Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013662.1 Corchorus capsularis cultivar CVL-1 contig13683, 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: 51671
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:53 original size:22 final size:22
Alignment explanation
Indices: 28--257 Score: 141
Period size: 22 Copynumber: 10.5 Consensus size: 22
18 AATCACATTT
*
28 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
50 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
* * * *
72 T-AGAATTTTGTTGACCCCTCTA
1 TGA-AATTTTGATAACCTCTTTA
* * * *
94 TGAAATTCTGATAATCACATTA
1 TGAAATTTTGATAACCTCTTTA
* *
116 TGTAATTTTGATAACCTCGCTT-
1 TGAAATTTTGATAACCTC-TTTA
** **
138 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTCTTTA
160 TGAAATTTTGATAA--TCTTCCTA
1 TGAAATTTTGATAACCTCTT--TA
* *
182 T-AAATTTTGATAATTCGATCTCTA
1 TGAAATTTTGATAA--C-CTCTTTA
* * * *
206 TGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCTCTTTA
*
228 TGAGA-TTTGATAACCT-TTTA
1 TGAAATTTTGATAACCTCTTTA
*
248 TCAAATTTTG
1 TGAAATTTTG
258 GTACTCATTA
Statistics
Matches: 158, Mismatches: 37, Indels: 27
0.71 0.17 0.12
Matches are distributed among these distances:
20 7 0.04
21 26 0.16
22 105 0.66
23 3 0.02
24 3 0.02
25 11 0.07
26 3 0.02
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:96 original size:44 final size:44
Alignment explanation
Indices: 4--194 Score: 138
Period size: 44 Copynumber: 4.4 Consensus size: 44
1 CAG
* * * * * **
4 TATGAAATTTTTG-TAATCACATTTTGAAAATTTGATAACCTCTT
1 TATGAAA-TTTTGATAACCACATTATGTAATTTTGATAACCCCGC
* * * * *
48 TATGAAATTTTGATAACCTCTTTATAG-AATTTTGTTGACCCCTC
1 TATGAAATTTTGATAACCACATTAT-GTAATTTTGATAACCCCGC
* * *
92 TATGAAATTCTGATAATCACATTATGTAATTTTGATAACCTCGC
1 TATGAAATTTTGATAACCACATTATGTAATTTTGATAACCCCGC
* * * * **
136 TTTGAAATTTTGATAACAACACTATGAAATTTTGATAATCTTC-C
1 TATGAAATTTTGATAACCACATTATGTAATTTTGATAA-CCCCGC
180 TAT-AAATTTTGATAA
1 TATGAAATTTTGATAA
195 TTCGATCTCT
Statistics
Matches: 118, Mismatches: 25, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
43 18 0.15
44 96 0.81
45 4 0.03
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (44 bp):
TATGAAATTTTGATAACCACATTATGTAATTTTGATAACCCCGC
Found at i:167 original size:88 final size:88
Alignment explanation
Indices: 4--169 Score: 203
Period size: 88 Copynumber: 1.9 Consensus size: 88
1 CAG
* * * ** *
4 TATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTCT
1 TATGAAATTTCTGTAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAACA
*
69 TTATAGAATTTTGTTGACCCCTC
66 CTATAGAATTTTGTTGACCCCTC
* *
92 TATGAAA-TTCTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACAA
1 TATGAAATTTCTG-TAATCACATTATGAAAATTTGATAACCTC-CTTATGAAATTTTGATAACAA
155 CACTAT-GAAATTTTG
64 CACTATAG-AATTTTG
170 ATAATCTTCC
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
87 5 0.08
88 59 0.89
89 2 0.03
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (88 bp):
TATGAAATTTCTGTAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAACA
CTATAGAATTTTGTTGACCCCTC
Found at i:309 original size:22 final size:21
Alignment explanation
Indices: 280--520 Score: 103
Period size: 22 Copynumber: 10.8 Consensus size: 21
270 AAATTGAGAC
280 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACC-TCATATGAAA
* *
301 TTTTGATAACCACACTATAAAA
1 TTTTGATAACCTCA-TATGAAA
*
323 TTTTGATAACCTCCCTATGAAA
1 TTTTGATAACCT-CATATGAAA
* *
345 -TATGAGTAACCTCCTAATGAAA
1 TTTTGA-TAACCTCAT-ATGAAA
* * *
367 TTCTGTTAACCACACTATGAAA
1 TTTTGATAACCTCA-TATGAAA
* *
389 TTCTT-ATAACCTCGCTATGACA
1 TT-TTGATAACCTC-ATATGAAA
* *
411 TTTTGATAATCTC-TTTGATAA
1 TTTTGATAACCTCATATGA-AA
* *
432 CTTTTCTATAAAATAACCACACTATGAAA
1 ---TT-T-T--GATAACCTCA-TATGAAA
*
461 TTTTGATAACCTCCTCATGAAA
1 TTTTGATAACCTCAT-ATGAAA
* * * *
483 TTATAATAATCATCTTATGAAA
1 TTTTGATAA-CCTCATATGAAA
*
505 TTTTGATAACCACATA
1 TTTTGATAACCTCATA
521 GAGACAAGAA
