Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013814.1 Corchorus capsularis cultivar CVL-1 contig13835, 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: 60124
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:12419 original size:2 final size:2
Alignment explanation
Indices: 12412--12437 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12402 CTTCTTTTAA
12412 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
12438 AGATATTGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:15242 original size:22 final size:22
Alignment explanation
Indices: 15185--15251 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 22
15175 AGAACCCGAT
*
15185 TATATGATTTTTATATA-TATAA
1 TATATG-TTTTTATATATTATTA
** * *
15207 TATATAATTATATAGATTATTA
1 TATATGTTTTTATATATTATTA
15229 TATATGTTTTTATATATT-TTA
1 TATATGTTTTTATATATTATTA
15250 TA
1 TA
15252 CCGAAAATAT
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
21 12 0.34
22 23 0.66
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (22 bp):
TATATGTTTTTATATATTATTA
Found at i:15606 original size:18 final size:20
Alignment explanation
Indices: 15585--15628 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
15575 AACTTAAACC
15585 CGACAAAATGGTGAACCCCGA
1 CGAC-AAATGGTGAACCCCGA
*
15606 CGACGACATGGTGAACCCCGA
1 CGAC-AAATGGTGAACCCCGA
15627 CG
1 CG
15629 CTGACAATGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.32, C:0.32, G:0.27, T:0.09
Consensus pattern (20 bp):
CGACAAATGGTGAACCCCGA
Found at i:16133 original size:2 final size:2
Alignment explanation
Indices: 16126--16160 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
16116 TTATGTTTGA
16126 AT AT 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 AT AT A
16161 CACATACTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16248 original size:15 final size:15
Alignment explanation
Indices: 16228--16259 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
16218 TTTTCAGTTT
16228 ATATATATATACTTA
1 ATATATATATACTTA
16243 ATATATATATACTTA
1 ATATATATATACTTA
16258 AT
1 AT
16260 GTTTCCTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATATATATACTTA
Found at i:16358 original size:2 final size:2
Alignment explanation
Indices: 16351--16383 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
16341 CTGTTCTGAA
16351 AT 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 AT A
16384 CACACACTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19338 original size:32 final size:32
Alignment explanation
Indices: 19293--19362 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
19283 TTGGTAATTT
* *
19293 TAAATTGAGTTTCTTAAATGATTAGAAACAAC
1 TAAATTGAATTTCTTAAACGATTAGAAACAAC
19325 TAAATTGAATTTCTTAAACGATTAGAAACAAC
1 TAAATTGAATTTCTTAAACGATTAGAAACAAC
19357 TAAATT
1 TAAATT
19363 TGATTATTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (32 bp):
TAAATTGAATTTCTTAAACGATTAGAAACAAC
Found at i:21357 original size:1 final size:1
Alignment explanation
Indices: 21351--21381 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
21341 AGGAGACTTC
21351 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
21382 CATTTCTCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:26584 original size:71 final size:71
Alignment explanation
Indices: 26468--26610 Score: 277
Period size: 71 Copynumber: 2.0 Consensus size: 71
26458 AAGTTGGACA
26468 TGCTGGTAGCATCATTTTTCTGCTTCTATTATATGCATTAACATATTATTTTGAATGATTACATT
1 TGCTGGTAGCATCATTTTTCTGCTTCTATTATATGCATTAACATATTATTTTGAATGATTACATT
26533 CAGCCT
66 CAGCCT
*
26539 TGCTGGTAGCATCATTTTTCTGCTTTTATTATATGCATTAACATATTATTTTGAATGATTACATT
1 TGCTGGTAGCATCATTTTTCTGCTTCTATTATATGCATTAACATATTATTTTGAATGATTACATT
26604 CAGCCT
66 CAGCCT
26610 T
1 T
26611 TTTATTTAGT
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.46
Consensus pattern (71 bp):
TGCTGGTAGCATCATTTTTCTGCTTCTATTATATGCATTAACATATTATTTTGAATGATTACATT
CAGCCT
Found at i:31743 original size:2 final size:2
Alignment explanation
Indices: 31736--31769 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
31726 ATAAGGTAAA
31736 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
31770 AAAAGAGCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:36572 original size:14 final size:15
Alignment explanation
Indices: 36545--36574 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
36535 GAAACTAACG
36545 AAAGAAAGAAAAGAA
1 AAAGAAAGAAAAGAA
36560 AAAGAAA-AAAAGAA
1 AAAGAAAGAAAAGAA
36574 A
1 A
36575 TTCAACCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAGAAAGAAAAGAA
Found at i:38131 original size:61 final size:60
Alignment explanation
Indices: 38018--38131 Score: 158
Period size: 61 Copynumber: 1.9 Consensus size: 60
38008 AGGAGACATT
* * *
38018 TAGATAATGAGCTCGCTTTGATAGCTGCAAGGCAAGTGCTTTCAACCTCTACAGAGCATA
