Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008512.1 Hibiscus syriacus cultivar Beakdansim tig00111372_pilon, whole genome shotgun sequence
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: 1759229
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 9
Found at i:529349 original size:34 final size:34
Alignment explanation
Indices: 529306--529476 Score: 148
Period size: 34 Copynumber: 4.9 Consensus size: 34
529296 AGTCAATTCG
* *
529306 CGTTGCGATAGTCTAATACGCTTTGCGATTTTCT
1 CGTTGCGATAGTCAAATACGCGTTGCGATTTTCT
* *
529340 CGTTGCGATAGTCAAATACCCGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATACGCGTTGCGAT--T----TTCT
*
529380 CGTTGCGATAGTCAAATTCGCGTTGCGATTTT-T
1 CGTTGCGATAGTCAAATACGCGTTGCGATTTTCT
* * *
529413 GAGTTGCGATAGTCAAATTCGCGTTGCGGTTTT-T
1 -CGTTGCGATAGTCAAATACGCGTTGCGATTTTCT
* * **
529447 GAGTTGCGATAATCAAATTTGCGTTGCGAT
1 -CGTTGCGATAGTCAAATACGCGTTGCGAT
529477 AGTCAAATTC
Statistics
Matches: 118, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
34 86 0.73
36 1 0.01
38 1 0.01
40 30 0.25
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (34 bp):
CGTTGCGATAGTCAAATACGCGTTGCGATTTTCT
Found at i:529421 original size:74 final size:74
Alignment explanation
Indices: 529300--529440 Score: 203
Period size: 74 Copynumber: 1.9 Consensus size: 74
529290 CGCGAAAGTC
* * * *
529300 AATTCGCGTTGCGATAGTCTAATACGCTTTGCGATTTTCTCGTTGCGATAGTCAAATACCCGTTG
1 AATTCACGTTGCGATAGTCAAATACGCGTTGCGATTTTCTAGTTGCGATAGTCAAATACCCGTTG
529365 CGATAATCA
66 CGATAATCA
* * *
529374 AATTCACGTTGCGATAGTCAAATTCGCGTTGCGATTTT-TGAGTTGCGATAGTCAAATTCGCGTT
1 AATTCACGTTGCGATAGTCAAATACGCGTTGCGATTTTCT-AGTTGCGATAGTCAAATACCCGTT
529438 GCG
65 GCG
529441 GTTTTTGAGT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
73 1 0.02
74 58 0.98
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (74 bp):
AATTCACGTTGCGATAGTCAAATACGCGTTGCGATTTTCTAGTTGCGATAGTCAAATACCCGTTG
CGATAATCA
Found at i:529440 original size:20 final size:20
Alignment explanation
Indices: 529291--529504 Score: 133
Period size: 20 Copynumber: 11.7 Consensus size: 20
529281 AAATCGCAAC
*
529291 GCGAAAGTC-AATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* * *
529310 GCGATAGTCTAATACGCTTT
1 GCGATAGTCAAATTCGCGTT
*
529330 GCGAT--T----TTCTCGTT
1 GCGATAGTCAAATTCGCGTT
* *
529344 GCGATAGTCAAATACCCGTT
1 GCGATAGTCAAATTCGCGTT
* *
529364 GCGATAATCAAATTCACGTT
1 GCGATAGTCAAATTCGCGTT
529384 GCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* *
529404 GCGAT--T----TTTGAGTT
1 GCGATAGTCAAATTCGCGTT
529418 GCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* * *
529438 GCG---GT---TTTTGAGTT
1 GCGATAGTCAAATTCGCGTT
* *
529452 GCGATAATCAAATTTGCGTT
1 GCGATAGTCAAATTCGCGTT
529472 GCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* *
529492 GCAATATTCAAAT
1 GCGATAGTCAAAT
529505 AAATGTGTAA
Statistics
Matches: 149, Mismatches: 27, Indels: 37
0.70 0.13 0.17
Matches are distributed among these distances:
14 30 0.20
16 2 0.01
17 3 0.02
18 2 0.01
19 8 0.05
20 104 0.70
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.34
Consensus pattern (20 bp):
GCGATAGTCAAATTCGCGTT
Found at i:529731 original size:140 final size:140
Alignment explanation
Indices: 529479--529757 Score: 522
Period size: 140 Copynumber: 2.0 Consensus size: 140
529469 GTTGCGATAG
*
529479 TCAAATTCGCGTTGCAATATTCAAATAAATGTGTAATAAGTGATAACAACTGAACAGATCATAGC
1 TCAAATTCGCATTGCAATATTCAAATAAATGTGTAATAAGTGATAACAACTGAACAGATCATAGC
529544 AATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAATA
66 AATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAATA
529609 CACATAATAA
131 CACATAATAA
* *
529619 TCAAATTCGCATTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCATAGC
1 TCAAATTCGCATTGCAATATTCAAATAAATGTGTAATAAGTGATAACAACTGAACAGATCATAGC
529684 AATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAATA
66 AATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAATA
*
529749 TACATAATA
131 CACATAATA
529758 CAACGTTTGC
Statistics
Matches: 135, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 135 1.00
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.28
Consensus pattern (140 bp):
TCAAATTCGCATTGCAATATTCAAATAAATGTGTAATAAGTGATAACAACTGAACAGATCATAGC
AATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAATA
CACATAATAA
Found at i:529838 original size:18 final size:18
Alignment explanation
Indices: 529815--529849 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
529805 AAGCCGGTTG
*
529815 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
529833 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
529850 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:532133 original size:24 final size:24
Alignment explanation
Indices: 532099--532152 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
532089 CTGAAACATC
532099 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
532123 ATCAAAGTCCGGGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
532147 ATCAAA
1 ATCAAA
532153 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:532996 original size:20 final size:20
Alignment explanation
Indices: 532971--533079 Score: 96
Period size: 20 Copynumber: 5.3 Consensus size: 20
532961 GAAATTCAGT
*
532971 GTTGCGATAGTCAGAATAGC
1 GTTGCGATAGTCAGAATCGC
**
532991 GTTGCGATTATGT-ATTATCGC
1 GTTGCGA-TA-GTCAGAATCGC
** *
533012 GTTGCGATTATGT-ATTATAGC
1 GTTGCGA-TA-GTCAGAATCGC
*
533033 GTTGCAATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
533053 GTTGCGATAGTCAAAATCGC
1 GTTGCGATAGTCAGAATCGC
533073 GTTGCGA
1 GTTGCGA
533080 ATCTGGAAAC
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
19 2 0.03
20 39 0.51
21 33 0.43
22 2 0.03
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.32
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:533015 original size:21 final size:21
Alignment explanation
Indices: 532986--533037 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
532976 GATAGTCAGA
532986 ATAGCGTTGCGATTATGTATT
1 ATAGCGTTGCGATTATGTATT
*
533007 ATCGCGTTGCGATTATGTATT
1 ATAGCGTTGCGATTATGTATT
533028 ATAGCGTTGC
1 ATAGCGTTGC
533038 AATAGTCAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.21, C:0.13, G:0.25, T:0.40
Consensus pattern (21 bp):
ATAGCGTTGCGATTATGTATT
Found at i:533117 original size:20 final size:19
Alignment explanation
Indices: 533094--533139 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
533084 GGAAACTGAT
* *
533094 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
533114 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
533133 TTGCGAT
1 TTGCGAT
533140 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:533129 original size:19 final size:19
Alignment explanation
Indices: 533105--533141 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
533095 TGCGATACTG
*
533105 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
533124 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
533142 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:533488 original size:11 final size:11
Alignment explanation
Indices: 533472--533519 Score: 62
Period size: 11 Copynumber: 4.5 Consensus size: 11
533462 ATATTTAAAT
533472 TTAATAATTTA
1 TTAATAATTTA
* *
533483 TTAATAGTTCA
1 TTAATAATTTA
533494 TTAATAATTTA
1 TTAATAATTTA
*
533505 -AAATAATTTA
1 TTAATAATTTA
533515 TTAAT
1 TTAAT
533520 GCTTTTTGAG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
10 9 0.30
11 21 0.70
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (11 bp):
TTAATAATTTA
Found at i:540961 original size:2 final size:2
Alignment explanation
Indices: 540954--540990 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
540944 AGCCATTGAA
540954 AT AT AT 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 AT AT AT A
540991 ACCGATTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:544742 original size:20 final size:19
Alignment explanation
Indices: 544706--544787 Score: 92
Period size: 20 Copynumber: 4.2 Consensus size: 19
544696 TAGTTAGACA
*
544706 GGGGGAATCAGTACCCCTT
1 GGGGGAATCAGTACCCCCT
* *
544725 GGGGGAGATCTGTTCCCCCT
1 GGGGGA-ATCAGTACCCCCT
*
544745 GGGGGGAATCGGTACCCCCT
1 -GGGGGAATCAGTACCCCCT
*
544765 GGGGGGAATCTGTACCCCCT
1 -GGGGGAATCAGTACCCCCT
544785 GGG
1 GGG
544788 CAATCTGATT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
19 9 0.16
20 40 0.73
21 6 0.11
ACGTcount: A:0.15, C:0.28, G:0.38, T:0.20
Consensus pattern (19 bp):
GGGGGAATCAGTACCCCCT
Found at i:544760 original size:40 final size:40
Alignment explanation
Indices: 544706--544787 Score: 121
Period size: 40 Copynumber: 2.0 Consensus size: 40
544696 TAGTTAGACA
* *
544706 GGGGGAATCAGTA-CCCCTTGGGGGAGATCTGTTCCCCCTG
1 GGGGGAATCAGTACCCCCTGGGGGGA-ATCTGTACCCCCTG
*
544746 GGGGGAATCGGTACCCCCTGGGGGGAATCTGTACCCCCTG
1 GGGGGAATCAGTACCCCCTGGGGGGAATCTGTACCCCCTG
544786 GG
1 GG
544788 CAATCTGATT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 27 0.71
41 11 0.29
ACGTcount: A:0.15, C:0.28, G:0.38, T:0.20
Consensus pattern (40 bp):
GGGGGAATCAGTACCCCCTGGGGGGAATCTGTACCCCCTG
Found at i:547134 original size:32 final size:34
Alignment explanation
Indices: 547097--547166 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
547087 CCTTACAAAC
* *
547097 TCCCTAG-TTTTTC-CGGGCTAAATTAGAACCTT
1 TCCCTAGCTTTTACACGGGCTAAACTAGAACCTT
*
547129 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAGCTTTTACACGGGCTAAACTAGAACCTT
547163 TCCC
1 TCCC
547167 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.21, C:0.30, G:0.16, T:0.33
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGCTAAACTAGAACCTT
Found at i:547549 original size:19 final size:20
