Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012154.1 Corchorus olitorius cultivar O-4 contig12187, 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: 16273
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.33
Found at i:943 original size:77 final size:77
Alignment explanation
Indices: 809--971 Score: 276
Period size: 77 Copynumber: 2.1 Consensus size: 77
799 CTATGCTTCA
* *
809 GACGATCGTGATTTTAGCTTGTTGACAAGTGACCTTATTTAAGGCTTCTTGTTAGAGTTAGTGAT
1 GACGATCGTGATTTCAGCTTGTTGACAAGTGACCTTATTTAAGGCTTCTTGTTAGAGTTAGCGAT
874 CCTGTTAGTGTT
66 CCTGTTAGTGTT
886 GACGATCGTGATTTCAGCTTGTTGACAAGTGACCTT-TTTAAAGGC-TCTTGTTAAGAGTTAGCG
1 GACGATCGTGATTTCAGCTTGTTGACAAGTGACCTTATTT-AAGGCTTCTTGTT-AGAGTTAGCG
949 ATCCTGTTAGTGTT
64 ATCCTGTTAGTGTT
963 GACGATCGT
1 GACGATCGT
972 CCTTCGCTTT
Statistics
Matches: 82, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
76 10 0.12
77 72 0.88
ACGTcount: A:0.21, C:0.15, G:0.25, T:0.39
Consensus pattern (77 bp):
GACGATCGTGATTTCAGCTTGTTGACAAGTGACCTTATTTAAGGCTTCTTGTTAGAGTTAGCGAT
CCTGTTAGTGTT
Found at i:8770 original size:329 final size:328
Alignment explanation
Indices: 8147--9291 Score: 1235
Period size: 329 Copynumber: 3.5 Consensus size: 328
8137 TGTCCTTTAC
* * * * **
8147 CAAAAATTGTGAGGGTTAATACACGATTTCGGTTAAAATTTTGCAAAAATTTACCCAAAATAATT
1 CAAAAACTGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGGAA-AATT
* * * *
8212 TTCCTAAATTTTTTGCCACGATACTCATAAAAAATATATAATTCAACGCC-AAAATATTGAAAGG
65 TTCCTCAATTTTTGGCCACGATACTCATAAAAAATATATAACTCAACGCCAAAAAGATTGAAAGG
* * ** *
8276 TTTTTCACGATTCTAATATCGGTTTTCCTA-T-TTTTTCCGAATTTATTTCTAGTTAAATCGAAA
130 CTTTTCACGCTTCTAATATC-GTTTTTTTATTATTTTTTCGAA-TTA-TTCTA-TTAAATCGAAA
* * *
8339 CATGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGGTTGAGATTTTGTTAGATGGA
191 CATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTCGTTAGATGGA
* *
8404 TATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACAGAGCCGCGGCCCCGAAACGC
256 TATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACTGAGCAG-GGCCCCGAAACGC
8469 GTTTTTAGT
320 GTTTTTAGT
* * * *
8478 CAAAAACTGTGATGGTTAGTATACGATTTCGGCTAAAATTTTGTAAAAATTGACAC-GAAACATT
1 CAAAAACTGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGGAAA-ATT
* * *
8542 TCTCCTCAATTTCTGGCCACCATATTCATAAAAAATATATAACTCAACGCCAAAAAAGATTGAAA
65 T-TCCTCAATTTTTGGCCACGATACTCATAAAAAATATATAACTCAACGCC-AAAAAGATTGAAA
* *
8607 GGCTTCTCACGCTTCTAATAT-GTTTTTTTTTTCATTTTTTCG-ATTATTCTATT-AATCGAAAC
128 GGCTTTTCACGCTTCTAATATCGTTTTTTTATT-ATTTTTTCGAATTATTCTATTAAATCGAAAC
* **
8669 -TGGATTGAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTCGTTAGATAAA
192 AT-GATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTCGTTAGATGGA
* * * * * *
8733 TATAGATATTCCAATGAGTCTTGGCGTCAAGAATCATGCAAAACTGAGCTGGGGCCCC-AGAAGG
256 TATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACTGAGC-AGGGCCCCGA-AACG
* *
8797 CCTTTTTAGC
319 CGTTTTTAGT
* * * *
8807 CAAACACCGTGA----TAACGTACACGATTTCGACTAAAATTTTGTAAAAATTGACCCGGAAGAA
1 CAAAAACTGTGATGGTTAA--TACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGGAA-AA
* * * **
