Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007651.1 Corchorus capsularis cultivar CVL-1 contig07672, 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: 15462
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:1418 original size:21 final size:21
Alignment explanation
Indices: 1392--1443 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
1382 GAAGAAGAAA
* *
1392 AAGAAGAAAGTGAGAACGAGG
1 AAGAAGAAAGTGAAAAAGAGG
*
1413 AAGAAGGAAGTGAAAAAGAGG
1 AAGAAGAAAGTGAAAAAGAGG
1434 AAGAAGAAAG
1 AAGAAGAAAG
1444 ACCTGCTGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.58, C:0.02, G:0.37, T:0.04
Consensus pattern (21 bp):
AAGAAGAAAGTGAAAAAGAGG
Found at i:1471 original size:18 final size:18
Alignment explanation
Indices: 1433--1473 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1423 TGAAAAAGAG
* *
1433 GAAGAAGAAAGACCTGCT
1 GAAGAAGAAAAACCTGAT
*
1451 GAAGAAGAAAAATCTGAT
1 GAAGAAGAAAAACCTGAT
1469 GAAGA
1 GAAGA
1474 GGTTGATGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.51, C:0.10, G:0.27, T:0.12
Consensus pattern (18 bp):
GAAGAAGAAAAACCTGAT
Found at i:3891 original size:235 final size:235
Alignment explanation
Indices: 3480--3949 Score: 904
Period size: 235 Copynumber: 2.0 Consensus size: 235
3470 GACTCAAGAA
3480 AAAGAACAGAAGAAAAAAGAAATACAACCAAGAAGCGCCACACTCAACTTTTTCATACTGCTTGG
1 AAAGAACAGAAGAAAAAAGAAATACAACCAAGAAGCGCCACACTCAACTTTTTCATACTGCTTGG
3545 TTTTTGCAAGATCACTCTAAACTCTATTCATTGTAAATCTTGCCTGAACTTAACCTTGAACCTAC
66 TTTTTGCAAGATCACTCTAAACTCTATTCATTGTAAATCTTGCCTGAACTTAACCTTGAACCTAC
3610 TCAGTGTATCTAGATCATATAGGATCACTCTACACACTCTTCAAACTATATCTTTGATTGTAAAC
131 TCAGTGTATCTAGATCATATAGGATCACTCTACACACTCTTCAAACTATATCTTTGATTGTAAAC
*
3675 AGTGCGGGGAGCACTTGTTCTAAGCTTGGGGAAAGCTTAG
196 AGTGCGAGGAGCACTTGTTCTAAGCTTGGGGAAAGCTTAG
* *
3715 AAAGAACATAAGAAAAAAGAAATACAACCAAGAAGCGCCACAGTCAACTTTTTCATACTGCTTGG
1 AAAGAACAGAAGAAAAAAGAAATACAACCAAGAAGCGCCACACTCAACTTTTTCATACTGCTTGG
3780 TTTTTGCAAGATCACTCTAAACTCTATTCATTGTAAATCTTGCCTGAACTTAACCTTGAACCTAC
66 TTTTTGCAAGATCACTCTAAACTCTATTCATTGTAAATCTTGCCTGAACTTAACCTTGAACCTAC
3845 TCAGTGTATCTAGATCATATAGGATCACTCTACACACTCTTCAAACTATATCTTTGATTGTAAAC
131 TCAGTGTATCTAGATCATATAGGATCACTCTACACACTCTTCAAACTATATCTTTGATTGTAAAC
*
3910 AGTGCGAGGAGCACTTGTTCTAAGTTTGGGGAAAGCTTAG
196 AGTGCGAGGAGCACTTGTTCTAAGCTTGGGGAAAGCTTAG
3950 GTTTTTGATC
Statistics
Matches: 231, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
235 231 1.00
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (235 bp):
AAAGAACAGAAGAAAAAAGAAATACAACCAAGAAGCGCCACACTCAACTTTTTCATACTGCTTGG
TTTTTGCAAGATCACTCTAAACTCTATTCATTGTAAATCTTGCCTGAACTTAACCTTGAACCTAC
TCAGTGTATCTAGATCATATAGGATCACTCTACACACTCTTCAAACTATATCTTTGATTGTAAAC
AGTGCGAGGAGCACTTGTTCTAAGCTTGGGGAAAGCTTAG
Found at i:6622 original size:33 final size:33
Alignment explanation
Indices: 6572--6695 Score: 144
Period size: 33 Copynumber: 3.7 Consensus size: 33