Alignment explanation
Indices: 547513--547554 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
547503 CCGTTAGACA
547513 GGGGGAATCGGTACCCCCTG
1 GGGGGAATCGGTACCCCCTG
*
547533 GGGGGAATCTGTACCCCCTG
1 GGGGGAATCGGTACCCCCTG
547553 GG
1 GG
547555 CAATCTGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.29, G:0.40, T:0.17
Consensus pattern (20 bp):
GGGGGAATCGGTACCCCCTG
Found at i:547561 original size:18 final size:19
Alignment explanation
Indices: 547513--547561 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
547503 CCGTTAGACA
* *
547513 GGGGGAATCGGTACCCCCT
1 GGGGCAATCTGTACCCCCT
*
547532 GGGGGGAATCTGTACCCCCT
1 -GGGGCAATCTGTACCCCCT
547552 -GGGCAATCTG
1 GGGGCAATCTG
547562 ATTTTTCTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 9 0.33
20 18 0.67
ACGTcount: A:0.16, C:0.29, G:0.37, T:0.18
Consensus pattern (19 bp):
GGGGCAATCTGTACCCCCT
Found at i:554540 original size:5 final size:5
Alignment explanation
Indices: 554530--554556 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
554520 CAACTCCGCT
554530 TTCCC TTCCC TTCCC TTCCC TTCCC TT
1 TTCCC TTCCC TTCCC TTCCC TTCCC TT
554557 TTTCATGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (5 bp):
TTCCC
Found at i:556118 original size:222 final size:219
Alignment explanation
Indices: 555604--556186 Score: 873
Period size: 222 Copynumber: 2.6 Consensus size: 219
555594 TATGATTAAG
* * ** *
555604 TCACTATGTTGCTCAGGTAACCGCTCAGGATTAACAAAATGGTCGAAAGTTTCATCAAGCATTCA
1 TCACTAGGTAGCTCAGGTAACCGCTCAGGATCGACACAATGGTCGAAAGTTTCATCAAGCATTCA
* *
555669 ACAAATGCCTT-CACTGATTCCAAAACCTCATCGTTGCAAACTAATTTGATAGCAAAAAGGGAGC
66 ACAAATGCCTTCCACTGATTCCAAAACCTCATCATTGCAAACTAATTTGATAACAAAAA-GGAGC
* *
555733 ATAAAATCAAACAAAAGTTAATTTCTCAGTCAAGTAAAGAACCTATGATGTTTCTTTTTCTTTTT
130 ATAAAATCCAACAAAAGCTAATTTCTCAGTCAAGTAAAGAACCTATGATGTTTCTTTTTCTTTTT
*
555798 TTTCAATCCATTCTAATAGATCAAA
195 TTTCAAACCATTCTAATAGATCAAA
*
555823 TCAGTAGGTAGCTCAGGTAACCGCTCAGGATCGACACAA-GGTCGAAAGTTTCATCAAGCATTCA
1 TCACTAGGTAGCTCAGGTAACCGCTCAGGATCGACACAATGGTCGAAAGTTTCATCAAGCATTCA
555887 ACAAAATGCCTTCCACTGATTCCAAAACCTCATCATTGCAAACTAATTTGATAACAAAAAGGAAG
66 AC-AAATGCCTTCCACTGATTCCAAAACCTCATCATTGCAAACTAATTTGATAACAAAAAGG-AG
* * * *
555952 CATAAGAATCCAACAAGAGCTCATTTCTCAGTCAAGTAAATAACCTATGATGTTTCTTTTTTTTC
129 CATAA-AATCCAACAAAAGCTAATTTCTCAGTCAAGTAAAGAACCTATGATGTTTCTTTTTCTT-
* *
556017 TTTTTTCAAAGCATTCTAATAGATCATA
192 TTTTTTCAAACCATTCTAATAGATCAAA
*
556045 TCACTAGGTCGCTCAGGTAACCGCTCAGGATCGACACAATGGTCGAAAGTTTCATCAAGCATTCA
1 TCACTAGGTAGCTCAGGTAACCGCTCAGGATCGACACAATGGTCGAAAGTTTCATCAAGCATTCA
* * * * *
556110 ACAAATGCCTTCCACTGATTCCAAAACATCATCACTGCAACCCAATTTGGTAACGAAAAAGGAGC
66 ACAAATGCCTTCCACTGATTCCAAAACCTCATCATTGCAAACTAATTTGATAAC-AAAAAGGAGC
*
556175 AAAAAAATCCAA
130 -ATAAAATCCAA
556187 GAGAAATTCA
Statistics
Matches: 331, Mismatches: 25, Indels: 13
0.90 0.07 0.04
Matches are distributed among these distances:
218 27 0.08
219 44 0.13
220 52 0.16
221 52 0.16
222 119 0.36
223 37 0.11
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (219 bp):
TCACTAGGTAGCTCAGGTAACCGCTCAGGATCGACACAATGGTCGAAAGTTTCATCAAGCATTCA
ACAAATGCCTTCCACTGATTCCAAAACCTCATCATTGCAAACTAATTTGATAACAAAAAGGAGCA
TAAAATCCAACAAAAGCTAATTTCTCAGTCAAGTAAAGAACCTATGATGTTTCTTTTTCTTTTTT
TTCAAACCATTCTAATAGATCAAA
Found at i:567461 original size:19 final size:19
Alignment explanation
Indices: 567418--567607 Score: 69
Period size: 20 Copynumber: 9.6 Consensus size: 19
567408 AAATGACCAA
* *
567418 CAAATTCACAACGCGATCT
1 CAAATTCGCAACGCGAACT
567437 CAAATTCGCAACGCGAACT
1 CAAATTCGCAACGCGAACT
* * **
567456 CCAATTTCGCAAC-CCAGTTT
1 -CAAATTCGCAACGCGA-ACT
*
567476 CCAATTTCGCAACGCGAA-T
1 -CAAATTCGCAACGCGAACT
* * ** **
567495 ATATAAATCGCATTGCGATTTTT
1 -CA-AATTCGCAACGCGA--ACT
* * *
567518 CAAATTCGCAACACAAAGT
1 CAAATTCGCAACGCGAACT
*
567537 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGA-ACT
* * * *
567557 CAAATTCACAACACAAAAGT
1 CAAATTCGCAACGC-GAACT
*
567577 CAAATTCGCAACGCGAATT
1 CAAATTCGCAACGCGAACT
* *
567596 TAATTTCGCAAC
1 CAAATTCGCAAC
567608 ACAAATGTTT
Statistics
Matches: 128, Mismatches: 34, Indels: 18
0.71 0.19 0.10
Matches are distributed among these distances:
19 49 0.38
20 65 0.51
21 12 0.09
22 1 0.01
23 1 0.01
ACGTcount: A:0.37, C:0.27, G:0.13, T:0.24
Consensus pattern (19 bp):
CAAATTCGCAACGCGAACT
Found at i:567559 original size:20 final size:20
Alignment explanation
Indices: 567517--567593 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
567507 TTGCGATTTT
567517 TCAAATTCGCAACAC-AAAG
1 TCAAATTCGCAACACGAAAG
* *
567536 TCAAATTCGCAACGCGATAG
1 TCAAATTCGCAACACGAAAG
* *
567556 TCAAATTCACAACACAAAAG
1 TCAAATTCGCAACACGAAAG
*
567576 TCAAATTCGCAACGCGAA
1 TCAAATTCGCAACACGAA
567594 TTTAATTTCG
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
19 14 0.29
20 34 0.71
ACGTcount: A:0.44, C:0.26, G:0.13, T:0.17
Consensus pattern (20 bp):
TCAAATTCGCAACACGAAAG
Found at i:567569 original size:39 final size:40
Alignment explanation
Indices: 567517--567592 Score: 136
Period size: 40 Copynumber: 1.9 Consensus size: 40
567507 TTGCGATTTT
*
567517 TCAAATTCGCAACAC-AAAGTCAAATTCGCAACGCGATAG
1 TCAAATTCACAACACAAAAGTCAAATTCGCAACGCGATAG
567556 TCAAATTCACAACACAAAAGTCAAATTCGCAACGCGA
1 TCAAATTCACAACACAAAAGTCAAATTCGCAACGCGA
567593 ATTTAATTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 14 0.40
40 21 0.60
ACGTcount: A:0.43, C:0.26, G:0.13, T:0.17
Consensus pattern (40 bp):
TCAAATTCACAACACAAAAGTCAAATTCGCAACGCGATAG
Found at i:567608 original size:39 final size:40
Alignment explanation
Indices: 567517--567612 Score: 142
Period size: 39 Copynumber: 2.5 Consensus size: 40
567507 TTGCGATTTT
567517 TCAAATTCGCAACAC-AAAGTCAAATTCGCAACGCGATAG
1 TCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGATAG
* *
567556 TCAAATTCACAACACAAAAGTCAAATTCGCAACGCGA-AT
1 TCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGATAG
* *
567595 TTAATTTCGCAACACAAA
1 TCAAATTCGCAACACAAA
567613 TGTTTTTTGT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
39 30 0.59
40 21 0.41
ACGTcount: A:0.44, C:0.25, G:0.11, T:0.20
Consensus pattern (40 bp):
TCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGATAG
Found at i:568358 original size:12 final size:12
Alignment explanation
Indices: 568343--568370 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
568333 TTTCCAATAC
568343 CAAACACAATCT
1 CAAACACAATCT
568355 CAAACACAATCT
1 CAAACACAATCT
568367 CAAA
1 CAAA
568371 ACTCACAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.32, G:0.00, T:0.14
Consensus pattern (12 bp):
CAAACACAATCT
Found at i:568508 original size:24 final size:24
Alignment explanation
Indices: 568480--568535 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
568470 GTGAGTACTA
**
568480 GTCAATATTCGAAATTTGATCTTG
1 GTCAATACCCGAAATTTGATCTTG
* *
568504 GTCAATACCCGGACTTTGATCTTG
1 GTCAATACCCGAAATTTGATCTTG
568528 GTCAATAC
1 GTCAATAC
568536 TCAGATTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.36
Consensus pattern (24 bp):
GTCAATACCCGAAATTTGATCTTG
Found at i:568545 original size:24 final size:24
Alignment explanation
Indices: 568494--568547 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
568484 ATATTCGAAA
*
568494 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
568518 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
568542 TTTGAT
1 TTTGAT
568548 GATGTGATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:570827 original size:18 final size:18
Alignment explanation
Indices: 570804--570838 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
570794 AGCAAAAGGT
*
570804 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
570822 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
570839 CAACCTAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:571695 original size:18 final size:18
Alignment explanation
Indices: 571674--571710 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
571664 GTAATTGGAG
571674 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
571692 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
571710 T
1 T
571711 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:571717 original size:24 final size:24
Alignment explanation
Indices: 571666--571718 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
571656 TTTCATATGT
* * *
571666 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
571690 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
571714 AATTT
1 AATTT
571719 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:572044 original size:39 final size:39
Alignment explanation
Indices: 571987--572073 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
571977 TCCTATGCTC
*
571987 ATCAAAATCCAAAGCTCATATGGTGTCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
*
572026 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
572065 ATCAAAATC
1 ATCAAAATC
572074 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.47, C:0.20, G:0.15, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:572345 original size:20 final size:20
Alignment explanation
Indices: 572312--572349 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
572302 GCAATGCTTA
*
572312 TTTCGAGTTTCGAATTTGAC
1 TTTCGAGTTGCGAATTTGAC
*
572332 TTTCGCGTTGCGAATTTG
1 TTTCGAGTTGCGAATTTG
572350 TACCTTCAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.16, G:0.24, T:0.45
Consensus pattern (20 bp):
TTTCGAGTTGCGAATTTGAC
Found at i:572488 original size:66 final size:60
Alignment explanation
Indices: 572408--572547 Score: 172
Period size: 66 Copynumber: 2.2 Consensus size: 60
