Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 60 of 135
Found at i:24371997 original size:34 final size:33
Alignment explanation
Indices: 24371914--24371997 Score: 107
Period size: 34 Copynumber: 2.5 Consensus size: 33
24371904 ATTCAATCCA
24371914 AAAAAAAAAAAAACAACAACAAAAACAAAAAAAC
1 AAAAAAAAAAAAA-AACAACAAAAACAAAAAAAC
* *
24371948 AAAAAAAATAAAAAAAGAACAAAAAC-CAAAAAC
1 AAAAAAAA-AAAAAAACAACAAAAACAAAAAAAC
24371981 AAAAAAAGAAACAAAAA
1 AAAAAAA-AAA-AAAAA
24371998 AATCTCTACC
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
33 15 0.33
34 25 0.56
35 5 0.11
ACGTcount: A:0.85, C:0.12, G:0.02, T:0.01
Consensus pattern (33 bp):
AAAAAAAAAAAAAAACAACAAAAACAAAAAAAC
Found at i:24372518 original size:7 final size:7
Alignment explanation
Indices: 24372506--24372557 Score: 54
Period size: 7 Copynumber: 7.3 Consensus size: 7
24372496 GAAAAATATG
24372506 TGAAAAA
1 TGAAAAA
24372513 TG-AAAA
1 TGAAAAA
*
24372519 TAAAAAAA
1 T-GAAAAA
24372527 TGAAAAA
1 TGAAAAA
24372534 TGAAAAA
1 TGAAAAA
24372541 TGGAAACAA
1 T-GAAA-AA
24372550 T-AAAAA
1 TGAAAAA
24372556 TG
1 TG
24372558 GAGAGGCTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
6 8 0.21
7 18 0.47
8 9 0.24
9 3 0.08
ACGTcount: A:0.69, C:0.02, G:0.13, T:0.15
Consensus pattern (7 bp):
TGAAAAA
Found at i:24372539 original size:14 final size:14
Alignment explanation
Indices: 24372506--24372557 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 14
24372496 GAAAAATATG
24372506 TGAAAAATG-AAAA
1 TGAAAAATGAAAAA
*
24372519 TAAAAAAATGAAAAA
1 T-GAAAAATGAAAAA
24372534 TGAAAAATGGAAACAA
1 TGAAAAAT-GAAA-AA
24372550 T-AAAAATG
1 TGAAAAATG
24372558 GAGAGGCTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
13 1 0.03
14 14 0.42
15 15 0.45
16 3 0.09
ACGTcount: A:0.69, C:0.02, G:0.13, T:0.15
Consensus pattern (14 bp):
TGAAAAATGAAAAA
Found at i:24374737 original size:50 final size:50
Alignment explanation
Indices: 24373866--24374731 Score: 560
Period size: 50 Copynumber: 17.4 Consensus size: 50
24373856 GCAGTGGAGC
* * *
24373866 AGATTGAAGTCACAACGGCAGATCTAGTTTCCCTGACAGTGCAATTAAAA
1 AGATTGAAGCCACAACGGCGGATCTGGTTTCCCTGACAGTGCAATTAAAA
*** * * * ** **
24373916 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGCAGTGGAGC
1 AGATTGAAGCCACAACGGCGGATCTGGTTTCCCTGACAGTGCAATTAAAA
* * * * *
24373966 AGATTGAAGTCACAACAGCGGATCTGGTTTCCCCGACAGCGTAATTAAAA
1 AGATTGAAGCCACAACGGCGGATCTGGTTTCCCTGACAGTGCAATTAAAA
*** * * * ** **
24374016 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGCAGTGGAGC
1 AGATTGAAGCCACAACGGCGGATCTGGTTTCCCTGACAGTGCAATTAAAA
* * *
24374066 AGATTGAAGTCACAACGGCGGATCTGGTTT-CCTCGACAGGGTAATTAAAA
1 AGATTGAAGCCACAACGGCGGATCTGGTTTCCCT-GACAGTGCAATTAAAA
*** * * * ** **
24374116 AGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGCAGTGGAGC
1 AGATTGAAGCCACAACGGCGGATCTGGTTTCCCTGACAGTGCAATTAAAA
* * * * * *
24374166 AGATTGAAGTCACAACAGCGGATCTGGTTTCCCCGGCAGCGCAACTAAAA
1 AGATTGAAGCCACAACGGCGGATCTGGTTTCCCTGACAGTGCAATTAAAA
* * *** * * * **
24374216 ATATTGAAGCTACAACGGCGGATCTTACTTCCCTGGCGGTGC-AGTAGAGC
1 AGATTGAAGCCACAACGGCGGATCTGGTTTCCCTGACAGTGCAATTA-AAA
* * *
24374266 AGATTGAAGTCACAACAGCGGATCTGGTTT-CCTCGACAGCGCAATTAAAA
1 AGATTGAAGCCACAACGGCGGATCTGGTTTCCCT-GACAGTGCAATTAAAA
* *** * * * ** **
24374316 AGATTGAAGCCACAACAGCGGATCTTACTTCCCTGGCGGTGCAGTGGAGC
1 AGATTGAAGCCACAACGGCGGATCTGGTTTCCCTGACAGTGCAATTAAAA
** * * *
24374366 AGATTGAAGTTACAACGGCAGATCTGGTTTCCCCGACAGCGCAATTAAAA
1 AGATTGAAGCCACAACGGCGGATCTGGTTTCCCTGACAGTGCAATTAAAA
* ** * * * * ** **
24374416 AGATTGAAGCTACAACGGCGGATCTTATTTCCTTGGCGGTGCAGTGGAGC
1 AGATTGAAGCCACAACGGCGGATCTGGTTTCCCTGACAGTGCAATTAAAA
* * ** *
24374466 AGATTGAAGTCACAACGGCAGATCTGGTTTCCCCCACAGCGCAATT-AAA
1 AGATTGAAGCCACAACGGCGGATCTGGTTTCCCTGACAGTGCAATTAAAA
* *** * * ** **
24374515 AGATTGAAGCCACAACGGCAGATCTTACTTCCCTGGA-GGTGCAGTGGAGC
1 AGATTGAAGCCACAACGGCGGATCTGGTTTCCCT-GACAGTGCAATTAAAA
* * *
24374565 AGATTGAAGTCACAACGGCAGATCTGGTTT-CGTCGACAGTGCAATT-AAA
1 AGATTGAAGCCACAACGGCGGATCTGGTTTCCCT-GACAGTGCAATTAAAA
* * * * * * ** *
24374614 AGATTGAAGCCACAACGGCAGATCTTAG-TTCCTTGGCGGTGCAGTGGAAC
1 AGATTGAAGCCACAACGGCGGATC-TGGTTTCCCTGACAGTGCAATTAAAA
* * **
24374664 AGATTGAAGTCACAACGGCAGATCTGGTTTCCCTGACAACGCAATTAAAA
1 AGATTGAAGCCACAACGGCGGATCTGGTTTCCCTGACAGTGCAATTAAAA
24374714 AGATTGAAGCCACAACGG
1 AGATTGAAGCCACAACGG
24374732 TAGATCTTAC
Statistics
Matches: 595, Mismatches: 208, Indels: 26
0.72 0.25 0.03
Matches are distributed among these distances:
49 84 0.14
50 502 0.84
51 9 0.02
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.22
Consensus pattern (50 bp):
AGATTGAAGCCACAACGGCGGATCTGGTTTCCCTGACAGTGCAATTAAAA
Found at i:24374822 original size:100 final size:100
Alignment explanation
Indices: 24373855--24374801 Score: 1432
Period size: 100 Copynumber: 9.5 Consensus size: 100
24373845 TCCTGGGCAT
* * * *
24373855 TGCAGTGGAGCAGATTGAAGTCACAACGGCAGATCTAGTTTCCCTGACAGTGCAATTAAAAAGAT
1 TGCAGTGGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGAT
24373920 TGAAGCCACAACGGCGGATCTTACTTCCCTGGCGG
66 TGAAGCCACAACGGCGGATCTTACTTCCCTGGCGG
* *
24373955 TGCAGTGGAGCAGATTGAAGTCACAACAGCGGATCTGGTTTCCCCGACAGCGTAATTAAAAAGAT
1 TGCAGTGGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGAT
24374020 TGAAGCCACAACGGCGGATCTTACTTCCCTGGCGG
66 TGAAGCCACAACGGCGGATCTTACTTCCCTGGCGG
* * *
24374055 TGCAGTGGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCTCGACAGGGTAATTAAAAAGAT
1 TGCAGTGGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGAT
24374120 TGAAGCCACAACGGCGGATCTTACTTCCCTGGCGG
66 TGAAGCCACAACGGCGGATCTTACTTCCCTGGCGG
* * * *
24374155 TGCAGTGGAGCAGATTGAAGTCACAACAGCGGATCTGGTTTCCCCGGCAGCGCAACTAAAAATAT
1 TGCAGTGGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGAT
*
24374220 TGAAGCTACAACGGCGGATCTTACTTCCCTGGCGG
66 TGAAGCCACAACGGCGGATCTTACTTCCCTGGCGG
* * *
24374255 TGCAGTAGAGCAGATTGAAGTCACAACAGCGGATCTGGTTTCCTCGACAGCGCAATTAAAAAGAT
1 TGCAGTGGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGAT
*
24374320 TGAAGCCACAACAGCGGATCTTACTTCCCTGGCGG
66 TGAAGCCACAACGGCGGATCTTACTTCCCTGGCGG
* *
24374355 TGCAGTGGAGCAGATTGAAGTTACAACGGCAGATCTGGTTTCCCCGACAGCGCAATTAAAAAGAT
1 TGCAGTGGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGAT
* * *
24374420 TGAAGCTACAACGGCGGATCTTATTTCCTTGGCGG
66 TGAAGCCACAACGGCGGATCTTACTTCCCTGGCGG
* *
24374455 TGCAGTGGAGCAGATTGAAGTCACAACGGCAGATCTGGTTTCCCCCACAGCGCAATT-AAAAGAT
1 TGCAGTGGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGAT
* *
24374519 TGAAGCCACAACGGCAGATCTTACTTCCCTGGAGG
66 TGAAGCCACAACGGCGGATCTTACTTCCCTGGCGG
* ** *
24374554 TGCAGTGGAGCAGATTGAAGTCACAACGGCAGATCTGGTTTCGTCGACAGTGCAATT-AAAAGAT
1 TGCAGTGGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGAT
* * *
24374618 TGAAGCCACAACGGCAGATCTTAGTTCCTTGGCGG
66 TGAAGCCACAACGGCGGATCTTACTTCCCTGGCGG
* * * *
24374653 TGCAGTGGAACAGATTGAAGTCACAACGGCAGATCTGGTTTCCCTGACAACGCAATTAAAAAGAT
1 TGCAGTGGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGAT
** * * *
24374718 TGAAGCCACAACGGTAGATCTTACCTCCTTAGCGG
66 TGAAGCCACAACGGCGGATCTTACTTCCCTGGCGG
* * * * *
24374753 TGCAGTTGAACAGATTGAAG-CTACGACGGCGGATCTTGTTTCCTCGACA
1 TGCAGTGGAGCAGATTGAAGTC-ACAACGGCGGATCTGGTTTCCCCGACA
24374802 TTGTAATTGG
Statistics
Matches: 782, Mismatches: 63, Indels: 4
0.92 0.07 0.00
Matches are distributed among these distances:
99 181 0.23
100 601 0.77
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.22
Consensus pattern (100 bp):
TGCAGTGGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGCGCAATTAAAAAGAT
TGAAGCCACAACGGCGGATCTTACTTCCCTGGCGG
Found at i:24378907 original size:5 final size:6
Alignment explanation
Indices: 24378892--24378916 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
24378882 AAAAATGCAA
24378892 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
24378917 CCTAATTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:24385304 original size:322 final size:323
Alignment explanation
Indices: 24384708--24385352 Score: 1283
Period size: 322 Copynumber: 2.0 Consensus size: 323
24384698 AAAAAAAAAT
24384708 GGGGAATTGGATGTTAATTAGAAAGGCGAATCCAAATATCCGACGCGTTTACTCCATCTCTGATC
1 GGGGAATTGGATGTTAATTAGAAAGGCGAATCCAAATATCCGACGCGTTTACTCCATCTCTGATC
24384773 ACAGCAACGCCGGTGCAATCCATTTACTCTCAAAATCTTATAAATATGCTTATTTTAAAATTAAT
66 ACAGCAACGCCGGTGCAATCCATTTACTCTCAAAATCTTATAAATATGCTTATTTTAAAATTAAT
24384838 GAGTTGGTGATATTGATATTAGACGCATTCAATAATATTTATGTTCATCAATATTTATTGAATTG
131 GAGTTGGTGATATTGATATTAGACGCATTCAATAATATTTATGTTCATCAATATTTATTGAATTG
24384903 AGTAGTAAACAGTTCGATATCATTCATATAATGAATCGAGTTTTAATTTTATGAATGAGAAATAT
196 AGTAGTAAACAGTTCGATATCATTCATATAATGAATCGAGTTTTAATTTTATGAATGAGAAATAT
24384968 GATATTAGAAGAGATTTATCATTTGTTAAAGTATTCGATTCATCTTAATTTTGAATTTAATTA
261 GATATTAGAAGAGATTTATCATTTGTTAAAGTATTCGATTCATCTTAATTTTGAATTTAATTA
24385031 GGGGAATTGG-TGTTAATTAGAAAGGCGAATCCAAATATCCGACGCGTTTACTCCATCTCTGATC
1 GGGGAATTGGATGTTAATTAGAAAGGCGAATCCAAATATCCGACGCGTTTACTCCATCTCTGATC
24385095 ACAGCAACGCCGGTGCAATCCATTTACTCTCAAAATCTTATAAATATGCTTATTTTAAAATTAAT
66 ACAGCAACGCCGGTGCAATCCATTTACTCTCAAAATCTTATAAATATGCTTATTTTAAAATTAAT
24385160 GAGTTGGTGATATTGATATTAGACGCATTCAATAATATTTATGTTCATCAATATTTATTGAATTG
131 GAGTTGGTGATATTGATATTAGACGCATTCAATAATATTTATGTTCATCAATATTTATTGAATTG
24385225 AGTAGTAAACAGTTCGATATCATTCATATAATGAATCGAGTTTTAATTTTATGAATGAGAAATAT
196 AGTAGTAAACAGTTCGATATCATTCATATAATGAATCGAGTTTTAATTTTATGAATGAGAAATAT
24385290 GATATTAGAAGAGATTTATCATTTGTTAAAGTATTCGATTCATCTTAATTTTGAATTTAATTA
261 GATATTAGAAGAGATTTATCATTTGTTAAAGTATTCGATTCATCTTAATTTTGAATTTAATTA
24385353 AGACTGAATG
Statistics
Matches: 322, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
322 312 0.97
323 10 0.03
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.38
Consensus pattern (323 bp):
GGGGAATTGGATGTTAATTAGAAAGGCGAATCCAAATATCCGACGCGTTTACTCCATCTCTGATC
ACAGCAACGCCGGTGCAATCCATTTACTCTCAAAATCTTATAAATATGCTTATTTTAAAATTAAT
GAGTTGGTGATATTGATATTAGACGCATTCAATAATATTTATGTTCATCAATATTTATTGAATTG
AGTAGTAAACAGTTCGATATCATTCATATAATGAATCGAGTTTTAATTTTATGAATGAGAAATAT
GATATTAGAAGAGATTTATCATTTGTTAAAGTATTCGATTCATCTTAATTTTGAATTTAATTA
Found at i:24388635 original size:58 final size:58
Alignment explanation
Indices: 24388551--24388710 Score: 178
Period size: 58 Copynumber: 2.8 Consensus size: 58
24388541 AATTTTTTGT
* * ** * *
24388551 CAAGTTAGGTCTTGAACTT-GATAAATATTCTTACATTGGGGCTTGAAAAACTTTTATC
1 CAAGTTAGGCCTTGAACTTAG-CAAATATTCCCACATTGAGGCTTGAAAAACTTTTACC
* * *** *
24388609 CAAGTCAGGCCTTGAACTTAGCAAATATCCCCACATTGAGGCTTGAAATTTTTTTGCC
1 CAAGTTAGGCCTTGAACTTAGCAAATATTCCCACATTGAGGCTTGAAAAACTTTTACC
