Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016540.1 Corchorus olitorius cultivar O-4 contig16573, 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: 238745
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:270 original size:2 final size:2
Alignment explanation
Indices: 263--294 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
253 AGAAGTGTGC
263 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
295 CTCCCAAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12355 original size:7 final size:7
Alignment explanation
Indices: 12323--12349 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
12313 AATAGAGATA
12323 ATATATT
1 ATATATT
12330 ATATATT
1 ATATATT
12337 ATATATT
1 ATATATT
12344 ATATAT
1 ATATAT
12350 ATTATAGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
ATATATT
Found at i:12362 original size:16 final size:16
Alignment explanation
Indices: 12329--12367 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
12319 GATAATATAT
*
12329 TATATATTATATATTA
1 TATATATTATATAGTA
12345 TATATATTATAGT-GTA
1 TATATATTATA-TAGTA
12361 TATATAT
1 TATATAT
12368 ACTCAACTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 20 0.95
17 1 0.05
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (16 bp):
TATATATTATATAGTA
Found at i:12679 original size:22 final size:22
Alignment explanation
Indices: 12625--12679 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
12615 CTTATTATGC
* *
12625 AATTTTGAAAATCTATCAAGGA
1 AATTTTGATAATCTATCAAAGA
*
12647 AATTTTAATAATC-ATCCAAAGA
1 AATTTTGATAATCTAT-CAAAGA
12669 AATTTTGATAA
1 AATTTTGATAA
12680 CCACATTATG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 2 0.07
22 26 0.93
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.35
Consensus pattern (22 bp):
AATTTTGATAATCTATCAAAGA
Found at i:12692 original size:22 final size:22
Alignment explanation
Indices: 12667--12736 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 22
12657 ATCATCCAAA
12667 GAAATTTTGATAACCACATTAT
1 GAAATTTTGATAACCACATTAT
* * *
12689 GAAATTTTGATAGCCTCATTGT
1 GAAATTTTGATAACCACATTAT
* * * *
12711 GAAATATTGGTAAGCACACTAT
1 GAAATTTTGATAACCACATTAT
12733 GAAA
1 GAAA
12737 AATTGTTGTA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.33
Consensus pattern (22 bp):
GAAATTTTGATAACCACATTAT
Found at i:13022 original size:25 final size:25
Alignment explanation
Indices: 12988--13061 Score: 139
Period size: 25 Copynumber: 3.0 Consensus size: 25
12978 CCAAACATTC
12988 TTGAGCACTCTCGCTCGGTCTCTAT
1 TTGAGCACTCTCGCTCGGTCTCTAT
*
13013 TTGAGTACTCTCGCTCGGTCTCTAT
1 TTGAGCACTCTCGCTCGGTCTCTAT
13038 TTGAGCACTCTCGCTCGGTCTCTA
1 TTGAGCACTCTCGCTCGGTCTCTA
13062 AAAATTAATC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.12, C:0.31, G:0.20, T:0.36
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCGGTCTCTAT
Found at i:13520 original size:22 final size:21
Alignment explanation
Indices: 13416--13872 Score: 117
Period size: 22 Copynumber: 21.5 Consensus size: 21
13406 ATCATATATA
* *
13416 CTATGAAATTATGATAACTTC
1 CTATGAAATTTTGATAACCTC
* *
13437 ATTATGATATTTTGATTAACCTTC
1 -CTATGAAATTTTGA-TAACC-TC
* **
13461 CTAT-ACAATTTCGATAAATTTTC
1 CTATGA-AATTTTGAT-AA-CCTC
* * *
13484 ATATAAAATTGTGATAACCTC
1 CTATGAAATTTTGATAACCTC
13505 CTTATGAAATTTTGATAA----
1 C-TATGAAATTTTGATAACCTC
* * *
13523 CTACG-AATTTTCATAACCTT
1 CTATGAAATTTTGATAACCTC
*
13543 CTCATG-ATTTTATGATAA---C
1 CT-ATGAAATTT-TGATAACCTC
* *
