Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3
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: 6198200
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 200361 characters in sequence are not A, C, G, or T
File 4 of 32
Found at i:349951 original size:15 final size:15
Alignment explanation
Indices: 349931--349977 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
349921 TACAAATTAG
349931 ATAAAATTATTAATA
1 ATAAAATTATTAATA
* *
349946 ATAAAAATATTTATA
1 ATAAAATTATTAATA
349961 ATAATAATT-TTAA-A
1 ATAA-AATTATTAATA
349975 ATA
1 ATA
349978 TAATAACTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.15
15 20 0.74
16 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAAAATTATTAATA
Found at i:351595 original size:24 final size:24
Alignment explanation
Indices: 351554--351599 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
351544 CTAATCAAAA
351554 TAATTTTTTAAAATAATTAAAATT
1 TAATTTTTTAAAATAATTAAAATT
*
351578 TAATTATTTTTAAA-AATTAAAA
1 TAATT-TTTTAAAATAATTAAAA
351600 AAAAAATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TAATTTTTTAAAATAATTAAAATT
Found at i:352221 original size:32 final size:32
Alignment explanation
Indices: 352161--352241 Score: 101
Period size: 32 Copynumber: 2.5 Consensus size: 32
352151 TTTAATTAAA
* * * *
352161 ATATAAAATGATAATATGAATATTTTAAAATTT
1 ATATAATATGA-ATTATTAATATATTAAAATTT
352194 ATATAATATGAATTATTAATATATTAAAATTT
1 ATATAATATGAATTATTAATATATTAAAATTT
*
352226 ATA-AATATAAATTATT
1 ATATAATATGAATTATT
352242 TTAAATATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
31 12 0.28
32 21 0.49
33 10 0.23
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (32 bp):
ATATAATATGAATTATTAATATATTAAAATTT
Found at i:352246 original size:16 final size:16
Alignment explanation
Indices: 352190--352255 Score: 57
Period size: 16 Copynumber: 4.1 Consensus size: 16
352180 ATATTTTAAA
352190 ATTTATATAATATGAATT
1 ATTTATA-AATAT-AATT
* * *
352208 ATTAATATAT-TAA-A
1 ATTTATAAATATAATT
352222 ATTTATAAATATAAATT
1 ATTTATAAATAT-AATT
352239 ATTT-TAAATATAATT
1 ATTTATAAATATAATT
352254 AT
1 AT
352256 AATAAAATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
14 8 0.21
15 9 0.23
16 10 0.26
17 6 0.15
18 6 0.15
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
ATTTATAAATATAATT
Found at i:352260 original size:25 final size:24
Alignment explanation
Indices: 352243--352294 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
352233 TAAATTATTT
352243 TAAATATAATTATAATAAAATAAAA
1 TAAATATAA-TATAATAAAATAAAA
*
352268 TAAATATAATATAATATAATATAAA
1 TAAATATAATATAATAAAATA-AAA
352293 TA
1 TA
352295 TATAAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 11 0.44
25 14 0.56
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
TAAATATAATATAATAAAATAAAA
Found at i:352263 original size:16 final size:15
Alignment explanation
Indices: 352244--352296 Score: 63
Period size: 16 Copynumber: 3.5 Consensus size: 15
352234 AAATTATTTT
352244 AAATATAATTATAATA
1 AAATATAA-TATAATA
*
352260 AAATAAAATA-AATA
1 AAATATAATATAATA
*
352274 TAATATAATATAATA
1 AAATATAATATAATA
352289 TAAATATA
1 -AAATATA
352297 TAAATTATCT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
14 12 0.39
15 6 0.19
16 13 0.42
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAATATAATATAATA
Found at i:352281 original size:21 final size:21
Alignment explanation
Indices: 352257--352296 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
352247 TATAATTATA
352257 ATAAAATAAAATAAATATAAT
1 ATAAAATAAAATAAATATAAT
* *
352278 ATAATATAATATAAATATA
1 ATAAAATAAAATAAATATA
352297 TAAATTATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAAAATAAAATAAATATAAT
Found at i:357576 original size:19 final size:21
Alignment explanation
Indices: 357540--357582 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
357530 ATTTTTTATT
*
357540 TATATATTTATTAATAAAGAA
1 TATATATTTATTAATAAAAAA
*
357561 TATAT-TTTA-TATTAAAAAA
1 TATATATTTATTAATAAAAAA
357580 TAT
1 TAT
357583 TTCAAAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 11 0.55
20 4 0.20
21 5 0.25
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
TATATATTTATTAATAAAAAA
Found at i:358657 original size:22 final size:23
Alignment explanation
Indices: 358613--358668 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 23
358603 TTTAATTTTT
* *
358613 ATATTAAAAA-TATAATCATTTA
1 ATATTAAAAATTATAATAAATTA
358635 ATATTAAAAATTATAA-AAATTA
1 ATATTAAAAATTATAATAAATTA
*
358657 A-ATTAATAATTA
1 ATATTAAAAATTA
358669 ATATTTAACA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 10 0.33
22 15 0.50
23 5 0.17
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
ATATTAAAAATTATAATAAATTA
Found at i:358735 original size:2 final size:2
Alignment explanation
Indices: 358728--358753 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
358718 ACATTCTAGC
358728 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
358754 GATAATCACC
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:358878 original size:3 final size:3
Alignment explanation
Indices: 358870--358911 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
358860 AACAAAACAT
358870 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
358912 ATCAAAGTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:359494 original size:5 final size:5
Alignment explanation
Indices: 359486--359536 Score: 50
Period size: 5 Copynumber: 10.2 Consensus size: 5
359476 TTATTGTATG
* * **
359486 AAAAT AAAAT AAAAT -AATT ATAAT AATAAT TTAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AA-AAT AAAAT AAAAT AAAAT AAAAT
359536 A
1 A
359537 GTTATGATAT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
4 3 0.08
5 30 0.83
6 3 0.08
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (5 bp):
AAAAT
Found at i:359648 original size:38 final size:37
Alignment explanation
Indices: 359606--359702 Score: 99
Period size: 36 Copynumber: 2.5 Consensus size: 37
359596 TTATCAAAAA
*
359606 TTAAAAAATTATTTAATAAAAAATATTGAA-TAATTATT
1 TTAAAAAATTATTTAATAAAAAATA--AAATTAATTATT
** *
359644 TTAAAATTTTATTAAAT-AAAAATAAAATTAATTATT
1 TTAAAAAATTATTTAATAAAAAATAAAATTAATTATT
359680 TTAAAAAATAAATATTTAATAAA
1 TTAAAAAAT---TATTTAATAAA
359703 TTAAATAATT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
35 2 0.04
36 15 0.32
37 7 0.15
38 14 0.30
39 7 0.15
40 2 0.04
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (37 bp):
TTAAAAAATTATTTAATAAAAAATAAAATTAATTATT
Found at i:359686 original size:16 final size:15
Alignment explanation
Indices: 359667--359709 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
359657 AAATAAAAAT
*
359667 AAAATTAATTATTTTA
1 AAAATTAAATA-TTTA
*
359683 AAAAATAAATATTTA
1 AAAATTAAATATTTA
359698 ATAAATTAAATA
1 A-AAATTAAATA
359710 ATTATATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 5 0.22
16 18 0.78
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAATTAAATATTTA
Found at i:360761 original size:19 final size:18
Alignment explanation
Indices: 360719--360776 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
360709 TGTTTGAATT
360719 ATATTTATTTTATTTTTTA
1 ATATTTATTTTA-TTTTTA
360738 ATATTATATTTTA-TTTTA
1 ATATT-TATTTTATTTTTA
* *
360756 ATTATTTTTTATTATATTTA
1 A-TATTTATT-TTATTTTTA
360776 A
1 A
360777 AACTATCAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
18 9 0.27
19 12 0.36
20 12 0.36
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
ATATTTATTTTATTTTTA
Found at i:361280 original size:2 final size:2
Alignment explanation
Indices: 361268--361301 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
361258 CCCCGAAAGC
361268 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
361302 GAGAGAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:361306 original size:2 final size:2
Alignment explanation
Indices: 361301--361344 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
361291 ATATATATAT
361301 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