572398 TTTTAGAAAC
* *
572408 AACAAATCAACTTTTACAAATTAATTAAACAAGCAAAAAAATAATTCTTATGTACACATCAAATT
1 AACAAATCAACTTTTACAAATCAATT----AAGC-AAAAAATAAATCTTATGTACACATC-AATT
572473 A
60 A
* * * *
572474 AACAAATCAACTTTTACAAATCAATTAATCAAAAAATAAATCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAGCAAAAAATAAATCTTATGTACACATCAATTA
572534 AACAAATCAACTTT
1 AACAAATCAACTTT
572548 CAATGTAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
60 19 0.28
61 21 0.31
62 3 0.04
66 25 0.37
ACGTcount: A:0.51, C:0.17, G:0.01, T:0.31
Consensus pattern (60 bp):
AACAAATCAACTTTTACAAATCAATTAAGCAAAAAATAAATCTTATGTACACATCAATTA
Found at i:574006 original size:21 final size:21
Alignment explanation
Indices: 573940--574012 Score: 62
Period size: 21 Copynumber: 3.5 Consensus size: 21
573930 GATGACAGGG
*
573940 GCCTCTTGAACGGTAGGATGT
1 GCCTCTTGAACGATAGGATGT
* * *
573961 GCTTCTT---CGATAATGAGAGGG
1 GCCTCTTGAACGAT-A-G-GATGT
573982 GCCTCTTGAACGATAGGATGT
1 GCCTCTTGAACGATAGGATGT
574003 GCCTCTTGAA
1 GCCTCTTGAA
574013 TGATGATAGG
Statistics
Matches: 39, Mismatches: 7, Indels: 12
0.67 0.12 0.21
Matches are distributed among these distances:
18 3 0.08
19 1 0.03
20 1 0.03
21 28 0.72
22 1 0.03
23 1 0.03
24 4 0.10
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (21 bp):
GCCTCTTGAACGATAGGATGT
Found at i:576262 original size:13 final size:13
Alignment explanation
Indices: 576244--576277 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
576234 GGGTTTCTTC
576244 AACAAAAAGAAAA
1 AACAAAAAGAAAA
*
576257 AACAAAAAGACAA
1 AACAAAAAGAAAA
576270 AACAAAAA
1 AACAAAAA
576278 CAAATATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.82, C:0.12, G:0.06, T:0.00
Consensus pattern (13 bp):
AACAAAAAGAAAA
Found at i:576723 original size:20 final size:20
Alignment explanation
Indices: 576698--576806 Score: 114
Period size: 20 Copynumber: 5.5 Consensus size: 20
576688 GCGTAAAAAC
576698 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
** * *
576718 ATTTGACTTAAGTGTTGTG-
1 ATTTGACTTTCGCGTTGCGA
*
576737 ATTT-ACAAATTCGCGTTGCGA
1 ATTTGAC--TTTCGCGTTGCGA
* *
576758 ATTTGACTTTTGTGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
576778 ATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
576798 ATTTGACTT
1 ATTTGACTT
576807 CTGTGTTGCG
Statistics
Matches: 69, Mismatches: 16, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
18 2 0.03
19 4 0.06
20 57 0.83
21 4 0.06
22 2 0.03
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.42
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:576761 original size:40 final size:40
Alignment explanation
Indices: 576706--576838 Score: 180
Period size: 40 Copynumber: 3.3 Consensus size: 40
576696 ACATTTGACT
* *
576706 TTCGCGTTGCGAATTTGACTTAAGTGTTGTGATTTACAAA
1 TTCGCGTTGCGAATTTGACTTATGTGTTGCGATTTACAAA
* *
576746 TTCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGAC-TA
1 TTCGCGTTGCGAATTTGACTTATGTGTTGCG-ATTT-ACAAA
* *
576787 -TCGCGTTGCGAATTTGACTTCTGTGTTGCGATTTACAGA
1 TTCGCGTTGCGAATTTGACTTATGTGTTGCGATTTACAAA
576826 TTCGCGTTGCGAA
1 TTCGCGTTGCGAA
576839 ATTGGAAACT
Statistics
Matches: 83, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
38 2 0.02
39 5 0.06
40 69 0.83
41 5 0.06
42 2 0.02
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.40
Consensus pattern (40 bp):
TTCGCGTTGCGAATTTGACTTATGTGTTGCGATTTACAAA
Found at i:576814 original size:20 final size:20
Alignment explanation
Indices: 576751--576817 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
576741 ACAAATTCGC
*
576751 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTCTGT
*
576771 GTTGCGAATTTGACTATC-GC
1 GTTGCGAATTTGACT-TCTGT
576791 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTCTGT
576811 GTTGCGA
1 GTTGCGA
576818 TTTACAGATT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
19 2 0.05
20 39 0.93
21 1 0.02
ACGTcount: A:0.16, C:0.15, G:0.27, T:0.42
Consensus pattern (20 bp):
GTTGCGAATTTGACTTCTGT
Found at i:576855 original size:80 final size:80
Alignment explanation
Indices: 576698--576882 Score: 230
Period size: 80 Copynumber: 2.3 Consensus size: 80
576688 GCGTAAAAAC
* *
576698 ATTTGACTTTCGCGTTGCGAATTTGACTTAAGTGTTGTGATTTACAAATTCGCGTTGCGAATTTG
1 ATTTGAC-TTCGCGTTGCGAATTTGACTTAAGTGTTGCGATTTACAAATTCGCGTTGCGAATTGG
*** *
576763 ACTTTTGTGTTGCG-A
65 ACAACTGAGTTGCGAA
** *
576778 ATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTGCGATTTACAGATTCGCGTTGCGAAATTG
1 ATTTGACT-TCGCGTTGCGAATTTGACTTAAGTGTTGCGATTTACAAATTCGCGTTGCG-AATTG
576843 GA-AACTGAGTTGCGAA
64 GACAACTGAGTTGCGAA
* *
576859 ATTGGAGTTCGCGTTGCGAATTTG
1 ATTTGACTTCGCGTTGCGAATTTG
576883 TTGGTCATTT
Statistics
Matches: 91, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
79 1 0.01
80 77 0.85
81 13 0.14
ACGTcount: A:0.21, C:0.15, G:0.26, T:0.38
Consensus pattern (80 bp):
ATTTGACTTCGCGTTGCGAATTTGACTTAAGTGTTGCGATTTACAAATTCGCGTTGCGAATTGGA
CAACTGAGTTGCGAA
Found at i:576874 original size:20 final size:19
Alignment explanation
Indices: 576824--576878 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
576814 GCGATTTACA
576824 GATTCGCGTTGCGAAATTG
1 GATTCGCGTTGCGAAATTG
** *
576843 GAAACTGAGTTGCGAAATTG
1 GATTC-GCGTTGCGAAATTG
576863 GAGTTCGCGTTGCGAA
1 GA-TTCGCGTTGCGAA
576879 TTTGTTGGTC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 3 0.11
20 24 0.86
21 1 0.04
ACGTcount: A:0.25, C:0.15, G:0.33, T:0.27
Consensus pattern (19 bp):
GATTCGCGTTGCGAAATTG
Found at i:580885 original size:21 final size:21
Alignment explanation
Indices: 580861--580910 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
580851 AATTAAAATG
* * *
580861 AATGAAATTCAAAAATTTAAT
1 AATGAAATTAAAAAAATTAAA
580882 AATGAAATTAAAAAAATTAAA
1 AATGAAATTAAAAAAATTAAA
*
580903 AATTAAAT
1 AATGAAAT
580911 GATTGAAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (21 bp):
AATGAAATTAAAAAAATTAAA
Found at i:582161 original size:94 final size:93
Alignment explanation
Indices: 582056--582230 Score: 296
Period size: 94 Copynumber: 1.9 Consensus size: 93
582046 GAAGTCATAG
582056 ATATAATTTACCCTAAATTTTAACCAAATCCAAACATAAAATATTTATTTATTTATTTTGATTAA
1 ATATAATTTACCCTAAATTTTAACCAAATCCAAACATAAAATATTTATTTATTTATTTTGATTAA
582121 TCTAAAGTGTATCATATATATATATATAT
66 TCTAAAGTGTAT-ATATATATATATATAT
* * * *
582150 ATATAGTTTACCCTAAATTTTAACCAAATCCATACGTAAACTATTTATTTATTTATTTTGATTAA
1 ATATAATTTACCCTAAATTTTAACCAAATCCAAACATAAAATATTTATTTATTTATTTTGATTAA
*
582215 TTTAAAGTGTATATAT
66 TCTAAAGTGTATATAT
582231 TTTAAAAATT
Statistics
Matches: 76, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
93 4 0.05
94 72 0.95
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.45
Consensus pattern (93 bp):
ATATAATTTACCCTAAATTTTAACCAAATCCAAACATAAAATATTTATTTATTTATTTTGATTAA
TCTAAAGTGTATATATATATATATATAT
Found at i:588240 original size:27 final size:28
Alignment explanation
Indices: 588193--588247 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
588183 GAGGTATTGG
588193 TTTAATAGTGAAATTATATGAAAATATTT
1 TTTAATAG-GAAATTATATGAAAATATTT
*
588222 TTTAATA-GAAATTGTATGAAAATATT
1 TTTAATAGGAAATTATATGAAAATATT
588248 GATATCTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 18 0.72
29 7 0.28
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.44
Consensus pattern (28 bp):
TTTAATAGGAAATTATATGAAAATATTT
Found at i:588279 original size:2 final size:2
Alignment explanation
Indices: 588272--588303 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
588262 GAGTGTCATC
588272 AT AT AT 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 AT AT AT
588304 GAAGATTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:589454 original size:13 final size:13
Alignment explanation
Indices: 589422--589476 Score: 65
Period size: 13 Copynumber: 4.2 Consensus size: 13
589412 CTAATTCTAG
* *
589422 TAACTGATTTAAC
1 TAACTGATTTGAT
589435 TAACTGATTTGAT
1 TAACTGATTTGAT
*
589448 TAGCTGATTTGAT
1 TAACTGATTTGAT
* *
589461 AAATTGATTTGAT
1 TAACTGATTTGAT
589474 TAA
1 TAA
589477 TTGTTTATAT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.44
Consensus pattern (13 bp):
TAACTGATTTGAT
Found at i:590474 original size:25 final size:26
Alignment explanation
Indices: 590443--590509 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 26
590433 TTTATATTTT
*
590443 AAGTTATGAATATATTTTAA-CAAAA
1 AAGTTATGAATATATTTTAAGAAAAA
* * *
590468 AATTTATGAA-AAAATTTAATGAAAAA
1 AAGTTATGAATATATTTTAA-GAAAAA
590494 AAGTTATGAATATATT
1 AAGTTATGAATATATT
590510 GGTAAATTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
24 7 0.22
25 9 0.28
26 13 0.41
27 3 0.09
ACGTcount: A:0.54, C:0.01, G:0.09, T:0.36
Consensus pattern (26 bp):
AAGTTATGAATATATTTTAAGAAAAA
Found at i:590480 original size:13 final size:13
Alignment explanation
Indices: 590464--590503 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
590454 ATATTTTAAC
590464 AAAAAATTTATG-
1 AAAAAATTTATGA
590476 AAAAAATTTAATGA
1 AAAAAATTT-ATGA
*
590490 AAAAAAGTTATGA
1 AAAAAATTTATGA
590503 A
1 A
590504 TATATTGGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 9 0.36
13 8 0.32
14 8 0.32
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (13 bp):
AAAAAATTTATGA
Found at i:590575 original size:34 final size:34
Alignment explanation
Indices: 590517--590583 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
590507 ATTGGTAAAT
*
590517 TTTTAAAAATAAATTTTAAAAAAAT-TTCGAGTGA
1 TTTTAAAAATAAAATTTAAAAAAATATT-GAGTGA
* **
590551 TTTTAATAATAAAATTTATGAAAATATTGAGTG
1 TTTTAAAAATAAAATTTAAAAAAATATTGAGTG
590584 TTACTTTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 26 0.93
35 2 0.07
ACGTcount: A:0.48, C:0.01, G:0.10, T:0.40
