Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011489.1 Corchorus capsularis cultivar CVL-1 contig11510, 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: 50488
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1303 original size:16 final size:16
Alignment explanation
Indices: 1282--1329 Score: 87
Period size: 16 Copynumber: 3.0 Consensus size: 16
1272 TCCTTGAGGG
*
1282 GAAAAGACGGGGTTTT
1 GAAAAGATGGGGTTTT
1298 GAAAAGATGGGGTTTT
1 GAAAAGATGGGGTTTT
1314 GAAAAGATGGGGTTTT
1 GAAAAGATGGGGTTTT
1330 ATAACACTGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.31, C:0.02, G:0.38, T:0.29
Consensus pattern (16 bp):
GAAAAGATGGGGTTTT
Found at i:8254 original size:31 final size:31
Alignment explanation
Indices: 8214--8373 Score: 167
Period size: 31 Copynumber: 5.5 Consensus size: 31
8204 ACGGTGTTCG
*
8214 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
1 ACGTGGCACGCCACATGTACCAAAAAGTGAC
*
8245 ATGTGGCACGCCACATGTACCAAAAAGT--C
1 ACGTGGCACGCCACATGTACCAAAAAGTGAC
8274 A--T-----GCCACATGTACCAAAAAGTGAC
1 ACGTGGCACGCCACATGTACCAAAAAGTGAC
* *
8298 ACATGGCACGCCACGTGTACCAAAAAGTGAC
1 ACGTGGCACGCCACATGTACCAAAAAGTGAC
* ** * *
8329 ACGTGGCATGCCACATGTTTCAAAAAATGGC
1 ACGTGGCACGCCACATGTACCAAAAAGTGAC
*
8360 ACGTGGCATGCCAC
1 ACGTGGCACGCCAC
8374 GTGCACAAAA
Statistics
Matches: 110, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
22 19 0.17
24 2 0.02
26 1 0.01
27 1 0.01
29 2 0.02
31 85 0.77
ACGTcount: A:0.34, C:0.28, G:0.23, T:0.16
Consensus pattern (31 bp):
ACGTGGCACGCCACATGTACCAAAAAGTGAC
Found at i:8302 original size:19 final size:20
Alignment explanation
Indices: 8256--8302 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
8246 TGTGGCACGC
*
8256 CACATGTACCAAAAAGTCATGC
1 CACATGTACCAAAAAG--ATGA
8278 CACATGTACCAAAAAG-TGA
1 CACATGTACCAAAAAGATGA
8297 CACATG
1 CACATG
8303 GCACGCCACG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 8 0.33
22 16 0.67
ACGTcount: A:0.43, C:0.26, G:0.15, T:0.17
Consensus pattern (20 bp):
CACATGTACCAAAAAGATGA
Found at i:8305 original size:53 final size:53
Alignment explanation
Indices: 8223--8325 Score: 170
Period size: 53 Copynumber: 1.9 Consensus size: 53
8213 GACGTGGCAC
* **
8223 GCCACGTGTACCAAAAAGTGACATGTGGCACGCCACATGTACCAAAAAGTCAT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCAT
*
8276 GCCACATGTACCAAAAAGTGACACATGGCACGCCACGTGTACCAAAAAGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGT
8326 GACACGTGGC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 46 1.00
ACGTcount: A:0.37, C:0.27, G:0.20, T:0.16
Consensus pattern (53 bp):
GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCAT
Found at i:8827 original size:32 final size:32
Alignment explanation
Indices: 8770--8853 Score: 159
Period size: 32 Copynumber: 2.6 Consensus size: 32
8760 TCCAATAACA
8770 ATAAGTTCGCTAAACAAATTTTTTTTTTTTGAG
1 ATAAGTTCGCTAAAC-AATTTTTTTTTTTTGAG
8803 ATAAGTTCGCTAAACAATTTTTTTTTTTTGAG
1 ATAAGTTCGCTAAACAATTTTTTTTTTTTGAG
8835 ATAAGTTCGCTAAACAATT
1 ATAAGTTCGCTAAACAATT
8854 AATTCCCATT
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
32 36 0.71
33 15 0.29
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (32 bp):
ATAAGTTCGCTAAACAATTTTTTTTTTTTGAG
Found at i:9734 original size:67 final size:67
Alignment explanation
Indices: 9623--9751 Score: 222
