Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020753.1 Corchorus olitorius cultivar O-4 contig20786, 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: 7095
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Found at i:1022 original size:252 final size:246
Alignment explanation
Indices: 536--1034 Score: 625
Period size: 252 Copynumber: 2.0 Consensus size: 246
526 ATTGAGATGC
* * * *
536 TCGTAAAAAAAAATTCTTAAATCCAATGTGGCTAAGATTTGATTAGATGAATATGGATATCTCAA
1 TCGTAAAAAAAAATCCTTAAATCCAATGTGGCTAAGATTTAATTAGATAAATATAGATATCTCAA
* * *
601 GGAGTCTTCGCGCCAAAATTCATCCAAAACTAAGCCGGGCCACGGAACGCTTTTTTAGCCAAAAA
66 GGAGTCTTCGAGCCAAAAATCATCCAAAACTAAGCCGGGCCACGGAACGCGTTTTTAGCCAAAAA
* ** *
666 CTGTGATGGTTTTTACACGATTTCGGCTAAAATTTTCTAAAAATTACCCCCAAAGATATTTCCCC
131 CTGTGATGGTTTTTACACGATTCCAACTAAAATTTTCTAAAAATTACCACCAAAGATATTTCCCC
*
731 AGTTTTGGCTAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGAT
196 AATTTTGGCTAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGAT
* * *
782 TCGTAAAAATAAATCCTTAAATCCAATGTGGCTGAGATTTAATTAGATAAATATAGATATTTCAA
1 TCGTAAAAAAAAATCCTTAAATCCAATGTGGCTAAGATTTAATTAGATAAATATAGATATCTCAA
* * * * *
847 GTAGTCTTGGAGCCAAAAAATCATGCAAAATTGAGCCGGGTCC-CTAGG-ACGCGTTTTTAGCCA
66 GGAGTCTTCGAGCC-AAAAATCATCCAAAACTAAGCCGGG-CCAC--GGAACGCGTTTTTAGCCA
* *
910 AAAACCT-TGATGGTTAATTAGTACACGATTCCAACTTAAATTTTGC-AAAAATTGA-CACGAAA
127 AAAA-CTGTGATGGTT--TT--TACACGATTCCAACTAAAATTTT-CTAAAAATT-ACCACCAAA
*
972 GAT-TTCTCCTCAATTTGTGGCTAAAATACTCAT-AAAAATATATAATTCAACGCCAAAAAGAT
185 GATATT-TCCCCAATTT-TGGCTAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGAT
1034 T
1 T
1035 GGAGGGCTAT
Statistics
Matches: 217, Mismatches: 23, Indels: 20
0.83 0.09 0.08
Matches are distributed among these distances:
246 69 0.32
247 22 0.10
248 28 0.13
249 4 0.02
250 2 0.01
251 2 0.01
252 72 0.33
253 18 0.08
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (246 bp):
TCGTAAAAAAAAATCCTTAAATCCAATGTGGCTAAGATTTAATTAGATAAATATAGATATCTCAA
GGAGTCTTCGAGCCAAAAATCATCCAAAACTAAGCCGGGCCACGGAACGCGTTTTTAGCCAAAAA
CTGTGATGGTTTTTACACGATTCCAACTAAAATTTTCTAAAAATTACCACCAAAGATATTTCCCC
AATTTTGGCTAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGAT
Found at i:1540 original size:15 final size:17
Alignment explanation
Indices: 1515--1548 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
1505 GCCTAAAAAT
1515 AATATTATTATAAT-TA
1 AATATTATTATAATCTA
1531 AATA-TATTATAATCTA
1 AATATTATTATAATCTA
1547 AA
1 AA
1549 AATAAGGGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
AATATTATTATAATCTA
Found at i:1569 original size:118 final size:118
Alignment explanation
Indices: 1435--1671 Score: 420
Period size: 118 Copynumber: 2.0 Consensus size: 118
1425 AAATAATTAT
