Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr1
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: 35726063
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1821929 characters in sequence are not A, C, G, or T
File 7 of 109
Found at i:2265998 original size:18 final size:18
Alignment explanation
Indices: 2265975--2266009 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2265965 AAAAAGAATT
*
2265975 AAAAAAGTATATTATTTA
1 AAAAAAATATATTATTTA
*
2265993 AAAAAAATATTTTATTT
1 AAAAAAATATATTATTT
2266010 CATGTCTACA
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:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (18 bp):
AAAAAAATATATTATTTA
Found at i:2271427 original size:6 final size:6
Alignment explanation
Indices: 2271418--2271469 Score: 104
Period size: 6 Copynumber: 8.7 Consensus size: 6
2271408 CATAAAAACT
2271418 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
2271466 TATA
1 TATA
2271470 TGCATTACAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (6 bp):
TATACA
Found at i:2274326 original size:14 final size:15
Alignment explanation
Indices: 2274309--2274347 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
2274299 AAAAATAATA
2274309 TAATAAACAAAA-CC
1 TAATAAACAAAAGCC
* *
2274323 TAATAAATAAAAGTC
1 TAATAAACAAAAGCC
2274338 TAATAAACAA
1 TAATAAACAA
2274348 TTCAGTCCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.64, C:0.13, G:0.03, T:0.21
Consensus pattern (15 bp):
TAATAAACAAAAGCC
Found at i:2275133 original size:26 final size:27
Alignment explanation
Indices: 2275104--2275156 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
2275094 TTTCAGAGAA
*
2275104 AAGGGAAAGAAGAGATG-ATTTTTTTT
1 AAGGGAAAGAAGAAATGAATTTTTTTT
* * *
2275130 AAGGTAGAGAGGAAATGAATTTTTTTT
1 AAGGGAAAGAAGAAATGAATTTTTTTT
2275157 TCTAAAATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.38, C:0.00, G:0.26, T:0.36
Consensus pattern (27 bp):
AAGGGAAAGAAGAAATGAATTTTTTTT
Found at i:2275690 original size:20 final size:20
Alignment explanation
Indices: 2275651--2275690 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2275641 TTATATTATT
*
2275651 TTTATGTATTATTTTATTTA
1 TTTATGTATTATTTCATTTA
* *
2275671 TTTATTTATTATTTCCTTTA
1 TTTATGTATTATTTCATTTA
2275691 CTTTTTTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.70
Consensus pattern (20 bp):
TTTATGTATTATTTCATTTA
Found at i:2275942 original size:14 final size:15
Alignment explanation
Indices: 2275913--2275944 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2275903 CTTTCATATT
2275913 TTATCATGCGCATTA
1 TTATCATGCGCATTA
2275928 TTATCATGC-CATTA
1 TTATCATGCGCATTA
2275942 TTA
1 TTA
2275945 CTACAAATTG
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:0.28, C:0.19, G:0.09, T:0.44
Consensus pattern (15 bp):
TTATCATGCGCATTA
Found at i:2294782 original size:27 final size:28
Alignment explanation
Indices: 2294752--2294806 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
2294742 TTTCAGAGAA
*
2294752 AAGGGAAAGAAGAGATG-ATTTTTTTTT
1 AAGGGAAAGAAGAAATGAATTTTTTTTT
* * *
2294779 AAGGTAGAGAGGAAATGAATTTTTTTTT
1 AAGGGAAAGAAGAAATGAATTTTTTTTT
2294807 CTAAAATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 13 0.57
28 10 0.43
ACGTcount: A:0.36, C:0.00, G:0.25, T:0.38
Consensus pattern (28 bp):
AAGGGAAAGAAGAAATGAATTTTTTTTT
Found at i:2295339 original size:20 final size:20
Alignment explanation
Indices: 2295300--2295339 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2295290 TTATATTATT
*
2295300 TTTATGTATTATTTTATTTA
1 TTTATGTATTATTTCATTTA
* *
2295320 TTTATTTATTATTTCCTTTA
1 TTTATGTATTATTTCATTTA
2295340 CTTTTTTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.70
Consensus pattern (20 bp):
TTTATGTATTATTTCATTTA
Found at i:2296206 original size:43 final size:43
Alignment explanation
Indices: 2296149--2296421 Score: 345
Period size: 43 Copynumber: 6.3 Consensus size: 43
2296139 TTATGGGAAA
* **
2296149 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTATAAC
1 AAACGCCGCTAAAGATCGTGACCTTTAGCGGCGCTTTTACCAC
* * * *
2296192 AAATGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTGCCAC
1 AAACGCCGCTAAAGATCGTGACCTTTAGCGGCGCTTTTACCAC
* * *
2296235 AAACGCCGCTAAAGATCTTGACCTTTAGCGGCGTTTTTATCAC
1 AAACGCCGCTAAAGATCGTGACCTTTAGCGGCGCTTTTACCAC
2296278 AAACGCCGCTAAAGATCGTGACCTTTAGCGGCGC-TTTAGCCAC
1 AAACGCCGCTAAAGATCGTGACCTTTAGCGGCGCTTTTA-CCAC
* **
2296321 AAACGCCGCTAAAGATCGTGATCTTTAGCGGCGC-TTTAGATAC
1 AAACGCCGCTAAAGATCGTGACCTTTAGCGGCGCTTTTA-CCAC
* * *
2296364 AAACGTCGCTAAAGATCGTGAGCTTTAGCGACGC-TTTAGCCAC
1 AAACGCCGCTAAAGATCGTGACCTTTAGCGGCGCTTTTA-CCAC
*
2296407 AAACGCCACTAAAGA
1 AAACGCCGCTAAAGA
2296422 ATAAACCTTT
Statistics
Matches: 205, Mismatches: 24, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
42 4 0.02
43 201 0.98
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAGATCGTGACCTTTAGCGGCGCTTTTACCAC
Found at i:2296257 original size:86 final size:86
Alignment explanation
Indices: 2296149--2296421 Score: 404
Period size: 86 Copynumber: 3.2 Consensus size: 86
2296139 TTATGGGAAA
* * *
2296149 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTATAACAAATGCCGCTAAAGAACATGAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTATAACAAACGCCGCTAAAGATCGTGAC
*
2296214 CTTTAGCGGCGCTTTTGCCAC
66 CTTTAGCGGCGCTTTAGCCAC
* * *
2296235 AAACGCCGCTAAAGATCTTGACCTTTAGCGGCGTTTTTATCACAAACGCCGCTAAAGATCGTGAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTATAACAAACGCCGCTAAAGATCGTGAC
2296300 CTTTAGCGGCGCTTTAGCCAC
66 CTTTAGCGGCGCTTTAGCCAC
* * * *
2296321 AAACGCCGCTAAAGATCGTGATCTTTAGCGGCGC-TTTAGATACAAACGTCGCTAAAGATCGTGA
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTATA-ACAAACGCCGCTAAAGATCGTGA
* *
2296385 GCTTTAGCGACGCTTTAGCCAC
65 CCTTTAGCGGCGCTTTAGCCAC
*
2296407 AAACGCCACTAAAGA
1 AAACGCCGCTAAAGA
2296422 ATAAACCTTT
Statistics
Matches: 170, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
85 4 0.02
86 166 0.98
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (86 bp):
AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTATAACAAACGCCGCTAAAGATCGTGAC
CTTTAGCGGCGCTTTAGCCAC
Found at i:2296301 original size:129 final size:129
Alignment explanation
Indices: 2296149--2296466 Score: 378
Period size: 129 Copynumber: 2.5 Consensus size: 129
2296139 TTATGGGAAA
* *
2296149 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTA-TAACAAATGCCGCTAAAGAACATGA
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGC-TTTAGCAACAAACGCCGCTAAAGAACATGA
* * * * * *
2296213 CCTTTAGCGGCGCTTTTGCCACAAACGCCGCTAAAGATCTTGACCTTTAGCGGCGTTTTTA-TCA
65 CCTTTAGCGGCGCTTTAGACACAAACGCCGCTAAAGATCGTGACCTTTAGCGACG-CTTTAGCCA
2296277 C
129 C
* * * * *
2296278 AAACGCCGCTAAAGATCGTGACCTTTAGCGGCGCTTTAGCCACAAACGCCGCTAAAGATCGTGAT
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTAGCAACAAACGCCGCTAAAGAACATGAC
* * *
2296343 CTTTAGCGGCGCTTTAGATACAAACGTCGCTAAAGATCGTGAGCTTTAGCGACGCTTTAGCCAC
66 CTTTAGCGGCGCTTTAGACACAAACGCCGCTAAAGATCGTGACCTTTAGCGACGCTTTAGCCAC
* * * *
2296407 AAACGCCACTAAAGA--ATAAACCTTTAGTGACGCTTCTAGCAA-AAACGCCGCTAAA-AACAT
1 AAACGCCGCTAAAGATCAT-GACCTTTAGCGGCGCTT-TAGCAACAAACGCCGCTAAAGAACAT
2296467 AANNNNNNNN
Statistics
Matches: 161, Mismatches: 24, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
127 4 0.02
128 35 0.22
129 122 0.76
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.24
Consensus pattern (129 bp):
AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTAGCAACAAACGCCGCTAAAGAACATGAC
CTTTAGCGGCGCTTTAGACACAAACGCCGCTAAAGATCGTGACCTTTAGCGACGCTTTAGCCAC
Found at i:2302802 original size:19 final size:19
Alignment explanation
Indices: 2302762--2302804 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2302752 AATTTTAATT
*
2302762 AATATAAATAAACAAATTA
1 AATATAAATAAACAAATAA
*
2302781 AATAGTAAAT-AACAGATAA
1 AATA-TAAATAAACAAATAA
2302800 AATAT
1 AATAT
2302805 TTTTGCGGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 15 0.71
20 5 0.24
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.26
Consensus pattern (19 bp):
AATATAAATAAACAAATAA
Found at i:2302866 original size:41 final size:41
Alignment explanation
Indices: 2302809--2302966 Score: 253
Period size: 41 Copynumber: 3.9 Consensus size: 41
2302799 AAATATTTTT
* *
2302809 GCGGCGCTTTCTCAAAAACGCCGCTAAAGCTCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
2302850 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
* *
2302891 GCGGCACTTTTTCAAAAACGGCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
* * *
2302932 GTGGCGCTTTTTTAAAAACGCCGCTAAAGACCTGA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGA
2302967 TAGGTCAAAA
Statistics
Matches: 108, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 108 1.00
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (41 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
Found at i:2303054 original size:41 final size:39
Alignment explanation
Indices: 2303006--2303098 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 39
2302996 AGGTTTTTTT
2303006 GCGGCGTTTTTCCAAAAAACGCCGCTAATGCTTGATCTTTA
1 GCGGCGTTTTT--AAAAAACGCCGCTAATGCTTGATCTTTA
** * *
2303047 GCGGCGTTTTGTGTAAAGCGCCGCTAATGCTTGATTTTTA
1 GCGGCGTTTT-TAAAAAACGCCGCTAATGCTTGATCTTTA
2303087 GCGGCGCTTTTT
1 GCGGCG-TTTTT
2303099 GTCCAAACGC
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
40 31 0.67
41 14 0.30
42 1 0.02
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.35
Consensus pattern (39 bp):
GCGGCGTTTTTAAAAAACGCCGCTAATGCTTGATCTTTA
Found at i:2304007 original size:14 final size:14
Alignment explanation
Indices: 2303988--2304038 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
2303978 ATGGTAGGGT
2303988 TTGGGCCTAGTGTA
1 TTGGGCCTAGTGTA
* *
2304002 TTGGGCCAAGGGTA
1 TTGGGCCTAGTGTA
*
2304016 TTTGGG-CTAATGTAA
1 -TTGGGCCTAGTGT-A
2304031 TTGGGCCT
1 TTGGGCCT
2304039 CGTAAATTAG
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
14 21 0.72
15 8 0.28
ACGTcount: A:0.18, C:0.14, G:0.35, T:0.33
