Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022935.1 Corchorus olitorius cultivar O-4 contig22968, 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: 18350
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:3031 original size:17 final size:17
Alignment explanation
Indices: 3009--3065 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
2999 TCATTACATC
3009 AATTAAAATTATAAATA
1 AATTAAAATTATAAATA
* *
3026 AATT--AATGTACCAAAAA
1 AATTAAAAT-TA-TAAATA
*
3043 AATTAAAATTATAAATT
1 AATTAAAATTATAAATA
3060 AATTAA
1 AATTAA
3066 TAATATAAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
15 3 0.10
16 2 0.06
17 21 0.68
18 2 0.06
19 3 0.10
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (17 bp):
AATTAAAATTATAAATA
Found at i:5148 original size:310 final size:307
Alignment explanation
Indices: 4565--5181 Score: 909
Period size: 310 Copynumber: 2.0 Consensus size: 307
4555 TAATTACTTA
* *
4565 GGGGTCGTTTGACATCGTTTTCGTTTTTCTGTTTTTTGTTTTTGTTTCGTTTTCGTTTTGTTTTT
1 GGGGTCGTTTGACATCATTTTCGTTTTTCTGTTTTTTGTTTTTGTTTCGTTTTCGTTTTATTTTT
* *
4630 GTTGCGTTGTCAATTTTTTGAAAACAAAAACATGTTTGAATATGCAATTTGGTTGTATGTTTTTA
66 GTTGCGCTGTCAATTTTTTGAAAACAAAAACATGTTTGAATATACAATTTGGTTGTATGTTTTTA
* *
4695 AATAAAAATGTAAAAAAAAAATAGTGAAAAAACATGTGAGTTACTGTTCATAAATGTGCTTCTGT
131 AATAAAAAAGT--AAAAAAAATAGTGAAAAAACATGTGAGTTACTGTTCATAAATATGCTTCTGT
*
4760 GAGTGTTTTGGAAAAACATGAAAACACAAAATTATTGTTTCAACTTTTTTCCAAAACACTGCTTC
194 GAGTGTTTTGGAAAAACATGAAAACACAAAATTATTGCTTCAACTTTTTTCCAAAACACTGCTTC
* * * *
4825 TGTTTCCAAAATTTTTGGAAACGGAAACAGCCTGCCAACCATTTTTTTT
259 TGTTTCCAAAATTTTTGAAAACAGAAACAGCCTGCCAAACATGTTTTTT
*
4874 GGGGTCGTTTGGCATCATTTTCGTTTTTCTGTTTTTTGTTTTTGTTTCGTTTTCG-TTTATTTTT
1 GGGGTCGTTTGACATCATTTTCGTTTTTCTGTTTTTTGTTTTTGTTTCGTTTTCGTTTTATTTTT
*
4938 GTTGCGCTGTCAA-TTTTTGAAAACAAAAACATGTTTGGATATACAATTTGGTTGTATGTTTTTA
66 GTTGCGCTGTCAATTTTTTGAAAACAAAAACATGTTTGAATATACAATTTGGTTGTATGTTTTTA
* * * * * *
5002 AATAAAAAAGT-AAAAAAA-GGTTAAAAAACATGTGATTTATTGTTCATGATTATGCTTCTGTGT
131 AATAAAAAAGTAAAAAAAATAGTGAAAAAACATGTGAGTTACTGTTCATAAATATGCTTC--TG-
* * *
5065 TTTGGAAGTGTTTTGGAAAAACATGAAAACACAAAATTCTTGCTTCCACTTTTTTCCAAAACATT
193 --T-G-AGTGTTTTGGAAAAACATGAAAACACAAAATTATTGCTTCAACTTTTTTCCAAAACACT
* *
5130 GCTTTTGTTTCCAAAATTTTTGAAAATAGAAACAGCCTGCCAAACATGTTTT
254 GCTTCTGTTTCCAAAATTTTTGAAAACAGAAACAGCCTGCCAAACATGTTTT
5182 CACTGTTTTG
Statistics
Matches: 277, Mismatches: 24, Indels: 13
0.88 0.08 0.04
Matches are distributed among these distances:
303 33 0.12
304 7 0.03
305 2 0.01
307 59 0.21
308 21 0.08
309 54 0.19
310 101 0.36
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.42
Consensus pattern (307 bp):
GGGGTCGTTTGACATCATTTTCGTTTTTCTGTTTTTTGTTTTTGTTTCGTTTTCGTTTTATTTTT
GTTGCGCTGTCAATTTTTTGAAAACAAAAACATGTTTGAATATACAATTTGGTTGTATGTTTTTA
AATAAAAAAGTAAAAAAAATAGTGAAAAAACATGTGAGTTACTGTTCATAAATATGCTTCTGTGA
GTGTTTTGGAAAAACATGAAAACACAAAATTATTGCTTCAACTTTTTTCCAAAACACTGCTTCTG
TTTCCAAAATTTTTGAAAACAGAAACAGCCTGCCAAACATGTTTTTT
Found at i:5261 original size:70 final size:70
Alignment explanation
