Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020603.1 Corchorus olitorius cultivar O-4 contig20636, 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: 3433
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.32
Found at i:53 original size:35 final size:35
Alignment explanation
Indices: 7--215 Score: 287
Period size: 35 Copynumber: 6.0 Consensus size: 35
1 AAATGT
* *
7 GATCAACTCTGATCACCGAAAACTTCTTAAAACGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
* *
42 GATCAACTCTGATCAT-AAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
* *
76 GATCAACTCTGATCAACGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
**
111 GATCAACTCTGATCATAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
* *
146 GATCAACTCTGATCATC-ATAAACTTCTTGGAATGA
1 GATCAACTCTGATCATCGA-AAACTTCTTGAAACGA
* *
181 GATCAACTCTGATCATCGAAAACTTATTGGAACGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
216 CCGCACTGGA
Statistics
Matches: 155, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
34 31 0.20
35 123 0.79
36 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.26
Consensus pattern (35 bp):
GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
Found at i:419 original size:55 final size:54
Alignment explanation
Indices: 180--447 Score: 220
Period size: 54 Copynumber: 5.0 Consensus size: 54
170 TCTTGGAATG
* * * * * * *
180 AGATCAACTCTGATCATC-GAAAACTTATTGGAACGACCGCACTGGATCATCTGG
1 AGATCAACTCTGATC-TCTAAAAACTTCTTTGAAAGACCGCACAGGGTCATCTGA
* * * * * *
234 GGATCAACTCTGATCTCTAAAAACTTCTTGGGACGACCGCACTGGATCATCTG-
1 AGATCAACTCTGATCTCTAAAAACTTCTTTGAAAGACCGCACAGGGTCATCTGA
* * * * * * *
287 GGATCAACTATGATCTCTACAAACTTCTTTGAAAGACCGCACGGGGTAAACTTA
1 AGATCAACTCTGATCTCTAAAAACTTCTTTGAAAGACCGCACAGGGTCATCTGA
* *
341 AGATCAACTCTGATCAT-TGAAAACTTCTTATGAAAGACTGCACAGGGTCATCTGA
1 AGATCAACTCTGATC-TCTAAAAACTTCTT-TGAAAGACCGCACAGGGTCATCTGA
* ** * * *
396 AGATCAACT-TAGATTTCTAAAAACTTCCATGAAAGACCACACTGGCTCATCT
1 AGATCAACTCT-GATCTCTAAAAACTTCTTTGAAAGACCGCACAGGGTCATCT
448 TAAACATCTG
Statistics
Matches: 177, Mismatches: 31, Indels: 12
0.80 0.14 0.05
Matches are distributed among these distances:
53 45 0.25
54 90 0.51
55 42 0.24
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (54 bp):
AGATCAACTCTGATCTCTAAAAACTTCTTTGAAAGACCGCACAGGGTCATCTGA
Found at i:450 original size:109 final size:107
Alignment explanation
Indices: 235--442 Score: 231
Period size: 109 Copynumber: 1.9 Consensus size: 107
225 ATCATCTGGG
* * * *
235 GATCAACTCTGATCTCTAAAAACTTCTTGGGACGACCGCACTGGATCATCTGGGATCAACTATGA
1 GATCAACTCTGATCTCTAAAAACTTCTTGGAAAGACCGCACAGGATCATCTGAGATCAACTATGA
* ** * *
300 TCTCTACAAACTTCTTTGAAAGACCGCACGGGGTAAACTTAA
66 TCTCTAAAAACTTCCATGAAAGACCACACGGGCTAAACTTAA
* * * *
342 GATCAACTCTGATCAT-TGAAAACTTCTTATGAAAGACTGCACAGGGTCATCTGAAGATCAACT-
1 GATCAACTCTGATC-TCTAAAAACTTCTT-GGAAAGACCGCACAGGATCATCTG-AGATCAACTA
* *
405 TAGATTTCTAAAAACTTCCATGAAAGACCACACTGGCT
63 T-GATCTCTAAAAACTTCCATGAAAGACCACACGGGCT
443 CATCTTAAAC
Statistics
Matches: 82, Mismatches: 15, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
107 25 0.30
108 20 0.24
109 37 0.45
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.26
