Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007932.1 Corchorus capsularis cultivar CVL-1 contig07953, 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: 49225
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:1270 original size:21 final size:21
Alignment explanation
Indices: 1241--1282 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1231 TCGCTCGGTC
*
1241 TCTACAAACCAATC-ATCACA
1 TCTACAAACCAAACAATCACA
1261 TCTACCAAACCAAACAATCACA
1 TCTA-CAAACCAAACAATCACA
1283 CACACCCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 9 0.47
22 6 0.32
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.17
Consensus pattern (21 bp):
TCTACAAACCAAACAATCACA
Found at i:5783 original size:18 final size:19
Alignment explanation
Indices: 5760--5797 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
5750 GAAATAGGAT
5760 TTCAAATCCAACAGA-AGA
1 TTCAAATCCAACAGATAGA
*
5778 TTCAAATTCAACAGATAGA
1 TTCAAATCCAACAGATAGA
5797 T
1 T
5798 ATGATAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.47, C:0.18, G:0.11, T:0.24
Consensus pattern (19 bp):
TTCAAATCCAACAGATAGA
Found at i:13506 original size:21 final size:21
Alignment explanation
Indices: 13477--13639 Score: 114
Period size: 21 Copynumber: 7.8 Consensus size: 21
13467 TCCTTGAACT
*
13477 TCAGCCTCTTCCATATCAAAA
1 TCAGCCTCTTCCATGTCAAAA
* * *
13498 TCAGTCTCTTCAATGTCATAA
1 TCAGCCTCTTCCATGTCAAAA
* *
13519 TTAGCCTCTTCCATGTCAAAG
1 TCAGCCTCTTCCATGTCAAAA
* * * *
13540 CCAGCCT-TGACAAAGTCAAAA
1 TCAGCCTCT-TCCATGTCAAAA
* * *
13561 TAAGCCTCTT-TAGCGTCAAAA
1 TCAGCCTCTTCCA-TGTCAAAA
* * *
13582 TCAGCATCTTTCATGTCGAAA
1 TCAGCCTCTTCCATGTCAAAA
* *
13603 TCAGCCTCTTCCATGTTAGAA
1 TCAGCCTCTTCCATGTCAAAA
* *
13624 TTAGACTCTTCCATGT
1 TCAGCCTCTTCCATGT
13640 TTGAACCATG
Statistics
Matches: 106, Mismatches: 32, Indels: 8
0.73 0.22 0.05
Matches are distributed among these distances:
20 2 0.02
21 102 0.96
22 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.31
Consensus pattern (21 bp):
TCAGCCTCTTCCATGTCAAAA
Found at i:14179 original size:45 final size:45
Alignment explanation
Indices: 14124--14228 Score: 124
Period size: 45 Copynumber: 2.3 Consensus size: 45
14114 GGGTCGACAT
* *
14124 TATTCAGATCGAGAAATTG-GTTAT-ATTAACCTTCTTCGACACCAA
1 TATTAAGATCGAGAAATTGAG-TATGA-AAACCTTCTTCGACACCAA
* * *
14169 TATTAAGATCGGGAATTTGAGTATGAAAACCTTCTTCGACAGCAA
1 TATTAAGATCGAGAAATTGAGTATGAAAACCTTCTTCGACACCAA
*
14214 TATTAAGATCTAGAA
1 TATTAAGATCGAGAA
14229 GCTCTACTGG
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
45 49 0.96
46 2 0.04
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (45 bp):
TATTAAGATCGAGAAATTGAGTATGAAAACCTTCTTCGACACCAA
Found at i:16129 original size:27 final size:27
Alignment explanation
Indices: 16092--16145 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
16082 GGTTTACATG
16092 TGTTTTGTTCATGAGAAAGAGAGAAGA
1 TGTTTTGTTCATGAGAAAGAGAGAAGA
*
16119 TGTTTTGTTCATGAGAAGGAGAGAAGA
