Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008392.1 Hibiscus syriacus cultivar Beakdansim tig00111157_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: 522134
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:469009 original size:16 final size:16
Alignment explanation
Indices: 468976--469009 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
468966 AAAATTTATT
* *
468976 TTAAAAAATAATTTTA
1 TTAAAAAATAAATATA
468992 TTAAAAAATAAATATA
1 TTAAAAAATAAATATA
469008 TT
1 TT
469010 TTAAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TTAAAAAATAAATATA
Found at i:469011 original size:34 final size:34
Alignment explanation
Indices: 468967--469034 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
468957 GTAATTTTAA
*
468967 AAATTTATTTTAAAAAATAA-TTTTATTAAAAAAT
1 AAATATATTTTAAAAAA-AACTTTTATTAAAAAAT
*
469001 AAATATATTTTAAAAAAAACCTTTTCTTAAAAAA
1 AAATATATTTTAAAAAAAA-CTTTTATTAAAAAA
469035 ATCCTCCCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 2 0.07
34 16 0.53
35 12 0.40
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (34 bp):
AAATATATTTTAAAAAAAACTTTTATTAAAAAAT
Found at i:469017 original size:20 final size:20
Alignment explanation
Indices: 468981--469019 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
468971 TTATTTTAAA
*
468981 AAATAATTTTATTAAAAAAT
1 AAATAATTTTATAAAAAAAT
469001 AAATATATTTTA-AAAAAAA
1 AAATA-ATTTTATAAAAAAA
469020 CCTTTTCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AAATAATTTTATAAAAAAAT
Found at i:471509 original size:18 final size:18
Alignment explanation
Indices: 471486--471521 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
471476 TCTTTGTAAC
471486 AAAATAAAATCGGTAAGT
1 AAAATAAAATCGGTAAGT
*
471504 AAAATAACATCGGTAAGT
1 AAAATAAAATCGGTAAGT
471522 GATTCCTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.08, G:0.17, T:0.22
Consensus pattern (18 bp):
AAAATAAAATCGGTAAGT
Found at i:473136 original size:15 final size:15
Alignment explanation
Indices: 473116--473162 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
473106 TAATATGAGT
*
473116 ATATGTTATAGGTGA
1 ATATGTTATACGTGA
473131 ATATGTTATACGTGA
1 ATATGTTATACGTGA
*
473146 AAAGTGTTATACGTGA
1 ATA-TGTTATACGTGA
473162 A
1 A
473163 AAATGATCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
15 16 0.55
16 13 0.45
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.36
Consensus pattern (15 bp):
ATATGTTATACGTGA
Found at i:473155 original size:16 final size:15
Alignment explanation
Indices: 473118--473164 Score: 67
Period size: 16 Copynumber: 3.1 Consensus size: 15
473108 ATATGAGTAT
* *
473118 ATGTTATAGGTGAAT
1 ATGTTATACGTGAAA
473133 ATGTTATACGTGAAA
1 ATGTTATACGTGAAA
473148 AGTGTTATACGTGAAA
1 A-TGTTATACGTGAAA
473164 A
1 A
473165 ATGATCTATG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
15 14 0.48
16 15 0.52
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.34
Consensus pattern (15 bp):
ATGTTATACGTGAAA
Found at i:473391 original size:23 final size:23
Alignment explanation
Indices: 473355--473456 Score: 114
Period size: 23 Copynumber: 4.4 Consensus size: 23
473345 AGTTGAAGGT
* *
473355 TCTACGCGGTCCTTTGGGACAAA
1 TCTACGTGGTCCTTCGGGACAAA
* *
473378 TCTACGTGGACCTTTGGGACAAA
1 TCTACGTGGTCCTTCGGGACAAA
* *
473401 TCTATGTGGTCCTTCGAGACAAA
1 TCTACGTGGTCCTTCGGGACAAA
** *
473424 TTCTACACGGTCCTTCGGGACATA
1 -TCTACGTGGTCCTTCGGGACAAA
473448 TCTACGTGG
1 TCTACGTGG
473457 AACTTCGGTG
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
23 47 0.72
24 18 0.28
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.28
