Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016173.1 Corchorus capsularis cultivar CVL-1 contig16194, 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: 23427
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:2334 original size:12 final size:11
Alignment explanation
Indices: 2304--2336 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
2294 ACAACAATTT
2304 AAAAAAAA-AA
1 AAAAAAAACAA
2314 AAAAAAAACTAA
1 AAAAAAAAC-AA
2326 AAAAAAAACAA
1 AAAAAAAACAA
2337 CACACACACA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 8 0.38
11 2 0.10
12 11 0.52
ACGTcount: A:0.91, C:0.06, G:0.00, T:0.03
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:9614 original size:21 final size:24
Alignment explanation
Indices: 9570--9614 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
9560 TTATCTTAGA
9570 TATAATATATATTATTAAATAAAT
1 TATAATATATATTATTAAATAAAT
9594 TATAA-ATATATT-TTAAA-AAAT
1 TATAATATATATTATTAAATAAAT
9615 AAATGATGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 4 0.19
22 5 0.24
23 7 0.33
24 5 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TATAATATATATTATTAAATAAAT
Found at i:11705 original size:31 final size:30
Alignment explanation
Indices: 11667--11830 Score: 111
Period size: 31 Copynumber: 5.5 Consensus size: 30
11657 TAGGGCTAAT
11667 TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
1 TGCTCAAATAAGGGCCTAACGTTT-TCAAAA
* * **
11698 TGCTCAAATAAGGGCTCGATC-TTTT-AATC
1 TGCTCAAATAAGGGC-CTAACGTTTTCAAAA
* *
11727 TAG-ACAAATAAGGGCCTAACGTTATCGAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTTC-AAAA
* * * **
11758 TCCTCAAATAAGGGCCCAATGTTTT-AATT
1 TGCTCAAATAAGGGCCTAACGTTTTCAAAA
** * * *
11787 TGGGCAAATAAGGGTCTAACGCTATCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTTCAAAA
*
11817 TGATCAAATAAGGG
1 TGCTCAAATAAGGG
11831 TCTGGGGTCA
Statistics
Matches: 97, Mismatches: 29, Indels: 15
0.69 0.21 0.11
Matches are distributed among these distances:
28 3 0.03
29 36 0.37
30 16 0.16
31 39 0.40
32 3 0.03
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.26
Consensus pattern (30 bp):
TGCTCAAATAAGGGCCTAACGTTTTCAAAA
Found at i:11764 original size:60 final size:59
Alignment explanation
Indices: 11671--11830 Score: 203
Period size: 60 Copynumber: 2.7 Consensus size: 59
11661 GCTAATTGCT
* * *
11671 CAAATAAGGGCCTAACGTTTGTCAAAATGCTCAAATAAGGGCTCGATCTTTTAATCTAGA
1 CAAATAAGGGCCTAACG-TTATCAAAATGCTCAAATAAGGGCCCAATCTTTTAATCTAGA
* * * * *
11731 CAAATAAGGGCCTAACGTTATCGAAAATCCTCAAATAAGGGCCCAATGTTTTAATTTGGG
1 CAAATAAGGGCCTAACGTTATC-AAAATGCTCAAATAAGGGCCCAATCTTTTAATCTAGA
* * *
11791 CAAATAAGGGTCTAACGCTATCAAAATGATCAAATAAGGG
1 CAAATAAGGGCCTAACGTTATCAAAATGCTCAAATAAGGG
11831 TCTGGGGTCA
Statistics
Matches: 87, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
59 20 0.23
60 67 0.77
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (59 bp):
CAAATAAGGGCCTAACGTTATCAAAATGCTCAAATAAGGGCCCAATCTTTTAATCTAGA
Found at i:11998 original size:61 final size:60
Alignment explanation
Indices: 11870--12036 Score: 244
Period size: 61 Copynumber: 2.8 Consensus size: 60
11860 ATTTTCGATG
*
11870 TCAGGCCCTTATTTGAGCATTTTGGCAAAAGTTAGGCCCTTATTTGGCCAAATTAAAAGA
1 TCAGGCCCTTATTTGAGCATTTTGGCAAAAGTTAGCCCCTTATTTGGCCAAATTAAAAGA
* *
11930 TCGGGCCCTTATTTGAGCATTTTGGCAAATGTTAGCCCCCTTATTTGGCCAAATTAAAAGA
1 TCAGGCCCTTATTTGAGCATTTTGGCAAAAGTTAG-CCCCTTATTTGGCCAAATTAAAAGA
* ** * **
11991 TCAGGCCCTTATTTGAACATTTTCACAAACGTTAGGTCCTTATTTG
1 TCAGGCCCTTATTTGAGCATTTTGGCAAAAGTTAGCCCCTTATTTG
12037 AGCAATTAGC
Statistics
Matches: 96, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
60 42 0.44
61 54 0.56
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (60 bp):
TCAGGCCCTTATTTGAGCATTTTGGCAAAAGTTAGCCCCTTATTTGGCCAAATTAAAAGA
Found at i:12005 original size:29 final size:29
Alignment explanation
Indices: 11903--12005 Score: 93
Period size: 29 Copynumber: 3.4 Consensus size: 29
11893 GGCAAAAGTT
11903 AGGCCCTTATTTGGCCAAATTAAAAGATC
1 AGGCCCTTATTTGGCCAAATTAAAAGATC
* ** * *
11932 GGGCCCTTATTTGAG-CATTTTGGCAAATG-TT
1 AGGCCCTTATTTG-GCCAAATT---AAAAGATC
*
11963 AGCCCCCTTATTTGGCCAAATTAAAAGATC
1 AG-GCCCTTATTTGGCCAAATTAAAAGATC
11993 AGGCCCTTATTTG
1 AGGCCCTTATTTG
12006 AACATTTTCA
Statistics
Matches: 55, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
29 30 0.55
30 4 0.07
31 3 0.05
32 18 0.33
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.32
Consensus pattern (29 bp):
AGGCCCTTATTTGGCCAAATTAAAAGATC
Found at i:14339 original size:2 final size:2
Alignment explanation
Indices: 14332--14373 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
14322 TTAATACATA
* *
14332 AT AT AT AT AT AT GT GT AT AT AT AT AT AT AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14373 A
1 A
14374 AATGAGCATA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22471 original size:19 final size:18
Alignment explanation
Indices: 22442--22483 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
22432 TGAGTAGTTT
* *
22442 TTAAGTAAAAATGTAATA
1 TTAAATAAAAATATAATA
22460 TATAAATAAAAATATAATA
1 T-TAAATAAAAATATAATA
22479 TTAAA
1 TTAAA
22484 ATAATTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (18 bp):
TTAAATAAAAATATAATA
Found at i:22487 original size:19 final size:19
Alignment explanation
Indices: 22447--22483 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
22437 AGTTTTTAAG
*
22447 TAAAAATGTAATATATAAA
1 TAAAAATATAATATATAAA
22466 TAAAAATATAATAT-TAAA
1 TAAAAATATAATATATAAA
22484 ATAATTAATA
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:0.03, T:0.32
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Done.