Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold100
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1174989
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.29
Warning! 153044 characters in sequence are not A, C, G, or T
File 3 of 4
Found at i:296044 original size:21 final size:21
Alignment explanation
Indices: 295999--296044 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
295989 GGTTTGTTCT
295999 TACATAAAATACAACTATAAG
1 TACATAAAATACAACTATAAG
* *
296020 -ACATAACATTACAAC-ATACG
1 TACATAA-AATACAACTATAAG
296040 TACAT
1 TACAT
296045 GATTTACTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.52, C:0.20, G:0.04, T:0.24
Consensus pattern (21 bp):
TACATAAAATACAACTATAAG
Found at i:296930 original size:26 final size:25
Alignment explanation
Indices: 296901--296959 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
296891 AAAAGTCTCA
*
296901 GACTTACAAT-CATGAGTCCTTGTTTT
1 GACTTACAATGCAT-AGTCCAT-TTTT
*
296927 GACTTAC-ATGTATAGTCCATTTTT
1 GACTTACAATGCATAGTCCATTTTT
296951 GACTTACAA
1 GACTTACAA
296960 GTCAATGTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
24 11 0.38
25 9 0.31
26 9 0.31
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.41
Consensus pattern (25 bp):
GACTTACAATGCATAGTCCATTTTT
Found at i:297079 original size:26 final size:26
Alignment explanation
Indices: 297050--297125 Score: 91
Period size: 26 Copynumber: 2.9 Consensus size: 26
297040 TCACATGTAC
297050 GAGTCTATGTTTTAGCTTACAAGTAT
1 GAGTCTATGTTTTAGCTTACAAGTAT
* *
297076 GAGTCCATGTTTT-GACTAACAAGTAT
1 GAGTCTATGTTTTAG-CTTACAAGTAT
* * *
297102 GAGTCTGTGTTTAAACTTACAAGT
1 GAGTCTATGTTTTAGCTTACAAGT
297126 TTGATTCCAT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
25 1 0.02
26 40 0.98
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (26 bp):
GAGTCTATGTTTTAGCTTACAAGTAT
Found at i:297113 original size:52 final size:52
Alignment explanation
Indices: 297050--297155 Score: 131
Period size: 52 Copynumber: 2.0 Consensus size: 52
297040 TCACATGTAC
* * ** *
297050 GAGTCTATGTTTTAGCTTACAAGTATGAGTCCATGTTTTGACTAACAAGTAT
1 GAGTCTATGTTTAAACTTACAAGTATGAGTCCATACTTTAACTAACAAGTAT
* * * *
297102 GAGTCTGTGTTTAAACTTACAAGTTTGATTCCATACTTTAATTAACAAGTAT
1 GAGTCTATGTTTAAACTTACAAGTATGAGTCCATACTTTAACTAACAAGTAT
297154 GA
1 GA
297156 AACCATGTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (52 bp):
GAGTCTATGTTTAAACTTACAAGTATGAGTCCATACTTTAACTAACAAGTAT
Found at i:297337 original size:26 final size:26
Alignment explanation
Indices: 297229--297336 Score: 121
Period size: 26 Copynumber: 4.2 Consensus size: 26
297219 TTCAAGTACA
*
297229 AGTCAATGTTCAGACTTACATGTATG
1 AGTCAATGTTCAGACTTACAAGTATG
*
297255 AGTCAATGTTCAGACTTACAAGTTTG
1 AGTCAATGTTCAGACTTACAAGTATG
* *
297281 AATCAATGTTTCA-A-TGAACAAGTATG
1 AGTCAATG-TTCAGACT-TACAAGTATG
* * *
297307 AGTCCATGTTCAGACTTACATGAATG
1 AGTCAATGTTCAGACTTACAAGTATG
297333 AGTC
1 AGTC
297337 CGTGTTCTGG
Statistics
Matches: 68, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
25 5 0.07
26 58 0.85
27 5 0.07
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (26 bp):
AGTCAATGTTCAGACTTACAAGTATG
Found at i:312576 original size:23 final size:22
Alignment explanation
Indices: 312521--312578 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 22
312511 AAAAATCAGT
*
312521 TTGAATGTTCTGATATCAAAAAA
1 TTGAAT-TTCTGATATAAAAAAA
*
312544 -T-CATTCTCTGATATAATAAAAA
1 TTGAATT-TCTGATATAA-AAAAA
312566 TTGAATTTCTGAT
1 TTGAATTTCTGAT
312579 GTCAGAAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
20 1 0.04
21 11 0.39
22 6 0.21
23 7 0.25
24 3 0.11
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (22 bp):
TTGAATTTCTGATATAAAAAAA
Found at i:312805 original size:23 final size:22
Alignment explanation
Indices: 312751--312807 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
312741 AAAAATCAGT
*
312751 TTGAATTTCTGATATCAAAAAA
1 TTGAATTTCTGATATAAAAAAA
*
312773 -T-CATTCTCTGATATAATAAAAA
1 TTGAATT-TCTGATATAA-AAAAA
312795 TTGAATTTCTGAT
1 TTGAATTTCTGAT
312808 GTCAGAAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
20 3 0.11
21 10 0.36
22 5 0.18
23 7 0.25
24 3 0.11
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (22 bp):
TTGAATTTCTGATATAAAAAAA
Found at i:312881 original size:22 final size:22
Alignment explanation
Indices: 312849--312910 Score: 106
Period size: 22 Copynumber: 2.8 Consensus size: 22
312839 TGGGTCGTTT
312849 TTTCTGATATCAAGAATCCGAA
1 TTTCTGATATCAAGAATCCGAA
*
312871 TTTCTGTTATCAAGAATCCGAA
1 TTTCTGATATCAAGAATCCGAA
*
312893 TTTCTGATATCAAAAATC
1 TTTCTGATATCAAGAATC
312911 ATTTTTATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.35
Consensus pattern (22 bp):
TTTCTGATATCAAGAATCCGAA
Found at i:331117 original size:38 final size:37
Alignment explanation
Indices: 331074--331145 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
331064 CTTTGTATCA
331074 TATGATATGATAAAATTATGTATCATATCATACAAAAG
1 TATGATATGATAAAA-TATGTATCATATCATACAAAAG
* * *
331112 TATGATATGATAAAATATTTATGATATGATACAA
1 TATGATATGATAAAATATGTATCATATCATACAA
331146 TATAATATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
37 16 0.52
38 15 0.48
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.36
Consensus pattern (37 bp):
TATGATATGATAAAATATGTATCATATCATACAAAAG
Found at i:335469 original size:166 final size:166
Alignment explanation
Indices: 335241--335985 Score: 1122
Period size: 166 Copynumber: 4.5 Consensus size: 166
335231 GGTCACGATT
* * * ** * * *
335241 TTTACAATCTTCACTATATATACAACCGTTTGTGTATGTATTGGCATTTTTGGTGAAGTGGTTTT
1 TTTAGAATCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCT
* * *
335306 TGAGAAGAA-AATTTTTAAACATTTTTCATATGTAGTTCT-ATGTTAAACTTTGAACCCCGCCTG
66 TGAGAAGAAGATTTTTTAAA-AATTTTCCTATGTA-TTCTAATGTTAAACTTTGAACCCCGCCTG
** * ** *
335369 GGGCTGCAGTTTTGATTTGAGGGTCACGATTTCTACAA
129 GGGCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAA
* *
335407 TTTAGAATCTTCATTATACATACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCT
1 TTTAGAATCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCT
* *
335472 TGAGAAGAAGATTTTTTAAACATTTTCCTAAGGTATATCT-ATGTTAAA-TTTGAACCCCGCCTG
66 TGAGAAGAAGATTTTTTAAAAATTTTCCT-ATGTAT-TCTAATGTTAAACTTTGAACCCCGCCTG
* *
335535 AGGCCACAGTTTTGGTCCGAGGGTCACGATTTTTACAA
129 GGGCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAA
* *
335573 TTTAGAATCTTCACTATGTATACAAGCTTATGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCT
1 TTTAGAATCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCT
* * *
335638 TAAGAAGAAGATTTTTTAAAAATTGTCCTATGTATTTTAATGTTAAACTTTGAACCCCGCCTGGG
66 TGAGAAGAAGATTTTTTAAAAATTTTCCTATGTATTCTAATGTTAAACTTTGAACCCCGCCTGGG
335703 GCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAA
131 GCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAA
* * *
335739 TTTAGAATCTTCACTATGTATACAAGCTTATGTGTAAATATTGGCATTTCTGGTGCAATGGTTCT
1 TTTAGAATCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCT
*
335804 TGAGAAGAAGATTTTTTAAAAATTTTCCTATGTATTTTAATGTTAAACTTTGAACCCCGCCTGGG
66 TGAGAAGAAGATTTTTTAAAAATTTTCCTATGTATTCTAATGTTAAACTTTGAACCCCGCCTGGG
335869 GCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAA
131 GCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAA
335905 TTTAGAATCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCAT-GTGCAGTGGTTC
1 TTTAGAATCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTC-TGGTGCAGTGGTTC
335969 TTGAGAAGAAGATTTTT
65 TTGAGAAGAAGATTTTT
335986 AAAGACATGC
Statistics
Matches: 534, Mismatches: 39, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
164 2 0.00
165 13 0.02
166 494 0.93
167 25 0.05
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (166 bp):
TTTAGAATCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCT
TGAGAAGAAGATTTTTTAAAAATTTTCCTATGTATTCTAATGTTAAACTTTGAACCCCGCCTGGG
GCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAA
Found at i:336167 original size:4 final size:4
Alignment explanation
Indices: 336158--336254 Score: 92
Period size: 4 Copynumber: 24.8 Consensus size: 4
336148 AAAGTTTACA
* * * *
336158 GACG GACG GACA GACG GACA GACG GACG GACG GACG GACG GGC- GACC
1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG
* * * *
336205 GAC- AAAG GNACA GACG GACA GACG GACG GACG GACG GACG GAC- GACG
1 GACG GACG G-ACG GACG GACG GACG GACG GACG GACG GACG GACG GACG
336252 GAC
1 GAC
336255 AACGGGTGAT
Statistics
Matches: 75, Mismatches: 14, Indels: 8
0.77 0.14 0.08
Matches are distributed among these distances:
3 6 0.08
4 67 0.89
5 2 0.03
ACGTcount: A:0.31, C:0.26, G:0.42, T:0.00
Consensus pattern (4 bp):
GACG
Found at i:336236 original size:47 final size:46
Alignment explanation
Indices: 336165--336256 Score: 157
Period size: 47 Copynumber: 2.0 Consensus size: 46
336155 ACAGACGGAC
*
336165 GGACAGACGGACAGACGGACGGACGGACGGACGGGCGACCGACAAA
1 GGACAGACGGACAGACGGACGGACGGACGGACGGACGACCGACAAA
*
336211 GGNACAGACGGACAGACGGACGGACGGACGGACGGACGACGGACAA
1 GG-ACAGACGGACAGACGGACGGACGGACGGACGGACGACCGACAA
336257 CGGGTGATCA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
46 2 0.05
47 41 0.95
ACGTcount: A:0.33, C:0.25, G:0.41, T:0.00
Consensus pattern (46 bp):
GGACAGACGGACAGACGGACGGACGGACGGACGGACGACCGACAAA
Found at i:337336 original size:21 final size:21
Alignment explanation
Indices: 337310--337426 Score: 101
Period size: 21 Copynumber: 5.6 Consensus size: 21
337300 ATATTTTCTA
*
337310 ACAAGTCGTCATAATTATCTG
1 ACAAGTCGACATAATTATCTG
* * *
337331 ACAAGTCGACATTATTATATA
1 ACAAGTCGACATAATTATCTG
** * *
337352 ACTGGTCGACATCATTATTTG
1 ACAAGTCGACATAATTATCTG
* *
337373 ACAAGGCGACATAA-GATCTG
1 ACAAGTCGACATAATTATCTG
* * *
337393 ACAAGTCAACATCATTAGCTG
1 ACAAGTCGACATAATTATCTG
*
337414 ACAAGTCAACATA
1 ACAAGTCGACATA
337427 TAATATGAAT
Statistics
Matches: 74, Mismatches: 21, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
20 15 0.20
21 59 0.80
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (21 bp):
ACAAGTCGACATAATTATCTG
Found at i:337515 original size:42 final size:42
Alignment explanation
Indices: 337463--337635 Score: 168
Period size: 42 Copynumber: 4.1 Consensus size: 42
337453 TAATTTTTTC
* *
337463 TGTCAAATAATTATGTTAACTTGTAAGATCATTATGTCCACT
1 TGTCAAATAATTATGTTAACTTGTCAGATCATTATGTCGACT
* * * * *
337505 TGTCAGATAATTATGTTAACTTATCAGATCTTTATATCGGCT
1 TGTCAAATAATTATGTTAACTTGTCAGATCATTATGTCGACT
* * * * * * *
337547 TGACATATAATAAT-TTCGACTTGTCATATAATTATGTCAACT
1 TGTCAAATAATTATGTT-AACTTGTCAGATCATTATGTCGACT
* ** *
337589 TGTCAAATAATGATGTCGACTTGTCAGATGATTATGTCGACT
1 TGTCAAATAATTATGTTAACTTGTCAGATCATTATGTCGACT
337631 TGTCA
1 TGTCA
337636 GATCCTTTTG
Statistics
Matches: 104, Mismatches: 25, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
41 2 0.02
42 101 0.97
43 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.40
Consensus pattern (42 bp):
TGTCAAATAATTATGTTAACTTGTCAGATCATTATGTCGACT
Found at i:337531 original size:21 final size:21
Alignment explanation
Indices: 337463--337638 Score: 111
Period size: 21 Copynumber: 8.4 Consensus size: 21
337453 TAATTTTTTC
*
337463 TGTCAAATAATTATGTTAACT
1 TGTCAGATAATTATGTTAACT
* * **
337484 TGTAAGATCATTATGTCCACT
1 TGTCAGATAATTATGTTAACT
337505 TGTCAGATAATTATGTTAACT
1 TGTCAGATAATTATGTTAACT
* ** * ***
337526 TATCAGATCTTTATATCGGCT
1 TGTCAGATAATTATGTTAACT
* * * *
337547 TGACATATAATAAT-TTCGACT
1 TGTCAGATAATTATGTT-AACT
* *
337568 TGTCATATAATTATGTCAACT
1 TGTCAGATAATTATGTTAACT
* * **
337589 TGTCAAATAATGATGTCGACT
1 TGTCAGATAATTATGTTAACT
* **
337610 TGTCAGATGATTATGTCGACT
1 TGTCAGATAATTATGTTAACT
337631 TGTCAGAT
1 TGTCAGAT
337639 CCTTTTGTCG
Statistics
Matches: 119, Mismatches: 34, Indels: 4
0.76 0.22 0.03
Matches are distributed among these distances:
