Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014029.1 Corchorus capsularis cultivar CVL-1 contig14050, 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: 6352
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Found at i:243 original size:24 final size:24
Alignment explanation
Indices: 216--265 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
206 ATTTATTCAT
216 TATTAATTAACTATTAACTAGATA
1 TATTAATTAACTATTAACTAGATA
* *
240 TATTAATTAGCTATTAATTAGATA
1 TATTAATTAACTATTAACTAGATA
264 TA
1 TA
266 GTATAATGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (24 bp):
TATTAATTAACTATTAACTAGATA
Found at i:1571 original size:20 final size:21
Alignment explanation
Indices: 1520--1572 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 21
1510 GCACTAGAGT
1520 ACATGGGTCG-CAAGACAAACC
1 ACATGGG-CGCCAAGACAAACC
1541 ACATGGGGCGCCAAG-CAAACC
1 ACAT-GGGCGCCAAGACAAACC
1562 ACATGGGCGCC
1 ACATGGGCGCC
1573 CAGCGCTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.23
21 16 0.53
22 7 0.23
ACGTcount: A:0.32, C:0.32, G:0.28, T:0.08
Consensus pattern (21 bp):
ACATGGGCGCCAAGACAAACC
Found at i:3894 original size:19 final size:19
Alignment explanation
Indices: 3870--3908 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
3860 AGCTCTTGGG
3870 ATTTCATCCCAAGCCGTGA
1 ATTTCATCCCAAGCCGTGA
3889 ATTTCATCCCAAGCCGTGA
1 ATTTCATCCCAAGCCGTGA
3908 A
1 A
3909 GGGAGCTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.26
Consensus pattern (19 bp):
ATTTCATCCCAAGCCGTGA
Found at i:4795 original size:52 final size:49
Alignment explanation
Indices: 4719--4876 Score: 130
Period size: 49 Copynumber: 3.2 Consensus size: 49
4709 ACAAAAATTA
* *
4719 AATCTTTA-GTCAAAA-ATGGGAGTTTTGA-TGAATGTGGAGTAATGAAAATGT
1 AATCTTTATGTCAAAAGAT-GAAGTTTTAAGT-AATGTGGA--AAT-AAAATGT
* * *
4770 AGTCTTTATGTCAAAAGATGAAGTTTTAAGTAATTTGTAAATAAAATGT
1 AATCTTTATGTCAAAAGATGAAGTTTTAAGTAATGTGGAAATAAAATGT
* *
4819 AATCTTTATGTTAAAAGATGAA-TCTTCTAAGTAACT-TGTAAATAAAAATGT
1 AATCTTTATGTCAAAAGATGAAGT-TT-TAAGTAA-TGTGGAAAT-AAAATGT
4870 AAT-TTTA
1 AATCTTTA
4877 AAGTGAAAAA
Statistics
Matches: 93, Mismatches: 7, Indels: 15
0.81 0.06 0.13
Matches are distributed among these distances:
48 1 0.01
49 29 0.31
50 21 0.23
51 18 0.19
52 21 0.23
53 3 0.03
ACGTcount: A:0.41, C:0.05, G:0.17, T:0.37
Consensus pattern (49 bp):
AATCTTTATGTCAAAAGATGAAGTTTTAAGTAATGTGGAAATAAAATGT
Found at i:4892 original size:51 final size:51
Alignment explanation
Indices: 4763--4926 Score: 180
Period size: 51 Copynumber: 3.3 Consensus size: 51
4753 TGGAGTAATG
* * *
4763 AAAATGTAGTCTTTATGTCAAAAGATGAAGT-T-TTAAGTAATTTGTAAAT-
1 AAAATGTAATCTTTAAGTGAAAAGATGAA-TCTCTTAAGTAATTTGTAAATA
* * *
4812 AAAATGTAATCTTTATGTTAAAAGATGAATCT-TCTAAGTAACTTGTAAATA
