Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024821.1 Corchorus olitorius cultivar O-4 contig24854, 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: 13558
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35
Found at i:2329 original size:7 final size:7
Alignment explanation
Indices: 2317--2357 Score: 73
Period size: 7 Copynumber: 5.7 Consensus size: 7
2307 GAAGACTAGG
2317 AAAAACA
1 AAAAACA
2324 AAAAACAA
1 AAAAAC-A
2332 AAAAACA
1 AAAAACA
2339 AAAAACA
1 AAAAACA
2346 AAAAACA
1 AAAAACA
2353 AAAAA
1 AAAAA
2358 GACAAGAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 26 0.79
8 7 0.21
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAACA
Found at i:2345 original size:22 final size:23
Alignment explanation
Indices: 2317--2362 Score: 85
Period size: 22 Copynumber: 2.0 Consensus size: 23
2307 GAAGACTAGG
2317 AAAAACAAAAAACAAAAAA-ACA
1 AAAAACAAAAAACAAAAAAGACA
2339 AAAAACAAAAAACAAAAAAGACA
1 AAAAACAAAAAACAAAAAAGACA
2362 A
1 A
2363 GAAGACTAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.85, C:0.13, G:0.02, T:0.00
Consensus pattern (23 bp):
AAAAACAAAAAACAAAAAAGACA
Found at i:2943 original size:40 final size:40
Alignment explanation
Indices: 2894--2974 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
2884 TTACAGCTCA
*
2894 AGCTAACCTATAATATGTATCTTGAATTGTAGAATTAAAC
1 AGCTAACCTATAATATGTATCTTGAATTCTAGAATTAAAC
*
2934 AGCTCACCTATAATATGTATCTTGAATTCTAGAATTAAAC
1 AGCTAACCTATAATATGTATCTTGAATTCTAGAATTAAAC
2974 A
1 A
2975 ACCCAATTCC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (40 bp):
AGCTAACCTATAATATGTATCTTGAATTCTAGAATTAAAC
Found at i:3928 original size:17 final size:17
Alignment explanation
Indices: 3883--3929 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
3873 TAATCAATTC
3883 TAATTAATATTTATTAT
1 TAATTAATATTTATTAT
*
3900 TATTTAAATATTTATT-T
1 TAATT-AATATTTATTAT
3917 TAATTGAATATTT
1 TAATT-AATATTT
3930 GTGATCTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 16 0.62
18 10 0.38
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
TAATTAATATTTATTAT
Found at i:4276 original size:33 final size:33
Alignment explanation
Indices: 4239--4301 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
4229 ACACCACTTT
4239 TTTATCTCTTTCTCAGTGACAGGTTGTATTTTC
1 TTTATCTCTTTCTCAGTGACAGGTTGTATTTTC
4272 TTTATCTCTTTCTCAGTGACAGGTTGTATT
1 TTTATCTCTTTCTCAGTGACAGGTTGTATT
4302 ATATAGTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.16, C:0.17, G:0.16, T:0.51
Consensus pattern (33 bp):
TTTATCTCTTTCTCAGTGACAGGTTGTATTTTC
Found at i:7313 original size:31 final size:31
Alignment explanation
Indices: 7278--7351 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
7268 AAGAGTTAGG
* *
7278 TGCAAAGTGGCAGTCCGTATAAATTTAAGGA
1 TGCAAAGTGACAATCCGTATAAATTTAAGGA
* *
7309 TGCAAAGTGACAATCTGTATAAATTTAAGGG
1 TGCAAAGTGACAATCCGTATAAATTTAAGGA
7340 TGCAAAGTGACA
1 TGCAAAGTGACA
7352 TTTATGCCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.26
Consensus pattern (31 bp):
TGCAAAGTGACAATCCGTATAAATTTAAGGA
Found at i:9307 original size:8 final size:8
Alignment explanation
Indices: 9294--9318 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
9284 TAGACATGTG
9294 TGATTTCT
1 TGATTTCT
9302 TGATTTCT
1 TGATTTCT
9310 TGATTTCT
1 TGATTTCT
9318 T
1 T
9319 TTATATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.64
Consensus pattern (8 bp):
TGATTTCT
Found at i:9982 original size:18 final size:19
Alignment explanation
