Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015359.1 Kokia drynarioides strain JFW-HI SEQ_130406, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 556503
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 929 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:294698 original size:59 final size:58
Alignment explanation
Indices: 294601--294774 Score: 244
Period size: 59 Copynumber: 3.0 Consensus size: 58
294591 GCCTTGGAGG
* *
294601 TCCCGAAACTTCCAAAAATTCCAATTTTGACCCCAAAACTACCAAAAATTCCATTTTTA
1 TCCCCAAACTTCCAAAAATTCCATTTTTGACCCCAAAACT-CCAAAAATTCCATTTTTA
294660 TCCCCAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTA
1 TCCCCAAACTTCCAAAAATTCCATTTTTGACCCCAAAAC-TCCAAAAATTCCATTTTTA
* * * * *
294719 -CCCTCGAACTTCCAAAAATTCCATTTTT-ACCCGAAACCTCTAAAATTTCCATTTTT
1 TCCC-CAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTCCAAAAATTCCATTTTT
294775 GACCTCAAAA
Statistics
Matches: 106, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
57 16 0.15
58 11 0.10
59 78 0.74
60 1 0.01
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32
Consensus pattern (58 bp):
TCCCCAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTCCAAAAATTCCATTTTTA
Found at i:294832 original size:59 final size:59
Alignment explanation
Indices: 294757--294931 Score: 176
Period size: 59 Copynumber: 2.9 Consensus size: 59
294747 ACCCGAAACC
** * *
294757 TCTAAAATTTCCATTTTTGACCTCAAAACTTTTGAAAATTACCATTTTACCCTCGAATG
1 TCTAAAAACTCCATTTTTAACCTCAAAACTTTTGAAAATTACCATTTTACCCTCGAATA
* * * * *
294816 TCTAAAAACTCTATTTTTTTACCTCAAAACTCTCG-AAATTACCCTTTTACCCTCGAATA
1 TCTAAAAACTCCA-TTTTTAACCTCAAAACTTTTGAAAATTACCATTTTACCCTCGAATA
* * * *
294875 TCTAAAAATTCCATTTTTAACC-CTAAA-TTTTCAAAAAAATTACCATTTTGCCCTCGA
1 TCTAAAAACTCCATTTTTAACCTCAAAACTTTT---GAAAATTACCATTTTACCCTCGA
294932 GAATCCAAAA
Statistics
Matches: 94, Mismatches: 17, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
56 2 0.02
57 4 0.04
58 8 0.09
59 43 0.46
60 37 0.39
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.38
Consensus pattern (59 bp):
TCTAAAAACTCCATTTTTAACCTCAAAACTTTTGAAAATTACCATTTTACCCTCGAATA
Found at i:294833 original size:87 final size:88
Alignment explanation
Indices: 294606--294813 Score: 269
Period size: 87 Copynumber: 2.4 Consensus size: 88
294596 GGAGGTCCCG
* * * *
294606 AAACTTCCAAAAATTCCAATTTTGACCC-CAAAACTACCAAAAATTCCATTTTTATCCCCAAACT
1 AAACTTCCAAAAATTCC-ATTTTTACCCTC-GAACTTCCAAAAATTCCATTTTTATCCCCAAACC
294670 TCCAAAAATTCCATTTTTGACCCCA
64 TCCAAAAATTCCATTTTTGACCCCA
*
294695 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTA-CCCGAAACCTC
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTATCCCCAAACCTC
* * *
294759 TAAAATTTCCATTTTTGACCTCA
66 CAAAAATTCCATTTTTGACCCCA
***
294782 AAACTTTTGAAAATTACCA-TTTTACCCTCGAA
1 AAACTTCCAAAAATT-CCATTTTTACCCTCGAA
294814 TGTCTAAAAA
Statistics
Matches: 106, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
87 54 0.51
88 34 0.32
89 18 0.17
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.32
Consensus pattern (88 bp):
AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTATCCCCAAACCTC
CAAAAATTCCATTTTTGACCCCA
Found at i:294883 original size:29 final size:29
Alignment explanation
Indices: 294791--294951 Score: 91
Period size: 30 Copynumber: 5.5 Consensus size: 29
294781 AAAACTTTTG
*
294791 AAAATTACCATTTTACCCTCGAATGTCTA
1 AAAATTACCATTTTACCCTCGAATATCTA
*** * *
294820 AAAACTCTATTTTTTTA-CCTC-AAAACTCTC
1 AAAA-T-TACCATTTTACCCTCGAATA-TCTA
* *
294850 GAAATTACCCTTTTACCCTCGAATATCTA
1 AAAATTACCATTTTACCCTCGAATATCTA
* * *
294879 AAAATT-CCATTTTTAACCCT-AAATTTTCAAA
1 AAAATTACCA-TTTT-ACCCTCGAA-TATC-TA
* *
294910 AAAATTACCATTTTGCCCTCGAGA-ATC-C
1 AAAATTACCATTTTACCCTCGA-ATATCTA
294938 AAAATTACCATTTT
1 AAAATTACCATTTT
294952 GCCCCTGTGT
Statistics
Matches: 99, Mismatches: 21, Indels: 25
0.68 0.14 0.17
Matches are distributed among these distances:
28 23 0.23
29 25 0.25
30 28 0.28
31 19 0.19
32 4 0.04
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.36
Consensus pattern (29 bp):
AAAATTACCATTTTACCCTCGAATATCTA
Found at i:299225 original size:16 final size:15
Alignment explanation
Indices: 299199--299229 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
299189 CCTCACCCCT
299199 TTAAACCTAATTTTA
1 TTAAACCTAATTTTA
299214 TTAAAGCCTAATTTTA
1 TTAAA-CCTAATTTTA
299230 ATAACAGCGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.39, C:0.13, G:0.03, T:0.45
Consensus pattern (15 bp):
TTAAACCTAATTTTA
Found at i:308174 original size:3 final size:3
Alignment explanation
Indices: 308166--308194 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
308156 AATATATCAA
308166 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
308195 AAAATATCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:309047 original size:24 final size:25
Alignment explanation
Indices: 308997--309051 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 25
308987 TAAAAACAAT
308997 TTTTTATTTTTTATACTTCTTTTAA
1 TTTTTATTTTTTATACTTCTTTTAA
309022 TTTTTATTTATTTA-A-TT-TTTTGAA
1 TTTTTATTT-TTTATACTTCTTTT-AA
309046 TTTTTA
1 TTTTTA
309052 AAATTTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
23 4 0.14
24 10 0.36
25 10 0.36
26 4 0.14
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.73
Consensus pattern (25 bp):
TTTTTATTTTTTATACTTCTTTTAA
Found at i:313494 original size:17 final size:18
Alignment explanation
Indices: 313472--313505 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
313462 TTGTTTAATT
313472 TTTCTT-TATTTTTCACA
1 TTTCTTGTATTTTTCACA
*
313489 TTTCTTGTTTTTTTCAC
1 TTTCTTGTATTTTTCAC
313506 TTTTTCAATC
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:0.12, C:0.18, G:0.03, T:0.68
Consensus pattern (18 bp):
TTTCTTGTATTTTTCACA
Found at i:318653 original size:20 final size:20
Alignment explanation
Indices: 318628--318667 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
318618 TAGTTGATAA
318628 CATGAAATGCAAGCCACGTT
1 CATGAAATGCAAGCCACGTT
318648 CATGAAATGCAAGCCACGTT
1 CATGAAATGCAAGCCACGTT
318668 TAGTTCATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
CATGAAATGCAAGCCACGTT
Found at i:322687 original size:43 final size:42
Alignment explanation
Indices: 322592--322913 Score: 198
Period size: 43 Copynumber: 7.5 Consensus size: 42
322582 TGTTAAAAAT
* ** ***
322592 CATGATCTTTTGCGGGGTTTGTGGGAAAAGTATCGCTAAAGAC
1 CATGATCTTTAGCGACGTTT-TGGGAAAAGCGCCGCTAAAGAC
** * **
322635 CATTTTCTTTAGCGACATTTTCAAGAAAAGCGCCGCTAAAGAC
1 CATGATCTTTAGCGACGTTTT-GGGAAAAGCGCCGCTAAAGAC
* *
322678 CATGATCTTTTAG-TAGCGTTAGTGGGAAAAGCGCCGCTAAAGAC
1 CATGATC-TTTAGCGA-CGTT-TTGGGAAAAGCGCCGCTAAAGAC
**
322722 CATGATCTTTAGCGGTGTTTGTGGGAAAAGCGCCGCTAAAGAC
1 CATGATCTTTAGCGACGTTT-TGGGAAAAGCGCCGCTAAAGAC
* * * * * *
322765 CATGTTCTTTAGTGGCCTTTGTGGGGAAAGCGCTGCTAAAGAC
1 CATGATCTTTAGCGACGTTT-TGGGAAAAGCGCCGCTAAAGAC
* * * ** * * *
322808 CATGTTTTTTAGTGGGGATTAT-GGAAAAGTGCCACTAAAGAC
1 CATGATCTTTAGCGACG-TTTTGGGAAAAGCGCCGCTAAAGAC
* * * * * * *
322850 AATGTTCTTTAACGGCGTTTGTGGGAAAAGCGTCGTTAATGAC
1 CATGATCTTTAGCGACGTTT-TGGGAAAAGCGCCGCTAAAGAC
* * *
322893 CATGTTCTATAGCGGCGTTTT
1 CATGATCTTTAGCGACGTTTT
322914 CCCACATAAA
Statistics
Matches: 220, Mismatches: 50, Indels: 19
0.76 0.17 0.07
Matches are distributed among these distances:
41 2 0.01
42 31 0.14
43 150 0.68
44 36 0.16
45 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (42 bp):
CATGATCTTTAGCGACGTTTTGGGAAAAGCGCCGCTAAAGAC
Found at i:322871 original size:85 final size:86
Alignment explanation
Indices: 322659--322907 Score: 252
Period size: 85 Copynumber: 2.9 Consensus size: 86
322649 ACATTTTCAA
* * * * * *
322659 GAAAAGCGCCGCTAAAGACCATGATCTTTTA-GTAGCGTTAGTGGGAAAAGCGCCGCTAAAGACC
1 GAAAAGCGCCACTAAAGACAATGTTCTTTAACG--GCGTTTGTGGGAAAAGCGCTGCTAAAGACC
* * * *
322723 ATGATCTTTAGCGGTGTTTGTGG
64 ATGTTCTTTAGCGGGGATTATGG
* * ** * *
322746 GAAAAGCGCCGCTAAAGACCATGTTCTTTAGTGGCCTTTGTGGGGAAAGCGCTGCTAAAGACCAT
1 GAAAAGCGCCACTAAAGACAATGTTCTTTAACGGCGTTTGTGGGAAAAGCGCTGCTAAAGACCAT
* *
322811 GTTTTTTAGTGGGGATTAT-G
66 GTTCTTTAGCGGGGATTATGG
* * *
322831 GAAAAGTGCCACTAAAGACAATGTTCTTTAACGGCGTTTGTGGGAAAAGCG-TCGTTAATGACCA
1 GAAAAGCGCCACTAAAGACAATGTTCTTTAACGGCGTTTGTGGGAAAAGCGCT-GCTAAAGACCA
*
322895 TGTTCTATAGCGG
65 TGTTCTTTAGCGG
322908 CGTTTTCCCA
Statistics
Matches: 135, Mismatches: 25, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
84 1 0.01
85 64 0.47
86 41 0.30
87 28 0.21
88 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.27
Consensus pattern (86 bp):
GAAAAGCGCCACTAAAGACAATGTTCTTTAACGGCGTTTGTGGGAAAAGCGCTGCTAAAGACCAT
GTTCTTTAGCGGGGATTATGG
Found at i:322894 original size:128 final size:130
Alignment explanation
Indices: 322593--322900 Score: 336
Period size: 130 Copynumber: 2.4 Consensus size: 130
322583 GTTAAAAATC
** * *** * * * *
322593 ATGATCTTTTGCGGGGTTTGTGGGAAAAGTATCGCTAAAGACCATTTTCTTTAGCGACATTT-TC
1 ATGATCTTTAACGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGTGGCCTTTGT-
** * *
322657 AAGAAAAGCGCCGCTAAAGACCATGATCTTTTAGTAGCGTTAGTGGGAAAAGCGCCGCTAAAGAC
65 GGGGAAAGCGCCGCTAAAGACCATGATCTTTTAGTAGCGTTAGTGGGAAAAGCGCCACTAAAGAC
*
322722 C
130 A
* *
322723 ATGATCTTTAGCGGTGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGTGGCCTTTGTG
1 ATGATCTTTAACGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGTGGCCTTTGTG
* * * * *
322788 GGGAAAGCGCTGCTAAAGACCATG-TTTTTTAGTGGGGATTA-T-GGAAAAGTGCCACTAAAGAC
66 GGGAAAGCGCCGCTAAAGACCATGATCTTTTAGTAGCG-TTAGTGGGAAAAGCGCCACTAAAGAC
322850 A
130 A
* * * *
322851 ATGTTCTTTAACGGCGTTTGTGGGAAAAGCGTCGTTAATGACCATGTTCT
1 ATGATCTTTAACGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
322901 ATAGCGGCGT
Statistics
Matches: 151, Mismatches: 25, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
128 62 0.41
129 11 0.07
130 77 0.51
131 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.30
Consensus pattern (130 bp):
ATGATCTTTAACGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGTGGCCTTTGTG
GGGAAAGCGCCGCTAAAGACCATGATCTTTTAGTAGCGTTAGTGGGAAAAGCGCCACTAAAGACA
