Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023418.1 Corchorus olitorius cultivar O-4 contig23451, 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: 10837
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:437 original size:21 final size:21
Alignment explanation
Indices: 413--483 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
403 CTTAGGCAAT
*
413 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
434 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
455 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
476 TCCAATGA
1 TCCAATGA
484 TCTCCTAGCA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
20 3 0.06
21 45 0.94
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:5732 original size:18 final size:19
Alignment explanation
Indices: 5698--5733 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5688 TCTGGTCGAA
*
5698 AAATTTTTTTTATTATTTT
1 AAATTTTTTTGATTATTTT
5717 AAATTTTTTTGA-TATTT
1 AAATTTTTTTGATTATTT
5734 GTCGATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (19 bp):
AAATTTTTTTGATTATTTT
Found at i:5885 original size:25 final size:24
Alignment explanation
Indices: 5848--5894 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
5838 CTAGAAAATT
5848 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAACTTTGAT-GAT-AGATGGA
5874 TGAAAAAC-TTGATGATAGATG
1 TGAAAAACTTTGATGATAGATG
5895 AATAGAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (24 bp):
TGAAAAACTTTGATGATAGATGGA
Found at i:6839 original size:21 final size:21
Alignment explanation
Indices: 6769--6827 Score: 102
Period size: 21 Copynumber: 2.8 Consensus size: 21
6759 CTTAGGCAAT
6769 TCCAATGAGCTT-GATACCTTC
1 TCCAATGAGCTTGGA-ACCTTC
6790 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
6811 TCCAATGAGCTTGGAAC
1 TCCAATGAGCTTGGAAC
6828 TTGCTCTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 35 0.95
22 2 0.05
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:7613 original size:60 final size:58
Alignment explanation
Indices: 7539--8304 Score: 910
Period size: 60 Copynumber: 12.9 Consensus size: 58
7529 AACCCCCTTT
*
7539 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTAGTAGAGAGTTTTCAGTTCAAAATCCAA
1 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAGTTCAAAATCC-A
* * * ** * *
7598 TTTTGCTTTTAAAAATCCTGTTCGAGGTCGCTGGTAGAGAGTTTTCAAATCAAAATTTCG
1 TCTTG-TTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAGTTCAAAA-TCCA
* * * * * * * *
7658 TCCTATTTTTTAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATTAAAAATTTCG
1 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAGTTCAAAA-TCCA
* * * * *
7717 TCTTGTTTTTAAAATCCTATTCGAGGTCTCTAGTAGAGAGTTTTCAATTCAAAGTCTTA
1 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAGTTCAAAATC-CA
*
7776 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCT-G-ATAGAGTTTTCAGTTCAAAAATCTCA
1 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAGTTC-AAAATC-CA
* * * *
7834 TCTTGTTTTGAAAATCCTATTCGAGGTCTCTGATAGAGAGTGTTCAGTTCAAAAATCTCA
1 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAGTTC-AAAATC-CA
7894 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAGTTCAAAAATCTCA
1 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAGTTC-AAAATC-CA
* * *
7954 TCTTGTTTTTAAAAGCCTGTTCGAGGTCTCTAGTAGAGAGTTTTCAGTTCAAAAATCTTA
1 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAGTTC-AAAATC-CA
** *
8014 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTAATAGAGAGTGTTCAGTTCAAAAATCTCA
1 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAGTTC-AAAATC-CA
* * *
8074 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGATAGAGAGTGTTCAGTTCAAAATCTTA
1 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAGTTCAAAATC-CA
* * * **
8133 TCTTGTTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGCTTTCAATTCGAAACAT-TG
1 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAGTTC-AAA-ATCCA
* * **
8192 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGCTTTCAATTCGAAACAT-TG
1 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAGTTC-AAA-ATCCA
* *
8251 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGATAGAGAGTTTTTAGTTCAAAA
1 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAGTTCAAAA
8305 ATCTTGTCTG
Statistics
Matches: 637, Mismatches: 62, Indels: 18
0.89 0.09 0.03
Matches are distributed among these distances:
57 15 0.02
58 41 0.06
59 286 0.45
60 291 0.46
61 4 0.01
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (58 bp):
TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAGTTCAAAATCCA
Found at i:7691 original size:59 final size:60
Alignment explanation
Indices: 7539--8306 Score: 963
Period size: 59 Copynumber: 12.9 Consensus size: 60
7529 AACCCCCTTT
* *
7539 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTAGTAGAGAGTTTTCAGTTC-AAAA-TCCAA
1 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAGTTCAAAAATTTC-A
* * * ** *
7598 TTTTGCTTTTAAAAATCCTGTTCGAGGTCGCTGGTAGAGAGTTTTCAAATC-AAAATTTCG
1 TCTTG-TTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAGTTCAAAAATTTCA
* * * * * *
7658 TCCTATTTTTTAAATCCTGATCGAGGTCTCTGGTAGAGAGTTTTCAATT-AAAAATTTCG
1 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAGTTCAAAAATTTCA
* * * *
7717 TCTTGTTTTTAAAATCCTATTCGAGGTCTCTAGTAGAGAGTTTTCAATTC-AAAGTCTT-A
1 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAGTTCAAAAAT-TTCA
* *
7776 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCT-G-ATAGAGTTTTCAGTTCAAAAATCTCA
1 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAGTTCAAAAATTTCA
* * * * *
7834 TCTTGTTTTGAAAATCCTATTCGAGGTCTCTGATAGAGAGTGTTCAGTTCAAAAATCTCA
1 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAGTTCAAAAATTTCA
*
7894 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAGTTCAAAAATCTCA
1 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAGTTCAAAAATTTCA
* *
7954 TCTTGTTTTTAAAAGCCTGTTCGAGGTCTCTAGTAGAGAGTTTTCAGTTCAAAAATCTT-A
1 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAGTTCAAAAAT-TTCA
** * *
8014 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTAATAGAGAGTGTTCAGTTCAAAAATCTCA
1 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAGTTCAAAAATTTCA
* *
8074 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGATAGAGAGTGTTCAGTTC-AAAATCTT-A
1 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAGTTCAAAAAT-TTCA
* * * * *
