Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004886.1 Hibiscus syriacus cultivar Beakdansim tig00011004_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: 92745
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1216 original size:23 final size:23
Alignment explanation
Indices: 1176--1219 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1166 TATGTTATGT
*
1176 GTCCTTGGGGACATTTCTACGCG
1 GTCCTTGGGGACAATTCTACGCG
1199 GTCCTT-GGGACAAATTCTACG
1 GTCCTTGGGGAC-AATTCTACG
1220 TGCCCCTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.18, C:0.25, G:0.27, T:0.30
Consensus pattern (23 bp):
GTCCTTGGGGACAATTCTACGCG
Found at i:5179 original size:4 final size:4
Alignment explanation
Indices: 5170--5196 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
5160 TTAACTTCAT
5170 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
5197 ACTTAAGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:6451 original size:2 final size:2
Alignment explanation
Indices: 6439--6474 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
6429 AGCTCAGATA
6439 AG AG A- AG AG AG 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 AG AG AG AG AG AG A
6475 AACGAATGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:15809 original size:35 final size:35
Alignment explanation
Indices: 15769--15843 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
15759 TTTATATCCG
* * *
15769 CAATTAGCATTCATTTTTATTTGAATTCTTTGAAT
1 CAATTAACATTCATTATTATTTGAATTCTATGAAT
* *
15804 TAATTAACATTCATTATTCTTTGAATTCTATGAAT
1 CAATTAACATTCATTATTATTTGAATTCTATGAAT
15839 CAATT
1 CAATT
15844 TAACTTTATT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (35 bp):
CAATTAACATTCATTATTATTTGAATTCTATGAAT
Found at i:21847 original size:14 final size:15
Alignment explanation
Indices: 21822--21859 Score: 60
Period size: 14 Copynumber: 2.5 Consensus size: 15
21812 GTTCTTTGCA
21822 TCATATTCTTTA-TT
1 TCATATTCTTTACTT
21836 TCATATTCTTTATCTT
1 TCATATTCTTTA-CTT
21852 TCATATTC
1 TCATATTC
21860 ATATTCCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 12 0.55
16 10 0.45
ACGTcount: A:0.21, C:0.18, G:0.00, T:0.61
Consensus pattern (15 bp):
TCATATTCTTTACTT
Found at i:24472 original size:2 final size:2
Alignment explanation
Indices: 24465--24504 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
24455 ACCTTTTCTA
24465 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
24505 GTAAAGCTTG
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:26484 original size:8 final size:7
Alignment explanation
Indices: 26470--26514 Score: 54
Period size: 7 Copynumber: 6.1 Consensus size: 7
26460 TATTACACTT
26470 AGAAAAA
1 AGAAAAA
26477 ATGAAAAA
1 A-GAAAAA
26485 AGAAAAA
1 AGAAAAA
**
26492 CTAAAAA
1 AGAAAAA
26499 AGAAAAGA
1 AGAAAA-A
26507 AGAAAAA
1 AGAAAAA
26514 A
1 A
26515 AACAAAATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
7 18 0.56
8 14 0.44
ACGTcount: A:0.80, C:0.02, G:0.13, T:0.04
Consensus pattern (7 bp):
AGAAAAA
Found at i:26497 original size:14 final size:15
Alignment explanation
Indices: 26470--26545 Score: 66
Period size: 15 Copynumber: 4.9 Consensus size: 15
26460 TATTACACTT
26470 AGAAAAAATGAAAAA
1 AGAAAAAATGAAAAA
*
26485 AGAAAAACT-AAAAA
1 AGAAAAAATGAAAAA
26499 AGAAAAGAA-GAAAAA
1 AGAAAA-AATGAAAAA
*
26514 AAACAAAATGATGAAAAA
1 AGA-AAAA--ATGAAAAA
**
26532 AGGGAAAATGAAAA
1 AGAAAAAATGAAAA
26546 GGAGGGTTCA
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
14 11 0.22
15 24 0.49
16 3 0.06
17 4 0.08
18 7 0.14
ACGTcount: A:0.75, C:0.03, G:0.16, T:0.07
Consensus pattern (15 bp):
AGAAAAAATGAAAAA
Found at i:26509 original size:22 final size:22
Alignment explanation
Indices: 26472--26513 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
26462 TTACACTTAG
26472 AAAAAATGAAAAAAGAAAAACT
1 AAAAAATGAAAAAAGAAAAACT
26494 AAAAAA-GAAAAGAAGAAAAA
1 AAAAAATGAAAA-AAGAAAAA
26514 AAACAAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.81, C:0.02, G:0.12, T:0.05
Consensus pattern (22 bp):
AAAAAATGAAAAAAGAAAAACT
Found at i:26516 original size:17 final size:18
Alignment explanation
Indices: 26494--26532 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
26484 AAGAAAAACT
*
26494 AAAAAAGAAAA-GAAGAA
