Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012826.1 Corchorus capsularis cultivar CVL-1 contig12847, 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: 35260
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:5560 original size:178 final size:177
Alignment explanation
Indices: 5263--5785 Score: 786
Period size: 178 Copynumber: 2.9 Consensus size: 177
5253 CAAATTCGAA
*
5263 ATTTGTCGTTTTCGGTCTTCTAGAAGTACAAACACAATAA--TTCCTCCAAACCGACAAAAAAGA
1 ATTTGTCGTTTTCGGTCTTCTAGAAGTACAAACACAATAATCTTCCTCCAAACCGACACAAAAGA
* ** *
5326 TACAGTTAATCAAGCAAAAG-ATATCGA-TTTATTTTGCAAATTATCCCAATTTGCATGTAATTG
66 TACAGTTAATCAAGCAAAAGTA-ATC-ATTTTATGTCACAAATTATCCCAAATTGCATGTAATTG
* *
5389 CCCAATATCAATGATCATGAGAGGTTTGCAGTACCCAAGACAGATAGGC
129 CCCAATATCAATGATCATGAGAGGTTTGCAGTACCAAAGACAAATAGGC
5438 ATTTGTCGTTTTCGGTCTTCTAGAAGTACAAACACAATAATTCTTCCTCCAAACCGACACAAAAG
1 ATTTGTCGTTTTCGGTCTTCTAGAAGTACAAACACAATAA-TCTTCCTCCAAACCGACACAAAAG
* *
5503 ATACAGGTAATCAAGCAAACGTAATCATTTTATGTCACAAATTATCCCAAATTGCATGTAATTGC
65 ATACAGTTAATCAAGCAAAAGTAATCATTTTATGTCACAAATTATCCCAAATTGCATGTAATTGC
*
5568 CCAATATCAATGATCATGAGAGGTTTGCAGTACTAAAGACAAATAGGC
130 CCAATATCAATGATCATGAGAGGTTTGCAGTACCAAAGACAAATAGGC
* ** *
5616 ATTTGTCGTTTTCGGTCTTCTAGAAGTAAAAACACAATAATACTTCCAACAAACCGGCACAAAAG
1 ATTTGTCGTTTTCGGTCTTCTAGAAGTACAAACACAATAAT-CTTCCTCCAAACCGACACAAAAG
* * *
5681 ATACAGTTAATCAAGCAAAAGGT-ATCGTTTTATGTCACAAATTATACAAAATTGCATGTAATTG
65 ATACAGTTAATCAAGCAAAA-GTAATCATTTTATGTCACAAATTATCCCAAATTGCATGTAATTG
*
5745 CCCAATATCAATGATAATTGAGAGGTTTGCAGGTACCAAAG
129 CCCAATATCAATGATCA-TGAGAGGTTTGCA-GTACCAAAG
5786 CCAGTGACAT
Statistics
Matches: 318, Mismatches: 21, Indels: 13
0.90 0.06 0.04
Matches are distributed among these distances:
175 40 0.13
177 2 0.01
178 252 0.79
179 16 0.05
180 8 0.03
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.28
Consensus pattern (177 bp):
ATTTGTCGTTTTCGGTCTTCTAGAAGTACAAACACAATAATCTTCCTCCAAACCGACACAAAAGA
TACAGTTAATCAAGCAAAAGTAATCATTTTATGTCACAAATTATCCCAAATTGCATGTAATTGCC
CAATATCAATGATCATGAGAGGTTTGCAGTACCAAAGACAAATAGGC
Found at i:10824 original size:8 final size:8
Alignment explanation
Indices: 10808--10858 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
10798 GGGTTATCAG
*
10808 TCTTCAGA
1 TCTTTAGA
10816 TCTTTAGA
1 TCTTTAGA
*
10824 TC-TTGGA
1 TCTTTAGA
*
10831 TGTTT-GA
1 TCTTTAGA
10838 GTCTTTAGA
1 -TCTTTAGA
10847 TCTTTAGA
1 TCTTTAGA
10855 TCTT
1 TCTT
10859 GGATGTTTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
7 7 0.19
8 27 0.75
9 2 0.06
ACGTcount: A:0.20, C:0.14, G:0.18, T:0.49
Consensus pattern (8 bp):
TCTTTAGA
Found at i:10848 original size:31 final size:31
Alignment explanation
Indices: 10806--10870 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
10796 TTGGGTTATC
10806 AGTCTTCAGATCTTTAGATCTTGGATGTTTG
1 AGTCTTCAGATCTTTAGATCTTGGATGTTTG
*
10837 AGTCTTTAGATCTTTAGATCTTGGATGTTTG
1 AGTCTTCAGATCTTTAGATCTTGGATGTTTG
10868 AGT
1 AGT
10871 TAGTTCAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.20, C:0.11, G:0.23, T:0.46
Consensus pattern (31 bp):
AGTCTTCAGATCTTTAGATCTTGGATGTTTG
Found at i:14622 original size:5 final size:5
Alignment explanation
Indices: 14612--14638 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
14602 AACTCATATT
14612 ATAAA ATAAA ATAAA ATAAA ATAAA AT
1 ATAAA ATAAA ATAAA ATAAA ATAAA AT
14639 CGTTTTGCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
ATAAA
Found at i:19148 original size:16 final size:16
Alignment explanation
Indices: 19127--19159 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
19117 TCAATTAATC
19127 ATGTTTGATATGAAAG
1 ATGTTTGATATGAAAG
19143 ATGTTTGATATGAAAG
1 ATGTTTGATATGAAAG
19159 A
1 A
19160 AATTCAGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.36
Consensus pattern (16 bp):
ATGTTTGATATGAAAG
Found at i:24704 original size:14 final size:14
Alignment explanation
Indices: 24685--24712 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
24675 TGCCTCTTTC
24685 CTTTTTAATTGACA
1 CTTTTTAATTGACA
24699 CTTTTTAATTGACA
1 CTTTTTAATTGACA
24713 TATCCTTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.07, T:0.50
Consensus pattern (14 bp):
CTTTTTAATTGACA
Found at i:26641 original size:32 final size:33
Alignment explanation
Indices: 26605--26670 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
26595 AAAAAAATTG
* * *
26605 ATTTTCCA-GAAAATATCCAAACAACATAAAAT
1 ATTTTCCATGAAAATACCCAAACAAAAGAAAAT
*
26637 ATTTTCCATGAAATTACCCAAACAAAAGAAAAT
1 ATTTTCCATGAAAATACCCAAACAAAAGAAAAT
26670 A
1 A
26671 GAAGATTTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 8 0.28
33 21 0.72
ACGTcount: A:0.53, C:0.18, G:0.05, T:0.24
Consensus pattern (33 bp):
ATTTTCCATGAAAATACCCAAACAAAAGAAAAT
Found at i:29254 original size:2 final size:2
Alignment explanation
Indices: 29247--29282 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
29237 ACCATACTTA
29247 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
29283 GATAATTATA
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.