Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 89 of 279
Found at i:29451029 original size:89 final size:89
Alignment explanation
Indices: 29450847--29451320 Score: 273
Period size: 89 Copynumber: 5.3 Consensus size: 89
29450837 CCGATACATG
* * * *
29450847 GAGATAAGATCTGTAACTTTTCAGTCTGCTTCCTGCAACTTCAGGAAGATAAGACTAG-TAGC-T
1 GAGATAAGATTTGTAA-TTTTCAGTCTGCTTCCTACAACTTCAGGAAGATAAGACTTGCTATCTT
* * *
29450910 GAGATCTGCTCCA-TAGCTGA-TACATG-
65 CAG-TCTGCTCCACT-G-TAACTTCA-GA
* * *
29450936 GAGATAAGATTTGTAATTTTCAGCCTGCTTCCTACAACTTCAAGAAGATAAGATTTGCTATCTTC
1 GAGATAAGATTTGTAATTTTCAGTCTGCTTCCTACAACTTCAGGAAGATAAGACTTGCTATCTTC
29451001 AGTCTGCTCCACTGTAACTTCAGA
66 AGTCTGCTCCACTGTAACTTCAGA
* * * * *
29451025 GAGATAAAACTTGCT-ATCTTT-AGTCTGC-TCCACAGCAACTTCAGGGAGATAAGGCTTGCTAT
1 GAGATAAGATTTG-TAAT-TTTCAGTCTGCTTCC-TA-CAACTTCAGGAAGATAAGACTTGCTAT
*
29451087 CTTCAGTCTGCTCCACTGCAACTTCA-A
62 CTTCAGTCTGCTCCACTGTAACTTCAGA
* * ** ** * * * * * ** *
29451114 GGAGATAAGGTTGGT-GGTTGAAATCTGC-TCCATAGCCGA-TACATGTAGATAAGACCCGCCA-
1 -GAGATAAGATTTGTAATTTTCAGTCTGCTTCC-TA--CAACTTCAGGAAGATAAGACTTGCTAT
** * *
29451175 CTTTTGATCTGCTCCA-TAGTCGA-TACATG-
62 CTTCAG-TCTGCTCCACT-GT-AACTTCA-GA
* * * * *
29451204 GAGATAAGATCTGTAA-TTTCGGTTTGCTTCCTGCAACTTCAGGAAGATAAGACTTGCTATTTTC
1 GAGATAAGATTTGTAATTTTCAGTCTGCTTCCTACAACTTCAGGAAGATAAGACTTGCTATCTTC
* *
29451268 AGTCTGCTCTACTGCAACTTCAGA
66 AGTCTGCTCCACTGTAACTTCAGA
* *
29451292 GAGATAAGACTTGTCATTTTC-GATCTGCT
1 GAGATAAGATTTGTAATTTTCAG-TCTGCT
29451321 CTATAGCCGA
Statistics
Matches: 289, Mismatches: 70, Indels: 52
0.70 0.17 0.13
Matches are distributed among these distances:
87 4 0.01
88 91 0.31
89 123 0.43
90 71 0.25
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (89 bp):
GAGATAAGATTTGTAATTTTCAGTCTGCTTCCTACAACTTCAGGAAGATAAGACTTGCTATCTTC
AGTCTGCTCCACTGTAACTTCAGA
Found at i:29451077 original size:134 final size:134
Alignment explanation
Indices: 29450866--29451880 Score: 919
Period size: 134 Copynumber: 7.6 Consensus size: 134
29450856 TCTGTAACTT
* * ** * *
29450866 TTCAGTCTGCTTC-CTGCAACTTCAG-GAAGATAAGACTAG-TAGCTGAGATCTGCTCCATAGCT
1 TTCAGTCTGCTCCACTGCAACTTCAGAG-AGATAAGACTCGCTATTTTAGATCTGCTCCATAGCC
* * * *
29450928 GATACATGGAGATAAGATTTGTAATTTTCAGCCTGCTTCCTACAACTTCAAGAAGATAAGATTTG
65 GATACATGGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTGCAACTTCAAGAAGATAAGACTTG
29450993 CTATC
130 CTATC
* * * *
29450998 TTCAGTCTGCTCCACTGTAACTTCAGAGAGATAAAACTTGCTATCTTTAG-TCTGCTCCACAG-C
1 TTCAGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTCGCTAT-TTTAGATCTGCTCCATAGCC
* * * * * * *
29451061 AACTTCAGGGAGATAAG-GCTTGCT-ATCTTCAGTCTGCTCCACTGCAACTTCAAGGAGATAAG-
65 GA-TACATGGAGATAAGATC-TG-TAATTTTCAGTCTGCTTC-CTGCAACTTCAAGAAGATAAGA
* * *
29451123 GTTGGTGGT-
126 CTTGCT-ATC
** * * * * * *
29451132 TGAAATCTGCTCCA-TAGCCGA-TACATG-TAGATAAGACCCGCCACTTTT-GATCTGCTCCATA
1 TTCAGTCTGCTCCACT-G-CAACTTCA-GAGAGATAAGACTCGCTA-TTTTAGATCTGCTCCATA
* * * *
29451193 GTCGATACATGGAGATAAGATCTGTAA-TTTCGGTTTGCTTCCTGCAACTTCAGGAAGATAAGAC
62 GCCGATACATGGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTGCAACTTCAAGAAGATAAGAC
*
29451257 TTGCTATT
127 TTGCTATC
* * * *
29451265 TTCAGTCTGCTCTACTGCAACTTCAGAGAGATAAGACTTG-TCATTTTCGATCTGCTCTATAGCC
1 TTCAGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTCGCT-ATTTTAGATCTGCTCCATAGCC
* *
29451329 GATACATGGAGATAAGATCTGTAAATTTTCAGTCTGCTTCCTGCAACTTCAGGAAGATAAGACTA
65 GATACATGGAGATAAGATCTGT-AATTTTCAGTCTGCTTCCTGCAACTTCAAGAAGATAAGACTT
**
29451394 G-TGGC
129 GCTATC
** * * * *
29451399 TAAAATCTGCTCCA-TAGCCGA-TACATG-GAGATAAGACTCGCCATTTCTA-ATCTGCTCCATA
1 TTCAGTCTGCTCCACT-G-CAACTTCA-GAGAGATAAGACTCGCTATTT-TAGATCTGCTCCATA
* * * *
29451460 GCCGATACATGGAGATAAGATCTGTAACTTTCAGTCTACTTCCTGCAACTTTAGGAAGATAAGAC
62 GCCGATACATGGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTGCAACTTCAAGAAGATAAGAC
*
29451525 TTGCTATT
127 TTGCTATC
* * *
29451533 TTTAGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTCG-TCATTTTCGATCTACTCCATAGCC
1 TTCAGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTCGCT-ATTTTAGATCTGCTCCATAGCC
29451597 GATACATGGAGATAAGATCTGTAAATTTTCAGTCTGCTTCCTGCAACTTCAAGAAGATAAGACTT
65 GATACATGGAGATAAGATCTGT-AATTTTCAGTCTGCTTCCTGCAACTTCAAGAAGATAAGACTT
*
29451662 CCTATC
129 GCTATC
* * * * * * *
29451668 TTCAGTCTACTCCACTGCAACTTTAGAGAGATAAGACTTG-TCATTTTCGATCTACTCTATAGCT
1 TTCAGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTCGCT-ATTTTAGATCTGCTCCATAGCC
* * * *
29451732 GGTACATGAAGATAAGATCTGTAACTTTTCGGTCTGCTTCCTGCAACTTCAGGAAGATAAGACTT
65 GATACATGGAGATAAGATCTGTAA-TTTTCAGTCTGCTTCCTGCAACTTCAAGAAGATAAGACTT
29451797 G-TATC
129 GCTATC
* ** * * * * * *** *
29451802 TCCAACCTGCT-CTCTGCAACTTCAGGGAAATAAGGCT-GGTGGCTTAAATCTGCTCCATAGCCG
1 TTCAGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTCGCTATTTTAGATCTGCTCCATAGCCG
29451865 ATACATGGAGATAAGA
66 ATACATGGAGATAAGA
29451881 CCCGCCATTT
Statistics
Matches: 717, Mismatches: 126, Indels: 80
0.78 0.14 0.09
Matches are distributed among these distances:
132 69 0.10
133 166 0.23
134 252 0.35
135 230 0.32
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (134 bp):
TTCAGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTCGCTATTTTAGATCTGCTCCATAGCCG
ATACATGGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTGCAACTTCAAGAAGATAAGACTTGC
TATC
Found at i:29451123 original size:45 final size:45
Alignment explanation
Indices: 29450935--29451707 Score: 228
Period size: 45 Copynumber: 17.3 Consensus size: 45
29450925 GCTGATACAT
* * * * *
29450935 GGAGATAAGATTTG-TAATTTTCAGCCTGCTTC-CTACAACTTCAA
1 GGAGATAAGACTTGCT-ATCTTCAGTCTGCTCCACTGCAACTTCAA
* * *
29450979 GAAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGTAACTTC-A
1 GGAGATAAGACTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAA
* * * *
29451023 GAGAGATAAAACTTGCTATCTTTAGTCTGCTCCACAGCAACTTCAG
1 G-GAGATAAGACTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAA
*
29451069 GGAGATAAGGCTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAA
1 GGAGATAAGACTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAA
* * * ** * * * *
29451114 GGAGATAAG-GTTGGTGGT-TGAAATCTGCTCCA-TAGCCGA-TACAT
1 GGAGATAAGACTTGCT-ATCTTCAGTCTGCTCCACT-G-CAACTTCAA
* ** * ** * * *
29451158 GTAGATAAGACCCGCCA-CTTTTGATCTGCTCCA-TAGTCGA-TACAT
1 GGAGATAAGACTTGCTATCTTCAG-TCTGCTCCACT-G-CAACTTCAA
* * *
29451203 GGAGATAAGA-TCTG-TAAT-TTCGGTTTGCTTC-CTGCAACTTC-A
1 GGAGATAAGACT-TGCT-ATCTTCAGTCTGCTCCACTGCAACTTCAA
* *
29451245 GGAAGATAAGACTTGCTATTTTCAGTCTGCTCTACTGCAACTTC-A
1 GG-AGATAAGACTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAA
* * * * *
29451290 GAGAGATAAGACTTG-TCATTTTC-GATCTGCTCTA-TAGCCGA-TACAT
1 G-GAGATAAGACTTGCT-ATCTTCAG-TCTGCTCCACT-G-CAACTTCAA
* *
29451336 GGAGATAAGA-TCTG-TAAATTTTCAGTCTGCTTC-CTGCAACTTC-A
1 GGAGATAAGACT-TGCT--ATCTTCAGTCTGCTCCACTGCAACTTCAA
* ** ** * * * *
29451380 GGAAGATAAGACTAG-TGGCTAAAATCTGCTCCA-TAGCCGA-TACAT
1 GG-AGATAAGACTTGCTATCTTCAGTCTGCTCCACT-G-CAACTTCAA
* * * * * *
29451425 GGAGATAAGACTCGCCAT-TTCTAATCTGCTCCA-TAGCCGA-TACAT
1 GGAGATAAGACTTGCTATCTTC-AGTCTGCTCCACT-G-CAACTTCAA
* * * *
29451470 GGAGATAAGA-TCTG-TAACTTTCAGTCTACTTC-CTGCAACTT-TA
1 GGAGATAAGACT-TGCTATC-TTCAGTCTGCTCCACTGCAACTTCAA
* *
29451513 GGAAGATAAGACTTGCTATTTTTAGTCTGCTCCACTGCAACTTC-A
1 GG-AGATAAGACTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAA
* * * * * *
29451558 GAGAGATAAGACTCG-TCATTTTC-GATCTACTCCA-TAGCCGA-TACAT
1 G-GAGATAAGACTTGCT-ATCTTCAG-TCTGCTCCACT-G-CAACTTCAA
* *
29451604 GGAGATAAGA-TCTG-TAAATTTTCAGTCTGCTTC-CTGCAACTTCAA
1 GGAGATAAGACT-TGCT--ATCTTCAGTCTGCTCCACTGCAACTTCAA
* * * *
29451649 GAAGATAAGACTTCCTATCTTCAGTCTACTCCACTGCAACTT-TA
1 GGAGATAAGACTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAA
29451693 GAGAGATAAGACTTG
1 G-GAGATAAGACTTG
29451708 TCATTTTCGA
Statistics
Matches: 549, Mismatches: 116, Indels: 127
0.69 0.15 0.16
Matches are distributed among these distances:
42 4 0.01
43 30 0.05
44 142 0.26
45 330 0.60
46 41 0.07
47 2 0.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (45 bp):
GGAGATAAGACTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAA
Found at i:29451578 original size:268 final size:267
Alignment explanation
Indices: 29450913--29451880 Score: 1041
Period size: 268 Copynumber: 3.6 Consensus size: 267
29450903 AGTAGCTGAG
* * * *
29450913 ATCTGCTCCATAGCTGATACATGGAGATAAGATTTGTAATTTTCAGCCTGCTTCCTACAACTTCA
1 ATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAA-TTTCAGTCTGCTTCCTGCAACTTCA
* * * * *
29450978 AGAAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGTAACTTCAGAGAGATAAAACTTG-CTAT
65 GGAAGATAAGACTTGCTATTTTCAGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTC-AT
* * * * * * * *
29451042 CTTTAG-TCTGCTCCACAG-CAACTTCAGGGAGATAAG-GCTTGCT--ATCTTCAGTCTGCTCCA
129 -TTTCGATCTGCTCCATAGCCGA-TACATGGAGATAAGATC-TG-TAAATTTTCAGTCTGCTTC-
** * * * *
29451102 CTGCAACTTCAAGG-AGATAAGGTTGGTGGTTGAAATCTGCTCCATAGCCGATACATGTAGATAA
189 CTGCAACTTC-AGGAAGATAAGACTAGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAA
*
29451166 GACCCGCCACTTTTG
253 GACCCGCCACTTTTA
* * *
29451181 ATCTGCTCCATAGTCGATACATGGAGATAAGATCTGTAATTTCGGTTTGCTTCCTGCAACTTCAG
1 ATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAATTTCAGTCTGCTTCCTGCAACTTCAG
*
29451246 GAAGATAAGACTTGCTATTTTCAGTCTGCTCTACTGCAACTTCAGAGAGATAAGACTTGTCATTT
66 GAAGATAAGACTTGCTATTTTCAGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTCATTT
*
29451311 TCGATCTGCTCTATAGCCGATACATGGAGATAAGATCTGTAAATTTTCAGTCTGCTTCCTGCAAC
131 TCGATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAAATTTTCAGTCTGCTTCCTGCAAC
*
29451376 TTCAGGAAGATAAGACTAGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGACTCGCC
196 TTCAGGAAGATAAGACTAGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGACCCGCC
29451441 A-TTTCTA
261 ACTTT-TA
* *
29451448 ATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAACTTTCAGTCTACTTCCTGCAACTTTA
1 ATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAA-TTTCAGTCTGCTTCCTGCAACTTCA
* *
29451513 GGAAGATAAGACTTGCTATTTTTAGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTCGTCATT
65 GGAAGATAAGACTTGCTATTTTCAGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTCATT
*
29451578 TTCGATCTACTCCATAGCCGATACATGGAGATAAGATCTGTAAATTTTCAGTCTGCTTCCTGCAA
130 TTCGATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAAATTTTCAGTCTGCTTCCTGCAA
* ** ** ** * * *