Consensus pattern (23 bp):
TCTACGTGGTCCTTCGGGACAAA
Found at i:473451 original size:47 final size:46
Alignment explanation
Indices: 473355--473456 Score: 114
Period size: 47 Copynumber: 2.2 Consensus size: 46
473345 AGTTGAAGGT
* * * ** *
473355 TCTACGCGGTCCTTTGGGACAAATCTACGTGGACCTTTGGGACAAA
1 TCTACGTGGTCCTTCGAGACAAATCTACACGGACCTTCGGGACAAA
* * *
473401 TCTATGTGGTCCTTCGAGACAAATTCTACACGGTCCTTCGGGACATA
1 TCTACGTGGTCCTTCGAGACAAA-TCTACACGGACCTTCGGGACAAA
473448 TCTACGTGG
1 TCTACGTGG
473457 AACTTCGGTG
Statistics
Matches: 45, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
46 19 0.42
47 26 0.58
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.28
Consensus pattern (46 bp):
TCTACGTGGTCCTTCGAGACAAATCTACACGGACCTTCGGGACAAA
Found at i:473462 original size:23 final size:23
Alignment explanation
Indices: 473355--473477 Score: 104
Period size: 23 Copynumber: 5.3 Consensus size: 23
473345 AGTTGAAGGT
* * *
473355 TCTACGCGGTCCTTTGGGACAAA
1 TCTACGTGGACCTTCGGGACAAA
*
473378 TCTACGTGGACCTTTGGGACAAA
1 TCTACGTGGACCTTCGGGACAAA
* * *
473401 TCTATGTGGTCCTTCGAGACAAA
1 TCTACGTGGACCTTCGGGACAAA
** * *
473424 TTCTACACGGTCCTTCGGGACATA
1 -TCTACGTGGACCTTCGGGACAAA
*
473448 TCTACGTGGAACTTCGGTG-CAAA
1 TCTACGTGGACCTTCGG-GACAAA
473471 TTCTACG
1 -TCTACG
473478 CGGCACTTCG
Statistics
Matches: 81, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
23 56 0.69
24 25 0.31
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (23 bp):
TCTACGTGGACCTTCGGGACAAA
Found at i:473477 original size:24 final size:24
Alignment explanation
Indices: 473448--473495 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
473438 TCGGGACATA
* *
473448 TCTACGTGGAACTTCGGTGCAAAT
1 TCTACGCGGAACTTCGATGCAAAT
*
473472 TCTACGCGGCACTTCGATGCAAAT
1 TCTACGCGGAACTTCGATGCAAAT
473496 ATATGAACAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (24 bp):
TCTACGCGGAACTTCGATGCAAAT
Found at i:477915 original size:90 final size:90
Alignment explanation
Indices: 477815--477991 Score: 291
Period size: 90 Copynumber: 2.0 Consensus size: 90
477805 TCATCATTTA
*
477815 AAAATAATATATAATTTAAACTTGTTTAAGAATAATTATTTTACAATTATTTTTAAATGATAAAT
1 AAAATAATATATAATTTAAACTTGTTTAACAATAATTATTTTACAATTATTTTTAAATGATAAAT
*
477880 GAATAATAAACATTGTAAGAAAGAC
66 GAATAACAAACATTGTAAGAAAGAC
* * *
477905 AAAATAATATATAATTTAAATTTGTTTAACAGTAATTATTTTATAATTATTTTTAAATGATAAAT
1 AAAATAATATATAATTTAAACTTGTTTAACAATAATTATTTTACAATTATTTTTAAATGATAAAT
* *
477970 GAATAGCAAACCTTGTAAGAAA
66 GAATAACAAACATTGTAAGAAA
477992 TACTTTTTTA
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 80 1.00
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.39
Consensus pattern (90 bp):
AAAATAATATATAATTTAAACTTGTTTAACAATAATTATTTTACAATTATTTTTAAATGATAAAT
GAATAACAAACATTGTAAGAAAGAC
Found at i:478659 original size:30 final size:30
Alignment explanation
Indices: 478623--478680 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
478613 AAAACAAATT
478623 TGAAAATGATCATTTCGATACTAACCCTTC
1 TGAAAATGATCATTTCGATACTAACCCTTC
*
478653 TGAAAATGGTCATTTCGATACTAACCCT
1 TGAAAATGATCATTTCGATACTAACCCT
478681 ATATTTGGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (30 bp):
TGAAAATGATCATTTCGATACTAACCCTTC
Found at i:482114 original size:16 final size:16
Alignment explanation
Indices: 482093--482125 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
482083 AAAACCTAAA
482093 CAGCCATTAGTGATTG
1 CAGCCATTAGTGATTG
482109 CAGCCATTAGTGATTG
1 CAGCCATTAGTGATTG
482125 C
1 C
482126 TATCTTTGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30
