Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009405.1 Hibiscus syriacus cultivar Beakdansim tig00113337_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: 1310060
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:195199 original size:15 final size:15
Alignment explanation
Indices: 195174--195215 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
195164 TACTTTACTC
195174 TTAAATTAAAAAT-T
1 TTAAATTAAAAATAT
195188 TTAAATTTAAAAATAT
1 TTAAA-TTAAAAATAT
*
195204 TGAAACTTAAAA
1 TTAAA-TTAAAA
195216 CAAAAATAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 5 0.21
15 8 0.33
16 11 0.46
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (15 bp):
TTAAATTAAAAATAT
Found at i:196308 original size:12 final size:12
Alignment explanation
Indices: 196291--196322 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
196281 CGACCCGATT
196291 ACCCGATACCCG
1 ACCCGATACCCG
196303 ACCCGATACCCG
1 ACCCGATACCCG
*
196315 GCCCGATA
1 ACCCGATA
196323 AATATTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.25, C:0.47, G:0.19, T:0.09
Consensus pattern (12 bp):
ACCCGATACCCG
Found at i:198052 original size:29 final size:29
Alignment explanation
Indices: 198020--198077 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
198010 TTGTTTAATC
198020 GGTTTCTAATTTGTATCTTGTATTTATTT
1 GGTTTCTAATTTGTATCTTGTATTTATTT
*
198049 GGTTTCTAATTTGTATGTTGTATTTATTT
1 GGTTTCTAATTTGTATCTTGTATTTATTT
198078 CAGTCTATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.17, C:0.05, G:0.16, T:0.62
Consensus pattern (29 bp):
GGTTTCTAATTTGTATCTTGTATTTATTT
Found at i:200962 original size:20 final size:20
Alignment explanation
Indices: 200929--200974 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
200919 ACCTCTTAAA
* *
200929 ATTTTAAATTTTTTTTATAT
1 ATTTTAAATATTTTTAATAT
*
200949 ATTTTTAATATTTTTAATAT
1 ATTTTAAATATTTTTAATAT
200969 ATTTTA
1 ATTTTA
200975 TTGAAAATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
ATTTTAAATATTTTTAATAT
Found at i:201152 original size:48 final size:48
Alignment explanation
Indices: 201065--201157 Score: 116
Period size: 48 Copynumber: 1.9 Consensus size: 48
201055 ACTCTTAAAT
* * ** *
201065 AGGGGTGGACCTCCATGGAGTCCGGGGTATCTCGGGCAACTCCTCATCC
1 AGGGGTGGACCTCCAT-GAGTCCCGGGTATCCCAAGCAACCCCTCATCC
201114 AGGGGTGGACCTCCAT-AGTACCCGGGTATCCCAAGCAACCCCTC
1 AGGGGTGGACCTCCATGAGT-CCCGGGTATCCCAAGCAACCCCTC
201158 CACAAGTGTC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
47 3 0.08
48 19 0.50
49 16 0.42
ACGTcount: A:0.19, C:0.33, G:0.29, T:0.18
Consensus pattern (48 bp):
AGGGGTGGACCTCCATGAGTCCCGGGTATCCCAAGCAACCCCTCATCC
Found at i:202395 original size:41 final size:41
Alignment explanation
Indices: 202350--202455 Score: 176
Period size: 41 Copynumber: 2.6 Consensus size: 41
202340 ATTCACGTTG
* *
202350 CATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGTTTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
202391 CATTTCGCGTTGCGATAGTTGGAGATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
202432 CATTTCGCGTTGCGATAGTTGAAA
1 CATTTCGCGTTGCGATAGTTGAAA
202456 TTGCAACGCT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:202446 original size:20 final size:20
Alignment explanation
Indices: 202375--202447 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
202365 TAGTTGAAAA
*
202375 TCGCGTTGCGTTTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
202395 TCGCGTTGCGATAGTTGGAGA
1 TCGCGTTGCGAT-TTTCCATT
202416 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
202436 TCGCGTTGCGAT
1 TCGCGTTGCGAT
202448 AGTTGAAATT
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.63
21 15 0.37
ACGTcount: A:0.11, C:0.22, G:0.27, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:202509 original size:19 final size:19
Alignment explanation
Indices: 202484--202552 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
202474 CATCGCAAAT
202484 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
* * * **
202503 CCGCAACGACAACTGTAGACTA
1 TCGCAACG--AA-TTTGGAAAA
202525 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
202544 TCGCAACGA
1 TCGCAACGA
202553 CAAGTAGACT
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 21 0.57
20 2 0.05
21 2 0.05
22 12 0.32
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.17
Consensus pattern (19 bp):
TCGCAACGAATTTGGAAAA
Found at i:202571 original size:39 final size:40
Alignment explanation
Indices: 202484--202571 Score: 151
Period size: 41 Copynumber: 2.2 Consensus size: 40
202474 CATCGCAAAT
202484 TCGCAACGAATTTGGAAAACCGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTGGAAAACCGCAACGACAAC-GTAGACTA
*
202525 TCGCAACGAATTTGGAAAATCGCAACGACAA-GTAGACTA
1 TCGCAACGAATTTGGAAAACCGCAACGACAACGTAGACTA
202564 TCGCAACG
1 TCGCAACG
202572 CGATTTTCAA
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
39 16 0.35
41 30 0.65
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (40 bp):
TCGCAACGAATTTGGAAAACCGCAACGACAACGTAGACTA
Found at i:202586 original size:21 final size:21
Alignment explanation
Indices: 202560--202657 Score: 83
Period size: 20 Copynumber: 4.8 Consensus size: 21
202550 CGACAAGTAG
** *
202560 ACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
*
202581 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* *
202602 A-AATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* * ** *
202622 A-AATCGCAACTCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
202642 ACTATCGCAACGCGAA
1 ACTATCGCAACGCGAA
202658 TTTGCGATAG
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
20 34 0.54
21 29 0.46
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:202609 original size:20 final size:20
Alignment explanation
Indices: 202584--202631 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
202574 ATTTTCAACT
202584 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
202604 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
202624 ATCGCAAC
1 ATCGCAAC
202632 TCGATTTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.10
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:202610 original size:61 final size:62
Alignment explanation
Indices: 202521--202658 Score: 185
Period size: 61 Copynumber: 2.3 Consensus size: 62
202511 ACAACTGTAG
* * **
202521 ACTATCGCAA--CGAATTTGGAAAATCGCAACGAC-AAGTAGACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAATATGGAAAATCGCAACG-CGAAATAGAAAATCGCAACGCGATTTTCA
* *
202581 ACTATCGCAACGCGAA-ATGGAAAATCGCAACGCGAAATGGAAAATCGCAACTCGATTTTCA
1 ACTATCGCAACGCGAATATGGAAAATCGCAACGCGAAATAGAAAATCGCAACGCGATTTTCA
202642 ACTATCGCAACGCGAAT
1 ACTATCGCAACGCGAAT
202659 TTGCGATAGT
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
60 11 0.16
61 53 0.78
62 4 0.06
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.20
Consensus pattern (62 bp):
ACTATCGCAACGCGAATATGGAAAATCGCAACGCGAAATAGAAAATCGCAACGCGATTTTCA
Found at i:205992 original size:23 final size:23
Alignment explanation
Indices: 205966--206028 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
205956 ATATAAGCAC
205966 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
205989 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
206012 TACCTATTACATCATAT
1 TACCTATTACATTATAT
206029 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:206473 original size:490 final size:490
Alignment explanation
Indices: 205553--206765 Score: 2365
Period size: 490 Copynumber: 2.5 Consensus size: 490
205543 TTATAATATG
205553 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATA-CTTTTTCTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACCTTTTT-TAAAGTTATGTAATTTATGT
205617 TTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAAGAATTTCATTTAC
65 TTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAAGAATTTCATTTAC
205682 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
130 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
205747 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
195 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
205812 TATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
260 TATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
205877 TCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGG
325 TCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGG
205942 ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGATACCTATTACATTATATA
390 ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGATACCTATTACATTATATA
206007 AGCGCTACCTATTACATCATATTTTTACCTATTATA
455 AGCGCTACCTATTACATCATATTTTTACCTATTATA
*
206043 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACCTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACCTTTTTTAAAGTTATGTAATTTATGTT
*
206108 TCAATTTTTTTTAATAGTGTTTCATGTTTTTCACCTACAATATTAATTTAAGAATTTCATTTACA
66 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAAGAATTTCATTTACA
*
206173 CAAAAAATTATTTGTTTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
131 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
206238 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
196 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
206303 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
261 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
206368 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
326 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
