Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017147.1 Corchorus olitorius cultivar O-4 contig17180, 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: 20581
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:2879 original size:19 final size:18
Alignment explanation
Indices: 2846--2881 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2836 TGGAAATAAT
2846 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
2864 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
2882 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:4690 original size:328 final size:329
Alignment explanation
Indices: 3209--4821 Score: 1429
Period size: 329 Copynumber: 4.9 Consensus size: 329
3199 ATTAATCGAA
* * * * * * * * * **
3209 ATCAAGGTTTTGGGCTAAAAACACGTTCCTGGGACCA-GGTTTAATGTTGCATGATTTTTTGCGT
1 ATCACGGTTTTTGGCTAAAAACGCGTTCCAGGG-CCATGGCTCAGTTTTGCATGATTTTTGGCAC
* * * * * *
3273 CAAGACTCCTTGAAATATCTACATTCATCTAA-CTAAATTTCAGCCAAATTGGATTTAAGGATTT
65 CGAGACTCATTGAAATATCTATATTCATCTAATC-AAATCTCAGACACATTGGATTTAAGGATTT
* *** * * * *
3337 -GTAAAACAAGCATCTGAATCATGATTCGATTTAATTAGAAATTAATTC-GAAAGATAATAGGAA
129 ATTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAG-AA-A-AATATGAA
* * * * * * *
3400 AAACGATATTAGAACCATG-AAAAATTCTTCAATATTTTTGGCGTTGAATTATATTATCTTTATA
191 AAACGATATTAGAAGCGTGTAAAAGTCCTTCAATTTTTTTGACGTTGAATTATATT-T-TTTATG
* * * * * *
3464 AGTATTGTGGCTAAAAATTGAGGAAATAACTTTCGAGTCAATTTTTGCAAAATTCTAGCCGATCG
254 AGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCC-A--G
*
3529 AAATCGTGTA-ATA
316 AAATCGTGTACATC
* * ** * *
3542 ATCACGGTTTTTGGCTGAAAACGCGTTCTGAGCCCCA-GGCTAAGTTTTGCATGGTTTTTGGCAC
1 ATCACGGTTTTTGGCTAAAAACGCGTTC-CAGGGCCATGGCTCAGTTTTGCATGATTTTTGGCAC
* * * * * ** * * *
3606 CAAGACTCTTTGAGATATCCATATTCATTTAATCAAATCTCAGTTAGATTGGATTTAAGAATTTG
65 CGAGACTCATTGAAATATCTATATTCATCTAATCAAATCTCAGACACATTGGATTTAAGGATTTA
* * * *
3671 TTTTTACGAGTATCTGAATCTTGTTTCGA-TT-ATTAGAAATTAATTCTG-AAAATATGAACAAT
130 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAAC
* * *
3733 GATATTA-AA-CGTGTGAAAAGTCCTCCAATTTTTTTGGCGTTGCATTATATATGTTTTATGAGT
195 GATATTAGAAGCGTGT-AAAAGTCCTTCAATTTTTTTGACGTTGAATTATAT-T-TTTTATGAGT
* * *
3796 ATTTTAGCCAAAAATTGACGG-AATAATTTTTCGGGTCATTTTTTGCAAAAATTTAGCC-GAAAT
257 ATTTTAGCCAAAAATTGA-GGAAAT-ATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCAGAAAT
* **
3859 CGTATATTGTTAC
320 CGTGTA--CAT-C
* * * *
3872 ATCACGGTTTTTGGCT-AAAACGCGTTTC-GGCGCCCTGGCTTAGTTTTGCATGATTTTTGGCGC
1 ATCACGGTTTTTGGCTAAAAACGCGTTCCAGG-GCCATGGCTCAGTTTTGCATGATTTTTGGCAC
* * *
3935 CGAGACTCATTGAAATGTCTATATTCATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTA
65 CGAGACTCATTGAAATATCTATATTCATCTAATCAAATCTCAGACACATTGGATTTAAGGATTTA
* ** * *
4000 TTTTTACGAGCATCTAAATCTTGTTTATATTTAATTAAAAATTAATTTAGAAAAATATGAAAAAC
130 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAAC
* * * * *
4065 GATATTAAAAGCGTGAAAAAGGCTTTCAATTTTTTT-AGCATTGAATTATA-TTTTTATGAGTAT
195 GATATTAGAAGCGTGTAAAAGTCCTTCAATTTTTTTGA-CGTTGAATTATATTTTTTATGAGTAT
* ** * * * * * * * *
4128 TTTCGTTAGAAATCGAGGAAAAATCTTTCGGATCAATTTTTGTAAAATTTTAGTC-GTAATAGTG
259 TTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCAGAAATCGTG
4192 TACTAATC
324 TAC--ATC
* * ** * **
4200 ATCACGGTTTTCGGTTAAAAACGCGTTCTGGGGCC-CGGCTCAGTTTTGCATGATTTTTGG-TGC
1 ATCACGGTTTTTGGCTAAAAACGCGTTCCAGGGCCATGGCTCAGTTTTGCATGATTTTTGGCACC
* *
4263 -A-A-TCATTGAAATATCTATATTCATATAA-CTAAATCTCAGACACATTAGATTTAAGGATTTA
66 GAGACTCATTGAAATATCTATATTCATCTAATC-AAATCTCAGACACATTGGATTTAAGGATTTA
* *
4324 TTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAT-TGGAAAAA
130 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATAT-GAAAAA
* * * * *
4388 CAATATTAGAAGCGT-TAAAAGCCCTTCAATCTTTTTGATGTCGAATTATGTATTTTTTATGAGT
194 CGATATTAGAAGCGTGTAAAAGTCCTTCAATTTTTTTGACGTTGAATTA--TATTTTTTATGAGT
*
4452 ATTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAG-CAAAAATCG
257 ATTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCAGAAATCG
4516 TGTACA-C
322 TGTACATC
* * * *
4523 ATCACGGTTTTTGGCTAAAAACGTGTTCCAGGACCATAGCTCTGTTTTGCATGATTTTTGGCACC
1 ATCACGGTTTTTGGCTAAAAACGCGTTCCAGGGCCATGGCTCAGTTTTGCATGATTTTTGGCACC
* * * * * * * * *
4588 GAGACTCCTTGAAATATATTTATTCATCTAATCATATATCAGGCATATCGGATTTAAGGATTTGT
66 GAGACTCATTGAAATATCTATATTCATCTAATCAAATCTCAGACACATTGGATTTAAGGATTTAT
* * * *
4653 TTTTATGTGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAAAATG-AAAA
131 TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAG--AAAAATATGAAAAA
* * * ** * * * *
4717 CGATATAAAAAGCGTG-AAAAGTCCTCCAATCCTTTTGGCGTTTAACTATATATATTTATGAGTA
194 CGATATTAGAAGCGTGTAAAAGTCCTTCAATTTTTTTGACGTTGAATTATAT-TTTTTATGAGTA
* * *
4781 GTTTT-GCCAAAAAAATGAGGAAAAATCTTTTGGGTC-ATTTT
258 -TTTTAGCC-AAAAATTGAGGAAATATCTTTCGGGTCAATTTT
4822 AGCATCATGG
Statistics
Matches: 1043, Mismatches: 191, Indels: 97
0.78 0.14 0.07
Matches are distributed among these distances:
323 56 0.05
324 146 0.14
325 5 0.00
326 79 0.08
327 9 0.01
328 152 0.15
329 305 0.29
330 83 0.08
331 17 0.02
332 34 0.03
333 130 0.12
334 27 0.03
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.37
Consensus pattern (329 bp):
ATCACGGTTTTTGGCTAAAAACGCGTTCCAGGGCCATGGCTCAGTTTTGCATGATTTTTGGCACC
GAGACTCATTGAAATATCTATATTCATCTAATCAAATCTCAGACACATTGGATTTAAGGATTTAT
TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACG
ATATTAGAAGCGTGTAAAAGTCCTTCAATTTTTTTGACGTTGAATTATATTTTTTATGAGTATTT
TAGCCAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCAGAAATCGTGTA
CATC
Found at i:5480 original size:31 final size:32
Alignment explanation
Indices: 5440--5516 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
5430 TGGTCTGACA
* * * *
5440 TGGCCTTGCCATGTGGCA-TTTTGGTCCAACG
1 TGGCATTGCCACGTGACATTTTTGGCCCAACG
* *
5471 TGTCATTGCCACGTGACATTTTTGGCCCGACG
1 TGGCATTGCCACGTGACATTTTTGGCCCAACG
5503 TGGCATTGCCACGT
1 TGGCATTGCCACGT
5517 CAGCAAAACC
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 14 0.37
32 24 0.63
ACGTcount: A:0.14, C:0.27, G:0.27, T:0.31
Consensus pattern (32 bp):
TGGCATTGCCACGTGACATTTTTGGCCCAACG
Found at i:6060 original size:19 final size:18
Alignment explanation
Indices: 6023--6067 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
6013 TGAAATTTAT
6023 TAATTATTTATTAAATAA
1 TAATTATTTATTAAATAA
6041 TAATTATTT-TTCAGAATAA
1 TAATTATTTATT-A-AATAA
*
6060 TTATTATT
1 TAATTATT
6068 AATATTCCCC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 2 0.08
18 10 0.42
19 12 0.50
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (18 bp):
TAATTATTTATTAAATAA
Found at i:10755 original size:21 final size:21
Alignment explanation
Indices: 10729--10781 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
10719 AACAGTGGAA
10729 ACAAGCTTTGCTTGAAGAGCT
1 ACAAGCTTTGCTTGAAGAGCT
10750 ACAAGCTTTGCTTGAAGAGCT
1 ACAAGCTTTGCTTGAAGAGCT
10771 ACAAGCTTTGC
1 ACAAGCTTTGC
10782 ATAAAAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (21 bp):
ACAAGCTTTGCTTGAAGAGCT
Found at i:12522 original size:21 final size:22
Alignment explanation
Indices: 12481--12522 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
12471 AAAATACATC
12481 AAAGCAAAGAAAAACAGTGAAA
1 AAAGCAAAGAAAAACAGTGAAA
12503 AAAGCAAAGAAAAACA-TGAA
1 AAAGCAAAGAAAAACAGTGAA
12523 GCTTTATTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.69, C:0.10, G:0.17, T:0.05
Consensus pattern (22 bp):
AAAGCAAAGAAAAACAGTGAAA
Found at i:14071 original size:163 final size:163
Alignment explanation
Indices: 13801--14128 Score: 656
Period size: 163 Copynumber: 2.0 Consensus size: 163
13791 ATGATATATC
13801 CTGTATAAAGGCCGGTGGTTCACTAGAGTAATAACCCAAATGAGTAAAAGCTTCCGAATTGCCCA
1 CTGTATAAAGGCCGGTGGTTCACTAGAGTAATAACCCAAATGAGTAAAAGCTTCCGAATTGCCCA
13866 AGCATTCAGGAATGGAACCAGATAAAGGTCATTTTGAAGCGCCACTAATGCCCCTTTTTCTTGTA
66 AGCATTCAGGAATGGAACCAGATAAAGGTCATTTTGAAGCGCCACTAATGCCCCTTTTTCTTGTA
13931 GTGAAGGGAAATTTGCAGAGTTCTTCTGGAATG
131 GTGAAGGGAAATTTGCAGAGTTCTTCTGGAATG
13964 CTGTATAAAGGCCGGTGGTTCACTAGAGTAATAACCCAAATGAGTAAAAGCTTCCGAATTGCCCA
1 CTGTATAAAGGCCGGTGGTTCACTAGAGTAATAACCCAAATGAGTAAAAGCTTCCGAATTGCCCA
