Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014610.1 Corchorus olitorius cultivar O-4 contig14643, 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: 54828
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:4608 original size:29 final size:30
Alignment explanation
Indices: 4550--4610 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
4540 ATTCTAATTA
* *
4550 ATGTATACATATAAATTATTCAATTTTATT
1 ATGTATAAATATAAATTATTCAATTATATT
* *
4580 ATGTATAAATAT-AATTATTTACTTATATT
1 ATGTATAAATATAAATTATTCAATTATATT
4609 AT
1 AT
4611 TTTATTTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (30 bp):
ATGTATAAATATAAATTATTCAATTATATT
Found at i:6431 original size:22 final size:22
Alignment explanation
Indices: 6391--6432 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
6381 GTTTATAATA
* *
6391 TTCTTGGGTCATTCGGGTTAAC
1 TTCTCGGGTCATTCAGGTTAAC
*
6413 TTCTCGGGTCATTTAGGTTA
1 TTCTCGGGTCATTCAGGTTA
6433 TGAATTTGTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.14, C:0.17, G:0.26, T:0.43
Consensus pattern (22 bp):
TTCTCGGGTCATTCAGGTTAAC
Found at i:10604 original size:43 final size:44
Alignment explanation
Indices: 10557--10643 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
10547 ACTAAAAAGC
10557 ACCGTGTTGATTTTTCTGCC-AAAAAAAAAAGCACCGTGTTGAT
1 ACCGTGTTGATTTTTCTGCCAAAAAAAAAAAGCACCGTGTTGAT
10600 ACCGTGTTGATTTTTCTGCCAAAAAAAAAAAGCACCGTGTTGAT
1 ACCGTGTTGATTTTTCTGCCAAAAAAAAAAAGCACCGTGTTGAT
10644 TTTTCTCGAC
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 20 0.47
44 23 0.53
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (44 bp):
ACCGTGTTGATTTTTCTGCCAAAAAAAAAAAGCACCGTGTTGAT
Found at i:31054 original size:48 final size:48
Alignment explanation
Indices: 30999--31146 Score: 287
Period size: 48 Copynumber: 3.1 Consensus size: 48
30989 AATTTATGCA
30999 GGTGACTATGAAAGCAGGAATGGAAGCCCTGAAATGAGATATCCTGCT
1 GGTGACTATGAAAGCAGGAATGGAAGCCCTGAAATGAGATATCCTGCT
*
31047 GGTGACTATGAAAGCAGGAATGGAAGCCCTGAAATGGGATATCCTGCT
1 GGTGACTATGAAAGCAGGAATGGAAGCCCTGAAATGAGATATCCTGCT
31095 GGTGACTATGAAAGCAGGAATGGAAGCCCTGAAATGAGATATCCTGCT
1 GGTGACTATGAAAGCAGGAATGGAAGCCCTGAAATGAGATATCCTGCT
31143 GGTG
1 GGTG
31147 CATTTGCTGA
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 98 1.00
ACGTcount: A:0.32, C:0.16, G:0.31, T:0.21
Consensus pattern (48 bp):
GGTGACTATGAAAGCAGGAATGGAAGCCCTGAAATGAGATATCCTGCT
Found at i:37561 original size:19 final size:19
Alignment explanation
Indices: 37550--37586 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
37540 AATTTTTAAG
37550 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
*
37569 TAAAAATTTAATAT-TAAA
1 TAAAAATATAATATATAAA
37587 ACAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:41729 original size:65 final size:65
Alignment explanation
Indices: 41652--41786 Score: 191
Period size: 65 Copynumber: 2.1 Consensus size: 65
41642 ATTTTTTAGG
*
41652 TCAACAAACTTTCTGAGAAACCCAATTTTCTTACAAAACAAACAGCCCAAAAATTTTTCTTCCAG
1 TCAACAAACTTTCCGAGAAACCCAATTTTCTTACAAAACAAACAGCCCAAAAA-TTTTCTTCCAG
41717 C
65 C
* * * * *
41718 TCAAC-AACTTTCCGAGAAACCCAATTTTCTTACGAAACAAATAGTCCAAGAATTTTCTTTCAGC
1 TCAACAAACTTTCCGAGAAACCCAATTTTCTTACAAAACAAACAGCCCAAAAATTTTCTTCCAGC
*
41782 CCAAC
1 TCAAC
41787 CCAATGACCA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
64 15 0.24
65 42 0.68
66 5 0.08
ACGTcount: A:0.38, C:0.27, G:0.07, T:0.27
Consensus pattern (65 bp):
TCAACAAACTTTCCGAGAAACCCAATTTTCTTACAAAACAAACAGCCCAAAAATTTTCTTCCAGC
Found at i:43682 original size:19 final size:19
Alignment explanation
Indices: 43642--43678 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
43632 AATTTTTAAG
43642 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
43661 TAAAAATATAATAT-TAAA
1 TAAAAATATAATATATAAA
43679 ATAATTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:46869 original size:26 final size:26
Alignment explanation
Indices: 46819--46869 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
46809 AAAAGTTAAA
* *
46819 GGGTTAAATCATGTAAAATAGAAATT
1 GGGTTAAATCATGTAAAACAAAAATT
*
46845 GGGTTAAATCATGTTAAACAAAAAT
1 GGGTTAAATCATGTAAAACAAAAAT
46870 CATAAACAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.29
Consensus pattern (26 bp):
GGGTTAAATCATGTAAAACAAAAATT
Found at i:47351 original size:17 final size:16
Alignment explanation
Indices: 47323--47355 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
47313 CTTGATATCA
47323 AATTTTTAATAATAAT
1 AATTTTTAATAATAAT
47339 AATTTTGTAATAATAAT
1 AATTTT-TAATAATAAT
47356 GTACTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
AATTTTTAATAATAAT
Found at i:53720 original size:15 final size:15
Alignment explanation
Indices: 53700--53728 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
53690 TTTCTCAATG
53700 TTTTGTTTTTTTTTT
1 TTTTGTTTTTTTTTT
53715 TTTTGTTTTTTTTT
1 TTTTGTTTTTTTTT
53729 CTCTCCATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (15 bp):
TTTTGTTTTTTTTTT
Done.