Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 18 of 172
Found at i:5796276 original size:8 final size:7
Alignment explanation
Indices: 5796265--5796316 Score: 58
Period size: 7 Copynumber: 7.9 Consensus size: 7
5796255 TTCTATTTCA
5796265 AAAAAAGG
1 AAAAAA-G
5796273 AAAAAAG
1 AAAAAAG
5796280 --AAAAG
1 AAAAAAG
5796285 -AAAAAG
1 AAAAAAG
*
5796291 AGAAAA-
1 AAAAAAG
5796297 AAAAAAG
1 AAAAAAG
5796304 AAAAAAG
1 AAAAAAG
5796311 AAAAAA
1 AAAAAA
5796317 TGGAGAGGCC
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
5 5 0.13
6 10 0.26
7 18 0.46
8 6 0.15
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:5796289 original size:13 final size:13
Alignment explanation
Indices: 5796267--5796316 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
5796257 CTATTTCAAA
*
5796267 AAAAGGAAAAAAG
1 AAAAGAAAAAAAG
*
5796280 AAAAGAAAAAGAG
1 AAAAGAAAAAAAG
*
5796293 AAAA-AAAAAAGAA
1 AAAAGAAAAAA-AG
5796306 AAAAGAAAAAA
1 AAAAGAAAAAA
5796317 TGGAGAGGCC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
12 5 0.16
13 20 0.65
14 6 0.19
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAAAG
Found at i:5796290 original size:19 final size:18
Alignment explanation
Indices: 5796266--5796316 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 18
5796256 TCTATTTCAA
5796266 AAAAAGGAAAAAAGAAAAG
1 AAAAAGGAAAAAA-AAAAG
5796285 AAAAAGAGAAAAAAAAAAG
1 AAAAAG-GAAAAAAAAAAG
*
5796304 AAAAAAGAAAAAA
1 AAAAAGGAAAAAA
5796317 TGGAGAGGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 7 0.23
19 16 0.53
20 7 0.23
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (18 bp):
AAAAAGGAAAAAAAAAAG
Found at i:5797350 original size:44 final size:44
Alignment explanation
Indices: 5797213--5797648 Score: 368
Period size: 44 Copynumber: 9.9 Consensus size: 44
5797203 CAAGATTTGG
*
5797213 CATCCCTGTGTTTATAGGAAACAGATCGAAGATAGCAGATCTGA
1 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
* * * * * ** *
5797257 CATTCATGTGCTTACAGCGAAGCAGATCGAAGATTTCAG--CATGG
1 CATCCCTGTGTTTATAGGGAA-CAGATCGAAGATAGCAGATC-TGA
* *
5797301 CATCCCTGTGTTTATAGGGAACA-AGTTGAAGATAGCAGATTTGA
1 CATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGCAGATCTGA
5797345 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
1 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
* * * * * ** *
5797389 CATTCCTGTGCTTACAGTGAAGCAGATCAAAGATTTCAG-TATGA
1 CATCCCTGTGTTTATAGGGAA-CAGATCGAAGATAGCAGATCTGA
* * *
5797433 CATCCCTGTGTTTATAGGGAACA-AGTTGAAGATAGCAGATTTGG
1 CATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGCAGATCTGA
*
5797477 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCTGA
1 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
* ** * * ** *
5797521 CA-CTCCTGTGCTTGCAGCGAAGCAGATCGAGGATTTCAG--CATGG
1 CATC-CCTGTGTTTATAGGGAA-CAGATCGAAGATAGCAGATC-TGA
* * *
5797565 CTTCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATTTGG
1 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
* * * * * *
5797609 CATCTCTGTATTGT-CAGAGAGCAGATCGAAGATACCAGAT
1 CATCCCTGTGTT-TATAGGGAACAGATCGAAGATAGCAGAT
5797649 TTGGCATCTC
Statistics
Matches: 308, Mismatches: 67, Indels: 34
0.75 0.16 0.08
Matches are distributed among these distances:
42 2 0.01
43 40 0.13
44 219 0.71
45 47 0.15
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.27
Consensus pattern (44 bp):
CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
Found at i:5797397 original size:88 final size:89
Alignment explanation
Indices: 5797210--5797661 Score: 406
Period size: 88 Copynumber: 5.1 Consensus size: 89
5797200 AAACAAGATT
* * * *
5797210 TGGCATCCCTGTGTTTATAGGAAACAGATCGAAGATAGCAGATCTGACATTCATGTGCTTACAGC
1 TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACATCCCTGTGTTTACAGC
**
5797275 GAAGCAGATCGAAGATTTCAG--CA
66 GAA-CAGATCGAAGATAGCAGATCA
* * *
5797298 TGGCATCCCTGTGTTTATAGGGAACA-AGTTGAAGATAGCAGATTTGACATCCCTGTGTTTATAG
1 TGGCATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGCAGATCTGACATCCCTGTGTTTACAG
*
5797362 GGAACAGATCGAAGATAGCAGATC-
65 CGAACAGATCGAAGATAGCAGATCA
* * * * * * ** * *
5797386 TGACATTCCTGTGCTTACAGTGAAGCAGATCAAAGATTTCAG-TATGACATCCCTGTGTTTATAG
1 TGGCATCCCTGTGTTTATAGGGAA-CAGATCGAAGATAGCAGATCTGACATCCCTGTGTTTACAG
* * *
5797450 GGAACA-AGTTGAAGATAGCAGAT-T
65 CGAACAGA-TCGAAGATAGCAGATCA
* * *
5797474 TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCTGACA-CTCCTGTGCTTGCAG
1 TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACATC-CCTGTGTTTACAG
* **
5797538 CGAAGCAGATCGAGGATTTCAG--CA
65 CGAA-CAGATCGAAGATAGCAGATCA
* * * * *
5797562 TGGCTTCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATTTGGCATCTCTGTATTGT-CAG
1 TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACATCCCTGTGTT-TACAG
* * * *
5797626 AGAGCAGATCGAAGATACCAGAT-T
65 CGAACAGATCGAAGATAGCAGATCA
*
5797650 TGGCATCTCTGT
1 TGGCATCCCTGT
5797662 ATTGGCGGAG
Statistics
Matches: 294, Mismatches: 54, Indels: 32
0.77 0.14 0.08
Matches are distributed among these distances:
87 46 0.16
88 221 0.75
89 25 0.09
90 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (89 bp):
TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACATCCCTGTGTTTACAGC
GAACAGATCGAAGATAGCAGATCA
Found at i:5797442 original size:132 final size:132
Alignment explanation
Indices: 5797205--5797648 Score: 685
Period size: 132 Copynumber: 3.4 Consensus size: 132
5797195 CAAAGAAACA
* *
5797205 AGATTTGGCATCCCTGTGTTTATAGGAAACAGATCGAAGATAGCAGATCTGACATTCATGTGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTT
5797270 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
5797335 GC
131 GC
*
5797337 AGATTTGACATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTT
* * * *
5797402 ACAGTGAAGCAGATCAAAGATTTCAGTATGACATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
5797467 GC
131 GC
* *
5797469 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCTGACACTCCTGTGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTT
* * * *
5797534 GCAGCGAAGCAGATCGAGGATTTCAGCATGGCTTCCCTGTGTTTATAGGGAAC-AGATCGAAGAT
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAG-TTGAAGAT
5797598 AGC
130 AGC
* * * * * *
5797601 AGATTTGGCATCTCTGTATTGT-CAGAGAGCAGATCGAAGATACCAGAT
1 AGATTTGGCATCCCTGTGTT-TATAGGGAACAGATCGAAGATAGCAGAT
5797649 TTGGCATCTC
Statistics
Matches: 286, Mismatches: 24, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
131 2 0.01
132 283 0.99
133 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (132 bp):
AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTT
ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
GC
Found at i:5797649 original size:44 final size:44
Alignment explanation
Indices: 5797586--5797684 Score: 162
Period size: 44 Copynumber: 2.2 Consensus size: 44
5797576 TTATAGGGAA
* *
5797586 CAGATCGAAGATAGCAGATTTGGCATCTCTGTATTGTCAGAGAG
1 CAGATCGAAGATACCAGATTTGGCATCTCTGTATTGGCAGAGAG
*
5797630 CAGATCGAAGATACCAGATTTGGCATCTCTGTATTGGCGGAGAG
1 CAGATCGAAGATACCAGATTTGGCATCTCTGTATTGGCAGAGAG
*
5797674 CAGATCAAAGA
1 CAGATCGAAGA
5797685 CATAGCTGAT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 51 1.00
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.24
Consensus pattern (44 bp):
CAGATCGAAGATACCAGATTTGGCATCTCTGTATTGGCAGAGAG
Found at i:5798651 original size:16 final size:15
Alignment explanation
Indices: 5798623--5798674 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 15
5798613 TCTATGCATG
5798623 TATATAT-ATTATAT
1 TATATATCATTATAT
5798637 TATATATCATGTATAT
1 TATATATCAT-TATAT
5798653 CGTATATCATCTATTATAT
1 --TATAT-ATC-ATTATAT
5798672 TAT
1 TAT
5798675 TTATGTTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
14 7 0.22
15 2 0.06
16 5 0.16
17 3 0.09
18 5 0.16
19 8 0.25
20 2 0.06
ACGTcount: A:0.37, C:0.08, G:0.04, T:0.52
Consensus pattern (15 bp):
TATATATCATTATAT
Found at i:5799238 original size:21 final size:21
Alignment explanation
Indices: 5799212--5799252 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
5799202 ATAAAAAAGG
5799212 CAATGCTTGGTATTTGGAAGA
1 CAATGCTTGGTATTTGGAAGA
5799233 CAATGCTTGGTATTTGGAAG
1 CAATGCTTGGTATTTGGAAG
5799253 CTCCGAGACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.10, G:0.29, T:0.34
Consensus pattern (21 bp):
CAATGCTTGGTATTTGGAAGA
Found at i:5806253 original size:23 final size:23
Alignment explanation
Indices: 5806227--5806271 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
5806217 TGATACATTG
*
5806227 CTAAAATGTCACTCATTGCTTGA
1 CTAAAATGTCACTCATTACTTGA
*
5806250 CTAAGATGTCACTCATTACTTG
1 CTAAAATGTCACTCATTACTTG
5806272 TAATGTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (23 bp):
CTAAAATGTCACTCATTACTTGA
Found at i:5807597 original size:23 final size:23
Alignment explanation
Indices: 5807515--5807601 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
5807505 CCTGATCAGT
*
5807515 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* *
5807537 A-ACGACACACGAGGTGCCTG--
1 ATACGACACACAAAGTGCCTGAA
* *
5807557 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
*
5807580 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
5807602 TCAGTAAAGC
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
20 1 0.02
21 34 0.62
22 1 0.02
23 19 0.35
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.15
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:5809081 original size:16 final size:17
Alignment explanation
Indices: 5809046--5809081 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
5809036 CCTAATTCTC
5809046 CCTT-TTTCTTTTCTTT
1 CCTTCTTTCTTTTCTTT
5809062 -CTTCTTTC-TTTCTTT
1 CCTTCTTTCTTTTCTTT
5809077 CCTTC
1 CCTTC
5809082 CCCTGCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (17 bp):
CCTTCTTTCTTTTCTTT
Found at i:5812791 original size:35 final size:34
Alignment explanation
Indices: 5812733--5812798 Score: 96
Period size: 35 Copynumber: 1.9 Consensus size: 34
5812723 AGTAAAATGT
*
5812733 TTTCCGTAAAATAATTTCTGGAAAATGTTTTATA
1 TTTCCGTAAAATAATTACTGGAAAATGTTTTATA
* *
5812767 TTTCTGTAAAATGACTTACTGGAAAATGTTTT
1 TTTCCGTAAAAT-AATTACTGGAAAATGTTTT
5812799 CTGGTGTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 11 0.39
35 17 0.61
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (34 bp):
TTTCCGTAAAATAATTACTGGAAAATGTTTTATA
Found at i:5813989 original size:18 final size:18
Alignment explanation
Indices: 5813937--5813981 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