206433 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGATACCTATTACATTATATAA
391 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGATACCTATTACATTATATAA
*
206498 GTGCTACCTATTACATCATATTTTTACCTATTATA
456 GCGCTACCTATTACATCATATTTTTACCTATTATA
*
206533 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACCTTTTTTAAAGTTATGTAATTTATGTT
206598 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAAGAATTTCATTTACA
66 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAAGAATTTCATTTACA
206663 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
131 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
206728 TAACCAAAGATAATAATAAATATGTAATATATATGTTT
196 TAACCAAAGATAATAATAAATATGTAATATATATGTTT
206766 CAATTATCAA
Statistics
Matches: 714, Mismatches: 8, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
490 708 0.99
491 6 0.01
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.41
Consensus pattern (490 bp):
TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACCTTTTTTAAAGTTATGTAATTTATGTT
TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAAGAATTTCATTTACA
CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGATACCTATTACATTATATAA
GCGCTACCTATTACATCATATTTTTACCTATTATA
Found at i:206482 original size:23 final size:23
Alignment explanation
Indices: 206456--206518 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
206446 ATATAAGCAC
206456 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
206479 TACCTATTACATTATATAAGTGC
1 TACCTATTACATTATATAAACGA
*
206502 TACCTATTACATCATAT
1 TACCTATTACATTATAT
206519 TTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:207853 original size:3 final size:3
Alignment explanation
Indices: 207845--207919 Score: 78
Period size: 3 Copynumber: 25.0 Consensus size: 3
207835 ACTTGTTTGG
* * * * *
207845 ATC ATC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GTC AGC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * *
207893 ATC GTC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
207920 GTCAGCTTCA
Statistics
Matches: 56, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.24, C:0.33, G:0.07, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:207902 original size:36 final size:36
Alignment explanation
Indices: 207855--207936 Score: 128
Period size: 36 Copynumber: 2.3 Consensus size: 36
207845 ATCATCATCA
*
207855 TCATCATCATCATCGTCATCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGTCAGCT
* *
207891 TCATCGTCATCATCATCGTCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGTCAGCT
*
207927 TCATCTTCAT
1 TCATCATCAT
207937 TGACCGCTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.21, C:0.33, G:0.09, T:0.38
Consensus pattern (36 bp):
TCATCATCATCATCATCATCATCTTCATCGTCAGCT
Found at i:207920 original size:12 final size:12
Alignment explanation
Indices: 207849--207936 Score: 95
Period size: 12 Copynumber: 7.3 Consensus size: 12
207839 GTTTGGATCA
* *
207849 TCATCATCATCA
1 TCATCTTCATCG
* * *
207861 TCATCATCGTCA
1 TCATCTTCATCG
207873 TCATCTTCATCG
1 TCATCTTCATCG
*
207885 TCAGCTTCATCG
1 TCATCTTCATCG
*
207897 TCATCATCATCG
1 TCATCTTCATCG
207909 TCATCTTCATCG
1 TCATCTTCATCG
* *
207921 TCAGCTTCATCT
1 TCATCTTCATCG
207933 TCAT
1 TCAT
207937 TGACCGCTTG
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 65 1.00
ACGTcount: A:0.22, C:0.33, G:0.08, T:0.38
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:207945 original size:18 final size:18
Alignment explanation
Indices: 207873--207936 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 18
207863 ATCATCGTCA
*
207873 TCATCTTCATCGTCAGCT
1 TCATCTTCATCGACAGCT
* * *
207891 TCATCGTCATC-ATCATCG
1 TCATCTTCATCGA-CAGCT
*
207909 TCATCTTCATCGTCAGCT
1 TCATCTTCATCGACAGCT
207927 TCATCTTCAT
1 TCATCTTCAT
207937 TGACCGCTTG
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.19, C:0.33, G:0.09, T:0.39
Consensus pattern (18 bp):
TCATCTTCATCGACAGCT
Found at i:209747 original size:200 final size:200
Alignment explanation
Indices: 209400--209977 Score: 1000
Period size: 201 Copynumber: 2.9 Consensus size: 200
209390 TTTAAATTAG
* * *
209400 TATCGACA-AAACATTAAACAGTGTCGATACA-TATTATATACCA-ATTCTCTCATAAAACCGGT
1 TATCGACACAAAC-TTAAAAAGTGTCGACACATTATT-TAGA-CATATTCTCTCATAAAACCGGT
* *
209462 ATACTTGTACTGGTTAGATTGAAAAATTACATATTACATTGTACTTTTGGTTTTCGATGTTTTTG
63 ATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTG
* *
209527 GGATCGACACTTTCTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGG
128 GGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTATGG
209592 ACCAAAAA
193 ACCAAAAA
*
209600 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
209665 CTTGTACCGGTTAGAATGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
209730 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCCTGTTTTCCATTCATTATGGAC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCA-CCCTGTTTTCCATTCATTATGGAC
209795 CAAAAA
195 CAAAAA
* *
209801 TATCGATACAAACTTAAAAAGTATCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
209866 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
209931 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTT
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTT
209978 GGCCATATTG
Statistics
Matches: 361, Mismatches: 13, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
199 2 0.01
200 156 0.43
201 203 0.56
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (200 bp):
TATCGACACAAACTTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTATGGACC
AAAAA
Found at i:210107 original size:18 final size:18
Alignment explanation
Indices: 210084--210144 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
210074 TCTCATTCAT
*
210084 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
210102 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
210121 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
210140 AATTA
1 AATTA
210145 ACCCTACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:210120 original size:19 final size:19
Alignment explanation
Indices: 210096--210144 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
210086 TTATATTCAC
210096 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
210115 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
210134 ATACAAAATTA
1 ATACAAAATTA
210145 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:211972 original size:33 final size:33
Alignment explanation
Indices: 211935--212000 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
211925 CATCTTAATA
* *
211935 TCACCCCTTAACACAACAACTTCTTTCACCACT
1 TCACCCCTCAACACAACAACTTATTTCACCACT
** *
211968 TCACCCCTCAACACCTCTACTTATTTCACCACT
1 TCACCCCTCAACACAACAACTTATTTCACCACT
212001 CCATCTATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.27, C:0.44, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACAACAACTTATTTCACCACT
Found at i:212059 original size:21 final size:21
Alignment explanation
Indices: 212034--212098 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
212024 CCCCTTATGC
* *
212034 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
212055 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
212076 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
212097 CT
1 CT
212099 TGATTGTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:214159 original size:24 final size:24
Alignment explanation
Indices: 214122--214174 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
214112 CTGTTCTATC
214122 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
214146 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
214170 TATTT
1 TATTT
214175 AATTGATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:214528 original size:20 final size:19
Alignment explanation
Indices: 214501--214561 Score: 79
Period size: 20 Copynumber: 3.1 Consensus size: 19
214491 TCTGGTAACG
214501 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
214520 TTCTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
*
214541 TTTTACCTGG-TATATCATT
1 TTTTACC-GGTTTTATCATT
214560 TT
1 TT
214562 GGATCGATAC
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
19 5 0.13
20 28 0.74
21 5 0.13
ACGTcount: A:0.18, C:0.16, G:0.10, T:0.56
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:214655 original size:182 final size:181
Alignment explanation
Indices: 214286--214759 Score: 612
Period size: 182 Copynumber: 2.6 Consensus size: 181
214276 CGTACTTACG
* * *** * *
214286 AAAGTATCGACACTTTCAATATATCCGATATTATTTTACCGGTTTTATCATTTTGATACATGTTT
1 AAAGTATCGACACTTTCAATATATCTGGTAACGTTTTACCGGTTTTATCATTTTCATACAGGTTT
* * * * *
214351 TATCATATTTTTACTTGTTATATCGTTGTGGATCGATATATTTTTTTTAAAGTATCTACACATTA
66 TATCATATTTTTACATGTTATATCGTTTTGGATCGATACA-TTTTTTAAAAGTATCAACACATTA
*
214416 TAGGCGCTAAAACTGTTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
130 TAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
* *
214468 AAAGTATCGACACTTTCAATATATCTGGTAACGTTTTACCGGTTTTATCATTTTCTTACCGGTTT
1 AAAGTATCGACACTTTCAATATATCTGGTAACGTTTTACCGGTTTTATCATTTTCATACAGGTTT
* * * *
214533 TATCATATTTTTACCTGGTATATCATTTTGGATCGATACATTTTTTAAAAGTATCAACACTTTAT
66 TATCATATTTTTACATGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCAACACATTAT
* *
214598 AGGAC-TTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGG-CGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
* * * * * *
214650 AAAGTACCGACACTTTAAATGTAT-TCGGTAGCGCTTTACCGGTTTTATCA-TTTCAATACTGGT
