Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 67 of 175
Found at i:20030188 original size:21 final size:20
Alignment explanation
Indices: 20030145--20030204 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
20030135 CACTAACTCT
* *
20030145 TAACCTCTAACCTCAAACCC
1 TAACCACTAACCTTAAACCC
* *
20030165 TAACCCCTAACCTTTAACCCC
1 TAACCACTAACC-TTAAACCC
20030186 TAACCACTAACCCTTAAAC
1 TAACCACTAA-CCTTAAAC
20030205 ATTATTTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
20 11 0.33
21 20 0.61
22 2 0.06
ACGTcount: A:0.35, C:0.43, G:0.00, T:0.22
Consensus pattern (20 bp):
TAACCACTAACCTTAAACCC
Found at i:20030307 original size:36 final size:35
Alignment explanation
Indices: 20030254--20030342 Score: 133
Period size: 35 Copynumber: 2.5 Consensus size: 35
20030244 ACCCTAACCC
*
20030254 AACCCCTGAATCCCTAAACCTTAAATCCCTAACTCTT
1 AACCCCT-AATCCCTAAACCTTAAATCCC-AACCCTT
*
20030291 AACCCCTAACCCCTAAACCTTAAATCCCAACCCTT
1 AACCCCTAATCCCTAAACCTTAAATCCCAACCCTT
*
20030326 AACCCATAATCCCTAAA
1 AACCCCTAATCCCTAAA
20030343 TCCATACTCC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.44
36 20 0.42
37 7 0.15
ACGTcount: A:0.36, C:0.40, G:0.01, T:0.22
Consensus pattern (35 bp):
AACCCCTAATCCCTAAACCTTAAATCCCAACCCTT
Found at i:20030323 original size:28 final size:28
Alignment explanation
Indices: 20030291--20030345 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
20030281 CCTAACTCTT
* *
20030291 AACCCCTAACCCCTAAACCTTAAATCCC
1 AACCCCTAACCCATAAACCCTAAATCCC
* *
20030319 AACCCTTAACCCATAATCCCTAAATCC
1 AACCCCTAACCCATAAACCCTAAATCC
20030346 ATACTCCCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.36, C:0.44, G:0.00, T:0.20
Consensus pattern (28 bp):
AACCCCTAACCCATAAACCCTAAATCCC
Found at i:20030765 original size:40 final size:39
Alignment explanation
Indices: 20030706--20030939 Score: 193
Period size: 40 Copynumber: 5.8 Consensus size: 39
20030696 TAAAATGTTT
* * *
20030706 TTAGCGGCGCTTTTCAAAAATGCCGCTAAAGCCCCCAGCA
1 TTAGCGGCGCTTTT-AAAAACGCCGCTAAAACCCACAGCA
* *
20030746 TTAGCGACGCGTTTTAAAAACGCCGCTAAAACCCAGAGCA
1 TTAGCGGCGC-TTTTAAAAACGCCGCTAAAACCCACAGCA
* * ** *
20030786 TTAGCGGTGCTTTTTAAAAAACACCGCTAAAACAAAGAGCA
1 TTAGCGGCGC-TTTT-AAAAACGCCGCTAAAACCCACAGCA
*
20030827 -TAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCA-AGCA
1 TTAGCGGCGC-TTTT-AAAAACGCCGCTAAA-ACCCACAGCA
* * * *
20030867 TTAGCAGCACTTTTTAAAAAGCGTCGCTAAAACCCAGAGCA
1 TTAGCGGCGC-TTTTAAAAA-CGCCGCTAAAACCCACAGCA
* * *
20030908 CTAGCGGCACTTTTTAAAAAACGCTGCTAAAA
1 TTAGCGGCGC-TTTT-AAAAACGCCGCTAAAA
20030940 AATGGCCGCT
Statistics
Matches: 162, Mismatches: 25, Indels: 13
0.81 0.12 0.06
Matches are distributed among these distances:
40 82 0.51
41 75 0.46
42 5 0.03
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.21
Consensus pattern (39 bp):
TTAGCGGCGCTTTTAAAAACGCCGCTAAAACCCACAGCA
Found at i:20030818 original size:41 final size:41
Alignment explanation
Indices: 20030706--20030939 Score: 251
Period size: 41 Copynumber: 5.8 Consensus size: 41
20030696 TAAAATGTTT
* * * **
20030706 TTAGCGGCGC-TTTTCAAAAATGCCGCTAAAGCCCCCAGCA
1 TTAGCGGCGCTTTTTAAAAAACGCCGCTAAAACCCAGAGCA
* *
20030746 TTAGCGACGCGTTTT-AAAAACGCCGCTAAAACCCAGAGCA
1 TTAGCGGCGCTTTTTAAAAAACGCCGCTAAAACCCAGAGCA
* * **
20030786 TTAGCGGTGCTTTTTAAAAAACACCGCTAAAACAAAGAGCA
1 TTAGCGGCGCTTTTTAAAAAACGCCGCTAAAACCCAGAGCA
* *
20030827 -TAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCA-AGCA
1 TTAGCGGCGCTTTTTAAAAAACGCCGCTAAA-ACCCAGAGCA
* * * *
20030867 TTAGCAGCACTTTTTAAAAAGCGTCGCTAAAACCCAGAGCA
1 TTAGCGGCGCTTTTTAAAAAACGCCGCTAAAACCCAGAGCA
* * *
20030908 CTAGCGGCACTTTTTAAAAAACGCTGCTAAAA
1 TTAGCGGCGCTTTTTAAAAAACGCCGCTAAAA
20030940 AATGGCCGCT
Statistics
Matches: 161, Mismatches: 28, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
40 77 0.48
41 84 0.52
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.21
Consensus pattern (41 bp):
TTAGCGGCGCTTTTTAAAAAACGCCGCTAAAACCCAGAGCA
Found at i:20030846 original size:81 final size:80
Alignment explanation
Indices: 20030742--20030939 Score: 227
Period size: 81 Copynumber: 2.4 Consensus size: 80
20030732 TAAAGCCCCC
* * * * **
20030742 AGCATTAGCGACGCGTTTTAAAAACGCCGCTAAAACCCAGAGCATTAGCGGTGCTTTTTAAAAAA
1 AGCACTAGCGGCGCTTTTTAAAAACGCCGCTAAAACCCA-AGCATTAGCAGCACTTTTTAAAAAA
20030807 CACCGCTAAAACAAAG
65 CACCGCTAAAACAAAG
*
20030823 AGCA-TAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCAAGCATTAGCAGCACTTTTTAAAAA
1 AGCACTAGCGGCGCTTTTT-AAAAACGCCGCTAAA-ACCCAAGCATTAGCAGCACTTTTTAAAAA
* ** **
20030887 GCGTCGCTAAAACCCAG
64 ACACCGCTAAAACAAAG
* *
20030904 AGCACTAGCGGCACTTTTTAAAAAACGCTGCTAAAA
1 AGCACTAGCGGCGCTTTTT-AAAAACGCCGCTAAAA
20030940 AATGGCCGCT
Statistics
Matches: 99, Mismatches: 15, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
80 12 0.12
81 56 0.57
82 31 0.31
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (80 bp):
AGCACTAGCGGCGCTTTTTAAAAACGCCGCTAAAACCCAAGCATTAGCAGCACTTTTTAAAAAAC
ACCGCTAAAACAAAG
Found at i:20031003 original size:38 final size:37
Alignment explanation
Indices: 20030955--20031028 Score: 112
Period size: 38 Copynumber: 2.0 Consensus size: 37
20030945 CCGCTAAATT
* * *
20030955 CCCCAGCATTAGCGGCGCTTTTTCAAAAATGCCGCTG
1 CCCCAGCATTAGCGACGCTTCTTAAAAAATGCCGCTG
20030992 CCCCGAGCATTAGCGACGCTTCTTAAAAAATGCCGCT
1 CCCC-AGCATTAGCGACGCTTCTTAAAAAATGCCGCT
20031029 AAAGCCTCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 4 0.12
38 29 0.88
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.23
Consensus pattern (37 bp):
CCCCAGCATTAGCGACGCTTCTTAAAAAATGCCGCTG
Found at i:20031186 original size:39 final size:41
Alignment explanation
Indices: 20031112--20031206 Score: 99
Period size: 39 Copynumber: 2.4 Consensus size: 41
20031102 GGAATTTGGT
* *
20031112 TTTTTA-CGGCGTTTTTCCAAAAAACGCCGCGAATGCTC-A
1 TTTTTAGCGGCATTTTTCCAAAAAACGCCACGAATGCTCGA
*
20031151 TTTTTAGCGGCATTTTT-CAAAAAA-GACCACTAATGCTCGA
1 TTTTTAGCGGCATTTTTCCAAAAAACG-CCACGAATGCTCGA
* *
20031191 TCTTTAGTGGCGATTT
1 TTTTTAGCGGC-ATTT
20031207 CCATATACAC
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
38 1 0.02
39 23 0.49
40 19 0.40
41 4 0.09
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (41 bp):
TTTTTAGCGGCATTTTTCCAAAAAACGCCACGAATGCTCGA
Found at i:20039787 original size:45 final size:45
Alignment explanation
Indices: 20039723--20039809 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
20039713 TAGATACTCG
* *
20039723 GTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTCCA
1 GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCA
* *
20039768 GTGGAATCAGCACATAGCAACCACTTTACTAATTAATGATGT
1 GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
20039810 TCGGTTCACA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (45 bp):
GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCA
Found at i:20039876 original size:51 final size:51
Alignment explanation
Indices: 20039818--20040002 Score: 250
Period size: 51 Copynumber: 3.6 Consensus size: 51
20039808 GTTCGGTTCA
*
20039818 CATAGTAGCCTGCACATAGTACTACACACATGATTGAAACTATCCGGTACG
1 CATAGTAGCCTGCACATAGTACTACACACGTGATTGAAACTATCCGGTACG
* *
20039869 CATAGTAGCCTGCACATAGTACTCCACACGTGATCGAAACTATCCGGTACG
1 CATAGTAGCCTGCACATAGTACTACACACGTGATTGAAACTATCCGGTACG
* * * * *
20039920 CATAGTAGCCTGCACATAGTACTACACATGCGACCT--ATC-ATTCCGGTACA
1 CATAGTAGCCTGCACATAGTACTACACACGTGA-TTGAAACTA-TCCGGTACG
*
20039970 CGTAGTAGCCTGCACATAGTACTACACACGTGA
1 CATAGTAGCCTGCACATAGTACTACACACGTGA
20040003 CCATCACTTT
Statistics
Matches: 119, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
49 1 0.01
50 40 0.34
51 78 0.66
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (51 bp):
CATAGTAGCCTGCACATAGTACTACACACGTGATTGAAACTATCCGGTACG
Found at i:20040026 original size:101 final size:100
Alignment explanation
Indices: 20039817--20040002 Score: 234
Period size: 101 Copynumber: 1.9 Consensus size: 100
20039807 TGTTCGGTTC
* * *
20039817 ACATAGTAGCCTGCACATAGTACTACACACATGATTGAAACTATCCGGTACGCATAGTAGCCTGC
1 ACATAGTAGCCTGCACATAGTACTACACACACGACTGAAACTATCCGGTACACATAGTAGCCTGC
* *
20039882 ACATAGTACTCCACACGTGATCGAAACTATCCGGT
66 ACATAGTACTACACACGTGATCCAAACTATCCGGT
** * *
20039917 ACGCATAGTAGCCTGCACATAGTACTACACATGCGACCT--ATC-ATTCCGGTACACGTAGTAGC
1 A--CATAGTAGCCTGCACATAGTACTACACACACGA-CTGAAACTA-TCCGGTACACATAGTAGC
20039979 CTGCACATAGTACTACACACGTGA
62 CTGCACATAGTACTACACACGTGA
20040003 CCATCACTTT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
100 2 0.03
101 41 0.55
102 30 0.41
103 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (100 bp):
ACATAGTAGCCTGCACATAGTACTACACACACGACTGAAACTATCCGGTACACATAGTAGCCTGC
ACATAGTACTACACACGTGATCCAAACTATCCGGT
Found at i:20041450 original size:15 final size:15
Alignment explanation
Indices: 20041427--20041468 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
20041417 CATACAAATT
*
20041427 AAAGAATTATTAGAA
1 AAAGAATTAATAGAA
*
20041442 AAAGTATTAATAGAA
1 AAAGAATTAATAGAA
*
20041457 AAA-AACTAATAG
1 AAAGAATTAATAG
20041469 TCCACATTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.62, C:0.02, G:0.12, T:0.24
Consensus pattern (15 bp):
AAAGAATTAATAGAA
Found at i:20044234 original size:42 final size:41
Alignment explanation
Indices: 20044171--20044303 Score: 169
Period size: 42 Copynumber: 3.2 Consensus size: 41
20044161 AAATATCAAG
* * *
20044171 GAAGCAACATGAGAAAGCAACATCCATG-TCTAAACAAAAAAA
1 GAAGCAACTTGGGAAAGCAACATCCAAGTTC-AAAC-AAAAAA
*
20044213 GAAGCAACTTGGGAAAACAACATCCAAGTTCAAACAAAAAA
1 GAAGCAACTTGGGAAAGCAACATCCAAGTTCAAACAAAAAA
* *
20044254 GAAAGCAACTTGGGAAAGCAACATCCAAGTTCAGATAAAAAA
1 G-AAGCAACTTGGGAAAGCAACATCCAAGTTCAAACAAAAAA
20044296 GGAAGCAA
1 -GAAGCAA
20044304 TGTGGAAACA
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
41 7 0.09
42 71 0.88
43 3 0.04
ACGTcount: A:0.53, C:0.18, G:0.17, T:0.12
Consensus pattern (41 bp):
GAAGCAACTTGGGAAAGCAACATCCAAGTTCAAACAAAAAA
Found at i:20046083 original size:12 final size:12
Alignment explanation
Indices: 20046066--20046093 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
20046056 AGTTTATAGA
