Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013143.1 Corchorus capsularis cultivar CVL-1 contig13164, 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: 14666
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Found at i:4657 original size:50 final size:50
Alignment explanation
Indices: 4596--4757 Score: 184
Period size: 50 Copynumber: 3.2 Consensus size: 50
4586 TTATATCAAT
* * *
4596 AAAAATGTACGTTACACAAAAGCGAAATCTAGAACTTATATG-GGTCTCAC
1 AAAAATATACGTTACTC-AAAGCGAAATCTAGAACTTTTATGTGGTCTCAC
* * *
4646 AAAAATATACGTTACTCAAAGCGAAAATCTAGAACTTCTTATGTGGGCCCAT
1 AAAAATATACGTTACTCAAAGCG-AAATCTAGAACTT-TTATGTGGTCTCAC
* * *
4698 AAAAATATACGTCACTCAAAGTGAAATCTAGAA-TTTTATGTGGATTTCAC
1 AAAAATATACGTTACTCAAAGCGAAATCTAGAACTTTTATGTGG-TCTCAC
*
4748 AAAAACATAC
1 AAAAATATAC
4758 ATCACGTGAC
Statistics
Matches: 95, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
49 14 0.15
50 41 0.43
51 14 0.15
52 26 0.27
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (50 bp):
AAAAATATACGTTACTCAAAGCGAAATCTAGAACTTTTATGTGGTCTCAC
Found at i:5763 original size:18 final size:18
Alignment explanation
Indices: 5742--5792 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 18
5732 TCATTTTTAT
5742 TCTTGATAATTTTGTTAA
1 TCTTGATAATTTTGTTAA
5760 TCTTGATTATTATTTTGTTAA
1 TCTTGA-TA--ATTTTGTTAA
*
5781 TCATG-TAATTTT
1 TCTTGATAATTTT
5793 TATTATGATT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 5 0.17
18 6 0.21
19 4 0.14
21 14 0.48
ACGTcount: A:0.25, C:0.06, G:0.10, T:0.59
Consensus pattern (18 bp):
TCTTGATAATTTTGTTAA
Found at i:9099 original size:23 final size:25
Alignment explanation
Indices: 9005--9109 Score: 69
Period size: 23 Copynumber: 4.3 Consensus size: 25
8995 ATCTAAAACT
* *
9005 TAATATATATA-TATA-TATATATA
1 TAATATATTTATTATATTTTATATA
* * **
9028 TAATATACGTATATAATAAATTATATAA
1 TAATATA--TTTATTATATTTTATAT-A
*
9056 TAAT-TA-TTATTATATTATATATA
1 TAATATATTTATTATATTTTATATA
9079 TAATATATTTATT-T-TTTTATATA
1 TAATATATTTATTATATTTTATATA
*
9102 AAATATAT
1 TAATATAT
9110 ATAATCGGGT
Statistics
Matches: 65, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
23 27 0.42
24 14 0.22
25 9 0.14
26 3 0.05
27 7 0.11
28 5 0.08
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (25 bp):
TAATATATTTATTATATTTTATATA
Found at i:9101 original size:2 final size:2
Alignment explanation
Indices: 9007--9086 Score: 63
Period size: 2 Copynumber: 45.0 Consensus size: 2
8997 CTAAAACTTA
* * *
9007 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AC GT AT AT A- AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9047 AT -T AT AT A- AT A- AT -T AT -T AT -T AT AT -T AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9081 AT AT AT
1 AT AT AT
9087 TTATTTTTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
1 10 0.16
2 52 0.84
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (2 bp):
AT
Found at i:11549 original size:197 final size:197
Alignment explanation
Indices: 11214--11602 Score: 742
Period size: 197 Copynumber: 2.0 Consensus size: 197
11204 CAACTTGATG
*
11214 TTAAAACTGCATTCTTACATGGTGATTTGCAAGAAGAAATTTACATGGACCAACCGGAGGGTTTT
1 TTAAAACTGCATTCTTACATGGTGATTTGCAAGAAGAAATTTACATGGACCAAACGGAGGGTTTT
11279 GAGGTTAAAGGGAAGGAACACATGGTTTGCAAGTTGAAGAAAAACTTGTATGGCTTGAAACAAGC
66 GAGGTTAAAGGGAAGGAACACATGGTTTGCAAGTTGAAGAAAAACTTGTATGGCTTGAAACAAGC
*
11344 TCCAAAGCAGTGGTACAAGAAGTTTTATTCCTTTATGGCGAGTCATCTCTTTACGAGAACTGCAT
131 TCCAAAGCAGTGGTACAAGAAGTTTGATTCCTTTATGGCGAGTCATCTCTTTACGAGAACTGCAT
11409 TC
196 TC
*
11411 TTAAAACTGTATTCTTACATGGTGATTTGCAAGAAGAAATTTACATGGACCAAACGGAGGGTTTT
1 TTAAAACTGCATTCTTACATGGTGATTTGCAAGAAGAAATTTACATGGACCAAACGGAGGGTTTT
11476 GAGGTTAAAGGGAAGGAACACATGGTTTGCAAGTTGAAGAAAAACTTGTATGGCTTGAAACAAGC
66 GAGGTTAAAGGGAAGGAACACATGGTTTGCAAGTTGAAGAAAAACTTGTATGGCTTGAAACAAGC
*
11541 TCCAAAGCAGTGGTACAAGAAGTTTGATTCCTTTATGGTGAGTCATCTCTTTACGAGAACTG
131 TCCAAAGCAGTGGTACAAGAAGTTTGATTCCTTTATGGCGAGTCATCTCTTTACGAGAACTG
11603 TAGCAGATCC
Statistics
Matches: 188, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
197 188 1.00
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.29
Consensus pattern (197 bp):
TTAAAACTGCATTCTTACATGGTGATTTGCAAGAAGAAATTTACATGGACCAAACGGAGGGTTTT
GAGGTTAAAGGGAAGGAACACATGGTTTGCAAGTTGAAGAAAAACTTGTATGGCTTGAAACAAGC
TCCAAAGCAGTGGTACAAGAAGTTTGATTCCTTTATGGCGAGTCATCTCTTTACGAGAACTGCAT
TC
Found at i:14306 original size:33 final size:33
Alignment explanation
Indices: 14256--14379 Score: 144
Period size: 33 Copynumber: 3.7 Consensus size: 33
14246 CCGCGCAACA
*
14256 CCGGCCACAAGACCGGCCACGCGACATGGACATGT
1 CCGGCCAC-A-ACCGGCCACGCGACATGGACATGC
*
14291 CCGGCCATC-ACCGGCCACGCGACATGGACATGG
1 CCGGCCA-CAACCGGCCACGCGACATGGACATGC
* ** *
14324 CCGGCTACAACCGGCCAAACGAC-TCGGCCATGC
1 CCGGCCACAACCGGCCACGCGACAT-GGACATGC
14357 CCGGCCACAACCGGCCACGCGAC
1 CCGGCCACAACCGGCCACGCGAC
14380 CCTTTGTCTA
Statistics
Matches: 77, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
32 2 0.03
33 67 0.87
35 7 0.09
36 1 0.01
ACGTcount: A:0.23, C:0.42, G:0.27, T:0.07
Consensus pattern (33 bp):
CCGGCCACAACCGGCCACGCGACATGGACATGC
Done.