Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011975.1 Corchorus olitorius cultivar O-4 contig12008, 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: 35420
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:11417 original size:21 final size:22
Alignment explanation
Indices: 11380--11421 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
11370 TTTTCAGTTG
*
11380 AAGCAAGAGAGGAAGTCGACTT
1 AAGCAAGAGAAGAAGTCGACTT
11402 AAGCAAG-GAAGAAGTCGACT
1 AAGCAAGAGAAGAAGTCGACT
11422 AAATTTTGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.43, C:0.14, G:0.31, T:0.12
Consensus pattern (22 bp):
AAGCAAGAGAAGAAGTCGACTT
Found at i:12767 original size:49 final size:49
Alignment explanation
Indices: 12710--12803 Score: 179
Period size: 49 Copynumber: 1.9 Consensus size: 49
12700 GGGGTGAATA
*
12710 CTTGATAGGTTTATTGTTTGAATAATTGAGTCATATGCTAGTTATGTTC
1 CTTGATAGGTTTATTGCTTGAATAATTGAGTCATATGCTAGTTATGTTC
12759 CTTGATAGGTTTATTGCTTGAATAATTGAGTCATATGCTAGTTAT
1 CTTGATAGGTTTATTGCTTGAATAATTGAGTCATATGCTAGTTAT
12804 TGTTTGCATG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.26, C:0.09, G:0.20, T:0.46
Consensus pattern (49 bp):
CTTGATAGGTTTATTGCTTGAATAATTGAGTCATATGCTAGTTATGTTC
Found at i:17734 original size:21 final size:21
Alignment explanation
Indices: 17686--17735 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
17676 GCTCATTGAA
* *
17686 TTCAAATTAGGGTTCTTGAGT
1 TTCAAATTAGGGTTCTAGAGC
17707 TTCAAATTAGGGTTCTAAGAGC
1 TTCAAATTAGGGTTCT-AGAGC
17729 TT-AAATT
1 TTCAAATT
17736 GGGCATTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 21 0.81
22 5 0.19
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (21 bp):
TTCAAATTAGGGTTCTAGAGC
Found at i:23636 original size:22 final size:22
Alignment explanation
Indices: 23588--23640 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
23578 TTCGTTCGAA
*
23588 GTTATCAAAATTTCATAGGAAT
1 GTTATCAAAACTTCATAGGAAT
* *
23610 ATTATCAAAACTTCATA-GTAT
1 GTTATCAAAACTTCATAGGAAT
23631 GGTTATCAAA
1 -GTTATCAAA
23641 CTTTCACAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 3 0.12
22 23 0.88
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (22 bp):
GTTATCAAAACTTCATAGGAAT
Found at i:23646 original size:22 final size:22
Alignment explanation
Indices: 23588--23646 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
23578 TTCGTTCGAA
*
23588 GTTATCAAAATTTCATAGGAAT
1 GTTATCAAACTTTCATAGGAAT
* *
23610 ATTATCAAAAC-TTCATA-GTAT
1 GTTATC-AAACTTTCATAGGAAT
23631 GGTTATCAAACTTTCA
1 -GTTATCAAACTTTCA
23647 CAAGGAATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
21 7 0.23
22 20 0.67
23 3 0.10
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (22 bp):
GTTATCAAACTTTCATAGGAAT
Found at i:23709 original size:22 final size:22
Alignment explanation
Indices: 23663--23710 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
