Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009540.1 Corchorus olitorius cultivar O-4 contig09572, 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: 9034
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:2358 original size:9 final size:8
Alignment explanation
Indices: 2335--2369 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
2325 GTTGAAGAAT
2335 AAATG-AA
1 AAATGAAA
2342 AAATGAAA
1 AAATGAAA
2350 AAATGGAAA
1 AAAT-GAAA
2359 AAATGAAA
1 AAATGAAA
2367 AAA
1 AAA
2370 CGGAAAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 5 0.19
8 13 0.50
9 8 0.31
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.11
Consensus pattern (8 bp):
AAATGAAA
Found at i:2362 original size:17 final size:17
Alignment explanation
Indices: 2340--2376 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
2330 AGAATAAATG
*
2340 AAAAATGAAAAAATGGA
1 AAAAATGAAAAAACGGA
2357 AAAAATGAAAAAACGGA
1 AAAAATGAAAAAACGGA
2374 AAA
1 AAA
2377 GAATCAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.73, C:0.03, G:0.16, T:0.08
Consensus pattern (17 bp):
AAAAATGAAAAAACGGA
Found at i:5349 original size:5 final size:5
Alignment explanation
Indices: 5339--5369 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
5329 TTTTTATTTA
5339 TTATT TTATT TTATT TTATT TTATT TT-TT TT
1 TTATT TTATT TTATT TTATT TTATT TTATT TT
5370 CTTATGATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (5 bp):
TTATT
Found at i:5590 original size:29 final size:29
Alignment explanation
Indices: 5558--5694 Score: 108
Period size: 29 Copynumber: 5.2 Consensus size: 29
5548 AACTTAATTT
5558 GCAACAGTCTCATTGGTTGAACTTTGCAA
1 GCAACAGTCTCATTGGTTGAACTTTGCAA
* *
5587 GCAACA---TC--T--TTCAA-TTTGAAAA
1 GCAACAGTCTCATTGGTTGAACTTTG-CAA
5609 GCAACAGTCTCATTGGTTGAACTTTGCAA
1 GCAACAGTCTCATTGGTTGAACTTTGCAA
* *
5638 GCAACA---TC--T--TTCAA-TTTGAAAA
1 GCAACAGTCTCATTGGTTGAACTTTG-CAA
5660 GCAACAGTCTCATTGGTTGAACTTTGCAA
1 GCAACAGTCTCATTGGTTGAACTTTGCAA
5689 GCAACA
1 GCAACA
5695 TCTTTCAATT
Statistics
Matches: 82, Mismatches: 8, Indels: 36
0.65 0.06 0.29
Matches are distributed among these distances:
21 8 0.10
22 24 0.29
24 2 0.02
25 4 0.05
26 4 0.05
27 2 0.02
29 30 0.37
30 8 0.10
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (29 bp):
GCAACAGTCTCATTGGTTGAACTTTGCAA
Found at i:5611 original size:22 final size:22
Alignment explanation
Indices: 5585--5665 Score: 65
Period size: 22 Copynumber: 3.4 Consensus size: 22
5575 TGAACTTTGC
5585 AAGCAACATCTTTCAATTTGAA
1 AAGCAACATCTTTCAATTTGAA
* *
5607 AAGCAACAGTCTCATTGGTTGAACTTTG-C
1 AAGCAACA---TC--T--TTCAA-TTTGAA
5636 AAGCAACATCTTTCAATTTGAA
1 AAGCAACATCTTTCAATTTGAA
5658 AAGCAACA
1 AAGCAACA
5666 GTCTCATTGG
Statistics
Matches: 46, Mismatches: 4, Indels: 18
0.68 0.06 0.26
Matches are distributed among these distances:
21 4 0.09
22 20 0.43
24 1 0.02
25 2 0.04
26 2 0.04
27 1 0.02
29 12 0.26
30 4 0.09
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (22 bp):
AAGCAACATCTTTCAATTTGAA
Found at i:5624 original size:51 final size:51
Alignment explanation
Indices: 5558--5711 Score: 308
Period size: 51 Copynumber: 3.0 Consensus size: 51
5548 AACTTAATTT
5558 GCAACAGTCTCATTGGTTGAACTTTGCAAGCAACATCTTTCAATTTGAAAA
1 GCAACAGTCTCATTGGTTGAACTTTGCAAGCAACATCTTTCAATTTGAAAA
5609 GCAACAGTCTCATTGGTTGAACTTTGCAAGCAACATCTTTCAATTTGAAAA
1 GCAACAGTCTCATTGGTTGAACTTTGCAAGCAACATCTTTCAATTTGAAAA
5660 GCAACAGTCTCATTGGTTGAACTTTGCAAGCAACATCTTTCAATTTGAAAA
