Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A08
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 123748673
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5630000 characters in sequence are not A, C, G, or T
File 32 of 373
Found at i:9045938 original size:2 final size:2
Alignment explanation
Indices: 9045931--9045955 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9045921 ATACCTTTTC
9045931 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
9045956 ATTTTATTCT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:9062388 original size:224 final size:224
Alignment explanation
Indices: 9061998--9062440 Score: 735
Period size: 224 Copynumber: 2.0 Consensus size: 224
9061988 ACCTACTAAC
* *
9061998 TCAATATTCCCACAACACGAAACATCCTTAACTAGCTGGATTGTCAACAATACATTGATTCCACC
1 TCAATATTCCCACAACACAAAACATCCTTAACTAGCTGGATTGCCAACAATACATTGATTCCACC
*
9062063 CCTTATGTCTCGACTCACCAATACAACACATTATTGTTGTCAGGTATCCAAGATACATATACAAT
66 CCTTATGTCTCGACTCACCAATACAACACATTATTGTTGTCAGGAATCCAAGATACATATACAAT
* * * *
9062128 CAACAAAAAGAACTAATAAAACATTAATATTATCAAGGAAATTTAAGCCAAGAACGAAGTTGAAA
131 CAAAAAAAAGAACTAATAAAACATTAATATTATCAAGGAAATTCAAGCCAAGAACAAAGTCGAAA
*
9062193 TCATCCAAGTGAATGACCTCAAAAGCTTG
196 TCATCCAAGTGAACGACCTCAAAAGCTTG
* *
9062222 TCAATATTCCTACAACACAAAACATCTTTAACTAGCTGGATTGCCAACAATACATTGATTCCACC
1 TCAATATTCCCACAACACAAAACATCCTTAACTAGCTGGATTGCCAACAATACATTGATTCCACC
* * *
9062287 CCTTATGTCTTGACTCACCAATACAACACATTATTGTTTTCGGGAATCCAAGATACATATACAAT
66 CCTTATGTCTCGACTCACCAATACAACACATTATTGTTGTCAGGAATCCAAGATACATATACAAT
* *
9062352 -AGAAAAAAAGAACTAATAAAGCATTAATATTATCAAGGAAATTCAAGCTAAGAACAAAGTCGAA
131 CA-AAAAAAAGAACTAATAAAACATTAATATTATCAAGGAAATTCAAGCCAAGAACAAAGTCGAA
9062416 ATCATCCAAGTGAACGACCTCAAAA
195 ATCATCCAAGTGAACGACCTCAAAA
9062441 CCTTTATTAT
Statistics
Matches: 203, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
223 1 0.00
224 202 1.00
ACGTcount: A:0.42, C:0.22, G:0.11, T:0.25
Consensus pattern (224 bp):
TCAATATTCCCACAACACAAAACATCCTTAACTAGCTGGATTGCCAACAATACATTGATTCCACC
CCTTATGTCTCGACTCACCAATACAACACATTATTGTTGTCAGGAATCCAAGATACATATACAAT
CAAAAAAAAGAACTAATAAAACATTAATATTATCAAGGAAATTCAAGCCAAGAACAAAGTCGAAA
TCATCCAAGTGAACGACCTCAAAAGCTTG
Found at i:9063324 original size:31 final size:31
Alignment explanation
Indices: 9063282--9063347 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
9063272 ATAAATTACA
*
9063282 ATTT-AGTCACTAAATTATTTGAAAA-TTTTC
1 ATTTAAGTCACTAAACTATTT-AAAAGTTTTC
*
9063312 ATTTAAGTCACTAAACTATTTAAAAGTTTTT
1 ATTTAAGTCACTAAACTATTTAAAAGTTTTC
9063343 ATTTA
1 ATTTA
9063348 TATGATTAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
30 8 0.25
31 24 0.75
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (31 bp):
ATTTAAGTCACTAAACTATTTAAAAGTTTTC
Found at i:9070379 original size:14 final size:14
Alignment explanation
Indices: 9070360--9070391 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
9070350 GTCGCTTCAC
9070360 CACACTTCACATGG
1 CACACTTCACATGG
*
9070374 CACACTTCGCATGG
1 CACACTTCACATGG
9070388 CACA
1 CACA
9070392 ACAAGCATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.28, C:0.38, G:0.16, T:0.19
Consensus pattern (14 bp):
CACACTTCACATGG
Found at i:9071981 original size:18 final size:18
Alignment explanation
Indices: 9071958--9071995 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
9071948 ACACAATAAA
9071958 ATATGTCAATAACAAAAT
1 ATATGTCAATAACAAAAT
*
9071976 ATATGTCAATAACATAAT
1 ATATGTCAATAACAAAAT
9071994 AT
1 AT
9071996 TTTCACAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATATGTCAATAACAAAAT
Found at i:9076036 original size:16 final size:16
Alignment explanation
Indices: 9076011--9076056 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
9076001 GTCTAGGCTG
*
9076011 GGTTTGGGGTGTTTAA
1 GGTTTAGGGTGTTTAA
*
9076027 GGTTTAGGGTGTTTAG
1 GGTTTAGGGTGTTTAA
9076043 GGTTTAGGGT-TTTA
1 GGTTTAGGGTGTTTA
9076057 GTAAAGTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
15 4 0.14
16 24 0.86
ACGTcount: A:0.13, C:0.00, G:0.41, T:0.46
Consensus pattern (16 bp):
GGTTTAGGGTGTTTAA
Found at i:9086917 original size:20 final size:20
Alignment explanation
Indices: 9086881--9086919 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
9086871 AGAAAATTTA
9086881 AAAAATAAAAAATAAAATCT
1 AAAAATAAAAAATAAAATCT
*
9086901 AAAAA-AAAGAATCAAAATC
1 AAAAATAAAAAAT-AAAATC
9086920 ATTTATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.74, C:0.08, G:0.03, T:0.15
Consensus pattern (20 bp):
AAAAATAAAAAATAAAATCT
Found at i:9091670 original size:65 final size:62
Alignment explanation
Indices: 9091601--9091722 Score: 163
Period size: 62 Copynumber: 1.9 Consensus size: 62
9091591 CATCAAGGAT
*
9091601 TTTTTTCATGTCCCAATGCAATTTATTTTTTTTACTTTTCTACACTAATAGCCGACACCAGAGAC
1 TTTTTTCATGTCCCAATACAA--T-TTTTTTTTACTTTTCTACACTAATAGCCGACACCAGAGAC
** * * *
9091666 TTTTTTTGTGTCCCAATACAATTTTTTTTTACTTTTCTACACTGATGGCCGGCACCA
1 TTTTTTCATGTCCCAATACAATTTTTTTTTACTTTTCTACACTAATAGCCGACACCA
9091723 AACCAGTAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
62 32 0.63
63 1 0.02
65 18 0.35
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.43
Consensus pattern (62 bp):
TTTTTTCATGTCCCAATACAATTTTTTTTTACTTTTCTACACTAATAGCCGACACCAGAGAC
Found at i:9091803 original size:48 final size:47
Alignment explanation
Indices: 9091738--9092015 Score: 278
Period size: 47 Copynumber: 5.9 Consensus size: 47
9091728 GTAATTTTTT
9091738 TTTTGTTCTAGCCTTCTAATGGCCGGCACCACACTAGTAAAAAAAAAA
1 TTTTGTTCTAGCCTTCTAATGGCCGGCACCACACTAGT-AAAAAAAAA
* *
9091786 TTTTGTTCTAGCCTTCTAATGGCTGGCACTACACTAGTAAAAAAAAA
1 TTTTGTTCTAGCCTTCTAATGGCCGGCACCACACTAGTAAAAAAAAA
* * * * * * *
9091833 ATTGGTACTCGCATTCTAATGGCCAGCACCACACTAGTAAAAAAAAT
1 TTTTGTTCTAGCCTTCTAATGGCCGGCACCACACTAGTAAAAAAAAA
* * *****
9091880 TTTTGATT-TTGTCCTTCTAATAGCCGGCACCACACTAGT---ATTTTT
1 TTTTG-TTCTAG-CCTTCTAATGGCCGGCACCACACTAGTAAAAAAAAA
**
9091925 TTTTGTTCT-GCCCTTCTAATGGTTGGCACCACACTAGTAAAAAAAAA
1 TTTTGTTCTAG-CCTTCTAATGGCCGGCACCACACTAGTAAAAAAAAA
* ** * *
9091972 TTTGGTTCTAGCCTTCTAATGGTTGGTACTACACTAGTAAAAAA
1 TTTTGTTCTAGCCTTCTAATGGCCGGCACCACACTAGTAAAAAA
9092016 TTTTTTTAAA
Statistics
Matches: 189, Mismatches: 34, Indels: 15
0.79 0.14 0.06
Matches are distributed among these distances:
44 27 0.14
45 8 0.04
47 92 0.49
48 62 0.33
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (47 bp):
TTTTGTTCTAGCCTTCTAATGGCCGGCACCACACTAGTAAAAAAAAA
Found at i:9091850 original size:47 final size:48
Alignment explanation
Indices: 9091745--9091919 Score: 192
Period size: 48 Copynumber: 3.7 Consensus size: 48
9091735 TTTTTTTGTT
* * *
9091745 CTAGCCTTCTAATGGCCGGCACCACACTAGTAAAAAAAAAATTTTGTT
1 CTAGCATTCTAATGGCCGGCACCACACTAGTAAAAAAAAAATTTGGTA
* * *
9091793 CTAGCCTTCTAATGGCTGGCACTACACTAGTAAAAAAAAAA-TTGGTA
1 CTAGCATTCTAATGGCCGGCACCACACTAGTAAAAAAAAAATTTGGTA
* * ** *
9091840 CTCGCATTCTAATGGCCAGCACCACACTAGTAAAAAAAATTTTTGAT-
1 CTAGCATTCTAATGGCCGGCACCACACTAGTAAAAAAAAAATTTGGTA
* * * *
9091887 TTTGTCCTTCTAATAGCCGGCACCACACTAGTA
1 CTAG-CATTCTAATGGCCGGCACCACACTAGTA
9091920 TTTTTTTTTG
Statistics
Matches: 108, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
47 40 0.37
48 68 0.63
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.27
Consensus pattern (48 bp):
CTAGCATTCTAATGGCCGGCACCACACTAGTAAAAAAAAAATTTGGTA
Found at i:9092511 original size:137 final size:135
Alignment explanation
Indices: 9092228--9092490 Score: 367
Period size: 137 Copynumber: 2.0 Consensus size: 135
9092218 AAGGCCAGAA
*
9092228 CCAAAAAAAAATTACTAGTGTGGTGCCGGCCATTACAAGACCAGAACTAATTTTTTTTAAATACT
1 CCAAAAAAAAATTACTAGTGTGGTGCCGGCCATTACAAGACCAGAACAAATTTTTTTTAAATACT
* * * *
9092293 GGTATTTTTGTATACCAGTATGATACGATTTTAAAAAAAATACCATAGTCCCTGCTGCTGGCCAT
66 AGTATTTTTGTATACCAGTACGATACGATTTT-AAAAAAATA-CATAGTCCCTGATGCTGACCAT
*
9092358 TAGAAGG
129 TAGAAGC
* *
9092365 CCAAAAAAAAATTACTAGTGTGGTGCCGGCCATTACAAGGCCAGATCCAAATTTTTTTTTTAAAT
1 CCAAAAAAAAATTACTAGTGTGGTGCCGGCCATTACAAGACCAGA-ACAAA--TTTTTTTTAAAT
9092430 ACTAGTATTTTTGTATACCAGTACGATACGA-TTT-AAAAAA-A-ATA-T-CCTGATGCTGACCA
63 ACTAGTATTTTTGTATACCAGTACGATACGATTTTAAAAAAATACATAGTCCCTGATGCTGACCA
9092489 TT
128 TT
9092491 GGATTCCCAA
Statistics
Matches: 116, Mismatches: 7, Indels: 11
0.87 0.05 0.08
Matches are distributed among these distances:
132 14 0.12
133 1 0.01
134 3 0.03
136 1 0.01
137 50 0.43
138 3 0.03
139 3 0.03
140 41 0.35
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (135 bp):
CCAAAAAAAAATTACTAGTGTGGTGCCGGCCATTACAAGACCAGAACAAATTTTTTTTAAATACT
AGTATTTTTGTATACCAGTACGATACGATTTTAAAAAAATACATAGTCCCTGATGCTGACCATTA
GAAGC
Found at i:9095700 original size:20 final size:20
Alignment explanation
Indices: 9095672--9095709 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
9095662 AAAAATAATT
9095672 ATAACTATTATATATATTAA
1 ATAACTATTATATATATTAA
* *
9095692 ATAATTATTATTTATATT
1 ATAACTATTATATATATT
9095710 TATATTAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
ATAACTATTATATATATTAA
Found at i:9100522 original size:9 final size:9
Alignment explanation
Indices: 9100508--9100536 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
9100498 AATTAAATAG
9100508 TTTGAGTTA
1 TTTGAGTTA
9100517 TTTGAGTTA
1 TTTGAGTTA
9100526 TTTGAGTTA
1 TTTGAGTTA
9100535 TT
1 TT
9100537 CGGATAAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.59
Consensus pattern (9 bp):
TTTGAGTTA
Found at i:9102357 original size:24 final size:23
Alignment explanation
Indices: 9102330--9102375 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
9102320 AATCATAGTA
*
9102330 TTGCATCGAAGTGTCACATTTCAG
1 TTGCACCGAAGTGTCAC-TTTCAG
9102354 TTGCACCGAAGTGTCACTTTCA
1 TTGCACCGAAGTGTCACTTTCA
9102376 TTTTCACACA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (23 bp):
TTGCACCGAAGTGTCACTTTCAG
Found at i:9113276 original size:22 final size:23
Alignment explanation
Indices: 9113243--9113285 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
9113233 ACATAACACG
9113243 TTGAGTATTTATT-TTTTAAACC
1 TTGAGTATTTATTGTTTTAAACC
9113265 TTGA-TATATTATTGTTTTAAA
1 TTGAGTAT-TTATTGTTTTAAA
9113286 AATAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 3 0.16
22 9 0.47
23 7 0.37
ACGTcount: A:0.30, C:0.05, G:0.09, T:0.56
Consensus pattern (23 bp):
TTGAGTATTTATTGTTTTAAACC
Found at i:9115254 original size:31 final size:31
Alignment explanation
Indices: 9115186--9115255 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
9115176 ACTTAATGAC
9115186 TTAGTGACTTAAATAAAGACTTTCAAATAGT
1 TTAGTGACTTAAATAAAGACTTTCAAATAGT
* * *
9115217 TCAGTGACTTAAATGAAA-ATTTTCCAATTA-T
1 TTAGTGACTTAAAT-AAAGACTTT-CAAATAGT
9115248 TTAGTGAC
1 TTAGTGAC
9115256 CATTTTTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
31 25 0.76
32 8 0.24
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (31 bp):
TTAGTGACTTAAATAAAGACTTTCAAATAGT
Found at i:9127502 original size:22 final size:19
Alignment explanation
Indices: 9127454--9127503 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
9127444 CCGTTATTAG
*
9127454 TTTGATTGTAATGATTGAA
1 TTTGATTATAATGATTGAA
*
9127473 TTTGATTATAATTATTCGAA
1 TTTGATTATAATGATT-GAA
9127493 TATTGTATTAT
1 T-TTG-ATTAT
9127504 TTGTGAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 14 0.54
20 4 0.15
21 3 0.12
22 5 0.19
ACGTcount: A:0.32, C:0.02, G:0.14, T:0.52
Consensus pattern (19 bp):
TTTGATTATAATGATTGAA
Found at i:9129357 original size:13 final size:13
Alignment explanation
Indices: 9129339--9129371 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
9129329 ATTTTGTGGA
9129339 TAAAAAATATTTT
1 TAAAAAATATTTT
9129352 T-AAAAATATTTT
1 TAAAAAATATTTT
9129364 TAATAAAA
1 TAA-AAAA
9129372 ATAATCATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 12 0.67
13 2 0.11
14 4 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TAAAAAATATTTT
Found at i:9129358 original size:12 final size:12
Alignment explanation
Indices: 9129341--9129366 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
9129331 TTTGTGGATA
9129341 AAAAATATTTTT
1 AAAAATATTTTT
9129353 AAAAATATTTTT
1 AAAAATATTTTT
9129365 AA
1 AA
9129367 TAAAAATAAT
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
AAAAATATTTTT
Found at i:9129592 original size:22 final size:20
Alignment explanation
Indices: 9129553--9129592 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
9129543 TCAGTTCCTC
*
9129553 TTTTTTTCCATTTTCTTTAA
1 TTTTTTTCCATTTCCTTTAA
9129573 TTTTTTTCCACCTTTCCTTT
1 TTTTTTTCCA--TTTCCTTT
9129593 TTTACTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.10, C:0.23, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTTTTCCATTTCCTTTAA
Found at i:9129656 original size:9 final size:9
Alignment explanation
Indices: 9129642--9129674 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
9129632 TCTCCCTTAC
9129642 TCTTTTTCT
1 TCTTTTTCT
9129651 TCTTTTTCT
1 TCTTTTTCT
*
9129660 TCTTCTTCT
1 TCTTTTTCT
9129669 T-TTTTT
1 TCTTTTT
9129675 TTACTTCCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 4 0.18
9 18 0.82
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (9 bp):
TCTTTTTCT
Found at i:9135338 original size:19 final size:19
Alignment explanation
Indices: 9135314--9135352 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
9135304 TCATAAAAAA
9135314 AGTAAAAAAAATAGTGCAT
1 AGTAAAAAAAATAGTGCAT
9135333 AGTAAAAAAAATAGTGCAT
1 AGTAAAAAAAATAGTGCAT
9135352 A
1 A
9135353 CCTCCCAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.59, C:0.05, G:0.15, T:0.21
Consensus pattern (19 bp):
AGTAAAAAAAATAGTGCAT
Found at i:9138890 original size:11 final size:11
Alignment explanation
Indices: 9138874--9138932 Score: 73
Period size: 11 Copynumber: 5.2 Consensus size: 11
9138864 CTTTATATAC
9138874 TAATAAAATAA
1 TAATAAAATAA
9138885 TAATAAAATAA
1 TAATAAAATAA
*
9138896 TAATAAAATATCT
1 TAATAAAATA--A
* *
9138909 TATTAAAATAT
1 TAATAAAATAA
9138920 TAATAAAATAA
1 TAATAAAATAA
9138931 TA
1 TA
9138933 TTTATCTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
11 33 0.79
13 9 0.21
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:9140789 original size:2 final size:2
Alignment explanation
Indices: 9140782--9140821 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
9140772 TAACATAAAA
9140782 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
9140822 CCCATATATG
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:9149962 original size:34 final size:34
Alignment explanation
Indices: 9149823--9149981 Score: 203
Period size: 35 Copynumber: 4.6 Consensus size: 34
9149813 ATTGAAATGT
* * * *
9149823 CATACTTACATTTCACAACTCGGTATGGGA-AATGC
1 CATACCTACGTTTCACAACT-AGTAT-GGATAATAC
**
9149858 CATACCTACGTTTCTTAACTCAGTATGGATAATAC
1 CATACCTACGTTTCACAACT-AGTATGGATAATAC
*
9149893 CATACCTACGTTTCACAACTTAGTATGGTTAATAC
1 CATACCTACGTTTCACAAC-TAGTATGGATAATAC
*
9149928 CATACCTACGTTTCACAACTAGTATGGATGATAC
1 CATACCTACGTTTCACAACTAGTATGGATAATAC
9149962 CATACCTACGTTTCACAACT
1 CATACCTACGTTTCACAACT
9149982 TTGCCATGGA
Statistics
Matches: 111, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
34 36 0.32
35 74 0.67
36 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.31
Consensus pattern (34 bp):
CATACCTACGTTTCACAACTAGTATGGATAATAC
Found at i:9149999 original size:69 final size:70
Alignment explanation
Indices: 9149857--9149992 Score: 202
Period size: 69 Copynumber: 1.9 Consensus size: 70
9149847 ATGGGAAATG
** * *
9149857 CCATACCTACGTTTCTTAACTCAGTATGGATAATACCATACCTACGTTTCACAACTTAGTATGGT
1 CCATACCTACGTTTCACAACTCAGTATGGATAATACCATACCTACGTTTCACAACTTAGCATGGA
9149922 TAATA
66 TAATA
* *
9149927 CCATACCTACGTTTCACAACT-AGTATGGATGATACCATACCTACGTTTCACAACTTTGCCATGG
1 CCATACCTACGTTTCACAACTCAGTATGGATAATACCATACCTACGTTTCACAACTTAG-CATGG
9149991 AT
65 AT
9149993 CAACCATGGT
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
69 35 0.59
70 24 0.41
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.32
Consensus pattern (70 bp):
CCATACCTACGTTTCACAACTCAGTATGGATAATACCATACCTACGTTTCACAACTTAGCATGGA
TAATA
Found at i:9150274 original size:16 final size:16
Alignment explanation
Indices: 9150253--9150283 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
9150243 CTTTTCCTCA
9150253 TTCGTCTTTTGATTCG
1 TTCGTCTTTTGATTCG
9150269 TTCGTCTTTTGATTC
1 TTCGTCTTTTGATTC
9150284 TTGATCTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.19, G:0.16, T:0.58
Consensus pattern (16 bp):
TTCGTCTTTTGATTCG
Found at i:9155329 original size:7 final size:7
Alignment explanation
Indices: 9155317--9155351 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
9155307 GTAACTTCTG
9155317 GAAAAAA
1 GAAAAAA