Found at i:332227 original size:17 final size:16
Alignment explanation
Indices: 332205--332238 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
332195 TTATAGTACT
*
332205 ATTATATATTATTATAA
1 ATTATATAATA-TATAA
332222 ATTATATAATATATAA
1 ATTATATAATATATAA
332238 A
1 A
332239 AATAACAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTATATAATATATAA
Found at i:332250 original size:22 final size:23
Alignment explanation
Indices: 332225--332277 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
332215 ATTATAAATT
*
332225 ATATAATATATAAAA-ATAACAA
1 ATATAAAATATAAAACATAACAA
* *
332247 ATATAAAATTTAAAACATTACAA
1 ATATAAAATATAAAACATAACAA
*
332270 ATTTAAAA
1 ATATAAAA
332278 AATTAGTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 13 0.50
23 13 0.50
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (23 bp):
ATATAAAATATAAAACATAACAA
Found at i:332273 original size:16 final size:16
Alignment explanation
Indices: 332252--332282 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
332242 AACAAATATA
*
332252 AAATTTAAAACATTAC
1 AAATTTAAAAAATTAC
332268 AAATTTAAAAAATTA
1 AAATTTAAAAAATTA
332283 GTCAGATCAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATTTAAAAAATTAC
Found at i:334433 original size:21 final size:21
Alignment explanation
Indices: 334407--334447 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
334397 TGGAAAAAAT
334407 TGTTCTTGA-GGTCTCGAGACA
1 TGTTCTT-ACGGTCTCGAGACA
*
334428 TGTTCTTACTGTCTCGAGAC
1 TGTTCTTACGGTCTCGAGAC
334448 TCTAAGGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (21 bp):
TGTTCTTACGGTCTCGAGACA
Found at i:337598 original size:6 final size:6
Alignment explanation
Indices: 337579--337617 Score: 69
Period size: 6 Copynumber: 6.3 Consensus size: 6
337569 TTTAAATGAA
337579 TTCATT TCTCATT TTCATT TTCATT TTCATT TTCATT TT
1 TTCATT T-TCATT TTCATT TTCATT TTCATT TTCATT TT
337618 GGAGAAAACC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 26 0.81
7 6 0.19
ACGTcount: A:0.15, C:0.18, G:0.00, T:0.67
Consensus pattern (6 bp):
TTCATT
Found at i:337687 original size:51 final size:48
Alignment explanation
Indices: 337597--337706 Score: 130
Period size: 51 Copynumber: 2.2 Consensus size: 48
337587 TCATTTTCAT
* *
337597 TTTCATTTTCATTTTCATTTTGGAGAAAACCATATTCATTTTAAAATG
1 TTTCATTTTCATTTTCATTTTGGAGAAAACCATAATCATTTGAAAATG
* * * *
337645 ATTTCATTTCTCCATTTTTATTTTGGAGAAAATCTTAATCATTTGCAAATG
1 -TTTCATTT-T-CATTTTCATTTTGGAGAAAACCATAATCATTTGAAAATG
337696 TTTCATATTTC
1 TTTCAT-TTTC
337707 TTCATTTCAC
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
49 9 0.17
50 8 0.15
51 35 0.67
ACGTcount: A:0.29, C:0.14, G:0.08, T:0.49
Consensus pattern (48 bp):
TTTCATTTTCATTTTCATTTTGGAGAAAACCATAATCATTTGAAAATG
Found at i:358517 original size:23 final size:23
Alignment explanation
Indices: 358491--358547 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
358481 GAAATTAAAT
358491 TATAATTTTTACGATAGTAAAAA
1 TATAATTTTTACGATAGTAAAAA
* *
358514 TATAATTTTTATGATGGTAAAAA
1 TATAATTTTTACGATAGTAAAAA
358537 TATAATTTTTA
1 TATAATTTTTA
358548 AAATATTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.46
Consensus pattern (23 bp):
TATAATTTTTACGATAGTAAAAA
Found at i:358557 original size:23 final size:23
Alignment explanation
Indices: 358491--358557 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
358481 GAAATTAAAT
*
358491 TATAATTTTTACGATAGTAAAAA
1 TATAATTTTTAAGATAGTAAAAA
* *
358514 TATAATTTTTATGATGGTAAAAA
1 TATAATTTTTAAGATAGTAAAAA
* *
358537 TATAATTTTTAAAATATTAAA
1 TATAATTTTTAAGATAGTAAA
358558 TCAAAATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.48, C:0.01, G:0.07, T:0.43
Consensus pattern (23 bp):
TATAATTTTTAAGATAGTAAAAA
Found at i:361418 original size:48 final size:46
Alignment explanation
Indices: 361347--361447 Score: 141
Period size: 48 Copynumber: 2.2 Consensus size: 46
361337 GAATAGATAA
* * * *
361347 ATAAT-AAAAATATAAAAAGTAATAGATACAATATTGGGATCATAT
1 ATAATAAAAAATATAAAAACTAATAAATACAATATTAGAATCATAT
361392 ATAATAAAAAATATATAAAACCTAATAAATACAATATTAGAATCATAT
1 ATAATAAAAAATATA-AAAA-CTAATAAATACAATATTAGAATCATAT
361440 ATAATAAA
1 ATAATAAA
361448 GATGAGCCTA
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
45 5 0.10
46 9 0.18
47 4 0.08
48 31 0.63
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.29
Consensus pattern (46 bp):
ATAATAAAAAATATAAAAACTAATAAATACAATATTAGAATCATAT
Found at i:364259 original size:23 final size:22
Alignment explanation
Indices: 364233--364294 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 22
364223 TTTTTTACTG
*
364233 TTTTGATTGTTGTTTTCGTGTTA
1 TTTTGATTGTT-TTTTCCTGTTA
*
364256 TTTTGCTATT-ATTTTTCCTGTTA
1 TTTTG--ATTGTTTTTTCCTGTTA
364279 TTTTGATTGTTATTTT
1 TTTTGATTGTT-TTTT
364295 TGTTGTTTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
21 3 0.09
22 1 0.03
23 24 0.75
24 1 0.03
25 3 0.09
ACGTcount: A:0.11, C:0.06, G:0.15, T:0.68
Consensus pattern (22 bp):
TTTTGATTGTTTTTTCCTGTTA
Found at i:364307 original size:21 final size:20
Alignment explanation
Indices: 364274--364317 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
364264 TTATTTTTCC
* *
364274 TGTTATTTTGATTGTTATTTT
1 TGTTATTTAGATT-TCATTTT
*
364295 TGTTGTTTAGATTTCATTTT
1 TGTTATTTAGATTTCATTTT
364315 TGT
1 TGT
364318 ACGTGTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.14, C:0.02, G:0.16, T:0.68
Consensus pattern (20 bp):
TGTTATTTAGATTTCATTTT
Found at i:365038 original size:27 final size:27
Alignment explanation
Indices: 365008--365059 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
364998 AAACTTCATT
*
365008 AAAAGA-AATGAAAAAGAGAGAAAAACA
1 AAAAGAGAA-GAAAAAGAGAAAAAAACA
*
365035 AAAAGAGAAGCAAAAGAGAAAAAAA
1 AAAAGAGAAGAAAAAGAGAAAAAAA
365060 ATAATAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.75, C:0.04, G:0.19, T:0.02
Consensus pattern (27 bp):
AAAAGAGAAGAAAAAGAGAAAAAAACA
Found at i:365068 original size:12 final size:11
Alignment explanation
Indices: 365053--365097 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 11
365043 AGCAAAAGAG
365053 AAAAAAAATAA
1 AAAAAAAATAA
365064 TAAAAAAAATAAA
1 -AAAAAAAAT-AA
365077 AAAAAAACATAA
1 AAAAAAA-ATAA
365089 AAGAAAAAA
1 AA-AAAAAA
365098 AATTTCTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 21 0.70
13 9 0.30
ACGTcount: A:0.87, C:0.02, G:0.02, T:0.09
Consensus pattern (11 bp):
AAAAAAAATAA
Found at i:365071 original size:22 final size:22
Alignment explanation
Indices: 365046--365099 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
365036 AAAGAGAAGC
* *
365046 AAAAGAGAAAAAAAATA-ATAA
1 AAAAAAGAAAAAAAAAACATAA
*
365067 AAAAAATAAAAAAAAAACATAA
1 AAAAAAGAAAAAAAAAACATAA
*
365089 AAGAAA-AAAAA
1 AAAAAAGAAAAA
365100 TTTCTCAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 19 0.68
22 9 0.32
ACGTcount: A:0.85, C:0.02, G:0.06, T:0.07
Consensus pattern (22 bp):
AAAAAAGAAAAAAAAAACATAA
Found at i:367652 original size:6 final size:7
Alignment explanation
Indices: 367635--367659 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
367625 TTAAGGAGAA
367635 AAAAAGG
1 AAAAAGG
367642 AAAAAGG
1 AAAAAGG
367649 AAAAAGG
1 AAAAAGG
367656 AAAA
1 AAAA
367660 CAAACCCGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (7 bp):
AAAAAGG
Found at i:376318 original size:16 final size:16
Alignment explanation
Indices: 376297--376329 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
376287 AAACAGTCAC
376297 TCAACTTTGATCTCAA
1 TCAACTTTGATCTCAA
376313 TCAACTTTGATCTCAA
1 TCAACTTTGATCTCAA
376329 T
1 T
376330 GACAAAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.24, G:0.06, T:0.39
Consensus pattern (16 bp):
TCAACTTTGATCTCAA
Found at i:380984 original size:23 final size:22
Alignment explanation
Indices: 380958--381007 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 22
380948 AGGTTTGTTC
380958 ATTT-TATTTTTTTAATTTTAAAT
1 ATTTATATTTTTTT-ATTTT-AAT
380981 ATTTATATTTTTTTATTTTAAT
1 ATTTATATTTTTTTATTTTAAT
381003 ATTTA
1 ATTTA
381008 ATAATTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 8 0.31
23 9 0.35
24 9 0.35
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (22 bp):
ATTTATATTTTTTTATTTTAAT
Found at i:380985 original size:22 final size:22
Alignment explanation
Indices: 380960--381007 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
380950 GTTTGTTCAT
380960 TTTAT-TTTTTTAATTTTAAATA
1 TTTATATTTTTTAATTTT-AATA
*
380982 TTTATATTTTTTTATTTTAATA
1 TTTATATTTTTTAATTTTAATA
381004 TTTA
1 TTTA
381008 ATAATTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTATATTTTTTAATTTTAATA
Found at i:381015 original size:22 final size:24
Alignment explanation
Indices: 380958--381016 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 24
380948 AGGTTTGTTC
*
380958 ATTT-TATTTTTTTAATTTTAAAT
1 ATTTATATATTTTTAATTTTAAAT
*
380981 ATTTATAT-TTTTTTATTTT-AAT
1 ATTTATATATTTTTAATTTTAAAT
*
381003 ATTTA-ATAATTTTA
1 ATTTATATATTTTTA
381017 TACATTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 2 0.06
22 12 0.39
23 14 0.45
24 3 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (24 bp):
ATTTATATATTTTTAATTTTAAAT
Found at i:381015 original size:23 final size:24
Alignment explanation
Indices: 380965--381015 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
380955 TTCATTTTAT
380965 TTTTTTAATTTTAAATATTTAT-A
1 TTTTTTAATTTTAAATATTTATAA
*
380988 TTTTTTTATTTT-AATATTTAATAA
1 TTTTTTAATTTTAAATATTT-ATAA
381012 TTTT
1 TTTT
381016 ATACATTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 7 0.28
23 13 0.52
24 5 0.20
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTTTTAATTTTAAATATTTATAA
Found at i:381072 original size:26 final size:25
Alignment explanation
Indices: 381036--381094 Score: 91
Period size: 25 Copynumber: 2.3 Consensus size: 25
381026 TTTCAAAAAA
381036 ATAATTTTATACATTTTTATTTATTG
1 ATAATTTTATA-ATTTTTATTTATTG
*
381062 ATAATTTTATATTTTTTATTTATTG
1 ATAATTTTATAATTTTTATTTATTG
*
381087 TTAATTTT
1 ATAATTTT
381095 TATATAGTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 20 0.65
