Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015038.1 Corchorus olitorius cultivar O-4 contig15071, 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: 32920
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Found at i:3442 original size:15 final size:15
Alignment explanation
Indices: 3412--3455 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
3402 TAACTTTGCT
3412 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
3428 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
3443 TTGCTTTT-TGTTT
1 TTG-TTTTCTGTTT
3456 TCTGTGTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 14 0.52
16 13 0.48
ACGTcount: A:0.11, C:0.07, G:0.14, T:0.68
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:13070 original size:13 final size:14
Alignment explanation
Indices: 13047--13075 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
13037 TCTCTAAATT
13047 AATGCATGTATGCA
1 AATGCATGTATGCA
13061 AATG-ATGTATGCA
1 AATGCATGTATGCA
13074 AA
1 AA
13076 GTCCAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.28
Consensus pattern (14 bp):
AATGCATGTATGCA
Found at i:16538 original size:28 final size:27
Alignment explanation
Indices: 16497--16603 Score: 106
Period size: 28 Copynumber: 3.9 Consensus size: 27
16487 TGTGAACTTA
* *
16497 AAATGACCACAATGCCCCTTGAGTGTGC
1 AAATGACCAAAATGCCCCTGGA-TGTGC
*
16525 AAATGACCAAAATGCCCCTGGATGTTC
1 AAATGACCAAAATGCCCCTGGATGTGC
* * * **
16552 AAATGACTAAAATGCCCCTGAATATAAA
1 AAATGACCAAAATGCCCCTGGATGT-GC
* *
16580 AAAAGACCAAAATGCCCCTAGATG
1 AAATGACCAAAATGCCCCTGGATG
16604 ACCCTAGTTT
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
27 26 0.40
28 39 0.60
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGGATGTGC
Found at i:16563 original size:27 final size:28
Alignment explanation
Indices: 16497--16571 Score: 107
Period size: 27 Copynumber: 2.7 Consensus size: 28
16487 TGTGAACTTA
* *
16497 AAATGACCACAATGCCCCTTGAGTGTGC
1 AAATGACCAAAATGCCCCTGGAGTGTGC
*
16525 AAATGACCAAAATGCCCCTGGA-TGTTC
1 AAATGACCAAAATGCCCCTGGAGTGTGC
*
16552 AAATGACTAAAATGCCCCTG
1 AAATGACCAAAATGCCCCTG
16572 AATATAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 23 0.53
28 20 0.47
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCTGGAGTGTGC
Found at i:17162 original size:50 final size:50
Alignment explanation
Indices: 17048--17475 Score: 631
Period size: 50 Copynumber: 8.3 Consensus size: 50
17038 ATGTTTGAAA
* **
17048 TGACTCGTATGGAAACGAGTTCGGCTTGTGGAAAAGCCTACGTGGCTTGGATAGC
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTA--T-G-TT-GATAAT
*
17103 TGACTCGTATGGAAACGAGCTTGGCTTGTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
*
17153 TGACTCGTATGGAAACGAGCTTGGCTTGTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
17203 TGACTCGTATGGAAACGAGTTTGGCTTGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGA---------GTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
* *
17262 TGACTCGTATGGAAATGAGTTTGGCTTGTGGAAAAGCCTGTGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
*
17312 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
*
17362 TGACTCGTATGGAAACGAGTTTGGCTTCTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
*
17412 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
*
17462 TGACTCATATGGAA
1 TGACTCGTATGGAA
17476 TGTTGATAAT
Statistics
Matches: 349, Mismatches: 15, Indels: 23
0.90 0.04 0.06
Matches are distributed among these distances:
50 259 0.74
51 2 0.01
52 1 0.00
53 1 0.00
55 38 0.11
59 48 0.14
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.31
Consensus pattern (50 bp):
TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
Found at i:17413 original size:209 final size:213
Alignment explanation
Indices: 17048--17440 Score: 677
Period size: 209 Copynumber: 1.9 Consensus size: 213
17038 ATGTTTGAAA
*
17048 TGACTCGTATGGAAACGAGTTCGGCTTGTGGAAAAGCCTACGTGGCTTGGATAGCTGACTCGTAT
1 TGACTCGTATGGAAACGAGTTCGGCTTGTGGAAAAGCCTA-GTGGCTTGGATAACTGACTCGTAT
