Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold1009
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: 1861391
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.29
Warning! 223269 characters in sequence are not A, C, G, or T
File 2 of 5
Found at i:65 original size:1 final size:1
Alignment explanation
Indices: 59--86 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
49 AAAATGGAAC
59 GGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGG
87 TGCATACAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:6879 original size:76 final size:76
Alignment explanation
Indices: 6657--7018 Score: 440
Period size: 76 Copynumber: 4.8 Consensus size: 76
6647 ATTTTACACC
* * * * *
6657 ATTTTACGTCGAGTTTCAAGTTTAATCACTCATTTTACTCGACTTATATTCCACATATAAATGTT
1 ATTTTACGTCGAGTTTCAAGTTTATTCACTCATTTTACGCAACTTAAATTCCACATTTAAATGTT
* *
6722 TATTATATCGA
66 TATTATACCCA
* * * * *
6733 ATTTTACGCCGAGTTTCAAGTTTAATCTAATCATTTTACGCAACTTAAATTCAAGATTTAAATGT
1 ATTTTACGTCGAGTTTCAAGTTTATTC-ACTCATTTTACGCAACTTAAATTCCACATTTAAATGT
6798 TTATTATACCCA
65 TTATTATACCCA
* * *
6810 ATTTTACGTCAAGTTTCAAGTTTATTCACTCATTTTACGCAAATTAAATTCCATATTTAAATGTT
1 ATTTTACGTCGAGTTTCAAGTTTATTCACTCATTTTACGCAACTTAAATTCCACATTTAAATGTT
***
6875 TATTATATAGA
66 TATTATACCCA
* * *
6886 ATTTTACGTCGAGTTTCAAGTTTATTCACTCATTTTACTCGACTTATATTCCACATTTAAATGTT
1 ATTTTACGTCGAGTTTCAAGTTTATTCACTCATTTTACGCAACTTAAATTCCACATTTAAATGTT
6951 CT-TTATACCCA
66 -TATTATACCCA
* ** * * *
6962 ATTTTACGTCGAGTTT-TAGTTTAATTTTCTCATTTTACTCAACTTATATTCTACATT
1 ATTTTACGTCGAGTTTCAAGTTT-ATTCACTCATTTTACGCAACTTAAATTCCACATT
7019 CATGTGTTTA
Statistics
Matches: 249, Mismatches: 34, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
75 5 0.02
76 179 0.72
77 65 0.26
ACGTcount: A:0.30, C:0.17, G:0.08, T:0.45
Consensus pattern (76 bp):
ATTTTACGTCGAGTTTCAAGTTTATTCACTCATTTTACGCAACTTAAATTCCACATTTAAATGTT
TATTATACCCA
Found at i:7053 original size:152 final size:153
Alignment explanation
Indices: 6657--7018 Score: 491
Period size: 153 Copynumber: 2.4 Consensus size: 153
6647 ATTTTACACC
*
6657 ATTTTACGTCGAGTTTCAAGTTTAA-TCACTCATTTTACTCGACTTATATTCCACATATAAATGT
1 ATTTTACGTCGAGTTTCAAGTTTAATTCACTCATTTTACTCAACTTATATTCCACAT-TAAATGT
*
6721 TTATTATATCGAATTTTACGCCGAGTTTCAAGTTTAATCTAATCATTTTACGCAACTTAAATTCA
65 TTATTATATCGAATTTTACGTCGAGTTTCAAGTTTAATCTAATCATTTTACGCAACTTAAATTCA
*
6786 AGATTTAAATGTTTATTATACCCA
130 ACATTTAAATGTTTATTATACCCA
* * * * *
6810 ATTTTACGTCAAGTTTCAAGTTT-ATTCACTCATTTTACGCAAATTAAATTCCATATTTAAATGT
1 ATTTTACGTCGAGTTTCAAGTTTAATTCACTCATTTTACTCAACTTATATTCCACA-TTAAATGT
* * * * * * *
6874 TTATTATATAGAATTTTACGTCGAGTTTCAAGTTTATTC-ACTCATTTTACTCGACTTATATTCC
65 TTATTATATCGAATTTTACGTCGAGTTTCAAGTTTAATCTAATCATTTTACGCAACTTAAATTCA
6938 ACATTTAAATGTTCT-TTATACCCA
130 ACATTTAAATGTT-TATTATACCCA
* ** *
6962 ATTTTACGTCGAGTTT-TAGTTTAATTTTCTCATTTTACTCAACTTATATTCTACATT
1 ATTTTACGTCGAGTTTCAAGTTTAATTCACTCATTTTACTCAACTTATATTCCACATT
7019 CATGTGTTTA
Statistics
Matches: 181, Mismatches: 24, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
151 7 0.04
152 82 0.45
153 91 0.50
154 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.08, T:0.45
Consensus pattern (153 bp):
ATTTTACGTCGAGTTTCAAGTTTAATTCACTCATTTTACTCAACTTATATTCCACATTAAATGTT
TATTATATCGAATTTTACGTCGAGTTTCAAGTTTAATCTAATCATTTTACGCAACTTAAATTCAA
CATTTAAATGTTTATTATACCCA
Found at i:9458 original size:96 final size:96
Alignment explanation
Indices: 9291--9599 Score: 399
Period size: 96 Copynumber: 3.2 Consensus size: 96
9281 CTAAAGCAGT
* * *
9291 ACACTTAGAGCA-A-ACGTATATACACATACATTTCTTACATACACACTTTACTGCTTTGTGAAG
1 ACACATAGAGCACACACGTATAAACACACACATTTCTTACATACACACTTTACTGCTTTGTGAAG
* *
9354 CCGGCACATACAATTATTTGTGTGAAGCTTG
66 TCAGCACATACAATTATTTGTGTGAAGCTTG
* **
9385 ACACATAGAGCACACACGTATAAACACACACATTTCCTACGCACACACTTTACTGCTTTGTGAAG
1 ACACATAGAGCACACACGTATAAACACACACATTTCTTACATACACACTTTACTGCTTTGTGAAG
*
9450 TCAGCACATAC-ATTTTTATGTGTGAAGCTTG
66 TCAGCACATACAATTATT-TGTGTGAAGCTTG
* * * * * *
9481 ACACATAGAGCACACATGTATATACACACACATTTCTTGCTTACACACTTTACCGCTTTGGGAAG
1 ACACATAGAGCACACACGTATAAACACACACATTTCTTACATACACACTTTACTGCTTTGTGAAG
* * * *
9546 TCAGCACATACATTTATATGTGTGATGTTTG
66 TCAGCACATACAATTATTTGTGTGAAGCTTG
* *
9577 ACACATAGGGCACACATGTATAA
1 ACACATAGAGCACACACGTATAA
9600 GTTTCCATTC
Statistics
Matches: 187, Mismatches: 24, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
94 11 0.06
95 6 0.03
96 167 0.89
97 3 0.02
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (96 bp):
ACACATAGAGCACACACGTATAAACACACACATTTCTTACATACACACTTTACTGCTTTGTGAAG
TCAGCACATACAATTATTTGTGTGAAGCTTG
Found at i:9876 original size:96 final size:96
Alignment explanation
Indices: 9712--9912 Score: 339
Period size: 96 Copynumber: 2.1 Consensus size: 96
9702 TAGAGTACAC
* * * * *
9712 GTATATACACATATATTTCTTACATACACACTTTACTGCTTTTTGAAGTCAGCATATACATTTAT
1 GTATATACACACACATTTCTTACATACACACTTTACCGCTTTGTGAAGTCAGCACATACATTTAT
*
9777 ATGTGTGAAGCTTGACACATAGGGCACACAT
66 ATGTGTGAAGCTTGACACATAGAGCACACAT
9808 GTATATACACACACATTTCTTACATACACACTTTACCGCTTTGTGAAGTCAGCACATACATTTAT
1 GTATATACACACACATTTCTTACATACACACTTTACCGCTTTGTGAAGTCAGCACATACATTTAT
*
9873 ATGTGTGAAGCTTGACACATAGATCACACAT
66 ATGTGTGAAGCTTGACACATAGAGCACACAT
9904 GTATATACA
1 GTATATACA
9913 AATTCTTTAA
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
96 98 1.00
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.33
Consensus pattern (96 bp):
GTATATACACACACATTTCTTACATACACACTTTACCGCTTTGTGAAGTCAGCACATACATTTAT
ATGTGTGAAGCTTGACACATAGAGCACACAT
Found at i:11000 original size:22 final size:22
Alignment explanation
Indices: 10958--11000 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
10948 ATATTTAATT
*
10958 ACATTAAAGGTAAAACTTTATG
1 ACATTAAAGGTAAAACGTTATG
* *
10980 ACATTAAAGGTGAAAGGTTAT
1 ACATTAAAGGTAAAACGTTAT
11001 ATTTAATTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (22 bp):
ACATTAAAGGTAAAACGTTATG
Found at i:12231 original size:36 final size:36
Alignment explanation
Indices: 12184--12258 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
12174 TGGGTTACTA
12184 ATATTGACAAAAAGTTCACTTATCATAATGTTGTAG
1 ATATTGACAAAAAGTTCACTTATCATAATGTTGTAG
12220 ATATTGACAAAAAGTTCACTTATCATAATGTTGTAG
1 ATATTGACAAAAAGTTCACTTATCATAATGTTGTAG
12256 ATA
1 ATA
12259 CTCTAATAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (36 bp):
ATATTGACAAAAAGTTCACTTATCATAATGTTGTAG
Found at i:24813 original size:12 final size:13
Alignment explanation
Indices: 24789--24823 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
24779 CTGGACTCTT
24789 AATAATAAATCAA
1 AATAATAAATCAA
24802 AATAAT-AATCAA
1 AATAATAAATCAA
24814 AATAAATAAA
1 AAT-AATAAA
24824 CATCGATCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 9 0.45
13 9 0.45
14 2 0.10
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (13 bp):
AATAATAAATCAA
Found at i:30275 original size:436 final size:439
Alignment explanation
Indices: 29450--30380 Score: 1361
Period size: 436 Copynumber: 2.1 Consensus size: 439
29440 NNNNNNNNNN
*
29450 TAAGT-TCTTCTTACAATAACTCTTTACTGAACAATAATTTGTTATTAGTTATAGAAGCAAAAAT
1 TAAGTGTCTTCTTACAATAACTCTTTACTGAACAATAATTTGTTATTAATTATAGAAGCAAAAAT
* * *
29514 GTTCATTGTACAGCTGTTTGTCTATACAGTACCATATTTAAGCCATATGTTACGTAATTAGGGGC
66 GTTCATTGTACAGCTGTTTGTCTATACAGTACCATACTTAAGCCATATATTACGTAATCAGGGGC
* *
29579 TTCAAGGGGCCAGAAGTTCAAAACTTTGATCATTAATATCTGAAAAAGGATAAATATTTTCAAAA
131 TTCAAGGGGCCAGAAGTTCAAAACTTTGATAATTAATATCTGAAAAAGGAGAAATATTTTCAAAA
* * **
29644 GCAATGTAGCACAAAAGTTGCTCAAAATAATGTTCTGTTCAATATGCAACCTTAAATGTTTTTGT
196 GCAATGTAGAACAAAAGTTGCTCAAAATAATGTTCTGTACAATATGCAACCAAAAATGTTTTTGT
**
29709 TTATGACCCCATTTAGGAGTTAAAGGGTCGGCCCCTAAAACACATTTGTACAGATATCTCAAGAA
261 TTATGACCCCATAAAGGAGTTAAAGGGTCGGCCCCTAAAACACATTTGTACAGATATCTCAAGAA
* **
29774 CCGTTAACATTTCATGAACACTTGTAAAACGAAATATGTTTATATTTTCGAGACCTTTCATTTGA
326 CCGTTAACATTTCATGAACACTTGTAAAACAAAATATGTTTATATTAGCGAGACCTTTCATTTGA
* *
29839 TATCAAGAAAAAGGGGCTGGCCCCTCAAATTAGGGGCCA-AGAGGGCTA-
391 TATCAAGAAAAAGGGACTGACCCCTCAAATTAGGGGCCAGA-AGGGCTAC
* * *
29887 TAA-TGTCTTCATACAATAAGTCTTTACTGAAAAATAATTTGTTATTAATTATAGAAGCAAAAAT
1 TAAGTGTCTTCTTACAATAACTCTTTACTGAACAATAATTTGTTATTAATTATAGAAGCAAAAAT
* *
29951 GTTCATTGTACAGCTGTTTGTCTATACAGTACCATACTTAAGTCATATATTACGTAATCAGGGGT
66 GTTCATTGTACAGCTGTTTGTCTATACAGTACCATACTTAAGCCATATATTACGTAATCAGGGGC
30016 TTCAAGGGGCCAGAA-TTCAAAACTTTGATAATTAATATCTGAAAAAGGAGAAATATTTTCAAAA
131 TTCAAGGGGCCAGAAGTTCAAAACTTTGATAATTAATATCTGAAAAAGGAGAAATATTTTCAAAA
30080 GCAATGTAGAACAAAAGTT-CTTCAAAATAATGTTCT-TAACAATATG-ATACCAAAAAT-TTTG
196 GCAATGTAGAACAAAAGTTGC-TCAAAATAATGTTCTGT-ACAATATGCA-ACCAAAAATGTTT-
* *
30141 TTG-TTAGTGGCCCCGGTAAAGG-GTTAAAGGGTCGGCCCCTAAAACACATTTGTACAGATATCT
257 TTGTTTA-TGACCCC-ATAAAGGAGTTAAAGGGTCGGCCCCTAAAACACATTTGTACAGATATCT
* * * ** *
30204 CGAGAACGGTTTACCA-TTCATGAACACTTGTTGAACAAAATATGTTTATATTAGCGATACCTTT
320 CAAGAACCG-TTAACATTTCATGAACACTTGTAAAACAAAATATGTTTATATTAGCGAGACCTTT
*
30268 TATTTGATATCAAGAAAAAGGGACTGACCCCTCAAATTAGGGGCCAGAAGGGCTAC
384 CATTTGATATCAAGAAAAAGGGACTGACCCCTCAAATTAGGGGCCAGAAGGGCTAC
* * * * *
30324 TAAGTGT-TT-TTATAATAACTCTTTTCTGACCAATAATTTGATATTAATCATA-AAGCA
1 TAAGTGTCTTCTTACAATAACTCTTTACTGAACAATAATTTGTTATTAATTATAGAAGCA
30381 GCAAATGAGC
Statistics
Matches: 444, Mismatches: 39, Indels: 24
0.88 0.08 0.05
Matches are distributed among these distances:
435 14 0.03
436 279 0.63
437 148 0.33
438 3 0.01
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.32
Consensus pattern (439 bp):
TAAGTGTCTTCTTACAATAACTCTTTACTGAACAATAATTTGTTATTAATTATAGAAGCAAAAAT
GTTCATTGTACAGCTGTTTGTCTATACAGTACCATACTTAAGCCATATATTACGTAATCAGGGGC
TTCAAGGGGCCAGAAGTTCAAAACTTTGATAATTAATATCTGAAAAAGGAGAAATATTTTCAAAA
