Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016328.1 Corchorus capsularis cultivar CVL-1 contig16349, 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: 29760
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:367 original size:33 final size:33
Alignment explanation
Indices: 327--461 Score: 177
Period size: 33 Copynumber: 4.1 Consensus size: 33
317 ACACTAGGCT
* *
327 CCCCACT-AGGACGGCTCAGCCACGGCGGAGCCT
1 CCCCACTGAGGA-GGCTCAACCACGGCGGAGCCG
360 CCCCACT-AGGGAGGCTCAACCACGGCGGAGCCG
1 CCCCACTGA-GGAGGCTCAACCACGGCGGAGCCG
* *
393 CCCCACTGGGGAGGCTAAACCACGGCGGAGCCG
1 CCCCACTGAGGAGGCTCAACCACGGCGGAGCCG
* *
426 CCCCACTGGGGAGGCTCAACCACGGC-AAGCCG
1 CCCCACTGAGGAGGCTCAACCACGGCGGAGCCG
458 CCCC
1 CCCC
462 GGTGGGACGG
Statistics
Matches: 94, Mismatches: 6, Indels: 5
0.90 0.06 0.05
Matches are distributed among these distances:
32 9 0.10
33 82 0.87
34 3 0.03
ACGTcount: A:0.20, C:0.41, G:0.32, T:0.07
Consensus pattern (33 bp):
CCCCACTGAGGAGGCTCAACCACGGCGGAGCCG
Found at i:1129 original size:61 final size:61
Alignment explanation
Indices: 1005--1119 Score: 151
Period size: 61 Copynumber: 1.9 Consensus size: 61
995 TTATTTTCGC
* * ** * * * *
1005 GGACAGTCTATCAGGCACCTGGCTGAAAATTTTCTAACCCATACAAGAACTGCAATCCCGT
1 GGACAATCTATCAGGCACCTGGCTGAAAATTTTCAAAAACAAAAAAGAACAGAAATCCCGT
1066 GGACAATCTATCAGGCACCTGGCTGAAAATTTTCAAAAACAAAAAAGAA-AGAAA
1 GGACAATCTATCAGGCACCTGGCTGAAAATTTTCAAAAACAAAAAAGAACAGAAA
1120 ATGGCGTGGA
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
60 3 0.07
61 43 0.93
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (61 bp):
GGACAATCTATCAGGCACCTGGCTGAAAATTTTCAAAAACAAAAAAGAACAGAAATCCCGT
Found at i:1152 original size:164 final size:166
Alignment explanation
Indices: 881--1331 Score: 852
Period size: 166 Copynumber: 2.7 Consensus size: 166
871 AGCAATCCAG
* *
881 ATACAAGAACTGCAATCCCGTGGACAGTCTATCAGGCACCTGGCTGAAAATTTTTAAAAACAAAA
1 ATACAAGAACTGCAATCCCGTGGACAATCTATCAGGCACCTGGCTGAAAATTTTCAAAAACAAAA
*
946 AAGAAAGAAAATGGCGTGGAGTGTTGCATGACTGACTTATGGCATAGGGTTATTTTCGCGGA-C-
66 AAGAAAGAAAATGGCGTGGAGTGCTGCATGACTGACTTATGGCATAGGGTTATTTTCGCGGATCA
1009 AGTCTATCAGGCACCTGGCTGAAAATTTTCTAACCC
131 AGTCTATCAGGCACCTGGCTGAAAATTTTCTAACCC
1045 ATACAAGAACTGCAATCCCGTGGACAATCTATCAGGCACCTGGCTGAAAATTTTCAAAAACAAAA
1 ATACAAGAACTGCAATCCCGTGGACAATCTATCAGGCACCTGGCTGAAAATTTTCAAAAACAAAA
1110 AAGAAAGAAAATGGCGTGGAGTGCTGCATGACTGACTTATGGCATAGGGTTATTTTCGCGGATCA
66 AAGAAAGAAAATGGCGTGGAGTGCTGCATGACTGACTTATGGCATAGGGTTATTTTCGCGGATCA
*
1175 AGTNTATCAGGCACCTGGCTGAAAATTTTCTAACCC
131 AGTCTATCAGGCACCTGGCTGAAAATTTTCTAACCC
1211 ATACAAGAACTGCAATCCCGTGGACAATCTATCAGGCACCTGGCTGAAAATTTTCAAAAACAAAA
1 ATACAAGAACTGCAATCCCGTGGACAATCTATCAGGCACCTGGCTGAAAATTTTCAAAAACAAAA
1276 AAGAAAGAAAATGGCGTGGAGTGCTGCATGACTGACTTATGGCATAGGGTTATTTT
66 AAGAAAGAAAATGGCGTGGAGTGCTGCATGACTGACTTATGGCATAGGGTTATTTT
1332 TGAGACACCT
Statistics
Matches: 281, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
164 124 0.44
165 1 0.00
166 156 0.56
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.24
Consensus pattern (166 bp):
ATACAAGAACTGCAATCCCGTGGACAATCTATCAGGCACCTGGCTGAAAATTTTCAAAAACAAAA
AAGAAAGAAAATGGCGTGGAGTGCTGCATGACTGACTTATGGCATAGGGTTATTTTCGCGGATCA
AGTCTATCAGGCACCTGGCTGAAAATTTTCTAACCC
