Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004870.1 Hibiscus syriacus cultivar Beakdansim tig00010979_pilon, 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: 97024
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:840 original size:12 final size:12
Alignment explanation
Indices: 806--846 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
796 GAGGGAAGAT
806 GAAG-AAGAGAA
1 GAAGAAAGAGAA
*
817 GAA-AACAAAGAA
1 GAAGAA-AGAGAA
829 GAAGAAAGAGAA
1 GAAGAAAGAGAA
841 GAAGAA
1 GAAGAA
847 TGAGGACGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 4 0.16
12 19 0.76
13 2 0.08
ACGTcount: A:0.68, C:0.02, G:0.29, T:0.00
Consensus pattern (12 bp):
GAAGAAAGAGAA
Found at i:2651 original size:31 final size:31
Alignment explanation
Indices: 2584--2643 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
2574 CAATTTAAGG
*
2584 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
2615 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
2644 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:2890 original size:20 final size:21
Alignment explanation
Indices: 2865--2905 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2855 ATTTGAATAT
*
2865 TATGAA-GGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
2885 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
2906 CCCATTCTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:2967 original size:21 final size:21
Alignment explanation
Indices: 2934--2973 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
2924 TTTTTGCAGA
*
2934 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
2956 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
2974 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:3228 original size:34 final size:32
Alignment explanation
Indices: 3189--3258 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
3179 TTTTGTAAAG
*
3189 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
3223 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
3255 GGGA
1 GGGA
3259 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:3759 original size:22 final size:22
Alignment explanation
Indices: 3731--3809 Score: 158
Period size: 22 Copynumber: 3.6 Consensus size: 22
3721 TCGAGGATCA
3731 GTATCGATACTGATTGAAGAAG
1 GTATCGATACTGATTGAAGAAG
3753 GTATCGATACTGATTGAAGAAG
1 GTATCGATACTGATTGAAGAAG
3775 GTATCGATACTGATTGAAGAAG
1 GTATCGATACTGATTGAAGAAG
3797 GTATCGATACTGA
1 GTATCGATACTGA
3810 AATGGGGGTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 57 1.00
ACGTcount: A:0.35, C:0.10, G:0.27, T:0.28
Consensus pattern (22 bp):
GTATCGATACTGATTGAAGAAG
Found at i:4509 original size:23 final size:23
Alignment explanation
Indices: 4459--4545 Score: 81
Period size: 23 Copynumber: 3.8 Consensus size: 23
4449 GGTTTCTATC
*
4459 CTATGTGGT-TCTTCGGGAC-AAT
1 CTATGTGGTAT-TTCGGGACAAAA
4481 CTTATGTGGTATTTCGGGACAAAA
1 C-TATGTGGTATTTCGGGACAAAA
* ** *
4505 CTATGCGGTCCTTAGGGACAAAA
1 CTATGTGGTATTTCGGGACAAAA
4528 CTATGTGGTCA-TTCGGGA
1 CTATGTGGT-ATTTCGGGA
4546 TAAATATGTG
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
22 1 0.02
23 48 0.91
24 4 0.08
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (23 bp):
CTATGTGGTATTTCGGGACAAAA
Found at i:16858 original size:23 final size:23
Alignment explanation
Indices: 16828--16877 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
16818 TCATTCAGAA
16828 ACTTTTCAGTGGCTAATTAATAC
1 ACTTTTCAGTGGCTAATTAATAC
*
16851 ACTTTTCAGTGGCTAATTAATTC
1 ACTTTTCAGTGGCTAATTAATAC
16874 ACTT
1 ACTT
16878 CAGACACTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.42
Consensus pattern (23 bp):
ACTTTTCAGTGGCTAATTAATAC
Found at i:17049 original size:101 final size:101
Alignment explanation
Indices: 16868--17049 Score: 233
Period size: 101 Copynumber: 1.8 Consensus size: 101
16858 AGTGGCTAAT
