Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007207.1 Corchorus capsularis cultivar CVL-1 contig07228, 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: 41687
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2534 original size:31 final size:31
Alignment explanation
Indices: 2490--2620 Score: 136
Period size: 31 Copynumber: 4.2 Consensus size: 31
2480 ATGGTGTCCG
* *
2490 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
1 ACGTGGCATGCCACATGCACCAAAAAGTGAC
* * *
2521 ATGTGGCACGCCACATGCACCAAAAAATGAC
1 ACGTGGCATGCCACATGCACCAAAAAGTGAC
** * **
2552 ACGTATCATGCAATGTGCACCAAAAAGTGAC
1 ACGTGGCATGCCACATGCACCAAAAAGTGAC
* ***
2583 ACGTGGCATGTCACATGTTTCAAAAAGTGAC
1 ACGTGGCATGCCACATGCACCAAAAAGTGAC
2614 ACGTGGC
1 ACGTGGC
2621 CGATCCGTTT
Statistics
Matches: 78, Mismatches: 22, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
31 78 1.00
ACGTcount: A:0.34, C:0.24, G:0.23, T:0.18
Consensus pattern (31 bp):
ACGTGGCATGCCACATGCACCAAAAAGTGAC
Found at i:9381 original size:11 final size:11
Alignment explanation
Indices: 9355--9386 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
9345 AGAAAGAAAA
9355 AGGTGTTCTT-
1 AGGTGTTCTTG
9365 -GGTGTTCTTG
1 AGGTGTTCTTG
9375 AGGTGTTCTTG
1 AGGTGTTCTTG
9386 A
1 A
9387 AAAAAGGGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
9 9 0.45
11 11 0.55
ACGTcount: A:0.09, C:0.09, G:0.34, T:0.47
Consensus pattern (11 bp):
AGGTGTTCTTG
Found at i:11506 original size:16 final size:15
Alignment explanation
Indices: 11466--11509 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
11456 AGAGGAAATA
11466 GGAAGGAAAGAAGAGG
1 GGAAGGAAAGAA-AGG
*
11482 GG-TGGAAAGAAATGG
1 GGAAGGAAAGAAA-GG
11497 GGAAGGAAAGAAA
1 GGAAGGAAAGAAA
11510 AGCTTCCTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 1 0.04
15 12 0.50
16 11 0.46
ACGTcount: A:0.50, C:0.00, G:0.45, T:0.05
Consensus pattern (15 bp):
GGAAGGAAAGAAAGG
Found at i:11955 original size:7 final size:8
Alignment explanation
Indices: 11925--11959 Score: 52
Period size: 8 Copynumber: 4.1 Consensus size: 8
11915 TTTTTAATAT
11925 ATTTTTTAA
1 ATTTTTT-A
11934 ATTCTTTTA
1 ATT-TTTTA
11943 ATTTTTTA
1 ATTTTTTA
11951 ATTTTTTA
1 ATTTTTTA
11959 A
1 A
11960 ACCGGTTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 14 0.56
9 7 0.28
10 4 0.16
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (8 bp):
ATTTTTTA
Found at i:12022 original size:30 final size:31
Alignment explanation
Indices: 11977--12034 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
11967 CAAATAGGTG
* *
11977 CTAAACGTTTGAAAA-TGGATCAATTTAATA
1 CTAAACATTTCAAAATTGGATCAATTTAATA
12007 CTAAACATTTCAAAATTGGATCAATTTA
1 CTAAACATTTCAAAATTGGATCAATTTA
12035 GATTTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 13 0.52
31 12 0.48
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.34
Consensus pattern (31 bp):
CTAAACATTTCAAAATTGGATCAATTTAATA
Found at i:14746 original size:12 final size:12
Alignment explanation
Indices: 14731--14756 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
14721 GGATTTTAGC
14731 CTCTTTTTTTTT
1 CTCTTTTTTTTT
14743 CTCTTTTTTTTT
1 CTCTTTTTTTTT
14755 CT
1 CT
14757 TTCTCCATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (12 bp):
CTCTTTTTTTTT
Found at i:17124 original size:16 final size:16