Period size: 67 Copynumber: 1.9 Consensus size: 67
9613 GTATTCAGGA
* * *
9623 TAACGGTGTACGAGTAATCTTGTGTGAACCGGATTGATCTATTATTATGTGATAAAACCCTCCAG
1 TAACGGTGTACGAGTAATCTTGTGTGAACCAGATTGACCCATTATTATGTGATAAAACCCTCCAG
9688 AG
66 AG
*
9690 TAACGGTGTACGAGTAATCTTGTGTGAGCCAGATTGACCCATTATTATGTGATAAAACCCTC
1 TAACGGTGTACGAGTAATCTTGTGTGAACCAGATTGACCCATTATTATGTGATAAAACCCTC
9752 TCAACAATCC
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 58 1.00
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (67 bp):
TAACGGTGTACGAGTAATCTTGTGTGAACCAGATTGACCCATTATTATGTGATAAAACCCTCCAG
AG
Found at i:16980 original size:27 final size:27
Alignment explanation
Indices: 16945--16999 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
16935 TTACTCTTTC
16945 TGTTCCTTTTTAATTGTCCATTTCCCT
1 TGTTCCTTTTTAATTGTCCATTTCCCT
*
16972 TGTTTCTTTTTAATTGTCCATTTCCCT
1 TGTTCCTTTTTAATTGTCCATTTCCCT
16999 T
1 T
17000 TCTTTCCATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.11, C:0.24, G:0.07, T:0.58
Consensus pattern (27 bp):
TGTTCCTTTTTAATTGTCCATTTCCCT
Found at i:21016 original size:48 final size:48
Alignment explanation
Indices: 20940--21058 Score: 148
Period size: 48 Copynumber: 2.5 Consensus size: 48
20930 CATCTCCTGG
* * * *
20940 ATCTTCATTTAAATCAAAATCATGAATGTTGGCTTCATCTCCTACCCA
1 ATCTTCGTTCAAATCAAAATCTTAAATGTTGGCTTCATCTCCTACCCA
* * * *
20988 ATCTTTGTTCAAATTAAAATCTTAAATGTTGGCTTTATCTCCTATCCA
1 ATCTTCGTTCAAATCAAAATCTTAAATGTTGGCTTCATCTCCTACCCA
* *
21036 ATCTTCGTTTAAATCAAAGTCTT
1 ATCTTCGTTCAAATCAAAATCTT
21059 CCAACCATTG
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 59 1.00
ACGTcount: A:0.30, C:0.21, G:0.08, T:0.40
Consensus pattern (48 bp):
ATCTTCGTTCAAATCAAAATCTTAAATGTTGGCTTCATCTCCTACCCA
Found at i:21122 original size:36 final size:37
Alignment explanation
Indices: 21055--21130 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 37
21045 TAAATCAAAG
* *
21055 TCTTCCAACCATTGATTTCTGTTCAATTCAAAAT-AT
1 TCTTCCAACCATTGATTTCTATTCAAATCAAAATGAT
* *
21091 TCTTCCATCCATTGATCTTC-ATTGAAATCAAAATGAT
1 TCTTCCAACCATTGAT-TTCTATTCAAATCAAAATGAT
21128 TCT
1 TCT
21131 CACTTGATGG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
36 26 0.76
37 8 0.24
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.41
Consensus pattern (37 bp):
TCTTCCAACCATTGATTTCTATTCAAATCAAAATGAT
Found at i:22940 original size:23 final size:24
Alignment explanation
Indices: 22907--22970 Score: 112
Period size: 23 Copynumber: 2.7 Consensus size: 24
22897 AAAAAAACCC
*
22907 TCAAAAAACAGAGCAAACCTCAGA
1 TCAAAAAACAGAGCAAACCCCAGA
22931 TC-AAAAACAGAGCAAACCCCAGA
1 TCAAAAAACAGAGCAAACCCCAGA
22954 TCAAAAAACAGAGCAAA
1 TCAAAAAACAGAGCAAA
22971 AGAAAGAAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
23 22 0.58
24 16 0.42
ACGTcount: A:0.56, C:0.25, G:0.12, T:0.06
Consensus pattern (24 bp):
TCAAAAAACAGAGCAAACCCCAGA
Found at i:24674 original size:40 final size:41
Alignment explanation
Indices: 24616--24697 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 41
24606 AATTGGTTAG
* *
24616 TTCAAGTAGTTCGATTCTA-CAATTGGTTAGTTTAAATAGT
1 TTCAAGTAGTTCGATTCTATCAATGGGTTAGTTCAAATAGT
* * *
24656 TTCAAGTAGTTCGGTTCTATTAATGGGTTAGTTCAAGTAGT
1 TTCAAGTAGTTCGATTCTATCAATGGGTTAGTTCAAATAGT
24697 T
1 T
24698 CGGTTCTATG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 18 0.50
