Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007440.1 Corchorus capsularis cultivar CVL-1 contig07461, 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: 49075
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Found at i:782 original size:16 final size:16
Alignment explanation
Indices: 751--806 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
741 GGTTAGGTTT
* *
751 ATTCGAGTTTCGGGTC
1 ATTCGGGTTTCAGGTC
*
767 ATACGGGTTTCAGGTC
1 ATTCGGGTTTCAGGTC
*
783 ATTC-GGTTTCCGGATC
1 ATTCGGGTTTCAGG-TC
799 ATTCGGGT
1 ATTCGGGT
807 CTTGGGTCTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
15 8 0.24
16 22 0.67
17 3 0.09
ACGTcount: A:0.14, C:0.20, G:0.30, T:0.36
Consensus pattern (16 bp):
ATTCGGGTTTCAGGTC
Found at i:792 original size:31 final size:30
Alignment explanation
Indices: 716--806 Score: 87
Period size: 31 Copynumber: 2.9 Consensus size: 30
706 GGTTTTCTCG
*
716 GGTCATTCGAGTTTTGGGTCATCTGGG-TTA
1 GGTCATTCGAGTTTCGGGTCATC-GGGTTTA
*
746 GGTTTATTCGAGTTTCGGGTCATACGGGTTTCA
1 GG-TCATTCGAGTTTCGGGTCAT-CGGGTTT-A
*
779 GGTCATTCG-GTTTCCGGATCATTCGGGT
1 GGTCATTCGAGTTT-CGGGTCA-TCGGGT
807 CTTGGGTCTA
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
30 2 0.04
31 25 0.49
32 20 0.39
33 4 0.08
ACGTcount: A:0.13, C:0.16, G:0.32, T:0.38
Consensus pattern (30 bp):
GGTCATTCGAGTTTCGGGTCATCGGGTTTA
Found at i:2552 original size:13 final size:13
Alignment explanation
Indices: 2530--2566 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
2520 AGTCAAAATG
2530 ATTAATTTAGTGTA
1 ATTAA-TTAGTGTA
*
2544 ATTAATTAGCGTA
1 ATTAATTAGTGTA
2557 ATTAATTAGT
1 ATTAATTAGT
2567 CTATATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 16 0.76
14 5 0.24
ACGTcount: A:0.38, C:0.03, G:0.14, T:0.46
Consensus pattern (13 bp):
ATTAATTAGTGTA
Found at i:3592 original size:21 final size:21
Alignment explanation
Indices: 3566--3610 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3556 ATTAAATTTT
*
3566 TAATAAATAATAAAATCTAAA
1 TAATAAATAATAAAATCAAAA
* *
3587 TAATAACTAATCAAATCAAAA
1 TAATAAATAATAAAATCAAAA
3608 TAA
1 TAA
3611 ATTGTGATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (21 bp):
TAATAAATAATAAAATCAAAA
Found at i:8074 original size:15 final size:14
Alignment explanation
Indices: 8041--8073 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
8031 AATTACATGG
8041 TTTTTCTTTCTTTC
1 TTTTTCTTTCTTTC
8055 TTTTTCCTTTCTTT-
1 TTTTT-CTTTCTTTC
8069 TTTTT
1 TTTTT
8074 TTTTTGGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTTCTTTCTTTC
Found at i:19228 original size:21 final size:21
Alignment explanation
Indices: 19204--19260 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 21
19194 GAAACATTAG
19204 AGGAAGACTCAAGAAGATTGT
1 AGGAAGACTCAAGAAGATTGT
*
19225 AGGATGACTCAAG-AGA---T
1 AGGAAGACTCAAGAAGATTGT
*
19242 -GGAAGACTCATGAAGATTG
1 AGGAAGACTCAAGAAGATTG
19261 GACTTTGGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 9
0.71 0.07 0.22
Matches are distributed among these distances:
16 10 0.34
17 4 0.14
20 3 0.10
21 12 0.41
ACGTcount: A:0.40, C:0.11, G:0.30, T:0.19
Consensus pattern (21 bp):
AGGAAGACTCAAGAAGATTGT
Found at i:37063 original size:17 final size:17
Alignment explanation
Indices: 37042--37076 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
37032 GTTTAATGAC
*
37042 TAAAAAGAATATTA-AT
1 TAAAAAAAATATTATAT
37058 TAAAAAAAATATTATAT
1 TAAAAAAAATATTATAT
37075 TA
1 TA
37077 TAATACTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
TAAAAAAAATATTATAT
Found at i:43034 original size:13 final size:13
Alignment explanation
Indices: 43016--43040 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43006 TTACAATTCC
43016 AAATAATATTTAT
1 AAATAATATTTAT
43029 AAATAATATTTA
1 AAATAATATTTA
43041 GAACATTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:44891 original size:29 final size:29
Alignment explanation
Indices: 44857--44931 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
44847 CTTGTAGCGT
*
44857 TTGGACATTTTGCCCCATGATCTTAAATC
1 TTGGACATTTTGCCCCATGAACTTAAATC
* * *
44886 TTGGACATTTTTCCCCATGAACTTCAATT
1 TTGGACATTTTGCCCCATGAACTTAAATC
*
44915 TTGGGACGTTTTGCCCC
1 TT-GGACATTTTGCCCC
44932 CTCAACATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 27 0.69
30 12 0.31
ACGTcount: A:0.20, C:0.25, G:0.16, T:0.39
Consensus pattern (29 bp):
TTGGACATTTTGCCCCATGAACTTAAATC
Found at i:45144 original size:28 final size:29
Alignment explanation
Indices: 45070--45146 Score: 111
Period size: 29 Copynumber: 2.7 Consensus size: 29
45060 CGTTAGGTTG
45070 AGGGGGCAAAACGTCCCAAAATTGAAGTTC
1 AGGGGGCAAAACGT-CCAAAATTGAAGTTC
* *
45100 AGGGGGCAAAATGTCCAAGATTGAAGTTC
1 AGGGGGCAAAACGTCCAAAATTGAAGTTC
*
45129 A-GGGGCAAAACATCCAAA
1 AGGGGGCAAAACGTCCAAA
45147 CGTTATAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
28 14 0.33
29 15 0.36
30 13 0.31
ACGTcount: A:0.39, C:0.18, G:0.27, T:0.16
Consensus pattern (29 bp):
AGGGGGCAAAACGTCCAAAATTGAAGTTC
Found at i:48280 original size:33 final size:33
Alignment explanation
Indices: 48224--48315 Score: 130
Period size: 33 Copynumber: 2.8 Consensus size: 33
48214 TTTGGATTCT
* *
48224 ATTGTTCCCACTAATATTATGCCTCAGAATGAG
1 ATTGCTCCCACTAATATTGTGCCTCAGAATGAG
* * * *
48257 ATTGCTGCCACTGATGTTGTGCCTCGGAATGAG
1 ATTGCTCCCACTAATATTGTGCCTCAGAATGAG
48290 ATTGCTCCCACTAATATTGTGCCTCA
1 ATTGCTCCCACTAATATTGTGCCTCA
48316 ACGAACACAC
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (33 bp):
ATTGCTCCCACTAATATTGTGCCTCAGAATGAG
Done.