Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022651.1 Corchorus olitorius cultivar O-4 contig22684, 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: 25111
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Found at i:58 original size:2 final size:2
Alignment explanation
Indices: 1--38 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1 TA TA TA TA TA 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 TA TA TA TA TA
39 ACATGATCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:322 original size:21 final size:20
Alignment explanation
Indices: 292--355 Score: 58
Period size: 25 Copynumber: 3.0 Consensus size: 20
282 TGTGACAGTA
292 TACTTATATACATATATTATG
1 TACTT-TATACATATATTATG
313 TACTTGTATATATACATATATTATG
1 TAC---T-T-TATACATATATTATG
*
338 TAC-TTATATATATATTAT
1 TACTTTATACATATATTAT
356 ATATATATAT
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
19 13 0.34
20 1 0.03
21 3 0.08
24 1 0.03
25 20 0.53
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.50
Consensus pattern (20 bp):
TACTTTATACATATATTATG
Found at i:328 original size:25 final size:25
Alignment explanation
Indices: 296--351 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
286 ACAGTATACT
*
296 TATATACATATATTATGTACTTGTA
1 TATATACATATATTATGTACTTATA
321 TATATACATATATTATGTACTTATA
1 TATATACATATATTATGTACTTATA
346 TATATA
1 TATATA
352 TTATATATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.48
Consensus pattern (25 bp):
TATATACATATATTATGTACTTATA
Found at i:365 original size:19 final size:19
Alignment explanation
Indices: 319--366 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
309 TATGTACTTG
* *
319 TATATATACATATATTATG
1 TATATATATATATATTATA
338 TACT-TATATATATATTATA
1 TA-TATATATATATATTATA
357 TATATATATA
1 TATATATATA
367 ATAATAAAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 1 0.04
19 23 0.92
20 1 0.04
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (19 bp):
TATATATATATATATTATA
Found at i:674 original size:22 final size:22
Alignment explanation
Indices: 649--699 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
639 ACCCTATTTG
649 AAAATTCACATGAAATAAGGTC
1 AAAATTCACATGAAATAAGGTC
671 AAAATTCACATGAAATAAGGTC
1 AAAATTCACATGAAATAAGGTC
693 AAAATTC
1 AAAATTC
700 TTTTTTTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.24
Consensus pattern (22 bp):
AAAATTCACATGAAATAAGGTC
Found at i:833 original size:2 final size:2
Alignment explanation
Indices: 826--873 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
816 AACTTGAAGT
826 GA GA GA GA 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 GA GA GA GA
868 GA GA GA
1 GA GA GA
874 ATAAAAGTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1629 original size:20 final size:20
Alignment explanation
Indices: 1604--1644 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1594 TAACCTTTTA
1604 ATTGGGTTAGTTAAGGATCC
1 ATTGGGTTAGTTAAGGATCC
1624 ATTGGGTTAGTTAAGGATCC
1 ATTGGGTTAGTTAAGGATCC
1644 A
1 A
1645 ACGCTTTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.10, G:0.29, T:0.34
Consensus pattern (20 bp):
ATTGGGTTAGTTAAGGATCC
Found at i:2431 original size:2 final size:2
