Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014982.1 Corchorus olitorius cultivar O-4 contig15015, 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: 80369
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Found at i:9634 original size:43 final size:42
Alignment explanation
Indices: 9573--9654 Score: 137
Period size: 42 Copynumber: 1.9 Consensus size: 42
9563 GCTAAGCCTT
9573 GAAAATTCTTTGTAAATTAAAAAAATACTCAACTCAAATCATA
1 GAAAATTCTTTGTAAATT-AAAAAATACTCAACTCAAATCATA
**
9616 GAAAATTCTTTGTAAATTAAGCAATACTCAACTCAAATC
1 GAAAATTCTTTGTAAATTAAAAAATACTCAACTCAAATC
9655 CTGATCCTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
42 19 0.51
43 18 0.49
ACGTcount: A:0.48, C:0.16, G:0.06, T:0.30
Consensus pattern (42 bp):
GAAAATTCTTTGTAAATTAAAAAATACTCAACTCAAATCATA
Found at i:9789 original size:55 final size:56
Alignment explanation
Indices: 9719--9830 Score: 217
Period size: 56 Copynumber: 2.0 Consensus size: 56
9709 TTTATTTTGT
9719 AGAATAATTAAGTAGAGAT-AGGGGATATGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATAAGGGGATATGATTTATTATAACATTTATTGTGTGAA
9774 AGAATAATTAAGTAGAGATAAGGGGATATGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATAAGGGGATATGATTTATTATAACATTTATTGTGTGAA
9830 A
1 A
9831 AGGAAACACA
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 19 0.34
56 37 0.66
ACGTcount: A:0.41, C:0.02, G:0.21, T:0.36
Consensus pattern (56 bp):
AGAATAATTAAGTAGAGATAAGGGGATATGATTTATTATAACATTTATTGTGTGAA
Found at i:9950 original size:11 final size:10
Alignment explanation
Indices: 9920--9944 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
9910 GACAAATGAG
9920 AAAAGACAAA
1 AAAAGACAAA
9930 AAAAGACAAA
1 AAAAGACAAA
9940 AAAAG
1 AAAAG
9945 TTCAAATGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.80, C:0.08, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAGACAAA
Found at i:20520 original size:31 final size:31
Alignment explanation
Indices: 20478--20541 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
20468 GATGAGAAGA
* * *
20478 AATCAAATAGGCTCTATCAACTAGGAACATG
1 AATCAAATAGGCACCATAAACTAGGAACATG
* *
20509 AATCAATTAGGCACCATAAACTAGGAGCATG
1 AATCAAATAGGCACCATAAACTAGGAACATG
20540 AA
1 AA
20542 CCAGGTAAGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.20
Consensus pattern (31 bp):
AATCAAATAGGCACCATAAACTAGGAACATG
Found at i:21828 original size:31 final size:32
Alignment explanation
Indices: 21792--21860 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
21782 CATTGGTCCT
*
21792 TAATTAG-AAGAGGAAATTAATGAATGAATAA
1 TAATTAGAAAGAGGAAAATAATGAATGAATAA
21823 TAATTAGAAAAAGAGGAAAATAATGAATGAATAA
1 TAATTAG--AAAGAGGAAAATAATGAATGAATAA
21857 TAAT
1 TAAT
21861 AAATAATTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
31 7 0.21
34 27 0.79
ACGTcount: A:0.58, C:0.00, G:0.17, T:0.25
Consensus pattern (32 bp):
TAATTAGAAAGAGGAAAATAATGAATGAATAA
Found at i:30951 original size:2 final size:2
Alignment explanation
Indices: 30946--30970 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30936 TTTTTTTTTT
30946 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
30971 TAAGGTTGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:31436 original size:31 final size:30
Alignment explanation
Indices: 31401--31477 Score: 102
Period size: 29 Copynumber: 2.6 Consensus size: 30
31391 ATACCGTACA
31401 GGTCCCTCTACTTACAAAAAAGGATCAATTT
1 GGTCCCTCTACTTACAAAAAAGG-TCAATTT
* **
31432 GGTCCCTCTAC-TATAAAAACTGTCAATTT
1 GGTCCCTCTACTTACAAAAAAGGTCAATTT
*
31461 GGTTCCTCTACTTACAA
1 GGTCCCTCTACTTACAA
31478 TTTGGTGTCG
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
29 17 0.43
30 12 0.30
31 11 0.28
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (30 bp):
GGTCCCTCTACTTACAAAAAAGGTCAATTT
Found at i:31523 original size:31 final size:30
Alignment explanation
Indices: 31401--31521 Score: 104
Period size: 31 Copynumber: 4.0 Consensus size: 30
31391 ATACCGTACA
* *
31401 GGTCCCTCTACTTACAAAAAAGGATCAATTT
1 GGTCCCTCTACTTACAAAATATG-TCAATTT
*
31432 GGTCCCTCTACTATA-AAAA-CTGTCAATTT
1 GGTCCCTCTACT-TACAAAATATGTCAATTT
* ** * *
31461 GGTTCCTCTACTTACAATTTGGTGTCGA-TT
1 GGTCCCTCTACTTACAAAAT-ATGTCAATTT
31491 GAGTCCCTCTACTTAACAAAATATGTCAATT
