Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024757.1 Corchorus olitorius cultivar O-4 contig24790, 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: 56396
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5531 original size:14 final size:14
Alignment explanation
Indices: 5512--5551 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
5502 TTAAGATTTC
*
5512 AAAAAAATCTCTAT
1 AAAAAAATCCCTAT
5526 AAAAAAATCCCTAT
1 AAAAAAATCCCTAT
5540 AAAAAAATCCCT
1 AAAAAAATCCCT
5552 CTTGATTATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.57, C:0.20, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAAAAATCCCTAT
Found at i:7945 original size:21 final size:21
Alignment explanation
Indices: 7919--7959 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
7909 TCGGTCTCGA
* *
7919 CAAACCAATCATCATATCAAC
1 CAAACCAAACACCATATCAAC
7940 CAAACCAAACACCATATCAA
1 CAAACCAAACACCATATCAA
7960 ACAATCACAC
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:0.51, C:0.34, G:0.00, T:0.15
Consensus pattern (21 bp):
CAAACCAAACACCATATCAAC
Found at i:9330 original size:35 final size:35
Alignment explanation
Indices: 9246--9382 Score: 193
Period size: 35 Copynumber: 3.8 Consensus size: 35
9236 GGCTTTGTTG
** *
9246 TTGCTTTGTTGATGGAGAAGAACTTTGCTGTTTTGTT
1 TTGCTTTGTTGATGGAGAAGAACTTTGC--TTCAGAT
*
9283 GTTGCTTTGTTGATGGAGAAGAACTTTACTTCAGAT
1 -TTGCTTTGTTGATGGAGAAGAACTTTGCTTCAGAT
*
9319 TTGCTTTGTTGATGGAGAAGAACTTTGCTTCAAAT
1 TTGCTTTGTTGATGGAGAAGAACTTTGCTTCAGAT
9354 TTGCTTTGCTTGATGGAGAAGAACTTTGC
1 TTGCTTTG-TTGATGGAGAAGAACTTTGC
9383 CTTGCCTCTT
Statistics
Matches: 92, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
35 41 0.45
36 24 0.26
38 27 0.29
ACGTcount: A:0.22, C:0.11, G:0.26, T:0.42
Consensus pattern (35 bp):
TTGCTTTGTTGATGGAGAAGAACTTTGCTTCAGAT
Found at i:9395 original size:73 final size:72
Alignment explanation
Indices: 9246--9380 Score: 202
Period size: 73 Copynumber: 1.9 Consensus size: 72
9236 GGCTTTGTTG
****
9246 TTGCTTTGTTGATGGAGAAGAACTTTGCTGTTTTGTTGTTGCTTTGTTGATGGAGAAGAACTTTA
1 TTGCTTTGTTGATGGAGAAGAACTTTGC-GTTCAAATGTTGCTTTGTTGATGGAGAAGAACTTTA
9311 CTTCAGAT
65 CTTCAGAT
9319 TTGCTTTGTTGATGGAGAAGAACTTTGC-TTCAAAT-TTGCTTTGCTTGATGGAGAAGAACTTT
1 TTGCTTTGTTGATGGAGAAGAACTTTGCGTTCAAATGTTGCTTTG-TTGATGGAGAAGAACTTT
9381 GCCTTGCCTC
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
70 8 0.14
71 21 0.37
73 28 0.49
ACGTcount: A:0.22, C:0.10, G:0.25, T:0.42
Consensus pattern (72 bp):
TTGCTTTGTTGATGGAGAAGAACTTTGCGTTCAAATGTTGCTTTGTTGATGGAGAAGAACTTTAC
TTCAGAT
Found at i:11445 original size:46 final size:46
Alignment explanation
Indices: 11378--11577 Score: 312
Period size: 46 Copynumber: 4.4 Consensus size: 46
11368 AACAACCTGT
* * ***
11378 ATCGGTTTCTTCGCGGGGTTGATTATTTATTGGCCTCTACCTCTGC
1 ATCGGCTTCTTGGCGGGGTTGATTATTTATCACCCTCTACCTCTGC
*
11424 ATCGGCTTCTTGGCGGGGTTGATTATTTATCACCCTCTACCGCTGC
1 ATCGGCTTCTTGGCGGGGTTGATTATTTATCACCCTCTACCTCTGC
*
11470 ATCGGCTTCTTGGCGGGGTTGATTATTTATCGCCCTCTACCTCTGC
1 ATCGGCTTCTTGGCGGGGTTGATTATTTATCACCCTCTACCTCTGC
*
11516 ATCAGCTTCTTGGCGGGGTTGATTATTTATCACCCTCTACCTCTGC
1 ATCGGCTTCTTGGCGGGGTTGATTATTTATCACCCTCTACCTCTGC
*
11562 ATCGACTTCTT-GCGGG
1 ATCGGCTTCTTGGCGGG
11578 ATGGTCACTC
Statistics
Matches: 142, Mismatches: 12, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
45 5 0.04
46 137 0.96
ACGTcount: A:0.12, C:0.27, G:0.23, T:0.37
Consensus pattern (46 bp):
ATCGGCTTCTTGGCGGGGTTGATTATTTATCACCCTCTACCTCTGC
Found at i:15067 original size:35 final size:35
Alignment explanation
Indices: 15000--15136 Score: 202
Period size: 35 Copynumber: 3.8 Consensus size: 35
14990 GGCTTTGTTG
* ** *
15000 TTGCTTTGTTTATGGAGAAGAACTTTGCTGCTTTGTT
1 TTGCTTTGTTGATGGAGAAGAACTTTGCT--TCAGAT
15037 GTTGCTTTGTTGATGGAGAAGAACTTTGCTTCAGAT
