Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015236.1 Corchorus capsularis cultivar CVL-1 contig15257, 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: 33405
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:1961 original size:24 final size:24
Alignment explanation
Indices: 1920--1983 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
1910 TCATTCAGGT
* * *
1920 TTCGGGTCATCTGGGTT-CGGGTTA
1 TTCGGGTCATC-GAGTTCCGAGTCA
1944 TTCGGGTCATACGAGTTCCGAGTCA
1 TTCGGGTCAT-CGAGTTCCGAGTCA
1969 TTCGGGTC-TCGAGTT
1 TTCGGGTCATCGAGTT
1984 GGGCGGGTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
23 6 0.17
24 15 0.43
25 14 0.40
ACGTcount: A:0.12, C:0.20, G:0.33, T:0.34
Consensus pattern (24 bp):
TTCGGGTCATCGAGTTCCGAGTCA
Found at i:2290 original size:42 final size:42
Alignment explanation
Indices: 2243--2324 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
2233 TTGATATTAA
* *
2243 TTTTGAATATTCAATACATAATTAATTATCACGTGGGGTACG
1 TTTTGAATATTAAATACATAATTAATTATCACGTAGGGTACG
*
2285 TTTTGAATATTAAATACATAATTAATTATCAGGTAGGGTA
1 TTTTGAATATTAAATACATAATTAATTATCACGTAGGGTA
2325 TGTATCAACA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.39
Consensus pattern (42 bp):
TTTTGAATATTAAATACATAATTAATTATCACGTAGGGTACG
Found at i:2867 original size:16 final size:16
Alignment explanation
Indices: 2831--2871 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
2821 TTATAATATG
* *
2831 CTCGGGTCATACGGGT
1 CTCGGGTCATACAGGA
*
2847 TTCGGGTCATACAGGA
1 CTCGGGTCATACAGGA
2863 CTCGGGTCA
1 CTCGGGTCA
2872 CAGGTCATTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.17, C:0.24, G:0.34, T:0.24
Consensus pattern (16 bp):
CTCGGGTCATACAGGA
Found at i:2883 original size:16 final size:16
Alignment explanation
Indices: 2864--2902 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
2854 CATACAGGAC
2864 TCGGGTCACAGGTCAT
1 TCGGGTCACAGGTCAT
* *
2880 TCGGGTTACGGGTCAT
1 TCGGGTCACAGGTCAT
2896 TCGGGTC
1 TCGGGTC
2903 TCGAGTTCGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.13, C:0.23, G:0.36, T:0.28
Consensus pattern (16 bp):
TCGGGTCACAGGTCAT
Found at i:14045 original size:22 final size:20
Alignment explanation
Indices: 14003--14044 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
13993 TTATACACAT
14003 ATATATATTACATATTAATA
1 ATATATATTACATATTAATA
*
14023 ATATATATTATATATTAA-A
1 ATATATATTACATATTAATA
14042 ATA
1 ATA
14045 AAATTCTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATATATTACATATTAATA
Found at i:15481 original size:16 final size:17
Alignment explanation
Indices: 15449--15483 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
15439 ACTCCTTTCA
15449 TTTTTTTTATTAATTAAT
1 TTTTTTTTATT-ATTAAT
15467 TTTTTTTTATT-TTAAT
1 TTTTTTTTATTATTAAT
15483 T
1 T
15484 AGAAAGATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
18 11 0.65
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTTTTTATTATTAAT
Found at i:16338 original size:20 final size:20
Alignment explanation
Indices: 16294--16332 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
16284 GGAAATAAAA
*
16294 ATATTATTAAAAAATTATAT
1 ATATTATTAAAAAATAATAT
*
16314 ATATTATTAAGAAATAATA
1 ATATTATTAAAAAATAATA
16333 GTTATTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (20 bp):
ATATTATTAAAAAATAATAT
Found at i:19191 original size:2 final size:2
Alignment explanation
Indices: 19184--19225 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
19174 TAGATATTAG
19184 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
19226 TAATACTTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:21866 original size:2 final size:2
Alignment explanation
Indices: 21859--21889 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
21849 TAATCTGAAG
21859 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
21890 TCTGTTTGTT
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:27562 original size:2 final size:2
Alignment explanation
Indices: 27555--27581 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
27545 GTTATTCTGT
27555 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 T
27582 TGATTGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31259 original size:13 final size:12
Alignment explanation
Indices: 31231--31323 Score: 68
Period size: 13 Copynumber: 7.5 Consensus size: 12
31221 CATGTTGAAG
31231 ATATTTGTAAACT
1 ATATTTGTAAA-T
31244 ATATATTGTAAAT
1 ATAT-TTGTAAAT
31257 ATATTTGGTGAAAT
1 ATATTT-GT-AAAT
31271 -TATTTGTAAAT
1 ATATTTGTAAAT
*
31282 GTATTTGTGAACA-
1 ATATTTGT-AA-AT
*
31295 AAATTTGTGAAAT
1 ATATTTGT-AAAT
*
31308 -TAATTGTAAAT
1 ATATTTGTAAAT
31319 -TATTT
1 ATATTT
31324 TGTGTTAATA
Statistics
Matches: 68, Mismatches: 5, Indels: 16
0.76 0.06 0.18
Matches are distributed among these distances:
11 12 0.18
12 17 0.25
13 27 0.40
14 12 0.18
ACGTcount: A:0.39, C:0.02, G:0.13, T:0.46
Consensus pattern (12 bp):
ATATTTGTAAAT
Found at i:31274 original size:24 final size:24
Alignment explanation
Indices: 31231--31323 Score: 75
Period size: 25 Copynumber: 3.8 Consensus size: 24
31221 CATGTTGAAG
31231 ATATTTGT-AAACTATATATTGTAAAT
1 ATATTTGTGAAA-T-TAT-TTGTAAAT
31257 ATATTTGGTGAAATTATTTGTAAAT
1 ATATTT-GTGAAATTATTTGTAAAT
* **
31282 GTATTTGTGAACAAAATTTGTGAAAT
1 ATATTTGTGAA-ATTATTTGT-AAAT
*
31308 -TAATTGT-AAATTATTT
1 ATATTTGTGAAATTATTT
31324 TGTGTTAATA
Statistics
Matches: 57, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
23 5 0.09
24 7 0.12
25 26 0.46
26 13 0.23
27 3 0.05
28 3 0.05
ACGTcount: A:0.39, C:0.02, G:0.13, T:0.46
Consensus pattern (24 bp):
ATATTTGTGAAATTATTTGTAAAT
Done.