GCAATGTAGAACAAAAGTTGCTCAAAATAATGTTCTGTACAATATGCAACCAAAAATGTTTTTGT
TTATGACCCCATAAAGGAGTTAAAGGGTCGGCCCCTAAAACACATTTGTACAGATATCTCAAGAA
CCGTTAACATTTCATGAACACTTGTAAAACAAAATATGTTTATATTAGCGAGACCTTTCATTTGA
TATCAAGAAAAAGGGACTGACCCCTCAAATTAGGGGCCAGAAGGGCTAC
Found at i:33110 original size:16 final size:16
Alignment explanation
Indices: 33089--33148 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 16
33079 GTCTTGAGTG
*
33089 AATGAATGAATGAATA
1 AATGAATGAATGAACA
* * **
33105 AATGAAGGAAGGAAGG
1 AATGAATGAATGAACA
33121 AATGAATGAATGAACA
1 AATGAATGAATGAACA
*
33137 TTATGAATGAAT
1 -AATGAATGAAT
33149 AGCAAATTCA
Statistics
Matches: 34, Mismatches: 9, Indels: 1
0.77 0.20 0.02
Matches are distributed among these distances:
16 24 0.71
17 10 0.29
ACGTcount: A:0.52, C:0.02, G:0.25, T:0.22
Consensus pattern (16 bp):
AATGAATGAATGAACA
Found at i:33148 original size:4 final size:4
Alignment explanation
Indices: 33087--33134 Score: 60
Period size: 4 Copynumber: 12.0 Consensus size: 4
33077 ATGTCTTGAG
* * * *
33087 TGAA TGAA TGAA TGAA TAAA TGAA GGAA GGAA GGAA TGAA TGAA TGAA
1 TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA
33135 CATTATGAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.52, C:0.00, G:0.29, T:0.19
Consensus pattern (4 bp):
TGAA
Found at i:47766 original size:4 final size:4
Alignment explanation
Indices: 47757--47808 Score: 63
Period size: 4 Copynumber: 13.5 Consensus size: 4
47747 AGTTTCGATT
* * *
47757 TTTA TTTA TTTA TTTA TTTA --TA TTTT TTTG TTTA TTTA CTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
47803 TTTA TT
1 TTTA TT
47809 ACTTGGGGCC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
2 2 0.05
4 39 0.95
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:49477 original size:13 final size:13
Alignment explanation
Indices: 49459--49484 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
49449 ACTCAGTCTC
49459 GGCTAAACATTGA
1 GGCTAAACATTGA
49472 GGCTAAACATTGA
1 GGCTAAACATTGA
49485 CTTCAGGAAA
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:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
GGCTAAACATTGA
Found at i:54887 original size:20 final size:20
Alignment explanation
Indices: 54858--54897 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
54848 TATTTATTTT
* *
54858 TTTTTTGGGGGGGGGGGTAG
1 TTTTTAGGGGAGGGGGGTAG
54878 TTTTTAGGGGAGGGGGGTAG
1 TTTTTAGGGGAGGGGGGTAG
54898 ATTTATTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.10, C:0.00, G:0.57, T:0.33
Consensus pattern (20 bp):
TTTTTAGGGGAGGGGGGTAG
Found at i:54902 original size:19 final size:20
Alignment explanation
Indices: 54864--54902 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
54854 TTTTTTTTTT
* *
54864 GGGGGGGGGGGTAGTTTTTA
1 GGGGAGGGGGGTAGTATTTA
54884 GGGGAGGGGGGTAG-ATTTA
1 GGGGAGGGGGGTAGTATTTA
54903 TTGTTATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.15, C:0.00, G:0.59, T:0.26
Consensus pattern (20 bp):
GGGGAGGGGGGTAGTATTTA
Found at i:58347 original size:177 final size:181
Alignment explanation
Indices: 58050--58421 Score: 594
Period size: 177 Copynumber: 2.1 Consensus size: 181
58040 TGGGGGAGGT
58050 GGGGGGGGGGTGGTAAAAATTTGAATCTTAGAAAATGATTTAATACTTAAGATATTTCAAAGTTT
1 GGGGGGGGGG-GGTAAAAATTTGAATCTTAGAAAATGATTTAATACTTAAGATATTTCAAAGTTT
*
58115 AGTCGGAGCAGTTTCATTACATATCATTTTTGTTGTTCAGTGATTAGCTATCA-TT-TT-TTTAG
65 AGTCGCAGCAGTTTCATTACATATCATTTTTGTTGTTCAGTGATTAGCTATCATTTATTATTTAG
*
58177 CTTT-CTCTATTTCACT-AAAACATTCTGAGATGAAAATGCATGATGAAGTGC
130 CTTTCCT-TATTTCACTAAAAACATTCTGAGATAAAAATGCATGATGAAGTGC
*
58228 GGGGGGGGGGGG-AACAAATTTGCATCTTAGAAAATGATTTAATACTTAAGATATTTCAAAGTTT
1 GGGGGGGGGGGGTAA-AAATTTGAATCTTAGAAAATGATTTAATACTTAAGATATTTCAAAGTTT
* * *
58292 AGTCGCAGTAGTTTCATTAGATATCATTTTTGTTGTTCAGTGATTAGCTATCATTTATTATTTTG
65 AGTCGCAGCAGTTTCATTACATATCATTTTTGTTGTTCAGTGATTAGCTATCATTTATTATTTAG
* *
58357 CTTTCCTTATTTCACTAAAAAACATTCTTAGATAAAAATGCATGATGAAGTGT
130 CTTTCCTTATTTCACT-AAAAACATTCTGAGATAAAAATGCATGATGAAGTGC
58410 GGGGGGGGGGGG
1 GGGGGGGGGGGG
58422 GGNTTGAGTC
Statistics
Matches: 179, Mismatches: 8, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
176 2 0.01
177 100 0.56
178 12 0.07
179 2 0.01
180 17 0.09
181 2 0.01
182 44 0.25
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (181 bp):
GGGGGGGGGGGGTAAAAATTTGAATCTTAGAAAATGATTTAATACTTAAGATATTTCAAAGTTTA
GTCGCAGCAGTTTCATTACATATCATTTTTGTTGTTCAGTGATTAGCTATCATTTATTATTTAGC
TTTCCTTATTTCACTAAAAACATTCTGAGATAAAAATGCATGATGAAGTGC
Found at i:62117 original size:2 final size:2
Alignment explanation
Indices: 62110--62168 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
62100 NNNNNNNNNN
62110 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
62152 CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT C
62169 GTGAAATTAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:66592 original size:2 final size:2
Alignment explanation
Indices: 66585--66746 Score: 224
Period size: 2 Copynumber: 82.0 Consensus size: 2
66575 GTCTTGACAT
66585 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
* *
66627 GA GA GA GA GA GA GA GA GA GA -A GA GA GA GA GA AA G- GA -A GG
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
*
66666 GA G- GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA TGA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA -GA
* * *
66708 GA GA GA GG GA GA GA GA GA AA TGA GA GA GG 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
66747 TTTAGAGATT
Statistics
Matches: 142, Mismatches: 12, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
1 4 0.03
2 136 0.96
3 2 0.01
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.01
Consensus pattern (2 bp):
GA
Found at i:75120 original size:2 final size:2
Alignment explanation
Indices: 75115--75139 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
75105 ATATANNNNN
75115 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
75140 TCAATGAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:93222 original size:18 final size:18
Alignment explanation
Indices: 93210--93599 Score: 396
Period size: 18 Copynumber: 21.4 Consensus size: 18
93200 CGTAGGCAAT
*
93210 GTTTGTTCTGTAGGAAAC
1 GTTTGTTCTGTAGGAAAG
93228 GTTTGTTCTGTAGGAAAG
1 GTTTGTTCTGTAGGAAAG
*
93246 GTTTGTTTTGTAGGAAAG
1 GTTTGTTCTGTAGGAAAG
*
93264 GTTTGTTTTGTAGGAAAG
1 GTTTGTTCTGTAGGAAAG
* *
93282 GTTTGTTCTGTAGGCAAT
1 GTTTGTTCTGTAGGAAAG
93300 GTTTGTTCTGTAGGAAAG
1 GTTTGTTCTGTAGGAAAG
**
93318 GTTTGTTCTGTAGG-ATT
1 GTTTGTTCTGTAGGAAAG
93335 GTTTGTTCTGTAGGAAAG
1 GTTTGTTCTGTAGGAAAG
**
93353 GTTTGTTCTGTAGG-ATT
1 GTTTGTTCTGTAGGAAAG
*
93370 GTTTGTTCTGTAGGCAAG
1 GTTTGTTCTGTAGGAAAG
93388 GTTTGTTCTGTAGGAATTTAAAG
1 GTTTGTTCTGTAGG-----AAAG
* * *
93411 GTTTTTATTTCGTAGGGAAG
1 GTTTGT-TCT-GTAGGAAAG
*
93431 GTTT-TTCCTGTAGGAAAC
1 GTTTGTT-CTGTAGGAAAG
93449 GTTTGTTCTGTAGGAAAG
1 GTTTGTTCTGTAGGAAAG
* *
93467 GTTTGTCCTGTAGGAAAC
1 GTTTGTTCTGTAGGAAAG
93485 GTTTGTTCTGTAGGAAAG
1 GTTTGTTCTGTAGGAAAG
* * *
93503 GTTTAATTC-ATAGAAAAG
1 GTTT-GTTCTGTAGGAAAG
* *
93521 GTTTGTCCTGTAGGCAAG
1 GTTTGTTCTGTAGGAAAG
*
93539 GTTTGTTCTGTATGAAAG
1 GTTTGTTCTGTAGGAAAG
*
93557 GTTTATT-TCGTA-GACAAG
1 GTTTGTTCT-GTAGGA-AAG
* * * *
93575 GTTTGCTCTATAGGCAAT
1 GTTTGTTCTGTAGGAAAG
93593 GTTTGTT
1 GTTTGTT
93600 TTATATGCTT
Statistics
Matches: 310, Mismatches: 45, Indels: 34
0.80 0.12 0.09
Matches are distributed among these distances:
17 35 0.11
18 244 0.79
19 9 0.03
20 7 0.02
23 8 0.03
24 2 0.01
25 5 0.02
ACGTcount: A:0.22, C:0.08, G:0.29, T:0.42
Consensus pattern (18 bp):
GTTTGTTCTGTAGGAAAG
Found at i:93781 original size:2 final size:2
Alignment explanation
Indices: 93774--93848 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
93764 ATTTCTGCAA
93774 AT AT AT AT AT AT 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
93816 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
93849 CTTTTAATTG
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:95103 original size:126 final size:126
Alignment explanation
Indices: 94914--95149 Score: 456
Period size: 126 Copynumber: 1.9 Consensus size: 126
94904 ATAATACGAG
94914 AAAAATTTGGGGTAGACTTATTTCTCAATGTCTTTTTAAATGACACGAATAACTTTACAAAAGTC
1 AAAAATTTGGGGTAGACTTATTTCTCAATGTCTTTTTAAATGACACGAATAACTTTACAAAAGTC
94979 AAATAGCCACGCAGTTTCAATAAAATGAAAAAGAAAAAATTAAAANGGGAGTGGGGATTCAT
66 AAATAGCCACGCAGTTTCAATAAAATGAAAAAGAAAAAATTAAAA-GGGAGTGGGGATTCAT
95041 AAAAATTTGGGGTAGACTTATTTCTCAATGTC-TTTTAAATGACACGAATAACTTTACAAAAGTC
1 AAAAATTTGGGGTAGACTTATTTCTCAATGTCTTTTTAAATGACACGAATAACTTTACAAAAGTC
95105 AAATAGCCACGCAGTTTCAATAAAATGAAAAAGAAAAAATTAAAA
66 AAATAGCCACGCAGTTTCAATAAAATGAAAAAGAAAAAATTAAAA
95150 AGGTTTTTTT
Statistics
Matches: 109, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
126 77 0.71
127 32 0.29
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.28
Consensus pattern (126 bp):
AAAAATTTGGGGTAGACTTATTTCTCAATGTCTTTTTAAATGACACGAATAACTTTACAAAAGTC
AAATAGCCACGCAGTTTCAATAAAATGAAAAAGAAAAAATTAAAAGGGAGTGGGGATTCAT
Found at i:99967 original size:2 final size:2
Alignment explanation
Indices: 99960--100011 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
99950 ACCCCACAAA
99960 CT CT CT CT CT C- 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
100001 CT CT CT CT CT C
1 CT CT CT CT CT C
100012 CAATCAAATT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:101212 original size:12 final size:11
Alignment explanation
Indices: 101193--101224 Score: 55
Period size: 12 Copynumber: 2.8 Consensus size: 11
101183 CTTTAGAAGC
101193 AAAAAAAACAA
1 AAAAAAAACAA
101204 AACAAAAAACAA
1 AA-AAAAAACAA
101216 AAAAAAAAC
1 AAAAAAAAC
101225 CCGAAAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:108839 original size:2 final size:2
