Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold150
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1854615
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 196055 characters in sequence are not A, C, G, or T
File 5 of 6
Found at i:1155745 original size:148 final size:148
Alignment explanation
Indices: 1155476--1155750 Score: 469
Period size: 148 Copynumber: 1.9 Consensus size: 148
1155466 TTAATGTAGG
1155476 ACTCACCATATGGGTACAGCATCAGGTACAGTATTAATGTAGAACTCACCATATGGGTACAGCAT
1 ACTCACCATATGGGTACAGCATCAGGTACAGTATTAATGTAGAACTCACCATATGGGTACAGCAT
* * * **
1155541 CAGGTACAGTATTATTGTAGGACTCACCATATGGGTACATCATCACATACTGTATTAATGTAGGA
66 CAGGTACAGTATTAATGTAGGACTCACCATATGGGTACAGCATCACAAACCATATTAATGTAGGA
1155606 CTCACATTATACATACAT
131 CTCACATTATACATACAT
* * *
1155624 ACTCACCATATGGGTACAGCATCAGGTACAGTATTAATGTAGGACTCACCATTTGGGTATAGCAT
1 ACTCACCATATGGGTACAGCATCAGGTACAGTATTAATGTAGAACTCACCATATGGGTACAGCAT
*
1155689 CAGGTACAGTATTAATGTAGGACTCACCATATGGGTACAGCATCAGAAACCATATTAATGTA
66 CAGGTACAGTATTAATGTAGGACTCACCATATGGGTACAGCATCACAAACCATATTAATGTA
1155751 CATACATATA
Statistics
Matches: 118, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
148 118 1.00
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.28
Consensus pattern (148 bp):
ACTCACCATATGGGTACAGCATCAGGTACAGTATTAATGTAGAACTCACCATATGGGTACAGCAT
CAGGTACAGTATTAATGTAGGACTCACCATATGGGTACAGCATCACAAACCATATTAATGTAGGA
CTCACATTATACATACAT
Found at i:1155750 original size:43 final size:43
Alignment explanation
Indices: 1155624--1155734 Score: 204
Period size: 43 Copynumber: 2.6 Consensus size: 43
1155614 ATACATACAT
1155624 ACTCACCATATGGGTACAGCATCAGGTACAGTATTAATGTAGG
1 ACTCACCATATGGGTACAGCATCAGGTACAGTATTAATGTAGG
* *
1155667 ACTCACCATTTGGGTATAGCATCAGGTACAGTATTAATGTAGG
1 ACTCACCATATGGGTACAGCATCAGGTACAGTATTAATGTAGG
1155710 ACTCACCATATGGGTACAGCATCAG
1 ACTCACCATATGGGTACAGCATCAG
1155735 AAACCATATT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 64 1.00
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.26
Consensus pattern (43 bp):
ACTCACCATATGGGTACAGCATCAGGTACAGTATTAATGTAGG
Found at i:1160648 original size:46 final size:46
Alignment explanation
Indices: 1160576--1160664 Score: 151
Period size: 46 Copynumber: 1.9 Consensus size: 46
1160566 TTTAGGTGTT
1160576 ACCTTATGACTCAGCATTACTATAGTGATTCTATCTCTAGTCAGTC
1 ACCTTATGACTCAGCATTACTATAGTGATTCTATCTCTAGTCAGTC
* * *
1160622 ACCTTATGATTTAGCATTACTGTAGTGATTCTATCTCTAGTCA
1 ACCTTATGACTCAGCATTACTATAGTGATTCTATCTCTAGTCA
1160665 CTGTTGTATA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.39
Consensus pattern (46 bp):
ACCTTATGACTCAGCATTACTATAGTGATTCTATCTCTAGTCAGTC
Found at i:1160712 original size:56 final size:56
Alignment explanation
Indices: 1160626--1160741 Score: 178
Period size: 56 Copynumber: 2.1 Consensus size: 56
1160616 TCAGTCACCT
* * *
1160626 TATGATTTAGCATTACTGTAGTGATTCTATCTCTAGTCACTGTTGTATACTACAGA
1 TATGATTCAGCATTACTGTAGTGATTCTATCCCTAGTCACTGTTGTACACTACAGA
* * *
1160682 TATGATTCAGTATTACTGTAGTTATTCTATCCCTAGTCATTGTTGTACACTACAGA
1 TATGATTCAGCATTACTGTAGTGATTCTATCCCTAGTCACTGTTGTACACTACAGA
1160738 TATG
1 TATG
1160742 GAGAACCCAC
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (56 bp):
TATGATTCAGCATTACTGTAGTGATTCTATCCCTAGTCACTGTTGTACACTACAGA
Found at i:1163073 original size:4 final size:4
Alignment explanation
Indices: 1163059--1163105 Score: 60
Period size: 4 Copynumber: 12.0 Consensus size: 4
1163049 GATCACATTT
* * *
1163059 TGTC TGTC -GTC CGTC TGTC TGTC TGTC CGTC CGTC TGTC TGTC TGTC
1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC
1163106 CGTAAACTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
3 3 0.08
4 36 0.92
ACGTcount: A:0.00, C:0.32, G:0.26, T:0.43
Consensus pattern (4 bp):
TGTC
Found at i:1163091 original size:20 final size:20
Alignment explanation
Indices: 1163059--1163108 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
1163049 GATCACATTT
1163059 TGTCTGT-CGTCCGTCTGTC
1 TGTCTGTCCGTCCGTCTGTC
1163078 TGTCTGTCCGTCCGTCTGTC
1 TGTCTGTCCGTCCGTCTGTC
1163098 TGTCTGTCCGT
1 TGTCTGTCCGT
1163109 AAACTTTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 7 0.23
20 23 0.77
ACGTcount: A:0.00, C:0.32, G:0.26, T:0.42
Consensus pattern (20 bp):
TGTCTGTCCGTCCGTCTGTC
Found at i:1163108 original size:16 final size:16
Alignment explanation
Indices: 1163059--1163101 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
1163049 GATCACATTT
1163059 TGTCTGTC-GTCCGTC
1 TGTCTGTCTGTCCGTC
1163074 TGTCTGTCTGTCCGTC
1 TGTCTGTCTGTCCGTC
*
1163090 CGTCTGTCTGTC
1 TGTCTGTCTGTC
1163102 TGTCCGTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 8 0.31
16 18 0.69
ACGTcount: A:0.00, C:0.33, G:0.26, T:0.42
Consensus pattern (16 bp):
TGTCTGTCTGTCCGTC
Found at i:1164004 original size:165 final size:165
Alignment explanation
Indices: 1163278--1164824 Score: 2150
Period size: 166 Copynumber: 9.2 Consensus size: 165
1163268 AGAAATTTTC
* * *
1163278 AAAAATCTTCTTCTCA-AGAACCAGA-AAGCCAGGAAAGCTGAATCTTGTGTGGAAGCATCCTCA
1 AAAAATCTTCTTCTCAGA-AACTA-ATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCA
* *
1163341 GGTAGTGTAGATTCAAAGTTGTGAAATTCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGG
64 GGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCTGGGGGTAGGGTGGGG-CACAATGGGGG
1163406 GTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
128 GTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
*
1163444 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATTCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* **
1163509 TAGTGTAGATTCAAAGTTGTGAAATTCATGACCCCTGGATGTAGGGTGGGGCCACAATGGGGGGT
66 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCTGGGGGTAGGGTGGGG-CACAATGGGGGGT
1163574 CGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
130 CGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
1163610 AAAAATCTTCTTCTCAGAAACTAGA-CAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAG
1 AAAAATCTTCTTCTCAGAAACTA-ATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAG
** * *
1163674 GTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCAGGGGTAGGGTGAGGCCACATTGGGGGG
65 GTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCTGGGGGTAGGGTG-GGGCACAAT------
* *
1163739 GGGGGGT-GTTAAAGATTTACAAAGGAATATATAGAGTAAATCTTT
123 GGGGGGTCG---AAGTTTTACATAGGAATATATAGAGTAAATCTTT
* * * * *
1163784 GAAAATCCTCTTCTCAAAAACTAATCAGCCAGGAAAGCTGAAACTTATGTGGAAGCATCCTGAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* *
1163849 TAGTGCAGATTCAAAGTTGTGAAAATCATGACCCCTGGGGGTAGGGTGGGGCACAATGGAGGGTC
66 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCTGGGGGTAGGGTGGGGCACAATGGGGGGTC
* * *
1163914 GAAGTTTTACATAGGAATATACACAGTTAATCTTT
131 GAAGTTTTACATAGGAATATATAGAGTAAATCTTT
*
1163949 AAAATTCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
** *
1164014 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCAGGGGTAGGGTGGGTCCACAATGGGGTGG
66 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCTGGGGGTAGGGTGGG-GCACAATGGGG-GG
*
1164079 TCGAAGTTTTACAAAGGAATATATAGAGTAAATCTTT
129 TCGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
* * * *
1164116 AAAAATCCTCTTCTCAAAAACTAATCAGCCAAGAAAGCTGAAACTTATGTGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* * *
1164181 TAGTGCAGATTCAAAGTTGTGAAAATCATGATCCCTGGGGGTAGGGTGGGGCACAATGGAGGGTC
66 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCTGGGGGTAGGGTGGGGCACAATGGGGGGTC
**
1164246 GAAGTTTTACATAGGAATATATATTGTAAATCTTT
131 GAAGTTTTACATAGGAATATATAGAGTAAATCTTT
1164281 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* **
1164346 CAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCAGGGGTAGGGTGGGGCCACAATGGGGGGT
66 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCTGGGGGTAGGGTGGGG-CACAATGGGGGGT
*
1164411 CAAAGTTTTACATAGGAATATATAGAGTAAATCTTT
130 CGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
* *
1164447 GAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTCGTGTGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* * * *
1164512 CAGTGTAGATTCAAAGTTGTGAAATTCATGATCCCTGGGGGTAGGGTGAGGCACAATGGGGGGGG
66 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCTGGGGGTAGGGTGGGGCACAAT-------G
* *
1164577 GGGGGGCGAAGTTGTACATAGGAATATATAGAGTAAATCTTT
124 GGGGGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
* * * * *
1164619 AAAAATCCTCTTCTCAGAAACTAAACAGCCAGGAAAGGTGAAACTTGTGTTGAAGTATCCTCAGG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
* * * *
1164684 TAGTGTAGATTCAAAGTTGTGAAAA-CATGATCCCTTGGGGTAGGGTGAGGCCACATTGGGGGGG
66 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCTGGGGGTAGGGTG-GGGCACAAT-------
** * *
1164748 GGGGGGGGTTAAAGTTTTACAAAGGAATATACAGAGTAAATCTTT
123 --GGGGGGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTT
* *
1164793 AGAAATCTTCTTCTCAGAAACTAATCAACCAG
1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAG
1164825 ATGATTCTTT
Statistics
Matches: 1245, Mismatches: 108, Indels: 48
0.89 0.08 0.03
Matches are distributed among these distances:
165 285 0.23
166 437 0.35
167 151 0.12
168 1 0.00
171 22 0.02
172 134 0.11
173 8 0.01
174 207 0.17
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.25
Consensus pattern (165 bp):
AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG
TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCTGGGGGTAGGGTGGGGCACAATGGGGGGTC
GAAGTTTTACATAGGAATATATAGAGTAAATCTTT
Found at i:1169850 original size:80 final size:80
Alignment explanation
Indices: 1169590--1170593 Score: 1316
Period size: 80 Copynumber: 12.7 Consensus size: 80
1169580 CCACAGTACA
* *
1169590 ATACATAAGTATACACTGTTATGATGTACATGTACGTACAGGT-CTCCTGTGCTCAGTGACATGA
1 ATACATATGTATACACTGTTATGAT-T-TAT-TA---ACAGGTGC-CCTGTGCTCAGTGACATGA
* * **
1169654 CAATATGTCGGTCTGATACATC
59 CAATGTGTCAGTCTGATGTATC
* * * *
1169676 ATACAAATGTATACACTGTTTGTGTTATGATTTATTAAAAGATGCCCTGTGCTGAGTGGCACA-G
1 ATACATATGTATACAC------TGTTATGATTTATTAACAGGTGCCCTGTGCTCAGT-G-ACATG
*
1169740 ACATTGTGTCAGTCTGATGTATC
58 ACAATGTGTCAGTCTGATGTATC
*
1169763 ATACATATGTATACACTGTTATGATTTATTAACAGGTCCCCTGTGCTCAGTGACATGACAATGTG
1 ATACATATGTATACACTGTTATGATTTATTAACAGGTGCCCTGTGCTCAGTGACATGACAATGTG
**
1169828 TTGGTCTGATGTATC
66 TCAGTCTGATGTATC
* * *
1169843 ATACATATGTATACACTGTTATGATTCATTAGCAGGTGCCCTGTGCTCAGTGACATGACATTGTG
1 ATACATATGTATACACTGTTATGATTTATTAACAGGTGCCCTGTGCTCAGTGACATGACAATGTG
1169908 TCAGTCTGATGTATC
66 TCAGTCTGATGTATC
*
1169923 ATACATATGTATACACTGTTATGATTTATTAACAGGTGCCCTGTGCTCAGTGACATGACATTGTG
1 ATACATATGTATACACTGTTATGATTTATTAACAGGTGCCCTGTGCTCAGTGACATGACAATGTG
*
1169988 TCGGTCTGATGTATC
66 TCAGTCTGATGTATC
*
1170003 ATACATATGTATACACTGTTATGATTTATTAACAGGTCCCCTGTGCTCAGTGACATGACAATGTG
1 ATACATATGTATACACTGTTATGATTTATTAACAGGTGCCCTGTGCTCAGTGACATGACAATGTG
** *
1170068 TTGGTTTGATGTATC
66 TCAGTCTGATGTATC
*
1170083 ATACATATGTATACACTGTTATGATTTATTAACAGGTGCCCTGTGCTCAGTGACATGACAATATG
1 ATACATATGTATACACTGTTATGATTTATTAACAGGTGCCCTGTGCTCAGTGACATGACAATGTG
* *
1170148 TCAATCTGATATATC
66 TCAGTCTGATGTATC
* * * *
1170163 ATACAAATGTATACACTGTTATGATTCATTAGCA---G----GTGCTCAGTGACATGACATTGTG
1 ATACATATGTATACACTGTTATGATTTATTAACAGGTGCCCTGTGCTCAGTGACATGACAATGTG
1170221 TCAGTCTGATGTATC
66 TCAGTCTGATGTATC
*
1170236 ATACATATGTATACACTGTTATGATTTATTAACAGGTGCCCTGTGCTCAGTGACATGACAATATG
1 ATACATATGTATACACTGTTATGATTTATTAACAGGTGCCCTGTGCTCAGTGACATGACAATGTG
* *
1170301 TCAATCTGATATATC
66 TCAGTCTGATGTATC
* * * *
1170316 ATACAAATGTATACACTGTTATGATTCATTAGCA---G----GTGCTCAGTGACATGACATTGTG
1 ATACATATGTATACACTGTTATGATTTATTAACAGGTGCCCTGTGCTCAGTGACATGACAATGTG
1170374 TCAGTCTGATGTATC
66 TCAGTCTGATGTATC
*
1170389 ATACATATGTATACACTGTTATGATTTATTAACAGGTGCCCTGTGCTCAGTGACATGACAATATG
1 ATACATATGTATACACTGTTATGATTTATTAACAGGTGCCCTGTGCTCAGTGACATGACAATGTG
* *
1170454 TCAATCTGATATATC
66 TCAGTCTGATGTATC
* * * *
1170469 ATACAAATGTATACACTGTTATGATTCATTAGCA---G----GTGCTCAGTGACATGACATTGTG
1 ATACATATGTATACACTGTTATGATTTATTAACAGGTGCCCTGTGCTCAGTGACATGACAATGTG
1170527 TCAGTCTGATGTATC
66 TCAGTCTGATGTATC
1170542 ATACATATGTATACACTGTTATGATTTATTAACAGGTGCCCTGTGCTCAGTG
1 ATACATATGTATACACTGTTATGATTTATTAACAGGTGCCCTGTGCTCAGTG
1170594 GCACAGAGAT
Statistics
Matches: 810, Mismatches: 77, Indels: 68
0.85 0.08 0.07
Matches are distributed among these distances:
73 195 0.24
76 3 0.00
77 3 0.00
79 3 0.00
80 493 0.61
81 31 0.04
86 29 0.04
87 36 0.04
88 3 0.00
89 2 0.00
90 2 0.00
91 1 0.00
92 9 0.01
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (80 bp):
ATACATATGTATACACTGTTATGATTTATTAACAGGTGCCCTGTGCTCAGTGACATGACAATGTG
TCAGTCTGATGTATC
Found at i:1170212 original size:73 final size:73
Alignment explanation
Indices: 1170125--1170580 Score: 597
Period size: 73 Copynumber: 6.1 Consensus size: 73
1170115 CAGGTGCCCT
1170125 GTGCTCAGTGACATGACAATATGTCAATCTGATATATCATACAAATGTATACACTGTTATGATTC
1 GTGCTCAGTGACATGACAATATGTCAATCTGATATATCATACAAATGTATACACTGTTATGATTC
*
1170190 ATTAGCAG
66 ATTAACAG
* * * * * *
1170198 GTGCTCAGTGACATGACATTGTGTCAGTCTGATGTATCATACATATGTATACACTGTTATGATTT
1 GTGCTCAGTGACATGACAATATGTCAATCTGATATATCATACAAATGTATACACTGTTATGATTC
1170263 ATTAACAGGTG
66 ATTAACA---G
1170274 CCCTGTGCTCAGTGACATGACAATATGTCAATCTGATATATCATACAAATGTATACACTGTTATG
1 ----GTGCTCAGTGACATGACAATATGTCAATCTGATATATCATACAAATGTATACACTGTTATG
*
1170339 ATTCATTAGCAG
62 ATTCATTAACAG
* * * * * *
1170351 GTGCTCAGTGACATGACATTGTGTCAGTCTGATGTATCATACATATGTATACACTGTTATGATTT
1 GTGCTCAGTGACATGACAATATGTCAATCTGATATATCATACAAATGTATACACTGTTATGATTC
1170416 ATTAACAGGTG
66 ATTAACA---G
1170427 CCCTGTGCTCAGTGACATGACAATATGTCAATCTGATATATCATACAAATGTATACACTGTTATG
1 ----GTGCTCAGTGACATGACAATATGTCAATCTGATATATCATACAAATGTATACACTGTTATG
*
1170492 ATTCATTAGCAG
62 ATTCATTAACAG
* * * * * *
1170504 GTGCTCAGTGACATGACATTGTGTCAGTCTGATGTATCATACATATGTATACACTGTTATGATTT
1 GTGCTCAGTGACATGACAATATGTCAATCTGATATATCATACAAATGTATACACTGTTATGATTC
1170569 ATTAACAG
66 ATTAACAG
1170577 GTGC
1 GTGC
1170581 CCTGTGCTCA
Statistics
Matches: 334, Mismatches: 35, Indels: 28
0.84 0.09 0.07
