Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021720.1 Corchorus olitorius cultivar O-4 contig21753, 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: 7753
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.34
Found at i:5793 original size:41 final size:42
Alignment explanation
Indices: 5735--5818 Score: 161
Period size: 41 Copynumber: 2.0 Consensus size: 42
5725 GATGATGAGC
5735 TTGGTTATGTCCCTGTTTTGTTCCTGTATTCATGTATGCATA
1 TTGGTTATGTCCCTGTTTTGTTCCTGTATTCATGTATGCATA
5777 TTGG-TATGTCCCTGTTTTGTTCCTGTATTCATGTATGCATA
1 TTGGTTATGTCCCTGTTTTGTTCCTGTATTCATGTATGCATA
5818 T
1 T
5819 GTCCCTGCTT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 38 0.90
42 4 0.10
ACGTcount: A:0.14, C:0.17, G:0.19, T:0.50
Consensus pattern (42 bp):
TTGGTTATGTCCCTGTTTTGTTCCTGTATTCATGTATGCATA
Found at i:7230 original size:13 final size:13
Alignment explanation
Indices: 7212--7563 Score: 127
Period size: 13 Copynumber: 24.2 Consensus size: 13
7202 CAAATTTTAT
7212 TTTCTAAATATAA
1 TTTCTAAATATAA
7225 TTTCTAAATATTTTAAAA
1 TTTCTAAATA---T--AA
*
7243 TTTCTAAATATTAT
1 TTTCTAAATA-TAA
*
7257 TTTCTAATTATAA
1 TTTCTAAATATAA
7270 TTTCATTACATATATAA
1 TTTC--TA-A-ATATAA
* * *
7287 TTGCTAATTATTAT
1 TTTCTAAATA-TAA
7301 TTTCTAAATATAA
1 TTTCTAAATATAA
* *
7314 TTTTTAAAAATTTTTAA
1 TTTCT--AAA--TATAA
*
7331 TTTCTAAATATTAT
1 TTTCTAAATA-TAA
*
7345 TTTCTAATTATAA
1 TTTCTAAATATAA
7358 TTTCCATACATATATAA
1 TTT-C-TA-A-ATATAA
7375 TTTCTAAATA-ATA
1 TTTCTAAATATA-A
7388 TTTCATTACATATATAA
1 TTTC--TA-A-ATATAA
*
7405 TTTAT-AATATAA
1 TTTCTAAATATAA
* *
7417 TTCCTAATTATAA
1 TTTCTAAATATAA
*
7430 TTTCTTCACATATATAG
1 TTTC-T-A-A-ATATAA
*
7447 TTTCTAAATATCAT
1 TTTCTAAATAT-AA
7461 TTTCTAAATA-ATA
1 TTTCTAAATATA-A
7474 TTTCATTACATATATAA
1 TTTC--TA-A-ATATAA
*
7491 TTTATAAATATAA
1 TTTCTAAATATAA
*
7504 TTCCT-AATAATAA
1 TTTCTAAAT-ATAA
*
7517 TTTCATTACATATATCA
1 TTTC--TA-A-ATATAA
*
7534 TTTCTAAATATTAT
1 TTTCTAAATA-TAA
* *
7548 TTTCTCATTATAA
1 TTTCTAAATATAA
7561 TTT
1 TTT
7564 ATGACCTATT
Statistics
Matches: 258, Mismatches: 37, Indels: 88
0.67 0.10 0.23
Matches are distributed among these distances:
12 14 0.05
13 80 0.31
14 58 0.22
15 26 0.10
16 10 0.04
17 54 0.21
18 16 0.06
ACGTcount: A:0.40, C:0.10, G:0.01, T:0.50
Consensus pattern (13 bp):
TTTCTAAATATAA
Found at i:7295 original size:30 final size:30
Alignment explanation
Indices: 7257--7505 Score: 122
Period size: 30 Copynumber: 8.5 Consensus size: 30
7247 TAAATATTAT
7257 TTTCTAATTATAATTTCATTACATATATAA
1 TTTCTAATTATAATTTCATTACATATATAA
* *
7287 TTGCTAATTATTATTT--TCTA-A-ATATAA
1 TTTCTAATTATAATTTCAT-TACATATATAA
* * * *
7314 TTTTTAAAAATTTTTAATTTC--TAAATAT-TAT
1 TTTCT---AA-TTATAATTTCATTACATATATAA
7345 TTTCTAATTATAATTTCCA-TACATATATAA
1 TTTCTAATTATAATTT-CATTACATATATAA