13562 CTATGAAATTTTGTTAATCTC
1 CTATGAAATTTTGATAACCTC
* ** *
13583 TCTATTAAATTTTGATATATATA
1 -CTATGAAATTTTGATA-ACCTC
*
13606 CTATGAAATTTTGATAACCAC
1 CTATGAAATTTTGATAACCTC
*
13627 ACTATAAAATTTTGATAACC-C
1 -CTATGAAATTTTGATAACCTC
* *
13648 CTTATGAAATTTTGA-AAACTAAA
1 C-TATGAAATTTTGATAACCT--C
** *
13671 CTATGAAATTTCAATAACCACC
1 CTATGAAATTTTGATAACC-TC
* * * *
13693 CTCTAAAATTATGATAACCTTT
1 CTATGAAATTTTGATAACC-TC
* *
13715 ATATGAAATTTTGATAACCATT
1 CTATGAAATTTTGATAACC-TC
* * * *
13737 ATATGAGATTTTTG-TTACTTC
1 CTATGA-AATTTTGATAACCTC
* * * *
13758 ACAATAAAATTTTAATAACATTC
1 -CTATGAAATTTTGATAAC-CTC
*
13781 CTATGAAATTTTGATAATCTCC
1 CTATGAAATTTTGATAACCT-C
* ** *
13803 CTTTGAAATACT-AT-A--TT
1 CTATGAAATTTTGATAACCTC
* *
13820 CTA--AAATTTTGATAATCAC
1 CTATGAAATTTTGATAACCTC
13839 ACTAT-AATATTTTGATAACCTC
1 -CTATGAA-ATTTTGATAACCTC
13861 CTTATGAAATTT
1 C-TATGAAATTT
13873 CTATCTATAT
Statistics
Matches: 313, Mismatches: 82, Indels: 80
0.66 0.17 0.17
Matches are distributed among these distances:
15 5 0.02
16 12 0.04
17 6 0.02
18 10 0.03
19 6 0.02
20 10 0.03
21 35 0.11
22 181 0.58
23 45 0.14
24 3 0.01
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (21 bp):
CTATGAAATTTTGATAACCTC
Found at i:13661 original size:65 final size:67
Alignment explanation
Indices: 13562--13731 Score: 193
Period size: 65 Copynumber: 2.6 Consensus size: 67
13552 TTATGATAAC
* * * * * * * **
13562 CTATGAAATTTTGTTAATCTCTCTATTAAATTTTGATATA-TATACTATGAAATTTTGATAACCA
1 CTATAAAATTTTGATAACCTCTATATGAAATTTTGATAAACTAAACTATGAAATTTCAATAACCA
13626 CA
66 CA
*
13628 CTATAAAATTTTGATAACCCCT-TATGAAATTTTGA-AAACTAAACTATGAAATTTCAATAACCA
1 CTATAAAATTTTGATAACCTCTATATGAAATTTTGATAAACTAAACTATGAAATTTCAATAACCA
*
13691 CC
66 CA
* * *
13693 CTCTAAAATTATGATAACCTTTATATGAAATTTTGATAA
1 CTATAAAATTTTGATAACCTCTATATGAAATTTTGATAA
13732 CCATTATATG
Statistics
Matches: 87, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
64 2 0.02
65 52 0.60
66 31 0.36
67 2 0.02
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.39
Consensus pattern (67 bp):
CTATAAAATTTTGATAACCTCTATATGAAATTTTGATAAACTAAACTATGAAATTTCAATAACCA
CA
Found at i:13688 original size:43 final size:43
Alignment explanation
Indices: 13607--13689 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
13597 ATATATATAC
* * **
13607 TATGAAATTTTGATAACCACACTATAAAATTTTGATAACCCCT
1 TATGAAATTTTGAAAACCAAACTATAAAATTTCAATAACCCCT
* *
13650 TATGAAATTTTGAAAACTAAACTATGAAATTTCAATAACC
1 TATGAAATTTTGAAAACCAAACTATAAAATTTCAATAACC
13690 ACCCTCTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (43 bp):
TATGAAATTTTGAAAACCAAACTATAAAATTTCAATAACCCCT
Found at i:15482 original size:2 final size:2
Alignment explanation
Indices: 15475--15504 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
15465 CAACATAAAG
15475 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
15505 AAAAACCTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:28525 original size:13 final size:13
Alignment explanation
Indices: 28507--28549 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
28497 TTTATGTCCT
28507 AAAATGACAGATA
1 AAAATGACAGATA
* *
28520 AAAATGGACAAAGA
1 AAAAT-GACAGATA
*
28534 AAAACGACAGATA
1 AAAATGACAGATA
28547 AAA
1 AAA
28550 TAGGAGGAGG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
13 14 0.58
14 10 0.42
ACGTcount: A:0.65, C:0.09, G:0.16, T:0.09
Consensus pattern (13 bp):
AAAATGACAGATA
Found at i:32771 original size:22 final size:21