23653 ATTATCAAAG
* * **
23663 AGGTTATCAAAATTTTATAGCA
1 AGGTTATAAAAATTTCATAAAA
23685 AGGTTATAAAAATTTCATAAAA
1 AGGTTATAAAAATTTCATAAAA
23707 AGGT
1 AGGT
23711 AAATTTCATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.46, C:0.06, G:0.15, T:0.33
Consensus pattern (22 bp):
AGGTTATAAAAATTTCATAAAA
Found at i:26063 original size:178 final size:179
Alignment explanation
Indices: 25740--26077 Score: 452
Period size: 178 Copynumber: 1.9 Consensus size: 179
25730 TAAGCACAAA
* * * * **
25740 TTATGTAATATTAAGTAAGACTGTCTATTTCCTTTAACTGAAACAATTAATTCTTTGAAAGCAAT
1 TTATATAATATTAAGTAAGACTGTCTATTCCCGTTAACCGAAACAACAAATTCTTTGAAAGCAAT
25805 TTTTATACCTCGAACATTAAATTTAGTTTTCGAGCCCTTCATGAAAGTTGTAAATCATGGAACAA
66 TTTTATACCTCGAACATTAAATTTAGTTTTCGAGCCCTTCATGAAAGTTGTAAATCATGGAACAA
* *
25870 CCTTTCAAGAGACACTTGAATCATCTCAATTAGACATCTGGAGGTAAAG
131 CCTTTCAAGAGACACTTAAATCACCTCAATTAGACATCTGGAGGTAAAG
* *
25919 TTATATAATATTAAGT-GGA-TCGTCTATTCCCGTTAACCGAAACAACAAATT-TTTCGGAAGC-
1 TTATATAATATTAAGTAAGACT-GTCTATTCCCGTTAACCGAAACAACAAATTCTTT-GAAAGCA
* * * *
25980 ATTTTTGATA-CTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATGATGGA
64 ATTTTT-ATACCTCG-AACATTAAATTTAGTTTTCGAGCCCTTCATGAAAGTTGTAAATCATGGA
* * *
26044 ACAATCTTTTAATAGACACTTAAATCACCTCAAT
127 ACAACCTTTCAAGAGACACTTAAATCACCTCAAT
26078 CGGATAACCG
Statistics
Matches: 138, Mismatches: 17, Indels: 9
0.84 0.10 0.05
Matches are distributed among these distances:
177 13 0.09
178 110 0.80
179 15 0.11
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (179 bp):
TTATATAATATTAAGTAAGACTGTCTATTCCCGTTAACCGAAACAACAAATTCTTTGAAAGCAAT
TTTTATACCTCGAACATTAAATTTAGTTTTCGAGCCCTTCATGAAAGTTGTAAATCATGGAACAA
CCTTTCAAGAGACACTTAAATCACCTCAATTAGACATCTGGAGGTAAAG
Found at i:26103 original size:178 final size:178
Alignment explanation
Indices: 25737--26119 Score: 441
Period size: 178 Copynumber: 2.1 Consensus size: 178
25727 CCATAAGCAC
* * * * **
25737 AAATTATGTAATATTAAGTAAGA-CTGTCTATTTCCTTTAACTGAAACAATTAATTCTTTGAAAG
1 AAATTATATAATATTAAGT-AGATC-GTCTATTCCCGTTAACCGAAACAACAAATTCTTTGAAAG
25801 CAATTTTTATACCTCGAACATTAAATTTAGTTTTCGAGCCCTTCATGAAAGTTGTAAATCATGGA
64 CAATTTTTATACCTCGAACATTAAATTTAGTTTTCGAGCCCTTCATGAAAGTTGTAAATCATGGA
* * * * * ***
25866 ACAACCTTTCAAGAGACACTTGAATCATCTCAATTAGACATCTGGAGGTA
129 ACAACCTTTCAAGAGACACTTAAATCACCTCAATCAGACAACCGGAAAAA
* * *
25916 AAGTTATATAATATTAAGTGGATCGTCTATTCCCGTTAACCGAAACAACAAATT-TTTCGGAAGC
1 AAATTATATAATATTAAGTAGATCGTCTATTCCCGTTAACCGAAACAACAAATTCTTT-GAAAGC
* * * *
25980 -ATTTTTGATA-CTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATGATGG
65 AATTTTT-ATACCTCG-AACATTAAATTTAGTTTTCGAGCCCTTCATGAAAGTTGTAAATCATGG
* * * * *
26043 AACAATCTTTTAATAGACACTTAAATCACCTCAATCGGATAACCGGAAAAA
128 AACAACCTTTCAAGAGACACTTAAATCACCTCAATCAGACAACCGGAAAAA
* *
26094 AAATTATATAATGTTAAATAGATCGT
1 AAATTATATAATATTAAGTAGATCGT
