Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013305.1 Corchorus capsularis cultivar CVL-1 contig13326, 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: 58119
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Found at i:6441 original size:33 final size:32
Alignment explanation
Indices: 6345--6483 Score: 136
Period size: 33 Copynumber: 4.2 Consensus size: 32
6335 AAGGATCATA
** **
6345 TGGCCGGTTGTGGCCGGGCATGGCCGA-GTCATG
1 TGGCCGG-TGTGGCCGGGCATCTCC-ATGTCGCG
**
6378 TGGCCAGGTGTGGCCGGGCATGGCCATGTCGCG
1 TGGCC-GGTGTGGCCGGGCATCTCCATGTCGCG
*
6411 TGGCCGGTGATGGCCGGGCATCTCCATGTCGCA
1 TGGCCGGTG-TGGCCGGGCATCTCCATGTCGCG
* * *
6444 TAGCCGGTGTTGCGCGGGCATCTCCAAGTCGCG
1 TGGCCGGTGTGGC-CGGGCATCTCCATGTCGCG
6477 TGGCCGG
1 TGGCCGG
6484 ATCTCCAAGT
Statistics
Matches: 92, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
32 8 0.09
33 82 0.89
34 2 0.02
ACGTcount: A:0.10, C:0.28, G:0.42, T:0.20
Consensus pattern (32 bp):
TGGCCGGTGTGGCCGGGCATCTCCATGTCGCG
Found at i:6489 original size:21 final size:21
Alignment explanation
Indices: 6463--6504 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
6453 TTGCGCGGGC
*
6463 ATCTCCAAGTCGCGTGGCCGG
1 ATCTCCAAGTCGCATGGCCGG
6484 ATCTCCAAGTCGCATGGCCGG
1 ATCTCCAAGTCGCATGGCCGG
6505 TCACTTGTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.17, C:0.33, G:0.31, T:0.19
Consensus pattern (21 bp):
ATCTCCAAGTCGCATGGCCGG
Found at i:9492 original size:16 final size:15
Alignment explanation
Indices: 9466--9495 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
9456 TTTCTGCTAA
9466 TCTTTTTTCTTTTCT
1 TCTTTTTTCTTTTCT
9481 TCTTTTTCTCTTTTC
1 TCTTTTT-TCTTTTC
9496 CCTCGCCTTC
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:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (15 bp):
TCTTTTTTCTTTTCT
Found at i:16044 original size:23 final size:22
Alignment explanation
Indices: 16014--16076 Score: 65
Period size: 23 Copynumber: 2.9 Consensus size: 22
16004 AAAAAAATTA
**
16014 TTTTTTTTAACACAAATCCTAAT
1 TTTTTTTTAACACAAAAAC-AAT
* *
16037 TTTTTTTTATCGCAAAAACAAT
1 TTTTTTTTAACACAAAAACAAT
*
16059 TTTTTTTTAA-AGAAAAAC
1 TTTTTTTTAACACAAAAAC
16077 GCAAATACAA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
21 6 0.18
22 12 0.36
23 15 0.45
ACGTcount: A:0.38, C:0.13, G:0.03, T:0.46
Consensus pattern (22 bp):
TTTTTTTTAACACAAAAACAAT
Found at i:16074 original size:21 final size:22
Alignment explanation
Indices: 16034--16076 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
16024 CACAAATCCT
**
16034 AATTTTTTTTTATCGCAAAAAC
1 AATTTTTTTTTAAAGCAAAAAC
16056 AATTTTTTTTTAAAG-AAAAAC
1 AATTTTTTTTTAAAGCAAAAAC
16077 GCAAATACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (22 bp):
AATTTTTTTTTAAAGCAAAAAC
Found at i:17102 original size:16 final size:16
Alignment explanation
Indices: 17081--17111 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17071 ACCCTAGTCT
*
17081 TAAAACTAGAGAAAAA
1 TAAAACTAAAGAAAAA
17097 TAAAACTAAAGAAAA
1 TAAAACTAAAGAAAA
17112 GTAGAAGAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.06, G:0.10, T:0.13
Consensus pattern (16 bp):
TAAAACTAAAGAAAAA
Found at i:19511 original size:25 final size:24
Alignment explanation
Indices: 19483--19541 Score: 75
Period size: 25 Copynumber: 2.5 Consensus size: 24
19473 TTCAAACCCT
**
19483 AAACTTCATTTCTAACCACTTCTTC
1 AAACTTCATTTCTAA-CAAATCTTC
*
19508 AAACTTCATTTTTAACAAATCTTC
1 AAACTTCATTTCTAACAAATCTTC
19532 AAA-TTCATTT
1 AAACTTCATTT
19542 TCCTTCATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 7 0.23
24 10 0.32
25 14 0.45
ACGTcount: A:0.34, C:0.24, G:0.00, T:0.42
Consensus pattern (24 bp):
AAACTTCATTTCTAACAAATCTTC
Found at i:19580 original size:26 final size:26
Alignment explanation
