Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013276.1 Corchorus capsularis cultivar CVL-1 contig13297, 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: 10969
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:3671 original size:41 final size:41
Alignment explanation
Indices: 3611--3693 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 41
3601 CCTAAATTTT
* * *
3611 AGGCATGGGGTTGTATCGTTCTTGAAATACAGGCATAGAGA
1 AGGCACGGGGTTGTATCGTTCCTGAAATACAGGCACAGAGA
*
3652 AGGCACGGGGTTGTGTCGTTCCTGAAATACAGGCACAGAGA
1 AGGCACGGGGTTGTATCGTTCCTGAAATACAGGCACAGAGA
3693 A
1 A
3694 CGCCTGTGCC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.29, C:0.16, G:0.33, T:0.23
Consensus pattern (41 bp):
AGGCACGGGGTTGTATCGTTCCTGAAATACAGGCACAGAGA
Found at i:7034 original size:197 final size:198
Alignment explanation
Indices: 6634--7196 Score: 827
Period size: 196 Copynumber: 2.8 Consensus size: 198
6624 TGCGAAAATT
** *
6634 TTTTTGCAACCA-TTTTAATTGGTTACAAATAACTTTTAAAAATGATTAAATGTCGTTTTCAAAA
1 TTTTTGCAACCACTTTTAATTGGTTATGAATAACTTTTAAAAATGATTAAATGTCGTTTCCAAAA
* * * * *
6698 CACTTACGTAACGACCTCTAGGTAGTTGACAAAATCATTTAAAAACGATT--T-T-TTTGCAAAA
66 CACTTACATAACGACCTCTAGGTAGTTGCCAAAATAATTTAAAAACGATTAATGTCGTTGCGAAA
* * *
6759 ACCATTACGCAACAACGTTGTTTTGGTTGTGAAATCTTTTACGTAGCAACATTTGATTGGTTGTG
131 ACCCTT---CAACGACGTTGTTTTGGTTGTGAAATCTTTTACGTAGCAACATTTGATTGGTTGCG
6824 TAATAA
193 TAATAA
*
6830 TTTTTGCAACCACTTTTAATTGGTTATGAATAACTTTTAAAAATGATTAAAAGTCGTTTCCAAAA
1 TTTTTGCAACCACTTTTAATTGGTTATGAATAACTTTTAAAAATGATTAAATGTCGTTTCCAAAA
6895 CACTTACATAACGACCTCTAGGTAGTTGCCAAAATAATTTAAAAACGATTAAATGTCGTTGCGAA
66 CACTTACATAACGACCTCTAGGTAGTTGCCAAAATAATTTAAAAACGATT-AATGTCGTTGCGAA
*
6960 AACCCTT-AACGACGTTGTTTTGGTTGTGAAATTTTTTACGTAGCAACATTTGATTGGTTGCGTA
130 AACCCTTCAACGACGTTGTTTTGGTTGTGAAATCTTTTACGTAGCAACATTTGATTGGTTGCGTA
7024 ATAA
195 ATAA
* * *
7028 -TTTTGCAATCAC-TTTAATTGGTTATGAATAACTTTTAGAAATGATTAAATGTCATTTCCAAAA
1 TTTTTGCAACCACTTTTAATTGGTTATGAATAACTTTTAAAAATGATTAAATGTCGTTTCCAAAA
* *
7091 CACTTACATAACGACCTCTAGGTAGTTACCAAAATGATTTAAAAACGATTATATGTCGTTGCGAA
66 CACTTACATAACGACCTCTAGGTAGTTGCCAAAATAATTTAAAAACGATTA-ATGTCGTTGCGAA
*
7156 AACCCTTACGCAACGACGTTGTTTTGGTTGTGAAATGTTTT
130 AACCCTT---CAACGACGTTGTTTTGGTTGTGAAATCTTTT
7197 GAATGGCTTT
Statistics
Matches: 336, Mismatches: 20, Indels: 18
0.90 0.05 0.05
Matches are distributed among these distances:
195 1 0.00
196 128 0.38
197 106 0.32
