Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007751.1 Corchorus capsularis cultivar CVL-1 contig07772, 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: 27076
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Found at i:4229 original size:166 final size:167
Alignment explanation
Indices: 3938--4268 Score: 443
Period size: 166 Copynumber: 2.0 Consensus size: 167
3928 AATGTCCCAA
* * * * ** *
3938 ACTTTAATAGAGTAGTGGAATTACTAAAAGATCCCTACCAAGGCTTACTTTTGGAGTTACAGAAG
1 ACTTGAATAGAGTAGTGGAATTAATAAAAGATCCCCACCAAGGATTACTGATGGAGCTACAGAAG
* * *
4003 TTATTTTTTTCGTCTTTTCCTACTTGGCAAATTACTTAAATGTCCTAACTTTTGATTCTTGAGGG
66 TTATATTTTTCGTCTTTACCTACTTGGCAAATTACTTAAATGTCCTAACTTTTGATTCTTGAGAG
* **
4068 GATTAAATAAGTAATTTTTTTGGTCATTTCTCAATGG
131 GATTAAATAACTAAACTTTTTGGTCATTTCTCAATGG
* * *
4105 ACTTGAATAGAGTAGTGGAATTAATAAATGATCCCCATCAAGGATTGA-TGAT-GAGCTAGAGAA
1 ACTTGAATAGAGTAGTGGAATTAATAAAAGATCCCCACCAAGGATT-ACTGATGGAGCTACAGAA
* * *
4168 -TTAATATTTTTCGTCTTTACCTACTTGGCAGATTACTTAAATGTCCTAATTTTTTATTCTTGAG
65 GTT-ATATTTTTCGTCTTTACCTACTTGGCAAATTACTTAAATGTCCTAACTTTTGATTCTTGAG
*
4232 AGTATTAAATAACTAAACTTTTTGGTCATTTCTCAAT
129 AGGATTAAATAACTAAACTTTTTGGTCATTTCTCAAT
4269 TGACAAATGA
Statistics
Matches: 142, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
165 2 0.01
166 97 0.68
167 42 0.30
168 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (167 bp):
ACTTGAATAGAGTAGTGGAATTAATAAAAGATCCCCACCAAGGATTACTGATGGAGCTACAGAAG
TTATATTTTTCGTCTTTACCTACTTGGCAAATTACTTAAATGTCCTAACTTTTGATTCTTGAGAG
GATTAAATAACTAAACTTTTTGGTCATTTCTCAATGG
Found at i:5094 original size:95 final size:92
Alignment explanation
Indices: 4911--5099 Score: 279
Period size: 95 Copynumber: 2.0 Consensus size: 92
4901 ATTTGGACTA
* *
4911 AACTTAGTGAATTAATTATATATTTTATTTCTAAAACCCTATAACAAGATTATTAATTATGGAAT
1 AACTTAGTGAATTAATTATATATTTTATTTCTAAAACCCTATAACAAAATTATTAATTATGAAAT
* *
4976 TTACCCTTAACATAAAAATAAAATTTT
66 ATACCCTTAAAATAAAAATAAAATTTT
* * * *
5003 AACTTAGTGAAATTAGTTTTGTATTTTATTTCTAAAACCCTATAACAATAAATTATTAATTTTGA
1 AACTTAGTG-AATTAATTATATATTTTATTTCTAAAACCCTATAAC-A-AAATTATTAATTATGA
5068 AATATACCCTTAAAATAAAAATAAAATTTT
63 AATATACCCTTAAAATAAAAATAAAATTTT
5098 AA
1 AA
5100 TTTGGGGCTA
Statistics
Matches: 86, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
92 9 0.10
93 33 0.38
94 1 0.01
95 43 0.50
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.40
Consensus pattern (92 bp):
AACTTAGTGAATTAATTATATATTTTATTTCTAAAACCCTATAACAAAATTATTAATTATGAAAT
ATACCCTTAAAATAAAAATAAAATTTT
Found at i:8574 original size:13 final size:13
Alignment explanation
Indices: 8553--8589 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
8543 GATAATTCTT
8553 TTTGACCCTCCAA
1 TTTGACCCTCCAA
*
8566 TTTGTCCCTCCAA
1 TTTGACCCTCCAA
*
8579 CTTGACCCTCC
1 TTTGACCCTCC
8590 TAATAATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.16, C:0.43, G:0.08, T:0.32
Consensus pattern (13 bp):
TTTGACCCTCCAA
