Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009554.1 Corchorus capsularis cultivar CVL-1 contig09575, 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: 44732
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:155 original size:3 final size:3
Alignment explanation
Indices: 147--207 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
137 TGAAATTAGG
147 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
195 ATT ATT ATT ATT A
1 ATT ATT ATT ATT A
208 CTACTACGAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:297 original size:31 final size:31
Alignment explanation
Indices: 256--392 Score: 136
Period size: 31 Copynumber: 4.5 Consensus size: 31
246 GTCAAATACT
* *
256 CAATTTAGGATATAACGTTTGTTG-CTGCAAG
1 CAATTAAGGATATAACGTTT-TTGACTTCAAG
* ** ***
287 CAATTAAGGATATAA--TGTTACAAAACAAG
1 CAATTAAGGATATAACGTTTTTGACTTCAAG
* *
316 CAATTAAGGATATAACGTTTTTGATTTCGAG
1 CAATTAAGGATATAACGTTTTTGACTTCAAG
* *
347 CAATTAAGGATATAACGTTTTCGATTTCAAG
1 CAATTAAGGATATAACGTTTTTGACTTCAAG
378 CAATTAAGGATATAA
1 CAATTAAGGATATAA
393 TCAGTTAGGG
Statistics
Matches: 87, Mismatches: 16, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
28 1 0.01
29 21 0.24
31 65 0.75
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.33
Consensus pattern (31 bp):
CAATTAAGGATATAACGTTTTTGACTTCAAG
Found at i:568 original size:29 final size:31
Alignment explanation
Indices: 515--573 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
505 ACGGACTATA
*
515 TCCTTATTTGCTCGATTTTCGTAACGTTATC
1 TCCTTAATTGCTCGATTTTCGTAACGTTATC
*
546 TCCTTAATTGCTTG-TTTT-GTAACGTTAT
1 TCCTTAATTGCTCGATTTTCGTAACGTTAT
574 ATCCCAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 10 0.38
30 4 0.15
31 12 0.46
ACGTcount: A:0.17, C:0.19, G:0.14, T:0.51
Consensus pattern (31 bp):
TCCTTAATTGCTCGATTTTCGTAACGTTATC
Found at i:1496 original size:31 final size:29
Alignment explanation
Indices: 1426--1483 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
1416 TCTCGTTTTT
*
1426 AAAAGTTAAGGGGTCAATTTGTCCCAAAA
1 AAAAGTTAAGGGGCCAATTTGTCCCAAAA
1455 AAAAGTTAAGGGGCCAATTTGTCCCAAAA
1 AAAAGTTAAGGGGCCAATTTGTCCCAAAA
1484 TGGATAGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (29 bp):
AAAAGTTAAGGGGCCAATTTGTCCCAAAA
Found at i:1505 original size:31 final size:29
Alignment explanation
Indices: 1426--1506 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 29
1416 TCTCGTTTTT
* *
1426 AAAAGTTAAGGGGTCAATTTGTCCCAAAA
1 AAAAGTTAAGGAGCCAATTTGTCCCAAAA
*
1455 AAAAGTTAAGGGGCCAATTTGTCCCAAAA
1 AAAAGTTAAGGAGCCAATTTGTCCCAAAA
* * *
1484 TGGATAGTTAAGGAGCTAATTTG
1 --AAAAGTTAAGGAGCCAATTTG
1507 GATATTAAGC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
29 28 0.62
31 17 0.38
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.26
Consensus pattern (29 bp):
AAAAGTTAAGGAGCCAATTTGTCCCAAAA
Found at i:3792 original size:28 final size:29
Alignment explanation
Indices: 3723--3796 Score: 98
Period size: 28 Copynumber: 2.6 Consensus size: 29
3713 AAAAATTTGT
* *
3723 AGAAATTAATAAAGTTTTGTTTTCTCATC
1 AGAAATTAATAAAGTTTTGTTTGCTCATA
*
3752 AGAAATTAATAAAGTTTT-TTTGGTACA-A
1 AGAAATTAATAAAGTTTTGTTTGCT-CATA
3780 AGAAATTAATAAAGTTT
1 AGAAATTAATAAAGTTT
3797 AGTTGATTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
28 21 0.51
29 20 0.49
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.41
Consensus pattern (29 bp):
AGAAATTAATAAAGTTTTGTTTGCTCATA
Found at i:6347 original size:6 final size:6
Alignment explanation
Indices: 6336--6366 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
6326 AAGGCAGTCA
