Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009474.1 Corchorus capsularis cultivar CVL-1 contig09495, 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: 62280
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:1389 original size:2 final size:2
Alignment explanation
Indices: 1335--1374 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
1325 TATGGGAGTA
1335 AT AT AT AT AT AT AT AT AT AT AT A- AT -T AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1374 A
1 A
1375 ATGGAGTACA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 32 0.91
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1712 original size:31 final size:31
Alignment explanation
Indices: 1677--1745 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
1667 AAGTTTAAGA
* **
1677 GGCAAAATGTCCAAACCGTACAAGTTCAGGG
1 GGCAAAACGTCCAAACCGTACAAGTTCAAAG
*
1708 GGCAAAACGTCCAAACTGTACAAGTTCAAAG
1 GGCAAAACGTCCAAACCGTACAAGTTCAAAG
1739 GGCAAAA
1 GGCAAAA
1746 AGAGGGCATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.41, C:0.22, G:0.23, T:0.14
Consensus pattern (31 bp):
GGCAAAACGTCCAAACCGTACAAGTTCAAAG
Found at i:3172 original size:3 final size:3
Alignment explanation
Indices: 3164--3198 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3154 TTTATTCATA
3164 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3199 ATATATGTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:4742 original size:14 final size:14
Alignment explanation
Indices: 4723--4750 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4713 GCAGCTAAAA
4723 GCAAGTCATATTGT
1 GCAAGTCATATTGT
4737 GCAAGTCATATTGT
1 GCAAGTCATATTGT
4751 TAGTTAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (14 bp):
GCAAGTCATATTGT
Found at i:5465 original size:12 final size:13
Alignment explanation
Indices: 5425--5458 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
5415 TATAGTATAG
5425 ATTATTATTTAAT
1 ATTATTATTTAAT
*
5438 -TTATTATTTATT
1 ATTATTATTTAAT
5450 ATTATTATT
1 ATTATTATT
5459 ACTATTACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
ATTATTATTTAAT
Found at i:6174 original size:6 final size:6
Alignment explanation
Indices: 6163--6189 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
6153 AAAAAATGAT
6163 ATTTTA ATTTTA ATTTTA ATTTTA ATT
1 ATTTTA ATTTTA ATTTTA ATTTTA ATT
6190 AATTTATTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
ATTTTA
Found at i:6612 original size:50 final size:51
Alignment explanation
Indices: 6543--6639 Score: 142
Period size: 52 Copynumber: 1.9 Consensus size: 51
6533 TTTGATTTGA
*
6543 TTTGATTTGATTCAAGGGTC-AAATGACTTGATCTTGAATTGATGAGTGAG
1 TTTGATTTGATTCAAGGGTCTAAATGACTTGATCTCGAATTGATGAGTGAG
* **
6593 TTTGATTTGATTCGAGGGTCTTTGATGACTTGATCTCGAATTGATGA
1 TTTGATTTGATTCAAGGGTC-TAAATGACTTGATCTCGAATTGATGA
6640 TAATTTGACT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
50 19 0.46
52 22 0.54
ACGTcount: A:0.25, C:0.09, G:0.26, T:0.40
Consensus pattern (51 bp):
TTTGATTTGATTCAAGGGTCTAAATGACTTGATCTCGAATTGATGAGTGAG
Found at i:6647 original size:50 final size:50
Alignment explanation
Indices: 6542--6647 Score: 135
Period size: 50 Copynumber: 2.1 Consensus size: 50
6532 GTTTGATTTG
*
6542 ATTTGATTTGATTCAAGGGTCAAATGACTTGATCTTGAATTGATGAGTGA
1 ATTTGATTTGATTCAAGGGTCAAATGACTTGATCTCGAATTGATGAGTGA
* * **
6592 GTTTGATTTGATTCGAGGGTCTTTGATGACTTGATCTCGAATTGATGA-T-A
1 ATTTGATTTGATTCAAGGGTC--AAATGACTTGATCTCGAATTGATGAGTGA
6642 ATTTGA
1 ATTTGA
6648 CTCAAGGGTC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
50 25 0.52
51 1 0.02
52 22 0.46
ACGTcount: A:0.26, C:0.08, G:0.25, T:0.41
Consensus pattern (50 bp):
ATTTGATTTGATTCAAGGGTCAAATGACTTGATCTCGAATTGATGAGTGA
Found at i:7690 original size:13 final size:12
Alignment explanation
Indices: 7667--7709 Score: 77
Period size: 12 Copynumber: 3.5 Consensus size: 12
7657 TTAATACAGG
7667 TATCGACGGATA
1 TATCGACGGATA
7679 TATCGAACGGATA
1 TATCG-ACGGATA
7692 TATCGACGGATA
1 TATCGACGGATA
7704 TATCGA
1 TATCGA
7710 GGTATCGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 18 0.60
13 12 0.40
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:9362 original size:21 final size:21
