Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005923.1 Corchorus capsularis cultivar CVL-1 contig05941, 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: 13351
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:3660 original size:21 final size:21
Alignment explanation
Indices: 3634--3677 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3624 TAGTACTGGA
*
3634 TTGCTAAAT-ACCGTCCCATTT
1 TTGCT-AATCACCGCCCCATTT
*
3655 TTGCTATTCACCGCCCCATTT
1 TTGCTAATCACCGCCCCATTT
3676 TT
1 TT
3678 TACGCTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.18, C:0.32, G:0.09, T:0.41
Consensus pattern (21 bp):
TTGCTAATCACCGCCCCATTT
Found at i:3929 original size:33 final size:34
Alignment explanation
Indices: 3859--3948 Score: 114
Period size: 33 Copynumber: 2.7 Consensus size: 34
3849 GGCGAAGTCG
* * *
3859 CCCCACTGGGGAGGC-TCAACCA-CGGCAGAGCCG
1 CCCCACTGGGGCGGCTTC-ACCATGGGCAGAGCCA
*
3892 CCCCAGTGGGGCGGCTTCACCATGGGCAG-GCCA
1 CCCCACTGGGGCGGCTTCACCATGGGCAGAGCCA
3925 CCCCACTGGGGCGGCTTCACCATG
1 CCCCACTGGGGCGGCTTCACCATG
3949 AAAAGGCTGC
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
33 43 0.86
34 7 0.14
ACGTcount: A:0.17, C:0.39, G:0.33, T:0.11
Consensus pattern (34 bp):
CCCCACTGGGGCGGCTTCACCATGGGCAGAGCCA
Found at i:3968 original size:33 final size:33
Alignment explanation
Indices: 3888--3973 Score: 109
Period size: 33 Copynumber: 2.6 Consensus size: 33
3878 CCACGGCAGA
***
3888 GCCGCCCCAGTGGGGCGGCTTCACCATGGGCAG
1 GCCGCCCCAGTGGGGCGGCTTCACCATGAAAAG
* *
3921 GCCACCCCACTGGGGCGGCTTCACCATGAAAAG
1 GCCGCCCCAGTGGGGCGGCTTCACCATGAAAAG
* *
3954 GCTGCCCCGGTGGGGCGGCT
1 GCCGCCCCAGTGGGGCGGCT
3974 CGGCTATTTT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.14, C:0.36, G:0.37, T:0.13
Consensus pattern (33 bp):
GCCGCCCCAGTGGGGCGGCTTCACCATGAAAAG
Found at i:9996 original size:45 final size:45
Alignment explanation
Indices: 9932--10025 Score: 181
Period size: 45 Copynumber: 2.1 Consensus size: 45
9922 CCCATTTCAA
9932 ATTAATTGTTCATTGTACATAAAGTAAGAAAATAATTAAAATTAG
1 ATTAATTGTTCATTGTACATAAAGTAAGAAAATAATTAAAATTAG
9977 ATTAATTGTTCATTGTACATAAAGTAAGAAAATAATTAAAATTAG
1 ATTAATTGTTCATTGTACATAAAGTAAGAAAATAATTAAAATTAG
10022 -TTAA
1 ATTAA
10026 ATTTATAATT
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 4 0.08
45 45 0.92
ACGTcount: A:0.49, C:0.04, G:0.11, T:0.36
Consensus pattern (45 bp):
ATTAATTGTTCATTGTACATAAAGTAAGAAAATAATTAAAATTAG
Found at i:11065 original size:16 final size:16
Alignment explanation
Indices: 11040--11077 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
11030 GTTTTACCAT
11040 TATA-ATTAATATAGA
1 TATATATTAATATAGA
*
11055 TATATATTAATATATA
1 TATATATTAATATAGA
11071 TATATAT
1 TATATAT
11078 ATTTAGCTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
TATATATTAATATAGA
Found at i:12526 original size:88 final size:89