Consensus pattern (14 bp):
TTGGGCCTAGTGTA
Found at i:2304796 original size:101 final size:101
Alignment explanation
Indices: 2304633--2305230 Score: 937
Period size: 101 Copynumber: 5.9 Consensus size: 101
2304623 ATTTAACTGT
* * * * * * * ** * *
2304633 AATGTCGCGGAAACAAGATTCGCCGTCAT-GACTTCAATCTATTCCACTACACTACTAGGAAAGT
1 AATGTCGGGGAAACCAGATCCGCTGTCGTAG-CTTCAATCTGTTCCACTGCACCGCCAAGAAAGT
*
2304697 AAGACCCGCCATTGTGGCTTCAATCTTTTTAAATTGC
65 AAGACCCGCCGTTGTGGCTTCAATCTTTTTAAATTGC
*
2304734 AATGTCGGGGAAACCAGATCCGCTGTCGTAGCTTCAATCTGCTCCACTGCACCGCCAAGAAAGTA
1 AATGTCGGGGAAACCAGATCCGCTGTCGTAGCTTCAATCTGTTCCACTGCACCGCCAAGAAAGTA
*
2304799 AGACCCGCCGTTGTGGCTTCAATCTTTCTAAATTGC
66 AGACCCGCCGTTGTGGCTTCAATCTTTTTAAATTGC
* *
2304835 AATATCGGGGAAACCAGATCTGCTGTCGTAGCTTCAATCTGTTCCACTGCACCGCCAAGAAAGTA
1 AATGTCGGGGAAACCAGATCCGCTGTCGTAGCTTCAATCTGTTCCACTGCACCGCCAAGAAAGTA
*
2304900 AGACCCGCCGTTGTGGCTTCAATTTTTTTAAATTGC
66 AGACCCGCCGTTGTGGCTTCAATCTTTTTAAATTGC
** *
2304936 AATGTCAAGGAAACCAGATCTGCTGTCGTAGCTTCAATCTGTTCCACTGCACCGCCAAGAAAGTA
1 AATGTCGGGGAAACCAGATCCGCTGTCGTAGCTTCAATCTGTTCCACTGCACCGCCAAGAAAGTA
2305001 AGACCCGCCGTTGTGGCTTCAATCTTTTTAAATTGC
66 AGACCCGCCGTTGTGGCTTCAATCTTTTTAAATTGC
* *
2305037 AATGTCGGGGAAACCAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGAAAGTA
1 AATGTCGGGGAAACCAGATCCGCTGTCGTAGCTTCAATCTGTTCCACTGCACCGCCAAGAAAGTA
*
2305102 AGACCCGTCGTTGTGGCTTCAATCTTTTTAAATTGC
66 AGACCCGCCGTTGTGGCTTCAATCTTTTTAAATTGC
* * *
2305138 AATGTCGAGGAAACCAGATCCGCTGTCGTAGCTTCAATCTGTTCCACTGCACCGCCAGGAAAGGA
1 AATGTCGGGGAAACCAGATCCGCTGTCGTAGCTTCAATCTGTTCCACTGCACCGCCAAGAAAGTA
*
2305203 AGACCCGCCGTTGTGGCTTTAATCTTTT
66 AGACCCGCCGTTGTGGCTTCAATCTTTT
2305231 CCACTGTAAT
Statistics
Matches: 462, Mismatches: 34, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
101 461 1.00
102 1 0.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (101 bp):
AATGTCGGGGAAACCAGATCCGCTGTCGTAGCTTCAATCTGTTCCACTGCACCGCCAAGAAAGTA
AGACCCGCCGTTGTGGCTTCAATCTTTTTAAATTGC
Found at i:2307383 original size:14 final size:14
Alignment explanation
Indices: 2307347--2307414 Score: 52
Period size: 14 Copynumber: 4.9 Consensus size: 14
2307337 AGGGCTACAT
2307347 TGTAGTTGGG-CTAG
1 TGTA-TTGGGCCTAG
*
2307361 GGT-TTGGGCCTAG
1 TGTATTGGGCCTAG
*
2307374 TGTATTGGGCCAAG
1 TGTATTGGGCCTAG
* *
2307388 GGTATTTGGG-CTAA
1 TGTA-TTGGGCCTAG
2307402 TGTAATTGGGCCT
1 TGT-ATTGGGCCT
2307415 CGTAAATTAG
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
12 5 0.12
13 6 0.14
14 23 0.55
15 8 0.19
ACGTcount: A:0.16, C:0.12, G:0.38, T:0.34
Consensus pattern (14 bp):
TGTATTGGGCCTAG
Found at i:2308001 original size:9 final size:9
Alignment explanation
Indices: 2307989--2308018 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
2307979 GATGAACATA
2307989 AAATTTAGT
1 AAATTTAGT
2307998 AAATTTAGT
1 AAATTTAGT
*
2308007 AAATTTACT
1 AAATTTAGT
2308016 AAA
1 AAA
2308019 CATAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (9 bp):
AAATTTAGT
Found at i:2308457 original size:27 final size:27
Alignment explanation
Indices: 2308419--2308480 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
2308409 TTTTAGTCCT
*
2308419 GTGCCGCCTCTGGCAAAGGCACCTTTG
1 GTGCCGCCTCTGCCAAAGGCACCTTTG
*
2308446 GTGCCGCCTCTGCCACAGGCACCTTTG
1 GTGCCGCCTCTGCCAAAGGCACCTTTG
2308473 GTGCCGCC
1 GTGCCGCC
2308481 CGTGGCATCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.11, C:0.39, G:0.29, T:0.21
Consensus pattern (27 bp):
GTGCCGCCTCTGCCAAAGGCACCTTTG
Found at i:2308917 original size:31 final size:32
Alignment explanation
Indices: 2308884--2308945 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
2308874 GAATTAGATA
*
2308884 TTTTGATTTAAATTTATTATGATA-TTTTTTAT
1 TTTTGACTTAAATTT-TTATGATAGTTTTTTAT
* *
2308916 TTTTTACTTGAATTTTTATGATAGTTTTTT
1 TTTTGACTTAAATTTTTATGATAGTTTTTT
2308946 CCTTAGCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 8 0.31
32 18 0.69
ACGTcount: A:0.24, C:0.02, G:0.08, T:0.66
Consensus pattern (32 bp):
TTTTGACTTAAATTTTTATGATAGTTTTTTAT
Found at i:2309667 original size:33 final size:33
Alignment explanation
Indices: 2309630--2309696 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
2309620 TGGTTGGGAC
2309630 TAAGGAAATAATTATCCAAATGCCCCTTCATGA
1 TAAGGAAATAATTATCCAAATGCCCCTTCATGA
*
2309663 TAAGGAAATAATTATCCAAATGTCCCTTCATGA
1 TAAGGAAATAATTATCCAAATGCCCCTTCATGA
2309696 T
1 T
2309697 CCATGTATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.30
Consensus pattern (33 bp):
TAAGGAAATAATTATCCAAATGCCCCTTCATGA
Found at i:2321206 original size:29 final size:29
Alignment explanation
Indices: 2321142--2321219 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 29
2321132 TAAAATAAAA
* * *
2321142 AATATTTTATAAATTTT-ATAATAATTTT
1 AATATTTTTTAATTTTTAAAAATAATTTT
*
2321170 AATGATTTTTTAATTTTTAAAAATAGTTTT
1 AAT-ATTTTTTAATTTTTAAAAATAATTTT
*
2321200 TATATTTTTTAATTTTTAAA
1 AATATTTTTTAATTTTTAAA
2321220 TTTTAAAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
28 3 0.07
29 29 0.67
30 11 0.26
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (29 bp):
AATATTTTTTAATTTTTAAAAATAATTTT
Found at i:2330451 original size:31 final size:31
Alignment explanation
Indices: 2330405--2330466 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
2330395 ATCAACTTAA
* *
2330405 GAAAAAGTGTCAAGTTTAGGTACTAAATTAG
1 GAAAAAGTGTAAAGTTTAGGTACCAAATTAG
*
2330436 GAAAAATTGTAAAGTTTAGGTACCAAATTAG
1 GAAAAAGTGTAAAGTTTAGGTACCAAATTAG
2330467 ACCAAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.29
Consensus pattern (31 bp):
GAAAAAGTGTAAAGTTTAGGTACCAAATTAG
Found at i:2330612 original size:16 final size:18
Alignment explanation
Indices: 2330575--2330614 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
2330565 TTTTTGAGAT
2330575 ATTT-TATATTATGTTAG
1 ATTTATATATTATGTTAG
*
2330592 TTTTATATATTATG-TA-
1 ATTTATATATTATGTTAG
2330608 ATTTATA
1 ATTTATA
2330615 ATACATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 6 0.30
17 5 0.25
18 9 0.45
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (18 bp):
ATTTATATATTATGTTAG
Found at i:2332631 original size:16 final size:18
Alignment explanation
Indices: 2332594--2332633 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
2332584 TTTTTGAGAT
2332594 ATTT-TATATTATGTTAG
1 ATTTATATATTATGTTAG
*
2332611 TTTTATATATTATG-TA-
1 ATTTATATATTATGTTAG
2332627 ATTTATA
1 ATTTATA
2332634 ATACATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 6 0.30
17 5 0.25
18 9 0.45
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (18 bp):
ATTTATATATTATGTTAG
Found at i:2334260 original size:52 final size:52
Alignment explanation
Indices: 2334203--2334307 Score: 167
Period size: 52 Copynumber: 2.0 Consensus size: 52
2334193 CAGGCCGGGC
*
2334203 TCGGGCTTAGGATTTTATTCCCGGGTCGGGCCTAG-ACAAAATTTCAGGCCCA
1 TCGGGCTTAGGATTTTATTCCCGGGCCGGGCCT-GTACAAAATTTCAGGCCCA
* *
2334255 TCGGGCTTAGGATTTTATTCCCGGGCCGGTCCTGTACAAAATTTTAGGCCCA
1 TCGGGCTTAGGATTTTATTCCCGGGCCGGGCCTGTACAAAATTTCAGGCCCA
2334307 T
1 T
2334308 ATTTCGGGTC
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
51 1 0.02
52 48 0.98
ACGTcount: A:0.20, C:0.25, G:0.26, T:0.30
Consensus pattern (52 bp):
TCGGGCTTAGGATTTTATTCCCGGGCCGGGCCTGTACAAAATTTCAGGCCCA
Found at i:2335805 original size:3 final size:3
Alignment explanation
Indices: 2335797--2335856 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
2335787 AAATTTTAGA
2335797 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2335845 TAT TAT TAT TAT
1 TAT TAT TAT TAT
2335857 ATTGTGTGTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2337756 original size:120 final size:119
Alignment explanation
Indices: 2337543--2337781 Score: 460
Period size: 120 Copynumber: 2.0 Consensus size: 119
2337533 GCACAGTTAA
2337543 ACTCCCATCATTTGCTGGCCCCGTACGAGGTAGGCGACCCCATCCGAAATCTACTTTTCTACAGA
1 ACTCCCATCATTTGCTGGCCCCGTACGAGGTAGGCGACCCCATCCGAAATCTACTTTTCTACAGA
2337608 GGCAACCGCATTTAAATATTTTCAATGAATTTTAATTACACGTCTGCTAAAACCT
66 GGCAACCGCATTTAAATATTTTCAATGAATTTTAATTACACGTC-GCTAAAACCT
*
2337663 ACTCCCATCATTTGCTGGCCCCGTACGAGGTAGGCGACCCCATCCGAAATCTACTTTTCTACATA
1 ACTCCCATCATTTGCTGGCCCCGTACGAGGTAGGCGACCCCATCCGAAATCTACTTTTCTACAGA
2337728 GGCAACCGCATTTAAATATTTTCAATGAATTTTAATTACACGTCGCTAAAACCT
66 GGCAACCGCATTTAAATATTTTCAATGAATTTTAATTACACGTCGCTAAAACCT
2337782 TACATGACTA
Statistics
Matches: 118, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
119 10 0.08
120 108 0.92
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (119 bp):
ACTCCCATCATTTGCTGGCCCCGTACGAGGTAGGCGACCCCATCCGAAATCTACTTTTCTACAGA
GGCAACCGCATTTAAATATTTTCAATGAATTTTAATTACACGTCGCTAAAACCT
Found at i:2338155 original size:33 final size:35
Alignment explanation
Indices: 2338117--2338213 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 35
2338107 ATGATTATAT
2338117 TTAAATATTTAAAATATATTTTATATATT-C-TAA
1 TTAAATATTTAAAATATATTTTATATATTGCTTAA
* *
2338150 TTAAAT-TTTATAAATA-ATTAATATTTATTGCTTAA
1 TTAAATATTTA-AAATATATT-TTATATATTGCTTAA
*
2338185 --AAATATTTAAAATTTATATTTCATATATT
1 TTAAATATTTAAAA--TATATTTTATATATT
2338214 AAAATGTTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
32 7 0.14
33 25 0.49
34 5 0.10
35 11 0.22
36 3 0.06
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (35 bp):
TTAAATATTTAAAATATATTTTATATATTGCTTAA
Found at i:2338400 original size:13 final size:13
Alignment explanation
Indices: 2338382--2338406 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2338372 GCTAAACACT
2338382 CACTTTTCAAAAG
1 CACTTTTCAAAAG
2338395 CACTTTTCAAAA
1 CACTTTTCAAAA
2338407 CTAGCCCTAA
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:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
CACTTTTCAAAAG
Found at i:2348456 original size:17 final size:17
Alignment explanation
Indices: 2348434--2348467 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2348424 TTGGTATAGT
2348434 TGGAATATAT-AACACAA
1 TGGAATAT-TCAACACAA
2348451 TGGAATATTCAACACAA
