Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012488.1 Corchorus olitorius cultivar O-4 contig12521, 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: 61795
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:837 original size:203 final size:200
Alignment explanation
Indices: 1--1136 Score: 1600
Period size: 199 Copynumber: 5.7 Consensus size: 200
* * * * *
1 AATCCCTATAAGAAAAATTACACAATACACAGTTAGTGGAGTTTAAGCAGATTGCACGTGCGAGG
1 AATCCCTATAAGAAAAATTATACAATACACCGTCAGTGGAGTTT-AGCAGACTGCACGTGCGGGG
* * *
66 TTTAAGGGTTGACATGTGTCCCATTAGGGAATATGTATCAATATTAAATATATCTAATTTATTAT
65 TTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATAT-T-TAATTAATTAT
** ** *
131 GAAATGGGGTATGTGTCAATTTCTTAACCAACTTATGGAGTCCAAATTTTACACTGACAGTGTAT
128 GAAATGGGGTATGTGTCAACCTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTAT
196 TGTATAAT
193 TGTATAAT
* * * *
204 AATCCCTATAAGAAAAATTATACAATACACCATTAGTGGAGTTTAGCAGAATGCACGTGTGGGGT
1 AATCCCTATAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGT
* * *
269 TTAAGGGTTGACATGTGTCCCATTAGGGAATATGTATTAATATTAAATATTGAATTGATTATGAA
66 TTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAA
*
334 ATGGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGT
131 ATGGGGTATGTGTCAACCTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGT
399 ATAAT
196 ATAAT
** * *
404 -ATTACTATAAGAAAAATTATACAATACACAGTCAGTGGAGTTTAGCAGACTGCATGTGCGGGGT
1 AATCCCTATAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGT
** *
468 TTAAGGGTCAACATGTGTCCCCTTAGGGAATATGTATTGATATTAAATATATTTAATTAATTATG
66 TTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATT-AA-ATATTTAATTAATTATG
* * * *
533 AAATGGGGTATGTGGCAA-CTTTCTAACCCGCTTATAGAGTCCAAAATTTACACCGACAGTGTAT
129 AAATGGGGTATGTGTCAACCTCT-TAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTAT
597 TGTATAAT
193 TGTATAAT
* *
605 AATCCCTATAAGAAAAATTATACAATACACCGTTAGTGGA-TCTTAGCAGACTGCACGTGTGGGG
1 AATCCCTATAAGAAAAATTATACAATACACCGTCAGTGGAGT-TTAGCAGACTGCACGTGCGGGG
669 TTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTCTTAATTAATATTAAATATTTAATTAATT
65 TTTAAGGGTTGACATGTGTCCCCTTAGGGAATATG---T-ATTAATATTAAATATTTAATTAATT
*
734 ATGAAAT-GGGTATGTGTCAACCTCTTAACCCACTTATGGAGTCCAAAATTTACACTGACAGTGT
126 ATGAAATGGGGTATGTGTCAACCTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGT
*
798 ATTGCATAAT
191 ATTGTATAAT
* *
808 AATCCCTATAAGAAAAATTATATAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGTGGGGT
1 AATCCCTATAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGT
* * *
873 TTAAGGGTTGGCATATGTCTCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAA
66 TTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAA
* * * * *
938 AT-GAGTATGTGTCAACCTTTTAACCCGTTTATGGAGTCCAAAATTTACACTTACAATGTATTGT
131 ATGGGGTATGTGTCAACCTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGT
1002 ATAAT
196 ATAAT
