Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 129 of 203
Found at i:40958563 original size:40 final size:39
Alignment explanation
Indices: 40958487--40958563 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 39
40958477 ATTGTGCTGA
* * *
40958487 GATTGTATCCGGGTTAGAGACCCGCTGGCTTCATGCTAG
1 GATTGTATCCGGGTTAAAGACCCGCAGGCTTAATGCTAG
*
40958526 GATTGTATCCGGGTTTAAAGTCCCGCAGGCTTAATGCT
1 GATTGTATCCGGG-TTAAAGACCCGCAGGCTTAATGCT
40958564 GGTGAATTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
39 13 0.39
40 20 0.61
ACGTcount: A:0.19, C:0.22, G:0.29, T:0.30
Consensus pattern (39 bp):
GATTGTATCCGGGTTAAAGACCCGCAGGCTTAATGCTAG
Found at i:40962903 original size:14 final size:14
Alignment explanation
Indices: 40962875--40962917 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
40962865 GATATGAATG
*
40962875 AAAAAA-ATTTGTA
1 AAAAAATATTTATA
*
40962888 AAAATATATTTATA
1 AAAAAATATTTATA
40962902 AAAAAATATTTA-A
1 AAAAAATATTTATA
40962915 AAA
1 AAA
40962918 CTAAACAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 9 0.35
14 17 0.65
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (14 bp):
AAAAAATATTTATA
Found at i:40968324 original size:197 final size:195
Alignment explanation
Indices: 40967844--40968608 Score: 976
Period size: 197 Copynumber: 4.0 Consensus size: 195
40967834 AAGCCTCTAT
40967844 AAAGAAGTACCGACCGA-CGTTCTACTTCAAAATAAGGTTCCTCTAATGTTACACAGCAAAACCA
1 AAAGAAGTACCGACC-ATCGTTCTACTTCAAAATAAGGTTCCTCTAATGTTACACAGCAAAACCA
* *
40967908 ATAACCCAATTTCAAATTATTTAAGCATTGCTATTGCAGCAACTCAGAGATTGTGGATTCGAGCA
65 ATAACCCAATTTCAAATTATTCAAGCATTGCTATTGCAGCAACTCGGAGATTGTGGATTCGAGCA
* *
40967973 CGCTTAACTGCGTAATATCATCAAATTTAATTAGCTTC-GGTTTAC-AGGTAGTTTAG-AATTGT
130 CACTTAAGTGCGTAATATCATCAAATTTAATTAG--TCGGGTTTACGA-GTAGTTTAGAAATTG-
*
40968035 CAAAA
191 CCAAA
* *
40968040 AAAGAAGTACCGACCATCGTTCTACTTCAAAATAAGGTTCCTCTAATGTCACACGGCAAAACCAA
1 AAAGAAGTACCGACCATCGTTCTACTTCAAAATAAGGTTCCTCTAATGTTACACAGCAAAACCAA
* * * * * * *
40968105 TAACCCAATTTTAAATTTATTCAAGTATTGCTATTGCAACAACTTGGAGGTTATGGATTCGAACA
66 TAACCCAATTTCAAA-TTATTCAAGCATTGCTATTGCAGCAACTCGGAGATTGTGGATTCGAGCA
*
40968170 CACTTAAGTGCGTAATATCATCAAATTTAATTAGTCGGGGTCTACGAGTAGTTTAGAAATTTGCC
130 CACTTAAGTGCGTAATATCATCAAATTTAATTAGTC-GGGTTTACGAGTAGTTTAGAAA-TTGCC
40968235 AAA
193 AAA
* *
40968238 AAAGAAGTTCCGACCATCGTTCTACTTCAAAATGAGGTTCCTCTAATGTTACACAGCAAAACCAA
1 AAAGAAGTACCGACCATCGTTCTACTTCAAAATAAGGTTCCTCTAATGTTACACAGCAAAACCAA
* * * * *
40968303 AAACCCAATTTCAAATTATTCAAGCATAGCTATTGCAGCAACTTGGAGCTTGTGGATTTGAGCAC
66 TAACCCAATTTCAAATTATTCAAGCATTGCTATTGCAGCAACTCGGAGATTGTGGATTCGAGCAC
* * *
40968368 ACTTAAGTGTGT-A-GT-ATC-----T--TT--T-GGGTTTACG-GTAGTTTAGAAAATTGTCAA
131 ACTTAAGTGCGTAATATCATCAAATTTAATTAGTCGGGTTTACGAGTAGTTTAG-AAATTGCCAA
40968419 A
195 A
* *
40968420 AAAGAAGTACCGACCATCGTTCTACTTCAAAAAAAGGTTCCTCTAATGTTTACACAG-GAAACCA
1 AAAGAAGTACCGACCATCGTTCTACTTCAAAATAAGGTTCCTCTAATG-TTACACAGCAAAACCA
*
40968484 ATAACCCAAATTTCAAATTATTCAAGCATTGCTATTGCAGCAACTCGGAGATTGTGGATTCTAGC
65 ATAACCC-AATTTCAAATTATTCAAGCATTGCTATTGCAGCAACTCGGAGATTGTGGATTCGAGC
* * * * *
40968549 ACAATTAAGTACATAATATCATCAAATTTAATTAGTTCAGGTTTAC-AGGTAATTTAGAAA
129 ACACTTAAGTGCGTAATATCATCAAATTTAATTAG-TCGGGTTTACGA-GTAGTTTAGAAA
40968609 ATCATCAAAA
Statistics
Matches: 494, Mismatches: 49, Indels: 51
0.83 0.08 0.09
Matches are distributed among these distances:
182 73 0.15
183 81 0.16
184 1 0.00
185 2 0.00
186 3 0.01
187 2 0.00
189 1 0.00
191 1 0.00
193 2 0.00
194 3 0.01
195 4 0.01
196 77 0.16
197 152 0.31
198 89 0.18
199 3 0.01
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (195 bp):
AAAGAAGTACCGACCATCGTTCTACTTCAAAATAAGGTTCCTCTAATGTTACACAGCAAAACCAA
TAACCCAATTTCAAATTATTCAAGCATTGCTATTGCAGCAACTCGGAGATTGTGGATTCGAGCAC
ACTTAAGTGCGTAATATCATCAAATTTAATTAGTCGGGTTTACGAGTAGTTTAGAAATTGCCAAA
Found at i:40968568 original size:380 final size:386
Alignment explanation
Indices: 40967844--40968584 Score: 1038
Period size: 380 Copynumber: 1.9 Consensus size: 386
40967834 AAGCCTCTAT
40967844 AAAGAAGTACCGACCGACGTTCTACTTCAAAATAAGGTTCCTCTAATGTTACACAGCAAAACCAA
1 AAAGAAGTACCGACCGACGTTCTACTTCAAAATAAGGTTCCTCTAATGTTACACAGCAAAACCAA
* * *
40967909 TAACCCAATTTCAAATTATTTAAGCATTGCTATTGCAGCAACTCAGAGATTGTGGATTCGAGCAC
66 AAACCCAATTTCAAATTATTCAAGCATAGCTATTGCAGCAACTCAGAGATTGTGGATTCGAGCAC
*
40967974 GCTTAACTGCGTAATATCATCAAATTTAATTAGCTTCGGTTTACAGGTAGTTTAGAATTGTCAAA
131 ACTTAACTGCGTAATATCATC--A-TT-ATTAG---CGGTTTACAGGTAGTTTAGAATTGTCAAA
*
40968039 AAAAGAAGTACCGACCATCGTTCTACTTCAAAATAAGGTTCCTCTAATGTCACACGGCAAAACCA
189 AAAAGAAGTACCGACCATCGTTCTACTTCAAAAAAAGGTTCCTCTAATGTCACACGG-AAAACCA
* * * *
40968104 ATAACCCAATTTTAAATTTATTCAAGTATTGCTATTGCAACAACTTGGAGGTTATGGATTCGAAC
253 ATAACCCAATTTCAAATTTATTCAAGCATTGCTATTGCAACAACTCGGAGATTATGGATTCGAAC
* * *
40968169 ACACTTAAGTGCGTAATATCATCAAATTTAATTAGTCGGGGTCTACGAGTAGTTTAGAAATTTGC
318 ACAATTAAGTACATAATATCATCAAATTTAATTAGTCGGGGTCTACGAGTAGTTTAGAAATTTGC
40968234 CAAA
383 CAAA
* *
40968238 AAAGAAGTTCCGACC-ATCGTTCTACTTCAAAATGAGGTTCCTCTAATGTTACACAGCAAAACCA
1 AAAGAAGTACCGACCGA-CGTTCTACTTCAAAATAAGGTTCCTCTAATGTTACACAGCAAAACCA
** * *
40968302 AAAACCCAATTTCAAATTATTCAAGCATAGCTATTGCAGCAACTTGGAGCTTGTGGATTTGAGCA
65 AAAACCCAATTTCAAATTATTCAAGCATAGCTATTGCAGCAACTCAGAGATTGTGGATTCGAGCA
* * *
40968367 CACTTAAGTGTGT-A-GT-ATC-TT-TT-G-GGTTTAC-GGTAGTTTAGAAAATTGTC-AAAAAA
130 CACTTAACTGCGTAATATCATCATTATTAGCGGTTTACAGGTAGTTTAG--AATTGTCAAAAAAA
*
40968423 GAAGTACCGACCATCGTTCTACTTCAAAAAAAGGTTCCTCTAATGTTTACACAGG-AAACCAATA
193 GAAGTACCGACCATCGTTCTACTTCAAAAAAAGGTTCCTCTAATG-TCACAC-GGAAAACCAATA
* * * *
40968487 ACCCAAATTTCAAA-TTATTCAAGCATTGCTATTGCAGCAACTCGGAGATTGTGGATTCTAGCAC
256 ACCC-AATTTCAAATTTATTCAAGCATTGCTATTGCAACAACTCGGAGATTATGGATTCGAACAC
40968551 AATTAAGTACATAATATCATCAAATTTAATTAGT
320 AATTAAGTACATAATATCATCAAATTTAATTAGT
40968585 TCAGGTTTAC
Statistics
Matches: 315, Mismatches: 26, Indels: 26
0.86 0.07 0.07
Matches are distributed among these distances:
379 10 0.03
380 144 0.46
381 20 0.06
382 2 0.01
384 1 0.00
385 2 0.01
387 2 0.01
391 3 0.01
392 1 0.00
393 2 0.01
394 128 0.41
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (386 bp):
AAAGAAGTACCGACCGACGTTCTACTTCAAAATAAGGTTCCTCTAATGTTACACAGCAAAACCAA
AAACCCAATTTCAAATTATTCAAGCATAGCTATTGCAGCAACTCAGAGATTGTGGATTCGAGCAC
ACTTAACTGCGTAATATCATCATTATTAGCGGTTTACAGGTAGTTTAGAATTGTCAAAAAAAGAA
GTACCGACCATCGTTCTACTTCAAAAAAAGGTTCCTCTAATGTCACACGGAAAACCAATAACCCA
ATTTCAAATTTATTCAAGCATTGCTATTGCAACAACTCGGAGATTATGGATTCGAACACAATTAA
GTACATAATATCATCAAATTTAATTAGTCGGGGTCTACGAGTAGTTTAGAAATTTGCCAAA
Found at i:40983688 original size:11 final size:11
Alignment explanation
Indices: 40983655--40983695 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
40983645 TACTTCATAT
40983655 TTTTTTTAAAA
1 TTTTTTTAAAA
*
40983666 ATTTTTTAAAA
1 TTTTTTTAAAA
40983677 TTTTTTTAAAA
1 TTTTTTTAAAA
40983688 TTATTTTT
1 TT-TTTTT
40983696 TGACATGTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 22 0.81
12 5 0.19
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TTTTTTTAAAA
Found at i:40984410 original size:37 final size:37
Alignment explanation
Indices: 40984333--40984410 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
40984323 TTTCGTTAGG
* ** *
40984333 TTTTATTATTATATAATTTTTAATGAAATATCTTGCT
1 TTTTATTATTATATAATTTTTAATCAAATAAATTGAT
*
40984370 TTTTATTATTATATAATTTTTATTCAATATAAATT-AT
1 TTTTATTATTATATAATTTTTAATCAA-ATAAATTGAT
40984407 TTTT
1 TTTT
40984411 TATATTTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
37 30 0.86
38 5 0.14
ACGTcount: A:0.33, C:0.04, G:0.03, T:0.60
Consensus pattern (37 bp):
TTTTATTATTATATAATTTTTAATCAAATAAATTGAT
Found at i:40986783 original size:18 final size:18
Alignment explanation
Indices: 40986760--40986795 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
40986750 ACCTGGAGTT
40986760 CAACTGAATAAAAGAGAC
1 CAACTGAATAAAAGAGAC
40986778 CAACTGAATAAAAGAGAC
1 CAACTGAATAAAAGAGAC
40986796 TGTTCTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.17, G:0.17, T:0.11
Consensus pattern (18 bp):
CAACTGAATAAAAGAGAC
Found at i:40991698 original size:16 final size:16
Alignment explanation
Indices: 40991673--40991703 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40991663 CACCACTTGG
*
40991673 ATTGTTTGCCATTAAA
1 ATTGTCTGCCATTAAA
40991689 ATTGTCTGCCATTAA
1 ATTGTCTGCCATTAA
40991704 TCATAATGTT
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:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (16 bp):
ATTGTCTGCCATTAAA
Found at i:41002153 original size:15 final size:16
Alignment explanation
Indices: 41002133--41002165 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
41002123 ATTAATTAAT
41002133 AATAAAAT-AAAATAA
1 AATAAAATAAAAATAA
41002148 AATAAAATAAAAATAA
1 AATAAAATAAAAATAA
41002164 AA
1 AA
41002166 ATTCTAACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (16 bp):
AATAAAATAAAAATAA
Found at i:41002167 original size:6 final size:5
Alignment explanation
Indices: 41002133--41002165 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
41002123 ATTAATTAAT
41002133 AATAA AATAA AATAA AATAA AATAAA AATAA AA
1 AATAA AATAA AATAA AATAA AAT-AA AATAA AA
41002166 ATTCTAACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AATAA
Found at i:41013798 original size:44 final size:46
Alignment explanation
Indices: 41013699--41013799 Score: 132
Period size: 49 Copynumber: 2.2 Consensus size: 46
41013689 ATCTTACAAT
* * *
41013699 TAAAAGAAGTTACATTTTATTATAATTTAATTTCGGCCTATAATAA
1 TAAAAAAAATTACATTTTATTATAATTTAATTTCAGCCTATAATAA
41013745 TTTTAAAAAAAATTACATTTTATTATAATTTAATTTCAGCCTATAA-AA
1 ---TAAAAAAAATTACATTTTATTATAATTTAATTTCAGCCTATAATAA
*
41013793 GAAAAAA
1 TAAAAAA
41013800 TCTTGACTTC
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
45 6 0.12
48 2 0.04
49 40 0.83
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.40
Consensus pattern (46 bp):
TAAAAAAAATTACATTTTATTATAATTTAATTTCAGCCTATAATAA
Found at i:41014479 original size:58 final size:57
Alignment explanation
Indices: 41014414--41014525 Score: 197
Period size: 58 Copynumber: 1.9 Consensus size: 57
41014404 AATTACAAGC
* *
41014414 AAAAACATGATATTGTAATATGTTCCCTATACAAGCAAATCAAACCCAAAAAAAACT
1 AAAAACATGATATTGTAATATGATCCCTACACAAGCAAATCAAACCCAAAAAAAACT
41014471 NAAAAACATGATATTGTAATATGATCCCTACACAAGCAAATCAAACCCAAAAAAA
1 -AAAAACATGATATTGTAATATGATCCCTACACAAGCAAATCAAACCCAAAAAAA
41014526 GCTTCAAAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.52, C:0.20, G:0.07, T:0.21
