Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold133
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: 2564099
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 17052 characters in sequence are not A, C, G, or T
File 5 of 17
Found at i:515883 original size:19 final size:18
Alignment explanation
Indices: 515822--515887 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 18
515812 TTAATATTAC
515822 ATATTTAAAATATATAATATTT
1 ATATTTAAAAT-T-T-ATA-TT
* *
515844 ATATTTAAAATTTTTAAT
1 ATATTTAAAATTTATATT
*
515862 ATATTTAACAATTTATCTT
1 ATATTTAA-AATTTATATT
515881 ATATTTA
1 ATATTTA
515888 TATGAGCATA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
18 9 0.24
19 16 0.42
20 1 0.03
21 1 0.03
22 11 0.29
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATTTAAAATTTATATT
Found at i:516461 original size:17 final size:18
Alignment explanation
Indices: 516414--516466 Score: 63
Period size: 17 Copynumber: 2.9 Consensus size: 18
516404 TCGTATTATT
516414 ATATTATAACTATTTTAAAA
1 ATATT-TAA-TATTTTAAAA
* *
516434 ATATTTTATATTTTATAA
1 ATATTTAATATTTTAAAA
516452 A-ATTTAATATTTTAA
1 ATATTTAATATTTTAA
516467 TAGTTTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 12 0.41
18 10 0.34
19 2 0.07
20 5 0.17
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATTTAATATTTTAAAA
Found at i:518209 original size:23 final size:22
Alignment explanation
Indices: 518170--518213 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
518160 TTTATTTAAA
518170 TTTAATATTAATATAAAATAATT
1 TTTAATATTAATAT-AAATAATT
* *
518193 TTTAATATTATTTTAAATAAT
1 TTTAATATTAATATAAATAAT
518214 AATTGAGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTAATATTAATATAAATAATT
Found at i:518761 original size:20 final size:20
Alignment explanation
Indices: 518699--518762 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 20
518689 ATTAGTTCAA
*
518699 ATATTTATATAAAAAAATTA
1 ATATTTATATAAAAAAATTT
* * *
518719 ATTTCTTTTTTAAAAAATTATTT
1 ATAT-TTATATAAAAAA--ATTT
518742 ATATTTATATAAAAAAATTT
1 ATATTTATATAAAAAAATTT
518762 A
1 A
518763 AGAACTATCA
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
20 8 0.24
21 10 0.29
22 10 0.29
23 6 0.18
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
ATATTTATATAAAAAAATTT
Found at i:518929 original size:17 final size:17
Alignment explanation
Indices: 518893--518936 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
518883 TCCTTTTGAT
** *
518893 TATTAATATTATTATCA
1 TATTAATATTAACATAA
518910 TATTAATATTAACATAA
1 TATTAATATTAACATAA
518927 TATATAATAT
1 TAT-TAATAT
518937 AAAAATGTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 17 0.74
18 6 0.26
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (17 bp):
TATTAATATTAACATAA
Found at i:519022 original size:22 final size:22
Alignment explanation
Indices: 518996--519037 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
518986 TTAAATATTA
*
518996 ATTTATTTAAAAAATTATTTTT
1 ATTTATATAAAAAATTATTTTT
* *
519018 ATTTATATCAAAATTTATTT
1 ATTTATATAAAAAATTATTT
519038 AATGATATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTATATAAAAAATTATTTTT
Found at i:521340 original size:21 final size:20
Alignment explanation
Indices: 521316--521356 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
521306 AATTTTTATT
521316 ATTTTAAATATATATTTTTTA
1 ATTTTAAATAT-TATTTTTTA
**
521337 ATTTTTTATATTATTTTTTA
1 ATTTTAAATATTATTTTTTA
521357 TAATAATACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
ATTTTAAATATTATTTTTTA
Found at i:521360 original size:22 final size:22
Alignment explanation
Indices: 521307--521360 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
521297 ATATCTTTAA
*
521307 ATTTTTATTATTTTAAATATAT
1 ATTTTTATAATTTTAAATATAT
**
521329 ATTTTT-TAATTTTTTATAT-T
1 ATTTTTATAATTTTAAATATAT
521349 ATTTTTTATAAT
1 A-TTTTTATAAT
521361 AATACCAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 2 0.07
21 15 0.56
22 10 0.37
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (22 bp):
ATTTTTATAATTTTAAATATAT
Found at i:521622 original size:2 final size:2
Alignment explanation
Indices: 521615--521647 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
521605 ACAAGACGAA
521615 AG AG 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 AG AG A
521648 ATTCTTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:521908 original size:20 final size:17
Alignment explanation
Indices: 521885--521928 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 17
521875 AAGTATATTT
521885 TTTAATTTAAATTTATATAA
1 TTTAATTTAAA-TTA-A-AA
521905 TTTAATTTAAATTAAAA
1 TTTAATTTAAATTAAAA
521922 TTTAATT
1 TTTAATT
521929 AATAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.38
18 1 0.04
19 3 0.12
20 11 0.46
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTAATTTAAATTAAAA
Found at i:523815 original size:2 final size:2
Alignment explanation
Indices: 523808--523834 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
523798 TACACCTACG
523808 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
523835 CACACACACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:524728 original size:24 final size:23
Alignment explanation
Indices: 524700--524753 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
524690 TTATTTTATT
524700 ATTTAAAATAATATTAAAAATTAA
1 ATTTAAAATAATATT-AAAATTAA
* * * *
524724 TTTTATATTAATATTATAATTAA
1 ATTTAAAATAATATTAAAATTAA
524747 ATTTAAA
1 ATTTAAA
524754 TAAAAATATT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
23 12 0.50
24 12 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTAAAATAATATTAAAATTAA
Found at i:534672 original size:20 final size:21
Alignment explanation
Indices: 534627--534672 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
534617 TTGTTTGTTT
* *
534627 TTATTCACGAACATATTTTTAA
1 TTATTCACGAACACA-TTTCAA
534649 TTATTCACGAACACA-TTCAA
1 TTATTCACGAACACATTTCAA
534669 TTAT
1 TTAT
534673 ATATTCAGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 8 0.36
22 14 0.64
ACGTcount: A:0.37, C:0.17, G:0.04, T:0.41
Consensus pattern (21 bp):
TTATTCACGAACACATTTCAA
Found at i:534754 original size:16 final size:16
Alignment explanation
Indices: 534729--534760 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
534719 TAAACACGAA
*
534729 TCAAACATAAATAAAC
1 TCAAAAATAAATAAAC
534745 TCAAAAATAAATAAAC
1 TCAAAAATAAATAAAC
534761 GAATACAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.16, G:0.00, T:0.19
Consensus pattern (16 bp):
TCAAAAATAAATAAAC
Found at i:536186 original size:27 final size:27
Alignment explanation
Indices: 536130--536186 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
536120 GCCGTTAATT
* * *
536130 TTGAAATTTAATTTGAAATAGTAAATG
1 TTGAAATTCAATTTGAAACAGTAAAGG
*
536157 TTGAAATTCAATTTGAAACAGTGAAGG
1 TTGAAATTCAATTTGAAACAGTAAAGG
536184 TTG
1 TTG
536187 TATAGTACCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.37
Consensus pattern (27 bp):
TTGAAATTCAATTTGAAACAGTAAAGG
Found at i:536608 original size:44 final size:44
Alignment explanation
Indices: 536548--536671 Score: 248
Period size: 44 Copynumber: 2.8 Consensus size: 44
536538 TGTGTTTTTA
536548 TTATTTATTTTTCCGTGGATTGGCATAGCCACCCAATTGCATAT
1 TTATTTATTTTTCCGTGGATTGGCATAGCCACCCAATTGCATAT
536592 TTATTTATTTTTCCGTGGATTGGCATAGCCACCCAATTGCATAT
1 TTATTTATTTTTCCGTGGATTGGCATAGCCACCCAATTGCATAT
536636 TTATTTATTTTTCCGTGGATTGGCATAGCCACCCAA
1 TTATTTATTTTTCCGTGGATTGGCATAGCCACCCAA
536672 ATTCTAACAA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 80 1.00
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (44 bp):
TTATTTATTTTTCCGTGGATTGGCATAGCCACCCAATTGCATAT
Found at i:540905 original size:12 final size:12
Alignment explanation
Indices: 540888--540913 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
540878 GAAAACAAAG
540888 GCTGCCAACTGT
1 GCTGCCAACTGT
540900 GCTGCCAACTGT
1 GCTGCCAACTGT
540912 GC
1 GC
540914 CGTCAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.35, G:0.27, T:0.23
Consensus pattern (12 bp):
GCTGCCAACTGT
Found at i:540938 original size:12 final size:12
Alignment explanation
Indices: 540916--540966 Score: 57
Period size: 12 Copynumber: 3.9 Consensus size: 12
540906 AACTGTGCCG
540916 TCAATTTTGAAAT
1 TCAA-TTTGAAAT
540929 TCAATTTGAAAT
1 TCAATTTGAAAT
*
540941 AGTAAATGTTGAAAT
1 --TCAAT-TTGAAAT
540956 TCAATTTGAAA
1 TCAATTTGAAA
540967 CAGTGAAGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
12 14 0.42
13 8 0.24
14 4 0.12
15 7 0.21
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (12 bp):
TCAATTTGAAAT
