Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008292.1 Corchorus capsularis cultivar CVL-1 contig08313, 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: 34631
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Found at i:5108 original size:2 final size:2
Alignment explanation
Indices: 5089--5135 Score: 53
Period size: 2 Copynumber: 24.0 Consensus size: 2
5079 CGGCCCCGAA
* *
5089 AT AT AT GT ACT AT GT AT AT AT AT AT AT AT AT AT AT AT -T A- AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5130 AT AT AT
1 AT AT AT
5136 GTTTTTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
1 2 0.05
2 34 0.89
3 2 0.05
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5634 original size:11 final size:11
Alignment explanation
Indices: 5600--5634 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
5590 GTACCGTTAA
5600 GCTATGACGTG
1 GCTATGACGTG
* *
5611 GATATGATGTG
1 GCTATGACGTG
5622 GCTATGACGTG
1 GCTATGACGTG
5633 GC
1 GC
5635 AATAAATATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.20, C:0.14, G:0.37, T:0.29
Consensus pattern (11 bp):
GCTATGACGTG
Found at i:6094 original size:19 final size:19
Alignment explanation
Indices: 6070--6106 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
6060 ATGACCAGTT
6070 TAAAACAAAATATTAAGTC
1 TAAAACAAAATATTAAGTC
**
6089 TAAAACAACTTATTAAGT
1 TAAAACAAAATATTAAGT
6107 TGTCTGCCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.11, G:0.05, T:0.30
Consensus pattern (19 bp):
TAAAACAAAATATTAAGTC
Found at i:9847 original size:2 final size:2
Alignment explanation
Indices: 9840--9880 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
9830 AGCTTTAAAT
* *
9840 TA TA TA TA TA TA TA TA TA TA TC TA TA TC TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9881 AGTCTAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18471 original size:2 final size:2
Alignment explanation
Indices: 18464--18490 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
18454 TAGAAAATGA
18464 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 A
18491 GCTCGTTCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19894 original size:37 final size:37
Alignment explanation
Indices: 19850--19920 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
19840 CTTGATCAAC
* *
19850 ATACATGTCTTTTCATATAGACATAACTTTATGATCA
1 ATACATGTCTTTCCAAATAGACATAACTTTATGATCA
19887 ATACATGTCTTTCCAAATAGACATAACTTTATGA
1 ATACATGTCTTTCCAAATAGACATAACTTTATGA
19921 ATAATCATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (37 bp):
ATACATGTCTTTCCAAATAGACATAACTTTATGATCA
Found at i:20353 original size:13 final size:13
Alignment explanation
Indices: 20335--20360 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20325 ACGAGATGAT
20335 CTAAGATCACCAA
1 CTAAGATCACCAA
20348 CTAAGATCACCAA
1 CTAAGATCACCAA
20361 TAGGTGAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.31, G:0.08, T:0.15
Consensus pattern (13 bp):
