Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016035.1 Corchorus capsularis cultivar CVL-1 contig16056, 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: 23025
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Found at i:44 original size:32 final size:33
Alignment explanation
Indices: 1--124 Score: 112
Period size: 32 Copynumber: 3.8 Consensus size: 33
*
1 ACCGGGGCGGCCTG-CCGTGGCGAAGCCGCCTC
1 ACCGGGGCGGCCTGCCCGTGGCGAAGCCGCCCC
* * *
33 ACCGGGACGGCCTGTCC-TGGCTAAGCCGCCCC
1 ACCGGGGCGGCCTGCCCGTGGCGAAGCCGCCCC
** * * *
65 AATGGGGCGGCCTGCCCATGGTGAAGCCACCCC
1 ACCGGGGCGGCCTGCCCGTGGCGAAGCCGCCCC
* *
98 A-TGAGGGCGGCTTG-CCGTGGCGAAGCC
1 ACCG-GGGCGGCCTGCCCGTGGCGAAGCC
125 TCCCAAGTGG
Statistics
Matches: 76, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
32 52 0.68
33 24 0.32
ACGTcount: A:0.14, C:0.37, G:0.37, T:0.12
Consensus pattern (33 bp):
ACCGGGGCGGCCTGCCCGTGGCGAAGCCGCCCC
Found at i:142 original size:32 final size:32
Alignment explanation
Indices: 4--140 Score: 109
Period size: 32 Copynumber: 4.2 Consensus size: 32
1 ACC
* **
4 GGGGCGGCCTG-CCGTGGCGAAGCCGCCTCACC
1 GGGGCGGCCTGCCCGTGGCGAAGCCACC-CAAT
* * * *
36 GGGACGGCCTGTCC-TGGCTAAGCCGCCCCAAT
1 GGGGCGGCCTGCCCGTGGCGAAGCC-ACCCAAT
* * *
68 GGGGCGGCCTGCCCATGGTGAAGCCACCCCAT
1 GGGGCGGCCTGCCCGTGGCGAAGCCACCCAAT
* *
100 GAGGGCGGCTTG-CCGTGGCGAAGCCTCCCAAGT
1 G-GGGCGGCCTGCCCGTGGCGAAGCCACCCAA-T
133 GGGGCGGC
1 GGGGCGGC
141 TTCGCCACGA
Statistics
Matches: 84, Mismatches: 16, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
32 61 0.73
33 23 0.27
ACGTcount: A:0.13, C:0.36, G:0.39, T:0.12
Consensus pattern (32 bp):
GGGGCGGCCTGCCCGTGGCGAAGCCACCCAAT
Found at i:1375 original size:1 final size:1
Alignment explanation
Indices: 1371--1410 Score: 53
Period size: 1 Copynumber: 40.0 Consensus size: 1
1361 CAGAAAAAGC
***
1371 AAAAAAAAAAAAAAAAGCCAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1411 CAAGGTTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.93, C:0.05, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:1387 original size:18 final size:19
Alignment explanation
Indices: 1364--1405 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
1354 CATGAAACAG
1364 AAAAAG-CAAAAAAAAAAA
1 AAAAAGCCAAAAAAAAAAA
1382 AAAAAGCCAAAAAAAAAAA
1 AAAAAGCCAAAAAAAAAAA
1401 AAAAA
1 AAAAA
1406 AAAAACAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.88, C:0.07, G:0.05, T:0.00
Consensus pattern (19 bp):
AAAAAGCCAAAAAAAAAAA
Found at i:4936 original size:4 final size:4
Alignment explanation
Indices: 4917--4968 Score: 74
Period size: 4 Copynumber: 13.8 Consensus size: 4
4907 ACACACACAC
*
4917 AAAG AGAG AAAG --AG AAAG -AAG AAAG AAAG AAAG AAAG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
4962 AAAG AAA
1 AAAG AAA
4969 AAAAAAAGCA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 3 0.07
4 38 0.88
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:7366 original size:165 final size:165
Alignment explanation
Indices: 6378--7366 Score: 1446
Period size: 165 Copynumber: 6.0 Consensus size: 165
6368 AGTTAACTGA
* * *