Matches are distributed among these distances:
73 200 0.60
76 2 0.01
77 2 0.01
80 130 0.39
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (73 bp):
GTGCTCAGTGACATGACAATATGTCAATCTGATATATCATACAAATGTATACACTGTTATGATTC
ATTAACAG
Found at i:1170301 original size:153 final size:155
Alignment explanation
Indices: 1169590--1170593 Score: 1430
Period size: 153 Copynumber: 6.3 Consensus size: 155
1169580 CCACAGTACA
* *
1169590 ATACATAAGTATACACTGTTATGATGTACATGTACGTACAGGT-CTCCTGTGCTCAGTGACATGA
1 ATACATATGTATACACTGTTATGAT-T-TAT-TA---ACAGGTGC-CCTGTGCTCAGTGACATGA
** * * **
1169654 CAATATGTCGGTCTGATACATCATACAAATGTATACACTGTTTGTGTTATGATTTATTAAAAGAT
59 CAATATGTCAATCTGATATATCATACAAATGTATACAC------TGTTATGATTCATTAGCAG--
*
1169719 GCCCTGTGCTGAGTGGCACA-GACATTGTGTCAGTCTGATGTATC
116 G--C-GTGCTCAGT-G-ACATGACATTGTGTCAGTCTGATGTATC
* *
1169763 ATACATATGTATACACTGTTATGATTTATTAACAGGTCCCCTGTGCTCAGTGACATGACAATGTG
1 ATACATATGTATACACTGTTATGATTTATTAACAGGTGCCCTGTGCTCAGTGACATGACAATATG
*** * *
1169828 TTGGTCTGATGTATCATACATATGTATACACTGTTATGATTCATTAGCAGGTGCCCTGTGCTCAG
66 TCAATCTGATATATCATACAAATGTATACACTGTTATGATTCATTAGCA-G-G--C-GTGCTCAG
1169893 TGACATGACATTGTGTCAGTCTGATGTATC
126 TGACATGACATTGTGTCAGTCTGATGTATC
* *
1169923 ATACATATGTATACACTGTTATGATTTATTAACAGGTGCCCTGTGCTCAGTGACATGACATTGTG
1 ATACATATGTATACACTGTTATGATTTATTAACAGGTGCCCTGTGCTCAGTGACATGACAATATG
** * * * *
1169988 TCGGTCTGATGTATCATACATATGTATACACTGTTATGATTTATTAACAGGTCCCCTGTGCTCAG
66 TCAATCTGATATATCATACAAATGTATACACTGTTATGATTCATTAGCAGG----C-GTGCTCAG
* ** *
1170053 TGACATGACAATGTGTTGGTTTGATGTATC
126 TGACATGACATTGTGTCAGTCTGATGTATC
1170083 ATACATATGTATACACTGTTATGATTTATTAACAGGTGCCCTGTGCTCAGTGACATGACAATATG
1 ATACATATGTATACACTGTTATGATTTATTAACAGGTGCCCTGTGCTCAGTGACATGACAATATG
1170148 TCAATCTGATATATCATACAAATGTATACACTGTTATGATTCATTAGCA-G-GTGCTCAGTGACA
66 TCAATCTGATATATCATACAAATGTATACACTGTTATGATTCATTAGCAGGCGTGCTCAGTGACA
1170211 TGACATTGTGTCAGTCTGATGTATC
131 TGACATTGTGTCAGTCTGATGTATC
1170236 ATACATATGTATACACTGTTATGATTTATTAACAGGTGCCCTGTGCTCAGTGACATGACAATATG
1 ATACATATGTATACACTGTTATGATTTATTAACAGGTGCCCTGTGCTCAGTGACATGACAATATG
1170301 TCAATCTGATATATCATACAAATGTATACACTGTTATGATTCATTAGCA-G-GTGCTCAGTGACA
66 TCAATCTGATATATCATACAAATGTATACACTGTTATGATTCATTAGCAGGCGTGCTCAGTGACA
1170364 TGACATTGTGTCAGTCTGATGTATC
131 TGACATTGTGTCAGTCTGATGTATC
1170389 ATACATATGTATACACTGTTATGATTTATTAACAGGTGCCCTGTGCTCAGTGACATGACAATATG
1 ATACATATGTATACACTGTTATGATTTATTAACAGGTGCCCTGTGCTCAGTGACATGACAATATG
1170454 TCAATCTGATATATCATACAAATGTATACACTGTTATGATTCATTAGCA-G-GTGCTCAGTGACA
66 TCAATCTGATATATCATACAAATGTATACACTGTTATGATTCATTAGCAGGCGTGCTCAGTGACA
1170517 TGACATTGTGTCAGTCTGATGTATC
131 TGACATTGTGTCAGTCTGATGTATC
1170542 ATACATATGTATACACTGTTATGATTTATTAACAGGTGCCCTGTGCTCAGTG
1 ATACATATGTATACACTGTTATGATTTATTAACAGGTGCCCTGTGCTCAGTG
1170594 GCACAGAGAT
Statistics
Matches: 794, Mismatches: 32, Indels: 30
0.93 0.04 0.04
Matches are distributed among these distances:
153 392 0.49
158 1 0.00
159 5 0.01
160 278 0.35
161 29 0.04
162 1 0.00
167 58 0.07
168 1 0.00
170 2 0.00
171 2 0.00
172 1 0.00
173 24 0.03
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (155 bp):
ATACATATGTATACACTGTTATGATTTATTAACAGGTGCCCTGTGCTCAGTGACATGACAATATG
TCAATCTGATATATCATACAAATGTATACACTGTTATGATTCATTAGCAGGCGTGCTCAGTGACA
TGACATTGTGTCAGTCTGATGTATC
Found at i:1174068 original size:2 final size:2
Alignment explanation
Indices: 1174061--1174098 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1174051 AAAAACAAAA
1174061 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1174099 CATAATAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1176098 original size:28 final size:28
Alignment explanation
Indices: 1176067--1176139 Score: 112
Period size: 28 Copynumber: 2.6 Consensus size: 28
1176057 TTACACGATA
*
1176067 ACTACAGATGATGAC-ACTTTGGCTGATG
1 ACTACAGATGATGACTA-TTTGGATGATG
*
1176095 ACTACAGATGATGACTATTTGGATGGTG
1 ACTACAGATGATGACTATTTGGATGATG
1176123 ACTACAGATGATGACTA
1 ACTACAGATGATGACTA
1176140 CAGATGAAGC
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
28 41 0.98
29 1 0.02
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.29
Consensus pattern (28 bp):
ACTACAGATGATGACTATTTGGATGATG
Found at i:1176108 original size:13 final size:13
Alignment explanation
Indices: 1176090--1176146 Score: 69
Period size: 13 Copynumber: 4.2 Consensus size: 13
1176080 ACACTTTGGC
1176090 TGATGACTACAGA
1 TGATGACTACAGA
**
1176103 TGATGACTATTTGGA
1 TGATGACTA--CAGA
*
1176118 TGGTGACTACAGA
1 TGATGACTACAGA
1176131 TGATGACTACAGA
1 TGATGACTACAGA
1176144 TGA
1 TGA
1176147 AGCATAGACT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
13 26 0.72
15 10 0.28
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.28
Consensus pattern (13 bp):
TGATGACTACAGA
Found at i:1181237 original size:20 final size:20
Alignment explanation
Indices: 1181212--1181254 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1181202 TGTCGATGTG
* * *
1181212 AACTTACGGACGGCAGTGTA
1 AACTTACAGACAGCACTGTA
1181232 AACTTACAGACAGCACTGTA
1 AACTTACAGACAGCACTGTA
1181252 AAC
1 AAC
1181255 ATATAGACCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (20 bp):
AACTTACAGACAGCACTGTA
Found at i:1181316 original size:20 final size:20
Alignment explanation
Indices: 1181291--1181589 Score: 314
Period size: 20 Copynumber: 14.9 Consensus size: 20
1181281 TATCACACTA
* *
1181291 AACTTACAGACTGCGATTTG
1 AACTTACAGACGGCGATGTG
* **
1181311 AACTTACATACGGCGATAAG
1 AACTTACAGACGGCGATGTG
* ** *
1181331 AATTTTACATTCTGCGATGTG
1 AA-CTTACAGACGGCGATGTG
* ** *
1181352 AACTTACATACAACGATATG
1 AACTTACAGACGGCGATGTG
* ** *
1181372 AATTTACATTCTGCGATGTG
1 AACTTACAGACGGCGATGTG
*
1181392 AACTTACAGACGGCAATGTG
1 AACTTACAGACGGCGATGTG
** *
1181412 AACTTACAGAATGCGATATG
1 AACTTACAGACGGCGATGTG
1181432 AACTTACAGACGGCGATGTG
1 AACTTACAGACGGCGATGTG
1181452 AACTTACAGACGGCGATGTG
1 AACTTACAGACGGCGATGTG
* *
1181472 AACTTACAGACGGTGATGTA
1 AACTTACAGACGGCGATGTG
*
1181492 AACTTACAGACGGCAATGTG
1 AACTTACAGACGGCGATGTG
*
1181512 AACTTACAGACGGCGATGTA
1 AACTTACAGACGGCGATGTG
*
1181532 AACTTACA-CCAGGCGATGTG
1 AACTTACAGAC-GGCGATGTG
*
1181552 AACTTACA-CCAGGCGATGTG
1 AACTTACAGAC-GGCGATGTG
1181572 AACTTACAGACGGCGATG
1 AACTTACAGACGGCGATG
1181590 AGGTCAAGGA
Statistics
Matches: 235, Mismatches: 41, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
19 1 0.00
20 218 0.93
21 16 0.07
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.24
Consensus pattern (20 bp):
AACTTACAGACGGCGATGTG
Found at i:1181389 original size:40 final size:41
Alignment explanation
Indices: 1181301--1181399 Score: 155
Period size: 41 Copynumber: 2.4 Consensus size: 41
1181291 AACTTACAGA
* **
1181301 CTGCGATTTGAACTTACATACGGCGATAAGAATTTTACATT
1 CTGCGATGTGAACTTACATACAACGATAAGAATTTTACATT
*
1181342 CTGCGATGTGAACTTACATACAACGATATGAA-TTTACATT
1 CTGCGATGTGAACTTACATACAACGATAAGAATTTTACATT
1181382 CTGCGATGTGAACTTACA
1 CTGCGATGTGAACTTACA
1181400 GACGGCAATG
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
40 26 0.48
41 28 0.52
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Consensus pattern (41 bp):
CTGCGATGTGAACTTACATACAACGATAAGAATTTTACATT
Found at i:1186188 original size:29 final size:29
Alignment explanation
Indices: 1186143--1186206 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
1186133 AAAAGAAGAT
* *
1186143 TAAATCTATATGTTTGACATATGTGGTTG
1 TAAATCTATATGGTTGACATATGTGGCTG
1186172 TAAATCTATATGGTTGACATATGTGGCTG
1 TAAATCTATATGGTTGACATATGTGGCTG
1186201 TAAATC
1 TAAATC
1186207 GTTCTTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (29 bp):
TAAATCTATATGGTTGACATATGTGGCTG
Found at i:1186555 original size:2 final size:2
Alignment explanation
Indices: 1186550--1186597 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1186540 GCTTTCTCTC
1186550 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1186592 TG TG TG
1 TG TG TG
1186598 AGAGAGAGAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1186602 original size:2 final size:2
Alignment explanation
Indices: 1186597--1186637 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1186587 GTGTGTGTGT
*
1186597 GA GA GA GA GA GA GA GA GA GA GT GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1186638 CTTCCATTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.51, T:0.02
Consensus pattern (2 bp):
GA
Found at i:1186837 original size:2 final size:2
Alignment explanation
Indices: 1186830--1186856 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1186820 TGTTTTAAAN
1186830 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1186857 CAGTCTGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1196925 original size:35 final size:35
Alignment explanation
Indices: 1196878--1197065 Score: 159
Period size: 35 Copynumber: 5.3 Consensus size: 35
1196868 CCACGGACTC
*
1196878 AACTTCACGTGTCCCCCACCCACCTTAGGTAAGGG
1 AACTTCAAGTGTCCCCCACCCACCTTAGGTAAGGG
* *
1196913 AACTTCAAGTGTCCCCCACCCACCTAAGGTAGGGG
1 AACTTCAAGTGTCCCCCACCCACCTTAGGTAAGGG
* * * * *
1196948 AAATTCACGTGCGCCCCCCCCCCCACCTCAGGTAAGGG
1 AACTTCAAGT--G-TCCCCCACCCACCTTAGGTAAGGG
* ** *
1196986 AACTTCACA-TG-CCCCCGCCCACAATAGCTAA-GG
1 AACTTCA-AGTGTCCCCCACCCACCTTAGGTAAGGG
* * * *
1197019 AACTTCACGTGCCCCCCAACCACGTTAGGTAAGGG
1 AACTTCAAGTGTCCCCCACCCACCTTAGGTAAGGG
1197054 AAC-TCAACGTGT
1 AACTTCAA-GTGT
1197066 TTCCCGCCTT
Statistics
Matches: 121, Mismatches: 24, Indels: 16
0.75 0.15 0.10
Matches are distributed among these distances:
33 11 0.09
34 33 0.27
35 48 0.40
36 1 0.01
37 1 0.01
38 27 0.22
ACGTcount: A:0.26, C:0.37, G:0.20, T:0.17
Consensus pattern (35 bp):
AACTTCAAGTGTCCCCCACCCACCTTAGGTAAGGG
Found at i:1196974 original size:38 final size:37
Alignment explanation
Indices: 1196890--1197007 Score: 116
Period size: 38 Copynumber: 3.2 Consensus size: 37
1196880 CTTCACGTGT
* * *
1196890 CCCCCACCCACCTTAGGTAAGGGAACTTCA-AGTG--T
1 CCCCCACCCACCTAAGGTAAGGGAAATTCACA-TGCCC
* *
1196925 CCCCCACCCACCTAAGGTAGGGGAAATTCACGTGCGCC
1 CCCCCACCCACCTAAGGTAAGGGAAATTCACATGC-CC
* * *
1196963 CCCCCCCCCACCTCAGGTAAGGGAACTTCACATGCCC
1 CCCCCACCCACCTAAGGTAAGGGAAATTCACATGCCC
1197000 CCGCCCAC
1 CC-CCCAC
1197008 AATAGCTAAG
Statistics
Matches: 67, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
35 29 0.43
37 4 0.06
38 34 0.51
ACGTcount: A:0.23, C:0.43, G:0.19, T:0.14
Consensus pattern (37 bp):
CCCCCACCCACCTAAGGTAAGGGAAATTCACATGCCC
Found at i:1199322 original size:39 final size:39
Alignment explanation
Indices: 1199242--1200296 Score: 778
Period size: 39 Copynumber: 27.6 Consensus size: 39
1199232 ATGTCCGGCG
* *
1199242 TACTCCATAACGATATAGACCTAGTATACAG-----ATA
1 TACTCCATAACGATATAGACCTAGCATAGAGATATAATA
* *
1199276 TACTCCATAACGATATAGACCTAGCATTGA-ATATACATG
1 TACTCCATAACGATATAGACCTAGCATAGAGATATA-ATA
* * * *
1199315 TACTCCATAACGATATAGACCTAGGATACAGACAGAATA
1 TACTCCATAACGATATAGACCTAGCATAGAGATATAATA
* * * * * *
1199354 TACTCTATAACGATAAAGACCTAGTAAACAGATAGAATA
1 TACTCCATAACGATATAGACCTAGCATAGAGATATAATA
* *
1199393 CACTCCATAACGATATAGACCTAGCATAGA-ATATACATG
1 TACTCCATAACGATATAGACCTAGCATAGAGATATA-ATA
* * ***
1199432 TACTCCATAACGATATAGACCTAGGATACAGACGGAATA
1 TACTCCATAACGATATAGACCTAGCATAGAGATATAATA
* * * * *
1199471 TATTCCATAACGATATAGACCTA-C-GACACATAGAATA
1 TACTCCATAACGATATAGACCTAGCATAGAGATATAATA
*
1199508 TACTCCATAACGATATAGACCTAGCATAGA-ATATACATG
1 TACTCCATAACGATATAGACCTAGCATAGAGATATA-ATA
*
1199547 TACTTCATAACGATATAGA-C---C-T--AG---T-ATA
1 TACTCCATAACGATATAGACCTAGCATAGAGATATAATA
*
1199575 TACTCCATAACGATATAGACCTAGCATAGA-ATATACATG
1 TACTCCATAACGATATAGACCTAGCATAGAGATATA-ATA
* * * *
1199614 TACTTCATAACGATATAGACCTAGCAGAGA-ATTTACATG
1 TACTCCATAACGATATAGACCTAGCATAGAGATATA-ATA
* * * * *
1199653 TACTCTATAACGATATAGACCTAGTATACAGACAGAATA
1 TACTCCATAACGATATAGACCTAGCATAGAGATATAATA
*
1199692 TACTCCATAACGATATAGACCTAGCATAGA-ATATACATG
1 TACTCCATAACGATATAGACCTAGCATAGAGATATA-ATA
* * * * *
1199731 TACTCCATAACGATATAGACCAAGTATACAGACAGAATA
1 TACTCCATAACGATATAGACCTAGCATAGAGATATAATA
* *
1199770 TACTCCATAACGATATAGACCTAGCATTGA-ATATACATG
1 TACTCCATAACGATATAGACCTAGCATAGAGATATA-ATA
* * * *
1199809 TACTCCATAACGATATAGACCTAGTATACAGACAGAATA
1 TACTCCATAACGATATAGACCTAGCATAGAGATATAATA
* *
1199848 TACTCCATAACGATATAGACCTAGCATTGA-ATATACATG
1 TACTCCATAACGATATAGACCTAGCATAGAGATATA-ATA
* * * * *
1199887 TACTCCATAACGATATGGACCTAGTATACAGACAGAATA
1 TACTCCATAACGATATAGACCTAGCATAGAGATATAATA
* *
1199926 TACTCCATAACGATAT--ACCTAGGATAGAGATAGAATA
1 TACTCCATAACGATATAGACCTAGCATAGAGATATAATA
* ** * * *
1199963 TACTCCATAACGATATAGGCCTAATATACAGACAGAATA
1 TACTCCATAACGATATAGACCTAGCATAGAGATATAATA
* * * * * *
1200002 CACTCCATATCGATATAGACCTAGGATACAGACAGAATA
1 TACTCCATAACGATATAGACCTAGCATAGAGATATAATA
* * *
1200041 TACTCCATGACGATATAGACCTACGGCA-CG-GATAGAATA
1 TACTCCATAACGATATAGACCTA--GCATAGAGATATAATA
* * * * * * *
1200080 TATTCCATATTATGATATAGACTTAGGAT-GCAGACAGAATT
1 TACTCCATA--ACGATATAGACCTAGCATAG-AGATATAATA
* * * * * *
1200121 TTCACCATAACGATATAGACCTAGGACACAGATAGAATA
1 TACTCCATAACGATATAGACCTAGCATAGAGATATAATA
* * * * * *
1200160 TATTCCATAACGATACAGACCTAGAATACAGACAGAATA
1 TACTCCATAACGATATAGACCTAGCATAGAGATATAATA
* * * * *
1200199 TACACCATAACGATACAGACCTAGTAT-GCAGACAGAATA
1 TACTCCATAACGATATAGACCTAGCATAG-AGATATAATA
* * *
1200238 TACACCGTAACGATAT--ACCTAGGAT-GCAGAT-TGAATA
1 TACTCCATAACGATATAGACCTAGCATAG-AGATAT-AATA
* * *
1200275 CACTCCATATCGATTTAGACCT
1 TACTCCATAACGATATAGACCT
1200297 CCATAACGAT
Statistics
Matches: 823, Mismatches: 152, Indels: 87
0.77 0.14 0.08
Matches are distributed among these distances:
28 20 0.02
29 1 0.00
30 1 0.00
32 2 0.00
33 1 0.00
34 28 0.03
35 2 0.00
37 94 0.11
38 19 0.02
39 612 0.74
40 16 0.02
41 27 0.03
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.24
Consensus pattern (39 bp):
TACTCCATAACGATATAGACCTAGCATAGAGATATAATA
Found at i:1199400 original size:78 final size:77
Alignment explanation
Indices: 1199242--1200296 Score: 959
Period size: 78 Copynumber: 13.8 Consensus size: 77
1199232 ATGTCCGGCG