361343 AG
1 AG
361345 TATACATATC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:362086 original size:38 final size:38
Alignment explanation
Indices: 362051--362188 Score: 177
Period size: 38 Copynumber: 3.6 Consensus size: 38
362041 AGTTGACGGT
* * * * *
362051 TAGAGAATTCAATTTAAAATTGATTGGCGGTTGACGAT
1 TAGAGAATTCAATTTGAAATTGACTGACGGCTGACGAC
* * *
362089 TAGAGAATTCAATTTGAAATTGGCTGACGGCTAACGGC
1 TAGAGAATTCAATTTGAAATTGACTGACGGCTGACGAC
* *
362127 TAGAGAATTCAATTTGGAATTGACCGACGGCTGACGAC
1 TAGAGAATTCAATTTGAAATTGACTGACGGCTGACGAC
*
362165 TAGAGAATTCAATTTGGAATTGAC
1 TAGAGAATTCAATTTGAAATTGAC
362189 CGGTGGCTGG
Statistics
Matches: 87, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 87 1.00
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (38 bp):
TAGAGAATTCAATTTGAAATTGACTGACGGCTGACGAC
Found at i:362136 original size:76 final size:76
Alignment explanation
Indices: 362046--362186 Score: 201
Period size: 76 Copynumber: 1.9 Consensus size: 76
362036 GAATTAGTTG
* ** * * *
362046 ACGGTTAGAGAATTCAATTTAAAATTGATTGGCGGTTGACGATTAGAGAATTCAATTTGAAATTG
1 ACGGCTAGAGAATTCAATTTAAAATTGACCGACGGCTGACGACTAGAGAATTCAATTTGAAATTG
362111 GCTGACGGCTA
66 GCTGACGGCTA
** *
362122 ACGGCTAGAGAATTCAATTTGGAATTGACCGACGGCTGACGACTAGAGAATTCAATTTGGAATTG
1 ACGGCTAGAGAATTCAATTTAAAATTGACCGACGGCTGACGACTAGAGAATTCAATTTGAAATTG
362187 ACCGGTGGCT
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
76 56 1.00
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.29
Consensus pattern (76 bp):
ACGGCTAGAGAATTCAATTTAAAATTGACCGACGGCTGACGACTAGAGAATTCAATTTGAAATTG
GCTGACGGCTA
Found at i:362206 original size:38 final size:38
Alignment explanation
Indices: 362044--362212 Score: 176
Period size: 38 Copynumber: 4.4 Consensus size: 38
362034 TTGAATTAGT
* ** ** * *
362044 TGACGGTTAGAGAATTCAATTTAAAATTGATTGGCGGT
1 TGACGGCTAGAGAATTCAATTTGGAATTGACCGACGGC
** * * *
362082 TGACGATTAGAGAATTCAATTTGAAATTGGCTGACGGC
1 TGACGGCTAGAGAATTCAATTTGGAATTGACCGACGGC
*
362120 TAACGGCTAGAGAATTCAATTTGGAATTGACCGACGGC
1 TGACGGCTAGAGAATTCAATTTGGAATTGACCGACGGC
* **
362158 TGACGACTAGAGAATTCAATTTGGAATTGACCGGTGGC
1 TGACGGCTAGAGAATTCAATTTGGAATTGACCGACGGC
**
362196 TGGTGGCTAGAGAATTC
1 TGACGGCTAGAGAATTC
362213 CAAATTGAAC
Statistics
Matches: 112, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 112 1.00
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (38 bp):
TGACGGCTAGAGAATTCAATTTGGAATTGACCGACGGC
Found at i:366807 original size:38 final size:38
Alignment explanation
Indices: 366758--366935 Score: 205
Period size: 38 Copynumber: 4.7 Consensus size: 38
366748 TTGAATTAGT
* *
366758 TGACGGTTAGAGAATTCAATTTGAAATTGACTGACGGC
1 TGACGGCTAGAGAATTCAATTTGAAATTGACTGGCGGC
366796 TGACGGCTAGAGAATTCAATTTGAAATT-AGCTGGCGGC
1 TGACGGCTAGAGAATTCAATTTGAAATTGA-CTGGCGGC
* * * *
366834 TGACGGCTAGAGAATTCAATTTGGAATTGGCCGGCAGC
1 TGACGGCTAGAGAATTCAATTTGAAATTGACTGGCGGC
* * * * *
366872 TGACGACTAGAGAATTCAATTTGGAATTGGCCGGTGGC
1 TGACGGCTAGAGAATTCAATTTGAAATTGACTGGCGGC
** *
366910 TGGTGGCTAGAGAATTCCAAATTGAA
1 TGACGGCTAGAGAATT-CAATTTGAA
366936 CTCTCTTTGA
Statistics
Matches: 123, Mismatches: 14, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
37 1 0.01
38 115 0.93
39 7 0.06
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.26
Consensus pattern (38 bp):
TGACGGCTAGAGAATTCAATTTGAAATTGACTGGCGGC
Found at i:367592 original size:29 final size:29
Alignment explanation
Indices: 367537--367604 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 29
367527 AAATTTTATA
*
367537 AAAAATATATTTATTTCTATAACGTTT-G
1 AAAAATATATTTATTTCTATAAAGTTTGG
*
367565 AAAAATACTTATTTATTT-TTTAAAGTTTGG
1 AAAAATA--TATTTATTTCTATAAAGTTTGG
*
367595 AAAAAAATAT
1 AAAAATATAT
367605 AATTACCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
28 10 0.29
29 8 0.24
30 16 0.47
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (29 bp):
AAAAATATATTTATTTCTATAAAGTTTGG
Found at i:367750 original size:26 final size:27
Alignment explanation
Indices: 367721--367779 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
367711 TTAGTTAATC
*
367721 TTAAAATT-TTTTTAA-TTATTATTAAA
1 TTAAAATTATTATTAAGTTA-TATTAAA
*
367747 TT-AAATTATTATTAAGTTATATTTAA
1 TTAAAATTATTATTAAGTTATATTAAA
367773 TTAAAAT
1 TTAAAAT
367780 GTATGTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
25 5 0.18
26 16 0.57
27 7 0.25
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (27 bp):
TTAAAATTATTATTAAGTTATATTAAA
Found at i:368386 original size:19 final size:17
Alignment explanation
Indices: 368362--368405 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 17
368352 GATAATAATT
*
368362 AAAAATAATTTTATAGTTA
1 AAAAATAATTTT-GAG-TA
368381 AAAAAT-ATTTTGAGTA
1 AAAAATAATTTTGAGTA
368397 AAAAATAAT
1 AAAAATAAT
368406 GAAAAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 8 0.35
17 4 0.17
18 5 0.22
19 6 0.26
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (17 bp):
AAAAATAATTTTGAGTA
Found at i:370978 original size:35 final size:35
Alignment explanation
Indices: 370909--370980 Score: 87
Period size: 34 Copynumber: 2.1 Consensus size: 35
370899 ATATAATTTT
*
370909 TTTTTAATTTAAATTATTATTTAATAATAAAAATA
1 TTTTTAATTTAAATTATAATTTAATAATAAAAATA
370944 TTTTT-ATTTAAATT-TAATTATAA-AATATATAAATA
1 TTTTTAATTTAAATTATAATT-TAATAATA-A-AAATA
370979 TT
1 TT
370981 AATATATGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
33 8 0.24
34 13 0.39
35 12 0.36
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (35 bp):
TTTTTAATTTAAATTATAATTTAATAATAAAAATA
Found at i:371510 original size:38 final size:38
Alignment explanation
Indices: 371467--371605 Score: 163
Period size: 38 Copynumber: 3.7 Consensus size: 38
371457 GCCAACCACT
* *
371467 AGCCAATTCTAAATTAAATTCTCTAGTTGCCAGCTACC
1 AGCCAATTCCAAATTAAATTCTCTAGTTGTCAGCTACC
* * * *
371505 GGCCAATTCCAAATTGAATTCTCTAGTCGTCAGCCACC
1 AGCCAATTCCAAATTAAATTCTCTAGTTGTCAGCTACC
** *
371543 AGCCAATTCCAAATTAAATTCTCTAACTGTCAGCTGCC
1 AGCCAATTCCAAATTAAATTCTCTAGTTGTCAGCTACC
**
371581 AGCCAATTTTAAA-TATAATTCTCTA
1 AGCCAATTCCAAATTA-AATTCTCTA
371606 ACCGTCAACC
Statistics
Matches: 85, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
37 2 0.02
38 83 0.98
ACGTcount: A:0.32, C:0.27, G:0.11, T:0.31
Consensus pattern (38 bp):
AGCCAATTCCAAATTAAATTCTCTAGTTGTCAGCTACC
Found at i:371577 original size:76 final size:76
Alignment explanation
Indices: 371451--371605 Score: 195
Period size: 76 Copynumber: 2.0 Consensus size: 76
371441 TCCCTAGCCA
* * ** *
371451 CTAGTCGCCAACCACTAGCCAATTCTAAATTAAATTCTCTAGTTGCCAGCTACCGGCCAATTCCA
1 CTAGTCGCCAACCACCAGCCAATTCCAAATTAAATTCTCTAACTGCCAGCTACCAGCCAATTCCA
371516 AAT-TGAATTCT
66 AATAT-AATTCT
* * * * **
371527 CTAGTCGTCAGCCACCAGCCAATTCCAAATTAAATTCTCTAACTGTCAGCTGCCAGCCAATTTTA
1 CTAGTCGCCAACCACCAGCCAATTCCAAATTAAATTCTCTAACTGCCAGCTACCAGCCAATTCCA
371592 AATATAATTCT
66 AATATAATTCT
371603 CTA
1 CTA
371606 ACCGTCAACC
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
76 66 0.99
77 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.30
Consensus pattern (76 bp):
CTAGTCGCCAACCACCAGCCAATTCCAAATTAAATTCTCTAACTGCCAGCTACCAGCCAATTCCA
AATATAATTCT
Found at i:379227 original size:13 final size:13
Alignment explanation
Indices: 379209--379233 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
379199 ACACATAGTA
379209 TGTATCGATACAT
1 TGTATCGATACAT
379222 TGTATCGATACA
1 TGTATCGATACA
379234 CCATAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:379230 original size:32 final size:33
Alignment explanation
Indices: 379189--379256 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
379179 GTAGCCAAAC
**
379189 TTGTATCGATACA-CATAGTATGTATCGATACA
1 TTGTATCGATACACCATAAAATGTATCGATACA
379221 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACACCATAAAATGTATCGATACA
379254 TTG
1 TTG
379257 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACACCATAAAATGTATCGATACA
Found at i:385764 original size:20 final size:20
