Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009862.1 Corchorus capsularis cultivar CVL-1 contig09883, 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: 24439
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Found at i:2661 original size:24 final size:26
Alignment explanation
Indices: 2605--2654 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
2595 GTAAAGTATT
*
2605 AAATTAAAACAACATATTACTCAAAAA
1 AAATTAAAACAACATAATACT-AAAAA
2632 AAATTAAAACAACATAATA-TAAA
1 AAATTAAAACAACATAATACTAAA
2655 CAAATTAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 3 0.14
26 1 0.05
27 18 0.82
ACGTcount: A:0.66, C:0.12, G:0.00, T:0.22
Consensus pattern (26 bp):
AAATTAAAACAACATAATACTAAAAA
Found at i:3454 original size:169 final size:164
Alignment explanation
Indices: 3162--3473 Score: 464
Period size: 169 Copynumber: 1.9 Consensus size: 164
3152 ATTGACTTAG
* *
3162 GACTAACTTGGTTCATCTATTTATTTAGCATGTTGAATCAATTTATTTTTCTAACATAATTACTA
1 GACTAACTTGATTCATCTATTTATTTAGCATGTTCAATCAATTTATTTTTCTAACATAATTACTA
** *
3227 ATTGATTCATTTATTTGGCAAAATGTAATAATCACCAATCAGTTATAACTTTGATTGACAAAGTT
66 ATTGATTCATTTATTTGGCAAAATCAAATAATCACCAATCAATTATAACTTTGATTGACAAAGTT
3292 AATTAACGACTAATTTTTTTGGAAATTAATTAAC
131 AATTAACGACTAATTTTTTTGGAAATTAATTAAC
* * *
3326 GACTAATTTGATTCA-CTAATTTATTTAGTATGTTCAATCAATCTATTTTTTTGCTAACATAATT
1 GACTAACTTGATTCATCT-ATTTATTTAGCATGTTCAATCAAT-T-TATTTTT-CTAACATAATT
* *
3390 ACTAATTGATTCATTTATTTATGGCAAATTCAAATAATCATCAATCAATTATAACTTTGATTGAC
62 ACTAATTGATTCATTTA-TT-TGGCAAAATCAAATAATCACCAATCAATTATAACTTTGATTGAC
*
3455 AAAGTTGATTAACGACTAA
125 AAAGTTAATTAACGACTAA
3474 CTTGATCAAT
Statistics
Matches: 131, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
163 2 0.02
164 35 0.27
165 1 0.01
166 6 0.05
167 28 0.21
168 2 0.02
169 57 0.44
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (164 bp):
GACTAACTTGATTCATCTATTTATTTAGCATGTTCAATCAATTTATTTTTCTAACATAATTACTA
ATTGATTCATTTATTTGGCAAAATCAAATAATCACCAATCAATTATAACTTTGATTGACAAAGTT
AATTAACGACTAATTTTTTTGGAAATTAATTAAC
Found at i:5008 original size:30 final size:30
Alignment explanation
Indices: 4974--5032 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
4964 TCAACTAATT
*
4974 AATCAATCAAAAGTAATTAATATATTTCCC
1 AATCAACCAAAAGTAATTAATATATTTCCC
* *
5004 AATCAACCTAAAGTAATTAATTTATTTCC
1 AATCAACCAAAAGTAATTAATATATTTCC
5033 TTTTGTCCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.44, C:0.17, G:0.03, T:0.36
Consensus pattern (30 bp):
AATCAACCAAAAGTAATTAATATATTTCCC
Found at i:5064 original size:2 final size:2
Alignment explanation
Indices: 5057--5082 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5047 CTTAGTTTTA
5057 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
5083 GATTTCTGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5953 original size:30 final size:31
Alignment explanation
Indices: 5895--5962 Score: 88
Period size: 30 Copynumber: 2.2 Consensus size: 31
5885 TATGTTTTTC
5895 TATGTTTTTCTTTTGAGACAAAATAATCCCT
1 TATGTTTTTCTTTTGAGACAAAATAATCCCT
5926 TATGTTTTT-TGTTTG-GAC-AAATAAATCCCT
1 TATGTTTTTCT-TTTGAGACAAAAT-AATCCCT
*
5956 TAAGTTT
1 TATGTTT
5963 GAAATATGAG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
29 4 0.12
30 17 0.50
31 13 0.38
ACGTcount: A:0.28, C:0.13, G:0.12, T:0.47
Consensus pattern (31 bp):
TATGTTTTTCTTTTGAGACAAAATAATCCCT
Found at i:6191 original size:20 final size:18
Alignment explanation
Indices: 6148--6183 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
6138 GTTAAACTTT
* *
6148 TGTTAAACATTTTATACA
1 TGTTAAAAAGTTTATACA
6166 TGTTAAAAAGTTTATACA
1 TGTTAAAAAGTTTATACA
6184 AATGTTAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (18 bp):
TGTTAAAAAGTTTATACA
Found at i:6386 original size:50 final size:51
Alignment explanation
Indices: 6332--6431 Score: 148
Period size: 50 Copynumber: 2.0 Consensus size: 51
6322 TTAGCTGCAA
6332 AAGGGATGAAAGTCAAAAATAGATCAGAACTGAAGAAA-GTTTAAGCAAAT
1 AAGGGATGAAAGTCAAAAATAGATCAGAACTGAAGAAATGTTTAAGCAAAT
