Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012895.1 Corchorus capsularis cultivar CVL-1 contig12916, 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: 43780
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1323 original size:3 final size:3
Alignment explanation
Indices: 1317--1349 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
1307 TATTATTATT
*
1317 ATA ATA ATA ATA ATA ATT ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1350 TTCTATCAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:5752 original size:21 final size:24
Alignment explanation
Indices: 5693--5773 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 24
5683 TTTAGTAATT
*
5693 AAATATATATTATTTATTTATTTTG
1 AAATATATATTA-TTATTTATTTAG
*
5718 AACTCAT-TA-T-TTA-TTATTTA-
1 AAAT-ATATATTATTATTTATTTAG
5738 AAATATAT-TTATTATTTATTTAG
1 AAATATATATTATTATTTATTTAG
*
5761 TAATATATATTAT
1 AAATATATATTAT
5774 ATCTAAGATA
Statistics
Matches: 45, Mismatches: 4, Indels: 15
0.70 0.06 0.23
Matches are distributed among these distances:
19 2 0.04
20 5 0.11
21 9 0.20
22 10 0.22
23 7 0.16
24 5 0.11
25 5 0.11
26 2 0.04
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (24 bp):
AAATATATATTATTATTTATTTAG
Found at i:5768 original size:25 final size:25
Alignment explanation
Indices: 5723--5771 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
5713 TTTTGAACTC
*
5723 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATGTAAAATATATTT
*
5748 ATTATTTATT-TAGTAATATATATT
1 ATTATTTATTAT-GTAAAATATATT
5772 ATATCTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (25 bp):
ATTATTTATTATGTAAAATATATTT
Found at i:8337 original size:18 final size:19
Alignment explanation
Indices: 8293--8345 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 19
8283 AAATATATAT
8293 TATTTATTTATTTTAAACACA
1 TATTTA-TTA-TTTAAACACA
*
8314 TAATTTATTATTTAAA-ATA
1 T-ATTTATTATTTAAACACA
8333 TATTTATTATTTA
1 TATTTATTATTTA
8346 TTTAATAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 12 0.40
19 3 0.10
20 6 0.20
21 4 0.13
22 5 0.17
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTTATTATTTAAACACA
Found at i:8356 original size:21 final size:22
Alignment explanation
Indices: 8283--8360 Score: 72
Period size: 22 Copynumber: 3.5 Consensus size: 22
8273 TTTAGTAATT
8283 AAATATATATTATTTATTTATTTTA
1 AAATATATA-TA-TTATTTA-TTTA
*
8308 AACACATA-AT-TTA-TTATTTA
1 AA-ATATATATATTATTTATTTA
*
8328 AAATATATTTATTATTTATTTA
1 AAATATATATATTATTTATTTA
8350 ATAATATATAT
1 A-AATATATAT
8361 TATATCTAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
19 4 0.09
20 7 0.16
21 6 0.14
22 11 0.25
23 8 0.18
24 1 0.02
25 3 0.07
26 4 0.09
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (22 bp):
AAATATATATATTATTTATTTA
Found at i:8361 original size:21 final size:21
Alignment explanation
Indices: 8281--8363 Score: 73
Period size: 21 Copynumber: 3.8 Consensus size: 21
8271 CGTTTAGTAA
8281 TTAAATATATATTATTTATTTATT
1 TTAAA-ATATATTA-TTATTTA-T
* *
8305 TTAAACACATAAT-TTA-TTAT
1 TTAAA-ATATATTATTATTTAT
8325 TTAAAATATATTTATTATTTAT
1 TTAAAATATA-TTATTATTTAT
8347 TTAATAATATA-TATTAT
1 TTAA-AATATATTATTAT
8364 ATCTAAGATA
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
19 4 0.08
20 7 0.14
21 12 0.24
22 11 0.22
23 6 0.12
24 10 0.20
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
TTAAAATATATTATTATTTAT
Found at i:16061 original size:30 final size:30
Alignment explanation
Indices: 16025--16098 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
16015 ATCAGATCAG
16025 GACATTTTG-CCTCAGAACTTTAAAATTCGA