20046066 ATTATCAGAATT
1 ATTATCAGAATT
20046078 ATTATCAGAATT
1 ATTATCAGAATT
20046090 ATTA
1 ATTA
20046094 GAACTACTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (12 bp):
ATTATCAGAATT
Found at i:20052296 original size:40 final size:40
Alignment explanation
Indices: 20052198--20052460 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
20052188 TCCTCGTTCA
* * * * *
20052198 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
20052237 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
20052277 AATGCCTTCGGGACTTAACCTGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
20052317 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
20052357 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
20052397 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
20052437 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
20052461 CAGCATTCAA
Statistics
Matches: 198, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
39 37 0.19
40 153 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:20072570 original size:45 final size:45
Alignment explanation
Indices: 20072449--20072578 Score: 154
Period size: 46 Copynumber: 2.9 Consensus size: 45
20072439 CAAATGGCCG
* *
20072449 TGGATACA-AAAAAATATCCTGTAGATGGAATCTACCTTTGGCTA
1 TGGATACACAAAAAATAACCTGTAGATGGAATCTACCTCTGGCTA
* ** *
20072493 TGGACTGCACAGGAAATAACCTGTAGAGGGAATCTACCTCTGGCTA
1 TGGA-TACACAAAAAATAACCTGTAGATGGAATCTACCTCTGGCTA
* * * *
20072539 TGGATACACAACAAATAACATGCAGATGGAATCTGCCTCT
1 TGGATACACAAAAAATAACCTGTAGATGGAATCTACCTCT
20072579 TGTTATGGGT
Statistics
Matches: 71, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
44 4 0.06
45 32 0.45
46 35 0.49
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.25
Consensus pattern (45 bp):
TGGATACACAAAAAATAACCTGTAGATGGAATCTACCTCTGGCTA
Found at i:20072586 original size:45 final size:44
Alignment explanation
Indices: 20072449--20072599 Score: 142
Period size: 45 Copynumber: 3.3 Consensus size: 44
20072439 CAAATGGCCG
* *
20072449 TGGATACAAAAAAATATCCTGTAGATGGAATCTACCT-TTGGCTA
1 TGGATACAAACAAATAACCTGTAGATGGAATCTACCTCTT-GCTA
* ** * *
20072493 TGGACTGCACAGGAAATAACCTGTAGAGGGAATCTACCTCTGGCTA
1 TGGA-TACA-AACAAATAACCTGTAGATGGAATCTACCTCTTGCTA
* * * *
20072539 TGGATACACAACAAATAACATGCAGATGGAATCTGCCTCTTGTTA
1 TGGATACA-AACAAATAACCTGTAGATGGAATCTACCTCTTGCTA
*
20072584 TGGGTACAAAGCAAAT
1 TGGATACAAA-CAAAT
20072600 TTGCAGATAA
Statistics
Matches: 87, Mismatches: 16, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
44 6 0.07
45 47 0.54
46 33 0.38
47 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (44 bp):
TGGATACAAACAAATAACCTGTAGATGGAATCTACCTCTTGCTA
Found at i:20084809 original size:22 final size:21
Alignment explanation
Indices: 20084784--20084827 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
20084774 TGATAAACTT
20084784 TAATATATA-ATTATATTATTTA
1 TAATATATATATTA-ATT-TTTA
*
20084806 TAATTTATATATTAATTTTTA
1 TAATATATATATTAATTTTTA
20084827 T
1 T
20084828 CAACTTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATATATATATTAATTTTTA
Found at i:20086403 original size:20 final size:21
Alignment explanation
Indices: 20086359--20086406 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
20086349 CAAATTTGAA
20086359 ATTTTTAGTCAATTTTACAATT
1 ATTTTTAGTCAATTTTA-AATT
* *
20086381 ATTTTTAGTGAATTTT-GATT
1 ATTTTTAGTCAATTTTAAATT
20086401 ATTTTT
1 ATTTTT
20086407 GACAGATTCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 9 0.38
22 15 0.62
ACGTcount: A:0.27, C:0.04, G:0.08, T:0.60
Consensus pattern (21 bp):
ATTTTTAGTCAATTTTAAATT
Found at i:20088560 original size:10 final size:10
Alignment explanation
Indices: 20088547--20088607 Score: 63
Period size: 10 Copynumber: 6.2 Consensus size: 10
20088537 AACCGAACAA
20088547 AACAGAATAG
1 AACAGAATAG
20088557 AACAGAATAG
1 AACAGAATAG
* *
20088567 AACAAAACA-
1 AACAGAATAG
20088576 AATCA-AATAG
1 AA-CAGAATAG
* *
20088586 AATAGAGTAG
1 AACAGAATAG
20088596 AACAGAATAG
1 AACAGAATAG
20088606 AA
1 AA
20088608 AATATATGTC
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
9 6 0.15
10 35 0.85
ACGTcount: A:0.62, C:0.10, G:0.16, T:0.11
Consensus pattern (10 bp):
AACAGAATAG
Found at i:20088596 original size:29 final size:30
Alignment explanation
Indices: 20088542--20088599 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
20088532 AACAGAACCG
20088542 AACAAAACAGAATAGAACAGAATAGAACAA
1 AACAAAACAGAATAGAACAGAATAGAACAA
* * *
20088572 AACAAATCA-AATAGAATAGAGTAGAACA
1 AACAAAACAGAATAGAACAGAATAGAACA
20088600 GAATAGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.64, C:0.12, G:0.14, T:0.10
Consensus pattern (30 bp):
AACAAAACAGAATAGAACAGAATAGAACAA
Found at i:20092453 original size:21 final size:21
Alignment explanation
Indices: 20092420--20092525 Score: 76
Period size: 21 Copynumber: 5.2 Consensus size: 21
20092410 CATGATCTGT
**
20092420 CCACACGGCCGTGTATCTCAG
1 CCACACGATCGTGTATCTCAG
20092441 CCACACGATCGTG----TCAG
1 CCACACGATCGTGTATCTCAG
* * * *
20092458 CCACATGGTCGTGTCTCTCAA
1 CCACACGATCGTGTATCTCAG
* *
20092479 CCACACAATCGCGTATCTCAG
1 CCACACGATCGTGTATCTCAG
* * * *
20092500 TCACACCATTGTGTTTCTCAG
1 CCACACGATCGTGTATCTCAG
20092521 CCACA
1 CCACA
20092526 TGGCTGTTTA
Statistics
Matches: 64, Mismatches: 17, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
17 15 0.23
21 49 0.77
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.24
Consensus pattern (21 bp):
CCACACGATCGTGTATCTCAG
Found at i:20092459 original size:17 final size:17
Alignment explanation
Indices: 20092437--20092472 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
20092427 GCCGTGTATC
20092437 TCAGCCACACGATCGTG
1 TCAGCCACACGATCGTG
* *
20092454 TCAGCCACATGGTCGTG
1 TCAGCCACACGATCGTG
20092471 TC
1 TC
20092473 TCTCAACCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.19, C:0.33, G:0.25, T:0.22
Consensus pattern (17 bp):
TCAGCCACACGATCGTG
Found at i:20093978 original size:24 final size:21
Alignment explanation
Indices: 20093951--20093995 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
20093941 TGTTTTTGGG
20093951 AATGAATTGAAAATGTGTGTATTA
1 AATGAATT--AAATGTGT-TATTA
*
20093975 AATGAGTTAAATGTGTTATTA
1 AATGAATTAAATGTGTTATTA
20093996 TATATCAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 8 0.40
24 7 0.35
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (21 bp):
AATGAATTAAATGTGTTATTA
Found at i:20096270 original size:15 final size:16
Alignment explanation
Indices: 20096238--20096271 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
20096228 ATTTCATCTC
20096238 ATTTGCATATAGGTTA
1 ATTTGCATATAGGTTA
*
20096254 ATTTGCATCTA-GTTA
1 ATTTGCATATAGGTTA
20096269 ATT
1 ATT
20096272 AATTTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.09, G:0.15, T:0.47
Consensus pattern (16 bp):
ATTTGCATATAGGTTA
Found at i:20098833 original size:22 final size:21
Alignment explanation
Indices: 20098793--20098833 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
20098783 AATCTTTTAA
* *
20098793 AAATAAATATTTATTTTTATC
1 AAATAAATAATTATATTTATC
20098814 AAATAACATAATTATATTTA
1 AAATAA-ATAATTATATTTA
20098834 GTACTTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (21 bp):
AAATAAATAATTATATTTATC
Found at i:20100986 original size:37 final size:37
Alignment explanation
Indices: 20100936--20101010 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
20100926 CTTCCTCGGT
20100936 GCAACACGAATCAATTGGTGTCTCGTCATTTTTTTTG
1 GCAACACGAATCAATTGGTGTCTCGTCATTTTTTTTG
20100973 GCAACACGAATCAATTGGTGTCTCGTCATTTTTTTTG
1 GCAACACGAATCAATTGGTGTCTCGTCATTTTTTTTG
20101010 G
1 G
20101011 ACTCCTAGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (37 bp):
GCAACACGAATCAATTGGTGTCTCGTCATTTTTTTTG
Found at i:20101746 original size:18 final size:20
Alignment explanation
Indices: 20101725--20101774 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 20
20101715 AAAGGAAGAC
20101725 AGAAAAAGA-AATCAAAAA-
1 AGAAAAAGAGAATCAAAAAG
*
20101743 AGAAAAAGAGAATGAAAAAG
1 AGAAAAAGAGAATCAAAAAG
20101763 AGCAAAAAGAGA
1 AG-AAAAAGAGA
20101775 TTGAGATTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 9 0.32
19 8 0.29
20 2 0.07
21 9 0.32
ACGTcount: A:0.72, C:0.04, G:0.20, T:0.04
Consensus pattern (20 bp):
AGAAAAAGAGAATCAAAAAG
Found at i:20110687 original size:14 final size:14
Alignment explanation
Indices: 20110670--20110698 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
20110660 ACCTCGACGA
20110670 GTAAACGTAGATAT
1 GTAAACGTAGATAT
20110684 GTAAACGTAGATAT
1 GTAAACGTAGATAT
20110698 G
1 G
20110699 GAGGCGACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.24, T:0.28
Consensus pattern (14 bp):
GTAAACGTAGATAT
Found at i:20122328 original size:16 final size:16
Alignment explanation
Indices: 20122307--20122339 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
20122297 TATTATCCCA
20122307 CTAACCTCTATCTCAC
1 CTAACCTCTATCTCAC
20122323 CTAACCTCTATCTCAC
1 CTAACCTCTATCTCAC
20122339 C
1 C
20122340 ATCGAAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.45, G:0.00, T:0.30
Consensus pattern (16 bp):
CTAACCTCTATCTCAC
Found at i:20136714 original size:1 final size:1
Alignment explanation
Indices: 20136628--20136698 Score: 142
Period size: 1 Copynumber: 71.0 Consensus size: 1
20136618 CACATTAACT
20136628 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
20136693 AAAAAA
1 AAAAAA
20136699 TTTCAGAGAT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 70 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:20151108 original size:26 final size:26
Alignment explanation
Indices: 20151079--20151137 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
20151069 TACCTACAAT
20151079 AGTTTCAGAATATCATAACATATATC
1 AGTTTCAGAATATCATAACATATATC
* *
20151105 AGTTTCAGAATATCATAGCATGTATC
1 AGTTTCAGAATATCATAACATATATC
20151131 AGTTTCA
1 AGTTTCA
20151138 TAACACTTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (26 bp):
AGTTTCAGAATATCATAACATATATC
Found at i:20151902 original size:33 final size:34
Alignment explanation
Indices: 20151850--20151915 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 34
