Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010044.1 Corchorus olitorius cultivar O-4 contig10076, 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: 6469
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Found at i:646 original size:26 final size:27
Alignment explanation
Indices: 617--685 Score: 86
Period size: 26 Copynumber: 2.6 Consensus size: 27
607 TCACCTATGA
*
617 GCATTTTGGTCATTTTTACACT-AGGG
1 GCATTTTGGTCATTTTCACACTCAGGG
* * *
643 GCATTTTGGTCATTTGCATATTCAGGG
1 GCATTTTGGTCATTTTCACACTCAGGG
*
670 GCATGTTGGTCATTTT
1 GCATTTTGGTCATTTT
686 AAGTCCACTT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
26 18 0.50
27 18 0.50
ACGTcount: A:0.17, C:0.14, G:0.25, T:0.43
Consensus pattern (27 bp):
GCATTTTGGTCATTTTCACACTCAGGG
Found at i:3350 original size:51 final size:50
Alignment explanation
Indices: 3295--3431 Score: 159
Period size: 50 Copynumber: 2.7 Consensus size: 50
3285 AGTGTAGTAT
3295 AATAAAAATATAATCTTT-ATGTTAAAAAATTGAATTTCGAGGCAATTTGTA
1 AATAAAAATATAATCTTTGA-G-TAAAAAATTGAATTTCGAGGCAATTTGTA
* * ** *
3346 AATAAAAATGTCATCTTTGAGTAAGCAATTGAATTTTGAGGCAATTTGTA
1 AATAAAAATATAATCTTTGAGTAAAAAATTGAATTTCGAGGCAATTTGTA
* * * * *
3396 AATAAAAATGTCACCTTTGAGTTAAAAATTGGATTT
1 AATAAAAATATAATCTTTGAGTAAAAAATTGAATTT
3432 TTATTTAAAA
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
50 57 0.76
51 17 0.23
52 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.36
Consensus pattern (50 bp):
AATAAAAATATAATCTTTGAGTAAAAAATTGAATTTCGAGGCAATTTGTA
Found at i:3426 original size:50 final size:49
Alignment explanation
Indices: 3319--3432 Score: 174
Period size: 50 Copynumber: 2.3 Consensus size: 49
3309 CTTTATGTTA
* *
3319 AAAAATTGAATTTCGAGGCAATTTGTAAATAAAAATGTCATCTTTGAGT
1 AAAAATTGAATTTTGAGGCAATTTGTAAATAAAAATGTCACCTTTGAGT
*
3368 AAGCAATTGAATTTTGAGGCAATTTGTAAATAAAAATGTCACCTTTGAGTT
1 AA-AAATTGAATTTTGAGGCAATTTGTAAATAAAAATGTCACCTTTGAG-T
*
3419 AAAAATTGGATTTT
1 AAAAATTGAATTTT
3433 TATTTAAAAG
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
49 2 0.03
50 53 0.91
51 3 0.05
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (49 bp):
AAAAATTGAATTTTGAGGCAATTTGTAAATAAAAATGTCACCTTTGAGT
Found at i:3584 original size:50 final size:51
Alignment explanation
Indices: 3438--3637 Score: 160
Period size: 50 Copynumber: 4.0 Consensus size: 51
3428 ATTTTTATTT
* * * *
3438 AAAAGTTCAAACTTTTAAGTAATTT-AAGAATAAAGATTGAAGTTTTAAGTG
1 AAAAGTTCAAACTTTTAAGTAATTTGTA-AATAAAGGTTGAATTTTTAAGTA
* * * * * * *
3489 GAAATTTGAAAC-TTTGAGAAATTTGTGAATAAAGTTTGAATTTTTAA-T-
1 AAAAGTTCAAACTTTTAAGTAATTTGTAAATAAAGGTTGAATTTTTAAGTA
