Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013982.1 Corchorus capsularis cultivar CVL-1 contig14003, 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: 52138
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Found at i:4476 original size:24 final size:23
Alignment explanation
Indices: 4449--4495 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
4439 AGTTATTTAG
4449 TTTATGTTT-TATCTTTAATTTTTC
1 TTTAT-TTTATATCTTT-ATTTTTC
*
4473 TTTATTTTATGTCTTTATTTTTC
1 TTTATTTTATATCTTTATTTTTC
4496 AAGTTTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.15, C:0.09, G:0.04, T:0.72
Consensus pattern (23 bp):
TTTATTTTATATCTTTATTTTTC
Found at i:4830 original size:13 final size:13
Alignment explanation
Indices: 4811--4849 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
4801 TATTTTCCCC
4811 AATTTTTGAAAAA
1 AATTTTTGAAAAA
*
4824 TATTTTTTCGAAAAA
1 -AATTTTT-GAAAAA
4839 AATTTTTGAAA
1 AATTTTTGAAA
4850 TTGAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 4 0.18
14 12 0.55
15 6 0.27
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (13 bp):
AATTTTTGAAAAA
Found at i:6037 original size:19 final size:18
Alignment explanation
Indices: 6013--6048 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
6003 TGAAGATTTC
6013 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
6032 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
6049 ATTATTTCAA
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:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:13121 original size:31 final size:31
Alignment explanation
Indices: 13052--13215 Score: 128
Period size: 31 Copynumber: 5.5 Consensus size: 31
13042 ATGGTATCCG
* ** * *
13052 ACGTGGCATGCCACGTGGATAAAAAAATAAC
1 ACGTGGCACGCCACGTGGACCAAAAAGTGAC
* * *
13083 ACATGGCAGGCCACGTGGATCAAAAAGTGAC
1 ACGTGGCACGCCACGTGGACCAAAAAGTGAC
*
13114 ATGTGGCACGCCACGTGTG-CCAAAAAGTGAC
1 ACGTGGCACGCCACGTG-GACCAAAAAGTGAC
* *
13145 ACGT--CA---CA--TGTACCAAAAAGTGAT
1 ACGTGGCACGCCACGTGGACCAAAAAGTGAC
*
13169 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
1 ACGTGGCACGCCACGTGGACCAAAAAGTGAC
* * *
13200 ATGCGGCATGCCACGT
1 ACGTGGCACGCCACGT
13216 TCACAAAAGG
Statistics
Matches: 108, Mismatches: 16, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
24 17 0.16
26 4 0.04
29 4 0.04
31 82 0.76
32 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.26, T:0.16
Consensus pattern (31 bp):
ACGTGGCACGCCACGTGGACCAAAAAGTGAC
Found at i:13147 original size:24 final size:24
Alignment explanation
Indices: 13120--13167 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
13110 TGACATGTGG
* *
13120 CACGCCACGTGTGCCAAAAAGTGA
1 CACGCCACATGTACCAAAAAGTGA
*
13144 CACGTCACATGTACCAAAAAGTGA
1 CACGCCACATGTACCAAAAAGTGA
13168 TACGTGGCAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.27, G:0.21, T:0.15
Consensus pattern (24 bp):
CACGCCACATGTACCAAAAAGTGA
Found at i:14947 original size:55 final size:54
Alignment explanation
Indices: 14881--14989 Score: 200
Period size: 55 Copynumber: 2.0 Consensus size: 54
14871 TGGAGAGACA
14881 ATAGAATATGGAGAAGAAGAAAATATGAAAAATGAGAGAAATTGTTCTTATTCAT
1 ATAGAATATGGAGAAGAAGAAAATATG-AAAATGAGAGAAATTGTTCTTATTCAT
*
14936 ATAGAATATGGAGAAGAAGAAAATATGAAAATGGGAGAAATTGTTCTTATTCAT
1 ATAGAATATGGAGAAGAAGAAAATATGAAAATGAGAGAAATTGTTCTTATTCAT
14990 CATATTCCAT
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
54 26 0.49
55 27 0.51
ACGTcount: A:0.48, C:0.04, G:0.21, T:0.28
Consensus pattern (54 bp):
ATAGAATATGGAGAAGAAGAAAATATGAAAATGAGAGAAATTGTTCTTATTCAT
Found at i:17232 original size:31 final size:31
Alignment explanation
Indices: 17194--17255 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