1 AAAAAACAAAATGAAGAA
*
26511 AAAAAACAAAATGATGAA
1 AAAAAACAAAATGAAGAA
26529 AAAA
1 AAAA
26533 GGGAAAATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.79, C:0.03, G:0.13, T:0.05
Consensus pattern (18 bp):
AAAAAACAAAATGAAGAA
Found at i:26521 original size:22 final size:22
Alignment explanation
Indices: 26472--26524 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
26462 TTACACTTAG
*
26472 AAAAAATGAAAAAAGAAAAACT
1 AAAAAATGAAAAAAGAAAAACA
26494 AAAAAA-GAAAAGAAGAAAAA-A
1 AAAAAATGAAAA-AAGAAAAACA
26515 AACAAAATGA
1 AA-AAAATGA
26525 TGAAAAAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 7 0.26
22 18 0.67
23 2 0.07
ACGTcount: A:0.79, C:0.04, G:0.11, T:0.06
Consensus pattern (22 bp):
AAAAAATGAAAAAAGAAAAACA
Found at i:39019 original size:115 final size:116
Alignment explanation
Indices: 38764--39026 Score: 293
Period size: 115 Copynumber: 2.3 Consensus size: 116
38754 TGGGTGTTAC
* *
38764 AAGAAGTTCCTAATGAGAAGAACTTGTTCAACATTTCACTCATCCATCACTAAAGGAGGTGGATC
1 AAGAAGTTCATAATGAGAAGAACTTATTCAACATTTCACTCATCCATCACTAAAGGAGGTGGATC
* * * *
38829 AACATTTCCAGTGGAGAGTTTATAACGATAAGAACTCATTCGATGAGGGAG
66 AACATTTCCAGTGGAGAGTTCATAACGAGAAGAACTCATTCGACGAGAGAG
* * * * * ** * *
38880 AA-AGAGTTTATAATAAGAATAACTTATTCAATCTTTTC-TTGGT-TATCAC-AGAAGGGGGTGG
1 AAGA-AGTTCATAATGAGAAGAACTTATTCAA-CATTTCACTCATCCATCACTA-AAGGAGGTGG
* *
38941 ATCAACATTTTCAG-GAGAGAGTTCATAATGAGAAGAACTCATTCGACGAGAGAG
63 ATCAACATTTCCAGTG-GAGAGTTCATAACGAGAAGAACTCATTCGACGAGAGAG
*
38995 AAGAAGTTCATAATGAGAAGAACTTCTTCAAC
1 AAGAAGTTCATAATGAGAAGAACTTATTCAAC
39027 CTTAGCTCGT
Statistics
Matches: 121, Mismatches: 21, Indels: 12
0.79 0.14 0.08
Matches are distributed among these distances:
114 3 0.02
115 86 0.71
116 27 0.22
117 5 0.04
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (116 bp):
AAGAAGTTCATAATGAGAAGAACTTATTCAACATTTCACTCATCCATCACTAAAGGAGGTGGATC
AACATTTCCAGTGGAGAGTTCATAACGAGAAGAACTCATTCGACGAGAGAG
Found at i:39385 original size:3 final size:3
Alignment explanation
Indices: 39371--39416 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
39361 TCAACCGTTA
*
39371 ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
39417 CAAATAAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:50835 original size:10 final size:10
Alignment explanation
Indices: 50806--50835 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
50796 ATGAAAGTAA
*
50806 TTTCGTTTTA
1 TTTCGTTTTT
50816 TTTCGTTTTT
1 TTTCGTTTTT
50826 TTTCGTTTTT
1 TTTCGTTTTT
50836 CTTGGTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.03, C:0.10, G:0.10, T:0.77
Consensus pattern (10 bp):
TTTCGTTTTT
Found at i:51018 original size:40 final size:40
Alignment explanation
Indices: 50957--51037 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
50947 GGCTCCCTAC
*
50957 ATTCATTATGTTTTGCAGTTTCTGTCTTTAGATTAGTTAA
1 ATTCATTATGTTTTCCAGTTTCTGTCTTTAGATTAGTTAA
*
50997 ATTCATTATGTTTTCCTGTTTCTGTCTTTAGATTAGTTAA
1 ATTCATTATGTTTTCCAGTTTCTGTCTTTAGATTAGTTAA
51037 A
1 A
51038 CTATTTTTAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.22, C:0.11, G:0.14, T:0.53
Consensus pattern (40 bp):
ATTCATTATGTTTTCCAGTTTCTGTCTTTAGATTAGTTAA
Found at i:51806 original size:13 final size:13
Alignment explanation
Indices: 51788--51814 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
51778 TAGAATGTTT
51788 GAAGAAACGGGTC
1 GAAGAAACGGGTC
51801 GAAGAAACGGGTC
1 GAAGAAACGGGTC
51814 G
1 G
51815 TTCTGCGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.41, T:0.07
Consensus pattern (13 bp):
GAAGAAACGGGTC
Found at i:51959 original size:23 final size:23
Alignment explanation
Indices: 51933--51980 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
51923 ATAAAGTACA
*
51933 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
51956 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
51979 AT
1 AT
51981 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:52730 original size:18 final size:18
Alignment explanation
Indices: 52707--52743 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
52697 CGAAATATAT
52707 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
52725 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
52743 A
1 A