Consensus pattern (107 bp):
GATCAACTCTGATCTCTAAAAACTTCTTGGAAAGACCGCACAGGATCATCTGAGATCAACTATGA
TCTCTAAAAACTTCCATGAAAGACCACACGGGCTAAACTTAA
Found at i:1325 original size:37 final size:39
Alignment explanation
Indices: 1247--1328 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 39
1237 TAAAAATCTT
**
1247 TTTGAAAAAAACATTTTTTTCTCGTTTCAAAAGATTGCAC
1 TTTGAAAAAAACA-TTTTTTCTCGTTTCAAAAGATCACAC
* * *
1287 TTTGAAGAAAACA-TTTTTC-CTTTTGAAAAGATCACAC
1 TTTGAAAAAAACATTTTTTCTCGTTTCAAAAGATCACAC
1324 TTTGA
1 TTTGA
1329 GGAAGGTTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
37 19 0.51
38 6 0.16
40 12 0.32
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (39 bp):
TTTGAAAAAAACATTTTTTCTCGTTTCAAAAGATCACAC
Found at i:1975 original size:19 final size:20
Alignment explanation
Indices: 1942--1998 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
1932 AAACACTTTC
1942 TTGAAAAACATTTTTGACTT
1 TTGAAAAACATTTTTGACTT
1962 TTGAAAAACATTTTTGACTT
1 TTGAAAAACATTTTTGACTT
1982 TTGAAAAAC-TTTTTGAC
1 TTGAAAAACATTTTTGAC
1999 CAAAATCCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 8 0.22
20 29 0.78
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.44
Consensus pattern (20 bp):
TTGAAAAACATTTTTGACTT
Found at i:2699 original size:19 final size:19
Alignment explanation
Indices: 2646--2700 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 19
2636 TTGAAACGAG
2646 ATCAACTCTGATCATCGAA
1 ATCAACTCTGATCATCGAA
* ** *
2665 AACTTCT-TGA--AACGAA
1 ATCAACTCTGATCATCGAA
2681 ATCAACTCTGATCATCGAA
1 ATCAACTCTGATCATCGAA
2700 A
1 A
2701 ACTTCTTCAA
Statistics
Matches: 25, Mismatches: 8, Indels: 6
0.64 0.21 0.15
Matches are distributed among these distances:
16 9 0.36
17 3 0.12
18 3 0.12
19 10 0.40
ACGTcount: A:0.40, C:0.24, G:0.11, T:0.25
Consensus pattern (19 bp):
ATCAACTCTGATCATCGAA
Found at i:3163 original size:35 final size:35
Alignment explanation
Indices: 2462--3156 Score: 896
Period size: 35 Copynumber: 19.7 Consensus size: 35
2452 ATCAAAGTGA
* *
2462 AGATCAACTCTGATCATCGAAAACTTCTTGAAATA
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
*
2497 AGATCAACTCTGATCATAAAAAAAACTTCTTGAAA-G
1 AGATCAACTCTGATCAT--CAAAAACTTCTTGAAATG
* *
2533 AAGATCAACTCTGACCATAAAAAAAAAAACTTCTTGAAATG
1 -AGATCAACTCTGATCAT-----CAAAAACTTCTTGAAATG
* *
2574 AGATCAACTCTGATCGA-CAAAAACTTCTTAAAAGG
1 AGATCAACTCTGATC-ATCAAAAACTTCTTGAAATG
* *
2609 AGATCAACTCTGATCATAAAAAACTTCTTGAAACG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* *
2644 AGATCAACTCTGATCATCGAAAACTTCTTGAAACG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* * *
2679 AAATCAACTCTGATCATCGAAAACTTCTTCAAATG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
2714 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
*
2749 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* * *
2784 CGATCAACTCTGATAATCGAAAACTTCTTGAAATG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* *
2819 AGATCAACTCTAATCATCGAAAACTTCTTGAAATG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
** * *
2854 TTATCAACCCTGATCATC-AAAACTTCTTAAAATG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* * *
