Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010851.1 Corchorus capsularis cultivar CVL-1 contig10872, 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: 24945
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.36
Found at i:312 original size:27 final size:27
Alignment explanation
Indices: 282--361 Score: 142
Period size: 27 Copynumber: 3.0 Consensus size: 27
272 AGGGGTATTG
*
282 TACGGAAGCCACGTATTTCCGGCGGGA
1 TACGGAAACCACGTATTTCCGGCGGGA
309 TACGGAAACCACGTATTTCCGGCGGGA
1 TACGGAAACCACGTATTTCCGGCGGGA
*
336 TATGGAAACCACGTATTTCCGGCGGG
1 TACGGAAACCACGTATTTCCGGCGGG
362 GTTCCTCATC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.24, C:0.25, G:0.31, T:0.20
Consensus pattern (27 bp):
TACGGAAACCACGTATTTCCGGCGGGA
Found at i:413 original size:9 final size:9
Alignment explanation
Indices: 399--428 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
389 GTTCAACCCC
399 TTCCTCCTA
1 TTCCTCCTA
408 TTCCTCCTA
1 TTCCTCCTA
417 TTCCTCCTA
1 TTCCTCCTA
426 TTC
1 TTC
429 ATACCATTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.10, C:0.43, G:0.00, T:0.47
Consensus pattern (9 bp):
TTCCTCCTA
Found at i:437 original size:18 final size:18
Alignment explanation
Indices: 399--439 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
389 GTTCAACCCC
*
399 TTCCTCCTATTCCTCCTA
1 TTCCTCCTATTCATCCTA
417 TTCCTCCTATTCATACC-A
1 TTCCTCCTATTCAT-CCTA
435 TTCCT
1 TTCCT
440 ACCATCCCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.15, C:0.41, G:0.00, T:0.44
Consensus pattern (18 bp):
TTCCTCCTATTCATCCTA
Found at i:502 original size:42 final size:42
Alignment explanation
Indices: 456--705 Score: 250
Period size: 42 Copynumber: 6.0 Consensus size: 42
446 CCTACCGGCC
456 GGGTTCCTCCGCCGCCTATTCCTCGGCCTCCTATTTCCGGAG
1 GGGTTCCTCCGCCGCCTATTCCTCGGCCTCCTATTTCCGGAG
* * **
498 GGGTTCCTCCGCCTCCTACCATTCCTAC--CATCCCTA---CCGGCC
1 GGGTTCCTCCGCCGCCT---ATTCCT-CGGCCT-CCTATTTCCGGAG
*
540 GGGTTCCTCCGCCGCCTATTCCTCGGCCTCCTATTTCTGGAG
1 GGGTTCCTCCGCCGCCTATTCCTCGGCCTCCTATTTCCGGAG
582 GGGTTCCTCCGCCGCCTATTCCTCGGCCTCCTATTTCCGGAG
1 GGGTTCCTCCGCCGCCTATTCCTCGGCCTCCTATTTCCGGAG
* * **
624 GGGTTCCTCCGCCTCCTACCATTCCTAC--CATCCCTA---CCGGCC
1 GGGTTCCTCCGCCGCCT---ATTCCT-CGGCCT-CCTATTTCCGGAG
*
666 GGGTTCCTCCGCCGCATATTCCTCGGCCTCCTATTTCCGG
1 GGGTTCCTCCGCCGCCTATTCCTCGGCCTCCTATTTCCGG
706 CGTGTTTCCT
Statistics
Matches: 171, Mismatches: 17, Indels: 40
0.75 0.07 0.18
Matches are distributed among these distances:
38 2 0.01
39 20 0.12
40 4 0.02
42 119 0.70
44 4 0.02
45 20 0.12
46 2 0.01
ACGTcount: A:0.09, C:0.43, G:0.20, T:0.28
Consensus pattern (42 bp):
GGGTTCCTCCGCCGCCTATTCCTCGGCCTCCTATTTCCGGAG
Found at i:523 original size:84 final size:84
Alignment explanation
Indices: 430--599 Score: 322
Period size: 84 Copynumber: 2.0 Consensus size: 84