Found at i:10881 original size:545 final size:531
Alignment explanation
Indices: 10038--11115 Score: 1949
Period size: 545 Copynumber: 2.0 Consensus size: 531
10028 AGAATATATA
*
10038 AAGTTAAAAGTAACAATTACATAAAACCCTTTTAGATATAAAAACTTATATAGAATTTTTGTTGG
1 AAGTTAAAAATAACAATTACATAAAACCCTTTTAGATATAAAAACTTATATAGAATTTTTGTTGG
*
10103 TACGTAGATGATGAAAATAAAGTAAAAAATAACAATTACATAAAAAGCTCTTTAGTAAAAAGAAT
66 CACGTAGATGATGAAAATAAAGTAAAAAATAACAATTACATAAAAAGCTCTTTAGTAAAAAGAAT
10168 AAACTCTTGCTTTTGTTTTTCTTAGAAGAAAGAATATTTCCCTTTATAGAAAAATGAAAAGAAAA
131 AAACTCTTGCTTTTGTTTTTCTTAGAAGAAAGAATATTTCCCTTTATAGAAAAATGAAAAGAAAA
* *
10233 AGTTGTTTAAAGAATTAAAACAAAATGAATAAATAGATAATTCTTTTAAAGAAATGAATAATAAA
196 AGTTGTTTAAAAAATTAAAACAAAATGAATAAATAGATAATTCTTTGAAAGAAATGAATAATAAA
* *
10298 CATAGAAATATAAACAAATGAAATGAATCTCTTATTACAACAAATTGAAAATTTTATACTTAGAC
261 CATAGAAATATAAACAAATGAAATGAATCTCTTATTACAACAAATTGAAAATTTTATACATAAAC
10363 TAAAAAATAATTAGAGGATTCCTTCAACAAAAAAAAAAGAAAGAAAAACAAAACAAATAAAGGGA
326 TAAAAAATAATTAGAGGATTCCTTCAAC---AAAAAAA-AAAGAAAAACAAAACAAATAAAGGGA
10428 AATCCTTTATGAATATATACTAAATTTTTTAAGCAAAAACAAAAAAAAATCTAGCTTTAAAACTC
387 AATCCTTTATGAATATATACTAAATTTTTTAAG------CAAAAAAAAA-CTA-CTTTAAAACTC
10493 ACAACATAAATCCTTTAGGTAAAAAGAAGTCTCCAATGAGATCAAATGAGATGAGAGAACCATTA
444 ACAACATAAATCCTTTAGGTAAAAAGAAGTCTCCAATGAGATCAAATGAGATGAGAGAACCATTA
10558 TTTATAGTGGTAATCTCACCATT
509 TTTATAGTGGTAATCTCACCATT
10581 AAGTTAAAAATAACAATTACATAAAACCCTTTTAGATATAAAAACTTATATAGAATTTTTGTTGG
1 AAGTTAAAAATAACAATTACATAAAACCCTTTTAGATATAAAAACTTATATAGAATTTTTGTTGG
*
10646 CACGTAGATGATGAAAATAAAGTAAAAAATAACAATTACATAAAACGCTCTTTAGTATAAAAAGA
66 CACGTAGATGATGAAAATAAAGTAAAAAATAACAATTACATAAAAAGCTCTTTAG--TAAAAAGA
10711 ATAAACTCTTGCTTTTGTTTTTCTTAGAAGAAAGAATATTTCCCTTTATAGAAAAATGAAAAGAA
129 ATAAACTCTTGCTTTTGTTTTTCTTAGAAGAAAGAATATTTCCCTTTATAGAAAAATGAAAAGAA
10776 AAAGTTGTTTAAAAAATTAAAACAAAATGAATAAATAGATAATTCTTTGAAAGAAATGAATAATA
194 AAAGTTGTTTAAAAAATTAAAACAAAATGAATAAATAGATAATTCTTTGAAAGAAATGAATAATA
*
10841 AACATAGAAATATAAACAAATGAAATGAATCTTTTATTACAACAAATTGAAAATTTTATACATAA
259 AACATAGAAATATAAACAAATGAAATGAATCTCTTATTACAACAAATTGAAAATTTTATACATAA
*
10906 ACTAAAAAATAATTAGAGGATTCCTTCAACAGAAAAAAAAGAAAAACAAAACAAATAAAGGGAAA
324 ACTAAAAAATAATTAGAGGATTCCTTCAACAAAAAAAAAAGAAAAACAAAACAAATAAAGGGAAA
10971 TCCTTTATGAATATATACTAAATTTTTTAAGCAAAAAAAAACTACTTTAAAACTCACAACATAAA
389 TCCTTTATGAATATATACTAAATTTTTTAAGCAAAAAAAAACTACTTTAAAACTCACAACATAAA
11036 TCCTTTAGGTAAAAAGAAGTCTCCAATGAGATCAAATGAGATGAGAGAACCATTATTTATAGTGG
454 TCCTTTAGGTAAAAAGAAGTCTCCAATGAGATCAAATGAGATGAGAGAACCATTATTTATAGTGG
11101 TAATCTCACCATT
519 TAATCTCACCATT
11114 AA
1 AA
11116 CTTTGATTGA
Statistics
Matches: 524, Mismatches: 9, Indels: 14
0.96 0.02 0.03
Matches are distributed among these distances:
533 101 0.19
534 3 0.01
535 10 0.02
541 59 0.11
542 6 0.01
543 117 0.22
545 228 0.44
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.29
Consensus pattern (531 bp):
