Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012956.1 Corchorus olitorius cultivar O-4 contig12989, 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: 31658
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:477 original size:27 final size:27
Alignment explanation
Indices: 400--477 Score: 120
Period size: 27 Copynumber: 2.9 Consensus size: 27
390 AGTGAACTTA
* *
400 AAATGACCAAACTGCCCCTGAATGTGC
1 AAATGACCAAAATGCCCCTGGATGTGC
*
427 AAATGACCAAAATGCCCCTTGATGTGC
1 AAATGACCAAAATGCCCCTGGATGTGC
*
454 AAATGACTAAAATGCCCCTGGATG
1 AAATGACCAAAATGCCCCTGGATG
478 ACCCTAATGC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.21
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGGATGTGC
Found at i:1828 original size:2 final size:2
Alignment explanation
Indices: 1821--1851 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1811 AAGTAAAGTA
1821 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1852 AAAGTGAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6541 original size:5 final size:6
Alignment explanation
Indices: 6523--6547 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6513 TAAGAAAGAT
6523 AATAAA AATAAA AATAAA AATAAA A
1 AATAAA AATAAA AATAAA AATAAA A
6548 GAACAATGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AATAAA
Found at i:6545 original size:21 final size:21
Alignment explanation
Indices: 6505--6545 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
6495 TGAATCACCC
* *
6505 AAAAATAATAAGAAAGATAAT
1 AAAAATAAAAAGAAAAATAAT
*
6526 AAAAATAAAAATAAAAATAA
1 AAAAATAAAAAGAAAAATAA
6546 AAGAACAATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (21 bp):
AAAAATAAAAAGAAAAATAAT
Found at i:8513 original size:3 final size:3
Alignment explanation
Indices: 8505--8548 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
8495 TAATTTTAGA
8505 TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
8549 AAGGGAATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:14330 original size:51 final size:52
Alignment explanation
Indices: 14236--14438 Score: 309
Period size: 52 Copynumber: 3.9 Consensus size: 52
14226 GATCTTTCCT
* *
14236 TAAATCGAACACTTTGAAAACTTGATGGGAATTTTCCCGCTTTGAAAAGACC
1 TAAATCGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACC
* *
14288 TAAATCAAACACTTTG-AAACTTGATGGTAACTTTCCCACTTTGAAAAGACC
1 TAAATCGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACC
* * *
14339 TAAATTGAATACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAATAGACC
1 TAAATCGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACC
* * *
14391 TGAATTGAACACTTTGAAAACTTGATGCGAACTTTCCCACTTTGAAAA
1 TAAATCGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAA
14439 CTTTGAAGGA
Statistics
Matches: 137, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
51 45 0.33
52 92 0.67
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (52 bp):
TAAATCGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACC
Found at i:14440 original size:28 final size:28
Alignment explanation
Indices: 14349--14441 Score: 88
Period size: 28 Copynumber: 3.5 Consensus size: 28
14339 TAAATTGAAT
*
14349 ACTTTGAAAACTTGATGGGAACTTTCCC
1 ACTTTGAAAACTTGATGCGAACTTTCCC
* * ***
14377 ACTTTG--AA-TAGA-CCTGAA-TTGAAC
1 ACTTTGAAAACTTGATGC-GAACTTTCCC
14401 ACTTTGAAAACTTGATGCGAACTTTCCC
1 ACTTTGAAAACTTGATGCGAACTTTCCC
14429 ACTTTGAAAACTT
1 ACTTTGAAAACTT
14442 TGAAGGAAAT
Statistics
