Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019358.1 Corchorus olitorius cultivar O-4 contig19391, 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: 14653
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Found at i:1060 original size:322 final size:320
Alignment explanation
Indices: 12--1233 Score: 1240
Period size: 322 Copynumber: 3.8 Consensus size: 320
2 TGTATAAAAT
* * * * * * * *
12 ATCACGGTTTTTGGCAAAAAAACGTGTTTCGGAGTCCCAATTCAATTTTGCATGATTTTTAGCGT
1 ATCAC-GTTTTTGACTAAAAAA-GCGTTCCGGAG-CCCGACTCACTTTTGCATGATTTTTGGCGT
* * * *
77 AAAGACTCCTTCAAATATCTATATTCATCGAATAAAATCTCAGCCACATTGTATATAACG-ATTT
63 AAAGACTCCTTGAAATATCTATATTCATCTAACAAAATCTCAGCCACATTGGATATAA-GAATTT
* * * * *
141 GTTTTTATGAGCATCCGAATCTTGTTTCAATTTAATTAAAAATTAATTTGGAAAAAAAATGGAAA
127 GTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGGAAA
*
206 AACGATATTAGAAGCGCGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAA
192 AACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAA
* * * * * *
271 TATT-TTGCAAAATATAGAGAAAAACTTTTCGGGTTAGTTTTTAGCCGAAATCGTGTAGTAACC
257 TATTGTAGCAAAAAATTGAGAAAAACTTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACA
* * * * * * * ** *
334 ATTACGATTTCTGTCTAAAAACGCGTTTCGGATCCCGACTCAGTTTTAAATGATTTTTTGCAG-A
1 ATCACG-TTTTTGACTAAAAAAGCGTTCCGGAGCCCGACTCACTTTTGCATGATTTTTGGC-GTA
* * *
398 AAGACTCCTTGAAATATCTATATTCATCTAACAAAATCTCAGTCACAATGGATTTAAGAATTTGT
64 AAGACTCCTTGAAATATCTATATTCATCTAACAAAATCTCAGCCACATTGGATATAAGAATTTGT
* * *
463 TTTTACGAGCATCTCAATCTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAAAGGAAAA
129 TTTTACGAGCATCTGAATC-TTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGGAAAA
* * * * * * * *
528 ACGATATTAGAAGTGTGAAAAACCCTTCAATTTTTTTGGTGTTAAATTATATATTTTTCCTGAGT
193 ACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAAT
* **
593 ATTGTAGC-AAAACTTGAGGAAAAACTTTTCGGGTAAATTTTTGCAAAATTTTAGCCGAAATCGT
258 ATTGTAGCAAAAAATTGA-GAAAAACTTTTCGGG--------T-C-AGTTTTTAGCCGAAATCGT
*
657 GTACAAACA
312 GTACTAACA
* * * *
666 ATCACGGGTTTTGGCTAAAAACA-CGTTCCGAAGCCCCGGCTCAACTTTT-CATGATTTTTGGCG
1 ATCAC-GTTTTTGACTAAAAA-AGCGTTCCGGAG-CCCGACTC-ACTTTTGCATGATTTTTGGCG
* * *
729 TAAAGACTCCTTGAAATAT-TCATATTCATCTAACCAAATGC-CAGCCACGTTGGATATAAGGAT
62 TAAAGACTCCTTGAAATATCT-ATATTCATCTAACAAAAT-CTCAGCCACATTGGATATAAGAAT
* *
792 TTG-TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAGTTTGG-AAAAAAATGGA
125 TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGGA
* *
855 AAAACGATATTAGAAGCGTGAAAAAG-CCGTCAATATTTTTTGCGTTGAATTATATATTTTTTTC
190 AAAACGATATTAGAAGCGTG-AAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATA-TTTTTTC
* * *
919 TGAATATTGTGGCAAAAAATTGAGAATAAACATTTCGGGTCAGTTTTTAGCCGAAATTGTGTACT
253 TGAATATTGTAGCAAAAAATTGAGAA-AAACTTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACT
*
984 AACT
317 AACA
* *
988 ATCACAGTTTTTGACTAAAAAAGCGTTCCGGGGCCACGACTCTA-TTTTGCATGATTTTTGGCGC
1 ATCAC-GTTTTTGACTAAAAAAGCGTTCCGGAGCC-CGACTC-ACTTTTGCATGATTTTTGGCGT
** * * * *
1052 CGAGACTCCTTGAAATATCTTTATTCATTTAATC-AAATCTCAGGCACATTGGATTTAAGAATTT
63 AAAGACTCCTTGAAATATCTATATTCATCTAA-CAAAATCTCAGCCACATTGGATATAAGAATTT
* * * * **
1116 -TCTTTTAC-ATGCATCTAAATTTTGTTTTGATTTAATTAGAAATTAATTCAG-AAAAGTATGTG
127 GT-TTTTACGA-GCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATG-G
