Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010669.1 Corchorus olitorius cultivar O-4 contig10701, 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: 3682
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Found at i:78 original size:35 final size:35
Alignment explanation
Indices: 4--324 Score: 237
Period size: 35 Copynumber: 9.1 Consensus size: 35
1 AAC
* * *
4 TGAAGAAAAGATCGCCCTGGATCGATT--A--AAG
1 TGAAGAAAAGATCACCCTGGATCAATTGAAGTAAA
* *
35 TGAAGGAAAGATCACCCTGGATCAATTGAAGGAAA
1 TGAAGAAAAGATCACCCTGGATCAATTGAAGTAAA
* *
70 TGAAGGAAAGATCGCCCTGGATCAATTGACA-TAAA
1 TGAAGAAAAGATCACCCTGGATCAATTGA-AGTAAA
105 CTGAAGAAAAGAT-AGCCCTGGATCAAATTGAAGTAAA
1 -TGAAGAAAAGATCA-CCCTGGATC-AATTGAAGTAAA
* * *
142 CTGAGGAAAAGATCGCCCTGGATCAACTGAAGTAAAA
1 -TGAAGAAAAGATCACCCTGGATCAATTGAAGT-AAA
* * *
179 TGAAGAAAAGATCGCCCTGGATCAAATGAAATAAA
1 TGAAGAAAAGATCACCCTGGATCAATTGAAGTAAA
* * * * * * *
214 CTGAA-TAAGGACCACCCTGGGTCAACTGAAATGAAT
1 -TGAAGAAAAGATCACCCTGGATCAATTGAAGT-AAA
* * * * *
250 TGAA-TAAGGATCGCCCT-GATCAAATCGAAATAAAA
1 TGAAGAAAAGATCACCCTGGATC-AATTGAAGT-AAA
* *
285 TGAAGAAAAGATCACCCTGGATCAACTGAAATAAA
1 TGAAGAAAAGATCACCCTGGATCAATTGAAGTAAA
320 CTGAA
1 -TGAA
325 TAAGGACCAC
Statistics
Matches: 240, Mismatches: 33, Indels: 29
0.79 0.11 0.10
Matches are distributed among these distances:
31 24 0.10
33 1 0.00
34 3 0.01
35 88 0.37
36 86 0.36
37 38 0.16
ACGTcount: A:0.43, C:0.17, G:0.22, T:0.18
Consensus pattern (35 bp):
TGAAGAAAAGATCACCCTGGATCAATTGAAGTAAA
Found at i:117 original size:36 final size:35
Alignment explanation
Indices: 1--324 Score: 277
Period size: 36 Copynumber: 9.2 Consensus size: 35
*
1 AACTGAAGAAAAGATCGCCCTGGATC----GATTA
1 AACTGAAGAAAAGATCGCCCTGGATCAATTGAATA
* * * *
32 AAGTGAAGGAAAGATCACCCTGGATCAATTGAAGGA
1 AACTGAAGAAAAGATCGCCCTGGATCAATTGAA-TA
*
68 AA-TGAAGGAAAGATCGCCCTGGATCAATTGACATA
1 AACTGAAGAAAAGATCGCCCTGGATCAATTGA-ATA
*
103 AACTGAAGAAAAGATAGCCCTGGATCAAATTGAAGTA
1 AACTGAAGAAAAGATCGCCCTGGATC-AATTGAA-TA
* *
140 AACTGAGGAAAAGATCGCCCTGGATCAACTGAAGTA
1 AACTGAAGAAAAGATCGCCCTGGATCAATTGAA-TA
* *
176 AAATGAAGAAAAGATCGCCCTGGATCAAATGAAATA
1 AACTGAAGAAAAGATCGCCCTGGATCAATTG-AATA
* * * * * * *
212 AACTGAA-TAAGGACCACCCTGGGTCAACTGAAATG
1 AACTGAAGAAAAGATCGCCCTGGATCAATTG-AATA
* * * *
247 AATTGAA-TAAGGATCGCCCT-GATCAAATCGAAATA
1 AACTGAAGAAAAGATCGCCCTGGATC-AATTG-AATA
* * *
282 AAATGAAGAAAAGATCACCCTGGATCAACTGAAATA
1 AACTGAAGAAAAGATCGCCCTGGATCAATTG-AATA
318 AACTGAA
1 AACTGAA
325 TAAGGACCAC
Statistics
Matches: 243, Mismatches: 37, Indels: 21
0.81 0.12 0.07
Matches are distributed among these distances:
31 23 0.09
34 3 0.01
35 84 0.35
36 95 0.39
37 38 0.16
ACGTcount: A:0.43, C:0.17, G:0.22, T:0.18
Consensus pattern (35 bp):
AACTGAAGAAAAGATCGCCCTGGATCAATTGAATA
Found at i:330 original size:71 final size:72
Alignment explanation
Indices: 30--324 Score: 310
Period size: 71 Copynumber: 4.1 Consensus size: 72
20 CTGGATCGAT
* * * * ** * *
30 TAAAGTGAAGGAAAGATCACCCTGGATCAATTG-AAGGAAATGAAGGAAAGATCGCCCTGGATCA
