Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007971.1 Corchorus capsularis cultivar CVL-1 contig07992, 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: 38911
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Found at i:9534 original size:29 final size:28
Alignment explanation
Indices: 9500--9580 Score: 101
Period size: 29 Copynumber: 2.8 Consensus size: 28
9490 ATATAGTACG
9500 TGCATA-TAATAGAATTCCTTTGATTCATA
1 TGCATAGTAATAGAATTCCTTTGATTC--A
*
9529 TGCATAGTTACTAGAAATTCCTTTGATTCA
1 TGCATAG-TAATAG-AATTCCTTTGATTCA
9559 TGCATAGTAACTAGAATTCCTT
1 TGCATAGTAA-TAGAATTCCTT
9581 GTGTGGAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
29 16 0.35
30 11 0.24
31 5 0.11
32 14 0.30
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (28 bp):
TGCATAGTAATAGAATTCCTTTGATTCA
Found at i:9536 original size:40 final size:38
Alignment explanation
Indices: 9433--9574 Score: 105
Period size: 40 Copynumber: 4.0 Consensus size: 38
9423 TGCGTAGTTG
9433 CTAGAATTCCTTTGATTC--ATGCATA-TATACTAGAA
1 CTAGAATTCCTTTGATTCATATGCATAGTATACTAGAA
* ** * *
9468 CTAGAA-TCCCTTGAATTCATATATATAGTACGTGCATATAA
1 CTAGAATTCCTTTG-ATTCATATGCATAGTA--TAC-TAGAA
9509 -TAGAATTCCTTTGATTCATATGCATAGT-TACTAG--
1 CTAGAATTCCTTTGATTCATATGCATAGTATACTAGAA
9543 --A-AATTCCTTTGATTC--ATGCATAGTA-ACTAGAA
1 CTAGAATTCCTTTGATTCATATGCATAGTATACTAGAA
9575 TTCCTTGTGT
Statistics
Matches: 86, Mismatches: 10, Indels: 25
0.71 0.08 0.21
Matches are distributed among these distances:
30 14 0.16
32 14 0.16
33 1 0.01
34 6 0.07
35 10 0.12
36 2 0.02
37 7 0.08
38 2 0.02
40 20 0.23
41 10 0.12
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.37
Consensus pattern (38 bp):
CTAGAATTCCTTTGATTCATATGCATAGTATACTAGAA
Found at i:9564 original size:30 final size:30
Alignment explanation
Indices: 9500--9580 Score: 114
Period size: 30 Copynumber: 2.7 Consensus size: 30
9490 ATATAGTACG
9500 TGCATA-TAA-TAGAATTCCTTTGATTCATA
1 TGCATAGTAACTAGAATTCCTTTGATTCA-A
*
9529 TGCATAGTTACTAGAAATTCCTTTGATTC-A
1 TGCATAGTAACTAG-AATTCCTTTGATTCAA
9559 TGCATAGTAACTAGAATTCCTT
1 TGCATAGTAACTAGAATTCCTT
9581 GTGTGGAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
29 14 0.30
30 16 0.34
31 3 0.06
32 14 0.30
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (30 bp):
TGCATAGTAACTAGAATTCCTTTGATTCAA
Found at i:10166 original size:1 final size:1
Alignment explanation
Indices: 10160--10190 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
10150 TCACCATCAT
10160 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
10191 CTCGTAAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:12653 original size:228 final size:228
