Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009787.1 Corchorus capsularis cultivar CVL-1 contig09808, 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: 40007
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:95 original size:33 final size:32
Alignment explanation
Indices: 19--148 Score: 134
Period size: 33 Copynumber: 3.9 Consensus size: 32
9 AAATTAGCCG
* * *
19 AGCCGCCCCATTGGGGCGGCCTACCCTGGCGA
1 AGCCGCCCCAGTGGGGCGGCCTACCATGGTGA
** * *
51 AGCCGTTCCAGTGGGGCGGCCTATTCATAGTGA
1 AGCCGCCCCAGTGGGGCGGCCTA-CCATGGTGA
*
84 AGCCGCCCCAGTGGGGCGGCCTGCCCAATGGTGA
1 AGCCGCCCCAGTGGGGCGGCCT-ACC-ATGGTGA
* *
118 AGCCGCCCAAGTGGGGCGGCCTGCCCATGGT
1 AGCCGCCCCAGTGGGGCGGCCT-ACCATGGT
149 CATCAATCCT
Statistics
Matches: 82, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
32 20 0.24
33 31 0.38
34 31 0.38
ACGTcount: A:0.15, C:0.34, G:0.36, T:0.15
Consensus pattern (32 bp):
AGCCGCCCCAGTGGGGCGGCCTACCATGGTGA
Found at i:123 original size:34 final size:33
Alignment explanation
Indices: 19--148 Score: 154
Period size: 34 Copynumber: 3.9 Consensus size: 33
9 AAATTAGCCG
* *
19 AGCCGCCCCATTGGGGCGGCCTACCC-TGGCGA
1 AGCCGCCCCAGTGGGGCGGCCTACCCATGGTGA
** ** *
51 AGCCGTTCCAGTGGGGCGGCCTATTCATAGTGA
1 AGCCGCCCCAGTGGGGCGGCCTACCCATGGTGA
*
84 AGCCGCCCCAGTGGGGCGGCCTGCCCAATGGTGA
1 AGCCGCCCCAGTGGGGCGGCCTACCC-ATGGTGA
* *
118 AGCCGCCCAAGTGGGGCGGCCTGCCCATGGT
1 AGCCGCCCCAGTGGGGCGGCCTACCCATGGT
149 CATCAATCCT
Statistics
Matches: 82, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
32 21 0.26
33 30 0.37
34 31 0.38
ACGTcount: A:0.15, C:0.34, G:0.36, T:0.15
Consensus pattern (33 bp):
AGCCGCCCCAGTGGGGCGGCCTACCCATGGTGA
Found at i:289 original size:18 final size:18
Alignment explanation
Indices: 262--300 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
252 GTTAACACTA
*
262 TTCTATGTTCGTGATAGT
1 TTCTACGTTCGTGATAGT
280 TTCTACGTTCGTGATAGT
1 TTCTACGTTCGTGATAGT
298 TTC
1 TTC
301 AAGATTAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.21, T:0.49
Consensus pattern (18 bp):
TTCTACGTTCGTGATAGT
Found at i:1923 original size:45 final size:45
Alignment explanation
Indices: 1867--1957 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
1857 GATTACTTCT
*
1867 CCAACTCATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCAC
1 CCAACTCATCATTAATCCGGGGTAGGGATCTTTTACTAATTCCAC
* *
1912 CCAACTTATCATTAATTCGGGGTAGGGATCTTTTACTAATTCCAC
1 CCAACTCATCATTAATCCGGGGTAGGGATCTTTTACTAATTCCAC
1957 C
1 C
1958 ACTCTATTCA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.33
Consensus pattern (45 bp):
CCAACTCATCATTAATCCGGGGTAGGGATCTTTTACTAATTCCAC
Found at i:2184 original size:325 final size:324
Alignment explanation
Indices: 1614--2404 Score: 1271
Period size: 325 Copynumber: 2.4 Consensus size: 324