198 58 0.17
200 30 0.09
201 1 0.00
202 12 0.04
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (198 bp):
TTTTTGCAACCACTTTTAATTGGTTATGAATAACTTTTAAAAATGATTAAATGTCGTTTCCAAAA
CACTTACATAACGACCTCTAGGTAGTTGCCAAAATAATTTAAAAACGATTAATGTCGTTGCGAAA
ACCCTTCAACGACGTTGTTTTGGTTGTGAAATCTTTTACGTAGCAACATTTGATTGGTTGCGTAA
TAA
Found at i:9632 original size:133 final size:131
Alignment explanation
Indices: 9222--9663 Score: 542
Period size: 132 Copynumber: 3.3 Consensus size: 131
9212 CCTTGAAAAG
* * ** * * * *
9222 GACTAATATAAGTCATTGCGACTAGAATAAGATTTCACAGCGACTTAATTTGTGGCTTCAAAGGT
1 GACTAACA-AAGTCGTTGCGAAAAGACTAAGATTTCGCAACGACTTAATTTGTGGCTTCAAAAGT
* * * *
9287 AATTATGTTTTTTTTAGCGACTTTTAAGGTTGCTACGAAAATCAATTAGCAAAATATATTAAGCA
65 AATTATGTTTTTTTTAGCGACTTTCAAGGTCGCTACGAAAATCAATTTGTAAAATATATTAAGCA
*
9352 AT
130 AC
* * *
9354 GACTAACAATAGTCGTTGCGAAAAGAGTAAGATTTCGGAGCGACTTAATTTGTGGCTTCAAAAGT
1 GACTAACAA-AGTCGTTGCGAAAAGACTAAGATTTCGCAACGACTTAATTTGTGGCTTCAAAAGT
* *
9419 AATTATGTTTTTTGTAGCGACTTTCAAGGTCGCTGCGAAAATCAATTTGTAAAATATATTAAGCA
65 AATTATGTTTTTTTTAGCGACTTTCAAGGTCGCTACGAAAATCAATTTGTAAAATATATTAAGCA
9484 AC
130 AC
* * ** * * *
9486 GATTAACAAAAGTCGTTGGGAAAAGTTTAAGATTTCGCAACGACTTAATCTGTCGTTTCAAAAGT
1 GACTAAC-AAAGTCGTTGCGAAAAGACTAAGATTTCGCAACGACTTAATTTGTGGCTTCAAAAGT
* * * **
9551 AATCATGTTTTTTTATAGCGACTATCAAGGTCGCTTCGAAAATCAATTTGTAAAATATATTAAAA
65 AATTATGTTTTTTT-TAGCGACTTTCAAGGTCGCTACGAAAATCAATTTGTAAAATATATTAAGC
9616 AAC
129 AAC
* * *
9619 GACTAATAGAAGTCGTTGCGAAAAGACTATGAATTCGCAACGACT
1 GACTAACA-AAGTCGTTGCGAAAAGACTAAGATTTCGCAACGACT
9664 GATAGAAGTC
Statistics
Matches: 269, Mismatches: 37, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
131 1 0.00
132 181 0.67
133 87 0.32
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (131 bp):
GACTAACAAAGTCGTTGCGAAAAGACTAAGATTTCGCAACGACTTAATTTGTGGCTTCAAAAGTA
ATTATGTTTTTTTTAGCGACTTTCAAGGTCGCTACGAAAATCAATTTGTAAAATATATTAAGCAA
C
Found at i:9704 original size:41 final size:41
Alignment explanation
Indices: 9616--9704 Score: 97
Period size: 41 Copynumber: 2.2 Consensus size: 41
9606 TATATTAAAA
* * *
9616 AACGACTAATAGAAGTCGTTGCGAAAAGACTATGAATTCGC
1 AACGACTAATAGAAGTCGTTGCAAAAAGACTAGGAATTAGC
* * ** *
9657 AACGACTGATAGAAGTCGTTGTAAAAAGGGTAGGATTTAGC
1 AACGACTAATAGAAGTCGTTGCAAAAAGACTAGGAATTAGC
*
9698 AGCGACT
1 AACGACT
9705 TTGTTTTTGT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (41 bp):
AACGACTAATAGAAGTCGTTGCAAAAAGACTAGGAATTAGC
Done.