Consensus pattern (34 bp):
TTTTAAAAATAAAATTTAAAAAAATATTGAGTGA
Found at i:593994 original size:12 final size:11
Alignment explanation
Indices: 593926--593996 Score: 56
Period size: 12 Copynumber: 6.3 Consensus size: 11
593916 TAATTGTTAG
593926 ATAAAAAATTAA
1 ATAAAAAA-TAA
*
593938 ATTAAAAATAA
1 ATAAAAAATAA
*
593949 A-AAGAAATAA
1 ATAAAAAATAA
593959 ATAAAAAATGAA
1 ATAAAAAAT-AA
**
593971 A-AAAATGTTAA
1 ATAAAA-AATAA
593982 ATAAAAACATAA
1 ATAAAAA-ATAA
593994 ATA
1 ATA
593997 TTAAAAAGGA
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
10 8 0.17
11 17 0.37
12 21 0.46
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.21
Consensus pattern (11 bp):
ATAAAAAATAA
Found at i:595396 original size:31 final size:31
Alignment explanation
Indices: 595358--595482 Score: 189
Period size: 31 Copynumber: 4.0 Consensus size: 31
595348 CCCGAAGGAC
* * *
595358 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
595389 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
595420 CAGTCCATATGTCCCGAAGAACATATGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
595451 CAGTCTATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
595482 C
1 C
595483 CCTCGACCCT
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 86 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:599082 original size:14 final size:14
Alignment explanation
Indices: 599065--599109 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
599055 CTATATATAT
599065 AAATATGTTTTCAA
1 AAATATGTTTTCAA
599079 AAATATGTTTTCAA
1 AAATATGTTTTCAA
*
599093 AAA-ACTGTTTCCAA
1 AAATA-TGTTTTCAA
599107 AAA
1 AAA
599110 CTATATTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 1 0.03
14 28 0.97
ACGTcount: A:0.47, C:0.11, G:0.07, T:0.36
Consensus pattern (14 bp):
AAATATGTTTTCAA
Found at i:599145 original size:24 final size:24
Alignment explanation
Indices: 599104--599174 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 24
599094 AAACTGTTTC
599104 CAAAAACTATAT-TA-TATATTTT
1 CAAAAACTATATATATTATATTTT
599126 CAAAAACTATATATATTATATATTT
1 CAAAAACTATATATATTATAT-TTT
** *
599151 TTAAAATTATTATATATATATATT
1 CAAAAACTA-TATATAT-TATATT
599175 ATCATATATA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
22 12 0.29
23 2 0.05
24 5 0.12
25 9 0.22
26 8 0.20
27 5 0.12
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (24 bp):
CAAAAACTATATATATTATATTTT
Found at i:599164 original size:28 final size:26
Alignment explanation
Indices: 599111--599174 Score: 87
Period size: 25 Copynumber: 2.5 Consensus size: 26
599101 TTCCAAAAAC
599111 TATATTATATATTTTCAAAAACTATA
1 TATATTATATATTTTCAAAAACTATA
* *
599137 TATATTATATATTTT-TAAAATTAT-
1 TATATTATATATTTTCAAAAACTATA
599161 TATATATATATATT
1 TATAT-TATATATT
599175 ATCATATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
24 5 0.14
25 15 0.43
26 15 0.43
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (26 bp):
TATATTATATATTTTCAAAAACTATA
Found at i:599743 original size:42 final size:42
Alignment explanation
Indices: 599639--599870 Score: 243
Period size: 42 Copynumber: 5.5 Consensus size: 42
599629 CAATAAGTCA
*
599639 AGATCTATAACGGCGTTTTTGGAACAAACG-CAGCAAAAGGTC
1 AGATCTATAGCGGCGTTTTTGGAACAAACGAC-GCAAAAGGTC
* * *
599681 AATATCTATAGAGGCGTTTTTGGAACAAACGTCGCAAAAGGTC
1 -AGATCTATAGCGGCGTTTTTGGAACAAACGACGCAAAAGGTC
* * **
599724 AGATCTATAGCTGTGTTTTTGGAACAAAC-ACTGCAAACTGTC
1 AGATCTATAGCGGCGTTTTTGGAACAAACGAC-GCAAAAGGTC
* * * * *
599766 ATATCTATAGCGACGTTTTTGGATACAAACGCCACAAAAAGTC
1 AGATCTATAGCGGCGTTTTTGGA-ACAAACGACGCAAAAGGTC
** * *
599809 AGATCTATAGTAGCATTTTTGGAACAAACGACGCAAAAGATC
1 AGATCTATAGCGGCGTTTTTGGAACAAACGACGCAAAAGGTC
**
599851 AGATCTATAGCATCGTTTTT
1 AGATCTATAGCGGCGTTTTT
599871 TATAAAAACA
Statistics
Matches: 155, Mismatches: 30, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
41 1 0.01
42 84 0.54
43 68 0.44
44 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (42 bp):
AGATCTATAGCGGCGTTTTTGGAACAAACGACGCAAAAGGTC
Found at i:599794 original size:85 final size:82
Alignment explanation
Indices: 599633--599870 Score: 255
Period size: 85 Copynumber: 2.8 Consensus size: 82
599623 ACACCGCAAT
* * * * *
599633 AAGTCAAGATCTATAACGGCGTTTTTGGAACAAACGCAGCAAAAGGTCAATATCTATAGAGGCGT
1 AAGTC-AGATCTATAGCTGCGTTTTTGGAACAAACAC-GCAAAA-GTC-ATATCTATAGCGACGT
* *
599698 TTTTGGAACAAACGTCGCAAA
62 TTTTGGAACAAACGCCACAAA
* * *
599719 AGGTCAGATCTATAGCTGTGTTTTTGGAACAAACACTGCAAACTGTCATATCTATAGCGACGTTT
1 AAGTCAGATCTATAGCTGCGTTTTTGGAACAAACAC-GCAAA-AGTCATATCTATAGCGACGTTT
599784 TTGGATACAAACGCCACAAA
64 TTGGA-ACAAACGCCACAAA
* *
599804 AAGTCAGATCTATAG-TAGCATTTTTGGAACAAACGACGCAAAAGATCAGATCTATAGC-ATCGT
1 AAGTCAGATCTATAGCT-GCGTTTTTGGAACAAAC-ACGCAAAAG-TCATATCTATAGCGA-CGT
599867 TTTT
62 TTTT
599871 TATAAAAACA
Statistics
Matches: 130, Mismatches: 16, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
84 24 0.18
85 100 0.77
86 6 0.05
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (82 bp):
AAGTCAGATCTATAGCTGCGTTTTTGGAACAAACACGCAAAAGTCATATCTATAGCGACGTTTTT
GGAACAAACGCCACAAA
Found at i:603760 original size:42 final size:40
Alignment explanation
Indices: 603656--603809 Score: 141
Period size: 41 Copynumber: 3.7 Consensus size: 40
603646 CAAAAAATCA
* *
603656 CCACTAAAGTATTATGTTTTAGCGGCGTTTATTG-GAAAACG
1 CCACTAAAGTACTA-GTTTTAGCGGCGTTT-TTGTTAAAACG
* *
603697 CCACTAAAATACGAGTATTTAGCGGCGTTTTTGCTTAAAACG
1 CCACTAAAGTACTAGT-TTTAGCGGCGTTTTTG-TTAAAACG
* * ** *
603739 CCATTAAAGTATTACGTTTTAGTAGCGTTTGT-TTAAAACCG
1 CCACTAAAGTACTA-GTTTTAGCGGCGTTTTTGTTAAAA-CG
*
603780 ACACTAAAGTACTAGGTTTTAGCGGCGTTT
1 CCACTAAAGTACTA-GTTTTAGCGGCGTTT
603810 GTCTAAAAAC
Statistics
Matches: 91, Mismatches: 17, Indels: 10
0.77 0.14 0.08
Matches are distributed among these distances:
40 11 0.12
41 50 0.55
42 28 0.31
43 2 0.02
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.34
Consensus pattern (40 bp):
CCACTAAAGTACTAGTTTTAGCGGCGTTTTTGTTAAAACG
Found at i:606201 original size:7 final size:7
Alignment explanation
Indices: 606189--606214 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
606179 CACACACAAA
606189 GGAAATT
1 GGAAATT
606196 GGAAATT
1 GGAAATT
606203 GGAAATT
1 GGAAATT
606210 GGAAA
1 GGAAA
606215 ATAGAAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (7 bp):
GGAAATT
Found at i:606479 original size:21 final size:20
Alignment explanation
Indices: 606455--606496 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
606445 TTCAACATGT
606455 TTTTAATTATCTATTATA-ATA
1 TTTTAATTA-C-ATTATATATA
*
606476 TTTTATTTACATTATATATA
1 TTTTAATTACATTATATATA
606496 T
1 T
606497 AATCATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 6 0.32
20 5 0.26
21 8 0.42
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTAATTACATTATATATA
Found at i:609887 original size:4 final size:4
Alignment explanation
Indices: 609880--609930 Score: 52
Period size: 4 Copynumber: 13.2 Consensus size: 4
609870 TAACAAAGTA
* * * *
609880 TATT TATT CATT TATA TATT TATA TATT TATA TATT T-TT TA-T TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
609926 TATT T
1 TATT T
609931 TTAATATTAT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
3 6 0.16
4 31 0.84
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (4 bp):
TATT
Found at i:609900 original size:8 final size:8
Alignment explanation
Indices: 609878--609992 Score: 73
Period size: 8 Copynumber: 14.6 Consensus size: 8
609868 TTTAACAAAG
609878 TATATTTA
1 TATATTTA
609886 T-TCATTTA
1 TAT-ATTTA
609894 TATATTTA
1 TATATTTA
609902 TATATTTA
1 TATATTTA
*
609910 TATATTTTT
1 TATA-TTTA
609919 TATTATTTA
1 TA-TATTTA
609928 T-T-TTTAA
1 TATATTT-A
609935 TATTATTT-
1 TA-TATTTA
*
609943 TAT-TTTT
1 TATATTTA
*
609950 TGT-TTTA
1 TATATTTA
*
609957 T-TGTTTA
1 TATATTTA
*
609964 TATATATA
1 TATATTTA
*
609972 TATATATA
1 TATATTTA
*
609980 TATATATA
1 TATATTTA
609988 TATAT
1 TATAT
609993 ATTTTACACG
Statistics
Matches: 90, Mismatches: 6, Indels: 22
0.76 0.05 0.19
Matches are distributed among these distances:
6 7 0.08
7 16 0.18
8 51 0.57
9 11 0.12
10 5 0.06
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.65
Consensus pattern (8 bp):
TATATTTA
Found at i:609967 original size:2 final size:2
Alignment explanation
Indices: 609962--609994 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
609952 TTTTATTGTT
609962 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 T
609995 TTTACACGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:610177 original size:16 final size:15
Alignment explanation
Indices: 610156--610191 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
610146 TTGTTTTATC
610156 TTTTATTATTATTTTA
1 TTTTATTATT-TTTTA
*
610172 TTTTATTATTTTTTC
1 TTTTATTATTTTTTA
610187 TTTTA
1 TTTTA
610192 CATATATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTATTATTTTTTA
Found at i:610313 original size:8 final size:8
Alignment explanation
Indices: 610300--610364 Score: 59
Period size: 8 Copynumber: 8.5 Consensus size: 8
610290 TTTCTTCATT
610300 TTTTATTA
1 TTTTATTA
610308 TTTTA-T-
1 TTTTATTA
610314 TTTTATTA
1 TTTTATTA
610322 TTTCT-TTA
1 TTT-TATTA
610330 TTTTATT-
1 TTTTATTA
*
610337 TGTT-TTA
1 TTTTATTA
*
610344 TTTTCTTA
1 TTTTATTA
610352 TTTTATTCA
1 TTTTATT-A
610361 TTTT
1 TTTT
610365 CGTTTTTTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 13
0.75 0.05 0.21
Matches are distributed among these distances:
6 7 0.15
7 9 0.19
8 25 0.53
9 6 0.13
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.77
Consensus pattern (8 bp):
TTTTATTA
Found at i:610316 original size:14 final size:14
Alignment explanation
Indices: 610299--610358 Score: 59
