Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012249.1 Corchorus olitorius cultivar O-4 contig12282, 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: 22125
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2185 original size:16 final size:16
Alignment explanation
Indices: 2155--2187 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2145 AGGGCACTTG
2155 GGGCACTTGGGCTCTT
1 GGGCACTTGGGCTCTT
2171 GGGC-CTTGGGCCTCTT
1 GGGCACTTGGG-CTCTT
2187 G
1 G
2188 ACTAATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.03, C:0.27, G:0.39, T:0.30
Consensus pattern (16 bp):
GGGCACTTGGGCTCTT
Found at i:5189 original size:3 final size:3
Alignment explanation
Indices: 5174--5211 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
5164 TTTCTTAAAA
* *
5174 AAG AAG AAA AAG AAG AAA AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
5212 AAACTTCACC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:5211 original size:9 final size:9
Alignment explanation
Indices: 5171--5208 Score: 67
Period size: 9 Copynumber: 4.2 Consensus size: 9
5161 CATTTTCTTA
5171 AAAAAGAAG
1 AAAAAGAAG
5180 AAAAAGAAG
1 AAAAAGAAG
5189 AAAAAGAAG
1 AAAAAGAAG
*
5198 AAGAAGAAG
1 AAAAAGAAG
5207 AA
1 AA
5209 GAAAAACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (9 bp):
AAAAAGAAG
Found at i:5777 original size:16 final size:16
Alignment explanation
Indices: 5758--5863 Score: 144
Period size: 16 Copynumber: 6.6 Consensus size: 16
5748 CGGGCTCGGG
5758 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
5774 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
* **
5790 CGGGCTCGGGT-TAAGT
1 CGGGTTCGGGTAT-TTT
5806 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
*
5822 CGGGTTCGGGT-TATGT
1 CGGGTTCGGGTAT-TTT
5838 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
5854 CGGGTTCGGG
1 CGGGTTCGGG
5864 CTCGGGTAGG
Statistics
Matches: 78, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
15 2 0.03
16 74 0.95
17 2 0.03
ACGTcount: A:0.07, C:0.14, G:0.42, T:0.38
Consensus pattern (16 bp):
CGGGTTCGGGTATTTT
Found at i:5800 original size:32 final size:32
Alignment explanation
Indices: 5758--5863 Score: 169
Period size: 32 Copynumber: 3.3 Consensus size: 32
5748 CGGGCTCGGG
*
5758 CGGGTTCGGG-TATTTTCGGGTTCGGGTATTTT
1 CGGGTTCGGGTTA-TGTCGGGTTCGGGTATTTT
* *
5790 CGGGCTCGGGTTAAGTCGGGTTCGGGTATTTT
1 CGGGTTCGGGTTATGTCGGGTTCGGGTATTTT
5822 CGGGTTCGGGTTATGTCGGGTTCGGGTATTTT
1 CGGGTTCGGGTTATGTCGGGTTCGGGTATTTT
5854 CGGGTTCGGG
1 CGGGTTCGGG
5864 CTCGGGTAGG
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
32 66 0.97
33 2 0.03
ACGTcount: A:0.07, C:0.14, G:0.42, T:0.38
Consensus pattern (32 bp):
CGGGTTCGGGTTATGTCGGGTTCGGGTATTTT
Found at i:5861 original size:6 final size:6
Alignment explanation
Indices: 5852--5894 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
5842 TTCGGGTATT
* * *
5852 TTCGGG TTCGGG CTCGGG -TAGGG TTCGGG TTCGGG CTCGGG TT
1 TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TT
5895 TGATTTTGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
5 4 0.13
6 27 0.87
ACGTcount: A:0.02, C:0.19, G:0.49, T:0.30
Consensus pattern (6 bp):
TTCGGG
Found at i:5870 original size:12 final size:12
Alignment explanation
Indices: 5853--5894 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
5843 TCGGGTATTT
5853 TCGGGTTCGGGC
1 TCGGGTTCGGGC
* *
5865 TCGGG-TAGGGT
1 TCGGGTTCGGGC
5876 TCGGGTTCGGGC
1 TCGGGTTCGGGC
5888 TCGGGTT
1 TCGGGTT
5895 TGATTTTGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.02, C:0.19, G:0.50, T:0.29
Consensus pattern (12 bp):
TCGGGTTCGGGC