20 1 0.01
21 117 0.98
22 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTCAGATAATTATGTTAACT
Found at i:337629 original size:63 final size:63
Alignment explanation
Indices: 337463--337656 Score: 181
Period size: 63 Copynumber: 3.1 Consensus size: 63
337453 TAATTTTTTC
** * * * *
337463 TGTCAAATAATTATGTTAACTTGTAAGATCATTATGTCCACTTGTCAGATAATTATGTTAACT
1 TGTCAAATAATTATGTCGACTTGTCAGATAATTATGTCGACTTGTCAGATAATTATGTCAACT
* * ** * * * * * * *
337526 TATCAGATCTTTATATCGGCTTGACATATAATAATTTCGACTTGTCATATAATTATGTCAACT
1 TGTCAAATAATTATGTCGACTTGTCAGATAATTATGTCGACTTGTCAGATAATTATGTCAACT
* * ** * *
337589 TGTCAAATAATGATGTCGACTTGTCAGATGATTATGTCGACTTGTCAGATCCTTTTGTCGACT
1 TGTCAAATAATTATGTCGACTTGTCAGATAATTATGTCGACTTGTCAGATAATTATGTCAACT
337652 TGTCA
1 TGTCA
337657 GAAAATGTTT
Statistics
Matches: 97, Mismatches: 34, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
63 97 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.40
Consensus pattern (63 bp):
TGTCAAATAATTATGTCGACTTGTCAGATAATTATGTCGACTTGTCAGATAATTATGTCAACT
Found at i:337647 original size:21 final size:21
Alignment explanation
Indices: 337481--337658 Score: 149
Period size: 21 Copynumber: 8.5 Consensus size: 21
337471 AATTATGTTA
* *
337481 ACTTGTAAGATCATTATGTCC
1 ACTTGTCAGATCATTATGTCG
* **
337502 ACTTGTCAGATAATTATGTTA
1 ACTTGTCAGATCATTATGTCG
* * *
337523 ACTTATCAGATCTTTATATCG
1 ACTTGTCAGATCATTATGTCG
* * * * * *
337544 GCTTGACATATAATAATTTCG
1 ACTTGTCAGATCATTATGTCG
* * *
337565 ACTTGTCATATAATTATGTCA
1 ACTTGTCAGATCATTATGTCG
* * *
337586 ACTTGTCAAATAATGATGTCG
1 ACTTGTCAGATCATTATGTCG
*
337607 ACTTGTCAGATGATTATGTCG
1 ACTTGTCAGATCATTATGTCG
* *
337628 ACTTGTCAGATCCTTTTGTCG
1 ACTTGTCAGATCATTATGTCG
337649 ACTTGTCAGA
1 ACTTGTCAGA
337659 AAATGTTTAT
Statistics
Matches: 125, Mismatches: 32, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 125 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (21 bp):
ACTTGTCAGATCATTATGTCG
Found at i:337781 original size:21 final size:21
Alignment explanation
Indices: 337724--337825 Score: 109
Period size: 21 Copynumber: 4.9 Consensus size: 21
337714 TTTTTCCAAC
**
337724 ACATGAATAAGTGACAAGTCG
1 ACATGAATATCTGACAAGTCG
* * *
337745 ACAT-AAGATCTTACAAGTCA
1 ACATGAATATCTGACAAGTCG
337765 ACAT-AATTATCTGACAAGTCG
1 ACATGAA-TATCTGACAAGTCG
* *
337786 TCATGGATATCTGACAAGTCG
1 ACATGAATATCTGACAAGTCG
*
337807 ACATGGATATCTGACAAGT
1 ACATGAATATCTGACAAGT
337826 AGTGGCAGAA
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
20 17 0.25
21 50 0.74
22 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (21 bp):
ACATGAATATCTGACAAGTCG
Found at i:337905 original size:21 final size:21
Alignment explanation
Indices: 337880--337927 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
337870 TTTTCTGACA
* *
337880 ACATAGAGATCTGAAAAGTTG
1 ACATAAAGATCTGAAAAGTCG
* *
337901 ACATAAATATCTGACAAGTCG
1 ACATAAAGATCTGAAAAGTCG
337922 ACATAA
1 ACATAA
337928 TCATCTGACG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.23
Consensus pattern (21 bp):
ACATAAAGATCTGAAAAGTCG
Found at i:337933 original size:21 final size:20
Alignment explanation
Indices: 337888--337961 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 20
337878 CAACATAGAG
* *
337888 ATCTGAAAAGTTGACATAAAT
1 ATCTGACAAGTCGACAT-AAT
337909 ATCTGACAAGTCGACATAAT
1 ATCTGACAAGTCGACATAAT
* * *
337929 CATCTGACGAGTCAACATAGTT
1 -ATCTGACAAGTCGACATA-AT
337951 ATCTGACAAGT
1 ATCTGACAAGT
337962 GGTGGCAGAC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
20 3 0.07
21 41 0.91
22 1 0.02
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (20 bp):
ATCTGACAAGTCGACATAAT
Found at i:352744 original size:2 final size:2
Alignment explanation
Indices: 352737--352778 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
352727 GCAGTAATAT
352737 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
352779 ATGAATAGCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:353129 original size:31 final size:32
Alignment explanation
Indices: 353091--353169 Score: 124
Period size: 31 Copynumber: 2.4 Consensus size: 32
353081 ACTCACACTC
353091 CAGGTAATGCTGTCCATTGGATGATG-AATTG
1 CAGGTAATGCTGTCCATTGGATGATGAAATTG
353122 CAGGTAATGCTGTCCATTGGATGATGAATTAATTG
1 CAGGTAATGCTGTCCATTGGATGATG-A--AATTG
353157 CAGGTAATGCTGT
1 CAGGTAATGCTGT
353170 TTATTCAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
31 26 0.59
35 18 0.41
ACGTcount: A:0.27, C:0.13, G:0.28, T:0.33
Consensus pattern (32 bp):
CAGGTAATGCTGTCCATTGGATGATGAAATTG
Found at i:353221 original size:37 final size:37
Alignment explanation
Indices: 353086--353396 Score: 201
Period size: 37 Copynumber: 8.6 Consensus size: 37
353076 GCTGGACTCA
* *
353086 CACTCCAGGTAATGCTGTCCATTGGATGAT-GAA--T
1 CACTCCAGGTAATGCCGTCCATTGGATGCTGGAATTT
* * *
353120 ---TGCAGGTAATGCTGTCCATTGGATGAT-GAA-TT
1 CACTCCAGGTAATGCCGTCCATTGGATGCTGGAATTT
* * * * ** ** *
353152 AATTGCAGGTAATGCTGTTTATTCAATACTGGAATTT
1 CACTCCAGGTAATGCCGTCCATTGGATGCTGGAATTT
* * **
353189 CACTCCAGGTAATGCTGTCCATTGGATGCTGGACTCC
1 CACTCCAGGTAATGCCGTCCATTGGATGCTGGAATTT
* * * * **
353226 CTCTCCAGGTAATGCCATCCATTGTATGCTGGACTCC
1 CACTCCAGGTAATGCCGTCCATTGGATGCTGGAATTT
* *
353263 CACTCTAGGTAATGCCATCCATTGGATGCT-GAAGTTT
1 CACTCCAGGTAATGCCGTCCATTGGATGCTGGAA-TTT
* * *
353300 TACTCCAGGTAATGCCATCCATTGGATGC-CGAAGTTT
1 CACTCCAGGTAATGCCGTCCATTGGATGCTGGAA-TTT
* * ** * *
353337 TACTCCAGGTAATGCCATCTTTTGGATGCTGGATCAGTG
1 CACTCCAGGTAATGCCGTCCATTGGATGCTGGA--ATTT
353376 CACTCCAGGTAATGCCGTCCA
1 CACTCCAGGTAATGCCGTCCA
353397 CTCTCACTGA
Statistics
Matches: 227, Mismatches: 39, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
31 29 0.13
32 1 0.00
35 21 0.09
36 5 0.02
37 150 0.66
38 2 0.01
39 18 0.08
40 1 0.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (37 bp):
CACTCCAGGTAATGCCGTCCATTGGATGCTGGAATTT
Found at i:354801 original size:25 final size:25
Alignment explanation
Indices: 354772--354848 Score: 78
Period size: 25 Copynumber: 3.4 Consensus size: 25
354762 TAGAAAGATC
354772 ATACAGCAATATCAATTTACAATTG
1 ATACAGCAATATCAATTTACAATTG
* * *
354797 ATACAGCAA-A-GAA---A-TA-TC
1 ATACAGCAATATCAATTTACAATTG
354815 ATACAGCAATATCAATTTACAATTG
1 ATACAGCAATATCAATTTACAATTG
354840 ATACAGCAA
1 ATACAGCAA
354849 AGCCATACCA
Statistics
Matches: 39, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
18 10 0.26
19 2 0.05
20 3 0.08
23 3 0.08
24 2 0.05
25 19 0.49
ACGTcount: A:0.48, C:0.17, G:0.09, T:0.26
Consensus pattern (25 bp):
ATACAGCAATATCAATTTACAATTG
Found at i:354822 original size:43 final size:43
Alignment explanation
Indices: 354763--354850 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
354753 ATGGATATTT
354763 AGAAAGATCATACAGCAATATCAATTTACAATTGATACAGCAA
1 AGAAAGATCATACAGCAATATCAATTTACAATTGATACAGCAA
*
354806 AGAAATATCATACAGCAATATCAATTTACAATTGATACAGCAA
1 AGAAAGATCATACAGCAATATCAATTTACAATTGATACAGCAA
354849 AG
1 AG
354851 CCATACCACA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.49, C:0.16, G:0.11, T:0.24
Consensus pattern (43 bp):
AGAAAGATCATACAGCAATATCAATTTACAATTGATACAGCAA
Found at i:358550 original size:46 final size:46
Alignment explanation
Indices: 358381--358551 Score: 170
Period size: 46 Copynumber: 3.8 Consensus size: 46
358371 CATATTTTTT
* * *
358381 TGGTGGTGGGATTAGCTCACAGAAAATGTATCTCAGTGGACCATAG
1 TGGTGGTGGGATTAGCTCATAGAGAATGTATCTTAGTGGACCATAG
** * * * *
358427 CAGTGGT--G-TTGGCTCATAGAGAATGCATCTGAATGGACCATAG
1 TGGTGGTGGGATTAGCTCATAGAGAATGTATCTTAGTGGACCATAG
** * *
358470 TGGTGGTGTTATTAGCTCATAGAGAATGTTTCTTAGTGAACC-TAAG
1 TGGTGGTGGGATTAGCTCATAGAGAATGTATCTTAGTGGACCAT-AG
* *
358516 TGGTGGTGGGGTTAGCTCAAAGAGAATGTATCTTAG
1 TGGTGGTGGGATTAGCTCATAGAGAATGTATCTTAG
358552 CATATCCCTA
Statistics
Matches: 99, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
43 34 0.34
44 1 0.01
45 1 0.01
46 63 0.64
ACGTcount: A:0.27, C:0.13, G:0.30, T:0.30
Consensus pattern (46 bp):
TGGTGGTGGGATTAGCTCATAGAGAATGTATCTTAGTGGACCATAG
Found at i:358678 original size:44 final size:44
Alignment explanation
Indices: 358617--358813 Score: 385
Period size: 44 Copynumber: 4.5 Consensus size: 44
358607 TAAAGGTGGT
*
358617 TGGGGTTAGCTCACAGAGAATATATCTCTGTAGACTTCTAATGG
1 TGGGGTTAGGTCACAGAGAATATATCTCTGTAGACTTCTAATGG
358661 TGGGGTTAGGTCACAGAGAATATATCTCTGTAGACTTCTAATGG
1 TGGGGTTAGGTCACAGAGAATATATCTCTGTAGACTTCTAATGG
358705 TGGGGTTAGGTCACAGAGAATATATCTCTGTAGACTTCTAATGG
1 TGGGGTTAGGTCACAGAGAATATATCTCTGTAGACTTCTAATGG
358749 TGGGGTTAGGTCACAGAGAATATATCTCTGTAGACTTCTAATGG
1 TGGGGTTAGGTCACAGAGAATATATCTCTGTAGACTTCTAATGG
358793 TGGGGTTAGGTCACAGAGAAT
1 TGGGGTTAGGTCACAGAGAAT
358814 TTTTTTGTAG
Statistics
Matches: 152, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
44 152 1.00
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (44 bp):
TGGGGTTAGGTCACAGAGAATATATCTCTGTAGACTTCTAATGG
Found at i:376630 original size:2 final size:2
Alignment explanation
Indices: 376623--376698 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
376613 TACATAACAC
376623 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
376665 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
376699 TTTAGAGAGA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:388782 original size:2 final size:2
Alignment explanation
Indices: 388775--388805 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
388765 TTGAATGAAT
388775 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
388806 TTGACTGGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:397284 original size:5 final size:5
Alignment explanation
Indices: 397254--397346 Score: 132
Period size: 5 Copynumber: 18.6 Consensus size: 5
397244 CCATTAAGCC
* * * * * *
397254 ACTAT GCTAT GCTAT GCTAT GCTAT ACTAT ACAAA ACTAT ACTAT ACTAT
1 ACTAT ACTAT ACTAT ACTAT ACTAT ACTAT ACTAT ACTAT ACTAT ACTAT
397304 ACTAT ACTAT ACTAT ACTAT ACTAT ACTAT ACTAT ACTAT ACT
1 ACTAT ACTAT ACTAT ACTAT ACTAT ACTAT ACTAT ACTAT ACT
397347 TTTTTCATAA
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 82 1.00
ACGTcount: A:0.38, C:0.20, G:0.04, T:0.38
Consensus pattern (5 bp):
ACTAT
Found at i:399803 original size:2 final size:2
Alignment explanation
Indices: 399796--399855 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
399786 TGAATTTAAC
399796 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
399838 GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA
399856 TTCGAAGCGA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:413218 original size:2 final size:2
Alignment explanation
Indices: 413211--413239 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
413201 GTTTTATTTT
413211 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
413240 TCNNNNNNNN
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:423385 original size:189 final size:188
Alignment explanation
Indices: 423099--423475 Score: 745
Period size: 189 Copynumber: 2.0 Consensus size: 188
423089 TGTCCGGTGC
423099 CCCCCGCCCCTTAGATCCGCGCATGCAGATGATTTTAATGTTAAGTTATTCAAATGCATGCCTTC
1 CCCCCGCCCCTTAGATCCGCGCATGCAGATGATTTTAATGTTAAGTTATTCAAATGCATGCCTTC
423164 AGTTCACACATATGTAAAACATATATATTATTAACGCACGTGTAACATGGTTTTTTGAACTCATG
66 AGTTCACACATATGTAAAACATATATATTATTAACGCACGTGTAACATGGTTTTTTGAACTCATG
423229 TTAACCATGTGTTTATTATAACATATGTGTAACATGTGGTTGAGATCTACATATGTAA
131 TTAACCATGTGTTTATTATAACATATGTGTAACATGTGGTTGAGATCTACATATGTAA
423287 NCCCCCGCCCCTTAGATCCGCGCATGCAGATGATTTTAATGTTAAGTTATTCAAATGCATGCCTT
1 -CCCCCGCCCCTTAGATCCGCGCATGCAGATGATTTTAATGTTAAGTTATTCAAATGCATGCCTT
423352 CAGTTCACACATATGTAAAACATATATATTATTAACGCACGTGTAACATGGTTTTTTGAACTCAT
65 CAGTTCACACATATGTAAAACATATATATTATTAACGCACGTGTAACATGGTTTTTTGAACTCAT
423417 GTTAACCATGTGTTTATTATAACATATGTGTAACATGTGGTTGAGATCTACATATGTAA
