Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018231.1 Corchorus olitorius cultivar O-4 contig18264, 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: 56673
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:4716 original size:21 final size:21
Alignment explanation
Indices: 4690--4760 Score: 108
Period size: 21 Copynumber: 3.4 Consensus size: 21
4680 TGCTAGGAGA
4690 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
4711 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
* *
4732 TCATTGGAAAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
4753 TCATTGGA
1 TCATTGGA
4761 ATTGCCTAAG
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
20 2 0.04
21 45 0.96
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:5663 original size:25 final size:24
Alignment explanation
Indices: 5627--5673 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
5617 TCCTTCTATT
5627 CATCTATCATC-AAGTTTTTCATC
1 CATCTATCATCAAAGTTTTTCATC
5650 CATCTCATCCATCAAAGTTTTTCA
1 CATCT-AT-CATCAAAGTTTTTCA
5674 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:11093 original size:21 final size:21
Alignment explanation
Indices: 11067--11158 Score: 159
Period size: 21 Copynumber: 4.4 Consensus size: 21
11057 TGCTTGGAGA
11067 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
11088 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
11109 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
11130 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
11151 TCATTGGA
1 TCATTGGA
11159 ATTGCCTAAG
Statistics
Matches: 69, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
20 2 0.03
21 67 0.97
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.26
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:24529 original size:2 final size:2
Alignment explanation
Indices: 24522--24549 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
24512 CAAGACATTC
24522 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24550 TAAAGTCAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25677 original size:21 final size:21
Alignment explanation
Indices: 25651--25692 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
25641 TCTTCTGTTG
25651 CAAAGTGTGAGGCTGCGTTTA
1 CAAAGTGTGAGGCTGCGTTTA
25672 CAAAGTGTGAGGCTGCGTTTA
1 CAAAGTGTGAGGCTGCGTTTA
25693 GTAGAAGTAG
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:0.14, G:0.33, T:0.29
Consensus pattern (21 bp):
CAAAGTGTGAGGCTGCGTTTA
Found at i:25772 original size:19 final size:19
Alignment explanation
Indices: 25748--25805 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
25738 TTGTTTAGCA
*
25748 ACTGTATAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
* *
25767 ACTGTACATATGAGATTAGAT
1 ACTGTACAGATGAGATT--AC
*
25788 ATTGTACAGATGAGATTA
1 ACTGTACAGATGAGATTA
25806 TTAGTGCAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.33
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:40991 original size:21 final size:22
Alignment explanation
Indices: 40967--41007 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
40957 GTTTATAATA
*
40967 TTCTTGGGTCA-TCGGGTTATC
1 TTCTCGGGTCATTCGGGTTATC
*
40988 TTCTCGGGTTATTCGGGTTA
1 TTCTCGGGTCATTCGGGTTA
41008 CGAGTTTGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.10, C:0.17, G:0.29, T:0.44
Consensus pattern (22 bp):
TTCTCGGGTCATTCGGGTTATC
Found at i:49353 original size:19 final size:20
Alignment explanation
Indices: 49325--49371 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
49315 TTAAATAGAA
*
49325 AAAGAATTTT-GGGAAGGA-G
1 AAAGAGTTTTCGGG-AGGAGG
49344 AAAGAGTTTTCCGGGAGGAGG
1 AAAGAGTTTT-CGGGAGGAGG
49365 AAAGAGT
1 AAAGAGT
49372 AAGTAAATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 9 0.38
20 4 0.17
21 11 0.46
ACGTcount: A:0.38, C:0.04, G:0.38, T:0.19
Consensus pattern (20 bp):
AAAGAGTTTTCGGGAGGAGG
Done.