14029 AGCATTCAGGAATGGAACCAGATAAAGGTCATTTTGAAGCGCCACTAATGCCCCTTTTTCTTGTA
66 AGCATTCAGGAATGGAACCAGATAAAGGTCATTTTGAAGCGCCACTAATGCCCCTTTTTCTTGTA
14094 GTGAAGGGAAATTTGCAGAGTTCTTCTGGAATG
131 GTGAAGGGAAATTTGCAGAGTTCTTCTGGAATG
14127 CT
1 CT
14129 TCCTGTCAAG
Statistics
Matches: 165, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
163 165 1.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.27
Consensus pattern (163 bp):
CTGTATAAAGGCCGGTGGTTCACTAGAGTAATAACCCAAATGAGTAAAAGCTTCCGAATTGCCCA
AGCATTCAGGAATGGAACCAGATAAAGGTCATTTTGAAGCGCCACTAATGCCCCTTTTTCTTGTA
GTGAAGGGAAATTTGCAGAGTTCTTCTGGAATG
Found at i:14393 original size:22 final size:20
Alignment explanation
Indices: 14368--14417 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
14358 AATTTATGAA
*
14368 GAGAGATAGTGAGTGGGAGGAG
1 GAGAGAGAGTGAGTGGG-GG-G
* *
14390 GAGAAAGAGTTAGTGGGGGG
1 GAGAGAGAGTGAGTGGGGGG
14410 GAGAGAGA
1 GAGAGAGA
14418 AGAAGGGCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 8 0.33
21 2 0.08
22 14 0.58
ACGTcount: A:0.34, C:0.00, G:0.54, T:0.12
Consensus pattern (20 bp):
GAGAGAGAGTGAGTGGGGGG
Found at i:15469 original size:17 final size:16
Alignment explanation
Indices: 15439--15495 Score: 64
Period size: 17 Copynumber: 3.6 Consensus size: 16
15429 CGTTCAAATG
15439 TCGGGTCA-TTTGGGT
1 TCGGGTCATTTTGGGT
15454 TCGGGTCAATTTTGGGT
1 TCGGGTC-ATTTTGGGT
* *
15471 T-GGGTCGTTTTCGGTT
1 TCGGGTCATTTT-GGGT
15487 TCGGGTCAT
1 TCGGGTCAT
15496 ACGGTTCGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
15 11 0.31
16 10 0.29
17 14 0.40
ACGTcount: A:0.07, C:0.14, G:0.37, T:0.42
Consensus pattern (16 bp):
TCGGGTCATTTTGGGT
Found at i:16099 original size:23 final size:25
Alignment explanation
Indices: 16069--16116 Score: 82
Period size: 23 Copynumber: 2.0 Consensus size: 25
16059 TAATTAATCG
16069 GTACAAATATA-A-TATATATATTT
1 GTACAAATATATAGTATATATATTT
16092 GTACAAATATATAGTATATATATTT
1 GTACAAATATATAGTATATATATTT
16117 AGGTCATGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 11 0.48
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (25 bp):
GTACAAATATATAGTATATATATTT
Found at i:17177 original size:16 final size:17
Alignment explanation
Indices: 17147--17222 Score: 72
Period size: 16 Copynumber: 4.7 Consensus size: 17
17137 GTCGGGTTGA
*
17147 TCGGGTTCGGATCATTT
1 TCGGGTTCGGGTCATTT
*
17164 T-GGGTTTGGGTCATTT
1 TCGGGTTCGGGTCATTT
17180 TCGGGTTCGGGT--TGTT
1 TCGGGTTCGGGTCAT-TT
* *
17196 T-GGATTCGGGT-AATT
1 TCGGGTTCGGGTCATTT
17211 TCGGGTTCGGGT
1 TCGGGTTCGGGT
17223 ACCCAAAATT
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
15 13 0.27
16 26 0.53
17 10 0.20
ACGTcount: A:0.08, C:0.12, G:0.38, T:0.42
Consensus pattern (17 bp):
TCGGGTTCGGGTCATTT
Done.