Alignment explanation
Indices: 108832--108873 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
108822 CACAAGGGCG
108832 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
108874 ACAACTTACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:112515 original size:4 final size:4
Alignment explanation
Indices: 112506--112555 Score: 66
Period size: 4 Copynumber: 12.8 Consensus size: 4
112496 AAAGTTTACA
* * *
112506 GACG GACG GACA GACA GACA GACG GACG GACG GACG GACG GAC- GACG
1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG
112553 GAC
1 GAC
112556 AACGGGTGAT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 3 0.07
4 40 0.93
ACGTcount: A:0.32, C:0.26, G:0.42, T:0.00
Consensus pattern (4 bp):
GACG
Found at i:116227 original size:4 final size:4
Alignment explanation
Indices: 116218--116253 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
116208 CATTAGTTTG
116218 GATT GATT GATT GATT GATT GATT GATT GATT GATT
1 GATT GATT GATT GATT GATT GATT GATT GATT GATT
116254 TCAATGAGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
GATT
Found at i:116327 original size:16 final size:16
Alignment explanation
Indices: 116308--116348 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
116298 GAATGAATGA
116308 ATGAATGAAAAGATGG
1 ATGAATGAAAAGATGG
116324 ATGAATGAAAAGATGG
1 ATGAATGAAAAGATGG
116340 ATGAATGAA
1 ATGAATGAA
116349 CGGACGGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.29, T:0.20
Consensus pattern (16 bp):
ATGAATGAAAAGATGG
Found at i:117432 original size:2 final size:2
Alignment explanation
Indices: 117425--117465 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
117415 AGCTCATAAA
*
117425 AG AG AG AG AG AG AA 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 AG AG A
117466 AAGGTTAAAT
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:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:127918 original size:14 final size:15
Alignment explanation
Indices: 127899--127932 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
127889 TGGGTTGTTG
127899 TTTTTTT-T-GTTTT
1 TTTTTTTGTGGTTTT
127912 TTTTTTTGTGGTTTT
1 TTTTTTTGTGGTTTT
127927 TTTTTT
1 TTTTTT
127933 GGGGGGGGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.37
14 1 0.05
15 11 0.58
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (15 bp):
TTTTTTTGTGGTTTT
Found at i:127933 original size:14 final size:12
Alignment explanation
Indices: 127893--127933 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
127883 CATTTCTGGG
*
127893 TTGTTGTTTTTT
1 TTGTTTTTTTTT
127905 TTGTTTTTTTTT
1 TTGTTTTTTTTT
127917 TTGTGGTTTTTTTT
1 TTGT--TTTTTTTT
127931 TTG
1 TTG
127934 GGGGGGGGGN
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 15 0.58
14 11 0.42
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (12 bp):
TTGTTTTTTTTT
Found at i:128407 original size:2 final size:2
Alignment explanation
Indices: 128400--128459 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
128390 NNNNNNNNNN
128400 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
128442 TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC
128460 CAAGAAGATG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:131310 original size:24 final size:21
Alignment explanation
Indices: 131267--131310 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
131257 TTACAAGGAA
*
131267 AAGAAAAAAAAATACCACAAC
1 AAGAAAAAAAAACACCACAAC
131288 AAGACAAAAACAAACACCTACAA
1 AAGA-AAAAA-AAACACC-ACAA
131311 GAATTGTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 4 0.21
22 5 0.26
23 6 0.32
24 4 0.21
ACGTcount: A:0.68, C:0.23, G:0.05, T:0.05
Consensus pattern (21 bp):
AAGAAAAAAAAACACCACAAC
Found at i:148961 original size:172 final size:172
Alignment explanation
Indices: 148675--149434 Score: 1288
Period size: 172 Copynumber: 4.4 Consensus size: 172
148665 TCACACTTTT
*
148675 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTT-TA
1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACAGATTTTCATTAAATTTATACCAAATGTTTAT-
* * * *
148739 ACCACTATTACTTTGGTCGAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGG
65 ACCACTATTACCTTGGTCAAGTTCGAAAATCAGCATTAGTCGATACTTTTTGTTGGCGTTATGGG
** *
148804 ACTTTGACTGCAATAATGACTCTGTTTTATCCAAAAATTGACC
130 ACTTTGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC
*
148847 TTGTAAGCGCTCTCATGCCTACAAATTTTGACAGATTTTCATTAAATTTATTCCAAATGTTTATA
1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACAGATTTTCATTAAATTTATACCAAATGTTTATA
148912 CCACTATTACCTTGGTCAAGTTCGAAAATCAGCATTAGTCGATACTTTTTGTTGGCGTTATGGGA
66 CCACTATTACCTTGGTCAAGTTCGAAAATCAGCATTAGTCGATACTTTTTGTTGGCGTTATGGGA
*
148977 CTTTGACCACAATCATGACTCCGTTTTATCCAAAAATTGACC
131 CTTTGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC
*
149019 TTGTAAGCGCTTTCATGCCTACAAATTTTGACAGATTTTCATTAAATTTATACCAAATGTTTATA
1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACAGATTTTCATTAAATTTATACCAAATGTTTATA
* * *
149084 CCACTATTACCTTGGTCAAGTTTGAAAATCAGCGTTATTCGATACTTTTTGTTGGCGTTATGGGA
66 CCACTATTACCTTGGTCAAGTTCGAAAATCAGCATTAGTCGATACTTTTTGTTGGCGTTATGGGA
149149 CTTTGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC
131 CTTTGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC
149191 TTGTAAGCGCTCTCATGCCTACAAATTTTGACAGATTTTCATTAAATTTATACCAAATGTTTATA
1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACAGATTTTCATTAAATTTATACCAAATGTTTATA
* * * *
149256 TCACTAATACTTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGCGTTATGGGA
66 CCACTATTACCTTGGTCAAGTTCGAAAATCAGCATTAGTCGATACTTTTTGTTGGCGTTATGGGA
*
149321 CTTTGACCACAATAATGACTCCGTTTTTTTCCAAAAATTGACC
131 CTTTGACCACAATAATGACTCCG-TTTTATCCAAAAATTGACC
* * * *
149364 TTGTTAGCGCGCTCATGCCTACAAATTTAGACGGATTTTCATTAAATTTATACCAAATGTTTATA
1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACAGATTTTCATTAAATTTATACCAAATGTTTATA
149429 CCACTA
66 CCACTA
149435 AGGTCACGTT
Statistics
Matches: 556, Mismatches: 30, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
172 471 0.85
173 85 0.15
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (172 bp):
TTGTAAGCGCTCTCATGCCTACAAATTTTGACAGATTTTCATTAAATTTATACCAAATGTTTATA
CCACTATTACCTTGGTCAAGTTCGAAAATCAGCATTAGTCGATACTTTTTGTTGGCGTTATGGGA
CTTTGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC
Found at i:150976 original size:24 final size:24
Alignment explanation
Indices: 150949--151023 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
150939 GAAAGAAAAT
* * *
150949 CAAATATGGCCTCTTTAAGAGGAC
1 CAAATACGGCCTCGTTAAGAGAAC
*
150973 CAAATACGGTCTCGTTAAGAGAAC
1 CAAATACGGCCTCGTTAAGAGAAC
* *
150997 CAAATGCGGTCTCGTTAAGAGAAC
1 CAAATACGGCCTCGTTAAGAGAAC
151021 CAA
1 CAA
151024 GAACGTAAGA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (24 bp):
CAAATACGGCCTCGTTAAGAGAAC
Found at i:154169 original size:18 final size:18
Alignment explanation
Indices: 154143--154177 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
154133 TATTCAACGT
154143 AAAAATATG-AAGTTTTA
1 AAAAATATGTAAGTTTTA
154160 AAAAAGTATGTAAGTTTT
1 AAAAA-TATGTAAGTTTT
154178 TATTCACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 4 0.25
19 7 0.44
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (18 bp):
AAAAATATGTAAGTTTTA
Found at i:159612 original size:165 final size:164
Alignment explanation
Indices: 159314--159841 Score: 507
Period size: 165 Copynumber: 3.2 Consensus size: 164
159304 GAAACAGATT
* * * ** ** * *
159314 CAGGTAGTGCAAATTTAAAGTTGTGAAAATCATG-TTCC-GGGGGTAGTATGTGGTCACAATGGG
1 CAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCAGAAGGTAGTATGGGGACACAATGGG
* * * *
159377 GG-TCGA-ATTTTTACATAGAAATATAAAGACTGAAT-TTTGAAAAA--TTCTTCTCGGACACCA
66 GGATC-ATA-TTTTACATAGAAATAT-AAGAGTAAATCTTT-AAAAATCTTCTTCTCAGAAACCA
* *
159437 ATCAGCCAGGAAAGCTCAAACTTGTGTGGAAGTATTCG
127 ATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGTATCCG
* * *
159475 CAAGTATTGTAGATTCAAAGTTGTGAATATCATGACCCTCAG-AGGTAGTATGGGGACACAATGG
1 CAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCC-CAGAAGGTAGTATGGGGACACAATGG
* *
159539 GGGATCATATTTCTACATAGAAATATAGGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAAT
65 GGGATCATATTT-TACATAGAAATATAAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACCAAT
* *
159604 CAGCCAGGAAAGCTGAAACTTGCGTGGAAGTAGCCG
129 CAGCCAGGAAAGCTGAAACTTGTGTGGAAGTATCCG
* * * * ** * *
159640 CAGGGAGTGTTGATTGAAAGTTGTGAAAATCATGACCCCCGAAGGTAGGGTGGGGCCACAAAGAG
1 CAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCAGAAGGTAGTATGGGGACACAATG-G
** * *
159705 GGGATGGTTGAACTTTTACATAGGAATATATATAGAGTAATTCTTTAAAAATCTTCTTCTCAAAA
65 GGGAT-CAT--A-TTTTACATA-GAA-ATATA-AGAGTAAATCTTTAAAAATCTTCTTCTCAGAA
* * * *
159770 ACCAATTAGCCATGATAA-CTGGAACTTGTGTGGAAGTATCCT
123 ACCAATCAGCCAGGA-AAGCTGAAACTTGTGTGGAAGTATCCG
*
159812 CAGGTAGTGTAGATTCAAATTTGTGAAAAT
1 CAGGTAGTGTAGATTCAAAGTTGTGAAAAT
159842 GATTAAAGTG
Statistics
Matches: 300, Mismatches: 48, Indels: 27
0.80 0.13 0.07
Matches are distributed among these distances:
161 28 0.09
162 1 0.00
163 39 0.13
164 22 0.07
165 96 0.32
166 6 0.02
167 1 0.00
169 7 0.02
170 6 0.02
171 5 0.02
172 87 0.29
173 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (164 bp):
CAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCAGAAGGTAGTATGGGGACACAATGGG
GGATCATATTTTACATAGAAATATAAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACCAATCA
GCCAGGAAAGCTGAAACTTGTGTGGAAGTATCCG
Found at i:167564 original size:81 final size:80
Alignment explanation
Indices: 167429--167578 Score: 282
Period size: 81 Copynumber: 1.9 Consensus size: 80
167419 TTCTCTCGCC
*
167429 TAATGCAAAATTGCTTTGAGGAGGTAAAGGTAACTTCTGTTCCTCTTTGTTCTCTGACAGGTATT
1 TAATGCAAAATTGCGTTGAGGAGGTAAAGGTAACTTCTGTTCCTCTTTGTTCTCTGACAGGTATT
167494 CAGANTCATTTGTTTT
