Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 118 of 427
Found at i:31152085 original size:28 final size:29
Alignment explanation
Indices: 31152012--31152099 Score: 94
Period size: 28 Copynumber: 3.1 Consensus size: 29
31152002 AGCATGGCTG
* * * *
31152012 CCAGATACAGA-AA-ATGTGACAGAGTCA
1 CCAGATACAGATAATTTGTGGCATAGCCA
*
31152039 CCAGATACAGATATTTTGTGGCAGT-GCCA
1 CCAGATACAGATAATTTGTGGCA-TAGCCA
31152068 CCAGA-ACAGATAATTTGTGGCATAGCCA
1 CCAGATACAGATAATTTGTGGCATAGCCA
31152096 CCAG
1 CCAG
31152100 GACGCTTCCT
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
27 12 0.24
28 25 0.49
29 14 0.27
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (29 bp):
CCAGATACAGATAATTTGTGGCATAGCCA
Found at i:31152252 original size:28 final size:28
Alignment explanation
Indices: 31152205--31152269 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
31152195 AAATTAACCC
*
31152205 TAGGGGTATAAAGGTCATTTAGCATACA
1 TAGGGGTATAAAGGTAATTTAGCATACA
* *
31152233 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTAGCATACA
31152261 TAGGGGTAT
1 TAGGGGTAT
31152270 TCTAGTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.32, C:0.08, G:0.28, T:0.32
Consensus pattern (28 bp):
TAGGGGTATAAAGGTAATTTAGCATACA
Found at i:31156074 original size:28 final size:26
Alignment explanation
Indices: 31156035--31156093 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
31156025 CCCTGTTTAG
*
31156035 AATACTTTAGTTTACTAAAATTACCGA
1 AATACTTTAGTTT-CTAAAAATACCGA
* *
31156062 AATACTCTTAGTTTGTAAAAATACTGA
1 AATACT-TTAGTTTCTAAAAATACCGA
31156089 AATAC
1 AATAC
31156094 CCTTGATTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 21 0.75
28 7 0.25
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (26 bp):
AATACTTTAGTTTCTAAAAATACCGA
Found at i:31156080 original size:27 final size:28
Alignment explanation
Indices: 31156050--31156140 Score: 98
Period size: 27 Copynumber: 3.4 Consensus size: 28
31156040 TTTAGTTTAC
31156050 TAAAATTACCGAAATACTCTTAG-TTTG
1 TAAAATTACCGAAATACTCTTAGATTTG
* * *
31156077 TAAAAATACTGAAATACCCTT-GATTTG
1 TAAAATTACCGAAATACTCTTAGATTTG
** * *
31156104 TAAAATTACTAAAATAC-CTTCGACTTG
1 TAAAATTACCGAAATACTCTTAGATTTG
31156131 TAAAATTACC
1 TAAAATTACC
31156141 AAAGTACCCC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
26 4 0.07
27 51 0.93
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (28 bp):
TAAAATTACCGAAATACTCTTAGATTTG
Found at i:31156354 original size:27 final size:27
Alignment explanation
Indices: 31156145--31156353 Score: 287
Period size: 27 Copynumber: 7.8 Consensus size: 27
31156135 ATTACCAAAG
31156145 TACCC-CGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
31156171 TACCC-CGATTTATATAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
31156197 TACCCTCGATTTACATAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * *
31156224 TACCCTTGACTTACAGAATTGCCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
31156251 TACCCTCAATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
31156278 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
31156305 TACCCTTGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
31156332 TACCCTTGATTTACAAAATTAC
1 TACCCTCGATTTACAGAATTAC
31156354 TAAAATACCC
Statistics
Matches: 165, Mismatches: 17, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
26 29 0.18
27 136 0.82
ACGTcount: A:0.27, C:0.23, G:0.10, T:0.40
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCGTTT
Found at i:31156362 original size:27 final size:27
Alignment explanation
Indices: 31156305--31156584 Score: 156
Period size: 27 Copynumber: 10.3 Consensus size: 27
31156295 ATTACTGTTT
* *****
31156305 TACCCTTGATTTACAGAATTACTGTTT
1 TACCCTTGATTTACAAAATTACCAAAA
*
31156332 TACCCTTGATTTACAAAATTACTAAAA
1 TACCCTTGATTTACAAAATTACCAAAA
* **
31156359 TACCCTTGGTTTGTAAAATTACCAAAA
1 TACCCTTGATTTACAAAATTACCAAAA
* **
31156386 TACCCCT-AGTTTGTAAAATTACCAAAA
1 TACCCTTGA-TTTACAAAATTACCAAAA
* *** *
31156413 TACCCTTGGTTTGTGAAATTACCGAAA
1 TACCCTTGATTTACAAAATTACCAAAA
** **
31156440 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTTGATTTACAAAATTACCAAAA
* *
31156467 TACCCCTGATTTACAAAGTTA-CAGAAA
1 TACCCTTGATTTACAAAATTACCA-AAA
*
31156494 TACCCTTGACTCTCTA-AAAATTA-TAGAAA
1 TACCCTTGA-T-T-TACAAAATTACCA-AAA
* **
31156523 TACCATT-AGTTTACAAAATTACTGAAA
1 TACCCTTGA-TTTACAAAATTACCAAAA
* ** * *
31156550 TACCCTTGGTTTGTAGATTTACCAAAA
1 TACCCTTGATTTACAAAATTACCAAAA
*
31156577 CACCCTTG
1 TACCCTTG
31156585 TAGGATGAAA
Statistics
Matches: 203, Mismatches: 41, Indels: 18
0.77 0.16 0.07
Matches are distributed among these distances:
26 4 0.02
27 175 0.86
28 4 0.02
29 18 0.09
30 2 0.01
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.33
Consensus pattern (27 bp):
TACCCTTGATTTACAAAATTACCAAAA
Found at i:31156363 original size:81 final size:81
Alignment explanation
Indices: 31156091--31156381 Score: 244
Period size: 81 Copynumber: 3.6 Consensus size: 81
31156081 AATACTGAAA
* ** * * * * **** *
31156091 TACCCTTGATTTGTAAAATTACTAAAATACCTTCGACTTGTAAAATTACCAAAGTACCC-CGATT
1 TACCCTCGATTTACAAAATTACCAAAATACCCTCGATTTATAAAATTACCGTTTTACCCTTGATT
31156155 TACAGAATTACCGTTT
66 TACAGAATTACCGTTT
* * **** * * *
31156171 TACCC-CGATTTATATAATTACCGTTTTACCCTCGATTTACATAATTACCGTTTTACCCTTGACT
1 TACCCTCGATTTACAAAATTACCAAAATACCCTCGATTTATAAAATTACCGTTTTACCCTTGATT
*
31156235 TACAGAATTGCCGTTT
66 TACAGAATTACCGTTT
* * **** * *
31156251 TACCCTCAATTTACAGAATTACCGTTTTACCCTCGATTTATAGAATTACTGTTTTACCCTTGATT
1 TACCCTCGATTTACAAAATTACCAAAATACCCTCGATTTATAAAATTACCGTTTTACCCTTGATT
*
31156316 TACAGAATTACTGTTT
66 TACAGAATTACCGTTT
* * * * *
31156332 TACCCTTGATTTACAAAATTACTAAAATACCCTTGGTTTGTAAAATTACC
1 TACCCTCGATTTACAAAATTACCAAAATACCCTCGATTTATAAAATTACC
31156382 AAAATACCCC
Statistics
Matches: 167, Mismatches: 42, Indels: 3
0.79 0.20 0.01
Matches are distributed among these distances:
79 36 0.22
80 28 0.17
81 103 0.62
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (81 bp):
TACCCTCGATTTACAAAATTACCAAAATACCCTCGATTTATAAAATTACCGTTTTACCCTTGATT
TACAGAATTACCGTTT
Found at i:31156379 original size:54 final size:54
Alignment explanation
Indices: 31156267--31156471 Score: 151
Period size: 54 Copynumber: 3.8 Consensus size: 54
31156257 CAATTTACAG
* * **** * ** *
31156267 AATTACCGTTTTACCCTCGATTTATAGAATTACTGTTTTACCCTTGATTTACAG
1 AATTACCGTTTTACCCTTGATTTATAAAATTACTAAAATACCCTTGGTTTGTAA
* *
31156321 AATTACTGTTTTACCCTTGATTTACAAAATTACTAAAATACCCTTGGTTTGTAA
1 AATTACCGTTTTACCCTTGATTTATAAAATTACTAAAATACCCTTGGTTTGTAA
**** * * * *
31156375 AATTACCAAAATACCCCT-AGTTTGTAAAATTACCAAAATACCCTTGGTTTGTGA
1 AATTACCGTTTTACCCTTGA-TTTATAAAATTACTAAAATACCCTTGGTTTGTAA
*** ** * *
31156429 AATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCC
1 AATTACCGTTTTACCCTTGATTTATAAAATTACTAAAATACCC
31156472 CTGATTTACA
Statistics
Matches: 124, Mismatches: 25, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
53 1 0.01
54 122 0.98
55 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.36
Consensus pattern (54 bp):
AATTACCGTTTTACCCTTGATTTATAAAATTACTAAAATACCCTTGGTTTGTAA
Found at i:31156390 original size:81 final size:81
Alignment explanation
Indices: 31156091--31156481 Score: 232
Period size: 81 Copynumber: 4.9 Consensus size: 81
31156081 AATACTGAAA
* ** * * * * * *
31156091 TACCCTTGATTTGTAAAATTACTAAAATACCTTCGACTTGTAAAATTACCAAAGTACCC-CGATT
1 TACCCTCGATTTACAAAATTACCAAAATACCCTCGATTTATAAAATTACCAAATTACCCTTGATT
31156155 TACAGAATTACCGTTT
66 TACAGAATTACCGTTT
* * **** * * *** *
31156171 TACCC-CGATTTATATAATTACCGTTTTACCCTCGATTTACATAATTACCGTTTTACCCTTGACT
1 TACCCTCGATTTACAAAATTACCAAAATACCCTCGATTTATAAAATTACCAAATTACCCTTGATT
*
31156235 TACAGAATTGCCGTTT
66 TACAGAATTACCGTTT
* * **** * ****
31156251 TACCCTCAATTTACAGAATTACCGTTTTACCCTCGATTTATAGAATTACTGTTTTACCCTTGATT
1 TACCCTCGATTTACAAAATTACCAAAATACCCTCGATTTATAAAATTACCAAATTACCCTTGATT
*
31156316 TACAGAATTACTGTTT
66 TACAGAATTACCGTTT
* * * * * * * *
31156332 TACCCTTGATTTACAAAATTACTAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCCTAGTT
1 TACCCTCGATTTACAAAATTACCAAAATACCCTCGATTTATAAAATTACCAAATTA-CCCTTGAT
****
31156397 TGTA-A-AATTACCAAAA
65 T-TACAGAATTACCGTTT
* * *** * * * * *
31156413 TACCCTTGGTTTGTGAAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATT
1 TACCCTCGATTTACAAAATTACCAAAATACCCTCGATTTATAAAATTACCAAATTACCCTTGATT
31156478 TACA
66 TACA
31156482 AAGTTACAGA
Statistics
Matches: 241, Mismatches: 65, Indels: 10
0.76 0.21 0.03
Matches are distributed among these distances:
79 38 0.16
80 35 0.15
81 158 0.66
82 8 0.03
83 2 0.01
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.36
Consensus pattern (81 bp):
TACCCTCGATTTACAAAATTACCAAAATACCCTCGATTTATAAAATTACCAAATTACCCTTGATT
TACAGAATTACCGTTT
Found at i:31156494 original size:54 final size:54
Alignment explanation
Indices: 31156346--31156584 Score: 177
Period size: 54 Copynumber: 4.4 Consensus size: 54
31156336 CTTGATTTAC
* *
31156346 AAAATTACTAAAATACCCTTGGTTTGTA-AAATTACCA-AAATACCC-CTAGTTTGT
1 AAAATTACCAAAATACCCTTGG-TT-TACAAATTA-CAGAAATACCCTCTAATTTGT
** *
31156400 AAAATTACCAAAATACCCTTGGTTTGTGAAATTACCGAAATACCCTC-AATTTGT
1 AAAATTACCAAAATACCCTTGGTTT-ACAAATTACAGAAATACCCTCTAATTTGT
* * * * *
31156454 AAAATTACCAAAATACCCCTGATTTACAAAGTTACAGAAATACCCT-TGACTCTCT
1 AAAATTACCAAAATACCCTTGGTTTACAAA-TTACAGAAATACCCTCT-AATTTGT
* * * * **
31156509 AAAAATTA-TAGAAATACCATTAGTTTACAAAATTACTGAAATACCCT-TGGTTTGT
1 -AAAATTACCA-AAATACCCTTGGTTTAC-AAATTACAGAAATACCCTCTAATTTGT
* * *
31156564 AGATTTACCAAAACACCCTTG
1 AAAATTACCAAAATACCCTTG
31156585 TAGGATGAAA
Statistics
Matches: 146, Mismatches: 28, Indels: 22
0.74 0.14 0.11
Matches are distributed among these distances:
52 1 0.01
53 6 0.04
54 91 0.62
55 10 0.07
56 35 0.24
57 3 0.02
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.31
Consensus pattern (54 bp):
AAAATTACCAAAATACCCTTGGTTTACAAATTACAGAAATACCCTCTAATTTGT
Found at i:31156645 original size:27 final size:27
Alignment explanation
Indices: 31156615--31156706 Score: 130
Period size: 27 Copynumber: 3.4 Consensus size: 27
31156605 ACCCCTATTA
*
31156615 GGTAAAAAGACCGTAATGCCCCTGTAG
1 GGTAAAATGACCGTAATGCCCCTGTAG
* *
31156642 GGTAAAGTGACCGTAAAGCCCCTGTAG
1 GGTAAAATGACCGTAATGCCCCTGTAG
* * *
31156669 GGTAAAGTGACCGTAATACCCCTGTAT
1 GGTAAAATGACCGTAATGCCCCTGTAG
31156696 GGTAAAATGAC
1 GGTAAAATGAC
31156707 GAATATGCCC
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.21
Consensus pattern (27 bp):
GGTAAAATGACCGTAATGCCCCTGTAG
Found at i:31157342 original size:26 final size:26
Alignment explanation
Indices: 31157313--31157462 Score: 230
Period size: 26 Copynumber: 5.8 Consensus size: 26
31157303 GAGGAAGTGC
*
31157313 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACTG
*
31157339 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACTG
* *
31157365 AAAAGGGCTTATGCCCCATTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACTG
* *
31157391 AAAAGGGCTTATACCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACTG
*
31157417 AAAAGGGCTTATGCCCTAGTTTACTG
1 AAAAGGGCTTATGCCCCAGTTTACTG
31157443 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
31157463 ATTAAAGAGG
Statistics
Matches: 111, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
25 9 0.08
26 102 0.92
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACTG
Found at i:31157391 original size:52 final size:52
Alignment explanation
Indices: 31157313--31157462 Score: 257
Period size: 52 Copynumber: 2.9 Consensus size: 52
31157303 GAGGAAGTGC
