Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016093.1 Corchorus capsularis cultivar CVL-1 contig16114, 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: 41801
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:807 original size:24 final size:25
Alignment explanation
Indices: 775--823 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
765 GATCAAGATT
*
775 TGAAGGAAAAGCAAAA-AAAAAAAA
1 TGAAGGAAAAGAAAAAGAAAAAAAA
799 TGAAGGAAAAGAAAAAGAAAAAAAA
1 TGAAGGAAAAGAAAAAGAAAAAAAA
824 GAAAAAATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.76, C:0.02, G:0.18, T:0.04
Consensus pattern (25 bp):
TGAAGGAAAAGAAAAAGAAAAAAAA
Found at i:813 original size:15 final size:15
Alignment explanation
Indices: 781--829 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
771 GATTTGAAGG
781 AAAAGCAAAAAAAA-A
1 AAAAG-AAAAAAAAGA
* **
796 AAATGAAGGAAAAGA
1 AAAAGAAAAAAAAGA
811 AAAAGAAAAAAAAGA
1 AAAAGAAAAAAAAGA
826 AAAA
1 AAAA
830 ATCAGAAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
14 6 0.22
15 21 0.78
ACGTcount: A:0.82, C:0.02, G:0.14, T:0.02
Consensus pattern (15 bp):
AAAAGAAAAAAAAGA
Found at i:874 original size:18 final size:18
Alignment explanation
Indices: 853--888 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
843 AAGATGCAAT
*
853 AAAAGGTGTTTTCAAAAA
1 AAAAAGTGTTTTCAAAAA
871 AAAAAGTGTTTTCAAAAA
1 AAAAAGTGTTTTCAAAAA
889 TCATGTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.14, T:0.28
Consensus pattern (18 bp):
AAAAAGTGTTTTCAAAAA
Found at i:2396 original size:2 final size:2
Alignment explanation
Indices: 2391--2415 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2381 CATATATGTG
2391 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 T
2416 CTACCAATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7022 original size:2 final size:2
Alignment explanation
Indices: 7015--7042 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
7005 TTATTAGATA
7015 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
7043 GTGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7047 original size:2 final size:2
Alignment explanation
Indices: 7042--7080 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
7032 TATATATATA
7042 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
7081 TGAATAGATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:8035 original size:15 final size:16
Alignment explanation
Indices: 8010--8042 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
8000 TTAGTTTTCC
*
8010 AAGATAAAAATTAAAA
1 AAGATAAAAATGAAAA
8026 AAGA-AAAAATGAAAA
1 AAGATAAAAATGAAAA
8041 AA
1 AA
8043 ATGAGTCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (16 bp):
AAGATAAAAATGAAAA
Found at i:8096 original size:7 final size:7
Alignment explanation
Indices: 8086--8110 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
8076 AAAATCCAAA
8086 AAAATTC
1 AAAATTC
8093 AAAATTC
1 AAAATTC
8100 AAAATTC
1 AAAATTC
8107 AAAA
1 AAAA
8111 CAAAATTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAATTC
Found at i:15292 original size:15 final size:14
Alignment explanation
Indices: 15257--15294 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
15247 AATTAGTAGA
15257 TTAG-CATTAGCAC
1 TTAGTCATTAGCAC
15270 TTAGGTCATTAGCAC
1 TTA-GTCATTAGCAC
15285 TTTAGTCATT
1 -TTAGTCATT
15295 CTATCTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 3 0.14
14 1 0.05
15 15 0.68
16 3 0.14
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.39
Consensus pattern (14 bp):
TTAGTCATTAGCAC
Found at i:17580 original size:30 final size:30
Alignment explanation
Indices: 17546--17614 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
17536 AGATGAAGTC
*
17546 TTTAAGTGATTCGTCAACAAAGATTGAATT
1 TTTAAGTGATTCGTCAACAAAGATTGAACT
* * * *
17576 TTTAAGTAATTTGTGAATAAAGATTGAACT
1 TTTAAGTGATTCGTCAACAAAGATTGAACT
17606 TTTAAGTGA