1 TGGAATATTCAACACAA
2348468 ACAGCTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.06
17 15 0.94
ACGTcount: A:0.50, C:0.15, G:0.12, T:0.24
Consensus pattern (17 bp):
TGGAATATTCAACACAA
Found at i:2352565 original size:16 final size:16
Alignment explanation
Indices: 2352541--2352578 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
2352531 TTAGAACATA
2352541 ATTTATTTTCCTTCTTTT
1 ATTT-TTTTCCTT-TTTT
2352559 -TTTTTTTCCTTTTTT
1 ATTTTTTTCCTTTTTT
2352574 ATTTT
1 ATTTT
2352579 CCATTGCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 4 0.21
16 12 0.63
17 3 0.16
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (16 bp):
ATTTTTTTCCTTTTTT
Found at i:2361555 original size:11 final size:11
Alignment explanation
Indices: 2361541--2361568 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
2361531 CTTTTTTTTT
2361541 TTTTTTTTGGG
1 TTTTTTTTGGG
2361552 TTTTTTTTGGG
1 TTTTTTTTGGG
2361563 TTTTTT
1 TTTTTT
2361569 AGGGTTAGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (11 bp):
TTTTTTTTGGG
Found at i:2384839 original size:4 final size:4
Alignment explanation
Indices: 2384830--2384884 Score: 74
Period size: 4 Copynumber: 13.8 Consensus size: 4
2384820 CAGGGGAGAA
* * * *
2384830 TATG TATG TATG TATG TATG CATG CATG TATG TATG TATG CATG CATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2384878 TATG TAT
1 TATG TAT
2384885 CAGTGCAGGC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.25, C:0.07, G:0.24, T:0.44
Consensus pattern (4 bp):
TATG
Found at i:2384858 original size:16 final size:16
Alignment explanation
Indices: 2384830--2384884 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
2384820 CAGGGGAGAA
*
2384830 TATGTATGTATGTATG
1 TATGTATGCATGTATG
*
2384846 TATGCATGCATGTATG
1 TATGTATGCATGTATG
*
2384862 TATGTATGCATGCATG
1 TATGTATGCATGTATG
2384878 TATGTAT
1 TATGTAT
2384885 CAGTGCAGGC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.25, C:0.07, G:0.24, T:0.44
Consensus pattern (16 bp):
TATGTATGCATGTATG
Found at i:2384891 original size:20 final size:20
Alignment explanation
Indices: 2384835--2384884 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
2384825 GAGAATATGT
2384835 ATGTATGTATGTATGCATGC
1 ATGTATGTATGTATGCATGC
2384855 ATGTATGTATGTATGCATGC
1 ATGTATGTATGTATGCATGC
2384875 ATGTATGTAT
1 ATGTATGTAT
2384885 CAGTGCAGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.08, G:0.24, T:0.42
Consensus pattern (20 bp):
ATGTATGTATGTATGCATGC
Found at i:2387314 original size:20 final size:21
Alignment explanation
Indices: 2387267--2387314 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
2387257 GCTTCCAGAA
* *
2387267 AATAATTTCTGAAAAATGACT
1 AATATTTTCTGAAAAATAACT
*
2387288 TAT-TTTTCTGAAAAA-AACT
1 AATATTTTCTGAAAAATAACT
2387307 AATATTTT
1 AATATTTT
2387315 TTGGTGTTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
19 5 0.23
20 15 0.68
21 2 0.09
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (21 bp):
AATATTTTCTGAAAAATAACT
Found at i:2394388 original size:14 final size:14
Alignment explanation
Indices: 2394357--2394431 Score: 73
Period size: 14 Copynumber: 5.3 Consensus size: 14
2394347 CGTACCACCT
*
2394357 TTTATAACAAATAAA
1 TTTATAA-AAATATA
*
2394372 TTTATATAAATATA
1 TTTATAAAAATATA
2394386 TTTATAAAAAT-TCGA
1 TTTATAAAAATAT--A
*
2394401 TATA-AAAAATATA
1 TTTATAAAAATATA
*
2394414 TTTATAAAAAAATA
1 TTTATAAAAATATA
2394428 TTTA
1 TTTA
2394432 AAATATAGAT
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
13 5 0.10
14 34 0.68
15 11 0.22
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (14 bp):
TTTATAAAAATATA
Found at i:2398452 original size:15 final size:15
Alignment explanation
Indices: 2398410--2398453 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
2398400 ATTAAATAAA
2398410 TAAAAAATATTAAATT
1 TAAAAAA-ATTAAATT
* * *
2398426 TAAATAATTTAATTT
1 TAAAAAAATTAAATT
2398441 TAAAAAAATTAAA
1 TAAAAAAATTAAA
2398454 AATAATATGG
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TAAAAAAATTAAATT
Found at i:2404164 original size:21 final size:21
Alignment explanation
Indices: 2404140--2404211 Score: 78
Period size: 20 Copynumber: 3.5 Consensus size: 21
2404130 AATACATGCA
*
2404140 TAAGGTATCGATACCTCGTAG
1 TAAGGTATCAATACCTCGTAG
**
2404161 TAA-GTATCAATACC-C-TCCC
1 TAAGGTATCAATACCTCGT-AG
2404180 TAAGGTATCAATACCTCGTAG
1 TAAGGTATCAATACCTCGTAG
*
2404201 CAAGGTATCAA
1 TAAGGTATCAA
2404212 AACTATAGAC
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
18 1 0.02
19 4 0.10
20 21 0.51
21 14 0.34
22 1 0.02
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (21 bp):
TAAGGTATCAATACCTCGTAG
Found at i:2412927 original size:34 final size:35
Alignment explanation
Indices: 2412861--2412927 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
2412851 CAAACACCAG
*
2412861 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATAATTTTACAGAAAAGT
* *
2412896 AAAATATTTTTCAG-AAATAATTTTACGGAAAA
1 AAAATATTTTCCAGTAAATAATTTTACAGAAAA
2412928 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.34
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATAATTTTACAGAAAAGT
Found at i:2419197 original size:3 final size:3
Alignment explanation
Indices: 2419189--2419233 Score: 67
Period size: 3 Copynumber: 15.3 Consensus size: 3
2419179 ATTAATTTTG
2419189 TTA TTA TTA TTA TTA TTA TTA -TA TTA -TA TATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
2419233 T
1 T
2419234 ACCTACATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.10
3 32 0.82
4 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:2429917 original size:31 final size:32
Alignment explanation
Indices: 2429857--2429931 Score: 98
Period size: 31 Copynumber: 2.3 Consensus size: 32
2429847 AAAAATGGGC
* *
2429857 CGGGTCGGGCTCGGGCTTATAATATTTTTTCCG
1 CGGGCCGGGCCCGGGCTTAT-ATATTTTTTCCG
* *
2429890 CGGGCCGGGCCCGGGCTTAT-TATTTTTTTCT
1 CGGGCCGGGCCCGGGCTTATATATTTTTTCCG
2429921 CGGGCCGGGCC
1 CGGGCCGGGCC
2429932 TGAGAAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
31 20 0.53
33 18 0.47
ACGTcount: A:0.08, C:0.27, G:0.33, T:0.32
Consensus pattern (32 bp):
CGGGCCGGGCCCGGGCTTATATATTTTTTCCG
Found at i:2438220 original size:25 final size:24
Alignment explanation
Indices: 2438184--2438302 Score: 69
Period size: 25 Copynumber: 4.7 Consensus size: 24
2438174 CGAAATGATT
* *
2438184 AAAAACTTGATGGAAAATTTTATG
1 AAAAACTTGATGAAAAACTTTATG
*
2438208 AAAAGACTTGATGAAAAACTTTA-A
1 AAAA-ACTTGATGAAAAACTTTATG
* * * *
2438232 AAAGAACTTGCTGCAAAACTTGATAA
1 AAA-AACTTGATGAAAAACTTTAT-G
* * *
2438258 AAAAACTTGGTAATTAAAAACTTGATA
1 AAAAACTT-G--ATGAAAAACTTTATG
*
2438285 AAAGAACTAGATGAAAAA
1 AAA-AACTTGATGAAAAA
2438303 TACTTGAAGA
Statistics
Matches: 76, Mismatches: 11, Indels: 15
0.75 0.11 0.15
Matches are distributed among these distances:
24 22 0.29
25 29 0.38
26 5 0.07
27 5 0.07
28 15 0.20
ACGTcount: A:0.52, C:0.08, G:0.14, T:0.25
Consensus pattern (24 bp):
AAAAACTTGATGAAAAACTTTATG
Found at i:2438223 original size:13 final size:12
Alignment explanation
Indices: 2438179--2438302 Score: 70
Period size: 12 Copynumber: 9.8 Consensus size: 12
2438169 AAAAACGAAA
*
2438179 TGATTAAAAACT
1 TGATGAAAAACT
* *
2438191 TGATGGAAAATT
1 TGATGAAAAACT
*
2438203 TTATGAAAAGACT
1 TGATGAAAA-ACT
2438216 TGATGAAAAACT
1 TGATGAAAAACT
* *
2438228 TTA-AAAAGAACT
1 TGATGAAA-AACT
* *
2438240 TGCTGCAAAACT
1 TGATGAAAAACT
*
2438252 TGATAAAAAAACT
1 TGAT-GAAAAACT
*
2438265 TGGTAATTAAAAACT
1 T-G--ATGAAAAACT
*
2438280 TGATAAAAGAACT
1 TGATGAAA-AACT
*
2438293 AGATGAAAAA
1 TGATGAAAAA
2438303 TACTTGAAGA
Statistics
Matches: 84, Mismatches: 20, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
11 3 0.04
12 40 0.48
13 29 0.35
14 2 0.02
15 8 0.10
16 2 0.02
ACGTcount: A:0.51, C:0.08, G:0.15, T:0.27
Consensus pattern (12 bp):
TGATGAAAAACT
Found at i:2438278 original size:15 final size:13
Alignment explanation
Indices: 2438246--2438309 Score: 65
Period size: 13 Copynumber: 4.7 Consensus size: 13
2438236 AACTTGCTGC
2438246 AAAACTTGATAAA
1 AAAACTTGATAAA
*
2438259 AAAACTTGGTAATTA
1 AAAACTTGATAA--A
2438274 AAAACTTGATAAA
1 AAAACTTGATAAA
* *
2438287 AGAACTAGATGAAA
1 AAAACTTGAT-AAA
*
2438301 AATACTTGA
1 AAAACTTGA
2438310 AGAATGAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
13 20 0.49
14 9 0.22
15 12 0.29
ACGTcount: A:0.55, C:0.08, G:0.12, T:0.25
Consensus pattern (13 bp):
AAAACTTGATAAA
Found at i:2438591 original size:17 final size:17
Alignment explanation
Indices: 2438569--2438602 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2438559 ATCTAGCCCA
*
2438569 ATTGTTTCCTTTTTCTT
1 ATTGTTTCATTTTTCTT
2438586 ATTGTTTCATTTTTCTT
1 ATTGTTTCATTTTTCTT
2438603 CTATTTAGCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.09, C:0.15, G:0.06, T:0.71
Consensus pattern (17 bp):
ATTGTTTCATTTTTCTT
Found at i:2439235 original size:14 final size:14
Alignment explanation
Indices: 2439216--2439242 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2439206 ATTATTCATT
2439216 TTTTCTTTTTTTTC
1 TTTTCTTTTTTTTC
2439230 TTTTCTTTTTTTT
1 TTTTCTTTTTTTT
2439243 TTTGAAAGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (14 bp):
TTTTCTTTTTTTTC
Found at i:2439982 original size:17 final size:17
Alignment explanation
Indices: 2439962--2440266 Score: 93
Period size: 17 Copynumber: 16.8 Consensus size: 17
2439952 AAAAAATCGG
2439962 GTTTCAAAAATTTCCGT
1 GTTTCAAAAATTTCCGT
* *
2439979 GTTTTAAAAAAAAATT-CGT
1 G-TTT--CAAAAATTTCCGT
*
2439998 GTTTTCAAAAACTTT-CAT
1 G-TTTCAAAAA-TTTCCGT
2440016 GTTTCAAAAATCTT-CGT
1 GTTTCAAAAAT-TTCCGT
*
2440033 GTTTTAAAAA-TTCCAGT
1 GTTTCAAAAATTTCC-GT
2440050 GTTTC-AAAATTT--GT
1 GTTTCAAAAATTTCCGT
2440064 GTTTTCAAAAAAATTTCCCGT
1 G-TTTC--AAAAATTT-CCGT
* *
2440085 GTTTTTAAAAAATTCTCGT
1 G-TTTCAAAAATTTC-CGT
* * * * *
2440104 ATATCGAAAATTTTCTT
1 GTTTCAAAAATTTCCGT
* *
2440121 GTTTTCAAAAAAAAAATTCCAT
1 G-TTTC----AAAAATTTCCGT
*
2440143 GTTTCATAAATTTCCGT
1 GTTTCAAAAATTTCCGT
*
2440160 GTTTTCAAAAAAAAATTCCCGT