Alignment explanation
Indices: 12247--12930 Score: 1037
Period size: 228 Copynumber: 3.0 Consensus size: 228
12237 TCACTGGGCA
* * * *
12247 CCACCACGAAGCCTGAGGACAAGGTGAAGGGTTGACTCCTTTTGGATATTGTAATCCGCCAAGGT
1 CCACCACGGAGCCTGAGGACGAGGTGAAGGGTTGACTCCTTCTGGATGTTGTAATCCGCCAAGGT
*
12312 GCGGCCGTCCTCCAGCTGCTTCCCGGCGAAGATCAATCGCTGCTGGTCAGGAGGGATTCCCTCCT
66 GCGGCCGTCCTCCAGCTGCTTCCCGGCGAAGATCAACCGCTGCTGGTCAGGAGGGATTCCCTCCT
* *
12377 TATCTTGGATCTTGGCCTTGACGTTATCGATTGTGTCTGAGCTCTCCACCTCGAGGGTGATGGTT
131 TATCTTGGATCTTGGCCTTGACGTTATCGATTGTGTCCGAGCTCTCCACCTCTAGGGTGATGGTT
*
12442 TTACCGGTGAGGGTTTTGACGAAGATCTGCATC
196 TTGCCGGTGAGGGTTTTGACGAAGATCTGCATC
* *
12475 CCACCTCGGAGCCTGAGGACGAGGTGAAGGGTTGATTCCTTCTGGATGTTGTAATCCG-CAAGGG
1 CCACCACGGAGCCTGAGGACGAGGTGAAGGGTTGACTCCTTCTGGATGTTGTAATCCGCCAA-GG
* ** * * * * * *
12539 TCCTTCCGTCCTCGAGCTGCTTTCCGGCGAAGATCAACCTCTGCTGGTCCGGTGGAATTCCCTCC
65 TGCGGCCGTCCTCCAGCTGCTTCCCGGCGAAGATCAACCGCTGCTGGTCAGGAGGGATTCCCTCC
* * * * * *
12604 TTATCCTGGATTTTTGCCTTGACGTTGTCGATCGTATCCGAGCTCTCCACCTCTAGGGTGATGGT
130 TTATCTTGGATCTTGGCCTTGACGTTATCGATTGTGTCCGAGCTCTCCACCTCTAGGGTGATGGT
* * *
12669 TTTGCCGGTGAGGGTTTTAACAAAAATCTGCATC
195 TTTGCCGGTGAGGGTTTTGACGAAGATCTGCATC
* *
12703 CCACCGCGGAGCCTGAGGACGAGGTGAAGGGTTGACTCCTTCTGGATGTTGTAATCGGCCAAGGT
1 CCACCACGGAGCCTGAGGACGAGGTGAAGGGTTGACTCCTTCTGGATGTTGTAATCCGCCAAGGT
* *
12768 GCGGCCGTCCTCCAGCTGCTTCCCGGCGAAGATCAACCGCTGCTGGTCGGGAGGGATCCCCTCCT
66 GCGGCCGTCCTCCAGCTGCTTCCCGGCGAAGATCAACCGCTGCTGGTCAGGAGGGATTCCCTCCT
* * *
12833 TATCTTGGAACTTGGCCTTGACGTTATCGATTGTGTCGGAGCTCTCCACCTCTAGGGTGATTGTT
131 TATCTTGGATCTTGGCCTTGACGTTATCGATTGTGTCCGAGCTCTCCACCTCTAGGGTGATGGTT
12898 TTGCCGGTGAGGGTTTTGACGAAGATCTGCATC
196 TTGCCGGTGAGGGTTTTGACGAAGATCTGCATC
12931 TTTCACGAGA
Statistics
Matches: 401, Mismatches: 53, Indels: 4
0.88 0.12 0.01
Matches are distributed among these distances:
227 3 0.01
228 395 0.99
229 3 0.01
ACGTcount: A:0.17, C:0.26, G:0.29, T:0.28
Consensus pattern (228 bp):
CCACCACGGAGCCTGAGGACGAGGTGAAGGGTTGACTCCTTCTGGATGTTGTAATCCGCCAAGGT
GCGGCCGTCCTCCAGCTGCTTCCCGGCGAAGATCAACCGCTGCTGGTCAGGAGGGATTCCCTCCT
TATCTTGGATCTTGGCCTTGACGTTATCGATTGTGTCCGAGCTCTCCACCTCTAGGGTGATGGTT
TTGCCGGTGAGGGTTTTGACGAAGATCTGCATC
Found at i:16913 original size:46 final size:46
Alignment explanation
Indices: 16860--16952 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
16850 AAGACAAGAG
16860 ATAACTGAATTAAAACAACTAAATGGAAATTAACCAGAGTCTGAAT
1 ATAACTGAATTAAAACAACTAAATGGAAATTAACCAGAGTCTGAAT
*
16906 ATAACTGAATTAAAACAACTAAATGGAAATTCACCAGAGTCTGAAT
1 ATAACTGAATTAAAACAACTAAATGGAAATTAACCAGAGTCTGAAT