1604 CCTTGATGGA
* * *
1614 GATCATTTATTAATTCCACTACTCTATTCAAATCCATTGAGAAATGATCAAAAAGATTACTTATT
1 GATCTTTTACTAATTCCACTACTCTATTCAAATCCATTGAGAAATGACCAAAAAGATTACTTATT
* *
1679 TAATCCCCTAAAGAATCAAAAGTTAGGACATTTAAATAATCTGCCAAATAGGAAAAGACGAAAAA
66 TAATCCCCTAAAGAATCAAAAGTTAGGACATTTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAA
*
1744 AATAAGTTCTCTAACTCCAAAAGCAAGTCTTGTTAGGGATCTTTTAGTAATTCCACTACTCTATG
131 AATAAGTTCTCTAACTCCAAAAGCAAGCCTTGTTAGGGATCTTTTAGTAATTCCACTACTCTATG
* *
1809 AAAGTTTTGGACATTTAAGTAATCTGCCAAGTAGGTAAAGACGAAAAAGATTACTTCTCCAACTC
196 AAAGTTTAGAACATTTAAGTAATCTGCCAAGTAGGTAAAGACGAAAAAGATTACTTCTCCAACTC
*
1874 ATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCACCCAACTTATCATTAATTCGGGGTAGG
261 ATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCACCCAACTTATCATTAATTCGGGGAAGG
* *
1938 GATCTTTTACTAATTCCACCACTCTATTCAAATCCATTGAAAAATGACCAAAAAGATTACTTATT
1 GATCTTTTACTAATTCCACTACTCTATTCAAATCCATTGAGAAATGACCAAAAAGATTACTTATT
* * * * *
2003 TAATCCCCTCAAGAATAAAAAATTAGGACATTTAAGTAATCTGCCAAGCAGGAAAAGACAAAAAA
66 TAATCCCCTAAAGAATCAAAAGTTAGGACATTTAAGTAATCTGCCAAGTAGGAAAAGAC-GAAAA
2068 AAATAAGTTCTCTAACTCCAAAAGCAAGCCTTGTTAGGGATCTTTTAGTAATTCCACTACTCTAT
130 AAATAAGTTCTCTAACTCCAAAAGCAAGCCTTGTTAGGGATCTTTTAGTAATTCCACTACTCTAT
* * *
2133 TAAAGTTTAGAACATTTAAGTAATCTGCCAGGTAGGTAAAGACGAAAAAGATTACTTCTCCAGCT
195 GAAAGTTTAGAACATTTAAGTAATCTGCCAAGTAGGTAAAGACGAAAAAGATTACTTCTCCAACT
2198 CATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCACCCAACTTATCATTAATTCGGGGAAGG
260 CATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCACCCAACTTATCATTAATTCGGGGAAGG
* * * *
2263 GATCTTTTAGTAATTCCACTACTCTATT-AAAGTCAAATGAGAAATGACCAAAAAG-TCTAGTTA
1 GATCTTTTACTAATTCCACTACTCTATTCAAA-TCCATTGAGAAATGACCAAAAAGAT-TACTTA
* ** * * *
2326 TTTAATCACCTTGAGAATCAAAAGTTAGGGCATTTAAGTAATCGGCCAAGTGGGAAAAGACGAAA
64 TTTAATCCCCTAAAGAATCAAAAGTTAGGACATTTAAGTAATCTGCCAAGTAGGAAAAGACGAAA
*
2391 AAAATTAGTTCTCT
129 AAAATAAGTTCTCT
2405 CGCTCCTCAT
Statistics
Matches: 428, Mismatches: 36, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
324 133 0.31
325 295 0.69
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.30
Consensus pattern (324 bp):
GATCTTTTACTAATTCCACTACTCTATTCAAATCCATTGAGAAATGACCAAAAAGATTACTTATT
TAATCCCCTAAAGAATCAAAAGTTAGGACATTTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAA
AATAAGTTCTCTAACTCCAAAAGCAAGCCTTGTTAGGGATCTTTTAGTAATTCCACTACTCTATG
AAAGTTTAGAACATTTAAGTAATCTGCCAAGTAGGTAAAGACGAAAAAGATTACTTCTCCAACTC
ATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCACCCAACTTATCATTAATTCGGGGAAGG
Found at i:2590 original size:149 final size:149
Alignment explanation
Indices: 2320--2621 Score: 595
Period size: 149 Copynumber: 2.0 Consensus size: 149
2310 CCAAAAAGTC