* *
1199242 TACTCCATAACGATATAGACCTAGTATAC---AG-ATATACTCCATAACGATATAGACCTAGCAT
1 TACTCCATAACGATATAGACCTAGGATACAATAGAATATACTCCATAACGATATAGACCTAGTAT
** * * *
1199303 TGA-ATATACATG
66 ACAGACAGA-ATA
* * *
1199315 TACTCCATAACGATATAGACCTAGGATACAGACAGAATATACTCTATAACGATAAAGACCTAGTA
1 TACTCCATAACGATATAGACCTAGGATACA-ATAGAATATACTCCATAACGATATAGACCTAGTA
* *
1199380 AACAGATAGAATA
65 TACAGACAGAATA
* * * * * *
1199393 CACTCCATAACGATATAGACCTAGCATAGAATATACATGTACTCCATAACGATATAGACCTAGGA
1 TACTCCATAACGATATAGACCTAGGATACAATAGA-ATATACTCCATAACGATATAGACCTAGTA
*
1199458 TACAGACGGAATA
65 TACAGACAGAATA
* * * *
1199471 TATTCCATAACGATATAGACCTACGACAC-ATAGAATATACTCCATAACGATATAGACCTAGCAT
1 TACTCCATAACGATATAGACCTAGGATACAATAGAATATACTCCATAACGATATAGACCTAGTAT
* * * *
1199535 AGA-ATATACATG
66 ACAGACAGA-ATA
* *
1199547 TACTTCATAACGATATAGACCTA-G------T---ATATACTCCATAACGATATAGACCTAGCAT
1 TACTCCATAACGATATAGACCTAGGATACAATAGAATATACTCCATAACGATATAGACCTAGTAT
* * * *
1199602 AGA-ATATACATG
66 ACAGACAGA-ATA
* * * * ** * *
1199614 TACTTCATAACGATATAGACCTAGCAGAGAATTTACATGTACTCTATAACGATATAGACCTAGTA
1 TACTCCATAACGATATAGACCTAGGATACAATAGA-ATATACTCCATAACGATATAGACCTAGTA
1199679 TACAGACAGAATA
65 TACAGACAGAATA
* * * * *
1199692 TACTCCATAACGATATAGACCTAGCATAGAATATACATGTACTCCATAACGATATAGACCAAGTA
1 TACTCCATAACGATATAGACCTAGGATACAATAGA-ATATACTCCATAACGATATAGACCTAGTA
1199757 TACAGACAGAATA
65 TACAGACAGAATA
* ** * *
1199770 TACTCCATAACGATATAGACCTAGCATTGAATATACATGTACTCCATAACGATATAGACCTAGTA
1 TACTCCATAACGATATAGACCTAGGATACAATAGA-ATATACTCCATAACGATATAGACCTAGTA
1199835 TACAGACAGAATA
65 TACAGACAGAATA
* ** * * *
1199848 TACTCCATAACGATATAGACCTAGCATTGAATATACATGTACTCCATAACGATATGGACCTAGTA
1 TACTCCATAACGATATAGACCTAGGATACAATAGA-ATATACTCCATAACGATATAGACCTAGTA
1199913 TACAGACAGAATA
65 TACAGACAGAATA
* * *
1199926 TACTCCATAACGATAT--ACCTAGGATAGAGATAGAATATACTCCATAACGATATAGGCCTAATA
1 TACTCCATAACGATATAGACCTAGGATACA-ATAGAATATACTCCATAACGATATAGACCTAGTA
1199989 TACAGACAGAATA
65 TACAGACAGAATA
* * * *
1200002 CACTCCATATCGATATAGACCTAGGATACAGACAGAATATACTCCATGACGATATAGACCTACG-
1 TACTCCATAACGATATAGACCTAGGATACA-ATAGAATATACTCCATAACGATATAGACCTA-GT
** * *
1200066 GCACGGATAGAATA
64 ATACAGACAGAATA
* * * * * * * *
1200080 TATTCCATATTATGATATAGACTTAGGATGCAGACAGAATTTTCACCATAACGATATAGACCTAG
1 TACTCCATA--ACGATATAGACCTAGGATACA-ATAGAATATACTCCATAACGATATAGACCTAG
* * *
1200145 GACACAGATAGAATA
63 TATACAGACAGAATA
* * * * * *
1200160 TATTCCATAACGATACAGACCTAGAATACAGACAGAATATACACCATAACGATACAGACCTAGTA
1 TACTCCATAACGATATAGACCTAGGATACA-ATAGAATATACTCCATAACGATATAGACCTAGTA
*
1200225 TGCAGACAGAATA
65 TACAGACAGAATA
* * * * * * *
1200238 TACACCGTAACGATAT--ACCTAGGATGCAGATTGAATACACTCCATATCGATTTAGACCT
1 TACTCCATAACGATATAGACCTAGGATACA-ATAGAATATACTCCATAACGATATAGACCT
1200297 CCATAACGAT
Statistics
Matches: 847, Mismatches: 108, Indels: 51
0.84 0.11 0.05
Matches are distributed among these distances:
67 65 0.08
70 1 0.00
73 28 0.03
74 1 0.00
75 3 0.00
76 149 0.18
77 13 0.02
78 513 0.61
79 8 0.01
80 66 0.08
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.24
Consensus pattern (77 bp):
TACTCCATAACGATATAGACCTAGGATACAATAGAATATACTCCATAACGATATAGACCTAGTAT
ACAGACAGAATA
Found at i:1199443 original size:117 final size:116
Alignment explanation
Indices: 1199242--1200222 Score: 1017
Period size: 117 Copynumber: 8.5 Consensus size: 116
1199232 ATGTCCGGCG
1199242 TACTCCATAACGATATAGACCTAGTATAC----AG-ATATACTCCATAACGATATAGACCTAGCA
1 TACTCCATAACGATATAGACCTAG-ATACAGATAGAATATACTCCATAACGATATAGACCTAGCA
*
1199302 TTGAATATACATGTACTCCATAACGATATAGACCTAGGATACAGACAGAATA
65 TAGAATATACATGTACTCCATAACGATATAGACCTAGGATACAGACAGAATA
* * * *
1199354 TACTCTATAACGATAAAGACCTAGTAAACAGATAGAATACACTCCATAACGATATAGACCTAGCA
1 TACTCCATAACGATATAGACCTAG-ATACAGATAGAATATACTCCATAACGATATAGACCTAGCA
*
1199419 TAGAATATACATGTACTCCATAACGATATAGACCTAGGATACAGACGGAATA
65 TAGAATATACATGTACTCCATAACGATATAGACCTAGGATACAGACAGAATA
* *
1199471 TATTCCATAACGATATAGACCTACG--ACACATAGAATATACTCCATAACGATATAGACCTAGCA
1 TACTCCATAACGATATAGACCTA-GATACAGATAGAATATACTCCATAACGATATAGACCTAGCA
*
1199534 TAGAATATACATGTACTTCATAACGATATAGACCTA-G-T---------ATA
65 TAGAATATACATGTACTCCATAACGATATAGACCTAGGATACAGACAGAATA
* * * *
1199575 TACTCCATAACGATATAGACCTAGCATAGA-ATATACATGTACTTCATAACGATATAGACCTAGC
1 TACTCCATAACGATATAGACCTAG-ATACAGATAGA-ATATACTCCATAACGATATAGACCTAGC
* * * *
1199639 AGAGAATTTACATGTACTCTATAACGATATAGACCTAGTATACAGACAGAATA
64 ATAGAATATACATGTACTCCATAACGATATAGACCTAGGATACAGACAGAATA
* * * * *
1199692 TACTCCATAACGATATAGACCTAGCATAGA-ATATACATGTACTCCATAACGATATAGACCAAGT
1 TACTCCATAACGATATAGACCTAG-ATACAGATAGA-ATATACTCCATAACGATATAGACCTAGC
* * * * * ** * * *
1199756 ATACAGACAGA-ATATACTCCATAACGATATAGACCTAGCATTGA-ATATACATG
64 ATAGA-ATATACATGTACTCCATAACGATATAGACCTAGGATACAGACAGA-ATA
*
1199809 TACTCCATAACGATATAGACCTAGTATACAGACAGAATATACTCCATAACGATATAGACCTAGCA
1 TACTCCATAACGATATAGACCTAG-ATACAGATAGAATATACTCCATAACGATATAGACCTAGCA
* * *
1199874 TTGAATATACATGTACTCCATAACGATATGGACCTAGTATACAGACAGAATA
65 TAGAATATACATGTACTCCATAACGATATAGACCTAGGATACAGACAGAATA
* * **
1199926 TACTCCATAACGATAT--ACCTAGGATAGAGATAGAATATACTCCATAACGATATAGGCCTAATA
1 TACTCCATAACGATATAGACCTA-GATACAGATAGAATATACTCCATAACGATATAGACCTAGCA
* * * ** *
1199989 TACAGACAGA-ATACACTCCATATCGATATAGACCTAGGATACAGACAGAATA
65 TAGA-ATATACATGTACTCCATAACGATATAGACCTAGGATACAGACAGAATA
* ** * * * *
1200041 TACTCCATGACGATATAGACCTACGGCACGGATAGAATATATTCCATATTATGATATAGACTTAG
1 TACTCCATAACGATATAGACCTA-GATACAGATAGAATATACTCCATA--ACGATATAGACCTAG
* * * * * * * *
1200106 GAT-GCAGACAGA-ATTTTCACCATAACGATATAGACCTAGGACACAGATAGAATA
63 CATAG-A-ATATACATGTACTCCATAACGATATAGACCTAGGATACAGACAGAATA
* * * * *
1200160 TATTCCATAACGATACAGACCTAGAATACAGACAGAATATACACCATAACGATACAGACCTAG
1 TACTCCATAACGATATAGACCTAG-ATACAGATAGAATATACTCCATAACGATATAGACCTAG
1200223 TATGCAGACA
Statistics
Matches: 732, Mismatches: 103, Indels: 63
0.82 0.11 0.07
Matches are distributed among these distances:
103 1 0.00
104 25 0.03
105 4 0.01
106 61 0.08
108 1 0.00
112 26 0.04
113 1 0.00
114 1 0.00
115 165 0.23
116 12 0.02
117 333 0.45
118 10 0.01
119 92 0.13
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.24
Consensus pattern (116 bp):
TACTCCATAACGATATAGACCTAGATACAGATAGAATATACTCCATAACGATATAGACCTAGCAT
AGAATATACATGTACTCCATAACGATATAGACCTAGGATACAGACAGAATA
Found at i:1199587 original size:67 final size:67
Alignment explanation
Indices: 1199505--1199637 Score: 266
Period size: 67 Copynumber: 2.0 Consensus size: 67
1199495 GACACATAGA
1199505 ATATACTCCATAACGATATAGACCTAGCATAGAATATACATGTACTTCATAACGATATAGACCTA
1 ATATACTCCATAACGATATAGACCTAGCATAGAATATACATGTACTTCATAACGATATAGACCTA
1199570 GT
66 GT
1199572 ATATACTCCATAACGATATAGACCTAGCATAGAATATACATGTACTTCATAACGATATAGACCTA
1 ATATACTCCATAACGATATAGACCTAGCATAGAATATACATGTACTTCATAACGATATAGACCTA
1199637 G
66 G
1199638 CAGAGAATTT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.28
Consensus pattern (67 bp):
ATATACTCCATAACGATATAGACCTAGCATAGAATATACATGTACTTCATAACGATATAGACCTA
GT
Found at i:1200446 original size:41 final size:41
Alignment explanation
Indices: 1200396--1200527 Score: 126
Period size: 41 Copynumber: 3.1 Consensus size: 41
1200386 ACGTACATGT
*
1200396 ACATGTAGACCTAGGAT-ATAGGCAGAATATACTACATAACG
1 ACATATAGACCTAGGATGA-AGGCAGAATATACTACATAACG
* *
1200437 ACATATAGACCTAGAATGAAGGCAGAATACACTACTAGTACTTAACG
1 ACATATAGACCTAGGATGAAGGCAGAAT--A-TAC---TACATAACG
* * *
1200484 AC--ATAGACCTTGGATGAAGGCAGAATATACTACAAAATG
1 ACATATAGACCTAGGATGAAGGCAGAATATACTACATAACG
1200523 ACATA
1 ACATA
1200528 GACCTAAGAT
Statistics
Matches: 74, Mismatches: 8, Indels: 18
0.74 0.08 0.18
Matches are distributed among these distances:
39 8 0.11
41 25 0.34
42 4 0.05
43 2 0.03
44 3 0.04
45 22 0.30
47 10 0.14
ACGTcount: A:0.43, C:0.17, G:0.18, T:0.21
Consensus pattern (41 bp):
ACATATAGACCTAGGATGAAGGCAGAATATACTACATAACG
Found at i:1200526 original size:39 final size:39
Alignment explanation
Indices: 1200401--1200533 Score: 133
Period size: 45 Copynumber: 3.2 Consensus size: 39
1200391 CATGTACATG
*
1200401 TAGACCTAGGAT-ATAGGCAGAATATACTACATAACGACATA
1 TAGACCTAGGATGA-AGGCAGAATATACTACAAAACGAC--A
* *
1200442 TAGACCTAGAATGAAGGCAGAATACACTACTAGTACTTAACGACA
1 TAGACCTAGGATGAAGGCAGAATATACTAC-A--A---AACGACA
* *
1200487 TAGACCTTGGATGAAGGCAGAATATACTACAAAATGACA
1 TAGACCTAGGATGAAGGCAGAATATACTACAAAACGACA
1200526 TAGACCTA
1 TAGACCTA
1200534 AGATTCAGAT
Statistics
Matches: 77, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
39 13 0.17
41 26 0.34
42 3 0.04
44 1 0.01
45 28 0.36
47 6 0.08
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.21
Consensus pattern (39 bp):
TAGACCTAGGATGAAGGCAGAATATACTACAAAACGACA
Found at i:1207689 original size:7 final size:8
Alignment explanation
Indices: 1207672--1207698 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
1207662 TTGGGTTCCA
1207672 TTTCTTTT
1 TTTCTTTT
1207680 TTTCTTTT
1 TTTCTTTT
1207688 TTTCTTTT
1 TTTCTTTT
1207696 TTT
1 TTT
1207699 TTGGTGTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTCTTTT
Found at i:1210338 original size:15 final size:15
Alignment explanation
Indices: 1210318--1210346 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1210308 ATGTATTTAC
1210318 TCTCCTCATCCTCAA
1 TCTCCTCATCCTCAA
1210333 TCTCCTCATCCTCA
1 TCTCCTCATCCTCA
1210347 GATTCCGCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.48, G:0.00, T:0.34
Consensus pattern (15 bp):
TCTCCTCATCCTCAA
Found at i:1212540 original size:66 final size:66
Alignment explanation
Indices: 1212432--1212563 Score: 255
Period size: 66 Copynumber: 2.0 Consensus size: 66
1212422 CGTGGGCGTT
*
1212432 GTTAATGGTCCCTACCCTCTTCCCTGTCTCCAGCTCCCAGATCTAACAAACAGAGTTTATAAATG
1 GTTAATGGTCCCTACCCTCTTCCCTGTCTCCAGCTCCAAGATCTAACAAACAGAGTTTATAAATG
1212497 A
66 A
1212498 GTTAATGGTCCCTACCCTCTTCCCTGTCTCCAGCTCCAAGATCTAACAAACAGAGTTTATAAATG
1 GTTAATGGTCCCTACCCTCTTCCCTGTCTCCAGCTCCAAGATCTAACAAACAGAGTTTATAAATG
1212563 A
66 A
1212564 ACTCTATAGA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.28, C:0.30, G:0.14, T:0.29
Consensus pattern (66 bp):
GTTAATGGTCCCTACCCTCTTCCCTGTCTCCAGCTCCAAGATCTAACAAACAGAGTTTATAAATG
A
Found at i:1212582 original size:35 final size:35
Alignment explanation
Indices: 1212536--1212605 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
1212526 TCCAGCTCCA
1212536 AGATCTAACAAACAGAGTTTATAAATGAACTCTAT
1 AGATCTAACAAACAGAGTTTATAAATGAACTCTAT
*
1212571 AGATCTAACAAACAGAGTTTATAAATGAGCTCTAT
1 AGATCTAACAAACAGAGTTTATAAATGAACTCTAT
1212606 GGCAAGGTCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.29
Consensus pattern (35 bp):
AGATCTAACAAACAGAGTTTATAAATGAACTCTAT
Found at i:1214169 original size:22 final size:22
Alignment explanation
Indices: 1214103--1214527 Score: 207
Period size: 22 Copynumber: 19.4 Consensus size: 22
1214093 TTGTGTAAAA
*
1214103 ACCTGTGTGACATTGTGTAGTC
1 ACCTGTGTGACAGTGTGTAGTC
* * *
1214125 ATCTTTGTGACAGTGTGCAGTC
1 ACCTGTGTGACAGTGTGTAGTC
* *
1214147 ACCTGTGTGACAGTGGGTGGTC
1 ACCTGTGTGACAGTGTGTAGTC
** * * * *
1214169 ATTTATGTGGCA-TGTATATTC
1 ACCTGTGTGACAGTGTGTAGTC
* *
1214190 AACTGTGTGA-AGAAGTGTAGTC
1 ACCTGTGTGACAG-TGTGTAGTC
*
1214212 ACCTGTTTGA-AGATGTGTAGTC
1 ACCTGTGTGACAG-TGTGTAGTC
* * *
1214234 ACCTGTGT-AAAGAGGGGTAGTC
1 ACCTGTGTGACAG-TGTGTAGTC
*
1214256 ACCTGTTTGA-AGATGTGTAGTC
1 ACCTGTGTGACAG-TGTGTAGTC
* * * *
1214278 ACCTGT-TTAAAGAGGGGTAGTC
1 ACCTGTGTGACAG-TGTGTAGTC
*
1214300 ACCTGTTTGA-AGATGTGTAGTC
1 ACCTGTGTGACAG-TGTGTAGTC
* * *
1214322 ACCTGTGT-AAAGAGAGGTAGTC
1 ACCTGTGTGACAGTG-TGTAGTC
*
1214344 ACCTGTTTGA-AGATGTGTAGTC
1 ACCTGTGTGACAG-TGTGTAGTC
* * *
1214366 ACCTGTGT-AAAGAGAGGTAGTC
1 ACCTGTGTGACAGTG-TGTAGTC
* *
1214388 ACCTGTTTTA-AGATGTGTAGTC
1 ACCTGTGTGACAG-TGTGTAGTC
* *
1214410 ACCTGTGT-AAAGATGGGTAGTC
1 ACCTGTGTGACAG-TGTGTAGTC
* *
1214432 ACCTGTGT-AAAGATGGGTAGTC
1 ACCTGTGTGACAG-TGTGTAGTC
* * *
1214454 ATCTGTGTAAACA-TGGGTAGTC
1 ACCTGTGT-GACAGTGTGTAGTC
*
1214476 ACCTGTTTGA-AGATGTGTAGTC
1 ACCTGTGTGACAG-TGTGTAGTC
* * *
1214498 ACCTGTGT-AAAGAGGGGTAGTC
1 ACCTGTGTGACAG-TGTGTAGTC
1214520 ACCTGTGT
1 ACCTGTGT
1214528 AAAGATGGAT
Statistics
Matches: 321, Mismatches: 62, Indels: 40
0.76 0.15 0.09
Matches are distributed among these distances:
20 2 0.01
21 21 0.07
22 289 0.90
23 7 0.02
24 2 0.01
ACGTcount: A:0.24, C:0.14, G:0.30, T:0.32
Consensus pattern (22 bp):
ACCTGTGTGACAGTGTGTAGTC
Found at i:1214255 original size:44 final size:44
Alignment explanation
Indices: 1214192--1214564 Score: 568
Period size: 44 Copynumber: 8.5 Consensus size: 44
1214182 GTATATTCAA
* * *
1214192 CTGTGTGAAGAAGTGTAGTCACCTGTTTGAAGATGTGTAGTCAC
1 CTGTGTAAAGAGGGGTAGTCACCTGTTTGAAGATGTGTAGTCAC
1214236 CTGTGTAAAGAGGGGTAGTCACCTGTTTGAAGATGTGTAGTCAC
1 CTGTGTAAAGAGGGGTAGTCACCTGTTTGAAGATGTGTAGTCAC
*
1214280 CTGTTTAAAGAGGGGTAGTCACCTGTTTGAAGATGTGTAGTCAC
1 CTGTGTAAAGAGGGGTAGTCACCTGTTTGAAGATGTGTAGTCAC
*
1214324 CTGTGTAAAGAGAGGTAGTCACCTGTTTGAAGATGTGTAGTCAC
1 CTGTGTAAAGAGGGGTAGTCACCTGTTTGAAGATGTGTAGTCAC
* *
1214368 CTGTGTAAAGAGAGGTAGTCACCTGTTTTAAGATGTGTAGTCAC
1 CTGTGTAAAGAGGGGTAGTCACCTGTTTGAAGATGTGTAGTCAC
* * * * *
1214412 CTGTGTAAAGATGGGTAGTCACCTGTGTAAAGATGGGTAGTCAT
1 CTGTGTAAAGAGGGGTAGTCACCTGTTTGAAGATGTGTAGTCAC
* *
1214456 CTGTGTAAACATGGGTAGTCACCTGTTTGAAGATGTGTAGTCAC
1 CTGTGTAAAGAGGGGTAGTCACCTGTTTGAAGATGTGTAGTCAC
* *
1214500 CTGTGTAAAGAGGGGTAGTCACCTGTGTAAAGATG-GATAGTCAC
1 CTGTGTAAAGAGGGGTAGTCACCTGTTTGAAGATGTG-TAGTCAC
* *
1214544 CCGTGTAAAGATGGGTAGTCA
1 CTGTGTAAAGAGGGGTAGTCA
1214565 TCGGTGTGAG
Statistics
Matches: 304, Mismatches: 24, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
43 1 0.00
44 303 1.00
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.30
Consensus pattern (44 bp):
CTGTGTAAAGAGGGGTAGTCACCTGTTTGAAGATGTGTAGTCAC
Found at i:1214571 original size:22 final size:22
Alignment explanation
Indices: 1214192--1214564 Score: 453
Period size: 22 Copynumber: 17.0 Consensus size: 22
1214182 GTATATTCAA
* * *
1214192 CTGTGTGAAGAAGTGTAGTCAC