8868 TTTTCCTCAATTTTTGACCACGATACTCATAAAAAATATATAATTCAACACTGAAAAGATTGAAA
63 TTTTCCTCAATTTTTGGCCACGATACTCATAAAAAATATATAACTCAACGCCAAAAAGATTGAAA
* * ** * * *
8933 GGCTATTCATGCTTCTAATATCGTTTTCCTATTA--TTTCCGTATTAATTCCTAATTGAATCGAA
128 GGCTTTTCACGCTTCTAATATCGTTTTTTTATTATTTTTTCGAATT-ATT-CT-ATTAAATCGAA
* * * *
8996 ACATGATTCATATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGGTAAGATTTGGTTAGATGG
190 ACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTCGTTAGATGG
* * * *
9061 ATATAGATATTTCAATGAGACTTGGCGCCAAAAATCGTGCATAACTGAGGCAGGGCTCCGGAACG
255 ATATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACTGA-GCAGGGCCCCGAAACG
9126 CGTTTTTACTTTTTAGT
319 CG-------TTTTTAGT
* * *
9143 CAAAAACTGTGATGGTTAATACACGATTTCAGCTAAAATGTTGCAAAAATTGA-CCTGAGAAATT
1 CAAAAACTGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGGA-AAATT
* * * * * *
9207 TCTCCTCAATTTTAGGTCACAATACTAATAAAAAATATATAACTCAATGCCAAAAAGACT-AAAG
65 T-TCCTCAATTTTTGGCCACGATACTCATAAAAAATATATAACTCAACGCCAAAAAGATTGAAA-
*
9271 GGCTTTTCATGCTTCTAATAT
128 GGCTTTTCACGCTTCTAATAT
9292 TGCTTTTCCT
Statistics
Matches: 680, Mismatches: 97, Indels: 67
0.81 0.11 0.08
Matches are distributed among these distances:
324 5 0.01
325 5 0.01
326 34 0.05
327 86 0.13
328 12 0.02
329 253 0.37
330 12 0.02
331 102 0.15
332 4 0.01
333 30 0.04
334 7 0.01
336 17 0.03
337 12 0.02
338 98 0.14
340 3 0.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32
Consensus pattern (328 bp):
CAAAAACTGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGGAAAATTT
TCCTCAATTTTTGGCCACGATACTCATAAAAAATATATAACTCAACGCCAAAAAGATTGAAAGGC
TTTTCACGCTTCTAATATCGTTTTTTTATTATTTTTTCGAATTATTCTATTAAATCGAAACATGA
TTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTCGTTAGATGGATATAG
ATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACTGAGCAGGGCCCCGAAACGCGTTTTT
AGT
Found at i:10006 original size:27 final size:26
Alignment explanation
Indices: 9965--10031 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 26
9955 CTAAATTTTC
*
9965 AATAT-TTTAATAATGG-AATAATTA-A
1 AATATATTTAAAAATGGCAAT--TTAGA
9990 AATATTATTTAAAAATGGCAATTTAGA
1 AATA-TATTTAAAAATGGCAATTTAGA
10017 AATATATTTGAAAAA
1 AATATATTT-AAAAA
10032 AAAAGAATAC
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
25 4 0.11
26 9 0.25
27 20 0.56
28 3 0.08
ACGTcount: A:0.52, C:0.01, G:0.09, T:0.37
Consensus pattern (26 bp):
AATATATTTAAAAATGGCAATTTAGA
Found at i:10442 original size:2 final size:2
Alignment explanation
Indices: 10435--10516 Score: 62
Period size: 2 Copynumber: 47.0 Consensus size: 2
10425 ACCGTTTAGT
*
10435 TA TA TA TA TA -A T- TA AA TA TA T- TA TA TA TA TA -A TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
10472 TA -A TA TA -A TA -A TA TA TA TA -A T- TA AA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10508 -A TA TA TA TA
1 TA TA TA TA TA
10517 ATGGTTAAAC
Statistics
Matches: 64, Mismatches: 4, Indels: 24
0.70 0.04 0.26
Matches are distributed among these distances:
1 12 0.19
2 52 0.81
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:10455 original size:12 final size:12
Alignment explanation
