Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015702.1 Corchorus capsularis cultivar CVL-1 contig15723, 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: 27376
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30
Found at i:3425 original size:30 final size:30
Alignment explanation
Indices: 3389--3449 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
3379 GACTTATTGA
3389 TGGGCATACTTGAAAATTGAATGTTTGATT
1 TGGGCATACTTGAAAATTGAATGTTTGATT
3419 TGGGCATACTTGAAAATTGAATGTTTGATT
1 TGGGCATACTTGAAAATTGAATGTTTGATT
3449 T
1 T
3450 TTTTTTTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.41
Consensus pattern (30 bp):
TGGGCATACTTGAAAATTGAATGTTTGATT
Found at i:6902 original size:25 final size:25
Alignment explanation
Indices: 6860--6940 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 25
6850 ATTTCTGACT
* **
6860 TTGGGCTTTTAACATATTTATGCAC
1 TTGGGCTTTTGATTTATTTATGCAC
*
6885 TTGGGCTTTTGATTTATTCATGCAC
1 TTGGGCTTTTGATTTATTTATGCAC
* * * * * *
6910 TTAGCCTTATGATTTCTTTGTGCAT
1 TTGGGCTTTTGATTTATTTATGCAC
6935 TTGGGC
1 TTGGGC
6941 CTAGGTTTTA
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.17, C:0.16, G:0.20, T:0.47
Consensus pattern (25 bp):
TTGGGCTTTTGATTTATTTATGCAC
Found at i:7682 original size:38 final size:38
Alignment explanation
Indices: 7631--7817 Score: 230
Period size: 38 Copynumber: 4.9 Consensus size: 38
7621 GAAATTTCCA
7631 AAAGTTTTCAATTTAGGGAAAGATCCCATCAAGTCTTC
1 AAAGTTTTCAATTTAGGGAAAGATCCCATCAAGTCTTC
* *
7669 AAAGTTTTCAATTTAGGGAAACATCCCGTCAAGTCTTC
1 AAAGTTTTCAATTTAGGGAAAGATCCCATCAAGTCTTC
* * * * *
7707 AAAATTTTTAGTTTAGGGAAAGATCCCACCAAGTTTTC
1 AAAGTTTTCAATTTAGGGAAAGATCCCATCAAGTCTTC
** ** * *
7745 AAAGTTTTCAATTTAGGGAAAGATATCATTTAGTTTTTTT
1 AAAGTTTTCAATTTAGGGAAAGATCCCATCAAG--TCTTC
*
7785 TAAGTTTTCAATTTAGGGAAAGATCCCATCAAG
1 AAAGTTTTCAATTTAGGGAAAGATCCCATCAAG
7818 CATTTTTCAA
Statistics
Matches: 124, Mismatches: 23, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
38 92 0.74
40 32 0.26
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (38 bp):
AAAGTTTTCAATTTAGGGAAAGATCCCATCAAGTCTTC
Found at i:11204 original size:87 final size:87
Alignment explanation
Indices: 11057--11297 Score: 301
Period size: 87 Copynumber: 2.8 Consensus size: 87
11047 GACGAGGGAA
** * * * *
11057 TCTCTTGGCGAGACGAACATGCCATCCCAATGAGGGAGTCTATTGGAGAGACGAACATGCGCTCT
1 TCTCTTGGAAAGACGAACATG-CATCCCGACGAGGGAGTCTCTTGGCGAGACGAACATGCGCTCT
** *
11122 TGGTGCTCCTCCATTCCAACGAG
65 TGGCACTCCTCCATCCCAACGAG
*
11145 TCTCTTGGAAAGACGAACATGCATCCCGACGAGGGAGTCTCTTAGCGAGACGAACATGCGCTCTT
1 TCTCTTGGAAAGACGAACATGCATCCCGACGAGGGAGTCTCTTGGCGAGACGAACATGCGCTCTT