29451643 CTTCAAGAAGATAAGACTTCCTATCTTCAGTCTACTCCACT-G-C-A-ACTTTAGAGAGATAAGA
195 CTTCAGGAAGATAAGAC-TAGTGGCTAAAATCTGCTCCA-TAGCCGATAC-AT-G-GAGATAAGA
** * *
29451704 CTTGTCA-TTTTCG
255 CCCGCCACTTTT-A
* * * * * *
29451717 ATCTACTCTATAGCTGGTACATGAAGATAAGATCTGTAACTTTTCGGTCTGCTTCCTGCAACTTC
1 ATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAA--TTTCAGTCTGCTTCCTGCAACTTC
* * ** * * * * * **
29451782 AGGAAGATAAGACTTG-TATCTCCAACCTGCT-CTCTGCAACTTCAGGGAAATAAGGCTGGT-GG
64 AGGAAGATAAGACTTGCTATTTTCAGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTCAT
* **
29451844 CTTAAATCTGCTCCATAGCCGATACATGGAGATAAGA
129 TTTCGATCTGCTCCATAGCCGATACATGGAGATAAGA
29451881 CCCGCCATTT
Statistics
Matches: 606, Mismatches: 78, Indels: 33
0.85 0.11 0.05
Matches are distributed among these distances:
266 13 0.02
267 237 0.39
268 243 0.40
269 75 0.12
270 38 0.06
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (267 bp):
ATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAATTTCAGTCTGCTTCCTGCAACTTCAG
GAAGATAAGACTTGCTATTTTCAGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTCATTT
TCGATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAAATTTTCAGTCTGCTTCCTGCAAC
TTCAGGAAGATAAGACTAGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGACCCGCC
ACTTTTA
Found at i:29451788 original size:45 final size:43
Alignment explanation
Indices: 29451472--29451795 Score: 166
Period size: 45 Copynumber: 7.2 Consensus size: 43
29451462 CGATACATGG
* *
29451472 AGATAAGATCTGTAACTTTCAGTCTACTTCCTGCAACTTTAGGA
1 AGATAAGA-CTGTAATTTTCAGTCTACTTCCTGCAACTTCAGGA
* * *
29451516 AGATAAGACTTGCT-ATTTTTAGTCTGCTCCACTGCAACTTCA-GA
1 AGATAAGAC-TG-TAATTTTCAGTCTACTTC-CTGCAACTTCAGGA
* * *
29451560 GAGATAAGACTCGTCATTTTC-GATCTAC-TCCATAGCCGA-TACATGG-
1 -AGATAAGACT-GTAATTTTCAG-TCTACTTCC-T-G-CAACTTCA-GGA
* *
29451606 AGATAAGATCTGTAAATTTTCAGTCTGCTTCCTGCAACTTCAAGA
1 AGATAAGA-CTGT-AATTTTCAGTCTACTTCCTGCAACTTCAGGA
* * * *
29451651 AGATAAGACT-TCCTATCTTCAGTCTACTCCACTGCAACTTTA-GA
1 AGATAAGACTGT--AATTTTCAGTCTACTTC-CTGCAACTTCAGGA
* ** * *
29451695 GAGATAAGACTTGTCATTTTC-GATCTAC-T-CTATAGCTGGTACATGA
1 -AGATAAGAC-TGTAATTTTCAG-TCTACTTCCTGCAACT--T-CAGGA
* *
29451741 AGATAAGATCTGTAACTTTTCGGTCTGCTTCCTGCAACTTCAGGA
1 AGATAAGA-CTGTAA-TTTTCAGTCTACTTCCTGCAACTTCAGGA
29451786 AGATAAGACT
1 AGATAAGACT
29451796 TGTATCTCCA
Statistics
Matches: 213, Mismatches: 34, Indels: 66
0.68 0.11 0.21
Matches are distributed among these distances:
42 5 0.02
43 3 0.01
44 53 0.25
45 110 0.52
46 29 0.14
47 8 0.04
48 5 0.02
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (43 bp):
AGATAAGACTGTAATTTTCAGTCTACTTCCTGCAACTTCAGGA
Found at i:29452102 original size:64 final size:64
Alignment explanation
Indices: 29451993--29452117 Score: 182
Period size: 64 Copynumber: 2.0 Consensus size: 64
29451983 TTCTATATCT
* *
29451993 ATGCTTATGCCAAATAACTAGGATGCTATGATCGAAATAATTCAAATGCTCCTACCTAGATGTG
1 ATGCTTATGCCAAATAACTAGGATGCTATGATCGAAAGAATTCAAATGCTCCTAACTAGATGTG
* *
29452057 ATGCTTATGTCAAATAATTAGGATGCTATGATC-AAGACGAA-TCAAATGCTCCTAACTAGAT
1 ATGCTTATGCCAAATAACTAGGATGCTATGATCGAA-A-GAATTCAAATGCTCCTAACTAGAT
29452118 TTACTATGAA
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
63 2 0.04
64 51 0.93
65 2 0.04
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.30
Consensus pattern (64 bp):
ATGCTTATGCCAAATAACTAGGATGCTATGATCGAAAGAATTCAAATGCTCCTAACTAGATGTG
Found at i:29463279 original size:130 final size:127
Alignment explanation
Indices: 29463051--29463426 Score: 388
Period size: 129 Copynumber: 2.9 Consensus size: 127
29463041 ATACGAAACG
* * **
29463051 TTGCCTCATTTTAA--TTTGAGAAAACATGGACGAAACTTCAAAAGGATATTTTGTATTTTAGTC
1 TTGCCTCATTTTAATTTTTAAGAAAA-ATGGACGAAATTTCAAAAGGATATTCCGTATTTTAGTC
* ** * * *
29463114 GAATG-GAAAATTGAAGCCCAGCACGATTGCGCACGA-CTCCCCAAACT-TCCAAGCATGAAATA
65 GAATGAAAAAAACGAAACCCAGCACGATTG-GCACGATCT-CCCAAACTCCCCAAACATGAAATA
* * ** *
29463176 TTGCCTCGTTTT-A-TTTTAAGAAAACGTGGGTGAAAATTTCAAAAAAAGGATATTCCATATTTT
1 TTGCCTCATTTTAATTTTTAAGAAAA-ATGGACG-AAATTTC---AAAAGGATATTCCGTATTTT
* * *
29463239 AGTCGAACGAAAAAAACGAAACCCAGCACGATTCGGCACGATCTCTCAAACTCCCCAAATATGAA
61 AGTCGAATGAAAAAAACGAAACCCAGCACGATT-GGCACGATCTCCCAAACTCCCCAAACATGAA
29463304 ATA
125 ATA
*** *
29463307 TTGCCTCATTTTAATTTTTTTTTAAAAATGGACGAAATTTCCAAAGGATATTCCGTATTTTAGTC
1 TTGCCTCATTTTAA-TTTTTAAGAAAAATGGACGAAATTTCAAAAGGATATTCCGTATTTTAGTC
* *
29463372 GAATGAAAAGAACGAAACCCAGCACGATTGGGCACGATCTCTCAAACTCCCCAAA
65 GAATGAAAAAAACGAAACCCAGCACGATT-GGCACGATCTCCCAAACTCCCCAAA
29463427 TACGAGATAT
Statistics
Matches: 209, Mismatches: 30, Indels: 20
0.81 0.12 0.08
Matches are distributed among these distances:
124 1 0.00
125 25 0.12
126 6 0.03
129 99 0.47
130 32 0.15
131 26 0.12
132 8 0.04
133 4 0.02
134 8 0.04
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (127 bp):
TTGCCTCATTTTAATTTTTAAGAAAAATGGACGAAATTTCAAAAGGATATTCCGTATTTTAGTCG
AATGAAAAAAACGAAACCCAGCACGATTGGCACGATCTCCCAAACTCCCCAAACATGAAATA
Found at i:29464139 original size:20 final size:21
Alignment explanation
Indices: 29464114--29464167 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
29464104 TTTAGAACGT
29464114 AAAATATTAAAAAAGA-TAAA
1 AAAATATTAAAAAAGAGTAAA
**
29464134 AAAATAAAAAAAAAGAGTAAA
