Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015832.1 Corchorus olitorius cultivar O-4 contig15865, 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: 27819
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:1670 original size:334 final size:333
Alignment explanation
Indices: 1035--1670 Score: 778
Period size: 334 Copynumber: 1.9 Consensus size: 333
1025 TTCGGCTAAA
* * *
1035 AACTAACCCGAAAAATTTTTTCTCAATTTTTTGCCAGAATACTCATAAAAAATATGTAATTCAAC
1 AACTAACCCGAAAAATTTTTCCTCAATTTTTTGCCACAATACTCATAAAAAATATATAATTCAAC
* ***
1100 GCCAAAAAGATTGACGGGCTTTTCGGGCTTCTATATCGATTTTCCATTTTTTTCCAAATTAATTT
66 GCCAAAAAGATTGAAGGGCTTTTCACACTTCTATATCGATTTTCCATTTTTTTCCAAATTAATTT
* * *
1165 CTAATTAAATCGAAACAAAATTCAGAAGCTCGTAAAAACAAATCTTTAAATCCAATGTGACTGAG
131 CTAATAAAATCAAAACAAAATTCAGAAGCACGTAAAAACAAATCTTTAAATCCAATGTGACTGAG
* * * * * *
1230 ATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGTAAAATTGAGCC
196 ATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTGTACGCCAAAAACCATGCAAAACTAAGCC
*
1295 GAGACTCTGGAACGCGTTTTGAGCCAAAAACCGTGATGGTTAGTACACGATATCGGCTAAAATTT
261 GAGACTCTGGAACGCGTTTTGAGCCAAAAACAGTGATGGTTAGTACACGATATCGGCTAAAATTT
1360 TGTAAAAG
326 TGTAAAAG
* * * * *
1368 AACTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCTCAATGCTC-TGAAAAAATATATAATTCGA
1 AACTAACCCGAAAAATTTTTCCTCAATTTTTTGCCACAATACTCAT-AAAAAATATATAATTCAA
* * * ** *
1432 CGCCAAAAA-ATTTGAAGGGGTTTTCACACTTTTAATATCGTTTTTCTTTTTTTTTCTAAACTT-
65 CGCCAAAAAGA-TTGAAGGGCTTTTCACACTTCT-ATATCGATTTTCCATTTTTTTCCAAA-TTA
* * * **
1495 ATTTTTAATAAAATCAAAACAAGATTCAGATGCACGTAAAAACAAATCTTTAAATCCAATGTGGT
127 ATTTCTAATAAAATCAAAACAAAATTCAGAAGCACGTAAAAACAAATCTTTAAATCCAATGTGAC
* * * * * *
1560 TGAGATTTGGTTAC-ATTAGTATAGATTTTTCTAGGATTCTGTATGCCAAAAACCATGCAAAACT
192 TGAGATTTGGTT-CGATGAATATAGATATTTCAAGGAGTCTGTACGCCAAAAACCATGCAAAACT
** * * * *
1624 AAGTGGAGGC-CTCGGTACGCGTTTTTAGCCAAAAACAGTTATGGTTA
256 AAGCCGAGACTCT-GGAACGCGTTTTGAGCCAAAAACAGTGATGGTTA
1671 TATATTTCAA
Statistics
Matches: 252, Mismatches: 45, Indels: 11
0.82 0.15 0.04
Matches are distributed among these distances:
332 2 0.01
333 81 0.32
334 166 0.66
335 3 0.01
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (333 bp):
AACTAACCCGAAAAATTTTTCCTCAATTTTTTGCCACAATACTCATAAAAAATATATAATTCAAC
GCCAAAAAGATTGAAGGGCTTTTCACACTTCTATATCGATTTTCCATTTTTTTCCAAATTAATTT
CTAATAAAATCAAAACAAAATTCAGAAGCACGTAAAAACAAATCTTTAAATCCAATGTGACTGAG
ATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTGTACGCCAAAAACCATGCAAAACTAAGCC
GAGACTCTGGAACGCGTTTTGAGCCAAAAACAGTGATGGTTAGTACACGATATCGGCTAAAATTT
TGTAAAAG
Found at i:2642 original size:8 final size:8
Alignment explanation
Indices: 2629--2697 Score: 78
Period size: 8 Copynumber: 9.1 Consensus size: 8
2619 CTTTATATAG
