Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01001106.1 Corchorus olitorius cultivar O-4 contig01106, 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, 741
Length: 1235
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Found at i:102 original size:54 final size:53
Alignment explanation
Indices: 16--382 Score: 384
Period size: 54 Copynumber: 6.8 Consensus size: 53
6 GACAGCACCT
* * *
16 GATCATCTGGAGATCAACTTTGATCTTTGAAAACTTCTAGGAA-GAACCGCACTG
1 GATCATCTGGAGATCAACTCTGA-CCTTGAAAACTTCTTGGAATG-ACCGCACTG
* * *
70 GATCATCTGGACATCAACTCTGAACTTCGAAAACTT-TTCGGAAGGACCGCACTG
1 GATCATCTGGAGATCAACTCTGACCTT-GAAAACTTCTT-GGAATGACCGCACTG
* ** **
124 GATCATCTGGAGATCAACTCTGATCATCAAAAACTTCTTGGAATGACCGCACAA
1 GATCATCTGGAGATCAACTCTGA-CCTTGAAAACTTCTTGGAATGACCGCACTG
* * * *
178 GATCATCT-GAGGATCAATTCTGATCAT-AAAACTTCTTGGAATGACAGCACTG
1 GATCATCTGGA-GATCAACTCTGACCTTGAAAACTTCTTGGAATGACCGCACTG
* * * *
230 GATC-TTTGGCGATCAATTCTGACCATTGAAAACTTCTTGGAGTGACCGCACTG
1 GATCATCTGGAGATCAACTCTGACC-TTGAAAACTTCTTGGAATGACCGCACTG
* * * *
283 GACCTTTTGGGGATCAACTCTGACCATTGAAAACTTCTTGGAATGACCGCACTG
1 GATCATCTGGAGATCAACTCTGACC-TTGAAAACTTCTTGGAATGACCGCACTG
* * *
337 GATCTTTTGGGGATCAACTCTGACCATTGAAAACTTCTTGGAATGA
1 GATCATCTGGAGATCAACTCTGACC-TTGAAAACTTCTTGGAATGA
383 GATCAACTCT
Statistics
Matches: 271, Mismatches: 32, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
51 15 0.06
52 28 0.10
53 31 0.11
54 193 0.71
55 4 0.01
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (53 bp):
GATCATCTGGAGATCAACTCTGACCTTGAAAACTTCTTGGAATGACCGCACTG
Found at i:387 original size:35 final size:35
Alignment explanation
Indices: 348--828 Score: 615
Period size: 35 Copynumber: 13.6 Consensus size: 35
338 ATCTTTTGGG
* ** *
348 GATCAACTCTGACCATTGAAAACTTCTTGGAATGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
*
383 GATCAACTCTGATCATAAAAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCAT--CAAAAACTTCTTGAAATGA
*
420 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
455 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
* *
490 GATCAACTCTGATAATCAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
* *
525 GATCAACTCTGATCATCAAAAACTTATTGAAAGGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
* **
560 GATCAACTCTGATCATAAAAAACTTCTTGAAACAA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
* *
595 GACCAACTCTGATCATC-GAAACTTCTT-AGAATGA
1 GATCAACTCTGATCATCAAAAACTTCTTGA-AATGA
*
629 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
* * *
664 GATCAACTCTGATCAACGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
* * *
699 GATCAACTCTGATCAACGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
* * * *
734 GATAAACTCTGATCATAAAAAAAACTTCTTTAAACGA
1 GATCAACTCTGATCAT--CAAAAACTTCTTGAAATGA
* * *
771 GATCAACTCTGATAATAAAAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCAT-CAAAAACTTCTTGAAATGA
* *
807 GATCAACTTTGATCATAAAAAA
1 GATCAACTCTGATCATCAAAAA
829 AACTTCATGG
Statistics
Matches: 404, Mismatches: 35, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
33 1 0.00
34 28 0.07
35 281 0.70
36 33 0.08
37 61 0.15