9155324 GAAAAAA
1 GAAAAAA
9155331 GAAAAAA
1 GAAAAAA
9155338 GAAAAAA
1 GAAAAAA
9155345 GAAAAAA
1 GAAAAAA
9155352 TGCTTTTGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:9162930 original size:24 final size:23
Alignment explanation
Indices: 9162903--9162962 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 23
9162893 TAGAGGTGAG
9162903 GAGAAAAGAAAAAGGAGGAGAAAA
1 GAGAAAAGAAAAAGGA-GAGAAAA
** *
9162927 GAGAAATA-AAAGTGGAGAGAAAT
1 GAGAAA-AGAAAAAGGAGAGAAAA
9162950 GAAGAAAAGAAAA
1 G-AGAAAAGAAAA
9162963 GAGAAAGAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
23 8 0.28
24 20 0.69
25 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.30, T:0.05
Consensus pattern (23 bp):
GAGAAAAGAAAAAGGAGAGAAAA
Found at i:9163015 original size:34 final size:34
Alignment explanation
Indices: 9162951--9163016 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 34
9162941 GAGAGAAATG
* *
9162951 AAGAAAAGAAAAGAGAAAGAGAGGAGAAAGGGGA
1 AAGAAAAGAAAAGAAAAAGAGAAGAGAAAGGGGA
9162985 AAGAAAAGAAAA-AAAAATGGAGAAGA-AAAGGG
1 AAGAAAAGAAAAGAAAAA--GAGAAGAGAAAGGG
9163017 TGGCTGGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 4 0.14
34 18 0.64
35 6 0.21
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (34 bp):
AAGAAAAGAAAAGAAAAAGAGAAGAGAAAGGGGA
Found at i:9177353 original size:16 final size:17
Alignment explanation
Indices: 9177332--9177368 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
9177322 ACTTGAAATT
9177332 TATTAAAT-TATTAAAA
1 TATTAAATATATTAAAA
*
9177348 TATTAATTATATTAAAA
1 TATTAAATATATTAAAA
9177365 -ATTA
1 TATTA
9177369 TAAGATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TATTAAATATATTAAAA
Found at i:9182371 original size:19 final size:22
Alignment explanation
Indices: 9182327--9182373 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 22
9182317 ATTGAGTGGT
*
9182327 TAATTAGACTTTAATTAAGTAA
1 TAATTAGACTTTAATTAAGGAA
9182349 -AATTAG-C-TTAATT-AGGAA
1 TAATTAGACTTTAATTAAGGAA
9182367 TAATTAG
1 TAATTAG
9182374 TGGAAAGGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 4 0.17
19 12 0.52
20 1 0.04
21 6 0.26
ACGTcount: A:0.45, C:0.04, G:0.13, T:0.38
Consensus pattern (22 bp):
TAATTAGACTTTAATTAAGGAA
Found at i:9182705 original size:5 final size:5
Alignment explanation
Indices: 9182681--9182736 Score: 67
Period size: 5 Copynumber: 10.6 Consensus size: 5
9182671 AAGAAATTGT
* *
9182681 TATTA TATGA TATTA TTATTA TATTA TAGTA TATTA TATTATA TATTA
1 TATTA TATTA TATTA -TATTA TATTA TATTA TATTA TA-T-TA TATTA
9182729 TATTA TAT
1 TATTA TAT
9182737 AAATAAGTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
5 33 0.75
6 7 0.16
7 4 0.09
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (5 bp):
TATTA
Found at i:9182727 original size:12 final size:12
Alignment explanation
Indices: 9182684--9182737 Score: 65
Period size: 12 Copynumber: 4.3 Consensus size: 12
9182674 AAATTGTTAT
*
9182684 TATATGATATTA
1 TATATTATATTA
9182696 T-TATTATATTATA
1 TATATTATA-T-TA
9182709 GTATATTATATTA
1 -TATATTATATTA
9182722 TATATTATATTA
1 TATATTATATTA
9182734 TATA
1 TATA
9182738 AATAAGTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
11 6 0.16
12 18 0.49
13 4 0.11
14 2 0.05
15 7 0.19
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.56
Consensus pattern (12 bp):
TATATTATATTA
Found at i:9182805 original size:29 final size:30
Alignment explanation
Indices: 9182767--9182829 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 30
9182757 GAAACAGAAT
* *
9182767 GAAAGCAAACTAAACAGAG-AAGAACAGGGA
1 GAAAGCAAACGAAACAAAGAAAGAA-AGGGA
*
9182797 GAAAG-AAACGAAAGAAAGAAAGAAAGGGA
1 GAAAGCAAACGAAACAAAGAAAGAAAGGGA
9182826 GAAA
1 GAAA
9182830 AGGGAAAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 19 0.66
30 10 0.34
ACGTcount: A:0.62, C:0.08, G:0.29, T:0.02
Consensus pattern (30 bp):
GAAAGCAAACGAAACAAAGAAAGAAAGGGA
Found at i:9183852 original size:15 final size:15
Alignment explanation
Indices: 9183832--9183888 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
9183822 CGATGAATTT
9183832 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* *
9183847 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
9183862 ATTGAATTTATATTG
1 ATTGAATTTATATTG
9183877 ATTGAA-TTATAT
1 ATTGAATTTATAT
9183889 AATATATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
14 6 0.16
15 32 0.84
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:9184291 original size:23 final size:23
Alignment explanation
Indices: 9184261--9184305 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
9184251 GCTTTATCGA
* *
9184261 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
9184284 TCAGGCACCTCGTGTGTCGTAT
1 TCAGGCACCTCATGTGTCGTAT
9184306 CGGCACGTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:9184316 original size:17 final size:18
Alignment explanation
Indices: 9184294--9184329 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
9184284 TCAGGCACCT
9184294 CGTGTGTCGTATC-GGCA
1 CGTGTGTCGTATCAGGCA
*
9184311 CGTGTGTTGTATCAGGCA
1 CGTGTGTCGTATCAGGCA
9184329 C
1 C
9184330 CTCGTGCGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.14, C:0.22, G:0.33, T:0.31
Consensus pattern (18 bp):
CGTGTGTCGTATCAGGCA
Found at i:9187248 original size:103 final size:103
Alignment explanation
Indices: 9187065--9187255 Score: 242
Period size: 103 Copynumber: 1.9 Consensus size: 103
9187055 CTATGGAGAC
* * *
9187065 TTTGGTGTGGTGAAGGGATGATATAATACATGACATGTAATAGTGCCTACGAGCTTTACATTACG
1 TTTGGTGTGGTGAAGGGATGATACAATACATGACACGTAATAGTGCCTACGAGCTTTACACTACG
*
9187130 GTGCATTGATATGGTGTAGTTATCACTCTTTTGAGCTA
66 GTGCATCGATATGGTGTAGTTATCACTCTTTTGAGCTA
* * * * *
9187168 TTTGGTGTGGTGGAGGGATGATACATTACATGATACG-ATATTGTGCCTAC-AGGCTTTGCACTA
1 TTTGGTGTGGTGAAGGGATGATACAATACATGACACGTA-ATAGTGCCTACGA-GCTTTACACTA
* * *
9187231 TGGTGCCTCGATGTGGTGTAGTTAT
64 CGGTGCATCGATATGGTGTAGTTAT
9187256 TGAGCTACCT
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
102 2 0.03
103 72 0.97
ACGTcount: A:0.24, C:0.13, G:0.28, T:0.36
Consensus pattern (103 bp):
TTTGGTGTGGTGAAGGGATGATACAATACATGACACGTAATAGTGCCTACGAGCTTTACACTACG
GTGCATCGATATGGTGTAGTTATCACTCTTTTGAGCTA
Found at i:9191403 original size:20 final size:20
Alignment explanation
Indices: 9191376--9191433 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
9191366 ATATTGGTTA
9191376 GCACTTTGGTGCCTCTGTTT
1 GCACTTTGGTGCCTCTGTTT
*
9191396 GTACTTTGGTGTCC-CTGTTT
1 GCACTTTGGTG-CCTCTGTTT
*
9191416 GCACTTCGGTGCCTCTGT
1 GCACTTTGGTGCCTCTGT
9191434 ATAGCATTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 2 0.06
20 29 0.88
21 2 0.06
ACGTcount: A:0.05, C:0.26, G:0.26, T:0.43
Consensus pattern (20 bp):
GCACTTTGGTGCCTCTGTTT
Found at i:9209720 original size:21 final size:19
Alignment explanation
Indices: 9209695--9209739 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
9209685 TCAATATAAA
9209695 TTTTAAAATTATTATTAT-TAT
1 TTTTAAAA-TA-T-TTATGTAT
9209716 TTTTAAAATATTTATGTAT
1 TTTTAAAATATTTATGTAT
9209735 TTTTA
1 TTTTA
9209740 TATATTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.17
19 9 0.39
20 2 0.09
21 8 0.35
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTTAAAATATTTATGTAT
Found at i:9213371 original size:16 final size:15
Alignment explanation
Indices: 9213345--9213374 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
9213335 CTACATACAC
9213345 AAAGTTGTTCTTTGA
1 AAAGTTGTTCTTTGA
9213360 AAAGTATGTTCTTTG
1 AAAGT-TGTTCTTTG
9213375 CTTGCGAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.07, G:0.20, T:0.47
Consensus pattern (15 bp):
AAAGTTGTTCTTTGA
Found at i:9215257 original size:10 final size:10
Alignment explanation
Indices: 9215224--9215265 Score: 57
Period size: 11 Copynumber: 4.0 Consensus size: 10
9215214 CCTCTCATAG
9215224 TTCTCTCTAAA
1 TTCTCTC-AAA
9215235 TTCTCTCCAAA
1 TTCTCT-CAAA
9215246 TTCTCTCAAA
1 TTCTCTCAAA
*
9215256 TTTTCTCAAA
1 TTCTCTCAAA
9215266 GCTCTCTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 13 0.45
11 15 0.52
12 1 0.03
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (10 bp):
TTCTCTCAAA
Found at i:9216394 original size:14 final size:14
Alignment explanation
Indices: 9216375--9216421 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
9216365 CAGAAGTATA
9216375 AGTAAATAAAAAAT
1 AGTAAATAAAAAAT
*