1 AAAGTATCGACACTTTCAATATATCT-GGTAACGTTTTACCGGTTTTATCATTTTC-ATACAGGT
* * *
214713 TTTGTCATAGTTTTACATGTTATATCGTTTTGGATCGACACATTTTT
64 TTTATCATATTTTTACATGTTATATCGTTTTGGATCGATACATTTTT
214760 AATTTGGATC
Statistics
Matches: 255, Mismatches: 33, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
181 72 0.28
182 183 0.72
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (181 bp):
AAAGTATCGACACTTTCAATATATCTGGTAACGTTTTACCGGTTTTATCATTTTCATACAGGTTT
TATCATATTTTTACATGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCAACACATTAT
AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
Found at i:230443 original size:33 final size:33
Alignment explanation
Indices: 230400--230473 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
230390 AGACTTCCAA
*
230400 ATCTAACATGTTGATACTTACCTTTGTCTGCAT
1 ATCTAACATGTTGATACTTAACTTTGTCTGCAT
* *
230433 GTCTAACATGTTGATACTTAACTTTGTTTGCAT
1 ATCTAACATGTTGATACTTAACTTTGTCTGCAT
230466 ATCTAACA
1 ATCTAACA
230474 ATACTTACCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (33 bp):
ATCTAACATGTTGATACTTAACTTTGTCTGCAT
Found at i:230486 original size:28 final size:29
Alignment explanation
Indices: 230413--230489 Score: 84
Period size: 33 Copynumber: 2.6 Consensus size: 29
230403 TAACATGTTG
* *
230413 ATACTTACCTTTGTCTGCATGTCTAACATGTT
1 ATACTTACCTTTGTTTGCATATCTAACA---T
*
230445 GATACTTAACTTTGTTTGCATATCTAACA-
1 -ATACTTACCTTTGTTTGCATATCTAACAT
230474 ATACTTACCTTTGTTT
1 ATACTTACCTTTGTTT
230490 TTATATTGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 15 0.38
33 25 0.62
ACGTcount: A:0.25, C:0.19, G:0.10, T:0.45
Consensus pattern (29 bp):
ATACTTACCTTTGTTTGCATATCTAACAT
Found at i:231072 original size:13 final size:14
Alignment explanation
Indices: 231054--231082 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
231044 GCATACTATT
231054 TCCTTGTAT-TTAG
1 TCCTTGTATATTAG
231067 TCCTTGTATATTAG
1 TCCTTGTATATTAG
231081 TC
1 TC
231083 ATCTAGTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.17, C:0.17, G:0.14, T:0.52
Consensus pattern (14 bp):
TCCTTGTATATTAG
Found at i:231817 original size:28 final size:28
Alignment explanation
Indices: 231780--231839 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
231770 TGATTCAGTC
*
231780 TTTGATTTTTCTTGCAAGACTATTTCAG
1 TTTGATTTTTCATGCAAGACTATTTCAG
231808 TTTGATTTTTCATGCAAGACTATTTCAG
1 TTTGATTTTTCATGCAAGACTATTTCAG
231836 TTTG
1 TTTG
231840 GATAAATTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.22, C:0.13, G:0.15, T:0.50
Consensus pattern (28 bp):
TTTGATTTTTCATGCAAGACTATTTCAG
Found at i:236384 original size:20 final size:20
Alignment explanation
Indices: 236348--236385 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
236338 ATCCTATTCC
**
236348 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
236368 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
236386 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:248498 original size:32 final size:34
Alignment explanation
Indices: 248457--248538 Score: 105
Period size: 35 Copynumber: 2.4 Consensus size: 34
248447 TTTAAATAGT
*
248457 TATTATTTTTTATATT-AAT-ATATTTATGTAAA
1 TATTATTTTTTATATTAAATAATATTTATATAAA
* *
248489 TATTATTTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTATATT-AAATAATATTTATATAAA
248524 TATTATTTATTTATA
1 TATTATTT-TTTATA
248539 ATTATTAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
32 15 0.36
34 3 0.07
35 19 0.45
36 5 0.12
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (34 bp):
TATTATTTTTTATATTAAATAATATTTATATAAA
Found at i:248500 original size:34 final size:33
Alignment explanation
Indices: 248424--248531 Score: 94
Period size: 35 Copynumber: 3.1 Consensus size: 33
248414 GTGGTAAGAA
* *
248424 ATTTATTTTTATGTTAGTAT-TTT-TTTAAATAGTT
1 ATTT-TTTTTAT-TTAATATATTTATATAAATA-TT
*
248458 ATTATTTTTTATATTAATATATTTATGTAAATATT
1 ATT-TTTTTTAT-TTAATATATTTATATAAATATT
* *
248493 ATTTTTTTTATTAAAATAATATTTATATAATTATT
1 ATTTTTTTTATT-TAAT-ATATTTATATAAATATT
248528 ATTT
1 ATTT
248532 ATTTATAATT
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
33 1 0.02
34 27 0.43
35 28 0.44
36 7 0.11
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (33 bp):
ATTTTTTTTATTTAATATATTTATATAAATATT
Found at i:248701 original size:17 final size:17
Alignment explanation
Indices: 248679--248732 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
248669 AATGTTAATA
248679 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
248696 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
248713 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
248730 TTT
1 TTT
248733 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:250340 original size:21 final size:21
Alignment explanation
Indices: 250314--250407 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
250304 TATGCCATCT
* *
250314 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
250335 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
250356 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
250377 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
250398 CCGCAGGGTT
1 CCGCAGGGTT
250408 TTATACCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 65 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.35, G:0.27, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:250980 original size:34 final size:34
Alignment explanation
Indices: 250930--251026 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
250920 AAATGTTTTT
*
250930 AAAATACAAATTATATTATTCAAAATTTAAAATA
1 AAAATAAAAATTATATTATTCAAAATTTAAAATA
* * *
250964 AAAATAAAAATAATATTATTCAAAA-TTAAATTT
1 AAAATAAAAATTATATTATTCAAAATTTAAAATA
* *
250997 AAAATATAAATTATAGTATTCAAAATTTAA
1 AAAATAAAAATTATATTATTCAAAATTTAA
251027 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCAAAATTTAAAATA
Found at i:250993 original size:28 final size:27
Alignment explanation
Indices: 250958--251010 Score: 63
Period size: 28 Copynumber: 1.9 Consensus size: 27
250948 TTCAAAATTT
250958 AAAATAAAAATAAAA-ATAATATTATTC
1 AAAATAAAAATAAAATATAA-ATTATTC
**
250985 AAAATTAAATTTAAAATATAAATTAT
1 AAAA-TAAAAATAAAATATAAATTAT
251011 AGTATTCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
27 4 0.18
28 14 0.64
29 4 0.18
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (27 bp):
AAAATAAAAATAAAATATAAATTATTC
Found at i:251033 original size:34 final size:33
Alignment explanation
Indices: 250928--251033 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
250918 ATAAATGTTT
*
250928 TTAAAATACAAATTATATTATTCAAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCAAAATTT-AAA
* *
250962 TAAAAATAAAAATAATATTATTCAAAA-TTAAA
1 TTAAAATAAAAATTATATTATTCAAAATTTAAA
* *
250994 TTTAAAATATAAATTATAGTATTCAAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCAAAATTTAA-A
251029 TTAAA
1 TTAAA
251034 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.58, C:0.05, G:0.01, T:0.37
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCAAAATTTAAA
Found at i:251655 original size:128 final size:127
Alignment explanation
Indices: 251427--252086 Score: 1151
Period size: 128 Copynumber: 5.2 Consensus size: 127
251417 TTACATGATT
251427 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
***
251492 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATGAGAAATAATAGG
251555 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
***
251620 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATGAGAAATAATAGG
251683 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
251748 TAACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAAT-GAGAAATAATAGG
*
251811 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGACAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
251876 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAAT-GAGAAATAATAGG
251939 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
252004 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAAT-AGTAAAATAATATG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATGAG--AAATAATAGG
252067 TACTGATATATCTAGTGTCC
1 TACTGATATATCTAGTGTCC
252087 AGCTCTGTTA
Statistics
Matches: 517, Mismatches: 12, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
126 1 0.00
127 1 0.00
128 515 1.00
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.23
Consensus pattern (127 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATGAGAAATAATAGG
Found at i:253785 original size:74 final size:74
Alignment explanation
Indices: 253651--253788 Score: 168
Period size: 74 Copynumber: 1.9 Consensus size: 74
253641 GAGTACAAAT
* * ** * * *
253651 AAAATTTCAGGGTGGGCATCGTCCGTAAAATAAGTAACTAATCGTAGAAAACTCATATTTCAGGG
1 AAAATTTCAGGGTGAGCATCATCAATAAAATAAGTAACTAATCGAAAAAAACTCAGATTTCAGGG
253716 TGGGCATGA
66 TGGGCATGA
* * * * *
253725 AAAATTTCAGGGTGAGTATCATCAATAAAATAAGTAATTGATCGAAAAAAATTCCGATTTCAGG
1 AAAATTTCAGGGTGAGCATCATCAATAAAATAAGTAACTAATCGAAAAAAACTCAGATTTCAGG
253789 ATGGACACGT
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
74 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27
Consensus pattern (74 bp):
AAAATTTCAGGGTGAGCATCATCAATAAAATAAGTAACTAATCGAAAAAAACTCAGATTTCAGGG
TGGGCATGA
Found at i:255629 original size:26 final size:26
Alignment explanation
Indices: 255571--255624 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
255561 ATTTTATGTT
*
255571 GATAAATTTATTAAATTTTAAGAAGA
