Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008356.1 Hibiscus syriacus cultivar Beakdansim tig00111095_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 12862612
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 26 of 56
Found at i:5341572 original size:21 final size:21
Alignment explanation
Indices: 5341546--5341601 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
5341536 GTTTTAACAG
5341546 TCACGTAAAGCACCAACCTCA
1 TCACGTAAAGCACCAACCTCA
**
5341567 TCACGTAAAGCACTGACCTCA
1 TCACGTAAAGCACCAACCTCA
5341588 TCACGTAAAGCACC
1 TCACGTAAAGCACC
5341602 TAACTTATCC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.36, C:0.36, G:0.12, T:0.16
Consensus pattern (21 bp):
TCACGTAAAGCACCAACCTCA
Found at i:5341942 original size:42 final size:42
Alignment explanation
Indices: 5341710--5341941 Score: 277
Period size: 42 Copynumber: 5.5 Consensus size: 42
5341700 GTGATGGAAT
* * * *
5341710 AGGTGATGGTTCTTGGTGTCGAGGTGTAGAATCGACTCGATC
1 AGGTGATGGATCTCGGTGTCGAGGTGTAGAATAGGCTCGATC
* *
5341752 AGGTGATGGCTCTCGGTGTCGAGGTGTAGAATTGGCTCGATC
1 AGGTGATGGATCTCGGTGTCGAGGTGTAGAATAGGCTCGATC
* * *
5341794 AGGTGATGGCTCTCAGTGTCGAGGTGTAGAATCGGCTCGATC
1 AGGTGATGGATCTCGGTGTCGAGGTGTAGAATAGGCTCGATC
* * * * *
5341836 AGGTGATGGATCTCGGTGTCGAAGTGGAGAAGAGACTCGATG
1 AGGTGATGGATCTCGGTGTCGAGGTGTAGAATAGGCTCGATC
* * * *
5341878 AGGTGATGGATCTTGGTGTCGAAGT-TGAGAAGAGGCTCGATG
1 AGGTGATGGATCTCGGTGTCGAGGTGT-AGAATAGGCTCGATC
*
5341920 AGGTGATGGATCTTGGTGTCGA
1 AGGTGATGGATCTCGGTGTCGA
5341942 AATGGGGGTG
Statistics
Matches: 172, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
42 172 1.00
ACGTcount: A:0.21, C:0.14, G:0.38, T:0.27
Consensus pattern (42 bp):
AGGTGATGGATCTCGGTGTCGAGGTGTAGAATAGGCTCGATC
Found at i:5343488 original size:20 final size:20
Alignment explanation
Indices: 5343445--5343498 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
5343435 TTAAATTCGC
* *
5343445 AAAATGAAAATCGCAACTCG
1 AAAATGAAAATCGCAACGCA
*
5343465 AAAATGAAATTCGCAACGCA
1 AAAATGAAAATCGCAACGCA
5343485 AAAACT-AAAATCGC
1 AAAA-TGAAAATCGC
5343499 GTTGCGAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.52, C:0.20, G:0.13, T:0.15
Consensus pattern (20 bp):
AAAATGAAAATCGCAACGCA
Found at i:5343519 original size:19 final size:19
Alignment explanation
Indices: 5343495--5343531 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5343485 AAAACTAAAA
*
5343495 TCGCGTTGCGAATTTCTTT
1 TCGCGTTACGAATTTCTTT
*
5343514 TCGCGTTACGATTTTCTT
1 TCGCGTTACGAATTTCTT
5343532 GTTGCTAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.11, C:0.22, G:0.19, T:0.49
Consensus pattern (19 bp):
TCGCGTTACGAATTTCTTT
Found at i:5343549 original size:20 final size:20
Alignment explanation
Indices: 5343524--5343562 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5343514 TCGCGTTACG
* *
5343524 ATTTTCTTGTTGCTAATTTT
1 ATTTTCGTGTTGCGAATTTT
5343544 ATTTTCGTGTTGCGAATTT
1 ATTTTCGTGTTGCGAATTT
5343563 AAGTTTCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.10, G:0.15, T:0.59
Consensus pattern (20 bp):
ATTTTCGTGTTGCGAATTTT
Found at i:5343569 original size:20 final size:20
Alignment explanation
Indices: 5343526--5343569 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
5343516 GCGTTACGAT
* * * *
5343526 TTTCTTGTTGCTAATTTTAT
1 TTTCGTGTTGCGAATTTAAG
5343546 TTTCGTGTTGCGAATTTAAG
1 TTTCGTGTTGCGAATTTAAG
5343566 TTTC
1 TTTC
5343570 AAAAACTACT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.16, C:0.11, G:0.16, T:0.57
Consensus pattern (20 bp):
TTTCGTGTTGCGAATTTAAG
Found at i:5344032 original size:20 final size:20
Alignment explanation
Indices: 5344009--5344057 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
5343999 AATATTCGCT
*
5344009 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTCTGTG
5344029 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGTG
5344049 TTGCGAATT
1 TTGCGAATT
5344058 CCAAATTCGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.16, C:0.12, G:0.24, T:0.47
Consensus pattern (20 bp):
TTGCGAATTTGACTTCTGTG
Found at i:5344562 original size:3 final size:3
Alignment explanation
Indices: 5344547--5344687 Score: 108
Period size: 3 Copynumber: 45.0 Consensus size: 3
5344537 AACTAAAATA
*
5344547 AAT AAT TAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- ATAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
* * * *
5344592 AAT AAT AAT AAAT AAT AAT GAT AAT AAT AAAT ATT AAT CAT ACT GCAAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT --AAT
* * *
5344641 AAAT AAT ACT -AT AAT AAAT AAA AAT ATAT AAT CAT AA- AAT CAAT AAT
1 -AAT AAT AAT AAT AAT -AAT AAT AAT A-AT AAT AAT AAT AAT -AAT AAT
5344688 GACACATTTA
Statistics
Matches: 110, Mismatches: 17, Indels: 22
0.74 0.11 0.15
Matches are distributed among these distances:
2 4 0.04
3 85 0.77
4 19 0.17
5 2 0.02
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5345097 original size:4 final size:4
Alignment explanation
Indices: 5345088--5345123 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
5345078 TTAGACAGGA
5345088 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA- AAAG A
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG A
5345124 TAATTTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 28 0.90
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:5345240 original size:16 final size:17
Alignment explanation
Indices: 5345194--5345244 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 17
5345184 TTTGTCGTTG
5345194 TTGTT-GATTAAATTAGT
1 TTGTTAGATTAAATTA-T
* *
5345211 TTGTTTGTTTAAATTAT
1 TTGTTAGATTAAATTAT
5345228 TT-TTAGATTAAATTAT
1 TTGTTAGATTAAATTAT
5345244 T
1 T
5345245 GTTGTTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
16 13 0.43
17 8 0.27
18 9 0.30
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (17 bp):
TTGTTAGATTAAATTAT
Found at i:5346376 original size:8 final size:8
Alignment explanation
Indices: 5346346--5346375 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
5346336 TAAAAAAAAG
5346346 GTATATAT
1 GTATATAT
5346354 GTATATAT
1 GTATATAT
*
5346362 GTATATGT
1 GTATATAT
5346370 GTATAT
1 GTATAT
5346376 GCATGTGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (8 bp):
GTATATAT
Found at i:5366719 original size:18 final size:18
Alignment explanation
Indices: 5366696--5366730 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
5366686 TCGAGGGTTA
5366696 TAGTGGTCCTTCGGGACG
1 TAGTGGTCCTTCGGGACG
5366714 TAGTGGTCCTTCGGGAC
1 TAGTGGTCCTTCGGGAC
5366731 ATATCCAGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.23, G:0.37, T:0.29
Consensus pattern (18 bp):
TAGTGGTCCTTCGGGACG
Found at i:5366770 original size:24 final size:22
Alignment explanation
Indices: 5366721--5366770 Score: 55
Period size: 24 Copynumber: 2.2 Consensus size: 22
5366711 ACGTAGTGGT
**
5366721 CCTTCGGGACATATCCAGTGGT
1 CCTTCGGGACATATCCAGTGCC
*
5366743 CCTTCGGGACAAATATTCAGTGCC
1 CCTTCGGGAC--ATATCCAGTGCC
5366767 CCTT
1 CCTT
5366771 GAGGGAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 10 0.43
24 13 0.57
ACGTcount: A:0.20, C:0.30, G:0.22, T:0.28
Consensus pattern (22 bp):
CCTTCGGGACATATCCAGTGCC
Found at i:5381070 original size:18 final size:18
Alignment explanation
Indices: 5381047--5381082 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5381037 AATACTTCAA
*
5381047 ATAAAATTTCTTCACACT
1 ATAAAATTTATTCACACT
5381065 ATAAAATTTATTCACACT
1 ATAAAATTTATTCACACT
5381083 TACTTGACTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAAAATTTATTCACACT
Found at i:5381463 original size:54 final size:53
Alignment explanation
Indices: 5381399--5381601 Score: 165
Period size: 53 Copynumber: 3.8 Consensus size: 53
5381389 ATTTTTCAAC
** *
5381399 ATTAAAGTTGAATCAAATATTTATCAAAACCCTGGTCTGCTCTCTTGCTTCTAT
1 ATTAAAGTTGAATCAAAT-TTTATCAAAACCCTACTCTGCTCCCTTGCTTCTAT
* * * *
5381453 ATTAAAGTTGAACCAAGTTTTATCAAAACCTTACTCTTCTCCCTTGCTTCTAT
1 ATTAAAGTTGAATCAAATTTTATCAAAACCCTACTCTGCTCCCTTGCTTCTAT
* * ** * ** * ** *
5381506 ATTTAACTTGAATTGAATCTTATCAAAATTCTAGTCAACTCCTTTGCTTCTAT
1 ATTAAAGTTGAATCAAATTTTATCAAAACCCTACTCTGCTCCCTTGCTTCTAT
* ** * * *
5381559 ATCT-AAGCTGAATTGAATCTTATCAAAATCCTAGTCTGCTCCC
1 AT-TAAAGTTGAATCAAATTTTATCAAAACCCTACTCTGCTCCC
5381602 CTACTCGTCT
Statistics
Matches: 121, Mismatches: 27, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
53 104 0.86
54 17 0.14
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.39
Consensus pattern (53 bp):
ATTAAAGTTGAATCAAATTTTATCAAAACCCTACTCTGCTCCCTTGCTTCTAT
Found at i:5382939 original size:17 final size:18
Alignment explanation
Indices: 5382917--5382953 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
5382907 TTGTTTTGAA
5382917 TTTAAAT-AA-AATTTTAT
1 TTTAAATGAATAA-TTTAT
5382934 TTTAAATGAATAATTTAT
1 TTTAAATGAATAATTTAT
5382952 TT
1 TT
5382954 ATGCTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 9 0.50
19 2 0.11
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TTTAAATGAATAATTTAT
Found at i:5389895 original size:22 final size:22
Alignment explanation
Indices: 5389870--5389918 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
5389860 GATTTTTGTG
*
5389870 CTCCACCGATCGAACATTTAAA
1 CTCCACCGATCAAACATTTAAA
5389892 CTCCACCGATCAAACATTTAAA
1 CTCCACCGATCAAACATTTAAA
5389914 CTCCA
1 CTCCA
5389919 TTCGATCAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.37, C:0.35, G:0.06, T:0.22
Consensus pattern (22 bp):
CTCCACCGATCAAACATTTAAA
Found at i:5390184 original size:19 final size:19
Alignment explanation
Indices: 5390156--5390204 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
5390146 AATGTCAACG
*
5390156 GTCAACGGGTCAGGTCAAA
1 GTCAATGGGTCAGGTCAAA
*
5390175 GTCAATGGGTCGGGTCAAA
1 GTCAATGGGTCAGGTCAAA
* *
5390194 ATCAATAGGTC
1 GTCAATGGGTC
5390205 GGGTTGGGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.31, C:0.18, G:0.31, T:0.20
Consensus pattern (19 bp):
GTCAATGGGTCAGGTCAAA
Found at i:5390205 original size:19 final size:19
Alignment explanation
Indices: 5390163--5390208 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
5390153 ACGGTCAACG
* * *
5390163 GGTCAGGTCAAAGTCAATG
1 GGTCGGGTCAAAATCAATA
5390182 GGTCGGGTCAAAATCAATA
1 GGTCGGGTCAAAATCAATA
5390201 GGTCGGGT
1 GGTCGGGT
5390209 TGGGTTGACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.28, C:0.15, G:0.35, T:0.22
Consensus pattern (19 bp):
GGTCGGGTCAAAATCAATA
Found at i:5393550 original size:21 final size:21
Alignment explanation
Indices: 5393509--5393550 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
5393499 CCACGAAGAC
* *
5393509 TCAAGTAACTCTATTAGATCA
1 TCAAGTAACCCTACTAGATCA
5393530 TCAAGATAACCCTACTA-ATCA
1 TCAAG-TAACCCTACTAGATCA
5393551 CAACAAGTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.40, C:0.24, G:0.07, T:0.29
Consensus pattern (21 bp):
TCAAGTAACCCTACTAGATCA
Found at i:5396527 original size:15 final size:15