Consensus pattern (57 bp):
AAAAACATGATATTGTAATATGATCCCTACACAAGCAAATCAAACCCAAAAAAAACT
Found at i:41015660 original size:16 final size:17
Alignment explanation
Indices: 41015633--41015681 Score: 68
Period size: 16 Copynumber: 3.0 Consensus size: 17
41015623 TATGACTCAA
41015633 CTTGAATGATCTAAACT
1 CTTGAATGATCTAAACT
41015650 C-T-AATTGATCTAAA-T
1 CTTGAA-TGATCTAAACT
41015665 CTTGAATGATCTAAACT
1 CTTGAATGATCTAAACT
41015682 TAAATATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 4 0.14
16 20 0.71
17 4 0.14
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (17 bp):
CTTGAATGATCTAAACT
Found at i:41019909 original size:21 final size:21
Alignment explanation
Indices: 41019883--41019923 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
41019873 TTAAAAATTA
* *
41019883 TTATAAGTTTTTGTATTTTTT
1 TTATAAATTTTTATATTTTTT
41019904 TTATAAATTTTTATATTTTT
1 TTATAAATTTTTATATTTTT
41019924 ATTTTTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (21 bp):
TTATAAATTTTTATATTTTTT
Found at i:41028552 original size:31 final size:29
Alignment explanation
Indices: 41028477--41028559 Score: 78
Period size: 31 Copynumber: 2.8 Consensus size: 29
41028467 ATACATAAAC
* *
41028477 TTAATT-TGGTACAATTATATAAATGAAAAT
1 TTAATTATGGTTCAA-T-TATACATGAAAAT
* *
41028507 TTGATTGTGGTTCAAATGTATACATGAAAAT
1 TTAATTATGGTTC-AAT-TATACATGAAAAT
*
41028538 TTAATTATGTTTCAATTATACA
1 TTAATTATGGTTCAATTATACA
41028560 CATTTGAAGA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
29 6 0.14
30 8 0.18
31 28 0.64
32 2 0.05
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.42
Consensus pattern (29 bp):
TTAATTATGGTTCAATTATACATGAAAAT
Found at i:41032870 original size:17 final size:17
Alignment explanation
Indices: 41032848--41032893 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
41032838 TTTCTTGGTT
41032848 TTTTTTTGGGGGTTAGG
1 TTTTTTTGGGGGTTAGG
***
41032865 TTTTTTTTTTGGTTAGG
1 TTTTTTTGGGGGTTAGG
41032882 TTTTTTTGGGGG
1 TTTTTTTGGGGG
41032894 GGGCTTAATG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.04, C:0.00, G:0.35, T:0.61
Consensus pattern (17 bp):
TTTTTTTGGGGGTTAGG
Found at i:41033563 original size:14 final size:13
Alignment explanation
Indices: 41033532--41033566 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
41033522 ATTGACTCTC
*
41033532 TAAAAACAGACAT
1 TAAAAACAGAAAT
41033545 TAAAAACAGAAAT
1 TAAAAACAGAAAT
*
41033558 TGAAAACAG
1 TAAAAACAG
41033567 CTCAGCACGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.63, C:0.11, G:0.11, T:0.14
Consensus pattern (13 bp):
TAAAAACAGAAAT
Found at i:41033764 original size:47 final size:49
Alignment explanation
Indices: 41033711--41033804 Score: 147
Period size: 49 Copynumber: 2.0 Consensus size: 49
41033701 ATTTTTGAAA
*
41033711 AACAGAAATT-AAAAGA-CTCAGCGTGTCTTGAGGCTCAACTCATTTTG
1 AACAGAAATTGAAAAGACCTCAACGTGTCTTGAGGCTCAACTCATTTTG
**
41033758 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTT
1 AACAGAAATTGAAAAGACCTCAACGTGTCTTGAGGCTCAACTCATTT
41033805 CTCGCAATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
47 10 0.24
48 4 0.10
49 28 0.67
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (49 bp):
AACAGAAATTGAAAAGACCTCAACGTGTCTTGAGGCTCAACTCATTTTG
Found at i:41033842 original size:72 final size:72
Alignment explanation
Indices: 41033758--41034127 Score: 573
Period size: 72 Copynumber: 5.0 Consensus size: 72
41033748 ACTCATTTTG
41033758 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
41033823 TTTTGAA
66 TTTTGAA
41033830 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
41033895 TTTTGAA
66 TTTTGAA
41033902 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
41033967 TTTTGAA
66 TTTTGAA
41033974 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
41034039 TTTTTTTTTTGAA
66 ------TTTTGAA
* * * * ** *
41034052 AGACAGAAATTGAAAATACCTCAGCATGTGAAC-CGAGGCTCAACTCACCTCTCGCAATATGAGC
1 A-ACAGAAATTGAAATTACCTCA--ACGTG-TCTTGAGGCTCAACTCATTTCTCGCAATATGAGT
41034116 TG-ATTTTGAA
62 TGAATTTTGAA
41034126 AA
1 AA
41034128 AGTAGAAATT
Statistics
Matches: 281, Mismatches: 7, Indels: 19
0.92 0.02 0.06
Matches are distributed among these distances:
72 209 0.74
73 1 0.00
74 8 0.03
78 8 0.03
79 20 0.07
80 1 0.00
81 33 0.12
82 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31
Consensus pattern (72 bp):
AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
TTTTGAA
Found at i:41034191 original size:54 final size:55
Alignment explanation
Indices: 41034091--41034196 Score: 135
Period size: 54 Copynumber: 1.9 Consensus size: 55
41034081 GAACCGAGGC
* * *
41034091 TCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCACAATATGAGCTGATTTTGAAAAAGCAGAAATTGAAAAGGT
* * *
41034145 TCAACCCACCTCTCACAATATGAGTTGATTCTTGAACAA-CATAAATTGAAAA
1 TCAACCCACCTCTCACAATATGAGCTGATT-TTGAAAAAGCAGAAATTGAAAA
41034197 CAGAAATTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
54 33 0.75
55 11 0.25
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (55 bp):
TCAACCCACCTCTCACAATATGAGCTGATTTTGAAAAAGCAGAAATTGAAAAGGT
Found at i:41034203 original size:13 final size:13
Alignment explanation
Indices: 41034176--41034209 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
41034166 GAGTTGATTC
*
41034176 TTGAACAACATAAA
1 TTGAA-AACAGAAA
41034190 TTGAAAACAGAAA
1 TTGAAAACAGAAA
41034203 TTGAAAA
1 TTGAAAA
41034210 TACCTCAGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.59, C:0.09, G:0.12, T:0.21
Consensus pattern (13 bp):
TTGAAAACAGAAA
Found at i:41034257 original size:140 final size:140
Alignment explanation
Indices: 41034047--41034534 Score: 852
Period size: 140 Copynumber: 3.5 Consensus size: 140
41034037 AATTTTTTTT
41034047 TTGAAAGACAGAAATTGAAAATACCTCAGCATGTGAACC-GAGGCTCAACTCACCTCTCGCAATA
1 TTGAAA-ACAGAAATTGAAAATACCTCAGC--GTG-ACCTGAGGCTCAACTCACCTCTCGCAATA
*
41034111 TGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCACAATATGAGTTGATTC
62 TGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTC
*
41034176 TTGAACAACATAAA
127 TTGAACAACGTAAA
41034190 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
* *
41034255 CTGATTTTAAAAAAGTAGAAATTAAAAGGTTCAACCCACTTCTCGCAATATGAGTTGATTCTTGA
66 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGA
41034320 ACAACGTAAA
131 ACAACGTAAA
* *
41034330 TTGAAAATAGAAATTGAAAATACCTTAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
*
41034395 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCATCTCTCGCAATATGAGTTGATTCTTGA
66 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGA
41034460 ACAACGTAAA
131 ACAACGTAAA
**
41034470 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCGTCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
41034535 TTGAGTTTCC
Statistics
Matches: 331, Mismatches: 13, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
139 3 0.01
140 299 0.90
142 23 0.07
143 6 0.02
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (140 bp):
TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTCTTGA
ACAACGTAAA
Found at i:41034331 original size:54 final size:54
Alignment explanation
Indices: 41034231--41034336 Score: 126
Period size: 54 Copynumber: 1.9 Consensus size: 54
41034221 GACCTGAGGC
*
41034231 TCAACTCACCTCTCGCAATATGAGCTGATTTTAAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCGCAATATGAGCTGATTTTAAAAAAGTA-AAATTGAAAAGGT
* * * *
41034285 TCAACCCACTTCTCGCAATATGAGTTGATTCTTGAACAACGT-AAATTGAAAA
1 TCAACCCACCTCTCGCAATATGAGCTGATT-TT-AAAAAAGTAAAATTGAAAA
41034337 TAGAAATTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
54 32 0.73
55 6 0.14
56 6 0.14
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (54 bp):
TCAACCCACCTCTCGCAATATGAGCTGATTTTAAAAAAGTAAAATTGAAAAGGT
Found at i:41034345 original size:13 final size:13
Alignment explanation
Indices: 41034327--41034351 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41034317 TGAACAACGT
41034327 AAATTGAAAATAG
1 AAATTGAAAATAG
41034340 AAATTGAAAATA
1 AAATTGAAAATA
41034352 CCTTAGCGTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (13 bp):
AAATTGAAAATAG
Found at i:41034471 original size:54 final size:54
Alignment explanation
Indices: 41034371--41034476 Score: 135
Period size: 54 Copynumber: 1.9 Consensus size: 54
41034361 GACCTGAGGC
*
41034371 TCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTA-AAATTGAAAAGGT
* * *
41034425 TCAACCCATCTCTCGCAATATGAGTTGATTCTTGAACAACGT-AAATTGAAAA
1 TCAACCCACCTCTCGCAATATGAGCTGATT-TTGAA-AAAGTAAAATTGAAAA
41034477 CAGAAATTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
54 32 0.71
55 9 0.20
56 4 0.09
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (54 bp):
TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAAAATTGAAAAGGT
Found at i:41042875 original size:12 final size:12
Alignment explanation
Indices: 41042858--41042893 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
41042848 TGGGATATGC
41042858 AATGTATGAATG
1 AATGTATGAATG
41042870 AATGTATGAATG
1 AATGTATGAATG
*
41042882 AATGGATGAATG
1 AATGTATGAATG
41042894 TCAAATGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.42, C:0.00, G:0.28, T:0.31
Consensus pattern (12 bp):
AATGTATGAATG
Found at i:41044871 original size:19 final size:17
Alignment explanation
Indices: 41044847--41044892 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
41044837 AGGGTTTCTT
41044847 GGTTTTTTTTGGAGGGTTA
1 GGTTTTTTTT--AGGGTTA
**
41044866 GGTTTTTTTTTTGGTTA
1 GGTTTTTTTTAGGGTTA
41044883 GGTTTTTTTT
1 GGTTTTTTTT
41044893 TTTGGGGACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 15 0.60
19 10 0.40
ACGTcount: A:0.07, C:0.00, G:0.28, T:0.65
Consensus pattern (17 bp):
GGTTTTTTTTAGGGTTA
Found at i:41044897 original size:18 final size:17
Alignment explanation
Indices: 41044861--41044894 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
41044851 TTTTTTGGAG
41044861 GGTTAGGTTTTTTTTTT
1 GGTTAGGTTTTTTTTTT
41044878 GGTTAGGTTTTTTTTTT
1 GGTTAGGTTTTTTTTTT
41044895 TGGGGACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.06, C:0.00, G:0.24, T:0.71
Consensus pattern (17 bp):
GGTTAGGTTTTTTTTTT
Found at i:41047619 original size:38 final size:38
Alignment explanation
Indices: 41047525--41047750 Score: 247
Period size: 38 Copynumber: 5.9 Consensus size: 38
41047515 CGAGGTATAA
* * * * *
41047525 AACCCAAACATAACACCAGCACGAAGCCTACGGGACTTT
1 AACCCAGATATAATACCAGCACAAAGCCTGCGGGA-TTT
* * *
41047564 AAACTCAGATATAATACCAGCACTAGGCCTGCGGGATTT
1 -AACCCAGATATAATACCAGCACAAAGCCTGCGGGATTT
*
41047603 AACCCAGATATAATACCAGCACGAAGCCTGCGGGATTT