9216389 AGTAAATAAAATAT
1 AGTAAATAAAAAAT
9216403 A-TACACATAATAAAAT
1 AGTA-A-ATAA-AAAAT
9216419 AGT
1 AGT
9216422 CGTTTTGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 2 0.07
14 15 0.56
15 4 0.15
16 5 0.19
17 1 0.04
ACGTcount: A:0.64, C:0.04, G:0.06, T:0.26
Consensus pattern (14 bp):
AGTAAATAAAAAAT
Found at i:9217086 original size:18 final size:18
Alignment explanation
Indices: 9217063--9217105 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
9217053 TGCCAGGTGC
* *
9217063 GTATCCTAGCCCTTATAT
1 GTATCCTAACCCCTATAT
9217081 GTATCCTAACCCCTATAT
1 GTATCCTAACCCCTATAT
*
9217099 GTTTCCT
1 GTATCCT
9217106 TTTCCGAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.21, C:0.30, G:0.09, T:0.40
Consensus pattern (18 bp):
GTATCCTAACCCCTATAT
Found at i:9225507 original size:27 final size:27
Alignment explanation
Indices: 9225469--9225522 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
9225459 CCGGAATAAG
9225469 GTATAATATAGCCTTCCAAACACACCA
1 GTATAATATAGCCTTCCAAACACACCA
9225496 GTATAATATAGCCTTCCAAACACACCA
1 GTATAATATAGCCTTCCAAACACACCA
9225523 ATAATGCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.30, G:0.07, T:0.22
Consensus pattern (27 bp):
GTATAATATAGCCTTCCAAACACACCA
Found at i:9227059 original size:24 final size:24
Alignment explanation
Indices: 9226996--9227060 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
9226986 TATCCATTAA
* *
9226996 ATAATCATAA-TAATTAT-AAACC
1 ATAATAATAATTAAATATAAAACC
**
9227018 ATAATAATAATTTTATATAAAACC
1 ATAATAATAATTAAATATAAAACC
*
9227042 ATGATAATAATTAAATATA
1 ATAATAATAATTAAATATA
9227061 TATAATACAT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
22 9 0.26
23 4 0.12
24 21 0.62
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.35
Consensus pattern (24 bp):
ATAATAATAATTAAATATAAAACC
Found at i:9229509 original size:41 final size:41
Alignment explanation
Indices: 9229464--9229589 Score: 146
Period size: 41 Copynumber: 3.1 Consensus size: 41
9229454 CTTTCTATCA
* * * *
9229464 GTGATTTATATTAGGCTCTGCACCCAGTAGGCTTCGTGCTG
1 GTGATTTATATCAGGCTCTGCGCCTAGCAGGCTTCGTGCTG
* * * *
9229505 GTGATTTATATCAAGCTTTGTGCCTAGCAGG-TGTCGTGCTT
1 GTGATTTATATCAGGCTCTGCGCCTAGCAGGCT-TCGTGCTG
* *
9229546 GTGATTTATATCAGGCTCTACGCCTAGCAGGCTTCGTGCCG
1 GTGATTTATATCAGGCTCTGCGCCTAGCAGGCTTCGTGCTG
9229587 GTG
1 GTG
9229590 CAATTGTATC
Statistics
Matches: 69, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
40 1 0.01
41 67 0.97
42 1 0.01
ACGTcount: A:0.17, C:0.21, G:0.28, T:0.34
Consensus pattern (41 bp):
GTGATTTATATCAGGCTCTGCGCCTAGCAGGCTTCGTGCTG
Found at i:9231713 original size:26 final size:26
Alignment explanation
Indices: 9231684--9231738 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
9231674 TTTAATTCTT
* *
9231684 TTATTTATCT-ATTTACTTTACATTCA
1 TTATTCATCTCATTT-CATTACATTCA
*
9231710 TTATTCATTTCATTTCATTACATTCA
1 TTATTCATCTCATTTCATTACATTCA
9231736 TTA
1 TTA
9231739 CTTGAAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 21 0.84
27 4 0.16
ACGTcount: A:0.27, C:0.16, G:0.00, T:0.56
Consensus pattern (26 bp):
TTATTCATCTCATTTCATTACATTCA
Found at i:9231810 original size:17 final size:17
Alignment explanation
Indices: 9231801--9231906 Score: 131
Period size: 17 Copynumber: 6.1 Consensus size: 17
9231791 CTTCAATGAT
9231801 ATGCAATCTTAGATGTG
1 ATGCAATCTTAGATGTG
*
9231818 ATGCAATCTTAGATATG
1 ATGCAATCTTAGATGTG
* *
9231835 ATACAATCTTAGATATG
1 ATGCAATCTTAGATGTG
*
9231852 ATTGCAATCTTAGATATG
1 A-TGCAATCTTAGATGTG
* *
9231870 ATACAATCTTAGATATG
1 ATGCAATCTTAGATGTG
*
9231887 ATTGCAATCTTAGATATG
1 A-TGCAATCTTAGATGTG
9231905 AT
1 AT
9231907 ATACAATCTT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
17 50 0.61
18 32 0.39
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (17 bp):
ATGCAATCTTAGATGTG
Found at i:9231859 original size:52 final size:54
Alignment explanation
Indices: 9231796--9231919 Score: 198
Period size: 52 Copynumber: 2.3 Consensus size: 54
9231786 ATAATCTTCA
* *
9231796 ATGATATGCAATCTTAGATGTGATGCAATCTTAGATATGA-TACAATCTTAGAT
1 ATGATATGCAATCTTAGATATGATACAATCTTAGATATGATTACAATCTTAGAT
*
9231849 ATGAT-TGCAATCTTAGATATGATACAATCTTAGATATGATTGCAATCTTAGAT
1 ATGATATGCAATCTTAGATATGATACAATCTTAGATATGATTACAATCTTAGAT
*
9231902 ATGATATACAATCTTAGA
1 ATGATATGCAATCTTAGA
9231920 AGATATGATT
Statistics
Matches: 65, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
52 32 0.49
53 22 0.34
54 11 0.17
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.36
Consensus pattern (54 bp):
ATGATATGCAATCTTAGATATGATACAATCTTAGATATGATTACAATCTTAGAT
Found at i:9231864 original size:35 final size:35
Alignment explanation
Indices: 9231804--9231919 Score: 198
Period size: 35 Copynumber: 3.3 Consensus size: 35
9231794 CAATGATATG
*
9231804 CAATCTTAGATGTGA-TGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
9231838 CAATCTTAGATATGATTGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
9231873 CAATCTTAGATATGATTGCAATCTTAGATATGATATA
1 CAATCTTAGATATGATTGCAATCTTAGATATG--ATA
9231910 CAATCTTAGA
1 CAATCTTAGA
9231920 AGATATGATT
Statistics
Matches: 78, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
34 14 0.18
35 51 0.65
37 13 0.17
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (35 bp):
CAATCTTAGATATGATTGCAATCTTAGATATGATA
Found at i:9237808 original size:28 final size:27
Alignment explanation
Indices: 9237749--9237808 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
9237739 TATATTTGTA
*
9237749 AAAATTTATAAATATTTTTAATGAAAT
1 AAAATTTATAAATATTTATAATGAAAT
*
9237776 AAAATTT-TAAATATATATATAATTAAAT
1 AAAATTTATAAATAT-T-TATAATGAAAT
9237804 AAAAT
1 AAAAT
9237809 AATATTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 7 0.24
27 8 0.28
28 14 0.48
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (27 bp):
AAAATTTATAAATATTTATAATGAAAT
Found at i:9239154 original size:20 final size:20
Alignment explanation
Indices: 9239131--9239182 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
9239121 AAAATTACAA
*
9239131 AAAAAATTCAAAATAAT-TTT
1 AAAAAATTCAAAA-AATATAT
* *
9239151 AAAAATTTCAAAACATATAT
1 AAAAAATTCAAAAAATATAT
9239171 AAAAAATTCAAA
1 AAAAAATTCAAA
9239183 TTTTATATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAAAATTCAAAAAATATAT
Found at i:9252322 original size:33 final size:33
Alignment explanation
Indices: 9252261--9252324 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
9252251 CGTAATCACT
* **
9252261 GTTTTCGACATTACTGAAAATTGAGTTGTTACA
1 GTTTCCGACATTACTGAAAAACGAGTTGTTACA
*
9252294 GTTTCCGACATTACTGAAAAACGGGTTGTTA
1 GTTTCCGACATTACTGAAAAACGAGTTGTTA
9252325 TATACACTGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (33 bp):
GTTTCCGACATTACTGAAAAACGAGTTGTTACA
Found at i:9256470 original size:12 final size:12
Alignment explanation
Indices: 9256453--9256478 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
9256443 GTTTTATTCA
9256453 TTTTTTCTTTAT
1 TTTTTTCTTTAT
9256465 TTTTTTCTTTAT
1 TTTTTTCTTTAT
9256477 TT
1 TT
9256479 GATTGGGATA
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:0.08, C:0.08, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTCTTTAT
Found at i:9258274 original size:15 final size:15
Alignment explanation
Indices: 9258254--9258283 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
9258244 CCACTCGCCC
9258254 AAACTTAAGTAACAA
1 AAACTTAAGTAACAA
9258269 AAACTTAAGTAACAA
1 AAACTTAAGTAACAA
9258284 CACTATCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.13, G:0.07, T:0.20
Consensus pattern (15 bp):
AAACTTAAGTAACAA
Found at i:9262903 original size:19 final size:19
Alignment explanation
Indices: 9262866--9262903 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
9262856 TTAATTAGGT
*
9262866 TTTAATTAGATGAATTTAG
1 TTTAATTAGATGAAATTAG
9262885 TTTAATTAAGA-GAAATTAG
1 TTTAATT-AGATGAAATTAG
9262904 AAAAAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (19 bp):
TTTAATTAGATGAAATTAG
Found at i:9263206 original size:33 final size:32
Alignment explanation
Indices: 9263164--9263235 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 32
9263154 AAATGAGTAC
9263164 ATTTATATTATTTA-TATATAATTAGTAAAAGGAT
1 ATTT-TATTATTTATTAT-TAATTAGTAAAA-GAT
9263198 ATTTTATTATTTATTATTAATTAGTAAAAGAT
1 ATTTTATTATTTATTATTAATTAGTAAAAGAT
9263230 -TTTTAT
1 ATTTTAT
9263236 ATGATAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
