Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 135 of 135
Found at i:41939453 original size:15 final size:15
Alignment explanation
Indices: 41939433--41939463 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
41939423 TTTTTATTAT
*
41939433 TTATAAATAATAAAA
1 TTATAAAAAATAAAA
41939448 TTATAAAAAATAAAA
1 TTATAAAAAATAAAA
41939463 T
1 T
41939464 AAAATAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
TTATAAAAAATAAAA
Found at i:41950990 original size:6 final size:6
Alignment explanation
Indices: 41950979--41951030 Score: 81
Period size: 6 Copynumber: 9.0 Consensus size: 6
41950969 AACGCCGTAT
*
41950979 CTTTTG CTTTTG CTTTTG CTTTTG CTTTTG CTTTTT CTTTT- CTTTT-
1 CTTTTG CTTTTG CTTTTG CTTTTG CTTTTG CTTTTG CTTTTG CTTTTG
41951025 CTTTTG
1 CTTTTG
41951031 ATAAAGCAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
5 10 0.23
6 34 0.77
ACGTcount: A:0.00, C:0.17, G:0.12, T:0.71
Consensus pattern (6 bp):
CTTTTG
Found at i:41961618 original size:33 final size:35
Alignment explanation
Indices: 41961564--41961643 Score: 87
Period size: 33 Copynumber: 2.4 Consensus size: 35
41961554 TGGGCCCAAC
* * *
41961564 AAAATTTAAA-TTATTTTAAAA-TTAAGTTTATTTT
1 AAAA-TTAAATTTATTTGAAAATTTAAATTTATTAT
41961598 AAAATTAAATTTA-TTGAAAATTTAAATTTATTAT
1 AAAATTAAATTTATTTGAAAATTTAAATTTATTAT
*
41961632 -AATTTAAATTTA
1 AAAATTAAATTTA
41961644 AATTTATTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
33 22 0.55
34 18 0.45
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (35 bp):
AAAATTAAATTTATTTGAAAATTTAAATTTATTAT
Found at i:41961656 original size:16 final size:17
Alignment explanation
Indices: 41961565--41961643 Score: 90
Period size: 17 Copynumber: 4.8 Consensus size: 17
41961555 GGGCCCAACA
41961565 AAATTTAAA-TTATTTT
1 AAATTTAAATTTATTTT
* *
41961581 AAAATTAAGTTTATTTT
1 AAATTTAAATTTATTTT
* **
41961598 AAAATTAAATTTATTGA
1 AAATTTAAATTTATTTT
*
41961615 AAATTTAAATTTATTAT
1 AAATTTAAATTTATTTT
41961632 -AATTTAAATTTA
1 AAATTTAAATTTA
41961644 AATTTATTTA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
16 19 0.35
17 35 0.65
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.51
Consensus pattern (17 bp):
AAATTTAAATTTATTTT
Found at i:41963576 original size:29 final size:29
Alignment explanation
Indices: 41963533--41963667 Score: 102
Period size: 29 Copynumber: 4.7 Consensus size: 29
41963523 CGAACCTTTA
41963533 AAAAATTACCATTTTACCCTTAAATGTCT
1 AAAAATTACCATTTTACCCTTAAATGTCT
41963562 AAAAATT-CCATTTTTGACCC-TAAACCT-TC-
1 AAAAATTACCA-TTTT-ACCCTTAAA--TGTCT
* **
41963591 CAAAATTACCATTTTACCCCCAAATGTCT
1 AAAAATTACCATTTTACCCTTAAATGTCT
* * * *
41963620 AAAAATT-CTATTTTTAACCTTGAACTTTC-
1 AAAAATTACCA-TTTTACCCTT-AAATGTCT
*
41963649 CAAAATTACCATTTTACCC
1 AAAAATTACCATTTTACCC
41963668 CAAAATTTTC
Statistics
Matches: 83, Mismatches: 12, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
27 1 0.01
28 11 0.13
29 54 0.65
30 16 0.19
31 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (29 bp):
AAAAATTACCATTTTACCCTTAAATGTCT
Found at i:41963618 original size:58 final size:58
Alignment explanation
Indices: 41963534--41963787 Score: 280
Period size: 58 Copynumber: 4.3 Consensus size: 58
41963524 GAACCTTTAA
** *
41963534 AAAATTACCATTTTACCCTTAAATGTCTAAAAATTCCATTTTTGACCCTAAACCTTCC
1 AAAATTACCATTTTACCCCCAAATGTCTAAAAATTCCATTTTTAACCCTAAACCTTCC
* * * *
41963592 AAAATTACCATTTTACCCCCAAATGTCTAAAAATTCTATTTTTAACCTTGAACTTTCC
1 AAAATTACCATTTTACCCCCAAATGTCTAAAAATTCCATTTTTAACCCTAAACCTTCC
* * * * * *
41963650 AAAATTACCATTTTACCCCAAAAT-TTTCCAAAATTTCATTTTTAA-CCTCGAACCTTTCA
1 AAAATTACCATTTTACCCCCAAATGTCT-AAAAATTCCATTTTTAACCCT-AAACC-TTCC
* * * * *
41963709 AAAATTATCATTTTACCCCCGAATATCTAAAAATTCCATTTTTTAACCCCAAACCTTTC
1 AAAATTACCATTTTACCCCCAAATGTCTAAAAATTCCA-TTTTTAACCCTAAACCTTCC
41963768 AAGAATTACCATTTT-CCCCC
1 AA-AATTACCATTTTACCCCC
41963788 TCCGAGTGTC
Statistics
Matches: 163, Mismatches: 26, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
57 4 0.02
58 92 0.56
59 41 0.25
60 24 0.15
61 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCCAAATGTCTAAAAATTCCATTTTTAACCCTAAACCTTCC
Found at i:41963677 original size:29 final size:28
Alignment explanation
Indices: 41963534--41963684 Score: 90
Period size: 29 Copynumber: 5.2 Consensus size: 28
41963524 GAACCTTTAA
** * *
41963534 AAAATTACCATTTTACCCTTAAATGTCTA
1 AAAATTACCATTTTACCCCAAAATTTC-C
* **
41963563 AAAATT-CCATTTTTGACCCTAAACCTTCC
1 AAAATTACCA-TTTT-ACCCCAAAATTTCC
* * *
41963592 AAAATTACCATTTTACCCCCAAATGTCTA
1 AAAATTACCATTTTACCCCAAAATTTC-C
* *** *
41963621 AAAATT-CTATTTTTAACCTTGAACTTTCC
1 AAAATTACCA-TTTT-ACCCCAAAATTTCC
41963650 AAAATTACCATTTTACCCCAAAATTTTCC
1 AAAATTACCATTTTACCCCAAAA-TTTCC
41963679 AAAATT
1 AAAATT
41963685 TCATTTTTAA
Statistics
Matches: 91, Mismatches: 23, Indels: 16
0.70 0.18 0.12
Matches are distributed among these distances:
28 18 0.20
29 51 0.56
30 22 0.24
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (28 bp):
AAAATTACCATTTTACCCCAAAATTTCC
Found at i:41963723 original size:30 final size:29
Alignment explanation
Indices: 41963631--41963723 Score: 91
Period size: 29 Copynumber: 3.2 Consensus size: 29
41963621 AAAATTCTAT
* *
41963631 TTTTAACCTTGAACTTTCCAAAATTACCA
1 TTTTAACCTCGAACTTTCCAAAATTATCA
* * *
41963660 TTTT-ACCCCAAAATTTTCCAAAATT-TCA
1 TTTTAACCTC-GAACTTTCCAAAATTATCA
*
41963688 TTTTTAACCTCGAACCTTTCAAAAATTATCA
1 -TTTTAACCTCGAA-CTTTCCAAAATTATCA
41963719 TTTTA
1 TTTTA
41963724 CCCCCGAATA
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
28 5 0.10
29 23 0.46
30 19 0.38
31 3 0.06
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.41
Consensus pattern (29 bp):
TTTTAACCTCGAACTTTCCAAAATTATCA
Found at i:41974638 original size:98 final size:98
Alignment explanation
Indices: 41974457--41974930 Score: 679
Period size: 98 Copynumber: 4.8 Consensus size: 98
41974447 CTACAGGTCT
* *
41974457 CAGTACCACGAA-ACACAAAGGGAAAGGTTTAAGTTGCAATGATGAACCTTATACCTTAGAGACA
1 CAGTACCACGAAGACACAAAGGGAAAGGTTTAAGTCGCAATGACGAACCTTATACCTTAGAGACA
*
41974521 TGAAGGGAAAGATTTAAGCCGCAACGACGAATC
66 TGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
*
41974554 CGGTACCACGAAGACACAAAGGGAAAGGTTTAAGTCGCAATGACGAACCTTATACCTTAGAGACA
1 CAGTACCACGAAGACACAAAGGGAAAGGTTTAAGTCGCAATGACGAACCTTATACCTTAGAGACA
41974619 TGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
