Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013358.1 Corchorus olitorius cultivar O-4 contig13391, 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: 23016
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:4148 original size:22 final size:22
Alignment explanation
Indices: 4123--4169 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
4113 TTTTTAATTG
*
4123 AGTAAAACTA-TAAAAGTAAAAT
1 AGTAAAA-TAGTAAAAATAAAAT
4145 AGTAAAATAGTAAAAATAAAAT
1 AGTAAAATAGTAAAAATAAAAT
4167 AGT
1 AGT
4170 TATAAGGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.64, C:0.02, G:0.11, T:0.23
Consensus pattern (22 bp):
AGTAAAATAGTAAAAATAAAAT
Found at i:4162 original size:9 final size:8
Alignment explanation
Indices: 4137--4169 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
4127 AAACTATAAA
4137 AGTAAAAT
1 AGTAAAAT
4145 AGTAAAAT
1 AGTAAAAT
4153 AGTAAAA-
1 AGTAAAAT
4160 A-TAAAAT
1 AGTAAAAT
4167 AGT
1 AGT
4170 TATAAGGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
6 5 0.22
7 2 0.09
8 16 0.70
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (8 bp):
AGTAAAAT
Found at i:4164 original size:14 final size:14
Alignment explanation
Indices: 4123--4169 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
4113 TTTTTAATTG
*
4123 AGTAAAACTATAAA-
1 AGTAAAAATA-AAAT
4137 AGTAAAATAGTAAAAT
1 AGTAAAA-A-TAAAAT
4153 AGTAAAAATAAAAT
1 AGTAAAAATAAAAT
4167 AGT
1 AGT
4170 TATAAGGATA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
14 16 0.55
15 4 0.14
16 9 0.31
ACGTcount: A:0.64, C:0.02, G:0.11, T:0.23
Consensus pattern (14 bp):
AGTAAAAATAAAAT
Found at i:4551 original size:425 final size:428
Alignment explanation
Indices: 3758--4615 Score: 1560
Period size: 425 Copynumber: 2.0 Consensus size: 428
3748 AAATGAATAA
*
3758 TTAATGATTGGACAACTTATTTTAATTTTTAAACTTGATAATAATACTTTTATTAGTTTATATAA
1 TTAATGATTGGACAACTTATTTTAACTTTTAAACTTGATAATAATACTTTTATTAGTTTATATAA
*
3823 TAAAATTGAAATGGGTCCAGAACTATCAAAAAATCTCCAATTTTTTTAAAATTAAAATGGTAAAA
66 TAAAATTGAAATGGGTCCAGAACTATCAAAAAATCTCCAATTTTCTTAAAATTAAAATGGTAAAA
*
3888 ATAAAATATTTATAAAAATATTGAATTTAATTAAATAAAAAAAAGAGTTTTAGCAGAATAACTGT
131 ATAAAATATTTATAAAAATATTGAAATTAATTAAATAAAAAAAAGAGTTTTAGCAGAATAACTGT
*
3953 AAAAGTTTATTTCTAACAAAAAAACTATAAAATTTAAACAATGTTATTTAAGAAATATATTTTTA
196 AAAAGTTTATTTCTAACAAAAAAACTATAAAATTTAAACAATGTCATTTAAGAAATATATTTTTA
4018 AAATTCTAATATATCTAAGCTTTTTAATTAAATTAGTAATATCGTAAAAATAAAATAGGTATAAG
261 AAATTCTAATATATCTAAGCTTTTTAATTAAATTAGTAATATCGTAAAAATAAAATAGGTATAAG
*
4083 GATATTAGATTTAATTAAATAAAAATAGAGTTTTTAATTGAGTAAAACTATAAAAGTAAAATAGT
326 GATATTAGATTTAATAAAATAAAAATAGAGTTTTTAATTGAGTAAAACTATAAAAGTAAAATAGT
4148 AAAATAGTAAAAATAAAATAGTTATAAGGATATTAGAT
391 AAAATAGTAAAAATAAAATAGTTATAAGGATATTAGAT
* *
4186 TTAATGATTGGGCAACTTATTTTAACTTTTAAACTTGATAATAATACTTTTATTAGTTTATATTA
1 TTAATGATTGGACAACTTATTTTAACTTTTAAACTTGATAATAATACTTTTATTAGTTTATATAA
* *
4251 TAAAATTGAAATGGGTCTAGAACTATCAAAAAATCTCTAA-TTTCTTAAAATTAAAATGGTAAAA
66 TAAAATTGAAATGGGTCCAGAACTATCAAAAAATCTCCAATTTTCTTAAAATTAAAATGGTAAAA
* *
4315 ATAAAATATTTATAAAAATATTGAAATTAATTAAAT-AAAAAAAGAGTTTTAGCATAATACCTGT
131 ATAAAATATTTATAAAAATATTGAAATTAATTAAATAAAAAAAAGAGTTTTAGCAGAATAACTGT
*
4379 AAAATTTTATTTCTAAC-AAAAAACTATAAAATTTAAACAATGTCATTTAAGAAATATATTTTTA
196 AAAAGTTTATTTCTAACAAAAAAACTATAAAATTTAAACAATGTCATTTAAGAAATATATTTTTA