1 AACCCAGATATAATACCAGCACAAAGCCTGCGGGATTT
* * *
41047641 AA-CCTGTATATATTACCAGCACAAAGCCTGTGGGATTT
1 AACCCAG-ATATAATACCAGCACAAAGCCTGCGGGATTT
* * *
41047679 AACCCGGATATATTACCAGCACAAAGCCCGCGGGATTT
1 AACCCAGATATAATACCAGCACAAAGCCTGCGGGATTT
* * * *
41047717 AACCCGGATATAATTCCAGCATATAGCCTGCGGG
1 AACCCAGATATAATACCAGCACAAAGCCTGCGGG
41047751 TCTTTAAGCC
Statistics
Matches: 162, Mismatches: 22, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
37 3 0.02
38 125 0.77
39 6 0.04
40 28 0.17
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (38 bp):
AACCCAGATATAATACCAGCACAAAGCCTGCGGGATTT
Found at i:41047714 original size:114 final size:116
Alignment explanation
Indices: 41047539--41047750 Score: 286
Period size: 114 Copynumber: 1.8 Consensus size: 116
41047529 CAAACATAAC
* * * * *
41047539 ACCAGCACGAAGCCTACGGGACTTTAAACTCAGATATAATACCAGCACTAGGCCTGCGGGATTTA
1 ACCAGCACAAAGCCTACGGGACTTTAAACCCAGATATAATACCAGCACAAAGCCCGCGGGATTTA
41047604 ACCCAGATATAATACCAGCACGA-AGCCTGCGGGATTTAACCTGTATATATT
66 ACCCAGATATAATACCAGCA-GATAGCCTGCGGGATTTAACCTGTATATATT
** * *
41047655 ACCAGCACAAAGCCTGTGGGA-TTT-AACCCGGATATATTACCAGCACAAAGCCCGCGGGATTTA
1 ACCAGCACAAAGCCTACGGGACTTTAAACCCAGATATAATACCAGCACAAAGCCCGCGGGATTTA
* * *
41047718 ACCCGGATATAATTCCAGCATATAGCCTGCGGG
66 ACCCAGATATAATACCAGCAGATAGCCTGCGGG
41047751 TCTTTAAGCC
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
113 1 0.01
114 61 0.73
115 3 0.04
116 18 0.22
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (116 bp):
ACCAGCACAAAGCCTACGGGACTTTAAACCCAGATATAATACCAGCACAAAGCCCGCGGGATTTA
ACCCAGATATAATACCAGCAGATAGCCTGCGGGATTTAACCTGTATATATT
Found at i:41051124 original size:11 final size:11
Alignment explanation
Indices: 41051108--41051132 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
41051098 CATAAATGAA
41051108 TTTTTATTATT
1 TTTTTATTATT
41051119 TTTTTATTATT
1 TTTTTATTATT
41051130 TTT
1 TTT
41051133 AAATTTTGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTATTATT
Found at i:41051849 original size:6 final size:6
Alignment explanation
Indices: 41051838--41051906 Score: 56
Period size: 6 Copynumber: 11.7 Consensus size: 6
41051828 AACATGTTTC
* *
41051838 TTTTAT TTTTAT TTTTAT TTCTAAT TTTTAT TTTCT-T CATTTA- TTTTAT
1 TTTTAT TTTTAT TTTTAT TT-TTAT TTTTAT TTT-TAT -TTTTAT TTTTAT
*
41051887 TTTT-T TTAT-T TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTT
41051907 GCTTATTACA
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
5 12 0.24
6 31 0.61
7 8 0.16
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTAT
Found at i:41051866 original size:13 final size:12
Alignment explanation
Indices: 41051838--41051905 Score: 54
Period size: 13 Copynumber: 5.8 Consensus size: 12
41051828 AACATGTTTC
*
41051838 TTTTATTTTTAT
1 TTTTATTTTAAT
41051850 TTTTATTTCTAAT
1 TTTTATTT-TAAT
*
41051863 TTTTATTTT-CT
1 TTTTATTTTAAT
41051874 TCATTTATTTT-A-
1 T--TTTATTTTAAT
*
41051886 TTTT-TTTTATT
1 TTTTATTTTAAT
41051897 TTTTATTTT
1 TTTTATTTT
41051906 TGCTTATTAC
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
9 4 0.09
10 3 0.07
11 6 0.13
12 14 0.30
13 19 0.41
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTATTTTAAT
Found at i:41052766 original size:12 final size:12
Alignment explanation
Indices: 41052751--41052780 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
41052741 ACAATAATAC
41052751 TATATATAAATG
1 TATATATAAATG
*
41052763 TATATATATATG
1 TATATATAAATG
41052775 TATATA
1 TATATA
41052781 ATAGAAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (12 bp):
TATATATAAATG
Found at i:41053461 original size:27 final size:27
Alignment explanation
Indices: 41053430--41053500 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
41053420 AATCACCATT
41053430 TCATTTTTTTTTACAT-AC-ATGATTA
1 TCATTTTTTTTTACATCACAATGATTA
* * *
41053455 TTCCATTTTATTTTGCTATCACAATGTTTA
1 -T-CATTTTTTTTTAC-ATCACAATGATTA
41053485 TCATTTTTTTTTACAT
1 TCATTTTTTTTTACAT
41053501 TATGCCCAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
26 1 0.03
27 13 0.36
28 13 0.36
29 3 0.08
30 6 0.17
ACGTcount: A:0.24, C:0.14, G:0.04, T:0.58
Consensus pattern (27 bp):
TCATTTTTTTTTACATCACAATGATTA
Found at i:41054470 original size:17 final size:17
Alignment explanation
Indices: 41054448--41054481 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
41054438 GTTGCAATCC
41054448 TTGAACTTTTTCACCCA
1 TTGAACTTTTTCACCCA
41054465 TTGAACTTTTTCACCCA
1 TTGAACTTTTTCACCCA
41054482 CCACACATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.29, G:0.06, T:0.41
Consensus pattern (17 bp):
TTGAACTTTTTCACCCA
Found at i:41055644 original size:18 final size:18
Alignment explanation
Indices: 41055610--41055644 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41055600 TTAACCGACT
* *
41055610 TATATTATATATTTATTA
1 TATATTATAAATATATTA
41055628 TATATTATAAATATATT
1 TATATTATAAATATATT
41055645 TAAATAGTTA
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TATATTATAAATATATTA
Found at i:41059630 original size:50 final size:51
Alignment explanation
Indices: 41059553--41059681 Score: 190
Period size: 50 Copynumber: 2.5 Consensus size: 51
41059543 GACCATGACA
*
41059553 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGA-AAAGTG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCCGATCAAGGACAAA-TG
*
41059604 A-AAGTGATAAGTGATAGCTTCGGCTACACTTATCCGATCAATGACAAATG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCCGATCAAGGACAAATG
* * *
41059654 ACAAGTGAAAAGTGGTAGCTTCAGCTAC
1 ACAAGTGATAAGTGATAGCTTCGGCTAC
41059682 CTGATCAGTG
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
50 44 0.62
51 27 0.38
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (51 bp):
ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCCGATCAAGGACAAATG
Found at i:41059695 original size:31 final size:31
Alignment explanation
Indices: 41059657--41059743 Score: 147
Period size: 31 Copynumber: 2.8 Consensus size: 31
41059647 ACAAATGACA
*
41059657 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
41059688 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
41059719 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
41059744 AAGTGACAAG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:41059827 original size:100 final size:100
Alignment explanation
Indices: 41059705--41059902 Score: 396
Period size: 100 Copynumber: 2.0 Consensus size: 100
41059695 AGTGGTAGCT
41059705 CCGGCTACCTGATCAGTGAATAGTGGTAGCTTCGGCTACAAGTGACAAGTGATTTCCGTACAAGA
1 CCGGCTACCTGATCAGTGAATAGTGGTAGCTTCGGCTACAAGTGACAAGTGATTTCCGTACAAGA
41059770 CCATATCTGGGATATGGCATCAGTGTGATGTATTA
66 CCATATCTGGGATATGGCATCAGTGTGATGTATTA
41059805 CCGGCTACCTGATCAGTGAATAGTGGTAGCTTCGGCTACAAGTGACAAGTGATTTCCGTACAAGA
1 CCGGCTACCTGATCAGTGAATAGTGGTAGCTTCGGCTACAAGTGACAAGTGATTTCCGTACAAGA
41059870 CCATATCTGGGATATGGCATCAGTGTGATGTAT
66 CCATATCTGGGATATGGCATCAGTGTGATGTAT
41059903 GCTACTGTAT
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 98 1.00
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (100 bp):
CCGGCTACCTGATCAGTGAATAGTGGTAGCTTCGGCTACAAGTGACAAGTGATTTCCGTACAAGA
CCATATCTGGGATATGGCATCAGTGTGATGTATTA
Found at i:41060013 original size:49 final size:47
Alignment explanation
Indices: 41059866--41060041 Score: 185
Period size: 47 Copynumber: 3.7 Consensus size: 47
41059856 ATTTCCGTAC
* * * * * * * *
41059866 AAGACCATATCTGGGATATGGCATCA-GTGTGATGTATGCTACTGTAT
1 AAGACCATAGCTGGGCTATGGCATCATATGTGATATGTGATTC-GTGT
** * * *
41059913 AAGACCATATTTGGGATATGGCATCA-GTGAGATATGTGATTCGTGT
1 AAGACCATAGCTGGGCTATGGCATCATATGTGATATGTGATTCGTGT
41059959 AAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTACGTGT
1 AAGACCATAGCTGGGCTATGGCATC-ATATGTGATATGTGATT-CGTGT
41060008 AAGACCATAGCTGGGCTATGGCATCATTATGTGA
1 AAGACCATAGCTGGGCTATGGCATCA-TATGTGA
41060042 AGATGTGTAA
Statistics
Matches: 113, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
46 25 0.22
47 37 0.33
48 14 0.12
49 37 0.33
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.31
Consensus pattern (47 bp):
AAGACCATAGCTGGGCTATGGCATCATATGTGATATGTGATTCGTGT
Found at i:41062424 original size:20 final size:20
Alignment explanation
Indices: 41062399--41062437 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
41062389 ATAAACCCTG
*
41062399 AATCTTGAACCTAGAACCCA
1 AATCTTAAACCTAGAACCCA
*
41062419 AATCTTAAACCTCGAACCC
1 AATCTTAAACCTAGAACCC
41062438 TGATGATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.33, G:0.08, T:0.21
Consensus pattern (20 bp):
AATCTTAAACCTAGAACCCA
Found at i:41063996 original size:131 final size:131
Alignment explanation
Indices: 41063734--41063993 Score: 371
Period size: 131 Copynumber: 2.0 Consensus size: 131
41063724 AATTTAGAGA
* ** *
41063734 ACATGAGTGAAATTCTAAAGGAATATTTGATTATTTTGAACAAACAAGAAATCGCAACCTAGCAC
1 ACATGAGTGAAATTCCAAAGGAATATTCAATTATTTTGAACAAACAAGAAATCGCAACCCAGCAC
* *
41063799 GATAGGGCACGATTCCCCAAATTGCCAAACATCGAGTATTACCTTCGTTTTGAAGAGTTTTTAAA
66 GATAGAGCACGATTCCCCAAATTGCCAAACATCGAGTATTACCTTCGTTTTGAAGAATTTTTAAA
41063864 G
131 G
* ** *
41063865 ACATGAGTGAAATTCCAAAGGAATATTCAATTGTTTTGAACAAACGGGAAATCGCAACCCATCAC
1 ACATGAGTGAAATTCCAAAGGAATATTCAATTATTTTGAACAAACAAGAAATCGCAACCCAGCAC
* * * *
41063930 GATAGAGCACGATT-CCCGAATTGCTAAACTTCGAGTATTGCCTTCGTTTT-AGAGAATTTTTAA
66 GATAGAGCACGATTCCCCAAATTGCCAAACATCGAGTATTACCTTCGTTTTGA-AGAATTTTTAA
41063993 A
130 A
41063994 AGAATAATTA
Statistics
Matches: 114, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
129 1 0.01
130 43 0.38
131 70 0.61
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (131 bp):
ACATGAGTGAAATTCCAAAGGAATATTCAATTATTTTGAACAAACAAGAAATCGCAACCCAGCAC
GATAGAGCACGATTCCCCAAATTGCCAAACATCGAGTATTACCTTCGTTTTGAAGAATTTTTAAA
G
Found at i:41064334 original size:6 final size:7
Alignment explanation
Indices: 41064316--41064344 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
41064306 ATGCAAGATG
41064316 TAAAAAA
1 TAAAAAA
41064323 TAAAAAA
1 TAAAAAA
41064330 TAAAAAA
1 TAAAAAA
41064337 TAAAAAA
1 TAAAAAA
41064344 T
1 T
41064345 GTGATATGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (7 bp):
TAAAAAA
Found at i:41066407 original size:21 final size:23
Alignment explanation
Indices: 41066374--41066415 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
41066364 ATTACATAGA
*
41066374 TATATACCTATATATATTAAAGG
1 TATATACCTATATATAATAAAGG
41066397 TATATA-C-ATATATAATAAA
1 TATATACCTATATATAATAAA
41066416 ACATATACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 1 0.06
23 6 0.33
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (23 bp):