Alignment explanation
Indices: 5396507--5396549 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
5396497 CAGGTCAGTT
5396507 TTTGTCTTAAAATGA
1 TTTGTCTTAAAATGA
5396522 TTTGTCTTAAAATGA
1 TTTGTCTTAAAATGA
5396537 TCTT-TCTTAAAAT
1 T-TTGTCTTAAAAT
5396550 TGTTTAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 25 0.93
16 2 0.07
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (15 bp):
TTTGTCTTAAAATGA
Found at i:5398793 original size:21 final size:23
Alignment explanation
Indices: 5398751--5398798 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 23
5398741 AATATTGGGG
5398751 TTATTTTTGAAAAATAATAAATTAT
1 TTATTTTT-AAAAATAATAAATT-T
5398776 TTATTTTT-AAAAT-A-AAATTT
1 TTATTTTTAAAAATAATAAATTT
5398796 TTA
1 TTA
5398799 AAAAGAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
20 4 0.17
21 5 0.22
22 1 0.04
23 5 0.22
25 8 0.35
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TTATTTTTAAAAATAATAAATTT
Found at i:5400098 original size:31 final size:31
Alignment explanation
Indices: 5400041--5400099 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
5400031 ATCACTTTAC
* * *
5400041 TTATTTTATTAATATTTTTATGATAAAAAAT
1 TTATTTTATTAATATTATCATCATAAAAAAT
5400072 TTATTTTATTAATATATATCA-CATAAAA
1 TTATTTTATTAATAT-TATCATCATAAAA
5400100 GTAAAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 21 0.88
32 3 0.12
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (31 bp):
TTATTTTATTAATATTATCATCATAAAAAAT
Found at i:5401158 original size:27 final size:27
Alignment explanation
Indices: 5401094--5401158 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
5401084 AAACTACTAA
* *
5401094 TAATAAGCTTAATTAGGATCATTAGAT
1 TAATAAGTTTAATTAGGATCATCAGAT
*
5401121 TAATAAGTTTAATTATGATCATCAGAT
1 TAATAAGTTTAATTAGGATCATCAGAT
*
5401148 TAATAATTTTA
1 TAATAAGTTTA
5401159 CTTTATATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.42
Consensus pattern (27 bp):
TAATAAGTTTAATTAGGATCATCAGAT
Found at i:5416255 original size:12 final size:12
Alignment explanation
Indices: 5416238--5416262 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5416228 GAATGCAAGG
5416238 TTGTTTTACAGT
1 TTGTTTTACAGT
5416250 TTGTTTTACAGT
1 TTGTTTTACAGT
5416262 T
1 T
5416263 GATCGTGATA
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:0.16, C:0.08, G:0.16, T:0.60
Consensus pattern (12 bp):
TTGTTTTACAGT
Found at i:5428101 original size:424 final size:424
Alignment explanation
Indices: 5427255--5428107 Score: 1345
Period size: 423 Copynumber: 2.0 Consensus size: 424
5427245 AAGGGTAAGA
* *
5427255 AAATTTTATTTTTCATTTTCAAGCTTATTTAGTTCATTTCTGGACTAAAGTGTGAAATAGTAAAA
1 AAATTTTATTTTTCATTTTCAAGCTTATTTAGTTCATTTCTAGACTAAAGTGTGAAATAGAAAAA
* *
5427320 TTATCTACAACAAATTCTCTACGAGTTGATGTAAATATTTCATGGTTTTCTTGCTTGGATAATTG
66 TTATATACAACAAATTATCTACGAGTTGATGTAAATATTTCATGGTTTTCTTGCTTGGATAATTG
* *
5427385 GTTTGGTTGTTAGGGTGGATAAAGAACAAGTTGGATTTTGATGATTTAAAGCTGGATTTTTATGT
131 GTTTGGTTATTAGGGTGGATAAAGAACAAGTTGGATTTTGATGATTTAAAGCTGGATTTTTATGG
* * *
5427450 TAGTGATGTTGTAGAGTTGTTTACAAGCATGTGTGATGATTAAAACCAAGTAAAAATGCATGTGT
196 TAGTGATGCTGTAGAGTTGTTTACAAGCATGTGTGATGATTAAAACCAAGTAAAAACGCATGTAT
* *
5427515 AAGGCTAGGCCACCTTAGGGTTTATGGAGGGATTTGTTTTTTTTAATTGAACTGATATGGAATCA
261 AAGGCTAGGCCACCTTAGGGTTTATGGAGAGATTTGTTTTGTTTAATTGAACTGATATGGAATCA
* *
5427580 TTTGAATTTCTTGGAAATGATGTTGGGAGGTTAAATTAATGCTTGAATCAAGTAGGAAATCATTG
326 TTTGAATTGCTTGGAAATGATGTTGAGAGGTTAAATTAATGCTTGAATCAAGTAGGAAATCATTG
*
5427645 AATCCTTACTCTGCAGTGTTCAACCCTAATGAAT
391 AATCCTTACTCTACAGTGTTCAACCCTAATGAAT
* *
5427679 AAATTTTATTTTTCATTTTCAAGCTTATTTAGTTGATTTTTAGACTAAAGTGTGAAATAGAAAAA
1 AAATTTTATTTTTCATTTTCAAGCTTATTTAGTTCATTTCTAGACTAAAGTGTGAAATAGAAAAA
* *
5427744 TTATATACATCAAATTATCTACGAGTTGATGT-AATATTTCATGGTTTTCTTG-TGTGGATCATT
66 TTATATACAACAAATTATCTACGAGTTGATGTAAATATTTCATGGTTTTCTTGCT-TGGATAATT
* * * *
5427807 GGTTTGGTTATTAGGGTGGATGAAGAACAAGTTGGATTTTGATGATTTCAAGTTGGATTTTTCTG
130 GGTTTGGTTATTAGGGTGGATAAAGAACAAGTTGGATTTTGATGATTTAAAGCTGGATTTTTATG
* *
5427872 GTATTGATGCTGTAGAGTTGTTTCCAAGCATGTGTGATGATTAAAACCAAGTAAAAACGCATGTA
195 GTAGTGATGCTGTAGAGTTGTTTACAAGCATGTGTGATGATTAAAACCAAGTAAAAACGCATGTA
*
5427937 TGAGGCTAGGCCACCTTAGGGTTTATGGAGAGA-TT-TTTTGTTTAGGATTGAACTGATATGGAA
260 TAAGGCTAGGCCACCTTAGGGTTTATGGAGAGATTTGTTTTGTTTA--ATTGAACTGATATGGAA
* * * *
5428000 TTCTTTTGAATTGCTTGGAAATGATGTTGAGAGGTTGAATTCATGCTTGAATCAAGTTGGAAATC
323 -TCATTTGAATTGCTTGGAAATGATGTTGAGAGGTTAAATTAATGCTTGAATCAAGTAGGAAATC
* * **
5428065 ATTGAATCCTTATTCTATAGTGTTTGACCCTAATGAAT
387 ATTGAATCCTTACTCTACAGTGTTCAACCCTAATGAAT
5428103 AAATT
1 AAATT
5428108 AGAGAAAATT
Statistics
Matches: 392, Mismatches: 33, Indels: 8
0.91 0.08 0.02
Matches are distributed among these distances:
421 8 0.02
422 3 0.01
423 195 0.50
424 186 0.47
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (424 bp):
AAATTTTATTTTTCATTTTCAAGCTTATTTAGTTCATTTCTAGACTAAAGTGTGAAATAGAAAAA
TTATATACAACAAATTATCTACGAGTTGATGTAAATATTTCATGGTTTTCTTGCTTGGATAATTG
GTTTGGTTATTAGGGTGGATAAAGAACAAGTTGGATTTTGATGATTTAAAGCTGGATTTTTATGG
TAGTGATGCTGTAGAGTTGTTTACAAGCATGTGTGATGATTAAAACCAAGTAAAAACGCATGTAT
AAGGCTAGGCCACCTTAGGGTTTATGGAGAGATTTGTTTTGTTTAATTGAACTGATATGGAATCA
TTTGAATTGCTTGGAAATGATGTTGAGAGGTTAAATTAATGCTTGAATCAAGTAGGAAATCATTG
AATCCTTACTCTACAGTGTTCAACCCTAATGAAT
Found at i:5429180 original size:21 final size:21
Alignment explanation
Indices: 5429156--5429210 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
5429146 TTTTTCAAGG
5429156 GGATCGATCCTTTGGTCAAAT
1 GGATCGATCCTTTGGTCAAAT
5429177 GGATCGATCCTTTGGTCAAAT
1 GGATCGATCCTTTGGTCAAAT
5429198 GGATCGATCCTTT
1 GGATCGATCCTTT
5429211 TGCTAGGGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.35
Consensus pattern (21 bp):
GGATCGATCCTTTGGTCAAAT
Found at i:5430415 original size:3 final size:3
Alignment explanation
Indices: 5430409--5430471 Score: 58
Period size: 3 Copynumber: 21.7 Consensus size: 3
5430399 TCATTATTTA
* * * * *
5430409 TAT TAT TAT TAT AAT TAT AAC TAT AAT TAT T-T TAT TAA TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
5430455 TAT TGT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
5430472 AAAATAATAA
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
2 4 0.09
3 43 0.91
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:5430735 original size:26 final size:26
Alignment explanation
Indices: 5430691--5430807 Score: 162
Period size: 26 Copynumber: 4.5 Consensus size: 26
5430681 GGGTTTCCAG
*
5430691 AACAGGCCACCTCCGCTTGGACCACTC
1 AACA-GCCACCACCGCTTGGACCACTC
* *
5430718 AACAGCCACCACCACTTGAACCACTC
1 AACAGCCACCACCGCTTGGACCACTC
*
5430744 AACAACCACCACCGCTTGGACCACTC
1 AACAGCCACCACCGCTTGGACCACTC
* *
5430770 AACAACCACCGCCGCTTGGACCACTC
1 AACAGCCACCACCGCTTGGACCACTC
*
5430796 AATAGCCACCAC
1 AACAGCCACCAC
5430808 TGTTGCCAAC
Statistics
Matches: 80, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
26 76 0.95
27 4 0.05
ACGTcount: A:0.30, C:0.45, G:0.13, T:0.12
Consensus pattern (26 bp):
AACAGCCACCACCGCTTGGACCACTC
Found at i:5434018 original size:25 final size:25
Alignment explanation
Indices: 5433981--5434043 Score: 117
Period size: 25 Copynumber: 2.5 Consensus size: 25
5433971 GGGTAGAAAT
5433981 CATGATTGGGTAGGATCTACTAAAG
1 CATGATTGGGTAGGATCTACTAAAG
*
5434006 CATGATTGAGTAGGATCTACTAAAG
1 CATGATTGGGTAGGATCTACTAAAG
5434031 CATGATTGGGTAG
1 CATGATTGGGTAG
5434044 CTAACATGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.32, C:0.11, G:0.29, T:0.29
Consensus pattern (25 bp):
CATGATTGGGTAGGATCTACTAAAG
Found at i:5441996 original size:115 final size:114
Alignment explanation
Indices: 5441794--5443192 Score: 2047
Period size: 115 Copynumber: 12.2 Consensus size: 114
5441784 TCTTAAAGAC
* *
5441794 AAGTGGAACAAGTCTGCCCCCATTCAGTGGATCAAACTCCTCCAAGATCTGATATTCCCTTCAGA
1 AAGTGGAACAAGTCTG-CCCGATTCAGTGGATCAAACTCCTCTAAGATCTGATATTCCCTTCAGA
*
5441859 GTAAGCGGAACAGGTCTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGT
65 GTAAGCGGAACATGTCTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGT
* * * *
5441909 AAGTGGAACAAGTCTAGCCCCATTCAGTGGATCAAACTCCCCCAAGATCTGATATTCTCTTCAGA
1 AAGTGGAACAAGTCT-GCCCGATTCAGTGGATCAAACTCCTCTAAGATCTGATATTCCCTTCAGA
* * * *
5441974 GTAAGCGAAACAGGTCTCTCTTTCCTAAGATTTGATATTTCCTTCAGAGT
65 GTAAGCGGAACATGTCTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGT
* *
5442024 AAGTGGAACAAGTCTGCCCCCATTTAGTGGATCAAACTCCTCTAAGATCTGATATTCCCTTCAGA
1 AAGTGGAACAAGTCTG-CCCGATTCAGTGGATCAAACTCCTCTAAGATCTGATATTCCCTTCAGA
* *
5442089 GTAAGCAGAACATGTCTTTCTTTCCCAAGATTTGATATTCCCTTCAGAGT
65 GTAAGCGGAACATGTCTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGT
* *
5442139 AAGTGGAACAAGTCTGCCATGATTCAGTAGATCAAACTCCTCTAAGATCTGATATTCCCTTCAGA
1 AAGTGGAACAAGTCTGCC-CGATTCAGTGGATCAAACTCCTCTAAGATCTGATATTCCCTTCAGA
*
5442204 GTAAGCGAAACATGTCTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGT
65 GTAAGCGGAACATGTCTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGT
* * **
5442254 AAGTGGAACAAGTCTGCCCTGATTCAAG-GAATCAAACTCCTCTAAGATATGATATAACCTTCAG
1 AAGTGGAACAAGTCTGCCC-GATTC-AGTGGATCAAACTCCTCTAAGATCTGATATTCCCTTCAG
* * *
5442318 AGTAAGTGGAACATGTCTTTCTTTCCCAAGATTTGATATTCCCTTCACAGT
64 AGTAAGCGGAACATGTCTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGT
* *
5442369 AAGTGGAACAAGTCTGCCATGATTCAGTAGATCAAACTCCTCTAAGATCTGATATTCCCTTCAGA
1 AAGTGGAACAAGTCTGCC-CGATTCAGTGGATCAAACTCCTCTAAGATCTGATATTCCCTTCAGA
* *
5442434 GTAAGCGGAACATGTCTCTCTTTCCCAATATTTGATATTACCTTCAGAGT
65 GTAAGCGGAACATGTCTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGT
* * **
5442484 AAGTGGAACAAGTCTGCCCTGATTCAAG-GAATCAAACTCCTCTAAGATATGATATAACCTTCAG
1 AAGTGGAACAAGTCTGCCC-GATTC-AGTGGATCAAACTCCTCTAAGATCTGATATTCCCTTCAG
5442548 AGTAAGCGGAACATGTCTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGT
64 AGTAAGCGGAACATGTCTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGT
* * * *
5442599 AAGTGGAACAAGTCTTCCCCCATTTAGTGGATCAAACTCCTCTAAGATATGATATTCCCTTCAGA
1 AAGTGGAACAAGTC-TGCCCGATTCAGTGGATCAAACTCCTCTAAGATCTGATATTCCCTTCAGA
* *
5442664 GTAAGCGGAACATGTCTCTCTTTCCCAATATTTGATATTCCATTCAGAGT
65 GTAAGCGGAACATGTCTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGT
*
5442714 AAGTGGAACAAGTCTGCCCTGATTTAGTGGATCAAACTCCTCTAAGATCTGATATTCCCTTCAGA
1 AAGTGGAACAAGTCTGCCC-GATTCAGTGGATCAAACTCCTCTAAGATCTGATATTCCCTTCAGA
* *
5442779 GTAAGCGGAACAGGTCTCTCTTTCCCAAGATTTGATATTCCCTTTAGAGT
65 GTAAGCGGAACATGTCTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGT
* ** *
5442829 AAGTGGAACAAGTCTGCCCTGATTCAAG-GAATCAAACTCCTCTAAGATCTGATATAACCTTCAA
1 AAGTGGAACAAGTCTGCCC-GATTC-AGTGGATCAAACTCCTCTAAGATCTGATATTCCCTTCAG
*
5442893 AGTAAGCGGAACATGTCTCTCTTTCCCAAGATTTGATATTCTCTTCAGAGT
64 AGTAAGCGGAACATGTCTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGT
* *
5442944 AAGTGGAACAAGTCTGCCCTGATTCAAG-GAATCAAACTCCT-TCAAGATCTGATATTCCTTTCA
1 AAGTGGAACAAGTCTGCCC-GATTC-AGTGGATCAAACTCCTCT-AAGATCTGATATTCCCTTCA