Found at i:540978 original size:27 final size:27
Alignment explanation
Indices: 540922--540978 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
540912 GCCGTCAATT
* *
540922 TTGAAATTCAATTTGAAATAGTAAATG
1 TTGAAATTCAATTTGAAACAGTAAAGG
*
540949 TTGAAATTCAATTTGAAACAGTGAAGG
1 TTGAAATTCAATTTGAAACAGTAAAGG
540976 TTG
1 TTG
540979 CATAGTACCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.35
Consensus pattern (27 bp):
TTGAAATTCAATTTGAAACAGTAAAGG
Found at i:541545 original size:14 final size:14
Alignment explanation
Indices: 541526--541555 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
541516 ACTCGCATGT
541526 TCGCTGCCCTTTTA
1 TCGCTGCCCTTTTA
541540 TCGCTGCCCTTTTA
1 TCGCTGCCCTTTTA
541554 TC
1 TC
541556 TCTAGAGCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.07, C:0.37, G:0.13, T:0.43
Consensus pattern (14 bp):
TCGCTGCCCTTTTA
Found at i:543125 original size:6 final size:6
Alignment explanation
Indices: 543114--543168 Score: 83
Period size: 6 Copynumber: 9.2 Consensus size: 6
543104 AAAATAATTA
* *
543114 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATATAT ATATAT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT
*
543162 TTTTAT A
1 ATTTAT A
543169 ATTAAATTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
ATTTAT
Found at i:544592 original size:17 final size:16
Alignment explanation
Indices: 544551--544590 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
544541 TGGCTTATTA
*
544551 TTTATTTAAATTTAGT
1 TTTATTTAAATTTAAT
*
544567 TTTAGTTTAATTTTAAT
1 TTTA-TTTAAATTTAAT
544584 TTTATTT
1 TTTATTT
544591 TACAATCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.68
Consensus pattern (16 bp):
TTTATTTAAATTTAAT
Found at i:544642 original size:18 final size:18
Alignment explanation
Indices: 544572--544643 Score: 56
Period size: 18 Copynumber: 3.8 Consensus size: 18
544562 TTAGTTTTAG
*
544572 TTTAATTTTAAT-TTTAT
1 TTTAATTTTAATAATTAT
544589 TTTACAATCTCTTAATTAATTAT
1 TTT--AAT-T-TTAA-TAATTAT
***
544612 TTTAATAAAAATAATTAT
1 TTTAATTTTAATAATTAT
544630 TTTAATTTTAATAA
1 TTTAATTTTAATAA
544644 ATAGCAAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 11
0.70 0.12 0.18
Matches are distributed among these distances:
17 3 0.07
18 18 0.43
19 5 0.12
20 1 0.02
21 7 0.17
22 1 0.02
23 7 0.17
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTAATTTTAATAATTAT
Found at i:544988 original size:143 final size:142
Alignment explanation
Indices: 544722--544988 Score: 297
Period size: 143 Copynumber: 1.9 Consensus size: 142
544712 ATTCAAGTAC
*
544722 ATATGATAAATATTTTAAACTTATTTTTAATACAATAAATTAACTTTAAAATAAATATATTAATT
1 ATATGATAAATATTTTAAACTTATATTTAATACAATAAATTAACTTTAAAATAAATATATTAATT
* * * * **
544787 TTTTATTTAAATAAGTTAATAAAATTATTTAAAGAAATTTAATGTTAAAAAATGATTAAAATTAA
66 TCTTATTTAAATAAATGAATAAAATTATTTAAAGAAATATAATAATAAAAAA-GATTAAAATTAA
544852 TTTTAATGTAAGT
130 TTTTAATGTAAGT
* * ** * ** * *
544865 ATATGTTAAATATTTTAAATTTATATTTAAT-CAAATACGTTAACTTTGAGTTGAATATATTGTA
1 ATATGATAAATATTTTAAACTTATATTTAATAC-AATAAATTAACTTTAAAATAAATATATT-AA
* * *
544929 TTTCTTATTTGAAATAAATGAATAAAATTATTTTAAA-AAGTATAGTAATAAAGAA-ATTAA
64 TTTCTTATTT-AAATAAATGAATAAAATTA-TTTAAAGAAATATAATAATAAAAAAGATTAA
544989 TTAAAAAAAT
Statistics
Matches: 101, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
142 1 0.01
143 55 0.54
144 10 0.10
145 29 0.29
146 6 0.06
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (142 bp):
ATATGATAAATATTTTAAACTTATATTTAATACAATAAATTAACTTTAAAATAAATATATTAATT
TCTTATTTAAATAAATGAATAAAATTATTTAAAGAAATATAATAATAAAAAAGATTAAAATTAAT
TTTAATGTAAGT
Found at i:545228 original size:14 final size:16
Alignment explanation
Indices: 545192--545230 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
545182 AAATATTAAT
*
545192 TTAAAATATTTTATAA
1 TTAAAAAATTTTATAA
545208 TTAAAAAATTTTA-AA
1 TTAAAAAATTTTATAA
545223 -TAAAAAAT
1 TTAAAAAAT
545231 GAAAACAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.36
15 2 0.09
16 12 0.55
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TTAAAAAATTTTATAA
Found at i:545283 original size:17 final size:16
Alignment explanation
Indices: 545242--545286 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
545232 AAAACAAAAA
*
545242 AATAAAAAATATTTTT
1 AATAAAAAATTTTTTT
*
545258 AAT-TAAAATTTTTTT
1 AATAAAAAATTTTTTT
545273 AATAAATAAATTTT
1 AATAAA-AAATTTT
545287 AAAAAATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 13 0.54
16 4 0.17
17 7 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AATAAAAAATTTTTTT
Found at i:548064 original size:63 final size:63
Alignment explanation
Indices: 547994--548155 Score: 263
Period size: 63 Copynumber: 2.6 Consensus size: 63
547984 ATATGTTTAG
* *
547994 ATTGTATCGATACATTATGAATTGTATCGATATATTTGGCCCAAC-AGCTAGAATTTCAAATGC
1 ATTGTATCGATACTTTATGAATTGTATCGATACATTTGGCCCAACGA-CTAGAATTTCAAATGC
*
548057 ATTGTATCGATACTTTATGAATTGTATCGATACATTTGGCTCAACGACTAGAATTTCAAATGC
1 ATTGTATCGATACTTTATGAATTGTATCGATACATTTGGCCCAACGACTAGAATTTCAAATGC
* *
548120 ATTGTATCGATACTTTATGAAATGTATTGATACATT
1 ATTGTATCGATACTTTATGAATTGTATCGATACATT
548156 GGAACGTGAA
Statistics
Matches: 93, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
63 92 0.99
64 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (63 bp):
ATTGTATCGATACTTTATGAATTGTATCGATACATTTGGCCCAACGACTAGAATTTCAAATGC
Found at i:548562 original size:35 final size:34
Alignment explanation
Indices: 548516--548581 Score: 105
Period size: 35 Copynumber: 1.9 Consensus size: 34
548506 GAAGTGATTG
*
548516 AGAGGCTCTATCTTAGCCTCTGAAAAAGATAGGGA
1 AGAGGCTCTATCTTAGCCTATG-AAAAGATAGGGA
*
548551 AGAGGTTCTATCTTAGCCTATGAAAAGATAG
1 AGAGGCTCTATCTTAGCCTATGAAAAGATAG
548582 AGTTGTAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 9 0.31
35 20 0.69
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (34 bp):
AGAGGCTCTATCTTAGCCTATGAAAAGATAGGGA
Found at i:549325 original size:2 final size:2
Alignment explanation
Indices: 549318--549346 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
549308 CCCTCGTGAC
549318 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
549347 GGTACCTCGC
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:549902 original size:18 final size:18
Alignment explanation
Indices: 549879--549913 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
549869 CCCTGGTGAA
*
549879 ATTTTATTTGAAGTTTGC
1 ATTTTATTTAAAGTTTGC
549897 ATTTTATTTAAAGTTTG
1 ATTTTATTTAAAGTTTG
549914 GCATGTCTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.03, G:0.14, T:0.57
Consensus pattern (18 bp):
ATTTTATTTAAAGTTTGC
Found at i:550284 original size:20 final size:18
Alignment explanation
Indices: 550259--550324 Score: 61
Period size: 20 Copynumber: 3.7 Consensus size: 18
550249 TAAAATATTA
550259 TATATATTTATATAAACTTT
1 TATATA-TTATATAAA-TTT
550279 TATATATTA-AT-AA--T
1 TATATATTATATAAATTT
550293 T-TATATTATATAAATTT
1 TATATATTATATAAATTT
550310 TAATATATTTATATA
1 T-ATATA-TTATATA
550325 TTTACATAGC
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 7 0.18
14 4 0.10
15 2 0.05
17 4 0.10
18 2 0.05
19 7 0.18
20 13 0.33
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
TATATATTATATAAATTT
Found at i:550303 original size:32 final size:34
Alignment explanation
Indices: 550252--550328 Score: 97
Period size: 32 Copynumber: 2.3 Consensus size: 34
550242 AAACAATTAA
*
550252 AATATTATATATATTTATATAAACTTTT-ATATATT
1 AATA-TATTTATATTTATATAAA-TTTTAATATATT
550287 AATA-ATTTATA-TTATATAAATTTTAATATATT
1 AATATATTTATATTTATATAAATTTTAATATATT
*
550319 TATATATTTA
1 AATATATTTA
550329 CATAGCATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
31 4 0.11
32 19 0.50
33 11 0.29
35 4 0.11
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (34 bp):
AATATATTTATATTTATATAAATTTTAATATATT
Found at i:555243 original size:16 final size:17
Alignment explanation
Indices: 555222--555258 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
555212 TCTATTTTCA
*
555222 TTTTAAAAAATATT-TT
1 TTTTAAAAAAAATTATT
555238 TTTTAAAAAAAATTATT
1 TTTTAAAAAAAATTATT
555255 TTTT
1 TTTT
555259 GACCTATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTTAAAAAAAATTATT
Found at i:556459 original size:29 final size:29
Alignment explanation
Indices: 556418--556493 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
556408 TATATGAAAC
* *
556418 ATTAAAA-TCAAAAACTTAAT-TAATATAT
1 ATTAAAATTTAAAAA-TTAATATAAAATAT
556446 ATTAAAATTTAAAAATTAATATAAAATAT
1 ATTAAAATTTAAAAATTAATATAAAATAT
*
556475 ATTCTAAAATTTTAAAATT
1 A-T-TAAAATTTAAAAATT
556494 TCTTAATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
