Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015560.1 Corchorus olitorius cultivar O-4 contig15593, 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: 4478
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:62 original size:14 final size:14
Alignment explanation
Indices: 43--89 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
33 TTTTCAAAAT
*
43 AAAAAACTTTTTTC
1 AAAAAACTATTTTC
*
57 AAAAAA-GATTTTC
1 AAAAAACTATTTTC
* *
70 AAGAAACTGTTTTC
1 AAAAAACTATTTTC
84 AAAAAA
1 AAAAAA
90 TGAGTTTTCC
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
13 10 0.38
14 16 0.62
ACGTcount: A:0.51, C:0.11, G:0.06, T:0.32
Consensus pattern (14 bp):
AAAAAACTATTTTC
Found at i:785 original size:4 final size:4
Alignment explanation
Indices: 734--811 Score: 71
Period size: 4 Copynumber: 20.8 Consensus size: 4
724 GAAGCAATCT
* *
734 AAAG AAA- AAAG AAA- AAA- AGAG AAAG CAAAG AAA- AAAG TGAA- AAA-
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG -AAAG AAAG AAAG -AAAG AAAG
778 AAAG AAAG AAAG AAAG AAAG AAAG AAAG -AAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
812 ATCAAAAGGA
Statistics
Matches: 63, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
3 19 0.30
4 38 0.60
5 6 0.10
ACGTcount: A:0.77, C:0.01, G:0.21, T:0.01
Consensus pattern (4 bp):
AAAG
Found at i:1091 original size:87 final size:87
Alignment explanation
Indices: 944--1113 Score: 259
Period size: 87 Copynumber: 2.0 Consensus size: 87
934 ATGTTTGAAC
* *
944 ATTTCTTAAGATGAGAAATTGATCCAGAAACATCAATTGAGTTGGGAATATCAATGCATGATCAA
1 ATTTCTTAAGATGAGAAATTGATCCAGAAACATCAATTGAGTTGGGAATATCAATACATGACCAA
*
1009 ATTGGAGGAAGATTTGGGAAAT
66 ATTGGAAGAAGATTTGGGAAAT
* * * * *
1031 ATTTCTTAAGGTGGGAAGTTGATCCAGAACCATCAGTTGAGTTGGGAATATCAATACATGACCAA
1 ATTTCTTAAGATGAGAAATTGATCCAGAAACATCAATTGAGTTGGGAATATCAATACATGACCAA
*
1096 ATTGGAAGAAGGTTTGGG
66 ATTGGAAGAAGATTTGGG
1114 GCATCAATCA
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
87 74 1.00
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.28
Consensus pattern (87 bp):
ATTTCTTAAGATGAGAAATTGATCCAGAAACATCAATTGAGTTGGGAATATCAATACATGACCAA
ATTGGAAGAAGATTTGGGAAAT
Found at i:2429 original size:37 final size:37
Alignment explanation
Indices: 1890--2422 Score: 520
Period size: 37 Copynumber: 14.4 Consensus size: 37
1880 TTCAAGATTT
*
1890 CTGTTTAGGTGTCTTATCAAATCTTTATTTAAGGTCC
1 CTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCC
* * * *
1927 CTGTTTAGGTGT-TTCATCAAAAT-CTTGTTCAAGATTC
1 CTGTTTAGGTGTCTT-ATC-AAATCCTTATTTAAGGTCC
*
1964 CTGTTTAGGTGTCTTATCAAATCCTTGTTTAAGGTCC
1 CTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCC
* * *
2001 CTATGTAGGTGTCTTATTAAATCCTTATTTAAGGTCC
1 CTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCC
*
2038 CTGTTTATGTGTCTTATCAAATCCTTATTTAAGGTCC