Alignment explanation
Indices: 32745--32814 Score: 68
Period size: 23 Copynumber: 3.1 Consensus size: 21
32735 TATTAATGGA
32745 TTAAAATAATAAAAATTAAAAG
1 TTAAAAT-ATAAAAATTAAAAG
*
32767 TTAAAGGATATAAAAATTAAAGGG
1 TTAAA--ATATAAAAATTAAA-AG
* *
32791 TTAAATTATATAAAATAAAAAG
1 TTAAAATATA-AAAATTAAAAG
32813 TT
1 TT
32815 TGAGTATTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
22 12 0.30
23 20 0.50
24 8 0.20
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.30
Consensus pattern (21 bp):
TTAAAATATAAAAATTAAAAG
Found at i:32793 original size:24 final size:23
Alignment explanation
Indices: 32753--32814 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
32743 GATTAAAATA
32753 ATAAAAATTAAAAGTTAAAGGAT
1 ATAAAAATTAAAAGTTAAAGGAT
* **
32776 ATAAAAATTAAAGGGTTAAATTAT
1 ATAAAAATTAAA-AGTTAAAGGAT
*
32800 AT-AAAATAAAAAGTT
1 ATAAAAATTAAAAGTT
32815 TGAGTATTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
22 3 0.09
23 20 0.61
24 10 0.30
ACGTcount: A:0.60, C:0.00, G:0.11, T:0.29
Consensus pattern (23 bp):
ATAAAAATTAAAAGTTAAAGGAT
Found at i:42339 original size:17 final size:18
Alignment explanation
Indices: 42306--42342 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
42296 GAGCCAATCC
42306 AGTCTTGCAAAGAAACAG
1 AGTCTTGCAAAGAAACAG
42324 AGTCTT-CAAATG-AACAG
1 AGTCTTGCAAA-GAAACAG
42341 AG
1 AG
42343 AAGAACAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.43, C:0.16, G:0.22, T:0.19
Consensus pattern (18 bp):
AGTCTTGCAAAGAAACAG
Found at i:43229 original size:20 final size:20
Alignment explanation
Indices: 43204--43248 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
43194 GTAGTAGTAG
*
43204 TAGATTTATTAA-TCTTGGAT
1 TAGATTAATTAAGT-TTGGAT
*
43224 TAGATTAATTAAGTTTGGCT
1 TAGATTAATTAAGTTTGGAT
43244 TAGAT
1 TAGAT
43249 CAACTTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 21 0.95
21 1 0.05
ACGTcount: A:0.31, C:0.04, G:0.18, T:0.47
Consensus pattern (20 bp):
TAGATTAATTAAGTTTGGAT
Found at i:44046 original size:2 final size:2
Alignment explanation
Indices: 44041--44069 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
44031 AGAACACAAG
44041 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 T
44070 GTATGTATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:46299 original size:22 final size:21
Alignment explanation
Indices: 46264--46314 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
46254 AAAAAACTGC
* *
46264 AATAAT-TATTATATGATCTAT
1 AATAATATA-TATATAAACTAT
46285 AATATATATATATATAAACTAT
1 AATA-ATATATATATAAACTAT
46307 AATAATAT
1 AATAATAT
46315 CTCTCTACAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 8 0.31
22 16 0.62
23 2 0.08
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (21 bp):
AATAATATATATATAAACTAT
Found at i:55155 original size:23 final size:22
Alignment explanation
Indices: 55122--55167 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
55112 TTTGATCTTG
* *
55122 TTTATTTATATTTATATTTATA
1 TTTATTTATATATATATATATA
55144 TTTATTTTATATATATATATATA
1 TTTA-TTTATATATATATATATA
55167 T
1 T
55168 AGTATACAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTATTTATATATATATATATA
Found at i:55168 original size:6 final size:6
Alignment explanation
Indices: 55124--55167 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
55114 TGATCTTGTT
* *
55124 TATTTA TATTTA TATTTA TATTTA T-TTTA TATATA TATATA TAT
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TAT
