Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016269.1 Corchorus capsularis cultivar CVL-1 contig16290, 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: 57647
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:145 original size:26 final size:26
Alignment explanation
Indices: 116--183 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 26
106 TACTTAATTT
116 ATTAGTTTATGTTTAATTAGTATCTA
1 ATTAGTTTATGTTTAATTAGTATCTA
*
142 ATTAGTTTAT-TATTAATTAGTATTTA
1 ATTAGTTTATGT-TTAATTAGTATCTA
*
168 ATTAGTTTATGATTAA
1 ATTAGTTTATGTTTAA
184 AATGAAGGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 1 0.03
26 37 0.97
ACGTcount: A:0.34, C:0.01, G:0.10, T:0.54
Consensus pattern (26 bp):
ATTAGTTTATGTTTAATTAGTATCTA
Found at i:183 original size:15 final size:13
Alignment explanation
Indices: 86--177 Score: 59
Period size: 11 Copynumber: 7.1 Consensus size: 13
76 TATGATTAGT
*
86 TTTAATTAGTTAA
1 TTTAATTAGTTTA
* * *
99 TTAAAATTACTTAA
1 TT-TAATTAGTTTA
113 TTT-ATTAGTTTA
1 TTTAATTAGTTTA
125 TGTTTAATTAG--TA
1 --TTTAATTAGTTTA
*
138 TCTAATTAGTTTA
1 TTTAATTAGTTTA
151 TTATTAATTAG--TA
1 -T-TTAATTAGTTTA
164 TTTAATTAGTTTA
1 TTTAATTAGTTTA
177 T
1 T
178 GATTAAAATG
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
11 16 0.26
12 8 0.13
13 11 0.18
14 15 0.24
15 12 0.19
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.55
Consensus pattern (13 bp):
TTTAATTAGTTTA
Found at i:231 original size:24 final size:25
Alignment explanation
Indices: 192--251 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
182 AAAATGAAGG
*
192 AAAATGAA-TTTGAAG-ATTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
215 AAAATGAAGTTTGAAGAAGTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
* *
240 GAAATTAAGTTT
1 AAAATGAAGTTT
252 AGGGTTTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 8 0.25
24 7 0.22
25 17 0.53
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (25 bp):
AAAATGAAGTTTGAAGAAGTTGTTA
Found at i:1979 original size:29 final size:29
Alignment explanation
Indices: 1947--2023 Score: 145
Period size: 29 Copynumber: 2.7 Consensus size: 29
1937 AAAACAGTCC
*
1947 CAAGTGCACAACCCGCATTTGAATCAACA
1 CAAGTGCACAACCCGCACTTGAATCAACA
1976 CAAGTGCACAACCCGCACTTGAATCAACA
1 CAAGTGCACAACCCGCACTTGAATCAACA
2005 CAAGTGCACAACCCGCACT
1 CAAGTGCACAACCCGCACT
2024 CGATACACCA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.36, C:0.35, G:0.14, T:0.14
Consensus pattern (29 bp):
CAAGTGCACAACCCGCACTTGAATCAACA
Found at i:11540 original size:13 final size:13
Alignment explanation
Indices: 11524--11550 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
11514 AGAACATAAG
11524 AAAAGAAAGCACT
1 AAAAGAAAGCACT
11537 AAAAGAAAGCACT
1 AAAAGAAAGCACT
11550 A
1 A
