Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold1024
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: 1774716
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 201941 characters in sequence are not A, C, G, or T
File 5 of 5
Found at i:1168169 original size:2 final size:2
Alignment explanation
Indices: 1168162--1168216 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
1168152 CTCACAACAT
1168162 GA GA GA GA GA GA GA 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
*
1168204 GA GT GA GA GA GA G
1 GA GA GA GA GA GA G
1168217 GCACCTGTCT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.47, C:0.00, G:0.51, T:0.02
Consensus pattern (2 bp):
GA
Found at i:1233746 original size:19 final size:20
Alignment explanation
Indices: 1233698--1233746 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
1233688 TTTTTCAAAG
*
1233698 AAAATATTATATTAATTATTA
1 AAAATA-TATATTAATTAGTA
*
1233719 ATAATTATATATTAATT-GTA
1 A-AAATATATATTAATTAGTA
1233739 AAAATATA
1 AAAATATA
1233747 ACACTTANTA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 6 0.25
20 3 0.12
21 11 0.46
22 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
AAAATATATATTAATTAGTA
Found at i:1238797 original size:12 final size:12
Alignment explanation
Indices: 1238780--1238805 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1238770 TTTTATATCT
1238780 AATTAATGTTAC
1 AATTAATGTTAC
1238792 AATTAATGTTAC
1 AATTAATGTTAC
1238804 AA
1 AA
1238806 ATAAGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (12 bp):
AATTAATGTTAC
Found at i:1243688 original size:2 final size:2
Alignment explanation
Indices: 1243681--1243721 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1243671 ACATACCGTA
1243681 TC TC TC TC TC TC TC TC TC TC TC TC TC TC 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
1243722 GATCCAGAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1246878 original size:62 final size:62
Alignment explanation
Indices: 1246759--1246881 Score: 192
Period size: 62 Copynumber: 2.0 Consensus size: 62
1246749 GATTATTATA
* * * *
1246759 TTTTATACTTTCATGTTAAATACTGAAATTTTATTGGTTAAGACACAGTTGACAATCCGTTT
1 TTTTATACTTTCATGTTAAATACTGAAATCTGATTGGTTAAGACACAGCTCACAATCCGTTT
* *
1246821 TTTTATACTTTCATGTTAAATACTGAAATCTGATTGGTTAAGACGCAGCTCATAATCCGTT
1 TTTTATACTTTCATGTTAAATACTGAAATCTGATTGGTTAAGACACAGCTCACAATCCGTT
1246882 CTATTACCCT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
62 55 1.00
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (62 bp):
TTTTATACTTTCATGTTAAATACTGAAATCTGATTGGTTAAGACACAGCTCACAATCCGTTT
Found at i:1253706 original size:3 final size:3
Alignment explanation
Indices: 1253691--1253729 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
1253681 GTCAGATACA
* *
1253691 GAT GAT GAC GAT GAT GAT GAT GAT GAC GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1253730 CATGTTCCAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.33, C:0.05, G:0.33, T:0.28
Consensus pattern (3 bp):
GAT
Found at i:1261526 original size:12 final size:12
Alignment explanation
Indices: 1261511--1261535 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1261501 TCCTCCAGAA
1261511 AAGGCTGAGGAG
1 AAGGCTGAGGAG
1261523 AAGGCTGAGGAG
1 AAGGCTGAGGAG
1261535 A
1 A
1261536 CTCAGGGAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.48, T:0.08
Consensus pattern (12 bp):
AAGGCTGAGGAG
Found at i:1261702 original size:21 final size:21
Alignment explanation
Indices: 1261679--1261943 Score: 262
Period size: 21 Copynumber: 12.5 Consensus size: 21
1261669 ACCCTCAGAG
* * * *
1261679 GAAAAGAAAGAAGAGGGGGAG
1 GAAAAGAAAGCAGAAGGAGAA
1261700 GAAAAGAAAGCAGAAGGAGAA
1 GAAAAGAAAGCAGAAGGAGAA
*
1261721 GAAAAGAAAGTAGAAGGAGAA
1 GAAAAGAAAGCAGAAGGAGAA
** *
1261742 GAAAAGAAAGTTGAGGGAGAA
1 GAAAAGAAAGCAGAAGGAGAA
*
1261763 GAAAAGAAAGAAGAAGGAGAA
1 GAAAAGAAAGCAGAAGGAGAA
*** *
1261784 GAAAAGAAAATTGAGGGAGAA
1 GAAAAGAAAGCAGAAGGAGAA
* * *
1261805 GAGAAGAAAGAGTCAGAGGGAGAG
1 GAAAAG-AA-AG-CAGAAGGAGAA
** * *
1261829 GAAAAGAAAGTTGATGGGGAA
1 GAAAAGAAAGCAGAAGGAGAA
* *
1261850 GAGAAGAAGGCAGAAGGAGAA
1 GAAAAGAAAGCAGAAGGAGAA
* *
1261871 GAAAAGAAAGCAGAAGGGGAG
1 GAAAAGAAAGCAGAAGGAGAA
1261892 GAAAAGAAAGCAGAAGGAG-A
1 GAAAAGAAAGCAGAAGGAGAA
*
1261912 GAAAAAGAAAGCAGAAGGAGAG
1 G-AAAAGAAAGCAGAAGGAGAA
1261934 GAAAAGAAAG
1 GAAAAGAAAG
1261944 TTGAAGATGA
Statistics
Matches: 201, Mismatches: 38, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
20 1 0.00
21 179 0.89
22 5 0.02
23 3 0.01
24 13 0.06
ACGTcount: A:0.56, C:0.02, G:0.38, T:0.03
Consensus pattern (21 bp):
GAAAAGAAAGCAGAAGGAGAA
Found at i:1261748 original size:63 final size:63
Alignment explanation
Indices: 1261679--1261943 Score: 300
Period size: 63 Copynumber: 4.2 Consensus size: 63
1261669 ACCCTCAGAG
* *
1261679 GAAAAGAAAGAAGAGGGGGAGGAAAAGAAAGCAGAAGGAGAAGAAAAGAAAGTAGAAGGAGAA
1 GAAAAGAAAGAAGAGGGAGAGGAAAAGAAAGCAGAAGGAGAAGAAAAGAAAGCAGAAGGAGAA
** * * *** *
1261742 GAAAAGAAAGTTGAGGGAGAAGAAAAGAAAGAAGAAGGAGAAGAAAAGAAAATTGAGGGAGAA
1 GAAAAGAAAGAAGAGGGAGAGGAAAAGAAAGCAGAAGGAGAAGAAAAGAAAGCAGAAGGAGAA
* ** * * * *
1261805 GAGAAGAAAGAGTCAGAGGGAGAGGAAAAGAAAGTTGATGGGGAAGAGAAGAAGGCAGAAGGAGA
1 GAAAAGAAAGA---AGAGGGAGAGGAAAAGAAAGCAGAAGGAGAAGAAAAGAAAGCAGAAGGAGA
1261870 A
63 A
* *
1261871 GAAAAGAAAGCAGAAGGG-GAGGAAAAGAAAGCAGAAGGAG-AGAAAAAGAAAGCAGAAGGAGAG
1 GAAAAGAAAGAAG-AGGGAGAGGAAAAGAAAGCAGAAGGAGAAG-AAAAGAAAGCAGAAGGAGAA
1261934 GAAAAGAAAG
1 GAAAAGAAAG
1261944 TTGAAGATGA
Statistics
Matches: 166, Mismatches: 31, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
62 2 0.01
63 111 0.67
64 4 0.02
66 49 0.30
ACGTcount: A:0.56, C:0.02, G:0.38, T:0.03
Consensus pattern (63 bp):
GAAAAGAAAGAAGAGGGAGAGGAAAAGAAAGCAGAAGGAGAAGAAAAGAAAGCAGAAGGAGAA
Found at i:1262025 original size:27 final size:29
Alignment explanation
Indices: 1261961--1262026 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 29
1261951 TGAAAAATCT
*
1261961 GAAGAGAAATCCAAAGATGCAGCAGAAGGG
1 GAAGA-AAATCCAAAGATGCAGCAGAAGAG
*
1261991 GATA-AAAAT-CAAA-ATGCTGCAGAAGAG
1 GA-AGAAAATCCAAAGATGCAGCAGAAGAG
1262018 GAAGAAAAT
1 GAAGAAAAT
1262027 GGTCAGTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
26 1 0.03
27 19 0.59
28 4 0.12
29 4 0.12
30 3 0.09
31 1 0.03
ACGTcount: A:0.52, C:0.11, G:0.27, T:0.11
Consensus pattern (29 bp):
GAAGAAAATCCAAAGATGCAGCAGAAGAG
Found at i:1280074 original size:22 final size:21
Alignment explanation
Indices: 1280025--1280212 Score: 196
Period size: 22 Copynumber: 8.8 Consensus size: 21
1280015 AAATATTTTA
* * **
1280025 ATCTCGTAATTACGAGAAAAC
1 ATCTCGTTATTACGAGTAATT
1280046 ATCTCGTTATTACGAGTTAATT
1 ATCTCGTTATTACGAG-TAATT
* **
1280068 ATCTCGTTATTACGAGAAAAG
1 ATCTCGTTATTACGAGTAATT
*
1280089 ATCTCGTTATTACGAGTTAGTT
1 ATCTCGTTATTACGAG-TAATT
* **
1280111 ATCTCGTTATTACGAGAAAAG
1 ATCTCGTTATTACGAGTAATT
1280132 ATCTCGTTATTACGAGATAATT
1 ATCTCGTTATTACGAG-TAATT
*
1280154 TTCTCGTTATTACGAGTTAATT
1 ATCTCGTTATTACGAG-TAATT
* * **
1280176 TTCTCGTTATTACGAGAAAAG
1 ATCTCGTTATTACGAGTAATT
1280197 ATCTCGTTATTACGAG
1 ATCTCGTTATTACGAG
1280213 AAAAGATCTA
Statistics
Matches: 140, Mismatches: 24, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
21 67 0.48
22 73 0.52
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.37
Consensus pattern (21 bp):
ATCTCGTTATTACGAGTAATT
Found at i:1280080 original size:43 final size:43
Alignment explanation
Indices: 1280025--1280221 Score: 270
Period size: 43 Copynumber: 4.6 Consensus size: 43
1280015 AAATATTTTA
* *
1280025 ATCTCGTAATTACGAGAAAACATCTCGTTATTACGAGTTAATT
1 ATCTCGTTATTACGAGAAAAGATCTCGTTATTACGAGTTAATT
*
1280068 ATCTCGTTATTACGAGAAAAGATCTCGTTATTACGAGTTAGTT
1 ATCTCGTTATTACGAGAAAAGATCTCGTTATTACGAGTTAATT
*
1280111 ATCTCGTTATTACGAGAAAAGATCTCGTTATTACGAGATAATT
1 ATCTCGTTATTACGAGAAAAGATCTCGTTATTACGAGTTAATT
* * *** * **
1280154 TTCTCGTTATTACGAGTTAATTTTCTCGTTATTACGAG-AAAAG
1 ATCTCGTTATTACGAG-AAAAGATCTCGTTATTACGAGTTAATT
1280197 ATCTCGTTATTACGAGAAAAGATCT
1 ATCTCGTTATTACGAGAAAAGATCT
1280222 ATATAAAATG
Statistics
Matches: 135, Mismatches: 18, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
42 5 0.04
43 113 0.84
44 17 0.13
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (43 bp):
ATCTCGTTATTACGAGAAAAGATCTCGTTATTACGAGTTAATT
Found at i:1280125 original size:65 final size:64
Alignment explanation
Indices: 1280046--1280221 Score: 262
Period size: 65 Copynumber: 2.7 Consensus size: 64
1280036 ACGAGAAAAC
* ** *
1280046 ATCTCGTTATTACGAGTTAATTATCTCGTTATTACGAGAAAAGATCTCGTTATTACGAGTTAGTT
1 ATCTCGTTATTACGAG-AAAAGATCTCGTTATTACGAGAAAAGATCTCGTTATTACGAGTTAATT
***
1280111 ATCTCGTTATTACGAGAAAAGATCTCGTTATTACGAGATAATTTTCTCGTTATTACGAGTTAATT
1 ATCTCGTTATTACGAGAAAAGATCTCGTTATTACGAGA-AAAGATCTCGTTATTACGAGTTAATT
*
1280176 TTCTCGTTATTACGAGAAAAGATCTCGTTATTACGAGAAAAGATCT
1 ATCTCGTTATTACGAGAAAAGATCTCGTTATTACGAGAAAAGATCT
1280222 ATATAAAATG
Statistics
Matches: 99, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
64 24 0.24
65 75 0.76
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.38
Consensus pattern (64 bp):
ATCTCGTTATTACGAGAAAAGATCTCGTTATTACGAGAAAAGATCTCGTTATTACGAGTTAATT
Found at i:1280940 original size:21 final size:21
Alignment explanation
Indices: 1280883--1281077 Score: 273
Period size: 21 Copynumber: 9.2 Consensus size: 21
1280873 TTTCAAAAAT
1280883 AGATCTTTTCTCGTAATTACG
1 AGATCTTTTCTCGTAATTACG
* ** *
1280904 AGATAATTAACTCGTAATAACG
1 AGAT-CTTTTCTCGTAATTACG
*
1280926 AGATCTTTTCTCGTAATAACG
1 AGATCTTTTCTCGTAATTACG
1280947 AGATCTTTTCTCGTAATTACG
1 AGATCTTTTCTCGTAATTACG
1280968 AGATCTTTTCTCGTAATTACG
1 AGATCTTTTCTCGTAATTACG
1280989 AGATCTTTTCTCGTAATTACG
1 AGATCTTTTCTCGTAATTACG
* ** * *
1281010 AGATAATTAACTCATAATAACG
1 AGAT-CTTTTCTCGTAATTACG
1281032 AGATCTTTTCTCGTAATTACG
1 AGATCTTTTCTCGTAATTACG
*
1281053 AGATCTTTTCTCGTTATTACG
1 AGATCTTTTCTCGTAATTACG
1281074 AGAT
1 AGAT
1281078 AANNNNNNNN
Statistics
Matches: 153, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
21 120 0.78
22 33 0.22
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (21 bp):
AGATCTTTTCTCGTAATTACG
Found at i:1281028 original size:85 final size:85
Alignment explanation
Indices: 1280883--1281079 Score: 297
Period size: 85 Copynumber: 2.3 Consensus size: 85
1280873 TTTCAAAAAT
* ** *
1280883 AGATCTTTTCTCGTAATTACGAGATAATTAACTCGTAATAACGAGATCTTTTCTCGTAATAACGA
1 AGATCTTTTCTCGTAATTACGAGATAATTAACTCGTAATAACGAGATATTAACTCATAATAACGA