31157313 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
* *
31157365 AAAAGGGCTTATGCCCCATTTTACCGAAAAGGGCTTATACCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
* *
31157417 AAAAGGGCTTATGCCCTAGTTTACTGAAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTT
31157463 ATTAAAGAGG
Statistics
Matches: 92, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
51 9 0.10
52 83 0.90
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (52 bp):
AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
Found at i:31157666 original size:42 final size:42
Alignment explanation
Indices: 31157607--31157698 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
31157597 TAGTCTCCCC
* ** *
31157607 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
31157649 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
31157691 AAATGGGC
1 AAATGGGC
31157699 CTATAGGCTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
Found at i:31157757 original size:31 final size:31
Alignment explanation
Indices: 31157722--31157800 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
31157712 CATTTACAGT
31157722 AAAGGCTTCGGCCCAGTGAAATGATTTATGA
1 AAAGGCTTCGGCCCAGTGAAATGATTTATGA
* * *
31157753 AAAGGCTTTGGCCCAATGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGAAATGATTTATGA
*
31157784 AAAGGTTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
31157801 AATCGTTAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.28
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGAAATGATTTATGA
Found at i:31164342 original size:25 final size:25
Alignment explanation
Indices: 31164312--31164389 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 25
31164302 TAGGATTTTA
31164312 TGTGATGAATGTGAACATGCGTATG
1 TGTGATGAATGTGAACATGCGTATG
* * * *
31164337 TGTGAT-AAGGCCG-A-ATG-GCCA-A
1 TGTGATGAATG-TGAACATGCG-TATG
31164359 TGTGATGAATGTGAACATGCGTATG
1 TGTGATGAATGTGAACATGCGTATG
31164384 TGTGAT
1 TGTGAT
31164390 AAGGCCGAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 14
0.63 0.13 0.23
Matches are distributed among these distances:
22 8 0.21
23 8 0.21
24 8 0.21
25 14 0.37
ACGTcount: A:0.28, C:0.10, G:0.32, T:0.29
Consensus pattern (25 bp):
TGTGATGAATGTGAACATGCGTATG
Found at i:31164362 original size:47 final size:47
Alignment explanation
Indices: 31164311--31164754 Score: 600
Period size: 47 Copynumber: 9.1 Consensus size: 47
31164301 TTAGGATTTT
31164311 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
31164358 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGAT--------AAGGCCGAATGGCCA
31164413 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
***
31164460 ATGTGATGAATGTGAACCCGTATATATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAA--C--ATGCGTATGTGTGATAAGGCCGAATGGCCA
31164511 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
*** *
31164558 ATGTGATGAATGTGAACCTGTATATATATATGCGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAA-C-----ATGCGTATGTGTGATAAGGCCGAATGGCCA
31164611 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
*
31164658 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCAAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
* ** * * *
31164705 ATATGATGAATGTGAACATGTATATATGTGGTAAGGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
31164752 ATG
1 ATG
31164755 CGAAATGTGT
Statistics
Matches: 356, Mismatches: 23, Indels: 36
0.86 0.06 0.09
Matches are distributed among these distances:
47 220 0.62
48 1 0.00
49 2 0.01
51 43 0.12
52 1 0.00
53 42 0.12
55 47 0.13
ACGTcount: A:0.31, C:0.13, G:0.30, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
Found at i:31164515 original size:24 final size:24
Alignment explanation
Indices: 31164487--31164562 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
31164477 CCGTATATAT
31164487 ATGTGTGATAAGGCCGAATGGCCA
1 ATGTGTGATAAGGCCGAATGGCCA
* * **
31164511 ATGTGATGA-ATGTG--AACAT-GCGT
1 ATGTG-TGATAAG-GCCGA-ATGGCCA
31164534 ATGTGTGATAAGGCCGAATGGCCA
1 ATGTGTGATAAGGCCGAATGGCCA
31164558 ATGTG
1 ATGTG
31164563 ATGAATGTGA
Statistics
Matches: 37, Mismatches: 8, Indels: 14
0.63 0.14 0.24
Matches are distributed among these distances:
22 4 0.11
23 12 0.32
24 17 0.46
25 4 0.11
ACGTcount: A:0.29, C:0.13, G:0.33, T:0.25
Consensus pattern (24 bp):
ATGTGTGATAAGGCCGAATGGCCA
Found at i:31164638 original size:23 final size:23
Alignment explanation
Indices: 31164611--31164685 Score: 57
Period size: 23 Copynumber: 3.2 Consensus size: 23
31164601 CGAATGGCCA
31164611 ATGTGATGAATGTGAACATGCGT
1 ATGTGATGAATGTGAACATGCGT
* * **
31164634 ATGTG-TGATAAG-G-CCGAATGGCCA
1 ATGTGATGA-ATGTGAAC--AT-GCGT
31164658 ATGTGATGAATGTGAACATGCGT
1 ATGTGATGAATGTGAACATGCGT
31164681 ATGTG
1 ATGTG
31164686 TGATAAGGCC
Statistics
Matches: 37, Mismatches: 8, Indels: 14
0.63 0.14 0.24
Matches are distributed among these distances:
21 1 0.03
22 4 0.11
23 16 0.43
24 11 0.30
25 4 0.11
26 1 0.03
ACGTcount: A:0.29, C:0.11, G:0.32, T:0.28
Consensus pattern (23 bp):
ATGTGATGAATGTGAACATGCGT
Found at i:31164653 original size:100 final size:98
Alignment explanation
Indices: 31164311--31164754 Score: 630
Period size: 100 Copynumber: 4.5 Consensus size: 98
31164301 TTAGGATTTT
*
31164311 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
* * *
31164376 TGCGTATGTGTGATAAG-GCCGA-AAGGCCGAATGGCCA
66 T--GTA--TAT-ATATGTG-TGATAAGGCCGAATGGCCA
31164413 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
*
31164478 CGTATATATATGTGTGATAAGGCCGAATGGCCA
66 TGTATATATATGTGTGATAAGGCCGAATGGCCA
31164511 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
*
31164576 TGTATATATATATGCGTGATAAGGCCGAATGGCCA
66 TG--TATATATATGTGTGATAAGGCCGAATGGCCA
31164611 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-C
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
*** *
31164675 ---ATGCGTATGTGTGATAAGGCCAAATGGCCA
66 TGTATATATATGTGTGATAAGGCCGAATGGCCA
* ** * * *
31164705 ATATGATGAATGTGAACATGTATATATGTGGTAAGGCCGAATGGCTAATG
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATG
31164755 CGAAATGTGT
Statistics
Matches: 320, Mismatches: 18, Indels: 16
0.90 0.05 0.05
Matches are distributed among these distances:
94 69 0.22
97 6 0.02
98 84 0.26
99 1 0.00
100 96 0.30
102 64 0.20
ACGTcount: A:0.31, C:0.13, G:0.30, T:0.26
Consensus pattern (98 bp):
ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
TGTATATATATGTGTGATAAGGCCGAATGGCCA
Found at i:31164704 original size:147 final size:147
Alignment explanation
Indices: 31164311--31164731 Score: 602
Period size: 147 Copynumber: 2.8 Consensus size: 147
31164301 TTAGGATTTT
31164311 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
***
31164376 TGCGTATGTGTGATAAGGCCGAAAGGCCGAATGGCCAATGTGATGAATGTGAA-C-----ATGCG
66 TGCGTATGTGTGATAAGGCC---A-----AATGGCCAATGTGATGAATGTGAACCTGTATATATA
*
31164435 TATGTGTGATAAGGCCGAATGGCCA
123 TATGCGTGATAAGGCCGAATGGCCA
***
31164460 ATGTGATGAATGTGAACCCGTATATATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTG
1 ATGTGATGAATGTGAA--C--ATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTG
*
31164525 AACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACCTGTATATATATATG
62 AACATGCGTATGTGTGATAAGGCCAAATGGCCAATGTGATGAATGTGAACCTGTATATATATATG
31164590 CGTGATAAGGCCGAATGGCCA
127 CGTGATAAGGCCGAATGGCCA
31164611 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
* *
31164676 TGCGTATGTGTGATAAGGCCAAATGGCCAATATGATGAATGTGAACATGTATATAT
66 TGCGTATGTGTGATAAGGCCAAATGGCCAATGTGATGAATGTGAACCTGTATATAT
31164732 GTGGTAAGGC
Statistics
Matches: 248, Mismatches: 14, Indels: 22
0.87 0.05 0.08
Matches are distributed among these distances:
145 24 0.10
146 1 0.00
147 98 0.40
149 17 0.07
151 43 0.17
153 65 0.26
ACGTcount: A:0.31, C:0.13, G:0.30, T:0.26
Consensus pattern (147 bp):
ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
TGCGTATGTGTGATAAGGCCAAATGGCCAATGTGATGAATGTGAACCTGTATATATATATGCGTG
ATAAGGCCGAATGGCCA
Found at i:31164862 original size:46 final size:46
Alignment explanation
Indices: 31164728--31164864 Score: 193
Period size: 46 Copynumber: 3.0 Consensus size: 46
31164718 GAACATGTAT
* *
31164728 ATATGTGGTAAGGCCGAATGGCTAATGCGAAATGTGTATGAGATAG
1 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
* *
31164774 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
* * * * *
31164820 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTTTGAGATG
1 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATG
31164865 TGTATATATA
Statistics
Matches: 80, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 80 1.00
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.26
Consensus pattern (46 bp):
ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
Found at i:31165056 original size:37 final size:37
Alignment explanation
Indices: 31165006--31165076 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
31164996 GGAAATATAT
31165006 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
31165043 TCCGGGTAAGACCCGATGACTACGTGTGGAGATT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATT
31165077 TCGTCTGAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.24
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:31168998 original size:21 final size:21
Alignment explanation
Indices: 31168974--31169016 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
31168964 ATTAGACAAG
**
31168974 AACTACTTATCTTTCAACCTC
1 AACTACTTATCTCCCAACCTC
31168995 AACTACTTATCTCCCAACCTC
1 AACTACTTATCTCCCAACCTC
31169016 A
1 A
31169017 CGGTCCAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.37, G:0.00, T:0.33
Consensus pattern (21 bp):
AACTACTTATCTCCCAACCTC
Found at i:31170767 original size:23 final size:23
Alignment explanation
Indices: 31170730--31170893 Score: 75
Period size: 23 Copynumber: 7.1 Consensus size: 23
31170720 CTCACCACAA
* *
31170730 CTCGTATGAGATTACCGATTTAG
1 CTCGTAAGAGCTTACCGATTTAG
*
31170753 CTCGTAAGAGCTTA-CTATTTCAG
1 CTCGTAAGAGCTTACCGATTT-AG
** * * *
31170776 CTTATTAGAGCTTGCCGATTCAG
1 CTCGTAAGAGCTTACCGATTTAG
* * * *
31170799 CTAG-ATAGAGGTTA-CTATTTCAT
1 CTCGTA-AGAGCTTACCGATTT-AG
* **
31170822 CTCATTGGAGCTTACCGATTTAG
1 CTCGTAAGAGCTTACCGATTTAG
* * * *
31170845 CTTG-ATGGAGCTTACAGTTTTAG
1 CTCGTA-AGAGCTTACCGATTTAG
* *
31170868 CTCGTTAGAGCTTACCGATTCAG
1 CTCGTAAGAGCTTACCGATTTAG
31170891 CTC
1 CTC
31170894 AATCGAGTTT
Statistics
Matches: 98, Mismatches: 35, Indels: 16
0.66 0.23 0.11
Matches are distributed among these distances:
22 9 0.09
23 80 0.82
24 9 0.09
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (23 bp):
CTCGTAAGAGCTTACCGATTTAG
Found at i:31170816 original size:46 final size:46
Alignment explanation
Indices: 31170741--31170892 Score: 164
Period size: 46 Copynumber: 3.3 Consensus size: 46
31170731 TCGTATGAGA
* * *
31170741 TTACCGATTTAGCTCG-TAAGAGCTTACTATTTCAGCTTATTAGAGC
1 TTACCGATTCAGCTAGAT-AGAGCTTACTATTTCAGCTCATTAGAGC
* * * *
31170787 TTGCCGATTCAGCTAGATAGAGGTTACTATTTCATCTCATTGGAGC
1 TTACCGATTCAGCTAGATAGAGCTTACTATTTCAGCTCATTAGAGC
* * * * *
31170833 TTACCGATTTAGCTTGATGGAGCTTAC-AGTTTTAGCTCGTTAGAGC
1 TTACCGATTCAGCTAGATAGAGCTTACTA-TTTCAGCTCATTAGAGC
31170879 TTACCGATTCAGCT
1 TTACCGATTCAGCT
31170893 CAATCGAGTT
Statistics
Matches: 87, Mismatches: 17, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
45 1 0.01
46 85 0.98
47 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (46 bp):
TTACCGATTCAGCTAGATAGAGCTTACTATTTCAGCTCATTAGAGC
Found at i:31184567 original size:40 final size:40
Alignment explanation
Indices: 31184519--31184706 Score: 245