6562 CCGCGCAACA
*
6572 CCGGCCACAAGACCGGCCACGCGACATGGACATGT
1 CCGGCCAC-A-ACCGGCCACGCGACATGGACATGC
*
6607 CCGGCCATC-ACCGGCCACGCGACATGGACATGG
1 CCGGCCA-CAACCGGCCACGCGACATGGACATGC
* ** *
6640 CCGGCTACAACCGGCCAAACGAC-TCGGCCATGC
1 CCGGCCACAACCGGCCACGCGACAT-GGACATGC
6673 CCGGCCACAACCGGCCACGCGAC
1 CCGGCCACAACCGGCCACGCGAC
6696 CCTTTGTCTA
Statistics
Matches: 77, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
32 2 0.03
33 67 0.87
35 7 0.09
36 1 0.01
ACGTcount: A:0.23, C:0.42, G:0.27, T:0.07
Consensus pattern (33 bp):
CCGGCCACAACCGGCCACGCGACATGGACATGC
Found at i:7611 original size:8 final size:8
Alignment explanation
Indices: 7598--7631 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
7588 CACCTTCTTG
7598 AAAAATTC
1 AAAAATTC
7606 AAAAATTC
1 AAAAATTC
*
7614 AGAAACTTC
1 A-AAAATTC
7623 AAAAATTC
1 AAAAATTC
7631 A
1 A
7632 TAGCTGATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24
Consensus pattern (8 bp):
AAAAATTC
Found at i:7726 original size:5 final size:5
Alignment explanation
Indices: 7710--7740 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
7700 ATCGAACAAT
7710 ATAAA A-AAA ATAAA ATAAA ATAAA ATAAA AT
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA AT
7741 TTCGACCAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:15150 original size:49 final size:49
Alignment explanation
Indices: 15089--15215 Score: 157
Period size: 48 Copynumber: 2.6 Consensus size: 49
15079 CAATTTTCAG
* * *
15089 TTTTTACCTGCTTTCCCCCAAAATGCCCTTCCCGGACGGAAGGCACTAA
1 TTTTTACCTGCTTTTCCCCAAAACGCCCTTCCCAGACGGAAGGCACTAA
* * * * **
15138 TTTTTACTTGCTTTTCCCTAAAACACCC-TCCCAGATGGAAGGCACTTG
1 TTTTTACCTGCTTTTCCCCAAAACGCCCTTCCCAGACGGAAGGCACTAA
*
15186 TTTTTACCTGCTTTTTCCCAAAACGCCCTT
1 TTTTTACCTGCTTTTCCCCAAAACGCCCTT
15216 TCAGACAAAG
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
48 40 0.62
49 24 0.38
ACGTcount: A:0.21, C:0.32, G:0.13, T:0.33
Consensus pattern (49 bp):
TTTTTACCTGCTTTTCCCCAAAACGCCCTTCCCAGACGGAAGGCACTAA
Found at i:15402 original size:63 final size:63
Alignment explanation
Indices: 15275--15462 Score: 188
Period size: 62 Copynumber: 3.0 Consensus size: 63
15265 TTCGATTTTT
* * * *
15275 GTCACATTCTTGCATTTAGGTTCTAGTTTTCCCAAAACACCCCCTTTTGGACAAAGGG-CTAGTT
1 GTCACATTCCTGCATTTAAGTT-TAGTATTCCCAAAATA--CCCTTTTGGACAAAGGGTC-AGTT
15339 TC
62 TC
** *
15341 GTCACATTCCTGCATTTAAGTTTAGTATTCCCAAAATACCCTTTCAGACAAAGGGTCAGTTTT
1 GTCACATTCCTGCATTTAAGTTTAGTATTCCCAAAATACCCTTTTGGACAAAGGGTCAGTTTC
* * *
15404 GTTACA-TCCT--AGTGTATAGTTT-CTATTTCCCAAAATACCCTTTTGGACAAAGGGTCAGT
1 GTCACATTCCTGCA-TTTA-AGTTTAGTA-TTCCCAAAATACCCTTTTGGACAAAGGGTCAGT
Statistics
Matches: 106, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
60 1 0.01
61 5 0.05
62 40 0.38
63 25 0.24
64 1 0.01
65 14 0.13
66 20 0.19
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (63 bp):
GTCACATTCCTGCATTTAAGTTTAGTATTCCCAAAATACCCTTTTGGACAAAGGGTCAGTTTC
Done.