* *
24388667 CAAGTTAGGGCTTGAACTTAGCAAATATTCCCACATTGTGGCTT
1 CAAGTTAGGCCTTGAACTTAGCAAATATTCCCACATTGAGGCTT
24388711 CAACTTTTTT
Statistics
Matches: 85, Mismatches: 16, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
58 84 0.99
59 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (58 bp):
CAAGTTAGGCCTTGAACTTAGCAAATATTCCCACATTGAGGCTTGAAAAACTTTTACC
Found at i:24388719 original size:58 final size:58
Alignment explanation
Indices: 24388602--24388737 Score: 182
Period size: 58 Copynumber: 2.3 Consensus size: 58
24388592 CTTGAAAAAC
* * *
24388602 TTTTATCCAAGTCAGGCCTTGAACTTAGCAAATATCCCCACATTGAGGCTTGAAATTT
1 TTTTACCCAAGTTAGGCCTTGAACTTAGCAAATATCCCCACATTGAGGCTTCAAATTT
* * * * *
24388660 TTTTGCCCAAGTTAGGGCTTGAACTTAGCAAATATTCCCACATTGTGGCTTCAACTTT
1 TTTTACCCAAGTTAGGCCTTGAACTTAGCAAATATCCCCACATTGAGGCTTCAAATTT
* *
24388718 TTTTATCCAAGTTAGTCCTT
1 TTTTACCCAAGTTAGGCCTT
24388738 AAAAATCCTA
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
58 66 1.00
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (58 bp):
TTTTACCCAAGTTAGGCCTTGAACTTAGCAAATATCCCCACATTGAGGCTTCAAATTT
Found at i:24414336 original size:23 final size:24
Alignment explanation
Indices: 24414301--24414345 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
24414291 AATTTTAAAA
*
24414301 AAAAATTTGATGATA-TAATTTTT
1 AAAAATTTGATGAGATTAATTTTT
* *
24414324 AAAATTTTTATGAGATTAATTT
1 AAAAATTTGATGAGATTAATTT
24414346 ACCAATAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (24 bp):
AAAAATTTGATGAGATTAATTTTT
Found at i:24415043 original size:31 final size:32
Alignment explanation
Indices: 24415007--24415075 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 32
24414997 TTTTTTTAGT
*
24415007 TAAATTTGACCGA-TAATCTTTTT-AAAAAAGTC
1 TAAATTTAACC-ATTAA-CTTTTTAAAAAAAGTC
24415039 -AAATTTAACCATTAACTTTTTGAAAAAAAGTC
1 TAAATTTAACCATTAACTTTTT-AAAAAAAGTC
24415071 TAAAT
1 TAAAT
24415076 GATATTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
30 7 0.22
31 12 0.38
32 9 0.28
33 4 0.12
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.36
Consensus pattern (32 bp):
TAAATTTAACCATTAACTTTTTAAAAAAAGTC
Found at i:24416926 original size:17 final size:18
Alignment explanation
Indices: 24416904--24416938 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
24416894 GGTGGATAAG
24416904 AAATAATGCCTA-TTTTT
1 AAATAATGCCTAGTTTTT
24416921 AAATAATGCCTAGTTTTT
1 AAATAATGCCTAGTTTTT
24416939 TTAGTAGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.46
Consensus pattern (18 bp):
AAATAATGCCTAGTTTTT
Found at i:24434358 original size:1 final size:1
Alignment explanation
Indices: 24434354--24434396 Score: 86
Period size: 1 Copynumber: 43.0 Consensus size: 1
24434344 CAAAAACCTT
24434354 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
24434397 GAAGAAGAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:24434409 original size:12 final size:14
Alignment explanation
Indices: 24434394--24434449 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
24434384 AAAAAAAAAA
24434394 AAAGA-AGA-AGAG
1 AAAGAGAGAGAGAG
24434406 AAAGA-AGA-AGAAG
1 AAAGAGAGAGAG-AG
24434419 AAGAGAGAGAGAGAG
1 AA-AGAGAGAGAGAG
*
24434434 AGAGAGAGAGAGAG
1 AAAGAGAGAGAGAG
24434448 AA
1 AA
24434450 GGGATAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
12 10 0.26
13 4 0.11
14 16 0.42
15 6 0.16
16 2 0.05
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (14 bp):
AAAGAGAGAGAGAG
Found at i:24434427 original size:2 final size:2
Alignment explanation
Indices: 24434420--24434448 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
24434410 AAGAAGAAGA
24434420 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
24434449 AGGGATAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:24440761 original size:53 final size:53
Alignment explanation
Indices: 24440659--24440764 Score: 133
Period size: 53 Copynumber: 2.0 Consensus size: 53
24440649 TTTCTTGATC
* *
24440659 TTTTACCAAACGATCTTCTTCGTTATCTTTAAACCTCTCAAATTACTTTGAGT
1 TTTTACCAAACGATCTTCTTCATTATCTTGAAACCTCTCAAATTACTTTGAGT
* * * * *
24440712 TTTTATCAAACGATCTTCTTTATTATCTTCGAACCCT-TCAGATTGCTTTGAGT
1 TTTTACCAAACGATCTTCTTCATTATCTT-GAAACCTCTCAAATTACTTTGAGT
24440765 GTGAGCTCAA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
53 40 0.89
54 5 0.11
ACGTcount: A:0.25, C:0.22, G:0.09, T:0.44
Consensus pattern (53 bp):
TTTTACCAAACGATCTTCTTCATTATCTTGAAACCTCTCAAATTACTTTGAGT
Found at i:24442008 original size:18 final size:18
Alignment explanation
Indices: 24441985--24442024 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
24441975 ATAAGTAATT
24441985 ATATTATA-TATTATTATA
1 ATATTATATTA-TATTATA
*
24442003 ATATTATATTATATTATT
1 ATATTATATTATATTATA
24442021 ATAT
1 ATAT
24442025 AAACAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATATTATATTATATTATA
Found at i:24442012 original size:13 final size:13
Alignment explanation
Indices: 24441982--24442024 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
24441972 TAAATAAGTA
24441982 ATTATATTAT-AT
1 ATTATATTATAAT
24441994 A-T-TATTATAAT
1 ATTATATTATAAT
*
24442005 ATTATATTATATT
1 ATTATATTATAAT
24442018 ATTATAT
1 ATTATAT
24442025 AAACAAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 6 0.22
11 4 0.15
12 2 0.07
13 15 0.56
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
ATTATATTATAAT
Found at i:24442103 original size:16 final size:19
Alignment explanation
Indices: 24442060--24442110 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
24442050 ATGGAAGTTG
24442060 AAACGAAAACAGAGAAGCAA
1 AAACGAAAA-AGAGAAGCAA
24442080 AAACGAAAAAGA-AAG-AA
1 AAACGAAAAAGAGAAGCAA
24442097 AAA-GAAAAAGAGAA
1 AAACGAAAAAGAGAA
24442111 AGAAGGAAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.27
17 7 0.23
18 3 0.10
19 3 0.10
20 9 0.30
ACGTcount: A:0.73, C:0.08, G:0.20, T:0.00
Consensus pattern (19 bp):
AAACGAAAAAGAGAAGCAA
Found at i:24442110 original size:18 final size:19
Alignment explanation
Indices: 24442060--24442114 Score: 64
Period size: 18 Copynumber: 3.0 Consensus size: 19
24442050 ATGGAAGTTG
24442060 AAACGAAAACAGAG-AAGCAA
1 AAACGAAAA-AGAGAAAG-AA
24442080 AAACG-AAAA-AGAAAGAA
1 AAACGAAAAAGAGAAAGAA
24442097 AAA-GAAAAAGAGAAAGAA
1 AAACGAAAAAGAGAAAGAA
24442115 GGAAGCCACG
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
16 1 0.03
17 11 0.34
18 12 0.38
19 3 0.09
20 5 0.16
ACGTcount: A:0.73, C:0.07, G:0.20, T:0.00
Consensus pattern (19 bp):
AAACGAAAAAGAGAAAGAA
Found at i:24442787 original size:27 final size:25
Alignment explanation
Indices: 24442731--24442788 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
24442721 ACTTTAGTGC
* * * *
24442731 GCTCTCTGATTATTAGCATGTTAGT
1 GCTCTCTGATCACTAGCACGTCAGT
24442756 GCTCTCTGATCACTAGCACGTCAGT
1 GCTCTCTGATCACTAGCACGTCAGT
*
24442781 GTTCTCTG
1 GCTCTCTG
24442789 TTTAGCACTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.17, C:0.24, G:0.21, T:0.38
Consensus pattern (25 bp):
GCTCTCTGATCACTAGCACGTCAGT
Found at i:24442803 original size:22 final size:22
Alignment explanation
Indices: 24442769--24442834 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
24442759 CTCTGATCAC
* *
24442769 TAGCACGTCAGTGTTCTCTGTT
1 TAGCACTTTAGTGTTCTCTGTT
*
24442791 TAGCACTTTAGTGGTCTCTGTT
1 TAGCACTTTAGTGTTCTCTGTT
24442813 TAGCACTTTAGTGTTCTCTGTT
1 TAGCACTTTAGTGTTCTCTGTT
24442835 CATTAGTGCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.14, C:0.20, G:0.21, T:0.45
Consensus pattern (22 bp):
TAGCACTTTAGTGTTCTCTGTT
Found at i:24443926 original size:17 final size:17
Alignment explanation
Indices: 24443904--24443942 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
24443894 TGCGGATGAA
24443904 AAATGCCCTTGGCTGAT
1 AAATGCCCTTGGCTGAT
* *
24443921 AAATGCTCTTGGCTGGT
1 AAATGCCCTTGGCTGAT
24443938 AAATG
1 AAATG
24443943 GACCTCGTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (17 bp):
AAATGCCCTTGGCTGAT
Found at i:24444690 original size:41 final size:41
Alignment explanation
Indices: 24444626--24444865 Score: 365
Period size: 41 Copynumber: 5.9 Consensus size: 41
24444616 CTTTCGGAGA
24444626 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGGGTC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGGGTC
* * **
24444667 TTTAGCGGCGTTTCT-AGGGAAGCGCCGCTAATGCTCTAGTC
1 TTTAGCGGCGTTTTTGA-GAAAGCGCCGCTAATGCTCGGGTC
* *
24444708 TTTAGCAGCGTTTTTGAGAAAGCGCCGCTAATGCTCTGGTC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGGGTC
24444749 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGGGTC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGGGTC
* *
24444790 TTTAGCGGCGTTTTTGAGAAAGAGCCACTAATGCTCGGGTC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGGGTC
* * *
24444831 TTTAGTGGTGTTTTTGATAAAGCGCCGCTAATGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCT
24444866 TAGGGATTTA
Statistics
Matches: 180, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
40 1 0.01
41 178 0.99
42 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.29, T:0.31
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGGGTC
Found at i:24446708 original size:32 final size:33
Alignment explanation
Indices: 24446662--24446726 Score: 123
Period size: 32 Copynumber: 2.0 Consensus size: 33
24446652 TTTTCTTTTA
24446662 TTTTTTTAATTTGAGAAGCAAAAAGTAAGAAAT
1 TTTTTTTAATTTGAGAAGCAAAAAGTAAGAAAT
24446695 TTTTTTTAA-TTGAGAAGCAAAAAGTAAGAAAT
1 TTTTTTTAATTTGAGAAGCAAAAAGTAAGAAAT
24446727 ACGAGTTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 23 0.72
33 9 0.28
ACGTcount: A:0.46, C:0.03, G:0.15, T:0.35
Consensus pattern (33 bp):
TTTTTTTAATTTGAGAAGCAAAAAGTAAGAAAT
Found at i:24448993 original size:6 final size:7
Alignment explanation
Indices: 24448982--24449012 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
24448972 AGTTTAAATT
24448982 TAAAAAA
1 TAAAAAA
24448989 TAAAAAA
1 TAAAAAA
24448996 TAAAAAA
1 TAAAAAA
*
24449003 TAAAACA
1 TAAAAAA
24449010 TAA
1 TAA
24449013 TATAATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAAAAA
Found at i:24449172 original size:43 final size:43
Alignment explanation
Indices: 24449081--24449428 Score: 468
Period size: 43 Copynumber: 8.1 Consensus size: 43
24449071 TGTTTTTAGT
* * * * * * *
24449081 GGCGTTTTTGCGAGAAGCGTCGCTAAAGCT-TTGGTCTATAGT
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGATCTATAGC
*** * *
24449123 GGCGTTTGTAAAAAAAGCGCCGCTAAAGGGCTTGACCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGATCTATAGC
* *
24449166 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGAGCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGATCTATAGC
*
24449209 GGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCTTGATCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGATCTATAGC
* * * *
24449252 GGCGTTTGT-GAAAAATGCGCCGCTAAAGGCCCTAATCTATAGC
1 GGCGTTTGTGGGAAAA-GCGCCGCTAAAGGTCTTGATCTATAGC
24449295 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGATCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGATCTATAGC
*
24449338 GGCGTTTGTGGG-AAAGTGCCGCTAAAGGTCTTGATCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGATCTATAGC
* *
24449380 GGCGTTTGTAGGAAAAGCGCCGCTAAAGGTCCTGATCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGATCTATAGC
24449423 GGCGTT
1 GGCGTT
24449429 GACAATAGCA
Statistics
Matches: 269, Mismatches: 33, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
42 67 0.25
43 197 0.73
44 5 0.02
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.26
Consensus pattern (43 bp):
GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGATCTATAGC
Found at i:24451197 original size:13 final size:13
Alignment explanation
Indices: 24451179--24451204 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
24451169 TTTCGTGCTT
24451179 ATTTTAATGTATA
1 ATTTTAATGTATA
24451192 ATTTTAATGTATA
1 ATTTTAATGTATA
24451205 TTGGGTTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
ATTTTAATGTATA
Found at i:24458829 original size:45 final size:45
Alignment explanation
Indices: 24458731--24458834 Score: 113
Period size: 45 Copynumber: 2.3 Consensus size: 45
24458721 AGAATATGTA
* *
24458731 TGTGTATATAAATTATATGAAAATATAAAAACATATAAGTATGTG
1 TGTGTATATAAATTATATGAAAATATAAAAACATATAAATATATG
* * * **
24458776 TATATATATATATT-TATGAAAATA-AAATATGTATATAAATATATG
1 TGTGTATATAAATTATATGAAAATATAAA-A-ACATATAAATATATG
24458821 TGTGTATATAAATT
1 TGTGTATATAAATT
24458835 GTAAGAGACA
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
43 3 0.06
44 11 0.23
45 33 0.70
ACGTcount: A:0.48, C:0.01, G:0.11, T:0.40
Consensus pattern (45 bp):
TGTGTATATAAATTATATGAAAATATAAAAACATATAAATATATG
Found at i:24459112 original size:3 final size:3
Alignment explanation
Indices: 24459098--24459168 Score: 54
Period size: 3 Copynumber: 23.0 Consensus size: 3
24459088 GAATGAGTAG
* * *
24459098 ATA ATT ATA ATA ATA ATCA AGTA ATA ATA ATA A-A TATA ATA CTA ACA
1 ATA ATA ATA ATA ATA AT-A A-TA ATA ATA ATA ATA -ATA ATA ATA ATA
* * *
24459145 ATA ATA ATA GTA GTA GTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA
24459169 TGATAAATAA
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
2 1 0.02
3 49 0.88
4 5 0.09
5 1 0.02
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:24466103 original size:13 final size:13
Alignment explanation
Indices: 24466062--24466109 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
24466052 AAGAATTTTT
*
24466062 TTTAATTTTCCTA
1 TTTAATTTTACTA
*
24466075 -TT-ATTATTATTA
1 TTTAATT-TTACTA
24466087 TTTAATTTTACTA
1 TTTAATTTTACTA
24466100 TTTAATTTTA
1 TTTAATTTTA
24466110 TTTTTGTAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
11 3 0.10
12 6 0.21
13 17 0.59
14 3 0.10
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (13 bp):
TTTAATTTTACTA
Found at i:24466493 original size:160 final size:160
Alignment explanation
Indices: 24466317--24466632 Score: 623
Period size: 160 Copynumber: 2.0 Consensus size: 160
24466307 AGTAGGTGGG
24466317 AGGGAAACATAAATTGGTTCTAATTTGCTTATCTGTCATCGCTATTTTTGCATGTTTTTGGTAAA
1 AGGGAAACATAAATTGGTTCTAATTTGCTTATCTGTCATCGCTATTTTTGCATGTTTTTGGTAAA
24466382 AGGTAAAATTTTTCTTTTAAATTGGGATGATACACTTATGGTTTGACCTATTTAGCTATTTAATT
66 AGGTAAAATTTTTCTTTTAAATTGGGATGATACACTTATGGTTTGACCTATTTAGCTATTTAATT
24466447 CTTTACACATGAAACTTTTCAATAACTTTT
131 CTTTACACATGAAACTTTTCAATAACTTTT
24466477 AGGGAAACATAAATTGGTTCTAATTTGCTTATCTGTCATCGCTATTTTTGCATGTTTTTGGTAAA
1 AGGGAAACATAAATTGGTTCTAATTTGCTTATCTGTCATCGCTATTTTTGCATGTTTTTGGTAAA
*
24466542 AGGTAAAATTTTTCTTTTAAATTGGGATGGTACACTTATGGTTTGACCTATTTAGCTATTTAATT
66 AGGTAAAATTTTTCTTTTAAATTGGGATGATACACTTATGGTTTGACCTATTTAGCTATTTAATT
24466607 CTTTACACATGAAACTTTTCAATAAC
131 CTTTACACATGAAACTTTTCAATAAC
24466633 CTAGACTTAG
Statistics
Matches: 155, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
160 155 1.00
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.44
Consensus pattern (160 bp):
AGGGAAACATAAATTGGTTCTAATTTGCTTATCTGTCATCGCTATTTTTGCATGTTTTTGGTAAA
AGGTAAAATTTTTCTTTTAAATTGGGATGATACACTTATGGTTTGACCTATTTAGCTATTTAATT
CTTTACACATGAAACTTTTCAATAACTTTT
Found at i:24467482 original size:52 final size:52
Alignment explanation
Indices: 24467413--24467514 Score: 159
Period size: 52 Copynumber: 2.0 Consensus size: 52
24467403 AGAAGAATTT
* * * *
24467413 TTCCAAGATTAATTAGCTGAAATTTTTGAGTTAGTGGGAGAATATTTTGGAG
1 TTCCAAGAATAATTAGCTAAAATTATTGACTTAGTGGGAGAATATTTTGGAG
*
24467465 TTCCAAGAATAATTAGCTAAAATTATTGACTTAGTGGGAGATTATTTTGG
1 TTCCAAGAATAATTAGCTAAAATTATTGACTTAGTGGGAGAATATTTTGG
24467515 GATATTTTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.32, C:0.07, G:0.23, T:0.38
Consensus pattern (52 bp):
TTCCAAGAATAATTAGCTAAAATTATTGACTTAGTGGGAGAATATTTTGGAG
Found at i:24469626 original size:29 final size:29
Alignment explanation
Indices: 24469594--24469659 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
24469584 CACCATTAAA
*
24469594 AGCCCTTTTTTTTAAAATTTATCGAAATG
1 AGCCCTTTTTTTTAAAATTTACCGAAATG
** * **
24469623 AGCCCGATATTTTATTATTTACCGAAATG
1 AGCCCTTTTTTTTAAAATTTACCGAAATG
24469652 -GCCCTTTT
1 AGCCCTTTT
24469660 CCTCGAAAGT
Statistics
Matches: 28, Mismatches: 9, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
28 5 0.18
29 23 0.82
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.42
Consensus pattern (29 bp):
AGCCCTTTTTTTTAAAATTTACCGAAATG
Found at i:24469848 original size:21 final size:22
Alignment explanation
Indices: 24469824--24469866 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
24469814 TTCTCTCCAT
*
24469824 GTTA-GGTTTTGGGTTTTTAGG
1 GTTAGGGTTTAGGGTTTTTAGG
24469845 GTTAGGGTTTAGGGTTTTTAGG
1 GTTAGGGTTTAGGGTTTTTAGG
24469867 ATTTTTAGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.12, C:0.00, G:0.40, T:0.49
Consensus pattern (22 bp):
GTTAGGGTTTAGGGTTTTTAGG
Found at i:24469864 original size:9 final size:9
Alignment explanation
Indices: 24469830--24469880 Score: 51
Period size: 9 Copynumber: 6.3 Consensus size: 9
24469820 CCATGTTAGG
24469830 TTTT-GGGT
1 TTTTAGGGT
24469838 TTTTAGGG-
1 TTTTAGGGT
24469846 --TTAGGG-
1 TTTTAGGGT
24469852 -TTTAGGGT
1 TTTTAGGGT
*
24469860 TTTTAGGAT
1 TTTTAGGGT
24469869 TTTTAGGGT
1 TTTTAGGGT
24469878 TTT
1 TTT
24469881 AGAGAAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
6 6 0.16
7 6 0.16
8 4 0.11
9 21 0.57
ACGTcount: A:0.12, C:0.00, G:0.33, T:0.55
Consensus pattern (9 bp):
TTTTAGGGT
Found at i:24470314 original size:125 final size:124
Alignment explanation
Indices: 24470048--24470334 Score: 484
Period size: 124 Copynumber: 2.3 Consensus size: 124
24470038 ATTTATTAAG
* * *
24470048 GAAATCGCTCCTACGTGAACGCGCTTTTGCTATAGTAGGTCTTGAAAAAATAATTTTGAGTTGAC
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTATAGTAGGTCCTGAAAAAATAATTTTGAGTTGAC
*
24470113 GTTTCTGAGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCT
66 GTTTCTAAGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCT
* *
24470172 AAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTTGAGTTGAC
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTATAGTAGGTCCTGAAAAAATAATTTTGAGTTGAC
*
24470237 GTTTCTAAGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTTT
66 GTTTCTAAGCAAATAGTAT-AAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCT
* *
24470297 GAAATCGCTCCCACGTGGACTCGCTTTTACTATAGTAG
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTATAGTAG
24470335 CATGTTTGAG
Statistics
Matches: 151, Mismatches: 11, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
124 78 0.52
125 73 0.48
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (124 bp):
GAAATCGCTCCCACGTGGACGCGCTTTTGCTATAGTAGGTCCTGAAAAAATAATTTTGAGTTGAC
GTTTCTAAGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCT
Found at i:24474061 original size:18 final size:18
Alignment explanation
Indices: 24474035--24474075 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
24474025 GACTAGAAAA
* * *
24474035 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
24474053 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
24474071 AGGAT
1 AGGAT
24474076 CATCTGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.44, C:0.07, G:0.29, T:0.20
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:24475910 original size:11 final size:11
Alignment explanation
Indices: 24475896--24475993 Score: 62
Period size: 11 Copynumber: 9.3 Consensus size: 11
24475886 GAGAAAGTTA
24475896 AGAGGAAATTG
1 AGAGGAAATTG
*
24475907 AGAGCAAATTG
1 AGAGGAAATTG
**
24475918 AGATTAAA-T-
1 AGAGGAAATTG
* *
24475927 A-TGG-ATTTG
1 AGAGGAAATTG
*
24475936 AGA-GAAATTT
1 AGAGGAAATTG
*
24475946 AGAAGGACATTG
1 AG-AGGAAATTG
* *
24475958 AGAGCAATTTG
1 AGAGGAAATTG
*
24475969 AGAGAAAATTG
1 AGAGGAAATTG
24475980 AGAGGAAATTG
1 AGAGGAAATTG
24475991 AGA
1 AGA
24475994 AAATAATTGA
Statistics
Matches: 63, Mismatches: 18, Indels: 12
0.68 0.19 0.13
Matches are distributed among these distances:
7 1 0.02
8 1 0.02
9 3 0.05
10 6 0.10
11 45 0.71
12 7 0.11
ACGTcount: A:0.45, C:0.03, G:0.29, T:0.23
Consensus pattern (11 bp):
AGAGGAAATTG
Found at i:24475940 original size:51 final size:51
Alignment explanation
Indices: 24475872--24475971 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 51
24475862 AAATAATTAA
24475872 AAATAGGGATTTAAGAGAAAGTTAAG-AGGAAATTGAGAGCAAATTGAGATT
1 AAATAGGGATTTAAGAGAAA-TTAAGAAGGAAATTGAGAGCAAATTGAGATT
* * * * *
24475923 AAATATGGATTTGAGAGAAATTTAGAAGGACATTGAGAGCAATTTGAGA
1 AAATAGGGATTTAAGAGAAATTAAGAAGGAAATTGAGAGCAAATTGAGA
24475972 GAAAATTGAG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
50 4 0.09
51 39 0.91
ACGTcount: A:0.45, C:0.03, G:0.27, T:0.25
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTAAGAAGGAAATTGAGAGCAAATTGAGATT
Found at i:24475958 original size:22 final size:22
Alignment explanation
Indices: 24475933--24476005 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
24475923 AAATATGGAT
* *
24475933 TTGAGAGAAATTTAGAAGGACA
1 TTGAGAGAAATTTAGAAGAAAA
*
24475955 TTGAGAGCAATTT-GAGAGAAAA
1 TTGAGAGAAATTTAGA-AGAAAA
*
24475977 TTGAGAGGAAATTGAGAA-AATAA
1 TTGAGA-GAAATTTAGAAGAA-AA
24476000 TTGAGA
1 TTGAGA
24476006 AAAGATTAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
21 2 0.05
22 24 0.57
23 14 0.33