* *
5443007 GAGTAA--GAAAAATAGATCTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGT
63 GAGTAAGCGGAACAT-G-TCTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGT
* * *
5443059 AAGTAGAACAAGTCTGCCCCCATTTAGTGGATCAAACTCCTCTAAGATCTGATATTCCCTTCAGA
1 AAGTGGAACAAGTCTG-CCCGATTCAGTGGATCAAACTCCTCTAAGATCTGATATTCCCTTCAGA
* * **
5443124 GTAAGCGGAACATGTGTCTTTTTTTTCAAGATTTGATATTCCCTTCAGAGT
65 GTAAGCGGAACATGTCTC-TCTTTCCCAAGATTTGATATTCCCTTCAGAGT
5443175 AAGTGGAACAAGTCTGCC
1 AAGTGGAACAAGTCTGCC
5443193 TCCATTCAAT
Statistics
Matches: 1169, Mismatches: 93, Indels: 44
0.90 0.07 0.03
Matches are distributed among these distances:
113 5 0.00
114 15 0.01
115 1084 0.93
116 60 0.05
117 5 0.00
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.30
Consensus pattern (114 bp):
AAGTGGAACAAGTCTGCCCGATTCAGTGGATCAAACTCCTCTAAGATCTGATATTCCCTTCAGAG
TAAGCGGAACATGTCTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGT
Found at i:5443201 original size:49 final size:49
Alignment explanation
Indices: 5443102--5443201 Score: 112
Period size: 49 Copynumber: 2.0 Consensus size: 49
5443092 AAACTCCTCT
* * * ***
5443102 AAGATCTGATATTCCCTTCAGAGTAAGCGGAACATGTGTCTTTTTTTTC
1 AAGATCTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTCTCCATTC
* *
5443151 AAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGC-CTCCATTC
1 AAGATCTGATATTCCCTTCAGAGTAAGCGGAACAAGTCT-CTCTCCATTC
5443200 AA
1 AA
5443202 TTTTCCCTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
49 41 0.98
50 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (49 bp):
AAGATCTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTCTCCATTC
Found at i:5443479 original size:17 final size:19
Alignment explanation
Indices: 5443457--5443496 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
5443447 TTGTCATTAT
5443457 TTATATTA-TAAT-TATAA
1 TTATATTATTAATATATAA
*
5443474 TTATATTATTAATATATTA
1 TTATATTATTAATATATAA
5443493 TTAT
1 TTAT
5443497 TAATAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
18 4 0.20
19 8 0.40
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTATATTATTAATATATAA
Found at i:5443497 original size:17 final size:17
Alignment explanation
Indices: 5443460--5443505 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
5443450 TCATTATTTA
*
5443460 TATTATAATT-ATA-AT
1 TATTATTATTAATATAT
5443475 TA-TATTATTAATATAT
1 TATTATTATTAATATAT
*
5443491 TATTATTAATAATAT
1 TATTATTATTAATAT
5443506 TAAAAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 6 0.23
15 5 0.19
16 4 0.15
17 11 0.42
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TATTATTATTAATATAT
Found at i:5443769 original size:26 final size:26
Alignment explanation
Indices: 5443721--5443829 Score: 146
Period size: 26 Copynumber: 4.2 Consensus size: 26
5443711 GGGTTTCCAG
* *
5443721 AACAGGCCACCTCCGCTTGGACCACTC
1 AACA-GCCACCACCACTTGGACCACTC
*
5443748 AACAGCCACCACCACTTTGACCACTC
1 AACAGCCACCACCACTTGGACCACTC
*
5443774 AACAGCCACCACCACTTAGACCACTC
1 AACAGCCACCACCACTTGGACCACTC
* * *
5443800 AACAACCACCGCCTCTTGGACCACTC
1 AACAGCCACCACCACTTGGACCACTC
5443826 AACA
1 AACA
5443830 ACCATCATTG
Statistics
Matches: 74, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
26 70 0.95
27 4 0.05
ACGTcount: A:0.30, C:0.45, G:0.11, T:0.14
Consensus pattern (26 bp):
AACAGCCACCACCACTTGGACCACTC
Found at i:5444839 original size:15 final size:15
Alignment explanation
Indices: 5444821--5444853 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
5444811 TATCATATTT
*
5444821 TGTATGTATTATATA
1 TGTAAGTATTATATA
5444836 TGTAAGTATTATATA
1 TGTAAGTATTATATA
5444851 TGT
1 TGT
5444854 TTTGTATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (15 bp):
TGTAAGTATTATATA
Found at i:5445857 original size:4 final size:4
Alignment explanation
Indices: 5445848--5445872 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
5445838 GTTTGATATG
5445848 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
5445873 CTTTGGCATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:5452070 original size:16 final size:16
Alignment explanation
Indices: 5452049--5452115 Score: 54
Period size: 16 Copynumber: 4.4 Consensus size: 16
5452039 TTTTCTCCCC
5452049 CTTCTTGCAGCTTCTT
1 CTTCTTGCAGCTTCTT
5452065 CTTCTT----CTTCTTT
1 CTTCTTGCAGCTTC-TT
*
5452078 CTTTTTGCAGCTTCTT
1 CTTCTTGCAGCTTCTT
* *
5452094 CTTCGTGACAACTTCTT
1 CTTCTTG-CAGCTTCTT
5452111 -TTCTT
1 CTTCTT
5452116 CTTTTTCTTG
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
12 4 0.10
13 7 0.17
16 17 0.43
17 12 0.30
ACGTcount: A:0.07, C:0.28, G:0.09, T:0.55
Consensus pattern (16 bp):
CTTCTTGCAGCTTCTT
Found at i:5453072 original size:22 final size:22
Alignment explanation
Indices: 5453046--5453098 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
5453036 TATGGGATTT
*
5453046 GAAGAATAATAAGAAGCTG-CAA
1 GAAGAAGAA-AAGAAGCTGCCAA
*
5453068 GAAGAAGAAAAGAAGCTGCCAC
1 GAAGAAGAAAAGAAGCTGCCAA
5453090 GAAGAAGAA
1 GAAGAAGAA
5453099 GCTGCAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 9 0.32
22 19 0.68
ACGTcount: A:0.55, C:0.11, G:0.26, T:0.08
Consensus pattern (22 bp):
GAAGAAGAAAAGAAGCTGCCAA
Found at i:5453099 original size:38 final size:40
Alignment explanation
Indices: 5453056--5453131 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 40
5453046 GAAGAATAAT
5453056 AAGAAGCTGCAAG-AA-GAAGAAAAGAAGCTGCCACGAAG
1 AAGAAGCTGCAAGAAAGGAAGAAAAGAAGCTGCCACGAAG
5453094 AAGAAGCTGCAAGAAAAGGAAGAAAAGAAGCTGCCACG
1 AAGAAGCTGCAAG-AAAGGAAGAAAAGAAGCTGCCACG
5453132 TCTGAGATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
38 13 0.37
40 2 0.06
41 20 0.57
ACGTcount: A:0.50, C:0.16, G:0.29, T:0.05
Consensus pattern (40 bp):
AAGAAGCTGCAAGAAAGGAAGAAAAGAAGCTGCCACGAAG
Found at i:5453383 original size:13 final size:13
Alignment explanation
Indices: 5453361--5453416 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
5453351 TCTTTTGTTC
*
5453361 TAATAAAATAATA
1 TAATAGAATAATA
*
5453374 TAATATAATAA-A
1 TAATAGAATAATA
5453386 TTAATAGAATAAATA
1 -TAATAGAAT-AATA
* *
5453401 GAATAGAAAAATA
1 TAATAGAATAATA
5453414 TAA
1 TAA
5453417 CAAAGGTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 1 0.03
13 24 0.69
14 9 0.26
15 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (13 bp):
TAATAGAATAATA
Found at i:5453384 original size:18 final size:18
Alignment explanation
Indices: 5453361--5453405 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
5453351 TCTTTTGTTC
*
5453361 TAATAAAATAATATAATA
1 TAATAAAATAATAGAATA
*
5453379 TAATAAATTAATAGAATA
1 TAATAAAATAATAGAATA
*
5453397 -AATAGAATA
1 TAATAAAATA
5453406 GAAAAATATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.31
Consensus pattern (18 bp):
TAATAAAATAATAGAATA
Found at i:5453492 original size:12 final size:12
Alignment explanation
Indices: 5453460--5453492 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
5453450 ATAAGAAATA
*
5453460 TATAATTAATTT
1 TATAATTATTTT
5453472 TATAATTATTTT
1 TATAATTATTTT
5453484 TATAATTAT
1 TATAATTAT
5453493 AAATTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TATAATTATTTT
Found at i:5453512 original size:17 final size:19
Alignment explanation
Indices: 5453471--5453514 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
5453461 ATAATTAATT
5453471 TTAT-AATTATTTTTATAA
1 TTATAAATTATTTTTATAA
*
5453489 TTATAAATTTTTTTTATAA
1 TTATAAATTATTTTTATAA
5453508 TTA-AAAT
1 TTATAAAT
5453515 ATCATATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTATAAATTATTTTTATAA
Found at i:5460649 original size:3 final size:3
Alignment explanation
Indices: 5460641--5460738 Score: 54
Period size: 3 Copynumber: 31.3 Consensus size: 3
5460631 CTTCTTGCAG
* ** * **
5460641 CTT CTT CTT CTT CTT CTT CTTT CTT TTT GCAG CTT CTT CTT CGTGA CAA
1 CTT CTT CTT CTT CTT CTT C-TT CTT CTT -CTT CTT CTT CTT C-T-T CTT
* * * *
5460690 CTT CTT -TT CTT CTT TTT CTT GCAT CTT CTT ATT CTT ATT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT -CTT CTT CTT CTT CTT CTT CTT CTT
5460735 CTT C
1 CTT C
5460739 AAAACTCTAA
Statistics
Matches: 71, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
2 2 0.03
3 62 0.87
4 6 0.08
5 1 0.01
ACGTcount: A:0.07, C:0.28, G:0.05, T:0.60
Consensus pattern (3 bp):
CTT
Found at i:5461657 original size:22 final size:22
Alignment explanation
Indices: 5461631--5461683 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
5461621 TATGGGATTT
*
5461631 GAAGAATAATAAGAAGCTG-CAA
1 GAAGAAGAA-AAGAAGCTGCCAA
*
5461653 GAAGAAGAAAAGAAGCTGCCAC
1 GAAGAAGAAAAGAAGCTGCCAA
5461675 GAAGAAGAA
1 GAAGAAGAA
5461684 GCTGCAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 9 0.32
22 19 0.68
ACGTcount: A:0.55, C:0.11, G:0.26, T:0.08
Consensus pattern (22 bp):
GAAGAAGAAAAGAAGCTGCCAA
Found at i:5461684 original size:38 final size:40
Alignment explanation
Indices: 5461641--5461716 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 40
5461631 GAAGAATAAT
5461641 AAGAAGCTGCAAG-AA-GAAGAAAAGAAGCTGCCACGAAG
1 AAGAAGCTGCAAGAAAGGAAGAAAAGAAGCTGCCACGAAG
*
5461679 AAGAAGCTGCAAGAAAAGGAAGAAAAGAAGTTGCCACG
1 AAGAAGCTGCAAG-AAAGGAAGAAAAGAAGCTGCCACG
5461717 TCTGAGATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
38 13 0.38
40 2 0.06
41 19 0.56
ACGTcount: A:0.50, C:0.14, G:0.29, T:0.07
Consensus pattern (40 bp):
AAGAAGCTGCAAGAAAGGAAGAAAAGAAGCTGCCACGAAG
Found at i:5461968 original size:13 final size:13
Alignment explanation
Indices: 5461946--5462001 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
5461936 TCTTTTGTTC
*
5461946 TAATAAAATAATA
1 TAATAGAATAATA
*
5461959 TAATATAATAA-A
1 TAATAGAATAATA
5461971 TTAATAGAATAAATA
1 -TAATAGAAT-AATA
* *
5461986 GAATAGAAAAATA
1 TAATAGAATAATA
5461999 TAA
1 TAA
5462002 AAAAGGTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 1 0.03
13 24 0.69
14 9 0.26
15 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (13 bp):
TAATAGAATAATA
Found at i:5461969 original size:18 final size:18
Alignment explanation
Indices: 5461946--5461990 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
5461936 TCTTTTGTTC
*
5461946 TAATAAAATAATATAATA
1 TAATAAAATAATAGAATA
*
5461964 TAATAAATTAATAGAATA
1 TAATAAAATAATAGAATA
*
5461982 -AATAGAATA
1 TAATAAAATA
5461991 GAAAAATATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.31
Consensus pattern (18 bp):
TAATAAAATAATAGAATA
Found at i:5462089 original size:12 final size:12
Alignment explanation
Indices: 5462046--5462089 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
5462036 ATAAGAAATA
*
5462046 TATAATTAATTT
1 TATAATTATTTT
5462058 TATAATTA-TTT
1 TATAATTATTTT
*
5462069 AATAATTATTTT
1 TATAATTATTTT
5462081 TATAATTAT
1 TATAATTAT
5462090 AAATTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 10 0.34
12 19 0.66
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TATAATTATTTT
Found at i:5462098 original size:18 final size:18
Alignment explanation
