Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007734.1 Hibiscus syriacus cultivar Beakdansim tig00109991_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: 739340
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:522996 original size:21 final size:21
Alignment explanation
Indices: 522972--523013 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
522962 ATTTGAATTT
**
522972 TATGAAGGGGTATTGATTCCC
1 TATGAAGGGGTACCGATTCCC
522993 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
523014 CCCATTCTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:523334 original size:34 final size:32
Alignment explanation
Indices: 523295--523364 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
523285 TTTTGTAAAG
*
523295 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
523329 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
523361 GGGA
1 GGGA
523365 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:524397 original size:5 final size:5
Alignment explanation
Indices: 524387--524420 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
524377 TTTTAATCCA
524387 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
524421 AATATGATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:525858 original size:30 final size:29
Alignment explanation
Indices: 525789--525858 Score: 72
Period size: 30 Copynumber: 2.3 Consensus size: 29
525779 AGAATTAAAG
525789 TAGGATTAAATTGATAAATTTTTAAATAC
1 TAGGATTAAATTGATAAATTTTTAAATAC
* *
525818 TAAGAGTTAAATTTATCAAATAATTTTAAAT-C
1 TAGGA-TTAAATTGAT-AAAT--TTTTAAATAC
525850 -AGGATTAAA
1 TAGGATTAAA
525859 CTAATATAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
29 4 0.12
30 14 0.41
31 7 0.21
32 1 0.03
33 8 0.24
ACGTcount: A:0.47, C:0.04, G:0.10, T:0.39
Consensus pattern (29 bp):
TAGGATTAAATTGATAAATTTTTAAATAC
Found at i:530229 original size:51 final size:51
Alignment explanation
Indices: 530161--530261 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 51
530151 AACTTGCTCG
*
530161 ATAATATTTACGAAACTGAATTCGATTCGAATAATTAACCTGTAAACAACA
1 ATAATAATTACGAAACTGAATTCGATTCGAATAATTAACCTGTAAACAACA
* * * *
530212 ATAATAATTACGGAACTGAATTTGGTTCGATTAATTAACCTGTAAACAAC
1 ATAATAATTACGAAACTGAATTCGATTCGAATAATTAACCTGTAAACAAC
530262 GGAAAATAAG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.31
Consensus pattern (51 bp):
ATAATAATTACGAAACTGAATTCGATTCGAATAATTAACCTGTAAACAACA
Found at i:531567 original size:363 final size:366
Alignment explanation
Indices: 530869--531609 Score: 1301
Period size: 363 Copynumber: 2.0 Consensus size: 366
530859 TTATTTTAAA
*
530869 AAAGTTAAAAATATTATATTTAACAAATAACCCTAATTTCTCTTAAATTAAAAAAAAACTCTAAA
1 AAAGTTAAAAATATTATATTTAAAAAATAACCCTAATTTCTCTTAAATTAAAAAAAAACTCTAAA
* *
530934 TTTCTAAAAATCCTAAATTCTTATTCCGCCGACGTCGTTCTTGTCGGCCAAGGTCACCGCTGTCA
66 TTTCTAAAAATCCTAAATTCTTAATCCACCGACGTCGTTCTTGTCGGCCAAGGTCACCGCTGT--
*
530999 CCGACGTCCTTGTCATCTTCCTAGTCAAATGTCATCATTCTTGCCACCGATTGGTCTTCAGGATC
129 ----CGTCCTTGTCATCTTCCTAGTCAAATGTCATCATTCTTGCCACCGATTGGTCGTCAGGATC
531064 GCTCGGGTTTGCGATTTGCAGTGTCGGGATTTGTCGAGGTACACACGACAATTGACCATTGATTG
190 GCTCGGGTTTGCGATTTGCAGTGTCGGGATTTGTCGAGGTACACACGACAATTGACCATTGATTG
531129 ACTCCTATTCTGATGGCTTTTCATGGGGTTATCGGTCGCCAGGTGGAGGTGAGGTTCATCGACGG
255 ACTCCTATTCTGATGGCTTTTCATGGGGTTATCGGTCGCCAGGTGGAGGTGAGGTTCATCGACGG
*
531194 CAAAGACGACAATATACGTGGGTTTAGACGTTAAAATTAGAATTCTC
320 CAAAGACGACAATATACGTGGGTTTAGACATTAAAATTAGAATTCTC
*
531241 AAAGTTAAAAATATTATATTTAAAAAATAACCCTAATTTCTCTTAAATTAAAAAAAAACTCTAGA
1 AAAGTTAAAAATATTATATTTAAAAAATAACCCTAATTTCTCTTAAATTAAAAAAAAACTCTAAA
531306 TTTCTAAAAATCCTAAATTCTTAATCCACCGACGTCGTTCTTGTCGGCCAAGGTCACCG-T-T-G
66 TTTCTAAAAATCCTAAATTCTTAATCCACCGACGTCGTTCTTGTCGGCCAAGGTCACCGCTGTCG
* * *
531368 TCCTTGTCATCTTCCTAGTCAAATGTCATCATTCTTGCCGCTGATTGGTCGTCGGGATCGCTCGG
131 TCCTTGTCATCTTCCTAGTCAAATGTCATCATTCTTGCCACCGATTGGTCGTCAGGATCGCTCGG
531433 GTTTGCGATTTGCAGTGTCGGGATTTGTCGAGGTACACACGACAATTGACCATTGATTGACTCCT
196 GTTTGCGATTTGCAGTGTCGGGATTTGTCGAGGTACACACGACAATTGACCATTGATTGACTCCT
531498 ATTCTGATGGCTTTTCATGGGGTTATC-GTCGCCAGGTGGAGGTGAGGTTCATCGACGGCAAAGG
261 ATTCTGATGGCTTTTCATGGGGTTATCGGTCGCCAGGTGGAGGTGAGGTTCATCGACGGCAAA-G
*
531562 ACGACAATATGCGTGGGTTTAGACATTAAAATTAGAATTCTC
325 ACGACAATATACGTGGGTTTAGACATTAAAATTAGAATTCTC
531604 AAAGTT
1 AAAGTT
531610 TTGAATTTTT
Statistics
Matches: 358, Mismatches: 10, Indels: 11
0.94 0.03 0.03
Matches are distributed among these distances:
362 35 0.10
363 201 0.56
370 1 0.00
371 1 0.00
372 120 0.34
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (366 bp):
AAAGTTAAAAATATTATATTTAAAAAATAACCCTAATTTCTCTTAAATTAAAAAAAAACTCTAAA
TTTCTAAAAATCCTAAATTCTTAATCCACCGACGTCGTTCTTGTCGGCCAAGGTCACCGCTGTCG
TCCTTGTCATCTTCCTAGTCAAATGTCATCATTCTTGCCACCGATTGGTCGTCAGGATCGCTCGG
GTTTGCGATTTGCAGTGTCGGGATTTGTCGAGGTACACACGACAATTGACCATTGATTGACTCCT
ATTCTGATGGCTTTTCATGGGGTTATCGGTCGCCAGGTGGAGGTGAGGTTCATCGACGGCAAAGA
CGACAATATACGTGGGTTTAGACATTAAAATTAGAATTCTC
Found at i:534953 original size:2 final size:2
Alignment explanation
Indices: 534948--534972 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
534938 AAAATAAAAA
534948 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
534973 AAGCGACTAG
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:536496 original size:189 final size:192
Alignment explanation
Indices: 536152--536532 Score: 678
Period size: 189 Copynumber: 2.0 Consensus size: 192
536142 TTTAAAAGTC
*
536152 TAGGGACTCAACAAAACAACTCCCTATAGTTGAGGGATCATTTTGTAACTTTTAATAGTCAAGGG
1 TAGGGACTCAACAAAACAACTCCCTATAGTTGAAGGATCATTTTGTAACTTTTAATAGTCAAGGG
536217 ACTCAATAAAACATTATCCTATAGTTAGTCGGAGAACCATTTTTATACTTCACCCATTATTTAAT
66 ACTCAATAAAACATTATCCTATAG-TAGTCGGAGAACCATTTTTATACTTCACCCATTATTTAAT
536282 TTCTTCTAACATTTATCTTGCTTTTCTTCTTCTTCTCATTTCATCTTTCTCAGGTGAACTGAT
130 TTCTTCTAACATTTATCTTGCTTTTCTTCTTCTTCTCATTTCATCTTTCTCAGGTGAACTGAT
* * *
536345 TAGGGACTCAACAAAACAATTCTCTATAGTTGAAGGATTATTTTGTAACTTTTAATAGTCAAGGG
1 TAGGGACTCAACAAAACAACTCCCTATAGTTGAAGGATCATTTTGTAACTTTTAATAGTCAAGGG
* *
536410 ACTCAATAAAATATTAT-C-GTA-TAGTCGGAGAACCATTTTTATACTTCACCCATTATTTAATT
66 ACTCAATAAAACATTATCCTATAGTAGTCGGAGAACCATTTTTATACTTCACCCATTATTTAATT
536472 TCTTCTAACATTTATCTTGCTTTTCTTCTTCTTCTCATTTCATCTTTCTCAGGTGAACTGA
131 TCTTCTAACATTTATCTTGCTTTTCTTCTTCTTCTCATTTCATCTTTCTCAGGTGAACTGA
536533 ATTTACAAAT
Statistics
Matches: 182, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
189 102 0.56
191 2 0.01
192 1 0.01
193 77 0.42
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (192 bp):
TAGGGACTCAACAAAACAACTCCCTATAGTTGAAGGATCATTTTGTAACTTTTAATAGTCAAGGG
ACTCAATAAAACATTATCCTATAGTAGTCGGAGAACCATTTTTATACTTCACCCATTATTTAATT
TCTTCTAACATTTATCTTGCTTTTCTTCTTCTTCTCATTTCATCTTTCTCAGGTGAACTGAT
Found at i:537020 original size:15 final size:16
Alignment explanation
Indices: 536990--537019 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
536980 AATGATTATT
536990 TTAAATTTT-TAAAAA
1 TTAAATTTTATAAAAA
537005 TTAAATTTTATAAAA
1 TTAAATTTTATAAAA
537020 TATATATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAATTTTATAAAAA
Found at i:537028 original size:16 final size:14
Alignment explanation
Indices: 536990--537033 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
536980 AATGATTATT
536990 TTAAATTTTTAAAAA
1 TTAAA-TTTTAAAAA
537005 TTAAATTTTATAAAA
1 TTAAATTTTA-AAAA
*
537020 TATATATTTTAAAA
1 T-TAAATTTTAAAA
537034 CTACTTGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 5 0.19
15 13 0.50
16 8 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTAAATTTTAAAAA
Found at i:539729 original size:2 final size:2
Alignment explanation
Indices: 539724--539762 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
539714 AAATAATAAT
539724 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
539763 TAATAAATTT
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:546652 original size:3 final size:3
Alignment explanation
Indices: 546646--546678 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
546636 TATGTAACAT
*
546646 TAA TAA TAA TAT TAA TAA TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
546679 TTTAATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:546661 original size:6 final size:6
Alignment explanation
Indices: 546633--546692 Score: 52
Period size: 6 Copynumber: 10.2 Consensus size: 6
546623 TGTAAAAAAA
* * * * *
546633 TAATAT GTAACAT TAATAA TAATAT TAATAA TAATAA TAATA- TAATTT
1 TAATAT -TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT
546681 TAATA- TAATAT T
1 TAATAT TAATAT T
546693 TATAATCCGA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
5 9 0.20
6 30 0.68
7 5 0.11
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (6 bp):
