Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024148.1 Corchorus olitorius cultivar O-4 contig24181, 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: 3897
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Found at i:422 original size:12 final size:11
Alignment explanation
Indices: 406--438 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
396 AAAATCTAAA
406 CAAAAAAAAAG
1 CAAAAAAAAAG
417 CAAAAAAAAAG
1 CAAAAAAAAAG
428 CAAAAACAAAA
1 CAAAAA-AAAA
439 AAAAAAGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.82, C:0.12, G:0.06, T:0.00
Consensus pattern (11 bp):
CAAAAAAAAAG
Found at i:443 original size:11 final size:11
Alignment explanation
Indices: 403--444 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
393 AAAAAAATCT
403 AAACAAAAAAA
1 AAACAAAAAAA
*
414 AAGCAAAAAAA
1 AAACAAAAAAA
*
425 AAGCAAAAACAA
1 AAACAAAAA-AA
437 AAA-AAAAA
1 AAACAAAAA
445 GTGAAAATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 24 0.86
12 4 0.14
ACGTcount: A:0.86, C:0.10, G:0.05, T:0.00
Consensus pattern (11 bp):
AAACAAAAAAA
Found at i:810 original size:22 final size:22
Alignment explanation
Indices: 784--842 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
774 GTGCATACAA
*
784 AAAAAATGATGAAAATGAAAATG
1 AAAAAATGAAGAAAATG-AAATG
*
807 -AAAAATGAAAAAAATGAAATG
1 AAAAAATGAAGAAAATGAAATG
828 AAAAAATGAAGAAAA
1 AAAAAATGAAGAAAA
843 GAAGCTCTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.16
22 27 0.84
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.14
Consensus pattern (22 bp):
AAAAAATGAAGAAAATGAAATG
Found at i:831 original size:13 final size:14
Alignment explanation
Indices: 809--837 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
799 TGAAAATGAA
809 AAATGAAAAAAATG
1 AAATGAAAAAAATG
823 AAATG-AAAAAATG
1 AAATGAAAAAAATG
836 AA
1 AA
838 GAAAAGAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
AAATGAAAAAAATG
Found at i:1173 original size:50 final size:50
Alignment explanation
Indices: 1117--1215 Score: 162
Period size: 50 Copynumber: 2.0 Consensus size: 50
1107 AAGTTTCATA
** *
1117 ATAAGATTGCATTCCATTTGTGAGTCTGATATCAAAATTCGATTTTCAAG
1 ATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGATTTTCAAG
*
1167 ATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAA
1 ATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGATTTTCAA
1216 AGGGCATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.36
Consensus pattern (50 bp):
ATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGATTTTCAAG
Found at i:1860 original size:68 final size:68
Alignment explanation
Indices: 1770--2014 Score: 393
Period size: 68 Copynumber: 3.6 Consensus size: 68
1760 AAGTCAGAAC
*
1770 CGTTTCCATACGAGTCAGTTTAGCCTTGGTTCCATCCAAGCAGCAGGGGCTTTTCTACAAGCGAA