52744 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:52973 original size:23 final size:23
Alignment explanation
Indices: 52947--53011 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
52937 ATGCGAGATA
52947 GATACCTATTACATTATATAAAC
1 GATACCTATTACATTATATAAAC
**
52970 GATACCTATTACATTATATAAGG
1 GATACCTATTACATTATATAAAC
* *
52993 GCTACCTATTACATCATAT
1 GATACCTATTACATTATAT
53012 GTTTACCTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.35
Consensus pattern (23 bp):
GATACCTATTACATTATATAAAC
Found at i:53395 original size:21 final size:20
Alignment explanation
Indices: 53365--53418 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
53355 GATAGACACT
*
53365 TTACAATATAACCATTACCTA
1 TTACATTATAACCA-TACCTA
*
53386 TTACATTATATAAACGATACCTA
1 TTACA-T-TAT-AACCATACCTA
53409 TTACATTATA
1 TTACATTATA
53419 TAAGGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
22 1 0.04
23 14 0.50
24 4 0.14
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:53406 original size:23 final size:23
Alignment explanation
Indices: 53380--53442 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
53370 ATATAACCAT
53380 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
53403 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
53426 TACCTATTACATCATAT
1 TACCTATTACATTATAT
53443 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:53763 original size:393 final size:395
Alignment explanation
Indices: 53100--53890 Score: 1550
Period size: 393 Copynumber: 2.0 Consensus size: 395
53090 TTTCAATTTT
53100 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
1 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
53165 ATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATACC
66 ATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATACC
53230 GTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
131 GTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
53295 AAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAG
196 AAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAG
*
53360 ACACTTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGG
261 ACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGG
53425 CTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATC
326 CTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATC
53490 GATAC
391 GATAC
53495 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
1 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
53560 ATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATACC
66 ATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATACC
53625 GTAACGT-AAAAA-AAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
131 GTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
53688 AAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAG
196 AAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAG
53753 ACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGG
261 ACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGG
*
53818 CTACCTATTACATCATATGTTTACCTATTTTATTGAAAGTGTCCATACTTTTTATAAAAAGGATC
326 CTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATC
53883 GATAC
391 GATAC
53888 TTT
1 TTT
53891 TTTTAAAACT
Statistics
Matches: 394, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
393 252 0.64
394 5 0.01
395 137 0.35
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (395 bp):
TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
ATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATACC
GTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
AAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAG
ACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGG
CTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATC
GATAC
Found at i:53788 original size:21 final size:22
Alignment explanation
Indices: 53763--53814 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
53753 ACACTTTACA
*
53763 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
53786 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
53809 ATATAA
1 ATATAA
53815 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:53799 original size:23 final size:23
Alignment explanation
Indices: 53773--53835 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