*
11210 GGCACTCGTCCATCCCAACGAG
66 GGCACTCCTCCATCCCAACGAG
* * *
11232 TC-C---CAATCAGATGAACATGCATCCCGACGAGGGAATCTCTTGGCGAGACGAACATGCGCTC
1 TCTCTTGGAA--AGACGAACATGCATCCCGACGAGGGAGTCTCTTGGCGAGACGAACATGCGCTC
11293 TTGGC
64 TTGGC
11298 GCTTGATCGA
Statistics
Matches: 136, Mismatches: 15, Indels: 7
0.86 0.09 0.04
Matches are distributed among these distances:
83 2 0.01
85 55 0.40
86 1 0.01
87 59 0.43
88 19 0.14
ACGTcount: A:0.25, C:0.29, G:0.26, T:0.21
Consensus pattern (87 bp):
TCTCTTGGAAAGACGAACATGCATCCCGACGAGGGAGTCTCTTGGCGAGACGAACATGCGCTCTT
GGCACTCCTCCATCCCAACGAG
Found at i:11707 original size:10 final size:10
Alignment explanation
Indices: 11694--11718 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
11684 TATATTCAGC
11694 CCATATAAGT
1 CCATATAAGT
11704 CCATATAAGT
1 CCATATAAGT
11714 CCATA
1 CCATA
11719 ATTGGAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.24, G:0.08, T:0.28
Consensus pattern (10 bp):
CCATATAAGT
Found at i:13280 original size:54 final size:54
Alignment explanation
Indices: 13132--13378 Score: 239
Period size: 54 Copynumber: 4.7 Consensus size: 54
13122 GACAAACATG
* * * * * **
13132 CCATCCCAAA-GAGGGAGTCTCATGGTGAGACGAACGTGAAAC-CTTTGCACTCCG
1 CCAT-CCAAACGAGGGAGTCTCTTGGTGAGACGAACATG-CACTCTTGGCGCTCTT
* *
13186 CCATCC---CGA-GG-GTCTCTTGGTGAGACGAACATGCAATCTTGGCGTTCTT
1 CCATCCAAACGAGGGAGTCTCTTGGTGAGACGAACATGCACTCTTGGCGCTCTT
* * *
13235 CTATCCAAACGTGGGAGTCTCCTGGTGAGACGAACATGCACTCTTGG-GACTCTT
1 CCATCCAAACGAGGGAGTCTCTTGGTGAGACGAACATGCACTCTTGGCG-CTCTT
* *
13289 CCATCCCAACGAGGGAGTCTCTTAGTGAGACGAACATGCACTCTTGGCGCTCTT
1 CCATCCAAACGAGGGAGTCTCTTGGTGAGACGAACATGCACTCTTGGCGCTCTT
* *
13343 CCATCCCAAC-A---AGTCTCTTGGAGAGACGAACATGCA
1 CCATCCAAACGAGGGAGTCTCTTGGTGAGACGAACATGCA
13379 TCCCGACGAG
Statistics
Matches: 163, Mismatches: 21, Indels: 22
0.79 0.10 0.11
Matches are distributed among these distances:
48 1 0.01
49 32 0.20
50 25 0.15
51 2 0.01
52 2 0.01
53 6 0.04
54 94 0.58
55 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.25, T:0.23
Consensus pattern (54 bp):
CCATCCAAACGAGGGAGTCTCTTGGTGAGACGAACATGCACTCTTGGCGCTCTT
Found at i:13396 original size:37 final size:38
Alignment explanation
Indices: 13354--13448 Score: 138
Period size: 38 Copynumber: 2.5 Consensus size: 38
13344 CATCCCAACA
* * *
13354 AGTCTCTTGGAGAGACGAACATG-CATCCCGACGAGGG
1 AGTCTCTTGGCGAGACGAACAAGCCATCCCAACGAGGG
*
13391 AGTCTCTTGGCGAGACGAACAAGCCATTCCAACGAGGG
1 AGTCTCTTGGCGAGACGAACAAGCCATCCCAACGAGGG
*
13429 AGTCTCTTGGCGAGATGAAC
1 AGTCTCTTGGCGAGACGAAC
13449 GTCCACTCTT
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
37 21 0.40
38 31 0.60
