Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013046.1 Corchorus olitorius cultivar O-4 contig13079, 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: 4336
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Found at i:382 original size:21 final size:21
Alignment explanation
Indices: 356--397 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
346 AAAATTCTAA
356 ACAACTCCTGCCCAGGACTTG
1 ACAACTCCTGCCCAGGACTTG
377 ACAACTCCTGCCCAGGACTTG
1 ACAACTCCTGCCCAGGACTTG
398 GTCTGTTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.38, G:0.19, T:0.19
Consensus pattern (21 bp):
ACAACTCCTGCCCAGGACTTG
Found at i:421 original size:71 final size:72
Alignment explanation
Indices: 304--469 Score: 246
Period size: 71 Copynumber: 2.3 Consensus size: 72
294 CCTAAAAACA
* * * *
304 GGACAAGTCCTGCCCAGGACCTGGTCTGTTGAAAGACGGAAGAAAATTCTA-AACAACTCCTGCC
1 GGACAACTCCTGCCCAGGACTTGGTCTGTTGAAAAACGAAAGAAAATTC-AGAACAACTCCTGCC
368 CAGGACTT
65 CAGGACTT
* *
376 -GACAACTCCTGCCCAGGACTTGGTCTGTTGAAAAACGAAAGAAAATTCAGAACAAGTCCTGTCC
1 GGACAACTCCTGCCCAGGACTTGGTCTGTTGAAAAACGAAAGAAAATTCAGAACAACTCCTGCCC
440 AGGACTT
66 AGGACTT
*
447 GGACAACTCCTGCCCTGGACTTG
1 GGACAACTCCTGCCCAGGACTTG
470 TTGCGGAAAA
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
70 1 0.01
71 63 0.74
72 21 0.25
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.20
Consensus pattern (72 bp):
GGACAACTCCTGCCCAGGACTTGGTCTGTTGAAAAACGAAAGAAAATTCAGAACAACTCCTGCCC
AGGACTT
Found at i:457 original size:22 final size:22
Alignment explanation
Indices: 427--469 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
417 AAAATTCAGA
* *
427 ACAAGTCCTGTCCAGGACTTGG
1 ACAACTCCTGCCCAGGACTTGG
*
449 ACAACTCCTGCCCTGGACTTG
1 ACAACTCCTGCCCAGGACTTG
470 TTGCGGAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.33, G:0.23, T:0.23
Consensus pattern (22 bp):
ACAACTCCTGCCCAGGACTTGG
Found at i:1050 original size:21 final size:21
Alignment explanation
Indices: 1028--1161 Score: 175
Period size: 21 Copynumber: 6.4 Consensus size: 21
1018 TGCTAGAAGT
*
1028 TCATTGGAGCAA-GTTCCAAGT
1 TCATTGGAG-AAGGTTCCAAGC
*
1049 TCATTGGA-ACAAGTTCCAAGC
1 TCATTGGAGA-AGGTTCCAAGC
1070 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
*
1091 TCATTGGAGAAGGTTCCAAGT
1 TCATTGGAGAAGGTTCCAAGC
*
1112 TCATTGGAGAAGGTTCCAAGA
1 TCATTGGAGAAGGTTCCAAGC
*
1133 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
1154 TCATTGGA
1 TCATTGGA
1162 ATTGCCTAAG
Statistics
Matches: 103, Mismatches: 5, Indels: 10
0.87 0.04 0.08
Matches are distributed among these distances:
19 1 0.01
20 3 0.03
21 97 0.94
22 1 0.01
23 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:1109 original size:63 final size:63
Alignment explanation
Indices: 1028--1161 Score: 193
Period size: 63 Copynumber: 2.1 Consensus size: 63
1018 TGCTAGAAGT
*
1028 TCATTGGAGCAAGTTCCAAGTTCATTGGA-ACAAGTTCCAAGCTCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGTTCATTGGAGA-AAGTTCCAAGATCATTGGAG-AAGGTTCCAAGC
* *
1091 TCATTGGAG-AAGGTTCCAAGTTCATTGGAGAAGGTTCCAAGATCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGCAA-GTTCCAAGTTCATTGGAGAAAGTTCCAAGATCATTGGAGAAGGTTCCAAGC
1154 TCATTGGA
1 TCATTGGA
1162 ATTGCCTAAG
Statistics
Matches: 65, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
62 4 0.06
63 60 0.92
64 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (63 bp):
TCATTGGAGCAAGTTCCAAGTTCATTGGAGAAAGTTCCAAGATCATTGGAGAAGGTTCCAAGC
Found at i:2056 original size:25 final size:24
Alignment explanation
Indices: 2020--2066 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
2010 TCCTTCTATT
2020 CATCTATCATC-AAGTTTTTCATC
1 CATCTATCATCAAAGTTTTTCATC
2043 CATCTCATCCATCAAAGTTTTTCA
1 CATCT-AT-CATCAAAGTTTTTCA
2067 AATTTTCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 4 0.19
26 10 0.48
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (24 bp):
CATCTATCATCAAAGTTTTTCATC
Found at i:3415 original size:21 final size:21
Alignment explanation
Indices: 3389--3430 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3379 GCATCTTAGG
3389 CAACTCCGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
*
3410 CAACTCTGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
3431 TTCTTCCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (21 bp):
CAACTCCGATGAGCTTGAAAC
Done.