130 GTTAACCATGTGTTTATTATAACATATGTGTAACATGTGGTTGAGATCTACATATGTAA
423476 AACATATGGT
Statistics
Matches: 188, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
189 188 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (188 bp):
CCCCCGCCCCTTAGATCCGCGCATGCAGATGATTTTAATGTTAAGTTATTCAAATGCATGCCTTC
AGTTCACACATATGTAAAACATATATATTATTAACGCACGTGTAACATGGTTTTTTGAACTCATG
TTAACCATGTGTTTATTATAACATATGTGTAACATGTGGTTGAGATCTACATATGTAA
Found at i:425219 original size:84 final size:84
Alignment explanation
Indices: 425128--425301 Score: 233
Period size: 84 Copynumber: 2.1 Consensus size: 84
425118 TTGTAATCAT
* ** * * * **
425128 GAGATATTTTCTCGTAATTTTGAGAAAATTACTCGTGAAAGCGAGATCTTCTTTCGTAATTACGA
1 GAGATATTTTCTCGTAATTTTGAGAAAATAACTCGAAAAAGCAAGATCTTCTTTCATAAATAAAA
425193 GATC-TTTTCTAGTAATAAC
66 GATCTTTTTCT-GTAATAAC
*
425212 GAGATATTTTCTCGTAATTTTGAGAAAATAACTCGAAAAAGCAAGATCTTTTTTCATAAATAAAA
1 GAGATATTTTCTCGTAATTTTGAGAAAATAACTCGAAAAAGCAAGATCTTCTTTCATAAATAAAA
* *
425277 GATCTTTTTCTTTAATTAC
66 GATCTTTTTCTGTAATAAC
425296 GAGATA
1 GAGATA
425302 AATAACTCTT
Statistics
Matches: 78, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
84 72 0.92
85 6 0.08
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (84 bp):
GAGATATTTTCTCGTAATTTTGAGAAAATAACTCGAAAAAGCAAGATCTTCTTTCATAAATAAAA
GATCTTTTTCTGTAATAAC
Found at i:425236 original size:21 final size:21
Alignment explanation
Indices: 425128--425230 Score: 77
Period size: 21 Copynumber: 4.9 Consensus size: 21
425118 TTGTAATCAT
**
425128 GAGATATTTTCTCGTAATTTT
1 GAGATATTTTCTCGTAATTAC
* * *
425149 GAGAAAATTACTCGTGAA--AGC
1 GAGATATTTTCTCGT-AATTA-C
*
425170 GAGATCTTCTT-TCGTAATTAC
1 GAGATATT-TTCTCGTAATTAC
* * *
425191 GAGATCTTTTCTAGTAATAAC
1 GAGATATTTTCTCGTAATTAC
425212 GAGATATTTTCTCGTAATT
1 GAGATATTTTCTCGTAATT
425231 TTGAGAAAAT
Statistics
Matches: 62, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
20 4 0.06
21 54 0.87
22 4 0.06
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.40
Consensus pattern (21 bp):
GAGATATTTTCTCGTAATTAC
Found at i:426050 original size:2 final size:2
Alignment explanation
Indices: 426043--426084 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
426033 TATTTCACAA
426043 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
426085 ATACATCTAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:428246 original size:20 final size:20
Alignment explanation
Indices: 428221--428262 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
428211 AAAACTCTAC
428221 ATAGGTAAAAACAAATCCTG
1 ATAGGTAAAAACAAATCCTG
428241 ATAGGTAAAAACAAATCCTG
1 ATAGGTAAAAACAAATCCTG
428261 AT
1 AT
428263 GACGTTGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.21
Consensus pattern (20 bp):
ATAGGTAAAAACAAATCCTG
Found at i:432853 original size:2 final size:2
Alignment explanation
Indices: 432846--432886 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
432836 TTTTTATATG
* *
432846 GT GT GT GT TT GT GT GT GT GT GT GT GT GT GT GT GT GT AT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
432887 GGGGGGGGGG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.02, C:0.00, G:0.46, T:0.51
Consensus pattern (2 bp):
GT
Found at i:433986 original size:2 final size:2
Alignment explanation
Indices: 433979--434019 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
433969 CGTAATACAC
433979 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
434020 TATAATTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:434311 original size:2 final size:2
Alignment explanation
Indices: 434304--434337 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
434294 GATAAACGCC
434304 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
434338 GGTACTCGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:440465 original size:3 final size:3
Alignment explanation
Indices: 440457--440482 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
440447 GAAGGCAAGA
440457 AGG AGG AGG AGG AGG AGG AGG AGG AG
1 AGG AGG AGG AGG AGG AGG AGG AGG AG
440483 AGAGAGAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:445917 original size:16 final size:17
Alignment explanation
Indices: 445889--445923 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
445879 AACAGGTAAA
445889 AAGTGTGAAATGAAATT
1 AAGTGTGAAATGAAATT
445906 AAGTGT-AAATGAAATT
1 AAGTGTGAAATGAAATT
445922 AA
1 AA
445924 AATCTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.51, C:0.00, G:0.20, T:0.29
Consensus pattern (17 bp):
AAGTGTGAAATGAAATT
Found at i:455150 original size:16 final size:16
Alignment explanation
Indices: 455129--455162 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
455119 AAAATATATA
*
455129 ATATATATATATGTTT
1 ATATATAAATATGTTT
455145 ATATATAAATATGTTT
1 ATATATAAATATGTTT
455161 AT
1 AT
455163 CATTACTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (16 bp):
ATATATAAATATGTTT
Found at i:461293 original size:2 final size:2
Alignment explanation
Indices: 461288--461360 Score: 139
Period size: 2 Copynumber: 37.0 Consensus size: 2
461278 AGCACACACT
461288 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
461330 GA GA -A GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
461361 TATTCCAACC
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 69 0.99
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:461688 original size:2 final size:2
Alignment explanation
Indices: 461681--461724 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
461671 AGTCTGGTAT
461681 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
461723 TC
1 TC
461725 NGAGAGAGAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:462043 original size:377 final size:376
Alignment explanation
Indices: 461349--462101 Score: 1497
Period size: 377 Copynumber: 2.0 Consensus size: 376
461339 GAGAGAGAGA
461349 GAGAGAGAGAGATATTCCAACCCTCATACATGCAGTGTAAAAATGAAGAAACTAAACATTTCAAA
1 GAGAGAGAGAGATATTCCAACCCTCATACATGCAGTGTAAAAATGAAGAAACTAAACATTTCAAA
461414 CACTAAATACTTCATTGTTAAACATTTTTTTATTTTGCGGTCTTGAAAAAAATAATAATAGAACG
66 CACTAAATACTTCATTGTTAAACATTTTTTTATTTTGCGGTCTTGAAAAAAATAATAATAGAACG
461479 ACATTTTTTCCTTATCATGGAAGGAGCACGTGGTCTATCTCGCAGGCTGATTTGATTGACAGGGA
131 ACATTTTTTCCTTATCATGGAAGGAGCACGTGGTCTATCTCGCAGGCTGATTTGATTGACAGGGA
461544 TAGCACGTGGACTCTGACTGCATAGATTCTATCGCAATTTTAGGGAAAAGGGTTCAATATAATGG
196 TAGCACGTGGACTCTGACTGCATAGATTCTATCGCAATTTTAGGGAAAAGGGTTCAATATAATGG
461609 AAACTATAAATCTAACTTATTACACTGAATTACAAGTAAAATGTACTTAAAATTAAACTCATAGT
261 AAACTATAAATCTAACTTATTACACTGAATTACAAGTAAAATGTACTTAAAATTAAACTCATAGT
461674 CTGGTATTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC
326 CTGGTATTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC
461725 NGAGAGAGAGAGATATTCCAACCCTCATACATGCAGTGTAAAAATGAAGAAACTAAACATTTCAA
1 -GAGAGAGAGAGATATTCCAACCCTCATACATGCAGTGTAAAAATGAAGAAACTAAACATTTCAA
461790 ACACTAAATACTTCATTGTTAAACATTTTTTTATTTTGCGGTCTTGAAAAAAATAATAATAGAAC
65 ACACTAAATACTTCATTGTTAAACATTTTTTTATTTTGCGGTCTTGAAAAAAATAATAATAGAAC
461855 GACATTTTTTCCTTATCATGGAAGGAGCACGTGGTCTATCTCGCAGGCTGATTTGATTGACAGGG
130 GACATTTTTTCCTTATCATGGAAGGAGCACGTGGTCTATCTCGCAGGCTGATTTGATTGACAGGG
461920 ATAGCACGTGGACTCTGACTGCATAGATTCTATCGCAATTTTAGGGAAAAGGGTTCAATATAATG
195 ATAGCACGTGGACTCTGACTGCATAGATTCTATCGCAATTTTAGGGAAAAGGGTTCAATATAATG
461985 GAAACTATAAATCTAACTTATTACACTGAATTACAAGTAAAATGTACTTAAAATTAAACTCATAG
260 GAAACTATAAATCTAACTTATTACACTGAATTACAAGTAAAATGTACTTAAAATTAAACTCATAG
462050 TCTGGTATTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC
325 TCTGGTATTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC
462102 TCTTATATGA
Statistics
Matches: 376, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
377 376 1.00
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.33
Consensus pattern (376 bp):
GAGAGAGAGAGATATTCCAACCCTCATACATGCAGTGTAAAAATGAAGAAACTAAACATTTCAAA
CACTAAATACTTCATTGTTAAACATTTTTTTATTTTGCGGTCTTGAAAAAAATAATAATAGAACG
ACATTTTTTCCTTATCATGGAAGGAGCACGTGGTCTATCTCGCAGGCTGATTTGATTGACAGGGA
TAGCACGTGGACTCTGACTGCATAGATTCTATCGCAATTTTAGGGAAAAGGGTTCAATATAATGG
AAACTATAAATCTAACTTATTACACTGAATTACAAGTAAAATGTACTTAAAATTAAACTCATAGT
CTGGTATTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC
Found at i:462065 original size:2 final size:2
Alignment explanation
Indices: 462058--462104 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
462048 AGTCTGGTAT
462058 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
462100 TC TC T
1 TC TC T
462105 TATATGACGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:471210 original size:1 final size:1
Alignment explanation
Indices: 471178--471202 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
471168 TTCGTCCTCC
471178 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
471203 ACATTTTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:479353 original size:2 final size:2
Alignment explanation
Indices: 479316--479343 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
479306 CATTTTGGAT
479316 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
479344 AGAGATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:482220 original size:17 final size:17
Alignment explanation
Indices: 482190--482258 Score: 70
Period size: 17 Copynumber: 3.9 Consensus size: 17
482180 TTGTTTTCAT
*
482190 TTTTGTTCTGTTGTTCTTG
1 TTTTGTT-TTTTGTT-TTG
482209 -TTTGTTTTTTGTTTTG
1 TTTTGTTTTTTGTTTTG
482225 TTTTGTTTTGTT-TTTTG
1 TTTTGTTTT-TTGTTTTG
*
482242 TTATTATTTTTTGTTTT
1 TT-TTGTTTTTTGTTTT
482259 TCTGTTTTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
16 3 0.07
17 23 0.52
18 18 0.41
ACGTcount: A:0.03, C:0.03, G:0.16, T:0.78
Consensus pattern (17 bp):
TTTTGTTTTTTGTTTTG
Found at i:482221 original size:7 final size:7
Alignment explanation
Indices: 482209--482267 Score: 59
Period size: 7 Copynumber: 8.3 Consensus size: 7
482199 GTTGTTCTTG
482209 TTTGTTT
1 TTTGTTT
482216 TTTGTTT
1 TTTGTTT
482223 TGTT-TTGT
1 T-TTGTT-T
482231 TTTGTTT
1 TTTGTTT
482238 TTTG-TT
1 TTTGTTT
* *
482244 ATTATTT
1 TTTGTTT
482251 TTTGTTT
1 TTTGTTT
482258 TTCTGTTT
1 TT-TGTTT
482266 TT
1 TT
482268 CGGGTGATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
6 4 0.09
7 26 0.60
8 13 0.30
ACGTcount: A:0.03, C:0.02, G:0.14, T:0.81
Consensus pattern (7 bp):
TTTGTTT
Found at i:482225 original size:5 final size:5
Alignment explanation
Indices: 482200--482238 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
482190 TTTTGTTCTG
*
482200 TTGTT CTTGTT TGTTTT TTGTT TTGTT TTGTT TTGTT TT
1 TTGTT -TTGTT T-TGTT TTGTT TTGTT TTGTT TTGTT TT
482239 TTGTTATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
5 21 0.70
6 9 0.30
ACGTcount: A:0.00, C:0.03, G:0.18, T:0.79
Consensus pattern (5 bp):
TTGTT
Found at i:482231 original size:35 final size:35
Alignment explanation
Indices: 482190--482258 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
482180 TTGTTTTCAT
*
482190 TTTTGTTCTGTTGTTCTTG-T-TTGTTTTTTGTTTTG
1 TTTTGTTCTGTT-TT-TTGTTATTATTTTTTGTTTTG
*
482225 TTTTGTTTTGTTTTTTGTTATTATTTTTTGTTTT
1 TTTTGTTCTGTTTTTTGTTATTATTTTTTGTTTT
482259 TCTGTTTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 3 0.10
34 3 0.10
35 24 0.80
ACGTcount: A:0.03, C:0.03, G:0.16, T:0.78
Consensus pattern (35 bp):
TTTTGTTCTGTTTTTTGTTATTATTTTTTGTTTTG
Found at i:482234 original size:22 final size:22
Alignment explanation
Indices: 482200--482266 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
482190 TTTTGTTCTG
482200 TTGTTCTTG-TTTGTTTTTTGTT
1 TTGTT-TTGTTTTGTTTTTTGTT
482222 TTGTTTTGTTTTGTTTTTTGTT
1 TTGTTTTGTTTTGTTTTTTGTT
* *
482244 AT-TATT-TTTTGTTTTTCTGTT
1 TTGTTTTGTTTTGTTTTT-TGTT
482265 TT
1 TT