1 TGTTTTGTTCATGAGAAAGAGAGAAGA
16146 GAGAAGAGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.35, C:0.04, G:0.31, T:0.30
Consensus pattern (27 bp):
TGTTTTGTTCATGAGAAAGAGAGAAGA
Found at i:16149 original size:7 final size:7
Alignment explanation
Indices: 16131--16163 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
16121 TTTTGTTCAT
16131 GAGAAGGA
1 GAGAA-GA
16139 GAGAAGA
1 GAGAAGA
16146 GAGAAGA
1 GAGAAGA
16153 GAGAAG-
1 GAGAAGA
16159 GAGAA
1 GAGAA
16164 TGAATTCTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 5 0.20
7 15 0.60
8 5 0.20
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (7 bp):
GAGAAGA
Found at i:16523 original size:16 final size:16
Alignment explanation
Indices: 16499--16529 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16489 TCCACCGACC
*
16499 GATGTCGGTTTCGGTG
1 GATGGCGGTTTCGGTG
16515 GATGGCGGTTTCGGT
1 GATGGCGGTTTCGGT
16530 CAGTTGGTCG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.06, C:0.13, G:0.45, T:0.35
Consensus pattern (16 bp):
GATGGCGGTTTCGGTG
Found at i:35725 original size:187 final size:187
Alignment explanation
Indices: 35405--35781 Score: 682
Period size: 187 Copynumber: 2.0 Consensus size: 187
35395 CTTAGAACCT
* * *
35405 AAAATTGTCAAATTTCCAATAGTATGTAAATCAACTAGCTCATTAGTGGATGTAATTCCCACTTG
1 AAAACTGTCAAATTTCCAATAGCATGTAAATCAACTAGCTCATTAATGGATGTAATTCCCACTTG
*
35470 GTCGGCCCAATCTAGGGAGTTGTTGGATCAAGCCGAACTACCATTAGCTTCATTAGTAAGACCAA
66 GTCGGCCCAATCTAGGGAGTTGTTGGATCAAACCGAACTACCATTAGCTTCATTAGTAAGACCAA
35535 GGCCACCAAGACCAATCCCCTTACTTTCAGCCACATGCTCAATGAAATCTCCCATAC
131 GGCCACCAAGACCAATCCCCTTACTTTCAGCCACATGCTCAATGAAATCTCCCATAC
*
35592 AAAACTGTCAAATTTCCAATAGCATGTAAATCAACTGGCTCATTAATGGATGTAATTCCCACTTG
1 AAAACTGTCAAATTTCCAATAGCATGTAAATCAACTAGCTCATTAATGGATGTAATTCCCACTTG
* *
35657 GTCGGCCCAATCTAGGGATTTGTTGGATCAAACCTAACTACCATTAGCTTCATTAGTAAGACCAA
66 GTCGGCCCAATCTAGGGAGTTGTTGGATCAAACCGAACTACCATTAGCTTCATTAGTAAGACCAA
*
35722 GGCCACCAAGACCAATCCCCTTACTTTCAGCCACATGCTTAATGAAATCTCCCATAC
131 GGCCACCAAGACCAATCCCCTTACTTTCAGCCACATGCTCAATGAAATCTCCCATAC
35779 AAA
1 AAA
35782 TTATTTTAGT
Statistics
Matches: 182, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
187 182 1.00
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (187 bp):
AAAACTGTCAAATTTCCAATAGCATGTAAATCAACTAGCTCATTAATGGATGTAATTCCCACTTG
GTCGGCCCAATCTAGGGAGTTGTTGGATCAAACCGAACTACCATTAGCTTCATTAGTAAGACCAA
GGCCACCAAGACCAATCCCCTTACTTTCAGCCACATGCTCAATGAAATCTCCCATAC
Found at i:36900 original size:35 final size:33
Alignment explanation
Indices: 36858--36979 Score: 144
Period size: 31 Copynumber: 3.7 Consensus size: 33
36848 TTCTTACTAA
* *
36858 ACTTAATTACCCTGAAATAAGTCGATCAATGACTT
1 ACTTAATTACCCTGAATTAAGT--ATCAATTACTT
*
36893 ACTTAATTACCCTGAATTAAGT-T-ACTTA-TT
1 ACTTAATTACCCTGAATTAAGTATCAATTACTT
36923 GACTTAATTACCCTGAATTAAGT-TACATATTACTT
1 -ACTTAATTACCCTGAATTAAGTAT-CA-ATTACTT
36958 ACTTAATTACCCTGAATTAAGT
1 ACTTAATTACCCTGAATTAAGT