* * * * * ** *
16868 TAATTCACTTCAGACACTTTTCATTGATATATCACTTATTTCAGAAACTTTTCATTGATAAATAA
1 TAATTCACTTCAAACACTTGTAATTGATATATCACTTACTACAGAAACTTTTCATACAAAAATAA
* *
16933 ATTCATTTTAGAAAAAGTCCTTTTCCAAACAAAAAA
66 ATTCATCTTACAAAAAGTCCTTTTCCAAACAAAAAA
16969 TAATTCACTTCAAACACTTGTAATTGATATATCACTTCACTACAGAAACTTTTTCATACAAAAAT
1 TAATTCACTTCAAACACTTGTAATTGATATATCACTT-ACTACAGAAAC-TTTTCATACAAAAAT
*
17034 TAATTCA-CTT-CAAAAA
64 AAATTCATCTTACAAAAA
17050 CTTTTCATTG
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
101 39 0.57
102 11 0.16
103 18 0.26
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (101 bp):
TAATTCACTTCAAACACTTGTAATTGATATATCACTTACTACAGAAACTTTTCATACAAAAATAA
ATTCATCTTACAAAAAGTCCTTTTCCAAACAAAAAA
Found at i:17082 original size:65 final size:65
Alignment explanation
Indices: 16952--17074 Score: 183
Period size: 65 Copynumber: 1.9 Consensus size: 65
16942 AGAAAAAGTC
* * * * * * *
16952 CTTTTCCAAACAAAAAATAATTCACTTCAAACACTTGTAATTGATATATCACTTCACTACAGAAA
1 CTTTTTCATACAAAAATTAATTCACTTCAAAAACTTTTCATTGATATATCACTCCACTACAGAAA
17017 CTTTTTCATACAAAAATTAATTCACTTCAAAAACTTTTCATTGATATATCACTCCACT
1 CTTTTTCATACAAAAATTAATTCACTTCAAAAACTTTTCATTGATATATCACTCCACT
17075 GTAGAAACCT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
65 51 1.00
ACGTcount: A:0.40, C:0.22, G:0.03, T:0.35
Consensus pattern (65 bp):
CTTTTTCATACAAAAATTAATTCACTTCAAAAACTTTTCATTGATATATCACTCCACTACAGAAA
Found at i:17088 original size:32 final size:32
Alignment explanation
Indices: 17047--17133 Score: 111
Period size: 32 Copynumber: 2.7 Consensus size: 32
17037 TTCACTTCAA
*
17047 AAACTTTTCATTGATATATCACTCCACTGTAG
1 AAACTTTTCAGTGATATATCACTCCACTGTAG
* * * * * *
17079 AAACCTTTCAGTGATAAATCAATTCATTGTAT
1 AAACTTTTCAGTGATATATCACTCCACTGTAG
17111 AAACTTTTCAGTGATATATCACT
1 AAACTTTTCAGTGATATATCACT
17134 TTATTTTACT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.38
Consensus pattern (32 bp):
AAACTTTTCAGTGATATATCACTCCACTGTAG
Found at i:17203 original size:19 final size:17
Alignment explanation
Indices: 17166--17202 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
17156 AATGACGGAC
17166 ATAAACCTATTTTTTAT
1 ATAAACCTATTTTTTAT
*
17183 ATAAACCTATTTTTTTT
1 ATAAACCTATTTTTTAT
17200 ATA
1 ATA
17203 TCAGCTCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.35, C:0.11, G:0.00, T:0.54
Consensus pattern (17 bp):
ATAAACCTATTTTTTAT
Found at i:19927 original size:214 final size:210
Alignment explanation
Indices: 19505--20317 Score: 1120
Period size: 212 Copynumber: 3.8 Consensus size: 210
19495 ATTTAAGAAT
*
19505 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAT
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACA-A---A--AG
*
19570 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATAC-AAAAA--ACTAAATTATAC
60 GGATCAAATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
* ** * * *
19632 CCATTTAAAAAGTTATGGGCCAATTAAAAAAATTTAATTAAGTAAAAAGTATGGATCAATTTCAT
125 CCATTTAAAAAGTTATGGGCCAATT-TAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAT
19697 ATGCAAATAAAATTTGGAGGAC
189 ATGCAAATAAAATTTGGAGGAC
*
19719 TAAATTGAAAAAATATGAAATTTA-AAA-AAAAA-TTAAATAAATTAAACAACACACATTGATGA
1 TAAATTGAACAAATATGAAA-TTACAAATAAAAATTTAAATAAATTAAACAACACA-A---A--A
* * *
19781 GGGATCAAATCTAAATAAATTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTATA
59 GGGATCAAATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATA
*
19846 CCCATTTAAAAGGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAT
124 CCCATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAT
19911 ATGCAAATAAAATTTGGAGGAC
189 ATGCAAATAAAATTTGGAGGAC
* * ** *
19933 TAAATTGAATAAATATAAAATTACAAATAAAAATTTAAATATGTTAAACAACACAAAAGAGATCA
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACAAAAGGGATCA
* * *
19998 AATCAAAAATAATTTTAAATTTTGAGGTTAAAATTAATACAAAAAAAGTACTAAATCATACCCAT