Alignment explanation
Indices: 2424--2451 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2414 ATGACAAAGC
2424 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
2452 TGATGTCACA
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):
AT
Found at i:4668 original size:5 final size:5
Alignment explanation
Indices: 4660--4709 Score: 63
Period size: 5 Copynumber: 10.8 Consensus size: 5
4650 TTATAAATCG
*
4660 ATATT ATA-T ATATT ATATT ATATT AT-GT -TATT ATATT ATA-T ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
4706 ATAT
1 ATAT
4710 ATACAACATA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
3 1 0.03
4 10 0.26
5 28 0.72
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (5 bp):
ATATT
Found at i:4693 original size:8 final size:8
Alignment explanation
Indices: 4661--4711 Score: 50
Period size: 9 Copynumber: 6.0 Consensus size: 8
4651 TATAAATCGA
4661 TATTATAT
1 TATTATAT
4669 ATATTATATT
1 -TATTATA-T
*
4679 ATATTATGT
1 -TATTATAT
4688 TATTATAT
1 TATTATAT
4696 TATATATAT
1 TAT-TATAT
4705 TA-TATAT
1 TATTATAT
4712 ACAACATATC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
7 5 0.13
8 10 0.26
9 15 0.39
10 8 0.21
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (8 bp):
TATTATAT
Found at i:4693 original size:18 final size:19
Alignment explanation
Indices: 4660--4711 Score: 70
Period size: 18 Copynumber: 2.7 Consensus size: 19
4650 TTATAAATCG
4660 ATATTATATATATTATATT
1 ATATTATATATATTATATT
*
4679 ATATTATGT-TATTATATT
1 ATATTATATATATTATATT
4697 ATATATATTATATAT
1 ATAT-TA-TATATAT
4712 ACAACATATC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 13 0.46
19 10 0.36
20 2 0.07
21 3 0.11
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
ATATTATATATATTATATT
Found at i:5778 original size:440 final size:433
Alignment explanation
Indices: 4856--6026 Score: 1360
Period size: 440 Copynumber: 2.7 Consensus size: 433
4846 TTAATATTTG
* ** **
4856 TTAATCGGACATTTGGATAAAAAATCATATGATATTAAATAAACCGTCAATCGAAACCATAAAAT
1 TTAATCGGACATATGGATCGAAAATCATATGATATTAAATAAACCGTCAATCGAAACCACCAAAT
* * * *
4921 TCTGGAAGATTTTTTAAAGTTGAACCATAAAAATTAGCTTTTGAGT-ACTTCATGAAAGTTGTAG
66 T-TGGAAGATTTTTTTAA-TTGAAACATAAAAATT-GCTTTTAAGTCA-TTTATGAAAGTTGTAG
* *
4985 ATCATGAAATTAACTTTTAATTGACATC-TAAATTACCTTAATTGGACAAATAG--AAAAA-AAA
127 ATCATGAAATTACCTTTTAATAGACA-CATAAATTACCTTAATTGGACAAATAGAAAAAAATAAA
** * * * *
5046 AACGTTAA--G--CG-TAAATCGAGTAATATAGAATTTGTAAAGGACTAAGTAGTATAAAGTAGA
191 AAAATTAAGTGAACGTTAAATCGATTAAGATAGAATTTGTAAA-AATTAAGTAGTATAAAGTAGA
* ** *
5106 AAAGTATGAGGGTCATTTGATAAATCATCCAAATAAGAAAATATTTGTTAATGGGGATCTTGAAA
255 AAAGTATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATATTCATTAATGGAGATCTTGAAA
* * * * *
5171 CATAAAAATTCCCTTTTGAATCCTTCATGAAACTCGTAGATTAAATTTAACTTTCGGGTTCATCA
320 CATAAAAATTCCCTTTTGAACCCTTAATGAAACTCGTAGATCAAATTTAACTTTCGGATCCATCA
* *
5236 TTAAAGTTGTAAATCATGCAATAACCTTTTAACCGACACTTGAATAACT
385 TGAAAGTCGTAAATCATGCAATAACCTTTTAACCGACACTTGAATAACT
* * * * * * *
5285 TTAATCGGACTTGTGAATCGAAAATTATATGGTATTAAATAAACCGGCAATCGAACCCACCAAAT
1 TTAATCGGACATATGGATCGAAAATCATATGATATTAAATAAACCGTCAATCGAAACCACCAAAT
*