31 6 0.16
32 3 0.08
33 21 0.57
34 7 0.19
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (32 bp):
ATTTTATTATTTATTATTAATTAGTAAAAGAT
Found at i:9263314 original size:23 final size:23
Alignment explanation
Indices: 9263288--9263331 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
9263278 AAAATACAAA
9263288 TGTAAAATATATATGTGTACATT
1 TGTAAAATATATATGTGTACATT
* * *
9263311 TGTAATATTTATATTTGTACA
1 TGTAAAATATATATGTGTACA
9263332 AAAGACCACA
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:0.36, C:0.05, G:0.11, T:0.48
Consensus pattern (23 bp):
TGTAAAATATATATGTGTACATT
Found at i:9268788 original size:76 final size:76
Alignment explanation
Indices: 9268701--9268854 Score: 308
Period size: 76 Copynumber: 2.0 Consensus size: 76
9268691 CCTCTGGGGC
9268701 AAACTATGTTAGTGAATCGAATATGTCGAAAATGCCCGTTAATGATCTAGGATAGAATCTTTTCT
1 AAACTATGTTAGTGAATCGAATATGTCGAAAATGCCCGTTAATGATCTAGGATAGAATCTTTTCT
9268766 GTTGATCTGTT
66 GTTGATCTGTT
9268777 AAACTATGTTAGTGAATCGAATATGTCGAAAATGCCCGTTAATGATCTAGGATAGAATCTTTTCT
1 AAACTATGTTAGTGAATCGAATATGTCGAAAATGCCCGTTAATGATCTAGGATAGAATCTTTTCT
9268842 GTTGATCTGTT
66 GTTGATCTGTT
9268853 AA
1 AA
9268855 TTATGCCATT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 78 1.00
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.36
Consensus pattern (76 bp):
AAACTATGTTAGTGAATCGAATATGTCGAAAATGCCCGTTAATGATCTAGGATAGAATCTTTTCT
GTTGATCTGTT
Found at i:9272146 original size:19 final size:20
Alignment explanation
Indices: 9272101--9272146 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 20
9272091 AGATGTGTTT
9272101 AATTAGGTTGTAATTAGATGA
1 AATTA-GTTGTAATTAGATGA
*
9272122 ATTTAGTT-TAATTAAGA-GA
1 AATTAGTTGTAATT-AGATGA
9272141 AATTAG
1 AATTAG
9272147 AAAAAAAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 12 0.55
20 6 0.27
21 4 0.18
ACGTcount: A:0.41, C:0.00, G:0.20, T:0.39
Consensus pattern (20 bp):
AATTAGTTGTAATTAGATGA
Found at i:9272448 original size:33 final size:32
Alignment explanation
Indices: 9272406--9272477 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 32
9272396 AAATGAGTAC
9272406 ATTTGTATTATTTA-TATATAATTAGTAAAAAGAT
1 ATTT-TATTATTTATTAT-TAATTAGT-AAAAGAT
9272440 ATTTTATTATTTATTATTAATTAGTAAAAGAT
1 ATTTTATTATTTATTATTAATTAGTAAAAGAT
9272472 -TTTTAT
1 ATTTTAT
9272478 ATGATAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
31 6 0.16
32 7 0.19
33 17 0.46
34 7 0.19
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (32 bp):
ATTTTATTATTTATTATTAATTAGTAAAAGAT
Found at i:9272878 original size:9 final size:9
Alignment explanation
Indices: 9272866--9272893 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
9272856 AAGAAAAGAA
9272866 GGAAATAGG
1 GGAAATAGG
9272875 GGAAATAGG
1 GGAAATAGG
9272884 GGAAATAGG
1 GGAAATAGG
9272893 G
1 G
9272894 AATTTGAAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.46, T:0.11
Consensus pattern (9 bp):
GGAAATAGG
Found at i:9278503 original size:27 final size:27
Alignment explanation
Indices: 9278395--9278505 Score: 125
Period size: 28 Copynumber: 4.0 Consensus size: 27
9278385 CACGAAAACT
* * *
9278395 AAGAATAGCCCTTATGGCTAACTCTAGA
1 AAGAATAGCCTTTGTGGCGAACTCT-GA
*
9278423 AAGAATAGCCTTTGTGGTGAACTCTGAA
1 AAGAATAGCCTTTGTGGCGAACTCTG-A
*
9278451 AAGAATAGCCTTTGTGGGGAACTCTGA
1 AAGAATAGCCTTTGTGGCGAACTCTGA
* *
9278478 AAGGAAT-GCCTTTGTGGCAAATTCTGA
1 AA-GAATAGCCTTTGTGGCGAACTCTGA
9278505 A
1 A
9278506 TGGATCGCCT
Statistics
Matches: 73, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
27 22 0.30
28 51 0.70
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.27
Consensus pattern (27 bp):
AAGAATAGCCTTTGTGGCGAACTCTGA
Found at i:9278979 original size:19 final size:19
Alignment explanation
Indices: 9278951--9278993 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
9278941 CACGTTTATG
* * *
9278951 TGCCAGGATGCACTTTGTA
1 TGCCAAGATGAACCTTGTA
*
9278970 TGCCAAGATGAACCTTGTG
1 TGCCAAGATGAACCTTGTA
9278989 TGCCA
1 TGCCA
9278994 TATATACGCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (19 bp):
TGCCAAGATGAACCTTGTA
Found at i:9283559 original size:19 final size:19
Alignment explanation
Indices: 9283511--9283565 Score: 103
Period size: 18 Copynumber: 2.9 Consensus size: 19
9283501 ATAATCTTCA
9283511 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
9283530 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
9283548 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
9283566 AGATATGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
18 18 0.51
19 17 0.49
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:9283591 original size:22 final size:22
Alignment explanation
Indices: 9283511--9283588 Score: 80
Period size: 18 Copynumber: 3.8 Consensus size: 22
9283501 ATAATCTTCA
9283511 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
9283530 ATGAT-TGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
9283548 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
9283570 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
9283589 GATTTAATTT
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
18 18 0.35
19 14 0.27
22 8 0.15
23 12 0.23
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:9283878 original size:18 final size:19
Alignment explanation
Indices: 9283855--9283891 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
9283845 TGTTTCCCTG
*
9283855 ATTTTTTTATAT-ATTTTA
1 ATTTTTTTAAATAATTTTA
9283873 ATTTTTTTAAATAATTTTA
1 ATTTTTTTAAATAATTTTA
9283892 GTATCATATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
ATTTTTTTAAATAATTTTA
Found at i:9287399 original size:26 final size:26
Alignment explanation
Indices: 9287368--9287475 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
9287358 TGAAATGCCC
*
9287368 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
9287394 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
9287420 ATCATGAAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
9287446 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
9287472 ATCA
1 ATCA
9287476 ATTTGTACCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:9294930 original size:26 final size:26
Alignment explanation
Indices: 9294894--9295003 Score: 177
Period size: 26 Copynumber: 4.2 Consensus size: 26
9294884 TGATACAAAT
9294894 TGATAATAGGTTAGGTAAATG-TTCAA
1 TGATAATAGGTTAGGTAAATGTTTC-A
*
9294920 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
9294946 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
9294972 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
9294998 TGATAA
1 TGATAA
9295004 GAATTTCATG
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
26 78 0.98
27 2 0.03
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:9296664 original size:27 final size:27
Alignment explanation
Indices: 9296623--9296735 Score: 138
Period size: 27 Copynumber: 4.2 Consensus size: 27
9296613 GAGGAAGCGT
*
9296623 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
9296650 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
9296677 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * *
9296705 TCTGGTGGCTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
9296731 TCTGG
1 TCTGG
9296736 CAGCCATGCT
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
26 5 0.07
27 55 0.72
28 16 0.21
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:9296728 original size:54 final size:54
Alignment explanation
Indices: 9296621--9296735 Score: 178
Period size: 54 Copynumber: 2.1 Consensus size: 54
9296611 TGGAGGAAGC
9296621 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT
* * * *
9296675 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGGCTCTGTCACAT-TATCT
1 GTTCTGGTGGCTATGCCACAAATATCTG-ATCTGGTGGCTCTGCCACATATATCT
9296729 GTTCTGG
1 GTTCTGG
9296736 CAGCCATGCT
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
54 37 0.66
55 19 0.34
ACGTcount: A:0.16, C:0.23, G:0.24, T:0.37
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT
Found at i:9298861 original size:16 final size:16
Alignment explanation
Indices: 9298839--9298892 Score: 58
Period size: 15 Copynumber: 3.4 Consensus size: 16
9298829 TAAATTAGAA
*
9298839 GAAAATTTA-AAAGAT
1 GAAAAATTAGAAAGAT
* *
9298854 GAAAAATTATAAGGAT
1 GAAAAATTAGAAAGAT
9298870 AGAAAAA-TAGAAAGAT
