Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012380.1 Corchorus capsularis cultivar CVL-1 contig12401, 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: 43246
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:6450 original size:134 final size:134
Alignment explanation
Indices: 6279--6551 Score: 537
Period size: 134 Copynumber: 2.0 Consensus size: 134
6269 TTAATAGTAC
6279 TAGCTCGTAAAAGCTTAGATAAGGAAAGTGGATTTGTATTAGCAAAGAAAGGTGAGGGTGAAGAA
1 TAGCTCGTAAAAGCTTAGATAAGGAAAGTGGATTTGTATTAGCAAAGAAAGGTGAGGGTGAAGAA
6344 ATGGGGAATCGTCCCATCACAAAAAGACACAGAGAAACTAAGAGAGTAAATGAAAAGCTGAAAGC
66 ATGGGGAATCGTCCCATCACAAAAAGACACAGAGAAACTAAGAGAGTAAATGAAAAGCTGAAAGC
6409 TCTT
131 TCTT
6413 TAGCTCGTAAAAGCTTAGATAAGGAAAGTGGATTTGTATTAGCAAAGAAAGGTGAGGGTGAAGAA
1 TAGCTCGTAAAAGCTTAGATAAGGAAAGTGGATTTGTATTAGCAAAGAAAGGTGAGGGTGAAGAA
*
6478 ATGGGGAATCGTCCCATCACAAAAAGATACAGAGAAACTAAGAGAGTAAATGAAAAGCTGAAAGC
66 ATGGGGAATCGTCCCATCACAAAAAGACACAGAGAAACTAAGAGAGTAAATGAAAAGCTGAAAGC
6543 TCTT
131 TCTT
6547 TAGCT
1 TAGCT
6552 AATGGCATTA
Statistics
Matches: 138, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
134 138 1.00
ACGTcount: A:0.42, C:0.12, G:0.26, T:0.20
Consensus pattern (134 bp):
TAGCTCGTAAAAGCTTAGATAAGGAAAGTGGATTTGTATTAGCAAAGAAAGGTGAGGGTGAAGAA
ATGGGGAATCGTCCCATCACAAAAAGACACAGAGAAACTAAGAGAGTAAATGAAAAGCTGAAAGC
TCTT
Found at i:6603 original size:122 final size:128
Alignment explanation
Indices: 6326--6605 Score: 367
Period size: 134 Copynumber: 2.2 Consensus size: 128
6316 ATTAGCAAAG
6326 AAAGGTGAGGGTGAAGAAATGGGGAATCGTCCCATCACAAAAAGACACAGAGAAACTAAGAGAGT
1 AAAGGTGAGGGTGAAGAAATGGGGAATCGTCCCATCACAAAAAGACACAGAGAAACTAAGAGAGT
* * * * *
6391 AAATGAAAAGCTGAAAGCTCTTTAGCTCGTAAAAGCTTAGATAAGGAAAGTGGATTTGTATTAGC
66 AAATGAAAAGCTGAAAGCTCTTTAGC-CGTAAAAGCTTAGAGAAGGAAAGT-G-CTCGCAATAGC
6456 AAA
128 --A
*
6459 GAAAGGTGAGGGTGAAGAAATGGGGAATCGTCCCATCACAAAAAGATACAGAGAAACTAAGAGAG
1 -AAAGGTGAGGGTGAAGAAATGGGGAATCGTCCCATCACAAAAAGACACAGAGAAACTAAGAGAG
**
6524 TAAATGAAAAGCTGAAAGCTCTTTAG-C-TAATGGCATTA-AGAAGGAAAGT-CTCGCAATA-C-
65 TAAATGAAAAGCTGAAAGCTCTTTAGCCGTAAAAGC-TTAGAGAAGGAAAGTGCTCGCAATAGCA
*
6583 AAAGG-GAGGGTGAAGGAATGGGG
1 AAAGGTGAGGGTGAAGAAATGGGG
6606 TTTTGTCTGT
Statistics
Matches: 136, Mismatches: 9, Indels: 14
0.86 0.06 0.09
Matches are distributed among these distances:
122 17 0.12
123 5 0.04
127 1 0.01
128 5 0.04
131 15 0.11
132 4 0.03
134 89 0.65
ACGTcount: A:0.42, C:0.12, G:0.28, T:0.18
Consensus pattern (128 bp):
AAAGGTGAGGGTGAAGAAATGGGGAATCGTCCCATCACAAAAAGACACAGAGAAACTAAGAGAGT
AAATGAAAAGCTGAAAGCTCTTTAGCCGTAAAAGCTTAGAGAAGGAAAGTGCTCGCAATAGCA
Found at i:7516 original size:217 final size:217
Alignment explanation
Indices: 7131--7575 Score: 691
Period size: 217 Copynumber: 2.0 Consensus size: 217
7121 CGGTCTCTTT
7131 TCAAGAAAAGGAAATTCGCTTAAACTATTTTCCTTCAATTGTCGATCACTAAGGTCCAAAAAATG
1 TCAAGAAAAGGAAATTCGCTTAAACTATTTTCCTTCAATTGTCGATCACTAAGGTCCAAAAAATG
* *
7196 CCCTGAAGTCCCTAAAATGCCCTCGACTATCAATTGAAATAAAAAAAAAAACAAGCACAAAAGTA
66 CCC---AG---C-AAAATACCCTCGACCATCAATTGAAAT---AAAAAAAACAAGCACAAAAGTA
*
7261 CCAAAATACCCATGACAATTTATTTTTAGGTGAATGTGGTGCAAGATAATATTTGGTTTTTCGGA
121 CCAAAATACCCATGACAATTTATTCTTAGGTGAATGTGGTGCAAGATAATATTTGGTTTTTCGGA
*
7326 CTTTTAACATCAAACTTTAGGAGATGTTTAAA