Indices: 19551--19621 Score: 99
Period size: 26 Copynumber: 2.8 Consensus size: 26
19541 TTCCTTCATT
19551 TTAATCATAAACTAAATAAATACTAA
1 TTAATCATAAACTAAATAAATACTAA
* * *
19577 TTAATAATAAACTAATTAGATACTAA
1 TTAATCATAAACTAAATAAATACTAA
*
19603 TTAAACATAAACT-AATAAA
1 TTAATCATAAACTAAATAAA
19622 CTAAGTAATT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
25 4 0.11
26 34 0.89
ACGTcount: A:0.58, C:0.10, G:0.01, T:0.31
Consensus pattern (26 bp):
TTAATCATAAACTAAATAAATACTAA
Found at i:22167 original size:22 final size:22
Alignment explanation
Indices: 22142--22185 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
22132 TTTTCCCACA
* *
22142 ACAAATTTTGTCCCGAAGTTGT
1 ACAAATTCTGGCCCGAAGTTGT
* *
22164 ACAAGTTCTGGGCCGAAGTTGT
1 ACAAATTCTGGCCCGAAGTTGT
22186 CCTGAAATTC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (22 bp):
ACAAATTCTGGCCCGAAGTTGT
Found at i:22247 original size:22 final size:22
Alignment explanation
Indices: 22215--22282 Score: 91
Period size: 22 Copynumber: 3.1 Consensus size: 22
22205 TTTCAACAGG
* *
22215 CCAAGTCCTGGGCTGAAGTTGT
1 CCAAGTTCTGGGCAGAAGTTGT
* *
22237 CTAAGTTCTGGGAAGAAGTTGT
1 CCAAGTTCTGGGCAGAAGTTGT
*
22259 CCAAGTTCTGGGCAGAACTTGT
1 CCAAGTTCTGGGCAGAAGTTGT
22281 CC
1 CC
22283 TGAATTTTAG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (22 bp):
CCAAGTTCTGGGCAGAAGTTGT
Found at i:25223 original size:27 final size:28
Alignment explanation
Indices: 25188--25255 Score: 95
Period size: 27 Copynumber: 2.5 Consensus size: 28
25178 ATTCTGGGGA
*
25188 ACTAACTTTGAATGGGA-AACTGTTTTG
1 ACTAACTTTGAATGGGAGAACTGTCTTG
*
25215 ACTAGCTTTGAAT-GGAGAACTGTCTTG
1 ACTAACTTTGAATGGGAGAACTGTCTTG
*
25242 ACTAACTTGGAATG
1 ACTAACTTTGAATG
25256 AGAGTCTGAC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
26 3 0.09
27 32 0.91
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.34
Consensus pattern (28 bp):
ACTAACTTTGAATGGGAGAACTGTCTTG
Found at i:29703 original size:27 final size:28
Alignment explanation
Indices: 29667--29733 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 28
29657 ATTCTAGGGA
* *
29667 ACTAAATTTGAATTGGA-AACTGTTTTG
1 ACTAACTTTGAATTGGAGAACTGTCTTG
*
29694 ACTAGCTTTGAA-TGGAGAACTGTCTTG
1 ACTAACTTTGAATTGGAGAACTGTCTTG
*
29721 ACTAACTTGGAAT
1 ACTAACTTTGAAT
29734 GAGAGTCTGA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.12
27 29 0.88
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (28 bp):
ACTAACTTTGAATTGGAGAACTGTCTTG
Found at i:33343 original size:22 final size:22
Alignment explanation
Indices: 33313--33356 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
33303 TTTTCTCGCA
33313 ACAACTTCT-GTCCCGAAGTTGT
1 ACAACTTCTAG-CCCGAAGTTGT
* *
33335 ACAAGTTCTAGGCCGAAGTTGT
1 ACAACTTCTAGCCCGAAGTTGT
33357 CCTACGCAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (22 bp):
ACAACTTCTAGCCCGAAGTTGT
Found at i:33391 original size:52 final size:52
Alignment explanation
Indices: 33309--33411 Score: 161
Period size: 52 Copynumber: 2.0 Consensus size: 52
33299 AGGTTTTTCT
* * *
33309 CGCAACAACTTCTGTCCCGAAGTTGTACAAGTTCTAGGCCGAAGTTGTCCTA
1 CGCAACAACTTCTGTCCCGAAGTTGAACAAGTTCCAGGCCGAAATTGTCCTA
* *
33361 CGCAACAACTTCTTTCCCGAAGTTGAACAAGTTCCGGGCCGAAATTGTCCT
1 CGCAACAACTTCTGTCCCGAAGTTGAACAAGTTCCAGGCCGAAATTGTCCT
33412 GAAACTCTTG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.26
Consensus pattern (52 bp):
CGCAACAACTTCTGTCCCGAAGTTGAACAAGTTCCAGGCCGAAATTGTCCTA
Found at i:36327 original size:12 final size:12
Alignment explanation
Indices: 36310--36363 Score: 58
Period size: 12 Copynumber: 4.6 Consensus size: 12
36300 GTAACTAAGA
36310 AAAATAAAAAGG
1 AAAATAAAAAGG
36322 AAAATAAAAA--
1 AAAATAAAAAGG
* * *
36332 ATAAACAAAACGA
1 A-AAATAAAAAGG
36345 AAAATAAAAAGG
1 AAAATAAAAAGG