ACGTcount: A:0.27, C:0.24, G:0.31, T:0.18
Consensus pattern (38 bp):
AGTCTCTTGGCGAGACGAACAAGCCATCCCAACGAGGG
Found at i:13539 original size:54 final size:54
Alignment explanation
Indices: 13414--13614 Score: 253
Period size: 54 Copynumber: 3.7 Consensus size: 54
13404 GACGAACAAG
* * * *
13414 CCATTCCAACGAGGGAGTCTCTTGGCGAGATGAACGTCCACTCTT-GCGCTCTT
1 CCATTCCAACGAGAGAGTCTCTTGGCGAGACGAACATGCACTCTTGGCGCTCTT
* * * * * *
13467 CCATACCAACAAGGGAGTCTCTTGGAGAGACGAACATGCGCTCTTGGCGCTTTT
1 CCATTCCAACGAGAGAGTCTCTTGGCGAGACGAACATGCACTCTTGGCGCTCTT
* *
13521 CCATTCCAACGAGAGAGTCTCTTGGCCAGATGAACATGCACTCTTGGCGCTCTT
1 CCATTCCAACGAGAGAGTCTCTTGGCGAGACGAACATGCACTCTTGGCGCTCTT
* *
13575 CCATCCCAAC-AAAGGAGTCTCTTGGCGAGACGAACATGCA
1 CCATTCCAACGAGA-GAGTCTCTTGGCGAGACGAACATGCA
13615 TTCCAACGAG
Statistics
Matches: 126, Mismatches: 20, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
53 40 0.32
54 86 0.68
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.23
Consensus pattern (54 bp):
CCATTCCAACGAGAGAGTCTCTTGGCGAGACGAACATGCACTCTTGGCGCTCTT
Found at i:13610 original size:108 final size:107
Alignment explanation
Indices: 13414--13613 Score: 328
Period size: 108 Copynumber: 1.9 Consensus size: 107
13404 GACGAACAAG
* * *
13414 CCATTCCAACGAGGGAGTCTCTTGGCGAGATGAACGTCCACTCTTGCGCTCTTCCATACCAACAA
1 CCATTCCAACGAGAGAGTCTCTTGGCCAGATGAACATCCACTCTTGCGCTCTTCCATACCAACAA
*
13479 GGGAGTCTCTTGGAGAGACGAACATGCGCTCTTGGCGCTTTT
66 AGGAGTCTCTTGGAGAGACGAACATGCGCTCTTGGCGCTTTT
* *
13521 CCATTCCAACGAGAGAGTCTCTTGGCCAGATGAACATGCACTCTTGGCGCTCTTCCATCCCAACA
1 CCATTCCAACGAGAGAGTCTCTTGGCCAGATGAACATCCACTCTT-GCGCTCTTCCATACCAACA
*
13586 AAGGAGTCTCTTGGCGAGACGAACATGC
65 AAGGAGTCTCTTGGAGAGACGAACATGC
13614 ATTCCAACGA
Statistics
Matches: 85, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
107 41 0.48
108 44 0.52
ACGTcount: A:0.23, C:0.29, G:0.24, T:0.23
Consensus pattern (107 bp):
CCATTCCAACGAGAGAGTCTCTTGGCCAGATGAACATCCACTCTTGCGCTCTTCCATACCAACAA
AGGAGTCTCTTGGAGAGACGAACATGCGCTCTTGGCGCTTTT
Found at i:13830 original size:76 final size:76
Alignment explanation
Indices: 13699--14003 Score: 466
Period size: 76 Copynumber: 4.0 Consensus size: 76
13689 AACCGTCAGA
* * *
13699 ATGAATGGCGTCTGCTTGGACGCTCAACCTCATTTAGAGTTAAACGGGGGTGCCAGTCTAGGCAC
1 ATGAGTGGCGTCTGCTTGGACGCTCGACCTCATTCAGAGTTAAACGGGGGTGCCAGTCTAGGCAC
** *
13764 TCAGTTGTTGG
66 TCAGCCGTCGG
*
13775 ATGAGTGGCGTCTGCTTGAACGCTCGACCTCATTCAGAGTTAAACGGGGGTGCCAGTCTAGGCAC
1 ATGAGTGGCGTCTGCTTGGACGCTCGACCTCATTCAGAGTTAAACGGGGGTGCCAGTCTAGGCAC
13840 TCAGCCGTCGG
66 TCAGCCGTCGG
* **
13851 ATGAGTGGCGTCTTCTTGGACGCTCGGTCTCATTCAGAGTTAAACGGGGGTGCCAGTCTAGGCAC