1 -TTGCTTTGTTGATGGAGAAGAACTTTGCTTCAGAT
15073 TTGCTTTGTTGATGGAGAAGAACTTTGCTTCAGAT
1 TTGCTTTGTTGATGGAGAAGAACTTTGCTTCAGAT
15108 TTGCTTTGCTTGATGGAGAAGAACTTTGC
1 TTGCTTTG-TTGATGGAGAAGAACTTTGC
15137 CTTGCCTTTG
Statistics
Matches: 94, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
35 43 0.46
36 23 0.24
38 28 0.30
ACGTcount: A:0.20, C:0.12, G:0.26, T:0.42
Consensus pattern (35 bp):
TTGCTTTGTTGATGGAGAAGAACTTTGCTTCAGAT
Found at i:15092 original size:73 final size:71
Alignment explanation
Indices: 15000--15136 Score: 204
Period size: 73 Copynumber: 1.9 Consensus size: 71
14990 GGCTTTGTTG
* ** *
15000 TTGCTTTGTTTATGGAGAAGAACTTTGCTGCTTTGTTGTTGCTTTG-TTGATGGAGAAGAACTTT
1 TTGCTTTGTTGATGGAGAAGAACTTTGCT--TCAGAT-TTGCTTTGCTTGATGGAGAAGAACTTT
15064 GCTTCAGAT
63 GCTTCAGAT
15073 TTGCTTTGTTGATGGAGAAGAACTTTGCTTCAGATTTGCTTTGCTTGATGGAGAAGAACTTTGC
1 TTGCTTTGTTGATGGAGAAGAACTTTGCTTCAGATTTGCTTTGCTTGATGGAGAAGAACTTTGC
15137 CTTGCCTTTG
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
70 8 0.14
71 23 0.39
73 28 0.47
ACGTcount: A:0.20, C:0.12, G:0.26, T:0.42
Consensus pattern (71 bp):
TTGCTTTGTTGATGGAGAAGAACTTTGCTTCAGATTTGCTTTGCTTGATGGAGAAGAACTTTGCT
TCAGAT
Found at i:16111 original size:26 final size:25
Alignment explanation
Indices: 16067--16119 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
16057 TATAAAATTG
*
16067 TCAAAAATATTTTCAAATTGCCATTA
1 TCAAAAATAATTTCAAATT-CCATTA
*
16093 TCAAAATATAATTTC-AATTCCTTTA
1 TCAAAA-ATAATTTCAAATTCCATTA
16118 TC
1 TC
16120 TATACTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 7 0.29
26 10 0.42
27 7 0.29
ACGTcount: A:0.40, C:0.17, G:0.02, T:0.42
Consensus pattern (25 bp):
TCAAAAATAATTTCAAATTCCATTA
Found at i:25092 original size:8 final size:7
Alignment explanation
Indices: 25066--25100 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
25056 CCCAAGTCTT
*
25066 CTTTCTC
1 CTTTTTC
25073 CTTTTTC
1 CTTTTTC
*
25080 GTTTTTC
1 CTTTTTC
25087 CTTTTTC
1 CTTTTTC
25094 CTTTTTC
1 CTTTTTC
25101 ATTTCCTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.00, C:0.29, G:0.03, T:0.69
Consensus pattern (7 bp):
CTTTTTC
Found at i:26510 original size:2 final size:2
Alignment explanation
Indices: 26503--26534 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
26493 GATTGAGCTG
26503 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26535 GTGTGTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26539 original size:2 final size:2
Alignment explanation
Indices: 26534--26582 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
26524 TATATATATA
26534 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
26576 TG TG TG T
1 TG TG TG T
26583 AAAAATATGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:29588 original size:32 final size:32
Alignment explanation
Indices: 29566--29718 Score: 234
Period size: 32 Copynumber: 4.8 Consensus size: 32
29556 TTTATTTAAG
*
29566 GAAACGCCGCTAAATAGTGGCGTTCCTGCACC
1 GAAACGCCGCTAAATAGTGGCGTTTCTGCACC
* *
29598 GAAATGCCGCTAAATAGTGGCGTCTCTGCACC
1 GAAACGCCGCTAAATAGTGGCGTTTCTGCACC
* *
29630 GAAACGCTGCTAAATAGTGGCGTTTCTGCATC
1 GAAACGCCGCTAAATAGTGGCGTTTCTGCACC
* *
29662 AAAACGCCGCTAAATAGTGGCGTTTCTACACC
1 GAAACGCCGCTAAATAGTGGCGTTTCTGCACC
*
29694 GAAACGCCGTTAAATAGTGGCGTTT
1 GAAACGCCGCTAAATAGTGGCGTTT
29719 TGGTTTAGAA
Statistics
Matches: 108, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 108 1.00
ACGTcount: A:0.27, C:0.25, G:0.24, T:0.24
Consensus pattern (32 bp):
GAAACGCCGCTAAATAGTGGCGTTTCTGCACC
Found at i:42563 original size:2 final size:2
Alignment explanation
Indices: 42556--42591 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
42546 CCAGTAAGTA
42556 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42592 TTTCGTTCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42632 original size:17 final size:18