1 AAAATGTAATCTTTAAGTGAAAAGATGAATCTCT-TAAGTAATTTGTAAATA
4863 AAAATGTAAT-TTTAAAGTGAAAA-ATTGAATCTCTTAAGTAATTTGTAAATA
1 AAAATGTAATCTTT-AAGTGAAAAGA-TGAATCTCTTAAGTAATTTGTAAATA
*
4914 AAGATG-AATCTTT
1 AAAATGTAATCTTT
4927 TAAATAATTT
Statistics
Matches: 101, Mismatches: 7, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
48 1 0.01
49 29 0.29
50 22 0.22
51 48 0.48
52 1 0.01
ACGTcount: A:0.43, C:0.05, G:0.13, T:0.38
Consensus pattern (51 bp):
AAAATGTAATCTTTAAGTGAAAAGATGAATCTCTTAAGTAATTTGTAAATA
Found at i:5047 original size:50 final size:51
Alignment explanation
Indices: 4925--5122 Score: 192
Period size: 51 Copynumber: 3.9 Consensus size: 51
4915 AGATGAATCT
* * * * *
4925 TTTAAA-TAATTTGAATATAAGGATTGGACTTTTAAGTGAAAGATTGAATC
1 TTTAAAGTAATTTGTATATAAAGATTGAATTTTTAAGTGAAAGATTGAACC
* * *
4975 TTTTAAGTAATTTG-ATGATAAAGATTGAGTTTTTAA-TTAGAAGA-TGAACC
1 TTTAAAGTAATTTGTAT-ATAAAGATTGAATTTTTAAGTGA-AAGATTGAACC
* * *
5025 TTTAAAGTAATTTGTATATAAAGATTAAATGTTTAAGTGAAAGATTGAATC
1 TTTAAAGTAATTTGTATATAAAGATTGAATTTTTAAGTGAAAGATTGAACC
* *
5076 TTTCAAGTAGTTTGTGA-ATAAAGATTGAATTTTTGAA-TGAAAAGATT
1 TTTAAAGTAATTTGT-ATATAAAGATTGAATTTTT-AAGTG-AAAGATT
5123 AATCTTTTTG
Statistics
Matches: 122, Mismatches: 17, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
50 47 0.39
51 65 0.53
52 10 0.08
ACGTcount: A:0.40, C:0.03, G:0.18, T:0.39
Consensus pattern (51 bp):
TTTAAAGTAATTTGTATATAAAGATTGAATTTTTAAGTGAAAGATTGAACC
Found at i:5097 original size:101 final size:101
Alignment explanation
Indices: 4914--5109 Score: 272
Period size: 101 Copynumber: 1.9 Consensus size: 101
4904 TTTGTAAATA
* * * * *
4914 AAGATGAATCTTTTAAATAATTTGAATATAAGGATTGGACTTTTAAGTGAAAGATTGAATCTTTT
1 AAGATGAATCCTTTAAATAATTTGAATATAAAGATTGAAATTTTAAGTGAAAGATTGAATCTTTC
*
4979 AAGTAATTTGATGATAAAGATTGAGTTTTTAATTAG
66 AAGTAATTTGATGATAAAGATTGAATTTTTAATTAG
*
5015 AAGATGAA-CCTTTAAAGTAATTTGTATATAAAGATT-AAATGTTTAAGTGAAAGATTGAATCTT
1 AAGATGAATCCTTTAAA-TAATTTGAATATAAAGATTGAAAT-TTTAAGTGAAAGATTGAATCTT
*
5078 TCAAGTAGTTTG-TGAATAAAGATTGAATTTTT
64 TCAAGTAATTTGATG-ATAAAGATTGAATTTTT
5110 GAATGAAAAG
Statistics
Matches: 84, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
100 11 0.13
101 73 0.87
ACGTcount: A:0.39, C:0.04, G:0.17, T:0.40
Consensus pattern (101 bp):
AAGATGAATCCTTTAAATAATTTGAATATAAAGATTGAAATTTTAAGTGAAAGATTGAATCTTTC
AAGTAATTTGATGATAAAGATTGAATTTTTAATTAG
Found at i:5197 original size:51 final size:51
Alignment explanation
Indices: 5128--5287 Score: 205
Period size: 51 Copynumber: 3.1 Consensus size: 51
5118 AGATTAATCT
** * * *
5128 TTTTGATTAAAGTG-AAATAAAAATGAGATCTTTGAGCTAAATGATGGAAC
1 TTTTGATTAATTTGTAAATAAAAATGAGATCTTTGAACTAAAAGATGAAAC
* * * *
5178 TTATGATTTATTTGTAAATAAAAATAAGATCTTTGAACTAAAAGATGAAAG
1 TTTTGATTAATTTGTAAATAAAAATGAGATCTTTGAACTAAAAGATGAAAC