1 CTGTGTAAAGATGGGTAGTCAC
* * *
1214214 CTGTTTGAAGATGTGTAGTCAC
1 CTGTGTAAAGATGGGTAGTCAC
*
1214236 CTGTGTAAAGAGGGGTAGTCAC
1 CTGTGTAAAGATGGGTAGTCAC
* * *
1214258 CTGTTTGAAGATGTGTAGTCAC
1 CTGTGTAAAGATGGGTAGTCAC
* *
1214280 CTGTTTAAAGAGGGGTAGTCAC
1 CTGTGTAAAGATGGGTAGTCAC
* * *
1214302 CTGTTTGAAGATGTGTAGTCAC
1 CTGTGTAAAGATGGGTAGTCAC
1214324 CTGTGTAAAGA-GAGGTAGTCAC
1 CTGTGTAAAGATG-GGTAGTCAC
* * *
1214346 CTGTTTGAAGATGTGTAGTCAC
1 CTGTGTAAAGATGGGTAGTCAC
1214368 CTGTGTAAAGA-GAGGTAGTCAC
1 CTGTGTAAAGATG-GGTAGTCAC
* * *
1214390 CTGTTTTAAGATGTGTAGTCAC
1 CTGTGTAAAGATGGGTAGTCAC
1214412 CTGTGTAAAGATGGGTAGTCAC
1 CTGTGTAAAGATGGGTAGTCAC
*
1214434 CTGTGTAAAGATGGGTAGTCAT
1 CTGTGTAAAGATGGGTAGTCAC
*
1214456 CTGTGTAAACATGGGTAGTCAC
1 CTGTGTAAAGATGGGTAGTCAC
* * *
1214478 CTGTTTGAAGATGTGTAGTCAC
1 CTGTGTAAAGATGGGTAGTCAC
*
1214500 CTGTGTAAAGAGGGGTAGTCAC
1 CTGTGTAAAGATGGGTAGTCAC
*
1214522 CTGTGTAAAGATGGATAGTCAC
1 CTGTGTAAAGATGGGTAGTCAC
*
1214544 CCGTGTAAAGATGGGTAGTCA
1 CTGTGTAAAGATGGGTAGTCA
1214565 TCGGTGTGAG
Statistics
Matches: 301, Mismatches: 46, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
21 2 0.01
22 297 0.99
23 2 0.01
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.30
Consensus pattern (22 bp):
CTGTGTAAAGATGGGTAGTCAC
Found at i:1221737 original size:17 final size:17
Alignment explanation
Indices: 1221715--1221747 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1221705 CAAATTAACT
1221715 TAAAATAACAGAACAAA
1 TAAAATAACAGAACAAA
*
1221732 TAAAATAACCGAACAA
1 TAAAATAACAGAACAA
1221748 CTGAAAAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.15, G:0.06, T:0.12
Consensus pattern (17 bp):
TAAAATAACAGAACAAA
Found at i:1221988 original size:18 final size:18
Alignment explanation
Indices: 1221967--1222002 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1221957 CTTAACGAAC
* *
1221967 GAAAATAATCGAACAACT
1 GAAAATAACCAAACAACT
1221985 GAAAATAACCAAACAACT
1 GAAAATAACCAAACAACT
1222003 TGCAAAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.58, C:0.19, G:0.08, T:0.14
Consensus pattern (18 bp):
GAAAATAACCAAACAACT
Found at i:1222426 original size:22 final size:22
Alignment explanation
Indices: 1222395--1222453 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 22
1222385 TATCTGTAAA
* *
1222395 TTGATATGGCTCTATTCGTTAG
1 TTGATATGGCTATATTCATTAG
*
1222417 TTGATGTGGCTATATTCATTAG
1 TTGATATGGCTATATTCATTAG
*
1222439 TTGATATGACTATAT
1 TTGATATGGCTATAT
1222454 CCGTTAATTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.24, C:0.10, G:0.20, T:0.46
Consensus pattern (22 bp):
TTGATATGGCTATATTCATTAG
Found at i:1222468 original size:22 final size:22
Alignment explanation
Indices: 1222443--1223386 Score: 1006
Period size: 22 Copynumber: 42.5 Consensus size: 22
1222433 CATTAGTTGA
1222443 TATGACTATATCCGTTAATTGT
1 TATGACTATATCCGTTAATTGT
1222465 TATGACTATATCCGTTACGACCGTTAGTT
1 TATGACTATATCCGTTA--A---TT-G-T
* *
1222494 GATATGAATATATCCATTAATTGT
1 --TATGACTATATCCGTTAATTGT
*
1222518 TATGACTATATCCGTTATTTGT
1 TATGACTATATCCGTTAATTGT
* *
1222540 TATTACTATATCCGTTAATTGG
1 TATGACTATATCCGTTAATTGT
* * * *
1222562 TATGGCTATATCCGTTAGTAGA
1 TATGACTATATCCGTTAATTGT
* *
1222584 TATGAATATATCCATTAATTGT
1 TATGACTATATCCGTTAATTGT
* * *
1222606 TATGACTATATCCGTTAGTAGA
1 TATGACTATATCCGTTAATTGT
* *
1222628 TATGAATATATCCATTAATTGT
1 TATGACTATATCCGTTAATTGT
* * *
1222650 TATGACAATATACGTTAATTGG
1 TATGACTATATCCGTTAATTGT
*
1222672 TATGACTATATACGTTAATTGT
1 TATGACTATATCCGTTAATTGT
* *
1222694 TATGACTATATACGTTAATTGG
1 TATGACTATATCCGTTAATTGT
*
1222716 TATGGCTATATCCGTTAATTGT
1 TATGACTATATCCGTTAATTGT
* * *
1222738 TATGACTATATCCGTTAGTAGA
1 TATGACTATATCCGTTAATTGT
* *
1222760 TATGAATATATCCATTAATTGT
1 TATGACTATATCCGTTAATTGT
* *
1222782 TATGACTATATACGTTAATTGA
1 TATGACTATATCCGTTAATTGT
* *
1222804 TATGGCTATATCCATTAATTGT
1 TATGACTATATCCGTTAATTGT
* *
1222826 TATGGCTATATCCGTTATTTGT
1 TATGACTATATCCGTTAATTGT
* *
1222848 TATTACTATATCCGTTAATTGG
1 TATGACTATATCCGTTAATTGT
* * * *
1222870 TATGGCTATATCCGTTAGTAGA
1 TATGACTATATCCGTTAATTGT
* *
1222892 TATGAATATATCCATTAATTGT
1 TATGACTATATCCGTTAATTGT
* *
1222914 TATGACTATATACGTTAATTGA
1 TATGACTATATCCGTTAATTGT
* *
1222936 TATGGCTATATCCATTAATTGT
1 TATGACTATATCCGTTAATTGT
* *
1222958 TATGGCTATATCCGTTATTTGT
1 TATGACTATATCCGTTAATTGT
* *
1222980 TATTACTATATCCGTTAATTGG
1 TATGACTATATCCGTTAATTGT
* * * *
1223002 TATGGCTATATCCGTTAGTAGA
1 TATGACTATATCCGTTAATTGT
* *
1223024 TATGAATATATCCATTAATTGT
1 TATGACTATATCCGTTAATTGT
** *
1223046 TATGACTATATAAGTTAATTGG
1 TATGACTATATCCGTTAATTGT
*
1223068 TATGACTATATACGTTAATTGT
1 TATGACTATATCCGTTAATTGT
* * *
1223090 TATGACTATATACGTTTATTGG
1 TATGACTATATCCGTTAATTGT
*
1223112 TATGGCTATATCCGTTAATTGT
1 TATGACTATATCCGTTAATTGT
* * *
1223134 TATGACTATATCCGTTAGTAGA
1 TATGACTATATCCGTTAATTGT
* *
1223156 TATGAATATATCCATTAATTGT
1 TATGACTATATCCGTTAATTGT
* *
1223178 TATGACTATATACGTTAATTGA
1 TATGACTATATCCGTTAATTGT
* *
1223200 TATGGCTATATCCGTTAATTGA
1 TATGACTATATCCGTTAATTGT
*
1223222 TATGGCTATATCCGTTAATTGT
1 TATGACTATATCCGTTAATTGT
* * *
1223244 TATGACTATATCCGTTAGTAGA
1 TATGACTATATCCGTTAATTGT
* * * *
1223266 TATGAATATATCCATTTATTTT
1 TATGACTATATCCGTTAATTGT
*
1223288 TATGACTATATCCGTTAATTGA
1 TATGACTATATCCGTTAATTGT
* *
1223310 TATGGCTATATCCGTTAATTGA
1 TATGACTATATCCGTTAATTGT
* * *
1223332 TATGACTATATACGTTAGTTGA
1 TATGACTATATCCGTTAATTGT
* *
1223354 TATGACTATATCTGTTAATTGC
1 TATGACTATATCCGTTAATTGT
1223376 TATGACTATAT
1 TATGACTATAT
1223387 ACGAGGACTG
Statistics
Matches: 761, Mismatches: 152, Indels: 18
0.82 0.16 0.02
Matches are distributed among these distances:
22 736 0.97
24 2 0.00
25 1 0.00
26 2 0.00
27 2 0.00
28 1 0.00
29 2 0.00
31 15 0.02
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.43
Consensus pattern (22 bp):
TATGACTATATCCGTTAATTGT
Found at i:1222726 original size:132 final size:132
Alignment explanation
Indices: 1222485--1223386 Score: 1257
Period size: 132 Copynumber: 6.8 Consensus size: 132
1222475 TCCGTTACGA
* * * * *
1222485 CCGTTAGTTGATATGAATATATCCATTAATTGTTATGACTATATCCGTTATTTGTTATTACTATA
1 CCGTTAGTAGATATGAATATATCCATTAATTGTTATGACTATATACGTTAATTGATATGACTATA
* * * * * *
1222550 TCCGTTAATTGGTATGGCTATATCCGTTAGTAGATATGAATATATCCATTAATTGTTATGACTAT
66 TCCGTTAATTGTTATGGCTATATCCGTTAATTGTTATGACTATATCCGTTAATTGTTATGACTAT
1222615 AT
131 AT
* *
1222617 CCGTTAGTAGATATGAATATATCCATTAATTGTTATGACAATATACGTTAATTGGTATGACTATA
1 CCGTTAGTAGATATGAATATATCCATTAATTGTTATGACTATATACGTTAATTGATATGACTATA
* * * * *
1222682 TACGTTAATTGTTATGACTATATACGTTAATTGGTATGGCTATATCCGTTAATTGTTATGACTAT
66 TCCGTTAATTGTTATGGCTATATCCGTTAATTGTTATGACTATATCCGTTAATTGTTATGACTAT
1222747 AT
131 AT
*
1222749 CCGTTAGTAGATATGAATATATCCATTAATTGTTATGACTATATACGTTAATTGATATGGCTATA
1 CCGTTAGTAGATATGAATATATCCATTAATTGTTATGACTATATACGTTAATTGATATGACTATA
* * * * *
1222814 TCCATTAATTGTTATGGCTATATCCGTTATTTGTTATTACTATATCCGTTAATTGGTATGGCTAT
66 TCCGTTAATTGTTATGGCTATATCCGTTAATTGTTATGACTATATCCGTTAATTGTTATGACTAT
1222879 AT
131 AT
*
1222881 CCGTTAGTAGATATGAATATATCCATTAATTGTTATGACTATATACGTTAATTGATATGGCTATA
1 CCGTTAGTAGATATGAATATATCCATTAATTGTTATGACTATATACGTTAATTGATATGACTATA
* * * * *
1222946 TCCATTAATTGTTATGGCTATATCCGTTATTTGTTATTACTATATCCGTTAATTGGTATGGCTAT
66 TCCGTTAATTGTTATGGCTATATCCGTTAATTGTTATGACTATATCCGTTAATTGTTATGACTAT
1223011 AT
131 AT
* *
1223013 CCGTTAGTAGATATGAATATATCCATTAATTGTTATGACTATATAAGTTAATTGGTATGACTATA
1 CCGTTAGTAGATATGAATATATCCATTAATTGTTATGACTATATACGTTAATTGATATGACTATA
* * * * * *
1223078 TACGTTAATTGTTATGACTATATACGTTTATTGGTATGGCTATATCCGTTAATTGTTATGACTAT
66 TCCGTTAATTGTTATGGCTATATCCGTTAATTGTTATGACTATATCCGTTAATTGTTATGACTAT
1223143 AT
131 AT
*
1223145 CCGTTAGTAGATATGAATATATCCATTAATTGTTATGACTATATACGTTAATTGATATGGCTATA
1 CCGTTAGTAGATATGAATATATCCATTAATTGTTATGACTATATACGTTAATTGATATGACTATA
* * * * *
1223210 TCCGTTAATTGATATGGCTATATCCGTTAATTGTTATGACTATATCCGTTAGTAGATATGAATAT
66 TCCGTTAATTGTTATGGCTATATCCGTTAATTGTTATGACTATATCCGTTAATTGTTATGACTAT
1223275 AT
131 AT
* *** * * * * *
1223277 CCATTTA-TTTTTATGACTATATCCGTTAATTGATATGGCTATATCCGTTAATTGATATGACTAT
1 CC-GTTAGTAGATATGAATATATCCATTAATTGTTATGACTATATACGTTAATTGATATGACTAT
* * * * * *
1223341 ATACGTTAGTTGATATGACTATATCTGTTAATTGCTATGACTATAT
65 ATCCGTTAATTGTTATGGCTATATCCGTTAATTGTTATGACTATAT
1223387 ACGAGGACTG
Statistics
Matches: 697, Mismatches: 72, Indels: 2
0.90 0.09 0.00
Matches are distributed among these distances:
132 694 1.00
133 3 0.00
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.43
Consensus pattern (132 bp):
CCGTTAGTAGATATGAATATATCCATTAATTGTTATGACTATATACGTTAATTGATATGACTATA
TCCGTTAATTGTTATGGCTATATCCGTTAATTGTTATGACTATATCCGTTAATTGTTATGACTAT
AT
Found at i:1225623 original size:4 final size:4
Alignment explanation
Indices: 1225614--1225648 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
1225604 ATTGCTTGAT
1225614 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCT
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCT
1225649 TTTTTTCTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.23, C:0.26, G:0.00, T:0.51
Consensus pattern (4 bp):
TCTA
Found at i:1226647 original size:22 final size:22
Alignment explanation
Indices: 1226621--1227005 Score: 182
Period size: 22 Copynumber: 17.9 Consensus size: 22
1226611 AATTAATTAA
1226621 TATTGCG-TTAAATCGCAATAGT
1 TATTGCGATTAAA-CGCAATAGT
* * * *
1226643 TATTGCGTTTTAATGCACT-GT
1 TATTGCGATTAAACGCAATAGT
* **
1226664 T-TTGCGTTTATTCGCAAT-GT
1 TATTGCGATTAAACGCAATAGT
* * *
1226684 ATTTTGCGTTTAAACGCAAAAG-
1 -TATTGCGATTAAACGCAATAGT
* **
1226706 -ATTGCGATAAAACGCAATAAC
1 TATTGCGATTAAACGCAATAGT
1226727 TATTGCGATTAAACGCAA-AGT
1 TATTGCGATTAAACGCAATAGT
*
1226748 GGATTGCG-TATAAACGCAA-AGT
1 -TATTGCGAT-TAAACGCAATAGT
*
1226770 T-TTGCGTTTAAACGCAA-AG-
1 TATTGCGATTAAACGCAATAGT
* ** *
1226789 TATTGCGTTTAATTGCAA-AAT
1 TATTGCGATTAAACGCAATAGT
* * * **
1226810 TATTGTGTTTAAACGCAAAAAAA
1 TATTGCGATTAAACGC-AATAGT
*
1226833 TATTGCGTTTAAACGCAA-AGCTAT
1 TATTGCGATTAAACGCAATAG---T
*
1226857 TATTGCGTTTAAACGCAATATGT
1 TATTGCGATTAAACGCAATA-GT
*
1226880 T-TTGCGAATAAACGCAACATA-T
1 TATTGCGATTAAACGC-A-ATAGT
*
1226902 T-TTGCGATTAAACGCAATAAT
1 TATTGCGATTAAACGCAATAGT
* * *
1226923 TTTTGTGATTAAACGCAATAAT
1 TATTGCGATTAAACGCAATAGT
*
1226945 T-TTGCGATTAAATGCAAT-GAT
1 TATTGCGATTAAACGCAATAG-T
*
1226966 T-TTGCGATTAAATGCAAT-GAT
1 TATTGCGATTAAACGCAATAG-T
* * *
1226987 TTTTGCGTTTAATCGCAAT
1 TATTGCGATTAAACGCAAT
1227006 TAATTCATTT
Statistics
Matches: 298, Mismatches: 41, Indels: 48
0.77 0.11 0.12
Matches are distributed among these distances:
19 1 0.00
20 63 0.21
21 62 0.21
22 124 0.42
23 25 0.08
24 21 0.07
25 1 0.00
26 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (22 bp):
TATTGCGATTAAACGCAATAGT
Found at i:1226744 original size:64 final size:62
Alignment explanation
Indices: 1226676--1227007 Score: 168
Period size: 64 Copynumber: 5.1 Consensus size: 62
1226666 TGCGTTTATT
* *
1226676 CGCAATGTATTTTGCGTTTAAACGCAAAAGATTGCGATAAAACGCAATAACTATTGCGATTAAA
1 CGCAAT-TATTTTGCGTTTAAACGCAAAAGATTGCGATTAAACGCAA-AATTATTGCGATTAAA
* *** * * * * * *
1226740 CGCAAAGTGGATTGCGTATAAACGC-AAAGTTTTGCGTTTAAACGC-AAAGTATTGCGTTTAAT
1 CGC-AATTATTTTGCGTTTAAACGCAAAAG-ATTGCGATTAAACGCAAAATTATTGCGATTAAA
* * * * * *
1226802 TGCAA-AATTATTGTGTTTAAACGCAAAAAAATATTGCGTTTAAACGCAAAGCTATTATTGCGTT
1 CGCAATTATT-TTGCGTTTAAACGC---AAAAGATTGCGATTAAACGCAAA---ATTATTGCGAT
1226866 TAAA
59 TAAA
* ** ** * *
1226870 CGCAATATGTTTTGCGAATAAACGCAACATATTTTGCGATTAAACGCAATAATTTTTGTGATTAA
1 CGCAAT-TATTTTGCGTTTAAACGCAA-A-AGATTGCGATTAAACGCAA-AATTATTGCGATTAA
1226935 A
62 A
* * * * * * * * *
1226936 CGCAATAATTTTGCGATTAAATGC-AATGATTTTGCGATTAAATGCAATGATTTTTGCGTTTAAT
1 CGCAATTATTTTGCGTTTAAACGCAAAAGA--TTGCGATTAAACGCAA-AATTATTGCGATTAAA
1227000 CGCAATTA
1 CGCAATTA
1227008 ATTCATTTGC
Statistics
Matches: 204, Mismatches: 46, Indels: 36
0.71 0.16 0.13
Matches are distributed among these distances:
61 14 0.07
62 15 0.07
63 6 0.03
64 79 0.39
65 21 0.10
66 20 0.10
67 1 0.00
68 34 0.17
69 12 0.06
70 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (62 bp):
CGCAATTATTTTGCGTTTAAACGCAAAAGATTGCGATTAAACGCAAAATTATTGCGATTAAA
Found at i:1226773 original size:84 final size:84
Alignment explanation
Indices: 1226684--1226918 Score: 217
Period size: 84 Copynumber: 2.7 Consensus size: 84
1226674 TTCGCAATGT
**
1226684 ATTTTGCGTTTAAACGCAAAAG-ATTGCGATAAAACGCAATAACTATTGCGATTAAACGCAAAGT
1 ATTTTGCGTTTAAACGCAAAAGTATTGCGATAAAACGCAA-AA-TATTGCGATTAAACGCAAAAA
*
1226748 GGATTGCGTATAAACGCAAAG
64 AGATTGCGTATAAACGCAAAG
* * ** * *
1226769 -TTTTGCGTTTAAACGC-AAAGTATTGCGTTTAATTGCAAAATTATTGTGTTTAAACGCAAAAAA
1 ATTTTGCGTTTAAACGCAAAAGTATTGCGATAAAACGCAAAA-TATTGCGATTAAACGC-AAAAA
* *
1226832 ATATTGCGTTTAAACGCAAAG
64 AGATTGCGTATAAACGCAAAG
* * *
1226853 CTATTATTGCGTTTAAACGCAATATGTTTTGCGA-ATAAACGCAACATATTTTGCGATTAAACGC
1 --ATT-TTGCGTTTAAACGCAA-AAGTATTGCGATA-AAACGCAA-A-ATATTGCGATTAAACGC
1226917 AA
59 AA
1226919 TAATTTTTGT
Statistics
Matches: 118, Mismatches: 21, Indels: 17
0.76 0.13 0.11
Matches are distributed among these distances:
83 20 0.17
84 50 0.42
87 2 0.02
88 14 0.12
89 1 0.01
90 16 0.14
91 14 0.12
92 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.31
Consensus pattern (84 bp):
ATTTTGCGTTTAAACGCAAAAGTATTGCGATAAAACGCAAAATATTGCGATTAAACGCAAAAAAG
ATTGCGTATAAACGCAAAG
Found at i:1226953 original size:21 final size:21
Alignment explanation
Indices: 1226684--1227010 Score: 191
Period size: 22 Copynumber: 15.1 Consensus size: 21
1226674 TTCGCAATGT
*
1226684 ATTTTGCGTTTAAACGCAA-A
1 ATTTTGCGATTAAACGCAATA
** *
1226704 AGATTGCGATAAAACGCAATA
1 ATTTTGCGATTAAACGCAATA
*
1226725 ACTATTGCGATTAAACGCAA-A
1 A-TTTTGCGATTAAACGCAATA
* *
1226746 GTGGATTGCG-TATAAACGCAA-A
1 AT--TTTGCGAT-TAAACGCAATA
* *
1226768 GTTTTGCGTTTAAACGCAA-A
1 ATTTTGCGATTAAACGCAATA
* * * **
1226788 GTATTGCGTTTAATTGCAA-A
1 ATTTTGCGATTAAACGCAATA
* * *
1226808 ATTATTGTGTTTAAACGCAAAAAA
1 ATT-TTGCGATTAAACGC--AATA
* *
1226832 ATATTGCGTTTAAACGCAA-A
1 ATTTTGCGATTAAACGCAATA
*