Alignment explanation
Indices: 17103--17135 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
17093 TTCAGAAAGC
17103 AGAAAAGCTCTGAAGT
1 AGAAAAGCTCTGAAGT
17119 AGAAAAGCTCTGAAGT
1 AGAAAAGCTCTGAAGT
17135 A
1 A
17136 TTTCAGATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.12, G:0.24, T:0.18
Consensus pattern (16 bp):
AGAAAAGCTCTGAAGT
Found at i:22165 original size:19 final size:19
Alignment explanation
Indices: 22141--22178 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
22131 CAAGGTCAAT
*
22141 CGGTTGAGAATTTGTTCTC
1 CGGTTGAGAATTTCTTCTC
22160 CGGTTGAGAATTTCTTCTC
1 CGGTTGAGAATTTCTTCTC
22179 AAATAAACAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.42
Consensus pattern (19 bp):
CGGTTGAGAATTTCTTCTC
Found at i:36481 original size:31 final size:31
Alignment explanation
Indices: 36443--36507 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
36433 TCCTTTATCA
36443 AAATTTATATTTTAATAGTTTTTATCAAATT
1 AAATTTATATTTTAATAGTTTTTATCAAATT
*
36474 AAATTTATATTTTAATAGTTTTTATTAAATT
1 AAATTTATATTTTAATAGTTTTTATCAAATT
36505 AAA
1 AAA
36508 ATCTTTATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.54
Consensus pattern (31 bp):
AAATTTATATTTTAATAGTTTTTATCAAATT
Found at i:38797 original size:15 final size:15
Alignment explanation
Indices: 38777--38863 Score: 88
Period size: 15 Copynumber: 5.7 Consensus size: 15
38767 GGCAATTGGG
*
38777 CGGGTTCGGGTACTT
1 CGGGTTCGGGTATTT
*
38792 CGGGTTTGGGTATTTT
1 CGGGTTCGGGTA-TTT
*
38808 CAGGTTCGGGT-TCTGT
1 CGGGTTCGGGTAT-T-T
38824 CGGGTTCGGGTATTT
1 CGGGTTCGGGTATTT
*
38839 TGGGTTCGGGTATTTT
1 CGGGTTCGGGTA-TTT
38855 C-GGTTCGGG
1 CGGGTTCGGG
38864 CTCGGATCGG
Statistics
Matches: 60, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
14 1 0.02
15 32 0.53
16 26 0.43
17 1 0.02
ACGTcount: A:0.06, C:0.14, G:0.40, T:0.40
Consensus pattern (15 bp):
CGGGTTCGGGTATTT
Found at i:38817 original size:31 final size:31
Alignment explanation
Indices: 38779--38863 Score: 102
Period size: 31 Copynumber: 2.8 Consensus size: 31
38769 CAATTGGGCG
*
38779 GGTTCGGGTACT-TCGGGTTTGGGTATTTTCA
1 GGTTCGGGTACTGTCGGGTTCGGGTATTTT-A
* *
38810 GGTTCGGGTTCTGTCGGGTTCGGGTATTTTG
1 GGTTCGGGTACTGTCGGGTTCGGGTATTTTA
* *
38841 GGTTCGGGTATTTTC-GGTTCGGG
1 GGTTCGGGTACTGTCGGGTTCGGG
38864 CTCGGATCGG
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
30 8 0.17
31 23 0.49
32 16 0.34
ACGTcount: A:0.06, C:0.13, G:0.40, T:0.41
Consensus pattern (31 bp):
GGTTCGGGTACTGTCGGGTTCGGGTATTTTA
Found at i:38831 original size:47 final size:47
Alignment explanation
Indices: 38777--38881 Score: 149
Period size: 47 Copynumber: 2.2 Consensus size: 47
38767 GGCAATTGGG
* * *
38777 CGGGTTCGGGTACTTCGGGTTTGGGTATTTTCAGGTTCGGGTTCTG-T
1 CGGGTTCGGGTACTTCGGGTTCGGGTATTTTC-GGTTCGGGCTCGGAT
* *
38824 CGGGTTCGGGTATTTTGGGTTCGGGTATTTTCGGTTCGGGCTCGGAT
1 CGGGTTCGGGTACTTCGGGTTCGGGTATTTTCGGTTCGGGCTCGGAT
38871 CGGGTTCGGGT
1 CGGGTTCGGGT
38882 TTAGGGTCGG
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
46 11 0.21
47 41 0.79
ACGTcount: A:0.06, C:0.15, G:0.41, T:0.38
Consensus pattern (47 bp):
CGGGTTCGGGTACTTCGGGTTCGGGTATTTTCGGTTCGGGCTCGGAT
Found at i:39687 original size:10 final size:11
Alignment explanation
Indices: 39660--39699 Score: 55
Period size: 10 Copynumber: 3.6 Consensus size: 11
39650 TATTTTGATC