* * * * * **
1007 AAT-CATATAAGAAAAATTATAGAATACAACGTCAGTAGAGTTTAGCAGACTGCACGGGCGATGT
1 AATCCCTATAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGT
* * ** * *
1071 GTAAGGGTTGACATGTGTCGCCTTAGGGAATACATGTTAATATTTAATATTTAATTAATTATGAA
66 TTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAA
1136 A
131 A
1137 AAGCTCAGTT
Statistics
Matches: 847, Mismatches: 75, Indels: 27
0.89 0.08 0.03
Matches are distributed among these distances:
198 111 0.13
199 191 0.23
200 83 0.10
201 81 0.10
202 155 0.18
203 190 0.22
204 25 0.03
205 3 0.00
206 8 0.01
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.33
Consensus pattern (200 bp):
AATCCCTATAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGT
TTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAA
ATGGGGTATGTGTCAACCTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGT
ATAAT
Found at i:1018 original size:401 final size:399
Alignment explanation
Indices: 1--1136 Score: 1631
Period size: 401 Copynumber: 2.8 Consensus size: 399
* * * *
1 AATCCCTATAAGAAAAATTACACAATACACAGTTAGTGGAGTTTAAGCAGATTGCACGTGCGAGG
1 AATCCCTATAAGAAAAATTATACAATACACAGTCAGTGGAGTTT-AGCAGACTGCACGTGCGGGG
* *
66 TTTAAGGGTTGACATGTGTCCCATTAGGGAATATGTATCAATATTAAATATATCTAATTTATTAT
65 TTTAAGGGTTGACATGTGTCCC-TTAGGGAATATGTATTAATATTAAATAT-T-TAATTAATTAT
* ** *
131 GAAATGGGGTATGTGTCAATTTCTTAACCAACTTATGGAGTCCAAATTTTACACTGACAGTGTAT
127 GAAATGGGGTATGTGTCAACTT-TTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTAT
* *
196 TGTATAATAATCCCTATAAGAAAAATTATACAATACACCATTAGTGGAGTTTAGCAGAATGCACG
191 TGTATAATAATCCCTATAAGAAAAATTATACAATACACCGTTAGTGGAGTTTAGCAGACTGCACG
* *
261 TGTGGGGTTTAAGGGTTGACATGTGTCCCATTAGGGAATATG-TATTAATATTAAATATTGAATT
256 TGTGGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGCTATTAATATTAAATATTTAATT
* * *
325 GATTATGAAATGGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACA
321 AATTATGAAATGGGGTATGTGTCAACCTCTTAACCCACTTATGGAGTCCAAAATTTACACTGACA
*
390 GTGTATTGTATAAT
386 GTGTATTGCATAAT
** *
404 -ATTACTATAAGAAAAATTATACAATACACAGTCAGTGGAGTTTAGCAGACTGCATGTGCGGGGT
1 AATCCCTATAAGAAAAATTATACAATACACAGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGT
** *
468 TTAAGGGTCAACATGTGTCCCCTTAGGGAATATGTATTGATATTAAATATATTTAATTAATTATG
66 TTAAGGGTTGACATGTGT-CCCTTAGGGAATATGTATTAATATT-AA-ATATTTAATTAATTATG
* * *
533 AAATGGGGTATGTGGCAACTTTCTAACCCGCTTATAGAGTCCAAAATTTACACCGACAGTGTATT
128 AAATGGGGTATGTGTCAACTTT-TAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATT
598 GTATAATAATCCCTATAAGAAAAATTATACAATACACCGTTAGTGGA-TCTTAGCAGACTGCACG
192 GTATAATAATCCCTATAAGAAAAATTATACAATACACCGTTAGTGGAGT-TTAGCAGACTGCACG
662 TGTGGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTCTTAATTAATATTAAATATTTA
256 TGTGGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATG-C-T-ATTAATATTAAATATTTA
727 ATTAATTATGAAAT-GGGTATGTGTCAACCTCTTAACCCACTTATGGAGTCCAAAATTTACACTG