1 G-TTTC----AAAAATTTCCGT
* * *
2440182 TTTTAAAAAATTTTCGT
1 GTTTCAAAAATTTCCGT
* *
2440199 GTTTTAAAAAATTGACCGT
1 G-TTTCAAAAATT-TCCGT
* *
2440218 GTTTCATAAATTTTCGT
1 GTTTCAAAAATTTCCGT
* **
2440235 GATTCAAAAAAATCTCGT
1 GTTTCAAAAATTTC-CGT
*
2440253 GTTTCAAAATTTTC
1 GTTTCAAAAATTTC
2440267 GGGTTTTTTT
Statistics
Matches: 211, Mismatches: 48, Indels: 57
0.67 0.15 0.18
Matches are distributed among these distances:
14 3 0.01
15 6 0.03
16 6 0.03
17 70 0.33
18 64 0.30
19 22 0.10
20 7 0.03
21 14 0.07
22 19 0.09
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (17 bp):
GTTTCAAAAATTTCCGT
Found at i:2440075 original size:33 final size:33
Alignment explanation
Indices: 2439988--2440075 Score: 101
Period size: 33 Copynumber: 2.7 Consensus size: 33
2439978 TGTTTTAAAA
* * *
2439988 AAAAATTCGTGTTTTCAAAAACTTTCATGTTTC
1 AAAAATTTGTGTTTTCAAAAAATTCCATGTTTC
2440021 AAAAATCTTCGTGTTTT--AAAAATTCCAGTGTTTC
1 AAAAAT-TT-GTGTTTTCAAAAAATTCCA-TGTTTC
2440055 -AAAATTTGTGTTTTCAAAAAA
1 AAAAATTTGTGTTTTCAAAAAA
2440076 ATTTCCCGTG
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
31 7 0.15
32 2 0.04
33 24 0.51
34 7 0.15
35 7 0.15
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.41
Consensus pattern (33 bp):
AAAAATTTGTGTTTTCAAAAAATTCCATGTTTC
Found at i:2440170 original size:38 final size:39
Alignment explanation
Indices: 2440111--2440273 Score: 141
Period size: 39 Copynumber: 4.4 Consensus size: 39
2440101 CGTATATCGA
* *
2440111 AAATTTTCTTGTTTTCAAAAAAAAAATT-CCATGTTTCAT
1 AAATTTTCGTGTTTTC-AAAAAAAAATTACCGTGTTTCAT
* * * * *
2440150 AAATTTCCGTGTTTTCAAAAAAAAATTCCCGTTTTTAAA
1 AAATTTTCGTGTTTTCAAAAAAAAATTACCGTGTTTCAT
2440189 AAATTTTCGTGTTTT----AAAAAATTGACCGTGTTTCAT
1 AAATTTTCGTGTTTTCAAAAAAAAATT-ACCGTGTTTCAT
*
2440225 AAATTTTCGTG-ATTC--AAAAAAA-T-CTCGTGTTTCA-
1 AAATTTTCGTGTTTTCAAAAAAAAATTAC-CGTGTTTCAT
*
2440259 AAATTTTCGGGTTTT
1 AAATTTTCGTGTTTT
2440274 TTTAAAAACA
Statistics
Matches: 104, Mismatches: 14, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
34 11 0.11
35 21 0.20
36 20 0.19
37 6 0.06
38 11 0.11
39 35 0.34
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.42
Consensus pattern (39 bp):
AAATTTTCGTGTTTTCAAAAAAAAATTACCGTGTTTCAT
Found at i:2440185 original size:21 final size:21
Alignment explanation
Indices: 2440150--2440191 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
2440140 CATGTTTCAT
*
2440150 AAATTTCCGTGTTTTCAAAAAA
1 AAATTCCCGTGTTTT-AAAAAA
2440172 AAATTCCCGT-TTTTAAAAAA
1 AAATTCCCGTGTTTTAAAAAA
2440192 TTTTCGTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 4 0.21
22 9 0.47
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (21 bp):
AAATTCCCGTGTTTTAAAAAA
Found at i:2440218 original size:19 final size:18
Alignment explanation
Indices: 2440169--2440221 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
2440159 TGTTTTCAAA
*
2440169 AAAAAATTCCCGT-TTTT
1 AAAAAATTACCGTGTTTT
**
2440186 AAAAAATTTTCGTGTTTT
1 AAAAAATTACCGTGTTTT
2440204 AAAAAATTGACCGTGTTT
1 AAAAAATT-ACCGTGTTT
2440222 CATAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 11 0.37
18 12 0.40
19 7 0.23
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (18 bp):
AAAAAATTACCGTGTTTT
Found at i:2440322 original size:16 final size:17
Alignment explanation
Indices: 2440303--2440335 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2440293 TCTAAAATTC
2440303 TCGTATTTT-AAAAAAA
1 TCGTATTTTCAAAAAAA
*
2440319 TCGTGTTTTCAAAAAAA
1 TCGTATTTTCAAAAAAA
2440336 GAAAAAGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (17 bp):
TCGTATTTTCAAAAAAA
Found at i:2441650 original size:17 final size:17
Alignment explanation
Indices: 2441628--2441675 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
2441618 GGGACCCAAA
2441628 AAATTATT-ATTTAATCG
1 AAATTATTAATTT-ATCG
2441645 AAATTATTAATTTATCG
1 AAATTATTAATTTATCG
*
2441662 -AA-TATTCATTTATC
1 AAATTATTAATTTATC
2441676 AAGATTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 11 0.38
16 2 0.07
17 12 0.41
18 4 0.14
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (17 bp):
AAATTATTAATTTATCG
Found at i:2442286 original size:15 final size:15
Alignment explanation
Indices: 2442266--2442299 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2442256 TTTATATTAT
**
2442266 TTTTGTTTTGTTTTC
1 TTTTGTTTTCCTTTC
2442281 TTTTGTTTTCCTTTC
1 TTTTGTTTTCCTTTC
2442296 TTTT
1 TTTT
2442300 TTCATGGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.09, T:0.79
Consensus pattern (15 bp):
TTTTGTTTTCCTTTC
Found at i:2443452 original size:30 final size:29
Alignment explanation
Indices: 2443418--2443474 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
2443408 TTACTTACTT
2443418 TTTTTATA-TATTAGTATGTATGTATCATTA
1 TTTTTATATTATTA-TATGTAT-TATCATTA
*
2443448 TTTTTATATTTTTATATGTATTATCAT
1 TTTTTATATTATTATATGTATTATCAT
2443475 GTCTTACTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 6 0.24
30 15 0.60
31 4 0.16
ACGTcount: A:0.28, C:0.04, G:0.07, T:0.61
Consensus pattern (29 bp):
TTTTTATATTATTATATGTATTATCATTA
Found at i:2464449 original size:16 final size:18
Alignment explanation
Indices: 2464414--2464451 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2464404 ATCTTTATTT
*
2464414 AAATAAAATACATTAGTA
1 AAATAAAATACATAAGTA
2464432 AAATAAAATA-A-AAGTA
1 AAATAAAATACATAAGTA
2464448 AAAT
1 AAAT
2464452 CCATATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 1 0.05
18 10 0.53
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (18 bp):
AAATAAAATACATAAGTA
Found at i:2469719 original size:15 final size:15
Alignment explanation
Indices: 2469699--2469748 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
2469689 AAACCAACAC
* *
2469699 AATAATAATACCCAT
1 AATAATAATAACAAT
2469714 AATAATAATAACAAT
1 AATAATAATAACAAT
* *
2469729 AATAATAACAGCAAT
1 AATAATAATAACAAT
2469744 AATAA
1 AATAA
2469749 CTTAATTAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.62, C:0.12, G:0.02, T:0.24
Consensus pattern (15 bp):
AATAATAATAACAAT
Found at i:2469729 original size:12 final size:12
Alignment explanation
Indices: 2469714--2469749 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
2469704 TAATACCCAT
2469714 AATAATAATAAC
1 AATAATAATAAC
2469726 AATAATAATAAC
1 AATAATAATAAC
**
2469738 AGCAATAATAAC
1 AATAATAATAAC
2469750 TTAATTAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.64, C:0.11, G:0.03, T:0.22
Consensus pattern (12 bp):
AATAATAATAAC
Found at i:2470227 original size:11 final size:12
Alignment explanation
Indices: 2470207--2470231 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2470197 TCCCTTCTTT
2470207 AAAACAAAAAAA
1 AAAACAAAAAAA
2470219 AAAACAAAAAAA
1 AAAACAAAAAAA
2470231 A
1 A
2470232 CTCTCTACCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAACAAAAAAA
Found at i:2472970 original size:17 final size:18
Alignment explanation
Indices: 2472929--2472964 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2472919 TTGTTATTAA
* *
2472929 ATATATTTTAATTAAAAT
1 ATATAATTTAATAAAAAT
2472947 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
2472965 CTTAATAATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:2473022 original size:61 final size:61
Alignment explanation
Indices: 2472957--2473143 Score: 159
Period size: 61 Copynumber: 3.1 Consensus size: 61
2472947 ATATAATTTA
* *
2472957 ATAAAAATCTTAATAATCAATATTGTTATATGAATTTACTCAAATCATAATATATGATACT
1 ATAAAAATCTTAATAATCAATATTATTATATGAATTTACTAAAATCATAATATATGATACT
* * * * * * ** * * *
2473018 AT-AAAAT-ATAAT-TTAAGATAATTATTAT-TCAATATATTTTAATTAAAATATATGAT-TT
1 ATAAAAATCTTAATAATCA-AT-ATTATTATATGAATTTACTAAAATCATAATATATGATACT
* * * *
2473076 AATAAAATTCTTAATAATCAATATTCTTATATGAATTTCCTAAAATCATAATATATGATAGT
1 -ATAAAAATCTTAATAATCAATATTATTATATGAATTTACTAAAATCATAATATATGATACT
2473138 ATAAAA
1 ATAAAA
2473144 TATAATTTGA
Statistics
Matches: 92, Mismatches: 26, Indels: 16
0.69 0.19 0.12
Matches are distributed among these distances:
58 3 0.03
59 29 0.32
60 23 0.25
61 34 0.37
62 3 0.03
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (61 bp):
ATAAAAATCTTAATAATCAATATTATTATATGAATTTACTAAAATCATAATATATGATACT
Found at i:2473122 original size:120 final size:119
Alignment explanation
Indices: 2472909--2473204 Score: 475
Period size: 120 Copynumber: 2.5 Consensus size: 119
2472899 TTAATCATAT
* * *
2472909 TTTAACATAATTGTTATTAAATATATTTTAATTAAAATATATAATTTAATAAAAATCTTAATAAT
1 TTTAA-ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAAT
* *
2472974 CAATATTGTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA
65 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
*
2473029 TTTAAGATAATTATTATTCAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAAT
1 TTTAA-ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAAT
* *
2473094 CAATATTCTTATATGAATTTCCTAAAATCATAATATATGATAGTATAAAATATAA
65 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
* *
2473149 TTTGAAATAATTATTATTAAAAATATTTTAATTAAAACATATGATTTAATAAAATT
1 TTT-AAATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
2473205 TAAAATAATA
Statistics
Matches: 163, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
120 161 0.99
121 2 0.01
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (119 bp):
TTTAAATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAATC
AATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
Found at i:2473211 original size:54 final size:55
Alignment explanation
Indices: 2472915--2473239 Score: 158
Period size: 57 Copynumber: 5.5 Consensus size: 55
2472905 ATATTTTAAC
* * *
2472915 ATAATTGTTATTAAATATATTTTAATTAAAATATATAATTTAATAAAAATCTTAATA
1 ATAATTATTATTAAAAATATTTTAATTAAAATATATGATTTAAT-AAAAT-TTAATA
* * * * * *
2472972 ATCAA-TATTGTTATATGAAT-TTACTCAAATCATAATATATGATACTATAAAATATAATTTAA-
1 AT-AATTATTATTA-A-AAATATT--T-TAATTAAAATATATGAT--T-T--AATAAAATTTAAT
*
2473034 G
55 A
* *
2473035 ATAATTATTATTCAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATA
1 ATAATTATTATTAAAAATATTTTAATTAAAATATATGATTTAATAAAA-T-TTAATA
* * * * * * *
2473092 ATCAA-TATTCTTATATGAAT-TTCCTAAAATCATAATATATGATAGT-ATAAAATATAATTTGA
1 AT-AATTATTATTA-A-AAATATT--T-TAATTAAAATATATGAT-TTAATAAAATTTAA--T--
2473154 A
55 A
*
2473155 ATAATTATTATTAAAAATATTTTAATTAAAACATATGATTTAATAAAATTTAAAATA
1 ATAATTATTATTAAAAATATTTTAATTAAAATATATGATTTAATAAAATTT--AATA
* *
2473212 ATAATTATTATTAAATATAATTTAATTA
1 ATAATTATTATTAAAAATATTTTAATTA
2473240 TATGAATTTG
Statistics
Matches: 198, Mismatches: 38, Indels: 64
0.66 0.13 0.21
Matches are distributed among these distances:
54 6 0.03
55 1 0.01
56 5 0.03
57 44 0.22
58 11 0.06
59 43 0.22
60 5 0.03
61 41 0.21
62 11 0.06
63 19 0.10
64 5 0.03
65 4 0.02
66 3 0.02
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.43
Consensus pattern (55 bp):
ATAATTATTATTAAAAATATTTTAATTAAAATATATGATTTAATAAAATTTAATA
Found at i:2473233 original size:29 final size:29
Alignment explanation
Indices: 2473154--2473236 Score: 80
Period size: 29 Copynumber: 2.9 Consensus size: 29
2473144 TATAATTTGA
* * *
2473154 AATAATTATTATTAAAAAT-ATTTTAATT
1 AATAATTATTATTAAATATAATTTAAAAT
* * * *
2473182 AA-AACATATGATTTAATAAAATTTAAAAT
1 AATAA-TTATTATTAAATATAATTTAAAAT
2473211 AATAATTATTATTAAATATAATTTAA
1 AATAATTATTATTAAATATAATTTAA
2473237 TTATATGAAT
Statistics
Matches: 41, Mismatches: 11, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
27 2 0.05
28 11 0.27
29 26 0.63
30 2 0.05
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (29 bp):
AATAATTATTATTAAATATAATTTAAAAT
Found at i:2488151 original size:26 final size:26
Alignment explanation
Indices: 2488096--2488178 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 26
2488086 ATGCAACGAC
* * * *
2488096 ATAATATATAACACAATTTTAAAGTAA
1 ATAATATACAAAACAA-ATTAAAATAA
* *
2488123 ATAATATGCAAAACAAATTAAAATGA
1 ATAATATACAAAACAAATTAAAATAA
* * *
2488149 ATAATATACACAGCAATTTAAAATAA
1 ATAATATACAAAACAAATTAAAATAA
2488175 ATAA
1 ATAA
2488179 CCTCCATCAC
Statistics
Matches: 45, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
26 32 0.71
27 13 0.29
ACGTcount: A:0.59, C:0.08, G:0.05, T:0.28
Consensus pattern (26 bp):
ATAATATACAAAACAAATTAAAATAA
Found at i:2488264 original size:21 final size:21
Alignment explanation
Indices: 2488226--2488265 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2488216 AAAAAGAAAT
* * *
2488226 TTAAAATAATATACAAAATAG
1 TTAAAAAAATAAAAAAAATAG
2488247 TTAAAAAAATAAAAAAAAT
1 TTAAAAAAATAAAAAAAAT
2488266 TAAATGGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.25
Consensus pattern (21 bp):
TTAAAAAAATAAAAAAAATAG
Found at i:2493137 original size:25 final size:25
Alignment explanation
Indices: 2493087--2493143 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
2493077 TTGTGTCAAG
* *
2493087 TTATTTGAAAAACCTATGTGGAGTA
1 TTATCTGAAAAACCTATATGGAGTA
*
2493112 TTATCTGAAAAACC-ATTATGGCGTA
1 TTATCTGAAAAACCTA-TATGGAGTA
2493137 TTATCTG
1 TTATCTG
2493144 GAAAGTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 1 0.04
25 27 0.96
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (25 bp):
TTATCTGAAAAACCTATATGGAGTA
Found at i:2493193 original size:75 final size:75
Alignment explanation
Indices: 2493055--2493193 Score: 176
Period size: 75 Copynumber: 1.9 Consensus size: 75
2493045 AAAGCCTATG
* * * *
2493055 TGGCGTATTGTCTAGAAAGCCTTTGTGTCAAGTTATTTGAAAAACCTATGTGGAGTATTATCTGA
1 TGGCGTATTATCTAGAAAGCCTTTGTGACAAGTTATGTGAAAAACCTATGTGGAGTATAATCTGA
2493120 AAAACCATTA
66 AAAACCATTA
* *
2493130 TGGCGTATTATCTGGAAAG-TTATTGTGACAAGTTATGT-AAAAAGCCTATGT-GAGTTATAATC
1 TGGCGTATTATCTAGAAAGCCT-TTGTGACAAGTTATGTGAAAAA-CCTATGTGGAG-TATAATC
2493192 TG
63 TG
2493194 GAAAGCCTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
74 9 0.16
75 46 0.84
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.35
Consensus pattern (75 bp):
TGGCGTATTATCTAGAAAGCCTTTGTGACAAGTTATGTGAAAAACCTATGTGGAGTATAATCTGA
AAAACCATTA
Found at i:2493216 original size:75 final size:75
Alignment explanation
Indices: 2493077--2493224 Score: 167
Period size: 75 Copynumber: 2.0 Consensus size: 75
2493067 TAGAAAGCCT
* * * *
2493077 TTGTGTCAAGTTATTTGAAAAACCTATGTGGAGTATTATCTGAAAAACCATTATGGCGTATTATC
1 TTGTGACAAGTTATGTGAAAAACCTATGTGGAGTATAATCTGAAAAACCATTATGGCGAATTATC
*
2493142 TGGAAAGTTA
66 TGAAAAGTTA
* * * *
2493152 TTGTGACAAGTTATGT-AAAAAGCCTATGT-GAGTTATAATCTGGAAAGCCTTTGTGGC-AAGTT
1 TTGTGACAAGTTATGTGAAAAA-CCTATGTGGAG-TATAATCTGAAAAACCATTATGGCGAA-TT
2493214 ATCTGAAAAGT
63 ATCTGAAAAGT
2493225 CTATCTAGCG
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
74 9 0.15
75 52 0.85
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.34
Consensus pattern (75 bp):
TTGTGACAAGTTATGTGAAAAACCTATGTGGAGTATAATCTGAAAAACCATTATGGCGAATTATC
TGAAAAGTTA
Found at i:2495588 original size:58 final size:58
Alignment explanation
Indices: 2495518--2495633 Score: 223
Period size: 58 Copynumber: 2.0 Consensus size: 58
2495508 ATCCGCGACC
*
2495518 TGTGTCATTAAGATTTGCTTCACATGAGTTCAAGTTGAGTTTGTTTGGCCATGTTCTA
1 TGTGTCATTAAGATTTGCTTCAAATGAGTTCAAGTTGAGTTTGTTTGGCCATGTTCTA
2495576 TGTGTCATTAAGATTTGCTTCAAATGAGTTCAAGTTGAGTTTGTTTGGCCATGTTCTA
1 TGTGTCATTAAGATTTGCTTCAAATGAGTTCAAGTTGAGTTTGTTTGGCCATGTTCTA
2495634 GGAGCTTTAA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.22, C:0.13, G:0.22, T:0.43
Consensus pattern (58 bp):
TGTGTCATTAAGATTTGCTTCAAATGAGTTCAAGTTGAGTTTGTTTGGCCATGTTCTA
Found at i:2495653 original size:58 final size:58
Alignment explanation
Indices: 2495521--2495653 Score: 178
Period size: 58 Copynumber: 2.3 Consensus size: 58
2495511 CGCGACCTGT
** * * *
2495521 GTCATTAAGATTTGCTTCACATGAGTTCAAGTTGAGTTTGTTTGGCCATGTTCTATGT
1 GTCATTAAGAAATGCTTCAAATGAGTTCAAGTTGAGTTTGTTTGGCCATGTTCTAGGA
**
2495579 GTCATTAAGATTTGCTTCAAATGAGTTCAAGTTGAGTTTGTTTGGCCATGTTCTAGGA
1 GTCATTAAGAAATGCTTCAAATGAGTTCAAGTTGAGTTTGTTTGGCCATGTTCTAGGA
*
2495637 G-CTTTAATGAAATGCTT
1 GTCATTAA-GAAATGCTT
2495654 GGATCTTTTT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
57 5 0.07
58 63 0.93
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.41
Consensus pattern (58 bp):
GTCATTAAGAAATGCTTCAAATGAGTTCAAGTTGAGTTTGTTTGGCCATGTTCTAGGA
Found at i:2503388 original size:20 final size:21
Alignment explanation
Indices: 2503351--2503391 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2503341 TTATATTTTT
*
2503351 AAAATATTAATTACTATAAAA
1 AAAATATTAAGTACTATAAAA
*
2503372 AAAATATT-AGTATTATAAAA
1 AAAATATTAAGTACTATAAAA
2503392 TTAAATCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (21 bp):
AAAATATTAAGTACTATAAAA
Found at i:2506675 original size:20 final size:20
Alignment explanation
Indices: 2506624--2506676 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
2506614 TGTATTAGCT
**
2506624 CACTACCTACCCAGGCCCCAA
1 CACT-CCTACCCAACCCCCAA
**
2506645 C-CTCCGGCCCAACCCCCAA
1 CACTCCTACCCAACCCCCAA
2506664 CACTCCTACCCAA
1 CACTCCTACCCAA
2506677 TATACATTTA
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
19 13 0.52
20 11 0.44
21 1 0.04
ACGTcount: A:0.26, C:0.57, G:0.08, T:0.09
Consensus pattern (20 bp):
CACTCCTACCCAACCCCCAA
Found at i:2511565 original size:6 final size:6
Alignment explanation
Indices: 2511554--2511579 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2511544 AGTTTTCTCC
2511554 AAAATG AAAATG AAAATG AAAATG AA
1 AAAATG AAAATG AAAATG AAAATG AA
2511580 GAAATGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (6 bp):
AAAATG
Found at i:2511612 original size:63 final size:64
Alignment explanation
Indices: 2511505--2511645 Score: 203
Period size: 63 Copynumber: 2.2 Consensus size: 64
2511495 ATAGAAATGG
* *
2511505 TGAAAATGGAGAAATGGGAAATCATTTGAAAATGATTATAGTTTTCTCCAAAATGAAAATGAAAA
1 TGAAAATGAAGAAAT-GGAAATCATTTGAAAATGAATATAGTTTTCTCCAAAATGAAAATGAAAA
* * * *
2511570 TGAAAATGAAGAAAT-GAAATCATTTGGAAATTAATGTGGTTTTCTCCAAAATGAAAATGAAAA
1 TGAAAATGAAGAAATGGAAATCATTTGAAAATGAATATAGTTTTCTCCAAAATGAAAATGAAAA
2511633 TGAAAAATGAAGA
1 TG-AAAATGAAGA
2511646 TGACCTGAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
63 45 0.65
64 10 0.14
65 14 0.20
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.27
Consensus pattern (64 bp):
TGAAAATGAAGAAATGGAAATCATTTGAAAATGAATATAGTTTTCTCCAAAATGAAAATGAAAA
Found at i:2511641 original size:19 final size:18
Alignment explanation
Indices: 2511617--2511661 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
2511607 GGTTTTCTCC
2511617 AAAATGAAAATGAAAATGA
1 AAAATGAAAATG-AAATGA
* **
2511636 AAAATGAAGATGACCTGA
1 AAAATGAAAATGAAATGA
2511654 AAAATGAA
1 AAAATGAA
2511662 TTTATGTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.62, C:0.04, G:0.18, T:0.16
Consensus pattern (18 bp):
AAAATGAAAATGAAATGA
Found at i:2513257 original size:21 final size:21
Alignment explanation
Indices: 2513224--2513272 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
2513214 AGTGTCAGTG
2513224 AGATTAATAATTGTAGCAATA
1 AGATTAATAATTGTAGCAATA
*
2513245 AGATTGAAT-ATTGTAGTAATA
1 AGATT-AATAATTGTAGCAATA
*
2513266 TGATTAA
1 AGATTAA
2513273 AATCAATGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 20 0.80
22 3 0.12
ACGTcount: A:0.45, C:0.02, G:0.16, T:0.37
Consensus pattern (21 bp):
AGATTAATAATTGTAGCAATA
Found at i:2513394 original size:24 final size:24
Alignment explanation
Indices: 2513350--2513396 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2513340 TTTAATAATA
*
2513350 TATGTAAAATAAATAATTATATTT
1 TATGTAAAATAAATAAATATATTT
*
2513374 TATGTTAAAT-AATAAAATATATT
1 TATGTAAAATAAAT-AAATATATT
2513397 AAATTTGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (24 bp):
TATGTAAAATAAATAAATATATTT
Found at i:2515552 original size:120 final size:120
Alignment explanation
Indices: 2515339--2515579 Score: 448
Period size: 120 Copynumber: 2.0 Consensus size: 120
2515329 TTAAAAGGCA
2515339 AAGGTTTGTTTAGCCTTGAGGCAAAGCCTTCAATTTCACTAGACAACACCAACCATTTTTGATCA
1 AAGGTTTGTTTAGCCTTGAGGCAAAGCCTTCAATTTCACTAGACAACACCAACCATTTTTGATCA
*
2515404 ACCCTCACCCTTTTAAACACCAACCCTGGAATTCCCCCTAACAAACCCAAAAAAT
