Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015788.1 Corchorus capsularis cultivar CVL-1 contig15809, 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: 16937
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:281 original size:154 final size:154
Alignment explanation
Indices: 1--1090 Score: 1772
Period size: 154 Copynumber: 7.1 Consensus size: 154
* *
1 TTAGCTCATTCAGAAAACTTTTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTAGAATCGT
1 TTAGCTCATTCAGAACACTTTTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGT
* *
66 CTTCGATTTGGCTAACCACAAACCTTTTCTTTCCATTGTTTATGGCCTAACTATAATTATTTTGA
66 CTTCGATTTGGCAAACCACAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATTATTTTGA
131 TGAGATTAGTCCATTGTGAAGTTT
131 TGAGATTAGTCCATTGTGAAGTTT
* * * *
155 TTAGCTCATTTAGAACACTTTTTATTCCGGGCCTTTCGAGGCCCATTAGTGCTATTTTGAATCGT
1 TTAGCTCATTCAGAACACTTTTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGT
220 CTTCGATTTGGCAAACCACAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATTATTTTGA
66 CTTCGATTTGGCAAACCACAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATTATTTTGA
285 TGAGATTAGTCCATTGTGAAGTTT
131 TGAGATTAGTCCATTGTGAAGTTT
*
309 TTAGCTCATTCAGAACACTTTTTATTTCGGGCCTTTCGGGGCCCATTAATGCTGTTTTGAATCGT
1 TTAGCTCATTCAGAACACTTTTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGT
*
374 CTTTGATTTGGCAAACCACAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATTATTTTGA
66 CTTCGATTTGGCAAACCACAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATTATTTTGA
439 TGAGATTAGTCCATTGTGAAGTTT
131 TGAGATTAGTCCATTGTGAAGTTT
* * * *
463 TTAGCTCATTTAGAACACTTTTTATTCCGGGCCTTTCGAGGCCCATTAGTGCTATTTTGAATCGT
1 TTAGCTCATTCAGAACACTTTTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGT
* * *
528 CTTCGATTTGGCAAACTACAAAGCTTATCTTTCCATTATTTATGGCCTAACTATAATTATTTTGA
66 CTTCGATTTGGCAAACCACAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATTATTTTGA
* * *
593 TAAGATTAGTCCATTCTGAAGTTC
131 TGAGATTAGTCCATTGTGAAGTTT
617 TTAGCTCATTCAGAACACTTTTTATTTCGGGCCTTTCGGGGCCCA-TAGTGCTGTTTTGAATCGT
1 TTAGCTCATTCAGAACACTTTTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGT
* * * *
681 CTTCGATTT-GC-AACCAACAAAGCTTTTCTTTCAATTGTTTACGACCTAACTATAATCATTTTG
66 CTTCGATTTGGCAAACC-ACAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATTATTTTG
* *
744 GTGAGATTAGTCCATTGTGCAGTTT
130 ATGAGATTAGTCCATTGTGAAGTTT
* * * ** * *
769 TTAGCTCATTCAGAAAAGTTGTTATTTCGGGCCTTTTAGGGCCCATTAATGCTCTTTTGAATCGT
1 TTAGCTCATTCAGAACACTTTTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGT
* *
834 CTTCAATTTGGCAAACCACAAATCTTTTCTTTCCATTGTTTATGGCCTAACTATAATTATTTTGA
66 CTTCGATTTGGCAAACCACAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATTATTTTGA
899 TGAGATTAGTCCATTGTGAAGTTT
131 TGAGATTAGTCCATTGTGAAGTTT
* * *
923 TTAGCTCATTTAGAACACTTTTTATTTCGGTCCTTTCGGGGCCCAATAGTGCTGTTTTGAATCGT
1 TTAGCTCATTCAGAACACTTTTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGT
* * * *
988 CTTCGATTTGGCAAACCCCAAAGCTTTTCTTTTCATTGTTTATGGCCTAAATTTAATTATTTTGA
66 CTTCGATTTGGCAAACCACAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATTATTTTGA
1053 TGAGATTAGTCCATTGTGAAGTTT
131 TGAGATTAGTCCATTGTGAAGTTT
1077 TTAGCTCATTCAGA
1 TTAGCTCATTCAGA
1091 GCATGATACG
Statistics
Matches: 858, Mismatches: 74, Indels: 8
0.91 0.08 0.01