Period size: 40 Copynumber: 4.7 Consensus size: 40
31184509 GCTACTCATT
* *
31184519 CAAATGCCTTAGAGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* *
31184559 CAATTGCCTTCGGGACTTAGCTCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * *
31184599 CAAATGCCTTCGGGACTTAGCCCAGATATAATAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * * * *
31184639 CAATTGCCTTCGGG-CTTAGCCCAG-AATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
31184678 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
31184707 CATCCTAATT
Statistics
Matches: 128, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
38 1 0.01
39 32 0.25
40 94 0.73
41 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:31198430 original size:2 final size:2
Alignment explanation
Indices: 31198423--31198451 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31198413 AGAACAAAAC
31198423 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31198452 AACTACTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31208404 original size:50 final size:50
Alignment explanation
Indices: 31208313--31208417 Score: 117
Period size: 50 Copynumber: 2.1 Consensus size: 50
31208303 GTCATTAGGG
* * *
31208313 TTACCGATTCTCAACTCGTATGAGCTTACAGATTTGTAGCTCTTGA-GAGC
1 TTACCGATTCTCAACTCATATGAGCTTACAGATTTGCAGCTCGT-ATGAGC
* *
31208363 TTACCGGTTCTCAACTCATGTGAGCTTACCA-ATTCT-CAGCTCGTATGAGC
1 TTACCGATTCTCAACTCATATGAGCTTA-CAGATT-TGCAGCTCGTATGAGC
31208413 TTACC
1 TTACC
31208418 TATTTACATC
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
49 1 0.02
50 43 0.91
51 3 0.06
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.33
Consensus pattern (50 bp):
TTACCGATTCTCAACTCATATGAGCTTACAGATTTGCAGCTCGTATGAGC
Found at i:31208437 original size:25 final size:25
Alignment explanation
Indices: 31208313--31208417 Score: 81
Period size: 25 Copynumber: 4.2 Consensus size: 25
31208303 GTCATTAGGG
* *
31208313 TTACCGATTCTCAACTCGTATGAGC
1 TTACCAATTCTCAGCTCGTATGAGC
* *
31208338 TTA-CAGATT-TGTAGCTCTTGA-GAGC
1 TTACCA-ATTCT-CAGCTCGT-ATGAGC
** * * *
31208363 TTACCGGTTCTCAACTCATGTGAGC
1 TTACCAATTCTCAGCTCGTATGAGC
31208388 TTACCAATTCTCAGCTCGTATGAGC
1 TTACCAATTCTCAGCTCGTATGAGC
31208413 TTACC
1 TTACC
31208418 TATTTACATC
Statistics
Matches: 59, Mismatches: 15, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
24 2 0.03
25 54 0.92
26 3 0.05
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.33
Consensus pattern (25 bp):
TTACCAATTCTCAGCTCGTATGAGC
Found at i:31217378 original size:14 final size:14
Alignment explanation
Indices: 31217359--31217387 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
31217349 AAGAGATAAA
31217359 CATATTTCTACATG
1 CATATTTCTACATG
31217373 CATATTTCTACATG
1 CATATTTCTACATG
31217387 C
1 C
31217388 CTTTACTTGG
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:0.28, C:0.24, G:0.07, T:0.41
Consensus pattern (14 bp):
CATATTTCTACATG
Found at i:31224809 original size:24 final size:24
Alignment explanation
Indices: 31224774--31224829 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
31224764 ATCCCTAAAA
*
31224774 CAATGAAAAGGTCGAATAGGATAC
1 CAATGAAAAGGTCGAAAAGGATAC
* *
31224798 CATTGAAAAGGTCGAAAAGGATAT
1 CAATGAAAAGGTCGAAAAGGATAC
31224822 CAATGAAA
1 CAATGAAA
31224830 TGGTTATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.48, C:0.11, G:0.23, T:0.18
Consensus pattern (24 bp):
CAATGAAAAGGTCGAAAAGGATAC
Found at i:31225492 original size:182 final size:182
Alignment explanation
Indices: 31225169--31225533 Score: 615
Period size: 182 Copynumber: 2.0 Consensus size: 182
31225159 TTTTGGGGAA
* *
31225169 TTATTTTTAAGTTTTAAATTTGTTTTAAGTTTTAAAAATAATTATTTATTTTTAGTTTTTATTTT
1 TTATTTTTAAATCTTAAATTTGTTTTAAGTTTTAAAAATAATTATTTATTTTTAGTTTTTATTTT
* * *
31225234 ATTTTTATCTCAAAACTCAACAGTTTCACCTTTTTTCCCCCATTTTCCCTGCACATTCTTTTTCC
66 ATTTTTATCTCAAAACTCAACAGTTTCACCTTTTTTCCACCACTTTCCCTGCACACTCTTTTTCC
31225299 AATTATTTTTTTTAGTCTTTTCATTTTGTTTCCTCTCCCTCCACGTTCTCCC
131 AATTATTTTTTTTAGTCTTTTCATTTTGTTTCCTCTCCCTCCACGTTCTCCC
*
31225351 TTATTTTTAAATCTTAAATTTGTTTTAAGTTTTCAAAATAATTATTTATTTTTAGTTTTTATTTT
1 TTATTTTTAAATCTTAAATTTGTTTTAAGTTTTAAAAATAATTATTTATTTTTAGTTTTTATTTT
* * * *
31225416 ATTTTTATCTCAAAACTCAATAGTTTCACGTTTTTT-CACCACTTTCTCTGCACGCTCTTTTTCC
66 ATTTTTATCTCAAAACTCAACAGTTTCACCTTTTTTCCACCACTTTCCCTGCACACTCTTTTTCC
* *
31225480 AATTATTTTTTTTAGTCTTTTCTTTTTGTTTCCTCTCCCTCTACGTTCTCCC
131 AATTATTTTTTTTAGTCTTTTCATTTTGTTTCCTCTCCCTCCACGTTCTCCC
31225532 TT
1 TT
31225534 CTCTTTTCAT
Statistics
Matches: 171, Mismatches: 12, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
181 75 0.44
182 96 0.56
ACGTcount: A:0.21, C:0.19, G:0.05, T:0.55
Consensus pattern (182 bp):
TTATTTTTAAATCTTAAATTTGTTTTAAGTTTTAAAAATAATTATTTATTTTTAGTTTTTATTTT
ATTTTTATCTCAAAACTCAACAGTTTCACCTTTTTTCCACCACTTTCCCTGCACACTCTTTTTCC
AATTATTTTTTTTAGTCTTTTCATTTTGTTTCCTCTCCCTCCACGTTCTCCC
Found at i:31227455 original size:40 final size:40
Alignment explanation
Indices: 31227371--31227458 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 40
31227361 ACATTCAAAT
* * *
31227371 GCCTTCGGGACATAGCCCGGTTACAGTAACTCGCACGAAT
1 GCCTTCGGGACATAACCCGGTTACAGTAACCCGCACGAAA
* * * *
31227411 GCCTTCGGGACTTAACCCGGATT-TAGTAGCCCGCTCGAAA
1 GCCTTCGGGACATAACCCGG-TTACAGTAACCCGCACGAAA
31227451 GCCTTCGG
1 GCCTTCGG
31227459 ATCTTAGTCC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
40 38 0.95
41 2 0.05
ACGTcount: A:0.22, C:0.31, G:0.26, T:0.22
Consensus pattern (40 bp):
GCCTTCGGGACATAACCCGGTTACAGTAACCCGCACGAAA
Found at i:31227545 original size:40 final size:40
Alignment explanation
Indices: 31227395--31227552 Score: 133
Period size: 40 Copynumber: 4.0 Consensus size: 40
31227385 GCCCGGTTAC
* * **
31227395 AGTAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGATTT
1 AGTAACTAGCACGAAAGCCTTC-GGATCTTAGTCCGGATTT
* ** * *
31227435 AGTAGCCCGCTCGAAAGCCTTCGGATCTTAGTCCAGATTT
1 AGTAACTAGCACGAAAGCCTTCGGATCTTAGTCCGGATTT
* * * *
31227475 AGTAACTCGCACGTATGCCGTCGGATCTTAGTCCGGATTT
1 AGTAACTAGCACGAAAGCCTTCGGATCTTAGTCCGGATTT
* *
31227515 AGTCACTTAGCAC-AAAGCCTTCGGGA-CTTAGCCCGGAT
1 AGTAAC-TAGCACGAAAGCCTTC-GGATCTTAGTCCGGAT
31227553 ATCATTCGAA
Statistics
Matches: 95, Mismatches: 20, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
39 3 0.03
40 84 0.88
41 8 0.08
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
AGTAACTAGCACGAAAGCCTTCGGATCTTAGTCCGGATTT
Found at i:31232207 original size:30 final size:29
Alignment explanation
Indices: 31232154--31232254 Score: 184
Period size: 29 Copynumber: 3.4 Consensus size: 29
31232144 AGTGAATCCT
31232154 CACACTTAGTGCTATATATTTTCAGCTCG
1 CACACTTAGTGCTATATATTTTCAGCTCG
31232183 CACACTTAGTGCTATATAATTTTCAGCTCG
1 CACACTTAGTGCTATAT-ATTTTCAGCTCG
*
31232213 CACACTTAGTGCTATATATTTTCAGTTCG
1 CACACTTAGTGCTATATATTTTCAGCTCG
31232242 CACACTTAGTGCT
1 CACACTTAGTGCT
31232255 GTACAATTTT
Statistics
Matches: 70, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
29 41 0.59
30 29 0.41
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.38
Consensus pattern (29 bp):
CACACTTAGTGCTATATATTTTCAGCTCG
Found at i:31232228 original size:59 final size:60
Alignment explanation
Indices: 31232154--31232284 Score: 201
Period size: 59 Copynumber: 2.2 Consensus size: 60
31232144 AGTGAATCCT
* * * *
31232154 CACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAA-TTTTCAGCTCG
1 CACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATACAATTTTTAAACCCG
* *
31232213 CACACTTAGTGCTATATATTTTCAGTTCGCACACTTAGTGCTGTACAATTTTTAAACCCG
1 CACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATACAATTTTTAAACCCG
31232273 CACACTTAGTGC
1 CACACTTAGTGC
31232285 CAATCTTGTC
Statistics
Matches: 65, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
59 45 0.69
60 20 0.31
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (60 bp):
CACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATACAATTTTTAAACCCG
Found at i:31235111 original size:12 final size:13
Alignment explanation
Indices: 31235073--31235115 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
31235063 TGCAAAAACT
31235073 AGAAAAGAAATG-A
1 AGAAAAGAAA-GAA
31235086 AGAAAAGAAAGAA
1 AGAAAAGAAAGAA
31235099 AGAAAAG-AAGAA
1 AGAAAAGAAAGAA
31235111 AGAAA
1 AGAAA
31235116 TGCACGGCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.02
Consensus pattern (13 bp):
AGAAAAGAAAGAA
Found at i:31236818 original size:12 final size:12
Alignment explanation
Indices: 31236801--31236831 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
31236791 TTACTGCCAA
31236801 TCTTGAAAATCT
1 TCTTGAAAATCT
31236813 TCTTGAAAATCT
1 TCTTGAAAATCT
31236825 TCTTGAA
1 TCTTGAA
31236832 TCTCCACGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (12 bp):
TCTTGAAAATCT
Found at i:31240717 original size:12 final size:12
Alignment explanation
Indices: 31240700--31240730 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
31240690 CAACTGCCAA
31240700 TCTTGAAAATCT
1 TCTTGAAAATCT
31240712 TCTTGAAAATCT
1 TCTTGAAAATCT
31240724 TCTTGAA
1 TCTTGAA
31240731 TCTCCACATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (12 bp):
TCTTGAAAATCT
Found at i:31246545 original size:31 final size:31
Alignment explanation
Indices: 31246498--31246612 Score: 187
Period size: 31 Copynumber: 3.7 Consensus size: 31
31246488 TTAGTCTTAA
*
31246498 CATAT-ACTGGGCCGAAGCCTTTCCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
*
31246528 CATATCACTGGGTCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
31246559 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
* *
31246590 CATATCATTGGGCTGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
31246613 ACTGTAAACG
Statistics
Matches: 79, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
30 5 0.06
31 74 0.94
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.30
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATAAAT
Found at i:31246683 original size:42 final size:42
Alignment explanation
Indices: 31246636--31246769 Score: 252
Period size: 42 Copynumber: 3.2 Consensus size: 42
31246626 TGGCCCTTAG
31246636 GCCCATTTCAATATCACATGTAATGTCAATGGAA-GTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAAT-GAATGTATGCAA
31246678 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
31246720 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
31246762 GCCCATTT
1 GCCCATTT
31246770 GGGGAGACTA
Statistics
Matches: 91, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
41 3 0.03
42 88 0.97
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
Found at i:31246958 original size:25 final size:25
Alignment explanation
Indices: 31246918--31246986 Score: 93
Period size: 25 Copynumber: 2.8 Consensus size: 25
31246908 TCTTTTAATT
*
31246918 ACTAGGGCAAAGCCCTTTTTGATAA
1 ACTAGGGCAAAGCCCTTTTCGATAA
* * *
31246943 ACTGGGGCAAAACCCTTTTCGGTAA
1 ACTAGGGCAAAGCCCTTTTCGATAA
*
31246968 ACTAGGGCAGAGCCCTTTT
1 ACTAGGGCAAAGCCCTTTT
31246987 AGCACTTCCT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (25 bp):
ACTAGGGCAAAGCCCTTTTCGATAA
Found at i:31247858 original size:27 final size:27
Alignment explanation
Indices: 31247797--31247860 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
31247787 GGCATATTCA
31247797 TCATTTTACCATACAGGGGTATTACGG
1 TCATTTTACCATACAGGGGTATTACGG
* *
31247824 TCACTTTACCCTACAGGGGCT-TTACGG
1 TCATTTTACCATACAGGGG-TATTACGG
*
31247851 TCTTTTTACC
1 TCATTTTACC
31247861 TATTAGGAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.36
Consensus pattern (27 bp):
TCATTTTACCATACAGGGGTATTACGG