1280948 GATCTTTTCTCGTAATTACG
66 GATCTTTTCTCGTAATTACG
* ** *
1280968 AGATCTTTTCTCGTAATTACGAGAT-CTTTTCTCGTAATTACGAGATAATTAACTCATAATAACG
1 AGATCTTTTCTCGTAATTACGAGATAATTAACTCGTAATAACGAGAT-ATTAACTCATAATAACG
1281032 AGATCTTTTCTCGTAATTACG
65 AGATCTTTTCTCGTAATTACG
*
1281053 AGATCTTTTCTCGTTATTACGAGATAA
1 AGATCTTTTCTCGTAATTACGAGATAA
1281080 NNNNNNNNNN
Statistics
Matches: 100, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
84 17 0.17
85 83 0.83
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (85 bp):
AGATCTTTTCTCGTAATTACGAGATAATTAACTCGTAATAACGAGATATTAACTCATAATAACGA
GATCTTTTCTCGTAATTACG
Found at i:1281072 original size:106 final size:106
Alignment explanation
Indices: 1280883--1281077 Score: 363
Period size: 106 Copynumber: 1.8 Consensus size: 106
1280873 TTTCAAAAAT
*
1280883 AGATCTTTTCTCGTAATTACGAGATAATTAACTCGTAATAACGAGATCTTTTCTCGTAATAACGA
1 AGATCTTTTCTCGTAATTACGAGATAATTAACTCATAATAACGAGATCTTTTCTCGTAATAACGA
1280948 GATCTTTTCTCGTAATTACGAGATCTTTTCTCGTAATTACG
66 GATCTTTTCTCGTAATTACGAGATCTTTTCTCGTAATTACG
*
1280989 AGATCTTTTCTCGTAATTACGAGATAATTAACTCATAATAACGAGATCTTTTCTCGTAATTACGA
1 AGATCTTTTCTCGTAATTACGAGATAATTAACTCATAATAACGAGATCTTTTCTCGTAATAACGA
*
1281054 GATCTTTTCTCGTTATTACGAGAT
66 GATCTTTTCTCGTAATTACGAGAT
1281078 AANNNNNNNN
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
106 86 1.00
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (106 bp):
AGATCTTTTCTCGTAATTACGAGATAATTAACTCATAATAACGAGATCTTTTCTCGTAATAACGA
GATCTTTTCTCGTAATTACGAGATCTTTTCTCGTAATTACG
Found at i:1281078 original size:64 final size:64
Alignment explanation
Indices: 1280914--1281079 Score: 253
Period size: 64 Copynumber: 2.6 Consensus size: 64
1280904 AGATAATTAA
* * * ** * *
1280914 CTCGTAATAACGAGATCTTTTCTCGTAATAACGAGAT-CTTTTCTCGTAATTACGAGATCTTTT
1 CTCGTAATTACGAGATCTTTTCTCGTAATTACGAGATAATTAACTCATAATAACGAGATCTTTT
1280977 CTCGTAATTACGAGATCTTTTCTCGTAATTACGAGATAATTAACTCATAATAACGAGATCTTTT
1 CTCGTAATTACGAGATCTTTTCTCGTAATTACGAGATAATTAACTCATAATAACGAGATCTTTT
*
1281041 CTCGTAATTACGAGATCTTTTCTCGTTATTACGAGATAA
1 CTCGTAATTACGAGATCTTTTCTCGTAATTACGAGATAA
1281080 NNNNNNNNNN
Statistics
Matches: 94, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
63 35 0.37
64 59 0.63
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.39
Consensus pattern (64 bp):
CTCGTAATTACGAGATCTTTTCTCGTAATTACGAGATAATTAACTCATAATAACGAGATCTTTT
Found at i:1285567 original size:136 final size:136
Alignment explanation
Indices: 1285324--1285591 Score: 457
Period size: 136 Copynumber: 2.0 Consensus size: 136
1285314 TGAAATATGT
*
1285324 AGTTATAGATGCATGCAAAAACTTTTAATAACGTAACCGCCGGTAAAATACGAAATTTCTGTTCG
1 AGTTATACATGCATGCAAAAACTTTTAATAACGTAACCGCCGGTAAAATACGAAATTTCTGTTCG
* * * *
1285389 AGGACTATTAGGATTTTTACATTTTTGAACTCCAAAATTCA-TTTTTTTCTACTCATAATTGACA
66 AGGACAAATAAGATTTTTACATTTTTAAACTCCAAAATTCATTTTTTTTCTACTCATAATTGACA
1285453 ATTTGC
131 ATTTGC
*
1285459 AGTTATACATGCATGCTAAAACTTTTAATAACGTAACCGCCGGTAAAATTACGAAATTTCTGTTC
1 AGTTATACATGCATGCAAAAACTTTTAATAACGTAACCGCCGGTAAAA-TACGAAATTTCTGTTC
*
1285524 GAGGACAAATAAGATTTTTACATTTTTAAACTCCCAAATTCATTTTTTTTCTACTCATAATTGAC
65 GAGGACAAATAAGATTTTTACATTTTTAAACTCCAAAATTCATTTTTTTTCTACTCATAATTGAC
1285589 AAT
130 AAT
1285592 ATGACAATAT
Statistics
Matches: 124, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
135 46 0.37
136 53 0.43
137 25 0.20
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (136 bp):
AGTTATACATGCATGCAAAAACTTTTAATAACGTAACCGCCGGTAAAATACGAAATTTCTGTTCG
AGGACAAATAAGATTTTTACATTTTTAAACTCCAAAATTCATTTTTTTTCTACTCATAATTGACA
ATTTGC
Found at i:1297335 original size:22 final size:22
Alignment explanation
Indices: 1297310--1297379 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
1297300 TATAAAAATA
1297310 AAAATCAAAGCACGAAACACTT
1 AAAATCAAAGCACGAAACACTT
* * * * *
1297332 AAAAT--TA-CTACTATAAAAATA
1 AAAATCAAAGC-ACGA-AACACTT
1297353 AAAATCAAAGCACGAAACACTT
1 AAAATCAAAGCACGAAACACTT
1297375 AAAAT
1 AAAAT
1297380 TTTAAGACAT
Statistics
Matches: 33, Mismatches: 10, Indels: 10
0.62 0.19 0.19
Matches are distributed among these distances:
19 1 0.03
20 4 0.12
21 9 0.27
22 14 0.42
23 4 0.12
24 1 0.03
ACGTcount: A:0.59, C:0.17, G:0.06, T:0.19
Consensus pattern (22 bp):
AAAATCAAAGCACGAAACACTT
Found at i:1297342 original size:43 final size:43
Alignment explanation
Indices: 1297295--1297380 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
1297285 GGCATCATTC
1297295 ACTACTATAAAAATAAAAATCAAAGCACGAAACACTTAAAATT
1 ACTACTATAAAAATAAAAATCAAAGCACGAAACACTTAAAATT
1297338 ACTACTATAAAAATAAAAATCAAAGCACGAAACACTTAAAATT
1 ACTACTATAAAAATAAAAATCAAAGCACGAAACACTTAAAATT
1297381 TTAAGACATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.58, C:0.16, G:0.05, T:0.21
Consensus pattern (43 bp):
ACTACTATAAAAATAAAAATCAAAGCACGAAACACTTAAAATT
Found at i:1299964 original size:24 final size:24
Alignment explanation
Indices: 1299921--1299967 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1299911 CACCTCCTGG
*
1299921 TCTATGGAATCTTTTCTGGGTGGC
1 TCTATGGAATCTTCTCTGGGTGGC
1299945 TCTATGGAATCCTTCT-TGGGTGG
1 TCTATGGAAT-CTTCTCTGGGTGG
1299968 ATTGTGAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.13, C:0.17, G:0.30, T:0.40
Consensus pattern (24 bp):
TCTATGGAATCTTCTCTGGGTGGC
Found at i:1302179 original size:146 final size:146
Alignment explanation
Indices: 1301917--1302718 Score: 1197
Period size: 146 Copynumber: 5.5 Consensus size: 146
1301907 TAAAACTGTT
* *
1301917 GGTCATAAGCAATATTTGTGTGAAGTAAGAACATT-CAATGCTTCTCCATAAGAAAGATAAT-GA
1 GGTCATAAGCAATCTTTGTGTGAAGTAAGAAC-TTCCAATGTTTCTCCATAAGAAAGAT-ATGGA
*
1301980 CCGGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAA
64 CCGGACACGAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAA
* * *
1302045 GGTCATGACAAACTCTTT
129 GGTCATGACACACCCTTA
* * * *
1302063 GGTCCTAAGCAATATTTGTGTGAAGTTAGAACATT-CAATGCTTCTCCATAAGAAAGATAAT-GA
1 GGTCATAAGCAATCTTTGTGTGAAGTAAGAAC-TTCCAATGTTTCTCCATAAGAAAGAT-ATGGA
* ** *
1302126 CCGGACACGAATTTTGCACTATTTTC-CCCAACGACCTTGACCTTGCCCAAATGACCTTGGATCA
64 CCGGACACGAATTTTGCACT-TTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCA
1302190 AGGTCATGACACACCCTTA
128 AGGTCATGACACACCCTTA
* * * *
1302209 GGTCATAAGCAATCTTTGTATGAATTAAGAACTTCAAATGTTTCTCCATAAGAAAGATATGGGCC
1 GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACC
* *
1302274 GGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCTAATGACCTTGGGTCAAGG
66 GGACACGAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGG
1302339 TCATGACACACCCTTA
131 TCATGACACACCCTTA
* * *
1302355 GATCATAAGCAATCTTTGTGTGAAGTAAAAACTTCCAATGTTTCTCCATTAGAAAGATATGGACC
1 GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACC
* * *
1302420 GGACACGAATTTTTGTA-TGTTTTCTGCCAGTGACCTTGAACTTGCCCGAATGACCTT--GTCAA
66 GGACACGAA-TTTTGCACT-TTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAA
*
1302482 GGTCATGACACACCTTTA
129 GGTCATGACACACCCTTA
*
1302500 GGTCATAAGCAATCTTTGTATGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACC
1 GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACC
* * *
1302565 GGACACGAATTTTGCATTTTTTCTGCCATTGACCTTGACCTTGCCCGAATGACCTTGGGTCAAGG
66 GGACACGAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGG
1302630 TCATGACACACCCTTA
131 TCATGACACACCCTTA
*
1302646 GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACT
1 GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACC
1302711 GGACACGA
66 GGACACGA
1302719 TTGCACAGAC
Statistics
Matches: 601, Mismatches: 46, Indels: 18
0.90 0.07 0.03
Matches are distributed among these distances:
144 42 0.07
145 102 0.17
146 410 0.68
147 47 0.08
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (146 bp):
GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACC
GGACACGAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGG
TCATGACACACCCTTA
Found at i:1302618 original size:291 final size:292
Alignment explanation
Indices: 1301917--1302718 Score: 1231
Period size: 291 Copynumber: 2.8 Consensus size: 292
1301907 TAAAACTGTT
* * *
1301917 GGTCATAAGCAATATTTGTGTGAAGTAAGAACATT-CAATGCTTCTCCATAAGAAAGATAAT-GA
1 GGTCATAAGCAATCTTTGTATGAAGTAAGAAC-TTCCAATGTTTCTCCATAAGAAAGAT-ATGGA
1301980 CCGGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAA
64 CCGGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAA
* * * * * * *
1302045 GGTCATGACAAACTCTTTGGTCCTAAGCAATATTTGTGTGAAGTTAGAACATT-CAATGCTTCTC
129 GGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAAC-TTCCAATGTTTCTC
*
1302109 CATAAGAAAGATAAT-GACCGGACACGAATTTTGCACTATTTTCCCCAACGACCTTGACCTTGCC
193 CATAAGAAAGAT-ATGGACCGGACACGAATTTTGCACTATTTTCCCCAACGACCTTGAACTTGCC
1302173 CAAATGACCTTGGATCAAGGTCATGACACACCCTTA
257 CAAATGACCTTGGATCAAGGTCATGACACACCCTTA
* * *
1302209 GGTCATAAGCAATCTTTGTATGAATTAAGAACTTCAAATGTTTCTCCATAAGAAAGATATGGGCC
1 GGTCATAAGCAATCTTTGTATGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACC
*
1302274 GGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCTAATGACCTTGGGTCAAGG
66 GGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGG
* *
1302339 TCATGACACACCCTTAGATCATAAGCAATCTTTGTGTGAAGTAAAAACTTCCAATGTTTCTCCAT
131 TCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCAT
* * * * ** *
1302404 TAGAAAGATATGGACCGGACACGAATTTTTGTA-TGTTTTCTGCCAGTGACCTTGAACTTGCCCG
196 AAGAAAGATATGGACCGGACACGAA-TTTTGCACTATTTTC-CCCAACGACCTTGAACTTGCCCA
*
1302468 AATGACCTT-G-TCAAGGTCATGACACACCTTTA
259 AATGACCTTGGATCAAGGTCATGACACACCCTTA
1302500 GGTCATAAGCAATCTTTGTATGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACC
1 GGTCATAAGCAATCTTTGTATGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACC
* * * *
1302565 GGACACGAATTTTGCATTTTTTCTGCCATTGACCTTGACCTTGCCCGAATGACCTTGGGTCAAGG
66 GGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGG
1302630 TCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCAT
131 TCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCAT
*
1302695 AAGAAAGATATGGACTGGACACGA
196 AAGAAAGATATGGACCGGACACGA
1302719 TTGCACAGAC
Statistics
Matches: 468, Mismatches: 36, Indels: 13
0.91 0.07 0.03
Matches are distributed among these distances:
291 237 0.51
292 198 0.42
293 33 0.07
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (292 bp):
GGTCATAAGCAATCTTTGTATGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACC
GGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGG
TCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCAT
AAGAAAGATATGGACCGGACACGAATTTTGCACTATTTTCCCCAACGACCTTGAACTTGCCCAAA
TGACCTTGGATCAAGGTCATGACACACCCTTA
Found at i:1302732 original size:4 final size:4
Alignment explanation
Indices: 1302730--1302764 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
1302720 TGCACAGACA
* *
1302730 GACG GACG GACA GACG GACG GACG GACA GACG GAC
1 GACG GACG GACG GACG GACG GACG GACG GACG GAC
1302765 AAGGTGATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.31, C:0.26, G:0.43, T:0.00
Consensus pattern (4 bp):
GACG
Found at i:1302743 original size:12 final size:12
Alignment explanation
Indices: 1302726--1302765 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
1302716 CGATTGCACA
1302726 GACAGACGGACG
1 GACAGACGGACG
1302738 GACAGACGGACG
1 GACAGACGGACG
* *
1302750 GACGGACAGACG
1 GACAGACGGACG
1302762 GACA
1 GACA
1302766 AGGTGATTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.35, C:0.25, G:0.40, T:0.00
Consensus pattern (12 bp):
GACAGACGGACG
Found at i:1302747 original size:8 final size:8
Alignment explanation
Indices: 1302723--1302765 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
1302713 ACACGATTGC
*
1302723 ACAGACAG
1 ACAGACGG
*
1302731 ACGGACGG
1 ACAGACGG
1302739 ACAGACGG
1 ACAGACGG
*
1302747 ACGGACGG
1 ACAGACGG
1302755 ACAGACGG
1 ACAGACGG
1302763 ACA
1 ACA
1302766 AGGTGATTCC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.37, C:0.26, G:0.37, T:0.00
Consensus pattern (8 bp):
ACAGACGG
Found at i:1302761 original size:16 final size:16
Alignment explanation
Indices: 1302723--1302764 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
1302713 ACACGATTGC
*
1302723 ACAGACAGACGGACGG
1 ACAGACGGACGGACGG
1302739 ACAGACGGACGGACGG
1 ACAGACGGACGGACGG
1302755 ACAGACGGAC
1 ACAGACGGAC
1302765 AAGGTGATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.36, C:0.26, G:0.38, T:0.00
Consensus pattern (16 bp):
ACAGACGGACGGACGG
Found at i:1307200 original size:21 final size:21
Alignment explanation
Indices: 1307148--1307203 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
1307138 ATGACAGGAT
*
1307148 TTACAGAAATGACACCTGAAA
1 TTACAGAAATGACACCTAAAA
1307169 TTACCAG-AATGACA-CTAAAA
1 TTA-CAGAAATGACACCTAAAA
1307189 TCTACAGAAATGACA
1 T-TACAGAAATGACA
1307204 TTTCAAATAC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 9 0.29
21 19 0.61
22 3 0.10
ACGTcount: A:0.48, C:0.20, G:0.12, T:0.20
Consensus pattern (21 bp):
TTACAGAAATGACACCTAAAA
Found at i:1308654 original size:21 final size:21
Alignment explanation
Indices: 1308630--1308687 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
1308620 ATCAACTTTA
*
1308630 AGTGTCATTTCTGTAGATTT-T
1 AGTGTCATTTCGGTA-ATTTCT
*
1308651 AGTGTCATTCCGGTAATTTCT
1 AGTGTCATTTCGGTAATTTCT
* *
1308672 GGTGTCATTTCCGTAA
1 AGTGTCATTTCGGTAA
1308688 ATACTATCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 4 0.13
21 27 0.87
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.45
Consensus pattern (21 bp):
AGTGTCATTTCGGTAATTTCT
Found at i:1320419 original size:25 final size:25
Alignment explanation
Indices: 1320389--1320444 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
1320379 TGTTAAACTT
1320389 AAATTTGTATTT-TACTTATAAAT-C
1 AAATTTGTATTTCTA-TTATAAATAC
* *
1320413 AAGATTTTTCTTTCTATTATAAATAC
1 AA-ATTTGTATTTCTATTATAAATAC
1320439 AAATTT
1 AAATTT
1320445 ATTACTGTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 2 0.07
25 20 0.74
26 5 0.19
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.50
Consensus pattern (25 bp):
AAATTTGTATTTCTATTATAAATAC
Found at i:1341747 original size:180 final size:180
Alignment explanation
Indices: 1341438--1342349 Score: 1509
Period size: 180 Copynumber: 5.1 Consensus size: 180
1341428 GCAGCTGCCA
* * * *
1341438 AAAGGGTACCCTTATTGTACGGATAACTCCTCCTACAGTTTTTAAGATAGGAAGTTGTTCTTTTG
1 AAAGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGCTCTTTTT
* * * *
1341503 CAGATCAATTGTATATATATCAGAGATGTGCATATTGCTAGGATTTTAATTTCTGATTATTTATG
66 CAGATCAATTGTACATATATCAGAGGTGTGCATATTGATAGGATTTTGATTTCTGATTATTTATG
* * *
1341568 AAAAAAATACCAGCTTTTGAACTTAGTAATTTTTTGGCAAAAAATTGCAC
131 AAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCAT
* * * *
1341618 ATAGGGTACCCTCATTGTACGTATAACTTCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTT
1 AAAGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGCTCTTTTT
* * *
1341683 CAGATCAATTGTACATATATCAGAGATGTGCATATTGCTAGGATTTTGATTTCTGATAATTTATG
66 CAGATCAATTGTACATATATCAGAGGTGTGCATATTGATAGGATTTTGATTTCTGATTATTTATG
1341748 AAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCAT
131 AAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCAT
*
1341798 AAAGGGTACCGTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGCTCTTTTT
1 AAAGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGCTCTTTTT
* * *
1341863 CAGATCAATTGTACATATATCAGTGGTGTGCATATTGATAGGATTTTGATTTCCGATTATTTTTG
66 CAGATCAATTGTACATATATCAGAGGTGTGCATATTGATAGGATTTTGATTTCTGATTATTTATG
*
1341928 AAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAAAATTGCAT
131 AAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCAT
* * * *
1341978 ATAGCGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAAGAAGTTGCTCTTTTG
1 AAAGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGCTCTTTTT
* *
1342043 CAGATCAATTGTACATATATCAGAGGTGTGCATATTGATAGGATTTTGATTTCCGATAATTTATG
66 CAGATCAATTGTACATATATCAGAGGTGTGCATATTGATAGGATTTTGATTTCTGATTATTTATG
1342108 AAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCAT
131 AAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCAT
* *
1342158 AAAGGGTACCGTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGCTCTTATT
1 AAAGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGCTCTTTTT
* * *
1342223 CAGATCAATTGTACATATATCAGTGGTGTGCATATTGATAAGATTTTGATTTCTGATTATTTTTG
66 CAGATCAATTGTACATATATCAGAGGTGTGCATATTGATAGGATTTTGATTTCTGATTATTTATG
*
1342288 AAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAGATATTGCAT
131 AAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCAT
1342338 AAAGGGTACCCT
1 AAAGGGTACCCT
1342350 TTCACCTTAT
Statistics
Matches: 686, Mismatches: 46, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
180 686 1.00
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (180 bp):
AAAGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGCTCTTTTT
CAGATCAATTGTACATATATCAGAGGTGTGCATATTGATAGGATTTTGATTTCTGATTATTTATG
AAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCAT
Found at i:1344643 original size:16 final size:16
Alignment explanation
Indices: 1344618--1344659 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1344608 AAACTAATCT
1344618 AAACTAAACTGACATA
1 AAACTAAACTGACATA
* *
1344634 AAACTCAACTGACCTA
1 AAACTAAACTGACATA
*
1344650 AAACTGAACT
1 AAACTAAACT
1344660 CAAACTGATC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.50, C:0.24, G:0.07, T:0.19
Consensus pattern (16 bp):
AAACTAAACTGACATA
Found at i:1353845 original size:93 final size:94
Alignment explanation
Indices: 1353686--1353872 Score: 358
Period size: 93 Copynumber: 2.0 Consensus size: 94
1353676 ACATATATTC
1353686 ATGAAAGTTGATCATCAAGTCATTGTTGAAAAAAAAGACAACAAAAACAAAATGCACATTTTATG
1 ATGAAAGTTGATCATCAAGTCATTGTTGAAAAAAAAGACAACAAAAACAAAATGCACATTTTATG
*
1353751 TGTTTG-TTTTGCAGGTTAATGTATTGAA
66 TGTTTGTTTTTACAGGTTAATGTATTGAA
1353779 ATGAAAGTTGATCATCAAGTCATTGTTGAAAAAAAAGACAACAAAAACAAAATGCACATTTTATG
1 ATGAAAGTTGATCATCAAGTCATTGTTGAAAAAAAAGACAACAAAAACAAAATGCACATTTTATG
1353844 TGTTTGTTTTTACAGGTTAATGTATTGAA
66 TGTTTGTTTTTACAGGTTAATGTATTGAA
1353873 TTTAAATACA
Statistics
Matches: 92, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
93 71 0.77
94 21 0.23
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.33
Consensus pattern (94 bp):
ATGAAAGTTGATCATCAAGTCATTGTTGAAAAAAAAGACAACAAAAACAAAATGCACATTTTATG
TGTTTGTTTTTACAGGTTAATGTATTGAA
Found at i:1359891 original size:21 final size:21
Alignment explanation
Indices: 1359865--1359928 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
1359855 TTCTATCAAA
*
1359865 TATGTCGACATGCAAGAGAAT
1 TATGTCGACATGCAAGAAAAT
* * *
1359886 TATGTCAACATGCAACATAAT
1 TATGTCGACATGCAAGAAAAT
1359907 TATG-CTGACATGCAAGAAAAT
1 TATGTC-GACATGCAAGAAAAT
1359928 T
1 T
1359929 GCAACCAGAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
20 1 0.03
21 35 0.97
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.27
Consensus pattern (21 bp):
TATGTCGACATGCAAGAAAAT
Found at i:1360080 original size:21 final size:21
Alignment explanation
Indices: 1360062--1360137 Score: 125
Period size: 21 Copynumber: 3.6 Consensus size: 21
1360052 TAAATATGCT
1360062 GACATGCAACTTATTTATGTC
1 GACATGCAACTTATTTATGTC
*
1360083 AACATGCAACTTATTTATGTC
1 GACATGCAACTTATTTATGTC
1360104 GACATGCAACTTATTTATGTC
1 GACATGCAACTTATTTATGTC
* *
1360125 AACACGCAACTTA
1 GACATGCAACTTA
1360138 CATGTACTTA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (21 bp):
GACATGCAACTTATTTATGTC
Found at i:1360108 original size:42 final size:42
Alignment explanation
Indices: 1360012--1360137 Score: 146
Period size: 42 Copynumber: 3.0 Consensus size: 42
1360002 ATGCTACCTT
* * * * * **
1360012 TTTATGTCGACAAGTAAATTATATATGTTAACATGCAAGATA
1 TTTATGTCGACATGCAACTTATTTATGTCAACATGCAACTTA
**
1360054 AATATG-CTGACATGCAACTTATTTATGTCAACATGCAACTTA
1 TTTATGTC-GACATGCAACTTATTTATGTCAACATGCAACTTA
*
1360096 TTTATGTCGACATGCAACTTATTTATGTCAACACGCAACTTA
1 TTTATGTCGACATGCAACTTATTTATGTCAACATGCAACTTA
1360138 CATGTACTTA
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 1 0.01
42 68 0.97
43 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.35
Consensus pattern (42 bp):
TTTATGTCGACATGCAACTTATTTATGTCAACATGCAACTTA
Found at i:1360198 original size:41 final size:42
Alignment explanation
Indices: 1360148--1360226 Score: 124
Period size: 41 Copynumber: 1.9 Consensus size: 42
1360138 CATGTACTTA
* *
1360148 TGTTGACATGCGAGATGAATATGTTGACAT-CAACTTAGTTT
1 TGTTGACATGCAAGATAAATATGTTGACATGCAACTTAGTTT
*
1360189 TGTTTACATGCAAGATAAATATGTTGACATGCAACTTA
1 TGTTGACATGCAAGATAAATATGTTGACATGCAACTTA
1360227 TAAGTTGTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
41 27 0.79
42 7 0.21
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (42 bp):
TGTTGACATGCAAGATAAATATGTTGACATGCAACTTAGTTT
Found at i:1360284 original size:21 final size:21
Alignment explanation
Indices: 1360258--1360340 Score: 94
Period size: 21 Copynumber: 4.0 Consensus size: 21
