Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014505.1 Corchorus capsularis cultivar CVL-1 contig14526, 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: 52953
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1166 original size:18 final size:18
Alignment explanation
Indices: 1132--1174 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1122 CCTAGCCAAG
*
1132 AAGAAGAAGAAATAAAGC
1 AAGAAGAAGAAAAAAAGC
*
1150 AAGAAGAA-AAACAAAAGG
1 AAGAAGAAGAAA-AAAAGC
1168 AAGAAGA
1 AAGAAGA
1175 TGCAGCAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.70, C:0.05, G:0.23, T:0.02
Consensus pattern (18 bp):
AAGAAGAAGAAAAAAAGC
Found at i:2497 original size:17 final size:17
Alignment explanation
Indices: 2465--2498 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2455 GTAAGCTTTG
*
2465 TATTCATTTTAAATTGT
1 TATTCATTTCAAATTGT
*
2482 TATTCATTTCAGATTGT
1 TATTCATTTCAAATTGT
2499 CATGAAAAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.56
Consensus pattern (17 bp):
TATTCATTTCAAATTGT
Found at i:6161 original size:14 final size:15
Alignment explanation
Indices: 6140--6182 Score: 65
Period size: 13 Copynumber: 3.1 Consensus size: 15
6130 TAAAATAGAG
6140 TCGAGTTGTAGGGAA
1 TCGAGTTGTAGGGAA
6155 T-GAGTTGTAGGG--
1 TCGAGTTGTAGGGAA
6167 TCGAGTTGTAGGGAA
1 TCGAGTTGTAGGGAA
6182 T
1 T
6183 AATTGCATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 1 0.04
13 11 0.44
14 11 0.44
15 2 0.08
ACGTcount: A:0.23, C:0.05, G:0.42, T:0.30
Consensus pattern (15 bp):
TCGAGTTGTAGGGAA
Found at i:6788 original size:13 final size:14
Alignment explanation
Indices: 6770--6799 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
6760 AAATGCTTGC
6770 AAAAATCA-TATAA
1 AAAAATCATTATAA
6783 AAAAATCATTATAA
1 AAAAATCATTATAA
6797 AAA
1 AAA
6800 TGAATAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAAATCATTATAA
Found at i:7610 original size:12 final size:13
Alignment explanation
Indices: 7595--7623 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
7585 TAACTTTGTC
7595 TTTTCT-TTTTTT
1 TTTTCTGTTTTTT
7607 TTTTCTGTTTTTT
1 TTTTCTGTTTTTT
7620 TTTT
1 TTTT
7624 ATTAATTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.00, C:0.07, G:0.03, T:0.90
Consensus pattern (13 bp):
TTTTCTGTTTTTT
Found at i:39779 original size:266 final size:266
Alignment explanation
Indices: 39291--40085 Score: 1191
Period size: 265 Copynumber: 3.0 Consensus size: 266
39281 CGCTTCCAAT
*
39291 ATTATTTTTCCCAC--TCTATTGTGTAATTCTAACGTAAAAATTACATGGATTTAGGATGAGGTG
1 ATTATTTTTCCCACGATCTATTGTGTAATTCTAAAGTAAAAATTACATGGATTTAGGATGAGGTG
* * *
39354 TCGTATCAGACAT-AA-GTACGTTATGTATTTTAAGGAATCTTTTA-TGTTATAACTTTTTGATA
66 TCGTATCTGACATAAATATACGTTATGTTTTTTAAGGAATCTTTTACT-TTATAACTTTTTGATA
* * * * *
39416 TATCGTAGTGAATATCAGATATTGTAACGTTAAGA-TGTAGTG-A---GTGTTATTATAAGTAAG
130 TCTCGTAATGATTATCAGATATTGTAACGTTAAGACAG-AGTGAAGTCGTGTTATTATAAGCAAG
*
39476 AGTCGAATTTAAAGTACTAACACATGGATAAAAAAAGGAAAGGCCAAGTGTAAATCAATGAGGGG
194 AGTCGAATTTAAAGTACT-A-ACATGGAT--AAAAAGGAAAAGCCAAGTGTAAATCAATGAGGGG
39541 ATTTCAAATAAG
255 ATTTCAAATAAG
*
39553 ATTATTTTTCCCACGATCTATTGTGTAATTCTAAAGTAAAAATTACATGAATTTAGGATGAGGTG
1 ATTATTTTTCCCACGATCTATTGTGTAATTCTAAAGTAAAAATTACATGGATTTAGGATGAGGTG
