Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012358.1 Corchorus olitorius cultivar O-4 contig12391, 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: 34375
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:2635 original size:4 final size:4
Alignment explanation
Indices: 2628--2761 Score: 241
Period size: 4 Copynumber: 33.5 Consensus size: 4
2618 TAATATATAC
*
2628 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT GCAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* *
2676 ACAT ACAT ACAT ACAT ACAT ACAT ACAT GCAT GCAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
2724 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC
2762 TGGAGTATAC
Statistics
Matches: 126, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 126 1.00
ACGTcount: A:0.48, C:0.25, G:0.02, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:7180 original size:42 final size:44
Alignment explanation
Indices: 7133--7222 Score: 139
Period size: 45 Copynumber: 2.1 Consensus size: 44
7123 CATTACTTAA
*
7133 ATTCTACT-T-CATCTCTAGGTAACTCATCAAAATAAAGCTAAT
1 ATTCTACTCTCCATCTCTAGATAACTCATCAAAATAAAGCTAAT
*
7175 ATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAGCTAAT
1 ATTCTACT-CTCCATCTCTAGATAACTCATCAAAATAAAGCTAAT
7220 ATT
1 ATT
7223 AATTGTTGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
42 8 0.19
44 1 0.02
45 34 0.79
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.34
Consensus pattern (44 bp):
ATTCTACTCTCCATCTCTAGATAACTCATCAAAATAAAGCTAAT
Found at i:9137 original size:8 final size:8
Alignment explanation
Indices: 9124--9148 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
9114 CCCTACCTCT
9124 TCCTCTCC
1 TCCTCTCC
9132 TCCTCTCC
1 TCCTCTCC
9140 TCCTCTCC
1 TCCTCTCC
9148 T
1 T
9149 GCTCCGACTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (8 bp):
TCCTCTCC
Found at i:20020 original size:3 final size:3
Alignment explanation
Indices: 20007--20036 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
19997 TTATAGTATC
20007 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
20037 GGCTGGTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:21163 original size:22 final size:22
Alignment explanation
Indices: 21138--21233 Score: 61
Period size: 22 Copynumber: 4.2 Consensus size: 22
21128 TAGGTTATTG
21138 AAATTTTGTAGAGTGGTTATCA
1 AAATTTTGTAGAGTGGTTATCA
** *
21160 AAATTATATCCAGAG-GAAGTTATAA
1 AAATT-T-TGTAGAGTG--GTTATCA
* * *
21185 AAATTTCGTTGTGTGGTTATCA
1 AAATTTTGTAGAGTGGTTATCA
* *
21207 AAATTTTATAGGAAT-GTTATCA
1 AAATTTTGTA-GAGTGGTTATCA
21229 AAATT
1 AAATT
21234 ACAAATATTA
Statistics
Matches: 54, Mismatches: 14, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
22 30 0.56
23 6 0.11
24 7 0.13
25 11 0.20
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.39
Consensus pattern (22 bp):
AAATTTTGTAGAGTGGTTATCA
Found at i:26303 original size:17 final size:17
Alignment explanation
Indices: 26273--26323 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
26263 CCACGTCACT
*
26273 TTTTTTATTTAAAAAATA
1 TTTTTT-TTAAAAAAATA
*
26291 TTTTTTTTCAAAAAATA
1 TTTTTTTTAAAAAAATA
* *
26308 ATTTCTTTAAAAAAAT
1 TTTTTTTTAAAAAAAT
26324 TGAAAAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 23 0.79
18 6 0.21
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTTTTTTAAAAAAATA
Found at i:27459 original size:75 final size:75
Alignment explanation
Indices: 27375--27522 Score: 251
Period size: 75 Copynumber: 2.0 Consensus size: 75
27365 TTCGTTACAC
* *
27375 CATTTTATTGTTGCTAAAAGAATTATATTTTACGCAACAACTCAATATTGTTGCGTAAAAATATT
1 CATTTTATTGTTGCTAAAAGAATTATATTTTACACAACAACTCAATATTGTAGCGTAAAAATATT
27440 TTAACAACGT
66 TTAACAACGT
* * *
27450 CATTTTATTGTTGTTAAAAGAATTGTATTTTACACAACAACTCAATTTTGTAGCGTAAAAATATT
1 CATTTTATTGTTGCTAAAAGAATTATATTTTACACAACAACTCAATATTGTAGCGTAAAAATATT
27515 TTAACAAC
66 TTAACAAC
27523 ATATATTCGT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 68 1.00
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (75 bp):
CATTTTATTGTTGCTAAAAGAATTATATTTTACACAACAACTCAATATTGTAGCGTAAAAATATT
TTAACAACGT
Done.