* *
5229 TTTTGATTAATTTGTAAGTAAAAATGAAATCTTTTGAACTAAAAGATGAAAC
1 TTTTGATTAATTTGTAAATAAAAATGAGATC-TTTGAACTAAAAGATGAAAC
5281 TTTTGAT
1 TTTTGAT
5288 AAGGTGAAGT
Statistics
Matches: 93, Mismatches: 15, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
50 10 0.11
51 57 0.61
52 26 0.28
ACGTcount: A:0.43, C:0.05, G:0.16, T:0.36
Consensus pattern (51 bp):
TTTTGATTAATTTGTAAATAAAAATGAGATCTTTGAACTAAAAGATGAAAC
Found at i:5271 original size:21 final size:21
Alignment explanation
Indices: 5247--5286 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
5237 AATTTGTAAG
5247 TAAAA-ATGAAATCTTTTGAAC
1 TAAAAGATGAAA-CTTTTGAAC
5268 TAAAAGATGAAACTTTTGA
1 TAAAAGATGAAACTTTTGA
5287 TAAGGTGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.33
Consensus pattern (21 bp):
TAAAAGATGAAACTTTTGAAC
Found at i:6110 original size:41 final size:41
Alignment explanation
Indices: 5969--6352 Score: 408
Period size: 41 Copynumber: 9.5 Consensus size: 41
5959 TTGTTTCCGA
* * *
5969 TTTCCCA-TTCTGCCCTTCCCCACCAGAAGGTGTTG-TTCAG
1 TTTCCCAGTT-TGCCCTTCCCCATCGGAAGGTGTTGTTTAAG
** *
6009 TTTCATAGTCTGCCCTTCCCCATCGGAAGGTGTTGTTTAAG
1 TTTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAAG
6050 TTT-CCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAAG
1 TTTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAAG
*
6090 TTTCCCAGTTTGCCATTCCCCATCGGAAGGTGTTGTTTAAG
1 TTTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAAG
**
6131 TTTCCCAGTTTGCCCTT-CCTGTCGGAAGGTGTTGTTTATA-
1 TTTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTA-AG
* * * *
6171 TTTCCCAGTTTGCCTTTCCCCGTCAGAAAGTGTTGTTTATA-
1 TTTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTA-AG
* * *
6212 TTTCCCAGTTTGCCCTTCCCCACCGAAAGATGTTGTTT-AG
1 TTTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAAG
* * * * * *
6252 AATGCCCAGTCTACCCTT-CCCACCGGAAGGAGTTGTTTACA-
1 -TTTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTA-AG
* * * * *
6293 TTTCCCAATCTGCCATTCCCCGTCAGAAGGTGTTGTTTAAG
1 TTTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAAG
*
6334 TTTTCCAGTTTGCCCTTCC
1 TTTCCCAGTTTGCCCTTCC
Statistics
Matches: 289, Mismatches: 44, Indels: 21
0.82 0.12 0.06
Matches are distributed among these distances:
39 1 0.00
40 130 0.45
41 157 0.54
42 1 0.00
ACGTcount: A:0.17, C:0.28, G:0.20, T:0.36
Consensus pattern (41 bp):
TTTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAAG
Found at i:6117 original size:81 final size:82
Alignment explanation
Indices: 5959--6352 Score: 401
Period size: 81 Copynumber: 4.8 Consensus size: 82
5949 CAATCTTGTC
* * * * ** *
5959 TTGTTTCCGATTTCCCA-TTCTGCCCTTCCCCACCAGAAGGTGTTG-TTCAGTTTCATAGTCTGC
1 TTGTTTAC-ATTTCCCAGTT-TGCCCTTCCCCATCGGAAGGTGTTGTTTAAGTTTCCCAGTTTGC
6022 CCTTCCCCATCGGAAGGTG
