Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018754.1 Corchorus olitorius cultivar O-4 contig18787, 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: 39833
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:269 original size:24 final size:24
Alignment explanation
Indices: 242--309 Score: 118
Period size: 24 Copynumber: 2.8 Consensus size: 24
232 TTGGTCTTTT
*
242 CCACGACCACTATGTGGCCGAATC
1 CCACGACCACCATGTGGCCGAATC
266 CCACGACCACCATGTGGCCGAATC
1 CCACGACCACCATGTGGCCGAATC
*
290 TCACGACCACCATGTGGCCG
1 CCACGACCACCATGTGGCCG
310 TTTGATTTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.24, C:0.40, G:0.22, T:0.15
Consensus pattern (24 bp):
CCACGACCACCATGTGGCCGAATC
Found at i:886 original size:23 final size:23
Alignment explanation
Indices: 859--933 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 23
849 ATTTCCCAAT
859 ATGGCTAGATTGAAAATCCAACC
1 ATGGCTAGATTGAAAATCCAACC
* * * *
882 ATGGCTTG-GTGAAATTTCCCAA-T
1 ATGGCTAGATTGAAA-AT-CCAACC
905 ATGGCTAGATTGAAAATCCAACC
1 ATGGCTAGATTGAAAATCCAACC
928 ATGGCT
1 ATGGCT
934 TGGTAAAATT
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
22 9 0.22
23 22 0.55
24 9 0.22
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (23 bp):
ATGGCTAGATTGAAAATCCAACC
Found at i:894 original size:22 final size:22
Alignment explanation
Indices: 869--942 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 22
859 ATGGCTAGAT
869 TGAAAATCCAACCATGGCTTGG
1 TGAAAATCCAACCATGGCTTGG
* * * *
891 TGAAATTTCCCAA-TATGGCTAGAT
1 TGAAA-AT-CCAACCATGGCTTG-G
915 TGAAAATCCAACCATGGCTTGG
1 TGAAAATCCAACCATGGCTTGG
937 T-AAAAT
1 TGAAAAT
943 TTCAACTATA
Statistics
Matches: 40, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
21 5 0.12
22 10 0.25
23 16 0.40
24 9 0.22
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (22 bp):
TGAAAATCCAACCATGGCTTGG
Found at i:897 original size:46 final size:46
Alignment explanation
Indices: 821--945 Score: 207
Period size: 46 Copynumber: 2.7 Consensus size: 46
811 TTTGCCAATA
* *
821 ATTGAAAA-CCAAACCATAGCTTTGTAAAATTTCCCAATATGGCTAG
1 ATTGAAAATCC-AACCATGGCTTGGTAAAATTTCCCAATATGGCTAG
*
867 ATTGAAAATCCAACCATGGCTTGGTGAAATTTCCCAATATGGCTAG
1 ATTGAAAATCCAACCATGGCTTGGTAAAATTTCCCAATATGGCTAG
913 ATTGAAAATCCAACCATGGCTTGGTAAAATTTC
1 ATTGAAAATCCAACCATGGCTTGGTAAAATTTC
946 AACTATAGCA
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
46 72 0.97
47 2 0.03
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (46 bp):
ATTGAAAATCCAACCATGGCTTGGTAAAATTTCCCAATATGGCTAG
Found at i:918 original size:24 final size:24
Alignment explanation
Indices: 847--919 Score: 80
Period size: 23 Copynumber: 3.1 Consensus size: 24
837 TAGCTTTGTA
847 AAATTTCCCAATATGGCTAGATTG
1 AAATTTCCCAATATGGCTAGATTG
* * * *
871 AAA-AT-CCAACCATGGCTTG-GTG
1 AAATTTCCCAA-TATGGCTAGATTG
893 AAATTTCCCAATATGGCTAGATTG
1 AAATTTCCCAATATGGCTAGATTG
917 AAA
1 AAA
920 ATCCAACCAT
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
22 9 0.24
23 16 0.43
24 12 0.32
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (24 bp):
AAATTTCCCAATATGGCTAGATTG
Found at i:6102 original size:36 final size:37
Alignment explanation
Indices: 6041--6114 Score: 141
Period size: 36 Copynumber: 2.0 Consensus size: 37
6031 AAGATTGTTA
6041 AGACAAGAGTCTTAAAAAGAGTAGACAAGAGTCTAAG
1 AGACAAGAGTCTTAAAAAGAGTAGACAAGAGTCTAAG
6078 AGACAAGAGTCTT-AAAAGAGTAGACAAGAGTCTAAG
1 AGACAAGAGTCTTAAAAAGAGTAGACAAGAGTCTAAG
6114 A
1 A
6115 AAACAAAAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 24 0.65
37 13 0.35
ACGTcount: A:0.49, C:0.11, G:0.24, T:0.16
Consensus pattern (37 bp):
AGACAAGAGTCTTAAAAAGAGTAGACAAGAGTCTAAG
Found at i:6704 original size:24 final size:24
Alignment explanation
Indices: 6677--6744 Score: 118
Period size: 24 Copynumber: 2.8 Consensus size: 24
6667 TTGGTCTTTT
*
6677 CCACGACCACTATGTGGCCGAATC
1 CCACGACCACCATGTGGCCGAATC
6701 CCACGACCACCATGTGGCCGAATC
1 CCACGACCACCATGTGGCCGAATC
*
6725 TCACGACCACCATGTGGCCG
1 CCACGACCACCATGTGGCCG
6745 TTTGATTTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.24, C:0.40, G:0.22, T:0.15
Consensus pattern (24 bp):
CCACGACCACCATGTGGCCGAATC
Found at i:7190 original size:6 final size:6
Alignment explanation