1 TAGATAATAAGCTCGCTTTGATAGCGGCAAGGAAAGTGCTTTCAACCTCTACAGAGCATA
* *
38078 TAGATATTAAGCTCGCTTTGATTAGCGGCAA-TAAGAGTGCTTTCAACCTCTACA
1 TAGATAATAAGCTCGCTTTGA-TAGCGGCAAGGAA-AGTGCTTTCAACCTCTACA
38132 AGGAGAAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
60 20 0.43
61 27 0.57
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (60 bp):
TAGATAATAAGCTCGCTTTGATAGCGGCAAGGAAAGTGCTTTCAACCTCTACAGAGCATA
Found at i:38334 original size:29 final size:27
Alignment explanation
Indices: 38275--38341 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
38265 TGTTTGGCGA
* **
38275 CATAAGCCATTGTTATATGTGTGGTGC
1 CATAGGCCATTGTTATATGTGTGGCAC
*
38302 CATAGGCCATTGTTATATACGTGTGGCAT
1 CATAGGCCATTGTTATAT--GTGTGGCAC
38331 CATAGGCCATT
1 CATAGGCCATT
38342 TTTGTATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 17 0.50
29 17 0.50
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (27 bp):
CATAGGCCATTGTTATATGTGTGGCAC
Found at i:38407 original size:35 final size:35
Alignment explanation
Indices: 38356--38441 Score: 145
Period size: 35 Copynumber: 2.5 Consensus size: 35
38346 TATATATGGA
* *
38356 GTGGCGTCATAGGCCAAGGTAATAGTTCATGATAT
1 GTGGCGACATAGGCCAAGGTAATAGTACATGATAT
*
38391 GTGGCGACATAAGCCAAGGTAATAGTACATGATAT
1 GTGGCGACATAGGCCAAGGTAATAGTACATGATAT
38426 GTGGCGACATAGGCCA
1 GTGGCGACATAGGCCA
38442 TCTAATATAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 47 1.00
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.23
Consensus pattern (35 bp):
GTGGCGACATAGGCCAAGGTAATAGTACATGATAT
Found at i:43357 original size:41 final size:41
Alignment explanation
Indices: 43305--43468 Score: 161
Period size: 48 Copynumber: 3.8 Consensus size: 41
43295 TTGATAATTA
43305 CCATAATTATCTCTAAAGATAATATGGTTAATAAATATAAT
1 CCATAATTATCTCTAAAGATAATATGGTTAATAAATATAAT
*
43346 TCATAATTATCTCTAATATATGTGGATAATATGGTTAATAAATATAAT
1 CCATAATTATCTCT-A-A-A----GATAATATGGTTAATAAATATAAT
*** *
43394 CCATAATTATCTCTGTGGATAATATGGTTAAT-TATATAAT
1 CCATAATTATCTCTAAAGATAATATGGTTAATAAATATAAT
* *
43434 CACCATAATTATCTCTTAA-ATATATATGGATAATA
1 --CCATAATTATCTCTAAAGATA-ATATGGTTAATA
43469 TGGTTAATAG
Statistics
Matches: 102, Mismatches: 10, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
40 7 0.07
41 31 0.30
42 25 0.25
43 1 0.01
44 1 0.01
48 37 0.36
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.40
Consensus pattern (41 bp):
CCATAATTATCTCTAAAGATAATATGGTTAATAAATATAAT
Found at i:43376 original size:48 final size:48
Alignment explanation
Indices: 43322--43477 Score: 193
Period size: 48 Copynumber: 3.3 Consensus size: 48
43312 TATCTCTAAA
*
43322 GATAATATGGTTAATAAATATAATTCATAATTATCTCTAATATATGTG
1 GATAATATGGTTAATAAATATAATCCATAATTATCTCTAATATATGTG
43370 GATAATATGGTTAATAAATATAATCCATAATTATCTC-------TGTG
1 GATAATATGGTTAATAAATATAATCCATAATTATCTCTAATATATGTG
* *
43411 GATAATATGGTTAAT-TATATAATCACCATAATTATCTCTTAAATATATATG
1 GATAATATGGTTAATAAATATAAT--CCATAATTATCTC-T-AATATATGTG
43462 GATAATATGGTTAATA
1 GATAATATGGTTAATA
43478 GAGGTAACTA
Statistics
Matches: 93, Mismatches: 3, Indels: 20
0.80 0.03 0.17
Matches are distributed among these distances:
40 7 0.08
41 19 0.20
42 13 0.14
48 36 0.39
51 18 0.19
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.40
Consensus pattern (48 bp):
GATAATATGGTTAATAAATATAATCCATAATTATCTCTAATATATGTG
Found at i:43461 original size:42 final size:41
Alignment explanation
Indices: 43371--43468 Score: 119
Period size: 42 Copynumber: 2.4 Consensus size: 41
43361 ATATATGTGG
**
43371 ATAATATGGTTAATAAATATAATCCATAATTATCTCTGTGG
1 ATAATATGGTTAATAAATATAATCCATAATTATCTCTGTAA
*
43412 ATAATATGGTTAAT-TATATAATCACCATAATTATCTCT-TAA
1 ATAATATGGTTAATAAATATAAT--CCATAATTATCTCTGTAA
*
43453 ATATATATGGATAATA
1 ATA-ATATGGTTAATA
43469 TGGTTAATAG
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
40 7 0.14
41 18 0.37
42 24 0.49
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (41 bp):
ATAATATGGTTAATAAATATAATCCATAATTATCTCTGTAA
Found at i:44003 original size:39 final size:39
Alignment explanation
Indices: 43949--44029 Score: 144
Period size: 39 Copynumber: 2.1 Consensus size: 39
43939 ATAAGTTTAG
43949 GCATATATTTAAGTTCATACCTAATTTAGTAGCAAAAAA
1 GCATATATTTAAGTTCATACCTAATTTAGTAGCAAAAAA
* *
43988 GCATATATTTAAGTTCGTACCTAATTTAGTAGCAAAAGA
1 GCATATATTTAAGTTCATACCTAATTTAGTAGCAAAAAA
44027 GCA
1 GCA
44030 ACACTTGAGG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.32
Consensus pattern (39 bp):
GCATATATTTAAGTTCATACCTAATTTAGTAGCAAAAAA
Found at i:53733 original size:6 final size:6
Alignment explanation
Indices: 53722--53751 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
53712 ATTAGCCCCC
53722 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG
53752 AAAGTCATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.33, T:0.17
Consensus pattern (6 bp):
TGAAAG
Done.