Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014025.1 Corchorus olitorius cultivar O-4 contig14058, 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: 30196
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:1795 original size:27 final size:27
Alignment explanation
Indices: 1749--1800 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
1739 GAAAAATAGA
* *
1749 AAAATGATAAAAATAGAATTTTAAATT
1 AAAATGATAAAAAAAGAATTATAAATT
* *
1776 AAAATGGTAAAAAAATAATTATAAA
1 AAAATGATAAAAAAAGAATTATAAA
1801 AATATTAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (27 bp):
AAAATGATAAAAAAAGAATTATAAATT
Found at i:2353 original size:314 final size:317
Alignment explanation
Indices: 1752--2384 Score: 1103
Period size: 314 Copynumber: 2.0 Consensus size: 317
1742 AAATAGAAAA
1752 ATGATAAAAATAGAATTTTAAATTAAAATGGTAAAAAAATAATTATAAAAATATTAAATTGAATT
1 ATGATAAAAATAGAATTTTAAATTAAAATGGTAAAAAAATAATTATAAAAATATTAAATTGAATT
*
1817 AAATGAAAATAGAGTTTTTAATAGAATAAAATTGTATGTTAAAAAATTTTAATATATCCTAGTTT
66 AAATGAAAATAGAGTTTTTAATAGAATAAAACTGTATGTTAAAAAATTTTAATATATCCTAGTTT
*
1882 TTAATGAAAAATAGTAGTAAAATGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAA
131 TTAATGAAAAATAGTAGTAAAATGGTAAAAACAAAGTAATTATAAAGATATTAGATTTAATTAAA
* *
1947 TAAAAATAGAGTTTTTAGTAGAATAAAACTATAATAGTTTAAGTAATGGCATTTAAGAATTATAT
196 TAAAAATAGAGTTTTTAGTAGAATAAAACTATAATAGTTTAAGTAATGACATTTAAGAAATATAT
* **
2012 TCGAAAAATAAAGATATAATCGTCGATTCAAAAGTTTTAAAAAACTCGTACTTTTAT
261 TCAAAAAATAAAGATATAATCGTCGATTCAAAAGTTTTAAAAAACTCAAACTTTTAT
*
2069 ATGATAAAAATA-AACTTTTAAATTAAAATGGTAAGAAAATAATTATAAAAATATTAAATTGAAT
1 ATGATAAAAATAGAA-TTTTAAATTAAAATGGTAAAAAAATAATTATAAAAATATTAAATTGAAT
* * *
2133 TAAATGAAATTAGTGTTTTTAATAGAATAAAGCTGTATGTTAAAAAATTTTAATATATCCTAGTT
65 TAAATGAAAATAGAGTTTTTAATAGAATAAAACTGTATGTTAAAAAATTTTAATATATCCTAGTT
2198 TTTAATG-AAAA-A-TAGTAAAATGGTAAAAACAAAGTAATTATAAAGATATTAGATTTAATTAA
130 TTTAATGAAAAATAGTAGTAAAATGGTAAAAACAAAGTAATTATAAAGATATTAGATTTAATTAA
2260 ATAAAAATAGAGTTTTTAGTAGAATAAAACTATAATAGTTTAAGTAATGACATTTAAGAAATATA
195 ATAAAAATAGAGTTTTTAGTAGAATAAAACTATAATAGTTTAAGTAATGACATTTAAGAAATATA
* * *
2325 TTCAAAAAATAAGGATATAATTGTCGATTCAAAAGTTTTACAAAACTCAAACTTTTAT
260 TTCAAAAAATAAAGATATAATCGTCGATTCAAAAGTTTTAAAAAACTCAAACTTTTAT
2383 AT
1 AT
2385 ATAGTATAGA
Statistics
Matches: 301, Mismatches: 14, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
314 166 0.55
315 1 0.00
316 6 0.02
317 128 0.43
ACGTcount: A:0.50, C:0.04, G:0.11, T:0.35
Consensus pattern (317 bp):
ATGATAAAAATAGAATTTTAAATTAAAATGGTAAAAAAATAATTATAAAAATATTAAATTGAATT
AAATGAAAATAGAGTTTTTAATAGAATAAAACTGTATGTTAAAAAATTTTAATATATCCTAGTTT
TTAATGAAAAATAGTAGTAAAATGGTAAAAACAAAGTAATTATAAAGATATTAGATTTAATTAAA
TAAAAATAGAGTTTTTAGTAGAATAAAACTATAATAGTTTAAGTAATGACATTTAAGAAATATAT
TCAAAAAATAAAGATATAATCGTCGATTCAAAAGTTTTAAAAAACTCAAACTTTTAT
Found at i:2544 original size:92 final size:92
Alignment explanation