24 2 0.05
ACGTcount: A:0.47, C:0.03, G:0.27, T:0.23
Consensus pattern (22 bp):
TTGAGAGAAATTTAGAAGAAAA
Found at i:24475973 original size:33 final size:33
Alignment explanation
Indices: 24475931--24475993 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
24475921 TTAAATATGG
* *
24475931 ATTTGAGAG-AAATTTAGAAGGACATTGAGAGCA
1 ATTTGAGAGAAAATTGAG-AGGAAATTGAGAGCA
24475964 ATTTGAGAGAAAATTGAGAGGAAATTGAGA
1 ATTTGAGAGAAAATTGAGAGGAAATTGAGA
24475994 AAATAATTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 20 0.74
34 7 0.26
ACGTcount: A:0.44, C:0.03, G:0.29, T:0.24
Consensus pattern (33 bp):
ATTTGAGAGAAAATTGAGAGGAAATTGAGAGCA
Found at i:24477750 original size:18 final size:18
Alignment explanation
Indices: 24477724--24477766 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
24477714 GACTAGAAAA
* * *
24477724 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
24477742 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
24477760 AGGATAC
1 AGGATAC
24477767 GCACCTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:24479549 original size:19 final size:19
Alignment explanation
Indices: 24479527--24479566 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
24479517 TACGATTTAA
24479527 AATTTTTTTAAAAAAAATT
1 AATTTTTTTAAAAAAAATT
*
24479546 AATTTTTTTAAAAATAATT
1 AATTTTTTTAAAAAAAATT
24479565 AA
1 AA
24479567 AAATAGGGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AATTTTTTTAAAAAAAATT
Found at i:24479635 original size:51 final size:51
Alignment explanation
Indices: 24479567--24479666 Score: 150
Period size: 51 Copynumber: 2.0 Consensus size: 51
24479557 AAATAATTAA
24479567 AAATAGGGATTTAAGAGAAATTTA-AGAGGAAATTGAGAGCACA-TTGAGATT
1 AAATAGGGATTTAAGAGAAATTTAGA-AGGAAATTGAGAGCA-ATTTGAGATT
* *
24479618 AAATATGGATTTGAGAGAAATTTAGAAGGAAATTGAGAGCAATTTGAGA
1 AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAATTTGAGA
24479667 GGAAATTGAG
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
50 1 0.02
51 43 0.96
52 1 0.02
ACGTcount: A:0.45, C:0.03, G:0.26, T:0.26
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAATTTGAGATT
Found at i:24479640 original size:11 final size:12
Alignment explanation
Indices: 24479626--24479688 Score: 66
Period size: 11 Copynumber: 5.7 Consensus size: 12
24479616 TTAAATATGG
24479626 ATTTGAGA-GAA
1 ATTTGAGAGGAA
24479637 ATTT-AGAAGGAA
1 ATTTGAG-AGGAA
*
24479649 A-TTGAGA-GCA
1 ATTTGAGAGGAA
24479659 ATTTGAGAGGAA
1 ATTTGAGAGGAA
24479671 A-TTGAGAGGAA
1 ATTTGAGAGGAA
24479682 A-TTGAGA
1 ATTTGAGA
24479689 AAATAATTGA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
10 5 0.11
11 31 0.69
12 9 0.20
ACGTcount: A:0.44, C:0.02, G:0.30, T:0.24
Consensus pattern (12 bp):
ATTTGAGAGGAA
Found at i:24479653 original size:22 final size:22
Alignment explanation
Indices: 24479628--24479689 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
24479618 AAATATGGAT
24479628 TTGAGAGAAATTTAGAAGGAAA
1 TTGAGAGAAATTTAGAAGGAAA
*
24479650 TTGAGAGCAATTT-GAGAGGAAA
1 TTGAGAGAAATTTAGA-AGGAAA
*
24479672 TTGAGAGGAAATTGAGAA
1 TTGAGA-GAAATTTAGAA
24479690 AATAATTGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 2 0.06
22 24 0.71
23 6 0.18
24 2 0.06
ACGTcount: A:0.45, C:0.02, G:0.31, T:0.23
Consensus pattern (22 bp):
TTGAGAGAAATTTAGAAGGAAA
Found at i:24479663 original size:33 final size:33
Alignment explanation
Indices: 24479626--24479688 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
24479616 TTAAATATGG
*
24479626 ATTTGAGA-GAAATTTAGAAGGAAATTGAGAGCA
1 ATTTGAGAGGAAATTGAG-AGGAAATTGAGAGCA
24479659 ATTTGAGAGGAAATTGAGAGGAAATTGAGA
1 ATTTGAGAGGAAATTGAGAGGAAATTGAGA
24479689 AAATAATTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
33 20 0.71
34 8 0.29
ACGTcount: A:0.44, C:0.02, G:0.30, T:0.24
Consensus pattern (33 bp):
ATTTGAGAGGAAATTGAGAGGAAATTGAGAGCA
Found at i:24479696 original size:23 final size:22
Alignment explanation
Indices: 24479628--24479700 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
24479618 AAATATGGAT
* *
24479628 TTGAGAG-AAATTTAGAAGGAAA
1 TTGAGAGCAAATTGAGAA-AAAA
* **
24479650 TTGAGAGCAATTTGAGAGGAAA
1 TTGAGAGCAAATTGAGAAAAAA
*
24479672 TTGAGAGGAAATTGAGAAAATAA
1 TTGAGAGCAAATTGAGAAAA-AA
24479695 TTGAGA
1 TTGAGA
24479701 AAAGATTAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
22 27 0.64
23 15 0.36
ACGTcount: A:0.47, C:0.01, G:0.29, T:0.23
Consensus pattern (22 bp):
TTGAGAGCAAATTGAGAAAAAA
Found at i:24482262 original size:18 final size:19
Alignment explanation
Indices: 24482229--24482270 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
24482219 ATAAAAAAAC
24482229 ATTTTGAAATTGAATAATG
1 ATTTTGAAATTGAATAATG
*
24482248 ATTTTTAAA-TGAATAATG
1 ATTTTGAAATTGAATAATG
24482266 -TTTTG
1 ATTTTG
24482271 GAAACGAGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 4 0.19
18 9 0.43
19 8 0.38
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (19 bp):
ATTTTGAAATTGAATAATG
Found at i:24482595 original size:25 final size:25
Alignment explanation
Indices: 24482553--24482633 Score: 85
Period size: 25 Copynumber: 3.2 Consensus size: 25
24482543 TAAACTGAAT
* *
24482553 CTGAAACTGTCT-TTGATAGTATATC
1 CTGAAACTG-CTATAGATAGTATATA
24482578 CTGAAACTGCTATAGATAGTATATA
1 CTGAAACTGCTATAGATAGTATATA
* * *
24482603 CTTAGACTACTATAGATAG-ACTATA
1 CTGAAACTGCTATAGATAGTA-TATA
24482628 CTGAAA
1 CTGAAA
24482634 ACACTTAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
24 3 0.06
25 44 0.94
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (25 bp):
CTGAAACTGCTATAGATAGTATATA
Found at i:24492719 original size:23 final size:23
Alignment explanation
Indices: 24492693--24492740 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
24492683 CTGATACATA
24492693 TTTGATTATTTGA-TTTCTCATTT
1 TTTGATTATTT-ACTTTCTCATTT
* *
24492716 TTTGTTTATTTACTTTCTTATTT
1 TTTGATTATTTACTTTCTCATTT
24492739 TT
1 TT
24492741 AGTATAGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 21 0.95
ACGTcount: A:0.15, C:0.08, G:0.06, T:0.71
Consensus pattern (23 bp):
TTTGATTATTTACTTTCTCATTT
Found at i:24492751 original size:24 final size:23
Alignment explanation
Indices: 24492706--24492751 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
24492696 GATTATTTGA
* *
24492706 TTTCTCATTTTTTGTTTATTTAC
1 TTTCTCATTTTTAGTATATTTAC
*
24492729 TTTCTTATTTTTAGTATAGTTTA
1 TTTCTCATTTTTAGTATA-TTTA
24492752 TCAAGCTCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.17, C:0.09, G:0.07, T:0.67
Consensus pattern (23 bp):
TTTCTCATTTTTAGTATATTTAC
Found at i:24493157 original size:16 final size:17
Alignment explanation
Indices: 24493117--24493158 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
24493107 AAACCATGTA
*
24493117 AATCTCCACTTTCTATT
1 AATCTCCACTCTCTATT
*
24493134 -ATCACCACTCTC-ATT
1 AATCTCCACTCTCTATT
24493149 AATCTCCACT
1 AATCTCCACT
24493159 ATATGGTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
15 3 0.14
16 18 0.86
ACGTcount: A:0.26, C:0.36, G:0.00, T:0.38
Consensus pattern (17 bp):
AATCTCCACTCTCTATT
Found at i:24507494 original size:15 final size:14
Alignment explanation
Indices: 24507460--24507494 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
24507450 GTAAAAATAT
24507460 TTAAAAATCAGTTC
1 TTAAAAATCAGTTC
24507474 TTAAAAATCACG-TC
1 TTAAAAATCA-GTTC
24507488 TTAAAAA
1 TTAAAAA
24507495 CCTACACCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 19 0.95
15 1 0.05
ACGTcount: A:0.49, C:0.14, G:0.06, T:0.31
Consensus pattern (14 bp):
TTAAAAATCAGTTC
Found at i:24514303 original size:18 final size:19
Alignment explanation
Indices: 24514232--24514324 Score: 62
Period size: 19 Copynumber: 4.6 Consensus size: 19
24514222 TAAAACTTAT
*
24514232 AAAAATCATAAAAACTTATATA
1 AAAAATTAT-AAAA-TTA-ATA
* *
24514254 AAAATTTATCAAATTAATA
1 AAAAATTATAAAATTAATA
*
24514273 AAAAATATTTAAAATTAA-A
1 AAAAAT-TATAAAATTAATA
* *
24514292 AAAACTTATAAAAATTCATA
1 AAAAATTAT-AAAATTAATA
*
24514312 AATAATATATAAA
1 AAAAAT-TATAAA
24514325 TAATATAAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
18 2 0.04
19 21 0.38
20 20 0.36
21 6 0.11
22 7 0.12
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAAATTATAAAATTAATA
Found at i:24514312 original size:10 final size:9
Alignment explanation
Indices: 24514160--24514335 Score: 67
Period size: 9 Copynumber: 18.6 Consensus size: 9
24514150 TTAATGAATA
24514160 AAAAATTCATT
1 AAAAATT-A-T
*
24514171 AAAAATCAT
1 AAAAATTAT
24514180 AAAAA-TATT
1 AAAAATTA-T
*
24514189 AAACA-T-T
1 AAAAATTAT
24514196 AAAAATTAT
1 AAAAATTAT
* *
24514205 TAAAATTCTT
1 AAAAATT-AT
* *
24514215 ATAAACT-T
1 AAAAATTAT
*
24514223 AAAACTTAT
1 AAAAATTAT
*
24514232 AAAAATCAT
1 AAAAATTAT
24514241 AAAAACTTATAT
1 AAAAA--T-TAT
24514253 AAAAATT-T
1 AAAAATTAT
*
24514261 ATCAAATTAAT
1 A-AAAATT-AT
*
24514272 AAAAAATATT
1 AAAAATTA-T
* *
24514282 TAAAATTAA
1 AAAAATTAT
24514291 AAAAACTTAT
1 AAAAA-TTAT
24514301 AAAAATTCAT
1 AAAAATT-AT
24514311 AAATAATATAT
1 AAA-AAT-TAT
24514322 AAATAA-TAT
1 AAA-AATTAT
24514331 AAAAA
1 AAAAA
24514336 AATTTAAACC
Statistics
Matches: 126, Mismatches: 23, Indels: 35
0.68 0.12 0.19
Matches are distributed among these distances:
7 5 0.04
8 11 0.09
9 51 0.40
10 31 0.25
11 20 0.16
12 8 0.06
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:24514334 original size:48 final size:50
Alignment explanation
Indices: 24514241--24514334 Score: 115
Period size: 48 Copynumber: 1.9 Consensus size: 50
24514231 TAAAAATCAT
* *
24514241 AAAAACTTATATAAAAATTTATCAAATTAATAAAAAATATTTAAAATTAA
1 AAAAACTTATATAAAAATTCATCAAATTAATAAAAAATATATAAAATTAA
*
24514291 AAAAAC-T-TATAAAAATTCAT-AAA-TAATATATAAATAATATAAAA
1 AAAAACTTATATAAAAATTCATCAAATTAATA-AAAAAT-ATATAAAA
24514335 AAATTTAAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
46 5 0.13
47 8 0.21
48 19 0.49
49 1 0.03
50 6 0.15
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (50 bp):
AAAAACTTATATAAAAATTCATCAAATTAATAAAAAATATATAAAATTAA
Found at i:24514343 original size:19 final size:18
Alignment explanation
Indices: 24514270--24514343 Score: 53
Period size: 19 Copynumber: 3.8 Consensus size: 18
24514260 TATCAAATTA
24514270 ATAAAAAATATTT-AAAAT
1 ATAAAAAA-ATTTAAAAAT
24514288 -TAAAAAAACTTATAAAAATT
1 ATAAAAAAA-TT-TAAAAA-T
* *
24514308 CATAAATAATATATAAATAAT
1 -ATAAA-AAAATTTAAA-AAT
24514329 ATAAAAAAATTTAAA
1 ATAAAAAAATTTAAA
24514344 CCCCTACAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 15
0.70 0.06 0.24
Matches are distributed among these distances:
16 1 0.02
17 9 0.20
18 1 0.02
19 12 0.27
20 6 0.14
21 5 0.11
22 7 0.16
23 3 0.07