TAATAT
Found at i:547063 original size:55 final size:54
Alignment explanation
Indices: 546981--547174 Score: 268
Period size: 55 Copynumber: 3.6 Consensus size: 54
546971 CCCTCTTTTT
* *
546981 TTCAGGGAGTAT-AGAACTCAAAC-ATCTTCAACACTCGTGTCTGTTCCCTATTCC
1 TTCAGAGAGTATAAG-ACTCGAACAATCTTCAACA-TCGTGTCTGTTCCCTATTCC
*
547035 TTCAGAGAGTATAAGACTTGAACAATCTTCAACAATCGTGTCT-TCTCCCTATTCC
1 TTCAGAGAGTATAAGACTCGAACAATCTTCAAC-ATCGTGTCTGT-TCCCTATTCC
* * *
547090 TTTAGAGAGTATAAGACTCGAACAATCTTCAACTATCATGTCTGCTCCCTATTCC
1 TTCAGAGAGTATAAGACTCGAACAATCTTCAAC-ATCGTGTCTGTTCCCTATTCC
547145 TTCAGAGAGTATAAGACTCGAACAATCTTC
1 TTCAGAGAGTATAAGACTCGAACAATCTTC
547175 TTCTTATGGG
Statistics
Matches: 126, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
54 18 0.14
55 107 0.85
56 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.31
Consensus pattern (54 bp):
TTCAGAGAGTATAAGACTCGAACAATCTTCAACATCGTGTCTGTTCCCTATTCC
Found at i:547192 original size:55 final size:55
Alignment explanation
Indices: 547025--547340 Score: 233
Period size: 55 Copynumber: 5.8 Consensus size: 55
547015 TCGTGTCTGT
* ** * *
547025 TCCCTATTCCTTCAGAGAGTATAAGACTTGAACAATCTTCAAC-AAT-CGTGTCTTC
1 TCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCTTCTAATGGGT-TC-GC
* **
547080 TCCCTATTCCTTTAGAGAGTATAAGACTCGAACAATCTTCAACTATCAT--G-TCTGC
1 TCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCTTCTA--ATGGGTTC-GC
*
547135 TCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCTTCTTATGGGTTCGC
1 TCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCTTCTAATGGGTTCGC
* * * * * * *
547190 TCCCTCTTTCTTCAGAGAGTAT-AGAACTTGAA-TATCTTCTTCAAACGGGTTTGC
1 TCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCTTCTAATGGGTTCGC
* * * * * * *
547244 TCCCTCTTTC-TCTAGGGAGTATAAAACTCGGAC-ATCTTCTTCAAACGGGTTCGC
1 TCCCTATTCCTTC-AGAGAGTATAAGACTCGAACAATCTTCTTCTAATGGGTTCGC
* * *
547298 TCCCTCTTTC-TCTAGGGAGTAT-AGAACTCGAAC-ATCTTCTTCT
1 TCCCTATTCCTTC-AGAGAGTATAAG-ACTCGAACAATCTTCTTCT
547341 GCTTCACTAC
Statistics
Matches: 227, Mismatches: 23, Indels: 23
0.83 0.08 0.08
Matches are distributed among these distances:
53 5 0.02
54 100 0.44
55 116 0.51
56 3 0.01
57 1 0.00
58 2 0.01
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (55 bp):
TCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCTTCTAATGGGTTCGC
Found at i:547193 original size:110 final size:109
Alignment explanation
Indices: 546958--547336 Score: 306
Period size: 110 Copynumber: 3.5 Consensus size: 109
546948 AGTATTTTGC
* * * *
546958 CAATGGGTTCGTTCCCTCTTTTTTTCAGGGAGTAT-AGAACTCAAACATCTTCAACACTCGTGTC
1 CAATGGGTTCGCTCCCTCTTTCTTT-AGAGAGTATAAGAACTCAAACATCTTCAACACTCATGTC
* *
547022 TGTTCCCTATTCCTTCAGAGAGTATAAGACTTGAACAATCTTCAA
65 TGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAA
* * * * *
547067 CAAT-CGTGTCTTCTCCCTATTCCTTTAGAGAGTATAAG-ACTCGAACAATCTTCAACTA-TCAT
1 CAATGGGT-TC-GCTCCCTCTTTCTTTAGAGAGTATAAGAACTCAAAC-ATCTTCAAC-ACTCAT
**
547129 GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCTT
62 GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAA
* * ** * ** ** ** *
547177 CTTATGGGTTCGCTCCCTCTTTCTTCAGAGAGTAT-AGAACTTGAATATCTTCTTCAAACGGGTT
1 C-AATGGGTTCGCTCCCTCTTTCTTTAGAGAGTATAAGAACTCAAACATCTTCAACACTCATGTC
* * * * * **
547241 TGCTCCCTCTTTC-TCTAGGGAGTATAAAACTCGGAC-ATCTTCTT
65 TGCTCCCTATTCCTTC-AGAGAGTATAAGACTCGAACAATCTTCAA
* * * *
547285 CAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTAT-AGAACTCGAACATCTTC
1 C-AATGGGTTCGCTCCCTCTTTCTTTAGAGAGTATAAGAACTCAAACATCTTC
547337 TTCTGCTTCA
Statistics
Matches: 220, Mismatches: 40, Indels: 21
0.78 0.14 0.07
Matches are distributed among these distances:
108 57 0.26
109 61 0.28
110 95 0.43
111 5 0.02
112 2 0.01
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (109 bp):
CAATGGGTTCGCTCCCTCTTTCTTTAGAGAGTATAAGAACTCAAACATCTTCAACACTCATGTCT
GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAA
Found at i:547248 original size:54 final size:54
Alignment explanation
Indices: 547148--547339 Score: 253
Period size: 54 Copynumber: 3.5 Consensus size: 54
547138 CTATTCCTTC
** *
547148 AGAGAGTATA-AGACTCGAACAATCTTCTTCTTATGGGTTCGCTCCCTCTTTCT-T
1 AGAGAGTATAGA-ACTCGAAC-ATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
* * *
547202 CAGAGAGTATAGAACTTGAATATCTTCTTCAAACGGGTTTGCTCCCTCTTTCTCT
1 -AGAGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
* * *
547257 AGGGAGTATAAAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
1 AGAGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
*
547311 AGGGAGTATAGAACTCGAACATCTTCTTC
1 AGAGAGTATAGAACTCGAACATCTTCTTC
547340 TGCTTCACTA
Statistics
Matches: 121, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
54 103 0.85
55 17 0.14
56 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (54 bp):
AGAGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
Found at i:561433 original size:3 final size:3
Alignment explanation
Indices: 561427--561459 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
561417 TATGTAACAT
*
561427 TAA TAA TAA TAT TAA TAA TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
561460 TTTAATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:561442 original size:6 final size:6
Alignment explanation
Indices: 561414--561473 Score: 52
Period size: 6 Copynumber: 10.2 Consensus size: 6
561404 TGTAAAAAAA
* * * * *
561414 TAATAT GTAACAT TAATAA TAATAT TAATAA TAATAA TAATA- TAATTT
1 TAATAT -TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT
561462 TAATA- TAATAT T
1 TAATAT TAATAT T
561474 TATAATCCGG
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
5 9 0.20
6 30 0.68
7 5 0.11
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (6 bp):
TAATAT
Found at i:561876 original size:59 final size:59
Alignment explanation
Indices: 561807--561918 Score: 215
Period size: 59 Copynumber: 1.9 Consensus size: 59
561797 CAGTGATTAA
*
561807 AGGGGTATTGTTCTCTCTAGAGATCTTGAATTCGAGCAGTTGTGCCTACGTCTACAGGG
1 AGGGGTATTGTTCTCTCTAGAAATCTTGAATTCGAGCAGTTGTGCCTACGTCTACAGGG
561866 AGGGGTATTGTTCTCTCTAGAAATCTTGAATTCGAGCAGTTGTGCCTACGTCT
1 AGGGGTATTGTTCTCTCTAGAAATCTTGAATTCGAGCAGTTGTGCCTACGTCT
561919 GCATGGAGTG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 52 1.00
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.34
Consensus pattern (59 bp):
AGGGGTATTGTTCTCTCTAGAAATCTTGAATTCGAGCAGTTGTGCCTACGTCTACAGGG
Found at i:562951 original size:2 final size:2
Alignment explanation
Indices: 562944--562983 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
562934 TTTTAAATTC
562944 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
562984 TCAATTAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:564453 original size:30 final size:30
Alignment explanation
Indices: 564417--564473 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
564407 CTACAGTTCG
564417 AATGAAGGTCGCC-GAGTGGTCAGGGCGACC
1 AATGAAGGTCGCCAG-GTGGTCAGGGCGACC
*
564447 AATGAAGGTCGCCAGGTGGTCTGGGCG
1 AATGAAGGTCGCCAGGTGGTCAGGGCG
564474 CCATGCAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.21, C:0.21, G:0.42, T:0.16
Consensus pattern (30 bp):
AATGAAGGTCGCCAGGTGGTCAGGGCGACC
Found at i:564689 original size:50 final size:50
Alignment explanation
Indices: 564626--564727 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
564616 TTTATCCTAT
564626 TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
1 TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
564676 TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
1 TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
564726 TT
1 TT
564728 CTATAATTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.25, C:0.02, G:0.16, T:0.57
Consensus pattern (50 bp):
TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
Found at i:565260 original size:20 final size:20
Alignment explanation
Indices: 565237--565276 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
565227 GTATTTAACC
565237 CAAACAACTAGTGTTTAGTG
1 CAAACAACTAGTGTTTAGTG
565257 CAAACAACTAGTGTTTAGTG
1 CAAACAACTAGTGTTTAGTG
565277 TTTTGTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (20 bp):
CAAACAACTAGTGTTTAGTG
Found at i:565531 original size:24 final size:24
Alignment explanation
Indices: 565504--565553 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
565494 AAATTGACGT
565504 CATAAATCACCTCAAAAACTAAAC
1 CATAAATCACCTCAAAAACTAAAC
565528 CATAAATCACCTCAAAAACTAAAC
1 CATAAATCACCTCAAAAACTAAAC
565552 CA
1 CA
565554 ATCCTCCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.54, C:0.30, G:0.00, T:0.16
Consensus pattern (24 bp):
CATAAATCACCTCAAAAACTAAAC
Found at i:575544 original size:22 final size:22
Alignment explanation
