Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012237.1 Corchorus capsularis cultivar CVL-1 contig12258, 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: 28790
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:11914 original size:3 final size:3
Alignment explanation
Indices: 11906--11939 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
11896 GCTCCATCAT
11906 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
11940 GTTTTTACGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:15726 original size:103 final size:101
Alignment explanation
Indices: 15539--15727 Score: 245
Period size: 103 Copynumber: 1.9 Consensus size: 101
15529 TATCCATTTT
* * **
15539 GTTCATTTAAAGACATAATTGTCATTTTATATGACGCGTGAGATGTGTGGATATTGTTGTATTGG
1 GTTCATTTAAAGACATAATTGTCATTTTATATGACGCGTGAGATGAGTGGATATTGTCGTATTAA
*
15604 CCCGTGAGATGAATGGGTATACCCATCTATTTCATA
66 CCCGTGAGATGAATAGGTATACCCATCTATTTCATA
* * * *
15640 GTTCATTT-AAGAACATAATTGTCATTTTATATATAGCTCGTGAGATGAGTGGGTGTTGTCGTAT
1 GTTCATTTAAAG-ACATAATTGTCATTTTATAT-GA-CGCGTGAGATGAGTGGATATTGTCGTAT
* *
15704 TAACCTGTGAGATGAGTAGGTATA
63 TAACCCGTGAGATGAATAGGTATA
15728 TGTATACCCA
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
100 3 0.04
101 28 0.38
102 1 0.01
103 42 0.57
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.38
Consensus pattern (101 bp):
GTTCATTTAAAGACATAATTGTCATTTTATATGACGCGTGAGATGAGTGGATATTGTCGTATTAA
CCCGTGAGATGAATAGGTATACCCATCTATTTCATA
Found at i:15922 original size:100 final size:101
Alignment explanation
Indices: 15748--15980 Score: 264
Period size: 98 Copynumber: 2.3 Consensus size: 101
15738 TCATTTTTAG
* *
15748 TGTTCATTT-AGGACATAATTGTCATTTT-TATGGTCCATGAGATTGGTGGATAATATCGTATTG
1 TGTTCATTTAAGGATATAATTGTCATTTTATATGGTCCATAAGATTGGTGGATAATATCGTATTG
*
15811 ACCCATAAGATGAGT-GGATAAATATCAATCCCTT-TCAC
66 ACCCATAAGATGAATAGG-T--ATATCAATCCCTTCT-AC
* *
15849 TGTTCATTTAAGGATATAATTGTCATTTTATATGGTCCGTAAGATT-GT-G-TATTATCGTATTG
1 TGTTCATTTAAGGATATAATTGTCATTTTATATGGTCCATAAGATTGGTGGATAATATCGTATTG
** * * *
15911 ACCTGTGAGATGAATAGGTATATCTATCCCTTCTAT
66 ACCCATAAGATGAATAGGTATATCAATCCCTTCTAC
* * *
15947 TGCTCATTGAAGGATGTAATTGTCATTTTATATG
1 TGTTCATTTAAGGATATAATTGTCATTTTATATG
15981 AGTTGTGAGA
Statistics
Matches: 115, Mismatches: 13, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
98 44 0.38
99 1 0.01
100 24 0.21
101 12 0.10
102 20 0.17
103 14 0.12
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (101 bp):
TGTTCATTTAAGGATATAATTGTCATTTTATATGGTCCATAAGATTGGTGGATAATATCGTATTG
ACCCATAAGATGAATAGGTATATCAATCCCTTCTAC
Found at i:21501 original size:18 final size:18
Alignment explanation
Indices: 21475--21512 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
21465 CCCTCTCATA
21475 GTACCTAGGTAGTATGAG
1 GTACCTAGGTAGTATGAG
*
21493 GTACTTAGGTAGTATGAG
1 GTACCTAGGTAGTATGAG
21511 GT
1 GT
21513 GCTGGATAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.26, C:0.08, G:0.34, T:0.32
Consensus pattern (18 bp):
GTACCTAGGTAGTATGAG
Found at i:22101 original size:156 final size:156
Alignment explanation
Indices: 21941--22226 Score: 337
Period size: 156 Copynumber: 1.8 Consensus size: 156
21931 TTGCCAATGT
** ** * * *
21941 ACTTAGAATATTTCCATGA-AACTAT-GGAAAAAATACCAAGTAAAACCGTGCTCCCCTTG-GTG
1 ACTTAGAATATCACCAT-ATAACTATGGGAAAAAAT-CCAAGTAAAACCGAACT-CCCTAGCATA
* * ** *
22003 GTGAACTAGGTTTGTCT-CTCTGTATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTA
63 GAGAACTAGGTTTGACTCCTC-AAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATACTA
22067 AGTCCAACAAGGCTAATTTTCCACCAGTAG
127 AGTCCAACAAGGCTAATTTTCCACCAGTAG
* * * *
22097 ACTTAGATTATCACCATATAGCTATGGGAAAAAATCTAAGTAAAACCGAACTCTCTAGCATAGAG
1 ACTTAGAATATCACCATATAACTATGGGAAAAAATCCAAGTAAAACCGAACTCCCTAGCATAGAG
* * *
22162 AAGTTGGTTTGACTCCTCAAATTGTCCTTAACTGAAAAACTAGCATAAGTTTTTCATACTAAGTC
66 AACTAGGTTTGACTCCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATACTAAGTC
22227 TGTTTGAGAT
Statistics
Matches: 107, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
155 5 0.05
156 90 0.84
157 12 0.11
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (156 bp):
ACTTAGAATATCACCATATAACTATGGGAAAAAATCCAAGTAAAACCGAACTCCCTAGCATAGAG
AACTAGGTTTGACTCCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATACTAAGTC
CAACAAGGCTAATTTTCCACCAGTAG
Found at i:23542 original size:2 final size:2
Alignment explanation
Indices: 23537--23568 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
23527 GTGTGTGAGG
23537 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23569 CTCTCTCTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23573 original size:2 final size:2
Alignment explanation
Indices: 23568--23594 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
23558 TATATATATA
23568 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
23595 GACAATCAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Done.