66 AATC-AAAATAATTTTAAATTGTGAGGTTGAAATTAATAC-AAAAAAGTACTAAATTATACCCAT
* **
20063 TTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTTAGGTGCA
129 TTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCATATGCA
*
20128 AATAAAATTTGGATGAC
194 AATAAAATTTGGAGGAC
20145 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATATAA-TAAACAACACAAAAGGGATC
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATA-AATTAAACAACACAAAAGGGATC
* * *
20209 AAATCAAAATAATTTTAAATTTTGAGGTTGAAATTAATACAAAAATGTACTAAATTATACTCATT
65 AAATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACCCATT
* * * *
20274 TAAAAAGTTATGAGCTAA-TTAATAAATATAAATAAGTATTAAGT
130 TAAAAAGTTATGGGCCAATTTAA-AAATAGAAATAAGTAATAAGT
20318 TGAGAAAAAA
Statistics
Matches: 547, Mismatches: 41, Indels: 26
0.89 0.07 0.04
Matches are distributed among these distances:
209 4 0.01
210 68 0.12
211 64 0.12
212 236 0.43
213 13 0.02
214 98 0.18
215 45 0.08
216 19 0.03
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.30
Consensus pattern (210 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACAAAAGGGATCA
AATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACCCATTT
AAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCATATGCAAA
TAAAATTTGGAGGAC
Found at i:20309 original size:422 final size:422
Alignment explanation
Indices: 19505--20317 Score: 1133
Period size: 422 Copynumber: 1.9 Consensus size: 422
19495 ATTTAAGAAT
* *
19505 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAT
1 TAAATTGAACAAATATAAAATTACAAATAAAAATTTAAATAAATTAAACAACACACA-T-AAGA-
* * *
19570 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAACTAAATTATACCCA
63 GGATCAAATCAAAATAATTTTAAATTGTGAGGTTAAAATTAATACAAAAAACTAAATCATACCCA
** * *
19635 TTTAAAAAGTTATGGGCCAATTAAAAAAATTTAATTAAGTAAAAAGTATGGATCAATTTCATATG
128 TTTAAAAAGTTATGGGCCAATTAAAAAAATAGAAATAAGTAAAAAGTATGGATCAATTTCAGATG
19700 CAAATAAAATTTGGAGGACTAAATTGAAAAAATATGAAATTTAAAAAAAAATTAAATAAATTAAA
193 CAAATAAAATTTGGAGGACTAAATTGAAAAAATATGAAATTTAAAAAAAAATTAAATAAATTAAA
* *
19765 CAACACACATTGATGAGGGATCAAATCTAAATAAATTTAAATTGTGATGTTGAAATTAATACAAA
258 CAACACACA-T-A-GAGGGATCAAATCAAAATAAATTTAAATTGTGAGGTTGAAATTAATACAAA
* *
19830 AAAGTACTAAATTATACCCATTTAAAAGGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAG
320 AAAGTACTAAATTATACCCATTTAAAAAGTTATGAGCCAATTTAAAAATAGAAATAAGTAATAAG
19895 TATGGGTCAATTTCATATGCAAATAAAATTTGGAGGAC
385 TATGGGTCAATTTCATATGCAAATAAAATTTGGAGGAC
* **
19933 TAAATTGAATAAATATAAAATTACAAATAAAAATTTAAATATGTTAAACAACACA-A-AAGA-GA
1 TAAATTGAACAAATATAAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATAAGAGGA
*
19995 TCAAATCAAAAATAATTTTAAATTTTGAGGTTAAAATTAATACAAAAAAAGTACTAAATCATACC
66 TCAAATC-AAAATAATTTTAAATTGTGAGGTTAAAATTAATAC--AAAAA--ACTAAATCATACC
* * * * *
20060 CATTTAAAAAGTTATGGGCCAATT-TAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTTAGG
126 CATTTAAAAAGTTATGGGCCAATTAAAAAAATAGAAATAAGTAAAAAGTATGGATCAATTTCAGA
* *
20124 TGCAAATAAAATTTGGATGACTAAATTGAACAAATATGAAA-TTACAAATAAAAATTTAAATATA
191 TGCAAATAAAATTTGGAGGACTAAATTGAAAAAATATGAAATTTA-AAA-AAAAA-TTAAATA-A
* *
20188 A-TAAACAACACA-A-A-AGGGATCAAATCAAAATAATTTTAAATTTTGAGGTTGAAATTAATAC
252 ATTAAACAACACACATAGAGGGATCAAATCAAAATAAATTTAAATTGTGAGGTTGAAATTAATAC
* * * * *
20249 AAAAATGTACTAAATTATACTCATTTAAAAAGTTATGAGCTAA-TTAATAAATATAAATAAGTAT
317 AAAAAAGTACTAAATTATACCCATTTAAAAAGTTATGAGCCAATTTAA-AAATAGAAATAAGTAA
20313 TAAGT
381 TAAGT
20318 TGAGAAAAAA
Statistics
Matches: 344, Mismatches: 31, Indels: 26
0.86 0.08 0.06
Matches are distributed among these distances:
421 4 0.01
422 109 0.32
423 32 0.09
424 4 0.01
425 8 0.02
426 73 0.21
427 43 0.12
428 69 0.20
429 2 0.01
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.30
Consensus pattern (422 bp):
TAAATTGAACAAATATAAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATAAGAGGA
TCAAATCAAAATAATTTTAAATTGTGAGGTTAAAATTAATACAAAAAACTAAATCATACCCATTT
AAAAAGTTATGGGCCAATTAAAAAAATAGAAATAAGTAAAAAGTATGGATCAATTTCAGATGCAA
ATAAAATTTGGAGGACTAAATTGAAAAAATATGAAATTTAAAAAAAAATTAAATAAATTAAACAA
CACACATAGAGGGATCAAATCAAAATAAATTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTA
CTAAATTATACCCATTTAAAAAGTTATGAGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGG
TCAATTTCATATGCAAATAAAATTTGGAGGAC
Found at i:20386 original size:22 final size:22
Alignment explanation
Indices: 20352--20406 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
20342 TATAGAGATA
* *
20352 TATATAATATAAAGTATAT-GTAT
1 TATAT-ATATAAACTATATACT-T
20375 TATATATATAAACTATATACTT
1 TATATATATAAACTATATACTT
20397 TATATATATA
1 TATATATATA
20407 TATTATGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 23 0.79
23 6 0.21
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (22 bp):
TATATATATAAACTATATACTT
Found at i:20435 original size:27 final size:28
Alignment explanation
Indices: 20401--20461 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
20391 ATACTTTATA
** * *
20401 TATATATATTATGTATAAAGTATAA-AT
1 TATATATACAATGTATAAACTATAATAC
20428 TATATATACAATGTATAAACTATAATAC
1 TATATATACAATGTATAAACTATAATAC
20456 TATATA
1 TATATA
20462 GTTTATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 22 0.76
28 7 0.24
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (28 bp):
TATATATACAATGTATAAACTATAATAC
Found at i:20443 original size:20 final size:19
Alignment explanation
Indices: 20403--20455 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
20393 ACTTTATATA
* *
20403 TATATATTATGTATA-AAG
1 TATAAATTATATATACAAG
20421 TATAAATTATATATACAATG
1 TATAAATTATATATACAA-G
*
20441 TATAAACTATA-ATAC
1 TATAAATTATATATAC
20456 TATATAGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 13 0.43
19 6 0.20
20 11 0.37
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (19 bp):
TATAAATTATATATACAAG
Found at i:20555 original size:17 final size:17
Alignment explanation
Indices: 20535--20628 Score: 66
Period size: 17 Copynumber: 5.3 Consensus size: 17
20525 CTATACAATT
* *
20535 TATATTTATATATTATG
1 TATATTTATAAATTATA
* *
20552 TATAATTATAAATAATA
1 TATATTTATAAATTATA
20569 TATATTGTATAAATTATA
1 TATATT-TATAAATTATA
20587 TAGTTTATTGATATAAATTATA
1 TA---TATT--TATAAATTATA
* *
20609 TA-GTTTATATA-TATA
1 TATATTTATAAATTATA
20624 TATAT
1 TATAT
20629 AGTATATATG
Statistics
Matches: 61, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
15 6 0.10
16 6 0.10
17 18 0.30
18 14 0.23
21 4 0.07
22 13 0.21
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TATATTTATAAATTATA
Found at i:20604 original size:22 final size:22
Alignment explanation
Indices: 20571--20631 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 22
20561 AAATAATATA
20571 TATTG-TATAAATTATATAGTT
1 TATTGATATAAATTATATAGTT
20592 TATTGATATAAATTATATAGTT
1 TATTGATATAAATTATATAGTT
*
20614 TA-T-ATATATA-TATATAGT
1 TATTGATATAAATTATATAGT
20632 ATATATGGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
19 8 0.21
20 6 0.16
21 6 0.16
22 18 0.47
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (22 bp):
TATTGATATAAATTATATAGTT
Found at i:20705 original size:20 final size:20
Alignment explanation
Indices: 20680--20740 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
20670 TATAAACTAC
20680 ATACTATAATTTATATTTAT
1 ATACTATAATTTATATTTAT
20700 ATAC--T-ATTTATA--TA-
1 ATACTATAATTTATATTTAT
*
20714 A-ACTATAGTTTATATTTAT
1 ATACTATAATTTATATTTAT
20733 ATACTATA
1 ATACTATA
20741 TATATATGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 14
0.69 0.02 0.29
Matches are distributed among these distances:
13 2 0.06
14 1 0.03
15 3 0.09
16 6 0.18
17 7 0.21
18 3 0.09
19 1 0.03
20 10 0.30
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.51
Consensus pattern (20 bp):
ATACTATAATTTATATTTAT