Indices: 575516--575573 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
575506 TTTTTTCAAA
575516 GTCAAAGTCAACGATCAGACCG
1 GTCAAAGTCAACGATCAGACCG
*
575538 GTCAAAGAT-AACGGTCAGACCG
1 GTCAAAG-TCAACGATCAGACCG
*
575560 ATCAACAGTCAACG
1 GTCAA-AGTCAACG
575574 GGTCAGGATG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 24 0.77
23 7 0.23
ACGTcount: A:0.38, C:0.26, G:0.22, T:0.14
Consensus pattern (22 bp):
GTCAAAGTCAACGATCAGACCG
Found at i:576939 original size:48 final size:48
Alignment explanation
Indices: 576884--577002 Score: 172
Period size: 48 Copynumber: 2.5 Consensus size: 48
576874 CACTAAAACA
*
576884 ACTTGATTCAAATAAATTAATTTTTTAAAATATATTCGACCCA-CCTCG
1 ACTTGATTCAAATAAATTAATTTTTTAAAATATATTC-AACCAGCCTCG
*
576932 ACTTGATTCGAAA-AAAATAATTTTTTAAAATATATTCAACCAGCCTCG
1 ACTTGATTC-AAATAAATTAATTTTTTAAAATATATTCAACCAGCCTCG
576980 ACTTGATT-AGAATAAATTAATTT
1 ACTTGATTCA-AATAAATTAATTT
577003 ATATTCAACC
Statistics
Matches: 64, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
46 1 0.02
47 6 0.09
48 54 0.84
49 3 0.05
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37
Consensus pattern (48 bp):
ACTTGATTCAAATAAATTAATTTTTTAAAATATATTCAACCAGCCTCG
Found at i:577006 original size:40 final size:40
Alignment explanation
Indices: 576962--577126 Score: 253
Period size: 40 Copynumber: 4.2 Consensus size: 40
576952 TTTTTTAAAA
576962 TATATTCAA-CCAGCCTCGACTTGATTAGAATAAATTAATT
1 TATATTCAACCCA-CCTCGACTTGATTAGAATAAATTAATT
*
577002 TATATTCAACCCACCTTGACTTGATTAGAATAAATTAATT
1 TATATTCAACCCACCTCGACTTGATTAGAATAAATTAATT
* *
577042 TATATTCAACCC-CCTCAACTTGATTCGAATAAATTAATT
1 TATATTCAACCCACCTCGACTTGATTAGAATAAATTAATT
* * *
577081 TATATTCAACCCACCTCGACTTGATTCGAAAAAATTAGTT
1 TATATTCAACCCACCTCGACTTGATTAGAATAAATTAATT
577121 TATATT
1 TATATT
577127 TGACCCTCCT
Statistics
Matches: 116, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
39 36 0.31
40 77 0.66
41 3 0.03
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.36
Consensus pattern (40 bp):
TATATTCAACCCACCTCGACTTGATTAGAATAAATTAATT
Found at i:577072 original size:79 final size:79
Alignment explanation
Indices: 576962--577161 Score: 265
Period size: 79 Copynumber: 2.5 Consensus size: 79
576952 TTTTTTAAAA
* * *
576962 TATATTCAACCAGCCTCGACTTGATTAGAATAAATTAATTTATATTCAACCCACCTTGACTTGAT
1 TATATTCAACC-CCCTCAACTTGATTAGAATAAATTAATTTATATTCAACCCACCTCGACTTGAT
*
577027 TAGAATAAATTAATT
65 TAGAAAAAATTAATT
*
577042 TATATTCAACCCCCTCAACTTGATTCGAATAAATTAATTTATATTCAACCCACCTCGACTTGATT
1 TATATTCAACCCCCTCAACTTGATTAGAATAAATTAATTTATATTCAACCCACCTCGACTTGATT
* *
577107 CGAAAAAATTAGTT
66 AGAAAAAATTAATT
** * * * *
577121 TATATTTGACCCTCCTTAACTTAATTTGGATAAATTAATTT
1 TATATTCAACCC-CCTCAACTTGATTAGAATAAATTAATTT
577162 GAATAAATTA
Statistics
Matches: 106, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
79 71 0.67
80 35 0.33
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.38
Consensus pattern (79 bp):
TATATTCAACCCCCTCAACTTGATTAGAATAAATTAATTTATATTCAACCCACCTCGACTTGATT
AGAAAAAATTAATT
Found at i:577156 original size:40 final size:40
Alignment explanation
Indices: 576962--577161 Score: 242
Period size: 40 Copynumber: 5.0 Consensus size: 40
576952 TTTTTTAAAA
* *
576962 TATATTCAA-CCAGCCTCGACTTGATTAGAATAAATTAATT
1 TATATTCAACCCA-CCTCAACTTGATTCGAATAAATTAATT
** *
577002 TATATTCAACCCACCTTGACTTGATTAGAATAAATTAATT
1 TATATTCAACCCACCTCAACTTGATTCGAATAAATTAATT
577042 TATATTCAACCC-CCTCAACTTGATTCGAATAAATTAATT
1 TATATTCAACCCACCTCAACTTGATTCGAATAAATTAATT
* * *
577081 TATATTCAACCCACCTCGACTTGATTCGAAAAAATTAGTT
1 TATATTCAACCCACCTCAACTTGATTCGAATAAATTAATT
** * * * * *
577121 TATATTTGACCCTCCTTAACTTAATTTGGATAAATTAATT
1 TATATTCAACCCACCTCAACTTGATTCGAATAAATTAATT
577161 T
1 T
577162 GAATAAATTA
Statistics
Matches: 141, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
39 36 0.26
40 102 0.72
41 3 0.02
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.38
Consensus pattern (40 bp):
TATATTCAACCCACCTCAACTTGATTCGAATAAATTAATT
Found at i:577160 original size:14 final size:14
Alignment explanation
Indices: 577141--577175 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
577131 CCTCCTTAAC
*
577141 TTAATTTGGATAAA
1 TTAATTTGAATAAA
577155 TTAATTTGAATAAA
1 TTAATTTGAATAAA
577169 TTAATTT
1 TTAATTT
577176 ATATTCGGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.49
Consensus pattern (14 bp):
TTAATTTGAATAAA
Found at i:580243 original size:9 final size:9
Alignment explanation
Indices: 580229--580255 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
580219 ATATATAATC
580229 TAAAAAATA
1 TAAAAAATA
580238 TAAAAAATA
1 TAAAAAATA
580247 TAAAAAATA
1 TAAAAAATA
580256 AAATTATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (9 bp):
TAAAAAATA
Found at i:586843 original size:13 final size:14
Alignment explanation
Indices: 586817--586849 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
586807 AGTGTTCAAA
*
586817 TTAATCCGTTACTG
1 TTAATCCGTAACTG
586831 TTAA-CCGTAACTG
1 TTAATCCGTAACTG
586844 TTAATC
1 TTAATC
586850 AGTGTAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.39
Consensus pattern (14 bp):
TTAATCCGTAACTG
Found at i:587623 original size:14 final size:14
Alignment explanation
Indices: 587606--587632 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
587596 GACTTCACAG
587606 TTTGAATTTCAAAC
1 TTTGAATTTCAAAC
587620 TTTGAATTTCAAA
1 TTTGAATTTCAAA
587633 GTTTATCATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.44
Consensus pattern (14 bp):
TTTGAATTTCAAAC
Found at i:589882 original size:19 final size:19
Alignment explanation
Indices: 589858--589895 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
589848 TTACCATTCT
589858 ACTACTTAAAAATATGAAG
1 ACTACTTAAAAATATGAAG
589877 ACTACTTAAAAATATGAAG
1 ACTACTTAAAAATATGAAG
589896 TTGCAAGAAG
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:0.53, C:0.11, G:0.11, T:0.26
Consensus pattern (19 bp):
ACTACTTAAAAATATGAAG
Found at i:596896 original size:2 final size:2
Alignment explanation
Indices: 596889--596925 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
596879 CGTAACCTAA
596889 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
596926 AAATAAACAG
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:600181 original size:72 final size:72
Alignment explanation
Indices: 600100--600243 Score: 288
Period size: 72 Copynumber: 2.0 Consensus size: 72
600090 CCCTCTCTTT
600100 TACTTTTTTTCTTATTTACAACTTTATCAATTTTATTGATTAATTCAACTTTTTCTTCTTTAATT
1 TACTTTTTTTCTTATTTACAACTTTATCAATTTTATTGATTAATTCAACTTTTTCTTCTTTAATT
600165 TTGTTTA
66 TTGTTTA
600172 TACTTTTTTTCTTATTTACAACTTTATCAATTTTATTGATTAATTCAACTTTTTCTTCTTTAATT
1 TACTTTTTTTCTTATTTACAACTTTATCAATTTTATTGATTAATTCAACTTTTTCTTCTTTAATT
600237 TTGTTTA
66 TTGTTTA
600244 ACTGACGGTG
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.24, C:0.12, G:0.03, T:0.61
Consensus pattern (72 bp):
TACTTTTTTTCTTATTTACAACTTTATCAATTTTATTGATTAATTCAACTTTTTCTTCTTTAATT
TTGTTTA
Found at i:601768 original size:19 final size:21
Alignment explanation
Indices: 601744--601793 Score: 68
Period size: 19 Copynumber: 2.4 Consensus size: 21
601734 AGTCAATTGT
*
601744 TTTATTAAATAT-TCAAT-AA
1 TTTATTAAATATATAAATAAA
601763 TTTATTAAATATATAAATAAAA
1 TTTATTAAATATATAAAT-AAA
601785 TTTATTAAA
1 TTTATTAAA
601794 CTTTCTATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 12 0.44
20 4 0.15
22 11 0.41
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
TTTATTAAATATATAAATAAA
Found at i:605071 original size:29 final size:29
Alignment explanation
Indices: 604987--605102 Score: 83
Period size: 29 Copynumber: 3.9 Consensus size: 29
604977 CCGTGTAATT
* *
604987 TAAAAAATGTTAGGTACCTAATTGCACCAA
1 TAAAAAA-ATTAGGTACCAAATTGCACCAA
* * ** *
605017 -AACATAAAAGTTGGGTGCCTGATTGCACCAT
1 TAA-A-AAAA-TTAGGTACCAAATTGCACCAA
*
605048 TAAAAAAAGTTA-GTACCAAATTGCACGAA
1 TAAAAAAA-TTAGGTACCAAATTGCACCAA
* *
605077 TACAAAAATTAGGTACCACATTGCAC
1 TAAAAAAATTAGGTACCAAATTGCAC
605103 ATAAATGCTA
Statistics
Matches: 68, Mismatches: 13, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
28 3 0.04
29 34 0.50
30 8 0.12
31 21 0.31
32 2 0.03
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (29 bp):
TAAAAAAATTAGGTACCAAATTGCACCAA
Found at i:614475 original size:21 final size:21
Alignment explanation
Indices: 614446--614498 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
614436 ATTCTGACTA
614446 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
614467 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
614488 TCGCAATGCGA
1 TCGCATTGCGA
614499 ATACATAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:614743 original size:22 final size:22
Alignment explanation
Indices: 614718--614783 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