Found at i:31248017 original size:27 final size:27
Alignment explanation
Indices: 31247977--31248100 Score: 124
Period size: 27 Copynumber: 4.6 Consensus size: 27
31247967 AGAAAGTCAA
* ** * *
31247977 GGGTATTTTTGTAATTTTGTAAATTGG
1 GGGTATTTTGGTAATTTTACAAACTAG
* *
31248004 GGGTATTTTGGTAAATTTACAAA-TTG
1 GGGTATTTTGGTAATTTTACAAACTAG
* * * *
31248030 AGGGTATTTCGATAATTTCACAAACCAG
1 -GGGTATTTTGGTAATTTTACAAACTAG
*
31248058 TGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACTAG
31248085 GGGTATTTTGGTAATT
1 GGGTATTTTGGTAATT
31248101 CTACCCTATA
Statistics
Matches: 78, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
26 2 0.03
27 75 0.96
28 1 0.01
ACGTcount: A:0.28, C:0.06, G:0.23, T:0.43
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACTAG
Found at i:31248073 original size:110 final size:108
Alignment explanation
Indices: 31247894--31248100 Score: 238
Period size: 110 Copynumber: 1.9 Consensus size: 108
31247884 CATCCTACAA
* ***
31247894 GGGTGTTTTGGTAAATCTACAAACCAAGGGTATTTCAGTAATTTTGTAAACCAATGGTATTTCTA
1 GGGTATTTTGGTAAATCTACAAACCAAGGGTATTTCAGTAATTTCACAAACCAATGGTATTTCTA
* * *
31247959 TAATTTTTAGAAAGTCAAGGGTATTTTTGTAATTTTGTAAATTGG
66 TAA-TTTTACAAACT-AAGGGTATTTTGGTAATTTTGTAAATTGG
* *** *
31248004 GGGTATTTTGGTAAATTTACAAATTGAGGGTATTTC-GATAATTTCACAAACCAGTGGTATTT-T
1 GGGTATTTTGGTAAATCTACAAACCAAGGGTATTTCAG-TAATTTCACAAACCAATGGTATTTCT
* *
31248067 GGTAATTTTACAAACTAGGGGTATTTTGGTAATT
65 -ATAATTTTACAAACTAAGGGTATTTTGGTAATT
31248101 CTACCCTATA
Statistics
Matches: 81, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
108 16 0.20
109 11 0.14
110 54 0.67
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.41
Consensus pattern (108 bp):
GGGTATTTTGGTAAATCTACAAACCAAGGGTATTTCAGTAATTTCACAAACCAATGGTATTTCTA
TAATTTTACAAACTAAGGGTATTTTGGTAATTTTGTAAATTGG
Found at i:31248115 original size:81 final size:81
Alignment explanation
Indices: 31247978--31248133 Score: 192
Period size: 81 Copynumber: 1.9 Consensus size: 81
31247968 GAAAGTCAAG
* ** * * *
31247978 GGTATTTTTGTAATTTTGTAAATTGGGGGTATTTTGGTAAATTTACAAATTGAGGGTATTTC-GA
1 GGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAAATTTACAAATTAAGGGTATTTCAG-
31248042 TAATTTCACAAACCAGT
65 TAATTTCACAAACCAGT
**
31248059 GGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGT-AATTCTAC-CCTATAAGGGTATTTCA
1 GGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAAATT-TACAAAT-TAAGGGTATTTCA
31248122 GTAATTTCACAA
64 GTAATTTCACAA
31248134 TCGAGGGTAA
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
80 5 0.08
81 58 0.91
82 1 0.02
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (81 bp):
GGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAAATTTACAAATTAAGGGTATTTCAGT
AATTTCACAAACCAGT
Found at i:31248119 original size:27 final size:27
Alignment explanation
Indices: 31247892--31248104 Score: 92
Period size: 27 Copynumber: 7.8 Consensus size: 27
31247882 TTCATCCTAC
* * *
31247892 AAGGGTGTTTTGGTAAATCTACAAACC
1 AAGGGTATTTTGGTAATTCTACAAACT
** * ** *
31247919 AAGGGTATTTCAGTAATTTTGTAAACC
1 AAGGGTATTTTGGTAATTCTACAAACT
* * * * *
31247946 AATGGTATTTCT-ATAATTTTTAGAAAGT
1 AAGGGTATTT-TGGTAA-TTCTACAAACT
* * ** *
31247974 CAAGGGTATTTTTGTAATTTTGTAAATT
1 -AAGGGTATTTTGGTAATTCTACAAACT
** *
31248002 GGGGGTATTTTGGTAAATT-TACAAATT
1 AAGGGTATTTTGGT-AATTCTACAAACT
* * *
31248029 GAGGGTATTTCGATAATT-TCACAAAC-
1 AAGGGTATTTTGGTAATTCT-ACAAACT
* *
31248055 CAGTGGTATTTTGGTAATTTTACAAACT
1 AAG-GGTATTTTGGTAATTCTACAAACT
*
31248083 AGGGGTATTTTGGTAATTCTAC
1 AAGGGTATTTTGGTAATTCTAC
31248105 CCTATAAGGG
Statistics
Matches: 143, Mismatches: 34, Indels: 18
0.73 0.17 0.09
Matches are distributed among these distances:
26 7 0.05
27 102 0.71
28 22 0.15
29 12 0.08
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (27 bp):
AAGGGTATTTTGGTAATTCTACAAACT
Found at i:31248151 original size:26 final size:26
Alignment explanation
Indices: 31248120--31248223 Score: 93
Period size: 27 Copynumber: 3.9 Consensus size: 26
31248110 AAGGGTATTT
31248120 CAGTAATTT-CACAATCGAGGGTAAAA
1 CAGTAATTTGCA-AATCGAGGGTAAAA
* * *
31248146 CGGTAATTTTGTAAATTGAGGGTAAAA
1 CAGTAA-TTTGCAAATCGAGGGTAAAA
* *
31248173 CAGTAATTCTGTAAATCAAGGGTAAAA
1 CAGTAATT-TGCAAATCGAGGGTAAAA
* **
31248200 CAGTGATTCTATAAATCGAGGGTA
1 CAGTAATT-TGCAAATCGAGGGTA
31248224 CTTTGGTAAT
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
26 7 0.11
27 58 0.88
28 1 0.02
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (26 bp):
CAGTAATTTGCAAATCGAGGGTAAAA
Found at i:31248169 original size:27 final size:27
Alignment explanation
Indices: 31248132--31248223 Score: 130
Period size: 27 Copynumber: 3.4 Consensus size: 27
31248122 GTAATTTCAC
* *
31248132 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACAGTAATTCTGTA
*
31248159 AATTGAGGGTAAAACAGTAATTCTGTA
1 AATCGAGGGTAAAACAGTAATTCTGTA
* * *
31248186 AATCAAGGGTAAAACAGTGATTCTATA
1 AATCGAGGGTAAAACAGTAATTCTGTA
31248213 AATCGAGGGTA
1 AATCGAGGGTA
31248224 CTTTGGTAAT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 57 1.00
ACGTcount: A:0.40, C:0.09, G:0.24, T:0.27
Consensus pattern (27 bp):
AATCGAGGGTAAAACAGTAATTCTGTA
Found at i:31249875 original size:12 final size:12
Alignment explanation
Indices: 31249858--31249889 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
31249848 CTAAAATTTC
31249858 TTTTATTATATA
1 TTTTATTATATA
31249870 TTTTATTATATA
1 TTTTATTATATA
31249882 TATTTATT
1 T-TTTATT
31249890 CTGTTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.68
13 6 0.32
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTATTATATA
Found at i:31250073 original size:5 final size:5
Alignment explanation
Indices: 31250032--31250109 Score: 69
Period size: 5 Copynumber: 16.6 Consensus size: 5
31250022 TATTTATTAC
* * *
31250032 ATATT ATATT TTACT ATA-T ATCATA ATATT -T-TT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT AT-ATT ATATT ATATT ATATT ATATT ATATT
*
31250080 ATA-T ACATT ATATT ATATT -T-TT ATATT ATA
1 ATATT ATATT ATATT ATATT ATATT ATATT ATA
31250110 ATTTACATTA
Statistics
Matches: 59, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
3 4 0.07
4 10 0.17
5 43 0.73
6 2 0.03
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (5 bp):
ATATT
Found at i:31250107 original size:37 final size:38
Alignment explanation
Indices: 31250032--31250109 Score: 108
Period size: 37 Copynumber: 2.1 Consensus size: 38
31250022 TATTTATTAC
31250032 ATATTATATTTTACTATATATCATAATATTTTTATATT
1 ATATTATATTTTACTATATATCATAATATTTTTATATT
*
31250070 ATATTATATTATATAC-AT-TAT-ATTATATTTTTATATT
1 ATATTATATT-T-TACTATATATCATAATATTTTTATATT
31250107 ATA
1 ATA
31250110 ATTTACATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
37 18 0.49
38 13 0.35
39 3 0.08
40 3 0.08
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (38 bp):
ATATTATATTTTACTATATATCATAATATTTTTATATT
Found at i:31250119 original size:30 final size:31
Alignment explanation
Indices: 31250068--31250133 Score: 91
Period size: 30 Copynumber: 2.1 Consensus size: 31
31250058 TATTTTTATA
31250068 TTATATTATATTATATACATTA-TATTATATTT
1 TTATATTATA-TATATACATTATTA-TATATTT
*
31250100 TTATATTATA-ATTTACATTATTATATATTT
1 TTATATTATATATATACATTATTATATATTT
31250130 TTAT
1 TTAT
31250134 TTGTAAATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 20 0.62
31 2 0.06
32 10 0.31
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (31 bp):
TTATATTATATATATACATTATTATATATTT
Found at i:31254686 original size:30 final size:30
Alignment explanation
Indices: 31254641--31254700 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
31254631 ATTTAATACG
*
31254641 AACTTTGGCAAAATTACATTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
* *
31254671 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
31254701 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.38
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTGCCCCTA
Found at i:31272944 original size:177 final size:176
Alignment explanation
Indices: 31272630--31273192 Score: 847
Period size: 176 Copynumber: 3.2 Consensus size: 176
31272620 CTTCGACGGA
* * *
31272630 GAGCAAATCGAAGACATAGCAAATCTGACTTTCAGATGTTTTCACATCAAAACAGATCCAAGATA
1 GAGCAAATCAAAGACATAGCAGATCTGACTTTCAGATGTTTTCACATCAAAGCAGATCCAAGATA
31272695 ACAGATCTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTAACCTTCAGATGTTT
66 ACAGATCTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTAACCTTCAGATGTTT
*
31272760 TTACTGAAGCAGATCCAAGATGATTTGGCATTCTTGTGTCTACAAG
131 TTACTGAAGCAGATCCAAGATGATTTGGCATTCTTGTGTTTACAAG
* * * * * *
31272806 GAGCAAATCAAAAACATAGCAGATTTGACTTTCGGATGTTCTCACATCAAAGTAGATCCCAGATA
1 GAGCAAATCAAAGACATAGCAGATCTGACTTTCAGATGTTTTCACATCAAAGCAGATCCAAGATA
* * * * * * * *
31272871 ACAGATCTGGCATCTCCATATGCAAATGGAGAGCAGATACATAGCAAATCTAACCTTCATATATT
66 ACAGATCTGGCGTCTCCATATTC-GACGGAGAGCAGACACATAGCAGATCTAACCTTCAGATGTT
* * *
31272936 TTTACTGAAGCATATCCAATATGATTTGGCGTTCTTGTGTTTACAAG
130 TTTACTGAAGCAGATCCAAGATGATTTGGCATTCTTGTGTTTACAAG
* *
31272983 AAGCAAATCGAAGACATAGCAGATCTGACTTTCAGATGTTTTCACATCAAAGCAGATCCAAGATA
1 GAGCAAATCAAAGACATAGCAGATCTGACTTTCAGATGTTTTCACATCAAAGCAGATCCAAGATA
*
31273048 ACAAATCTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTAACCTTCAGATGTTT
66 ACAGATCTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTAACCTTCAGATGTTT
* * *
31273113 ATACTGAAGTAGATCCAAGATGATTTGGCATCCTTGTGTTTACAAG
131 TTACTGAAGCAGATCCAAGATGATTTGGCATTCTTGTGTTTACAAG
* * *
31273159 GAACAAATCAAAGACATAGCAGATTTGGCTTTCA
1 GAGCAAATCAAAGACATAGCAGATCTGACTTTCA
31273193 CGTGTTTACG
Statistics
Matches: 337, Mismatches: 49, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
176 182 0.54
177 155 0.46
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (176 bp):
GAGCAAATCAAAGACATAGCAGATCTGACTTTCAGATGTTTTCACATCAAAGCAGATCCAAGATA
ACAGATCTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTAACCTTCAGATGTTT
TTACTGAAGCAGATCCAAGATGATTTGGCATTCTTGTGTTTACAAG
Found at i:31274249 original size:40 final size:40
Alignment explanation
Indices: 31274194--31274273 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
31274184 CTGAAGAACA
31274194 GAGGTGATACTTTCAATTTTCTTTTCATTATTTATTTTCT
1 GAGGTGATACTTTCAATTTTCTTTTCATTATTTATTTTCT
31274234 GAGGTGATACTTTCAATTTTCTTTTCATTATTTATTTTCT
1 GAGGTGATACTTTCAATTTTCTTTTCATTATTTATTTTCT
31274274 TTCTGATACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.20, C:0.12, G:0.10, T:0.57
Consensus pattern (40 bp):
GAGGTGATACTTTCAATTTTCTTTTCATTATTTATTTTCT
Found at i:31275232 original size:22 final size:19
Alignment explanation
Indices: 31275207--31275263 Score: 57
Period size: 18 Copynumber: 3.0 Consensus size: 19
31275197 ATATTTATTA
31275207 CATATTATATTTTACTATATAT
1 CATATTATATTTT--T-TATAT
31275229 CATA--ATATTTTTTATAT
1 CATATTATATTTTTTATAT
*
31275246 TATATTATA-TTTTTATAT
1 CATATTATATTTTTTATAT
31275264 TATAATTTAC
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
17 8 0.25
18 10 0.31
19 3 0.09
20 7 0.22
22 4 0.12
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (19 bp):
CATATTATATTTTTTATAT
Found at i:31275283 original size:20 final size:18
Alignment explanation
Indices: 31275240--31275283 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
31275230 ATAATATTTT
* *
31275240 TTATATTATATTATATTT
1 TTATATTATATTACATTA
31275258 TTATATTATAATTTACATTA
1 TTATATTAT-A-TTACATTA
31275278 TTATAT
1 TTATAT
31275284 ATTTTTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 9 0.41
19 1 0.05
20 12 0.55
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (18 bp):