1 ATGAGTGGCGTCTGCTTGGACGCTCGACCTCATTCAGAGTTAAACGGGGGTGCCAGTCTAGGCAC
13916 TCAGCCGTCGG
66 TCAGCCGTCGG
* * * * * *
13927 ATGAGTGGCATATGTTTGGACGCTCGGCCTCATTCAGAGTTAAACGAGGGTACCAGTCTAGGCAC
1 ATGAGTGGCGTCTGCTTGGACGCTCGACCTCATTCAGAGTTAAACGGGGGTGCCAGTCTAGGCAC
13992 TCAGCCGTCGG
66 TCAGCCGTCGG
14003 A
1 A
14004 GACGAAGGGC
Statistics
Matches: 211, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
76 211 1.00
ACGTcount: A:0.20, C:0.24, G:0.31, T:0.25
Consensus pattern (76 bp):
ATGAGTGGCGTCTGCTTGGACGCTCGACCTCATTCAGAGTTAAACGGGGGTGCCAGTCTAGGCAC
TCAGCCGTCGG
Found at i:15486 original size:76 final size:75
Alignment explanation
Indices: 15360--15567 Score: 294
Period size: 76 Copynumber: 2.8 Consensus size: 75
15350 AACTTGTGCA
* *
15360 AACTCTTAGCGAGGTCGAGCGTCCAAGCAGACGCCACCCGCAGATGGCTGAGCGCCTAGACTGGC
1 AACTCTTAGCGAGGTCGAGCGTCCAAGCAGACGCCACACGCAGACGGCTGAGCGCCTAGACTGGC
*
15425 GCCCCCGTATT
66 GCCCCCGT-GT
* *
15436 AACTCTTAGCGAGGTCGAGCGTCCAAGCAGACGCCACTCGCAGACGGCTGAGCGCCTAGACTGGT
1 AACTCTTAGCGAGGTCGAGCGTCCAAGCAGACGCCACACGCAGACGGCTGAGCGCCTAGACTGGC
15501 GCCCCCGTGT
66 GCCCCCGTGT
* * * *
15511 AACTCTCAGTC-AGGCCGAGCGTCCAAGCAGACGACC-CACGCAGACGACTGAGAGCCT
1 AACTCTTAG-CGAGGTCGAGCGTCCAAGCAGACG-CCACACGCAGACGGCTGAGCGCCT
15568 TGAATGGTGC
Statistics
Matches: 121, Mismatches: 9, Indels: 5
0.90 0.07 0.04
Matches are distributed among these distances:
75 48 0.40
76 73 0.60
ACGTcount: A:0.23, C:0.34, G:0.29, T:0.14
Consensus pattern (75 bp):
AACTCTTAGCGAGGTCGAGCGTCCAAGCAGACGCCACACGCAGACGGCTGAGCGCCTAGACTGGC
GCCCCCGTGT
Found at i:18744 original size:22 final size:21
Alignment explanation
Indices: 18704--18746 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
18694 CAGAAGGAAT
*
18704 ACTTAAACCAAAAATCAAAAC
1 ACTTAAACCAAAAACCAAAAC
*
18725 ACTTAATCCAAAAAACCAAAAC
1 ACTTAAACC-AAAAACCAAAAC
18747 CCCCAGTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.60, C:0.26, G:0.00, T:0.14
Consensus pattern (21 bp):
ACTTAAACCAAAAACCAAAAC
Found at i:20588 original size:14 final size:14
Alignment explanation
Indices: 20571--20611 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
20561 CAGAAAAAAG
*
20571 AAAGAAAAAAATAA
1 AAAGAAAAAAAGAA
20585 AAAGAATAAAAAGAA
1 AAAGAA-AAAAAGAA
20600 AAAGATAAAAAA
1 AAAGA-AAAAAA
20612 AATTGAATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 6 0.25
15 17 0.71
16 1 0.04
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (14 bp):
AAAGAAAAAAAGAA
Found at i:20703 original size:14 final size:14
Alignment explanation
Indices: 20683--20721 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
20673 TTTAAAAATT
20683 GTTTTCAAGAAAAGA