1360248 TAAGTTATAA
*
1360258 GTTGCATGTCGACATAAATAT
1 GTTGCATGTCAACATAAATAT
**
1360279 GTTGCATGTCAACATATTTAT
1 GTTGCATGTCAACATAAATAT
* * * *
1360300 CTTGCATGTTAACATAACTAA
1 GTTGCATGTCAACATAAATAT
*
1360321 GTTGCATGTCGACATAAATA
1 GTTGCATGTCAACATAAATA
1360341 GGTAGCGTAT
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Consensus pattern (21 bp):
GTTGCATGTCAACATAAATAT
Found at i:1360445 original size:21 final size:21
Alignment explanation
Indices: 1360419--1360499 Score: 90
Period size: 21 Copynumber: 3.9 Consensus size: 21
1360409 ATTGCAGTTT
* *
1360419 TCTTGCATGTCAACCTAGTTA
1 TCTTGCATGTCAACATAATTA
* ** *
1360440 TGTTGCATGTTGACATAACTA
1 TCTTGCATGTCAACATAATTA
*
1360461 TCTTGCATGTCAACATATTTA
1 TCTTGCATGTCAACATAATTA
*
1360482 TCTTGCATGTCGACATAA
1 TCTTGCATGTCAACATAA
1360500 CTAATAGAAA
Statistics
Matches: 47, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (21 bp):
TCTTGCATGTCAACATAATTA
Found at i:1360488 original size:42 final size:42
Alignment explanation
Indices: 1360419--1360502 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
1360409 ATTGCAGTTT
* * *
1360419 TCTTGCATGTCAACCTAGTTATGTTGCATGTTGACATAACTA
1 TCTTGCATGTCAACATAGTTATCTTGCATGTCGACATAACTA
*
1360461 TCTTGCATGTCAACATATTTATCTTGCATGTCGACATAACTA
1 TCTTGCATGTCAACATAGTTATCTTGCATGTCGACATAACTA
1360503 ATAGAAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.38
Consensus pattern (42 bp):
TCTTGCATGTCAACATAGTTATCTTGCATGTCGACATAACTA
Found at i:1360647 original size:21 final size:20
Alignment explanation
Indices: 1360582--1360658 Score: 73
Period size: 21 Copynumber: 3.8 Consensus size: 20
1360572 TTCTTCTAAT
*
1360582 TATGTCGACATGCAAGATAA
1 TATGTCGACATGCAACATAA
* * * *
1360602 AATGTTGACATGCAATATAGT
1 TATGTCGACATGCAACATA-A
*
1360623 TATGTCAACATGCAACATAA
1 TATGTCGACATGCAACATAA
*
1360643 CTATGTTGACATGCAA
1 -TATGTCGACATGCAA
1360659 GAAAACTGCA
Statistics
Matches: 44, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
20 16 0.36
21 28 0.64
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.29
Consensus pattern (20 bp):
TATGTCGACATGCAACATAA
Found at i:1360791 original size:21 final size:21
Alignment explanation
Indices: 1360746--1360870 Score: 115
Period size: 21 Copynumber: 5.9 Consensus size: 21
1360736 CTACCTACTG
*
1360746 ATGTCAAAATGCAACTTATTTT
1 ATGTCAACATGCAACTTA-TTT
* *
1360768 ATGTTAACATGCAACTTCTTT
1 ATGTCAACATGCAACTTATTT
* *
1360789 ATGTCGACATGCAACTTAGTT
1 ATGTCAACATGCAACTTATTT
* *
1360810 ATGTTAACATGCAACATATTT
1 ATGTCAACATGCAACTTATTT
* * * *
1360831 ATGTCGACATGCACCTAAGTT
1 ATGTCAACATGCAACTTATTT
** *
1360852 ATGTTGACATACAACTTAT
1 ATGTCAACATGCAACTTAT
1360871 AAGTTGCATG
Statistics
Matches: 81, Mismatches: 22, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
21 66 0.81
22 15 0.19
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.37
Consensus pattern (21 bp):
ATGTCAACATGCAACTTATTT
Found at i:1360822 original size:42 final size:42
Alignment explanation
Indices: 1360754--1360870 Score: 162
Period size: 42 Copynumber: 2.8 Consensus size: 42
1360744 TGATGTCAAA
* *
1360754 ATGCAACTTATTTTATGTTAACATGCAACTTCTTTATGTCGAC
1 ATGCAACTTA-GTTATGTTAACATGCAACTTATTTATGTCGAC
*
1360797 ATGCAACTTAGTTATGTTAACATGCAACATATTTATGTCGAC
1 ATGCAACTTAGTTATGTTAACATGCAACTTATTTATGTCGAC
* * * *
1360839 ATGCACCTAAGTTATGTTGACATACAACTTAT
1 ATGCAACTTAGTTATGTTAACATGCAACTTAT
1360871 AAGTTGCATG
Statistics
Matches: 66, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
42 56 0.85
43 10 0.15
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.38
Consensus pattern (42 bp):
ATGCAACTTAGTTATGTTAACATGCAACTTATTTATGTCGAC
Found at i:1360963 original size:21 final size:21
Alignment explanation
Indices: 1360869--1361079 Score: 190
Period size: 21 Copynumber: 10.0 Consensus size: 21
1360859 CATACAACTT
*
1360869 ATAAGTTGCATGTCAACATAT
1 ATAAGTTGCATGTCAACATAA
* ** * *
1360890 TTATCTCGCATGTAAACATAA
1 ATAAGTTGCATGTCAACATAA
* *
1360911 CTAAGTTGCATGTCAACATAT
1 ATAAGTTGCATGTCAACATAA
* ** *
1360932 TTATCTCGCATGTCAACATAA
1 ATAAGTTGCATGTCAACATAA
* *
1360953 CTAAGTTGCATG-CTGACATAA
1 ATAAGTTGCATGTC-AACATAA
*
1360974 ATAAGTTGCATGTCGACATAA
1 ATAAGTTGCATGTCAACATAA
*
1360995 ATAAGTTGCATGTTAACATAA
1 ATAAGTTGCATGTCAACATAA
* *
1361016 ATAAGTTGCATTTCAGCATAA
1 ATAAGTTGCATGTCAACATAA
* ** **
1361037 TTATCTTGCATGTTTACATAA
1 ATAAGTTGCATGTCAACATAA
*
1361058 ATAAGTTGCATGTCGACATAA
1 ATAAGTTGCATGTCAACATAA
1361079 A
1 A
1361080 AAGGTAGCAT
Statistics
Matches: 148, Mismatches: 40, Indels: 4
0.77 0.21 0.02
Matches are distributed among these distances:
20 1 0.01
21 146 0.99
22 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.33
Consensus pattern (21 bp):
ATAAGTTGCATGTCAACATAA
Found at i:1361238 original size:42 final size:42
Alignment explanation
Indices: 1361169--1361248 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
1361159 TTGCAATTTT
*
1361169 TCTTGCATGTCAACATAGTTATGTTGCATGTCGACATAATTA
1 TCTTGCATGTCAACATAGTTATCTTGCATGTCGACATAATTA
* *
1361211 TCTTGCATGTCAAGATATTTATCTTGCATGTCGACATA
1 TCTTGCATGTCAACATAGTTATCTTGCATGTCGACATA
1361249 TTTAATAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (42 bp):
TCTTGCATGTCAACATAGTTATCTTGCATGTCGACATAATTA
Found at i:1361249 original size:21 final size:21
Alignment explanation
Indices: 1361164--1361252 Score: 115
Period size: 21 Copynumber: 4.2 Consensus size: 21
1361154 TCTAATTGCA
*
1361164 ATTTTTCTTGCATGTCAACAT
1 ATTTATCTTGCATGTCAACAT
* * *
1361185 AGTTATGTTGCATGTCGACAT
1 ATTTATCTTGCATGTCAACAT
* *
1361206 AATTATCTTGCATGTCAAGAT
1 ATTTATCTTGCATGTCAACAT
*
1361227 ATTTATCTTGCATGTCGACAT
1 ATTTATCTTGCATGTCAACAT
1361248 ATTTA
1 ATTTA
1361253 ATAGAAAATA
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.43
Consensus pattern (21 bp):
ATTTATCTTGCATGTCAACAT
Found at i:1361303 original size:21 final size:21
Alignment explanation
Indices: 1361277--1361318 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1361267 TGCACACAAT
1361277 GGGCAGAGATATGCCACCATA
1 GGGCAGAGATATGCCACCATA
1361298 GGGCAGAGATATGCCACCATA
1 GGGCAGAGATATGCCACCATA
1361319 ATTAATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.24, G:0.29, T:0.14
Consensus pattern (21 bp):
GGGCAGAGATATGCCACCATA
Found at i:1366402 original size:24 final size:24
Alignment explanation
Indices: 1366370--1366421 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
1366360 CGTGTACAAA
1366370 TGGAGAGATTTCTTGTTTTACCCT
1 TGGAGAGATTTCTTGTTTTACCCT
1366394 TGGAGAGATTTCTTGTTTTACCCT
1 TGGAGAGATTTCTTGTTTTACCCT
1366418 TGGA
1 TGGA
1366422 CCCTGGCAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.17, C:0.15, G:0.23, T:0.44
Consensus pattern (24 bp):
TGGAGAGATTTCTTGTTTTACCCT
Found at i:1368504 original size:18 final size:18
Alignment explanation
Indices: 1368449--1368505 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
1368439 ATTTGATCAC
*
1368449 ATAATACAATATCATAAAAT
1 ATAATACAATATCAT--ATT
1368469 ATAATACAATAT-AGTATT
1 ATAATACAATATCA-TATT
*
1368487 ATATTACAATATCATATT
1 ATAATACAATATCATATT
1368505 A
1 A
1368506 CATAATACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 18 0.55
19 2 0.06
20 13 0.39
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.37
Consensus pattern (18 bp):
ATAATACAATATCATATT
Found at i:1368747 original size:15 final size:15
Alignment explanation
Indices: 1368718--1368866 Score: 79
Period size: 15 Copynumber: 9.4 Consensus size: 15
1368708 ATACATATAG
* *
1368718 TATCATATGACACAA
1 TATCATATAATACAA
*
1368733 TAAT-ATATATTACAA
1 T-ATCATATAATACAA
1368748 TATCATATAATACAA
1 TATCATATAATACAA
*
1368763 TTTCATGTGATATCATA-ATA
1 TATCA--T-ATA--ATACA-A
*
1368783 TATTATATAA-ACCAA
1 TATCATATAATA-CAA
*
1368798 TATCATATCATACAA
1 TATCATATAATACAA
* *
1368813 TATCGTATGATACAA
1 TATCATATAATACAA
*
1368828 TATTATATAATATTACAA
1 TATCATAT-A-A-TACAA
*
1368846 TATAATATAATACAA
1 TATCATATAATACAA
*
1368861 TTTCAT
1 TATCAT
1368867 GTGATGTAAT
Statistics
Matches: 103, Mismatches: 17, Indels: 28
0.70 0.11 0.19
Matches are distributed among these distances:
14 3 0.03
15 65 0.63
16 5 0.05
17 6 0.06
18 16 0.16
19 1 0.01
20 7 0.07
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (15 bp):
TATCATATAATACAA
Found at i:1368846 original size:18 final size:18
Alignment explanation
Indices: 1368823--1368857 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1368813 TATCGTATGA
*
1368823 TACAATATTATATAATAT
1 TACAATATAATATAATAT
1368841 TACAATATAATATAATA
1 TACAATATAATATAATA
1368858 CAATTTCATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (18 bp):
TACAATATAATATAATAT
Found at i:1368862 original size:98 final size:98
Alignment explanation
Indices: 1368718--1368945 Score: 313
Period size: 98 Copynumber: 2.4 Consensus size: 98
1368708 ATACATATAG
* * * *
1368718 TATCATATGACACAATA--ATAT-ATATTACAATATCATATAATACAATTTCATGTGATATCATA
1 TATCGTATGATACAATATTATATAATATTACAATATAATATAATACAATTTCATGTGATATAATA
*
1368780 ATATATTA-TATAAACCAATATCATATCATACAA
66 ATATATTACT-GAAACCAATATCATATCATACAA
* *
1368813 TATCGTATGATACAATATTATATAATATTACAATATAATATAATACAATTTCATGTGATGTAATT
1 TATCGTATGATACAATATTATATAATATTACAATATAATATAATACAATTTCATGTGATATAATA
* *
1368878 CTATATTACTGAAACCAATATCATATTATACAA
66 ATATATTACTGAAACCAATATCATATCATACAA
* *
1368911 TATTGTATGATACAATATTATAGAATA-TACAATAT
1 TATCGTATGATACAATATTATATAATATTACAATAT
1368946 TGTATCATAG
Statistics
Matches: 118, Mismatches: 11, Indels: 6
0.87 0.08 0.04
Matches are distributed among these distances:
95 15 0.13
97 12 0.10
98 90 0.76
99 1 0.01
ACGTcount: A:0.46, C:0.11, G:0.05, T:0.38
Consensus pattern (98 bp):
TATCGTATGATACAATATTATATAATATTACAATATAATATAATACAATTTCATGTGATATAATA
ATATATTACTGAAACCAATATCATATCATACAA
Found at i:1368970 original size:32 final size:32
Alignment explanation
Indices: 1368904--1368970 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
1368894 AATATCATAT
* **
1368904 TATACAATATTGTATGATACAATATTATAGAA
1 TATACAATATTGTATCATACAATACAATAGAA
** *
1368936 TATACAATATTGTATCATAGGATACAATATAA
1 TATACAATATTGTATCATACAATACAATAGAA
1368968 TAT
1 TAT
1368971 TTTGCAATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.37
Consensus pattern (32 bp):
TATACAATATTGTATCATACAATACAATAGAA
Found at i:1369194 original size:20 final size:20
Alignment explanation
Indices: 1369171--1369214 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1369161 ATATGATATC
1369171 ATATTGTATCATATCAAACA
1 ATATTGTATCATATCAAACA