26 11 0.35
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (25 bp):
ATAATTTTATAATTTTTATTTATTG
Found at i:381095 original size:26 final size:25
Alignment explanation
Indices: 381036--381099 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 25
381026 TTTCAAAAAA
*
381036 ATAATTTTATACATTTTTATTTATTG
1 ATAATTTTATA-TTTTTTATTTATTG
381062 ATAATTTTATATTTTTTATTTATTG
1 ATAATTTTATATTTTTTATTTATTG
*
381087 TTAATTTTTATAT
1 ATAA-TTTTATAT
381100 AGTAATCTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 16 0.46
26 19 0.54
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.66
Consensus pattern (25 bp):
ATAATTTTATATTTTTTATTTATTG
Found at i:391968 original size:16 final size:17
Alignment explanation
Indices: 391941--391973 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
391931 TGTTAAAAAT
391941 ATAATCTTATATTTTTA
1 ATAATCTTATATTTTTA
391958 ATAAT-TTATATTTTTA
1 ATAATCTTATATTTTTA
391974 TCTTTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (17 bp):
ATAATCTTATATTTTTA
Found at i:407018 original size:33 final size:34
Alignment explanation
Indices: 406966--407031 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 34
406956 CTAATTAACT
406966 TTTTTTAAGAAAAGATTAATGAAAATTTTCAAAG
1 TTTTTTAAGAAAAGATTAATGAAAATTTTCAAAG
* * *
407000 TTTTTTGAG-AAAGCTTAATTAAAATTTTCAAA
1 TTTTTTAAGAAAAGATTAATGAAAATTTTCAAA
407032 AATTTTAAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 21 0.72
34 8 0.28
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.41
Consensus pattern (34 bp):
TTTTTTAAGAAAAGATTAATGAAAATTTTCAAAG
Found at i:407122 original size:29 final size:30
Alignment explanation
Indices: 407057--407129 Score: 94
Period size: 29 Copynumber: 2.4 Consensus size: 30
407047 CTACAAAAAC
*
407057 AATCACTTTTGTTTGACTCATATTACATTTT
1 AATCACTTTTGTTTGAC-AATATTACATTTT
* *
407088 AGTCACTTTTGTTTGA-AATGTTACATTTT
1 AATCACTTTTGTTTGACAATATTACATTTT
*
407117 AATCACTTATGTT
1 AATCACTTTTGTT
407130 ATTTTTTTTG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 22 0.59
31 15 0.41
ACGTcount: A:0.26, C:0.14, G:0.10, T:0.51
Consensus pattern (30 bp):
AATCACTTTTGTTTGACAATATTACATTTT
Found at i:407281 original size:18 final size:18
Alignment explanation
Indices: 407258--407300 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
407248 GAATAGATTT
407258 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
407276 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
407294 TTAATTA
1 TTAATTA
407301 CACCTTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:410153 original size:2 final size:2
Alignment explanation
Indices: 410146--410170 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
410136 CTATTCTTTA
410146 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 A
410171 GATAGATAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:411877 original size:30 final size:30
Alignment explanation
Indices: 411841--411901 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
411831 AGACATTCCA
411841 GATTCATTTGGAACACATTCTGGAGTACCT
1 GATTCATTTGGAACACATTCTGGAGTACCT
411871 GATTCATTTGGAACACATTCTGGAGTACCT
1 GATTCATTTGGAACACATTCTGGAGTACCT
411901 G
1 G
411902 CTGAAACCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (30 bp):
GATTCATTTGGAACACATTCTGGAGTACCT
Found at i:415985 original size:28 final size:27
Alignment explanation
Indices: 415913--415987 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 27
415903 GAGTTGGTGT
* * *
415913 TTTGGGTTTAA-TGTTCAAGGTTTATG
1 TTTGGGTTTAAGGGTTTAAGATTTATG
*
415939 TTTAGGGTTT-AGGTTTTTAAGATTTAGTG
1 TTT-GGGTTTAAGG-GTTTAAGATTTA-TG
415968 TTTGGGTTTAAGGGTTTAAG
1 TTTGGGTTTAAGGGTTTAAG
415988 GTCATGGGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
26 4 0.10
27 6 0.15
28 21 0.54
29 8 0.21
ACGTcount: A:0.20, C:0.01, G:0.29, T:0.49
Consensus pattern (27 bp):
TTTGGGTTTAAGGGTTTAAGATTTATG
Found at i:417409 original size:3 final size:3
Alignment explanation
Indices: 417401--417434 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
417391 TTGTTCGGCA
417401 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
417435 TTGTTAACTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:422685 original size:58 final size:58
Alignment explanation
Indices: 422580--422745 Score: 205
Period size: 58 Copynumber: 2.8 Consensus size: 58
422570 TCTAATTTTA
* *
422580 TATATTATAATTTTTA-TTAATTTATATTTTAATAATAATTATATTAAAA-ACGTTATTAAAT
1 TATA-TATTATTTTTATTTAA-TTATA-TTTAATAATAATTATATTAAAATA--TAATTAAAT
*
422641 TATATATTA-TTTTATTTAATTATATTTAATAATAATTATGTTAAAATATAATTAAAT
1 TATATATTATTTTTATTTAATTATATTTAATAATAATTATATTAAAATATAATTAAAT
* *
422698 TATTTATTATTTTTATTAAATTATATTTAATAATAATCT-TATTAAAAT
1 TATATATTATTTTTATTTAATTATATTTAATAATAAT-TATATTAAAAT
422746 TTCATAACAA
Statistics
Matches: 95, Mismatches: 6, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
57 16 0.17
58 55 0.58
59 12 0.13
60 8 0.08
61 4 0.04
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (58 bp):
TATATATTATTTTTATTTAATTATATTTAATAATAATTATATTAAAATATAATTAAAT
Found at i:422961 original size:32 final size:32
Alignment explanation
Indices: 422917--423005 Score: 142
Period size: 32 Copynumber: 2.8 Consensus size: 32
422907 TACAGTTATA
*
422917 TTCATTACAGCTCTATTCCATTGCAACTCTAT
1 TTCATTACAGCTCTATTCCATTACAACTCTAT
*
422949 TTTATTACAGCTCTATTCCATTACAACTCTAT
1 TTCATTACAGCTCTATTCCATTACAACTCTAT
* *
422981 TTCATTACAGTTATATTCCATTACA
1 TTCATTACAGCTCTATTCCATTACA
423006 GCGAACCAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.28, C:0.25, G:0.04, T:0.43
Consensus pattern (32 bp):
TTCATTACAGCTCTATTCCATTACAACTCTAT
Found at i:423006 original size:16 final size:16
Alignment explanation
Indices: 422905--423007 Score: 109
Period size: 16 Copynumber: 6.5 Consensus size: 16
422895 TGAATTACTG
* *
422905 ATTACAGTTATATT-C
1 ATTACAGCTCTATTCC
422920 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
* * **
422936 ATTGCAACTCTATTTT
1 ATTACAGCTCTATTCC
422952 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
* *
422968 ATTACAACTCTATTTC
1 ATTACAGCTCTATTCC
* *
422984 ATTACAGTTATATTCC
1 ATTACAGCTCTATTCC
423000 ATTACAGC
1 ATTACAGC
423008 GAACCAAACG
Statistics
Matches: 70, Mismatches: 17, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
15 12 0.17
16 58 0.83
ACGTcount: A:0.29, C:0.23, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:423087 original size:19 final size:20
Alignment explanation
Indices: 423046--423095 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
423036 TATGCGTAAG
* *
423046 TTTTAAGTTAATC-TTTATA
1 TTTTAATTTGATCTTTTATA
* *
423065 TTTTAATTTGATCTTTTTTT
1 TTTTAATTTGATCTTTTATA
423085 TTTTAATTTGA
1 TTTTAATTTGA
423096 AATTTCAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.24, C:0.04, G:0.06, T:0.66
Consensus pattern (20 bp):
TTTTAATTTGATCTTTTATA
Found at i:426765 original size:18 final size:16
Alignment explanation
Indices: 426747--426779 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
426737 TGGATAAAAT
426747 AATAATA-AAAAGAAA
1 AATAATATAAAAGAAA
*
426762 AATAATGTAAAAGAAA
1 AATAATATAAAAGAAA
426778 AA
1 AA
426780 AATGAAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AATAATATAAAAGAAA
Found at i:426767 original size:15 final size:16
Alignment explanation
Indices: 426747--426786 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
426737 TGGATAAAAT
426747 AATAAT-AAAAAGAAA
1 AATAATGAAAAAGAAA
*
426762 AATAATGTAAAAGAAA
1 AATAATGAAAAAGAAA
426778 AA-AATGAAA
1 AATAATGAAA
426787 GAATTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.75, C:0.00, G:0.10, T:0.15
Consensus pattern (16 bp):
AATAATGAAAAAGAAA
Found at i:426775 original size:16 final size:15
Alignment explanation
Indices: 426754--426783 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
426744 AATAATAATA
426754 AAAAGAAAAATAATGT
1 AAAAGAAAAA-AATGT
426770 AAAAGAAAAAAATG
1 AAAAGAAAAAAATG
426784 AAAGAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (15 bp):
AAAAGAAAAAAATGT
Found at i:427188 original size:21 final size:20
Alignment explanation
Indices: 427160--427202 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
427150 ATAATCATGC
*
427160 ATGAAAATGAAAATTTGAAG
1 ATGAAAATGAAAATTTAAAG
*
427180 ATGATAAATGTAAATTTAAAG
1 ATGA-AAATGAAAATTTAAAG
427201 AT
1 AT
427203 AATGCATGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.30
Consensus pattern (20 bp):
ATGAAAATGAAAATTTAAAG
Found at i:427697 original size:16 final size:18
Alignment explanation
Indices: 427676--427713 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
427666 AAGATCATAC
427676 AAAACTT-CTAAA-AATG
1 AAAACTTACTAAAGAATG
*
427692 AAAACTTAGTAAAGAATG
1 AAAACTTACTAAAGAATG
427710 AAAA
1 AAAA
427714 AAAGACGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 4 0.21
18 8 0.42
ACGTcount: A:0.61, C:0.08, G:0.11, T:0.21
Consensus pattern (18 bp):
AAAACTTACTAAAGAATG
Found at i:431512 original size:6 final size:6
Alignment explanation
Indices: 431491--431573 Score: 64
Period size: 6 Copynumber: 13.8 Consensus size: 6
431481 TTTAAATTGG
** **
431491 TTTAAA TTTATT TTTAAA TTTAAA TTT--A TGTTAAA TTTAAA TTTATCTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTA--AA
**
431540 TTTAAA TTTAAA TTT-GC TTTAAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
431574 TTAGATTTGA
Statistics
Matches: 59, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
4 2 0.03
5 5 0.08
6 46 0.78
7 2 0.03
8 4 0.07
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:431526 original size:17 final size:18
Alignment explanation
Indices: 431491--431572 Score: 105
Period size: 17 Copynumber: 4.6 Consensus size: 18
431481 TTTAAATTGG
431491 TTTAAATTTATTTTTAAA
1 TTTAAATTTATTTTTAAA
*
431509 TTTAAATTTA-TGTTAAA
1 TTTAAATTTATTTTTAAA
431526 TTTAAATTTATCTTTTTAAA
1 TTTAAATTTA--TTTTTAAA
**
431546 TTTAAATTT-GCTTTAAA
1 TTTAAATTTATTTTTAAA
431563 TTTAAATTTA
1 TTTAAATTTA
431573 ATTAGATTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
17 31 0.55
18 10 0.18
20 15 0.27