5350 TTGGAAAGCATTTTCTTTAATTGAAACATAAAAATTGCCTTTTAAGTCATTTATGAAAGTTGTAA
66 TTGG-AAG-ATTTT-TTTAATTGAAACATAAAAATTG-CTTTTAAGTCATTTATGAAAGTTGTAG
* * * * *
5415 ATCATGAAATTACCTTTTAATAGGCAGATGAATCACCTTAATCGGACAAATAGAAAAAAATAAAA
127 ATCATGAAATTACCTTTTAATAGACACATAAATTACCTTAATTGGACAAATAGAAAAAAATAAAA
*
5480 AAATTAAGCTGAAACGTTAAATCGATTAAGATAGAATTAGTAAACAATTAAGTAGTATAAAGTAG
192 AAATTAAG-TG-AACGTTAAATCGATTAAGATAGAATTTGTAAA-AATTAAGTAGTATAAAGTAG
** * * *
5545 AAAAACATGAGGGTCATTTGATAAATAATCCAATTAAGAAAATGTTCATTGATGGAGATCTTGAA
254 AAAAGTATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATATTCATTAATGGAGATCTTGAA
* * * *
5610 ACATAAAAATTTCCTTTTGAACCCTTAATGAAACTCGTATATCAAATTTAGC-TTCTGGATCCTT
319 ACATAAAAATTCCCTTTTGAACCCTTAATGAAACTCGTAGATCAAATTTAACTTTC-GGATCCAT
** *
5674 CATGATGGTCGTAAATCATGCAATAACCTTTTAACTGACACTTGAATAACT
383 CATGAAAGTCGTAAATCATGCAATAACCTTTTAACCGACACTTGAATAACT
* * *
5725 TTAATTGGACATATGGATCGAAAATCATATGATATCAAATAGACCGTCAATCGAAACCACCAAAT
1 TTAATCGGACATATGGATCGAAAATCATATGATATTAAATAAACCGTCAATCGAAACCACCAAA-
* *
5790 TTTCGGAAGTATTTTTTTTTTTAAATTGAAACATAAAAATTGACTTTCGAA-TCCTTTATGAAAG
65 TTT-GGAAG-A----TTTTTTT-AATTGAAACATAAAAATTG-CTTT-TAAGTCATTTATGAAAG
* *
5854 TTGTAGATCATGAAATTACCTTTTAATAGACACTTAAATTAACTTAATTGGACAAATAGAAAAAA
121 TTGTAGATCATGAAATTACCTTTTAATAGACACATAAATTACCTTAATTGGACAAATAG--AAAA
* * * *
5919 AGAATAAAAAAAATAAAGATGAAGCGTTAAATCGGTTAAGATAGAATTTGTAAAAGATTAAATAA
184 A-AAT-AAAAAAATTAAG-TGAA-CGTTAAATCGATTAAGATAGAATTTGTAAAA-ATTAAGTAG
* *
5984 CATAAAGTAGAAAAGTAT-AGGGATGATTTGATAAATAATCCAA
244 TATAAAGTAGAAAAGTATGAGGG-TCATTTGATAAATAATCCAA
6027 GCAAGCAAGA
Statistics
Matches: 624, Mismatches: 86, Indels: 44
0.83 0.11 0.06
Matches are distributed among these distances:
428 3 0.00
429 59 0.09
430 87 0.14
431 5 0.01
432 5 0.01
433 9 0.01
436 1 0.00
439 5 0.01
440 249 0.40
441 7 0.01
442 2 0.00
444 3 0.00
445 90 0.14
446 2 0.00
447 5 0.01
448 10 0.02
449 82 0.13
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.31
Consensus pattern (433 bp):
TTAATCGGACATATGGATCGAAAATCATATGATATTAAATAAACCGTCAATCGAAACCACCAAAT
TTGGAAGATTTTTTTAATTGAAACATAAAAATTGCTTTTAAGTCATTTATGAAAGTTGTAGATCA
TGAAATTACCTTTTAATAGACACATAAATTACCTTAATTGGACAAATAGAAAAAAATAAAAAAAT
TAAGTGAACGTTAAATCGATTAAGATAGAATTTGTAAAAATTAAGTAGTATAAAGTAGAAAAGTA
TGAGGGTCATTTGATAAATAATCCAAATAAGAAAATATTCATTAATGGAGATCTTGAAACATAAA
AATTCCCTTTTGAACCCTTAATGAAACTCGTAGATCAAATTTAACTTTCGGATCCATCATGAAAG
TCGTAAATCATGCAATAACCTTTTAACCGACACTTGAATAACT
Found at i:7420 original size:27 final size:27
Alignment explanation
Indices: 7390--7443 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
7380 TGGTAAGTGC
*
7390 ATTACTTTAAGTTTTTTGAACCTTTTA
1 ATTACTTTAAGTCTTTTGAACCTTTTA
7417 ATTACTTTAAGTCTTTTGAACCTTTTA
1 ATTACTTTAAGTCTTTTGAACCTTTTA
7444 GTGTCTAGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.26, C:0.13, G:0.07, T:0.54
Consensus pattern (27 bp):
ATTACTTTAAGTCTTTTGAACCTTTTA
Found at i:7479 original size:2 final size:2
Alignment explanation
Indices: 7472--7504 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
7462 ACAAGTCTAT
*
7472 TA TA TA TA TA TA TA TA TA -A TA AA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7505 GCCGGGTTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:8211 original size:19 final size:19