Found at i:20726 original size:33 final size:35
Alignment explanation
Indices: 20653--20760 Score: 132
Period size: 35 Copynumber: 3.1 Consensus size: 35
20643 AGAGTTTAGG
* * * *
20653 GTTTATATTTATAT-TTATATAAACTACATACTATA
1 GTTTATATTTATATACTATATATA-TATAAACTATA
*
20688 ATTTATATTTATATACTAT-T-TATATAAACTATA
1 GTTTATATTTATATACTATATATATATAAACTATA
*
20721 GTTTATATTTATATACTATATATATATGAACTATA
1 GTTTATATTTATATACTATATATATATAAACTATA
20756 GTTTA
1 GTTTA
20761 CATATGAACT
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
33 27 0.43
34 2 0.03
35 31 0.49
36 3 0.05
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.50
Consensus pattern (35 bp):
GTTTATATTTATATACTATATATATATAAACTATA
Found at i:20754 original size:35 final size:33
Alignment explanation
Indices: 20682--20760 Score: 122
Period size: 33 Copynumber: 2.3 Consensus size: 33
20672 TAAACTACAT
*
20682 ACTATAATTTATATTTATATACTATTTATATAA
1 ACTATAGTTTATATTTATATACTATTTATATAA
*
20715 ACTATAGTTTATATTTATATACTATATATATATGA
1 ACTATAGTTTATATTTATATACTAT-T-TATATAA
20750 ACTATAGTTTA
1 ACTATAGTTTA
20761 CATATGAACT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
33 24 0.57
34 1 0.02
35 17 0.40
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (33 bp):
ACTATAGTTTATATTTATATACTATTTATATAA
Found at i:20772 original size:33 final size:34
Alignment explanation
Indices: 20682--20779 Score: 105
Period size: 33 Copynumber: 2.9 Consensus size: 34
20672 TAAACTACAT
* *
20682 ACTATAATTTATATTTATATACTAT-T-TATATAA
1 ACTATAGTTTACA-TTATATACTATATATATATAA
* *
20715 ACTATAGTTTATATTTATATACTATATATATATGA
1 ACTATAGTTTACA-TTATATACTATATATATATAA
20750 ACTATAGTTTACA-TATGA-ACTATATATATA
1 ACTATAGTTTACATTAT-ATACTATATATATA
20780 AATATATATA
Statistics
Matches: 59, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
33 39 0.66
34 2 0.03
35 18 0.31
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (34 bp):
ACTATAGTTTACATTATATACTATATATATATAA
Found at i:20839 original size:2 final size:2
Alignment explanation
Indices: 20832--20902 Score: 56
Period size: 2 Copynumber: 34.0 Consensus size: 2
20822 ACATATGACC
* *
20832 TA TA TA TA TA CTA TA GTT TA TA TT TA TA TA CTA TA TA T- TA TA
1 TA TA TA TA TA -TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA
*
20874 TA TA TA AA CTA TA TA TA -A TA TA TA GTA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA
20903 ATTTACATAT
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
1 2 0.04
2 46 0.82
3 8 0.14
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:20861 original size:20 final size:20
Alignment explanation
Indices: 20832--20902 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
20822 ACATATGACC
20832 TATATATATACTATAGT-TTA
1 TATATATATACTATA-TATTA
*
20852 TATTTATATACTATATATTA
1 TATATATATACTATATATTA
* *
20872 TATATATAAACTATATATAA
1 TATATATATACTATATATTA
20892 TATATAGTATA
1 TATATA-TATA
20903 ATTTACATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
19 1 0.02
20 40 0.91
21 3 0.07
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (20 bp):
TATATATATACTATATATTA
Found at i:20867 original size:51 final size:51
Alignment explanation
Indices: 20770--20907 Score: 144
Period size: 51 Copynumber: 2.8 Consensus size: 51
20760 ACATATGAAC
* * *
20770 TATATATATAAA-TATATATACACTA-AGGTTGATA-TTATATACTATATAGT
1 TATACATATAAACTATATATATACTATA-GTTTATATTTATATACTATATA-T
* *
20820 T-TACATATGACCTATATATATACTATAGTTTATATTTATATACTATATAT
1 TATACATATAAACTATATATATACTATAGTTTATATTTATATACTATATAT
* *
20870 TATATATATAAACTATATATAATA-TATAGTATA-ATTTA
1 TATACATATAAACTATATAT-ATACTATAGTTTATATTTA
20908 CATATGAACT
Statistics
Matches: 74, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
49 7 0.09
50 26 0.35
51 38 0.51
52 3 0.04
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (51 bp):
TATACATATAAACTATATATATACTATAGTTTATATTTATATACTATATAT