Consensus pattern (16 bp):
CAGCCATTAGTGATTG
Found at i:482268 original size:2 final size:2
Alignment explanation
Indices: 482263--482296 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
482253 GTGTGTGTGT
482263 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
482297 TGTTGCCTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:488458 original size:6 final size:6
Alignment explanation
Indices: 488447--489379 Score: 1817
Period size: 6 Copynumber: 156.7 Consensus size: 6
488437 TATAGAATCG
488447 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
488495 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
488543 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
488591 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
488639 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
488687 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
488735 AATTTT AA-TTT AA-TTT AATTTT AATTTT AATTTT AATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
488781 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
488829 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
488877 AATTTT AATTTT AATTTT AATTTT AATTTT AA-TTT --TTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
488922 AATTTT AATTTT AATTTT AATTTT AA-TTT AATTTT AATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
488969 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
489017 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
489065 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
489113 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
489161 AATTTT AATTTT AATTTT AA-TTT AATTTT AATTTT AATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
489208 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
489256 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
489304 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
489352 AATTTT AATTTT AATTTT AATTTT AATT
1 AATTTT AATTTT AATTTT AATTTT AATT
489380 AAACCCTTGT
Statistics
Matches: 921, Mismatches: 0, Indels: 12
0.99 0.00 0.01
Matches are distributed among these distances:
4 3 0.00
5 23 0.02
6 895 0.97
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
AATTTT
Found at i:490466 original size:32 final size:32
Alignment explanation
Indices: 490378--490479 Score: 125
Period size: 32 Copynumber: 3.2 Consensus size: 32
490368 GAGCTAGCCT
* * *
490378 AAGGGAATGCCTTGGGTCCTTAGAGCCTACCC
1 AAGGGAATACCTTGGGGCCTCAGAGCCTACCC
* * *
490410 AA-TGAATACATTGGGGACTCAGAGCCTACCC
1 AAGGGAATACCTTGGGGCCTCAGAGCCTACCC
* *
490441 AAGGGAGTACCTTGGGGCCTGAGAGCCTACCC
1 AAGGGAATACCTTGGGGCCTCAGAGCCTACCC
490473 AAGGGAA
1 AAGGGAA
490480 CATCTCGGAA
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
31 25 0.44
32 32 0.56
ACGTcount: A:0.27, C:0.25, G:0.29, T:0.18
Consensus pattern (32 bp):
AAGGGAATACCTTGGGGCCTCAGAGCCTACCC
Found at i:491345 original size:22 final size:22
Alignment explanation
Indices: 491320--491365 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
491310 GGCATGTGAA
491320 ATTTGGCCAGAATGACCTATGT
1 ATTTGGCCAGAATGACCTATGT
* *
491342 ATTTGTCCCGAATGACCTATGT
1 ATTTGGCCAGAATGACCTATGT
491364 AT
1 AT
491366 ATGTCCCGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.35
Consensus pattern (22 bp):
ATTTGGCCAGAATGACCTATGT
Found at i:491370 original size:22 final size:22
Alignment explanation
Indices: 491329--491375 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
491319 AATTTGGCCA
*
491329 GAATGACCTATGTATTTGTCCC
1 GAATGACCTATGTATATGTCCC
491351 GAATGACCTATGTATATGTCCC
