Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018726.1 Corchorus olitorius cultivar O-4 contig18759, 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: 27152
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Found at i:468 original size:32 final size:32
Alignment explanation
Indices: 427--487 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
417 AAATATGTTT
* *
427 GAAAAATAAGGATATAATGGTCGATTCAATTA
1 GAAAAATAAGGATATAATAGTCAATTCAATTA
*
459 GAAAAATAAGGGTATAATAGTCAATTCAA
1 GAAAAATAAGGATATAATAGTCAATTCAA
488 AAGTTTTACA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26
Consensus pattern (32 bp):
GAAAAATAAGGATATAATAGTCAATTCAATTA
Found at i:2302 original size:357 final size:347
Alignment explanation
Indices: 1530--2448 Score: 1371
Period size: 357 Copynumber: 2.6 Consensus size: 347
1520 AAAAAAATAA
* * *
1530 TTAATCATAATATGTGAAATTATAATAATAATATAAATTTTATTGAATAAATGAT-A---AT--T
1 TTAATCATAATAGGTAAAATTATAACAATAATATAAATTTTATTGAATAAATGATAATTTATAAT
*
1589 -TTAAAATTATAACAATGTGGATTTGACTGAATAAAACATAATTTTAGTTTATAATATTTTTGCG
66 GTTAAAATTATAACAATGTGGATTTGACTGAATAAAACATAATTTTAGTTTATAATATTCTTGCG
*
1653 TCTTTCGGGTTAACTTATCGGGTCATTCG-AGTTACGAGTTTGTCGAGTCTGGATATGACAGGTT
131 TCTTTCGGGTTAACTTCTCGGGTCATTCGTA--TACGAGTTTGTCG-GTCTGGATATGACAGGTT
1717 TGGAACGTTTACTTTTTCTGGT--AA-AATAATTATTATTATTTATTCATTATGTAAAAAAAAAT
193 TGGAACGTTTACTTTTTCTGGTCAAATAATAATTATTATTATTTATTCATTATGTAAAAAAAAAT
* *
1779 TACTAATTTTAAACTTATCATAAATTATTCATATAAATGATTTAGTATTTATCCATATATATTAT
258 TACTAATTATAAACTTATCATAAATTATTCATATAAAGGATTTAGTATTTAT-CATATATATTAT
*
1844 TGTTCATATAATGAAATTTAGTAATT
322 TGTTCATATAATGAAATTTAGTAAAT
*
1870 TTAATCATAATAGGTAAAATTATAACAATAATATAAATTTTATTGAATAAATGATAATTTAGAAT
1 TTAATCATAATAGGTAAAATTATAACAATAATATAAATTTTATTGAATAAATGATAATTTATAAT
*
1935 GGTTAAAATTATAACAATGTTGATTTGACTGAATAAAACATAATTTTAGTTTATAATATTCTTGC
66 -GTTAAAATTATAACAATGTGGATTTGACTGAATAAAACATAATTTTAGTTTATAATATTCTTGC
*
2000 GTCTTTCGGGTTAACTTCTCGGGTCATTCGTATAACGAGTTTGTCAGGTCTAGATATATGACAGG
130 GTCTTTCGGGTTAACTTCTCGGGTCATTCGTAT-ACGAGTTTGTC-GGTCT-G-GATATGACAGG
2065 TTTGGAACGTTTACTTTTTCTGGTCAAATAATAATTATTATTTATATTTATTCATTATGTAAAAA
191 TTTGGAACGTTTACTTTTTCTGGTCAAATAATAATTATTA--T-TATTTATTCATTATGT-AAAA
* *
2130 AACAAATTACTAATTATAAACTTATCATAAATTATTCATATAACGGATTTAGTATTTAT-TTATA
252 AA-AAATTACTAATTATAAACTTATCATAAATTATTCATATAAAGGATTTAGTATTTATCATATA
*
2194 TGATTATTGTTCATATAATGAAGTTTAGTAAAT
316 T-ATTATTGTTCATATAATGAAATTTAGTAAAT
*
2227 TTAATCATAATAGGTAAAATTATAACAATAACATAAATTTTATTGAATAAATGATAATTTATAAT
1 TTAATCATAATAGGTAAAATTATAACAATAATATAAATTTTATTGAATAAATGATAATTTATAAT
*
2292 AGTTAAAATTATAACAATGTGGATTTGACAGAATAAAACATAATTTTAGTTTATAATATTCTTGC
66 -GTTAAAATTATAACAATGTGGATTTGACTGAATAAAACATAATTTTAGTTTATAATATTCTTGC
* * * *
2357 GTCTCTCGGGTTAATTTCTCGAGTCATTCAGGT-TACGAGTTTGTCGGGTCTGGATATGACGGGT
130 GTCTTTCGGGTTAACTTCTCGGGTCATTC--GTATACGAGTTTGTC-GGTCTGGATATGACAGGT
*
2421 TT-GAATCGTTTACTTTTTCTAGTCAAAT
192 TTGGAA-CGTTTACTTTTTCTGGTCAAAT
2449 TGGGTTCAAC
Statistics
Matches: 528, Mismatches: 26, Indels: 35
0.90 0.04 0.06
Matches are distributed among these distances:
340 52 0.10
341 1 0.00
344 1 0.00
346 1 0.00
347 1 0.00
348 105 0.20
349 3 0.01
350 34 0.06
352 2 0.00
353 11 0.02
354 3 0.01
355 34 0.06