Found at i:20878 original size:62 final size:61
Alignment explanation
Indices: 20708--20879 Score: 172
Period size: 62 Copynumber: 2.7 Consensus size: 61
20698 ATATACTATT
*
20708 TATATAAACTATAGTTTATATTTATATACTATATATATATGAACTATAGTTTACATATGAACTA
1 TATATATACTATAGTTTATATTTATATACTATATATATAT--A-TATAGTTTACATATGAACTA
* * * * * *
20772 TATATATAAATATA-TATACACTAAGGT-TGA-TAT-TATATACTATATAGTTTACATATGACCT
1 TATATAT-ACTATAGTTTATATTTA--TAT-ACTATATATATA-TATATAGTTTACATATGAACT
20833 A
61 A
20834 TATATATACTATAGTTTATATTTATATACTATATATTATATATATA
1 TATATATACTATAGTTTATATTTATATACTATATA-TATATATATA
20880 AACTATATAT
Statistics
Matches: 86, Mismatches: 12, Indels: 22
0.72 0.10 0.18
Matches are distributed among these distances:
60 2 0.02
61 9 0.10
62 40 0.47
63 5 0.06
64 18 0.21
65 10 0.12
66 2 0.02
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.45
Consensus pattern (61 bp):
TATATATACTATAGTTTATATTTATATACTATATATATATATATAGTTTACATATGAACTA
Found at i:20895 original size:34 final size:34
Alignment explanation
Indices: 20856--20925 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 34
20846 AGTTTATATT
* *
20856 TATATACTATATATTATATATATAAACTATATATAA
1 TATATAGTATA-ATT-TACATATAAACTATATATAA
*
20892 TATATAGTATAATTTACATATGAACTATATATAA
1 TATATAGTATAATTTACATATAAACTATATATAA
20926 AAATTCTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
34 18 0.58
35 3 0.10
36 10 0.32
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (34 bp):
TATATAGTATAATTTACATATAAACTATATATAA
Found at i:20948 original size:14 final size:14
Alignment explanation
Indices: 20926--20956 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
20916 CTATATATAA
*
20926 AAATTCTAAACCCT
1 AAATCCTAAACCCT
20940 AAATCCTAAACCCT
1 AAATCCTAAACCCT
20954 AAA
1 AAA
20957 CTATACATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.29, G:0.00, T:0.23
Consensus pattern (14 bp):
AAATCCTAAACCCT
Found at i:21002 original size:33 final size:33
Alignment explanation
Indices: 20953--21105 Score: 173
Period size: 33 Copynumber: 4.5 Consensus size: 33
20943 TCCTAAACCC
* * *
20953 TAAACTATACATTATATAGTTTATTAGTATATA
1 TAAACTATATAATATATAGTTCATTAGTATATA
* *
20986 TAAACTATATAATATATAG-ACTATATGGTATATA
1 TAAACTATATAATATATAGTTC-AT-TAGTATATA
* *
21020 TAAACTATACATTATATATAATTCATTAGTATATA
1 TAAACTAT--ATAATATATAGTTCATTAGTATATA
* *
21055 TACACTATATATTATATAGTTCATTAGTATATA
1 TAAACTATATAATATATAGTTCATTAGTATATA
*
21088 TAAACTATATAGTATATA
1 TAAACTATATAATATATA
21106 TAAACTATAT
Statistics
Matches: 100, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
33 57 0.57
34 16 0.16
35 15 0.15
36 11 0.11
37 1 0.01
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.42
Consensus pattern (33 bp):
TAAACTATATAATATATAGTTCATTAGTATATA
Found at i:21003 original size:18 final size:18
Alignment explanation
Indices: 20977--21116 Score: 134
Period size: 18 Copynumber: 8.1 Consensus size: 18
20967 TATAGTTTAT
20977 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
*
20995 TA--ATATATAGACTATA
1 TAGTATATATAAACTATA
*
21011 TGGTATATATAAACTATA
1 TAGTATATATAAACTATA
* * *
21029 CATTATATAT-AATTCAT-
1 TAGTATATATAAACT-ATA
*
21046 TAGTATATATACACTATA
1 TAGTATATATAAACTATA
**
21064 TA-T-TATAT-AGTTCAT-
1 TAGTATATATAAACT-ATA
21079 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
21097 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
21115 TA
1 TA
21117 TTAATTTATT
Statistics
Matches: 96, Mismatches: 16, Indels: 20
0.73 0.12 0.15
Matches are distributed among these distances:
15 3 0.03
16 22 0.23
17 21 0.22
18 50 0.52
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.41
Consensus pattern (18 bp):
TAGTATATATAAACTATA
Found at i:21261 original size:62 final size:61
Alignment explanation
Indices: 21171--21306 Score: 184
Period size: 62 Copynumber: 2.2 Consensus size: 61
21161 AAATATATAA
* * *