8133 TCTTGTTTTTAAAATCCTGATCGAGGTCTCTGGTAGAGAGCTTTCAATTCGAAACA-TT-G
1 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAGTTC-AAAAATTTCA
* * * *
8192 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGCTTTCAATTCGAAACA-TT-G
1 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAGTTC-AAAAATTTCA
* *
8251 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGATAGAGAGTTTTTAGTTCAAAAAT
1 TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAGTTCAAAAAT
8307 CTTGTCTGGC
Statistics
Matches: 634, Mismatches: 60, Indels: 30
0.88 0.08 0.04
Matches are distributed among these distances:
57 15 0.02
58 39 0.06
59 287 0.45
60 287 0.45
61 6 0.01
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (60 bp):
TCTTGTTTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAGTTCAAAAATTTCA
Found at i:8415 original size:59 final size:58
Alignment explanation
Indices: 8343--8661 Score: 390
Period size: 59 Copynumber: 5.3 Consensus size: 58
8333 AACCCCCTTT
*
8343 TCTTGTTTTTAAAATCCTGTTCGAGGTTTCTGATAGAGAGTTTTCAGTTCAAAATCTTA
1 TCTTG-TTTTAAAATCCTGTTCGAGGTTTCTGATAGAGAGTTTTCAATTCAAAATCTTA
* * * * *
8402 TCTTGTATTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTTTTTAATTCAAAATATTG
1 TCTTGT-TTTAAAATCCTGTTCGAGGTTTCTGATAGAGAG---TTTTCAATTCAAAATCTTA
* *
8464 TCTTGTTTTAAAATCCTGTTCGAGGTCTT-TGATAGAGAGTTTTCAGTTCAAAAATCTTG
1 TCTTGTTTTAAAATCCTGTTCGAGGT-TTCTGATAGAGAGTTTTCAATTC-AAAATCTTA
* **
8523 TCTTGTTCTTAAAATCCTGTTCGAGGTTTCTGGTAGAGAGTTTTCAATTCAAAATAATA
1 TCTTGTT-TTAAAATCCTGTTCGAGGTTTCTGATAGAGAGTTTTCAATTCAAAATCTTA
* *
8582 TCTTGTTATTAAAATCCTGTTCCAGGTCTCTGATAGAGAGTTTTTCAATATCAAAATCTT-
1 TCTTGTT-TTAAAATCCTGTTCGAGGTTTCTGATAGAGAG-TTTTCAAT-TCAAAATCTTA
*
8642 TCTTTGTTTTTAAATCCTGT
1 TC-TTGTTTTAAAATCCTGT
8662 CTTGTTTTTA
Statistics
Matches: 226, Mismatches: 23, Indels: 21
0.84 0.09 0.08
Matches are distributed among these distances:
58 9 0.04
59 95 0.42
60 58 0.26
61 42 0.19
62 22 0.10
ACGTcount: A:0.26, C:0.14, G:0.16, T:0.44
Consensus pattern (58 bp):
TCTTGTTTTAAAATCCTGTTCGAGGTTTCTGATAGAGAGTTTTCAATTCAAAATCTTA
Found at i:8557 original size:121 final size:115
Alignment explanation
Indices: 8343--8661 Score: 433
Period size: 120 Copynumber: 2.7 Consensus size: 115
8333 AACCCCCTTT
8343 TCTTGTTTTTAAAATCCTGTTCGAGGT-TTCTGATAGAGAGTTTTCAGTTCAAAATCTTATCTTG
1 TCTTG-TTTTAAAATCCTGTTCGAGGTCTT-TGATAGAGAGTTTTCAGTTCAAAATCTT-TCTTG
* * *
8407 TATTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTTTTTAATTCAAAATATTG
63 T-TTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAG---TTTTCAATTCAAAATAATA
8464 TCTTGTTTTAAAATCCTGTTCGAGGTCTTTGATAGAGAGTTTTCAGTTCAAAAATCTTGTCTTGT
1 TCTTGTTTTAAAATCCTGTTCGAGGTCTTTGATAGAGAGTTTTCAGTTC-AAAATCTT-TCTTGT
*
8529 TCTTAAAATCCTGTTCGAGGTTTCTGGTAGAGAGTTTTCAATTCAAAATAATA
64 T-TTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATAATA
* * *
8582 TCTTGTTATTAAAATCCTGTTCCAGGTCTCTGATAGAGAGTTTTTCAATATCAAAATCTTTCTTT
1 TCTTGTT-TTAAAATCCTGTTCGAGGTCTTTGATAGAGAG-TTTTCAGT-TCAAAATCTTTC-TT
*
8647 GTTTTTAAATCCTGT
62 GTTTTAAAATCCTGT
8662 CTTGTTTTTA
Statistics
Matches: 182, Mismatches: 9, Indels: 16
0.88 0.04 0.08
Matches are distributed among these distances:
118 23 0.13
119 43 0.24
