Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017673.1 Corchorus olitorius cultivar O-4 contig17706, 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: 55935
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:98 original size:42 final size:42
Alignment explanation
Indices: 52--136 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
42 TTTGTATTAA
*
52 TTTTGAATATTAAATACATAAATAATTATCAGGTGGGGTATG
1 TTTTGAATATTAAATACATAAATAATTATCAGGTAGGGTATG
* * *
94 TTTTGAATATTAAATACATAATTTATTATTAGGTAGGGTATG
1 TTTTGAATATTAAATACATAAATAATTATCAGGTAGGGTATG
136 T
1 T
137 GTCAACATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.36, C:0.04, G:0.18, T:0.42
Consensus pattern (42 bp):
TTTTGAATATTAAATACATAAATAATTATCAGGTAGGGTATG
Found at i:718 original size:16 final size:16
Alignment explanation
Indices: 699--752 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
689 CTCGGGTCAC
*
699 TTGGGCTACGGGTTAT
1 TTGGGTTACGGGTTAT
* *
715 TTGGGTTTCGGGTCAT
1 TTGGGTTACGGGTTAT
* *
731 CTGGGTTACGAGTTAT
1 TTGGGTTACGGGTTAT
*
747 TCGGGT
1 TTGGGT
753 CTCGGGTCGG
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.11, C:0.13, G:0.37, T:0.39
Consensus pattern (16 bp):
TTGGGTTACGGGTTAT
Found at i:746 original size:32 final size:32
Alignment explanation
Indices: 681--760 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 32
671 GTCACAGGTC
* *
681 ATTCAGGTCTCGGGTCACTTGGGCTACGGGTT
1 ATTCGGGTCTCGGGTCACTTGGGCTACGAGTT
* * *
713 ATTTGGGTTTCGGGTCA-TCTGGGTTACGAGTT
1 ATTCGGGTCTCGGGTCACT-TGGGCTACGAGTT
745 ATTCGGGTCTCGGGTC
1 ATTCGGGTCTCGGGTC
761 GGGCGGGTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 1 0.03
32 39 0.98
ACGTcount: A:0.11, C:0.19, G:0.35, T:0.35
Consensus pattern (32 bp):
ATTCGGGTCTCGGGTCACTTGGGCTACGAGTT
Found at i:774 original size:15 final size:16
Alignment explanation
Indices: 748--777 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
738 ACGAGTTATT
748 CGGGTCTCGGGTCGGG
1 CGGGTCTCGGGTCGGG
764 CGGGT-TCGGGTCGG
1 CGGGTCTCGGGTCGG
778 TTACTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.00, C:0.23, G:0.57, T:0.20
Consensus pattern (16 bp):
CGGGTCTCGGGTCGGG
Found at i:2057 original size:40 final size:40
Alignment explanation
Indices: 2011--2086 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
2001 AAAGAAAGAT
*
2011 ATTAGTTTGTTAAATCTTAAAACAAATAAAAAGAAAAAAA
1 ATTAGTTTGTTAAATCTTAAAACAAAGAAAAAGAAAAAAA
*
2051 ATTAGTTTGTTAAATCTTAAATCAAAGAAAAAGAAA
1 ATTAGTTTGTTAAATCTTAAAACAAAGAAAAAGAAA
2087 TATGACAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.57, C:0.05, G:0.09, T:0.29
Consensus pattern (40 bp):
ATTAGTTTGTTAAATCTTAAAACAAAGAAAAAGAAAAAAA
Found at i:7225 original size:16 final size:16
Alignment explanation
Indices: 7188--7227 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
7178 AGAGGTTGAA
*
7188 AGAAAGCAATTAAACT
1 AGAAAACAATTAAACT
*
7204 -GAAAACAATTATACT
1 AGAAAACAATTAAACT
7219 AGAAAACAA
1 AGAAAACAA
7228 AACAAAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.60, C:0.12, G:0.10, T:0.17
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:8630 original size:29 final size:30
Alignment explanation
Indices: 8592--8651 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
8582 CAATTCTTGC
*
8592 TCTTGAAATAAATCTTCAA-AGTCTTCAAA
1 TCTTCAAATAAATCTTCAAGAGTCTTCAAA
*
8621 TCTTCAAATAAGTCTTCAATGAGTCTTCAAA
1 TCTTCAAATAAATCTTCAA-GAGTCTTCAAA
8652 CACGAACTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 17 0.63
31 10 0.37
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.35
Consensus pattern (30 bp):
TCTTCAAATAAATCTTCAAGAGTCTTCAAA
Found at i:15103 original size:21 final size:21
Alignment explanation
Indices: 15079--15128 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
15069 CTTAGGCAAT
15079 TCCAATGAGCTTGGAACCTT-C
1 TCCAATGAGCTTGGAA-CTTGC
15100 TCCAATGAGCTTGGAACTTGC
1 TCCAATGAGCTTGGAACTTGC
15121 TCCAATGA
1 TCCAATGA
15129 TCTCCTAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 3 0.11
21 25 0.89
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACTTGC
Found at i:20639 original size:25 final size:24