Period size: 14 Copynumber: 4.1 Consensus size: 14
610289 TTTTCTTCAT
610299 TTTTTATTATTTTA
1 TTTTTATTATTTTA
*
610313 TTTTTATTATTTCTT
1 TTTTTATTATTT-TA
*
610328 TATTTTATTTGTTTTA
1 T-TTTTA-TTATTTTA
*
610344 -TTTTCTTATTTTA
1 TTTTTATTATTTTA
610357 TT
1 TT
610359 CATTTTCGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
13 7 0.19
14 17 0.46
15 2 0.05
16 6 0.16
17 5 0.14
ACGTcount: A:0.17, C:0.03, G:0.02, T:0.78
Consensus pattern (14 bp):
TTTTTATTATTTTA
Found at i:610333 original size:22 final size:22
Alignment explanation
Indices: 610300--610358 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
610290 TTTCTTCATT
*
610300 TTTTATTATTTTATTT-TTATTA
1 TTTTCTTATTTTATTTGTT-TTA
610322 -TTTCTTTATTTTATTTGTTTTA
1 TTTTC-TTATTTTATTTGTTTTA
610344 TTTTCTTATTTTATT
1 TTTTCTTATTTTATT
610359 CATTTTCGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 3 0.09
22 24 0.73
23 6 0.18
ACGTcount: A:0.17, C:0.03, G:0.02, T:0.78
Consensus pattern (22 bp):
TTTTCTTATTTTATTTGTTTTA
Found at i:611854 original size:21 final size:21
Alignment explanation
Indices: 611828--611910 Score: 114
Period size: 21 Copynumber: 4.0 Consensus size: 21
611818 AATAGAATGT
*
611828 CCAGGGGGTACAAATT-CCCC
1 CCAGGGGGTACAGATTCCCCC
* *
611848 CCAAGGGGTACCGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
611869 CCAGGGGGTACAGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
* *
611890 CCAGGGGGTACCGAATCCCCC
1 CCAGGGGGTACAGATTCCCCC
611911 TGTCTAACGA
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
20 13 0.24
21 42 0.76
ACGTcount: A:0.20, C:0.40, G:0.27, T:0.13
Consensus pattern (21 bp):
CCAGGGGGTACAGATTCCCCC
Found at i:611886 original size:41 final size:42
Alignment explanation
Indices: 611828--611910 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
611818 AATAGAATGT
*
611828 CCAGGGGGTACAAATT-CCCCCCAAGGGGTACCGATTCCCCC
1 CCAGGGGGTACAAATTCCCCCCCAAGGGGTACCGAATCCCCC
* *
611869 CCAGGGGGTACAGATTCCCCCCCAGGGGGTACCGAATCCCCC
1 CCAGGGGGTACAAATTCCCCCCCAAGGGGTACCGAATCCCCC
611911 TGTCTAACGA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
41 15 0.39
42 23 0.61
ACGTcount: A:0.20, C:0.40, G:0.27, T:0.13
Consensus pattern (42 bp):
CCAGGGGGTACAAATTCCCCCCCAAGGGGTACCGAATCCCCC
Found at i:617213 original size:22 final size:20
Alignment explanation
Indices: 617183--617263 Score: 63
Period size: 23 Copynumber: 3.8 Consensus size: 20
617173 TAGTGCAGGA
*
617183 GGAATCGATACCCCCTTGAAGG
1 GGAACCGATACCCCCTTG-A-G
*
617205 GGAACCGATTCCCCCTTTGTATG
1 GGAACCGATACCCCC-TTG-A-G
* *
617228 GGAACCGATTCCCTCATTGAG
1 GGAACCGATACCC-CCTTGAG
*
617249 GGAATCGATACCCCC
1 GGAACCGATACCCCC
617264 CACGGGTTCT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
20 1 0.02
21 12 0.24
22 14 0.29
23 21 0.43
24 1 0.02
ACGTcount: A:0.23, C:0.31, G:0.23, T:0.22
Consensus pattern (20 bp):
GGAACCGATACCCCCTTGAG
Found at i:617251 original size:21 final size:23
Alignment explanation
Indices: 617204--617263 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
617194 CCCCTTGAAG
*
617204 GGGAACCGATTCCCCCTTTGTAT
1 GGGAACCGATTCCCCCATTGTAT
*
617227 GGGAACCGATTCCCTCATTG-A-
1 GGGAACCGATTCCCCCATTGTAT
* *
617248 GGGAATCGATACCCCC
1 GGGAACCGATTCCCCC
617264 CACGGGTTCT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 13 0.41
22 1 0.03
23 18 0.56
ACGTcount: A:0.22, C:0.32, G:0.23, T:0.23
Consensus pattern (23 bp):
GGGAACCGATTCCCCCATTGTAT
Found at i:619252 original size:136 final size:135
Alignment explanation
Indices: 619009--619283 Score: 514
Period size: 136 Copynumber: 2.0 Consensus size: 135
618999 AGGGGGAGTA
619009 ATTTCAAATTTGATTTCAAAATGATTTCTTAAAAATCTTAAAATTACTCAAATGTTTTGTTATAT
1 ATTTCAAATTTGATTTCAAAATGATTTCTTAAAAATCTTAAAATTACTCAAATGTTTTGTTATAT
* *
619074 CAAAAAGGGGGAGATTGTTGAAAGCATTTTGATGTTTCGATATTACAAATTAAGTTAAATGAATT
66 CAAAAAGGGGGAGATTGTTGAAAACATTTTGATGTTTCGATATAACAAATTAAGTTAAATGAATT
619139 TTAAG
131 TTAAG
*
619144 ATTTCAAATTTGATTTCAAAATTATTTTCTTAAAAATCTTAAAATTACTCAAATGTTTTGTTATA
1 ATTTCAAATTTGATTTCAAAATGA-TTTCTTAAAAATCTTAAAATTACTCAAATGTTTTGTTATA
619209 TCAAAAAGGGGGAGATTGTTGAAAACATTTTGATGTTTCGATATAACAAATTAAGTTAAATGAAT
65 TCAAAAAGGGGGAGATTGTTGAAAACATTTTGATGTTTCGATATAACAAATTAAGTTAAATGAAT
619274 TTTAAG
130 TTTAAG
619280 ATTT
1 ATTT
619284 TACAAAAGAT
Statistics
Matches: 136, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
135 23 0.17
136 113 0.83
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.41
Consensus pattern (135 bp):
ATTTCAAATTTGATTTCAAAATGATTTCTTAAAAATCTTAAAATTACTCAAATGTTTTGTTATAT
CAAAAAGGGGGAGATTGTTGAAAACATTTTGATGTTTCGATATAACAAATTAAGTTAAATGAATT
TTAAG
Found at i:619564 original size:20 final size:20
Alignment explanation
Indices: 619539--619617 Score: 113
Period size: 20 Copynumber: 4.0 Consensus size: 20
619529 ACAAAATGTT
619539 CAGGGGGTACAGATTCCCCC
1 CAGGGGGTACAGATTCCCCC
* *
619559 CAGGGGATACCGATTCCCCC
1 CAGGGGGTACAGATTCCCCC
*
619579 CAGGGGGTACATATTCCCCC
1 CAGGGGGTACAGATTCCCCC
* *
619599 CATGGGGTACCGATTCCCC
1 CAGGGGGTACAGATTCCCC
619618 TGTCTAACGA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.19, C:0.37, G:0.27, T:0.18
Consensus pattern (20 bp):
CAGGGGGTACAGATTCCCCC
Found at i:619595 original size:40 final size:40
Alignment explanation
Indices: 619539--619617 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
619529 ACAAAATGTT
619539 CAGGGGGTACAGATTCCCCCCA-GGGGATACCGATTCCCCC
1 CAGGGGGTACAGATTCCCCCCATGGGG-TACCGATTCCCCC
*
619579 CAGGGGGTACATATTCCCCCCATGGGGTACCGATTCCCC
1 CAGGGGGTACAGATTCCCCCCATGGGGTACCGATTCCCC
619618 TGTCTAACGA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
40 33 0.89
41 4 0.11
ACGTcount: A:0.19, C:0.37, G:0.27, T:0.18
Consensus pattern (40 bp):
CAGGGGGTACAGATTCCCCCCATGGGGTACCGATTCCCCC
Found at i:620636 original size:259 final size:257
Alignment explanation
Indices: 620179--620694 Score: 1014
Period size: 259 Copynumber: 2.0 Consensus size: 257
620169 GTAGACTTTG
620179 GTTGAGAAAGTTGAACCACTCTAAATCGCTGTGCAAATATTTTCAATTTTCTACAAAAGCTTCCA
1 GTTGAGAAAGTTGAACCACTCTAAATCGCTGTGCAAATATTTTCAATTTTCTACAAAAGCTTCCA
620244 CCAAAATTTTAATTGCCAATTCACCCCCTCTGGACATTTCCATCGATCGATTAACTCAACACCCA
66 CCAAAATTTTAATTGCCAATTCACCCCCTCTGGACATTTCCATCGATCGATTAACTCAACACCCA
620309 GAGAGTCCTTTTGAAGATTACGAGACCCTAGCTGAGCTGGAGGCCACTATTGATAAGTTCAAGAA
131 GAGAGTCCTTTTGAAGATTACGAGACCCTAGCTGAGCTGGAGGCCACTATTGATAAGTTCAAGAA
620374 GCAAGCTTCGGATAGTTCCTATCGATGAAGGACTCCAATAACGTTTTCGTTAGGAACAGGCT
196 GCAAGCTTCGGATAGTTCCTATCGATGAAGGACTCCAATAACGTTTTCGTTAGGAACAGGCT
620436 GTTGAGAAAGTTGAACCACTCTAAATCGCTGTGCAAATATTTTCAATTTTCTACAAAAGCTTCCA
1 GTTGAGAAAGTTGAACCACTCTAAATCGCTGTGCAAATATTTTCAATTTTCTACAAAAGCTTCCA
620501 CCAAAATTTTTAATTGCCAATTCACCCCCTCTTGGACATTTCCATCGATCGATTAACTCAACACC
66 CCAAAA-TTTTAATTGCCAATTCACCCCCTC-TGGACATTTCCATCGATCGATTAACTCAACACC
620566 CAGAGAGTCCTTTTGAAGATTACGAGACCCTAGCTGAGCTGGAGGCCACTATTGATAAGTTCAAG
129 CAGAGAGTCCTTTTGAAGATTACGAGACCCTAGCTGAGCTGGAGGCCACTATTGATAAGTTCAAG
620631 AAGCAAGCTTCGGATAGTTCCTATCGATGAAGGACTCCAATAACGTTTTCGTTAGGAACAGGCT
194 AAGCAAGCTTCGGATAGTTCCTATCGATGAAGGACTCCAATAACGTTTTCGTTAGGAACAGGCT
620695 CAAAAAAGAG
Statistics
Matches: 257, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
257 71 0.28
258 24 0.09
259 162 0.63
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (257 bp):
GTTGAGAAAGTTGAACCACTCTAAATCGCTGTGCAAATATTTTCAATTTTCTACAAAAGCTTCCA
CCAAAATTTTAATTGCCAATTCACCCCCTCTGGACATTTCCATCGATCGATTAACTCAACACCCA
GAGAGTCCTTTTGAAGATTACGAGACCCTAGCTGAGCTGGAGGCCACTATTGATAAGTTCAAGAA
GCAAGCTTCGGATAGTTCCTATCGATGAAGGACTCCAATAACGTTTTCGTTAGGAACAGGCT
Found at i:621211 original size:14 final size:14
Alignment explanation
Indices: 621194--621221 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
621184 ACACTCAAGA
621194 ATAATACAATTGAG
1 ATAATACAATTGAG
621208 ATAATACAATTGAG
1 ATAATACAATTGAG
621222 CACAATAAGT
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:0.14, T:0.29
Consensus pattern (14 bp):
ATAATACAATTGAG
Found at i:621591 original size:18 final size:17
Alignment explanation
Indices: 621537--621585 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
621527 TTAGACCCTT
* *
621537 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
621555 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
621573 AGTGCATTCGATG
1 AGTGCA-TCGATG
621586 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:621668 original size:54 final size:53
Alignment explanation
Indices: 621558--621669 Score: 138
Period size: 53 Copynumber: 2.1 Consensus size: 53
621548 GCACTAAGAG
* * * *
621558 TGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCATAGTGCATCGA
1 TGCATCGATACATCAAATGCATTCGACGTTTCAAAATAGCCATAATGCATCGA
*
621611 TGCATCGATACATCAAATGCATTCGACGTTTTCATAAA-ATCC-TCAATGCATCGA
1 TGCATCGATACATCAAATGCATTCGACG-TTTCA-AAATAGCCAT-AATGCATCGA
621665 TGCAT
1 TGCAT
621670 GAAATGCATT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
53 26 0.51
54 22 0.43
55 3 0.06
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.29
Consensus pattern (53 bp):
TGCATCGATACATCAAATGCATTCGACGTTTCAAAATAGCCATAATGCATCGA
Found at i:622093 original size:19 final size:19
Alignment explanation
Indices: 622069--622106 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
622059 TTAACACTTC
622069 TCCCCTTTAAAACATTTTA
1 TCCCCTTTAAAACATTTTA
622088 TCCCCTTTAAAACATTTTA
1 TCCCCTTTAAAACATTTTA
622107 ACTTTAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.26, G:0.00, T:0.42
Consensus pattern (19 bp):
TCCCCTTTAAAACATTTTA
Found at i:622203 original size:2 final size:2
Alignment explanation
Indices: 622196--622220 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