482267 TCGGGTGATA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
20 10 0.25
21 11 0.28
22 19 0.47
ACGTcount: A:0.03, C:0.03, G:0.15, T:0.79
Consensus pattern (22 bp):
TTGTTTTGTTTTGTTTTTTGTT
Found at i:482253 original size:13 final size:12
Alignment explanation
Indices: 482167--482258 Score: 52
Period size: 12 Copynumber: 7.8 Consensus size: 12
482157 TTAAAGCATA
482167 TTTTT-TTTTA-
1 TTTTTGTTTTAT
*
482177 TTATTGTTTTCA-
1 TTTTTGTTTT-AT
* *
482189 TTTTTGTTCTGT
1 TTTTTGTTTTAT
*
482201 TGTTCTTG-TTTGT
1 T-TT-TTGTTTTAT
482214 TTTTTG-TTT-T
1 TTTTTGTTTTAT
* *
482224 GTTTTGTTTTGT
1 TTTTTGTTTTAT
482236 TTTTTGTTATTAT
1 TTTTTGTT-TTAT
482249 TTTTTGTTTT
1 TTTTTGTTTT
482259 TCTGTTTTTC
Statistics
Matches: 66, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
10 10 0.15
11 13 0.20
12 22 0.33
13 18 0.27
14 3 0.05
ACGTcount: A:0.05, C:0.03, G:0.13, T:0.78
Consensus pattern (12 bp):
TTTTTGTTTTAT
Found at i:486430 original size:17 final size:17
Alignment explanation
Indices: 486402--486451 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
486392 TAAGAAGTTT
486402 ATAAATCAAAAAATATAATA
1 ATAAATC-AAAAATA-AA-A
486422 AT-AAT-AAAAATAAAA
1 ATAAATCAAAAATAAAA
486437 ATAAATCAAAAATAA
1 ATAAATCAAAAATAA
486452 TGGTGGTGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 3 0.11
16 5 0.18
17 15 0.54
19 3 0.11
20 2 0.07
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (17 bp):
ATAAATCAAAAATAAAA
Found at i:486874 original size:6 final size:6
Alignment explanation
Indices: 486853--486931 Score: 87
Period size: 6 Copynumber: 13.8 Consensus size: 6
486843 NNNNNNNAAA
* *
486853 AAAAAC CAAAAC -AAAAC AAAAA- AACAAA- AAAAAC AAAAAC -AAAAT
1 AAAAAC AAAAAC AAAAAC AAAAAC AA-AAAC AAAAAC AAAAAC AAAAAC
*
486898 AAAAAC AAAAAC AAAAAC AAACA- AAAAAC AAAAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAA
486932 AACCCCAAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
5 18 0.29
6 45 0.71
ACGTcount: A:0.84, C:0.15, G:0.00, T:0.01
Consensus pattern (6 bp):
AAAAAC
Found at i:486891 original size:23 final size:22
Alignment explanation
Indices: 486850--486932 Score: 96
Period size: 23 Copynumber: 3.6 Consensus size: 22
486840 NNNNNNNNNN
**
486850 AAAAAAAACCAAAAC-AAAACA
1 AAAAAAAAAAAAAACAAAAACA
486871 AAAAAACAAAAAAAACAAAAACA
1 AAAAAA-AAAAAAAACAAAAACA
*
486894 AAATAAAAACAAAAACAAAAACA
1 AAA-AAAAAAAAAAACAAAAACA
486917 AACAAAAAACAAAAAA
1 AA-AAAAAA-AAAAAA
486933 ACCCCAAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
21 6 0.11
22 7 0.13
23 31 0.58
24 9 0.17
ACGTcount: A:0.84, C:0.14, G:0.00, T:0.01
Consensus pattern (22 bp):
AAAAAAAAAAAAAACAAAAACA
Found at i:486942 original size:1 final size:1
Alignment explanation
Indices: 486850--486933 Score: 51
Period size: 1 Copynumber: 84.0 Consensus size: 1
486840 NNNNNNNNNN
** * * * * * * * *
486850 AAAAAAAACCAAAACAAAACAAAAAAACAAAAAAAACAAAAACAAAATAAAAACAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
486915 CAAACAAAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAA
486934 CCCCAAAAAG
Statistics
Matches: 59, Mismatches: 24, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 59 1.00
ACGTcount: A:0.85, C:0.14, G:0.00, T:0.01
Consensus pattern (1 bp):
A
Found at i:486942 original size:17 final size:16
Alignment explanation
Indices: 486853--486933 Score: 99
Period size: 17 Copynumber: 4.8 Consensus size: 16
486843 NNNNNNNAAA
*
486853 AAAAACCAAAACAAAAC
1 AAAAA-CAAAAAAAAAC
*
486870 AAAAAAACAAAAAAAAC
1 AAAAACA-AAAAAAAAC
486887 AAAAACAAAATAAAAAC
1 AAAAACAAAA-AAAAAC
*
486904 AAAAACAAAAACAAAC
1 AAAAACAAAAAAAAAC
486920 AAAAAACAAAAAAA
1 -AAAAACAAAAAAA
486934 CCCCAAAAAG
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
16 9 0.16
17 47 0.84
ACGTcount: A:0.84, C:0.15, G:0.00, T:0.01
Consensus pattern (16 bp):
AAAAACAAAAAAAAAC
Found at i:488549 original size:4 final size:4
Alignment explanation
Indices: 488523--488583 Score: 97
Period size: 4 Copynumber: 15.0 Consensus size: 4
488513 ATGTTGATGA
488523 AAAT AAAAT AAAAT AAA- AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT -AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
488572 AAAT AAAT AAAT
1 AAAT AAAT AAAT
488584 GAANNNNNNN
Statistics
Matches: 55, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
3 3 0.05
4 43 0.78
5 9 0.16
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:506695 original size:12 final size:12
Alignment explanation
Indices: 506678--506730 Score: 61
Period size: 12 Copynumber: 4.2 Consensus size: 12
506668 NNNNNNNNNA
506678 AAAAAAAAAAAT
1 AAAAAAAAAAAT
506690 AAAAAAAAATAGAT
1 AAAAAAAAA-A-AT
*
506704 AAATAAAAAAAT
1 AAAAAAAAAAAT
* *
506716 AAAATAAAATAT
1 AAAAAAAAAAAT
506728 AAA
1 AAA
506731 TAAATAAAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
12 23 0.66
13 2 0.06
14 10 0.29
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.15
Consensus pattern (12 bp):
AAAAAAAAAAAT
Found at i:506718 original size:26 final size:28
Alignment explanation
Indices: 506682--506739 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
506672 NNNNNAAAAA
*
506682 AAAAAAATAAAA-AAAA-ATAGATAAAT
1 AAAAAAATAAAATAAAATATAAATAAAT
506708 AAAAAAATAAAATAAAATATAAATAAAT
1 AAAAAAATAAAATAAAATATAAATAAAT
506736 AAAA
1 AAAA
506740 CGAAAATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 12 0.41
27 4 0.14
28 13 0.45
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (28 bp):
AAAAAAATAAAATAAAATATAAATAAAT
Found at i:506732 original size:32 final size:31
Alignment explanation
Indices: 506677--506738 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
506667 NNNNNNNNNN
*
506677 AAAAAAAAAAAATAAAAAAAAATAGATAAAT
1 AAAAAAAAAAAATAAAAAAAAATAAATAAAT
* *
506708 AAAAAAATAAAATAAAATATAAATAAATAAA
1 AAAAAAAAAAAATAAAA-AAAAATAAATAAA
506739 ACGAAAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 16 0.59
32 11 0.41
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (31 bp):
AAAAAAAAAAAATAAAAAAAAATAAATAAAT
Found at i:518956 original size:22 final size:22
Alignment explanation
Indices: 518930--519324 Score: 252
Period size: 22 Copynumber: 18.4 Consensus size: 22
518920 ATAATTTCTT
*
518930 TTGCGTTTAAACGCAATAACTA
1 TTGCGTTTAAACGCAATAAGTA
* * *
518952 TTGCGTTTAATCGCAAT--CTT
1 TTGCGTTTAAACGCAATAAGTA
*
518972 TTGCG-TTAAATCGCAATAAGTT
1 TTGCGTTTAAA-CGCAATAAGTA
518994 TTGCGTTTAAACGCAA-AAG-A
1 TTGCGTTTAAACGCAATAAGTA
** *
519014 TTGCAATTAAACGCAAT-AGCAA
1 TTGCGTTTAAACGCAATAAG-TA
* **
519036 TTGCTTTTAAACGCAA-AGAACA
1 TTGCGTTTAAACGCAATA-AGTA
* * *
519058 TTGCGTTTTAACACAA-AGGT-
1 TTGCGTTTAAACGCAATAAGTA
*
519078 TTGCGTTTAAACGC-A-AAGTT
1 TTGCGTTTAAACGCAATAAGTA
*
519098 TTGCGTTTAAACGC-A-AAGTT
1 TTGCGTTTAAACGCAATAAGTA
519118 TTGCGTTTAAACGCAA-AAGTA
1 TTGCGTTTAAACGCAATAAGTA
* * *
519139 TTGCGTTTAAATGCAAAAAAATA
1 TTGCGTTTAAACGC-AATAAGTA
519162 TTGCGTTTAAACGCAAAGGTAA-TA
1 TTGCGTTTAAACGC-AA--TAAGTA
* * *
519186 TTGCGTTTTAACGCAATAATTT
1 TTGCGTTTAAACGCAATAAGTA
* ** * *
519208 TTGTGAATAAACGCAAT-TGTTT
1 TTGCGTTTAAACGCAATAAG-TA
* * *
519230 TTGCGATTAAACGCAACAA-TT
1 TTGCGTTTAAACGCAATAAGTA
* *
519251 TTGCGATTAAACGCAATAA-TCG
1 TTGCGTTTAAACGCAATAAGT-A
*
519273 TTGCGTTTAATCGCAA-AAGGTA
1 TTGCGTTTAAACGCAATAA-GTA
* *
519295 TTGGGTTTAAACGCAATAGGTA
1 TTGCGTTTAAACGCAATAAGTA
519317 TTGCGTTT
1 TTGCGTTT
519325 TATTGCAAAA
Statistics
Matches: 305, Mismatches: 46, Indels: 44
0.77 0.12 0.11
Matches are distributed among these distances:
19 8 0.03
20 75 0.25
21 47 0.15
22 128 0.42
23 30 0.10
24 15 0.05
25 2 0.01
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (22 bp):
TTGCGTTTAAACGCAATAAGTA
Found at i:519083 original size:20 final size:20
Alignment explanation
Indices: 518929--519181 Score: 166
Period size: 20 Copynumber: 12.1 Consensus size: 20
518919 AATAATTTCT
**
518929 TTTGCGTTTAAACGCAATAAC
1 TTTGCGTTTAAACGCAA-AGG
* ***
518950 TATTGCGTTTAATCGCAATCT
1 T-TTGCGTTTAAACGCAAAGG
*
518971 TTTGCG-TTAAATCGCAATAAGT
1 TTTGCGTTTAAA-CGC-A-AAGG
*
518993 TTTGCGTTTAAACGCAAAAG
1 TTTGCGTTTAAACGCAAAGG
* ** *
519013 ATTGCAATTAAACGCAATAGCA
1 TTTGCGTTTAAACGCAA-AG-G
* * *
519035 ATTGCTTTTAAACGCAAAGAAC
1 TTTGCGTTTAAACGCAAAG--G
* * *
519057 ATTGCGTTTTAACACAAAGG
1 TTTGCGTTTAAACGCAAAGG
*
519077 TTTGCGTTTAAACGCAAAGT
1 TTTGCGTTTAAACGCAAAGG
*
519097 TTTGCGTTTAAACGCAAAGT
1 TTTGCGTTTAAACGCAAAGG
*
519117 TTTGCGTTTAAACGCAAAAG
1 TTTGCGTTTAAACGCAAAGG
* **
519137 TATTGCGTTTAAATGCAAAAAAA
1 T-TTGCGTTTAAACGC--AAAGG
519160 TATTGCGTTTAAACGCAAAGG
1 T-TTGCGTTTAAACGCAAAGG
519181 T
1 T
519182 AATATTGCGT
Statistics
Matches: 188, Mismatches: 33, Indels: 22
0.77 0.14 0.09
Matches are distributed among these distances:
19 4 0.02
20 79 0.42
21 24 0.13
22 57 0.30
23 24 0.13
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.32
Consensus pattern (20 bp):
TTTGCGTTTAAACGCAAAGG
Found at i:519163 original size:23 final size:23
Alignment explanation
Indices: 519078--519201 Score: 102
Period size: 20 Copynumber: 5.7 Consensus size: 23
519068 ACACAAAGGT
* *
519078 TTGCGTTTAAACGC---AAAGTT
1 TTGCGTTTAAACGCAAAAAAATA
* *
519098 TTGCGTTTAAACGC---AAAGTT
1 TTGCGTTTAAACGCAAAAAAATA
*
519118 TTGCGTTTAAACGC--AAAAGTA
1 TTGCGTTTAAACGCAAAAAAATA
*
519139 TTGCGTTTAAATGCAAAAAAATA
1 TTGCGTTTAAACGCAAAAAAATA
**
519162 TTGCGTTTAAACGCAAAGGTAATA
1 TTGCGTTTAAACGCAAA-AAAATA
*
519186 TTGCGTTTTAACGCAA
1 TTGCGTTTAAACGCAA
519202 TAATTTTTGT
Statistics
Matches: 93, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
20 34 0.37
21 18 0.19
23 22 0.24
24 19 0.20
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (23 bp):
TTGCGTTTAAACGCAAAAAAATA
Found at i:519165 original size:104 final size:106
Alignment explanation
Indices: 518930--519181 Score: 273
Period size: 104 Copynumber: 2.4 Consensus size: 106
518920 ATAATTTCTT
* * * ***
518930 TTGCGTTTAAACGC-AATAACTATTGCGTTTAATCGCAATCTTTTGCGTTAAATCGCAATAAGTT
1 TTGCGTTTAAACGCAAAAAAC-ATTGCGTTTAAACACAAAGGTTTGCGTTAAATCGCAATAAGTT
*
518994 TTGCGTTTAAACGCAAAAGATTGCAATTAAACGCAATAGCAA
65 TTGCGTTTAAACGCAAAAGATTGCAATTAAACGCAAAAGCAA
* * *
519036 TTGCTTTTAAACGCAAAGAACATTGCGTTTTAACACAAAGGTTTGCGTTTAAA-CGC-A-AAGTT
1 TTGCGTTTAAACGCAAAAAACATTGCGTTTAAACACAAAGGTTTGCG-TTAAATCGCAATAAGTT
* ** *
519098 TTGCGTTTAAACGC-AAAGTTTTGCGTTTAAACGCAAAAG-TA
65 TTGCGTTTAAACGCAAAAG-ATTGCAATTAAACGCAAAAGCAA
* * *
519139 TTGCGTTTAAATGCAAAAAAATATTGCGTTTAAACGCAAAGGT
1 TTGCGTTTAAACGC-AAAAAACATTGCGTTTAAACACAAAGGT
519182 AATATTGCGT
Statistics
Matches: 123, Mismatches: 19, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
103 17 0.14
104 59 0.48
105 1 0.01
106 36 0.29
107 10 0.08
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.32
Consensus pattern (106 bp):
TTGCGTTTAAACGCAAAAAACATTGCGTTTAAACACAAAGGTTTGCGTTAAATCGCAATAAGTTT
TGCGTTTAAACGCAAAAGATTGCAATTAAACGCAAAAGCAA
Found at i:519321 original size:44 final size:42
Alignment explanation
Indices: 518930--519339 Score: 201
Period size: 42 Copynumber: 9.5 Consensus size: 42
518920 ATAATTTCTT
* * * * ** *
518930 TTGCGTTTAAACGCAATAACTATTGCGTTTAATCGC-AATCTT
1 TTGCGTTTAATCGCAA-AAGTTTTGCGTTTAAACGCAAAGGTA
* *
518972 TTGCGTTAAATCGCAATAAGTTTTGCGTTTAAACGCAAAAG-A
1 TTGCGTTTAATCGCAA-AAGTTTTGCGTTTAAACGCAAAGGTA
** * * ** * **
519014 TTGCAATTAAACGCAATAGCAATTGCTTTTAAACGCAAAGAACA
1 TTGCGTTTAATCGCAAAAG-TTTTGCGTTTAAACGCAAAG-GTA
* * *
519058 TTGCGTTTTAA-CAC-AAAGGTTTGCGTTTAAACGCAAA-GTT
1 TTGCG-TTTAATCGCAAAAGTTTTGCGTTTAAACGCAAAGGTA
* *
519098 TTGCGTTTAAACGC-AAAGTTTTGCGTTTAAACGCAAAAGTA
1 TTGCGTTTAATCGCAAAAGTTTTGCGTTTAAACGCAAAGGTA
* *
519139 TTGCGTTTAAAT-GCAAAAAAATATTGCGTTTAAACGCAAAGGTAATA
1 TTGCGTTT-AATCGC--AAAAGTTTTGCGTTTAAACGCAAAGG---TA
* * ** * * *
519186 TTGCGTTTTAA-CGCAATAATTTTTGTGAATAAACGCAATTGTTT