Indices: 5462067--5462110 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
5462057 TTATAATTAT
5462067 TTAATAATTATTTTTATAA
1 TTAA-AATTATTTTTATAA
5462086 TTATAAATT-TTTTTATAA
1 TTA-AAATTATTTTTATAA
5462104 TTAAAAT
1 TTAAAAT
5462111 ATCATACAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.17
18 12 0.50
19 7 0.29
20 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTAAAATTATTTTTATAA
Found at i:5469517 original size:21 final size:21
Alignment explanation
Indices: 5469458--5469521 Score: 78
Period size: 20 Copynumber: 3.1 Consensus size: 21
5469448 AATGATTTAT
*
5469458 TTTTATTTATATTA-TTAAAA
1 TTTTATTTATATTATTTTAAA
* *
5469478 TTTTATCTATATT-TATTAAA
1 TTTTATTTATATTATTTTAAA
*
5469498 TTTTGTTTATATTATTTTAAA
1 TTTTATTTATATTATTTTAAA
5469519 TTT
1 TTT
5469522 CAGTTTGTTG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 27 0.75
21 9 0.25
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTATTTATATTATTTTAAA
Found at i:5476979 original size:4 final size:4
Alignment explanation
Indices: 5476970--5477066 Score: 50
Period size: 4 Copynumber: 24.2 Consensus size: 4
5476960 TAACCCAATT
* * * * * * * * *
5476970 AGAC AGAC AGAC AAAC AGAT AGAG AGAT AGAT AGAC ACAA AGAT AGAG
1 AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC
* * * * * * *
5477018 AGAT AGAC AGAG AGAT AGAG AGAC AGAC AGAG AGAT AGAT AGAC AGAC
1 AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC
5477066 A
1 A
5477067 AACATAGATA
Statistics
Matches: 73, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
4 73 1.00
ACGTcount: A:0.53, C:0.11, G:0.28, T:0.08
Consensus pattern (4 bp):
AGAC
Found at i:5477065 original size:24 final size:24
Alignment explanation
Indices: 5476970--5477183 Score: 111
Period size: 24 Copynumber: 9.2 Consensus size: 24
5476960 TAACCCAATT
* * *
5476970 AGACAGACAGACAAACAGATAGAG
1 AGACAGACAGACAGATAGATAGAC
* * * *
5476994 AGATAGATAGACACAAAGATAG--
1 AGACAGACAGACAGATAGATAGAC
* * *
5477016 AG--AGATAGACAGAGAGATAGAG
1 AGACAGACAGACAGATAGATAGAC
*
5477038 AGACAGACAGAGAGATAGATAGAC
1 AGACAGACAGACAGATAGATAGAC
* * * * *
5477062 AGACAAACATAGATATAAATAGAC
1 AGACAGACAGACAGATAGATAGAC
* * * * **
5477086 AAAGAGATAGAAAGAGGGATAGAC
1 AGACAGACAGACAGATAGATAGAC
* *
5477110 A-A-AG--AGACAGAGAGATAGCC
1 AGACAGACAGACAGATAGATAGAC
* * *
5477130 AAATAGACAGATAGATAGATAGAC
1 AGACAGACAGACAGATAGATAGAC
*
5477154 AGATAGACAGACAGATAGATAGAC
1 AGACAGACAGACAGATAGATAGAC
*
5477178 ATACAG
1 AGACAG
5477184 TTAGACGGAC
Statistics
Matches: 148, Mismatches: 34, Indels: 16
0.75 0.17 0.08
Matches are distributed among these distances:
20 30 0.20
21 1 0.01
22 8 0.05
23 1 0.01
24 108 0.73
ACGTcount: A:0.53, C:0.11, G:0.26, T:0.11
Consensus pattern (24 bp):
AGACAGACAGACAGATAGATAGAC
Found at i:5477126 original size:20 final size:20
Alignment explanation
Indices: 5476998--5477148 Score: 110
Period size: 20 Copynumber: 7.3 Consensus size: 20
5476988 ATAGAGAGAT
5476998 AGATAGACACAA-AGATAGAG
1 AGATAGACA-AAGAGATAGAG
*
5477018 AGATAGACAGAGAGATAGAG
1 AGATAGACAAAGAGATAGAG
* * *
5477038 AGACAGACAGAGAGATAGAT
1 AGATAGACAAAGAGATAGAG
* * *
5477058 AGACAGACAAACATAGATATA-
1 AGATAGAC-AA-AGAGATAGAG
5477079 A-ATAGACAAAGAGATAGAAAG
1 AGATAGACAAAGAGATAG--AG
*
5477100 AGGGATAGACAAAGAGACAGAG
1 A--GATAGACAAAGAGATAGAG
* * * *
5477122 AGATAGCCAAATAGACAGAT
1 AGATAGACAAAGAGATAGAG
5477142 AGATAGA
1 AGATAGA
5477149 TAGACAGATA
Statistics
Matches: 108, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
18 6 0.06
19 3 0.03
20 71 0.66
21 3 0.03
22 10 0.09
24 15 0.14
ACGTcount: A:0.54, C:0.09, G:0.26, T:0.11
Consensus pattern (20 bp):
AGATAGACAAAGAGATAGAG
Found at i:5477143 original size:8 final size:8
Alignment explanation
Indices: 5477122--5477178 Score: 69
Period size: 8 Copynumber: 7.1 Consensus size: 8
5477112 AGAGACAGAG
*
5477122 AGATAGCC
1 AGATAGAC
*
5477130 AAATAGAC
1 AGATAGAC
*
5477138 AGATAGAT
1 AGATAGAC
5477146 AGATAGAC
1 AGATAGAC
5477154 AGATAGAC
1 AGATAGAC
* *
5477162 AGACAGAT
1 AGATAGAC
5477170 AGATAGAC
1 AGATAGAC
5477178 A
1 A
5477179 TACAGTTAGA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
8 40 1.00
ACGTcount: A:0.51, C:0.12, G:0.23, T:0.14
Consensus pattern (8 bp):
AGATAGAC
Found at i:5477147 original size:4 final size:4
Alignment explanation
Indices: 5477132--5477176 Score: 54
Period size: 4 Copynumber: 11.2 Consensus size: 4
5477122 AGATAGCCAA
* * * *
5477132 ATAG ACAG ATAG ATAG ATAG ACAG ATAG ACAG ACAG ATAG ATAG A
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG A
5477177 CATACAGTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.51, C:0.09, G:0.24, T:0.16
Consensus pattern (4 bp):
ATAG
Found at i:5477171 original size:20 final size:20
Alignment explanation
Indices: 5476978--5477188 Score: 106
Period size: 20 Copynumber: 10.8 Consensus size: 20
5476968 TTAGACAGAC
* *
5476978 AGACAAACAGATAGAGAGAT
1 AGACAGACAGATAGATAGAT
* * * *
5476998 AGATAGACACAAAGATAGAG
1 AGACAGACAGATAGATAGAT
* * *
5477018 AGATAGACAGAGAGATAGAG
1 AGACAGACAGATAGATAGAT
*
5477038 AGACAGACAGAGAGATAGAT
1 AGACAGACAGATAGATAGAT
*
5477058 AGACAGACA-A-ACATAGAT
1 AGACAGACAGATAGATAGAT
* * * * *
5477076 ATA-A-ATAGACAAAGAGAT
1 AGACAGACAGATAGATAGAT
* ** * * *
5477094 AGAAAGAGGGATAGACAAAG
1 AGACAGACAGATAGATAGAT
* ** *
5477114 AGACAGAGAGATAGCCAAAT
1 AGACAGACAGATAGATAGAT
* *
5477134 AGACAGATAGATAGATAGAC
1 AGACAGACAGATAGATAGAT
* *
5477154 AGATAGACAGACAGATAGAT
1 AGACAGACAGATAGATAGAT
* *
5477174 AGACATACAGTTAGA
1 AGACAGACAGATAGA
5477189 CGGACGGATA
Statistics
Matches: 147, Mismatches: 40, Indels: 8
0.75 0.21 0.04
Matches are distributed among these distances:
16 2 0.01
17 2 0.01
18 17 0.12
19 2 0.01
20 124 0.84
ACGTcount: A:0.53, C:0.10, G:0.26, T:0.12
Consensus pattern (20 bp):
AGACAGACAGATAGATAGAT
Found at i:5477183 original size:16 final size:16
Alignment explanation
Indices: 5476969--5477188 Score: 71
Period size: 16 Copynumber: 13.2 Consensus size: 16
5476959 ATAACCCAAT
* *
5476969 TAGACAGACAGACAAA
1 TAGATAGACAGACAGA
* * *
5476985 CAGATAGAGAGATAGA
1 TAGATAGACAGACAGA
* * * *
5477001 TAGACACAAAGATAGA
1 TAGATAGACAGACAGA
* *
5477017 GAGATAGACAGAGAGA
1 TAGATAGACAGACAGA
*
5477033 TAGAGAGACAGACAGAGAGA
1 TAGATAGACAGAC----AGA
*
5477053 TAGATAGACAGACAAACA
1 TAGATAGACAGAC--AGA
* * *
5477071 TAGATATAAATAGACAAA
1 TAG--ATAGACAGACAGA
* * **
5477089 GAGATAGAAAGAGGGA
1 TAGATAGACAGACAGA
* * *
5477105 TAGACAAAGAGACAGA
1 TAGATAGACAGACAGA
* * * *
5477121 GAGATAGCCAAATAGA
1 TAGATAGACAGACAGA
* * *
5477137 CAGATAGATAGATAGA
1 TAGATAGACAGACAGA
*
5477153 CAGATAGACAGACAGA
1 TAGATAGACAGACAGA
* *
5477169 TAGATAGACATACAGT
1 TAGATAGACAGACAGA
5477185 TAGA
1 TAGA
5477189 CGGACGGATA
Statistics
Matches: 147, Mismatches: 51, Indels: 12
0.70 0.24 0.06
Matches are distributed among these distances:
16 114 0.78
18 10 0.07
20 23 0.16
ACGTcount: A:0.52, C:0.10, G:0.25, T:0.12
Consensus pattern (16 bp):
TAGATAGACAGACAGA
Found at i:5484812 original size:20 final size:20
Alignment explanation
Indices: 5484767--5484817 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
5484757 ACACACTTTC
*
5484767 CAAATTCGCAACACAAATTT
1 CAAATTCGCAACACAAATGT
**
5484787 GTAATTCGCAACACAGAA-GT
1 CAAATTCGCAACACA-AATGT
5484807 CAAATTCGCAA
1 CAAATTCGCAA
5484818 AGCGCGTTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
20 23 0.92
21 2 0.08
ACGTcount: A:0.43, C:0.24, G:0.12, T:0.22
Consensus pattern (20 bp):
CAAATTCGCAACACAAATGT
Found at i:5484978 original size:22 final size:22
Alignment explanation
Indices: 5484953--5485010 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
5484943 TCACTCTCTA
*
5484953 CGGCGACATCCGTCCCCATCTC
1 CGGCGAAATCCGTCCCCATCTC
* *
5484975 CGGCAAAATCCATCCCCATCTC
1 CGGCGAAATCCGTCCCCATCTC
5484997 CGGCGAAATCCGTC
1 CGGCGAAATCCGTC
5485011 TATCTTCATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.21, C:0.45, G:0.17, T:0.17
Consensus pattern (22 bp):
CGGCGAAATCCGTCCCCATCTC
Found at i:5485372 original size:20 final size:20
Alignment explanation
Indices: 5485349--5485387 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
5485339 TTTGAAATTT
*
5485349 AAATTCGCAACACGAAAATG
1 AAATTCACAACACGAAAATG
5485369 AAATTCACAACACGAAAAT
1 AAATTCACAACACGAAAAT
5485388 CGCAACGCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.21, G:0.10, T:0.15
Consensus pattern (20 bp):
AAATTCACAACACGAAAATG
Found at i:5486983 original size:21 final size:21
Alignment explanation
Indices: 5486940--5487037 Score: 83
Period size: 21 Copynumber: 4.7 Consensus size: 21
5486930 GTTAGGGGAG
*
5486940 TTACGTGATGAGGTCAGTGCT
1 TTACGTGATGAGGTCGGTGCT
* *
5486961 TTGCGTGATGAGGTCGGTACT
1 TTACGTGATGAGGTCGGTGCT
* ** *
5486982 TTACATGATGACAAT-GGTGCA
1 TTACGTGATGA-GGTCGGTGCT
**
5487003 TGGCGTGATGAGGTACGGT-CT
1 TTACGTGATGAGGT-CGGTGCT
5487024 TTACGTGATGAGGT
1 TTACGTGATGAGGT
5487038 AGTCGCTCTA
Statistics
Matches: 57, Mismatches: 17, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
20 1 0.02
21 52 0.91
22 4 0.07
ACGTcount: A:0.20, C:0.13, G:0.35, T:0.32
Consensus pattern (21 bp):
TTACGTGATGAGGTCGGTGCT
Found at i:5486991 original size:42 final size:41
Alignment explanation
Indices: 5486940--5487040 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 41
5486930 GTTAGGGGAG
* *
5486940 TTACGTGATGAGGTCAGTGCTTTGCGTGATGAGGT-CGGTACT
1 TTACGTGATGAGGT-AGTGCATGGCGTGATGAGGTACGGT-CT
* ** *
5486982 TTACATGATGACAATGGTGCATGGCGTGATGAGGTACGGTCT
1 TTACGTGATGA-GGTAGTGCATGGCGTGATGAGGTACGGTCT
5487024 TTACGTGATGAGGTAGT
1 TTACGTGATGAGGTAGT
5487041 CGCTCTATGT
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
41 3 0.06
42 39 0.83
43 5 0.11
ACGTcount: A:0.21, C:0.13, G:0.35, T:0.32
Consensus pattern (41 bp):
TTACGTGATGAGGTAGTGCATGGCGTGATGAGGTACGGTCT
Found at i:5487157 original size:4 final size:4
Alignment explanation
Indices: 5487148--5487189 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
5487138 TTTTTCAGCA
* * *
5487148 TTAT TTAT TTAT TTAT TTAT TGAT TTAT GTAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
5487190 TTAGTGGCCC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:5487361 original size:21 final size:20
Alignment explanation
Indices: 5487333--5487453 Score: 71
Period size: 21 Copynumber: 5.8 Consensus size: 20
5487323 GATTCACCTG
5487333 TCATCGTTCAAGAGACCCCTC
1 TCATCGTTCAAGAG-CCCCTC
* * * * *
5487354 TTATCGTTAAAGAGGCCATG
1 TCATCGTTCAAGAGCCCCTC
5487374 TCATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGA-GCCCCTC
* * * ** *
5487395 CCACCGTTCAAAAGGCCTTTG
1 TCATCGTTCAAGA-GCCCCTC
* *
5487416 TCATTGTTCAAGAGGTCCCTC
1 TCATCGTTCAAGA-GCCCCTC
* *
5487437 CCACCGTTCAAGAGCCC
1 TCATCGTTCAAGAGCCC
5487454 GATTCACATG
Statistics
Matches: 71, Mismatches: 28, Indels: 3
0.70 0.27 0.03
Matches are distributed among these distances:
20 17 0.24
21 54 0.76
ACGTcount: A:0.23, C:0.33, G:0.19, T:0.25
Consensus pattern (20 bp):