622186 AATTGATTAA
622196 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 A
622221 GCTTAAGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:624391 original size:23 final size:22
Alignment explanation
Indices: 624363--624442 Score: 81
Period size: 22 Copynumber: 3.6 Consensus size: 22
624353 GCATGGCCTT
*
624363 GTGCATTGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
624385 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
* *
624407 GTGTATCAATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
*
624429 ATGCATCGATGCAC
1 GTGCATCGATGCAC
624443 TGTTAGGTGT
Statistics
Matches: 44, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
21 14 0.32
22 15 0.34
23 15 0.34
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:634265 original size:73 final size:76
Alignment explanation
Indices: 634168--634313 Score: 178
Period size: 73 Copynumber: 1.9 Consensus size: 76
634158 CTTGAGATTG
* **
634168 TTTTTCTTAAAACATATTTTGTCTCACTT-GATG-CTGTTTT-ACTCGAAAGAAG-ATTT-ATTT
1 TTTTTCTTAAAACATAATTTGTCTC-CTTCGA-GACCATTTTCACTCGAAAGAAGAATTTCATTT
634228 CACTCAAGATTTT
64 CACTCAAGATTTT
*
634241 TTTTTCTTAAAACA-AGATTTGTCTCGTTCGAGACCATTTTCACTCGAAAGAAGACATTTCATTT
1 TTTTTCTTAAAACATA-ATTTGTCTCCTTCGAGACCATTTTCACTCGAAAGAAGA-ATTTCATTT
634305 CACTCAAGA
64 CACTCAAGA
634314 CTATTTTTAA
Statistics
Matches: 62, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
72 4 0.06
73 29 0.47
74 12 0.19
76 4 0.06
77 13 0.21
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (76 bp):
TTTTTCTTAAAACATAATTTGTCTCCTTCGAGACCATTTTCACTCGAAAGAAGAATTTCATTTCA
CTCAAGATTTT
Found at i:634379 original size:39 final size:39
Alignment explanation
Indices: 634326--634478 Score: 202
Period size: 39 Copynumber: 4.0 Consensus size: 39
634316 ATTTTTAAAG
* *
634326 AAGATCTTATCTCGCTTGAGATAGTTTCCCTCGAAACAA
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAA
*
634365 AAGATTTTATCTCGCTTGAGATAGTTTCCCTTTAAACAA
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAA
* * *
634404 AAGATTTTATCTTGCTTGACATAGTTTTCCTTGAAAC-A
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAA
* * * *
634442 AA-ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACA
634479 TAAACATTGA
Statistics
Matches: 99, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
37 27 0.27
38 3 0.03
39 69 0.70
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (39 bp):
AAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAA
Found at i:634541 original size:36 final size:36
Alignment explanation
Indices: 634494--634579 Score: 118
Period size: 36 Copynumber: 2.4 Consensus size: 36
634484 ATTGAAAACA
* * **
634494 TTTCCCTTGAAATAAATTTTGTCTTTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTCGTCTCCCTTGAGATAG
*
634530 TTTCCCTTGAAACAAATTTCGTCTCCCTTGAGATAT
1 TTTCCCTTGAAACAAATTTCGTCTCCCTTGAGATAG
*
634566 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
634580 TAAACTTTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.43
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTCGTCTCCCTTGAGATAG
Found at i:634583 original size:101 final size:102
Alignment explanation
Indices: 634407--634606 Score: 312
Period size: 101 Copynumber: 2.0 Consensus size: 102
634397 TAAACAAAAG
* *
634407 ATTTTATCTTGCTTGACATAGTTTTCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
1 ATTTTATCTTGCTTGACATAGTTTCCCTTGAAACAAAATTTCGTCTCCCTTGAGACAGTTTCTCT
634472 TGAAACATAAACATTGAAAACATTTCCCTTGAAATAA
66 TGAAACATAAACATTGAAAACATTTCCCTTGAAATAA
* * * * *
634509 ATTTTGTCTTTCTTGAGATAGTTTCCCTTGAAAC-AAATTTCGTCTCCCTTGAGATATTTTCTCT
1 ATTTTATCTTGCTTGACATAGTTTCCCTTGAAACAAAATTTCGTCTCCCTTGAGACAGTTTCTCT
* *
634573 TGAAACATAAACTTTGAAAACGTTTCCCTTGAAA
66 TGAAACATAAACATTGAAAACATTTCCCTTGAAA
634607 CACAAAATAT
Statistics
Matches: 89, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
101 59 0.66
102 30 0.34
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.40
Consensus pattern (102 bp):
ATTTTATCTTGCTTGACATAGTTTCCCTTGAAACAAAATTTCGTCTCCCTTGAGACAGTTTCTCT
TGAAACATAAACATTGAAAACATTTCCCTTGAAATAA
Found at i:634779 original size:66 final size:66
Alignment explanation
Indices: 634644--634797 Score: 193
Period size: 66 Copynumber: 2.3 Consensus size: 66
634634 AAAACGAGTT
* * ** *
634644 TTGAAACAGTTTCCCTTGAAACACCTACATTTGAGATTGTTTCCCTTGAAACATGTTTTGTCTCT
1 TTGAGACAGTTTCCCTTGAAACACCAACATTTGAGATTGTTTCCCTTGAAACAAATTTCGTCTCT
634709 C
66 C
** * *
634710 TTGAGACAGTTTCTTTTGAAATACCAACCTTTGAGATTGTTTCCCTTGAAACAAATTTCGTCT-T
1 TTGAGACAGTTTCCCTTGAAACACCAACATTTGAGATTGTTTCCCTTGAAACAAATTTCGTCTCT
634774 GC
66 -C
*
634776 TTGAGACAATTTTCCCTTGAAA
1 TTGAGAC-AGTTTCCCTTGAAA
634798 TAAGAAATTT
Statistics
Matches: 74, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
65 1 0.01
66 62 0.84
67 11 0.15
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (66 bp):
TTGAGACAGTTTCCCTTGAAACACCAACATTTGAGATTGTTTCCCTTGAAACAAATTTCGTCTCT
C
Found at i:637221 original size:18 final size:16
Alignment explanation
Indices: 637200--637245 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 16
637190 ACAAAGTTTA
637200 TTTATTCATTTATATATT
1 TTTATT-ATTTAT-TATT
637218 TTTATTATTTATTATT
1 TTTATTATTTATTATT
637234 TTAATATTATTT
1 TT--TATTATTT
637246 TGTTTTTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.23
17 6 0.23
18 14 0.54
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTATTATTTATTATT
Found at i:637272 original size:2 final size:2
Alignment explanation
Indices: 637265--637301 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
637255 TTTATTGTTT
637265 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 T
637302 TATTTTTACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:637410 original size:3 final size:3
Alignment explanation
Indices: 637394--637500 Score: 57
Period size: 3 Copynumber: 36.3 Consensus size: 3
637384 AATTTATTTT
* *
637394 TTA TTA CTA CTA TTA TTA TTA TTA TTA TT- TATA CTTCA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA -TT-A TTA TTA TTA
* * * *
637441 TTA -TA TT- TCA -TA TGTT TTA TT- TTG TT- TTA TCTT TTA TTA TTA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
*
637483 TT- TTA TTA TTA TTT TTA T
1 TTA TTA TTA TTA TTA TTA T
637501 ATGCATTTTA
Statistics
Matches: 82, Mismatches: 10, Indels: 24
0.71 0.09 0.21
Matches are distributed among these distances:
2 11 0.13
3 62 0.76
4 7 0.09
5 2 0.02
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:637436 original size:20 final size:19
Alignment explanation
Indices: 637411--637451 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
637401 TACTATTATT
637411 ATTATTATTATTTATACTTC
1 ATTATTATTA-TTATACTTC
*
637431 ATTATTATTATTATATTTC
1 ATTATTATTATTATACTTC
637450 AT
1 AT
637452 ATGTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTATTATTATTATACTTC
Found at i:637484 original size:23 final size:23
Alignment explanation
Indices: 637406--637537 Score: 89
Period size: 23 Copynumber: 5.8 Consensus size: 23
637396 ATTACTACTA
637406 TTATTATTATTATTA-TTTATAC-T
1 TTATTATTATT-TTATTTTAT-CTT
* * *
637429 TCATTATTATTATTATATT-TCAT
1 TTATTATTATT-TTATTTTATCTT
* * *
637452 ATGTT-TTATTTTGTTTTATCTT
1 TTATTATTATTTTATTTTATCTT
637474 TTATTATTATTTTATTATTAT-TT
1 TTATTATTATTTTATT-TTATCTT
* *
637497 TTA-TATGCATTTTATTTTTTCCTT
1 TTATTAT-TATTTTATTTTAT-CTT
637521 TTATT-TTATTTTATTTT
1 TTATTATTATTTTATTTT
637538 TTATTTTACA
Statistics
Matches: 86, Mismatches: 14, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
21 5 0.06
22 18 0.21
23 50 0.58
24 12 0.14
25 1 0.01
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (23 bp):
TTATTATTATTTTATTTTATCTT
Found at i:637488 original size:18 final size:17
Alignment explanation
Indices: 637455--637545 Score: 61
Period size: 17 Copynumber: 5.6 Consensus size: 17
637445 ATTTCATATG
*
637455 TTTTATTTTGTTTTATC
1 TTTTATTTTATTTTATC
637472 TTTTATTATTATTTTAT-
1 TTTTATT-TTATTTTATC
* *
637489 TATTA-TTT-TTATATGC
1 TTTTATTTTATTTTAT-C
*
637505 ATTTTA--TT-TTTT-CC
1 -TTTTATTTTATTTTATC
*
637519 TTTTATTTTATTTTATT
1 TTTTATTTTATTTTATC
637536 TTTTATTTTA
1 TTTTATTTTA
637546 CATATATATA
Statistics
Matches: 58, Mismatches: 8, Indels: 16
0.71 0.10 0.20
Matches are distributed among these distances:
13 5 0.09
14 6 0.10
15 4 0.07
16 10 0.17
17 25 0.43
18 8 0.14
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (17 bp):
TTTTATTTTATTTTATC
Found at i:637545 original size:5 final size:5
Alignment explanation
Indices: 637455--637537 Score: 53
Period size: 5 Copynumber: 15.8 Consensus size: 5
637445 ATTTCATATG
* **
637455 TTTTA TTTTG TTTTA TCTTTTA TTATTA TTTTA TTATTA TTTTTA TATGCA
1 TTTTA TTTTA TTTTA --TTTTA TT-TTA TTTTA TT-TTA -TTTTA T-TTTA
**
637506 TTTTA -TTT- TTTCC TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
637538 TTATTTTACA
Statistics
Matches: 61, Mismatches: 9, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
4 5 0.08
5 35 0.57
6 14 0.23
7 7 0.11
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:637690 original size:19 final size:19
Alignment explanation
Indices: 637649--637703 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
637639 ACTTTTCTTC
* *
637649 ATTTTTTTATTAT-TTTTA
1 ATTTATTTATTTTATTTTA
*
637667 ATTTATTTGTTTTATTTTA
1 ATTTATTTATTTTATTTTA
* *
637686 TTTTATTTATTTTCTTTT
1 ATTTATTTATTTTATTTT
637704 TTTCCTCTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 10 0.33
19 20 0.67
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (19 bp):
ATTTATTTATTTTATTTTA
Found at i:637694 original size:14 final size:14
Alignment explanation
Indices: 637631--637703 Score: 55
Period size: 14 Copynumber: 5.3 Consensus size: 14