20151840 GCATAGTTGA
* *
20151850 ACAGTCTTGGGCCTAAGCCC-TTTCAGTATCAGTG
1 ACAGTCTTAGGCCTAAGCCCATCTCAGTA-CAGTG
*
20151884 ACAG-CTTAGGCCTTAGCCCATCTCAGTACAGT
1 ACAGTCTTAGGCCTAAGCCCATCTCAGTACAGT
20151916 ATAAAAATGG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 17 0.61
34 11 0.39
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (34 bp):
ACAGTCTTAGGCCTAAGCCCATCTCAGTACAGTG
Found at i:20155755 original size:20 final size:18
Alignment explanation
Indices: 20155710--20155757 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
20155700 TTAGAAAAAC
20155710 TTTA-TTTTTATTAATTT
1 TTTATTTTTTATTAATTT
*
20155727 TTCTGTTTTTATATTAATATT
1 TT-TATTTTT-TATTAAT-TT
20155748 TTTATTTTTT
1 TTTATTTTTT
20155758 TTTCAATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 2 0.08
18 1 0.04
19 5 0.20
20 13 0.52
21 4 0.16
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (18 bp):
TTTATTTTTTATTAATTT
Found at i:20156886 original size:16 final size:15
Alignment explanation
Indices: 20156861--20156890 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
20156851 ATGTTGGCTA
20156861 AATTGATTTCAAAAG
1 AATTGATTTCAAAAG
20156876 AATTCGATTTCAAAA
1 AATT-GATTTCAAAA
20156891 CATGGAAGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (15 bp):
AATTGATTTCAAAAG
Found at i:20160498 original size:14 final size:14
Alignment explanation
Indices: 20160481--20160518 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
20160471 TTTTTTATTT
*
20160481 TTATTTTTATTTTA
1 TTATTGTTATTTTA
*
20160495 TTATTGTTATTATA
1 TTATTGTTATTTTA
20160509 TTATTGTTAT
1 TTATTGTTAT
20160519 ATCTTACTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (14 bp):
TTATTGTTATTTTA
Found at i:20162399 original size:42 final size:41
Alignment explanation
Indices: 20162286--20162429 Score: 119
Period size: 43 Copynumber: 3.4 Consensus size: 41
20162276 CGAAAAGCTC
* * * * *
20162286 ATACAATGCCAACGTCTCAGACGAGGTCTTACATGTAATCAA
1 ATACGATGCCAATGTCTCAGAC-AGGTCTTACACGAAACCAA
* * * * *
20162328 ATGTCGATGCCACTGTCCCAAACAGGGTCTTACACGAAACCAT
1 AT-ACGATGCCAATGTCTCAGACA-GGTCTTACACGAAACCAA
*
20162371 ATACGATGCCAATGTCTCAGACACGGTCTTACACATAAATCTCAA
1 ATACGATGCCAATGTCTCAGACA-GGTCTTACAC-GAAA-C-CAA
20162416 AT-CGATGCCAATGT
1 ATACGATGCCAATGT
20162430 TCCAAACATT
Statistics
Matches: 80, Mismatches: 17, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
42 30 0.38
43 33 0.41
44 13 0.16
45 4 0.05
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (41 bp):
ATACGATGCCAATGTCTCAGACAGGTCTTACACGAAACCAA
Found at i:20162427 original size:44 final size:42
Alignment explanation
Indices: 20162331--20162454 Score: 126
Period size: 44 Copynumber: 2.9 Consensus size: 42
20162321 TAATCAAATG
* * * * *
20162331 TCGATGCCACTGTCCCAAACAGGGTCTTACACGAAA-CCATA
1 TCGATGCCAATGTCTCAAACACGGTCTTACACAAAATCCAAA
*
20162372 TACGATGCCAATGTCTCAGACACGGTCTTACACATAAATCTCAAA
1 T-CGATGCCAATGTCTCAAACACGGTCTTACACA-AAATC-CAAA
**
20162417 TCGATGCCAATGT-TCCAAACATTGTCTTACACAAAATC
1 TCGATGCCAATGTCT-CAAACACGGTCTTACACAAAATC
20162455 ACATATCAGA
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
41 1 0.01
42 27 0.39
43 9 0.13
44 28 0.41
45 4 0.06
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (42 bp):
TCGATGCCAATGTCTCAAACACGGTCTTACACAAAATCCAAA
Found at i:20171069 original size:14 final size:14
Alignment explanation
Indices: 20171050--20171085 Score: 58
Period size: 12 Copynumber: 2.7 Consensus size: 14
20171040 AAACTAGCTC
20171050 TTTTTTTTCACAAT
1 TTTTTTTTCACAAT
20171064 TTTTTTTT--CAAT
1 TTTTTTTTCACAAT
20171076 TTTTTTTTCA
1 TTTTTTTTCA
20171086 AGAAACTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 12 0.60
14 8 0.40
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTTTTTCACAAT
Found at i:20176623 original size:25 final size:25
Alignment explanation
Indices: 20176590--20176711 Score: 65
Period size: 25 Copynumber: 4.9 Consensus size: 25
20176580 ATATATAAAG
* * * *
20176590 TATAAAAATATATTTTATCAAAATA
1 TATAAAAATAAAATATATAAAAATA
*
20176615 TATACAAATAAAATATATAAAAATA
1 TATAAAAATAAAATATATAAAAATA
* * * *
20176640 TAT-ATAAT--ATTTTA-AAAAACA
1 TATAAAAATAAAATATATAAAAATA
* *
20176661 TATAAAAATAATATATATACAAAAAAA
1 TATAAAAATAA-A-ATATATAAAAATA
*
20176688 TTATAAATATAAAAT-TATTAAAAA
1 -TATAAAAATAAAATATA-TAAAAA
20176712 CGTAAATCTA
Statistics
Matches: 73, Mismatches: 16, Indels: 15
0.70 0.15 0.14
Matches are distributed among these distances:
21 9 0.12
22 8 0.11
24 3 0.04
25 26 0.36
26 10 0.14
27 7 0.10
28 10 0.14
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (25 bp):
TATAAAAATAAAATATATAAAAATA
Found at i:20176649 original size:17 final size:16
Alignment explanation
Indices: 20176576--20176701 Score: 56
Period size: 15 Copynumber: 8.2 Consensus size: 16
20176566 ATTACTTTTG
20176576 AAAAATATATAAAGTAT
1 AAAAATATATAAA-TAT
**
20176593 AAAAATATAT-TTTAT
1 AAAAATATATAAATAT
*
20176608 CAAAATATATACAA-AT
1 AAAAATATATA-AATAT
*
20176624 AAAATATATAAAAATAT
1 AAAA-ATATATAAATAT
* *
20176641 ATATAATAT-T--TTA-
1 A-AAAATATATAAATAT
* *
20176654 AAAAACATATAAAAAT
1 AAAAATATATAAATAT
* *
20176670 -AATATATATACA-A-
1 AAAAATATATAAATAT
20176683 AAAAAT-TATAAATAT
1 AAAAATATATAAATAT
20176698 AAAA
1 AAAA
20176702 TTATTAAAAA
Statistics
Matches: 78, Mismatches: 19, Indels: 26
0.63 0.15 0.21
Matches are distributed among these distances:
12 5 0.06
13 7 0.09
14 8 0.10
15 26 0.33
16 7 0.09
17 23 0.29
18 2 0.03
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (16 bp):
AAAAATATATAAATAT
Found at i:20176817 original size:15 final size:16
Alignment explanation
Indices: 20176797--20176829 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
20176787 TTAATCTATA
20176797 TTTATAT-TTTTAAAT
1 TTTATATATTTTAAAT
*
20176812 TTTATATATTTTCAAT
1 TTTATATATTTTAAAT
20176828 TT
1 TT
20176830 CAAAATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTATATATTTTAAAT
Found at i:20178054 original size:50 final size:51
Alignment explanation
Indices: 20177995--20178092 Score: 180
Period size: 50 Copynumber: 1.9 Consensus size: 51
20177985 AGGGGAAGCC
20177995 ATGGTTAGGGTTTTCAAGCTTCCAAGCTCGA-TGTAAGTCCGTTCTAAGTT
1 ATGGTTAGGGTTTTCAAGCTTCCAAGCTCGATTGTAAGTCCGTTCTAAGTT
*
20178045 ATGGTTAGGGTTTTCAAGCTTTCAAGCTCGATTGTAAGTCCGTTCTAA
1 ATGGTTAGGGTTTTCAAGCTTCCAAGCTCGATTGTAAGTCCGTTCTAA
20178093 CCCCGTTTTT
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
50 30 0.65
51 16 0.35
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.37
Consensus pattern (51 bp):
ATGGTTAGGGTTTTCAAGCTTCCAAGCTCGATTGTAAGTCCGTTCTAAGTT
Found at i:20178871 original size:51 final size:50
Alignment explanation
Indices: 20178702--20178892 Score: 183
Period size: 51 Copynumber: 3.8 Consensus size: 50
20178692 TAAAAGTGAA
* * * *
20178702 AGTGATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-
1 AGTGATGGTCACATGTGTAGTACTATGTGCAGGCTACTA-ATGCATCAGAT
* * * *
20178752 A-AGATAGGTCGCATGTGTAGTACTATGTGCAGGCTACT-ATGCGTACCGAAT
1 AGTGAT-GGTCACATGTGTAGTACTATGTGCAGGCTACTAATGCAT-CAG-AT
* * * *
20178803 AGCT-TTGATCACGTGTGTAGTACTATGTGCAGGCAACTAAATGCATCAGAT
1 AG-TGATGGTCACATGTGTAGTACTATGTGCAGGCTACT-AATGCATCAGAT
*
20178854 AGTGATGGTCACATGTGTAGTACTATGTGTAGGCTACTA
1 AGTGATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
20178893 TGTGAACCGG
Statistics
Matches: 111, Mismatches: 21, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
48 2 0.02
49 5 0.05
50 34 0.31
51 62 0.56
52 3 0.03
53 5 0.05
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (50 bp):
AGTGATGGTCACATGTGTAGTACTATGTGCAGGCTACTAATGCATCAGAT
Found at i:20178893 original size:102 final size:101
Alignment explanation
Indices: 20178710--20178894 Score: 273
Period size: 101 Copynumber: 1.8 Consensus size: 101
20178700 AAAGTGATGG
* ** * *
20178710 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAAAGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGCAGGCAACTAAATGCACCAGAAAGATAGGTCACATGTGTAGTAC
20178775 TATGTGCAGGCTACTATGCGTACCGAATAGCTTTGA
66 TATGTGCAGGCTACTATGCGTACCGAATAGCTTTGA
* *
20178811 TCACGTGTGTAGTACTATGTGCAGGCAACTAAATGCATCAGATAG-TGATGGTCACATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCAACTAAATGCACCAGAAAGAT-A-GGTCACATGTGTAGT
*
20178875 ACTATGTGTAGGCTACTATG
64 ACTATGTGCAGGCTACTATG
20178895 TGAACCGGTA
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
100 1 0.01
101 40 0.54
102 33 0.45
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGCAGGCAACTAAATGCACCAGAAAGATAGGTCACATGTGTAGTAC
TATGTGCAGGCTACTATGCGTACCGAATAGCTTTGA
Found at i:20178970 original size:46 final size:43
Alignment explanation
Indices: 20178898--20178996 Score: 119
Period size: 46 Copynumber: 2.2 Consensus size: 43
20178888 TACTATGTGA
*
20178898 ACCGGTATCATTAATTATAAGGTGGTTGCTATGTGCT-AATCCC
1 ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGAAT-CC
* *
20178941 ACCGGATATCATTGATTACAAAGGGTGGTTGCTGTGTGCTGAATCC
1 ACCGG-TATCATTAATTA-AAA-GGTGGTTGCTATGTGCTGAATCC
20178987 ACCGTGTATC
1 ACCG-GTATC
20178997 TGTTATTATT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
43 5 0.10
44 11 0.23
45 2 0.04
46 26 0.54
47 4 0.08
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.32
Consensus pattern (43 bp):
ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGAATCC
Found at i:20179166 original size:37 final size:38
Alignment explanation
Indices: 20179097--20179169 Score: 112
Period size: 37 Copynumber: 1.9 Consensus size: 38
20179087 ATGTGTGGAA
* *
20179097 TTGAATTGAATATTGACTTAAAAATGACAAAGTGAATT
1 TTGAATTGAATAGTGACTTAAAAATGAAAAAGTGAATT
*
20179135 TTGAATTGAATAGTGAC-TAAAAGTGAAAAAGTGAA
1 TTGAATTGAATAGTGACTTAAAAATGAAAAAGTGAA
20179170 ATTATGAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 16 0.50
38 16 0.50
ACGTcount: A:0.47, C:0.04, G:0.19, T:0.30
Consensus pattern (38 bp):
TTGAATTGAATAGTGACTTAAAAATGAAAAAGTGAATT
Found at i:20187632 original size:41 final size:41
Alignment explanation
Indices: 20187572--20187763 Score: 173
Period size: 41 Copynumber: 4.8 Consensus size: 41
20187562 GACTTTAGTG
* *
20187572 GCGTTTTTCAAAAAGCGCCGCTAATGCT-AGAGGATTTAGCA