* * ** *
6382 AAGGGATGAAAGTCAGAAATATATCAGATTTGAAGAAATGTTTAATCAAA
1 AAGGGATGAAAGTCAAAAATAGATCAGAACTGAAGAAATGTTTAAGCAAA
6432 CAGTGAGAGA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
50 34 0.77
51 10 0.23
ACGTcount: A:0.50, C:0.07, G:0.21, T:0.22
Consensus pattern (51 bp):
AAGGGATGAAAGTCAAAAATAGATCAGAACTGAAGAAATGTTTAAGCAAAT
Found at i:6550 original size:10 final size:11
Alignment explanation
Indices: 6535--6602 Score: 79
Period size: 12 Copynumber: 6.2 Consensus size: 11
6525 CTTTCTTCCT
6535 TCTCTTTT-TC
1 TCTCTTTTCTC
6545 TCTCTTTTCTC
1 TCTCTTTTCTC
6556 T-TCTTTTCTTC
1 TCTCTTTTC-TC
*
6567 TCTCTTCTCTCC
1 TCTCTTTTCT-C
6579 TCTCTTTTCTGC
1 TCTCTTTTCT-C
6591 TCT-TTTTCTC
1 TCTCTTTTCTC
6601 TC
1 TC
6603 CCTCGTCGAC
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
10 18 0.35
11 13 0.25
12 20 0.39
ACGTcount: A:0.00, C:0.35, G:0.01, T:0.63
Consensus pattern (11 bp):
TCTCTTTTCTC
Found at i:6555 original size:7 final size:7
Alignment explanation
Indices: 6542--6594 Score: 52
Period size: 7 Copynumber: 7.3 Consensus size: 7
6532 CCTTCTCTTT
6542 TTCTCTC
1 TTCTCTC
*
6549 TTTTCTC
1 TTCTCTC
*
6556 TTCTTTTC
1 TTC-TCTC
6564 TTCTCTC
1 TTCTCTC
6571 TTCTCTC
1 TTCTCTC
* *
6578 CTCTCTT
1 TTCTCTC
6585 TTCTGCTC
1 TTCT-CTC
6593 TT
1 TT
6595 TTTCTCTCCC
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
7 26 0.72
8 10 0.28
ACGTcount: A:0.00, C:0.36, G:0.02, T:0.62
Consensus pattern (7 bp):
TTCTCTC
Found at i:6567 original size:22 final size:22
Alignment explanation
Indices: 6533--6601 Score: 79
Period size: 22 Copynumber: 3.1 Consensus size: 22
6523 TTCTTTCTTC
6533 CTTCTCTTT-TTCTCTCTTTTCT
1 CTTCT-TTTCTTCTCTCTTTTCT
*
6555 CTTCTTTTCTTCTCTCTTCTCT
1 CTTCTTTTCTTCTCTCTTTTCT
*
6577 CCTCTCTTTTCTGCTCT-TTTTCT
1 -CT-TCTTTTCTTCTCTCTTTTCT
6600 CT
1 CT
6602 CCCTCGTCGA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
21 3 0.07
22 19 0.46
23 7 0.17
24 12 0.29
ACGTcount: A:0.00, C:0.35, G:0.01, T:0.64
Consensus pattern (22 bp):
CTTCTTTTCTTCTCTCTTTTCT
Found at i:8209 original size:2 final size:2
Alignment explanation
Indices: 8170--8195 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8160 ATTACACTTC
8170 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
8196 GATTCTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9471 original size:26 final size:26
Alignment explanation
Indices: 9442--9491 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
9432 GTTATTATAT
9442 TGTTAGGATTATTAGGATTGAGATTC
1 TGTTAGGATTATTAGGATTGAGATTC
9468 TGTTAGGATTATTAGGATTGAGAT
1 TGTTAGGATTATTAGGATTGAGAT
9492 GCTTTTGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.28, C:0.02, G:0.28, T:0.42
Consensus pattern (26 bp):
TGTTAGGATTATTAGGATTGAGATTC
Found at i:10237 original size:20 final size:20
Alignment explanation
Indices: 10212--10250 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
10202 CCTCAAACGC
10212 TGAACATACGAAATCAATGT
1 TGAACATACGAAATCAATGT
*
10232 TGAACATACGACATCAATG
1 TGAACATACGAAATCAATG
10251 CTGCAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.18, G:0.15, T:0.23
Consensus pattern (20 bp):
TGAACATACGAAATCAATGT
Found at i:17168 original size:15 final size:15
Alignment explanation
Indices: 17148--17186 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
17138 GAACAATCAA
*
17148 ATCAACCACCCCCAG
1 ATCAACCACCACCAG
17163 ATCAACCACCACCAG
1 ATCAACCACCACCAG
*
17178 AACAACCAC
1 ATCAACCAC
17187 TAAATCAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.41, C:0.49, G:0.05, T:0.05
Consensus pattern (15 bp):
ATCAACCACCACCAG
Found at i:17211 original size:18 final size:18
Alignment explanation
Indices: 17188--17224 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
17178 AACAACCACT
17188 AAATCAACCCCCAAACCA
1 AAATCAACCCCCAAACCA
*
17206 AAATCAACCTCCAAACCA
1 AAATCAACCCCCAAACCA
17224 A
1 A
17225 CCTGTAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.41, G:0.00, T:0.08
Consensus pattern (18 bp):
AAATCAACCCCCAAACCA
Done.