Indices: 2432--2614 Score: 312
Period size: 92 Copynumber: 2.0 Consensus size: 92
2422 CCTTTTTAAT
* * *
2432 TAAATTAGTAATATGGTAAAAATAAAATAGGTATAAGGATATTATATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
2497 AGTTTTTAGTTGAGTAAAACTATAAAG
66 AGTTTTTAGTTGAGTAAAACTATAAAG
* *
2524 TAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAGTAG
1 TAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
*
2589 AGTTTTTAGTTGATTAAAACTATAAA
66 AGTTTTTAGTTGAGTAAAACTATAAA
2615 AGTTTAAACA
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
92 85 1.00
ACGTcount: A:0.51, C:0.01, G:0.14, T:0.34
Consensus pattern (92 bp):
TAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
AGTTTTTAGTTGAGTAAAACTATAAAG
Found at i:3127 original size:24 final size:22
Alignment explanation
Indices: 3072--3128 Score: 73
Period size: 20 Copynumber: 2.6 Consensus size: 22
3062 AAAAATTGTT
*
3072 TATCATTAGTTTGAATCCTTAC
1 TATCATTAGTTTGAATCCTAAC
3094 -A-CATTAGTTTGAATCCTAAAC
1 TATCATTAGTTTGAATCCT-AAC
3115 ATATCATTAGTTTG
1 -TATCATTAGTTTG
3129 TGTAGAAGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
20 16 0.53
21 3 0.10
23 1 0.03
24 10 0.33
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.42
Consensus pattern (22 bp):
TATCATTAGTTTGAATCCTAAC
Found at i:6582 original size:19 final size:19
Alignment explanation
Indices: 6532--6582 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
6522 TGTGGGTTTT
6532 TTAATAA-TAATTATTCAA
1 TTAATAATTAATTATTCAA
* *
6550 TAAAATAATT-ATTATTTAA
1 T-TAATAATTAATTATTCAA
6569 TTAATAATTAATTA
1 TTAATAATTAATTA
6583 ATTTCAGCCC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 8 0.30
19 18 0.67
20 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAATAATTAATTATTCAA
Found at i:6956 original size:13 final size:13
Alignment explanation
Indices: 6938--6963 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6928 AAGGTAGCAA
6938 CAAAAATCATCAC
1 CAAAAATCATCAC
6951 CAAAAATCATCAC
1 CAAAAATCATCAC
6964 TCATGCCAAG
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:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (13 bp):
CAAAAATCATCAC
Found at i:8540 original size:22 final size:22
Alignment explanation
Indices: 8491--8541 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
8481 AAATATTACC
**
8491 ATAATTATTTTTGACAGCCATA
1 ATAATTATTTTTGACAGAAATA
*
8513 ATAATTATTTTTGCCAAGAAATA
1 ATAATTATTTTTGAC-AGAAATA
8536 A-AATTA
1 ATAATTA
8542 GGGAACAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.39
Consensus pattern (22 bp):
ATAATTATTTTTGACAGAAATA
Found at i:21865 original size:18 final size:19
Alignment explanation
Indices: 21829--21885 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 19
21819 TGGGATTTTT
*
21829 AATAA-TAATTATTCAATTA
1 AATAATTAATAATT-AATTA
21848 AATAATTAATAATT-ATTA
1 AATAATTAATAATTAATTA
**
21866 TTTAATTAATAATTAATTA
1 AATAATTAATAATTAATTA
21885 A
1 A