1 -GAAAAATTAGAAAGAT
9298886 GAAAAAT
1 GAAAAAT
9298893 ATAATTTTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
15 14 0.44
16 12 0.38
17 6 0.19
ACGTcount: A:0.63, C:0.00, G:0.17, T:0.20
Consensus pattern (16 bp):
GAAAAATTAGAAAGAT
Found at i:9306791 original size:32 final size:34
Alignment explanation
Indices: 9306710--9306792 Score: 98
Period size: 34 Copynumber: 2.5 Consensus size: 34
9306700 GATTTTGTGC
* * *
9306710 TGCATATCTGTTACTGAGATGGGCTAAGGCCTTAA
1 TGCATA-CTGATACTGAAATGGGCTAAGGCCTAAA
* *
9306745 TGCTTACTGTTACTGAAATGGGCTAAGGCC-AAA
1 TGCATACTGATACTGAAATGGGCTAAGGCCTAAA
9306778 TG-ATACTGATACTGA
1 TGCATACTGATACTGA
9306793 TATTAAAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
32 11 0.26
33 4 0.09
34 23 0.53
35 5 0.12
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (34 bp):
TGCATACTGATACTGAAATGGGCTAAGGCCTAAA
Found at i:9308910 original size:33 final size:33
Alignment explanation
Indices: 9308833--9308910 Score: 102
Period size: 33 Copynumber: 2.4 Consensus size: 33
9308823 AGCCACGAGA
* * * *
9308833 GGCTATGGTCAAGTTAAAGGTGGTAACGGGTTT
1 GGCTGTGGTCAGGTCAAAGGTGGTAACGAGTTT
* *
9308866 GGCTGTGGTCAGGTCAAAGGTGGTGATGAGTTT
1 GGCTGTGGTCAGGTCAAAGGTGGTAACGAGTTT
9308899 GGCTGTGGTCAG
1 GGCTGTGGTCAG
9308911 AGAGCACCAG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.19, C:0.10, G:0.41, T:0.29
Consensus pattern (33 bp):
GGCTGTGGTCAGGTCAAAGGTGGTAACGAGTTT
Found at i:9317319 original size:20 final size:20
Alignment explanation
Indices: 9317279--9317340 Score: 92
Period size: 19 Copynumber: 3.2 Consensus size: 20
9317269 CATGCGGCAA
9317279 AAAATTTATTAAAAATA-TT
1 AAAATTTATTAAAAATATTT
* *
9317298 AAAATTTAATAATAATATTT
1 AAAATTTATTAAAAATATTT
9317318 AAAATTTATTAAAAAT-TTT
1 AAAATTTATTAAAAATATTT
9317337 AAAA
1 AAAA
9317341 AAAAACTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 22 0.58
20 16 0.42
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AAAATTTATTAAAAATATTT
Found at i:9317640 original size:36 final size:38
Alignment explanation
Indices: 9317593--9317672 Score: 110
Period size: 36 Copynumber: 2.2 Consensus size: 38
9317583 TTGTATGATC
* * *
9317593 ATTTTTATAATTTTTTTACGAATTT-T-ATGTTTTTTA
1 ATTTTTATAATTTTATTACGAATTTATAAAGTTTTATA
*
9317629 ATTTTTATAATTTTATTACGACTTTATAAAGTTTTATA
1 ATTTTTATAATTTTATTACGAATTTATAAAGTTTTATA
9317667 ATTTTT
1 ATTTTT
9317673 TTTATATTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
36 23 0.61
37 1 0.03
38 14 0.37
ACGTcount: A:0.29, C:0.04, G:0.05, T:0.62
Consensus pattern (38 bp):
ATTTTTATAATTTTATTACGAATTTATAAAGTTTTATA
Found at i:9317731 original size:11 final size:12
Alignment explanation
Indices: 9317707--9317742 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
9317697 CTTTCTACGA
9317707 TTTTTATAATTT
1 TTTTTATAATTT
*
9317719 TTTTTCTAATTT
1 TTTTTATAATTT
*
9317731 TTTTTAAAATTT
1 TTTTTATAATTT
9317743 AAGTATTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTTTATAATTT
Found at i:9321374 original size:16 final size:15
Alignment explanation
Indices: 9321346--9321383 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
9321336 TGAAATTTGG
*
9321346 ATTAAATTCAATAAA
1 ATTAAATTAAATAAA
9321361 ATTATAATTAAAT-AA
1 ATTA-AATTAAATAAA
9321376 ATTAAATT
1 ATTAAATT
9321384 TGATTATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 4 0.19
15 10 0.48
16 7 0.33
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (15 bp):
ATTAAATTAAATAAA
Found at i:9332144 original size:13 final size:13
Alignment explanation
Indices: 9332128--9332152 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9332118 TTGAAAATCT
9332128 AGAAAAAAAAAAA
1 AGAAAAAAAAAAA
9332141 AGAAAAAAAAAA
1 AGAAAAAAAAAA
9332153 GTCAAATTGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AGAAAAAAAAAAA
Found at i:9350758 original size:16 final size:16
Alignment explanation
Indices: 9350737--9350790 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
9350727 TTTAGTTCAC
*
9350737 TGTAATGGAATAGGGT
1 TGTAATGGAATAGAGT
*
9350753 TGTAATTGAATAGAGT
1 TGTAATGGAATAGAGT
* *
9350769 TGTAATGGAATAAAGC
1 TGTAATGGAATAGAGT
9350785 TGTAAT
1 TGTAAT
9350791 CAGAAATTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.37, C:0.02, G:0.28, T:0.33
Consensus pattern (16 bp):
TGTAATGGAATAGAGT
Found at i:9354364 original size:17 final size:19
Alignment explanation
Indices: 9354324--9354364 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
9354314 ATTATCATTA
9354324 GGTATCGATATCTTATTTT
1 GGTATCGATATCTTATTTT
* *
9354343 AGTATCGATA-C-TGTTTT
1 GGTATCGATATCTTATTTT
9354360 GGTAT
1 GGTAT
9354365 TCTATTTTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
17 9 0.47
18 1 0.05
19 9 0.47
ACGTcount: A:0.22, C:0.10, G:0.20, T:0.49
Consensus pattern (19 bp):
GGTATCGATATCTTATTTT
Found at i:9363284 original size:8 final size:8
Alignment explanation
Indices: 9363261--9363299 Score: 51
Period size: 9 Copynumber: 4.6 Consensus size: 8
9363251 TAAATAAATT
*
9363261 ATTACAAA
1 ATTAAAAA
9363269 ATTAAAAA
1 ATTAAAAA
9363277 TATTAAAAA
1 -ATTAAAAA
9363286 ATTATAAAA
1 ATTA-AAAA
9363295 ATTAA
1 ATTAA
9363300 TTCAACTACT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
8 12 0.43
9 16 0.57
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (8 bp):
ATTAAAAA
Found at i:9363286 original size:17 final size:18
Alignment explanation
Indices: 9363254--9363299 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
9363244 TTCAAAGTAA
* *
9363254 ATAAATTATTACAAAATT
1 ATAAAATATTAAAAAATT
9363272 A-AAAATATTAAAAAATT
1 ATAAAATATTAAAAAATT
9363289 ATAAAA-ATTAA
1 ATAAAATATTAA
9363300 TTCAACTACT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 20 0.80
18 5 0.20
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
ATAAAATATTAAAAAATT
Found at i:9363575 original size:11 final size:12
Alignment explanation
Indices: 9363549--9363581 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
9363539 TTCAAAAATA
9363549 AAAATAATTATTT
1 AAAATAA-TATTT
9363562 AAAATAAT-TTT
1 AAAATAATATTT
9363573 AAAATAATA
1 AAAATAATA
9363582 AAATTCTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 11 0.58
12 1 0.05
13 7 0.37
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
AAAATAATATTT
Found at i:9374433 original size:3 final size:3
Alignment explanation
Indices: 9374425--9374457 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
9374415 AAAAAAGTGG
*
9374425 AGA AGA AGA AGA AGA AAA AGA AGA AGA A-A AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
9374458 AAAAATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:9375001 original size:3 final size:3
Alignment explanation
Indices: 9374995--9375038 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
9374985 GGAGGAGGAA
*
9374995 AAG AAG AAA AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
9375039 AAATTACTAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:9375005 original size:9 final size:9
Alignment explanation
Indices: 9374993--9375041 Score: 71
Period size: 9 Copynumber: 5.4 Consensus size: 9
9374983 GAGGAGGAGG
9374993 AAAAGAAGA
1 AAAAGAAGA
9375002 AAAAGAAGA
1 AAAAGAAGA
*
9375011 AGAAGAAGA
1 AAAAGAAGA
*
9375020 AGAAGAAGA
1 AAAAGAAGA
*
9375029 AGAAGAAGA
1 AAAAGAAGA
9375038 AAAA
1 AAAA
9375042 TTACTAGCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (9 bp):
AAAAGAAGA
Found at i:9376395 original size:30 final size:31
Alignment explanation
Indices: 9376330--9376398 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
9376320 ACTGTTAGTC
* *
9376330 AGTGACTGTTTCGTCACTTTTTTATAACGTT
1 AGTGACTGTTTCGTCACTTTTTCAAAACGTT
* *
9376361 AGTGACTGTTTTGTTA-TTTTTCAAAAC-TT
1 AGTGACTGTTTCGTCACTTTTTCAAAACGTT
9376390 AAGTGACTG
1 -AGTGACTG
9376399 AAATAAAACT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 2 0.06
30 17 0.52
31 14 0.42
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.46
Consensus pattern (31 bp):
AGTGACTGTTTCGTCACTTTTTCAAAACGTT
Found at i:9380394 original size:29 final size:29
Alignment explanation
Indices: 9380360--9380417 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
9380350 AATTTAGCTC
*
9380360 TTTTTAAAGATT-AATGGTTAAATTTAATT
1 TTTTTAAAGATTGAA-GGGTAAATTTAATT
9380389 TTTTTAAAGATTGAAGGGTAAATTTAATT
1 TTTTTAAAGATTGAAGGGTAAATTTAATT
9380418 AAAAAAAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 25 0.93
