Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017757.1 Corchorus olitorius cultivar O-4 contig17790, 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: 25561
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.36
Found at i:7168 original size:18 final size:18
Alignment explanation
Indices: 7147--7182 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
7137 TCTCTTCAAA
7147 GCTAATTCTCTCAGCGGT
1 GCTAATTCTCTCAGCGGT
7165 GCTAATTCTCTCAGCGGT
1 GCTAATTCTCTCAGCGGT
7183 CTTCAATGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.28, G:0.22, T:0.33
Consensus pattern (18 bp):
GCTAATTCTCTCAGCGGT
Found at i:15228 original size:13 final size:13
Alignment explanation
Indices: 15210--15234 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15200 TATTTGGAAT
15210 ATTTTTATTTATA
1 ATTTTTATTTATA
15223 ATTTTTATTTAT
1 ATTTTTATTTAT
15235 TTAATTTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTTTATTTATA
Found at i:16195 original size:332 final size:325
Alignment explanation
Indices: 15474--16697 Score: 1301
Period size: 324 Copynumber: 3.7 Consensus size: 325
15464 CATCGGCAAT
* * * * *
15474 ATTGGATTTAAAAATTTATTTTTACGTGTATTTGAATCTTATTTCGATTT-ATTAGAAATTAATT
1 ATTGGATTT-AAGATTTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATT
* * ** *
15538 TAGAAAAAATAAGAAATACGATATTAAAAGCGT-AAAATGCCCTCCAATCTTTTTGATGTTCAAT
65 TA-AAAAAATATGAAAAACGATATTAAAAGCGTGAAAA-GCCCTCCAATCTTTTTGGCGTTGAAT
* * *
15602 TATATACTTTTATGAGTATTTTAGCCAAAAGTTGAGGAGAAATCTTTCGAGTCAATTTTTGCAAA
128 TATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGA-AAATCTTTCGGGTCAATTTTTGCAAA
* * *
15667 ATTTTAGCCGAAATCGTCTACTAATAGTTTAACCATCACGGTTTTTGGCTAAAAACA-CGTTCCG
192 ATTTTAGCCGAAATCG--T-GT-A-A---TAATCATCACAGTTTTTGGCTAAAAA-AGCGTT-C-
* * * * * *
15731 AGGATCCGA-CTCAATTTTGCATGA-TTTTGGCTCCGAGACTACTTGAAATATCTATATTCATCT
246 AGGGTCCCAGCTCAGTTTTGCATGATTTTTGGCGCC-AGACTCCTT-AAAAATCTATATTCATCT
*
15794 AATCAATTCTCAGCCAC
309 AATCAAATCTCAGCCAC
* ** *
15811 ATTGGATTTAAAGATTTGTTTTTACGAGCATATGAATCTCGTTTCAATTTAATTAGAAATTAATT
1 ATTGGATTT-AAGATTTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATT
** * * * * *
15876 TGGAAAAATAGGAAAAACGATATTAGAAA-CGTCAAAAACCCTTCAATCTTTTTGGTGTTGAATT
65 TAAAAAAATATGAAAAACGATATTA-AAAGCGTGAAAAGCCCTCCAATCTTTTTGGCGTTGAATT
* * *
15940 ATATATTTTTTATGAGCATTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCAACTTTTACAAA
129 ATATA-TTTTTATGAGTATTTTAGCCAAAAATTGAGGAAA-ATCTTTCGGGTCAATTTTTGCAAA
* *
16005 ATTTTTAACCGAAATCGTGTAATAATCATCACAGTTTTTGCCTAAAAAAGCGTTCTAGGGTCCCA
192 A-TTTTAGCCGAAATCGTGTAATAATCATCACAGTTTTTGGCTAAAAAAGCGTTC-AGGGTCCCA
*
16070 GCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTAAGAAATCCATATTCATCTAATCAAATC
255 GCTCAGTTTTGCATGATTTTTGGCGCC-AGACTCCTTAA-AAATCTATATTCATCTAATCAAATC
* *
16135 TCAACTAC
318 TCAGCCAC