Alignment explanation
Indices: 385739--385776 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
385729 GTAAAAAGAC
385739 AGAATGCATCGATACATTAA
1 AGAATGCATCGATACATTAA
*
385759 AGAATGTATCGATACATT
1 AGAATGCATCGATACATT
385777 CATACATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (20 bp):
AGAATGCATCGATACATTAA
Found at i:386382 original size:127 final size:128
Alignment explanation
Indices: 386232--386486 Score: 503
Period size: 127 Copynumber: 2.0 Consensus size: 128
386222 TTAGAGTAAG
386232 AAAATTATTTTGTTGGATTCGACACCTACCAAATTTCTGTGTTATTGCCGAGGATCAAACCTAGG
1 AAAATTATTTTGTTGGATTCGACACCTACCAAATTTCTGTGTTATTGCCGAGGATCAAACCTAGG
386297 ATGCCCGCATGACAAGCGAGAATACTTACCATTATACTAACCAAATTTTGGC-GCTGTTGCCA
66 ATGCCCGCATGACAAGCGAGAATACTTACCATTATACTAACCAAATTTTGGCTGCTGTTGCCA
386359 AAAATTATTTTGTTGGATTCGACACCTACCAAATTTCTGTGTTATTGCCGAGGATCAAACCTAGG
1 AAAATTATTTTGTTGGATTCGACACCTACCAAATTTCTGTGTTATTGCCGAGGATCAAACCTAGG
386424 ATGCCCGCATGACAAGCGAGAATACTTACCATTATACTAACCAAATTTTGGCTGCTGTTGCCA
66 ATGCCCGCATGACAAGCGAGAATACTTACCATTATACTAACCAAATTTTGGCTGCTGTTGCCA
386487 GGGAGTAGTG
Statistics
Matches: 127, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
127 117 0.92
128 10 0.08
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (128 bp):
AAAATTATTTTGTTGGATTCGACACCTACCAAATTTCTGTGTTATTGCCGAGGATCAAACCTAGG
ATGCCCGCATGACAAGCGAGAATACTTACCATTATACTAACCAAATTTTGGCTGCTGTTGCCA
Found at i:387408 original size:74 final size:74
Alignment explanation
Indices: 387287--387434 Score: 260
Period size: 74 Copynumber: 2.0 Consensus size: 74
387277 ACCTTTTATG
** *
387287 AATATTGAGAGAGATTTAAACAGTTTTGTGCAAGTTGTCATCAACATCAAATTCTTAAACAACTG
1 AATATTGAGAGAGATTTAAACAGTTTTGTGCAAGTTGTCATCAACATCAAATTCCCAAACAACCG
387352 TTGATCCAA
66 TTGATCCAA
*
387361 AATATTTAGAGAGATTTAAACAGTTTTGTGCAAGTTGTCATCAACATCAAATTCCCAAACAACCG
1 AATATTGAGAGAGATTTAAACAGTTTTGTGCAAGTTGTCATCAACATCAAATTCCCAAACAACCG
387426 TTGATCCAA
66 TTGATCCAA
387435 TATTTTTATG
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 70 1.00
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (74 bp):
AATATTGAGAGAGATTTAAACAGTTTTGTGCAAGTTGTCATCAACATCAAATTCCCAAACAACCG
TTGATCCAA
Found at i:394550 original size:18 final size:18
Alignment explanation
Indices: 394513--394550 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
394503 ATTTATTTTA
*
394513 TTTTAATTTATTTTGCAT
1 TTTTAATTTATTTTGAAT
394531 TTTTAATTTATCTTT-AAT
1 TTTTAATTTAT-TTTGAAT
394549 TT
1 TT
394551 ATCTATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TTTTAATTTATTTTGAAT
Found at i:398925 original size:3 final size:3
Alignment explanation
Indices: 398917--398953 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
398907 AACAAAACAT
398917 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
398954 GAATCAAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:399660 original size:15 final size:16
Alignment explanation
Indices: 399640--399673 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
399630 TTAAACAGTT
399640 AAATAA-TTTATAATA
1 AAATAATTTTATAATA
399655 AAATAATTTTTATAATA
1 AAATAA-TTTTATAATA
399672 AA
1 AA
399674 TCAAACATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
17 11 0.65
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATAATTTTATAATA
Found at i:400883 original size:18 final size:18
Alignment explanation
Indices: 400843--400896 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
400833 TATATATTTG
*
400843 TATTATA-TTTAATTTACA
1 TATTATATTTTATTTTA-A
400861 T-TTATATTATT-TTTTAA
1 TATTATATT-TTATTTTAA
400878 TATTATATTTTATTTTAA
1 TATTATATTTTATTTTAA
400896 T
1 T
400897 TAATTTTGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
17 9 0.29
18 20 0.65
19 2 0.06
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
TATTATATTTTATTTTAA
Found at i:402368 original size:7 final size:7
Alignment explanation
Indices: 402356--402385 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
402346 AATATGATAT
402356 TTATTAA
1 TTATTAA
402363 TTATTAA
1 TTATTAA
402370 TTATTAA
1 TTATTAA
402377 TTATTAA
1 TTATTAA
402384 TT
1 TT
402386 TTTATTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TTATTAA
Found at i:403374 original size:19 final size:16
Alignment explanation
Indices: 403319--403378 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 16
403309 ATATCTATCA
403319 TAATTTA-A-ATGAAT
1 TAATTTATATATGAAT
403333 TAATTTATATATGAAT
1 TAATTTATATATGAAT
*
403349 TAGATTTATGTATTGATAT
1 TA-ATTTATATA-TGA-AT
403368 TATATTTATAT
1 TA-ATTTATAT
403379 TTTATATCTA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
14 7 0.18
15 1 0.03
16 8 0.21
17 8 0.21
18 3 0.08
19 11 0.29
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (16 bp):
TAATTTATATATGAAT
Found at i:403383 original size:13 final size:13
Alignment explanation
Indices: 403367--403400 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
403357 TGTATTGATA
403367 TTATATTTATATT
1 TTATATTTATATT
*
403380 TTATATCTATATT
1 TTATATTTATATT
403393 TTAT-TTTA
1 TTATATTTA
403401 AAAATTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 3 0.16
13 16 0.84
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (13 bp):
TTATATTTATATT
Found at i:403397 original size:18 final size:18
Alignment explanation
Indices: 403364--403400 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
403354 TTATGTATTG
403364 ATATTATATTTATATTTT
1 ATATTATATTTATATTTT
403382 ATATCTATATTT-TATTTT
1 ATAT-TATATTTATATTTT
403400 A
1 A
403401 AAAATTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (18 bp):
ATATTATATTTATATTTT
Found at i:403850 original size:16 final size:17
Alignment explanation
Indices: 403808--403855 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 17
403798 TTATAATTAA
403808 ATTTAAATAAAATATATT
1 ATTTAAAT-AAATATATT
*
403826 TTATTAAATAAATA-ATT
1 AT-TTAAATAAATATATT
403843 ATTTAAATTAAAT
1 ATTTAAA-TAAAT
403856 CCATCTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 5 0.19
17 9 0.35
18 6 0.23
19 6 0.23
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATTTAAATAAATATATT
Found at i:404309 original size:3 final size:3
Alignment explanation
Indices: 404301--404342 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
404291 AAATTTTATG
404301 ATA ATA 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 ATA ATA
404343 CCGTAAAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:404600 original size:26 final size:28
Alignment explanation
Indices: 404550--404613 Score: 96
Period size: 26 Copynumber: 2.3 Consensus size: 28
404540 ATATCACATA
*
404550 ATATAATATAAATATATATTCTAAAATTT
1 ATATAA-ATAAATATATAATCTAAAATTT
404579 ATATAAATAAATAT-TAAT-TAAAATTT
1 ATATAAATAAATATATAATCTAAAATTT
404605 ATATAAATA
1 ATATAAATA
404614 TAAAAATATT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
26 17 0.50
27 3 0.09
28 8 0.24
29 6 0.18
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (28 bp):
ATATAAATAAATATATAATCTAAAATTT
Found at i:406177 original size:2 final size:2
Alignment explanation
Indices: 406170--406196 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
406160 TATGTGGATA
406170 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 A
406197 AAGTTCATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:406279 original size:11 final size:11
Alignment explanation
Indices: 406259--406298 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
406249 TTATCTTAAC
406259 ATATA-AATAT
1 ATATATAATAT
406269 A-ATAT-ATAT
1 ATATATAATAT
406278 ATATATAATAT
1 ATATATAATAT
*
406289 ATATAGAATA
1 ATATATAATA
406299 ACGAACTGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
9 8 0.31
10 5 0.19
11 13 0.50
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (11 bp):
ATATATAATAT
Found at i:406283 original size:15 final size:15
Alignment explanation
Indices: 406259--406298 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
406249 TTATCTTAAC
406259 ATATAAATATAATAT
1 ATATAAATATAATAT
*