*
7375 TTTCTAAATA-ATATTTCATTACATATATAA
1 TTTCTAATTATA-ATTTCATTACATATATAA
* *
7405 TTTATAA-TATAA-TTC-CTA-AT-TATAA
1 TTTCTAATTATAATTTCATTACATATATAA
* *
7430 TTTCTTCACATATATAGTTTC--TA-A-ATATCAT
1 TTTC-T-A-AT-TATAATTTCATTACATATAT-AA
*
7461 TTTCTAAATA-ATATTTCATTACATATATAA
1 TTTCTAATTATA-ATTTCATTACATATATAA
* *
7491 TTTATAAATATAATT
1 TTTCTAATTATAATT
7506 CCTAATAATA
Statistics
Matches: 170, Mismatches: 21, Indels: 56
0.69 0.09 0.23
Matches are distributed among these distances:
25 8 0.05
26 4 0.02
27 26 0.15
28 10 0.06
29 17 0.10
30 76 0.45
31 27 0.16
32 2 0.01
ACGTcount: A:0.40, C:0.09, G:0.01, T:0.50
Consensus pattern (30 bp):
TTTCTAATTATAATTTCATTACATATATAA
Found at i:7313 original size:44 final size:42
Alignment explanation
Indices: 7203--7390 Score: 187
Period size: 44 Copynumber: 4.3 Consensus size: 42
7193 CGCTATATTC
* *
7203 AAATTTTATTTTCTAAATATAATTTCTAAATATTTTAAAATTTCT
1 AAATATTATTTTCTAAATATAATTTCTAAATA---TATAATTTCT
* * *
7248 AAATATTATTTTCTAATTATAATTTCATTACATATATAATTGCT
1 AAATATTATTTTCTAAATATAATTTC--TAAATATATAATTTCT
* * * *
7292 AATTATTATTTTCTAAATATAATTTTTAAAAATTTTTAATTTCT
1 AAATATTATTTTCTAAATATAATTTCT--AAATATATAATTTCT
* *
7336 AAATATTATTTTCTAATTATAATTTCCATACATATATAATTTCT
1 AAATATTATTTTCTAAATATAATTT-C-TAAATATATAATTTCT
*
7380 AAATAATATTT
1 AAATATTATTT
7391 CATTACATAT
Statistics
Matches: 118, Mismatches: 19, Indels: 13
0.79 0.13 0.09
Matches are distributed among these distances:
42 1 0.01
44 87 0.74
45 24 0.20
46 1 0.01
47 5 0.04
ACGTcount: A:0.40, C:0.07, G:0.01, T:0.52
Consensus pattern (42 bp):
AAATATTATTTTCTAAATATAATTTCTAAATATATAATTTCT
Found at i:7358 original size:88 final size:89
Alignment explanation
Indices: 7204--7390 Score: 290
Period size: 88 Copynumber: 2.1 Consensus size: 89
7194 GCTATATTCA
*
7204 AATT-TTATTTTCTAAATATAATTTCTAAATATTTTAAAATTTCTAAATATTATTTTCTAATTAT
1 AATTATTATTTTCTAAATATAATTTCTAAAAATTTTAAAATTTCTAAATATTATTTTCTAATTAT
7268 AATTT-CATTACATATATAATTGCT
66 AATTTCCA-TACATATATAATTGCT
* *
7292 AATTATTATTTTCTAAATATAATTTTTAAAAATTTT-TAATTTCTAAATATTATTTTCTAATTAT
1 AATTATTATTTTCTAAATATAATTTCTAAAAATTTTAAAATTTCTAAATATTATTTTCTAATTAT
*
7356 AATTTCCATACATATATAATTTCT
66 AATTTCCATACATATATAATTGCT
* *
7380 AAATAATATTT
1 AATTATTATTT
7391 CATTACATAT
Statistics
Matches: 91, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
88 60 0.66
89 31 0.34
ACGTcount: A:0.40, C:0.07, G:0.01, T:0.52
Consensus pattern (89 bp):
AATTATTATTTTCTAAATATAATTTCTAAAAATTTTAAAATTTCTAAATATTATTTTCTAATTAT
AATTTCCATACATATATAATTGCT
Found at i:7415 original size:44 final size:43
Alignment explanation
Indices: 7328--7549 Score: 217
Period size: 44 Copynumber: 5.1 Consensus size: 43
7318 TAAAAATTTT
*
7328 TAATTTCTAAATATTATTT--TCTA-AT-TATAATTTCCATACATATA