66 TGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* * *
41974652 CGGTACCACGAAGACACAAAGGGAAATGTTTAAGTCGCAATGGA-GAACCTTATACCTTAAAGAC
1 CAGTACCACGAAGACACAAAGGGAAAGGTTTAAGTCGCAAT-GACGAACCTTATACCTTAGAGAC
*
41974716 ATGAAGGGAAAGATTTAAGCCGCAACGGCAAATC
65 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* * * * *
41974750 CAGTACCACGACGACACAAAGGGAAAGGTTTAAGTTGTAATGGCGAACCTTATACCTCAGA-AGC
1 CAGTACCACGAAGACACAAAGGGAAAGGTTTAAGTCGCAATGACGAACCTTATACCTTAGAGA-C
* *
41974814 ATGAAAGGGAACGATTTAAGCCGCAACGGTGAATC
65 ATG-AAGGGAAAGATTTAAGCCGCAACGGCGAATC
* * * * *
41974849 CAGTACCGCGAAGACACAAGGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAGA-AGC
1 CAGTACCACGAAGACACAAAGGGAAAGGTTTAAGTCGCAATGACGAACCTTATACCTTAGAGA-C
* *
41974913 ATAAAAGGAAA-ATTTAAG
65 ATGAAGGGAAAGATTTAAG
41974931 TCGCGATGGT
Statistics
Matches: 345, Mismatches: 27, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
97 20 0.06
98 235 0.68
99 90 0.26
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.18
Consensus pattern (98 bp):
CAGTACCACGAAGACACAAAGGGAAAGGTTTAAGTCGCAATGACGAACCTTATACCTTAGAGACA
TGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
Found at i:41974904 original size:49 final size:49
Alignment explanation
Indices: 41974459--41974939 Score: 320
Period size: 49 Copynumber: 9.8 Consensus size: 49
41974449 ACAGGTCTCA
* **
41974459 GTACCACGAA-ACACAAAGGGAAAGGTTTAAGTTGCAATGATGAACCTT
1 GTACCACGAAGACACAAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTT
* ** * * * * *
41974507 ATACCTTA-G-AGACATGAAGGGAAAGATTTAAGCCGCAACGACGAATCC-G
1 GTACC--ACGAAGACACAAAGGGAAAGGTTTAAGTCGCAATGGCGAA-CCTT
*
41974556 GTACCACGAAGACACAAAGGGAAAGGTTTAAGTCGCAATGACGAACCTT
1 GTACCACGAAGACACAAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTT
* ** * * * *
41974605 ATACCTTA-G-AGACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCC-G
1 GTACC--ACGAAGACACAAAGGGAAAGGTTTAAGTCGCAATGGCGAA-CCTT
* *
41974654 GTACCACGAAGACACAAAGGGAAATGTTTAAGTCGCAATGGAGAACCTT
1 GTACCACGAAGACACAAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTT
* *** ** * * * * *
41974703 ATACCTTAAAGACATGAAGGGAAAGATTTAAGCCGCAACGGCAAATCC-A
1 GTACCACGAAGACACAAAGGGAAAGGTTTAAGTCGCAATGGCGAA-CCTT
* * *
41974752 GTACCACGACGACACAAAGGGAAAGGTTTAAGTTGTAATGGCGAACCTT
1 GTACCACGAAGACACAAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTT
* * * * * * * * *
41974801 ATACCTCAGAAG-CATGAAAGGGAACGATTTAAGCCGCAACGGTGAATCC-A
1 GTACCAC-GAAGACA-CAAAGGGAAAGGTTTAAGTCGCAATGGCGAA-CCTT
* *
41974851 GTACCGCGAAGACACAAGGGGAAAGGTTTAAGTCGCAATGGCGAACCTT
1 GTACCACGAAGACACAAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTT
* * * * *
41974900 GTACCTCAGAAG-CATAAAAGGAAA-ATTTAAGTCGCGATGG
1 GTACCAC-GAAGACACAAAGGGAAAGGTTTAAGTCGCAATGG
41974940 TGAATTTAGT
Statistics
Matches: 324, Mismatches: 88, Indels: 42
0.71 0.19 0.09
Matches are distributed among these distances:
47 2 0.01
48 29 0.09
49 245 0.76
50 45 0.14
51 3 0.01
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.18
Consensus pattern (49 bp):
GTACCACGAAGACACAAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTT
Found at i:41975390 original size:17 final size:17
Alignment explanation
Indices: 41975365--41975430 Score: 78
Period size: 17 Copynumber: 3.8 Consensus size: 17
41975355 CCAACAGAAT
41975365 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
* *
41975382 TTAAGTTTATTTTAAAT
1 TTAAATTTATTTTAAAA
* *
41975399 TTAAATTTATTATAAAT
1 TTAAATTTATTTTAAAA
*
41975416 TTATATTTATATTTA
1 TTAAATTTAT-TTTA
41975431 TTTAAATAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
17 39 0.93
18 3 0.07
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:41975418 original size:23 final size:22
Alignment explanation
Indices: 41975392--41975437 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
41975382 TTAAGTTTAT
41975392 TTTAAATTTAAATTTATTATAAA
1 TTTAAATTTAAATTTATT-TAAA
* *
41975415 TTTATATTTATATTTATTTAAA
1 TTTAAATTTAAATTTATTTAAA
41975437 T
1 T
41975438 AATGTCCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTAAATTTAAATTTATTTAAA
Found at i:41975425 original size:34 final size:34
Alignment explanation
Indices: 41975362--41975437 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 34
41975352 GGCCCAACAG
*
41975362 AATTTAAATTTATTTTAAAATTAAGTTTAT-TTT
1 AATTTAAATTTATTATAAAATTAAGTTTATATTT
*
41975395 AAATTTAAATTTATTATAAATTTATA-TTTATATTT
1 -AATTTAAATTTATTATAAAATTA-AGTTTATATTT
41975430 -ATTTAAAT
1 AATTTAAAT
41975438 AATGTCCAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
33 8 0.21
34 26 0.68
35 4 0.11
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (34 bp):
AATTTAAATTTATTATAAAATTAAGTTTATATTT
Found at i:41977293 original size:30 final size:30
Alignment explanation
Indices: 41977259--41977330 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
41977249 TCCAGGAATC
* *
41977259 ATATTTTGACTCCCGAACTTTCT-AAAAATT
1 ATATTTTGAC-CCCCAAATTTCTCAAAAATT
41977289 ATATTTTGACCCCCAAATTTCTCAAAAATT
1 ATATTTTGACCCCCAAATTTCTCAAAAATT
* *
41977319 ACATTTTTACCC
1 ATATTTTGACCC
41977331 TTGAATTGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 10 0.27
30 27 0.73
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (30 bp):
ATATTTTGACCCCCAAATTTCTCAAAAATT
Found at i:41977606 original size:19 final size:19
Alignment explanation
Indices: 41977584--41977640 Score: 71
Period size: 19 Copynumber: 3.0 Consensus size: 19
41977574 TTTAAATACA
*
41977584 ATTTATATTATTATTTAAT
1 ATTTAAATTATTATTTAAT
* *
41977603 ATTTAAAATATTATTTATT
1 ATTTAAATTATTATTTAAT
41977622 ATTTAAATT-TGTATTTAAT
1 ATTTAAATTAT-TATTTAAT
41977641 TTATGTTTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 1 0.03
19 31 0.97
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
ATTTAAATTATTATTTAAT
Found at i:41978744 original size:28 final size:28
Alignment explanation
Indices: 41978669--41978975 Score: 193
Period size: 29 Copynumber: 10.6 Consensus size: 28
41978659 CATCACGAAT
* * *
41978669 TTTCCAAAATTTCATTTTTAACCTTAAAC
1 TTTCCAAAATTCCA-TTTTAACCCTGAAC
* *
41978698 TTTCCAAAAATTACA-TTT-ACCTCTGAAT
1 TTTCC-AAAATTCCATTTTAACC-CTGAAC
41978726 TTTCCAAAATTCCATTTTAACCC-GAAC
1 TTTCCAAAATTCCATTTTAACCCTGAAC
*
41978753 CTTCCAAAATTACCATTTT-ACCCTCGAA-
1 TTTCCAAAATT-CCATTTTAACCCT-GAAC
* * *
41978781 TGTCTAAAAATTCCATTTTTAACCCCGAAC