21886 TTTCAGCCCT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 16 0.50
19 9 0.28
20 7 0.22
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
AATAATTAATAATTAATTA
Found at i:21865 original size:26 final size:25
Alignment explanation
Indices: 21827--21887 Score: 86
Period size: 26 Copynumber: 2.4 Consensus size: 25
21817 TGTGGGATTT
*
21827 TTAATAATAATTATTCAATTAAATAA
1 TTAATAATTATTATTCAATT-AATAA
*
21853 TTAATAATTATTATTTAATTAATAA
1 TTAATAATTATTATTCAATTAATAA
21878 TTAATTAATT
1 TTAA-TAATT
21888 TCAGCCCTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 9 0.28
26 23 0.72
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (25 bp):
TTAATAATTATTATTCAATTAATAA
Found at i:21873 original size:11 final size:11
Alignment explanation
Indices: 21827--21886 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
21817 TGTGGGATTT
21827 TTAATAA-TAA
1 TTAATAATTAA
*
21837 TTATTCAATTAA
1 TTAAT-AATTAA
*
21849 ATAATTAA-TAA
1 TTAA-TAATTAA
* *
21860 TTATTATTTAA
1 TTAATAATTAA
21871 TTAATAATTAA
1 TTAATAATTAA
21882 TTAAT
1 TTAAT
21887 TTCAGCCCTT
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
10 6 0.16
11 24 0.63
12 7 0.18
13 1 0.03
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (11 bp):
TTAATAATTAA
Found at i:21875 original size:15 final size:15
Alignment explanation
Indices: 21827--21887 Score: 56
Period size: 15 Copynumber: 4.1 Consensus size: 15
21817 TGTGGGATTT
21827 TTAATAA-TAATT-A
1 TTAATAATTAATTAA
*
21840 TTCAATTAAATAATTAA
1 TT-AA-TAATTAATTAA
* *
21857 -TAATTATTATTTAA
1 TTAATAATTAATTAA
21871 TTAATAATTAATTAA
1 TTAATAATTAATTAA
21886 TT
1 TT
21888 TCAGCCCTTG
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
13 2 0.05
14 10 0.26
15 19 0.50
16 6 0.16
17 1 0.03
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
TTAATAATTAATTAA
Found at i:21906 original size:4 final size:4
Alignment explanation
Indices: 21834--21887 Score: 53
Period size: 4 Copynumber: 14.2 Consensus size: 4
21824 TTTTTAATAA
* *
21834 TAAT T-AT TCAAT TAAA TAAT TAA- TAAT T-AT TATT TAAT TAA- TAAT
1 TAAT TAAT T-AAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT
21879 TAAT TAAT T
1 TAAT TAAT T
21888 TCAGCCCTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
3 12 0.29
4 26 0.63
5 3 0.07
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (4 bp):
TAAT
Found at i:22136 original size:32 final size:31
Alignment explanation
Indices: 22095--22171 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 31
22085 GGTTAGCTTT
22095 GGGTTAAATTTGAGTCAGATTGATTC-GGATTC
1 GGGTTAAATTTG-GTCAGATTGATTCAGG-TTC
*
22127 GGGTTAAATTTGGATTAGATTGATTCAGGTTC
1 GGGTTAAATTTGG-TCAGATTGATTCAGGTTC
* *
22159 GGATCAAATTTGG
1 GGGTTAAATTTGG
22172 GTCATGTTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
31 1 0.03
32 37 0.93
33 2 0.05
ACGTcount: A:0.26, C:0.08, G:0.29, T:0.38
Consensus pattern (31 bp):
GGGTTAAATTTGGTCAGATTGATTCAGGTTC
Found at i:22365 original size:20 final size:20
