Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009239.1 Corchorus capsularis cultivar CVL-1 contig09260, 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: 46494
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:3565 original size:11 final size:12
Alignment explanation
Indices: 3529--3558 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
3519 ATAAAAATCA
3529 TAAAAATAATAAT
1 TAAAAA-AATAAT
3542 TAAAAAAATAAT
1 TAAAAAAATAAT
3554 TAAAA
1 TAAAA
3559 GATAATTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
TAAAAAAATAAT
Found at i:3729 original size:26 final size:26
Alignment explanation
Indices: 3665--3721 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
3655 GACTAAATAA
* *
3665 TAAAGATATGATTAAAATTCAAAAAT
1 TAAAAATATGATTAAAATTCAAAAAC
3691 TAAAAATATGATTAAAATTCAAAAAC
1 TAAAAATATGATTAAAATTCAAAAAC
3717 TAAAA
1 TAAAA
3722 GTGAGATTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.28
Consensus pattern (26 bp):
TAAAAATATGATTAAAATTCAAAAAC
Found at i:5983 original size:26 final size:28
Alignment explanation
Indices: 5951--6004 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 28
5941 TTTTTATTTG
5951 AGTTTG-TTTTTTAGTCAGTTT-GAGTC
1 AGTTTGTTTTTTTAGTCAGTTTCGAGTC
5977 AGTTTGTTTTTTTAGTCAGTTTCGAGTC
1 AGTTTGTTTTTTTAGTCAGTTTCGAGTC
6005 TAGTCTCAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 6 0.23
27 15 0.58
28 5 0.19
ACGTcount: A:0.15, C:0.09, G:0.22, T:0.54
Consensus pattern (28 bp):
AGTTTGTTTTTTTAGTCAGTTTCGAGTC
Found at i:16170 original size:3 final size:3
Alignment explanation
Indices: 16162--16211 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
16152 TATAAGCATA
16162 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16210 AA
1 AA
16212 AAGAACTTGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:21082 original size:12 final size:12
Alignment explanation
Indices: 21067--21091 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
21057 TCGATTAAAA
21067 AGAAAAGGATTT
1 AGAAAAGGATTT
21079 AGAAAAGGATTT
1 AGAAAAGGATTT
21091 A
1 A
21092 CAATGACAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (12 bp):
AGAAAAGGATTT
Found at i:29734 original size:79 final size:78
Alignment explanation
Indices: 29584--29733 Score: 212
Period size: 79 Copynumber: 1.9 Consensus size: 78
29574 TACGTAGTTC
* ** *
29584 ATTTTTTTTTGTGCTCTAAGTTTTGCCTAAGCCGTCCTTTGTAGGATTTTCAACTTAGCGAGTCT
1 ATTTTTTTTTGTGCTCTAACTTTTGCCTAAGCCGTCCTTTACAAGATTTTCAACTTAGCGAGTCT
29649 CTTTTTTATTTTT
66 CTTTTTTATTTTT
* * *
29662 ATTTTTATTTTTTGCTCTAACTTTTGTCTAAGTCGTCCTTTACAAGATTTTCAACTTAGCGAG-C
1 ATTTTT-TTTTGTGCTCTAACTTTTGCCTAAGCCGTCCTTTACAAGATTTTCAACTTAGCGAGTC
*
29726 TTTTTTTT
65 TCTTTTTT
29734 TTGTTCTGGT
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
78 14 0.22
79 49 0.78
ACGTcount: A:0.17, C:0.17, G:0.13, T:0.53
Consensus pattern (78 bp):
ATTTTTTTTTGTGCTCTAACTTTTGCCTAAGCCGTCCTTTACAAGATTTTCAACTTAGCGAGTCT
CTTTTTTATTTTT
Found at i:34774 original size:2 final size:2
Alignment explanation
