Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012885.1 Corchorus olitorius cultivar O-4 contig12918, 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: 20311
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:8240 original size:19 final size:18
Alignment explanation
Indices: 8219--8254 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
8209 AGGGTAAATA
*
8219 AAAAAAAATTGTTTTCAT
1 AAAAAAAAGTGTTTTCAT
*
8237 AAAAAGAAGTGTTTTCAT
1 AAAAAAAAGTGTTTTCAT
8255 GAAAGAAGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.36
Consensus pattern (18 bp):
AAAAAAAAGTGTTTTCAT
Found at i:9127 original size:19 final size:18
Alignment explanation
Indices: 9103--9138 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
9093 TGAAGATTTA
9103 TTGAAGATAATTTGAAGAC
1 TTGAAGATAA-TTGAAGAC
*
9122 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
9139 ATTATTTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.31
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAC
Found at i:10234 original size:24 final size:24
Alignment explanation
Indices: 10207--10281 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
10197 GATCAAAAGG
10207 TAATTATTTAAAGAATAAAAGGGA
1 TAATTATTTAAAGAATAAAAGGGA
* ** * *
10231 TAATTCA--CACTGGAT-TAAGAGG-
1 TAATT-ATTTAAAGAATAAAAG-GGA
10253 TAATTATTTAAAGAATAAAAGGGA
1 TAATTATTTAAAGAATAAAAGGGA
10277 TAATT
1 TAATT
10282 CACACTGGAT
Statistics
Matches: 35, Mismatches: 10, Indels: 12
0.61 0.18 0.21
Matches are distributed among these distances:
21 1 0.03
22 8 0.23
23 12 0.34
24 13 0.37
25 1 0.03
ACGTcount: A:0.48, C:0.04, G:0.17, T:0.31
Consensus pattern (24 bp):
TAATTATTTAAAGAATAAAAGGGA
Found at i:10254 original size:46 final size:46
Alignment explanation
Indices: 10189--10297 Score: 200
Period size: 46 Copynumber: 2.4 Consensus size: 46
10179 TGAGTAATTA
*
10189 TCACACTGGATCAAAAGGTAATTATTTAAAGAATAAAAGGGATAAT
1 TCACACTGGATCAAGAGGTAATTATTTAAAGAATAAAAGGGATAAT
*
10235 TCACACTGGATTAAGAGGTAATTATTTAAAGAATAAAAGGGATAAT
1 TCACACTGGATCAAGAGGTAATTATTTAAAGAATAAAAGGGATAAT
10281 TCACACTGGATCAAGAG
1 TCACACTGGATCAAGAG
10298 TTTTATCTAA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 60 1.00
ACGTcount: A:0.45, C:0.10, G:0.19, T:0.26
Consensus pattern (46 bp):
TCACACTGGATCAAGAGGTAATTATTTAAAGAATAAAAGGGATAAT
Found at i:16866 original size:28 final size:28
Alignment explanation
Indices: 16823--16952 Score: 165
Period size: 28 Copynumber: 4.6 Consensus size: 28
16813 GTCACTTAAG
* *
16823 GGGGCATTTTGATCATTTTACATGACCA
1 GGGGCATTTTGGTCATTTTGCATGACCA
* *
16851 AGGGCATTTTGGTCATTTTGCATGTCCA
1 GGGGCATTTTGGTCATTTTGCATGACCA
16879 GGGGCATTTTGGTCATTTTGCAT-ATCCA
1 GGGGCATTTTGGTCATTTTGCATGA-CCA
*
16907 GGGGCATTTTGGTCATTTTGCA-CATCCA
1 GGGGCATTTTGGTCATTTTGCATGA-CCA
16935 GGGGGCATTTTGGGTCAT
1 -GGGGCATTTT-GGTCAT
16953 CTCAAGTACT
Statistics
Matches: 92, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
28 76 0.83
29 10 0.11
30 6 0.07
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (28 bp):
GGGGCATTTTGGTCATTTTGCATGACCA
Found at i:16884 original size:56 final size:57
Alignment explanation
Indices: 16821--16946 Score: 184
Period size: 56 Copynumber: 2.2 Consensus size: 57
16811 GGGTCACTTA
**
16821 AGGGGGCATTTTGATCATTTTACATGA-CCAAGGGCATTTTGGTCATTTTGCATGTCC
1 AGGGGGCATTTTGATCATTTTACAT-ATCCAAGGGCATTTTGGTCATTTTGCACATCC
* * *
16878 A-GGGGCATTTTGGTCATTTTGCATATCCAGGGGCATTTTGGTCATTTTGCACATCC
1 AGGGGGCATTTTGATCATTTTACATATCCAAGGGCATTTTGGTCATTTTGCACATCC
16934 AGGGGGCATTTTG
1 AGGGGGCATTTTG
16947 GGTCATCTCA
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
55 1 0.02
56 49 0.79
57 12 0.19
ACGTcount: A:0.19, C:0.17, G:0.27, T:0.37
Consensus pattern (57 bp):
AGGGGGCATTTTGATCATTTTACATATCCAAGGGCATTTTGGTCATTTTGCACATCC
Found at i:17340 original size:35 final size:35
Alignment explanation
Indices: 17300--17370 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
17290 GCCTCATGCA
* *
17300 TTATTTTGATTTTCTTTGCTTGGCATTGCATGTAT
1 TTATTTTGATTTTCTTTGCTTCGCATTGCATATAT
17335 TTATTTTGATTTTCTTTGCTTCGCATTGCATATAT
1 TTATTTTGATTTTCTTTGCTTCGCATTGCATATAT
17370 T
1 T
17371 CGATTGCATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.15, C:0.13, G:0.14, T:0.58
Consensus pattern (35 bp):
TTATTTTGATTTTCTTTGCTTCGCATTGCATATAT
Found at i:17568 original size:25 final size:25
Alignment explanation
Indices: 17517--17568 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
17507 TGGTGGTTTT
* *
17517 ACTCTACATTTACATTTCGTTTTGC
1 ACTCCACATTTACATTTCGTTTGGC
17542 ACTCCACATTTACATTTTC-TTTGGC
1 ACTCCACATTTACA-TTTCGTTTGGC
17567 AC
1 AC
17569 CAAATGATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.21, C:0.27, G:0.08, T:0.44
Consensus pattern (25 bp):
ACTCCACATTTACATTTCGTTTGGC
Found at i:18507 original size:22 final size:22
Alignment explanation
Indices: 18453--18500 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
18443 GCCAGCCGAG
*
18453 CAAGGTAGCAAAGTCAGATCGC
1 CAAGGTAGCCAAGTCAGATCGC
18475 CAAGGTAGCCAAGTCAGATCGC
1 CAAGGTAGCCAAGTCAGATCGC
18497 CAAG
1 CAAG
18501 TCAGCCACTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.35, C:0.25, G:0.27, T:0.12
Consensus pattern (22 bp):
CAAGGTAGCCAAGTCAGATCGC
Found at i:18928 original size:25 final size:27
Alignment explanation
Indices: 18895--18956 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
18885 GAACAGACTC
18895 TCCCTCTCTCTCAAGGCAGTCTCATTT
1 TCCCTCTCTCTCAAGGCAGTCTCATTT
18922 TCCCTCTCTCTCAAGGCAGTCTCATTT
1 TCCCTCTCTCTCAAGGCAGTCTCATTT
18949 TCCCTCTC
1 TCCCTCTC
18957 CGTTTTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.13, C:0.40, G:0.10, T:0.37
Consensus pattern (27 bp):
TCCCTCTCTCTCAAGGCAGTCTCATTT
Done.