1 GAATGACCTATGTATATGTCCC
491373 GAA
1 GAA
491376 GGATCGCGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (22 bp):
GAATGACCTATGTATATGTCCC
Found at i:496079 original size:24 final size:24
Alignment explanation
Indices: 496052--496159 Score: 87
Period size: 24 Copynumber: 4.5 Consensus size: 24
496042 AATTATTTTA
*
496052 TCTGATTTCCGACTTGAATTCTGT
1 TCTGATTTCTGACTTGAATTCTGT
* * *
496076 TCTGA-TACATGACCTGAATTATGT
1 TCTGATTTC-TGACTTGAATTCTGT
*
496100 TCTGATTTCTGA-TCTGGATTCTGT
1 TCTGATTTCTGACT-TGAATTCTGT
* * *
496124 TCTGATATCTG-TTCTAAATTCTGT
1 TCTGATTTCTGACT-TGAATTCTGT
*
496148 TTTGATTTCTGA
1 TCTGATTTCTGA
496160 TACCTCCGTA
Statistics
Matches: 66, Mismatches: 13, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
23 2 0.03
24 62 0.94
25 2 0.03
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.47
Consensus pattern (24 bp):
TCTGATTTCTGACTTGAATTCTGT
Found at i:496104 original size:12 final size:12
Alignment explanation
Indices: 496089--496158 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
496079 GATACATGAC
*
496089 CTGAATTATGTT
1 CTGAATTCTGTT
* *
496101 CTGATTTCTGAT
1 CTGAATTCTGTT
*
496113 CTGGATTCTGTT
1 CTGAATTCTGTT
496125 CTG-ATATCTGTT
1 CTGAAT-TCTGTT
*
496137 CTAAATTCTGTT
1 CTGAATTCTGTT
* *
496149 TTGATTTCTG
1 CTGAATTCTG
496159 ATACCTCCGT
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
11 2 0.04
12 42 0.91
13 2 0.04
ACGTcount: A:0.17, C:0.14, G:0.17, T:0.51
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:496154 original size:48 final size:48
Alignment explanation
Indices: 496052--496160 Score: 123
Period size: 48 Copynumber: 2.3 Consensus size: 48
496042 AATTATTTTA
* * *
496052 TCTGATTTCCGA-CTTGAATTCTGTTCTGATACATGACCTGAATTATGT
1 TCTGATTTCTGATC-TGGATTCTGTTCTGATACATGACCTAAATTATGT
** *
496100 TCTGATTTCTGATCTGGATTCTGTTCTGATATC-TGTTCTAAATTCTGT
1 TCTGATTTCTGATCTGGATTCTGTTCTGATA-CATGACCTAAATTATGT
*
496148 TTTGATTTCTGAT
1 TCTGATTTCTGAT
496161 ACCTCCGTAT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
48 50 0.96
49 2 0.04
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.48
Consensus pattern (48 bp):
TCTGATTTCTGATCTGGATTCTGTTCTGATACATGACCTAAATTATGT
Found at i:497940 original size:15 final size:15
Alignment explanation
Indices: 497907--497942 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
497897 AATAAATATT
*
497907 TATTTTAGAATTTAA
1 TATTTTAGAAATTAA
497922 -ATTTTAGAAATTAA
1 TATTTTAGAAATTAA
497936 TATTTTA
1 TATTTTA
497943 TTCGATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (15 bp):
TATTTTAGAAATTAA
Found at i:498352 original size:23 final size:23
Alignment explanation
Indices: 498332--498376 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
498322 AATGCACTTC
*
498332 TGTGCTGAATCATTCAACACTGT
1 TGTGCTGAATCAGTCAACACTGT
* *
498355 TTTGTTGAATCAGTCAACACTG
1 TGTGCTGAATCAGTCAACACTG
498377 AATCATTCAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.36
Consensus pattern (23 bp):
TGTGCTGAATCAGTCAACACTGT
Found at i:501157 original size:29 final size:29
Alignment explanation
Indices: 501072--501159 Score: 113
Period size: 29 Copynumber: 3.0 Consensus size: 29
501062 ATCCAACCAT
* ****
501072 AGGTCGCCATGCACTCCCAGCGACCTCCT
1 AGGTCGCCATGCACTCCCGGCGACCAAGG
*
501101 AGGTCGCCATGCACGCCCGGCGACCAAGG
1 AGGTCGCCATGCACTCCCGGCGACCAAGG
*
501130 AGGTCGCCATGCACTCGCGGCGACCAAGG
1 AGGTCGCCATGCACTCCCGGCGACCAAGG
501159 A
1 A
501160 TTCATGCATG
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.20, C:0.39, G:0.30, T:0.11
Consensus pattern (29 bp):
AGGTCGCCATGCACTCCCGGCGACCAAGG