30 2 0.07
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (29 bp):
TTTTTAAAGATTGAAGGGTAAATTTAATT
Found at i:9380945 original size:21 final size:21
Alignment explanation
Indices: 9380892--9380938 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
9380882 TATGATTGTA
9380892 TGATATAATTCAAATGAAAAG
1 TGATATAATTCAAATGAAAAG
9380913 TGATATAATTCAAATGAAAAG
1 TGATATAATTCAAATGAAAAG
9380934 T-ATAT
1 TGATAT
9380939 GCATTCAGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.51, C:0.04, G:0.13, T:0.32
Consensus pattern (21 bp):
TGATATAATTCAAATGAAAAG
Found at i:9385319 original size:19 final size:20
Alignment explanation
Indices: 9385288--9385329 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
9385278 ATTTTATTTA
9385288 TTTACCGAATAAACAAGATT
1 TTTACCGAATAAACAAGATT
* *
9385308 TTTACC-AATAAAGAATATT
1 TTTACCGAATAAACAAGATT
9385327 TTT
1 TTT
9385330 TTATATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (20 bp):
TTTACCGAATAAACAAGATT
Found at i:9385330 original size:20 final size:21
Alignment explanation
Indices: 9385282--9385330 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
9385272 CTTTATATTT
9385282 TATTTATTTACCGAATAAACAA
1 TATTT-TTTACCGAATAAACAA
* *
9385304 GA-TTTTTACC-AATAAAGAA
1 TATTTTTTACCGAATAAACAA
9385323 TATTTTTT
1 TATTTTTT
9385331 TATATTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 9 0.39
20 11 0.48
21 2 0.09
22 1 0.04
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.43
Consensus pattern (21 bp):
TATTTTTTACCGAATAAACAA
Found at i:9392835 original size:21 final size:22
Alignment explanation
Indices: 9392811--9392861 Score: 79
Period size: 21 Copynumber: 2.4 Consensus size: 22
9392801 TTTTTCTCTC
9392811 TTCTATTAACAAATTTAA-TC-T
1 TTCTATTAA-AAATTTAATTCAT
9392832 TTCTATTAAAAATTTAATTCAT
1 TTCTATTAAAAATTTAATTCAT
9392854 TTCTATTA
1 TTCTATTA
9392862 TTTAACTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.29
21 11 0.39
22 9 0.32
ACGTcount: A:0.37, C:0.12, G:0.00, T:0.51
Consensus pattern (22 bp):
TTCTATTAAAAATTTAATTCAT
Found at i:9398722 original size:121 final size:121
Alignment explanation
Indices: 9398508--9398750 Score: 486
Period size: 121 Copynumber: 2.0 Consensus size: 121
9398498 TGTTAGTTAT
9398508 TTAAACGCGTAGGTTAAGATTTATCAGGGAGCTTGAACTTCAACTTGGGAGCATCGCATCACTAT
1 TTAAACGCGTAGGTTAAGATTTATCAGGGAGCTTGAACTTCAACTTGGGAGCATCGCATCACTAT
9398573 TTGAGGTTTTAAAGTTTCTTTCGTAACTATATTGGTTATTATTTGTCTAAGAATAA
66 TTGAGGTTTTAAAGTTTCTTTCGTAACTATATTGGTTATTATTTGTCTAAGAATAA
9398629 TTAAACGCGTAGGTTAAGATTTATCAGGGAGCTTGAACTTCAACTTGGGAGCATCGCATCACTAT
1 TTAAACGCGTAGGTTAAGATTTATCAGGGAGCTTGAACTTCAACTTGGGAGCATCGCATCACTAT
9398694 TTGAGGTTTTAAAGTTTCTTTCGTAACTATATTGGTTATTATTTGTCTAAGAATAA
66 TTGAGGTTTTAAAGTTTCTTTCGTAACTATATTGGTTATTATTTGTCTAAGAATAA
9398750 T
1 T
9398751 GACATGTACA
Statistics
Matches: 122, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
121 122 1.00
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (121 bp):
TTAAACGCGTAGGTTAAGATTTATCAGGGAGCTTGAACTTCAACTTGGGAGCATCGCATCACTAT
TTGAGGTTTTAAAGTTTCTTTCGTAACTATATTGGTTATTATTTGTCTAAGAATAA
Found at i:9403819 original size:7 final size:7
Alignment explanation
Indices: 9403801--9403832 Score: 50
Period size: 6 Copynumber: 4.9 Consensus size: 7
9403791 TTGCAATTCA
9403801 AATTTTT
1 AATTTTT
9403808 -ATTTTT
1 AATTTTT
9403814 -ATTTTT
1 AATTTTT
9403820 AATTTTT
1 AATTTTT
9403827 AATTTT
1 AATTTT
9403833 CTTTTCTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 12 0.50
7 12 0.50
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (7 bp):
AATTTTT
Found at i:9403856 original size:19 final size:20
Alignment explanation
Indices: 9403810--9403858 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
9403800 AAATTTTTAT
*
9403810 TTTTATTTT-TAATTTTTAA
1 TTTTATTTTCTAATTCTTAA
* *
9403829 TTTTCTTTTCTAATTCTTCA
1 TTTTATTTTCTAATTCTTAA
9403849 -TTTATTTTCT
1 TTTTATTTTCT
9403859 TTTGACAGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTATTTTCTAATTCTTAA
Found at i:9424561 original size:46 final size:48
Alignment explanation
Indices: 9424504--9424624 Score: 156
Period size: 46 Copynumber: 2.6 Consensus size: 48
9424494 TGATATGTGT
* *
9424504 GCTAGTGTAAGACATGTCTGGGACATGCATCGACATTGAGA-CGA-GA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGACATTGAGATAGACAA
* * * * *
9424550 GCTAGTGTAAGACATGTTTGGGACATGTATCGGCCTTGAGATATACAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGACATTGAGATAGACAA
*
9424598 GCTAGTGTAAGACTTGTCTGGGACATG
1 GCTAGTGTAAGACATGTCTGGGACATG
9424625 ACGTCAGCTT
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
46 37 0.58
47 1 0.02
48 26 0.41
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.26
Consensus pattern (48 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGACATTGAGATAGACAA
Found at i:9427489 original size:15 final size:15
Alignment explanation
Indices: 9427469--9427500 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
9427459 CAGGGGTCAC
9427469 ACCATATTGAAATCA
1 ACCATATTGAAATCA
9427484 ACCATATTGAAATCA
1 ACCATATTGAAATCA
9427499 AC
1 AC
9427501 TAACCACTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.22, G:0.06, T:0.25
Consensus pattern (15 bp):
ACCATATTGAAATCA
Found at i:9436316 original size:25 final size:26
Alignment explanation
Indices: 9436288--9436356 Score: 70
Period size: 25 Copynumber: 2.7 Consensus size: 26
9436278 CCTTGGTTTC
*
9436288 ATTTTTTTTGTTTTATTT-TATTTTT
1 ATTTTTTTTGTTTTATTTCTATTCTT
* * *
9436313 ATTTATTAT-TCTTATTTCTATTCTT
1 ATTTTTTTTGTTTTATTTCTATTCTT
*
9436338 ATTTATTTTTGTTATATTT
1 ATTT-TTTTTGTTTTATTT
9436357 AGTTTCATTT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
24 7 0.21
25 17 0.52
26 3 0.09
27 6 0.18
ACGTcount: A:0.17, C:0.04, G:0.03, T:0.75
Consensus pattern (26 bp):
ATTTTTTTTGTTTTATTTCTATTCTT
Found at i:9436321 original size:18 final size:17
Alignment explanation
Indices: 9436300--9436356 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 17
9436290 TTTTTTTGTT
9436300 TTATTTTATTTTTATTTA
1 TTATTTTATTTTTA-TTA
* *
9436318 TTATTCTTATTTCTATTC
1 TTATT-TTATTTTTATTA
*
9436336 TTA-TTTATTTTTGTTA
1 TTATTTTATTTTTATTA
9436352 -TATTT
1 TTATTT
9436357 AGTTTCATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 2 0.06
16 11 0.34
17 1 0.03
18 10 0.31
19 8 0.25
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (17 bp):
TTATTTTATTTTTATTA
Found at i:9436366 original size:25 final size:25
Alignment explanation
Indices: 9436283--9436371 Score: 67
Period size: 25 Copynumber: 3.6 Consensus size: 25
9436273 AGTTTCCTTG
*
9436283 GTTTCATTT-TTTTTGTTTTATTTTA
1 GTTTCATTTATTTTTGTTATA-TTTA
* * * *
9436308 TTTTTATTTATTATTCTTAT-TTCTA
1 GTTTCATTTATTTTTGTTATATT-TA
*
9436333 -TTCTTATTTATTTTTGTTATATTTA
1 GTT-TCATTTATTTTTGTTATATTTA
*
9436358 GTTTCATTTGTTTT
1 GTTTCATTTATTTT
9436372 ATTATTCTCC
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
24 4 0.08
25 35 0.70
26 11 0.22
ACGTcount: A:0.16, C:0.06, G:0.06, T:0.73
Consensus pattern (25 bp):
GTTTCATTTATTTTTGTTATATTTA
Found at i:9438183 original size:26 final size:26
Alignment explanation
Indices: 9438120--9438183 Score: 60
Period size: 26 Copynumber: 2.5 Consensus size: 26
9438110 TTTTTAGTTG
*
9438120 TTTTATTTTTATTTTCTTAAACTTAT
1 TTTTATTTTTATCTTCTTAAACTTAT
* * *
9438146 TTCGT-TTCTTATCTT-TTGAACTATAT
1 TT-TTATTTTTATCTTCTTAAACT-TAT
9438172 TTTTATTTTTAT
1 TTTTATTTTTAT
9438184 GGTTTTTTCT
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
25 7 0.24
26 21 0.72
27 1 0.03
ACGTcount: A:0.20, C:0.09, G:0.03, T:0.67
Consensus pattern (26 bp):
TTTTATTTTTATCTTCTTAAACTTAT
Found at i:9438815 original size:21 final size:21
Alignment explanation
Indices: 9438774--9438815 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 21
9438764 TGGTTACGAA
*
9438774 TCTATGAACTTGATTTGTTAT
1 TCTATGAACTTGATTCGTTAT
*
9438795 TCTA-GAACTTGCTTCGATTAT
1 TCTATGAACTTGATTCG-TTAT
9438816 GCATGTCAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.48
Consensus pattern (21 bp):
TCTATGAACTTGATTCGTTAT
Found at i:9441572 original size:70 final size:70
Alignment explanation
Indices: 9441496--9441630 Score: 234
Period size: 70 Copynumber: 1.9 Consensus size: 70
9441486 TAGTTTATTA
* * * *
9441496 CTAATTAATTTGCTGCTGTAATGCTGTAAATTATTGGCTGTCCAAATTAGGACAAATTTATGGTG