55168 AGTATACAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
5 5 0.14
6 31 0.86
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
TATTTA
Found at i:58153 original size:15 final size:15
Alignment explanation
Indices: 58133--58173 Score: 82
Period size: 15 Copynumber: 2.7 Consensus size: 15
58123 TCTAAATAAA
58133 TTTGAAACTAACTAC
1 TTTGAAACTAACTAC
58148 TTTGAAACTAACTAC
1 TTTGAAACTAACTAC
58163 TTTGAAACTAA
1 TTTGAAACTAA
58174 TATGCTATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.34
Consensus pattern (15 bp):
TTTGAAACTAACTAC
Found at i:61915 original size:72 final size:72
Alignment explanation
Indices: 61798--61942 Score: 263
Period size: 72 Copynumber: 2.0 Consensus size: 72
61788 TATACGGCGG
*
61798 TGTAAATTTTGGACTCCACAAGCAGGTTGCGGGGTTGACACAGGTCCATGCTGCTTGTGGAGTTG
1 TGTAAATTTTGGACTCCACAAGCAGGTTGCGGAGTTGACACAGGTCCATGCTGCTTGTGGAGTTG
61863 ACACAGA
66 ACACAGA
* *
61870 TGTAAATTTTGGACTCCACAAGCAGGTTGCGGAGTTGATAGAGGTCCATGCTGCTTGTGGAGTTG
1 TGTAAATTTTGGACTCCACAAGCAGGTTGCGGAGTTGACACAGGTCCATGCTGCTTGTGGAGTTG
61935 ACACAGA
66 ACACAGA
61942 T
1 T
61943 CCAATCTGCT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (72 bp):
TGTAAATTTTGGACTCCACAAGCAGGTTGCGGAGTTGACACAGGTCCATGCTGCTTGTGGAGTTG
ACACAGA
Found at i:62447 original size:22 final size:23
Alignment explanation
Indices: 62422--62473 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
62412 CTTTACGGTC
62422 TATCTGTA-TTT-TTTCTTTTATT
1 TATCTGTACTTTATTT-TTTTATT
*
62444 TATCTCTACTTTATTTTTTTATT
1 TATCTGTACTTTATTTTTTTATT
62467 TAT-TGTA
1 TATCTGTA
62474 AAATTGTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 10 0.38
23 13 0.50
24 3 0.12
ACGTcount: A:0.17, C:0.10, G:0.04, T:0.69
Consensus pattern (23 bp):
TATCTGTACTTTATTTTTTTATT
Found at i:66420 original size:19 final size:19
Alignment explanation
Indices: 66384--66426 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
66374 CGGATGTCTT
66384 ATTTTTAAATTAATTTTTA
1 ATTTTTAAATTAATTTTTA
* *
66403 GTTTTTAAATT-TTCTTTTA
1 ATTTTTAAATTAAT-TTTTA
66422 ATTTT
1 ATTTT
66427 ATTTTAGTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
ATTTTTAAATTAATTTTTA
Found at i:70536 original size:31 final size:32
Alignment explanation
Indices: 70476--70537 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
70466 AAATTATGCC
* ** *
70476 AAGACAAGTAGACTACGTAAATTGTACAAAAA
1 AAGACAAGTAGACGACGTAAAAAGAACAAAAA
70508 AAGA-AAGTAGACGACGTAAAAAGAACAAAA
1 AAGACAAGTAGACGACGTAAAAAGAACAAAA
70538 GAATATTCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.58, C:0.11, G:0.18, T:0.13
Consensus pattern (32 bp):
AAGACAAGTAGACGACGTAAAAAGAACAAAAA
Found at i:76116 original size:60 final size:60
Alignment explanation
Indices: 76043--76161 Score: 193
Period size: 60 Copynumber: 2.0 Consensus size: 60
76033 AAATTTTACT
* *
76043 CTGACTAATTCGGATTCGACCCGGCTCTATGTACGCAAGGTCTCGAACCGGAACAAGTTG
1 CTGACTAATTCGGATTCGACCCGGCTCTACGTACGCAAAGTCTCGAACCGGAACAAGTTG
** *
76103 CTGACTAATTCGGATTCGGGCCGGGTCTACGTACGCAAAGTCTCGAACCGGAACAAGTT
1 CTGACTAATTCGGATTCGACCCGGCTCTACGTACGCAAAGTCTCGAACCGGAACAAGTT
76162 ACTTACCACT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.25, C:0.26, G:0.26, T:0.23
Consensus pattern (60 bp):
CTGACTAATTCGGATTCGACCCGGCTCTACGTACGCAAAGTCTCGAACCGGAACAAGTTG
Found at i:83577 original size:6 final size:6
Alignment explanation
Indices: 83568--83604 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
83558 GCGTCCACGA
* *
