Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013139.1 Corchorus olitorius cultivar O-4 contig13172, 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: 7275
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1045 original size:27 final size:27
Alignment explanation
Indices: 1015--1071 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
1005 AAATCACTAC
1015 TATAAACTATGGAATATGCAGGTCTAA
1 TATAAACTATGGAATATGCAGGTCTAA
1042 TATAAACTATGGAATATGCAGGTCTAA
1 TATAAACTATGGAATATGCAGGTCTAA
1069 TAT
1 TAT
1072 GGAAAATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.32
Consensus pattern (27 bp):
TATAAACTATGGAATATGCAGGTCTAA
Found at i:1612 original size:35 final size:35
Alignment explanation
Indices: 1559--1829 Score: 449
Period size: 35 Copynumber: 7.8 Consensus size: 35
1549 AATTCTGGTC
*
1559 TTTGAAGA-GCTGCACCGAGTCATCTGGATTCAAT
1 TTTGAAGATGCTACACCGAGTCATCTGGATTCAAT
*
1593 TTTGAAGATGCTGCACCGAGTCATCTGGATTCAAT
1 TTTGAAGATGCTACACCGAGTCATCTGGATTCAAT
*
1628 TTTGAAGATGCTGCACCGAGTCATCTGGATTCAAT
1 TTTGAAGATGCTACACCGAGTCATCTGGATTCAAT
*
1663 TTTGAAGATGCTGCACCGAGTCATCTGGATTCAAT
1 TTTGAAGATGCTACACCGAGTCATCTGGATTCAAT
1698 TTTGAAGATGCTACACCGAGTCATCT-GAGTTC-AT
1 TTTGAAGATGCTACACCGAGTCATCTGGA-TTCAAT
*
1732 CTTTGAAGATGCTACACCGAGTCATCTGGATTCAAC
1 -TTTGAAGATGCTACACCGAGTCATCTGGATTCAAT
*
1768 TTTGAAGATGCTACACCGAGTCATCTGGATTCAAC
1 TTTGAAGATGCTACACCGAGTCATCTGGATTCAAT
1803 TTTGAAGATGCTACACCGAGTCATCTG
1 TTTGAAGATGCTACACCGAGTCATCTG
1830 AAGATGGTAA
Statistics
Matches: 230, Mismatches: 2, Indels: 9
0.95 0.01 0.04
Matches are distributed among these distances:
34 12 0.05
35 215 0.93
36 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (35 bp):
TTTGAAGATGCTACACCGAGTCATCTGGATTCAAT
Found at i:2081 original size:106 final size:105
Alignment explanation
Indices: 1847--2351 Score: 769
Period size: 105 Copynumber: 4.8 Consensus size: 105
1837 TAATGCACCG
* * * ** * ** * * *
1847 TATGGAAACGAACTGTGGCTTGTGGAAAAGCCTATGTGGCTTGGACGGAACCAAGGTTTGAATTG
1 TATGGAAATGAGCT-TGGCTTATGGAAAAGCCCCTGTTGCTTGGGTGGAACCAAGGCTTCAACTG
*
1912 ACTCGCATGGAAACGAGTTTAGTCTTGGAAGACTGAATTCA
65 ACTCGTATGGAAACGAGTTTAGTCTTGGAAGACTGAATTCA
* * * *
1953 TATGGAAATGAACTTGGCTTATGGGAAAGCCTCTATTGCTTGGGTGGAACCAAGGCTTCAACTGA
1 TATGGAAATGAGCTTGGCTTATGGAAAAGCCCCTGTTGCTTGGGTGGAACCAAGGCTTCAACTGA
*
2018 CTCGTATGGAAACAAGTTTAGTCTTGGGAAGACTGAATTCA
66 CTCGTATGGAAACGAGTTTAGTCTT-GGAAGACTGAATTCA
*
2059 TATGGAAATGAGCTTGGCTTATGGAAAAACCCCTGTTGCTTGGGTGGAACCAAGGCTTCAACTGA
1 TATGGAAATGAGCTTGGCTTATGGAAAAGCCCCTGTTGCTTGGGTGGAACCAAGGCTTCAACTGA
* *
2124 CTCGCATGGAAACGAGTTTAGTCTTGGAAGATTGAATTCA
66 CTCGTATGGAAACGAGTTTAGTCTTGGAAGACTGAATTCA
**
2164 TATGGAAATGAGCTTGGCTGGTGGAAAAGCCCCTGTTGCTTGGGTGGAACCAAGGCTTCAACTGA
1 TATGGAAATGAGCTTGGCTTATGGAAAAGCCCCTGTTGCTTGGGTGGAACCAAGGCTTCAACTGA
* *
2229 CTCGTATGGAAACGAGTTT-GGCTTAGAAGACTGAATTCA
66 CTCGTATGGAAACGAGTTTAGTCTTGGAAGACTGAATTCA
2268 TATGGAAATGAGCTTGGCTTATGGAAAAGCCCCTGTTGCTTGGGTGGAACCAAGGCTTCAACTGA
1 TATGGAAATGAGCTTGGCTTATGGAAAAGCCCCTGTTGCTTGGGTGGAACCAAGGCTTCAACTGA
2333 CTCGTATGGAAACGAGTTT
66 CTCGTATGGAAACGAGTTT
2352 GGCTTATGGA
Statistics
Matches: 368, Mismatches: 30, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
104 99 0.27
105 158 0.43
106 111 0.30
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27
Consensus pattern (105 bp):