1 AAAATATTAAAAAAGAGTAAA
*
29464155 AGAAT-TTAAAAAA
1 AAAATATTAAAAAA
29464168 CTAAGAAAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 20 0.71
21 8 0.29
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (21 bp):
AAAATATTAAAAAAGAGTAAA
Found at i:29472873 original size:23 final size:23
Alignment explanation
Indices: 29472847--29472891 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
29472837 CAAACCTGTG
*
29472847 ATGACGTTATCTT-ATAAATATGC
1 ATGAAGTTATCTTGA-AAATATGC
*
29472870 ATGAATTTATCTTGAAAATATG
1 ATGAAGTTATCTTGAAAATATG
29472892 TTGAATTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (23 bp):
ATGAAGTTATCTTGAAAATATGC
Found at i:29477015 original size:22 final size:23
Alignment explanation
Indices: 29476990--29477035 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
29476980 CAACCAAACG
29476990 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
29477012 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
29477035 A
1 A
29477036 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:29477041 original size:23 final size:23
Alignment explanation
Indices: 29476997--29477041 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
29476987 ACGAATTCAA
*
29476997 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
29477020 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
29477042 CACATACCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:29478692 original size:47 final size:47
Alignment explanation
Indices: 29478623--29478718 Score: 183
Period size: 47 Copynumber: 2.0 Consensus size: 47
29478613 CTTATACCGT
29478623 TTATTCTATGAGAAACTAGACTCAATAAGCTTTAATTCCATATTTTG
1 TTATTCTATGAGAAACTAGACTCAATAAGCTTTAATTCCATATTTTG
*
29478670 TTATTCTTTGAGAAACTAGACTCAATAAGCTTTAATTCCATATTTTG
1 TTATTCTATGAGAAACTAGACTCAATAAGCTTTAATTCCATATTTTG
29478717 TT
1 TT
29478719 CATCTTCTAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (47 bp):
TTATTCTATGAGAAACTAGACTCAATAAGCTTTAATTCCATATTTTG
Found at i:29481908 original size:3 final size:3
Alignment explanation
Indices: 29481900--29481947 Score: 62
Period size: 3 Copynumber: 15.7 Consensus size: 3
29481890 CTTTATTAAA
*
29481900 TAT TAT TAT TAT T-T CTAA TAT TAT TAT TAT TAT TAT TAT TAT ATAT
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
29481946 TA
1 TA
29481948 GTGTATATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
2 1 0.03
3 36 0.90
4 3 0.08
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:29482099 original size:26 final size:27
Alignment explanation
Indices: 29482070--29482160 Score: 77
Period size: 26 Copynumber: 3.4 Consensus size: 27
29482060 TGATCATTAT
29482070 TATTATTATTATTATATAT-TA-ATGTA
1 TATTATT-TTATTATATATGTATATGTA
*
29482096 TATT-TTTTATTGTATATGTATATGTA
1 TATTATTTTATTATATATGTATATGTA
* *
29482122 TA-TATATTTA-TATATA-GTATTATTTTT
1 TATTAT-TTTATTATATATGTA-TA-TGTA
29482149 TATTATTTTATT
1 TATTATTTTATT
29482161 TTAATACTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
24 10 0.19
25 8 0.15
26 19 0.36
27 12 0.23
28 4 0.08
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (27 bp):
TATTATTTTATTATATATGTATATGTA
Found at i:29482235 original size:287 final size:288
Alignment explanation
Indices: 29481921--29482468 Score: 856
Period size: 287 Copynumber: 1.9 Consensus size: 288
29481911 TTTCTAATAT
* *
29481921 TATTATTATTATTATTATTATATATTAGTGTATATTTTTTATTGTATATGTATATGTATATATAT
1 TATTATTATTATCATTATTATATATTAGTGTATATTTTTTATTATATATGTATATGTATATATAT
*
29481986 TTATATATAGTATTATTTTTTATTACTTTATTTTAATATTTTTATTATATTTGCTTTTT-T-TTT
66 TTATATATAGTATTATTTTTTATTACTTTATTTTAATATTTTTATTATATTGGCTTTTTGTATTT
* *
29482049 -GTATT-TCAATATGA-TCA-TTATTATTATTATTATTATATATTAATGTATATTTTTTATTGTA
131 AGTATTATCAATATGATTCATTTATTATTATTATTATTATATATTAATGTATA-CTTTTATTATA
* *
29482110 TATGTATATGTATATATATTTATATATAGTATTATTTTTTATTATTTTATTTTAATACTTTTATT
195 TACGTATATG----TATATTTATATATAGTATTATTTTTTATTACTTTATTTTAATACTTTTATT
29482175 ATATTTGCTTTTTTTGCATTTCAACATGATTAC
256 ATATTTGCTTTTTTTGCATTTCAACATGATTAC
29482208 TATTATTATTATCATTATTATATATTAGTGTATATTTTTTATTATATATGTATATGTATATATAT
1 TATTATTATTATCATTATTATATATTAGTGTATATTTTTTATTATATATGTATATGTATATATAT
*
29482273 TTATATATAGTATTATTTTTTATTACTTTGTTTTAATATTTTTATTATATTGGCTTTTTGTATTT
66 TTATATATAGTATTATTTTTTATTACTTTATTTTAATATTTTTATTATATTGGCTTTTTGTATTT
* * * * * *
29482338 CATTATTATTATTATTATTTTATTTATTATTATTATTATTATATATTAGTGTATACTTTTATTAT
131 -AGTATTATCAATATGA-TTCATTTATTATTATTATTATTATATATTAATGTATACTTTTATTAT
*
29482403 ATACGTATATGTATATTTATATATAGTATTATTTTTTATTACTTTATTTTAATATTTTTATTATA
194 ATACGTATATGTATATTTATATATAGTATTATTTTTTATTACTTTATTTTAATACTTTTATTATA
29482468 T
259 T
29482469 ATGTATGTAT
Statistics
Matches: 238, Mismatches: 15, Indels: 13
0.89 0.06 0.05
Matches are distributed among these distances:
287 120 0.50
288 1 0.00
289 3 0.01
290 53 0.22
291 4 0.02
292 6 0.03
294 20 0.08
295 31 0.13
ACGTcount: A:0.30, C:0.03, G:0.06, T:0.62
Consensus pattern (288 bp):
TATTATTATTATCATTATTATATATTAGTGTATATTTTTTATTATATATGTATATGTATATATAT
TTATATATAGTATTATTTTTTATTACTTTATTTTAATATTTTTATTATATTGGCTTTTTGTATTT
AGTATTATCAATATGATTCATTTATTATTATTATTATTATATATTAATGTATACTTTTATTATAT