66 CAGA-TCATTTGTTTT
167510 TAATGCAAAATTGCGTTGAGGAGGTAAAGGTAACTTCTGTTCCTCTTTGTTCTCTGACAGGTATT
1 TAATGCAAAATTGCGTTGAGGAGGTAAAGGTAACTTCTGTTCCTCTTTGTTCTCTGACAGGTATT
167575 CAGA
66 CAGA
167579 AACTGTACAC
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 68 1.00
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.38
Consensus pattern (80 bp):
TAATGCAAAATTGCGTTGAGGAGGTAAAGGTAACTTCTGTTCCTCTTTGTTCTCTGACAGGTATT
CAGATCATTTGTTTT
Found at i:178632 original size:164 final size:163
Alignment explanation
Indices: 178249--178874 Score: 977
Period size: 164 Copynumber: 3.8 Consensus size: 163
178239 GTAAACTGCA
* * * *
178249 ACCATGATTTGAACAAAC-AAGAATATTCACT-TCTAAAGGATGCTTCCATTTTAATTTGAGCTT
1 ACCATGATTTGAACAAACTAA-AATCTACACTACCT-GAGGATGCTTCCATTTTAATTTGAGCTT
*
178312 TCCTGGCGTCATAGTTTTTGAGAAGAAAGTTTAAAGATTTTCTCTATATACATGTATTCGTATGT
64 TCCTGGCGTCATAGTTTTTGAGAAGAAAGTTTAAAGATTTTCTC--TAT--A--TATTCCTATGT
*
178377 AAAACTTGATCCCCCTACTGTGGCCCAACCCTACCCCCGGCG
123 AAAACTTGATCCCCCTACTGTGGCCCTACCCTACCCCCGG-G
* *
178419 ACCATGATTTGAACAGACTAAAATCTATACTACCTGAGGATGCTTCCATTTTAATTTGAGCTTTC
1 ACCATGATTTGAACAAACTAAAATCTACACTACCTGAGGATGCTTCCATTTTAATTTGAGCTTTC
178484 CTGGCGTCATAGTTTTTGAGAAGAAAGTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTG
66 CTGGCGTCATAGTTTTTGAGAAGAAAGTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTG
*
178549 ATCCCCCTACTGTGGCCCTACCCTACCCCTGGG
131 ATCCCCCTACTGTGGCCCTACCCTACCCCCGGG
* ** * *
178582 AACCATTATTTGAACAAACTAAAATCTACACTACCTGAGGATTATTCCATTTCAATTTTAGCTTT
1 -ACCATGATTTGAACAAACTAAAATCTACACTACCTGAGGATGCTTCCATTTTAATTTGAGCTTT
* *
178647 CCTGGCGTCATAGTTTTTGAGACGAAAGTTTAAAGATTTTCTCTATATATTCCTATGTAAAAATT
65 CCTGGCGTCATAGTTTTTGAGAAGAAAGTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTT
*
178712 GATCCCCCTACTGCGGCCCTACCCTACCCCCGGGG
130 GATCCCCCTACTGTGGCCCTACCCTACCCCC-GGG
178747 ACCATGATTTGAACAAACTAAAATCTACACTACCTGAGGATGCTTCCATTTTAATTTGAGCTTTC
1 ACCATGATTTGAACAAACTAAAATCTACACTACCTGAGGATGCTTCCATTTTAATTTGAGCTTTC
*
178812 CTGGCGTCATAGTTTTTGAGAATAAAGTTTAAAGATTTTCTCTATATATTCCTATGTAAAACT
66 CTGGCGTCATAGTTTTTGAGAAGAAAGTTTAAAGATTTTCTCTATATATTCCTATGTAAAACT
178875 NNNNNNNNNN
Statistics
Matches: 424, Mismatches: 28, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
163 1 0.00
164 317 0.75
165 3 0.01
166 1 0.00
168 3 0.01
170 95 0.22
171 4 0.01
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (163 bp):
ACCATGATTTGAACAAACTAAAATCTACACTACCTGAGGATGCTTCCATTTTAATTTGAGCTTTC
CTGGCGTCATAGTTTTTGAGAAGAAAGTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTG
ATCCCCCTACTGTGGCCCTACCCTACCCCCGGG
Found at i:179402 original size:31 final size:30
Alignment explanation
Indices: 179343--179407 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
179333 TCAAAAAGGT
* *
179343 TTTTGTTAAGTCGTACTTAAAATCATTCGGA
1 TTTTGTTAAGTCGTACTCAAAATAATTC-GA
*
179374 TTTTGTTAAGTCGTAC-CAGGAATAATTCGA
1 TTTTGTTAAGTCGTACTCA-AAATAATTCGA
179404 TTTT
1 TTTT
179408 TTTCATCTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 7 0.23
31 23 0.77
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.43
Consensus pattern (30 bp):
TTTTGTTAAGTCGTACTCAAAATAATTCGA
Found at i:181930 original size:4 final size:4
Alignment explanation
Indices: 181923--181960 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
181913 ATAGATAGAC
181923 AGCT AGCT AGCT AGCT AGCT AGCT AGCT AGCT AGCT AG
1 AGCT AGCT AGCT AGCT AGCT AGCT AGCT AGCT AGCT AG
181961 ATAGATAGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (4 bp):
AGCT
Found at i:181973 original size:12 final size:12
Alignment explanation
Indices: 181907--181975 Score: 57
Period size: 12 Copynumber: 5.8 Consensus size: 12
181897 ACAGACAGAC
*
181907 AGATAGATAGAT
1 AGATAGATAGCT
* *
181919 AGACAGCTAGCT
1 AGATAGATAGCT
* *
181931 AGCTAGCTAGCT
1 AGATAGATAGCT
* *
181943 AGCTAGCTAGCT
1 AGATAGATAGCT
* *
181955 AGCTAGATAGAT
1 AGATAGATAGCT
181967 AGATAGATA
1 AGATAGATA
181976 AAACGAGGAT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 49 1.00
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.23
Consensus pattern (12 bp):
AGATAGATAGCT
Found at i:181975 original size:8 final size:8
Alignment explanation
Indices: 181910--181972 Score: 63
Period size: 8 Copynumber: 7.9 Consensus size: 8
181900 GACAGACAGA
*
181910 TAGATAGA
1 TAGATAGC
*
181918 TAGACAGC
1 TAGATAGC
*
181926 TAGCTAGC
1 TAGATAGC
*
181934 TAGCTAGC
1 TAGATAGC
*
181942 TAGCTAGC
1 TAGATAGC
*
181950 TAGCTAGC
1 TAGATAGC
*
181958 TAGATAGA
1 TAGATAGC
181966 TAGATAG
1 TAGATAG
181973 ATAAAACGAG
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 49 1.00
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (8 bp):
TAGATAGC
Found at i:182233 original size:5 final size:5
Alignment explanation
Indices: 182225--182251 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
182215 AAGTTAAGTT
182225 CTATC CTATC CTATC CTATC CTATC CT
1 CTATC CTATC CTATC CTATC CTATC CT
182252 GCATCCTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.41, G:0.00, T:0.41
Consensus pattern (5 bp):
CTATC
Found at i:195214 original size:165 final size:167
Alignment explanation
Indices: 194990--195434 Score: 592
Period size: 165 Copynumber: 2.7 Consensus size: 167
194980 TTTTTTTAAA
* * * * * * *
194990 ATTTAATACTTTTTTACTACATAGG-CATATGGGCCCCTCCCTAGAGCCTGAAACCCTGACCCAG
1 ATTTAATACATATTTACTATAT-GGCCATATTGGCCCCACCCTAGAGCCAGAACCCCTGACCCAG
* *
195054 GGGCCATAAATTTCACAATTCTGGTAGAAGGCTTCATGGACATCATAAGCATCCATTAAGTTTTT
65 GGGCCATGAATTTCACAATTTTGGTAGAAGGCTTCATGGACATCATAAGCATCCATTAAGTTTTT
*
195119 AACAAATAT-ATTGGAGT-AAGAAGGAGATTTTCTAAG
130 AACAAATATAATTGGAGTAAAGAAGAAGATTTTCTAAG
* *
195155 ATTTAATACATATTTATTATATGGCCATATTGGCCCCACTCTAGAGCCAGAACCCCTGACCCAGG
1 ATTTAATACATATTTACTATATGGCCATATTGGCCCCACCCTAGAGCCAGAACCCCTGACCCAGG
* * * * *
195220 GGCCATGAATTTCACAATTTTGGTAGAGGGCTTCAGGGACATCATAATCATGCATTTAGTTTTTA
66 GGCCATGAATTTCACAATTTTGGTAGAAGGCTTCATGGACATCATAAGCATCCATTAAGTTTTTA
195285 ACAAATATACATTGGAGTAAAGAAGAAGATTTTCTAAG
131 ACAAATATA-ATTGGAGTAAAGAAGAAGATTTTCTAAG
* * * * *
195323 ATTTAATACATTTTTACTATATGGCTATATTGGCCCCACCCTAGAG-CATGTACCCCTGACACAA
1 ATTTAATACATATTTACTATATGGCCATATTGGCCCCACCCTAGAGCCA-GAACCCCTGACCCAG
** * * *
195387 GGGTAATGAATTTCACAATTTTGATAGAAGGTTTAATGGACATCATAA
65 GGGCCATGAATTTCACAATTTTGGTAGAAGGCTTCATGGACATCATAA
195435 CCATGCAAAC
Statistics
Matches: 244, Mismatches: 31, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
164 2 0.01
165 119 0.49
167 10 0.04
168 113 0.46
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Consensus pattern (167 bp):
ATTTAATACATATTTACTATATGGCCATATTGGCCCCACCCTAGAGCCAGAACCCCTGACCCAGG
GGCCATGAATTTCACAATTTTGGTAGAAGGCTTCATGGACATCATAAGCATCCATTAAGTTTTTA
ACAAATATAATTGGAGTAAAGAAGAAGATTTTCTAAG
Found at i:195398 original size:168 final size:164
Alignment explanation
Indices: 194990--195441 Score: 600
Period size: 168 Copynumber: 2.7 Consensus size: 164
194980 TTTTTTTAAA
* * * * * *
194990 ATTTAATACTTTTTTACTACATAGGCATATGGGCCCCTCCCTAGAGCCTGAAACCCTGACCCAGG
1 ATTTAATACATTTTTACTATAT-GGCATATTGGCCCCACCCTAGAGCATGAACCCCTGACCCAGG
* * * *
195055 GGCCATAAATTTCACAATTCTGGTAGAAGGCTTCATGGACATCATAAGCATCCATTAAGTTTTTA
65 GGCCATGAATTTCACAATTTTGGTAGAAGGCTTCATGGACATCATAACCATGCATTAAGTTTTTA
*
195120 ACAAATATATTGGAGTAAGAAGGAGATTTTCTAAG
130 ACAAATATATTGGAGTAAGAAGAAGATTTTCTAAG
* * *
195155 ATTTAATACATATTTATTATATGGCCATATTGGCCCCACTCTAGAGCCA-GAACCCCTGACCCAG
1 ATTTAATACATTTTTACTATATGG-CATATTGGCCCCACCCTAGAG-CATGAACCCCTGACCCAG
* * * *
195219 GGGCCATGAATTTCACAATTTTGGTAGAGGGCTTCAGGGACATCATAATCATGCATTTAGTTTTT
64 GGGCCATGAATTTCACAATTTTGGTAGAAGGCTTCATGGACATCATAACCATGCATTAAGTTTTT
195284 AACAAATATACATTGGAGTAAAGAAGAAGATTTTCTAAG
129 AACAAATAT--ATTGGAGT-AAGAAGAAGATTTTCTAAG
* * *
195323 ATTTAATACATTTTTACTATATGGCTATATTGGCCCCACCCTAGAGCATGTACCCCTGACACAAG
1 ATTTAATACATTTTTACTATATGGC-ATATTGGCCCCACCCTAGAGCATGAACCCCTGACCCAGG
** * * *
195388 GGTAATGAATTTCACAATTTTGATAGAAGGTTTAATGGACATCATAACCATGCA
65 GGCCATGAATTTCACAATTTTGGTAGAAGGCTTCATGGACATCATAACCATGCA
195442 AACAGTTTTT
Statistics
Matches: 249, Mismatches: 31, Indels: 11
0.86 0.11 0.04
Matches are distributed among these distances:
164 2 0.01
165 117 0.47
166 1 0.00
167 11 0.04
168 118 0.47
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (164 bp):
ATTTAATACATTTTTACTATATGGCATATTGGCCCCACCCTAGAGCATGAACCCCTGACCCAGGG
GCCATGAATTTCACAATTTTGGTAGAAGGCTTCATGGACATCATAACCATGCATTAAGTTTTTAA
CAAATATATTGGAGTAAGAAGAAGATTTTCTAAG
Found at i:197141 original size:4 final size:4
Alignment explanation
Indices: 197132--197222 Score: 164
Period size: 4 Copynumber: 22.8 Consensus size: 4
197122 ACAAGGTAAA
197132 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
* *
197180 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT GGAT GGAT AGA
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGA
197223 CAGACAAGGG
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
4 85 1.00
ACGTcount: A:0.48, C:0.00, G:0.27, T:0.24
Consensus pattern (4 bp):
AGAT
Found at i:200887 original size:1 final size:1
Alignment explanation
Indices: 200878--200924 Score: 85
Period size: 1 Copynumber: 47.0 Consensus size: 1
200868 TAAAAATTTG
*
200878 AAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
200925 GATTTGTGTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.98, C:0.00, G:0.00, T:0.02
Consensus pattern (1 bp):
A
Found at i:202651 original size:14 final size:15
Alignment explanation
Indices: 202632--202664 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
202622 TGCGTATTTA
202632 TTTGTTGTTGTT-TT
1 TTTGTTGTTGTTGTT
202646 TTTGTTGTTGTTGTT
1 TTTGTTGTTGTTGTT
202661 TTTG
1 TTTG
202665 GGTTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.00, C:0.00, G:0.24, T:0.76