* *
1369191 ATATTGTTTCATATCATACA
1 ATATTGTATCATATCAAACA
1369211 ATAT
1 ATAT
1369215 CATAGGAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.41
Consensus pattern (20 bp):
ATATTGTATCATATCAAACA
Found at i:1370271 original size:177 final size:177
Alignment explanation
Indices: 1369833--1370577 Score: 935
Period size: 177 Copynumber: 4.2 Consensus size: 177
1369823 TGTGACCTGT
* * ** * * *
1369833 TCCAAAAAACTTAACTTTATCCAGCATCCGAAACCTATGGCTCACACTCAGCATTCAAGCCTGTC
1 TCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATTGCTCAGATTCAGCATTCAAGCCTGTC
** * * * *
1369898 AGGTGCATCAGTATCATAAGACACACCATCCATGGAAGTCTGGTGAAGTAAGGACAAGTAATAAC
66 AGGTGCATCAGTATCATAAGACACACCATCCATACAAGTTTGGTGAAGTTAGGACCAGTAGTAAC
***
1369963 TAAGATA-T-CATCATCAGAGGGCACCTGTTTCAAAAACTTTATTTAACCAGC
131 TAAGATATTGC-T-ATCAGAGGGCACCTGCAACAAAAAC----TTTAACCAGC
*** * *
1370014 TTTTAAAACCTTAACCTCCTCCAGCATCCGAAACCTTTTGCTCAGATTCAGCATTCAAGCTTGTC
1 TCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATTGCTCAGATTCAGCATTCAAGCCTGTC
*
1370079 AGGTGCATCAGTATCATAAGACGCACCATCCATACAAGTTTGGTGAAGTTAGGACCAGTAGTAAC
66 AGGTGCATCAGTATCATAAGACACACCATCCATACAAGTTTGGTGAAGTTAGGACCAGTAGTAAC
*
1370144 TAAGATATAAT-C-ATCAGAGGGCAACTGCAACAAAAACTTTAACCAGC
131 TAAGATAT--TGCTATCAGAGGGCACCTGCAACAAAAACTTTAACCAGC
* * * * *
1370191 TCTAAAAACCTTAACCTCTTCCAGCATCTGAAACCTATTGCTCATATTCAGCATTCAAGCTTGTC
1 TCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATTGCTCAGATTCAGCATTCAAGCCTGTC
* * *
1370256 AGGTGCATTAGTATCATAAGACACATCATTCATACAAGTTTGGTGAAGTTAGGACCAGTAGTAAC
66 AGGTGCATCAGTATCATAAGACACACCATCCATACAAGTTTGGTGAAGTTAGGACCAGTAGTAAC
* * ** *
1370321 TTAGATATTGCTACCACTGGGCACCTGCAACAAAAACTTTAACCTGC
131 TAAGATATTGCTATCAGAGGGCACCTGCAACAAAAACTTTAACCAGC
* * * *
1370368 TCCAAAAACCTTAACCTCCTCCAGCATCCGCAACCTATAGCTCAGATTCAGCACTCAAACCTGTC
1 TCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATTGCTCAGATTCAGCATTCAAGCCTGTC
* * *
1370433 TGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAG-TACGGACCAGCAGTAA
66 AGGTGCATCAGTATCATAAGACACACCATCCATACAAGTTTGGTGAAGTTA-GGACCAGTAGTAA
* * *
1370497 CTAAGATATTGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCTGG
130 CTAAGATATTGCTATCAGAGGGCACCTGCAACAAAAACTTTAACCAGC
*
1370545 TCCAACAAA-CTTAACCTCCTCCAGCATCTGAAA
1 TCCAA-AAACCTTAACCTCCTCCAGCATCCGAAA
1370578 TTTAGGACCC
Statistics
Matches: 496, Mismatches: 61, Indels: 18
0.86 0.11 0.03
Matches are distributed among these distances:
175 1 0.00
176 3 0.01
177 348 0.70
178 3 0.01
181 139 0.28
184 2 0.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.25
Consensus pattern (177 bp):
TCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATTGCTCAGATTCAGCATTCAAGCCTGTC
AGGTGCATCAGTATCATAAGACACACCATCCATACAAGTTTGGTGAAGTTAGGACCAGTAGTAAC
TAAGATATTGCTATCAGAGGGCACCTGCAACAAAAACTTTAACCAGC
Found at i:1370367 original size:19 final size:19
Alignment explanation
Indices: 1370343--1370384 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1370333 ACCACTGGGC
*
1370343 ACCTGCAACAAAAACTTTA
1 ACCTGCAACAAAAACCTTA
**
1370362 ACCTGCTCCAAAAACCTTA
1 ACCTGCAACAAAAACCTTA
1370381 ACCT
1 ACCT
1370385 CCTCCAGCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.33, G:0.05, T:0.21
Consensus pattern (19 bp):
ACCTGCAACAAAAACCTTA
Found at i:1370389 original size:19 final size:19
Alignment explanation
Indices: 1370351--1370390 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1370341 GCACCTGCAA
* *
1370351 CAAAAACTTTAACCTGCTC
1 CAAAAACCTTAACCTCCTC
1370370 CAAAAACCTTAACCTCCTC
1 CAAAAACCTTAACCTCCTC
1370389 CA
1 CA
1370391 GCATCCGCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.38, G:0.03, T:0.23
Consensus pattern (19 bp):
CAAAAACCTTAACCTCCTC
Found at i:1370653 original size:354 final size:352
Alignment explanation
Indices: 1369833--1370681 Score: 888
Period size: 354 Copynumber: 2.4 Consensus size: 352
1369823 TGTGACCTGT
* * ** * * * * * *
1369833 TCCAAAAAACTTAACTTTATCCAGCATCCGAAACCTATGGCTCACACTCAGCATTCAAGCCTGTC
1 TCCAAAAACCTTAACCTCCTCCAGCATCTGAAACCTATGGCCCAGATTCAGCATCCAAGCTTGTC
* * * ** ** *
1369898 AGGTGCATCAGTATCATAAGACACACCATCCATGGAAGTCTGGTGAAGTA-AGGACAAGTAATAA
66 AAGTCCATAAGTATCA-AAGACACATAATCCATACAAGTTTGGTGAAG-ACAGGACAAGTAATAA
* * ** *** * ***
1369962 CTAAGATA-T-CATCATCAGAGGGCACCTGTTTCAAAAACTTTATTTAACCAGCTTTTAAAACCT
129 CTTAGATATTGC-T-ACCACTGGGCACCTGCAACAAAAAC----TTTAACCTGCTCCAAAAACCT
* * * * *
1370025 TAACCTCCTCCAGCATCCGAAACCTTTTGCTCAGATTCAGCATTCAAGCTTGTCAGGTGCATCAG
188 TAACCTCCTCCAGCATCCGAAACCTATAGCTCAGATTCAGCACTCAAACCTGTCAGGTGCATCAG
* *
1370090 TATCATAAGACGCACCATCCATACAAGTTTGGTGAAGTTAGGACCAGTAGTAACTAAGATATAAT
253 TATCATAAGACACACCATCCATACAAGTTTGGTGAAGTTAGGACCAGCAGTAACTAAGATAT-AT
*
1370155 CATCAGAGGGCAACTGCAACAAAAACTTTAACCAGC
317 CATCAAAGGGCAACTGCAACAAAAACTTTAACCAGC
* * * * * *
1370191 TCTAAAAACCTTAACCTCTTCCAGCATCTGAAACCTATTGCTCATATTCAGCATTCAAGCTTGTC
1 TCCAAAAACCTTAACCTCCTCCAGCATCTGAAACCTATGGCCCAGATTCAGCATCCAAGCTTGTC
* * * * * ** * *
1370256 AGGTGCATTAGTATCATAAGACACATCATTCATACAAGTTTGGTGAAGTTAGGACCAGTAGTAAC
66 AAGTCCATAAGTATCA-AAGACACATAATCCATACAAGTTTGGTGAAGACAGGACAAGTAATAAC
1370321 TTAGATATTGCTACCACTGGGCACCTGCAACAAAAACTTTAACCTGCTCCAAAAACCTTAACCTC
130 TTAGATATTGCTACCACTGGGCACCTGCAACAAAAACTTTAACCTGCTCCAAAAACCTTAACCTC
* *
1370386 CTCCAGCATCCGCAACCTATAGCTCAGATTCAGCACTCAAACCTGTCTGGTGCATCAGTATCATA
195 CTCCAGCATCCGAAACCTATAGCTCAGATTCAGCACTCAAACCTGTCAGGTGCATCAGTATCATA
*
1370451 AGACACACCATCCATGCAAGTTTGGTGAAG-TACGGACCAGCAGTAACTAAGATAT-TGCTATCA
260 AGACACACCATCCATACAAGTTTGGTGAAGTTA-GGACCAGCAGTAACTAAGATATAT-C-ATCA
* * *
1370514 AAGGGCACCTGCAACAAAAACTTTAACCTGG
322 AAGGGCAACTGCAACAAAAACTTTAACCAGC
**
1370545 TCCAACAAA-CTTAACCTCCTCCAGCATCTGAAATTTA-GGACCCAGATTCAGCATCCAAGTCTT
1 TCCAA-AAACCTTAACCTCCTCCAGCATCTGAAACCTATGG-CCCAGATTCAGCATCCAAG-CTT
* ** *
1370608 -TCAAGTCCATAAGTAGGTC-CAGATGCATAATCCATGCAAGTTTGGTGAAGACAGGACAAGTAA
63 GTCAAGTCCATAAGTA--TCAAAGACACATAATCCATACAAGTTTGGTGAAGACAGGACAAGTAA
*
1370671 TAGCTTAGATA
126 TAACTTAGATA
1370682 CAGGACCTGC
Statistics
Matches: 414, Mismatches: 66, Indels: 26
0.82 0.13 0.05
Matches are distributed among these distances:
352 1 0.00
353 4 0.01
354 263 0.64
355 6 0.01
356 2 0.00
358 135 0.33
359 2 0.00
360 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (352 bp):
TCCAAAAACCTTAACCTCCTCCAGCATCTGAAACCTATGGCCCAGATTCAGCATCCAAGCTTGTC
AAGTCCATAAGTATCAAAGACACATAATCCATACAAGTTTGGTGAAGACAGGACAAGTAATAACT
TAGATATTGCTACCACTGGGCACCTGCAACAAAAACTTTAACCTGCTCCAAAAACCTTAACCTCC
TCCAGCATCCGAAACCTATAGCTCAGATTCAGCACTCAAACCTGTCAGGTGCATCAGTATCATAA
GACACACCATCCATACAAGTTTGGTGAAGTTAGGACCAGCAGTAACTAAGATATATCATCAAAGG
GCAACTGCAACAAAAACTTTAACCAGC
Found at i:1370726 original size:6 final size:6
Alignment explanation
Indices: 1370715--1370752 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
1370705 ACCAGGTCCG
1370715 GACGCC GACGCC GACGCC -ACCGCC GACGCC GACGCC GA
1 GACGCC GACGCC GACGCC GA-CGCC GACGCC GACGCC GA
1370753 GGGTATAGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 1 0.03
6 28 0.93
7 1 0.03
ACGTcount: A:0.18, C:0.50, G:0.32, T:0.00
Consensus pattern (6 bp):
GACGCC
Found at i:1371583 original size:18 final size:19
Alignment explanation
Indices: 1371532--1371573 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
1371522 ACAAAGAGAT
*
1371532 ATAAACCTTTACAAGTGTC
1 ATAAACCTTAACAAGTGTC
1371551 ATAAACCTTAACAAGTGTC
1 ATAAACCTTAACAAGTGTC
1371570 ATAA
1 ATAA
1371574 TTTCAACAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.43, C:0.19, G:0.10, T:0.29
Consensus pattern (19 bp):
ATAAACCTTAACAAGTGTC
Found at i:1381014 original size:17 final size:18
Alignment explanation
Indices: 1380984--1381017 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1380974 TCTACTCATA
1380984 TTATTTTCTCTTTCTCTT
1 TTATTTTCTCTTTCTCTT
1381002 TTATTTT-TCTTTCTCT
1 TTATTTTCTCTTTCTCT
1381018 CTCAATTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.74
Consensus pattern (18 bp):
TTATTTTCTCTTTCTCTT
Found at i:1401109 original size:42 final size:41
Alignment explanation
Indices: 1401050--1401130 Score: 135
Period size: 42 Copynumber: 2.0 Consensus size: 41
1401040 ATGAAAGTAC
1401050 AAAGATGGCGGAAAACCTAATTAAGTTATCAAAACTGTTNGA
1 AAAGATGGCGGAAAACCTAATTAAGTTATCAAAACTGTT-GA
**
1401092 AAAGATGGCGGAAAACCTCGTTAAGTTATCAAAACTGTT
1 AAAGATGGCGGAAAACCTAATTAAGTTATCAAAACTGTT
1401131 AGGAAGCTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (41 bp):
AAAGATGGCGGAAAACCTAATTAAGTTATCAAAACTGTTGA
Found at i:1410320 original size:16 final size:16
Alignment explanation
Indices: 1410301--1410332 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1410291 CCCTATAAAT
1410301 TGGGTACGTTTTCTCC
1 TGGGTACGTTTTCTCC
1410317 TGGGTACGTTTTCTCC
1 TGGGTACGTTTTCTCC
1410333 AGCATTCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.25, G:0.25, T:0.44
Consensus pattern (16 bp):
TGGGTACGTTTTCTCC
Found at i:1433913 original size:164 final size:164
Alignment explanation
Indices: 1433642--1434104 Score: 793
Period size: 164 Copynumber: 2.8 Consensus size: 164
1433632 GTATTTTAAC
* *
1433642 GTTCTGCACTGG-AGTGGATGACCAATTTGAGTCTGAACACGCTCATTCCGCCCTTGACACTGTT
1 GTTCTGCCCTGGAAG-GGATGACCAATTTGAGTCTGATCACGCTCATTCCGCCCTTGACACTGTT
* *
1433706 ATTGAGCTGCTTGTCACAGTGGAGACTCTAGCCTTTCTGTTTTGTTTAGGCATGTCTTTTCTTTA
65 ATTGAGCTGCTTGCCACAGTGGAGACTCTAGCCCTTCTGTTTTGTTTAGGCATGTCTTTTCTTTA
1433771 ATTTACAATCCGTCCAGTCACCCGTTGCATGTATT
130 ATTTACAATCCGTCCAGTCACCCGTTGCATGTATT
1433806 GTTCTGCCCTGGAAGGGATGACCAATTTGAGTCTGATCACGCTCATTCCGCCCTTGACACTGTTA
1 GTTCTGCCCTGGAAGGGATGACCAATTTGAGTCTGATCACGCTCATTCCGCCCTTGACACTGTTA
1433871 TTGAGCTGCTTGCCACAGTGGAGACTCTAGCCCTTCTGTTTTGTTTAGGCATGTCTTTTCTTTAA
66 TTGAGCTGCTTGCCACAGTGGAGACTCTAGCCCTTCTGTTTTGTTTAGGCATGTCTTTTCTTTAA
* * * *
1433936 TGTATAATCTGTCCAGTCACCTGTTGCATGTATT
131 TTTACAATCCGTCCAGTCACCCGTTGCATGTATT
*
1433970 GTTCTGCCCTGGAAGGGATGACCAATTTGAGTCTGATCACGCTCATTCCGCCCTTGACACTGTTG
1 GTTCTGCCCTGGAAGGGATGACCAATTTGAGTCTGATCACGCTCATTCCGCCCTTGACACTGTTA
* * * *
1434035 TCGAGCTGCTTGCCACAATGGAGACTCTGGCCCTTCTGCTTTGTTTAGGCATGTCTTTTCTTTAA
66 TTGAGCTGCTTGCCACAGTGGAGACTCTAGCCCTTCTGTTTTGTTTAGGCATGTCTTTTCTTTAA
1434100 TTTAC
131 TTTAC
1434105 TAAAGAATTT
Statistics
Matches: 283, Mismatches: 15, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
164 281 0.99
165 2 0.01
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.36
Consensus pattern (164 bp):