Matches: 48, Mismatches: 11, Indels: 12
0.68 0.15 0.17
Matches are distributed among these distances:
24 9 0.19
25 6 0.12
26 4 0.08
27 6 0.12
28 23 0.48
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.32
Consensus pattern (28 bp):
ACTTTGAAAACTTGATGCGAACTTTCCC
Found at i:14454 original size:28 final size:28
Alignment explanation
Indices: 14400--14454 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
14390 CTGAATTGAA
* *
14400 CACTTTGAAAACTTGATGCGAACTTTCC
1 CACTTTGAAAACTTGAAGCGAAATTTCC
14428 CACTTTGAAAACTTTGAAG-GAAATTTC
1 CACTTTGAAAAC-TTGAAGCGAAATTTC
14455 TTTTTTTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.33
Consensus pattern (28 bp):
CACTTTGAAAACTTGAAGCGAAATTTCC
Found at i:15300 original size:101 final size:101
Alignment explanation
Indices: 15125--15324 Score: 373
Period size: 101 Copynumber: 2.0 Consensus size: 101
15115 TGTGATGCAC
* *
15125 CCAAGGTTGATCATGGACTTGAAGATGACATTGGAGAGCAAGAAAAGGATGAGCATGGGCTTCAA
1 CCAAGGTTGATCATGGACTTGAAGATGACAATGGAGAGCAAGAAAAGGATGAGCATGGGCTGCAA
15190 GGAAGCATGAAGATGCATGGAGATCATGGAGATAAT
66 GGAAGCATGAAGATGCATGGAGATCATGGAGATAAT
*
15226 CCAAGGTTGATCATGGACTTGAAGATGACAATGGAGAGCAAGGAAAGGATGAGCATGGGCTGCAA
1 CCAAGGTTGATCATGGACTTGAAGATGACAATGGAGAGCAAGAAAAGGATGAGCATGGGCTGCAA
15291 GGAAGCATGAAGATGCATGGAGATCATGGAGATA
66 GGAAGCATGAAGATGCATGGAGATCATGGAGATA
15325 TCGAAAAGCA
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
101 96 1.00
ACGTcount: A:0.36, C:0.12, G:0.33, T:0.18
Consensus pattern (101 bp):
CCAAGGTTGATCATGGACTTGAAGATGACAATGGAGAGCAAGAAAAGGATGAGCATGGGCTGCAA
GGAAGCATGAAGATGCATGGAGATCATGGAGATAAT
Found at i:22612 original size:13 final size:13
Alignment explanation
Indices: 22596--22623 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
22586 GATAAAGCTA
22596 AAAGCAAATAATT
1 AAAGCAAATAATT
22609 AAAGCAAATAATT
1 AAAGCAAATAATT
22622 AA
1 AA
22624 CAAGGAGGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.21
Consensus pattern (13 bp):
AAAGCAAATAATT
Found at i:22927 original size:19 final size:18
Alignment explanation
Indices: 22903--22938 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
22893 TGAAGACTTA
22903 TTGAAGATAATTTGAAGAC
1 TTGAAGATAA-TTGAAGAC
*
22922 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
22939 ATTATCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.31
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAC
Found at i:30560 original size:42 final size:39
Alignment explanation
Indices: 30469--30552 Score: 100
Period size: 40 Copynumber: 2.1 Consensus size: 39
30459 TCGATTAAAC
* *
30469 AAGGAGCAAAGTCGACAAGAGGAAGCAAGTTATCGACTTT
1 AAGGAGCAAAGTCGAAAAGAGGAAGCAAATTATCGAC-TT
30509 AAGGAGCAAAGTCGATAAAGAAGG-AGCAAAATTATCGAC-T
1 AAGGAGCAAAGTCGA-AAAG-AGGAAGC-AAATTATCGACTT
30549 AAGG
1 AAGG
30553 GAAGCAAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
40 20 0.51
41 6 0.15
42 13 0.33
ACGTcount: A:0.44, C:0.13, G:0.27, T:0.15
Consensus pattern (39 bp):
AAGGAGCAAAGTCGAAAAGAGGAAGCAAATTATCGACTT
Found at i:31114 original size:12 final size:12
Alignment explanation
Indices: 31097--31121 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31087 GGTTTCATGA
31097 TCCTAATTTTGC
1 TCCTAATTTTGC
31109 TCCTAATTTTGC
1 TCCTAATTTTGC
31121 T
1 T
31122 TCTAGTGATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.08, T:0.52
Consensus pattern (12 bp):
TCCTAATTTTGC
Done.