1 TAAACTGAAGAAAAGATCGCCCTGGATCAAATGAAATAAAATGAAGAAAAGATCACCCTGGATCA
* *
94 ATTGACA
66 ACTGAAA
* * * * *
101 TAAACTGAAGAAAAGATAGCCCTGGATCAAATTGAAGTAAACTGAGGAAAAGATCGCCCTGGATC
1 TAAACTGAAGAAAAGATCGCCCTGGATCAAA-TGAAATAAAATGAAGAAAAGATCACCCTGGATC
*
166 AACTGAAG
65 AACTGAAA
* * * * * *
174 TAAAATGAAGAAAAGATCGCCCTGGATCAAATGAAATAAACTGAA-TAAGGACCACCCTGGGTCA
1 TAAACTGAAGAAAAGATCGCCCTGGATCAAATGAAATAAAATGAAGAAAAGATCACCCTGGATCA
238 ACTGAAA
66 ACTGAAA
* * * *
245 TGAATTGAA-TAAGGATCGCCCT-GATCAAATCGAAATAAAATGAAGAAAAGATCACCCTGGATC
1 TAAACTGAAGAAAAGATCGCCCTGGATCAAAT-GAAATAAAATGAAGAAAAGATCACCCTGGATC
308 AACTGAAA
65 AACTGAAA
316 TAAACTGAA
1 TAAACTGAA
325 TAAGGACCAC
Statistics
Matches: 185, Mismatches: 35, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
69 8 0.04
70 23 0.12
71 82 0.44
72 14 0.08
73 58 0.31
ACGTcount: A:0.44, C:0.17, G:0.21, T:0.18
Consensus pattern (72 bp):
TAAACTGAAGAAAAGATCGCCCTGGATCAAATGAAATAAAATGAAGAAAAGATCACCCTGGATCA
ACTGAAA
Found at i:472 original size:21 final size:21
Alignment explanation
Indices: 446--558 Score: 133
Period size: 21 Copynumber: 5.4 Consensus size: 21
436 GGCTAGGAGT
* *
446 TCATTGCAGCAAATTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
*
467 TCATTGGAGCATGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
488 TCATTGGAG-AAGGTTCCAAGC
1 TCATTGGAGCAA-GTTCCAAGC
*
509 TCATTGGAG-AAGGTCCCAAGC
1 TCATTGGAGCAA-GTTCCAAGC
*
530 TCATTGGAG-AAGGTTTCAAGC
1 TCATTGGAGCAA-GTTCCAAGC
551 TCATTGGA
1 TCATTGGA
559 ATTGCCTAAG
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
20 1 0.01
21 83 0.99
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (21 bp):
TCATTGGAGCAAGTTCCAAGC
Found at i:493 original size:42 final size:42
Alignment explanation
Indices: 459--558 Score: 164
Period size: 42 Copynumber: 2.4 Consensus size: 42
449 TTGCAGCAAA
* * *
459 TTCCAAGCTCATTGGAGCATGTTCCAAGCTCATTGGAGAAGG
1 TTCCAAGCTCATTGGAGAAGGTCCCAAGCTCATTGGAGAAGG
501 TTCCAAGCTCATTGGAGAAGGTCCCAAGCTCATTGGAGAAGG
1 TTCCAAGCTCATTGGAGAAGGTCCCAAGCTCATTGGAGAAGG
*
543 TTTCAAGCTCATTGGA
1 TTCCAAGCTCATTGGA
559 ATTGCCTAAG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (42 bp):
TTCCAAGCTCATTGGAGAAGGTCCCAAGCTCATTGGAGAAGG
Found at i:1453 original size:25 final size:24
Alignment explanation
Indices: 1417--1463 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
1407 TCCTTCTATT
1417 CATCTATCATC-AAGTTTTTCATC
1 CATCTATCATCAAAGTTTTTCATC
1440 CATCTCATCCATCAAAGTTTTTCA
1 CATCT-AT-CATCAAAGTTTTTCA
1464 AATTTTCAAG
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:3494 original size:21 final size:21
Alignment explanation
Indices: 3470--3544 Score: 114
Period size: 21 Copynumber: 3.6 Consensus size: 21
3460 GATGTGAAAG
* *
3470 AAGCTCATTGGAGCATGTTCC
1 AAGCTCATTGGAGAAGGTTCC
*
3491 AAGCTCCTTGGAGAAGGTTCC
1 AAGCTCATTGGAGAAGGTTCC
*
3512 AAGCTCATTGGAGAAGGTTTC
1 AAGCTCATTGGAGAAGGTTCC
3533 AAGCTCATTGGA
1 AAGCTCATTGGA
3545 ATTGCCTAAG
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (21 bp):
AAGCTCATTGGAGAAGGTTCC
Done.