TTATATTATATTACATTA
Found at i:31276897 original size:70 final size:70
Alignment explanation
Indices: 31276783--31276922 Score: 253
Period size: 70 Copynumber: 2.0 Consensus size: 70
31276773 ACAGAAAACT
* *
31276783 TAAAAATATATTCCTCTTCATCTGAATCAGAATCTGTTTCTGATATTAACTCATATAATGTTTCT
1 TAAAAATATATTCCTCTTCATCTGAATCAGAATCTGTTTATGATATTAACTCATATAATATTTCT
31276848 TTAGG
66 TTAGG
*
31276853 TAAATATATATTCCTCTTCATCTGAATCAGAATCTGTTTATGATATTAACTCATATAATATTTCT
1 TAAAAATATATTCCTCTTCATCTGAATCAGAATCTGTTTATGATATTAACTCATATAATATTTCT
31276918 TTAGG
66 TTAGG
31276923 ATTTATTTCC
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 67 1.00
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.44
Consensus pattern (70 bp):
TAAAAATATATTCCTCTTCATCTGAATCAGAATCTGTTTATGATATTAACTCATATAATATTTCT
TTAGG
Found at i:31278201 original size:3 final size:3
Alignment explanation
Indices: 31278193--31278228 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
31278183 AGAACAAGGT
31278193 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
31278229 TAGAGTCAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:31281149 original size:40 final size:40
Alignment explanation
Indices: 31281047--31281198 Score: 155
Period size: 40 Copynumber: 3.8 Consensus size: 40
31281037 AAATTGAATG
* * * * *
31281047 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAAAT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGAT
* *
31281086 GATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 -ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGAT
* * *
31281127 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCCAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTAGAT
* * *
31281167 AAATCTGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
31281199 AAATCGTGAT
Statistics
Matches: 95, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
39 3 0.03
40 87 0.92
41 5 0.05
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGAT
Found at i:31290614 original size:41 final size:41
Alignment explanation
Indices: 31290565--31290695 Score: 172
Period size: 41 Copynumber: 3.2 Consensus size: 41
31290555 CAAAAAATTG
31290565 AGCAATAGCGGCATTTTTGGTCCAAACGCCGCTAAAAACTA
1 AGCAATAGCGGCATTTTTGGTCCAAACGCCGCTAAAAACTA
* *
31290606 AGCGATAGCGGCATTTTTGGTCCAAATGCCGCTAAAAACTA
1 AGCAATAGCGGCATTTTTGGTCCAAACGCCGCTAAAAACTA
** * ** *
31290647 AGCAATAGTAGCGTTTTTCATCCAAACGCCGCGAAAAAACTA
1 AGCAATAGCGGCATTTTTGGTCCAAACGCCGC-TAAAAACTA
*
31290689 AACAATA
1 AGCAATA
31290696 TTGAAGCTTT
Statistics
Matches: 78, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
41 64 0.82
42 14 0.18
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (41 bp):
AGCAATAGCGGCATTTTTGGTCCAAACGCCGCTAAAAACTA
Found at i:31290932 original size:40 final size:41
Alignment explanation
Indices: 31290836--31291001 Score: 226
Period size: 41 Copynumber: 4.1 Consensus size: 41
31290826 ATTGCTCAGT
*
31290836 TTTTAGCAGCGCTTTTGGAAAAACGCCGCTATAGATCGAGG
1 TTTTAGCGGCGCTTTTGGAAAAACGCCGCTATAGATCGAGG
* * * ** *
31290877 TTTTAGCGGCACTTTTGGAAAAACGCTGCTATTG-TTTAGT
1 TTTTAGCGGCGCTTTTGGAAAAACGCCGCTATAGATCGAGG
* *
31290917 TTTTAGCTGCGCTTTTGGAAAAACGCTGCTATAGATCGAGG
1 TTTTAGCGGCGCTTTTGGAAAAACGCCGCTATAGATCGAGG
* *
31290958 TTTTAACGGCGCTTTTGGAAAAACGCCGCTATAGATTGAGG
1 TTTTAGCGGCGCTTTTGGAAAAACGCCGCTATAGATCGAGG
31290999 TTT
1 TTT
31291002 AGGGTTTAGA
Statistics
Matches: 107, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
40 34 0.32
41 73 0.68
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (41 bp):
TTTTAGCGGCGCTTTTGGAAAAACGCCGCTATAGATCGAGG
Found at i:31290959 original size:81 final size:81
Alignment explanation
Indices: 31290824--31290989 Score: 269
Period size: 81 Copynumber: 2.0 Consensus size: 81
31290814 ATAACAGCGT
*
31290824 CTATTGCTCAGTTTTTAGCAGCGCTTTTGGAAAAACGCCGCTATAGATCGAGGTTTTAGCGGCAC
1 CTATTGCTCAGTTTTTAGCAGCGCTTTTGGAAAAACGCCGCTATAGATCGAGGTTTTAACGGCAC
*
31290889 TTTTGGAAAAACGCTG
66 TTTTGGAAAAACGCCG
* * * * *
31290905 CTATTGTTTAGTTTTTAGCTGCGCTTTTGGAAAAACGCTGCTATAGATCGAGGTTTTAACGGCGC
1 CTATTGCTCAGTTTTTAGCAGCGCTTTTGGAAAAACGCCGCTATAGATCGAGGTTTTAACGGCAC
31290970 TTTTGGAAAAACGCCG
66 TTTTGGAAAAACGCCG
31290986 CTAT
1 CTAT
31290990 AGATTGAGGT
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 78 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (81 bp):
CTATTGCTCAGTTTTTAGCAGCGCTTTTGGAAAAACGCCGCTATAGATCGAGGTTTTAACGGCAC
TTTTGGAAAAACGCCG
Found at i:31291763 original size:21 final size:21
Alignment explanation
Indices: 31291733--31291775 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
31291723 ATATATGTTC
31291733 ATGGTCTAGGATTTAGGG-TTT
1 ATGGTCTAGGATTT-GGGATTT
*
31291754 ATGGTTTAGGATTTGGGATTT
1 ATGGTCTAGGATTTGGGATTT
31291775 A
1 A
31291776 ATTTTTAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.21, C:0.02, G:0.33, T:0.44
Consensus pattern (21 bp):
ATGGTCTAGGATTTGGGATTT
Found at i:31292196 original size:7 final size:7
Alignment explanation
Indices: 31292183--31292231 Score: 62
Period size: 8 Copynumber: 6.6 Consensus size: 7
31292173 AAATCTTCAA
31292183 AAAAATT
1 AAAAATT
*
31292190 GAAAATTT
1 -AAAAATT
31292198 AAAAATT
1 AAAAATT
31292205 AAAAATT
1 AAAAATT
31292212 AAAAACTT
1 AAAAA-TT
31292220 AAAAACTT
1 AAAAA-TT
31292228 AAAA
1 AAAA
31292232 TTTTAATATT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
7 18 0.47
8 20 0.53
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (7 bp):
AAAAATT
Found at i:31292202 original size:8 final size:8
Alignment explanation
Indices: 31292159--31292237 Score: 54
Period size: 8 Copynumber: 9.6 Consensus size: 8
31292149 TATATGTTAG
31292159 TTTAAAAA
1 TTTAAAAA
*
31292167 TGATAAAAA
1 T-TTAAAAA
31292176 TCTTCAAAAAA
1 T-TT--AAAAA
* *
31292187 ATTGAAAA
1 TTTAAAAA
31292195 TTTAAAAA
1 TTTAAAAA
31292203 -TTAAAAA
1 TTTAAAAA
31292210 -TTAAAAA
1 TTTAAAAA
*
31292217 CTTAAAAA
1 TTTAAAAA
* *
31292225 CTTAAAAT
1 TTTAAAAA
31292233 TTTAA
1 TTTAA
31292238 TATTTAGTAT
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
7 14 0.24
8 29 0.50
9 8 0.14
10 2 0.03
11 5 0.09
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.32
Consensus pattern (8 bp):
TTTAAAAA
Found at i:31292237 original size:16 final size:15
Alignment explanation
Indices: 31292183--31292231 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
31292173 AAATCTTCAA
* *
31292183 AAAAATTGAAAATTT
1 AAAAATTAAAAACTT
31292198 AAAAATTAAAAA-TT
1 AAAAATTAAAAACTT
31292212 AAAAACTTAAAAACTT
1 AAAAA-TTAAAAACTT
31292228 AAAA
1 AAAA
31292232 TTTTAATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
14 7 0.23
15 18 0.58
16 6 0.19
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (15 bp):
AAAAATTAAAAACTT
Found at i:31292305 original size:23 final size:24
Alignment explanation
Indices: 31292265--31292310 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
31292255 CATATTTCAG
* * *
31292265 TTAAAAAGATCAATATT-CAAAAT
1 TTAAAAAAATAAAAATTCCAAAAT
31292288 TTAAAAAAATAAAAATTCCAAAA
1 TTAAAAAAATAAAAATTCCAAAA
31292311 AATGATAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.63, C:0.09, G:0.02, T:0.26
Consensus pattern (24 bp):
TTAAAAAAATAAAAATTCCAAAAT
Found at i:31292357 original size:25 final size:26
Alignment explanation
Indices: 31292328--31292376 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
31292318 ATCTCAGCAC
*
31292328 AAAAATTTTAAAA-GAAAAAAATAGA
1 AAAAATATTAAAATGAAAAAAATAGA
*
31292353 AAAAATATTAAAATGAAGAAAATA
1 AAAAATATTAAAATGAAAAAAATA
31292377 AAATTGAGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.20
Consensus pattern (26 bp):
AAAAATATTAAAATGAAAAAAATAGA
Found at i:31298208 original size:43 final size:42
Alignment explanation
Indices: 31298102--31298208 Score: 142
Period size: 42 Copynumber: 2.5 Consensus size: 42
31298092 ACAAAAGACG
*
31298102 CTAAAGATCATGATCTTTAGCGGCGTTTGCGAAAAAGCGCCA
1 CTAAAGATCATGATCTTTAGCGGCGTTTGCGAAAAAACGCCA
* * * *
31298144 CTAAAGGTCATGGTCTATAGCGGCGTTTGCGAAAAAAACGTCA
1 CTAAAGATCATGATCTTTAGCGGCGTTTGCG-AAAAAACGCCA
* *
31298187 CTAAAGACCATGACCTTTAGCG
1 CTAAAGATCATGATCTTTAGCG
31298209 ACGCTTTTTC
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
42 28 0.52
43 26 0.48
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.23
Consensus pattern (42 bp):
CTAAAGATCATGATCTTTAGCGGCGTTTGCGAAAAAACGCCA
Found at i:31298235 original size:42 final size:42
Alignment explanation
Indices: 31298187--31298276 Score: 121
Period size: 42 Copynumber: 2.1 Consensus size: 42
31298177 AAAAACGTCA
31298187 CTAAAGACCATGACCTTTAGC-GACGCTTTT-TCGCAAACACCG
1 CTAAAGACCATGACCTTTAGCAG-CGCTTTTAT-GCAAACACCG
* *
31298229 CTAAAGACCATGACTTTTAGCAGCGCTTTTAATGCAAACGCCG
1 CTAAAGACCATGACCTTTAGCAGCGCTTTT-ATGCAAACACCG
31298272 CTAAA
1 CTAAA
31298277 AGTCATGGTC
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
42 27 0.63
43 15 0.35
44 1 0.02
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (42 bp):
CTAAAGACCATGACCTTTAGCAGCGCTTTTATGCAAACACCG
Found at i:31309440 original size:17 final size:17
Alignment explanation
Indices: 31309390--31309440 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 17
31309380 TGGAAACATG
*
31309390 ATCTTCGAAGATATGCA
1 ATCTTAGAAGATATGCA
*
31309407 ATCTTAGATATGATATGTA
1 ATCTTAGA-A-GATATGCA
31309426 ATCTTAGAAGATATG
1 ATCTTAGAAGATATG
31309441 ATTTTGTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 13 0.43
18 2 0.07
19 15 0.50
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (17 bp):
ATCTTAGAAGATATGCA
Found at i:31309440 original size:22 final size:21
Alignment explanation
Indices: 31309412--31309469 Score: 80
Period size: 22 Copynumber: 2.7 Consensus size: 21
31309402 ATGCAATCTT
*
31309412 AGATATGATATGTAATCTTAG
1 AGATATGATTTGTAATCTTAG
31309433 AAGATATGATTTTGTAATCTTAG
1 -AGATATGA-TTTGTAATCTTAG
*
31309456 AGATTTGATTTGTA
1 AGATATGATTTGTA
31309470 GATACCCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 6 0.18
22 15 0.45
23 12 0.36
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.43
Consensus pattern (21 bp):
AGATATGATTTGTAATCTTAG
Found at i:31311575 original size:17 final size:17
Alignment explanation
Indices: 31311553--31311588 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
31311543 AGTCATTTCA
31311553 AGATGTAATGCCCATGG
1 AGATGTAATGCCCATGG
31311570 AGATGTAATGCCCATGG
1 AGATGTAATGCCCATGG
31311587 AG
1 AG
31311589 TTGCCAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.22
Consensus pattern (17 bp):
AGATGTAATGCCCATGG
Found at i:31314598 original size:17 final size:17
Alignment explanation
Indices: 31314548--31314598 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 17
31314538 TGGAAACATG
*
31314548 ATCTTTGAAGATATGCA
1 ATCTTAGAAGATATGCA
**
31314565 ATCTTAGATATGATATGTT
1 ATCTTAGA-A-GATATGCA
31314584 ATCTTAGAAGATATG
1 ATCTTAGAAGATATG
31314599 ATTTTGTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 13 0.45
18 2 0.07
19 14 0.48
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (17 bp):
ATCTTAGAAGATATGCA
Found at i:31314598 original size:22 final size:21
Alignment explanation
Indices: 31314557--31314627 Score: 65
Period size: 22 Copynumber: 3.4 Consensus size: 21
31314547 GATCTTTGAA
*
31314557 GATATGCAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
31314576 GATATGTTATCTTAGAAGATAT
1 GATATGTAATCTTAG-AGATAT
* *
31314598 GATTTTGTAATCTTAGAGATTT
1 GA-TATGTAATCTTAGAGATAT
*
31314620 GATTTGTA
1 GATATGTA
31314628 GATACCCTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
19 11 0.26