6336 GAATCC GAATCC GAATCC GAATCC GAATCC G
1 GAATCC GAATCC GAATCC GAATCC GAATCC G
6367 GTGGGCCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.32, G:0.19, T:0.16
Consensus pattern (6 bp):
GAATCC
Found at i:9320 original size:1 final size:1
Alignment explanation
Indices: 9314--9357 Score: 52
Period size: 1 Copynumber: 44.0 Consensus size: 1
9304 ACCTGCTGGG
* * * *
9314 TTTTTTTTTTCTTTTGTTTTGTTTTTTTGTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
9358 GCTGAAGGAT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.00, C:0.02, G:0.07, T:0.91
Consensus pattern (1 bp):
T
Found at i:13756 original size:156 final size:157
Alignment explanation
Indices: 13344--13720 Score: 554
Period size: 156 Copynumber: 2.4 Consensus size: 157
13334 CATCTTGGCT
*
13344 AAGTTTCATCTCAAACGGACTTAAGATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTG
1 AAGTTTCATCTCAATCGGACTTAAGATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTG
13409 GGGAGAGAAACCAAGTTCACCATCAAGGAGAGCTCGGTTTTACTTAGAATTTTTTCCATAGTCTT
66 GGGAGAGAAACCAAGTTCA-CATCAAGGAGAGCTCGGTTTTACTTAGAATTTTTTCCATAGTCTT
* *
13474 ATGGAGATAATCTAAGCCTACTGGTGGAA
130 ATGAAGATAATCTAAG-CTACTCGTGGAA
* *
13503 AA---TCAGCCTC-ATTGGACTT-AGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTT
1 AAGTTTCA-TCTCAATCGGACTTAAG-ATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTT
13563 TGGGGAGAGAAACCAAGTTCAGCATCAAGGAGAGCTCGGTTTTACTTAGAATTTTTTCCATAGTC
64 TGGGGAGAGAAACCAAGTTCA-CATCAAGGAGAGCTCGGTTTTACTTAGAATTTTTTCCATAGTC
*
13628 TTATGAAGATATTCTAAG-T-CTCGT-GACA
128 TTATGAAGATAATCTAAGCTACTCGTGGA-A
* ** *
13656 AAGTTTCATCTCAATCAGACTTAAGATGAAAAAGGTATGCAAGTTTTTCATTTAAGGACAGTTTG
1 AAGTTTCATCTCAATCGGACTTAAGATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTG
13721 AGGTGTGAAG
Statistics
Matches: 197, Mismatches: 13, Indels: 19
0.86 0.06 0.08
Matches are distributed among these distances:
152 2 0.01
153 7 0.04
154 1 0.01
155 5 0.03
156 175 0.89
157 5 0.03
159 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.32
Consensus pattern (157 bp):
AAGTTTCATCTCAATCGGACTTAAGATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTG
GGGAGAGAAACCAAGTTCACATCAAGGAGAGCTCGGTTTTACTTAGAATTTTTTCCATAGTCTTA
TGAAGATAATCTAAGCTACTCGTGGAA
Found at i:14101 original size:17 final size:18
Alignment explanation
Indices: 14051--14101 Score: 63
Period size: 17 Copynumber: 3.0 Consensus size: 18
14041 AGACTACAGC
14051 TCATGCTACCTAGTACC-
1 TCATGCTACCTAGTACCA
*
14068 TCATGCTA-CTGGTACCA
1 TCATGCTACCTAGTACCA
*
14085 T-GTGCTACCTAGTACCA
1 TCATGCTACCTAGTACCA
14102 CAGAAGGGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 12 0.41
17 17 0.59
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.29
Consensus pattern (18 bp):
TCATGCTACCTAGTACCA
Found at i:17115 original size:2 final size:2
Alignment explanation
Indices: 17104--17138 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
17094 CTAAAATACG
17104 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17139 GCATACCTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:18761 original size:76 final size:76
Alignment explanation
Indices: 18635--18902 Score: 398
Period size: 76 Copynumber: 3.5 Consensus size: 76
18625 AAATTTCTAT
* *
18635 AAATTAATAATGTTGGAATCT-TGAAAAATTATTAATTTAGAGA-TATTATTAATTTATCGAGTG
1 AAATTAATAATGTTGGGA-CTATGAAAAATTATTAATTTAGAAAGT-TTATTAATTTATCGAGTG
*
18698 TTAATTTATATGG
64 TTAAATTATATGG
18711 AAATTAATAATGTTGGGACTATGAAAAATTATTAATTTAGAAAGTTTATTAATTTAT-GAGTGTT
1 AAATTAATAATGTTGGGACTATGAAAAATTATTAATTTAGAAAGTTTATTAATTTATCGAGTGTT
*
18775 AACTTATATGG
66 AAATTATATGG
