Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014724.1 Corchorus olitorius cultivar O-4 contig14757, 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: 42857
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:19 original size:2 final size:2
Alignment explanation
Indices: 7--40 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
1 GCATTT
7 TA TA TA CTA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA T
41 TCTTTAGGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35753 original size:22 final size:22
Alignment explanation
Indices: 35725--35766 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
35715 ATATCATATT
35725 TATGAGTAGGAAAAAATTATCA
1 TATGAGTAGGAAAAAATTATCA
35747 TATGAGTAGGAAAAAATTAT
1 TATGAGTAGGAAAAAATTAT
35767 GATGCCGATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.02, G:0.19, T:0.29
Consensus pattern (22 bp):
TATGAGTAGGAAAAAATTATCA
Found at i:37298 original size:15 final size:16
Alignment explanation
Indices: 37280--37309 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
37270 ATCATGTTAT
37280 ATCC-TTAAAAAATAA
1 ATCCTTTAAAAAATAA
37295 ATCCTTTAAAAAATA
1 ATCCTTTAAAAAATA
37310 CGTTCTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (16 bp):
ATCCTTTAAAAAATAA
Found at i:39000 original size:4 final size:4
Alignment explanation
Indices: 38993--39036 Score: 63
Period size: 4 Copynumber: 11.2 Consensus size: 4
38983 TACGTATATA
* *
38993 TATG TATG TGTG TACG TATG TATG TATG TATG TAT- TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG T
39037 GTGTGTATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 3 0.09
4 32 0.91
ACGTcount: A:0.23, C:0.02, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:39678 original size:36 final size:36
Alignment explanation
Indices: 39638--39710 Score: 85
Period size: 36 Copynumber: 2.0 Consensus size: 36
39628 AGTGTGTCTC
*
39638 ATATGTACAAAG-ATACGTTAGTTAATTACAGTTGAT
1 ATATG-ACAAAGAATACGGTAGTTAATTACAGTTGAT
* * **
39674 ATATGATAGAGAATGGGGTAGTTAATTACAGTTGAT
1 ATATGACAAAGAATACGGTAGTTAATTACAGTTGAT
39710 A
1 A
39711 AAATGGCTCG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
35 4 0.13
36 27 0.87
ACGTcount: A:0.38, C:0.05, G:0.22, T:0.34
Consensus pattern (36 bp):
ATATGACAAAGAATACGGTAGTTAATTACAGTTGAT
Found at i:40420 original size:29 final size:29
Alignment explanation
Indices: 40379--40486 Score: 128
Period size: 29 Copynumber: 3.7 Consensus size: 29
40369 GGTTTTTTCA
40379 AGTTCAAGGGCTTATTTGGCTGCAATTAG
1 AGTTCAAGGGCTTATTTGGCTGCAATTAG
* * ***
40408 AGTTCAGGGGCTTATTTGGGT-TTTTTCAAG
1 AGTTCAAGGGCTTATTTGGCTGCAATT--AG
40438 AGTTCAAGGGCTTATTTGGCTGCAATTAG
1 AGTTCAAGGGCTTATTTGGCTGCAATTAG
* *
40467 AGTTCATGAGCTTATTTGGC
1 AGTTCAAGGGCTTATTTGGC
40487 CGTTTTGTGT
Statistics
Matches: 64, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
28 2 0.03
29 39 0.61
30 21 0.33
31 2 0.03
ACGTcount: A:0.21, C:0.13, G:0.28, T:0.38
Consensus pattern (29 bp):
AGTTCAAGGGCTTATTTGGCTGCAATTAG
Found at i:40442 original size:30 final size:29
Alignment explanation
Indices: 40356--40456 Score: 116
Period size: 29 Copynumber: 3.5 Consensus size: 29
40346 GCCGTCAGAA
*
40356 AAGGGTTTATTTGGGTTTTTTCA-AGTTC
1 AAGGGCTTATTTGGGTTTTTTCAGAGTTC
* ***
40384 AAGGGCTTATTTGGCTGCAATT-AGAGTTC
1 AAGGGCTTATTTGGGT-TTTTTCAGAGTTC
*
40413 AGGGGCTTATTTGGGTTTTTTCAAGAGTTC
1 AAGGGCTTATTTGGGTTTTTTC-AGAGTTC
40443 AAGGGCTTATTTGG
1 AAGGGCTTATTTGG
40457 CTGCAATTAG
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
28 17 0.29
29 21 0.36
30 20 0.34
ACGTcount: A:0.20, C:0.10, G:0.29, T:0.42
Consensus pattern (29 bp):
AAGGGCTTATTTGGGTTTTTTCAGAGTTC
Found at i:40450 original size:59 final size:57
Alignment explanation
Indices: 40362--40485 Score: 212
Period size: 59 Copynumber: 2.1 Consensus size: 57
40352 AGAAAAGGGT
*
40362 TTATTTGGGTTTTTTCAAGTTCAAGGGCTTATTTGGCTGCAATTAGAGTTCAGGGGC
1 TTATTTGGGTTTTTTCAAGTTCAAGGGCTTATTTGGCTGCAATTAGAGTTCAGGAGC
*
40419 TTATTTGGGTTTTTTCAAGAGTTCAAGGGCTTATTTGGCTGCAATTAGAGTTCATGAGC
1 TTATTTGGGTTTTTTC-A-AGTTCAAGGGCTTATTTGGCTGCAATTAGAGTTCAGGAGC
40478 TTATTTGG
1 TTATTTGG
40486 CCGTTTTGTG
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
57 16 0.25
58 1 0.02
59 46 0.73
ACGTcount: A:0.20, C:0.11, G:0.27, T:0.42
Consensus pattern (57 bp):
TTATTTGGGTTTTTTCAAGTTCAAGGGCTTATTTGGCTGCAATTAGAGTTCAGGAGC
Found at i:41289 original size:2 final size:2
Alignment explanation
Indices: 41282--41312 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
41272 GCCTTACATG
41282 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41313 TATGATAATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42828 original size:2 final size:2
Alignment explanation
Indices: 42821--42857 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
42811 CTTATCACTA
42821 AT AT AT 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 AT AT AT A
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.