83568 CCACCT CCACCT CCACCA CCACCT CCACGT CCACCT C
1 CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT C
83605 TGCCTCTAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.19, C:0.65, G:0.03, T:0.14
Consensus pattern (6 bp):
CCACCT
Found at i:83588 original size:18 final size:18
Alignment explanation
Indices: 83561--83602 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
83551 CTCCTGAGCG
*
83561 TCCACGACCACCTCCACC
1 TCCACCACCACCTCCACC
*
83579 TCCACCACCACCTCCACG
1 TCCACCACCACCTCCACC
83597 TCCACC
1 TCCACC
83603 TCTGCCTCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.21, C:0.62, G:0.05, T:0.12
Consensus pattern (18 bp):
TCCACCACCACCTCCACC
Found at i:84998 original size:4 final size:4
Alignment explanation
Indices: 84989--85014 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
84979 GTTTATTAAC
84989 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
85015 GCCCATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:86199 original size:228 final size:227
Alignment explanation
Indices: 85794--86250 Score: 869
Period size: 228 Copynumber: 2.0 Consensus size: 227
85784 CGGGTTTATA
85794 TATATATACTAAATAGTATTTGAAAGACCCATGGAATTTACCAAAGGCCCCTTTTGAGGATCGAT
1 TATATATACTAAATAGTATTTGAAAGACCCATGGAATTTACCAAAGGCCCCTTTTGAGGATCGAT
*
85859 GAGGATGCTCTATTTGAACTTTTTTGTCTTTTTCTGTCTTTTCTCACTTGCCAAATTACTAAGAA
66 GAGGATGCTCTATTTGAACTTTTTTGTCCTTTTCTGTCTTTTCTCACTTGCCAAATTACTAAGAA
*
85924 GACCCTAGGTTAGTTTCTAGCCAGTTTTTGCCCTTAAGCCCTTTTTTGTAATTATCCTTTCCTTT
131 GACCCTAGGTTAGTTTCTAGACAGTTTTTGCCCTTAAGCCCTTTTTTGTAATTATCCTTTCCTTT
85989 CACATAAATGTTATAATAAATCATATATCCCT
196 CACATAAATGTTATAATAAATCATATATCCCT
86021 TATATATACTAAATAGTATTTGAAAGACCCATGGAATTTACCAAAGGCCCCTTTTGAGGATCGAT
1 TATATATACTAAATAGTATTTGAAAGACCCATGGAATTTACCAAAGGCCCCTTTTGAGGATCGAT
* *
86086 GAGGATGCTCTATTTGAACTTTTTTTGTCCTTTTCTGTTTTTTCTCACTTGTCAAATTACTAAGA
66 GAGGATGCTCTATTTGAAC-TTTTTTGTCCTTTTCTGTCTTTTCTCACTTGCCAAATTACTAAGA
86151 AGACCCTAGGTTAGTTTCTAGACAGTTTTTGCCCTTAAGCCCTTTTTTGTAATTATCCTTTCCTT
130 AGACCCTAGGTTAGTTTCTAGACAGTTTTTGCCCTTAAGCCCTTTTTTGTAATTATCCTTTCCTT
86216 TCACATAAATGTTATAATAAATCATATATCCCT
195 TCACATAAATGTTATAATAAATCATATATCCCT
86249 TA
1 TA
86251 ATTATATAGA
Statistics
Matches: 225, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
227 84 0.37
228 141 0.63
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.40
Consensus pattern (227 bp):
TATATATACTAAATAGTATTTGAAAGACCCATGGAATTTACCAAAGGCCCCTTTTGAGGATCGAT
GAGGATGCTCTATTTGAACTTTTTTGTCCTTTTCTGTCTTTTCTCACTTGCCAAATTACTAAGAA
GACCCTAGGTTAGTTTCTAGACAGTTTTTGCCCTTAAGCCCTTTTTTGTAATTATCCTTTCCTTT
CACATAAATGTTATAATAAATCATATATCCCT
Found at i:90584 original size:22 final size:21
Alignment explanation
Indices: 90559--90633 Score: 80
Period size: 22 Copynumber: 3.4 Consensus size: 21
90549 TTGAATGTTT
90559 TTATGAAATTTTGATAACTACC
1 TTATGAAATTTTGATAA-TACC
* **
90581 TTATTAAATTTTGATAATCATG
1 TTATGAAATTTTGATAAT-ACC
90603 TTATGAAATTTTGATAATTTACC
1 TTATGAAATTTTGATAA--TACC
90626 -TATGAAAT
1 TTATGAAAT
90634 ATGAAACTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
21 1 0.02
22 41 0.93
23 1 0.02
24 1 0.02
ACGTcount: A:0.37, C:0.08, G:0.09, T:0.45
Consensus pattern (21 bp):
TTATGAAATTTTGATAATACC
Found at i:90719 original size:21 final size:23
Alignment explanation
Indices: 90633--90726 Score: 113
Period size: 23 Copynumber: 4.2 Consensus size: 23
90623 ACCTATGAAA
* **
90633 TATGAAACTTTAAT-AACCTAAC
1 TATGAAATTTTAATAAACCTTCC