* **
16143 ATTGGATTTAAGTATTTGTTTTTACAAGCATCTGAATCTTATTTCGATTTAATTAGACTTTAATT
1 ATTGGATTTAAG-ATTTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATT
* * * *
16208 TAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTCGGCATT-ATATT
65 TAAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCCTCCAATCTTTTTGGCGTTGA-ATT
* * * *
16272 ATATAAATTTTATGAGTA-TTTAGCCAAAAAGTGAGGAAAATTTTTTCGGGT-AATTTCTTGTAA
129 ATAT-ATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAA-TCTTTCGGGTCAATTT-TTGCAA
* * * * *
16335 ATTTTTAGCCAAAATCGTG---T-A-CATCACCGTTTTTGGCTAAAAACGCGCTTC-GTGGCCCC
191 AATTTTAGCCGAAATCGTGTAATAATCATCACAGTTTTTGGCTAAAAAAGCG-TTCAG-GGTCCC
* * * * *
16394 GGCTCAGTTTTACATGATTTTTGGTGCCGGAACTCCTTAAAATATCTATATTCATCAAAT-AAAT
254 AGCTCAGTTTTGCATGATTTTTGGCGCCAG-ACTCCTTAAAA-ATCTATATTCATCTAATCAAAT
*
16458 CTTAGCCAC
317 CTCAGCCAC
* * * *
16467 ATTGCATTTAAGGCTTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAGTTAGAAATTAATT
1 ATTGGATTTAA-GATTTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATT
* ** *
16532 CAAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCCTTAAATCTTTTTGGCGTTGAATCA
65 TAAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCCTCCAATCTTTTTGGCGTTGAATTA
* * * * * * *
16597 TATATTTTTATGAGTGTTATGGCTAAAAATTGAGGAAATATCTTTCGGGTGATTTTTTGGAAAAT
130 TATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAA-ATCTTTCGGGTCAATTTTTGCAAAAT
16662 TTTAGCCGAAATCGTGTAATAATCATCACAGTTTTT
194 TTTAGCCGAAATCGTGTAATAATCATCACAGTTTTT
16698 TTGATAAAAA
Statistics
Matches: 752, Mismatches: 105, Indels: 68
0.81 0.11 0.07
Matches are distributed among these distances:
323 11 0.01
324 176 0.23
325 84 0.11
326 4 0.01
327 2 0.00
328 1 0.00
329 12 0.02
330 29 0.04
331 84 0.11
332 162 0.22
333 1 0.00
334 1 0.00
335 1 0.00
336 1 0.00
337 96 0.13
338 73 0.10
339 14 0.02
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (325 bp):
ATTGGATTTAAGATTTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTT
AAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCCTCCAATCTTTTTGGCGTTGAATTAT
ATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAATCTTTCGGGTCAATTTTTGCAAAATTT
TAGCCGAAATCGTGTAATAATCATCACAGTTTTTGGCTAAAAAAGCGTTCAGGGTCCCAGCTCAG
TTTTGCATGATTTTTGGCGCCAGACTCCTTAAAAATCTATATTCATCTAATCAAATCTCAGCCAC
Found at i:17599 original size:47 final size:47
Alignment explanation
Indices: 17545--17642 Score: 187
Period size: 47 Copynumber: 2.1 Consensus size: 47
17535 TTTCAGGCCA
17545 TTTTCCCAAAGTTTTAGCCGATATCGTGTACAAACCATCACAGTTTT
1 TTTTCCCAAAGTTTTAGCCGATATCGTGTACAAACCATCACAGTTTT
*
17592 TTTTCCCAAAGTTTTAGCCGATATTGTGTACAAACCATCACAGTTTT
1 TTTTCCCAAAGTTTTAGCCGATATCGTGTACAAACCATCACAGTTTT
17639 TTTT
1 TTTT
17643 TTTTTTCTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (47 bp):
TTTTCCCAAAGTTTTAGCCGATATCGTGTACAAACCATCACAGTTTT