1 GTTTTCAA-AAAAGA
*
20698 -TTTTCAAAAATGA
1 GTTTTCAAAAAAGA
20711 GTTTTCAAAAA
1 GTTTTCAAAAA
20722 GTTTTTAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (14 bp):
GTTTTCAAAAAAGA
Found at i:22973 original size:2 final size:2
Alignment explanation
Indices: 22966--22991 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
22956 AGTAGGTTTA
22966 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
22992 TCACTTCTAA
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):
AT
Found at i:24643 original size:16 final size:16
Alignment explanation
Indices: 24622--24654 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
24612 CTCGAAAAAC
24622 CCAAAACCCAAATGAT
1 CCAAAACCCAAATGAT
*
24638 CCAAAACCCAAGTGAT
1 CCAAAACCCAAATGAT
24654 C
1 C
24655 TGCGGCCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.33, G:0.09, T:0.12
Consensus pattern (16 bp):
CCAAAACCCAAATGAT
Found at i:24861 original size:421 final size:423
Alignment explanation
Indices: 24074--24918 Score: 1107
Period size: 421 Copynumber: 2.0 Consensus size: 423
24064 ATCCTATGCA
* *
24074 GGCCCGACAAATCCGTAGGCTGAATAATCTCAGAAGTTAACCCAAATGATCCAAAAATATTATAA
1 GGCCCGACAAACCCGTAGGCCGAATAATCTCAGAAGTTAACCCAAATGATCCAAAAATATTATAA
* * *
24139 ACTAAAATTATGTTTTATTTAATAAAATCTCAATTGAATCTGAGTCTTATATCCGAAAAAACCCA
66 ACTAAAATTATGTTTTATTTAATAAAATCTCAACTGAATCTGAGCCCTATATCCGAAAAAACCCA
* * * * ** * *
24204 ATACTCGAATGACCCATAACCCGTGTGACTTGAGGCCAAAACCCAAATAGCCTGACCCAAGATCT
131 AAACCCAAATGACCCAAAACCCAAGTGACTTGAGGCCAAAACCCAAATAGCCTGACCCAAGACCC
* * *
24269 AGCAGATCCGAGACCAAAATGACCTGAATCTAGATGAGCCGAAACCCGAATGTCTTGAGAAAATT
196 AGCAGACCCGAGACCAAAATGACCTGAACCTAGATGAGCCGAAACCCGAATGTCATGAGAAAATT
* * *
24334 ACCTGCCACATTTGATCTATACCTAGATGACTCGAACTCGAAACCCATCCAATCCGCCCGATTGA
261 ACCTGCCACATTTGATCTATACCAAGATGACTCGAACTCAAAACCCATCCAATCCGCCCGATTAA
*
24399 CTCATCTAACTTTATCAGTCAAATGAAATAATTGCATGTTACTCTTCTTTTTATTTAT-AAAACT
326 CTCATCTAACTTTATAAGTCAAATGAAATAATTGCATGTTACTCTTCTTTTTATTTATAAAAACT
24463 TTATATA-TTTTTTTAATTAAATTAGTAAAATGG
391 TTATA-AGTTTTTTTAATTAAATTAGTAAAATGG
** *
24496 GGCCCGACAAACCCGTAGGCCGAATAATC-CGAGAAGTTAACCTGAATGATCCAAGAATATTATA
1 GGCCCGACAAACCCGTAGGCCGAATAATCTC-AGAAGTTAACCCAAATGATCCAAAAATATTATA
24560 AACTAAAATTATGTTTTATTTAATAAAAT-TCCAACTGAATCTGAGCCCTATA-CTCG-AAAAAC
65 AACTAAAATTATGTTTTATTTAATAAAATCT-CAACTGAATCTGAGCCCTATATC-CGAAAAAAC
* * * ** *
24622 CCAAAACCCAAATGATCCAAAACCCAAGTGA-TCTGCGGCCAAAACCCGAACCT-GTTTGACCCT
128 CCAAAACCCAAATGACCCAAAACCCAAGTGACT-TGAGGCCAAAACCC-AA-ATAGCCTGACCCA
* * * *
24685 AGACCCAGCAGACCCGAGATC-GAATGACCTGGACCTAGATGAGCCGAAACCCGAATTTCATGAG
