Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014377.1 Corchorus olitorius cultivar O-4 contig14410, 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: 70836
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:249 original size:24 final size:25
Alignment explanation
Indices: 216--272 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
206 GTCAGCCTTG
*
216 AATTT-TTTAATGT-TTAATTCTTA
1 AATTTATTTAATGTCTTAATTATTA
*
239 AATTTATTTAATGTCTTAATTATTC
1 AATTTATTTAATGTCTTAATTATTA
264 AATTTATTT
1 AATTTATTT
273 TACAATCCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.17
24 8 0.27
25 17 0.57
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.60
Consensus pattern (25 bp):
AATTTATTTAATGTCTTAATTATTA
Found at i:3728 original size:66 final size:66
Alignment explanation
Indices: 3596--3723 Score: 199
Period size: 66 Copynumber: 2.0 Consensus size: 66
3586 AAGTTTCTTA
*
3596 ACAAGTTTTTATATATTTTGAATTCCATTTCTTCTTTTGATTTTTCAAAGTTACTAAGTAATATT
1 ACAAGTTTCTATATATTTTGAATTCCATTTCTTCTTTTGATTTTTCAAAGTTACTAAGTAATATT
3661 G
66 G
* *
3662 ACAAGTTTCTCTATATTTTGAATTCCATTT-TGTCTTTTGA-TTTTCAAAGTT-TTAAGTAATAT
1 ACAAGTTTCTATATATTTTGAATTCCATTTCT-TCTTTTGATTTTTCAAAGTTACTAAGTAATAT
3724 ATTGAGTTGA
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
64 10 0.17
65 12 0.21
66 36 0.62
ACGTcount: A:0.28, C:0.11, G:0.09, T:0.52
Consensus pattern (66 bp):
ACAAGTTTCTATATATTTTGAATTCCATTTCTTCTTTTGATTTTTCAAAGTTACTAAGTAATATT
G
Found at i:4147 original size:12 final size:12
Alignment explanation
Indices: 4130--4169 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
4120 GATTTTTGTT
*
4130 AAAAAAAAAGAA
1 AAAAAAAAATAA
*
4142 AAAAAAAAATAT
1 AAAAAAAAATAA
*
4154 AAAATAAAATAA
1 AAAAAAAAATAA
4166 AAAA
1 AAAA
4170 TTGAAATTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.88, C:0.00, G:0.03, T:0.10
Consensus pattern (12 bp):
AAAAAAAAATAA
Found at i:27372 original size:20 final size:21
Alignment explanation
Indices: 27347--27389 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
27337 GAAAACTGAA
27347 TTGCTA-ATACCGTCCCCTTT
1 TTGCTACATACCGTCCCCTTT
*
27367 TTGCTACTTACCGTCCCCTTT
1 TTGCTACATACCGTCCCCTTT
27388 TT
1 TT
27390 ACACTTTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.12, C:0.35, G:0.09, T:0.44
Consensus pattern (21 bp):
TTGCTACATACCGTCCCCTTT
Found at i:27395 original size:20 final size:21
Alignment explanation
Indices: 27354--27395 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
27344 GAATTGCTAA
*
27354 TACCGTCCCCTTTTTGCTACT
1 TACCGTCCCCTTTTTACTACT
27375 TACCGTCCCCTTTTTAC-ACT
1 TACCGTCCCCTTTTTACTACT
27395 T
1 T
27396 TTGTCATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.12, C:0.38, G:0.07, T:0.43
Consensus pattern (21 bp):
TACCGTCCCCTTTTTACTACT
Found at i:35457 original size:17 final size:17
Alignment explanation
Indices: 35426--35466 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
35416 ATTTTTAATG
35426 TTTAA-TTCTTAAATTTA
1 TTTAATTTCTTAAA-TTA
35443 TTTAATTTCTT-AATTA
1 TTTAATTTCTTAAATTA
*
35459 TTCAATTT
1 TTTAATTT
35467 ATTTTACAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 10 0.45
17 7 0.32
18 5 0.23
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTAATTTCTTAAATTA
Found at i:35457 original size:25 final size:24
Alignment explanation
Indices: 35419--35470 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
35409 CCTTGAAATT
*
35419 TTTAATGTTTAATTCTTAAATTTA
1 TTTAATGTTTAATTATTAAATTTA
* *
35443 TTTAATTTCTTAATTATTCAATTTA
1 TTTAATGT-TTAATTATTAAATTTA
35468 TTT
1 TTT
35471 TACAATCCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.62
Consensus pattern (24 bp):
TTTAATGTTTAATTATTAAATTTA
Found at i:37348 original size:56 final size:56
Alignment explanation
Indices: 37281--37387 Score: 196
Period size: 56 Copynumber: 1.9 Consensus size: 56
37271 CATTTGGCAT
37281 TTCATTCTAGAACTGCAGGGTTGGAAAGTTTGTTCATGTAACCTTTCTATTGTTAA
1 TTCATTCTAGAACTGCAGGGTTGGAAAGTTTGTTCATGTAACCTTTCTATTGTTAA
* *
37337 TTCATTCTAGAACTGCAGGGTTTGAAAGTTTGTTCATTTAACCTTTCTATT