TATATACCTATATATAATAAAGG
Found at i:41067290 original size:18 final size:19
Alignment explanation
Indices: 41067267--41067303 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
41067257 AAAGAAAAAA
41067267 AAAGAGA-AGAAGGGAGAG
1 AAAGAGAGAGAAGGGAGAG
*
41067285 AAAGAGAGAGGAGGGAGAG
1 AAAGAGAGAGAAGGGAGAG
41067304 GGGAAAGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (19 bp):
AAAGAGAGAGAAGGGAGAG
Found at i:41067365 original size:18 final size:18
Alignment explanation
Indices: 41067325--41067366 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
41067315 GAGGGGGGCT
41067325 GCCGGCCATCGTCCGGTC
1 GCCGGCCATCGTCCGGTC
* *
41067343 ACCGGACCATCGTGC-GTC
1 GCCGG-CCATCGTCCGGTC
41067361 GCCGGC
1 GCCGGC
41067367 GCTGGCCACC
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
17 1 0.05
18 11 0.55
19 8 0.40
ACGTcount: A:0.10, C:0.43, G:0.33, T:0.14
Consensus pattern (18 bp):
GCCGGCCATCGTCCGGTC
Found at i:41068323 original size:13 final size:13
Alignment explanation
Indices: 41068305--41068330 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41068295 CTCATACAAG
41068305 ATTAAATTAATAT
1 ATTAAATTAATAT
41068318 ATTAAATTAATAT
1 ATTAAATTAATAT
41068331 TACTACATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATTAAATTAATAT
Found at i:41068362 original size:5 final size:5
Alignment explanation
Indices: 41068352--41068384 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
41068342 TACGTTGTGA
41068352 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
41068385 AACACACAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:41068377 original size:9 final size:9
Alignment explanation
Indices: 41068353--41068383 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
41068343 ACGTTGTGAA
41068353 AAATAAAAT
1 AAATAAAAT
41068362 AAAATAAAAT
1 -AAATAAAAT
41068372 AAATAAAAT
1 AAATAAAAT
41068381 AAA
1 AAA
41068384 AAACACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:41068377 original size:14 final size:15
Alignment explanation
Indices: 41068352--41068384 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
41068342 TACGTTGTGA
41068352 AAAATAAAATAAAAT
1 AAAATAAAATAAAAT
41068367 AAAAT-AAATAAAAT
1 AAAATAAAATAAAAT
41068381 AAAA
1 AAAA
41068385 AACACACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAATAAAATAAAAT
Found at i:41074387 original size:3 final size:3
Alignment explanation
Indices: 41074362--41074419 Score: 61
Period size: 3 Copynumber: 20.3 Consensus size: 3
41074352 GTTTTTTAGT
* *
41074362 TTA TT- TTA TTA ATA -TA GTTA TTA TTA TTA TTA TTA CTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
41074406 TTA TT- TT- TTA TTA T
1 TTA TTA TTA TTA TTA T
41074420 ACTTGCATAC
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
2 8 0.17
3 38 0.79
4 2 0.04
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:41074557 original size:13 final size:13
Alignment explanation
Indices: 41074526--41074550 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41074516 ACCATATTTT
41074526 TTTATATATATAG
1 TTTATATATATAG
41074539 TTTATATATATA
1 TTTATATATATA
41074551 TTATATACAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (13 bp):
TTTATATATATAG
Found at i:41076141 original size:21 final size:22
Alignment explanation
Indices: 41076112--41076158 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
41076102 CAGAAGGAGT
*
41076112 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
41076134 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
41076155 GAGT
1 GAGT
41076159 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:41079158 original size:38 final size:38
Alignment explanation
Indices: 41079107--41079185 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
41079097 AACTACAAAG
*
41079107 AGATTGTCTCTCTTAATTTGATTAAAAAGGAACCTATC
1 AGATTGTCTCTCTTAATTTGATTAAAAAGGAACCTAAC
41079145 AGATTGTCTCTCTTAATTTGATTAAAAAGGAACCTAAC
1 AGATTGTCTCTCTTAATTTGATTAAAAAGGAACCTAAC
41079183 AGA
1 AGA
41079186 ATCCCATGAG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (38 bp):
AGATTGTCTCTCTTAATTTGATTAAAAAGGAACCTAAC
Found at i:41083263 original size:26 final size:26
Alignment explanation
Indices: 41083234--41083289 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
41083224 AATTTTTAAC
* *
41083234 TTTGACCACATTATCATAGTTTTTGT
1 TTTGACCACACTATCATAGTTTGTGT
* * *
41083260 TTTGTCTACACTATCATGGTTTGTGT
1 TTTGACCACACTATCATAGTTTGTGT
41083286 TTTG
1 TTTG
41083290 TTTATTCTGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.18, C:0.14, G:0.16, T:0.52
Consensus pattern (26 bp):
TTTGACCACACTATCATAGTTTGTGT
Found at i:41087837 original size:3 final size:3
Alignment explanation
Indices: 41087829--41087890 Score: 56
Period size: 3 Copynumber: 21.0 Consensus size: 3
41087819 ATAAGTAAAG
* * *
41087829 ATA ATA ATA ATA ATA ATA ATA ATG ATA ATA A-A TATA GTA ATG ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA
* *
41087874 ATA GTA AGA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA
41087891 TATAGTATTA
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
2 3 0.07
3 42 0.91
4 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:41091974 original size:62 final size:62
Alignment explanation
Indices: 41091908--41092091 Score: 314
Period size: 62 Copynumber: 3.0 Consensus size: 62
41091898 CACGTATCTC
*
41091908 TTCATTCATTAACATTACATTTCATTACATACAATAAATTTCCTAAAATCCAAAAATACGCG
1 TTCATGCATTAACATTACATTTCATTACATACAATAAATTTCCTAAAATCCAAAAATACGCG
* *
41091970 TTCATGCATTAACATTACATTTTATTACATACAATAAATTTCCTAAAATCAAAAAATACGCG
1 TTCATGCATTAACATTACATTTCATTACATACAATAAATTTCCTAAAATCCAAAAATACGCG
* * *
41092032 TTCATGCATCAACATTACATTTCATTGCATACAATAAATTTCCTAAAATCCAAAAGTACG
1 TTCATGCATTAACATTACATTTCATTACATACAATAAATTTCCTAAAATCCAAAAATACG
41092092 TCGAGTTTAG
Statistics
Matches: 114, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 114 1.00
ACGTcount: A:0.42, C:0.20, G:0.05, T:0.33
Consensus pattern (62 bp):
TTCATGCATTAACATTACATTTCATTACATACAATAAATTTCCTAAAATCCAAAAATACGCG
Found at i:41092187 original size:96 final size:96
Alignment explanation
Indices: 41092023--41092215 Score: 350
Period size: 96 Copynumber: 2.0 Consensus size: 96
41092013 TAAAATCAAA
*
41092023 AAATACGCGTTCATGCATCAACATTACATTTCATTGCATACAATAAATTTCCTAAAATCCAAAAG
1 AAATACGCGTTCATGCATCAACATTACATTTCATTACATACAATAAATTTCCTAAAATCCAAAAG
*
41092088 TACGTCGAGTTTAGAACTCTAGTACAAAACC
66 TACGTCGAGTGTAGAACTCTAGTACAAAACC
* *
41092119 AAATACGCGTTCATGCATTAACATTACATTTTATTACATACAATAAATTTCCTAAAATCCAAAAG
1 AAATACGCGTTCATGCATCAACATTACATTTCATTACATACAATAAATTTCCTAAAATCCAAAAG
41092184 TACGTCGAGTGTAGAACTCTAGTACAAAACC
66 TACGTCGAGTGTAGAACTCTAGTACAAAACC
41092215 A
1 A
41092216 GATGGATTGG
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
96 93 1.00
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.28
Consensus pattern (96 bp):
AAATACGCGTTCATGCATCAACATTACATTTCATTACATACAATAAATTTCCTAAAATCCAAAAG
TACGTCGAGTGTAGAACTCTAGTACAAAACC
Found at i:41093426 original size:10 final size:10
Alignment explanation
Indices: 41093411--41093461 Score: 57
Period size: 10 Copynumber: 4.7 Consensus size: 10
41093401 CAGTGGAGAC
41093411 AAAAAAAAGA
1 AAAAAAAAGA
41093421 AAAAAAAAGTA
1 AAAAAAAAG-A
41093432 AAAAAAACGAGA
1 AAAAAAA--AGA
*
41093444 AAATAAAAATA
1 AAA-AAAAAGA
41093455 AAAAAAA
1 AAAAAAA
41093462 CCAAATAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
10 13 0.36
11 13 0.36
12 4 0.11
13 6 0.17
ACGTcount: A:0.84, C:0.02, G:0.08, T:0.06
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:41093444 original size:23 final size:22
Alignment explanation
Indices: 41093411--41093462 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
41093401 CAGTGGAGAC
41093411 AAAAAAA-AGAAAA-AAAAAGTA
1 AAAAAAACAGAAAATAAAAA-TA
41093432 AAAAAAACGAGAAAATAAAAATA
1 AAAAAAAC-AGAAAATAAAAATA
41093455 AAAAAAAC
1 AAAAAAAC
41093463 CAAATAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.25
23 16 0.57
24 5 0.18
ACGTcount: A:0.83, C:0.04, G:0.08, T:0.06
Consensus pattern (22 bp):
AAAAAAACAGAAAATAAAAATA
Found at i:41093906 original size:13 final size:13
Alignment explanation
Indices: 41093888--41093949 Score: 54
Period size: 13 Copynumber: 4.6 Consensus size: 13
41093878 ACTTCACTTG
41093888 AAAAAAAAATGAA
1 AAAAAAAAATGAA
*
41093901 AAAAAAAAATAAA
1 AAAAAAAAATGAA
*
41093914 AAAATGAAAAAAGAA
1 AAAA--AAAAATGAA
* *
41093929 AAGAAGAAA-GAA
1 AAAAAAAAATGAA
41093941 AAAGAAAAA
1 AAA-AAAAA
41093950 GGAGAGGCCA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
12 5 0.13
13 24 0.62
15 10 0.26
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (13 bp):
AAAAAAAAATGAA
Found at i:41093916 original size:21 final size:21
Alignment explanation
Indices: 41093890--41093930 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
41093880 TTCACTTGAA
41093890 AAAAAAATGAAAAAAAAAAAT
1 AAAAAAATGAAAAAAAAAAAT
*
41093911 AAAAAAATGAAAAAAGAAAA
1 AAAAAAATGAAAAAAAAAAA
41093931 GAAGAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.07, T:0.07
Consensus pattern (21 bp):
AAAAAAATGAAAAAAAAAAAT
Found at i:41093950 original size:12 final size:11
Alignment explanation
Indices: 41093887--41093949 Score: 65
Period size: 11 Copynumber: 5.5 Consensus size: 11
41093877 TACTTCACTT
*
41093887 GAAAAAAAAAT
1 GAAAAAAAAAA
41093898 GAAAAAAAAAA
1 GAAAAAAAAAA
* *
41093909 -ATAAAAAAAT
1 GAAAAAAAAAA
41093919 GAAAAAAGAAAA
1 GAAAAAA-AAAA
41093931 GAAGAAAGAAAAA
1 GAA-AAA-AAAAA
41093944 GAAAAA
1 GAAAAA
41093950 GGAGAGGCCA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
10 8 0.19
11 15 0.35
12 9 0.21
13 10 0.23
14 1 0.02
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.05
Consensus pattern (11 bp):
GAAAAAAAAAA
Found at i:41094471 original size:108 final size:108
Alignment explanation
Indices: 41094272--41094471 Score: 276
Period size: 108 Copynumber: 1.9 Consensus size: 108
41094262 TAATTTATTC
* * *
41094272 TCATTTTGTATTCTAGCAAAATTTGCTATCCTGATTAATGTGTTCATTTAGAGTTTTGTTCTCAA
1 TCATCTTGTATTCTAGCAAAATTTGCTATCCTGATTAATGTGTTCATTTAGAGCTTTGCTCTCAA
*
41094337 CAAATTTTCATCTTATCCATTGTGATAATATTTTCCATCTTAT
66 CAAAATTTCATCTTATCCATTGTGATAATATTTTCCATCTTAT
* * * **
41094380 TCATCTTGTA-TCTCAGCAAAATTTGCTATCTTGATTGATTTGTTTGTTTAGAGCTTTGCTCTCA
1 TCATCTTGTATTCT-AGCAAAATTTGCTATCCTGATTAATGTGTTCATTTAGAGCTTTGCTCTCA
* * *
41094444 ACAAAATTTCATTTTGTCCATTTTGATA
65 ACAAAATTTCATCTTATCCATTGTGATA
41094472 NNNNNNNNNN
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
107 3 0.04
108 76 0.96