*
90655 TATGAAATTTTAATAAACATTCC
1 TATGAAATTTTAATAAACCTTCC
90678 TATGAAATTTTAATAAACCTTCC
1 TATGAAATTTTAATAAACCTTCC
**
90701 TATGAAA-TTTCGT-AACCTTCC
1 TATGAAATTTTAATAAACCTTCC
90722 TATGA
1 TATGA
90727 TTTTTGATAA
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
21 13 0.20
22 17 0.27
23 34 0.53
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.37
Consensus pattern (23 bp):
TATGAAATTTTAATAAACCTTCC
Found at i:90737 original size:21 final size:22
Alignment explanation
Indices: 90633--90739 Score: 101
Period size: 23 Copynumber: 4.9 Consensus size: 22
90623 ACCTATGAAA
* * **
90633 TATGAAACTTTAATAACCTAAC
1 TATGAAATTTTGATAACCTTCC
* *
90655 TATGAAATTTTAATAAACATTCC
1 TATGAAATTTTGAT-AACCTTCC
*
90678 TATGAAATTTTAATAAACCTTCC
1 TATGAAATTTTGAT-AACCTTCC
*
90701 TATGAAATTTCG-TAACCTTCC
1 TATGAAATTTTGATAACCTTCC
*
90722 TATG-ATTTTTGATAACCT
1 TATGAAATTTTGATAACCT
90740 CTCTGTGACA
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
20 5 0.07
21 18 0.24
22 14 0.19
23 37 0.50
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:94322 original size:2 final size:2
Alignment explanation
Indices: 94315--94342 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
94305 ATAGACAGAG
94315 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
94343 AAATATTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:95107 original size:124 final size:127
Alignment explanation
Indices: 94971--95216 Score: 374
Period size: 124 Copynumber: 1.9 Consensus size: 127
94961 ACTTTTATAA
*
94971 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATAT-CTT-TA-TA-ATTTTTAC
1 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACTATATTTTTAA
*
95032 CATTTTACTATTTAAATTAAAAAAACTTATATATATCAGAATTTTTTAAATATACTATTACAG
66 CATTTTACTATTTAAATT-AAAAAACTTATATATATCAGAATTTTTAAAATATACTATTACAG
*
95095 TTTTATTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACTTATTTTATTT
1 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAC-TA---TATTT
* *
95160 TTAACATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTAAAATATA
62 TTAACATTTTACTATTTAAATTAAAAAACTTATATATATCAGAATTTTTAAAATATA
95217 TTTCTTAAAT
Statistics
Matches: 109, Mismatches: 5, Indels: 9
0.89 0.04 0.07
Matches are distributed among these distances:
124 45 0.41
125 3 0.03
126 2 0.02
128 2 0.02
131 33 0.30
132 24 0.22
ACGTcount: A:0.40, C:0.10, G:0.01, T:0.49
Consensus pattern (127 bp):
TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACTATATTTTTAA
CATTTTACTATTTAAATTAAAAAACTTATATATATCAGAATTTTTAAAATATACTATTACAG
Found at i:96793 original size:5 final size:5
Alignment explanation
Indices: 96785--96809 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
96775 TATCTTCAAA
96785 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
96810 TCCATCCCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:135785 original size:2 final size:2
Alignment explanation
Indices: 135778--135808 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
135768 CTTTTCAACA
135778 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
135809 ATTAAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:137588 original size:27 final size:27
Alignment explanation
Indices: 137554--137607 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
137544 TTATTGTTTA
137554 GCTATAAATTAAGGGTAATTATTTGAT
1 GCTATAAATTAAGGGTAATTATTTGAT
137581 GCTATAAATTAAGGGTAATTATTTGAT
1 GCTATAAATTAAGGGTAATTATTTGAT