2629 TAGTAAGA
1 TAGTAAGA
2637 TAGTAAGA
1 TAGTAAGA
2645 TAGTAAG-
1 TAGTAAGA
2652 -A-TAAGA
1 TAGTAAGA
2658 TAGTAAGA
1 TAGTAAGA
2666 TAGTAAG-
1 TAGTAAGA
2673 -A-TAAGA
1 TAGTAAGA
2679 TAAGATAAGA
1 T-AG-TAAGA
2689 TAGTAAGA
1 TAGTAAGA
2697 T
1 T
2698 TTATATTGCT
Statistics
Matches: 53, Mismatches: 0, Indels: 16
0.77 0.00 0.23
Matches are distributed among these distances:
5 8 0.15
6 2 0.04
7 1 0.02
8 34 0.64
9 2 0.04
10 6 0.11
ACGTcount: A:0.52, C:0.00, G:0.23, T:0.25
Consensus pattern (8 bp):
TAGTAAGA
Found at i:2658 original size:5 final size:5
Alignment explanation
Indices: 2632--2690 Score: 62
Period size: 5 Copynumber: 13.4 Consensus size: 5
2622 TATATAGTAG
2632 TAAGA T-AG- TAAGA T-AG- TAAGA TAAGA T-AG- TAAGA T-AG- TAAGA
1 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA
2674 TAAGA TAAGA TAAGA TA
1 TAAGA TAAGA TAAGA TA
2691 GTAAGATTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 16
0.74 0.00 0.26
Matches are distributed among these distances:
3 4 0.09
4 16 0.35
5 26 0.57
ACGTcount: A:0.54, C:0.00, G:0.22, T:0.24
Consensus pattern (5 bp):
TAAGA
Found at i:2658 original size:13 final size:13
Alignment explanation
Indices: 2640--2697 Score: 71
Period size: 13 Copynumber: 4.1 Consensus size: 13
2630 AGTAAGATAG
2640 TAAGATAGTAAGA
1 TAAGATAGTAAGA
2653 TAAGATAGTAAGATA
1 TAAGATAGTAAG--A
2668 GTAAGATAAGATAAGA
1 -TAAGAT-AG-TAAGA
2684 TAAGATAGTAAGA
1 TAAGATAGTAAGA
2697 T
1 T
2698 TTATATTGCT
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
13 18 0.45
14 2 0.05
15 7 0.17
16 7 0.17
17 2 0.05
18 4 0.10
ACGTcount: A:0.53, C:0.00, G:0.22, T:0.24
Consensus pattern (13 bp):
TAAGATAGTAAGA
Found at i:2658 original size:21 final size:21
Alignment explanation
Indices: 2625--2697 Score: 114
Period size: 21 Copynumber: 3.5 Consensus size: 21
2615 GTGACTTTAT
2625 ATAGT-AG-TAAGATAGTAAG
1 ATAGTAAGATAAGATAGTAAG
2644 ATAGTAAGATAAGATAGTAAG
1 ATAGTAAGATAAGATAGTAAG
2665 ATAGTAAGATAAGATAAGATAAG
1 ATAGTAAGATAAGAT-AG-TAAG
2688 ATAGTAAGAT
1 ATAGTAAGAT
2698 TTATATTGCT
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
19 5 0.10
20 2 0.04
21 27 0.54
22 2 0.04
23 14 0.28
ACGTcount: A:0.52, C:0.00, G:0.23, T:0.25
Consensus pattern (21 bp):
ATAGTAAGATAAGATAGTAAG
Found at i:4036 original size:1 final size:1
Alignment explanation
Indices: 4030--4060 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
4020 ATTTTCATTC
4030 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4061 GTGTGTCTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:8257 original size:21 final size:21
Alignment explanation
Indices: 8200--8261 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 21
8190 CTCTTTGTGG
8200 AATGAATTTTATAATATGATA
1 AATGAATTTTATAATATGATA
* * *