ACGTATATGTATATTTATATATAGTATTATTTTTTATTACTTTATTTTAATACTTTTATTATATT
TGCTTTTTTTGCATTTCAACATGATTAC
Found at i:29482261 original size:144 final size:145
Alignment explanation
Indices: 29481921--29482468 Score: 817
Period size: 143 Copynumber: 3.8 Consensus size: 145
29481911 TTTCTAATAT
*
29481921 TATTATTATTATTATTATTATATATTAGTGTATATTTTTTATTGTATATGTATATGTATATATAT
1 TATTATTATTATTATTATTATATATTAGTGTATATTTTTTATTATATATGTATATGTATATATAT
*
29481986 TTATATATAGTATTATTTTTTATTACTTTATTTTAATATTTTTATTATATTTGCTTTTTTTTTGT
66 TTATATATAGTATTATTTTTTATTACTTTATTTTAATATTTTTATTATATTTGC-TTTTTTTTGC
29482051 ATTTCAATATGA-T-C
130 ATTTCAATATGATTAC
* *
29482065 -ATTATTATTATTATTATTATATATTAATGTATATTTTTTATTGTATATGTATATGTATATATAT
1 TATTATTATTATTATTATTATATATTAGTGTATATTTTTTATTATATATGTATATGTATATATAT
* *
29482129 TTATATATAGTATTATTTTTTATTATTTTATTTTAATACTTTTATTATATTTGC-TTTTTTTGCA
66 TTATATATAGTATTATTTTTTATTACTTTATTTTAATATTTTTATTATATTTGCTTTTTTTTGCA
*
29482193 TTTCAACATGATTAC
131 TTTCAATATGATTAC
*
29482208 TATTATTATTATCATTATTATATATTAGTGTATATTTTTTATTATATATGTATATGTATATATAT
1 TATTATTATTATTATTATTATATATTAGTGTATATTTTTTATTATATATGTATATGTATATATAT
* * *
29482273 TTATATATAGTATTATTTTTTATTACTTTGTTTTAATATTTTTATTATATTGGCTTTTTGTATTT
66 TTATATATAGTATTATTTTTTATTACTTTATTTTAATATTTTTATTATATTTGCTTTTT-T-TTG
* * * *
29482338 CATTATTATTATTATTATTT
129 CATT-TCAATATGATTA--C
* *
29482358 TATTTATTATTATTATTATTATATATTAGTGTATA-CTTTTATTATATACGTATATG----TATA
1 TA-TTATTATTATTATTATTATATATTAGTGTATATTTTTTATTATATATGTATATGTATATATA
29482418 TTTATATATAGTATTATTTTTTATTACTTTATTTTAATATTTTTATTATAT
65 TTTATATATAGTATTATTTTTTATTACTTTATTTTAATATTTTTATTATAT
29482469 ATGTATGTAT
Statistics
Matches: 372, Mismatches: 22, Indels: 18
0.90 0.05 0.04
Matches are distributed among these distances:
141 19 0.05
142 1 0.00
143 116 0.31
144 111 0.30
145 4 0.01
146 55 0.15
147 6 0.02
148 8 0.02
150 21 0.06
151 31 0.08
ACGTcount: A:0.30, C:0.03, G:0.06, T:0.62
Consensus pattern (145 bp):
TATTATTATTATTATTATTATATATTAGTGTATATTTTTTATTATATATGTATATGTATATATAT
TTATATATAGTATTATTTTTTATTACTTTATTTTAATATTTTTATTATATTTGCTTTTTTTTGCA
TTTCAATATGATTAC
Found at i:29482347 original size:3 final size:3
Alignment explanation
Indices: 29482339--29482385 Score: 69
Period size: 3 Copynumber: 15.3 Consensus size: 3
29482329 TTTGTATTTC
29482339 ATT ATT ATT ATT ATT ATT -TT ATTT ATT ATT ATT ATT ATT ATAT ATT
1 ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT AT-T ATT
29482385 A
1 A
29482386 GTGTATACTT
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 2 0.05
3 33 0.80
4 6 0.15
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:29482536 original size:72 final size:73
Alignment explanation
Indices: 29482402--29482540 Score: 199
Period size: 72 Copynumber: 1.9 Consensus size: 73
29482392 ACTTTTATTA
* * * * * *
29482402 TATACGTATATGTATATTTATATATAGTATTATTTTTTATTACTTTATTTTAATATTTTTATTAT
1 TATACGTATA-GTATATTTATACATAGTACTATTTTTAATTACTTTATTTTAACACTATTATTAT
29482467 ATATGTATG
65 ATATGTATG
*
29482476 TATACGTATA-TATATTTATACATAGTACTATTTTTAATTACTTTATTTTAACGCTATTATTATA
1 TATACGTATAGTATATTTATACATAGTACTATTTTTAATTACTTTATTTTAACACTATTATTATA
29482540 T
66 T
29482541 TATATTTGTT
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
72 48 0.83
74 10 0.17
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.56
Consensus pattern (73 bp):
TATACGTATAGTATATTTATACATAGTACTATTTTTAATTACTTTATTTTAACACTATTATTATA
TATGTATG
Found at i:29491515 original size:77 final size:76
Alignment explanation
Indices: 29491385--29491770 Score: 560
Period size: 76 Copynumber: 5.1 Consensus size: 76
29491375 TGATATTTTT
* *
29491385 ATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAAAGGTGAGTTG-GACCTCGGATCACACGC
1 ATTTCTGTTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG-CCTCGGGTCACACGC
*
29491449 CGAGGTATTTTCA
64 TGAGGTATTTTCA
29491462 ATTTCTGTTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCT
1 ATTTCTGTTTTTCAA-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCT
29491527 GAGGTATCTTT-A
65 GAGGTAT-TTTCA
* * *
29491539 ATTCCTATTTTTCAATAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTG
1 ATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTG
*
29491604 AGGTATTTTTA
66 AGGTATTTTCA
* *
29491615 GTCTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTG
1 ATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTG
*
29491680 AGGTATTTTTA
66 AGGTATTTTCA
* * ** * * * *
29491691 GTCTCTGTTTTTCAAAAAATCAACTCATATTGTAAAAGGTGAGTTGAACCTTGGGTCACACACTG
1 ATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTG
29491756 AGGTATTTTCA
66 AGGTATTTTCA
29491767 ATTT
1 ATTT
29491771 TTTTTTACTT
Statistics
Matches: 285, Mismatches: 20, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
75 3 0.01
76 200 0.70
77 78 0.27
78 4 0.01
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.33
Consensus pattern (76 bp):
ATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTG
AGGTATTTTCA
Found at i:29493431 original size:3 final size:3
Alignment explanation
Indices: 29493423--29493485 Score: 65
Period size: 3 Copynumber: 20.7 Consensus size: 3
29493413 CTTTATTAAA
* * * *
29493423 TAT TAT TAT TAT T-T CTAA TAT TAT TAA TAT TAT CAC TAT TAT TAT
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
