Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020589.1 Corchorus olitorius cultivar O-4 contig20622, 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: 63110
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:12111 original size:31 final size:31
Alignment explanation
Indices: 12076--12137 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
12066 AAAGTCATTA
*
12076 ATGAATATTGTGATTATTCATGAATCAAGAG
1 ATGAATATTGTAATTATTCATGAATCAAGAG
12107 ATGAATATTGTAATTATTCATGAATCAAGAG
1 ATGAATATTGTAATTATTCATGAATCAAGAG
12138 TTCTCTTGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.40, C:0.06, G:0.18, T:0.35
Consensus pattern (31 bp):
ATGAATATTGTAATTATTCATGAATCAAGAG
Found at i:13365 original size:15 final size:15
Alignment explanation
Indices: 13345--13374 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13335 TTAGAGAGGT
13345 TATTAATTAATGGAG
1 TATTAATTAATGGAG
*
13360 TATTAATTTATGGAG
1 TATTAATTAATGGAG
13375 GTTATACTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (15 bp):
TATTAATTAATGGAG
Found at i:13366 original size:76 final size:76
Alignment explanation
Indices: 13227--13370 Score: 225
Period size: 76 Copynumber: 1.9 Consensus size: 76
13217 CTCTATAAAT
* * *
13227 TAATAATGTTGGGACCATGAAAAATTATTAATTTAGAGAGATTATTAATTTATCTAGTGTTAATT
1 TAATAATGTTGGGACCATGAAAAATTATTAATTTAGAGAGATTATTAATTAATCGAGTATTAATT
13292 TATATGGAAAC
66 TATATGGAAAC
** * *
13303 TAATAATGTTGGGACTGTGAAAAATTATTAATTTAGAGAGGTTATTAATTAATGGAGTATTAATT
1 TAATAATGTTGGGACCATGAAAAATTATTAATTTAGAGAGATTATTAATTAATCGAGTATTAATT
13368 TAT
66 TAT
13371 GGAGGTTATA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
76 61 1.00
ACGTcount: A:0.39, C:0.03, G:0.17, T:0.40
Consensus pattern (76 bp):
TAATAATGTTGGGACCATGAAAAATTATTAATTTAGAGAGATTATTAATTAATCGAGTATTAATT
TATATGGAAAC
Found at i:14369 original size:39 final size:39
Alignment explanation
Indices: 14315--14391 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
14305 ATCACTCATC
* *
14315 TTGATATTATTCATGTGAAGACCAATATACCCTCAATTT
1 TTGATACTATTCATGTGAAGACCAATAAACCCTCAATTT
14354 TTGATACTATTCATGTGAAGACCAATAAACCCTCAATT
1 TTGATACTATTCATGTGAAGACCAATAAACCCTCAATT
14392 GTAAATTGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.35
Consensus pattern (39 bp):
TTGATACTATTCATGTGAAGACCAATAAACCCTCAATTT
Found at i:19075 original size:32 final size:31
Alignment explanation
Indices: 19038--19106 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 31
19028 ATAAGAACTC
* *
19038 AATTGACCTAATCTTACGAGTATAAGTGACTA
1 AATTGACCCAATCTTACGAGTAAAAG-GACTA
*
19070 AATTGACCCAATCTTATGAGTAAAAGGACTA
1 AATTGACCCAATCTTACGAGTAAAAGGACTA
*
19101 AGTTGA
1 AATTGA
19107 TCACTTTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
31 10 0.30
32 23 0.70
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.29
Consensus pattern (31 bp):
AATTGACCCAATCTTACGAGTAAAAGGACTA
Found at i:19135 original size:29 final size:28
Alignment explanation
Indices: 19086--19143 Score: 64
Period size: 29 Copynumber: 2.0 Consensus size: 28
19076 CCCAATCTTA
* *
19086 TGAGTAAAAGGACTAAGTTGATCACTTTT
1 TGAGTAAAAGGACTAAATTGAACA-TTTT
*
19115 TGAGTACAAGGA-TGAAATTGAACATTTT
1 TGAGTAAAAGGACT-AAATTGAACATTTT
19143 T
1 T
19144 ATATAGTACA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
28 6 0.24
29 19 0.76
