Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021811.1 Corchorus olitorius cultivar O-4 contig21844, 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: 74890
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:590 original size:21 final size:21
Alignment explanation
Indices: 566--636 Score: 142
Period size: 21 Copynumber: 3.4 Consensus size: 21
556 AACCTGGAGC
566 GGGTCGAACTCGACCTTCTCA
1 GGGTCGAACTCGACCTTCTCA
587 GGGTCGAACTCGACCTTCTCA
1 GGGTCGAACTCGACCTTCTCA
608 GGGTCGAACTCGACCTTCTCA
1 GGGTCGAACTCGACCTTCTCA
629 GGGTCGAA
1 GGGTCGAA
637 ACAGGCTACT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.20, C:0.31, G:0.27, T:0.23
Consensus pattern (21 bp):
GGGTCGAACTCGACCTTCTCA
Found at i:8491 original size:50 final size:50
Alignment explanation
Indices: 8416--8516 Score: 184
Period size: 50 Copynumber: 2.0 Consensus size: 50
8406 GACATGTGTC
* *
8416 CCCTATGGATTAGATTGAAATATTTAAAATTTAATTAATTTAAAAATGAA
1 CCCTAGGGACTAGATTGAAATATTTAAAATTTAATTAATTTAAAAATGAA
8466 CCCTAGGGACTAGATTGAAATATTTAAAATTTAATTAATTTAAAAATGAA
1 CCCTAGGGACTAGATTGAAATATTTAAAATTTAATTAATTTAAAAATGAA
8516 C
1 C
8517 ATGTGTCAAC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.46, C:0.08, G:0.11, T:0.36
Consensus pattern (50 bp):
CCCTAGGGACTAGATTGAAATATTTAAAATTTAATTAATTTAAAAATGAA
Found at i:8877 original size:24 final size:25
Alignment explanation
Indices: 8840--8887 Score: 80
Period size: 24 Copynumber: 1.9 Consensus size: 25
8830 ACAGCTAATT
8840 TCTCTTGCTATTTTTCCTGCGAAAGC
1 TCTCTTGC-ATTTTTCCTGCGAAAGC
8866 TCTCTTGC-TTTTTCCTGCGAAA
1 TCTCTTGCATTTTTCCTGCGAAA
8888 ACACCATCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 14 0.64
26 8 0.36
ACGTcount: A:0.15, C:0.27, G:0.15, T:0.44
Consensus pattern (25 bp):
TCTCTTGCATTTTTCCTGCGAAAGC
Found at i:12542 original size:21 final size:19
Alignment explanation
Indices: 12508--12548 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
12498 TTCTGTTTCA
12508 GTATTGGGGTTTGTATTTT
1 GTATTGGGGTTTGTATTTT
*
12527 GTATATGGGGCTTTGTGTTTT
1 GTAT-TGGGG-TTTGTATTTT
12548 G
1 G
12549 CACCAAAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 5 0.26
21 10 0.53
ACGTcount: A:0.10, C:0.02, G:0.34, T:0.54
Consensus pattern (19 bp):
GTATTGGGGTTTGTATTTT
Found at i:23695 original size:7 final size:7
Alignment explanation
Indices: 23683--23713 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
23673 TTTACTTAAG
23683 CTCTCAA
1 CTCTCAA
23690 CTCTCAA
1 CTCTCAA
23697 CTCTCAA
1 CTCTCAA
23704 CTCTCAA
1 CTCTCAA
23711 CTC
1 CTC
23714 ATCATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.45, G:0.00, T:0.29
Consensus pattern (7 bp):
CTCTCAA
Found at i:29016 original size:2 final size:2
Alignment explanation
Indices: 29009--29033 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28999 GATGGGGGAG
29009 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
29034 CATTTAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:29793 original size:29 final size:30
Alignment explanation
Indices: 29743--29820 Score: 72
Period size: 32 Copynumber: 2.6 Consensus size: 30
29733 CCTGATTTTG
* *
29743 CAAA-TTCAAGGGGCAAAGTGG-CACAATTT
1 CAAAGTTCAGGGGGCAAACTGGCCA-AATTT
*
29772 -AAAGTTCAGGGGGCAATCTGGCCTAAATTT
1 CAAAGTTCAGGGGGCAAACTGGCC-AAATTT
*
29802 GCAAAGTTCAGGGGACAAA
1 -CAAAGTTCAGGGGGCAAA
29821 TGGGCTATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
28 3 0.08
29 14 0.36
30 6 0.15
31 1 0.03
32 15 0.38
ACGTcount: A:0.36, C:0.17, G:0.27, T:0.21
Consensus pattern (30 bp):
CAAAGTTCAGGGGGCAAACTGGCCAAATTT
Found at i:30820 original size:39 final size:39
Alignment explanation
Indices: 30766--30844 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
30756 TTAAGAGTTG
* * *
30766 ATGAGTTCTTTCTACTCTATTCAACAAGTATTGGTAGAA
1 ATGAGTTCATTCTACTCTATTCAACAAGCATTGATAGAA
30805 ATGAGTTCATTCTACTCTATTCAACAAGCATTGATAGAA
1 ATGAGTTCATTCTACTCTATTCAACAAGCATTGATAGAA
30844 A
1 A
30845 AACACAAAGC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.35
Consensus pattern (39 bp):
ATGAGTTCATTCTACTCTATTCAACAAGCATTGATAGAA
Found at i:36170 original size:39 final size:40
Alignment explanation
Indices: 36114--36194 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
36104 TTTAATTCCT
