Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023762.1 Corchorus olitorius cultivar O-4 contig23795, 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: 14517
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Found at i:2235 original size:24 final size:25
Alignment explanation
Indices: 2206--2256 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
2196 ATAGAGTAAC
*
2206 AATAAAATAAATAAACAAGA-AAAT
1 AATAAAATAAAGAAACAAGATAAAT
*
2230 AATAAAATTAAGAAACAAGATAAAT
1 AATAAAATAAAGAAACAAGATAAAT
2255 AA
1 AA
2257 ATACTCCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.73, C:0.04, G:0.06, T:0.18
Consensus pattern (25 bp):
AATAAAATAAAGAAACAAGATAAAT
Found at i:2734 original size:27 final size:28
Alignment explanation
Indices: 2684--2736 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
2674 AAATCAATTA
*
2684 GAAATCATAAAAACATAAAGATAAATCT
1 GAAATCATAAAAACACAAAGATAAATCT
2712 GAAATCATAAAATAC-CAAA-ATAAAT
1 GAAATCATAAAA-ACACAAAGATAAAT
2737 AATCAGATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 6 0.26
28 15 0.65
29 2 0.09
ACGTcount: A:0.62, C:0.11, G:0.06, T:0.21
Consensus pattern (28 bp):
GAAATCATAAAAACACAAAGATAAATCT
Found at i:4050 original size:33 final size:33
Alignment explanation
Indices: 4013--4077 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
4003 CTAAGTTATT
4013 GCTTCATATGCAATGCCCCTTAAGCCAAAAGGA
1 GCTTCATATGCAATGCCCCTTAAGCCAAAAGGA
*
4046 GCTTCATATGCAATGCCCCTTATGCCAAAAGG
1 GCTTCATATGCAATGCCCCTTAAGCCAAAAGG
4078 CAAGGCTCCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (33 bp):
GCTTCATATGCAATGCCCCTTAAGCCAAAAGGA
Found at i:8475 original size:22 final size:21
Alignment explanation
Indices: 8446--8491 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
8436 AATTTCTTGA
* *
8446 AAATCAGAATATCAATAAATC
1 AAATCAGAAAATCAAGAAATC
8467 AAATACAGAAAATCAAGAAATC
1 AAAT-CAGAAAATCAAGAAATC
8489 AAA
1 AAA
8492 AACAACAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.63, C:0.13, G:0.07, T:0.17
Consensus pattern (21 bp):
AAATCAGAAAATCAAGAAATC
Found at i:9561 original size:29 final size:30
Alignment explanation
Indices: 9524--9584 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
9514 TTTTCACAGA
*
9524 TGGTCAAATAAG-CCTCT-AACTTTTTATTT
1 TGGTCAAATAAGTCCT-TGAACTTTTAATTT
*
9553 TGGTTAAATAAGTCCTTGAACTTTTAATTT
1 TGGTCAAATAAGTCCTTGAACTTTTAATTT
9583 TG
1 TG
9585 ACCAAATAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 12 0.43
30 16 0.57
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (30 bp):
TGGTCAAATAAGTCCTTGAACTTTTAATTT
Found at i:9592 original size:30 final size:29
Alignment explanation
Indices: 9528--9592 Score: 69
Period size: 30 Copynumber: 2.2 Consensus size: 29
9518 CACAGATGGT
* **
9528 CAAATAAGCCTCTAACTTTTTATTTTGGT
1 CAAATAAGCCTCTAACTTTTAATTTTGAC
*
9557 TAAATAAGTCCT-TGAACTTTTAATTTTGAC
1 CAAATAAG-CCTCT-AACTTTTAATTTTGAC
9587 CAAATA
1 CAAATA
9593 GACCCAGCCG
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
29 8 0.28
30 21 0.72
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.42
Consensus pattern (29 bp):
CAAATAAGCCTCTAACTTTTAATTTTGAC
Found at i:13338 original size:2 final size:2
Alignment explanation
Indices: 13331--13360 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
13321 CTAGGATCGG
13331 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
13361 TGTATACATA
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:13541 original size:24 final size:23
Alignment explanation
Indices: 13514--13565 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 23
13504 TTTTGAATTA
13514 AAGAAACAATAAAAATAAATAAAC
1 AAGAAACAATAAAAATAAA-AAAC
* * *
13538 AAGAAAATAATAAAATTAAACAAC
1 AAG-AAACAATAAAAATAAAAAAC
13562 AAGA
1 AAGA
13566 TAAAAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
23 1 0.04
24 9 0.38
25 14 0.58
ACGTcount: A:0.73, C:0.08, G:0.06, T:0.13
Consensus pattern (23 bp):
AAGAAACAATAAAAATAAAAAAC
Found at i:13559 original size:21 final size:21
Alignment explanation
Indices: 13521--13574 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
13511 TTAAAGAAAC
* *
13521 AATAAAAATAAATAAACAAGAA
1 AATAAAAA-AATTAAACAACAA
*
13543 AATAATAAAATTAAACAACAA
1 AATAAAAAAATTAAACAACAA
*
13564 GATAAAAAAAT
1 AATAAAAAAAT
13575 ACTCCAATCC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 20 0.74
22 7 0.26
ACGTcount: A:0.74, C:0.06, G:0.04, T:0.17
Consensus pattern (21 bp):
AATAAAAAAATTAAACAACAA
Found at i:14038 original size:20 final size:20
Alignment explanation
Indices: 14003--14043 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
13993 AATCAATTAG
14003 AAATCATAAAAACATAAGAAT
1 AAATCATAAAAACATAA-AAT
*
14024 AAATC-TAAAATCATAAAAT
1 AAATCATAAAAACATAAAAT
14043 A
1 A
14044 CCAAGATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 10 0.53
21 5 0.26
ACGTcount: A:0.66, C:0.10, G:0.02, T:0.22
Consensus pattern (20 bp):
AAATCATAAAAACATAAAAT
Done.