5813927 GCTTCGAAAC
5813937 GGGAAAGGGAAGGAGAAG
1 GGGAAAGGGAAGGAGAAG
5813955 GGGAAAGGGAAGGAGAAG
1 GGGAAAGGGAAGGAGAAG
5813973 GGGAAAGGG
1 GGGAAAGGG
5813982 GAGAAGAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (18 bp):
GGGAAAGGGAAGGAGAAG
Found at i:5821368 original size:32 final size:32
Alignment explanation
Indices: 5821330--5821390 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
5821320 TAATCAATAT
* *
5821330 GAGTTATCAAATTAAATTAATTAATTTATCAC
1 GAGTTATCAAATTAAAGTAATCAATTTATCAC
* *
5821362 GAGTTATTAAATTCAAGTAATCAATTTAT
1 GAGTTATCAAATTAAAGTAATCAATTTAT
5821391 AAGTTTATGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (32 bp):
GAGTTATCAAATTAAAGTAATCAATTTATCAC
Found at i:5823226 original size:42 final size:42
Alignment explanation
Indices: 5823171--5823291 Score: 147
Period size: 43 Copynumber: 2.9 Consensus size: 42
5823161 TAGGGTTACT
*
5823171 GAGATTACATGTAAGACCATATCTGAGATATGACATCGATAT
1 GAGATTACATGTAAGACCATATCTGAGATATGACATCGATAC
* * * * *
5823213 GAGACTT-CGTGTAAGACCATAAT-TGGGCTATTGGCATTGATAC
1 GAGA-TTACATGTAAGACCAT-ATCTGAGATA-TGACATCGATAC
5823256 GAGATTACATGTAAGACCATATCTGAGATATGACAT
1 GAGATTACATGTAAGACCATATCTGAGATATGACAT
5823292 TGGTACGGTA
Statistics
Matches: 64, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
42 30 0.47
43 34 0.53
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (42 bp):
GAGATTACATGTAAGACCATATCTGAGATATGACATCGATAC
Found at i:5829087 original size:29 final size:28
Alignment explanation
Indices: 5829029--5829110 Score: 82
Period size: 28 Copynumber: 3.0 Consensus size: 28
5829019 TAATATTAAA
5829029 TAAATATG-TATATAATT-TAATTAAAA-T
1 TAAATATGATATATAATTAT-A-TAAAATT
* * *
5829056 TAAAGTTTTATATATAATTATATCAAATT
1 TAAA-TATGATATATAATTATATAAAATT
5829085 TAAATATGATATATAA-TATATAAAAT
1 TAAATATGATATATAATTATATAAAAT
5829111 CAAATAAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
27 13 0.29
28 16 0.36
29 15 0.33
30 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (28 bp):
TAAATATGATATATAATTATATAAAATT
Found at i:5830946 original size:14 final size:14
Alignment explanation
Indices: 5830929--5830955 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5830919 TATGTTAGAA
5830929 TGTTTATAAAAAAG
1 TGTTTATAAAAAAG
5830943 TGTTTATAAAAAA
1 TGTTTATAAAAAA
5830956 AAAAAAAGTC
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:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (14 bp):
TGTTTATAAAAAAG
Found at i:5835808 original size:46 final size:46
Alignment explanation
Indices: 5835710--5835811 Score: 141
Period size: 46 Copynumber: 2.2 Consensus size: 46
5835700 TGAGAAGTCA
*
5835710 GCAAGGGGAGCTCGCGGTCTCAGCTCGCACATGCCAAGGAGTGCTC
1 GCAAGGGGAGCTCACGGTCTCAGCTCGCACATGCCAAGGAGTGCTC
** * * * *
5835756 ATAAGGGGAGCTTACGGTCTCAGCTCGCACATGCCAATGTGTGCTT
1 GCAAGGGGAGCTCACGGTCTCAGCTCGCACATGCCAAGGAGTGCTC
5835802 GCAAGGGGAG
1 GCAAGGGGAG
5835812 TTTGTGGTCC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.22, C:0.25, G:0.34, T:0.19
Consensus pattern (46 bp):
GCAAGGGGAGCTCACGGTCTCAGCTCGCACATGCCAAGGAGTGCTC
Found at i:5839563 original size:23 final size:23
Alignment explanation
Indices: 5839519--5839564 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
5839509 TACATCAGCA
* *
5839519 AGGTACTCCAAAATGATGAAATG
1 AGGTACTCAAAAATGATAAAATG
5839542 AGGTACTCAAAAATTGA-AAAATG
1 AGGTACTCAAAAA-TGATAAAATG
5839565 TATCTTTGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.48, C:0.11, G:0.20, T:0.22
Consensus pattern (23 bp):
AGGTACTCAAAAATGATAAAATG
Found at i:5841073 original size:38 final size:38
Alignment explanation
Indices: 5841031--5841128 Score: 126
Period size: 38 Copynumber: 2.5 Consensus size: 38
5841021 GCACTAGGCT
*
5841031 TGCGGGATTTAACCCGGATATAATACCAGTACGA-AGCC
1 TGCGGGATTTAACCCGGATATAATACCAGCA-GATAGCC
* *
5841069 TGCGGGATTTAACCCGGATATAATTCCAGCATATAGCC
1 TGCGGGATTTAACCCGGATATAATACCAGCAGATAGCC
*
5841107 TGCGGGTCTTTAAGCCCGGATA
1 TGCGGG-ATTTAA-CCCGGATA
5841129 CACATCAAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
37 1 0.02
38 39 0.74
39 5 0.09
40 8 0.15
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.24
Consensus pattern (38 bp):
TGCGGGATTTAACCCGGATATAATACCAGCAGATAGCC
Found at i:5853458 original size:12 final size:12
Alignment explanation
Indices: 5853443--5853476 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5853433 TTAAAAAAGA
*
5853443 TTAATTTACTCT
1 TTAATTTAATCT
5853455 TTAATTTAATCT
1 TTAATTTAATCT
*
5853467 TTAATCTAAT
1 TTAATTTAAT
5853477 GTACAAGAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (12 bp):
TTAATTTAATCT
Found at i:5864151 original size:120 final size:120
Alignment explanation
Indices: 5864013--5864299 Score: 538
Period size: 120 Copynumber: 2.4 Consensus size: 120
5864003 TTGCTTTTAC
* * *
5864013 ATTAAATTATATAGTTTAATTAAAATTTATTTAATAATAATTATGTTAATTTATATTTTATAGTA
1 ATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTA
5864078 TCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTT
66 TCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTT
5864133 ATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTA
1 ATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTA
*
5864198 TCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTT
66 TCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTT
5864253 ATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 ATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
5864300 TAAATATGAT
Statistics
Matches: 163, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 163 1.00
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (120 bp):
ATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTA
TCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTT
Found at i:5864167 original size:15 final size:15
Alignment explanation
Indices: 5864132--5864183 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
5864122 TTAAGAATTT
*
5864132 TATTAAATTAT-ATA
1 TATTTAATTATAATA
5864146 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
5864160 TATTTAATAATAAT-
1 TATTTAATTATAATA
5864174 TATGTTAATT
1 TAT-TTAATT
5864184 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:5864265 original size:61 final size:61
Alignment explanation
Indices: 5864080--5864267 Score: 199
Period size: 61 Copynumber: 3.1 Consensus size: 61
5864070 TTATAGTATC
*
5864080 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
* * * * * * * * * *
5864141 ATATATTTTAATTAT-AATATATTTA-ATAATAAT-TATG-TTAATTTA-TATTTTA-TAGTATC
1 ATATATTATGATT-TGAGTAAATTCATATAAGAATAT-TGATT-ATTAAGAATTTTATTA-AATT
5864200 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
5864261 ATATATT
1 ATATATT
5864268 TTAATTATAA
Statistics
Matches: 96, Mismatches: 21, Indels: 20
0.70 0.15 0.15
Matches are distributed among these distances:
58 3 0.03
59 29 0.30
60 25 0.26
61 36 0.38
62 3 0.03
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
Found at i:5864282 original size:16 final size:16
Alignment explanation
Indices: 5864261--5864302 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
5864251 TTATTAAATT
*
5864261 ATATATTTTAATTATA
1 ATATATTTTAATAATA
5864277 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
5864292 AT-TATGTTTAA
1 ATATAT-TTTAA
5864303 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:5864287 original size:15 final size:15
Alignment explanation
Indices: 5864252--5864293 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
5864242 TTAAGAATTT
*
5864252 TATTAAATTAT-ATA
1 TATTTAATTATAATA
5864266 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
5864280 TATTTAATAATAAT
1 TATTTAATTATAAT
5864294 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:5864532 original size:45 final size:43
Alignment explanation
Indices: 5864428--5864537 Score: 113
Period size: 45 Copynumber: 2.6 Consensus size: 43
5864418 TTTTCCATTA
5864428 TGCTATTACACCTCTATT-C---CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATACATTCAACCAAACACAAGAT
* * * *
5864467 TACTATTACGCCTTTATTCCATTACATTCAACCAAACA-ATTGATT
1 TGCTATTACACCTCTATTCCA-TACATTCAACCAAACACA-AGA-T
5864512 TGCTATTACACCTCTATTCCAATACA
1 TGCTATTACACCTCTATTCC-ATACA
5864538 CCTCTAATCC
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
39 15 0.27
40 1 0.02
43 1 0.02
44 16 0.29
45 22 0.39
46 1 0.02
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.34
Consensus pattern (43 bp):
TGCTATTACACCTCTATTCCATACATTCAACCAAACACAAGAT
Found at i:5864539 original size:16 final size:16
Alignment explanation
Indices: 5864518--5864585 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
5864508 GATTTGCTAT
*
5864518 TACACCTCTATTCCAA
1 TACACCTCTAATCCAA
*
5864534 TACACCTCTAATCCAT
1 TACACCTCTAATCCAA
5864550 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
5864566 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
5864582 TACA
1 TACA
5864586 GCGAACCAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:5877032 original size:6 final size:6
Alignment explanation
Indices: 5877021--5877060 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
5877011 AACGTGTGAA
5877021 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
5877061 TACACACAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:5886039 original size:7 final size:7
Alignment explanation
Indices: 5886023--5886077 Score: 51
Period size: 7 Copynumber: 8.0 Consensus size: 7
5886013 ATCCATTTCC
5886023 AAAAAT-
1 AAAAATA
5886029 AAAAATA
1 AAAAATA
5886036 AAAAATA
1 AAAAATA
**
5886043 AAAAAGC
1 AAAAATA
*
5886050 AAAAAGA
1 AAAAATA
5886057 AAAAA-A
1 AAAAATA
*
5886063 AAAGAAAA
1 AAA-AATA
5886071 AAAAATA
1 AAAAATA
5886078 TATAACTGCA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
6 10 0.24
7 28 0.67
8 4 0.10
ACGTcount: A:0.85, C:0.02, G:0.05, T:0.07
Consensus pattern (7 bp):
AAAAATA
Found at i:5886070 original size:10 final size:11
Alignment explanation
Indices: 5886023--5886075 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
5886013 ATCCATTTCC
*
5886023 AAAAATAAAAAT
1 AAAAA-AAAAAG
*
5886035 AAAAAATAAA-
1 AAAAAAAAAAG
**
5886045 AAAGCAAAAAG
1 AAAAAAAAAAG
5886056 AAAAAAAAAAG
1 AAAAAAAAAAG
5886067 AAAAAAAAA
1 AAAAAAAAA
5886076 TATATAACTG
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
10 7 0.21
11 22 0.65
12 5 0.15
ACGTcount: A:0.87, C:0.02, G:0.06, T:0.06