1 GACATTTTGCCCT-AGAACTTTAAAATTCGA
* * * *
16055 GACATTTTGCCCTTGAACTTTCATATTTGA
1 GACATTTTGCCCTAGAACTTTAAAATTCGA
*
16085 GACATTTTGTCCTA
1 GACATTTTGCCCTA
16099 TAAACTTCTC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
30 34 0.92
31 3 0.08
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (30 bp):
GACATTTTGCCCTAGAACTTTAAAATTCGA
Found at i:18429 original size:2 final size:2
Alignment explanation
Indices: 18422--18465 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
18412 AGTAGTAATC
* *
18422 AT AT AT AT AT AT AT AT AT AT AT AT AT GT GT AT AT 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
18464 AT
1 AT
18466 TAAAACTGAG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18776 original size:79 final size:79
Alignment explanation
Indices: 18689--18847 Score: 291
Period size: 79 Copynumber: 2.0 Consensus size: 79
18679 TATTAATTAA
*
18689 ATGATTTGATTTGATTATATAGATCCAAAATTAACTCCCTAATAAACTGATTAATACAAAAATTA
1 ATGATTTGATTTGATTATATAGATCCAAAATTAACTCCCTAATAAACTAATTAATACAAAAATTA
*
18754 AGGTAATTAGGGTT
66 AGGAAATTAGGGTT
*
18768 ATGATTTGATTTGATTATATAGATCCAAAATTAACTCCCTAATAAACTAATTAATTCAAAAATTA
1 ATGATTTGATTTGATTATATAGATCCAAAATTAACTCCCTAATAAACTAATTAATACAAAAATTA
18833 AGGAAATTAGGGTT
66 AGGAAATTAGGGTT
18847 A
1 A
18848 GAAATTTCCG
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 77 1.00
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (79 bp):
ATGATTTGATTTGATTATATAGATCCAAAATTAACTCCCTAATAAACTAATTAATACAAAAATTA
AGGAAATTAGGGTT
Found at i:21997 original size:12 final size:12
Alignment explanation
Indices: 21980--22004 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
21970 TGTCATTTTG
21980 TATGTATTTAAC
1 TATGTATTTAAC
21992 TATGTATTTAAC
1 TATGTATTTAAC
22004 T
1 T
22005 GGCTCCAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (12 bp):
TATGTATTTAAC
Found at i:22564 original size:27 final size:27
Alignment explanation
Indices: 22531--22587 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
22521 ACATGTTGAA
* *
22531 AATGTTTATATATACATACAATAAAAT
1 AATGTTTATATATACAGACAACAAAAT
22558 AATGTTTATATATACAGACAACAAAAT
1 AATGTTTATATATACAGACAACAAAAT
22585 AAT
1 AAT
22588 AAAATTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.53, C:0.09, G:0.05, T:0.33
Consensus pattern (27 bp):
AATGTTTATATATACAGACAACAAAAT
Found at i:23379 original size:376 final size:377
Alignment explanation
Indices: 22923--23680 Score: 1147
Period size: 383 Copynumber: 2.0 Consensus size: 377
22913 AAATTGGTAT
* **
22923 AATCTTCGTTTACAAAAGCAATTTTAGTAAATATAAATAAGAAATTTGATAATTAAAAATATTGA
1 AATCTTCGTTTACAAAAGCAATTTTAGTAAATATAAATAAGAAACTTGATAACCAAAAATATTGA
* *
22988 GACTGTAAAGTTATTAGATTAGTTAATAGTACTATACATTTTTTTATAATCATTATAGAAT-TT-
66 GAATGTAAAGTTATTAGATTAGTTAATAATACTATACATTTTTTT-T--T-ATTATAGAATATTA
23051 T-TTTTTTCAAAA-AAAAAT-ATAGAAAATTGGTAATCTTCACAAAAAATTAGATAGAAAATTGG
127 TATTTTTTCAAAACAAAAATAATAGAAAATTGGTAATCTTCACAAAAAATTAGATAGAAAATTGG
* *
23113 TGATC-TT-CACCATTAATGAAAGTTTACTAAAGTTAATAAGAATGTAAGGTTTATTGAATTTGT
192 TAATCTTTGCA-CATTAATGAAAGTTTACTAAAGTTAATAAGAATGTAAGG-TTATTGAATTTAT
* * **
23176 TCATAGTATCATAATTGTTTTAATAACATTTAATTGATACTCCCTT-TTTTCCTATTTATTTGTC
255 TCATAGTATCATAATTGTTTTAATAACATTCAATCGATACT-CCTTACGTTCCTATTTATTTGTC
23240 ACATTTTGGTTAACCAATCTTCAAGTTTGACAATATTTTTCT-AAAAATATATAAAGTAA
319 ACATTTTGGTTAACCAATCTTCAAGTTTGACAATATTTTTCTCAAAAA-ATATAAAGTAA
23299 AATCTTCGTTTACAAAAGCAATTTTAGTAAATATAAATAAGAAACTTGATAACCAAAAATATTGA
1 AATCTTCGTTTACAAAAGCAATTTTAGTAAATATAAATAAGAAACTTGATAACCAAAAATATTGA
* * * *
23364 GAATGTAAGGTTATTAGATTAGTTGATAATACTATACCTTTTTTTTTATTATATAATCATTATAG