1 TTTC-CAAAATTCCA-TTTTAACCCTGAAC
* * *
41978811 CTTCCAAAATTACTATTTT-ACTCCCGAA-
1 TTTCCAAAATT-CCATTTTAAC-CCTGAAC
* *
41978839 TGTCTAAAAATTCCATTTTTAACCCTGAAC
1 TTTC-CAAAATTCCA-TTTTAACCCTGAAC
* *
41978869 TTTCCAAAAATTACCATTTTACCCCT-AAA
1 TTTCC-AAAATT-CCATTTTAACCCTGAAC
*
41978898 TATTCCAAAATTCCATTTTTAACCCCGAAC
1 T-TTCCAAAATTCCA-TTTTAACCCTGAAC
*
41978928 CTTCCACAAATTTCCATTTT-ACCCTCGAA-
1 TTTCCA-AAA-TTCCATTTTAACCCT-GAAC
* *
41978957 TATCTAAAAATTCCATTTT
1 TTTC-CAAAATTCCATTTT
41978976 TTAACCCTAA
Statistics
Matches: 220, Mismatches: 32, Indels: 53
0.72 0.10 0.17
Matches are distributed among these distances:
27 28 0.13
28 45 0.20
29 86 0.39
30 53 0.24
31 8 0.04
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36
Consensus pattern (28 bp):
TTTCCAAAATTCCATTTTAACCCTGAAC
Found at i:41978791 original size:29 final size:30
Alignment explanation
Indices: 41978758--41979097 Score: 166
Period size: 29 Copynumber: 11.5 Consensus size: 30
41978748 CGAACCTTCC
41978758 AAAATTACCATTTT-ACCCTCGAATGTCTA
1 AAAATTACCATTTTAACCCTCGAATGTCTA
*
41978787 AAAATT-CCATTTTTAACCC-CGAACCT-TC-C
1 AAAATTACCA-TTTTAACCCTCGAA--TGTCTA
*
41978816 AAAATTACTATTTT-ACTCC-CGAATGTCTA
1 AAAATTACCATTTTAAC-CCTCGAATGTCTA
* *
41978845 AAAATT-CCATTTTTAACCCT-GAACTTTCCA
1 AAAATTACCA-TTTTAACCCTCGAA-TGTCTA
* * * *
41978875 AAAATTACCATTTTACCCCT-AAATAT-TCC
1 AAAATTACCATTTTAACCCTCGAATGTCT-A
*
41978904 AAAATT-CCATTTTTAACCC-CGAACCT-TCCA
1 AAAATTACCA-TTTTAACCCTCGAA--TGTCTA
* * *
41978934 CAAATTTCCATTTT-ACCCTCGAATATCTA
1 AAAATTACCATTTTAACCCTCGAATGTCTA
* * *
41978963 AAAATT-CCATTTTTTAACCCT-AAATTTTTTA
1 AAAATTACCA--TTTTAACCCTCGAA-TGTCTA
*
41978994 AAAATTACCATTTT-ACCCCCGAATGTCTA
1 AAAATTACCATTTTAACCCTCGAATGTCTA
* *
41979023 AAAATT-CCATTTTTTGA-CCTCGAACCT-TCCA
1 AAAATTACCA--TTTTAACCCTCGAA--TGTCTA
** * *
41979054 AAAATTACCATTTTGCCCCCCGAGTGTCT-
1 AAAATTACCATTTTAACCCTCGAATGTCTA
*
41979083 AAAATTACCGTTTTA
1 AAAATTACCATTTTA
41979098 CCTTTCGAGC
Statistics
Matches: 242, Mismatches: 33, Indels: 72
0.70 0.10 0.21
Matches are distributed among these distances:
27 1 0.00
28 19 0.08
29 103 0.43
30 74 0.31
31 38 0.16
32 7 0.03
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.36
Consensus pattern (30 bp):
AAAATTACCATTTTAACCCTCGAATGTCTA
Found at i:41978908 original size:59 final size:59
Alignment explanation
Indices: 41978674--41979086 Score: 418
Period size: 59 Copynumber: 7.1 Consensus size: 59
41978664 CGAATTTTCC
* * * * * * *
41978674 AAAATTTCATTTTTAACCTTAAACTTTCCAAAAATTA-CA-TTTACCTCTGAAT-TTTCC
1 AAAATTCCATTTTTAACCCTGAACCTTCCAAAAATTACCATTTTACCCCTGAATGTCT-A
41978731 AAAATTCCA-TTTTAACCC-GAACCTTCC-AAAATTACCATTTTA-CCCTCGAATGTCTA
1 AAAATTCCATTTTTAACCCTGAACCTTCCAAAAATTACCATTTTACCCCT-GAATGTCTA
* *
41978787 AAAATTCCATTTTTAACCCCGAACCTTCC-AAAATTACTATTTTACTCCC-GAATGTCTA
1 AAAATTCCATTTTTAACCCTGAACCTTCCAAAAATTACCATTTTAC-CCCTGAATGTCTA
* * * *
41978845 AAAATTCCATTTTTAACCCTGAACTTTCCAAAAATTACCATTTTACCCCTAAATAT-TCC
1 AAAATTCCATTTTTAACCCTGAACCTTCCAAAAATTACCATTTTACCCCTGAATGTCT-A
* * * *
41978904 AAAATTCCATTTTTAACCCCGAACCTTCCACAAATTTCCATTTTA-CCCTCGAATATCTA
1 AAAATTCCATTTTTAACCCTGAACCTTCCAAAAATTACCATTTTACCCCT-GAATGTCTA
* ** ** *
41978963 AAAATTCCATTTTTTAACCCTAAATTTTTTAAAAATTACCATTTTACCCCCGAATGTCTA
1 AAAATTCCA-TTTTTAACCCTGAACCTTCCAAAAATTACCATTTTACCCCTGAATGTCTA
* * * *
41979023 AAAATTCCATTTTTTGA-CCTCGAACCTTCCAAAAATTACCATTTTGCCCCCCGAGTGTCTA
1 AAAATTCCA-TTTTTAACCCT-GAACCTTCCAAAAATTACCATTTT-ACCCCTGAATGTCTA
41979084 AAA
1 AAA
41979087 TTACCGTTTT
Statistics
Matches: 301, Mismatches: 38, Indels: 30
0.82 0.10 0.08
Matches are distributed among these distances:
54 7 0.02
55 12 0.04
56 25 0.08
57 19 0.06
58 67 0.22
59 77 0.26
60 75 0.25
61 19 0.06
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (59 bp):
AAAATTCCATTTTTAACCCTGAACCTTCCAAAAATTACCATTTTACCCCTGAATGTCTA
Found at i:41978923 original size:30 final size:31
Alignment explanation
Indices: 41978669--41979067 Score: 152
Period size: 29 Copynumber: 13.6 Consensus size: 31
41978659 CATCACGAAT
* *
41978669 TTTCC-AAAATTTCATTTTTAA--CCTTAAA
1 TTTCCAAAAATTCCATTTTTAACCCCTGAAA
* * *
41978697 CTTTCCAAAAATTACA--TTT-ACCTCTGAAT
1 -TTTCCAAAAATTCCATTTTTAACCCCTGAAA
*
41978726 TTTCC-AAAATTCCA-TTTTAA-CCC-GAAC
1 TTTCCAAAAATTCCATTTTTAACCCCTGAAA
*
41978753 CTTCC-AAAATTACCA-TTTT-A-CCCTCG-AA
1 TTTCCAAAAATT-CCATTTTTAACCCCT-GAAA
* * *
41978781 TGTCTAAAAATTCCATTTTTAACCCC-GAAC
1 TTTCCAAAAATTCCATTTTTAACCCCTGAAA
* *
41978811 CTTCC-AAAATTAC-TATTTT-ACTCCC-G-AA
1 TTTCCAAAAATTCCAT-TTTTAAC-CCCTGAAA
* * *
41978839 TGTCTAAAAATTCCATTTTTAA-CCCTGAAC
1 TTTCCAAAAATTCCATTTTTAACCCCTGAAA
41978869 TTTCCAAAAATTACCA-TTTT-ACCCCT-AAA
1 TTTCCAAAAATT-CCATTTTTAACCCCTGAAA
*
41978898 TATTCC-AAAATTCCATTTTTAACCCC-GAAC
1 T-TTCCAAAAATTCCATTTTTAACCCCTGAAA
* *
41978928 CTTCCACAAATTTCCA-TTTT-A-CCCTCG-AA
1 TTTCCA-AAAATTCCATTTTTAACCCCT-GAAA
* *
41978957 TATCTAAAAATTCCATTTTTTAA-CCCT-AAA
1 TTTCCAAAAATTCCA-TTTTTAACCCCTGAAA
** *
41978987 TTTTTTAAAAATTACCA-TTTT-ACCCCCG-AA
1 -TTTCCAAAAATT-CCATTTTTAACCCCTGAAA
* * * * *
41979017 TGTCTAAAAATTCCATTTTTTGACCTC-GAAC
1 TTTCCAAAAATTCCA-TTTTTAACCCCTGAAA
*
41979048 CTTCCAAAAATTACCATTTT
1 TTTCCAAAAATT-CCATTTT
41979068 GCCCCCCGAG
Statistics
Matches: 283, Mismatches: 44, Indels: 84
0.69 0.11 0.20
Matches are distributed among these distances:
27 26 0.09
28 52 0.18
29 83 0.29
30 69 0.24
31 47 0.17
32 6 0.02
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.37
Consensus pattern (31 bp):
TTTCCAAAAATTCCATTTTTAACCCCTGAAA
Found at i:41991314 original size:22 final size:23
Alignment explanation
Indices: 41991288--41991340 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
41991278 ATGTGTGTTT
* *
41991288 AATAATAAATTAT-ATATATTAA
1 AATAAAAAATTATAAAATATTAA
41991310 AATAAAAAATTATAAAAATATTAA
1 AATAAAAAATTAT-AAAATATTAA
41991334 AATAAAA
1 AATAAAA
41991341 TTTTAATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 12 0.44
24 15 0.56
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (23 bp):
AATAAAAAATTATAAAATATTAA
Found at i:41992233 original size:13 final size:12
Alignment explanation
Indices: 41992184--41992234 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
41992174 AACTTGATCA
*
41992184 AACATGTTCATG
1 AACATGTTAATG
*
41992196 AACAT-ATAATTG
1 AACATGTTAA-TG
*
41992208 AACATGTTCATG