1 TAATTTCTAAATAATATTTCAT-TACATATATAATTT--ATA-A-ATA
7372 TAATTTCTAAATAATATTTCATTACATATATAATTTAT-AATA
1 TAATTTCTAAATAATATTTCATTACATATATAATTTATAAATA
* * * *
7414 TAATTCCT-AATTATAATTTC-TTCACATATATAGTTTCTAAATA
1 TAATTTCTAAATAAT-ATTTCATT-ACATATATAATTTATAAATA
*
7457 TCATTTTCTAAATAATATTTCATTACATATATAATTTATAAATA
1 T-AATTTCTAAATAATATTTCATTACATATATAATTTATAAATA
* * *
7501 TAATTCCT-AATAATAATTTCATTACATATATCATTTCTAAATA
1 TAATTTCTAAATAAT-ATTTCATTACATATATAATTTATAAATA
*
7544 TTATTT
1 TAATTT
7550 TCTCATTATA
Statistics
Matches: 151, Mismatches: 16, Indels: 23
0.79 0.08 0.12
Matches are distributed among these distances:
41 7 0.05
42 34 0.23
43 41 0.27
44 47 0.31
45 11 0.07
46 3 0.02
47 8 0.05
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (43 bp):
TAATTTCTAAATAATATTTCATTACATATATAATTTATAAATA
Found at i:7455 original size:116 final size:118
Alignment explanation
Indices: 7269--7500 Score: 285
Period size: 116 Copynumber: 2.0 Consensus size: 118
7259 TCTAATTATA
* * * * *
7269 ATTTCATTACATATATAATTGCTAATTATTATTTTCTAAATATAATTTTTAAAAATTTTTAATTT
1 ATTTCATTACATATATAATTGATAATTATTAATTCCTAAATATAATTTTTAAAAATATATAATTT
* *
7334 CTAAATATTATTTTCTAATTATAAT-TTCCA-TACATATATAATTTCTAAATAAT
66 CTAAATATCATTTTCTAA--ATAATATTCCATTACATATATAATTTATAAATAAT
* * * * *
7387 ATTTCATTACATATATAATTTATAA-TA-TAATTCCTAATTATAATTTCTT-CACATATATAGTT
1 ATTTCATTACATATATAATTGATAATTATTAATTCCTAAATATAATTT-TTAAAAATATATAATT
*
7449 TCTAAATATCATTTTCTAAATAATATTTCATTACATATATAATTTATAAATA
65 TCTAAATATCATTTTCTAAATAATATTCCATTACATATATAATTTATAAATA
7501 TAATTCCTAA
Statistics
Matches: 98, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
114 5 0.05
115 4 0.04
116 62 0.63
117 4 0.04
118 23 0.23
ACGTcount: A:0.41, C:0.09, G:0.01, T:0.49
Consensus pattern (118 bp):
ATTTCATTACATATATAATTGATAATTATTAATTCCTAAATATAATTTTTAAAAATATATAATTT
CTAAATATCATTTTCTAAATAATATTCCATTACATATATAATTTATAAATAAT
Found at i:7465 original size:86 final size:87
Alignment explanation
Indices: 7375--7552 Score: 299
Period size: 87 Copynumber: 2.1 Consensus size: 87
7365 ACATATATAA
*
7375 TTTCTAAATAATATTTCATTACATATATAATTTAT-AATATAATTCCTAATTATAATTTC-TTCA
1 TTTCTAAATAATATTTCATTACATATATAATTTATAAATATAATTCCTAATAATAATTTCATT-A
7438 CATATAT-AGTTTCTAAATATCAT
65 CATATATCA-TTTCTAAATATCAT
7461 TTTCTAAATAATATTTCATTACATATATAATTTATAAATATAATTCCTAATAATAATTTCATTAC
1 TTTCTAAATAATATTTCATTACATATATAATTTATAAATATAATTCCTAATAATAATTTCATTAC
*
7526 ATATATCATTTCTAAATATTAT
66 ATATATCATTTCTAAATATCAT
7548 TTTCT
1 TTTCT
7553 CATTATAATT
Statistics
Matches: 87, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
86 35 0.40
87 49 0.56
88 3 0.03
ACGTcount: A:0.40, C:0.11, G:0.01, T:0.48
Consensus pattern (87 bp):
TTTCTAAATAATATTTCATTACATATATAATTTATAAATATAATTCCTAATAATAATTTCATTAC
ATATATCATTTCTAAATATCAT
Done.