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAAAAAAATTTAAAAAT
Found at i:24514858 original size:2 final size:2
Alignment explanation
Indices: 24514851--24514880 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
24514841 TTGGTGAATA
24514851 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
24514881 GTATGTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24516128 original size:19 final size:18
Alignment explanation
Indices: 24516074--24516131 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 18
24516064 TTATTAATAA
*
24516074 ATTAAATTTATAAAAAAAT
1 ATTAAATTTAT-AATAAAT
* * *
24516093 ATTAGTATTCATTATAAAT
1 ATTA-AATTTATAATAAAT
24516112 ATTAAATTTATGAATAAAT
1 ATTAAATTTAT-AATAAAT
24516131 A
1 A
24516132 CAAATTTTAA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
18 5 0.17
19 20 0.67
20 5 0.17
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.41
Consensus pattern (18 bp):
ATTAAATTTATAATAAAT
Found at i:24516369 original size:25 final size:23
Alignment explanation
Indices: 24516325--24516370 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
24516315 AGTTTCAAAA
* *
24516325 TTATATATTTTAATATTTTTTAG
1 TTATATATTTCAATAATTTTTAG
24516348 TTATATATTTGCATATAATTTTT
1 TTATATATTT-CA-ATAATTTTT
24516371 TATTAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 10 0.53
24 1 0.05
25 8 0.42
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.63
Consensus pattern (23 bp):
TTATATATTTCAATAATTTTTAG
Found at i:24516591 original size:43 final size:43
Alignment explanation
Indices: 24516525--24516679 Score: 147
Period size: 43 Copynumber: 3.6 Consensus size: 43
24516515 NNNNNNCGGC
** *
24516525 GTTTGTGGAAAAAGCGCCCCTAAAGATCATGGTCTTTAGCGGT
1 GTTTGTGGGGAAAGCGCCGCTAAAGATCATGGTCTTTAGCGGT
* * *
24516568 GTTTGTGGGGAAAGCGCTGCTAAAGATTA-GGTTCTTTAGTGGCT
1 GTTTGTGGGGAAAGCGCCGCTAAAGATCATGG-TCTTTAGCGG-T
* * * *
24516612 -TTTGTGGTCG-AAGCGCCGCTATAGATCATGGTCTTTTGCGGC
1 GTTTGTGG-GGAAAGCGCCGCTAAAGATCATGGTCTTTAGCGGT
*
24516654 GTTT-TAGGGAGAAGCGCCGCTAAAGA
1 GTTTGTGGGGA-AAGCGCCGCTAAAGA
24516680 CCCTAATCTT
Statistics
Matches: 89, Mismatches: 16, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
41 1 0.01
42 4 0.04
43 80 0.90
44 4 0.04
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.30
Consensus pattern (43 bp):
GTTTGTGGGGAAAGCGCCGCTAAAGATCATGGTCTTTAGCGGT
Found at i:24516715 original size:43 final size:42
Alignment explanation
Indices: 24516668--24516849 Score: 170
Period size: 43 Copynumber: 4.3 Consensus size: 42
24516658 TAGGGAGAAG
24516668 CGCCGCTAAAGACCCTAATCTTTAGCGGCGCTTGTCGCAAAAA
1 CGCCGCTAAAGACCCTAATCTTTAGCGGCGCTTGTC-CAAAAA
* ** * * *
24516711 CGCCGCTAACGACCCTGGTCTATAGCGGCGCTTCGACCACAAA
1 CGCCGCTAAAGACCCTAATCTTTAGCGGCGCTT-GTCCAAAAA
* *
24516754 CGCCACTAAAGAACCTAATCTTTAGCGGCGCTT-TCCCAACAAA
1 CGCCGCTAAAGACCCTAATCTTTAGCGGCGCTTGT-CCAA-AAA
* * * * * *
24516797 CGCCGCAAAAGACCCTGATCTATA-CGACGCTTCGACCACAAA
1 CGCCGCTAAAGACCCTAATCTTTAGCGGCGCTT-GTCCAAAAA
*
24516839 CGCCACTAAAG
1 CGCCGCTAAAG
24516850 GTCTTAGTCT
Statistics
Matches: 110, Mismatches: 24, Indels: 11
0.76 0.17 0.08
Matches are distributed among these distances:
42 22 0.20
43 86 0.78
44 2 0.02
ACGTcount: A:0.30, C:0.34, G:0.19, T:0.18
Consensus pattern (42 bp):
CGCCGCTAAAGACCCTAATCTTTAGCGGCGCTTGTCCAAAAA
Found at i:24516887 original size:85 final size:86
Alignment explanation
Indices: 24516668--24516868 Score: 262
Period size: 86 Copynumber: 2.3 Consensus size: 86
24516658 TAGGGAGAAG
* * * * * * *
24516668 CGCCGCTAAAGACCCTAATCTTTAGCGGCGCTTGTCGCAA-AAACGCCGCTAACGACCCTGGTCT
1 CGCCACTAAAGAACCTAATCTTCAGCGGCGCTT-TCCCAACAAACGCCGCAAAAGACCCTGATCT
*
24516732 ATAGCGGCGCTTCGACCACAAA
65 ATAGCGACGCTTCGACCACAAA
*
24516754 CGCCACTAAAGAACCTAATCTTTAGCGGCGCTTTCCCAACAAACGCCGCAAAAGACCCTGATCTA
1 CGCCACTAAAGAACCTAATCTTCAGCGGCGCTTTCCCAACAAACGCCGCAAAAGACCCTGATCTA
24516819 TA-CGACGCTTCGACCACAAA
66 TAGCGACGCTTCGACCACAAA
** * *
24516839 CGCCACTAAAGGTCTTAGTCTTCAGCGGCG
1 CGCCACTAAAGAACCTAATCTTCAGCGGCG
24516869 TTTGTGCTAG
Statistics
Matches: 102, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
85 47 0.46
86 55 0.54
ACGTcount: A:0.28, C:0.33, G:0.20, T:0.19
Consensus pattern (86 bp):
CGCCACTAAAGAACCTAATCTTCAGCGGCGCTTTCCCAACAAACGCCGCAAAAGACCCTGATCTA
TAGCGACGCTTCGACCACAAA
Found at i:24517036 original size:22 final size:22
Alignment explanation
Indices: 24517008--24517050 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
24516998 TTGCGGCACT
*
24517008 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
24517030 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
24517051 GTTTTGGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.28, G:0.21, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:24524138 original size:5 final size:5
Alignment explanation
Indices: 24524128--24524154 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
24524118 GTTGATTAGA
24524128 AAAAG AAAAG AAAAG AAAAG AAAAG AA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AA
24524155 TTCAGTGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:24528610 original size:43 final size:44
Alignment explanation
Indices: 24528558--24528643 Score: 102
Period size: 44 Copynumber: 2.0 Consensus size: 44
24528548 ATCTCACTGG
* * *
24528558 GCAACAGT-GGAATAGATTGAAGATTACAGATCTTATCTCCCTA
1 GCAACAGTGGGAATAGATCGAAGATGACAGATCTTACCTCCCTA
* * * *
24528601 GCAATAGTGGGAGTAGATCGAAGATGGCAGATTTTACCTCCCT
1 GCAACAGTGGGAATAGATCGAAGATGACAGATCTTACCTCCCT
24528644 GAAGTTACAG
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
43 7 0.20
44 28 0.80
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (44 bp):
GCAACAGTGGGAATAGATCGAAGATGACAGATCTTACCTCCCTA
Found at i:24528683 original size:132 final size:131
Alignment explanation
Indices: 24528383--24528684 Score: 387
Period size: 132 Copynumber: 2.3 Consensus size: 131
24528373 AACTACTGTG
* *
24528383 GTTACAGTGGAGTACATTGAAGCCAGTAATTCTA-CTTCCCTGGGCAGCAGTGGAATAGATTGAA
1 GTTACAGTGGAGTACATTGAAGCCAGTAATTCTATC-TCACTGGGCAACAGTGGAATAGATTGAA
* * * * * *
24528447 GATTTCGGATATTGTCTCCCCAAGCAGTAGTAGAGCATATCAAAGATGGTGAATTTTACCTCCCT
65 GATTACAGATATTATCTCCCCAAGCAATAGTAGAGCAGATCAAAGATGGAGAATTTTACCTCCCT
24528512 GA
130 GA
* *
24528514 GATTACAGTGGAGTACATTGAAGCCACTAATTTTATCTCACTGGGCAACAGTGGAATAGATTGAA
1 G-TTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCACTGGGCAACAGTGGAATAGATTGAA
* * * * *
24528579 GATTACAGATCTTATCT-CCCTAGCAATAGTGGGAGTAGATCGAAGATGGCAG-ATTTTACCTCC
65 GATTACAGATATTATCTCCCCAAGCAATAGT-AGAGCAGATCAAAGATGG-AGAATTTTACCTCC
24528642 CTGAA
128 CTG-A
24528647 GTTACAGTGGAGTACATTGAAGCCAGT-ATTCCTATCTC
1 GTTACAGTGGAGTACATTGAAGCCAGTAATT-CTATCTC
24528685 CTTGAAGTTG
Statistics
Matches: 148, Mismatches: 17, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
131 15 0.10
132 129 0.87
133 4 0.03
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (131 bp):
GTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCACTGGGCAACAGTGGAATAGATTGAAG
ATTACAGATATTATCTCCCCAAGCAATAGTAGAGCAGATCAAAGATGGAGAATTTTACCTCCCTG
A
Found at i:24530192 original size:25 final size:25
Alignment explanation
Indices: 24530145--24530192 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
24530135 ACGCATCTTT
*
24530145 TTTTTTTATAAAGTATACCTATACA
1 TTTTTTTATAAAGTATACATATACA
*
24530170 TTTTTTTATATA-TAGTACATATA
1 TTTTTTTATAAAGTA-TACATATA
24530193 TATGTATCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 18 0.90
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.52
Consensus pattern (25 bp):
TTTTTTTATAAAGTATACATATACA
Found at i:24530343 original size:34 final size:35
Alignment explanation
Indices: 24530290--24530379 Score: 110
Period size: 34 Copynumber: 2.6 Consensus size: 35
24530280 CTTTTATATA
* * *
24530290 TTTTATGTTTTATAGATATATACATATACA-TTTC
1 TTTTATGTTGTAAATATATATACATATACATTTTC
* *
24530324 TTTTATGTTGTAAATATATATACTTATACATTTTT
1 TTTTATGTTGTAAATATATATACATATACATTTTC
*
24530359 TTTCTATTTTGTAAATATATA
1 TTT-TATGTTGTAAATATATA
24530380 CCCATGTGCA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
34 26 0.54
35 6 0.12
36 16 0.33
ACGTcount: A:0.32, C:0.07, G:0.06, T:0.56
Consensus pattern (35 bp):
TTTTATGTTGTAAATATATATACATATACATTTTC
Found at i:24531380 original size:17 final size:19
Alignment explanation
Indices: 24531358--24531394 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
24531348 TTATATATTT
*
24531358 TTAATT-TT-TAATAAATA
1 TTAATTATTATAAAAAATA
24531375 TTAATTATTATAAAAAATA
1 TTAATTATTATAAAAAATA
24531394 T
1 T
24531395 CCATAATTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 2 0.12
19 9 0.53
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTAATTATTATAAAAAATA
Found at i:24533379 original size:40 final size:39
Alignment explanation
Indices: 24533335--24533450 Score: 110
Period size: 40 Copynumber: 2.9 Consensus size: 39
24533325 TGTTTGGACA
* * *
24533335 AAAAACGCCACTAAAAATCGAGCATTAACGGCGCTTTTAT
1 AAAAACGCCGCTAAAAAT-GAGCATTAGCGGCGCTTTTAC
* ** *
24533375 AAAAACACCGCTAAAGGTAGAGCATTAGTGGCGC-TTTAC
1 AAAAACGCCGCTAAAAAT-GAGCATTAGCGGCGCTTTTAC
* *
24533414 AGAAAACGCTGCTAAAAATTAGCATTAGCGGCG-TTTT
1 A-AAAACGCCGCTAAAAATGAGCATTAGCGGCGCTTTT
24533451 CTGAAAATCG
Statistics
Matches: 60, Mismatches: 14, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
39 20 0.33
40 40 0.67
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (39 bp):
AAAAACGCCGCTAAAAATGAGCATTAGCGGCGCTTTTAC
Found at i:24533469 original size:38 final size:39
Alignment explanation
Indices: 24533336--24533469 Score: 103
Period size: 40 Copynumber: 3.4 Consensus size: 39
24533326 GTTTGGACAA
* * * *
24533336 AAAACGCCACTAAAAATCGAGCATTAACGGCGCTTTTATA-
1 AAAACGCCGCTAAAAAT-TAGCATTAGCGGCGC-TTTACAG
* ** * *
24533376 AAAACACCGCTAAAGGTAGAGCATTAGTGGCGCTTTACAG
1 AAAACGCCGCTAAAAAT-TAGCATTAGCGGCGCTTTACAG
* * *
24533416 AAAACGCTGCTAAAAATTAGCATTAGCGGCG-TTTTCTG
1 AAAACGCCGCTAAAAATTAGCATTAGCGGCGCTTTACAG
24533454 AAAATCGCCGC-AAAAA
1 AAAA-CGCCGCTAAAAA
24533470 GCCTAAGCCA
Statistics
Matches: 75, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
38 14 0.19
39 22 0.29
40 39 0.52
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (39 bp):
AAAACGCCGCTAAAAATTAGCATTAGCGGCGCTTTACAG
Found at i:24533574 original size:41 final size:41
Alignment explanation
Indices: 24533511--24533746 Score: 223
Period size: 41 Copynumber: 5.7 Consensus size: 41
24533501 TTTGGGGCCC
*
24533511 TTAGCGGCGTTTTTTAGGAAGCGCCGCTAATGCTCTAG-CCT
1 TTAGCGGCGTTTTTGA-GAAGCGCCGCTAATGCTCTAGACCT
* * *
24533552 TTAGCGGCGTTTTTGAGTAAGCGCCGCTAAAGGC-C-AGAGCA