21 6 0.14
22 15 0.35
23 11 0.26
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (21 bp):
GATATGTAATCTTAGAGATAT
Found at i:31314614 original size:23 final size:22
Alignment explanation
Indices: 31314570--31314624 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
31314560 ATGCAATCTT
* *
31314570 AGATATGA-TATGTTATCTTAG
1 AGATATGATTTTGTAATCTTAG
31314591 AAGATATGATTTTGTAATCTTAG
1 -AGATATGATTTTGTAATCTTAG
*
31314614 AGATTTGATTT
1 AGATATGATTT
31314625 GTAGATACCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 18 0.62
23 11 0.38
ACGTcount: A:0.33, C:0.04, G:0.18, T:0.45
Consensus pattern (22 bp):
AGATATGATTTTGTAATCTTAG
Found at i:31315688 original size:45 final size:46
Alignment explanation
Indices: 31315639--31315730 Score: 152
Period size: 46 Copynumber: 2.0 Consensus size: 46
31315629 TTTAAAATTT
31315639 AAAATTTCAA-AAAAAAATTAAAACCTTCT-ATAAAGAGGTAAACAA
1 AAAATTTCAATAAAAAAATTAAAACCTT-TGATAAAGAGGTAAACAA
*
31315684 AAAATTTCAATAAAAAATTTAAAACCTTTGATAAAGAGGTAAACAA
1 AAAATTTCAATAAAAAAATTAAAACCTTTGATAAAGAGGTAAACAA
31315730 A
1 A
31315731 TACAAATTGC
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
45 11 0.25
46 33 0.75
ACGTcount: A:0.59, C:0.10, G:0.08, T:0.24
Consensus pattern (46 bp):
AAAATTTCAATAAAAAAATTAAAACCTTTGATAAAGAGGTAAACAA
Found at i:31319894 original size:16 final size:16
Alignment explanation
Indices: 31319873--31319916 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
31319863 CCTTGCATCA
*
31319873 AATTTTTAAAATTTTT
1 AATTTTTAAAATTTAT
*
31319889 AATTTTTTTAAA-TTAT
1 AA-TTTTTAAAATTTAT
31319905 AATTTTTAAAAT
1 AATTTTTAAAAT
31319917 GCATGCTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 8 0.35
16 7 0.30
17 8 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
AATTTTTAAAATTTAT
Found at i:31322135 original size:17 final size:18
Alignment explanation
Indices: 31322113--31322148 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
31322103 ATCTGACAAA
*
31322113 GCCCGATAAGTGAT-AAT
1 GCCCGATAAATGATGAAT
31322130 GCCCGATAAATGATGAAT
1 GCCCGATAAATGATGAAT
31322148 G
1 G
31322149 ATAAAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (18 bp):
GCCCGATAAATGATGAAT
Found at i:31322670 original size:24 final size:24
Alignment explanation
Indices: 31322643--31322703 Score: 113
Period size: 24 Copynumber: 2.5 Consensus size: 24
31322633 TGATAAGCTC
31322643 TATGAGCTTCCTGAGTAAAACTCT
1 TATGAGCTTCCTGAGTAAAACTCT
31322667 TATGAGCTTCCTGAGTAAAACTCT
1 TATGAGCTTCCTGAGTAAAACTCT
*
31322691 TATGAGTTTCCTG
1 TATGAGCTTCCTG
31322704 TTTAGCCTGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (24 bp):
TATGAGCTTCCTGAGTAAAACTCT
Found at i:31326202 original size:17 final size:17
Alignment explanation
Indices: 31326161--31326275 Score: 72
Period size: 17 Copynumber: 6.7 Consensus size: 17
31326151 ATCTTTCTAC
* * *
31326161 GAACTCAAGCAATTTTT
1 GAACTTAAGCAAATCTT
* * *
31326178 GAATTTAATCCAATCTT
1 GAACTTAAGCAAATCTT
*
31326195 GAACTTAAGCAAATTTT
1 GAACTTAAGCAAATCTT
*
31326212 GAACTTTCAA-CAAATTTT
1 GAAC-TT-AAGCAAATCTT
**
31326230 GGGCTTAAGCAAAAT-TT
1 GAACTTAAGC-AAATCTT
* * *
31326247 GAACTTAAGGATATTTT
1 GAACTTAAGCAAATCTT
31326264 GAACTTAAGCAA
1 GAACTTAAGCAA
31326276 GTTCTGAACT
Statistics
Matches: 75, Mismatches: 18, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
16 5 0.07
17 52 0.69
18 16 0.21
19 2 0.03
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (17 bp):
GAACTTAAGCAAATCTT
Found at i:31326284 original size:34 final size:32
Alignment explanation
Indices: 31326161--31326287 Score: 92
Period size: 34 Copynumber: 3.7 Consensus size: 32
31326151 ATCTTTCTAC
* * * * *
31326161 GAACTCAAGCAATTTTTGAATTTAATCCAATCTT
1 GAACTTAAGCAA-ATTTGAACTTAA-CAAATTTT
31326195 GAACTTAAGCAAATTTTGAACTTTCAACAAATTTT
1 GAACTTAAGCAAA-TTTGAAC-TT-AACAAATTTT
** * *
31326230 GGGCTTAAGCAAAATTTGAACTTAAGGATATTTT
1 GAACTTAAGC-AAATTTGAACTTAA-CAAATTTT
*
31326264 GAACTTAAGCAAGTTCTGAACTTA
1 GAACTTAAGCAAATT-TGAACTTA
31326288 GGTGGATTTC
Statistics
Matches: 75, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
33 6 0.08
34 41 0.55
35 23 0.31
36 5 0.07
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.35
Consensus pattern (32 bp):
GAACTTAAGCAAATTTGAACTTAACAAATTTT
Found at i:31326706 original size:138 final size:138
Alignment explanation
Indices: 31326437--31326851 Score: 537
Period size: 138 Copynumber: 3.0 Consensus size: 138
31326427 AGCTGATAGT
* * *
31326437 TTAACTCTTCGAGCTCTTAGAATATTAGTTAGGAGCGTAGGTCTA-CTAGCTATTTTTGGAGGTT
1 TTAACTCTACGAGCTCTTAGAATACTAGTTAGGAGCATAGGTC-AGCTAGCTATTTTTGGAGGTT
* * * * * * * * **
31326501 GCAATCATAAACTGGAAAACCTTTATAACATAAGCTGGGAGCATACGTTCACTACCTATGTAAGA
65 GCAATCATAAACCGGAAAACCTTTATAACATCAGCTAGGAGCGTAGGTTCGCTAGCTGTGTTGGA
31326566 GCTGCAAGC
130 GCTGCAAGC
* * *
31326575 TTAACTCTACAAGCTCTTAGAATACTAGTTGGGAGCATAGGTCCGCTAGCTATTTTTGGAGGTTG
1 TTAACTCTACGAGCTCTTAGAATACTAGTTAGGAGCATAGGTCAGCTAGCTATTTTTGGAGGTTG
* * * *
31326640 CGATCATAAACCGAAAAACCTTTATAACATCAGCTAGGAGTGTAGGTTCGTTAGCTGTGTTGGAG
66 CAATCATAAACCGGAAAACCTTTATAACATCAGCTAGGAGCGTAGGTTCGCTAGCTGTGTTGGAG
31326705 CTGCAAGC
131 CTGCAAGC
* * *
31326713 TTAACTCTGCGAGCTCTTAGAATACTAGCTAAGAGCATAGGTCAGCTAGCTATTTTTGGAGGTTG
1 TTAACTCTACGAGCTCTTAGAATACTAGTTAGGAGCATAGGTCAGCTAGCTATTTTTGGAGGTTG
** * *
31326778 CAATTGTAAACCGGCAAACCTTTATAACATCAGCTAGAAGCGTAGG-TCTGCTAGCTGTGTTGGA
66 CAATCATAAACCGGAAAACCTTTATAACATCAGCTAGGAGCGTAGGTTC-GCTAGCTGTGTTGGA
* *
31326842 GTTGCGAGC
130 GCTGCAAGC
31326851 T
1 T
31326852 CTTAAAATAC
Statistics
Matches: 239, Mismatches: 36, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
137 2 0.01
138 237 0.99
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (138 bp):
TTAACTCTACGAGCTCTTAGAATACTAGTTAGGAGCATAGGTCAGCTAGCTATTTTTGGAGGTTG
CAATCATAAACCGGAAAACCTTTATAACATCAGCTAGGAGCGTAGGTTCGCTAGCTGTGTTGGAG
CTGCAAGC
Found at i:31327061 original size:262 final size:262
Alignment explanation
Indices: 31326634--31327113 Score: 617
Period size: 262 Copynumber: 1.8 Consensus size: 262
31326624 CTATTTTTGG
* * * *
31326634 AGGTTGCGATCATAAACCGAAAAACCTTTATAACATCAGCTAGGAGTGTAGGTTCGTTAGCTGTG
1 AGGTTGCGATCATAAACCGAAAAACCATTATAACATCAGCTAGGAGTGTAGATCCGTTAGCTATG
* *
31326699 TTGGAGCTGCAAGCTTAACTCTGCGAGCTCTTAGAATACTAGCTAAGAGCATAGGTCAGCTAGCT
66 TTGGAGCTGCAAGCTTAACTCTGCAAGCTCTTAGAATACTAGCTAAGAGCATAAGTCAGCTAGCT
* * * * *
31326764 ATTTTTGGAGGTTGCAATTGTAAACCGGCAAACCTTTATAACA-TCAGCTAGAAGCGTAGGTCTG
131 ATTTTTAGAGGTTGCAATTATAAACCGGAAAACCTTTATAACACT-AGCTAGAAGAGTAGGCCTG
31326828 CTAGCTGTGTTGGAGTTGCGAGCTCTTAAAATACTAACTAGGAGCGTGGGTCCACTAGTTGTTTT
195 CTAGCTGTGTTGGAGTTGCGAGCTCTTAAAATACTAACTAGGAGCGTGGGTCCACTAGTTGTTTT
31326893 TAA
260 TAA
* ** * *
31326896 AGGTTGCGATTATAAATTGGAAAACCATTATAACATTAGCT-GG-GTGCATAGATCCGTTAGCTA
1 AGGTTGCGATCATAAACCGAAAAACCATTATAACATCAGCTAGGAGTG--TAGATCCGTTAGCTA
** * * * ** *
31326959 TGTTGGAGCTGTGAGTTTTATTCTGCAAGCTCTTAGAATACTAGCTGGGAGTATAAGTCCA-CTA
64 TGTTGGAGCTGCAAGCTTAACTCTGCAAGCTCTTAGAATACTAGCTAAGAGCATAAGT-CAGCTA
* ** * * *
31327023 GTTATTTTTAGAGGTTGGGATTATAAACTGGAAAACCTTTATAACACTAGCTGGGAGAGTAGGCC
128 GCTATTTTTAGAGGTTGCAATTATAAACCGGAAAACCTTTATAACACTAGCTAGAAGAGTAGGCC
*
31327088 TGCTAGCTGTGTTGGAGTTTCGAGCT
193 TGCTAGCTGTGTTGGAGTTGCGAGCT
31327114 TGACTTTACG
Statistics
Matches: 183, Mismatches: 31, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
260 3 0.02
261 2 0.01
262 175 0.96
263 3 0.02
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (262 bp):
AGGTTGCGATCATAAACCGAAAAACCATTATAACATCAGCTAGGAGTGTAGATCCGTTAGCTATG
TTGGAGCTGCAAGCTTAACTCTGCAAGCTCTTAGAATACTAGCTAAGAGCATAAGTCAGCTAGCT
ATTTTTAGAGGTTGCAATTATAAACCGGAAAACCTTTATAACACTAGCTAGAAGAGTAGGCCTGC
TAGCTGTGTTGGAGTTGCGAGCTCTTAAAATACTAACTAGGAGCGTGGGTCCACTAGTTGTTTTT
AA
Found at i:31327128 original size:138 final size:138
Alignment explanation
Indices: 31326877--31327203 Score: 333
Period size: 138 Copynumber: 2.4 Consensus size: 138
31326867 AGGAGCGTGG
* * * * * * *
31326877 GTCCACTAGTTGTTTTTAAAGGTTGCGATTATAAATTGGAAAACCATTATAACATTAGCTGGGTG
1 GTCCACTAGTTATTTTTAGAGGTTGGGATTATAAACTGGAAAACCTTTATAACACTAGCTGGGAG
* * * * * * *
31326942 CATAGATCCGTTAGCTATGTTGGAGCTGTGAGTTTTATTCTGCAAGCTCTTAGAATACTAGCTGG
66 CATAGAGCCGCTAGCTATGTTGGAGCTGTGAGCTTGATTCTACAAGCTCTTAGAACAATAGCTGG
31327007 GAGTATAA
131 GAGTATAA
31327015 GTCCACTAGTTATTTTTAGAGGTTGGGATTATAAACTGGAAAACCTTTATAACACTAGCTGGGAG
1 GTCCACTAGTTATTTTTAGAGGTTGGGATTATAAACTGGAAAACCTTTATAACACTAGCTGGGAG
* * * *
31327080 -AGTAG-GCCTGCTAGCTGTGTTGGAG-TTTCGAGCTTGACTT-TACGAGCTCTTAGAACAATGG
66 CA-TAGAGCC-GCTAGCTATGTTGGAGCTGT-GAGCTTGA-TTCTACAAGCTCTTAGAACAATAG
* * *
31327141 TTGGGAGTGTAG
127 CTGGGAGTATAA
* * * *
31327153 GTCCACTAGCTAGTTTTGGAGGTTGCGG-TCATAAACT-GAGAAACCTTTATA
1 GTCCACTAGTTATTTTTAGAGGTTG-GGATTATAAACTGGA-AAACCTTTATA
31327204 TAATACTAAG
Statistics
Matches: 158, Mismatches: 25, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
137 7 0.04
138 147 0.93
139 4 0.03
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (138 bp):
GTCCACTAGTTATTTTTAGAGGTTGGGATTATAAACTGGAAAACCTTTATAACACTAGCTGGGAG
CATAGAGCCGCTAGCTATGTTGGAGCTGTGAGCTTGATTCTACAAGCTCTTAGAACAATAGCTGG
GAGTATAA
Found at i:31327199 original size:400 final size:400
Alignment explanation
Indices: 31326446--31327203 Score: 880
Period size: 400 Copynumber: 1.9 Consensus size: 400
31326436 TTTAACTCTT
* * ** * **
31326446 CGAGCTCTTAGAATATTAGTTAGGAGCGTAGGTCTACTAGCTATTTTTGGAGGTTGCAATCATAA
1 CGAGCTCTTAAAATACTAACTAGGAGCGTAGGTCCACTAGCTATTTTTAAAGGTTGCAATCATAA
* *
31326511 ACTGGAAAACCTTTATAACATAAGCTGGGAGCATACGTTCACTACCTATGTAAGAGCTGCAAGCT
66 ACTGGAAAACCATTATAACATAAGCTGGGAGCATACGATCACTACCTATGTAAGAGCTGCAAGCT
* * * *
31326576 TAACTCTACAAGCTCTTAGAATACTAGTTGGGAGCATAGGTCCGCTAGCTATTTTTGGAGGTTGC
131 TAACTCTACAAGCTCTTAGAATACTAGCTGGGAGCATAAGTCCACTAGCTATTTTTAGAGGTTGC
* * *
31326641 GATCATAAACCGAAAAACCTTTATAACATCAGCTAGGAGTGTAGGTTCGTTAGCTGTGTTGGAGC
196 GATCATAAACCGAAAAACCTTTATAACATCAGCTAGGAGAGTAGGCTCGCTAGCTGTGTTGGAGC
* * * *
31326706 TGCAAGCTTAACTCTGCGAGCTCTTAGAATACTAGCTAAGAGCATAGGTCAGCTAGCTATTTTTG
261 TGCAAGCTTAACTCTACGAGCTCTTAGAACAATAGCTAAGAGCATAGGTCAGCTAGCTAGTTTTG
**
31326771 GAGGTTGCAATTGTAAACCGGCAAACCTTTATAACATCAGCTAGAAGCGTAGGTCTGCTAGCTGT
326 GAGGTTGCAATCATAAACCGGCAAACCTTTATAACATCAGCTAGAAGCGTAGGTCTGCTAGCTGT
31326836 GTTGGAGTTG
391 GTTGGAGTTG
* * * * *
31326846 CGAGCTCTTAAAATACTAACTAGGAGCGTGGGTCCACTAGTTGTTTTTAAAGGTTGCGATTATAA
1 CGAGCTCTTAAAATACTAACTAGGAGCGTAGGTCCACTAGCTATTTTTAAAGGTTGCAATCATAA
* * * * ** **
31326911 ATTGGAAAACCATTATAACATTAGCTGGGTGCATA-GATC-CGTTAGCTATGTTGGAGCTGTGAG
66 ACTGGAAAACCATTATAACATAAGCTGGGAGCATACGATCAC--TACCTATGTAAGAGCTGCAAG
* * * * * *
31326974 TTTTATTCTGCAAGCTCTTAGAATACTAGCTGGGAGTATAAGTCCACTAGTTATTTTTAGAGGTT
129 CTTAACTCTACAAGCTCTTAGAATACTAGCTGGGAGCATAAGTCCACTAGCTATTTTTAGAGGTT
* * * * *
31327039 GGGATTATAAACTGGAAAACCTTTATAACA-CTAGCTGGGAGAGTAGGC-CTGCTAGCTGTGTTG
194 GCGATCATAAACCGAAAAACCTTTATAACATC-AGCTAGGAGAGTAGGCTC-GCTAGCTGTGTTG
* * * * * * * ** **
31327102 GAGTTTCGAGCTTGACTTTACGAGCTCTTAGAACAATGGTTGGGAGTGTAGGTCCA-CTAGCTAG
257 GAGCTGCAAGCTTAACTCTACGAGCTCTTAGAACAATAGCTAAGAGCATAGGT-CAGCTAGCTAG
** *
31327166 TTTTGGAGGTTGCGGTCATAAACTGAG-AAACCTTTATA
321 TTTTGGAGGTTGCAATCATAAACCG-GCAAACCTTTATA
31327204 TAATACTAAG
Statistics
Matches: 292, Mismatches: 60, Indels: 12
0.80 0.16 0.03
Matches are distributed among these distances:
398 1 0.00
399 5 0.02
400 283 0.97
401 3 0.01
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.31
Consensus pattern (400 bp):