637621 ACTTTGTTTC
637631 TTTTATTTACTTTT-
1 TTTTATTTA-TTTTA
* *
637645 CTTCATTT-TTTTA
1 TTTTATTTATTTTA
*
637658 TTATT-TTTAATTTA
1 TT-TTATTTATTTTA
637672 TTTGT-TTTATTTTA
1 TTT-TATTTATTTTA
*
637686 TTTTATTTATTTTC
1 TTTTATTTATTTTA
637700 TTTT
1 TTTT
637704 TTTCCTCTTC
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
12 4 0.09
13 6 0.13
14 37 0.79
ACGTcount: A:0.16, C:0.05, G:0.01, T:0.77
Consensus pattern (14 bp):
TTTTATTTATTTTA
Found at i:637697 original size:9 final size:9
Alignment explanation
Indices: 637593--637698 Score: 63
Period size: 9 Copynumber: 11.3 Consensus size: 9
637583 CTTTACCTTA
637593 TTTATTTAT
1 TTTATTTAT
* *
637602 TTTGTTTTT
1 TTTATTTAT
*
637611 CCTTTAATTTAC
1 --TTT-ATTTAT
* *
637623 TTTGTTTCT
1 TTTATTTAT
637632 TTTATTTACT
1 TTTATTTA-T
* *
637642 TTTCTTCAT
1 TTTATTTAT
637651 TTT-TTTAT
1 TTTATTTAT
*
637659 TATT-TTTAA
1 T-TTATTTAT
*
637668 TTTATTTGT
1 TTTATTTAT
637677 TTTATTTTAT
1 TTTA-TTTAT
637687 TTTATTTAT
1 TTTATTTAT
637696 TTT
1 TTT
637699 CTTTTTTTCC
Statistics
Matches: 73, Mismatches: 17, Indels: 14
0.70 0.16 0.13
Matches are distributed among these distances:
8 7 0.10
9 42 0.58
10 18 0.25
11 3 0.04
12 3 0.04
ACGTcount: A:0.16, C:0.07, G:0.03, T:0.75
Consensus pattern (9 bp):
TTTATTTAT
Found at i:642982 original size:3 final size:3
Alignment explanation
Indices: 642974--643030 Score: 71
Period size: 3 Copynumber: 18.7 Consensus size: 3
642964 TGCCTATTTG
* *
642974 TAA TAA TAA TAA TAA TAT TAA TAA TAA AAA TATA TAA TAAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA T-AA TAA TAA
643021 T-A TAA TAA TA
1 TAA TAA TAA TA
643031 TAAATAAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 2 0.04
3 39 0.83
4 6 0.13
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:643011 original size:31 final size:31
Alignment explanation
Indices: 642976--643036 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
642966 CCTATTTGTA
642976 ATAAT-AATAATAATATTAATAATAAAAATAT
1 ATAATAAATAATAATA-TAATAATAAAAATAT
*
643007 ATAATAAATAATAATATAATAATATAAATA
1 ATAATAAATAATAATATAATAATAAAAATA
643037 AATTCGGGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 18 0.64
32 10 0.36
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (31 bp):
ATAATAAATAATAATATAATAATAAAAATAT
Found at i:643830 original size:113 final size:112
Alignment explanation
Indices: 643632--644478 Score: 1428
Period size: 113 Copynumber: 7.5 Consensus size: 112
643622 AAGTCGAACA
* * * *
643632 AGTTCTTCTCATTATGAACTTCCTCTGGAAATACTGATCCATCAAGTGATGAATTTAAGCAAAAG
1 AGTTCTTCTCATTATGAACTTTCTCTGGAAA-GCTGATCCATCAAGTGATGGATTTGAGCAAAAG
* * *
643697 GTTGAACAAGCTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATG
65 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATG
* *
643745 AGTTCTTCTCATTATGAACTTTTTCTGGAGAAGTTGATCCATCAAGTGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTTTCTCTGGA-AAGCTGATCCATCAAGTGATGGATTTGAGCAAAAG
*
643810 GTTGAACAAGTTATTCTCATTATGAACTTCTTCTTCCTTCTTTAGATG
65 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATG
*
643858 AGTTCTTCTCATTATGAACTTTATCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTTTCTCTGG-AAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAG
* *
643923 GTTGAACAAGTTATTCTCATTATGAACTTCTTATTCCTTCTTTAGATG
65 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATG
* *
643971 AGTTCTTCTCATTATGAACTTTTTCTGGAGAACCTGATCCATCAAGTGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTTTCTCTGGA-AAGCTGATCCATCAAGTGATGGATTTGAGCAAAAG
*
644036 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATG
65 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATG
644084 AGTTCTTCTCATTATGAACTTTCTCTGGAAATGCTGATCCATCAAGTGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTTTCTCTGGAAA-GCTGATCCATCAAGTGATGGATTTGAGCAAAAG
*
644149 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATG
65 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATG
644197 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTTTCTCTGG-AAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAG
644262 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATG
65 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATG
644310 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTTTCTCTGG-AAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAG
644375 GTTGAACAAGTTCTT-TCATTATGAACTTCTTCTT-CTTCTTTAGATG
65 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATG
* * *
644421 AGTTCTTTTCATTATAAACTTTCTCTGGAAAATCTGATCCATCAAGTGATGGATTTGA
1 AGTTCTTCTCATTATGAACTTTCTCTGG-AAAGCTGATCCATCAAGTGATGGATTTGA
644479 ATCTTTGCTA
Statistics
Matches: 705, Mismatches: 24, Indels: 12
0.95 0.03 0.02
Matches are distributed among these distances:
111 67 0.10
112 22 0.03
113 610 0.87
114 6 0.01
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (112 bp):
AGTTCTTCTCATTATGAACTTTCTCTGGAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGG
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATG
Found at i:646003 original size:23 final size:25
Alignment explanation
Indices: 645968--646014 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
645958 TGACCCCCTC
645968 TTTTTTCCTTTTTT-TTCTTCTTCTC
1 TTTTTTCCTTTTTTCTT-TTCTTCTC
645993 TTTTTT-C-TTTTTCTTTTCTTCT
1 TTTTTTCCTTTTTTCTTTTCTTCT
646015 TTTCATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 12 0.57
24 3 0.14
25 6 0.29
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (25 bp):
TTTTTTCCTTTTTTCTTTTCTTCTC
Found at i:646005 original size:21 final size:20
Alignment explanation
Indices: 645979--646029 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
645969 TTTTTCCTTT
*
645979 TTTTTCTTCTTCTCTTTTTTC
1 TTTTTCTTCTTCT-TCTTTTC
646000 TTTTTCTT-TTCTTCTTTTC
1 TTTTTCTTCTTCTTCTTTTC
*
646019 ATTTT-TTCTTC
1 TTTTTCTTCTTC
646030 AAGCATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 2 0.07
19 13 0.48
20 4 0.15
21 8 0.30
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTTCTTCTTCTTCTTTTC
Found at i:646009 original size:26 final size:25
Alignment explanation
Indices: 645965--646028 Score: 92
Period size: 25 Copynumber: 2.5 Consensus size: 25
645955 TCTTGACCCC
*
645965 CTCTTTTTTCCTTTTTTTTCTTCTT
1 CTCTTTTTTCTTTTTTTTTCTTCTT
645990 CTCTTTTTTCTTTTTCTTTTCTTCTT
1 CTCTTTTTTCTTTTT-TTTTCTTCTT
*
646016 TTCATTTTTTCTT
1 CTC-TTTTTTCTT
646029 CAAGCATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 14 0.40
26 12 0.34
27 9 0.26
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.77
Consensus pattern (25 bp):
CTCTTTTTTCTTTTTTTTTCTTCTT
Found at i:649748 original size:9 final size:9
Alignment explanation
Indices: 649731--649769 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
649721 GAAATAAATG
649731 AATGT-AAA
1 AATGTAAAA
649739 AATGTAAAA
1 AATGTAAAA
649748 AATGTAAAA
1 AATGTAAAA
*
649757 AATGTAAAG
1 AATGTAAAA
649766 AATG
1 AATG
649770 ATTGCTACTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
8 5 0.17
9 24 0.83
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (9 bp):
AATGTAAAA
Found at i:657174 original size:19 final size:19
Alignment explanation
Indices: 657150--657192 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
657140 TAATGCCCAA
657150 AATTTGGTATC-ATTAATAT
1 AATTT-GTATCTATTAATAT
* *
657169 AATTTGTCTCTATTATTAT
1 AATTTGTATCTATTAATAT
657188 AATTT
1 AATTT
657193 AAATATTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (19 bp):
AATTTGTATCTATTAATAT
Found at i:658949 original size:3 final size:3
Alignment explanation
Indices: 658928--658991 Score: 67
Period size: 3 Copynumber: 21.0 Consensus size: 3
658918 GGCCTGTTTG
* * *
658928 TAA TAG TAA TAA TAT TAA TAA TAA AAA TATA TAA TAAA TAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA T-AA TAA TAA TAA
*
658974 TAA TAA TAA TAA TTA TAA
1 TAA TAA TAA TAA TAA TAA
658992 ATAAAATCGG
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
2 2 0.04
3 42 0.84
4 6 0.12
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:658956 original size:15 final size:15
Alignment explanation
Indices: 658928--658986 Score: 75
Period size: 15 Copynumber: 3.9 Consensus size: 15
658918 GGCCTGTTTG
*
658928 TAATAGTAATAATAT
1 TAATAATAATAATAT
*
658943 TAATAATAAAAATAT
1 TAATAATAATAATAT
658958 ATAATAAATAATAATA-
1 -TAAT-AATAATAATAT
658974 TAATAATAATAAT
1 TAATAATAATAAT
658987 TATAAATAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
14 9 0.23
15 17 0.44
16 4 0.10
17 9 0.23
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.36
Consensus pattern (15 bp):
TAATAATAATAATAT
Found at i:658967 original size:17 final size:17
Alignment explanation
Indices: 658938--658982 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
658928 TAATAGTAAT
658938 AATAT-TAAT-AATAAA
1 AATATATAATAAATAAA
*
658953 AATATATAATAAATAAT
1 AATATATAATAAATAAA
658970 AATATAATAATAA
1 AATAT-ATAATAA
658983 TAATTATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 5 0.19
16 4 0.15
17 10 0.38
18 7 0.27
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AATATATAATAAATAAA
Found at i:659422 original size:2 final size:2
Alignment explanation
Indices: 659415--659477 Score: 119
Period size: 2 Copynumber: 32.0 Consensus size: 2
659405 CATCACACCA
659415 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
659457 -T AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
659478 CATTTGACAG
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 59 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:662114 original size:12 final size:11
Alignment explanation
Indices: 662099--662175 Score: 58
Period size: 10 Copynumber: 7.2 Consensus size: 11