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:5886259 original size:60 final size:60
Alignment explanation
Indices: 5886187--5886304 Score: 227
Period size: 60 Copynumber: 2.0 Consensus size: 60
5886177 AACAAATTAT
*
5886187 AGAAGATGACCGAGACTGGTAAAAATTGGCATAAGAAACTACTGCCTACTCTCTATGCAC
1 AGAAGATGACCGAGACTGGTAAAAATTGGCATAAGAAACTACCGCCTACTCTCTATGCAC
5886247 AGAAGATGACCGAGACTGGTAAAAATTGGCATAAGAAACTACCGCCTACTCTCTATGC
1 AGAAGATGACCGAGACTGGTAAAAATTGGCATAAGAAACTACCGCCTACTCTCTATGC
5886305 TTACGCTGGG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.21
Consensus pattern (60 bp):
AGAAGATGACCGAGACTGGTAAAAATTGGCATAAGAAACTACCGCCTACTCTCTATGCAC
Found at i:5887636 original size:7 final size:7
Alignment explanation
Indices: 5887624--5887684 Score: 56
Period size: 7 Copynumber: 8.7 Consensus size: 7
5887614 TTATTTCAAA
5887624 AAAAAAG
1 AAAAAAG
5887631 AAAAAA-
1 AAAAAAG
5887637 AAGAAAA-
1 AA-AAAAG
*
5887644 AAATAA-
1 AAAAAAG
*
5887650 TAAAAAG
1 AAAAAAG
5887657 AAAAAAG
1 AAAAAAG
5887664 AGAAAAATG
1 A-AAAAA-G
5887673 AAAAAAG
1 AAAAAAG
5887680 AAAAA
1 AAAAA
5887685 TGGAGAGGCC
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
6 9 0.20
7 25 0.54
8 10 0.22
9 2 0.04
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (7 bp):
AAAAAAG
Found at i:5887645 original size:16 final size:16
Alignment explanation
Indices: 5887624--5887684 Score: 79
Period size: 16 Copynumber: 3.8 Consensus size: 16
5887614 TTATTTCAAA
5887624 AAAAAAGAAAAAAAAG
1 AAAAAAGAAAAAAAAG
5887640 AAAAAA-ATAATAAAAAG
1 AAAAAAGA-AA-AAAAAG
* *
5887657 AAAAAAGAGAAAAATG
1 AAAAAAGAAAAAAAAG
5887673 AAAAAAGAAAAA
1 AAAAAAGAAAAA
5887685 TGGAGAGGCC
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
15 1 0.03
16 24 0.62
17 13 0.33
18 1 0.03
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (16 bp):
AAAAAAGAAAAAAAAG
Found at i:5887678 original size:9 final size:8
Alignment explanation
Indices: 5887623--5887684 Score: 65
Period size: 9 Copynumber: 7.6 Consensus size: 8
5887613 TTTATTTCAA
5887623 AAAAAAAG
1 AAAAAAAG
5887631 AAAAAAAAG
1 -AAAAAAAG
*
5887640 AAAAAAAT
1 AAAAAAAG
5887648 AATAAAAAG
1 AA-AAAAAG
5887657 -AAAAAAG
1 AAAAAAAG
*
5887664 AGAAAAATG
1 A-AAAAAAG
5887673 -AAAAAAG
1 AAAAAAAG
5887680 AAAAA
1 AAAAA
5887685 TGGAGAGGCC
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
7 12 0.27
8 14 0.31
9 19 0.42
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (8 bp):
AAAAAAAG
Found at i:5887691 original size:26 final size:23
Alignment explanation
Indices: 5887623--5887684 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 23
5887613 TTTATTTCAA
*
5887623 AAAAAAAGAAAAAAAAGAAAAAAAT
1 AAAAAAAG--AAAAAAGAGAAAAAT
5887648 AATAAAAAGAAAAAAGAGAAAAAT
1 AA-AAAAAGAAAAAAGAGAAAAAT
*
5887672 GAAAAAAGAAAAA
1 AAAAAAAGAAAAA
5887685 TGGAGAGGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 11 0.32
24 15 0.44
25 2 0.06
26 6 0.18
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (23 bp):
AAAAAAAGAAAAAAGAGAAAAAT
Found at i:5888821 original size:88 final size:88
Alignment explanation
Indices: 5888543--5888884 Score: 338
Period size: 88 Copynumber: 3.9 Consensus size: 88
5888533 AAACAAGATT
5888543 TGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGCTTACAGC
1 TGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGCTTACAGC
* *
5888608 GAAGCAGATCAAAGATTTCAGCA
66 GAAGAAGATCGAAGATTTCAGCA
* ** * * * ** * * * *
5888631 TCGTGTCCCTGTGTTTATAGGGAACGAGTTGAAGATTTCAG--CATGGCATCCCTGTGTTTATAG
1 TGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATC-TGACATTCCTGTGCTTACAG
* * * **
5888694 GGAACAAG-TTGAAGATAGCAG-A
65 CGAAGAAGATCGAAGATTTCAGCA
* *
5888716 TTTGGCATCCCCGTGTTTATAGGGAACAAATCGAAGATAACAGATCTGACATTCCTGTGCTTACA
1 --TGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGCTTACA
* *
5888781 GCGAAGTAGATCGAAGATTTTAGCA
64 GCGAAGAAGATCGAAGATTTCAGCA
* * * *
5888806 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCA-TCCTTGTGCTTACAA
1 TGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCC-TGTGCTTAC-A
*
5888870 G-GAACAA-ATCGAAGA
64 GCGAAGAAGATCGAAGA
5888885 CATAGCTGAT
Statistics
Matches: 198, Mismatches: 47, Indels: 19
0.75 0.18 0.07
Matches are distributed among these distances:
85 1 0.01
86 10 0.05
87 64 0.32
88 110 0.56
89 12 0.06
90 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (88 bp):
TGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGCTTACAGC
GAAGAAGATCGAAGATTTCAGCA
Found at i:5888884 original size:44 final size:44
Alignment explanation
Indices: 5888538--5888899 Score: 261
Period size: 44 Copynumber: 8.2 Consensus size: 44
5888528 TAAAGAAACA
5888538 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGC
* * * * * * * * **
5888582 AGATCTGACATTCCTGTGCTTACAGCGAAGCAGATCAAAGATTTC
1 AGATTTGGCATCCCTGTGTTTATAGGGAA-CAAATCGAAGATAGC
* * * * **
5888627 AGCA-TCGTG--TCCCTGTGTTTATAGGGAACGAGTTGAAGATTTC
1 AG-ATTTG-GCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGC
* *
5888670 AGCA--TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGC
1 AG-ATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGC
* *
5888713 AGATTTGGCATCCCCGTGTTTATAGGGAACAAATCGAAGATAAC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGC
* * * * * * * * ***
5888757 AGATCTGACATTCCTGTGCTTACAGCGAAGTAGATCGAAGATTTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAA-CAAATCGAAGATAGC
* *
5888802 AGCA--TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGC
1 AG-ATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGC
* * * *
5888845 AGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAG--ATAGC
*
5888891 TGATTTGGC
1 AGATTTGGC
5888900 TTTCACGGTT
Statistics
Matches: 244, Mismatches: 61, Indels: 24
0.74 0.19 0.07
Matches are distributed among these distances:
41 1 0.00
42 3 0.01
43 57 0.23
44 142 0.58
45 26 0.11
46 15 0.06
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.28
Consensus pattern (44 bp):
AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGC
Found at i:5889204 original size:205 final size:205
Alignment explanation
Indices: 5888846--5889784 Score: 1525
Period size: 205 Copynumber: 4.6 Consensus size: 205
5888836 GAAGATAGCA
5888846 GATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACG-GTT
1 GATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTT
* * * * * *
5888910 TACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTGTTGTTAGAGAACAAACCAAAGTTTGG
66 TACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTCTGG
* * * ** *
5888975 CGTCTCCATATTCGACGAAGAGCAGGCACATAGCAGATCTGGCCTTCATATGTTTATACTGAAGC
131 CATCTCCAT-TTCGACGGAGAGCAGACACATAGCAGATCTAACCTTCAGATGTTTATACTGAAGC
*
5889040 AGATCCAAGGT
195 AGATCCAAGAT
5889051 GATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACG-GTT
1 GATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTT
* *
5889115 TACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGG
66 TACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTCTGG
* *
5889180 CGTCTCCATATTCGACGGAGAGCAGACACATAGTAGATCTAACCTTCAGATGTTTATACTGAAGC
131 CATCTCCAT-TTCGACGGAGAGCAGACACATAGCAGATCTAACCTTCAGATGTTTATACTGAAGC
*
5889245 AAATCCAAGAT
195 AGATCCAAGAT
** *
5889256 GATTTGGCATTTTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGCT
1 GATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTT
5889321 TACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTCTGG
66 TACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTCTGG
* * * *
5889386 TATCTCCATTTCGACGGAGAGCGGATACATAGTAGATCTAACCTTCAGATGTTTATACTGAAGCA
131 CATCTCCATTTCGACGGAGAGCAGACACATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCA
5889451 GATCCAAGAT
196 GATCCAAGAT
* * *
5889461 GGTTTGGCATCCTTGTGCTTACAAGGAACAAATCAAAGACATAGCTGATTTGGCTTTCACGTGCT
1 GATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTT
*
5889526 TACGATGAAGCAAATCTAAGATGATTTGGCATCTCT-TATAGTCAGAGAACAAATCGAAGTCTGG
66 TACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTCTGG
*
5889590 CATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTAACCTTCAGATG-----ACTGAAGCA
131 CATCTCCATTTCGACGGAGAGCAGACACATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCA
5889650 GATCCAAGAT
196 GATCCAAGAT
*
5889660 GGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTT
1 GATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTT
5889725 TACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAG
66 TACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAG
5889785 AAATAGATTT
Statistics
Matches: 699, Mismatches: 33, Indels: 9
0.94 0.04 0.01
Matches are distributed among these distances:
199 118 0.17
200 22 0.03
204 75 0.11
205 412 0.59
206 72 0.10
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (205 bp):
GATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTT
TACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTCTGG
CATCTCCATTTCGACGGAGAGCAGACACATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCA
GATCCAAGAT
Found at i:5890040 original size:87 final size:85
Alignment explanation
Indices: 5889686--5890046 Score: 213
Period size: 87 Copynumber: 4.2 Consensus size: 85
5889676 GCTTACAAGG
* * *
5889686 AACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATT
1 AACAAATCGAAGACATAGCAGATTTGGCTTTCA-GTGTTTACGATGAAGCAGATCTAAGATAATT
*
5889751 TGGCATCTCTGTATTGTCAGAG
65 TGGCATCTCTGT-TTGTCAGAA
* * * *
5889773 AACAAATCGAAGA-A-A-TAGATTTGGCGTCTCAGT-ATT-CGATGGAGAGCAGATCAAAGATAT
1 AACAAATCGAAGACATAGCAGATTTGGC-TTTCAGTGTTTACGAT-GA-AGCAGATCTAAGATA-
*** ** *
5889833 CAACAGGACAGTCATAAGTTT-ACA-AGA
62 -ATTTGG-CA-TC-TCTGTTTGTCAGA-A
* * ** * * * * *
5889860 AGCAGATTAAAGACATAGCAGATCTGACCTTCAGATGATTTTAC--TGAAGCAGATCCAAGATGA
1 AACAAATCGAAGACATAGCAGATTTGGCTTTCAG-TG--TTTACGATGAAGCAGATCTAAGATAA
* * *
5889923 TTTGACATC-CT-TCTGTTCACAA
63 TTTGGCATCTCTGTTTG-TCAGAA
* * *
5889945 GGAGCAAATCGAAGACACAGCAGATTTGGCTTTCACGTGTTTACGCTGAAGCAGATCTAAGATAA
1 --AACAAATCGAAGACATAGCAGATTTGGCTTTCA-GTGTTTACGATGAAGCAGATCTAAGATAA
5890010 TTTGGCATCTCTGTATTGTCAGAA
63 TTTGGCATCTCTGT-TTGTCAGAA
5890034 AACAAATCGAAGA
1 AACAAATCGAAGA
5890047 AGTAGATTTG
Statistics
Matches: 199, Mismatches: 47, Indels: 56
0.66 0.16 0.19
Matches are distributed among these distances:
82 4 0.02
83 6 0.03
84 22 0.11
85 13 0.07
86 8 0.04
87 93 0.47
88 10 0.05
89 14 0.07
90 23 0.12
91 2 0.01
92 1 0.01
93 2 0.01
94 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (85 bp):