1226852 GCTATTATTGCGTTTAAACGCAATA
1 ---ATT-TTGCGATTAAACGCAATA
* * *
1226877 TGTTTTGCGAATAAACGCAACA
1 -ATTTTGCGATTAAACGCAATA
1226899 TATTTTGCGATTAAACGCAATA
1 -ATTTTGCGATTAAACGCAATA
*
1226921 ATTTTTGTGATTAAACGCAATA
1 A-TTTTGCGATTAAACGCAATA
* *
1226943 ATTTTGCGATTAAATGCAATG
1 ATTTTGCGATTAAACGCAATA
*
1226964 ATTTTGCGATTAAATGCAATGA
1 ATTTTGCGATTAAACGCAAT-A
* * *
1226986 TTTTTGCGTTTAATCGCAATTA
1 ATTTTGCGATTAAACGCAA-TA
1227008 ATT
1 ATT
1227011 CATTTGCTGA
Statistics
Matches: 253, Mismatches: 36, Indels: 34
0.78 0.11 0.11
Matches are distributed among these distances:
20 50 0.20
21 56 0.22
22 106 0.42
23 21 0.08
24 19 0.08
25 1 0.00
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (21 bp):
ATTTTGCGATTAAACGCAATA
Found at i:1228024 original size:2 final size:2
Alignment explanation
Indices: 1228017--1228051 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1228007 TTTAAATATA
1228017 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1228052 TGGAAAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1230436 original size:5 final size:5
Alignment explanation
Indices: 1230426--1230473 Score: 55
Period size: 5 Copynumber: 9.6 Consensus size: 5
1230416 ATTTAATTAA
*
1230426 TTTGT TTTGT TTTGT TTTGT TTTG- TTTGT ATGTT-T TTTGG TTTGT TTT
1 TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT -T-TTGT TTTGT TTTGT TTT
1230474 TAAAAAGGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
4 6 0.16
5 27 0.73
6 2 0.05
7 2 0.05
ACGTcount: A:0.02, C:0.00, G:0.21, T:0.77
Consensus pattern (5 bp):
TTTGT
Found at i:1233289 original size:19 final size:20
Alignment explanation
Indices: 1233267--1233311 Score: 67
Period size: 19 Copynumber: 2.3 Consensus size: 20
1233257 GTCTTTTACA
1233267 AATTTTTT-TATCTTCTTTT-
1 AATTTTTTGT-TCTTCTTTTC
1233286 AATTTTTTGTTCTTCTTTTC
1 AATTTTTTGTTCTTCTTTTC
1233306 AATTTT
1 AATTTT
1233312 ATGAATTAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.16, C:0.11, G:0.02, T:0.71
Consensus pattern (20 bp):
AATTTTTTGTTCTTCTTTTC
Found at i:1237265 original size:90 final size:90
Alignment explanation
Indices: 1237164--1237339 Score: 214
Period size: 90 Copynumber: 2.0 Consensus size: 90
1237154 CTAAAGTTCC
* * *
1237164 TTTCTTTAAAAGTT-TTT-TTTTAATAGAAAAAAAAATGTATT-AAATGACAAAAAGGCAGAAAA
1 TTTCTTAAAAAGTTATTTCTTTTAA-ACAAAAAAAAATGT-TTGAAATGA-AAAAAGGAAGAAAA
* *
1237226 TTTCCCAACAATTTTACAAAAAAAATCT
63 TGTCCCAACAATTTGACAAAAAAAATCT
* * * *
1237254 TTTCTTAAAAAGTTATTTCTTTTGAACAAAAAGAAATGTTTGTAATGATAAAAGGAAGAAAATGT
1 TTTCTTAAAAAGTTATTTCTTTTAAACAAAAAAAAATGTTTGAAATGAAAAAAGGAAGAAAATGT
*
1237319 CCCAACAATTTGATAAAAAAA
66 CCCAACAATTTGACAAAAAAA
1237340 CTAATAAATA
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
90 48 0.66
91 20 0.27
92 5 0.07
ACGTcount: A:0.48, C:0.09, G:0.10, T:0.32
Consensus pattern (90 bp):
TTTCTTAAAAAGTTATTTCTTTTAAACAAAAAAAAATGTTTGAAATGAAAAAAGGAAGAAAATGT
CCCAACAATTTGACAAAAAAAATCT
Found at i:1241975 original size:16 final size:17
Alignment explanation
Indices: 1241944--1241976 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1241934 TTGAACATTT
*
1241944 TGGAAGTGTGAAATAAA
1 TGGAAGTGTAAAATAAA
1241961 TGGAAGTG-AAAATAAA
1 TGGAAGTGTAAAATAAA
1241977 GAATTCAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.52, C:0.00, G:0.27, T:0.21
Consensus pattern (17 bp):
TGGAAGTGTAAAATAAA
Found at i:1242096 original size:12 final size:12
Alignment explanation
Indices: 1242081--1242117 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
1242071 TTTTCCCTGG
1242081 TTTTGGTTTTTT
1 TTTTGGTTTTTT
1242093 TTTTGGTTTTGTT
1 TTTTGGTTTT-TT
1242106 TTTT-GTTTTTT
1 TTTTGGTTTTTT
1242117 T
1 T
1242118 GTGTGTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 3 0.12
12 15 0.62
13 6 0.25
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (12 bp):
TTTTGGTTTTTT
Found at i:1242099 original size:18 final size:18
Alignment explanation
Indices: 1242078--1242114 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1242068 TTTTTTTCCC
1242078 TGGTTTTGGTTTTTT-TTT
1 TGGTTTT-GTTTTTTGTTT
1242096 TGGTTTTGTTTTTTGTTT
1 TGGTTTTGTTTTTTGTTT
1242114 T
1 T
1242115 TTTGTGTGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (18 bp):
TGGTTTTGTTTTTTGTTT
Found at i:1242127 original size:26 final size:24
Alignment explanation
Indices: 1242081--1242131 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
1242071 TTTTCCCTGG
*
1242081 TTTTGGTTTTTTTTTTGGTTTTGT
1 TTTTGGTTTTTTTTGTGGTTTTGT
*
1242105 TTTTTGTTTTTTTGTGTGTGTTTTGT
1 TTTTGGTTTTTTT-TGTG-GTTTTGT
1242131 T
1 T
1242132 AGTTTTTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 12 0.52
25 3 0.13
26 8 0.35
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (24 bp):
TTTTGGTTTTTTTTGTGGTTTTGT
Found at i:1242639 original size:16 final size:16
Alignment explanation
Indices: 1242618--1242668 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
1242608 AATCATAAAC
1242618 AAAAACAAAACCAAAA
1 AAAAACAAAACCAAAA
1242634 AAAAACAAAACCAAAA
1 AAAAACAAAACCAAAA
*
1242650 AAAAA-AAACCCAAGAA
1 AAAAACAAAACCAA-AA
1242666 AAA
1 AAA
1242669 TCTGAAATCG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
15 7 0.21
16 26 0.79
ACGTcount: A:0.80, C:0.18, G:0.02, T:0.00
Consensus pattern (16 bp):
AAAAACAAAACCAAAA
Found at i:1242642 original size:22 final size:20
Alignment explanation
Indices: 1242614--1242657 Score: 61
Period size: 22 Copynumber: 2.1 Consensus size: 20
1242604 TTTTAATCAT
1242614 AAACAAAAACAAAACCAAAAAA
1 AAACAAAAACAAAA--AAAAAA
*
1242636 AAACAAAACCAAAAAAAAAA
1 AAACAAAAACAAAAAAAAAA
1242656 AA
1 AA
1242658 CCCAAGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.38
22 13 0.62
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (20 bp):
AAACAAAAACAAAAAAAAAA
Found at i:1242668 original size:15 final size:14
Alignment explanation
Indices: 1242618--1242659 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
1242608 AATCATAAAC
*
1242618 AAAAACAAAACCAAA
1 AAAAAAAAAACC-AA
1242633 AAAAAACAAAACCAA
1 AAAAAA-AAAACCAA
1242648 AAAAAAAAAACC
1 AAAAAAAAAACC
1242660 CAAGAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 6 0.24
15 13 0.52
16 6 0.24
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAACCAA
Found at i:1260091 original size:19 final size:19
Alignment explanation
Indices: 1260064--1261005 Score: 1296
Period size: 19 Copynumber: 48.4 Consensus size: 19
1260054 GTAAAAATTT
*
1260064 CTCCATTGTATATAGTATA
1 CTCCATTGTATATAGGATA
*
1260083 CTACATTGTATATAGGATA
1 CTCCATTGTATATAGGATA
1260102 CTCCATTGTATATAGGATA
1 CTCCATTGTATATAGGATA
* *
1260121 CTCCATTGTATCTAAGATA
1 CTCCATTGTATATAGGATA
*
1260140 CTCCATTGTATCTAGGATA
1 CTCCATTGTATATAGGATA
*
1260159 CTCCATGGTATATAGGATA
1 CTCCATTGTATATAGGATA
*
1260178 CTCCATTGTATATATGATA
1 CTCCATTGTATATAGGATA
*
1260197 TTCCATTGTATATAGGATA
1 CTCCATTGTATATAGGATA
*
1260216 CTCCATGGTATATAGGATA
1 CTCCATTGTATATAGGATA
*
1260235 CTCCATGGTATATAGGATA
1 CTCCATTGTATATAGGATA
1260254 CTCCATTGTATATAGGATA
1 CTCCATTGTATATAGGATA
*
1260273 CTCCATGGTATATAGGATA
1 CTCCATTGTATATAGGATA
1260292 CTCCATTGTATATATAGGATA
1 CTCCATTG--TATATAGGATA
* *
1260313 CTCCATAGCATATAGGATA
1 CTCCATTGTATATAGGATA
* *
1260332 CTCCATGGTATATAGTATA
1 CTCCATTGTATATAGGATA
*
1260351 CTCCATGGTATATAAAGGATA
1 CTCCATTGTATAT--AGGATA
1260372 CTCCATTGTATATAGGATA
1 CTCCATTGTATATAGGATA
*
1260391 CTCCATGGTATATAGGATA
1 CTCCATTGTATATAGGATA
1260410 CTCCA-TGATATATAGGATA
1 CTCCATTG-TATATAGGATA
1260429 CTCCATTGTATATATAGGATA
1 CTCCATTG--TATATAGGATA
1260450 CTCCATTGTATATAGGATA
1 CTCCATTGTATATAGGATA
1260469 CTCCATTGTATATAGGATA
1 CTCCATTGTATATAGGATA
*
1260488 ATCCATTGTATATAGGATA
1 CTCCATTGTATATAGGATA
*
1260507 CTCCATTGTATCTAGGATA
1 CTCCATTGTATATAGGATA
* *
1260526 CTCCATGGTATCTAGGATA
1 CTCCATTGTATATAGGATA
* *
1260545 CTCCATGGTATCTAGGATA
1 CTCCATTGTATATAGGATA
*
1260564 CTCCATGGTATATAGGATA
1 CTCCATTGTATATAGGATA
*
1260583 CTCCATGGTATATAGGATA
1 CTCCATTGTATATAGGATA
1260602 CTCCATTGTATATATAGGATA
1 CTCCATTG--TATATAGGATA
1260623 CTCCATTGTATATAGGATA
1 CTCCATTGTATATAGGATA
1260642 CTCCATTGTATATAGGATA
1 CTCCATTGTATATAGGATA
*
1260661 CTCCATGGTATATAGGATA
1 CTCCATTGTATATAGGATA
1260680 CTCCATTGTATATATAGGATA
1 CTCCATTG--TATATAGGATA
1260701 CTCCATTGTATATATAGGATA
1 CTCCATTG--TATATAGGATA
1260722 CTCCATTGTATATA-GAGTA
1 CTCCATTGTATATAGGA-TA
*
1260741 CTCCATTGTATATATGATA
1 CTCCATTGTATATAGGATA
1260760 CTCCATTGTATATATAGGATA
1 CTCCATTG--TATATAGGATA
*
1260781 CTCCATTGTATATAGGGTA
1 CTCCATTGTATATAGGATA
* *
1260800 TTCCATTGTATATATGATA
1 CTCCATTGTATATAGGATA
1260819 CTCCATTGTATATATAGGATA
1 CTCCATTG--TATATAGGATA
1260840 CTCCATTGTATATAGGATA
1 CTCCATTGTATATAGGATA
*
1260859 CTCCATTGTATATAGGGTA
1 CTCCATTGTATATAGGATA
*
1260878 CTCCATTGTATATATGATA
1 CTCCATTGTATATAGGATA
*
1260897 CTCCATAAACCATTGTATAT-GTGTTA
1 ---C-T---CCATTGTATATAG-GATA
1260923 CTCCATTGTATATAGGATA
1 CTCCATTGTATATAGGATA
*
1260942 ATCCATTGTATATAGGATA
1 CTCCATTGTATATAGGATA
*
1260961 CTACATTGTATATAGGATA
1 CTCCATTGTATATAGGATA
* *
1260980 CTCTATTGTATCTAGGATA
1 CTCCATTGTATATAGGATA
1260999 CTCCATT
1 CTCCATT
1261006 TCTCTAGATA
Statistics
Matches: 843, Mismatches: 54, Indels: 52
0.89 0.06 0.05
Matches are distributed among these distances:
18 3 0.00
19 667 0.79
20 5 0.01
21 150 0.18
22 2 0.00
23 2 0.00
26 14 0.02
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (19 bp):
CTCCATTGTATATAGGATA
Found at i:1260156 original size:57 final size:57
Alignment explanation
Indices: 1260064--1261005 Score: 1235
Period size: 59 Copynumber: 16.1 Consensus size: 57
1260054 GTAAAAATTT
*
1260064 CTCCATTGTATAT-AGTATACTACATTGTATATAGGATACTCCATTGTATATAGGATA
1 CTCCATTGTATATAAG-ATACTCCATTGTATATAGGATACTCCATTGTATATAGGATA
* * *
1260121 CTCCATTGTATCTAAGATACTCCATTGTATCTAGGATACTCCATGGTATATAGGATA
1 CTCCATTGTATATAAGATACTCCATTGTATATAGGATACTCCATTGTATATAGGATA
* * *
1260178 CTCCATTGTATATATGATATTCCATTGTATATAGGATACTCCATGGTATATAGGATA
1 CTCCATTGTATATAAGATACTCCATTGTATATAGGATACTCCATTGTATATAGGATA
* * *
1260235 CTCCATGGTATATAGGATACTCCATTGTATATAGGATACTCCATGGTATATAGGATA
1 CTCCATTGTATATAAGATACTCCATTGTATATAGGATACTCCATTGTATATAGGATA
* * * *
1260292 CTCCATTGTATATATAGGATACTCCATAGCATATAGGATACTCCATGGTATATAGTATA
1 CTCCATTGTATATA-A-GATACTCCATTGTATATAGGATACTCCATTGTATATAGGATA
* *
1260351 CTCCATGGTATATAAAGGATACTCCATTGTATATAGGATACTCCATGGTATATAGGATA
1 CTCCATTGTATAT-AA-GATACTCCATTGTATATAGGATACTCCATTGTATATAGGATA
*
1260410 CTCCA-TGATATATAGGATACTCCATTGTATATATAGGATACTCCATTGTATATAGGATA
1 CTCCATTG-TATATAAGATACTCCATTG--TATATAGGATACTCCATTGTATATAGGATA
* * *
1260469 CTCCATTGTATATAGGATAATCCATTGTATATAGGATACTCCATTGTATCTAGGATA
1 CTCCATTGTATATAAGATACTCCATTGTATATAGGATACTCCATTGTATATAGGATA
* * * * * *
1260526 CTCCATGGTATCTAGGATACTCCATGGTATCTAGGATACTCCATGGTATATAGGATA
1 CTCCATTGTATATAAGATACTCCATTGTATATAGGATACTCCATTGTATATAGGATA
* *
1260583 CTCCATGGTATATAGGATACTCCATTGTATATATAGGATACTCCATTGTATATAGGATA
1 CTCCATTGTATATAAGATACTCCATTG--TATATAGGATACTCCATTGTATATAGGATA
* *
1260642 CTCCATTGTATATAGGATACTCCATGGTATATAGGATACTCCATTGTATATATAGGATA
1 CTCCATTGTATATAAGATACTCCATTGTATATAGGATACTCCATTG--TATATAGGATA
*
1260701 CTCCATTGTATATATAGGATACTCCATTGTATATA-GAGTACTCCATTGTATATATGATA
1 CTCCATTGTATATA-A-GATACTCCATTGTATATAGGA-TACTCCATTGTATATAGGATA
* * *
1260760 CTCCATTGTATATATAGGATACTCCATTGTATATAGGGTATTCCATTGTATATATGATA
1 CTCCATTGTATATA-A-GATACTCCATTGTATATAGGATACTCCATTGTATATAGGATA
*
1260819 CTCCATTGTATATATAGGATACTCCATTGTATATAGGATACTCCATTGTATATAGGGTA
1 CTCCATTGTATATA-A-GATACTCCATTGTATATAGGATACTCCATTGTATATAGGATA
* *
1260878 CTCCATTGTATATATGATACTCCATAAACCATTGTATAT-GTGTTACTCCATTGTATATAGGATA
1 CTCCATTGTATATAAGATA---C-T---CCATTGTATATAG-GATACTCCATTGTATATAGGATA
* * * * *
1260942 ATCCATTGTATATAGGATACTACATTGTATATAGGATACTCTATTGTATCTAGGATA
1 CTCCATTGTATATAAGATACTCCATTGTATATAGGATACTCCATTGTATATAGGATA
1260999 CTCCATT
1 CTCCATT
1261006 TCTCTAGATA
Statistics
Matches: 803, Mismatches: 57, Indels: 50
0.88 0.06 0.05
Matches are distributed among these distances:
57 345 0.43
58 5 0.01
59 366 0.46
60 8 0.01
61 29 0.04
63 1 0.00
64 49 0.06
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (57 bp):
CTCCATTGTATATAAGATACTCCATTGTATATAGGATACTCCATTGTATATAGGATA
Found at i:1260925 original size:45 final size:45
Alignment explanation
Indices: 1260861--1260947 Score: 131
Period size: 45 Copynumber: 1.9 Consensus size: 45
1260851 ATAGGATACT
* *
1260861 CCATTGTATATAGGGTACTCCATTGTATATATGATACTCCATAAA
1 CCATTGTATATAGGGTACTCCATTGTATATAGGATAATCCATAAA
*
1260906 CCATTGTATAT-GTGTTACTCCATTGTATATAGGATAATCCAT
1 CCATTGTATATAG-GGTACTCCATTGTATATAGGATAATCCAT
1260948 TGTATATAGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 1 0.03
45 37 0.97
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (45 bp):
CCATTGTATATAGGGTACTCCATTGTATATAGGATAATCCATAAA
Found at i:1261833 original size:17 final size:17
Alignment explanation
Indices: 1261813--1261845 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1261803 AACTCTCAGT
1261813 TTAGCCGATAACTGGTC
1 TTAGCCGATAACTGGTC
1261830 TTAGCCGATAACTGGT
1 TTAGCCGATAACTGGT
1261846 ACAGTACCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30
Consensus pattern (17 bp):
TTAGCCGATAACTGGTC
Found at i:1268728 original size:67 final size:63
Alignment explanation
Indices: 1268512--1268765 Score: 391
Period size: 63 Copynumber: 4.0 Consensus size: 63
1268502 GATAACCCAT
1268512 GAAAGCTCTACAAGTGTTTATTCTGGAGCTAATACATGCAGGGAAGCTCCCACCTCACGGGAA
1 GAAAGCTCTACAAGTGTTTATTCTGGAGCTAATACATGCAGGGAAGCTCCCACCTCACGGGAA
1268575 GAAAGCTCTACAAGTGTTTATTCTGGAGCTAATACATGCAGGGAAGCTCCCACCTCACGGGAA
1 GAAAGCTCTACAAGTGTTTATTCTGGAGCTAATACATGCAGGGAAGCTCCCACCTCACGGGAA
* *
1268638 GAAAGCTCTACAAGTGTTTATTCTGGAGCTGATACATCCAGGCAGAGAAGCTCCCACCTCACGGG
1 GAAAGCTCTACAAGTGTTTATTCTGGAGCTAATACAT----GCAGGGAAGCTCCCACCTCACGGG
1268703 AA
62 AA
* ** * * * *
1268705 GAAAGCTCTACAAGTGTTCATTCTAAAGCGAATACATGCAAGAAAGCTCCGACCTCACGGG
1 GAAAGCTCTACAAGTGTTTATTCTGGAGCTAATACATGCAGGGAAGCTCCCACCTCACGGG
1268766 GTGAACGCAA
Statistics
Matches: 176, Mismatches: 11, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