1 TTGCG-TTTAATCGCAA-AAGTTTTGCGTTTAAACGCAA-AGGTA
* * * * *
519230 TTGCGATTAAACGCAACAA-TTTTGCGATTAAACGCAATA-ATCG
1 TTGCGTTTAATCGCAA-AAGTTTTGCGTTTAAACGCAA-AGGT-A
* *
519273 TTGCGTTTAATCGCAAAAGGTATTGGGTTTAAACGCAATAGGTA
1 TTGCGTTTAATCGCAAAA-GTTTTGCGTTTAAACGCAA-AGGTA
* * *
519317 TTGCGTTTTATTGCAAAACTTTT
1 TTGCGTTTAATCGCAAAAGTTTT
519340 TTTTAAAATT
Statistics
Matches: 284, Mismatches: 61, Indels: 45
0.73 0.16 0.12
Matches are distributed among these distances:
39 5 0.02
40 29 0.10
41 14 0.05
42 80 0.28
43 43 0.15
44 75 0.26
45 7 0.02
46 16 0.06
47 12 0.04
48 3 0.01
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34
Consensus pattern (42 bp):
TTGCGTTTAATCGCAAAAGTTTTGCGTTTAAACGCAAAGGTA
Found at i:520462 original size:21 final size:21
Alignment explanation
Indices: 520420--520803 Score: 167
Period size: 22 Copynumber: 17.8 Consensus size: 21
520410 AAATGAAGTA
*
520420 ATTGCGATTAAACGCAAAAATC
1 ATTGCGTTTAAACGC-AAAATC
*
520442 ATTGCGTTTAATCGCAAAATC
1 ATTGCGTTTAAACGCAAAATC
* * *
520463 ATTGCATTTAATCGCAAAATG
1 ATTGCGTTTAAACGCAAAATC
* * *
520484 TTTGCGTTTAATCGCAAAAATT
1 ATTGCGTTTAAACGC-AAAATC
* *
520506 ATTGCGTTTAATCGCAAAAAC
1 ATTGCGTTTAAACGCAAAATC
* * * ** *
520527 GTTTGCATCTATTCGCAAAATAT
1 -ATTGCGTTTAAACGCAAAAT-C
520550 ATTGCGTTTAAACGCAATAATAGC
1 ATTGCGTTTAAACGCAA-AAT--C
* * *
520574 TTTGCGTTTAAACGCAATATTTGT
1 ATTGCGTTTAAACGCAA-A-AT-C
* * *
520598 TTTGTGTTTAAACGCAATGAT-
1 ATTGCGTTTAAACGCAA-AATC
* * *
520619 TTTGCGATTAAACGCAATA-C
1 ATTGCGTTTAAACGCAAAATC
*
520639 ATTGCGTTTAAACGCAGAA-C
1 ATTGCGTTTAAACGCAAAATC
*
520659 TTTGCGTTTAAACGC--AATCC
1 ATTGCGTTTAAACGCAAAAT-C
* * *
520679 ACTTTGCGTTTAATCGCATAACTT
1 A--TTGCGTTTAAACGCA-AAATC
* * *
520703 TTTGCGTTTTATCGC--AATC
1 ATTGCGTTTAAACGCAAAATC
*
520722 TTTTGCGTTTAAACGCAAAATAC
1 -ATTGCGTTTAAACGCAAAAT-C
** *
520745 ATTGCGAATAAACGCAAAA-G
1 ATTGCGTTTAAACGCAAAATC
* *
520765 ATTGCATTAAAACGCAATAA-C
1 ATTGCGTTTAAACGCAA-AATC
520786 TATTGCGATTT-AACGCAA
1 -ATTGCG-TTTAAACGCAA
520804 TATAAATTAA
Statistics
Matches: 283, Mismatches: 58, Indels: 42
0.74 0.15 0.11
Matches are distributed among these distances:
18 2 0.01
19 2 0.01
20 58 0.20
21 59 0.21
22 116 0.41
23 7 0.02
24 36 0.13
25 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (21 bp):
ATTGCGTTTAAACGCAAAATC
Found at i:520685 original size:22 final size:20
Alignment explanation
Indices: 520551--520805 Score: 149
Period size: 20 Copynumber: 11.9 Consensus size: 20
520541 GCAAAATATA
520551 TTGCGTTTAAACGCAATAATAGCT
1 TTGCGTTTAAACGC---AATA-CT
*
520575 TTGCGTTTAAACGCAATATTTGTT
1 TTGCGTTTAAACGCAATA----CT
* *
520599 TTGTGTTTAAACGCAATGATT
1 TTGCGTTTAAACGCAAT-ACT
* *
520620 TTGCGATTAAACGCAATACA
1 TTGCGTTTAAACGCAATACT
520640 TTGCGTTTAAACGCAGA-ACT
1 TTGCGTTTAAACGCA-ATACT
520660 TTGCGTTTAAACGCAATCCACT
1 TTGCGTTTAAACGCAAT--ACT
*
520682 TTGCGTTTAATCGC-ATAACTTT
1 TTGCGTTTAAACGCAAT-AC--T
* *
520704 TTGCGTTTTATCGCAAT-CTT
1 TTGCGTTTAAACGCAATAC-T
*
520724 TTGCGTTTAAACGCAAAATACA
1 TTGCGTTTAAACGC--AATACT
** * **
520746 TTGCGAATAAACGCAAAAGA
1 TTGCGTTTAAACGCAATACT
* *
520766 TTGCATTAAAACGCAATAACT
1 TTGCGTTTAAACGCAAT-ACT
520787 ATTGCGATTT-AACGCAATA
1 -TTGCG-TTTAAACGCAATA
520806 TAAATTAATT
Statistics
Matches: 187, Mismatches: 27, Indels: 37
0.75 0.11 0.15
Matches are distributed among these distances:
19 1 0.01
20 64 0.34
21 27 0.14
22 57 0.30
23 5 0.03
24 32 0.17
25 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Consensus pattern (20 bp):
TTGCGTTTAAACGCAATACT
Found at i:520702 original size:42 final size:42
Alignment explanation
Indices: 520618--520738 Score: 140
Period size: 42 Copynumber: 2.9 Consensus size: 42
520608 AACGCAATGA
* *
520618 TTTTGCGATTAAACGCAAT-ACATTGCGTTTAAACGCAGAAC
1 TTTTGCGTTTAAACGCAATCACTTTGCGTTTAAACGCAGAAC
* *
520659 -TTTGCGTTTAAACGCAATCCACTTTGCGTTTAATCGCATAAC
1 TTTTGCGTTTAAACGCAAT-CACTTTGCGTTTAAACGCAGAAC
* * *
520701 TTTTTGCGTTTTATCGCAATC-TTTTGCGTTTAAACGCA
1 -TTTTGCGTTTAAACGCAATCACTTTGCGTTTAAACGCA
520739 AAATACATTG
Statistics
Matches: 68, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
40 17 0.25
42 34 0.50
43 1 0.01
44 16 0.24
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (42 bp):
TTTTGCGTTTAAACGCAATCACTTTGCGTTTAAACGCAGAAC
Found at i:522291 original size:15 final size:16
Alignment explanation
Indices: 522224--522291 Score: 66
Period size: 16 Copynumber: 4.0 Consensus size: 16
522214 TTGTTAAAAT
522224 TTGGGGGCGAGTTGTC
1 TTGGGGGCGAGTTGTC
522240 TTGAGCTGGTGCCGAGTTGTC
1 TTG-G--GG-G-CGAGTTGTC
* *
522261 TTGGGGGTGAGATGTC
1 TTGGGGGCGAGTTGTC
522277 TT-GGGGCGAGTTGTC
1 TTGGGGGCGAGTTGTC
522292 CAGCATTCAT
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
15 11 0.26
16 12 0.28
17 2 0.05
18 2 0.05
19 2 0.05
20 2 0.05
21 12 0.28
ACGTcount: A:0.09, C:0.13, G:0.46, T:0.32
Consensus pattern (16 bp):
TTGGGGGCGAGTTGTC
Found at i:531141 original size:12 final size:12
Alignment explanation
Indices: 531124--531148 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
531114 GTCTATTATT
531124 TTAATATAGTAG
1 TTAATATAGTAG
531136 TTAATATAGTAG
1 TTAATATAGTAG
531148 T
1 T
531149 ATAGATTATT
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:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (12 bp):
TTAATATAGTAG
Found at i:536139 original size:382 final size:384
Alignment explanation
Indices: 535416--536157 Score: 953
Period size: 382 Copynumber: 1.9 Consensus size: 384
535406 TTACATCCCT
* * **
535416 TGTACTGTGTAAATTTTAAGTCCCCGTACAGGCTATAGTCGCCGTTTGATCTCAGGAATTTCTTC
1 TGTACTGTGTAAATTTTAAGTCCACGTACAGGCTATAGTCGCCGTTTAATCTCAGGAATTTAGTC
** *
535481 TTAATTGTTCAATCCGCTGCATATTTGGCAGAAAATAAGAATTGGGTCCGAGGTACATGTACACA
66 TTAATTGTTCAATCCGCTGCATATTTCACAGAAAATAAGAATGGGGTCCGAGGTACATGTACACA
* * *
535546 AAATTTCATTAGGATTGAGTAAGGGGCTCGGGAGTTAGAATTTTTTTCTACAGTACATGTCCAGC
131 AAATTTCATTAGGATTGAGTAAGGGGCTCGGGAGTTAGAATTTTTTTCTAAAGTACATGTCAAAC
* * * *
535611 AAGCCAATCAAAACTCGAATGCCAAAAAATTCATATCTTTCTTAAAAATGAACGAATAGGTCTGG
196 AAGACAATCAAAACTCAAATGCCAAAAAATTCATAACTCTCTTAAAAATGAACGAATAGGTCTGG
* * * ** * *
535676 TCATTAGTACAGTAATCTAGACTTGAAGTAGGTTGAAAAAAAAGGTTCAAGATGACAGATCCAGT
261 TAATTAGTACAGTAATCTAGAATGGAAGTAGGTTGAAAAAAAAGGCCCAAGATCAAAGATCCAGT
*
535741 AAAATCAGGCCAGAAAAACTAAATGATTTTGTGAAAACGAAAGGGGGGGGGTCGGTGGG
326 AAAATCAGGCCAGAAAAACTAAATGATTTTATGAAAACGAAAGGGGGGGGGTCGGTGGG
* *
535800 TGTACTGTGTAAA-TTTAATTTCCACGTATAGGC-ATTAAG-CGCCGTTTAAT-TCAGGAATTTA
1 TGTACTGTGTAAATTTTAA-GTCCACGTACAGGCTA-T-AGTCGCCGTTTAATCTCAGGAATTTA
* * * *
535861 GTCTTAATTGTTCAATCCGCTGCATATTTCACAGACAAA-CAGAATGGGGTCCGAGGTCCATTTT
63 GTCTTAATTGTTCAATCCGCTGCATATTTCACAGA-AAATAAGAATGGGGTCCGAGGTACATGTA
* * *
535925 CACGAATTTTCATTAGGATTGAGTGAA-GGGCTTGGGAGTTAGAATTTTTTT-TAAAGTACATGT
127 CACAAAATTTCATTAGGATTGAGT-AAGGGGCTCGGGAGTTAGAATTTTTTTCTAAAGTACATGT
* ** ** * ** *
535988 CAAACACGACAATTGAAACTCAAATGCCAAAACCTTCATAACTCTGTTATTAATGAACGAATTGG
191 CAAACAAGACAATCAAAACTCAAATGCCAAAAAATTCATAACTCTCTTAAAAATGAACGAATAGG
** **
536053 TCTGGTAATTAGTACAGTAATCTAGAATGGTATTTA-GTTGAAATTAAAGGCCCAAGATCAAAGA
256 TCTGGTAATTAGTACAGTAATCTAGAATGG-AAGTAGGTTGAAAAAAAAGGCCCAAGATCAAAGA
*
536117 -CCAAGTAAAATCGGGCCAGAAAAACTAAATGATTTTATGAA
320 TCC-AGTAAAATCAGGCCAGAAAAACTAAATGATTTTATGAA
536158 TTGGGAGGGG
Statistics
Matches: 306, Mismatches: 45, Indels: 16
0.83 0.12 0.04
Matches are distributed among these distances:
381 2 0.01
382 146 0.48
383 116 0.38
384 40 0.13
385 2 0.01
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (384 bp):
TGTACTGTGTAAATTTTAAGTCCACGTACAGGCTATAGTCGCCGTTTAATCTCAGGAATTTAGTC
TTAATTGTTCAATCCGCTGCATATTTCACAGAAAATAAGAATGGGGTCCGAGGTACATGTACACA
AAATTTCATTAGGATTGAGTAAGGGGCTCGGGAGTTAGAATTTTTTTCTAAAGTACATGTCAAAC
AAGACAATCAAAACTCAAATGCCAAAAAATTCATAACTCTCTTAAAAATGAACGAATAGGTCTGG
TAATTAGTACAGTAATCTAGAATGGAAGTAGGTTGAAAAAAAAGGCCCAAGATCAAAGATCCAGT
AAAATCAGGCCAGAAAAACTAAATGATTTTATGAAAACGAAAGGGGGGGGGTCGGTGGG
Found at i:537392 original size:63 final size:63
Alignment explanation
Indices: 537315--537443 Score: 240
Period size: 63 Copynumber: 2.0 Consensus size: 63
537305 AAAAAAATAA
* *
537315 TAATAATAGGGGAAAAGAAACAAAGCAATAACAATAAGGTCTTCCGTTGGAAACGGAAGACCT
1 TAATAATAGAGGAAAAGAAACAAAGCAATAACAATAAGGTATTCCGTTGGAAACGGAAGACCT
537378 TAATAATAGAGGAAAAGAAACAAAGCAATAACAATAAGGTATTCCGTTGGAAACGGAAGACCT
1 TAATAATAGAGGAAAAGAAACAAAGCAATAACAATAAGGTATTCCGTTGGAAACGGAAGACCT
537441 TAA
1 TAA
537444 CTAAAGGTTC
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.48, C:0.13, G:0.21, T:0.18
Consensus pattern (63 bp):
TAATAATAGAGGAAAAGAAACAAAGCAATAACAATAAGGTATTCCGTTGGAAACGGAAGACCT
Found at i:544582 original size:2 final size:2
Alignment explanation
Indices: 544575--544615 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
544565 TCAACTCTAA
544575 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
544616 NNNNNNNNNN
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:567558 original size:12 final size:12
Alignment explanation
Indices: 567541--567575 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
567531 ATACTTCTTC
567541 TCCATCATAATA
1 TCCATCATAATA
567553 TCCATCATAATA
1 TCCATCATAATA
567565 TCCATCATAAT
1 TCCATCATAAT
567576 TAAGTAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.34
Consensus pattern (12 bp):
TCCATCATAATA
Found at i:570473 original size:25 final size:25
Alignment explanation
Indices: 570418--570483 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 25
570408 TTAAGATTGC
* *
570418 TTTTTGTGTTCGTTTTTATTGTTTGG
1 TTTTTTTGTT-GTTTTTATTGTATGG
570444 -TTTTTTGTTGTTTTT-TTGGTATGG
1 TTTTTTTGTTGTTTTTATT-GTATGG
*
570468 TGTTTTTTGTGGTTTT
1 T-TTTTTTGTTGTTTT
570484 GGGGGTGGGG
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
23 2 0.06
24 11 0.32
25 8 0.24
26 13 0.38
ACGTcount: A:0.03, C:0.02, G:0.24, T:0.71
Consensus pattern (25 bp):
TTTTTTTGTTGTTTTTATTGTATGG
Found at i:573687 original size:7 final size:7
Alignment explanation
Indices: 573677--573764 Score: 86
Period size: 7 Copynumber: 12.6 Consensus size: 7
573667 GAAAAGGATC
*
573677 ATTCGAT
1 ATTCGAG
573684 ATTCGAG
1 ATTCGAG
* *
573691 ATTCAAA
1 ATTCGAG
*
573698 ATACGAG
1 ATTCGAG
*
573705 ATTCGAA
1 ATTCGAG
*
573712 ATACGAG
1 ATTCGAG
573719 ATTCGAG
1 ATTCGAG
*
573726 ATTCGAA
1 ATTCGAG
* *
573733 ATACGCG
1 ATTCGAG
573740 ATTCGAG
1 ATTCGAG
*
573747 ATTCGAA
1 ATTCGAG
573754 ATTCGAG
1 ATTCGAG
573761 ATTC
1 ATTC
573765 AATATCTAAA
Statistics
Matches: 62, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
7 62 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.27
Consensus pattern (7 bp):
ATTCGAG
Found at i:573710 original size:21 final size:21
Alignment explanation
Indices: 573701--573764 Score: 110
Period size: 21 Copynumber: 3.0 Consensus size: 21
573691 ATTCAAAATA
573701 CGAGATTCGAAATACGAGATT
1 CGAGATTCGAAATACGAGATT
*
573722 CGAGATTCGAAATACGCGATT
1 CGAGATTCGAAATACGAGATT
*
573743 CGAGATTCGAAATTCGAGATT
1 CGAGATTCGAAATACGAGATT
573764 C
1 C
573765 AATATCTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.25
Consensus pattern (21 bp):
CGAGATTCGAAATACGAGATT
Found at i:573723 original size:14 final size:14
Alignment explanation
Indices: 573677--573764 Score: 95
Period size: 14 Copynumber: 6.3 Consensus size: 14
573667 GAAAAGGATC
*
573677 ATTCGATATTCGAG
1 ATTCGAAATTCGAG
* *
573691 ATTCAAAATACGAG
1 ATTCGAAATTCGAG
*
573705 ATTCGAAATACGAG
1 ATTCGAAATTCGAG
* *
573719 ATTCGAGATTCGAA
1 ATTCGAAATTCGAG
* **
573733 ATACGCGATTCGAG
1 ATTCGAAATTCGAG
573747 ATTCGAAATTCGAG
1 ATTCGAAATTCGAG
573761 ATTC
1 ATTC
573765 AATATCTAAA
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 61 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.27
Consensus pattern (14 bp):