1 TTCATTCTAGAACTGCAGGGTTGGAAAGTTTGTTCATGTAACCTTTCTATT
37388 CTTAGTTGTG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.43
Consensus pattern (56 bp):
TTCATTCTAGAACTGCAGGGTTGGAAAGTTTGTTCATGTAACCTTTCTATTGTTAA
Found at i:48905 original size:21 final size:21
Alignment explanation
Indices: 48861--48901 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
48851 ATCCGTGAAG
48861 GAGAAAAATTGGGGATGAAAAT
1 GAGAAAAATTGGGGA-GAAAAT
48883 GAGAAAAATTGGGG-GAAAA
1 GAGAAAAATTGGGGAGAAAA
48902 ATGAAGGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
22 14 0.74
ACGTcount: A:0.51, C:0.00, G:0.34, T:0.15
Consensus pattern (21 bp):
GAGAAAAATTGGGGAGAAAAT
Found at i:58420 original size:30 final size:30
Alignment explanation
Indices: 58384--58440 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
58374 ATAAAGTAGA
58384 AAACTCATCATAAGACAAACCATCACAAGC
1 AAACTCATCATAAGACAAACCATCACAAGC
58414 AAACTCATCATAAGACAAACCATCACA
1 AAACTCATCATAAGACAAACCATCACA
58441 GGCGCATAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.51, C:0.30, G:0.05, T:0.14
Consensus pattern (30 bp):
AAACTCATCATAAGACAAACCATCACAAGC
Found at i:58422 original size:15 final size:15
Alignment explanation
Indices: 58384--58440 Score: 71
Period size: 15 Copynumber: 3.7 Consensus size: 15
58374 ATAAAGTAGA
*
58384 AAACTCATCATAAGAC
1 AAAC-CATCACAAGAC
58400 AAACCATCACAAG-C
1 AAACCATCACAAGAC
*
58414 AAACTCATCATAAGAC
1 AAAC-CATCACAAGAC
58430 AAACCATCACA
1 AAACCATCACA
58441 GGCGCATAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
14 5 0.14
15 22 0.61
16 9 0.25
ACGTcount: A:0.51, C:0.30, G:0.05, T:0.14
Consensus pattern (15 bp):
AAACCATCACAAGAC
Found at i:66254 original size:26 final size:26
Alignment explanation
Indices: 66218--66269 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
66208 TTTTTGACTA
* *
66218 TATGTGAAATTATGTGGAATTATATG
1 TATGTGAAATTATGTGAAACTATATG
66244 TATGTGAAATTATGTGAAACTATATG
1 TATGTGAAATTATGTGAAACTATATG
66270 CTTGAGGCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.37, C:0.02, G:0.21, T:0.40
Consensus pattern (26 bp):
TATGTGAAATTATGTGAAACTATATG
Found at i:66294 original size:13 final size:13
Alignment explanation
Indices: 66276--66300 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
66266 TATGCTTGAG
66276 GCCTCTGTTTTGC
1 GCCTCTGTTTTGC
66289 GCCTCTGTTTTG
1 GCCTCTGTTTTG
66301 TCATGACTAT
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:0.00, C:0.28, G:0.24, T:0.48
Consensus pattern (13 bp):
GCCTCTGTTTTGC
Found at i:67419 original size:17 final size:17
Alignment explanation
Indices: 67397--67435 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
67387 AAAGGCCCCC
67397 TACTAGTAATAAAACAT
1 TACTAGTAATAAAACAT
* *
67414 TACTAGTACTAAACCAT
1 TACTAGTAATAAAACAT
67431 TACTA
1 TACTA
67436 ATCATGTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.18, G:0.05, T:0.31
Consensus pattern (17 bp):
TACTAGTAATAAAACAT
Found at i:68263 original size:33 final size:33
Alignment explanation
Indices: 68226--68291 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
68216 ACAACAGAAA
* *
68226 GGCATAATATGAATGGCTAATAATGAGAGATAG
1 GGCATAACATGAATGGCTAATAATGAGAAATAG
68259 GGCATAACATGAATGGCTAATAATGAGAAATAG
1 GGCATAACATGAATGGCTAATAATGAGAAATAG
68292 CTGGTGCCCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.44, C:0.08, G:0.26, T:0.23
Consensus pattern (33 bp):
GGCATAACATGAATGGCTAATAATGAGAAATAG
Found at i:69726 original size:42 final size:43
Alignment explanation
Indices: 69663--69751 Score: 128
Period size: 42 Copynumber: 2.1 Consensus size: 43
69653 TATATTAAAG
* *
69663 TTATCCCTAAACTGTTGTATGCTCAGCATTCAGTTTTTTTTT-
1 TTATCCCTAAACTGCTATATGCTCAGCATTCAGTTTTTTTTTC
*
69705 TTAT-CCTCAAACTGCTATATGCTCAGCATTTAGTTTTTTTTTC
1 TTATCCCT-AAACTGCTATATGCTCAGCATTCAGTTTTTTTTTC
69748 TTAT
1 TTAT
69752 GACATTTGTC
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
41 3 0.07
42 35 0.83
43 4 0.10
ACGTcount: A:0.20, C:0.19, G:0.10, T:0.51
Consensus pattern (43 bp):
TTATCCCTAAACTGCTATATGCTCAGCATTCAGTTTTTTTTTC
Done.