28 12 0.29
29 14 0.34
30 1 0.02
31 14 0.34
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (29 bp):
ATTAAAATTTAAAAATTAATATAAAATAT
Found at i:556807 original size:110 final size:111
Alignment explanation
Indices: 556613--556834 Score: 376
Period size: 110 Copynumber: 2.0 Consensus size: 111
556603 CAACAAAGCG
*
556613 TTGGTAGCACAGGTGGGGGAGACGTAGCACTCCCCCTATCACTGATCCGACTCAATCATATCGGT
1 TTGGTAGCACAGGTGGGGGAGACGTAGCACTCCCCCTATCACTGATCCGACTCAATCATACCGGT
* *
556678 TGCTGAACTGAAATATCTAACCAGTCCTTTTGGCTATTGGCTTTGA
66 TGCTGAACTGAAATATCTAACCAGTCCTTTCGGCTATCGGCTTTGA
*
556724 TTGGTAGCACAGGT-GGGGAGAC-TAAGCTCTCCCCCTATCACTGATCCGACTCAATCATACCGG
1 TTGGTAGCACAGGTGGGGGAGACGT-AGCACTCCCCCTATCACTGATCCGACTCAATCATACCGG
*
556787 TTGCTGAACTGAAATATCTAACCAGTGCTTTCGGCTATCGGCTTTGA
65 TTGCTGAACTGAAATATCTAACCAGTCCTTTCGGCTATCGGCTTTGA
556834 T
1 T
556835 CTTTACACTG
Statistics
Matches: 105, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
109 1 0.01
110 90 0.86
111 14 0.13
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.28
Consensus pattern (111 bp):
TTGGTAGCACAGGTGGGGGAGACGTAGCACTCCCCCTATCACTGATCCGACTCAATCATACCGGT
TGCTGAACTGAAATATCTAACCAGTCCTTTCGGCTATCGGCTTTGA
Found at i:556994 original size:2 final size:2
Alignment explanation
Indices: 556987--557015 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
556977 TATATGTTTG
556987 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
557016 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:557020 original size:2 final size:2
Alignment explanation
Indices: 557015--557045 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
557005 ACACACACAC
557015 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
557046 AATCAATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:557092 original size:18 final size:17
Alignment explanation
Indices: 557069--557102 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
557059 AAAATAAATT
*
557069 TTTTAAATATATAAAAAA
1 TTTTAAAAAT-TAAAAAA
557087 TTTTAAAAATTAAAAA
1 TTTTAAAAATTAAAAA
557103 TATTCATACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TTTTAAAAATTAAAAAA
Found at i:558897 original size:72 final size:72
Alignment explanation
Indices: 558773--559146 Score: 543
Period size: 72 Copynumber: 5.2 Consensus size: 72
558763 AGTGAAACGA
* * * *
558773 TAATTCGAGATAATCTGCACGATAAATGCAATCAACAACTATTTCTGTATATTTAAAACTACTAT
1 TAATCCGAGATAATCTGCACGATAAATACAATCAACAAATATTTCTGCATATTTAAAACTACTAT
558838 CAACAAC
66 CAACAAC
* * *
558845 TAATCCGAGATAATCTGCACGATAAATACAATCAATAACTATTTCTACATATTTAAAACTACTAT
1 TAATCCGAGATAATCTGCACGATAAATACAATCAACAAATATTTCTGCATATTTAAAACTACTAT
*
558910 CAATAAC
66 CAACAAC
* * *
558917 TAATTCGAGATAATCTGCACGATAACTACAATCAACAAATATTTCTGCATATTTAAAACTACAAT
1 TAATCCGAGATAATCTGCACGATAAATACAATCAACAAATATTTCTGCATATTTAAAACTACTAT
558982 CAACAAC
66 CAACAAC
* * * * * *
558989 AAATCCGAGATAATCTGTATGATAACA-ACAATCAATAAATGTTTTTGCATATTTAAAACTACTA
1 TAATCCGAGATAATCTGCACGATAA-ATACAATCAACAAATATTTCTGCATATTTAAAACTACTA
559053 TCAACAAC
65 TCAACAAC
* * *
559061 TAATCCAAGATAATCTGCACGATAACTACAATCAACAAATATTTCTACATATTTAAAACTACTAT
1 TAATCCGAGATAATCTGCACGATAAATACAATCAACAAATATTTCTGCATATTTAAAACTACTAT
559126 CAACAAC
66 CAACAAC
*
559133 TAATCTGAGATAAT
1 TAATCCGAGATAAT
559147 TTGTTTAAAA
Statistics
Matches: 267, Mismatches: 33, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
72 267 1.00
ACGTcount: A:0.44, C:0.19, G:0.07, T:0.30
Consensus pattern (72 bp):
TAATCCGAGATAATCTGCACGATAAATACAATCAACAAATATTTCTGCATATTTAAAACTACTAT
CAACAAC
Found at i:559494 original size:15 final size:15
Alignment explanation
Indices: 559456--559496 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
559446 TGGGTATACA
559456 GGTGGTGGATGCACG
1 GGTGGTGGATGCACG
**
559471 GGTTATGGATGCACG
1 GGTGGTGGATGCACG
559486 GGTGGTGGATG
1 GGTGGTGGATG
559497 AACAGAATCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.15, C:0.10, G:0.51, T:0.24
Consensus pattern (15 bp):
GGTGGTGGATGCACG
Found at i:564393 original size:15 final size:14
Alignment explanation
Indices: 564368--564412 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
564358 ACATTTTTTA
*
564368 TACCATAAACTAAT
1 TACCCTAAACTAAT
564382 TACCCCTAAACTAAT
1 TA-CCCTAAACTAAT
*
564397 TACTCTAAACCTAAT
1 TACCCTAAA-CTAAT
564412 T
1 T
564413 CAACATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 8 0.30
15 19 0.70
ACGTcount: A:0.42, C:0.27, G:0.00, T:0.31
Consensus pattern (14 bp):
TACCCTAAACTAAT
Found at i:564598 original size:28 final size:30
Alignment explanation
Indices: 564534--564602 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 30
564524 GATTTACTGT
* *
564534 TAAAAAAATAATAATCAAAATTTTAACATAT
1 TAAAAAAATAATAATCAAAA-TTTAACAAAA
564565 TAAAAAAATAATAAT-AAAA-TTAA-AAAA
1 TAAAAAAATAATAATCAAAATTTAACAAAA
*
564592 TAGAAAAATAA
1 TAAAAAAATAA
564603 ATATTAAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 12 0.34
28 4 0.11
30 4 0.11
31 15 0.43
ACGTcount: A:0.70, C:0.03, G:0.01, T:0.26
Consensus pattern (30 bp):
TAAAAAAATAATAATCAAAATTTAACAAAA
Found at i:565248 original size:2 final size:2
Alignment explanation
Indices: 565241--565277 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
565231 ACCCTTTTAT
565241 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
565278 TTGGTCAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:565460 original size:17 final size:19
Alignment explanation
Indices: 565436--565480 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 19
565426 GTCATGTTAT
565436 TATTTAAAAAATT-CAAAA
1 TATTTAAAAAATTACAAAA
*
565454 T-TTT-AAAAATTAGAAAA
1 TATTTAAAAAATTACAAAA
565471 TATTTAAAAA
1 TATTTAAAAA
565481 TTTTAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 7 0.30
17 8 0.35
18 4 0.17
19 4 0.17
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (19 bp):
TATTTAAAAAATTACAAAA
Found at i:565476 original size:18 final size:17
Alignment explanation
Indices: 565436--565482 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 17
565426 GTCATGTTAT
565436 TATTTAAAAAATTCAAAA
1 TATTT-AAAAATTCAAAA
*
565454 T-TTTAAAAATTAGAAAA
1 TATTTAAAAATT-CAAAA
565471 TATTTAAAAATT
1 TATTTAAAAATT
565483 TTAAATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 7 0.27
17 8 0.31
18 11 0.42
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (17 bp):
TATTTAAAAATTCAAAA
Found at i:565488 original size:17 final size:17
Alignment explanation
Indices: 565436--565488 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
565426 GTCATGTTAT
*
565436 TATTTAAAAAATTCAAAA
1 TATTT-AAAAATTTAAAA
*
565454 T-TTTAAAAATTAGAAAA
1 TATTTAAAAATT-TAAAA
*
565471 TATTTAAAAATTTTAAA
1 TATTTAAAAATTTAAAA
565488 T
1 T
565489 TTATTTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 7 0.23
17 12 0.40
18 11 0.37
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
TATTTAAAAATTTAAAA
Found at i:565821 original size:3 final size:3
Alignment explanation
Indices: 565813--565865 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
565803 TTGGTTTCTT
565813 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
565861 TTA TT
1 TTA TT
565866 TATTTCTCAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:576800 original size:3 final size:3
Alignment explanation
Indices: 576794--576824 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
576784 CAAAAAAAAA
576794 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
576825 CGAATAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:576882 original size:8 final size:8
Alignment explanation
Indices: 576839--576923 Score: 59
Period size: 8 Copynumber: 10.8 Consensus size: 8
576829 TAAAATAACA
576839 TAAAATA-
1 TAAAATAT
576846 TAAAA-AT
1 TAAAATAT
* *
576853 TAATATAGA
1 TAAAATA-T
*
576862 TATAATAT
1 TAAAATAT
*
576870 CAAAATAT
1 TAAAATAT
576878 TAAAATAT
1 TAAAATAT
576886 TAAAAT-T
1 TAAAATAT
* *
576893 TATAAAAAA
1 TA-AAATAT
*
576902 TAAATTAT
1 TAAAATAT
*
576910 TAACATAT
1 TAAAATAT
576918 TAAAAT
1 TAAAAT
576924 TTATATATAT
Statistics
Matches: 57, Mismatches: 16, Indels: 9
0.70 0.20 0.11
Matches are distributed among these distances:
6 1 0.02
7 12 0.21
8 37 0.65
9 7 0.12
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.35
Consensus pattern (8 bp):
TAAAATAT
Found at i:577082 original size:14 final size:14
Alignment explanation
Indices: 577044--577090 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
577034 TTATTAAAAA
577044 ATATTAATATTTTT
1 ATATTAATATTTTT
**
577058 -TAAAAATTATTTTT
1 ATATTAA-TATTTTT
*
577072 ATATTAATATTTAT