406274 ATATATATATAATAT
1 ATATAAATATAATAT
406289 ATATAGAATA
1 ATATA-AATA
406299 ACGAACTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 19 0.86
16 3 0.14
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (15 bp):
ATATAAATATAATAT
Found at i:407580 original size:28 final size:27
Alignment explanation
Indices: 407538--407590 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
407528 TCAATTCTCA
* *
407538 TATTATTATTTTTTATATTTAAAATTTT
1 TATTATTATTATTTA-ATATAAAATTTT
407566 TATTATTATTATTTAATATAAAATT
1 TATTATTATTATTTAATATAAAATT
407591 GGAAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (27 bp):
TATTATTATTATTTAATATAAAATTTT
Found at i:412925 original size:12 final size:12
Alignment explanation
Indices: 412864--412937 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
412854 AATTTTTTTA
412864 TAAATATAATATT
1 TAAA-ATAATATT
412877 TACAAAT-AT-TT
1 TA-AAATAATATT
*
412888 TAATAAATAATACT
1 T-A-AAATAATATT
* **
412902 TCAAATTTTATT
1 TAAAATAATATT
*
412914 TAGAATAATATT
1 TAAAATAATATT
412926 TAAAATAATATT
1 TAAAATAATATT
412938 ATTTAAAATA
Statistics
Matches: 46, Mismatches: 11, Indels: 9
0.70 0.17 0.14
Matches are distributed among these distances:
11 3 0.07
12 33 0.72
13 6 0.13
14 4 0.09
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (12 bp):
TAAAATAATATT
Found at i:412957 original size:17 final size:17
Alignment explanation
Indices: 412921--412991 Score: 64
Period size: 15 Copynumber: 4.5 Consensus size: 17
412911 ATTTAGAATA
*
412921 ATATTTAAAATA-ATAT
1 ATATTTAAAATATAAAT
412937 -TATTTAAAATATAAAT
1 ATATTTAAAATATAAAT
*
412953 ATATTT--TATATAAA-
1 ATATTTAAAATATAAAT
*
412967 ATATTT-AAATAAAAAT
1 ATATTTAAAATATAAAT
412983 AATATTTAA
1 -ATATTTAA
412992 GCATTAAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
14 6 0.13
15 24 0.53
16 3 0.07
17 11 0.24
18 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATTTAAAATATAAAT
Found at i:412961 original size:22 final size:21
Alignment explanation
Indices: 412928--412970 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
412918 ATAATATTTA
*
412928 AAATAATATTATTTAAAATAT
1 AAATAATATTATATAAAATAT
*
412949 AAATATATTTTATATAAAATAT
1 AAATA-ATATTATATAAAATAT
412971 TTAAATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AAATAATATTATATAAAATAT
Found at i:413002 original size:19 final size:17
Alignment explanation
Indices: 412917--412991 Score: 54
Period size: 17 Copynumber: 4.7 Consensus size: 17
412907 TTTTATTTAG
*
412917 AATAATATTT-AA-AAT
1 AATAATATTTAAATAAA
* *
412932 AATATTATTTAAAATATA
1 AATAATATTT-AAATAAA
* *
412950 AAT-ATATTT-TAT-AT
1 AATAATATTTAAATAAA
412964 AA-AATATTTAAATAAA
1 AATAATATTTAAATAAA
412980 AATAATATTTAA
1 AATAATATTTAA
412992 GCATTAAAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 12
0.68 0.14 0.18
Matches are distributed among these distances:
14 8 0.18
15 13 0.30
16 3 0.07
17 16 0.36
18 4 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AATAATATTTAAATAAA
Found at i:414018 original size:20 final size:21
Alignment explanation
Indices: 413965--414018 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
413955 TATTTTTATT
413965 TAAAT-TTAATTATAAAATATA
1 TAAATATT-ATTATAAAATATA
413986 TAAATATTATTATAAAA-ATA
1 TAAATATTATTATAAAATATA
*
414006 -AAATTATTTTTAT
1 TAAA-TATTATTAT
414019 TATTTTATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 3 0.10
20 11 0.37
21 14 0.47
22 2 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TAAATATTATTATAAAATATA
Found at i:415484 original size:2 final size:2
Alignment explanation
Indices: 415477--415515 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
415467 TAACTTTCTT
415477 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
415516 TTCTATTAGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:415729 original size:16 final size:17
Alignment explanation
Indices: 415704--415737 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
415694 AATCAATTTT
415704 AACTCAAAATAAT-CTA
1 AACTCAAAATAATACTA
*
415720 AACTCGAAATAATACTA
1 AACTCAAAATAATACTA
415737 A
1 A
415738 TTTAAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.56, C:0.18, G:0.03, T:0.24
Consensus pattern (17 bp):
AACTCAAAATAATACTA
Found at i:416743 original size:16 final size:16
Alignment explanation
Indices: 416705--416806 Score: 84
Period size: 16 Copynumber: 6.4 Consensus size: 16
416695 ATTTTTTAAG
*
416705 TTATTTTGATGTTCAAA
1 TTATTTTAAT-TTCAAA
* *
416722 TCATTTTAATTTCAAG
1 TTATTTTAATTTCAAA
416738 TTATTTTTAATTT-AAA
1 TTA-TTTTAATTTCAAA
* *
416754 TT-TTTCAATATCAAA
1 TTATTTTAATTTCAAA
416769 TTATTTTAAGTTT-AAA
1 TTATTTTAA-TTTCAAA
* * *
416785 TCATTTTAATTTTAAT
1 TTATTTTAATTTCAAA
416801 TTATTT
1 TTATTT
416807 CAAGTTTAAG
Statistics
Matches: 68, Mismatches: 12, Indels: 11
0.75 0.13 0.12
Matches are distributed among these distances:
14 7 0.10
15 8 0.12
16 34 0.50
17 19 0.28
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.57
Consensus pattern (16 bp):
TTATTTTAATTTCAAA
Found at i:416783 original size:31 final size:30
Alignment explanation
Indices: 416725--416794 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 30
416715 GTTCAAATCA
* *
416725 TTTTAATTTCAAGTTATTTTTAATTTAAAT
1 TTTTAATATCAAATTATTTTTAATTTAAAT
416755 TTTTCAATATCAAATTA-TTTTAAGTTTAAAT
1 TTTT-AATATCAAATTATTTTTAA-TTTAAAT
416786 CATTTTAAT
1 --TTTTAAT
416795 TTTAATTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
30 10 0.29
31 17 0.50
32 3 0.09
33 4 0.12
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.56
Consensus pattern (30 bp):
TTTTAATATCAAATTATTTTTAATTTAAAT
Found at i:416814 original size:16 final size:16
Alignment explanation
Indices: 416699--416815 Score: 71
Period size: 16 Copynumber: 7.3 Consensus size: 16
416689 CAGTTAATTT
* *
416699 TTTAAGTTATTTTGATG
1 TTTAAATTATTTT-AAG
* *
416716 TTCAAATCATTTTAA-
1 TTTAAATTATTTTAAG
*
416731 TTTCAAGTTATTTTTAA-
1 TTT-AAATTA-TTTTAAG
*
416748 TTTAAATT-TTTCAA-
1 TTTAAATTATTTTAAG
*
416762 TATCAAATTATTTTAAG
1 T-TTAAATTATTTTAAG
* *
416779 TTTAAATCATTTTAAT
1 TTTAAATTATTTTAAG
* *
416795 TTTAATTTATTTCAAG
1 TTTAAATTATTTTAAG
416811 TTTAA
1 TTTAA
416816 GTCAATTAGA
Statistics
Matches: 77, Mismatches: 18, Indels: 11
0.73 0.17 0.10
Matches are distributed among these distances:
14 6 0.08
15 8 0.10
16 43 0.56
17 20 0.26
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.55
Consensus pattern (16 bp):
TTTAAATTATTTTAAG
Found at i:417858 original size:15 final size:15
Alignment explanation
Indices: 417830--417868 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
417820 ATCATTAAAC
* *
417830 TAATAATTTTAAATAT
1 TAAT-ATTTCAAATAG
417846 TAATATTTCAAATAG
1 TAATATTTCAAATAG
417861 TAATATTT
1 TAATATTT
417869 TAATGATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (15 bp):
TAATATTTCAAATAG
Found at i:417906 original size:14 final size:14
Alignment explanation
Indices: 417887--417914 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
417877 ATATCTATTG
417887 CTAAAATATTATAT
1 CTAAAATATTATAT
417901 CTAAAATATTATAT
1 CTAAAATATTATAT
417915 TAATGTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
CTAAAATATTATAT
Found at i:417966 original size:21 final size:21
Alignment explanation
Indices: 417932--417997 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
417922 AAATATTTTA
417932 AAAAATAA-TATAT-ATTATT
1 AAAAATAATTATATAATTATT
*
417951 AAAACATAATTATATAAATATT
1 AAAA-ATAATTATATAATTATT
*
417973 TAAAAT-ATTATAATAATTATT
1 AAAAATAATTAT-ATAATTATT
417994 AAAA
1 AAAA
417998 TATTATTTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
19 4 0.10
20 9 0.23
21 18 0.46
22 8 0.21
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
AAAAATAATTATATAATTATT
Found at i:417975 original size:23 final size:22
Alignment explanation
Indices: 417921--417977 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 22
417911 ATATTAATGT
417921 TAAATATTTTAAAAAATAATATA
1 TAAATA-TTTAAAAAATAATATA
* *
417944 T-ATTA-TTAAAACATAATTATA