41 18 0.50
ACGTcount: A:0.27, C:0.10, G:0.21, T:0.43
Consensus pattern (41 bp):
TTCAAGTAGTTCGATTCTATCAATGGGTTAGTTCAAATAGT
Found at i:24823 original size:80 final size:81
Alignment explanation
Indices: 24677--24830 Score: 265
Period size: 81 Copynumber: 1.9 Consensus size: 81
24667 CGGTTCTATT
* * *
24677 AATGGGTTAGTTCAAGTAGTTCGGTTCTATGACTGGTTCGATTTTATAACTCTGACTAGTTTAAA
1 AATGGGTTAGTTCAAGTAGTTCGATTCTATGACTAGTTCGATTTTACAACTCTGACTAGTTTAAA
24742 TAGTTTCAATTCTAAC
66 TAGTTTCAATTCTAAC
*
24758 AATGGGTTAGTTCAAGTAGTTCGATTCTATGACTAGTTCG-TTTTACAACTCTGGCTAGTTTAAA
1 AATGGGTTAGTTCAAGTAGTTCGATTCTATGACTAGTTCGATTTTACAACTCTGACTAGTTTAAA
24822 TAGTTTCAA
66 TAGTTTCAA
24831 GTAGTTCGAT
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
80 31 0.45
81 38 0.55
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.40
Consensus pattern (81 bp):
AATGGGTTAGTTCAAGTAGTTCGATTCTATGACTAGTTCGATTTTACAACTCTGACTAGTTTAAA
TAGTTTCAATTCTAAC
Found at i:24884 original size:98 final size:99
Alignment explanation
Indices: 24762--24951 Score: 330
Period size: 99 Copynumber: 1.9 Consensus size: 99
24752 TCTAACAATG
*
24762 GGTTAGTTCAAGTAGTTCGATTCTATGACTAGTTC-GTTTTACAACTCTGGCTAGTTTAAATAGT
1 GGTTAGTTCAAGTAGTTCGATTCTACGACTAGTTCGGTTTTACAACTCTGGCTAGTTTAAATAGT
24826 TTCAAGTAGTTCGATTCTAACAATTGGAATAATT
66 TTCAAGTAGTTCGATTCTAACAATTGGAATAATT
* *
24860 GGTTAGTTCAAGTAGTTC-AGTTCTACGACTGGTTCGGTTTTACAACTCTGGTTAGTTTAAATAG
1 GGTTAGTTCAAGTAGTTCGA-TTCTACGACTAGTTCGGTTTTACAACTCTGGCTAGTTTAAATAG
24924 TTTCAAGTAGTTCGATTCTAACAATTGG
65 TTTCAAGTAGTTCGATTCTAACAATTGG
24952 TTAGTTCAAA
Statistics
Matches: 87, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
97 1 0.01
98 31 0.36
99 55 0.63
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (99 bp):
GGTTAGTTCAAGTAGTTCGATTCTACGACTAGTTCGGTTTTACAACTCTGGCTAGTTTAAATAGT
TTCAAGTAGTTCGATTCTAACAATTGGAATAATT
Found at i:24960 original size:31 final size:30
Alignment explanation
Indices: 24925--25001 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 30
24915 TTTAAATAGT
*
24925 TTCAAGTAGTTCGATTCTAACAATTGGTTAG
1 TTCAAATAGTTCGATTCT-ACAATTGGTTAG
* * *
24956 TTCAAATAGTTGGGTTCTATAATTGGTTAG
1 TTCAAATAGTTCGATTCTACAATTGGTTAG
*
24986 TTTAAATAGTTC-ATTC
1 TTCAAATAGTTCGATTC
25002 GGTTCTAACA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 3 0.08
30 21 0.54
31 15 0.38
ACGTcount: A:0.29, C:0.10, G:0.18, T:0.43
Consensus pattern (30 bp):
TTCAAATAGTTCGATTCTACAATTGGTTAG
Found at i:29187 original size:35 final size:35
Alignment explanation
Indices: 29141--29213 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
29131 TTTTTACCCC
29141 ATTTGGTATCTAGAGCATTGTTCTGATTAATCCGG
1 ATTTGGTATCTAGAGCATTGTTCTGATTAATCCGG
29176 ATTTGGTATCTAGAGCATTGTTCTGATTAATCCGG
1 ATTTGGTATCTAGAGCATTGTTCTGATTAATCCGG
29211 ATT
1 ATT
29214 CGACCTATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.23, C:0.14, G:0.22, T:0.41
Consensus pattern (35 bp):
ATTTGGTATCTAGAGCATTGTTCTGATTAATCCGG
Found at i:30715 original size:4 final size:4
Alignment explanation
Indices: 30706--30734 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
30696 TGGGTTCTTA
30706 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
30735 CTTATTAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:34873 original size:32 final size:33
Alignment explanation