1 GCGTTTTTTAGAAAGCGCCGCTAATGCTCAG-GGATTTAGCA
* * *
20187613 GCGTTTTTTAGAAACCGCCGCTAATGCTCTGGGCTTTAGCA
1 GCGTTTTTTAGAAAGCGCCGCTAATGCTCAGGGATTTAGCA
* * * *
20187654 GCATTTTTTAGAAAGCGCCGCTAATTCTC-TGG-----GCG
1 GCGTTTTTTAGAAAGCGCCGCTAATGCTCAGGGATTTAGCA
* * * * * * *
20187689 GCGTTTTTGAAGAAAGTGCCACTATTGCTCTGGGCTTTAGCG
1 GCGTTTTT-TAGAAAGCGCCGCTAATGCTCAGGGATTTAGCA
20187731 GCGTTTTTTAGAAAGCGCCGCTAATGCTCAGGG
1 GCGTTTTTTAGAAAGCGCCGCTAATGCTCAGGG
20187764 GCTTTTAACG
Statistics
Matches: 121, Mismatches: 22, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
35 9 0.07
36 16 0.13
37 2 0.02
40 2 0.02
41 80 0.66
42 12 0.10
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (41 bp):
GCGTTTTTTAGAAAGCGCCGCTAATGCTCAGGGATTTAGCA
Found at i:20187993 original size:7 final size:7
Alignment explanation
Indices: 20187983--20188042 Score: 50
Period size: 7 Copynumber: 8.7 Consensus size: 7
20187973 AGAGTTTTGA
20187983 GTTTAGG
1 GTTTAGG
*
20187990 GTTTATG
1 GTTTAGG
*
20187997 GTGTA-G
1 GTTTAGG
*
20188003 GTTTAAG
1 GTTTAGG
* *
20188010 GCTTGGG
1 GTTTAGG
20188017 GTTTAGG
1 GTTTAGG
* *
20188024 GTATAAG
1 GTTTAGG
20188031 GTTTAGG
1 GTTTAGG
20188038 GTTTA
1 GTTTA
20188043 CGTTGTAATG
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
6 5 0.12
7 35 0.88
ACGTcount: A:0.18, C:0.02, G:0.38, T:0.42
Consensus pattern (7 bp):
GTTTAGG
Found at i:20203041 original size:27 final size:27
Alignment explanation
Indices: 20203010--20203160 Score: 187
Period size: 27 Copynumber: 5.6 Consensus size: 27
20203000 TAAATTGTAC
20203010 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
20203037 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
20203063 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
20203091 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
20203119 AGCACTAAGTGTGCGATTTGATTAAGT
1 AGCACTAAGTGTGCGATTTGACTATGT
20203146 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
20203161 CACTGAGTGT
Statistics
Matches: 106, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
27 83 0.78
28 23 0.22
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:20203124 original size:82 final size:81
Alignment explanation
Indices: 20203011--20203160 Score: 230
Period size: 82 Copynumber: 1.8 Consensus size: 81
20203001 AAATTGTACA
* *
20203011 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATAAGTA-GCACTAAGTG
20203075 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
20203092 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTAAGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATAAGTAGCACTAAGTG
20203157 TGCG
65 TGCG
20203161 CACTGAGTGT
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 15 0.24
82 46 0.74
83 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATAAGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:20204890 original size:12 final size:12
Alignment explanation
Indices: 20204873--20204900 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
20204863 GCTAGCCATG
20204873 ATGTTACTATTA
1 ATGTTACTATTA
20204885 ATGTTACTATTA
1 ATGTTACTATTA
20204897 ATGT
1 ATGT
20204901 CCTTAATCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.50
Consensus pattern (12 bp):
ATGTTACTATTA
Found at i:20206243 original size:43 final size:43
Alignment explanation
Indices: 20206196--20206330 Score: 200
Period size: 43 Copynumber: 3.1 Consensus size: 43
20206186 TTTTTATGAC
20206196 CTTTAGCGGCGTTTGTGGGTAAAGTGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGTTTGTGGGTAAAGTGCCGCTAAAGATCATGTT
* * *
20206239 CTTTAGCGGCGTTTGTGGGTAAAGCGTCGCTAAAGATGATGTT
1 CTTTAGCGGCGTTTGTGGGTAAAGTGCCGCTAAAGATCATGTT
* * *
20206282 CTTTAGTGGCGTTTGTGGGTAAAGCT-CCGCTAAAGAACATGAT
1 CTTTAGCGGCGTTTGTGGGTAAAG-TGCCGCTAAAGATCATGTT
20206325 CTTTAG
1 CTTTAG
20206331 TGGAGTTTTT
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
43 82 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.33
Consensus pattern (43 bp):
CTTTAGCGGCGTTTGTGGGTAAAGTGCCGCTAAAGATCATGTT
Found at i:20218794 original size:57 final size:58
Alignment explanation
Indices: 20218727--20218891 Score: 217
Period size: 58 Copynumber: 2.9 Consensus size: 58
20218717 TGAATGAAAA
** * ** *
20218727 TGAACAGGAAATATTCTCTGGCAAGAACAGTAAATATTCTCT--TTAGAAAAAGACGAG
1 TGAACAGGAAATATTCTCTGGCGTGAACAGTAAATATTCCCTGACAAG-AAAAGACAAG
20218784 TGAACAGGAAATATTCTCTGGCGTGAACAGTAAATATTCCCTGACAAGAAAAGACAAG
1 TGAACAGGAAATATTCTCTGGCGTGAACAGTAAATATTCCCTGACAAGAAAAGACAAG
* * * *
20218842 TGAACAGAAAATATTCTCTAGCGTGAATAGTAAATATTCCCTGGCAAGAA
1 TGAACAGGAAATATTCTCTGGCGTGAACAGTAAATATTCCCTGACAAGAA
20218892 CAGTAGAAAT
Statistics
Matches: 96, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
57 39 0.41
58 55 0.57
59 2 0.02
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (58 bp):
TGAACAGGAAATATTCTCTGGCGTGAACAGTAAATATTCCCTGACAAGAAAAGACAAG
Found at i:20218896 original size:23 final size:23
Alignment explanation
Indices: 20218843--20218896 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
20218833 AAAGACAAGT
* * **
20218843 GAACAGAAAATATTCTCTAGCGT
1 GAACAGTAAATATTCCCTAGCAA
* *
20218866 GAATAGTAAATATTCCCTGGCAA
1 GAACAGTAAATATTCCCTAGCAA
20218889 GAACAGTA
1 GAACAGTA
20218897 GAAATCTCTA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.24
Consensus pattern (23 bp):
GAACAGTAAATATTCCCTAGCAA
Found at i:20219339 original size:57 final size:59
Alignment explanation
Indices: 20219186--20219350 Score: 239
Period size: 58 Copynumber: 2.9 Consensus size: 59
20219176 ATTTCTACTG
* * * *
20219186 TTCTTGCCAGGGAATATTTACTGTTC-ACGCTATAGAATATTTCCTGTTCACTCGTCTT
1 TTCTTGCCAGGGAATATTTATTGTTCTACGCCAAAGAATATTTCCTGTTCACTAGTCTT
*
20219244 TTCTTGCCAGGGAATATTTATTGTT-TACGCCAGAGAATATTTCCTGTTCACTAGTCTT
1 TTCTTGCCAGGGAATATTTATTGTTCTACGCCAAAGAATATTTCCTGTTCACTAGTCTT
* *
20219302 TTCTTG-CAGGGAATATTTATTGTTCTA-GCCAAAGAATATTCCCTATTCA
1 TTCTTGCCAGGGAATATTTATTGTTCTACGCCAAAGAATATTTCCTGTTCA
20219351 TCTCTAAAGA
Statistics
Matches: 98, Mismatches: 7, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
57 37 0.38
58 61 0.62
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.41
Consensus pattern (59 bp):
TTCTTGCCAGGGAATATTTATTGTTCTACGCCAAAGAATATTTCCTGTTCACTAGTCTT
Found at i:20234600 original size:13 final size:13
Alignment explanation
Indices: 20234582--20234606 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20234572 ATTAAAAATG
20234582 TTTTAAAATTTAT
1 TTTTAAAATTTAT
20234595 TTTTAAAATTTA
1 TTTTAAAATTTA
20234607 AAATGATTTA
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTAAAATTTAT
Found at i:20234617 original size:30 final size:33
Alignment explanation
Indices: 20234567--20234627 Score: 83
Period size: 30 Copynumber: 1.9 Consensus size: 33
20234557 AATTAAAATA
*
20234567 AAAATATTAAAAATGTTTTAAA-ATTTATTTTT
1 AAAATATTAAAAATGATTTAAATATTTATTTTT
*
20234599 AAAAT-TT-AAAATGATTTAAATTTTTATTT
1 AAAATATTAAAAATGATTTAAATATTTATTT
20234628 CAAATTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 12 0.46
31 9 0.35
32 5 0.19
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (33 bp):
AAAATATTAAAAATGATTTAAATATTTATTTTT
Found at i:20235217 original size:40 final size:40
Alignment explanation
Indices: 20235171--20235264 Score: 134
Period size: 40 Copynumber: 2.4 Consensus size: 40
20235161 ATTTGGATAC
* * *
20235171 AAAACGCCGCTAAAGATCGAGCGTTAGCGGTGCTTTTTGG
1 AAAACGCCGCTAAAGATCGAGAGTTAGCGGCGCTTTATGG
* *
20235211 AAAACGCCGCTAAAGATCGAGATTTAGTGGCGCTTTATGG
1 AAAACGCCGCTAAAGATCGAGAGTTAGCGGCGCTTTATGG
*
20235251 AAATCGCCGCTAAA
1 AAAACGCCGCTAAA
20235265 AATAAGCATT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (40 bp):
AAAACGCCGCTAAAGATCGAGAGTTAGCGGCGCTTTATGG
Found at i:20235472 original size:41 final size:41
Alignment explanation
Indices: 20235411--20235515 Score: 131
Period size: 41 Copynumber: 2.6 Consensus size: 41
20235401 GCTAAAGCCC
* *
20235411 TTTTTGAGAAAGCG-TCGCTAATGCTTAAGGCTCTATCTACG
1 TTTTTGAGAAAGCGCT-GCTAATGCTTAAGGCTCTAGCGACG
* * * **
20235452 TTTTTGGGAAAGCGCTGCTAATGCTTAGGGCTTTAGCGGTG
1 TTTTTGAGAAAGCGCTGCTAATGCTTAAGGCTCTAGCGACG
20235493 TTTTTGAGAAAGCGCTGCTAATG
1 TTTTTGAGAAAGCGCTGCTAATG
20235516 TTCTATTTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
41 54 0.98
42 1 0.02
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.34
Consensus pattern (41 bp):
TTTTTGAGAAAGCGCTGCTAATGCTTAAGGCTCTAGCGACG
Found at i:20235820 original size:22 final size:21
Alignment explanation
Indices: 20235795--20235848 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
20235785 GTGTTACCAT
20235795 TTTAAGGTTTATGGATTATGGG
1 TTTAAGGTTTATGGATTA-GGG
* * *
20235817 TTTAGGGTTTTTGGTTTAGGG
1 TTTAAGGTTTATGGATTAGGG
* *
20235838 TATATGGTTTA
1 TTTAAGGTTTA
20235849 GACAGGTTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (21 bp):
TTTAAGGTTTATGGATTAGGG
Found at i:20235828 original size:75 final size:75
Alignment explanation
Indices: 20235741--20235925 Score: 298
Period size: 75 Copynumber: 2.5 Consensus size: 75
20235731 TATCACTATA
* *
20235741 GTTTAGGGTTTTTTGTTTAGGGTATATGGTTTAAATAGGTTTAGGTGTTACCATTTTAAGGTTTA
1 GTTTAGGGTTTTTGGTTTAGGGTATATGGTTTAAACAGGTTTAGGTGTTACCATTTTAAGGTTTA
20235806 TGGATTATGG
66 TGGATTATGG
* *
20235816 GTTTAGGGTTTTTGGTTTAGGGTATATGGTTTAGACAGGTTTAGGTGTTGCCATTTTAAGGTTTA
1 GTTTAGGGTTTTTGGTTTAGGGTATATGGTTTAAACAGGTTTAGGTGTTACCATTTTAAGGTTTA
20235881 TGGATTATGG
66 TGGATTATGG
* * * *
20235891 GTTTAGGGATTATGGTTTATGGTTTATGGTTTAAA
1 GTTTAGGGTTTTTGGTTTAGGGTATATGGTTTAAA
20235926 GGTTGGGGTT
Statistics
Matches: 101, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 101 1.00
ACGTcount: A:0.21, C:0.03, G:0.30, T:0.47
Consensus pattern (75 bp):
GTTTAGGGTTTTTGGTTTAGGGTATATGGTTTAAACAGGTTTAGGTGTTACCATTTTAAGGTTTA
TGGATTATGG
Found at i:20235834 original size:14 final size:14
Alignment explanation
Indices: 20235815--20235849 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
20235805 ATGGATTATG
* *
20235815 GGTTTAGGGTTTTT
1 GGTTTAGGGTATAT
20235829 GGTTTAGGGTATAT
1 GGTTTAGGGTATAT
20235843 GGTTTAG
1 GGTTTAG