CTAAGATCACCAA
Found at i:23166 original size:12 final size:12
Alignment explanation
Indices: 23149--23203 Score: 65
Period size: 12 Copynumber: 4.5 Consensus size: 12
23139 CATCGATACC
*
23149 TCGATAAATCCG
1 TCGATATATCCG
* *
23161 TCGATATCTCTG
1 TCGATATATCCG
23173 TCGATATATCCG
1 TCGATATATCCG
*
23185 TTCGATATATCCA
1 -TCGATATATCCG
23198 TCGATA
1 TCGATA
23204 CATGTATTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
12 25 0.69
13 11 0.31
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.35
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:23201 original size:25 final size:24
Alignment explanation
Indices: 23149--23203 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
23139 CATCGATACC
* **
23149 TCGATAAATCCGTCGATATCTCTG
1 TCGATAAATCCGTCGATATATCCA
*
23173 TCGATATATCCGTTCGATATATCCA
1 TCGATAAATCCG-TCGATATATCCA
23198 TCGATA
1 TCGATA
23204 CATGTATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 11 0.42
25 15 0.58
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.35
Consensus pattern (24 bp):
TCGATAAATCCGTCGATATATCCA
Found at i:29055 original size:21 final size:21
Alignment explanation
Indices: 29029--29072 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
29019 TTTAACTGGA
29029 TTGCTAAAT-ACCGCCCCATTT
1 TTGCT-AATCACCGCCCCATTT
*
29050 TTGCTATTCACCGCCCCATTT
1 TTGCTAATCACCGCCCCATTT
29071 TT
1 TT
29073 TACGCTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.18, C:0.34, G:0.09, T:0.39
Consensus pattern (21 bp):
TTGCTAATCACCGCCCCATTT
Found at i:29343 original size:32 final size:32
Alignment explanation
Indices: 29302--29375 Score: 114
Period size: 32 Copynumber: 2.3 Consensus size: 32
29292 GGGTATGAAT
* *
29302 AGGCCGCCCCACTG-GGGCGGCTTCGCCAGGGC
1 AGGCCGCCCCA-TGAGAGCGGCTTCGCCACGGC
29334 AGGCCGCCCCATGAGAGCGGCTTCGCCACGGC
1 AGGCCGCCCCATGAGAGCGGCTTCGCCACGGC
29366 AGGCCGCCCC
1 AGGCCGCCCC
29376 GGGCCGGCTC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
31 2 0.05
32 37 0.95
ACGTcount: A:0.12, C:0.43, G:0.36, T:0.08
Consensus pattern (32 bp):
AGGCCGCCCCATGAGAGCGGCTTCGCCACGGC
Found at i:31778 original size:31 final size:31
Alignment explanation
Indices: 31736--31808 Score: 137
Period size: 31 Copynumber: 2.4 Consensus size: 31
31726 TTTCTCTCTC
31736 GATCGATCGCCATGGGTCTCTCAGTTTTCAA
1 GATCGATCGCCATGGGTCTCTCAGTTTTCAA
*
31767 GATCGAGCGCCATGGGTCTCTCAGTTTTCAA
1 GATCGATCGCCATGGGTCTCTCAGTTTTCAA
31798 GATCGATCGCC
1 GATCGATCGCC
31809 TTGCTTCTCA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.19, C:0.27, G:0.25, T:0.29
Consensus pattern (31 bp):
GATCGATCGCCATGGGTCTCTCAGTTTTCAA
Found at i:32199 original size:172 final size:165
Alignment explanation
Indices: 31913--32233 Score: 498
Period size: 172 Copynumber: 1.9 Consensus size: 165
31903 CTTTCTCTGA
*
31913 TCTGAATTTTCGAAACCCTAAGATTTTCGCATATGACCCAAATTCATAGTGTTTTTGGTACTCCT
1 TCTGAATTTTCGAAACCCTAAAATTTTCGCATATGACCCAAATTCATAGTGTTTTTGGTACTCCT