*
39660 TCGGGCTCGGG
1 TCGGGTTCGGG
39671 TCGGGTTCGGG
1 TCGGGTTCGGG
39682 -CGGGTTCGGG
1 TCGGGTTCGGG
39692 TTCGGGTT
1 -TCGGGTT
39700 GTCTCGAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 10 0.38
11 10 0.38
12 6 0.23
ACGTcount: A:0.00, C:0.20, G:0.53, T:0.28
Consensus pattern (11 bp):
TCGGGTTCGGG
Found at i:39691 original size:6 final size:6
Alignment explanation
Indices: 39660--39699 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
39650 TATTTTGATC
*
39660 TCGGGC TCGGG- TCGGGT TCGGG- -CGGGT TCGGGT TCGGGT T
1 TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT T
39700 GTCTCGAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
4 4 0.13
5 5 0.16
6 22 0.71
ACGTcount: A:0.00, C:0.20, G:0.53, T:0.28
Consensus pattern (6 bp):
TCGGGT
Found at i:39692 original size:16 final size:15
Alignment explanation
Indices: 39667--39697 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
39657 ATCTCGGGCT
39667 CGGGTCGGGTTCGGG
1 CGGGTCGGGTTCGGG
39682 CGGGTTCGGGTTCGGG
1 CGGG-TCGGGTTCGGG
39698 TTGTCTCGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (15 bp):
CGGGTCGGGTTCGGG
Found at i:39726 original size:16 final size:16
Alignment explanation
Indices: 39707--39744 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
39697 GTTGTCTCGA
*
39707 GTTCGGGTATTTTCAG
1 GTTCGGGTAATTTCAG
39723 GTTCGGGTAATTTCAG
1 GTTCGGGTAATTTCAG
39739 GTTCGG
1 GTTCGG
39745 ACGGGTTCGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.13, C:0.13, G:0.34, T:0.39
Consensus pattern (16 bp):
GTTCGGGTAATTTCAG
Found at i:39797 original size:6 final size:6
Alignment explanation
Indices: 39786--39838 Score: 60
Period size: 6 Copynumber: 9.3 Consensus size: 6
39776 TTCGGGTAAT
*
39786 TTCGGG TTCGGG TTCGGG --CGGG TTCGGA TTCGGG --CGGG TTCGGG
1 TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG
39830 TTTCGGG TT
1 -TTCGGG TT
39839 AGAAAGCCGC
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
4 8 0.20
6 26 0.65
7 6 0.15
ACGTcount: A:0.02, C:0.17, G:0.49, T:0.32
Consensus pattern (6 bp):
TTCGGG
Found at i:39807 original size:16 final size:16
Alignment explanation
Indices: 39788--39836 Score: 80
Period size: 16 Copynumber: 3.0 Consensus size: 16
39778 CGGGTAATTT
39788 CGGGTTCGGGTTCGGG
1 CGGGTTCGGGTTCGGG
*
39804 CGGGTTCGGATTCGGG
1 CGGGTTCGGGTTCGGG
39820 CGGGTTCGGGTTTCGGG
1 CGGGTTCGGG-TTCGGG
39837 TTAGAAAGCC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 24 0.80
17 6 0.20
ACGTcount: A:0.02, C:0.18, G:0.53, T:0.27
Consensus pattern (16 bp):
CGGGTTCGGGTTCGGG
Found at i:41274 original size:19 final size:20
Alignment explanation
Indices: 41246--41283 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
41236 TTGCTGTTGA
41246 AAAAAGAAAATGGCAACAAG
1 AAAAAGAAAATGGCAACAAG
41266 AAAAA-AAAATGGCAACAA
1 AAAAAGAAAATGGCAACAA
41284 TGCCAAACAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.68, C:0.11, G:0.16, T:0.05
Consensus pattern (20 bp):
AAAAAGAAAATGGCAACAAG
Found at i:41640 original size:2 final size:2
Alignment explanation
Indices: 41633--41686 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
41623 ACTGAAACAC
41633 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
41675 AG AG AG AG AG AG
1 AG AG AG AG AG AG
41687 C
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.