* *
4443 AAATTCTGATATATCTAAGTTTTTTAATTAAATTAGTAATATCGTAAAAATAAAATAGGTATAAG
261 AAATTCTAATATATCTAAGCTTTTTAATTAAATTAGTAATATCGTAAAAATAAAATAGGTATAAG
*
4508 GATATTAGATTTAATAAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTAAAATAGT
326 GATATTAGATTTAATAAAATAAAAATAGAGTTTTTAATTGAGTAAAACTATAAAAGTAAAATAGT
4573 AAAATAGTAAAAATAAAATAGTTATAAGGATATTAGAT
391 AAAATAGTAAAAATAAAATAGTTATAAGGATATTAGAT
4611 TTAAT
1 TTAAT
4616 TAAATAAAAA
Statistics
Matches: 415, Mismatches: 15, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
425 215 0.52
426 42 0.10
427 58 0.14
428 100 0.24
ACGTcount: A:0.48, C:0.05, G:0.09, T:0.37
Consensus pattern (428 bp):
TTAATGATTGGACAACTTATTTTAACTTTTAAACTTGATAATAATACTTTTATTAGTTTATATAA
TAAAATTGAAATGGGTCCAGAACTATCAAAAAATCTCCAATTTTCTTAAAATTAAAATGGTAAAA
ATAAAATATTTATAAAAATATTGAAATTAATTAAATAAAAAAAAGAGTTTTAGCAGAATAACTGT
AAAAGTTTATTTCTAACAAAAAAACTATAAAATTTAAACAATGTCATTTAAGAAATATATTTTTA
AAATTCTAATATATCTAAGCTTTTTAATTAAATTAGTAATATCGTAAAAATAAAATAGGTATAAG
GATATTAGATTTAATAAAATAAAAATAGAGTTTTTAATTGAGTAAAACTATAAAAGTAAAATAGT
AAAATAGTAAAAATAAAATAGTTATAAGGATATTAGAT
Found at i:4573 original size:22 final size:22
Alignment explanation
Indices: 4548--4594 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
4538 TTTTTAGTTG
*
4548 AGTAAAACTA-TAAAAGTAAAAT
1 AGTAAAA-TAGTAAAAATAAAAT
4570 AGTAAAATAGTAAAAATAAAAT
1 AGTAAAATAGTAAAAATAAAAT
4592 AGT
1 AGT
4595 TATAAGGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.64, C:0.02, G:0.11, T:0.23
Consensus pattern (22 bp):
AGTAAAATAGTAAAAATAAAAT
Found at i:4573 original size:93 final size:93
Alignment explanation
Indices: 4471--4655 Score: 298
Period size: 93 Copynumber: 2.0 Consensus size: 93
4461 GTTTTTTAAT
* * *
4471 TAAATTAGTAATATCGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATAAAATAAAAATAG
1 TAAAATAGTAAAATAGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATAAAATAAAAATAG
* * *
4536 AGTTTTTAGTTGAGTAAAACTATAAAAG
66 AGTTCTTAGTTAACTAAAACTATAAAAG
* *
4564 TAAAATAGTAAAATAGTAAAAATAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATAGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATAAAATAAAAATAG
4629 AGTTCTTAGTTAACTAAAACTATAAAA
66 AGTTCTTAGTTAACTAAAACTATAAAA
4656 ATTTAAACAA
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 84 1.00
ACGTcount: A:0.54, C:0.03, G:0.12, T:0.32
Consensus pattern (93 bp):
TAAAATAGTAAAATAGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATAAAATAAAAATAG
AGTTCTTAGTTAACTAAAACTATAAAAG
Found at i:4587 original size:9 final size:8
Alignment explanation
Indices: 4562--4594 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
4552 AAACTATAAA
4562 AGTAAAAT
1 AGTAAAAT
4570 AGTAAAAT
1 AGTAAAAT
4578 AGTAAAA-
1 AGTAAAAT
4585 A-TAAAAT
1 AGTAAAAT
4592 AGT
1 AGT
4595 TATAAGGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
6 5 0.22
7 2 0.09
8 16 0.70
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (8 bp):
AGTAAAAT
Found at i:4589 original size:14 final size:14
Alignment explanation
Indices: 4548--4594 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
4538 TTTTTAGTTG
*
4548 AGTAAAACTATAAA-
1 AGTAAAAATA-AAAT
4562 AGTAAAATAGTAAAAT
1 AGTAAAA-A-TAAAAT
4578 AGTAAAAATAAAAT
1 AGTAAAAATAAAAT
4592 AGT
1 AGT
4595 TATAAGGATA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
14 16 0.55