2888 TGATCAAATCTGACCATCAAAAACTTCTTGAAATG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* * *
2923 CGATCAACTATGATCATC-AAAACTTCTTAAAATG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* * * * *
2957 TGATCAACTCAGATCACCGAAAACTTCTTAAAATG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
2992 AGATCAACTCTGATCAT-AAAAACTTCTTGAAATG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* * *
3026 AGATCAACTCTGATCAACGAAAACTTCTTGAAAGG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* *
3061 AGATCAACTCTGATCATAAAAAACTTCTTGAAACG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
*
3096 AGATCAACTCTGATCATCAAAAACTTCTTGGAATG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
*
3131 AGATCAACTCTGATCATCGAAAACTT
1 AGATCAACTCTGATCATCAAAAACTT
3157 ATTGGAACGA
Statistics
Matches: 588, Mismatches: 60, Indels: 24
0.88 0.09 0.04
Matches are distributed among these distances:
34 90 0.15
35 434 0.74
37 30 0.05
40 32 0.05
41 2 0.00
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (35 bp):
AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
Found at i:3221 original size:54 final size:54
Alignment explanation
Indices: 3131--3398 Score: 249
Period size: 54 Copynumber: 5.0 Consensus size: 54
3121 TCTTGGAATG
* * * *
3131 AGATCAACTCTGATCATC-GAAAACTTATTGGAACGACCGCACTGGATCATCTGG
1 AGATCAACTCTGATC-TCTAAAAACTTCTTGGAAAGACCGCACTGGATCATCTGA
* * *
3185 GGATCAACTCTGATCTCTAAAAACTTCTTGGGACGACCGCACTGGATCATCTG-
1 AGATCAACTCTGATCTCTAAAAACTTCTTGGAAAGACCGCACTGGATCATCTGA
* * * * * * * *
3238 GGATCAACTATGATCTCTACAAACTTCTTTGAAAGACCGCACGGGGTCAACTTA
1 AGATCAACTCTGATCTCTAAAAACTTCTTGGAAAGACCGCACTGGATCATCTGA
* * * * *
3292 AGATCAACTCTGATCAT-TGAAAACTTCTTATGAAAGACTGCACAGGGTCATCTGA
1 AGATCAACTCTGATC-TCTAAAAACTTCTT-GGAAAGACCGCACTGGATCATCTGA
* * *
3347 AGATCAACT-TAGATTTCTAAAAACTTCTAT-GAAAGACCACACTGGCTCATCT
1 AGATCAACTCT-GATCTCTAAAAACTTCT-TGGAAAGACCGCACTGGATCATCT
3399 TAAACATCTG
Statistics
Matches: 180, Mismatches: 27, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
53 46 0.26
54 89 0.49
55 44 0.24
56 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (54 bp):
AGATCAACTCTGATCTCTAAAAACTTCTTGGAAAGACCGCACTGGATCATCTGA
Found at i:3401 original size:109 final size:107
Alignment explanation
Indices: 3186--3401 Score: 247
Period size: 109 Copynumber: 2.0 Consensus size: 107
3176 ATCATCTGGG
* * * *
3186 GATCAACTCTGATCTCTAAAAACTTCTTGGGACGACCGCACTGGATCATCTGGGATCAACTATGA
1 GATCAACTCTGATCTCTAAAAACTTCTTGGAAAGACCGCACAGGATCATCTGAGATCAACTATGA
* * * *
3251 TCTCTACAAACTTCTTTGAAAGACCGCACGGGGTCAACTTAA
66 TCTCTAAAAACTTCTATGAAAGACCACACGGGCTCAACTTAA
* * * *
3293 GATCAACTCTGATCAT-TGAAAACTTCTTATGAAAGACTGCACAGGGTCATCTGAAGATCAACT-
1 GATCAACTCTGATC-TCTAAAAACTTCTT-GGAAAGACCGCACAGGATCATCTG-AGATCAACTA
* * *
3356 TAGATTTCTAAAAACTTCTATGAAAGACCACACTGGCTCATCTTAA
63 T-GATCTCTAAAAACTTCTATGAAAGACCACACGGGCTCAACTTAA
3402 ACATCTGTAC
Statistics
Matches: 90, Mismatches: 15, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
107 25 0.28
108 20 0.22
109 45 0.50
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (107 bp):
GATCAACTCTGATCTCTAAAAACTTCTTGGAAAGACCGCACAGGATCATCTGAGATCAACTATGA
TCTCTAAAAACTTCTATGAAAGACCACACGGGCTCAACTTAA
Done.