Consensus pattern (15 bp):
TTTGTTGTTGTTGTT
Found at i:204625 original size:13 final size:12
Alignment explanation
Indices: 204607--204642 Score: 56
Period size: 11 Copynumber: 3.0 Consensus size: 12
204597 ACCAAACCCC
204607 GGGTTTACTTTCT
1 GGGTTTACTTT-T
204620 GGGTTTAC-TTT
1 GGGTTTACTTTT
204631 GGGTTTACTTTT
1 GGGTTTACTTTT
204643 TGAAAATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 9 0.41
12 5 0.23
13 8 0.36
ACGTcount: A:0.08, C:0.11, G:0.25, T:0.56
Consensus pattern (12 bp):
GGGTTTACTTTT
Found at i:204644 original size:13 final size:13
Alignment explanation
Indices: 204607--204644 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
204597 ACCAAACCCC
*
204607 GGGTTTACTTTCT
1 GGGTTTACTTTTT
204620 GGGTTTAC--TTT
1 GGGTTTACTTTTT
204631 GGGTTTACTTTTT
1 GGGTTTACTTTTT
204644 G
1 G
204645 AAAATTTGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
11 10 0.45
13 12 0.55
ACGTcount: A:0.08, C:0.11, G:0.26, T:0.55
Consensus pattern (13 bp):
GGGTTTACTTTTT
Found at i:204917 original size:22 final size:23
Alignment explanation
Indices: 204851--204917 Score: 59
Period size: 22 Copynumber: 3.0 Consensus size: 23
204841 TTTCTGATCG
** *
204851 GGGTTTACTCTCTGTGTCCACTCT
1 GGGTTTACTCTGGGT-TCCACTCA
*
204875 GGGTTTACT-TGGGGTT-TACTCA
1 GGGTTTACTCT-GGGTTCCACTCA
204897 GGGTTTACTCT-GGTTCCACTC
1 GGGTTTACTCTGGGTTCCACTC
204918 TACTAAACCC
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
21 4 0.11
22 17 0.49
23 3 0.09
24 11 0.31
ACGTcount: A:0.10, C:0.24, G:0.25, T:0.40
Consensus pattern (23 bp):
GGGTTTACTCTGGGTTCCACTCA
Found at i:204935 original size:11 final size:12
Alignment explanation
Indices: 204921--204953 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
204911 TCCACTCTAC
204921 TAAACCCAG-AG
1 TAAACCCAGAAG
204932 TAAACCCAGAAAG
1 TAAACCCAG-AAG
204945 TAAACCCAG
1 TAAACCCAG
204954 GGTTTAGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
13 11 0.55
ACGTcount: A:0.48, C:0.27, G:0.15, T:0.09
Consensus pattern (12 bp):
TAAACCCAGAAG
Found at i:205744 original size:41 final size:41
Alignment explanation
Indices: 205687--205772 Score: 118
Period size: 41 Copynumber: 2.1 Consensus size: 41
205677 ATGATTTACT
* *
205687 AAATTTGCTAAAACCTGTATACAACCTGGTATAGTTAAATA
1 AAATTTGCTAAAACCTGAATACAACCTGCTATAGTTAAATA
* * * *
205728 AAATTTGCTTAAACCTGAATACAGCCTGCTATGGTTAAATT
1 AAATTTGCTAAAACCTGAATACAACCTGCTATAGTTAAATA
205769 AAAT
1 AAAT
205773 AGGATTAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.33
Consensus pattern (41 bp):
AAATTTGCTAAAACCTGAATACAACCTGCTATAGTTAAATA
Found at i:206966 original size:18 final size:17
Alignment explanation
Indices: 206935--206984 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
206925 CTTAATCTTA
206935 TAAAAAGAT-A-ATATC
1 TAAAAAGATCATATATC
206950 TTAAAAAGATCATATATC
1 -TAAAAAGATCATATATC
*
206968 AAAAAAGTATCATATAT
1 TAAAAAG-ATCATATAT
206985 TTACTTACCC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 9 0.30
17 7 0.23
18 14 0.47
ACGTcount: A:0.56, C:0.08, G:0.06, T:0.30
Consensus pattern (17 bp):
TAAAAAGATCATATATC
Found at i:208991 original size:16 final size:16
Alignment explanation
Indices: 208959--208990 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
208949 GTTTGGTTTT
208959 GTTTTGTTTTGTGGGG
1 GTTTTGTTTTGTGGGG
208975 GTTTT-TTTTGTGGGG
1 GTTTTGTTTTGTGGGG
208990 G
1 G
208991 GGGGGGGGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.00, C:0.00, G:0.44, T:0.56
Consensus pattern (16 bp):
GTTTTGTTTTGTGGGG
Found at i:211547 original size:29 final size:28
Alignment explanation
Indices: 211515--211592 Score: 77
Period size: 29 Copynumber: 2.8 Consensus size: 28
211505 AGTCGATGAC
*
211515 GATGCGATGTTCATGTTGATGACGACGAT
1 GATG-GATGGTCATGTTGATGACGACGAT
* * * *
211544 GATGTTATGGTGATGATGACGACGACGAT
1 GATG-GATGGTCATGTTGATGACGACGAT
*
211573 GAT-GATGGTCATGTCGATGA
1 GATGGATGGTCATGTTGATGA
211593 AGATGATGTA
Statistics
Matches: 38, Mismatches: 11, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
27 12 0.32
29 26 0.68
ACGTcount: A:0.26, C:0.12, G:0.33, T:0.29
Consensus pattern (28 bp):
GATGGATGGTCATGTTGATGACGACGAT
Found at i:211557 original size:23 final size:24
Alignment explanation
Indices: 211520--211565 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
211510 ATGACGATGC
*
211520 GATGTTCATGTTGATGACGACGAT
1 GATGTTCATGGTGATGACGACGAT
*
211544 GATGTT-ATGGTGATGATGACGA
1 GATGTTCATGGTGATGACGACGA
211566 CGACGATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.26, C:0.09, G:0.33, T:0.33
Consensus pattern (24 bp):
GATGTTCATGGTGATGACGACGAT
Found at i:220657 original size:24 final size:22
Alignment explanation
Indices: 220622--220666 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
220612 GATCAAATCT
220622 AAAAAATAATATTTTTGGAAAAA
1 AAAAAATAATATTTTT-GAAAAA
220645 AAAAAATATATATTTTTGAAAA
1 AAAAAATA-ATATTTTTGAAAA
220667 TTGAGATTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (22 bp):
AAAAAATAATATTTTTGAAAAA
Found at i:222887 original size:15 final size:15
Alignment explanation
Indices: 222867--222897 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
222857 TTCCGTAACA
222867 GATAAAAAGATATTT
1 GATAAAAAGATATTT
*
222882 GATAAAAAGTTATTT
1 GATAAAAAGATATTT
222897 G
1 G
222898 CGGTGACGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.35
Consensus pattern (15 bp):
GATAAAAAGATATTT
Found at i:226140 original size:2 final size:2
Alignment explanation
Indices: 226133--226175 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
226123 TTTGTTTTCT
226133 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
226175 G
1 G
226176 GTGTTAAAAC
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:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:226559 original size:2 final size:2
Alignment explanation
Indices: 226552--226610 Score: 82
Period size: 2 Copynumber: 29.5 Consensus size: 2
226542 CCAGGATTAA
* * * *
226552 CT CT CT CT CT CT AT CT TT TT CT CT TT 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
226594 CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT C
226611 ACTCACTCTG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.02, C:0.44, G:0.00, T:0.54
Consensus pattern (2 bp):
CT
Found at i:227521 original size:23 final size:22
Alignment explanation
Indices: 227465--227522 Score: 62
Period size: 23 Copynumber: 2.6 Consensus size: 22
227455 GTATATCCGT
** *
227465 AATTCGTTATACGTTTATAGCG
1 AATTCGTTATATATTTATAACG
**
227487 AATTCGAAATATATCTTATAACG
1 AATTCGTTATATAT-TTATAACG
227510 AATTCGTTATATA
1 AATTCGTTATATA
227523 ACGATAAGTT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (22 bp):
AATTCGTTATATATTTATAACG
Found at i:246705 original size:2 final size:2
Alignment explanation
Indices: 246698--246743 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
246688 ATTAACTCCT
246698 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
246740 TC TC
1 TC TC
246744 ATAAAACATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:255607 original size:2 final size:2
Alignment explanation
Indices: 255600--255638 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
255590 ATACAGTCAA
*
255600 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AC AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
255639 AACAGAGACA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.03, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:255645 original size:14 final size:14
Alignment explanation
Indices: 255600--255650 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
255590 ATACAGTCAA
*
255600 AGAGAGAGAGAGAG
1 AGAGACAGAGAGAG
*
255614 AGAGAGAGAGAGAG
1 AGAGACAGAGAGAG
* *
255628 AGAGACAGAGAAAC
1 AGAGACAGAGAGAG
255642 AGAGACAGA
1 AGAGACAGA
255651 TATATATACA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.53, C:0.06, G:0.41, T:0.00
Consensus pattern (14 bp):
AGAGACAGAGAGAG
Found at i:256503 original size:2 final size:2
Alignment explanation
Indices: 256496--256564 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
256486 AATACATGTG
256496 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
256538 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
256565 CGCGTTAACC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:266800 original size:165 final size:165
Alignment explanation
Indices: 266585--267364 Score: 1065
Period size: 166 Copynumber: 4.8 Consensus size: 165
266575 ATAAAAATGT
*
266585 ATCCCCCATTGTGGCCCCACCCTACCCCAAGGGACCATGATTTGAACAAACTTGAATCTACA-TC
1 ATCCCCCATTGTGGCCCCACCCTACCCCCAGGGACCATGATTTGAACAAACTTGAATCTACACT-
* * * *
266649 ATCTGAGGATGGTTACC-CGCCAATTTGAGC-TTTCTTGGTC-ATATAGTTTTTGAGAAGAAGAT
65 ATCTGAGGATGCTT-CCACTCAAATTTGAGCTTTTC-TGGCCTA-ATAGTTTTTGAGAAGAAGAT
266711 TTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTG
127 TTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTG
* *
266750 ATCCCCCATTGTGGCCCCACCATACCCCCAGGGACCATAATTTGAACAAACTTGAATCTACACTA
1 ATCCCCCATTGTGGCCCCACCCTACCCCCAGGGACCATGATTTGAACAAACTTGAATCTACACTA
* * * * *
266815 CCTGAGGATGCTTTCATTTAAATTTGAGCTTTTCTGGCCTAATAGTTTTTGAGAAGAAGAATTTT
66 TCTGAGGATGCTTCCACTCAAATTTGAGCTTTTCTGGCCTAATAGTTTTTGAGAAGAAGATTTTT
*
266880 --A-A-------TATATATTCCTATGTTAAACTTG
131 AAAGATTTTCTCTATATATTCCTATGTAAAACTTG
*
266905 ATCCCCCCATTGTGGCCCCACCCTACCCCCAGGGACTATGATTTGAACAAACTTGAATCTACACT
1 AT-CCCCCATTGTGGCCCCACCCTACCCCCAGGGACCATGATTTGAACAAACTTGAATCTACACT
* ** * *
266970 ATCTGAGGATGCTTCCATTTTAATTTGATCTTTTCTGGCCTAATTGTTTTT--G-AGAAGATTTT
65 ATCTGAGGATGCTTCCACTCAAATTTGAGCTTTTCTGGCCTAATAGTTTTTGAGAAGAAGATTTT
*
267032 TATAGATTTTCTCTATATATTCCTATGTAAAACTTG
130 TAAAGATTTTCTCTATATATTCCTATGTAAAACTTG
* *
