Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007832.1 Corchorus capsularis cultivar CVL-1 contig07853, 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: 6823
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Found at i:3326 original size:22 final size:22
Alignment explanation
Indices: 3278--3327 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
3268 TCGGGGTAGG
*
3278 AAAAAACTCAAAAAAATACAGG
1 AAAAAACTCAAAAAAATACAGC
* *
3300 GAAAAGCTCGAAAAAAATACA-C
1 AAAAAACTC-AAAAAAATACAGC
3322 AAAAAA
1 AAAAAA
3328 TAGAAATAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.68, C:0.14, G:0.10, T:0.08
Consensus pattern (22 bp):
AAAAAACTCAAAAAAATACAGC
Found at i:4722 original size:48 final size:48
Alignment explanation
Indices: 4650--5076 Score: 561
Period size: 48 Copynumber: 8.9 Consensus size: 48
4640 TTTCACTCGC
* * * * *
4650 TTTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTTACTTGT
1 TTTTCCTAAAACGCCCTTCCCGGACGGAAGGCACTAATTTTTACCTGT
* * * *
4698 TTTTCCCAACACGCCCTTCACGGACGGAAGGCACTGATTTTTACCTGT
1 TTTTCCTAAAACGCCCTTCCCGGACGGAAGGCACTAATTTTTACCTGT
* * * *
4746 TTTTCCTAAAATGCCTTTCCCGGA-GGAAGGCACTGATTTTTACCTAT
1 TTTTCCTAAAACGCCCTTCCCGGACGGAAGGCACTAATTTTTACCTGT
* * *
4793 TTTTCATAAAACGCCCTTCCCGGACGGAGGGCACTGATTTTTACCTGT
1 TTTTCCTAAAACGCCCTTCCCGGACGGAAGGCACTAATTTTTACCTGT
* * *
4841 TTTTCCTAAAACGCCCTTCCCGGACGGAAGGCACTAATCTTCACTTGT
1 TTTTCCTAAAACGCCCTTCCCGGACGGAAGGCACTAATTTTTACCTGT
* *
4889 TTTTCCCAAACCGCCCTTCCCGGACGGAAGGCACTAATTTTTACCTGT
1 TTTTCCTAAAACGCCCTTCCCGGACGGAAGGCACTAATTTTTACCTGT
* * * *
4937 TTTTCCTAAAACGCCCTTCTCGGATGGAAGTCACTAATTTTTACTTGCT
1 TTTTCCTAAAACGCCCTTCCCGGACGGAAGGCACTAATTTTTACCTG-T
*
4986 TTTTCCTAAAACGCCCTTCCCGGACGGAAGGCACCAATTTTTA-CTCGCTT
1 TTTTCCTAAAACGCCCTTCCCGGACGGAAGGCACTAATTTTTACCT-G--T
*
5036 TTTTCCTAAAACGCCCTTCCCGGACGGAAGGCGCTAATTTT
1 TTTTCCTAAAACGCCCTTCCCGGACGGAAGGCACTAATTTT
5077 ACTCGCTTTT
Statistics
Matches: 333, Mismatches: 42, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
47 43 0.13
48 209 0.63
49 41 0.12
50 40 0.12
ACGTcount: A:0.22, C:0.29, G:0.17, T:0.32
Consensus pattern (48 bp):
TTTTCCTAAAACGCCCTTCCCGGACGGAAGGCACTAATTTTTACCTGT
Found at i:5107 original size:48 final size:49
Alignment explanation
Indices: 4639--5116 Score: 521
Period size: 48 Copynumber: 9.9 Consensus size: 49
4629 CAATTTTCGG
* * * * *
4639 TTTTCACTCGC-TTTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTA
1 TTTTTACTCGCTTTTTCCTAAAACGCCCTTCCCGGACGGAAGGCACTAA
* * * * *
4687 TTTTTACTTG-TTTTTCCCAACACGCCCTTCACGGACGGAAGGCACTGA
1 TTTTTACTCGCTTTTTCCTAAAACGCCCTTCCCGGACGGAAGGCACTAA
* * *
4735 TTTTTAC-CTG-TTTTTCCTAAAATGCCTTTCCCGGA-GGAAGGCACTGA
1 TTTTTACTC-GCTTTTTCCTAAAACGCCCTTCCCGGACGGAAGGCACTAA
** * * *
4782 TTTTTAC-CTATTTTTCATAAAACGCCCTTCCCGGACGGAGGGCACTGA