GTTCTGCCCTGGAAGGGATGACCAATTTGAGTCTGATCACGCTCATTCCGCCCTTGACACTGTTA
TTGAGCTGCTTGCCACAGTGGAGACTCTAGCCCTTCTGTTTTGTTTAGGCATGTCTTTTCTTTAA
TTTACAATCCGTCCAGTCACCCGTTGCATGTATT
Found at i:1438283 original size:14 final size:16
Alignment explanation
Indices: 1438251--1438284 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1438241 AGGTAAGCTC
1438251 TCTCTCTCTCTTCCTA
1 TCTCTCTCTCTTCCTA
1438267 TCTCTCTCT-TTCC-A
1 TCTCTCTCTCTTCCTA
1438281 TCTC
1 TCTC
1438285 GGTCATTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 4 0.22
16 9 0.50
ACGTcount: A:0.06, C:0.44, G:0.00, T:0.50
Consensus pattern (16 bp):
TCTCTCTCTCTTCCTA
Found at i:1438916 original size:12 final size:12
Alignment explanation
Indices: 1438899--1438924 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1438889 TTTTAAAATC
1438899 AAAAGTATAATA
1 AAAAGTATAATA
1438911 AAAAGTATAATA
1 AAAAGTATAATA
1438923 AA
1 AA
1438925 GATGAATGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (12 bp):
AAAAGTATAATA
Found at i:1465945 original size:12 final size:12
Alignment explanation
Indices: 1465925--1466198 Score: 196
Period size: 12 Copynumber: 22.6 Consensus size: 12
1465915 ACAATCATTA
*
1465925 CTTTCTCTCTCT
1 CTTTCTTTCTCT
* *
1465937 CTCTCTCTCTCT
1 CTTTCTTTCTCT
*
1465949 CTCTCCATTTCTCT
1 CT-TTC-TTTCTCT
*
1465963 CCTT-TTT-TCT
1 CTTTCTTTCTCT
* *
1465973 CTTTCTCTACCCT
1 CTTTCT-TTCTCT
*
1465986 CTTTCTTTCTTT
1 CTTTCTTTCTCT
*
1465998 CTTTCTTTCTTT
1 CTTTCTTTCTCT
*
1466010 CTTTCTTTCTTT
1 CTTTCTTTCTCT
*
1466022 CTTTCTTTCTTT
1 CTTTCTTTCTCT
*
1466034 CTTTCTTTCTTT
1 CTTTCTTTCTCT
1466046 CTTTCTTTCT-T
1 CTTTCTTTCTCT
* * *
1466057 CTCTCTCTCTTT
1 CTTTCTTTCTCT
* *
1466069 C-TTCTCTCTAT
1 CTTTCTTTCTCT
* *
1466080 CTGTCTCTCTCT
1 CTTTCTTTCTCT
* *
1466092 CTATCTTTATCT
1 CTTTCTTTCTCT
*
1466104 CTCTCCATTTCTCT
1 CT-TTC-TTTCTCT
1466118 CTTTTCTTTCTCT
1 C-TTTCTTTCTCT
** *
1466131 CTCCCTTCTCTTT
1 CTTTCTT-TCTCT
*
1466144 CTTTCTTTCTTT
1 CTTTCTTTCTCT
* *
1466156 CTTTCATTCTTT
1 CTTTCTTTCTCT
1466168 CTTTCTTTCTCT
1 CTTTCTTTCTCT
*
1466180 CTTTCTTTCTTT
1 CTTTCTTTCTCT
1466192 CTTTCTT
1 CTTTCTT
1466199 ATTGTATCTT
Statistics
Matches: 217, Mismatches: 34, Indels: 22
0.79 0.12 0.08
Matches are distributed among these distances:
10 6 0.03
11 22 0.10
12 144 0.66
13 28 0.13
14 16 0.07
15 1 0.00
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.64
Consensus pattern (12 bp):
CTTTCTTTCTCT
Found at i:1465994 original size:4 final size:4
Alignment explanation
Indices: 1465985--1466198 Score: 225
Period size: 4 Copynumber: 53.0 Consensus size: 4
1465975 TTCTCTACCC
1465985 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT
* * * *
1466033 TCTT TCTT TCTT TCTT TCTT TC-T TCTC TCTC TCTT TC-T TCTC TCTA
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT
* * * * * * * * *
1466079 TCTG TCTC TCTC TCTA TCTT TATC TCTCT CCATT TCTC TCTTT TCTT TCTC
1 TCTT TCTT TCTT TCTT TCTT TCTT TCT-T TC-TT TCTT TC-TT TCTT TCTT
* * * *
1466130 TCTC CCTT CTCTT TCTT TCTT TCTT TCTT TCAT TCTT TCTT TCTT TCTC
1 TCTT TCTT -TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT
1466179 TCTT TCTT TCTT TCTT TCTT
1 TCTT TCTT TCTT TCTT TCTT
1466199 ATTGTATCTT
Statistics
Matches: 180, Mismatches: 24, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
3 6 0.03
4 164 0.91
5 9 0.05
6 1 0.01
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.66
Consensus pattern (4 bp):
TCTT
Found at i:1475105 original size:2 final size:2
Alignment explanation
Indices: 1475098--1475145 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
1475088 CCAATACAAC
1475098 GA GA GA GA GA GA GA G- 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
1475139 GA GA GA G
1 GA GA GA G
1475146 GGGTTATATT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1503965 original size:11 final size:11
Alignment explanation
Indices: 1503951--1503980 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1503941 CATTGTTGTT
*
1503951 TCATGCGAATA
1 TCATGCAAATA
1503962 TCATGCAAATA
1 TCATGCAAATA
1503973 TCATGCAA
1 TCATGCAA
1503981 TTTTCATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (11 bp):
TCATGCAAATA
Found at i:1513621 original size:2 final size:2
Alignment explanation
Indices: 1513616--1513655 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1513606 ATTTTTATAT
*
1513616 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1513656 CTTTTTCGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1522198 original size:5 final size:5
Alignment explanation
Indices: 1522179--1522358 Score: 173
Period size: 5 Copynumber: 35.6 Consensus size: 5
1522169 TGGTTTTGAG
* * * * * *
1522179 CTATG CTATG CTATA CTATA CTACA CTATA CTACA CT-TCA CTACA CTACA
1 CTATA CTATA CTATA CTATA CTATA CTATA CTATA CTAT-A CTATA CTATA
* * * * * * * * * *
1522229 CTACA CTACA CTACA CTACA CTACA CTACA CTACA CTACA CTACA CTACA
1 CTATA CTATA CTATA CTATA CTATA CTATA CTATA CTATA CTATA CTATA
*
1522279 CTATATA CTATA CTATT CTATA CTATA CTATA CTATA CTATA CTATA CTATA
1 C--TATA CTATA CTATA CTATA CTATA CTATA CTATA CTATA CTATA CTATA
1522331 CTATA CTATA CTATA CTATA CTATA CTA
1 CTATA CTATA CTATA CTATA CTATA CTA
1522359 GCATCCACAA
Statistics
Matches: 162, Mismatches: 9, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
5 158 0.98
7 4 0.02
ACGTcount: A:0.38, C:0.28, G:0.01, T:0.33
Consensus pattern (5 bp):
CTATA
Found at i:1527790 original size:4 final size:4
Alignment explanation
Indices: 1527781--1527840 Score: 84
Period size: 4 Copynumber: 15.0 Consensus size: 4
1527771 ACTGAAGCGA
* * *
1527781 GACG GACG GACG GACG GACG GACA GACG AACG GACG GACG GACA GACG
1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG
*
1527829 GACT GACG GACG
1 GACG GACG GACG
1527841 CAGAGAAAAG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 48 1.00
ACGTcount: A:0.30, C:0.25, G:0.43, T:0.02
Consensus pattern (4 bp):
GACG
Found at i:1527813 original size:20 final size:20
Alignment explanation
Indices: 1527785--1527840 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
1527775 AAGCGAGACG
1527785 GACGGACGGACGGACGGACA
1 GACGGACGGACGGACGGACA
*
1527805 GACGAACGGACGGACGGACA
1 GACGGACGGACGGACGGACA
*
1527825 GACGGACTGACGGACG
1 GACGGACGGACGGACG
1527841 CAGAGAAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.30, C:0.25, G:0.43, T:0.02
Consensus pattern (20 bp):
GACGGACGGACGGACGGACA
Found at i:1528730 original size:2 final size:2
Alignment explanation
Indices: 1528723--1528753 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1528713 ATAAAACATT
*
1528723 GA GA GA GA GA GA GA GA GA GA GA AA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1528754 TGATAAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1530045 original size:8 final size:8
Alignment explanation
Indices: 1530024--1530093 Score: 96
Period size: 8 Copynumber: 9.4 Consensus size: 8
1530014 GATCACATTT
1530024 TGTCCGTC
1 TGTCCGTC
1530032 -GTCCGTC
1 TGTCCGTC
1530039 TGT-C--C
1 TGTCCGTC
1530044 -GTCCGTC
1 TGTCCGTC
1530051 TGTCCGTC
1 TGTCCGTC
1530059 TGTCCGTC
1 TGTCCGTC
1530067 TGTCCGTC
1 TGTCCGTC
*
1530075 CGTCCGTC
1 TGTCCGTC
1530083 TGTCCGTC
1 TGTCCGTC
1530091 TGT
1 TGT
1530094 AAACTTTTTA
Statistics
Matches: 55, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
4 2 0.04
5 2 0.04
7 9 0.16
8 42 0.76
ACGTcount: A:0.00, C:0.39, G:0.26, T:0.36
Consensus pattern (8 bp):
TGTCCGTC
Found at i:1530047 original size:4 final size:4
Alignment explanation
Indices: 1530025--1530090 Score: 80
Period size: 4 Copynumber: 16.8 Consensus size: 4
1530015 ATCACATTTT
* * * *
1530025 GTCC GT-C GTCC GTCT GTCC GTCC GTCT GTCC GTCT GTCC GTCT GTCC
1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC
*
1530072 GTCC GTCC GTCT GTCC GTC
1 GTCC GTCC GTCC GTCC GTC
1530091 TGTAAACTTT
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
3 3 0.06
4 48 0.94
ACGTcount: A:0.00, C:0.41, G:0.26, T:0.33
Consensus pattern (4 bp):
GTCC
Found at i:1535483 original size:16 final size:17
Alignment explanation
Indices: 1535453--1535488 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1535443 TCATACTTGT
*
1535453 CTGTGTTTGTTTTTTTC
1 CTGTGTTTGTGTTTTTC
1535470 CTGT-TTTGTGTTTTTC
1 CTGTGTTTGTGTTTTTC
1535486 CTG
1 CTG
1535489 GAGGTATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.00, C:0.14, G:0.19, T:0.67
Consensus pattern (17 bp):
CTGTGTTTGTGTTTTTC
Found at i:1537270 original size:15 final size:15
Alignment explanation
Indices: 1537250--1537282 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1537240 GGGGGGGGGT
1537250 TTTTTGTGTTT-TTTG
1 TTTTTGT-TTTGTTTG
1537265 TTTTTGTTTTGTTTG
1 TTTTTGTTTTGTTTG
1537280 TTT
1 TTT
1537283 GGTTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (15 bp):
TTTTTGTTTTGTTTG
Found at i:1537274 original size:11 final size:10
Alignment explanation
Indices: 1537249--1537304 Score: 53
Period size: 11 Copynumber: 5.6 Consensus size: 10
1537239 GGGGGGGGGG
*
1537249 TTTTTTG-TG
1 TTTTTTGTTT
1537258 TTTTTTGTTT
1 TTTTTTGTTT
1537268 TTGTTTTG-TT
1 TT-TTTTGTTT
* *
1537278 TGTTTGGTTT
1 TTTTTTGTTT
1537288 TTTTTTGGTTT
1 TTTTTT-GTTT
1537299 TTTTTT
1 TTTTTT
1537305 ATGTAGGCTA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
9 11 0.29
10 12 0.32
11 15 0.39
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:1537276 original size:20 final size:19
Alignment explanation
Indices: 1537249--1537301 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1537239 GGGGGGGGGG
1537249 TTTTTTGTGTTTTTTGTTT
1 TTTTTTGTGTTTTTTGTTT
*
1537268 TTGTTTTGT-TTGTTTGGTTT
1 TT-TTTTGTGTT-TTTTGTTT
1537288 TTTTTTG-GTTTTTT
1 TTTTTTGTGTTTTTT
1537302 TTTATGTAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
18 3 0.10
19 11 0.38
20 15 0.52
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (19 bp):
TTTTTTGTGTTTTTTGTTT
Found at i:1537303 original size:15 final size:14
Alignment explanation
Indices: 1537248--1537304 Score: 51
Period size: 16 Copynumber: 3.7 Consensus size: 14
1537238 GGGGGGGGGG
1537248 GTTTTTTGTGTTTTTT
1 GTTTTTT-T-TTTTTT
*
1537264 GTTTTTGTTTTGTTT
1 GTTTTT-TTTTTTTT
*
1537279 GTTTGGTTTTTTTTTG
1 GTTT--TTTTTTTTTT
1537295 GTTTTTTTTT
1 GTTTTTTTTT
1537305 ATGTAGGCTA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
14 6 0.17
15 9 0.26
16 17 0.49
17 3 0.09
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (14 bp):
GTTTTTTTTTTTTT
Found at i:1541891 original size:87 final size:86