ATTCGAAATTCGAG
Found at i:581062 original size:23 final size:23
Alignment explanation
Indices: 581036--581107 Score: 144
Period size: 23 Copynumber: 3.1 Consensus size: 23
581026 TTATGTTATC
581036 GAATTTGATGCTGTCCTTTGTTT
1 GAATTTGATGCTGTCCTTTGTTT
581059 GAATTTGATGCTGTCCTTTGTTT
1 GAATTTGATGCTGTCCTTTGTTT
581082 GAATTTGATGCTGTCCTTTGTTT
1 GAATTTGATGCTGTCCTTTGTTT
581105 GAA
1 GAA
581108 CTCAATATAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.15, C:0.12, G:0.22, T:0.50
Consensus pattern (23 bp):
GAATTTGATGCTGTCCTTTGTTT
Found at i:584143 original size:3 final size:3
Alignment explanation
Indices: 584137--584164 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
584127 ATCATCATGA
584137 CCT CCT CCT CCT CCT CCT CCT CCT CCT C
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT C
584165 ATTATCAACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (3 bp):
CCT
Found at i:584181 original size:15 final size:15
Alignment explanation
Indices: 584163--584208 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
584153 CTCCTCCTCC
*
584163 TCATTATCAACGTCA
1 TCATTATCATCGTCA
*
584178 TC---ATCATCGTTA
1 TCATTATCATCGTCA
584190 TCATTATCATCGTCA
1 TCATTATCATCGTCA
584205 TCAT
1 TCAT
584209 CATCGTTATC
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
12 10 0.40
15 15 0.60
ACGTcount: A:0.28, C:0.26, G:0.07, T:0.39
Consensus pattern (15 bp):
TCATTATCATCGTCA
Found at i:584227 original size:27 final size:27
Alignment explanation
Indices: 584163--584218 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
584153 CTCCTCCTCC
*
584163 TCATTATCAACGTCATCATCATCGTTA
1 TCATTATCATCGTCATCATCATCGTTA
584190 TCATTATCATCGTCATCATCATCGTTA
1 TCATTATCATCGTCATCATCATCGTTA
584217 TC
1 TC
584219 GTATTCATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.27, C:0.27, G:0.07, T:0.39
Consensus pattern (27 bp):
TCATTATCATCGTCATCATCATCGTTA
Found at i:592594 original size:2 final size:2
Alignment explanation
Indices: 592587--592638 Score: 70
Period size: 2 Copynumber: 26.0 Consensus size: 2
592577 GGACATTTAA
*
592587 TC TC TC TC TC TC TC TC TC TC TC TC TC AT- TC TC CC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC -TC TC TC TC TC TC TC TC
*
592629 CC TC TC TC TC
1 TC TC TC TC TC
592639 AAGCTTGCAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
1 1 0.02
2 42 0.95
3 1 0.02
ACGTcount: A:0.02, C:0.52, G:0.00, T:0.46
Consensus pattern (2 bp):
TC
Found at i:594579 original size:112 final size:112
Alignment explanation
Indices: 594373--594595 Score: 392
Period size: 112 Copynumber: 2.0 Consensus size: 112
594363 AGTTTTGTTC
*
594373 GTTTGGGTATATCTAATTAGAGGCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACACA
1 GTTTGGGTATATCTAATTAAAGGCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACACA
* *
594438 GAATATACAAGATATACACAGCAGTTGTGTCGTGTGCCCAGGTGCAT
66 GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCAT
* * *
594485 GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTCCAACTTAGGAAAACCCCTGGAACTAACACA
1 GTTTGGGTATATCTAATTAAAGGCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACACA
594550 GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCA
66 GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCA
594596 CGTCAGGGTT
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
112 105 1.00
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.29
Consensus pattern (112 bp):
GTTTGGGTATATCTAATTAAAGGCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACACA
GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCAT
Found at i:595621 original size:11 final size:11
Alignment explanation
Indices: 595607--595660 Score: 99
Period size: 11 Copynumber: 4.9 Consensus size: 11
595597 TTTTTTTTAA
595607 TGGCTTAAAGG
1 TGGCTTAAAGG
595618 TGGCTTAAAGG
1 TGGCTTAAAGG
*
595629 TAGCTTAAAGG
1 TGGCTTAAAGG
595640 TGGCTTAAAGG
1 TGGCTTAAAGG
595651 TGGCTTAAAG
1 TGGCTTAAAG
595661 AAGTTTGGAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 41 1.00
ACGTcount: A:0.30, C:0.09, G:0.33, T:0.28
Consensus pattern (11 bp):
TGGCTTAAAGG
Found at i:595708 original size:11 final size:11
Alignment explanation
Indices: 595692--595720 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
595682 ATAAGTTGTC
595692 CTTAAAGGTGG
1 CTTAAAGGTGG
595703 CTTAAAGGTGG
1 CTTAAAGGTGG
595714 CTTAAAG
1 CTTAAAG
595721 ATAGTCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.28
Consensus pattern (11 bp):
CTTAAAGGTGG
Found at i:595802 original size:11 final size:11
Alignment explanation
Indices: 595786--595817 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
595776 GCAATACATA
595786 TAGCTTAAAGG
1 TAGCTTAAAGG
595797 TAGCTTAAAGG
1 TAGCTTAAAGG
*
595808 TGGCTTAAAG
1 TAGCTTAAAG
595818 ATCGTCTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.34, C:0.09, G:0.28, T:0.28
Consensus pattern (11 bp):
TAGCTTAAAGG
Found at i:595839 original size:11 final size:11
Alignment explanation
Indices: 595823--595861 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
595813 TAAAGATCGT
595823 CTTTAAGCTAC
1 CTTTAAGCTAC
*
595834 CTTTAAAC-AC
1 CTTTAAGCTAC
*
595844 CTTTAAGCTAT
1 CTTTAAGCTAC
595855 CTTTAAG
1 CTTTAAG
595862 GAGGACTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (11 bp):
CTTTAAGCTAC
Found at i:596781 original size:33 final size:31
Alignment explanation
Indices: 596703--596769 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
596693 ACAATGGTAA
596703 CATTCTCAGCAGTTATCTCTCTTTGCCCATT
1 CATTCTCAGCAGTTATCTCTCTTTGCCCATT
596734 CATTCTCAGCAGTTATCTCTCTTTGCCCATT
1 CATTCTCAGCAGTTATCTCTCTTTGCCCATT
596765 C-TTCT
1 CATTCT
596770 TATGCATAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 4 0.11
31 32 0.89
ACGTcount: A:0.15, C:0.33, G:0.09, T:0.43
Consensus pattern (31 bp):
CATTCTCAGCAGTTATCTCTCTTTGCCCATT
Found at i:596970 original size:16 final size:16
Alignment explanation
Indices: 596949--596986 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
596939 ACGGAAGAGT
*
596949 GACAGACGGACGGACG
1 GACAGAAGGACGGACG
596965 GACAGAAGGACGGACG
1 GACAGAAGGACGGACG
596981 GACAGA
1 GACAGA
596987 GTGATTACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.37, C:0.21, G:0.42, T:0.00
Consensus pattern (16 bp):
GACAGAAGGACGGACG
Found at i:599480 original size:177 final size:179
Alignment explanation
Indices: 599107--599644 Score: 947
Period size: 177 Copynumber: 3.0 Consensus size: 179
599097 CGGCTGCCAG
* *
599107 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAATTCTCAAGATAGGAAGTTGTTCTTTTGCA
*
599172 GATCAATTTTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTTATCG-
66 GATCAATTGTACATATATCAGAGGTGTGCATATT-CTAGGATTTTGATTTCCGATAATTTAT-GA
*
599236 AAAAAATACTAGCTTTTGAACTAAGTCATTTTTTGGCAAAATATTGCATAT
129 AAAAAATACTAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
*
599287 AGGGAACCCTCATTGTACGGATAACTCCTCCTACAATTCTCAAGATAGGAAGTTGTTCTTTTGCA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAATTCTCAAGATAGGAAGTTGTTCTTTTGCA
*
599352 GATCAATTGTACATATATCAGAGGTGTGCATA-T-TAGGATTTTGATTTCCGATAATTTGTGAAA
66 GATCAATTGTACATATATCAGAGGTGTGCATATTCTAGGATTTTGATTTCCGATAATTTATGAAA
*
599415 AAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
131 AAAATACTAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
599464 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAATTCTCAAGATAGGAAGTTGTTCTTTTGCA
1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAATTCTCAAGATAGGAAGTTGTTCTTTTGCA
599529 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTTATGAA
66 GATCAATTGTACATATATCAGAGGTGTGCATATT-CTAGGATTTTGATTTCCGATAATTTATGAA
* *
599594 AAAAATACTAGCTTTTGAACTTGGTCATTTTTTGGCAAAATGTTGCATAT
130 AAAAATACTAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
599644 A
1 A
599645 CATGTAGGGT
Statistics
Matches: 342, Mismatches: 12, Indels: 8
0.94 0.03 0.02
Matches are distributed among these distances:
176 1 0.00
177 170 0.50
178 1 0.00
179 1 0.00
180 169 0.49
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (179 bp):
AGGGTACCCTCATTGTACGGATAACTCCTCCTACAATTCTCAAGATAGGAAGTTGTTCTTTTGCA
GATCAATTGTACATATATCAGAGGTGTGCATATTCTAGGATTTTGATTTCCGATAATTTATGAAA
AAAATACTAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT
Found at i:600492 original size:168 final size:167
Alignment explanation
Indices: 599976--600594 Score: 718
Period size: 168 Copynumber: 3.7 Consensus size: 167
599966 CCATATTTTC
* * * ** *
599976 AAAAATCTTCTTCTCTACTCCCACGCA--TGAGGAAAAAACCGGTTGCATGGTTATGATGTCCAT
1 AAAAATCTTCTTCTCTACTCCCACACATGTGAGCAAAAAACTGAATACATGGTTATGATGTCCAT
* ** * *
600039 GAAGCCCTCTACCAAAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGGCTCTAGGGTGGG
66 G-AGGCCTCTACCAAAATTGTGAAATTCATGACCCCTTTGTTAGGTGTTCAGGCTCTAGGGTGGG
* *
600104 GCCAATATGGCCAAATAGTAAAAAC-GTATTAAATCTTA
130 GCCAATATGGCCATATAGT-AAAACTGTTTTAAATCTTA
* * * * * ** * * *
600142 GAAAATCTTTTTCTTTACTCCCATATACATGTATATTTGTTAAAAACTAAATGCATAGTTATGAT
1 AAAAATCTTCTTCTCTACTCCC--ACACATGT-GA---GCAAAAAACTGAATACATGGTTATGAT
*
600207 GTCCATGAGGCCCTCTACCAAAATTGTAAAATTCATGACCCCTTTGTTAGGTG-T-----TC-AG
60 GTCCATGAGG-CCTCTACCAAAATTGTGAAATTCATGACCCCTTTGTTAGGTGTTCAGGCTCTAG
600265 GGTGGGGCCAATATGGCCATATAGTAAAACTGTTTTAAATCTTA
124 GGTGGGGCCAATATGGCCATATAGTAAAACTGTTTTAAATCTTA
600309 AAAAATCTTCTTCTCTACTCCCACACATGTGAGCAAAAAACTGAATACATGGTTATGATGTCCAT
1 AAAAATCTTCTTCTCTACTCCCACACATGTGAGCAAAAAACTGAATACATGGTTATGATGTCCAT
* *
600374 GAGTGCCTCTACTAAGATTGTGAAATTCATGACCCCTTTGTTAGGTGTTCAGGCTCTAGGGTGGG
66 GAG-GCCTCTACCAAAATTGTGAAATTCATGACCCCTTTGTTAGGTGTTCAGGCTCTAGGGTGGG
600439 GCCAATATGGCCATATAGTAAAACTGTTTTAAATCTTA
130 GCCAATATGGCCATATAGTAAAACTGTTTTAAATCTTA
* * *
600477 AAAAATCTTCTTCTCTACTCCCACACATGTGGGCAAAAAACTGAATACATGGTTATGATATCCAC
1 AAAAATCTTCTTCTCTACTCCCACACATGTGAGCAAAAAACTGAATACATGGTTATGATGTCCAT
* ** * * * * * * *
600542 AATCTCCTTTACCTAAATTGTGTAATTCATGGCCCCTTGGTCAGGGGTTCAGG
66 GA-GGCCTCTACCAAAATTGTGAAATTCATGACCCCTTTGTTAGGTGTTCAGG
600595 ACATGGAGGG
Statistics
Matches: 385, Mismatches: 49, Indels: 36
0.82 0.10 0.08
Matches are distributed among these distances:
161 70 0.18
162 2 0.01
164 1 0.00
165 7 0.02
166 24 0.06
167 59 0.15
168 153 0.40
170 1 0.00
171 1 0.00
173 3 0.01
174 64 0.17
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (167 bp):
AAAAATCTTCTTCTCTACTCCCACACATGTGAGCAAAAAACTGAATACATGGTTATGATGTCCAT
GAGGCCTCTACCAAAATTGTGAAATTCATGACCCCTTTGTTAGGTGTTCAGGCTCTAGGGTGGGG
CCAATATGGCCATATAGTAAAACTGTTTTAAATCTTA
Found at i:606097 original size:4 final size:4
Alignment explanation
Indices: 606090--606129 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
606080 CTCTGAGACA
* * *
606090 GACG GACG GACG GACA GACA GACG GACT GACG GACG GACG
1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG
606130 CAGAGGAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.30, C:0.25, G:0.42, T:0.03
Consensus pattern (4 bp):
GACG
Found at i:606110 original size:20 final size:20
Alignment explanation
Indices: 606085--606124 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
606075 TCCGCCTCTG
606085 AGACAGACGGACGGACGGAC
1 AGACAGACGGACGGACGGAC
*
606105 AGACAGACGGACTGACGGAC
1 AGACAGACGGACGGACGGAC
606125 GGACGCAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.25, G:0.38, T:0.03
Consensus pattern (20 bp):
AGACAGACGGACGGACGGAC
Found at i:606492 original size:21 final size:22
Alignment explanation
Indices: 606457--606498 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
606447 CTGCTATAAC
* *
606457 TGTCCGATGCTTGGT-AAATAT
1 TGTCCGATCCATGGTGAAATAT
606478 TGTCCGATCCATGGTGAAATA
1 TGTCCGATCCATGGTGAAATA
606499 GTTCAACACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (22 bp):