318 ATTAATTATGAAATGGGGTATGTGTCAACCTCTTAACCCACTTATGGAGTCCAAAATTTACACTG
791 ACAGTGTATTGCATAAT
383 ACAGTGTATTGCATAAT
* * *
808 AATCCCTATAAGAAAAATTATATAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGTGGGGT
1 AATCCCTATAAGAAAAATTATACAATACACAGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGT
* *
873 TTAAGGGTTGGCATATGTCTCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAA
66 TTAAGGGTTGACATGTGTC-CCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAA
* * * *
938 AT-GAGTATGTGTCAACCTTTTAACCCGTTTATGGAGTCCAAAATTTACACTTACAATGTATTGT
130 ATGGGGTATGTGTCAA-CTTTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGT
* * * * * * *
1002 ATAATAAT-CATATAAGAAAAATTATAGAATACAACGTCAGTAGAGTTTAGCAGACTGCACGGGC
194 ATAATAATCCCTATAAGAAAAATTATACAATACACCGTTAGTGGAGTTTAGCAGACTGCACGTGT
** * * * *
1066 GATGTGTAAGGGTTGACATGTGTCGCCTTAGGGAATA--CATGTTAATATTTAATATTTAATTAA
259 GGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGC-TATTAATATTAAATATTTAATTAA
1129 TTATGAAA
323 TTATGAAA
1137 AAGCTCAGTT
Statistics
Matches: 661, Mismatches: 59, Indels: 32
0.88 0.08 0.04
Matches are distributed among these distances:
397 29 0.04
398 2 0.00
400 2 0.00
401 302 0.46
402 104 0.16
403 29 0.04
404 68 0.10
405 125 0.19
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.33
Consensus pattern (399 bp):
AATCCCTATAAGAAAAATTATACAATACACAGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGT
TTAAGGGTTGACATGTGTCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAA
TGGGGTATGTGTCAACTTTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTAT
AATAATCCCTATAAGAAAAATTATACAATACACCGTTAGTGGAGTTTAGCAGACTGCACGTGTGG
GGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGCTATTAATATTAAATATTTAATTAATTA
TGAAATGGGGTATGTGTCAACCTCTTAACCCACTTATGGAGTCCAAAATTTACACTGACAGTGTA
TTGCATAAT
Found at i:1166 original size:16 final size:16
Alignment explanation
Indices: 1145--1175 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1135 AAAAGCTCAG
*
1145 TTAATAAGGTTACTAA
1 TTAATAAGATTACTAA
1161 TTAATAAGATTACTA
1 TTAATAAGATTACTA
1176 TACAACTTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (16 bp):
TTAATAAGATTACTAA
Found at i:6805 original size:12 final size:12
Alignment explanation
Indices: 6788--6896 Score: 85
Period size: 12 Copynumber: 9.1 Consensus size: 12
6778 CGTGACCGCA
*
6788 ATAGGGATAGGG
1 ATAGGGACAGGG
6800 ATAGGGACAGGG
1 ATAGGGACAGGG
*
6812 ACAGGGACAGGG
1 ATAGGGACAGGG
* *
6824 ACAGGGGCAGGG
1 ATAGGGACAGGG
* *
6836 ATTGGGATC-GTG
1 ATAGGGA-CAGGG
* * *
6848 ATAAGGAAAGGC
1 ATAGGGACAGGG
* *
6860 AGAGGGAGAGGG
1 ATAGGGACAGGG
*
6872 ATAGGGGCAGGG
1 ATAGGGACAGGG
*
6884 ACAGGGACAGGG
1 ATAGGGACAGGG
6896 A
1 A
6897 CCGGGACCGT
Statistics
Matches: 74, Mismatches: 21, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
12 73 0.99
13 1 0.01
ACGTcount: A:0.32, C:0.09, G:0.50, T:0.08