Alignment explanation
Indices: 1541784--1541957 Score: 262
Period size: 87 Copynumber: 2.0 Consensus size: 86
1541774 GTTGTATGCT
*
1541784 ATGCTATTAAGAATTGAGATGAAGGGCTTAACAATATTGTATGCTATGCT-ATAGTATGCTATGA
1 ATGCTATTAAGAATTAAGATGAAGGGCTTAACAATATTGTATGCTATGCTGA-AGTATGCTATGA
1541848 GGTTTGAACAAAAACGCCTTCAA
65 GGTTTGAACAAAAACGCC-TCAA
** *
1541871 ATGCT-TTAAGGAATTAAGATGAAGGGCTTAATGATATTGTATGCTATGCTGAGGTATGCTATGA
1 ATGCTATTAA-GAATTAAGATGAAGGGCTTAACAATATTGTATGCTATGCTGAAGTATGCTATGA
*
1541935 TGTTTGAACAAAAACGCCTCAA
65 GGTTTGAACAAAAACGCCTCAA
1541957 A
1 A
1541958 ATACAAAAAG
Statistics
Matches: 80, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
86 9 0.11
87 70 0.88
88 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (86 bp):
ATGCTATTAAGAATTAAGATGAAGGGCTTAACAATATTGTATGCTATGCTGAAGTATGCTATGAG
GTTTGAACAAAAACGCCTCAA
Found at i:1542177 original size:21 final size:21
Alignment explanation
Indices: 1542153--1542193 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1542143 TGTATGCAAT
1542153 GGTACGAGATTCCAATGCTAA
1 GGTACGAGATTCCAATGCTAA
*
1542174 GGTATGAGATTCCAATGCTA
1 GGTACGAGATTCCAATGCTA
1542194 TGCTATGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (21 bp):
GGTACGAGATTCCAATGCTAA
Found at i:1542200 original size:21 final size:21
Alignment explanation
Indices: 1542158--1542221 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
1542148 GCAATGGTAC
* *
1542158 GAGATTCCAATGCTAAGGTAT
1 GAGATTCCAATGCTATGCTAT
1542179 GAGATTCCAATGCTATGCTAT
1 GAGATTCCAATGCTATGCTAT
* *
1542200 GAGATTTCATTGCTATGCTAT
1 GAGATTCCAATGCTATGCTAT
1542221 G
1 G
1542222 GTGTATGTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (21 bp):
GAGATTCCAATGCTATGCTAT
Found at i:1544923 original size:2 final size:2
Alignment explanation
Indices: 1544918--1544960 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1544908 AACTAGAAAA
1544918 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
1544960 T
1 T
1544961 AAAGTACATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1549658 original size:63 final size:63
Alignment explanation
Indices: 1549559--1549689 Score: 262
Period size: 63 Copynumber: 2.1 Consensus size: 63
1549549 TATTCATAAT
1549559 TTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTCTTGTTATTGCTTTGTTTCTTTTTCACTA
1 TTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTCTTGTTATTGCTTTGTTTCTTTTTCACTA
1549622 TTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTCTTGTTATTGCTTTGTTTCTTTTTCACTA
1 TTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTCTTGTTATTGCTTTGTTTCTTTTTCACTA
1549685 TTATT
1 TTATT
1549690 NNNNNNNNNN
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 68 1.00
ACGTcount: A:0.18, C:0.20, G:0.14, T:0.49
Consensus pattern (63 bp):
TTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTCTTGTTATTGCTTTGTTTCTTTTTCACTA
Found at i:1552128 original size:22 final size:22
Alignment explanation
Indices: 1552100--1552146 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
1552090 AAATTAATTT
1552100 ACTCATCAATTTTTTCGAGTGA
1 ACTCATCAATTTTTTCGAGTGA
1552122 ACTCATCAATTTTTTCGAGTGA
1 ACTCATCAATTTTTTCGAGTGA
1552144 ACT
1 ACT
1552147 ATGTCATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (22 bp):
ACTCATCAATTTTTTCGAGTGA
Found at i:1554493 original size:2 final size:2
Alignment explanation
Indices: 1554486--1554533 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1554476 CGGGAAAATT
1554486 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
1554528 AG AG AG
1 AG AG AG
1554534 GTTCAAACTC
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:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1558120 original size:2 final size:2
Alignment explanation
Indices: 1558113--1558161 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1558103 AGGTACCGGG
1558113 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
1558155 TC TC TC T
1 TC TC TC T
1558162 GGGAAGTGGG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1562213 original size:11 final size:11
Alignment explanation
Indices: 1562194--1562238 Score: 63
Period size: 11 Copynumber: 4.1 Consensus size: 11
1562184 AATACAATTT
1562194 CCAAGTAAACC
1 CCAAGTAAACC
*
1562205 CCGAGTAAACC
1 CCAAGTAAACC
*
1562216 CAAAGTAAACC
1 CCAAGTAAACC
*
1562227 CCAAGTGAACC
1 CCAAGTAAACC
1562238 C
1 C
1562239 AAATTTTCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.42, C:0.36, G:0.13, T:0.09
Consensus pattern (11 bp):
CCAAGTAAACC
Found at i:1562221 original size:22 final size:22
Alignment explanation
Indices: 1562196--1562241 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
1562186 TACAATTTCC
*
1562196 AAGTAAACCCCGAGTAAACCCA
1 AAGTAAACCCCAAGTAAACCCA
*
1562218 AAGTAAACCCCAAGTGAACCCA
1 AAGTAAACCCCAAGTAAACCCA
1562240 AA
1 AA
1562242 TTTTCAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.48, C:0.30, G:0.13, T:0.09
Consensus pattern (22 bp):
AAGTAAACCCCAAGTAAACCCA
Found at i:1568550 original size:2 final size:2
Alignment explanation
Indices: 1568543--1568651 Score: 173
Period size: 2 Copynumber: 54.5 Consensus size: 2
1568533 TCAATGAATT
* * *
1568543 AG AG AG AG AC AG AG AG AA AG AG AG AG AG AG AG AG AA 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
* *
1568585 AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AA 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
1568627 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 A
1568652 CGCATTACAC
Statistics
Matches: 97, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 97 1.00
ACGTcount: A:0.54, C:0.01, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1572250 original size:21 final size:20
Alignment explanation
Indices: 1572207--1572258 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
1572197 AAAACATAGC
*
1572207 TGTTTGTTTTTTTGCTTTGT
1 TGTTTGGTTTTTTGCTTTGT
1572227 TGTATTGGTTTTTTG-TTTGTT
1 TGT-TTGGTTTTTTGCTTTG-T
*
1572248 TGTTTTGTTTT
1 TGTTTGGTTTT
1572259 GCTTTTTGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.02, C:0.02, G:0.21, T:0.75
Consensus pattern (20 bp):
TGTTTGGTTTTTTGCTTTGT
Found at i:1572268 original size:33 final size:34
Alignment explanation
Indices: 1572207--1572279 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
1572197 AAAACATAGC
1572207 TGTTTGTTTTTTTGCTTTGTTGTATTGGT-TTTT
1 TGTTTGTTTTTTTGCTTTGTTGTATTGGTGTTTT
*
1572240 TGTTTGTTTGTTTTGTTTTGCTT-T-TTGGTGTTTT
1 TGTTTGTTT-TTTTGCTTTG-TTGTATTGGTGTTTT
*
1572274 TTTTTG
1 TGTTTG
1572280 GTACCAGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
33 14 0.40
34 19 0.54
35 2 0.06
ACGTcount: A:0.01, C:0.03, G:0.22, T:0.74
Consensus pattern (34 bp):
TGTTTGTTTTTTTGCTTTGTTGTATTGGTGTTTT
Found at i:1574132 original size:4 final size:4
Alignment explanation
Indices: 1574123--1574180 Score: 100
Period size: 4 Copynumber: 14.8 Consensus size: 4
1574113 AAAGTTTACA
*
1574123 GACG GACG GACA GACG GACG GACG GACG GACG GACG GACG GACG GACG
1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG
1574171 GAC- GACG GAC
1 GACG GACG GAC
1574181 AACAGGTGAT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
3 3 0.06
4 48 0.94
ACGTcount: A:0.28, C:0.26, G:0.47, T:0.00
Consensus pattern (4 bp):
GACG
Found at i:1576194 original size:15 final size:15
Alignment explanation
Indices: 1576171--1576207 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1576161 TTACAATTTA
*
1576171 TGTTGTTTTTGTTGT
1 TGTTTTTTTTGTTGT
1576186 TGTTTTTTTTGTTGT
1 TGTTTTTTTTGTTGT
1576201 T-TTTTTT
1 TGTTTTTT
1576208 AGCTTCATGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (15 bp):
TGTTTTTTTTGTTGT
Found at i:1576205 original size:12 final size:12
Alignment explanation
Indices: 1576171--1576207 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
1576161 TTACAATTTA
*
1576171 TGTTGTTTTTGT
1 TGTTGTTTTTTT
1576183 TGTTGTTTTTTT
1 TGTTGTTTTTTT
1576195 TGTTGTTTTTTT
1 TGTTGTTTTTTT
1576207 T
1 T
1576208 AGCTTCATGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (12 bp):
TGTTGTTTTTTT
Found at i:1577111 original size:3 final size:3
Alignment explanation
Indices: 1577105--1577138 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1577095 CAACAACAAC
*
1577105 AAT AAT AAT AAT TAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1577139 NNNNNNNNNN
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:1583273 original size:2 final size:2
Alignment explanation
Indices: 1583268--1583315 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1583258 ATATATTCAA
1583268 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
1583310 AG AG AG
1 AG AG AG
1583316 TATTTCATAA
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:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1587803 original size:22 final size:22
Alignment explanation
Indices: 1587753--1587805 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
1587743 TATACGTGTT
*
1587753 GCTTAAAGGTGGCTTAAAGAAA
1 GCTTAAAGATGGCTTAAAGAAA
* **
1587775 GCGTAAAGATGGCTTAAAGGCA
1 GCTTAAAGATGGCTTAAAGAAA
1587797 GCTTAAAGA
1 GCTTAAAGA
1587806 CTATCTTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.40, C:0.11, G:0.28, T:0.21
Consensus pattern (22 bp):
GCTTAAAGATGGCTTAAAGAAA
Found at i:1587826 original size:11 final size:11
Alignment explanation
Indices: 1587810--1587838 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1587800 TAAAGACTAT
1587810 CTTTAAGCCAC
1 CTTTAAGCCAC
1587821 CTTTAAGCCAC
1 CTTTAAGCCAC
1587832 CTTTAAG
1 CTTTAAG
1587839 GACAACTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.31
Consensus pattern (11 bp):
CTTTAAGCCAC
Found at i:1587886 original size:11 final size:11
Alignment explanation
Indices: 1587870--1587923 Score: 90
Period size: 11 Copynumber: 4.9 Consensus size: 11
1587860 GTCCAAACTT
1587870 CTTTAAGCCAC
1 CTTTAAGCCAC
1587881 CTTTAAGCCAC
1 CTTTAAGCCAC
*
1587892 CTTTAAGCTAC
1 CTTTAAGCCAC
*
1587903 CTTTAAGCCGC
1 CTTTAAGCCAC
1587914 CTTTAAGCCA
1 CTTTAAGCCA
1587924 TTAAAAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 39 1.00
ACGTcount: A:0.26, C:0.33, G:0.11, T:0.30
Consensus pattern (11 bp):
CTTTAAGCCAC
Found at i:1594924 original size:135 final size:135
Alignment explanation
Indices: 1594734--1595027 Score: 364
Period size: 135 Copynumber: 2.2 Consensus size: 135
1594724 TATAATCATG
* * * *
1594734 ACCCCTAAACCATATATATTCTTGTTTCTGATGTCAAGGGGCATCAAATGTTATGTCGGTGATGG