1 GATAAATTTATAAAATTTTAAGAAGA
255597 GATAAATTTATAAAATTTTAA-AAG-
1 GATAAATTTATAAAATTTTAAGAAGA
255621 GATA
1 GATA
255625 CAAATAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 4 0.15
25 3 0.11
26 20 0.74
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (26 bp):
GATAAATTTATAAAATTTTAAGAAGA
Found at i:257113 original size:24 final size:24
Alignment explanation
Indices: 257081--257140 Score: 113
Period size: 24 Copynumber: 2.5 Consensus size: 24
257071 TCATTTTATA
257081 AAAAT-AAATTTAATTTAATTGAT
1 AAAATGAAATTTAATTTAATTGAT
257104 AAAATGAAATTTAATTTAATTGAT
1 AAAATGAAATTTAATTTAATTGAT
257128 AAAATGAAATTTA
1 AAAATGAAATTTA
257141 TTCATTTTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 5 0.14
24 31 0.86
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (24 bp):
AAAATGAAATTTAATTTAATTGAT
Found at i:257210 original size:23 final size:22
Alignment explanation
Indices: 257167--257210 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
257157 TATTTAATTA
*
257167 ATTTTATTTGATTAAATATTTG
1 ATTTTATTTGATTAAAAATTTG
257189 ATTTTAATTT-ATTCAAAAATTT
1 ATTTT-ATTTGATT-AAAAATTT
257211 TGAAATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (22 bp):
ATTTTATTTGATTAAAAATTTG
Found at i:265100 original size:16 final size:16
Alignment explanation
Indices: 265051--265102 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
265041 ATAAAAAATA
265051 AATTTGAAAGTTAGAGT
1 AATTTGAAAGTTA-AGT
265068 AA-TT-AAA-TTAGAAGT
1 AATTTGAAAGTT--AAGT
265083 AATTTGAAAGTTAAGT
1 AATTTGAAAGTTAAGT
265099 AATT
1 AATT
265103 AAATTAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 11
0.73 0.00 0.27
Matches are distributed among these distances:
14 2 0.07
15 8 0.27
16 13 0.43
17 5 0.17
18 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.37
Consensus pattern (16 bp):
AATTTGAAAGTTAAGT
Found at i:273125 original size:39 final size:39
Alignment explanation
Indices: 273071--273160 Score: 144
Period size: 39 Copynumber: 2.3 Consensus size: 39
273061 GTATCTCCTT
* *
273071 TGACGATCTTGATTCCCCACCGTCTGATGCGTTGGTTGA
1 TGACGATCTCGATTCCCCACCGTCTGACGCGTTGGTTGA
*
273110 TGACGATCTCGATTCCCCACCTTCTGACGCGTTGGTTGA
1 TGACGATCTCGATTCCCCACCGTCTGACGCGTTGGTTGA
*
273149 TGATGATCTCGA
1 TGACGATCTCGA
273161 CAGCATTGAG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.17, C:0.27, G:0.24, T:0.32
Consensus pattern (39 bp):
TGACGATCTCGATTCCCCACCGTCTGACGCGTTGGTTGA
Found at i:273917 original size:42 final size:42
Alignment explanation
Indices: 273868--273993 Score: 189
Period size: 42 Copynumber: 3.0 Consensus size: 42
273858 GTTAGTGGCG
* * * *
273868 CAGGGGCAAACAGGATTTGTCCAATTTCAGGGTGGGAAAGCA
1 CAGGGGCATACAGAATTTGCCCGATTTCAGGGTGGGAAAGCA
* **
273910 CGGGGGCATACAGAATTTGCCCGATTTCAAAGTGGGAAAGCA
1 CAGGGGCATACAGAATTTGCCCGATTTCAGGGTGGGAAAGCA
273952 CAGGGGCATACAGAATTTGCCCGATTTCAGGGTGGGAAAGCA
1 CAGGGGCATACAGAATTTGCCCGATTTCAGGGTGGGAAAGCA
273994 GTGTTCAGAG
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 74 1.00
ACGTcount: A:0.30, C:0.18, G:0.33, T:0.19
Consensus pattern (42 bp):
CAGGGGCATACAGAATTTGCCCGATTTCAGGGTGGGAAAGCA
Found at i:275207 original size:20 final size:21
Alignment explanation
Indices: 275169--275218 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 21
275159 GAATAGGTTA
275169 TATTTAATTTTAAAATATTAT
1 TATTTAATTTTAAAATATTAT
275190 TATTTAA-TTT--AAT-TTAT
1 TATTTAATTTTAAAATATTAT
*
275207 TATTTTATTTTA
1 TATTTAATTTTA
275219 CATTGAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 10 0.38
18 6 0.23
20 3 0.12
21 7 0.27
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TATTTAATTTTAAAATATTAT
Found at i:275859 original size:8 final size:8
Alignment explanation
Indices: 275840--275893 Score: 56
Period size: 8 Copynumber: 6.8 Consensus size: 8
275830 ATGGTATGTT
275840 TATTTTTAA
1 TATTTTT-A
275849 TATTTTTA
1 TATTTTTA
275857 TATTTTTA
1 TATTTTTA
275865 TA-TTTTA
1 TATTTTTA
* * *
275872 AAATTTAA
1 TATTTTTA
*
275880 AATTTTTA
1 TATTTTTA
275888 TATTTT
1 TATTTT
275894 AAAAATCAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
7 6 0.15
8 26 0.67
9 7 0.18
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TATTTTTA
Found at i:276841 original size:18 final size:18
Alignment explanation
Indices: 276799--276842 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 18
276789 TTGATACAAA
276799 ACACCCAAATTTGATGAG
1 ACACCCAAATTTGATGAG
276817 --A--CAAATTTGATGAG
1 ACACCCAAATTTGATGAG
276831 ACACCCAAATTT
1 ACACCCAAATTT
276843 AACAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 8
0.73 0.00 0.27
Matches are distributed among these distances:
14 13 0.59
16 2 0.09
18 7 0.32
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (18 bp):
ACACCCAAATTTGATGAG
Found at i:279390 original size:31 final size:30
Alignment explanation
Indices: 279352--279431 Score: 106
Period size: 31 Copynumber: 2.6 Consensus size: 30
279342 TATTAGCATA
*
279352 TAATTAAAATAAAAAAATTTGAAAGTTAGAG
1 TAATTAAATTAAAAAAATTTGAAAGTTA-AG
* **
279383 TAATTAAATTAGGAGTAATTTGAAAGTTAAG
1 TAATTAAATTA-AAAAAATTTGAAAGTTAAG
279414 TAATTAAATTAAAAAAAT
1 TAATTAAATTAAAAAAAT
279432 AAGCTTCAAC
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
30 4 0.10
31 23 0.56
32 14 0.34
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (30 bp):
TAATTAAATTAAAAAAATTTGAAAGTTAAG
Found at i:279400 original size:15 final size:14
Alignment explanation
Indices: 279377--279424 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 14
279367 AATTTGAAAG
279377 TTAGAGTAATTAAA
1 TTAGAGTAATTAAA
279391 TTAGGAGTAATTTGAAA
1 TTA-GAGTAA-TT-AAA
279408 GTTA-AGTAATTAAA
1 -TTAGAGTAATTAAA
279422 TTA
1 TTA
279425 AAAAAATAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
13 3 0.10
14 6 0.20
15 8 0.27
16 7 0.23
17 3 0.10
18 3 0.10
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.38
Consensus pattern (14 bp):
TTAGAGTAATTAAA
Found at i:279417 original size:16 final size:17
Alignment explanation
Indices: 279367--279418 Score: 67
Period size: 16 Copynumber: 3.2 Consensus size: 17
279357 AAAATAAAAA
279367 AATTTGAAAGTTAGAGT
1 AATTTGAAAGTTAGAGT
279384 AA-TT-AAA-TTAGGAGT
1 AATTTGAAAGTTA-GAGT
279399 AATTTGAAAGTTA-AGT
1 AATTTGAAAGTTAGAGT
279415 AATT
1 AATT
279419 AAATTAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
14 3 0.10
15 9 0.29
16 11 0.35
17 5 0.16
18 3 0.10
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.37
Consensus pattern (17 bp):
AATTTGAAAGTTAGAGT
Found at i:286663 original size:141 final size:141
Alignment explanation
Indices: 286409--286693 Score: 561
Period size: 141 Copynumber: 2.0 Consensus size: 141
286399 AAAAGTGTAC
286409 CTACAGAAGTCATGATTTTAGAATGTAAAACTTCGATTAACCTTGTAATTAATGGATGGAATAAT
1 CTACAGAAGTCATGATTTTAGAATGTAAAACTTCGATTAACCTTGTAATTAATGGATGGAATAAT
286474 GTGACCTCACCATCAGACAAATTGTGAAGATAAGATACAAGTGAACAAACTCGACTGAATGATGA
66 GTGACCTCACCATCAGACAAATTGTGAAGATAAGATACAAGTGAACAAACTCGACTGAATGATGA
286539 GTTTAAATCGT
131 GTTTAAATCGT
*
286550 CTACAGAATTCATGATTTTAGAATGTAAAACTTCGATTAACCTTGTAATTAATGGATGGAATAAT
1 CTACAGAAGTCATGATTTTAGAATGTAAAACTTCGATTAACCTTGTAATTAATGGATGGAATAAT
286615 GTGACCTCACCATCAGACAAATTGTGAAGATAAGATACAAGTGAACAAACTCGACTGAATGATGA
66 GTGACCTCACCATCAGACAAATTGTGAAGATAAGATACAAGTGAACAAACTCGACTGAATGATGA
286680 GTTTAAATCGT
131 GTTTAAATCGT
286691 CTA
1 CTA
286694 TTAGTAGATA
Statistics
Matches: 143, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
141 143 1.00
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (141 bp):
CTACAGAAGTCATGATTTTAGAATGTAAAACTTCGATTAACCTTGTAATTAATGGATGGAATAAT
GTGACCTCACCATCAGACAAATTGTGAAGATAAGATACAAGTGAACAAACTCGACTGAATGATGA
GTTTAAATCGT
Found at i:292294 original size:25 final size:24
Alignment explanation
Indices: 292242--292288 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
292232 GCAAAGAATC
292242 AAAAAAATGCCAAAAAAACATAAA
1 AAAAAAATGCCAAAAAAACATAAA
*
292266 AAAAAATATGCCATAAAAACATA
1 AAAAAA-ATGCCAAAAAAACATA
292289 TGAAAACGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.70, C:0.13, G:0.04, T:0.13
Consensus pattern (24 bp):
AAAAAAATGCCAAAAAAACATAAA
Found at i:292644 original size:16 final size:16
Alignment explanation
Indices: 292623--292653 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
292613 CAAATTTAAT
*
292623 CCGAACCGAAAGTAAA
1 CCGAACAGAAAGTAAA
292639 CCGAACAGAAAGTAA
1 CCGAACAGAAAGTAA
292654 CTCAAACCAA
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:0.52, C:0.23, G:0.19, T:0.06
Consensus pattern (16 bp):
CCGAACAGAAAGTAAA
Found at i:293255 original size:20 final size:20
Alignment explanation
Indices: 293227--293276 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
293217 CACCCAATCT
* *
293227 AAATCTAATCCGATCTGAATA
1 AAAT-TAATCAGATCTAAATA
293248 AAATTAATCAGATCTAAATA
1 AAATTAATCAGATCTAAATA
293268 AAATTAATC
1 AAATTAATC
293277 TGAATATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 23 0.85
21 4 0.15
ACGTcount: A:0.50, C:0.14, G:0.06, T:0.30
Consensus pattern (20 bp):
AAATTAATCAGATCTAAATA
Found at i:297391 original size:20 final size:20
Alignment explanation
Indices: 297363--297401 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
297353 TGGCAACAAA
* *
297363 AATGATTTATAATTGACATC
1 AATGATTTAAAAGTGACATC
*
297383 AATGGTTTAAAAGTGACAT
1 AATGATTTAAAAGTGACAT
297402 GGAAAAATTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (20 bp):
AATGATTTAAAAGTGACATC