29493468 TAT TAT TAT TAT ATAT TA
1 TAT TAT TAT TAT -TAT TA
29493486 GTGTATATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
2 1 0.02
3 45 0.92
4 3 0.06
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:29493444 original size:9 final size:9
Alignment explanation
Indices: 29493415--29493485 Score: 63
Period size: 9 Copynumber: 7.7 Consensus size: 9
29493405 TTTCGTTTCT
29493415 TTATTAAATA
1 TTATT-AATA
*
29493425 TTATTATTA
1 TTATTAATA
29493434 TT-TCTAATA
1 TTAT-TAATA
29493443 TTATTAATA
1 TTATTAATA
* *
29493452 TTATCACTA
1 TTATTAATA
*
29493461 TTATTATTA
1 TTATTAATA
*
29493470 TTATTATTA
1 TTATTAATA
29493479 TATATTA
1 T-TATTA
29493486 GTGTATATTT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
8 1 0.02
9 40 0.77
10 11 0.21
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (9 bp):
TTATTAATA
Found at i:29493444 original size:18 final size:18
Alignment explanation
Indices: 29493421--29493473 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
29493411 TTCTTTATTA
29493421 AATATTATTATTATT-TC
1 AATATTATTATTATTATC
*
29493438 TAATATTATTAATATTATC
1 -AATATTATTATTATTATC
*
29493457 ACTATTATTATTATTAT
1 AATATTATTATTATTAT
29493474 TATTATATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
18 29 0.94
19 2 0.06
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.57
Consensus pattern (18 bp):
AATATTATTATTATTATC
Found at i:29493542 original size:6 final size:6
Alignment explanation
Indices: 29493502--29493532 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
29493492 ATTTTTTTAT
29493502 TGTATA TGTATA TGTATA TGTATA TGTATA T
1 TGTATA TGTATA TGTATA TGTATA TGTATA T
29493533 ATATTTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (6 bp):
TGTATA
Found at i:29493543 original size:18 final size:18
Alignment explanation
Indices: 29493504--29493549 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
29493494 TTTTTTATTG
* *
29493504 TATATGTATATGTATATG
1 TATATGTATATATATATA
*
29493522 TATATGTATATATATTTA
1 TATATGTATATATATATA
29493540 TATATAGTAT
1 TATAT-GTAT
29493550 TATTTTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (18 bp):
TATATGTATATATATATA
Found at i:29493758 original size:3 final size:3
Alignment explanation
Indices: 29493750--29493785 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
29493740 TGTATTTCAA
29493750 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA
29493786 GTGTATACTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:29493784 original size:143 final size:142
Alignment explanation
Indices: 29493516--29494345 Score: 1160
Period size: 143 Copynumber: 5.8 Consensus size: 142
29493506 TATGTATATG
*
29493516 TATATGTATATGTATATATATTTATATATAGTATTATTTTTTATTACTTTATTTTAATACTTTTA
1 TATATGTATATGTATATATATTTATATATAGTATTATTTTTTATTACTTTATTTTAATATTTTTA
* * *
29493581 TTATATTTACTTTTTTTGTATTTCAATATGATTACTATTATTATTATCATTATTATATATTA-TA
66 TTATATTTGC--TTTTTGTATTTCAATATTATTACTATTATTATTATTATTATTATATATTAGT-
29493645 GTATATTTTTTTATTA
128 GTATA-TTTTTTATTA
* *
29493661 TATATGTATATGTATATATATTTATATATAGTATTATTTTTTATTATTTTGTTTTAATATTTTTA
1 TATATGTATATGTATATATATTTATATATAGTATTATTTTTTATTACTTTATTTTAATATTTTTA
* *
29493726 TTATATTGGCTTTTTGTATTTCAATATTATTATTATTATTATTATTATTATTATATATTAGTGTA
66 TTATATTTGCTTTTTGTATTTCAATATTATTACTATTATTATTATTATTATTATATATTAGTGTA
*
29493791 TACTTTTTATTA
131 TATTTTTTATTA
*
29493803 TATACGTATATGTATATATATTTATATATAGTATTATTTTTTATTACTTTATTTTAATATTTTTA
1 TATATGTATATGTATATATATTTATATATAGTATTATTTTTTATTACTTTATTTTAATATTTTTA
* *
29493868 TTATATTTGCTTTTTTTTTGTATTTCAATATGA-T-C-ATTATTATTATTATTATTATATATTAA
66 TTATATTTGC----TTTTTGTATTTCAATATTATTACTATTATTATTATTATTATTATATATTAG
29493930 TGTATATTTTTTATTA
127 TGTATATTTTTTATTA
* *
29493946 TATATGTATATGTATATATATTTATATATAGTATTATTTTTTATTATTTTGTTTTAATATTTTTA
1 TATATGTATATGTATATATATTTATATATAGTATTATTTTTTATTACTTTATTTTAATATTTTTA
*
29494011 TTATATTGGCTTTTTGTATTTCAATATTATTACTATTATTATTATTATTATTATATATTAGTGTA
66 TTATATTTGCTTTTTGTATTTCAATATTATTACTATTATTATTATTATTATTATATATTAGTGTA
*
29494076 TACTTTTTATTA
131 TATTTTTTATTA
* * * * * *
29494088 TATACGTATACGTAAATGTATATTTATATATAATATT-TTTATTATTATTTTATTTTAATATTTT
1 TATATGTATATGT--ATATATATTTATATATAGTATTATTTTTTATTACTTTATTTTAATATTTT
*
29494152 TATTATATTTGCTTTTTGTATTTCAATATTATTACTATTATCATTATTATTATTA-ATATTAGTG
64 TATTATATTTGCTTTTTGTATTTCAATATTATTACTATTATTATTATTATTATTATATATTAGTG
29494216 TATA-TTTTTATTA
129 TATATTTTTTATTA
* * * **
29494229 TATATGTATGTATACGTATATATATTTATACATAGTACTATTTTTAATTACTTTATTTTAACGTT
1 TATATGTA--TAT--GTATATATATTTATATATAGTATTATTTTTTATTACTTTATTTTAATATT
* * * *
29494294 ATTATTAT-TTT--TTTTTGTATTTCATTATTATTGCTAGTT-TTATTATCATTAT
62 TTTATTATATTTGCTTTTTGTATTTCAATATTATTACTA-TTATTATTATTATTAT
29494346 CATCATTATT
Statistics
Matches: 621, Mismatches: 48, Indels: 36
0.88 0.07 0.05
Matches are distributed among these distances:
139 18 0.03
140 1 0.00
141 51 0.08
142 147 0.24
143 265 0.43
144 48 0.08
145 73 0.12
146 18 0.03
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (142 bp):
TATATGTATATGTATATATATTTATATATAGTATTATTTTTTATTACTTTATTTTAATATTTTTA
TTATATTTGCTTTTTGTATTTCAATATTATTACTATTATTATTATTATTATTATATATTAGTGTA
TATTTTTTATTA
