Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019394.1 Corchorus olitorius cultivar O-4 contig19427, 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: 84707
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:620 original size:4 final size:4
Alignment explanation
Indices: 611--637 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
601 TCTCGGTTCT
611 AATA AATA AATA AATA AATA AATA AAT
1 AATA AATA AATA AATA AATA AATA AAT
638 GAGACCGAGC
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:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:25656 original size:26 final size:26
Alignment explanation
Indices: 25604--25656 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
25594 TTAAGTTATC
* * **
25604 AAAAGAAGTTATGATATTTTCTTCAA
1 AAAAAAAGTTATGATATTATCAACAA
25630 AAAAAAAGTTATGATATTATCAACAA
1 AAAAAAAGTTATGATATTATCAACAA
25656 A
1 A
25657 TTAAGTAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.51, C:0.08, G:0.09, T:0.32
Consensus pattern (26 bp):
AAAAAAAGTTATGATATTATCAACAA
Found at i:27572 original size:20 final size:21
Alignment explanation
Indices: 27535--27574 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
27525 ATTTTTCTAT
27535 GGTTACTAAAAAAGTAATAAA
1 GGTTACTAAAAAAGTAATAAA
27556 GGTTA-TAAAAGAA-TAATAA
1 GGTTACTAAAA-AAGTAATAA
27575 TGCTATAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.57, C:0.03, G:0.15, T:0.25
Consensus pattern (21 bp):
GGTTACTAAAAAAGTAATAAA
Found at i:28605 original size:16 final size:16
Alignment explanation
Indices: 28564--28605 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
28554 TTCAAAAAAA
28564 TAATAATAATTATAAT
1 TAATAATAATTATAAT
* *
28580 TATTATTAATTATAAT
1 TAATAATAATTATAAT
28596 TAATAATAAT
1 TAATAATAAT
28606 CAAAAATAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TAATAATAATTATAAT
Found at i:37055 original size:6 final size:6
Alignment explanation
Indices: 37044--37079 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
37034 CCTAATGGAA
37044 GATTCC GATTCC GATTCC GATTCC GATTCC GATTCC
1 GATTCC GATTCC GATTCC GATTCC GATTCC GATTCC
37080 AAGGGGATCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.17, C:0.33, G:0.17, T:0.33
Consensus pattern (6 bp):
GATTCC
Found at i:39619 original size:88 final size:88
Alignment explanation
Indices: 39467--39723 Score: 426
Period size: 88 Copynumber: 2.9 Consensus size: 88
39457 GATTTTGGTT
*
39467 ATGATTAGGGTTTGACTGTGTCTGGGTATTAATTCATTTATGTTTTTTTGATAACTTCAACTCGA
1 ATGATTAGGGTTTCACTGTGTCTGGGTATTAATTCATTTATGTTTTTTTGATAACTTCAACTCGA
39532 ATGCAAAATTAATTTGTTCGGTG
66 ATGCAAAATTAATTTGTTCGGTG
* * * *
39555 ATTATTAGAGTTTCACTGTGTCTGGGTATTAGTTCATTTATGTTTTTTTGATTACTTCAACTCGA
1 ATGATTAGGGTTTCACTGTGTCTGGGTATTAATTCATTTATGTTTTTTTGATAACTTCAACTCGA
*
39620 ATGCAAAATTAATTCAAGTTCGGTG
66 ATGCAAAATTAATT--TGTTCGGTG
*
39645 ATGATTAGGGTTTCATTGTGTCTGGGTATTAATTCATTTATG-TTTTTTGATAACTTCAACTCGA
1 ATGATTAGGGTTTCACTGTGTCTGGGTATTAATTCATTTATGTTTTTTTGATAACTTCAACTCGA
39709 ATGCAAAATTAATTT
66 ATGCAAAATTAATTT
39724 TAGTTGTTTC
Statistics
Matches: 155, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
88 74 0.48
89 35 0.23
90 46 0.30
ACGTcount: A:0.26, C:0.11, G:0.18, T:0.45
Consensus pattern (88 bp):
ATGATTAGGGTTTCACTGTGTCTGGGTATTAATTCATTTATGTTTTTTTGATAACTTCAACTCGA
ATGCAAAATTAATTTGTTCGGTG
Found at i:48134 original size:108 final size:108
Alignment explanation
Indices: 47945--48154 Score: 368
Period size: 108 Copynumber: 1.9 Consensus size: 108
47935 GACAGCACTA
47945 GGTTTTCTGACTCAGAATTTATTGGACCTTGTGCCTGCTCACATGGTGTAGTAACTGGTGCAGCC
1 GGTTTTCTGACTCAGAATTTATTGGACCTTGTGCCTGCTCACATGGTGTAGTAACTGGTGCAGCC
*
48010 AACCTCCCAAACCCAGGTGGATTATCCCGAATAGCAGGGACTG
66 AACCTCCCAAACCCAGGTGGATAATCCCGAATAGCAGGGACTG
* *
48053 GGTTTTCTGACTCTGAAGTTT-TTGGACCTTGTGCCTGCTCACTTGGTGTAGTAACTGGTGCAGC
1 GGTTTTCTGACTCAGAA-TTTATTGGACCTTGTGCCTGCTCACATGGTGTAGTAACTGGTGCAGC
*
48117 CAACCTCCCACACCCAGGTGGATAATCCCGAATAGCAG
65 CAACCTCCCAAACCCAGGTGGATAATCCCGAATAGCAG
48155 AAACTCTACG
Statistics
Matches: 97, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
108 94 0.97
109 3 0.03
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.28
Consensus pattern (108 bp):
GGTTTTCTGACTCAGAATTTATTGGACCTTGTGCCTGCTCACATGGTGTAGTAACTGGTGCAGCC
AACCTCCCAAACCCAGGTGGATAATCCCGAATAGCAGGGACTG