63 119 0.68
67 57 0.32
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.21
Consensus pattern (63 bp):
GAAAGCTCTACAAGTGTTTATTCTGGAGCTAATACATGCAGGGAAGCTCCCACCTCACGGGAA
Found at i:1268741 original size:130 final size:126
Alignment explanation
Indices: 1268512--1268765 Score: 391
Period size: 130 Copynumber: 2.0 Consensus size: 126
1268502 GATAACCCAT
*
1268512 GAAAGCTCTACAAGTGTTTATTCTGGAGCTAATACATGCAGGGAAGCTCCCACCTCACGGGAAGA
1 GAAAGCTCTACAAGTGTTTATTCTGGAGCTAATACATGCAGAGAAGCTCCCACCTCACGGGAAGA
* ** * * *
1268577 AAGCTCTACAAGTGTTTATTCTGGAGCTAATACATGCAGGGAAGCTCCCACCTCACGGGAA
66 AAGCTCTACAAGTGTTCATTCTAAAGCGAATACATGCAAGAAAGCTCCCACCTCACGGGAA
*
1268638 GAAAGCTCTACAAGTGTTTATTCTGGAGCTGATACATCCAGGCAGAGAAGCTCCCACCTCACGGG
1 GAAAGCTCTACAAGTGTTTATTCTGGAGCTAATACAT----GCAGAGAAGCTCCCACCTCACGGG
*
1268703 AAGAAAGCTCTACAAGTGTTCATTCTAAAGCGAATACATGCAAGAAAGCTCCGACCTCACGGG
62 AAGAAAGCTCTACAAGTGTTCATTCTAAAGCGAATACATGCAAGAAAGCTCCCACCTCACGGG
1268766 GTGAACGCAA
Statistics
Matches: 115, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
126 36 0.31
130 79 0.69
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.21
Consensus pattern (126 bp):
GAAAGCTCTACAAGTGTTTATTCTGGAGCTAATACATGCAGAGAAGCTCCCACCTCACGGGAAGA
AAGCTCTACAAGTGTTCATTCTAAAGCGAATACATGCAAGAAAGCTCCCACCTCACGGGAA
Found at i:1268846 original size:13 final size:13
Alignment explanation
Indices: 1268828--1268857 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1268818 TTTATACAAG
1268828 AACTTTGAATGAA
1 AACTTTGAATGAA
*
1268841 AACTTTGACTGAA
1 AACTTTGAATGAA
1268854 AACT
1 AACT
1268858 GCCAAGTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (13 bp):
AACTTTGAATGAA
Found at i:1268953 original size:38 final size:38
Alignment explanation
Indices: 1268911--1269031 Score: 95
Period size: 38 Copynumber: 3.2 Consensus size: 38
1268901 AGGCAATGGT
1268911 AATATAGATTTATTTGGTGTCATGAAATCATACATATA
1 AATATAGATTTATTTGGTGTCATGAAATCATACATATA
* ** *** * *
1268949 AATATACATACACAAGGATTGT-ATG-AA-CACTGCCATAGA
1 AATATAGATTTATTTGG--TGTCATGAAATCA-T-ACATATA
* *
1268988 AAGATAGATTTATTTGGTGTCATGAAATCCTACATATA
1 AATATAGATTTATTTGGTGTCATGAAATCATACATATA
1269026 AATATA
1 AATATA
1269032 CATACACAAG
Statistics
Matches: 57, Mismatches: 19, Indels: 14
0.63 0.21 0.16
Matches are distributed among these distances:
37 5 0.09
38 27 0.47
39 21 0.37
40 4 0.07
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (38 bp):
AATATAGATTTATTTGGTGTCATGAAATCATACATATA
Found at i:1268995 original size:77 final size:77
Alignment explanation
Indices: 1268914--1269114 Score: 384
Period size: 77 Copynumber: 2.6 Consensus size: 77
1268904 CAATGGTAAT
*
1268914 ATAGATTTATTTGGTGTCATGAAATCATACATATAAATATACATACACAAGGATTGTATGAACAC
1 ATAGATTTATTTGGTGTCATGAAATCCTACATATAAATATACATACACAAGGATTGTATGAACAC
1268979 TGCCATAGAAAG
66 TGCCATAGAAAG
1268991 ATAGATTTATTTGGTGTCATGAAATCCTACATATAAATATACATACACAAGGATTGTATGAACAC
1 ATAGATTTATTTGGTGTCATGAAATCCTACATATAAATATACATACACAAGGATTGTATGAACAC
1269056 TGCCATAGAAAG
66 TGCCATAGAAAG
*
1269068 ATAGATTTATTTGGTATCATGAAATCCTACATATAAATATACATACA
1 ATAGATTTATTTGGTGTCATGAAATCCTACATATAAATATACATACA
1269115 ATATAAAACA
Statistics
Matches: 122, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
77 122 1.00
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.31
Consensus pattern (77 bp):
ATAGATTTATTTGGTGTCATGAAATCCTACATATAAATATACATACACAAGGATTGTATGAACAC
TGCCATAGAAAG
Found at i:1270231 original size:54 final size:55
Alignment explanation
Indices: 1270145--1270387 Score: 311
Period size: 54 Copynumber: 4.4 Consensus size: 55
1270135 ATATATTTAT
1270145 ATTGACATTGACTTTTACCTGTGTCGTA-TAATTACTGACCTTTACTGTTTTTCC
1 ATTGACATTGACTTTTACCTGTGTCGTATTAATTACTGACCTTTACTGTTTTTCC
*
1270199 ATTGACATTGACTTTTACTTGTGTCGT-TTAATTACTGACCTTTACTG----TCC
1 ATTGACATTGACTTTTACCTGTGTCGTATTAATTACTGACCTTTACTGTTTTTCC
*
1270249 ATTGACATTGACTTTTACCTGTGTCATATTACTATAGTATTACTGACCTTTACTGTTTTTCC
1 ATTGACATTGACTTTTACCTGTGTC---GTA-T-TA--ATTACTGACCTTTACTGTTTTTCC
* * *
1270311 ATTGACCTTGACTCTTACCTGTGTCGTATT-ATTGCTGACCTTTACTGTTTTTCC
1 ATTGACATTGACTTTTACCTGTGTCGTATTAATTACTGACCTTTACTGTTTTTCC
* *
1270365 ATTGACCTTGACTCTTACCTGTG
1 ATTGACATTGACTTTTACCTGTG
1270388 ATGTATTTCC
Statistics
Matches: 169, Mismatches: 7, Indels: 26
0.84 0.03 0.13
Matches are distributed among these distances:
50 27 0.16
53 1 0.01
54 91 0.54
55 1 0.01
56 2 0.01
57 1 0.01
58 18 0.11
59 2 0.01
62 26 0.15
ACGTcount: A:0.19, C:0.21, G:0.14, T:0.46
Consensus pattern (55 bp):
ATTGACATTGACTTTTACCTGTGTCGTATTAATTACTGACCTTTACTGTTTTTCC
Found at i:1270237 original size:27 final size:27
Alignment explanation
Indices: 1270153--1270244 Score: 75
Period size: 27 Copynumber: 3.4 Consensus size: 27
1270143 ATATTGACAT
* * *
1270153 TGACTTTTACCTGTGTCGTATAATTAC
1 TGACCTTTACTTGTGTCGTTTAATTAC
*
1270180 TGACCTTTAC-TGT-T--TTTCCATTGAC
1 TGACCTTTACTTGTGTCGTTT-AATT-AC
*
1270205 ATTGACTTTTACTTGTGTCGTTTAATTAC
1 --TGACCTTTACTTGTGTCGTTTAATTAC
1270234 TGACCTTTACT
1 TGACCTTTACT
1270245 GTCCATTGAC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
23 2 0.04
24 3 0.06
25 3 0.06
26 3 0.06
27 28 0.55
28 3 0.06
29 3 0.06
30 3 0.06
31 3 0.06
ACGTcount: A:0.20, C:0.20, G:0.13, T:0.48
Consensus pattern (27 bp):
TGACCTTTACTTGTGTCGTTTAATTAC
Found at i:1270382 original size:27 final size:27
Alignment explanation
Indices: 1270298--1270382 Score: 74
Period size: 27 Copynumber: 3.1 Consensus size: 27
1270288 TTACTGACCT
1270298 TTACTGTTTTTCCATTGACCTTGACTC
1 TTACTGTTTTTCCATTGACCTTGACTC
1270325 TTACCTGTGTCGTATT--ATTG--C-TGAC-C
1 TTA-CTGT-T--T-TTCCATTGACCTTGACTC
1270351 TTTACTGTTTTTCCATTGACCTTGACTC
1 -TTACTGTTTTTCCATTGACCTTGACTC
1270379 TTAC
1 TTAC
1270383 CTGTGATGTA
Statistics
Matches: 46, Mismatches: 0, Indels: 24
0.66 0.00 0.34
Matches are distributed among these distances:
22 2 0.04
23 1 0.02
24 4 0.09
25 1 0.02
26 6 0.13
27 18 0.39
28 6 0.13
29 1 0.02
30 4 0.09
31 1 0.02
32 2 0.04
ACGTcount: A:0.15, C:0.25, G:0.13, T:0.47
Consensus pattern (27 bp):
TTACTGTTTTTCCATTGACCTTGACTC
Found at i:1271140 original size:30 final size:30
Alignment explanation
Indices: 1271106--1271166 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
1271096 CTGAAAGGCT
1271106 TTCTTCCTCAGTGGCTGTTGACGCCTCAAA
1 TTCTTCCTCAGTGGCTGTTGACGCCTCAAA
1271136 TTCTTCCTCAGTGGCTGTTGACGCCTCAAA
1 TTCTTCCTCAGTGGCTGTTGACGCCTCAAA
1271166 T
1 T
1271167 GCATCCAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.16, C:0.30, G:0.20, T:0.34
Consensus pattern (30 bp):
TTCTTCCTCAGTGGCTGTTGACGCCTCAAA
Found at i:1272870 original size:33 final size:33
Alignment explanation
Indices: 1272818--1272880 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
1272808 GGTCAGTAAT
* *
1272818 AATACAACACAGGTAAGAGTCGATGTCAATATA
1 AATACAACACAGGTAAGAGTCAATGCCAATATA
* * *
1272851 AATACATCACGGGTGAGAGTCAATGCCAAT
1 AATACAACACAGGTAAGAGTCAATGCCAAT
1272881 GGAAAAACAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 25 1.00
ACGTcount: A:0.41, C:0.17, G:0.21, T:0.21
Consensus pattern (33 bp):
AATACAACACAGGTAAGAGTCAATGCCAATATA
Found at i:1272938 original size:54 final size:54
Alignment explanation
Indices: 1272866--1272986 Score: 197
Period size: 54 Copynumber: 2.2 Consensus size: 54
1272856 ATCACGGGTG
*
1272866 AGAGTCAATGCCAATGGAAAAACAATAAAGGTCAGTAATAATACGACACAGGTA
1 AGAGTCAATGTCAATGGAAAAACAATAAAGGTCAGTAATAATACGACACAGGTA
* * *
1272920 AGAGTCAATGTCATTGGAAAAACAGTAAAGGTCAGTAATAATACGACACAGGTG
1 AGAGTCAATGTCAATGGAAAAACAATAAAGGTCAGTAATAATACGACACAGGTA
*
1272974 AGAGTCAAGGTCA
1 AGAGTCAATGTCA
1272987 CAAGTAAGAG
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 62 1.00
ACGTcount: A:0.45, C:0.14, G:0.23, T:0.18
Consensus pattern (54 bp):
AGAGTCAATGTCAATGGAAAAACAATAAAGGTCAGTAATAATACGACACAGGTA
Found at i:1273299 original size:33 final size:33
Alignment explanation
Indices: 1273257--1273392 Score: 137
Period size: 33 Copynumber: 4.1 Consensus size: 33
1273247 GATAGGGGTA
* * *
1273257 AAGGTCAGTGAAAATATATCACATGTTACAGTC
1 AAGGTCAGTGGAAATACATCACATGTAACAGTC
* * * * *
1273290 AAGGTCAGTGGAAATACATCTCAAGTTAGAGCC
1 AAGGTCAGTGGAAATACATCACATGTAACAGTC
* ** ** *
1273323 AATGTCTTTGGAAATACATCGTATGTAAGAGTC
1 AAGGTCAGTGGAAATACATCACATGTAACAGTC
*
1273356 AAGGTCAGTGGAAATTCATCACATGTAACAGTC
1 AAGGTCAGTGGAAATACATCACATGTAACAGTC
1273389 AAGG
1 AAGG
1273393 ACGATGGAAA
Statistics
Matches: 82, Mismatches: 21, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 82 1.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (33 bp):
AAGGTCAGTGGAAATACATCACATGTAACAGTC
Found at i:1274692 original size:2 final size:2
Alignment explanation
Indices: 1274685--1274725 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
1274675 CAAGCCATAT
* * *
1274685 TC TC TC TC TC TC TT TC TC TC TC TT TC TT TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1274726 TCTTCTTCTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (2 bp):
TC
Found at i:1274703 original size:14 final size:14
Alignment explanation
Indices: 1274684--1274726 Score: 77
Period size: 14 Copynumber: 3.1 Consensus size: 14
1274674 TCAAGCCATA
1274684 TTCTCTCTCTCTCT
1 TTCTCTCTCTCTCT
*
1274698 TTCTCTCTCTTTCT
1 TTCTCTCTCTCTCT
1274712 TTCTCTCTCTCTCT
1 TTCTCTCTCTCTCT
1274726 T
1 T
1274727 CTTCTTCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (14 bp):
TTCTCTCTCTCTCT
Found at i:1274704 original size:10 final size:10
Alignment explanation
Indices: 1274689--1274740 Score: 58
Period size: 10 Copynumber: 5.5 Consensus size: 10
1274679 CCATATTCTC
1274689 TCTCTCTCTT
1 TCTCTCTCTT
1274699 TCTCTCTCTT
1 TCTCTCTCTT
*
1274709 TCT-T-TCTC
1 TCTCTCTCTT
1274717 TCTCTCTC-T
1 TCTCTCTCTT
1274726 TCT-TCTTCTT
1 TCTCTC-TCTT
1274736 TCTCT
1 TCTCT
1274741 TTCACATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
8 8 0.23
9 7 0.20
10 19 0.54
11 1 0.03
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (10 bp):
TCTCTCTCTT
Found at i:1274829 original size:21 final size:21
Alignment explanation
Indices: 1274805--1274844 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1274795 CTACATTAAT
**
1274805 TTTTTCTCTTTCTCAATCTCC
1 TTTTTCTCACTCTCAATCTCC
1274826 TTTTTCTCACTCTCAATCT
1 TTTTTCTCACTCTCAATCT
1274845 ATCTCACACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.12, C:0.33, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTTCTCACTCTCAATCTCC
Found at i:1274851 original size:16 final size:16
Alignment explanation
Indices: 1274830--1274864 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1274820 ATCTCCTTTT
*
1274830 TCTCACTCTCAATCTA
1 TCTCACACTCAATCTA
*
1274846 TCTCACACTCCATCTA
1 TCTCACACTCAATCTA
1274862 TCT
1 TCT
1274865 ATGTCTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.23, C:0.40, G:0.00, T:0.37
Consensus pattern (16 bp):
TCTCACACTCAATCTA
Found at i:1277659 original size:28 final size:28
Alignment explanation
Indices: 1277619--1277676 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
1277609 ATCCTGTTTA
1277619 ATTCAGTCTGAGTATGAGTACACCCAAT
1 ATTCAGTCTGAGTATGAGTACACCCAAT
1277647 ATTCAGTCTGAGTATGAGTACACCCAAT
1 ATTCAGTCTGAGTATGAGTACACCCAAT
1277675 AT
1 AT
1277677 AAACAGTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (28 bp):
ATTCAGTCTGAGTATGAGTACACCCAAT
Found at i:1279072 original size:28 final size:28
Alignment explanation
Indices: 1279032--1279089 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
1279022 ATCCTGTTTA
1279032 ATTCAGTCTGAGTATGAGTACACCCAAT
1 ATTCAGTCTGAGTATGAGTACACCCAAT
1279060 ATTCAGTCTGAGTATGAGTACACCCAAT
1 ATTCAGTCTGAGTATGAGTACACCCAAT
1279088 AT
1 AT
1279090 AAACAGTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (28 bp):
ATTCAGTCTGAGTATGAGTACACCCAAT
Found at i:1296620 original size:2 final size:2
Alignment explanation
Indices: 1296613--1296658 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
1296603 NNNNNNNNNN
* *
1296613 AT AT AT AT AA AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1296655 AT AT
1 AT AT
1296659 CATGTATATG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1297376 original size:13 final size:13
Alignment explanation
Indices: 1297358--1297383 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1297348 AAACTTGAAT
1297358 CTACCATACCAGA
1 CTACCATACCAGA
1297371 CTACCATACCAGA
1 CTACCATACCAGA
1297384 AAAATGACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.38, G:0.08, T:0.15
Consensus pattern (13 bp):
CTACCATACCAGA
Found at i:1300772 original size:26 final size:28
Alignment explanation
Indices: 1300743--1300796 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
1300733 GGTCTGTACA
1300743 GTATTG-AAT-ATTCTATGGTGTTATAT
1 GTATTGTAATGATTCTATGGTGTTATAT
*
1300769 GTATTGTTAATGTTTCTATGGTGTTATA
1 GTATTG-TAATGATTCTATGGTGTTATA
1300797 ATGTTAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 6 0.25
28 3 0.12
29 15 0.62
ACGTcount: A:0.24, C:0.04, G:0.20, T:0.52
Consensus pattern (28 bp):
GTATTGTAATGATTCTATGGTGTTATAT
Found at i:1304207 original size:33 final size:33
Alignment explanation
Indices: 1304170--1304595 Score: 342
Period size: 33 Copynumber: 12.9 Consensus size: 33
1304160 GACGAATGCC
*
1304170 AGCTGTAATAAAGTGGGCGACATAATAAAGGAT
1 AGCTGTAATAAAGTGGGCGATATAATAAAGGAT
* * * * *
1304203 AGCTGTAACAGAGTCGGCGATATGAT-AAGGACC
1 AGCTGTAATAAAGTGGGCGATATAATAAAGGA-T
* * * *
1304236 AGCTGAAATAAAATGGGCGACATAATAAAGAAT
1 AGCTGTAATAAAGTGGGCGATATAATAAAGGAT
* * *
1304269 AGCTGTAATAGAGTGGGCGATATGAT-AAGGACC
1 AGCTGTAATAAAGTGGGCGATATAATAAAGGA-T
** * * *
1304302 AGCTGTAATGGAGTGGGCAATATACTGAAGGAT
1 AGCTGTAATAAAGTGGGCGATATAATAAAGGAT
* * * * *
1304335 AGCTGTTATAATGTGGGTGATATTATAAA-GACC
1 AGCTGTAATAAAGTGGGCGATATAATAAAGGA-T
* * * *
1304368 GGCAGTAATAAAGTGGGCGATATAATTAGGGAT
1 AGCTGTAATAAAGTGGGCGATATAATAAAGGAT
* * *
1304401 AGCTGTAATAGAGTGGACGATATGATAAAGG-T
1 AGCTGTAATAAAGTGGGCGATATAATAAAGGAT
* * *
1304433 CAGCTGTAATAAAGTGGGCGATATGATTAAGAAT
1 -AGCTGTAATAAAGTGGGCGATATAATAAAGGAT
* * * *