Alignment explanation
Indices: 20602--20648 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
20592 CTGGAAAATT
20602 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAACTTTGAT-GAT-AGATGGA
20628 TGAAAAAC-TTGATGATAGATG
1 TGAAAAACTTTGATGATAGATG
20649 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:21542 original size:21 final size:21
Alignment explanation
Indices: 21518--21609 Score: 168
Period size: 21 Copynumber: 4.4 Consensus size: 21
21508 CTTAGGCAAT
21518 TCCAATGAGCTTGGAACCTT-C
1 TCCAATGAGCTTGGAA-CTTGC
21539 TCCAATGAGCTTGGAACTTGC
1 TCCAATGAGCTTGGAACTTGC
21560 TCCAATGAGCTTGGAACTTGC
1 TCCAATGAGCTTGGAACTTGC
21581 TCCAATGAGCTTGGAACTTGC
1 TCCAATGAGCTTGGAACTTGC
21602 TCCAATGA
1 TCCAATGA
21610 TCTCCTAGCA
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
20 3 0.04
21 67 0.96
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACTTGC
Found at i:27501 original size:52 final size:53
Alignment explanation
Indices: 27430--27533 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 53
27420 TTTCTTTCTT
* *
27430 CAACAACTTTTTGTCCCGAAGTTGAACAAGTTTTGGGCCGAAGTTGTCCTGCG
1 CAACAACTTTCTGTCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTCCTGCG
27483 CAACAAC-TTCTGTCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTCCTGC
1 CAACAACTTTCTGTCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTCCTGC
27534 AATTCTTGTT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 42 0.86
53 7 0.14
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.28
Consensus pattern (53 bp):
CAACAACTTTCTGTCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTCCTGCG
Found at i:27510 original size:22 final size:22
Alignment explanation
Indices: 27484--27527 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
27474 TGTCCTGCGC
*
27484 AACAACTTCTGTCCCGAAGTTG
1 AACAACTTCTGGCCCGAAGTTG
* *
27506 AACAAGTTCTGGGCCGAAGTTG
1 AACAACTTCTGGCCCGAAGTTG
27528 TCCTGCAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (22 bp):
AACAACTTCTGGCCCGAAGTTG
Found at i:27583 original size:21 final size:21
Alignment explanation
Indices: 27559--27599 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
27549 TTCGACAGGC
*
27559 CAACTTCTGGGCAGAAGTTGA
1 CAACATCTGGGCAGAAGTTGA
*
27580 CAACATCTGGGCCGAAGTTG
1 CAACATCTGGGCAGAAGTTG
27600 TCCTGTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (21 bp):
CAACATCTGGGCAGAAGTTGA
Found at i:31794 original size:11 final size:10
Alignment explanation
Indices: 31778--31822 Score: 54
Period size: 11 Copynumber: 4.2 Consensus size: 10
31768 AAGTTCGTGT
31778 TTGAAGATTTA
1 TTGAAGA-TTA
*
31789 TTGAAGATAA
1 TTGAAGATTA
31799 TTTGAAGATTA
1 -TTGAAGATTA
31810 TTGAAGAATTA
1 TTGAAG-ATTA
31821 TT
1 TT
31823 TCAAGAAGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 8 0.27
11 22 0.73
ACGTcount: A:0.40, C:0.00, G:0.18, T:0.42
Consensus pattern (10 bp):
TTGAAGATTA
Found at i:31828 original size:22 final size:22
Alignment explanation
Indices: 31781--31828 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
31771 TTCGTGTTTG
*
31781 AAGATTTATTGAAGATAATTTG
1 AAGATTTATTGAAGATAATTTC
*
31803 AAGA-TTATTGAAGAATTATTTC
1 AAGATTTATTGAAG-ATAATTTC
31825 AAGA
1 AAGA
31829 AGCAAGAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.44, C:0.02, G:0.17, T:0.38
Consensus pattern (22 bp):
AAGATTTATTGAAGATAATTTC
Found at i:38222 original size:22 final size:23
Alignment explanation
Indices: 38178--38231 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
38168 TGATATAGTC
* * *
38178 ATTATAGTTAATTAAGGAGGTTA
1 ATTATGGTTAATTAAGCAAGTTA
38201 ATTATGGTT-ATTAAGCAAGTTA
1 ATTATGGTTAATTAAGCAAGTTA
38223 ATTAATGGT
1 ATT-ATGGT
38232 CGGTTACTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 14 0.52
23 13 0.48
ACGTcount: A:0.37, C:0.02, G:0.20, T:0.41
Consensus pattern (23 bp):
ATTATGGTTAATTAAGCAAGTTA
Found at i:40058 original size:12 final size:12
Alignment explanation
Indices: 40027--40059 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
40017 TCGAAGTTCG
40027 TATTTGAAGACT
1 TATTTGAAGACT
*
40039 CA-TTGAAGACT
1 TATTTGAAGACT
