Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009561.1 Corchorus capsularis cultivar CVL-1 contig09582, 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: 63568
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1342 original size:60 final size:59
Alignment explanation
Indices: 1278--1469 Score: 153
Period size: 60 Copynumber: 3.1 Consensus size: 59
1268 AGAGATAGTA
1278 TTAGATTACATATTAACCCTTAAAATTATAGCTAAAATTTTTAAAACTAAAAAGGGTATT
1 TTAGATTACATATTAACCCTTAAAATTATAGCTAAAA-TTTTAAAACTAAAAAGGGTATT
** * *
1338 TTAGATATTA-ATAAGATGCTTAACGTGATTTAAAA-T-T-GC-ATTAATTTTAAAA-TTAAAAG
1 TTAG--ATTACAT---A---TTAAC---CCTTAAAATTATAGCTA-AAATTTTAAAACTAAAAAG
* *
1397 AGATAGTA
54 -GGTA-TT
1405 TTAGATTACATATTAACCCTTAAAATTATAGCTAAAATTTTAAAACTAAAAAGGGTATT
1 TTAGATTACATATTAACCCTTAAAATTATAGCTAAAATTTTAAAACTAAAAAGGGTATT
1464 TTAGAT
1 TTAGAT
1470 ATTTCAGGTC
Statistics
Matches: 100, Mismatches: 12, Indels: 41
0.65 0.08 0.27
Matches are distributed among these distances:
57 6 0.06
58 1 0.01
59 8 0.08
60 24 0.24
61 9 0.09
62 4 0.04
63 1 0.01
64 1 0.01
65 10 0.10
66 14 0.14
67 14 0.14
68 1 0.01
69 1 0.01
70 6 0.06
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.37
Consensus pattern (59 bp):
TTAGATTACATATTAACCCTTAAAATTATAGCTAAAATTTTAAAACTAAAAAGGGTATT
Found at i:1371 original size:127 final size:126
Alignment explanation
Indices: 1220--1472 Score: 488
Period size: 127 Copynumber: 2.0 Consensus size: 126
1210 TAATTATAAC
1220 AATAAGATGCTTAACGTGATTTAAAATTGCACTAATTTTAAAATTAAAAGAGATAGTATTAGATT
1 AATAAGATGCTTAACGTGATTTAAAATTGCACTAATTTTAAAATTAAAAGAGATAGTATTAGATT
1285 ACATATTAACCCTTAAAATTATAGCTAAAATTTTTAAAACTAAAAAGGGTATTTTAGATATT
66 ACATATTAACCCTTAAAATTATAGCTAAAA-TTTTAAAACTAAAAAGGGTATTTTAGATATT
*
1347 AATAAGATGCTTAACGTGATTTAAAATTGCATTAATTTTAAAATTAAAAGAGATAGTATTAGATT
1 AATAAGATGCTTAACGTGATTTAAAATTGCACTAATTTTAAAATTAAAAGAGATAGTATTAGATT
1412 ACATATTAACCCTTAAAATTATAGCTAAAATTTTAAAACTAAAAAGGGTATTTTAGATATT
66 ACATATTAACCCTTAAAATTATAGCTAAAATTTTAAAACTAAAAAGGGTATTTTAGATATT
1473 TCAGGTCAAG
Statistics
Matches: 125, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
126 31 0.25
127 94 0.75
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.36
Consensus pattern (126 bp):
AATAAGATGCTTAACGTGATTTAAAATTGCACTAATTTTAAAATTAAAAGAGATAGTATTAGATT
ACATATTAACCCTTAAAATTATAGCTAAAATTTTAAAACTAAAAAGGGTATTTTAGATATT
Found at i:1528 original size:2 final size:2
Alignment explanation
Indices: 1521--1563 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
1511 AAAGATAAAG
*
1521 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1562 AT
1 AT
1564 TTCGGGCCCG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:8001 original size:18 final size:18
Alignment explanation
Indices: 7962--8005 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
7952 TTATTAATCT
*
7962 TATATATATAATATATAC
1 TATATATATAATATATAA
*
7980 TATATATATACTACT-TAA
1 TATATATATAATA-TATAA
7998 TATATATA
1 TATATATA
8006 GCTTTGGTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 22 0.96
19 1 0.04
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (18 bp):
TATATATATAATATATAA
Found at i:8158 original size:1 final size:1
Alignment explanation
Indices: 8147--8179 Score: 57
Period size: 1 Copynumber: 33.0 Consensus size: 1
8137 TGCAGATTAT
*
8147 AAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
8180 GTAAAACATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:26683 original size:12 final size:12
Alignment explanation
Indices: 26651--26689 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
26641 ATGGAATTAA
26651 ATATCCGTCG--
1 ATATCCGTCGAT
26661 ATA-CC-TCGAT
1 ATATCCGTCGAT
26671 ATATCCGTCGAT
1 ATATCCGTCGAT
26683 ATATCCG
1 ATATCCG
26690 ATATCTGTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
8 3 0.12
9 2 0.08
10 6 0.24
11 2 0.08
12 12 0.48
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (12 bp):