Found at i:501350 original size:29 final size:29
Alignment explanation
Indices: 501316--501390 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
501306 ATGTCGTCGC
* **
501316 GAGTGCATGGCGACCTCCTTGGTCGCCGG
1 GAGTGCATGGCGACCTACGAGGTCGCCGG
* * * *
501345 GCGTGCATGGCGATCTAGGAGGTCGCTGG
1 GAGTGCATGGCGACCTACGAGGTCGCCGG
501374 GAGTGCATGGCGACCTA
1 GAGTGCATGGCGACCTA
501391 TGGTTGGGCT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.15, C:0.25, G:0.40, T:0.20
Consensus pattern (29 bp):
GAGTGCATGGCGACCTACGAGGTCGCCGG
Found at i:502045 original size:3 final size:3
Alignment explanation
Indices: 502037--502113 Score: 147
Period size: 3 Copynumber: 26.0 Consensus size: 3
502027 TGCCCTCAAC
502037 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
502085 TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
502114 CTCCAAACAA
Statistics
Matches: 73, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 71 0.97
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:509678 original size:26 final size:26
Alignment explanation
Indices: 509649--509700 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
509639 CACAACATAC
509649 AGCATAAATATCTACAAGGACTTCAA
1 AGCATAAATATCTACAAGGACTTCAA
509675 AGCATAAATATCTACAAGGACTTCAA
1 AGCATAAATATCTACAAGGACTTCAA
509701 GAATTGGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.23
Consensus pattern (26 bp):
AGCATAAATATCTACAAGGACTTCAA
Found at i:517376 original size:19 final size:20
Alignment explanation
Indices: 517346--517383 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
517336 ATGTGATTTG
*
517346 TTGAGAAGAAAAACAGTTGA
1 TTGAGAAGAAAAAAAGTTGA
517366 TTGAG-AGAAAAAAAGTTG
1 TTGAGAAGAAAAAAAGTTG
517384 TTTTGTGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.50, C:0.03, G:0.26, T:0.21
Consensus pattern (20 bp):
TTGAGAAGAAAAAAAGTTGA
Found at i:520203 original size:21 final size:21
Alignment explanation
Indices: 520177--520219 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
520167 TTTCTGGGTT
* *
520177 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
520198 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
520219 A
1 A
520220 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:520618 original size:29 final size:29
Alignment explanation
Indices: 520584--520655 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
520574 CATATTATGA
**
520584 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
* *
520613 TACATGACATGAATTCATCTTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
520642 TACATGACATGAAT
1 TACATGACATGAAT
520656 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:520706 original size:30 final size:30
Alignment explanation
Indices: 520670--520727 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
520660 AGAAAAGTTC
*
520670 TATGCCTATGTGATAAAAGTATGTAAATGA
1 TATGCCTATGTGATAAAAGTATGGAAATGA
* *
520700 TATGCCTATGTGTTAAAGGTATGGAAAT
1 TATGCCTATGTGATAAAAGTATGGAAAT
520728 ACTATGTCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.36, C:0.07, G:0.22, T:0.34
Consensus pattern (30 bp):
TATGCCTATGTGATAAAAGTATGGAAATGA
Found at i:521019 original size:22 final size:22
Alignment explanation
Indices: 520945--521011 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
520935 TTATGGACAT
520945 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
520967 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
520989 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
521011 A
1 A
521012 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Done.