614708 GGCGACATCC
*
614718 GTCCCCATCTTCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
* *
614740 GTCCCCATCTCCAACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
614762 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
614784 TTCACGGTCA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.26, C:0.38, G:0.14, T:0.23
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:615208 original size:20 final size:20
Alignment explanation
Indices: 615159--615209 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
615149 TCAAATTCGC
*
615159 GTTGCGATTGTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
**
615179 GTTGCGATTTTCATTTTTGT
1 GTTGCGATTTTCATTTTCAT
615199 GTTGCGATTTT
1 GTTGCGATTTT
615210 AAGTTTCAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.12, C:0.12, G:0.22, T:0.55
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:627162 original size:20 final size:20
Alignment explanation
Indices: 627137--627259 Score: 143
Period size: 20 Copynumber: 6.5 Consensus size: 20
627127 AGAATAGTTT
627137 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
627157 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* *
627177 ACTATCACAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
627193 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
** *
627210 AAAATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
627230 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
627250 ACTATCGCAA
1 ACTATCGCAA
627260 CGAAAGAATC
Statistics
Matches: 88, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
14 6 0.07
16 6 0.07
17 4 0.05
18 2 0.02
19 10 0.11
20 60 0.68
ACGTcount: A:0.42, C:0.22, G:0.20, T:0.16
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:627261 original size:73 final size:73
Alignment explanation
Indices: 627140--627291 Score: 250
Period size: 73 Copynumber: 2.1 Consensus size: 73
627130 ATAGTTTACT
* * *
627140 ATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCACAACGAGAGAATCGCAATGCG
1 ATCGCAACGCGAAAATGACTATCGCAACGCGAAAATGACTATCACAACGAAAGAATCGCAATACG
627205 AAATGAAA
66 AAATGAAA
* * *
627213 ATCGCAACGCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAACGAAAGAATCGTAATACG
1 ATCGCAACGCGAAAATGACTATCGCAACGCGAAAATGACTATCACAACGAAAGAATCGCAATACG
627278 AAATGAAA
66 AAATGAAA
627286 ATCGCA
1 ATCGCA
627292 TTGCGATTTT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.44, C:0.20, G:0.20, T:0.16
Consensus pattern (73 bp):
ATCGCAACGCGAAAATGACTATCGCAACGCGAAAATGACTATCACAACGAAAGAATCGCAATACG
AAATGAAA
Found at i:627331 original size:20 final size:20
Alignment explanation
Indices: 627306--627408 Score: 154
Period size: 20 Copynumber: 5.2 Consensus size: 20
627296 GATTTTCTCG
**
627306 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
627326 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
627346 TTACGATAGTCATTTTCG-A
1 TTGCGATAGTCATTTTCGCA
*
627365 GTTGCGATAGTCATTTTCGCG
1 -TTGCGATAGTCATTTTCGCA
627386 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
627406 TTG
1 TTG
627409 TGATTTTAAG
Statistics
Matches: 75, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
19 1 0.01
20 74 0.99
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.39
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:627937 original size:18 final size:19
Alignment explanation
Indices: 627898--627941 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 19
627888 TTCACCTATC
627898 ATCATTCAAAAGGCCTCCCCT
1 ATCATTCAAAAGG-C-CCCCT
627919 ATCATTCAAAAGG-CCCCT
1 ATCATTCAAAAGGCCCCCT
627937 ATCAT
1 ATCAT
627942 CCCTCAAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.43
21 13 0.57
ACGTcount: A:0.32, C:0.34, G:0.09, T:0.25
Consensus pattern (19 bp):
ATCATTCAAAAGGCCCCCT
Found at i:629408 original size:14 final size:14
Alignment explanation
Indices: 629389--629424 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
629379 ATTGTTTAAT
629389 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
629403 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
629417 TGATTTGT
1 TGATTTGT
629425 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:629549 original size:14 final size:14
Alignment explanation
Indices: 629530--629583 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
629520 AAAACAGACT
629530 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
629544 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
629563 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
629577 ATCGCAA
1 ATCGCAA
629584 TGCGAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:629567 original size:33 final size:34
Alignment explanation
Indices: 629530--629605 Score: 145
Period size: 33 Copynumber: 2.3 Consensus size: 34
629520 AAAACAGACT
629530 ATCGCAACGAGAGAATCGCAATGCG-AAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
629563 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
629597 ATCGCAACG
1 ATCGCAACG
629606 CGAAATTCTC
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 25 0.60
34 17 0.40
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.12
Consensus pattern (34 bp):
ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
Found at i:629601 original size:20 final size:19
Alignment explanation
Indices: 629543--629611 Score: 76
Period size: 19 Copynumber: 3.8 Consensus size: 19
629533 GCAACGAGAG
629543 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
629562 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
629576 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
629596 AATCGCAACGCGAAAT
1 AATCGCAATGCGAAAT
629612 TCTCGTTGCA
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
14 10 0.24
15 1 0.02
16 2 0.05
17 2 0.05
19 13 0.32
20 13 0.32
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:629675 original size:20 final size:20
Alignment explanation
Indices: 629650--629741 Score: 159
Period size: 20 Copynumber: 4.6 Consensus size: 20
629640 GATTCTCTCA
629650 TTGCGATAGTCATTTCCGCG
1 TTGCGATAGTCATTTCCGCG
629670 TTGCGATAGTCATTTCCGCG
1 TTGCGATAGTCATTTCCGCG
*
629690 TTGCGATAGTCATTTCCGTG
1 TTGCGATAGTCATTTCCGCG
629710 TTGCGATAGTCATATT-CGCG
1 TTGCGATAGTCAT-TTCCGCG
629730 TTGCGATAGTCA
1 TTGCGATAGTCA
629742 AATGAATGTC
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
20 67 0.97
21 2 0.03
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCGCG
Found at i:631947 original size:14 final size:14
Alignment explanation
Indices: 631928--631963 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
631918 TCCCGTGGCA
631928 TTTTCTTAGGGGAT
1 TTTTCTTAGGGGAT
*
631942 TTTTCTTTGGGGAT
1 TTTTCTTAGGGGAT
631956 TTCTTCTT
1 TT-TTCTT
631964 CTTCTTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.08, C:0.11, G:0.22, T:0.58
Consensus pattern (14 bp):
TTTTCTTAGGGGAT
Found at i:632188 original size:24 final size:24
Alignment explanation
Indices: 632154--632207 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
632144 CTGAAAAATC
632154 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
632178 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
*
632202 AACAAA
1 ATCAAA
632208 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:0.43, C:0.20, G:0.19, T:0.19
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:633074 original size:20 final size:20
Alignment explanation
Indices: 633049--633155 Score: 169
Period size: 20 Copynumber: 5.3 Consensus size: 20
633039 AAATTCAGTA
633049 TTGCGATAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCG
*
633069 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
* *
633089 TTGCGATAGTTAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
633109 TTGCGATAGTCATAATCGCG
1 TTGCGATAGTCAGAATCGCG
*
633129 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
633149 TTGCGAT
1 TTGCGAT
633156 TTACATATTC
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 80 1.00
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:633165 original size:20 final size:20
Alignment explanation
Indices: 633142--633210 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
633132 CGATAGTCAG
*
633142 ATTCGCGTTGCGATTTACAT
1 ATTCGCATTGCGATTTACAT
*
633162 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACAT
* *
633182 AGTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACAT
633202 ATTCGCATT
1 ATTCGCATT
633211 ACGAATTAGG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACAT
Found at i:633173 original size:40 final size:40
Alignment explanation
Indices: 633048--633175 Score: 159
Period size: 40 Copynumber: 3.2 Consensus size: 40
633038 GAAATTCAGT
* *
633048 ATTGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCTC
1 ATTGCGATAGTCAGAATCGCGTTGCGATAGTCATAATCGC