1 ACCCTTAAACCATATATATTCTTGTTCCTGATGTCAAGGGGCATCAAATGTTATGTAGGTCATGG
* * * * * * *
1594799 GCCCTGTGGGTGGTCTTGACCCCCCTCGAACAGCAAGT-CCCTTAATATCTTAAAAACAGTTG-G
66 GCCCCGGGGGTGGTCGTGACCCACCTCGAAAAGCAAGTGCAC-GAATATCTTAAAAACAGTTGAG
1594862 AATCCCC
130 -ATCCCC
1594869 ACCCTTAAACCATATATATTCTTGTTCCTTG-TGTCAAGGGGCATCAAACTG-TATGTAGGTCAT
1 ACCCTTAAACCATATATATTCTTGTTCC-TGATGTCAAGGGGCATCAAA-TGTTATGTAGGTCAT
* * *
1594932 GGGCCCCGGGGGTGGTCGTGACCCACCTCGAAAAGGAAGTGCACGAATATCTTGAAAACGGTTGA
64 GGGCCCCGGGGGTGGTCGTGACCCACCTCGAAAAGCAAGTGCACGAATATCTTAAAAACAGTTGA
1594997 GATCCCC
129 GATCCCC
* *
1595004 ACCCCTT-ACCCATATATTTTCTTG
1 A-CCCTTAAACCATATATATTCTTG
1595028 ATCATAGATC
Statistics
Matches: 138, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
135 126 0.91
136 12 0.09
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.28
Consensus pattern (135 bp):
ACCCTTAAACCATATATATTCTTGTTCCTGATGTCAAGGGGCATCAAATGTTATGTAGGTCATGG
GCCCCGGGGGTGGTCGTGACCCACCTCGAAAAGCAAGTGCACGAATATCTTAAAAACAGTTGAGA
TCCCC
Found at i:1595327 original size:166 final size:166
Alignment explanation
Indices: 1595037--1595380 Score: 512
Period size: 166 Copynumber: 2.1 Consensus size: 166
1595027 GATCATAGAT
1595037 CAAGATATGATGTGTCTATCCATTAAATCATAAGAAGAGTTCTAGCTAGGATCTATGTTTTTTTT
1 CAAGATATGATGTGTCTATCCATTAAATCATAAGAAGAGTTCTAG--AGGATCTATGTTTTTTTT
*
1595102 TTGAGTGATGAACGTCAATTTTCTGCTACTATTTGACTCCCTGGATGAAATTAAAATTTTAAAAA
64 TTGAGTGATAAACGTCAATTTTCTGCTACTATTTGACTCCCTGGATGAAATTAAAATTTTAAAAA
* *
1595167 CCTTACTGCACATCTATAGAACAGTCCCTATCATATCC
129 CCTTACTGCACATCTATAGAACAGCCCCAATCATATCC
*
1595205 CAAGATATGATGTGTCTATCCATTAAATCATAAGAGGAGTTCT-G-GGATCTATGGTTTTTTTTT
1 CAAGATATGATGTGTCTATCCATTAAATCATAAGAAGAGTTCTAGAGGATCTAT-G-TTTTTTTT
* * * * *
1595268 TTTAGTGATAAAGGTCAATTTTTTGCTACTATTTGACTCCCTGGATGAAATTTAAATTTTTAAAA
64 TTGAGTGATAAACGTCAATTTTCTGCTACTATTTGACTCCCTGGATGAAATTAAAATTTTAAAAA
* * * *
1595333 CCTTATTGCATATCTATAGGACAGCCCCAATTATATCC
129 CCTTACTGCACATCTATAGAACAGCCCCAATCATATCC
*
1595371 CAAGAGATGA
1 CAAGATATGA
1595381 CGTAGCTACT
Statistics
Matches: 160, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
164 8 0.05
165 1 0.01
166 108 0.68
167 1 0.01
168 42 0.26
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.37
Consensus pattern (166 bp):
CAAGATATGATGTGTCTATCCATTAAATCATAAGAAGAGTTCTAGAGGATCTATGTTTTTTTTTT
GAGTGATAAACGTCAATTTTCTGCTACTATTTGACTCCCTGGATGAAATTAAAATTTTAAAAACC
TTACTGCACATCTATAGAACAGCCCCAATCATATCC
Found at i:1600298 original size:18 final size:19
Alignment explanation
Indices: 1600269--1600322 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1600259 GATTTTTTTA
1600269 AATTCCTGTAGGAATTA-T
1 AATTCCTGTAGGAATTAGT
* * *
1600287 ATTTCCTATAGGAGAATAGT
1 AATTCCTGTAGGA-ATTAGT
1600307 AATTCCTGTAGGAATT
1 AATTCCTGTAGGAATT
1600323 TGATTCAGAC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
18 11 0.39
19 5 0.18
20 12 0.43
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (19 bp):
AATTCCTGTAGGAATTAGT
Found at i:1600510 original size:11 final size:11
Alignment explanation
Indices: 1600494--1600534 Score: 73
Period size: 11 Copynumber: 3.7 Consensus size: 11
1600484 TAAGCAAGTC
1600494 CTTAAAGGTGG
1 CTTAAAGGTGG
1600505 CTTAAAGGTGG
1 CTTAAAGGTGG
*
1600516 CGTAAAGGTGG
1 CTTAAAGGTGG
1600527 CTTAAAGG
1 CTTAAAGG
1600535 AGATACGATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.29, C:0.10, G:0.37, T:0.24
Consensus pattern (11 bp):
CTTAAAGGTGG
Found at i:1600560 original size:11 final size:11
Alignment explanation
Indices: 1600544--1600573 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1600534 GAGATACGAT
1600544 CTTTAAGCCAC
1 CTTTAAGCCAC
*
1600555 CTTTAAGTCAC
1 CTTTAAGCCAC
1600566 CTTTAAGC
1 CTTTAAGC
1600574 TGAGCTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.27, C:0.30, G:0.10, T:0.33
Consensus pattern (11 bp):
CTTTAAGCCAC
Found at i:1600647 original size:21 final size:22
Alignment explanation
Indices: 1600603--1600654 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
1600593 TGTCCAAACT
1600603 TCTTTAAGTCACCTTTAAGCCA
1 TCTTTAAGTCACCTTTAAGCCA
*
1600625 TCTTTAAG-CTACTTTTAAG-CA
1 TCTTTAAGTC-ACCTTTAAGCCA
1600646 TCTTTAAGT
1 TCTTTAAGT
1600655 GGCATTTACG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.42
Consensus pattern (22 bp):
TCTTTAAGTCACCTTTAAGCCA
Found at i:1601023 original size:2 final size:2
Alignment explanation
Indices: 1601016--1601062 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1601006 CGGTGAAATA
1601016 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
1601058 TC TC T
1 TC TC T
1601063 TAGTTCATCC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1603033 original size:11 final size:11
Alignment explanation
Indices: 1603017--1603045 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1603007 ATAAGTTGTC
1603017 CTTAAAGGTGG
1 CTTAAAGGTGG
1603028 CTTAAAGGTGG
1 CTTAAAGGTGG
1603039 CTTAAAG
1 CTTAAAG
1603046 ATAGTCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.28
Consensus pattern (11 bp):
CTTAAAGGTGG
Found at i:1603076 original size:11 final size:11
Alignment explanation
Indices: 1603062--1603102 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
1603052 TTTAAGCTGC
1603062 CTTTAAGCCAT
1 CTTTAAGCCAT
* **
1603073 CTTTACGCTTT
1 CTTTAAGCCAT
1603084 CTTTAAGCCAT
1 CTTTAAGCCAT
1603095 CTTTAAGC
1 CTTTAAGC
1603103 AACAAATATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.22, C:0.27, G:0.10, T:0.41
Consensus pattern (11 bp):
CTTTAAGCCAT
Found at i:1603127 original size:11 final size:11
Alignment explanation
Indices: 1603111--1603142 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1603101 GCAACAAATA
1603111 TAGCTTAAAGG
1 TAGCTTAAAGG
1603122 TAGCTTAAAGG
1 TAGCTTAAAGG
*
1603133 TGGCTTAAAG
1 TAGCTTAAAG
1603143 ATCGTCTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.34, C:0.09, G:0.28, T:0.28
Consensus pattern (11 bp):
TAGCTTAAAGG
Found at i:1603173 original size:21 final size:21
Alignment explanation
Indices: 1603147--1603186 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1603137 TTAAAGATCG
1603147 TCTTTAAGCTACCTTTAAGCA
1 TCTTTAAGCTACCTTTAAGCA
*
1603168 TCTTTAAGCTATCTTTAAG
1 TCTTTAAGCTACCTTTAAG
1603187 GAGAACTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.20, G:0.10, T:0.42
Consensus pattern (21 bp):
TCTTTAAGCTACCTTTAAGCA
Found at i:1603174 original size:10 final size:11
Alignment explanation
Indices: 1603147--1603186 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
1603137 TTAAAGATCG
1603147 TCTTTAAGCTA
1 TCTTTAAGCTA
*
1603158 CCTTTAAGC-A
1 TCTTTAAGCTA
1603168 TCTTTAAGCTA
1 TCTTTAAGCTA
1603179 TCTTTAAG
1 TCTTTAAG
1603187 GAGAACTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.28, C:0.20, G:0.10, T:0.42
Consensus pattern (11 bp):
TCTTTAAGCTA
Found at i:1607405 original size:2 final size:2
Alignment explanation
Indices: 1607398--1607441 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1607388 TATCTATTTA
1607398 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
1607440 TC
1 TC
1607442 CACAACATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1620414 original size:1 final size:1
Alignment explanation
Indices: 1620410--1620458 Score: 53
Period size: 1 Copynumber: 49.0 Consensus size: 1
1620400 CAAAAATGTG
* ** * *
1620410 TTTTTGTTTTTTTAGTTTTTTGTTTGTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1620459 ATAAAATATT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.02, C:0.00, G:0.08, T:0.90
Consensus pattern (1 bp):
T
Found at i:1629252 original size:4 final size:4
Alignment explanation
Indices: 1629231--1629295 Score: 87
Period size: 4 Copynumber: 16.2 Consensus size: 4
1629221 CCGGTTTTCA
* * *
1629231 CCGT CCGT CAGT CAGT CCGT CCGT CTG- CCTGT CCGT CCGT CCGT CCGT
1 CCGT CCGT CCGT CCGT CCGT CCGT CCGT CC-GT CCGT CCGT CCGT CCGT
1629279 CCGT CCGT CCGT CCGT C
1 CCGT CCGT CCGT CCGT C
1629296 TGTCTGTCTG
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
3 1 0.02
4 52 0.95
5 2 0.04
ACGTcount: A:0.03, C:0.46, G:0.25, T:0.26
Consensus pattern (4 bp):
CCGT
Found at i:1629300 original size:4 final size:4
Alignment explanation
Indices: 1629293--1629357 Score: 98
Period size: 4 Copynumber: 16.8 Consensus size: 4
1629283 CCGTCCGTCC
1629293 GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GT-T
1 GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT
* *
1629340 -TTT TTCT GTCT GTCT GTC
1 GTCT GTCT GTCT GTCT GTC
1629358 CCACTTCAGT
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
2 1 0.02
3 2 0.04
4 54 0.95
ACGTcount: A:0.00, C:0.23, G:0.23, T:0.54
Consensus pattern (4 bp):
GTCT
Found at i:1631274 original size:112 final size:112
Alignment explanation
Indices: 1631055--1631531 Score: 519
Period size: 112 Copynumber: 4.3 Consensus size: 112
1631045 CGAAAGAGGA
* * * * * ** *
1631055 CAACTAACCTCATCGATTGTTAATTAGTCAACAAACTTTATCGATAGGTAATTGGTCATCTAACC
1 CAACTAACCTCATCGATAGGTAATTGGTCAACTAACCTTATCGATAGGTAATAAGTCAACTAACC
* * * *
1631120 TCATCGATACGTAATT-GTACAACTAACCTCATCGCTTGGTAATTGGT
66 TCATCGATAGGTAATTGGT-CAACTAACCTCTTCGATAGGTAATTGGT
** * * ** * * *
1631167 CAACTAACCTCATAAAAAGGCAATAAGTCCACTAACCTTATCTATAGGAAATAAGTCAACTAACC
1 CAACTAACCTCATCGATAGGTAATTGGTCAACTAACCTTATCGATAGGTAATAAGTCAACTAACC
* * *
1631232 TCATCGATAGGTAATTGGTTAGCTATA-CTCTTCGATATGTAATTGGT
66 TCATCGATAGGTAATTGGTCAACTA-ACCTCTTCGATAGGTAATTGGT
* * *
1631279 CAACTAAACTCATCGATGGGTAATTGGTCAACTAACCTTATCGATAGGTAATAGGTCAACTAACC
1 CAACTAACCTCATCGATAGGTAATTGGTCAACTAACCTTATCGATAGGTAATAAGTCAACTAACC
* * * *
1631344 TTATCGATAGGTAAGTAGTCAACTAACCTCTTCGATAGGTAATTCGT
66 TCATCGATAGGTAATTGGTCAACTAACCTCTTCGATAGGTAATTGGT
* * * *
1631391 CTACTAACCTCATCGATAGATAATTGGTCAACTAACCTTATCGAAAGGTAATAAGTCAACCAACC
1 CAACTAACCTCATCGATAGGTAATTGGTCAACTAACCTTATCGATAGGTAATAAGTCAACTAACC
* * * * *
1631456 TCATCGATAGGTAGTTGGTCTACTGACCTCATCGAAAGGTAATT-GT
66 TCATCGATAGGTAATTGGTCAACTAACCTCTTCGATAGGTAATTGGT
* * *
1631502 ACCACTAACCTCATCAAAAGGTAATTGGTC
1 -CAACTAACCTCATCGATAGGTAATTGGTC
1631532 CACGTTGAGG
Statistics
Matches: 301, Mismatches: 60, Indels: 8
0.82 0.16 0.02
Matches are distributed among these distances:
111 3 0.01
112 295 0.98
113 3 0.01
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.30
Consensus pattern (112 bp):
CAACTAACCTCATCGATAGGTAATTGGTCAACTAACCTTATCGATAGGTAATAAGTCAACTAACC
TCATCGATAGGTAATTGGTCAACTAACCTCTTCGATAGGTAATTGGT
Done.