20235850 ACAGGTTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.14, C:0.00, G:0.37, T:0.49
Consensus pattern (14 bp):
GGTTTAGGGTATAT
Found at i:20235888 original size:7 final size:7
Alignment explanation
Indices: 20235870--20236009 Score: 70
Period size: 7 Copynumber: 19.6 Consensus size: 7
20235860 GTGTTGCCAT
*
20235870 TTTAAGG
1 TTTATGG
20235877 TTTATGG
1 TTTATGG
*
20235884 ATTATGGG
1 TTTAT-GG
*
20235892 TTTAGGG
1 TTTATGG
*
20235899 ATTATGG
1 TTTATGG
20235906 TTTATGG
1 TTTATGG
20235913 TTTATGG
1 TTTATGG
*
20235920 TTTAAAGG
1 TTT-ATGG
**
20235928 -TTGGGG
1 TTTATGG
*
20235934 TTTAAGG
1 TTTATGG
20235941 TTTA-GAG
1 TTTATG-G
* *
20235948 GTCATGTG
1 TTTATG-G
* *
20235956 TTAAGGG
1 TTTATGG
20235963 TTTATGG
1 TTTATGG
*
20235970 TTTTAGGG
1 -TTTATGG
*
20235978 TTTTAAGG
1 -TTTATGG
20235986 TTTA-GG
1 TTTATGG
20235992 TTTATGG
1 TTTATGG
*
20235999 TTTAGGG
1 TTTATGG
20236006 TTTA
1 TTTA
20236010 GATTAACTAG
Statistics
Matches: 103, Mismatches: 23, Indels: 14
0.74 0.16 0.10
Matches are distributed among these distances:
6 9 0.09
7 68 0.66
8 26 0.25
ACGTcount: A:0.20, C:0.01, G:0.33, T:0.46
Consensus pattern (7 bp):
TTTATGG
Found at i:20236007 original size:14 final size:14
Alignment explanation
Indices: 20235870--20236009 Score: 97
Period size: 14 Copynumber: 9.8 Consensus size: 14
20235860 GTGTTGCCAT
*
20235870 TTTAAGGTTTATGG
1 TTTAGGGTTTATGG
* *
20235884 ATTATGGGTTTAGGG
1 TTTA-GGGTTTATGG
* *
20235899 ATTATGGTTTATGG
1 TTTAGGGTTTATGG
* *
20235913 TTTATGGTTTAAAGG
1 TTTAGGGTTT-ATGG
* *
20235928 -TTGGGGTTTAAGG
1 TTTAGGGTTTATGG
*
20235941 TTTAGAGG-TCATGTG
1 TTTAG-GGTTTATG-G
*
20235956 TTAAGGGTTTATGG
1 TTTAGGGTTTATGG
*
20235970 TTTTAGGGTTTTAAGG
1 -TTTAGGG-TTTATGG
20235986 TTTA-GGTTTATGG
1 TTTAGGGTTTATGG
20235999 TTTAGGGTTTA
1 TTTAGGGTTTA
20236010 GATTAACTAG
Statistics
Matches: 100, Mismatches: 17, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
13 14 0.14
14 44 0.44
15 36 0.36
16 6 0.06
ACGTcount: A:0.20, C:0.01, G:0.33, T:0.46
Consensus pattern (14 bp):
TTTAGGGTTTATGG
Found at i:20236710 original size:24 final size:25
Alignment explanation
Indices: 20236674--20236721 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
20236664 TTAAAATGAA
20236674 TTTTAAAAGATTT-TAAACTTTTAT
1 TTTTAAAAGATTTATAAACTTTTAT
* * *
20236698 TTTTATAATATTTATATACTTTTA
1 TTTTAAAAGATTTATAAACTTTTA
20236722 AAGAAAAGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.58
Consensus pattern (25 bp):
TTTTAAAAGATTTATAAACTTTTAT
Found at i:20240549 original size:43 final size:43
Alignment explanation
Indices: 20240488--20240578 Score: 123
Period size: 43 Copynumber: 2.1 Consensus size: 43
20240478 CTTTGACTTC
* *
20240488 ATTA-CAAGATTTCTTTGATTAAGTAAATGTATTATATCTTTT
1 ATTACCAAGATTTCTTTGATTAAGAAAATGCATTATATCTTTT
* *
20240530 ATTACCAAGATTTAC-TTGATTAAGAAAATGCATTGTATTTTTT
1 ATTACCAAGATTT-CTTTGATTAAGAAAATGCATTATATCTTTT
20240573 ATTACC
1 ATTACC
20240579 TTGCAATGTG
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
42 4 0.09
43 38 0.88
44 1 0.02
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (43 bp):
ATTACCAAGATTTCTTTGATTAAGAAAATGCATTATATCTTTT
Found at i:20241039 original size:43 final size:43
Alignment explanation
Indices: 20240965--20241249 Score: 369
Period size: 43 Copynumber: 6.7 Consensus size: 43
20240955 CGAGAAGCAT
* * *
20240965 CGCTAAAGGT-TTGTTCTGTAGCGGCGCTTGTGGGAAAAGCGC
1 CGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGGAAAAGCGC
* **
20241007 CGCTAAAGGTCTTGATCTATAGCGGCATTTGTGAAAAAAGCGC
1 CGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGGAAAAGCGC
*
20241050 CGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAAAAGCGC
1 CGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGGAAAAGCGC
* * *
20241093 CGCTAAAGGTCTTGAGCTATAGCTGCGTTTGT-GGTAAAGCGC
1 CGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGGAAAAGCGC
* * * * *
20241135 TGCTAAAAGTCTTGATCTATAGTGGCGTTTGT-GTAAAAGCAC
1 CGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGGAAAAGCGC
* * *
20241177 CGCTAAAGGTCCTGATCTATAGCGGCATTTGTGGGAAAAGCAC
1 CGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGGAAAAGCGC
* *
20241220 CGGTAAAGGTCATGATCTATAGCGGCGTTT
1 CGCTAAAGGTCTTGATCTATAGCGGCGTTT
20241250 ATTTCCAAAA
Statistics
Matches: 212, Mismatches: 29, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
42 79 0.37
43 133 0.63
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.27
Consensus pattern (43 bp):
CGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGGAAAAGCGC
Found at i:20241154 original size:85 final size:85
Alignment explanation
Indices: 20240965--20241249 Score: 376
Period size: 85 Copynumber: 3.4 Consensus size: 85
20240955 CGAGAAGCAT
* * * *
20240965 CGCTAAAGGT-TTGTTCTGTAGCGGCGCTTGTGGGAAAAGCGCCGCTAAAGGTCTTGATCTATAG
1 CGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGATCTATAG
*
20241029 CGGCATTTGTGAAAAAAGCGC
66 CGGCATTTGTG-GAAAAGCGC
*
20241050 CGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGAGCTATAG
1 CGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGATCTATAG
* * *
20241115 CTGCGTTTGTGGTAAAGCGC
66 CGGCATTTGTGGAAAAGCGC
* * * * * *
20241135 TGCTAAAAGTCTTGATCTATAGTGGCGTTTGT-GTAAAAGCACCGCTAAAGGTCCTGATCTATAG
1 CGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGATCTATAG
*
20241199 CGGCATTTGTGGGAAAAGCAC
66 CGGCATTTGT-GGAAAAGCGC
* *
20241220 CGGTAAAGGTCATGATCTATAGCGGCGTTT
1 CGCTAAAGGTCTTGATCTATAGCGGCGTTT
20241250 ATTTCCAAAA
Statistics
Matches: 173, Mismatches: 25, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
84 36 0.21
85 79 0.46
86 58 0.34
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.27
Consensus pattern (85 bp):
CGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGATCTATAG
CGGCATTTGTGGAAAAGCGC
Found at i:20241227 original size:127 final size:128
Alignment explanation
Indices: 20240983--20241249 Score: 374
Period size: 127 Copynumber: 2.1 Consensus size: 128
20240973 GTTTGTTCTG
* * *
20240983 TAGCGGCGCTTGTGGGAAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCATTTGTGAAAAAAGC
1 TAGCGGCGTTTGT-GGTAAAGCGCCGCTAAAAGTCTTGATCTATAGCGGCATTTGTGAAAAAAGC
* * * * *
20241048 GCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCTTGAGCTA
65 ACCGCTAAAGGTCCTGATCTATAGCGGCATTTGTGGAAAAAGCACCGCTAAAGGTCATGAGCTA
* * * * *
20241112 TAGCTGCGTTTGTGGTAAAGCGCTGCTAAAAGTCTTGATCTATAGTGGCGTTTGTG-TAAAAGCA
1 TAGCGGCGTTTGTGGTAAAGCGCCGCTAAAAGTCTTGATCTATAGCGGCATTTGTGAAAAAAGCA
* * *
20241176 CCGCTAAAGGTCCTGATCTATAGCGGCATTTGTGGGAAAAGCACCGGTAAAGGTCATGATCTA
66 CCGCTAAAGGTCCTGATCTATAGCGGCATTTGTGGAAAAAGCACCGCTAAAGGTCATGAGCTA
20241239 TAGCGGCGTTT
1 TAGCGGCGTTT
20241250 ATTTCCAAAA
Statistics
Matches: 121, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
127 72 0.60
128 38 0.31
129 11 0.09
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (128 bp):
TAGCGGCGTTTGTGGTAAAGCGCCGCTAAAAGTCTTGATCTATAGCGGCATTTGTGAAAAAAGCA
CCGCTAAAGGTCCTGATCTATAGCGGCATTTGTGGAAAAAGCACCGCTAAAGGTCATGAGCTA
Found at i:20256615 original size:27 final size:27
Alignment explanation
Indices: 20256584--20256761 Score: 189
Period size: 27 Copynumber: 6.6 Consensus size: 27
20256574 TAAATTGTAC
20256584 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
20256611 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
20256637 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
20256665 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
*
20256693 AGCACTAAGTGTGCGATTTGA-TTTCGT
1 AGCACTAAGTGTGCGATTTGACTAT-GT
* * *
20256720 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
**
20256747 AGCACTGTGTGTGCG
1 AGCACTAAGTGTGCG
20256762 GACTCAATAT
Statistics
Matches: 127, Mismatches: 19, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
26 2 0.02
27 100 0.79
28 25 0.20
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:20260417 original size:21 final size:20
Alignment explanation
Indices: 20260385--20260423 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
20260375 TTTGCCATGA
*
20260385 TTAGATTCAATTTTTATATG
1 TTAGATTCAATTTGTATATG
*
20260405 TTAGCATTTAATTTGTATA
1 TTAG-ATTCAATTTGTATA
20260424 ATTGTTTATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.31, C:0.05, G:0.10, T:0.54
Consensus pattern (20 bp):
TTAGATTCAATTTGTATATG
Found at i:20262983 original size:121 final size:121
Alignment explanation
Indices: 20262657--20263009 Score: 471
Period size: 121 Copynumber: 2.9 Consensus size: 121
20262647 TGGGCTACAA
* * *
20262657 TTGGTCCTGGAAGAAATAATTTCGAGTTGACA-TTTCTAAGCAAATAGTATAAAATCTCTTCTAC
1 TTGGTCCTGGAAGAAATAATTTCGAGTTGA-AGTTTCTGAGCAAATAGTATAAAATCGCTTCTAG
* *
20262721 CAGGATCCTTTATGAGAAGAATTTGTGAAATCGAGCCCACGTGGACGCGCTTTTGCTATAG
65 CAGGATGCTTTATGAGAAGAATTTATGAAATCGAGCCCACGT----GCGCTTTTGCTATAG
* * * * *
20262782 TAGGTCCT-GAAAAAATTATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTT-TAA
1 TTGGTCCTGGAAGAAATAATTTCGAGTTGAAGTTTCTGAGCAAATAGTAT-AAAATCGCTTCT-A
* * *
20262845 GCAGGATGCTATT-TGAGAAGAATTTCTGAAATCGTGCCCTCGTGCGCTTTTGCTATAG
64 GCAGGATGCT-TTATGAGAAGAATTTATGAAATCGAGCCCACGTGCGCTTTTGCTATAG
*
20262903 TTGGTCTTGGAAGAAATAATTTCGAGTTGAAGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
1 TTGGTCCTGGAAGAAATAATTTCGAGTTGAAGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
*
20262968 AGGATGCTTTATGAGAAGAATTTATGAAATCGCGCCCACGTG
66 AGGATGCTTTATGAGAAGAATTTATGAAATCGAGCCCACGTG
20263010 GACGCGCTTT
Statistics
Matches: 200, Mismatches: 21, Indels: 18
0.84 0.09 0.08
Matches are distributed among these distances:
120 2 0.01
121 69 0.34
122 39 0.19
124 37 0.19
125 51 0.25
126 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (121 bp):
TTGGTCCTGGAAGAAATAATTTCGAGTTGAAGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
AGGATGCTTTATGAGAAGAATTTATGAAATCGAGCCCACGTGCGCTTTTGCTATAG
Found at i:20266242 original size:22 final size:22
Alignment explanation
Indices: 20266217--20266509 Score: 263
Period size: 22 Copynumber: 13.7 Consensus size: 22
20266207 AAGTTAAGGT
*
20266217 TTTAGGGTTTATGGTTTTTAAG
1 TTTAGGGTTTAGGGTTTTTAAG
**
20266239 TTTAGGGTTTATAGTTTTTAAG