1 TTAGCGGCGTTTTTGAG-AAGCGCCGCT-AATGCTCTAGACCT
* * * * *
24533593 TTAGCGGCGCTTCTTAAAAAACGCCGCTAATGCTCTA-TCCT
1 TTAGCGGCG-TTTTTGAGAAGCGCCGCTAATGCTCTAGACCT
* * *
24533634 TTAGCGACGTTTTTGAAGAAGCGCCGGTAATGTTCT-GACCT
1 TTAGCGGCGTTTTTG-AGAAGCGCCGCTAATGCTCTAGACCT
* * *
24533675 TTAGCGGCATTTTTGAAGAAGCGCCGCTAATGCT-AAGATCT
1 TTAGCGGCGTTTTTG-AGAAGCGCCGCTAATGCTCTAGACCT
*
24533716 TTAGCGGCGTTTTTGAAAAAGCGCCGCTAAT
1 TTAGCGGCGTTTTTG-AGAAGCGCCGCTAAT
24533747 ATATTTTTAT
Statistics
Matches: 158, Mismatches: 28, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
40 11 0.07
41 137 0.87
42 10 0.06
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.29
Consensus pattern (41 bp):
TTAGCGGCGTTTTTGAGAAGCGCCGCTAATGCTCTAGACCT
Found at i:24533735 original size:123 final size:123
Alignment explanation
Indices: 24533511--24533746 Score: 300
Period size: 123 Copynumber: 1.9 Consensus size: 123
24533501 TTTGGGGCCC
* * * *
24533511 TTAGCGGCGTTTTTTAGGAAGCGCCGCTAATGCTCTAGCCTTTAGCGGCGTTTTTGAGTAAGCGC
1 TTAGCGACGTTTTTGAAGAAGCGCCGCTAATGCTCTAGCCTTTAGCGGCATTTTTGAGTAAGCGC
*
24533576 CGCTAAAGGCCAGAGCATTAGCGGCGCTTCTTAAAAAACGCCGCTAATGCTCTATCCT
66 CGCTAAAGGCAAGAGCATTAGCGGCGCTTCTTAAAAAACGCCGCTAATGCTCTATCCT
* *
24533634 TTAGCGACGTTTTTGAAGAAGCGCCGGTAATGTTCT-GACCTTTAGCGGCATTTTTGAAG-AAGC
1 TTAGCGACGTTTTTGAAGAAGCGCCGCTAATGCTCTAG-CCTTTAGCGGCATTTTTG-AGTAAGC
* * * * *
24533697 GCCGCT-AATGCTAAGATCTTTAGCGGCG-TTTTTGAAAAAGCGCCGCTAAT
64 GCCGCTAAAGGC-AAGAGCATTAGCGGCGCTTCTT-AAAAAACGCCGCTAAT
24533747 ATATTTTTAT
Statistics
Matches: 97, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
122 9 0.09
123 86 0.89
124 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.29
Consensus pattern (123 bp):
TTAGCGACGTTTTTGAAGAAGCGCCGCTAATGCTCTAGCCTTTAGCGGCATTTTTGAGTAAGCGC
CGCTAAAGGCAAGAGCATTAGCGGCGCTTCTTAAAAAACGCCGCTAATGCTCTATCCT
Found at i:24534053 original size:15 final size:16
Alignment explanation
Indices: 24534033--24534066 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
24534023 CAAATATGGT
24534033 GTTTATGGATTT-AGG
1 GTTTATGGATTTAAGG
24534048 GTTTATGGATTTAAGG
1 GTTTATGGATTTAAGG
24534064 GTT
1 GTT
24534067 AGAGGTTAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.47
Consensus pattern (16 bp):
GTTTATGGATTTAAGG
Found at i:24545307 original size:43 final size:43
Alignment explanation
Indices: 24545260--24545447 Score: 220
Period size: 43 Copynumber: 4.3 Consensus size: 43
24545250 AGGTGTTGGC
*
24545260 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATCATGGT
1 CTTTAGCGGCGTTTTTGGTCAAAGCGCCGCTAAAGATCATGGT
* **
24545303 CTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGATCATGGT
1 CTTTAGCGGCGTTTTTGGTCAAAGCGCCGCTAAAGATCATGGT
** * *
24545346 CTTTAGCGGCGTTTTTGGGGAAAGCGCTGCTAAAGATTA-GGTT
1 CTTTAGCGGCGTTTTTGGTCAAAGCGCCGCTAAAGATCATGG-T
* * *
24545389 CTTTAGTGGCGTTTTGTGGTCGAAA-CGCCGCTATAGATCAGGGT
1 CTTTAGCGGCGTTTT-TGGTC-AAAGCGCCGCTAAAGATCATGGT
24545433 CTATT-GCGGCGTTTT
1 CT-TTAGCGGCGTTTT
24545448 AGGGGAAAAA
Statistics
Matches: 124, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
42 2 0.02
43 88 0.71
44 27 0.22
45 7 0.06
ACGTcount: A:0.20, C:0.18, G:0.30, T:0.32
Consensus pattern (43 bp):
CTTTAGCGGCGTTTTTGGTCAAAGCGCCGCTAAAGATCATGGT
Found at i:24545453 original size:87 final size:85
Alignment explanation
Indices: 24545280--24545521 Score: 258
Period size: 75 Copynumber: 2.9 Consensus size: 85
24545270 GTTTTTGGTC
* * ** * *
24545280 AAAGCGCCGCTAAAGATCATGG-TCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGATCATG
1 AAAGCG-CGCTAAAGATTA-GGTTCTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGG
*
24545344 GTCT-TTAGCGGCGTTTTTGGGG
64 GTCTATT-GCGGCGTTTTAGGGG
24545366 AAAGCGCTGCTAAAGATTAGGTTCTTTAGTGGCGTTTTGTGGTCGAAA-CGCCGCTATAGATCAG
1 AAAGCGC-GCTAAAGATTAGGTTCTTTAGTGGCG-TTTGTGGTC-AAAGCGCCGCTATAGATCAG
24545430 GGTCTATTGCGGCGTTTTAGGGG
63 GGTCTATTGCGGCGTTTTAGGGG
*
24545453 --A-------AAA-ATTAGGTTCTTTAGTGGCGTTTGTAGTCAAAGCGCCGCTATAGATCAGGGT
1 AAAGCGCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGGT
*
24545508 CTATTCCGGCGTTT
66 CTATTGCGGCGTTT
24545522 GAGAAAAAAA
Statistics
Matches: 141, Mismatches: 9, Indels: 23
0.82 0.05 0.13
Matches are distributed among these distances:
74 3 0.02
75 40 0.28
76 19 0.13
77 3 0.02
85 4 0.03
86 27 0.19
87 40 0.28
88 5 0.04
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (85 bp):
AAAGCGCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGGT
CTATTGCGGCGTTTTAGGGG
Found at i:24552610 original size:3 final size:3
Alignment explanation
Indices: 24552602--24552663 Score: 67
Period size: 3 Copynumber: 21.3 Consensus size: 3
24552592 TAATATATGT
* *
24552602 ATA ATA ATA ATA ATA ATA AT- ATA AT- ATA ATA ATA ATAA ATG CTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA
*
24552646 ATA ATA AT- ATA GTA ATA A
1 ATA ATA ATA ATA ATA ATA A
24552664 ACAATTTAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
2 6 0.12
3 40 0.82
4 3 0.06
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:24552632 original size:16 final size:17
Alignment explanation
Indices: 24552605--24552663 Score: 77
Period size: 16 Copynumber: 3.6 Consensus size: 17
24552595 TATATGTATA
24552605 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
24552622 ATAAT-ATAATAATAAT
1 ATAATAATAATAATAAT
**
24552638 A-AATGCTAATAATAAT
1 ATAATAATAATAATAAT
*
24552654 ATAGTAATAA
1 ATAATAATAA
24552664 ACAATTTAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
15 3 0.08
16 23 0.64
17 10 0.28
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (17 bp):
ATAATAATAATAATAAT
Found at i:24552649 original size:19 final size:20
Alignment explanation
Indices: 24552601--24552654 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
24552591 ATAATATATG
24552601 TATAATAATAATAATAATAA
1 TATAATAATAATAATAATAA
24552621 TATAAT-ATAATAATAATAA
1 TATAATAATAATAATAATAA
**
24552640 -ATGCTAATAATAATA
1 TATAATAATAATAATA
24552655 TAGTAATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
18 3 0.10
19 22 0.71
20 6 0.19
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (20 bp):
TATAATAATAATAATAATAA
Found at i:24553618 original size:41 final size:41
Alignment explanation
Indices: 24553602--24553796 Score: 327
Period size: 41 Copynumber: 4.8 Consensus size: 41
24553592 CTTATAGCTT
* *
24553602 GATTCAGATCACCGGCACGTAGCCTGCTAGGTTTATAACCT
1 GATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCC
*
24553643 GATTCAAATCACCGGCACGTATCCTGCTAGGTTTATAACCC
1 GATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCC
** *
24553684 GATTCAAATCACTAGCACGTAGCCTACTAGGTTTATAACCC
1 GATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCC
*
24553725 GATTCAAATCACCGGCACATAGCCTGCTAGGTTTATAACCC
1 GATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCC
24553766 GATTCAAATCACCGGCACGTAGCCTGCTAGG
1 GATTCAAATCACCGGCACGTAGCCTGCTAGG
24553797 CGCTTAGCCT
Statistics
Matches: 142, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 142 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (41 bp):
GATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCC
Found at i:24553714 original size:82 final size:82
Alignment explanation
Indices: 24553573--24553796 Score: 331
Period size: 82 Copynumber: 2.7 Consensus size: 82
24553563 ACAGATTCAA
* ** * ** *
24553573 CGGCACATAGACTGCTAGACTTATAGCTTGATTCAGATCACCGGCACGTAGCCTGCTAGGTTTAT
1 CGGCACATAGCCTGCTAGGTTTATAACCCGATTCAAATCACCGGCACGTAGCCTGCTAGGTTTAT
*
24553638 AACCTGATTCAAATCAC
66 AACCCGATTCAAATCAC
* * ** *
24553655 CGGCACGTATCCTGCTAGGTTTATAACCCGATTCAAATCACTAGCACGTAGCCTACTAGGTTTAT
1 CGGCACATAGCCTGCTAGGTTTATAACCCGATTCAAATCACCGGCACGTAGCCTGCTAGGTTTAT
24553720 AACCCGATTCAAATCAC
66 AACCCGATTCAAATCAC
24553737 CGGCACATAGCCTGCTAGGTTTATAACCCGATTCAAATCACCGGCACGTAGCCTGCTAGG
1 CGGCACATAGCCTGCTAGGTTTATAACCCGATTCAAATCACCGGCACGTAGCCTGCTAGG
24553797 CGCTTAGCCT
Statistics
Matches: 124, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
82 124 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (82 bp):
CGGCACATAGCCTGCTAGGTTTATAACCCGATTCAAATCACCGGCACGTAGCCTGCTAGGTTTAT
AACCCGATTCAAATCAC
Found at i:24557649 original size:100 final size:100
Alignment explanation
Indices: 24557468--24557663 Score: 241
Period size: 100 Copynumber: 2.0 Consensus size: 100
24557458 ATTATTTAAC
* * *
24557468 TGCAATGTCGAGGAAACAAGATTCACCGTCGTGACTTCAATATATTCCACTACACCGCTAAGGAA
1 TGCAATGTCGAGGAAACAAGATCCACCGTCGTGACTTCAATACATTCCACTACACCGCCAAGGAA
*
24557533 GTAAGATCAGCCGTTGTGGCCTCAATCTTTTAAAT
66 GTAAAATCAGCCGTTGTGGCCTCAATCTTTTAAAT
* * * * * * * *
24557568 TGCAATGTCGGGGGAACCAGATCCACCGTCGT-AGCTTCAATCCGTTCCACTATACTGCCAGGGA
1 TGCAATGTCGAGGAAACAAGATCCACCGTCGTGA-CTTCAATACATTCCACTACACCGCCAAGGA
* * *
24557632 AGTAAAATCCGCTGTTGTGGCTTCAATCTTTT
65 AGTAAAATCAGCCGTTGTGGCCTCAATCTTTT
24557664 TCCACTGTAA
Statistics
Matches: 80, Mismatches: 15, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
99 1 0.01
100 79 0.99
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (100 bp):
TGCAATGTCGAGGAAACAAGATCCACCGTCGTGACTTCAATACATTCCACTACACCGCCAAGGAA
GTAAAATCAGCCGTTGTGGCCTCAATCTTTTAAAT
Found at i:24557872 original size:40 final size:41
Alignment explanation
Indices: 24557819--24558064 Score: 169
Period size: 40 Copynumber: 5.9 Consensus size: 41
24557809 AGGTCTTCAG
24557819 TCTGCTCCACTGCAACCTCAGGGAGATAAGACTTGATGTGA
1 TCTGCTCCACTGCAACCTCAGGGAGATAAGACTTGATGTGA
* * * * *
24557860 TCTACT-CTCTGCAACCTCAGAGAGATAAGA-TCCGTATGTCAA
1 TCTGCTCCACTGCAACCTCAGGGAGATAAGACT-TG-ATGT-GA
* * ** *
24557902 TCCGCTCCACTGCAACCTCAGGGAGATAGGATCGATTTCTTCTG-
1 TCTGCTCCACTGCAACCTCAGGGAGATA--A--GACTTGATGTGA
* * *
24557946 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGA
1 TCTGCTCCACTGCAACCTCAGGGAGATAAGACTTGATGTGA
* ** * *
24557987 TCTGCT-CTCTGCAACCTCAGAAAGATAAGATCTGGATGTTAA
1 TCTGCTCCACTGCAACCTCAGGGAGATAAGA-CTTGATG-TGA
** * * *
24558029 TCCACTCCGCTGCAACTTCAGGGAGATATGA-TTGAT
1 TCTGCTCCACTGCAACCTCAGGGAGATAAGACTTGAT
24558065 TTATTCTGCC
Statistics
Matches: 156, Mismatches: 36, Indels: 26
0.72 0.17 0.12
Matches are distributed among these distances:
39 1 0.01
40 48 0.31
41 26 0.17
42 11 0.07
43 38 0.24
44 26 0.17
45 1 0.01
46 2 0.01
47 2 0.01
48 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.26
Consensus pattern (41 bp):
TCTGCTCCACTGCAACCTCAGGGAGATAAGACTTGATGTGA
Found at i:24557997 original size:127 final size:127
Alignment explanation
Indices: 24557812--24558106 Score: 428
Period size: 127 Copynumber: 2.3 Consensus size: 127
24557802 TAGGATTAGG
* * * *