TATGGAAATGAGCTTGGCTTATGGAAAAGCCCCTGTTGCTTGGGTGGAACCAAGGCTTCAACTGA
CTCGTATGGAAACGAGTTTAGTCTTGGAAGACTGAATTCA
Found at i:2233 original size:211 final size:209
Alignment explanation
Indices: 1847--2351 Score: 776
Period size: 211 Copynumber: 2.4 Consensus size: 209
1837 TAATGCACCG
* * * ** * ** * * *
1847 TATGGAAACGAACTGTGGCTTGTGGAAAAGCCTATGTGGCTTGGACGGAACCAAGGTTTGAATTG
1 TATGGAAATGAGCT-TGGCTTATGGAAAAGCCCCTGTTGCTTGGGTGGAACCAAGGCTTCAACTG
*
1912 ACTCGCATGGAAACGAGTTTAGTCTTGGAAGACTGAATTCATATGGAAATGAACTTGGCTTATGG
65 ACTCGCATGGAAACGAGTTTAGTCTTGGAAGACTGAATTCATATGGAAATGAACTTGGCTGATGG
* * *
1977 GAAAGCCTCTATTGCTTGGGTGGAACCAAGGCTTCAACTGACTCGTATGGAAACAAGTTTAGTCT
130 AAAAGCCCCTATTGCTTGGGTGGAACCAAGGCTTCAACTGACTCGTATGGAAACAAGTTT-GGCT
*
2042 TGGGAAGACTGAATTCA
194 T-AGAAGACTGAATTCA
*
2059 TATGGAAATGAGCTTGGCTTATGGAAAAACCCCTGTTGCTTGGGTGGAACCAAGGCTTCAACTGA
1 TATGGAAATGAGCTTGGCTTATGGAAAAGCCCCTGTTGCTTGGGTGGAACCAAGGCTTCAACTGA
* * *
2124 CTCGCATGGAAACGAGTTTAGTCTTGGAAGATTGAATTCATATGGAAATGAGCTTGGCTGGTGGA
66 CTCGCATGGAAACGAGTTTAGTCTTGGAAGACTGAATTCATATGGAAATGAACTTGGCTGATGGA
* *
2189 AAAGCCCCTGTTGCTTGGGTGGAACCAAGGCTTCAACTGACTCGTATGGAAACGAGTTTGGCTTA
131 AAAGCCCCTATTGCTTGGGTGGAACCAAGGCTTCAACTGACTCGTATGGAAACAAGTTTGGCTTA
2254 GAAGACTGAATTCA
196 GAAGACTGAATTCA
2268 TATGGAAATGAGCTTGGCTTATGGAAAAGCCCCTGTTGCTTGGGTGGAACCAAGGCTTCAACTGA
1 TATGGAAATGAGCTTGGCTTATGGAAAAGCCCCTGTTGCTTGGGTGGAACCAAGGCTTCAACTGA
*
2333 CTCGTATGGAAACGAGTTT
66 CTCGCATGGAAACGAGTTT
2352 GGCTTATGGA
Statistics
Matches: 269, Mismatches: 24, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
209 96 0.36
210 4 0.01
211 157 0.58
212 12 0.04
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27
Consensus pattern (209 bp):
TATGGAAATGAGCTTGGCTTATGGAAAAGCCCCTGTTGCTTGGGTGGAACCAAGGCTTCAACTGA
CTCGCATGGAAACGAGTTTAGTCTTGGAAGACTGAATTCATATGGAAATGAACTTGGCTGATGGA
AAAGCCCCTATTGCTTGGGTGGAACCAAGGCTTCAACTGACTCGTATGGAAACAAGTTTGGCTTA
GAAGACTGAATTCA
Found at i:3157 original size:49 final size:49
Alignment explanation
Indices: 3101--3195 Score: 138
Period size: 49 Copynumber: 1.9 Consensus size: 49
3091 TGATCTTAGA
*
3101 CTCACAAAT-TAAATGCAATCTTACTTTGAAAAGCGAATTTTAATCTGGG
1 CTCACAAATGGAAA-GCAATCTTACTTTGAAAAGCGAATTTTAATCTGGG
** *
3150 CTCACAAATGGAAAGCAATCTTGTTTTGAAAAGCGAATTTTGATCT
1 CTCACAAATGGAAAGCAATCTTACTTTGAAAAGCGAATTTTAATCT
3196 TGCAAACTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
49 38 0.93
50 3 0.07
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (49 bp):
CTCACAAATGGAAAGCAATCTTACTTTGAAAAGCGAATTTTAATCTGGG
Found at i:3211 original size:33 final size:33
Alignment explanation
Indices: 3164--3230 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
3154 CAAATGGAAA
*
3164 GCAATCTTGTTTTGAAAAGCGAATTTTGATCTT
1 GCAAACTTGTTTTGAAAAGCGAATTTTGATCTT
3197 GCAAACTTGTTTTGAAAAGCGAATTTTGATCTT
1 GCAAACTTGTTTTGAAAAGCGAATTTTGATCTT
3230 G
1 G
3231 AACTCACAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.40
Consensus pattern (33 bp):
GCAAACTTGTTTTGAAAAGCGAATTTTGATCTT
Found at i:3911 original size:12 final size:12
Alignment explanation
Indices: 3894--3925 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
3884 TTTTGCTTTT
3894 GATTTGAACTTC
1 GATTTGAACTTC
3906 GATTTGAACTTC
1 GATTTGAACTTC
3918 GATTTGAA
1 GATTTGAA
3926 TTATTTGATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (12 bp):
GATTTGAACTTC
Done.