1 AACATGTTAATG
41992220 AACAATGTTAATG
1 AAC-ATGTTAATG
41992233 AA
1 AA
41992235 TAATAAACAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
11 2 0.06
12 17 0.55
13 12 0.39
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (12 bp):
AACATGTTAATG
Found at i:42000289 original size:20 final size:20
Alignment explanation
Indices: 42000253--42000291 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
42000243 CAAGTATCCA
*
42000253 CCATCATTGGTAAATTACTT
1 CCATCATTGGAAAATTACTT
42000273 CCATC-TTGGAAAGATTACT
1 CCATCATTGGAAA-ATTACT
42000292 AAAGGTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.36
Consensus pattern (20 bp):
CCATCATTGGAAAATTACTT
Found at i:42002226 original size:115 final size:115
Alignment explanation
Indices: 42002059--42002289 Score: 453
Period size: 115 Copynumber: 2.0 Consensus size: 115
42002049 TGCATTAGGT
42002059 TCTCTTTTTTGCTACACTAAAACTACCAAATTATATGAAATAGGAAAGCATGTAGGTTTTATAAT
1 TCTCTTTTTTGCTACACTAAAACTACCAAATTATATGAAATAGGAAAGCATGTAGGTTTTATAAT
42002124 CTTGAGACTGATAACATTATTGAATCTACTCATATAATATATTTTGAGCA
66 CTTGAGACTGATAACATTATTGAATCTACTCATATAATATATTTTGAGCA
*
42002174 TCTCTTTTTTGCTACACTAAAACTGCCAAATTATATGAAATAGGAAAGCATGTAGGTTTTATAAT
1 TCTCTTTTTTGCTACACTAAAACTACCAAATTATATGAAATAGGAAAGCATGTAGGTTTTATAAT
42002239 CTTGAGACTGATAACATTATTGAATCTACTCATATAATATATTTTGAGCA
66 CTTGAGACTGATAACATTATTGAATCTACTCATATAATATATTTTGAGCA
42002289 T
1 T
42002290 TTAGTAATAA
Statistics
Matches: 115, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
115 115 1.00
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.38
Consensus pattern (115 bp):
TCTCTTTTTTGCTACACTAAAACTACCAAATTATATGAAATAGGAAAGCATGTAGGTTTTATAAT
CTTGAGACTGATAACATTATTGAATCTACTCATATAATATATTTTGAGCA
Found at i:42004354 original size:2 final size:2
Alignment explanation
Indices: 42004318--42004343 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42004308 TTTTCTACAA
42004318 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
42004344 TATTGTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42006730 original size:6 final size:6
Alignment explanation
Indices: 42006719--42006743 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
42006709 AATCATTTAC
42006719 AAATAT AAATAT AAATAT AAATAT A
1 AAATAT AAATAT AAATAT AAATAT A
42006744 TAACATTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATAT
Found at i:42006813 original size:17 final size:17
Alignment explanation
Indices: 42006793--42006834 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
42006783 TATTTCAAAA
42006793 TAAAAATACCAAAATTC
1 TAAAAATACCAAAATTC
42006810 TAAAAATACCAAAATTC
1 TAAAAATACCAAAATTC
*
42006827 TCAAAATA
1 TAAAAATA
42006835 GAATGTATTT
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:0.60, C:0.17, G:0.00, T:0.24
Consensus pattern (17 bp):
TAAAAATACCAAAATTC
Found at i:42008009 original size:14 final size:14
Alignment explanation
Indices: 42007990--42008078 Score: 133
Period size: 14 Copynumber: 6.4 Consensus size: 14
42007980 CAAAGTTAAA
*
42007990 GTCAACGATGAACG
1 GTCAACGATCAACG
*
42008004 GTCAACGATGAACG
1 GTCAACGATCAACG
*
42008018 GTCAACTATCAACG
1 GTCAACGATCAACG
*
42008032 GCCAACGATCAACG
1 GTCAACGATCAACG
*
42008046 GTCAACGATCAACA
1 GTCAACGATCAACG
42008060 GTCAACGATCAACG
1 GTCAACGATCAACG
42008074 GTCAA
1 GTCAA
42008079 AGGTCGATCA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 68 1.00
ACGTcount: A:0.37, C:0.27, G:0.21, T:0.15
Consensus pattern (14 bp):
GTCAACGATCAACG
Found at i:42008010 original size:7 final size:7
Alignment explanation
Indices: 42007990--42008083 Score: 80
Period size: 7 Copynumber: 13.4 Consensus size: 7
42007980 CAAAGTTAAA
42007990 GTCAACG
1 GTCAACG
* *
42007997 ATGAACG
1 GTCAACG
42008004 GTCAACG
1 GTCAACG
* *
42008011 ATGAACG
1 GTCAACG
*
42008018 GTCAACT
1 GTCAACG
*
42008025 ATCAACG
1 GTCAACG
*
42008032 GCCAACG
1 GTCAACG
*
42008039 ATCAACG
1 GTCAACG
42008046 GTCAACG
1 GTCAACG
* *
42008053 ATCAACA
1 GTCAACG
42008060 GTCAACG
1 GTCAACG
*
42008067 ATCAACG
1 GTCAACG
*
42008074 GTCAAAG
1 GTCAACG
42008081 GTC
1 GTC
42008084 GATCAATACT
Statistics
Matches: 64, Mismatches: 23, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
7 64 1.00
ACGTcount: A:0.36, C:0.27, G:0.22, T:0.15
Consensus pattern (7 bp):
GTCAACG
Found at i:42008122 original size:22 final size:22
Alignment explanation
Indices: 42008082--42008124 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
42008072 CGGTCAAAGG
*
42008082 TCGATCAATACTCGGTCAACGC
1 TCGATCAATACTCGATCAACGC
**
42008104 TCGATCAATGGTCGATCAACG
1 TCGATCAATACTCGATCAACG
42008125 GTCAGTCAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (22 bp):
TCGATCAATACTCGATCAACGC
Found at i:42008133 original size:22 final size:22
Alignment explanation
Indices: 42008108--42008151 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
42008098 CAACGCTCGA
* *
42008108 TCAATGGTCGATCAACGGTCAG
1 TCAATGATCGATCAACAGTCAG
*
42008130 TCAATGATCGGTCAACAGTCAG
1 TCAATGATCGATCAACAGTCAG
42008152 AATTGGTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.23, G:0.25, T:0.23
Consensus pattern (22 bp):
TCAATGATCGATCAACAGTCAG
Found at i:42010989 original size:30 final size:30
Alignment explanation
Indices: 42010953--42011012 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
42010943 ACAGGTTGTT
42010953 TCCAGCCCATAATAGCCTCAATCTTCTTCG
1 TCCAGCCCATAATAGCCTCAATCTTCTTCG
42010983 TCCAGCCCATAATAGCCTCAATCTTCTTCG
1 TCCAGCCCATAATAGCCTCAATCTTCTTCG
42011013 GATCCACACG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.37, G:0.10, T:0.30
Consensus pattern (30 bp):
TCCAGCCCATAATAGCCTCAATCTTCTTCG
Found at i:42013919 original size:12 final size:13
Alignment explanation
Indices: 42013904--42013944 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
42013894 AATCATTTAC
42013904 AAATATA-AATAT
1 AAATATATAATAT
42013916 AAATATATAATATT
1 AAATATATAATA-T
*
42013930 AAGTATATAAT-T
1 AAATATATAATAT
42013942 AAA
1 AAA
42013945 ACAAAATAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 10 0.40
13 4 0.16
14 11 0.44
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (13 bp):
AAATATATAATAT
Found at i:42015155 original size:14 final size:14
Alignment explanation
Indices: 42015138--42015164 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42015128 ACGGGTCAAA
42015138 GTCAATGATCAACG