ATATCCGTCGAT
Found at i:27781 original size:3 final size:3
Alignment explanation
Indices: 27769--27801 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
27759 AGCTCAGGAA
27769 GAT G-T GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
27802 GGGGAAATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.30, C:0.00, G:0.36, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:29119 original size:2 final size:2
Alignment explanation
Indices: 29112--29148 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
29102 TCTATGTTGT
29112 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29149 TTTCTTCCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31821 original size:22 final size:22
Alignment explanation
Indices: 31796--31839 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
31786 TATGTGGCAC
31796 AAATTGGAATTTTAACTCCAAT
1 AAATTGGAATTTTAACTCCAAT
31818 AAATTGGAATTTTAACTCCAAT
1 AAATTGGAATTTTAACTCCAAT
31840 TGTGGGTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (22 bp):
AAATTGGAATTTTAACTCCAAT
Found at i:31999 original size:18 final size:19
Alignment explanation
Indices: 31976--32015 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
31966 CCTTGAAAAT
31976 AATTCTTC-AATGATCTTC
1 AATTCTTCAAATGATCTTC
*
31994 AATTCTTCAAATTATCTTC
1 AATTCTTCAAATGATCTTC
32013 AAT
1 AAT
32016 AAGTCTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.33, C:0.20, G:0.03, T:0.45
Consensus pattern (19 bp):
AATTCTTCAAATGATCTTC
Found at i:35145 original size:3 final size:3
Alignment explanation
Indices: 35137--35187 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
35127 AACTAATTCA
35137 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
35185 AAT
1 AAT
35188 GTAGAAATCA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:37835 original size:3 final size:3
Alignment explanation
Indices: 37827--37861 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
37817 CGCTAAAGTT
37827 TAA TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
37862 AATGAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:42670 original size:2 final size:2
Alignment explanation
Indices: 42663--42692 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
42653 GCACCCGAGA
42663 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42693 TGAGTACTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43653 original size:12 final size:12
Alignment explanation
Indices: 43636--43661 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
43626 AAACCTTTTG
43636 AAATTATGATAA
1 AAATTATGATAA
43648 AAATTATGATAA
1 AAATTATGATAA
43660 AA
1 AA
43662 CAAGGGACTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (12 bp):
AAATTATGATAA
Found at i:56252 original size:11 final size:11
Alignment explanation
Indices: 56220--56257 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
56210 TCTAGGACTC
*
56220 CAAAAAAAAGAA
1 CAAAACAAA-AA
56232 CAAAAC-AAAA
1 CAAAACAAAAA
56242 CAAAACAAAAA
1 CAAAACAAAAA
56253 CAAAA
1 CAAAA
56258 TGACTGACTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 8 0.33
11 11 0.46
12 5 0.21
ACGTcount: A:0.82, C:0.16, G:0.03, T:0.00
Consensus pattern (11 bp):
CAAAACAAAAA
Found at i:58072 original size:58 final size:58
Alignment explanation
Indices: 58006--58126 Score: 235
Period size: 58 Copynumber: 2.1 Consensus size: 58
57996 ATCTTTTGTT
58006 AGATAAATCTCAATGTACCAATTCAACTACCCAGTTTGATCATATCTTTCAAAAGATC
1 AGATAAATCTCAATGTACCAATTCAACTACCCAGTTTGATCATATCTTTCAAAAGATC
58064 AGATAAATCTCAATGTACCAATTCAACTACCCAGTTTGATCATATCTTTCAAAAGATC
1 AGATAAATCTCAATGTACCAATTCAACTACCCAGTTTGATCATATCTTTCAAAAGATC
58122 A-ATAA
1 AGATAA
58127 GGGATAAACT
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
57 4 0.06
58 59 0.94
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (58 bp):
AGATAAATCTCAATGTACCAATTCAACTACCCAGTTTGATCATATCTTTCAAAAGATC
Done.