Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018465.1 Corchorus olitorius cultivar O-4 contig18498, 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: 27229
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Found at i:1909 original size:31 final size:31
Alignment explanation
Indices: 1768--1908 Score: 149
Period size: 31 Copynumber: 4.5 Consensus size: 31
1758 GCATGCCATG
** * * **
1768 TGTCACTTTTTGGTACACATGACGTGACATG
1 TGTCACTTTTTGGTACATGTGGCGTGCCACA
* *
1799 TGTCACTTTTTGGTACATGTGGCGTACCACT
1 TGTCACTTTTTGGTACATGTGGCGTGCCACA
*
1830 TGTCACTTTTTGGTACATGTGGTGTGCCACA
1 TGTCACTTTTTGGTACATGTGGCGTGCCACA
* *
1861 TGTCGCTTTTTGGTACACT-TGGCGTGTCACA
1 TGTCACTTTTTGGTACA-TGTGGCGTGCCACA
* *
1892 TGTCGCTTTTTAGTACA
1 TGTCACTTTTTGGTACA
1909 CATGGCATGC
Statistics
Matches: 95, Mismatches: 14, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
31 94 0.99
32 1 0.01
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.39
Consensus pattern (31 bp):
TGTCACTTTTTGGTACATGTGGCGTGCCACA
Found at i:7532 original size:149 final size:148
Alignment explanation
Indices: 7255--7571 Score: 483
Period size: 149 Copynumber: 2.1 Consensus size: 148
7245 CGGTCTCATT
* * ** * * *
7255 GGAGACGTTCATTTCTTTTTTTTTATACGGGGACACCTGGGCTGGTGTTTGACCGTTTGTGACGA
1 GGAGACGATCATTT-TGTTTTTTTATACGGGGACACCAAGGCTGGTGTTCGACCGTTCGTAACGA
*
7320 AAGTCTCTAAGGAGACGATCGTTTTTTTTTATTATACGGGGACACCAAGGCTGGTGTTCGGCCGT
65 AAGTCTCAAAGGAGACGATCGTTTTTTTTTATTATACGGGGACACCAAGGCTGGTGTTCGGCCGT
7385 TCGTAACGAGAGTCTCAAA
130 TCGTAACGAGAGTCTCAAA
* *
7404 GGAGACGATCATTTTGTTTTTTTATACGGGGACACCAAGGCTGGTGTTCGGCCGTTCGTAACGAG
1 GGAGACGATCATTTTGTTTTTTTATACGGGGACACCAAGGCTGGTGTTCGACCGTTCGTAACGAA
*
7469 AGTCTCAAAGGAGACGATCGTTTTGTTTATT-TTATACGGGGACACCAAGGTTGGTGTTCGGCCG
66 AGTCTCAAAGGAGACGATCGTTTT-TTT-TTATTATACGGGGACACCAAGGCTGGTGTTCGGCCG
*
7533 TTCGTAACGAGGGTCTCAAA
129 TTCGTAACGAGAGTCTCAAA
*
7553 GGAGACGATCGTTTTGTTT
1 GGAGACGATCATTTTGTTT
7572 GCTTCTTCAA
Statistics
Matches: 153, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
148 66 0.43
149 85 0.56
150 2 0.01
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (148 bp):
GGAGACGATCATTTTGTTTTTTTATACGGGGACACCAAGGCTGGTGTTCGACCGTTCGTAACGAA
AGTCTCAAAGGAGACGATCGTTTTTTTTTATTATACGGGGACACCAAGGCTGGTGTTCGGCCGTT
CGTAACGAGAGTCTCAAA
Found at i:7568 original size:75 final size:74
Alignment explanation
Indices: 7272--7571 Score: 476
Period size: 74 Copynumber: 4.0 Consensus size: 74
7262 TTCATTTCTT
** * * * * * *
7272 TTTTTTTATACGGGGACACCTGGGCTGGTGTTTGACCGTTTGTGACGAAAGTCTCTAAGGAGACG
1 TTTTTTTATACGGGGACACCAAGGCTGGTGTTCGGCCGTTCGTAACGAGAGTCTCAAAGGAGACG
7337 ATCGTTTT-
66 ATCGTTTTG
7345 TTTTTATTATACGGGGACACCAAGGCTGGTGTTCGGCCGTTCGTAACGAGAGTCTCAAAGGAGAC
1 TTTTT-TTATACGGGGACACCAAGGCTGGTGTTCGGCCGTTCGTAACGAGAGTCTCAAAGGAGAC
*
7410 GATCATTTTG
65 GATCGTTTTG
7420 TTTTTTTATACGGGGACACCAAGGCTGGTGTTCGGCCGTTCGTAACGAGAGTCTCAAAGGAGACG
1 TTTTTTTATACGGGGACACCAAGGCTGGTGTTCGGCCGTTCGTAACGAGAGTCTCAAAGGAGACG
7485 ATCGTTTTG
66 ATCGTTTTG
* *
7494 TTTATTTTATACGGGGACACCAAGGTTGGTGTTCGGCCGTTCGTAACGAGGGTCTCAAAGGAGAC