Found at i:297649 original size:28 final size:28
Alignment explanation
Indices: 297618--297679 Score: 124
Period size: 28 Copynumber: 2.2 Consensus size: 28
297608 TAGATCGAGA
297618 GAAATTGTAATTCCTATTTTCTCATAGT
1 GAAATTGTAATTCCTATTTTCTCATAGT
297646 GAAATTGTAATTCCTATTTTCTCATAGT
1 GAAATTGTAATTCCTATTTTCTCATAGT
297674 GAAATT
1 GAAATT
297680 CTTCTACCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.45
Consensus pattern (28 bp):
GAAATTGTAATTCCTATTTTCTCATAGT
Found at i:304102 original size:2 final size:2
Alignment explanation
Indices: 304097--304133 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
304087 ACAAAAAATG
304097 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
304134 TTATTTAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:313282 original size:4 final size:4
Alignment explanation
Indices: 313273--313355 Score: 157
Period size: 4 Copynumber: 20.8 Consensus size: 4
313263 TATAATACAT
*
313273 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AAAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
313321 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
313356 TATATATATA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 77 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:314635 original size:57 final size:57
Alignment explanation
Indices: 314545--314662 Score: 200
Period size: 57 Copynumber: 2.1 Consensus size: 57
314535 GGCTTCCCAT
* * *
314545 ATAAGTAATTTAACCAAACATAAAGGCTACTTAGGTTGGTGGATTGGTTAATTCTTA
1 ATAAGTAATTTAACCAAACATAAAGGCTACTTAGGTTGGTGCATAGGTTAATGCTTA
*
314602 ATAAGTAATTTAACCAAACATAAAGGCTCCTTAGGTTGGTGCATAGGTTAATGCTTA
1 ATAAGTAATTTAACCAAACATAAAGGCTACTTAGGTTGGTGCATAGGTTAATGCTTA
314659 ATAA
1 ATAA
314663 ATGCGCTAAC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (57 bp):
ATAAGTAATTTAACCAAACATAAAGGCTACTTAGGTTGGTGCATAGGTTAATGCTTA
Found at i:315048 original size:2 final size:2
Alignment explanation
Indices: 315036--315067 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
315026 ACAAGTCGAG
*
315036 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
315068 CACACTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:318295 original size:15 final size:15
Alignment explanation
Indices: 318275--318303 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
318265 TTTGTGTTAT
318275 TAATTTTTAATTAAA
1 TAATTTTTAATTAAA
318290 TAATTTTTAATTAA
1 TAATTTTTAATTAA
318304 TTAAAAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TAATTTTTAATTAAA
Found at i:318832 original size:64 final size:64
Alignment explanation
Indices: 318740--318866 Score: 209
Period size: 64 Copynumber: 2.0 Consensus size: 64
318730 TTCTAAACGT
* *
318740 AAAAAATAGTAAATATTAAAATATGATATATATACTTAGATCAAATTAATAATTGTATCTGGTA
1 AAAAAATAATAAATATTAAAATACGATATATATACTTAGATCAAATTAATAATTGTATCTGGTA
* * *
318804 AAAAAATAATAAATATTAGAATACGATATATATACTTAGGTCAAATTAATATTTGTATCTGGT
1 AAAAAATAATAAATATTAAAATACGATATATATACTTAGATCAAATTAATAATTGTATCTGGT
318867 TTATTAGAAG
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 58 1.00
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.36
Consensus pattern (64 bp):
AAAAAATAATAAATATTAAAATACGATATATATACTTAGATCAAATTAATAATTGTATCTGGTA
Found at i:321035 original size:32 final size:31
Alignment explanation
Indices: 320999--321069 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
320989 TCAAATAACA
*
320999 TAATATATG-TTCGCTTTCATTTTTTATTTAAT
1 TAATATATGATT-ACTTTCA-TTTTTATTTAAT
* *
321031 TAATATATGATTATTTTTATTTTTATTTAAT
1 TAATATATGATTACTTTCATTTTTATTTAAT
*
321062 TAAGATAT
1 TAATATAT
321070 TGTCACAACG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 19 0.56
32 13 0.38
33 2 0.06
ACGTcount: A:0.31, C:0.04, G:0.06, T:0.59
Consensus pattern (31 bp):
TAATATATGATTACTTTCATTTTTATTTAAT
Found at i:324319 original size:21 final size:22
Alignment explanation
Indices: 324290--324330 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
324280 TAGTCTTGAT
*
324290 GTTTCGTGTTGTATTATTTTAC
1 GTTTCGTGTTGTAGTATTTTAC
324312 GTTT-GTGTTGTAGTATTTT
1 GTTTCGTGTTGTAGTATTTT
324331 TCTCTAGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.12, C:0.05, G:0.22, T:0.61
Consensus pattern (22 bp):
GTTTCGTGTTGTAGTATTTTAC
Found at i:326281 original size:19 final size:20
Alignment explanation
Indices: 326239--326311 Score: 58
Period size: 22 Copynumber: 3.4 Consensus size: 20
326229 TAATCTTTAT
* *
326239 TTTTAAAAAATAAAATTCATAA
1 TTTT-AAAAA-AAAACTCAAAA
326261 TTTTAAAAAAAAACT-AAAA
1 TTTTAAAAAAAAACTCAAAA
*
326280 TTTTCTATTAAAAAAACTCAAAA
1 -TTT-TA-AAAAAAAACTCAAAA
326303 TTCTTAAAA
1 TT-TTAAAA
326312 CCTTAATTCT
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
19 3 0.07
20 8 0.19
21 9 0.21
22 17 0.40
23 5 0.12
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (20 bp):
TTTTAAAAAAAAACTCAAAA
Found at i:336113 original size:64 final size:64
Alignment explanation
Indices: 336060--336222 Score: 220
Period size: 65 Copynumber: 2.5 Consensus size: 64
336050 CGGTGCACCA
* *
336060 AGTGTGCATCGATCCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCCAGAGTGCATCGATGCATGG
* * **
336124 ATTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
* * *
336189 AGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
336223 CAATTAATTC
Statistics
Matches: 86, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
64 39 0.45
65 47 0.55
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:336194 original size:19 final size:19
Alignment explanation
Indices: 336170--336220 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
336160 GAAAATATTC
336170 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
336189 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
336208 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
336221 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:336262 original size:65 final size:64
Alignment explanation
Indices: 336064--336271 Score: 203
Period size: 65 Copynumber: 3.2 Consensus size: 64
336054 GCACCAAGTG
* * * ** *
336064 TGCATCGATCCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGGATTG
1 TGCATCGGTGCATGAAATGCATTCGATGTTT-CAAAATATTCAGAGTGCATCGATGCATGGA-TG
336128 -
64 A
* * *
336128 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGA-GA
1 TGCATCGGTGCATGAAATGCATTCGATG-TTTCAAAATATTCAGAGTGCATCGATGCATGGATGA
* *
336192 GTGCATCGGTGCATGGAATGCATTCGATG-TTC-AATTAATTCATCGA-TGCATCGATGCATGGA
1 -TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAAT-ATTCA--GAGTGCATCGATGCATGGA
336254 CTGA
62 -TGA
336258 TGCATCGGTGCATG
1 TGCATCGGTGCATG
336272 CCTTTGAATT
Statistics
Matches: 124, Mismatches: 11, Indels: 17
0.82 0.07 0.11
Matches are distributed among these distances:
62 3 0.02
63 8 0.06
64 50 0.40
65 61 0.49
66 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (64 bp):
TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAATATTCAGAGTGCATCGATGCATGGATGA
Found at i:337559 original size:21 final size:20
Alignment explanation
Indices: 337473--337630 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
337463 AAATGACCAA
**
337473 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
337492 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
337512 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
337532 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
337553 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
337574 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
337594 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
337615 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
337631 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 40 0.39
21 46 0.45
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:337623 original size:20 final size:20
Alignment explanation
Indices: 337598--337790 Score: 246
Period size: 20 Copynumber: 9.6 Consensus size: 20
337588 GATTTTCCAG
* ** *
337598 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
337618 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
337638 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
337658 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
337678 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
337698 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
337718 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
337738 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
337759 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
337779 AATCGCAACGCG
1 AATCGCAACGCG
337791 ATTTTTAAAG
Statistics
Matches: 151, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
19 1 0.01
20 131 0.87
21 19 0.13
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:338209 original size:33 final size:33
Alignment explanation
Indices: 338170--338240 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
338160 TTCACTTAGA
338170 TTTCATTTCGCGTTACGATTCTCTAGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTAGTTGCGAT
* * *
338203 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTAGTTGCGAT
338236 TTTCA
1 TTTCA
338241 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTAGTTGCGAT
Found at i:338346 original size:21 final size:21
Alignment explanation
Indices: 338320--338396 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
338310 TGCAGAAGAG
338320 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
* **