1 CGTTTCCATACGAGTCAGTTTAGCCTTGGTTCCATCCAAGCAGCAGGGGCTTTTCTACAAGCCAA
1835 ACT
66 ACT
* * * *
1838 CGTTTCCATACGAGTCAGTTTAGCCTTGGTTCCATCCAAGCATTCAGGAGCTTTTCCACGAGCCA
1 CGTTTCCATACGAGTCAGTTTAGCCTTGGTTCCATCCAAGCA-GCAGGGGCTTTTCTACAAGCCA
1903 AACT
65 AACT
* *
1907 CGTTTCCATACGAGTCAGTTTAGCCTTGGTTCCATCCAAGCAGCAAGGGC-TTTCTCATAAGCCA
1 CGTTTCCATACGAGTCAGTTTAGCCTTGGTTCCATCCAAGCAGCAGGGGCTTTTCT-ACAAGCCA
1971 AACT
65 AACT
*
1975 CGTTTCCATACGAGTCAGTTTAGCCTTGGTCCCATCCAAG
1 CGTTTCCATACGAGTCAGTTTAGCCTTGGTTCCATCCAAG
2015 TTCAGTGAGG
Statistics
Matches: 163, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
67 4 0.02
68 96 0.59
69 63 0.39
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (68 bp):
CGTTTCCATACGAGTCAGTTTAGCCTTGGTTCCATCCAAGCAGCAGGGGCTTTTCTACAAGCCAA
ACT
Found at i:1997 original size:137 final size:136
Alignment explanation
Indices: 1770--2031 Score: 438
Period size: 137 Copynumber: 1.9 Consensus size: 136
1760 AAGTCAGAAC
* *
1770 CGTTTCCATACGAGTCAGTTTAGCCTTGGTTCCATCCAAGCAGCAGGGGCTTTTCTACAAGCGAA
1 CGTTTCCATACGAGTCAGTTTAGCCTTGGTTCCATCCAAGCAGCAAGGGCTTTTCTACAAGCCAA
*
1835 ACTCGTTTCCATACGAGTCAGTTTAGCCTTGGTTCCATCCAAGCATTCAG-GAGCTTTTCCACGA
66 ACTCGTTTCCATACGAGTCAGTTTAGCCTTGGTCCCATCCAAG--TTCAGTGAGCTTTTCCACGA
1899 GCCAAACT
129 GCCAAACT
*
1907 CGTTTCCATACGAGTCAGTTTAGCCTTGGTTCCATCCAAGCAGCAAGGGC-TTTCTCATAAGCCA
1 CGTTTCCATACGAGTCAGTTTAGCCTTGGTTCCATCCAAGCAGCAAGGGCTTTTCT-ACAAGCCA
*
1971 AACTCGTTTCCATACGAGTCAGTTTAGCCTTGGTCCCATCCAAGTTCAGTGAGGTTTTCCA
65 AACTCGTTTCCATACGAGTCAGTTTAGCCTTGGTCCCATCCAAGTTCAGTGAGCTTTTCCA
2032 AACCGGACTC
Statistics
Matches: 118, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
135 5 0.04
136 15 0.13
137 98 0.83
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.29
Consensus pattern (136 bp):
CGTTTCCATACGAGTCAGTTTAGCCTTGGTTCCATCCAAGCAGCAAGGGCTTTTCTACAAGCCAA
ACTCGTTTCCATACGAGTCAGTTTAGCCTTGGTCCCATCCAAGTTCAGTGAGCTTTTCCACGAGC
CAAACT
Found at i:2114 original size:16 final size:16
Alignment explanation
Indices: 2093--2123 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2083 TTAAGCTTGT
2093 TTCCATACAAGTTAAG
1 TTCCATACAAGTTAAG
*
2109 TTCCATCCAAGTTAA
1 TTCCATACAAGTTAA
2124 TCTTTTCTCG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.10, T:0.32
Consensus pattern (16 bp):
TTCCATACAAGTTAAG
Found at i:2186 original size:47 final size:47
Alignment explanation
Indices: 2124--2477 Score: 489
Period size: 47 Copynumber: 7.5 Consensus size: 47
2114 TCCAAGTTAA
2124 TCTTTTCTCGCTTCCACGCGAGTCTACGATTTGGTGACCAAAGTTGG
1 TCTTTTCTCGCTTCCACGCGAGTCTACGATTTGGTGACCAAAGTTGG
* * * * *
2171 TCTTTTCTCACTTCCATGCGA-CCTTACAATTTAGTGACCAAAGTTGG
1 TCTTTTCTCGCTTCCACGCGAGTC-TACGATTTGGTGACCAAAGTTGG
*