AACAAATCGAAGACATAGCAGATTTGGCTTTCAGTGTTTACGATGAAGCAGATCTAAGATAATTT
GGCATCTCTGTTTGTCAGAA
Found at i:5890106 original size:261 final size:255
Alignment explanation
Indices: 5889616--5890128 Score: 726
Period size: 261 Copynumber: 2.0 Consensus size: 255
5889606 GAGAGCAGAT
* * *
5889616 ACATAGCAGATCTAACCTTCAGATGACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTA
1 ACATAGCAGATCTAACCTTCAGATGACTGAAGCAGATCCAAGATGATTTGACATCCTTCTGCTTA
* *
5889681 CAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGA
66 CAAGGAACAAATCGAAGACACAGCAGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGA
* *
5889746 TGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGAAATAGATTTGGCGTCTCAGTATTCG
131 TAATTTGGCATCTCTGTATTGTCAGAAAACAAATCGAAGAAATAGATTTGGCGTCTCAGTATTCG
*
5889811 ATGGAGAGCAGATCAAAGATATCAACAGGACAGTCATAAGTTTACAA-GAAGCAGATTAAAG
196 A-GGAGAGCAGATCAAAGATATAAACAGGACAGTCATAAGTTTACAATG-AGCAGATTAAAG
*
5889872 ACATAGCAGATCTGACCTTCAGATGATTTTACTGAAGCAGATCCAAGATGATTTGACATCCTTCT
1 ACATAGCAGATCTAACCTTCAGATG-----ACTGAAGCAGATCCAAGATGATTTGACATCCTTCT
* * *
5889937 G-TTCACAAGGAGCAAATCGAAGACACAGCAGATTTGGCTTTCACGTGTTTACGCTGAAGCAGAT
61 GCTT-ACAAGGAACAAATCGAAGACACAGCAGATTTGGCTTTCACGTGTTTACGATGAAGCAAAT
* *
5890001 CTAAGATAATTTGGCATCTCTGTATTGTCAGAAAACAAATCGAAGAAGTAGATTTGGCGTCTCTG
125 CTAAGATAATTTGGCATCTCTGTATTGTCAGAAAACAAATCGAAGAAATAGATTTGGCGTCTCAG
* * * * * * *
5890066 TGTTC-AGCAGAGAGCATATCGAAGATATAAACATGACAGTCTTGAGTTTGCAATGAGCAGATT
190 TATTCGAG--GAGAGCAGATCAAAGATATAAACAGGACAGTCATAAGTTTACAATGAGCAGATT
5890129 GAGGACCATG
Statistics
Matches: 227, Mismatches: 21, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
256 24 0.11
259 1 0.00
260 3 0.01
261 198 0.87
262 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (255 bp):
ACATAGCAGATCTAACCTTCAGATGACTGAAGCAGATCCAAGATGATTTGACATCCTTCTGCTTA
CAAGGAACAAATCGAAGACACAGCAGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGA
TAATTTGGCATCTCTGTATTGTCAGAAAACAAATCGAAGAAATAGATTTGGCGTCTCAGTATTCG
AGGAGAGCAGATCAAAGATATAAACAGGACAGTCATAAGTTTACAATGAGCAGATTAAAG
Found at i:5890437 original size:19 final size:19
Alignment explanation
Indices: 5890413--5890473 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
5890403 AATCTTTAAG
*
5890413 GATATGCAATCTTAGGTAT
1 GATATGCAATCTTAGATAT
5890432 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
5890451 GATAT--AATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
5890468 AATATG
1 GATATG
5890474 ATATGATATG
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
17 16 0.41
19 23 0.59
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:5893862 original size:24 final size:25
Alignment explanation
Indices: 5893809--5893856 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
5893799 TTAGCCCTCT
* *
5893809 CGAGCTTCCCATTATATGGTTCTTG
1 CGAGCTTCCCATTATATAGCTCTTG
5893834 CGAGCTTCCCATTA-ATAGCTCTT
1 CGAGCTTCCCATTATATAGCTCTT
5893857 CAGAGCATCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.19, C:0.27, G:0.17, T:0.38
Consensus pattern (25 bp):
CGAGCTTCCCATTATATAGCTCTTG
Found at i:5893978 original size:26 final size:25
Alignment explanation
Indices: 5893931--5894002 Score: 108
Period size: 26 Copynumber: 2.8 Consensus size: 25
5893921 CCCGATATAT
5893931 GGCTCTTTGGAGCTTCCCGATTAAA
1 GGCTCTTTGGAGCTTCCCGATTAAA
* *
5893956 GGCTCTTTGTGAGCTTCCTGATTAAT
1 GGCTCTTTG-GAGCTTCCCGATTAAA
*
5893982 GGCTCTTCGGAGCTTCCCGAT
1 GGCTCTTTGGAGCTTCCCGAT
5894003 ATGGCTTGCT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
25 20 0.48
26 22 0.52
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.35
Consensus pattern (25 bp):
GGCTCTTTGGAGCTTCCCGATTAAA
Found at i:5894045 original size:25 final size:25
Alignment explanation
Indices: 5893920--5894033 Score: 105
Period size: 25 Copynumber: 4.6 Consensus size: 25
5893910 CTTATGAGTG
5893920 TCCCGATATATGGCTCTTTGGAGCT
1 TCCCGATATATGGCTCTTTGGAGCT
*
5893945 TCCCGAT-TAAAGGCTCTTTGTGAGCT
1 TCCCGATAT-ATGGCTCTTTG-GAGCT
* *
5893971 TCCTGAT-TAATGGCTCTTCGGAGCT
1 TCCCGATAT-ATGGCTCTTTGGAGCT
*
5893996 TCCCG--ATATGGCT-TGCTT-GAACT
1 TCCCGATATATGGCTCT--TTGGAGCT
5894019 TCCCGATATATGGCT
1 TCCCGATATATGGCT
5894034 ATCCGGAGCT
Statistics
Matches: 75, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
22 1 0.01
23 15 0.20
24 3 0.04
25 34 0.45
26 22 0.29
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.35
Consensus pattern (25 bp):
TCCCGATATATGGCTCTTTGGAGCT
Found at i:5894105 original size:24 final size:24
Alignment explanation
Indices: 5894039--5894108 Score: 72
Period size: 24 Copynumber: 2.9 Consensus size: 24
5894029 TGGCTATCCG
*
5894039 GAGCTTCTTGATTAATGGCTCTTCA
1 GAGCTTCTTGATT-ATGGCTCTACA
* *
5894064 GAGCTACTCG-TTATTGGCTC-ACA
1 GAGCTTCTTGATTA-TGGCTCTACA
5894087 TGAGCTTCTTGATTATGGCTCT
1 -GAGCTTCTTGATTATGGCTCT
5894109 TTTGAGCTCC
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
23 3 0.08
24 22 0.61
25 11 0.31
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (24 bp):
GAGCTTCTTGATTATGGCTCTACA
Found at i:5894116 original size:73 final size:73
Alignment explanation
Indices: 5893943--5894116 Score: 163
Period size: 73 Copynumber: 2.4 Consensus size: 73
5893933 CTCTTTGGAG
* * *
5893943 CTTCCCGAT-TAAAGGCTCTTTGTGAGCTTCCTGATTAATGGCTCTTCGGAGCTTCCCGATATGG
1 CTTCCCGATAT-ATGGCTCTTT-TGAGCTTCCTGATTAATGGCTCTTCAGAGCTACCCGATATGG
** *
5894007 CTTGCTTGAA
64 CTCACATGAA
* *** * * *
5894017 CTTCCCGATATATGGCTATCCGGAGCTTCTTGATTAATGGCTCTTCAGAGCTACTCGTTATTGGC
1 CTTCCCGATATATGGCTCTTTTGAGCTTCCTGATTAATGGCTCTTCAGAGCTACCCGATA-TGGC
*
5894082 TCACATGAG
65 TCACATGAA
**
5894091 CTTCTTGAT-TATGGCTCTTTTGAGCT
1 CTTCCCGATATATGGCTCTTTTGAGCT
5894117 CCCCATTATA
Statistics
Matches: 78, Mismatches: 20, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
73 46 0.59
74 31 0.40
75 1 0.01
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.37
Consensus pattern (73 bp):
CTTCCCGATATATGGCTCTTTTGAGCTTCCTGATTAATGGCTCTTCAGAGCTACCCGATATGGCT
CACATGAA
Found at i:5904696 original size:25 final size:25
Alignment explanation
Indices: 5904660--5904714 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
5904650 GACATACCAC
5904660 AGCTCTCTTGAGCTTCTCGATATTT
1 AGCTCTCTTGAGCTTCTCGATATTT
5904685 AGCTCT-TATGAGCTTCTCGATATTT
1 AGCTCTCT-TGAGCTTCTCGATATTT
*
5904710 TGCTC
1 AGCTC
5904715 GTAAGGGCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 1 0.04
25 27 0.96
ACGTcount: A:0.16, C:0.24, G:0.16, T:0.44
Consensus pattern (25 bp):
AGCTCTCTTGAGCTTCTCGATATTT
Found at i:5904724 original size:25 final size:25
Alignment explanation
Indices: 5904669--5904725 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
5904659 CAGCTCTCTT
* *
5904669 GAGCTTCTCGATATTTAGCTCTTAT
1 GAGCTTCTCGATATTTAGCTCGTAA
*
5904694 GAGCTTCTCGATATTTTGCTCGTAA
1 GAGCTTCTCGATATTTAGCTCGTAA
*
5904719 GGGCTTC
1 GAGCTTC
5904726 CAGATATACA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.40
Consensus pattern (25 bp):
GAGCTTCTCGATATTTAGCTCGTAA
Found at i:5904740 original size:25 final size:25
Alignment explanation
Indices: 5904712--5904776 Score: 112
Period size: 25 Copynumber: 2.6 Consensus size: 25
5904702 CGATATTTTG
* *
5904712 CTCGTAAGGGCTTCCAGATATACAA
1 CTCGTATGAGCTTCCAGATATACAA
5904737 CTCGTATGAGCTTCCAGATATACAA
1 CTCGTATGAGCTTCCAGATATACAA
5904762 CTCGTATGAGCTTCC
1 CTCGTATGAGCTTCC
5904777 TGTTACTCAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (25 bp):
CTCGTATGAGCTTCCAGATATACAA
Found at i:5912723 original size:27 final size:27
Alignment explanation
Indices: 5912693--5912746 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
5912683 TTATGGGTAA
* *
5912693 AAATATAATTTTATTATTTAAAAAATT
1 AAATATAAATTTATAATTTAAAAAATT
*
5912720 AAATATAAATTTATAATTTAATAAATT
1 AAATATAAATTTATAATTTAAAAAATT
5912747 TTAAAATACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
AAATATAAATTTATAATTTAAAAAATT
Found at i:5913912 original size:17 final size:16
Alignment explanation
Indices: 5913892--5913949 Score: 50
Period size: 15 Copynumber: 3.6 Consensus size: 16
5913882 TTTTAAAGCT
5913892 TAAAATTATTAAAAACA
1 TAAAATTATTAAAAA-A
5913909 TAAAA--ATTATAAAAA
1 TAAAATTATTA-AAAAA
*
5913924 TAAATTTA-TAAAAAA
1 TAAAATTATTAAAAAA
5913939 TTTAAAATTAT
1 --TAAAATTAT
5913950 AATTTTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 11
0.72 0.04 0.24
Matches are distributed among these distances:
15 14 0.42
16 6 0.18
17 13 0.39
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (16 bp):
TAAAATTATTAAAAAA
Found at i:5913950 original size:17 final size:16
Alignment explanation
Indices: 5913891--5913951 Score: 63
Period size: 17 Copynumber: 3.8 Consensus size: 16
5913881 CTTTTAAAGC
5913891 TTAAAATTATTAAAAACA
1 TTAAAATTA-TAAAAA-A
*
5913909 TAAAAATTAT-AAAAA
1 TTAAAATTATAAAAAA
*
5913924 -TAAATTTATAAAAAA
1 TTAAAATTATAAAAAA
5913939 TTTAAAATTATAA
1 -TTAAAATTATAA
5913952 TTTTTTTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
14 7 0.19
15 6 0.17
16 4 0.11
17 11 0.31
18 8 0.22
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (16 bp):
TTAAAATTATAAAAAA
Found at i:5917423 original size:21 final size:21
Alignment explanation
Indices: 5917397--5917440 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
5917387 AGACGAGCAA
* *
5917397 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
5917418 TACTCCAAAACAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
5917439 TA
1 TA
5917441 ACAGCCCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:5920671 original size:18 final size:18
Alignment explanation
Indices: 5920631--5920679 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
5920621 CTTATAATTC
* *
5920631 TTTTAATATTTTTTTAAA
1 TTTTAATATATTTATAAA
5920649 TTTTAATATATTTATAATA
1 TTTTAATATATTTATAA-A
*
5920668 TTTAAAT-TATTT
1 TTTTAATATATTT
5920680 GTTGATGGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 20 0.74
19 7 0.26
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTAATATATTTATAAA
Found at i:5926914 original size:10 final size:10
Alignment explanation
Indices: 5926894--5926959 Score: 64
Period size: 10 Copynumber: 6.5 Consensus size: 10
5926884 CATTTGTTGC
5926894 TTTTA-AATT
1 TTTTATAATT
5926903 TTTTATAA-T
1 TTTTATAATT
5926912 TTTTATAATT
1 TTTTATAATT
*
5926922 TTTTAATATTT
1 TTTT-ATAATT
**
5926933 TTTTATAACA
1 TTTTATAATT
5926943 TTTTATTAATT
1 TTTTA-TAATT
5926954 ATTTTA
1 -TTTTA
5926960 AAAAAAAACT