1 GTCAATGATCAACG
42015152 GTCAATGATCAAC
1 GTCAATGATCAAC
42015165 TATCAAAGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (14 bp):
GTCAATGATCAACG
Found at i:42015163 original size:21 final size:20
Alignment explanation
Indices: 42015131--42015198 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 20
42015121 AAAGTTAACG
*
42015131 GGTCAAAGTCAA-TGATCAAC
1 GGTCAATGTCAACT-ATCAAC
*
42015151 GGTCAATGATCAACTATCAAA
1 GGTCAATG-TCAACTATCAAC
*
42015172 GGTCAATGGTAAACTATCAAC
1 GGTCAAT-GTCAACTATCAAC
42015193 GGTCAA
1 GGTCAA
42015199 CAGTCAACGG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 7 0.17
21 32 0.78
22 2 0.05
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (20 bp):
GGTCAATGTCAACTATCAAC
Found at i:42015232 original size:22 final size:22
Alignment explanation
Indices: 42015199--42015260 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
42015189 CAACGGTCAA
*
42015199 CAGTCAACGGTCGATCAACGCT
1 CAGTCAATGGTCGATCAACGCT
* * *
42015221 CTA-TCAATGGTCAATTAACGGT
1 C-AGTCAATGGTCGATCAACGCT
*
42015243 CAGTCAATGGTCGGTCAA
1 CAGTCAATGGTCGATCAA
42015261 TGGTCAGAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
21 1 0.03
22 29 0.94
23 1 0.03
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (22 bp):
CAGTCAATGGTCGATCAACGCT
Found at i:42018447 original size:3 final size:3
Alignment explanation
Indices: 42018439--42018465 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
42018429 ATACTTCTTA
42018439 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
42018466 GTTGTTGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:42018470 original size:3 final size:3
Alignment explanation
Indices: 42018464--42018498 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
42018454 ATTATTATTA
* *
42018464 TTG TTG TTG TTG TTG TTG CTG TTG TTG TTG CTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
42018499 ATCTAAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.06, G:0.31, T:0.63
Consensus pattern (3 bp):
TTG
Found at i:42018479 original size:12 final size:12
Alignment explanation
Indices: 42018464--42018498 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
42018454 ATTATTATTA
*
42018464 TTGTTGTTGTTG
1 TTGTTGCTGTTG
42018476 TTGTTGCTGTTG
1 TTGTTGCTGTTG
42018488 TTGTTGCTGTT
1 TTGTTGCTGTT
42018499 ATCTAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.06, G:0.31, T:0.63
Consensus pattern (12 bp):
TTGTTGCTGTTG
Found at i:42020424 original size:11 final size:11
Alignment explanation
Indices: 42020407--42020444 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
42020397 ATTCATGAAT
42020407 ATAAGAAGTTG
1 ATAAGAAGTTG
*
42020418 GTAAGAAGTTG
1 ATAAGAAGTTG
*
42020429 ATAAGAAGCTG
1 ATAAGAAGTTG
42020440 ATAAG
1 ATAAG
42020445 TGATTAGTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.45, C:0.03, G:0.29, T:0.24
Consensus pattern (11 bp):
ATAAGAAGTTG
Found at i:42031138 original size:2 final size:2
Alignment explanation
Indices: 42031131--42031156 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42031121 CAACAAAGGC
42031131 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
42031157 GACTCTATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:42037370 original size:183 final size:183
Alignment explanation
Indices: 42037062--42037427 Score: 714
Period size: 183 Copynumber: 2.0 Consensus size: 183
42037052 GTAGCACATA
42037062 ATCTAGCATATTCTCTTTTGATTCTTTCCATATCCTTTGTAATCTCTTATCTTAAGAATGTTTGA
1 ATCTAGCATATTCTCTTTTGATTCTTTCCATATCCTTTGTAATCTCTTATCTTAAGAATGTTTGA
42037127 TTTGAATTCCTTAGATTAAGGGATATTATAGATGTCATTGTATCTAGACCGTCGATGTACTCTAA
66 TTTGAATTCCTTAGATTAAGGGATATTATAGATGTCATTGTATCTAGACCGTCGATGTACTCTAA
42037192 TCTTAACCGTTGGATGTAGGGGGCTTCAACTATAAATAAAGGCTTACCCCCAC
131 TCTTAACCGTTGGATGTAGGGGGCTTCAACTATAAATAAAGGCTTACCCCCAC
*
42037245 ATCTAGCATATTCTCTTTTGATTCTTTCCATATCCTTTGTAATCTCTTATCTTAGGAATGTTTGA
1 ATCTAGCATATTCTCTTTTGATTCTTTCCATATCCTTTGTAATCTCTTATCTTAAGAATGTTTGA
*
42037310 TTTGAATTCCTTATATTAAGGGATATTATAGATGTCATTGTATCTAGACCGTCGATGTACTCTAA
66 TTTGAATTCCTTAGATTAAGGGATATTATAGATGTCATTGTATCTAGACCGTCGATGTACTCTAA
42037375 TCTTAACCGTTGGATGTAGGGGGCTTCAACTATAAATAAAGGCTTACCCCCAC
131 TCTTAACCGTTGGATGTAGGGGGCTTCAACTATAAATAAAGGCTTACCCCCAC
42037428 CTCATTTTAC
Statistics
Matches: 181, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
183 181 1.00
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.39
Consensus pattern (183 bp):
ATCTAGCATATTCTCTTTTGATTCTTTCCATATCCTTTGTAATCTCTTATCTTAAGAATGTTTGA
TTTGAATTCCTTAGATTAAGGGATATTATAGATGTCATTGTATCTAGACCGTCGATGTACTCTAA
TCTTAACCGTTGGATGTAGGGGGCTTCAACTATAAATAAAGGCTTACCCCCAC
Found at i:42041891 original size:18 final size:19
Alignment explanation
Indices: 42041868--42041903 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
42041858 GTTGTGTTAT
42041868 TGTTG-TTACTTGAACTTA
1 TGTTGTTTACTTGAACTTA
42041886 TGTTGTTTACTTGAACTT
1 TGTTGTTTACTTGAACTT
42041904 TTGCGCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.19, C:0.11, G:0.17, T:0.53
Consensus pattern (19 bp):
TGTTGTTTACTTGAACTTA
Found at i:42043582 original size:20 final size:21
Alignment explanation
Indices: 42043553--42043596 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
42043543 TTTCCTGATA
*
42043553 TTTTCATTCTT-TCTCTTTTG
1 TTTTCATTCTTCTCTCTTCTG
*
42043573 TTTTCCTTCTTCTCTCTTCTG
1 TTTTCATTCTTCTCTCTTCTG
42043594 TTT
1 TTT
42043597 CAGATCTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.02, C:0.25, G:0.05, T:0.68
Consensus pattern (21 bp):
TTTTCATTCTTCTCTCTTCTG
Found at i:42045927 original size:26 final size:26
Alignment explanation
Indices: 42045891--42045944 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
42045881 ATGGTAAATA
*
42045891 CAGCACATCTTGGAACTCTTCTTGTT
1 CAGCACATCTTGGAACTCTTCTTATT
*
42045917 CAGCACATCTTGGAAGTCTTCTTATT
1 CAGCACATCTTGGAACTCTTCTTATT
42045943 CA
1 CA
42045945 TGAATTGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (26 bp):
CAGCACATCTTGGAACTCTTCTTATT
Found at i:42046232 original size:95 final size:95
Alignment explanation
Indices: 42046069--42046259 Score: 382
Period size: 95 Copynumber: 2.0 Consensus size: 95
42046059 CTCGATCGTC
42046069 ACGGTGGTTGTCACGGAGGACATCGCTGATGACGATCTGTTCGTGGTGCCTATCGCCGTCGGTCG
1 ACGGTGGTTGTCACGGAGGACATCGCTGATGACGATCTGTTCGTGGTGCCTATCGCCGTCGGTCG