1 ATATTAATATTTTT
577086 ATATT
1 ATATT
577091 TTATAATTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
13 4 0.15
14 18 0.69
15 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
ATATTAATATTTTT
Found at i:577094 original size:21 final size:21
Alignment explanation
Indices: 577068--577109 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
577058 TAAAAATTAT
577068 TTTTAT-ATTAATATTTATATA
1 TTTTATAATTAA-ATTTATATA
*
577089 TTTTATAATTAAATTTTTATA
1 TTTTATAATTAAATTTATATA
577110 AAAATAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTATAATTAAATTTATATA
Found at i:577141 original size:48 final size:49
Alignment explanation
Indices: 577046--577150 Score: 126
Period size: 50 Copynumber: 2.1 Consensus size: 49
577036 ATTAAAAAAT
* *
577046 ATTAATATTTTTTAAAAATTATTTTTATATTAATATTTATATATTTTATA
1 ATTAA-ATTTTTTAAAAATAATTTTTATATTAATATTTATATATTTTAAA
*
577096 ATTAAATTTTTATAAAAATAATTTTTAATATT-A-A-TTATATCTTTTAAA
1 ATTAAATTTTT-TAAAAATAATTTTT-ATATTAATATTTATATATTTTAAA
577144 ACTTAAA
1 A-TTAAA
577151 AAAATATAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
48 13 0.27
49 12 0.24
50 19 0.39
51 5 0.10
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (49 bp):
ATTAAATTTTTTAAAAATAATTTTTATATTAATATTTATATATTTTAAA
Found at i:585584 original size:18 final size:18
Alignment explanation
Indices: 585543--585585 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
585533 TTAATTTAAA
585543 TTTAATTATAAAAATATAT
1 TTTAA-TATAAAAATATAT
*
585562 ATTAATAT-AAAATAATAT
1 TTTAATATAAAAAT-ATAT
585580 TTTAAT
1 TTTAAT
585586 GATATTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 5 0.24
18 12 0.57
19 4 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTAATATAAAAATATAT
Found at i:589282 original size:19 final size:20
Alignment explanation
Indices: 589237--589283 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
589227 TGATTTGTAA
589237 TAATATTTTATAATTAAAA-
1 TAATATTTTATAATTAAAAT
* * *
589256 TAATATATTTTTATTTAAATT
1 TAATAT-TTTATAATTAAAAT
589277 TAATATT
1 TAATATT
589284 AAAATTATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 6 0.26
20 11 0.48
21 6 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TAATATTTTATAATTAAAAT
Found at i:589282 original size:21 final size:21
Alignment explanation
Indices: 589234--589274 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
589224 ATTTGATTTG
589234 TAATAATATTTTATAATTAAAA
1 TAAT-ATATTTTATAATTAAAA
*
589256 TAATATATTTT-TATTTAAA
1 TAATATATTTTATAATTAAA
589275 TTTAATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TAATATATTTTATAATTAAAA
Found at i:589325 original size:12 final size:12
Alignment explanation
Indices: 589288--589326 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
589278 AATATTAAAA
*
589288 TTATAAATATTA
1 TTATAAATATTT
589300 TTATAAACTATTT
1 TTATAAA-TATTT
589313 TT-TAAATATTT
1 TTATAAATATTT
589324 TTA
1 TTA
589327 ACAAATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
11 7 0.29
12 11 0.46
13 6 0.25
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (12 bp):
TTATAAATATTT
Found at i:589656 original size:40 final size:40
Alignment explanation
Indices: 589611--589688 Score: 106
Period size: 40 Copynumber: 1.9 Consensus size: 40
589601 ATTTATAAAG
589611 TTATT-ATTATAAT-TTATTTTTAAAATAAAATTATATATTT
1 TTATTAATTAT-ATGTTATTTTTAAAA-AAAATTATATATTT
* *
589651 TTATTAATTATTTGTTATTTTTTAAAAAAATTATATAT
1 TTATTAATTATATGTTATTTTTAAAAAAAATTATATAT
589689 AAAATAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 18 0.53
41 16 0.47
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (40 bp):
TTATTAATTATATGTTATTTTTAAAAAAAATTATATATTT
Found at i:589726 original size:20 final size:18
Alignment explanation
Indices: 589696--589736 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
589686 TATAAAATAA
589696 TTTTATTTTTATCTTAATT
1 TTTTATTTTTAT-TTAATT
*
589715 TTTTATTTTTTATTTTATT
1 TTTTA-TTTTTATTTAATT
589734 TTT
1 TTT
589737 ATATATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTATTTTTATTTAATT
Found at i:590435 original size:16 final size:16
Alignment explanation
Indices: 590406--590443 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
590396 AATATAATTT
590406 TATTTTATAATTTAAA
1 TATTTTATAATTTAAA
590422 TGATTTTA-AATTTAAA
1 T-ATTTTATAATTTAAA
590438 TATTTT
1 TATTTT
590444 TAAGTTTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.24
16 10 0.48
17 6 0.29
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (16 bp):
TATTTTATAATTTAAA
Found at i:590451 original size:16 final size:15
Alignment explanation
Indices: 590406--590451 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
590396 AATATAATTT
590406 TATTTTATAATTTAAA
1 TATTTT-TAATTTAAA
*
590422 TGATTTTAAATTTAAA
1 T-ATTTTTAATTTAAA
590438 TATTTTTAAGTTTA
1 TATTTTTAA-TTTA
590452 GTTTTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 7 0.27
16 14 0.54
17 5 0.19
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (15 bp):
TATTTTTAATTTAAA
Found at i:590504 original size:18 final size:18
Alignment explanation
Indices: 590481--590515 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
590471 TTAAATTAAA
590481 TTTAAATAATTTTAGATT
1 TTTAAATAATTTTAGATT
**
590499 TTTAAATTTTTTTAGAT
1 TTTAAATAATTTTAGAT
590516 GAATTTTCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (18 bp):
TTTAAATAATTTTAGATT
Found at i:590715 original size:15 final size:15
Alignment explanation
Indices: 590695--590741 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
590685 TGAGATAATA
590695 TTTAAATTTAATATT
1 TTTAAATTTAATATT
*
590710 TTTAAATATAAT-TT
1 TTTAAATTTAATATT
* *
590724 TTAAAATTATATTATT
1 TTTAAATT-TAATATT
590740 TT
1 TT
590742 AATTTTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 8 0.31
15 14 0.54
16 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTAAATTTAATATT
Found at i:590780 original size:17 final size:18
Alignment explanation
Indices: 590753--590796 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
590743 ATTTTATTTA
590753 AATATAAAAATA-TTAATT
1 AATA-AAAAATATTTAATT
*
590771 ATTAAAAAATATTTAATT
1 AATAAAAAATATTTAATT
590789 AATAAAAA
1 AATAAAAA
590797 TTTTATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AATAAAAAATATTTAATT
Found at i:590811 original size:17 final size:17
Alignment explanation
Indices: 590757--590812 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
590747 TATTTAAATA
*
590757 TAAAAATATTAATT-AT
1 TAAAAATATTTATTAAT
590773 TAAAAAATATTTAATTAA-
1 T-AAAAATATTT-ATTAAT
590791 TAAAAAT-TTTATTAAAT
1 TAAAAATATTTATT-AAT
590808 TAAAA
1 TAAAA
590813 TAATCAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
15 3 0.09
16 6 0.18
17 20 0.59
18 4 0.12
19 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAAAATATTTATTAAT
Found at i:591637 original size:21 final size:20
Alignment explanation
Indices: 591595--591637 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
591585 ATAAGTAGAT
* *
591595 AATTTTTTAAAGAGTTACTA
1 AATTTTTTAAAAAGTTAATA
*
591615 AATTTTTTAAAAAATTTAATA
1 AATTTTTT-AAAAAGTTAATA
591636 AA
1 AA
591638 AAATTTAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (20 bp):
AATTTTTTAAAAAGTTAATA
Found at i:592699 original size:21 final size:20
Alignment explanation
Indices: 592669--592707 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
592659 AATTATGTCA
*
592669 TTTTATTTTTATTACTTTACT
1 TTTTAATTTTATTA-TTTACT
*
592690 TTTTAATTTTTTTATTTA
1 TTTTAATTTTATTATTTA
592708 AGTTTCTGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTAATTTTATTATTTACT
Found at i:594058 original size:12 final size:12
Alignment explanation
Indices: 594041--594065 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
594031 CTTATTAGAC
594041 AGTGAAATAATG
1 AGTGAAATAATG
594053 AGTGAAATAATG
1 AGTGAAATAATG
594065 A
1 A
594066 TATGATGTCC
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:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (12 bp):
AGTGAAATAATG
Found at i:594841 original size:3 final size:3
Alignment explanation
Indices: 594833--594864 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
594823 TCGTTGGTGT
*
594833 TGA TGA TGA TGA TGA TGA TGA TGA CGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
594865 GGGGACTGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.34, T:0.31
Consensus pattern (3 bp):
TGA
Found at i:598067 original size:15 final size:15
Alignment explanation
Indices: 598047--598079 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
598037 TTTACCCTTT
598047 TTTTCTAATTTTTTA
1 TTTTCTAATTTTTTA
*
598062 TTTTCTTATTTTTTA