* * * * *
18786 AAATTAATAATCTTGGGACTAAGAAAAATTATTAATTTAGAAAGTTTATTAATTCACCGAATGTT
1 AAATTAATAATGTTGGGACTATGAAAAATTATTAATTTAGAAAGTTTATTAATTTATCGAGTGTT
*
18851 AAATTATCTGG
66 AAATTATATGG
*
18862 AAATTAATAATATTGGGACTATGAAAAATTATTAATTTAGA
1 AAATTAATAATGTTGGGACTATGAAAAATTATTAATTTAGA
18903 GAGGTTAATT
Statistics
Matches: 177, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
75 72 0.41
76 104 0.59
77 1 0.01
ACGTcount: A:0.42, C:0.04, G:0.14, T:0.40
Consensus pattern (76 bp):
AAATTAATAATGTTGGGACTATGAAAAATTATTAATTTAGAAAGTTTATTAATTTATCGAGTGTT
AAATTATATGG
Found at i:24333 original size:1 final size:1
Alignment explanation
Indices: 24327--24360 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
24317 CACATCAGAG
24327 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
24361 GCATCTCTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:24940 original size:18 final size:18
Alignment explanation
Indices: 24917--24957 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
24907 TAAAGCTGAG
*
24917 TTTTCCCCCTTTTCAAAA
1 TTTTCCCCCTTTCCAAAA
24935 TTTTCCCCCTTTCCAAAA
1 TTTTCCCCCTTTCCAAAA
24953 TTTTC
1 TTTTC
24958 AAATTTCCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.34, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTTCCCCCTTTCCAAAA
Found at i:37837 original size:69 final size:70
Alignment explanation
Indices: 37711--37847 Score: 231
Period size: 70 Copynumber: 2.0 Consensus size: 70
37701 AATCCTTAAG
*
37711 AAAAAAATCAATCAATTAAATCAAGTTAAGGTACTAATTATAAAAAAAATTACAAAGAACAATGC
1 AAAAAAATCAATCAATTAAATCAAGTTAAGGTACCAATTATAAAAAAAATTACAAAGAACAATGC
37776 AATGA
66 AATGA
* * *
37781 AAAAAAATCAATTAATTAAATCAAGTTAATGTACCACTTAT-AAAAAAATTACAAAGAACAATGC
1 AAAAAAATCAATCAATTAAATCAAGTTAAGGTACCAATTATAAAAAAAATTACAAAGAACAATGC
37845 AAT
66 AAT
37848 TAAACGTAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
69 26 0.41
70 37 0.59
ACGTcount: A:0.58, C:0.11, G:0.07, T:0.24
Consensus pattern (70 bp):
AAAAAAATCAATCAATTAAATCAAGTTAAGGTACCAATTATAAAAAAAATTACAAAGAACAATGC
AATGA
Found at i:38350 original size:58 final size:59
Alignment explanation
Indices: 38278--38393 Score: 189
Period size: 58 Copynumber: 2.0 Consensus size: 59
38268 TTATCAAACA
* * *
38278 TACCAAAATACACAAATAAATAAATTATAAATAAACTCACATTTCGTAAGACTAGAACT
1 TACCAAAATACACAAACAAATAAATTACAAATAAACTCACATTCCGTAAGACTAGAACT
*
38337 TACC-AAATACACAAACAAATAAATTACAAATAAACTCACATTCCGTGAGACTAGAAC
1 TACCAAAATACACAAACAAATAAATTACAAATAAACTCACATTCCGTAAGACTAGAAC
38394 CCAAGACCTC
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
58 49 0.92
59 4 0.08
ACGTcount: A:0.52, C:0.20, G:0.06, T:0.22
Consensus pattern (59 bp):
TACCAAAATACACAAACAAATAAATTACAAATAAACTCACATTCCGTAAGACTAGAACT
Found at i:43426 original size:35 final size:35
Alignment explanation
Indices: 43380--43449 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
43370 CTCAAATATC
43380 TAAGTTGACTTTTGACATTTAGCTACAGACTTGCT
1 TAAGTTGACTTTTGACATTTAGCTACAGACTTGCT
43415 TAAGTTGACTTTTGACATTTAGCTACAGACTTGCT
1 TAAGTTGACTTTTGACATTTAGCTACAGACTTGCT
43450 ACGGACTTGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (35 bp):
TAAGTTGACTTTTGACATTTAGCTACAGACTTGCT
Found at i:44360 original size:21 final size:21
Alignment explanation
Indices: 44336--44381 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
44326 TTGAAAAGCA
*
44336 TTATAGCTATTTTAATAACTT
1 TTATAACTATTTTAATAACTT
* * *
44357 TTATAACTTTTTTAGTAATTT
1 TTATAACTATTTTAATAACTT
44378 TTAT
1 TTAT
44382 TACAAGATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (21 bp):
TTATAACTATTTTAATAACTT
Done.