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
9 14 0.30
10 15 0.33
11 12 0.26
12 5 0.11
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTTATAATT
Found at i:5926923 original size:19 final size:21
Alignment explanation
Indices: 5926894--5926958 Score: 66
Period size: 23 Copynumber: 3.1 Consensus size: 21
5926884 CATTTGTTGC
5926894 TTTTA-AATTTTTT-ATA-AT
1 TTTTATAATTTTTTAATATAT
*
5926912 TTTTATAATTTTTTAATATTT
1 TTTTATAATTTTTTAATATAT
5926933 TTTTATAACATTTTATTAAT-TAT
1 TTTTAT-A-ATTTT-TTAATATAT
5926956 TTT
1 TTT
5926959 AAAAAAAAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
18 5 0.13
19 8 0.21
20 3 0.08
21 7 0.18
22 1 0.03
23 10 0.26
24 5 0.13
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTTATAATTTTTTAATATAT
Found at i:5926925 original size:11 final size:11
Alignment explanation
Indices: 5926901--5926940 Score: 50
Period size: 9 Copynumber: 3.9 Consensus size: 11
5926891 TGCTTTTAAA
5926901 TTTTTTATAA-
1 TTTTTTATAAT
5926911 -TTTTTATAAT
1 TTTTTTATAAT
*
5926921 TTTTTAAT-AT
1 TTTTTTATAAT
5926931 TTTTTTATAA
1 TTTTTTATAA
5926941 CATTTTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
9 9 0.36
10 9 0.36
11 7 0.28
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTTTTATAAT
Found at i:5927830 original size:61 final size:61
Alignment explanation
Indices: 5927757--5927882 Score: 252
Period size: 61 Copynumber: 2.1 Consensus size: 61
5927747 ATTCGATTCT
5927757 ATTCTATTTCAGATAATCGAAACTTTTAAAATTATATCTTATAAACTATTTAAATACCTCA
1 ATTCTATTTCAGATAATCGAAACTTTTAAAATTATATCTTATAAACTATTTAAATACCTCA
5927818 ATTCTATTTCAGATAATCGAAACTTTTAAAATTATATCTTATAAACTATTTAAATACCTCA
1 ATTCTATTTCAGATAATCGAAACTTTTAAAATTATATCTTATAAACTATTTAAATACCTCA
5927879 ATTC
1 ATTC
5927883 AGATTCAATT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.40, C:0.15, G:0.03, T:0.41
Consensus pattern (61 bp):
ATTCTATTTCAGATAATCGAAACTTTTAAAATTATATCTTATAAACTATTTAAATACCTCA
Found at i:5942465 original size:10 final size:10
Alignment explanation
Indices: 5942451--5942527 Score: 58
Period size: 10 Copynumber: 8.0 Consensus size: 10
5942441 AAATTACTTG
5942451 TTATTATTT-
1 TTATTATTTA
5942460 TCTATTATTTA
1 T-TATTATTTA
*
5942471 TTATTATTAA
1 TTATTATTTA
*
5942481 TTATAATCTCTA
1 TTATTAT-T-TA
5942493 -TA-TATTTA
1 TTATTATTTA
5942501 TTA-TATTTA
1 TTATTATTTA
*
5942510 TT-GTATTTA
1 TTATTATTTA
5942519 TTATT-TTTA
1 TTATTATTTA
5942528 GTAGTGTATA
Statistics
Matches: 56, Mismatches: 5, Indels: 14
0.75 0.07 0.19
Matches are distributed among these distances:
8 2 0.04
9 24 0.43
10 25 0.45
11 4 0.07
12 1 0.02
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (10 bp):
TTATTATTTA
Found at i:5942466 original size:20 final size:21
Alignment explanation
Indices: 5942425--5942478 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
5942415 TTGTGTTAGT
5942425 TTAC-TGTT-TTATTTTCAAA
1 TTACTTGTTATTATTTTCAAA
*
5942444 TTACTTGTTATTATTTTC-TA
1 TTACTTGTTATTATTTTCAAA
* *
5942464 TTATTTATTATTATT
1 TTACTTGTTATTATT
5942479 AATTATAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.13
20 18 0.60
21 8 0.27
ACGTcount: A:0.24, C:0.07, G:0.04, T:0.65
Consensus pattern (21 bp):
TTACTTGTTATTATTTTCAAA
Found at i:5942505 original size:9 final size:9
Alignment explanation
Indices: 5942465--5942527 Score: 56
Period size: 9 Copynumber: 6.7 Consensus size: 9
5942455 TATTTTCTAT
5942465 TATTTATTA
1 TATTTATTA
*
5942474 TTATTAATTA
1 -TATTTATTA
5942484 TAATCTCTA-TA
1 T-AT-T-TATTA
5942495 TATTTATTA
1 TATTTATTA
*
5942504 TATTTATTG
1 TATTTATTA
5942513 TATTTATTA
1 TATTTATTA
*
5942522 TTTTTA
1 TATTTA
5942528 GTAGTGTATA
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
8 2 0.05
9 25 0.57
10 12 0.27
11 4 0.09
12 1 0.02
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (9 bp):
TATTTATTA
Found at i:5942803 original size:24 final size:24
Alignment explanation
Indices: 5942749--5942881 Score: 76
Period size: 24 Copynumber: 5.2 Consensus size: 24
5942739 CGTTTTTTTT
* *
5942749 TATTTCTAATATGTATATATTATGTAAA
1 TATTT-TAATAT-TAT-TA-TATATATA
5942777 TATTTTAATATTATGT-TATATATA
1 TATTTTAATATTAT-TATATATATA
*
5942801 TATTTTTCATA-TATTATATATATA
1 TA-TTTTAATATTATTATATATATA
* *
5942825 TGTTTTTAATATTACATTTTATATAT-
1 T-ATTTTAATATT--ATTATATATATA
*
5942851 TATTATGT-ATATTTTTAGTATATATA
1 TATT-T-TAATATTATTA-TATATATA
5942877 TATTT
1 TATTT
5942882 GTGAAGTATT
Statistics
Matches: 85, Mismatches: 10, Indels: 23
0.72 0.08 0.19
Matches are distributed among these distances:
23 1 0.01
24 29 0.34
25 18 0.21
26 15 0.18
27 17 0.20
28 5 0.06
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (24 bp):
TATTTTAATATTATTATATATATA
Found at i:5942817 original size:22 final size:22
Alignment explanation
Indices: 5942792--5942838 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
5942782 TAATATTATG
5942792 TTATATATATAT-TTTTCATATA
1 TTATATATATATGTTTTCA-ATA
*
5942814 TTATATATATATGTTTTTAATA
1 TTATATATATATGTTTTCAATA
5942836 TTA
1 TTA
5942839 CATTTTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (22 bp):
TTATATATATATGTTTTCAATA
Found at i:5942982 original size:17 final size:19
Alignment explanation
Indices: 5942956--5943001 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 19
5942946 TTAATACTAC
*
5942956 ATTATATATATATTT-A-T
1 ATTATGTATATATTTAAGT
5942973 ATTATGTATATATTTCAAGT
1 ATTATGTATATATTT-AAGT
5942993 ATTATGTAT
1 ATTATGTAT
5943002 TAAGCATTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 14 0.56
19 1 0.04
20 10 0.40
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (19 bp):
ATTATGTATATATTTAAGT
Found at i:5954749 original size:27 final size:27
Alignment explanation
Indices: 5954701--5954859 Score: 193
Period size: 27 Copynumber: 5.9 Consensus size: 27
5954691 GCGAGGCTGC
* *
5954701 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
5954728 CAGATATTGTGGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
5954754 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
5954781 CAGATAATCGTGGCATAGCCACCAGA-A
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
5954808 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
*
5954835 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
5954860 GACGCTTCCT
Statistics
Matches: 117, Mismatches: 7, Indels: 16
0.84 0.05 0.11
Matches are distributed among these distances:
26 10 0.09
27 102 0.87
28 5 0.04
ACGTcount: A:0.35, C:0.23, G:0.25, T:0.18
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:5954794 original size:54 final size:54
Alignment explanation
Indices: 5954719--5954859 Score: 248
Period size: 54 Copynumber: 2.6 Consensus size: 54
5954709 GTGACGAAGT
*
5954719 CACCAGATACAGAT-ATTGTGGCAGAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
*
5954773 CACCAGATCAGATAATCGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
5954827 CACCAGATCAGATAATTGTGGCATAGCCACCAG
1 CACCAGATCAGATAATTGTGGCATAGCCACCAG
5954860 GACGCTTCCT
Statistics
Matches: 83, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
53 5 0.06
54 78 0.94
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
Found at i:5956141 original size:26 final size:26
Alignment explanation
Indices: 5956111--5956218 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
5956101 TGAAATTCCC
*
5956111 ATCATGGAACATTTACCGAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
5956137 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
5956163 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
5956189 ATCATGGAATATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
5956215 ATCA
1 ATCA
5956219 ATTTGTATCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.36, C:0.26, G:0.07, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:5957538 original size:43 final size:42
Alignment explanation
Indices: 5957478--5957592 Score: 135
Period size: 43 Copynumber: 2.7 Consensus size: 42
5957468 AAGAAGAAGG
5957478 AAAAGATCAAGGTGAAAACCCGAAAAGGGAGCCTTGATGAAC
1 AAAAGATCAAGGTGAAAACCCGAAAAGGGAGCCTTGATGAAC
* ** *
5957520 AAAAGGATCAAGGTGAAAACCCGAAAAGGGTGTTTTGATTAACAC
1 AAAA-GATCAAGGTGAAAACCCGAAAAGGGAGCCTTGA-TGA-AC
*
5957565 AAAAGAT-TAGGATGAAAACCC-AAAAGGG
1 AAAAGATCAAGG-TGAAAACCCGAAAAGGG
5957593 CATTTTAATG
Statistics
Matches: 64, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
42 4 0.06
43 40 0.62
44 14 0.22
45 6 0.09
ACGTcount: A:0.46, C:0.14, G:0.25, T:0.15
Consensus pattern (42 bp):
AAAAGATCAAGGTGAAAACCCGAAAAGGGAGCCTTGATGAAC
Found at i:5958719 original size:74 final size:74
Alignment explanation
Indices: 5958442--5958865 Score: 659
Period size: 74 Copynumber: 5.6 Consensus size: 74
5958432 TATTTTCAAT
* * *
5958442 TTTGTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTC
1 TTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
5958507 AATATTCTG
66 AATATTCTG
* *
5958516 TTTGTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAA
1 TTTGTC----AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAA
5958581 TTTCAATATTCTG
62 TTTCAATATTCTG
*
5958594 TTTGTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGGACACGCTGAGGTAA
1 TTTGTC----AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAA
*
5958659 TTTCAATATTCTA
62 TTTCAATATTCTG
* * *
5958672 TTTGTCGAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGAAACGCTGAGGTAATTTC
1 TTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
5958737 AATATTCTG
66 AATATTCTG
* *
5958746 TTTGTCGAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
1 TTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
*
5958811 AGTATTCTG
66 AATATTCTG
5958820 TTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
1 TTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
5958866 CTCACATGTT
Statistics
Matches: 330, Mismatches: 16, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
74 182 0.55
78 148 0.45
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (74 bp):
TTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
AATATTCTG
Found at i:5959055 original size:82 final size:81
Alignment explanation
Indices: 5958824--5959069 Score: 224
Period size: 89 Copynumber: 2.9 Consensus size: 81
5958814 ATTCTGTTTG
* * * * *
5958824 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCTCACATGTTGAGGTATTTTCAG
1 TCAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGTCGAGCTATTTTCAA
** * *
5958889 TTTCTGTTTTTTAATTTATATTTT
66 AATCTG----CT--TTTA-A-GTT