1 TTTAGGGTTTAGGGTTTTTAAG
20266261 TTTAGGGTTT-GTGGTTTTTAAG
1 TTTAGGGTTTAG-GGTTTTTAAG
* * *
20266283 TTTAAGGTTTATGGTTTTTAGG
1 TTTAGGGTTTAGGGTTTTTAAG
20266305 TTTAGGGTTT-GTGGTTTTTAAG
1 TTTAGGGTTTAG-GGTTTTTAAG
* *
20266327 TTAAGGG-TTAGGGTTTTTAGG
1 TTTAGGGTTTAGGGTTTTTAAG
* *
20266348 TTTAGGGGTT-GGG-GTTT---
1 TTTAGGGTTTAGGGTTTTTAAG
*
20266365 TTTA-AGTTTAGGGTTTTTAGA-
1 TTTAGGGTTTAGGGTTTTTA-AG
*
20266386 TTTAGGGTTTGGGGTTTTTAAG
1 TTTAGGGTTTAGGGTTTTTAAG
*
20266408 TTTAGGGTTTAGGGTTTTTAGG
1 TTTAGGGTTTAGGGTTTTTAAG
* * *
20266430 TCTAAGGTTTGGGGTTTTTAAG
1 TTTAGGGTTTAGGGTTTTTAAG
* *
20266452 TTAAGGG-TTAGCGTTTTTAA-
1 TTTAGGGTTTAGGGTTTTTAAG
*
20266472 TTTAAGGG-TTAGGGTTTCT-AG
1 TTT-AGGGTTTAGGGTTTTTAAG
*
20266493 TTTAAGGGTTTATGGTT
1 TTT-AGGGTTTAGGGTT
20266510 CGTCAATTAA
Statistics
Matches: 223, Mismatches: 33, Indels: 30
0.78 0.12 0.10
Matches are distributed among these distances:
16 3 0.01
17 7 0.03
18 3 0.01
20 6 0.03
21 57 0.26
22 147 0.66
ACGTcount: A:0.17, C:0.01, G:0.31, T:0.50
Consensus pattern (22 bp):
TTTAGGGTTTAGGGTTTTTAAG
Found at i:20266255 original size:29 final size:29
Alignment explanation
Indices: 20266200--20266255 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
20266190 TAAGGGTTAG
* *
20266200 GGTTTTAAAGTTAAGGTTTTAGGGTTTAT
1 GGTTTTAAAGTTAAGGGTTTAGAGTTTAT
* * *
20266229 GGTTTTTAAGTTTAGGGTTTATAGTTT
1 GGTTTTAAAGTTAAGGGTTTAGAGTTT
20266256 TTAAGTTTAG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.21, C:0.00, G:0.27, T:0.52
Consensus pattern (29 bp):
GGTTTTAAAGTTAAGGGTTTAGAGTTTAT
Found at i:20266267 original size:66 final size:66
Alignment explanation
Indices: 20266196--20266335 Score: 167
Period size: 66 Copynumber: 2.1 Consensus size: 66
20266186 AACTTAAGGG
*
20266196 TTAGGGTTT-T-AAAGTTAAGGTTTTAGGGTTTATGGTTTTTAAGTTTAGGGTTTATAGTTTTTA
1 TTAGGGTTTGTGAAAGTTAA-G-TTTAAGGTTTATGGTTTTTAAGTTTAGGGTTTATAGTTTTTA
20266259 AGT
64 AGT
**** * * *
20266262 TTAGGGTTTGTGGTTTTTAAGTTTAAGGTTTATGGTTTTTAGGTTTAGGGTTTGTGGTTTTTAAG
1 TTAGGGTTTGTGAAAGTTAAGTTTAAGGTTTATGGTTTTTAAGTTTAGGGTTTATAGTTTTTAAG
20266327 T
66 T
*
20266328 TAAGGGTT
1 TTAGGGTT
20266336 AGGGTTTTTA
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
66 57 0.90
67 2 0.03
68 4 0.06
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.52
Consensus pattern (66 bp):
TTAGGGTTTGTGAAAGTTAAGTTTAAGGTTTATGGTTTTTAAGTTTAGGGTTTATAGTTTTTAAG
T
Found at i:20266380 original size:16 final size:16
Alignment explanation
Indices: 20266359--20266395 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
20266349 TTAGGGGTTG
20266359 GGGTTTTTTA-AGTTTA
1 GGGTTTTTTAGA-TTTA
20266375 GGG-TTTTTAGATTTA
1 GGGTTTTTTAGATTTA
20266390 GGGTTT
1 GGGTTT
20266396 GGGGTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.16, C:0.00, G:0.30, T:0.54
Consensus pattern (16 bp):
GGGTTTTTTAGATTTA
Found at i:20266417 original size:125 final size:124
Alignment explanation
Indices: 20266252--20266488 Score: 359
Period size: 125 Copynumber: 1.9 Consensus size: 124
20266242 AGGGTTTATA
* * * * *
20266252 GTTTTTAAGTTTAGGGTTTGTGGTTTTTAAGTTTAAGGTTTATGGTTTTTAGGTTTAGGGTTTGT
1 GTTTTTAAGTTTAGGGTTTGGGGTTTTTAAGTTTAAGGTTTAGGGTTTTTAGGTCTAAGGTTTGG
* * * *
20266317 GGTTTTTAAGTTAAGGGTTAGGGTTTTTAGGTTTAGGGGTTGGGGTTTTTTAAGTTTAGG
66 GGTTTTTAAGTTAAGGGTTAGCGTTTTTA-ATTTAAGGGTTAGGGTTTTTTAAGTTTAGG
*
20266377 GTTTTT-AGATTTAGGGTTTGGGGTTTTTAAGTTTAGGGTTTAGGGTTTTTAGGTCTAAGGTTTG
1 GTTTTTAAG-TTTAGGGTTTGGGGTTTTTAAGTTTAAGGTTTAGGGTTTTTAGGTCTAAGGTTTG
20266441 GGGTTTTTAAGTTAAGGGTTAGCGTTTTTAATTTAAGGGTTAGGGTTT
65 GGGTTTTTAAGTTAAGGGTTAGCGTTTTTAATTTAAGGGTTAGGGTTT
20266489 CTAGTTTAAG
Statistics
Matches: 101, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
124 17 0.17
125 84 0.83
ACGTcount: A:0.17, C:0.01, G:0.32, T:0.50
Consensus pattern (124 bp):
GTTTTTAAGTTTAGGGTTTGGGGTTTTTAAGTTTAAGGTTTAGGGTTTTTAGGTCTAAGGTTTGG
GGTTTTTAAGTTAAGGGTTAGCGTTTTTAATTTAAGGGTTAGGGTTTTTTAAGTTTAGG
Found at i:20269015 original size:11 final size:11
Alignment explanation
Indices: 20268999--20269054 Score: 69
Period size: 11 Copynumber: 5.0 Consensus size: 11
20268989 ATTAAATATG
20268999 AATTTGAGAGA
1 AATTTGAGAGA
*
20269010 AATTTG-GAAGG
1 AATTTGAG-AGA
20269021 AATTTGAGAGA
1 AATTTGAGAGA
*
20269032 AAATTGAGAGGA
1 AATTTGAGA-GA
20269044 AATTTGAGAGA
1 AATTTGAGAGA
20269055 GGATTTGTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
10 1 0.03
11 26 0.68
12 11 0.29
ACGTcount: A:0.45, C:0.00, G:0.30, T:0.25
Consensus pattern (11 bp):
AATTTGAGAGA
Found at i:20269023 original size:22 final size:22
Alignment explanation
Indices: 20268998--20269054 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 22
20268988 GATTAAATAT
*
20268998 GAATTTGAGAGAAATTTG-GAAG
1 GAATTTGAGAGAAAATTGAG-AG
20269020 GAATTTGAGAGAAAATTGAGAG
1 GAATTTGAGAGAAAATTGAGAG
20269042 GAAATTTGAGAGA
1 G-AATTTGAGAGA
20269055 GGATTTGTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
22 20 0.62
23 12 0.38
ACGTcount: A:0.44, C:0.00, G:0.32, T:0.25
Consensus pattern (22 bp):
GAATTTGAGAGAAAATTGAGAG
Found at i:20269060 original size:12 final size:12
Alignment explanation
Indices: 20268998--20269061 Score: 57
Period size: 11 Copynumber: 5.6 Consensus size: 12
20268988 GATTAAATAT
20268998 GAATTTGAGAGA
1 GAATTTGAGAGA
20269010 -AATTTG-GA-A
1 GAATTTGAGAGA
20269019 GGAATTTGAGAGA
1 -GAATTTGAGAGA
*
20269032 -AAATTGAGAG-
1 GAATTTGAGAGA
20269042 GAAATTTGAGAGA
1 G-AATTTGAGAGA
*
20269055 GGATTTG
1 GAATTTG
20269062 TTTGTGAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
9 1 0.02
10 2 0.05
11 21 0.50
12 16 0.38
13 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.33, T:0.27
Consensus pattern (12 bp):
GAATTTGAGAGA
Found at i:20272117 original size:13 final size:13
Alignment explanation
Indices: 20272099--20272135 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
20272089 AAACACTCAA
20272099 ATTTCTCAAAAAT
1 ATTTCTCAAAAAT
*
20272112 ATTTCTGAAAAAT
1 ATTTCTCAAAAAT
*
20272125 ACTTCTCAAAA
1 ATTTCTCAAAA
20272136 GCAATAAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.46, C:0.16, G:0.03, T:0.35
Consensus pattern (13 bp):
ATTTCTCAAAAAT
Found at i:20272704 original size:13 final size:13
Alignment explanation
Indices: 20272688--20272718 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
20272678 CAGAGCACTG
20272688 TTTCTCTTCCCGA
1 TTTCTCTTCCCGA
20272701 TTTCTCTTCCCGA
1 TTTCTCTTCCCGA
20272714 TTTCT
1 TTTCT
20272719 TGCACCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.06, C:0.35, G:0.06, T:0.52
Consensus pattern (13 bp):
TTTCTCTTCCCGA
Found at i:20274856 original size:20 final size:20
Alignment explanation
Indices: 20274820--20274858 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
20274810 AATTTTTTAA
*
20274820 AAATATATTTATAATATAAT
1 AAATATATTAATAATATAAT
20274840 AAATATA-TAATACATATAA
1 AAATATATTAATA-ATATAA
20274859 ATTTAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATATATTAATAATATAAT
Found at i:20278557 original size:26 final size:24
Alignment explanation
Indices: 20278522--20278573 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 24
20278512 ACATTTTATG
20278522 AAATTATATTTAATAATAATTATTTT
1 AAATTATATTTAATAAT-A-TATTTT
* *
20278548 AAATTGTATTTAATCATATATTTT
1 AAATTATATTTAATAATATATTTT
20278572 AA
1 AA
20278574 TTAAAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 8 0.33
25 1 0.04
26 15 0.62
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (24 bp):
AAATTATATTTAATAATATATTTT
Found at i:20278680 original size:18 final size:17
Alignment explanation
Indices: 20278652--20278686 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
20278642 ATTATTAAGA
*
20278652 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
20278669 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
20278687 TTAATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:20278686 original size:16 final size:16
Alignment explanation
Indices: 20278652--20278706 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
20278642 ATTATTAAGA
20278652 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA--ATAT
20278669 ATTTTAATTAAAATAT
1 ATTTTAATTAAAATAT
*
20278685 A-TTTAA-TAAAAAAT
1 ATTTTAATTAAAATAT
20278699 ATGTTTAA
1 AT-TTTAA
20278707 ATATGATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 8 0.24
15 5 0.15
16 10 0.29
17 5 0.15
18 6 0.18
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
ATTTTAATTAAAATAT
Found at i:20278820 original size:155 final size:157
Alignment explanation
Indices: 20278640--20278954 Score: 571
Period size: 155 Copynumber: 2.0 Consensus size: 157
20278630 ATAAGAATAT
20278640 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAAAAAATATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAAAAAATATGTTT
* *
20278705 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATT-AAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
20278769 TAATCATTTACCAAAACAAATTTATGC
131 TAATCATTTACCAAAACAAATTTATGC
* *
20278796 TAATTA-TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAAAAAATATGTTT
20278860 AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
20278925 TAATCATTTACCAAAACAATTTTATGC
131 TAATCATTTACCAAAACAAATTTATGC
20278952 TAA
1 TAA
20278955 GGGTATTCTA
Statistics
Matches: 153, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
155 97 0.63
156 56 0.37
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAAAAAATATGTTT
AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATCATTTACCAAAACAAATTTATGC
Found at i:20278835 original size:18 final size:17
Alignment explanation
Indices: 20278807--20278841 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
20278797 AATTATAAGA
*
20278807 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
20278824 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
20278842 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:20279071 original size:44 final size:45
Alignment explanation
Indices: 20279006--20279096 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
20278996 ACCTCTATTC
* * *