11551 GCTGCTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.15, G:0.15, T:0.07
Consensus pattern (13 bp):
AAAAGAAAGCACT
Found at i:13968 original size:114 final size:114
Alignment explanation
Indices: 13810--14767 Score: 1170
Period size: 114 Copynumber: 8.6 Consensus size: 114
13800 TTTTTATAAT
* * *
13810 TTTTAAGCTTCATTTTTAAGGCTTTTTTGCATTTCTCCGGAAAAAA-TAAA-AGTAGCAGCGTCT
1 TTTTAGGCTTCATTTTT-AGGTTTTTTTGCATTTCTCC-GAAAAAATTAAATA-TAGCGGCGTCT
* * * * *
13873 GAGAATCTCAGACACCACCATTTAGTGGTGTCTAGGGTCAAGACGCCGCTAC
63 GGGAACCTCAGACGCCACCATTTAGCGGCGTCTAGGGTCAAGACGCCGCTAC
13925 TTTTAGGCTTCATTTTTAGGTTTTTTTGCATTTCTCCGAAAAAATTAAATATAGCGGCGTCTGGG
1 TTTTAGGCTTCATTTTTAGGTTTTTTTGCATTTCTCCGAAAAAATTAAATATAGCGGCGTCTGGG
* ** ** ** *
13990 AACCTCAGACGCCACCATTTAGCGGTGTCTCTA-CTTTTAG--GCTTC-AT
66 AACCTCAGACGCCACCATTTAGCGGCG--TCTAGGGTCAAGACGCCGCTAC
* * * *
14037 TTTTAGG---------T-----TTTTTGCATTTCTCCGTAAAAATTAAATACAGCGGCATTTGGG
1 TTTTAGGCTTCATTTTTAGGTTTTTTTGCATTTCTCCGAAAAAATTAAATATAGCGGCGTCTGGG
** * * * *
14088 AACAACAAACGCCACCATTTAGGGGCGTTTAGTGTCAAGACGCCGCTAC
66 AACCTCAGACGCCACCATTTAGCGGCGTCTAGGGTCAAGACGCCGCTAC
* * *
14137 TTTTAGGCTTCAATTTTAGG-TTTTTTGCATTTCTCTGAAAAAATTAAATATAGCGGCGTCTAGG
1 TTTTAGGCTTCATTTTTAGGTTTTTTTGCATTTCTCCGAAAAAATTAAATATAGCGGCGTCTGGG
* * * *
14201 AACCTTAGACGCCACCATTTAGCGTCGTTTAGTGTCAAGACGCCGCTAC
66 AACCTCAGACGCCACCATTTAGCGGCGTCTAGGGTCAAGACGCCGCTAC
* **
14250 TTTTAGGCTTCAATTTTAGG-TTTTTTGCATTTCTCTTAAAAAATTAAATATAGCGGCGTCTGGG
1 TTTTAGGCTTCATTTTTAGGTTTTTTTGCATTTCTCCGAAAAAATTAAATATAGCGGCGTCTGGG
14314 AACCTCAGACGCCACCATTTAGCGGCGTCTAGGGTCAAGACGCCGCTAC
66 AACCTCAGACGCCACCATTTAGCGGCGTCTAGGGTCAAGACGCCGCTAC
** *
14363 TTTTAGGCTTCATTTTTAGGTTGATTTGCATTTCTCCGAAAAAATCAAATATAGCGGCGTCTGGG
1 TTTTAGGCTTCATTTTTAGGTTTTTTTGCATTTCTCCGAAAAAATTAAATATAGCGGCGTCTGGG
14428 AACCTCAGACGCCACCATTTAGCGGCGTCTAGGGTCAAGACGCCGCTAC
66 AACCTCAGACGCCACCATTTAGCGGCGTCTAGGGTCAAGACGCCGCTAC
* * ** *
14477 TTTTAGACTTCAATTTTAGGTTGATTTGCATTTCTCTGAAAAAATTAAATATAGCGGCGTCTGGG
1 TTTTAGGCTTCATTTTTAGGTTTTTTTGCATTTCTCCGAAAAAATTAAATATAGCGGCGTCTGGG
* * *
14542 AACCTCAGACACCACCATTTAGCGGCGTTTAGGGTCAAGATC-CCGTTAC
66 AACCTCAGACGCCACCATTTAGCGGCGTCTAGGGTCAAGA-CGCCGCTAC
** ** *
14591 TTTTAGGCTTCATTTTTAGGTTGATTTGTTTTTCTCCGAAAATATTAAATATAGCGGCGTCTGGG
1 TTTTAGGCTTCATTTTTAGGTTTTTTTGCATTTCTCCGAAAAAATTAAATATAGCGGCGTCTGGG
* *
14656 AACCTCAGACGCCACCATTTAACGGCGTCTAAGGTCAAGACGCCGCTAC
66 AACCTCAGACGCCACCATTTAGCGGCGTCTAGGGTCAAGACGCCGCTAC
** ** *
14705 TTTTAGGCTTCATTTTTAGGTTGATTTGTTTTTCTCCGAAAAAATTAAATATAGCGACGTCTG
1 TTTTAGGCTTCATTTTTAGGTTTTTTTGCATTTCTCCGAAAAAATTAAATATAGCGGCGTCTG
14768 AAATTCAATT
Statistics
Matches: 744, Mismatches: 75, Indels: 49
0.86 0.09 0.06
Matches are distributed among these distances:
96 3 0.00
97 3 0.00
98 61 0.08
99 3 0.00