1 TAAATATTTAAAAAATAA-TATA
417965 TAAATATTTAAAA
1 TAAATATTTAAAA
417978 TATTATAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 10 0.36
21 5 0.18
22 6 0.21
23 7 0.25
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATATTTAAAAAATAATATA
Found at i:417998 original size:20 final size:19
Alignment explanation
Indices: 417933--418003 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 19
417923 AATATTTTAA
*
417933 AAAATAATATAT-ATTATT
1 AAAATATTATATAATTATT
*
417951 AAAACATAATTATATAAATATTT
1 -AAA-AT-ATTATATAATTA-TT
417974 AAAATATTATAATAATTATT
1 AAAATATTAT-ATAATTATT
417994 AAAATATTAT
1 AAAATATTAT
418004 TTCAATTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
19 3 0.07
20 19 0.43
21 14 0.32
22 6 0.14
23 2 0.05
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAATATTATATAATTATT
Found at i:418159 original size:30 final size:30
Alignment explanation
Indices: 418111--418188 Score: 77
Period size: 30 Copynumber: 2.5 Consensus size: 30
418101 TATCATTAAA
* * *
418111 ATTA-TAAATTATATTAATATTTTACTATAT
1 ATTATTAAATTA-AATAATACTATACTATAT
*
418141 ATTATTAAATTAAATAATACTATATTATAT
1 ATTATTAAATTAAATAATACTATACTATAT
*
418171 ATGATTAAAATATAAATA
1 ATTATT-AAAT-TAAATA
418189 TGTATATTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 23 0.57
31 11 0.28
32 6 0.15
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (30 bp):
ATTATTAAATTAAATAATACTATACTATAT
Found at i:418195 original size:30 final size:30
Alignment explanation
Indices: 418162--418220 Score: 59
Period size: 31 Copynumber: 1.9 Consensus size: 30
418152 AAATAATACT
*
418162 ATATTATATATGATTAAAATATAAATAT-GT
1 ATATTATATAT-ATTAAAATATAAATATACT
418192 ATATT-TAATAATATTCAAAATATAAATAT
1 ATATTAT-AT-ATATT-AAAATATAAATAT
418221 TTAAAAGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 1 0.04
30 10 0.38
31 15 0.58
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (30 bp):
ATATTATATATATTAAAATATAAATATACT
Found at i:425407 original size:20 final size:20
Alignment explanation
Indices: 425359--425460 Score: 73
Period size: 20 Copynumber: 5.1 Consensus size: 20
425349 GTTTGTAGTT
*
425359 TTATTTGTACAAAAACTATAAG
1 TTATTTGT--AAAAGCTATAAG
* * * *
425381 CTGTTTGTCAAAGCTGTAAG
1 TTATTTGTAAAAGCTATAAG
* *
425401 TTATTTGTGAGA-CTATAAG
1 TTATTTGTAAAAGCTATAAG
* *
425420 TTGTTTGTAAAAGCTCTAAG
1 TTATTTGTAAAAGCTATAAG
* *
425440 TTATTTGTGAGA-CTATAAG
1 TTATTTGTAAAAGCTATAAG
425459 TT
1 TT
425461 TGTAAAAACT
Statistics
Matches: 61, Mismatches: 18, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
19 23 0.38
20 32 0.52
22 6 0.10
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (20 bp):
TTATTTGTAAAAGCTATAAG
Found at i:425421 original size:19 final size:19
Alignment explanation
Indices: 425397--425460 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
425387 GTCAAAGCTG
425397 TAAGTTATTTGTGAGACTA
1 TAAGTTATTTGTGAGACTA
* * * *
425416 TAAGTTGTTTGTAAAAGCTC
1 TAAGTTATTTGTGAGA-CTA
425436 TAAGTTATTTGTGAGACTA
1 TAAGTTATTTGTGAGACTA
425455 TAAGTT
1 TAAGTT
425461 TGTAAAAACT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
19 21 0.58
20 15 0.42
ACGTcount: A:0.31, C:0.06, G:0.20, T:0.42
Consensus pattern (19 bp):
TAAGTTATTTGTGAGACTA
Found at i:425459 original size:39 final size:39
Alignment explanation
Indices: 425373--425460 Score: 149
Period size: 39 Copynumber: 2.3 Consensus size: 39
425363 TTGTACAAAA
* * *
425373 ACTATAAGCTGTTTGTCAAAGCTGTAAGTTATTTGTGAG
1 ACTATAAGTTGTTTGTAAAAGCTCTAAGTTATTTGTGAG
425412 ACTATAAGTTGTTTGTAAAAGCTCTAAGTTATTTGTGAG
1 ACTATAAGTTGTTTGTAAAAGCTCTAAGTTATTTGTGAG
425451 ACTATAAGTT
1 ACTATAAGTT
425461 TGTAAAAACT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (39 bp):
ACTATAAGTTGTTTGTAAAAGCTCTAAGTTATTTGTGAG
Found at i:427469 original size:20 final size:19
Alignment explanation
Indices: 427421--427469 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
427411 TATTATTATC
*
427421 AATTTTT-ATTGATTAAAT
1 AATTTTTAATTAATTAAAT
* *
427439 AATATTAAATTAATTTAAAT
1 AATTTTTAATTAA-TTAAAT
427459 AATTTTTAATT
1 AATTTTTAATT
427470 TTTTATATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 5 0.21
19 4 0.17
20 15 0.62
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
AATTTTTAATTAATTAAAT
Found at i:428215 original size:23 final size:24
Alignment explanation
Indices: 428189--428250 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 24
428179 AAAATTTATA
428189 AAAATATAAATAT-AATAAAATTT
1 AAAATATAAATATAAATAAAATTT
*
428212 AAAATATAAAT-TAAATAATATTT
1 AAAATATAAATATAAATAAAATTT
428235 ATTAAATATATAATAT
1 A--AAATATA-AATAT
428251 TCATATTATG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 1 0.03
23 21 0.64
25 7 0.21
26 3 0.09
27 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
AAAATATAAATATAAATAAAATTT
Found at i:428702 original size:6 final size:6
Alignment explanation
Indices: 428670--428701 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
428660 GAAATGGCCT
*
428670 CAACAG CAACAG CAACAG CAACAG CAGCAG CA
1 CAACAG CAACAG CAACAG CAACAG CAACAG CA
428702 GTTTCGTCTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.47, C:0.34, G:0.19, T:0.00
Consensus pattern (6 bp):
CAACAG
Found at i:433571 original size:18 final size:18
Alignment explanation
Indices: 433543--433585 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
433533 CAAAAATTAA
433543 AAAATAA-AATG-ATTTAT
1 AAAATAATAATGCATTT-T
433560 AAAATAATAATGCATTTT
1 AAAATAATAATGCATTTT
*
433578 ACAATAAT
1 AAAATAAT
433586 TAAATTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 7 0.30
18 12 0.52
19 4 0.17
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.35
Consensus pattern (18 bp):
AAAATAATAATGCATTTT
Found at i:434559 original size:22 final size:21
Alignment explanation
Indices: 434534--434579 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
434524 TTAATTATTC
434534 AAAATTATATC-TATTAGATTTA
1 AAAATTATATCATA-TA-ATTTA
*
434556 AAAATTTTATCATATAATTTA
1 AAAATTATATCATATAATTTA
434577 AAA
1 AAA
434580 TATATTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 8 0.36
22 12 0.55
23 2 0.09
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (21 bp):
AAAATTATATCATATAATTTA
Found at i:443460 original size:15 final size:15
Alignment explanation
Indices: 443433--443465 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
443423 GATTTTTTTT
443433 GGGAAGGGAGGGAGTG
1 GGGAAGGGAGGGA-TG
443449 GGGAAGGG-GGGATG
1 GGGAAGGGAGGGATG
443463 GGG
1 GGG
443466 CAGTGGAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 4 0.24
16 8 0.47
ACGTcount: A:0.21, C:0.00, G:0.73, T:0.06
Consensus pattern (15 bp):
GGGAAGGGAGGGATG
Found at i:455562 original size:2 final size:2
Alignment explanation
Indices: 455551--455579 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
455541 AACAGCCTGG
455551 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
455580 AACTGGTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:459195 original size:13 final size:14
Alignment explanation
Indices: 459181--459213 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
459171 ATCAAATTGA
459181 TTAATTAAATCGAT
1 TTAATTAAATCGAT
*
459195 TTAATT-AATCAAT
1 TTAATTAAATCGAT
459208 TTAATT
1 TTAATT
459214 GAAAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (14 bp):
TTAATTAAATCGAT
Found at i:459727 original size:4 final size:4
Alignment explanation
Indices: 459691--459753 Score: 72
Period size: 4 Copynumber: 15.8 Consensus size: 4
459681 ATTATAATAA
* * * * * *
459691 ATAC ACAC ACAC ATAC GTAC GTAC GTAC GTAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
459739 ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATA
459754 TACACATAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 55 1.00
ACGTcount: A:0.44, C:0.27, G:0.06, T:0.22
Consensus pattern (4 bp):
ATAC
Found at i:464591 original size:13 final size:14
Alignment explanation
Indices: 464573--464606 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