267068 ATCCCCCGATTTTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACT
1 ATCCCCC-ATTGTGGCCCCACCCTACCCCCAGGGACCATGATTTGAACAAACTTGAATCTACACT
* * *
267133 ATCTGACGATGCTTCCACTCAAATTTGAGCTTTCCTGGCCTAATAGTTTTTTAGAAGAAGATTTT
65 ATCTGAGGATGCTTCCACTCAAATTTGAGCTTTTCTGGCCTAATAGTTTTTGAGAAGAAGATTTT
267198 TAAAGATTTTCTCTATATATTCCTATGTAAAACTTG
130 TAAAGATTTTCTCTATATATTCCTATGTAAAACTTG
*
267234 ATCCCCCAAATGTGGCCCCACCCTACCCCC-GGTGACCATGATTTGAACAAACTTGAATCTACAC
1 ATCCCCC-ATTGTGGCCCCACCCTACCCCCAGG-GACCATGATTTGAACAAACTTGAATCTACAC
* * * * * * *
267298 TACCTGAGGATGCCTCCACACAAGTTTTAGCTTTTCAGGCCAAATAGTTTTTGAGAAGAAGATTT
64 TATCTGAGGATGCTTCCACTCAAATTTGAGCTTTTCTGGCCTAATAGTTTTTGAGAAGAAGATTT
267363 TT
129 TT
267365 GAAAAATACC
Statistics
Matches: 548, Mismatches: 47, Indels: 39
0.86 0.07 0.06
Matches are distributed among these distances:
153 10 0.02
154 1 0.00
155 25 0.05
156 106 0.19
162 6 0.01
163 123 0.22
164 1 0.00
165 110 0.20
166 166 0.30
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (165 bp):
ATCCCCCATTGTGGCCCCACCCTACCCCCAGGGACCATGATTTGAACAAACTTGAATCTACACTA
TCTGAGGATGCTTCCACTCAAATTTGAGCTTTTCTGGCCTAATAGTTTTTGAGAAGAAGATTTTT
AAAGATTTTCTCTATATATTCCTATGTAAAACTTG
Found at i:267547 original size:9 final size:9
Alignment explanation
Indices: 267533--267572 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
267523 GTGAAAAGTT
267533 AACAACGAC
1 AACAACGAC
267542 AACAACGAC
1 AACAACGAC
*
267551 AACGACGAC
1 AACAACGAC
*
267560 AACGACAGAC
1 AACAAC-GAC
267570 AAC
1 AAC
267573 GGACAAATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
9 23 0.79
10 6 0.21
ACGTcount: A:0.53, C:0.33, G:0.15, T:0.00
Consensus pattern (9 bp):
AACAACGAC
Found at i:267554 original size:15 final size:15
Alignment explanation
Indices: 267534--267566 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
267524 TGAAAAGTTA
267534 ACAACGACAACAACG
1 ACAACGACAACAACG
*
267549 ACAACGACGACAACG
1 ACAACGACAACAACG
267564 ACA
1 ACA
267567 GACAACGGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.52, C:0.33, G:0.15, T:0.00
Consensus pattern (15 bp):
ACAACGACAACAACG
Found at i:268521 original size:57 final size:57
Alignment explanation
Indices: 268418--268528 Score: 170
Period size: 58 Copynumber: 1.9 Consensus size: 57
268408 TTATTAAGGA
*
268418 GCTAAACATACATCACTGCATATCAAGGAATAAGGAATTTAGTCTTTGAATATTCAT
1 GCTAAACATACATCACTGCATATCAAAGAATAAGGAATTTAGTCTTTGAATATTCAT
* **
268475 GCTAAACATTATATCACTGCATATCAAAGAATATTGAA-TTAGTCTTTGAATATT
1 GCTAAACA-TACATCACTGCATATCAAAGAATAAGGAATTTAGTCTTTGAATATT
268529 AATGGCCAGT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
57 24 0.49
58 25 0.51
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (57 bp):
GCTAAACATACATCACTGCATATCAAAGAATAAGGAATTTAGTCTTTGAATATTCAT
Found at i:271308 original size:2 final size:2
Alignment explanation
Indices: 271301--271355 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
271291 GTATCTTAAA
271301 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
271343 AG AG AG AG AG AG A
1 AG AG AG AG AG AG A
271356 CTTCTATGTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:274174 original size:6 final size:6
Alignment explanation
Indices: 274160--274217 Score: 66
Period size: 6 Copynumber: 9.5 Consensus size: 6
274150 TTTTCAGATG
*
274160 ATTGAT ATTGCT ATTGATT ATTGAT ATTGATAT ATTGAT ATTGAT A-T-AT
1 ATTGAT ATTGAT ATTGA-T ATTGAT ATTG--AT ATTGAT ATTGAT ATTGAT
274209 ATTGAT ATT
1 ATTGAT ATT
274218 CAGGTGCCAA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
4 3 0.07
5 2 0.04
6 28 0.62
7 6 0.13
8 6 0.13
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.52
Consensus pattern (6 bp):
ATTGAT
Found at i:274197 original size:14 final size:14
Alignment explanation
Indices: 274164--274208 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
274154 CAGATGATTG
*
274164 ATATTGCTATTGAT
1 ATATTGATATTGAT
274178 -TATTGATATTGAT
1 ATATTGATATTGAT
274191 ATATTGATATTGAT
1 ATATTGATATTGAT
274205 ATAT
1 ATAT
274209 ATTGATATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.41
14 17 0.59
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.51
Consensus pattern (14 bp):
ATATTGATATTGAT
Found at i:279626 original size:2 final size:2
Alignment explanation
Indices: 279619--279688 Score: 133
Period size: 2 Copynumber: 35.5 Consensus size: 2
279609 TATGCATAGA
279619 CT CT CT CT CT CT CT CT CT CT CT CT C- 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
279660 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
279689 ATGAAAGTTG
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 66 0.99
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:280756 original size:20 final size:20
Alignment explanation
Indices: 280720--280759 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
280710 GACTTGCTAC
280720 CCAACAAAATCAAATTTTAT
1 CCAACAAAATCAAATTTTAT
*
280740 CCAA-AAAACTCACATTTTAT
1 CCAACAAAA-TCAAATTTTAT
280760 TTCTAACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (20 bp):
CCAACAAAATCAAATTTTAT
Found at i:282304 original size:11 final size:12
Alignment explanation
Indices: 282274--282386 Score: 67
Period size: 11 Copynumber: 9.7 Consensus size: 12
282264 AATAAACCCA
*
282274 GGGTTTACTTTCG
1 GGGTTTAC-ATCG
*
282287 TGGTTTACAT-G
1 GGGTTTACATCG
*
282298 GGGTTTAC-TCT
1 GGGTTTACATCG
*
282309 GGGTTTACTTTCG
1 GGGTTTAC-ATCG
* *
282322 TGGTTTACAT-T
1 GGGTTTACATCG
*
282333 GGGTTTAC-TCT
1 GGGTTTACATCG
*
282344 GGGTTTACTTTCG
1 GGGTTTAC-ATCG
*
282357 TGGTTTACAT-G
1 GGGTTTACATCG
*
282368 GGGTTTAC-TCT
1 GGGTTTACATCG
282379 GGGTTTAC
1 GGGTTTAC
282387 TTTTTACTGA
Statistics
Matches: 79, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
10 3 0.04
11 48 0.61
12 3 0.04
13 25 0.32
ACGTcount: A:0.12, C:0.14, G:0.28, T:0.46
Consensus pattern (12 bp):
GGGTTTACATCG
Found at i:282306 original size:24 final size:23
Alignment explanation
Indices: 282274--282386 Score: 106
Period size: 24 Copynumber: 4.8 Consensus size: 23
282264 AATAAACCCA
282274 GGGTTTACTTTCGTGGTTTACAT-G
1 GGGTTTACTTT-G-GGTTTACATCG
* *
282298 GGGTTTACTCTGGGTTTACTTTCG
1 GGGTTTACTTTGGGTTTAC-ATCG
* * *
282322 TGGTTTACATTGGGTTTAC-TCT
1 GGGTTTACTTTGGGTTTACATCG
282344 GGGTTTACTTTCGTGGTTTACAT-G
1 GGGTTTACTTT-G-GGTTTACATCG
*
282368 GGGTTTACTCTGGGTTTAC
1 GGGTTTACTTTGGGTTTAC
282387 TTTTTACTGA
Statistics
Matches: 74, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
22 25 0.34
23 4 0.05
24 44 0.59
25 1 0.01
ACGTcount: A:0.12, C:0.14, G:0.28, T:0.46
Consensus pattern (23 bp):
GGGTTTACTTTGGGTTTACATCG
Found at i:282320 original size:35 final size:35
Alignment explanation
Indices: 282274--282389 Score: 223
Period size: 35 Copynumber: 3.3 Consensus size: 35
282264 AATAAACCCA
282274 GGGTTTACTTTCGTGGTTTACATGGGGTTTACTCT
1 GGGTTTACTTTCGTGGTTTACATGGGGTTTACTCT
*
282309 GGGTTTACTTTCGTGGTTTACATTGGGTTTACTCT
1 GGGTTTACTTTCGTGGTTTACATGGGGTTTACTCT
282344 GGGTTTACTTTCGTGGTTTACATGGGGTTTACTCT
1 GGGTTTACTTTCGTGGTTTACATGGGGTTTACTCT
282379 GGGTTTACTTT
1 GGGTTTACTTT
282390 TTACTGATTC
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 79 1.00
ACGTcount: A:0.11, C:0.14, G:0.28, T:0.47
Consensus pattern (35 bp):
GGGTTTACTTTCGTGGTTTACATGGGGTTTACTCT
Found at i:282387 original size:11 final size:11
Alignment explanation
Indices: 282298--282387 Score: 85
Period size: 11 Copynumber: 7.8 Consensus size: 11
282288 GGTTTACATG
282298 GGGTTTACTCT
1 GGGTTTACTCT
*
282309 GGGTTTACTTT
1 GGGTTTACTCT
282320 CGTGGTTTACAT-T
1 -G-GGTTTAC-TCT
282333 GGGTTTACTCT
1 GGGTTTACTCT
*
282344 GGGTTTACTTT
1 GGGTTTACTCT
*
282355 CGTGGTTTACAT-G
1 -G-GGTTTAC-TCT
282368 GGGTTTACTCT
1 GGGTTTACTCT
282379 GGGTTTACT
1 GGGTTTACT
282388 TTTTACTGAT
Statistics
Matches: 67, Mismatches: 4, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
10 2 0.03
11 44 0.66
12 4 0.06
13 15 0.22
14 2 0.03
ACGTcount: A:0.11, C:0.14, G:0.28, T:0.47
Consensus pattern (11 bp):
GGGTTTACTCT
Found at i:284647 original size:50 final size:49
Alignment explanation
Indices: 284568--284664 Score: 151
Period size: 50 Copynumber: 2.0 Consensus size: 49
284558 GGCTTTATAA
284568 CCAGACAGGATACTCCAGACCCGCACCCCCCCCCCCCCGCGCCCATTNAC
1 CCAGACAGGATACTCCAGACCCGCACCCCCCCCCCCCCGCGCCCATT-AC
* *
284618 CCAGACAGGATGCTCCAGCCCCGC-CCCCCCCCCCTCCCGCGCCCATT
1 CCAGACAGGATACTCCAGACCCGCACCCCCCCCCC-CCCGCGCCCATT
284665 CCCCCCGGCT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
49 10 0.23
50 34 0.77
ACGTcount: A:0.16, C:0.58, G:0.15, T:0.09
Consensus pattern (49 bp):
CCAGACAGGATACTCCAGACCCGCACCCCCCCCCCCCCGCGCCCATTAC
Found at i:286010 original size:17 final size:17
Alignment explanation
Indices: 285988--286020 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
285978 GTTTCCCGAA
285988 AGTGACGGAGTTAGGGT
1 AGTGACGGAGTTAGGGT
286005 AGTGACGGAGTTAGGG
1 AGTGACGGAGTTAGGG
286021 GGCTATGCGA
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:0.06, G:0.48, T:0.21
Consensus pattern (17 bp):
AGTGACGGAGTTAGGGT
Found at i:296029 original size:23 final size:23
Alignment explanation
Indices: 295999--296042 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
295989 GCACATGTGC
*
295999 AGCTTGAATAAATACTTAGAATA
1 AGCTTGAATAAAAACTTAGAATA
296022 AGCTTGAATAAAAACTTAGAA
1 AGCTTGAATAAAAACTTAGAA
296043 ACTACAGCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.50, C:0.09, G:0.14, T:0.27
Consensus pattern (23 bp):
AGCTTGAATAAAAACTTAGAATA
Found at i:296102 original size:5 final size:5
Alignment explanation
Indices: 296087--296121 Score: 61
Period size: 5 Copynumber: 6.8 Consensus size: 5
296077 TTGGGGGGTT
296087 TTTTGG TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
1 TTTT-G TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