Indices: 9959--9997 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
9949 TGTTCATTAA
9959 AAAGGTATTT-AA-GTTATC
1 AAAGGT-TTTGAATGTTATC
9977 AAAGGTTTTGAATGTTATC
1 AAAGGTTTTGAATGTTATC
9996 AA
1 AA
9998 TAAATTCAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.16
18 8 0.42
19 8 0.42
ACGTcount: A:0.38, C:0.05, G:0.18, T:0.38
Consensus pattern (19 bp):
AAAGGTTTTGAATGTTATC
Found at i:11341 original size:60 final size:60
Alignment explanation
Indices: 11254--11416 Score: 247
Period size: 60 Copynumber: 2.7 Consensus size: 60
11244 GCTAATTGCT
* * *
11254 CAAATAAGGGCCTAACGTT-TGCCAAAATGATCAAATAATGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTAT-CAAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
11314 CAAATAAGGGCCTAACGTTATCAAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTATCAAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
** * *
11374 CAAATAATAGTCTAACGTTATCGAAAATGCTCAAATAAGGGCC
1 CAAATAAGGGCCTAACGTTATCAAAAATGCTCAAATAAGGGCC
11417 TGACATCAGT
Statistics
Matches: 95, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
60 94 0.99
61 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTATCAAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
Found at i:11498 original size:31 final size:30
Alignment explanation
Indices: 11458--11623 Score: 121
Period size: 31 Copynumber: 5.5 Consensus size: 30
11448 TTGATGCCAT
11458 GCCCTTATTTGAGCATTTTGGCAAACGTTAG
1 GCCCTTATTTGAGCATTTT-GCAAACGTTAG
* ** * *
11489 GCTCTTATTTG-GCCAAATT--AAA-ATATCG
1 GCCCTTATTTGAG-CATTTTGCAAACGT-TAG
11517 GCCCCTTATTTGAGCATTTTGGCAAACGTTAG
1 G-CCCTTATTTGAGCATTTT-GCAAACGTTAG
** * *
11549 GCCCTTATTTG-GCCAAATT--AAAAGATCAG
1 GCCCTTATTTGAG-CATTTTGCAAACG-TTAG
*
11578 ACCCTTATTTGAGCATTTTGACAAACGTTAG
1 GCCCTTATTTGAGCATTTTG-CAAACGTTAG
11609 GCCCTTATTTGAGCA
1 GCCCTTATTTGAGCA
11624 ATTAGCCTAT
Statistics
Matches: 101, Mismatches: 20, Indels: 28
0.68 0.13 0.19
Matches are distributed among these distances:
27 1 0.01
28 10 0.10
29 30 0.30
30 4 0.04
31 45 0.45
32 10 0.10
33 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (30 bp):
GCCCTTATTTGAGCATTTTGCAAACGTTAG
Found at i:11556 original size:60 final size:60
Alignment explanation
Indices: 11459--11619 Score: 277
Period size: 60 Copynumber: 2.7 Consensus size: 60
11449 TGATGCCATG
* * * *
11459 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCTCTTATTTGGCCAAATTAAAATATCGGC
1 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA
11519 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA
1 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA
*
11579 CCCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTG
1 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
11620 AGCAATTAGC
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 96 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (60 bp):
CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA
Found at i:12901 original size:36 final size:35
Alignment explanation
Indices: 12861--12930 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 35
12851 TTCAATAACC
*
12861 TTACATCTTTTATG-ATTTTGGTTATCATATTTCTTA
1 TTACA-CTTTT-TGAATTTTGATTATCATATTTCTTA
12897 TTACACTTTTTGTAATTTTGATTATCATATTTCT
1 TTACACTTTTTG-AATTTTGATTATCATATTTCT
12931 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 2 0.06
35 5 0.16
36 24 0.77
ACGTcount: A:0.23, C:0.11, G:0.07, T:0.59
Consensus pattern (35 bp):
TTACACTTTTTGAATTTTGATTATCATATTTCTTA
Done.