Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009639.1 Corchorus capsularis cultivar CVL-1 contig09660, 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: 12303
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.35
Found at i:1013 original size:27 final size:27
Alignment explanation
Indices: 981--1044 Score: 119
Period size: 27 Copynumber: 2.3 Consensus size: 27
971 ATTTCTGAAA
981 AACAAGGGAAATGGACAATTAAAAAGG
1 AACAAGGGAAATGGACAATTAAAAAGG
1008 AACAAGGGAAATGGACAATTAAAAAGG
1 AACAAGGGAAATGGACAATTAAAAAGG
1035 AACAGAGGGA
1 AACA-AGGGA
1045 GTATATATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 31 0.86
28 5 0.14
ACGTcount: A:0.55, C:0.08, G:0.28, T:0.09
Consensus pattern (27 bp):
AACAAGGGAAATGGACAATTAAAAAGG
Found at i:5657 original size:17 final size:17
Alignment explanation
Indices: 5635--5668 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5625 ACACATAAAA
*
5635 GCAAATCATGTGAAGGG
1 GCAAATCAAGTGAAGGG
5652 GCAAATCAAGTGAAGGG
1 GCAAATCAAGTGAAGGG
5669 TCATGTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.35, T:0.15
Consensus pattern (17 bp):
GCAAATCAAGTGAAGGG
Found at i:7444 original size:12 final size:11
Alignment explanation
Indices: 7424--7454 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
7414 CCAAAGATTA
7424 TATTATTTATT
1 TATTATTTATT
7435 TATCTATTTATT
1 TAT-TATTTATT
7447 TATTATTT
1 TATTATTT
7455 TCTTAAGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (11 bp):
TATTATTTATT
Found at i:9173 original size:86 final size:85
Alignment explanation
Indices: 8990--9163 Score: 235
Period size: 86 Copynumber: 2.0 Consensus size: 85
8980 ATAAAATTTG
* * * * *
8990 TAAAGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGGTTTAGGAGATATTTTAAGAAATAAA
1 TAAAGATAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGAAGATA-TTTAAAAAAGAAA
*
9055 TAAATTATAAAGATTGAATAA
65 TAAATTATAAAGATTAAATAA
*
9076 TAAAGATAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGAAGATA-TTAAAAAAGGAAA
1 TAAAGATAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGAAGATATTTAAAAAA-GAAA
9140 TAAAATTAATAAA-ATTAAATAA
65 T-AAATT-ATAAAGATTAAATAA
9162 TA
1 TA
9164 TTGTTAATAT
Statistics
Matches: 78, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
84 7 0.09
85 4 0.05
86 62 0.79
87 5 0.06
ACGTcount: A:0.48, C:0.05, G:0.14, T:0.33
Consensus pattern (85 bp):
TAAAGATAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGAAGATATTTAAAAAAGAAAT
AAATTATAAAGATTAAATAA
Found at i:10982 original size:26 final size:27
Alignment explanation
Indices: 10937--10988 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
10927 AAACTATCGA
*
10937 GTCTGTTAACTTGAT-TTTTTTGCTGG
1 GTCTGTTAACTCGATGTTTTTTGCTGG
*
10963 GTCTGTTATCTCGATGTTTTTTGCTG
1 GTCTGTTAACTCGATGTTTTTTGCTG
10989 ACGTGAAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.10, C:0.13, G:0.23, T:0.54
Consensus pattern (27 bp):
GTCTGTTAACTCGATGTTTTTTGCTGG
Found at i:11977 original size:106 final size:108
Alignment explanation
Indices: 11745--12038 Score: 423
Period size: 106 Copynumber: 2.6 Consensus size: 108
11735 ATTATTATAG
* *
11745 TTTTATTCTACTAAAAACTCTATTTTTATTCAATTAAATTAAATTTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAA-TTAATATTTTTATAATTACTT
11810 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
60 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
11859 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATTTTTATAATTACTTTA-TT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TAATATTTTTATAATTACTTTATTT
*
11923 TTACC-AAAAATTTGGATATA-TTAAATTTTTTCTAATATACAA
65 TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
**
11965 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCAATATTTTATATAAGTTTTTTTTA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATT-AATATTTT-TATAA--TTACTTTA
12030 TTTTTACCA
62 TTTTTACCA
12039 TTTTAATTTA
Statistics
Matches: 168, Mismatches: 5, Indels: 17
0.88 0.03 0.09
Matches are distributed among these distances:
105 1 0.01
106 68 0.40
107 20 0.12
108 8 0.05
109 37 0.22
110 10 0.06
111 2 0.01
114 22 0.13
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.51
Consensus pattern (108 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTAATATTTTTATAATTACTTTATTTT
TACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
Done.