* * * *
3537 CAAAGTTCAAACTTTTAAGCAATTTGTAAATAAAGGTTAAAATTTTTAATTA
1 AAAAGTTCAAACTTTTAAGTAATTTGTAAATAAAGGTT-GAATTTTTAAGTA
* * * *
3589 AAAAGATT-GAACTTTTAAGTAATTTGTAAGTAAAGATTG-GTTTTTAAGT
1 AAAAG-TTCAAACTTTTAAGTAATTTGTAAATAAAGGTTGAATTTTTAAGT
3638 GAAAGATGGA
Statistics
Matches: 118, Mismatches: 25, Indels: 13
0.76 0.16 0.08
Matches are distributed among these distances:
48 9 0.08
49 22 0.19
50 45 0.38
51 10 0.08
52 30 0.25
53 2 0.02
ACGTcount: A:0.42, C:0.04, G:0.15, T:0.39
Consensus pattern (51 bp):
AAAAGTTCAAACTTTTAAGTAATTTGTAAATAAAGGTTGAATTTTTAAGTA
Found at i:4704 original size:43 final size:44
Alignment explanation
Indices: 4597--4815 Score: 201
Period size: 43 Copynumber: 4.8 Consensus size: 44
4587 GTTTTCCCTC
*
4597 TTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCC-TAGTTTTCAA
1 TTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCTTA-TCTTCAA
* *
4641 TATCTCTTCAAAAACTGCCCCTTCCTGGTTGGAAGGTCCTTATCTTC-A
1 T-T-TC--CAAAAA-TGCCCCTTCCCGGTCGGAAGGTCCTTATCTTCAA
* * **
4689 TTTCCAAAAATGCCCCTTCCCGGTCGAAAGGTCCCAATTTTCGATATCTC
1 TTTCCAAAAATGCCCCTTCCCGGTCGGAAGGT-CC--TTATC--T-TCAA
* * *
4739 TTTCCAAAAATGCCCCTTCCCAGTCGGAAGGTCCTTGTTTTC-A
1 TTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCTTATCTTCAA
**
4782 TTTCCAAAAATGCCCCTTCCTAGTCGGAAGGTCC
1 TTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCC
4816 CAGTTTTCCT
Statistics
Matches: 148, Mismatches: 14, Indels: 27
0.78 0.07 0.14
Matches are distributed among these distances:
43 52 0.35
44 11 0.07
45 2 0.01
46 8 0.05
47 4 0.03
48 9 0.06
49 30 0.20
50 32 0.22
ACGTcount: A:0.22, C:0.31, G:0.16, T:0.31
Consensus pattern (44 bp):
TTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCTTATCTTCAA
Found at i:4813 original size:93 final size:92
Alignment explanation
Indices: 4597--4823 Score: 330
Period size: 93 Copynumber: 2.5 Consensus size: 92
4587 GTTTTCCCTC
*
4597 TTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCTAGTTTTCAATATCTCTTCAAAAACTGCCCC
1 TTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCAGTTTTCAATATCTCTTCAAAAACTGCCCC
** *
4662 TTCCTGGTTGGAAGGTCCTTATCTTCA
66 TTCCCAGTCGGAAGGTCCTTATCTTCA
* * *
4689 TTTCCAAAAATGCCCCTTCCCGGTCGAAAGGTCCCAATTTTCGATATCTCTTTCCAAAAA-TGCC
1 TTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCAGTTTTCAATATCTC-TT-CAAAAACTGCC
* *
4753 CCTTCCCAGTCGGAAGGTCCTTGTTTTCA
64 CCTTCCCAGTCGGAAGGTCCTTATCTTCA
**
4782 TTTCCAAAAATGCCCCTTCCTAGTCGGAAGGTCCCAGTTTTC
1 TTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCAGTTTTC
4824 CTTCGATAAT
Statistics