1 TTTTCTAATTTTTTA
598077 TTT
1 TTT
598080 AAAACTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTCTAATTTTTTA
Found at i:598573 original size:18 final size:19
Alignment explanation
Indices: 598541--598578 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
598531 AATATTAATA
598541 AATTATTATTTTAAT-TTT
1 AATTATTATTTTAATATTT
598559 AATT-TTATTTATAATATTT
1 AATTATTATTT-TAATATTT
598578 A
1 A
598579 TAATTTTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
18 8 0.44
19 4 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
AATTATTATTTTAATATTT
Found at i:599251 original size:20 final size:19
Alignment explanation
Indices: 599226--599269 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
599216 ACATATATTT
599226 TAATTTAATATCTTTAATA
1 TAATTTAATATCTTTAATA
** *
599245 GTAATTTTTTATTTTTAATA
1 -TAATTTAATATCTTTAATA
599265 TAATT
1 TAATT
599270 CATTTTACAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (19 bp):
TAATTTAATATCTTTAATA
Found at i:599336 original size:21 final size:21
Alignment explanation
Indices: 599298--599353 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
599288 AAATACATAG
599298 TTTACTA-T-TAAT-TTTAAT
1 TTTACTATTATAATATTTAAT
*
599316 TTTATTATTATAATATTTAAT
1 TTTACTATTATAATATTTAAT
*
599337 TTTACTATTACAATATT
1 TTTACTATTATAATATT
599354 AATCTCATCG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.19
19 1 0.03
20 4 0.12
21 21 0.66
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTACTATTATAATATTTAAT
Found at i:599629 original size:19 final size:18
Alignment explanation
Indices: 599607--599643 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
599597 TTATTAAATT
599607 AATTATTAATTATTTTAAA
1 AATTATTAATT-TTTTAAA
599626 AATTATTAATTTTTTAAA
1 AATTATTAATTTTTTAAA
599644 TTTATAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AATTATTAATTTTTTAAA
Found at i:599644 original size:16 final size:18
Alignment explanation
Indices: 599607--599648 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
599597 TTATTAAATT
599607 AATTATTAATTATTTTAAA
1 AATTATTAATTATTTT-AA
599626 AATTATTAATT-TTTTAA
1 AATTATTAATTATTTTAA
*
599643 ATTTAT
1 AATTAT
599649 AAAATTACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.32
18 4 0.18
19 11 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
AATTATTAATTATTTTAA
Found at i:600137 original size:20 final size:21
Alignment explanation
Indices: 600104--600150 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
600094 ATTTTAGATT
**
600104 AAAATAATTTTATT-TTTTAG
1 AAAATAATCATATTATTTTAG
*
600124 AAAATAATCATATTATTTT-T
1 AAAATAATCATATTATTTTAG
600144 AAAATAA
1 AAAATAA
600151 AATTTTGTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (21 bp):
AAAATAATCATATTATTTTAG
Found at i:600986 original size:3 final size:3
Alignment explanation
Indices: 600980--601038 Score: 50
Period size: 3 Copynumber: 18.7 Consensus size: 3
600970 GTCAAAAAAA
*
600980 ATT ATT ATT ATT ATT ATT CTTT ATT ATCT A-T ATT -TAT ATTT ATT ATT
1 ATT ATT ATT ATT ATT ATT -ATT ATT AT-T ATT ATT AT-T A-TT ATT ATT
601027 ATT ATTT ATT AT
1 ATT A-TT ATT AT
601039 CTATCTATCT
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
2 3 0.06
3 34 0.72
4 9 0.19
5 1 0.02
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:601005 original size:19 final size:19
Alignment explanation
Indices: 600981--601035 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
600971 TCAAAAAAAA
*
600981 TTATTATTATTA-TTATTCT
1 TTATTATTATTATTTA-TAT
601000 TTATTATCTA-TATTTATAT
1 TTATTAT-TATTATTTATAT
601019 TTATTATTATTATTTAT
1 TTATTATTATTATTTAT
601036 TATCTATCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
18 2 0.06
19 25 0.78
20 5 0.16
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATTATTATTATTTATAT
Found at i:601474 original size:2 final size:2
Alignment explanation
Indices: 601467--601493 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
601457 CATATAGATT
601467 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
601494 GCATGCAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:602166 original size:23 final size:23
Alignment explanation
Indices: 602131--602175 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
602121 AAAAAATACA
* *
602131 TATTTATATTTTTTATTATTTAT
1 TATTCATAATTTTTATTATTTAT
602154 TATTCATAATTTTTATTATTTA
1 TATTCATAATTTTTATTATTTA
602176 AAATATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (23 bp):
TATTCATAATTTTTATTATTTAT
Found at i:602244 original size:23 final size:22
Alignment explanation
Indices: 602216--602274 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 22
602206 AAAAAATTTA
602216 TATTTTTATGTTTATGTTATATT
1 TATTTTTATGTTTATGTTA-ATT
* *
602239 TATTTTTATATTTTATTTTAATT
1 TATTTTTAT-GTTTATGTTAATT
*
602262 AATTTTTAATGTT
1 TATTTTT-ATGTT
602275 ATAGGCATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
23 20 0.67
24 10 0.33
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.69
Consensus pattern (22 bp):
TATTTTTATGTTTATGTTAATT
Found at i:603250 original size:26 final size:27
Alignment explanation
Indices: 603193--603252 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
603183 ATAATTATTT
*
603193 AATA-TAATTTAACTTAAATTTATATG
1 AATATTAATTTAACTTAAATTTATATA
*
603219 ATTATTAATTTAA-TTAAATGTT-TATA
1 AATATTAATTTAACTTAAAT-TTATATA
603245 AATATTAA
1 AATATTAA
603253 AAATCTTCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 19 0.66
27 10 0.34
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (27 bp):
AATATTAATTTAACTTAAATTTATATA
Found at i:603403 original size:13 final size:13
Alignment explanation
Indices: 603385--603430 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
603375 AAAAACTTCA
*
603385 TATTTTTTATTTG
1 TATTTTTTATTTT
603398 TATTTTTTAATTTT
1 TATTTTTT-ATTTT
*
603412 TA-ATTTTATTTT
1 TATTTTTTATTTT
603424 TATTTTT
1 TATTTTT
603431 AAATTATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
12 7 0.25
13 15 0.54
14 6 0.21
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (13 bp):
TATTTTTTATTTT
Found at i:603443 original size:26 final size:26
Alignment explanation
Indices: 603384--603445 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
603374 TAAAAACTTC
* *
603384 ATATTTTTTATTTGTATTTTTTAATT
1 ATATATTTTATTTGTATTTTTAAATT
* *
603410 -TTTAATTTTATTTTTATTTTTAAATT
1 ATAT-ATTTTATTTGTATTTTTAAATT
603436 ATATATTTTA
1 ATATATTTTA
603446 ATGTTAATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
25 2 0.07
26 25 0.86
27 2 0.07
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (26 bp):
ATATATTTTATTTGTATTTTTAAATT
Found at i:603560 original size:6 final size:6
Alignment explanation
Indices: 603525--603575 Score: 50
Period size: 6 Copynumber: 8.0 Consensus size: 6
603515 TTTTTTTATC
*
603525 TTTTATA TTTTAA ATTTAGA TTTTAA TTTTAA TTTTTTAA TTTT-A TTTTAA
1 TTTTA-A TTTTAA TTTTA-A TTTTAA TTTTAA --TTTTAA TTTTAA TTTTAA
603576 AATAATATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
5 5 0.13
6 17 0.45
7 10 0.26
8 6 0.16
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (6 bp):
TTTTAA
Found at i:603564 original size:14 final size:13
Alignment explanation
Indices: 603525--603573 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
603515 TTTTTTTATC
*
603525 TTTTATATTTTAA
1 TTTTATTTTTTAA
* **
603538 ATTTAGATTTTAA
1 TTTTATTTTTTAA
603551 TTTTAATTTTTTAA
1 TTTT-ATTTTTTAA
603565 TTTTATTTT
1 TTTTATTTT
603574 AAAATAATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
13 19 0.63
14 11 0.37
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (13 bp):
TTTTATTTTTTAA
Found at i:603819 original size:18 final size:18
Alignment explanation
Indices: 603791--603825 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
603781 ATTTTAGATT
603791 TTTTATATTTAAGTTTTTA
1 TTTTATATTTAA-TTTTTA
603810 TTTT-TATTTAATTTTT
1 TTTTATATTTAATTTTT
603826 CAATGGTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 7 0.44
19 4 0.25
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (18 bp):
TTTTATATTTAATTTTTA
Found at i:605188 original size:11 final size:10
Alignment explanation
Indices: 605168--605202 Score: 61
Period size: 10 Copynumber: 3.4 Consensus size: 10
605158 AATTAACGAT
605168 AAAAAATTTA
1 AAAAAATTTA
605178 AAAAAATTTTA
1 AAAAAA-TTTA
605189 AAAAAATTTA
1 AAAAAATTTA
605199 AAAA
1 AAAA
605203 TTTTTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 14 0.58
11 10 0.42
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
AAAAAATTTA
Found at i:605518 original size:20 final size:20
Alignment explanation