16952 A
1 A
16953 GAAAAGTGAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.49, C:0.14, G:0.13, T:0.24
Consensus pattern (46 bp):
ATAACTGAATTAAAACAACTAAATGGAAATTAACCAGAGTCTGAAT
Found at i:17849 original size:228 final size:228
Alignment explanation
Indices: 17452--18114 Score: 815
Period size: 228 Copynumber: 2.9 Consensus size: 228
17442 CCTGAGGACA
* * * * * *
17452 AGGTGAAGGGTGGACTCCTTCTGAATGTTATAATCAGCAAGGGTGCGCCCATCCTCCAATTGCTT
1 AGGTGAAGGGTAGACTCCTTCTGGATGTTGTAATCCGCAAGGGTGCGCCCGTCCTCCAACTGCTT
* * * * * *
17517 TCCGGCAAAGATGAGCCTCTGCTGATCGGGAGGAATACCCTCCTTATCCTGGATCTTCGCTTTCA
66 TCCGGCGAAGATCAACCTCTGCTGGTCGGGAGGAATACCCTCCTTATCCTGGATCTTCGCCTTAA
* * * * *
17582 CATTATCAATTGTATCGGAGCTCTCCACCTCAAGGGTGATTGTTTTTCCGGTGAGTGTTTTGACA
131 CGTTATCGATTGTATCCGAGCTCTCCACCTCAAGGGTGATTGTTTTACCGGTGAGGGTTTTGACA
*
17647 AAGATCTGCATCCCTCCGCGGAGCCTCAGCACG
196 AAGATCTGCATCCCACCGCGGAGCCTCAGCACG
* * **
17680 AGGTGAAGGGTAGACTCCTTCTGGATATTGTAATCCGCAAGGGTCCTTCCGTCCTCCAACTGCTT
1 AGGTGAAGGGTAGACTCCTTCTGGATGTTGTAATCCGCAAGGGTGCGCCCGTCCTCCAACTGCTT
* * * * * * *
17745 TCCGGCGAAGATCAACCTCTGCTGGTCCGGTGGAATTCCCTCCTTATCGTGGATTTTTGCCTTGA
66 TCCGGCGAAGATCAACCTCTGCTGGTCGGGAGGAATACCCTCCTTATCCTGGATCTTCGCCTTAA
* * * * * *
17810 CGTTGTCGATCGTATCCGAACTCTCCACCTCTAGGGTGATTGTTTTGCCGGTGAGGGTTTTAACA
131 CGTTATCGATTGTATCCGAGCTCTCCACCTCAAGGGTGATTGTTTTACCGGTGAGGGTTTTGACA
* * *
17875 AAAATCTGCATCCCACCGCGGAGCCTGAGGACG
196 AAGATCTGCATCCCACCGCGGAGCCTCAGCACG
* * * * *
17908 AGGTGAAGGGTTGATTCCTTCTGGATGTTGTAATCCGCCAA-GGTGCGGCCGTCCTCGAGCTGCT
1 AGGTGAAGGGTAGACTCCTTCTGGATGTTGTAATCCG-CAAGGGTGCGCCCGTCCTCCAACTGCT
* * * * * * *
17972 TGCCGGCGAAGATCAATCGCTGCTGGTCGGGAGGGATGCCCTCCTTATCTTGGATCTTGGCCTTA
65 TTCCGGCGAAGATCAACCTCTGCTGGTCGGGAGGAATACCCTCCTTATCCTGGATCTTCGCCTTA
* * * *
18037 ACGTTATCGATTGTGTCTGAGCTTTCCACCTCGAGGGTGATTGTTTTACCGGTGAGGGTTTTGAC
130 ACGTTATCGATTGTATCCGAGCTCTCCACCTCAAGGGTGATTGTTTTACCGGTGAGGGTTTTGAC
*
18102 GAAGATCTGCATC
195 AAAGATCTGCATC
18115 TTTCACGAGA
Statistics
Matches: 368, Mismatches: 66, Indels: 2
0.84 0.15 0.00
Matches are distributed among these distances:
228 365 0.99
229 3 0.01
ACGTcount: A:0.19, C:0.25, G:0.27, T:0.29
Consensus pattern (228 bp):
AGGTGAAGGGTAGACTCCTTCTGGATGTTGTAATCCGCAAGGGTGCGCCCGTCCTCCAACTGCTT
TCCGGCGAAGATCAACCTCTGCTGGTCGGGAGGAATACCCTCCTTATCCTGGATCTTCGCCTTAA
CGTTATCGATTGTATCCGAGCTCTCCACCTCAAGGGTGATTGTTTTACCGGTGAGGGTTTTGACA
AAGATCTGCATCCCACCGCGGAGCCTCAGCACG
Found at i:19768 original size:21 final size:21
Alignment explanation
Indices: 19725--19768 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