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (18 bp):
TTTAAATTTATTTTTAAA
Found at i:431550 original size:37 final size:35
Alignment explanation
Indices: 431491--431572 Score: 121
Period size: 37 Copynumber: 2.3 Consensus size: 35
431481 TTTAAATTGG
431491 TTTAAATTTATTTTTAAATTTAAATTT-ATGTTAAA
1 TTTAAATTTATTTTTAAATTTAAATTTGAT-TTAAA
*
431526 TTTAAATTTATCTTTTTAAATTTAAATTTGCTTTAAA
1 TTTAAATTTA--TTTTTAAATTTAAATTTGATTTAAA
431563 TTTAAATTTA
1 TTTAAATTTA
431573 ATTAGATTTG
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
35 10 0.23
37 32 0.74
38 1 0.02
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (35 bp):
TTTAAATTTATTTTTAAATTTAAATTTGATTTAAA
Found at i:432286 original size:3 final size:3
Alignment explanation
Indices: 432280--432364 Score: 64
Period size: 3 Copynumber: 27.3 Consensus size: 3
432270 TTATATTGAC
* * * *
432280 AAT AAT AAT AAT AAT AAT ATT ACT AAT -AT AATT AAC AAT ATT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
* * *
432325 GAT AAC AAT AAT AAT GACAT CAAT AAT AAT ATT AAT AAT A
1 AAT AAT AAT AAT AAT -A-AT -AAT AAT AAT AAT AAT AAT A
432365 GTATTAATTA
Statistics
Matches: 64, Mismatches: 14, Indels: 8
0.74 0.16 0.09
Matches are distributed among these distances:
2 2 0.03
3 53 0.83
4 6 0.09
5 3 0.05
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:432296 original size:36 final size:36
Alignment explanation
Indices: 432255--432329 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 36
432245 AAAATGTCAT
* *
432255 TAATAACATTATTAAT-TATATTGACAATAATAATAA
1 TAATAACATTACTAATATA-ATTAACAATAATAATAA
* * *
432291 TAATAATATTACTAATATAATTAACAATATTAATGA
1 TAATAACATTACTAATATAATTAACAATAATAATAA
432327 TAA
1 TAA
432330 CAATAATAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
36 31 0.94
37 2 0.06
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (36 bp):
TAATAACATTACTAATATAATTAACAATAATAATAA
Found at i:432369 original size:12 final size:12
Alignment explanation
Indices: 432255--432372 Score: 71
Period size: 12 Copynumber: 10.1 Consensus size: 12
432245 AAAATGTCAT
* *
432255 TAATAACATTAT
1 TAATAATATTAA
* *
432267 TAATTATATTGA
1 TAATAATATTAA
* *
432279 CAATAATAATAA
1 TAATAATATTAA
*
432291 TAATAATATTAC
1 TAATAATATTAA
*
432303 TAAT-ATA--AT
1 TAATAATATTAA
*
432312 TAACAATATTAA
1 TAATAATATTAA
* * *
432324 TGATAACAATAA
1 TAATAATATTAA
* * *
432336 TAATGACATCAA
1 TAATAATATTAA
432348 TAATAATATTAA
1 TAATAATATTAA
*
432360 TAATAGTATTAA
1 TAATAATATTAA
432372 T
1 T
432373 TAAAAAAGAA
Statistics
Matches: 77, Mismatches: 26, Indels: 6
0.71 0.24 0.06
Matches are distributed among these distances:
9 4 0.05
10 3 0.04
11 3 0.04
12 67 0.87
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.37
Consensus pattern (12 bp):
TAATAATATTAA
Found at i:432599 original size:30 final size:27
Alignment explanation
Indices: 432489--432825 Score: 262
Period size: 30 Copynumber: 11.4 Consensus size: 27
432479 CTAAAATTAT
* * * *
432489 CATTTTATCCTCGAACTTCTAAAATTCC
1 CATTTTA-CCCCGAACTTCCAAAAATAC
* *
432517 CATTTTTGACCCCAAACCTTCCAAAAATTAT
1 CA-TTTT-ACCCCGAA-CTTCCAAAAA-TAC
* *
432548 TATTTTACCCCCGAACTTCCAAAAATCC
1 CATTTTA-CCCCGAACTTCCAAAAATAC
**
432576 CATTTTTGATGCCGAACCTTCCAAAAATTAC
1 CA-TTTT-ACCCCGAA-CTTCCAAAAA-TAC
* *
432607 CATTTTACCCCCAACTTCCAAAAATCC
1 CATTTTACCCCGAACTTCCAAAAATAC
432634 CATTTTTGACCCCGAAACTTCCAAAAATTAC
1 CA-TTTT-ACCCCG-AACTTCCAAAAA-TAC
432665 CATTTTACTCCCGAACCTTCCAAAAATTAC
1 CATTTTAC-CCCGAA-CTTCCAAAAA-TAC
*
432695 CATTTTACCCCCGAACTTCCAAAAATCC
1 CATTTTA-CCCCGAACTTCCAAAAATAC
*
432723 CATTTTGACCCCGAAACTTCCAAAAATTTC
1 CATTTT-ACCCCG-AACTTCCAAAAA-TAC
*
432753 CTTTTTACCCCCGAACTTCCAAAAAT-C
1 CATTTTA-CCCCGAACTTCCAAAAATAC
*
432780 TCTTTTTTGACCCCGATACTTCCAAAAAATTAC
1 -C-ATTTT-ACCCCGA-ACTTCC-AAAAA-TAC
432813 CATTTTACTCCCG
1 CATTTTAC-CCCG
432826 GATGTTCGAA
Statistics
Matches: 257, Mismatches: 24, Indels: 53
0.77 0.07 0.16
Matches are distributed among these distances:
27 5 0.02
28 33 0.13
29 90 0.35
30 102 0.40
31 24 0.09
32 2 0.01
33 1 0.00
ACGTcount: A:0.32, C:0.32, G:0.05, T:0.31
Consensus pattern (27 bp):
CATTTTACCCCGAACTTCCAAAAATAC
Found at i:432649 original size:58 final size:58
Alignment explanation
Indices: 432467--432778 Score: 316
Period size: 58 Copynumber: 5.3 Consensus size: 58
432457 CGTCACGAAG
* * * * * *
432467 CCCCGAAACC-TCCTAAAATTATCATTTTATCCTCGAACTTCTAAAATTCCCATTTTTGA
1 CCCCG-AACCTTCCAAAAATTACCATTTTA-CCCCCAACTTCCAAAAATCCCATTTTTGA
* **
432526 CCCCAAACCTTCCAAAAATTATTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
1 CCCCGAACCTTCCAAAAATTACCATTTTACCCCC-AACTTCCAAAAATCCCATTTTTGA
**
432585 TGCCGAACCTTCCAAAAATTACCATTTTACCCCCAACTTCCAAAAATCCCATTTTTGA
1 CCCCGAACCTTCCAAAAATTACCATTTTACCCCCAACTTCCAAAAATCCCATTTTTGA
* * *
432643 CCCCGAAACTTCCAAAAATTACCATTTTACTCCCGAACCTTCCAAAAATTACCA-TTTT-A
1 CCCCGAACCTTCCAAAAATTACCATTTTAC-CCCCAA-CTTCCAAAAA-TCCCATTTTTGA
* * *
432702 CCCCCGAA-CTTCCAAAAA-TCCCATTTTGACCCCGAAACTTCCAAAAATTTCC-TTTTT-A
1 -CCCCGAACCTTCCAAAAATTACCATTTT-ACCCC-CAACTTCCAAAAA-TCCCATTTTTGA
432760 CCCCCGAA-CTTCCAAAAAT
1 -CCCCGAACCTTCCAAAAAT
432779 CTCTTTTTTG
Statistics
Matches: 223, Mismatches: 20, Indels: 20
0.85 0.08 0.08
Matches are distributed among these distances:
58 106 0.48
59 92 0.41
60 21 0.09
61 4 0.02
ACGTcount: A:0.33, C:0.33, G:0.04, T:0.30
Consensus pattern (58 bp):
CCCCGAACCTTCCAAAAATTACCATTTTACCCCCAACTTCCAAAAATCCCATTTTTGA
Found at i:432729 original size:88 final size:85
Alignment explanation
Indices: 432467--432778 Score: 344
Period size: 88 Copynumber: 3.6 Consensus size: 85
432457 CGTCACGAAG
* * * * * *
432467 CCCCGAAACCTCCTAAAATTATCATTTTATCCTCGAACTT-CTAAAATTCCCATTTTTGACCCCA
1 CCCCGAAACTTCCAAAAATTACCATTTTATCC-CGAACTTCCAAAAATTACCA-TTTT-ACCCCC
***
432531 AACCTTCCAAAAATTATTATTTT-A
63 AA-CTTCCAAAAA-TCCCATTTTGA
* *
432555 CCCCCG-AACTTCCAAAAA-TCCCATTTTTGATGCCGAACCTTCCAAAAATTACCATTTTACCCC
1 -CCCCGAAACTTCCAAAAATTACCA-TTTT-ATCCCGAA-CTTCCAAAAATTACCATTTTACCCC
432618 CAACTTCCAAAAATCCCATTTTTGA
62 CAACTTCCAAAAATCCCA-TTTTGA
432643 CCCCGAAACTTCCAAAAATTACCATTTTACTCCCGAACCTTCCAAAAATTACCATTTTACCCCCG
1 CCCCGAAACTTCCAAAAATTACCATTTTA-TCCCGAA-CTTCCAAAAATTACCATTTTACCCCC-
432708 AACTTCCAAAAATCCCATTTTGA
63 AACTTCCAAAAATCCCATTTTGA
* * *
432731 CCCCGAAACTTCCAAAAATTTCCTTTTTACCCCCGAACTTCCAAAAAT
1 CCCCGAAACTTCCAAAAATTACCATTTTA-TCCCGAACTTCCAAAAAT
432779 CTCTTTTTTG
Statistics
Matches: 197, Mismatches: 16, Indels: 22
0.84 0.07 0.09
Matches are distributed among these distances:
86 2 0.01
87 34 0.17
88 115 0.58
89 36 0.18
90 10 0.05
ACGTcount: A:0.33, C:0.33, G:0.04, T:0.30
Consensus pattern (85 bp):
CCCCGAAACTTCCAAAAATTACCATTTTATCCCGAACTTCCAAAAATTACCATTTTACCCCCAAC
TTCCAAAAATCCCATTTTGA
Found at i:432779 original size:58 final size:58
Alignment explanation
Indices: 432467--432825 Score: 290
Period size: 58 Copynumber: 6.1 Consensus size: 58
432457 CGTCACGAAG
* * * * * *
432467 CCCCGAAACCTCCTAAAATTATCATTTTATCCTCG-AACTT-CTAAAATTCCCATTTTTGA-
1 CCCCG-AACTTCCAAAAATTACCATTTTA-CCCCGAAACTTCCAAAAATTACCA-TTTT-AC
* ** *
432526 CCCCAAACCTTCCAAAAATTATTATTTTACCCCCG-AACTTCCAAAAA-TCCCATTTTTGA-
1 CCCCGAA-CTTCCAAAAATTACCATTTTA-CCCCGAAACTTCCAAAAATTACCA-TTTT-AC
** * *
432585 TGCCGAACCTTCCAAAAATTACCATTTTACCCC-CAACTTCCAAAAA-TCCCATTTTTGA-
1 CCCCGAA-CTTCCAAAAATTACCATTTTACCCCGAAACTTCCAAAAATTACCA-TTTT-AC
*
432643 CCCCGAAACTTCCAAAAATTACCATTTTACTCCCGAACCTTCCAAAAATTACCATTTTAC
1 CCCCG-AACTTCCAAAAATTACCATTTTAC-CCCGAAACTTCCAAAAATTACCATTTTAC
* * *
432703 CCCCGAACTTCCAAAAA-TCCCATTTTGACCCCGAAACTTCCAAAAATTTCCTTTTTAC
1 CCCCGAACTTCCAAAAATTACCATTTT-ACCCCGAAACTTCCAAAAATTACCATTTTAC
** *
432761 CCCCGAACTTCCAAAAATCT-CTTTTTTGACCCCGATACTTCCAAAAAATTACCATTTTAC
1 CCCCGAACTTCCAAAAAT-TACCATTTT-ACCCCGAAACTTCC-AAAAATTACCATTTTAC
*
432821 TCCCG
1 CCCCG
432826 GATGTTCGAA
Statistics
Matches: 261, Mismatches: 27, Indels: 23
0.84 0.09 0.07
Matches are distributed among these distances:
58 106 0.41
59 106 0.41
60 45 0.17
61 4 0.02
ACGTcount: A:0.32, C:0.33, G:0.05, T:0.31
Consensus pattern (58 bp):
CCCCGAACTTCCAAAAATTACCATTTTACCCCGAAACTTCCAAAAATTACCATTTTAC
Found at i:433166 original size:14 final size:14
Alignment explanation
Indices: 433147--433175 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
433137 TTCAAAATTG
433147 TTTTTCTTTTTTTT
1 TTTTTCTTTTTTTT
433161 TTTTTCTTTTTTTT
1 TTTTTCTTTTTTTT
433175 T
1 T
433176 ATACAAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (14 bp):
TTTTTCTTTTTTTT
Found at i:435150 original size:23 final size:23
Alignment explanation
Indices: 435124--435168 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
435114 ATTTTCGAAT
**
435124 TTCGAATTATTCAAATCGAGTTA
1 TTCGAATTAAACAAATCGAGTTA
*
435147 TTCGAGTTAAACAAATCGAGTT
1 TTCGAATTAAACAAATCGAGTT
435169 GAATTTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.36
Consensus pattern (23 bp):
TTCGAATTAAACAAATCGAGTTA
Found at i:435230 original size:9 final size:9
Alignment explanation
Indices: 435214--435243 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
435204 TTTAATTTTT
435214 TAATTCGAA
1 TAATTCGAA
*
435223 TTATTCGAA
1 TAATTCGAA
435232 TAATTCGAA
1 TAATTCGAA
435241 TAA
1 TAA
435244 ACCGAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (9 bp):
TAATTCGAA
Found at i:435249 original size:18 final size:18
Alignment explanation
Indices: 435214--435252 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
435204 TTTAATTTTT
* **
435214 TAATTCGAATTATTCGAA
1 TAATTCGAATAAACCGAA
435232 TAATTCGAATAAACCGAA
1 TAATTCGAATAAACCGAA
435250 TAA
1 TAA
435253 AACTATAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.31
Consensus pattern (18 bp):
TAATTCGAATAAACCGAA
Found at i:435442 original size:42 final size:42
Alignment explanation
Indices: 435390--435477 Score: 128
Period size: 42 Copynumber: 2.1 Consensus size: 42
435380 ACTCATCAAC
435390 AAACTAAACCCAAATATAATTTCATTATT-C-AAA-AACACTCAT
1 AAACTAAACCCAAATATAA-TT--TTATTCCAAAATAACACTCAT
435432 AAACTAAACCCAAATATAATTTTATTCCAAAATAACACTCAT