420 CTCCTATTCA
430 TACCATTCCTACCATCCCTACCGGCCGGGTTCCTCCGCCGCCTATTCCTCGGCCTCCTATTTCCG
1 TACCATTCCTACCATCCCTACCGGCCGGGTTCCTCCGCCGCCTATTCCTCGGCCTCCTATTTCCG
*
495 GAGGGGTTCCTCCGCCTCC
66 GAGGGGTTCCTCCGCCGCC
*
514 TACCATTCCTACCATCCCTACCGGCCGGGTTCCTCCGCCGCCTATTCCTCGGCCTCCTATTTCTG
1 TACCATTCCTACCATCCCTACCGGCCGGGTTCCTCCGCCGCCTATTCCTCGGCCTCCTATTTCCG
579 GAGGGGTTCCTCCGCCGCC
66 GAGGGGTTCCTCCGCCGCC
598 TA
1 TA
600 TTCCTCGGCC
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.10, C:0.44, G:0.19, T:0.26
Consensus pattern (84 bp):
TACCATTCCTACCATCCCTACCGGCCGGGTTCCTCCGCCGCCTATTCCTCGGCCTCCTATTTCCG
GAGGGGTTCCTCCGCCGCC
Found at i:604 original size:126 final size:126
Alignment explanation
Indices: 456--702 Score: 485
Period size: 126 Copynumber: 2.0 Consensus size: 126
446 CCTACCGGCC
456 GGGTTCCTCCGCCGCCTATTCCTCGGCCTCCTATTTCCGGAGGGGTTCCTCCGCCTCCTACCATT
1 GGGTTCCTCCGCCGCCTATTCCTCGGCCTCCTATTTCCGGAGGGGTTCCTCCGCCTCCTACCATT
*
521 CCTACCATCCCTACCGGCCGGGTTCCTCCGCCGCCTATTCCTCGGCCTCCTATTTCTGGAG
66 CCTACCATCCCTACCGGCCGGGTTCCTCCGCCGCATATTCCTCGGCCTCCTATTTCTGGAG
582 GGGTTCCTCCGCCGCCTATTCCTCGGCCTCCTATTTCCGGAGGGGTTCCTCCGCCTCCTACCATT
1 GGGTTCCTCCGCCGCCTATTCCTCGGCCTCCTATTTCCGGAGGGGTTCCTCCGCCTCCTACCATT
647 CCTACCATCCCTACCGGCCGGGTTCCTCCGCCGCATATTCCTCGGCCTCCTATTTC
66 CCTACCATCCCTACCGGCCGGGTTCCTCCGCCGCATATTCCTCGGCCTCCTATTTC
703 CGGCGTGTTT
Statistics
Matches: 120, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
126 120 1.00
ACGTcount: A:0.09, C:0.43, G:0.20, T:0.28
Consensus pattern (126 bp):
GGGTTCCTCCGCCGCCTATTCCTCGGCCTCCTATTTCCGGAGGGGTTCCTCCGCCTCCTACCATT
CCTACCATCCCTACCGGCCGGGTTCCTCCGCCGCATATTCCTCGGCCTCCTATTTCTGGAG
Found at i:628 original size:84 final size:84
Alignment explanation
Indices: 450--727 Score: 254
Period size: 84 Copynumber: 3.3 Consensus size: 84
440 ACCATCCCTA
* *
450 CCGGCCGGGTTCCTCCGCCGCCTATTCCTCGGCCTCCTATTTCCGGAGGGGTTCCTCCGCCTCCT
1 CCGGACGGGTTCCTCCGCCGCCTATTCCTCGGCCTCCTATTTCCGGAGGGGTTCCTCCGCCGCCT
*
515 ACCATTCCTAC--CATCCCTA---
66 ---ATTCCT-CGGCCT-CCTATTT
* *
534 CCGGCCGGGTTCCTCCGCCGCCTATTCCTCGGCCTCCTATTTCTGGAGGGGTTCCTCCGCCGCCT
1 CCGGACGGGTTCCTCCGCCGCCTATTCCTCGGCCTCCTATTTCCGGAGGGGTTCCTCCGCCGCCT
599 ATTCCTCGGCCTCCTATTT
66 ATTCCTCGGCCTCCTATTT
* * * **
618 CCGGAGGGGTTCCTCCGCCTCCTACCATTCCTAC--CATCCCTA---CCGGCCGGGTTCCTCCGC
1 CCGGACGGGTTCCTCCGCCGCCT---ATTCCT-CGGCCT-CCTATTTCCGGAGGGGTTCCTCCGC
*
678 CGCATATTCCTCGGCCTCCTATTT
61 CGCCTATTCCTCGGCCTCCTATTT
* * *
702 CCGG-CGTGTTTCCTCGGCCTCCTATT
1 CCGGACG-GGTTCCTCCGCCGCCTATT
728 TCCCGCGGGG
Statistics
Matches: 169, Mismatches: 14, Indels: 25
0.81 0.07 0.12
Matches are distributed among these distances:
80 1 0.01
81 13 0.08
82 2 0.01
83 1 0.01
84 139 0.82
86 2 0.01
87 10 0.06
88 1 0.01
ACGTcount: A:0.08, C:0.43, G:0.21, T:0.28
Consensus pattern (84 bp):