Statistics
Matches: 164, Mismatches: 34, Indels: 44
0.68 0.14 0.18
Matches are distributed among these distances:
20 4 0.02
21 21 0.13
22 109 0.66
23 10 0.06
24 3 0.02
25 2 0.01
26 3 0.02
28 6 0.04
29 2 0.01
30 4 0.02
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (21 bp):
TTTTGATAACCTCATATGAAA
Found at i:342 original size:44 final size:43
Alignment explanation
Indices: 28--515 Score: 172
Period size: 44 Copynumber: 10.9 Consensus size: 43
18 AATCACATTT
* * **
28 TGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTC-CTATGAAATTTTGATAACCTCCCTA
* * * * * * **
72 T-AGAATTTTGTTGACCCCTCTATGAAATTCTGATAATCACATTA
1 TGA-AATTTTGATAACCTC-CTATGAAATTTTGATAACCTCCCTA
* * ** *
116 TGTAATTTTGATAACCTCGCTTTGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTC-CTATGAAATTTTGATAACCTCCCTA
* * *
160 TGAAATTTTGATAATCTTCCTAT-AAATTTTGATAATTCGATCTCTA
1 TGAAATTTTGATAA-CCTCCTATGAAATTTTGATAA--C-CTCCCTA
* * **
206 TGAAATTTCGATAATCACT-CTATGAGA-TTTGATAACCT-TTTA
1 TGAAATTTTGATAA-C-CTCCTATGAAATTTTGATAACCTCCCTA
* * * * * * *
248 TCAAATTTTGGT-A-CTCATTATAAAATTGAGACTTTTATAACCTTCATA
1 TGAAATTTTGATAACCTC-CTATGAAA-T-----TTTGATAACCTCCCTA
* *
296 TGAAATTTTGATAACCACACTATAAAATTTTGATAACCTCCCTA
1 TGAAATTTTGATAACCTC-CTATGAAATTTTGATAACCTCCCTA
* * * * *
340 TGAAA-TATGAGTAACCTCCTAATGAAATTCTGTTAACCACACTA
1 TGAAATTTTGA-TAACCTCCT-ATGAAATTTTGATAACCTCCCTA
* * *
384 TGAAATTCTT-ATAACCTCGCTATGACATTTTGATAA--TCTCTT
1 TGAAATT-TTGATAACCTC-CTATGAAATTTTGATAACCTCCCTA
* *
426 TGATAACTTTTCTATAAAATAACCACACTATGAAATTTTGATAACCT-CCTCA
1 TGA-AA---TT-T-T--GATAACCTC-CTATGAAATTTTGATAACCTCCCT-A
* * * *
478 TGAAATTATAATAATCATCTTATGAAATTTTGATAACC
1 TGAAATTTTGATAA-CCTCCTATGAAATTTTGATAACC
516 ACATAGAGAC
Statistics
Matches: 339, Mismatches: 68, Indels: 74
0.70 0.14 0.15
Matches are distributed among these distances:
38 2 0.01
40 5 0.01
41 1 0.00
42 18 0.05
43 22 0.06
44 172 0.51
45 10 0.03
46 38 0.11
47 14 0.04
48 14 0.04
49 2 0.01
50 33 0.10
51 4 0.01
52 4 0.01
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (43 bp):
TGAAATTTTGATAACCTCCTATGAAATTTTGATAACCTCCCTA
Found at i:2056 original size:31 final size:31
Alignment explanation
Indices: 2021--2086 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
2011 TGGCAATTTA
*
2021 GAAATATGTTTTAAAAAAAAGGATACAATTG
1 GAAATATGTTTTAAAAAAAAGGATACAATAG
* *
2052 GAAATATGTTTTAAAAATAAGGGTACAATAG
1 GAAATATGTTTTAAAAAAAAGGATACAATAG
2083 GAAA
1 GAAA
2087 ACATAAAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.52, C:0.03, G:0.18, T:0.27
Consensus pattern (31 bp):
GAAATATGTTTTAAAAAAAAGGATACAATAG
Found at i:6314 original size:43 final size:44
Alignment explanation
Indices: 6266--6354 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
6256 GTAAGAGGAA
6266 GACCGG-TTTTTCTTAAAGAGACTACTATTAATTAAGTCAAAAT
1 GACCGGTTTTTTCTTAAAGAGACTACTATTAATTAAGTCAAAAT
6309 GACCGGTTTTTTCTTAAAGAGACTACTATTAATTAAGTCAAAAT
1 GACCGGTTTTTTCTTAAAGAGACTACTATTAATTAAGTCAAAAT
6353 GA
1 GA
6355 TCAATCAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 6 0.13
44 39 0.87
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (44 bp):
GACCGGTTTTTTCTTAAAGAGACTACTATTAATTAAGTCAAAAT
Found at i:14383 original size:2 final size:2
Alignment explanation
Indices: 14376--14405 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
14366 GAATGAATAG
14376 TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
14406 CCTCCGGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17971 original size:24 final size:25
Alignment explanation
Indices: 17934--17985 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
17924 TTTTTCTTTA
* * *
17934 CTTTTTCTGATTTTCCCTGCTTTCT
1 CTTTATCTGATTTTCCATGCATTCT
*
17959 CTTTATCTG-TTTTGCATGCATTCT
1 CTTTATCTGATTTTCCATGCATTCT
17983 CTT
1 CTT
17986 GGCTTGCCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.08, C:0.25, G:0.10, T:0.58