338341 TCGCAACGTGA-AAATGACTA
1 TCGCAACGAGAGAAATGAAAA
*
338361 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAGAGAAATGAAAA
338383 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
338397 TCGCAACGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 9 0.19
21 29 0.62
22 9 0.19
ACGTcount: A:0.48, C:0.17, G:0.22, T:0.13
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:338400 original size:14 final size:14
Alignment explanation
Indices: 338381--338437 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
338371 GAAAAATGAA
338381 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
338395 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
338414 AATCGCAACGAGAG
1 AATCGCAACGAGAG
338428 AATCGCAACG
1 AATCGCAACG
338438 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:338412 original size:33 final size:33
Alignment explanation
Indices: 338374--338453 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
338364 GCAACGAGAA
338374 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
338407 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
338440 AAACCAAAATCGCA
1 AAATGAAAATCGCA
338454 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:338471 original size:19 final size:19
Alignment explanation
Indices: 338449--338576 Score: 87
Period size: 19 Copynumber: 7.1 Consensus size: 19
338439 GAAACCAAAA
*
338449 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
338468 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
338482 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
338501 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
338515 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
338535 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
338555 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
338575 TC
1 TC
338577 AACCAAAAGA
Statistics
Matches: 87, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
14 20 0.23
16 6 0.07
17 6 0.07
19 22 0.25
20 19 0.22
21 14 0.16
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:338490 original size:14 final size:14
Alignment explanation
Indices: 338471--338527 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
338461 TTTCATTTCG
338471 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
338485 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
338504 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
338518 CGTTGCGATT
1 CGTTGCGATT
338528 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:338496 original size:33 final size:33
Alignment explanation
Indices: 338454--338576 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
338444 CAAAATCGCA
338454 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
338487 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
338520 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
338561 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
338577 AACCAAAAGA
Statistics
Matches: 81, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
33 45 0.56
34 2 0.02
35 6 0.07
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.02
41 21 0.26
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:338538 original size:21 final size:21
Alignment explanation
Indices: 338512--338576 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
338502 CGCGTTGCGA
338512 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
338533 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
338553 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
338574 TTC
1 TTC
338577 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:340420 original size:93 final size:93
Alignment explanation
Indices: 340261--340483 Score: 437
Period size: 93 Copynumber: 2.4 Consensus size: 93
340251 TAGATTGCTT
*
340261 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
340326 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
340354 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
340419 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
340447 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
340484 AATACCCTGA
Statistics
Matches: 129, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 129 1.00
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:340637 original size:19 final size:18
Alignment explanation
Indices: 340613--340704 Score: 65
Period size: 19 Copynumber: 5.4 Consensus size: 18
340603 GCAACGAGAG
340613 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAAT-AA
*
340632 AATCGCAA--CGACAT--
1 AATCGCAACGCGAAATAA
*
340646 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-TAA
*
340665 AATCGCAA--CG--ACAA
1 AATCGCAACGCGAAATAA
*
340679 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-TAA
340698 AATCGCA
1 AATCGCA
340705 TTGCGATTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 19 0.32
15 1 0.02
16 6 0.10
17 7 0.12
18 1 0.02
19 26 0.43
ACGTcount: A:0.47, C:0.28, G:0.16, T:0.09
Consensus pattern (18 bp):
AATCGCAACGCGAAATAA
Found at i:340639 original size:33 final size:33
Alignment explanation
Indices: 340581--340704 Score: 176
Period size: 33 Copynumber: 3.7 Consensus size: 33
340571 TAGTTTACTT
* * * *
340581 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGACAAAA
** *
340615 TCGCAACGCGAAATGAAAATCGCAACGACATAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
340648 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
340681 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
340705 TTGCGATTTT
Statistics
Matches: 82, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
33 70 0.85
34 12 0.15
ACGTcount: A:0.46, C:0.27, G:0.17, T:0.10
Consensus pattern (33 bp):
TCGCAACGCGAAACCAAAATCGCAACGACAAAA
Found at i:340651 original size:14 final size:14
Alignment explanation
Indices: 340630--340688 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
340620 ACGCGAAATG
340630 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
340644 ATAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
340663 AAAATCGCAACGAC
1 AAAATCGCAACGAC
340677 AAAATCGCAACG
1 AAAATCGCAACG
340689 CGAAACCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.47, C:0.29, G:0.15, T:0.08
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:340722 original size:19 final size:19
Alignment explanation
Indices: 340700--340872 Score: 159
Period size: 19 Copynumber: 9.6 Consensus size: 19
340690 GAAACCAAAA
*
340700 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
340719 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
340733 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
340752 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
340768 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
340785 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
340804 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
340823 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
340842 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
340862 TCGTGTTGCGA
1 TCGCGTTGCGA
340873 AAGTAAACTA
Statistics
Matches: 126, Mismatches: 17, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
14 17 0.13
16 8 0.06
17 8 0.06
19 81 0.64
20 12 0.10
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:340741 original size:14 final size:14
Alignment explanation
Indices: 340722--340778 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
340712 TTTCATTTCG
340722 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
340736 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
*
340753 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTCT
340769 CGTTGCGATT
1 CGTTGCGATT
340779 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 7 0.19
17 7 0.19
19 6 0.17
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:340830 original size:38 final size:38
Alignment explanation
Indices: 340700--340872 Score: 168
Period size: 33 Copynumber: 4.8 Consensus size: 38
340690 GAAACCAAAA
*
340700 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
340735 T--CGTTGCGATTTTCATTTCGCATTGCGA-T-TC-TG
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* **
340768 T--CGTTGCGATTTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
** *
340804 TCGCGTTGCGATTTTGGTTTCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
340842 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTTCA-TTTCGCGTTGCGA
340873 AAGTAAACTA
Statistics
Matches: 115, Mismatches: 15, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
31 2 0.02
32 1 0.01
33 52 0.45
34 1 0.01
35 2 0.02
36 2 0.02
38 44 0.38
39 11 0.10
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
Found at i:342815 original size:14 final size:14
Alignment explanation
Indices: 342795--342859 Score: 121
Period size: 14 Copynumber: 4.6 Consensus size: 14
342785 GATTGTTTAA
342795 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
*
342809 ATGATTTGTAAAAG
1 TTGATTTGTAAAAG
342823 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
342837 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
342851 TTGATTTGT
1 TTGATTTGT
342860 GTAATTGATG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 49 1.00
ACGTcount: A:0.34, C:0.00, G:0.22, T:0.45
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:342982 original size:19 final size:19
Alignment explanation
Indices: 342966--343063 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