Indices: 7172--7206 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
7162 TTTTTTTTCA
*
7172 ATTTTT ATATTT ATTTTT ATTTTT ATTTTT ATTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTT
7207 ATAGTTTGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:7568 original size:15 final size:16
Alignment explanation
Indices: 7542--7571 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
7532 GAAAAAACGA
7542 TTTTTTCTTTGTCAAC
1 TTTTTTCTTTGTCAAC
7558 TTTTTTC-TTGTCAA
1 TTTTTTCTTTGTCAA
7572 AAGAAACACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63
Consensus pattern (16 bp):
TTTTTTCTTTGTCAAC
Found at i:9102 original size:14 final size:14
Alignment explanation
Indices: 9077--9122 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
9067 CGTCCATTCC
9077 TTTTTATCTGTCGT
1 TTTTTATCTGTCGT
* * *
9091 TTTTTCTTTGTCCT
1 TTTTTATCTGTCGT
9105 TTTTTATCTGTCGT
1 TTTTTATCTGTCGT
9119 TTTT
1 TTTT
9123 GGGCATAATT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.04, C:0.15, G:0.11, T:0.70
Consensus pattern (14 bp):
TTTTTATCTGTCGT
Found at i:10008 original size:47 final size:47
Alignment explanation
Indices: 9934--10027 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
9924 ACCGTCAACA
*
9934 CCGTTAGTCACGTGCCATCATGTGCACGGTTCTGTCAACCCCCTAGT
1 CCGTTAGTCACGTGCCATCATGCGCACGGTTCTGTCAACCCCCTAGT
9981 CCGTTAGTCACGTGCCATCATGCGCACGGTTCTGTCAACCCCCTAGT
1 CCGTTAGTCACGTGCCATCATGCGCACGGTTCTGTCAACCCCCTAGT
10028 TAACTGCTTA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.17, C:0.35, G:0.21, T:0.27
Consensus pattern (47 bp):
CCGTTAGTCACGTGCCATCATGCGCACGGTTCTGTCAACCCCCTAGT
Found at i:11066 original size:35 final size:34
Alignment explanation
Indices: 11023--11090 Score: 127
Period size: 35 Copynumber: 2.0 Consensus size: 34
11013 TGAAGATCGC
11023 AGGAGATGAAGGAAAATAGAAAGAAAAAGGGAAGG
1 AGGAGATGAAGGAAAATAGAAAG-AAAAGGGAAGG
11058 AGGAGATGAAGGAAAATAGAAAGAAAAGGGAAG
1 AGGAGATGAAGGAAAATAGAAAGAAAAGGGAAG
11091 AAAAAAGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 10 0.30
35 23 0.70
ACGTcount: A:0.57, C:0.00, G:0.37, T:0.06
Consensus pattern (34 bp):
AGGAGATGAAGGAAAATAGAAAGAAAAGGGAAGG
Found at i:15186 original size:29 final size:29
Alignment explanation
Indices: 15144--15202 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
15134 AAAATTTTAA
15144 GGCTAGTTAAATTCAGTCTAAAGAATTAG
1 GGCTAGTTAAATTCAGTCTAAAGAATTAG
15173 GGCTAGTTAAATTCAGTCTAAAGAATTAG
1 GGCTAGTTAAATTCAGTCTAAAGAATTAG
15202 G
1 G
15203 CCTAAATTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (29 bp):
GGCTAGTTAAATTCAGTCTAAAGAATTAG
Found at i:19175 original size:31 final size:31
Alignment explanation
Indices: 19140--19211 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
19130 TAAATTATTG
*
19140 CAAATTAAAACAAATTAA-GCATTAAATTAAA
1 CAAATTAAAA-AAATGAATGCATTAAATTAAA
* *
19171 CAAA-TAATTAAAATGAATGCCTTAAATTAAA
1 CAAATTAA-AAAAATGAATGCATTAAATTAAA
19202 CAAATTAAAA
1 CAAATTAAAA
19212 GATGATAGAC
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
30 9 0.26
31 22 0.65
32 3 0.09
ACGTcount: A:0.60, C:0.10, G:0.04, T:0.26
Consensus pattern (31 bp):
CAAATTAAAAAAATGAATGCATTAAATTAAA
Found at i:31792 original size:21 final size:21
Alignment explanation
Indices: 31768--31833 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
31758 GAGAATATTC
*
31768 TTATCTATACAGTAATAAATT
1 TTATCTATACAGTAACAAATT
* * *
31789 TTATCTGTATAGTAACAAATC
1 TTATCTATACAGTAACAAATT
* * * *
31810 TAATCCATACAATAACCAATT
1 TTATCTATACAGTAACAAATT
31831 TTA
1 TTA
31834 CTCTTACCGA
Statistics
Matches: 33, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.42, C:0.15, G:0.05, T:0.38
Consensus pattern (21 bp):
TTATCTATACAGTAACAAATT
Found at i:38042 original size:37 final size:37
Alignment explanation
Indices: 37996--38066 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
37986 AGTTATCGGG
*
37996 AAAAAAGGACATGACTATGGAGAAGGCAGAATAGGGA
1 AAAAAAGGACATGAATATGGAGAAGGCAGAATAGGGA
38033 AAAAAAGGACATGAATATGGAGAAGGCAGAATAG
1 AAAAAAGGACATGAATATGGAGAAGGCAGAATAG
38067 TACATATACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.51, C:0.07, G:0.31, T:0.11
Consensus pattern (37 bp):
AAAAAAGGACATGAATATGGAGAAGGCAGAATAGGGA
Done.