TGTCCGATCCATGGTGAAATAT
Found at i:608680 original size:181 final size:181
Alignment explanation
Indices: 608345--608699 Score: 416
Period size: 181 Copynumber: 2.0 Consensus size: 181
608335 AATTTAAGGC
* * *
608345 AAAATCTTTTTATTTGGAAATTACACCCCCATGAAGGAGCCCATATTCTTCGTTTTAACGTTAAC
1 AAAATCTTTTTATTTAGAAATTACACCCCCATGAAGGAACCCATATTCTTCATTTTAACGTTAAC
* * *
608410 AAACTGATATAATTAAACGCTTAAGAGACTCCCTAAATCTTTAGGTATGAATACTTACGCCCTAA
66 AAAATGATATAATTAAACGCTTAAGAGACTCCCTAAAACTTTAGGTATGAATACTTACACCCTAA
*
608475 TATAACCTTAATTACATGAATACAAAGAAATAAACAGCATTAGTCAATTGA
131 TATAACCTTAAGTACATGAATACAAAGAAATAAACAGCATTAGTCAATTGA
* * *
608526 AAAATCTTTTTATTTAGAAATTACATCCCCATGAATGAACCCATATTCTTCATTTTAACTTTAA-
1 AAAATCTTTTTATTTAGAAATTACACCCCCATGAAGGAACCCATATTCTTCATTTTAACGTTAAC
* * * * *
608590 AAAATGGATATAGTTTAACGCTT-AGTAGAC-CTCTTAAAACTTTTGAG-AT-TATGACTTACAC
66 AAAAT-GATATAATTAAACGCTTAAG-AGACTC-CCTAAAACTTTAG-GTATGAAT-ACTTACAC
*** * * * *
608651 CCTCAAT-TCTTCTTTAGTACATTAATACAAAGAAATAATCAGCTTTAGT
126 CCT-AATATAACCTTAAGTACATGAATACAAAGAAATAAACAGCATTAGT
608700 TTCAGAAAAA
Statistics
Matches: 146, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
180 9 0.06
181 133 0.91
182 4 0.03
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.34
Consensus pattern (181 bp):
AAAATCTTTTTATTTAGAAATTACACCCCCATGAAGGAACCCATATTCTTCATTTTAACGTTAAC
AAAATGATATAATTAAACGCTTAAGAGACTCCCTAAAACTTTAGGTATGAATACTTACACCCTAA
TATAACCTTAAGTACATGAATACAAAGAAATAAACAGCATTAGTCAATTGA
Found at i:609433 original size:166 final size:166
Alignment explanation
Indices: 608827--609783 Score: 1361
Period size: 166 Copynumber: 5.8 Consensus size: 166
608817 GTGAATATGC
* * * * * * *
608827 AAAATAAGCAAAGTCGACATTTAACAGAAAGCTGGCATCCGATTGGTACAGAAATATATCCCACA
1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACATCCGATTGGTACAAAAATATATCCCACG
* * *
608892 ATATGGCATGCCTATACAAATAGTGTGTTAAAATTTCAAGCATCTGCGATAAATAGCTGCTAAGA
66 ATATGGCATGCCTATACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAGA
*
608957 AATCTTTGAGGAAAATTTGTTTGAAAATTTTGGCT-
131 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTA
* * *
608992 AAAATAAACAAAGTAC-TCATTTAACAGGAAGATGACGTCTGATTGGTACAAAAATATATCCCAC
1 AAAATAAACAAAGT-CGTCATTTAACAGGAAGTTGACATCCGATTGGTACAAAAATATATCCCAC
* *
609056 GATATGGCATGCCT-TAACAAACACTGTGTAAAAATTTCAAGCATCTCCGATAAATAGCTGCTGA
65 GATATGGCATGCCTAT-ACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGCTGCTGA
* *
609120 GAAATCTTTGACGAAAATTTGTTTAAAAATTTTGGCAA
129 GAAATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTA
* * * *
609158 AAAATAAAC--AGTCATTATTTAACAGGAAGTTGACATCCGATTGATACAAAAATATATCCCACA
1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACATCCGATTGGTACAAAAATATATCCCACG
* * * * *
609221 ATATGGCATGCCAAAACAAATAGTGTGTTAAAATTTTAAGCATCTGCGATAAATAGCTGCTGAGA
66 ATATGGCATGCCTATACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAGA
*
609286 AATCTTTGACAAAAATTTGTTTGAAAATTTTGGCTA
131 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTA
* * * *
609322 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACACCCGATTGGTAGAGAAATATATCCCACC
1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACATCCGATTGGTACAAAAATATATCCCACG
* * * * *
609387 ATATGGAATGCCTATACAAATATTGTGTAAAAATTTCGAGCATCTGCAATAAATAGTTGCTGAGA
66 ATATGGCATGCCTATACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAGA
609452 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTA
131 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTA
* * *
609488 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGA-AGTCTGATTGGTACAAAAATACATCCTAC
1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACA-TCCGATTGGTACAAAAATATATCCCAC
* * * * *
609552 GATATAGCACGCCTATACAAATACTGTGTAAAAATTTCAAGCATCTGCAATAAACAGTTGCTGAG
65 GATATGGCATGCCTATACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAG
* *
609617 AATTCTTTGACGGAAATTTGTTTGAAAATTTTGGCTA
130 AAATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTA
* *
609654 AAAATAAACAAAGTCATCATTTAACAGGAAGTTGATATCCGATTGGTACAAAAATATATCCCACG
1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACATCCGATTGGTACAAAAATATATCCCACG
* * *
609719 ATATGGCATGCCT-TAACAAACACTGTGTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG
66 ATATGGCATGCCTAT-ACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAG
609783 A
130 A
609784 TAAATGCGAC
Statistics
Matches: 707, Mismatches: 75, Indels: 19
0.88 0.09 0.02
Matches are distributed among these distances:
163 1 0.00
164 146 0.21
165 146 0.21
166 413 0.58
167 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (166 bp):
AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACATCCGATTGGTACAAAAATATATCCCACG
ATATGGCATGCCTATACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAGA
AATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTA
Found at i:609819 original size:4 final size:4
Alignment explanation
Indices: 609810--609877 Score: 109
Period size: 4 Copynumber: 17.0 Consensus size: 4
609800 TTTTGTTACG
* *
609810 GACA GACA GACA GACG GACA GACA GACA GACA GACA GACA GACA GACG
1 GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA
*
609858 GACG GACA GACA GACA GACA
1 GACA GACA GACA GACA GACA
609878 CACAAGGGTA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 60 1.00
ACGTcount: A:0.46, C:0.25, G:0.29, T:0.00
Consensus pattern (4 bp):
GACA
Found at i:610254 original size:8 final size:8
Alignment explanation
Indices: 610241--610293 Score: 88
Period size: 8 Copynumber: 6.6 Consensus size: 8
610231 TGCGTCTACA
610241 GACAGACG
1 GACAGACG
610249 GACAGACG
1 GACAGACG
610257 GACAGACG
1 GACAGACG
610265 GACAGACG
1 GACAGACG
* *
610273 GACGGACA
1 GACAGACG
610281 GACAGACG
1 GACAGACG
610289 GACAG
1 GACAG
610294 GGTGAAACCA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 41 1.00
ACGTcount: A:0.38, C:0.25, G:0.38, T:0.00
Consensus pattern (8 bp):
GACAGACG
Found at i:610255 original size:12 final size:12
Alignment explanation
Indices: 610241--610293 Score: 70
Period size: 12 Copynumber: 4.4 Consensus size: 12
610231 TGCGTCTACA
* *
610241 GACAGACGGACA
1 GACAGACAGACG
*
610253 GACGGACAGACG
1 GACAGACAGACG
*
610265 GACAGACGGACG
1 GACAGACAGACG
610277 GACAGACAGACG
1 GACAGACAGACG
610289 GACAG
1 GACAG
610294 GGTGAAACCA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.38, C:0.25, G:0.38, T:0.00
Consensus pattern (12 bp):
GACAGACAGACG
Found at i:611260 original size:21 final size:21
Alignment explanation
Indices: 611024--611271 Score: 162
Period size: 21 Copynumber: 11.8 Consensus size: 21
611014 ACCCTTACCA
* * *
611024 TCCCCATTCTGTTCACAGCTC
1 TCCCCATTCTGCTCACAGATT
*
611045 TCCCCATTCTGC-CGACACATT
1 TCCCCATTCTGCTC-ACAGATT
* * *
611066 TCCCCACTT-TTCTGAAAGATT
1 TCCCCA-TTCTGCTCACAGATT
* *
611087 TCCCCTTTCTGTTCACAGATT
1 TCCCCATTCTGCTCACAGATT
* * * * * *
611108 CCCCCATTCAGCTGATATAGT
1 TCCCCATTCTGCTCACAGATT
* * * *
611129 TCTCCTTTCTGGTCACAGATA
1 TCCCCATTCTGCTCACAGATT
*
611150 TCCCCATT-TAGCTTACAGATT
1 TCCCCATTCT-GCTCACAGATT
* * *
611171 TCCCCTTTCTGTTCACAGATA
1 TCCCCATTCTGCTCACAGATT
*
611192 TCCCCATT-TAGCTTACAGATT
1 TCCCCATTCT-GCTCACAGATT
* *
611213 TCCCCTTTCTGTTCACAGATT
1 TCCCCATTCTGCTCACAGATT
* * *
611234 CCCCCATTCTGCTGACAGGTT
1 TCCCCATTCTGCTCACAGATT
*
611255 TCCCCATTTTGCTCACA
1 TCCCCATTCTGCTCACA
611272 ATGCCCCCCA
Statistics
Matches: 164, Mismatches: 55, Indels: 16
0.70 0.23 0.07
Matches are distributed among these distances:
20 5 0.03
21 155 0.95
22 4 0.02
ACGTcount: A:0.19, C:0.34, G:0.11, T:0.36
Consensus pattern (21 bp):
TCCCCATTCTGCTCACAGATT
Found at i:611271 original size:42 final size:42
Alignment explanation
Indices: 611077--611284 Score: 228
Period size: 42 Copynumber: 5.0 Consensus size: 42
611067 CCCCACTTTT
* *
611077 CTGAAAGATTTCCCCTTTCTGTTCACAGATTCCCCCATTCAG
1 CTGACAGATTTCCCCTTTCTGTTCACAGATTCCCCCATTTAG
* * * * *
611119 CTGATATAGTTCTCCTTTCTGGTCACAGATAT-CCCCATTTAG
1 CTGACAGATTTCCCCTTTCTGTTCACAGAT-TCCCCCATTTAG
*
611161 CTTACAGATTTCCCCTTTCTGTTCACAGATAT-CCCCATTTAG
1 CTGACAGATTTCCCCTTTCTGTTCACAGAT-TCCCCCATTTAG
*
611203 CTTACAGATTTCCCCTTTCTGTTCACAGATTCCCCCATTCT-G
1 CTGACAGATTTCCCCTTTCTGTTCACAGATTCCCCCATT-TAG
* * *
611245 CTGACAGGTTTCCCCATTT-TGCTCACA-ATGCCCCCCATTT
1 CTGACAGATTTCCCC-TTTCTGTTCACAGAT-TCCCCCATTT
611285 TGTACACAGT
Statistics
Matches: 145, Mismatches: 16, Indels: 11
0.84 0.09 0.06
Matches are distributed among these distances:
41 4 0.03
42 136 0.94
43 5 0.03
ACGTcount: A:0.20, C:0.33, G:0.12, T:0.36
Consensus pattern (42 bp):
CTGACAGATTTCCCCTTTCTGTTCACAGATTCCCCCATTTAG
Found at i:617484 original size:4 final size:4
Alignment explanation
Indices: 617475--617555 Score: 117
Period size: 4 Copynumber: 20.2 Consensus size: 4
617465 ATCTTTCCCC
* * * * *
617475 CTCT CTCT CTCT GTCT GTCT GTCT GTCT GTCT CTCT CTCT CTCT CTCT
1 CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT
617523 CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT C
1 CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT C
617556 AACATATGGC
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 75 1.00
ACGTcount: A:0.00, C:0.44, G:0.06, T:0.49
Consensus pattern (4 bp):
CTCT
Found at i:619307 original size:14 final size:14
Alignment explanation
Indices: 619288--619318 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
619278 AATAACTAAT
619288 CGATAAACTTACAA
1 CGATAAACTTACAA
*
619302 CGATAAACTTATAA
1 CGATAAACTTACAA
619316 CGA
1 CGA
619319 GACTACGGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.19, G:0.10, T:0.23
Consensus pattern (14 bp):
CGATAAACTTACAA
Found at i:621656 original size:162 final size:161
Alignment explanation
Indices: 621389--621685 Score: 576
Period size: 162 Copynumber: 1.8 Consensus size: 161
621379 TTGTAACCGA
*
621389 TATCTTTCTAATGATATTAACACAAGCGGATCCAGAAAATTTTTGCAGGGAGGTCCGACAGTTAT
1 TATCTTTCTAATGATATGAACACAAGCGGATCCAGAAAATTTTTGCAGGGAGGTCCGACAGTTAT
621454 TCAAGTTTGTCGTGGGTGGGGAAGGGGTGTCTCAGGCATAATTTTGGTATTTTTATGATGTAAAT
66 TCAAGTTTGTCGTGGGTGGGGAAGGGGTGTCTCAGGCATAATTTTGGTATTTTTATGATGTAAAT
621519 TTAAAGAAACTTGACTTTTGGGGGGGGGGGG
131 TTAAAGAAACTTGACTTTTGGGGGGGGGGGG
621550 NTATCTTTCTAATGATATGAACACAAGCGGATCCAGAAAATTTTTGCAGGGAGGTCCGACAGTTA
1 -TATCTTTCTAATGATATGAACACAAGCGGATCCAGAAAATTTTTGCAGGGAGGTCCGACAGTTA
621615 TTCAAGTTTGTCGTGGGTGGGGAAGGGGTGTCTCAGGCATAATTTTGGTATTTTTATGATGTAAA
65 TTCAAGTTTGTCGTGGGTGGGGAAGGGGTGTCTCAGGCATAATTTTGGTATTTTTATGATGTAAA
621680 TTTAAA
130 TTTAAA
621686 NTTTATACAT
Statistics
Matches: 134, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
162 134 1.00
ACGTcount: A:0.27, C:0.11, G:0.28, T:0.33
Consensus pattern (161 bp):
TATCTTTCTAATGATATGAACACAAGCGGATCCAGAAAATTTTTGCAGGGAGGTCCGACAGTTAT
TCAAGTTTGTCGTGGGTGGGGAAGGGGTGTCTCAGGCATAATTTTGGTATTTTTATGATGTAAAT
TTAAAGAAACTTGACTTTTGGGGGGGGGGGG
Found at i:622093 original size:16 final size:16
Alignment explanation
Indices: 622072--622106 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
622062 TACGAATTAC
622072 AACTAAAGATTACCAT
1 AACTAAAGATTACCAT
622088 AACTAAAGATTACCAT
1 AACTAAAGATTACCAT
622104 AAC
1 AAC
622107 AGGTTACAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.20, G:0.06, T:0.23
Consensus pattern (16 bp):
AACTAAAGATTACCAT
Found at i:626872 original size:41 final size:42
Alignment explanation
Indices: 626809--626890 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 42
626799 GCAAATTTTA
626809 ATTATTAAGAAAAGAAAAGAAAAATACATTTTAACAATGTAT
1 ATTATTAAGAAAAGAAAAGAAAAATACATTTTAACAATGTAT
* * *
626851 ATTATTAAGTATA-AAAAGAAAATTACATTTTAACAATGTA
1 ATTATTAAGAAAAGAAAAGAAAAATACATTTTAACAATGTA
626891 AACAAAAAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
41 26 0.70
42 11 0.30