* * *
633088 GTTGCGATAGTTAGAATCTCGTTGCGATAGTCATAATCGC
1 ATTGCGATAGTCAGAATCGCGTTGCGATAGTCATAATCGC
* * * *
633128 GTTGCGATAGTCAGATTCGCGTTGCGAT-TTACATATTCGC
1 ATTGCGATAGTCAGAATCGCGTTGCGATAGT-CATAATCGC
633168 ATTGCGAT
1 ATTGCGAT
633176 TTACGTAGTC
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
39 1 0.01
40 75 0.99
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (40 bp):
ATTGCGATAGTCAGAATCGCGTTGCGATAGTCATAATCGC
Found at i:633173 original size:60 final size:60
Alignment explanation
Indices: 633048--633175 Score: 172
Period size: 60 Copynumber: 2.1 Consensus size: 60
633038 GAAATTCAGT
* *
633048 ATTGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCTCGTTGCGATAGTTAGAATCTCG
1 ATTGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGATA-TTACAATCTCG
* *
633109 -TTGCGATAGTCATAATCGCGTTGCGATAGTCAGATTCGCGTTGCGAT-TTACATAT-TCG
1 ATTGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGATATTACA-ATCTCG
633167 CATTGCGAT
1 -ATTGCGAT
633176 TTACGTAGTC
Statistics
Matches: 60, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
58 7 0.12
59 2 0.03
60 51 0.85
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (60 bp):
ATTGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGATATTACAATCTCG
Found at i:634191 original size:20 final size:20
Alignment explanation
Indices: 634155--634192 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
634145 ATCCTATTCC
**
634155 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
634175 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
634193 GTGAACCAAA
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:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:640399 original size:21 final size:21
Alignment explanation
Indices: 640373--640414 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
640363 TGGACGAATA
640373 TCGGAGACAAGACAGTTGGGG
1 TCGGAGACAAGACAGTTGGGG
640394 TCGGAGACAAGACAGTTGGGG
1 TCGGAGACAAGACAGTTGGGG
640415 ACTTACTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.43, T:0.14
Consensus pattern (21 bp):
TCGGAGACAAGACAGTTGGGG
Found at i:642333 original size:2 final size:2
Alignment explanation
Indices: 642322--642385 Score: 70
Period size: 2 Copynumber: 35.0 Consensus size: 2
642312 ATATTCAAAT
642322 TA TA -A TA TA TA T- TA TA T- TA TA -A T- TA -A TGA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA
642359 TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
642386 GTTAATATTC
Statistics
Matches: 54, Mismatches: 0, Indels: 16
0.77 0.00 0.23
Matches are distributed among these distances:
1 7 0.13
2 45 0.83
3 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:643532 original size:11 final size:11
Alignment explanation
Indices: 643518--643552 Score: 70
Period size: 11 Copynumber: 3.2 Consensus size: 11
643508 ATTTTAATAG
643518 AAAAAATCTAA
1 AAAAAATCTAA
643529 AAAAAATCTAA
1 AAAAAATCTAA
643540 AAAAAATCTAA
1 AAAAAATCTAA
643551 AA
1 AA
643553 TTTATAGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAAAATCTAA
Found at i:654914 original size:19 final size:19
Alignment explanation
Indices: 654903--654952 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
654893 CTTGGAAAAT
654903 CTAGTATAACTTGGCAAGC
1 CTAGTATAACTTGGCAAGC
654922 CTAGTATAACTTGGCAAGC
1 CTAGTATAACTTGGCAAGC
654941 CTAGTATAACTT
1 CTAGTATAACTT
654953 TTGTAATAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (19 bp):
CTAGTATAACTTGGCAAGC
Found at i:657128 original size:116 final size:116
Alignment explanation
Indices: 656924--657155 Score: 446
Period size: 116 Copynumber: 2.0 Consensus size: 116
656914 GTATTCCATT
*
656924 GCCATTCTCTCTTCAAATCCCAGTTAAGAAAACACGAAACCTAAAACACATCAATAACAAATTAA
1 GCCATTCTCTCTTCAAATCCCAGTTAAGAAAACACGAAACCTAAAACACATCAATAACAAAGTAA
656989 GAAGAGAAATGTAAGATTTACAACAAAAGACTAACTTTACACGAAAATTTA
66 GAAGAGAAATGTAAGATTTACAACAAAAGACTAACTTTACACGAAAATTTA
657040 GCCATTCTCTCTTCAAATCCCAGTTAAGAAAACACGAAACCTAAAACACATCAATAACAAAGTAA
1 GCCATTCTCTCTTCAAATCCCAGTTAAGAAAACACGAAACCTAAAACACATCAATAACAAAGTAA
*
657105 GAAGATAAATGTAAGATTTACAACAAAAGACTAACTTTACACGAAAATTTA
66 GAAGAGAAATGTAAGATTTACAACAAAAGACTAACTTTACACGAAAATTTA
657156 TATAAAAAGG
Statistics
Matches: 114, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
116 114 1.00
ACGTcount: A:0.48, C:0.20, G:0.09, T:0.22
Consensus pattern (116 bp):
GCCATTCTCTCTTCAAATCCCAGTTAAGAAAACACGAAACCTAAAACACATCAATAACAAAGTAA
GAAGAGAAATGTAAGATTTACAACAAAAGACTAACTTTACACGAAAATTTA
Found at i:658986 original size:37 final size:37
Alignment explanation
Indices: 658918--658988 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
658908 TTGAGTTTAA
* * * **
658918 TCGAGTGGAGGATGTAAAATTTTTGGGTCGGATCGAG
1 TCGAGTAGAGGATATAAAATTTTCGAATCGGATCGAG
658955 TCGAGTAGAGGATATAAAATTTTCGAATCGGATC
1 TCGAGTAGAGGATATAAAATTTTCGAATCGGATC
658989 AAATTGACCA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.30, C:0.10, G:0.31, T:0.30
Consensus pattern (37 bp):
TCGAGTAGAGGATATAAAATTTTCGAATCGGATCGAG
Found at i:659300 original size:15 final size:15
Alignment explanation
Indices: 659282--659323 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
659272 ATTTTTTAAA
659282 AAAATATTTAAAATT
1 AAAATATTTAAAATT
* *
659297 AAAAAATTTTAAATT
1 AAAATATTTAAAATT
*
659312 -ATATATTTAAAA
1 AAAATATTTAAAA
659324 AAACAGAAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAATATTTAAAATT
Found at i:659913 original size:31 final size:31
Alignment explanation
Indices: 659855--659913 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
659845 GAGACAAAAT
*
659855 TAGTTTAGACACCTATTTGGTTTTTAAGGTA
1 TAGTTTAGACACCTATTTGGTTATTAAGGTA
*
659886 TAGTTTAGACACTTATTTTGG-TATTAAG
1 TAGTTTAGACACCTA-TTTGGTTATTAAG
659914 TCAATGTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 20 0.80
32 5 0.20
ACGTcount: A:0.27, C:0.08, G:0.19, T:0.46
Consensus pattern (31 bp):
TAGTTTAGACACCTATTTGGTTATTAAGGTA
Found at i:661114 original size:15 final size:15
Alignment explanation
Indices: 661090--661128 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
661080 GGAGGGGCGT
*
661090 TTTTAATTTCAATTA
1 TTTTATTTTCAATTA
661105 TTTTATTTTCAATTA
1 TTTTATTTTCAATTA
661120 TTTTATTTT
1 TTTTATTTT
661129 ATTTTCCACC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTATTTTCAATTA
Found at i:661198 original size:474 final size:463
Alignment explanation
Indices: 660273--661114 Score: 1301
Period size: 474 Copynumber: 1.8 Consensus size: 463
660263 TTTGGTCTGT
* *
660273 TTTAGTGCCTAAACTTTAAATTTTTTCAAAACTTAACATTACATTTTTAACGGGTACTAAAATGA
1 TTTAGTACCTAAACTTTAAATTTTTTCAAAACTTAACATTAAATTTTTAACGGGTACTAAAATGA
660338 ATTTAATTTAATTATATATTTGGTCCTTAATGCTTATACATTTTATTAAGTTAGTCCCTAATACT
66 ATTTAATTTAATTATATATTTGGTCCTTAATGCTTATACATTTTATTAAGTTAGTCCCTAATACT
*
660403 TAACAAAACTGGTATAATTATATACTTAACAAGATTTAACATTAAATTTTTAACGGATACTAAAA
131 TAACAAAACTGGTATAATTATATACTTAACAAGACTTAACATTAAATTTTTAACGGATACTAAAA
* * *
660468 TGAATTTAATTTTAATTTTTTTCAAAACTTAACAAAATTGGTATAATTTTATATTTGGTCCTTAA
196 TGAATTTAATTTCAATTTTTTTCAAAACTTAACAAAAATGGTATAATTTTATATTTGATCCTTAA
*
660533 TATTTATACATATTATTAATTTGGTCCTAATTTTAATCGAATTAATAAATTTAAACATCTAACCA
261 TACTTATACATATTATTAATTTGG--C--ATTTTAAT---ATT-ATAAATTTAAACATCT-A-CA
660598 GATTTTGAAATGTATCACAACATAATTGGAGGGTATTTTTTTAATTTCAATCATTTTATTTTCCA
316 GATTTTGAAATGTATCACAACATAATTGGAGGGTATTTTTTTAATTTCAATCATTTTATTTTCCA
*
660663 CCCATATCACCATCAGATTATATAGAAAATTAGTAGAAGAATAAGCACTACAAAGGTGATACTCG
381 CCCATATCACCATCAGATTAGATAGAAAATTAGTAGAAGAATAAGCACTACAAAGGTGATACTCG
660728 TGTTAAAAACTTAACATG
446 TGTTAAAAACTTAACATG
* *
660746 TTTAGTACCTAAATTTTCAATTTTTTTCAAAACTTAACATTAAATTTTTAACGGGTACTAAAATG
1 TTTAGTACCTAAACTTT-AAATTTTTTCAAAACTTAACATTAAATTTTTAACGGGTACTAAAATG
* *
660811 AATTTAATTTAATTATATATTTGGTCCTTAATGCTTATACATTTTATTAATTTAGTCCTTAATAC
65 AATTTAATTTAATTATATATTTGGTCCTTAATGCTTATACATTTTATTAAGTTAGTCCCTAATAC
* *
660876 TTAGCAAAACTGGTATAATTATATACTTAACAAGACTTAACATTAAATTTTTAACGGGTACTAAA
130 TTAACAAAACTGGTATAATTATATACTTAACAAGACTTAACATTAAATTTTTAACGGATACTAAA
*
660941 ATGAATTTAATTTCAATTTTTTTTCAACACTTAACAAAAATGGTATAATTTTATATTTGATCCTT
195 ATGAATTTAATTTCAA-TTTTTTTCAAAACTTAACAAAAATGGTATAATTTTATATTTGATCCTT
* * *
661006 AATACTTCTACATTTTATTAATTT-G-ATTTTAAT-TT-T-AA-TT-GA-AT-T-CAGATTTTGA
259 AATACTTATACATATTATTAATTTGGCATTTTAATATTATAAATTTAAACATCTACAGATTTTGA
*** *
661061 AATGTATCACAACATAATTGGAGGG-GCGTTTTTAATTTCAATTATTTTATTTTC
324 AATGTATCACAACATAATTGGAGGGTATTTTTTTAATTTCAATCATTTTATTTTC
661115 AATTATTTTA
Statistics
Matches: 346, Mismatches: 21, Indels: 23
0.89 0.05 0.06
Matches are distributed among these distances:
454 25 0.07
455 35 0.10
458 1 0.00
459 2 0.01
460 1 0.00
461 2 0.01
462 2 0.01
463 1 0.00
465 2 0.01
469 8 0.02
473 15 0.04
474 186 0.54