CCGGACGGGTTCCTCCGCCGCCTATTCCTCGGCCTCCTATTTCCGGAGGGGTTCCTCCGCCGCCT
ATTCCTCGGCCTCCTATTT
Found at i:719 original size:27 final size:27
Alignment explanation
Indices: 684--757 Score: 112
Period size: 27 Copynumber: 2.7 Consensus size: 27
674 CCGCCGCATA
* * *
684 TTCCTCGGCCTCCTATTTCCGGCGTGT
1 TTCCTCGGCCTCCTATTTCCCGCGGGG
711 TTCCTCGGCCTCCTATTTCCCGCGGGG
1 TTCCTCGGCCTCCTATTTCCCGCGGGG
*
738 TTCCTCCGCCTCCTATTTCC
1 TTCCTCGGCCTCCTATTTCC
758 AAGCTTCTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.04, C:0.42, G:0.19, T:0.35
Consensus pattern (27 bp):
TTCCTCGGCCTCCTATTTCCCGCGGGG
Found at i:2217 original size:38 final size:38
Alignment explanation
Indices: 2161--2247 Score: 165
Period size: 38 Copynumber: 2.3 Consensus size: 38
2151 AATAAGAAAG
*
2161 AAACTATATTTATGTATTAAATATAGAAAAAACCAACA
1 AAACCATATTTATGTATTAAATATAGAAAAAACCAACA
2199 AAACCATATTTATGTATTAAATATAGAAAAAACCAACA
1 AAACCATATTTATGTATTAAATATAGAAAAAACCAACA
2237 AAACCATATTT
1 AAACCATATTT
2248 GATTCAAGGA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.54, C:0.13, G:0.05, T:0.29
Consensus pattern (38 bp):
AAACCATATTTATGTATTAAATATAGAAAAAACCAACA
Found at i:3431 original size:1 final size:1
Alignment explanation
Indices: 3425--3462 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
3415 TCATGTTGGG
3425 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3463 AACATCAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:5706 original size:164 final size:164
Alignment explanation
Indices: 5435--5763 Score: 658
Period size: 164 Copynumber: 2.0 Consensus size: 164
5425 GATATGAGTG
5435 ACCGAGGATGATCAGCAATAAAGATTTTAATAGGACTTGGCCTCGATCTGTTTAGACAACAGTAT
1 ACCGAGGATGATCAGCAATAAAGATTTTAATAGGACTTGGCCTCGATCTGTTTAGACAACAGTAT
5500 GACTGGAAGTACATATATAATTGGTTATCCCATTTGCTAACATCTCTTTGTAACATAATTGGTTA
66 GACTGGAAGTACATATATAATTGGTTATCCCATTTGCTAACATCTCTTTGTAACATAATTGGTTA
5565 CTGTTAGGCATCTCTCCACCTGTTCTGTCACCAA
131 CTGTTAGGCATCTCTCCACCTGTTCTGTCACCAA
5599 ACCGAGGATGATCAGCAATAAAGATTTTAATAGGACTTGGCCTCGATCTGTTTAGACAACAGTAT
1 ACCGAGGATGATCAGCAATAAAGATTTTAATAGGACTTGGCCTCGATCTGTTTAGACAACAGTAT
5664 GACTGGAAGTACATATATAATTGGTTATCCCATTTGCTAACATCTCTTTGTAACATAATTGGTTA
66 GACTGGAAGTACATATATAATTGGTTATCCCATTTGCTAACATCTCTTTGTAACATAATTGGTTA
5729 CTGTTAGGCATCTCTCCACCTGTTCTGTCACCAA
131 CTGTTAGGCATCTCTCCACCTGTTCTGTCACCAA
5763 A
1 A
5764 GTCTGTCCTG
Statistics
Matches: 165, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
164 165 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (164 bp):
ACCGAGGATGATCAGCAATAAAGATTTTAATAGGACTTGGCCTCGATCTGTTTAGACAACAGTAT
GACTGGAAGTACATATATAATTGGTTATCCCATTTGCTAACATCTCTTTGTAACATAATTGGTTA
CTGTTAGGCATCTCTCCACCTGTTCTGTCACCAA
Found at i:7708 original size:2 final size:2
Alignment explanation