ACGTcount: A:0.55, C:0.05, G:0.09, T:0.32
Consensus pattern (42 bp):
ATTATTAAGAAAAGAAAAGAAAAATACATTTTAACAATGTAT
Found at i:630641 original size:15 final size:15
Alignment explanation
Indices: 630621--630654 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
630611 ATATCATGAC
630621 ATCTACATACTAGGT
1 ATCTACATACTAGGT
630636 ATCTACATACTAGGT
1 ATCTACATACTAGGT
630651 ATCT
1 ATCT
630655 TACCTTTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (15 bp):
ATCTACATACTAGGT
Found at i:638038 original size:41 final size:41
Alignment explanation
Indices: 637993--638531 Score: 930
Period size: 41 Copynumber: 13.3 Consensus size: 41
637983 GTGGATACGA
*
637993 AACAGTACAGATTACTGGTAAATGTCCTGTGTAGGATATAC
1 AACAGTACAGATTACTGGTAAATGCCCTGTGTAGGATATAC
638034 AACAGTACAGATTACT-GT--ATGCCCTGTGTAGGATATAC
1 AACAGTACAGATTACTGGTAAATGCCCTGTGTAGGATATAC
638072 AACAGTACAGATTACTGGTAAATGCCCTGTGTAGGATATAC
1 AACAGTACAGATTACTGGTAAATGCCCTGTGTAGGATATAC
*
638113 AACAGTACAGATTACTGGTAAATGCCCTGTG-ATGGGTATAC
1 AACAGTACAGATTACTGGTAAATGCCCTGTGTA-GGATATAC
638154 AACAGTACAGATTACTGGTAAATGCCCTGTGTAGGATATAC
1 AACAGTACAGATTACTGGTAAATGCCCTGTGTAGGATATAC
* *
638195 AACAGTACAGATTACTGGTAAATGCCCTGTGAAGGGTATAC
1 AACAGTACAGATTACTGGTAAATGCCCTGTGTAGGATATAC
638236 AACAGTACAGATTACTGGTAAATGCCCTGTGTAGGATATAC
1 AACAGTACAGATTACTGGTAAATGCCCTGTGTAGGATATAC
*
638277 AACAGTACAGATTACTGGTAAATGCCCTGTGTAGGGTATAC
1 AACAGTACAGATTACTGGTAAATGCCCTGTGTAGGATATAC
*
638318 AACAGTACAGATTACT-GT--ATGCCCTGTTTAGGATATAC
1 AACAGTACAGATTACTGGTAAATGCCCTGTGTAGGATATAC
638356 AACAGTACAGATTACTGGTAAATGCCCTGTGTAGGATATAC
1 AACAGTACAGATTACTGGTAAATGCCCTGTGTAGGATATAC
638397 AACAGTACAGATTACTGGTAAATGCCCTGTGTAGGATATAC
1 AACAGTACAGATTACTGGTAAATGCCCTGTGTAGGATATAC
*
638438 AACAGTACCGATTACTGGTAAATGCCCTGTGTAGGATATAC
1 AACAGTACAGATTACTGGTAAATGCCCTGTGTAGGATATAC
* *
638479 AACAGTACAGATTACTGGTAAATGTCCTGTGTAGGGTATAC
1 AACAGTACAGATTACTGGTAAATGCCCTGTGTAGGATATAC
*
638520 AACAATACAGAT
1 AACAGTACAGAT
638532 GCAAAGTCCT
Statistics
Matches: 474, Mismatches: 16, Indels: 16
0.94 0.03 0.03
Matches are distributed among these distances:
38 69 0.15
39 4 0.01
40 5 0.01
41 395 0.83
42 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (41 bp):
AACAGTACAGATTACTGGTAAATGCCCTGTGTAGGATATAC
Found at i:638517 original size:284 final size:284
Alignment explanation
Indices: 637993--638531 Score: 990
Period size: 284 Copynumber: 1.9 Consensus size: 284
637983 GTGGATACGA
*
637993 AACAGTACAGATTACTGGTAAATGTCCTGTGTAGGATATACAACAGTACAGATTACTGTATGCCC
1 AACAGTACAGATTACTGGTAAATGCCCTGTGTAGGATATACAACAGTACAGATTACTGTATGCCC
638058 TGTGTAGGATATACAACAGTACAGATTACTGGTAAATGCCCTGTGTAGGATATACAACAGTACAG
66 TGTGTAGGATATACAACAGTACAGATTACTGGTAAATGCCCTGTGTAGGATATACAACAGTACAG
*
638123 ATTACTGGTAAATGCCCTGTGATGGGTATACAACAGTACAGATTACTGGTAAATGCCCTGTGTAG
131 ATTACTGGTAAATGCCCTGTGATGGATATACAACAGTACAGATTACTGGTAAATGCCCTGTGTAG
*
638188 GATATACAACAGTACAGATTACTGGTAAATGCCCTGTGAAGGGTATACAACAGTACAGATTACTG
196 GATATACAACAGTACAGATTACTGGTAAATGCCCTGTGAAGGGTATACAACAATACAGATTACTG
638253 GTAAATGCCCTGTGTAGGATATAC
261 GTAAATGCCCTGTGTAGGATATAC
*
638277 AACAGTACAGATTACTGGTAAATGCCCTGTGTAGGGTATACAACAGTACAGATTACTGTATGCCC
1 AACAGTACAGATTACTGGTAAATGCCCTGTGTAGGATATACAACAGTACAGATTACTGTATGCCC
*
638342 TGTTTAGGATATACAACAGTACAGATTACTGGTAAATGCCCTGTGTAGGATATACAACAGTACAG
66 TGTGTAGGATATACAACAGTACAGATTACTGGTAAATGCCCTGTGTAGGATATACAACAGTACAG
*
638407 ATTACTGGTAAATGCCCTGTG-TAGGATATACAACAGTACCGATTACTGGTAAATGCCCTGTGTA
131 ATTACTGGTAAATGCCCTGTGAT-GGATATACAACAGTACAGATTACTGGTAAATGCCCTGTGTA
* *
638471 GGATATACAACAGTACAGATTACTGGTAAATGTCCTGTGTAGGGTATACAACAATACAGAT
195 GGATATACAACAGTACAGATTACTGGTAAATGCCCTGTGAAGGGTATACAACAATACAGAT
638532 GCAAAGTCCT
Statistics
Matches: 246, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
283 1 0.00
284 245 1.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (284 bp):
AACAGTACAGATTACTGGTAAATGCCCTGTGTAGGATATACAACAGTACAGATTACTGTATGCCC
TGTGTAGGATATACAACAGTACAGATTACTGGTAAATGCCCTGTGTAGGATATACAACAGTACAG
ATTACTGGTAAATGCCCTGTGATGGATATACAACAGTACAGATTACTGGTAAATGCCCTGTGTAG
GATATACAACAGTACAGATTACTGGTAAATGCCCTGTGAAGGGTATACAACAATACAGATTACTG
GTAAATGCCCTGTGTAGGATATAC
Found at i:638805 original size:17 final size:17
Alignment explanation
Indices: 638783--638820 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
638773 AATGTTCTAT
* *
638783 ACACATGTTTACGTTAA
1 ACACATGATCACGTTAA
638800 ACACATGATCACGTTAA
1 ACACATGATCACGTTAA
638817 ACAC
1 ACAC
638821 TTTGAAAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.26
Consensus pattern (17 bp):
ACACATGATCACGTTAA
Found at i:647158 original size:40 final size:40
Alignment explanation
Indices: 647051--647242 Score: 187
Period size: 38 Copynumber: 4.8 Consensus size: 40
647041 GGTACCCCCA
* ** *
647051 TTAGTACTACAGTAAG-TACCTACAAAATATTGTGTCTTCC
1 TTAGTACTACACTAAGTTACC-ACCTAATATTGTGTCTCCC
* * *
647091 TTAGTAC-ATA-TAAGTGACCACCAAATATTGTGTCTCCC
1 TTAGTACTACACTAAGTTACCACCTAATATTGTGTCTCCC
*
647129 TTAGTACTACACTAAGTTACCATCTAATATTGT-T-TCCC
1 TTAGTACTACACTAAGTTACCACCTAATATTGTGTCTCCC
* *
647167 TTAGTACTAAACTAAGTTACTACCTAATATTGTGTCATCCC
1 TTAGTACTACACTAAGTTACCACCTAATATTGTGTC-TCCC
* * * * *
647208 ATTAGTACTACAGTTAGTGATCACTTAATATTGTG
1 -TTAGTACTACACTAAGTTACCACCTAATATTGTG
647243 CCCAATATTG
Statistics
Matches: 127, Mismatches: 18, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
38 62 0.49
39 9 0.07
40 25 0.20
41 4 0.03
42 27 0.21
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.36
Consensus pattern (40 bp):
TTAGTACTACACTAAGTTACCACCTAATATTGTGTCTCCC
Found at i:648667 original size:44 final size:44
Alignment explanation
Indices: 648603--649308 Score: 876
Period size: 44 Copynumber: 16.0 Consensus size: 44
648593 GACGGTCGAT
*
648603 TATCTCAGACAGAATGGTGAGTGTTACCTCAGTCATATTGAGAC
1 TATCTCAGACAGAATGGTGAGTGTTATCTCAGTCATATTGAGAC
* *
648647 AATCTCAGAGAGAATGGTGAGTGTTATCTCAGTCAT-TTCGAGAC
1 TATCTCAGACAGAATGGTGAGTGTTATCTCAGTCATATT-GAGAC
* * *
648691 TATCTCAGACAGAATGGTGAGTGTTTTCACAGTCGTATTGAGAC
1 TATCTCAGACAGAATGGTGAGTGTTATCTCAGTCATATTGAGAC
* * ** *
648735 AATCTCAGACAAAATGGCAAGTGTTATCTCAGTCAT-TTCAAGAC
1 TATCTCAGACAGAATGGTGAGTGTTATCTCAGTCATATT-GAGAC
* ** * *
648779 TATCTCAGAAAGAATGGCAAGTGTTATCTCAGTCTTAATGAGAC
1 TATCTCAGACAGAATGGTGAGTGTTATCTCAGTCATATTGAGAC
648823 TATCTCAGACAGAATGGTGAGTGTTATCTCAGTCATATTGAGAC
1 TATCTCAGACAGAATGGTGAGTGTTATCTCAGTCATATTGAGAC
** *
648867 TATCTCAGACAGAATGGCAAGTGTCATCTCAGTCATATTGAGAC
1 TATCTCAGACAGAATGGTGAGTGTTATCTCAGTCATATTGAGAC
* *
648911 TATCTCAGACAGAATGGTGAGAGTTATCTTAGTCATATTGAGAC
1 TATCTCAGACAGAATGGTGAGTGTTATCTCAGTCATATTGAGAC
* * ** ** *
648955 TAACTCAGACAGAATGGTGAGTGTTTTAACAGTTGTATTGAAAC
1 TATCTCAGACAGAATGGTGAGTGTTATCTCAGTCATATTGAGAC
* ** * **
648999 TATCTCAGACGGAATGGCAAGTGTCATCTCAGTTGTATTGAGAC
1 TATCTCAGACAGAATGGTGAGTGTTATCTCAGTCATATTGAGAC
*
649043 TATCTCAGACAGAATGGTGAGAGTTATCTCAGTCATATTGAGAC
1 TATCTCAGACAGAATGGTGAGTGTTATCTCAGTCATATTGAGAC
* * * ** *
649087 TAACTCAGACAGAATGGTGAGTGTTTTCACAGTTGTATTGAAAC
1 TATCTCAGACAGAATGGTGAGTGTTATCTCAGTCATATTGAGAC
** *
649131 TATCTCAGACAGAATGGCAAGTGTCATCTCAGTCATATTGAGAC
1 TATCTCAGACAGAATGGTGAGTGTTATCTCAGTCATATTGAGAC
* * *
649175 TATCTCAGACAAAATGGTGAGAGTTATCTCAGTCATATTGAGAT
1 TATCTCAGACAGAATGGTGAGTGTTATCTCAGTCATATTGAGAC
* * * ** *
649219 TATCTCAGACAGAATGATGAGTGTTTTCACAGTTGTATTGAGCC
1 TATCTCAGACAGAATGGTGAGTGTTATCTCAGTCATATTGAGAC
* * *
649263 AATATCAGACAGAATGGTGAGTGTTATCTCAGTCATAATGAGAC
1 TATCTCAGACAGAATGGTGAGTGTTATCTCAGTCATATTGAGAC
649307 TA
1 TA
649309 CTGTAGATTT
Statistics
Matches: 557, Mismatches: 101, Indels: 8
0.84 0.15 0.01
Matches are distributed among these distances:
43 4 0.01
44 550 0.99
45 3 0.01
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (44 bp):
TATCTCAGACAGAATGGTGAGTGTTATCTCAGTCATATTGAGAC
Found at i:648838 original size:20 final size:20
Alignment explanation
Indices: 648815--648926 Score: 62
Period size: 20 Copynumber: 5.2 Consensus size: 20
648805 TCTCAGTCTT
648815 AATGAGACTATCTCAGACAG
1 AATGAGACTATCTCAGACAG
** * *
648835 AATGGTGAGTGTTATCTCAGTCAT
1 AA---TGAG-ACTATCTCAGACAG
*
648859 ATTGAGACTATCTCAGACAG
1 AATGAGACTATCTCAGACAG
** * *
648879 AATGGCAAGTGTCATCTCAGTCAT
1 AAT-G--AGACT-ATCTCAGACAG
*
648903 ATTGAGACTATCTCAGACAG
1 AATGAGACTATCTCAGACAG
648923 AATG
1 AATG
648927 GTGAGAGTTA
Statistics
Matches: 64, Mismatches: 20, Indels: 16
0.64 0.20 0.16
Matches are distributed among these distances:
20 26 0.41
21 8 0.12
23 8 0.12
24 22 0.34
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (20 bp):
AATGAGACTATCTCAGACAG
Found at i:648841 original size:132 final size:132
Alignment explanation
Indices: 648603--649308 Score: 995
Period size: 132 Copynumber: 5.3 Consensus size: 132
648593 GACGGTCGAT
** * * * *
648603 TATCTCAGACAGAATGGTGAGTGTTACCTCAGTCATATTGAGACAATCTCAGAGAGAATGGTGAG
1 TATCTCAGACAGAATGGCAAGTGTCATCTCAGTCATATTGAGACTATCTCAGAAAGAATGGTGAG
* *
648668 TGTTATCTCAGTCAT-TTCGAGACTATCTCAGACAGAATGGTGAGTGTTTTCACAGTCGTATTGA
66 AGTTATCTCAGTCATATT-GAGACTATCTCAGACAGAATGGTGAGTGTTTTCACAGTTGTATTGA
648732 GAC
130 GAC
* * * * **
648735 AATCTCAGACAAAATGGCAAGTGTTATCTCAGTCAT-TTCAAGACTATCTCAGAAAGAATGGCAA
1 TATCTCAGACAGAATGGCAAGTGTCATCTCAGTCATATT-GAGACTATCTCAGAAAGAATGGTGA
* * * * * **
648799 GTGTTATCTCAGTCTTAATGAGACTATCTCAGACAGAATGGTGAGTGTTATCTCAGTCATATTGA
65 GAGTTATCTCAGTCATATTGAGACTATCTCAGACAGAATGGTGAGTGTTTTCACAGTTGTATTGA
648864 GAC
130 GAC
*
648867 TATCTCAGACAGAATGGCAAGTGTCATCTCAGTCATATTGAGACTATCTCAGACAGAATGGTGAG
1 TATCTCAGACAGAATGGCAAGTGTCATCTCAGTCATATTGAGACTATCTCAGAAAGAATGGTGAG
* * * *
648932 AGTTATCTTAGTCATATTGAGACTAACTCAGACAGAATGGTGAGTGTTTTAACAGTTGTATTGAA
66 AGTTATCTCAGTCATATTGAGACTATCTCAGACAGAATGGTGAGTGTTTTCACAGTTGTATTGAG
648997 AC
131 AC
* ** *
648999 TATCTCAGACGGAATGGCAAGTGTCATCTCAGTTGTATTGAGACTATCTCAGACAGAATGGTGAG
1 TATCTCAGACAGAATGGCAAGTGTCATCTCAGTCATATTGAGACTATCTCAGAAAGAATGGTGAG
* *
649064 AGTTATCTCAGTCATATTGAGACTAACTCAGACAGAATGGTGAGTGTTTTCACAGTTGTATTGAA
66 AGTTATCTCAGTCATATTGAGACTATCTCAGACAGAATGGTGAGTGTTTTCACAGTTGTATTGAG
649129 AC
131 AC
649131 TATCTCAGACAGAATGGCAAGTGTCATCTCAGTCATATTGAGACTATCTCAGACAA-AATGGTGA
1 TATCTCAGACAGAATGGCAAGTGTCATCTCAGTCATATTGAGACTATCTCAGA-AAGAATGGTGA
* *
649195 GAGTTATCTCAGTCATATTGAGATTATCTCAGACAGAATGATGAGTGTTTTCACAGTTGTATTGA
65 GAGTTATCTCAGTCATATTGAGACTATCTCAGACAGAATGGTGAGTGTTTTCACAGTTGTATTGA
*
649260 GCC
130 GAC
* * ** * *
649263 AATATCAGACAGAATGGTGAGTGTTATCTCAGTCATAATGAGACTA
1 TATCTCAGACAGAATGGCAAGTGTCATCTCAGTCATATTGAGACTA
649309 CTGTAGATTT
Statistics
Matches: 517, Mismatches: 53, Indels: 8
0.89 0.09 0.01
Matches are distributed among these distances:
131 2 0.00
132 511 0.99
133 4 0.01
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (132 bp):
TATCTCAGACAGAATGGCAAGTGTCATCTCAGTCATATTGAGACTATCTCAGAAAGAATGGTGAG
AGTTATCTCAGTCATATTGAGACTATCTCAGACAGAATGGTGAGTGTTTTCACAGTTGTATTGAG
AC
Found at i:648850 original size:24 final size:23
Alignment explanation
Indices: 648823--648939 Score: 66
Period size: 24 Copynumber: 5.2 Consensus size: 23
648813 TTAATGAGAC
648823 TATCTCAGACAGAATGGTGAGTGT
1 TATCTCAGACAGAATGGTGAG-GT
* * **
648847 TATCTCAGTCA-TAT--TGAGAC
1 TATCTCAGACAGAATGGTGAGGT
**
648867 TATCTCAGACAGAATGGCAAGTGT
1 TATCTCAGACAGAATGGTGAG-GT
* * * **
648891 CATCTCAGTCA-TAT--TGAGAC
1 TATCTCAGACAGAATGGTGAGGT
648911 TATCTCAGACAGAATGGTGAGAGT
1 TATCTCAGACAGAATGGTGAG-GT
648935 TATCT
1 TATCT
648940 TAGTCATATT
Statistics
Matches: 63, Mismatches: 22, Indels: 16
0.62 0.22 0.16
Matches are distributed among these distances:
20 19 0.30
21 10 0.16
23 10 0.16
24 24 0.38
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (23 bp):
TATCTCAGACAGAATGGTGAGGT
Done.