475 66 0.19
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.43
Consensus pattern (463 bp):
TTTAGTACCTAAACTTTAAATTTTTTCAAAACTTAACATTAAATTTTTAACGGGTACTAAAATGA
ATTTAATTTAATTATATATTTGGTCCTTAATGCTTATACATTTTATTAAGTTAGTCCCTAATACT
TAACAAAACTGGTATAATTATATACTTAACAAGACTTAACATTAAATTTTTAACGGATACTAAAA
TGAATTTAATTTCAATTTTTTTCAAAACTTAACAAAAATGGTATAATTTTATATTTGATCCTTAA
TACTTATACATATTATTAATTTGGCATTTTAATATTATAAATTTAAACATCTACAGATTTTGAAA
TGTATCACAACATAATTGGAGGGTATTTTTTTAATTTCAATCATTTTATTTTCCACCCATATCAC
CATCAGATTAGATAGAAAATTAGTAGAAGAATAAGCACTACAAAGGTGATACTCGTGTTAAAAAC
TTAACATG
Found at i:661833 original size:19 final size:18
Alignment explanation
Indices: 661799--661837 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
661789 TTTTAACTCA
661799 AAATTATTTAGAAAAACTT
1 AAATTATTTAGAAAAA-TT
661818 AAATTATTT-GATAAAATT
1 AAATTATTTAGA-AAAATT
661836 AA
1 AA
661838 CAATAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (18 bp):
AAATTATTTAGAAAAATT
Found at i:661923 original size:19 final size:20
Alignment explanation
Indices: 661880--661924 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
661870 TTTTTTAGCT
*
661880 TATTA-TAATAATTTTAATT
1 TATTATTAATAATTTTAATA
*
661899 TTTTATTAATAATTTT-ATA
1 TATTATTAATAATTTTAATA
661918 TATTATT
1 TATTATT
661925 TTTATTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTATTAATAATTTTAATA
Found at i:662028 original size:19 final size:18
Alignment explanation
Indices: 661993--662039 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
661983 CATATATATG
661993 AAAATATTTTTAAAAATTT
1 AAAATATTTTTAAAAA-TT
*
662012 AAAATTATTTTT-TAAATT
1 AAAA-TATTTTTAAAAATT
662030 AAAAATATTT
1 -AAAATATTT
662040 AATTTAAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 7 0.28
19 11 0.44
20 7 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AAAATATTTTTAAAAATT
Found at i:662047 original size:20 final size:18
Alignment explanation
Indices: 661993--662039 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
661983 CATATATATG
*
661993 AAAATATTTTTAAAAATTTA
1 AAAATATTTTT-TAAA-TTA
*
662013 AAATTATTTTTTAAATTA
1 AAAATATTTTTTAAATTA
662031 AAAATATTT
1 AAAATATTT
662040 AATTTAAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 11 0.46
19 3 0.12
20 10 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AAAATATTTTTTAAATTA
Found at i:664092 original size:20 final size:20
Alignment explanation
Indices: 664064--664111 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
664054 ATAAAATGCG
**
664064 ATGCAAAAATCTAAATGCAT
1 ATGCAAAAATAAAAATGCAT
664084 -TGCATAAAATAAAAATGCAT
1 ATGCA-AAAATAAAAATGCAT
664104 ATGCAAAA
1 ATGCAAAA
664112 TGTAGGGTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 4 0.17
20 16 0.67
21 4 0.17
ACGTcount: A:0.54, C:0.12, G:0.10, T:0.23
Consensus pattern (20 bp):
ATGCAAAAATAAAAATGCAT
Found at i:670446 original size:24 final size:25
Alignment explanation
Indices: 670409--670457 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
670399 TGGGTCTGGG
670409 CCAGTATGGGTTGTAA-TTGGGCCT
1 CCAGTATGGGTTGTAATTTGGGCCT
* *
670433 CCAGTCTGGTTTGTAATTTGGGCCT
1 CCAGTATGGGTTGTAATTTGGGCCT
670458 GTAATATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.14, C:0.18, G:0.31, T:0.37
Consensus pattern (25 bp):
CCAGTATGGGTTGTAATTTGGGCCT
Found at i:670490 original size:5 final size:5
Alignment explanation
Indices: 670460--670573 Score: 61
Period size: 5 Copynumber: 21.4 Consensus size: 5
670450 TTGGGCCTGT
* *
670460 AATAT AATAA AAT-T AATAA CAATAA AATAAA AATAAA AATAA TAATAAA
1 AATAA AATAA AATAA AATAA -AATAA AAT-AA AAT-AA AATAA -AAT-AA
* * * * *
670509 AATAA TAATAT TATAA TATAA TATAA TAATAA TATTAA AATAA AATAA
1 AATAA -AATAA AATAA AATAA AATAA -AATAA -AATAA AATAA AATAA
*
670557 TAAT-A AATGA AATAA AA
1 -AATAA AATAA AATAA AA
670574 AACTAGTGTC
Statistics
Matches: 90, Mismatches: 10, Indels: 18
0.76 0.08 0.15
Matches are distributed among these distances:
4 6 0.07
5 44 0.49
6 38 0.42
7 2 0.02
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.29
Consensus pattern (5 bp):
AATAA
Found at i:670494 original size:11 final size:11
Alignment explanation
Indices: 670474--670563 Score: 85
Period size: 11 Copynumber: 8.1 Consensus size: 11
670464 TAATAAAATT
*
670474 AATAACAATAA
1 AATAATAATAA
*
670485 AATAAAAATAAA
1 AATAATAAT-AA
670497 AATAATAATAAA
1 AATAATAAT-AA
*
670509 AATAATAATAT
1 AATAATAATAA
*
670520 TATAAT-ATAA
1 AATAATAATAA
*
670530 TATAATAATAA
1 AATAATAATAA
*
670541 TATTAA-AATAA
1 -AATAATAATAA
670552 AATAATAATAA
1 AATAATAATAA
670563 A
1 A
670564 TGAAATAAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
10 13 0.19
11 29 0.43
12 25 0.37
ACGTcount: A:0.70, C:0.01, G:0.00, T:0.29
Consensus pattern (11 bp):
AATAATAATAA
Found at i:670505 original size:3 final size:3
Alignment explanation
Indices: 670459--670562 Score: 89
Period size: 3 Copynumber: 37.0 Consensus size: 3
670449 TTTGGGCCTG
* * *
670459 TAA T-A TAA TAA -AA TTAA TAA CAA TAA -AA TAA AAA TAA AAA TAA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
670502 TAA TAA AAA TAA TAA T-A TTA TAA T-A TAA T-A TAA TAA TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
670547 -AA TAA -AA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
670563 ATGAAATAAA
Statistics
Matches: 81, Mismatches: 11, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
2 16 0.20
3 63 0.78
4 2 0.02
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:670515 original size:38 final size:39
Alignment explanation
Indices: 670463--670574 Score: 115
Period size: 38 Copynumber: 2.9 Consensus size: 39
670453 GGCCTGTAAT
* *
670463 ATAATAAAATTAATAACAATAAAATA-AAAATAAAAATA
1 ATAATAAAAATAATAATAATAAAATATAAAATAAAAATA
* * * *
670501 ATAATAAAAATAATAATATTATAATATAATATAATAATA
1 ATAATAAAAATAATAATAATAAAATATAAAATAAAAATA
* *
670540 AT-ATTAAAATAA-AATAATAATAA-ATGAAATAAAAA
1 ATAATAAAAATAATAATAATAA-AATATAAAATAAAAA
670575 ACTAGTGTCT
Statistics
Matches: 60, Mismatches: 12, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
37 15 0.25
38 33 0.55
39 12 0.20
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.29
Consensus pattern (39 bp):
ATAATAAAAATAATAATAATAAAATATAAAATAAAAATA
Found at i:670529 original size:13 final size:13
Alignment explanation
Indices: 670459--670558 Score: 51
Period size: 14 Copynumber: 7.4 Consensus size: 13
670449 TTTGGGCCTG
*
670459 TAATATAATAAAA
1 TAATATAATAATA
* *
670472 TTAATAACAATAAAA
1 -TAAT-ATAATAATA
*
670487 TAA-A-AATAAAAA
1 TAATATAAT-AATA
*
670499 TAATAATAAAAATAA
1 TAAT-ATAATAAT-A
*
670514 TAATATTATAATA
1 TAATATAATAATA
670527 TAATATAATAATAA
1 TAATATAATAAT-A
* * *
670541 TATTAAAATAAAA
1 TAATATAATAATA
670554 TAATA
1 TAATA
670559 ATAAATGAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
11 3 0.04
12 8 0.12
13 17 0.25
14 26 0.38
15 15 0.22
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (13 bp):
TAATATAATAATA
Found at i:671007 original size:123 final size:121
Alignment explanation
Indices: 670796--671658 Score: 995
Period size: 112 Copynumber: 7.3 Consensus size: 121
670786 GTTGAACAAA
** * * *
670796 TTCTT-CTCTTTCAGATGAGTTCTTCTCATTATGAACACT-TCTGGCAA-TGTTGATGCTGACCT
1 TTCTTCCTC-TTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGTG-T-ATGCTAATCT
* * *
670858 ATCTTCTTCTGTGATAGAATCTTGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTT
63 ATC-TCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
* *
670918 TTCTTCCTCTTCAGATGAGTTATTCTCATTATGAACTTTCTCTGGAAAAGTTTATGCTAATCTAT
1 TTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG-AAAGTGTATGCTAATCTAT
* *
670983 CTCCTTCTGTGATAGAGTCATGCAAACGGTTGAACAAGTTCTTCTCATTATGAACTTT
65 CT-CTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
* *
671041 TTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG-AA----ATGCTGATCCA--
1 TTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGTGTATGCTAATCTATC
** * * * * *
671099 TC--AAGTGATGGATTTGA-GCAAAAAGTTGAACAAGCTCTTCTCATTATGAACTTC
66 TCTTCTGTGATAGA-GTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
* *
671153 TTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTCCTCTGGAAAAGTGTGTGCTAATCTAT
1 TTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG-AAAGTGTATGCTAATCTAT
671218 CTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
65 CT-CTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
671276 TTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAGAGTGTATGCTAATCTAT
1 TTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA-AGTGTATGCTAATCTAT
671341 CTCCTTCTGTGAT--AGTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
65 CT-CTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
* * * *
671397 TTCTTCCTCTTCATATGAGTTTTTCTCATTATGAACTTTCTCTGG-AA----ATGCTGATCCA--