137608 ACATCGACGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.04, G:0.19, T:0.41
Consensus pattern (27 bp):
GCTATAAATTAAGGGTAATTATTTGAT
Found at i:138114 original size:7 final size:7
Alignment explanation
Indices: 138102--138130 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
138092 ATCAACGATG
138102 TCTCTAC
1 TCTCTAC
138109 TCTCTAC
1 TCTCTAC
138116 TCTCTAC
1 TCTCTAC
138123 TCTCTAC
1 TCTCTAC
138130 T
1 T
138131 AGGCCTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.41, G:0.00, T:0.45
Consensus pattern (7 bp):
TCTCTAC
Found at i:140012 original size:3 final size:3
Alignment explanation
Indices: 139998--140047 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
139988 AAAGAAAACC
* * * * *
139998 CAT CAT CCT CAT CAT CTT CCT CAT CAC CAT CAT CAT CAT CAT TAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
140046 CA
1 CA
140048 AATGATAAAT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.28, C:0.38, G:0.00, T:0.34
Consensus pattern (3 bp):
CAT
Found at i:154866 original size:13 final size:13
Alignment explanation
Indices: 154850--154874 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
154840 TGAGATTGTT
154850 TCAATGTCCATAA
1 TCAATGTCCATAA
154863 TCAATGTCCATA
1 TCAATGTCCATA
154875 TTGTTTCAGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (13 bp):
TCAATGTCCATAA
Found at i:155449 original size:56 final size:59
Alignment explanation
Indices: 155342--155458 Score: 188
Period size: 56 Copynumber: 2.0 Consensus size: 59
155332 TATCCATTTC
*
155342 CTTTCACATAATAAATGTTATAATAATAAATTCTATCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAATAAATTCTATCCCCCTATCTCTACTTAATTATT
155401 CTTTCACACAATAAATG-T-TAA-AAT-AATTCCTATCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAATAAATT-CTATCCCCCTATCTCTACTTAATTATT
155457 CT
1 CT
155459 ACAAAATAAA
Statistics
Matches: 56, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
55 4 0.07
56 32 0.57
57 3 0.05
58 1 0.02
59 16 0.29
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.41
Consensus pattern (59 bp):
CTTTCACACAATAAATGTTATAATAATAAATTCTATCCCCCTATCTCTACTTAATTATT
Found at i:155583 original size:42 final size:41
Alignment explanation
Indices: 155524--155612 Score: 151
Period size: 42 Copynumber: 2.1 Consensus size: 41
155514 TAAGGATCAG
*
155524 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC-AA
*
155566 GATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTTCAA
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCAA
155607 GATTTG
1 GATTTG
155613 GCTAAGGCCT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
41 7 0.16
42 38 0.84
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (41 bp):
GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCAA
Found at i:161915 original size:190 final size:190
Alignment explanation
Indices: 161563--161926 Score: 516
Period size: 190 Copynumber: 1.9 Consensus size: 190
161553 AGATTTAGAC
* * * *
161563 ATTAAACACCTATCAACTACACGGCTTCACTAGCAGTGTGATCGTCTGATTGACGTGTCAATAGG
1 ATTAAACACCTATCAACTACACAGCTCCACTAGCAGTGTGATCATCTGATTGACGTGTCAAAAGG
* * * *
161628 AAATTGTGAAAATGTTCTTTCTTTATTTTCATCAAATTCAGAAGATTTTCTTATAGTGACTTTAA
66 AAATTATGAAAATGTTCTTTCTTTATTTTCATCAAATTCAAAAGATTTTCTTACAATGACTTTAA
*
161693 GCAGCTTTTAGAGTCATCAACCAATAAATGTTAGCACCACTCAAGTCTCAAACAAAAGGA
131 GCAGCTTTTAGAATCATCAACCAATAAATGTTAGCACCACTCAAGTCTCAAACAAAAGGA
* * * * * *
161753 ATTAAACACCTGTCAACTACACAGC-CCACTTTGTAGTTTGATCATTTGGTTGACGTGTCAAAAG