Indices: 605493--605530 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
605483 ATTAATCAAA
605493 TTAATTAAAATAATTTTTGT
1 TTAATTAAAATAATTTTTGT
* *
605513 TTAATTAATATGATTTTT
1 TTAATTAAAATAATTTTT
605531 TAATTTAATT
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:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (20 bp):
TTAATTAAAATAATTTTTGT
Found at i:605538 original size:18 final size:17
Alignment explanation
Indices: 605512--605545 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
605502 ATAATTTTTG
605512 TTTAATTAATATGATTT
1 TTTAATTAATATGATTT
*
605529 TTTAATTTAATTTGATT
1 TTTAA-TTAATATGATT
605546 AATAATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (17 bp):
TTTAATTAATATGATTT
Found at i:606936 original size:20 final size:20
Alignment explanation
Indices: 606906--606959 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
606896 ATTCGATGTT
606906 AAATATTTTTTAATTAA-TTA
1 AAAT-TTTTTTAATTAATTTA
* *
606926 AAATTTATTTTATTTAATTTT
1 AAATTT-TTTTAATTAATTTA
606947 AAATTTTTTTAAT
1 AAATTTTTTTAAT
606960 ATTATAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 2 0.07
20 19 0.66
21 8 0.28
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
AAATTTTTTTAATTAATTTA
Found at i:607005 original size:15 final size:15
Alignment explanation
Indices: 606982--607015 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
606972 ATATATATTT
*
606982 TTAATTTTTTTAAAA
1 TTAAATTTTTTAAAA
*
606997 TTAAATTTTTTAAGA
1 TTAAATTTTTTAAAA
607012 TTAA
1 TTAA
607016 TAAGTCAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (15 bp):
TTAAATTTTTTAAAA
Found at i:607440 original size:19 final size:18
Alignment explanation
Indices: 607406--607441 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
607396 TCTTTCAATT
*
607406 TTTAAAAAATATTTACTC
1 TTTAAAAAATACTTACTC
607424 TTTAAAAAATCACTTACT
1 TTTAAAAAAT-ACTTACT
607442 TCGAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (18 bp):
TTTAAAAAATACTTACTC
Found at i:607923 original size:24 final size:24
Alignment explanation
Indices: 607869--607931 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
607859 AGTTGTATAC
* *
607869 TTATATTTTT-TTAACTTTTATCTT
1 TTAT-TTTTTATTTACTTTTATATT
607893 TTATTTTTTATTTACTTTTATATT
1 TTATTTTTTATTTACTTTTATATT
607917 ATT-TTTTTTACTTTA
1 -TTATTTTTTA-TTTA
607932 GAGATTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 5 0.15
24 23 0.68
25 6 0.18
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (24 bp):
TTATTTTTTATTTACTTTTATATT
Found at i:607931 original size:19 final size:18
Alignment explanation
Indices: 607884--607931 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
607874 TTTTTTTAAC
607884 TTTTATCTTT-TATTTTTT
1 TTTTA-CTTTATATTTTTT
*
607902 ATTTACTTTTATATTATTTT
1 TTTTAC-TTTATATT-TTTT
607922 TTTTACTTTA
1 TTTTACTTTA
607932 GAGATTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 1 0.04
18 7 0.28
19 8 0.32
20 9 0.36
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTACTTTATATTTTTT
Found at i:607941 original size:20 final size:19
Alignment explanation
Indices: 607895--607943 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
607885 TTTATCTTTT
* * *
607895 ATTTTTTATTTACTTTTAT
1 ATTTTTTTTTTACTTTGAG
607914 ATTATTTTTTTTACTTTAGAG
1 ATT-TTTTTTTTACTTT-GAG
607935 ATTTTTTTT
1 ATTTTTTTT
607944 GCATGCATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 3 0.12
20 18 0.72
21 4 0.16
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.71
Consensus pattern (19 bp):
ATTTTTTTTTTACTTTGAG
Found at i:608239 original size:19 final size:18
Alignment explanation
Indices: 608212--608248 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
608202 ATTATTATTT
608212 TTAAAATATTTTTAATAA
1 TTAAAATATTTTTAATAA
608230 TTAAATATATTTTTAATAA
1 TTAAA-ATATTTTTAATAA
608249 ATTTTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTAAAATATTTTTAATAA
Found at i:608254 original size:12 final size:13
Alignment explanation
Indices: 608209--608267 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 13
608199 TATATTATTA
608209 TTTTTAA-AATAT
1 TTTTTAATAATAT
608221 TTTTAATAATTAAATAT
1 TTTT--TAA-T-AATAT
608238 ATTTTTAATAA-AT
1 -TTTTTAATAATAT
*
608251 TTTTTATTAATAT
1 TTTTTAATAATAT
608264 TTTT
1 TTTT
608268 AAAAAAATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 13
0.74 0.02 0.25
Matches are distributed among these distances:
12 13 0.33
13 8 0.21
14 5 0.13
15 1 0.03
16 3 0.08
17 5 0.13
18 4 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TTTTTAATAATAT
Found at i:608268 original size:12 final size:12
Alignment explanation
Indices: 608207--608269 Score: 50
Period size: 11 Copynumber: 5.8 Consensus size: 12
608197 TATATATTAT
608207 TATTTTTAA-AA
1 TATTTTTAATAA
608218 TATTTTTAAT-A
1 TATTTTTAATAA
*
608229 -A--TTAAAT-A
1 TATTTTTAATAA
608237 TATTTTTAATAA
1 TATTTTTAATAA
*
608249 -ATTTTTTATTAA
1 TA-TTTTTAATAA
608261 TATTTTTAA
1 TATTTTTAA
608270 AAAAATATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
8 6 0.15
9 1 0.02
10 1 0.02
11 16 0.39
12 16 0.39
13 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TATTTTTAATAA
Found at i:608371 original size:21 final size:22
Alignment explanation
Indices: 608302--608382 Score: 73
Period size: 20 Copynumber: 3.9 Consensus size: 22
608292 ATTATAAAAA
*
608302 TATT-TTATCAAATT-AATAAC
1 TATTATTATAAAATTAAATAAC
* **
608322 TAGTAAAATAAAATT--ATAAC
1 TATTATTATAAAATTAAATAAC
*
608342 TATTATTATAAAATTAAATAAT
1 TATTATTATAAAATTAAATAAC
608364 TA-TATTATAAAATATAAAT
1 TATTATTATAAAAT-TAAAT
608383 TTTATAATTA
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
20 20 0.41
21 18 0.37
22 11 0.22
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (22 bp):
TATTATTATAAAATTAAATAAC
Found at i:608396 original size:21 final size:21
Alignment explanation
Indices: 608329--608382 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
608319 AACTAGTAAA
*
608329 ATAAAATT--ATAACTATTATT
1 ATAAAATTAAATAATTA-TATT
608349 ATAAAATTAAATAATTATATT
1 ATAAAATTAAATAATTATATT
608370 ATAAAATATAAAT
1 ATAAAAT-TAAAT
608383 TTTATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 8 0.27
21 11 0.37
22 11 0.37
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
ATAAAATTAAATAATTATATT
Found at i:608946 original size:21 final size:21
Alignment explanation
Indices: 608922--608964 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
608912 AGTTTTCTAG
* * *
608922 TAAAAACTCAATATTTTAAAA
1 TAAAAAATAAATATTTAAAAA
608943 TAAAAAATAAATATTTAAAAA
1 TAAAAAATAAATATTTAAAAA
608964 T
1 T
608965 TATTTCAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAAAAATAAATATTTAAAAA
Found at i:613754 original size:4 final size:4
Alignment explanation
Indices: 613739--614082 Score: 301
Period size: 4 Copynumber: 86.0 Consensus size: 4
613729 TCTTTTGTAC
* * * * * *
613739 ATAT ACAT ATAT ATAT ATAC ATAT ACAT ATAT ATAC ATAC ATAC ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * * * * * *
613787 ATAT ACAT ACAT ACAT ACAT ATAC ATAT ATAT ACAT ACAT ACAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * * * *
613835 ATAT ATAC ATAT ACAT ATAT ATAC ATAC ATAC ATAT ATAT ATAC ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * * * * *
613883 ACAT ATAT ATAC ATAC ATAC ATAT ATAT ATAC ATAT ACAT ATAT ATAC
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * * * * *
613931 ATAC ATAC ATAT ATAT ACAC ATAC ATAT ATAT ACAT ACAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * * * *
613979 ACAT ATAT ACAT ACAT ATAT ATAT ATAT ACAT ACAT ATAT ATAC ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * *
614027 ATAT ATAC ATAT ATAT ACAT ATAC ATAT ATAT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
614075 ATAT ATAT
1 ATAT ATAT
614083 GAGCATTCTC
Statistics
Matches: 288, Mismatches: 52, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 288 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (4 bp):
ATAT
Found at i:613758 original size:14 final size:14
Alignment explanation
Indices: 613736--614082 Score: 333
Period size: 14 Copynumber: 24.5 Consensus size: 14
613726 TCCTCTTTTG
*
613736 TACATATACATATA
1 TACATATATATATA
*
613750 T--ATATATACATA
1 TACATATATATATA
*
613762 TACATATATATACA
1 TACATATATATATA
*
613776 TACATACATATATA
1 TACATATATATATA
* *
613790 TACATACATACATA
1 TACATATATATATA
* * *
613804 CATATACATATATA
1 TACATATATATATA
* *
613818 TACATACATACATA
1 TACATATATATATA
* *
613832 TATATATATACATA
1 TACATATATATATA
*
613846 TACATATATATACA
1 TACATATATATATA
613860 TACATACATATATATA
1 TACAT--ATATATATA
613876 TACATATACATATATA
1 TACATAT--ATATATA
* *