1 TTTAAGTGA
17615 AAGATGAAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (30 bp):
TTTAAGTGATTCGTCAACAAAGATTGAACT
Found at i:18338 original size:89 final size:89
Alignment explanation
Indices: 18176--18352 Score: 216
Period size: 89 Copynumber: 2.0 Consensus size: 89
18166 AAGACTAGAT
* *
18176 TTGTTTAGTTTTCCCAATTTGCCCTTCCCAGTCGGAAGGTGTTGTCTCATCCTGCTTTTTCCCAA
1 TTGTTTAGTTTTCCCAATTTGCCCTTCCCAGCCGGAAGGTGTTGTCTCATCCTGCTTGTTCCCAA
*
18241 ATTGCCCTTCCCAGTCAGAAGGTG
66 AATGCCCTTCCCAGTCAGAAGGTG
* * * * *
18265 TTGTTTAGTTTTCTCAGTTTGCTCTTTCCCA-CCGGAAGGTGTTGTCTGC-T-TTTCTTGTTCCC
1 TTGTTTAGTTTTCCCAATTTGC-CCTTCCCAGCCGGAAGGTGTTGTCT-CATCCTGCTTGTTCCC
* *
18327 AAAATGCCCCTTCCCGGTCGGAAGGT
64 AAAATG-CCCTTCCCAGTCAGAAGGT
18353 CACGGTCTTC
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
88 14 0.19
89 53 0.71
90 8 0.11
ACGTcount: A:0.14, C:0.27, G:0.20, T:0.38
Consensus pattern (89 bp):
TTGTTTAGTTTTCCCAATTTGCCCTTCCCAGCCGGAAGGTGTTGTCTCATCCTGCTTGTTCCCAA
AATGCCCTTCCCAGTCAGAAGGTG
Found at i:18389 original size:49 final size:49
Alignment explanation
Indices: 18308--18757 Score: 515
Period size: 49 Copynumber: 9.2 Consensus size: 49
18298 GGAAGGTGTT
* * * * *
18308 GTCTGCTTTTCTTGTTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCACG
1 GTCTTCTTTACTTATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACA
* * *
18357 GTCTTCTTTACTTATTCCAAAAATGCCCCTTCCCAGTCGTAAGGTCACC
1 GTCTTCTTTACTTATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACA
* *
18406 GTCTTCTTTACTTATTCCAAAAATGCCCCTTCCCGGTCGAAAGGTCATA
1 GTCTTCTTTACTTATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACA
*
18455 GT-TCTCTTCT-CTTGTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACA
1 GTCT-TCTT-TACTTATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACA
*
18504 GTCTTCTTTACTTATTCCAAAAATGCCCCTTCCCGGCCGGAAGGTCACA
1 GTCTTCTTTACTTATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACA
**
18553 GTCTTCTTCCCTTATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACA
1 GTCTTCTTTACTTATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACA
*
18602 GT-TCTCTTCT-CTTATTCAAAAAATGCCCCTTCCCGGTCGGAAGGTCACA
1 GTCT-TCTT-TACTTATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACA
* ** * * *
18651 GTTTTCTCTT--TTGGGTCCCAAAATGCCCCTTCCCGGTTGGAAGGTC-CTT
1 GTCTTCT-TTACTT-ATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCAC-A
* * *
18700 GT-TTCCTTAATTTGTTTCTC-AAAATGCCCCTTCCCGGTCGGAAGGTC-CA
1 GTCTT-CTTTACTT-ATTC-CAAAAATGCCCCTTCCCGGTCGGAAGGTCACA
*
18749 GTTTTCTTT
1 GTCTTCTTT
18758 TCACATCTGT
Statistics
Matches: 353, Mismatches: 33, Indels: 30
0.85 0.08 0.07
Matches are distributed among these distances:
48 9 0.03
49 305 0.86
50 38 0.11
51 1 0.00
ACGTcount: A:0.19, C:0.31, G:0.17, T:0.33
Consensus pattern (49 bp):
GTCTTCTTTACTTATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACA
Found at i:18584 original size:147 final size:147
Alignment explanation
Indices: 18317--18756 Score: 577
Period size: 147 Copynumber: 3.0 Consensus size: 147
18307 TGTCTGCTTT
* *
18317 TCTTGTTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCACGGTCTTCTTTACTTATTCCAAAAATG
1 TCTTGTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCTTCTTTACTTATTCCAAAAATG
* * * *
18382 CCCCTTCCCAGTCGTAAGGTCACCGTCTTCTTTACTTATTCCAAAAATGCCCCTTCCCGGTCGAA
66 CCCCTTCCCGGTCGGAAGGTCACAGTCTTCTTCACTTATTCCAAAAATGCCCCTTCCCGGTCGAA
*
18447 AGGTCATAGTTCTCTTC
131 AGGTCACAGTTCTCTTC
18464 TCTTGTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCTTCTTTACTTATTCCAAAAATG
1 TCTTGTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCTTCTTTACTTATTCCAAAAATG
* * *
18529 CCCCTTCCCGGCCGGAAGGTCACAGTCTTCTTCCCTTATTCCAAAAATGCCCCTTCCCGGTCGGA
66 CCCCTTCCCGGTCGGAAGGTCACAGTCTTCTTCACTTATTCCAAAAATGCCCCTTCCCGGTCGAA
18594 AGGTCACAGTTCTCTTC
131 AGGTCACAGTTCTCTTC
* * * ** *