1 ATTAAACACCTATCAACTACACAGCTCCAC-TAGCAGTGTGATCATCTGATTGACGTGTCAAAAG
* *
161817 GAAATTATGAAAATGTTCTCTTTTTTTTTTTCATCAAATTCAAAAGATTTTCTTACAATGACTTT
65 GAAATTATGAAAATGTTCT-TTCTTTATTTTCATCAAATTCAAAAGATTTTCTTACAATGACTTT
* * *
161882 AAGCAGCTTTTAGAATCA-CTACCTATGAATGTTAGCACCACTCAA
129 AAGCAGCTTTTAGAATCATCAACCAATAAATGTTAGCACCACTCAA
161927 AACAAAGAAA
Statistics
Matches: 152, Mismatches: 20, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
189 3 0.02
190 92 0.61
191 57 0.38
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (190 bp):
ATTAAACACCTATCAACTACACAGCTCCACTAGCAGTGTGATCATCTGATTGACGTGTCAAAAGG
AAATTATGAAAATGTTCTTTCTTTATTTTCATCAAATTCAAAAGATTTTCTTACAATGACTTTAA
GCAGCTTTTAGAATCATCAACCAATAAATGTTAGCACCACTCAAGTCTCAAACAAAAGGA
Found at i:172771 original size:20 final size:21
Alignment explanation
Indices: 172732--172772 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
172722 ATATCTTCCA
*
172732 TTTCCAAAGCATCAACAAAAT
1 TTTCCAAAGCATCAAAAAAAT
172753 TTTCCAAAGCAT-AAAAAAAT
1 TTTCCAAAGCATCAAAAAAAT
172773 AACATTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.51, C:0.20, G:0.05, T:0.24
Consensus pattern (21 bp):
TTTCCAAAGCATCAAAAAAAT
Found at i:200367 original size:34 final size:35
Alignment explanation
Indices: 200301--200366 Score: 100
Period size: 33 Copynumber: 1.9 Consensus size: 35
200291 CTATTTTAGT
*
200301 TTCTCTTCTCTTTTTTCTTTTCCTTTTTTTTTTCC
1 TTCTCTTCTCTTTCTTCTTTTCCTTTTTTTTTTCC
*
200336 TTCTC-TCTCTTTCTTC-TTTCTTTTTTTTTTT
1 TTCTCTTCTCTTTCTTCTTTTCCTTTTTTTTTT
200367 TTAAATATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 14 0.48
34 10 0.34
35 5 0.17
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (35 bp):
TTCTCTTCTCTTTCTTCTTTTCCTTTTTTTTTTCC
Found at i:215792 original size:7 final size:7
Alignment explanation
Indices: 215780--215808 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
215770 CATCGATCAT
215780 GTGAAAA
1 GTGAAAA
215787 GTGAAAA
1 GTGAAAA
215794 GTGAAAA
1 GTGAAAA
215801 GTGAAAA
1 GTGAAAA
215808 G
1 G
215809 CACAAATCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.31, T:0.14
Consensus pattern (7 bp):
GTGAAAA
Found at i:216619 original size:6 final size:6
Alignment explanation
Indices: 216608--216632 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
216598 TTAATGAAAC
216608 TCTTTT TCTTTT TCTTTT TCTTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT T
216633 TTTAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TCTTTT
Found at i:227546 original size:7 final size:7
Alignment explanation
Indices: 227534--227559 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
227524 AGTATTATTA
227534 TAAATGT
1 TAAATGT
227541 TAAATGT
1 TAAATGT
227548 TAAATGT
1 TAAATGT
227555 TAAAT
1 TAAAT
227560 ATATACTCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.42
Consensus pattern (7 bp):
TAAATGT
Found at i:227812 original size:32 final size:32
Alignment explanation
Indices: 227756--227827 Score: 119
Period size: 32 Copynumber: 2.2 Consensus size: 32
227746 AATTGATGTA
227756 AAGTTAATAAAAAAATAGAAGGGTAAATTGGAG
1 AAGTTAATAAAAAAATAG-AGGGTAAATTGGAG
227789 AAGTTAATAAAAAATATAG-GGGTAAATTGGAG
1 AAGTTAATAAAAAA-ATAGAGGGTAAATTGGAG
227821 AAGTTAA
1 AAGTTAA
227828 GTGTGAGTAG
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
32 20 0.53
33 14 0.37
34 4 0.11
ACGTcount: A:0.53, C:0.00, G:0.24, T:0.24
Consensus pattern (32 bp):
AAGTTAATAAAAAAATAGAGGGTAAATTGGAG
Done.