Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024550.1 Corchorus olitorius cultivar O-4 contig24583, 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: 7020
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Found at i:5216 original size:67 final size:67
Alignment explanation
Indices: 5102--5421 Score: 389
Period size: 67 Copynumber: 5.0 Consensus size: 67
5092 AGAGGATTTT
*
5102 AGAAGTACACCGGAAGACGGTTTGTTAGAAAGAATTTTCAAAAATTGATTGGAAGACAATCTCAT
1 AGAAGAACACCGGAAGACGGTTTGTTAGAAAGAATTTTCAAAAATTGATTGGAAGACAATCTCAT
5167 TA
66 TA
* *
5169 AGGAGAACACCGGAAGACGGTTTGTTAAAAAGAATTTTCAAAAATTGATTGGAAGACAATCTCAT
1 AGAAGAACACCGGAAGACGGTTTGTTAGAAAGAATTTTCAAAAATTGATTGGAAGACAATCTCAT
5234 TA
66 TA
* ** *
5236 AGAAGTACACCGGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTTGATTGGAAGACAA-CACA-
1 AGAAGAACACCGGAAGACGGTTTGTTAGAAAGAATTTTCAAAAATTGATTGGAAGACAATCTCAT
5299 T-
66 TA
* * * ** *
5300 CG--G-A-A---G-A--CGGGTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTTAT
1 AGAAGAACACCGGAAGACGGTTTGTTAGAAAGAATTTTCAAAAATTGATTGGAAGACAATCTCAT
5355 TA
66 TA
* **
5357 AGGAGAAC-CTCGGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCA
1 AGAAGAACAC-CGGAAGACGGTTTGTTAGAAAGAATTTTCAAAAATTGATTGGAAGACAATCTCA
5421 T
65 T
5422 CGGAAGACAG
Statistics
Matches: 221, Mismatches: 18, Indels: 28
0.83 0.07 0.10
Matches are distributed among these distances:
54 40 0.18
55 2 0.01
56 2 0.01
57 2 0.01
59 1 0.00
60 2 0.01
61 1 0.00
62 1 0.00
64 2 0.01
65 2 0.01
66 3 0.01
67 163 0.74
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (67 bp):
AGAAGAACACCGGAAGACGGTTTGTTAGAAAGAATTTTCAAAAATTGATTGGAAGACAATCTCAT
TA
Found at i:5328 original size:54 final size:54
Alignment explanation
Indices: 5246--5348 Score: 188
Period size: 54 Copynumber: 1.9 Consensus size: 54
5236 AGAAGTACAC
* *
5246 CGGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTTGATTGGAAGACAACACAT
1 CGGAAGACGGGTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAACACAT
5300 CGGAAGACGGGTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAA
1 CGGAAGACGGGTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAA
5349 TCTTATTAAG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.26
Consensus pattern (54 bp):
CGGAAGACGGGTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAACACAT
Found at i:5501 original size:122 final size:120
Alignment explanation
Indices: 5179--5488 Score: 442
Period size: 121 Copynumber: 2.5 Consensus size: 120
5169 AGGAGAACAC
* * * *
5179 CGGAAGACGGTTTGTTAAAAAGAATTTTCAAAAATTGATTGGAAGACAATCTCATTAAGAAGTAC
1 CGGAAGACGGTTTGCTAGAAAGAATTTTC-AAAGTTGATTGGAAGACAATCTTATTAAGAAGTAC
5244 ACCGGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTTGATTGGAAGACAACACAT
65 ACCGGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTTGATTGGAAGACAACACAT
* * *
5300 CGGAAGACGGGTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTTATTAAGGAGAAC
1 CGGAAGACGGTTTGCTAGAAAGAATTTTCAAA-GTTGATTGGAAGACAATCTTATTAAGAAGTAC
*
5365 -CTCGGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCAT
65 AC-CGGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTTGATTGGAAGACAA-CACAT
* * ** * *
5422 CGGAAGACAGTTTGCTAGAAAGAATTTTCAGAAGTTGATCGGAAGATGATCTTGTCAAGAAGTAC
1 CGGAAGACGGTTTGCTAGAAAGAATTTTCA-AAGTTGATTGGAAGACAATCTTATTAAGAAGTAC
5487 AC
65 AC
5489 AAGAAGATGG
Statistics
Matches: 167, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
120 4 0.02
121 103 0.62
122 57 0.34
123 3 0.02
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (120 bp):
CGGAAGACGGTTTGCTAGAAAGAATTTTCAAAGTTGATTGGAAGACAATCTTATTAAGAAGTACA