* * * *
5958913 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCATATGTCGAGGTATTTTCAA
1 TCAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGTCGAGCTATTTTCAA
5958978 AATCTGCTTTTAAGTT
66 AATCTGCTTTTAAGTT
** * *
5958994 TCAAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGTTTTGGCTCACGTG-CTGAGCTATTTTC
1 TC-AAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGTC-GAGCTATTTTC
**
5959058 AATTTCTGCTTT
64 AAAATCTGCTTT
5959070 AATGTTTGTT
Statistics
Matches: 136, Mismatches: 19, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
81 5 0.04
82 62 0.46
83 4 0.03
85 1 0.01
89 64 0.47
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.37
Consensus pattern (81 bp):
TCAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGTCGAGCTATTTTCAA
AATCTGCTTTTAAGTT
Found at i:5960727 original size:9 final size:9
Alignment explanation
Indices: 5960715--5960746 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
5960705 ATAATCTCTA
5960715 TATATTTAT
1 TATATTTAT
5960724 TATATTTAT
1 TATATTTAT
*
5960733 TGTATTTAT
1 TATATTTAT
5960742 TATAT
1 TATAT
5960747 GTAGTAGTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (9 bp):
TATATTTAT
Found at i:5960757 original size:21 final size:20
Alignment explanation
Indices: 5960717--5960771 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 20
5960707 AATCTCTATA
*
5960717 TATTTATTATAT-T-TATTG
1 TATTTATTATATGTATAGTG
5960735 TATTTATTATATGTAGTAGTG
1 TATTTATTATATGTA-TAGTG
5960756 TATATT-TTATTATGTA
1 TAT-TTATTA-TATGTA
5960772 CGTATATGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
18 12 0.39
19 1 0.03
21 10 0.32
22 8 0.26
ACGTcount: A:0.29, C:0.00, G:0.11, T:0.60
Consensus pattern (20 bp):
TATTTATTATATGTATAGTG
Found at i:5960913 original size:14 final size:14
Alignment explanation
Indices: 5960894--5960942 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
5960884 AGTGCATAAT
5960894 TTTATATATATATA
1 TTTATATATATATA
*
5960908 TTTATATATATGTA
1 TTTATATATATATA
*
5960922 TTTA-ATATATTTA
1 TTTATATATATATA
*
5960935 TGTATATA
1 TTTATATA
5960943 CTTATGTAGC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
13 11 0.35
14 20 0.65
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (14 bp):
TTTATATATATATA
Found at i:5960942 original size:29 final size:29
Alignment explanation
Indices: 5960892--5960950 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
5960882 TCAGTGCATA
* *
5960892 ATTTTATATATATATATTTATA-TATATGT
1 ATTTAATATATATATATATATACT-TATGT
* *
5960921 ATTTAATATATTTATGTATATACTTATGT
1 ATTTAATATATATATATATATACTTATGT
5960950 A
1 A
5960951 GCATTATTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
29 24 0.96
30 1 0.04
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (29 bp):
ATTTAATATATATATATATATACTTATGT
Found at i:5961072 original size:22 final size:20
Alignment explanation
Indices: 5961001--5961105 Score: 74
Period size: 22 Copynumber: 5.0 Consensus size: 20
5960991 TATTTTGTAA
5961001 ATATTTTA-ATA-TTATATT
1 ATATTTTATATATTTATATT
* *
5961019 ATATTATATATATTTTTCA-T
1 ATATTTTATATATTTAT-ATT
5961039 ATATTATATATATATGTTAATATT
1 ATATT-T-TATATAT-TT-ATATT
5961063 ATATTTTATATA-TTATTATGT
1 ATATTTTATATATTTA-TAT-T
*
5961084 ATATTTTTAGTATATATATATT
1 ATA-TTTTA-TATATTTATATT
5961106 TGTGAAATAT
Statistics
Matches: 69, Mismatches: 5, Indels: 22
0.72 0.05 0.23
Matches are distributed among these distances:
18 7 0.10
19 4 0.06
20 14 0.20
21 5 0.07
22 19 0.28
23 11 0.16
24 9 0.13
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (20 bp):
ATATTTTATATATTTATATT
Found at i:5961098 original size:49 final size:51
Alignment explanation
Indices: 5960983--5961102 Score: 130
Period size: 49 Copynumber: 2.5 Consensus size: 51
5960973 TTATTTCTAA
*
5960983 TATGTATATATTTT-GTA-A-ATATTTTAATATTATATTATATTATATATAT
1 TATGTATAT-TTTTAGTATATATATGTTAATATTATATTATATTATATATAT
* * *
5961032 T-TTTCATA-TATTA-TATATATATGTTAATATTATATTTTA-TATAT-TAT
1 TATGT-ATATTTTTAGTATATATATGTTAATATTATATTATATTATATATAT
5961079 TATGTATATTTTTAGTATATATAT
1 TATGTATATTTTTAGTATATATAT
5961103 ATTTGTGAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
47 12 0.21
48 14 0.24
49 32 0.55
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (51 bp):
TATGTATATTTTTAGTATATATATGTTAATATTATATTATATTATATATAT
Found at i:5961173 original size:57 final size:54
Alignment explanation
Indices: 5960973--5961217 Score: 186
Period size: 57 Copynumber: 4.4 Consensus size: 54
5960963 GTCGTTTTTT
* *
5960973 TTATTTCTAATATGTATATATTTTGTAAATATTTTAATATTATATTA-TATTA-TA
1 TTATTTTTAATATGTATATA-TTTGTAAATATTATAATATT-TATTATTATTATTA
*
5961027 TATATTTTTCATATAT-TATATATATATGTTAATATTAT-AT-TTTATATATTATTATGTA
1 T-TATTTTT-A-ATATGTATATAT-T-TGTAAATATTATAATATTTAT-TATTATTAT-TA
* *
5961085 -TATTTTTAGTATATATATATTTGTGAAATATTATCAATAGTTTATTATTATTATTA
1 TTATTTTTAATATGTATATATTTGT-AAATATTAT-AATA-TTTATTATTATTATTA
* * * * *
5961141 TTATTATTAATATGTATATATTGTGTATATATTTTAATA-CTA-CATTA-TA-TA
1 TTATTTTTAATATGTATATATT-TGTAAATATTATAATATTTATTATTATTATTA
5961192 TATATTTTTATATTATGTATATATTT
1 T-TATTTTTA-A-TATGTATATATTT
5961218 CAAGTATTAT
Statistics
Matches: 158, Mismatches: 13, Indels: 41
0.75 0.06 0.19
Matches are distributed among these distances:
51 3 0.02
52 9 0.06
53 9 0.06
54 30 0.19
55 19 0.12
56 30 0.19
57 48 0.30
58 10 0.06
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (54 bp):
TTATTTTTAATATGTATATATTTGTAAATATTATAATATTTATTATTATTATTA
Found at i:5962465 original size:127 final size:127
Alignment explanation
Indices: 5962239--5962493 Score: 447
Period size: 127 Copynumber: 2.0 Consensus size: 127
5962229 TAAATGTCAA
*
5962239 ATTGAATTCGTATTTTGAAAATTAAGACGACACAAGTTTAACAAGACACCAATTTTGGGCGTCGC
1 ATTGAATTCGTATTTTGAAAATTAAGACGACACAAGTTTAACAAGACACCAATTTTGAGCGTCGC
*
5962304 GAAGGTGCTAATACCTTCCTCGCGCGTAACTAACTCTGAACCTTATTTTTCCTCTGGCTTTT
66 GAAGGTGCTAATACCTTCCTCGCGCGTAACTAACTCCGAACCTTATTTTTCCTCTGGCTTTT
* * *
5962366 ATTGAATTCGTATTTTGAAAATTAAGACGACACAAGTTTAACAAGATACCAGTTTTGAGTGTCGC
1 ATTGAATTCGTATTTTGAAAATTAAGACGACACAAGTTTAACAAGACACCAATTTTGAGCGTCGC
* *
5962431 GAGGGTGCTAATACCTTCCTCGCGCGTAACTAACTCCGAACCTTCTTTTTCCTCTGGCTTTT
66 GAAGGTGCTAATACCTTCCTCGCGCGTAACTAACTCCGAACCTTATTTTTCCTCTGGCTTTT
5962493 A
1 A
5962494 ACGTAGACCC
Statistics
Matches: 121, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
127 121 1.00
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (127 bp):
ATTGAATTCGTATTTTGAAAATTAAGACGACACAAGTTTAACAAGACACCAATTTTGAGCGTCGC
GAAGGTGCTAATACCTTCCTCGCGCGTAACTAACTCCGAACCTTATTTTTCCTCTGGCTTTT
Found at i:5963131 original size:23 final size:23
Alignment explanation
Indices: 5963105--5963203 Score: 76
Period size: 23 Copynumber: 4.2 Consensus size: 23
5963095 CCCTCATGCA
5963105 AACCCTTATGGATTTAGTATGTG
1 AACCCTTATGGATTTAGTATGTG
* * *
5963128 AACCCTAATAT-GTTTTAATATG-C
1 AACCCT--TATGGATTTAGTATGTG
* * * *
5963151 AAACTTTAATATGATTTACTATGTG
1 AACCCTT-AT-GGATTTAGTATGTG
*
5963176 AACCCTTATGGATTTAGTATGCG
1 AACCCTTATGGATTTAGTATGTG
5963199 AACCC
1 AACCC
5963204 CTATACGATT
Statistics
Matches: 57, Mismatches: 13, Indels: 12
0.70 0.16 0.15
Matches are distributed among these distances:
21 1 0.02
22 2 0.04
23 26 0.46
24 20 0.35
25 8 0.14
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.37
Consensus pattern (23 bp):
AACCCTTATGGATTTAGTATGTG
Found at i:5963149 original size:24 final size:24
Alignment explanation
Indices: 5963115--5963203 Score: 74
Period size: 24 Copynumber: 3.8 Consensus size: 24
5963105 AACCCTTATG
*
5963115 GATTTAGTATGTGAACCCTAATAT
1 GATTTAATATGTGAACCCTAATAT
* ** **
5963139 GTTTTAATATGCAAACTTTAATAT
1 GATTTAATATGTGAACCCTAATAT
*
5963163 GATTTACTATGTGAACCCT--TAT
1 GATTTAATATGTGAACCCTAATAT
* *
5963185 GGATTTAGTATGCGAACCC
1 -GATTTAATATGTGAACCC
5963204 CTATACGATT
Statistics
Matches: 50, Mismatches: 14, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
22 3 0.06
23 16 0.32
24 31 0.62
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (24 bp):
GATTTAATATGTGAACCCTAATAT
Found at i:5963213 original size:24 final size:23
Alignment explanation
Indices: 5963163--5963249 Score: 59
Period size: 24 Copynumber: 3.7 Consensus size: 23
5963153 ACTTTAATAT
* * * *
5963163 GATTTACTATGTGAACCCTTATG
1 GATTTAGTATGCGAACCCCTATC
5963186 GATTTAGTATGCGAACCCCTATAC
1 GATTTAGTATGCGAACCCCTAT-C
* * * *
5963210 GA-TTATGTTTGTGAACCTCTATGT
1 GATTTA-GTATGCGAACCCCTAT-C
*
5963234 GATTTATTATGCGAAC
1 GATTTAGTATGCGAAC
5963250 TCTCATGTGA
Statistics
Matches: 49, Mismatches: 12, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
23 22 0.45
24 24 0.49
25 3 0.06
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.38
Consensus pattern (23 bp):
GATTTAGTATGCGAACCCCTATC
Found at i:5963257 original size:24 final size:23
Alignment explanation
Indices: 5963226--5963273 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
5963216 GTTTGTGAAC
* * *
5963226 CTCTATGTGATTTATTATGCGAA
1 CTCTATGTGACTTAATATCCGAA
5963249 CTCTCATGTGACTTAATATCCGAA
1 CTCT-ATGTGACTTAATATCCGAA
5963273 C
1 C
5963274 CCTGTATGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.38
Consensus pattern (23 bp):
CTCTATGTGACTTAATATCCGAA
Found at i:5963385 original size:26 final size:26
Alignment explanation
Indices: 5963269--5963387 Score: 71
Period size: 28 Copynumber: 4.5 Consensus size: 26
5963259 ACTTAATATC
*
5963269 CGAACCCTGTATGTGCAAACCCTACATG
1 CGAACCCTGTA--TGCGAACCCTACATG
* * *
5963297 CAAACTCTGTATGTTCGAACCCTATATG
1 CGAACCCTGTATG--CGAACCCTACATG
* * * * *
5963325 TGATCCCTATGTGTGAACCCT-CATG
1 CGAACCCTGTATGCGAACCCTACATG
* ***
5963350 TG-ATTTTGTATGCGAACCCTACATG
1 CGAACCCTGTATGCGAACCCTACATG
5963375 CGAACCCTGTATG
1 CGAACCCTGTATG
5963388 TGTGACCTGT
Statistics
Matches: 64, Mismatches: 23, Indels: 10
0.66 0.24 0.10
Matches are distributed among these distances:
24 11 0.17
25 10 0.16
26 16 0.25
28 27 0.42
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.29
Consensus pattern (26 bp):
CGAACCCTGTATGCGAACCCTACATG
Found at i:5964892 original size:17 final size:18
Alignment explanation
Indices: 5964858--5964894 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
5964848 GTGTTGGTTA
*
5964858 TAATTATATATTTTTTTG
1 TAATTATATATATTTTTG
5964876 TAATTATA-ATATTTTTG
1 TAATTATATATATTTTTG
5964893 TA
1 TA
5964895 TGAATTGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
TAATTATATATATTTTTG
Found at i:5972693 original size:19 final size:19