24557812 TCTTCAGTCTGCTCCACTGCAACCTCAGGGAGATAAGACTTGATGTGATCTACTCTCTGCAACCT
1 TCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTACTCTCTGCAACCT
* * *
24557877 CAGAGAGATAAGATCCGTATGTCAATCCGCTCCACTGCAACCTCAGGGAGATAGGATCGATT
66 CAGAAAGATAAGATCCGGATGTCAATCCACTCCACTGCAACCTCAGGGAGATAGGATCGATT
*
24557939 TCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTCTGCAACCT
1 TCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTACTCTCTGCAACCT
* * * * * *
24558004 CAGAAAGATAAGATCTGGATGTTAATCCACTCCGCTGCAACTTCAGGGAGATATGATTGATT
66 CAGAAAGATAAGATCCGGATGTCAATCCACTCCACTGCAACCTCAGGGAGATAGGATCGATT
* * * *
24558066 TATTCTGCCTGCTCCACTGTAATTTCAGGGAGATAAGACTG
1 TCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTG
24558107 AAGTTTCACC
Statistics
Matches: 150, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
127 150 1.00
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (127 bp):
TCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTACTCTCTGCAACCT
CAGAAAGATAAGATCCGGATGTCAATCCACTCCACTGCAACCTCAGGGAGATAGGATCGATT
Found at i:24559294 original size:1 final size:1
Alignment explanation
Indices: 24559288--24559390 Score: 53
Period size: 1 Copynumber: 103.0 Consensus size: 1
24559278 TCCTTTTCCC
* * * * * * * * * * *
24559288 TTTTTTTTCTTTTCTTTTCTTTCTTTCTTTTTTTCTTTTTCTTTTCTTTCTTTCTTCTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * *
24559353 CTTTTCTTTTTATTTTTTCTTTTCTTTTTCTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
24559391 AAGAAAAGTA
Statistics
Matches: 68, Mismatches: 34, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
1 68 1.00
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.83
Consensus pattern (1 bp):
T
Found at i:24559302 original size:5 final size:5
Alignment explanation
Indices: 24559287--24559390 Score: 93
Period size: 4 Copynumber: 22.0 Consensus size: 5
24559277 CTCCTTTTCC
24559287 CTTTT -TTTT CTTTT CTTTT C-TTT C-TTT C-TTT -TTTT CTTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT C-TTTT CTTTT
*
24559333 C-TTT CTTTCTT CTTTT -TTTT CTTTT CTTTT -TATT -TTTT CTTTT CTTTTT
1 CTTTT C-TT-TT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT C-TTTT
24559382 CTTTT -TTTT
1 CTTTT CTTTT
24559391 AAGAAAAGTA
Statistics
Matches: 87, Mismatches: 2, Indels: 21
0.79 0.02 0.19
Matches are distributed among these distances:
4 36 0.41
5 35 0.40
6 13 0.15
7 3 0.03
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.83
Consensus pattern (5 bp):
CTTTT
Found at i:24559316 original size:18 final size:17
Alignment explanation
Indices: 24559290--24559390 Score: 97
Period size: 17 Copynumber: 5.9 Consensus size: 17
24559280 CTTTTCCCTT
24559290 TTTTTTCTTTTCTTTTC
1 TTTTTTCTTTTCTTTTC
24559307 TTTCTTTC-TTT-TTTTC
1 TTT-TTTCTTTTCTTTTC
24559323 -TTTTTCTTTTCTTTCTTTC
1 TTTTTTCTTTTC--T-TTTC
24559342 TTCTTTT-TTTTCTTTTC
1 TT-TTTTCTTTTCTTTTC
*
24559359 TTTTTATTTTTTCTTTTC
1 TTTTT-TCTTTTCTTTTC
24559377 -TTTTTCTTTT-TTTT
1 TTTTTTCTTTTCTTTT
24559391 AAGAAAAGTA
Statistics
Matches: 73, Mismatches: 1, Indels: 22
0.76 0.01 0.23
Matches are distributed among these distances:
14 4 0.05
15 9 0.12
16 13 0.18
17 17 0.23
18 16 0.22
19 4 0.05
20 6 0.08
21 4 0.05
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTTCTTTTCTTTTC
Found at i:24559341 original size:31 final size:31
Alignment explanation
Indices: 24559291--24559387 Score: 121
Period size: 30 Copynumber: 3.2 Consensus size: 31
24559281 TTTTCCCTTT
24559291 TTTTTCTTTTCTTTTCTTTCTTTCTTTTTTTC
1 TTTTTCTTTTC-TTTCTTTCTTTCTTTTTTTC
24559323 TTTTTCTTTTCTTTCTTTC-TTCTTTTTTT-
1 TTTTTCTTTTCTTTCTTTCTTTCTTTTTTTC
* *
24559352 TCTTTTCTTTT-TATTTTTTCTTT-TCTTTTTC
1 T-TTTTCTTTTCT-TTCTTTCTTTCTTTTTTTC
24559383 TTTTT
1 TTTTT
24559388 TTTAAGAAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
29 2 0.03
30 35 0.59
31 11 0.19
32 11 0.19
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.82
Consensus pattern (31 bp):
TTTTTCTTTTCTTTCTTTCTTTCTTTTTTTC
Found at i:24559391 original size:27 final size:26
Alignment explanation
Indices: 24559289--24559385 Score: 130
Period size: 27 Copynumber: 3.8 Consensus size: 26
24559279 CCTTTTCCCT
24559289 TTTTTTTCTTTTCTTTTCTTTCTTTC
1 TTTTTTTCTTTTCTTTTCTTTCTTTC
24559315 TTTTTTTCTTTTTCTTTTCTTTCTTTC
1 TTTTTTTC-TTTTCTTTTCTTTCTTTC
*
24559342 TTCTTTT-TTTTCTTTTC-TT-TTT-
1 TTTTTTTCTTTTCTTTTCTTTCTTTC
*
24559364 ATTTTTTCTTTTCTTTTTCTTT
1 TTTTTTTCTTTTC-TTTTCTTT
24559386 TTTTTAAGAA
Statistics
Matches: 64, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
22 5 0.08
23 8 0.12
24 7 0.11
25 12 0.19
26 8 0.12
27 24 0.38
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.82
Consensus pattern (26 bp):
TTTTTTTCTTTTCTTTTCTTTCTTTC
Found at i:24562868 original size:27 final size:27
Alignment explanation
Indices: 24562811--24562868 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
24562801 ATGATGTAGC
* *
24562811 AAAAAAGAATAAAAGAATAATTACTCG
1 AAAAAAGAATAAAAGAATAATGACTCA
* *
24562838 AAAAAAGAATAAAAGAATACTGGCTCA
1 AAAAAAGAATAAAAGAATAATGACTCA
24562865 AAAA
1 AAAA
24562869 TGCATACGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.64, C:0.09, G:0.12, T:0.16
Consensus pattern (27 bp):
AAAAAAGAATAAAAGAATAATGACTCA
Found at i:24563943 original size:15 final size:15
Alignment explanation
Indices: 24563923--24563958 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
24563913 TTCCTTTACA
24563923 CCGAGCAGTAATGTG
1 CCGAGCAGTAATGTG
24563938 CCGAGCAGTAATGTG
1 CCGAGCAGTAATGTG
*
24563953 CAGAGC
1 CCGAGC
24563959 TTTAGTAGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.28, C:0.22, G:0.33, T:0.17
Consensus pattern (15 bp):
CCGAGCAGTAATGTG
Found at i:24573252 original size:24 final size:24
Alignment explanation
Indices: 24573214--24573465 Score: 152
Period size: 24 Copynumber: 10.8 Consensus size: 24
24573204 TGAATTGGAT
* *
24573214 AATTTACAATAAATAATATATAATA
1 AATTTAAAAT-AATAATATATGATA
* *
24573239 AATTTGAAATAATAATACAT-ATAA
1 AATTTAAAATAATAATATATGAT-A
*
24573263 AATTT-AAA-AAT--TTTGATGAT-
1 AATTTAAAATAATAATAT-ATGATA
* * **
24573283 AATTCTAGAATAATCATACGTGATA
1 AATT-TAAAATAATAATATATGATA
** * *
24573308 AATCCAAAATAATAGTATATAATA
1 AATTTAAAATAATAATATATGATA
*
24573332 AATTT-AAA-AATATTA-ATGATA
1 AATTTAAAATAATAATATATGATA
* *
24573353 AATTTGAAATAGAT-ATACATGATA
1 AATTTAAAATA-ATAATATATGATA
** **
24573377 AATTTAAAATAATGTTA-ACAATA
1 AATTTAAAATAATAATATATGATA
24573400 AATTTAAAATAATAATAT-TGATA
1 AATTTAAAATAATAATATATGATA
* *
24573423 AA-TTACAAATAATAAAACATGATA
1 AATTTA-AAATAATAATATATGATA
*
24573447 AATCTAAAATAATAATATA
1 AATTTAAAATAATAATATA
24573466 CAATATACTT
Statistics
Matches: 174, Mismatches: 35, Indels: 37
0.71 0.14 0.15
Matches are distributed among these distances:
20 5 0.03
21 13 0.07
22 19 0.11
23 50 0.29
24 73 0.42
25 14 0.08
ACGTcount: A:0.56, C:0.05, G:0.06, T:0.34
Consensus pattern (24 bp):
AATTTAAAATAATAATATATGATA
Found at i:24573310 original size:69 final size:69
Alignment explanation
Indices: 24573236--24573463 Score: 198
Period size: 69 Copynumber: 3.3 Consensus size: 69
24573226 ATAATATATA
* * *
24573236 ATAAATTTGAAATAATAATACAT-ATAAAATTTAAAAATTTTGATGAT-AATTCT-AGAATA-AT
1 ATAAATTTAAAATAATAATACATAAT-AAATTTAAAAATATTAATGATAAATT-TGA-AATAGAT
*
24573297 CATACGTG
63 -ATACATG
** * *
24573305 ATAAATCCAAAATAATAGTATATAATAAATTTAAAAATATTAATGATAAATTTGAAATAGATATA
1 ATAAATTTAAAATAATAATACATAATAAATTTAAAAATATTAATGATAAATTTGAAATAGATATA
24573370 CATG
66 CATG
** * * * **
24573374 ATAAATTTAAAATAATGTTA-ACAATAAATTTAAAATAATAATATTGATAAATTACAAATA-ATA
1 ATAAATTTAAAATAATAATACATAATAAATTT-AAA-AATATTAATGATAAATTTGAAATAGAT-
*
24573437 AAACATG
63 ATACATG
*
24573444 ATAAATCTAAAATAATAATA
1 ATAAATTTAAAATAATAATA
24573464 TACAATATAC
Statistics
Matches: 131, Mismatches: 21, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
68 10 0.08
69 69 0.53
70 52 0.40
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.34
Consensus pattern (69 bp):
ATAAATTTAAAATAATAATACATAATAAATTTAAAAATATTAATGATAAATTTGAAATAGATATA
CATG
Found at i:24573443 original size:70 final size:68
Alignment explanation
Indices: 24573303--24573459 Score: 183
Period size: 70 Copynumber: 2.3 Consensus size: 68
24573293 TAATCATACG
* * * **
24573303 TGATAAATCCAAAATAATAG-TATATAATAAATTTAAAAATATTAATGATAAATTTGAAATAGAT
1 TGATAAATCTAAAATAAT-GTTA-ACAATAAATTTAAAAATAATAATGATAAATTACAAATAGAT
*
24573367 ATACA
64 AAACA
* *
24573372 TGATAAATTTAAAATAATGTTAACAATAAATTTAAAATAATAATATTGATAAATTACAAATA-AT
1 TGATAAATCTAAAATAATGTTAACAATAAATTT-AAA-AATAATAATGATAAATTACAAATAGAT
24573436 AAAACA
64 -AAACA
24573442 TGATAAATCTAAAATAAT
1 TGATAAATCTAAAATAAT
24573460 AATATACAAT
Statistics
Matches: 75, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
68 11 0.15
69 23 0.31
70 41 0.55
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (68 bp):
TGATAAATCTAAAATAATGTTAACAATAAATTTAAAAATAATAATGATAAATTACAAATAGATAA
ACA
Found at i:24573448 original size:47 final size:48
Alignment explanation
Indices: 24573347--24573464 Score: 129
Period size: 47 Copynumber: 2.5 Consensus size: 48
24573337 AAAAATATTA
* * **
24573347 ATGATAAATTTGAAATAGAT-ATACATGATAAATTTAAAATAATGTTAAC
1 ATGATAAATTTAAAATA-ATAATA-TTGATAAATTTAAAATAATGAAAAC
24573396 A--ATAAATTTAAAATAATAATATTGATAAA-TTACAAATAAT-AAAAC
1 ATGATAAATTTAAAATAATAATATTGATAAATTTA-AAATAATGAAAAC
*
24573441 ATGATAAATCTAAAATAATAATAT
1 ATGATAAATTTAAAATAATAATAT
24573465 ACAATATACT
Statistics
Matches: 60, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
45 7 0.12
46 16 0.27
47 36 0.60
49 1 0.02
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (48 bp):
ATGATAAATTTAAAATAATAATATTGATAAATTTAAAATAATGAAAAC
Found at i:24576158 original size:34 final size:34
Alignment explanation
Indices: 24576102--24576172 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
24576092 ATAGAAATAA
**
24576102 ATTATTTTGTGTTTGACGTTGATACTATCGACCT
1 ATTATTTTGTGTTTGAAATTGATACTATCGACCT
* * *
24576136 ATTATTTTGTGTTTGAAATTGATGCTATGGATCT
1 ATTATTTTGTGTTTGAAATTGATACTATCGACCT
24576170 ATT
1 ATT
24576173 GGAGGTAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.23, C:0.10, G:0.18, T:0.49
Consensus pattern (34 bp):
ATTATTTTGTGTTTGAAATTGATACTATCGACCT
Found at i:24592786 original size:3 final size:3
Alignment explanation
Indices: 24592778--24592802 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
24592768 TTTGTTTTTA
24592778 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
24592803 TTTCCTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:24593583 original size:15 final size:15
Alignment explanation