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.47
Consensus pattern (108 bp):
TCATCTTGTATTCTAGCAAAATTTGCTATCCTGATTAATGTGTTCATTTAGAGCTTTGCTCTCAA
CAAAATTTCATCTTATCCATTGTGATAATATTTTCCATCTTAT
Found at i:41098351 original size:3 final size:3
Alignment explanation
Indices: 41098336--41098397 Score: 61
Period size: 3 Copynumber: 20.0 Consensus size: 3
41098326 NNNNNNNTTA
* * * *
41098336 TAT TAT TAG TAT TAT TAG TAT TAC TAT TAT TAT TAT TAT GTAT TAG
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT
*
41098382 TAT ATAT TTT TAT TAT
1 TAT -TAT TAT TAT TAT
41098398 GTACGCGTAT
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
3 41 0.87
4 6 0.13
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:41098394 original size:23 final size:22
Alignment explanation
Indices: 41098339--41098400 Score: 81
Period size: 23 Copynumber: 2.8 Consensus size: 22
41098329 NNNNTTATAT
*
41098339 TATTAGTATTATTA-GTATTAC
1 TATTATTATTATTATGTATTAC
*
41098360 TATTATTATTATTATGTATTAG
1 TATTATTATTATTATGTATTAC
*
41098382 TATATATTTTTATTATGTA
1 TAT-TATTATTATTATGTA
41098401 CGCGTATACA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 13 0.36
22 9 0.25
23 14 0.39
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58
Consensus pattern (22 bp):
TATTATTATTATTATGTATTAC
Found at i:41098407 original size:23 final size:23
Alignment explanation
Indices: 41098363--41098408 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
41098353 GTATTACTAT
**
41098363 TATTATTATTATGTATTAGTATA
1 TATTATTATTATGTACGAGTATA
* *
41098386 TATTTTTATTATGTACGCGTATA
1 TATTATTATTATGTACGAGTATA
41098409 CATATATATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.04, G:0.11, T:0.54
Consensus pattern (23 bp):
TATTATTATTATGTACGAGTATA
Found at i:41098472 original size:25 final size:24
Alignment explanation
Indices: 41098425--41098472 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
41098415 TATTTTTTCA
*
41098425 TATTTAATATTTTTATTTCATTTT
1 TATTTAATATTTTTATTTAATTTT
41098449 TATTCTAATA-TTTTATTATAATTT
1 TATT-TAATATTTTTATT-TAATTT
41098473 ATATATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (24 bp):
TATTTAATATTTTTATTTAATTTT
Found at i:41102454 original size:34 final size:34
Alignment explanation
Indices: 41102415--41102481 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
41102405 AACTTGTTTA
41102415 GAAGCCTTACTTTGTAAACAATACATAGTTATTC
1 GAAGCCTTACTTTGTAAACAATACATAGTTATTC
41102449 GAAGCCTTACTTTGTAAACAATACATAGTTATT
1 GAAGCCTTACTTTGTAAACAATACATAGTTATT
41102482 ATTTCTTTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (34 bp):
GAAGCCTTACTTTGTAAACAATACATAGTTATTC
Found at i:41104634 original size:28 final size:28
Alignment explanation
Indices: 41104580--41104634 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
41104570 TTTGTCTACA
* *
41104580 CTTGGATGTCGTTTTCCCAAGTTGCTTT
1 CTTGGATGTCATTTTCCCAAGTAGCTTT
* *
41104608 CTTGGATGTCATTTTCTCACGTAGCTT
1 CTTGGATGTCATTTTCCCAAGTAGCTT
41104635 CCTTTTTTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.45
Consensus pattern (28 bp):
CTTGGATGTCATTTTCCCAAGTAGCTTT
Found at i:41104670 original size:71 final size:71
Alignment explanation
Indices: 41104554--41104709 Score: 269
Period size: 71 Copynumber: 2.2 Consensus size: 71
41104544 ATGGTTGCTT
* *
41104554 CCACGTTGCTTTC-TTTTTTGTCTACACTTGGATGTCGTTTTCCCAAGTTGCTTTCTTGGATGTC
1 CCACGTAGCTTCCTTTTTTTGTCTACACTTGGATGTCGTTTTCCCAAGTTGCTTTCTTGGATGTC
41104618 ATTTTC
66 ATTTTC
* *
41104624 TCACGTAGCTTCCTTTTTTTGTCTACATTTGGATGTCGTTTTCCCAAGTTGCTTTCTTGGATGTC
1 CCACGTAGCTTCCTTTTTTTGTCTACACTTGGATGTCGTTTTCCCAAGTTGCTTTCTTGGATGTC
41104689 ATTTTC
66 ATTTTC
41104695 CCACGTAGCTTCCTT
1 CCACGTAGCTTCCTT
41104710 GATATTTTAA
Statistics
Matches: 80, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
70 10 0.12
71 70 0.88
ACGTcount: A:0.12, C:0.24, G:0.17, T:0.47
Consensus pattern (71 bp):
CCACGTAGCTTCCTTTTTTTGTCTACACTTGGATGTCGTTTTCCCAAGTTGCTTTCTTGGATGTC
ATTTTC
Found at i:41104705 original size:28 final size:28
Alignment explanation
Indices: 41104652--41104710 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
41104642 TTGTCTACAT
* * *
41104652 TTGGATGTCGTTTTCCCAAGTTGCTTTC
1 TTGGATGTCATTTTCCCAAGTAGCTTCC
*
41104680 TTGGATGTCATTTTCCCACGTAGCTTCC
1 TTGGATGTCATTTTCCCAAGTAGCTTCC
41104708 TTG
1 TTG
41104711 ATATTTTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.44
Consensus pattern (28 bp):
TTGGATGTCATTTTCCCAAGTAGCTTCC
Found at i:41105454 original size:16 final size:17
Alignment explanation
Indices: 41105424--41105455 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
41105414 TTTAAATCGT
41105424 TTGTAAAAAACATATAC
1 TTGTAAAAAACATATAC
41105441 TTGTAAAAAA-ATATA
1 TTGTAAAAAACATATA
41105456 TTCTGAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.31
Consensus pattern (17 bp):
TTGTAAAAAACATATAC
Found at i:41115740 original size:20 final size:20
Alignment explanation
Indices: 41115699--41115740 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
41115689 TCATAACATA
* *
41115699 TCTCTCATTCTATATTCTTT
1 TCTCTCATTCCATATTCCTT
41115719 TCTCTCATTCCAT-TTCCCTT
1 TCTCTCATTCCATATT-CCTT
41115739 TC
1 TC
41115741 CTTTTCCCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.12, C:0.33, G:0.00, T:0.55
Consensus pattern (20 bp):
TCTCTCATTCCATATTCCTT
Found at i:41119848 original size:12 final size:11
Alignment explanation
Indices: 41119825--41119867 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
41119815 TTACAATAAC
41119825 AAACAA-ATTAA
1 AAACAATATT-A
41119836 AAACAATATTA
1 AAACAATATTA
*
41119847 AAACAATTCTTA
1 AAACAA-TATTA
41119859 AAACAATAT
1 AAACAATAT
41119868 ACAGATTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 15 0.54
12 13 0.46
ACGTcount: A:0.63, C:0.12, G:0.00, T:0.26
Consensus pattern (11 bp):
AAACAATATTA
Found at i:41119946 original size:22 final size:22
Alignment explanation
Indices: 41119901--41119947 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
41119891 GTGGTTATAT
*
41119901 TAAGATAGTAACAACTAACAAG
1 TAAGATAGTAACAACTAAAAAG
*
41119923 TAAGA-AGTTACAACTAAAATAG
1 TAAGATAGTAACAACTAAAA-AG
41119945 TAA
1 TAA
41119948 CAAAACTAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.55, C:0.11, G:0.13, T:0.21
Consensus pattern (22 bp):
TAAGATAGTAACAACTAAAAAG
Found at i:41124280 original size:44 final size:45
Alignment explanation
Indices: 41124217--41124329 Score: 165
Period size: 44 Copynumber: 2.5 Consensus size: 45
41124207 TACTCCAGAA
*
41124217 ATGAGTAAGACCATAGTTGAAAGATGCTATGGCATC-TGATAAAG
1 ATGAGTAAGACCATAGTTGAAAGATGCTATGGCATCATAATAAAG
* * * *
41124261 ATGAGTAAGACTATAGTTGAAAGATGCTATGGCGTCATAATACAT
1 ATGAGTAAGACCATAGTTGAAAGATGCTATGGCATCATAATAAAG
*
41124306 ATGAGTAAGGCCATAGTTGAAAGA
1 ATGAGTAAGACCATAGTTGAAAGA
41124330 AACTATGACA
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
44 34 0.56
45 27 0.44
ACGTcount: A:0.39, C:0.11, G:0.25, T:0.26
Consensus pattern (45 bp):
ATGAGTAAGACCATAGTTGAAAGATGCTATGGCATCATAATAAAG
Found at i:41125752 original size:102 final size:102
Alignment explanation
Indices: 41125576--41125781 Score: 403
Period size: 102 Copynumber: 2.0 Consensus size: 102
41125566 TTGAGAACAT
41125576 GATTCAAAGGTGTTTGCCATATATTTAGGTTTTTGTATCATTTGGAACCTAGACTCGAAGAGTGG
1 GATTCAAAGGTGTTTGCCATATATTTAGGTTTTTGTATCATTTGGAACCTAGACTCGAAGAGTGG
41125641 GTCGGGTACAAGTGTTACAAATCCTTTCCAAATAAAA
66 GTCGGGTACAAGTGTTACAAATCCTTTCCAAATAAAA
41125678 GATTCAAAGGTGTTTGCCATATATTTAGGTTTTTGTATCATTTGGAACCTAGACTCGAAGAGTGG
1 GATTCAAAGGTGTTTGCCATATATTTAGGTTTTTGTATCATTTGGAACCTAGACTCGAAGAGTGG
*
41125743 GTCGGGTACAAGTGTTACAAATTCTTTCCAAATAAAA
66 GTCGGGTACAAGTGTTACAAATCCTTTCCAAATAAAA
41125780 GA
1 GA
41125782 AGGTTTGTTA
Statistics
Matches: 103, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 103 1.00
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (102 bp):
GATTCAAAGGTGTTTGCCATATATTTAGGTTTTTGTATCATTTGGAACCTAGACTCGAAGAGTGG
GTCGGGTACAAGTGTTACAAATCCTTTCCAAATAAAA
Found at i:41128717 original size:16 final size:18
Alignment explanation
Indices: 41128690--41128722 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
41128680 TAGAATTGAG
41128690 TTGAGAAAATT-ATTTAA
1 TTGAGAAAATTAATTTAA
41128707 TTGAG-AAATTAATTTA
1 TTGAGAAAATTAATTTA
41128723 TTTAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (18 bp):
TTGAGAAAATTAATTTAA
Found at i:41135596 original size:3 final size:3
Alignment explanation
Indices: 41135588--41135618 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
41135578 TAATATCTCC
41135588 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
41135619 GTTTTTTTAC
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:41135971 original size:40 final size:40
Alignment explanation
Indices: 41135926--41136005 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
41135916 AAATATTATG
41135926 ACTATATACTATTATTTACATTAAGATTTTTTTTTACTTA
1 ACTATATACTATTATTTACATTAAGATTTTTTTTTACTTA
41135966 ACTATATACTATTATTTACATTAAGATTTTTTTTTACTTA
1 ACTATATACTATTATTTACATTAAGATTTTTTTTTACTTA
41136006 TAAATCAAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.33, C:0.10, G:0.03, T:0.55
Consensus pattern (40 bp):
ACTATATACTATTATTTACATTAAGATTTTTTTTTACTTA
Found at i:41141826 original size:14 final size:15
Alignment explanation
Indices: 41141797--41141834 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
41141787 TTTGAGTAAA
41141797 AAAAAGATGAAAAATG
1 AAAAA-ATGAAAAATG
41141813 AAAAAATG-AAAATG
1 AAAAAATGAAAAATG
*
41141827 TAAAAATG
1 AAAAAATG
41141835 GAGAAGCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.62
15 3 0.14
16 5 0.24
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (15 bp):
AAAAAATGAAAAATG
Found at i:41143306 original size:88 final size:86
Alignment explanation
Indices: 41143076--41143343 Score: 419
Period size: 86 Copynumber: 3.1 Consensus size: 86
41143066 AGATCAGTGA
*
41143076 AGATCGAAAACAAACCCTGCCTCCCTCGGTTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGCC
1 AGATCGAAAACAAACCTTGCCTCCCTCGGTTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGCC
41143141 TTCCTGCATCGACAGTGAAGC
66 TTCCTGCATCGACAGTGAAGC
* * * **
41143162 AGATCGAAAACAAACCTTGCCTCCATCGGTTGTAGTGGAACTGGTTGAAGATAGCAGATTTTGTT
1 AGATCGAAAACAAACCTTGCCTCCCTCGGTTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGCC
*
41143227 TTCTTGCATCGACAGTGAAGC
66 TTCCTGCATCGACAGTGAAGC
* *
41143248 AGATCGAAGACACAAACCTTGCCTCCCTCGGTTGTAGTGGAGTTGGTTGAGGATAGCAGATCTTG
1 AGATCGAA-A-ACAAACCTTGCCTCCCTCGGTTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTG
* *
41143313 CCTTCCTGCATCGACAGTTAAGT
64 CCTTCCTGCATCGACAGTGAAGC
41143336 AGATCGAA
1 AGATCGAA
41143344 TACGGCTAAT
Statistics
Matches: 163, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
86 87 0.53
87 1 0.01
88 75 0.46
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.26
Consensus pattern (86 bp):
AGATCGAAAACAAACCTTGCCTCCCTCGGTTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGCC
TTCCTGCATCGACAGTGAAGC
Found at i:41143744 original size:44 final size:44
Alignment explanation
Indices: 41143549--41143941 Score: 188
Period size: 44 Copynumber: 9.1 Consensus size: 44
41143539 TAGAGAAGCG
* *
41143549 GATTGAAGTAATAGATCTTATCTCTCTGAAGTTGCAGT--AG-A
1 GATTGAAGTAATAAATCTTATCTCCCTGAAGTTGCAGTGGAGCA
* * * * * ** *
41143590 G-TGGATCGCAACAAGTCTTATC-CCTCTGAAGTCACAGTGGGGCA
1 GATTGA-AGTAATAAATCTTATCTCC-CTGAAGTTGCAGTGGAGCA
* * * *
41143634 GACTGAAG-AAGAAAATATTATCTCCCTGAGGTTGCAGTGGAGCA
1 GATTGAAGTAA-TAAATCTTATCTCCCTGAAGTTGCAGTGGAGCA
* * * *
41143678 GATTGAAGTCGAT-AATCCTATCTCCCTGAAGTTGTAGTGGAGCG
1 GATTGAAGT-AATAAATCTTATCTCCCTGAAGTTGCAGTGGAGCA
* * ** * * **
41143722 GATTAAAGTAATAAATCTTATCTCTCTGACA-TTATACTAGAGTG
1 GATTGAAGTAATAAATCTTATCTCCCTGA-AGTTGCAGTGGAGCA
* * * ** * *
41143766 GATCGCA-T--CAGGTCTTATTTCCCTGAAG-T-CAAGGTGGGGCA
1 GATTGAAGTAATAAATCTTATCTCCCTGAAGTTGC-A-GTGGAGCA
* *
41143807 GACTGAAG-AAGCAAATCTTATCTCCCT-AAGGTTGCAGTGGAGCA
1 GATTGAAGTAA-TAAATCTTATCTCCCTGAA-GTTGCAGTGGAGCA
* * * *
41143851 GATTGAAGTCGAT-AATCCTATCTCCCTGAAGTTGTAGTGGAGCG
1 GATTGAAGT-AATAAATCTTATCTCCCTGAAGTTGCAGTGGAGCA
* * * * *
41143895 GATTAAAGTAATAGATTTTATCTCTCTGAAGTTGCAGTAGAGCA
1 GATTGAAGTAATAAATCTTATCTCCCTGAAGTTGCAGTGGAGCA
41143939 GAT
1 GAT
41143942 CGCATCAAGT
Statistics
Matches: 254, Mismatches: 72, Indels: 49
0.68 0.19 0.13
Matches are distributed among these distances:
40 7 0.03
41 43 0.17
43 10 0.04
44 182 0.72
45 9 0.04
46 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (44 bp):
GATTGAAGTAATAAATCTTATCTCCCTGAAGTTGCAGTGGAGCA
Found at i:41143794 original size:173 final size:173
Alignment explanation
Indices: 41143501--41143954 Score: 662
Period size: 173 Copynumber: 2.6 Consensus size: 173
41143491 AGTGTAAGGA
* * * * * *
41143501 AGCAGATTGAAGCCGATAATCCTATCTTCCTTAAGTTGTAGAGAAGCGGATTGAAGTAATAGATC
1 AGCAGATTGAAGTCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATC
* *
41143566 TTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCAACAAGTCTTATCCCTCTGAAGTCACA-GTGG
66 TTATCTCTCTGAAGTTACACTAGAGTGGATCGCAACAAGTCTTATCCCTCTGAAGTCA-AGGTGG
*
41143630 GGCAGACTGAAGAAGAAAATATTATCTCCCTGAGGTTGCAGTGG
130 GGCAGACTGAAGAAGAAAATATTATCTCCCTAAGGTTGCAGTGG
*
41143674 AGCAGATTGAAGTCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAAATC
1 AGCAGATTGAAGTCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATC
* * * *
41143739 TTATCTCTCTGACA-TTATACTAGAGTGGATCGCATCAGGTCTTATTTCC-CTGAAGTCAAGGTG
66 TTATCTCTCTGA-AGTTACACTAGAGTGGATCGCAACAAGTCTTA-TCCCTCTGAAGTCAAGGTG
* *
41143802 GGGCAGACTGAAGAAGCAAATCTTATCTCCCTAAGGTTGCAGTGG
129 GGGCAGACTGAAGAAGAAAATATTATCTCCCTAAGGTTGCAGTGG
*
41143847 AGCAGATTGAAGTCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATT
1 AGCAGATTGAAGTCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATC
* * ** *
41143912 TTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAGTCTT
66 TTATCTCTCTGAAGTTACACTAGAGTGGATCGCAACAAGTCTT
41143955 GCCAACTAAA
Statistics
Matches: 253, Mismatches: 24, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
172 2 0.01
173 247 0.98
174 4 0.02
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.29
Consensus pattern (173 bp):
AGCAGATTGAAGTCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATC
TTATCTCTCTGAAGTTACACTAGAGTGGATCGCAACAAGTCTTATCCCTCTGAAGTCAAGGTGGG
GCAGACTGAAGAAGAAAATATTATCTCCCTAAGGTTGCAGTGG
Found at i:41145426 original size:3 final size:3
Alignment explanation
Indices: 41145418--41145474 Score: 96
Period size: 3 Copynumber: 19.0 Consensus size: 3
41145408 TAATATCTCC
*
41145418 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ACT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
41145466 ACT ATT ATT
1 ATT ATT ATT
41145475 TTTTTACTTA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:41150091 original size:18 final size:18
Alignment explanation
Indices: 41150068--41150109 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
41150058 ATTAAATGAT
41150068 TTAATAATAATCAATTTA
1 TTAATAATAATCAATTTA
41150086 TTAATAATAATCAATTTA
1 TTAATAATAATCAATTTA
41150104 TATAAT
1 T-TAAT
41150110 TTAGCTAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (18 bp):
TTAATAATAATCAATTTA
Found at i:41150421 original size:2 final size:2
Alignment explanation
Indices: 41150414--41150445 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
41150404 TGACAACCGA
*
41150414 AT AT AT AT AT AT AT AT AA AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41150446 TTCATTATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:41150648 original size:41 final size:41
Alignment explanation
Indices: 41150590--41150694 Score: 97
Period size: 41 Copynumber: 2.6 Consensus size: 41
41150580 TGTAATAATG
* *
41150590 CACCGGCATAAA-ACCTGCTAGGCTCA-AGCCTCATAAAAACT
1 CACCGGCA-AAAGGCCTGCTAGGCTCATAGCCTCAT-AAAACA
** * * * * *
41150631 CACCGGCACTAGGCCTGCAAGGCTTATAGCCTGATATATCA
1 CACCGGCAAAAGGCCTGCTAGGCTCATAGCCTCATAAAACA
41150672 CACCGGCAAAAGGCCTGCTAGGC
1 CACCGGCAAAAGGCCTGCTAGGC
41150695 ACGAAGCTCG
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
40 1 0.02
41 42 0.84
42 7 0.14
ACGTcount: A:0.30, C:0.31, G:0.21, T:0.17
Consensus pattern (41 bp):
CACCGGCAAAAGGCCTGCTAGGCTCATAGCCTCATAAAACA
Found at i:41156904 original size:52 final size:53
Alignment explanation
Indices: 41156795--41156908 Score: 140
Period size: 52 Copynumber: 2.2 Consensus size: 53
41156785 GTGATTTACT
* * **
41156795 TTATTTAGTAGGCCTTGAGTCGGTGTATATTTTTAGCAAGATTTGAGCTGGTGA
1 TTATTTAGAAGGCCTTAAGTCGGTGTATA-TTTTAGCAAGATTTGAGCCAGTGA
* * * *
41156849 TTATTTAGAAGGCTTTAAGTCGGTGTGTA-TTTAGCAGGCTTTGAGCCAGTGA
1 TTATTTAGAAGGCCTTAAGTCGGTGTATATTTTAGCAAGATTTGAGCCAGTGA
41156901 TTATTTAG
1 TTATTTAG
41156909 CAGGTACCAC
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
52 27 0.52
54 25 0.48
ACGTcount: A:0.23, C:0.10, G:0.27, T:0.40
Consensus pattern (53 bp):
TTATTTAGAAGGCCTTAAGTCGGTGTATATTTTAGCAAGATTTGAGCCAGTGA
Found at i:41156909 original size:26 final size:26
Alignment explanation
Indices: 41156795--41156912 Score: 103
Period size: 26 Copynumber: 4.5 Consensus size: 26
41156785 GTGATTTACT
* * *
41156795 TTATTTAGTAGGCCTTGAGTCGGTGTA
1 TTATTTAGCAGGCTTTGAGCCGGTG-A
* * * *
41156822 TATTTTTAGCAAGATTTGAGCTGGTGA
1 T-TATTTAGCAGGCTTTGAGCCGGTGA
* * *
41156849 TTATTTAGAAGGCTTTAAGTCGGTG-
1 TTATTTAGCAGGCTTTGAGCCGGTGA
*
41156874 TGTATTTAGCAGGCTTTGAGCCAGTGA
1 T-TATTTAGCAGGCTTTGAGCCGGTGA
41156901 TTATTTAGCAGG
1 TTATTTAGCAGG
41156913 TACCACATAT
Statistics
Matches: 70, Mismatches: 18, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
25 1 0.01
26 48 0.69
27 4 0.06
28 17 0.24
ACGTcount: A:0.23, C:0.10, G:0.28, T:0.39
Consensus pattern (26 bp):
TTATTTAGCAGGCTTTGAGCCGGTGA
Found at i:41157582 original size:101 final size:101
Alignment explanation
Indices: 41157407--41157613 Score: 405
Period size: 101 Copynumber: 2.0 Consensus size: 101
41157397 ATATAGGATG
41157407 ATGTTATGTTAAGGTTGTTACTGTCTTGGTATTTTGGTTGTAAATATCTTTGGGTGTAAAGTTGG
1 ATGTTATGTTAAGGTTGTTACTGTCTTGGTATTTTGGTTGTAAATATCTTTGGGTGTAAAGTTGG
41157472 TATATGTTTTGATAAAAGTGACTATTTTGGTAATGA
66 TATATGTTTTGATAAAAGTGACTATTTTGGTAATGA
41157508 ATGTTATGTTAAGGTTGTTACTGTCTTGGTATTTTGGTTGTAAATATCTTTGGGTGTAAAGTTGG
1 ATGTTATGTTAAGGTTGTTACTGTCTTGGTATTTTGGTTGTAAATATCTTTGGGTGTAAAGTTGG
*
41157573 TATATGTTTTGATAAAGGTGACTATTTTGGTAATGA
66 TATATGTTTTGATAAAAGTGACTATTTTGGTAATGA
41157609 ATGTT
1 ATGTT
41157614 TATAGTCATC
Statistics
Matches: 105, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
101 105 1.00
ACGTcount: A:0.24, C:0.04, G:0.25, T:0.47
Consensus pattern (101 bp):
ATGTTATGTTAAGGTTGTTACTGTCTTGGTATTTTGGTTGTAAATATCTTTGGGTGTAAAGTTGG
TATATGTTTTGATAAAAGTGACTATTTTGGTAATGA
Found at i:41157646 original size:101 final size:98
Alignment explanation
Indices: 41157439--41157643 Score: 266
Period size: 101 Copynumber: 2.0 Consensus size: 98
41157429 GTCTTGGTAT
41157439 TTTGGTTGTAAATATCTTTGGGTGTAAAGTTGGTATATGTTTTGATAAAAGTGACTATTTTGGTA
1 TTTGGTTGTAAATATCTTTGGGTGTAAAGTTGGTATATGTTTTGATAAAAGTGACTATTTTGGTA
* * * * * *
41157504 ATGAATGTTATGTTAAGGTTGTTACTGTCTTGG
66 ATGAATGTTATGTCAACGTTGTAACAGCCCTGG
*
41157537 TATTTTGGTTGTAAATATCTTTGGGTGTAAAGTTGGTATATGTTTTGATAAAGGTGACTATTTTG
1 ---TTTGGTTGTAAATATCTTTGGGTGTAAAGTTGGTATATGTTTTGATAAAAGTGACTATTTTG
* *
41157602 GTAATGAATGTTTATAGTCATCTTTGTAACAGCACCCTGG
63 GTAATGAATG-TTAT-GTCAACGTTGTAACAG--CCCTGG
41157642 TT
1 TT
41157644 GGTATATGGT
Statistics
Matches: 91, Mismatches: 9, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
101 71 0.78
102 6 0.07
103 10 0.11
105 4 0.04
ACGTcount: A:0.25, C:0.06, G:0.24, T:0.45
Consensus pattern (98 bp):
TTTGGTTGTAAATATCTTTGGGTGTAAAGTTGGTATATGTTTTGATAAAAGTGACTATTTTGGTA
ATGAATGTTATGTCAACGTTGTAACAGCCCTGG
Found at i:41171257 original size:11 final size:12
Alignment explanation
Indices: 41171241--41171273 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
41171231 GGACCCAAGA
41171241 TGAATTAATTT-
1 TGAATTAATTTG
*
41171252 TGAATTCATTTG
1 TGAATTAATTTG
41171264 TGAATTAATT
1 TGAATTAATT
41171274 CACTTGTGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.33, C:0.03, G:0.12, T:0.52
Consensus pattern (12 bp):
TGAATTAATTTG
Found at i:41177348 original size:15 final size:15
Alignment explanation
Indices: 41177328--41177358 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
41177318 ATGAATTTAG
41177328 TTAATGTACATGCAT
1 TTAATGTACATGCAT
*
41177343 TTAATGTACATTCAT
1 TTAATGTACATGCAT
41177358 T
1 T
41177359 CATGCACGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.45
Consensus pattern (15 bp):
TTAATGTACATGCAT
Found at i:41184356 original size:21 final size:21
Alignment explanation
Indices: 41184326--41184366 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
41184316 CGTTACTTTG
*
41184326 GTTTAATGATTTTGA-AAATC
1 GTTTAATGATATTGAGAAATC
41184346 GTTTATATGATATTGAGAAAT
1 GTTTA-ATGATATTGAGAAAT
41184367 GGTCTAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.37, C:0.02, G:0.17, T:0.44
Consensus pattern (21 bp):
GTTTAATGATATTGAGAAATC