1 CTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCC
* ** * *
2075 CTGTTTAGGTGTCTCATCGAAAT-CTGGTTCAAGATCC
1 CTGTTTAGGTGTCTTATC-AAATCCTTATTTAAGGTCC
* * * * * *
2112 CTATTTAGGTGTCTCATCAAAAT-CTTGTTCAAGATTC
1 CTGTTTAGGTGTCTTATC-AAATCCTTATTTAAGGTCC
* * *
2149 CTGTTTAGGTTTCTTATTAAATCTTTATTTAAGGTCC
1 CTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCC
* * * *
2186 CTATTTAGGTGTCTCATCAAAAT-CTTGTTTAAGATCC
1 CTGTTTAGGTGTCTTATC-AAATCCTTATTTAAGGTCC
* *
2223 CTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTGC
1 CTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCC
* * ** * *
2260 CTGTTTAGGTTTCTTGTCAAAATTTTTGTTTAA-GACC
1 CTGTTTAGGTGTCTTATC-AAATCCTTATTTAAGGTCC
* *
2297 CTTGTTTAAGTTTCTTATCAAATCCTTATTTAAGGTCC
1 C-TGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCC
* * * * * * * *
2335 ATGTTTAAGTGTCTCATCAAAACCTTGTTCAAGATCA
1 CTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCC
* *
2372 CTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTAC
1 CTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCC
*
2409 ATGTTTAGGTGTCT
1 CTGTTTAGGTGTCT
2423 CTTCAAAATC
Statistics
Matches: 405, Mismatches: 80, Indels: 22
0.80 0.16 0.04
Matches are distributed among these distances:
36 14 0.03
37 348 0.86
38 43 0.11
ACGTcount: A:0.23, C:0.17, G:0.16, T:0.44
Consensus pattern (37 bp):
CTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCC
Found at i:2470 original size:149 final size:149
Alignment explanation
Indices: 2158--2458 Score: 379
Period size: 149 Copynumber: 2.0 Consensus size: 149
2148 CCTGTTTAGG
* * * * * * *
2158 TTTCTTATTAAATCTTTATTTAAGGTCCCTATTTAGGTGTCTCATCAAAATCTTGTTTAAGATCC
1 TTTCTTATCAAATCCTTATTTAAGGTCCATATTTAAGTGTCTCATCAAAACCTTGTTCAAGATCA
* * * ****
2223 CTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTGCCTGTTTAGGTTTCTTGTCAAAATTTTTG
66 CTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTACATGTTTAGGTGTCTTGTCAAAATCCCAG
* ** *
2288 TTTAAGACCCTTGTTTAAG
131 TTTAAGACCCTTATCAAAA
*
2307 TTTCTTATCAAATCCTTATTTAAGGTCCATGTTTAAGTGTCTCATCAAAACCTTGTTCAAGATCA
1 TTTCTTATCAAATCCTTATTTAAGGTCCATATTTAAGTGTCTCATCAAAACCTTGTTCAAGATCA
2372 CTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTACATGTTTAGGTGTCTCT-TCAAAATCCCA
66 CTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTACATGTTTAGGTGTCT-TGTCAAAATCCCA
* ***
2436 GTTTAGGTTTCTTATCAAAA
130 GTTTAAGACCCTTATCAAAA
2456 TTT
1 TTT
2459 TGTTCAAAAT
Statistics
Matches: 128, Mismatches: 23, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
149 127 0.99
150 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.13, T:0.45
Consensus pattern (149 bp):
TTTCTTATCAAATCCTTATTTAAGGTCCATATTTAAGTGTCTCATCAAAACCTTGTTCAAGATCA
CTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTACATGTTTAGGTGTCTTGTCAAAATCCCAG
TTTAAGACCCTTATCAAAA