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (35 bp):
GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
Found at i:658 original size:174 final size:176
Alignment explanation
Indices: 348--828 Score: 700
Period size: 174 Copynumber: 2.7 Consensus size: 176
338 ATCTTTTGGG
* * * *
348 GATCAACTCTGACCATTGAAAACTTCTTGGAATGAGATCAACTCTGATCATAAAAAAAACTTCTT
1 GATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCAT-AAAAAAACTTCTT
*
413 GAAATGAGATCAACTCTGATCATAAAAAACTTCTTGAAATGAGATCAACTCTGATCATCAAAAAC
65 GAAACGAGATCAACTCTGATCATAAAAAACTTCTTGAAATGAGATCAACTCTGATCATCAAAAAC
478 TTCTTGAAATGAGATCAACTCTGAT-AATCAAAAACTTCTTGAAACGA
130 TTCTTGAAATGAGATCAACTCTGATCAA-CAAAAACTTCTTGAAACGA
* *
525 GATCAACTCTGATCATCAAAAACTTATTGAAAGGAGATCAACTCTGATCAT-AAAAAACTTCTTG
1 GATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAAACTTCTTG
* * ** *
589 AAACAAGACCAACTCTGATCAT-CGAAACTTCTT-AGAATGAGATCAACTCTGATCATCGAAAAC
66 AAACGAGATCAACTCTGATCATAAAAAACTTCTTGA-AATGAGATCAACTCTGATCATCAAAAAC
* *
652 TTCTTGAAATGAGATCAACTCTGATCAACGAAAACTTCTTGAAAGGA
130 TTCTTGAAATGAGATCAACTCTGATCAACAAAAACTTCTTGAAACGA
* *
699 GATCAACTCTGATCAACGAAAACTTCTTGAAAGGAGATAAACTCTGATCATAAAAAAAACTTCTT
1 GATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCAT-AAAAAAACTTCTT
* * * * *
764 TAAACGAGATCAACTCTGATAATAAAAAAACTTCTTGAAAGGAGATCAACTTTGATCATAAAAAA
65 GAAACGAGATCAACTCTGATCAT-AAAAAACTTCTTGAAATGAGATCAACTCTGATCATCAAAAA
829 AACTTCATGG
Statistics
Matches: 269, Mismatches: 28, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
173 1 0.00
174 125 0.46
175 34 0.13
176 31 0.12
177 45 0.17
178 32 0.12
179 1 0.00
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (176 bp):
GATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAAACTTCTTG
AAACGAGATCAACTCTGATCATAAAAAACTTCTTGAAATGAGATCAACTCTGATCATCAAAAACT
TCTTGAAATGAGATCAACTCTGATCAACAAAAACTTCTTGAAACGA
Found at i:711 original size:209 final size:211
Alignment explanation
Indices: 348--828 Score: 664
Period size: 209 Copynumber: 2.3 Consensus size: 211
338 ATCTTTTGGG
* ** * *
348 GATCAACTCTGACCATTGAAAACTTCTTGGAATGAGATCAACTCTGATCATAAAAAAAACTTCTT
1 GATCAACTCTGATCATAAAAAACTTCTTGAAACGAGATCAACTCTGATCAT--AAAAAACTTCTT
*
413 GAAATGAGATCAACTCTGATCATAAAAAACTTCTTGAAATGAGATCAACTCTGATCATCAAAAAC
64 GAAATGAGATCAACTCTGATCATAAAAAACTTCTTGAAATGAGATCAACTCTGATCAACAAAAAC
* *
478 TTCTTGAAATGAGATCAACTCTGAT-AATCAAAAACTTCTTGAAACGAGATCAACTCTGATCAT-
129 TTCTTGAAAGGAGATCAACTCTGATCAA-CAAAAACTTCTTGAAACGAGATAAACTCTGATCATA
* *
541 CAAAAACTTATTGAAAGGA
193 AAAAAACTTATTGAAACGA
* * **
560 GATCAACTCTGATCATAAAAAACTTCTTGAAACAAGACCAACTCTGATCAT-CGAAACTTCTT-A
1 GATCAACTCTGATCATAAAAAACTTCTTGAAACGAGATCAACTCTGATCATAAAAAACTTCTTGA
** *
623 GAATGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGAGATCAACTCTGATCAACGAAAACT
66 -AATGAGATCAACTCTGATCATAAAAAACTTCTTGAAATGAGATCAACTCTGATCAACAAAAACT
* *
688 TCTTGAAAGGAGATCAACTCTGATCAACGAAAACTTCTTGAAAGGAGATAAACTCTGATCATAAA
130 TCTTGAAAGGAGATCAACTCTGATCAACAAAAACTTCTTGAAACGAGATAAACTCTGATCAT-AA
* *
753 AAAAACTTCTTTAAACGA
194 AAAAACTTATTGAAACGA
* * *
771 GATCAACTCTGATAATAAAAAAACTTCTTGAAAGGAGATCAACTTTGATCATAAAAAA