Found at i:41184434 original size:24 final size:23
Alignment explanation
Indices: 41184415--41184483 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
41184405 AATGATATTG
41184415 AGAAATAGTATAATCTTGATTTA
1 AGAAATAGTATAATCTTGATTTA
* * * *
41184438 ATGATATTG-AGAAT-TATGATTTTT
1 A-GAAATAGTATAATCT-TGA-TTTA
41184462 AGAAATAGTATAATCTTGATTT
1 AGAAATAGTATAATCTTGATTT
41184484 TTAGAATTAT
Statistics
Matches: 34, Mismatches: 7, Indels: 10
0.67 0.14 0.20
Matches are distributed among these distances:
22 1 0.03
23 16 0.47
24 16 0.47
25 1 0.03
ACGTcount: A:0.39, C:0.03, G:0.14, T:0.43
Consensus pattern (23 bp):
AGAAATAGTATAATCTTGATTTA
Found at i:41184484 original size:24 final size:24
Alignment explanation
Indices: 41184415--41184489 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 24
41184405 AATGATATTG
*
41184415 AGAAATAGTATAATCTTGA-TTTA
1 AGAAATAGTATAATCTTGATTTTT
* * *
41184438 ATGATATTG-AGAAT-TATGATTTTT
1 A-GAAATAGTATAATCT-TGATTTTT
41184462 AGAAATAGTATAATCTTGATTTTT
1 AGAAATAGTATAATCTTGATTTTT
41184486 AGAA
1 AGAA
41184490 TTATGTTGTG
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
22 1 0.03
23 13 0.32
24 25 0.62
25 1 0.03
ACGTcount: A:0.40, C:0.03, G:0.15, T:0.43
Consensus pattern (24 bp):
AGAAATAGTATAATCTTGATTTTT
Found at i:41197046 original size:13 final size:13
Alignment explanation
Indices: 41197028--41197053 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41197018 TACGTAAAGA
41197028 AATTAATTAATTT
1 AATTAATTAATTT
41197041 AATTAATTAATTT
1 AATTAATTAATTT
41197054 TACATTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AATTAATTAATTT
Found at i:41200158 original size:51 final size:50
Alignment explanation
Indices: 41199987--41200170 Score: 171
Period size: 51 Copynumber: 3.6 Consensus size: 50
41199977 TGAAATTGAA
* *
41199987 AGTGATGGTCACATGTGTAGTACTACGTGCAGGC-GACTACGTGTACCAGA-
1 AGTGATGGTCACATGTGTAGTACTATGTGCAGGCTG-CTACGTGTA-CGGAT
* * * *
41200037 A-TGATAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACTGGAT
1 AGTGAT-GGTCACATGTGTAGTACTATGTGCAGGCTGCTACGTGTAC-GGAT
* * * *
41200088 AGCT--TCGATCACGTCTGTAGTACTATGTGTAGGCTGCTACGTGTATCGGAT
1 AG-TGAT-GGTCACATGTGTAGTACTATGTGCAGGCTGCTACGTGTA-CGGAT
*
41200139 AGTGATGGCCACATGTGTAGTACTATGTGCAG
1 AGTGATGGTCACATGTGTAGTACTATGTGCAG
41200171 ACTACTATGT
Statistics
Matches: 105, Mismatches: 20, Indels: 17
0.74 0.14 0.12
Matches are distributed among these distances:
49 5 0.05
50 37 0.35
51 60 0.57
52 2 0.02
53 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.29
Consensus pattern (50 bp):
AGTGATGGTCACATGTGTAGTACTATGTGCAGGCTGCTACGTGTACGGAT
Found at i:41200426 original size:16 final size:16
Alignment explanation
Indices: 41200405--41200436 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
41200395 TGATTGAAAG
*
41200405 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
41200421 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
41200437 GCAACAAAAC
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:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:41205827 original size:24 final size:24
Alignment explanation
Indices: 41205800--41205861 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
41205790 CCTAGAAAGT
* *
41205800 AATAAAAACACAAACCCATAAATC
1 AATAAAAACGCAAACCCACAAATC
* *
41205824 AATAAAAATGCAAACTCACAAATC
1 AATAAAAACGCAAACCCACAAATC
*
41205848 AATAGAAACGCAAA
1 AATAAAAACGCAAA
41205862 ATCACAAACC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.61, C:0.21, G:0.05, T:0.13
Consensus pattern (24 bp):
AATAAAAACGCAAACCCACAAATC
Found at i:41205866 original size:24 final size:24
Alignment explanation
Indices: 41205800--41205869 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
41205790 CCTAGAAAGT
* ** *
41205800 AATAAAAACACAAACCCATAAATC
1 AATAAAAACGCAAAATCACAAATC
* *
41205824 AATAAAAATGCAAACTCACAAATC
1 AATAAAAACGCAAAATCACAAATC
*
41205848 AATAGAAACGCAAAATCACAAA
1 AATAAAAACGCAAAATCACAAA
41205870 CCTTGAAGAC
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.61, C:0.21, G:0.04, T:0.13
Consensus pattern (24 bp):
AATAAAAACGCAAAATCACAAATC
Found at i:41207291 original size:36 final size:36
Alignment explanation
Indices: 41207216--41207291 Score: 84
Period size: 36 Copynumber: 2.1 Consensus size: 36
41207206 CATACATACG
*
41207216 TTTTATAATATATACATATACGTACACATTTTTTAAT
1 TTTTATAATATATACATATACG-ACACATTTTATAAT
* *
41207253 TTTTATAA-ATATATATATAC-ACATACTTTTATATAT
1 TTTTATAATATATACATATACGACACA-TTTTATA-AT
41207289 TTT
1 TTT
41207292 CTATGTTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
34 4 0.12
35 6 0.18
36 16 0.47
37 8 0.24
ACGTcount: A:0.38, C:0.09, G:0.01, T:0.51
Consensus pattern (36 bp):
TTTTATAATATATACATATACGACACATTTTATAAT
Found at i:41207399 original size:21 final size:20
Alignment explanation
Indices: 41207373--41207411 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
41207363 TAATTCACAC
*
41207373 ACATATATTTTTCTTATATGT
1 ACATATATATTT-TTATATGT
41207394 ACATATATATTTTTATAT
1 ACATATATATTTTTATAT
41207412 TTTATAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.56
Consensus pattern (20 bp):
ACATATATATTTTTATATGT
Found at i:41212437 original size:44 final size:44
Alignment explanation
Indices: 41212371--41213129 Score: 672
Period size: 44 Copynumber: 17.7 Consensus size: 44
41212361 TACAAAGCTT
* *
41212371 TATCTCCCTGGTCAGTAGTGGAATAGGTTAAAGATTGTAAGTCC
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
* *
41212415 TACCTCCCTGGTCAGCAGTGGAATAGGCTGAAGATTGTGAA-TCC
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGT-AAGTCC
* * *
41212459 TATCTCCCTAGTCAACAGTGGAATAGGTTGAAGATTGTGAGTCC
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
41212503 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
* *
41212547 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAGTTC
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
*
41212591 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAGTCC
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
* * *
41212635 TATCTCTCTGGCCAGTAGTGGAATAGGTTGAAGATTGTAAGTCC
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
* *
41212679 TATTTCCCTGGTCAGTAGTGGAATA----G--G--TG-AA-TCC
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
*
41212713 TATCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGTGAA-TCC
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGT-AAGTCC
* * **
41212757 TATCTCCCTGGTGAGCCG-AAAATAGGTTGAAGATTGTGAA-TCC
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGT-AAGTCC
* * *
41212800 TATCTCCCTGAG-CAGCAGTGGAGTAGGTTGAA-AAT-TACAGATCT
1 TATCTCCCTG-GTCAGCAGTGGAATAGGTTGAAGATTGTA-AG-TCC
* * ** * * * ** * *
41212844 TATCTCCCTAAG-CAGTAGTGGAGCAGATCGAAAACGGCGAA-TCT
1 TATCTCCCT-GGTCAGCAGTGGAATAGGTTGAAGATTG-TAAGTCC
* * * * * ****
41212888 TATCTTCCCAAGGT-AGTAG-GGAAGCAGATTTAAGCCACT-AG-CC
1 TATC-TCCC-TGGTCAGCAGTGGAA-TAGGTTGAAGATTGTAAGTCC
* *
41212931 TTATCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCT
1 -TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
41212976 TATCTCCCTGGTCAGCAGTGGAATA----G--G--TG-AA-TCC
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
* *
41213010 TATCTCCCTTGTCAGTAGTGGAATAGGTTGAAGATTGTGAA-TCC
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGT-AAGTCC
* * *
41213054 CATCTTCCTGGTCAGCAGTAGAATAGGTTGAAGATTGTGAA-TCC
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGT-AAGTCC
*
41213098 TATCTCCCTGAG-CAGCAGTGGAGTAGGTTGAA
1 TATCTCCCTG-GTCAGCAGTGGAATAGGTTGAA
41213130 AATTACAGAT
Statistics
Matches: 593, Mismatches: 80, Indels: 84
0.78 0.11 0.11
Matches are distributed among these distances:
34 50 0.08
35 4 0.01
36 4 0.01
38 4 0.01
40 4 0.01
41 1 0.00
42 8 0.01
43 58 0.10
44 435 0.73
45 23 0.04
46 1 0.00
47 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (44 bp):
TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
Found at i:41212610 original size:132 final size:132
Alignment explanation
Indices: 41212371--41213129 Score: 743
Period size: 132 Copynumber: 5.9 Consensus size: 132
41212361 TACAAAGCTT
* *
41212371 TATCTCCCTGGTCAGTAGTGGAATAGGTTAAAGATTGTAAGTCCTACCTCCCTGGTCAGCAGTGG
1 TATCTCCCTGGTCAGTAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTGGTCAGCAGTGG
* * * *
41212436 AATAGGCTGAAGATTGTGAATCCTATCTCCCTAGTCAACAGTGGAATAGGTTGAAGATTGTGAGT
66 AATAGGTTGAAGATTGTGAGTCCTATCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
41212501 CC
131 CC
*
41212503 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTGGTCAGCAGTGG
1 TATCTCCCTGGTCAGTAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTGGTCAGCAGTGG
* * *
41212568 AATAGGTTGAAGATTGTGAGTTCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAGT
66 AATAGGTTGAAGATTGTGAGTCCTATCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
41212633 CC
131 CC
* * * *
41212635 TATCTCTCTGGCCAGTAGTGGAATAGGTTGAAGATTGTAAGTCCTATTTCCCTGGTCAGTAGTGG
1 TATCTCCCTGGTCAGTAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTGGTCAGCAGTGG
41212700 AATAGG-T---GA-----A-TCCTATCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
66 AATAGGTTGAAGATTGTGAGTCCTATCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
41212755 CC
131 CC
* ** **
41212757 TATCTCCCTGGTGAGCCG-AAAATAGGTTGAAGATTGTGAA-TCCTATCTCCCTGAG-CAGCAGT
1 TATCTCCCTGGTCAGTAGTGGAATAGGTTGAAGATTGT-AAGTCCTATCTCCCTG-GTCAGCAGT
* * ** * * ** * * * ** *
41212819 GGAGTAGGTTGAAAATT-ACAGATCTTATCTCCCTAAG-CAGTAGTGGAGCAGATCGAAAACGGC
64 GGAATAGGTTGAAGATTGTGAG-TCCTATCTCCCT-AGTCAGCAGTGGAATAGGTTGAAGATTGT
*
41212882 GAATCT
127 GAATCC
* * * * **** *
41212888 TATCTTCCCAAGGT-AGTAG-GGAAGCAGATTTAAGCCACT-AG-CCTTATCTCCCTAGTCAGCA
1 TATC-TCCC-TGGTCAGTAGTGGAA-TAGGTTGAAGATTGTAAGTCC-TATCTCCCTGGTCAGCA
* * *
41212949 GTGGAATAGGTTGAAGATTGTAAGTCTTATCTCCCTGGTCAGCAGTGG-A-A---T--AG---GT
62 GTGGAATAGGTTGAAGATTGTGAGTCCTATCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGT
41213004 GAATCC
127 GAATCC
* * * *
41213010 TATCTCCCTTGTCAGTAGTGGAATAGGTTGAAGATTGTGAA-TCCCATCTTCCTGGTCAGCAGTA
1 TATCTCCCTGGTCAGTAGTGGAATAGGTTGAAGATTGT-AAGTCCTATCTCCCTGGTCAGCAGTG
* *
41213074 GAATAGGTTGAAGATTGTGAATCCTATCTCCCTGAG-CAGCAGTGGAGTAGGTTGAA
65 GAATAGGTTGAAGATTGTGAGTCCTATCTCCCT-AGTCAGCAGTGGAATAGGTTGAA
41213130 AATTACAGAT
Statistics
Matches: 513, Mismatches: 80, Indels: 71
0.77 0.12 0.11
Matches are distributed among these distances:
120 2 0.00
121 59 0.12
122 130 0.25
123 5 0.01
124 1 0.00
125 2 0.00
127 1 0.00
128 2 0.00
129 2 0.00
130 1 0.00
131 43 0.08
132 252 0.49
133 13 0.03
