Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013424.1 Corchorus capsularis cultivar CVL-1 contig13445, 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: 33211
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:6627 original size:17 final size:18
Alignment explanation
Indices: 6605--6642 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
6595 GAGAAAATAG
*
6605 AATATGTAGAAGAAGA-A
1 AATATGAAGAAGAAGAGA
*
6622 AATATGAAGAATAAGAGA
1 AATATGAAGAAGAAGAGA
6640 AAT
1 AAT
6643 TGTTCTCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.61, C:0.00, G:0.21, T:0.18
Consensus pattern (18 bp):
AATATGAAGAAGAAGAGA
Found at i:6844 original size:11 final size:11
Alignment explanation
Indices: 6830--6867 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
6820 ATTCATAACA
6830 AATTTATAATT
1 AATTTATAATT
6841 AATTTATAATT
1 AATTTATAATT
6852 -ATTTGATAATT
1 AATTT-ATAATT
*
6863 TATTT
1 AATTT
6868 TATATATAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:7562 original size:18 final size:18
Alignment explanation
Indices: 7541--7575 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
7531 TCGATATTTA
* *
7541 TCGATATCTCGATAAATC
1 TCGATATATCCATAAATC
7559 TCGATATATCCATAAAT
1 TCGATATATCCATAAAT
7576 ATCCGTAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.34
Consensus pattern (18 bp):
TCGATATATCCATAAATC
Found at i:8192 original size:3 final size:3
Alignment explanation
Indices: 8184--8209 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
8174 ACGGAAAATG
8184 TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TG
8210 GGGGAAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.35, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:9306 original size:13 final size:12
Alignment explanation
Indices: 9276--9318 Score: 68
Period size: 12 Copynumber: 3.5 Consensus size: 12
9266 CATCGATACC
*
9276 TCGATATATCCA
1 TCGATATATCCG
9288 TCGATATATCCG
1 TCGATATATCCG
9300 TTCGATATATCCG
1 -TCGATATATCCG
9313 TCGATA
1 TCGATA
9319 CCTGTATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 17 0.59
13 12 0.41
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:10972 original size:13 final size:12
Alignment explanation
Indices: 10944--10997 Score: 90
Period size: 13 Copynumber: 4.3 Consensus size: 12
10934 TCGATATCTT
10944 GATATATCCGTC
1 GATATATCCGTC
10956 GATATATCCGTTC
1 GATATATCCG-TC
10969 GATATATCCGTTC
1 GATATATCCG-TC
10982 GATATATCCGTC
1 GATATATCCGTC
10994 GATA
1 GATA
10998 CCTGTATTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
12 16 0.39
13 25 0.61
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (12 bp):
GATATATCCGTC
Found at i:10972 original size:25 final size:25
Alignment explanation
Indices: 10944--10997 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
10934 TCGATATCTT
10944 GATATATCCG-TCGATATATCCGTTC
1 GATATATCCGTTCGATATATCCG-TC
10969 GATATATCCGTTCGATATATCCGTC
1 GATATATCCGTTCGATATATCCGTC
10994 GATA
1 GATA
10998 CCTGTATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 16 0.57
26 12 0.43
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (25 bp):
GATATATCCGTTCGATATATCCGTC
Found at i:31360 original size:105 final size:105
Alignment explanation
Indices: 31168--31424 Score: 336
Period size: 105 Copynumber: 2.4 Consensus size: 105
31158 TTGTAAAAAG
* ** * *
31168 TAATTCATTTTAAGGGTAAATTAGGACATTAAAGATTTATTAGTATAGGGTTTTAGAAAAAATAG
1 TAATTCATTTTAAGGGTAAGTTATCAAATTAAAGATTTATTA-T-TAGGGTTTTAGAAAAAATAA
* *
31233 AATCAACCAATTTCGCTAAGTTTAACCCCAAATTAAAAAATT
64 AAACAACCAATTTCACTAAGTTTAACCCCAAATTAAAAAATT
*
31275 TAATTCATTTTAAGGGTAAGTTATCAAATTAAAGATTTATTATTAGTGTTTTAGAAAAAATAAAA
1 TAATTCATTTTAAGGGTAAGTTATCAAATTAAAGATTTATTATTAGGGTTTTAGAAAAAATAAAA
** ** *
31340 ACAACCAATTTCACTAAGTTTAGTCTTAAATTAAAACATT
66 ACAACCAATTTCACTAAGTTTAACCCCAAATTAAAAAATT
** *
31380 TAATTCATTTCGAGGGTAAGTTGTCAAATTAAA-ATTTTATTATTA
1 TAATTCATTTTAAGGGTAAGTTATCAAATTAAAGA-TTTATTATTA
31425 TTATAGGGTT
Statistics
Matches: 133, Mismatches: 16, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
104 1 0.01
105 93 0.70
106 1 0.01
107 38 0.29
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (105 bp):
TAATTCATTTTAAGGGTAAGTTATCAAATTAAAGATTTATTATTAGGGTTTTAGAAAAAATAAAA
ACAACCAATTTCACTAAGTTTAACCCCAAATTAAAAAATT
Done.