Indices: 5181--5315 Score: 225
Period size: 70 Copynumber: 1.9 Consensus size: 70
5171 AAACATGTTT
*
5181 TCACTGTTTTGTTTCCAAAAACAGAAAATTGGCAACAGAAAACAGGAAACAGAAACGATGCCAAA
1 TCACTATTTTGTTTCCAAAAACAGAAAATTGGCAACAGAAAACAGGAAACAGAAACGATGCCAAA
5246 TGAGC
66 TGAGC
* * * *
5251 TCACTATTTTGTTTCCAAAAACAGAAAATTGGCAGCAGAAAACTGGAAACGGAAACTATGCCAAA
1 TCACTATTTTGTTTCCAAAAACAGAAAATTGGCAACAGAAAACAGGAAACAGAAACGATGCCAAA
5316 CAAGCTCTTA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
70 60 1.00
ACGTcount: A:0.44, C:0.19, G:0.18, T:0.20
Consensus pattern (70 bp):
TCACTATTTTGTTTCCAAAAACAGAAAATTGGCAACAGAAAACAGGAAACAGAAACGATGCCAAA
TGAGC
Found at i:5582 original size:35 final size:35
Alignment explanation
Indices: 5542--5616 Score: 150
Period size: 35 Copynumber: 2.1 Consensus size: 35
5532 AGTTCGTTTA
5542 TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
1 TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
5577 TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
1 TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
5612 TGTTC
1 TGTTC
5617 GTTTATATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.41
Consensus pattern (35 bp):
TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
Found at i:5679 original size:16 final size:16
Alignment explanation
Indices: 5658--5689 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5648 TATAATTATT
5658 TATATATTAATAATAA
1 TATATATTAATAATAA
*
5674 TATATATTATTAATAA
1 TATATATTAATAATAA
5690 AAATTATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATATATTAATAATAA
Found at i:5684 original size:19 final size:19
Alignment explanation
Indices: 5642--5689 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
5632 GAACGTTCAT
* *
5642 TTATTATATAATTATTTATA
1 TTATTA-ATAATAATATATA
5662 -TATTAATAATAATATATA
1 TTATTAATAATAATATATA
5680 TTATTAATAA
1 TTATTAATAA
5690 AAATTATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTATTAATAATAATATATA
Found at i:5856 original size:18 final size:18
Alignment explanation
Indices: 5829--5863 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5819 AATTATTACA
5829 TTGTTCATGAACAATTTT
1 TTGTTCATGAACAATTTT
*
5847 TTGTTTATGAACAATTT
1 TTGTTCATGAACAATTT
5864 CAATTTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (18 bp):
TTGTTCATGAACAATTTT
Found at i:7484 original size:438 final size:435
Alignment explanation
Indices: 6533--7558 Score: 1257
Period size: 436 Copynumber: 2.3 Consensus size: 435
6523 TCCCTTCTAT
6533 TTTTATATTT-TTTTTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCA
1 TTTTAT-TTTCTTTTTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCA
* * * * * * *
6597 TGATCTACAAATTTCATTAACA-ACTCCAAAGTCAATTTTAATGTTTTGATTCTAAAAAATACTT
65 TGATCTACAACTTTCATGAA-AGACTCAAAAG-CAATTTTTATATTTTAATTCTAAAAAATGCTT
* * * * * *
6661 CCGAAATTTTGTGGTTTTGATTGCCGGTTGATTTAATATCGTATAATTTTTTCCACATATCCAAT
128 CCGAAATTTTGTCGTTTCGATTGCCGATTGATTTAATACCATATAATTTTATCCACATATCCAAT
* * * **
6726 TGAAATTATTGAAGTATCGGTTAAAAGATTATTGCATGATTTACGACTTTCATGAAGGACCCGAA