Alignment explanation
Indices: 12320--12537 Score: 339
Period size: 88 Copynumber: 2.5 Consensus size: 89
12310 AAATGTGAAT
* *
12320 AATTATGACATTAGGTGGGATGGGCCATGCCAGTGAATATTAAACTGTTTCTTTCATATTTATGA
1 AATTATGACATTAGGTGGGATAGGCCATGCCAGTGAATATTAAACTGTTTCTTTCAAATTTATGA
12385 AAAACTTATCTATATATCTATATA
66 AAAACTTATCTATATATCTATATA
* * * *
12409 AATTATGACTTTAGCTGGGATAGGTCATGCCAGTGAATATTAAACTGTTTCTTTTAAATTTAT-A
1 AATTATGACATTAGGTGGGATAGGCCATGCCAGTGAATATTAAACTGTTTCTTTCAAATTTATGA
* *
12473 AAAACTTATTTATATATTTATATA
66 AAAACTTATCTATATATCTATATA
* *
12497 AATTATGACATTAGGTGGAACAGGCCATGCCAGTGAATATT
1 AATTATGACATTAGGTGGGATAGGCCATGCCAGTGAATATT
12538 TATCTATATC
Statistics
Matches: 116, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
88 59 0.51
89 57 0.49
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.38
Consensus pattern (89 bp):
AATTATGACATTAGGTGGGATAGGCCATGCCAGTGAATATTAAACTGTTTCTTTCAAATTTATGA
AAAACTTATCTATATATCTATATA
Found at i:12566 original size:57 final size:57
Alignment explanation
Indices: 12485--12594 Score: 184
Period size: 57 Copynumber: 1.9 Consensus size: 57
12475 AACTTATTTA
*
12485 TATATTTATATAAATTATGACATTAGGTGGAACAGGCCATGCCAGTGAATATTTATC
1 TATATCTATATAAATTATGACATTAGGTGGAACAGGCCATGCCAGTGAATATTTATC
* * *
12542 TATATCTATATAAATTATGGCATTAGGTGGGACAGGTCATGCCAGTGAATATT
1 TATATCTATATAAATTATGACATTAGGTGGAACAGGCCATGCCAGTGAATATT
12595 AAACTGTTTC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.35
Consensus pattern (57 bp):
TATATCTATATAAATTATGACATTAGGTGGAACAGGCCATGCCAGTGAATATTTATC
Found at i:12581 original size:145 final size:145
Alignment explanation
Indices: 12397--12682 Score: 509
Period size: 145 Copynumber: 2.0 Consensus size: 145
12387 AACTTATCTA
* *
12397 TATATCTATATAAATTATGACTTTAGCTGGGATAGGTCATGCCAGTGAATATTAAACTGTTTCTT
1 TATATCTATATAAATTATGACATTAGCTGGGACAGGTCATGCCAGTGAATATTAAACTGTTTCTT
* *
12462 TTAAATTTATAAAAACTTATTTATATATTTATATAAATTATGACATTAGGTGGAACAGGCCATGC
66 TCAAATTTATAAAAACTTATCTATATATTTATATAAATTATGACATTAGGTGGAACAGGCCATGC
12527 CAGTGAATATTTATC
131 CAGTGAATATTTATC
* *
12542 TATATCTATATAAATTATGGCATTAGGTGGGACAGGTCATGCCAGTGAATATTAAACTGTTTCTT
1 TATATCTATATAAATTATGACATTAGCTGGGACAGGTCATGCCAGTGAATATTAAACTGTTTCTT
*
12607 TCAAATTTATAAAAACTTATCTATATATTTATATAAATTATGACATTAGGTGGAACAGGCCATTC
66 TCAAATTTATAAAAACTTATCTATATATTTATATAAATTATGACATTAGGTGGAACAGGCCATGC
12672 CAGTGAATATT
131 CAGTGAATATT
12683 AAACTATTTC
Statistics
Matches: 134, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
145 134 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (145 bp):
TATATCTATATAAATTATGACATTAGCTGGGACAGGTCATGCCAGTGAATATTAAACTGTTTCTT
TCAAATTTATAAAAACTTATCTATATATTTATATAAATTATGACATTAGGTGGAACAGGCCATGC
CAGTGAATATTTATC
Found at i:12693 original size:88 final size:88
Alignment explanation