53763 ATATAACCAC
53773 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
53796 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
53819 TACCTATTACATCATAT
1 TACCTATTACATTATAT
53836 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:56698 original size:184 final size:184
Alignment explanation
Indices: 56389--57427 Score: 1972
Period size: 184 Copynumber: 5.7 Consensus size: 184
56379 TTTTAAATGG
*
56389 TATGGACATAAAGTACCGACACAATATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCA
56454 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
56519 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
*
56573 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCA
*
56638 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
*
56703 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
*
56757 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTGGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCA
56822 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
56887 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
*
56941 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTGGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCA
57006 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
57071 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
*
57125 TATGGACATAAAGTACCGACACAATATT-AAAAGTGTCGATATAGGTTGTAGACCTATTGGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCA
57189 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
57254 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
*
57308 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCA
* **
57373 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTTTATTATAAT
66 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAT
57428 ATGTTGAAAG
Statistics
Matches: 841, Mismatches: 13, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
183 183 0.22
184 658 0.78
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (184 bp):
TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCA
TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
Found at i:58902 original size:3 final size:3
Alignment explanation
Indices: 58894--58938 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
58884 ACTTGTTTGG
* * *
58894 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
58939 GCCAGCTTCA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.27, C:0.33, G:0.02, T:0.38
Consensus pattern (3 bp):
ATC
Found at i:58911 original size:12 final size:12
Alignment explanation
Indices: 58898--58974 Score: 73
Period size: 12 Copynumber: 6.4 Consensus size: 12
58888 GTTTGGATCA
* *
58898 TCATCTTCATCA
1 TCATCGTCATCT
* *
58910 TCATCATCATCA
1 TCATCGTCATCT
* *
58922 TCGTCATCATCT
1 TCATCGTCATCT
* *
58934 TCATCGCCAGCT
1 TCATCGTCATCT
58946 TCATCGTCATCT
1 TCATCGTCATCT
*
58958 TCATCGTCAGCT
1 TCATCGTCATCT
58970 TCATC
1 TCATC
58975 TTCTGCGACC
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 55 1.00
ACGTcount: A:0.21, C:0.35, G:0.08, T:0.36
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:58955 original size:24 final size:24
Alignment explanation
Indices: 58928--58974 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
58918 ATCATCGTCA
58928 TCATCTTCATCGCCAGCTTCATCG
1 TCATCTTCATCGCCAGCTTCATCG
*
58952 TCATCTTCATCGTCAGCTTCATC
1 TCATCTTCATCGCCAGCTTCATC
58975 TTCTGCGACC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.17, C:0.36, G:0.11, T:0.36
Consensus pattern (24 bp):
TCATCTTCATCGCCAGCTTCATCG
Found at i:58961 original size:6 final size:6
Alignment explanation
Indices: 58898--58977 Score: 61
Period size: 6 Copynumber: 13.3 Consensus size: 6
58888 GTTTGGATCA
* * * * * * * *
58898 TCATCT TCATCA TCATCA TCATCA TCGTCA TCATCT TCATCG CCAGCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * *
58946 TCATCG TCATCT TCATCG TCAGCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TC
58978 TGCGACCGAT
Statistics
Matches: 58, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.20, C:0.35, G:0.07, T:0.38
Consensus pattern (6 bp):
TCATCT
Found at i:60773 original size:199 final size:199
Alignment explanation
Indices: 60433--61655 Score: 2270