342956 AAAAATGACT
342966 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
342985 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
343004 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
343018 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
343037 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
343057 ATCGCAA
1 ATCGCAA
343064 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:343095 original size:53 final size:53
Alignment explanation
Indices: 342966--343082 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
342956 AAAAATGACT
342966 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
343018 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
343071 ATCGCAATGCGA
1 ATCGCAATGCGA
343083 TTTTCATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.45
53 35 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:343139 original size:34 final size:34
Alignment explanation
Indices: 343096--343389 Score: 177
Period size: 34 Copynumber: 8.5 Consensus size: 34
343086 TCATTTCGCA
343096 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
*
343130 TTGCGATTTTCATTT-CGCATTGCGATT-T-TCAT
1 TTGCGATTTTCATTTCCGCATTGCGATTCTCTC-G
* * *
343162 TTCCGCA-TTGCGATTCTCTCG--TTGCGATT-T-TCAT
1 TTGCG-ATTTTC-ATT-TC-CGCATTGCGATTCTCTC-G
* * *
343196 TTACGCA-TTGCGATTCTCTCG--TTGCGATTTTCATTTCG
1 TTGCG-ATTTTC-ATT-TC-CGCATTGCGA--TTC-TCTCG
343234 CATTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
* * *
343270 TTACGATTTTCATTT-CGCATTGCGTTTCATTTCG
1 TTGCGATTTTCATTTCCGCATTGCGATTC-TCTCG
*
343304 CATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 --TTGCGATTTTCATTTCCGCATTGCGATTCTC-TCG
*
343340 TTG-GTATTTTCATTT-CGCATTGCGATTCTCTCA
1 TTGCG-ATTTTCATTTCCGCATTGCGATTCTCTCG
* *
343373 TTGCGATTGTAATTTCC
1 TTGCGATTTTCATTTCC
343390 ATGTTGCGAT
Statistics
Matches: 216, Mismatches: 19, Indels: 50
0.76 0.07 0.18
Matches are distributed among these distances:
31 2 0.01
32 9 0.04
33 54 0.25
34 88 0.41
36 24 0.11
37 17 0.08
38 3 0.01
39 12 0.06
40 7 0.03
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (34 bp):
TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
Found at i:343141 original size:53 final size:52
Alignment explanation
Indices: 343078--343366 Score: 301
Period size: 53 Copynumber: 5.5 Consensus size: 52
343068 AGAATCGCAA
343078 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATT-TCTCGT
343131 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATT-TCTCGT
* * * * *
343184 TGCGATTTTCATTTACGCATTGCGATTCTCTC-GTTGCG-ATTTTC-ATTTCGCAT
1 TGCGATTTTCATTT-CGCATTGCGATT-T-TCATTTCCGCA-TTGCGATTTCTCGT
* * * * *
343237 TGCGATTTTCATTTCCGCATTGCGATTCTCTC-GTTACG-ATTTTC-ATTTCGCAT
1 TGCGATTTTCATTT-CGCATTGCGATT-T-TCATTTCCGCA-TTGCGATTTCTCGT
343290 TGCG--TTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTT-TCATGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTCTC--GT
343341 TG-GTATTTTCATTTCGCATTGCGATT
1 TGCG-ATTTTCATTTCGCATTGCGATT
343367 CTCTCATTGC
Statistics
Matches: 212, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
48 2 0.01
49 9 0.04
50 18 0.08
51 11 0.05
53 146 0.69
54 16 0.08
55 8 0.04
56 2 0.01
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (52 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTCTCGT
Found at i:343197 original size:87 final size:86
Alignment explanation
Indices: 343096--343338 Score: 405
Period size: 87 Copynumber: 2.8 Consensus size: 86
343086 TCATTTCGCA
343096 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCA
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCA
343161 TTTCCGCATTGCGATTCTCTCG
65 TTTCCGCATTGCGATTCTCTCG
343183 TTGCGATTTTCATTTACGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCA
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCA
343248 TTTCCGCATTGCGATTCTCTCG
65 TTTCCGCATTGCGATTCTCTCG
* * *
343270 TTACGATTTTCATTTCGCATTGCGTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTT
1 TTGCGATTTTCATTTCGCATTGCGATTC-TCTCG--TTGCGATTTTCATTT-CGCATTGCGATTT
343335 TCAT
62 TCAT
343339 GTTGGTATTT
Statistics
Matches: 148, Mismatches: 4, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
86 12 0.08
87 104 0.70
89 15 0.10
90 17 0.11
ACGTcount: A:0.14, C:0.24, G:0.16, T:0.46
Consensus pattern (86 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
TTCCGCATTGCGATTCTCTCG
Found at i:345668 original size:12 final size:12
Alignment explanation
Indices: 345651--345675 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
345641 TCTTCGGAGA
345651 CTTTTTCTTCTT
1 CTTTTTCTTCTT
345663 CTTTTTCTTCTT
1 CTTTTTCTTCTT
345675 C
1 C
345676 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:345884 original size:24 final size:24
Alignment explanation
Indices: 345850--345896 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
345840 CTGAAACATC
345850 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
345874 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
345897 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:346617 original size:20 final size:20
Alignment explanation
Indices: 346589--346817 Score: 253
Period size: 20 Copynumber: 11.4 Consensus size: 20
346579 AAATTTCAGT
* * *
346589 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
346609 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
346629 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
346649 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
346669 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
346689 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
346709 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
346729 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
346749 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
346769 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
346789 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
346809 GTTGCGATT
1 GTTGCGATT
346818 CTGGAAAATC
Statistics
Matches: 185, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
20 184 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:347626 original size:27 final size:27
Alignment explanation
Indices: 347583--347636 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
347573 ATAATAAGAG
*
347583 ATATAATCAATGGTTGTGGTTTTACGC
1 ATATAATCAATAGTTGTGGTTTTACGC
*
347610 ATATAATCAATATTTGTGGTTTTACGC
1 ATATAATCAATAGTTGTGGTTTTACGC
347637 TAAGTGAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.43
Consensus pattern (27 bp):
ATATAATCAATAGTTGTGGTTTTACGC
Found at i:351898 original size:17 final size:17
Alignment explanation
Indices: 351874--351917 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
351864 ATATATCATC
351874 AATA-AAAATATAAGAA-
1 AATATAAAATATAA-AAG
351890 AATATAAAATATAAAAG
1 AATATAAAATATAAAAG
351907 AATATGAAAAT
1 AATAT-AAAAT
351918 TTTAAGGGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.24
17 14 0.56
18 5 0.20
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (17 bp):
AATATAAAATATAAAAG
Found at i:352268 original size:16 final size:16
Alignment explanation
Indices: 352243--352276 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
352233 TGATTAAGTA
*
352243 CTGAATGATTCAAATG
1 CTGAACGATTCAAATG
*
352259 CTGAACGATTCAGATG
1 CTGAACGATTCAAATG
352275 CT
1 CT
352277 CTGAATGAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (16 bp):
CTGAACGATTCAAATG
Found at i:352545 original size:18 final size:19
Alignment explanation
Indices: 352510--352546 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
352500 CACGGAATGT
352510 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
352530 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
352547 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:353897 original size:29 final size:30
Alignment explanation
Indices: 353840--353922 Score: 141
Period size: 29 Copynumber: 2.8 Consensus size: 30
353830 GTAACTTTAG
353840 TACCTAAAGTTTTATTTTTTTTCAAAATCA
1 TACCTAAAGTTTTATTTTTTTTCAAAATCA
353870 TACCTAAAGTTTTATTTTTTTT-AAAATCA
1 TACCTAAAGTTTTATTTTTTTTCAAAATCA
* *
353899 TACCTAAAGTTTTGTTTTGTTTCA
1 TACCTAAAGTTTTATTTTTTTTCA
353923 TTTTAGCACT
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
29 27 0.54
30 23 0.46
ACGTcount: A:0.30, C:0.12, G:0.06, T:0.52
Consensus pattern (30 bp):
TACCTAAAGTTTTATTTTTTTTCAAAATCA
Found at i:362941 original size:19 final size:19
Alignment explanation
Indices: 362917--362953 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
362907 CGTAGATCTA
362917 AACCCT-AAAGATACTTAAT
1 AACCCTAAAAG-TACTTAAT
362936 AACCCTAAAAGTACTTAA
1 AACCCTAAAAGTACTTAA
362954 CTGCCCTAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.49, C:0.22, G:0.05, T:0.24
Consensus pattern (19 bp):
AACCCTAAAAGTACTTAAT
Found at i:373907 original size:44 final size:44
Alignment explanation
Indices: 373803--373888 Score: 136
Period size: 44 Copynumber: 2.0 Consensus size: 44
373793 TTTAATAGCC
* *
373803 CCCTATTGGTCGTGGGTTGTATCACGATTCATAGATTTTTATCT
1 CCCTATTGGTCGTGGGGTGTATCACGATTCATAGATTTGTATCT
* *
373847 CCCTGTTGGTCGTGGGGTGTATCACTATTCATAGATTTGTAT
1 CCCTATTGGTCGTGGGGTGTATCACGATTCATAGATTTGTAT
373889 TTCCTTATCT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.42
Consensus pattern (44 bp):
CCCTATTGGTCGTGGGGTGTATCACGATTCATAGATTTGTATCT
Found at i:385225 original size:10 final size:10
Alignment explanation