1 TTT-TTTTATACGGGGACACCAAGGCTGGTGTTCGGCCGTTCGTAACGAGAGTCTCAAAGGAGAC
7559 GATCGTTTTG
65 GATCGTTTTG
7569 TTT
1 TTT
7572 GCTTCTTCAA
Statistics
Matches: 212, Mismatches: 12, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
73 5 0.02
74 130 0.61
75 77 0.36
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (74 bp):
TTTTTTTATACGGGGACACCAAGGCTGGTGTTCGGCCGTTCGTAACGAGAGTCTCAAAGGAGACG
ATCGTTTTG
Found at i:15770 original size:186 final size:193
Alignment explanation
Indices: 15457--15950 Score: 591
Period size: 186 Copynumber: 2.5 Consensus size: 193
15447 GGTGCCAAAG
* *
15457 GATTTGGAACGGAGTTGGCACGAATTTTCCCCATGTAGGTTCCAAATGTCGTGCGAAAGTTGTTT
1 GATTTGGAACGGAGTTGGCACGAGTTTTCCCCATGTAGGTTCCAAATGTCGTGCCAAAGTTG-TT
** * *
15522 TTTTTTTTTAAAAAAAAAGATTTCACCCAGTCAAAATAATGTCTGTAGAGGGAATCAAATTAAAT
65 TTTTTTTAAAAAAAAAAAGATTTCACCCAGTCAAAATAATGTCTGTAGAAGGAATCAAATTAAAA
*
15587 ACCTCACC--T--TCCCTCCTTAAATTCCACTATGGTAGCATTCAATTGA-TTT-T-A-T-TTA
130 ACCTCACCTTTACTCCCTCCTTAAATTCCACTATGGCAGCATTCAATTGATTTTGTCACTATTA
15642 GATTTGGAACGGAGTTCGGCACGAGTTTTCCCCATGTAGGTTCCAAATGTCGTGCCAAAGTTGTT
1 GATTTGGAACGGAGTT-GGCACGAGTTTTCCCCATGTAGGTTCCAAATGTCGTGCCAAAGTTGTT
*
15707 TTTTTTTAAAAAAAAAAAGAATTTCACCCGGTCAAAATAATGTCTGTAGAAGGAATCAAATTAAA
65 TTTTTTTAAAAAAAAAAAG-ATTTCACCCAGTCAAAATAATGTCTGTAGAAGGAATCAAATTAAA
*
15772 AACCTCACCTAATTTTGCAGGAAAGAGCTTCCCTTCTTAAATTCCACTATGGCAGCATTCAATTG
129 AACCTCACC----TTT---------A-C-TCCCTCCTTAAATTCCACTATGGCAGCATTCAATTG
15837 ATTTTGTCACGTGATTA
179 ATTTTGTCAC-T-ATTA
* * *
15854 GATTTGGAAGGGAGTTTGGCACGAGTTTTCCCCATTTAGGTTCCAAATGTCGTGCCAAA-TT-TG
1 GATTTGGAACGGAG-TTGGCACGAGTTTTCCCCATGTAGGTTCCAAATGTCGTGCCAAAGTTGTT
*
15917 TTTTTTTAATAAAAAAAA-A-TTCACCCAGTCAAAA
65 TTTTTTTAAAAAAAAAAAGATTTCACCCAGTCAAAA
15951 CCAGTGTTTT
Statistics
Matches: 266, Mismatches: 14, Indels: 36
0.84 0.04 0.11
Matches are distributed among these distances:
185 35 0.13
186 95 0.36
192 1 0.00
205 35 0.13
206 3 0.01
207 15 0.06
208 2 0.01
210 19 0.07
211 2 0.01
212 57 0.21
213 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (193 bp):
GATTTGGAACGGAGTTGGCACGAGTTTTCCCCATGTAGGTTCCAAATGTCGTGCCAAAGTTGTTT
TTTTTTAAAAAAAAAAAGATTTCACCCAGTCAAAATAATGTCTGTAGAAGGAATCAAATTAAAAA
CCTCACCTTTACTCCCTCCTTAAATTCCACTATGGCAGCATTCAATTGATTTTGTCACTATTA
Found at i:16617 original size:57 final size:60
Alignment explanation
Indices: 16506--16622 Score: 159
Period size: 57 Copynumber: 2.0 Consensus size: 60
16496 TTAGTCCCAA
** * *
16506 ATAACACGTGTATATATTATAGTATAAATATCTTTATAAAGCTTTACCTATAAAAAGTGT
1 ATAACACGTGTATATATTATAGTATAAATATCAGTATAAAGATGTACCTATAAAAAGTGT
* *
16566 ATAACACGTGTATATA-TATA-TATATATAT-AGTATAAATATGTACCTATAAAAAGTGT
1 ATAACACGTGTATATATTATAGTATAAATATCAGTATAAAGATGTACCTATAAAAAGTGT
16623 GTATATATAT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
57 23 0.45
58 8 0.16
59 4 0.08
60 16 0.31
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.38
Consensus pattern (60 bp):
ATAACACGTGTATATATTATAGTATAAATATCAGTATAAAGATGTACCTATAAAAAGTGT
Found at i:18995 original size:54 final size:54