66 ACCCTCACCCTCTTAAACACCAACCCTGGAATTCCCCCTAACAAACCCAAAAAAT
*
2515459 AAGGTTTGTTTAGCCTTGAGGCAAAGCCTTCAATTTCACTAGTCAACACCAACCATTTTTGA-CG
1 AAGGTTTGTTTAGCCTTGAGGCAAAGCCTTCAATTTCACTAGACAACACCAACCATTTTTGATC-
2515523 AACCCTCACCCTCTTAAACACCAACCCTGGAATTCCCCCTAACAAACCCAAAAAAT
65 AACCCTCACCCTCTTAAACACCAACCCTGGAATTCCCCCTAACAAACCCAAAAAAT
2515579 A
1 A
2515580 TGAAGGTCCA
Statistics
Matches: 118, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
119 1 0.01
120 117 0.99
ACGTcount: A:0.34, C:0.31, G:0.10, T:0.24
Consensus pattern (120 bp):
AAGGTTTGTTTAGCCTTGAGGCAAAGCCTTCAATTTCACTAGACAACACCAACCATTTTTGATCA
ACCCTCACCCTCTTAAACACCAACCCTGGAATTCCCCCTAACAAACCCAAAAAAT
Found at i:2522383 original size:6 final size:6
Alignment explanation
Indices: 2522374--2522402 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2522364 TAAAAGAAGA
2522374 AGAGGG AGAGGG AGAGGG AGAGGG AGAGG
1 AGAGGG AGAGGG AGAGGG AGAGGG AGAGG
2522403 TCAAGCAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (6 bp):
AGAGGG
Found at i:2525465 original size:21 final size:21
Alignment explanation
Indices: 2525432--2525480 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
2525422 AGTGTCAGTG
2525432 AGATTAATAATTGTAGCAATA
1 AGATTAATAATTGTAGCAATA
*
2525453 AGATTGAAT-ATTGTAGTAATA
1 AGATT-AATAATTGTAGCAATA
*
2525474 TGATTAA
1 AGATTAA
2525481 AATCAATGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 20 0.80
22 3 0.12
ACGTcount: A:0.45, C:0.02, G:0.16, T:0.37
Consensus pattern (21 bp):
AGATTAATAATTGTAGCAATA
Found at i:2527530 original size:24 final size:24
Alignment explanation
Indices: 2527503--2527548 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
2527493 ATAAAATTAA
*
2527503 ATGAAATGTCAAGAGTTATGTTAT
1 ATGAAAGGTCAAGAGTTATGTTAT
2527527 ATGAAAGGTCAAGAGTTATGTT
1 ATGAAAGGTCAAGAGTTATGTT
2527549 GTTTTTAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35
Consensus pattern (24 bp):
ATGAAAGGTCAAGAGTTATGTTAT
Found at i:2528723 original size:42 final size:42
Alignment explanation
Indices: 2528664--2528824 Score: 222
Period size: 42 Copynumber: 3.9 Consensus size: 42
2528654 AAAAATAAAC
2528664 GACCTTTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGAACAA
1 GACCTTTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGAACAA
*
2528706 GACCTTTAGCGGCGCTTTCCCAAAAACGTCGCTAAAGAACAA
1 GACCTTTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGAACAA
* ** *
2528748 GACCTTTAGCAGCGCTTTTTACAAAAACGCTGCTAAAGAACAA
1 GACCTTTAGCGGCGC-TTTCCCAAAAACGCCGCTAAAGAACAA
*
2528791 GA----TAGCGACGCTTTCCCCAAAAACGCCGCTAAAG
1 GACCTTTAGCGGCGCTTT-CCCAAAAACGCCGCTAAAG
2528825 GTCATGAAAA
Statistics
Matches: 106, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
38 3 0.03
39 23 0.22
42 55 0.52
43 25 0.24
ACGTcount: A:0.34, C:0.29, G:0.19, T:0.19
Consensus pattern (42 bp):
GACCTTTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGAACAA
Found at i:2530100 original size:24 final size:24
Alignment explanation
Indices: 2530073--2530118 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
2530063 ATAAAATTAA
*
2530073 ATGAAATGTCAAGAGTTATGTTAT
1 ATGAAAGGTCAAGAGTTATGTTAT
2530097 ATGAAAGGTCAAGAGTTATGTT
1 ATGAAAGGTCAAGAGTTATGTT
2530119 GTTTTTAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35
Consensus pattern (24 bp):
ATGAAAGGTCAAGAGTTATGTTAT
Found at i:2531293 original size:42 final size:42
Alignment explanation
Indices: 2531234--2531394 Score: 222
Period size: 42 Copynumber: 3.9 Consensus size: 42
2531224 AAAAATAAAC
2531234 GACCTTTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGAACAA
1 GACCTTTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGAACAA
*
2531276 GACCTTTAGCGGCGCTTTCCCAAAAACGTCGCTAAAGAACAA
1 GACCTTTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGAACAA
* ** *
2531318 GACCTTTAGCAGCGCTTTTTACAAAAACGCTGCTAAAGAACAA
1 GACCTTTAGCGGCGC-TTTCCCAAAAACGCCGCTAAAGAACAA
*
2531361 GA----TAGCGACGCTTTCCCCAAAAACGCCGCTAAAG
1 GACCTTTAGCGGCGCTTT-CCCAAAAACGCCGCTAAAG
2531395 GTCATGAAAA
Statistics
Matches: 106, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
38 3 0.03
39 23 0.22
42 55 0.52
43 25 0.24
ACGTcount: A:0.34, C:0.29, G:0.19, T:0.19
Consensus pattern (42 bp):
GACCTTTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGAACAA
Found at i:2532317 original size:23 final size:23
Alignment explanation
Indices: 2532252--2532319 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
2532242 ACAATAGAAA
*
2532252 GTAGCACTTTAACACTTCAAGTT
1 GTAGCACTTTAACACTTCAATTT
**
2532275 ACAGCA-TTTAAACACTTCAATTT
1 GTAGCACTTT-AACACTTCAATTT
2532298 GTAGCACTTTAACA-TATCAATT
1 GTAGCACTTTAACACT-TCAATT
2532320 AACAACATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
22 4 0.11
23 30 0.81
24 3 0.08
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (23 bp):
GTAGCACTTTAACACTTCAATTT
Found at i:2532340 original size:46 final size:46
Alignment explanation
Indices: 2532252--2532342 Score: 114
Period size: 46 Copynumber: 2.0 Consensus size: 46
2532242 ACAATAGAAA
* * *
2532252 GTAGCACTTTAACACTTCAAGTTACAGCATTTAAACACTTCAATTT
1 GTAGCACTTTAACACTTCAAGTTACAACATATAAACAATTCAATTT
*
2532298 GTAGCACTTTAACA-TATCAA-TTAACAACATATACACAATTCAATT
1 GTAGCACTTTAACACT-TCAAGTT-ACAACATATAAACAATTCAATT
2532343 AACATAGCAC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
45 3 0.08
46 36 0.92
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.33
Consensus pattern (46 bp):
GTAGCACTTTAACACTTCAAGTTACAACATATAAACAATTCAATTT
Found at i:2533826 original size:39 final size:38
Alignment explanation
Indices: 2533783--2533896 Score: 95
Period size: 39 Copynumber: 3.2 Consensus size: 38
2533773 CCATTTTGGT
2533783 ATTGTAAATATTTGTGGCGCTTATAAAAAAACGCCACTA
1 ATTGTAAATATTTGTGGCGCTTATAAAAAAA-GCCACTA
* * *
2533822 ATTGTATAAT-TTT-T---GC-TA-AAAATTAA---ATTT
1 ATTGTA-AATATTTGTGGCGCTTATAAAA-AAAGCCACTA
2533852 ATTGTAAATATTTGTGGCGCTTATAAAAAAATGCCACTA
1 ATTGTAAATATTTGTGGCGCTTATAAAAAAA-GCCACTA
2533891 ATTGTA
1 ATTGTA
2533897 TAAATTTTGC
Statistics
Matches: 56, Mismatches: 6, Indels: 26
0.64 0.07 0.30
Matches are distributed among these distances:
29 3 0.05
30 11 0.20
31 1 0.02
33 4 0.07
34 6 0.11
35 6 0.11
36 4 0.07
38 1 0.02
39 17 0.30
40 3 0.05
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.38
Consensus pattern (38 bp):
ATTGTAAATATTTGTGGCGCTTATAAAAAAAGCCACTA
Found at i:2533893 original size:69 final size:69
Alignment explanation
Indices: 2533782--2533920 Score: 260
Period size: 69 Copynumber: 2.0 Consensus size: 69
2533772 GCCATTTTGG
*
2533782 TATTGTAAATATTTGTGGCGCTTATAAAAAAACGCCACTAATTGTATAATTTTTGCTAAAAATTA
1 TATTGTAAATATTTGTGGCGCTTATAAAAAAACGCCACTAATTGTATAAATTTTGCTAAAAATTA
2533847 AATT
66 AATT
*
2533851 TATTGTAAATATTTGTGGCGCTTATAAAAAAATGCCACTAATTGTATAAATTTTGCTAAAAATTA
1 TATTGTAAATATTTGTGGCGCTTATAAAAAAACGCCACTAATTGTATAAATTTTGCTAAAAATTA
2533916 AATT
66 AATT
2533920 T
1 T
2533921 CTGTATCAAA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.40
Consensus pattern (69 bp):
TATTGTAAATATTTGTGGCGCTTATAAAAAAACGCCACTAATTGTATAAATTTTGCTAAAAATTA
AATT
Found at i:2534105 original size:19 final size:17
Alignment explanation
Indices: 2534050--2534107 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 17
2534040 TATCAATTTT
*
2534050 AAATAAATAATTTTTGAA
1 AAATTAATAATTTTT-AA
2534068 AAATTAAGTAATATTTTAA
1 AAATTAA-TAAT-TTTTAA
2534087 AGAATTAGATAATTTTTAA
1 A-AATTA-ATAATTTTTAA
2534106 AA
1 AA
2534108 TTTTTATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
18 7 0.20
19 14 0.40
20 13 0.37
21 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (17 bp):
AAATTAATAATTTTTAA
Found at i:2534400 original size:10 final size:10
Alignment explanation
Indices: 2534385--2534438 Score: 56
Period size: 10 Copynumber: 5.3 Consensus size: 10
2534375 GTTTAAATTC
2534385 TTTTTAAAAT
1 TTTTTAAAAT
2534395 TTTTTAAAA-
1 TTTTTAAAAT
* *
2534404 ATTTTGAAAT
1 TTTTTAAAAT
*
2534414 CTTTTAAAATT
1 TTTTTAAAA-T
2534425 TATTTTAAAAT
1 T-TTTTAAAAT
2534436 TTT
1 TTT
2534439 AAATCACGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
9 7 0.19
10 18 0.50
11 3 0.08
12 8 0.22
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (10 bp):
TTTTTAAAAT
Found at i:2534418 original size:29 final size:29
Alignment explanation
Indices: 2534371--2534443 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 29
2534361 TTATAAAAAT
*
2534371 AAAAGTTTAAATTCTTTTTAAAATTT-TTTA
1 AAAATTTTAAA-TC-TTTTAAAATTTATTTA
*
2534401 AAAATTTTGAAATCTTTTAAAATTTATTTT
1 AAAATTTT-AAATCTTTTAAAATTTATTTA
2534431 AAAATTTTAAATC
1 AAAATTTTAAATC
2534444 ACGAAAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
29 16 0.41
30 20 0.51
31 3 0.08
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (29 bp):
AAAATTTTAAATCTTTTAAAATTTATTTA
Found at i:2534725 original size:15 final size:15
Alignment explanation
Indices: 2534698--2534735 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
2534688 AGCCTTTAAA
2534698 CCATAAA-CCATAAC
1 CCATAAACCCATAAC
* *
2534712 CCCTAAACCCATAAT
1 CCATAAACCCATAAC
2534727 CCATAAACC
1 CCATAAACC
2534736 TTAAAATGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.45, C:0.39, G:0.00, T:0.16
Consensus pattern (15 bp):
CCATAAACCCATAAC
Found at i:2534740 original size:22 final size:21
Alignment explanation
Indices: 2534693--2534798 Score: 63
Period size: 21 Copynumber: 5.0 Consensus size: 21
2534683 ACCCCAGCCT
*
2534693 TTAAACCATAAACCATAACCC
1 TTAAACCATAAACCATAAACC
* *
2534714 CTAAACCCATAATCCATAAACC
1 TTAAA-CCATAAACCATAAACC
*** *
2534736 TTAAAATGGTAACACC-TAAACT
1 TT-AAACCATAA-ACCATAAACC
*
2534758 TTAAACTC-TAAACCATATACC
1 TTAAAC-CATAAACCATAAACC
* * *
2534779 CTAAACCAAAAACCCTAAAC
1 TTAAACCATAAACCATAAAC
2534799 TATAGTGATA
Statistics
Matches: 62, Mismatches: 17, Indels: 12
0.68 0.19 0.13
Matches are distributed among these distances:
20 4 0.06
21 28 0.45
22 25 0.40
23 5 0.08
ACGTcount: A:0.47, C:0.30, G:0.02, T:0.21
Consensus pattern (21 bp):