17184 AGTTTTGAGA
*
17194 AACTTTTGAAACACCTATTGTACCCTTATTT
1 AACTTTTGAAACACCTATTATACCCTTATTT
** *
17225 AACTTTTGAAATGCCTATTATATCCTTATTT
1 AACTTTTGAAACACCTATTATACCCTTATTT
17256 TTCTAACATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.29, C:0.19, G:0.06, T:0.45
Consensus pattern (31 bp):
AACTTTTGAAACACCTATTATACCCTTATTT
Found at i:19824 original size:17 final size:17
Alignment explanation
Indices: 19802--19835 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
19792 AGTAGATGTA
19802 ATTTGAAATACATGAAT
1 ATTTGAAATACATGAAT
19819 ATTTGAAATACATGAAT
1 ATTTGAAATACATGAAT
19836 CAACATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (17 bp):
ATTTGAAATACATGAAT
Found at i:24624 original size:61 final size:59
Alignment explanation
Indices: 24555--24679 Score: 169
Period size: 61 Copynumber: 2.1 Consensus size: 59
24545 AAAAATTGTT
* *** * *
24555 GAAAATTGTCCTTATTTTGATAGTTTAAGTGGTGAAATTTCCAAAATTAAAAGTTTAAGAA
1 GAAAATTGTCCTAATTTTGATAGTTTAAGAAATGAAA-ATCC-AAATTAAAAGTTCAAGAA
*
24616 GAAAATTGTCCTAATTTTGATAGTTTAAGAAATGAAAATCCAAATTAAAAGTTCAAGGA
1 GAAAATTGTCCTAATTTTGATAGTTTAAGAAATGAAAATCCAAATTAAAAGTTCAAGAA
24675 GAAAA
1 GAAAA
24680 AAATGTCCAT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 21 0.37
60 3 0.05
61 33 0.58
ACGTcount: A:0.44, C:0.07, G:0.16, T:0.33
Consensus pattern (59 bp):
GAAAATTGTCCTAATTTTGATAGTTTAAGAAATGAAAATCCAAATTAAAAGTTCAAGAA
Found at i:24644 original size:31 final size:31
Alignment explanation
Indices: 24555--24646 Score: 89
Period size: 31 Copynumber: 3.0 Consensus size: 31
24545 AAAAATTGTT
* **
24555 GAAAATTGTCCTTATTTTGATAGTTTAAGTG
1 GAAAATTGTCCTAATTTTGATAGTTTAAGAA
* ** * *
24586 GTGAAATT-TCC-AAAATTAAAAGTTTAAGAA
1 G-AAAATTGTCCTAATTTTGATAGTTTAAGAA
24616 GAAAATTGTCCTAATTTTGATAGTTTAAGAA
1 GAAAATTGTCCTAATTTTGATAGTTTAAGAA
24647 ATGAAAATCC
Statistics
Matches: 45, Mismatches: 13, Indels: 6
0.70 0.20 0.09
Matches are distributed among these distances:
29 5 0.11
30 16 0.36
31 19 0.42
32 5 0.11
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.38
Consensus pattern (31 bp):
GAAAATTGTCCTAATTTTGATAGTTTAAGAA
Found at i:24692 original size:59 final size:60
Alignment explanation
Indices: 24568--24693 Score: 141
Period size: 61 Copynumber: 2.1 Consensus size: 60
24558 AATTGTCCTT
*** * * * *
24568 ATTTTGATAGTTTAAGTGGTGAAATTTCCAAAATTAAAAGTTTAAGAAGAAAATTGTCCTA
1 ATTTTGATAGTTTAAGAAATGAAATATCCAAAATTAAAAGTTCAAGAAAAAAAATGTCC-A
24629 ATTTTGATAGTTTAAGAAATGAAA-ATCC-AAATTAAAAGTTCAAGGAGAAAAAAATGTCC-
1 ATTTTGATAGTTTAAGAAATGAAATATCCAAAATTAAAAGTTCAA-GA-AAAAAAATGTCCA
24688 ATTTTG
1 ATTTTG
24694 TAAAAGTTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
59 20 0.36
60 5 0.09
61 31 0.55
ACGTcount: A:0.44, C:0.07, G:0.16, T:0.33
Consensus pattern (60 bp):
ATTTTGATAGTTTAAGAAATGAAATATCCAAAATTAAAAGTTCAAGAAAAAAAATGTCCA
Found at i:37496 original size:11 final size:11
Alignment explanation
Indices: 37465--37498 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
37455 GAATTTGAGG
*
37465 TCACTTATCAC
1 TCACTTATCCC
37476 TCACTTATCCC
1 TCACTTATCCC
37487 TCACTTATCCC
1 TCACTTATCCC
37498 T
1 T
37499 ATCTCTTCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.21, C:0.41, G:0.00, T:0.38
Consensus pattern (11 bp):
TCACTTATCCC
Found at i:37878 original size:15 final size:15
Alignment explanation
Indices: 37858--37888 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
37848 CTGCCCCTAT
37858 TGGGAGACTCATCCA
1 TGGGAGACTCATCCA
37873 TGGGAGACTCATCCA
1 TGGGAGACTCATCCA
37888 T
1 T
37889 CATAACTAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.23
Consensus pattern (15 bp):
TGGGAGACTCATCCA
Done.