26120 TTAGCCAAAC
Statistics
Matches: 170, Mismatches: 30, Indels: 9
0.81 0.14 0.04
Matches are distributed among these distances:
177 12 0.07
178 140 0.82
179 18 0.11
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (178 bp):
AAATTATATAATATTAAGTAGATCGTCTATTCCCGTTAACCGAAACAACAAATTCTTTGAAAGCA
ATTTTTATACCTCGAACATTAAATTTAGTTTTCGAGCCCTTCATGAAAGTTGTAAATCATGGAAC
AACCTTTCAAGAGACACTTAAATCACCTCAATCAGACAACCGGAAAAA
Found at i:28666 original size:2 final size:2
Alignment explanation
Indices: 28654--28688 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
28644 TAATTATAAC
*
28654 TA TA T- TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28689 GATAGATAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:29250 original size:16 final size:16
Alignment explanation
Indices: 29231--29261 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
29221 AGTTAGTGGG
29231 GGAGAGAGAAGAAGGC
1 GGAGAGAGAAGAAGGC
29247 GGAGAGAGAAGAAGG
1 GGAGAGAGAAGAAGG
29262 GAAACTTGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.52, T:0.00
Consensus pattern (16 bp):
GGAGAGAGAAGAAGGC
Found at i:30414 original size:29 final size:29
Alignment explanation
Indices: 30381--30439 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
30371 CTAATCTAGC
30381 AAAGATCGCATTGCCTTTACTAAACCAGA
1 AAAGATCGCATTGCCTTTACTAAACCAGA
30410 AAAGATCGCATTGCCTTTACTAAACCAGA
1 AAAGATCGCATTGCCTTTACTAAACCAGA
30439 A
1 A
30440 TTCGGCAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.39, C:0.24, G:0.14, T:0.24
Consensus pattern (29 bp):
AAAGATCGCATTGCCTTTACTAAACCAGA
Found at i:31456 original size:20 final size:20
Alignment explanation
Indices: 31431--31469 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
31421 CCTTATGCCT
31431 TGAGTGCTCCTTTAAGGTCG
1 TGAGTGCTCCTTTAAGGTCG
31451 TGAGTGCTCCTTTAAGGTC
1 TGAGTGCTCCTTTAAGGTC
31470 TTAAATGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.21, G:0.28, T:0.36
Consensus pattern (20 bp):
TGAGTGCTCCTTTAAGGTCG
Found at i:33179 original size:75 final size:75
Alignment explanation
Indices: 33046--33208 Score: 164
Period size: 75 Copynumber: 2.2 Consensus size: 75
33036 ATGATAATTT
* * * * * * ** **
33046 GCAACATCTTGAAGCTGATTCACTTTATCAGGTTTCTGATTCGAATTCAAATTTTGAGCATCGTA
1 GCAACATCTTGAAGCTGATCCACGTAATCAGGATGCTGATTCAAATTCAAATACTGAGCATCCCA
*
33111 ACGATGATAG
66 ACGACGATAG
* * * * *
33121 GCAACATCTTGAAGTTGATCCTCGTAATCAGGATGCTGTTTCAAATTCTAATACTGAGCTTCCCA
1 GCAACATCTTGAAGCTGATCCACGTAATCAGGATGCTGATTCAAATTCAAATACTGAGCATCCCA
*
33186 ATGACGATAG
66 ACGACGATAG
*
33196 GCAACATTTTGAA
1 GCAACATCTTGAA
33209 AATGTTATTG
Statistics
Matches: 70, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
75 70 1.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (75 bp):
GCAACATCTTGAAGCTGATCCACGTAATCAGGATGCTGATTCAAATTCAAATACTGAGCATCCCA
ACGACGATAG
Done.