662089 TTTTACCCTT
662099 TTTATTTATTTA
1 TTTATTTA-TTA
662111 TTTA-TTATTA
1 TTTATTTATTA
662121 -TTATTATAATTA
1 TTTATT-T-ATTA
*
662133 TTATATATATTA
1 TT-TATTTATTA
*
662145 -TTATATATTA
1 TTTATTTATTA
662155 -TTA-TTATTA
1 TTTATTTATTA
662164 -TTATTTATTA
1 TTTATTTATTA
662174 TT
1 TT
662176 AAATAATTAC
Statistics
Matches: 56, Mismatches: 2, Indels: 15
0.77 0.03 0.21
Matches are distributed among these distances:
9 11 0.20
10 22 0.39
11 6 0.11
12 12 0.21
13 2 0.04
14 3 0.05
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TTTATTTATTA
Found at i:662120 original size:3 final size:3
Alignment explanation
Indices: 662112--662176 Score: 87
Period size: 3 Copynumber: 21.0 Consensus size: 3
662102 ATTTATTTAT
*
662112 TTA TTA TTA TTA TTA TAA TTA TTA -TA TATA TTA TTA TATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA T-TA TTA TTA
662158 TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA
662177 AATAATTACA
Statistics
Matches: 56, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
2 2 0.04
3 45 0.80
4 9 0.16
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:662155 original size:19 final size:19
Alignment explanation
Indices: 662104--662176 Score: 89
Period size: 19 Copynumber: 3.8 Consensus size: 19
662094 CCCTTTTTAT
662104 TTATT-TAT-TTATTATTA
1 TTATTATATATTATTATTA
662121 TTATTATA-ATTATTATATATA
1 TTATTATATATTA-T-TAT-TA
662142 TTATTATATATTATTATTA
1 TTATTATATATTATTATTA
*
662161 TTATTATTTATTATTA
1 TTATTATATATTATTA
662177 AATAATTACA
Statistics
Matches: 49, Mismatches: 1, Indels: 10
0.82 0.02 0.17
Matches are distributed among these distances:
17 5 0.10
18 5 0.10
19 18 0.37
20 6 0.12
21 11 0.22
22 4 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATTATATATTATTATTA
Found at i:663477 original size:3 final size:3
Alignment explanation
Indices: 663464--663523 Score: 54
Period size: 3 Copynumber: 20.3 Consensus size: 3
663454 TTATTTGCAA
* * *
663464 TAT TAT T-T TAT TAT TAT TAT TGT TTT TAAT TAT TAT T-T CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT
663508 TAT TAT T-T TCAT TAT T
1 TAT TAT TAT T-AT TAT T
663524 TATATAAATA
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
2 5 0.11
3 38 0.81
4 4 0.09
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:663497 original size:16 final size:14
Alignment explanation
Indices: 663464--663523 Score: 75
Period size: 14 Copynumber: 4.1 Consensus size: 14
663454 TTATTTGCAA
663464 TATTATTTTATTAT
1 TATTATTTTATTAT
*
663478 TATTATTGTTTTTAAT
1 TATTATT-TTATT-AT
*
663494 TATTATTTCATTAT
1 TATTATTTTATTAT
663508 TATTATTTTCATTAT
1 TATTATTTT-ATTAT
663523 T
1 T
663524 TATATAAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
14 17 0.44
15 13 0.33
16 9 0.23
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (14 bp):
TATTATTTTATTAT
Found at i:664323 original size:16 final size:17
Alignment explanation
Indices: 664304--664336 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
664294 TTTTCAAAAT
664304 TTTTATA-TACTTATTA
1 TTTTATAGTACTTATTA
*
664320 TTTTATAGTATTTATTA
1 TTTTATAGTACTTATTA
664337 ATATTTCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (17 bp):
TTTTATAGTACTTATTA
Found at i:665956 original size:14 final size:14
Alignment explanation
Indices: 665918--665971 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
665908 ATTTTAAATA
*
665918 ATTTACATTTACAT
1 ATTTACATTTGCAT
*
665932 TTTTACATTTGCAT
1 ATTTACATTTGCAT
665946 ATTTACATTTGGCAT
1 ATTTACATTT-GCAT
* *
665961 CTTTGCATTTG
1 ATTTACATTTG
665972 TATTTTTATG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.52
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:669625 original size:7 final size:7
Alignment explanation
Indices: 669615--669670 Score: 51
Period size: 7 Copynumber: 7.4 Consensus size: 7
669605 AAGAAGAAGG
669615 AAAAAGA
1 AAAAAGA
669622 AAAAAGA
1 AAAAAGA
669629 AAAGAA-A
1 AAA-AAGA
*
669636 AAAGATGA
1 AAA-AAGA
669644 AAAAAGA
1 AAAAAGA
669651 AAAATGAGA
1 AAAA--AGA
669660 AAAAAGGA
1 AAAAA-GA
669668 AAA
1 AAA
669671 TTGAATCAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
7 24 0.57
8 11 0.26
9 7 0.17
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.04
Consensus pattern (7 bp):
AAAAAGA
Found at i:669633 original size:12 final size:12
Alignment explanation
Indices: 669616--669653 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
669606 AGAAGAAGGA
669616 AAAAGAAAAAAG
1 AAAAGAAAAAAG
669628 AAAAGAAAAAAG
1 AAAAGAAAAAAG
*
669640 --ATGAAAAAAG
1 AAAAGAAAAAAG
669650 AAAA
1 AAAA
669654 ATGAGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 9 0.41
12 13 0.59
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.03
Consensus pattern (12 bp):
AAAAGAAAAAAG
Found at i:669648 original size:17 final size:16
Alignment explanation
Indices: 669600--669670 Score: 60
Period size: 17 Copynumber: 4.5 Consensus size: 16
669590 CTCATCCAGC
* *
669600 AAAGAAAGAAGAAGGAA
1 AAAGAAAAAAG-AGAAA
669617 AAAG-AAAAA-AG--A
1 AAAGAAAAAAGAGAAA
669629 AAAGAAAAAAGATGAAA
1 AAAGAAAAAAGA-GAAA
*
669646 AAAGAAAAATGAGAAA
1 AAAGAAAAAAGAGAAA
669662 AAAGGAAAA
1 AAA-GAAAA
669671 TTGAATCAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
12 5 0.11
13 5 0.11
14 3 0.07
15 1 0.02
16 11 0.24
17 21 0.46
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (16 bp):
AAAGAAAAAAGAGAAA
Found at i:669671 original size:16 final size:17
Alignment explanation
Indices: 669628--669671 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
669618 AAGAAAAAAG
*
669628 AAAAGAAAAAAGATGAA
1 AAAAGAAAAATGATGAA
669645 AAAAGAAAAATGA-GAA
1 AAAAGAAAAATGATGAA
*
669661 AAAAGGAAAAT
1 AAAAGAAAAAT
669672 TGAATCAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 13 0.52
17 12 0.48
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.07
Consensus pattern (17 bp):
AAAAGAAAAATGATGAA
Found at i:671944 original size:113 final size:114
Alignment explanation
Indices: 671745--672083 Score: 554
Period size: 113 Copynumber: 3.0 Consensus size: 114
671735 AAGTGCCATG
*
671745 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* *
671810 TGGTTTGATATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATT
66 TGGTTTGGTATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAATT
*
671859 TGCTCATAGTAGAAATAAGGAG-CCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
*
671923 TGGTTTGGTATGAACCCCAAAACCAATCATTAAATTTGAAAGATGAATT
66 TGGTTTGGTATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAATT
* *
671972 TACTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * * * * *
672037 TGGTTCGGTAGGAACCACAGAACCAATCATTAGAATTGAGAGATGAA
66 TGGTTTGGTATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAA
672084 CTGCATGATC
Statistics
Matches: 209, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
113 108 0.52
114 101 0.48
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (114 bp):
TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGGTTTGGTATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAATT
Found at i:674637 original size:22 final size:22
Alignment explanation
Indices: 674606--674660 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
674596 ATCTACACTC
*
674606 TTCAAAGATGATAGATTCCCTT
1 TTCAAAGATGACAGATTCCCTT
* *
674628 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCCCTT
674650 TTCAAAGATGA
1 TTCAAAGATGA
674661 AAGCTTTATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCCCTT
Found at i:675264 original size:113 final size:113
Alignment explanation
Indices: 675055--675729 Score: 937
Period size: 113 Copynumber: 6.0 Consensus size: 113
675045 TAGCAAAGAT
* *
675055 TCAAATCCATCACTTAATGGATCAACTTTTCCAGAAAAAGTTCATAAT--G-AGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
*
675117 AGAAGGAAGAACAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
675165 TCAAATCCATTATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
*
675230 AGAAGGAAGAAGAAATTCATAATGAGAAAAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
675278 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTAA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
*
675343 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * *
675391 TCGAATTCATCACTCGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTAATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* * *
675456 AGAAGGAATAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTT-GC
** ** * * *** *
675504 TTGAATTTATCA-TTCGATGGATCAGCATTGCCAGAGCGAGTTCATAATGAGAAGAACTCATTTG
1 TCAAATCCATCACTT-GATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
* * *
675568 AAGAAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGC
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * * *
675617 TCGAATTCATCACTTGATAGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* * ** *
675682 AGAAAGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
675730 ATGACTCTAT
Statistics
Matches: 512, Mismatches: 46, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
110 44 0.09
112 7 0.01
113 455 0.89
114 6 0.01
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (113 bp):
TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:676089 original size:3 final size:3
Alignment explanation
Indices: 676081--676128 Score: 64
Period size: 3 Copynumber: 16.0 Consensus size: 3
676071 ATTTATTTAT
676081 TTA TTA TTA TTA TTA -TA TATA TTA TTA -TA TATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T-TA TTA TTA TTA TTA
676126 TTA
1 TTA
676129 AAAAATAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
2 4 0.10
3 31 0.76
4 6 0.15
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Done.