356 22 0.04
357 202 0.38
358 54 0.10
359 2 0.00
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.42
Consensus pattern (347 bp):
TTAATCATAATAGGTAAAATTATAACAATAATATAAATTTTATTGAATAAATGATAATTTATAAT
GTTAAAATTATAACAATGTGGATTTGACTGAATAAAACATAATTTTAGTTTATAATATTCTTGCG
TCTTTCGGGTTAACTTCTCGGGTCATTCGTATACGAGTTTGTCGGTCTGGATATGACAGGTTTGG
AACGTTTACTTTTTCTGGTCAAATAATAATTATTATTATTTATTCATTATGTAAAAAAAAATTAC
TAATTATAAACTTATCATAAATTATTCATATAAAGGATTTAGTATTTATCATATATATTATTGTT
CATATAATGAAATTTAGTAAAT
Found at i:4218 original size:2 final size:2
Alignment explanation
Indices: 4211--4242 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4201 AAATCTTTAG
4211 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
4243 TAAAAAAAGT
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:8797 original size:21 final size:20
Alignment explanation
Indices: 8751--8804 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
8741 TTAAAAACCC
*
8751 GTTCGATTTCGCATGGATTA
1 GTTCGATTTCACATGGATTA
* *
8771 GCTTCGATTTCACAGTGGGTTT
1 G-TTCGATTTCACA-TGGATTA
8793 GTTCGATTTCAC
1 GTTCGATTTCAC
8805 CCTTTGACAG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 1 0.03
21 22 0.76
22 6 0.21
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.41
Consensus pattern (20 bp):
GTTCGATTTCACATGGATTA
Found at i:12527 original size:24 final size:24
Alignment explanation
Indices: 12487--12551 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
12477 CTGCACCCCA
* *
12487 AGCCCCTACCTCCAACAAT-CAACC
1 AGCCCCTCCCTCAAACAATACAA-C
* *
12511 AGCTCCTCCCTCAAACACTACAAC
1 AGCCCCTCCCTCAAACAATACAAC
*
12535 AGCCCCTGCCTCAAACA
1 AGCCCCTCCCTCAAACA
12552 TTGGAAATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 31 0.91
25 3 0.09
ACGTcount: A:0.32, C:0.48, G:0.06, T:0.14
Consensus pattern (24 bp):
AGCCCCTCCCTCAAACAATACAAC
Found at i:13088 original size:3 final size:3
Alignment explanation
Indices: 13080--13126 Score: 67
Period size: 3 Copynumber: 15.0 Consensus size: 3
13070 CTGGTACTTT
*
13080 GAA GAA GAA GAA GAA GAA GAA GAA GAAA GAA GAAA GAA GAA GTA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA G-AA GAA G-AA GAA GAA GAA GAA
13127 AACCCTAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
3 34 0.85
4 6 0.15
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:14410 original size:15 final size:15
Alignment explanation
Indices: 14387--14425 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
14377 GGTTCAAATG
14387 AGGGAGGGGCGGGGT
1 AGGGAGGGGCGGGGT
*
14402 -GGTGAGGGGTGGGGT
1 AGG-GAGGGGCGGGGT
14417 AGGGAGGGG
1 AGGGAGGGG
14426 GATGGTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 2 0.10
15 17 0.81
16 2 0.10
ACGTcount: A:0.13, C:0.03, G:0.74, T:0.10
Consensus pattern (15 bp):
AGGGAGGGGCGGGGT
Found at i:15330 original size:17 final size:17
Alignment explanation
Indices: 15308--15342 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
15298 GGGTGGTAAG
15308 CACCCTT-TCCTACCCCT
1 CACCCTTCT-CTACCCCT
15325 CACCCTTCTCTACCCCT
1 CACCCTTCTCTACCCCT
15342 C
1 C
15343 CAACAAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 16 0.94
18 1 0.06
ACGTcount: A:0.11, C:0.60, G:0.00, T:0.29
Consensus pattern (17 bp):
CACCCTTCTCTACCCCT
Found at i:19207 original size:12 final size:12
Alignment explanation
