Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014346.1 Corchorus olitorius cultivar O-4 contig14379, 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: 37220
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:1890 original size:16 final size:16
Alignment explanation
Indices: 1869--1922 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
1859 TTAAGTTAGC
1869 TAACTTATGAAACAAT
1 TAACTTATGAAACAAT
*
1885 TAACTTATGAAAACAGCCT
1 TAACTTATG-AAACA--AT
*
1904 TAACTTATGAAACCAT
1 TAACTTATGAAACAAT
1920 TAA
1 TAA
1923 TATGTTAGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
16 13 0.41
17 5 0.16
18 4 0.12
19 10 0.31
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.30
Consensus pattern (16 bp):
TAACTTATGAAACAAT
Found at i:3164 original size:15 final size:15
Alignment explanation
Indices: 3146--3190 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
3136 CATCATTCCT
3146 ATCCTCTACATTGAC
1 ATCCTCTACATTGAC
*
3161 ATCCTCTACATTAAC
1 ATCCTCTACATTGAC
*
3176 ATCCTCTAGATTGAC
1 ATCCTCTACATTGAC
3191 TGCATCATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.29, C:0.31, G:0.07, T:0.33
Consensus pattern (15 bp):
ATCCTCTACATTGAC
Found at i:11627 original size:231 final size:231
Alignment explanation
Indices: 11212--11656 Score: 634
Period size: 231 Copynumber: 1.9 Consensus size: 231
11202 CCCGGCTTAA
* * * *
11212 TTTTGTATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAATCTCAGGCT
1 TTTTGCATGATTTTTGACAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAA---CA-GAT
*
11277 CTCAGCCACATTAGATTTAAGGATTTTTTTTACGAGTATCTGAATATTGTTTCGATTTAATTAGA
62 CCCAGCCACATTAGATTTAAGGATTTTTTTTACGAGTATCTGAATATTGTTTCGATTTAATTAGA
* *
11342 AATAGATTCGGAAAAAAAAATATAAAAATGATATTTAAAGCGAGAAAATATTTCAATTTTTTTTT
127 AATAGATTCGGAAAAAAAAATAGAAAAATGATATTTAAAGCAAGAAAATATTTC-A-TTTTTTTT
11407 G-AGTTGAATTGTGTATTTTTTGCCGAAAATATTTTTGTTTGT
190 GCA-TTGAATTGTGTATTTTTTGCCGAAAATATTTTTGTTTGT
*
11449 TTTTGCATGATTTTTGAC-GTAAATACTCCTTGAAATATCTATATTCATCGAA-CAA-A-ATCCC
1 TTTTGCATGATTTTTGACAG-AAAGACTCCTTGAAATATCTATATTCATCGAACCAACAGATCCC
* * * *
11510 AGCCACGTTCGATTTAAGTATTTGTTTTTACGA-TCATCTGAATCTTGTTTCGATTTAATTAGAA
65 AGCCACATTAGATTTAAGGATTT-TTTTTACGAGT-ATCTGAATATTGTTTCGATTTAATTAGAA
11574 ATAGATTCGG-AAAAAAAATAGAAAAATGATATTTAAAGCAAGAAAAATATTTCATTTTTTTTGC
128 ATAGATTCGGAAAAAAAAATAGAAAAATGATATTTAAAGCAAG-AAAATATTTCATTTTTTTTGC
11638 ATTGAATTGTGTATTTTTT
192 ATTGAATTGTGTATTTTTT
11657 CTGACTATCG
Statistics
Matches: 191, Mismatches: 12, Indels: 18
0.86 0.05 0.08
Matches are distributed among these distances:
229 27 0.14
230 56 0.29
231 57 0.30
232 1 0.01
236 4 0.02
237 46 0.24
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (231 bp):
TTTTGCATGATTTTTGACAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAACAGATCCCA
GCCACATTAGATTTAAGGATTTTTTTTACGAGTATCTGAATATTGTTTCGATTTAATTAGAAATA
GATTCGGAAAAAAAAATAGAAAAATGATATTTAAAGCAAGAAAATATTTCATTTTTTTTGCATTG
AATTGTGTATTTTTTGCCGAAAATATTTTTGTTTGT
Found at i:15019 original size:23 final size:23
Alignment explanation
Indices: 14970--15020 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
14960 ATTGATTATC
* * *
14970 TTGGTTTTACTTTTTTTATGGTT
1 TTGGTTTTAATTGTTTTATGGTG
* *
14993 TTGGTTTTAATTGTTTTCTTGTG
1 TTGGTTTTAATTGTTTTATGGTG
15016 TTGGT
1 TTGGT
15021 GCACTTCTCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.08, C:0.04, G:0.22, T:0.67
Consensus pattern (23 bp):
TTGGTTTTAATTGTTTTATGGTG
Found at i:15198 original size:37 final size:37
Alignment explanation
Indices: 15148--15232 Score: 143
Period size: 37 Copynumber: 2.3 Consensus size: 37