Indices: 12542--13169 Score: 977
Period size: 88 Copynumber: 7.1 Consensus size: 88
12532 AATATTTATC
*
12542 TATATCTATATAAATTATGGCATTAGGTGGGACAGGTCATGCCAGTGAATATTAAACTGTTTCTT
1 TATATCTATATAAATTATGACATTAGGTGGGACAGGTCATGCCAGTGAATATTAAACTGTTTCTT
* * *
12607 TCAAATTTATAAAAACTTATCTA
66 TCATATGTATAGAAACTTATCTA
* * * * *
12630 TATATTTATATAAATTATGACATTAGGTGGAACAGGCCATTCCAGTGAATATTAAACTATTTCTT
1 TATATCTATATAAATTATGACATTAGGTGGGACAGGTCATGCCAGTGAATATTAAACTGTTTCTT
12695 TCATATGTATAGAAACTTATCTA
66 TCATATGTATAGAAACTTATCTA
* *
12718 TATATCTATATAAATTATGACATTAGGTGGGATAGGTCATACCAGTGAATATTAAACTGTTTCTT
1 TATATCTATATAAATTATGACATTAGGTGGGACAGGTCATGCCAGTGAATATTAAACTGTTTCTT
* * *
12783 TCAAATTTATAAAAACTTATCTA
66 TCATATGTATAGAAACTTATCTA
* * * *
12806 TATATTTATATAAATTATGAGATTAGGTGGAACAGGCCATGCCAGTGAATATTAAACTGTTTTCT
1 TATATCTATATAAATTATGACATTAGGTGGGACAGGTCATGCCAGTGAATATTAAACTG-TTTCT
12871 TTCATATGTATAGAAACTTATCTA
65 TTCATATGTATAGAAACTTATCTA
12895 TATATCTATATAAATTATGACATTAGGTGGGACAGGTCATGCCAGTGAATATTAAACTGTTTCTT
1 TATATCTATATAAATTATGACATTAGGTGGGACAGGTCATGCCAGTGAATATTAAACTGTTTCTT
* * * *
12960 TCAAATTTATAAAAATTTATCTA
66 TCATATGTATAGAAACTTATCTA
* * * * *
12983 TATATTTATATAAATTATGACATTAGGTGGAACAGGCCAAGCCAGTGAATATTAAACTGATTCTT
1 TATATCTATATAAATTATGACATTAGGTGGGACAGGTCATGCCAGTGAATATTAAACTGTTTCTT
13048 TCATATGTATAGAAACTTATCTA
66 TCATATGTATAGAAACTTATCTA
*
13071 TATATCTATATAAATTATGACATTAGGTGGGATAGGTCATGCCAGTGAATATTAAACTGTTTCTT
1 TATATCTATATAAATTATGACATTAGGTGGGACAGGTCATGCCAGTGAATATTAAACTGTTTCTT
* *
13136 TTATATGTATAGAAATTTATCTA
66 TCATATGTATAGAAACTTATCTA
13159 TATATCTATAT
1 TATATCTATAT
13170 TTATATAAAG
Statistics
Matches: 487, Mismatches: 52, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
88 406 0.83
89 81 0.17
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (88 bp):
TATATCTATATAAATTATGACATTAGGTGGGACAGGTCATGCCAGTGAATATTAAACTGTTTCTT
TCATATGTATAGAAACTTATCTA
Found at i:12730 original size:233 final size:234
Alignment explanation
Indices: 12320--12770 Score: 688
Period size: 233 Copynumber: 1.9 Consensus size: 234
12310 AAATGTGAAT
** *
12320 AATTATGACATTAGGTGGGATGGGCCATGCCAGTGAATATTAAACTGTTTCTTTCATATTTATGA
1 AATTATGACATTAGGTGGGACAGGCCATGCCAGTGAATATTAAACTGTTTCTTTCAAATTTATGA
* * * *
12385 AAAACTTATCTATATATCTATATAAATTATGACTTTAGCTGGGATAGGTCATGCCAGTGAATATT
66 AAAACTTATCTATATATCTATATAAATTATGACATTAGCTGGAACAGGCCATGCCAGTGAATATT
* * * * *
12450 AAACTGTTTCTTTTAAATTTATAAAAACTTATTTATATATTTATATAAATTATGACATTAGGTGG
131 AAACTATTTCTTTCAAATGTATAAAAACTTATCTATATATCTATATAAATTATGACATTAGGTGG
*
12515 AACAGGCCATGCCAGTGAATATTTATCTATATCTATATA
196 AACAGGCCATACCAGTGAATATTTATCTATATCTATATA
* *
12554 AATTATGGCATTAGGTGGGACAGGTCATGCCAGTGAATATTAAACTGTTTCTTTCAAATTTAT-A
1 AATTATGACATTAGGTGGGACAGGCCATGCCAGTGAATATTAAACTGTTTCTTTCAAATTTATGA
* * *