TCATCGTTCAAGAGCCCCTC
Found at i:5487428 original size:42 final size:42
Alignment explanation
Indices: 5487331--5487447 Score: 148
Period size: 42 Copynumber: 2.8 Consensus size: 42
5487321 CCGATTCACC
* ** *
5487331 TGTCATCGTTCAAGAGACCCCTCTTATCGTT-AAAGAGGCCA
1 TGTCATCGTTCAAGAGGCCCCTCCCACCGTTCAAAGAGGCCA
*
5487372 TGTCATCGTTCAAGAGGCCCCTCCCACCGTTCAAA-AGGCCTT
1 TGTCATCGTTCAAGAGGCCCCTCCCACCGTTCAAAGAGGCC-A
* *
5487414 TGTCATTGTTCAAGAGGTCCCTCCCACCGTTCAA
1 TGTCATCGTTCAAGAGGCCCCTCCCACCGTTCAA
5487448 GAGCCCGATT
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
41 32 0.48
42 35 0.52
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.26
Consensus pattern (42 bp):
TGTCATCGTTCAAGAGGCCCCTCCCACCGTTCAAAGAGGCCA
Found at i:5488910 original size:207 final size:206
Alignment explanation
Indices: 5488555--5488950 Score: 652
Period size: 207 Copynumber: 1.9 Consensus size: 206
5488545 GTGCTGAAAG
*
5488555 TGTGCATAAACAACCATTTGTTATTGGTAAGTTTGAGCAAGTGTTGTTAACATATATACTCTTTG
1 TGTGCATAAACAACCAATTGTTATTGGTAAGTTTGAGCAAGTGTTGTTAACATATATAC-CTTTG
* *
5488620 CTGGTTTGAAAATGTTTGGTTAAGTACCTAGAATTCAATAATTTGTTGTTTGTTGGTTTTAGATG
65 CTGGTTTGAAAATGTTTGGTTAAGTACCTAGAATTCAATAATTTGATGTTTGTTGGGTTTAGATG
*
5488685 TGTAGAAAGTGTTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTGAAGTAAGCTACGTGA
130 TGTAGAAAGTGTTGTTTGAGCAAATGTTTGGTTTATGCAGGTTAATCCTGAAGTAAGCTACGTGA
5488750 AATTGATGTATT
195 AATTGATGTATT
* *
5488762 TGTGCATAAACAACCAATTGTTATTGGTAAGTTTGTGCAAGTGTTGTTAACTGTTATATA-C-TT
1 TGTGCATAAACAACCAATTGTTATTGGTAAGTTTGAGCAAGTGTTGTTAAC--ATATATACCTTT
*
5488825 GTTGGTTTGAAAATGTTTGGTTTAAGTACCTAGAATTCAATAATTTGATGTTTGTTGGGTTTAGA
64 GCTGGTTTGAAAATGTTTGG-TTAAGTACCTAGAATTCAATAATTTGATGTTTGTTGGGTTTAGA
* * *
5488890 TGTGTAGAAAGTGTTGTTTGAGCAAATGTTTGGTTTATGTAGGTTAATTCTGAAGTGAGCT
128 TGTGTAGAAAGTGTTGTTTGAGCAAATGTTTGGTTTATGCAGGTTAATCCTGAAGTAAGCT
5488951 GCATGAATGT
Statistics
Matches: 176, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
206 21 0.12
207 149 0.85
209 6 0.03
ACGTcount: A:0.27, C:0.08, G:0.23, T:0.42
Consensus pattern (206 bp):
TGTGCATAAACAACCAATTGTTATTGGTAAGTTTGAGCAAGTGTTGTTAACATATATACCTTTGC
TGGTTTGAAAATGTTTGGTTAAGTACCTAGAATTCAATAATTTGATGTTTGTTGGGTTTAGATGT
GTAGAAAGTGTTGTTTGAGCAAATGTTTGGTTTATGCAGGTTAATCCTGAAGTAAGCTACGTGAA
ATTGATGTATT
Found at i:5491772 original size:24 final size:24
Alignment explanation
Indices: 5491745--5491791 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
5491735 ATCATCATAA
5491745 TCCGAGTATTAACCAAGATCAAAG
1 TCCGAGTATTAACCAAGATCAAAG
* *
5491769 TCCGGGTATTGACCAAGATCAAA
1 TCCGAGTATTAACCAAGATCAAA
5491792 TTTCAAATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.21
Consensus pattern (24 bp):
TCCGAGTATTAACCAAGATCAAAG
Found at i:5492771 original size:52 final size:52
Alignment explanation
Indices: 5492697--5492795 Score: 155
Period size: 52 Copynumber: 1.9 Consensus size: 52
5492687 TATGATTGTC
* *
5492697 TTTAGTCACCGATTTTTTAATTAAGA-GCATTTGATCTCTTATATTATTTGAT
1 TTTAGTCACCGATTTTTTAATTAA-ATGCATTTAATCTCTTACATTATTTGAT
*
5492749 TTTAGTCACCGATTTTTTAATTAAATGCGTTTAATCTCTTACATTAT
1 TTTAGTCACCGATTTTTTAATTAAATGCATTTAATCTCTTACATTAT
5492796 CGATCTATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 1 0.02
52 42 0.98
ACGTcount: A:0.27, C:0.13, G:0.10, T:0.49
Consensus pattern (52 bp):
TTTAGTCACCGATTTTTTAATTAAATGCATTTAATCTCTTACATTATTTGAT
Found at i:5492979 original size:23 final size:23
Alignment explanation
Indices: 5492921--5493005 Score: 163
Period size: 23 Copynumber: 3.7 Consensus size: 23
5492911 GTCTTCTTCT
5492921 TCTCTACAGCTTAACCAGCTCTC
1 TCTCTACAGCTTAACCAGCTCTC
5492944 TCTCT-CAGCTTAACCAGCTCTC
1 TCTCTACAGCTTAACCAGCTCTC
5492966 TCTCTACAGCTTAACCAGCTCTC
1 TCTCTACAGCTTAACCAGCTCTC
5492989 TCTCTACAGCTTAACCA
1 TCTCTACAGCTTAACCA
5493006 CTAACCTGTT
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
22 22 0.36
23 39 0.64
ACGTcount: A:0.22, C:0.39, G:0.08, T:0.31
Consensus pattern (23 bp):
TCTCTACAGCTTAACCAGCTCTC
Found at i:5493841 original size:28 final size:29
Alignment explanation
Indices: 5493787--5493844 Score: 73
Period size: 31 Copynumber: 2.0 Consensus size: 29
5493777 AAAGTATGGT
*
5493787 AAGAAGAAGAAACAACTTGAAAAAGAAGAAG
1 AAGAAGAAGAAACAACCTG--AAAGAAGAAG
*
5493818 AAGAAGAAGAAACAACCTG-GAGAAGAA
1 AAGAAGAAGAAACAACCTGAAAGAAGAA
5493845 ATAGAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 7 0.28
31 18 0.72
ACGTcount: A:0.62, C:0.09, G:0.24, T:0.05
Consensus pattern (29 bp):
AAGAAGAAGAAACAACCTGAAAGAAGAAG
Found at i:5495796 original size:12 final size:12
Alignment explanation
Indices: 5495758--5495796 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
5495748 ATAATAAATC
5495758 AAAGTTTACATT
1 AAAGTTTACATT
*
5495770 AAAGTGTA-ATAT
1 AAAGTTTACAT-T
5495782 AAAGTTTACATT
1 AAAGTTTACATT
5495794 AAA
1 AAA
5495797 ATTACATGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 2 0.09
12 19 0.83
13 2 0.09
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.36
Consensus pattern (12 bp):
AAAGTTTACATT
Found at i:5502423 original size:29 final size:31
Alignment explanation
Indices: 5502342--5502425 Score: 88
Period size: 29 Copynumber: 2.8 Consensus size: 31
5502332 CAAAATATAT
* *
5502342 AACTTTT-GAAAA-TTATACTTTAGTCT-CTA
1 AACTTTTCCAAAATTTATACTTTGGT-TACTA
*
5502371 AACTTTTCCAAAGTTTATACTTTGGTTACTA
1 AACTTTTCCAAAATTTATACTTTGGTTACTA
*
5502402 AAC-TTT-CAAAATTTATATTTTGGT
1 AACTTTTCCAAAATTTATACTTTGGT
5502426 CCTAACTAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
29 23 0.49
30 7 0.15
31 17 0.36
ACGTcount: A:0.32, C:0.13, G:0.08, T:0.46
Consensus pattern (31 bp):
AACTTTTCCAAAATTTATACTTTGGTTACTA
Found at i:5505050 original size:62 final size:63
Alignment explanation
Indices: 5504923--5505063 Score: 151
Period size: 62 Copynumber: 2.3 Consensus size: 63
5504913 CTCGGGGTCT
** ** *
5504923 AGTATCGATA-TTGAGGTATTTTTGGAAACATCAAATCCAAATTTGGTATAGATACTCACAAG
1 AGTATCGATACTCAAGGTATTTTTCAAAACATCAAAGCCAAATTTGGTATAGATACTCACAAG
* * * * * ***
5504985 AGTATCGGTAC-CAAGGTATTTTTCAAAACATCAAAGCTAATTTTGGTATCGATACTTAGGTG
1 AGTATCGATACTCAAGGTATTTTTCAAAACATCAAAGCCAAATTTGGTATAGATACTCACAAG
5505047 AGTATCGATACTCAAGG
1 AGTATCGATACTCAAGG
5505064 GGTCAGTATA
Statistics
Matches: 63, Mismatches: 14, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
62 58 0.92
63 5 0.08
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (63 bp):
AGTATCGATACTCAAGGTATTTTTCAAAACATCAAAGCCAAATTTGGTATAGATACTCACAAG
Found at i:5514808 original size:7 final size:7
Alignment explanation
Indices: 5514796--5514902 Score: 62
Period size: 7 Copynumber: 15.6 Consensus size: 7
5514786 ATTCATATTC
5514796 AAGAAAA
1 AAGAAAA
5514803 AAGAAAA
1 AAGAAAA
5514810 AAGAAAA
1 AAGAAAA
*
5514817 TATAG-TAA
1 -A-AGAAAA
5514825 AAGAAAA
1 AAGAAAA
*
5514832 GAGAAAA
1 AAGAAAA
* *
5514839 GATAAAA
1 AAGAAAA
*
5514846 AA-ACAA
1 AAGAAAA
* *
5514852 AATAGAA
1 AAGAAAA
5514859 AAGAAATA
1 AAGAAA-A
*
5514867 AA-AAGA
1 AAGAAAA
5514873 AAGAAAA
1 AAGAAAA
*
5514880 AAG-AAT
1 AAGAAAA
5514886 AAG-AAA
1 AAGAAAA
*
5514892 AAGAAGA
1 AAGAAAA
5514899 AAGA
1 AAGA
5514903 GAACATATTA
Statistics
Matches: 79, Mismatches: 14, Indels: 14
0.74 0.13 0.13
Matches are distributed among these distances:
6 20 0.25
7 51 0.65
8 6 0.08
9 2 0.03
ACGTcount: A:0.77, C:0.01, G:0.16, T:0.07
Consensus pattern (7 bp):
AAGAAAA
Found at i:5514848 original size:22 final size:22
Alignment explanation
Indices: 5514799--5514905 Score: 92
Period size: 22 Copynumber: 4.7 Consensus size: 22
5514789 CATATTCAAG
* *
5514799 AAAAAAGAAAAAAGAAAATATA
1 AAAAAAGAAAAGAGAAAAGATA
**
5514821 GTAAAAGAAAAGAGAAAAGATA
1 AAAAAAGAAAAGAGAAAAGATA
* *
5514843 AAAAAACAAAATAGAAAAGA-A
1 AAAAAAGAAAAGAGAAAAGATA
*
5514864 ATAAAAAG-AAAGAAAAAAGAATA
1 A-AAAAAGAAAAGAGAAAAG-ATA
5514887 AGAAAAAGAAGAAAGAGAA
1 A-AAAAAG-A-AAAGAGAA
5514906 CATATTAAGT
Statistics
Matches: 66, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
21 11 0.17
22 40 0.61
23 8 0.12
26 7 0.11
ACGTcount: A:0.77, C:0.01, G:0.16, T:0.07
Consensus pattern (22 bp):
AAAAAAGAAAAGAGAAAAGATA
Found at i:5514894 original size:19 final size:20
Alignment explanation
Indices: 5514857--5514902 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
5514847 AACAAAATAG
5514857 AAAAGAAATAAAAAGAAAGAA
1 AAAAG-AATAAAAAGAAAGAA
*
5514878 AAAAGAATAAGAA-AAAGAA
1 AAAAGAATAAAAAGAAAGAA
*
5514897 GAAAGA
1 AAAAGA
5514903 GAACATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 11 0.48
20 7 0.30
21 5 0.22
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.04
Consensus pattern (20 bp):
AAAAGAATAAAAAGAAAGAA
Found at i:5518137 original size:104 final size:104
Alignment explanation
Indices: 5517952--5518144 Score: 253
Period size: 104 Copynumber: 1.9 Consensus size: 104
5517942 CTTTAAATTA
* * * * *
5517952 TCCAGATTGACCCAACTTCCTCAACGAGAATGAACAATGTCATATGAAAGCAGCCAGAACTATTC
1 TCCAAATTGACCCAACTTCCTCAACAAGAAGGAACAACGTCATATGAAAACAGCCAGAACTATTC
** *
5518017 AACATGGATGAGCAGTGTCGTCTTCAACACTAGATTATC
66 AACATAAATGAGCAGTGTCATCTTCAACACTAGATTATC
* * * * *
5518056 TCCAAATTGACTCGACTTCCTCAACAAGAAGGAACAACGTCATTTGAAAAC-GATCAGAACTCTT
1 TCCAAATTGACCCAACTTCCTCAACAAGAAGGAACAACGTCATATGAAAACAG-CCAGAACTATT
5518120 CAACATAAATGAGCAGTGTCATCTT
65 CAACATAAATGAGCAGTGTCATCTT
5518145 TAGCAAACAA
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
103 1 0.01
104 74 0.99
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (104 bp):
TCCAAATTGACCCAACTTCCTCAACAAGAAGGAACAACGTCATATGAAAACAGCCAGAACTATTC
AACATAAATGAGCAGTGTCATCTTCAACACTAGATTATC
Found at i:5522245 original size:32 final size:32
Alignment explanation
Indices: 5522209--5522321 Score: 111
Period size: 32 Copynumber: 3.5 Consensus size: 32
5522199 GTACATTTTT
* *
5522209 TGAATGCAATACTAACTAT-GTGGTGCATTATC
1 TGAATGCAATACTAACTATACT-ATGCATTATC
* * *
5522241 TGAATGCCATGCTAACTTTACTATGCATTATC
1 TGAATGCAATACTAACTATACTATGCATTATC
* * *
5522273 TGAATGCAATATTACCTCTACTATGCATTATC
1 TGAATGCAATACTAACTATACTATGCATTATC
* **
5522305 TAAATATAATACTAACT
1 TGAATGCAATACTAACT
5522322 TTATTGTGAC
Statistics
Matches: 65, Mismatches: 15, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
32 64 0.98
33 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.36
Consensus pattern (32 bp):
TGAATGCAATACTAACTATACTATGCATTATC
Found at i:5522810 original size:16 final size:16
Alignment explanation
Indices: 5522785--5522817 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5522775 TTGTTGTTTC
5522785 TAGCTATTACTATTTT
1 TAGCTATTACTATTTT
*
5522801 TAGCTGTTACTATTTT
1 TAGCTATTACTATTTT
5522817 T
1 T
5522818 GTTTTTGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.58
Consensus pattern (16 bp):
TAGCTATTACTATTTT
Found at i:5526271 original size:23 final size:22
Alignment explanation
Indices: 5526214--5526278 Score: 103
Period size: 22 Copynumber: 2.9 Consensus size: 22
5526204 AGTCGAGGGT