Matches are distributed among these distances:
151 3 0.00
152 103 0.12
153 52 0.06
154 696 0.81
155 4 0.00
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.41
Consensus pattern (154 bp):
TTAGCTCATTCAGAACACTTTTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGT
CTTCGATTTGGCAAACCACAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATTATTTTGA
TGAGATTAGTCCATTGTGAAGTTT
Found at i:1594 original size:22 final size:21
Alignment explanation
Indices: 1564--1606 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1554 CTTTCCCTTA
1564 ACAACTTCTGTCCCGAAGTTGT
1 ACAACTTCTG-CCCGAAGTTGT
* *
1586 ACAAGTTCTGGCCGAAGTTGT
1 ACAACTTCTGCCCGAAGTTGT
1607 CCTGAAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (21 bp):
ACAACTTCTGCCCGAAGTTGT
Found at i:3757 original size:33 final size:33
Alignment explanation
Indices: 3714--3802 Score: 119
Period size: 33 Copynumber: 2.7 Consensus size: 33
3704 TTTCAATGCC
*
3714 ATCAACCAAAACAGGATTA-TTTGTAATGCTATG
1 ATCAACCAAAACAGAATTAGTTT-TAATGCTATG
* *
3747 ATCAATCAAAACAAAATTAGTTTTAATGCTATG
1 ATCAACCAAAACAGAATTAGTTTTAATGCTATG
*
3780 TTCAACCAAAACAGAATT-GTTTT
1 ATCAACCAAAACAGAATTAGTTTT
3803 CATCACAATT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
32 5 0.10
33 41 0.84
34 3 0.06
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.33
Consensus pattern (33 bp):
ATCAACCAAAACAGAATTAGTTTTAATGCTATG
Found at i:7024 original size:155 final size:154
Alignment explanation
Indices: 6629--7234 Score: 969
Period size: 154 Copynumber: 3.9 Consensus size: 154
6619 CCTTGGCGCA
* * * * ** *
6629 TCAGAACACTGGTTATTTTGGGCCTTTTGGGGTCCATTACAGCTGTTTTGAATCGTATTCGATTT
1 TCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTT
* * * *
6694 GGCAAACCACAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATTATTTTGATGAAATTAG
66 GGCAAACCACAAAGCTTTTCTTTCAATTGTTTACGGCCTAACTATAATCATTTTGATGAGATTAG
6759 TCCATTGTGAAGTTTTTAGCTCAT
131 TCCATTGTGAAGTTTTTAGCTCAT
* *
6783 TCAGAAAACTTTTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTT
1 TCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTT
* * * *
6848 GGCAAACCACAAAGCTTTTCTTTCCATTGTTTATGGCCTAGCTATAATTATTTTGATGAGATTAG
66 GGCAAACCACAAAGCTTTTCTTTCAATTGTTTACGGCCTAACTATAATCATTTTGATGAGATTAG
6913 TCCATTGTGAAGTTTTTTAGCTCAT
131 TCCATTGTGAAG-TTTTTAGCTCAT
*
6938 TTAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTT
1 TCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTT
* *
7003 GGCAAACCACAAAGCTTTTCTTTCAATTGTTTACGACCTAACTATAATCATTTTGGTGAGATTAG
66 GGCAAACCACAAAGCTTTTCTTTCAATTGTTTACGGCCTAACTATAATCATTTTGATGAGATTAG
7068 TCCATTGTGAAGTTTTTAGCTCAT
131 TCCATTGTGAAGTTTTTAGCTCAT
* *
7092 TCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGTTGTTTTGAATCGGCTTCGATTT
1 TCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTT
* * *
7157 GACAAACCACAAAGCTTTTCTTTCAATTTTTTACGGCCTAACTATAATCATTTTGGTGAGATTAG
66 GGCAAACCACAAAGCTTTTCTTTCAATTGTTTACGGCCTAACTATAATCATTTTGATGAGATTAG
*
7222 TCCACTGTGAAGT
131 TCCATTGTGAAGT
7235 GATGCGCCCA
Statistics
Matches: 424, Mismatches: 27, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
154 279 0.66
155 145 0.34
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (154 bp):
TCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTT
GGCAAACCACAAAGCTTTTCTTTCAATTGTTTACGGCCTAACTATAATCATTTTGATGAGATTAG