Period size: 199 Copynumber: 6.1 Consensus size: 199
60423 TTTAAATTAG
* *
60433 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
60498 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
60563 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
60628 AAAA
196 AAAA
*
60632 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATT
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
60697 ATTGTACCGGTTAGATTGAAAAACTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
60762 CGACACTTTTTATATATGGATCGACACTTT-TTGTTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
60826 AAAA
196 AAAA
* *
60830 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATT
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
60895 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
60960 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
61025 AAAA
196 AAAA
61029 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
61094 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
61159 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAA
61224 AAAAA
195 AAAAA
*
61229 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACTGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
61294 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
61359 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
61424 AAAA
196 AAAA
61428 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
61493 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
61557 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAA
61622 AAAAA
195 AAAAA
*
61627 TATCGACACAAACTATATTAGTATCGACA
1 TATCGACACAAACTATATTAGTGTCGACA
61656 TGACCCTTAA
Statistics
Matches: 996, Mismatches: 25, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
198 223 0.22
199 578 0.58
200 195 0.20
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (199 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
AAAA
Found at i:61472 original size:399 final size:399
Alignment explanation
Indices: 60433--61655 Score: 2308
Period size: 399 Copynumber: 3.1 Consensus size: 399
60423 TTTAAATTAG
*
60433 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
60498 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
60563 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
60628 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
* * *
60693 TATTATTGTACCGGTTAGATTGAAAAACTACATATTACATTATACTTTTGGGTTCGATGATTTTG
261 TATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
* *
60758 GGATCGACAC-TTTTTATATATGGATCGACACTTT-TTGTTGCACCTTGTTTTTAATTCATTCTG
326 GGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
*
60821 GGAAAAAAA
391 GAAAAAAAA
*
60830 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATT
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
60895 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
60960 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
61025 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
61090 TATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
261 TATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
61155 GGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
326 GGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
61220 GAAAAAAAA
391 GAAAAAAAA
* *
61229 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACTGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
61294 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
61359 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
61424 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
61489 TATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTTG
261 TATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
61553 GGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
326 GGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
61618 GAAAAAAAA
391 GAAAAAAAA
*
61627 TATCGACACAAACTATATTAGTATCGACA
1 TATCGACACAAACTATATTAGTGTCGACA
61656 TGACCCTTAA
Statistics
Matches: 810, Mismatches: 14, Indels: 3
0.98 0.02 0.00
Matches are distributed among these distances:
397 330 0.41
398 145 0.18
399 335 0.41
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (399 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
TATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
GGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
GAAAAAAAA
Found at i:61764 original size:19 final size:19
Alignment explanation
Indices: 61737--61781 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
61727 ATTCACATAA
*
61737 AAAAATATAAATCGTATAC
1 AAAATTATAAATCGTATAC
*
61756 AAAATTATAAATCTTATAC
1 AAAATTATAAATCGTATAC
61775 AAAATTA
1 AAAATTA
61782 ACTCGACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAATTATAAATCGTATAC
Found at i:63603 original size:33 final size:33
Alignment explanation
Indices: 63566--63631 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
63556 CATCTTAATA
*
63566 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
63599 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
63632 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:65771 original size:24 final size:24
Alignment explanation
Indices: 65734--65786 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
65724 CCGTTCTATC
65734 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
65758 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
65782 TATTT
1 TATTT
65787 AATTGATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:65948 original size:17 final size:18
Alignment explanation
Indices: 65926--65967 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
65916 ATATATCCGG
*
65926 TATCATTT-TACCGTTTT
1 TATCATTTATACCGGTTT
65943 TATCATTTGATACCGGTTT
1 TATCATTT-ATACCGGTTT
65962 TATCAT
1 TATCAT
65968 ATTTTTACCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.36
19 14 0.64
ACGTcount: A:0.21, C:0.17, G:0.10, T:0.52
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:73258 original size:30 final size:29
Alignment explanation
Indices: 73224--73283 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
73214 AAATGGATTT
* *
73224 AGTTTAATGACCAAATTATAAGATTTTGAA
1 AGTTTAATGACCAAAGTATAA-ACTTTGAA
**
73254 AGTTTGGTGACCAAAGTATAAACTTTGAA
1 AGTTTAATGACCAAAGTATAAACTTTGAA
73283 A
1 A
73284 AGTTAAGGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33
Consensus pattern (29 bp):
AGTTTAATGACCAAAGTATAAACTTTGAA
Found at i:73286 original size:30 final size:31
Alignment explanation
Indices: 73231--73304 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 31
73221 TTTAGTTTAA
* * *
73231 TGACCAAATTATAAGATTTTGAAAGTT-TGG
1 TGACCAAAATATAAGACTTTGAAAGTTAAGG
*
73261 TGACCAAAGTATAA-ACTTTGAAAAGTTAAGG
1 TGACCAAAATATAAGACTTTG-AAAGTTAAGG
73292 -GACCAAAATATAA
1 TGACCAAAATATAA
73305 TTTTAAAAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
29 5 0.13
30 31 0.82
31 2 0.05
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.28
Consensus pattern (31 bp):
TGACCAAAATATAAGACTTTGAAAGTTAAGG
Found at i:74248 original size:30 final size:32
Alignment explanation
Indices: 74211--74279 Score: 92
Period size: 31 Copynumber: 2.2 Consensus size: 32
74201 TCTATTGGCC
74211 TTAGAAAAATTT-GGGGACC-ATTCT-GTAATT
1 TTAGAAAAATTTGGGGGACCAATT-TGGTAATT
*
74241 TTTG-AAAATTTGGGGGACCAATTTGGTAATT
1 TTAGAAAAATTTGGGGGACCAATTTGGTAATT
74272 TTAGAAAA
1 TTAGAAAA
74280 GTTGTAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
29 7 0.21
30 11 0.33
31 12 0.36
32 3 0.09
ACGTcount: A:0.35, C:0.07, G:0.22, T:0.36
Consensus pattern (32 bp):
TTAGAAAAATTTGGGGGACCAATTTGGTAATT
Found at i:75330 original size:14 final size:14
Alignment explanation
Indices: 75311--75343 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
75301 CACATGAGAA
75311 ATGATATAAGCTAT
1 ATGATATAAGCTAT
*
75325 ATGATATAATCTAT
1 ATGATATAAGCTAT
75339 ATGAT
1 ATGAT
75344 TACATGCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.39
Consensus pattern (14 bp):
ATGATATAAGCTAT
Found at i:75588 original size:18 final size:18
Alignment explanation
Indices: 75565--75627 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
75555 ATATGATAGG
75565 TCCTTCGGGACACAGACA
1 TCCTTCGGGACACAGACA
* * *
75583 TCCTTCGGGATGATAG--G
1 TCCTTCGGGA-CACAGACA
*
75600 TCATTCGGGACACAGACA
1 TCCTTCGGGACACAGACA
*
75618 TCCTTTGGGA
1 TCCTTCGGGA
75628 TGATAGGTCC
Statistics
Matches: 33, Mismatches: 9, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
16 3 0.09
17 9 0.27
18 18 0.55
19 3 0.09
