Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006159.1 Corchorus capsularis cultivar CVL-1 contig06177, 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: 11602
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1421 original size:21 final size:22
Alignment explanation
Indices: 1397--1442 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
1387 TTTGTTTAAT
1397 TAAC-AATTGTCCTTTTCCAAG
1 TAACAAATTGTCCTTTTCCAAG
1418 TAACAAATTGTCCTTTTCCAAG
1 TAACAAATTGTCCTTTTCCAAG
1440 TAA
1 TAA
1443 GGATGTTCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.37
Consensus pattern (22 bp):
TAACAAATTGTCCTTTTCCAAG
Found at i:1807 original size:14 final size:13
Alignment explanation
Indices: 1788--1834 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
1778 CTGCAAAATT
1788 AACAAAAACACAAA
1 AACAAAAACA-AAA
1802 AACAAAAACAAAA
1 AACAAAAACAAAA
* *
1815 TACGAAAAA-TAAA
1 AAC-AAAAACAAAA
1828 AACAAAA
1 AACAAAA
1835 CTAAAGGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 4 0.14
13 10 0.34
14 15 0.52
ACGTcount: A:0.79, C:0.15, G:0.02, T:0.04
Consensus pattern (13 bp):
AACAAAAACAAAA
Found at i:1813 original size:20 final size:20
Alignment explanation
Indices: 1788--1834 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1778 CTGCAAAATT
1788 AACAAAA-ACACAAAAACAAA
1 AACAAAATAC-CAAAAACAAA
* *
1808 AACAAAATACGAAAAATAAA
1 AACAAAATACCAAAAACAAA
1828 AACAAAA
1 AACAAAA
1835 CTAAAGGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 22 0.92
21 2 0.08
ACGTcount: A:0.79, C:0.15, G:0.02, T:0.04
Consensus pattern (20 bp):
AACAAAATACCAAAAACAAA
Found at i:1814 original size:5 final size:6
Alignment explanation
Indices: 1792--1834 Score: 50
Period size: 6 Copynumber: 6.7 Consensus size: 6
1782 AAAATTAACA
*
1792 AAAACAC AAAAAC AAAAAC AAAATAC GAAAAAT AAAAAC AAAA
1 AAAA-AC AAAAAC AAAAAC AAAA-AC -AAAAAC AAAAAC AAAA
1835 CTAAAGGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
6 21 0.66
7 7 0.22
8 4 0.12
ACGTcount: A:0.79, C:0.14, G:0.02, T:0.05
Consensus pattern (6 bp):
AAAAAC
Found at i:5544 original size:33 final size:33
Alignment explanation
Indices: 5502--5567 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
5492 GGCTGCAATC
5502 TTTGAATGTTCTTAGTGTTCATAATAGTTCATG
1 TTTGAATGTTCTTAGTGTTCATAATAGTTCATG
5535 TTTGAATGTTCTTAGTGTTCATAATAGTTCATG
1 TTTGAATGTTCTTAGTGTTCATAATAGTTCATG
5568 ATAAAATAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.24, C:0.09, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTGAATGTTCTTAGTGTTCATAATAGTTCATG
Found at i:6007 original size:17 final size:17
Alignment explanation
Indices: 5985--6018 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5975 GCTTTATATT
*
5985 ATAAAAAACAATTATAA
1 ATAAAAAACAATAATAA
6002 ATAAAAAACAATAATAA
1 ATAAAAAACAATAATAA
6019 TAAGAAGTGA
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:0.74, C:0.06, G:0.00, T:0.21
Consensus pattern (17 bp):
ATAAAAAACAATAATAA
Found at i:6364 original size:217 final size:214
Alignment explanation
Indices: 6005--6437 Score: 724
Period size: 217 Copynumber: 2.0 Consensus size: 214
5995 ATTATAAATA
* *
6005 AAAAACAATAATAATAAGAAGTGAAATGTCTAAAAAACCGGTCAAAAGATTTAGCTTCATTACTT
1 AAAAACAATAATAATAAAAAGTGAAATGTCTAAAAAACCGGTCAAAAGATTTAGCATCATTACTT
*
6070 TAAGAATTGATAGGGGTATTTCAGTCATTTCGTGTTTGGTTTTTTAGTTATTTGAGTTGAAGACC
66 TAAGAATTGATAGGGGTATTTCAGTCATTTCATGTTTGGTTTTTTAGTTATTTGAGTTGAAGACC
* *
6135 GAGGGCATTTTAGGAAGTTTGCC-AAAAAAAACCCTCTGTTGGTCCCATATTCCATCATAATCAC
131 GAGGGCATTTTAGGAAGTTTGCCAAAAAAAAACCCTCCGTGGGTCCCATATTCCATCATAATCAC
6199 TTTATAAATTGGGTAATTT
196 TTTATAAATTGGGTAATTT
*
6218 AAAAACATTAATAATAAAAAGTGAAATGTCTAAAAAACCGGTCAAAAGATTTAGCATCATTACTT
1 AAAAACAATAATAATAAAAAGTGAAATGTCTAAAAAACCGGTCAAAAGATTTAGCATCATTACTT
* *
6283 TAAGAATAAATTGATAGGGGTATTTCGGTCATTTCATGTTTGGTTTTTTAGTTATTTGAGTTGAT
66 TAAG----AATTGATAGGGGTATTTCAGTCATTTCATGTTTGGTTTTTTAGTTATTTGAGTTGAA
* *
6348 GATCGAGGGTATTTTAGGAAGTTTGCCAAAAAAAAAACCCTCCGTGGGTCCCATATTCCATCATA
127 GACCGAGGGCATTTTAGGAAGTTTGCC-AAAAAAAAACCCTCCGTGGGTCCCATATTCCATCATA
6413 ATCACTTTATAAATTGGGTAATTT
191 ATCACTTTATAAATTGGGTAATTT
6437 A
1 A
6438 TCAAATAGCC
Statistics
Matches: 204, Mismatches: 10, Indels: 6
0.93 0.05 0.03
Matches are distributed among these distances:
213 66 0.32
217 79 0.39
219 59 0.29
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.35
Consensus pattern (214 bp):
AAAAACAATAATAATAAAAAGTGAAATGTCTAAAAAACCGGTCAAAAGATTTAGCATCATTACTT
TAAGAATTGATAGGGGTATTTCAGTCATTTCATGTTTGGTTTTTTAGTTATTTGAGTTGAAGACC
GAGGGCATTTTAGGAAGTTTGCCAAAAAAAAACCCTCCGTGGGTCCCATATTCCATCATAATCAC
TTTATAAATTGGGTAATTT
Found at i:9271 original size:42 final size:43
Alignment explanation
Indices: 9224--9311 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 43
9214 TTACCTAAAC
*
9224 TCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATAT
1 TCTACCTCCATCTCTAGATAATTCATCAAAATAAAGCTAATAT
9266 TCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAGCTAATAT
1 TCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAGCTAATAT
9311 T
1 T
9312 AATTGTTGTT
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
42 4 0.10
45 38 0.90
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.34
Consensus pattern (43 bp):
TCTACCTCCATCTCTAGATAATTCATCAAAATAAAGCTAATAT
Done.