20279006 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
20279050 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
20279095 CA
1 CA
20279097 GCGAATCAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:20280160 original size:13 final size:13
Alignment explanation
Indices: 20280142--20280178 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
20280132 TATTTGTTTA
20280142 TATTCCCACCGAT
1 TATTCCCACCGAT
20280155 TATTCCCACCGAT
1 TATTCCCACCGAT
20280168 TATTCCCACCG
1 TATTCCCACCG
20280179 GCCGAATGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.22, C:0.41, G:0.08, T:0.30
Consensus pattern (13 bp):
TATTCCCACCGAT
Found at i:20281675 original size:12 final size:13
Alignment explanation
Indices: 20281651--20281682 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
20281641 GTTATTTATT
20281651 TTCTTTT-GCTCG
1 TTCTTTTGGCTCG
20281663 TT-TTTTGGCTCG
1 TTCTTTTGGCTCG
20281675 TTCTTTTG
1 TTCTTTTG
20281683 CTTAAAATGC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.22
12 9 0.50
13 5 0.28
ACGTcount: A:0.00, C:0.19, G:0.19, T:0.62
Consensus pattern (13 bp):
TTCTTTTGGCTCG
Found at i:20284886 original size:49 final size:49
Alignment explanation
Indices: 20284829--20284932 Score: 136
Period size: 49 Copynumber: 2.1 Consensus size: 49
20284819 TCATGTGTTA
* * ** * *
20284829 TAATTTTATACAGTCTTGAGTTTTTTATTCATGATATTGAACTCAATTT
1 TAATTTTATAAAGTCTTCACCTTTTGATTCATGATATTAAACTCAATTT
* *
20284878 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTCTTCACCTTTTGATTCATGATATTAAACTCAATTT
20284927 TAATTT
1 TAATTT
20284933 GTTTTTTTTC
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.31, C:0.10, G:0.09, T:0.51
Consensus pattern (49 bp):
TAATTTTATAAAGTCTTCACCTTTTGATTCATGATATTAAACTCAATTT
Found at i:20286384 original size:26 final size:28
Alignment explanation
Indices: 20286330--20286393 Score: 87
Period size: 26 Copynumber: 2.4 Consensus size: 28
20286320 TAAGAATAAG
* * *
20286330 AATTTTATTTAATTATTTATTATTATTA
1 AATTATATTTAATTAATAATTATTATTA
20286358 AATTATATTTAA-TAATAATTATT-TTA
1 AATTATATTTAATTAATAATTATTATTA
20286384 AATTATATTT
1 AATTATATTT
20286394 TAGTATTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 13 0.39
27 9 0.27
28 11 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
AATTATATTTAATTAATAATTATTATTA
Found at i:20286495 original size:16 final size:15
Alignment explanation
Indices: 20286449--20286486 Score: 67
Period size: 16 Copynumber: 2.5 Consensus size: 15
20286439 TTTATTAACA
20286449 ATTTTATTAAATTAT
1 ATTTTATTAAATTAT
20286464 ATATTTATTAAATTAT
1 AT-TTTATTAAATTAT
20286480 ATTTTAT
1 ATTTTAT
20286487 AACAATTATG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTTTATTAAATTAT
Found at i:20286684 original size:39 final size:41
Alignment explanation
Indices: 20286628--20286733 Score: 135
Period size: 44 Copynumber: 2.5 Consensus size: 41
20286618 TTTCCTTATG
* *
20286628 CTATTACACCTCTATTCCATTCAACCAAACACAAGAA-TAC
1 CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
20286668 C-ATTACGCCTCTATTCCATTACATTCAACCAAACAAAAGAATTAC
1 CTATTACGCCTCTATT-C----CATTCAACCAAACAAAAGAATTAC
20286713 CTATTACGCCTCTATTCCATT
1 CTATTACGCCTCTATTCCATT
20286734 ACGCCTCTAT
Statistics
Matches: 57, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
39 13 0.23
40 2 0.04
41 4 0.07
44 19 0.33
45 5 0.09
46 14 0.25
ACGTcount: A:0.36, C:0.31, G:0.04, T:0.29
Consensus pattern (41 bp):
CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
Found at i:20286708 original size:44 final size:46
Alignment explanation
Indices: 20286645--20286735 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
20286635 ACCTCTATTC
*
20286645 CATTCAACCAAACACAAGAA-TACC-ATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
20286689 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
20286735 C
1 C
20286736 GCCTCTATTC
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 19 0.43
45 4 0.09
46 21 0.48
ACGTcount: A:0.38, C:0.31, G:0.04, T:0.26
Consensus pattern (46 bp):
CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
Found at i:20286736 original size:16 final size:16
Alignment explanation
Indices: 20286715--20286751 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
20286705 AGAATTACCT
20286715 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
20286731 ATTACGCCTCTATTCT
1 ATTACGCCTCTATTCC
20286747 ATTAC
1 ATTAC
20286752 AGCGAACCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.22, C:0.32, G:0.05, T:0.41
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:20287946 original size:18 final size:17
Alignment explanation
Indices: 20287914--20287952 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
20287904 ATTTTTATAA
20287914 TTTTTTAAAAATATTGAT
1 TTTTTTAAAAATATTG-T
**
20287932 TTTTTTAAATCTATTGT
1 TTTTTTAAAAATATTGT
20287949 TTTT
1 TTTT
20287953 ATGTTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (17 bp):
TTTTTTAAAAATATTGT
Found at i:20288773 original size:3 final size:3
Alignment explanation
Indices: 20288767--20288795 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
20288757 ACTACTTCTT
20288767 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
20288796 GAGAACTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:20289219 original size:22 final size:22
Alignment explanation
Indices: 20289193--20289242 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
20289183 ACAAATCCTA
*
20289193 TCTCAATTTCCTTCCAAAATTC
1 TCTCAATTTCCTTCCAAAATCC
20289215 TCTCAATTTCCTTCCAAAATCC
1 TCTCAATTTCCTTCCAAAATCC
20289237 TCTCAA
1 TCTCAA
20289243 ACTCTCAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.28, C:0.34, G:0.00, T:0.38
Consensus pattern (22 bp):
TCTCAATTTCCTTCCAAAATCC
Found at i:20289250 original size:30 final size:30
Alignment explanation
Indices: 20289214--20289272 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
20289204 TTCCAAAATT
20289214 CTCTCAATTTCCTTCCAAAATCCTCTCAAA
1 CTCTCAATTTCCTTCCAAAATCCTCTCAAA
*
20289244 CTCTCAATTTCCTTCCAAAATCCTTTCAA
1 CTCTCAATTTCCTTCCAAAATCCTCTCAA
20289273 TTTCCTTCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.29, C:0.36, G:0.00, T:0.36
Consensus pattern (30 bp):
CTCTCAATTTCCTTCCAAAATCCTCTCAAA
Found at i:20289250 original size:52 final size:52
Alignment explanation
Indices: 20289193--20289295 Score: 172
Period size: 52 Copynumber: 2.0 Consensus size: 52
20289183 ACAAATCCTA
*
20289193 TCTCAATTTCCTTCCAAAATTCTCTCAATTTCCTTCC-AAAATCCTCTCAAAC
1 TCTCAATTTCCTTCCAAAATCCTCTCAATTTCCTTCCAAAAAT-CTCTCAAAC
*
20289245 TCTCAATTTCCTTCCAAAATCCTTTCAATTTCCTTCCAAAAATCTCTCAAA
1 TCTCAATTTCCTTCCAAAATCCTCTCAATTTCCTTCCAAAAATCTCTCAAA
20289296 TCCATATTAA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
52 43 0.90
53 5 0.10
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.37
Consensus pattern (52 bp):
TCTCAATTTCCTTCCAAAATCCTCTCAATTTCCTTCCAAAAATCTCTCAAAC
Found at i:20289294 original size:22 final size:22
Alignment explanation
Indices: 20289244--20289294 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
20289234 TCCTCTCAAA
20289244 CTCTCAATTTCCTTCCAAAATC
1 CTCTCAATTTCCTTCCAAAATC
*
20289266 CTTTCAATTTCCTTCCAAAAAT-
1 CTCTCAATTTCCTTCC-AAAATC
20289288 CTCTCAA
1 CTCTCAA
20289295 ATCCATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.29, C:0.33, G:0.00, T:0.37
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAATC
Found at i:20289355 original size:10 final size:10
Alignment explanation
Indices: 20289328--20289391 Score: 51
Period size: 10 Copynumber: 6.5 Consensus size: 10
20289318 CCTCAATTTC
*
20289328 ATTTTTTAAA
1 ATTTTTTTAA
**
20289338 ATAATTTTAA
1 ATTTTTTTAA
20289348 ATTTTTTT--
1 ATTTTTTTAA
20289356 ATTTTTTTAAA
1 ATTTTTTT-AA
**
20289367 ATAATTTTAA
1 ATTTTTTTAA
*
20289377 ATTTTTTTAT
1 ATTTTTTTAA
20289387 ATTTT
1 ATTTT
20289392 CATCAATGGC
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
8 8 0.20
10 27 0.66
11 6 0.15
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
ATTTTTTTAA
Found at i:20289361 original size:29 final size:29
Alignment explanation
Indices: 20289329--20289391 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
20289319 CTCAATTTCA
20289329 TTTTTTAAAATAATTTTAAATTTTTTTAT
1 TTTTTTAAAATAATTTTAAATTTTTTTAT
20289358 TTTTTTAAAATAATTTTAAATTTTTTTAT
1 TTTTTTAAAATAATTTTAAATTTTTTTAT
*
20289387 ATTTT
1 TTTTT
20289392 CATCAATGGC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (29 bp):
TTTTTTAAAATAATTTTAAATTTTTTTAT
Found at i:20290485 original size:7 final size:7
Alignment explanation
Indices: 20290473--20290511 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
20290463 AGTGGATTGA
20290473 TATTTAG
1 TATTTAG
20290480 TATTTAG
1 TATTTAG
20290487 TATTTAG
1 TATTTAG
*
20290494 TATTTTG
1 TATTTAG
*
20290501 TATTTTG
1 TATTTAG
20290508 TATT
1 TATT
20290512 ATGTATATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.23, C:0.00, G:0.13, T:0.64
Consensus pattern (7 bp):
TATTTAG
Found at i:20290516 original size:7 final size:7
Alignment explanation
Indices: 20290473--20290517 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
20290463 AGTGGATTGA
*
20290473 TATTTAG
1 TATTTTG
*
20290480 TATTTAG
1 TATTTTG
*
20290487 TATTTAG
1 TATTTTG
20290494 TATTTTG
1 TATTTTG
20290501 TATTTTG
1 TATTTTG
*
20290508 TATTATG
1 TATTTTG
20290515 TAT
1 TAT
20290518 ATAACTAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.24, C:0.00, G:0.13, T:0.62
Consensus pattern (7 bp):
TATTTTG
Found at i:20291690 original size:29 final size:29
Alignment explanation
Indices: 20291605--20292022 Score: 557
Period size: 29 Copynumber: 13.9 Consensus size: 29
20291595 TAAAAAAAAT
*
20291605 CCTAATTTAATTAAAAACCCTAAACACTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
*
20291635 CCTAATTTAATTAAAAACCTTAAACCCTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
20291665 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
20291694 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
20291723 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
20291752 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