*
2320 TAGTTATTTAATCACCTTGAGAATCAAAAGTTAGGGCATTTAAGTAATCGGCCAAGTGGGAAAAG
1 TAGTTATTTAATCACCTTAAGAATCAAAAGTTAGGGCATTTAAGTAATCGGCCAAGTGGGAAAAG
2385 ACGAAAAAAATTAGTTCTCTCGCTCCTCATTAATCTGGGGTAAGGATCTTTTAGTAATTTCCATA
66 ACGAAAAAAATTAGTTCTCTCGCTCCTCATTAATCTGGGGTAAGGATCTTTTAGTAATTTCCATA
2450 TGTTTATTCAAATAATATG
131 TGTTTATTCAAATAATATG
2469 TAGTTATTTAATCACCTTAAGAATCAAAAGTTAGGGCATTTAAGTAATCGGCCAAGTGGGAAAAG
1 TAGTTATTTAATCACCTTAAGAATCAAAAGTTAGGGCATTTAAGTAATCGGCCAAGTGGGAAAAG
2534 ACGAAAAAAATTAGTTCTCTCGCTCCTCATTAATCTGGGGTAAGGATCTTTTAGTAATTTCCATA
66 ACGAAAAAAATTAGTTCTCTCGCTCCTCATTAATCTGGGGTAAGGATCTTTTAGTAATTTCCATA
2599 TGTTTATTCAAATAATATG
131 TGTTTATTCAAATAATATG
2618 TAGT
1 TAGT
2622 ATATATATGG
Statistics
Matches: 152, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (149 bp):
TAGTTATTTAATCACCTTAAGAATCAAAAGTTAGGGCATTTAAGTAATCGGCCAAGTGGGAAAAG
ACGAAAAAAATTAGTTCTCTCGCTCCTCATTAATCTGGGGTAAGGATCTTTTAGTAATTTCCATA
TGTTTATTCAAATAATATG
Found at i:2977 original size:22 final size:22
Alignment explanation
Indices: 2949--3076 Score: 100
Period size: 22 Copynumber: 5.9 Consensus size: 22
2939 GTTACCACAC
2949 TATGAAATTTTGATAACCTCCA
1 TATGAAATTTTGATAACCTCCA
* * *
2971 TATGAAATTTCGATATCC-ACA
1 TATGAAATTTTGATAACCTCCA
* * **
2992 TAATGAAATTTTAATAACATTGA
1 T-ATGAAATTTTGATAACCTCCA
* *
3015 TATGAAATTTTGGT-A-CTACAA
1 TATGAAATTTTGATAACCT-CCA
* ** *
3036 TAAGAAATTTTGATAATTTCCT
1 TATGAAATTTTGATAACCTCCA
3058 TATGAAATTTTGATAACCT
1 TATGAAATTTTGATAACCT
3077 TATAAAGACA
Statistics
Matches: 79, Mismatches: 22, Indels: 10
0.71 0.20 0.09
Matches are distributed among these distances:
20 1 0.01
21 17 0.22
22 58 0.73
23 3 0.04
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCA
Found at i:3009 original size:44 final size:44
Alignment explanation
Indices: 2941--3072 Score: 135
Period size: 44 Copynumber: 3.0 Consensus size: 44
2931 AAAGTTTAGT
* * *
2941 TACCACACT-ATGAAATTTTGATAACCTCCATATGAAATTTCGA
1 TACCACAATAATGAAATTTTGATAACATCCATATGAAATTTTGA
* ** *
2984 TATCCAC-ATAATGAAATTTTAATAACATTGATATGAAATTTTGG
1 TA-CCACAATAATGAAATTTTGATAACATCCATATGAAATTTTGA
* ** *
3028 TACTACAATAA-GAAATTTTGATAATTTCCTTATGAAATTTTGA
1 TACCACAATAATGAAATTTTGATAACATCCATATGAAATTTTGA
3071 TA
1 TA
3073 ACCTTATAAA
Statistics
Matches: 71, Mismatches: 15, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
43 33 0.46
44 38 0.54
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (44 bp):
TACCACAATAATGAAATTTTGATAACATCCATATGAAATTTTGA
Found at i:4775 original size:15 final size:15
Alignment explanation
Indices: 4755--4786 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4745 GTGTTTATCA
4755 TTCTTCATCCCCTTT
1 TTCTTCATCCCCTTT
*
4770 TTCTTCATCTCCTTT
1 TTCTTCATCCCCTTT
4785 TT
1 TT
