Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015781.1 Corchorus olitorius cultivar O-4 contig15814, 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: 14009
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:5596 original size:12 final size:12
Alignment explanation
Indices: 5555--5594 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
5545 TTTTTTTAAA
*
5555 AAAAGGAAATCTG
1 AAAAGGAAA-GTG
5568 AAAAGGAAAGTG
1 AAAAGGAAAGTG
5580 AAAAGGAAAG-G
1 AAAAGGAAAGTG
5591 AAAA
1 AAAA
5595 AGATGAAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 5 0.19
12 12 0.46
13 9 0.35
ACGTcount: A:0.62, C:0.03, G:0.28, T:0.07
Consensus pattern (12 bp):
AAAAGGAAAGTG
Found at i:6915 original size:141 final size:141
Alignment explanation
Indices: 6747--7705 Score: 1492
Period size: 141 Copynumber: 6.8 Consensus size: 141
6737 AGTTGTTGAG
* *
6747 CAAAGTTGCATTTAAGTTTCAAAAAAACCTTGCTCAAGGTCGAGTTTGCATTTGTAAGACCTCCG
1 CAAAGTTGCGTTTAAGTTTC-AAAAAACCTTGCTCAAGGTTGAGTTTGCATTTGTAAGACCTCCG
*
6812 GGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGATATCACCTCATTTCAT
65 GGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCACCTCATTTCAT
6877 -AAATTGTTAAT
130 CAAATTGTTAAT
* *
6888 CAAAGTTGCATTTAAGTTTCAAAAAAACCTTGCTCAAGGTCGAGTTTGCATTTGTAAGACCTCCG
1 CAAAGTTGCGTTTAAGTTTC-AAAAAACCTTGCTCAAGGTTGAGTTTGCATTTGTAAGACCTCCG
* * *
6953 GGTATAATTTCAGAAACCTCCGAGTATTAATTCTGATAAATCCTCCGGGTATCACCTCATTTCAT
65 GGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCACCTCATTTCAT
7018 -AAATTGTTAAT
130 CAAATTGTTAAT
* * *
7029 CGAATTTGCGTTTAAGTTTCAAAAAACCTTGCTCAAGGTTGAGTTTGCATTTGTAAGACCTTCGG
1 CAAAGTTGCGTTTAAGTTTCAAAAAACCTTGCTCAAGGTTGAGTTTGCATTTGTAAGACCTCCGG
* * *
7094 GCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCATCCGGTTATCACATCATTTCATC
66 GCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCACCTCATTTCATC
*
7159 AAGTTGTTAAT
131 AAATTGTTAAT
* *
7170 CAAAGTTGCATTTAAGTTTCAAAAAACCTTGCTCAAGGTTGACTTTGCATTTGTAAGACCTCCGG
1 CAAAGTTGCGTTTAAGTTTCAAAAAACCTTGCTCAAGGTTGAGTTTGCATTTGTAAGACCTCCGG
** * *
7235 GCATGATTTCAGAAACCTCCGGGTATCAATTCTGATAAATCCTCCAGGTATCACCTCATTTCATC
66 GCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCACCTCATTTCATC
*
7300 AAGTTGTTAAT
131 AAATTGTTAAT
* *
7311 CAAAGTTGCGTTTAAGTTTCAAAAAATCTTGCTCAAGGTTGAGTTTGCATTTGTAAGACCTCTGG
1 CAAAGTTGCGTTTAAGTTTCAAAAAACCTTGCTCAAGGTTGAGTTTGCATTTGTAAGACCTCCGG
*
7376 GCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCTGGGTATCACCTCATTTCAT-
66 GCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCACCTCATTTCATC
7440 AAATTGTTAAT
131 AAATTGTTAAT
*
7451 CAAAGTTGCGTTTAAGTTTCAAAAAAACCTTGCTCAAGGTTGAGTTTGCATTTGTAAGACCTCCA
1 CAAAGTTGCGTTTAAGTTTC-AAAAAACCTTGCTCAAGGTTGAGTTTGCATTTGTAAGACCTCCG
* ** * *
7516 GGCACAATTTCAAAAACCTCTTGGTATTAATTCTGATAAATCATCTGGGTATCACCTCATTTCAT
65 GGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCACCTCATTTCAT
*
7581 CAAGTTGTTAAT
130 CAAATTGTTAAT
* * * *
7593 CAAAGTTGCGCTTAAGTTTCAAAAAACCTTGCACAAGGTTGATTTTGCATTTGTAAAACCTCCGG
1 CAAAGTTGCGTTTAAGTTTCAAAAAACCTTGCTCAAGGTTGAGTTTGCATTTGTAAGACCTCCGG
* * * * * *
7658 GCACGATTTCAGAAACCTCTGAGTATTAATTCTTACAAGTCCTCCGGG
66 GCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGG
7706 CATCTGACAT
Statistics
Matches: 755, Mismatches: 60, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
140 131 0.17
141 595 0.79
142 29 0.04
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.33
Consensus pattern (141 bp):
CAAAGTTGCGTTTAAGTTTCAAAAAACCTTGCTCAAGGTTGAGTTTGCATTTGTAAGACCTCCGG
GCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCACCTCATTTCATC
AAATTGTTAAT
Found at i:6971 original size:22 final size:23
Alignment explanation
Indices: 6946--7004 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 23
6936 CATTTGTAAG
6946 ACCTCCGGGTATAATT-TCAGAA
1 ACCTCCGGGTATAATTCTCAGAA
* * *
6968 ACCTCCGAGTATTAATTCTGATAA
1 ACCTCCGGGTA-TAATTCTCAGAA
6992 ATCCTCCGGGTAT
1 A-CCTCCGGGTAT
7005 CACCTCATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 10 0.33
23 5 0.17
24 6 0.20
25 9 0.30
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.31
Consensus pattern (23 bp):
ACCTCCGGGTATAATTCTCAGAA
Found at i:7872 original size:40 final size:39
Alignment explanation
Indices: 7753--7900 Score: 167
Period size: 39 Copynumber: 3.8 Consensus size: 39
7743 AGGAACTATT
*
7753 TTGCTTTATTAGTTAA-TTCAGAAGCCTATTCAGGATCA
1 TTGCTTTATCAGTTAATTTCAGAAGCCTATTCAGGATCA
* * *
7791 TTGCTTTGTCAGTTAATTTCAGAAGCCTATTTAGGACCA
1 TTGCTTTATCAGTTAATTTCAGAAGCCTATTCAGGATCA
* *
7830 TTGCTTTATCAAGTTAATTTCAGAATCCTGTTCATGG-TCA
1 TTGCTTTATC-AGTTAATTTCAGAAGCCTATTCA-GGATCA
* * *
7870 TTGCTTTCTCGGTTAACTTCA-AAGTCCTATT
1 TTGCTTTATCAGTTAATTTCAGAAG-CCTATT
7901 TTAGGATATC
Statistics
Matches: 92, Mismatches: 14, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
38 16 0.17
39 43 0.47
40 31 0.34
41 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41
Consensus pattern (39 bp):
TTGCTTTATCAGTTAATTTCAGAAGCCTATTCAGGATCA
Found at i:7885 original size:79 final size:78
Alignment explanation
Indices: 7753--7906 Score: 197
Period size: 79 Copynumber: 2.0 Consensus size: 78
7743 AGGAACTATT
* * *
7753 TTGCTTTATTAGTTAATTCAGAAGCCTATTCAGGATCATTGCTTTGTCAGTTAATTTCAGAAG-C
1 TTGCTTTATAAGTTAATTCAGAAGCCTATTCAGGATCATTGCTTTCTCAGTTAACTTCA-AAGTC
7817 CTA-TTTAGGACCA
65 CTATTTTAGGACCA
* * *
7830 TTGCTTTATCAAGTTAATTTCAGAATCCTGTTCATGG-TCATTGCTTTCTCGGTTAACTTCAAAG
1 TTGCTTTAT-AAGTTAA-TTCAGAAGCCTATTCA-GGATCATTGCTTTCTCAGTTAACTTCAAAG
7894 TCCTATTTTAGGA
63 TCCTATTTTAGGA
7907 TATCTCCCAC
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
77 9 0.14
78 9 0.14
79 39 0.59
80 9 0.14
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41
Consensus pattern (78 bp):
TTGCTTTATAAGTTAATTCAGAAGCCTATTCAGGATCATTGCTTTCTCAGTTAACTTCAAAGTCC
TATTTTAGGACCA
Found at i:9394 original size:142 final size:142
Alignment explanation
Indices: 9138--9423 Score: 536
Period size: 142 Copynumber: 2.0 Consensus size: 142
9128 TGCACATGTG
* *
9138 CAAACATCATGGCATTTCATATAAGTTGCATTCATGTTAGAATTATCACGCATAGTTAATTACTT
1 CAAACATCATGGCATTTCATATAAGCTGCATTCATCTTAGAATTATCACGCATAGTTAATTACTT
9203 GACTTCCCCACCAAAATCATATCATATATTCATATTTCAGTTCATGTACACTCAAAATACCAAAA
66 GACTTCCCCACCAAAATCATATCATATATTCATATTTCAGTTCATGTACACTCAAAATACCAAAA
9268 ACAGAGCATACA
131 ACAGAGCATACA
9280 CAAACATCATGGCATTTCATATAAGCTGCATTCATCTTAGAATTATCACGCATAGTTAATTACTT
1 CAAACATCATGGCATTTCATATAAGCTGCATTCATCTTAGAATTATCACGCATAGTTAATTACTT
* *
9345 GACTTCCCCATCAATATCATATCATATATTCATATTTCAGTTCATGTACACTCAAAATACCAAAA
66 GACTTCCCCACCAAAATCATATCATATATTCATATTTCAGTTCATGTACACTCAAAATACCAAAA
9410 ACAGAGCATACA
131 ACAGAGCATACA
9422 CA
1 CA
9424 CATATAATTA
Statistics
Matches: 140, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
142 140 1.00
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (142 bp):
CAAACATCATGGCATTTCATATAAGCTGCATTCATCTTAGAATTATCACGCATAGTTAATTACTT
GACTTCCCCACCAAAATCATATCATATATTCATATTTCAGTTCATGTACACTCAAAATACCAAAA
ACAGAGCATACA
Done.