Indices: 7694--7729 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
7684 CCATGCTACA
*
7694 AT AT AT TT A- 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 AT A
7730 CTAAATCTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11929 original size:15 final size:16
Alignment explanation
Indices: 11909--11948 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
11899 TTTACGCCCC
11909 TAAGCCTCCTC-AGCG
1 TAAGCCTCCTCGAGCG
11924 TAAGCCTCC-CGAGCG
1 TAAGCCTCCTCGAGCG
*
11939 TAAGGCTCCT
1 TAAGCCTCCT
11949 ATATCCGGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 21 0.95
ACGTcount: A:0.20, C:0.38, G:0.23, T:0.20
Consensus pattern (16 bp):
TAAGCCTCCTCGAGCG
Found at i:12035 original size:15 final size:14
Alignment explanation
Indices: 12015--12079 Score: 57
Period size: 15 Copynumber: 4.8 Consensus size: 14
12005 TATTTCTGGG
12015 CCTATTTCCGAGCCT
1 CCTATTTCCGA-CCT
12030 CCTATTTCCGA--T
1 CCTATTTCCGACCT
**
12042 CCTAAGTCC--CCT
1 CCTATTTCCGACCT
*
12054 CGTATTTCCGAGCCT
1 CCTATTTCCGA-CCT
12069 CCTATTTCCGA
1 CCTATTTCCGA
12080 TAAGTCCACT
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
12 15 0.38
15 24 0.62
ACGTcount: A:0.15, C:0.38, G:0.12, T:0.34
Consensus pattern (14 bp):
CCTATTTCCGACCT
Found at i:12096 original size:36 final size:37
Alignment explanation
Indices: 12015--12102 Score: 133
Period size: 39 Copynumber: 2.4 Consensus size: 37
12005 TATTTCTGGG
*
12015 CCTATTTCCGAGCCTCCTATTTCCGATCCTAAGTCCCCT
1 CCTATTTCCGAGCCTCCTATTTCCGA--CTAAGTCCACT
*
12054 CGTATTTCCGAGCCTCCTATTTCCGA-TAAGTCCACT
1 CCTATTTCCGAGCCTCCTATTTCCGACTAAGTCCACT
12090 CCTATTTCCGAGC
1 CCTATTTCCGAGC
12103 ACCGTATACC
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
36 21 0.46
39 25 0.54
ACGTcount: A:0.17, C:0.38, G:0.12, T:0.33
Consensus pattern (37 bp):
CCTATTTCCGAGCCTCCTATTTCCGACTAAGTCCACT
Found at i:15875 original size:24 final size:24
Alignment explanation
Indices: 15801--15877 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 24
15791 TTTATTTTTG
* *
15801 GTTTGTTAATTTCTTTCAATATAA
1 GTTTGTTAATTTCATTCAATTTAA
* * * *
15825 GTTTG-TAATATGCATACAGTTT-G
1 GTTTGTTAAT-TTCATTCAATTTAA
15848 GTTTGTTAATTTCATTCAATTTAA
1 GTTTGTTAATTTCATTCAATTTAA
15872 GTTTGT
1 GTTTGT
15878 ATTATGTATA
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
23 18 0.45
24 22 0.55
ACGTcount: A:0.26, C:0.08, G:0.14, T:0.52
Consensus pattern (24 bp):
GTTTGTTAATTTCATTCAATTTAA
Found at i:22725 original size:20 final size:20
Alignment explanation
Indices: 22700--22739 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
22690 TTTCTATGTG
22700 AATTTGTTCTTTAAATCATA
1 AATTTGTTCTTTAAATCATA
22720 AATTTGTTCTTTAAATCATA
1 AATTTGTTCTTTAAATCATA
22740 GATGAAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.50
Consensus pattern (20 bp):
AATTTGTTCTTTAAATCATA
Done.