Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012057.1 Corchorus capsularis cultivar CVL-1 contig12078, 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: 16631
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5089 original size:41 final size:41
Alignment explanation
Indices: 5032--5246 Score: 241
Period size: 41 Copynumber: 5.2 Consensus size: 41
5022 AATGACCTAG
* * *
5032 TCTTCAATTGACAATTTAATTCAAGGTTCTTGACGACTTGA
1 TCTTGAATTGATAATTTAATTCAAGGGTCTTGACGACTTGA
* *
5073 CCTTGAATTGATAATTTAATTCAAGGGTCTTGACGATTTGA
1 TCTTGAATTGATAATTTAATTCAAGGGTCTTGACGACTTGA
** * * *
5114 TCTTGAATTGAAAATAATTCGATTCAAGGGTCTCGATGACTTGT
1 TCTTGAATTG---ATAATTTAATTCAAGGGTCTTGACGACTTGA
* * **
5158 TCTTGAATTGATAATTTAGTTCAAGGGTCTTGATGACTCAA
1 TCTTGAATTGATAATTTAATTCAAGGGTCTTGACGACTTGA
* * **
5199 TCTTGAATTGATAATTTAATTCAAGGGTCTCGATGACTCAA
1 TCTTGAATTGATAATTTAATTCAAGGGTCTTGACGACTTGA
5240 TCTTGAA
1 TCTTGAA
5247 CAAACGAAAA
Statistics
Matches: 150, Mismatches: 21, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
41 115 0.77
44 35 0.23
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (41 bp):
TCTTGAATTGATAATTTAATTCAAGGGTCTTGACGACTTGA
Found at i:5155 original size:85 final size:82
Alignment explanation
Indices: 5032--5236 Score: 248
Period size: 85 Copynumber: 2.5 Consensus size: 82
5022 AATGACCTAG
* * * * * *
5032 TCTTCAATTGACAATTTAATTCAAGGTTCTTGACGACTTGACCTTGAATTGATAATTTAATTCAA
1 TCTTGAATTGATAATTCAATTCAAGGGTCTCGATGACTTGACCTTGAATTGATAATTTAATTCAA
* **
5097 GGGTCTTGACGATTTGA
66 GGGTCTTGACGACTCAA
* ** *
5114 TCTTGAATTGAAAATAATTCGATTCAAGGGTCTCGATGACTTGTTCTTGAATTGATAATTTAGTT
1 TCTTGAATTG---ATAATTCAATTCAAGGGTCTCGATGACTTGACCTTGAATTGATAATTTAATT
*
5179 CAAGGGTCTTGATGACTCAA
63 CAAGGGTCTTGACGACTCAA
*
5199 TCTTGAATTGATAATTTAATTCAAGGGTCTCGATGACT
1 TCTTGAATTGATAATTCAATTCAAGGGTCTCGATGACT
5237 CAATCTTGAA
Statistics
Matches: 104, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
82 35 0.34
85 69 0.66
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.39
Consensus pattern (82 bp):
TCTTGAATTGATAATTCAATTCAAGGGTCTCGATGACTTGACCTTGAATTGATAATTTAATTCAA
GGGTCTTGACGACTCAA
Found at i:5363 original size:16 final size:16
Alignment explanation
Indices: 5342--5376 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
5332 TCTGAAAATA
5342 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
5358 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
5374 CTT
1 CTT
5377 TCTGAATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (16 bp):
CTTCAGAGCTTTTCTG
Found at i:7525 original size:19 final size:18
Alignment explanation
Indices: 7493--7530 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
7483 TTGAATTAAT
*
7493 TCTTCAATTGTCTTCAAA
1 TCTTCAATTATCTTCAAA
7511 TCTTCAAATTATCTTCAAA
1 TCTTC-AATTATCTTCAAA
7530 T
1 T
7531 AATCTTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.32, C:0.21, G:0.03, T:0.45
Consensus pattern (18 bp):
TCTTCAATTATCTTCAAA
Found at i:7526 original size:11 final size:11
Alignment explanation
Indices: 7509--7540 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
7499 ATTGTCTTCA
7509 AATCTTCAAAT
1 AATCTTCAAAT
*
7520 TATCTTCAAAT
1 AATCTTCAAAT
7531 AATCTTCAAA
1 AATCTTCAAA
7541 CACGAAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (11 bp):
AATCTTCAAAT
Found at i:10482 original size:15 final size:15
Alignment explanation
Indices: 10462--10500 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
10452 TGCAAGTTGT
*
10462 TCATCTTCTTGTGCC
1 TCATCTTCTAGTGCC
*
10477 TCATCTTCTAGTGGC
1 TCATCTTCTAGTGCC
10492 TCATCTTCT
1 TCATCTTCT
10501 GGCTTAGCAA
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:0.10, C:0.31, G:0.13, T:0.46
Consensus pattern (15 bp):
TCATCTTCTAGTGCC
Found at i:11955 original size:6 final size:6
Alignment explanation
Indices: 11939--11969 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
11929 CAAAACAAAA
11939 TAAAT- TAAATC TAAATC TAAATC TAAATC TA
1 TAAATC TAAATC TAAATC TAAATC TAAATC TA
11970 TAGCAATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATC
Found at i:13346 original size:19 final size:18
Alignment explanation
Indices: 13314--13351 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
13304 TTGAATTAAT
*
13314 TCTTCAATTGTCTTCAAA
1 TCTTCAATTATCTTCAAA
13332 TCTTCAAATTATCTTCAAA
1 TCTTC-AATTATCTTCAAA
13351 T
1 T
13352 AATCTTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.32, C:0.21, G:0.03, T:0.45
Consensus pattern (18 bp):
TCTTCAATTATCTTCAAA
Found at i:13347 original size:11 final size:11
Alignment explanation
Indices: 13330--13361 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
13320 ATTGTCTTCA
13330 AATCTTCAAAT
1 AATCTTCAAAT
*
13341 TATCTTCAAAT
1 AATCTTCAAAT
13352 AATCTTCAAA
1 AATCTTCAAA
13362 CACGAACTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (11 bp):
AATCTTCAAAT
Found at i:13539 original size:21 final size:21
Alignment explanation
Indices: 13513--13566 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
13503 AGCAAAATAG
13513 AGTAAAAACA-CATATAAAAAT
1 AGTAAAAA-ATCATATAAAAAT
*
13534 AGTAAAAAATTATATAAAAAT
1 AGTAAAAAATCATATAAAAAT
13555 AGCTATAAAAAT
1 AG-TA-AAAAAT
13567 ATGCATAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 1 0.03
21 20 0.69
22 2 0.07
23 6 0.21
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (21 bp):
AGTAAAAAATCATATAAAAAT
Found at i:13561 original size:12 final size:11
Alignment explanation
Indices: 13525--13567 Score: 54
Period size: 12 Copynumber: 3.9 Consensus size: 11
13515 TAAAAACACA
13525 TATAAAAATAG
1 TATAAAAATAG
13536 TA-AAAAATTA-
1 TATAAAAA-TAG
13546 TATAAAAATAG
1 TATAAAAATAG
13557 CTATAAAAATA
1 -TATAAAAATA
13568 TGCATAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
10 9 0.32
11 9 0.32
12 10 0.36
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (11 bp):
TATAAAAATAG
Done.