36980 TACTGACTTA
Statistics
Matches: 78, Mismatches: 4, Indels: 11
0.84 0.04 0.12
Matches are distributed among these distances:
30 2 0.03
31 26 0.33
32 1 0.01
33 1 0.01
34 25 0.32
35 23 0.29
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.38
Consensus pattern (33 bp):
ACTTAATTACCCTGAATTAAGTATCAATTACTT
Found at i:36931 original size:31 final size:31
Alignment explanation
Indices: 36889--36991 Score: 154
Period size: 31 Copynumber: 3.2 Consensus size: 31
36879 TCGATCAATG
36889 ACTTACTTAATTACCCTGAATTAAGTTACTT
1 ACTTACTTAATTACCCTGAATTAAGTTACTT
36920 A-TTGACTTAATTACCCTGAATTAAGTTACATATT
1 ACTT-ACTTAATTACCCTGAATTAAGTTAC---TT
*
36954 ACTTACTTAATTACCCTGAATTAAGTTACTG
1 ACTTACTTAATTACCCTGAATTAAGTTACTT
36985 ACTTACT
1 ACTTACT
36992 GTCTTACTAA
Statistics
Matches: 66, Mismatches: 1, Indels: 10
0.86 0.01 0.13
Matches are distributed among these distances:
30 2 0.03
31 34 0.52
34 28 0.42
35 2 0.03
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (31 bp):
ACTTACTTAATTACCCTGAATTAAGTTACTT
Found at i:36974 original size:65 final size:66
Alignment explanation
Indices: 36858--36983 Score: 202
Period size: 65 Copynumber: 1.9 Consensus size: 66
36848 TTCTTACTAA
36858 ACTTAATTACCCTGAAATAAGTCGATCAATGACTTACTTAATTACCCTGAATTAAGTTACTTATT
1 ACTTAATTACCCTGAAATAAGTCGATCAATGACTTACTTAATTACCCTGAATTAAGTTACTTATT
36923 G
66 G
* * *
36924 ACTTAATTACCCTGAATTAAGT-TA-CATATTACTTACTTAATTACCCTGAATTAAGTTACT
1 ACTTAATTACCCTGAAATAAGTCGATCA-ATGACTTACTTAATTACCCTGAATTAAGTTACT
36984 GACTTACTGT
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
64 2 0.04
65 33 0.59
66 21 0.38
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.38
Consensus pattern (66 bp):
ACTTAATTACCCTGAAATAAGTCGATCAATGACTTACTTAATTACCCTGAATTAAGTTACTTATT
G
Found at i:37077 original size:184 final size:182
Alignment explanation
Indices: 36858--37251 Score: 666
Period size: 184 Copynumber: 2.2 Consensus size: 182
36848 TTCTTACTAA
* * * *
36858 ACTTAATTACCCTGAAATAAGTCGA-TCAATGACTTACTTAATTACCCTGAATTAAGTTACTTAT
1 ACTTAATTACCCTGAATTAAG-CTACTTAATGACTTAATTAATTACCCTGAATTAAGTTACTTAT
36922 TGACTTAATTACCCTGAATTAAGTTACATATTACTTACTTAATTACCCTGAATTAAGTTACTGAC
65 TGACTTAATTACCCTGAATTAAGTTACATATTACTTACTTAATTACCCTGAATTAAGTTACTGAC
*
36987 TTACTGTCTTACTAACTTACTTAATTACCCTGAATTAAAGTTGATT-ACTGACTTT
130 TTACTGTCTTACTAACTTACTTAATTACCCTGAATT-AAGTT-ATTCACTGAC-CT
*
37042 ACTTAATTACCCTGAATTAAGCTACTTACTGACTTAATTAATTACCCTGAATTAAGTTACTTATT
1 ACTTAATTACCCTGAATTAAGCTACTTAATGACTTAATTAATTACCCTGAATTAAGTTACTTATT
37107 GACTTAATTACCCTGAATTAAGTTACATATTACTTACTTAATTACCCTGAATTAAGTTACTGACT
66 GACTTAATTACCCTGAATTAAGTTACATATTACTTACTTAATTACCCTGAATTAAGTTACTGACT
37172 TACTGTCTTACTAACTTACTTAATTACCCTGAATTAAGTTATTCACTGACCT
131 TACTGTCTTACTAACTTACTTAATTACCCTGAATTAAGTTATTCACTGACCT
* *
37224 ATTTAATTACCCTGAATTAAGTTACTTA
1 ACTTAATTACCCTGAATTAAGCTACTTA
37252 TTACTGATTC
Statistics
