Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016333.1 Corchorus olitorius cultivar O-4 contig16366, 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: 47187
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:62 original size:29 final size:27
Alignment explanation
Indices: 29--96 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 27
19 TTACTTTTTC
29 TACATAATCTAATTCTTTTTTTTGGCCAG
1 TACATAATCTAATTC-TTTTTTT-GCCAG
58 TACATAATCTAA---TTTTTTTGCCAG
1 TACATAATCTAATTCTTTTTTTGCCAG
*
82 AACATAATCTAATTC
1 TACATAATCTAATTC
97 AATGTGAACA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
24 16 0.46
25 7 0.20
29 12 0.34
ACGTcount: A:0.31, C:0.18, G:0.07, T:0.44
Consensus pattern (27 bp):
TACATAATCTAATTCTTTTTTTGCCAG
Found at i:3036 original size:2 final size:2
Alignment explanation
Indices: 3031--3093 Score: 80
Period size: 2 Copynumber: 32.5 Consensus size: 2
3021 TTCAGAAAAA
3031 AT AT AT AT AT AT AT AT AT AT -T AT -T AT AT AT -T A- AT AGT ACT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T A-T
3071 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
3094 CTAAATCAAA
Statistics
Matches: 55, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
1 4 0.07
2 47 0.85
3 4 0.07
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:14318 original size:13 final size:13
Alignment explanation
Indices: 14300--14324 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14290 TGTCCCCCCC
14300 AAAAAAAAAGAAA
1 AAAAAAAAAGAAA
14313 AAAAAAAAAGAA
1 AAAAAAAAAGAA
14325 CTTGAAAAAG
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAGAAA
Found at i:23248 original size:51 final size:51
Alignment explanation
Indices: 23188--23290 Score: 188
Period size: 51 Copynumber: 2.0 Consensus size: 51
23178 CTTCATTTCC
* *
23188 ACTTGAGGTAAAGAAGGTTAGCTTAAATAGAGATATGAACCAAAAACTCTA
1 ACTTGAGGTAAAGAAGGTTAGCTTAAAGAGAGACATGAACCAAAAACTCTA
23239 ACTTGAGGTAAAGAAGGTTAGCTTAAAGAGAGACATGAACCAAAAACTCTA
1 ACTTGAGGTAAAGAAGGTTAGCTTAAAGAGAGACATGAACCAAAAACTCTA
23290 A
1 A
23291 AAAAACACGG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.46, C:0.13, G:0.20, T:0.21
Consensus pattern (51 bp):
ACTTGAGGTAAAGAAGGTTAGCTTAAAGAGAGACATGAACCAAAAACTCTA
Found at i:29788 original size:88 final size:88
Alignment explanation
Indices: 29634--29803 Score: 322
Period size: 88 Copynumber: 1.9 Consensus size: 88
29624 TACATTAAAC
*
29634 ATCAGCCTGCTTTCGATGTTCTTACCACTGGCGGCAGGGTTACTGAATCAAGGTTCTTTGGATAG
1 ATCAGCCTGCTTTCGATGTTCTCACCACTGGCGGCAGGGTTACTGAATCAAGGTTCTTTGGATAG
29699 GGTGTCCACAAGCCAAAAAAAAA
66 GGTGTCCACAAGCCAAAAAAAAA
*
29722 ATCAGCCTGCTTTCGATGTTCTCACCACTGGCGGCAGGGTTACTGAATCAAGGTTCTTTGGGTAG
1 ATCAGCCTGCTTTCGATGTTCTCACCACTGGCGGCAGGGTTACTGAATCAAGGTTCTTTGGATAG
29787 GGTGTCCACAAGCCAAA
66 GGTGTCCACAAGCCAAA
29804 TCCACCTCTG
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 80 1.00
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.26
Consensus pattern (88 bp):
ATCAGCCTGCTTTCGATGTTCTCACCACTGGCGGCAGGGTTACTGAATCAAGGTTCTTTGGATAG
GGTGTCCACAAGCCAAAAAAAAA
Found at i:37359 original size:56 final size:56
Alignment explanation
Indices: 37273--37392 Score: 195
Period size: 56 Copynumber: 2.1 Consensus size: 56
37263 AACTTACACA
* * *
37273 AAACGGTCAAATAAGCCTTTGAACTCTTTAAAAATATCAAATCAGTCCTTCCCTCT
1 AAACGGTCAAATAAGCCCTTGAACTCTTTAAAAATACCAAATCAGCCCTTCCCTCT
* *
37329 AAACGGTCAAATAAGCCCTTGAACTCTTTAAAAATGCCAAATCAGCCCTTCCGTCT
1 AAACGGTCAAATAAGCCCTTGAACTCTTTAAAAATACCAAATCAGCCCTTCCCTCT
37385 AAACGGTC
1 AAACGGTC
37393 CGTCTATTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.27
Consensus pattern (56 bp):
AAACGGTCAAATAAGCCCTTGAACTCTTTAAAAATACCAAATCAGCCCTTCCCTCT
Found at i:40589 original size:25 final size:25
Alignment explanation
Indices: 40555--40603 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
40545 GATTGATTTG
40555 TAGAGACCGAGCGAGAGTGCTCAAA
1 TAGAGACCGAGCGAGAGTGCTCAAA
*
40580 TAGAGACCGAGTGAGAGTGCTCAA
1 TAGAGACCGAGCGAGAGTGCTCAA
40604 GATTGTTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.18, G:0.33, T:0.14
Consensus pattern (25 bp):
TAGAGACCGAGCGAGAGTGCTCAAA
Found at i:46751 original size:22 final size:24
Alignment explanation
Indices: 46716--46774 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 24
46706 ATAAATGTTG
* *
46716 CTGATAA-TCTTCT-CTTTTATCT
1 CTGATAATTCTTCTCCATTTATCA
46738 CTGATAATTC-TCTCCATTTATCA
1 CTGATAATTCTTCTCCATTTATCA
46761 CTTGATAATATCTT
1 C-TGATAAT-TCTT
46775 GCCAGATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
22 10 0.33
23 10 0.33
24 7 0.23
25 2 0.07
26 1 0.03
ACGTcount: A:0.24, C:0.22, G:0.05, T:0.49
Consensus pattern (24 bp):
CTGATAATTCTTCTCCATTTATCA
Done.