Alignment explanation
Indices: 42612--42652 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
42602 ATCAAAATGT
42612 AAAAAGAAAGA-AAAAAA
1 AAAAAGAAAGAGAAAAAA
*
42629 AAAAGGAAAGAGAAAAAA
1 AAAAAGAAAGAGAAAAAA
42647 AAAAAG
1 AAAAAG
42653 GAAAAGTGCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAGAGAAAAAA
Found at i:42658 original size:20 final size:19
Alignment explanation
Indices: 42620--42656 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
42610 GTAAAAAGAA
42620 AGAAAAAAAAAAAGGAAAG
1 AGAAAAAAAAAAAGGAAAG
42639 AGAAAAAAAAAAAGGAAA
1 AGAAAAAAAAAAAGGAAA
42657 AGTGCCTGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (19 bp):
AGAAAAAAAAAAAGGAAAG
Found at i:44023 original size:19 final size:20
Alignment explanation
Indices: 43999--44056 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 20
43989 CTGTTTGACA
43999 ACTGTACAGATGAGATTA-C
1 ACTGTACAGATGAGATTAGC
* *
44018 ACTGTACAGATTAGATTAGGT
1 ACTGTACAGATGAGATTA-GC
*
44039 ACTATACAGATGAGATTA
1 ACTGTACAGATGAGATTA
44057 TTAGAGCAGC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.52
21 16 0.48
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (20 bp):
ACTGTACAGATGAGATTAGC
Found at i:45444 original size:2 final size:2
Alignment explanation
Indices: 45437--45464 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
45427 CTTCATCTTT
45437 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
45465 AAAGTACGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:50595 original size:7 final size:6
Alignment explanation
Indices: 50576--50610 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
50566 TTTGATTTAC
50576 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT GTTCT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT -TTCT
50611 ATTATTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 24 0.86
7 4 0.14
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (6 bp):
TTCTTT
Found at i:50827 original size:16 final size:17
Alignment explanation
Indices: 50801--50832 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
50791 CCTAGGTATG
50801 TAAATTTTATAATATTA
1 TAAATTTTATAATATTA
50818 TAAA-TTTATAATATT
1 TAAATTTTATAATATT
50833 TTATCTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAAATTTTATAATATTA
Found at i:51481 original size:2 final size:2
Alignment explanation
Indices: 51474--51504 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
51464 CTTAAAATGA
51474 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
51505 CTAGTACTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54320 original size:31 final size:31
Alignment explanation
Indices: 54273--54351 Score: 115
Period size: 31 Copynumber: 2.5 Consensus size: 31
54263 ATTTTTAGCC
* * *
54273 ACCAACTTGAGTCTAAATCTTTCAAAAGTTG
1 ACCAATTTGAGGCTAAACCTTTCAAAAGTTG
54304 -CTCAATTTGAGGCTAAACCTTTCAAAAGTTG
1 AC-CAATTTGAGGCTAAACCTTTCAAAAGTTG
54335 ACCAATTTGAGGCTAAA
1 ACCAATTTGAGGCTAAA
54352 ATAAAAACGG
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
30 1 0.02
31 41 0.95
32 1 0.02
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.30
Consensus pattern (31 bp):
ACCAATTTGAGGCTAAACCTTTCAAAAGTTG
Found at i:56369 original size:52 final size:52
Alignment explanation
Indices: 56287--56389 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 52
56277 ATAGAGAAAA
56287 CAAAAATTGACAAGATTATAATAGATAAAATATATTATTTCATTTGCTATAG
1 CAAAAATTGACAAGATTATAATAGATAAAATATATTATTTCATTTGCTATAG
*
56339 CAAAAATTGGCAAGATTATAATAGGA-AAAATATATTATTTCATTTGCTATA
1 CAAAAATTGACAAGATTATAATA-GATAAAATATATTATTTCATTTGCTATA
56390 TCCATGC
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
52 47 0.96
53 2 0.04
ACGTcount: A:0.46, C:0.08, G:0.11, T:0.36
Consensus pattern (52 bp):
CAAAAATTGACAAGATTATAATAGATAAAATATATTATTTCATTTGCTATAG
Done.