15138 CCCGTTGAGG
* *
15148 AAAATGTTTTATTACTGTTTTTATTTAAATGCTTTAT
1 AAAATGTTTTATTACTGATTTTATTTAAATGCTTAAT
15185 AAAATGTTTTATTACTGATTTTATTTAAATGCTTAAT
1 AAAATGTTTTATTACTGATTTTATTTAAATGCTTAAT
*
15222 AAAATATTTTA
1 AAAATGTTTTA
15233 ATAAATTATT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.35, C:0.05, G:0.07, T:0.53
Consensus pattern (37 bp):
AAAATGTTTTATTACTGATTTTATTTAAATGCTTAAT
Found at i:19325 original size:21 final size:21
Alignment explanation
Indices: 19299--19354 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
19289 AGGGTCTAAT
*
19299 CTCATATTATCCATGGT-TGTG
1 CTCATATTATCCAT-GTCTGCG
*
19320 CTCATATTACCCATGTCTGCG
1 CTCATATTATCCATGTCTGCG
*
19341 TTCATATTATCCAT
1 CTCATATTATCCAT
19355 ATCCATGGCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 2 0.07
21 28 0.93
ACGTcount: A:0.21, C:0.25, G:0.12, T:0.41
Consensus pattern (21 bp):
CTCATATTATCCATGTCTGCG
Found at i:21173 original size:177 final size:176
Alignment explanation
Indices: 20687--21195 Score: 601
Period size: 178 Copynumber: 2.9 Consensus size: 176
20677 AGTGGTCTAT
* * * * *
20687 TTAATATTATATAATTTTCGCTCCGGATATCCGATCAAGATGATTCAAGTATCTATTAAAAGGTT
1 TTAATATTACATAATTTT-GCTCCAGATGTCCGATTAAGGTGATTCAAGTATCTATTAAAAGGTT
* * *
20752 G-TTCTATGATTTACAACTTTCATGAAGGACTCGAAAACTAAATTTAATGTTTCAAGTACAAAAA
65 GTTTC-ATGATCTACAACTTTCATGAAGGACTCGAAAGCTAAATTT-ATGTTTCAAGTACTAAAA
* * **
20816 ATGCTTTCGAAAAATTAGTTCTTTCGGTTAACAGGAATGGATGGTCCAC
128 ATGCTTCCAAAAAATTAGTTCTTTCGGTTAACAGGAATGGACCGTCCAC
** * * *
20865 TTAATATTACATAACTTTTGCTCCAGATGTCTAATTGAGGTGATTCAATTATCTCTTAAAAGGTT
1 TTAATATTACATAA-TTTTGCTCCAGATGTCCGATTAAGGTGATTCAAGTATCTATTAAAAGGTT
* * * *
20930 GTTCCATGATCTATAACTTTCATAAAGGACTCAAAAGCTAAATTTATTGTTTCAAGTA-TAAAAA
65 GTTTCATGATCTACAACTTTCATGAAGGACTCGAAAGCTAAATTTA-TGTTTCAAGTACT-AAAA
* * * *
20994 ATGGTTCCAAAAAATTAGTTGTTTCGGTT-ACTTGGAATGGACCGTTCAC
128 ATGCTTCCAAAAAATTAGTTCTTTCGGTTAAC-AGGAATGGACCGTCCAC
* * * *
21043 TTAATATTACATAATTTTGCACCAGATGTCCGATTAAGGCGATTCAAGTATCTGTTAAAAAGTTG
1 TTAATATTACATAATTTTGCTCCAGATGTCCGATTAAGGTGATTCAAGTATCTATTAAAAGGTTG
* * *
21108 TTTCGTGATCTACAACTTTCATGAAGGACTCGAAAGCTAAATTTGATATTTCAAATACTAAAAAT
66 TTTCATGATCTACAACTTTCATGAAGGACTCGAAAGCTAAATTT-ATGTTTCAAGTACTAAAAAT
** * *
21173 GCTTCTGAAAAATTTGTTATTTC
130 GCTTCCAAAAAATTAGTTCTTTC
21196 AGTGGATTGT
Statistics
Matches: 279, Mismatches: 45, Indels: 15
0.82 0.13 0.04
Matches are distributed among these distances:
177 118 0.42
178 155 0.56
179 6 0.02
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (176 bp):
TTAATATTACATAATTTTGCTCCAGATGTCCGATTAAGGTGATTCAAGTATCTATTAAAAGGTTG
TTTCATGATCTACAACTTTCATGAAGGACTCGAAAGCTAAATTTATGTTTCAAGTACTAAAAATG
CTTCCAAAAAATTAGTTCTTTCGGTTAACAGGAATGGACCGTCCAC
Found at i:21965 original size:67 final size:67
Alignment explanation
Indices: 21850--22024 Score: 244
Period size: 67 Copynumber: 2.6 Consensus size: 67
21840 ATAATGTTGA
* * *
21850 AAAATTGTTTGACTCTTTTGTAACTTTGAAC-ACTTATTCCATCTTGAATGTCTTCATGAACAAA
1 AAAATTGTTTGACTCTTTTGTAACTTTGAACAAC-TATTTCATCCTGAATGCCTTCATGAACAAA
21914 ACT
65 ACT
* * ** *
21917 AAAATTGTTTCACTCTTTTATAACTTTGAACAACTATTTCATCCTGAATGCCTTGGTGCACAAAA
1 AAAATTGTTTGACTCTTTTGTAACTTTGAACAACTATTTCATCCTGAATGCCTTCATGAACAAAA
21982 CT
66 CT
* *
21984 AAAATTATTTGACTCTTTTGTAACTTTGAACACCTATTTCA
1 AAAATTGTTTGACTCTTTTGTAACTTTGAACAACTATTTCA
22025 AATGTTAATA
Statistics
Matches: 95, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
67 93 0.98
68 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (67 bp):
AAAATTGTTTGACTCTTTTGTAACTTTGAACAACTATTTCATCCTGAATGCCTTCATGAACAAAA
CT
Done.