AAGTTAAAAATAACAATTACATAAAACCCTTTTAGATATAAAAACTTATATAGAATTTTTGTTGG
CACGTAGATGATGAAAATAAAGTAAAAAATAACAATTACATAAAAAGCTCTTTAGTAAAAAGAAT
AAACTCTTGCTTTTGTTTTTCTTAGAAGAAAGAATATTTCCCTTTATAGAAAAATGAAAAGAAAA
AGTTGTTTAAAAAATTAAAACAAAATGAATAAATAGATAATTCTTTGAAAGAAATGAATAATAAA
CATAGAAATATAAACAAATGAAATGAATCTCTTATTACAACAAATTGAAAATTTTATACATAAAC
TAAAAAATAATTAGAGGATTCCTTCAACAAAAAAAAAAGAAAAACAAAACAAATAAAGGGAAATC
CTTTATGAATATATACTAAATTTTTTAAGCAAAAAAAAACTACTTTAAAACTCACAACATAAATC
CTTTAGGTAAAAAGAAGTCTCCAATGAGATCAAATGAGATGAGAGAACCATTATTTATAGTGGTA
ATCTCACCATT
Found at i:11254 original size:68 final size:68
Alignment explanation
Indices: 11167--11302 Score: 245
Period size: 68 Copynumber: 2.0 Consensus size: 68
11157 ATTTTTATCA
11167 AAAAGATTAATCAAGGAGGAAATTGTGGATCTAACATATTGTAATTAGAATGTAATTAATCAATC
1 AAAAGATTAATCAAGGAGGAAATTGTGGATCTAACATATTGTAATTAGAATGTAATTAATCAATC
11232 AAT
66 AAT
* * *
11235 AAAAGATTAATTAATGAGGAAATTTTGGATCTAACATATTGTAATTAGAATGTAATTAATCAATC
1 AAAAGATTAATCAAGGAGGAAATTGTGGATCTAACATATTGTAATTAGAATGTAATTAATCAATC
11300 AAT
66 AAT
11303 TAGATACAAG
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 65 1.00
ACGTcount: A:0.46, C:0.07, G:0.15, T:0.33
Consensus pattern (68 bp):
AAAAGATTAATCAAGGAGGAAATTGTGGATCTAACATATTGTAATTAGAATGTAATTAATCAATC
AAT
Found at i:13493 original size:21 final size:20
Alignment explanation
Indices: 13454--13504 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
13444 CATATAAAAT
13454 ATAACTTAGTAAGCATTTTA
1 ATAACTTAGTAAGCATTTTA
* * *
13474 GTAACTTTATTAAGCTTTTTA
1 ATAAC-TTAGTAAGCATTTTA
13495 ATAACCTTAG
1 ATAA-CTTAG
13505 AAAGTTTTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
20 4 0.17
21 19 0.79
22 1 0.04
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (20 bp):
ATAACTTAGTAAGCATTTTA
Found at i:18644 original size:28 final size:28
Alignment explanation
Indices: 18612--18668 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
18602 TATATGGTTG
18612 TTTCTCTAAATATAGTAAAAGGCTTATA
1 TTTCTCTAAATATAGTAAAAGGCTTATA
18640 TTTCTCTAAATATAGTAAAAGGCTTATA
1 TTTCTCTAAATATAGTAAAAGGCTTATA
18668 T
1 T
18669 ATATAAGATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.40
Consensus pattern (28 bp):
TTTCTCTAAATATAGTAAAAGGCTTATA
Found at i:19765 original size:21 final size:21
Alignment explanation
Indices: 19705--19765 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
19695 GCCTTATATT
* *
19705 GTTTTTTAGTCACCTTATTAA
1 GTTTTTTAGTAACCTTACTAA
**
19726 GTATTTTTACCCAACCTTACTAA
1 GT-TTTTTA-GTAACCTTACTAA
*
19749 GTTTTTTAGTAATCTTA
1 GTTTTTTAGTAACCTTA
19766 TTGTGGATTT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
21 8 0.26
22 12 0.39
23 11 0.35
ACGTcount: A:0.26, C:0.16, G:0.08, T:0.49
Consensus pattern (21 bp):
GTTTTTTAGTAACCTTACTAA
Found at i:20739 original size:20 final size:21
Alignment explanation
Indices: 20703--20742 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
20693 TATAATAATC