Matches: 120, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
92 46 0.38
93 68 0.57
94 6 0.05
ACGTcount: A:0.22, C:0.30, G:0.16, T:0.32
Consensus pattern (92 bp):
TTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCAGTTTTCAATATCTCTTCAAAAACTGCCCC
TTCCCAGTCGGAAGGTCCTTATCTTCA
Found at i:4888 original size:41 final size:40
Alignment explanation
Indices: 4831--5112 Score: 298
Period size: 41 Copynumber: 7.0 Consensus size: 40
4821 TTCCTTCGAT
* *
4831 AATTCCTAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTTA
1 AATTCCCAGTTTGTCCTTCCTCATCGGAAGGTGTTG-TTTA
* * *
4872 AATTCCCGGTTTGCCCTTCCTCATCGGAAGGTGTTG-TCA
1 AATTCCCAGTTTGTCCTTCCTCATCGGAAGGTGTTGTTTA
* * *
4911 GCATTCCCCGTTTGTCCTTCCTCATCGGAAGGTATTGTTTA
1 -AATTCCCAGTTTGTCCTTCCTCATCGGAAGGTGTTGTTTA
* * *
4952 AGTTCACCAGTTTGTCCTTCCTCACCGGAAGGTGTTG-TCA
1 AATTC-CCAGTTTGTCCTTCCTCATCGGAAGGTGTTGTTTA
* * * *
4992 GCATTCCCCGTTTGTCCTTCCTCATTGGAAGGTATTGTTTA
1 -AATTCCCAGTTTGTCCTTCCTCATCGGAAGGTGTTGTTTA
* * * *
5033 AGTTCACCAGTTTGTCCTTCCTCACCGGAAGGCGTTATTTA
1 AATTC-CCAGTTTGTCCTTCCTCATCGGAAGGTGTTGTTTA
* * * *
5074 GATTTCCAGTTTGCCCTTCCTCATCGGAACGTGTTGTTT
1 AATTCCCAGTTTGTCCTTCCTCATCGGAAGGTGTTGTTT
5113 CAAGCCCATT
Statistics
Matches: 198, Mismatches: 37, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
39 2 0.01
40 96 0.48
41 100 0.51
ACGTcount: A:0.16, C:0.26, G:0.21, T:0.38
Consensus pattern (40 bp):
AATTCCCAGTTTGTCCTTCCTCATCGGAAGGTGTTGTTTA
Found at i:4971 original size:81 final size:81
Alignment explanation
Indices: 4839--5112 Score: 381
Period size: 81 Copynumber: 3.4 Consensus size: 81
4829 ATAATTCCTA
* * * * *
4839 GTTTGCCCTTCCTCATCGGAAGGTGTTGTTTTAAATTC-CCGGTTTGCCCTTCCTCATCGGAAGG
1 GTTTGCCCTTCCTCATCGGAAGGTATTG-TTTAAGTTCACCAGTTTGTCCTTCCTCACCGGAAGG
4903 TGTTGTCAGCATTCCCC
65 TGTTGTCAGCATTCCCC
*
4920 GTTTGTCCTTCCTCATCGGAAGGTATTGTTTAAGTTCACCAGTTTGTCCTTCCTCACCGGAAGGT
1 GTTTGCCCTTCCTCATCGGAAGGTATTGTTTAAGTTCACCAGTTTGTCCTTCCTCACCGGAAGGT
4985 GTTGTCAGCATTCCCC
66 GTTGTCAGCATTCCCC
* * *
5001 GTTTGTCCTTCCTCATTGGAAGGTATTGTTTAAGTTCACCAGTTTGTCCTTCCTCACCGGAAGGC
1 GTTTGCCCTTCCTCATCGGAAGGTATTGTTTAAGTTCACCAGTTTGTCCTTCCTCACCGGAAGGT
* * * *
5066 GTTATTTAG-ATTTCCA
66 GTT-GTCAGCATTCCCC
* *
5082 GTTTGCCCTTCCTCATCGGAACGTGTTGTTT
1 GTTTGCCCTTCCTCATCGGAAGGTATTGTTT
5113 CAAGCCCATT
Statistics
Matches: 175, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
80 8 0.05
81 164 0.94
82 3 0.02
ACGTcount: A:0.15, C:0.26, G:0.21, T:0.38
Consensus pattern (81 bp):
GTTTGCCCTTCCTCATCGGAAGGTATTGTTTAAGTTCACCAGTTTGTCCTTCCTCACCGGAAGGT
GTTGTCAGCATTCCCC
Done.