* * *
1178 --AAACGATATTAAAAGCGTGAAAAGTCC-TCCAATCTTTTTGGCGTTGCATTATATAT
189 AAAAACGATATTAGAAGCGTGAAAAGCCCGT-CAATCTTTTTGGCGTTGAATTATATAT
1234 ATTGATGAGT
Statistics
Matches: 746, Mismatches: 115, Indels: 79
0.79 0.12 0.08
Matches are distributed among these distances:
319 1 0.00
320 95 0.13
321 131 0.18
322 196 0.26
323 51 0.07
324 2 0.00
330 55 0.07
331 51 0.07
332 84 0.11
333 74 0.10
334 6 0.01
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Consensus pattern (320 bp):
ATCACGTTTTTGACTAAAAAAGCGTTCCGGAGCCCGACTCACTTTTGCATGATTTTTGGCGTAAA
GACTCCTTGAAATATCTATATTCATCTAACAAAATCTCAGCCACATTGGATATAAGAATTTGTTT
TTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGGAAAAACG
ATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAATATT
GTAGCAAAAAATTGAGAAAAACTTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACA
Found at i:3790 original size:6 final size:6
Alignment explanation
Indices: 3781--3813 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
3771 TCATACAACC
3781 AAAAA- AAAAAG AAAAAG AAAAAG -AAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
3814 CAGCTTTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 10 0.38
6 16 0.62
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:3801 original size:11 final size:12
Alignment explanation
Indices: 3781--3813 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
3771 TCATACAACC
3781 AAAAA-AAAAAG
1 AAAAAGAAAAAG
3792 AAAAAGAAAAAG
1 AAAAAGAAAAAG
3804 -AAAAGAAAAA
1 AAAAAGAAAAA
3814 CAGCTTTGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 15 0.71
12 6 0.29
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAG
Found at i:3807 original size:17 final size:17
Alignment explanation
Indices: 3781--3813 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3771 TCATACAACC
3781 AAAAAAAAAAGAAAAAG
1 AAAAAAAAAAGAAAAAG
*
3798 AAAAAGAAAAGAAAAA
1 AAAAAAAAAAGAAAAA
3814 CAGCTTTGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAGAAAAAG
Found at i:4760 original size:22 final size:22
Alignment explanation
Indices: 4732--4775 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
4722 TTTCCCTGTT
4732 TCGACCTTCATCAGGGTC-AAAC
1 TCGACCTTC-TCAGGGTCGAAAC
*
4754 TCGACCTTCTCTGGGTCGAAAC
1 TCGACCTTCTCAGGGTCGAAAC
4776 AGGGCTGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.25
Consensus pattern (22 bp):
TCGACCTTCTCAGGGTCGAAAC
Found at i:6139 original size:16 final size:16
Alignment explanation
Indices: 6118--6164 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
6108 GATTTTCATC
*
6118 ACTTGATATCTATTTT
1 ACTTGATATATATTTT
*
6134 ACTTGATTTATATTTT
1 ACTTGATATATATTTT
*
6150 -CTTGAATATTTATTT
1 ACTTG-ATATATATTT
6165 ATTTGCAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
15 4 0.15
16 22 0.85
ACGTcount: A:0.26, C:0.09, G:0.06, T:0.60
Consensus pattern (16 bp):
ACTTGATATATATTTT
Found at i:13968 original size:20 final size:20
Alignment explanation
Indices: 13943--13987 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
13933 ATGTAAGTAC
13943 AGTGTGATGATGTGAAAATA
1 AGTGTGATGATGTGAAAATA
13963 AGTGTGATGATGTGAAAATA
1 AGTGTGATGATGTGAAAATA
13983 AGTGT
1 AGTGT
13988 TAGGTGAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (20 bp):
AGTGTGATGATGTGAAAATA
Done.