*
5526214 TACATAGGTCTTTCGGGACATA
1 TACATAGGTCCTTCGGGACATA
*
5526236 TACATAGGTCCTTCAGGACATA
1 TACATAGGTCCTTCGGGACATA
5526258 TACATGAGGTCCTTCGGGACA
1 TACAT-AGGTCCTTCGGGACA
5526279 AATTTTATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 25 0.64
23 14 0.36
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.28
Consensus pattern (22 bp):
TACATAGGTCCTTCGGGACATA
Found at i:5526449 original size:26 final size:26
Alignment explanation
Indices: 5526419--5526468 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
5526409 TTTCTTATAA
5526419 GATATTATGTTATTATTTGTTAATTT
1 GATATTATGTTATTATTTGTTAATTT
5526445 GATATTATGTTATTATTTGTTAAT
1 GATATTATGTTATTATTTGTTAAT
5526469 AATAGATCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (26 bp):
GATATTATGTTATTATTTGTTAATTT
Found at i:5529198 original size:12 final size:14
Alignment explanation
Indices: 5529169--5529197 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5529159 TAAAGTGAAC
5529169 AAATTTTAACACAA
1 AAATTTTAACACAA
5529183 AAATTTTAACA-AA
1 AAATTTTAACACAA
5529196 AA
1 AA
5529198 TCTTACGGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (14 bp):
AAATTTTAACACAA
Found at i:5531377 original size:29 final size:27
Alignment explanation
Indices: 5531299--5531392 Score: 116
Period size: 28 Copynumber: 3.3 Consensus size: 27
5531289 AATGTAGTGA
5531299 TTGTAAAAATATAGGTTGTTATTGTAAT
1 TTGTAAAAATATA-GTTGTTATTGTAAT
*
5531327 ATGTAAAAATATGAGTTGTTATTGTAAT
1 TTGTAAAAATAT-AGTTGTTATTGTAAT
**
5531355 TTGTAAAAAATATATGTCATTATTGTAAT
1 TTGT-AAAAATATA-GTTGTTATTGTAAT
*
5531384 TTATAAAAA
1 TTGTAAAAA
5531393 GATTTGTTCT
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
28 34 0.59
29 24 0.41
ACGTcount: A:0.41, C:0.01, G:0.14, T:0.44
Consensus pattern (27 bp):
TTGTAAAAATATAGTTGTTATTGTAAT
Found at i:5531407 original size:29 final size:28
Alignment explanation
Indices: 5531317--5531537 Score: 173
Period size: 29 Copynumber: 7.7 Consensus size: 28
5531307 ATATAGGTTG
* * * ** *
5531317 TTATTGTAATATGTAAAAATATGAGTTG
1 TTATTGTAATTTATAAAAAGATTTGTTC
*
5531345 TTATTGTAATTTGTAAAAA-ATATATG-TC
1 TTATTGTAATTTATAAAAAGAT-T-TGTTC
5531373 ATTATTGTAATTTATAAAAAGATTTGTTC
1 -TTATTGTAATTTATAAAAAGATTTGTTC
* *
5531402 TCTATT-TAAAATTATAAAAAGATTTGTCC
1 T-TATTGT-AATTTATAAAAAGATTTGTTC
* *
5531431 TTTATTGTAATTTATAAGAAGATTT-ATC
1 -TTATTGTAATTTATAAAAAGATTTGTTC
* *
5531459 TTCTATTATAATTTATAAAAAGATTTGTCTG
1 -T-TATTGTAATTTATAAAAAGATTTGT-TC
*
5531490 TTATTGTAATTTATAAAAA-ACTTTGTCC
1 TTATTGTAATTTATAAAAAGA-TTTGTTC
*
5531518 TTAAATGTAATTTATAAAAA
1 TT-ATTGTAATTTATAAAAA
5531538 TTATTTAATT
Statistics
Matches: 160, Mismatches: 19, Indels: 27
0.78 0.09 0.13
Matches are distributed among these distances:
27 2 0.01
28 29 0.18
29 123 0.77
30 5 0.03
31 1 0.01
ACGTcount: A:0.39, C:0.05, G:0.10, T:0.46
Consensus pattern (28 bp):
TTATTGTAATTTATAAAAAGATTTGTTC
Found at i:5531440 original size:58 final size:58
Alignment explanation
Indices: 5531374--5531508 Score: 195
Period size: 58 Copynumber: 2.3 Consensus size: 58
5531364 ATATATGTCA
*
5531374 TTATTGTAATTTATAAAAAGATTTGT-TCTCTATT-TAAAATTATAAAAAGATTTGTCCT-
1 TTATTGTAATTTATAAAAAGATTTATCT-TCTATTAT-AAATTATAAAAAGATTTGT-CTG
* *
5531432 TTATTGTAATTTATAAGAAGATTTATCTTCTATTATAATTTATAAAAAGATTTGTCTG
1 TTATTGTAATTTATAAAAAGATTTATCTTCTATTATAAATTATAAAAAGATTTGTCTG
5531490 TTATTGTAATTTATAAAAA
1 TTATTGTAATTTATAAAAA
5531509 ACTTTGTCCT
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
57 2 0.03
58 66 0.94
59 2 0.03
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.47
Consensus pattern (58 bp):
TTATTGTAATTTATAAAAAGATTTATCTTCTATTATAAATTATAAAAAGATTTGTCTG
Found at i:5531471 original size:87 final size:87
Alignment explanation
Indices: 5531375--5531534 Score: 227
Period size: 87 Copynumber: 1.8 Consensus size: 87
5531365 TATATGTCAT
* * *
5531375 TATTGTAATTTATAAAAAGATTTGTTCT-CTATT-TAAAATTATAAAAAGA-TTTGTCCTTTATT
1 TATTATAATTTATAAAAAGATTTG-TCTGCTATTGT-AAATTATAAAAA-ACTTTGTCCTTAAAT
5531437 GTAATTTATAAGAAGATTTATCTTC
63 GTAATTTATAAGAAGATTTATCTTC
* *
5531462 TATTATAATTTATAAAAAGATTTGTCTGTTATTGTAATTTATAAAAAACTTTGTCCTTAAATGTA
1 TATTATAATTTATAAAAAGATTTGTCTGCTATTGTAAATTATAAAAAACTTTGTCCTTAAATGTA
5531527 ATTTATAA
66 ATTTATAA
5531535 AAATTATTTA
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
86 4 0.06
87 60 0.92
88 1 0.02
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (87 bp):
TATTATAATTTATAAAAAGATTTGTCTGCTATTGTAAATTATAAAAAACTTTGTCCTTAAATGTA
ATTTATAAGAAGATTTATCTTC
Found at i:5531545 original size:24 final size:23
Alignment explanation
Indices: 5531518--5531569 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
5531508 AACTTTGTCC
5531518 TTAAATGTAATTTATAAAAATTAT
1 TTAAATGTAATTTATAAAAATT-T
* * * *
5531542 TTAATTTTAATTTGTATAAATTT
1 TTAAATGTAATTTATAAAAATTT
5531565 TTAAA
1 TTAAA
5531570 AATTTTAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (23 bp):
TTAAATGTAATTTATAAAAATTT
Found at i:5534324 original size:17 final size:17
Alignment explanation
Indices: 5534290--5534341 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
5534280 ACCGGACAAA
* *
5534290 TTTATTATTTTAGAGAG
1 TTTATTAATTTACAGAG
*
5534307 TTTATTAATTTACCGAG
1 TTTATTAATTTACAGAG
*
5534324 --TATTAATTTAAAGAG
1 TTTATTAATTTACAGAG
5534339 TTT
1 TTT
5534342 CTACTGTATA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (17 bp):
TTTATTAATTTACAGAG
Found at i:5538893 original size:23 final size:22
Alignment explanation
Indices: 5538829--5538893 Score: 85
Period size: 22 Copynumber: 2.9 Consensus size: 22
5538819 AGTCAAGGGT
*
5538829 TACATAGGTCCTTCGGGATATA
1 TACATAGGTCCTTCGGGACATA
* **
5538851 TAGATAGGTCCTTCAAGACATA
1 TACATAGGTCCTTCGGGACATA
5538873 TACATAAGGTCCTTCGGGACA
1 TACAT-AGGTCCTTCGGGACA
5538894 AATTTCATAT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
22 22 0.63
23 13 0.37
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (22 bp):
TACATAGGTCCTTCGGGACATA
Found at i:5541025 original size:40 final size:39
Alignment explanation
Indices: 5540981--5541121 Score: 128
Period size: 38 Copynumber: 3.6 Consensus size: 39
5540971 TTCAAAAATT
*
5540981 ATATATTATATATGTTTCCAAAAAAAATATTTTTGAAACA
1 ATATATTATATATGTTT-CAAAAAAAATATTTTCGAAACA
* *
5541021 ATATATTATATATGCTTTC--AAAAAATGTTTTCGAAACT
1 ATATATTATATATG-TTTCAAAAAAAATATTTTCGAAACA
* * * * *
5541059 ATATAATATATATGTTTTC--AAAAATTGTTTTCCCAAACT
1 ATATATTATATATG-TTTCAAAAAAAATATTTT-CGAAACA
*
5541098 ATATAATATATATGTTTTCAAAAA
1 ATATATTATATATG-TTTCAAAAA
5541122 TTGTTTTCCC
Statistics
Matches: 90, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
38 44 0.49
39 25 0.28
40 15 0.17
41 6 0.07
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.42
Consensus pattern (39 bp):
ATATATTATATATGTTTCAAAAAAAATATTTTCGAAACA
Found at i:5541044 original size:38 final size:38
Alignment explanation
Indices: 5540980--5541364 Score: 303
Period size: 37 Copynumber: 10.1 Consensus size: 38
5540970 CTTCAAAAAT
* * * *
5540980 TATATATTATATATGTTTCCAAAAAAAATATTTTTGAAAC
1 TATATAATATATATGTTTTC--AAAAAATGTTTTCGAAAC
* * *
5541020 AATATATTATATATGCTTTCAAAAAATGTTTTCGAAAC
1 TATATAATATATATGTTTTCAAAAAATGTTTTCGAAAC
* *
5541058 TATATAATATATATGTTTTCAAAAATTGTTTTCCCAAAC
1 TATATAATATATATGTTTTCAAAAAATGTTTT-CGAAAC
* *
5541097 TATATAATATATATGTTTTCAAAAATTGTTTTCCCAAAC
1 TATATAATATATATGTTTTCAAAAAATGTTTT-CGAAAC
* * * * *
5541136 TATATAATATATATGGTTTC-ATAGATCCTTTTCAAAAC
1 TATATAATATATATGTTTTCAAAAAAT-GTTTTCGAAAC
* *
5541174 TATAT-A-GTATATGTTTTCAAAAAATTGTTTTCAAAAC
1 TATATAATATATATGTTTTCAAAAAA-TGTTTTCGAAAC
* *
5541211 TATAT-A-ATATACGTTTTCAAAAAAATTGTTTT-TAAAC
1 TATATAATATATATGTTTTC-AAAAAA-TGTTTTCGAAAC
* * *
5541248 TCTAT-A-ATATACGTTTTCAAAAAAAATGTTTTTCAAAAC
1 TATATAATATATATGTTTTC--AAAAAATG-TTTTCGAAAC
*
5541287 TATAT-A-ATATACGTTTT-AAAAAATTGTTTTTCGAAAC
1 TATATAATATATATGTTTTCAAAAAA-TG-TTTTCGAAAC
* *
5541324 TATAT-A-ATATCTGTTTTC-AAAAATGTGTTTTGAAAAC
1 TATATAATATATATGTTTTCAAAAAATGT-TTTCG-AAAC
5541361 TATA
1 TATA
5541365 ATATATGTTT
Statistics
Matches: 302, Mismatches: 31, Indels: 27
0.84 0.09 0.08
Matches are distributed among these distances:
35 1 0.00
36 22 0.07
37 93 0.31
38 82 0.27
39 87 0.29
40 17 0.06
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.42
Consensus pattern (38 bp):
TATATAATATATATGTTTTCAAAAAATGTTTTCGAAAC
Found at i:5541108 original size:39 final size:36
Alignment explanation
Indices: 5541022--5541404 Score: 349
Period size: 37 Copynumber: 10.3 Consensus size: 36
5541012 TTTGAAACAA
* * * *
5541022 TATATTATATATGCTTTCAAAAAATGTTTTCGAAAC
1 TATATAATATATGTTTTCAAAAATTGTTTTCAAAAC
*
5541058 TATATAATATATATGTTTTCAAAAATTGTTTTCCCAAAC
1 TATAT-A-ATATATGTTTTCAAAAATTGTTTT-CAAAAC
*
5541097 TATATAATATATATGTTTTCAAAAATTGTTTTCCCAAAC
1 TATAT-A-ATATATGTTTTCAAAAATTGTTTT-CAAAAC
* * * **
5541136 TATATAATATATATGGTTTCATAGATCCTTTTCAAAAC
1 TATAT-A-ATATATGTTTTCAAAAATTGTTTTCAAAAC
*
5541174 TATATAGTATATGTTTTCAAAAAATTGTTTTCAAAAC
1 TATATAATATATGTTTTC-AAAAATTGTTTTCAAAAC
* *
5541211 TATATAATATACGTTTTCAAAAAAATTGTTTT-TAAAC
1 TATATAATATATGTTTTC--AAAAATTGTTTTCAAAAC
* * *
5541248 TCTATAATATACGTTTTCAAAAAAAATGTTTTTCAAAAC
1 TATATAATATATGTTTTC--AAAAATTG-TTTTCAAAAC
* * *
5541287 TATATAATATACGTTTTAAAAAATTGTTTTTCGAAAC
1 TATATAATATATGTTTTCAAAAATTG-TTTTCAAAAC
* *
5541324 TATATAATATCTGTTTTCAAAAATGTGTTTTGAAAAC
1 TATATAATATATGTTTTCAAAAAT-TGTTTTCAAAAC
* *** *
5541361 --TATAATATATGTTTTTAAATCGTATTTTCAAAAC
1 TATATAATATATGTTTTCAAAAATTGTTTTCAAAAC
*
5541395 CATATAATAT
1 TATATAATAT
5541405 GTTTTTAAAT
Statistics
Matches: 299, Mismatches: 38, Indels: 20
0.84 0.11 0.06
Matches are distributed among these distances:
34 10 0.03
35 17 0.06
36 23 0.08
37 107 0.36
38 51 0.17
39 91 0.30
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (36 bp):
TATATAATATATGTTTTCAAAAATTGTTTTCAAAAC
Found at i:5541272 original size:76 final size:75
Alignment explanation
Indices: 5541040--5541346 Score: 279
Period size: 76 Copynumber: 4.0 Consensus size: 75
5541030 ATATGCTTTC
* * * *
5541040 AAAAAATG-TTTTCGAAACTATATAATATATATGTTTTCAAAAATTGTTTTCCCAAACTATATAA
1 AAAAAATGTTTTTCAAAACTATAT-A-ATATACGTTTTAAAAAATTGTTTT-TCAAACTATAT-A
*
5541104 TATATATGTTTTC--
62 -ATATACGTTTTCAA
* * * * * * * * ** *
5541117 AAAAATTGTTTTCCCAAACTATATAATATATATGGTTTCATAGA-TCCTTTTCAAAACTATATAG
1 AAAAAATGTTTTTCAAAACTATAT-A-ATATACGTTTTAAAAAATTGTTTTTC-AAACTATATAA
*
5541181 TATATGTTTTC-A
63 TATACGTTTTCAA
* *
5541193 AAAAATTG-TTTTCAAAACTATATAATATACGTTTTCAAAAAAATTGTTTTT-AAACTCTATAAT
1 AAAAAATGTTTTTCAAAACTATATAATATACGTTTT--AAAAAATTGTTTTTCAAACTATATAAT
5541256 ATACGTTTTCAA
64 ATACGTTTTCAA
5541268 AAAAAATGTTTTTCAAAACTATATAATATACGTTTTAAAAAATTGTTTTTCGAAACTATATAATA
1 AAAAAATGTTTTTCAAAACTATATAATATACGTTTTAAAAAATTGTTTTTC-AAACTATATAATA
5541333 T-CTGTTTTCAA
65 TAC-GTTTTCAA
5541344 AAA
1 AAA
5541347 TGTGTTTTGA
Statistics
Matches: 195, Mismatches: 24, Indels: 23
0.81 0.10 0.10