12618 AAAACTTATCTATATATTTATATAAATTATGACATTAGGTGGAACAGGCCATTCCAGTGAATATT
66 AAAACTTATCTATATATCTATATAAATTATGACATTAGCTGGAACAGGCCATGCCAGTGAATATT
* *
12683 AAACTATTTCTTTCATATGTATAGAAACTTATCTATATATCTATATAAATTATGACATTAGGTGG
131 AAACTATTTCTTTCAAATGTATAAAAACTTATCTATATATCTATATAAATTATGACATTAGGTGG
* * *
12748 GATAGGTCATACCAGTGAATATT
196 AACAGGCCATACCAGTGAATATT
12771 AAACTGTTTC
Statistics
Matches: 194, Mismatches: 23, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
233 136 0.70
234 58 0.30
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (234 bp):
AATTATGACATTAGGTGGGACAGGCCATGCCAGTGAATATTAAACTGTTTCTTTCAAATTTATGA
AAAACTTATCTATATATCTATATAAATTATGACATTAGCTGGAACAGGCCATGCCAGTGAATATT
AAACTATTTCTTTCAAATGTATAAAAACTTATCTATATATCTATATAAATTATGACATTAGGTGG
AACAGGCCATACCAGTGAATATTTATCTATATCTATATA
Found at i:12836 original size:176 final size:177
Alignment explanation
Indices: 12542--13169 Score: 1107
Period size: 176 Copynumber: 3.6 Consensus size: 177
12532 AATATTTATC
*
12542 TATATCTATATAAATTATGGCATTAGGTGGGACAGGTCATGCCAGTGAATATTAAACTGTTTCTT
1 TATATCTATATAAATTATGACATTAGGTGGGACAGGTCATGCCAGTGAATATTAAACTGTTTCTT
*
12607 TCAAATTTATAAAAACTTATCTATATATTTATATAAATTATGACATTAGGTGGAACAGGCCATTC
66 TCAAATTTATAAAAACTTATCTATATATTTATATAAATTATGACATTAGGTGGAACAGGCCATGC
12672 CAGTGAATATTAAACT-ATTTCTTTCATATGTATAGAAACTTATCTA
131 CAGTGAATATTAAACTGATTTCTTTCATATGTATAGAAACTTATCTA
* *
12718 TATATCTATATAAATTATGACATTAGGTGGGATAGGTCATACCAGTGAATATTAAACTGTTTCTT
1 TATATCTATATAAATTATGACATTAGGTGGGACAGGTCATGCCAGTGAATATTAAACTGTTTCTT
*
12783 TCAAATTTATAAAAACTTATCTATATATTTATATAAATTATGAGATTAGGTGGAACAGGCCATGC
66 TCAAATTTATAAAAACTTATCTATATATTTATATAAATTATGACATTAGGTGGAACAGGCCATGC
*
12848 CAGTGAATATTAAACTGTTTTCTTTCATATGTATAGAAACTTATCTA
131 CAGTGAATATTAAACTGATTTCTTTCATATGTATAGAAACTTATCTA
12895 TATATCTATATAAATTATGACATTAGGTGGGACAGGTCATGCCAGTGAATATTAAACTGTTTCTT
1 TATATCTATATAAATTATGACATTAGGTGGGACAGGTCATGCCAGTGAATATTAAACTGTTTCTT
* *
12960 TCAAATTTATAAAAATTTATCTATATATTTATATAAATTATGACATTAGGTGGAACAGGCCAAGC
66 TCAAATTTATAAAAACTTATCTATATATTTATATAAATTATGACATTAGGTGGAACAGGCCATGC
13025 CAGTGAATATTAAACTGA-TTCTTTCATATGTATAGAAACTTATCTA
131 CAGTGAATATTAAACTGATTTCTTTCATATGTATAGAAACTTATCTA
*
13071 TATATCTATATAAATTATGACATTAGGTGGGATAGGTCATGCCAGTGAATATTAAACTGTTTCTT
1 TATATCTATATAAATTATGACATTAGGTGGGACAGGTCATGCCAGTGAATATTAAACTGTTTCTT
* * * * * *
13136 TTATATGTATAGAAATTTATCTATATATCTATAT
66 TCAAATTTATAAAAACTTATCTATATATTTATAT
13170 TTATATAAAG
Statistics
Matches: 433, Mismatches: 18, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
176 262 0.61
177 171 0.39
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (177 bp):
TATATCTATATAAATTATGACATTAGGTGGGACAGGTCATGCCAGTGAATATTAAACTGTTTCTT
TCAAATTTATAAAAACTTATCTATATATTTATATAAATTATGACATTAGGTGGAACAGGCCATGC
CAGTGAATATTAAACTGATTTCTTTCATATGTATAGAAACTTATCTA
Done.