CCGGAAGACGGTTTGTTAGAAAGAATTTTCAAATGTTGATTGGAAGACAACACAT
Found at i:5545 original size:64 final size:64
Alignment explanation
Indices: 5444--5737 Score: 374
Period size: 64 Copynumber: 4.6 Consensus size: 64
5434 TGCTAGAAAG
* *
5444 AATTTTCAGAAGTTGATCGGAAGATGATCTTGTCAAGAAGTACACAAGAAGATGGTTTCTCAAA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
** * *
5508 AATTTTCCTAAGTTGATCGGAAGATGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAC
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
* * * * *
5572 AGTTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAACTACGCCAGAAGATGGATTCT-TAA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
* * * * * * *
5635 AATTTTCAAAAGTCGGTCGGAAGACGATCTTGTTAAAAAGCACACCAGAAGATGGTTTCTCGGAA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTC-AAA
* * * *
5700 AAGTTTCAGAAGTGGGTCGGAAGACGATCTTGTTAAGA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGA
5738 GATGCACCGG
Statistics
Matches: 200, Mismatches: 28, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
63 51 0.25
64 113 0.56
65 36 0.18
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.27
Consensus pattern (64 bp):
AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
Found at i:5969 original size:50 final size:49
Alignment explanation
Indices: 5912--6037 Score: 182
Period size: 50 Copynumber: 2.5 Consensus size: 49
5902 GGTTTTCTCG
*
5912 AGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTA
1 AGATTGAATTGG-AGACAGTTCAAAGGATAAGCAGAAGACGGTCCTTTTA
5962 AGATTGAATTGGTAGACAGTTCAAAGGATAAGCAGAAGACGGTCCTTTTA
1 AGATTGAATTGG-AGACAGTTCAAAGGATAAGCAGAAGACGGTCCTTTTA
* *
6012 ATATT-AGATTGGAGAACAATTCAAAG
1 AGATTGA-ATTGGAG-ACAGTTCAAAG
6038 AAATTGATCG
Statistics
Matches: 70, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
49 3 0.04
50 67 0.96
ACGTcount: A:0.38, C:0.11, G:0.25, T:0.25
Consensus pattern (49 bp):
AGATTGAATTGGAGACAGTTCAAAGGATAAGCAGAAGACGGTCCTTTTA
Found at i:6146 original size:50 final size:50
Alignment explanation
Indices: 6087--6216 Score: 206
Period size: 50 Copynumber: 2.6 Consensus size: 50
6077 AAGTGAAACA
*
6087 TTCCACAAGCCAAACTCTTTTCCATACGAGTCAATTATCAACATAGGCTT
1 TTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATAGGCTT
*
6137 TTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATGGGCTT
1 TTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATAGGCTT
* **
6187 TTCCATAAGCCACAGTTCGTTTCCATACGA
1 TTCCACAAGCCA-AACTCGTTTCCATACGA
6217 TACATTACCA
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
50 59 0.80
51 15 0.20
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.29
Consensus pattern (50 bp):
TTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATAGGCTT
Found at i:6278 original size:35 final size:35
Alignment explanation
Indices: 6232--6389 Score: 246
Period size: 35 Copynumber: 4.5 Consensus size: 35
6222 TACCATCTTC
*
6232 TCAGATGACTCGGTGTAGCATCTTCAAAGTT-ATAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAATTGA-AT
* *
6267 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGAAC
1 TCAGATGACTCGGTGTAGCATCTTCAAAATTGAAT
*
6302 TCAGATGACTCGGTGTAGCATTTTCAAAATTGAAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAATTGAAT
*
6337 CCAGATGACTCGGTGTAGCATCTTCAAAATTGAAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAATTGAAT
*
6372 CCAGATGACTCGGTGTAG
1 TCAGATGACTCGGTGTAG
6390 ACACCCCATT
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 115 0.99
36 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.30
Consensus pattern (35 bp):
TCAGATGACTCGGTGTAGCATCTTCAAAATTGAAT
Done.