464563 AGCATCTCAA
464573 TCAGCAGTCAG-AG
1 TCAGCAGTCAGCAG
464586 TCAGCAGTCAGCAG
1 TCAGCAGTCAGCAG
464600 TCAGCAG
1 TCAGCAG
464607 AAAATTGTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.29, C:0.26, G:0.29, T:0.15
Consensus pattern (14 bp):
TCAGCAGTCAGCAG
Found at i:464594 original size:7 final size:7
Alignment explanation
Indices: 464573--464606 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
464563 AGCATCTCAA
464573 TCAGCAG
1 TCAGCAG
464580 TCAG-AG
1 TCAGCAG
464586 TCAGCAG
1 TCAGCAG
464593 TCAGCAG
1 TCAGCAG
464600 TCAGCAG
1 TCAGCAG
464607 AAAATTGTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.29, C:0.26, G:0.29, T:0.15
Consensus pattern (7 bp):
TCAGCAG
Found at i:466026 original size:36 final size:34
Alignment explanation
Indices: 465986--466066 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 34
465976 AATAATTATA
*
465986 ATATAATCA-TATAAATATATTAAAATTTATATAAAT
1 ATATAAT-ATTATAAATATA--AAAATTAATATAAAT
* *
466022 ATATAATATTTTAAATATAATAATTAATATAAAT
1 ATATAATATTATAAATATAAAAATTAATATAAAT
466056 ATATAA-ATTAT
1 ATATAATATTAT
466067 TACGTTTTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
33 4 0.10
34 19 0.47
35 1 0.03
36 16 0.40
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (34 bp):
ATATAATATTATAAATATAAAAATTAATATAAAT
Found at i:466061 original size:20 final size:19
Alignment explanation
Indices: 465988--466061 Score: 70
Period size: 20 Copynumber: 4.1 Consensus size: 19
465978 TAATTATAAT
*
465988 ATAATCATATAAATATATTA
1 ATAATTATATAAATATA-TA
466008 A-AATTTATATAAATATATA
1 ATAA-TTATATAAATATATA
466027 AT-ATT-T-T-AA-ATATA
1 ATAATTATATAAATATATA
466041 ATAATTAATATAAATATATA
1 ATAATT-ATATAAATATATA
466061 A
1 A
466062 ATTATTACGT
Statistics
Matches: 45, Mismatches: 1, Indels: 16
0.73 0.02 0.26
Matches are distributed among these distances:
14 7 0.16
15 5 0.11
16 1 0.02
17 2 0.04
18 3 0.07
19 8 0.18
20 19 0.42
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (19 bp):
ATAATTATATAAATATATA
Found at i:466065 original size:18 final size:18
Alignment explanation
Indices: 465994--466065 Score: 71
Period size: 18 Copynumber: 4.0 Consensus size: 18
465984 TAATATAATC
*
465994 ATATAAATATATTAAAATTT
1 ATATAAATATA-T-AAATTA
466014 ATATAAATATATAATATT-
1 ATATAAATATATAA-ATTA
466032 -T-TAAATATA-ATAATTA
1 ATATAAATATATA-AATTA
466048 ATATAAATATATAAATTA
1 ATATAAATATATAAATTA
466066 TTACGTTTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
15 4 0.09
16 9 0.20
17 2 0.04
18 15 0.33
19 5 0.11
20 11 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATAAATATATAAATTA
Found at i:467828 original size:43 final size:39
Alignment explanation
Indices: 467779--467872 Score: 120
Period size: 37 Copynumber: 2.4 Consensus size: 39
467769 TAAATAGGTC
467779 AAATAAAGCAAAAAAAAAAATCAATTCCCTTAAATAGAAGTTA
1 AAATAAAGCAAAAAAAAAAATC----CCCTTAAATAGAAGTTA
*
467822 AAATAAAGC--AAAAAAAAATCCCTTTAAATAGAAGTTA
1 AAATAAAGCAAAAAAAAAAATCCCCTTAAATAGAAGTTA
*
467859 AAATAAACCAAAAA
1 AAATAAAGCAAAAA
467873 TGAATCCATC
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
37 24 0.51
39 3 0.06
41 11 0.23
43 9 0.19
ACGTcount: A:0.63, C:0.12, G:0.06, T:0.19
Consensus pattern (39 bp):
AAATAAAGCAAAAAAAAAAATCCCCTTAAATAGAAGTTA
Found at i:468416 original size:2 final size:2
Alignment explanation
Indices: 468409--468437 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
468399 ACGCGCTTCC
468409 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
468438 TGAGAGTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:468449 original size:66 final size:66
Alignment explanation
Indices: 468343--468473 Score: 226
Period size: 66 Copynumber: 2.0 Consensus size: 66
468333 ATGCAACATT
*
468343 ATATATGTATATATATATATATATAATATTGAAAGTAAAAGATGTGAATACCTTGGACGCGCTTC
1 ATATATATATATATATATATATATAATATTGAAAGTAAAAGATGTGAATACCTTGGACGCGCTTC
468408 C
66 C
* * *
468409 ATATATATATATATATATATATATAATATTGAGAGTAAAAGATGTGAATGCCTTGGATGCGCTTC
1 ATATATATATATATATATATATATAATATTGAAAGTAAAAGATGTGAATACCTTGGACGCGCTTC
468474 TTTGACTTTA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (66 bp):
ATATATATATATATATATATATATAATATTGAAAGTAAAAGATGTGAATACCTTGGACGCGCTTC
C
Found at i:471261 original size:15 final size:15
Alignment explanation
Indices: 471233--471277 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
471223 TTATCTGAAA
471233 ATAAAATCTATTTTTT
1 ATAAAAT-TATTTTTT
*
471249 TTAAAATTATTTTTT
1 ATAAAATTATTTTTT
*
471264 AAAAAATTATTTTT
1 ATAAAATTATTTTT
471278 AACACATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 20 0.77
16 6 0.23
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (15 bp):
ATAAAATTATTTTTT
Found at i:471568 original size:2 final size:2
Alignment explanation
Indices: 471561--471595 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
471551 GTACTGGCAT
471561 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
471596 TGAAAGTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:474235 original size:31 final size:31
Alignment explanation
Indices: 474161--474235 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
474151 GTTTACATTT
*
474161 AATAAACGTAAATTGTTTAAAGTTTATTAAA
1 AATAAACATAAATTGTTTAAAGTTTATTAAA
*
474192 AATAAACGTAAATTGTTTAAAGTTTATTAAA
1 AATAAACATAAATTGTTTAAAGTTTATTAAA
*
474223 AATAAATATAAAT
1 AATAAACATAAAT
474236 AATTTTATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.52, C:0.03, G:0.08, T:0.37
Consensus pattern (31 bp):
AATAAACATAAATTGTTTAAAGTTTATTAAA
Found at i:485007 original size:22 final size:22
Alignment explanation
Indices: 484980--485022 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
484970 TCAATACTTA
*
484980 ATTTTTATTAACATCAATTTAT
1 ATTTTTAGTAACATCAATTTAT
*
485002 ATTTTTAGTAACATCTATTTA
1 ATTTTTAGTAACATCAATTTA
485023 GCATCACGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.53
Consensus pattern (22 bp):
ATTTTTAGTAACATCAATTTAT
Found at i:485518 original size:21 final size:20
Alignment explanation
Indices: 485477--485518 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
485467 ATTTTAATAT
**
485477 TTATAATTTTTTAAATTAAA
1 TTATAATTTTTTAAAAAAAA
485497 TTATAATTTTTTTAAAAAAAA
1 TTATAA-TTTTTTAAAAAAAA
485518 T
1 T
485519 AAAAAATAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTATAATTTTTTAAAAAAAA
Found at i:487310 original size:18 final size:19
Alignment explanation
Indices: 487268--487303 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
487258 ATCGAAAATC
487268 AATTTAATTTATAGTTTTT
1 AATTTAATTTATAGTTTTT
487287 AATTTAA-TTATAGTTTT
1 AATTTAATTTATAGTTTT
487304 ACTTTTATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (19 bp):
AATTTAATTTATAGTTTTT
Found at i:487991 original size:28 final size:28
Alignment explanation
Indices: 487934--487993 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
487924 AATTTTAGTT
**
487934 TTAAATTAAATTTTTTATAATTTTTTAA
1 TTAAATTAAATTTTTTATAATTTTGAAA
487962 TTAAATT-AATTTTATT-TAATTTGTGAAA
1 TTAAATTAAATTTT-TTATAATTT-TGAAA
487990 TTAA
1 TTAA
487994 TGCAATCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 12 0.43
28 16 0.57
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (28 bp):
TTAAATTAAATTTTTTATAATTTTGAAA
Found at i:490720 original size:49 final size:49
Alignment explanation
Indices: 490658--490757 Score: 121
Period size: 49 Copynumber: 2.0 Consensus size: 49
490648 CGGTGACGGA
* *
490658 ATTATTAACTAGTTTAAAAA-TCTGTAAATGATGATATAAAATTTAATTT
1 ATTATTAACTAGTTTAAAAATTC-ATAAATGATGATATAAAATTCAATTT
* * * * *
490707 ATTATTAATTAGTTTGAATATTCATAAATGGTGATATAAGATTCAATTT
1 ATTATTAACTAGTTTAAAAATTCATAAATGATGATATAAAATTCAATTT
490756 AT
1 AT
490758 GATAGTTTCA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
49 41 0.95
50 2 0.05
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.44
Consensus pattern (49 bp):
ATTATTAACTAGTTTAAAAATTCATAAATGATGATATAAAATTCAATTT
Found at i:492382 original size:17 final size:18
Alignment explanation