42046134 AACCATCGCAGGAGATTATCACCGTTCAAT
66 AACCATCGCAGGAGATTATCACCGTTCAAT
42046164 ACGGTGGTTGTCACGGAGGACATCGCTGATGACGATCTGTTCGTGGTGCCTATCGCCGTCGGTCG
1 ACGGTGGTTGTCACGGAGGACATCGCTGATGACGATCTGTTCGTGGTGCCTATCGCCGTCGGTCG
42046229 AACCATCGCAGGAGATTATCACCGTTCAAT
66 AACCATCGCAGGAGATTATCACCGTTCAAT
42046259 A
1 A
42046260 ATTCTTCCTT
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 96 1.00
ACGTcount: A:0.20, C:0.25, G:0.29, T:0.25
Consensus pattern (95 bp):
ACGGTGGTTGTCACGGAGGACATCGCTGATGACGATCTGTTCGTGGTGCCTATCGCCGTCGGTCG
AACCATCGCAGGAGATTATCACCGTTCAAT
Found at i:42047395 original size:19 final size:21
Alignment explanation
Indices: 42047357--42047401 Score: 67
Period size: 19 Copynumber: 2.2 Consensus size: 21
42047347 TTTAAAAGTA
*
42047357 GCATTAAAAAAATTGTCCGTT
1 GCATTAAAAAAATTGACCGTT
42047378 GCATT-AAAAAA-TGACCGTT
1 GCATTAAAAAAATTGACCGTT
42047397 GCATT
1 GCATT
42047402 TACTGCTCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.52
20 6 0.26
21 5 0.22
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.31
Consensus pattern (21 bp):
GCATTAAAAAAATTGACCGTT
Found at i:42048264 original size:12 final size:12
Alignment explanation
Indices: 42048247--42048272 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42048237 GTTGAATCTG
42048247 TTACTTCTTTCA
1 TTACTTCTTTCA
42048259 TTACTTCTTTCA
1 TTACTTCTTTCA
42048271 TT
1 TT
42048273 GGTAGTGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.23, G:0.00, T:0.62
Consensus pattern (12 bp):
TTACTTCTTTCA
Found at i:42050588 original size:14 final size:13
Alignment explanation
Indices: 42050551--42050602 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
42050541 GGGTCATAAA
*
42050551 TTTAGGGTTTTGAG
1 TTTAGGGGTTTG-G
*
42050565 ATTTATGGGTTGTGG
1 -TTTAGGGGTT-TGG
42050580 TTTAGGGGTTTGG
1 TTTAGGGGTTTGG
42050593 TTT-GGGGTTT
1 TTTAGGGGTTT
42050603 TAAGGTGTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
12 7 0.21
13 6 0.18
14 9 0.27
15 9 0.27
16 2 0.06
ACGTcount: A:0.10, C:0.00, G:0.40, T:0.50
Consensus pattern (13 bp):
TTTAGGGGTTTGG
Found at i:42050633 original size:7 final size:7
Alignment explanation
Indices: 42050621--42050676 Score: 51
Period size: 7 Copynumber: 7.9 Consensus size: 7
42050611 GAAGGCTTGG
42050621 GGGTTTA
1 GGGTTTA
42050628 GGGTTTGA
1 GGGTTT-A
*
42050636 GGTTTTA
1 GGGTTTA
42050643 GGGTTT-
1 GGGTTTA
*
42050649 GGGTTATG
1 GGGTT-TA
**
42050657 GGGTTCG
1 GGGTTTA
42050664 GGGTTTA
1 GGGTTTA
42050671 GGGTTT
1 GGGTTT
42050677 GGGGCTTGGG
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
6 5 0.12
7 25 0.61
8 11 0.27
ACGTcount: A:0.09, C:0.02, G:0.46, T:0.43
Consensus pattern (7 bp):
GGGTTTA
Found at i:42050680 original size:14 final size:14
Alignment explanation
Indices: 42050620--42050680 Score: 70
Period size: 14 Copynumber: 4.3 Consensus size: 14
42050610 TGAAGGCTTG
42050620 GGGGTTTAGGGTTT
1 GGGGTTTAGGGTTT
*
42050634 GAGGTTTTAGGGTTT
1 G-GGGTTTAGGGTTT
* *
42050649 -GGGTTATGGGGTTC
1 GGGGTT-TAGGGTTT
42050663 GGGGTTTAGGGTTT
1 GGGGTTTAGGGTTT
42050677 GGGG
1 GGGG
42050681 CTTGGGGCTC
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
13 4 0.11
14 17 0.45
15 17 0.45
ACGTcount: A:0.08, C:0.02, G:0.51, T:0.39
Consensus pattern (14 bp):
GGGGTTTAGGGTTT
Found at i:42050686 original size:28 final size:28
Alignment explanation
Indices: 42050639--42050693 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
42050629 GGTTTGAGGT
* *
42050639 TTTAGGGTTTGGGTTATGGGGTTCGGGG
1 TTTAGGGTTTGGGCTATGGGGCTCGGGG
42050667 TTTAGGGTTTGGGGCT-TGGGGCTCGGG
1 TTTAGGGTTT-GGGCTATGGGGCTCGGG
42050694 TTTCGGGGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 20 0.83
29 4 0.17
ACGTcount: A:0.05, C:0.07, G:0.51, T:0.36
Consensus pattern (28 bp):
TTTAGGGTTTGGGCTATGGGGCTCGGGG
Found at i:42050687 original size:21 final size:21
Alignment explanation
Indices: 42050614--42050717 Score: 81
Period size: 21 Copynumber: 4.9 Consensus size: 21
42050604 AAGGTGTGAA
42050614 GGCTTGGGGGTTTAGGGTTTGAG
1 GGCTT-GGGGTTTAGGGTTTG-G
** *
42050637 GTTTTAGGGTTT-GGGTTATGG
1 GGCTTGGGGTTTAGGGTT-TGG
42050658 GG-TTCGGGGTTTAGGGTTTGG
1 GGCTT-GGGGTTTAGGGTTTGG
* *
42050679 GGCTTGGGG-CTCGGGTTTCGG
1 GGCTTGGGGTTTAGGGTTT-GG
*
42050700 GGCTT-GGGTTTCGGGTTT
1 GGCTTGGGGTTTAGGGTTT
42050718 CGGGTTTCGG
Statistics
Matches: 67, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
20 12 0.18
21 37 0.55
22 15 0.22
23 3 0.04
ACGTcount: A:0.05, C:0.08, G:0.49, T:0.38
Consensus pattern (21 bp):
GGCTTGGGGTTTAGGGTTTGG
Found at i:42050788 original size:26 final size:25
Alignment explanation
Indices: 42050749--42050830 Score: 67
Period size: 27 Copynumber: 3.1 Consensus size: 25
42050739 CGGGGCTCGG
42050749 GGGTCGAGGCTCGGGGGTCTGGGGTC
1 GGGTCGAGGCTC-GGGGTCTGGGGTC
* * * *
42050775 GGGTCTAGGTTCGGGGTTTGGGGTTT
1 GGGTCGAGGCTCGGGGTCTGGGG-TC
*
42050801 GGGCTCGGGGCTCGGGG-CTCGGGGTTC
1 GGG-TCGAGGCTCGGGGTCT-GGGG-TC
42050828 GGG
1 GGG
42050831 GTTCGGGGTT
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
25 10 0.23
26 15 0.34
27 19 0.43
ACGTcount: A:0.02, C:0.17, G:0.56, T:0.24
Consensus pattern (25 bp):
GGGTCGAGGCTCGGGGTCTGGGGTC
Found at i:42051183 original size:7 final size:7
Alignment explanation
Indices: 42050656--42051247 Score: 162
Period size: 7 Copynumber: 84.9 Consensus size: 7
42050646 TTTGGGTTAT
42050656 GGGGTTC
1 GGGGTTC
*
42050663 GGGGTTT
1 GGGGTTC
* *
42050670 AGGGTTT
1 GGGGTTC
42050677 GGGGCTT-
1 GGGG-TTC
*
42050684 GGGGCTC
1 GGGGTTC
*
42050691 GGGTTTC
1 GGGGTTC
42050698 GGGGCTT-
1 GGGG-TTC
*
42050705 GGGTTTC
1 GGGGTTC
*
42050712 GGGTTTC
1 GGGGTTC
*
42050719 GGGTTTC
1 GGGGTTC
*
42050726 GGGGCTC
1 GGGGTTC
* *
42050733 GGTGCTC
1 GGGGTTC
*
42050740 GGGGCTC
1 GGGGTTC
*
42050747 GGGGGTC
1 GGGGTTC
* *
42050754 GAGGCTC
1 GGGGTTC
*
42050761 GGGGGTC
1 GGGGTTC
42050768 TGGGG-TC
1 -GGGGTTC
42050775 -GGG-TC
1 GGGGTTC
**
42050780 TAGGTTC
1 GGGGTTC
*
42050787 GGGGTTT
1 GGGGTTC
42050794 GGGGTT-
1 GGGGTTC
* *
42050800 TGGGCTC
1 GGGGTTC
*
42050807 GGGGCTC
1 GGGGTTC
*
42050814 GGGGCTC
1 GGGGTTC
42050821 GGGGTTC
1 GGGGTTC
42050828 GGGGTTC
1 GGGGTTC
42050835 GGGGTTC
1 GGGGTTC
42050842 GGGGTTC
1 GGGGTTC
* *
42050849 GGGTTTA
1 GGGGTTC
* *
42050856 GGGTTTA
1 GGGGTTC
* *
42050863 GGGTTTA
1 GGGGTTC
* *
42050870 GGGTTTA
1 GGGGTTC
** *
42050877 GGTTTTA
1 GGGGTTC
