Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021947.1 Corchorus olitorius cultivar O-4 contig21980, 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: 19150
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:230 original size:20 final size:19
Alignment explanation
Indices: 188--232 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
178 AGGCCCCTGG
*
188 ATTA-GTTTAATTTGGTCC
1 ATTAGGTTTAATTTGGTCA
*
206 CTTAGGTTTAAATTTGGTCA
1 ATTAGGTTT-AATTTGGTCA
226 ATTAGGT
1 ATTAGGT
233 GCCTGTCAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 4 0.18
20 15 0.68
ACGTcount: A:0.24, C:0.09, G:0.20, T:0.47
Consensus pattern (19 bp):
ATTAGGTTTAATTTGGTCA
Found at i:10112 original size:2 final size:2
Alignment explanation
Indices: 10105--10143 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
10095 ATCTTCTTTA
10105 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10144 GTTGTGTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11083 original size:21 final size:23
Alignment explanation
Indices: 11043--11084 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
11033 AGAAATGTTC
11043 AATATAGAATTAATAAAATTATA
1 AATATAGAATTAATAAAATTATA
*
11066 AATA-AGAA-TAATAGAATTA
1 AATATAGAATTAATAAAATTA
11085 AAGGGAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 4 0.22
23 4 0.22
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (23 bp):
AATATAGAATTAATAAAATTATA
Found at i:11384 original size:33 final size:32
Alignment explanation
Indices: 11313--11415 Score: 142
Period size: 33 Copynumber: 3.2 Consensus size: 32
11303 TTTGATGGGG
11313 TAAAAAAATTGACATATAATATATATAT-ATA
1 TAAAAAAATTGACATATAATATATATATAATA
*
11344 T---ATAATTGACATATAATATATATAATAATA
1 TAAAAAAATTGACATATAATATATAT-ATAATA
11374 TAAAAAAATTGACATATAATATATATATATATA
1 TAAAAAAATTGACATATAATATATATATA-ATA
11407 TAACAAAAA
1 TAA-AAAAA
11416 AGAACTTGAA
Statistics
Matches: 63, Mismatches: 2, Indels: 11
0.83 0.03 0.14
Matches are distributed among these distances:
28 21 0.33
29 2 0.03
30 4 0.06
31 1 0.02
32 3 0.05
33 27 0.43
34 5 0.08
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.35
Consensus pattern (32 bp):
TAAAAAAATTGACATATAATATATATATAATA
Found at i:11398 original size:35 final size:32
Alignment explanation
Indices: 11316--11415 Score: 120
Period size: 28 Copynumber: 3.2 Consensus size: 32
11306 GATGGGGTAA
11316 AAAAATTGACATATAATATATATATATAT---
1 AAAAATTGACATATAATATATATATATATAAC
*
11345 -ATAATTGACATATAATATATATAATAATATAA-
1 AAAAATTGACATATAATATATAT-AT-ATATAAC
11377 AAAAATTGACATATAATATATATATATATATAAC
1 AAAAATTGACATAT-A-ATATATATATATATAAC
11411 AAAAA
1 AAAAA
11416 AGAACTTGAA
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
28 21 0.34
29 2 0.03
30 4 0.07
33 18 0.30
34 8 0.13
35 8 0.13
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.35
Consensus pattern (32 bp):
AAAAATTGACATATAATATATATATATATAAC
Found at i:11442 original size:18 final size:20
Alignment explanation
Indices: 11411--11448 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
11401 TATATATAAC
11411 AAAAAAGAACTTGAAGCTTT
1 AAAAAAGAACTTGAAGCTTT
11431 AAAAAA-AA-TTGAAGCTTT
1 AAAAAAGAACTTGAAGCTTT
11449 GGCCTAGTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.56
19 2 0.11
20 6 0.33
ACGTcount: A:0.53, C:0.08, G:0.13, T:0.26
Consensus pattern (20 bp):
AAAAAAGAACTTGAAGCTTT
Found at i:12260 original size:2 final size:2
Alignment explanation
Indices: 12253--12282 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12243 ATTAGGAGAA
12253 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12283 TCTGCATGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12368 original size:2 final size:2
Alignment explanation
Indices: 12361--12397 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
12351 AATTGGAGAA
12361 AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT ACT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A
12398 AGTCTAAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 30 0.91
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12379 original size:109 final size:109
Alignment explanation
Indices: 12177--12390 Score: 394
Period size: 109 Copynumber: 2.0 Consensus size: 109
12167 TTCCAGCAGA
*
12177 GCATGGGGCTTTCAGTAATCCACATGCCATTCAGAAAATGGGTTGGTATGAATTCAAGTCAGTTT
1 GCATGGGGCTTTCAGTAATCCACATGCCATTCAGAAAATGGGTTGATATGAATTCAAGTCAGTTT
12242 AATTAGGAGAAATATATATATATATATATATATATATATATTCT
66 AATTAGGAGAAATATATATATATATATATATATATATATATTCT
*