Found at i:29493937 original size:26 final size:27
Alignment explanation
Indices: 29493908--29493979 Score: 84
Period size: 26 Copynumber: 2.8 Consensus size: 27
29493898 TGATCATTAT
29493908 TATTATTATTATTATATAT-TA-ATGTA
1 TATTATT-TTATTATATATGTATATGTA
29493934 TATT-TTTTATTATATATGTATATGTA
1 TATTATTTTATTATATATGTATATGTA
29493960 TA-TATATTTA-TATATA-GTAT
1 TATTAT-TTTATTATATATGTAT
29493980 TATTTTTTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
24 11 0.26
25 9 0.21
26 18 0.43
27 4 0.10
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (27 bp):
TATTATTTTATTATATATGTATATGTA
Found at i:29493947 original size:24 final size:26
Alignment explanation
Indices: 29493916--29493982 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 26
29493906 ATTATTATTA
*
29493916 TTATTATATATTA-ATGTATAT-TTT
1 TTATTATATATTATATGTATATATAT
29493940 TTATTATATATGTATATGTATATATAT
1 TTATTATATAT-TATATGTATATATAT
29493967 TTATATATAGTATTAT
1 TTAT-TATA-TATTAT
29493983 TTTTTATTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
24 11 0.30
25 2 0.05
26 8 0.22
27 6 0.16
28 7 0.19
29 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (26 bp):
TTATTATATATTATATGTATATATAT
Found at i:29493952 original size:20 final size:20
Alignment explanation
Indices: 29493929--29493992 Score: 65
Period size: 24 Copynumber: 2.9 Consensus size: 20
29493919 TTATATATTA
29493929 ATGTATATTTTTTATTATAT
1 ATGTATATTTTTTATTATAT
*
29493949 ATGTATATGTATATATATTTATAT
1 ATGTATAT-T-T-TTTA-TTATAT
29493973 ATAGTATTATTTTTTATTAT
1 AT-GTA-TATTTTTTATTAT
29493993 TTTGTTTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
20 8 0.22
21 1 0.03
22 5 0.14
23 6 0.17
24 9 0.25
25 4 0.11
26 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (20 bp):
ATGTATATTTTTTATTATAT
Found at i:29493961 original size:14 final size:13
Alignment explanation
Indices: 29493911--29493964 Score: 51
Period size: 12 Copynumber: 4.2 Consensus size: 13
29493901 TCATTATTAT
29493911 TATTATTAT-TATA
1 TATTA-TATGTATA
29493924 TATTA-ATGTATA
1 TATTATATGTATA
* *
29493936 TTTTTTAT-TATA
1 TATTATATGTATA
29493948 TATGTATATGTATA
1 TAT-TATATGTATA
29493962 TAT
1 TAT
29493965 ATTTATATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
11 2 0.06
12 13 0.39
13 11 0.33
14 7 0.21
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (13 bp):
TATTATATGTATA
Found at i:29493995 original size:285 final size:286
Alignment explanation
Indices: 29493450--29494325 Score: 1242
Period size: 285 Copynumber: 3.1 Consensus size: 286
29493440 ATATTATTAA
* * * * *
29493450 TATTATCACTATTATTATTATTATTATTATATATTAGTGTATATTTTTTTATTGTATA-TGTATA
1 TATT-TCAATATTATTATTATTATTATTAT-TATTA-T-TATA---TATTAGTGTATACTTTTTA
*
29493514 TGTATAT--GTATATGTATATATATTTATATATAGTATTATTTTTTATTACTTTATTTTAATACT
59 T-TATATACGTATATGTATATATATTTATATATAGTATTATTTTTTATTACTTTATTTTAATATT
* *
29493577 TTTATTATATTTACTTTTTTTGTATTTCAATATGATTACTATTATTATTATCATTATTATATATT
123 TTTATTATATTTGCTTTTTTTGTATTTCAATATGATTACTATTATTATTATTATTATTATATATT
29493642 -ATAGTATATTTTTTTATTATATATGTATATGTATATATATTTATATATAGTATTATTTTTTATT
188 AAT-GTATA-TTTTTTATTATATATGTATATGTATATATATTTATATATAGTATTATTTTTTATT
29493706 ATTTTGTTTTAATATTTTTATTATATTGGCTTTTTG
251 ATTTTGTTTTAATATTTTTATTATATTGGCTTTTTG
29493742 TATTTCAATATTATTATTATTATTATTATTATTATTATATATTAGTGTATACTTTTTATTATATA
1 TATTTCAATATTATTATTATTATTATTATTATTATTATATATTAGTGTATACTTTTTATTATATA
29493807 CGTATATGTATATATATTTATATATAGTATTATTTTTTATTACTTTATTTTAATATTTTTATTAT
66 CGTATATGTATATATATTTATATATAGTATTATTTTTTATTACTTTATTTTAATATTTTTATTAT
29493872 ATTTGCTTTTTTTTTGTATTTCAATATGA-T-C-ATTATTATTATTATTATTATATATTAATGTA
131 ATTTGC--TTTTTTTGTATTTCAATATGATTACTATTATTATTATTATTATTATATATTAATGTA
29493934 TATTTTTTATTATATATGTATATGTATATATATTTATATATAGTATTATTTTTTATTATTTTGTT
194 TATTTTTTATTATATATGTATATGTATATATATTTATATATAGTATTATTTTTTATTATTTTGTT
29493999 TTAATATTTTTATTATATTGGCTTTTTG
259 TTAATATTTTTATTATATTGGCTTTTTG
*
29494027 TATTTCAATATTATTACTATTATTATTATTATTATTATATATTAGTGTATACTTTTTATTATATA
1 TATTTCAATATTATTATTATTATTATTATTATTATTATATATTAGTGTATACTTTTTATTATATA
* * * * *
29494092 CGTATACGTAAATGTATATTTATATATAATATT-TTTATTATTATTTTATTTTAATATTTTTATT
66 CGTATATGT--ATATATATTTATATATAGTATTATTTTTTATTACTTTATTTTAATATTTTTATT
* * *
29494156 ATATTTGC--TTTTTGTATTTCAATATTATTACTATTATCATTATTATTATTA-ATATTAGTGTA
129 ATATTTGCTTTTTTTGTATTTCAATATGATTACTATTATTATTATTATTATTATATATTAATGTA
* * * *
29494218 TA-TTTTTATTATATATGTATGTATACGTATATATATTTATACATAGTACTATTTTTAATTACTT
194 TATTTTTTATTATATATGTA--TAT--GTATATATATTTATATATAGTATTATTTTTTATTATTT
* ** * *
29494282 TATTTTAACGTTATTATTAT-TT--TTTTTTG
255 TGTTTTAATATTTTTATTATATTGGCTTTTTG
*
29494311 TATTTCATTATTATT
1 TATTTCAATATTATT
29494326 GCTAGTTTTA
Statistics
Matches: 542, Mismatches: 27, Indels: 38
0.89 0.04 0.06
Matches are distributed among these distances:
282 18 0.03
283 18 0.03
284 33 0.06
285 199 0.37
286 73 0.13
287 141 0.26
288 5 0.01
289 22 0.04
290 5 0.01
291 24 0.04
292 4 0.01
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.61
Consensus pattern (286 bp):
TATTTCAATATTATTATTATTATTATTATTATTATTATATATTAGTGTATACTTTTTATTATATA
CGTATATGTATATATATTTATATATAGTATTATTTTTTATTACTTTATTTTAATATTTTTATTAT
ATTTGCTTTTTTTGTATTTCAATATGATTACTATTATTATTATTATTATTATATATTAATGTATA