1 G-GTCCCTCTACTT-ACAAAATATGTCAATT
31522 GATTATATAT
Statistics
Matches: 71, Mismatches: 12, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
28 2 0.03
29 20 0.28
30 4 0.06
31 37 0.52
32 8 0.11
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (30 bp):
GGTCCCTCTACTTACAAAATATGTCAATTT
Found at i:31816 original size:29 final size:31
Alignment explanation
Indices: 31770--31846 Score: 104
Period size: 29 Copynumber: 2.5 Consensus size: 31
31760 TGACACCAAA
* *
31770 TTGTAAGTAAAGGGACCAAATTGA-CAGTTT
1 TTGTAAGTAGAGGGACCAAATTGATCACTTT
* *
31800 TTGT-AGTAGGGGGACCAAATTGATCCCTTT
1 TTGTAAGTAGAGGGACCAAATTGATCACTTT
31830 TTGTAAGTAGAGGGACC
1 TTGTAAGTAGAGGGACC
31847 TGTACGGTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
29 17 0.43
30 12 0.30
31 11 0.28
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.30
Consensus pattern (31 bp):
TTGTAAGTAGAGGGACCAAATTGATCACTTT
Found at i:32172 original size:64 final size:64
Alignment explanation
Indices: 32071--32197 Score: 245
Period size: 64 Copynumber: 2.0 Consensus size: 64
32061 AGGAGGAGAA
32071 TTCCACCTAGTCAACTTCCAATTTTATCAATTAAACACCTTAAATTGCATTATGTGACCCTTAT
1 TTCCACCTAGTCAACTTCCAATTTTATCAATTAAACACCTTAAATTGCATTATGTGACCCTTAT
*
32135 TTCCACCTAGTCAACTTCCAATTTTATCAATTAAACACCTTAATTTGCATTATGTGACCCTTA
1 TTCCACCTAGTCAACTTCCAATTTTATCAATTAAACACCTTAAATTGCATTATGTGACCCTTA
32198 CTTGGAGGAA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.38
Consensus pattern (64 bp):
TTCCACCTAGTCAACTTCCAATTTTATCAATTAAACACCTTAAATTGCATTATGTGACCCTTAT
Found at i:38241 original size:18 final size:18
Alignment explanation
Indices: 38218--38254 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
38208 AAAACAAATC
38218 TATGCAATTGTTGGAAAA
1 TATGCAATTGTTGGAAAA
38236 TATGCAATTGTTGGAAAA
1 TATGCAATTGTTGGAAAA
38254 T
1 T
38255 TAAACCTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.22, T:0.35
Consensus pattern (18 bp):
TATGCAATTGTTGGAAAA
Found at i:58047 original size:2 final size:2
Alignment explanation
Indices: 58040--58065 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
58030 TGATGTCGAA
58040 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
58066 TATTGATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58134 original size:28 final size:28
Alignment explanation
Indices: 58106--58160 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 28
58096 AATTTGTTTA
58106 AAATT-GACCTTTTGTCCCCTAAACTTT
1 AAATTAGACCTTTTGTCCCCTAAACTTT
* * *
58133 AATTTGAGACTTTTTGTCCTCTAAACTT
1 AAATT-AGACCTTTTGTCCCCTAAACTT
58161 GCAATATGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 4 0.17
29 19 0.83
ACGTcount: A:0.25, C:0.22, G:0.09, T:0.44
Consensus pattern (28 bp):
AAATTAGACCTTTTGTCCCCTAAACTTT
Found at i:59384 original size:47 final size:47
Alignment explanation
Indices: 59315--59409 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
59305 TAAAAATTAC
59315 GAATACAAATTGTATTCAAAATCCTTCTTCTAATCATCTAAAGTATT
1 GAATACAAATTGTATTCAAAATCCTTCTTCTAATCATCTAAAGTATT
59362 GAATACAAATTGTATTCAAAATCCTTCTTCTAATCATCTAAAGTATT
1 GAATACAAATTGTATTCAAAATCCTTCTTCTAATCATCTAAAGTATT
59409 G
1 G
59410 TAATGGACAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.38, C:0.17, G:0.07, T:0.38
Consensus pattern (47 bp):
GAATACAAATTGTATTCAAAATCCTTCTTCTAATCATCTAAAGTATT
Found at i:64745 original size:21 final size:21
Alignment explanation
Indices: 64720--64770 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
64710 TATCTTAGAT
64720 ATAAT-ATATATTATTAAATAA
1 ATAATAATATATT-TTAAATAA
64741 ATAATAAATATATTTTAAAT-A
1 ATAAT-AATATATTTTAAATAA
64762 ATAAATAAT
1 AT-AATAAT
64771 GAGTTCAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
21 11 0.41
22 9 0.33
23 7 0.26
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
ATAATAATATATTTTAAATAA
Found at i:64753 original size:25 final size:25
Alignment explanation
Indices: 64722--64770 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
64712 TCTTAGATAT
*
64722 AATATATATT-ATTAAATAAATAATA
1 AATATATATTAAAT-AATAAATAATA
*
64747 AATATATTTTAAATAATAAATAAT
1 AATATATATTAAATAATAAATAAT
64771 GAGTTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AATATATATTAAATAATAAATAATA
Done.