Consensus pattern (12 bp):
ATAGGGACAGGG
Found at i:6817 original size:18 final size:18
Alignment explanation
Indices: 6790--6903 Score: 86
Period size: 18 Copynumber: 6.3 Consensus size: 18
6780 TGACCGCAAT
*
6790 AGGGATAGGGATAGGGAC
1 AGGGACAGGGATAGGGAC
*
6808 AGGGACAGGGACAGGGAC
1 AGGGACAGGGATAGGGAC
* *
6826 AGGGGCAGGGATTGGGATC
1 AGGGACAGGGATAGGGA-C
* * * * * *
6845 -GTGATAAGGAAAGGCAG
1 AGGGACAGGGATAGGGAC
* *
6862 AGGGAGAGGGATAGGGGC
1 AGGGACAGGGATAGGGAC
*
6880 AGGGACAGGGACAGGGAC
1 AGGGACAGGGATAGGGAC
*
6898 CGGGAC
1 AGGGAC
6904 CGTGATTGGG
Statistics
Matches: 70, Mismatches: 24, Indels: 4
0.71 0.24 0.04
Matches are distributed among these distances:
18 69 0.99
19 1 0.01
ACGTcount: A:0.31, C:0.11, G:0.51, T:0.07
Consensus pattern (18 bp):
AGGGACAGGGATAGGGAC
Found at i:6905 original size:6 final size:6
Alignment explanation
Indices: 6790--6903 Score: 77
Period size: 6 Copynumber: 19.0 Consensus size: 6
6780 TGACCGCAAT
* * * *
6790 AGGGAT AGGGAT AGGGAC AGGGAC AGGGAC AGGGAC AGGGGC AGGGAT
1 AGGGAC AGGGAC AGGGAC AGGGAC AGGGAC AGGGAC AGGGAC AGGGAC
* * * * * * * * * *
6838 TGGGATC -GTGAT AAGGAA AGGCAG AGGGAG AGGGAT AGGGGC AGGGAC
1 AGGGA-C AGGGAC AGGGAC AGGGAC AGGGAC AGGGAC AGGGAC AGGGAC
*
6886 AGGGAC AGGGAC CGGGAC
1 AGGGAC AGGGAC AGGGAC
6904 CGTGATTGGG
Statistics
Matches: 86, Mismatches: 20, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
6 86 1.00
ACGTcount: A:0.31, C:0.11, G:0.51, T:0.07
Consensus pattern (6 bp):
AGGGAC
Found at i:6979 original size:6 final size:6
Alignment explanation
Indices: 6970--6995 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
6960 GGACAAGGAG
6970 AGGGAT AGGGAT AGGGAT AGGGAT AG
1 AGGGAT AGGGAT AGGGAT AGGGAT AG
6996 AAGGCACGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.50, T:0.15
Consensus pattern (6 bp):
AGGGAT
Found at i:11899 original size:14 final size:15
Alignment explanation
Indices: 11874--11902 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
11864 TAAACCACTG
11874 AAATGTAAAAAAAAA
1 AAATGTAAAAAAAAA
11889 AAATG-AAAAAAAAA
1 AAATGTAAAAAAAAA
11903 GAAAGAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (15 bp):
AAATGTAAAAAAAAA
Found at i:13645 original size:47 final size:47
Alignment explanation
Indices: 13593--14042 Score: 582
Period size: 47 Copynumber: 10.0 Consensus size: 47
13583 GAAGAATTTT
*
13593 GTAGTAAAAGAAGGAGAAATTAGTTTAATTCTAGGTAATTAAACTAA
1 GTAGTAAAAGAAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAA
* *
13640 GTAGTAAAA-AAGAAGAAATTAGTTTAATTCAAGGTAGTTAAAC---
1 GTAGTAAAAGAAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAA
* *
13683 ----T-----AAGAAGAATTTGGTTTAATTCTAGGTAATTAAACTAA
1 GTAGTAAAAGAAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAA
13721 GTAGTAAAA-AAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAA
1 GTAGTAAAAGAAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAA
* *
13767 GTAGTAAAAAAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAA
1 GTAGTAAAAGAAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAA
*
13814 GTAGTAAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACT-A
1 GTAGTAAAAGAAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAA
* * *
13860 --AGCAAAAGGAGAAGAGATTAGTTTAATTCTAGGTAATTAAACT-A
1 GTAGTAAAAGAAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAA
* *
13904 --AGTAAAAGGAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAA
1 GTAGTAAAAGAAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAA
* *
13949 GTAGTAAAAGAAGAAGAGACTAGTTTAATTCTAGGTAATTAAACTAA
1 GTAGTAAAAGAAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAA
* * *
13996 GTAGTAGAAGAAGGAA-AGATTAGTTTAATTCTAGGTAACTAAACTAA
1 GTAGTAAAAGAA-GAAGAAATTAGTTTAATTCTAGGTAATTAAACTAA
14043 AAGAAGAAGT
Statistics
Matches: 368, Mismatches: 19, Indels: 32
0.88 0.05 0.08
Matches are distributed among these distances:
35 30 0.08
39 1 0.00
42 1 0.00
44 84 0.23
45 1 0.00
46 76 0.21
47 172 0.47
48 3 0.01
ACGTcount: A:0.47, C:0.05, G:0.19, T:0.30
Consensus pattern (47 bp):
GTAGTAAAAGAAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAA
Found at i:13688 original size:35 final size:35
Alignment explanation
Indices: 13649--13721 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
13639 AGTAGTAAAA
*
13649 AAGAAGAAATTAGTTTAATTCAAGGTAGTTAAACT
1 AAGAAGAAATTAGTTTAATTCAAGGTAATTAAACT
* * *
13684 AAGAAGAATTTGGTTTAATTCTAGGTAATTAAACT
1 AAGAAGAAATTAGTTTAATTCAAGGTAATTAAACT
13719 AAG
1 AAG
13722 TAGTAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.44, C:0.05, G:0.18, T:0.33
Consensus pattern (35 bp):
AAGAAGAAATTAGTTTAATTCAAGGTAATTAAACT
Found at i:13730 original size:81 final size:85
Alignment explanation
Indices: 13611--14051 Score: 491
Period size: 91 Copynumber: 5.0 Consensus size: 85
13601 AGAAGGAGAA
*
13611 ATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAAAGAAGAAATTAGTTTAATTCAAGGTA
1 ATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAAAGAAGAAATTAGTTTAATTCTAGGTA
*
13676 GTTAAACTAAG-AAG-A-A-
66 ATTAAACTAAGAAAGAAGAG
* *
13692 TTTGGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAAAGAAGAAATTAGTTTAATTCTAGGTA
1 ATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAAAGAAGAAATTAGTTTAATTCTAGGTA
13757 ATTAAACTAAGTAGTAAAAAAAGAAGAG
66 ATTAAACT-A--AG-----AAAGAAGAG
*
13785 ATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGATTAGTTTAATTCTAGGT
1 ATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAA-AAGAAGAAATTAGTTTAATTCTAGGT
13850 AATTAAACTAAGCAAAAGGAGAAGAG
65 AATTAAACTAAG---AA--AGAAGAG
** *
13876 ATTAGTTTAATTCTAGGTAATTAAACTAAGTA--AAAGGAGAAGAGATTAGTTTAATTCTAGGTA
1 ATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAAAGAAGAAATTAGTTTAATTCTAGGTA