Found at i:19051 original size:337 final size:333
Alignment explanation
Indices: 17654--19127 Score: 1431
Period size: 337 Copynumber: 4.4 Consensus size: 333
17644 TTTTTCTTTT
* * * * * * *
17654 CTAAAAACGCCTTTTGG-GCCCCGGACTCAGTTTTGCATGA-TTTTTAGCGTCGAGATTTCTTGA
1 CTAAAAACGCGTTTCGGAACCCCGG-CTTAGTTTTGCATGATTTTTTA-CGCCGAGACTCCTTGA
*
17717 AATATCTATATTCATCTAATCAAATCTCAGCCACATT-ACATTTAAGAATTTGTTTTTACGAACA
64 AATATCTATATTCATCTAATCAAATCTCAGCCACATTGA-ATTTAAGAATTTGTTTTTACGAGCA
* * *
17781 TTTGAATCTTGTTTCGA-TTAAATTAGAAATTAATTCTAAAAAATATGAAAAACGAT-TTAAAAA
128 TCTGAATCTTGTTTCGATTTAAA-TAGAAATTAATTCAAAAAAATATGAAAAACGATATTAAAAG
* *
17844 CGTGAAAAGTCCTCCAATCTTTTTGG-AGTTGAATATATATATATATATATATTGAGTATTTTAG
192 CATGAAAAGTCCTCCAATCTTTTTGGCA-TT-AA-AT-TATATATAT-TTTA-TGAGTATTTTAG
* * * * * * **
17908 ACAAAAACCT-AGGAAAAATATCTTT-G-GTAACTTTTTGCAAAATATTAGTTGAAATCGTGTAC
251 CCAAAAA-TTGAGGGAAAATATCTTTCGAGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTAC
* * *
17970 GTTAGTCGAAGTCACGATTTTTGG
315 --TA-AC-CA-TTACGATTTTTGG
* * * * * * *
17994 CTAAAAAAGCATTCCAGG-ACCCCGG-TTCAGTGTTGCAT--TTTTTTTCGCCGATACTCATTGA
1 CTAAAAACGCGTTTC-GGAACCCCGGCTT-AGTTTTGCATGATTTTTTACGCCGAGACTCCTTGA
* * *** *
18055 AATATCTATATTCATCTAA-CTAAATCTCAGCCACATTGGATTTAAGGATTTG-TAAAACAAGCA
64 AATATCTATATTCATCTAATC-AAATCTCAGCCACATTGAATTTAAGAATTTGTTTTTACGAGCA
* * * * * * *
18118 TCTGAATCATCTTTCGATTTAACTAGAAATTAATTCGGAAAATAATAGGAAACACGATATTAGAA
128 TCTGAATCTTGTTTCGATTTAAATAGAAATTAATTC--AAAAAAATATGAAAAACGATATTAAAA
* * * * * * *
18183 GCATGAAAAGGCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTGTGGCTAAA
191 GCATGAAAAGTCCTCCAATCTTTTTGGCATTAAATTATATATATTTTATGAGTATTTTAGCCAAA
* * * * * *
18248 AATTGA--GTAAATAACTTTCGAATCAATTTTTGC-AAATTTCTAGCCGAAATCGTGTAATAATC
256 AATTGAGGGAAAATATCTTTCGAGTCATTTTTTGCAAAATTT-TAGCCGAAATCGTGTACTAACC
*
18310 ATTAC-AGTATTTGG
320 ATTACGA-TTTTTGG
* * * * * * *
18324 CTAAAAACGCG-TTCCGATGCCCC-GATTAAGTTTTGC-----TTTTGACGCCAAGTCTCTTTGA
1 CTAAAAACGCGTTTCGGA-ACCCCGGCTT-AGTTTTGCATGATTTTTTACGCCGAGACTCCTTGA
* * * * *
18382 GATATCCATATTCATTTAATCAAATCTCAGCTACATTGGATTTAAGAATTTGTTTTTACGAGCAT
64 AATATCTATATTCATCTAATCAAATCTCAGCCACATTGAATTTAAGAATTTGTTTTTACGAGCAT
* * *
18447 CTGAATCTTGTTTC-ATTTAATTAGAAATTAATTTAGAAAAATATG-AAAACGATATTAAAAGCA
129 CTGAATCTTGTTTCGATTTAAATAGAAATTAATTCAAAAAAATATGAAAAACGATATTAAAAGCA
* * *
18510 TGAAAAGTACTCCAATGTTTTTGACATTAAATTATATATATTTTATGAGTATTTTAGCCAAAAAT
194 TGAAAAGTCCTCCAATCTTTTTGGCATTAAATTATATATATTTTATGAGTATTTTAGCCAAAAAT
* *
18575 TG-GCTGGAAAAT-T-TTTCGAGTCATTTTTTGCAAAATTTTAGCTGAAATCGTGTA-T----GT
259 TGAG--GGAAAATATCTTTCGAGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCAT
18632 TACGATTTTTGG
322 TACGATTTTTGG
* ** * *
18644 CTAAAAACGCGTTTCGGGACCCCGGCTTAGTTTTGCATGATTTTTGGCGCCGATACTCCATGAAA