31978 ATTATACATGAAGGTATAATGGTACCAATAAGAAACATTCGGTGTAAATAAATACGTAAAGTGTT
66 ATTATACATGAAGGTATAATGGTACCAATAAGAAACATTCGGTGTAAATAAATACGTAAAGTGTT
* *
32043 TTACTTGGCATTCCTATTGGTTTTGACAAAGTTTT
131 TTAATTGACATTCCTATTGGTTTTGACAAAGTTTT
32078 TCTGAATTTTCGAAACCCTAAAATTTTCGCATATGACCCAAATTCATATTGTGTTTAAGTGCTGG
1 TCTGAATTTTCGAAACCCTAAAATTTTCGCATATGACCCAAATTCATA--GTGTTT---T--TGG
* * * * * *
32143 TACTCCTATTATACATGAAGGTATAATGGTACCAATTAGAGACATTTGTTGTAAATAACTATGTA
59 TACTCCTATTATACATGAAGGTATAATGGTACCAATAAGAAACATTCGGTGTAAATAAATACGTA
32208 AAGTGTTTTAATTGACATTCCTATTG
124 AAGTGTTTTAATTGACATTCCTATTG
32234 TGTAGTAAAG
Statistics
Matches: 140, Mismatches: 9, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
165 47 0.34
167 6 0.04
170 1 0.01
172 86 0.61
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (165 bp):
TCTGAATTTTCGAAACCCTAAAATTTTCGCATATGACCCAAATTCATAGTGTTTTTGGTACTCCT
ATTATACATGAAGGTATAATGGTACCAATAAGAAACATTCGGTGTAAATAAATACGTAAAGTGTT
TTAATTGACATTCCTATTGGTTTTGACAAAGTTTT
Found at i:34041 original size:481 final size:482
Alignment explanation
Indices: 32982--34631 Score: 2691
Period size: 481 Copynumber: 3.4 Consensus size: 482
32972 TTGAATGCAA
* * *
32982 TAAAAGGCACAACAGTGGCACTCCTATTATACATCAAGGTATAATGGTGCCTCTGATTCAAAGTT
1 TAAAAGGCACAACAGTGGCGCTCCTATTATACATCAAGGTATAATGGTGCCTCTGAATAAAAGTT
**** * * * *
33047 GGTGACAATATTTTGTATTTGCAGCAGAAGAGATGGCATTCCTATTATACATTAAGGTATAGTGG
66 GGTGATGGGAATTTCTATTTGCAGCAAAAGAGATGGCATTCCTATTATACATCAAGGTATAGTGG
* * *
33112 TGCATCCAAATGAAGGTTGGTAATGAGATTTCTTATAATGCAGTTAAAGGCACAATGTGGTGGCA
131 TGCATCCAAATAAAGGTTGGTAATGAGAATTCTTATAATGCGGTTAAAGGCACAATGTGGTGGCA
*
33177 TTCCTACTATACATAAAGGTATAGTGGTGCCAGTTCGTGTAATATACCTGGAACTCTTATAGTGC
196 TTCCTACTATACATAAAGGTATAGTGGTGCCAGTTCGTGTAATATGCCTGGAACTCTTATAGTGC
* *
33242 AATGAAATATG-AAAATCTTGAAGGCTCATGCACCCTCGCCCACTCCATTTTTTCTGATTCACCA
261 AATGAAATATGAAAAATCTTGAAGGCTCATGCTCCCTCGCCCACTCCATTTTTCCTGATTCACCA
* *
33306 CCATGAGCAATTTAAGTTTTGTACTCAAAGTTGTTTTTTGACT-TTTAGTATACACTGCACACCC
326 CCATGAGCAATTTAAGTTTTATACTCAAAGTTGTTTTTTGACTGTTTAGTATTCACTGCACACCC
*
33370 ATGAAATGGCAGCTATGCCTTGTTTTGATTTTGTTCTATCTATTTTCAAACGATGCAAGTTCTTT
391 ATGAAATGGCAGCTATGCCTTGTTTTGATTTTGTTCTATCTATTTTCAAAAGATGCAAGTTCTTT
33435 TGTTACATGGCATTTTTTTTTAAATGC
456 TGTTACATGGCATTTTTTTTTAAATGC
*
33462 TAAAAGGCACAACAGTGGCGCTCCTATTATACATCAAGGTATAATGGCGCCTCTGAATAAAAGTT
1 TAAAAGGCACAACAGTGGCGCTCCTATTATACATCAAGGTATAATGGTGCCTCTGAATAAAAGTT
* *
33527 GGTGATGGGAATTTCAATTTGCAGCAAAAGAGATGCCATTCCTATTATACATCAAGGTATAGTGG
66 GGTGATGGGAATTTCTATTTGCAGCAAAAGAGATGGCATTCCTATTATACATCAAGGTATAGTGG
* *
33592 TGCATCCAAAAAAAGGTTGGGAATGAGAATTCTTATAATGCGGTTAAAGGCACAATGTGGTGGCA
131 TGCATCCAAATAAAGGTTGGTAATGAGAATTCTTATAATGCGGTTAAAGGCACAATGTGGTGGCA
*
33657 TTCCTACTATACATAAAAGTATAGTGGTGCCAGTTCGTGTAATATGCCTGGAACTCTTATAGTGC
196 TTCCTACTATACATAAAGGTATAGTGGTGCCAGTTCGTGTAATATGCCTGGAACTCTTATAGTGC