1 GATCAACTCTGATCAT-AAAAAACTTCTTGAAACGAGATCAACTCTGATCATAAAAAA
829 AACTTCATGG
Statistics
Matches: 235, Mismatches: 28, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
208 1 0.00
209 124 0.53
210 2 0.01
211 30 0.13
212 75 0.32
213 3 0.01
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (211 bp):
GATCAACTCTGATCATAAAAAACTTCTTGAAACGAGATCAACTCTGATCATAAAAAACTTCTTGA
AATGAGATCAACTCTGATCATAAAAAACTTCTTGAAATGAGATCAACTCTGATCAACAAAAACTT
CTTGAAAGGAGATCAACTCTGATCAACAAAAACTTCTTGAAACGAGATAAACTCTGATCATAAAA
AAACTTATTGAAACGA
Found at i:1049 original size:54 final size:54
Alignment explanation
Indices: 827--1158 Score: 375
Period size: 54 Copynumber: 6.2 Consensus size: 54
817 GATCATAAAA
* * * *
827 AAAACTTCATGGAATGACCGCACCGGTTCATCTGGGGATCAACTCCGATCACTG
1 AAAACTTCTTGGAATGACCGCACTGGATCATCTGGGGATCAACTCTGATCACTG
* * * *
881 AAAACTTCTTTTGAATGATCGCACTGGATCATCTAGGGATCAACTCTGATCTCT-
1 AAAACTTC-TTGGAATGACCGCACTGGATCATCTGGGGATCAACTCTGATCACTG
* * * ** * *
935 AAAACTTATAGGAATGACCGTACTGGGCCATCT-GGAATCAATTCTGATCAAC-G
1 AAAACTTCTTGGAATGACCGCACTGGATCATCTGGGGATCAACTCTGATC-ACTG
988 AAAACTTCTTGGAATGACCGCACTGGATCATCTGGGGATCAACTCTGATCACTG
1 AAAACTTCTTGGAATGACCGCACTGGATCATCTGGGGATCAACTCTGATCACTG
* * * * * *
1042 AAAACTTCTTGAAATGATCGCACTAGATCATTTGGGGATCAACTCTAATCATTCG
1 AAAACTTCTTGGAATGACCGCACTGGATCATCTGGGGATCAACTCTGATCACT-G
* * * * *
1097 -AAACTTCTTGGAATGATCTCACTGGACCATCTGGGGATCAACTCTGATCTCTA
1 AAAACTTCTTGGAATGACCGCACTGGATCATCTGGGGATCAACTCTGATCACTG
1150 AAAACTTCT
1 AAAACTTCT
1159 ATGAAAGACA
Statistics
Matches: 231, Mismatches: 40, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
52 14 0.06
53 50 0.22
54 129 0.56
55 38 0.16
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (54 bp):
AAAACTTCTTGGAATGACCGCACTGGATCATCTGGGGATCAACTCTGATCACTG
Found at i:1112 original size:161 final size:161
Alignment explanation
Indices: 827--1145 Score: 430
Period size: 161 Copynumber: 2.0 Consensus size: 161
817 GATCATAAAA
*
827 AAAACTTCATGGAATGACCGCACCGGTTCATCTGGGGATCAACTCCGATCACTGAAAACTTCTTT
1 AAAACTTCATGGAATGACCGCACCGGATCATCTGGGGATCAACTCCGATCACTGAAAACTTC-TT
* *
892 TGAATGATCGCACTGGATCATCTAGGGATCAACTCTGATCTCTAAAACTTATAGGAATGACCGT-
65 TGAATGATCGCACTAGATCATCTAGGGATCAACTCTAATCTCTAAAACTTATAGGAATGACC-TC
* *
956 ACTGGGCCATCT-GGAATCAATTCTGATCAACG
129 ACTGGACCATCTGGGAATCAACTCTGATCAACG
* * *
988 AAAACTTCTTGGAATGACCGCACTGGATCATCTGGGGATCAACTCTGATCACTGAAAACTTC-TT
1 AAAACTTCATGGAATGACCGCACCGGATCATCTGGGGATCAACTCCGATCACTGAAAACTTCTTT
* * * * * *
1052 GAAATGATCGCACTAGATCATTTGGGGATCAACTCTAATCAT-TCGAAACTTCTTGGAATGATCT
66 G-AATGATCGCACTAGATCATCTAGGGATCAACTCTAATC-TCT-AAAACTTATAGGAATGACCT
*
1116 CACTGGACCATCTGGGGATCAACTCTGATC
128 CACTGGACCATCTGGGAATCAACTCTGATC
1146 TCTAAAAACT
Statistics
Matches: 138, Mismatches: 15, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
159 3 0.02
160 36 0.26
161 85 0.62
162 14 0.10
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (161 bp):
AAAACTTCATGGAATGACCGCACCGGATCATCTGGGGATCAACTCCGATCACTGAAAACTTCTTT
GAATGATCGCACTAGATCATCTAGGGATCAACTCTAATCTCTAAAACTTATAGGAATGACCTCAC
TGGACCATCTGGGAATCAACTCTGATCAACG
Done.