18611 TCTTATTCAAAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTTTTCTCTT--TTGGGTCCCAAAA
1 TCTTGTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCTTCT-TTACTT-ATTCCAAAAA
* * * * *
18674 TGCCCCTTCCCGGTTGGAAGGTC-CTTGT-TTCCTTAATTTGTTTCTC-AAAATGCCCCTTCCCG
64 TGCCCCTTCCCGGTCGGAAGGTCAC-AGTCTT-CTTCACTT-ATTC-CAAAAATGCCCCTTCCCG
* *
18736 GTCGGAAGGTC-CAGTTTTCTT
125 GTCGAAAGGTCACAGTTCTCTT
18757 TTCACATCTG
Statistics
Matches: 263, Mismatches: 24, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
146 5 0.02
147 225 0.86
148 32 0.12
149 1 0.00
ACGTcount: A:0.20, C:0.31, G:0.17, T:0.32
Consensus pattern (147 bp):
TCTTGTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCTTCTTTACTTATTCCAAAAATG
CCCCTTCCCGGTCGGAAGGTCACAGTCTTCTTCACTTATTCCAAAAATGCCCCTTCCCGGTCGAA
AGGTCACAGTTCTCTTC
Found at i:19355 original size:152 final size:152
Alignment explanation
Indices: 19079--19385 Score: 614
Period size: 152 Copynumber: 2.0 Consensus size: 152
19069 GCCTAGAATT
19079 ATGATTAGTGGCGACTGCATATGGTATCAGTAGTGTTTTCCATACCAAGTCGTTCAGCGGCAGGG
1 ATGATTAGTGGCGACTGCATATGGTATCAGTAGTGTTTTCCATACCAAGTCGTTCAGCGGCAGGG
19144 TTCGGACCCCGGACCCGCACGTTGCGACAAAAGGGCGCAAAAAGATCATCTTTGAACCTGGTGAT
66 TTCGGACCCCGGACCCGCACGTTGCGACAAAAGGGCGCAAAAAGATCATCTTTGAACCTGGTGAT
19209 TGGGTTTGGTTGCATCTAAGGA
131 TGGGTTTGGTTGCATCTAAGGA
19231 ATGATTAGTGGCGACTGCATATGGTATCAGTAGTGTTTTCCATACCAAGTCGTTCAGCGGCAGGG
1 ATGATTAGTGGCGACTGCATATGGTATCAGTAGTGTTTTCCATACCAAGTCGTTCAGCGGCAGGG
19296 TTCGGACCCCGGACCCGCACGTTGCGACAAAAGGGCGCAAAAAGATCATCTTTGAACCTGGTGAT
66 TTCGGACCCCGGACCCGCACGTTGCGACAAAAGGGCGCAAAAAGATCATCTTTGAACCTGGTGAT
19361 TGGGTTTGGTTGCATCTAAGGA
131 TGGGTTTGGTTGCATCTAAGGA
19383 ATG
1 ATG
19386 TGAGGTTCCC
Statistics
Matches: 155, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
152 155 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (152 bp):
ATGATTAGTGGCGACTGCATATGGTATCAGTAGTGTTTTCCATACCAAGTCGTTCAGCGGCAGGG
TTCGGACCCCGGACCCGCACGTTGCGACAAAAGGGCGCAAAAAGATCATCTTTGAACCTGGTGAT
TGGGTTTGGTTGCATCTAAGGA
Found at i:31426 original size:78 final size:78
Alignment explanation
Indices: 31301--31460 Score: 216
Period size: 78 Copynumber: 2.1 Consensus size: 78
31291 TACTTTTATA
* * *
31301 ATTTTACTCAACTAAAAACTCTATATTTATTCAACTAAATCTAATATCTTTATAATTATTTTA-T
1 ATTTTACTCAACTAAAAACTCTATATTTATTCAACTAAACCTAATATCCTTATAACTATTTTAGT
*
31365 TTCACTTATTTTACT
66 TT-AC-CATTTTACT
* * * *
31380 ATTTTACTTAACT-AAAACTCTATTTTTATTTAATTAAACCTAATATCCTTATAACTATTTTAGT
1 ATTTTACTCAACTAAAAACTCTATATTTATTCAACTAAACCTAATATCCTTATAACTATTTTAGT
31444 TTACCATTTTACT
66 TTACCATTTTACT
31457 ATTT
1 ATTT
31461 CAATTATTTT
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
77 12 0.17
78 45 0.62
79 15 0.21
ACGTcount: A:0.34, C:0.15, G:0.01, T:0.50
Consensus pattern (78 bp):
ATTTTACTCAACTAAAAACTCTATATTTATTCAACTAAACCTAATATCCTTATAACTATTTTAGT
TTACCATTTTACT
Found at i:36812 original size:24 final size:24
Alignment explanation
Indices: 36784--36831 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
36774 GCACTCGTCA
*
36784 AAACTTTGTAATAGATTGTGTTTT
1 AAACTTTGTAATAAATTGTGTTTT
36808 AAACTTTGTAATAAATTGTGTTTT
1 AAACTTTGTAATAAATTGTGTTTT
36832 GATCTTCTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.04, G:0.15, T:0.50
Consensus pattern (24 bp):
AAACTTTGTAATAAATTGTGTTTT
Found at i:40358 original size:2 final size:2
Alignment explanation
Indices: 40351--40392 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
40341 ATGGATATAA
40351 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
40393 GTAGCGGAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:41561 original size:2 final size:2
Alignment explanation
Indices: 41556--41582 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
41546 TTTCATAAAT
41556 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 T
41583 TATGTGCTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.