1435 AGGGAGTAAATTATTATAATTATATTTTATATTTATAATATCTTTACATAATTAAAATAAAAAGT
1 AGGGAGTAAATTATTATAATTATATTTTATATTTATAATATCTTTACATAATTAAAATAAAAAGT
* *
1500 TTCATGCCTAAAAATAATATTATTATAATTAAATATATTATAATCTAAAAATA
66 TTCATGACTAAAAATAATAATATTATAATTAAATATATTATAATCTAAAAATA
* *
1553 AGGGAGTAAATTATTATAATTATATTTTGTATTTATAATATCTTTATATAATTAAAATAAAAAGT
1 AGGGAGTAAATTATTATAATTATATTTTATATTTATAATATCTTTACATAATTAAAATAAAAAGT
* *
1618 TTCATGACTATAAATAATAATATTATAATTAAATATATTATAATTTAAAAATA
66 TTCATGACTAAAAATAATAATATTATAATTAAATATATTATAATCTAAAAATA
1671 A
1 A
1672 TTATTAGAAG
Statistics
Matches: 113, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
118 113 1.00
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (118 bp):
AGGGAGTAAATTATTATAATTATATTTTATATTTATAATATCTTTACATAATTAAAATAAAAAGT
TTCATGACTAAAAATAATAATATTATAATTAAATATATTATAATCTAAAAATA
Found at i:1630 original size:59 final size:59
Alignment explanation
Indices: 1449--1630 Score: 167
Period size: 59 Copynumber: 3.1 Consensus size: 59
1439 AGTAAATTAT
* *
1449 TATAATTATATTTTATATTTATAATATCTTTACATAATTAAAATAAAAAGTTTCATGCC
1 TATAATTATATTTTATATTTATAATATCTTTATATAATTAAAATAAAAAGTTTCATGAC
* * * * ** ** * *
1508 TAAAAATAATATTATTATAATTA-AATA--TAT-TATAATCTAAAAATAAGGGAG-TAAATTAT
1 T-ATAATTATATT-TTATATTTATAATATCTTTATATAAT-T-AAAATAA-AAAGTTTCATGAC
*
1567 TATAATTATATTTTGTATTTATAATATCTTTATATAATTAAAATAAAAAGTTTCATGAC
1 TATAATTATATTTTATATTTATAATATCTTTATATAATTAAAATAAAAAGTTTCATGAC
1626 TATAA
1 TATAA
1631 ATAATAATAT
Statistics
Matches: 90, Mismatches: 23, Indels: 20
0.68 0.17 0.15
Matches are distributed among these distances:
57 12 0.13
58 18 0.20
59 28 0.31
60 18 0.20
61 14 0.16
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (59 bp):
TATAATTATATTTTATATTTATAATATCTTTATATAATTAAAATAAAAAGTTTCATGAC
Found at i:1669 original size:59 final size:59
Alignment explanation
Indices: 1488--1671 Score: 160
Period size: 59 Copynumber: 3.1 Consensus size: 59
1478 TTACATAATT
* * * *
1488 AAAATAAAAAGTTTCATGCCTAAAAATAATATTATTATAATTAAATATATTATAATCTA
1 AAAATAAAAAGTTTCATGACTATAAATAATAATATTATAATTAAATATATTATAATTTA
** ** * * * * * * * *
1547 AAAATAAGGGAG-TAAATTATTAT-AATTAT-ATTTTGTATTTATAATATCTTTATATAATT-
1 AAAATAA-AAAGTTTCATGACTATAAATAATAATATTATAATTA-AATAT-ATTATA-ATTTA
1606 AAAATAAAAAGTTTCATGACTATAAATAATAATATTATAATTAAATATATTATAATTTA
1 AAAATAAAAAGTTTCATGACTATAAATAATAATATTATAATTAAATATATTATAATTTA
1665 AAAATAA
1 AAAATAA
1672 TTATTAGAAG
Statistics
Matches: 89, Mismatches: 28, Indels: 16
0.67 0.21 0.12
Matches are distributed among these distances:
57 8 0.09
58 15 0.17
59 43 0.48
60 14 0.16
61 9 0.10
ACGTcount: A:0.51, C:0.04, G:0.05, T:0.40
Consensus pattern (59 bp):
AAAATAAAAAGTTTCATGACTATAAATAATAATATTATAATTAAATATATTATAATTTA