1 AAACTAAACCCAAATATAATTTTATTCCAAAATAACACTCAT
435474 AAAC
1 AAAC
435478 AACTCCTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
39 5 0.12
40 1 0.02
41 5 0.12
42 32 0.74
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (42 bp):
AAACTAAACCCAAATATAATTTTATTCCAAAATAACACTCAT
Found at i:440583 original size:12 final size:12
Alignment explanation
Indices: 440566--440592 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
440556 GTTCTACTCA
440566 GATGTGATGCAG
1 GATGTGATGCAG
440578 GATGTGATGCAG
1 GATGTGATGCAG
440590 GAT
1 GAT
440593 TTGCTTCTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.07, G:0.41, T:0.26
Consensus pattern (12 bp):
GATGTGATGCAG
Found at i:447890 original size:10 final size:10
Alignment explanation
Indices: 447875--447899 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
447865 AAGGGAAAGT
447875 AAAAAAATAA
1 AAAAAAATAA
447885 AAAAAAATAA
1 AAAAAAATAA
447895 AAAAA
1 AAAAA
447900 TAAAAAGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:455960 original size:2 final size:2
Alignment explanation
Indices: 455953--455977 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
455943 GCTTTAAAAC
455953 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 T
455978 TCACCGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:458094 original size:9 final size:9
Alignment explanation
Indices: 458076--458152 Score: 63
Period size: 9 Copynumber: 8.3 Consensus size: 9
458066 GTCAGTAAAT
458076 AATT-TTAA
1 AATTATTAA
458084 AATTATTAA
1 AATTATTAA
458093 AATTACTTTTTAA
1 AATTA----TTAA
*
458106 AAATA-TAA
1 AATTATTAA
458114 AATTATTAA
1 AATTATTAA
458123 AATTATTTTAA
1 AATTA--TTAA
458134 AA-TA-TAA
1 AATTATTAA
458141 AATTATTAA
1 AATTATTAA
458150 AAT
1 AAT
458153 AATCAATATT
Statistics
Matches: 57, Mismatches: 2, Indels: 19
0.73 0.03 0.24
Matches are distributed among these distances:
7 5 0.09
8 13 0.23
9 23 0.40
10 2 0.04
11 6 0.11
13 8 0.14
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (9 bp):
AATTATTAA
Found at i:458103 original size:22 final size:21
Alignment explanation
Indices: 458078--458118 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
458068 CAGTAAATAA
*
458078 TTTTAAAATTATTAAAATTACT
1 TTTTAAAAATA-TAAAATTACT
458100 TTTTAAAAATATAAAATTA
1 TTTTAAAAATATAAAATTA
458119 TTAAAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
TTTTAAAAATATAAAATTACT
Found at i:458135 original size:27 final size:29
Alignment explanation
Indices: 458081--458152 Score: 121
Period size: 27 Copynumber: 2.5 Consensus size: 29
458071 TAAATAATTT
458081 TAAAATTATTAAAATTACTTTTTAAAAATA
1 TAAAATTATTAAAATTAC-TTTTAAAAATA
458111 TAAAATTATTAAAATTA-TTTT-AAAATA
1 TAAAATTATTAAAATTACTTTTAAAAATA
458138 TAAAATTATTAAAAT
1 TAAAATTATTAAAAT
458153 AATCAATATT
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
27 21 0.50
28 4 0.10
30 17 0.40
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (29 bp):
TAAAATTATTAAAATTACTTTTAAAAATA
Found at i:458151 original size:16 final size:16
Alignment explanation
Indices: 458105--458153 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
458095 TTACTTTTTA
458105 AAAATATAAAATTATT
1 AAAATATAAAATTATT
458121 AAAAT-T---ATT-TT
1 AAAATATAAAATTATT
458132 AAAATATAAAATTATT
1 AAAATATAAAATTATT
458148 AAAATA
1 AAAATA
458154 ATCAATATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
11 7 0.25
12 4 0.14
15 4 0.14
16 13 0.46
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAAATATAAAATTATT
Found at i:458816 original size:16 final size:17
Alignment explanation
Indices: 458795--458834 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 17
458785 AAGTGATGAT
458795 TATTTT-AATAATTTTA
1 TATTTTAAATAATTTTA
458811 TATTTTAAAATAATTTTA
1 TATTTT-AAATAATTTTA
458829 TATTTT
1 TATTTT
458835 TGAAAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 6 0.27
18 16 0.73
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTTTAAATAATTTTA
Found at i:458841 original size:21 final size:18
Alignment explanation
Indices: 458801--458860 Score: 75
Period size: 21 Copynumber: 3.1 Consensus size: 18
458791 TGATTATTTT
458801 AATAATTTTATATTTTAA
1 AATAATTTTATATTTTAA
458819 AATAATTTTATATTTTTGAAA
1 AATAATTTTATA-TTTT--AA
*
458840 AATAATTTTAATAATTTAA
1 AATAATTTT-ATATTTTAA
458859 AA
1 AA
458861 ATCATTTGCT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
18 12 0.32
19 8 0.22
21 14 0.38
22 3 0.08
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
AATAATTTTATATTTTAA
Found at i:458862 original size:20 final size:19
Alignment explanation
Indices: 458801--458867 Score: 73
Period size: 21 Copynumber: 3.4 Consensus size: 19
458791 TGATTATTTT
*
458801 AATAATTTTAT-ATTTTAA
1 AATAATTTTATAATTTAAA
*
458819 AATAATTTTATATTTTTGAAA
1 AATAATTTTATA-ATTT-AAA
458840 AATAATTTTAATAATTTAAA
1 AATAATTTT-ATAATTTAAA
*
458860 AATCATTT
1 AATAATTT
458868 GCTGACATGG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
18 11 0.27
20 13 0.32
21 14 0.34
22 3 0.07
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (19 bp):
AATAATTTTATAATTTAAA
Found at i:460231 original size:3 final size:3
Alignment explanation
Indices: 460223--460248 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
460213 TAAATAAGTT
460223 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
460249 TATTAATAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:460484 original size:3 final size:3
Alignment explanation
Indices: 460476--460512 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
460466 AAAGTTTTCT
*
460476 TAA TAA TAA CAA TAA TAA TAA TAA TAA TAA TACA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
460513 AAAGAACGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:461399 original size:29 final size:29
Alignment explanation
Indices: 461366--461738 Score: 236
Period size: 29 Copynumber: 12.8 Consensus size: 29
461356 GGAGGTTCTT
*
461366 AAACTATCCAAAAATTACATTTTGACCCC
1 AAACTTTCCAAAAATTACATTTTGACCCC
* *
461395 AAACTTTCCAAAAATTACATTTTTACCCTT
1 AAACTTTCCAAAAATTACATTTTGACCC-C
*
461425 AAACTTTCCAAAAATTACATTTT-ACCCTT
1 AAACTTTCCAAAAATTACATTTTGACCC-C
461454 AAACTTTCC-AAAATTACATTTGTGACCCCC
1 AAACTTTCCAAAAATTACATTT-TGA-CCCC
* * *
461484 AAACTTTCTAAAAATTACATTTTTACCTTC
1 AAACTTTCCAAAAATTACATTTTGACC-CC
*
461514 AAACTTTCC-AAAATTCCATTTTTGACCCC
1 AAACTTTCCAAAAATTACA-TTTTGACCCC
* *
461543 AAACCTTCC-AATATTACCATTTT-ACCCC
1 AAACTTTCCAAAAATTA-CATTTTGACCCC
** * * * *
461571 TGA-TGTCTAAAAATTCCATTTTGACCTCG
1 AAACTTTCCAAAAATTACATTTTGACC-CC
*
461600 AACCTTT-C-AAAATTACCATTTT-ACCCC
1 AAACTTTCCAAAAATTA-CATTTTGACCCC
* * * * *
461627 TGAA-TGTCTAAAAATTCCATTTTTAACCCC
1 -AAACTTTCCAAAAATTACA-TTTTGACCCC
* *
461657 GAACCTTCC-AAAATTACCATTTT-ACCCTC
1 AAACTTTCCAAAAATTA-CATTTTGACCC-C
* * *
461686 -GA-TTGTCAAAAAATTCCATTTTTGACCCC
1 AAACTT-TCCAAAAATTACA-TTTTGACCCC
*
461715 AAA-TTTATCAAAAATTACCATTTT
1 AAACTTT-CCAAAAATTA-CATTTT
461739 ACCTCCCAAG
Statistics
Matches: 270, Mismatches: 46, Indels: 55
0.73 0.12 0.15
Matches are distributed among these distances:
27 12 0.04
28 47 0.17
29 113 0.42
30 81 0.30
31 17 0.06
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (29 bp):
AAACTTTCCAAAAATTACATTTTGACCCC
Found at i:461458 original size:59 final size:58
Alignment explanation
Indices: 461366--461569 Score: 236
Period size: 59 Copynumber: 3.5 Consensus size: 58
461356 GGAGGTTCTT
* * *
461366 AAACTATCCAAAAATTACATTTTGACCC-CAAACTTTCCAAAAATTACATTTTTACCCTT
1 AAACTTTCCAAAAATTACATTTT-ACCCTTAAACTTTCC-AAAATTACATTTTTACCCTC
* *
461425 AAACTTTCCAAAAATTACATTTTACCCTTAAACTTTCCAAAATTACATTTGTGACCCCC
1 AAACTTTCCAAAAATTACATTTTACCCTTAAACTTTCCAAAATTACATTT-TTACCCTC
* *
461484 AAACTTTCTAAAAATTACATTTTTA-CCTTCAAACTTTCCAAAATTCCATTTTTGACCC-C
1 AAACTTTCCAAAAATTACA-TTTTACCCTT-AAACTTTCCAAAATTACATTTTT-ACCCTC
* *
461543 AAACCTTCC-AATATTACCATTTTACCC
1 AAACTTTCCAAAAATTA-CATTTTACCC
461570 CTGATGTCTA
Statistics
Matches: 127, Mismatches: 11, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
58 27 0.21
59 71 0.56
60 29 0.23
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.35
Consensus pattern (58 bp):
AAACTTTCCAAAAATTACATTTTACCCTTAAACTTTCCAAAATTACATTTTTACCCTC
Found at i:461676 original size:58 final size:58
Alignment explanation
Indices: 461523--461741 Score: 300
Period size: 58 Copynumber: 3.8 Consensus size: 58
461513 CAAACTTTCC
*
461523 AAAATTCCATTTTTGACCCCAAACCTTCCAATATTACCATTTTACCCCTG-ATGTCTA
1 AAAATTCCATTTTTGACCCCAAACCTTCCAAAATTACCATTTTACCCCTGAATGTCTA
* * *
461580 AAAATTCCA-TTTTGACCTCGAACCTTTCAAAATTACCATTTTACCCCTGAATGTCTA
1 AAAATTCCATTTTTGACCCCAAACCTTCCAAAATTACCATTTTACCCCTGAATGTCTA
* * * *
461637 AAAATTCCATTTTTAACCCCGAACCTTCCAAAATTACCATTTTA-CCCTCGATTGTCAA
1 AAAATTCCATTTTTGACCCCAAACCTTCCAAAATTACCATTTTACCCCT-GAATGTCTA
** *
461695 AAAATTCCATTTTTGACCCCAAATTTATCAAAAATTACCATTTTACC
1 AAAATTCCATTTTTGACCCCAAACCT-TCCAAAATTACCATTTTACC
461742 TCCCAAGTGT
Statistics
Matches: 143, Mismatches: 14, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
56 36 0.25
57 29 0.20
58 60 0.42
59 17 0.12
60 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (58 bp):
AAAATTCCATTTTTGACCCCAAACCTTCCAAAATTACCATTTTACCCCTGAATGTCTA
Found at i:461786 original size:29 final size:30
Alignment explanation
Indices: 461723--461787 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
461713 CCAAATTTAT
* **
461723 CAAAAATTACCATTTTACCTCCCAAGTGTC
1 CAAAAATTACCATTCTACCTCCCAAGCATC
*
461753 C-AAAATTACCATTCTACC-CCCAGGCATC
1 CAAAAATTACCATTCTACCTCCCAAGCATC
461781 CAAAAAT
1 CAAAAAT
461788 CACATTTTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 8 0.27
29 21 0.70
30 1 0.03
ACGTcount: A:0.37, C:0.32, G:0.06, T:0.25
Consensus pattern (30 bp):
CAAAAATTACCATTCTACCTCCCAAGCATC
Found at i:472843 original size:59 final size:58
Alignment explanation
Indices: 472712--472913 Score: 189
Period size: 59 Copynumber: 3.4 Consensus size: 58
472702 CCATCTTTTA
* * *
472712 ATCTGATAAAAAAATTCAAATTTTTGGGTGTTGACCATGCAAT-AGCCGACACCTCCT-TTCT
1 ATCTGATAAAAAAATT-AAATTTTT-TGTGTTGGCTATGCAATGA-CCGACACC-CCTATT-T
* * *