Alignment explanation
Indices: 8189--8239 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
8179 GGGCTGAAAT
8189 TAATTAATTATTAATTAAA
1 TAATTAATTATTAATTAAA
* *
8208 TAA-TAATTATTTTATTGAA
1 TAATTAATTA-TTAATTAAA
8227 TAATT-ATTATTAA
1 TAATTAATTATTAA
8240 AAATCCCACA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 9 0.33
19 17 0.63
20 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TAATTAATTATTAATTAAA
Found at i:10565 original size:23 final size:25
Alignment explanation
Indices: 10528--10579 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 25
10518 TATAGAAATA
* *
10528 ATAAAATGATGATATGA-TATAT-T
1 ATAAAATAATAATATGACTATATCT
*
10551 ATAAAATAATAATATTACTATATCT
1 ATAAAATAATAATATGACTATATCT
10576 ATAA
1 ATAA
10580 TAACAAGAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 14 0.58
24 5 0.21
25 5 0.21
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (25 bp):
ATAAAATAATAATATGACTATATCT
Found at i:12137 original size:2 final size:2
Alignment explanation
Indices: 12130--12157 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12120 ATGCAGCCAA
12130 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
12158 TATTGGAAAC
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):
AT
Found at i:12878 original size:2 final size:2
Alignment explanation
Indices: 12871--12903 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
12861 TGTTTTTAGT
12871 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12904 TTGGGTGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13910 original size:41 final size:41
Alignment explanation
Indices: 13865--14034 Score: 205
Period size: 41 Copynumber: 4.4 Consensus size: 41
13855 CAACAAACAT
* *
13865 AGTCTTCAAAGTTTTTTTTCAAATTAGGAAAGATCCTATCA
1 AGTCTTCAAAGTTTTTTTTCAAATTGGGAAAGATCCCATCA
*
13906 AGTCTTCAAAGTTTGTTTTCAAATTGGGAAAGATCCCATCA
1 AGTCTTCAAAGTTTTTTTTCAAATTGGGAAAGATCCCATCA
*
13947 AGTTTTCAAAG----TTTTCAAATTGGGAAAGATCCCATCA
1 AGTCTTCAAAGTTTTTTTTCAAATTGGGAAAGATCCCATCA
* *
13984 AGTTTTCAAAG----TTTTC-AATTGGAAAAGATCCCATCA
1 AGTCTTCAAAGTTTTTTTTCAAATTGGGAAAGATCCCATCA
* *
14020 AGTTTTCAAAATTTT
1 AGTCTTCAAAGTTTT
14035 CAATTTAGGG
Statistics
Matches: 119, Mismatches: 6, Indels: 9
0.89 0.04 0.07
Matches are distributed among these distances:
36 29 0.24
37 42 0.35
41 48 0.40
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.36
Consensus pattern (41 bp):
AGTCTTCAAAGTTTTTTTTCAAATTGGGAAAGATCCCATCA
Found at i:14011 original size:36 final size:37
Alignment explanation
Indices: 13880--14064 Score: 246
Period size: 37 Copynumber: 4.9 Consensus size: 37
13870 TCAAAGTTTT
* * *
13880 TTTTCAAATTAGGAAAGATCCTATCAAGTCTTCAAAGTTTG
1 TTTTCAAATTGGGAAAGATCCCATCAAGTTTTCAAA----G
13921 TTTTCAAATTGGGAAAGATCCCATCAAGTTTTCAAAG
1 TTTTCAAATTGGGAAAGATCCCATCAAGTTTTCAAAG
13958 TTTTCAAATTGGGAAAGATCCCATCAAGTTTTCAAAG
1 TTTTCAAATTGGGAAAGATCCCATCAAGTTTTCAAAG
* *
13995 TTTTC-AATTGGAAAAGATCCCATCAAGTTTTCAAAA
1 TTTTCAAATTGGGAAAGATCCCATCAAGTTTTCAAAG
* *
14031 TTTTCAATTTAGGGAAAGATCCCATTAAAGTTTT
1 TTTTCAAATT-GGGAAAGATCCCA-TCAAGTTTT