613892 TACATACATACATA
1 TACATATATATATA
*
613906 T--ATATATACATA
1 TACATATATATATA
*
613918 TACATATATATACA
1 TACATATATATATA
613932 TACATACATATATATA
1 TACAT--ATATATATA
* *
613948 CACATACATATATA
1 TACATATATATATA
613962 TACATACATATATATA
1 TACAT--ATATATATA
*
613978 TACATATATACATA
1 TACATATATATATA
* *
613992 CATATATATATATA
1 TACATATATATATA
*
614006 TACATACATATATA
1 TACATATATATATA
614020 TACATATATATATA
1 TACATATATATATA
* * *
614034 CATATATATACATA
1 TACATATATATATA
614048 TACATATATATATA
1 TACATATATATATA
*
614062 TATATATATATATA
1 TACATATATATATA
*
614076 TATATAT
1 TACATAT
614083 GAGCATTCTC
Statistics
Matches: 277, Mismatches: 44, Indels: 24
0.80 0.13 0.07
Matches are distributed among these distances:
12 21 0.08
14 205 0.74
16 51 0.18
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (14 bp):
TACATATATATATA
Found at i:613761 original size:20 final size:20
Alignment explanation
Indices: 613736--614082 Score: 356
Period size: 20 Copynumber: 18.1 Consensus size: 20
613726 TCCTCTTTTG
613736 TACATATACATATATATATA
1 TACATATACATATATATATA
*
613756 TACATATACATATATATACA
1 TACATATACATATATATATA
*
613776 TAC--ATACATATATATACA
1 TACATATACATATATATATA
613794 TACATACATACATATACATATATA
1 TACAT--ATACATAT--ATATATA
613818 TACATACATACATATATATATA
1 TACAT--ATACATATATATATA
*
613840 TACATATACATATATATACA
1 TACATATACATATATATATA
613860 TAC--ATAC--ATATATATA
1 TACATATACATATATATATA
*
613876 TACATATACATATATATACA
1 TACATATACATATATATATA
613896 TAC--ATAC--ATATATATA
1 TACATATACATATATATATA
613912 TACATATAC----ATATATA
1 TACATATACATATATATATA
*
613928 TAC--ATACATACATATATA
1 TACATATACATATATATATA
* *
613946 TACACATACATATATATACA
1 TACATATACATATATATATA
* *
613966 TACATATATATATACATATA
1 TACATATACATATATATATA
613986 TAC--ATACATATATATATA
1 TACATATACATATATATATA
* * *
614004 TATACATACATATATATACA
1 TACATATACATATATATATA
* *
614024 T--ATATATATACATATATA
1 TACATATACATATATATATA
614042 TACATATACATATATATATA
1 TACATATACATATATATATA
* *
614062 TATATATATATATATATATA
1 TACATATACATATATATATA
614082 T
1 T
614083 GAGCATTCTC
Statistics
Matches: 281, Mismatches: 24, Indels: 44
0.81 0.07 0.13
Matches are distributed among these distances:
14 4 0.01
16 32 0.11
18 73 0.26
20 131 0.47
22 20 0.07
24 21 0.07
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (20 bp):
TACATATACATATATATATA
Found at i:613776 original size:36 final size:36
Alignment explanation
Indices: 613736--614075 Score: 408
Period size: 36 Copynumber: 9.5 Consensus size: 36
613726 TCCTCTTTTG
*
613736 TACATATACATATATATATATACATATACATATATA
1 TACATATACATATATATACATACATATACATATATA
*
613772 TACATACATACATATATATACATAC--ATACATACATA
1 TACAT--ATACATATATATACATACATATACATATATA
*
613808 TACATAT--ATATACATACATACATAT--ATATATA
1 TACATATACATATATATACATACATATACATATATA
* *
613840 TACATATACATATATATACATACATACATATATATA
1 TACATATACATATATATACATACATATACATATATA
* *
613876 TACATATACATATATATACATACATACATATATATA
1 TACATATACATATATATACATACATATACATATATA
613912 TACATATACATATATATACATAC--ATACATATATA
1 TACATATACATATATATACATACATATACATATATA
* *
613946 TACACATACATATATATACATACATATATATATACATA
1 TACATATACATATATATACATACATATACATAT--ATA
* * * * *
613984 TATACATACATATATATATATATACATACATATATA
1 TACATATACATATATATACATACATATACATATATA
* *
614020 TACATATATATATACATATATATACATATACATATATA
1 TACATATACATAT--ATATACATACATATACATATATA
* *
614058 TATATATATATATATATA
1 TACATATACATATATATA
614076 TATATATGAG
Statistics
Matches: 269, Mismatches: 21, Indels: 28
0.85 0.07 0.09
Matches are distributed among these distances:
32 26 0.10
34 51 0.19
36 111 0.41
38 81 0.30
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (36 bp):
TACATATACATATATATACATACATATACATATATA
Found at i:616259 original size:29 final size:29
Alignment explanation
Indices: 616218--616278 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
616208 ATGTATAAAT
*
616218 ATATTAAAATTTATATAATATAA-ATATTA
1 ATATCAAAATTTATAT-ATATAATATATTA
*
616247 ATATCAAAATTTATATATATAATATTTTA
1 ATATCAAAATTTATATATATAATATATTA
616276 ATA
1 ATA
616279 CGATTTTGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 6 0.21
29 23 0.79
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (29 bp):
ATATCAAAATTTATATATATAATATATTA
Found at i:616618 original size:19 final size:20
Alignment explanation
Indices: 616590--616628 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
616580 TACATTTGTT
616590 ATAATATTTTT-ATTTTTTG
1 ATAATATTTTTAATTTTTTG
*
616609 ATAATTTTTTTAATTTTTTG
1 ATAATATTTTTAATTTTTTG
616629 TCATTAACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (20 bp):
ATAATATTTTTAATTTTTTG
Found at i:616887 original size:2 final size:2
Alignment explanation
Indices: 616880--616907 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
616870 TTAATTTTGT
616880 TA 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
616908 GAGAGAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:616912 original size:2 final size:2
Alignment explanation
Indices: 616907--616946 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
616897 ATATATATAT
616907 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
616947 TTAAGGTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:617639 original size:20 final size:21
Alignment explanation
Indices: 617597--617649 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
617587 TTTAATAATT
617597 TGTATCGATACAATAAGGCAA
1 TGTATCGATACAATAAGGCAA
*
617618 TGTATCGATAC-GTAAGTG-AA
1 TGTATCGATACAATAAG-GCAA
*
617638 TGTATCAATACA
1 TGTATCGATACA
617650 TGCCTAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (21 bp):
TGTATCGATACAATAAGGCAA
Found at i:621296 original size:17 final size:18
Alignment explanation
Indices: 621263--621297 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
621253 AATTATTATC
621263 ATATAAAAACATATAAAT
1 ATATAAAAACATATAAAT
*
621281 ATATAAATAC-TATAAAT
1 ATATAAAAACATATAAAT
621298 GTTATCCCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (18 bp):
ATATAAAAACATATAAAT
Found at i:621588 original size:28 final size:27
Alignment explanation
Indices: 621557--621609 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
621547 TATGCATTCA
621557 TATTATATTAGTGTTATTTTTCATATTG
1 TATTATATT-GTGTTATTTTTCATATTG
* * *
621585 TATTATGTTTTGTTATTTTTTATAT
1 TATTATATTGTGTTATTTTTCATAT
621610 CACGCTCATG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 14 0.64
28 8 0.36
ACGTcount: A:0.23, C:0.02, G:0.09, T:0.66
Consensus pattern (27 bp):
TATTATATTGTGTTATTTTTCATATTG
Found at i:623018 original size:15 final size:16
Alignment explanation
Indices: 622992--623024 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
622982 TATAAATTAG
622992 ATAAATATTATTAATA
1 ATAAATATTATTAATA
*
623008 ATAAA-ATTATTTATA
1 ATAAATATTATTAATA
623023 AT
1 AT
623025 GATAATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATAAATATTATTAATA
Found at i:624198 original size:15 final size:16
Alignment explanation
Indices: 624178--624210 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
624168 AGATTAGGAG
*
624178 TTTAATTTCT-TATAA
1 TTTAATTACTCTATAA
624193 TTTAATTACTCTATAA
1 TTTAATTACTCTATAA
624209 TT
1 TT
624211 ACTCCACTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTAATTACTCTATAA
Found at i:626612 original size:20 final size:19
Alignment explanation
Indices: 626566--626643 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 19
626556 TTTTGCCCTG
* *
626566 ATGTATCGATACATTTTTCA
1 ATGTATCGATACA-TTATGA
*
626586 ATATATCGATACATGTATGA
1 ATGTATCGATACAT-TATGA
* * *
626606 ATGTATCGATATAATCTGTA
1 ATGTATCGATACATTATG-A
626626 ATGTATCGATACATTATG
1 ATGTATCGATACATTATG
626644 TCTTTTTACC
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
19 4 0.09
20 42 0.91
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.40
Consensus pattern (19 bp):
ATGTATCGATACATTATGA
Found at i:627587 original size:22 final size:22
Alignment explanation
Indices: 627553--627606 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
627543 AGCCTTTGAC
627553 CATGCA-TTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
627574 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
627596 CATGCATTTTT
1 CATGCATTTTT
627607 AACATGTCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 6 0.19
22 26 0.81
ACGTcount: A:0.19, C:0.11, G:0.09, T:0.61
Consensus pattern (22 bp):
CATGCATTTTTTTATTATGTTT
Found at i:633783 original size:21 final size:21
Alignment explanation
Indices: 633759--633805 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
633749 AAATGAAAAG
633759 AAAAAGTGCAAAAAC-AAAATAA
1 AAAAAG-G-AAAAACAAAAATAA