4787 TTTTCTTCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.34, G:0.00, T:0.59
Consensus pattern (15 bp):
TTCTTCATCCCCTTT
Found at i:10331 original size:18 final size:18
Alignment explanation
Indices: 10308--10346 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
10298 TAATACTAAC
*
10308 ATACTAACAAAAACCATA
1 ATACTAACAAAAAACATA
10326 ATACTAACAAAAAACATA
1 ATACTAACAAAAAACATA
10344 ATA
1 ATA
10347 AGGAGAAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.64, C:0.18, G:0.00, T:0.18
Consensus pattern (18 bp):
ATACTAACAAAAAACATA
Found at i:17604 original size:18 final size:18
Alignment explanation
Indices: 17578--17636 Score: 100
Period size: 18 Copynumber: 3.3 Consensus size: 18
17568 CGCATGAGGC
* *
17578 GCCAACCGGCCACAACCG
1 GCCATCCGGGCACAACCG
17596 GCCATCCGGGCACAACCG
1 GCCATCCGGGCACAACCG
17614 GCCATCCGGGCACAACCG
1 GCCATCCGGGCACAACCG
17632 GCCAT
1 GCCAT
17637 TTGATCCTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.24, C:0.46, G:0.25, T:0.05
Consensus pattern (18 bp):
GCCATCCGGGCACAACCG
Found at i:22250 original size:15 final size:15
Alignment explanation
Indices: 22230--22259 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
22220 CCCAGCCTGC
22230 CCCCTCTTTTAAATA
1 CCCCTCTTTTAAATA
22245 CCCCTCTTTTAAATA
1 CCCCTCTTTTAAATA
22260 TATATTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.00, T:0.40
Consensus pattern (15 bp):
CCCCTCTTTTAAATA
Found at i:23609 original size:12 final size:12
Alignment explanation
Indices: 23568--23611 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
23558 ACACACACAC
*
23568 ACATATGTATAT
1 ACATATATATAT
*
23580 ACATACATATAT
1 ACATATATATAT
23592 ACATATATATAT
1 ACATATATATAT
*
23604 ATATATAT
1 ACATATAT
23612 TTACACAAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (12 bp):
ACATATATATAT
Found at i:26118 original size:53 final size:53
Alignment explanation
Indices: 26019--26121 Score: 125
Period size: 53 Copynumber: 1.9 Consensus size: 53
26009 ATATATGATA
* * * * *
26019 GTATTTACAATAAGATAAAAGCATAGTTCAGACATAACTTATACTTAGTTCAT
1 GTATTTACAACAAAATAAAAGCATAGTTCAAACATAACTCACACTTAGTTCAT
* * * *
26072 GTATTTACAACAAAATAGATGCATAGTTGAAACATGACTCACACTTAGTT
1 GTATTTACAACAAAATAAAAGCATAGTTCAAACATAACTCACACTTAGTT
26122 TAGCCATCCA
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
53 41 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.32
Consensus pattern (53 bp):
GTATTTACAACAAAATAAAAGCATAGTTCAAACATAACTCACACTTAGTTCAT
Found at i:39602 original size:2 final size:2
Alignment explanation
Indices: 39595--39630 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
39585 TCTATCAAGC
39595 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39631 CAAGAAGTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.