Found at i:2036 original size:24 final size:25
Alignment explanation
Indices: 1988--2036 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
1978 ATATAATTTG
1988 GTGACAGCCCTGTTTGCTTCGTTTC
1 GTGACAGCCCTGTTTGCTTCGTTTC
2013 GTGACAGCCCT-TTTGTCTTC-TTTC
1 GTGACAGCCCTGTTTG-CTTCGTTTC
2037 CTCTCCTCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.08, C:0.29, G:0.20, T:0.43
Consensus pattern (25 bp):
GTGACAGCCCTGTTTGCTTCGTTTC
Found at i:4702 original size:13 final size:13
Alignment explanation
Indices: 4684--4708 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4674 TCTGACTAAC
4684 GAAAAAGAAAAAA
1 GAAAAAGAAAAAA
4697 GAAAAAGAAAAA
1 GAAAAAGAAAAA
4709 CAAAGAAACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
GAAAAAGAAAAAA
Found at i:4875 original size:24 final size:24
Alignment explanation
Indices: 4843--4892 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
4833 GCCTGAACTT
4843 AGTTATATTAAAGGCAACCATAAC
1 AGTTATATTAAAGGCAACCATAAC
*
4867 AGTTATATTAAAGGCAACCATGAC
1 AGTTATATTAAAGGCAACCATAAC
4891 AG
1 AG
4893 AACATAACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (24 bp):
AGTTATATTAAAGGCAACCATAAC
Found at i:6504 original size:9 final size:8
Alignment explanation
Indices: 6488--6546 Score: 56
Period size: 7 Copynumber: 7.9 Consensus size: 8
6478 GAAAGGAAAT
6488 TTATTTTA
1 TTATTTTA
6496 TTATATTTA
1 TTAT-TTTA
6505 -T-TTTT-
1 TTATTTTA
**
6510 TTCGTTTA
1 TTATTTTA
6518 TTATTTTA
1 TTATTTTA
6526 TTA-TTTA
1 TTATTTTA
6533 TTA-TTTA
1 TTATTTTA
6540 TTATTTT
1 TTATTTT
6547 CATTTATTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
6 4 0.09
7 18 0.42
8 17 0.40
9 4 0.09
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.75
Consensus pattern (8 bp):
TTATTTTA
Found at i:6524 original size:15 final size:15
Alignment explanation
Indices: 6488--6559 Score: 71
Period size: 14 Copynumber: 5.0 Consensus size: 15
6478 GAAAGGAAAT
*
6488 TTATTTTATTATAT-
1 TTATTTTATTATTTA
* *
6502 TTATTTTTTTCGTTTA
1 TTATTTTATT-ATTTA
6518 TTATTTTATTATTTA
1 TTATTTTATTATTTA
6533 TTA-TTTATTATTT-
1 TTATTTTATTATTTA
*
6546 TCA-TTTATTATTTA
1 TTATTTTATTATTTA
6560 ATTTTTCCTT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
13 12 0.24
14 19 0.39
15 9 0.18
16 9 0.18
ACGTcount: A:0.24, C:0.03, G:0.01, T:0.72
Consensus pattern (15 bp):
TTATTTTATTATTTA
Found at i:6534 original size:7 final size:7
Alignment explanation
Indices: 6514--6559 Score: 67
Period size: 7 Copynumber: 6.6 Consensus size: 7
6504 ATTTTTTTCG
6514 TTTATTA
1 TTTATTA
6521 TTTTATTA
1 -TTTATTA
6529 TTTATTA
1 TTTATTA
6536 TTTATTA
1 TTTATTA
*
6543 TTT-TCA
1 TTTATTA
6549 TTTATTA
1 TTTATTA
6556 TTTA
1 TTTA
6560 ATTTTTCCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
6 5 0.14
7 23 0.66
8 7 0.20
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTATTA
Found at i:13264 original size:2 final size:2
Alignment explanation
Indices: 13257--13288 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
13247 AATTACCTGT
13257 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
13289 TATATATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:16895 original size:11 final size:11
Alignment explanation
Indices: 16879--16903 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16869 CCCTTGTCAC
16879 TTTATTTTATT
1 TTTATTTTATT