1 CTAAAAACGCGTTTCGGAACCCCGGCTTAGTTTTGCATGATTTTTTACGCCGAGACTCCTTGAAA
* * * *
18709 TATCTATATTCATCTAATCAAATATCATCCATATTGAATTTAAGGATTTGTTTTTACGAGCATCT
66 TATCTATATTCATCTAATCAAATCTCAGCCACATTGAATTTAAGAATTTGTTTTTACGAGCATCT
18774 GAATCTTGTTTCGATTTAAATAGAAATTAATTCAAAAAAAATAATATGAAAAACGATATTAAAAG
131 GAATCTTGTTTCGATTTAAATAGAAATTAATTC---AAAAA-AATATGAAAAACGATATTAAAAG
** * * * *
18839 TGTGAAAATTCCTCCAATCTTTTTGGCGTTAAACTATATGTATTTTATGAGTATTTTAGCCAAAA
192 CATGAAAAGTCCTCCAATCTTTTTGGCATTAAATTATATATATTTTATGAGTATTTTAGCCAAAA
* * *
18904 ATTGAGGGAAAAT-TTTTTCGGGTCACTTTTTTTCAAAATTTTAGCCGAAATCGTGTACTAACCA
257 ATTGAGGGAAAATATCTTTCGAGTCA-TTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCA
*
18968 TTACGGTTTTTGG
321 TTACGATTTTTGG
* *
18981 CGAAAAACGCGTTTCGGAACCCCGGCTTAGTTTTGCATGATTTTTTACGCCGAGACTCCTTAAAA
1 CTAAAAACGCGTTTCGGAACCCCGGCTTAGTTTTGCATGATTTTTTACGCCGAGACTCCTTGAAA
* * * ** * *
19046 TATCTATATTCATCTAATCAAATTTCTA-CCAGATTAAATTTAAGTTTTTATTTTTACGAGCATT
66 TATCTATATTCATCTAATCAAATCTC-AGCCACATTGAATTTAAGAATTTGTTTTTACGAGCATC
19110 TGAATCTTGTTTCGATTT
130 TGAATCTTGTTTCGATTT
19128 CATTCAAATT
Statistics
Matches: 932, Mismatches: 154, Indels: 99
0.79 0.13 0.08
Matches are distributed among these distances:
320 33 0.04
321 8 0.01
324 74 0.08
325 125 0.13
326 24 0.03
327 84 0.09
328 22 0.02
329 8 0.01
330 45 0.05
331 86 0.09
332 30 0.03
333 12 0.01
334 7 0.01
335 39 0.04
336 3 0.00
337 185 0.20
338 65 0.07
339 23 0.02
340 50 0.05
341 9 0.01
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (333 bp):
CTAAAAACGCGTTTCGGAACCCCGGCTTAGTTTTGCATGATTTTTTACGCCGAGACTCCTTGAAA
TATCTATATTCATCTAATCAAATCTCAGCCACATTGAATTTAAGAATTTGTTTTTACGAGCATCT
GAATCTTGTTTCGATTTAAATAGAAATTAATTCAAAAAAATATGAAAAACGATATTAAAAGCATG
AAAAGTCCTCCAATCTTTTTGGCATTAAATTATATATATTTTATGAGTATTTTAGCCAAAAATTG
AGGGAAAATATCTTTCGAGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATTACG
ATTTTTGG
Found at i:20396 original size:21 final size:22
Alignment explanation
Indices: 20372--20412 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
20362 GTTTATAATA
*
20372 TTCTTGGGTCA-TCGGGTTATC
1 TTCTCGGGTCATTCGGGTTATC
*
20393 TTCTCGGGTTATTCGGGTTA
1 TTCTCGGGTCATTCGGGTTA
20413 CGAGTTTGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.10, C:0.17, G:0.29, T:0.44
Consensus pattern (22 bp):
TTCTCGGGTCATTCGGGTTATC
Found at i:21625 original size:45 final size:45
Alignment explanation
Indices: 21588--21677 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
21578 ATATTGTTTT
*
21588 TTGTTAATCTCTTTGTTCTAATCTTTCTCTTGAGAATAGAAATTG
1 TTGTTAATCTCTTTGATCTAATCTTTCTCTTGAGAATAGAAATTG
* *
21633 TTGTTAATCTCTTTGATCTGATCTTTCTCTTGAAAATAGAAATTG
1 TTGTTAATCTCTTTGATCTAATCTTTCTCTTGAGAATAGAAATTG
21678 CTGCGTATCA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (45 bp):
TTGTTAATCTCTTTGATCTAATCTTTCTCTTGAGAATAGAAATTG
Done.