Indices: 492356--492389 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
492346 AATAAATAAT
*
492356 AAAAACGAAAA-AAAAAG
1 AAAAAAGAAAAGAAAAAG
492373 AAAAAAGAAAAGAAAAA
1 AAAAAAGAAAAGAAAAA
492390 ATTCCCCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (18 bp):
AAAAAAGAAAAGAAAAAG
Found at i:496085 original size:24 final size:24
Alignment explanation
Indices: 496058--496103 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
496048 ATTATTATGA
* *
496058 TGATGATGATTACGATGATGATAC
1 TGATGAGGAATACGATGATGATAC
*
496082 TGATGAGGAATACTATGATGAT
1 TGATGAGGAATACGATGATGAT
496104 GAAGAATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.35, C:0.07, G:0.26, T:0.33
Consensus pattern (24 bp):
TGATGAGGAATACGATGATGATAC
Found at i:496103 original size:18 final size:18
Alignment explanation
Indices: 496082--496123 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
496072 ATGATGATAC
*
496082 TGATGAGGAATACTATGA
1 TGATGAAGAATACTATGA
*
496100 TGATGAAGAATATTATGA
1 TGATGAAGAATACTATGA
496118 TG-TGAA
1 TGATGAA
496124 AAAGGAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.40, C:0.02, G:0.26, T:0.31
Consensus pattern (18 bp):
TGATGAAGAATACTATGA
Found at i:498525 original size:9 final size:9
Alignment explanation
Indices: 498490--498532 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
498480 TTGAGTTTAA
498490 TTAATA-AT
1 TTAATATAT
*
498498 TTATTATAT
1 TTAATATAT
*
498507 ATATATATAT
1 TTA-ATATAT
498517 TTAATATAT
1 TTAATATAT
498526 TTAATAT
1 TTAATAT
498533 TTATTTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
8 5 0.17
9 17 0.59
10 7 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TTAATATAT
Found at i:498525 original size:11 final size:10
Alignment explanation
Indices: 498496--498550 Score: 53
Period size: 9 Copynumber: 5.7 Consensus size: 10
498486 TTAATTAATA
498496 ATTTAT-TAT
1 ATTTATATAT
*
498505 ATATATATAT
1 ATTTATATAT
498515 ATTTA-ATAT
1 ATTTATATAT
*
498524 ATTTAATATTT
1 ATTT-ATATAT
*
498535 ATTT-TATTT
1 ATTTATATAT
498544 ATTTATA
1 ATTTATA
498551 ATAAAAAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
9 22 0.56
10 10 0.26
11 7 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
ATTTATATAT
Found at i:499173 original size:23 final size:20
Alignment explanation
Indices: 499132--499176 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 20
499122 ATATGAAATA
*
499132 TTAATTTTTTATTTATTAAT
1 TTAATTTATTATTTATTAAT
*
499152 TTAATTTATTA-TTA-TGAT
1 TTAATTTATTATTTATTAAT
499170 TTAATTT
1 TTAATTT
499177 TTGTGAATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 10 0.43
19 3 0.13
20 10 0.43
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
TTAATTTATTATTTATTAAT
Found at i:499602 original size:28 final size:29
Alignment explanation
Indices: 499571--499657 Score: 83
Period size: 28 Copynumber: 3.0 Consensus size: 29
499561 TGTTTAAATT
* *
499571 AATATTTAATAAATAAATAATTTAT-TAA
1 AATATTTAATATATAAATAATTAATATAA
*
499599 AATATTAAAT-TATAATATATATTAATATAA
1 AATATTTAATATATAA-ATA-ATTAATATAA
*
499629 AAT-TTTAATATTATAAATAA-TAATTTAA
1 AATATTTAATA-TATAAATAATTAATATAA
499657 A
1 A
499658 TTAAATTATA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
27 4 0.08
28 20 0.41
29 11 0.22
30 9 0.18
31 5 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
AATATTTAATATATAAATAATTAATATAA
Found at i:499651 original size:23 final size:22
Alignment explanation
Indices: 499593--499647 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
499583 ATAAATAATT
*
499593 TATTA-AAATATTAAATTATAA
1 TATTATAAATATAAAATTATAA
* *
499614 TATATATTAATATAAAATTTTAA
1 TAT-TATAAATATAAAATTATAA
499637 TATTATAAATA
1 TATTATAAATA
499648 ATAATTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 3 0.11
22 9 0.32
23 16 0.57
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TATTATAAATATAAAATTATAA
Found at i:499672 original size:28 final size:27
Alignment explanation
Indices: 499582--499682 Score: 69
Period size: 28 Copynumber: 3.6 Consensus size: 27
499572 ATATTTAATA
*
499582 AATAAATAATTTATTAAAATATTAAATTAT
1 AATAAATAA-TAATT-AAA-ATTAAATTAT
* * *
499612 AATATATATTAATATAAAATTTTAA-TAT
1 AATAAATAATAAT-TAAAA-TTAAATTAT
* *
499640 TATAAATAATAATTTAAATTAAATTAT
1 AATAAATAATAATTAAAATTAAATTAT
* *
499667 AAATAAAAAATTATTA
1 -AATAAATAATAATTA
499683 TTTAAAATTT
Statistics
Matches: 54, Mismatches: 13, Indels: 10
0.70 0.17 0.13
Matches are distributed among these distances:
26 4 0.07
27 7 0.13
28 25 0.46
29 10 0.19
30 8 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
AATAAATAATAATTAAAATTAAATTAT
Found at i:500034 original size:28 final size:28
Alignment explanation
Indices: 500002--500069 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
499992 TTAAAATTTA
500002 ATTTAATTAA-TTTAAATAATAAATTAAT
1 ATTTAA-TAATTTTAAATAATAAATTAAT
** *
500030 ATTTAATAATTTTAAATTTTAATTTAAT
1 ATTTAATAATTTTAAATAATAAATTAAT
500058 ATTT-ATAATTTT
1 ATTTAATAATTTT
500070 TTAAATTTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 11 0.31
28 25 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
ATTTAATAATTTTAAATAATAAATTAAT
Found at i:500037 original size:18 final size:17
Alignment explanation
Indices: 500006--500039 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
499996 AATTTAATTT
500006 AATTAATTTAAATAATA
1 AATTAATTTAAATAATA
*
500023 AATTAATATTTAATAAT
1 AATTAAT-TTAAATAAT
500040 TTTAAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTAATTTAAATAATA
Found at i:500248 original size:15 final size:15
Alignment explanation
Indices: 500228--500256 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
500218 GATGGGTTAA
500228 AAAAGAATTAAATTG
1 AAAAGAATTAAATTG
500243 AAAAGAATTAAATT
1 AAAAGAATTAAATT
500257 TAATTATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (15 bp):
AAAAGAATTAAATTG
Found at i:500287 original size:23 final size:22
Alignment explanation
Indices: 500243--500290 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
500233 AATTAAATTG
500243 AAAAGAATTAAATTTAATTATA
1 AAAAGAATTAAATTTAATTATA
*
500265 AAAATAATATAAATATTAA-TATA
1 AAAAGAAT-TAAAT-TTAATTATA
500288 AAA
1 AAA
500291 TTAAAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 7 0.30
23 12 0.52
24 4 0.17
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAAGAATTAAATTTAATTATA
Found at i:501283 original size:16 final size:16
Alignment explanation
Indices: 501258--501310 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
501248 ATTCTATGAG
501258 TTTTTT-TATTAAATA
1 TTTTTTATATTAAATA
*
501273 TTTTTTATATTTAATA
1 TTTTTTATATTAAATA
501289 TTTATTTAATATTTAAA-A
1 TTT-TTT-ATA-TTAAATA
501307 TTTT
1 TTTT
501311 AATTTAATTG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 6 0.19
16 11 0.34
17 4 0.12
18 7 0.22
19 4 0.12
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTTTATATTAAATA
Found at i:501302 original size:18 final size:16
Alignment explanation
Indices: 501258--501310 Score: 63
Period size: 18 Copynumber: 3.2 Consensus size: 16
501248 ATTCTATGAG
*
501258 TTTTTT-TATTAAATA
1 TTTTTTATATTTAATA
501273 TTTTTTATATTTAATA
1 TTTTTTATATTTAATA
*
501289 TTTATTTAATATTTAAAA
1 TTT-TTT-ATATTTAATA
501307 TTTT
1 TTTT
501311 AATTTAATTG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 6 0.18
16 11 0.33
17 4 0.12
18 12 0.36
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTTTATATTTAATA
Found at i:504414 original size:22 final size:22
Alignment explanation
Indices: 504381--504444 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
504371 ATATGAACAT
504381 ATATAAAAAATAAT-TATAATATA
1 ATAT-AAAAATAATATA-AATATA
*
504404 ATATAAAAATAATATAAATATT
1 ATATAAAAATAATATAAATATA
*
504426 ATATAAATAT-ATA-AAATAT
1 ATATAAAAATAATATAAATAT
504445 TAAAATTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
20 6 0.16
21 3 0.08
22 23 0.61
23 6 0.16
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
ATATAAAAATAATATAAATATA
Found at i:504415 original size:11 final size:11
Alignment explanation