TTAAACCATAAACCATAAACC
Found at i:2534782 original size:14 final size:14
Alignment explanation
Indices: 2534760--2534798 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
2534750 CCTAAACTTT
* *
2534760 AAACTCTAAACCAT
1 AAACCCTAAACCAA
*
2534774 ATACCCTAAACCAA
1 AAACCCTAAACCAA
2534788 AAACCCTAAAC
1 AAACCCTAAAC
2534799 TATAGTGATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.51, C:0.33, G:0.00, T:0.15
Consensus pattern (14 bp):
AAACCCTAAACCAA
Found at i:2535281 original size:74 final size:73
Alignment explanation
Indices: 2535097--2535337 Score: 261
Period size: 72 Copynumber: 3.3 Consensus size: 73
2535087 CTGAGCATTA
** * * *
2535097 GCGGCGCTTTCCT-AAAAACATCGCTAAATCCCCGAAAGCTCATAAAACGGCGTCATTTTGG-AT
1 GCGGCGC-TTCCTAAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTTGGCTT
*
2535160 AGATTTTTT
65 AGGTTTTTT
* * * * *
2535169 GCGGCGCTTCCTCATAAACGCCACTAAATCCCCCAAAGCTCACAAAACGACGTCGTTTTGGCTTA
1 GCGGCGCTTCCTAAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTTGGCTTA
*
2535234 GGTTCTTT
66 GGTTTTTT
* * * * *
2535242 GTGGTGCTTTCTTAAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAAATGGCGTTGTTTTGGCT
1 GCGGCGC-TTCCTAAAAAACGCCGCTAAATCCCCGAAAGCTCAC-AAAACGGCGTCGTTTTGGCT
2535307 TAGGTTTTTT
64 TAGGTTTTTT
* * *
2535317 GCGACGCTTTCTCAAAAACGC
1 GCGGCGCTTCCTAAAAAACGC
2535338 TGCTGAAGCC
Statistics
Matches: 137, Mismatches: 28, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
71 5 0.04
72 47 0.34
73 13 0.09
74 42 0.31
75 30 0.22
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.29
Consensus pattern (73 bp):
GCGGCGCTTCCTAAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTTGGCTTA
GGTTTTTT
Found at i:2535527 original size:73 final size:72
Alignment explanation
Indices: 2535359--2535531 Score: 217
Period size: 73 Copynumber: 2.4 Consensus size: 72
2535349 TGAGCATTAG
* * *
2535359 CGGCGCTTTCCTAAAAA-CATCGCTAAATCCCCGAAAGCTCATAAAACGGCGTCGTTTTGCCTTA
1 CGGCGCTTTCCTAAAAAGC--CGCTAAATCCCCCAAAGCTCACAAAACGACGTCGTTTTGCCTTA
2535423 GGTTTTTTA
64 GGTTTTTTA
* * *
2535432 CGGCGC-TTCATCGAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACGACGTCGTTTTGGCTTA
1 CGGCGCTTTC--CTAAAAAGCCGCTAAATCCCCCAAAGCTCACAAAACGACGTCGTTTTGCCTTA
2535496 GGTTCTTTT-
64 GGTT-TTTTA
2535505 CGGCGCTTTCCTAAAATAGCCGCTAAA
1 CGGCGCTTTCCTAAAA-AGCCGCTAAA
2535532 GCCTTGAGCA
Statistics
Matches: 86, Mismatches: 8, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
72 8 0.09
73 65 0.76
74 12 0.14
75 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.27
Consensus pattern (72 bp):
CGGCGCTTTCCTAAAAAGCCGCTAAATCCCCCAAAGCTCACAAAACGACGTCGTTTTGCCTTAGG
TTTTTTA
Found at i:2535529 original size:261 final size:261
Alignment explanation
Indices: 2534983--2535531 Score: 944
Period size: 261 Copynumber: 2.1 Consensus size: 261
2534973 TAAGCATTAG
*
2534983 CGGCGCTTTTCTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAAATGGCGTTGTTTTGGCTTA
1 CGGCGCTTTCCTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAAATGGCGTTGTTTTGGCTTA
2535048 GGTTTTTTGCGACGCTTTCTCAAAAACGCTGCTGAAGCCCTGAGCATTAGCGGCGCTTTCCTAAA
66 GGTTTTTTGCGACGCTTTCTCAAAAACGCTGCTGAAGCCCTGAGCATTAGCGGCGCTTTCCTAAA
* *
2535113 AACATCGCTAAATCCCCGAAAGCTCATAAAACGGCGTCATTTTGGATAGATTTTTTGCGGCGCTT
131 AACATCGCTAAATCCCCGAAAGCTCATAAAACGGCGTCATTTTGCATAGATTTTTTACGGCGCTT
*
2535178 CCTCATAAACGCCACTAAATCCCCCAAAGCTCACAAAACGACGTCGTTTTGGCTTAGGTTCTTTG
196 CATCATAAACGCCACTAAATCCCCCAAAGCTCACAAAACGACGTCGTTTTGGCTTAGGTTCTTTG
2535243 T
261 T
* *
2535244 -GGTGCTTTCTTAAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAAATGGCGTTGTTTTGGCTT
1 CGGCGCTTTCCT-AAAAACGCCGCTAAATCCCCGAAAGCTCACAAAAATGGCGTTGTTTTGGCTT
2535308 AGGTTTTTTGCGACGCTTTCTCAAAAACGCTGCTGAAGCCCTGAGCATTAGCGGCGCTTTCCTAA
65 AGGTTTTTTGCGACGCTTTCTCAAAAACGCTGCTGAAGCCCTGAGCATTAGCGGCGCTTTCCTAA
* * *
2535373 AAACATCGCTAAATCCCCGAAAGCTCATAAAACGGCGTCGTTTTGCCTTAGGTTTTTTACGGCGC
130 AAACATCGCTAAATCCCCGAAAGCTCATAAAACGGCGTCATTTTG-CATAGATTTTTTACGGCGC
*
2535438 TTCATCGA-AAACGCCGCTAAATCCCCCAAAGCTCACAAAACGACGTCGTTTTGGCTTAGGTTCT
194 TTCATC-ATAAACGCCACTAAATCCCCCAAAGCTCACAAAACGACGTCGTTTTGGCTTAGGTTCT
2535502 TT-T
258 TTGT
2535505 CGGCGCTTTCCTAAAATA-GCCGCTAAA
1 CGGCGCTTTCCTAAAA-ACGCCGCTAAA
2535532 GCCTTGAGCA
Statistics
Matches: 271, Mismatches: 12, Indels: 10
0.92 0.04 0.03
Matches are distributed among these distances:
260 8 0.03
261 175 0.65
262 87 0.32
263 1 0.00
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (261 bp):
CGGCGCTTTCCTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAAATGGCGTTGTTTTGGCTTA
GGTTTTTTGCGACGCTTTCTCAAAAACGCTGCTGAAGCCCTGAGCATTAGCGGCGCTTTCCTAAA
AACATCGCTAAATCCCCGAAAGCTCATAAAACGGCGTCATTTTGCATAGATTTTTTACGGCGCTT
CATCATAAACGCCACTAAATCCCCCAAAGCTCACAAAACGACGTCGTTTTGGCTTAGGTTCTTTG
T
Found at i:2535572 original size:187 final size:188
Alignment explanation
Indices: 2535192--2535646 Score: 551
Period size: 187 Copynumber: 2.4 Consensus size: 188
2535182 ATAAACGCCA
* * * * * *
2535192 CTAAATCCCCCAAAGCTCACAAAACGACGTCGTTTTGGCTTAGGTTCTTTGTGGTGCTTTCTTAA
1 CTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTTGGCTTAGGTTTTTTGCGGCGCTTTC-TCA
* * * *
2535257 AAAACGCCGCTAAATCCCCGAAAGCTCACAAAAATGGCGTTGTTTTGGCTTAGGTTTTTTGCGAC
65 AAAACGCCGCTAAATCCCCCAAAGCTCACAAAAACGACGTCGTTTTGGCTTAGGTTTTTTGCGAC
* * * * *
2535322 GCTTTCTCAAAAACGCTGCTGAAGCCCTGAGCATTAGCGGCGCTTTCCTAAAAACATCG
130 GCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCACTTTCATAAAAACACCG
* * * *
2535381 CTAAATCCCCGAAAGCTCATAAAACGGCGTCGTTTTGCCTTAGGTTTTTTACGGCGC-TTCATCG
1 CTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTTGGCTTAGGTTTTTTGCGGCGCTTTC-TCA
*
2535445 AAAACGCCGCTAAATCCCCCAAAGCTCAC-AAAACGACGTCGTTTTGGCTTAGGTTCTTTT-CGG
65 AAAACGCCGCTAAATCCCCCAAAGCTCACAAAAACGACGTCGTTTTGGCTTAGGTT-TTTTGCGA
* * **
2535508 CGCTTTC-CTAAAATA-GCCGCTAAAGCCTTGAGCATTAGTGGCACTTTCATAAAAATGCCG
129 CGCTTTCTC-AAAA-ACGCCGCTAAAGCCCTGAGCATTAGCGGCACTTTCATAAAAACACCG
*** * *
2535568 CTAAATCGTTGAAAGCTCACAAAACGGCGTTGTTTTGGCTTAAGTTTTTTTGCGGCGCTTTCTCA
1 CTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTTGGCTT-AGGTTTTTTGCGGCGCTTTCTCA
*
2535633 AAAACGTCGCTAAA
65 AAAACGCCGCTAAA
2535647 GCCCTGAGCA
Statistics
Matches: 226, Mismatches: 35, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
186 1 0.00
187 107 0.47
188 66 0.29
189 52 0.23
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (188 bp):
CTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTTGGCTTAGGTTTTTTGCGGCGCTTTCTCAA
AAACGCCGCTAAATCCCCCAAAGCTCACAAAAACGACGTCGTTTTGGCTTAGGTTTTTTGCGACG
CTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCACTTTCATAAAAACACCG
Found at i:2535670 original size:115 final size:115
Alignment explanation
Indices: 2535445--2535760 Score: 415
Period size: 114 Copynumber: 2.8 Consensus size: 115
2535435 CGCTTCATCG
** * * *
2535445 AAAACGCCGCTAAATCCCCCAAAGCTCACAAAACGACGTCGTTTTGGCTTAGGTTCTTTT-CGGC
1 AAAACGCCGCTAAATCCCTGAAAGCTCACAAAACGGCGTCGTTTTGGCTTAAGTTTTTTTGCGGC
* *
2535509 GCTTTC-CTAAAATA-GCCGCTAAAGCCTTGAGCATTAGTGGCACTTTCATA
66 GCTTTCTC-AAAA-ACGCCGCTAAAGCCCTGAGCATTAGCGGCACTTTCATA
* ** *
2535559 AAAATGCCGCTAAATCGTTGAAAGCTCACAAAACGGCGTTGTTTTGGCTTAAGTTTTTTTGCGGC
1 AAAACGCCGCTAAATCCCTGAAAGCTCACAAAACGGCGTCGTTTTGGCTTAAGTTTTTTTGCGGC
* * *
2535624 GCTTTCTCAAAAACGTCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCCTA
66 GCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCACTTTCATA
* * * * *
2535674 AAAACGCCGCTAAATCCCTGAAAGCTTATAAATCGGCGTCGTTTTAGCTT-AGATTTTTTGCGGC
1 AAAACGCCGCTAAATCCCTGAAAGCTCACAAAACGGCGTCGTTTTGGCTTAAGTTTTTTTGCGGC
2535738 GCTTTCTCAAAAACGCCGCTAAA
66 GCTTTCTCAAAAACGCCGCTAAA
2535761 TCCCCCAAAG
Statistics
Matches: 175, Mismatches: 24, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
114 87 0.50
115 87 0.50
116 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (115 bp):
AAAACGCCGCTAAATCCCTGAAAGCTCACAAAACGGCGTCGTTTTGGCTTAAGTTTTTTTGCGGC
GCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCACTTTCATA
Found at i:2536080 original size:186 final size:185
Alignment explanation
Indices: 2535551--2536104 Score: 482
Period size: 186 Copynumber: 3.0 Consensus size: 185
2535541 ATTAGTGGCA
* * **** * * * *
2535551 CTTTCATAAAAATGCCGCTAAATCGTTGAAAGCTCACAAAACGGCGTTGTTTTGGCTTAAGTTTT
1 CTTTCTTAAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACGACGTCGTTTTGGCTTATG-TTA
* *
2535616 TTTGCGGCGCTTTCTCAAAAACGTCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCCTAAAAACGC
65 TTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTT-CTTAAAACGC
* * * * * * * *
2535681 CGCTAAATCCCTGAAAGCTTATAAATCGGCGTCGTTTTAGCTTAGATTTTTTGCGGCG
129 CGCTAAATCCCCGAAAACTCACAAAACGGCGTCGTTTTGGCTTAG-GTTTTTGCGACG
* * * *
2535739 CTTTCTCAAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACGACGCCGTTTTGTGAGTTTTCGG
1 CTTTCTTAAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACGACGTCGTTTTG-G-CTTAT--G
** * * * * * * * *
2535804 GGATTTAGCAGCG-TTT-T-AAGAAAGCGCCGCTAATGCTCAGGGCTTTAGTGGC-ATTT-TTGA
62 TTATTT-GCGGCGCTTTCTCAA-AAA-CGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTT-A
*** * * * *
2535864 GAAAGCGCCGC-AAA-GAAC-ATAA-GC-CAAAACGACGTCGTTTTGGCTTAGGTTCTTTGCGAT
123 -AAA-CGCCGCTAAATCCCCGAAAACTCACAAAACGGCGTCGTTTTGGCTTAGGTT-TTTGCGAC
2535924 G
185 G
*
2535925 CTTTCTTAAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACGACGTCGTTTTGGCTTATGTTCT
1 CTTTCTTAAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACGACGTCGTTTTGGCTTATGTTAT
* * *
2535990 TTGCGGCGCTTTCTCAAAAATGCCACTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAACGCTG
66 TTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAACGCCG
* *
2536055 CTAAATCCCCGAAAACTCACAAAACGGCGTCG-TTGGGCTTATGTTTTTGC
131 CTAAATCCCCGAAAACTCACAAAACGGCGTCGTTTTGGCTTAGGTTTTTGC
2536105 AGAAGGCGTT
Statistics
Matches: 278, Mismatches: 67, Indels: 46
0.71 0.17 0.12
Matches are distributed among these distances:
181 10 0.04
182 33 0.12
183 9 0.03
184 15 0.05
185 15 0.05