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (132 bp):
TATCTCCCTGGTCAGTAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTGGTCAGCAGTGG
AATAGGTTGAAGATTGTGAGTCCTATCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
CC
Found at i:41212721 original size:34 final size:34
Alignment explanation
Indices: 41212676--41212740 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
41212666 AGATTGTAAG
* * *
41212676 TCCTATTTCCCTGGTCAGTAGTGGAATAGGTGAA
1 TCCTATCTCCCTAGTCAGCAGTGGAATAGGTGAA
41212710 TCCTATCTCCCTAGTCAGCAGTGGAATAGGT
1 TCCTATCTCCCTAGTCAGCAGTGGAATAGGT
41212741 TGAAGATTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.31
Consensus pattern (34 bp):
TCCTATCTCCCTAGTCAGCAGTGGAATAGGTGAA
Found at i:41213064 original size:78 final size:78
Alignment explanation
Indices: 41212932--41213081 Score: 230
Period size: 78 Copynumber: 1.9 Consensus size: 78
41212922 CCACTAGCCT
** *
41212932 TATCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCTTATCTCCCTGGTCAGCAGTGG
1 TATCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCCCATCTCCCTGGTCAGCAGTAG
41212997 AATAGGTGAATCC
66 AATAGGTGAATCC
* * *
41213010 TATCTCCCTTGTCAGTAGTGGAATAGGTTGAAGATTGTGAA-TCCCATCTTCCTGGTCAGCAGTA
1 TATCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGT-AAGTCCCATCTCCCTGGTCAGCAGTA
41213074 GAATAGGT
65 GAATAGGT
41213082 TGAAGATTGT
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
78 63 0.97
79 2 0.03
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (78 bp):
TATCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCCCATCTCCCTGGTCAGCAGTAG
AATAGGTGAATCC
Found at i:41213279 original size:298 final size:297
Alignment explanation
Indices: 41212651--41213282 Score: 1054
Period size: 298 Copynumber: 2.1 Consensus size: 297
41212641 TCTGGCCAGT
* * * *
41212651 AGTGGAATAGGTTGAAGATTGTAAGTCCTATTTCCCTGGTCAGTAGTGGAATAGGTGAATCCTAT
1 AGTGGAATAGGTTGAAGAATGTAAGTCTTATCTCCCTGGTCAGCAGTGGAATAGGTGAATCCTAT
* * *
41212716 CTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCCTATCTCCCTGGTGAGCCGAAAATA
66 CTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCCCATCTCCCTGGTCAGCAGAAAATA
41212781 GGTTGAAGATTGTGAATCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTA
131 GGTTGAAGATTGTGAATCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTA
41212846 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAAACGGCGAATCTTATCTTCCCAAGGTAGTAGGGAA
196 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAAACGGCGAATCTTATCTTCCCAAGGTAGTAGGGAA
* *
41212911 GCAGATTTAAGCCACTAGCCTTATCTCCCTAGTCAGC
261 GCAGACTCAAGCCACTAGCCTTATCTCCCTAGTCAGC
*
41212948 AGTGGAATAGGTTGAAGATTGTAAGTCTTATCTCCCTGGTCAGCAGTGGAATAGGTGAATCCTAT
1 AGTGGAATAGGTTGAAGAATGTAAGTCTTATCTCCCTGGTCAGCAGTGGAATAGGTGAATCCTAT
* * * *
41213013 CTCCCTTGTCAGTAGTGGAATAGGTTGAAGATTGTGAATCCCATCTTCCTGGTCAGCAGTAGAAT
66 CTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCCCATCTCCCTGGTCAGCAG-AAAAT
41213078 AGGTTGAAGATTGTGAATCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCTT
130 AGGTTGAAGATTGTGAATCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCTT
*
41213143 ATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCAAGGTAGTAGGGA
195 ATCTCCCTAAGCAGTAGTGGAGCAGATCGAAAACGGCGAATCTTATCTTCCCAAGGTAGTAGGGA
41213208 AGCAGACTCAAGCCACTAGCCTTATCTCCCTAAG-CAGC
260 AGCAGACTCAAGCCACTAGCCTTATCTCCCT-AGTCAGC
* *
41213246 AGTGGAGTAGGTTGAA-AAT-TACAGATTTTATCTCCCT
1 AGTGGAATAGGTTGAAGAATGTA-AG-TCTTATCTCCCT
41213283 AAGTTACAGT
Statistics
Matches: 315, Mismatches: 16, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
296 2 0.01
297 119 0.38
298 192 0.61
299 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (297 bp):
AGTGGAATAGGTTGAAGAATGTAAGTCTTATCTCCCTGGTCAGCAGTGGAATAGGTGAATCCTAT
CTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCCCATCTCCCTGGTCAGCAGAAAATA
GGTTGAAGATTGTGAATCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTA
TCTCCCTAAGCAGTAGTGGAGCAGATCGAAAACGGCGAATCTTATCTTCCCAAGGTAGTAGGGAA
GCAGACTCAAGCCACTAGCCTTATCTCCCTAGTCAGC
Found at i:41213351 original size:87 final size:88
Alignment explanation
Indices: 41213230--41213389 Score: 198
Period size: 88 Copynumber: 1.8 Consensus size: 88
41213220 CCACTAGCCT
* * * * *
41213230 TATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATTACAGATTTTATCTCCCT-AAGTTACAGTG
1 TATCTCCCTAAGCAGCAGTGGAGCAGATTGAAAATAACAGATCTTATCTCCCTGAAGTTACAGTA
41213294 GAGCAGATTGAAGACAGTAATCC
66 GAGCAGATTGAAGACAGTAATCC
** * * *
41213317 TATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAATAATAGATCTTATCTCTCTGAAGTTGCAGT
1 TATCTCCCT-AAGCAGCAGTGGAGCAGATTGAAAATAACAGATCTTATCTCCCTGAAGTTACAGT
*
41213381 AGAGTAGAT
65 AGAGCAGAT
41213390 CGTATCAGGT
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
87 28 0.47
88 32 0.53
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (88 bp):
TATCTCCCTAAGCAGCAGTGGAGCAGATTGAAAATAACAGATCTTATCTCCCTGAAGTTACAGTA
GAGCAGATTGAAGACAGTAATCC
Found at i:41213365 original size:44 final size:44
Alignment explanation
Indices: 41213228--41213466 Score: 154
Period size: 44 Copynumber: 5.5 Consensus size: 44
41213218 AGCCACTAGC
** * * * *
41213228 CTTATCTCCCT-AAGCAGCAGTGGAGTAGGTTGAAAATTACAGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAATAATAGAT
* * * * *
41213272 TTTATCTCCCT-AAGTTACAGTGGAGCAGATTGAAGACAGTA-AT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAATAATAGAT
*
41213315 CCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAATAGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAATAGAT
* * * ** *
41213359 CTTATCTCTCTGAAGTTGCAGTAGAGTAGA-T--CGT-ATCAGGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAAT-AGAT
* * * *
41213400 CTTATCTCCCTGAGGTTGCAGCGGAGCAGACTAAGA-AATCA-AGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAAT-AGA-T
* *
41213444 CTTATCCCCCTAAAGTTGCAGTG
1 CTTATCTCCCTGAAGTTGCAGTG
41213467 AGGCAAACTA
Statistics
Matches: 151, Mismatches: 36, Indels: 16
0.74 0.18 0.08
Matches are distributed among these distances:
40 2 0.01
41 29 0.19
42 1 0.01
43 18 0.12
44 101 0.67
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAATAGAT
Found at i:41213477 original size:44 final size:44
Alignment explanation
Indices: 41213393--41213480 Score: 106
Period size: 44 Copynumber: 2.0 Consensus size: 44
41213383 AGTAGATCGT
* * * * *
41213393 ATCAGGTCTTATCTCCCTGAGGTTGCAGCGGAGCAGACTAAGAA
1 ATCAAGTCTTATCCCCCTAAAGTTGCAGCGGAGCAAACTAAGAA
*
41213437 ATCAAGTCTTATCCCCCTAAAGTTGCAG-TGAGGCAAACTAAGAA
1 ATCAAGTCTTATCCCCCTAAAGTTGCAGCGGA-GCAAACTAAGAA
41213481 TAGAAAATCT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
43 2 0.05
44 35 0.95
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.23
Consensus pattern (44 bp):
ATCAAGTCTTATCCCCCTAAAGTTGCAGCGGAGCAAACTAAGAA
Found at i:41213999 original size:22 final size:22
Alignment explanation
Indices: 41213939--41213996 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 22
41213929 AACCTTCAAG
41213939 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
41213958 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
41213980 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
41213997 GATTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.39
22 8 0.24
23 12 0.36
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:41214601 original size:36 final size:36
Alignment explanation
Indices: 41214526--41214601 Score: 84
Period size: 36 Copynumber: 2.1 Consensus size: 36
41214516 CATACATACG
*
41214526 TTTTATAATATATACATATACGTACACATTTTTTAAT
1 TTTTATAATATATACATATACG-ACACATTTTATAAT
* *
41214563 TTTTATAA-ATATATATATAC-ACATACTTTTATATAT
1 TTTTATAATATATACATATACGACACA-TTTTATA-AT
41214599 TTT
1 TTT
41214602 CTATGTTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
34 4 0.12
35 6 0.18
36 16 0.47
37 8 0.24
ACGTcount: A:0.38, C:0.09, G:0.01, T:0.51
Consensus pattern (36 bp):
TTTTATAATATATACATATACGACACATTTTATAAT
Found at i:41216805 original size:28 final size:29
Alignment explanation
Indices: 41216752--41216855 Score: 81
Period size: 31 Copynumber: 3.4 Consensus size: 29
41216742 CAGAATTAAA
*
41216752 TTATATATTTTTACGATAATAAAAATATAATT
1 TTAT-TATTTTTAAGAT-A-AAAAATATAATT
41216784 TTATTATTTTTAA-A-AAATAAAT-TAAATT
1 TTATTATTTTTAAGATAAA-AAATAT-AATT
*
41216812 TT-TATAATTTTAAGGGATAAAAAATATAATT
1 TTAT-TATTTTTAA--GATAAAAAATATAATT
*
41216843 TTATTATTATTAA
1 TTATTATTTTTAA
41216856 TTTAAAATGA
Statistics
Matches: 59, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
27 4 0.07
28 19 0.32
30 1 0.02
31 26 0.44
32 9 0.15
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (29 bp):
TTATTATTTTTAAGATAAAAAATATAATT
Found at i:41217801 original size:56 final size:55
Alignment explanation
Indices: 41217732--41217855 Score: 178
Period size: 55 Copynumber: 2.2 Consensus size: 55
41217722 TATATTAAAA
*
41217732 AATATATCAAAAAAATTAATTGATGT-TTTTAAAAAATAAAATATATTTGACATAAT
1 AATATAT-AAAAAAATTAATTGATGTATTTTAAAAAAT-AAATATATTTAACATAAT
* * *
41217788 AATATATAGAAAAATTAGTTGATGTATTTTAAAAAATAAATATATTTAATATAAT
1 AATATATAAAAAAATTAATTGATGTATTTTAAAAAATAAATATATTTAACATAAT
*
41217843 CATATATAAAAAA
1 AATATATAAAAAA
41217856 TATTTTATTA
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
55 43 0.70
56 18 0.30
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (55 bp):
AATATATAAAAAAATTAATTGATGTATTTTAAAAAATAAATATATTTAACATAAT
Found at i:41227606 original size:20 final size:20
Alignment explanation
Indices: 41227581--41227620 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
41227571 GGCCACACGA
*
41227581 GCATGTGTGAGGTTGTGTGG
1 GCATGTGTGAGGCTGTGTGG
41227601 GCATGTGTGAGGCTGTGTGG
1 GCATGTGTGAGGCTGTGTGG
41227621 ACCACATTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.07, G:0.50, T:0.33
Consensus pattern (20 bp):
GCATGTGTGAGGCTGTGTGG
Found at i:41228304 original size:34 final size:34
Alignment explanation
Indices: 41228264--41228387 Score: 158
Period size: 34 Copynumber: 3.6 Consensus size: 34
41228254 TTCTGATCTG
* *
41228264 ATATGACATTCTGATATGATATATGTTTCTGAAA
1 ATATGACATTCTAATATGATATATGTTTCTGGAA
* * *
41228298 ATATGACATTCTGATATGGTATATGTTTTTGGAA
1 ATATGACATTCTAATATGATATATGTTTCTGGAA
* * * *
41228332 ATATGACATTCTAATTTAATATATATTTCTGGTA
1 ATATGACATTCTAATATGATATATGTTTCTGGAA
*
41228366 ATGTGACATTCTAATATGATAT
1 ATATGACATTCTAATATGATAT
41228388 TTGTATATGT
Statistics
Matches: 77, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 77 1.00
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.44
Consensus pattern (34 bp):
ATATGACATTCTAATATGATATATGTTTCTGGAA
Done.