* ** ****
20291781 CCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAA
1 -CCTAA---T---TTAA-TTAA--AAACCCTAAC--CCTAA
*
20291822 CCTAATTTAAGTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
20291851 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
20291880 CTTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
20291909 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
* *
20291938 CTTGATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
20291967 CCTAATTTAATTAAAAACCCTAAAACCCTAA
1 CCTAATTTAATTAAAAACCCT--AACCCTAA
* *
20291998 CTTAATTTAATTAAAAACTCTAACC
1 CCTAATTTAATTAAAAACCCTAACC
20292023 ATTAACAAAA
Statistics
Matches: 347, Mismatches: 27, Indels: 29
0.86 0.07 0.07
Matches are distributed among these distances:
29 234 0.67
30 53 0.15
31 31 0.09
33 4 0.01
34 3 0.01
36 3 0.01
37 5 0.01
39 4 0.01
40 5 0.01
41 5 0.01
ACGTcount: A:0.45, C:0.27, G:0.00, T:0.28
Consensus pattern (29 bp):
CCTAATTTAATTAAAAACCCTAACCCTAA
Found at i:20291737 original size:58 final size:58
Alignment explanation
Indices: 20291605--20292022 Score: 620
Period size: 58 Copynumber: 6.9 Consensus size: 58
20291595 TAAAAAAAAT
* *
20291605 CCTAATTTAATTAAAAACCCTAAACACTAACCTAATTTAATTAAAAACCTTAAACCCTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAACCTAATTTAATTAAAAACCCT-AACCCTAA
20291665 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAA
20291723 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCCTAAC
1 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATT----A----AA----AACCCTAAC
20291788 CCTAA
54 CCTAA
*
20291793 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAAGTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAA
*
20291851 CCTAATTTAATTAAAAACCCTAACCCTAACTTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAA
* *
20291909 CCTAATTTAATTAAAAACCCTAACCCTAACTTGATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAA
* *
20291967 CCTAATTTAATTAAAAACCCTAAAACCCTAACTTAATTTAATTAAAAACTCTAACC
1 CCTAATTTAATTAAAAACCCT--AACCCTAACCTAATTTAATTAAAAACCCTAACC
20292023 ATTAACAAAA
Statistics
Matches: 336, Mismatches: 8, Indels: 28
0.90 0.02 0.08
Matches are distributed among these distances:
58 197 0.59
59 27 0.08
60 52 0.15
62 3 0.01
66 3 0.01
70 54 0.16
ACGTcount: A:0.45, C:0.27, G:0.00, T:0.28
Consensus pattern (58 bp):
CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAA
Found at i:20291766 original size:87 final size:87
Alignment explanation
Indices: 20291605--20292022 Score: 620
Period size: 87 Copynumber: 4.6 Consensus size: 87
20291595 TAAAAAAAAT
* *
20291605 CCTAATTTAATTAAAAACCCTAAACACTAACCTAATTTAATTAAAAACCTTAAACCCTAACCTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAACCTAATTTAATTAAAAACCCT-AACCCTAACCTAA
20291670 TTTAATTAAAAACCCTAACCCTAA
64 TTTAATTAAAAACCCTAACCCTAA
20291694 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATT
1 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATT
20291759 TAATTAAAAACCCTAACCCTAACCCTAACCCTAA
66 TAATT----A----AA----AACCCTAACCCTAA
*
20291793 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAAGTAAAAACCCTAACCCTAACCTAATT
1 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATT
20291858 TAATTAAAAACCCTAACCCTAA
66 TAATTAAAAACCCTAACCCTAA
* * *
20291880 CTTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACTTGATT
1 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATT
20291945 TAATTAAAAACCCTAACCCTAA
66 TAATTAAAAACCCTAACCCTAA
* *
20291967 CCTAATTTAATTAAAAACCCTAAAACCCTAACTTAATTTAATTAAAAACTCTAACC
1 CCTAATTTAATTAAAAACCCT--AACCCTAACCTAATTTAATTAAAAACCCTAACC
20292023 ATTAACAAAA
Statistics
Matches: 305, Mismatches: 10, Indels: 28
0.89 0.03 0.08
Matches are distributed among these distances:
87 137 0.45
88 27 0.09
89 52 0.17
91 3 0.01
95 3 0.01
99 83 0.27
ACGTcount: A:0.45, C:0.27, G:0.00, T:0.28
Consensus pattern (87 bp):
CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATT
TAATTAAAAACCCTAACCCTAA
Found at i:20291778 original size:6 final size:6
Alignment explanation
Indices: 20291767--20291794 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
20291757 TTTAATTAAA
20291767 AACCCT AACCCT AACCCT AACCCT AACC
1 AACCCT AACCCT AACCCT AACCCT AACC
20291795 TAATTTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.50, G:0.00, T:0.14
Consensus pattern (6 bp):
AACCCT
Found at i:20291783 original size:41 final size:41
Alignment explanation
Indices: 20291738--20291823 Score: 172
Period size: 41 Copynumber: 2.1 Consensus size: 41
20291728 TTTAATTAAA
20291738 AACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCT
1 AACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCT
20291779 AACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCT
1 AACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCT
20291820 AACC
1 AACC
20291824 TAATTTAAGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.42, C:0.35, G:0.00, T:0.23
Consensus pattern (41 bp):
AACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCT
Found at i:20295993 original size:27 final size:26
Alignment explanation
Indices: 20295912--20295980 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 26
20295902 ATATTGAGTC
** * *
20295912 CGCACACACAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACA-AATCAAAT
20295939 CGCACACTTAGTGCTACGAAATCAAAT
1 CGCACACTTAGTGCTAC-AAATCAAAT
20295966 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
20295981 GTACAATTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
27 36 0.97
28 1 0.03
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.23
Consensus pattern (26 bp):
CGCACACTTAGTGCTACAAATCAAAT
Found at i:20296271 original size:27 final size:27
Alignment explanation
Indices: 20296236--20296310 Score: 114
Period size: 27 Copynumber: 2.8 Consensus size: 27
20296226 GTGCCGCATG
*
20296236 GTCAATTCGCACACTTAGTGCATCATA
1 GTCAATTCGCACACTTAGTGCAACATA
* *
20296263 TTCATTTCGCACACTTAGTGCAACATA
1 GTCAATTCGCACACTTAGTGCAACATA
*
20296290 GTCAAATCGCACACTTAGTGC
1 GTCAATTCGCACACTTAGTGC
20296311 TGTACAATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (27 bp):
GTCAATTCGCACACTTAGTGCAACATA
Found at i:20304221 original size:27 final size:27
Alignment explanation
Indices: 20304191--20304368 Score: 171
Period size: 27 Copynumber: 6.6 Consensus size: 27
20304181 ATATTGAGTC
** *
20304191 CGCACACACAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
20304218 CGCACACTTAGTGCTACGA-AATCAAAT
1 CGCACACTTAGTGCTAC-ATAATCAACT
*
20304245 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
20304273 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
20304300 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
20304327 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
20304354 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
20304369 GTACAATTTA
Statistics
Matches: 128, Mismatches: 18, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
26 1 0.01
27 102 0.80
28 25 0.20
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:20307026 original size:123 final size:123
Alignment explanation
Indices: 20306748--20307026 Score: 470
Period size: 123 Copynumber: 2.3 Consensus size: 123
20306738 CCACGATGGT
*
20306748 GCGATTTTATACTATTTGCTTAGAAATGTCAAAAAAAATTATTTCTTACATGACCAACTGTAGCG
1 GCGATTTTATACTATTTGCTCAGAAATGTC-AAAAAAATTATTTCTTACATGACCAACTGTAGCG
*
20306813 AAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAACATCCTAGTTGAA
65 AAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAACATCCTAGTAGAA
*
20306872 GCGATTTTATACTATTTGCTCACAAATGTCAAAAAAATTATTTCTTACATGACCAACTGTAGCGA
1 GCGATTTTATACTATTTGCTCAGAAATGTCAAAAAAATTATTTCTTACATGACCAACTGTAGCGA
* * *
20306937 AATCGTGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
66 AATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAACATCCTAGTAGAA
*
20306995 GCGATTTTATACTATTTGAC-CAGAAACGTCAA
1 GCGATTTTATACTATTTG-CTCAGAAATGTCAA
20307027 CTCGAAATAA
Statistics
Matches: 146, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
123 117 0.80
124 29 0.20
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.31
Consensus pattern (123 bp):
GCGATTTTATACTATTTGCTCAGAAATGTCAAAAAAATTATTTCTTACATGACCAACTGTAGCGA
AATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAACATCCTAGTAGAA
Found at i:20307985 original size:28 final size:27
Alignment explanation
Indices: 20307938--20308016 Score: 81
Period size: 27 Copynumber: 2.9 Consensus size: 27
20307928 TGGAAGTCCA
*
20307938 AAACAAATAACAA-ACAAAACCCAAA-C
1 AAACAAA-AGCAAGACAAAACCCAAACC
* *
20307964 AGAACAAATGTTAAGACAAAACCCAAACC
1 A-AACAAAAG-CAAGACAAAACCCAAACC
*
20307993 AAACAAAAGCAAGACAACACCCAA
1 AAACAAAAGCAAGACAAAACCCAA
20308017 TAAAAGTCAG
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
26 1 0.02
27 21 0.49
28 19 0.44
29 2 0.05
ACGTcount: A:0.62, C:0.27, G:0.06, T:0.05
Consensus pattern (27 bp):
AAACAAAAGCAAGACAAAACCCAAACC
Found at i:20308080 original size:16 final size:16
Alignment explanation
Indices: 20308058--20308097 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
20308048 CGTTTGGTTC
*
20308058 ACTGTAATGGAATAGA
1 ACTGTAATGGAATAAA
*
20308074 GCTGTAATGGAATAAA
1 ACTGTAATGGAATAAA
20308090 ACTGTAAT
1 ACTGTAAT
20308098 TAGTAATTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.42, C:0.07, G:0.23, T:0.28
Consensus pattern (16 bp):
ACTGTAATGGAATAAA
Found at i:20308354 original size:58 final size:58
Alignment explanation
Indices: 20308275--20308398 Score: 178
Period size: 58 Copynumber: 2.1 Consensus size: 58
20308265 TTTTAATGAG
* *
20308275 ATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAACCATATT-TTAATATA
1 ATTATTATTAAAAATAATTTAAT-AAAATAATAAATAATTTAACAAAATTCTTAATATA
* * * *
20308333 ATTATTATTAAATATAATTTAATAAAATAATATATAATTTAATAAAATTCTTCATATA
1 ATTATTATTAAAAATAATTTAATAAAATAATAAATAATTTAACAAAATTCTTAATATA
20308391 ATTATTAT
1 ATTATTAT
20308399 ATGAATTAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 22 0.37
58 37 0.63
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (58 bp):
ATTATTATTAAAAATAATTTAATAAAATAATAAATAATTTAACAAAATTCTTAATATA
Done.