CGAGCTCTTAAAATACTAACTAGGAGCGTAGGTCCACTAGCTATTTTTAAAGGTTGCAATCATAA
ACTGGAAAACCATTATAACATAAGCTGGGAGCATACGATCACTACCTATGTAAGAGCTGCAAGCT
TAACTCTACAAGCTCTTAGAATACTAGCTGGGAGCATAAGTCCACTAGCTATTTTTAGAGGTTGC
GATCATAAACCGAAAAACCTTTATAACATCAGCTAGGAGAGTAGGCTCGCTAGCTGTGTTGGAGC
TGCAAGCTTAACTCTACGAGCTCTTAGAACAATAGCTAAGAGCATAGGTCAGCTAGCTAGTTTTG
GAGGTTGCAATCATAAACCGGCAAACCTTTATAACATCAGCTAGAAGCGTAGGTCTGCTAGCTGT
GTTGGAGTTG
Found at i:31329134 original size:17 final size:17
Alignment explanation
Indices: 31329094--31329135 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
31329084 CCGTCAACAT
*
31329094 AAACTAACCAACTTTTC
1 AAACTATCCAACTTTTC
31329111 AAACTATCCAACTTTTC
1 AAACTATCCAACTTTTC
31329128 AAACTATC
1 AAACTATC
31329136 AGTTGTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.40, C:0.29, G:0.00, T:0.31
Consensus pattern (17 bp):
AAACTATCCAACTTTTC
Found at i:31334463 original size:126 final size:125
Alignment explanation
Indices: 31334322--31334693 Score: 503
Period size: 126 Copynumber: 2.9 Consensus size: 125
31334312 TTTGACCTTG
*
31334322 AAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCAAAAATGCTTCAAGAAGGATGCAC
1 AAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGAAGGATGCAC
* * * * *
31334387 TGTTAGTAAAATTACAGGAAAAAGCACCCACGTAGACGCTCTTTTTCTACAGTAGTTCCCA
66 TGTCAGCAAAATTA-TGAAAAAAGCTCCCACGTAGACGCTCTTTTTCTACAGTAGTTCCCA
* * * *
31334448 AAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCAAAAAGGTTTCAAGCAGGATACAC
1 AAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGAAGGATGCAC
* * * **
31334513 TATCAGCAAAATTTATGAAAAAAGCTCCCACGTGGACACTCTTTTTCTACAGTAGTTCTTA
66 TGTCAGCAAAA-TTATGAAAAAAGCTCCCACGTAGACGCTCTTTTTCTACAGTAGTTCCCA
* * *
31334574 AAATAATAATTTTGAGAAGATGTTTCTGAACAAATAGTGTCAGAAACGCTTCAA-ATAGGATGCA
1 AAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGA-AGGATGCA
* * *
31334638 CTGCCAGCAAAATTTTTGAAAAAAGCTCTCACGTAGACGCTCTTTTTTCTACAGTA
65 CTGTCAGCAAAA-TTATGAAAAAAGCTCCCACGTAGACGCTC-TTTTTCTACAGTA
31334694 TTCATGCTTG
Statistics
Matches: 216, Mismatches: 27, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
126 200 0.93
127 16 0.07
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (125 bp):
AAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGAAGGATGCAC
TGTCAGCAAAATTATGAAAAAAGCTCCCACGTAGACGCTCTTTTTCTACAGTAGTTCCCA
Found at i:31339432 original size:48 final size:48
Alignment explanation
Indices: 31339373--31339537 Score: 165
Period size: 48 Copynumber: 3.5 Consensus size: 48
31339363 TATGAGAGTA
* * *
31339373 AGTGTAAGACATGTTTGGGACATGCATCGGCTTCAAGATATACAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTTCGAGATATACAAGCT
* * * * ** *
31339421 AGTGTAAGACATCTCTAGGACATGCATTGACATT-GAGA-CGA-GAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGC-TTCGAGATATACAAGCT
* *
31339467 AGTGTAAGACATGTCTGGGACATACATCGGCCTCGAGATATACAAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTTCGAGATATACAAGCT
* * *
31339515 AGTGTTAGACCTATCTGGGACAT
1 AGTGTAAGACATGTCTGGGACAT
31339538 TGCGTCAGCT
Statistics
Matches: 91, Mismatches: 22, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
45 1 0.01
46 33 0.36
47 2 0.02
48 53 0.58
49 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (48 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCTTCGAGATATACAAGCT
Found at i:31344089 original size:31 final size:31
Alignment explanation
Indices: 31344054--31344113 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
31344044 AACTAAATAG
31344054 AAATAAATTTAATATATATTAAATCTATTCA
1 AAATAAATTTAATATATATTAAATCTATTCA
*
31344085 AAATAAATTTAATCTATATTAAATCTATT
1 AAATAAATTTAATATATATTAAATCTATT
31344114 AAATCGATCG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (31 bp):
AAATAAATTTAATATATATTAAATCTATTCA
Found at i:31344190 original size:17 final size:17
Alignment explanation
Indices: 31344168--31344206 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
31344158 AATTTAGATG
*
31344168 TAAAATATACTA-AAATA
1 TAAAATAAACTAGAAA-A
31344185 TAAAATAAACTAGAAAA
1 TAAAATAAACTAGAAAA
31344202 TAAAA
1 TAAAA
31344207 ATGGAGTCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.23
Consensus pattern (17 bp):
TAAAATAAACTAGAAAA
Found at i:31344307 original size:19 final size:19
Alignment explanation
Indices: 31344246--31344311 Score: 62
Period size: 19 Copynumber: 3.3 Consensus size: 19
31344236 TTACTATATT
*
31344246 AATATAAAAGAAATATAACTA
1 AATAT-AAAGAAAGATAA-TA
* *
31344267 AGATATAAAAAAAGATATTA
1 A-ATATAAAGAAAGATAATA
31344287 AATATAAAGATAA-ATAATA
1 AATATAAAGA-AAGATAATA
31344306 AATATA
1 AATATA
31344312 TATATAAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
19 19 0.50
20 5 0.13
21 10 0.26
22 4 0.11
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.26
Consensus pattern (19 bp):
AATATAAAGAAAGATAATA
Found at i:31344512 original size:13 final size:13
Alignment explanation
Indices: 31344496--31344523 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
31344486 ATTCGAGTCT
31344496 ATAATTCATATTA
1 ATAATTCATATTA
31344509 ATAATTCATATTA
1 ATAATTCATATTA
31344522 AT
1 AT
31344524 TATGAATAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (13 bp):
ATAATTCATATTA
Found at i:31345942 original size:27 final size:27
Alignment explanation
Indices: 31345893--31346361 Score: 246
Period size: 27 Copynumber: 17.3 Consensus size: 27
31345883 CCAATTATTG
* **
31345893 AAATACCCTCGACTTGCAAAATTACCA
1 AAATACCCTCGATTTATAAAATTACCA
* * *
31345920 AAGTACCCTCGATTTATAGAATTACCG
1 AAATACCCTCGATTTATAAAATTACCA
*** * *
31345947 TTTTACCCTCGATTTATAGAATTACCG
1 AAATACCCTCGATTTATAAAATTACCA
*** * **
31345974 TTTTACCCTCGATTTATAGAATTATTA
1 AAATACCCTCGATTTATAAAATTACCA
*** * * **
31346001 TTTTACCCTTGATTTATAGAATTACTG
1 AAATACCCTCGATTTATAAAATTACCA
*** * *
31346028 TTTTACCCTCGATTTAAAAAATTACTA
1 AAATACCCTCGATTTATAAAATTACCA
* * *
31346055 AAATACCCTTGGTTTACAAAATTACCA
1 AAATACCCTCGATTTATAAAATTACCA
*
31346082 AAATACCCTCGA-TCAGTAAAATTACCA
1 AAATACCCTCGATTTA-TAAAATTACCA
* * * *
31346109 AAATACCCTAG-TCTGTAAAATTACTA
1 AAATACCCTCGATTTATAAAATTACCA
* * *
31346135 AAATACCCTTGGTTTGTAAAATTACCA
1 AAATACCCTCGATTTATAAAATTACCA
* *
31346162 AAATACCC-CTAGTTTGTAAAATTACCA
1 AAATACCCTCGA-TTTATAAAATTACCA
* * * *
31346189 AAATACCACT-GGTTTGTGAAATTACCG
1 AAATACC-CTCGATTTATAAAATTACCA
* * *
31346216 AAACACCCTCAATTTGTAAAATTACCA
1 AAATACCCTCGATTTATAAAATTACCA
* *
31346243 AAATACCC-CTGATTTACAAAATTACAA
1 AAATACCCTC-GATTTATAAAATTACCA
* * **
31346270 AAATACCCTTGACTTTCTAAAAATTATAA
1 AAATACCCTCGA-TTTAT-AAAATTACCA
* * * * **
31346299 AAATACCATTGGTTTACAAAATTACTG
1 AAATACCCTCGATTTATAAAATTACCA
* * * * *
31346326 AAATACCCTTGGTTTGTAGATTTACCA
1 AAATACCCTCGATTTATAAAATTACCA
*
31346353 AAACACCCT
1 AAATACCCT
31346362 TGTAGGGTGA
Statistics
Matches: 357, Mismatches: 74, Indels: 22
0.79 0.16 0.05
Matches are distributed among these distances:
26 25 0.07
27 306 0.86
28 7 0.02
29 19 0.05
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.33
Consensus pattern (27 bp):
AAATACCCTCGATTTATAAAATTACCA
Found at i:31346089 original size:54 final size:54
Alignment explanation
Indices: 31346031--31346361 Score: 274
Period size: 54 Copynumber: 6.1 Consensus size: 54
31346021 ATTACTGTTT
* * * **
31346031 TACCCTCGATTTAAAAAATTACTAAAATACCCTTGGTTTACAAAATTACCAAAA
1 TACCCTCGATTTATAAAATTACCAAAATACCCTTAGTTTGTAAAATTACCAAAA
* * *
31346085 TACCCTCGA-TCAGTAAAATTACCAAAATACCC-TAGTCTGTAAAATTACTAAAA
1 TACCCTCGATTTA-TAAAATTACCAAAATACCCTTAGTTTGTAAAATTACCAAAA
* * * *
31346138 TACCCTTGGTTTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAA
1 TACCCTCGATTTATAAAATTACCAAAATACCCTTAGTTTGTAAAATTACCAAAA
* * * * * * *
31346192 TACCACT-GGTTTGTGAAATTACCGAAACACCCTCAATTTGTAAAATTACCAAAA
1 TACC-CTCGATTTATAAAATTACCAAAATACCCTTAGTTTGTAAAATTACCAAAA
* * * * **
31346246 TACCC-CTGATTTACAAAATTACAAAAATACCCTTGACTTTCTAAAAATTATAAAAA
1 TACCCTC-GATTTATAAAATTACCAAAATACCCTT-AGTTTGT-AAAATTACCAAAA
* * * * ** * * *
31346302 TACCATTGGTTTACAAAATTACTGAAATACCCTTGGTTTGTAGATTTACCAAAA
1 TACCCTCGATTTATAAAATTACCAAAATACCCTTAGTTTGTAAAATTACCAAAA
*
31346356 CACCCT
1 TACCCT
31346362 TGTAGGGTGA
Statistics
Matches: 222, Mismatches: 46, Indels: 18
0.78 0.16 0.06
Matches are distributed among these distances:
53 45 0.20
54 127 0.57
55 11 0.05
56 39 0.18
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.30
Consensus pattern (54 bp):
TACCCTCGATTTATAAAATTACCAAAATACCCTTAGTTTGTAAAATTACCAAAA
Found at i:31346812 original size:20 final size:20
Alignment explanation
Indices: 31346776--31346852 Score: 118
Period size: 20 Copynumber: 3.8 Consensus size: 20
31346766 CGATGGTAAG
*
31346776 TTGGGCCTCAATAGGCTGAAA
1 TTGGGCC-CAATGGGCTGAAA
*
31346797 TTGGGCCCAATTGGCTGAAA
1 TTGGGCCCAATGGGCTGAAA
*
31346817 TTGGGCCCAATGGGCTAAAA
1 TTGGGCCCAATGGGCTGAAA
31346837 TTGGGCCCAATGGGCT
1 TTGGGCCCAATGGGCT
31346853 TCAGGCCCAT
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
20 46 0.87
21 7 0.13
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (20 bp):
TTGGGCCCAATGGGCTGAAA
Found at i:31347345 original size:25 final size:25
Alignment explanation
Indices: 31347307--31347400 Score: 127
Period size: 25 Copynumber: 3.8 Consensus size: 25
31347297 AGGAAGTGCT
*
31347307 AAAAGGGCTATGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
* *
31347332 AAAAGGGCTTTGCCCTAGTTTACAG
1 AAAAGGGCTTTGCCCCAGTTTACCG
* * *
31347357 AAAAGGGCTTTTCCTCAGTTTATC-
1 AAAAGGGCTTTGCCCCAGTTTACCG
31347381 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
31347401 ATTAAAAGAG
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
24 18 0.31
25 41 0.69
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCG
Found at i:31347413 original size:24 final size:24
Alignment explanation
Indices: 31347307--31347413 Score: 110
Period size: 25 Copynumber: 4.4 Consensus size: 24
31347297 AGGAAGTGCT
* *
31347307 AAAAGGGCTATGCCCCAGTTTACC
1 AAAAGGGCTTTGCCCCAGTTTATC
*
31347331 GAAAAGGGCTTTGCCCTAGTTTA-C
1 -AAAAGGGCTTTGCCCCAGTTTATC
* *
31347355 AGAAAAGGGCTTTTCCTCAGTTTATC
1 --AAAAGGGCTTTGCCCCAGTTTATC
*
31347381 AAAAGGGCTTTGCCCCAG-TTATT
1 AAAAGGGCTTTGCCCCAGTTTATC
31347404 AAAAGAGGCT
1 AAAAG-GGCT
31347414 AAGCCTCCAA
Statistics
Matches: 71, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
23 9 0.13
24 21 0.30
25 40 0.56
26 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTTATC
Found at i:31347657 original size:31 final size:31
Alignment explanation
Indices: 31347619--31347759 Score: 228
Period size: 31 Copynumber: 4.5 Consensus size: 31
31347609 TGTTTACAGT
* *
31347619 AAAGGCTTCGCCCCAATGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
31347650 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
* *
31347681 TAATGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
* *
31347712 TAAGGCTTTGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
31347743 AAAGGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
31347760 AACCGTTAAA
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 102 1.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:31348576 original size:17 final size:17
Alignment explanation
Indices: 31348556--31348589 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
31348546 TTCGTATATT
*
31348556 ATACTAATTATATCTAA
1 ATACTAAGTATATCTAA
*
31348573 ATACTAAGTGTATCTAA
1 ATACTAAGTATATCTAA
31348590 GCGAATCTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (17 bp):
ATACTAAGTATATCTAA
Found at i:31353460 original size:46 final size:45
Alignment explanation