20703 TTAAACTATTTTAGTGATTTA
1 TTAAACTATTTTAGTGATTTA
*
20724 TTAAACT-TTTTTGTGATTT
1 TTAAACTATTTTAGTGATTT
20743 TCTTTTGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.28, C:0.05, G:0.10, T:0.57
Consensus pattern (21 bp):
TTAAACTATTTTAGTGATTTA
Found at i:20809 original size:20 final size:20
Alignment explanation
Indices: 20780--20818 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
20770 TATTACGCCT
*
20780 TTTTAGTAACATTATTAAGC
1 TTTTAATAACATTATTAAGC
*
20800 TTTTAATAACTTTATTAAG
1 TTTTAATAACATTATTAAG
20819 ACTGCTATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.49
Consensus pattern (20 bp):
TTTTAATAACATTATTAAGC
Found at i:22973 original size:20 final size:22
Alignment explanation
Indices: 22919--22977 Score: 68
Period size: 24 Copynumber: 2.7 Consensus size: 22
22909 ATAACTTTTC
* *
22919 ATATATAAAACAAAAAAAGGTA
1 ATATATATACCAAAAAAAGGTA
22941 CATATATGATACCAAAAAAAGGT-
1 -ATATAT-ATACCAAAAAAAGGTA
22964 ATATAT-TACCAAAA
1 ATATATATACCAAAA
22978 TTTTTTTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
20 8 0.24
22 6 0.18
23 6 0.18
24 13 0.39
ACGTcount: A:0.59, C:0.10, G:0.08, T:0.22
Consensus pattern (22 bp):
ATATATATACCAAAAAAAGGTA
Found at i:24602 original size:23 final size:23
Alignment explanation
Indices: 24572--24617 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
24562 CAAACAATCT
24572 TGAGCACTCTCGCTCGGTCTCTA
1 TGAGCACTCTCGCTCGGTCTCTA
*
24595 TGAGCACTCTCGTTCGGTCTCTA
1 TGAGCACTCTCGCTCGGTCTCTA
24618 ACAAACTAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.13, C:0.33, G:0.22, T:0.33
Consensus pattern (23 bp):
TGAGCACTCTCGCTCGGTCTCTA
Found at i:24643 original size:21 final size:22
Alignment explanation
Indices: 24614--24656 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
24604 TCGTTCGGTC
*
24614 TCTAACAAA-CTAACAATCACA
1 TCTAACAAACCAAACAATCACA
*
24635 TCTACCAAACCAAACAATCACA
1 TCTAACAAACCAAACAATCACA
24657 CGCACACACA
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:0.51, C:0.33, G:0.00, T:0.16
Consensus pattern (22 bp):
TCTAACAAACCAAACAATCACA
Found at i:25676 original size:30 final size:30
Alignment explanation
Indices: 25642--25705 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
25632 AAAAAACCCA
*
25642 TGAAATTTAGCAATTTAGCAAAATTTTAGG
1 TGAAAATTAGCAATTTAGCAAAATTTTAGG
25672 TGAAAATTAGCAATTTAGCAAAATTTTAGG
1 TGAAAATTAGCAATTTAGCAAAATTTTAGG
25702 TGAA
1 TGAA
25706 TTAGAATATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.34
Consensus pattern (30 bp):
TGAAAATTAGCAATTTAGCAAAATTTTAGG
Found at i:26982 original size:2 final size:2
Alignment explanation
Indices: 26975--27076 Score: 204
Period size: 2 Copynumber: 51.0 Consensus size: 2
26965 CTACATTTCA
26975 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
27017 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
27059 AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 100 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.