12286 GCATGGGGCTTTCAGTAATCCACATGCCATTCAGAAAATGGGTTGATATGAATTTAAGTCAGTTT
1 GCATGGGGCTTTCAGTAATCCACATGCCATTCAGAAAATGGGTTGATATGAATTCAAGTCAGTTT
12351 AATT-GGAGAAATATATATATATATTATATATATATATATA
66 AATTAGGAGAAATATATATATATA-TATATATATATATATA
12391 CTATATAAGT
Statistics
Matches: 102, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
108 19 0.19
109 83 0.81
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.36
Consensus pattern (109 bp):
GCATGGGGCTTTCAGTAATCCACATGCCATTCAGAAAATGGGTTGATATGAATTCAAGTCAGTTT
AATTAGGAGAAATATATATATATATATATATATATATATATTCT
Found at i:12383 original size:17 final size:17
Alignment explanation
Indices: 12361--12397 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
12351 AATTGGAGAA
*
12361 ATATATATATATATTAT
1 ATATATATATATACTAT
12378 ATATATATATATACTAT
1 ATATATATATATACTAT
12395 ATA
1 ATA
12398 AGTCTAAACT
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:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATATATATATACTAT
Found at i:12397 original size:15 final size:15
Alignment explanation
Indices: 12361--12389 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12351 AATTGGAGAA
12361 ATATATATATATATT
1 ATATATATATATATT
12376 ATATATATATATAT
1 ATATATATATATAT
12390 ACTATATAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATATATATATATATT
Found at i:12645 original size:18 final size:18
Alignment explanation
Indices: 12624--12688 Score: 53
Period size: 18 Copynumber: 3.4 Consensus size: 18
12614 ATATATATAA
12624 TAATTAAAATACTTACAT
1 TAATTAAAATACTTACAT
12642 TAATTAAATGCAATACTATA-A-
1 TAATT-AA---AATACT-TACAT
* *
12663 TAACTGAAATACTTACAT
1 TAATTAAAATACTTACAT
12681 TAATTAAA
1 TAATTAAA
12689 TTCTTAGGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 14
0.67 0.07 0.26
Matches are distributed among these distances:
16 2 0.06
17 7 0.19
18 11 0.31
19 2 0.06
20 1 0.03
21 4 0.11
22 7 0.19
23 2 0.06
ACGTcount: A:0.51, C:0.11, G:0.03, T:0.35
Consensus pattern (18 bp):
TAATTAAAATACTTACAT
Found at i:12689 original size:17 final size:17
Alignment explanation
Indices: 12624--12694 Score: 52
Period size: 17 Copynumber: 3.8 Consensus size: 17
12614 ATATATATAA
12624 TAATTAAAATACTTACAT
1 TAATT-AAATACTTACAT
* *
12642 TAATTAAATGCAATACTAT
1 TAATTAAATAC-TTAC-AT
*
12661 AATAACTGAAATACTTACAT
1 --TAA-TTAAATACTTACAT
*
12681 TAATTAAATTCTTA
1 TAATTAAATACTTA
12695 GGTTTTTTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 11
0.69 0.12 0.19
Matches are distributed among these distances:
17 14 0.34
18 11 0.27
19 2 0.05
20 2 0.05
21 6 0.15
22 6 0.15
ACGTcount: A:0.48, C:0.11, G:0.03, T:0.38
Consensus pattern (17 bp):
TAATTAAATACTTACAT
Found at i:14041 original size:2 final size:2
Alignment explanation
Indices: 14034--14061 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
14024 ATATTTAGTG
14034 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14062 ATCTTAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15209 original size:6 final size:7
Alignment explanation
Indices: 15178--15206 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
15168 GAAAATTGGC
15178 AACAAAA
1 AACAAAA
15185 AACAAAA
1 AACAAAA
15192 AACAAAA
1 AACAAAA
15199 AACAAAA
1 AACAAAA
15206 A
1 A
15207 CAATACCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (7 bp):
AACAAAA
Found at i:15349 original size:2 final size:2
Alignment explanation
Indices: 15342--15379 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
15332 CTTTAACTAG
15342 TA TA TA TA TA TA TA TA T- TA TA TA T- TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15380 GATCCTTGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 30 0.91
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:15886 original size:32 final size:32
Alignment explanation
Indices: 15826--15887 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
15816 GCTCTTAATA
* *
15826 AAATTGAACAAAATCTTTTTCTTTTTGAAATC
1 AAATCGAACAAAATCTTTTTCTTGTTGAAATC
15858 AAATCGAACAAAATCTTTGTT-TTGTTGAAA
1 AAATCGAACAAAATCTTT-TTCTTGTTGAAA
15888 AAAAAAACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 25 0.93
33 2 0.07
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.40
Consensus pattern (32 bp):
AAATCGAACAAAATCTTTTTCTTGTTGAAATC
Found at i:16144 original size:2 final size:2
Alignment explanation
Indices: 16137--16169 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
16127 GTGATTAAAT
16137 TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16170 CGACGTATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Done.