1304467 AGCTGTAATAGAGTTGGCGATATGATAATA-AAT
1 AGCTGTAATAAAGTGGGCGATATAATAA-AGGAT
* **
1304500 A-ATGTAATAAAGTGGGCGATATAATAAAGGCC
1 AGCTGTAATAAAGTGGGCGATATAATAAAGGAT
* * * *
1304532 AACTGTAACAAAGTGGGCGATATAATTAATGAT
1 AGCTGTAATAAAGTGGGCGATATAATAAAGGAT
* * *
1304565 AGCTGTAATAGAGTAGGCGATATCATAAAGG
1 AGCTGTAATAAAGTGGGCGATATAATAAAGG
1304596 GTGGGCAATT
Statistics
Matches: 302, Mismatches: 80, Indels: 22
0.75 0.20 0.05
Matches are distributed among these distances:
31 1 0.00
32 35 0.12
33 253 0.84
34 13 0.04
ACGTcount: A:0.39, C:0.09, G:0.28, T:0.24
Consensus pattern (33 bp):
AGCTGTAATAAAGTGGGCGATATAATAAAGGAT
Found at i:1304258 original size:66 final size:66
Alignment explanation
Indices: 1304168--1304595 Score: 423
Period size: 66 Copynumber: 6.5 Consensus size: 66
1304158 AGGACGAATG
* * *
1304168 CCAGCTGTAATAAAGTGGGCGACATAATAAAGGATAGCTGTAACAGAGTCGGCGATATGATAAGG
1 CCAGCTGTAATAAAGTGGGCGATATAATAAAGGATAGCTGTAATAGAGTGGGCGATATGATAAGG
1304233 A
66 A
* * * *
1304234 CCAGCTGAAATAAAATGGGCGACATAATAAAGAATAGCTGTAATAGAGTGGGCGATATGATAAGG
1 CCAGCTGTAATAAAGTGGGCGATATAATAAAGGATAGCTGTAATAGAGTGGGCGATATGATAAGG
1304299 A
66 A
** * * * * * * *
1304300 CCAGCTGTAATGGAGTGGGCAATATACTGAAGGATAGCTGTTATA-ATGTGGGTGATATTATAAA
1 CCAGCTGTAATAAAGTGGGCGATATAATAAAGGATAGCTGTAATAGA-GTGGGCGATATGATAAG
1304364 GA
65 GA
* * * * *
1304366 CCGGCAGTAATAAAGTGGGCGATATAATTAGGGATAGCTGTAATAGAGTGGACGATATGATAAAG
1 CCAGCTGTAATAAAGTGGGCGATATAATAAAGGATAGCTGTAATAGAGTGGGCGATATGAT-AAG
1304431 G-
65 GA
* * * * * **
1304432 TCAGCTGTAATAAAGTGGGCGATATGATTAAGAATAGCTGTAATAGAGTTGGCGATATGATAATA
1 CCAGCTGTAATAAAGTGGGCGATATAATAAAGGATAGCTGTAATAGAGTGGGCGATATGATAAGG
1304497 A
66 A
** * ** * * * * *
1304498 ATA-ATGTAATAAAGTGGGCGATATAATAAAGGCCAACTGTAACAAAGTGGGCGATATAATTAAT
1 CCAGCTGTAATAAAGTGGGCGATATAATAAAGGATAGCTGTAATAGAGTGGGCGATATGA-TAAG
1304562 GA
65 GA
* * * *
1304564 -TAGCTGTAATAGAGTAGGCGATATCATAAAGG
1 CCAGCTGTAATAAAGTGGGCGATATAATAAAGG
1304596 GTGGGCAATT
Statistics
Matches: 297, Mismatches: 59, Indels: 12
0.81 0.16 0.03
Matches are distributed among these distances:
65 50 0.17
66 243 0.82
67 4 0.01
ACGTcount: A:0.39, C:0.10, G:0.28, T:0.24
Consensus pattern (66 bp):
CCAGCTGTAATAAAGTGGGCGATATAATAAAGGATAGCTGTAATAGAGTGGGCGATATGATAAGG
A
Found at i:1304538 original size:98 final size:98
Alignment explanation
Indices: 1304404--1304592 Score: 281
Period size: 98 Copynumber: 1.9 Consensus size: 98
1304394 TAGGGATAGC
* * * * * *
1304404 TGTAATAGAGTGGACGATATGATAAAGGTCAGCTGTAATAAAGTGGGCGATATGATTAA-GAATA
1 TGTAATAAAGTGGACGATATAATAAAGGCCAACTGTAACAAAGTGGGCGATATAATTAATG-ATA
* *
1304468 GCTGTAATAGAGTTGGCGATATGATAATAAATAA
65 GCTGTAATAGAGTAGGCGATATCATAATAAATAA
*
1304502 TGTAATAAAGTGGGCGATATAATAAAGGCCAACTGTAACAAAGTGGGCGATATAATTAATGATAG
1 TGTAATAAAGTGGACGATATAATAAAGGCCAACTGTAACAAAGTGGGCGATATAATTAATGATAG
1304567 CTGTAATAGAGTAGGCGATATCATAA
66 CTGTAATAGAGTAGGCGATATCATAA
1304593 AGGGTGGGCA
Statistics
Matches: 81, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
98 80 0.99
99 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.25, T:0.26
Consensus pattern (98 bp):
TGTAATAAAGTGGACGATATAATAAAGGCCAACTGTAACAAAGTGGGCGATATAATTAATGATAG
CTGTAATAGAGTAGGCGATATCATAATAAATAA
Found at i:1305619 original size:38 final size:38
Alignment explanation
Indices: 1305568--1306391 Score: 1199
Period size: 38 Copynumber: 21.8 Consensus size: 38
1305558 AGAGGATCAG
1305568 GATGGTTATAGCACAGCCTGTAAAATATCGGGGGTAAA
1 GATGGTTATAGCACAGCCTGTAAAATATCGGGGGTAAA
* *
1305606 GATGGTTATAGCACAGCCTGTAACATATCGGGAGTAAA
1 GATGGTTATAGCACAGCCTGTAAAATATCGGGGGTAAA
* * *
1305644 GATAGTTATAGCACAGCTTGTAAAATATCGGGGGTGAA
1 GATGGTTATAGCACAGCCTGTAAAATATCGGGGGTAAA
* *
1305682 GATGGTTATAGCACAGCTTGTAAAATATCGGGGGTGAA
1 GATGGTTATAGCACAGCCTGTAAAATATCGGGGGTAAA
* *
1305720 GATGGTTATAGCACAGCCTGTAAAATATCGGGGATGAA
1 GATGGTTATAGCACAGCCTGTAAAATATCGGGGGTAAA
* * *
1305758 GATGGTTATAGAACAGCATGTAAAATATCGGGGGTGAA
1 GATGGTTATAGCACAGCCTGTAAAATATCGGGGGTAAA
* * *
1305796 GATGATTATAGCACAGCATGTAATATATCGGGGGTAAA
1 GATGGTTATAGCACAGCCTGTAAAATATCGGGGGTAAA
* * *
1305834 GATGGCTATAGGACAGCCTGTAAAATATCGGGGGTGAA
1 GATGGTTATAGCACAGCCTGTAAAATATCGGGGGTAAA
** * *
1305872 GATGGTTATATAACAGCATGTAAAATATCGGGGGTGAA
1 GATGGTTATAGCACAGCCTGTAAAATATCGGGGGTAAA
* * *
1305910 GATGGTTATAGAACAGCATGTAAAATATCGGGGGTGAA
1 GATGGTTATAGCACAGCCTGTAAAATATCGGGGGTAAA
*
1305948 GATGGTTATAGAACAGCCTGTAAAATATCGGGGGTAAA
1 GATGGTTATAGCACAGCCTGTAAAATATCGGGGGTAAA
* *
1305986 GATGTTTATCGCACAGCCTGTAAAATATCGGGGGTAAA
1 GATGGTTATAGCACAGCCTGTAAAATATCGGGGGTAAA
1306024 GATGGTTATAGCACAGCCTGTAAAATATC-GGGGTAAA
1 GATGGTTATAGCACAGCCTGTAAAATATCGGGGGTAAA
*
1306061 GATGGTTATTGCACAGCCTGTAAAATATCGGGGGTAAA
1 GATGGTTATAGCACAGCCTGTAAAATATCGGGGGTAAA
* * *
1306099 GATGTTTATCGCACAGCCTGTAAAATATCGGGGGTTAA
1 GATGGTTATAGCACAGCCTGTAAAATATCGGGGGTAAA
1306137 GATGGTTATAGCACAGCCTGTAAAATATCGGGGGTAAA
1 GATGGTTATAGCACAGCCTGTAAAATATCGGGGGTAAA
*
1306175 GATGGTTATCGCACAGCCTGTAAAATATCGGGGGTAAA
1 GATGGTTATAGCACAGCCTGTAAAATATCGGGGGTAAA
1306213 GATGGTTATAGCACAGCCTGTAAAATATCGGGGGTAAA
1 GATGGTTATAGCACAGCCTGTAAAATATCGGGGGTAAA
* * *
1306251 GAT-GTTATAGTATACCCTGTAAAATATCGGGGGTTAAA
1 GATGGTTATAGCACAGCCTGTAAAATATCGGGGG-TAAA
* * * *
1306289 -TTGCTTATTGCACAGCCTGTAAAATATGGGGGGTAAA
1 GATGGTTATAGCACAGCCTGTAAAATATCGGGGGTAAA
1306326 GAT-GTTATAGCACAGCCTGTAAAATATCGGGGGTTAAA
1 GATGGTTATAGCACAGCCTGTAAAATATCGGGGG-TAAA
* * * *
1306364 -TTGCTTATTGCACAGCCTGTAAATTATC
1 GATGGTTATAGCACAGCCTGTAAAATATC
1306392 AAGGGTGACG
Statistics
Matches: 718, Mismatches: 62, Indels: 12
0.91 0.08 0.02
Matches are distributed among these distances:
37 96 0.13
38 622 0.87
ACGTcount: A:0.33, C:0.13, G:0.28, T:0.26
Consensus pattern (38 bp):
GATGGTTATAGCACAGCCTGTAAAATATCGGGGGTAAA
Found at i:1307482 original size:2 final size:2
Alignment explanation
Indices: 1307475--1307545 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
1307465 GTTCGCAAAC
1307475 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1307517 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1307546 CACCAGCTCA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1320733 original size:2 final size:2
Alignment explanation
Indices: 1320726--1320763 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1320716 TCAGAATTTG
*
1320726 GA GA GA GA GA GA GA GA GA GA GA GA GA TA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1320764 CGTGTATAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.47, T:0.03
Consensus pattern (2 bp):
GA
Found at i:1320898 original size:2 final size:2
Alignment explanation
Indices: 1320893--1321008 Score: 187
Period size: 2 Copynumber: 58.0 Consensus size: 2
1320883 CTCTAAAAAA
1320893 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * * * *
1320935 AG AG AG AC AG AC AG AC AG AG AG AG AG AG AG AG AC AG AG AG TG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1320977 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1321009 TAGGAGAGTA
Statistics
Matches: 104, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 104 1.00
ACGTcount: A:0.49, C:0.03, G:0.47, T:0.01
Consensus pattern (2 bp):
AG
Found at i:1322316 original size:9 final size:9
Alignment explanation
Indices: 1322304--1322328 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1322294 ATTATAATTA
1322304 TTATTAATG
1 TTATTAATG
1322313 TTATTAATG
1 TTATTAATG
1322322 TTATTAA
1 TTATTAA
1322329 CGTTTAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (9 bp):
TTATTAATG
Found at i:1323599 original size:2 final size:2
Alignment explanation
Indices: 1323592--1323644 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
1323582 ATTACAAGCT
*
1323592 GA GA GA GA GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1323634 GA GA GA GA GA G
1 GA GA GA GA GA G
1323645 TTTTTTCTGA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1327083 original size:15 final size:15
Alignment explanation
Indices: 1327063--1327093 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1327053 TTGGAAAGAC
1327063 ACTCTTTAATATTTA
1 ACTCTTTAATATTTA
1327078 ACTCTTTAATATTTA
1 ACTCTTTAATATTTA
1327093 A
1 A
1327094 AATTGCTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.13, G:0.00, T:0.52
Consensus pattern (15 bp):
ACTCTTTAATATTTA
Found at i:1328142 original size:65 final size:65
Alignment explanation
Indices: 1327929--1328130 Score: 395
Period size: 65 Copynumber: 3.1 Consensus size: 65
1327919 GTCTTACACT
*
1327929 TTTGAATATGATATTTTTTGGCCATGAACTGTTATTTATTAAATAAGAAATCCAAATATTCTAGC
1 TTTGAATATGATATTTTTTGGCCACGAACTGTTATTTATTAAATAAGAAATCCAAATATTCTAGC
1327994 TTTGAATATGATATTTTTTGGCCACGAACTGTTATTTATTAAATAAGAAATCCAAATATTCTAGC
1 TTTGAATATGATATTTTTTGGCCACGAACTGTTATTTATTAAATAAGAAATCCAAATATTCTAGC
1328059 TTTGAATATGATATTTTTTGGCCACGAACTGTTATTTATTAAATAAGAAATCCAAATATTCTAGC
1 TTTGAATATGATATTTTTTGGCCACGAACTGTTATTTATTAAATAAGAAATCCAAATATTCTAGC
1328124 TTTGAAT
1 TTTGAAT
1328131 TTGAACATTT
Statistics
Matches: 136, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 136 1.00
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.41
Consensus pattern (65 bp):
TTTGAATATGATATTTTTTGGCCACGAACTGTTATTTATTAAATAAGAAATCCAAATATTCTAGC
Found at i:1329189 original size:2 final size:2
Alignment explanation
Indices: 1329182--1329218 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1329172 GGTATGCTTA
1329182 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1329219 TATGGAAGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1330303 original size:214 final size:210
Alignment explanation
Indices: 1329934--1330357 Score: 812
Period size: 214 Copynumber: 2.0 Consensus size: 210
1329924 AATACGGATC
1329934 GAGTTGGGTATAAATGCTAACTTCCAAGGACTCCAAAAAAACCGCCAGAAAATCCAATATGTTTG
1 GAGTTGGGTATAAATGCTAACTTCCAAGGACTCCAAAAAAACCGCCAGAAAATCCAATATGTTTG
1329999 TTTAACGTCTTTCTAGTAGAATTAATATATCCTCTGCGCTTCTGATCCCGGTATTCATATATTTA
66 TTTAACGTCTTTCTAGTAGAATTAATATATCCTCTGCGCTTCTGATCCCGGTATTCATATATTTA
1330064 ATACTGAGGCAGGACCCATTGATTCACTTCGCCTCCCGTTGCTAGGCAACCGAATCGACGAGCAG
131 ATACTGAGGCAGGACCCATTGATTCACTTCGCCTCCCGTTGCTAGGCAACCGAATCGACGAGCAG
1330129 GTAGATCGATTTTGG
196 GTAGATCGATTTTGG
1330144 NNNNGAGTTGGGTATAAATGCTAACTTCCAAGGACTCCAAAAAAACCGCCAGAAAATCCAATATG
1 ----GAGTTGGGTATAAATGCTAACTTCCAAGGACTCCAAAAAAACCGCCAGAAAATCCAATATG
1330209 TTTGTTTAACGTCTTTCTAGTAGAATTAATATATCCTCTGCGCTTCTGATCCCGGTATTCATATA
62 TTTGTTTAACGTCTTTCTAGTAGAATTAATATATCCTCTGCGCTTCTGATCCCGGTATTCATATA
1330274 TTTAATACTGAGGCAGGACCCATTGATTCACTTCGCCTCCCGTTGCTAGGCAACCGAATCGACGA
127 TTTAATACTGAGGCAGGACCCATTGATTCACTTCGCCTCCCGTTGCTAGGCAACCGAATCGACGA
1330339 GCAGGTAGATCGATTTTGG
192 GCAGGTAGATCGATTTTGG
1330358 CCGTGTTCTA
Statistics
Matches: 210, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
214 210 1.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.29
Consensus pattern (210 bp):
GAGTTGGGTATAAATGCTAACTTCCAAGGACTCCAAAAAAACCGCCAGAAAATCCAATATGTTTG
TTTAACGTCTTTCTAGTAGAATTAATATATCCTCTGCGCTTCTGATCCCGGTATTCATATATTTA
ATACTGAGGCAGGACCCATTGATTCACTTCGCCTCCCGTTGCTAGGCAACCGAATCGACGAGCAG
GTAGATCGATTTTGG
Found at i:1334224 original size:21 final size:23
Alignment explanation
Indices: 1334183--1334225 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1334173 AATGTGTTTG
*
1334183 TAGTCAGTAGACAACGAAAATTC
1 TAGTCAATAGACAACGAAAATTC
1334206 TAGTCAATAGAC-A-GAAAATT
1 TAGTCAATAGACAACGAAAATT
1334226 GTATCTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 1 0.05
23 11 0.58
ACGTcount: A:0.47, C:0.14, G:0.16, T:0.23
Consensus pattern (23 bp):
TAGTCAATAGACAACGAAAATTC
Found at i:1337224 original size:2 final size:2
Alignment explanation
Indices: 1337217--1337272 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1337207 TTGAAGAAGG
1337217 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1337259 TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC
1337273 GCTTTAAAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1337677 original size:2 final size:2
Alignment explanation
Indices: 1337670--1337734 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
1337660 CTTAATAATA
1337670 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1337712 TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC T
1337735 TCATTCATGT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1348742 original size:31 final size:31
Alignment explanation
Indices: 1348701--1349542 Score: 1066
Period size: 31 Copynumber: 27.3 Consensus size: 31
1348691 TCCTCACCTG
* **
1348701 TCAGTTCAACCAACATCAGTAAGTATGATTA
1 TCAGTCCAACCAACATCAGTAAGTACAATTA
* *
1348732 TCAGTCCAACCAACATTAGCAA-TACAATTA
1 TCAGTCCAACCAACATCAGTAAGTACAATTA
*
1348762 TCAGTCCAACCAACATCAATAAGTACAATTA
1 TCAGTCCAACCAACATCAGTAAGTACAATTA
1348793 TCAGTCCAACCAACATCAGTAAGTACAATTA
1 TCAGTCCAACCAACATCAGTAAGTACAATTA
* * *
1348824 TCTGTCCAACCAACATCAGTGAGTTCAATTA
1 TCAGTCCAACCAACATCAGTAAGTACAATTA
* * *
1348855 TCA-ACCAACCAACATTAGCAAGTACAATTA
1 TCAGTCCAACCAACATCAGTAAGTACAATTA
*
1348885 TCAGTCCAACCAACATCAGTGAGTACAATTA
1 TCAGTCCAACCAACATCAGTAAGTACAATTA
* * * *
1348916 TTAGTTCAACCAACATTAGCAAGTACAATTA
1 TCAGTCCAACCAACATCAGTAAGTACAATTA
* *
1348947 TCA-ACCAACCAACATCAGTGAGTACAATTA
1 TCAGTCCAACCAACATCAGTAAGTACAATTA
* *
1348977 TCAGTTCAACCAACATCAGTAAGTAAAATTA
1 TCAGTCCAACCAACATCAGTAAGTACAATTA
* *
1349008 TCTGTCCAACCAACATCAGTGAGTACAATTA
1 TCAGTCCAACCAACATCAGTAAGTACAATTA
* *
1349039 TCAGTTCAACCAACATCAGTGAGTACAATTA
1 TCAGTCCAACCAACATCAGTAAGTACAATTA
1349070 TCAGTCCAACCAACATCAGTAAGTACAATTA
1 TCAGTCCAACCAACATCAGTAAGTACAATTA
*
1349101 TCAGTCCAACCAACAAT-AGCAAGTACAATTA
1 TCAGTCCAACCAAC-ATCAGTAAGTACAATTA
*
1349132 TCAGTCCAACCAACATCAGTGAGTACAATTA
1 TCAGTCCAACCAACATCAGTAAGTACAATTA
*
1349163 TCAGTCCAACTAACATCAGTAAGTACAATTA
1 TCAGTCCAACCAACATCAGTAAGTACAATTA
* *
1349194 TCAGTCCAACCAACATCAGTAATTACAATGA
1 TCAGTCCAACCAACATCAGTAAGTACAATTA
** *
1349225 TCAGTCCAACCAACATCAGTGGGTGCAATTA
1 TCAGTCCAACCAACATCAGTAAGTACAATTA
* * * * *
1349256 TTAGTTCAACCAACATCAATGAGTTCAATTA