36114 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
36154 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
36193 AT
1 AT
36195 TCTTAGGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:36221 original size:25 final size:24
Alignment explanation
Indices: 36185--36231 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
36175 AATACTTACA
*
36185 TTAATTAAATTCTTAGGTATTTTT
1 TTAATTAAATTCTTAGGCATTTTT
36209 TTAATTCAAATTCTTAGGCATTT
1 TTAATT-AAATTCTTAGGCATTT
36232 GTGCAAACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.53
Consensus pattern (24 bp):
TTAATTAAATTCTTAGGCATTTTT
Found at i:37081 original size:36 final size:36
Alignment explanation
Indices: 37034--37103 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
37024 GAGATTTTGG
* *
37034 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
37070 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
37104 GGTTATTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Found at i:48147 original size:2 final size:2
Alignment explanation
Indices: 48140--48164 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
48130 CAAGCAAGTA
48140 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
48165 CCAAGTACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:52283 original size:4 final size:4
Alignment explanation
Indices: 52274--52307 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
52264 TTTGGCCAAA
52274 ATTT ATTT ATTT ATTT ATTT A-TT ATTT ATTT ATT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATT
52308 ATTAATAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:52300 original size:11 final size:11
Alignment explanation
Indices: 52274--52310 Score: 65
Period size: 11 Copynumber: 3.3 Consensus size: 11
52264 TTTGGCCAAA
52274 ATTTATTTATTT
1 ATTTATTTA-TT
52286 ATTTATTTATT
1 ATTTATTTATT
52297 ATTTATTTATT
1 ATTTATTTATT
52308 ATT
1 ATT
52311 AATAAGTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
ATTTATTTATT
Found at i:66954 original size:9 final size:9
Alignment explanation
Indices: 66942--66977 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
66932 CATATTTCAT
66942 TCATCAATA
1 TCATCAATA
66951 TCATCAATCA
1 TCATCAAT-A
*
66961 CCATCAATA
1 TCATCAATA
66970 TCATCAAT
1 TCATCAAT
66978 CATTTACTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.31
Consensus pattern (9 bp):
TCATCAATA
Found at i:66967 original size:19 final size:19
Alignment explanation
Indices: 66943--66979 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
66933 ATATTTCATT
66943 CATCAATATCATCAATCAC
1 CATCAATATCATCAATCAC
66962 CATCAATATCATCAATCA
1 CATCAATATCATCAATCA
66980 TTTACTTAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.30, G:0.00, T:0.27
Consensus pattern (19 bp):
CATCAATATCATCAATCAC
Found at i:67008 original size:20 final size:20
Alignment explanation
Indices: 66972--67012 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
66962 CATCAATATC
*
66972 ATCAATCATTTACTTAGCAA
1 ATCAATCATATACTTAGCAA
66992 ATCAATCATCATA-TTAGCAA
1 ATCAATCAT-ATACTTAGCAA
67012 A
1 A
67013 AAATGAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.44, C:0.20, G:0.05, T:0.32
Consensus pattern (20 bp):
ATCAATCATATACTTAGCAA
Found at i:67786 original size:11 final size:11
Alignment explanation
Indices: 67770--67794 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
67760 ATAAATAACT
67770 TATTATATATA
1 TATTATATATA
67781 TATTATATATA
1 TATTATATATA
67792 TAT
1 TAT
67795 ATCTGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTATATATA
Found at i:74006 original size:25 final size:25
Alignment explanation
Indices: 73875--73999 Score: 214
Period size: 25 Copynumber: 5.0 Consensus size: 25
73865 TGTGTTTTCC
73875 AAACGCAAGCACAGGCTCGTTTGCT
1 AAACGCAAGCACAGGCTCGTTTGCT
*
73900 AAACGCAAGCACAGGCTCGTTTACT
1 AAACGCAAGCACAGGCTCGTTTGCT
* *
73925 AAACGCAAACACAGGTTCGTTTGCT
1 AAACGCAAGCACAGGCTCGTTTGCT
*
73950 AAACGCAAACACAGGCTCGTTTGCT
1 AAACGCAAGCACAGGCTCGTTTGCT
73975 AAACGCAAGCACAGGCTCGTTTGCT
1 AAACGCAAGCACAGGCTCGTTTGCT
74000 CAGCGCACAC
Statistics
Matches: 94, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 94 1.00
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.21
Consensus pattern (25 bp):
AAACGCAAGCACAGGCTCGTTTGCT
Done.