15 4 0.14
16 9 0.31
ACGTcount: A:0.64, C:0.02, G:0.11, T:0.23
Consensus pattern (14 bp):
AGTAAAAATAAAAT
Found at i:4726 original size:31 final size:31
Alignment explanation
Indices: 4691--4752 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
4681 ATATTAAAAA
*
4691 AATAAGGGTATAATAGGTGATTCAAAAGTTT
1 AATAAGGATATAATAGGTGATTCAAAAGTTT
4722 AATAAGGATATAATAGGTGATTCAAAAGTTT
1 AATAAGGATATAATAGGTGATTCAAAAGTTT
4753 TACAAAACTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.44, C:0.03, G:0.21, T:0.32
Consensus pattern (31 bp):
AATAAGGATATAATAGGTGATTCAAAAGTTT
Found at i:6183 original size:2 final size:2
Alignment explanation
Indices: 6176--6222 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
6166 TTAACTAGTG
**
6176 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A CC TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6217 TA TA TA
1 TA TA TA
6223 CTTTATAATG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:8146 original size:3 final size:3
Alignment explanation
Indices: 8140--8185 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
8130 TTTTTACTCT
8140 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
8186 ATGATCATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:8549 original size:31 final size:31
Alignment explanation
Indices: 8514--8652 Score: 172
Period size: 31 Copynumber: 4.5 Consensus size: 31
8504 GGTGTCCGAC
*
8514 GTGGCATGCCACGTGTACCAAAAAACGACAT
1 GTGGCATGCCACGTGTACCAAAAAATGACAT
*
8545 GTGGCACGCCACGTGTA-CAAAAAAGTGACAT
1 GTGGCATGCCACGTGTACCAAAAAA-TGACAT
* *
8576 GTGGCACGCCACGTGTACCAAAAAGTGACAT
1 GTGGCATGCCACGTGTACCAAAAAATGACAT
* ** ** *
8607 GTGGCATGCCATGTGTTTCAAAAGGTGACAC
1 GTGGCATGCCACGTGTACCAAAAAATGACAT
8638 GTGGCATGCCACGTG
1 GTGGCATGCCACGTG
8653 CACAAAAGGA
Statistics
Matches: 96, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
30 7 0.07
31 83 0.86
32 6 0.06
ACGTcount: A:0.30, C:0.24, G:0.27, T:0.19
Consensus pattern (31 bp):
GTGGCATGCCACGTGTACCAAAAAATGACAT
Found at i:8611 original size:62 final size:62
Alignment explanation
Indices: 8512--8652 Score: 194
Period size: 62 Copynumber: 2.3 Consensus size: 62
8502 ACGGTGTCCG
8512 ACGTGGCATGCCACGTGTACCAAAAAACGACATGTGGCACGCCACGTG-TACAAAAAAGTGAC
1 ACGTGGCATGCCACGTGTACCAAAAAACGACATGTGGCACGCCACGTGTTAC-AAAAAGTGAC
* * ** * * * *
8574 ATGTGGCACGCCACGTGTACCAAAAAGTGACATGTGGCATGCCATGTGTTTCAAAAGGTGAC
1 ACGTGGCATGCCACGTGTACCAAAAAACGACATGTGGCACGCCACGTGTTACAAAAAGTGAC
8636 ACGTGGCATGCCACGTG
1 ACGTGGCATGCCACGTG
8653 CACAAAAGGA
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
62 66 0.97
63 2 0.03
ACGTcount: A:0.30, C:0.24, G:0.27, T:0.18
Consensus pattern (62 bp):
ACGTGGCATGCCACGTGTACCAAAAAACGACATGTGGCACGCCACGTGTTACAAAAAGTGAC
Found at i:12490 original size:48 final size:48
Alignment explanation
Indices: 12435--12533 Score: 146
Period size: 48 Copynumber: 2.1 Consensus size: 48
12425 TATACCGGGT
12435 TTGGGTGGGCCGAGAACAGGTTTGGTGCGTGATGG-TATAGGGCCAGAC
1 TTGGGTGGGCCGAGAACAGGTTTGGTGCGTGATGGAT-TAGGGCCAGAC
* * * *
12483 TTGGGTGGGTCGAGTACGGGTTTGGTGCGTGATGGATTTGGGCCAGAC
1 TTGGGTGGGCCGAGAACAGGTTTGGTGCGTGATGGATTAGGGCCAGAC
12531 TTG
1 TTG
12534 ATGGGTTTGG
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
48 45 0.98
49 1 0.02
ACGTcount: A:0.15, C:0.13, G:0.44, T:0.27
Consensus pattern (48 bp):