Alignment explanation
Indices: 9338--9379 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
9328 GTCTATCTCA
9338 TAATTTCTCCCTTTGAACATC
1 TAATTTCTCCCTTTGAACATC
9359 TAATTTCTCCCTTTGAACATC
1 TAATTTCTCCCTTTGAACATC
9380 GTATCGTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.29, G:0.05, T:0.43
Consensus pattern (21 bp):
TAATTTCTCCCTTTGAACATC
Found at i:9398 original size:2 final size:2
Alignment explanation
Indices: 9386--9414 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
9376 CATCGTATCG
9386 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9415 CTTTCTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15656 original size:7 final size:7
Alignment explanation
Indices: 15634--15672 Score: 60
Period size: 7 Copynumber: 5.4 Consensus size: 7
15624 AAATATGTTG
15634 TATTATTA
1 TATTA-TA
*
15642 TATAATA
1 TATTATA
15649 TATTATA
1 TATTATA
15656 TATTATA
1 TATTATA
15663 TATTATA
1 TATTATA
15670 TAT
1 TAT
15673 ATAGACTGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
7 25 0.86
8 4 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TATTATA
Found at i:33975 original size:17 final size:16
Alignment explanation
Indices: 33935--33983 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
33925 CATGTAATCT
*
33935 TTGATCACCGGTGATC
1 TTGATCACTGGTGATC
33951 TTGCATCACTGGTGATC
1 TTG-ATCACTGGTGATC
*
33968 TTAGATCACTAGTGAT
1 TT-GATCACTGGTGAT
33984 TTGGGGGGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 3 0.10
17 25 0.86
18 1 0.03
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:35040 original size:3 final size:3
Alignment explanation
Indices: 35032--35086 Score: 56
Period size: 3 Copynumber: 17.3 Consensus size: 3
35022 GATTTCTATG
* * *
35032 TTA TTA TTA TTG TTA TTA TTA TTA TTA TATA TATA CGTA TTA TTA TCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA T-TA -TTA TTA TTA TTA
35080 TTA TTA T
1 TTA TTA T
35087 ATATCTACTA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
3 36 0.82
4 8 0.18
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:35311 original size:34 final size:34
Alignment explanation
Indices: 35241--35309 Score: 106
Period size: 32 Copynumber: 2.1 Consensus size: 34
35231 GGAAAATAAG
*
35241 TATTTCAATTTTGGGGAGAAATCATTATTATATA
1 TATTTCAATTTTGGGCAGAAATCATTATTATATA
*
35275 TATTTCAA-TTTGGGCA-ATATCATTATTATATA
1 TATTTCAATTTTGGGCAGAAATCATTATTATATA
35307 TAT
1 TAT
35310 ATATATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 18 0.55
33 7 0.21
34 8 0.24
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.46
Consensus pattern (34 bp):
TATTTCAATTTTGGGCAGAAATCATTATTATATA
Found at i:37023 original size:15 final size:17
Alignment explanation
Indices: 37003--37039 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
36993 TGTGAGTTTA
37003 GTTTGTA-ATTTATT-T
1 GTTTGTATATTTATTAT
*
37018 GTTTGTATATTTGTTAT
1 GTTTGTATATTTATTAT
37035 GTTTG
1 GTTTG
37040 GTAGTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 7 0.37
16 6 0.32
17 6 0.32
ACGTcount: A:0.16, C:0.00, G:0.19, T:0.65
Consensus pattern (17 bp):
GTTTGTATATTTATTAT
Found at i:49682 original size:13 final size:13
Alignment explanation
Indices: 49664--49691 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
49654 TTTTTATGGC
49664 ATCTATACTAATT
1 ATCTATACTAATT
49677 ATCTATACTAATT
1 ATCTATACTAATT
49690 AT
1 AT
49692 TATTATTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.46
Consensus pattern (13 bp):
ATCTATACTAATT
Found at i:50094 original size:14 final size:14
Alignment explanation
Indices: 50075--50102 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
50065 TACTATGCTT
50075 CTTAATCTAACAAA
1 CTTAATCTAACAAA
50089 CTTAATCTAACAAA
1 CTTAATCTAACAAA
50103 AAACCATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (14 bp):
CTTAATCTAACAAA
Found at i:55591 original size:6 final size:7
Alignment explanation
Indices: 55560--55590 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
55550 AGCAATAAAC
55560 TGCAATT
1 TGCAATT
55567 TGCAATT
1 TGCAATT
55574 TGCAATT
1 TGCAATT
55581 TGC-ATT
1 TGCAATT
55587 TGCA
1 TGCA
55591 TCAATCTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (7 bp):
TGCAATT
Done.