8221 AAT-TATTTCTGT-ATATGTTA
1 AATGAATTT-TATAATATGATA
8241 AATGAATTTTATAATAT-ATA
1 AATGAATTTTATAATATGATA
8261 A
1 A
8262 TAGTATTACT
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
20 19 0.59
21 13 0.41
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.47
Consensus pattern (21 bp):
AATGAATTTTATAATATGATA
Found at i:8419 original size:22 final size:22
Alignment explanation
Indices: 8390--8537 Score: 101
Period size: 22 Copynumber: 6.8 Consensus size: 22
8380 TGAATATTTT
8390 TATGAAATTTTGATAACTACCC
1 TATGAAATTTTGATAACTACCC
* * **
8412 TATTAAATTTTGATAACCACAT
1 TATGAAATTTTGATAACTACCC
*
8434 TATGAAATTTT-ACTAATTA-CC
1 TATGAAATTTTGA-TAACTACCC
* *
8455 TATGAAATTGTGATAAACT-CCA
1 TATGAAATTTTGAT-AACTACCC
* **
8477 TATGAAACTTTGATAACCTA-AA
1 TATGAAATTTTGATAA-CTACCC
* *
8499 TATGAAATTTTAATAAACCT-TCC
1 TATGAAATTTTGAT-AA-CTACCC
8522 TATGAAATTTTG-TAAC
1 TATGAAATTTTGATAAC
8538 CTTCTTCTGA
Statistics
Matches: 98, Mismatches: 20, Indels: 18
0.72 0.15 0.13
Matches are distributed among these distances:
20 1 0.01
21 16 0.16
22 65 0.66
23 16 0.16
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACTACCC
Found at i:8481 original size:43 final size:44
Alignment explanation
Indices: 8389--8493 Score: 119
Period size: 43 Copynumber: 2.4 Consensus size: 44
8379 TTGAATATTT
* *
8389 TTATGAAATTTTGATAACTACCCTATTAAATTTTGATAACCACA
1 TTATGAAATTTTGATAACTACCCTATGAAATTGTGATAACCACA
*
8433 TTATGAAATTTT-ACTAATTA-CCTATGAAATTGTGATAAACTC-CA
1 TTATGAAATTTTGA-TAACTACCCTATGAAATTGTGAT-AAC-CACA
*
8477 -TATGAAACTTTGATAAC
1 TTATGAAATTTTGATAAC
8494 CTAAATATGA
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
43 28 0.54
44 23 0.44
45 1 0.02
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (44 bp):
TTATGAAATTTTGATAACTACCCTATGAAATTGTGATAACCACA
Found at i:13107 original size:20 final size:19
Alignment explanation
Indices: 13079--13117 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
13069 AATAGTTAAG
*
13079 ATATGTATTATAATATATAT
1 ATATATATTATAATA-ATAT
13099 ATATATATTATAATAATAT
1 ATATATATTATAATAATAT
13118 GGCCGGGCCG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
ATATATATTATAATAATAT
Found at i:18379 original size:33 final size:33
Alignment explanation
Indices: 18335--18411 Score: 93
Period size: 33 Copynumber: 2.4 Consensus size: 33
18325 TTATCACAGC
* * **
18335 ATCCAA-TCAGCAAAAGGTTAGTGAGTTGATTG
1 ATCCAAGTCAGCAAAAGGTCAGTGAGATGATCA
*
18367 ATCCAAGTCAGCAAAATGTCAGTGAGATGATCA
1 ATCCAAGTCAGCAAAAGGTCAGTGAGATGATCA
*
18400 ATCCAAGCCAGC
1 ATCCAAGTCAGC
18412 TGAAGGAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
32 6 0.16
33 32 0.84
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.22
Consensus pattern (33 bp):
ATCCAAGTCAGCAAAAGGTCAGTGAGATGATCA
Done.