1 GCAACAGTCTCATTGGTTGAACTTTGCAAGCAACATCTTTCAATTTGAAAA
5711 G
1 G
5712 GCTAAAAGTT
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 103 1.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.31
Consensus pattern (51 bp):
GCAACAGTCTCATTGGTTGAACTTTGCAAGCAACATCTTTCAATTTGAAAA
Found at i:7267 original size:60 final size:60
Alignment explanation
Indices: 7171--7335 Score: 210
Period size: 60 Copynumber: 2.8 Consensus size: 60
7161 GCTAATTGCT
* * * * *
7171 CAAATAAGGGTCTAATGTTTGTC-AAAATGTTCAAATAGGGGCCTGATCTTTTAGTTTGGC
1 CAAATAAGGGCCTAACG-TTATCGAAAATGCTCAAATAGGGGCCTGATCTTTTAATTTGGC
**
7231 CAAAT-AGAGGCCTAACGTTATCGAAAATGCTCAAATAAGGATCC-GATCTTTTAATTTGGC
1 CAAATAAG-GGCCTAACGTTATCGAAAATGCTCAAAT-AGGGGCCTGATCTTTTAATTTGGC
*
7291 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCTG
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAGGGGCCTG
7336 GCGTCAGTTT
Statistics
Matches: 90, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
59 10 0.11
60 73 0.81
61 7 0.08
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.28
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAGGGGCCTGATCTTTTAATTTGGC
Found at i:7329 original size:31 final size:31
Alignment explanation
Indices: 7231--7334 Score: 92
Period size: 31 Copynumber: 3.4 Consensus size: 31
7221 TTAGTTTGGC
7231 CAAAT-AGAGGCCTAACGTTATCGAAAATGCT
1 CAAATAAG-GGCCTAACGTTATCGAAAATGCT
* * * * **
7262 CAAATAAGGATCCGATC-TT-T-TAATTTGGC-
1 CAAATAAGG-GCCTAACGTTATCGAAAAT-GCT
7291 CAAATAAGGGCCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
7322 CAAATAAGGGCCT
1 CAAATAAGGGCCT
7335 GGCGTCAGTT
Statistics
Matches: 54, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
28 4 0.07
29 14 0.26
30 6 0.11
31 24 0.44
32 6 0.11
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (31 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCT
Found at i:7411 original size:31 final size:30
Alignment explanation
Indices: 7373--7476 Score: 106
Period size: 31 Copynumber: 3.4 Consensus size: 30
7363 TTTCTATGTC
7373 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTTGG-AAACGTT
** * *
7404 AGGCCCTTATTTG-GCCAAATT--AAAAGATC
1 AGGCCCTTATTTGAG-CATTTTGGAAACG-TT
*
7433 GGGCCCTTATTTGAGCATTTTGGTAAACGTT
1 AGGCCCTTATTTGAGCATTTTGG-AAACGTT
7464 AGGCCCTTATTTG
1 AGGCCCTTATTTG
7477 CCTAAATTAA
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
28 4 0.07
29 17 0.30
30 2 0.04
31 30 0.53
32 4 0.07
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (30 bp):
AGGCCCTTATTTGAGCATTTTGGAAACGTT
Found at i:7467 original size:60 final size:61
Alignment explanation
Indices: 7371--7536 Score: 255
Period size: 60 Copynumber: 2.8 Consensus size: 61
7361 ATTTTCTATG
7371 TCAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCC-AAATTAAAAGA
1 TCAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCTAAATTAAAAGA
* *
7431 TCGGGCCCTTATTTGAGCATTTTGGTAAACGTTAGGCCCTTATTT-GCCTAAATTAAAAGA
1 TCAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCTAAATTAAAAGA
* * * * *
7491 TCAGACCCTTATTTGAACATTTTGACAAACATTAGACCCTTATTTG
1 TCAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
7537 AGCAATTAGC
Statistics
Matches: 95, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
59 3 0.03
60 92 0.97
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.34
Consensus pattern (61 bp):
TCAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCTAAATTAAAAGA
Done.