100 8 0.01
103 1 0.00
109 1 0.00
112 8 0.01
113 217 0.29
114 414 0.56
115 21 0.03
116 4 0.01
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (114 bp):
TTTTAGGCTTCATTTTTAGGTTTTTTTGCATTTCTCCGAAAAAATTAAATATAGCGGCGTCTGGG
AACCTCAGACGCCACCATTTAGCGGCGTCTAGGGTCAAGACGCCGCTAC
Found at i:14100 original size:98 final size:99
Alignment explanation
Indices: 13921--14109 Score: 308
Period size: 98 Copynumber: 1.9 Consensus size: 99
13911 CAAGACGCCG
* *
13921 CTACTTTTAGGCTTCATTTTTAGGTTTTTTTGCATTTCTCCGAAAAAATTAAATATAGCGGCGTC
1 CTACTTTTAGGCTTCATTTTTAGGTTTTTTTGCATTTCTCCGAAAAAATTAAATACAGCGGCATC
** *
13986 TGGGAACCTCAGACGCCACCATTTAGCGGTGTCT
66 TGGGAACAACAAACGCCACCATTTAGCGGTGTCT
* *
14020 CTACTTTTAGGCTTCATTTTTAGG-TTTTTTGCATTTCTCCGTAAAAATTAAATACAGCGGCATT
1 CTACTTTTAGGCTTCATTTTTAGGTTTTTTTGCATTTCTCCGAAAAAATTAAATACAGCGGCATC
14084 TGGGAACAACAAACGCCACCATTTAG
66 TGGGAACAACAAACGCCACCATTTAG
14110 GGGCGTTTAG
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
98 59 0.71
99 24 0.29
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (99 bp):
CTACTTTTAGGCTTCATTTTTAGGTTTTTTTGCATTTCTCCGAAAAAATTAAATACAGCGGCATC
TGGGAACAACAAACGCCACCATTTAGCGGTGTCT
Found at i:16003 original size:42 final size:43
Alignment explanation
Indices: 15921--16019 Score: 125
Period size: 42 Copynumber: 2.3 Consensus size: 43
15911 TTAGAGAGTT
*
15921 ATCAAATTTCATA-AACAAGATTACCAAAATTAATATGGGGTG
1 ATCAAATTTCATACAACAAGATTACCAAAACTAATATGGGGTG
* *
15963 ATCAAATTT-ATACAA-AAG-TTGCCAAAACTAATATTGGGGGTT
1 ATCAAATTTCATACAACAAGATTACCAAAACTAATA-T-GGGGTG
16005 ATCAAATTTCATACA
1 ATCAAATTTCATACA
16020 CAATGTTATG
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
40 13 0.26
41 7 0.14
42 25 0.50
43 5 0.10
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (43 bp):
ATCAAATTTCATACAACAAGATTACCAAAACTAATATGGGGTG
Found at i:22160 original size:33 final size:32
Alignment explanation
Indices: 22090--22230 Score: 131
Period size: 33 Copynumber: 4.3 Consensus size: 32
22080 AAAGAATCAT
* * **
22090 GTGGCCAGTTGTGGCCGGGCATGGCCGA-GTCAT
1 GTGGCC-GGTGTGGCCGGGCATCGCC-ATGTCGC
* *
22123 GTGGCCTGTTGTGGCCGGGCATGGCCATGTCGC
1 GTGGCC-GGTGTGGCCGGGCATCGCCATGTCGC
*
22156 GTGGCCGGTGATGGCCGGGCATCTCCATGTCGC
1 GTGGCCGGTG-TGGCCGGGCATCGCCATGTCGC
* * * *
22189 ATGGCCGGTGTTGCGCGGGCATCTCCAAGTCGC
1 GTGGCCGGTGTGGC-CGGGCATCGCCATGTCGC
22222 GTGGCCGGT
1 GTGGCCGGT
22231 CACAAGTGCT
Statistics
Matches: 95, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
32 7 0.07
33 88 0.93
ACGTcount: A:0.09, C:0.28, G:0.41, T:0.22
Consensus pattern (32 bp):
GTGGCCGGTGTGGCCGGGCATCGCCATGTCGC
Found at i:29141 original size:18 final size:17
Alignment explanation
Indices: 29109--29143 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
29099 AAAGACAATA
*