120 62 0.34
121 54 0.30
ACGTcount: A:0.26, C:0.14, G:0.16, T:0.44
Consensus pattern (115 bp):
TCTTGTTTTAAAATCCTGTTCGAGGTCTTTGATAGAGAGTTTTCAGTTCAAAATCTTTCTTGTTT
TAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTCAATTCAAAATAATA
Found at i:8666 original size:18 final size:19
Alignment explanation
Indices: 8645--8680 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
8635 AAATCTTTCT
8645 TTGTTTTT-AAATCCTGTC
1 TTGTTTTTAAAATCCTGTC
8663 TTGTTTTTAAAATCCTGT
1 TTGTTTTTAAAATCCTGT
8681 TCGAGGTGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.19, C:0.14, G:0.11, T:0.56
Consensus pattern (19 bp):
TTGTTTTTAAAATCCTGTC
Found at i:8763 original size:138 final size:138
Alignment explanation
Indices: 8514--8798 Score: 439
Period size: 138 Copynumber: 2.1 Consensus size: 138
8504 TTTCAGTTCA
* *
8514 AAAATCTTGTCTTGTTCTTAAAATCCTGTTCGAGGTTTCTGGTAGAGAGTTTTCAATTCAAAATA
1 AAAATCCTGTCTTGTTCTTAAAATCCTGTTCGAGGTGTCTGGTAGAGAGTTTTCAATTCAAAATA
* * *
8579 ATATCTTGTTATTAAAATCCTGTTCCAGGTCTCTGATAGAGAG-TTTTTCAATATCAAAATCTT-
66 ATATCTTGTTATTAAAATCCTGGTACAGGTCTCTGATAGAAAGTTTTTTCAAT-TCAAAATCTTG
8642 TCTTTGTTTT
130 TC-TTGTTTT
* * *
8652 TAAATCCTGTCTTGTTTTTAAAATCCTGTTCGAGGTGTCTGGTAGAGAGTTTTCAATTCAAAATC
1 AAAATCCTGTCTTGTTCTTAAAATCCTGTTCGAGGTGTCTGGTAGAGAGTTTTCAATTCAAAATA
* * *
8717 ATATCTTGTTTTTAAAATCCTGGTAGAGGTCTCTGGTAGAAAGTTTTTTCAATTCAAAATCTTGT
66 ATATCTTGTTATTAAAATCCTGGTACAGGTCTCTGATAGAAAGTTTTTTCAATTCAAAATCTTGT
8782 CTTGTTTT
131 CTTGTTTT
8790 AAAATCCTG
1 AAAATCCTG
8799 ATTGAGGTCT
Statistics
Matches: 133, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
138 122 0.92
139 11 0.08
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (138 bp):
AAAATCCTGTCTTGTTCTTAAAATCCTGTTCGAGGTGTCTGGTAGAGAGTTTTCAATTCAAAATA
ATATCTTGTTATTAAAATCCTGGTACAGGTCTCTGATAGAAAGTTTTTTCAATTCAAAATCTTGT
CTTGTTTT
Found at i:8820 original size:60 final size:59
Alignment explanation
Indices: 8653--8809 Score: 210
Period size: 59 Copynumber: 2.6 Consensus size: 59
8643 CTTTGTTTTT
* * *
8653 AAATCCTGTCTTGTTTTTAAAATCCTGTTCGAGGTGTCTGGTAGAGAG-TTTTCAATTCA
1 AAATCATGTCTTGTTTTTAAAATCCTGTT-GAGGTCTCTGGTAGAAAGTTTTTCAATTCA
* *
8712 AAATCATATCTTGTTTTTAAAATCCTGGTAGAGGTCTCTGGTAGAAAGTTTTTTCAATTCA
1 AAATCATGTCTTGTTTTTAAAATCCT-GTTGAGGTCTCTGGTAGAAAG-TTTTTCAATTCA
*
8773 AAATCTTGTCTTG-TTTTAAAATCCTGATTGAGGTCTC
1 AAATCATGTCTTGTTTTTAAAATCCTG-TTGAGGTCTC
8810 CGATTGAAAG
Statistics
Matches: 86, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
59 41 0.48
60 23 0.27
61 22 0.26
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (59 bp):
AAATCATGTCTTGTTTTTAAAATCCTGTTGAGGTCTCTGGTAGAAAGTTTTTCAATTCA
Found at i:9097 original size:29 final size:29
Alignment explanation
Indices: 9049--9116 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
9039 TGTCTCTTAA
*
9049 ATTGGTCA--TTTGCACGTTCAGGGGCAT
1 ATTGGTCATTTTTGCACATTCAGGGGCAT
* *
9076 TTTGGTCATTTTTGCACATTCAGGGGCGT
1 ATTGGTCATTTTTGCACATTCAGGGGCAT
9105 ATTGGTCATTTT
1 ATTGGTCATTTT
9117 GCATACTAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 7 0.20
29 28 0.80
ACGTcount: A:0.16, C:0.16, G:0.26, T:0.41
Consensus pattern (29 bp):
ATTGGTCATTTTTGCACATTCAGGGGCAT
Done.