472773 GTCAGAT-AAAAAATTTAATTTTTTAGTGTTGGCTATGCAATGACCGACACCCCTATTT
1 ATCTGATAAAAAAATTAAATTTTTT-GTGTTGGCTATGCAATGACCGACACCCCTATTT
* * ** *
472831 ATCTGATAAAAAAATCAAAATTTATTGTGTTGG-TCATGCAATGACTAACACCCTTATTT
1 ATCTGATAAAAAAAT-TAAATTTTTTGTGTTGGCT-ATGCAATGACCGACACCCCTATTT
*
472890 A-CTGATAAAAAAATCAAATTTTTT
1 ATCTGATAAAAAAATTAAATTTTTT
472914 TTTAGATAAA
Statistics
Matches: 119, Mismatches: 16, Indels: 16
0.79 0.11 0.11
Matches are distributed among these distances:
57 8 0.07
58 23 0.19
59 67 0.56
60 16 0.13
61 5 0.04
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (58 bp):
ATCTGATAAAAAAATTAAATTTTTTGTGTTGGCTATGCAATGACCGACACCCCTATTT
Found at i:472923 original size:25 final size:26
Alignment explanation
Indices: 472893--472942 Score: 84
Period size: 27 Copynumber: 1.9 Consensus size: 26
472883 CTTATTTACT
472893 GATAAAAAAA-TCAAATTTTTTTTTA
1 GATAAAAAAATTCAAATTTTTTTTTA
472918 GATAAAAAAATTTCAAATTTTTTTT
1 GATAAAAAAA-TTCAAATTTTTTTT
472943 GGTGTTGGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 10 0.43
27 13 0.57
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (26 bp):
GATAAAAAAATTCAAATTTTTTTTTA
Found at i:473156 original size:60 final size:60
Alignment explanation
Indices: 472922--473148 Score: 217
Period size: 60 Copynumber: 3.8 Consensus size: 60
472912 TTTTTAGATA
* * * *
472922 AAAAAATTTCAAATTTTTTTTGGTGTTGGTCAT-TACATGACCGACA-CTCTTTTTTATCTGAAT
1 AAAAAA-TTC-AATTTTTTTT-GTGTTGGCCATGT-CATGGCAGACACCCCTTTTTTATCTG-AT
* ** * * * *
472985 AAAAAA-TCAAATTTTTGGGTGTTGACCATGTCATGGCTGACACCCCTTTTTTGTCAGAT
1 AAAAAATTCAATTTTTTTTGTGTTGGCCATGTCATGGCAGACACCCCTTTTTTATCTGAT
* * * * * *
473044 AAACAATTCGATTTTTTTTTTGTTGGTCATGCCATGGCCGACACCCCTTTTTTATCTGAT
1 AAAAAATTCAATTTTTTTTGTGTTGGCCATGTCATGGCAGACACCCCTTTTTTATCTGAT
* *
473104 AAAAAATTTAATTTTTTTTGTGTTGGCCATGTAATGGCAGACACC
1 AAAAAATTCAATTTTTTTTGTGTTGGCCATGTCATGGCAGACACC
473149 AACTTTTTCT
Statistics
Matches: 131, Mismatches: 30, Indels: 9
0.77 0.18 0.05
Matches are distributed among these distances:
59 25 0.19
60 98 0.75
61 2 0.02
63 6 0.05
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.41
Consensus pattern (60 bp):
AAAAAATTCAATTTTTTTTGTGTTGGCCATGTCATGGCAGACACCCCTTTTTTATCTGAT
Found at i:473156 original size:120 final size:120
Alignment explanation
Indices: 472934--473156 Score: 288
Period size: 120 Copynumber: 1.9 Consensus size: 120
472924 AAAATTTCAA
* *
472934 ATTTTTTTTGGTGTTGGTCATTACATGACCGACACTCTTTTTTATCTGAATAAAAAATCAAATTT
1 ATTTTTTTTGGTGTTGGTCATGACATGACCGACACCCTTTTTTATCTGAATAAAAAATCAAATTT
* * *
472999 TTGGGTGTTGACCATGTCATGGCTGACACCCCTTTTTTGTCAGATAAACAATTCG
66 TTGGGTGTTGACCATGTAATGGCAGACACCACTTTTTTGTCAGATAAACAATTCG
* * * * *
473054 ATTTTTTTT-TTGTTGGTCATGCCATGGCCGACACCCCTTTTTTATCTG-ATAAAAAATTTAATT
1 ATTTTTTTTGGTGTTGGTCATGACATGACCGACA-CCCTTTTTTATCTGAATAAAAAA-TCAAAT
** *
473117 TTTTTTGTGTTGGCCATGTAATGGCAGACACCAACTTTTT
64 TTTTGGGTGTTGACCATGTAATGGCAGACACC-ACTTTTT
473157 CTTATTCTCT
Statistics
Matches: 87, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
119 28 0.32
120 53 0.61
121 6 0.07
ACGTcount: A:0.24, C:0.17, G:0.16, T:0.42
Consensus pattern (120 bp):
ATTTTTTTTGGTGTTGGTCATGACATGACCGACACCCTTTTTTATCTGAATAAAAAATCAAATTT
TTGGGTGTTGACCATGTAATGGCAGACACCACTTTTTTGTCAGATAAACAATTCG
Found at i:474712 original size:61 final size:60
Alignment explanation
Indices: 474626--475053 Score: 228
Period size: 61 Copynumber: 7.1 Consensus size: 60
474616 CATTGCATGG
* *
474626 CCAACACCAAAAAAATTTAATTTTTTACCAGATAAAAAAGGGGGTGTCGCCCATGGATGA
1 CCAACACAAAAAAAATTTAATTTTTTACCAGATAAAAAAGGGGGTGTCGACCATGGATGA
* *** * * ** *
474686 CCAACATAAAAAAAATTTTAAATTTTTTATTTGA-CAAAAACGGGGTGTCGATTATTGCATGA
1 CCAACACAAAAAAAA-TTT-AATTTTTTACCAGATAAAAAAGGGGGTGTCGACCA-TGGATGA
* * * * * *
474748 CCAATACAAAAAAAATTGATTTTTTTACCAGATAAAAAAGGGAGTGTTGGCCATGGCATGA
1 CCAACACAAAAAAAATTTAATTTTTTACCAGATAAAAAAGGGGGTGTCGACCATGG-ATGA
* *** * * * * *
474809 CCAACACAAAAAAAATTCGAATTTTTTATTTGA-CAAAAAGGGGGTGTCGGCTATGGCGTAA
1 CCAACACAAAAAAAATT-TAATTTTTTACCAGATAAAAAAGGGGGTGTCGACCATGG-ATGA
* ** * * * * *
474870 CCAATAC-TCAAAAATTTGATTTTTTATCTGA-ATAAAAA-GGGGTGTCGACCATGCAATGG
1 CCAACACAAAAAAAATTTAATTTTTTACCAGATA-AAAAAGGGGGTGTCGACCATG-GATGA
* * * * * * *
474929 CCAACACCAAAAAAATTGATTTTTTTTATCA-ATAAATAA--GGGTGTCGATCATTGCATGA
1 CCAACACAAAAAAAATTTA-ATTTTTTACCAGATAAAAAAGGGGGTGTCGACCA-TGGATGA
* * * * * * * * * *
474988 CCAATA-ACAAAAAATTGAATTTTTTATCTGA-CAAAAAGAGGATGTCGACCATTGCATGG
1 CCAACACAAAAAAAATTTAATTTTTTACCAGATAAAAAAGGGGGTGTCGACCA-TGGATGA
475047 CCAACAC
1 CCAACAC
475054 TTGAAATTTT
Statistics
Matches: 280, Mismatches: 72, Indels: 32
0.73 0.19 0.08
Matches are distributed among these distances:
57 13 0.05
58 11 0.04
59 73 0.26
60 51 0.18
61 91 0.32
62 41 0.15
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.28
Consensus pattern (60 bp):
CCAACACAAAAAAAATTTAATTTTTTACCAGATAAAAAAGGGGGTGTCGACCATGGATGA
Found at i:474822 original size:60 final size:59
Alignment explanation
Indices: 474620--475172 Score: 311
Period size: 59 Copynumber: 9.2 Consensus size: 59
474610 CAATTTCATT
* * * *
474620 GCATGGCCAACACCAAAAAAATTTAATTTTTTACCAGATAAAAAAGGGGGTGTCGCCCATG
1 GCATGACCAACA-CAAAAAAATTGAATTTTTTATCAGATAAAAAA-GGGGTGTCGACCATG
* * ** * * ** *
474681 G-ATGACCAACATAAAAAAAATTTTAAATTTTTTATTTGACAAAAACGGGGTGTCGATTATT
1 GCATGACCAACA-CAAAAAAA--TTGAATTTTTTATCAGATAAAAAAGGGGTGTCGACCATG
* * * * *
474742 GCATGACCAATACAAAAAAAATTGATTTTTTTACCAGATAAAAAAGGGAGTGTTGGCCATG
1 GCATGACCAACAC-AAAAAAATTGAATTTTTTATCAGATAAAAAAGGG-GTGTCGACCATG
** * * * *
474803 GCATGACCAACACAAAAAAAATTCGAATTTTTTATTTGACAAAAAGGGGGTGTCGGCTATG
1 GCATGACCAACAC-AAAAAAATT-GAATTTTTTATCAGATAAAAAAGGGGTGTCGACCATG
* * * * * *
474864 GCGTAACCAATACTCAAAAATTTG-ATTTTTTATCTGA-ATAAAAAGGGGTGTCGACCAT-
1 GCATGACCAACAC-AAAAAAATTGAATTTTTTATCAGATA-AAAAAGGGGTGTCGACCATG
* * * * *
474922 GCAATGGCCAACACCAAAAAAATTGATTTTTTTTATCA-ATAAATAA-GGGTGTCGATCATT
1 GC-ATGACCAACA-CAAAAAAATTGA-ATTTTTTATCAGATAAAAAAGGGGTGTCGACCATG
* * * * *
474982 GCATGACCAATA-ACAAAAAATTGAATTTTTTATCTGA-CAAAAAGAGGATGTCGACCATT
1 GCATGACCAACACA-AAAAAATTGAATTTTTTATCAGATAAAAAAG-GGGTGTCGACCATG
* ** ** * * * *
475041 GCATGGCCAACACTTGAAATTTTGATTTTTTTATCAGAT-TAAAAGGGAGTATTGACCAT-
1 GCATGACCAACAC-AAAAAAATTGAATTTTTTATCAGATAAAAAAGGG-GTGTCGACCATG
* * * ** * * *
475100 GCAATGGCCAACAC-GAAAACTT-TTTTTTTCTATCAAATAAAAAAGGGGGTGTCGGCCATC
1 GC-ATGACCAACACAAAAAAATTGAATTTTT-TATCAGATAAAAAA-GGGGTGTCGACCATG
*
475160 GCATGGCCAACAC
1 GCATGACCAACAC
475173 TAAATTTTTT
Statistics
Matches: 382, Mismatches: 84, Indels: 54
0.73 0.16 0.10
Matches are distributed among these distances:
57 20 0.05
58 27 0.07
59 111 0.29
60 92 0.24
61 79 0.21
62 53 0.14
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (59 bp):
GCATGACCAACACAAAAAAATTGAATTTTTTATCAGATAAAAAAGGGGTGTCGACCATG
Found at i:474834 original size:122 final size:120
Alignment explanation
Indices: 474617--475053 Score: 408
Period size: 122 Copynumber: 3.6 Consensus size: 120
474607 CTACAATTTC
* * * * *
474617 ATTGCATGGCCAACACCAAAAAAATTTAATTTTTTACCAGATAAAAAAGGGGGTGTCGCCCATGG
1 ATTGCATGACCAATACAAAAAAAATTGAATTTTTTACCAGATAAAAAA-GGGGTGTCGACCATGG
* * *
474682 -ATGACCAACATAAAAAAAATTTTAAATTTTTTATTTGACAAAAACGGGGTGTCGATT
65 CATGACCAACACAAAAAAAA--TTGAATTTTTTATTTGACAAAAAAGGGGTGTCGATT
* * *
474739 ATTGCATGACCAATACAAAAAAAATTGATTTTTTTACCAGATAAAAAAGGGAGTGTTGGCCATGG
1 ATTGCATGACCAATACAAAAAAAATTGAATTTTTTACCAGATAAAAAAGGG-GTGTCGACCATGG
* **
474804 CATGACCAACACAAAAAAAATTCGAATTTTTTATTTGACAAAAAGGGGGTGTCGGCT
65 CATGACCAACACAAAAAAAATT-GAATTTTTTATTTGACAAAAAAGGGGTGTCGATT
* * * ** * * *
474861 ATGGCGTAACCAATACTCAAAAATTTG-ATTTTTTATCTGA-ATAAAAAGGGGTGTCGACCAT-G
1 ATTGCATGACCAATACAAAAAAAATTGAATTTTTTACCAGATA-AAAAAGGGGTGTCGACCATGG
* * * *
474923 CAATGGCCAACACCAAAAAAATTG-A-TTTTT-TTT-ATCAATAAATAAGGGTGTCGATC
65 C-ATGACCAACACAAAAAAAATTGAATTTTTTATTTGA-CAA-AAA-AGGGGTGTCGATT
* * * * * *
474979 ATTGCATGACCAATA-ACAAAAAATTGAATTTTTTATCTGA-CAAAAAGAGGATGTCGACCATTG
1 ATTGCATGACCAATACAAAAAAAATTGAATTTTTTACCAGATAAAAAAG-GGGTGTCGACCATGG
*
475042 CATGGCCAACAC
65 CATGACCAACAC
475054 TTGAAATTTT
Statistics
Matches: 267, Mismatches: 37, Indels: 26
0.81 0.11 0.08
Matches are distributed among these distances:
115 1 0.00
116 6 0.02
117 23 0.09
118 57 0.21
119 5 0.02
120 29 0.11
121 23 0.09
122 105 0.39
123 18 0.07
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (120 bp):
ATTGCATGACCAATACAAAAAAAATTGAATTTTTTACCAGATAAAAAAGGGGTGTCGACCATGGC
ATGACCAACACAAAAAAAATTGAATTTTTTATTTGACAAAAAAGGGGTGTCGATT
Found at i:476005 original size:36 final size:37
Alignment explanation
Indices: 475965--476068 Score: 120
Period size: 41 Copynumber: 2.6 Consensus size: 37
475955 TCGATTATAA
*
475965 TATGAGA-AAGTCAAATACTGAAAAAATTATTAGTGT
1 TATGAGAGAAGACAAATACTGAAAAAATTATTAGTGT
476001 TATGAGACAGTGAAGACAAATACTGAAAAAATTATTAGTGT
1 TATGAG--A--GAAGACAAATACTGAAAAAATTATTAGTGT
476042 TATGAGACAGTGAAGACAAATACTGAA
1 TATGAG--A--GAAGACAAATACTGAA
476069 GGCATTTGGA
Statistics
Matches: 62, Mismatches: 1, Indels: 5
0.91 0.01 0.07
Matches are distributed among these distances:
36 6 0.10
38 1 0.02
41 55 0.89
ACGTcount: A:0.47, C:0.08, G:0.19, T:0.26
Consensus pattern (37 bp):
TATGAGAGAAGACAAATACTGAAAAAATTATTAGTGT
Found at i:476033 original size:41 final size:41
Alignment explanation
Indices: 475976--476068 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
475966 ATGAGAAAGT
475976 CAAATACTGAAAAAATTATTAGTGTTATGAGACAGTGAAGA
1 CAAATACTGAAAAAATTATTAGTGTTATGAGACAGTGAAGA
476017 CAAATACTGAAAAAATTATTAGTGTTATGAGACAGTGAAGA
1 CAAATACTGAAAAAATTATTAGTGTTATGAGACAGTGAAGA
476058 CAAATACTGAA
1 CAAATACTGAA
476069 GGCATTTGGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.47, C:0.09, G:0.18, T:0.26
Consensus pattern (41 bp):
CAAATACTGAAAAAATTATTAGTGTTATGAGACAGTGAAGA
Found at i:487761 original size:26 final size:27
Alignment explanation
Indices: 487723--487775 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
487713 GTTATTAAAT
*