Alignment explanation
Indices: 5972647--5972694 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
5972637 GTATATATTT
5972647 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
5972665 TAAATCTTATTT-GGATAGA
1 TAAATTTTATTTAGG-TAGA
*
5972684 TAAGTTTTATT
1 TAAATTTTATT
5972695 CATATTCTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:5972756 original size:43 final size:43
Alignment explanation
Indices: 5972708--5972843 Score: 238
Period size: 43 Copynumber: 3.2 Consensus size: 43
5972698 ATTCTAGAAA
* *
5972708 TATTTT-TATTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC
1 TATTTTCT-TTTTATGTTTTAGTAGTTTATTAGAATAAGGGAAC
5972751 TATTTTCTTTTTATGTTTTAGTAGTTTATTAGAATAAGGGAAC
1 TATTTTCTTTTTATGTTTTAGTAGTTTATTAGAATAAGGGAAC
5972794 TATTTTCTTTTTATGTTTTAGTAGTTTATTAGAATAAGGGAAC
1 TATTTTCTTTTTATGTTTTAGTAGTTTATTAGAATAAGGGAAC
5972837 TATTTTC
1 TATTTTC
5972844 CCAATTAGGA
Statistics
Matches: 90, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
43 89 0.99
44 1 0.01
ACGTcount: A:0.28, C:0.06, G:0.15, T:0.51
Consensus pattern (43 bp):
TATTTTCTTTTTATGTTTTAGTAGTTTATTAGAATAAGGGAAC
Found at i:5981957 original size:100 final size:100
Alignment explanation
Indices: 5981784--5981981 Score: 396
Period size: 100 Copynumber: 2.0 Consensus size: 100
5981774 AAAAAAGACG
5981784 AGAAAAAACTGCTAGAAAATGGAACTTATCAGGATCAACACTACCTAAACTCTGCTTTGGTCTAA
1 AGAAAAAACTGCTAGAAAATGGAACTTATCAGGATCAACACTACCTAAACTCTGCTTTGGTCTAA
5981849 ACGATTCATGCTATTGACCATCAACTCATAGATTT
66 ACGATTCATGCTATTGACCATCAACTCATAGATTT
5981884 AGAAAAAACTGCTAGAAAATGGAACTTATCAGGATCAACACTACCTAAACTCTGCTTTGGTCTAA
1 AGAAAAAACTGCTAGAAAATGGAACTTATCAGGATCAACACTACCTAAACTCTGCTTTGGTCTAA
5981949 ACGATTCATGCTATTGACCATCAACTCATAGAT
66 ACGATTCATGCTATTGACCATCAACTCATAGAT
5981982 CTAGCAACTA
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:0.37, C:0.21, G:0.14, T:0.27
Consensus pattern (100 bp):
AGAAAAAACTGCTAGAAAATGGAACTTATCAGGATCAACACTACCTAAACTCTGCTTTGGTCTAA
ACGATTCATGCTATTGACCATCAACTCATAGATTT
Found at i:5983729 original size:93 final size:94
Alignment explanation
Indices: 5983603--5983791 Score: 344
Period size: 93 Copynumber: 2.0 Consensus size: 94
5983593 GTACACTCCT
*
5983603 TTGTTCTACCTCCCCCCCCCCCTTCCTACTTGGATAGCACATGGGACTTGAACAAGATCACACCA
1 TTGTTCTACCT--CCCCCCCCCTCCCTACTTGGATAGCACATGGGACTTGAACAAGATCACACCA
5983668 GTCTATTCACAGTCTGATTGTCAAATACAAC
64 GTCTATTCACAGTCTGATTGTCAAATACAAC
5983699 TTGTTCTACCT-CCCCCCCCTCCCTACTTGGATAGCACATGGGACTTGAACAAGATCACACCAGT
1 TTGTTCTACCTCCCCCCCCCTCCCTACTTGGATAGCACATGGGACTTGAACAAGATCACACCAGT
5983763 CTATTCACAGTCTGATTGTCAAATACAAC
66 CTATTCACAGTCTGATTGTCAAATACAAC
5983792 AATCTCATCG
Statistics
Matches: 92, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
93 81 0.88
96 11 0.12
ACGTcount: A:0.26, C:0.33, G:0.14, T:0.27
Consensus pattern (94 bp):
TTGTTCTACCTCCCCCCCCCTCCCTACTTGGATAGCACATGGGACTTGAACAAGATCACACCAGT
CTATTCACAGTCTGATTGTCAAATACAAC
Found at i:5990353 original size:11 final size:11
Alignment explanation
Indices: 5990332--5990390 Score: 59
Period size: 10 Copynumber: 5.1 Consensus size: 11
5990322 TGGGTAAAGA
5990332 TTTTTATTAATT
1 TTTTTA-TAATT
5990344 TTTTTATAA-T
1 TTTTTATAATT
5990354 TTTTTATAAATTT
1 TTTTTAT-AA-TT
5990367 TATATTTATAATT
1 T-T-TTTATAATT
5990380 TTTTTA-AATT
1 TTTTTATAATT
5990390 T
1 T
5990391 ATAATATTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
10 13 0.31
11 9 0.21
12 7 0.17
13 5 0.12
14 3 0.07
15 5 0.12
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTTATAATT
Found at i:5990380 original size:25 final size:26
Alignment explanation
Indices: 5990346--5990400 Score: 87
Period size: 25 Copynumber: 2.2 Consensus size: 26
5990336 TATTAATTTT
5990346 TTTATAATTTTTTATAAATTT-T-ATA
1 TTTATAATTTTTT-TAAATTTATAATA
5990371 TTTATAATTTTTTTAAATTTATAATA
1 TTTATAATTTTTTTAAATTTATAATA
5990397 TTTA
1 TTTA
5990401 ATATATTACA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 7 0.25
25 14 0.50
26 7 0.25
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (26 bp):
TTTATAATTTTTTTAAATTTATAATA
Found at i:5991118 original size:23 final size:23
Alignment explanation
Indices: 5991092--5991166 Score: 68
Period size: 23 Copynumber: 3.4 Consensus size: 23
5991082 ATAAATATTG
5991092 TTAAGAATATGCCTTAGACTTGC
1 TTAAGAATATGCCTTAGACTTGC
* * * *
5991115 TTAATAATA-G--GTAAATATTG-
1 TTAAGAATATGCCTTAGA-CTTGC
5991135 TTAAGAATATGCCTTAGACTTGC
1 TTAAGAATATGCCTTAGACTTGC
*
5991158 TTAATAATA
1 TTAAGAATA
5991167 GGTTTGTAGA
Statistics
Matches: 38, Mismatches: 9, Indels: 10
0.67 0.16 0.18
Matches are distributed among these distances:
20 11 0.29
21 4 0.11
22 4 0.11
23 19 0.50
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (23 bp):
TTAAGAATATGCCTTAGACTTGC
Found at i:5991144 original size:43 final size:43
Alignment explanation
Indices: 5991083--5991169 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
5991073 GAAAATTACA
5991083 TAAATATTGTTAAGAATATGCCTTAGACTTGCTTAATAATAGG
1 TAAATATTGTTAAGAATATGCCTTAGACTTGCTTAATAATAGG
5991126 TAAATATTGTTAAGAATATGCCTTAGACTTGCTTAATAATAGG
1 TAAATATTGTTAAGAATATGCCTTAGACTTGCTTAATAATAGG
5991169 T
1 T
5991170 TTGTAGATCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (43 bp):
TAAATATTGTTAAGAATATGCCTTAGACTTGCTTAATAATAGG
Found at i:5996510 original size:28 final size:28
Alignment explanation
Indices: 5996470--5996533 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
5996460 TAACATAGAA
*
5996470 CTTGTTTTTGTGCGTTTCTTGTTATCTC
1 CTTGATTTTGTGCGTTTCTTGTTATCTC
*
5996498 CTTGATTTTGTGCGTTTCTTGTTATCTT
1 CTTGATTTTGTGCGTTTCTTGTTATCTC
5996526 CTTGATTT
1 CTTGATTT
5996534 AGACAGTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.06, C:0.16, G:0.17, T:0.61
Consensus pattern (28 bp):
CTTGATTTTGTGCGTTTCTTGTTATCTC
Found at i:5996981 original size:62 final size:60
Alignment explanation
Indices: 5996870--5997009 Score: 165
Period size: 62 Copynumber: 2.3 Consensus size: 60
5996860 TTAATATAAA
* *
5996870 AATAATTATAATAAGAATGATATTAAATTATATATTTTAATTTAATTAAATTATATTTAGT
1 AATAATTATATTAA-AATGATATTAAATTATATATTTTAATTTAATTAAATTATATTTAAT
* * * *
5996931 ACTAATTATATTAAAAT-ATGATTAAATTATTTATTATTTATTTTTATTAAATTATATTTAAT
1 AATAATTATATTAAAATGAT-ATTAAATTATATA-T-TTTAATTTAATTAAATTATATTTAAT
**
5996993 AATAATCCTATTAAAAT
1 AATAATTATATTAAAAT
5997010 TTAATAACAA
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
59 2 0.03
60 15 0.22
61 13 0.19
62 37 0.55
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (60 bp):
AATAATTATATTAAAATGATATTAAATTATATATTTTAATTTAATTAAATTATATTTAAT
Found at i:5998908 original size:16 final size:17
Alignment explanation
Indices: 5998877--5998909 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5998867 ATTAGTTAAA
5998877 TTAACTAAATTAATTTT
1 TTAACTAAATTAATTTT
*
5998894 TTAATTAAA-TAATTTT
1 TTAACTAAATTAATTTT
5998910 CTCAACCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
TTAACTAAATTAATTTT
Found at i:6003539 original size:35 final size:35
Alignment explanation
Indices: 6003500--6003674 Score: 350
Period size: 35 Copynumber: 5.0 Consensus size: 35
6003490 ATCAAGAGAG
6003500 AAAGATAGCAAGGAGATGATGGGGAGCAAGAATAT
1 AAAGATAGCAAGGAGATGATGGGGAGCAAGAATAT
6003535 AAAGATAGCAAGGAGATGATGGGGAGCAAGAATAT
1 AAAGATAGCAAGGAGATGATGGGGAGCAAGAATAT
6003570 AAAGATAGCAAGGAGATGATGGGGAGCAAGAATAT
1 AAAGATAGCAAGGAGATGATGGGGAGCAAGAATAT
6003605 AAAGATAGCAAGGAGATGATGGGGAGCAAGAATAT
1 AAAGATAGCAAGGAGATGATGGGGAGCAAGAATAT
6003640 AAAGATAGCAAGGAGATGATGGGGAGCAAGAATAT
1 AAAGATAGCAAGGAGATGATGGGGAGCAAGAATAT
6003675 CAAGTTGGAT
Statistics
Matches: 140, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 140 1.00
ACGTcount: A:0.46, C:0.06, G:0.34, T:0.14
Consensus pattern (35 bp):
AAAGATAGCAAGGAGATGATGGGGAGCAAGAATAT
Found at i:6003703 original size:20 final size:20
Alignment explanation
Indices: 6003666--6003703 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
6003656 TGATGGGGAG
*
6003666 CAAGAATATCAAGTTGGATT
1 CAAGAATATCAAGCTGGATT
6003686 CAAGAA-ATCGAAGCTGGA
1 CAAGAATATC-AAGCTGGA
6003704 GGAGAGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.21
Consensus pattern (20 bp):
CAAGAATATCAAGCTGGATT
Found at i:6005039 original size:46 final size:46
Alignment explanation
Indices: 6004734--6005009 Score: 489
Period size: 46 Copynumber: 6.0 Consensus size: 46
6004724 AGTGTGCTCT
*
6004734 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTGAGACCATGGTTGAAAGATACCATGGCAAC
6004780 CTGATATGAAATGTGTGAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTGAGACCATGGTTGAAAGATACCATGGCAAC
6004826 CTGATATGAAATGTGTGAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTGAGACCATGGTTGAAAGATACCATGGCAAC
6004872 CTGATATGAAATGTGTGAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTGAGACCATGGTTGAAAGATACCATGGCAAC
6004918 CTGATATGAAATGTGTGAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTGAGACCATGGTTGAAAGATACCATGGCAAC
* **** *
6004964 GTGATATGAAATGAACAAGACTATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTGAGACCATGGTTGAAAGATACCATGGCAAC
6005010 ATGACAGAAA
Statistics
Matches: 223, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 223 1.00
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (46 bp):
CTGATATGAAATGTGTGAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:6006204 original size:42 final size:42
Alignment explanation
Indices: 6006157--6006259 Score: 116
Period size: 42 Copynumber: 2.5 Consensus size: 42
6006147 CTTTATGGCT
* * * ***
6006157 CATTCTGTTAGCCTTTGTGGCATTATGATATGGTTTTTGTGG
1 CATTCTGTTAGCCTTTGTGGCATTATAAAATAGCCATTGTGG
* * *
6006199 CATTCTATTAGCCTTTGTAGCATTCTAAAATAGCCATTGTGG
1 CATTCTGTTAGCCTTTGTGGCATTATAAAATAGCCATTGTGG
*
6006241 GATTCTGTTAGCCTTTGTG
1 CATTCTGTTAGCCTTTGTG
6006260 TCGTATTCTA
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.18, C:0.16, G:0.22, T:0.44
Consensus pattern (42 bp):
CATTCTGTTAGCCTTTGTGGCATTATAAAATAGCCATTGTGG
Found at i:6006221 original size:20 final size:20
Alignment explanation
Indices: 6006157--6006259 Score: 80
Period size: 22 Copynumber: 5.0 Consensus size: 20
6006147 CTTTATGGCT
*
6006157 CATTCTGTTAGCCTTTGTGG
1 CATTCTATTAGCCTTTGTGG
* * **
6006177 CATTATGATATGGTTTTTGTGG
1 CATTCT-AT-TAGCCTTTGTGG
*
6006199 CATTCTATTAGCCTTTGTAG
1 CATTCTATTAGCCTTTGTGG
* *
6006219 CATTCTAAAATAGCCATTGTGG
1 CATTCT--ATTAGCCTTTGTGG
* *
6006241 GATTCTGTTAGCCTTTGTG
