Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023826.1 Corchorus olitorius cultivar O-4 contig23859, 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: 21507
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:370 original size:5 final size:6
Alignment explanation
Indices: 343--399 Score: 53
Period size: 6 Copynumber: 9.0 Consensus size: 6
333 TTACTTCCAC
* *
343 TTTCTT TTTCAATT TTTCTT TTTCTT TTTCTT CTTTCATT TTTC-A TTTCAT
1 TTTCTT TTTC--TT TTTCTT TTTCTT TTTCTT -TTTC-TT TTTCTT TTTCTT
394 TTTCTT
1 TTTCTT
400 CCCTTTTCCT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
5 4 0.09
6 23 0.53
7 8 0.19
8 8 0.19
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.74
Consensus pattern (6 bp):
TTTCTT
Found at i:372 original size:12 final size:13
Alignment explanation
Indices: 343--396 Score: 67
Period size: 12 Copynumber: 4.2 Consensus size: 13
333 TTACTTCCAC
343 TTTCTTTTTCAATT
1 TTTCTTTTTC-ATT
357 TTTCTTTTTC-TT
1 TTTCTTTTTCATT
369 TTTCTTCTTTCATT
1 TTTCTT-TTTCATT
*
383 TTTC-ATTTCATT
1 TTTCTTTTTCATT
395 TT
1 TT
397 CTTCCCTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
12 17 0.46
13 4 0.11
14 16 0.43
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTCTTTTTCATT
Found at i:384 original size:20 final size:19
Alignment explanation
Indices: 343--396 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
333 TTACTTCCAC
343 TTTCTTTTTCAATTTTTCTT
1 TTTCTTTTTC-ATTTTTCTT
363 TTTCTTTTTC-TTCTTTCATT
1 TTTCTTTTTCATT-TTTC-TT
*
383 TTTC-ATTTCATTTT
1 TTTCTTTTTCATTTT
397 CTTCCCTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 2 0.07
19 10 0.33
20 18 0.60
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTCTTTTTCATTTTTCTT
Found at i:405 original size:27 final size:27
Alignment explanation
Indices: 343--400 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 27
333 TTACTTCCAC
* *
343 TTTCTT-TTTCAATTTTTCTTTTTCTT
1 TTTCTTCTTTCAATTTTTCTATTTCAT
369 TTTCTTCTTTC-ATTTTTC-ATTTCAT
1 TTTCTTCTTTCAATTTTTCTATTTCAT
394 TTTCTTC
1 TTTCTTC
401 CCTTTTCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 12 0.41
26 13 0.45
27 4 0.14
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.72
Consensus pattern (27 bp):
TTTCTTCTTTCAATTTTTCTATTTCAT
Found at i:17808 original size:46 final size:47
Alignment explanation
Indices: 17755--17851 Score: 160
Period size: 47 Copynumber: 2.1 Consensus size: 47
17745 ACAAATTCTA
* *
17755 ATTTACTCAATC-AATGCTTCAATTTTACTTATTTAATTTTTGTTTT
1 ATTTACTCAATCTAACGCTTCAATTTTACTTATTTAATTTTAGTTTT
*
17801 ATTTACTCGATCTAACGCTTCAATTTTACTTATTTAATTTTAGTTTT
1 ATTTACTCAATCTAACGCTTCAATTTTACTTATTTAATTTTAGTTTT
17848 ATTT
1 ATTT
17852 GTCCGATTAA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
46 11 0.23
47 36 0.77
ACGTcount: A:0.26, C:0.13, G:0.05, T:0.56
Consensus pattern (47 bp):
ATTTACTCAATCTAACGCTTCAATTTTACTTATTTAATTTTAGTTTT
Found at i:18124 original size:1 final size:1
Alignment explanation
Indices: 18120--18146 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
18110 TTCAAGTCTT
18120 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
18147 CCGGTCTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:19490 original size:19 final size:19
Alignment explanation
Indices: 19462--19505 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
19452 ATCTCCTCTT
19462 TATTTAGCCACGTGGATTG
1 TATTTAGCCACGTGGATTG
* *
19481 TATTTTGCCACGTGGATTT
1 TATTTAGCCACGTGGATTG
19500 TATTTA
1 TATTTA
19506 CTTTAATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.20, C:0.14, G:0.20, T:0.45
Consensus pattern (19 bp):
TATTTAGCCACGTGGATTG
Found at i:19969 original size:18 final size:18
Alignment explanation
Indices: 19948--20008 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
19938 GATTTAGGAT
19948 TTCGAATTGATTTGGGGC
1 TTCGAATTGATTTGGGGC
* *** *
19966 TTCG-GTTCGATTTAAAGA
1 TTCGAATT-GATTTGGGGC
19984 TTCGAATTGATTTGGGGC
1 TTCGAATTGATTTGGGGC
20002 TTTCGAA
1 -TTCGAA
20009 GGGTGAAACT
Statistics
Matches: 30, Mismatches: 10, Indels: 5
0.67 0.22 0.11
Matches are distributed among these distances:
17 2 0.07
18 20 0.67
19 8 0.27
ACGTcount: A:0.21, C:0.11, G:0.28, T:0.39
Consensus pattern (18 bp):
TTCGAATTGATTTGGGGC
Found at i:19988 original size:36 final size:36
Alignment explanation
Indices: 19935--20003 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
19925 GCGGTTTAAT
*
19935 TTCGATTTAGGATTTCGAATTGATTTGGGGCTTCGG
1 TTCGATTTAAGATTTCGAATTGATTTGGGGCTTCGG
19971 TTCGATTTAAAGA-TTCGAATTGATTTGGGGCTT
1 TTCGATTT-AAGATTTCGAATTGATTTGGGGCTT
20004 TCGAAGGGTG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
36 28 0.90
37 3 0.10
ACGTcount: A:0.20, C:0.10, G:0.28, T:0.42
Consensus pattern (36 bp):
TTCGATTTAAGATTTCGAATTGATTTGGGGCTTCGG
Done.