Indices: 10438--10518 Score: 64
Period size: 13 Copynumber: 6.8 Consensus size: 12
10428 GTTTAGTTAT
10438 ATATATAATT-A
1 ATATATAATTAA
*
10449 A-ATAT-ATTAT
1 ATATATAATTAA
10459 ATATATAA-TATA
1 ATATATAATTA-A
10471 ATAATATAA-TAA
1 AT-ATATAATTAA
10483 TATATATAATTAA
1 -ATATATAATTAA
*
10496 ATATATATAATAA
1 ATATATA-ATTAA
10509 TATATATAAT
1 -ATATATAAT
10519 GGTTAAACGG
Statistics
Matches: 57, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
9 3 0.05
10 5 0.09
11 7 0.12
12 17 0.30
13 18 0.32
14 7 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
ATATATAATTAA
Found at i:10455 original size:14 final size:14
Alignment explanation
Indices: 10436--10518 Score: 84
Period size: 14 Copynumber: 5.8 Consensus size: 14
10426 CCGTTTAGTT
10436 ATATATATAATTAA
1 ATATATATAATTAA
10450 ATATAT-TATATATATA
1 ATATATATA-AT-TA-A
10466 ATATA-ATAATATAATA
1 ATATATATAAT-T-A-A
10482 ATATATATAATTAA
1 ATATATATAATTAA
10496 ATATATATAA-T-A
1 ATATATATAATTAA
10508 ATATATATAAT
1 ATATATATAAT
10519 GGTTAAACGG
Statistics
Matches: 62, Mismatches: 0, Indels: 15
0.81 0.00 0.19
Matches are distributed among these distances:
12 11 0.18
13 3 0.05
14 19 0.31
15 7 0.11
16 17 0.27
17 5 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATATATATAATTAA
Found at i:10460 original size:21 final size:21
Alignment explanation
Indices: 10434--10501 Score: 91
Period size: 21 Copynumber: 3.0 Consensus size: 21
10424 AACCGTTTAG
10434 TTATATATATAATTAAATATA
1 TTATATATATAATTAAATATA
10455 TTATATATATAATATAATAATATAA
1 TTATATATATAAT-T-A-AATAT-A
*
10480 TAATATATATAATTAAATATA
1 TTATATATATAATTAAATATA
10501 T
1 T
10502 ATAATAATAT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
21 15 0.36
22 6 0.14
23 2 0.05
24 6 0.14
25 13 0.31
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TTATATATATAATTAAATATA
Found at i:10468 original size:16 final size:15
Alignment explanation
Indices: 10435--10516 Score: 77
Period size: 16 Copynumber: 5.5 Consensus size: 15
10425 ACCGTTTAGT
10435 TATATATATA-ATTAAA
1 TATATATATATA-T-AA
10451 TATATTATATATATAA
1 TATA-TATATATATAA
10467 TATA-ATA-ATATAA
1 TATATATATATATAA
10480 TA-ATATATATAATTAA
1 TATATATATAT-A-TAA
10496 -ATATATATA-ATAA
1 TATATATATATATAA
10509 TATATATA
1 TATATATA
10517 ATGGTTAAAC
Statistics
Matches: 58, Mismatches: 0, Indels: 18
0.76 0.00 0.24
Matches are distributed among these distances:
12 1 0.02
13 14 0.24
14 13 0.22
15 2 0.03
16 20 0.34
17 7 0.12
18 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TATATATATATATAA
Found at i:10478 original size:34 final size:34
Alignment explanation
Indices: 10440--10518 Score: 99
Period size: 34 Copynumber: 2.3 Consensus size: 34
10430 TTAGTTATAT
* *
10440 ATATAATTAA-ATATATTA-TATATATAATATAATA
1 ATATAA-TAATATATATAATTAAATAT-ATATAATA
10474 ATATAATAATATATATAATTAAATATATATAATA
1 ATATAATAATATATATAATTAAATATATATAATA
10508 ATATATATAAT
1 ATATA-ATAAT
10519 GGTTAAACGG
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
33 3 0.08
34 26 0.65
35 11 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (34 bp):
ATATAATAATATATATAATTAAATATATATAATA
Done.