193 TGAAATTATTCAAGTATCGGTTAAAAGATTACTGCATAATTTACGACTTTCATGAAAAACCCGAA
* * *
6791 AGCTAAATTTGATCTACGAGTTTCGTGAAGGGTTCAAAAGGGAATTTCTATGTTTCAAGATCTCC
258 AGCTAAATTCGATCTACGAGTTTCATGAAGGGTTCAAAAGAGAATTTCTATGTTTCAAGATCTCC
** * *
6856 ATTAACAAACATTTTCTTATTTGGATTATTTATCAAATGACCCTCATACTTTTCTACTTTATACT
323 ATTAACAAACATTTTCTTATTTCAATTAGTTATCAAATCACCCTCATACTTTTCTACTTTATACT
* *
6921 ACTTAGTCCTTTACAAATTCTATCTTAATCTAATGTTTAAGTTTTATA
388 ACTTAGTCCTTTACAAATTCTATCTTAATCTAATGTTAAACTTTTATA
* *
6969 TTTT-TGTTCTTTGTTCTATTTGTCCGATTAAGGTGATTCATGTGTCTATTAAAAGGTAATTTCA
1 TTTTATTTTCTTT-TTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCA
* * *
7033 TGATCTACAACTTTCATGAAGGACTCAAAAGCAAATTTTTATATTTCAATTCAAAAAAATGCTTC
65 TGATCTACAACTTTCATGAAAGACTCAAAAGC-AATTTTTATATTTTAATTCTAAAAAATGCTTC
* ** * *
7098 CTAAA-TTTGTTCGTTTCGATTGTTGATAT-ATTTAATACCATATAATTTTCGATCCCCATGTCC
129 CGAAATTTTG-TCGTTTCGATTGCCGAT-TGATTTAATACCATATAATTTT--ATCCACATATCC
* * * * *
7161 AATT-AAAGTTATTCAAGTGTCGGTTAGAAGGTTACTGTATAATTTATGACTTTCATGAAAAACC
190 AATTGAAA-TTATTCAAGTATCGGTTAAAAGATTACTGCATAATTTACGACTTTCATGAAAAACC
* * *
7225 CGAGAG-TTAATTCGATCTACGAGTTTCATGAAGGGTTCAAAAGAGAATTTTTATGTTTCAAGAT
254 CGAAAGCTAAATTCGATCTACGAGTTTCATGAAGGGTTCAAAAGAGAATTTCTATGTTTCAAGAT
* *
7289 CTCCATTAACAAATATTTTCTTATTTCAATTAGTTAT-AAATCACCCTCATACTTTTCTATTTTA
319 CTCCATTAACAAACATTTTCTTATTTCAATTAGTTATCAAATCACCCTCATACTTTTCTACTTTA
* * * *
7353 TGCTACTTAGTCCTTTCCAAATTCTATCTTACTC-GAT-TTAATACTTCATT-TA
384 TACTACTTAGTCCTTTACAAATTCTATCTTAATCTAATGTTAA-ACTT--TTATA
* * * * * *
7405 CTTTTATTTTCTTTATTCCATTTTTCCAATTAAGGTAATTCAAATGTCTATTAAAAGGTAATTTT
1 -TTTTATTTTCTTT-TTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTC
* *
7470 ATGATCTACAACTTTCTTGAAAGACTCAAAAACTAATTTTTATAATTTTAATTCTAAAAAATGCT
64 ATGATCTACAACTTTCATGAAAGACTCAAAAGC-AATTTTTAT-ATTTTAATTCTAAAAAATGCT
**
7535 TTTGAAATTTTGT-GATTTCGATTG
127 TCCGAAATTTTGTCG-TTTCGATTG
7559 AAAATCTATT
Statistics
Matches: 504, Mismatches: 69, Indels: 31
0.83 0.11 0.05
Matches are distributed among these distances:
434 5 0.01
435 14 0.03
436 198 0.39
437 96 0.19
438 154 0.31
439 33 0.07
440 4 0.01
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (435 bp):
TTTTATTTTCTTTTTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCAT
GATCTACAACTTTCATGAAAGACTCAAAAGCAATTTTTATATTTTAATTCTAAAAAATGCTTCCG
AAATTTTGTCGTTTCGATTGCCGATTGATTTAATACCATATAATTTTATCCACATATCCAATTGA
AATTATTCAAGTATCGGTTAAAAGATTACTGCATAATTTACGACTTTCATGAAAAACCCGAAAGC
TAAATTCGATCTACGAGTTTCATGAAGGGTTCAAAAGAGAATTTCTATGTTTCAAGATCTCCATT
AACAAACATTTTCTTATTTCAATTAGTTATCAAATCACCCTCATACTTTTCTACTTTATACTACT
TAGTCCTTTACAAATTCTATCTTAATCTAATGTTAAACTTTTATA
Found at i:10288 original size:15 final size:15
Alignment explanation
Indices: 10268--10306 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
10258 AAGCGAGGGT
10268 GATGAAGACAAGGAA
1 GATGAAGACAAGGAA
**
10283 GATGAAGATGAGGAA
1 GATGAAGACAAGGAA
*
10298 GAAGAAGAC
1 GATGAAGAC
10307 GTAAAACCCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.51, C:0.05, G:0.36, T:0.08
Consensus pattern (15 bp):
GATGAAGACAAGGAA
Done.