* * * **
33722 AATGAAATATGAAAAATCTTTAAGGCTCATGCTCCCTTGCCCACTCCA-CTTTCCTGATTCATTA
261 AATGAAATATGAAAAATCTTGAAGGCTCATGCTCCCTCGCCCACTCCATTTTTCCTGATTCACCA
* *
33786 CTATGAGCAATTCAAGTTTTATACTCAAAGTTGTTTTTTGACTGTTTAGTATTCACTGCACACCC
326 CCATGAGCAATTTAAGTTTTATACTCAAAGTTGTTTTTTGACTGTTTAGTATTCACTGCACACCC
* * * * * *
33851 ATGAAATGGCCGCTATGTCTTGTTTTGATTTTATTCTATCAATTTTCAAATGATACAAGTTCTTT
391 ATGAAATGGCAGCTATGCCTTGTTTTGATTTTGTTCTATCTATTTTCAAAAGATGCAAGTTCTTT
33916 TGTTACATGGCATTTTTTTTTAAATGC
456 TGTTACATGGCATTTTTTTTTAAATGC
*
33943 TAAAAGGCACAACAGTGGTGCTCCTATTATACATCAAGGTATAATGGTGCCTCTGAATAAAAGTT
1 TAAAAGGCACAACAGTGGCGCTCCTATTATACATCAAGGTATAATGGTGCCTCTGAATAAAAGTT
* *
34008 GGTGATGGGAATTTCTATTTGCAGCCAAAGAGATGGCATTCCTGTTATACATCAAGGTATAGTGG
66 GGTGATGGGAATTTCTATTTGCAGCAAAAGAGATGGCATTCCTATTATACATCAAGGTATAGTGG
34073 TGCATCCAAATAAAGGTTGGTAATGAGAATTCTTATAATGCGGTTAAAGGCACAATGTGGTGGCA
131 TGCATCCAAATAAAGGTTGGTAATGAGAATTCTTATAATGCGGTTAAAGGCACAATGTGGTGGCA
*
34138 TTCCTACTATACATAAAGGTATAGTGGTGCCAGTTCGTGTAATATGCCTGGAACTCTTATAGTGA
196 TTCCTACTATACATAAAGGTATAGTGGTGCCAGTTCGTGTAATATGCCTGGAACTCTTATAGTGC
* ** * *
34203 AATGAAATATGAACAATCTTGAAGGCTGGTACTCCCTCGCCCAGTCCATTTTTTCC-GATTCACC
261 AATGAAATATGAAAAATCTTGAAGGCTCATGCTCCCTCGCCCACTCCA-TTTTTCCTGATTCACC
* *
34267 ACCATGAGCAATTTAAGTTTTATAGTCATAGTTGTTTTTTGACTGTTTAGTATTCACTGCACACC
325 ACCATGAGCAATTTAAGTTTTATACTCAAAGTTGTTTTTTGACTGTTTAGTATTCACTGCACACC
* *
34332 CATGAAATGGCAGCTATGCCTTGTTTTGGATCTTGTTCTATCTATTTTTAAAAGATGCAAGTTC-
390 CATGAAATGGCAGCTATGCCTTGTTTT-GATTTTGTTCTATCTATTTTCAAAAGATGCAAGTTCT
34396 TTT-TTACATGGCATATTTTTTTTAAAATGC
454 TTTGTTACATGGCAT-TTTTTTTT-AAATGC
* *
34426 TAAAAGGCACAACAGCGGCGCTCGTATTATACATCAAGGTATAATGGTGCCTCTGAATAAAAGTT
1 TAAAAGGCACAACAGTGGCGCTCCTATTATACATCAAGGTATAATGGTGCCTCTGAATAAAAGTT
*
34491 GGTGATGGGAATTTCTATTTGCAGCAAAAGAGATGGCATTTCTATTATACATCAAGGTATAGTGG
66 GGTGATGGGAATTTCTATTTGCAGCAAAAGAGATGGCATTCCTATTATACATCAAGGTATAGTGG
* * * *
34556 TGCATCCAAATGAAGGTTGGTAATGAGAATTCTTATAATCCGGTTAAAGGCACAATATGGTGACA
131 TGCATCCAAATAAAGGTTGGTAATGAGAATTCTTATAATGCGGTTAAAGGCACAATGTGGTGGCA
34621 TTCCTACTATA
196 TTCCTACTATA
Statistics
Matches: 1083, Mismatches: 80, Indels: 11
0.92 0.07 0.01
Matches are distributed among these distances:
480 302 0.28
481 441 0.41
482 103 0.10
483 237 0.22
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.34
Consensus pattern (482 bp):
TAAAAGGCACAACAGTGGCGCTCCTATTATACATCAAGGTATAATGGTGCCTCTGAATAAAAGTT
GGTGATGGGAATTTCTATTTGCAGCAAAAGAGATGGCATTCCTATTATACATCAAGGTATAGTGG
TGCATCCAAATAAAGGTTGGTAATGAGAATTCTTATAATGCGGTTAAAGGCACAATGTGGTGGCA
TTCCTACTATACATAAAGGTATAGTGGTGCCAGTTCGTGTAATATGCCTGGAACTCTTATAGTGC
AATGAAATATGAAAAATCTTGAAGGCTCATGCTCCCTCGCCCACTCCATTTTTCCTGATTCACCA
CCATGAGCAATTTAAGTTTTATACTCAAAGTTGTTTTTTGACTGTTTAGTATTCACTGCACACCC
ATGAAATGGCAGCTATGCCTTGTTTTGATTTTGTTCTATCTATTTTCAAAAGATGCAAGTTCTTT
TGTTACATGGCATTTTTTTTTAAATGC
Done.