*
39618 TCGTATCTGACATAAATATACGTTATGTTTTTTAAGGAATCCTTTACTTTATAACTTTTTGATAT
66 TCGTATCTGACATAAATATACGTTATGTTTTTTAAGGAATCTTTTACTTTATAACTTTTTGATAT
*
39683 CTCGTAATGATTATCAGATATTGTAACATTAAGACAGAGTGAAGTCGTGTTATTATAAGCAAGAG
131 CTCGTAATGATTATCAGATATTGTAACGTTAAGACAGAGTGAAGTCGTGTTATTATAAGCAAGAG
* *
39748 TCAAATTTAAAGTACTAACATGGATAAAAAGGAAAAGCCAAGTGTAAATCAATG-GGGGGTTTCA
196 TCGAATTTAAAGTACTAACATGGATAAAAAGGAAAAGCCAAGTGTAAATCAATGAGGGGATTTCA
*
39812 AATAAT
261 AATAAG
*
39818 ATTA-TTTTCTCCACGATCTATCGTGTAATTCTAAAGTAAAAATTACATGGATTTAGGATGAGGT
1 ATTATTTTTC-CCACGATCTATTGTGTAATTCTAAAGTAAAAATTACATGGATTTAGGATGAGGT
* *
39882 GTCGTATCTGACATAAGTATACGTTATGTTTTTTAAGGAATCTTTTACATTATAACTTTTTGATA
65 GTCGTATCTGACATAAATATACGTTATGTTTTTTAAGGAATCTTTTACTTTATAACTTTTTGATA
* * * *
39947 TCTCGTTATGATTATCAAATATTATTGTAACGTTAAGACAGACTGAAGTCGTGTTATTATAAACA
130 TCTCGTAATGATTATC--AGA-TATTGTAACGTTAAGACAGAGTGAAGTCGTGTTATTATAAGCA
* *
40012 AGAGTCGAATTTAAAGTACTAATATGGATAAAAAGGAAAAGCCAAGTGTAAATCAATGAGAGGAT
192 AGAGTCGAATTTAAAGTACTAACATGGATAAAAAGGAAAAGCCAAGTGTAAATCAATGAGGGGAT
40077 TTCAAATAA
257 TTCAAATAA
40086 TACTAAATTA
Statistics
Matches: 488, Mismatches: 30, Indels: 23
0.90 0.06 0.04
Matches are distributed among these distances:
262 14 0.03
264 64 0.13
265 149 0.31
266 105 0.22
267 5 0.01
268 104 0.21
269 14 0.03
270 33 0.07
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (266 bp):
ATTATTTTTCCCACGATCTATTGTGTAATTCTAAAGTAAAAATTACATGGATTTAGGATGAGGTG
TCGTATCTGACATAAATATACGTTATGTTTTTTAAGGAATCTTTTACTTTATAACTTTTTGATAT
CTCGTAATGATTATCAGATATTGTAACGTTAAGACAGAGTGAAGTCGTGTTATTATAAGCAAGAG
TCGAATTTAAAGTACTAACATGGATAAAAAGGAAAAGCCAAGTGTAAATCAATGAGGGGATTTCA
AATAAG
Found at i:46599 original size:53 final size:53
Alignment explanation
Indices: 46536--46645 Score: 186
Period size: 53 Copynumber: 2.1 Consensus size: 53
46526 CAAAAAAAAA
46536 AGTTTCTTCCATTTGATGATTACTCTACTCTTGCTGTCTTGCATGCATTAGC-C
1 AGTTTCTTCCATTTGATGATTACTCTACTCTTGCTGTCTTGCATGCATT-GCTC
* *
46589 AGTTTCTTCCATTTGATTATTACTCTACTCTTGCTGTCTTGCCTGCATTGCTC
1 AGTTTCTTCCATTTGATGATTACTCTACTCTTGCTGTCTTGCATGCATTGCTC
46642 AGTT
1 AGTT
46646 GGACACGTCA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
52 2 0.04
53 52 0.96
ACGTcount: A:0.15, C:0.25, G:0.15, T:0.45
Consensus pattern (53 bp):
AGTTTCTTCCATTTGATGATTACTCTACTCTTGCTGTCTTGCATGCATTGCTC
Found at i:48680 original size:3 final size:3
Alignment explanation
Indices: 48674--48719 Score: 83
Period size: 3 Copynumber: 15.0 Consensus size: 3
48664 ACTACTACTA
48674 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT
48720 ATATATTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:49466 original size:14 final size:14
Alignment explanation
Indices: 49421--49470 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
49411 AAAAAAAATC
49421 AATTTAATTATTTAT
1 AATTTAATT-TTTAT
* *
49436 GA-TT-ATTATTAT
1 AATTTAATTTTTAT
*
49448 TATTTAATTTTTAT
1 AATTTAATTTTTAT
49462 AATTTAATT
1 AATTTAATT
49471 GTTAATTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
12 5 0.18
13 5 0.18
14 17 0.61
15 1 0.04
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (14 bp):
AATTTAATTTTTAT
Done.