14065 TTTAAAAAAA
Statistics
Matches: 133, Mismatches: 8, Indels: 8
0.89 0.05 0.05
Matches are distributed among these distances:
36 34 0.26
37 46 0.35
38 12 0.09
39 8 0.06
41 33 0.25
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (37 bp):
TTTTCAAATTGGGAAAGATCCCATCAAGTTTTCAAAG
Found at i:14018 original size:73 final size:75
Alignment explanation
Indices: 13880--14064 Score: 248
Period size: 73 Copynumber: 2.4 Consensus size: 75
13870 TCAAAGTTTT
* * * *
13880 TTTTCAAATTAGGAAAGATCCTATCAAGTCTTCAAAGTTTGTTTTCAAATTGGGAAAGATCCCAT
1 TTTTCAAATTGGGAAAGATCCCATCAAGTTTTCAAA---TGTTTTCAAATTGGAAAAGATCCCAT
*
13945 CAAGTTTTCAAAG
63 CAAGTTTTCAAAA
13958 TTTTCAAATTGGGAAAGATCCCATCAAGTTTTCAAA-GTTTTC-AATTGGAAAAGATCCCATCAA
1 TTTTCAAATTGGGAAAGATCCCATCAAGTTTTCAAATGTTTTCAAATTGGAAAAGATCCCATCAA
14021 GTTTTCAAAA
66 GTTTTCAAAA
* *
14031 TTTTCAATTTAGGGAAAGATCCCATTAAAGTTTT
1 TTTTCAAATT-GGGAAAGATCCCA-TCAAGTTTT
14065 TTTAAAAAAA
Statistics
Matches: 98, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
73 38 0.39
74 19 0.19
75 8 0.08
78 33 0.34
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (75 bp):
TTTTCAAATTGGGAAAGATCCCATCAAGTTTTCAAATGTTTTCAAATTGGAAAAGATCCCATCAA
GTTTTCAAAA
Found at i:15520 original size:13 final size:13
Alignment explanation
Indices: 15502--15527 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
15492 TATTATGAAA
15502 TTACATGAGAAGG
1 TTACATGAGAAGG
15515 TTACATGAGAAGG
1 TTACATGAGAAGG
15528 CATTTACCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.31, T:0.23
Consensus pattern (13 bp):
TTACATGAGAAGG
Found at i:15905 original size:24 final size:24
Alignment explanation
Indices: 15878--15963 Score: 75
Period size: 24 Copynumber: 3.5 Consensus size: 24
15868 TCCCATCAAA
15878 TTTTCAAAGTGTTCAATTTAGCTC
1 TTTTCAAAGTGTTCAATTTAGCTC
** * **
15902 TTTTCAAAGTG-GGAAGTTCCCGTC
1 TTTTCAAAGTGTTCAATTTAGC-TC
*
15926 AAGCTTTCAAAGTGTTCAATTTAGCTC
1 ---TTTTCAAAGTGTTCAATTTAGCTC
15953 TTTTCAAAGTG
1 TTTTCAAAGTG
15964 GGAAAGGTCC
Statistics
Matches: 45, Mismatches: 12, Indels: 10
0.67 0.18 0.15
Matches are distributed among these distances:
23 5 0.11
24 23 0.51
27 12 0.27
28 5 0.11
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (24 bp):
TTTTCAAAGTGTTCAATTTAGCTC
Found at i:16007 original size:52 final size:52
Alignment explanation
Indices: 15854--16262 Score: 622
Period size: 52 Copynumber: 7.9 Consensus size: 52
15844 TCAAAGTTTC
*
15854 CAAAGTGGGAAAGTTCCCATCAAATTTTCAAAGTGTTCAATTTAGCTCTTTT
1 CAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTGTTCAATTTAGCTCTTTT
* *
15906 CAAAGTGGG-AAGTTCCCGTCAAGCTTTCAAAGTGTTCAATTTAGCTCTTTT
1 CAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTGTTCAATTTAGCTCTTTT
* * *
15957 CAAAGTGGGAAAGGTCCCATCAAGTTTTTAAAGTGTTCAATTTAGTTCTTTT
1 CAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTGTTCAATTTAGCTCTTTT
16009 CAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTGTTCAATTTAGCTCTTTT
1 CAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTGTTCAATTTAGCTCTTTT
* *
16061 CAACGTGGGAAAGTTCCTATCAAGTTTTCAAAGTGTTCAATTTAGCTCTTTT
1 CAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTGTTCAATTTAGCTCTTTT
* * * *