Indices: 385210--385259 Score: 52
Period size: 10 Copynumber: 5.0 Consensus size: 10
385200 GTCTATAAAA
385210 ATATTATATT
1 ATATTATATT
385220 ATATTATATT
1 ATATTATATT
385230 -TATT-TATT
1 ATATTATATT
385238 -TATTATTATT
1 ATATTA-TATT
385248 ATTATTAATATT
1 A-TATT-ATATT
385260 TTTTATTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
8 8 0.23
9 4 0.11
10 14 0.40
12 8 0.23
13 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
ATATTATATT
Found at i:385239 original size:8 final size:9
Alignment explanation
Indices: 385211--385252 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
385201 TCTATAAAAA
385211 TATTATATT
1 TATTATATT
385220 ATATTATATT
1 -TATTATATT
385230 TATT-TATT
1 TATTATATT
385238 TATTAT-TAT
1 TATTATAT-T
385247 TATTAT
1 TATTAT
385253 TAATATTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
8 9 0.30
9 12 0.40
10 9 0.30
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TATTATATT
Found at i:385360 original size:33 final size:33
Alignment explanation
Indices: 385323--385388 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
385313 GAAAATAAAT
*
385323 CAACGTATTTGAGTCCTATTGAAA-CACTAAAAC
1 CAACGTATTTGAGTCATATT-AAAGCACTAAAAC
385356 CAACGTATTTGAGTCATATTAAAGCACTAAAAC
1 CAACGTATTTGAGTCATATTAAAGCACTAAAAC
385389 TGAAGCATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 3 0.10
33 28 0.90
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (33 bp):
CAACGTATTTGAGTCATATTAAAGCACTAAAAC
Found at i:385716 original size:26 final size:26
Alignment explanation
Indices: 385687--385749 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
385677 TTTTTATTTC
*
385687 ATTTTTTATTT-AT-TTACTTTATATAT
1 ATTTTTTATTTCATCTTAATTT-TA-AT
*
385713 ATTTTTCATTTCATCTTAATTTTAAT
1 ATTTTTTATTTCATCTTAATTTTAAT
385739 A-TTTTTATTTC
1 ATTTTTTATTTC
385750 TTTTTACATT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
25 9 0.28
26 13 0.41
27 4 0.12
28 6 0.19
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (26 bp):
ATTTTTTATTTCATCTTAATTTTAAT
Found at i:385944 original size:12 final size:13
Alignment explanation
Indices: 385922--385950 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
385912 CGGATTAAAT
385922 TTTTGAATTTTAA
1 TTTTGAATTTTAA
385935 TTTT-AATTTTAA
1 TTTTGAATTTTAA
385947 TTTT
1 TTTT
385951 CGCAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (13 bp):
TTTTGAATTTTAA
Found at i:387617 original size:17 final size:17
Alignment explanation
Indices: 387597--387629 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
387587 TATTCGTAAT
387597 CAACACT-TATTACATAC
1 CAACACTCTA-TACATAC
387614 CAACACTCTATACATA
1 CAACACTCTATACATA
387630 ATCAAGTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.27
Consensus pattern (17 bp):
CAACACTCTATACATAC
Found at i:388095 original size:15 final size:15
Alignment explanation
Indices: 388072--388149 Score: 138
Period size: 15 Copynumber: 5.2 Consensus size: 15
388062 CGTAGGACTC
388072 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
388087 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
388102 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
388117 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
388132 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
388147 CTA
1 CTA
388150 TTATACCCTC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 59 1.00
ACGTcount: A:0.31, C:0.33, G:0.22, T:0.14
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:388108 original size:30 final size:30
Alignment explanation
Indices: 388072--388149 Score: 156
Period size: 30 Copynumber: 2.6 Consensus size: 30
388062 CGTAGGACTC
388072 CTACATCCCGAAGGACTACGTCCCGAAGGA
1 CTACATCCCGAAGGACTACGTCCCGAAGGA
388102 CTACATCCCGAAGGACTACGTCCCGAAGGA
1 CTACATCCCGAAGGACTACGTCCCGAAGGA
388132 CTACATCCCGAAGGACTA
1 CTACATCCCGAAGGACTA
388150 TTATACCCTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.31, C:0.33, G:0.22, T:0.14
Consensus pattern (30 bp):
CTACATCCCGAAGGACTACGTCCCGAAGGA
Found at i:388276 original size:29 final size:29
Alignment explanation
Indices: 388234--388307 Score: 132
Period size: 29 Copynumber: 2.6 Consensus size: 29
388224 TTTCATATGT
388234 TCATGTA-CTCATGTCATTTCTCCTGTGA
1 TCATGTAGCTCATGTCATTTCTCCTGTGA
*
388262 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCCTGTGA
388291 TCATGTAGCTCATGTCA
1 TCATGTAGCTCATGTCA
388308 CTTCATATCA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 7 0.16
29 37 0.84
ACGTcount: A:0.19, C:0.23, G:0.16, T:0.42
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCCTGTGA
Found at i:388754 original size:19 final size:19
Alignment explanation
Indices: 388730--388816 Score: 76
Period size: 19 Copynumber: 4.7 Consensus size: 19
388720 TATTGTTGGG
388730 ATGCATCGATGCACTCCTT
1 ATGCATCGATGCACTCCTT
**
388749 ATGCATCGATGCAC-CGAT
1 ATGCATCGATGCACTCCTT
**
388767 -TGCATTCGATG-TTTCAC-T
1 ATGCA-TCGATGCACTC-CTT
*
388785 AT-CATCGATGCACTACTT
1 ATGCATCGATGCACTCCTT
388803 ATGCATCGATGCAC
1 ATGCATCGATGCAC
388817 GAATTGCATT
Statistics
Matches: 53, Mismatches: 8, Indels: 14
0.71 0.11 0.19
Matches are distributed among these distances:
17 11 0.21
18 16 0.30
19 26 0.49
ACGTcount: A:0.24, C:0.28, G:0.17, T:0.31
Consensus pattern (19 bp):
ATGCATCGATGCACTCCTT
Found at i:392410 original size:37 final size:37
Alignment explanation
Indices: 392360--392471 Score: 181
Period size: 37 Copynumber: 3.1 Consensus size: 37
392350 TTTCCAAGTT
*
392360 TTGTCTCTCTTGAGACACTTTCCCTTGAAACAAAATC
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATC
*
392397 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATC
* *
392433 TTATCTCTCTTGAGACAGTTTCCCTTGAAATAAAATC
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATC
392470 TT
1 TT
392472 TGAATATCTT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
36 33 0.48
37 36 0.52
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (37 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATC
Found at i:392601 original size:31 final size:31
Alignment explanation
Indices: 392563--392623 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
392553 CTTAAAACAC
392563 AAAAAAACC-CTCAAAATTATTTCTCTTGAAG
1 AAAAAAACCTCTCAAAA-TATTTCTCTTGAAG
* *
392594 AAAAAAACCTTTGAAAATATTTCTCTTGAA
1 AAAAAAACCTCTCAAAATATTTCTCTTGAA
392624 ACATCAAACC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 22 0.81
32 5 0.19
ACGTcount: A:0.46, C:0.16, G:0.07, T:0.31
Consensus pattern (31 bp):
AAAAAAACCTCTCAAAATATTTCTCTTGAAG
Found at i:392780 original size:83 final size:82
Alignment explanation
Indices: 392631--392888 Score: 288
Period size: 83 Copynumber: 3.1 Consensus size: 82
392621 GAAACATCAA
* ** * *
392631 ACCTTCGAGTTCGACTACGCTCAGCTTCAAAACACATCATTTACAACATAACTCAAGACTATAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAACATAACTCAAGGCTAGAAG
392696 GGTTATCTGCCAACAAAG
66 GGTTATCTG-CAACAAAG
* * * *
392714 ACCTTCGAGTTCAACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAAATCCAGGCTAGAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAACATAACTCAAGGCTAGAAG
392779 GGTTATCTGTCAAC-AAG
66 GGTTATCTG-CAACAAAG
* * * * * * * * * *
392796 AAGCTCCGAGTTCGACTCCACTCAACTCAAAGGCACCATTATTTGCAACATAACGCAAGGCAAGA
1 -ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA-CATCATTTACAACATAACTCAAGGCTAGA
392861 AGGGTTATCTGC--CAAAG
64 AGGGTTATCTGCAACAAAG
392878 ACCTTCGAGTT
1 ACCTTCGAGTT
392889 TGATTCCATT
Statistics
Matches: 146, Mismatches: 26, Indels: 8
0.81 0.14 0.04
Matches are distributed among these distances:
81 10 0.07
82 6 0.04
83 97 0.66
84 33 0.23
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (82 bp):
ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAACATAACTCAAGGCTAGAAG
GGTTATCTGCAACAAAG
Found at i:393280 original size:21 final size:22
Alignment explanation
Indices: 393231--393290 Score: 56
Period size: 21 Copynumber: 2.9 Consensus size: 22
393221 GGTCTACAAA
393231 AATAT-TTTATTATATTTTATT
1 AATATATTTATTATATTTTATT
* *
393252 TATTTATTTA-TA-ATTATTATT
1 AATATATTTATTATATT-TTATT
*
393273 AATATATTTTTTAT-TTTT
1 AATATATTTATTATATTTT
393291 GCAGGCCCCA
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
20 3 0.10
21 19 0.63
22 8 0.27
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
AATATATTTATTATATTTTATT
Found at i:393417 original size:33 final size:33
Alignment explanation
Indices: 393347--393422 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 33
393337 AAATCAACGT
* * *
393347 ATTTGAGTCATATTGAAATACTAAAACCAATGT
1 ATTTGAGTCCTATTGAAACACTAAAACCAATGC
**
393380 ATTTGAGTCCTATTGAAACACTAAAATTGAA-GC
1 ATTTGAGTCCTATTGAAACACTAAAA-CCAATGC
393413 ATTTGAGTCC
1 ATTTGAGTCC
393423 AAGTAGGACT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 35 0.95
34 2 0.05
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.33
Consensus pattern (33 bp):
ATTTGAGTCCTATTGAAACACTAAAACCAATGC
Found at i:393809 original size:19 final size:19
Alignment explanation
Indices: 393761--393820 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 19
393751 TCTATAAAAA
393761 TATT-TTATTATATTA-TATT
1 TATTATTATT-TATTATTA-T
393780 TATTTATTTATTTATTATTAT
1 TA-TTA-TTATTTATTATTAT
393801 TATTATTATTTTATT-TTAT
1 TATTATTA-TTTATTATTAT
393820 T
1 T
393821 TGCAAGTCCT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
19 10 0.28
20 11 0.31
21 8 0.22
22 7 0.19
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TATTATTATTTATTATTAT
Done.