*
633781 AAAAAGGAACAACAAAAATAA
1 AAAAAGGAAAAACAAAAATAA
633802 AAAA
1 AAAA
633806 TGAGGACATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 5 0.22
21 12 0.52
22 6 0.26
ACGTcount: A:0.77, C:0.09, G:0.09, T:0.06
Consensus pattern (21 bp):
AAAAAGGAAAAACAAAAATAA
Found at i:635228 original size:28 final size:28
Alignment explanation
Indices: 635120--636301 Score: 1274
Period size: 28 Copynumber: 40.9 Consensus size: 28
635110 TGGCATTTCT
* * *
635120 TTTCAAAGTCCACAACTCTGTGGCA-TC
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
* * * * *
635147 CTTCTAAAGTCCACAACTCCGTGGCACCC
1 TTTC-AAAGCCCACAAGTCAGTGGCACTC
* * * * *
635176 TTT-TAAGTCCATAACTCCGTGGCACTC
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
635203 TTTCAAAGCCCACAAGTCAGTGGCACTC
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
* *
635231 TTTTCAAAGCCCACACAAGTCGGTGGCAACCC
1 -TTTCAAAG-CC-CACAAGTCAGTGGC-ACTC
635263 ATTTCAAAGCCCACAAGTCAGTGGCACTC
1 -TTTCAAAGCCCACAAGTCAGTGGCACTC
* * *
635292 TTTTTAAAGCCCACGCAAGTTAGTGGCACCC
1 -TTTCAAAGCCCA--CAAGTCAGTGGCACTC
* *
635323 TTTTAAAGCCCACAAGTTAGTGGCACTC
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
*
635351 TTTTCAAAGCCCACAAGTCAGTGGCACCC
1 -TTTCAAAGCCCACAAGTCAGTGGCACTC
*
635380 TTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
635408 TTTTCAAAGCCCACGCAAGTCAGTGGCAC-C
1 -TTTCAAAGCCCA--CAAGTCAGTGGCACTC
635438 ATTTCAAAGCCCACAAGTCAGTGGCAC-C
1 -TTTCAAAGCCCACAAGTCAGTGGCACTC
* * *
635466 ATTGCGAAGCCCACAATTCAGTGGCACTC
1 -TTTCAAAGCCCACAAGTCAGTGGCACTC
*
635495 TTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
*
635523 TTTTAAAGCCCACACAAGTCAGTGGCACTCC
1 TTTCAAAG-CC-CACAAGTCAGTGGCACT-C
635554 TTTCAAAGCCCACAAGTCAGTGGCACTCC
1 TTTCAAAGCCCACAAGTCAGTGGCACT-C
635583 TTTCAAAGCCCACAAGTCAGTGGCACTC
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
*
635611 TTTTCAAAGCCCACAAATCAGTGGCACTC
1 -TTTCAAAGCCCACAAGTCAGTGGCACTC
*
635640 TTTTCAAAGCCCACAAGTCAGTGGCACCC
1 -TTTCAAAGCCCACAAGTCAGTGGCACTC
* *
635669 TTTCAAAGCCCACAAGTTAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
* *
635697 TTTCAGAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
* *
635725 TTTCGAAGCTCACAAGTCAGTGGCAC-C
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
* * *
635752 ATTGCGAAGCCCACAATTCAGTGGCACTC
1 -TTTCAAAGCCCACAAGTCAGTGGCACTC
*
635781 TTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
* *
635809 TTTTAAAGCCCACACAAGTCAGTGACACTCC
1 TTTCAAAG-CC-CACAAGTCAGTGGCACT-C
* * *
635840 TTTTAAAGCTCACGCAAGTCAGTGGTAC-C
1 TTTCAAAGC-C-CACAAGTCAGTGGCACTC
*
635869 TTTTCAAAGCCCACGAGTCAGTGGCACTC
1 -TTTCAAAGCCCACAAGTCAGTGGCACTC
*
635898 TTTCAAAGCCTACAAGTCAGTGGCA-TCC
1 TTTCAAAGCCCACAAGTCAGTGGCACT-C
* * *
635926 TTTCAAAGCCCACGAGTTAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
635954 TTTCAAAGCCCACACAAGTCAGTGGCACTCC
1 TTTCAAAG-CC-CACAAGTCAGTGGCACT-C
635985 TTTCAAAGCCCACGCAAGTCAGTGGCAC-C
1 TTTCAAAGCCCA--CAAGTCAGTGGCACTC
*
636014 TTTTCAAAGCCCACGAGTCAGTGGCACTC
1 -TTTCAAAGCCCACAAGTCAGTGGCACTC
*
636043 TTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
* *
636071 TTTC-AAGCCCACGAGTCAGTGGTAC-C
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
*
636097 TTTTCAAAGCCCACGAGTCAGTGGCAC-C
1 -TTTCAAAGCCCACAAGTCAGTGGCACTC
636125 TTTCAAAGCCCACAAGTCAGTGGCACTC
1 TTTCAAAGCCCACAAGTCAGTGGCACTC
**
636153 TTTCAAAGCCCATGAGTCAGTGGCA-TCC
1 TTTCAAAGCCCACAAGTCAGTGGCACT-C
*
636181 TTTCAAAGCCCACGCAAGTCAGTGGCACCC
1 TTTCAAAGCCCA--CAAGTCAGTGGCACTC
* **
636211 TTTTAAAGCCCACGCAAGTCAGTAACACTC
1 TTTCAAAGCCCA--CAAGTCAGTGGCACTC
* *
636241 TTTTCAAAGCCCACATGTGTCAGTGGCAACTTT
1 -TTTCAAAGCCCACA--AGTCAGTGGC-AC-TC
636274 TTTCAAAGCCTACACAAGGT-AGTGGCAC
1 TTTCAAAGCC--CACAA-GTCAGTGGCAC
636302 ATTTTTTTTA
Statistics
Matches: 1012, Mismatches: 93, Indels: 96
0.84 0.08 0.08
Matches are distributed among these distances:
26 1 0.00
27 78 0.08
28 452 0.45
29 179 0.18
30 148 0.15
31 118 0.12
32 29 0.03
33 3 0.00
34 4 0.00
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (28 bp):
TTTCAAAGCCCACAAGTCAGTGGCACTC
Found at i:635565 original size:145 final size:141
Alignment explanation
Indices: 635120--636255 Score: 1353
Period size: 145 Copynumber: 7.9 Consensus size: 141
635110 TGGCATTTCT
* * * * * * * *
635120 TTTCAAAGTCCACAACTCTGTGGCATCCTTCT-AAAGTCCACAACTCCGTGGCACCCTTT-TAAG
1 TTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTCAAAG
* * * * *
635183 TCCATAACTCCGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACACA
64 CCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTT-AAAGCCCACACA
*
635248 AGTCGGTGGCAACCC
128 AGTCAGTGGC-ACCC
* * *
635263 ATTTCAAAGCCCACAAGTCAGTGGCACTCTTTTTAAAGCCCACGCAAGTTAGTGGCACCCTTTTA
1 -TTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCA--CAAGTCAGTGGCA-CCTTTCA
* *
635328 AAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG-CC-C
61 AAGCCCACAAGTCAGTGGCACTC-TTTCAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCAC
635391 ACAAGTCAGTGGCACCC
125 ACAAGTCAGTGGCACCC
* * *
635408 TTTTCAAAGCCCACGCAAGTCAGTGGCACCATTTCAAAGCCCACAAGTCAGTGGCACCATTGCGA
1 -TTTCAAAGCCCA--CAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACC-TTTCAA
*
635473 AGCCCACAATTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACAC
62 AGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACAC
635538 AAGTCAGTGGCACTCC
127 AAGTCAGTGGCAC-CC
*
635554 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGCAC-C-TTTCAAA
* *
635619 GCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG-CC-CAC
63 GCCCACAAGTCAGTGGCACTC-TTTCAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACAC
*
635682 AAGTTAGTGGCACCC
127 AAGTCAGTGGCACCC
* * * * * *
635697 TTTCAGAGCCCACAAGTCAGTGGCACCCTTTCGAAGCTCACAAGTCAGTGGCACCATTGCGAAGC
1 TTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACC-TTTCAAAGC
*
635762 CCACAATTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACACAAG
65 CCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACACAAG
*
635827 TCAGTGACACTCC
130 TCAGTGGCAC-CC
* * * *
635840 TTTTAAAGCTCACGCAAGTCAGTGGTACCTTTTCAAAGCCCACGAGTCAGTGGCACTCTTTCAAA
1 TTTCAAAGC-C-CACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTCAAA
* * * *
635905 GCCTACAAGTCAGTGGCA-TCCTTTCAAAGCCCACGAGTTAGTGGCACCCTTTCAAAGCCCACAC
63 GCCCACAAGTCAGTGGCACT-CTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACAC
635969 AAGTCAGTGGCACTCC
127 AAGTCAGTGGCAC-CC
*
635985 TTTCAAAGCCCACGCAAGTCAGTGGCACCTTTTCAAAGCCCACGAGTCAGTGGCACTCTTTCAAA
1 TTTCAAAGCCCA--CAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTCAAA
* * *
636050 GCCCACAAGTCAGTGGCACCCTTTC-AAGCCCACGAGTCAGTGGTA-CCTTTTCAAAG-CC-CAC
63 GCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTT-AAAGCCCACAC
*
636111 GAGTCAGTGGCA-CC
127 AAGTCAGTGGCACCC
**
636125 TTTCAAAGCCCACAAGTCAGTGGCA-CTCTTTCAAAGCCCATGAGTCAGTGGCATCCTTTCAAAG
1 TTTCAAAGCCCACAAGTCAGTGGCACCT-TTTCAAAGCCCACAAGTCAGTGGCA-CCTTTCAAAG
* * ** *
636189 CCCACGCAAGTCAGTGGCACCCTTTTAAAGCCCACGCAAGTCAGTAACACTCTTTTCAAAGCCCA
64 CCCA--CAAGTCAGTGGCACTCTTTCAAAGCCCA--CAAGTCAGTGGCACCCTTTT-AAAGCCCA
636254 CA
124 CA
636256 TGTGTCAGTG
Statistics
Matches: 880, Mismatches: 76, Indels: 70
0.86 0.07 0.07
Matches are distributed among these distances:
137 2 0.00
138 50 0.06
139 1 0.00
140 68 0.08
141 35 0.04
142 54 0.06
143 105 0.12
144 140 0.16
145 276 0.31
146 65 0.07
147 32 0.04
148 22 0.03
149 30 0.03
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (141 bp):
TTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTCAAAGCC
CACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACACAAGT
CAGTGGCACCC
Found at i:636457 original size:47 final size:47
Alignment explanation
Indices: 636403--636577 Score: 187
Period size: 47 Copynumber: 3.7 Consensus size: 47
636393 GGCACCTTTA
* * *
636403 TTAGCTCAATGTTGCTGGCCTTGAATCAGCACATTTTCGATTTTCCC
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCATTTTCCC
* * * *
636450 TTAGCTCAATGTTGCTGGCCTTGAATCAGCACGTTGTCCACTTT-AC
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCATTTTCCC
* *
636496 -TAGCCCAATGTCGCTGGCCTTG-ATCAGCACGTTAGTCCACTTTTCCC
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATT-GTCCA-TTTTCCC
* **
636543 TTAG-TCCAAAGTCGCTGGCCTTGAATTGGCACATT
1 TTAGCT-CAATGTCGCTGGCCTTGAATCAGCACATT
636578 AGCAATCGTC
Statistics
Matches: 108, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
44 11 0.10
45 25 0.23
46 4 0.04
47 41 0.38
48 19 0.18
49 8 0.07
ACGTcount: A:0.19, C:0.27, G:0.19, T:0.34
Consensus pattern (47 bp):
TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCATTTTCCC
Done.