13939 ATTAAACTAAGTAGTAAAAGAAGAAGAG
66 ATTAAACT-A--AG----A-AAGAAGAG
* * *
13967 ACTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAGAAGAAGGAA-AGATTAGTTTAATTCTAGG
1 ATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTA-AA-AAAGAAGAAATTAGTTTAATTCTAGG
* *
14031 TAACTAAACTAAAAGAAGAAG
64 TAATTAAACTAAGA-AAGAAG
14052 TAAACAGAGA
Statistics
Matches: 319, Mismatches: 17, Indels: 42
0.84 0.04 0.11
Matches are distributed among these distances:
81 69 0.22
82 1 0.00
84 2 0.01
87 8 0.03
88 34 0.11
89 8 0.03
90 3 0.01
91 83 0.26
92 4 0.01
93 40 0.13
94 64 0.20
95 3 0.01
ACGTcount: A:0.47, C:0.05, G:0.18, T:0.30
Consensus pattern (85 bp):
ATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAAAGAAGAAATTAGTTTAATTCTAGGTA
ATTAAACTAAGAAAGAAGAG
Found at i:13957 original size:182 final size:174
Alignment explanation
Indices: 13593--14047 Score: 657
Period size: 182 Copynumber: 2.6 Consensus size: 174
13583 GAAGAATTTT
* * *
13593 GTAGTAAAAGAAGGAGAAATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAA-AAGAAGAA
1 GTAGTAAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAG
* * * *
13657 ATTAGTTTAATTCAAGGTAGTTAAACTAAGAAGAATTTGGTTTAATTCTAGGTAATTAAACTAAG
66 ATTAGTTTAATTCTAGGTAATTAAACTAAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAAG
13722 TAGTAAAAAAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAA
131 TAG-AAAAAAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAA
*
13767 GTAGTAAAAAAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAG
1 GTAGTAAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAG
13832 ATTAGTTTAATTCTAGGTAATTAAACTAAGCAAAAGGAGAAGAGATTAGTTTAATTCTAGGTAAT
66 ATTAGTTTAATTCTAGGTAATTAAACTAAG----A--AG-A-A-ATTAGTTTAATTCTAGGTAAT
** *
13897 TAAACTAAGTA-AAAGGAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAA
122 TAAACTAAGTAGAAAAAAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAA
* *
13949 GTAGTAAAAGAAGAAGAGACTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAGAAGAAGGAA-A
1 GTAGTAAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAA-GAAGA
*
14013 GATTAGTTTAATTCTAGGTAACTAAACTAA-AAGAA
65 GATTAGTTTAATTCTAGGTAATTAAACTAAGAAGAA
14048 GAAGTAAACA
Statistics
Matches: 255, Mismatches: 15, Indels: 23
0.87 0.05 0.08
Matches are distributed among these distances:
173 1 0.00
174 54 0.21
175 37 0.15
177 1 0.00
179 1 0.00
181 2 0.01
182 125 0.49
183 4 0.02
184 30 0.12
ACGTcount: A:0.47, C:0.05, G:0.19, T:0.29
Consensus pattern (174 bp):
GTAGTAAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAG
ATTAGTTTAATTCTAGGTAATTAAACTAAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAAG
TAGAAAAAAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAA
Found at i:28484 original size:152 final size:151
Alignment explanation
Indices: 28202--28504 Score: 579
Period size: 152 Copynumber: 2.0 Consensus size: 151