40050 TATTTGAAGA
1 TATTTGAAGA
40060 TTTGAAGACA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.36
Consensus pattern (12 bp):
TATTTGAAGACT
Found at i:40081 original size:29 final size:30
Alignment explanation
Indices: 40028--40088 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 30
40018 CGAAGTTCGT
* *
40028 ATTTGAAGACTCATTGAAGACTTATTTGAAG
1 ATTTGAAGAC-CATTGAAGAATTATTTCAAG
40059 ATTTGAAGA-CATTGAAGAATTATTTCAAG
1 ATTTGAAGACCATTGAAGAATTATTTCAAG
40088 A
1 A
40089 GGAAAGAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 19 0.68
31 9 0.32
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.34
Consensus pattern (30 bp):
ATTTGAAGACCATTGAAGAATTATTTCAAG
Found at i:41468 original size:15 final size:16
Alignment explanation
Indices: 41435--41474 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
41425 TTACTTTGCT
41435 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
41451 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
41466 TTGCTTTCT
1 TTGTTTTCT
41475 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:41847 original size:30 final size:28
Alignment explanation
Indices: 41811--41888 Score: 75
Period size: 30 Copynumber: 2.7 Consensus size: 28
41801 TTTTTCTAAA
**
41811 AAAAAAATTTGTTTTGTGTTTTTGCGTCAT
1 AAAAAAATTTGTTTTGTGTTTTT-AAT-AT
*** * *
41841 AAAAAAAAGGGTTTTGCGTTTTTAATTT
1 AAAAAAATTTGTTTTGTGTTTTTAATAT
41869 AAAAAAATTTGTTTTGTGTT
1 AAAAAAATTTGTTTTGTGTT
41889 GCGTTTTTGA
Statistics
Matches: 37, Mismatches: 11, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
28 17 0.46
29 1 0.03
30 19 0.51
ACGTcount: A:0.32, C:0.04, G:0.17, T:0.47
Consensus pattern (28 bp):
AAAAAAATTTGTTTTGTGTTTTTAATAT
Found at i:41931 original size:28 final size:28
Alignment explanation
Indices: 41900--41959 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
41890 CGTTTTTGAA
* *
41900 AAAAAAAAAGAGTTTT-TGCGTTATATAT
1 AAAAAAAAAG-GTTTTCTGCGTCATAAAT
*
41928 AAAAAAAAAGTTTTTCTGCGTCATAAAT
1 AAAAAAAAAGGTTTTCTGCGTCATAAAT
41956 AAAA
1 AAAA
41960 TTTTTTTTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 4 0.14
28 24 0.86
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.32
Consensus pattern (28 bp):
AAAAAAAAAGGTTTTCTGCGTCATAAAT
Found at i:47036 original size:25 final size:25
Alignment explanation
Indices: 46987--47039 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
46977 AGAGAGTCTG
*
46987 CATGCATCATAATCTTAATCAATGC
1 CATGCATCATAATCTTAATAAATGC
47012 CATGCATCATAATCTTAA-AATATGC
1 CATGCATCATAATCTTAATAA-ATGC
47037 CAT
1 CAT
47040 AATTTTTTCG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 1 0.04
25 25 0.96
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.32
Consensus pattern (25 bp):
CATGCATCATAATCTTAATAAATGC
Found at i:48316 original size:29 final size:30
Alignment explanation
Indices: 48269--48328 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
48259 GAAGTTCGTG
* *
48269 TTTGAAGACTCATTGAAGACTTATTTGAAGA
1 TTTGAAGAC-CATTGAAGAATTATTTCAAGA
48300 TTTGAAGA-CATTGAAGAATTATTTCAAGA
1 TTTGAAGACCATTGAAGAATTATTTCAAGA
48329 GGAAAGAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 19 0.70
31 8 0.30
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.35
Consensus pattern (30 bp):
TTTGAAGACCATTGAAGAATTATTTCAAGA
Found at i:49735 original size:15 final size:16
Alignment explanation
Indices: 49702--49741 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
49692 TTACTTTGCT
49702 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
49718 TTGTTTTC-AGTTTAA
1 TTGTTTTCTAGTATAA
*
49733 TTGCTTTCT
1 TTGTTTTCT
49742 TTCAACCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.17, C:0.10, G:0.12, T:0.60
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:49993 original size:15 final size:15
Alignment explanation
Indices: 49973--50003 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
49963 TCAAATTATC
*
49973 AATATCCTTATAAGT
1 AATATCCTAATAAGT
49988 AATATCCTAATAAGT
1 AATATCCTAATAAGT
50003 A
1 A
50004 GGCAAGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.35
Consensus pattern (15 bp):
AATATCCTAATAAGT
Done.