Indices: 24593565--24593594 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
24593555 ACAATATTCA
24593565 TTTTTTTCTTAAAAT
1 TTTTTTTCTTAAAAT
24593580 TTTTTTTCTTAAAAT
1 TTTTTTTCTTAAAAT
24593595 CTTATTAGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTTTTCTTAAAAT
Found at i:24597836 original size:51 final size:51
Alignment explanation
Indices: 24597760--24597860 Score: 193
Period size: 51 Copynumber: 2.0 Consensus size: 51
24597750 CTAATCAATG
*
24597760 ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTA
1 ACAAGTGATAAGTGGTAACTTTAGCTACACTTATCTGATCAGTGACAAGTA
24597811 ACAAGTGATAAGTGGTAACTTTAGCTACACTTATCTGATCAGTGACAAGT
1 ACAAGTGATAAGTGGTAACTTTAGCTACACTTATCTGATCAGTGACAAGT
24597861 GGCTACACTT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.30
Consensus pattern (51 bp):
ACAAGTGATAAGTGGTAACTTTAGCTACACTTATCTGATCAGTGACAAGTA
Found at i:24597877 original size:28 final size:28
Alignment explanation
Indices: 24597834--24597889 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
24597824 GGTAACTTTA
24597834 GCTACACTTATCTGATCAGTGACAAGTG
1 GCTACACTTATCTGATCAGTGACAAGTG
*
24597862 GCTACACTTATTTGATCAGTGACAAGTG
1 GCTACACTTATCTGATCAGTGACAAGTG
24597890 ACAAGTGATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (28 bp):
GCTACACTTATCTGATCAGTGACAAGTG
Found at i:24597914 original size:79 final size:79
Alignment explanation
Indices: 24597783--24597937 Score: 283
Period size: 79 Copynumber: 2.0 Consensus size: 79
24597773 GGTAGCTTTA
24597783 GCTACACTTATCTGATCAGTGACAAGTAACAAGTGATAAGTGGTAACTTTAGCTACACTTATCTG
1 GCTACACTTATCTGATCAGTGACAAGTAACAAGTGATAAGTGGTAACTTTAGCTACACTTATCTG
24597848 ATCAGTGACAAGTG
66 ATCAGTGACAAGTG
* * *
24597862 GCTACACTTATTTGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTG
1 GCTACACTTATCTGATCAGTGACAAGTAACAAGTGATAAGTGGTAACTTTAGCTACACTTATCTG
24597927 ATCAGTGACAA
66 ATCAGTGACAA
24597938 ATGAAAAGTG
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 73 1.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (79 bp):
GCTACACTTATCTGATCAGTGACAAGTAACAAGTGATAAGTGGTAACTTTAGCTACACTTATCTG
ATCAGTGACAAGTG
Found at i:24597947 original size:51 final size:52
Alignment explanation
Indices: 24597862--24598009 Score: 181
Period size: 58 Copynumber: 2.7 Consensus size: 52
24597852 GTGACAAGTG
* *
24597862 GCTACACTTATTTGATCAGTGACAAGTGA-CAAGTGATAAGTGGTAGCTTTA
1 GCTACACTTATCTGATCAGTGACAAGTGAGAAAGTGATAAGTGGTAGCTTTA
*
24597913 GCTACACTTATCTGATCAGTGACAAATGAAAAGTGACAAGTGATAAGTGGTAGCTTTA
1 GCTACACTTATCTGATCAGTGACAAGTG---A--GA-AAGTGATAAGTGGTAGCTTTA
* *
24597971 GCTACACTTATCTAATCAGTGACAAGTGATAAATGTGAT
1 GCTACACTTATCTGATCAGTGACAAGTGAGAAA-GTGAT
24598010 CCGTATAAGA
Statistics
Matches: 83, Mismatches: 6, Indels: 14
0.81 0.06 0.14
Matches are distributed among these distances:
51 26 0.31
52 2 0.02
53 6 0.07
54 1 0.01
55 1 0.01
58 47 0.57
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (52 bp):
GCTACACTTATCTGATCAGTGACAAGTGAGAAAGTGATAAGTGGTAGCTTTA
Found at i:24597975 original size:58 final size:58
Alignment explanation
Indices: 24597885--24597995 Score: 213
Period size: 58 Copynumber: 1.9 Consensus size: 58
24597875 GATCAGTGAC
*
24597885 AAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAATGAA
1 AAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAGTGACAAATGAA
24597943 AAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAGTGACAA
1 AAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAGTGACAA
24597996 GTGATAAATG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (58 bp):
AAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAGTGACAAATGAA
Found at i:24605108 original size:6 final size:6
Alignment explanation
Indices: 24605092--24605146 Score: 78
Period size: 6 Copynumber: 9.5 Consensus size: 6
24605082 AGTCCATTTG
*
24605092 TTTTA- TTTTAT TTTTA- TTTTAT TTTTAT TTTTAT TTTTAT GTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
*
24605138 TGTTAT TTT
1 TTTTAT TTT
24605147 CTTAAACTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
5 10 0.23
6 34 0.77
ACGTcount: A:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (6 bp):
TTTTAT
Found at i:24621595 original size:22 final size:22
Alignment explanation
Indices: 24621551--24621616 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
24621541 AATATAATAG
* * * *
24621551 CGAAATGGTACCAAAATAGCAA
1 CGAAATGGCAGCAAAACAACAA
24621573 CGAAATGGCAGCAAAACAACAA
1 CGAAATGGCAGCAAAACAACAA
* * *
24621595 CAAAATAGCTGCAAAACAACAA
1 CGAAATGGCAGCAAAACAACAA
24621617 AATCGGGCCA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.55, C:0.21, G:0.15, T:0.09
Consensus pattern (22 bp):
CGAAATGGCAGCAAAACAACAA
Found at i:24622180 original size:16 final size:17
Alignment explanation
Indices: 24622154--24622187 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
24622144 GAAATTAATA
*
24622154 ATAATATTATTTAAATT
1 ATAATATTATTAAAATT
24622171 ATAATA-TATTAAAATT
1 ATAATATTATTAAAATT
24622187 A
1 A
24622188 ACGTTCAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATAATATTATTAAAATT
Found at i:24623346 original size:19 final size:20
Alignment explanation
Indices: 24623319--24623393 Score: 52
Period size: 19 Copynumber: 3.9 Consensus size: 20
24623309 AAAATATAAA
*
24623319 ATTACAAAT-TATAAAAATT
1 ATTAAAAATATATAAAAATT
* *
24623338 ATTAAAAATATGTAAAAATC
1 ATTAAAAATATATAAAAATT
* *
24623358 A-T-AGAATAAAT-AAAA-T
1 ATTAAAAATATATAAAAATT
24623374 ATCTAAAAATATATATAAAA
1 AT-TAAAAATATATA-AAAA
24623394 AATAAAAAAG
Statistics
Matches: 41, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
16 1 0.02
17 4 0.10
18 7 0.17
19 16 0.39
20 9 0.22
21 4 0.10
ACGTcount: A:0.63, C:0.04, G:0.03, T:0.31
Consensus pattern (20 bp):
ATTAAAAATATATAAAAATT
Found at i:24623346 original size:33 final size:32
Alignment explanation
Indices: 24623278--24623348 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 32
24623268 TGAAAAAAGT
**
24623278 AAATATAAAATATAAAATATTTAAATTATAGA
1 AAATATAAAATATAAAATATAAAAATTATAGA
24623310 AAATATAAAAT-TACAAATTATAAAAATTATTA-A
1 AAATATAAAATATA-AAA-TATAAAAATTA-TAGA
24623343 AAATAT
1 AAATAT
24623349 GTAAAAATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
31 2 0.06
32 14 0.41
33 16 0.47
34 2 0.06
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (32 bp):
AAATATAAAATATAAAATATAAAAATTATAGA
Found at i:24623372 original size:28 final size:29
Alignment explanation
Indices: 24623340--24623401 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 29
24623330 TAAAAATTAT
* *
24623340 TAAAAATATGTAAAAAT-CATAGAATAAA
1 TAAAAATATCTAAAAATACATAGAAAAAA
* *
24623368 T-AAAATATCTAAAAATATATATAAAAAA
1 TAAAAATATCTAAAAATACATAGAAAAAA
24623396 TAAAAA
1 TAAAAA
24623402 AGATACATCT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
27 14 0.50
28 10 0.36
29 4 0.14
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (29 bp):
TAAAAATATCTAAAAATACATAGAAAAAA
Found at i:24623926 original size:24 final size:24
Alignment explanation
Indices: 24623898--24623949 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
24623888 TTAGTAGGTC
* * *
24623898 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAACAAATACT
* *
24623922 AAATATATTATACTAACAAATACT
1 AAATAAACTATACTAACAAATACT
24623946 AAAT
1 AAAT
24623950 TTTCTAGAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.54, C:0.12, G:0.04, T:0.31
Consensus pattern (24 bp):
AAATAAACTATACTAACAAATACT
Found at i:24632052 original size:3 final size:3
Alignment explanation
Indices: 24632044--24632073 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
24632034 GGGCTAAGTT
24632044 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
24632074 CTACATTGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:24636237 original size:16 final size:15
Alignment explanation
Indices: 24636218--24636293 Score: 57
Period size: 16 Copynumber: 4.8 Consensus size: 15
24636208 AAAAAATAAA
24636218 AAATATTTAAAAACAT
1 AAATATTTAAAAA-AT
24636234 AAATATTTAAAAAATCT
1 AAATATTTAAAAAA--T
* *
24636251 AAATATTATAAATATT
1 AAATATT-TAAAAAAT
24636267 ATAA-ATTTAAAAACA-
1 A-AATATTTAAAAA-AT
*
24636282 AAATATATAAAA
1 AAATATTTAAAA
24636294 TTTTAAAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
14 2 0.04
15 14 0.29
16 18 0.37
17 10 0.20
18 5 0.10
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATATTTAAAAAAT
Found at i:24636246 original size:17 final size:17
Alignment explanation
Indices: 24636218--24636262 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
24636208 AAAAAATAAA
24636218 AAATATTT-AAAAA-CAT
1 AAATATTTAAAAAATC-T
24636234 AAATATTTAAAAAATCT
1 AAATATTTAAAAAATCT
24636251 AAATATTATAAA
1 AAATATT-TAAA
24636263 TATTATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 8 0.31
17 13 0.50
18 5 0.19
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATATTTAAAAAATCT
Found at i:24636294 original size:22 final size:23
Alignment explanation
Indices: 24636260--24636302 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
24636250 TAAATATTAT
24636260 AAATATTATAAA-TTTAAAAACA
1 AAATATTATAAATTTTAAAAACA
24636282 AAATA-TATAAAATTTTAAAAA
1 AAATATTAT-AAATTTTAAAAA
24636303 ATCAATTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 3 0.16
22 8 0.42
23 8 0.42
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
AAATATTATAAATTTTAAAAACA
Found at i:24636798 original size:24 final size:25
Alignment explanation
Indices: 24636762--24636809 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
24636752 TAAATTGATT
*
24636762 TTTTTTTAAATTTA-AAATTTTTTG
1 TTTTATTAAATTTATAAATTTTTTG
* *
24636786 TTTTATTATATTTATATATTTTTT
1 TTTTATTAAATTTATAAATTTTTT
24636810 AGGTTTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (25 bp):
TTTTATTAAATTTATAAATTTTTTG
Found at i:24643061 original size:2 final size:2
Alignment explanation
Indices: 24643054--24643085 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
24643044 GAAGTCTCTG
24643054 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
24643086 TCTGATAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24645887 original size:44 final size:44
Alignment explanation
Indices: 24645837--24645926 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
24645827 TATAATCCAG
24645837 TTTTATTTTTTTAATCCCGATAGTTTATTAACCAATAGAATCAC
1 TTTTATTTTTTTAATCCCGATAGTTTATTAACCAATAGAATCAC
*
24645881 TTTTATTTTTTTAATCCCGATAGTTTGTTAACCAATAGAATCAC
1 TTTTATTTTTTTAATCCCGATAGTTTATTAACCAATAGAATCAC
24645925 TT
1 TT
24645927 ATCAAAACCC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.47
Consensus pattern (44 bp):
TTTTATTTTTTTAATCCCGATAGTTTATTAACCAATAGAATCAC
Done.