Indices: 34769--34793 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
34759 GTAGTATATA
34769 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
34794 ACACCAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:37702 original size:2 final size:2
Alignment explanation
Indices: 37697--37816 Score: 61
Period size: 2 Copynumber: 61.5 Consensus size: 2
37687 TTAACGTTAG
* ** * * *
37697 AT AT AT AT AT AT AT AT AT AT -T TT CC AG AT TT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
37738 AA AT A- AT AT AT AT TT AT AT -T AT AT AT AT ACC A- AA ACT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT
* * *
37779 AT A- AT AT AT AT TT AT AT AA AT AT AT AA AT 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 A
37817 CCAAAACTAA
Statistics
Matches: 89, Mismatches: 22, Indels: 14
0.71 0.18 0.11
Matches are distributed among these distances:
1 5 0.06
2 82 0.92
3 2 0.02
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:38447 original size:16 final size:16
Alignment explanation
Indices: 38426--38458 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
38416 AAGTTGTCAA
38426 AATGCTATTGATTTGT
1 AATGCTATTGATTTGT
38442 AATGCTATTGATTTGT
1 AATGCTATTGATTTGT
38458 A
1 A
38459 TTATAAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.27, C:0.06, G:0.18, T:0.48
Consensus pattern (16 bp):
AATGCTATTGATTTGT
Found at i:44659 original size:121 final size:121
Alignment explanation
Indices: 44445--44688 Score: 479
Period size: 121 Copynumber: 2.0 Consensus size: 121
44435 CGAGCTAAAA
44445 TTATGCATGTTTTTATAGTTATTTTTATATACTTTTTACTACTTTTACATGTGTTTTTACCCTAT
1 TTATGCATGTTTTTATAGTTATTTTTATATACTTTTTACTACTTTTACATGTGTTTTTACCCTAT
44510 TTTGTTAGTATTTGTGTTTTTAGGTCTTGAAGACAAGAAAAGTGAAAACTTATTGT
66 TTTGTTAGTATTTGTGTTTTTAGGTCTTGAAGACAAGAAAAGTGAAAACTTATTGT
*
44566 TTATGCATGTTTTTATAGTTATTTTTATATACTTTTTACTACTTTTATATGTGTTTTTACCCTAT
1 TTATGCATGTTTTTATAGTTATTTTTATATACTTTTTACTACTTTTACATGTGTTTTTACCCTAT
44631 TTTGTTAGTATTTGTGTTTTTAGGTCTTGAAGACAAGAAAAGTGAAAACTTATTGT
66 TTTGTTAGTATTTGTGTTTTTAGGTCTTGAAGACAAGAAAAGTGAAAACTTATTGT
44687 TT
1 TT
44689 TTCACTCTTT
Statistics
Matches: 122, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
121 122 1.00
ACGTcount: A:0.25, C:0.09, G:0.14, T:0.52
Consensus pattern (121 bp):
TTATGCATGTTTTTATAGTTATTTTTATATACTTTTTACTACTTTTACATGTGTTTTTACCCTAT
TTTGTTAGTATTTGTGTTTTTAGGTCTTGAAGACAAGAAAAGTGAAAACTTATTGT
Found at i:46459 original size:35 final size:35
Alignment explanation
Indices: 46418--46494 Score: 111
Period size: 36 Copynumber: 2.2 Consensus size: 35
46408 TCCAAGAATT
* *
46418 AGTTTTT-GTTTTTTCGATTTTTCTAAAAAAAAGAA
1 AGTTTTTCCTTTTTCCGATTTTTCTAAAAAAAA-AA
*
46453 AGTTTTTCCTTTTTCCGTTTTTTCTAAAAAAAAAA
1 AGTTTTTCCTTTTTCCGATTTTTCTAAAAAAAAAA
46488 AGTTTTT
1 AGTTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 16 0.42
36 22 0.58
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.51
Consensus pattern (35 bp):
AGTTTTTCCTTTTTCCGATTTTTCTAAAAAAAAAA
Done.