Found at i:1930 original size:11 final size:11
Alignment explanation
Indices: 1914--1938 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1904 ATATATATAT
1914 ATAGTAGTAAG
1 ATAGTAGTAAG
1925 ATAGTAGTAAG
1 ATAGTAGTAAG
1936 ATA
1 ATA
1939 AGATATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.24, T:0.28
Consensus pattern (11 bp):
ATAGTAGTAAG
Found at i:2731 original size:15 final size:14
Alignment explanation
Indices: 2681--2728 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
2671 TGTCATGTCA
2681 TAATTTT-CCTCAAT
1 TAATTTTACCT-AAT
* *
2695 TTATTTTA-TTAAT
1 TAATTTTACCTAAT
2708 TAATTTTACCTAAT
1 TAATTTTACCTAAT
2722 TAATTTT
1 TAATTTT
2729 TACAAGTTCG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 10 0.36
14 18 0.64
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.58
Consensus pattern (14 bp):
TAATTTTACCTAAT
Found at i:5331 original size:22 final size:22
Alignment explanation
Indices: 5306--5380 Score: 89
Period size: 22 Copynumber: 3.4 Consensus size: 22
5296 TTGAATATTT
5306 TTATGAAATTTTGATAACTACC
1 TTATGAAATTTTGATAACTACC
* * **
5328 TTATTAAATTTTGATAACCATG
1 TTATGAAATTTTGATAACTACC
*
5350 TTATGAAATTTTGATAATTTACC
1 TTATGAAATTTTGATAA-CTACC
5373 -TATGAAAT
1 TTATGAAAT
5381 ATGAAACTTT
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
22 42 0.98
23 1 0.02
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.44
Consensus pattern (22 bp):
TTATGAAATTTTGATAACTACC
Found at i:5406 original size:29 final size:29
Alignment explanation
Indices: 5351--5409 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
5341 ATAACCATGT
* * *
5351 TATGAAATTTTGATAATTTACCTATGAAA
1 TATGAAACTTTGATAACTAACCTATGAAA
5380 TATGAAACTTTGATAACCTAACC-ATGAAA
1 TATGAAACTTTGATAA-CTAACCTATGAAA
5409 T
1 T
5410 TTTAATAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (29 bp):
TATGAAACTTTGATAACTAACCTATGAAA
Found at i:6600 original size:11 final size:11
Alignment explanation
Indices: 6580--6631 Score: 68
Period size: 11 Copynumber: 4.7 Consensus size: 11
6570 ATCAGTAATT
6580 ATGATGCAGTA
1 ATGATGCAGTA
* *
6591 ATGATTCAGTC
1 ATGATGCAGTA
6602 ATGATGCAGTA
1 ATGATGCAGTA
* *
6613 ATGATTCAGTC
1 ATGATGCAGTA
6624 ATGATGCA
1 ATGATGCA
6632 AGCATTGTTA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 34 1.00
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (11 bp):
ATGATGCAGTA
Found at i:6606 original size:22 final size:22
Alignment explanation
Indices: 6580--6631 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
6570 ATCAGTAATT
6580 ATGATGCAGTAATGATTCAGTC
1 ATGATGCAGTAATGATTCAGTC
6602 ATGATGCAGTAATGATTCAGTC
1 ATGATGCAGTAATGATTCAGTC
6624 ATGATGCA
1 ATGATGCA
6632 AGCATTGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (22 bp):
ATGATGCAGTAATGATTCAGTC
Done.