Indices: 31353363--31353471 Score: 134
Period size: 46 Copynumber: 2.4 Consensus size: 45
31353353 ATATGTGTGC
* *
31353363 CAGTGTAAGACATGTCTGGGACATGCATCGGCTACATTATAAGAGT
1 CAGTGTAAGACATGTCTAGGACATGCATCGGC-ACATTAGAAGAGT
31353409 CAGTGTAAGACATGTCTAGGACATGCATC-G-ACATTGAGACGAGAG-
1 CAGTGTAAGACATGTCTAGGACATGCATCGGCACATT-AGA--AGAGT
31353454 CTAGTGTAAGACATGTCT
1 C-AGTGTAAGACATGTCT
31353472 GCGATATACA
Statistics
Matches: 57, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
43 5 0.09
44 2 0.04
45 2 0.04
46 48 0.84
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (45 bp):
CAGTGTAAGACATGTCTAGGACATGCATCGGCACATTAGAAGAGT
Found at i:31353678 original size:49 final size:49
Alignment explanation
Indices: 31353544--31353679 Score: 155
Period size: 49 Copynumber: 2.8 Consensus size: 49
31353534 CTTGTTGTGT
** * ** * *
31353544 GTCAGTGTAAGACCCGTCTGGGACATAGCATTAACACCGATAGATGAGA
1 GTCAGTGTAAGACCTATCTGGGACATGGCATTGGCATCGATAGATGAAA
* * * * * *
31353593 GCCAATGTAAGACCTATCTGGGACATGGCGTCGGCATTGATATATGAAA
1 GTCAGTGTAAGACCTATCTGGGACATGGCATTGGCATCGATAGATGAAA
31353642 GTCAGTGTAAGACCTATCTGGGACATGGCATTGGCATC
1 GTCAGTGTAAGACCTATCTGGGACATGGCATTGGCATC
31353680 TTATCCCATG
Statistics
Matches: 69, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
49 69 1.00
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (49 bp):
GTCAGTGTAAGACCTATCTGGGACATGGCATTGGCATCGATAGATGAAA
Found at i:31355013 original size:21 final size:20
Alignment explanation
Indices: 31354983--31355021 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
31354973 GTCAAAATGG
*
31354983 CCACATGGGCGTGTCGCCTTT
1 CCACACGGGCGTGT-GCCTTT
31355004 CCACACGGGCGTGTGCCT
1 CCACACGGGCGTGTGCCT
31355022 CTATTTCAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.10, C:0.36, G:0.31, T:0.23
Consensus pattern (20 bp):
CCACACGGGCGTGTGCCTTT
Found at i:31356129 original size:30 final size:30
Alignment explanation
Indices: 31356093--31356154 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
31356083 GCATTAGGCT
*
31356093 CGGTGATACTATGGGTACTGTTGATGGGCC
1 CGGTGATACTATGGGTACTGTTGAGGGGCC
** * *
31356123 CGGTGATTGTGTGGGTGCTGTTGAGGGGCC
1 CGGTGATACTATGGGTACTGTTGAGGGGCC
31356153 CG
1 CG
31356155 TCTCATCATC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.11, C:0.16, G:0.44, T:0.29
Consensus pattern (30 bp):
CGGTGATACTATGGGTACTGTTGAGGGGCC
Found at i:31358614 original size:49 final size:49
Alignment explanation
Indices: 31358530--31358689 Score: 279
Period size: 49 Copynumber: 3.3 Consensus size: 49
31358520 CTCTTCGGGA
* *
31358530 CTTATCACAT-T-TATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACCTTCACATTCATCACATCGGCCATTAGGC
*
31358577 CTTATCACATCTATACACACCTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACCTTCACATTCATCACATCGGCCATTAGGC
31358626 CTTATCACATATATACACACCTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACCTTCACATTCATCACATCGGCCATTAGGC
31358675 CTTATCACATATATA
1 CTTATCACATATATA
31358690 TATCTCATAC
Statistics
Matches: 108, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
47 10 0.09
48 1 0.01
49 97 0.90
ACGTcount: A:0.30, C:0.31, G:0.07, T:0.31
Consensus pattern (49 bp):
CTTATCACATATATACACACCTTCACATTCATCACATCGGCCATTAGGC
Found at i:31361966 original size:21 final size:21
Alignment explanation
Indices: 31361933--31361973 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
31361923 TATAAAGAGC
*
31361933 TTTGAGAAATTTAATGAGAAA
1 TTTGAGAAATTTAAAGAGAAA
**
31361954 TTTGAGAGCTTTAAAGAGAA
1 TTTGAGAAATTTAAAGAGAA
31361974 TTGTTAGAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.02, G:0.22, T:0.32
Consensus pattern (21 bp):
TTTGAGAAATTTAAAGAGAAA
Found at i:31363712 original size:26 final size:26
Alignment explanation
Indices: 31363676--31363728 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
31363666 GTGATGGTTA
31363676 ATACATTACTTTTAAAAGTTATTTGT
1 ATACATTACTTTTAAAAGTTATTTGT
31363702 ATACATTACTTTTAAAAGTTATTTGT
1 ATACATTACTTTTAAAAGTTATTTGT
31363728 A
1 A
31363729 ATGGATCTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.49
Consensus pattern (26 bp):
ATACATTACTTTTAAAAGTTATTTGT
Found at i:31367007 original size:47 final size:47
Alignment explanation
Indices: 31366936--31367028 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 47
31366926 TTTTAACCAT
*
31366936 ACTTTCATTAAATTTATTAGAAAAAACAAATTGATA-AAGAAAAACAC
1 ACTTTCATTAAATTTATTAAAAAAAACAAATTGA-AGAAGAAAAACAC
31366983 ACTTTCATTAAATTTATTAAAAAAAACAAATTGAAGAAGAAAAACA
1 ACTTTCATTAAATTTATTAAAAAAAACAAATTGAAGAAGAAAAACA
31367029 GAGGTTGATG
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 1 0.02
47 43 0.98
ACGTcount: A:0.57, C:0.10, G:0.06, T:0.27
Consensus pattern (47 bp):
ACTTTCATTAAATTTATTAAAAAAAACAAATTGAAGAAGAAAAACAC
Found at i:31369175 original size:21 final size:21
Alignment explanation
Indices: 31369151--31369190 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
31369141 TACTCCGACT
*
31369151 CTTCCTCCTCTTCTTCCTCCA
1 CTTCCTCCTCCTCTTCCTCCA
31369172 CTTCCTCCTCCTCTTCCTC
1 CTTCCTCCTCCTCTTCCTC
31369191 TTCCAAGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.03, C:0.55, G:0.00, T:0.42
Consensus pattern (21 bp):
CTTCCTCCTCCTCTTCCTCCA
Found at i:31369188 original size:12 final size:12
Alignment explanation
Indices: 31369153--31369190 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
31369143 CTCCGACTCT
*
31369153 TCCTCCTCTTCT
1 TCCTCCTCTTCC
*
31369165 TCCTCCACTTCC
1 TCCTCCTCTTCC
31369177 TCCTCCTCTTCC
1 TCCTCCTCTTCC
31369189 TC
1 TC
31369191 TTCCAAGAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.03, C:0.55, G:0.00, T:0.42
Consensus pattern (12 bp):
TCCTCCTCTTCC
Found at i:31370116 original size:93 final size:94
Alignment explanation
Indices: 31369943--31370132 Score: 265
Period size: 93 Copynumber: 2.0 Consensus size: 94
31369933 CACCGATGGT
* * * * * *
31369943 CCTCTAACTTTTAGAGTATTTCAATTTTGGTTATCCAATTGCGGAAAATTTTAAACTTCAAGCCC
1 CCTCTAACGTTTAAAGCATTTCAATTTTGGTTATCCAATTACGAAAAATTTTAAACCTCAAGCCC
*
31370008 TTTTAAAAAATTAAATAATTCTATTTAAG
66 TTTTAAAAAATTAAATAATCCTATTTAAG
* * *
31370037 CCTCTAACGTTTAAAGCATTTCAATTTTGGTTATCTAATTAC-AAAAATTTTAACCCTCGAGCCC
1 CCTCTAACGTTTAAAGCATTTCAATTTTGGTTATCCAATTACGAAAAATTTTAAACCTCAAGCCC
* *
31370101 TTTTGAAACATTAAATAATCCTATTTAAG
66 TTTTAAAAAATTAAATAATCCTATTTAAG
31370130 CCT
1 CCT
31370133 TTTAGTTCTT
Statistics
Matches: 84, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
93 47 0.56
94 37 0.44
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (94 bp):
CCTCTAACGTTTAAAGCATTTCAATTTTGGTTATCCAATTACGAAAAATTTTAAACCTCAAGCCC
TTTTAAAAAATTAAATAATCCTATTTAAG
Found at i:31370497 original size:28 final size:28
Alignment explanation
Indices: 31370465--31370521 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
31370455 AGAAACTGCA
31370465 CTTAAACAACTCATGAAGAAGTTACAAT
1 CTTAAACAACTCATGAAGAAGTTACAAT
31370493 CTTAAACAACTCATGAAGAAGTTACAAT
1 CTTAAACAACTCATGAAGAAGTTACAAT
31370521 C
1 C
31370522 CTTTGAGTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.46, C:0.19, G:0.11, T:0.25
Consensus pattern (28 bp):
CTTAAACAACTCATGAAGAAGTTACAAT
Found at i:31375624 original size:33 final size:34
Alignment explanation
Indices: 31375554--31375639 Score: 111
Period size: 33 Copynumber: 2.5 Consensus size: 34
31375544 ACAACAGACG
* * *
31375554 TTTGGGGAAAAACTAAGGGATTTGGGGAAAATTA
1 TTTGGGGAAAAACTAAGGGATTTCGAGAAAATGA
* *
31375588 TTTGGGGAAAAA-TAATGGATTTCGAGAAACTGA
1 TTTGGGGAAAAACTAAGGGATTTCGAGAAAATGA
31375621 TTTGGGGATAAAACTAAGG
1 TTTGGGGA-AAAACTAAGG
31375640 CTATCAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
33 24 0.55
34 16 0.36
35 4 0.09
ACGTcount: A:0.38, C:0.05, G:0.30, T:0.27
Consensus pattern (34 bp):
TTTGGGGAAAAACTAAGGGATTTCGAGAAAATGA
Found at i:31377356 original size:60 final size:60
Alignment explanation
Indices: 31377282--31377404 Score: 237
Period size: 60 Copynumber: 2.0 Consensus size: 60
31377272 AGTTTTTCGT
31377282 ACATACATGTACCAACTCGTGACTTAACATACTCTTTCTTGTTCTTGACATACCCGTTGA
1 ACATACATGTACCAACTCGTGACTTAACATACTCTTTCTTGTTCTTGACATACCCGTTGA
*
31377342 ACATACCTGTACCAACTCGTGACTTAACATACTCTTTCTTGTTCTTGACATACCCGTTGA
1 ACATACATGTACCAACTCGTGACTTAACATACTCTTTCTTGTTCTTGACATACCCGTTGA
31377402 ACA
1 ACA
31377405 CTTAGAATAC
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.27, C:0.28, G:0.11, T:0.34
Consensus pattern (60 bp):
ACATACATGTACCAACTCGTGACTTAACATACTCTTTCTTGTTCTTGACATACCCGTTGA
Found at i:31378508 original size:10 final size:11
Alignment explanation
Indices: 31378484--31378511 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
31378474 CAATCAAGAA
31378484 TTTTCTTCACT
1 TTTTCTTCACT
31378495 TTTTCTTCACT
1 TTTTCTTCACT
31378506 TTTTCT
1 TTTTCT
31378512 GACTAGATCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.07, C:0.25, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTTCTTCACT
Found at i:31384590 original size:26 final size:26
Alignment explanation
Indices: 31384561--31384837 Score: 171
Period size: 26 Copynumber: 10.6 Consensus size: 26
31384551 AAACGAAACA
*
31384561 AAATAATATATAAAACAATTTAAAGT
1 AAATAATATATAAAACAATTTAAAAT
31384587 AAAT-A-ATATAAAACAATTTAAAAT
1 AAATAATATATAAAACAATTTAAAAT
* *
31384611 -AATCAATATGTAAAACAAATTAAAAT
1 AAAT-AATATATAAAACAATTTAAAAT
* * *
31384637 AAATAATATACAAAGCAATTTAAAGT
1 AAATAATATATAAAACAATTTAAAAT
* *
31384663 AAATAATATATAAGACACTTT---A-
1 AAATAATATATAAAACAATTTAAAAT
** * * * *
31384685 AAATAGCATATAAAAGAGTTCAAGAT
1 AAATAATATATAAAACAATTTAAAAT
* *
31384711 AAATAATATGTAAAAAGAAATTTAAAAT
1 AAATAATATAT-AAAA-CAATTTAAAAT
*
31384739 AAATAATATA-AAAA-AAGGTTTAAAAACA
1 AAATAATATATAAAACAA--TTT-AAAA-T
* *
31384767 AAAGACATATATATAAAAATATAATTCAAAAT
1 AAATA-ATATATA-AAACA-AT--TT-AAAAT
* *
31384799 AAATAATATAT--AATAGTTTAAAAT
1 AAATAATATATAAAACAATTTAAAAT
31384823 AAATAATATATAAAA
1 AAATAATATATAAAA
31384838 TTTAAAATGG
Statistics
Matches: 194, Mismatches: 34, Indels: 46
0.71 0.12 0.17
Matches are distributed among these distances:
22 15 0.08
23 3 0.02
24 36 0.19
25 5 0.03
26 72 0.37
27 12 0.06
28 23 0.12
29 5 0.03
30 1 0.01
31 10 0.05
32 5 0.03
33 7 0.04
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (26 bp):
AAATAATATATAAAACAATTTAAAAT
Found at i:31384686 original size:52 final size:50
Alignment explanation
Indices: 31384561--31384837 Score: 209
Period size: 50 Copynumber: 5.3 Consensus size: 50
31384551 AAACGAAACA
*
31384561 AAATAATATATAAAACAATTTAAAGTAAATAATATAAAACAATTTAAAAT
1 AAATAATATATAAAACAATTTAAAATAAATAATATAAAACAATTTAAAAT
* * *
31384611 -AATCAATATGTAAAACAAATTAAAATAAATAATATACAAAGCAATTTAAAGT
1 AAAT-AATATATAAAACAATTTAAAATAAATAATATA-AAA-CAATTTAAAAT
* * ** * * * *
31384663 AAATAATATATAAGACACTTTAAAAT--AGCATATAAAAGAGTTCAAGAT
1 AAATAATATATAAAACAATTTAAAATAAATAATATAAAACAATTTAAAAT
* * * *
31384711 AAATAATATGTAAAAAGAAATTTAAAATAAATAATATAAAAAAAGGTTTAAAAACA
1 AAATAATATAT-AAAA-CAATTTAAAATAAATAATATAAAACAA--TTT-AAAA-T
* * * * *
31384767 AAAGACATATATATAAAAATATAATTCAAAATAAATAATATATAATAGTTTAAAAT
1 AAATA-ATATATA-AAACA-AT--TT-AAAATAAATAATATAAAACAATTTAAAAT
31384823 AAATAATATATAAAA
1 AAATAATATATAAAA
31384838 TTTAAAATGG
Statistics
Matches: 176, Mismatches: 33, Indels: 32
0.73 0.14 0.13
Matches are distributed among these distances:
48 16 0.09
49 9 0.05
50 44 0.25
51 3 0.02
52 38 0.22
53 3 0.02
54 5 0.03
55 10 0.06
56 11 0.06
57 14 0.08
58 3 0.02
59 2 0.01
60 18 0.10
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (50 bp):
AAATAATATATAAAACAATTTAAAATAAATAATATAAAACAATTTAAAAT
Done.