Alignment explanation
Indices: 18828--18996 Score: 176
Period size: 54 Copynumber: 3.1 Consensus size: 54
18818 GTGCCTGTTT
* *
18828 GAAAATCTCGTGCCAAATAGCATGACAAATTTGAGAGCCATTCCAAATTCCGTGA
1 GAAAATCTCGTGCCAAATAACATGAC-AATTTGAGAGCCGTTCCAAATTCCGTGA
*** * * * * * * * * *
18883 GAAAAAAACAATGCCAAATACCGTGCCAATTTGAGAGCTGTGCCAAATACAGTCA
1 GAAAATCTC-GTGCCAAATAACATGACAATTTGAGAGCCGTTCCAAATTCCGTGA
* *
18938 GAAAATCTCGTGCCAAACAACATGACAATTTGAGAGCCGTTCAAAATTCCGTGA
1 GAAAATCTCGTGCCAAATAACATGACAATTTGAGAGCCGTTCCAAATTCCGTGA
18992 GAAAA
1 GAAAA
18997 GACAATGCCA
Statistics
Matches: 86, Mismatches: 27, Indels: 3
0.74 0.23 0.03
Matches are distributed among these distances:
54 39 0.45
55 34 0.40
56 13 0.15
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (54 bp):
GAAAATCTCGTGCCAAATAACATGACAATTTGAGAGCCGTTCCAAATTCCGTGA
Found at i:23056 original size:14 final size:14
Alignment explanation
Indices: 23037--23078 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
23027 GCCACATGCT
23037 TTATTATCTTCTCC
1 TTATTATCTTCTCC
*
23051 TTATTATC-TC-CA
1 TTATTATCTTCTCC
*
23063 TTATTATTTTCTCC
1 TTATTATCTTCTCC
23077 TT
1 TT
23079 TTCCTTTACA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
12 8 0.35
13 4 0.17
14 11 0.48
ACGTcount: A:0.17, C:0.24, G:0.00, T:0.60
Consensus pattern (14 bp):
TTATTATCTTCTCC
Found at i:23496 original size:91 final size:93
Alignment explanation
Indices: 23335--23505 Score: 274
Period size: 91 Copynumber: 1.9 Consensus size: 93
23325 GCTGTGGAGA
* * *
23335 TTTAACACACTCAACATTCTATATAATACAAAATGACTAGAGAATATCTGCAGCTTTCATCGTTT
1 TTTAACACACTCAACATTCTATATAATACAAAATGACTAGAGAATATATGCAGCTTTCAGCCTTT
*
23400 GATAAGTTTAATGCTGAAACGCTAGAGT
66 AATAAGTTTAATGCTGAAACGCTAGAGT
* *
23428 TTTAACACACTCAACA-TCTATATAATA-TAAATTACTAGAGAATATATGCAGCTTTCAGCCTTT
1 TTTAACACACTCAACATTCTATATAATACAAAATGACTAGAGAATATATGCAGCTTTCAGCCTTT
23491 AATAAGTTTAATGCT
66 AATAAGTTTAATGCT
23506 CCTCTTGCAA
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
91 45 0.62
92 11 0.15
93 16 0.22
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (93 bp):
TTTAACACACTCAACATTCTATATAATACAAAATGACTAGAGAATATATGCAGCTTTCAGCCTTT
AATAAGTTTAATGCTGAAACGCTAGAGT
Found at i:27010 original size:69 final size:70
Alignment explanation
Indices: 26870--27025 Score: 219
Period size: 69 Copynumber: 2.2 Consensus size: 70
26860 CAGATCTTGG
*
26870 CCAAGTCCTGTCCAGGACTTGGGTTGTTGAGGTATGCAGAAATACAGAACAAGACCGGGGCAGGA
1 CCAAGTCCTGTCCAGGACTTGGGCTGTTGAGGTATGCAGAAATACAGAACAAGACCGGGGCAGGA
26935 GTTAC
66 GTTAC
* * * *
26940 CCAAGTCCTGTCCCGGACTTGTGCTGTTGAGG-A-GC-GCAAATTACAGGACAAGACCTGGGCAG
1 CCAAGTCCTGTCCAGGACTTGGGCTGTTGAGGTATGCAG-AAA-TACAGAACAAGACCGGGGCAG
27002 GAGTTAC
64 GAGTTAC
*
27009 CCAAGTCCTGTTCAGGA
1 CCAAGTCCTGTCCAGGA
27026 GTTGTTGCGG
Statistics
Matches: 77, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
67 1 0.01
68 5 0.06
69 42 0.55
70 29 0.38
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.21
Consensus pattern (70 bp):
CCAAGTCCTGTCCAGGACTTGGGCTGTTGAGGTATGCAGAAATACAGAACAAGACCGGGGCAGGA
GTTAC
Done.