1 TTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGTGTATGCTAATCTATC
** * * * *
671455 TC--AAGTGATGGATTTGA-GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
66 TCTTCTGTGATAGA-GTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
*
671509 TTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA-TGT-TG---ATCCA--
1 TTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGTGTATGCTAATCTATC
** * * * *
671567 TC--AAGTGATGGATTTGA-GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
66 TCTTCTGTGATAGA-GTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
671621 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 TTCTTCC-TCTTCAGATGAGTTCTTCTCATTATGAACT
671659 CTACCTGGAA
Statistics
Matches: 668, Mismatches: 46, Indels: 63
0.86 0.06 0.08
Matches are distributed among these distances:
110 5 0.01
112 231 0.35
113 37 0.06
114 3 0.00
115 12 0.02
117 9 0.01
118 8 0.01
119 1 0.00
120 2 0.00
121 89 0.13
122 37 0.06
123 230 0.34
124 3 0.00
125 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (121 bp):
TTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGTGTATGCTAATCTATC
TCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
Found at i:671814 original size:76 final size:76
Alignment explanation
Indices: 671688--671865 Score: 277
Period size: 76 Copynumber: 2.3 Consensus size: 76
671678 GAAAAGAAAA
* * *
671688 AAACATTC-TGCACTGTAGGGCTTACAGCTGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCA
1 AAACA-TCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCA
671752 AAGGCTTTTTGG
65 AAGGCTTTTTGG
* *
671764 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCAA
671829 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
671840 ACACATCATGCATTGTAGGACTTACA
1 AAACATCATGCACTGTAGGACTTACA
671866 TATGTGAGAA
Statistics
Matches: 94, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
75 2 0.02
76 92 0.98
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (76 bp):
AAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCAA
AGGCTTTTTGG
Found at i:675298 original size:114 final size:114
Alignment explanation
Indices: 675106--675329 Score: 394
Period size: 114 Copynumber: 2.0 Consensus size: 114
675096 AGACTATCAT
* *
675106 CAAATTCATCTTTCAAATTCAATGATTGGTTTTGGGGTTCCTACCAAACCAGATCAGATAACTCA
1 CAAATTCATCTTTCAAATTCAATGATTGGTTTTAGGGTTCATACCAAACCAGATCAGATAACTCA
*
675171 AAAAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAC
66 AAAAACACTTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAC
*
675220 CAAATTCATCTTTCAAATTTAATGATTGGTTTTAGGGTTCATACCAAACCAGATCAGATAACTCA
1 CAAATTCATCTTTCAAATTCAATGATTGGTTTTAGGGTTCATACCAAACCAGATCAGATAACTCA
* *
675285 AAGAACACTTCCAGAAGATGCTATTGGGGCTCTTTATTTCTACTA
66 AAAAACACTTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTA
675330 CGAGAACATG
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 104 1.00
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (114 bp):
CAAATTCATCTTTCAAATTCAATGATTGGTTTTAGGGTTCATACCAAACCAGATCAGATAACTCA
AAAAACACTTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAC
Found at i:684135 original size:3 final size:3
Alignment explanation
Indices: 684117--684207 Score: 57
Period size: 3 Copynumber: 32.0 Consensus size: 3
684107 TTTGGGCCTG
* * * * * * *
684117 TAA T-A TAA TAA AAA TAA TAA AAA TAA AAA TAA AAA AAA TAA AAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
684164 TAA T-A TTA TAA T-A TAA TAA TAA TAT TAA -AA CAA -AA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
684208 ATGAAATAAA
Statistics
Matches: 70, Mismatches: 13, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
2 10 0.14
3 60 0.86
ACGTcount: A:0.73, C:0.01, G:0.00, T:0.26
Consensus pattern (3 bp):
TAA
Found at i:684143 original size:15 final size:15
Alignment explanation
Indices: 684123--684166 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
684113 CCTGTAATAT
684123 AATAAAAATAATAAA
1 AATAAAAATAATAAA
*
684138 AATAAAAATAAAAAA
1 AATAAAAATAATAAA
*
684153 AATAAAAAAAATAA
1 AATAAAAATAATAA
684167 TATTATAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (15 bp):
AATAAAAATAATAAA
Found at i:684147 original size:21 final size:21
Alignment explanation
Indices: 684121--684168 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
684111 GGCCTGTAAT
*
684121 ATAATAAAAATAATAAAAATAA
1 ATAATAAAAAAAATAAAAA-AA
684143 A-AATAAAAAAAATAAAAAAA
1 ATAATAAAAAAAATAAAAAAA
684163 ATAATA
1 ATAATA
684169 TTATAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 3 0.12
21 20 0.83
22 1 0.04
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (21 bp):
ATAATAAAAAAAATAAAAAAA
Found at i:684153 original size:24 final size:24
Alignment explanation
Indices: 684121--684166 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
684111 GGCCTGTAAT
* *
684121 ATAATAAAAATAATAAAAATAAAA
1 ATAAAAAAAATAAAAAAAATAAAA
684145 ATAAAAAAAATAAAAAAAATAA
1 ATAAAAAAAATAAAAAAAATAA
684167 TATTATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (24 bp):
ATAAAAAAAATAAAAAAAATAAAA
Found at i:684186 original size:19 final size:19
Alignment explanation
Indices: 684157--684206 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
684147 AAAAAAAATA
* * *
684157 AAAAAAATAATATTATAAT
1 AAAATAATAATATTAAAAC
*
684176 ATAATAATAATATTAAAAC
1 AAAATAATAATATTAAAAC
684195 AAAATAATAATA
1 AAAATAATAATA
684207 AATGAAATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAATAATAATATTAAAAC
Found at i:684220 original size:22 final size:22
Alignment explanation
Indices: 684176--684220 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
684166 ATATTATAAT
* *
684176 ATAATAATAATATTAAAACAAA
1 ATAATAATAATATGAAAAAAAA
684198 ATAATAATAA-ATGAAATAAAAA
1 ATAATAATAATATGAAA-AAAAA
684220 A
1 A
684221 CTAGTGTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (22 bp):
ATAATAATAATATGAAAAAAAA
Found at i:686349 original size:38 final size:38
Alignment explanation
Indices: 686296--686390 Score: 138
Period size: 38 Copynumber: 2.5 Consensus size: 38
686286 TTATAAATCC
* *
686296 TCCACCCGATTCGAACCCGACCAAAAAAATATACACCT
1 TCCACCCGATCCGAACCCGACCAAAAAAATATACACAT
* *
686334 TCCACCCAATCCGAACTCC-ACCCAAAAAATATACACAT
1 TCCACCCGATCCGAAC-CCGACCAAAAAAATATACACAT
686372 TCCACCCGATCCGAACCCG
1 TCCACCCGATCCGAACCCG
686391 GCCCGCTTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
37 2 0.04
38 46 0.92
39 2 0.04
ACGTcount: A:0.37, C:0.41, G:0.07, T:0.15
Consensus pattern (38 bp):
TCCACCCGATCCGAACCCGACCAAAAAAATATACACAT
Found at i:686795 original size:15 final size:13
Alignment explanation
Indices: 686774--686810 Score: 56
Period size: 14 Copynumber: 2.7 Consensus size: 13
686764 ATTCTAGGGA
686774 TAAAAAAATATTAT
1 TAAAAAAATA-TAT
686788 TAATAAAAATATAT
1 TAA-AAAAATATAT
686802 TAAAAAAAT
1 TAAAAAAAT
686811 CCTTAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.27
14 9 0.41
15 7 0.32
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAAAAAATATAT
Found at i:689864 original size:16 final size:15
Alignment explanation
Indices: 689838--689867 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
689828 ATGAAATCTC
689838 ATGTCTGTCCCTTTA
1 ATGTCTGTCCCTTTA
689853 ATGTCATGTCCCTTT
1 ATGTC-TGTCCCTTT
689868 TATAAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.13, C:0.27, G:0.13, T:0.47
Consensus pattern (15 bp):
ATGTCTGTCCCTTTA
Found at i:690854 original size:3 final size:3
Alignment explanation
Indices: 690846--690879 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
690836 CATCCATTTC
690846 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
690880 GGGTTAGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:697096 original size:25 final size:25
Alignment explanation
Indices: 697062--697111 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
697052 AGAAACTGAG
697062 AGTGGTATTAAAAAATCGAGTTCGT
1 AGTGGTATTAAAAAATCGAGTTCGT
697087 AGTGGTATTAAAAAATCGAGTTCGT
1 AGTGGTATTAAAAAATCGAGTTCGT
697112 CTCCATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (25 bp):
AGTGGTATTAAAAAATCGAGTTCGT
Found at i:703272 original size:3 final size:3
Alignment explanation
Indices: 703264--703289 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
703254 TATTTAACCA
703264 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
703290 GCTATTAGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:704368 original size:19 final size:18
Alignment explanation
Indices: 704333--704369 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
704323 AATTCTCCCC
*
704333 AAAATTATTACAAATATA
1 AAAATTATTAAAAATATA
704351 AAAATTATTATAAAATATA
1 AAAATTATTA-AAAATATA
704370 TTATTTTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAATTATTAAAAATATA
Found at i:705014 original size:31 final size:31