296122 TTGTGGTCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 25 0.86
6 4 0.14
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (5 bp):
TTTTG
Found at i:296231 original size:23 final size:23
Alignment explanation
Indices: 296205--296248 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
296195 TTTGGCATTT
*
296205 GAAAAAAAACCAACAACAACAAC
1 GAAAAAAAACCAACAAAAACAAC
**
296228 GAAAAAACCCCAACAAAAACA
1 GAAAAAAAACCAACAAAAACA
296249 CGTAATATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.68, C:0.27, G:0.05, T:0.00
Consensus pattern (23 bp):
GAAAAAAAACCAACAAAAACAAC
Found at i:299105 original size:2 final size:2
Alignment explanation
Indices: 299098--299144 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
299088 TGTGCATAAA
299098 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
299140 TC TC T
1 TC TC T
299145 GTTTTTTTTT
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:305461 original size:2 final size:2
Alignment explanation
Indices: 305454--305493 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
305444 GTAAATTTAA
305454 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
305494 CAAGTCTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:317919 original size:2 final size:2
Alignment explanation
Indices: 317912--317954 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
317902 TAAAGACCAC
*
317912 CT CT CT CT CT CT CT CA 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
317954 C
1 C
317955 GTTTTAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.02, C:0.51, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:319203 original size:2 final size:2
Alignment explanation
Indices: 319196--319276 Score: 162
Period size: 2 Copynumber: 40.5 Consensus size: 2
319186 NNNNNNNNNN
319196 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
319238 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
319277 ATTGTAATGT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:325262 original size:11 final size:12
Alignment explanation
Indices: 325230--325272 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
325220 TTAGGGTATG
* *
325230 TCTTAGGACGTA
1 TCTTAGGACATC
325242 TCTTAGGACAT-
1 TCTTAGGACATC
*
325253 TCTTATGACATC
1 TCTTAGGACATC
325265 TCTTAGGA
1 TCTTAGGA
325273 TGTAAAACGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.37
Consensus pattern (12 bp):
TCTTAGGACATC
Found at i:325535 original size:2 final size:2
Alignment explanation
Indices: 325528--325575 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
325518 TTTCAGAACA
325528 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
325570 TC TC TC
1 TC TC TC
325576 CTCAGTAGTC
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:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:331825 original size:11 final size:11
Alignment explanation
Indices: 331805--331841 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
331795 TCTGCAGTGT
*
331805 TTTATTAACAG
1 TTTATAAACAG
331816 TTTATAAACAG
1 TTTATAAACAG
331827 TTTATAAACAG
1 TTTATAAACAG
331838 TTTA
1 TTTA
331842 ACCTATCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (11 bp):
TTTATAAACAG
Found at i:340282 original size:2 final size:2
Alignment explanation
Indices: 340275--340319 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
340265 TAAAGGTCAG
340275 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
340317 CT C
1 CT C
340320 GTAGCAATGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:347373 original size:40 final size:40
Alignment explanation
Indices: 347322--347432 Score: 197
Period size: 40 Copynumber: 2.8 Consensus size: 40
347312 TATTTCTATA
347322 TTTAGAAAGTACAGGTCAATCTGAGTTTTTAAAGCTTATT
1 TTTAGAAAGTACAGGTCAATCTGAGTTTTTAAAGCTTATT
*
347362 TTTAGAAAGTACAGGTCAATCCGAGTTTTTAAAGCTTATT
1 TTTAGAAAGTACAGGTCAATCTGAGTTTTTAAAGCTTATT
347402 TTTAGAAAGTACAGGTCAATCTGCA-TTTTTA
1 TTTAGAAAGTACAGGTCAATCTG-AGTTTTTA
347433 TACTTTGACA
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
40 67 0.99
41 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (40 bp):
TTTAGAAAGTACAGGTCAATCTGAGTTTTTAAAGCTTATT
Found at i:357311 original size:41 final size:42
Alignment explanation
Indices: 357189--357337 Score: 142
Period size: 41 Copynumber: 3.6 Consensus size: 42
357179 AAAATTTGAA
** *
357189 ATAACGAATTCAGCGAATTTGTTATAACAGA-TTAAATTCGTT
1 ATAACGAATTCA-AAAATTCGTTATAACAGATTTAAATTCGTT
* * * * *
357231 ATAACGAATTCCTAAAATTTGTTTTAACAAATTT-GATTCGTT
1 ATAACGAATT-CAAAAATTCGTTATAACAGATTTAAATTCGTT
*
357273 ATAACGGATTCAAAAATTCGTTATAAC-GATTTAAATTCGTT
1 ATAACGAATTCAAAAATTCGTTATAACAGATTTAAATTCGTT
* * * *
357314 TTAACAAATTTAAGAATTCGTTAT
1 ATAACGAATTCAAAAATTCGTTAT
357338 CTCAAATTCA
Statistics
Matches: 87, Mismatches: 17, Indels: 7
0.78 0.15 0.06
Matches are distributed among these distances:
40 4 0.05
41 40 0.46
42 40 0.46
43 3 0.03
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.39
Consensus pattern (42 bp):
ATAACGAATTCAAAAATTCGTTATAACAGATTTAAATTCGTT
Found at i:357333 original size:22 final size:21
Alignment explanation
Indices: 357204--357337 Score: 91
Period size: 19 Copynumber: 6.5 Consensus size: 21
357194 GAATTCAGCG
* *
357204 AATTTGTTATAACAGA-TT-A
1 AATTCGTTATAACAAATTTAA
*
357223 AATTCGTTATAACGAATTCCTAA
1 AATTCGTTATAACAAATT--TAA
* *
357246 AATTTGTTTTAACAAATTT--
1 AATTCGTTATAACAAATTTAA
* ** *
357265 GATTCGTTATAACGGATTCAAA
1 AATTCGTTATAACAAATT-TAA
*
357287 AATTCGTTATAAC-GATTT-A
1 AATTCGTTATAACAAATTTAA
*
357306 AATTCGTTTTAACAAATTTAA
1 AATTCGTTATAACAAATTTAA
357327 GAATTCGTTAT
1 -AATTCGTTAT
357338 CTCAAATTCA
Statistics
Matches: 88, Mismatches: 17, Indels: 17
0.72 0.14 0.14
Matches are distributed among these distances:
19 39 0.44
20 5 0.06
21 6 0.07
22 22 0.25
23 16 0.18
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.41
Consensus pattern (21 bp):
AATTCGTTATAACAAATTTAA
Found at i:357352 original size:63 final size:63
Alignment explanation
Indices: 357222--357352 Score: 160
Period size: 63 Copynumber: 2.1 Consensus size: 63
357212 ATAACAGATT
* **
357222 AAATTCGTTATAACGAATTCCTAAAATTTGTTTTAACAAATTTGATTCGTTATAACGGATTCAA
1 AAATTCGTTATAACGAATT-CTAAAATTCGTTTTAACAAATTTGATTCGTTATAACAAATTCAA
**
357286 AAATTCGTTATAACG-ATT-T-AAATTCGTTTTAACAAATTTAAGAATTCGTTATCTCAAATTCA
1 AAATTCGTTATAACGAATTCTAAAATTCGTTTTAACAAATTT--G-ATTCGTTATAACAAATTCA
357348 A
63 A
357349 AAAT
1 AAAT
357353 ATTTTTGATA
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
60 19 0.32
61 1 0.02
62 1 0.02
63 23 0.39
64 15 0.25
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39
Consensus pattern (63 bp):
AAATTCGTTATAACGAATTCTAAAATTCGTTTTAACAAATTTGATTCGTTATAACAAATTCAA
Found at i:357756 original size:2 final size:2
Alignment explanation
Indices: 357749--357797 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
357739 CATGGAAGTC
357749 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
357791 AG AG AG A
1 AG AG AG A
357798 TTAATCTATA
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:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:358343 original size:2 final size:2
Alignment explanation
Indices: 358336--358372 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
358326 GCACATTCTG
*
358336 GA GA GA GA GA GA GA GA GA GA GA GA GA GG GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
358373 TATTAATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (2 bp):
GA
Found at i:364856 original size:17 final size:17
Alignment explanation
Indices: 364836--364868 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
364826 AACCCTCAGT
364836 TTAGCCGATAACTGGTC
1 TTAGCCGATAACTGGTC
364853 TTAGCCGATAACTGGT
1 TTAGCCGATAACTGGT
364869 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:370591 original size:16 final size:16
Alignment explanation
Indices: 370567--370597 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
370557 GAATTCGTTA
*
370567 TACGGATATAACGAAT
1 TACGCATATAACGAAT
370583 TACGCATATAACGAA
1 TACGCATATAACGAA
370598 GTAATTCCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.23
Consensus pattern (16 bp):
TACGCATATAACGAAT
Found at i:370844 original size:17 final size:17
Alignment explanation
Indices: 370813--370845 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
370803 TGTTTTAAGA
370813 AAGAAAAAATAATTTTT
1 AAGAAAAAATAATTTTT
370830 AAGATAAAAAT-ATTTT
1 AAGA-AAAAATAATTTT
370846 AGTTGAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (17 bp):
AAGAAAAAATAATTTTT
Found at i:371235 original size:2 final size:2
Alignment explanation
Indices: 371228--371277 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
371218 GAAAATAATT
371228 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
371270 TC TC TC TC
1 TC TC TC TC
371278 AGTATTTGTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:371993 original size:21 final size:21
Alignment explanation
Indices: 371967--372067 Score: 112
Period size: 21 Copynumber: 4.8 Consensus size: 21
371957 ATCTGCCACC
* *
371967 ACTTGTCAGATAATTATATTG
1 ACTTGTCAGATAATTATGTCG
*
371988 ACTTGTCAGATGATTATGTCG
1 ACTTGTCAGATAATTATGTCG
* *
372009 ACTTGTCAGATATTTATGTCA
1 ACTTGTCAGATAATTATGTCG
** * *
372030 ACTTGTCAGATCTTTTTGTTG
1 ACTTGTCAGATAATTATGTCG
*
372051 ACTTGTCAGAAAATTAT
1 ACTTGTCAGATAATTAT
372068 CGTATTGAGT
Statistics
Matches: 66, Mismatches: 14, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
21 66 1.00
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.43
Consensus pattern (21 bp):
ACTTGTCAGATAATTATGTCG
Found at i:372170 original size:21 final size:21
Alignment explanation
Indices: 372139--372228 Score: 90
Period size: 21 Copynumber: 4.3 Consensus size: 21
372129 AACTTGTCAT
* *
372139 CATAATTATCTGACAAGCCGA