1 TTTTTACTCGCTTTTTCCTAAAACGCCCTTCCCGGACGGAAGGCACTAA
4830 TTTTTAC-CTG-TTTTTCCTAAAACGCCCTTCCCGGACGGAAGGCACTAA
1 TTTTTACTC-GCTTTTTCCTAAAACGCCCTTCCCGGACGGAAGGCACTAA
* * * * *
4878 TCTTCACTTG-TTTTTCCCAAACCGCCCTTCCCGGACGGAAGGCACTAA
1 TTTTTACTCGCTTTTTCCTAAAACGCCCTTCCCGGACGGAAGGCACTAA
* * *
4926 TTTTTAC-CTG-TTTTTCCTAAAACGCCCTTCTCGGATGGAAGTCACTAA
1 TTTTTACTC-GCTTTTTCCTAAAACGCCCTTCCCGGACGGAAGGCACTAA
* *
4974 TTTTTACTTGCTTTTTCCTAAAACGCCCTTCCCGGACGGAAGGCACCAA
1 TTTTTACTCGCTTTTTCCTAAAACGCCCTTCCCGGACGGAAGGCACTAA
*
5023 TTTTTACTCGCTTTTTTCCTAAAACGCCCTTCCCGGACGGAAGGCGCTAA
1 TTTTTACTCGC-TTTTTCCTAAAACGCCCTTCCCGGACGGAAGGCACTAA
* * ** * *
5073 -TTTTACTCGCTTTTTCTTGAAGTGCCCTTTCCGGACGAAAGGCA
1 TTTTTACTCGCTTTTTCCTAAAACGCCCTTCCCGGACGGAAGGCA
5117 AGTTCATTTT
Statistics
Matches: 370, Mismatches: 50, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
47 42 0.11
48 238 0.64
49 54 0.15
50 36 0.10
ACGTcount: A:0.21, C:0.29, G:0.18, T:0.32
Consensus pattern (49 bp):
TTTTTACTCGCTTTTTCCTAAAACGCCCTTCCCGGACGGAAGGCACTAA
Found at i:6134 original size:23 final size:23
Alignment explanation
Indices: 6108--6219 Score: 63
Period size: 23 Copynumber: 4.9 Consensus size: 23
6098 ATAAATTTTA
6108 TTTTTTTTAGAAAAACGCAATTT
1 TTTTTTTTAGAAAAACGCAATTT
*****
6131 TTTTTTCTT--TTTTTCGCAATTT
1 TTTTTT-TTAGAAAAACGCAATTT
** * *
6153 TTTTTAATCGCAAAAA-GCAA-AT
1 TTTTTTTTAG-AAAAACGCAATTT
6175 TTTTTTTTAGGGAAAAA-GCAATTT
1 TTTTTTTTA--GAAAAACGCAATTT
6199 TTTTTTTTAGAAAAAACGCAA
1 TTTTTTTTAG-AAAAACGCAA
6220 AAACAAAATT
Statistics
Matches: 63, Mismatches: 17, Indels: 17
0.65 0.18 0.18
Matches are distributed among these distances:
21 1 0.02
22 21 0.33
23 24 0.38
24 17 0.27
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.47
Consensus pattern (23 bp):
TTTTTTTTAGAAAAACGCAATTT
Found at i:6175 original size:24 final size:23
Alignment explanation
Indices: 6148--6204 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
6138 TTTTTTTCGC
6148 AATTTTTTTTAATCGCAAAAAGCA
1 AATTTTTTTTAA-CGCAAAAAGCA
* * *
6172 AATTTTTTTTTAGGGAAAAAGCA
1 AATTTTTTTTAACGCAAAAAGCA
*
6195 ATTTTTTTTT
1 AATTTTTTTT
6205 TTAGAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 18 0.62
24 11 0.38
ACGTcount: A:0.35, C:0.07, G:0.11, T:0.47
Consensus pattern (23 bp):
AATTTTTTTTAACGCAAAAAGCA
Found at i:6214 original size:24 final size:23
Alignment explanation
Indices: 6164--6220 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
6154 TTTTAATCGC
**
6164 AAAAAGCAAATTTTTTTTTAGGG
1 AAAAAGCAAATTTTTTTTTAGAA
*
6187 AAAAAGCAATTTTTTTTTTTAGAA
1 AAAAAGCAA-ATTTTTTTTTAGAA
*
6211 AAAACGCAAA
1 AAAAAGCAAA
6221 AACAAAATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
23 9 0.32
24 19 0.68
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.35
Consensus pattern (23 bp):
AAAAAGCAAATTTTTTTTTAGAA
Done.