487723 TTTAATAAGATTATTATT-AAATATAA
1 TTTAATAAGATTATCATTAAAATATAA
487749 TTTAATATA-ATTATCATTAAAATATAA
1 TTTAATA-AGATTATCATTAAAATATAA
487776 ATGAATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 15 0.62
27 9 0.38
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (27 bp):
TTTAATAAGATTATCATTAAAATATAA
Found at i:487782 original size:27 final size:26
Alignment explanation
Indices: 487732--487782 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
487722 TTTTAATAAG
* * *
487732 ATTATTATTAAATATAATTTAATATA
1 ATTATCATTAAATATAAATGAATATA
487758 ATTATCATTAAAATATAAATGAATA
1 ATTATCATT-AAATATAAATGAATA
487783 AAAATAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 8 0.38
27 13 0.62
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (26 bp):
ATTATCATTAAATATAAATGAATATA
Found at i:503923 original size:22 final size:22
Alignment explanation
Indices: 503897--503938 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
503887 TTAAAAAAAA
503897 TTTTTATGTA-GATTTTTTTTTT
1 TTTTTAT-TATGATTTTTTTTTT
*
503919 TTTTTATTATTATTTTTTTT
1 TTTTTATTATGATTTTTTTT
503939 ATGAACTGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.14, C:0.00, G:0.05, T:0.81
Consensus pattern (22 bp):
TTTTTATTATGATTTTTTTTTT
Found at i:505643 original size:15 final size:16
Alignment explanation
Indices: 505623--505655 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
505613 ATAACTTAAA
*
505623 TTCAATA-TTTAATTT
1 TTCAATACTTAAATTT
505638 TTCAATACTTAAATTT
1 TTCAATACTTAAATTT
505654 TT
1 TT
505656 AATTTATAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (16 bp):
TTCAATACTTAAATTT
Found at i:508098 original size:21 final size:21
Alignment explanation
Indices: 508074--508148 Score: 141
Period size: 21 Copynumber: 3.6 Consensus size: 21
508064 AGGAGAAGCA
*
508074 TGTCTTGAGACATGACTTCGC
1 TGTCTCGAGACATGACTTCGC
508095 TGTCTCGAGACATGACTTCGC
1 TGTCTCGAGACATGACTTCGC
508116 TGTCTCGAGACATGACTTCGC
1 TGTCTCGAGACATGACTTCGC
508137 TGTCTCGAGACA
1 TGTCTCGAGACA
508149 CAACACACAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.20, C:0.27, G:0.24, T:0.29
Consensus pattern (21 bp):
TGTCTCGAGACATGACTTCGC
Found at i:514953 original size:22 final size:21
Alignment explanation
Indices: 514928--514974 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
514918 TGATTGATAA
514928 AAAAAGGTAAATAGAAAATTAT
1 AAAAAGGTAAATA-AAAATTAT
** *
514950 AAAAATTTAAATATAAATTAT
1 AAAAAGGTAAATAAAAATTAT
514971 AAAA
1 AAAA
514975 TTTAAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (21 bp):
AAAAAGGTAAATAAAAATTAT
Found at i:516741 original size:3 final size:3
Alignment explanation
Indices: 516735--516926 Score: 181
Period size: 3 Copynumber: 62.7 Consensus size: 3
516725 TCATAACGAC
516735 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
516783 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATT AAT ATT AAT GAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* ** ** *
516831 ATT AAT AAT AAT AA- ACAGTT TTT TTT AAT AAT CATT AAT AAT AAT AACT
1 AAT AAT AAT AAT AAT A-A--T AAT AAT AAT AAT -AAT AAT AAT AAT AA-T
* ** * *
516880 -GT TTT AAT GAT AAT AAT AAT AAT AAT AAT AAT ATT AATT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT
516925 AA
1 AA
516927 AAAAAGAAAC
Statistics
Matches: 157, Mismatches: 24, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
2 2 0.01
3 149 0.95
4 6 0.04
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:518034 original size:29 final size:28
Alignment explanation
Indices: 517992--518181 Score: 173
Period size: 29 Copynumber: 6.9 Consensus size: 28
517982 TAGGAGGTCT
517992 CGAAACTTCCAAAAATTCCATTTTGACCC
1 CGAAACTTCCAAAAATTCCATTTT-ACCC
*
518021 CGAAACTTCCAAAAATTCTATTTTACCCC
1 CGAAACTTCCAAAAATTCCATTTTA-CCC
*
518050 CG-AACTTCCAAAAATTCTATTTT----
1 CGAAACTTCCAAAAATTCCATTTTACCC
* *
518073 --TAAC-T-CAAAACTTCCATTTTAACCC
1 CGAAACTTCCAAAAATTCCATTTT-ACCC
* *
518098 CAAAACTTCCAAAAATTCAAATTTTACCC
1 CGAAACTTCCAAAAATTC-CATTTTACCC
* *
518127 CTAAACTTCCAAAAATTCCATTTTTGACCT
1 CGAAACTTCCAAAAATTCCA-TTTT-ACCC
*
518157 CAAAACTTCCAAAAATTACCATTTT
1 CGAAACTTCCAAAAATT-CCATTTT
518182 GCCCTCGGAT
Statistics
Matches: 136, Mismatches: 10, Indels: 29
0.78 0.06 0.17
Matches are distributed among these distances:
20 13 0.10
21 1 0.01
22 3 0.02
27 3 0.02
28 24 0.18
29 61 0.45
30 28 0.21
31 3 0.02
ACGTcount: A:0.37, C:0.28, G:0.03, T:0.32
Consensus pattern (28 bp):
CGAAACTTCCAAAAATTCCATTTTACCC
Found at i:518123 original size:49 final size:48
Alignment explanation
Indices: 518029--518137 Score: 128
Period size: 49 Copynumber: 2.2 Consensus size: 48
518019 CCCGAAACTT
* * ** * *
518029 CCAAAAATTCTATTTTACCCCCGAACTTCCAAAAATTCTATTTTTAAC
1 CCAAAACTTCCATTTTACCCCAAAACTTCCAAAAATTCAAATTTTAAC
* *
518077 TCAAAACTTCCATTTTAACCCCAAAACTTCCAAAAATTCAAATTTTACC
1 CCAAAACTTCCATTTT-ACCCCAAAACTTCCAAAAATTCAAATTTTAAC
*
518126 CCTAAACTTCCA
1 CCAAAACTTCCA
518138 AAAATTCCAT
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
48 13 0.26
49 37 0.74
ACGTcount: A:0.38, C:0.29, G:0.01, T:0.32
Consensus pattern (48 bp):
CCAAAACTTCCATTTTACCCCAAAACTTCCAAAAATTCAAATTTTAAC
Found at i:518266 original size:58 final size:59
Alignment explanation
Indices: 518078--518267 Score: 178
Period size: 59 Copynumber: 3.3 Consensus size: 59
518068 ATTTTTAACT
* * * * **
518078 CAAAACTTCCATTTT-AACCCCAAAACTTCCAAAAATT-CAAATTTTACCCCTAAACT-TC
1 CAAAAATTCCATTTTCGACCTCAAAACTTCCAAAAATTAC-CATTTTACCCCCGAA-TGTC
* * * *
518136 CAAAAATTCCATTTTTGACCTCAAAACTTCCAAAAATTACCATTTTGCCCTCGGATGTC
1 CAAAAATTCCATTTTCGACCTCAAAACTTCCAAAAATTACCATTTTACCCCCGAATGTC
* *
518195 CAAAAACTT-CATTTTCGACCTCGAAAC-TCTC-AAAATTACCCTTTTACCCCCGAATG-C
1 CAAAAA-TTCCATTTTCGACCTCAAAACTTC-CAAAAATTACCATTTTACCCCCGAATGTC
518252 CTAAAAATTCCATTTT
1 C-AAAAATTCCATTTT
518268 AACTCTGAAT
Statistics
Matches: 110, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
57 4 0.04
58 49 0.45
59 54 0.49
60 3 0.03
ACGTcount: A:0.35, C:0.29, G:0.05, T:0.31
Consensus pattern (59 bp):
CAAAAATTCCATTTTCGACCTCAAAACTTCCAAAAATTACCATTTTACCCCCGAATGTC
Found at i:529054 original size:19 final size:19
Alignment explanation
Indices: 529032--529090 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 19
529022 TTTATTTCTT
529032 ATATT-AATTTCAATTTTAA
1 ATATTAAATTT-AATTTTAA
*
529051 ATATTAAATTTATTTTTAA
1 ATATTAAATTTAATTTTAA
529070 A-ATTTAAATTT-ATTTATAA
1 ATA-TTAAATTTAATTT-TAA
529089 AT
1 AT
529091 TTTTCTAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
18 4 0.12
19 25 0.74
20 5 0.15
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (19 bp):
ATATTAAATTTAATTTTAA
Found at i:529092 original size:18 final size:17
Alignment explanation
Indices: 529044--529092 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 17
529034 ATTAATTTCA
529044 ATTTTAAATATTAAATTT
1 ATTTTAAAT-TTAAATTT
529062 ATTTTTAAAATTTAAATTT
1 A-TTTT-AAATTTAAATTT
529081 ATTTATAAATTT
1 ATTT-TAAATTT
529093 TTCTAATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 10 0.36
19 14 0.50
20 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:529890 original size:30 final size:30
Alignment explanation
Indices: 529856--529915 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
529846 TTAGCCATCC
*
529856 AACTTTAGTAAGTTTTCATTTTGGTCACTT
1 AACTTTAGTAAGTTTTCATTTTGGCCACTT
529886 AACTTTAGTAAGTTTTCATTTTGGCCACTT
1 AACTTTAGTAAGTTTTCATTTTGGCCACTT
529916 GTTTTATCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.23, C:0.15, G:0.13, T:0.48
Consensus pattern (30 bp):
AACTTTAGTAAGTTTTCATTTTGGCCACTT
Found at i:532379 original size:14 final size:15
Alignment explanation
Indices: 532360--532391 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
532350 AGAGATAAAT
532360 AAATAAAA-TTGTGA
1 AAATAAAATTTGTGA
532374 AAATAAAATTTGTGA
1 AAATAAAATTTGTGA
532389 AAA
1 AAA
532392 AGAAAGGAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.28
Consensus pattern (15 bp):
AAATAAAATTTGTGA
Found at i:533114 original size:27 final size:27
Alignment explanation
Indices: 533060--533115 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
533050 TTATTTTCTT
* **
533060 TTTATGTAAATACATACTAATTTTTTA
1 TTTATGTAAATACATACTAAATAATTA
*
533087 TTTATGTAAATACATATTAAATAATTA
1 TTTATGTAAATACATACTAAATAATTA
533114 TT
1 TT
533116 GTTTTTTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.50
Consensus pattern (27 bp):
TTTATGTAAATACATACTAAATAATTA
Found at i:537036 original size:15 final size:13
Alignment explanation
Indices: 537004--537046 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 13
536994 TTTAATGATA
537004 AATAGTTTTATTTT
1 AATA-TTTTATTTT
537018 AATATTTTATTAATT
1 AATATTTTATT--TT
537033 AATATTTTCATTTT
1 AATATTTT-ATTTT
537047 TTGTAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 7 0.27
14 6 0.23
15 10 0.38
16 3 0.12
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (13 bp):
AATATTTTATTTT
Found at i:537680 original size:24 final size:23
Alignment explanation
Indices: 537615--537686 Score: 81
Period size: 23 Copynumber: 3.1 Consensus size: 23
537605 AAAGTAGACG
*
537615 AAACGTGCCACAAGGTAGAGAAA
1 AAACGTGCCACAAGGCAGAGAAA
* * *
537638 AAACATGCCACAAGACAGAGGAA
1 AAACGTGCCACAAGGCAGAGAAA
* *
537661 AAACGTGCCATAAAGGCAGATAAA
1 AAACGTGCCA-CAAGGCAGAGAAA
537685 AA
1 AA
537687 CTAGAAAAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 28 0.72
24 11 0.28
ACGTcount: A:0.51, C:0.18, G:0.22, T:0.08
Consensus pattern (23 bp):
AAACGTGCCACAAGGCAGAGAAA
Found at i:540096 original size:58 final size:58
Alignment explanation
Indices: 540054--540276 Score: 274
Period size: 59 Copynumber: 3.8 Consensus size: 58
540044 TTCGAGGTCG
* *
540054 AAAATGGAGA-TTTTGGAGGTT-AAGGGAAAAAATGGAATTTTTGGAAGTTTCGGGGTGA
1 AAAATGG-GATTTTTGGAAGTTCAAGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGT-A
* * * *
540112 AAAATGGGATTTTTGAAAGTTCGAGGGTAAAAATGGAATTTTTAGAAGTATT-AGGGTAA
1 AAAATGGGATTTTTGGAAGTTCAAGGGTAAAAATGGAATTTTTGGAAGT-TTCGGGGT-A
* * * *
540171 AAAATGGGATTCTTGGAAATTC-GGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTTA
1 AAAATGGGATTTTTGGAAGTTCAAGGGTAAAAATGGAATTTTTGGAAGTTTCGGGG-TA
*
540229 AAAATGGAATTTTTGGAAGTTCAAGGGTAAAAATGGAATTTTTGGAAG
1 AAAATGGGATTTTTGGAAGTTCAAGGGTAAAAATGGAATTTTTGGAAG
540277 GTGTAGGGAC
Statistics
Matches: 142, Mismatches: 17, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
57 4 0.03
58 63 0.44
59 73 0.51
60 2 0.01
ACGTcount: A:0.36, C:0.02, G:0.30, T:0.32
Consensus pattern (58 bp):
AAAATGGGATTTTTGGAAGTTCAAGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTA
Found at i:540124 original size:29 final size:29
Alignment explanation
Indices: 539956--540276 Score: 241
Period size: 29 Copynumber: 10.9 Consensus size: 29
539946 TTTCGGATAC
* * *
539956 TCGGGGGAAAAATGGTAATTTTGGGAAAATT
1 TCGGGGTAAAAATGG-AATTTTTGG-AAGTT
* *
539987 TAGGGTTTAAAAATGGAATTTTTGGACA-TT
1 TCGGG-GTAAAAATGGAATTTTTGGA-AGTT
*
540017 T-GGGAGT-AAAAGGGTAA-TTTT-GAGAGTT
1 TCGGG-GTAAAAATGG-AATTTTTGGA-AGTT
* * *
540045 TCGAGGTCGAAAATGGAGA-TTTTGG-AGGT
1 TCGGGGT-AAAAATGGA-ATTTTTGGAAGTT
** *
540074 TAAGGGAAAAAATGGAATTTTTGGAAGTT
1 TCGGGGTAAAAATGGAATTTTTGGAAGTT
* *
540103 TCGGGGTGAAAAATGGGATTTTTGAAAG-T
1 TCGGGGT-AAAAATGGAATTTTTGGAAGTT
*
540132 TCGAGGGTAAAAATGGAATTTTTAGAAGTAT
1 TCG-GGGTAAAAATGGAATTTTTGGAAGT-T
* * * *
540163 T-AGGGTAAAAAATGGGATTCTTGGAA-AT
1 TCGGGGT-AAAAATGGAATTTTTGGAAGTT
540191 TCGGGGTAAAAATGGAATTTTTGGAAGTT
1 TCGGGGTAAAAATGGAATTTTTGGAAGTT
*
540220 TTGGGGTTAAAAATGGAATTTTTGGAAG-T
1 TCGGGG-TAAAAATGGAATTTTTGGAAGTT
*
540249 TCAAGGGTAAAAATGGAATTTTTGGAAG
1 TC-GGGGTAAAAATGGAATTTTTGGAAG
540277 GTGTAGGGAC
Statistics
Matches: 233, Mismatches: 37, Indels: 42
0.75 0.12 0.13
Matches are distributed among these distances:
27 4 0.02
28 48 0.21
29 80 0.34
30 77 0.33
31 16 0.07
32 8 0.03
ACGTcount: A:0.35, C:0.03, G:0.31, T:0.32
Consensus pattern (29 bp):
TCGGGGTAAAAATGGAATTTTTGGAAGTT
Found at i:540284 original size:29 final size:29
Alignment explanation
Indices: 540054--540284 Score: 197
Period size: 30 Copynumber: 7.9 Consensus size: 29
540044 TTCGAGGTCG
* *
540054 AAAATGGAGA-TTTTGG-AGGTTAAGGGAA
1 AAAATGGA-ATTTTTGGAAGGTTTAGGGTA
*
540082 AAAATGGAATTTTTGGAA-GTTTCGGGGTGA
1 AAAATGGAATTTTTGGAAGGTTT-AGGGT-A
* * *
540112 AAAATGGGATTTTT-GAAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGGTT-TAGGGTA
*
540141 AAAATGGAATTTTTAGAA-GTATTAGGGTAA
1 AAAATGGAATTTTTGGAAGGT-TTAGGGT-A
* * * **
540171 AAAATGGGATTCTTGGAA-ATTCGGGGTA
1 AAAATGGAATTTTTGGAAGGTTTAGGGTA
* *
540199 AAAATGGAATTTTTGGAAGTTTTGGGGTTA
1 AAAATGGAATTTTTGGAAGGTTTAGGG-TA
*
540229 AAAATGGAATTTTTGGAA-GTTCAAGGGTA
1 AAAATGGAATTTTTGGAAGGTT-TAGGGTA
*
540258 AAAATGGAATTTTTGGAAGGTGTAGGG
1 AAAATGGAATTTTTGGAAGGTTTAGGG
540285 ACCTCCAGGG
Statistics
Matches: 167, Mismatches: 23, Indels: 25
0.78 0.11 0.12
Matches are distributed among these distances:
27 1 0.01
28 34 0.20
29 65 0.39
30 67 0.40
ACGTcount: A:0.35, C:0.02, G:0.31, T:0.32
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGGTTTAGGGTA
Found at i:541239 original size:24 final size:21
Alignment explanation
Indices: 541201--541261 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 21
541191 TTTGTCTCCT
541201 TTTATTTATTTATTAACAATAATAA
1 TTTA-TTA-TTATTAACAA-AA-AA
* *
541226 TATTATTATTATTATCAAAACA
1 T-TTATTATTATTAACAAAAAA
541248 TTTATTATTATTAA
1 TTTATTATTATTAA
541262 TGAATATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
21 12 0.38
22 2 0.06
23 2 0.06
24 9 0.28
25 4 0.12
26 3 0.09
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTATTATTATTAACAAAAAA
Found at i:545526 original size:30 final size:29
Alignment explanation
Indices: 545480--545855 Score: 284
Period size: 30 Copynumber: 12.7 Consensus size: 29
545470 AGGTTAAGGG
545480 AAAAATTGGAATTTTTGGAAGTTTTGGGGT
1 AAAAA-TGGAATTTTTGGAAGTTTTGGGGT
* *
545510 CAAAAATGGGATTTTTGGAAG-TTCGAGGGT
1 -AAAAATGGAATTTTTGGAAGTTTTG-GGGT
**
545540 AAAAATGGAATTTTTGGAAGTTTTAAGGT
1 AAAAATGGAATTTTTGGAAGTTTTGGGGT
545569 AAAAAATGGAATTTTTGGAAG-TTTGAGGGT
1 -AAAAATGGAATTTTTGGAAGTTTTG-GGGT
* * *** *
545599 AAAAA-CGAATTTTTTAGAAGTTTCAAAGTT
1 AAAAATGGAA-TTTTTGGAAGTTT-TGGGGT
* * **
545629 AAAAAT-GAGATTCTTGGAAATTCGGGGGT
1 AAAAATGGA-ATTTTTGGAAGTTTTGGGGT
* *
545658 AAAAATGGAATTTTTGGAAGTTTTAGTGTT
1 AAAAATGGAATTTTTGGAAGTTTT-GGGGT
*
545688 AAAAAAT-GAGATTTTTGGAAG-TTCGAGGGT
1 -AAAAATGGA-ATTTTTGGAAGTTTTG-GGGT
*
545718 -AAAATGAAATTTTTGGAAGTTTTGGGGT
1 AAAAATGGAATTTTTGGAAGTTTTGGGGT
* * *
545746 CAAAAATGGGATTTTTGGAAG-TTCGATGGT
1 -AAAAATGGAATTTTTGGAAGTTTTG-GGGT
* **
545776 AAAAACGGAATTTTTTGGAAGTTTTGAGATT
1 AAAAATGGAA-TTTTTGGAAGTTTTG-GGGT
* *
545807 AAAAATGGGATTTTTGGAAG-TTCGAGGGT
1 AAAAATGGAATTTTTGGAAGTTTTG-GGGT
**
545836 AAAAATAAAATTTTTGGAAG
1 AAAAATGGAATTTTTGGAAG
545856 GTTTAGGGAC
Statistics
Matches: 273, Mismatches: 51, Indels: 44
0.74 0.14 0.12
Matches are distributed among these distances:
28 23 0.08
29 100 0.37
30 114 0.42
31 36 0.13
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTTTGGGGT
Found at i:545561 original size:59 final size:59
Alignment explanation
Indices: 545395--545855 Score: 476
Period size: 59 Copynumber: 7.8 Consensus size: 59
545385 TTTGGGGTTT
* * *
545395 AAAAATGGAATTTTTGGACA-TTC-AGGAGT-AAAAGGGTAA-TTTT-GAGAGTTTCGAGGTC
1 AAAAATGGGATTTTTGGA-AGTTCGAGG-GTAAAAATGG-AATTTTTGGA-AGTTTTGAGGTC
* * * *
545453 GAAAATGGAGA-TTTTGGAGGTT-AAGGG-AAAAATTGGAATTTTTGGAAGTTTTGGGGTC
1 AAAAATGG-GATTTTTGGAAGTTCGAGGGTAAAAA-TGGAATTTTTGGAAGTTTTGAGGTC
* *
545511 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTAAGGTA
1 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGAGGTC
* * * * ** * *
545570 AAAAATGGAATTTTTGGAAGTTTGAGGGTAAAAA-CGAATTTTTTAGAAGTTTCAAAGTT
1 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAA-TTTTTGGAAGTTTTGAGGTC
* * * * *
545629 AAAAATGAGATTCTTGGAAATTCGGGGGTAAAAATGGAATTTTTGGAAGTTTT-AGTGTTA
1 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGAG-G-TC
* * *
545689 AAAAATGAGATTTTTGGAAGTTCGAGGGT-AAAATGAAATTTTTGGAAGTTTTGGGGTC
1 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGAGGTC
* * * *
545747 AAAAATGGGATTTTTGGAAGTTCGATGGTAAAAACGGAATTTTTTGGAAGTTTTGAGATT
1 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAA-TTTTTGGAAGTTTTGAGGTC
**
545807 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATAAAATTTTTGGAAG
1 AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAG
545856 GTTTAGGGAC
Statistics
Matches: 339, Mismatches: 47, Indels: 33
0.81 0.11 0.08
Matches are distributed among these distances:
57 9 0.03
58 84 0.25
59 158 0.47
60 88 0.26
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (59 bp):
AAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGAGGTC
Found at i:546578 original size:7 final size:7
Alignment explanation
Indices: 546566--546590 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
546556 CCTCTCCTTC
546566 CCACGCA
1 CCACGCA
546573 CCACGCA
1 CCACGCA
546580 CCACGCA
1 CCACGCA
546587 CCAC
1 CCAC
546591 CGTCGAAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.60, G:0.12, T:0.00
Consensus pattern (7 bp):
CCACGCA
Found at i:546840 original size:15 final size:15
Alignment explanation
Indices: 546822--546870 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
546812 TTTATTTATT
546822 TATTATTATTATTAA
1 TATTATTATTATTAA
*
546837 TATTATTATTATCAAAA
1 TATTATTATTAT--TAA
546854 TATTTATTATTATTAA
1 TA-TTATTATTATTAA
546870 T
1 T
546871 GAATATTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 12 0.41
16 3 0.10
17 4 0.14
18 10 0.34
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTATTATTATTAA
Found at i:546842 original size:18 final size:18
Alignment explanation
Indices: 546821--546878 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
546811 ATTTATTTAT
*
546821 TTATTATTATTATTAATA
1 TTATTATTATTATAAATA
*
546839 TTATTATTATCA-AAATA
1 TTATTATTATTATAAATA
*
546856 TTTATTATTATTAATGAATA
1 -TTATTATTATT-ATAAATA
546876 TTA
1 TTA
546879 AGAAAAACTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
17 4 0.12
18 21 0.64
19 4 0.12
20 4 0.12
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (18 bp):
TTATTATTATTATAAATA
Found at i:552889 original size:6 final size:6
Alignment explanation
Indices: 552870--552978 Score: 79
Period size: 6 Copynumber: 19.2 Consensus size: 6
552860 CAATCTTTAA
* * * *
552870 TTAAAT TT--AT TTAAAT TTAAAT TT-ATT TTAAGT CTAACT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* * * **
552915 TT-ATT TTAAAT TTAAA- TTAAAT TT-AAT TTAAAC TAAAAT TTATTT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
552960 TTAAA- TTAAATT TTAAAT T
1 TTAAAT TTAAA-T TTAAAT T
552979 GAGTTTAAAG
Statistics
Matches: 79, Mismatches: 16, Indels: 16
0.71 0.14 0.14
Matches are distributed among these distances:
4 4 0.05
5 23 0.29
6 47 0.59
7 5 0.06
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (6 bp):
TTAAAT
Found at i:552913 original size:23 final size:22
Alignment explanation
Indices: 552883--552950 Score: 84
Period size: 23 Copynumber: 3.1 Consensus size: 22
552873 AATTTATTTA
*
552883 AATTTAAATTTATTTTAAGTCT
1 AATTTAAATTTATTTTAAATCT
*
552905 AACTTTAAATTTATTTTAAATTT
1 AA-TTTAAATTTATTTTAAATCT
* *
552928 AAATTAAATTTAATTTAAA-CT
1 AATTTAAATTTATTTTAAATCT
552949 AA
1 AA
552951 AATTTATTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
21 3 0.08
22 17 0.43
23 20 0.50
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.50
Consensus pattern (22 bp):
AATTTAAATTTATTTTAAATCT
Found at i:552924 original size:11 final size:11
Alignment explanation
Indices: 552878--552946 Score: 75
Period size: 11 Copynumber: 6.1 Consensus size: 11
552868 AATTAAATTT
552878 ATTTAAATTTAA
1 ATTT-AATTTAA
*
552890 ATTTATTTTAA
1 ATTTAATTTAA
* *
552901 GTCTAACTTTAA
1 ATTTAA-TTTAA
*
552913 ATTTATTTTAA
1 ATTTAATTTAA
*
552924 ATTTAAATTAA
1 ATTTAATTTAA
552935 ATTTAATTTAA
1 ATTTAATTTAA
552946 A
1 A
552947 CTAAAATTTA
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
11 34 0.74
12 12 0.26
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.52
Consensus pattern (11 bp):
ATTTAATTTAA
Done.