29109 AAAATTAAAGTGATAGT
1 AAAATTAAACTGATAGT
29126 AAAATTAAACTAGATAGT
1 AAAATTAAACT-GATAGT
29144 TTATTAATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.54, C:0.03, G:0.14, T:0.29
Consensus pattern (17 bp):
AAAATTAAACTGATAGT
Found at i:36113 original size:33 final size:33
Alignment explanation
Indices: 36073--36169 Score: 124
Period size: 33 Copynumber: 2.9 Consensus size: 33
36063 AGCACTTGTG
* *
36073 ACCGGCCACGCGACTTGGAGATGCCC-GCGCAAC
1 ACCGGCCAAGCGACATGGAGATGCCCGGC-CAAC
* *
36106 ACCGGCCATGCGACATGGAGATGCCCGGCCATC
1 ACCGGCCAAGCGACATGGAGATGCCCGGCCAAC
**
36139 ACCGGCCAAGCGACATGGCCATGCCCGGCCA
1 ACCGGCCAAGCGACATGGAGATGCCCGGCCA
36170 CAACAGGACA
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
33 55 0.96
34 2 0.04
ACGTcount: A:0.22, C:0.39, G:0.30, T:0.09
Consensus pattern (33 bp):
ACCGGCCAAGCGACATGGAGATGCCCGGCCAAC
Found at i:36192 original size:33 final size:33
Alignment explanation
Indices: 36155--36217 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
36145 CAAGCGACAT
36155 GGCCATGCCCGGCCACAACAGGACACATGACTC
1 GGCCATGCCCGGCCACAACAGGACACATGACTC
* *
36188 GGCCATGCCCGGCCACAACCGGCCACATGA
1 GGCCATGCCCGGCCACAACAGGACACATGA
36218 TTCTTTAGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.25, C:0.41, G:0.25, T:0.08
Consensus pattern (33 bp):
GGCCATGCCCGGCCACAACAGGACACATGACTC
Found at i:38879 original size:13 final size:14
Alignment explanation
Indices: 38857--38892 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 14
38847 TTAATACTTG
38857 TTTTT-CTTTTT-C
1 TTTTTACTTTTTCC
38869 TTTTTA-TTTTTCC
1 TTTTTACTTTTTCC
38882 TTTTTACTTTT
1 TTTTTACTTTT
38893 ACACTTGATC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 10 0.48
13 7 0.33
14 4 0.19
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTACTTTTTCC
Found at i:54218 original size:20 final size:20
Alignment explanation
Indices: 54193--54245 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
54183 TACTGTTCTC
54193 TATGAAATTTGGACTAACTA
1 TATGAAATTTGGACTAACTA
** *
54213 TATGAAATTTGGACTTTCTG
1 TATGAAATTTGGACTAACTA
54233 TATGAAATTTGGA
1 TATGAAATTTGGA
54246 AATTATGGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.34, C:0.08, G:0.19, T:0.40
Consensus pattern (20 bp):
TATGAAATTTGGACTAACTA
Found at i:55974 original size:23 final size:22
Alignment explanation
Indices: 55948--56000 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
55938 TCACAAAGCC
*
55948 TAATGCATAAATAAAAGCCCAAA
1 TAATGCATAAAGAAAAGCCC-AA
** *
55971 TAATGGGTAAAGCAAAGCCCAA
1 TAATGCATAAAGAAAAGCCCAA
55993 -AATGCATA
1 TAATGCATA
56001 TAAAGTTTAA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 6 0.25
22 2 0.08
23 16 0.67
ACGTcount: A:0.51, C:0.17, G:0.15, T:0.17
Consensus pattern (22 bp):
TAATGCATAAAGAAAAGCCCAA
Done.