16113 CAAAGTGGGAAAGTTCTCATCAAGTTTTCAAAGCGTTCGATTTAGGTCTTTT
1 CAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTGTTCAATTTAGCTCTTTT
* * * *
16165 AAAAGTGGGAAAGTTCCTATCAAATTTTCAAAGTGTTCAATTTAGCACTTTTT
1 CAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTGTTCAATTTAGCTC-TTTT
* * * *
16218 CAAAATGGGAAAATTCCCACCAAGTTTTCAAAGTGTTCGATTTAG
1 CAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTGTTCAATTTAG
16263 GGAAATATCC
Statistics
Matches: 321, Mismatches: 34, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
51 48 0.15
52 231 0.72
53 42 0.13
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (52 bp):
CAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTGTTCAATTTAGCTCTTTT
Found at i:22477 original size:29 final size:30
Alignment explanation
Indices: 22438--22498 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
22428 TATAAATAAT
* *
22438 ATAATATAATT-AGATAA-TTATATTTATAC
1 ATAATAAAATTGA-ATAATTTATATGTATAC
22467 ATAATAAAATTGAATAATTTATATGTATAC
1 ATAATAAAATTGAATAATTTATATGTATAC
22497 AT
1 AT
22499 TAATTAGAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 14 0.50
30 14 0.50
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (30 bp):
ATAATAAAATTGAATAATTTATATGTATAC
Found at i:23727 original size:2 final size:2
Alignment explanation
Indices: 23722--23747 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
23712 GCCAAATGTC
23722 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
23748 CTAATTTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:24038 original size:45 final size:45
Alignment explanation
Indices: 23978--24065 Score: 115
Period size: 45 Copynumber: 2.0 Consensus size: 45
23968 TAAAAACCTC
* * *
23978 ACTATGAAATTTTGATAACTTTCGA-ATGAAATTTTGATAACCAAT
1 ACTATGAAATGTTGATAACCTTC-ATATGAAATATTGATAACCAAT
* *
24023 ACTATGAGATGTTGATAACCTTCATATGATATATTGATAACCA
1 ACTATGAAATGTTGATAACCTTCATATGAAATATTGATAACCA
24066 CGTTATGAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
44 1 0.03
45 36 0.97
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (45 bp):
ACTATGAAATGTTGATAACCTTCATATGAAATATTGATAACCAAT
Found at i:24250 original size:22 final size:22
Alignment explanation
Indices: 23942--24403 Score: 191
Period size: 22 Copynumber: 21.3 Consensus size: 22
23932 TTTCTAAATT
* *
23942 TTTTCGATAACCTCCCTAAGGAA
1 TTTT-GATAACCTCCCTATGAAA
* * *
23965 TTTTAAAAACCTCACTATGAAA
1 TTTTGATAACCTCCCTATGAAA
* * **
23987 TTTTGATAACTTTCGAATGAAA
1 TTTTGATAACCTCCCTATGAAA
* *
24009 TTTTGATAACCAAT-ACTATGAGA
1 TTTTGATAACC--TCCCTATGAAA
* * * *
24032 TGTTGATAACCTTCATATGATA
1 TTTTGATAACCTCCCTATGAAA
* * **
24054 TATTGATAACCACGTTATGAAA
1 TTTTGATAACCTCCCTATGAAA
* * * * *
24076 ATTTAAGAACCTCCATTTG-AA
1 TTTTGATAACCTCCCTATGAAA
* * * *
24097 TTGTT-AGTAATCACACTCTGAAA
1 TT-TTGA-TAACCTCCCTATGAAA
* * *
24120 TTTTGATAATCACACTATGAAA
1 TTTTGATAACCTCCCTATGAAA
* ** *
24142 TTGTGATAACCTTGCTATAAAA
1 TTTTGATAACCTCCCTATGAAA
* *
24164 TTTTGATAAACCTCCTTATAAAA
1 TTTTGAT-AACCTCCCTATGAAA
* *
24187 TTTT-ATAACCTTCTTATGAAA
1 TTTTGATAACCTCCCTATGAAA
* *
24208 TCTTGATAA-----CTA-CAAA
1 TTTTGATAACCTCCCTATGAAA
**
24224 TTTTGATAACCTCCCTATGATT
1 TTTTGATAACCTCCCTATGAAA