1 CATTCTATTAGCCTTTGTG
6006260 TCGTATTCTA
Statistics
Matches: 62, Mismatches: 17, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
20 29 0.47
21 3 0.05
22 30 0.48
ACGTcount: A:0.18, C:0.16, G:0.22, T:0.44
Consensus pattern (20 bp):
CATTCTATTAGCCTTTGTGG
Found at i:6033000 original size:14 final size:14
Alignment explanation
Indices: 6032981--6033025 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
6032971 AATTAAGTTA
6032981 AATTTAATATAAAT
1 AATTTAATATAAAT
*
6032995 AATTT-ATTTAAAT
1 AATTTAATATAAAT
* *
6033008 AATTAAAAATAAAT
1 AATTTAATATAAAT
6033022 AATT
1 AATT
6033026 AACATAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AATTTAATATAAAT
Found at i:6043172 original size:10 final size:10
Alignment explanation
Indices: 6043159--6043183 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
6043149 CATTTAATTA
6043159 ATTTTAAAAT
1 ATTTTAAAAT
6043169 ATTTTAAAAT
1 ATTTTAAAAT
6043179 ATTTT
1 ATTTT
6043184 TGTACTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
ATTTTAAAAT
Found at i:6046842 original size:16 final size:16
Alignment explanation
Indices: 6046821--6046857 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
6046811 GTAGCTAATG
6046821 TTTTAGATAATTTCTA
1 TTTTAGATAATTTCTA
**
6046837 TTTTAGATCGTTTCTA
1 TTTTAGATAATTTCTA
6046853 TTTTA
1 TTTTA
6046858 ATCACTTTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.59
Consensus pattern (16 bp):
TTTTAGATAATTTCTA
Found at i:6047107 original size:24 final size:24
Alignment explanation
Indices: 6047049--6047107 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
6047039 CTAAAATTTA
6047049 ATTAAATAAAA-ATTTATATTAAT
1 ATTAAATAAAATATTTATATTAAT
6047072 -TTAAATAAAAATATTTATATTAAT
1 ATTAAAT-AAAATATTTATATTAAT
*
6047096 ATTATATAAAAT
1 ATTAAATAAAAT
6047108 TCAAAACATT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
22 6 0.19
23 4 0.12
24 17 0.53
25 5 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
ATTAAATAAAATATTTATATTAAT
Found at i:6047948 original size:76 final size:75
Alignment explanation
Indices: 6047826--6047974 Score: 244
Period size: 76 Copynumber: 2.0 Consensus size: 75
6047816 GAAAACCAGA
6047826 ATTATTCCCTTATTAATAGAAAAGGCAAATGGAAAGTTAGAAAAAAGAATCATAATCTTTCCAAA
1 ATTATTCCCTTATTAATAGAAAAGGCAAATGGAAAGTTAGAAAAAAGAATCATAATCTTTCCAAA
6047891 AGAATATAGG
66 AGAATATAGG
* * * *
6047901 ATTATTCCCTTATTAATAGAGGAAGGCAAATGGAAAGTTAGAAAAAAGAATTATATTCTTTCTAA
1 ATTATTCCCTTATTAATAGA-AAAGGCAAATGGAAAGTTAGAAAAAAGAATCATAATCTTTCCAA
*
6047966 AATAATATA
65 AAGAATATA
6047975 AATTTCCATG
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
75 20 0.29
76 48 0.71
ACGTcount: A:0.47, C:0.09, G:0.14, T:0.30
Consensus pattern (75 bp):
ATTATTCCCTTATTAATAGAAAAGGCAAATGGAAAGTTAGAAAAAAGAATCATAATCTTTCCAAA
AGAATATAGG
Found at i:6048144 original size:138 final size:138
Alignment explanation
Indices: 6047949--6048231 Score: 444
Period size: 138 Copynumber: 2.1 Consensus size: 138
6047939 TAGAAAAAAG
* * * * *
6047949 AATTATATTCTTTCTAAAATAATATAAATTTCCATGTCTTTTATATTTTGCCTGAAATTAATTAA
1 AATTATAATCTTTCCAAAAGAATATAAATTTCCATGTCTTTAATATTTTGACTGAAATTAATTAA
*
6048014 TATAATTGTTTATATTAATAAATTC-GATAAAATATATACAATTATTACTTTGCATGAATCAAAT
66 TATAATTGTTTATATTAATAAATTCAG-TAAAATATATACAATTAATACTTTGCATGAATCAAAT
6048078 TCATATATT
130 TCATATATT
*
6048087 AATTATAATCTTTCCAAAAGAATATTAACTTT-CATGTCTTTAATATTTTGACTGAAATTAATTA
1 AATTATAATCTTTCCAAAAGAATA-TAAATTTCCATGTCTTTAATATTTTGACTGAAATTAATTA
* * *
6048151 ATATAATTTTTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
65 ATATAATTGTTTATATTAATAAATTCAGTAAAATATATACAATTAATACTTTGCATGAATCAAAT
6048216 TCATATATT
130 TCATATATT
6048225 AATTATA
1 AATTATA
6048232 TATATATGTT
Statistics
Matches: 133, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
138 126 0.95
139 7 0.05
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.45
Consensus pattern (138 bp):
AATTATAATCTTTCCAAAAGAATATAAATTTCCATGTCTTTAATATTTTGACTGAAATTAATTAA
TATAATTGTTTATATTAATAAATTCAGTAAAATATATACAATTAATACTTTGCATGAATCAAATT
CATATATT
Found at i:6048927 original size:25 final size:25
Alignment explanation
Indices: 6048893--6048942 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
6048883 ATCTCAAGTT
6048893 TGAGGATCATATACATAGTTGTAAC
1 TGAGGATCATATACATAGTTGTAAC
6048918 TGAGGATCATATACATAGTTGTAAC
1 TGAGGATCATATACATAGTTGTAAC
6048943 AGCCCGTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (25 bp):
TGAGGATCATATACATAGTTGTAAC
Found at i:6054048 original size:24 final size:23
Alignment explanation
Indices: 6053994--6054049 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
6053984 ATTTAATAAA
*
6053994 TAAATAAATATTTTAATATATTT
1 TAAATAAATATTTTAATATAATT
*
6054017 TAATATAATTATTATTAAATATAATT
1 TAA-ATAAATATT-TT-AATATAATT
6054043 T-AATAAA
1 TAAATAAA
6054050 AAATAATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
23 3 0.11
24 12 0.44
25 3 0.11
26 9 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TAAATAAATATTTTAATATAATT
Found at i:6054109 original size:21 final size:21
Alignment explanation
Indices: 6054080--6054129 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
6054070 ACATTCTTAG
*
6054080 TATAATTATTTTATATTAAAT
1 TATATTTATTTTATATTAAAT
*
6054101 TATATTTATTTTTTATTAAAT
1 TATATTTATTTTATATTAAAT
6054122 TATATTTA
1 TATATTTA
6054130 ATATTTTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TATATTTATTTTATATTAAAT
Found at i:6056062 original size:21 final size:21
Alignment explanation
Indices: 6056010--6056095 Score: 64
Period size: 21 Copynumber: 3.9 Consensus size: 21
6056000 ATGTAAGAAA
* *
6056010 ATAAAAATATATAAAATTATC
1 ATAAAAATAAATAATATTATC
* **
6056031 ACAAAGGTAAATAATATTATC
1 ATAAAAATAAATAATATTATC
*
6056052 ATAAATATAAATATTATTTAATTATC
1 ATAAAAATAAATA--A--T-ATTATC
*
6056078 ATAAAAATAAATATTATT
1 ATAAAAATAAATAATATT
6056096 TATTTAAATA
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
21 29 0.58
22 1 0.02
23 1 0.02
25 1 0.02
26 18 0.36
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (21 bp):
ATAAAAATAAATAATATTATC
Found at i:6056080 original size:26 final size:26
Alignment explanation
Indices: 6056046--6056097 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
6056036 GGTAAATAAT
*
6056046 ATTATCATAAATATAAATATTATTTA
1 ATTATCATAAAAATAAATATTATTTA
6056072 ATTATCATAAAAATAAATATTATTTA
1 ATTATCATAAAAATAAATATTATTTA
6056098 TTTAAATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (26 bp):
ATTATCATAAAAATAAATATTATTTA
Found at i:6056098 original size:22 final size:22
Alignment explanation
Indices: 6056038--6056098 Score: 61
Period size: 26 Copynumber: 2.6 Consensus size: 22
6056028 ATCACAAAGG
* *
6056038 TAAATAATA-TTATCATAAATA
1 TAAATATTATTTATCATAAAAA
6056059 TAAATATTATTTAATTATCATAAAAA
1 TAAATATTA--T--TTATCATAAAAA
6056085 TAAATATTATTTAT
1 TAAATATTATTTAT
6056099 TTAAATATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
21 8 0.24
22 4 0.12
24 1 0.03
26 20 0.61
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (22 bp):
TAAATATTATTTATCATAAAAA
Found at i:6060570 original size:30 final size:30
Alignment explanation
Indices: 6060536--6060607 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
6060526 GCCTTTTTTT
* *
6060536 AAAGTTAAATTTGGCCCTCAACCTTTAAAA
1 AAAGTTAAATTTGACCATCAACCTTTAAAA
* * *
6060566 AAAGTCAAAATTGACCATTAACCTTTAAAA
1 AAAGTTAAATTTGACCATCAACCTTTAAAA
6060596 AAGAGTTAAATT
1 AA-AGTTAAATT
6060608 ATTTTTTTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
30 27 0.79
31 7 0.21
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.29
Consensus pattern (30 bp):
AAAGTTAAATTTGACCATCAACCTTTAAAA
Found at i:6068509 original size:26 final size:26
Alignment explanation
Indices: 6068461--6068510 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
6068451 ACTTTCAAAT
*
6068461 TCACTCAAGCAAAAGGAGGAAAAGAA
1 TCACTCAAGCAAAAGGAGAAAAAGAA
* *
6068487 TCACTCAAGCAATATGAGAAAAAG
1 TCACTCAAGCAAAAGGAGAAAAAG
6068511 GACTCTTACG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.52, C:0.16, G:0.20, T:0.12
Consensus pattern (26 bp):
TCACTCAAGCAAAAGGAGAAAAAGAA
Found at i:6073738 original size:44 final size:45
Alignment explanation
Indices: 6073649--6073739 Score: 132
Period size: 44 Copynumber: 2.0 Consensus size: 45
6073639 AAGTATAATA
*
6073649 GAATAGAGGCGTAATAGCAATTCAATTGTTTGGTTGAATGTAATG
1 GAATAGAGGCGTAATAGCAATTCAATTGTTTGGTTGAATGGAATG
* *
6073694 GAATAGAGGCGTAATAG-TATTC-TTGTGTTTGGTTGAATGGAATG
1 GAATAGAGGCGTAATAGCAATTCAAT-TGTTTGGTTGAATGGAATG
6073738 GA
1 GA
6073740 GGTGTAATAG
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 24 0.57
45 17 0.40
ACGTcount: A:0.31, C:0.05, G:0.30, T:0.34
Consensus pattern (45 bp):
GAATAGAGGCGTAATAGCAATTCAATTGTTTGGTTGAATGGAATG
Found at i:6073889 original size:35 final size:35
Alignment explanation
Indices: 6073824--6073912 Score: 92
Period size: 35 Copynumber: 2.5 Consensus size: 35
6073814 ATTGTTTTGT
6073824 TATAAA-ATTTTAATAAGATTATTAAAATAATATAA
1 TATAAATATTTTAATAAGATTATTAAAATAAT-TAA
* * * *
6073859 TATAAATATTTTAATCATATT-TTAACATAATTAT
1 TATAAATATTTTAATAAGATTATTAAAATAATTAA
6073893 TATTAAATATAATTTAATAA
1 TA-TAAATAT--TTTAATAA
6073913 AAAATATATA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
34 4 0.09
35 22 0.49
36 12 0.27
37 7 0.16
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (35 bp):
TATAAATATTTTAATAAGATTATTAAAATAATTAA
Found at i:6077689 original size:14 final size:14
Alignment explanation
Indices: 6077670--6077697 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6077660 AGCAGAAATC
6077670 TGGAGAAAAGAAAA
1 TGGAGAAAAGAAAA
6077684 TGGAGAAAAGAAAA
1 TGGAGAAAAGAAAA
6077698 GAAATGTGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.29, T:0.07
Consensus pattern (14 bp):
TGGAGAAAAGAAAA
Found at i:6077697 original size:19 final size:18
Alignment explanation
Indices: 6077652--6077717 Score: 59
Period size: 18 Copynumber: 3.7 Consensus size: 18
6077642 GAAAAAATTT
*
6077652 AGAAGAAAAGCAGAAATCTG
1 AGAAGAAAAG-A-AAATGTG
6077672 -G-AGAAAAGAAAATG-G
1 AGAAGAAAAGAAAATGTG
6077687 AGAAAAGAAAAG-AAATGTG
1 AG--AAGAAAAGAAAATGTG
6077706 AGAAGAAAAGAA
1 AGAAGAAAAGAA
6077718 GCATACTGTA
Statistics
Matches: 39, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
15 1 0.03
16 5 0.13
17 9 0.23
18 13 0.33
19 11 0.28
ACGTcount: A:0.62, C:0.03, G:0.27, T:0.08
Consensus pattern (18 bp):
AGAAGAAAAGAAAATGTG
Done.