ACGTcount: A:0.24, C:0.25, G:0.27, T:0.24
Consensus pattern (18 bp):
TCCTTCGGGACACAGACA
Found at i:75607 original size:35 final size:35
Alignment explanation
Indices: 75557--75648 Score: 166
Period size: 35 Copynumber: 2.6 Consensus size: 35
75547 TATTAAACAT
75557 ATGATAGGTCCTTCGGGACACAGACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGACATCCTTCGGG
* *
75592 ATGATAGGTCATTCGGGACACAGACATCCTTTGGG
1 ATGATAGGTCCTTCGGGACACAGACATCCTTCGGG
75627 ATGATAGGTCCTTCGGGACACA
1 ATGATAGGTCCTTCGGGACACA
75649 TTTTATACGA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 54 1.00
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (35 bp):
ATGATAGGTCCTTCGGGACACAGACATCCTTCGGG
Found at i:75644 original size:17 final size:17
Alignment explanation
Indices: 75583--75644 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
75573 GACACAGACA
75583 TCCTTCGGGATGATAGG
1 TCCTTCGGGATGATAGG
* * * *
75600 TCATTCGGGA-CACAGACA
1 TCCTTCGGGATGATAG--G
*
75618 TCCTTTGGGATGATAGG
1 TCCTTCGGGATGATAGG
75635 TCCTTCGGGA
1 TCCTTCGGGA
75645 CACATTTTAT
Statistics
Matches: 32, Mismatches: 10, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
16 3 0.09
17 18 0.56
18 8 0.25
19 3 0.09
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.27
Consensus pattern (17 bp):
TCCTTCGGGATGATAGG
Found at i:77772 original size:2 final size:2
Alignment explanation
Indices: 77765--77791 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
77755 CACATTTAAA
77765 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
77792 CACTCTATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:79558 original size:8 final size:8
Alignment explanation
Indices: 79547--79580 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
79537 ATATTTTATA
79547 TATTTAAT
1 TATTTAAT
*
79555 TATTCAAT
1 TATTTAAT
*
79563 TATTTAAC
1 TATTTAAT
79571 TATTTAAT
1 TATTTAAT
79579 TA
1 TA
79581 CTTATCCGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (8 bp):
TATTTAAT
Found at i:79940 original size:55 final size:54
Alignment explanation
Indices: 79848--80004 Score: 185
Period size: 55 Copynumber: 2.9 Consensus size: 54
79838 ATATTCGGAA
* * *
79848 AACGAGCTCGCTCCCTCATT-TTAGGGAGTATAGAACTCGAACAATTTTCTG-C
1 AACGAGTTCGCTCCCTCTTTCTTAGGGAGTATAGAACTCGAACAATCTTCTGTC
* *
79900 GAACGAGTTCACTCCCTCTTTCTTCGGAGAGTATAGAACTCGAACAATCTTCTGTC
1 -AACGAGTTCGCTCCCTCTTTCTTAGG-GAGTATAGAACTCGAACAATCTTCTGTC
* * * * *
79956 AACGGGTTCGTTCCCTCTTTCTTAGGGAGTA-GGAACTTGAAGAATCTTC
1 AACGAGTTCGCTCCCTCTTTCTTAGGGAGTATAGAACTCGAACAATCTTC
80005 ATCAATCGTG
Statistics
Matches: 89, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
53 32 0.36
54 9 0.10
55 47 0.53
56 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (54 bp):
AACGAGTTCGCTCCCTCTTTCTTAGGGAGTATAGAACTCGAACAATCTTCTGTC
Found at i:80059 original size:55 final size:55
Alignment explanation
Indices: 79911--80499 Score: 735
Period size: 55 Copynumber: 10.7 Consensus size: 55
79901 AACGAGTTCA
* * * *
79911 CTCCCTCTTTCTTCGGAGAGTAT-AGAACTCGAACAATCTTCTGTCAA-CGGGT-TCG
1 CTCCCTATTTCTTCAGAGAGTATAAG-ACTCGAACAATCTTC-ATCAATCGTGTCT-G
* * * ** * *
79966 TTCCCTCTTTCTT-AGGGAGTAGGA-ACTTGAAGAATCTTCATCAATCGTGTCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
* * * * *
80019 CTCCCTATTTCCTCAGAGAGTATAAGACCCAAACAATCTTCAACAAATCCTGTCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATC-AATCGTGTCTG
*
80075 CTCCCTATTTCTTCAGAGAGTATAAGAC-CTAAACAATCTTCATCAATCGTGTCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTC-GAACAATCTTCATCAATCGTGTCTG
* *
80130 CTCCCCA-TTCTTTCAGAGAGTATAAGACTTGAACAATCTTCATCAATCGTGTCTG
1 CTCCCTATTTC-TTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
** *
80185 CTCCCTATTTCCGCAGAGAGTATATGACTCGAACAATCTTCATCAATCGTGTCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
* * * *
80240 CTCCCTATTT-TGCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGCGTCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
* *
80294 CTCCCTATTTCTTCAGAGAGTACAAGACTCGAACAATCTTCATCCATCGTGTCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
* * * *
80349 CTCCATATTTCTGCAGAGAGTATAAGACTCGAACAATTTTCAACAATCGTGTCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
* * * *
80404 CTTCCTATTTTTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