186 CTTTTAACATCAAACTTTAAGAGATGTTTAAA
7358 TCAAGAAAAGGAAATTCGCTTAAACTATTTTCCTTCAATTGTCCTCTGATCACTAAGGTCCAAAA
1 TCAAGAAAAGGAAATTCGCTTAAACTATTTTCCTTCAATTG---TC-GATCACTAAGGTCCAAAA
7423 AATGCCC-G-AAAATACCCTCGACCATCAATTGAAAT-AAAAAAA-AAGCACAAAAGTACCAAAA
62 AATGCCCAGCAAAATACCCTCGACCATCAATTGAAATAAAAAAAACAAGCACAAAAGTACCAAAA
*
7484 TACCCATGACAATTTATTCTTAGGTGAATGTGGTGCAAGATAATGTTTGGTTTTTCGGACTTTTA
127 TACCCATGACAATTTATTCTTAGGTGAATGTGGTGCAAGATAATATTTGGTTTTTCGGACTTTTA
7549 ACATCAAACTTTAAGAGATGTTTAAA
192 ACATCAAACTTTAAGAGATGTTTAAA
7575 T
1 T
7576 ATATTTCATG
Statistics
Matches: 209, Mismatches: 5, Indels: 18
0.90 0.02 0.08
Matches are distributed among these distances:
217 108 0.52
218 7 0.03
222 25 0.12
227 42 0.20
230 2 0.01
231 25 0.12
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (217 bp):
TCAAGAAAAGGAAATTCGCTTAAACTATTTTCCTTCAATTGTCGATCACTAAGGTCCAAAAAATG
CCCAGCAAAATACCCTCGACCATCAATTGAAATAAAAAAAACAAGCACAAAAGTACCAAAATACC
CATGACAATTTATTCTTAGGTGAATGTGGTGCAAGATAATATTTGGTTTTTCGGACTTTTAACAT
CAAACTTTAAGAGATGTTTAAA
Found at i:19664 original size:2 final size:2
Alignment explanation
Indices: 19657--19685 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19647 TTTCGATAAT
19657 TA 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 TA T
19686 GGTCCCTTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30067 original size:30 final size:31
Alignment explanation
Indices: 29983--30070 Score: 115
Period size: 30 Copynumber: 2.9 Consensus size: 31
29973 CGTGTTCCAA
* *
29983 AAAAAGTGATATGTGGCACGCCACATGTACC
1 AAAAAGTGACACGTGGCACGCCACATGTACC
* * *
30014 AAAAAGTGACACATGTCACGCCACGTGTA-C
1 AAAAAGTGACACGTGGCACGCCACATGTACC
*
30044 AAAAAGTGACACGTGGCATGCCACATG
1 AAAAAGTGACACGTGGCACGCCACATG
30071 ACATGCCACA
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
30 24 0.50
31 24 0.50
ACGTcount: A:0.36, C:0.24, G:0.23, T:0.17
Consensus pattern (31 bp):
AAAAAGTGACACGTGGCACGCCACATGTACC
Found at i:33802 original size:16 final size:16
Alignment explanation
Indices: 33781--33813 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
33771 GTAAGTTCAT
33781 ATAGCGTGTTTCATTG
1 ATAGCGTGTTTCATTG
33797 ATAGCGTGTTTCATTG
1 ATAGCGTGTTTCATTG
33813 A
1 A
33814 CTCTGGATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.12, G:0.24, T:0.42
Consensus pattern (16 bp):
ATAGCGTGTTTCATTG
Found at i:36975 original size:16 final size:16
Alignment explanation
Indices: 36954--36988 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
36944 AATCCATTAG
36954 GTGCTTTCCG-AGGAGA
1 GTGCTTT-CGAAGGAGA
36970 GTGCTTTCGAAGGAGA
1 GTGCTTTCGAAGGAGA
36986 GTG
1 GTG
36989 ATTCCCAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 2 0.11
16 16 0.89
ACGTcount: A:0.20, C:0.14, G:0.40, T:0.26
Consensus pattern (16 bp):
GTGCTTTCGAAGGAGA
Found at i:40831 original size:21 final size:20
Alignment explanation
Indices: 40787--40831 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
40777 GTGTCAATTG
**
40787 CCATGTCATCACATAACGTT
1 CCATGTCATCACATAACGCC
*
40807 CCATGTCATCACTTTAACGCC
1 CCATGTCATCAC-ATAACGCC
40828 CCAT
1 CCAT
40832 TTAACAGAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.27, C:0.36, G:0.09, T:0.29
Consensus pattern (20 bp):
CCATGTCATCACATAACGCC
Done.