Found at i:2611 original size:54 final size:54
Alignment explanation
Indices: 2532--2840 Score: 315
Period size: 54 Copynumber: 5.7 Consensus size: 54
2522 CTCTAGAAAA
* * *
2532 TTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTTAGAGGTCTAAA
1 TTGATCTTAAGATGACCCAGTGTGGTCTTCCATAGAAGTTTTTAGAGATCTAAG
* * *
2586 TTGATCTTAAGATGACCCAGTGTGGTCTTTCA-AAAAATTTTTCAGAGATCTAAG
1 TTGATCTTAAGATGACCCAGTGTGGTCTTCCATAGAAGTTTTT-AGAGATCTAAG
* * *
2640 TTGATCTTAAGATGACCCAGTTTGGTCTTCCATAGAAGCTTTTAGAGGTCTAAG
1 TTGATCTTAAGATGACCCAGTGTGGTCTTCCATAGAAGTTTTTAGAGATCTAAG
* * * * * * *
2694 TTGATCTTCAGACGACCCTGTGTGGTCTTCCATAGAAGTTTTCAAAAATCCAAG
1 TTGATCTTAAGATGACCCAGTGTGGTCTTCCATAGAAGTTTTTAGAGATCTAAG
* * *
2748 TTGATCTTAAAGTTGATCCAGTGTGGTCATTCCA-AGAAGTTTAT-GATGATC-AGAG
1 TTGATCTT-AAGATGACCCAGTGTGGTC-TTCCATAGAAGTTTTTAGA-GATCTA-AG
* *
2803 TTGATCTCTAA-ATTGATCCAGTGCGGTCGTTCCA-AGAA
1 TTGATCT-TAAGA-TGACCCAGTGTGGTC-TTCCATAGAA
2841 ATGTTTCCAT
Statistics
Matches: 215, Mismatches: 32, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
53 8 0.04
54 135 0.63
55 66 0.31
56 6 0.03
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (54 bp):
TTGATCTTAAGATGACCCAGTGTGGTCTTCCATAGAAGTTTTTAGAGATCTAAG
Found at i:2935 original size:33 final size:33
Alignment explanation
Indices: 2893--2970 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
2883 ATTAATTAAG
* * * *
2893 AAGTTCAAAATTTGCATTTCATTTCAAAATTCA
1 AAGTTCAAAATCTGCATATCATATCAAAACTCA
2926 AAGTTCAAAATCTGCATATCATATCAAAACTCA
1 AAGTTCAAAATCTGCATATCATATCAAAACTCA
2959 AAGTTCAAAATC
1 AAGTTCAAAATC
2971 CACAATTTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.32
Consensus pattern (33 bp):
AAGTTCAAAATCTGCATATCATATCAAAACTCA
Found at i:3362 original size:7 final size:7
Alignment explanation
Indices: 3127--3342 Score: 405
Period size: 7 Copynumber: 30.9 Consensus size: 7
3117 AATAGGCAAT
*
3127 TCAAAAT
1 TCAAAAC
*
3134 TCAAAAT
1 TCAAAAC
*
3141 TCAAAAT
1 TCAAAAC
3148 TCAAAAC
1 TCAAAAC
3155 TCAAAAC
1 TCAAAAC
3162 TCAAAAC
1 TCAAAAC
3169 TCAAAAC
1 TCAAAAC
3176 TCAAAAC
1 TCAAAAC
3183 TCAAAAC
1 TCAAAAC
3190 TCAAAAC
1 TCAAAAC
3197 TCAAAAC
1 TCAAAAC
3204 TCAAAAC
1 TCAAAAC
3211 TCAAAAC
1 TCAAAAC
3218 TCAAAAC
1 TCAAAAC
3225 TCAAAAC
1 TCAAAAC
3232 TCAAAAC
1 TCAAAAC
3239 TCAAAAC
1 TCAAAAC
3246 TCAAAAC
1 TCAAAAC
3253 TCAAAAC
1 TCAAAAC
3260 TCAAAAC
1 TCAAAAC
3267 TCAAAAC
1 TCAAAAC
3274 TCAAAAC
1 TCAAAAC
3281 TCAAAAC
1 TCAAAAC
3288 TCAAAAC
1 TCAAAAC
3295 TCAAAAC
1 TCAAAAC
3302 TCAAAAC
1 TCAAAAC
3309 TCAAAAC
1 TCAAAAC
3316 TCAAAAC
1 TCAAAAC
3323 TCAAAAC
1 TCAAAAC
3330 TCAAAAC
1 TCAAAAC
3337 TCAAAA
1 TCAAAA
3343 TTCATGGTTC
Statistics
Matches: 208, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 208 1.00
ACGTcount: A:0.57, C:0.27, G:0.00, T:0.16
Consensus pattern (7 bp):
TCAAAAC
Done.