* *
42050884 GGGTTTA
1 GGGGTTC
** *
42050891 GGTTTTA
1 GGGGTTC
* *
42050898 GGGTTTT
1 GGGGTTC
* *
42050905 AGGGTTG
1 GGGGTTC
42050912 GGGGTTC
1 GGGGTTC
42050919 GGGGTTC
1 GGGGTTC
*
42050926 CGGGTTCC
1 GGGGTT-C
* *
42050934 GGGTTTTA
1 GGG-GTTC
*
42050942 GGGGTTTA
1 GGGG-TTC
* *
42050950 GGGTTTA
1 GGGGTTC
* *
42050957 GGGTTTA
1 GGGGTTC
* *
42050964 GGGTTTA
1 GGGGTTC
* *
42050971 GGGTTTT
1 GGGGTTC
42050978 GGGGTT-
1 GGGGTTC
* *
42050984 TGGGTTT
1 GGGGTTC
*
42050991 GTGGTTTC
1 G-GGGTTC
42050999 GGGGTTC
1 GGGGTTC
42051006 GGGGTTC
1 GGGGTTC
*
42051013 GGGTTTC
1 GGGGTTC
* *
42051020 GGGTTTT
1 GGGGTTC
*
42051027 AGGGTTC
1 GGGGTTC
* * *
42051034 GAGTTTT
1 GGGGTTC
* *
42051041 AGGGTTT
1 GGGGTTC
*
42051048 GGGGTTTT
1 GGGG-TTC
*
42051056 GGGTTTC
1 GGGGTTC
*
42051063 GGGTTTC
1 GGGGTTC
* *
42051070 GGTGCTC
1 GGGGTTC
*
42051077 GGGGCTC
1 GGGGTTC
*
42051084 GGGGCTC
1 GGGGTTC
*
42051091 GGGGCTC
1 GGGGTTC
*
42051098 GGGGGTC
1 GGGGTTC
*
42051105 GGGGGTC
1 GGGGTTC
42051112 -GGG-TC
1 GGGGTTC
**
42051117 TAGGTTC
1 GGGGTTC
*
42051124 GGGGTTT
1 GGGGTTC
42051131 GGGGTTC
1 GGGGTTC
*
42051138 -GGGCTC
1 GGGGTTC
*
42051144 GGGGCTC
1 GGGGTTC
*
42051151 GGGGCTC
1 GGGGTTC
*
42051158 GGGGCTC
1 GGGGTTC
*
42051165 GGGGCTC
1 GGGGTTC
42051172 GGGGTTC
1 GGGGTTC
*
42051179 GGGGTTT
1 GGGGTTC
*
42051186 AGGGTT-
1 GGGGTTC
* *
42051192 TGGGTTG
1 GGGGTTC
*
42051199 GGGGTTTA
1 GGGG-TTC
* *
42051207 GGGTTTT
1 GGGGTTC
* *
42051214 AGGGTTG
1 GGGGTTC
*
42051221 GGGGTTG
1 GGGGTTC
42051228 GGGGTTC
1 GGGGTTC
42051235 GGGGTTC
1 GGGGTTC
*
42051242 TGGGTT
1 GGGGTT
42051248 TAGGGGTTTA
Statistics
Matches: 476, Mismatches: 90, Indels: 38
0.79 0.15 0.06
Matches are distributed among these distances:
5 7 0.01
6 29 0.06
7 402 0.84
8 36 0.08
9 2 0.00
ACGTcount: A:0.04, C:0.12, G:0.51, T:0.34
Consensus pattern (7 bp):
GGGGTTC
Found at i:42051226 original size:29 final size:29
Alignment explanation
Indices: 42051183--42051292 Score: 91
Period size: 29 Copynumber: 3.8 Consensus size: 29
42051173 GGGTTCGGGG
*
42051183 TTTAGGGTT-TGGGTTGGGGGTTTAGGGT
1 TTTAGGGTTGGGGGTTGGGGGTTTAGGGT
**
42051211 TTTAGGGTTGGGGGTTGGGGGTTCGGGGT
1 TTTAGGGTTGGGGGTTGGGGGTTTAGGGT
* * **
42051240 TCT-GGGTTTAGGGGTTTAGGGTTTAGGG-
1 TTTAGGG-TTGGGGGTTGGGGGTTTAGGGT
* * *
42051268 TTTAGGTTTTGGGGTTTCGGGGTTT
1 TTTAGG-GTTGGGGGTTGGGGGTTT
42051293 CCATGGACTT
Statistics
Matches: 63, Mismatches: 15, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
28 14 0.22
29 49 0.78
ACGTcount: A:0.06, C:0.03, G:0.49, T:0.42
Consensus pattern (29 bp):
TTTAGGGTTGGGGGTTGGGGGTTTAGGGT
Found at i:42051261 original size:7 final size:7
Alignment explanation
Indices: 42051180--42051284 Score: 79
Period size: 7 Copynumber: 14.9 Consensus size: 7
42051170 TCGGGGTTCG
42051180 GGGTTTA
1 GGGTTTA
42051187 GGGTTT-
1 GGGTTTA
**
42051193 GGGTTGG
1 GGGTTTA
42051200 GGGTTTA
1 GGGTTTA
42051207 GGGTTTTA
1 GGG-TTTA
**
42051215 GGGTTGG
1 GGGTTTA
**
42051222 GGGTTGG
1 GGGTTTA
**
42051229 GGGTTCG
1 GGGTTTA
42051236 GGGTTCT-
1 GGGTT-TA
42051243 GGGTTTA
1 GGGTTTA
42051250 GGGGTTTA
1 -GGGTTTA
42051258 GGGTTTA
1 GGGTTTA
42051265 GGGTTTA
1 GGGTTTA
* *
42051272 GGTTTTG
1 GGGTTTA
42051279 GGGTTT
1 GGGTTT
42051285 CGGGGTTTCC
Statistics
Matches: 83, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
6 6 0.07
7 63 0.76
8 14 0.17
ACGTcount: A:0.07, C:0.02, G:0.50, T:0.41
Consensus pattern (7 bp):
GGGTTTA
Found at i:42052066 original size:18 final size:19
Alignment explanation
Indices: 42052043--42052078 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
42052033 GTTGTGTTAT
42052043 TGTTG-TTACTTGAACTTA
1 TGTTGTTTACTTGAACTTA
42052061 TGTTGTTTACTTGAACTT
1 TGTTGTTTACTTGAACTT
42052079 TTGCGCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.19, C:0.11, G:0.17, T:0.53
Consensus pattern (19 bp):
TGTTGTTTACTTGAACTTA
Found at i:42053757 original size:20 final size:21
Alignment explanation
Indices: 42053728--42053771 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
42053718 TTTCCTGATA
*
42053728 TTTTCATTCTT-TCTCTTTTG
1 TTTTCATTCTTCTCTCTTCTG
*
42053748 TTTTCCTTCTTCTCTCTTCTG
1 TTTTCATTCTTCTCTCTTCTG
42053769 TTT
1 TTT
42053772 CAGATCTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.02, C:0.25, G:0.05, T:0.68
Consensus pattern (21 bp):
TTTTCATTCTTCTCTCTTCTG
Found at i:42056103 original size:26 final size:26
Alignment explanation
Indices: 42056067--42056120 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
42056057 ATGGTAAATA
*
42056067 CAGCACATCTTGGAACTCTTCTTGTT
1 CAGCACATCTTGGAACTCTTCTTATT
*
42056093 CAGCACATCTTGGAAGTCTTCTTATT
1 CAGCACATCTTGGAACTCTTCTTATT
42056119 CA
1 CA
42056121 TGAATTGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (26 bp):
CAGCACATCTTGGAACTCTTCTTATT
Found at i:42056408 original size:95 final size:95
Alignment explanation
Indices: 42056245--42056435 Score: 382
Period size: 95 Copynumber: 2.0 Consensus size: 95
42056235 CTCGATCGTC
42056245 ACGGTGGTTGTCACGGAGGACATCGCTGATGACGATCTGTTCGTGGTGCCTATCGCCGTCGGTCG
1 ACGGTGGTTGTCACGGAGGACATCGCTGATGACGATCTGTTCGTGGTGCCTATCGCCGTCGGTCG
42056310 AACCATCGCAGGAGATTATCACCGTTCAAT
66 AACCATCGCAGGAGATTATCACCGTTCAAT
42056340 ACGGTGGTTGTCACGGAGGACATCGCTGATGACGATCTGTTCGTGGTGCCTATCGCCGTCGGTCG
1 ACGGTGGTTGTCACGGAGGACATCGCTGATGACGATCTGTTCGTGGTGCCTATCGCCGTCGGTCG
42056405 AACCATCGCAGGAGATTATCACCGTTCAAT
66 AACCATCGCAGGAGATTATCACCGTTCAAT
42056435 A
1 A
42056436 ATTCTTCCTT
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 96 1.00
ACGTcount: A:0.20, C:0.25, G:0.29, T:0.25
Consensus pattern (95 bp):
ACGGTGGTTGTCACGGAGGACATCGCTGATGACGATCTGTTCGTGGTGCCTATCGCCGTCGGTCG
AACCATCGCAGGAGATTATCACCGTTCAAT
Found at i:42057571 original size:19 final size:21
Alignment explanation
Indices: 42057533--42057577 Score: 67
Period size: 19 Copynumber: 2.2 Consensus size: 21
42057523 TTTAAAAGTA
*
42057533 GCATTAAAAAAATTGTCCGTT
1 GCATTAAAAAAATTGACCGTT
42057554 GCATT-AAAAAA-TGACCGTT
1 GCATTAAAAAAATTGACCGTT
42057573 GCATT
1 GCATT
42057578 TACTGCTCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.52
20 6 0.26
21 5 0.22
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.31
Consensus pattern (21 bp):
GCATTAAAAAAATTGACCGTT
Found at i:42058439 original size:12 final size:12
Alignment explanation