**
24246 TTTTGATAACCTCATTATGAAA
1 TTTTGATAACCTCCCTATGAAA
* *
24268 TTTTGTTAATCTCCCTATGAAA
1 TTTTGATAACCTCCCTATGAAA
* * *
24290 TTTTGATCTACAT-ACTATGAAA
1 TTTTGAT-AACCTCCCTATGAAA
* *
24312 TTTTGGTAACC-CTCTTATGAAA
1 TTTTGATAACCTC-CCTATGAAA
* ** *
24334 TTTTGA-AA-ATAAACTACGAAA
1 TTTTGATAACCT-CCCTATGAAA
* * *
24355 TTTTGATAATCTTCATATGAAA
1 TTTTGATAACCTCCCTATGAAA
*
24377 TTTTGATATCCTCCC--TGAAA
1 TTTTGATAACCTCCCTATGAAA
24397 TTTTGAT
1 TTTTGAT
24404 TACTCCATAG
Statistics
Matches: 322, Mismatches: 95, Indels: 47
0.69 0.20 0.10
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
20 12 0.04
21 40 0.12
22 213 0.66
23 43 0.13
24 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (22 bp):
TTTTGATAACCTCCCTATGAAA
Found at i:24291 original size:126 final size:129
Alignment explanation
Indices: 24120--24363 Score: 280
Period size: 126 Copynumber: 1.9 Consensus size: 129
24110 CACTCTGAAA
* ** * *
24120 TTTTGATAATCACACTATGAAATTGTGATAACCTTGCTATAAAATTTTGATAAACCTCCTTATAA
1 TTTTGATAACCACACTATGAAATTGTGATAACCTCCCTATAAAATTTTGATAAACATAC-TATAA
*
24185 AATTTT-ATAACCTTCTTATGAAATCTTG-AT-AACTAC-AAATTTTGATAACCTCCCTATGATT
65 AATTTTGATAACCCTCTTATGAAATCTTGAATAAACTACGAAATTTTGATAACCTCCCTATGATT
* * * * * * ** *
24246 TTTTGATAACCTCATTATGAAATTTTGTTAATCTCCCTATGAAATTTTGATCTACATACTATGAA
1 TTTTGATAACCACACTATGAAATTGTGATAACCTCCCTATAAAATTTTGATAAACATACTATAAA
* *
24311 ATTTTGGTAACCCTCTTATGAAATTTTGAAAATAAACTACGAAATTTTGATAA
66 ATTTTGATAACCCTCTTATGAAATCTTG--AATAAACTACGAAATTTTGATAA
24364 TCTTCATATG
Statistics
Matches: 95, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
125 10 0.11
126 65 0.68
129 2 0.02
130 6 0.06
131 12 0.13
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (129 bp):
TTTTGATAACCACACTATGAAATTGTGATAACCTCCCTATAAAATTTTGATAAACATACTATAAA
ATTTTGATAACCCTCTTATGAAATCTTGAATAAACTACGAAATTTTGATAACCTCCCTATGATT
Found at i:24374 original size:43 final size:45
Alignment explanation
Indices: 24264--24382 Score: 127
Period size: 43 Copynumber: 2.7 Consensus size: 45
24254 ACCTCATTAT
* * * ** *
24264 GAAATTTTGTTAATCTCCCTATGAAATTTTG-ATCTACATACTAT
1 GAAATTTTGATAATCTTCATATGAAATTTTGAAAATACATACTAC
* * * *
24308 GAAATTTTGGTAACCCTCTTATGAAATTTTGAAAATA-A-ACTAC
1 GAAATTTTGATAATCTTCATATGAAATTTTGAAAATACATACTAC
24351 GAAATTTTGATAATCTTCATATGAAATTTTGA
1 GAAATTTTGATAATCTTCATATGAAATTTTGA
24383 TATCCTCCCT
Statistics
Matches: 62, Mismatches: 12, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
43 32 0.52
44 27 0.44
45 3 0.05
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (45 bp):
GAAATTTTGATAATCTTCATATGAAATTTTGAAAATACATACTAC
Found at i:24534 original size:22 final size:22
Alignment explanation
Indices: 24509--24587 Score: 79
Period size: 22 Copynumber: 3.6 Consensus size: 22
24499 AATCACATTT
*
24509 TGAAAATTTGATAACCTTTTTA
1 TGAAAATTTGATAACCTCTTTA
*
24531 TGAAATTTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
* * * *
24553 T-AAAATTTTGTTGACCCCTCTA
1 TGAAAA-TTTGATAACCTCTTTA
*
24575 TGAAATTTTGATA
1 TGAAAATTTGATA
24588 TTTTCATTAT
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
21 3 0.07
22 39 0.87
23 3 0.07
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCTTTA
Found at i:24733 original size:24 final size:22
Alignment explanation
Indices: 24679--24853 Score: 88
Period size: 22 Copynumber: 7.9 Consensus size: 22
24669 GAAAACCACA
*
24679 CTATGAAATTTCAATAACCTTC
1 CTATGAAATTTTAATAACCTTC
**
24701 CTAAAAAATTTTAATAACCTGATC
1 CTATGAAATTTTAATAACCT--TC
** *
24725 CTATGAAATTTTGGTAACC-AC
1 CTATGAAATTTTAATAACCTTC
* *
24746 ACTATAAAATTTTGATAA-CTTC
1 -CTATGAAATTTTAATAACCTTC
* ** *
24768 CATGTGAAATTTTGGTAACC-AC
1 C-TATGAAATTTTAATAACCTTC
* * *
24790 ACTATGGAATATTGATAACC-TC
1 -CTATGAAATTTTAATAACCTTC
* *
24812 CTCATGAAATTATAATAACCATC
1 CT-ATGAAATTTTAATAACCTTC
* * *
24835 TTATTAAATTTTGATAACC
1 CTATGAAATTTTAATAACC
24854 ACACAGAGAC
Statistics
Matches: 116, Mismatches: 28, Indels: 18
0.72 0.17 0.11
Matches are distributed among these distances:
21 5 0.04
22 89 0.77
23 5 0.04
24 17 0.15
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (22 bp):
CTATGAAATTTTAATAACCTTC
Found at i:24743 original size:46 final size:43
Alignment explanation
Indices: 24701--24793 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 43
24691 AATAACCTTC
24701 CTAAAAAATTTTAATAACCTGATCCTATGAAATTTTGGTAACCACA
1 CTAAAAAATTTTAATAA-CT--TCCTATGAAATTTTGGTAACCACA
* * *
24747 CTATAAAATTTTGATAACTTCCATGTGAAATTTTGGTAACCACA
1 CTAAAAAATTTTAATAACTTCC-TATGAAATTTTGGTAACCACA
24791 CTA
1 CTA
24794 TGGAATATTG
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 3 0.07
44 23 0.53
45 2 0.05
46 15 0.35
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (43 bp):
CTAAAAAATTTTAATAACTTCCTATGAAATTTTGGTAACCACA
Found at i:24820 original size:44 final size:43
Alignment explanation
Indices: 24723--24822 Score: 137
Period size: 44 Copynumber: 2.3 Consensus size: 43
24713 AATAACCTGA
* *
24723 TCCTATGAAATTTTGGTAACCACACTATAAAATTTTGATAACT
1 TCCTATGAAATTTTGGTAACCACACTATAAAATATTGATAACC
* **
24766 TCCATGTGAAATTTTGGTAACCACACTATGGAATATTGATAACC
1 TCC-TATGAAATTTTGGTAACCACACTATAAAATATTGATAACC
24810 TCCTCATGAAATT
1 TCCT-ATGAAATT
24823 ATAATAACCA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
43 4 0.08
44 45 0.92
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (43 bp):
TCCTATGAAATTTTGGTAACCACACTATAAAATATTGATAACC
Found at i:24831 original size:44 final size:44
Alignment explanation
Indices: 24739--24832 Score: 100
Period size: 44 Copynumber: 2.1 Consensus size: 44
24729 GAAATTTTGG
* * * * **
24739 TAACCACACTATAAAATTTTGATAACTTCCATGTGAAATTTTGG
1 TAACCACACTATAAAATATTGATAACCTCCATATGAAATTATAA
**
24783 TAACCACACTATGGAATATTGATAACCTCC-TCATGAAATTATAA
1 TAACCACACTATAAAATATTGATAACCTCCAT-ATGAAATTATAA
24827 TAACCA
1 TAACCA
24833 TCTTATTAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
43 1 0.02
44 40 0.98
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (44 bp):
TAACCACACTATAAAATATTGATAACCTCCATATGAAATTATAA
Found at i:25052 original size:19 final size:20
Alignment explanation
Indices: 25021--25058 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
25011 TATTGACATT
25021 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
25040 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
25059 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Done.