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.34
Consensus pattern (28 bp):
TGAGTAAAAGGACTAAATTGAACATTTT
Found at i:21766 original size:2 final size:2
Alignment explanation
Indices: 21759--21784 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21749 AATTAATTTA
21759 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
21785 AGCATGCTCG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:26731 original size:5 final size:5
Alignment explanation
Indices: 26721--26745 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
26711 TTTTTTTAAT
26721 GTCTG GTCTG GTCTG GTCTG GTCTG
1 GTCTG GTCTG GTCTG GTCTG GTCTG
26746 CCTTTGTGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.40, T:0.40
Consensus pattern (5 bp):
GTCTG
Found at i:37724 original size:20 final size:20
Alignment explanation
Indices: 37683--37725 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
37673 CTCTCACAAG
* *
37683 TTTCTAGCCGTTGGAGCTCT
1 TTTCTAGCCGTTAGAGCACT
*
37703 TTTCTAGCCGTTATAGCACT
1 TTTCTAGCCGTTAGAGCACT
37723 TTT
1 TTT
37726 TCCACTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (20 bp):
TTTCTAGCCGTTAGAGCACT
Found at i:46492 original size:18 final size:18
Alignment explanation
Indices: 46469--46505 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
46459 ATCCACGGTT
46469 CAAGCTATCT-AATCCCTC
1 CAAGCTAT-TAAATCCCTC
46487 CAAGCTATTAAATCCCTC
1 CAAGCTATTAAATCCCTC
46505 C
1 C
46506 CCAAGGGCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.30, C:0.38, G:0.05, T:0.27
Consensus pattern (18 bp):
CAAGCTATTAAATCCCTC
Found at i:52196 original size:51 final size:51
Alignment explanation
Indices: 52094--52196 Score: 118
Period size: 51 Copynumber: 2.0 Consensus size: 51
52084 CGTTCTTCAA
* ** * **
52094 TATTTCCTTGTTTCAATCTTGTCTCCGGACACCCAAACACTCTTTTAGTGT
1 TATTTCCTTGTTTCAATCTTGTCTCCGAACACAAAAACACTCGTACAGTGT
* *
52145 TATTTTCTTGTTTCAATCTTGTCTCCGAACATAAAAACACT-GTACACGTGT
1 TATTTCCTTGTTTCAATCTTGTCTCCGAACACAAAAACACTCGTACA-GTGT
52196 T
1 T
52197 TCTCTCTCAG
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
50 2 0.05
51 41 0.95
ACGTcount: A:0.23, C:0.24, G:0.12, T:0.41
Consensus pattern (51 bp):
TATTTCCTTGTTTCAATCTTGTCTCCGAACACAAAAACACTCGTACAGTGT
Found at i:52902 original size:13 final size:13
Alignment explanation
Indices: 52884--52909 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52874 TAAATTTTAA
52884 GATGCATTTTGGC
1 GATGCATTTTGGC
52897 GATGCATTTTGGC
1 GATGCATTTTGGC
52910 ATTTATGCCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.31, T:0.38
Consensus pattern (13 bp):
GATGCATTTTGGC
Found at i:57414 original size:1 final size:1
Alignment explanation
Indices: 57408--57440 Score: 57
Period size: 1 Copynumber: 33.0 Consensus size: 1
57398 TCCAAACTAT
*
57408 AAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
57441 TAGCTTCTTC
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:0.97, C:0.03, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:62348 original size:5 final size:5
Alignment explanation
Indices: 62340--62366 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
62330 TTTTATAAAC
62340 CTTGT CTTGT CTTGT CTTGT CTTGT CT
1 CTTGT CTTGT CTTGT CTTGT CTTGT CT
62367 CATGTTGTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.22, G:0.19, T:0.59
Consensus pattern (5 bp):
CTTGT
Done.