TTGGGTGGGCCGAGAACAGGTTTGGTGCGTGATGGATTAGGGCCAGAC
Found at i:17106 original size:13 final size:13
Alignment explanation
Indices: 17088--17116 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
17078 TCTACAATTA
17088 AAAAAATATATTG
1 AAAAAATATATTG
17101 AAAAAATATATTG
1 AAAAAATATATTG
17114 AAA
1 AAA
17117 GTAATTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.28
Consensus pattern (13 bp):
AAAAAATATATTG
Found at i:17734 original size:44 final size:44
Alignment explanation
Indices: 17671--17766 Score: 120
Period size: 44 Copynumber: 2.2 Consensus size: 44
17661 CTCCACCAAT
* * *
17671 AACCCAGATTTCTGTTTTCATTTGGATTCAAAAAAAGCAAAGTA
1 AACCCAAATTTCTATTTTCATTTGGATTCAAAAAAAGCAAAATA
* * * *
17715 AACCCAAATTTTTATTTTCATTTTGATTCAAAAGAAGTAAAATA
1 AACCCAAATTTCTATTTTCATTTGGATTCAAAAAAAGCAAAATA
17759 AACACCAA
1 AAC-CCAA
17767 TTCTTTTTTC
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 40 0.91
45 4 0.09
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (44 bp):
AACCCAAATTTCTATTTTCATTTGGATTCAAAAAAAGCAAAATA
Found at i:18469 original size:3 final size:3
Alignment explanation
Indices: 18461--18533 Score: 146
Period size: 3 Copynumber: 24.3 Consensus size: 3
18451 TTAAATATAC
18461 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
18509 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
18534 TATTGGTTTT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:22343 original size:14 final size:14
Alignment explanation
Indices: 22326--22354 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
22316 TATAGTTACC
22326 GGTTTAGGAGGAAT
1 GGTTTAGGAGGAAT
22340 GGTTTAGGAGGAAT
1 GGTTTAGGAGGAAT
22354 G
1 G
22355 CTCAAGAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.45, T:0.28
Consensus pattern (14 bp):
GGTTTAGGAGGAAT
Found at i:22430 original size:15 final size:15
Alignment explanation
Indices: 22410--22441 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
22400 AATTTTTTTT
*
22410 TATCTATACTATCTA
1 TATCTATACTATATA
22425 TATCTATACTATATA
1 TATCTATACTATATA
22440 TA
1 TA
22442 AAATTACGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.47
Consensus pattern (15 bp):
TATCTATACTATATA
Found at i:22497 original size:31 final size:31
Alignment explanation
Indices: 22454--22520 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
22444 ATTACGAGCT
* * * * *
22454 TTATAAAACTTTTGAATCGTGTATTATATCC
1 TTATTAAACTTTTGAATCATCTATCATACCC
22485 TTATTAAACTTTTGAATCATCTATCATACCC
1 TTATTAAACTTTTGAATCATCTATCATACCC
22516 TTATT
1 TTATT
22521 TTTCGAATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.46
Consensus pattern (31 bp):
TTATTAAACTTTTGAATCATCTATCATACCC
Found at i:22643 original size:77 final size:77
Alignment explanation
Indices: 22556--22701 Score: 265
Period size: 77 Copynumber: 1.9 Consensus size: 77
22546 TGGTTTAAAT
*
22556 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCTTATAACTA
22621 TTTTATTTTTAC
66 TTTTATTTTTAC
* *
22633 TTTTATAGTTTTACTCAATTAAAAACTCTATTTTTATTTAATTAAATATAATATCCTTATACCTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCTTATAACTA
22698 TTTT
66 TTTT
22702 TTTACGATAT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 66 1.00
ACGTcount: A:0.34, C:0.12, G:0.01, T:0.52
Consensus pattern (77 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCTTATAACTA
TTTTATTTTTAC
Done.