19715 TAGGGTTTAG
* *
19725 AAACAATTAATTAAAAGCCTT
1 AAACAATTAATTAAAAACATT
19746 AAAC-ATTAATTAAAAACAATT
1 AAACAATTAATTAAAAAC-ATT
19767 AA
1 AA
19769 GGAAGGGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.59, C:0.11, G:0.02, T:0.27
Consensus pattern (21 bp):
AAACAATTAATTAAAAACATT
Found at i:19953 original size:2 final size:2
Alignment explanation
Indices: 19940--19976 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
19930 AATTAAAATA
19940 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19977 TTTTGTAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29518 original size:1 final size:1
Alignment explanation
Indices: 29512--29544 Score: 57
Period size: 1 Copynumber: 33.0 Consensus size: 1
29502 TAGTTGATTC
*
29512 TTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
29545 GTTTCTTATA
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:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:30610 original size:44 final size:43
Alignment explanation
Indices: 30541--30623 Score: 112
Period size: 44 Copynumber: 1.9 Consensus size: 43
30531 CAGATGTCTT
* *
30541 AATATATAAATGACAAACTATTGTATGGTGAATAAAAATAATA
1 AATATATAAATAACAAACTATTGTATGATGAATAAAAATAATA
* * *
30584 AATATATAAATCAACAAATTGTTGTATGATGAATATAAAT
1 AATATATAAAT-AACAAACTATTGTATGATGAATAAAAAT
30624 GATTTAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
43 11 0.32
44 23 0.68
ACGTcount: A:0.52, C:0.05, G:0.11, T:0.33
Consensus pattern (43 bp):
AATATATAAATAACAAACTATTGTATGATGAATAAAAATAATA
Found at i:31132 original size:41 final size:41
Alignment explanation
Indices: 31074--31182 Score: 182
Period size: 41 Copynumber: 2.7 Consensus size: 41
31064 ACAACTCTTG
* *
31074 CAGAATAAGAAAAATTTGCCTACATTTTCCAAGCAACTAAT
1 CAGAATAACAAACATTTGCCTACATTTTCCAAGCAACTAAT
31115 CAGAATAACAAACATTTGCCTACATTTTCCAAGCAACTAAT
1 CAGAATAACAAACATTTGCCTACATTTTCCAAGCAACTAAT
* *
31156 TAGAGTAACAAACATTTGCCTACATTT
1 CAGAATAACAAACATTTGCCTACATTT
31183 CTTTGCCTAA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 64 1.00
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.28
Consensus pattern (41 bp):
CAGAATAACAAACATTTGCCTACATTTTCCAAGCAACTAAT
Found at i:36967 original size:33 final size:33
Alignment explanation
Indices: 36925--36991 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
36915 CCAAAAGAAA
*
36925 AAAGTTATGAGTATCAACTCAGACTATGACTGG
1 AAAGTTATGAGTATCAACTCAAACTATGACTGG
36958 AAAGTTATGAGTATCAACTCAAACTATGACTGG
1 AAAGTTATGAGTATCAACTCAAACTATGACTGG
36991 A
1 A
36992 TTTAATTTGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (33 bp):
AAAGTTATGAGTATCAACTCAAACTATGACTGG
Done.