16890 TTTATTTTATT
1 TTTATTTTATT
16901 TTT
1 TTT
16904 TGGTATCTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:17075 original size:5 final size:5
Alignment explanation
Indices: 17060--17126 Score: 98
Period size: 5 Copynumber: 12.8 Consensus size: 5
17050 CCAGTCCATA
17060 ATTATT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTATAT
1 ATTA-T ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT A-T-TAT
*
17113 ATTAT ATTAG ATTA
1 ATTAT ATTAT ATTA
17127 ATATATGTAA
Statistics
Matches: 58, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
5 48 0.83
6 6 0.10
7 4 0.07
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (5 bp):
ATTAT
Found at i:17987 original size:12 final size:13
Alignment explanation
Indices: 17963--18037 Score: 64
Period size: 13 Copynumber: 5.8 Consensus size: 13
17953 CAATTCCAAT
17963 AATA-ATAATATA
1 AATATATAATATA
17975 AATATATAA-ATA
1 AATATATAATATA
*
17987 AATATATACTATA
1 AATATATAATATA
* * *
18000 AATAAATATTATT
1 AATATATAATATA
*
18013 ATTATATATATATA
1 AATATATA-ATATA
*
18027 TATACTATAAT
1 AATA-TATAAT
18038 CCGAGACAAG
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
12 15 0.31
13 23 0.47
14 7 0.14
15 4 0.08
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (13 bp):
AATATATAATATA
Found at i:17999 original size:17 final size:17
Alignment explanation
Indices: 17966--18036 Score: 72
Period size: 17 Copynumber: 4.1 Consensus size: 17
17956 TTCCAATAAT
*
17966 AATAATATAAATA-TATA
1 AATAA-ATATATACTATA
17983 AATAAATATATACTATA
1 AATAAATATATACTATA
*
18000 AATAAATATTATTATTATA
1 AATAAATA-TA-TACTATA
* *
18019 TATATATATATACTATA
1 AATAAATATATACTATA
18036 A
1 A
18037 TCCGAGACAA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
16 6 0.13
17 23 0.51
18 4 0.09
19 12 0.27
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
AATAAATATATACTATA
Found at i:18113 original size:3 final size:3
Alignment explanation
Indices: 18100--18145 Score: 74
Period size: 3 Copynumber: 14.7 Consensus size: 3
18090 AAAAATGACA
18100 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AA
18146 GAAAGAAACA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 35 0.85
4 6 0.15
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:23314 original size:72 final size:72
Alignment explanation
Indices: 23197--23341 Score: 263
Period size: 72 Copynumber: 2.0 Consensus size: 72
23187 TTGTTCTTTC
* *
23197 TGGTTCCATGTTTCAACTTTTCTTCATTTTGGAATGAAGATGTTTGCTTTTGCATCTCAATATAT
1 TGGTTCCATGTTTCAACTTTTCTTCATTTTAGAATGAAGATGTTTGCTTTTGCATCTCAAGATAT
23262 AGACTCT
66 AGACTCT
*
23269 TGGTTCCATGTTTCAACTTTTCTTCATTTTAGAATGAAGATGTTTGCTTTTGTATCTCAAGATAT
1 TGGTTCCATGTTTCAACTTTTCTTCATTTTAGAATGAAGATGTTTGCTTTTGCATCTCAAGATAT
23334 AGACTCT
66 AGACTCT
23341 T
1 T
23342 AATTTGTCAA
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.23, C:0.16, G:0.15, T:0.46
Consensus pattern (72 bp):
TGGTTCCATGTTTCAACTTTTCTTCATTTTAGAATGAAGATGTTTGCTTTTGCATCTCAAGATAT
AGACTCT
Found at i:26272 original size:4 final size:4
Alignment explanation
Indices: 26263--26307 Score: 90
Period size: 4 Copynumber: 11.2 Consensus size: 4
26253 AAATTAAGCA
26263 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
26308 CCTCTTTGCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (4 bp):
ATGT
Done.