Indices: 34832--34904 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 33
34822 ACAAAGTTTA
* * *
34832 TTTAACATGCATGATCT-CTTCTTCTACCTTTC
1 TTTATCATGCATAATCTCCTCCTTCTACCTTTC
34864 TTTATCATGCATAATCTCCTCCTTCTACCTTTC
1 TTTATCATGCATAATCTCCTCCTTCTACCTTTC
34897 TTTATCAT
1 TTTATCAT
34905 TAAAAATTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
32 15 0.41
33 22 0.59
ACGTcount: A:0.19, C:0.29, G:0.04, T:0.48
Consensus pattern (33 bp):
TTTATCATGCATAATCTCCTCCTTCTACCTTTC
Found at i:35016 original size:29 final size:29
Alignment explanation
Indices: 34972--35032 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
34962 CATCAAAAAT
34972 ATAGTATCACTATGACACCCGAAGTTGTC
1 ATAGTATCACTATGACACCCGAAGTTGTC
* * *
35001 ATAGTATCATTTTGACACCTGAAGTTGTC
1 ATAGTATCACTATGACACCCGAAGTTGTC
35030 ATA
1 ATA
35033 TTAAGGATGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (29 bp):
ATAGTATCACTATGACACCCGAAGTTGTC
Found at i:36308 original size:35 final size:35
Alignment explanation
Indices: 36257--36354 Score: 133
Period size: 35 Copynumber: 2.8 Consensus size: 35
36247 TCAAATGGTG
* *
36257 CAAATTTGATTTAAGGCTCCAGAAGAGCCAGTATT
1 CAAAATTGATTGAAGGCTCCAGAAGAGCCAGTATT
* *
36292 TAAAATTGATTGAAGGCTCCAGACGAGCCAGTATT
1 CAAAATTGATTGAAGGCTCCAGAAGAGCCAGTATT
* **
36327 CAAATTTGATTGAAGGCTCTGGAAGAGC
1 CAAAATTGATTGAAGGCTCCAGAAGAGC
36355 TACTATTGTT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 54 1.00
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (35 bp):
CAAAATTGATTGAAGGCTCCAGAAGAGCCAGTATT
Found at i:44441 original size:17 final size:17
Alignment explanation
Indices: 44419--44452 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
44409 CTCCGGTCCC
44419 TTTGAGATGTATTAAAA
1 TTTGAGATGTATTAAAA
44436 TTTGAGATGTATTAAAA
1 TTTGAGATGTATTAAAA
44453 AAAAGTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (17 bp):
TTTGAGATGTATTAAAA
Found at i:44486 original size:49 final size:49
Alignment explanation
Indices: 44414--44512 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
44404 AAATCCTCCG
44414 GTCCCTTTGAGATGTATTAAAATTTGAGATGTATTAAAAAAAAGTTTAA
1 GTCCCTTTGAGATGTATTAAAATTTGAGATGTATTAAAAAAAAGTTTAA
44463 GTCCCTTTGAGATGTATTAAAATTTGAGATGTATTAAAAAAAAGTTTAA
1 GTCCCTTTGAGATGTATTAAAATTTGAGATGTATTAAAAAAAAGTTTAA
44512 G
1 G
44513 GTATTTTATT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.36
Consensus pattern (49 bp):
GTCCCTTTGAGATGTATTAAAATTTGAGATGTATTAAAAAAAAGTTTAA
Found at i:44490 original size:17 final size:17
Alignment explanation
Indices: 44468--44501 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
44458 TTTAAGTCCC
44468 TTTGAGATGTATTAAAA
1 TTTGAGATGTATTAAAA
44485 TTTGAGATGTATTAAAA
1 TTTGAGATGTATTAAAA
44502 AAAAGTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (17 bp):
TTTGAGATGTATTAAAA
Found at i:46147 original size:21 final size:23
Alignment explanation
Indices: 46121--46171 Score: 61
Period size: 26 Copynumber: 2.2 Consensus size: 23
46111 AGGAGAACCC
46121 TACCCTA-A-TTTTTAAAATGAG
1 TACCCTACACTTTTTAAAATGAG
46142 TACCCTACCTCACTTTTTAAAATGAG
1 TACCCTA---CACTTTTTAAAATGAG
46168 TACC
1 TACC
46172 ATATCATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 7 0.28
25 1 0.04
26 17 0.68
ACGTcount: A:0.33, C:0.24, G:0.08, T:0.35
Consensus pattern (23 bp):
TACCCTACACTTTTTAAAATGAG
Done.