Indices: 19190--19214 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19180 CCTTCTTTCG
19190 AATCCTATGTTA
1 AATCCTATGTTA
19202 AATCCTATGTTA
1 AATCCTATGTTA
19214 A
1 A
19215 TTTAGATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (12 bp):
AATCCTATGTTA
Found at i:21391 original size:21 final size:21
Alignment explanation
Indices: 21350--21391 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
21340 TCTTCTCTTG
*
21350 ATCCTACTCACTTTTAAGACA
1 ATCCTACTCACTTCTAAGACA
*
21371 ATCCTACTCACTTCTAGGACA
1 ATCCTACTCACTTCTAAGACA
21392 TTGCGTGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.31, G:0.07, T:0.31
Consensus pattern (21 bp):
ATCCTACTCACTTCTAAGACA
Found at i:21998 original size:290 final size:290
Alignment explanation
Indices: 21478--22055 Score: 1102
Period size: 290 Copynumber: 2.0 Consensus size: 290
21468 AATTTTCAAT
*
21478 TGGTTGCATATCGAGACTGCATGTTTATGTGCTATTATGAAATCAAGTGAATTCCTTCATACAAC
1 TGGTTGCATATCGAGAATGCATGTTTATGTGCTATTATGAAATCAAGTGAATTCCTTCATACAAC
21543 TTTCACTCTTTGCAAGTTTCAAATCCTCTCTGCTTCTTAATTTGATTTTGAAACAAATATATGAT
66 TTTCACTCTTTGCAAGTTTCAAATCCTCTCTGCTTCTTAATTTGATTTTGAAACAAATATATGAT
* *
21608 TTGTCTCCTTGTCCAAGTTCTTTGCTTTTGGTCTATACAATATTACTATTTACTTTTCTCACACA
131 ATGTCTCCTTGTCCAAGTTCTTTGCTTTTGGTCTATACAATATTACAATTTACTTTTCTCACACA
*
21673 AGATTGATATCTTAAGATAAATTATCAACTTCTATCAAAAGAGAACAAAAAGACCTGCGACGAAG
196 AGATTGATATCTTAAGATAAATTATCAACTTCTATCAAAAGAGAACAAAAAGACCCGCGACGAAG
21738 CGCAGGTAGTCCACCTAGTATGTATACATA
261 CGCAGGTAGTCCACCTAGTATGTATACATA
*
21768 TGGTTGCATATCGAGAATGCATGTTTATGTGCTATTATGAAATCAAGTGAATTCTTTCATACAAC
1 TGGTTGCATATCGAGAATGCATGTTTATGTGCTATTATGAAATCAAGTGAATTCCTTCATACAAC
*
21833 TTTCACTCTTTGCAAGTTTCAAATCCTCTCTGCTTCTTAATTTGATTTTGAAACAGATATATGAT
66 TTTCACTCTTTGCAAGTTTCAAATCCTCTCTGCTTCTTAATTTGATTTTGAAACAAATATATGAT
21898 ATGTCTCCTTGTCCAAGTTCTTTGCTTTTGGTCTATACAATATTACAATTTACTTTTCTCACACA
131 ATGTCTCCTTGTCCAAGTTCTTTGCTTTTGGTCTATACAATATTACAATTTACTTTTCTCACACA
21963 AGATTGATATCTTAAGATAAATTATCAACTTCTATCAAAAGAGAACAAAAAGACCCGCGACGAAG
196 AGATTGATATCTTAAGATAAATTATCAACTTCTATCAAAAGAGAACAAAAAGACCCGCGACGAAG
22028 CGCAGGTAGTCCACCTAGTATGTATACA
261 CGCAGGTAGTCCACCTAGTATGTATACA
22056 CACACACACA
Statistics
Matches: 282, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
290 282 1.00
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (290 bp):
TGGTTGCATATCGAGAATGCATGTTTATGTGCTATTATGAAATCAAGTGAATTCCTTCATACAAC
TTTCACTCTTTGCAAGTTTCAAATCCTCTCTGCTTCTTAATTTGATTTTGAAACAAATATATGAT
ATGTCTCCTTGTCCAAGTTCTTTGCTTTTGGTCTATACAATATTACAATTTACTTTTCTCACACA
AGATTGATATCTTAAGATAAATTATCAACTTCTATCAAAAGAGAACAAAAAGACCCGCGACGAAG
CGCAGGTAGTCCACCTAGTATGTATACATA
Found at i:22060 original size:2 final size:2
Alignment explanation
Indices: 22053--22089 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
22043 TAGTATGTAT
22053 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
22090 TATATATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:22094 original size:2 final size:2
Alignment explanation
Indices: 22089--22124 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
22079 ACACACACAC
22089 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
22125 CAATTGTTGA
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
Done.