TCCATTGTGAAGTTTTTAGCTCAT
Found at i:7204 original size:309 final size:309
Alignment explanation
Indices: 6631--7234 Score: 983
Period size: 309 Copynumber: 2.0 Consensus size: 309
6621 TTGGCGCATC
* * *
6631 AGAACACTGGTTATTTTGGGCCTTTTGGGGTCCATTACAGCTGTTTTGAATCGTATTCGATTTGG
1 AGAACACTGGTTATTTCGGGCCTTTCGGGGCCCATTACAGCTGTTTTGAATCGTATTCGATTTGG
* * * *
6696 CAAACCACAAAGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATTATTTTGATGAAATTAGTC
66 CAAACCACAAAGCTTTTCTTTCAATTGTTTACGACCTAACTATAATCATTTTGATGAAATTAGTC
*
6761 CATTGTGAAGTTTTTAGCTCATTCAGAAAACTTTTTATTTCGGGCCTTTCGGGGCCCATTAGTGC
131 CATTGTGAAGTTTTTAGCTCATTCAGAAAACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGC
* * * * *
6826 TGTTTTGAATCGTCTTCGATTTGGCAAACCACAAAGCTTTTCTTTCCATTGTTTATGGCCTAGCT
196 TGTTTTGAATCGGCTTCGATTTGACAAACCACAAAGCTTTTCTTTCAATTGTTTACGGCCTAACT
* *
6891 ATAATTATTTTGATGAGATTAGTCCATTGTGAAGTTTTTTAGCTCATTT
261 ATAATCATTTTGATGAGATTAGTCCACTGTGAAGTTTTTTAGCTCATTT
* ** *
6940 AGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGTCTTCGATTTGG
1 AGAACACTGGTTATTTCGGGCCTTTCGGGGCCCATTACAGCTGTTTTGAATCGTATTCGATTTGG
* *
7005 CAAACCACAAAGCTTTTCTTTCAATTGTTTACGACCTAACTATAATCATTTTGGTGAGATTAGTC
66 CAAACCACAAAGCTTTTCTTTCAATTGTTTACGACCTAACTATAATCATTTTGATGAAATTAGTC
* *
7070 CATTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGT
131 CATTGTGAAGTTTTTAGCTCATTCAGAAAACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGC
*
7135 TGTTTTGAATCGGCTTCGATTTGACAAACCACAAAGCTTTTCTTTCAATTTTTTACGGCCTAACT
196 TGTTTTGAATCGGCTTCGATTTGACAAACCACAAAGCTTTTCTTTCAATTGTTTACGGCCTAACT
*
7200 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGT
261 ATAATCATTTTGATGAGATTAGTCCACTGTGAAGT
7235 GATGCGCCCA
Statistics
Matches: 270, Mismatches: 25, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
309 270 1.00
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (309 bp):
AGAACACTGGTTATTTCGGGCCTTTCGGGGCCCATTACAGCTGTTTTGAATCGTATTCGATTTGG
CAAACCACAAAGCTTTTCTTTCAATTGTTTACGACCTAACTATAATCATTTTGATGAAATTAGTC
CATTGTGAAGTTTTTAGCTCATTCAGAAAACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGC
TGTTTTGAATCGGCTTCGATTTGACAAACCACAAAGCTTTTCTTTCAATTGTTTACGGCCTAACT
ATAATCATTTTGATGAGATTAGTCCACTGTGAAGTTTTTTAGCTCATTT
Found at i:11162 original size:33 final size:33
Alignment explanation
Indices: 11120--11222 Score: 109
Period size: 33 Copynumber: 3.1 Consensus size: 33
11110 CTAGTGACCA
* *
11120 GCCATGCGACTTGGAGAAGCTCGGCCAACACCG
1 GCCACGCGACTTGGAGAAGCCCGGCCAACACCG
* *
11153 GCCACGCGACTCGGAGATGCCCGGCCAACACCG
1 GCCACGCGACTTGGAGAAGCCCGGCCAACACCG
* * * * *
11186 GCCACGTGACATGGACATGTCCGGCC-ACAACCG
1 GCCACGCGACTTGGAGAAGCCCGGCCAAC-ACCG
11219 GCCA
1 GCCA
11223 TCGCTAGGCG
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
32 2 0.03
33 58 0.97
ACGTcount: A:0.23, C:0.38, G:0.29, T:0.10
Consensus pattern (33 bp):
GCCACGCGACTTGGAGAAGCCCGGCCAACACCG
Found at i:12204 original size:17 final size:17
Alignment explanation
Indices: 12179--12212 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12169 CACCCTTCTT
12179 GAAAATTCAAAAATTCA
1 GAAAATTCAAAAATTCA
*
12196 GAAACTTCAAAAATTCA
1 GAAAATTCAAAAATTCA
12213 TAGCCGATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.15, G:0.06, T:0.24
Consensus pattern (17 bp):
GAAAATTCAAAAATTCA
Done.