Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015075.1 Corchorus olitorius cultivar O-4 contig15108, 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: 11856
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--36 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1 TA TA TA TA 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 TA TA TA TA
37 CTAGTCTTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1974 original size:25 final size:26
Alignment explanation
Indices: 1931--1980 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
1921 GGTACAGTAC
1931 AAATTGAATTTTTCTAAATAAAATAA
1 AAATTGAATTTTTCTAAATAAAATAA
*
1957 AAATTGAA-TTTTGTAAATAAAATA
1 AAATTGAATTTTTCTAAATAAAATA
1981 TTTTAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (26 bp):
AAATTGAATTTTTCTAAATAAAATAA
Found at i:2162 original size:25 final size:27
Alignment explanation
Indices: 2110--2175 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
2100 AAAAGTACAC
*
2110 AAAATTATATTTTAATAGTGGCATAA-TT
1 AAAA-TATATTTTAATAATGGCA-AATTT
*
2138 AAAATATTTTTTAATAATGGC-AATTT
1 AAAATATATTTTAATAATGGCAAATTT
2164 AGAAATATATTT
1 A-AAATATATTT
2176 GGAGAAAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
25 2 0.06
26 3 0.09
27 24 0.73
28 4 0.12
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (27 bp):
AAAATATATTTTAATAATGGCAAATTT
Found at i:3166 original size:351 final size:351
Alignment explanation
Indices: 2516--3207 Score: 975
Period size: 351 Copynumber: 2.0 Consensus size: 351
2506 ATTGCCAAGT
* * *
2516 CAGATGTCTTGAAGTCTAAATCTGATATTCTTAGACCCAAATTGTTAATATGGAAGCCCAAAGAA
1 CAGATGTCTTGAACTCTAAATCCGATATTCTTAGACCCAAATTGTTAATATGGAAACCCAAAGAA
* *
2581 GTAGTTCAAGACCAATCAGTAATTATGATGCAGTAATGATTCAGCCCTGATACAGCATTGTGAAA
66 GGAGTCCAAGACCAATCAGTAATTATGATGCAGTAATGATTCAGCCCTGATACAGCATTGTGAAA
*
2646 TCATATTCAAATGAGGACTTAACAAGAGCAATTTTGGAAGAAAATTCATAACTTTTGATGCAAAA
131 TCATATTCAAAAGAGGACTTAACAAGAGCAATTTTGGAAGAAAATTCATAACTTTTGATGCAAAA
2711 CTCAGAAAAATGCAAATGAAATACCGTTGGAAAGAGAATTCCAAGATCTACAACATTTATGTTTA
196 CTCAGAAAAATGCAAATGAAATACCGTTGGAAAGAGAATTCCAAGATCTACAACATTTATGTTTA
* * * *
2776 CCTTGAGACCTAATTTTGCAGCTTCGATAGACGATTTTGCCCTTAAAATTTCTAGA-TTGAATTG
261 CCTCGAGACCTAATTATGCAGCTTCGATAGACAATTTTGCCCTTAAAATTTCTAGACAT-AATTG
* *
2840 ATTTTCTTCTAAACCGATTTGGAGAGC
325 ATCTTCTCCTAAACCGATTTGGAGAGC
*
2867 CAGATGTCTTGAAACT-TAAATCCGATATTCTTAGGCCC-AATTCGTTAATATGGAAACCCAAAG
1 CAGATGTCTTG-AACTCTAAATCCGATATTCTTAGACCCAAATT-GTTAATATGGAAACCCAAAG
* * * *
2930 AAGGAGTCCAAGTCCAATCAGTAATTATGATGCAGTAATGGTTCAGCCCTGATGCAGCATTGTTA
64 AAGGAGTCCAAGACCAATCAGTAATTATGATGCAGTAATGATTCAGCCCTGATACAGCATTGTGA
* * *
2995 AATCCTATTCAAAAGAGGACTTCACAAGAGCAGTTTTGGAAGAAAATTCATAACTTTTGAT-CTA
129 AATCATATTCAAAAGAGGACTTAACAAGAGCAATTTTGGAAGAAAATTCATAACTTTTGATGC-A
* * * ** * *
3059 GAGCTCATAAAAATGCAAATGAGGTACCGTTGGATAGAGGATTCCAAGATCTACAAC-TATTATG
193 AAACTCAGAAAAATGCAAATGAAATACCGTTGGAAAGAGAATTCCAAGATCTACAACAT-TTATG
* * * * * *
3123 TTTATCTCGAGACCTAATTATGTC-G-TTCCGGTGGATAATTTTGCCCTTGAAATTTCTGGACAT
257 TTTACCTCGAGACCTAATTATG-CAGCTT-CGATAGACAATTTTGCCCTTAAAATTTCTAGACAT
3186 AATTGATCTTCTCCTAAACCGA
320 AATTGATCTTCTCCTAAACCGA
3208 CTTGAAGAAT
Statistics
Matches: 301, Mismatches: 33, Indels: 14
0.86 0.09 0.04
Matches are distributed among these distances:
350 8 0.03
351 288 0.96
352 5 0.02
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (351 bp):
CAGATGTCTTGAACTCTAAATCCGATATTCTTAGACCCAAATTGTTAATATGGAAACCCAAAGAA