66 GAATGTAAAGTTATTAGATTAGTTAATAATACTATACATTTTTTTTTATTATAGAAT-ATTATA-
* *
23429 TTTTTTTAAAACAAAAATAGATAGAAAATTGGTAATCTTCATAAAAAATTAGATAGAAAATTGGT
129 TTTTTTCAAAACAAAAATA-ATAGAAAATTGGTAATCTTCACAAAAAATTAGATAGAAAATTGGT
*
23494 AATCTTTTGGGTACATTAATGAAAGTTTACTAAAGTTAATAAGAATGTAAGGTTATTGAATTTAT
193 AATC-TTT--GCACATTAATGAAAGTTTACTAAAGTTAATAAGAATGTAAGGTTATTGAATTTAT
*
23559 TCATAGTATCATAATTGTTTTAATAACCTTCAATCGATACTCCTTACGTTCCTATTTATTTGTCA
255 TCATAGTATCATAATTGTTTTAATAACATTCAATCGATACTCCTTACGTTCCTATTTATTTGTCA
*
23624 CATTTTGGTTAACCAATCTTCAAGTTTGACAATATTTTTCTCAAAAAATATGAAGTA
320 CATTTTGGTTAACCAATCTTCAAGTTTGACAATATTTTTCTCAAAAAATATAAAGTA
23681 CAACATTTTT
Statistics
Matches: 347, Mismatches: 20, Indels: 23
0.89 0.05 0.06
Matches are distributed among these distances:
372 9 0.03
373 1 0.00
374 2 0.01
375 2 0.01
376 102 0.29
377 10 0.03
378 6 0.02
380 47 0.14
382 6 0.02
383 117 0.34
384 44 0.13
385 1 0.00
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (377 bp):
AATCTTCGTTTACAAAAGCAATTTTAGTAAATATAAATAAGAAACTTGATAACCAAAAATATTGA
GAATGTAAAGTTATTAGATTAGTTAATAATACTATACATTTTTTTTTATTATAGAATATTATATT
TTTTCAAAACAAAAATAATAGAAAATTGGTAATCTTCACAAAAAATTAGATAGAAAATTGGTAAT
CTTTGCACATTAATGAAAGTTTACTAAAGTTAATAAGAATGTAAGGTTATTGAATTTATTCATAG
TATCATAATTGTTTTAATAACATTCAATCGATACTCCTTACGTTCCTATTTATTTGTCACATTTT
GGTTAACCAATCTTCAAGTTTGACAATATTTTTCTCAAAAAATATAAAGTAA
Found at i:30776 original size:37 final size:38
Alignment explanation
Indices: 30671--30778 Score: 173
Period size: 38 Copynumber: 2.9 Consensus size: 38
30661 GGCTGTGCAT
** * *
30671 AGTGGACCCGCACCTCAGGGGGTTAAACTGATGGTAAG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGCTAAG
30709 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGCTAAG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGCTAAG
30747 AGTGGACCCGTGCCTC-GGGGGTTAAACTGTTG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTG
30779 GCTTGATTGT
Statistics
Matches: 66, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
37 16 0.24
38 50 0.76
ACGTcount: A:0.21, C:0.21, G:0.35, T:0.22
Consensus pattern (38 bp):
AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGCTAAG
Found at i:42194 original size:16 final size:16
Alignment explanation
Indices: 42173--42206 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
42163 TCTGAAGTAT
42173 TTCAGAACTTTTCTGC
1 TTCAGAACTTTTCTGC
*
42189 TTCAGAGCTTTTCTGC
1 TTCAGAACTTTTCTGC
42205 TT
1 TT
42207 TCTGAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.15, C:0.24, G:0.15, T:0.47
Consensus pattern (16 bp):
TTCAGAACTTTTCTGC
Found at i:43099 original size:66 final size:65
Alignment explanation
Indices: 42959--43167 Score: 337
Period size: 65 Copynumber: 3.2 Consensus size: 65
42949 ACGTAGTTCA
* *
42959 TTTTTTTTTTTTGTGCTCTAAGTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGC
1 TTTTTTTTTTTTTTGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGC
***
43024 TTTTTTTTTTTTTTGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGTTT
1 TTTTTTTTTTTTTTGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGC
* *
43089 TTTTTTTTTTTTTTGCTCTTAACTTTTGCCTAAGTCGTCCTTTGCAGGATTTTCAACTTAGCGAC
1 TTTTTTTTTTTTTTGCTC-TAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAG
43154 C
65 C
*
43155 CTTTTTTTTTTTT
1 TTTTTTTTTTTTT
43168 GGGTTGACTG
Statistics
Matches: 133, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
65 78 0.59
66 55 0.41
ACGTcount: A:0.14, C:0.20, G:0.14, T:0.52
Consensus pattern (65 bp):
TTTTTTTTTTTTTTGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGC
Done.