Matches: 200, Mismatches: 8, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
182 30 0.15
183 13 0.06
184 157 0.79
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.40
Consensus pattern (182 bp):
ACTTAATTACCCTGAATTAAGCTACTTAATGACTTAATTAATTACCCTGAATTAAGTTACTTATT
GACTTAATTACCCTGAATTAAGTTACATATTACTTACTTAATTACCCTGAATTAAGTTACTGACT
TACTGTCTTACTAACTTACTTAATTACCCTGAATTAAGTTATTCACTGACCT
Found at i:37090 original size:35 final size:35
Alignment explanation
Indices: 36994--37251 Score: 242
Period size: 35 Copynumber: 7.1 Consensus size: 35
36984 GACTTACTGT
*
36994 CTTACTAACTTACTTAATTACCCTGAATTAAAGTTGA
1 CTTACTGACTTACTTAATTACCCTGAATT-AAGTT-A
*
37031 -TTACTGACTTTACTTAATTACCCTGAATTAAGCTA
1 CTTACTGAC-TTACTTAATTACCCTGAATTAAGTTA
*
37066 CTTACTGACTTAATTAATTACCCTGAATTAAGTTA
1 CTTACTGACTTACTTAATTACCCTGAATTAAGTTA
*
37101 CTTA-T---TGACTTAATTACCCTGAATTAAGTTA
1 CTTACTGACTTACTTAATTACCCTGAATTAAGTTA
* *
37132 CATA-TTACTTACTTAATTACCCTGAATTAAGTTACTGA
1 CTTACTGACTTACTTAATTACCCTGAATTAAG-T--T-A
*
37170 CTTACTGTCTTACTAACTTACTTAATTACCCTGAATTAAGTTA
1 CTTACTG----ACTTAC-T---TAATTACCCTGAATTAAGTTA
* *
37213 -TTCACTGACCTATTTAATTACCCTGAATTAAGTTA
1 CTT-ACTGACTTACTTAATTACCCTGAATTAAGTTA
37248 CTTA
1 CTTA
37252 TTACTGATTC
Statistics
Matches: 187, Mismatches: 14, Indels: 42
0.77 0.06 0.17
Matches are distributed among these distances:
31 28 0.15
34 23 0.12
35 52 0.28
36 21 0.11
37 21 0.11
38 5 0.03
39 4 0.02
42 2 0.01
43 10 0.05
44 2 0.01
46 1 0.01
47 18 0.10
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.40
Consensus pattern (35 bp):
CTTACTGACTTACTTAATTACCCTGAATTAAGTTA
Found at i:37096 original size:14 final size:15
Alignment explanation
Indices: 37077--37132 Score: 53
Period size: 14 Copynumber: 3.7 Consensus size: 15
37067 TTACTGACTT
37077 AATTAA-TTACCCTG
1 AATTAAGTTACCCTG
**
37091 AATTAAGTTACTTATTG
1 AATTAAGTTAC--CCTG
*
37108 ACTTAA-TTACCCTG
1 AATTAAGTTACCCTG
37122 AATTAAGTTAC
1 AATTAAGTTAC
37133 ATATTACTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
14 13 0.41
15 8 0.25
16 4 0.12
17 7 0.22
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (15 bp):
AATTAAGTTACCCTG
Found at i:37194 original size:81 final size:80
Alignment explanation
Indices: 37108--37257 Score: 221
Period size: 81 Copynumber: 1.9 Consensus size: 80
37098 TTACTTATTG
* *
37108 ACTTAATTACCCTGAATTAAGTTA-CATATTACTTACTTAATTACCCTGAATTAAGTTACTGACT
1 ACTTAATTACCCTGAATTAAGTTATCA-ATGACCTACTTAATTACCCTGAATTAAGTTACTGA-T
37172 TACTGTCTTACTAACTT
64 TACTGTCTTACTAACTT
* * *
37189 ACTTAATTACCCTGAATTAAGTTATTCACTGACCTATTTAATTACCCTGAATTAAGTTACTTATT
1 ACTTAATTACCCTGAATTAAGTTA-TCAATGACCTACTTAATTACCCTGAATTAAGTTACTGATT
37254 ACTG
65 ACTG
37258 ATTCACCTTT
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
81 30 0.48
82 30 0.48
83 2 0.03
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.41
Consensus pattern (80 bp):
ACTTAATTACCCTGAATTAAGTTATCAATGACCTACTTAATTACCCTGAATTAAGTTACTGATTA
CTGTCTTACTAACTT
Done.