GGAGTCCAAGACCAATCAGTAATTATGATGCAGTAATGATTCAGCCCTGATACAGCATTGTGAAA
TCATATTCAAAAGAGGACTTAACAAGAGCAATTTTGGAAGAAAATTCATAACTTTTGATGCAAAA
CTCAGAAAAATGCAAATGAAATACCGTTGGAAAGAGAATTCCAAGATCTACAACATTTATGTTTA
CCTCGAGACCTAATTATGCAGCTTCGATAGACAATTTTGCCCTTAAAATTTCTAGACATAATTGA
TCTTCTCCTAAACCGATTTGGAGAGC
Found at i:3363 original size:27 final size:25
Alignment explanation
Indices: 3314--3369 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 25
3304 TTTCCACTAT
3314 TTTAATAATGAAATAATTAAAATATTA
1 TTTAATAATGAAAT-ATTAAAATA-TA
3341 TTTAATAATGACAAT-TTAGAAATATA
1 TTTAATAATGA-AATATTA-AAATATA
3367 TTT
1 TTT
3370 GAAAATAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
26 8 0.30
27 16 0.59
28 3 0.11
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (25 bp):
TTTAATAATGAAATATTAAAATATA
Found at i:3514 original size:22 final size:22
Alignment explanation
Indices: 3489--3570 Score: 94
Period size: 22 Copynumber: 3.8 Consensus size: 22
3479 TTGAACATTT
3489 TTATGAAATTTTGATAACTACC
1 TTATGAAATTTTGATAACTACC
* *
3511 TTATTAAATTTTGATAACCACC
1 TTATGAAATTTTGATAACTACC
* * *
3533 ATATGAAATTTTGGTAATTACC
1 TTATGAAATTTTGATAACTACC
* *
3555 -TATAAAATTGTGATAA
1 TTATGAAATTTTGATAA
3571 ACTCCATAAG
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
21 13 0.26
22 37 0.74
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.40
Consensus pattern (22 bp):
TTATGAAATTTTGATAACTACC
Found at i:3578 original size:43 final size:44
Alignment explanation
Indices: 3490--3593 Score: 120
Period size: 43 Copynumber: 2.4 Consensus size: 44
3480 TGAACATTTT
* * *
3490 TATGAAATTTTGATAACTACCTTATTAAATTTTGATAACCACCA
1 TATGAAATTTTGATAACTACCTTATAAAATTGTGATAAACACCA
* * *
3534 TATGAAATTTTGGTAATTACC-TATAAAATTGTGATAAACTCCA
1 TATGAAATTTTGATAACTACCTTATAAAATTGTGATAAACACCA
* **
3577 TAAGAAACCTTGATAAC
1 TATGAAATTTTGATAAC
3594 CTAACTATGA
Statistics
Matches: 49, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
43 30 0.61
44 19 0.39
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (44 bp):
TATGAAATTTTGATAACTACCTTATAAAATTGTGATAAACACCA
Found at i:8525 original size:19 final size:18
Alignment explanation
Indices: 8497--8538 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
8487 AATTAATTGT
8497 TTTAATATTAAATTTTTA
1 TTTAATATTAAATTTTTA
*
8515 TTTATATATTATATTTTTA
1 TTTA-ATATTAAATTTTTA
*
8534 CTTAA
1 TTTAA
8539 AAATTACTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTAATATTAAATTTTTA
Found at i:8966 original size:20 final size:20
Alignment explanation
Indices: 8941--8988 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
8931 CCAAATTAAA
*
8941 AAAAAATATGAGG-CAAATT
1 AAAAAATAGGAGGTCAAATT
* *
8960 CAAAAAAAAGGGGGTCAAATT
1 -AAAAAATAGGAGGTCAAATT
8981 AAAAAATA
1 AAAAAATA
8989 AAAATTATGG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.60, C:0.06, G:0.17, T:0.17
Consensus pattern (20 bp):
AAAAAATAGGAGGTCAAATT
Found at i:8986 original size:22 final size:21
Alignment explanation
Indices: 8932--8991 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
8922 TTAAGAGGGC
*
8932 CAAATTAAAAAAAAATATGAGG
1 CAAATTAAAAAAAAA-AGGAGG
* *
8954 CAAATT-CAAAAAAAAGGGGG
1 CAAATTAAAAAAAAAAGGAGG
8974 TCAAATTAAAAAATAAAA
1 -CAAATTAAAAAA-AAAA
8992 ATTATGGGGG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
20 4 0.13
21 13 0.42
22 10 0.32
23 4 0.13
ACGTcount: A:0.63, C:0.07, G:0.13, T:0.17
Consensus pattern (21 bp):
CAAATTAAAAAAAAAAGGAGG
Done.