190 AGACCCAGCAGACCCGAGACCAAAATGACCTGAACCTAGATGAGCCGAAACCCGAATGTCATGAG
** * * * * * * * *
24749 AAAATTTTCTGTCTCATTTGATTTGTACCAAGATGACTCGAA-TCCAAAACTCGTCCAATTCGCT
255 AAAATTACCTGCCACATTTGATCTATACCAAGATGACTCGAACT-CAAAACCCATCCAATCCGCC
** * * *
24813 CGATTAACTTTTCTAACTTTATAATTCAAATGAAATAATTGGATGTTACTCTTCTTTTTATTTTT
319 CGATTAACTCATCTAACTTTATAAGTCAAATGAAATAATTGCATGTTACTCTTCTTTTTATTTAT
24878 AAAAACTTTATAAGTTTTTTTTAATTAAATTAGTAAAATGG
384 AAAAACTTTATAAG-TTTTTTTAATTAAATTAGTAAAATGG
24919 TAAAAATAAA
Statistics
Matches: 365, Mismatches: 48, Indels: 19
0.84 0.11 0.04
Matches are distributed among these distances:
420 2 0.01
421 193 0.53
422 143 0.39
423 27 0.07
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (423 bp):
GGCCCGACAAACCCGTAGGCCGAATAATCTCAGAAGTTAACCCAAATGATCCAAAAATATTATAA
ACTAAAATTATGTTTTATTTAATAAAATCTCAACTGAATCTGAGCCCTATATCCGAAAAAACCCA
AAACCCAAATGACCCAAAACCCAAGTGACTTGAGGCCAAAACCCAAATAGCCTGACCCAAGACCC
AGCAGACCCGAGACCAAAATGACCTGAACCTAGATGAGCCGAAACCCGAATGTCATGAGAAAATT
ACCTGCCACATTTGATCTATACCAAGATGACTCGAACTCAAAACCCATCCAATCCGCCCGATTAA
CTCATCTAACTTTATAAGTCAAATGAAATAATTGCATGTTACTCTTCTTTTTATTTATAAAAACT
TTATAAGTTTTTTTAATTAAATTAGTAAAATGG
Found at i:25088 original size:134 final size:130
Alignment explanation
Indices: 24888--25127 Score: 327
Period size: 134 Copynumber: 1.8 Consensus size: 130
24878 AAAAACTTTA
* * * **
24888 TAAGTTTTTTTTAATTAAATTAGTAAAATGGTAAAAATAAAATAGGTATAAAAATATTAGGTTTA
1 TAAGTTTTTTTTAAATAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAAAATACTAGACTTA
* *
24953 ATAAAATAAAAATAGAATTTTTAATTGAGTAATACTATAAAAATATATTATAAAAATTCTAATAT
66 ATAAAATAAAAATAG-AGTTTTAATTGAGTAAAACTATAAAAATATATTATAAAAATTCTAATAT
25018 T
130 T
* * **
25019 TAAGTTTTTTAATTAAAATAAAATAGTAAATTGGTAAAAATAAAATAGTTATAAGGATACTAGAC
1 TAAGTTTTTT--TT-AAATAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAAAATACTAGAC
* *
25084 TTAATTAAATAAAAATAGAGTTTTAGTTGAGTAAAACTATAAAA
63 TTAATAAAATAAAAATAGAGTTTTAATTGAGTAAAACTATAAAA
25128 CTTTAAACAA
Statistics
Matches: 93, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
131 10 0.11
133 25 0.27
134 58 0.62
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.37
Consensus pattern (130 bp):
TAAGTTTTTTTTAAATAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAAAATACTAGACTTA
ATAAAATAAAAATAGAGTTTTAATTGAGTAAAACTATAAAAATATATTATAAAAATTCTAATATT
Found at i:26257 original size:2 final size:2
Alignment explanation
Indices: 26250--26285 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
26240 TGTGTATGTG
26250 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
26286 CTAGAGAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.