*
80459 CTCCCTATTTCTTCAGAGAGTATAAGACTCGATCAATCTTC
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTC
80500 GATTATCGTT
Statistics
Matches: 466, Mismatches: 57, Indels: 22
0.86 0.10 0.04
Matches are distributed among these distances:
52 4 0.01
53 28 0.06
54 67 0.14
55 314 0.67
56 53 0.11
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (55 bp):
CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
Found at i:80295 original size:219 final size:220
Alignment explanation
Indices: 79998--80499 Score: 744
Period size: 219 Copynumber: 2.3 Consensus size: 220
79988 GAACTTGAAG
* *
79998 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCTCAGAGAGTATAAGACCCAAACAATCTTCAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTT-CTCAGAGAGTATAAGACTCGAACAATCTTCAAC
*
80063 AAATCCTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGAC-CTAAACAATCTTCATCAATCGTGT
65 AAATCCTGTCTGCTCCCTATTTCTTCAGAGAGTACAAGACTC-AAACAATCTTCATCAATCGTGT
* * * *
80127 CTGCTCCCCA-TTCTTTCAGAGAGTATAAGACTTGAACAATCTTCATCAATCGTGTCTGCTCCCT
129 CTGCTCCACATTTC-TGCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCT
*
80191 ATTTCCGCAGAGAGTATATGACTCGAAC
193 ATTTCCGCAGAGAGTATAAGACTCGAAC
80219 AATCTTCATCAATCGTGTCTGCTCCCTATTT-TGCAGAGAGTATAAGACTCGAACAATCTTCAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCT-CAGAGAGTATAAGACTCGAACAATCTTCAAC
* *
80283 AAA-CGC-GTCTGCTCCCTATTTCTTCAGAGAGTACAAGACTCGAACAATCTTCATCCATCGTGT
65 AAATC-CTGTCTGCTCCCTATTTCTTCAGAGAGTACAAGACTCAAACAATCTTCATCAATCGTGT
* * *
80346 CTGCTCCATATTTCTGCAGAGAGTATAAGACTCGAACAATTTTCAACAATCGTGTCTGCTTCCTA
129 CTGCTCCACATTTCTGCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTA
***
80411 TTTTTTCAGAGAGTATAAGACTCGAAC
194 TTTCCGCAGAGAGTATAAGACTCGAAC
* * *
80438 AATCTTCAACAATCGCGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGATCAATCTTC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTC-TCAGAGAGTATAAGACTCGAACAATCTTC
80500 GATTATCGTT
Statistics
Matches: 256, Mismatches: 19, Indels: 13
0.89 0.07 0.05
Matches are distributed among these distances:
219 160 0.62
220 64 0.25
221 32 0.12
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.31
Consensus pattern (220 bp):
AATCTTCATCAATCGTGTCTGCTCCCTATTTCTCAGAGAGTATAAGACTCGAACAATCTTCAACA
AATCCTGTCTGCTCCCTATTTCTTCAGAGAGTACAAGACTCAAACAATCTTCATCAATCGTGTCT
GCTCCACATTTCTGCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATT
TCCGCAGAGAGTATAAGACTCGAAC
Found at i:81521 original size:8 final size:8
Alignment explanation
Indices: 81499--81557 Score: 63
Period size: 8 Copynumber: 7.5 Consensus size: 8
81489 GAACCCTTCC
81499 TTTTTTCCA
1 TTTTTT-CA
81508 TTTTTTCA
1 TTTTTTCA
81516 TTTTTT-A
1 TTTTTTCA
81523 TTATTTT-A
1 TT-TTTTCA
81531 TTTTTT-A
1 TTTTTTCA
81538 TTTTTTTCA
1 -TTTTTTCA
81547 -TTTTTCA
1 TTTTTTCA
81554 TTTT
1 TTTT
81558 CACTCATTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
7 15 0.33
8 24 0.52
9 7 0.15
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTTCA
Found at i:81533 original size:15 final size:16
Alignment explanation
Indices: 81510--81551 Score: 68
Period size: 15 Copynumber: 2.7 Consensus size: 16
81500 TTTTTCCATT
81510 TTTTCATTTTTTATTA
1 TTTTCATTTTTTATTA
*
81526 TTTT-ATTTTTTATTT
1 TTTTCATTTTTTATTA
81541 TTTTCATTTTT
1 TTTTCATTTTT
81552 CATTTTCACT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTCATTTTTTATTA
Found at i:81557 original size:15 final size:15
Alignment explanation
Indices: 81500--81557 Score: 64
Period size: 15 Copynumber: 3.7 Consensus size: 15
81490 AACCCTTCCT
81500 TTTTTCCATTTTTTCA
1 TTTTT-CATTTTTTCA
*
81516 TTTTTTATTATTTT-A
1 TTTTTCATT-TTTTCA
*
81531 TTTTTTATTTTTTTCA
1 TTTTTCA-TTTTTTCA
81547 TTTTTCATTTT
1 TTTTTCATTTT
81558 CACTCATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
15 19 0.51
16 18 0.49
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTCATTTTTTCA
Found at i:85065 original size:8 final size:8
Alignment explanation
Indices: 85052--85079 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
85042 AAAAGAAGAT
85052 ATATATAC
1 ATATATAC
85060 ATATATAC
1 ATATATAC
85068 ATATATAC
1 ATATATAC
85076 ATAT
1 ATAT
85080 GGGAGAATCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATATAC
Done.