Consensus pattern (25 bp):
CTTTATCTGATTTTCCATGCATTCT
Found at i:18275 original size:2 final size:2
Alignment explanation
Indices: 18268--18293 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18258 TGTAATTATC
18268 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
18294 GAGTAATTTC
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:22253 original size:13 final size:13
Alignment explanation
Indices: 22235--22269 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
22225 TGCGAAATGA
*
22235 GCCTTTCATCAAT
1 GCCTTTCACCAAT
22248 GCCTTTCACCAAT
1 GCCTTTCACCAAT
22261 GCCTTTCAC
1 GCCTTTCAC
22270 AAACTTAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.20, C:0.37, G:0.09, T:0.34
Consensus pattern (13 bp):
GCCTTTCACCAAT
Found at i:30223 original size:6 final size:6
Alignment explanation
Indices: 30212--30236 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
30202 AAGGTTTCAT
30212 TTCTTG TTCTTG TTCTTG TTCTTG T
1 TTCTTG TTCTTG TTCTTG TTCTTG T
30237 CTTTCTGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.16, T:0.68
Consensus pattern (6 bp):
TTCTTG
Found at i:34366 original size:2 final size:2
Alignment explanation
Indices: 34359--34393 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
34349 ATAAACCTTC
34359 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34394 CCCTTCCTCG
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35457 original size:39 final size:39
Alignment explanation
Indices: 35412--35502 Score: 182
Period size: 39 Copynumber: 2.3 Consensus size: 39
35402 AAATTCAAAG
35412 CCAAATTTCTTATAATTTACCTTGAATTAAGCAATTAGC
1 CCAAATTTCTTATAATTTACCTTGAATTAAGCAATTAGC
35451 CCAAATTTCTTATAATTTACCTTGAATTAAGCAATTAGC
1 CCAAATTTCTTATAATTTACCTTGAATTAAGCAATTAGC
35490 CCAAATTTCTTAT
1 CCAAATTTCTTAT
35503 CAAGGCCATA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.40
Consensus pattern (39 bp):
CCAAATTTCTTATAATTTACCTTGAATTAAGCAATTAGC
Found at i:36806 original size:51 final size:52
Alignment explanation
Indices: 36730--36838 Score: 184
Period size: 51 Copynumber: 2.1 Consensus size: 52
36720 GTAAGAAGTT
*
36730 ATCTCAATATTCACCAATCACCGTAAAAC-AAAAAGAATGAACGTATATATC
1 ATCTCAATATTCACCAATCACCGTAAAACAAAAAAGAATGAACATATATATC
36781 ATCTCAATATTCACCAATCACCGTAAAACAAAAAAAGAATGAACATATATATC
1 ATCTCAATATTCACCAATCACCGTAAAAC-AAAAAAGAATGAACATATATATC
*
36834 TTCTC
1 ATCTC
36839 TGTTGGTATT
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
51 29 0.54
53 25 0.46
ACGTcount: A:0.47, C:0.22, G:0.06, T:0.25
Consensus pattern (52 bp):
ATCTCAATATTCACCAATCACCGTAAAACAAAAAAGAATGAACATATATATC
Found at i:40223 original size:15 final size:15
Alignment explanation
Indices: 40203--40231 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40193 AGCAAGTCTT
40203 AGATTCAAGACCTTA
1 AGATTCAAGACCTTA
40218 AGATTCAAGACCTT
1 AGATTCAAGACCTT
40232 GAATACGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.28
Consensus pattern (15 bp):
AGATTCAAGACCTTA
Found at i:40340 original size:35 final size:35
Alignment explanation
Indices: 40301--40374 Score: 148
Period size: 35 Copynumber: 2.1 Consensus size: 35
40291 CGATGCAGGT
40301 CAGATCTTGGTCTTAGGTTCAAGACCTTGCATACA
1 CAGATCTTGGTCTTAGGTTCAAGACCTTGCATACA
40336 CAGATCTTGGTCTTAGGTTCAAGACCTTGCATACA
1 CAGATCTTGGTCTTAGGTTCAAGACCTTGCATACA
40371 CAGA
1 CAGA
40375 CACTCCCGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (35 bp):
CAGATCTTGGTCTTAGGTTCAAGACCTTGCATACA
Found at i:43084 original size:15 final size:15
Alignment explanation
Indices: 43066--43100 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
43056 TAACTCTCCA
*
43066 TGGGAGAGTGATTCT
1 TGGGAGAGTGATTCC
43081 TGGGAGAGTGATTCC
1 TGGGAGAGTGATTCC
43096 TGGGA
1 TGGGA
43101 AAGTAACTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.20, C:0.09, G:0.43, T:0.29
Consensus pattern (15 bp):
TGGGAGAGTGATTCC
Done.