186 91 0.33
188 47 0.17
189 4 0.01
190 15 0.05
191 33 0.12
192 6 0.02
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (185 bp):
CTTTCTTAAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACGACGTCGTTTTGGCTTATGTTAT
TTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAACGCCG
CTAAATCCCCGAAAACTCACAAAACGGCGTCGTTTTGGCTTAGGTTTTTGCGACG
Found at i:2539553 original size:17 final size:17
Alignment explanation
Indices: 2539533--2539569 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
2539523 AGTTATGTTA
*
2539533 TATGAAAGGTTAAGAGT
1 TATGAAAGGTCAAGAGT
2539550 TATGAAAGGTCAAGAGT
1 TATGAAAGGTCAAGAGT
2539567 TAT
1 TAT
2539570 ATTGTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.41, C:0.03, G:0.27, T:0.30
Consensus pattern (17 bp):
TATGAAAGGTCAAGAGT
Found at i:2546506 original size:25 final size:25
Alignment explanation
Indices: 2546472--2546519 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
2546462 CAAAAAAAGC
2546472 CTGCCGTCTCTGGCACGGGTTCTGT
1 CTGCCGTCTCTGGCACGGGTTCTGT
*
2546497 CTGCCGTCTCTGGCATGGGTTCT
1 CTGCCGTCTCTGGCACGGGTTCT
2546520 TAGGTTTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.04, C:0.31, G:0.31, T:0.33
Consensus pattern (25 bp):
CTGCCGTCTCTGGCACGGGTTCTGT
Found at i:2548144 original size:82 final size:82
Alignment explanation
Indices: 2548007--2548171 Score: 294
Period size: 82 Copynumber: 2.0 Consensus size: 82
2547997 CAAGGTGTGA
*
2548007 AATGGAGATTCACAGGATTTTATGGTTCCCCATATGTCCAGGACAGGAACGTTTCATGGGATACT
1 AATGGAGATTCACAGGATTCTATGGTTCCCCATATGTCCAGGACAGGAACGTTTCATGGGATACT
*
2548072 TTGAAAAGATTGGCCAC
66 TTGAAAAGATTGACCAC
*
2548089 AATGGAGATTCACAGGATTCTATGGTTCCCCATATGTCCAGGACAGGAATGTTTCATGGGATACT
1 AATGGAGATTCACAGGATTCTATGGTTCCCCATATGTCCAGGACAGGAACGTTTCATGGGATACT
*
2548154 TTTAAAAGATTGACCAC
66 TTGAAAAGATTGACCAC
2548171 A
1 A
2548172 GGAGTGGAAA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.28
Consensus pattern (82 bp):
AATGGAGATTCACAGGATTCTATGGTTCCCCATATGTCCAGGACAGGAACGTTTCATGGGATACT
TTGAAAAGATTGACCAC
Found at i:2572522 original size:19 final size:21
Alignment explanation
Indices: 2572488--2572527 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
2572478 CGAATAACTC
2572488 AATTTTTTTAATTTAAAATTT
1 AATTTTTTTAATTTAAAATTT
2572509 AATTTTTTT-A-TTAAAATTT
1 AATTTTTTTAATTTAAAATTT
2572528 TCAAACCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.47
20 1 0.05
21 9 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
AATTTTTTTAATTTAAAATTT
Found at i:2576126 original size:12 final size:12
Alignment explanation
Indices: 2576109--2576138 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2576099 CCCGTATTAA
*
2576109 TTTTTATATCAT
1 TTTTTATATAAT
2576121 TTTTTATATAAT
1 TTTTTATATAAT
2576133 TTTTTA
1 TTTTTA
2576139 AAAAATGTTA
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:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTTTATATAAT
Found at i:2577654 original size:17 final size:17
Alignment explanation
Indices: 2577622--2577655 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2577612 AATTAATATA
* *
2577622 ATTATTAAGTTGTTAAT
1 ATTATTAAATTATTAAT
2577639 ATTATTAAATTATTAAT
1 ATTATTAAATTATTAAT
2577656 TTTTTTATGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
ATTATTAAATTATTAAT
Found at i:2578586 original size:20 final size:20
Alignment explanation
Indices: 2578561--2578604 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
2578551 GAGATTAGTG
2578561 CCTATCTACAAAATGAGAGT
1 CCTATCTACAAAATGAGAGT
*
2578581 CCTATCTATAAAATGAGAGT
1 CCTATCTACAAAATGAGAGT
2578601 CCTA
1 CCTA
2578605 AGAGGTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (20 bp):
CCTATCTACAAAATGAGAGT
Found at i:2590698 original size:67 final size:67
Alignment explanation
Indices: 2590590--2590721 Score: 237
Period size: 67 Copynumber: 2.0 Consensus size: 67
2590580 TTTTCAATTC
* * *
2590590 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGTGGGATTACCAGTCCAGGCTAAATCCCCTG
1 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTACCAGTACAAGCTAAATCCCCTG
2590655 CA
66 CA
2590657 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTACCAGTACAAGCTAAATCCCCTG
1 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTACCAGTACAAGCTAAATCCCCTG
2590722 TAATATAAAC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.28, C:0.33, G:0.19, T:0.20
Consensus pattern (67 bp):
AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTACCAGTACAAGCTAAATCCCCTG
CA
Found at i:2590936 original size:57 final size:57
Alignment explanation
Indices: 2590848--2590956 Score: 175
Period size: 57 Copynumber: 1.9 Consensus size: 57
2590838 AATTCGGATT
2590848 ACCCGTCCGGGCTAAATCCATTTTCCACATATTCTTCGGGAGGGCTATATCAAGATC
1 ACCCGTCCGGGCTAAATCCATTTTCCACATATTCTTCGGGAGGGCTATATCAAGATC
* * *
2590905 ACCCGTTCGGGCTAGAT-CTTTTTCACACATATTCTTCGGGAGGGCTATATCA
1 ACCCGTCCGGGCTAAATCCATTTTC-CACATATTCTTCGGGAGGGCTATATCA
2590957 GGATAGGATC
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
56 6 0.12
57 42 0.88
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (57 bp):
ACCCGTCCGGGCTAAATCCATTTTCCACATATTCTTCGGGAGGGCTATATCAAGATC
Found at i:2595732 original size:106 final size:106
Alignment explanation
Indices: 2595547--2595750 Score: 390
Period size: 106 Copynumber: 1.9 Consensus size: 106
2595537 ATAATATTCA
2595547 TACATGTGTACCACTTAACCAACTAACTAAACATATTTTACTATTATAAAACATCATATCGTAAT
1 TACATGTGTACCACTTAACCAACTAACTAAACATATTTTACTATTATAAAACATCATATCGTAAT
*
2595612 AAATATACATTATAATTCTATTAGCCGAATTTTACATATTT
66 AAATATACATTATAATTCCATTAGCCGAATTTTACATATTT
2595653 TACATGTGTACCACTTAACCAACTAACTAAACATATTTTACTATTATAAAACATCATATCGTAAT
1 TACATGTGTACCACTTAACCAACTAACTAAACATATTTTACTATTATAAAACATCATATCGTAAT
*
2595718 ACATATACATTATAATTCCATTAGCCGAATTTT
66 AAATATACATTATAATTCCATTAGCCGAATTTT
2595751 GTGTCTATAT
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
106 96 1.00
ACGTcount: A:0.40, C:0.18, G:0.05, T:0.37
Consensus pattern (106 bp):
TACATGTGTACCACTTAACCAACTAACTAAACATATTTTACTATTATAAAACATCATATCGTAAT
AAATATACATTATAATTCCATTAGCCGAATTTTACATATTT
Found at i:2596018 original size:22 final size:23
Alignment explanation
Indices: 2595968--2596013 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2595958 TTGAACTATA
2595968 CCATACGAAAAAATGGGCAAAAT
1 CCATACGAAAAAATGGGCAAAAT
2595991 CCATACGAAAAAATGGGCAAAAT
1 CCATACGAAAAAATGGGCAAAAT
2596014 TATACAAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.52, C:0.17, G:0.17, T:0.13
Consensus pattern (23 bp):
CCATACGAAAAAATGGGCAAAAT
Found at i:2600382 original size:43 final size:44
Alignment explanation
Indices: 2600331--2600487 Score: 183
Period size: 44 Copynumber: 3.6 Consensus size: 44
2600321 GTGGACTAAG
* * * *
2600331 CCACCAAATTTGCAGACAAACTGTCATGTAGGTTGTGGAT-AAA
1 CCACCAAATTAGTAGACAAGCTGCCATGTAGGTTGTGGATGAAA
* * *
2600374 CCACCAAATTAATAGACAAGCTGCCATATAGGTTGTGGATGAAG
1 CCACCAAATTAGTAGACAAGCTGCCATGTAGGTTGTGGATGAAA
* * * *
2600418 CTACCAAATTCGTAGACAAGCTGCCACGTAGGTTTTGGATGAAA
1 CCACCAAATTAGTAGACAAGCTGCCATGTAGGTTGTGGATGAAA
*
2600462 CCACCAAATTCA-TAGACAAGTTGCCA
1 CCACCAAATT-AGTAGACAAGCTGCCA
2600488 AATCTTCCTC
Statistics
Matches: 95, Mismatches: 17, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
43 34 0.36
44 61 0.64
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (44 bp):
CCACCAAATTAGTAGACAAGCTGCCATGTAGGTTGTGGATGAAA
Found at i:2600696 original size:40 final size:40
Alignment explanation
Indices: 2600641--2600719 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 40
2600631 TTTTGACATG
*
2600641 CAATTCTCATTTTGTCTCGATGTATCAAAACATCACATTA
1 CAATTCACATTTTGTCTCGATGTATCAAAACATCACATTA
2600681 CAATTCACATTTTGTCTCGATGTATCAAAACATCACATT
1 CAATTCACATTTTGTCTCGATGTATCAAAACATCACATT
2600720 TTTAATAGTC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.33, C:0.23, G:0.08, T:0.37
Consensus pattern (40 bp):
CAATTCACATTTTGTCTCGATGTATCAAAACATCACATTA
Found at i:2603080 original size:16 final size:16
Alignment explanation
Indices: 2603061--2603091 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2603051 GCATGGCTTT
2603061 CTATTTCTTTTATTAC
1 CTATTTCTTTTATTAC
*
2603077 CTATTTGTTTTATTA
1 CTATTTCTTTTATTA
2603092 TACTTTATTT
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:0.19, C:0.13, G:0.03, T:0.65
Consensus pattern (16 bp):
CTATTTCTTTTATTAC
Found at i:2606371 original size:28 final size:30
Alignment explanation
Indices: 2606314--2606371 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 30
2606304 ACATATTCTC
* *
2606314 AACAATACAAATCTTTAATAATACACAGTA
1 AACAATACAAATCTGTAATAATACAAAGTA
*
2606344 AACAATAC-AAT-TGTAATAATATAAAGTA
1 AACAATACAAATCTGTAATAATACAAAGTA
2606372 TATGAGACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 14 0.56
29 3 0.12
30 8 0.32
ACGTcount: A:0.55, C:0.12, G:0.05, T:0.28
Consensus pattern (30 bp):
AACAATACAAATCTGTAATAATACAAAGTA
Found at i:2607170 original size:21 final size:22
Alignment explanation
Indices: 2607146--2607198 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 22
2607136 TTAAAAACAT
2607146 TTATTTTAATGATAATATTA-A
1 TTATTTTAATGATAATATTATA
*
2607167 TTATTTTAATGATAATTTTATA
1 TTATTTTAATGATAATATTATA
*
2607189 TTTTTTTAAT
1 TTATTTTAAT
2607199 TTCTTAGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 19 0.66
22 10 0.34
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (22 bp):
TTATTTTAATGATAATATTATA
Found at i:2610156 original size:27 final size:27
Alignment explanation
Indices: 2610113--2610176 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
2610103 TGGGATTAAG
2610113 TTTGAATTT-ATAATTTGGTAATT-GA
1 TTTGAATTTCATAATTTGGTAATTAGA
2610138 TGTTGAATTTCATAATTTGGTAATTAGA
1 T-TTGAATTTCATAATTTGGTAATTAGA
2610166 TTTGAAATTTC
1 TTTG-AATTTC
2610177 TTTTGTATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
25 1 0.03
26 8 0.23
27 17 0.49
28 9 0.26
ACGTcount: A:0.31, C:0.03, G:0.16, T:0.50
Consensus pattern (27 bp):
TTTGAATTTCATAATTTGGTAATTAGA
Done.