Found at i:48841 original size:11 final size:12
Alignment explanation
Indices: 48813--48854 Score: 68
Period size: 12 Copynumber: 3.5 Consensus size: 12
48803 GCGTCCACTG
48813 CAAAAATTGAAA
1 CAAAAATTGAAA
48825 CAAAAATTGAAA
1 CAAAAATTGAAA
48837 CAAAAATTTGAAA
1 CAAAAA-TTGAAA
48850 -AAAAA
1 CAAAAA
48855 AAATGAGTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 23 0.79
13 6 0.21
ACGTcount: A:0.69, C:0.07, G:0.07, T:0.17
Consensus pattern (12 bp):
CAAAAATTGAAA
Found at i:55708 original size:45 final size:45
Alignment explanation
Indices: 55644--55733 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
55634 TAACAAGCCA
55644 ACAAGACAAATATAGCACATTCAAGTGCATCAGCAGTTTAAAAAT
1 ACAAGACAAATATAGCACATTCAAGTGCATCAGCAGTTTAAAAAT
55689 ACAAGACAAATATAGCACATTCAAGTGCATCAGCAGTTTAAAAAT
1 ACAAGACAAATATAGCACATTCAAGTGCATCAGCAGTTTAAAAAT
55734 GCATGCATGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (45 bp):
ACAAGACAAATATAGCACATTCAAGTGCATCAGCAGTTTAAAAAT
Found at i:67190 original size:13 final size:14
Alignment explanation
Indices: 67172--67208 Score: 51
Period size: 12 Copynumber: 2.7 Consensus size: 14
67162 GTAATACATG
67172 ATAAAAAAAAT-AA
1 ATAAAAAAAATAAA
67185 AT-AAAAAAATAAA
1 ATAAAAAAAATAAA
67198 ATAAAATAAAA
1 ATAAAA-AAAA
67209 AAAGAAGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 8 0.38
13 6 0.29
14 3 0.14
15 4 0.19
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (14 bp):
ATAAAAAAAATAAA
Found at i:67204 original size:18 final size:16
Alignment explanation
Indices: 67174--67211 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 16
67164 AATACATGAT
67174 AAAAAAAATAAATAAA
1 AAAAAAAATAAATAAA
67190 AAAATAAAATAAAATAAA
1 AAAA-AAAAT-AAATAAA
67208 AAAA
1 AAAA
67212 GAAGAAGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 4 0.20
17 5 0.25
18 11 0.55
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (16 bp):
AAAAAAAATAAATAAA
Found at i:69195 original size:16 final size:17
Alignment explanation
Indices: 69174--69205 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
69164 ATGTTAGGTC
69174 TAAATAT-AACTTTTTA
1 TAAATATCAACTTTTTA
69190 TAAATATCAACTTTTT
1 TAAATATCAACTTTTT
69206 CAAATGTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (17 bp):
TAAATATCAACTTTTTA
Found at i:77265 original size:46 final size:46
Alignment explanation
Indices: 77198--77310 Score: 226
Period size: 46 Copynumber: 2.5 Consensus size: 46
77188 ATTTATTAGG
77198 AATATAGGTGCAAGATATTTAAGGACAGAGTTTCAGTTCCTCATAT
1 AATATAGGTGCAAGATATTTAAGGACAGAGTTTCAGTTCCTCATAT
77244 AATATAGGTGCAAGATATTTAAGGACAGAGTTTCAGTTCCTCATAT
1 AATATAGGTGCAAGATATTTAAGGACAGAGTTTCAGTTCCTCATAT
77290 AATATAGGTGCAAGATATTTA
1 AATATAGGTGCAAGATATTTA
77311 TGATGGTAAA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 67 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (46 bp):
AATATAGGTGCAAGATATTTAAGGACAGAGTTTCAGTTCCTCATAT
Found at i:81299 original size:50 final size:50
Alignment explanation
Indices: 81224--81326 Score: 188
Period size: 50 Copynumber: 2.1 Consensus size: 50
81214 TAGTGTTCGG
81224 TAATCAAACTGAAATCCTATTAATCCAGAACTGAGAATCACATTAGACCT
1 TAATCAAACTGAAATCCTATTAATCCAGAACTGAGAATCACATTAGACCT
* *
81274 TAATCAAATTGAAATCCTATTAATCCAGAACTGAGAGTCACATTAGACCT
1 TAATCAAACTGAAATCCTATTAATCCAGAACTGAGAATCACATTAGACCT
81324 TAA
1 TAA
81327 ATAGGGAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.27
Consensus pattern (50 bp):
TAATCAAACTGAAATCCTATTAATCCAGAACTGAGAATCACATTAGACCT
Found at i:83920 original size:17 final size:17
Alignment explanation
Indices: 83876--83933 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
83866 AATTAAATCT
* *
83876 TAATACTAATAT-ATAT
1 TAATAATAATATAATAA
*
83892 TAA-AAAAATATAATAA
1 TAATAATAATATAATAA
*
83908 TAATAATAATATAATCA
1 TAATAATAATATAATAA
*
83925 TAACAATAA
1 TAATAATAA
83934 AAGAAAAACG
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
15 6 0.18
16 9 0.26
17 19 0.56
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (17 bp):
TAATAATAATATAATAA
Found at i:84684 original size:2 final size:2
Alignment explanation
Indices: 84677--84705 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
84667 CCTCCCTACT
84677 TA TA TA TA T- 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
84706 AT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.