2218 TCTTTTCTCGCTTCCACGCGAGTCTACGATTTGGTGAGCAAAGTTGG
1 TCTTTTCTCGCTTCCACGCGAGTCTACGATTTGGTGACCAAAGTTGG
* * * * *
2265 TCTTTTCTCGCTTCCATGCGA-ACTTACAATTTAGTGACCAAGGTTGG
1 TCTTTTCTCGCTTCCACGCGAGTC-TACGATTTGGTGACCAAAGTTGG
* *
2312 TCTTTTCTCCCTTCCACGCGAGACTACGATTTGGTGACCAAAGTTGG
1 TCTTTTCTCGCTTCCACGCGAGTCTACGATTTGGTGACCAAAGTTGG
* * * *
2359 TCTTTTCTCGCTTCCATGCGA-ACTTACAATTTAGTGACCAAAGTTGG
1 TCTTTTCTCGCTTCCACGCGAGTC-TACGATTTGGTGACCAAAGTTGG
*
2406 TCTTTTCTTGCTTCCACGCGAGTCTACGATTTGGTGACCAAAGTTGG
1 TCTTTTCTCGCTTCCACGCGAGTCTACGATTTGGTGACCAAAGTTGG
*
2453 TCTTTTCTCGCTTCCATGCGAGTCT
1 TCTTTTCTCGCTTCCACGCGAGTCT
2478 TCAATTTCAG
Statistics
Matches: 268, Mismatches: 33, Indels: 12
0.86 0.11 0.04
Matches are distributed among these distances:
46 4 0.01
47 260 0.97
48 4 0.01
ACGTcount: A:0.19, C:0.25, G:0.20, T:0.36
Consensus pattern (47 bp):
TCTTTTCTCGCTTCCACGCGAGTCTACGATTTGGTGACCAAAGTTGG
Found at i:2484 original size:94 final size:94
Alignment explanation
Indices: 2124--2473 Score: 637
Period size: 94 Copynumber: 3.7 Consensus size: 94
2114 TCCAAGTTAA
*
2124 TCTTTTCTCGCTTCCACGCGAGTCTACGATTTGGTGACCAAAGTTGGTCTTTTCTCACTTCCATG
1 TCTTTTCTCGCTTCCACGCGAGTCTACGATTTGGTGACCAAAGTTGGTCTTTTCTCGCTTCCATG
*
2189 CGACCTTACAATTTAGTGACCAAAGTTGG
66 CGAACTTACAATTTAGTGACCAAAGTTGG
*
2218 TCTTTTCTCGCTTCCACGCGAGTCTACGATTTGGTGAGCAAAGTTGGTCTTTTCTCGCTTCCATG
1 TCTTTTCTCGCTTCCACGCGAGTCTACGATTTGGTGACCAAAGTTGGTCTTTTCTCGCTTCCATG
*
2283 CGAACTTACAATTTAGTGACCAAGGTTGG
66 CGAACTTACAATTTAGTGACCAAAGTTGG
* *
2312 TCTTTTCTCCCTTCCACGCGAGACTACGATTTGGTGACCAAAGTTGGTCTTTTCTCGCTTCCATG
1 TCTTTTCTCGCTTCCACGCGAGTCTACGATTTGGTGACCAAAGTTGGTCTTTTCTCGCTTCCATG
2377 CGAACTTACAATTTAGTGACCAAAGTTGG
66 CGAACTTACAATTTAGTGACCAAAGTTGG
*
2406 TCTTTTCTTGCTTCCACGCGAGTCTACGATTTGGTGACCAAAGTTGGTCTTTTCTCGCTTCCATG
1 TCTTTTCTCGCTTCCACGCGAGTCTACGATTTGGTGACCAAAGTTGGTCTTTTCTCGCTTCCATG
2471 CGA
66 CGA
2474 GTCTTCAATT
Statistics
Matches: 245, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
94 245 1.00
ACGTcount: A:0.19, C:0.25, G:0.20, T:0.35
Consensus pattern (94 bp):
TCTTTTCTCGCTTCCACGCGAGTCTACGATTTGGTGACCAAAGTTGGTCTTTTCTCGCTTCCATG
CGAACTTACAATTTAGTGACCAAAGTTGG
Found at i:2760 original size:49 final size:49
Alignment explanation
Indices: 2688--2787 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
2678 ATAATTAAAA
2688 AAGTTCGCAAAGAGGGGCAGCTGTAGACACCCAATTTTGGGTTTAGGAT
1 AAGTTCGCAAAGAGGGGCAGCTGTAGACACCCAATTTTGGGTTTAGGAT
2737 AAGTTCGCAAAGAGGGGCAGCTGTAGACACCCAATTTTGGGTTTAGGAT
1 AAGTTCGCAAAGAGGGGCAGCTGTAGACACCCAATTTTGGGTTTAGGAT
2786 AA
1 AA
2788 TTAATCTCCT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.24
Consensus pattern (49 bp):
AAGTTCGCAAAGAGGGGCAGCTGTAGACACCCAATTTTGGGTTTAGGAT
Done.