Matches are distributed among these distances:
73 9 0.05
74 34 0.17
75 36 0.18
76 66 0.34
77 20 0.10
78 30 0.15
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.42
Consensus pattern (75 bp):
AAAAAATGTTTTTCAAAACTATATAATATACGTTTTAAAAAATTGTTTTTCAAACTATATAATAT
ACGTTTTCAA
Found at i:5541405 original size:34 final size:34
Alignment explanation
Indices: 5541367--5541443 Score: 118
Period size: 34 Copynumber: 2.3 Consensus size: 34
5541357 AAACTATAAT
*
5541367 ATATGTTTTTAAATCGTATTTTCAAAACCATATA
1 ATATGTTTTTAAATCATATTTTCAAAACCATATA
* *
5541401 ATATGTTTTTAAATCATATTTTCCAAACCATATT
1 ATATGTTTTTAAATCATATTTTCAAAACCATATA
*
5541435 ATATATTTT
1 ATATGTTTT
5541444 CAAACTGATT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.36, C:0.12, G:0.04, T:0.48
Consensus pattern (34 bp):
ATATGTTTTTAAATCATATTTTCAAAACCATATA
Found at i:5543021 original size:176 final size:177
Alignment explanation
Indices: 5542726--5543075 Score: 585
Period size: 176 Copynumber: 2.0 Consensus size: 177
5542716 AAAAATTTAA
*
5542726 AATATTTGCACAAACCAACTTACCTTAGTGGTTAAAGGAATCATTGTTGTTCCTAGATGTCACGA
1 AATATTTGCACAAACCAACTTACCTTAGTGGTTAAAGGAATCATTGTTGTTCCTAGAGGTCACGA
* * *
5542791 GTTCAAGCACCAGCGACTGCAGCAGGGTGATTGAGTGTTCATTGTTAAATGGTTGAGAGTATTTA
66 GTTCAAGCACCAGCGACTGCAGCAGGGTAATTGAGTGTTCATTGTCAAATGGTTGAAAGTATTTA
*
5542856 GAACAAATACTACTTTATAATCACCTTAG-TTTAATAAAAAAATCAG
131 GAACAAATACTACTTTATAATCACCTTAGAGTTAATAAAAAAATCAG
*
5542902 AATATTTGCACAAACCAACTTACCTTAGTGGTTAAAGGAATCATTGTTGTTCCTAGAGGTCACGG
1 AATATTTGCACAAACCAACTTACCTTAGTGGTTAAAGGAATCATTGTTGTTCCTAGAGGTCACGA
* * *
5542967 GTTCAAGCACCAGCTACTGTAGCAGGGTAATTGAGTGTTCATTGTCAGATGGTTGAAAGTATTTA
66 GTTCAAGCACCAGCGACTGCAGCAGGGTAATTGAGTGTTCATTGTCAAATGGTTGAAAGTATTTA
* **
5543032 GAACAAATACTACTTTGTAATCGTCTTAGAGTTAATAAAAAAAT
131 GAACAAATACTACTTTATAATCACCTTAGAGTTAATAAAAAAAT
5543076 TTAAAATATT
Statistics
Matches: 161, Mismatches: 12, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
176 148 0.92
177 13 0.08
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.31
Consensus pattern (177 bp):
AATATTTGCACAAACCAACTTACCTTAGTGGTTAAAGGAATCATTGTTGTTCCTAGAGGTCACGA
GTTCAAGCACCAGCGACTGCAGCAGGGTAATTGAGTGTTCATTGTCAAATGGTTGAAAGTATTTA
GAACAAATACTACTTTATAATCACCTTAGAGTTAATAAAAAAATCAG
Found at i:5543130 original size:21 final size:23
Alignment explanation
Indices: 5543081--5543136 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 23
5543071 AAAATTTAAA
5543081 ATATTTTATAAAATCATACTTATT
1 ATATTTT-TAAAATCATACTTATT
*
5543105 -T-TTTTTCAAATCA-A-TTATT
1 ATATTTTTAAAATCATACTTATT
5543124 ATATTTTTAAAAT
1 ATATTTTTAAAAT
5543137 AGTTATATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
19 5 0.18
20 2 0.07
21 16 0.57
22 4 0.14
23 1 0.04
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (23 bp):
ATATTTTTAAAATCATACTTATT
Found at i:5543165 original size:23 final size:22
Alignment explanation
Indices: 5543120--5543165 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
5543110 TCAAATCAAT
* *
5543120 TATTATATTTTTAAAATAGTTA
1 TATTATATTTTTAAAAAAATTA
5543142 TATTATATTTATTAAAAAAATTA
1 TATTATATTT-TTAAAAAAATTA
5543165 T
1 T
5543166 TATTTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
TATTATATTTTTAAAAAAATTA
Found at i:5550364 original size:22 final size:22
Alignment explanation
Indices: 5550334--5550411 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 22
5550324 TTGACAAATA
*
5550334 ACTAAAGTGCCTTACCACTGGT
1 ACTAAAGTGCCTTAACACTGGT
* * * *
5550356 ATTAAAGTGCCTCATCACTGCT
1 ACTAAAGTGCCTTAACACTGGT
* *
5550378 ACAAAAGTGCATTTAACACT-GT
1 ACTAAAGTGC-CTTAACACTGGT
5550400 ACTAAAGTGCCT
1 ACTAAAGTGCCT
5550412 CAGTACTGAT
Statistics
Matches: 43, Mismatches: 12, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
21 1 0.02
22 36 0.84
23 6 0.14
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.28
Consensus pattern (22 bp):
ACTAAAGTGCCTTAACACTGGT
Found at i:5553858 original size:21 final size:21
Alignment explanation
Indices: 5553832--5553884 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
5553822 TTGTGCATAG
* *
5553832 GATCGATCTCTTAG-GGAACAA
1 GATCGATC-CCTAGAGGAAAAA
5553853 GATCGATCCCTAGAGGAAAAA
1 GATCGATCCCTAGAGGAAAAA
*
5553874 GATCAATCCCT
1 GATCGATCCCT
5553885 CTAAATAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 4 0.14
21 24 0.86
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.21
Consensus pattern (21 bp):
GATCGATCCCTAGAGGAAAAA
Found at i:5563501 original size:53 final size:53
Alignment explanation
Indices: 5563443--5563548 Score: 185
Period size: 53 Copynumber: 2.0 Consensus size: 53
5563433 TTGAGTCATA
*
5563443 AACTCTGTATTTTAAGTTAATGATATATATTGGAGACTTATGTCGGGAGCTCC
1 AACTCTGTATTTTAAGTTAATGATATATATTGGAGACTTATGTCGGGAACTCC
* *
5563496 AACTCTGTATTTTAAGTTAATGATATATTTTGGAGACTTATGTTGGGAACTCC
1 AACTCTGTATTTTAAGTTAATGATATATATTGGAGACTTATGTCGGGAACTCC
5563549 CCCGTATTAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (53 bp):
AACTCTGTATTTTAAGTTAATGATATATATTGGAGACTTATGTCGGGAACTCC
Found at i:5571262 original size:22 final size:20
Alignment explanation
Indices: 5571218--5571284 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
5571208 CCTAAATTTG
*
5571218 GTATCGATAC-TAGTC-A-A
1 GTATCGATACATAGACTAGA
*
5571235 GTATCGATACCATAGCACTGGA
1 GTATCGATA-CATAG-ACTAGA
* *
5571257 GTATCGGTACTTAGACTAGA
1 GTATCGATACATAGACTAGA
5571277 GTATCGAT
1 GTATCGAT
5571285 TCTTTCTTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
17 9 0.23
18 1 0.03
19 3 0.08
20 13 0.33
21 4 0.10
22 9 0.23
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.28
Consensus pattern (20 bp):
GTATCGATACATAGACTAGA
Found at i:5571342 original size:20 final size:19
Alignment explanation
Indices: 5571317--5571355 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
5571307 ATTAGTTAAG
5571317 GGGTATCAATACCAATAGGT
1 GGGTATCAATACCAA-AGGT
**
5571337 GGGTATGGATACCAAAGGT
1 GGGTATCAATACCAAAGGT
5571356 CTAGTATCGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.33, C:0.13, G:0.31, T:0.23
Consensus pattern (19 bp):
GGGTATCAATACCAAAGGT
Found at i:5572287 original size:29 final size:29
Alignment explanation
Indices: 5572253--5572311 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
5572243 CCTAAATTAA
*
5572253 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTACTTACATCAATTTAGT
5572282 TTTGATGTCATTACTTACATCAATTTAGT
1 TTTGATGTCATTACTTACATCAATTTAGT
5572311 T
1 T
5572312 AAGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTACTTACATCAATTTAGT
Found at i:5578458 original size:19 final size:19
Alignment explanation
Indices: 5578434--5578503 Score: 99
Period size: 19 Copynumber: 3.7 Consensus size: 19
5578424 TAATTAAATC
5578434 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
5578453 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
*
5578472 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
5578491 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
5578504 TTTCAATTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
17 4 0.08
18 6 0.12
19 38 0.79
ACGTcount: A:0.24, C:0.16, G:0.37, T:0.23
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:5578460 original size:64 final size:62
Alignment explanation
Indices: 5578308--5578469 Score: 157
Period size: 64 Copynumber: 2.5 Consensus size: 62
5578298 TTGGACTCCT
* * * * *
5578308 AGTGCATCGGTGCACT-AAGAGTGCACCGATGCATGAAGTGCATTCGATGTTTGAAAAATAGCC
1 AGTGCATCGATGCA-TGGAGAGTGCATCGATGCATCAAATGCATTCGATGTTTGAAAAATAG-C
* *** *
5578371 TGGTGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATCAG
1 -AGTGCATCGATGCATGGAGAGTGCATCGATGCATCAAATGCATTCGATGTTTGAA--AAAT-AG
5578436 -
62 C
*
5578436 AGTGCATCGATGCATGGAGAGTGCATCGGTGCAT
1 AGTGCATCGATGCATGGAGAGTGCATCGATGCAT
5578470 GGAGAGTGCA
Statistics
Matches: 79, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
63 1 0.01
64 72 0.91
66 4 0.05
67 2 0.03
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (62 bp):
AGTGCATCGATGCATGGAGAGTGCATCGATGCATCAAATGCATTCGATGTTTGAAAAATAGC
Found at i:5578479 original size:83 final size:84
Alignment explanation
Indices: 5578373--5578535 Score: 211
Period size: 83 Copynumber: 2.0 Consensus size: 84
5578363 AAATAGCCTG
*** *
5578373 GTGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATCA-GA
1 GTGCATCGATGCATGGAGAGTGCATCGATGCATCAAATGCATTCGATGTTTCAATTAAATCATGA
*
5578437 GTGCATCGATGCATGGAGA
66 ATGCATCGATGCATGGAGA
* * ** * * *
5578456 GTGCATCGGTGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTTTCAATTTATTCATTA
1 GTGCATCGATGCATGGAGAGTGCATCGATGCATCAAATGCATTCGATGTTTCAATTAAATCATGA
5578521 ATGCATCGATGCATG
66 ATGCATCGATGCATG
5578536 ATATTGATGC
Statistics
Matches: 67, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
83 52 0.78
84 15 0.22
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (84 bp):
GTGCATCGATGCATGGAGAGTGCATCGATGCATCAAATGCATTCGATGTTTCAATTAAATCATGA
ATGCATCGATGCATGGAGA
Found at i:5581198 original size:24 final size:23
Alignment explanation
Indices: 5581127--5581206 Score: 85
Period size: 24 Copynumber: 3.5 Consensus size: 23
5581117 TATGGTCTAG
*
5581127 TGCATCGATGCACATTCAAGGCA
1 TGCATCGATGCACATTCAAGGGA
* * *
5581150 TACATCGGTG--CA-TCATGCGGA
1 TGCATCGATGCACATTCAAG-GGA
5581171 TGCATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTC-AAGGGA
5581195 TGCATCGATGCA
1 TGCATCGATGCA
5581207 TTGTTAAGTG
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
20 4 0.09
21 12 0.27
23 10 0.22
24 17 0.38
25 2 0.04
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.23
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAGGGA
Found at i:5581219 original size:44 final size:42
Alignment explanation
Indices: 5581104--5581226 Score: 113
Period size: 44 Copynumber: 2.8 Consensus size: 42
5581094 AAAACCCGAC
* *
5581104 GGATGCATCGATGTATGGTCTAGTGCATCGATGCACATTCAAG
1 GGATGCATCGATGCATTGT-TAGTGCATCGATGCACATTCAAG
* * * **
5581147 GCATACATCGGTGCATCATG-CGGATGCATCGATGCACATTCAAAG
1 GGATGCATCGATGCAT--TGTTAG-TGCATCGATGCACATTC-AAG
*
5581192 GGATGCATCGATGCATTGTTAAGTGCATCGGTGCA
1 GGATGCATCGATGCATTGTT-AGTGCATCGATGCA
5581227 TTAAGAACAA
Statistics
Matches: 61, Mismatches: 13, Indels: 11
0.72 0.15 0.13
Matches are distributed among these distances:
43 15 0.25
44 28 0.46
45 18 0.30
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (42 bp):
GGATGCATCGATGCATTGTTAGTGCATCGATGCACATTCAAG
Found at i:5587115 original size:45 final size:42
Alignment explanation
Indices: 5587018--5587124 Score: 115
Period size: 45 Copynumber: 2.4 Consensus size: 42
5587008 CGGTGCACTA
* * *
5587018 AGAGTGCATCGAAGCATGAAGTGCATTCGATGTTTGAAAAAT
1 AGAGTGCATCGATGCATCAAATGCATTCGATGTTTGAAAAAT
* *
5587060 AGCCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAAT
1 AG---AGTGCATCGATGCATCAAATGCATTCGATGTTTGAA--AAAT
5587107 CAGAGTGCATCGATGCAT
1 -AGAGTGCATCGATGCAT
5587125 GGAGAGTGCA
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.04