Indices: 504381--504432 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
504371 ATATGAACAT
504381 ATATAAAAAATA
1 ATAT-AAAAATA
*
504393 AT-TATAATATA
1 ATATA-AAAATA
504404 ATATAAAAATA
1 ATATAAAAATA
* *
504415 ATATAAATATT
1 ATATAAAAATA
504426 ATATAAA
1 ATATAAA
504433 TATATAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
10 1 0.03
11 29 0.85
12 4 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
ATATAAAAATA
Found at i:504429 original size:27 final size:27
Alignment explanation
Indices: 504390--504464 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 27
504380 TATATAAAAA
* *
504390 ATAATTATAATATAATATAAAAATAAT
1 ATAAATATTATATAATATAAAAATAAT
*
504417 ATAAATATTATATAAATATATAAAATATT
1 ATAAATATTATAT-AATATA-AAAATAAT
504446 A-AAAT-TTATATAATATAAA
1 ATAAATATTATATAATATAAA
504465 TTATTAATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
25 2 0.05
26 6 0.14
27 17 0.40
28 10 0.23
29 8 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
ATAAATATTATATAATATAAAAATAAT
Found at i:504433 original size:11 final size:11
Alignment explanation
Indices: 504398--504446 Score: 57
Period size: 11 Copynumber: 4.6 Consensus size: 11
504388 AAATAATTAT
*
504398 AATATAATATA
1 AATATTATATA
* *
504409 AAAATAATATA
1 AATATTATATA
504420 AATATTATATA
1 AATATTATATA
504431 AATA-TATA-A
1 AATATTATATA
504440 AATATTA
1 AATATTA
504447 AAATTTATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
9 5 0.15
10 6 0.18
11 23 0.68
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
AATATTATATA
Found at i:504433 original size:20 final size:20
Alignment explanation
Indices: 504386--504446 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
504376 AACATATATA
*
504386 AAAAATAATTATAATATAATAT
1 AAAAATAA-TATAA-ATATTAT
504408 AAAAATAATATAAATATTAT
1 AAAAATAATATAAATATTAT
*
504428 ATAAAT-ATATAAAATATTA
1 AAAAATAATAT-AAATATTA
504447 AAATTTATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.11
20 19 0.53
21 5 0.14
22 8 0.22
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAAATAATATAAATATTAT
Found at i:504500 original size:32 final size:32
Alignment explanation
Indices: 504428--504501 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
504418 TAAATATTAT
* *
504428 ATAAA-TATATAAAATATTAAAATTTATATAAT
1 ATAAATTAT-TAATATATTAAAATTTATATAAC
*
504460 ATAAATTATTAATATATTAAAATTTATTTAAC
1 ATAAATTATTAATATATTAAAATTTATATAAC
*
504492 ATATATTATT
1 ATAAATTATT
504502 TTAAATATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
32 34 0.92
33 3 0.08
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (32 bp):
ATAAATTATTAATATATTAAAATTTATATAAC
Found at i:504551 original size:20 final size:19
Alignment explanation
Indices: 504404--504551 Score: 71
Period size: 20 Copynumber: 7.7 Consensus size: 19
504394 TTATAATATA
504404 ATATAAAAATA-ATATAAAT
1 ATATAAAAATATAT-TAAAT
*
504423 ATTATATAAATATA-TAAA-
1 A-TATAAAAATATATTAAAT
* *
504441 ATAT-TAAA-AT-TTATAT
1 ATATAAAAATATATTAAAT
*
504457 A-ATATAAAT-TATT-AAT
1 ATATAAAAATATATTAAAT
* *
504473 ATATTAAAATTTATTTAACAT
1 ATATAAAAATATA-TTAA-AT
*
504494 ATATTATTTTAAATATAATTAAAT
1 ATA-TA---AAAATAT-ATTAAAT
504518 ATATAAAAATATATTAAAT
1 ATATAAAAATATATTAAAT
*
504537 ATAATACAAATATAT
1 AT-ATAAAAATATAT
504552 AAAACTAACG
Statistics
Matches: 101, Mismatches: 10, Indels: 35
0.69 0.07 0.24
Matches are distributed among these distances:
15 7 0.07
16 13 0.13
17 11 0.11
18 3 0.03
19 16 0.16
20 27 0.27
21 6 0.06
22 1 0.01
23 2 0.02
24 5 0.05
25 9 0.09
26 1 0.01
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (19 bp):
ATATAAAAATATATTAAAT
Found at i:504566 original size:30 final size:29
Alignment explanation
Indices: 504503--504573 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 29
504493 TATATTATTT
* *
504503 TAAATATAATTAAATATATAAAAATATAT
1 TAAATATAATCAAATATATAAAAATATAG
*
504532 TAAATATAATACAAATATATAAAACTA-ACG
1 TAAATATAAT-CAAATATATAAAAATATA-G
504562 TAAATA-AATCAA
1 TAAATATAATCAA
504574 CCTCAGTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 3 0.08
29 14 0.38
30 20 0.54
ACGTcount: A:0.62, C:0.06, G:0.01, T:0.31
Consensus pattern (29 bp):
TAAATATAATCAAATATATAAAAATATAG
Found at i:504849 original size:2 final size:2
Alignment explanation
Indices: 504842--504872 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
504832 TCAAGAACAA
504842 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
504873 ATTAAGGACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:506124 original size:50 final size:50
Alignment explanation
Indices: 506014--506113 Score: 184
Period size: 50 Copynumber: 2.0 Consensus size: 50
506004 ACTCTCTGCG
506014 CTAAAACCTTTACTAATTTAAACATTAGAGCGCGAATGGAACAATAAACT
1 CTAAAACCTTTACTAATTTAAACATTAGAGCGCGAATGGAACAATAAACT
506064 CTAAAACCTTTACTAATTTAAACATTAGAGCGCGAATGGAA-ACATAAACT
1 CTAAAACCTTTACTAATTTAAACATTAGAGCGCGAATGGAACA-ATAAACT
506114 TTAACTCCTT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
49 1 0.02
50 48 0.98
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.26
Consensus pattern (50 bp):
CTAAAACCTTTACTAATTTAAACATTAGAGCGCGAATGGAACAATAAACT
Found at i:506231 original size:34 final size:34
Alignment explanation
Indices: 506176--506392 Score: 258
Period size: 34 Copynumber: 6.4 Consensus size: 34
506166 GCCTCCTTTC
*
506176 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* * *
506209 TGTTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* * *
506243 TGTTGACTAAATGGGAGATTTGATAGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* * **
506277 TGTTTATTAAATGAGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* *
506311 TATTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* * * *
506345 TGTTGACTAAAT-GATAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGT-GATTTGGTAGCTTACCAT
506379 TGTTGATTAAATGG
1 TGTTGATTAAATGG
506393 TGGTTTTTAC
Statistics
Matches: 155, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
33 14 0.09
34 140 0.90
35 1 0.01
ACGTcount: A:0.26, C:0.08, G:0.25, T:0.41
Consensus pattern (34 bp):
TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
Found at i:506379 original size:102 final size:102
Alignment explanation
Indices: 506176--506391 Score: 317
Period size: 102 Copynumber: 2.1 Consensus size: 102
506166 GCCTCCTTTC
** * * * *
506176 TGTTGATTAAATG-GTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTGC
1 TGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTAC
*
506240 CATTGTTGACTAAATGGGAGATTTGATAGCTTACCAT
66 CATTGTTGACTAAATGAGAGATTTGATAGCTTACCAT
*
506277 TGTTTATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTAC
1 TGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTAC
* * * *
506342 CATTGTTGACTAAATGATAGATTTGGTAGGTTGCCAT
66 CATTGTTGACTAAATGAGAGATTTGATAGCTTACCAT
506379 TGTTGATTAAATG
1 TGTTGATTAAATG
506392 GTGGTTTTTA
Statistics
Matches: 101, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
101 12 0.12
102 89 0.88
ACGTcount: A:0.26, C:0.08, G:0.25, T:0.41
Consensus pattern (102 bp):
TGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTAC
CATTGTTGACTAAATGAGAGATTTGATAGCTTACCAT
Found at i:510862 original size:34 final size:34
Alignment explanation
Indices: 510805--511023 Score: 271
Period size: 34 Copynumber: 6.5 Consensus size: 34
510795 AAGTGGGAGA
*
510805 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
510838 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
510872 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
**** *
510906 ATTGTTGATTAAATGAAAAATTTGATAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
510940 ATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
510974 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
511008 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
511024 TGGTTTTTAC
Statistics
Matches: 158, Mismatches: 25, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
33 17 0.11
34 140 0.89
35 1 0.01
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Done.