36357 AAAATAA
1 AAAATAA
36364 CGAAAAAGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
10 1 0.03
11 7 0.21
12 25 0.74
13 1 0.03
ACGTcount: A:0.78, C:0.04, G:0.09, T:0.09
Consensus pattern (12 bp):
AAAATAAAAAGG
Found at i:36365 original size:22 final size:23
Alignment explanation
Indices: 36322--36379 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 23
36312 AATAAAAAGG
*
36322 AAAATAAAAAATAAACAAAACGA
1 AAAATAAAAAAGAAACAAAACGA
* *
36345 AAAATAAAAAGGAAA-ATAACGA
1 AAAATAAAAAAGAAACAAAACGA
*
36367 AAAAGAAAAAAGA
1 AAAATAAAAAAGA
36380 TAAATGTAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 17 0.57
23 13 0.43
ACGTcount: A:0.78, C:0.05, G:0.10, T:0.07
Consensus pattern (23 bp):
AAAATAAAAAAGAAACAAAACGA
Found at i:37244 original size:21 final size:21
Alignment explanation
Indices: 37218--37266 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
37208 GCACTGGAGG
* * *
37218 ACATGGGTCGCGAGGCAAACC
1 ACATGGGGCGCCAAGCAAACC
*
37239 ACATGGGGCGCCAAGCATACC
1 ACATGGGGCGCCAAGCAAACC
37260 ACATGGG
1 ACATGGG
37267 CCCCCAGCTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.29, G:0.33, T:0.10
Consensus pattern (21 bp):
ACATGGGGCGCCAAGCAAACC
Found at i:44504 original size:11 final size:10
Alignment explanation
Indices: 44486--44519 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
44476 AATTGTCTTC
44486 AAATCTTCAA
1 AAATCTTCAA
44496 AATATCTTCAA
1 AA-ATCTTCAA
44507 GAAATCTTCAA
1 -AAATCTTCAA
44518 AA
1 AA
44520 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Found at i:46592 original size:29 final size:29
Alignment explanation
Indices: 46560--46629 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
46550 ACTGGCGTGG
46560 GGCATGGCGCGGGTTGAGCGACAACGCCA
1 GGCATGGCGCGGGTTGAGCGACAACGCCA
46589 GGCATGGCGCGGGTTGAGCGACAACGCCA
1 GGCATGGCGCGGGTTGAGCGACAACGCCA
46618 GGCATGGC-CGGG
1 GGCATGGCGCGGG
46630 CAGGAGGTGC
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 4 0.10
29 37 0.90
ACGTcount: A:0.19, C:0.27, G:0.44, T:0.10
Consensus pattern (29 bp):
GGCATGGCGCGGGTTGAGCGACAACGCCA
Found at i:50372 original size:11 final size:10
Alignment explanation
Indices: 50354--50387 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
50344 AATTGTCTTC
50354 AAATCTTCAA
1 AAATCTTCAA
50364 AATATCTTCAA
1 AA-ATCTTCAA
50375 GAAATCTTCAA
1 -AAATCTTCAA
50386 AA
1 AA
50388 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Found at i:51837 original size:55 final size:55
Alignment explanation
Indices: 51750--51926 Score: 227
Period size: 55 Copynumber: 3.2 Consensus size: 55
51740 ATTAAATATT
51750 ACACCATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAGTTGAAGGCA
1 ACACCATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAGTTGAAGGCA
* * * * * * *
51805 ACACCATCAGGATCAATTTATTAGT-CACGATGATTTG-A-G-TAATTTTTAATTGACA
1 ACACCATCAGGACCAATTTTTTGGTCCA-GATGATCTGAATGATAA-GTTGAA--GGCA
51860 ACACCATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAGTTGAAGGCA
1 ACACCATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAGTTGAAGGCA
51915 ACACCATCAGGA
1 ACACCATCAGGA
51927 TCAAGCTATT
Statistics
Matches: 100, Mismatches: 14, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
52 3 0.03
53 5 0.05
54 3 0.03
55 78 0.78
56 3 0.03
57 5 0.05
58 3 0.03
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (55 bp):
ACACCATCAGGACCAATTTTTTGGTCCAGATGATCTGAATGATAAGTTGAAGGCA
Found at i:53023 original size:16 final size:15
Alignment explanation
Indices: 52998--53028 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
52988 CTTTCCTCTT
52998 GATAGAATTAATTGC
1 GATAGAATTAATTGC
53013 GATAGGAATTAATTGC
1 GATA-GAATTAATTGC
53029 ACTTTGTGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (15 bp):
GATAGAATTAATTGC
Done.