21171 GGATCAAATTGAACAAAATTTAAATATGAAGCTTAAATTAATAAATGATAA-CATTAAATTT
1 GGATTAAATTGAAAAAAATTGAAATATGAAGCTTAAATTAATAAATGA-AATCATTAAATTT
* * *
21232 GGATTAAATTGAAAAAAAGTTGAAATATGAAGCTTAAATTAATATATTAAATTATTAAATTT
1 GGATTAAATTGAAAAAAA-TTGAAATATGAAGCTTAAATTAATAAATGAAATCATTAAATTT
*
21294 GGAATAAATTGAA
1 GGATTAAATTGAA
21307 TAAATTTAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
61 18 0.27
62 48 0.73
ACGTcount: A:0.51, C:0.04, G:0.12, T:0.34
Consensus pattern (61 bp):
GGATTAAATTGAAAAAAATTGAAATATGAAGCTTAAATTAATAAATGAAATCATTAAATTT
Found at i:23858 original size:14 final size:14
Alignment explanation
Indices: 23839--23885 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
23829 ATTTTTTCTT
23839 TATATAAATTAAAC
1 TATATAAATTAAAC
23853 TATAT-AATT----
1 TATATAAATTAAAC
23862 TATATAAATTAAAC
1 TATATAAATTAAAC
*
23876 TATATTAATT
1 TATATAAATT
23886 TTCCTTTGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
13 4 0.15
14 14 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:23863 original size:23 final size:24
Alignment explanation
Indices: 23837--23886 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
23827 TTATTTTTTC
23837 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
23860 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
23884 TTT
1 TTT
23887 TCCTTTGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:24176 original size:16 final size:16
Alignment explanation
Indices: 24155--24238 Score: 159
Period size: 16 Copynumber: 5.2 Consensus size: 16
24145 CGGATCATTT
*
24155 ACAGGTCAGGTTAAAA
1 ACAGGTCAGGTTGAAA
24171 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAA
24187 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAA
24203 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAA
24219 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAA
24235 ACAG
1 ACAG
24239 ATCGGGTAAT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
16 67 1.00
ACGTcount: A:0.39, C:0.13, G:0.30, T:0.18
Consensus pattern (16 bp):
ACAGGTCAGGTTGAAA
Found at i:25987 original size:2 final size:2
Alignment explanation
Indices: 25980--26053 Score: 139
Period size: 2 Copynumber: 37.0 Consensus size: 2
25970 TTATTTTTAC
25980 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
26022 AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26054 GATTAGGTAA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:36461 original size:22 final size:22
Alignment explanation
Indices: 36433--36476 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
36423 TTTGTATCGA
36433 GTTATCCCGTTTATCCTAAATT
1 GTTATCCCGTTTATCCTAAATT
*
36455 GTTATCCCGTTTGTCCTAAATT
1 GTTATCCCGTTTATCCTAAATT
36477 TTTCAGAACG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.23, G:0.11, T:0.45
Consensus pattern (22 bp):
GTTATCCCGTTTATCCTAAATT
Found at i:38053 original size:29 final size:29
Alignment explanation
Indices: 38010--38092 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
38000 CTCACCTAAC
38010 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
38040 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
* *
38069 TAAATGATGTAGGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
38093 ATTTAGTTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 45 0.92
30 4 0.08
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:42817 original size:29 final size:29
Alignment explanation
Indices: 42774--42856 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
42764 CTCACCTAAC
42774 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
42804 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
42833 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
42857 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:44095 original size:3 final size:3
Alignment explanation
Indices: 44087--44161 Score: 150