28192 TTTAATGAGA
28202 AGATGGAGAACCAATTTATATATTCAGTCATTTAATCTGGTACATCCATCAAATAGCCAGTTTAA
1 AGATGGAGAACCAATTTATATATTCAGTCATTTAATCTGGTACATCCATCAAATAGCCAGTTTAA
28267 CGGTTGAGATTCATTTGACTATTAAATGTACTTAAATATCTCCCCATTGACATAATTAGACAGAT
66 CGGTTGAGATTCATTTGACTATTAAATGTACTTAAATATCTCCCCATTGACATAATTAGACAGAT
28332 TTGATATTAAACCACAATAATG
131 TTGATA-TAAACCACAATAATG
28354 AGATGGAGAACCAATTTATATATTCAGTCATTTAATCTGGTACATCCATCAAATAGCCAGTTTAA
1 AGATGGAGAACCAATTTATATATTCAGTCATTTAATCTGGTACATCCATCAAATAGCCAGTTTAA
**
28419 CGGTTGAGATTCATTTGACTATTAAATGTACTTAAATATCTCCCCATTGACATAATTAGGTAGAT
66 CGGTTGAGATTCATTTGACTATTAAATGTACTTAAATATCTCCCCATTGACATAATTAGACAGAT
28484 TTGATATAAACCACAATAATG
131 TTGATATAAACCACAATAATG
28505 TTGGTCAAAT
Statistics
Matches: 149, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
151 15 0.10
152 134 0.90
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.34
Consensus pattern (151 bp):
AGATGGAGAACCAATTTATATATTCAGTCATTTAATCTGGTACATCCATCAAATAGCCAGTTTAA
CGGTTGAGATTCATTTGACTATTAAATGTACTTAAATATCTCCCCATTGACATAATTAGACAGAT
TTGATATAAACCACAATAATG
Found at i:38498 original size:52 final size:52
Alignment explanation
Indices: 38432--38573 Score: 230
Period size: 52 Copynumber: 2.7 Consensus size: 52
38422 AGTTTTTCAA
* * *
38432 ACTTTTTAAAGTGGGAAAGATCCCATCAAGTTTTCAGAGTATTCAATTTAGG
1 ACTTTTCAAAGTGGGAAAGATCCCATCAAGTTTTCAAAGTATTCAATTTAGC
*
38484 ACTTTTCAAAGTGGGAAAGATCCCATCAAGTTTTCAAAGTGTTCAATTTAGC
1 ACTTTTCAAAGTGGGAAAGATCCCATCAAGTTTTCAAAGTATTCAATTTAGC
* *
38536 TCTTCTCAAAGTGGGAAAGATCCCATCAAGTTTTCAAA
1 ACTTTTCAAAGTGGGAAAGATCCCATCAAGTTTTCAAA
38574 CTTTTCAAAG
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 84 1.00
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (52 bp):
ACTTTTCAAAGTGGGAAAGATCCCATCAAGTTTTCAAAGTATTCAATTTAGC
Found at i:38591 original size:37 final size:38
Alignment explanation
Indices: 38541--38691 Score: 153
Period size: 42 Copynumber: 3.8 Consensus size: 38
38531 TTAGCTCTTC
*
38541 TCAAAGTGGGAAAGATCCCATC-AAGTTTTCAAACTTT
1 TCAAAGTGGGAAAGATCCCATCAAAGTTTTCAAAATTT
38578 TCAAAGTGGGAAAGATCCCATCAAGTAGTTTTCAAAAATTT
1 TCAAAGTGGGAAAGATCCCATCAA--AGTTTTC-AAAATTT
** * * *
38619 TCAATTTAGGGAAAGATCCCATCCAATTCTTTTATAAAGTTT
1 TCAAAGT-GGGAAAGATCCCATCAAAGT-TTTCA-AAA-TTT
38661 TCAATCAG-GGGAAAGATCCCATCAAAGTTTT
1 TCAA--AGTGGGAAAGATCCCATCAAAGTTTT
38692 TTTTTTTTAA
Statistics
Matches: 94, Mismatches: 10, Indels: 16
0.78 0.08 0.13
Matches are distributed among these distances:
37 22 0.23
38 1 0.01
40 10 0.11
41 20 0.21
42 41 0.44
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (38 bp):
TCAAAGTGGGAAAGATCCCATCAAAGTTTTCAAAATTT
Found at i:39311 original size:34 final size:34
Alignment explanation
Indices: 39268--39335 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
39258 TCATATATCA
39268 TAATAAAATCCATAAATAACATACATTTCAAATG