64 CCTTCCCCATCGGAAGGTG
6041 TTGTTTA-AGTTT-CCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAAGTTTCCCAGTTTGCC
1 TTGTTTACA-TTTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAAGTTTCCCAGTTTGCC
*
6104 ATTCCCCATCGGAAGGTG
65 CTTCCCCATCGGAAGGTG
**
6122 TTGTTTA-AGTTTCCCAGTTTGCCCTT-CCTGTCGGAAGGTGTTGTTTATA-TTTCCCAGTTTGC
1 TTGTTTACA-TTTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTA-AGTTTCCCAGTTTGC
* * * *
6184 CTTTCCCCGTCAGAAAGTG
64 CCTTCCCCATCGGAAGGTG
* * * * * * * *
6203 TTGTTTATATTTCCCAGTTTGCCCTTCCCCACCGAAAGATGTTGTTT-AGAATGCCCAGTCTACC
1 TTGTTTACATTTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAAG-TTTCCCAGTTTGCC
* *
6267 CTT-CCCACCGGAAGGAG
65 CTTCCCCATCGGAAGGTG
* * * * * *
6284 TTGTTTACATTTCCCAATCTGCCATTCCCCGTCAGAAGGTGTTGTTTAAGTTTTCCAGTTTGCCC
1 TTGTTTACATTTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAAGTTTCCCAGTTTGCCC
6349 TTCC
66 TTCC
Statistics
Matches: 258, Mismatches: 43, Indels: 22
0.80 0.13 0.07
Matches are distributed among these distances:
80 28 0.11
81 179 0.69
82 51 0.20
ACGTcount: A:0.16, C:0.27, G:0.20, T:0.37
Consensus pattern (82 bp):
TTGTTTACATTTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAAGTTTCCCAGTTTGCCC
TTCCCCATCGGAAGGTG
Found at i:6217 original size:122 final size:120
Alignment explanation
Indices: 5969--6352 Score: 459
Period size: 122 Copynumber: 3.2 Consensus size: 120
5959 TTGTTTCCGA
* * **
5969 TTTCCCA-TTCTGCCCTTCCCCACCAGAAGGTGTTGTTCAGTTTCATAGTCTGCCCTTCCCCATC
1 TTTCCCAGTT-TGCCCTTCCCCACCGGAAGGTGTTGTTTAGTTTCCCAGTCTGCCCTT-CCCATC
* * *
6033 GGAAGGTGTTGTTTAAGTTT-CCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAAG
64 GGAAGGTGTTGTTTAA-TTTCCCAGTTTGCCATTCCCCGTCAGAAGGTGTTGTTTAAG
* * * **
6090 TTTCCCAGTTTGCCATTCCCCATCGGAAGGTGTTGTTTAAGTTTCCCAGTTTGCCCTTCCTGTCG
1 TTTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTT-AGTTTCCCAGTCTGCCCTTCCCATCG
* *
6155 GAAGGTGTTGTTTATATTTCCCAGTTTGCCTTTCCCCGTCAGAAAGTGTTGTTTATA-
65 GAAGGTGTTGTTTA-ATTTCCCAGTTTGCCATTCCCCGTCAGAAGGTGTTGTTTA-AG
* * * * * *
6212 TTTCCCAGTTTGCCCTTCCCCACCGAAAGATGTTGTTTAGAATGCCCAGTCTACCCTTCCCACCG
1 TTTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAG-TTTCCCAGTCTGCCCTTCCCATCG
* * *
6277 GAAGGAGTTGTTTACATTTCCCAATCTGCCATTCCCCGTCAGAAGGTGTTGTTTAAG
65 GAAGGTGTTGTTTA-ATTTCCCAGTTTGCCATTCCCCGTCAGAAGGTGTTGTTTAAG
*
6334 TTTTCCAGTTTGCCCTTCC
1 TTTCCCAGTTTGCCCTTCC
Statistics
Matches: 225, Mismatches: 31, Indels: 13
0.84 0.12 0.05
Matches are distributed among these distances:
121 56 0.25
122 168 0.75
123 1 0.00
ACGTcount: A:0.17, C:0.28, G:0.20, T:0.36
Consensus pattern (120 bp):
TTTCCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAGTTTCCCAGTCTGCCCTTCCCATCGG
AAGGTGTTGTTTAATTTCCCAGTTTGCCATTCCCCGTCAGAAGGTGTTGTTTAAG
Done.