*
17113 GGAAACGAGCTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGCTTGGC
65 GGAAACGAGCTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACTCGTATGGAAACGAGCTTGGC
*
17178 TTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGTTTGGCTTGTTTGGCTTGTGG
130 TTCTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGTTTGGCTTGTTTGGCTTGTGG
17243 AAAAGCCTATGTTGATAAT
195 AAAAGCCTATGTTGATAAT
* * *
17262 TGACTCGTATGGAAATGAGTTTGGCTTGTGGAAAAGCCT-GT-G-TT-GATAATTGACTCGTATG
1 TGACTCGTATGGAAACGAGTTCGGCTTGTGGAAAAGCCTAGTGGCTTGGATAACTGACTCGTATG
* *
17323 GAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACTCGTATGGAAACGAGTTTGGCT
66 GAAACGAGCTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACTCGTATGGAAACGAGCTTGGCT
17388 TCTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGTTTGGCTTGT
131 TCTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGTTTGGCTTGT
17441 GGAAAAGCCC
Statistics
Matches: 171, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
209 129 0.75
210 2 0.01
211 1 0.01
212 2 0.01
214 37 0.22
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (213 bp):
TGACTCGTATGGAAACGAGTTCGGCTTGTGGAAAAGCCTAGTGGCTTGGATAACTGACTCGTATG
GAAACGAGCTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACTCGTATGGAAACGAGCTTGGCT
TCTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGTTTGGCTTGTTTGGCTTGTGGA
AAAGCCTATGTTGATAAT
Found at i:17483 original size:24 final size:24
Alignment explanation
Indices: 17451--17499 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
17441 GGAAAAGCCC
17451 ATGTTGATAATTGACTCATATGGA
1 ATGTTGATAATTGACTCATATGGA
*
17475 ATGTTGATAATTGACTCGTATGGA
1 ATGTTGATAATTGACTCATATGGA
17499 A
1 A
17500 ACAAGTTTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.22, T:0.37
Consensus pattern (24 bp):
ATGTTGATAATTGACTCATATGGA
Found at i:17522 original size:74 final size:74
Alignment explanation
Indices: 17401--17549 Score: 271
Period size: 74 Copynumber: 2.0 Consensus size: 74
17391 GGAAAAGCCT
*
17401 ATGTTGATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGAC
1 ATGTTGATAATTGACTCGTATGGAAACAAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGAC
17466 TCATATGGA
66 TCATATGGA
*
17475 ATGTTGATAATTGACTCGTATGGAAACAAGTTTGGCTTGTGGAAAAGCCCATGTTTATAATTGAC
1 ATGTTGATAATTGACTCGTATGGAAACAAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGAC
*
17540 TCGTATGGA
66 TCATATGGA
17549 A
1 A
17550 ACGAGTTTGG
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 72 1.00
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (74 bp):
ATGTTGATAATTGACTCGTATGGAAACAAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGAC
TCATATGGA
Found at i:17535 original size:50 final size:50
Alignment explanation
Indices: 17475--17578 Score: 181
Period size: 50 Copynumber: 2.1 Consensus size: 50
17465 CTCATATGGA
17475 ATGTTGATAATTGACTCGTATGGAAACAAGTTTGGCTTGTGGAAAAGCCC
1 ATGTTGATAATTGACTCGTATGGAAACAAGTTTGGCTTGTGGAAAAGCCC
* * *
17525 ATGTTTATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCT
1 ATGTTGATAATTGACTCGTATGGAAACAAGTTTGGCTTGTGGAAAAGCCC
17575 ATGT
1 ATGT
17579 ATTCGGATGG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (50 bp):
ATGTTGATAATTGACTCGTATGGAAACAAGTTTGGCTTGTGGAAAAGCCC
Found at i:17571 original size:124 final size:124
Alignment explanation
Indices: 17351--17578 Score: 411
Period size: 124 Copynumber: 1.8 Consensus size: 124
17341 GGAAAAGCCC
* *
17351 ATGTTGATAATTGACTCGTATGGAAACGAGTTTGGCTTCTGGAAAAGCCTATGTTGATAATTGAC
1 ATGTTGATAATTGACTCGTATGGAAACAAGTTTGGCTTCTGGAAAAGCCCATGTTGATAATTGAC
17416 TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACTCATATGGA
66 TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACTCATATGGA
* *
17475 ATGTTGATAATTGACTCGTATGGAAACAAGTTTGGCTTGTGGAAAAGCCCATGTTTATAATTGAC
1 ATGTTGATAATTGACTCGTATGGAAACAAGTTTGGCTTCTGGAAAAGCCCATGTTGATAATTGAC
*
17540 TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGT
66 TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGT
17579 ATTCGGATGG
Statistics
Matches: 99, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
124 99 1.00
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (124 bp):
ATGTTGATAATTGACTCGTATGGAAACAAGTTTGGCTTCTGGAAAAGCCCATGTTGATAATTGAC
TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACTCATATGGA
Found at i:17789 original size:79 final size:80
Alignment explanation
Indices: 17658--17811 Score: 274
Period size: 79 Copynumber: 1.9 Consensus size: 80
17648 ATACCTTTGG
*
17658 AAAATAACTCTGAATCTGATGTTGTAACTGAAAACTTCTTGATTGATGATG-AAAAAGGACCAAT
1 AAAATAACTCTGAATCTGATGTTGTAACTGAAAACCTCTTGATTGATGATGAAAAAAGGACCAAT
17722 GTGCGGTCAACTTGA
66 GTGCGGTCAACTTGA
*
17737 AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACCTCTTGATTGATGATGAAAAAAGGACCAAT
1 AAAATAACTCTGAATCTGATGTTGTAACTGAAAACCTCTTGATTGATGATGAAAAAAGGACCAAT
*
17802 TTGCGGTCAA
66 GTGCGGTCAA
17812 TTTTGATAAC
Statistics
Matches: 71, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
79 49 0.69
80 22 0.31
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (80 bp):
AAAATAACTCTGAATCTGATGTTGTAACTGAAAACCTCTTGATTGATGATGAAAAAAGGACCAAT
GTGCGGTCAACTTGA
Found at i:18463 original size:50 final size:50
Alignment explanation
Indices: 18264--18459 Score: 320
Period size: 50 Copynumber: 3.9 Consensus size: 50
18254 CTTCAATGTC
* * *
18264 CTTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTA
1 CTTTGAAAAGCAAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTA
*
18314 CTTTGAAAAGCAAATTTTGATCTTGAACTCACAAATGGAATGCAATCTTA
1 CTTTGAAAAGCAAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTA
* *
18364 CTTTGAAAAGAAAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
1 CTTTGAAAAGCAAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTA
* *
18414 CTTTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAAT
1 CTTTGAAAAGCAAATTTTGATCTTGAACTCACAAATGGAAAGCAAT
18460 TTTATTGTAA
Statistics
Matches: 138, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 138 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (50 bp):
CTTTGAAAAGCAAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTA
Found at i:19501 original size:7 final size:8
Alignment explanation
Indices: 19484--19508 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
19474 AGTGCCTTTA
19484 TTTTCATT
1 TTTTCATT
19492 TTTTCATT
1 TTTTCATT
19500 TTTTCATT
1 TTTTCATT
19508 T
1 T
19509 CATTTTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTCATT
Found at i:22256 original size:12 final size:14
Alignment explanation
Indices: 22235--22265 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
22225 CTACTAACAA
22235 TTTTTGTTTTGAGT
1 TTTTTGTTTTGAGT
22249 TTTTT-TTTTGAGT
1 TTTTTGTTTTGAGT
22262 TTTT
1 TTTT
22266 CTAGGAAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.06, C:0.00, G:0.16, T:0.77
Consensus pattern (14 bp):
TTTTTGTTTTGAGT
Found at i:25052 original size:32 final size:33
Alignment explanation
Indices: 25002--25082 Score: 83
Period size: 33 Copynumber: 2.5 Consensus size: 33
24992 CCGAGCCGCG
* * * *
25002 CCGAGACAGCTGCTCGGCCA-CAGCCCGGCCAC
1 CCGAGCCACCTGCCCGGCCACCAGCCCGACCAC
* * *
25034 CCGAGCCATCTGCCCGGCCACCAGCGCTACCAC
1 CCGAGCCACCTGCCCGGCCACCAGCCCGACCAC
*
25067 CCGCGCCACCTGCCCG
1 CCGAGCCACCTGCCCG
25083 ACCATCCGCG
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
32 17 0.43
33 23 0.57
ACGTcount: A:0.16, C:0.52, G:0.25, T:0.07
Consensus pattern (33 bp):
CCGAGCCACCTGCCCGGCCACCAGCCCGACCAC
Found at i:25086 original size:21 final size:21
Alignment explanation
Indices: 25062--25101 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
25052 CACCAGCGCT
25062 ACCACCCGCGCCACC-TGCCCG
1 ACCACCCGCG-CACCATGCCCG
*
25083 ACCATCCGCGCACCATGCC
1 ACCACCCGCGCACCATGCC
25102 TGGCTAGCCG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.17, C:0.57, G:0.17, T:0.07
Consensus pattern (21 bp):
ACCACCCGCGCACCATGCCCG
Done.