Alignment explanation
Indices: 22327--22365 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
22317 CATAGATGAA
*
22327 ATTTTCAGAATTTATTATTT
1 ATTTTCAGAATTTAGTATTT
22347 ATTTTCA-AATATTAGTATT
1 ATTTTCAGAAT-TTAGTATT
22366 GAATTCGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.56
Consensus pattern (20 bp):
ATTTTCAGAATTTAGTATTT
Found at i:22426 original size:16 final size:16
Alignment explanation
Indices: 22391--22430 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
22381 CAGGTTTAGA
*
22391 TTCGGG-TTTAGGTTT
1 TTCGGGTTTTAGATTT
*
22406 ATCGGGTTTTAGATTT
1 TTCGGGTTTTAGATTT
22422 TTCGGGTTT
1 TTCGGGTTT
22431 GAATTTTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 5 0.24
16 16 0.76
ACGTcount: A:0.10, C:0.07, G:0.30, T:0.53
Consensus pattern (16 bp):
TTCGGGTTTTAGATTT
Found at i:22438 original size:15 final size:16
Alignment explanation
Indices: 22391--22438 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
22381 CAGGTTTAGA
*
22391 TTCGGGTTT-AGGTTT
1 TTCGGGTTTGAGATTT
* *
22406 ATCGGGTTTTAGATTT
1 TTCGGGTTTGAGATTT
22422 TTCGGGTTTGA-ATTT
1 TTCGGGTTTGAGATTT
22437 TT
1 TT
22439 TCGAGTTCGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 14 0.50
16 14 0.50
ACGTcount: A:0.12, C:0.06, G:0.27, T:0.54
Consensus pattern (16 bp):
TTCGGGTTTGAGATTT
Found at i:28913 original size:19 final size:19
Alignment explanation
Indices: 28889--28925 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
28879 CAGATTCCAT
*
28889 TATATATCTATATACTATC
1 TATATATATATATACTATC
28908 TATATATATATATACTAT
1 TATATATATATATACTAT
28926 ATAAATCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.49
Consensus pattern (19 bp):
TATATATATATATACTATC
Found at i:29719 original size:13 final size:11
Alignment explanation
Indices: 29601--29714 Score: 67
Period size: 11 Copynumber: 10.8 Consensus size: 11
29591 ATTATGCTAT
*
29601 TATATATCAAA
1 TATATATAAAA
* **
29612 TATATTTATGA
1 TATATATAAAA
29623 TATATATAAAA
1 TATATATAAAA
*
29634 TATAT-T-TAA
1 TATATATAAAA
* **
29643 T-TATTTATGA
1 TATATATAAAA
29653 TATATATAAAA
1 TATATATAAAA
* *
29664 TACATGT-AAA
1 TATATATAAAA
*
29674 -ATATATAAAT
1 TATATATAAAA
* **
29684 TATATTTATGA
1 TATATATAAAA
29695 TATATATAAAA
1 TATATATAAAA
29706 TATATATAA
1 TATATATAA
29715 CAAATTTTTT
Statistics
Matches: 74, Mismatches: 24, Indels: 10
0.69 0.22 0.09
Matches are distributed among these distances:
8 3 0.04
9 8 0.11
10 9 0.12
11 54 0.73
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (11 bp):
TATATATAAAA
Found at i:29845 original size:10 final size:10
Alignment explanation
Indices: 29830--29854 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
29820 ATTTCCTATT
29830 TTAAAACCGA
1 TTAAAACCGA
29840 TTAAAACCGA
1 TTAAAACCGA
29850 TTAAA
1 TTAAA
29855 TTAAATTGAA
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:0.52, C:0.16, G:0.08, T:0.24
Consensus pattern (10 bp):
TTAAAACCGA
Done.