Alignment explanation
Indices: 704979--705040 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
704969 GAGACATGGC
* *
704979 CAAATTGTGTGGAGATCAATACATGAGAGGT
1 CAAATTGTGTGCAGATCAATAAATGAGAGGT
*
705010 CAAATTGTGTGCATATCAATAAATGAGAGGT
1 CAAATTGTGTGCAGATCAATAAATGAGAGGT
705041 GGCTTCTCAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.37, C:0.10, G:0.26, T:0.27
Consensus pattern (31 bp):
CAAATTGTGTGCAGATCAATAAATGAGAGGT
Found at i:708033 original size:25 final size:24
Alignment explanation
Indices: 707996--708043 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
707986 TGTTCTATTT
*
707996 TATGTATGGTATGTACATTTTTATG
1 TATGTATGGTATGCA-ATTTTTATG
*
708021 TATGTATGTTATGCAATTTTTAT
1 TATGTATGGTATGCAATTTTTAT
708044 TTATTTTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.25, C:0.04, G:0.17, T:0.54
Consensus pattern (24 bp):
TATGTATGGTATGCAATTTTTATG
Found at i:720116 original size:54 final size:55
Alignment explanation
Indices: 719964--720285 Score: 541
Period size: 54 Copynumber: 5.9 Consensus size: 55
719954 AGATTTCCCA
*
719964 ACGATTATTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
720019 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
720074 ACGATTGTTGAAGA-TGTTCGAGTC-CTATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTC-ATACTCTCTGAAGAAATAGGGAGCAGAC
720128 ACGATTG-TGAAGATTGTTCGAGTCTCATACTCTCTGAAG-AATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
720181 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCA-AC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* * *
720235 ACGATTG-TGAAGATTGTTCGAGTTTCATACTCCCT-AGAGAAAGAGGGAGCA
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGA-AGAAATAGGGAGCA
720286 AACCCGTTTG
Statistics
Matches: 257, Mismatches: 4, Indels: 14
0.93 0.01 0.05
Matches are distributed among these distances:
52 1 0.00
53 67 0.26
54 109 0.42
55 80 0.31
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.27
Consensus pattern (55 bp):
ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
Found at i:720320 original size:52 final size:51
Alignment explanation
Indices: 720198--720553 Score: 271
Period size: 52 Copynumber: 6.8 Consensus size: 51
720188 TTGAAGATTG
* * * *
720198 TTCGAG-TCTCATACTCTCTGAAGAAATAGGGAGC-AACACGATTGTGAAGATTG-
1 TTCGAGTTCT-ATACTCCCTG-AGAAAGAGGGAGCGAACCCG-TT-TGAAGA-AGA
*
720251 TTCGAGTT-TCATACTCCCTAGAGAAAGAGGGAGCAAACCCGTTTGAAGAAGA
1 TTCGAGTTCT-ATACTCCCT-GAGAAAGAGGGAGCGAACCCGTTTGAAGAAGA
* * * *
720303 TTCGAGTTCTATTCTCCCTGA-AGAAGAGGGAGTGAACCCGTTTAAAGACG-
1 TTCGAGTTCTATACTCCCTGAGA-AAGAGGGAGCGAACCCGTTTGAAGAAGA
* * * ** * *
720353 TTCGAGTTCCACA-TCCCTAGATAAAGAGGGAATGAACCCGCTTGCAGAAGA
1 TTCGAGTTCTATACTCCCT-GAGAAAGAGGGAGCGAACCCGTTTGAAGAAGA
*
720404 TTGTTCGAGTTCCATACTCCCTGAAGAAAGA-GGAGCGAACCCG-TTGAAGAAGA
1 ---TTCGAGTTCTATACTCCCTG-AGAAAGAGGGAGCGAACCCGTTTGAAGAAGA
* * *
720457 TGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCAGTTAGCAGAAGATTA
1 --TTCGAGTTCTATACTCCCTG-AGAAAGAGGGAGCGAACCCGTTTGAAGAAG---A
* *
720514 TTCGAGTTCTATACTCCCTGAAACAATAGGGAGCGAACCC
1 TTCGAGTTCTATACTCCCTGAGA-AAGAGGGAGCGAACCC
720554 CGTCCCCAGA
Statistics
Matches: 254, Mismatches: 29, Indels: 38
0.79 0.09 0.12
Matches are distributed among these distances:
49 5 0.02
50 35 0.14
51 27 0.11
52 51 0.20
53 51 0.20
54 39 0.15
55 45 0.18
57 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.23
Consensus pattern (51 bp):
TTCGAGTTCTATACTCCCTGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGA
Found at i:720444 original size:54 final size:54
Alignment explanation
Indices: 719973--720553 Score: 476
Period size: 54 Copynumber: 10.9 Consensus size: 54
719963 AACGATTATT
* * * *
719973 GAAGATTGTTCGAG-TCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
1 GAAGATTGTTCGAGTTC-CATACTCCCTGAAGAAAGAGGGAGCA-ACCCGATTGTA
* * * *
720028 GAAGATTGTTCGAG-TCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
1 GAAGATTGTTCGAGTTC-CATACTCCCTGAAGAAAGAGGGAGCA-ACCCGATTGTA
* * *
720083 GAAGA-TGTTCGAG-TCCTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT-
1 GAAGATTGTTCGAGTTCC-ATACTCCCTGAAGAAAGAGGGAGCA-ACCCGATTGTA
* * * *
720136 GAAGATTGTTCGAG-TCTCATACTCTCTGAAG-AATAGGGAGCAGACACGATTGTT
1 GAAGATTGTTCGAGTTC-CATACTCCCTGAAGAAAGAGGGAGCA-ACCCGATTGTA
* * *
720190 GAAGATTGTTCGAG-TCTCATACTCTCTGAAGAAATAGGGAGCAACACGATTGT-
1 GAAGATTGTTCGAGTTC-CATACTCCCTGAAGAAAGAGGGAGCAACCCGATTGTA
* * *
720243 GAAGATTGTTCGAGTTTCATACTCCCT-AGAGAAAGAGGGAGCAAACCCGTTTGAA
1 GAAGATTGTTCGAGTTCCATACTCCCTGA-AGAAAGAGGGAGC-AACCCGATTGTA
* * *
720298 GAAGA---TTCGAGTTCTATTCTCCCTGAAG-AAGAGGGAGTGAACCCG-TT-TA
1 GAAGATTGTTCGAGTTCCATACTCCCTGAAGAAAGAGGGAG-CAACCCGATTGTA
* * * * *
720347 -AAGA-CGTTCGAGTTCCACA-TCCCT-AGATAAAGAGGGAATG-AACCCGCTTGCA
1 GAAGATTGTTCGAGTTCCATACTCCCTGA-AGAAAGAGGG-A-GCAACCCGATTGTA
*
720399 GAAGATTGTTCGAGTTCCATACTCCCTGAAGAAAGA-GGAGCGAACCCG-TTGAA
1 GAAGATTGTTCGAGTTCCATACTCCCTGAAGAAAGAGGGAGC-AACCCGATTGTA
* * *
720452 GAAGA-TGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCAG-TTAGCA
1 GAAGATTGTTCGAGTTCCATACTCCCTGAAGAAAGAGGGAGC-AACCCGATT-GTA
* * *
720506 GAAGATTATTCGAGTTCTATACTCCCTGAA-ACAATAGGGAGCGAACCC
1 GAAGATTGTTCGAGTTCCATACTCCCTGAAGA-AAGAGGGAGC-AACCC
720554 CGTCCCCAGA
Statistics
Matches: 471, Mismatches: 26, Indels: 58
0.85 0.05 0.10
Matches are distributed among these distances:
48 5 0.01
49 7 0.01
50 25 0.05
51 18 0.04
52 51 0.11
53 91 0.19
54 148 0.31
55 125 0.27
56 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (54 bp):
GAAGATTGTTCGAGTTCCATACTCCCTGAAGAAAGAGGGAGCAACCCGATTGTA
Found at i:720518 original size:107 final size:107
Alignment explanation
Indices: 719973--720547 Score: 494
Period size: 107 Copynumber: 5.4 Consensus size: 107
719963 AACGATTATT
*
719973 GAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTT
1 GAAGATTGTTCGAGTC-CATACTCCCTGAAGAAATAGGGAGCA-ACACGATTG-TGAAGATTGTT
* * * **
720038 CGAG-TCTCATACTCTCTGAAGAAATAGGGAGCAGACACGA-TTGTT
63 CGAGTTCTCATACTCCCTGAAGAAAGAGGGAGC-GA-ACCAGTTGCA
*
720083 GAAGA-TGTTCGAGTCCTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTGAAGATTGTTC
1 GAAGATTGTTCGAGTCC-ATACTCCCTGAAGAAATAGGGAGCA-ACACGATTGTGAAGATTGTTC
* * * **
720147 GAG-TCTCATACTCTCTGAAG-AATAGGGAGCAGACACGA-TTGTT
64 GAGTTCTCATACTCCCTGAAGAAAGAGGGAGC-GA-ACCAGTTGCA
*
720190 GAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAACACGATTGTGAAGATTGTTCG
1 GAAGATTGTTCGAGTC-CATACTCCCTGAAGAAATAGGGAGCAACACGATTGTGAAGATTGTTCG
* * *
720255 AGTT-TCATACTCCCT-AGAGAAAGAGGGAGCAAACCCGTTTGAA
65 AGTTCTCATACTCCCTGA-AGAAAGAGGGAGCGAACCAG-TTGCA
* * * * * * *
720298 GAAGA---TTCGAGTTCTATTCTCCCTGAAG-AAGAGGGAGTGAACCCG-TT-TAAAGA-CGTTC
1 GAAGATTGTTCGAG-TCCATACTCCCTGAAGAAATAGGGAG-CAACACGATTGTGAAGATTGTTC
* * ** *
720356 GAGTTC-CACA-TCCCT-AGATAAAGAGGGAATGAACCCGCTTGCA
64 GAGTTCTCATACTCCCTGA-AGAAAGAGGGAGCGAACCAG-TTGCA
* * *
720399 GAAGATTGTTCGAGTTCCATACTCCCTGAAGAAAGA-GGAGCGAACCCG-TTGAAGAAGA-TGTT
1 GAAGATTGTTCGAG-TCCATACTCCCTGAAGAAATAGGGAGC-AACACGATTG-TGAAGATTGTT
720461 CGAGTTCT-ATACTCCCTGAAGAAAGAGGGAGCGAACCAGTTAGCA
63 CGAGTTCTCATACTCCCTGAAGAAAGAGGGAGCGAACCAGTT-GCA
* *
720506 GAAGATTATTCGAGTTCTATACTCCCTGAA-ACAATAGGGAGC
1 GAAGATTGTTCGAG-TCCATACTCCCTGAAGA-AATAGGGAGC
720548 GAACCCCGTC
Statistics
Matches: 405, Mismatches: 36, Indels: 50
0.82 0.07 0.10
Matches are distributed among these distances:
101 32 0.08
102 12 0.03
103 5 0.01
104 43 0.11
105 26 0.06
106 24 0.06
107 120 0.30
108 92 0.23
109 46 0.11
110 5 0.01
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (107 bp):
GAAGATTGTTCGAGTCCATACTCCCTGAAGAAATAGGGAGCAACACGATTGTGAAGATTGTTCGA
GTTCTCATACTCCCTGAAGAAAGAGGGAGCGAACCAGTTGCA
Found at i:720590 original size:56 final size:56
Alignment explanation
Indices: 720397--720609 Score: 188
Period size: 56 Copynumber: 3.9 Consensus size: 56
720387 AACCCGCTTG
* * * * **
720397 CAGAAGATTGTTCGAGTTCCATACTCCCTG-AAGAA-AGAGGAGCGAA-CCCGT-TG
1 CAGAAGATTATTCAAGTTCTATACTCCCTGAAACAATAG-GGAGCGAACCCCGTCCC
* * * * * ***
720450 AAGAAGA-TGTTCGAGTTCTATACTCCCTGAAGA-AAGAGGGAGCGAA-CCAGTTAG
1 CAGAAGATTATTCAAGTTCTATACTCCCTGAA-ACAATAGGGAGCGAACCCCGTCCC
*
720504 CAGAAGATTATTCGAGTTCTATACTCCCTGAAACAATAGGGAGCGAACCCCGTCCC
1 CAGAAGATTATTCAAGTTCTATACTCCCTGAAACAATAGGGAGCGAACCCCGTCCC
* ** *
720560 CAGAAGATTCTTCAAGTTCTATGTTCCCTGAAACGATAGGGAGCGAACCC
1 CAGAAGATTATTCAAGTTCTATACTCCCTGAAACAATAGGGAGCGAACCC
720610 GATTTTGAAG
Statistics
Matches: 137, Mismatches: 16, Indels: 11
0.84 0.10 0.07
Matches are distributed among these distances:
52 21 0.15
53 21 0.15
54 11 0.08
55 35 0.26
56 49 0.36
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.22
Consensus pattern (56 bp):
CAGAAGATTATTCAAGTTCTATACTCCCTGAAACAATAGGGAGCGAACCCCGTCCC
Done.