Period size: 3 Copynumber: 25.0 Consensus size: 3
44077 AACTTTGGAC
44087 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
44135 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
44162 TGAACTGTTT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:50088 original size:23 final size:23
Alignment explanation
Indices: 50062--50114 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
50052 TCCCGAAGGA
50062 CCACATAGGTTTGCACCGAAATG
1 CCACATAGGTTTGCACCGAAATG
50085 CCACATAGGTTTGCACCGAAATG
1 CCACATAGGTTTGCACCGAAATG
50108 CCACATA
1 CCACATA
50115 ATTGTCTCGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (23 bp):
CCACATAGGTTTGCACCGAAATG
Found at i:53081 original size:24 final size:24
Alignment explanation
Indices: 53054--53099 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
53044 TACCACAGCT
53054 CGTATAAAT-TGCACCAAAGTGCCA
1 CGTA-AAATATGCACCAAAGTGCCA
*
53078 CGTAGAATATGCACCAAAGTGC
1 CGTAAAATATGCACCAAAGTGC
53100 GACATAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.20
Consensus pattern (24 bp):
CGTAAAATATGCACCAAAGTGCCA
Found at i:53107 original size:24 final size:24
Alignment explanation
Indices: 53063--53132 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 24
53053 TCGTATAAAT
*
53063 TGCACCAAAGTGCCACGTAGAATA
1 TGCACCAAAGTGCCACATAGAATA
*
53087 TGCACCAAAGTGCGACATAGAA-A
1 TGCACCAAAGTGCCACATAGAATA
*
53110 TGTC-CCGAA-TGACCACATAGAAT
1 TG-CACCAAAGTG-CCACATAGAAT
53133 TGTCCCGAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
22 2 0.05
23 16 0.41
24 21 0.54
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (24 bp):
TGCACCAAAGTGCCACATAGAATA
Found at i:53200 original size:23 final size:23
Alignment explanation
Indices: 53104--53192 Score: 106
Period size: 23 Copynumber: 3.9 Consensus size: 23
53094 AAGTGCGACA
* *
53104 TAGAAATGTCCCGAATGACCACA
1 TAGAAATGTCCCGAAGGACCACG
* *
53127 TAGAATTGTCCCGAAGGCCCACG
1 TAGAAATGTCCCGAAGGACCACG
***
53150 TAGAAATGTCTTAAAGGACCACG
1 TAGAAATGTCCCGAAGGACCACG
*
53173 TAGAATTGTCCCGAAGGACC
1 TAGAAATGTCCCGAAGGACC
53193 GTGTAGAACC
Statistics
Matches: 53, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.34, C:0.25, G:0.22, T:0.19
Consensus pattern (23 bp):
TAGAAATGTCCCGAAGGACCACG
Found at i:56320 original size:16 final size:16
Alignment explanation
Indices: 56301--56335 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
56291 ATTCTTACGA
*
56301 GACAAAATTCAATGTG
1 GACAAAATACAATGTG
56317 GACAAAATACAATGTG
1 GACAAAATACAATGTG
56333 GAC
1 GAC
56336 TTTCCGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.46, C:0.14, G:0.20, T:0.20
Consensus pattern (16 bp):
GACAAAATACAATGTG
Found at i:58582 original size:2 final size:2
Alignment explanation
Indices: 58575--58602 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
58565 CTAATTTAAC
58575 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58603 TAACATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:88670 original size:11 final size:11
Alignment explanation
Indices: 88648--88683 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
88638 GTTTGATGCT
88648 TTCTCT-TTGA
1 TTCTCTCTTGA
88658 TTCTCTCTTGA
1 TTCTCTCTTGA
88669 TTCTCTCTTGA
1 TTCTCTCTTGA
88680 TTCT
1 TTCT
88684 AGTTGCTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 6 0.24
11 19 0.76
ACGTcount: A:0.08, C:0.25, G:0.08, T:0.58
Consensus pattern (11 bp):
TTCTCTCTTGA
Found at i:91690 original size:20 final size:20
Alignment explanation
Indices: 91662--91713 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
91652 CAAAGGGGGA
*
91662 ATCGGTTCCCTCATGAGGGT
1 ATCGATTCCCTCATGAGGGT
91682 ATCGATTCCCTCATGAGGGT
1 ATCGATTCCCTCATGAGGGT
91702 ATCGATTCCCTC
1 ATCGATTCCCTC
91714 TACACCAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.17, C:0.29, G:0.23, T:0.31
Consensus pattern (20 bp):
ATCGATTCCCTCATGAGGGT
Done.