Indices: 42058422--42058447 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42058412 GTTGAATCTG
42058422 TTACTTCTTTCA
1 TTACTTCTTTCA
42058434 TTACTTCTTTCA
1 TTACTTCTTTCA
42058446 TT
1 TT
42058448 GGTAGTGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.23, G:0.00, T:0.62
Consensus pattern (12 bp):
TTACTTCTTTCA
Found at i:42060754 original size:14 final size:13
Alignment explanation
Indices: 42060717--42060768 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
42060707 GGGTCATAAA
*
42060717 TTTAGGGTTTTGAG
1 TTTAGGGGTTTG-G
*
42060731 ATTTATGGGTTGTGG
1 -TTTAGGGGTT-TGG
42060746 TTTAGGGGTTTGG
1 TTTAGGGGTTTGG
42060759 TTT-GGGGTTT
1 TTTAGGGGTTT
42060769 TAAGGTGTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
12 7 0.21
13 6 0.18
14 9 0.27
15 9 0.27
16 2 0.06
ACGTcount: A:0.10, C:0.00, G:0.40, T:0.50
Consensus pattern (13 bp):
TTTAGGGGTTTGG
Found at i:42060810 original size:15 final size:14
Alignment explanation
Indices: 42060790--42060848 Score: 73
Period size: 14 Copynumber: 4.1 Consensus size: 14
42060780 GGCTTGGGGG
42060790 TTAGGGTTTGAGGTT
1 TTAGGGTTTG-GGTT
42060805 TTAGGGTTTGGGTT
1 TTAGGGTTTGGGTT
* * *
42060819 ATGGGGTTTGGGGT
1 TTAGGGTTTGGGTT
42060833 TTAGGGTTTAGGGTT
1 TTAGGGTTT-GGGTT
42060848 T
1 T
42060849 GGGGCTTGGG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
14 22 0.59
15 15 0.41
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (14 bp):
TTAGGGTTTGGGTT
Found at i:42060817 original size:21 final size:21
Alignment explanation
Indices: 42060786--42060858 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
42060776 TGAAGGCTTG
* *
42060786 GGGGTTAGGGTTTGAGGTTTT
1 GGGGTTTGGGTTTGAGGGTTT
*
42060807 AGGGTTTGGGTTATG-GGGTTT
1 GGGGTTTGGGTT-TGAGGGTTT
42060828 GGGGTTTAGGGTTT-AGGGTTT
1 GGGGTTT-GGGTTTGAGGGTTT
*
42060849 GGGGCTTGGG
1 GGGGTTTGGG
42060859 GCTCGGGTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
20 3 0.07
21 34 0.77
22 7 0.16
ACGTcount: A:0.08, C:0.01, G:0.51, T:0.40
Consensus pattern (21 bp):
GGGGTTTGGGTTTGAGGGTTT
Found at i:42060823 original size:7 final size:6
Alignment explanation
Indices: 42060787--42060894 Score: 54
Period size: 7 Copynumber: 16.0 Consensus size: 6
42060777 GAAGGCTTGG
*
42060787 GGGTTA GGGTTT GAGGTTTT AGGGTTT GGGTTAT GGGGTTT GGGGTTT
1 GGGTTT GGGTTT G-GG-TTT -GGGTTT GGGTT-T -GGGTTT -GGGTTT
* * * * *
42060835 AGGGTTT AGGGTTT GGGGCTTG GGGCTC GGGTTT CGGGCTT GGGTTT CGGGTTC
1 -GGGTTT -GGGTTT -GGG-TTT GGGTTT GGGTTT -GGGTTT GGGTTT -GGGTTT
42060889 GGGTTT
1 GGGTTT
42060895 CGGGGCTCGG
Statistics
Matches: 82, Mismatches: 12, Indels: 16
0.75 0.11 0.15
Matches are distributed among these distances:
6 26 0.32
7 43 0.52
8 12 0.15
9 1 0.01
ACGTcount: A:0.06, C:0.06, G:0.48, T:0.40
Consensus pattern (6 bp):
GGGTTT
Found at i:42060825 original size:8 final size:7
Alignment explanation
Indices: 42060783--42060859 Score: 66
Period size: 7 Copynumber: 10.9 Consensus size: 7
42060773 GTGTGAAGGC
*
42060783 TTGGGGG
1 TTGGGGT
*
42060790 TTAGGGT
1 TTGGGGT
*
42060797 TTGAGGTT
1 TTG-GGGT
*
42060805 TTAGGGT
1 TTGGGGT
42060812 TT-GGGT
1 TTGGGGT
42060818 TATGGGGT
1 T-TGGGGT
42060826 TTGGGGT
1 TTGGGGT
*
42060833 TTAGGGT
1 TTGGGGT
*
42060840 TTAGGGT
1 TTGGGGT
*
42060847 TTGGGGC
1 TTGGGGT
42060854 TTGGGG
1 TTGGGG
42060860 CTCGGGTTTC
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
6 5 0.09
7 43 0.74
8 10 0.17
ACGTcount: A:0.08, C:0.01, G:0.51, T:0.40
Consensus pattern (7 bp):
TTGGGGT
Found at i:42060879 original size:13 final size:13
Alignment explanation
Indices: 42060857--42060898 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
42060847 TTGGGGCTTG
*
42060857 GGGCTCGGGTTTC
1 GGGCTTGGGTTTC
42060870 GGGCTTGGGTTTC
1 GGGCTTGGGTTTC
42060883 GGG-TTCGGGTTTC
1 GGGCTT-GGGTTTC
42060896 GGG
1 GGG
42060899 GCTCGGTGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 2 0.07
13 25 0.93
ACGTcount: A:0.00, C:0.17, G:0.50, T:0.33
Consensus pattern (13 bp):
GGGCTTGGGTTTC
Found at i:42060884 original size:20 final size:20
Alignment explanation
Indices: 42060812--42060891 Score: 72
Period size: 20 Copynumber: 4.0 Consensus size: 20
42060802 GTTTTAGGGT
* * *
42060812 TTGGGTTATGGGGTTTGGGGT
1 TTGGGTT-TCGGGTTTCGGGC
* *
42060833 TTAGGGTTTAGGGTTTGGGGC
1 TT-GGGTTTCGGGTTTCGGGC
**
42060854 TTGGGGCTCGGGTTTCGGGC
1 TTGGGTTTCGGGTTTCGGGC
42060874 TTGGGTTTCGGG-TTCGGG
1 TTGGGTTTCGGGTTTCGGG
42060892 TTTCGGGGCT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
19 6 0.12
20 24 0.48
21 15 0.30
22 5 0.10
ACGTcount: A:0.04, C:0.09, G:0.50, T:0.38
Consensus pattern (20 bp):
TTGGGTTTCGGGTTTCGGGC
Found at i:42060896 original size:7 final size:7
Alignment explanation
Indices: 42060808--42060898 Score: 64
Period size: 7 Copynumber: 13.4 Consensus size: 7
42060798 TGAGGTTTTA
42060808 GGGTTT-
1 GGGTTTC
*
42060814 GGGTTATG
1 GGGTT-TC
*
42060822 GGGTTTG
1 GGGTTTC
*
42060829 GGGTTTA
1 GGGTTTC
*
42060836 GGGTTTA
1 GGGTTTC
*
42060843 GGGTTTG
1 GGGTTTC
*
42060850 GGGCTT-
1 GGGTTTC
**
42060856 GGGGCTC
1 GGGTTTC
42060863 GGGTTTC
1 GGGTTTC
*
42060870 GGGCTT-
1 GGGTTTC
42060876 GGGTTTC
1 GGGTTTC
42060883 GGG-TTC
1 GGGTTTC
42060889 GGGTTTC
1 GGGTTTC
42060896 GGG
1 GGG
42060899 GCTCGGTGCT
Statistics
Matches: 71, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
6 20 0.28
7 46 0.65
8 5 0.07
ACGTcount: A:0.03, C:0.09, G:0.51, T:0.37
Consensus pattern (7 bp):
GGGTTTC
Found at i:42060904 original size:7 final size:7
Alignment explanation
Indices: 42060894--42061019 Score: 91
Period size: 7 Copynumber: 18.7 Consensus size: 7
42060884 GGTTCGGGTT
42060894 TCGGGGC
1 TCGGGGC
*
42060901 TCGGTGC
1 TCGGGGC
42060908 TCGGGGC
1 TCGGGGC
*
42060915 TCGGGGG
1 TCGGGGC
*
42060922 TCGAGGC
1 TCGGGGC
*
42060929 TCGGGGG
1 TCGGGGC
42060936 TCGGGG-
1 TCGGGGC
42060942 TC-GGG-
1 TCGGGGC
** *
42060947 TCTAGGT
1 TCGGGGC
42060954 TCGGGG-
1 TCGGGGC
**
42060960 TTTGGG-
1 TCGGGGC
**
42060966 TTTGGGC
1 TCGGGGC
42060973 TCGGGGC
1 TCGGGGC
42060980 TCGGGGC
1 TCGGGGC
42060987 TCGGGGC
1 TCGGGGC
*
42060994 TCGGGGT
1 TCGGGGC
*
42061001 TCGGGGT
1 TCGGGGC
*
42061008 TCGGGGT
1 TCGGGGC
42061015 TCGGG
1 TCGGG
Statistics
Matches: 101, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
5 5 0.05
6 14 0.14
7 82 0.81
ACGTcount: A:0.02, C:0.20, G:0.56, T:0.23
Consensus pattern (7 bp):
TCGGGGC
Done.