1 CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTGTCCAAATTAGGACAAAATCATGGTG
9441561 CTTAG
66 CTTAG
9441566 CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTGTCCAAATTAGGACAAAATCATGGTG
1 CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTGTCCAAATTAGGACAAAATCATGGTG
9441631 TTATGTGCTA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 61 1.00
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.36
Consensus pattern (70 bp):
CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTGTCCAAATTAGGACAAAATCATGGTG
CTTAG
Found at i:9442463 original size:43 final size:43
Alignment explanation
Indices: 9442399--9442557 Score: 212
Period size: 43 Copynumber: 3.7 Consensus size: 43
9442389 ATTGTTTATC
* * * *
9442399 GAAATGTTA-CGGGCTTTGGGCCTAGTAGGCTATAATGCCGGT
1 GAAATGATATCGGGCTTCGGGCCTAGCAGGCTATAATGCCAGT
9442441 GAAATGATATCGGGCTTCGGGCCTAGCAGGCTATAATGCCAGT
1 GAAATGATATCGGGCTTCGGGCCTAGCAGGCTATAATGCCAGT
* * * *
9442484 GAGATAATATCGGGCCTCGGGCCTAGCAGGCTATAATACCAGT
1 GAAATGATATCGGGCTTCGGGCCTAGCAGGCTATAATGCCAGT
* **
9442527 GAAACGATATCGGGCTTCAAGCCTAGCAGGC
1 GAAATGATATCGGGCTTCGGGCCTAGCAGGC
9442558 GAAATGTCGG
Statistics
Matches: 102, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
42 8 0.08
43 94 0.92
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (43 bp):
GAAATGATATCGGGCTTCGGGCCTAGCAGGCTATAATGCCAGT
Found at i:9447822 original size:23 final size:24
Alignment explanation
Indices: 9447795--9447853 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
9447785 AATGTTAGAT
9447795 ATTAAATATTTTATT-TAAGTATA
1 ATTAAATATTTTATTATAAGTATA
* *
9447818 ATTAAATA-TTAATTATAATTATA
1 ATTAAATATTTTATTATAAGTATA
*
9447841 ATTATTATATTTT
1 ATTA-AATATTTT
9447854 TTAGATACGT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 5 0.17
23 19 0.66
24 3 0.10
25 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
ATTAAATATTTTATTATAAGTATA
Found at i:9448148 original size:55 final size:55
Alignment explanation
Indices: 9448053--9448170 Score: 209
Period size: 55 Copynumber: 2.1 Consensus size: 55
9448043 TGTTTCCTTT
*
9448053 ACAAGTAAAAGAAAACCTACTATCGGATTTCAGTGTTTCATATAGGAAAGATTCC
1 ACAATTAAAAGAAAACCTACTATCGGATTTCAGTGTTTCATATAGGAAAGATTCC
* *
9448108 ACAATTAAAGGAAACCCTACTATCGGATTTCAGTGTTTCATATAGGAAAGATTCC
1 ACAATTAAAAGAAAACCTACTATCGGATTTCAGTGTTTCATATAGGAAAGATTCC
9448163 ACAATTAA
1 ACAATTAA
9448171 CTTGTATTCC
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 60 1.00
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (55 bp):
ACAATTAAAAGAAAACCTACTATCGGATTTCAGTGTTTCATATAGGAAAGATTCC
Found at i:9455832 original size:3 final size:3
Alignment explanation
Indices: 9455824--9455894 Score: 72
Period size: 3 Copynumber: 23.7 Consensus size: 3
9455814 CTGCAGACTA
* * * * *
9455824 ATT ATT ATT ATT ACT ATT ATT GTT GTT GTT ATT ATT AGT ATT -TCT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
*
9455869 ATT ATT GTT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
9455895 AGAAGAGTCT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
2 1 0.02
3 56 0.97
4 1 0.02
ACGTcount: A:0.27, C:0.03, G:0.07, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:9456249 original size:6 final size:6
Alignment explanation
Indices: 9456240--9456276 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
9456230 AGAGAGAATT
* *
9456240 TTAAAA TTAAAA TTAAAA TTAAAA CTAAAA CTAAAA T
1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA T
9456277 CATTAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (6 bp):
TTAAAA
Found at i:9458067 original size:16 final size:16
Alignment explanation
Indices: 9458046--9458077 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
9458036 AATTCATTTA
*
9458046 AATTAATTAATTTTCT
1 AATTAAATAATTTTCT
9458062 AATTAAATAATTTTCT
1 AATTAAATAATTTTCT
9458078 CAACCCAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (16 bp):
AATTAAATAATTTTCT
Found at i:9459039 original size:40 final size:41
Alignment explanation
Indices: 9458979--9459069 Score: 139
Period size: 40 Copynumber: 2.2 Consensus size: 41
9458969 TCATGCGAGT
* *
9458979 AGGCCGTGTGTGACACAAGGTCGTGTAACAGCCCGTAT-CC
1 AGGCCGTGTGTGACAAAAGGTCGTGTAACAGCCCATATCCC
*
9459019 AGGCCGTGTGTGACAAAAGGTCGTGTAATAGCCCATATCCC
1 AGGCCGTGTGTGACAAAAGGTCGTGTAACAGCCCATATCCC
*
9459060 AGGCCATGTG
1 AGGCCGTGTG
9459070 CATCCAAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
40 35 0.76
41 11 0.24
ACGTcount: A:0.24, C:0.25, G:0.30, T:0.21
Consensus pattern (41 bp):
AGGCCGTGTGTGACAAAAGGTCGTGTAACAGCCCATATCCC
Found at i:9462611 original size:108 final size:108
Alignment explanation
Indices: 9462485--9462700 Score: 378
Period size: 108 Copynumber: 2.0 Consensus size: 108
9462475 TATACCTAAG
*
9462485 CTTACAATTATCATTCCATAACCAAGCATCAATCAAAGCATATTACATAACATATCATTTTCTCC
1 CTTACAATTATCATTCCATAACCAAGCATCAATCAAAGCATATCACATAACATATCATTTTCTCC
9462550 ACCATTAAACATTAAACATATGATCTAAGCTACCTAGCAAAAT
66 ACCATTAAACATTAAACATATGATCTAAGCTACCTAGCAAAAT
* *
9462593 CTTACAATTATCATTCCATAACCAAGCATCATTCAAAGCATATCATATAACATATCATTTTCTCC
1 CTTACAATTATCATTCCATAACCAAGCATCAATCAAAGCATATCACATAACATATCATTTTCTCC
* * *
9462658 ACCATTAAACATTAAATATATTATTTAAGCTACCTAGCAAAAT
66 ACCATTAAACATTAAACATATGATCTAAGCTACCTAGCAAAAT
9462701 AATAACATGA
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
108 102 1.00
ACGTcount: A:0.41, C:0.23, G:0.04, T:0.31
Consensus pattern (108 bp):
CTTACAATTATCATTCCATAACCAAGCATCAATCAAAGCATATCACATAACATATCATTTTCTCC
ACCATTAAACATTAAACATATGATCTAAGCTACCTAGCAAAAT
Found at i:9464059 original size:16 final size:17
Alignment explanation
Indices: 9464038--9464079 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
9464028 CCAAATCCAC
9464038 ATTCAATTTCT-AATTT
1 ATTCAATTTCTCAATTT
* *
9464054 ATTCAATTTTTCATTTT
1 ATTCAATTTCTCAATTT
9464071 ATTCAATTT
1 ATTCAATTT
9464080 AGTCCTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTCAATTTCTCAATTT
Found at i:9465612 original size:30 final size:30
Alignment explanation
Indices: 9465578--9465639 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 30
9465568 ATTATTAACA
9465578 TATTTAATA-T-AATTTATTATTTTAATAAAT
1 TATTTAATATTCAA-TT-TTATTTTAATAAAT
9465608 TATTTAATATTTCAATTTTATTTTAATAAAT
1 TATTTAATA-TTCAATTTTATTTTAATAAAT
9465639 T
1 T
9465640 TTAAAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
30 9 0.31
31 15 0.52
32 3 0.10
33 2 0.07
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (30 bp):
TATTTAATATTCAATTTTATTTTAATAAAT
Found at i:9465652 original size:16 final size:16
Alignment explanation
Indices: 9465631--9465664 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
9465621 AATTTTATTT
9465631 TAATAAATTTTAAA-AA
1 TAAT-AATTTTAAATAA
9465647 TAATAATTTTAAATAA
1 TAATAATTTTAAATAA
9465663 TA
1 TA
9465665 TTCTTCACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATTTTAAATAA
Found at i:9465657 original size:30 final size:31
Alignment explanation
Indices: 9465594--9465657 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
9465584 ATATAATTTA
* * *
9465594 TTATTTTAATAAATTATTTAATATTTCAATT
1 TTATTTTAATAAATTATTAAAAATATCAATT
9465625 TTATTTTAATAAATT-TTAAAAATAAT-AATT
1 TTATTTTAATAAATTATTAAAAAT-ATCAATT
9465655 TTA
1 TTA
9465658 AATAATATTC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 13 0.45
31 16 0.55
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (31 bp):
TTATTTTAATAAATTATTAAAAATATCAATT
Found at i:9465717 original size:15 final size:15
Alignment explanation
Indices: 9465697--9465753 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
9465687 ATTCAATATT
9465697 AATATTTTAATAATA
1 AATATTTTAATAATA
*
9465712 AATATTTATTATAATTATA
1 AATA--T-TT-TAATAATA
*
9465731 AATATATTAATAATA
1 AATATTTTAATAATA
*
9465746 AATGTTTT
1 AATATTTT
9465754 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 17 0.52
16 1 0.03
17 2 0.06
18 2 0.06
19 11 0.33
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:9465726 original size:19 final size:19
Alignment explanation
Indices: 9465699--9465735 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
9465689 TCAATATTAA
*
9465699 TATTTTAATAATAAATATT
1 TATTATAATAATAAATATT
*
9465718 TATTATAATTATAAATAT
1 TATTATAATAATAAATAT
9465736 ATTAATAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTATAATAATAAATATT
Done.