1 CATAATGATCTGACAAGTCGA
* * * **
372160 TATAAAGATCTGATAAGTTAA
1 CATAATGATCTGACAAGTCGA
*
372181 CATAATTATCTGACAAGTCGA
1 CATAATGATCTGACAAGTCGA
**
372202 CATAATGATCTGACAAGTTAA
1 CATAATGATCTGACAAGTCGA
372223 CATAAT
1 CATAAT
372229 AAATTGACAG
Statistics
Matches: 53, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (21 bp):
CATAATGATCTGACAAGTCGA
Found at i:372212 original size:42 final size:42
Alignment explanation
Indices: 372139--372228 Score: 144
Period size: 42 Copynumber: 2.1 Consensus size: 42
372129 AACTTGTCAT
* *
372139 CATAATTATCTGACAAGCCGATATAAAGATCTGATAAGTTAA
1 CATAATTATCTGACAAGCCGACATAAAGATCTGACAAGTTAA
* *
372181 CATAATTATCTGACAAGTCGACATAATGATCTGACAAGTTAA
1 CATAATTATCTGACAAGCCGACATAAAGATCTGACAAGTTAA
372223 CATAAT
1 CATAAT
372229 AAATTGACAG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (42 bp):
CATAATTATCTGACAAGCCGACATAAAGATCTGACAAGTTAA
Found at i:372357 original size:18 final size:21
Alignment explanation
Indices: 372274--372447 Score: 147
Period size: 21 Copynumber: 8.3 Consensus size: 21
372264 ATTCATATTA
* *
372274 TATGTTGACTTGTCAGAA-AGT
1 TATGTCGACTTGTCA-AATAAT
* * *
372295 GATGTTGACTTGTCAGAT-AT
1 TATGTCGACTTGTCAAATAAT
*
372315 TATGTCGACTTGTCAAAAAAT
1 TATGTCGACTTGTCAAATAAT
* * * *
372336 AATTTTGACTTGTCATATAAT
1 TATGTCGACTTGTCAAATAAT
372357 TATGTCGACTTGTCAAATAAT
1 TATGTCGACTTGTCAAATAAT
* * *
372378 GATGTCGACTTGTCAGATGAT
1 TATGTCGACTTGTCAAATAAT
* **
372399 TATGTCGACTTGTCAGATCCT
1 TATGTCGACTTGTCAAATAAT
*
372420 TACGTCGACTTGTCAGAA-AAT
1 TATGTCGACTTGTCA-AATAAT
372441 ATATGTC
1 -TATGTC
372448 AACTGGATGG
Statistics
Matches: 122, Mismatches: 27, Indels: 7
0.78 0.17 0.04
Matches are distributed among these distances:
20 16 0.13
21 100 0.82
22 6 0.05
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.37
Consensus pattern (21 bp):
TATGTCGACTTGTCAAATAAT
Found at i:372370 original size:42 final size:41
Alignment explanation
Indices: 372274--372413 Score: 190
Period size: 42 Copynumber: 3.4 Consensus size: 41
372264 ATTCATATTA
* * *
372274 TATGTTGACTTGTCAGAAAGTGATGTTGACTTGTCAGATAT
1 TATGTCGACTTGTCAAAAAATGATGTTGACTTGTCAGATAT
* * *
372315 TATGTCGACTTGTCAAAAAATAATTTTGACTTGTCATATAAT
1 TATGTCGACTTGTCAAAAAATGATGTTGACTTGTCAGAT-AT
* *
372357 TATGTCGACTTGTCAAATAATGATGTCGACTTGTCAGATGAT
1 TATGTCGACTTGTCAAAAAATGATGTTGACTTGTCAGAT-AT
372399 TATGTCGACTTGTCA
1 TATGTCGACTTGTCA
372414 GATCCTTACG
Statistics
Matches: 86, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
41 33 0.38
42 53 0.62
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (41 bp):
TATGTCGACTTGTCAAAAAATGATGTTGACTTGTCAGATAT
Found at i:372410 original size:63 final size:62
Alignment explanation
Indices: 372274--372434 Score: 171
Period size: 63 Copynumber: 2.6 Consensus size: 62
372264 ATTCATATTA
* * * *
372274 TATGTTGACTTGTCAGA-AAGTGATGTTGACTTGTCAGATATTATGTCGACTTGTCAAAAAAT
1 TATGTTGACTTGTCAGATAA-TTATGTCGACTTGTCAAATATGATGTCGACTTGTCAAAAAAT
* * * * **
372336 AATTTTGACTTGTCATATAATTATGTCGACTTGTCAAATAATGATGTCGACTTGTCAGATGAT
1 TATGTTGACTTGTCAGATAATTATGTCGACTTGTCAAAT-ATGATGTCGACTTGTCAAAAAAT
* ** *
372399 TATGTCGACTTGTCAGATCCTTACGTCGACTTGTCA
1 TATGTTGACTTGTCAGATAATTATGTCGACTTGTCA
372435 GAAAATATAT
Statistics
Matches: 80, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
62 30 0.38
63 50 0.62
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (62 bp):
TATGTTGACTTGTCAGATAATTATGTCGACTTGTCAAATATGATGTCGACTTGTCAAAAAAT
Found at i:372427 original size:42 final size:41
Alignment explanation
Indices: 372274--372436 Score: 166
Period size: 42 Copynumber: 3.9 Consensus size: 41
372264 ATTCATATTA
* * * *
372274 TATGTTGACTTGTCAGAA-AGTGATGTTGACTTGTCAGATAT
1 TATGTCGACTTGTCA-AATAATAATGTCGACTTGTCAGATAT
* * * *
372315 TATGTCGACTTGTCAAAAAATAATTTTGACTTGTCATATAAT
1 TATGTCGACTTGTCAAATAATAATGTCGACTTGTCAGAT-AT
*
372357 TATGTCGACTTGTCAAATAATGATGTCGACTTGTCAGATGAT
1 TATGTCGACTTGTCAAATAATAATGTCGACTTGTCAGAT-AT
* ** * *
372399 TATGTCGACTTGTCAGATCCTTACGTCGACTTGTCAGA
1 TATGTCGACTTGTCAAATAATAATGTCGACTTGTCAGA
372437 AAATATATGT
Statistics
Matches: 104, Mismatches: 16, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
40 2 0.02
41 31 0.30
42 71 0.68
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (41 bp):
TATGTCGACTTGTCAAATAATAATGTCGACTTGTCAGATAT
Found at i:372539 original size:21 final size:21
Alignment explanation
Indices: 372513--372583 Score: 92
Period size: 21 Copynumber: 3.4 Consensus size: 21
372503 CGTGAATAAA
372513 TGACAAGTCGACATAATTATC
1 TGACAAGTCGACATAATTATC
*
372534 TGACAAGTCGACATCAA-GATC
1 TGACAAGTCGACAT-AATTATC
*
372555 TGACAAGTCGACAT-GTATATC
1 TGACAAGTCGACATAAT-TATC
372576 TGACAAGT
1 TGACAAGT
372584 GGTGGCAGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
21 42 0.95
22 2 0.05
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (21 bp):
TGACAAGTCGACATAATTATC
Found at i:401792 original size:2 final size:2
Alignment explanation
Indices: 401787--401844 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
401777 CACACACACA
401787 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
401829 CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT
401845 AAAAATAAAG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:403070 original size:19 final size:17
Alignment explanation
Indices: 403036--403074 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
403026 CGTGTGAGTT
*
403036 AAAATAAAATTTAGAATA
1 AAAAAAAAATTTAGAA-A
403054 AAAAAAAAATTTAAGAAA
1 AAAAAAAAATTT-AGAAA
403072 AAA
1 AAA
403075 GTTAAAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (17 bp):
AAAAAAAAATTTAGAAA
Found at i:405840 original size:13 final size:13
Alignment explanation
Indices: 405822--405847 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
405812 TAAAGGGCTA
405822 AGACTTTTAAAAG
1 AGACTTTTAAAAG
405835 AGACTTTTAAAAG
1 AGACTTTTAAAAG
405848 TTTTCGTTAG
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:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (13 bp):
AGACTTTTAAAAG
Found at i:429015 original size:20 final size:20
Alignment explanation
Indices: 428990--429053 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
428980 AGGGGCATGC
*
428990 ACAGGGGTAT-ACAGTGGCTT
1 ACAGGGG-ATGACAGTGGCGT
429010 ACAGGGGATGACAGTGGCGT
1 ACAGGGGATGACAGTGGCGT
* * *
429030 ACAGGGGGTGACAGGGGCTT
1 ACAGGGGATGACAGTGGCGT
429050 ACAG
1 ACAG
429054 TGGCACACAG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 2 0.05
20 37 0.95
ACGTcount: A:0.25, C:0.16, G:0.42, T:0.17
Consensus pattern (20 bp):
ACAGGGGATGACAGTGGCGT
Found at i:429044 original size:30 final size:30
Alignment explanation
Indices: 429010--429180 Score: 105
Period size: 32 Copynumber: 5.5 Consensus size: 30
429000 ACAGTGGCTT
**
429010 ACAGGGGATGACAGTGGCGTACAGGGGGTG
1 ACAGGGGATGACAGTGGCACACAGGGGGTG
* *
429040 ACAGGGGCTTACAGTGGCACACAGGGGTTGTG
1 ACAGGGGATGACAGTGGCACACAGGGG--GTG
* * * **
429072 TACAGGGG-CGCACAG-GGGATGACAGGGTAT-
1 -ACAGGGGATG-ACAGTGGCA-CACAGGGGGTG
* *
429102 ACAGGGGCTCTGTACAGTGGCACACAGGGGATG
1 ACAGGGG--ATG-ACAGTGGCACACAGGGGGTG
**
429135 TACAGGGGATGACAGTGAAAACACAGGGGGTG
1 -ACAGGGGATGACAGTG-GCACACAGGGGGTG
*
429167 ACAGGGGAAGACAG
1 ACAGGGGATGACAG
429181 GGGATTTTCA
Statistics
Matches: 109, Mismatches: 20, Indels: 23
0.72 0.13 0.15
Matches are distributed among these distances:
29 7 0.06
30 23 0.21
31 20 0.18
32 32 0.29
33 20 0.18
34 7 0.06
ACGTcount: A:0.27, C:0.16, G:0.43, T:0.13
Consensus pattern (30 bp):
ACAGGGGATGACAGTGGCACACAGGGGGTG
Found at i:429128 original size:23 final size:22
Alignment explanation
Indices: 429049--429139 Score: 82
Period size: 23 Copynumber: 4.2 Consensus size: 22
429039 GACAGGGGCT
*
429049 TACAGTGGCACACAGGGGTTGTG
1 TACAGTGGCACACAGGGG-TATG
* *
429072 TACAGGGGCGCACAGGGG-ATG
1 TACAGTGGCACACAGGGGTATG
* * *
429093 -ACAG-GGTATACAGGGGCTCTG
1 TACAGTGGCACACAGGGG-TATG
429114 TACAGTGGCACACAGGGG-ATG
1 TACAGTGGCACACAGGGGTATG
429135 TACAG
1 TACAG
429140 GGGATGACAG
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
19 9 0.17
20 4 0.07
21 11 0.20
22 4 0.07
23 26 0.48
ACGTcount: A:0.25, C:0.19, G:0.40, T:0.16
Consensus pattern (22 bp):
TACAGTGGCACACAGGGGTATG
Found at i:429128 original size:42 final size:43
Alignment explanation
Indices: 429060--429141 Score: 121
Period size: 42 Copynumber: 1.9 Consensus size: 43
429050 ACAGTGGCAC
* * *
429060 ACAGGGGTTGTGTACAGGGGCGCACAGGGGATG-ACAGGGTAT
1 ACAGGGGCTCTGTACAGGGGCACACAGGGGATGTACAGGGTAT
*
429102 ACAGGGGCTCTGTACAGTGGCACACAGGGGATGTACAGGG
1 ACAGGGGCTCTGTACAGGGGCACACAGGGGATGTACAGGG
429142 GATGACAGTG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
42 29 0.83
43 6 0.17
ACGTcount: A:0.24, C:0.17, G:0.43, T:0.16
Consensus pattern (43 bp):
ACAGGGGCTCTGTACAGGGGCACACAGGGGATGTACAGGGTAT
Found at i:429141 original size:11 final size:10
Alignment explanation
Indices: 429125--429185 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
429115 ACAGTGGCAC
429125 ACAGGGGATG
1 ACAGGGGATG
429135 TACAGGGGATG
1 -ACAGGGGATG
** **
429146 ACAGTGAAAAC
1 ACAG-GGGATG
*
429157 ACAGGGGGTG
1 ACAGGGGATG
*
429167 ACAGGGGAAG
1 ACAGGGGATG
429177 ACAGGGGAT
1 ACAGGGGAT
429186 TTTCATACGG
Statistics
Matches: 37, Mismatches: 12, Indels: 3
0.71 0.23 0.06
Matches are distributed among these distances:
10 21 0.57
11 16 0.43
ACGTcount: A:0.34, C:0.11, G:0.44, T:0.10
Consensus pattern (10 bp):
ACAGGGGATG
Found at i:432933 original size:12 final size:13
Alignment explanation
Indices: 432910--432939 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
432900 TAGCAGCTAG
432910 TTTTTCATTTTTT
1 TTTTTCATTTTTT
432923 TTTTTCATTTTTT
1 TTTTTCATTTTTT
432936 TTTT
1 TTTT
432940 AACACATGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTTCATTTTTT
Done.