1 TCAGTCCAACCAACATCAGTAAGTACAATTA
* * *
1349287 TCTGTTCAACCAACATCAGTAAGTACAATGA
1 TCAGTCCAACCAACATCAGTAAGTACAATTA
* * *
1349318 TCAGTTCAACCAACATTAGCAA-TACAATTA
1 TCAGTCCAACCAACATCAGTAAGTACAATTA
1349348 TCAGTCCAACCAACATCAGTAAGTACAATTA
1 TCAGTCCAACCAACATCAGTAAGTACAATTA
* *
1349379 TCAGT-CAACCAACATTAGCAAGTACAATTA
1 TCAGTCCAACCAACATCAGTAAGTACAATTA
* * * * *
1349409 TCAGTCCAAGCAACACCAATGAGTTCAATTA
1 TCAGTCCAACCAACATCAGTAAGTACAATTA
* * * * *
1349440 TCAGTTCAAACAACATCACTGAGTAGAATTA
1 TCAGTCCAACCAACATCAGTAAGTACAATTA
* * * * *
1349471 TCTGTTCAATCAACATCAATGAGTACAATTA
1 TCAGTCCAACCAACATCAGTAAGTACAATTA
* *
1349502 TAAGTCCAACCAACATCAGTGAGTACAATTA
1 TCAGTCCAACCAACATCAGTAAGTACAATTA
1349533 TCAGTCCAAC
1 TCAGTCCAAC
1349543 TTTATACAAA
Statistics
Matches: 703, Mismatches: 101, Indels: 14
0.86 0.12 0.02
Matches are distributed among these distances:
30 131 0.19
31 570 0.81
32 2 0.00
ACGTcount: A:0.41, C:0.24, G:0.11, T:0.25
Consensus pattern (31 bp):
TCAGTCCAACCAACATCAGTAAGTACAATTA
Found at i:1365334 original size:30 final size:28
Alignment explanation
Indices: 1365310--1365453 Score: 126
Period size: 30 Copynumber: 4.9 Consensus size: 28
1365300 TTCTAGCATT
*
1365310 TCAACCACGCTCACCACCGCTTCTATCA
1 TCAACCACGCCCACCACCGCTTCTATCA
*
1365338 GCACGACCACGCCCACCACCGCTTCTATCA
1 TCA--ACCACGCCCACCACCGCTTCTATCA
*
1365368 TCACCGTCACGCCCACCACCGCTTCTATCA
1 TCAAC--CACGCCCACCACCGCTTCTATCA
* * *
1365398 GCACGACCACACCCACCACCGTTTCTATCTGA
1 TCA--ACCACGCCCACCACCGCTTCTATC--A
* * * *
1365430 ACGACCACGCCGAGCACCGCTTCT
1 TCAACCACGCCCACCACCGCTTCT
1365454 GCGTTAAAAT
Statistics
Matches: 94, Mismatches: 14, Indels: 14
0.77 0.11 0.11
Matches are distributed among these distances:
28 3 0.03
30 88 0.94
32 3 0.03
ACGTcount: A:0.23, C:0.47, G:0.12, T:0.17
Consensus pattern (28 bp):
TCAACCACGCCCACCACCGCTTCTATCA
Found at i:1365439 original size:60 final size:61
Alignment explanation
Indices: 1365313--1365453 Score: 196
Period size: 60 Copynumber: 2.3 Consensus size: 61
1365303 TAGCATTTCA
* * *
1365313 ACCACGCTCACCACCGCTTCTATCAGCACGACCACGCCCACCACCGCTTCTATCATCACCG
1 ACCACGCCCACCACCGCTTCTATCAGCACGACCACACCCACCACCGCTTCTATCATCAACG
* * *
1365374 -TCACGCCCACCACCGCTTCTATCAGCACGACCACACCCACCACCGTTTCTATC-TGAACG
1 ACCACGCCCACCACCGCTTCTATCAGCACGACCACACCCACCACCGCTTCTATCATCAACG
* *
1365433 ACCACGCCGAGCACCGCTTCT
1 ACCACGCCCACCACCGCTTCT
1365454 GCGTTAAAAT
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
59 4 0.06
60 66 0.94
ACGTcount: A:0.23, C:0.48, G:0.13, T:0.17
Consensus pattern (61 bp):
ACCACGCCCACCACCGCTTCTATCAGCACGACCACACCCACCACCGCTTCTATCATCAACG
Found at i:1366524 original size:2 final size:2
Alignment explanation
Indices: 1366517--1366576 Score: 93
Period size: 2 Copynumber: 30.0 Consensus size: 2
1366507 CAATCGATTG
*
1366517 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT AT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* *
1366559 CA AT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT
1366577 GTTTATTGTA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.05, C:0.47, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1368118 original size:15 final size:15
Alignment explanation
Indices: 1368098--1368160 Score: 58
Period size: 15 Copynumber: 4.2 Consensus size: 15
1368088 TCATGATACA
1368098 ATATTGTATAATATG
1 ATATTGTATAATATG
*
1368113 ATATTGTACTAA-A-C
1 ATATTGTA-TAATATG
*
1368127 ATTATTGTATCATATG
1 A-TATTGTATAATATG
* *
1368143 ATATTGTTTCATATG
1 ATATTGTATAATATG
1368158 ATA
1 ATA
1368161 CTGAGTCATA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
14 3 0.08
15 33 0.82
16 4 0.10
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (15 bp):
ATATTGTATAATATG
Found at i:1368169 original size:15 final size:15
Alignment explanation
Indices: 1368136--1368176 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1368126 CATTATTGTA
* **
1368136 TCATATGATATTGTT
1 TCATATGATACTGAG
1368151 TCATATGATACTGAG
1 TCATATGATACTGAG
1368166 TCATATGATAC
1 TCATATGATAC
1368177 GATATTGTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (15 bp):
TCATATGATACTGAG
Found at i:1368545 original size:18 final size:20
Alignment explanation
Indices: 1368510--1368560 Score: 70
Period size: 18 Copynumber: 2.6 Consensus size: 20
1368500 AATAACACCC
*
1368510 TATCATATCATATGATACGA
1 TATCATATCATATGATACAA
1368530 TATCATATC-T-TGATACAA
1 TATCATATCATATGATACAA
*
1368548 TGTCATATCATAT
1 TATCATATCATAT
1368561 ATTACATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 15 0.56
19 2 0.07
20 10 0.37
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (20 bp):
TATCATATCATATGATACAA
Found at i:1368591 original size:28 final size:28
Alignment explanation
Indices: 1368558--1368611 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
1368548 TGTCATATCA
* *
1368558 TATATTACATTTTTATATTCTATCATTT
1 TATATTACAGTATTATATTCTATCATTT
*
1368586 TATATTACAGTATTATATTGTATCAT
1 TATATTACAGTATTATATTCTATCAT
1368612 ATGATATATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.31, C:0.09, G:0.04, T:0.56
Consensus pattern (28 bp):
TATATTACAGTATTATATTCTATCATTT
Found at i:1368618 original size:28 final size:28
Alignment explanation
Indices: 1368559--1368618 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
1368549 GTCATATCAT
* * * *
1368559 ATATTACATTTTTATATTCTATCATTTT
1 ATATTACAGTATTATATTCTATCATATG
*
1368587 ATATTACAGTATTATATTGTATCATATG
1 ATATTACAGTATTATATTCTATCATATG
1368615 ATAT
1 ATAT
1368619 ATGATATATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.33, C:0.08, G:0.05, T:0.53
Consensus pattern (28 bp):
ATATTACAGTATTATATTCTATCATATG
Found at i:1368843 original size:16 final size:16
Alignment explanation
Indices: 1368822--1368855 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1368812 AAAGGTGGTG
1368822 TCATAAAGGTGACGCC
1 TCATAAAGGTGACGCC
*
1368838 TCATAAAGGTGATGCC
1 TCATAAAGGTGACGCC
1368854 TC
1 TC
1368856 GTCTCGGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (16 bp):
TCATAAAGGTGACGCC
Found at i:1369490 original size:15 final size:15
Alignment explanation
Indices: 1369470--1369505 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
1369460 TATTATACAT
1369470 TATTGTATCATATGA
1 TATTGTATCATATGA
*
1369485 TATTGTTTCATATGA
1 TATTGTATCATATGA
1369500 TATTGT
1 TATTGT
1369506 CATATGTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.28, C:0.06, G:0.14, T:0.53
Consensus pattern (15 bp):
TATTGTATCATATGA
Found at i:1369510 original size:13 final size:14
Alignment explanation
Indices: 1369470--1369511 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 14
1369460 TATTATACAT
1369470 TATTGTATCATATGA
1 TATTGT-TCATATGA
1369485 TATTGTTTCATATGA
1 TATTG-TTCATATGA
1369500 TATTG-TCATATG
1 TATTGTTCATATG
1369512 TAACATTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 7 0.27
15 18 0.69
16 1 0.04
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (14 bp):
TATTGTTCATATGA
Found at i:1369692 original size:15 final size:15
Alignment explanation
Indices: 1369674--1369721 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
1369664 ATTATACCAC
1369674 ATGAAATTGTATCAT
1 ATGAAATTGTATCAT
** *
1369689 ATGATTTTGTAACAT
1 ATGAAATTGTATCAT
1369704 AT-AATATTGTATCAT
1 ATGAA-ATTGTATCAT
1369719 ATG
1 ATG
1369722 GTACGATATG
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
14 1 0.04
15 24 0.96
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (15 bp):
ATGAAATTGTATCAT
Found at i:1370436 original size:18 final size:17
Alignment explanation
Indices: 1370409--1370443 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
1370399 TCATATTATA
1370409 TTAAACAATATCATATC
1 TTAAACAATATCATATC
1370426 TTAATACAATATCATATC
1 TTAA-ACAATATCATATC
1370444 ATATGTTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (17 bp):
TTAAACAATATCATATC
Found at i:1370508 original size:17 final size:17
Alignment explanation
Indices: 1370486--1370521 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
1370476 ATTACAGTAT
1370486 TATATTGTATCA-TATGA
1 TATATTGTAT-AGTATGA
1370503 TATATTGTATAGTATGA
1 TATATTGTATAGTATGA
1370520 TA
1 TA
1370522 AGATGCAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 1 0.06
17 17 0.94
ACGTcount: A:0.36, C:0.03, G:0.14, T:0.47
Consensus pattern (17 bp):
TATATTGTATAGTATGA
Found at i:1371928 original size:2 final size:2
Alignment explanation
Indices: 1371921--1371976 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1371911 CTACAACTAA
1371921 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1371963 CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT
1371977 TATACAACCA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1373533 original size:166 final size:165
Alignment explanation
Indices: 1373259--1373590 Score: 637
Period size: 166 Copynumber: 2.0 Consensus size: 165
1373249 CATGCCGAAT
*
1373259 TTTTAACTAATTTTTAAGTGTTAATGAATACAAACATATTACGATATGATGAAATTAAATGCCTA
1 TTTTAACTAATTTTTAAGTGTTAATGAATACAAAAATATTACGATATGATGAAATTAAATGCCTA
1373324 CGAAATTTTATTTGTTTTAGAAACAACAAAATTTTGACCCAACGAAAATATGTGCTTCTACAGTA
66 CGAAATTTTATTTGTTTTAGAAACAACAAAATTTTGACCCAACGAAAATATGTGCTTCTACAGTA
*
1373389 CTTAAAATTTTTACAGAATGCATAATTTCAGTTTTG
131 CTT-AAATTTATACAGAATGCATAATTTCAGTTTTG
1373425 TTTTAACTAATTTTTAAGTGTTAATGAATACAAAAATATTACGATATGATGAAATTAAATGCCTA
1 TTTTAACTAATTTTTAAGTGTTAATGAATACAAAAATATTACGATATGATGAAATTAAATGCCTA
1373490 CGAAATTTTATTTGTTTTAGAAACAACAAAATTTTGACCCAACGAAAATATGTGCTTCTACAGTA
66 CGAAATTTTATTTGTTTTAGAAACAACAAAATTTTGACCCAACGAAAATATGTGCTTCTACAGTA
1373555 CTTAAATTTATACAGAATGCATAATTTCAGTTTTG
131 CTTAAATTTATACAGAATGCATAATTTCAGTTTTG
1373590 T
1 T
1373591 ACTTTTAAAA
Statistics
Matches: 164, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
165 32 0.20
166 132 0.80
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (165 bp):
TTTTAACTAATTTTTAAGTGTTAATGAATACAAAAATATTACGATATGATGAAATTAAATGCCTA
CGAAATTTTATTTGTTTTAGAAACAACAAAATTTTGACCCAACGAAAATATGTGCTTCTACAGTA
CTTAAATTTATACAGAATGCATAATTTCAGTTTTG
Found at i:1377270 original size:13 final size:13
Alignment explanation
Indices: 1377252--1377276 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1377242 GTAAAGTTAA
1377252 TTAGCAAATAAAG
1 TTAGCAAATAAAG
1377265 TTAGCAAATAAA
1 TTAGCAAATAAA
1377277 TTTGTACGTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.12, T:0.24
Consensus pattern (13 bp):
TTAGCAAATAAAG
Found at i:1377952 original size:29 final size:29
Alignment explanation
Indices: 1377910--1378197 Score: 324
Period size: 29 Copynumber: 9.9 Consensus size: 29
1377900 CGTTCTACCA
*
1377910 CAACCATCTACAACAGGCAATAGAACATT
1 CAACCATCTACAACAGGTAATAGAACATT
* *
1377939 CAACCATCTACAACAGGCAGTAGAACATT
1 CAACCATCTACAACAGGTAATAGAACATT
* *
1377968 CAACAATCTACAACAGGTAATAGACCATT
1 CAACCATCTACAACAGGTAATAGAACATT
* * *
1377997 CAACCATCTACAACAGGCAGTAGATCATT
1 CAACCATCTACAACAGGTAATAGAACATT
*** * *
1378026 CAAATGTCTACAACAGGTGATATAACATT
1 CAACCATCTACAACAGGTAATAGAACATT
* *
1378055 CAACCATCTACAACAGGTGATATAACATT
1 CAACCATCTACAACAGGTAATAGAACATT
* * *
1378084 CAACCATCTACAACAAGTGATATAACATT
1 CAACCATCTACAACAGGTAATAGAACATT
* * * *
1378113 CAACCACCTACAACAAGTGATATAACATT
1 CAACCATCTACAACAGGTAATAGAACATT
* *
1378142 CAACCATCTACAACAGGTGATATAACATT
1 CAACCATCTACAACAGGTAATAGAACATT
* * * *
1378171 CAACCATATACAAAAGGCAGTAGAACA
1 CAACCATCTACAACAGGTAATAGAACA
1378198 CGAATCCATA
Statistics
Matches: 229, Mismatches: 30, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 229 1.00
ACGTcount: A:0.43, C:0.25, G:0.11, T:0.21
Consensus pattern (29 bp):
CAACCATCTACAACAGGTAATAGAACATT
Found at i:1378005 original size:58 final size:58
Alignment explanation
Indices: 1377910--1378197 Score: 366
Period size: 58 Copynumber: 5.0 Consensus size: 58
1377900 CGTTCTACCA
** *
1377910 CAACCATCTACAACAGGCAATAGAACATTCAACCATCTACAACAGGCAGTAGAACATT
1 CAACCATCTACAACAGGTGATATAACATTCAACCATCTACAACAGGCAGTAGAACATT
* * * * *
1377968 CAACAATCTACAACAGGTAATAGACCATTCAACCATCTACAACAGGCAGTAGATCATT
1 CAACCATCTACAACAGGTGATATAACATTCAACCATCTACAACAGGCAGTAGAACATT
*** * *
1378026 CAAATGTCTACAACAGGTGATATAACATTCAACCATCTACAACAGG-TGATATAACATT
1 CAACCATCTACAACAGGTGATATAACATTCAACCATCTACAACAGGCAG-TAGAACATT
* * *
1378084 CAACCATCTACAACAAGTGATATAACATTCAACCACCTACAACAAGTG-A-TATAACATT
1 CAACCATCTACAACAGGTGATATAACATTCAACCATCTACAAC-AG-GCAGTAGAACATT
* *
1378142 CAACCATCTACAACAGGTGATATAACATTCAACCATATACAAAAGGCAGTAGAACA
1 CAACCATCTACAACAGGTGATATAACATTCAACCATCTACAACAGGCAGTAGAACA
1378198 CGAATCCATA
Statistics
Matches: 201, Mismatches: 24, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
56 1 0.00
57 4 0.02
58 193 0.96
59 2 0.01
60 1 0.00
ACGTcount: A:0.43, C:0.25, G:0.11, T:0.21
Consensus pattern (58 bp):
CAACCATCTACAACAGGTGATATAACATTCAACCATCTACAACAGGCAGTAGAACATT
Found at i:1378056 original size:87 final size:87
Alignment explanation
Indices: 1377910--1378197 Score: 384
Period size: 87 Copynumber: 3.3 Consensus size: 87
1377900 CGTTCTACCA
* * * *
1377910 CAACCATCTACAACAGGCAATAGAACATTCAACCATCTACAACAGG-CAGTAGAACATTCAACAA
1 CAACCATCTACAACAGGCAGTAGAACATTCAACCATCTACAACAGGTGA-TATAACATTCAACCA
* * *
1377974 TCTACAACAGGTAATAGACCATT
65 TCTACAACAGGTGATATAACATT
* ***
1377997 CAACCATCTACAACAGGCAGTAGATCATTCAAATGTCTACAACAGGTGATATAACATTCAACCAT
1 CAACCATCTACAACAGGCAGTAGAACATTCAACCATCTACAACAGGTGATATAACATTCAACCAT
1378062 CTACAACAGGTGATATAACATT
66 CTACAACAGGTGATATAACATT
* * *
1378084 CAACCATCTACAACAAGTG-A-TATAACATTCAACCACCTACAACAAGTGATATAACATTCAACC
1 CAACCATCTACAAC-AG-GCAGTAGAACATTCAACCATCTACAACAGGTGATATAACATTCAACC
1378147 ATCTACAACAGGTGATATAACATT
64 ATCTACAACAGGTGATATAACATT
* *
1378171 CAACCATATACAAAAGGCAGTAGAACA
1 CAACCATCTACAACAGGCAGTAGAACA
1378198 CGAATCCATA
Statistics
Matches: 175, Mismatches: 21, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
85 1 0.01
86 3 0.02
87 166 0.95
88 4 0.02
89 1 0.01
ACGTcount: A:0.43, C:0.25, G:0.11, T:0.21
Consensus pattern (87 bp):
CAACCATCTACAACAGGCAGTAGAACATTCAACCATCTACAACAGGTGATATAACATTCAACCAT
CTACAACAGGTGATATAACATT
Done.