6378 TCATTTTCAGAATTAACAGCAGCCTGGAGAGCCGGTGCAACATCTTCAGAAGGCATTTCTCTCTC
1 TCATTTTCAGAATTAACAGCAACCTGGGGAGCCAGTGCAACATCTTCAGAAGGCATTTCTCTCTC
* * * *
6443 GCTCAAGCCATTGTCTGGCTTTGGATCATGGAGATTGCTAATC-CTCTCTGTAGGTAAAGTTTCT
66 ACTCAAGCCATTGTCTGGCTTTGAATCTTGGAGATTGCTCATCTCT-TCTGTAGGTAAAGTTTCT
*
6507 GAACTCAATATGGTAGAAGAATCAGTTTGAACCCGT
130 GAACTCAATATGGTAGAAGAATCAGTTTGAACCCAT
* * *
6543 TCATTTTCAGAATTAACAGCAACCAGGGGAGCCAATGCAACATCTTCCA-AAGGCATTTCTCTAT
1 TCATTTTCAGAATTAACAGCAACCTGGGGAGCCAGTGCAACATCTT-CAGAAGGCATTTCTCTCT
* * *
6607 CACTCAAGCCGTTGTCTGGCTTTGAATCTTGGAGGTTGCTCATCTCTTCTGTAGGTAAATTTTCT
65 CACTCAAGCCATTGTCTGGCTTTGAATCTTGGAGATTGCTCATCTCTTCTGTAGGTAAAGTTTCT
*
6672 GAACTCAATATGGTAGAAGAATCAGTTTGAA-CGACT
130 GAACTCAATATGGTAGAAGAATCAGTTTGAACCCA-T
* *
6708 TCATTTTCAGAATTAGCAGCAACCTGGGGAGCCAGTGCAACATCTTCAGAAGGCATTTCTCTCTT
1 TCATTTTCAGAATTAACAGCAACCTGGGGAGCCAGTGCAACATCTTCAGAAGGCATTTCTCTCTC
* * * * * *
6773 ACTCAAGCCATTGACTGGCTTTGAATCTCGGAGATTGCTCCTTTCTTCCGTTGGTAAAGTTTCTG
66 ACTCAAGCCATTGTCTGGCTTTGAATCTTGGAGATTGCTCATCTCTTCTGTAGGTAAAGTTTCTG
*
6838 AACTCAATATTGTAGAAGAATCAGTTTGAACGCC-T
131 AACTCAATATGGTAGAAGAATCAGTTTGAAC-CCAT
* *
6873 TCATTTTCAGAGTTAGCAGCAACCTGGGGAGCCAGTGCAACATCTTCAGAAGGCATTTCTCTCTC
1 TCATTTTCAGAATTAACAGCAACCTGGGGAGCCAGTGCAACATCTTCAGAAGGCATTTCTCTCTC
* * * * *
6938 ACTCAAGCCATTGACTGGCTCTGAATCTTGGAAATTGCTCCTTTCTTCTGTAGGTAAAGTTTCTG
66 ACTCAAGCCATTGTCTGGCTTTGAATCTTGGAGATTGCTCATCTCTTCTGTAGGTAAAGTTTCTG
*
7003 AACTCAATATTGTAGAAGAATCAGTTTGAACCCAT
131 AACTCAATATGGTAGAAGAATCAGTTTGAACCCAT
* * * * *
7038 CCATTTACAGAACTAACAGCAACCTGGGCAGCCAGTGCAACATCTTCAGAAGGCATTTCTCTCTT
1 TCATTTTCAGAATTAACAGCAACCTGGGGAGCCAGTGCAACATCTTCAGAAGGCATTTCTCTCTC
* * * * * *
7103 ACTCAAGCCATTGTCTAGCTTTGAATCTTGGAGACTGCCCGTCTTTTCTGTAGGTAAAGTTCCTG
66 ACTCAAGCCATTGTCTGGCTTTGAATCTTGGAGATTGCTCATCTCTTCTGTAGGTAAAGTTTCTG
* *
7168 AACTCAATATGGTAGAAGACTCATTTTGAACCCAT
131 AACTCAATATGGTAGAAGAATCAGTTTGAACCCAT
* *
7203 TCATTCTCAGAATTAACAGCAACCTGGGGAGCCAGTGCAACATCTTCAGAAGGCATTTCTCCCTC
1 TCATTTTCAGAATTAACAGCAACCTGGGGAGCCAGTGCAACATCTTCAGAAGGCATTTCTCTCTC
*
7268 ACTCAAGCCATAGTCTGGCTTTGAATCTTGGAGATTGCTCATCTCTTCTGTAGGTAAAGTTTCTG
66 ACTCAAGCCATTGTCTGGCTTTGAATCTTGGAGATTGCTCATCTCTTCTGTAGGTAAAGTTTCTG
* * * *
7333 AGCTCAACATTGTAGAAGAACCAGTTTGAACCCA
131 AACTCAATATGGTAGAAGAATCAGTTTGAACCCA
7367 ATCTGGGTTC
Statistics
Matches: 739, Mismatches: 78, Indels: 14
0.89 0.09 0.02
Matches are distributed among these distances:
164 5 0.01
165 729 0.99
166 4 0.01
167 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.31
Consensus pattern (165 bp):
TCATTTTCAGAATTAACAGCAACCTGGGGAGCCAGTGCAACATCTTCAGAAGGCATTTCTCTCTC
ACTCAAGCCATTGTCTGGCTTTGAATCTTGGAGATTGCTCATCTCTTCTGTAGGTAAAGTTTCTG
AACTCAATATGGTAGAAGAATCAGTTTGAACCCAT
Found at i:16489 original size:14 final size:14
Alignment explanation
Indices: 16472--16503 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
16462 AAGCTTATAT
16472 AGTCTTTTCGTTAC
1 AGTCTTTTCGTTAC
*
16486 AGTCTTTTTGTTAC
1 AGTCTTTTCGTTAC
16500 AGTC
1 AGTC
16504 GCAATTTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.50
Consensus pattern (14 bp):
AGTCTTTTCGTTAC
Done.