45 45 0.85
47 4 0.08
48 2 0.04
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (42 bp):
AGAGTGCATCGATGCATCAAATGCATTCGATGTTTGAAAAAT
Found at i:5587132 original size:19 final size:19
Alignment explanation
Indices: 5587108--5587158 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
5587098 TAATTAAATC
5587108 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
5587127 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
5587146 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
5587159 TTTCAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:5590331 original size:20 final size:20
Alignment explanation
Indices: 5590306--5590380 Score: 64
Period size: 20 Copynumber: 3.6 Consensus size: 20
5590296 AAATGATGGT
5590306 AATAATAATAAAGATAAAAA
1 AATAATAATAAAGATAAAAA
* *
5590326 AATAATAAAAAAAATAAAAA
1 AATAATAATAAAGATAAAAA
*
5590346 GAT-ATATATAATAGTAATAAAAA
1 AATAATA-ATAA-AG--ATAAAAA
5590369 AACTAA-AATAAA
1 AA-TAATAATAAA
5590381 TAAATAACTA
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
19 3 0.07
20 23 0.53
21 1 0.02
22 1 0.02
23 12 0.28
24 2 0.05
25 1 0.02
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.21
Consensus pattern (20 bp):
AATAATAATAAAGATAAAAA
Found at i:5592714 original size:105 final size:105
Alignment explanation
Indices: 5592592--5593260 Score: 1320
Period size: 105 Copynumber: 6.4 Consensus size: 105
5592582 TATTGTTCAG
5592592 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACC
*
5592657 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGT
5592697 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACC
5592762 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGT
5592802 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACC
5592867 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGT
5592907 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACC
5592972 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGT
5593012 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACC
*
5593077 AACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGT
5593117 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACC
5593182 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGT
5593222 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
5593261 GGTAAAACCT
Statistics
Matches: 561, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 561 1.00
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGT
Found at i:5598305 original size:744 final size:744
Alignment explanation
Indices: 5596879--5598365 Score: 2902
Period size: 744 Copynumber: 2.0 Consensus size: 744
5596869 CTTCGGGATG
5596879 CATCTTGATCTGATTGTACCCCGAAAATCCATCCATGAATGAAAAGTAGGCGTTCCCGGCCGTAT
1 CATCTTGATCTGATTGTACCCCGAAAATCCATCCATGAATGAAAAGTAGGCGTTCCCGGCCGTAT
5596944 TGTCCACCAGAGTGTCTATGTGTGGCAGAGGAAAGTTGTCCTTGGGACTGGCCTTATTAAGGTCC
66 TGTCCACCAGAGTGTCTATGTGTGGCAGAGGAAAGTTGTCCTTGGGACTGGCCTTATTAAGGTCC
*
5597009 CGGTAATCGACACACATGCGTACTTTCCCGTCCTTCTTCGGCACAGGCACTATGTTGGCCACCCA
131 CGGTAATCGACACACATGCGTACTTTCCCCTCCTTCTTCGGCACAGGCACTATGTTGGCCACCCA
*
5597074 TTCAGGGTATTTGGCTACTTGGAGAAAACCGGCATCAAATTGCTTCTTAACTTCCTCCTTGATCT
196 TTCAGGGTATTTGGCTACTTGGAGAAAACCGACATCAAATTGCTTCTTAACTTCCTCCTTGATCT
*
5597139 TAAGGAGCATTTCTGGTCTCATTCTTCTCAGTTTTTGCTGCACTGGTTTGAATTCTGGTTTGATT
261 TAAGGAGCATTTCTGGTCGCATTCTTCTCAGTTTTTGCTGCACTGGTTTGAATTCTGGTTTGATT
5597204 GGCAGTTTGTGAACAACCATATCTGTGTCTAGTCCCGGCATGTCTTGATACGACCAAGCAAACAC
326 GGCAGTTTGTGAACAACCATATCTGTGTCTAGTCCCGGCATGTCTTGATACGACCAAGCAAACAC
5597269 ATCTTCGTACTCCTGAAGTAAGGCTATCAGGTTTTTTCTTGCTTCAGTCGAAAGAGTTGTGCCGA
391 ATCTTCGTACTCCTGAAGTAAGGCTATCAGGTTTTTTCTTGCTTCAGTCGAAAGAGTTGTGCCGA
5597334 TTTTAACCTCTTTTCGATCTTCCTCAGTGCCCAAATTTAAGATTTCGATCGCCTCCTCATGTGGC
456 TTTTAACCTCTTTTCGATCTTCCTCAGTGCCCAAATTTAAGATTTCGATCGCCTCCTCATGTGGC
5597399 AGTATTTGCTTTTCTTCTTTTTCTATCATTCTCAACAATTCGGTAGGCAAGTTATACTCTTCTTC
521 AGTATTTGCTTTTCTTCTTTTTCTATCATTCTCAACAATTCGGTAGGCAAGTTATACTCTTCTTC
5597464 ATTATCGCCTTCTTCAAATTCCCCAAGACAAATGGTTGATTCAAAATCCACCTCCGGATCAGGGT
586 ATTATCGCCTTCTTCAAATTCCCCAAGACAAATGGTTGATTCAAAATCCACCTCCGGATCAGGGT
5597529 CATTAGTGCCCACATTATCATTATCTGGGAACCTGAAAGGAGGAAGATGTGTATGTGTGAGAGGA
651 CATTAGTGCCCACATTATCATTATCTGGGAACCTGAAAGGAGGAAGATGTGTATGTGTGAGAGGA
5597594 TAATATCCCACACGGAATGGTCAAGAACA
716 TAATATCCCACACGGAATGGTCAAGAACA
5597623 CATCTTGATCTGATTGTACCCCGAAAATCCATCCATGAATGAAAAGTAGGCGTTCCCGGCCGTAT
1 CATCTTGATCTGATTGTACCCCGAAAATCCATCCATGAATGAAAAGTAGGCGTTCCCGGCCGTAT
5597688 TGTCCACCAGAGTGTCTATGTGTGGCAGAGGAAAGTTGTCCTTGGGACTGGCCTTATTAAGGTCC
66 TGTCCACCAGAGTGTCTATGTGTGGCAGAGGAAAGTTGTCCTTGGGACTGGCCTTATTAAGGTCC
* *
5597753 CGGTAATCGATACAGATGCGTACTTTCCCCTCCTTCTTCGGCACAGGCACTATGTTGGCCACCCA
131 CGGTAATCGACACACATGCGTACTTTCCCCTCCTTCTTCGGCACAGGCACTATGTTGGCCACCCA
* *
5597818 TTCAGGGTATTTGGCTAGTTGGAGAAAACCGACATCAAATTGCTTCTTGACTTCCTCCTTGATCT
196 TTCAGGGTATTTGGCTACTTGGAGAAAACCGACATCAAATTGCTTCTTAACTTCCTCCTTGATCT
5597883 TAAGGAGCATTTCTGGTCGCATTCTTCTCAGTTTTTGCTGCACTGGTTTGAATTCTGGTTTGATT
261 TAAGGAGCATTTCTGGTCGCATTCTTCTCAGTTTTTGCTGCACTGGTTTGAATTCTGGTTTGATT
5597948 GGCAGTTTGTGAACAACCATATCTGTGTCTAGTCCCGGCATGTCTTGATACGACCAAGCAAACAC
326 GGCAGTTTGTGAACAACCATATCTGTGTCTAGTCCCGGCATGTCTTGATACGACCAAGCAAACAC
5598013 ATCTTCGTACTCCTGAAGTAAGGCTATCAGGTTTTTTCTTGCTTCAGTCGAAAGAGTTGTGCCGA
391 ATCTTCGTACTCCTGAAGTAAGGCTATCAGGTTTTTTCTTGCTTCAGTCGAAAGAGTTGTGCCGA
5598078 TTTTAACCTCTTTTCGATCTTCCTCAGTGCCCAAATTTAAGATTTCGATCGCCTCCTCATGTGGC
456 TTTTAACCTCTTTTCGATCTTCCTCAGTGCCCAAATTTAAGATTTCGATCGCCTCCTCATGTGGC
5598143 AGTATTTGCTTTTCTTCTTTTTCTATCATTCTCAACAATTCGGTAGGCAAGTTATACTCTTCTTC
521 AGTATTTGCTTTTCTTCTTTTTCTATCATTCTCAACAATTCGGTAGGCAAGTTATACTCTTCTTC
5598208 ATTATCGCCTTCTTCAAATTCCCCAAGACAAATGGTTGATTCAAAATCCACCTCCGGATCAGGGT
586 ATTATCGCCTTCTTCAAATTCCCCAAGACAAATGGTTGATTCAAAATCCACCTCCGGATCAGGGT
*
5598273 CATTAGTGCCCACATTATCGTTATCTGGGAACCTGAAAGGAGGAAGATGTGTATGTGTGAGAGGA
651 CATTAGTGCCCACATTATCATTATCTGGGAACCTGAAAGGAGGAAGATGTGTATGTGTGAGAGGA
5598338 TAATATCCCACACGGAATGGTCAAGAAC
716 TAATATCCCACACGGAATGGTCAAGAAC
5598366 TAACTTTGAG
Statistics
Matches: 735, Mismatches: 8, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
744 735 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (744 bp):
CATCTTGATCTGATTGTACCCCGAAAATCCATCCATGAATGAAAAGTAGGCGTTCCCGGCCGTAT
TGTCCACCAGAGTGTCTATGTGTGGCAGAGGAAAGTTGTCCTTGGGACTGGCCTTATTAAGGTCC
CGGTAATCGACACACATGCGTACTTTCCCCTCCTTCTTCGGCACAGGCACTATGTTGGCCACCCA
TTCAGGGTATTTGGCTACTTGGAGAAAACCGACATCAAATTGCTTCTTAACTTCCTCCTTGATCT
TAAGGAGCATTTCTGGTCGCATTCTTCTCAGTTTTTGCTGCACTGGTTTGAATTCTGGTTTGATT
GGCAGTTTGTGAACAACCATATCTGTGTCTAGTCCCGGCATGTCTTGATACGACCAAGCAAACAC
ATCTTCGTACTCCTGAAGTAAGGCTATCAGGTTTTTTCTTGCTTCAGTCGAAAGAGTTGTGCCGA
TTTTAACCTCTTTTCGATCTTCCTCAGTGCCCAAATTTAAGATTTCGATCGCCTCCTCATGTGGC
AGTATTTGCTTTTCTTCTTTTTCTATCATTCTCAACAATTCGGTAGGCAAGTTATACTCTTCTTC
ATTATCGCCTTCTTCAAATTCCCCAAGACAAATGGTTGATTCAAAATCCACCTCCGGATCAGGGT
CATTAGTGCCCACATTATCATTATCTGGGAACCTGAAAGGAGGAAGATGTGTATGTGTGAGAGGA
TAATATCCCACACGGAATGGTCAAGAACA
Found at i:5604271 original size:20 final size:20
Alignment explanation
Indices: 5604233--5604276 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
5604223 ATGGTTAGTA
*
5604233 AAATAAAAATAAATGGAAAT
1 AAATAAAAATAAATAGAAAT
5604253 AAATAAAAATAACA-AGAAAT
1 AAATAAAAATAA-ATAGAAAT
5604273 AAAT
1 AAAT
5604277 GGCAATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 21 0.95
21 1 0.05
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (20 bp):
AAATAAAAATAAATAGAAAT
Found at i:5605289 original size:19 final size:19
Alignment explanation
Indices: 5605267--5605305 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
5605257 AAATGATGGT
* *
5605267 AATAATAATAAAGATAAAA
1 AATAATAAAAAAAATAAAA
5605286 AATAATAAAAAAAATAAAA
1 AATAATAAAAAAAATAAAA
5605305 A
1 A
5605306 GATATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (19 bp):
AATAATAAAAAAAATAAAA
Found at i:5605576 original size:23 final size:22
Alignment explanation
Indices: 5605542--5605585 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
5605532 GGAGAGAGGG
*
5605542 AAAAATATATAATAATAATAGA
1 AAAAATAAATAATAATAATAGA
*
5605564 AAAAATTAAATAATAATTATAG
1 AAAAA-TAAATAATAATAATAG
5605586 CGTATAAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.30
Consensus pattern (22 bp):
AAAAATAAATAATAATAATAGA
Found at i:5605744 original size:130 final size:128
Alignment explanation
Indices: 5605479--5605745 Score: 287
Period size: 130 Copynumber: 2.1 Consensus size: 128
5605469 AGGTAAAATT
* * **
5605479 AATAA-AAAACATATAATAATATTAATTCCATATATATATAATAGCTAAATATGGGAGAGAGGGA
1 AATAATAAAACATATAATAATATTAATACCATATATATATAATAACTAAATAT-GGAGAGAGAAA
* * ** *
5605543 AAAATATATAATAATAATAGAAAAAATTAAATAATAATTATAGCGTATAAAGTAAAATAAATGA
65 AAAATATATAATAATAATAGAAAAAACTAAATAATAATGATAGAATATAAAGAAAAATAAATGA
*
5605607 AGTTAATAAAACATATAATAATATTAATACCATATATATATAATAACTAAATAT-GAGAGA-AAA
1 A-ATAATAAAACATATAATAATATTAATACCATATATATATAATAACTAAATATGGAGAGAGAAA
* *
5605670 AAAATCTATATAATAGTAAT-GGAAAAACTAAATAATGAA-GATA-AATATAATAAGAAAAAGAG
65 AAAA--TATATAATAATAATAGAAAAAACTAAATAAT-AATGATAGAATAT-A-AAG-AAAA-A-
5605732 TAAA-GA
122 TAAATGA
5605738 AATAATAA
1 AATAATAA
5605746 GATAAAATAC
Statistics
Matches: 116, Mismatches: 13, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
127 8 0.07
128 25 0.22
129 21 0.18
130 54 0.47
131 4 0.03
132 4 0.03
ACGTcount: A:0.59, C:0.04, G:0.10, T:0.27
Consensus pattern (128 bp):
AATAATAAAACATATAATAATATTAATACCATATATATATAATAACTAAATATGGAGAGAGAAAA
AAATATATAATAATAATAGAAAAAACTAAATAATAATGATAGAATATAAAGAAAAATAAATGA
Found at i:5608434 original size:120 final size:126
Alignment explanation
Indices: 5608306--5608561 Score: 416
Period size: 128 Copynumber: 2.0 Consensus size: 126
5608296 ATTAAGCAAA
*
5608306 AATAATCAATGAAGAAAAAAGAGTATACGTATATAATAATAATAACG-TA-A-ATATATATATAT
1 AATAATCAATGAAGAAAAAAAAGTATACGTATATAATAATAATAACGATATATATATATATATAT
*
5608368 ATA-AA-TTAGTAAAAAGAAGATAATAGTAATAGTTAAATTAAAAATAATATAT-GTATAT
66 ATATAACTTAGTAAAAAGAAGATAATAGTAATAGTTAAATTAAAAATAATATATAATATAT
5608426 AATAATCAATGAAGAAAAAAAAGTATACGTATATAATAATAATAACGTATATATATATATATATA
1 AATAATCAATGAAGAAAAAAAAGTATACGTATATAATAATAATAACG---ATATATATATATATA
5608491 TATATATAACTTAGTAAAAAGAAGATAATAGTAATAGTTAAATTAAAAATAATATATACATATAT
63 TATATATAACTTAGTAAAAAGAAGATAATAGTAATAGTTAAATTAAAAATAATATATA-ATATAT
5608556 AATAAT
1 AATAAT
5608562 TTGTAAAACA
Statistics
Matches: 124, Mismatches: 2, Indels: 10
0.91 0.01 0.07
Matches are distributed among these distances:
120 46 0.37
124 2 0.02
125 1 0.01
126 15 0.12
127 2 0.02
128 47 0.38
130 11 0.09
ACGTcount: A:0.57, C:0.03, G:0.09, T:0.32
Consensus pattern (126 bp):
AATAATCAATGAAGAAAAAAAAGTATACGTATATAATAATAATAACGATATATATATATATATAT
ATATAACTTAGTAAAAAGAAGATAATAGTAATAGTTAAATTAAAAATAATATATAATATAT
Done.