Found at i:6753 original size:16 final size:16
Alignment explanation
Indices: 6728--6770 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
6718 TCGGGCTGCC
* *
6728 TCGGGTTCGGGTATTT
1 TCGGGCTCGGGTAATT
*
6744 TTGGGCTCGGGTAATT
1 TCGGGCTCGGGTAATT
*
6760 TCGGGTTCGGG
1 TCGGGCTCGGG
6771 ACGTTGACTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.07, C:0.14, G:0.42, T:0.37
Consensus pattern (16 bp):
TCGGGCTCGGGTAATT
Found at i:10493 original size:296 final size:293
Alignment explanation
Indices: 9959--10548 Score: 939
Period size: 296 Copynumber: 2.0 Consensus size: 293
9949 AATCTTGATT
* * **
9959 GCAATTGTTAAATTAATGAACTCGGGTAGACACATTTACAGCACTAATCCTTTGGAATTCTGGCA
1 GCAATTGTTAAATTAATGAACTCGGGTAGACACATTTACAACACCAATCCTTTGGAATTCCAGCA
10024 GAGGAGTTGAACCGGTAAATCCTAATATCCACACACAATCAATATGTAATTAAAACACACTTAAT
66 GAGGAGTTGAACCGGTAAATCCTAATATCCACACACAATCAATATGTAATTAAAACACACTTAAT
* * * *
10089 CATAAATATAAAAATAGTAAATTACAAAAAATGGCAGCATGAAAAGTAAGGGAGAAAATTCATCG
131 CATAAATACAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGTAAGGGAGAAAATTCATCA
* *
10154 AGAGCCTTTTTAGTCACCCGAAAAGTGAGAAAAGACAAAAAAAAAAACCAAAAGGAGGCACCACA
196 AGAGCCTTTTTAGTCACCCAAAAAGTAAGAAAAGAC--AAAAAAAAACCAAAAGGAGGCACCACA
10219 TTAATCCTCAATTTGGCCTTTTAAGTAATTTCCATA
259 TTAATCCTCAATTTGGCC-TTTAAGTAATTTCCATA
* * *
10255 GCAATTGTTAAATTAATGAACTCGGGTAGATACATTTATAACACCAATCCTTTGGAATTCCATCA
1 GCAATTGTTAAATTAATGAACTCGGGTAGACACATTTACAACACCAATCCTTTGGAATTCCAGCA
*
10320 GAGGAGTTGAACCGGTAAATCCTAATATCCACACACAATTAATATGTAATTAAAACACACTTAAT
66 GAGGAGTTGAACCGGTAAATCCTAATATCCACACACAATCAATATGTAATTAAAACACACTTAAT
* * * *
10385 CATAAATACAAAAATAGTAAATTACAAAAAAGGGTAGGAGGAAAAGTAAGGTAGGAAATTCATCA
131 CATAAATACAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGTAAGGGAGAAAATTCATCA
* * *
10450 AGGGCCTTTTTAGTCACTCAAAAAGTAAGAAAAGATC-AAAAAAAGCCAAAAGGAGGCACCACAT
196 AGAGCCTTTTTAGTCACCCAAAAAGTAAGAAAAGA-CAAAAAAAAACCAAAAGGAGGCACCACAT
*
10514 TAATTCTCAATTTGGCCTTTAAGTAATTTCCATA
260 TAATCCTCAATTTGGCCTTTAAGTAATTTCCATA
10548 G
1 G
10549 TCACTAAAAA
Statistics
Matches: 271, Mismatches: 22, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
293 18 0.07
294 42 0.15
296 210 0.77
297 1 0.00
ACGTcount: A:0.43, C:0.17, G:0.16, T:0.25
Consensus pattern (293 bp):
GCAATTGTTAAATTAATGAACTCGGGTAGACACATTTACAACACCAATCCTTTGGAATTCCAGCA
GAGGAGTTGAACCGGTAAATCCTAATATCCACACACAATCAATATGTAATTAAAACACACTTAAT
CATAAATACAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGTAAGGGAGAAAATTCATCA
AGAGCCTTTTTAGTCACCCAAAAAGTAAGAAAAGACAAAAAAAAACCAAAAGGAGGCACCACATT
AATCCTCAATTTGGCCTTTAAGTAATTTCCATA
Found at i:21887 original size:26 final size:27
Alignment explanation
Indices: 21858--21908 Score: 95
Period size: 26 Copynumber: 1.9 Consensus size: 27
21848 CAAATTAATT
21858 ATCATTAAATTTTAAACAC-TTAAAAA
1 ATCATTAAATTTTAAACACATTAAAAA
21884 ATCATTAAATTTTAAACACATTAAA
1 ATCATTAAATTTTAAACACATTAAA
21909 TTATAGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (27 bp):
ATCATTAAATTTTAAACACATTAAAAA
Found at i:21907 original size:16 final size:16
Alignment explanation
Indices: 21860--21910 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 16
21850 AATTAATTAT
21860 CATTAAATTTTAAACA
1 CATTAAATTTTAAACA
*
21876 C-TTAAA----AAA-T
1 CATTAAATTTTAAACA
21886 CATTAAATTTTAAACA
1 CATTAAATTTTAAACA
21902 CATTAAATT
1 CATTAAATT
21911 ATAGAAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 12
0.66 0.05 0.29
Matches are distributed among these distances:
10 1 0.04
11 8 0.30
15 8 0.30
16 10 0.37
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (16 bp):
CATTAAATTTTAAACA
Done.