1 TAATAAAATCCATAAATAACATACATTTCAAATG
39302 TAATAAAATCCATAAATAACATACATTTCAAATG
1 TAATAAAATCCATAAATAACATACATTTCAAATG
39336 CACCATATGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.53, C:0.15, G:0.03, T:0.29
Consensus pattern (34 bp):
TAATAAAATCCATAAATAACATACATTTCAAATG
Found at i:40986 original size:30 final size:30
Alignment explanation
Indices: 40950--41051 Score: 89
Period size: 30 Copynumber: 3.3 Consensus size: 30
40940 TCCATTAAAA
40950 AAAAAACAGCATTTTTTACCTCAAACTTAT
1 AAAAAACAGCATTTTTTACCTCAAACTTAT
* ** * * *
40980 AAAAAACAGAACTTTTATATATATGGAAACCT-C
1 AAAAAACAGCA-TTTT-T-TACCT-CAAACTTAT
* *
41013 AAAAAACAACATCTTTTACCTCAAACTTAT
1 AAAAAACAGCATTTTTTACCTCAAACTTAT
41043 AAAAAACAG
1 AAAAAACAG
41052 ACAATTTGTA
Statistics
Matches: 52, Mismatches: 15, Indels: 10
0.68 0.19 0.13
Matches are distributed among these distances:
29 5 0.10
30 21 0.40
31 5 0.10
32 4 0.08
33 12 0.23
34 5 0.10
ACGTcount: A:0.49, C:0.19, G:0.05, T:0.27
Consensus pattern (30 bp):
AAAAAACAGCATTTTTTACCTCAAACTTAT
Found at i:41032 original size:63 final size:63
Alignment explanation
Indices: 40950--41154 Score: 304
Period size: 63 Copynumber: 3.3 Consensus size: 63
40940 TCCATTAAAA
* *
40950 AAAAAACAGCATTTTTTACCTCAAACTTATAAAAAACAGAACTTTTATATATATGGAAACCTC
1 AAAAAACAGCATCTTTTACCTCAAACTTATAAAAAACAGAACTTTTGTATATATGGAAACCTC
* *
41013 AAAAAACAACATCTTTTACCTCAAACTTATAAAAAACAG-ACAATTTGTATATATGGAAACCTC
1 AAAAAACAGCATCTTTTACCTCAAACTTATAAAAAACAGAAC-TTTTGTATATATGGAAACCTC
* * * * * *
41076 AAATAACAGCATCTTTTACCTCAAACATATAACAAACTGAAATTTTGTATATATGGAAACCTA
1 AAAAAACAGCATCTTTTACCTCAAACTTATAAAAAACAGAACTTTTGTATATATGGAAACCTC
41139 AAAAAACAGCATCTTT
1 AAAAAACAGCATCTTT
41155 GTTCTCCATT
Statistics
Matches: 127, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
62 2 0.02
63 124 0.98
64 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.07, T:0.29
Consensus pattern (63 bp):
AAAAAACAGCATCTTTTACCTCAAACTTATAAAAAACAGAACTTTTGTATATATGGAAACCTC
Found at i:41625 original size:18 final size:18
Alignment explanation
Indices: 41602--41638 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
41592 CAATGGAAGG
41602 ATTGACAATAGGGACCTC
1 ATTGACAATAGGGACCTC
41620 ATTGACAATAGGGACCTC
1 ATTGACAATAGGGACCTC
41638 A
1 A
41639 GAAGGAGGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (18 bp):
ATTGACAATAGGGACCTC
Found at i:61746 original size:23 final size:23
Alignment explanation
Indices: 61720--61795 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
61710 GACAAATAAG
*
61720 CAAAACAACAACATTTTGAACAT
1 CAAAACAGCAACATTTTGAACAT
*
61743 CAAAACAGTAACATTTTGAACAT
1 CAAAACAGCAACATTTTGAACAT
* *
61766 CAAAACAGCAACATCTTGAACAG
1 CAAAACAGCAACATTTTGAACAT
61789 CAAAACA
1 CAAAACA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.51, C:0.22, G:0.08, T:0.18
Consensus pattern (23 bp):
CAAAACAGCAACATTTTGAACAT
Done.