TTTTTTATTATATATGTATATGTATATATATTTATATATAGTATTATTTTTTATTATTTTGTTTT
AATATTTTTATTATATTGGCTTTTTG
Found at i:29494050 original size:3 final size:3
Alignment explanation
Indices: 29494035--29494070 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
29494025 TGTATTTCAA
*
29494035 TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT ATAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA
29494071 GTGTATACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:29494151 original size:13 final size:12
Alignment explanation
Indices: 29494107--29494161 Score: 58
Period size: 13 Copynumber: 4.5 Consensus size: 12
29494097 ACGTAAATGT
*
29494107 ATATTTATATATA
1 ATATTTTTAT-TA
29494120 ATATTTTTATTA
1 ATATTTTTATTA
* *
29494132 TTATTTTATTTTA
1 ATATTTT-TATTA
29494145 ATATTTTTATT-
1 ATATTTTTATTA
29494156 ATATTT
1 ATATTT
29494162 GCTTTTTGTA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
11 6 0.17
12 11 0.31
13 19 0.53
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTTTTATTA
Found at i:29494174 original size:24 final size:25
Alignment explanation
Indices: 29494118--29494167 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
29494108 TATTTATATA
*
29494118 TAATATTTTTATTATTATTTTATTT
1 TAATATTTTTATTATTATTTGATTT
*
29494143 TAATATTTTTATTA-TATTTGCTTT
1 TAATATTTTTATTATTATTTGATTT
29494167 T
1 T
29494168 TGTATTTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (25 bp):
TAATATTTTTATTATTATTTGATTT
Found at i:29495792 original size:3 final size:3
Alignment explanation
Indices: 29495784--29495846 Score: 65
Period size: 3 Copynumber: 20.7 Consensus size: 3
29495774 CTTTATTAAA
* * * *
29495784 TAT TAT TAT TAT T-T CTAA TAT TAT TAA TAT TAT CAC TAT TAT TAT
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
29495829 TAT TAT TAT TAT ATAT TA
1 TAT TAT TAT TAT -TAT TA
29495847 GTGTATATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
2 1 0.02
3 45 0.92
4 3 0.06
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:29495805 original size:9 final size:9
Alignment explanation
Indices: 29495776--29495846 Score: 63
Period size: 9 Copynumber: 7.7 Consensus size: 9
29495766 TTTCGTTTCT
29495776 TTATTAAATA
1 TTATT-AATA
*
29495786 TTATTATTA
1 TTATTAATA
29495795 TT-TCTAATA
1 TTAT-TAATA
29495804 TTATTAATA
1 TTATTAATA
* *
29495813 TTATCACTA
1 TTATTAATA
*
29495822 TTATTATTA
1 TTATTAATA
*
29495831 TTATTATTA
1 TTATTAATA
29495840 TATATTA
1 T-TATTA
29495847 GTGTATATTT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
8 1 0.02
9 40 0.77
10 11 0.21
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (9 bp):
TTATTAATA
Found at i:29495805 original size:18 final size:18
Alignment explanation
Indices: 29495782--29495834 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
29495772 TTCTTTATTA
29495782 AATATTATTATTATT-TC
1 AATATTATTATTATTATC
*
29495799 TAATATTATTAATATTATC
1 -AATATTATTATTATTATC
*
29495818 ACTATTATTATTATTAT
1 AATATTATTATTATTAT
29495835 TATTATATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
18 29 0.94
19 2 0.06
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.57
Consensus pattern (18 bp):
AATATTATTATTATTATC
Found at i:29495874 original size:6 final size:6
Alignment explanation
Indices: 29495863--29495893 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
29495853 ATTTTTTTAT
29495863 TGTATA TGTATA TGTATA TGTATA TGTATA T
1 TGTATA TGTATA TGTATA TGTATA TGTATA T
29495894 ATATTTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (6 bp):
TGTATA
Found at i:29495904 original size:18 final size:18
Alignment explanation
Indices: 29495865--29495910 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
29495855 TTTTTTATTG
* *
29495865 TATATGTATATGTATATG
1 TATATGTATATATATATA
*
29495883 TATATGTATATATATTTA
1 TATATGTATATATATATA
29495901 TATATAGTAT
1 TATAT-GTAT
29495911 TATTTTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (18 bp):
TATATGTATATATATATA
Found at i:29495984 original size:3 final size:3
Alignment explanation
Indices: 29495976--29496005 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
29495966 ATATGATCAC
29495976 TAT TAT TAT TAT TAT TAT TAT TAT ATAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA
29496006 ATGTATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:29496272 original size:3 final size:3
Alignment explanation
Indices: 29496257--29496292 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
29496247 TGTATTTCAA
*
29496257 TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT ATAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA
29496293 GTGTATACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:29496283 original size:143 final size:142
Alignment explanation
Indices: 29495877--29496567 Score: 907
Period size: 143 Copynumber: 4.8 Consensus size: 142
29495867 TATGTATATG
29495877 TATATGTATATGTATATATATTTATATATAGTATTA-TTTTT-TTACTTTATTTTAATATTTTTA
1 TATATGTATATGTATATATATTTATATATAGTATTATTTTTTATTACTTTATTTTAATATTTTTA
* *
29495940 TTATATTTGCTTTTTTTTGTATTTCAATATGATCACTATTATTATTATTATTATTATTATATATT
66 TTATATTTGC---TTTTTGTATTTCAATAT--T-ATTACTATTATTATTATTATTATTATATATT
* *
29496005 AATGTATATTTTTTATTG
125 AGTGTATATTTTTTATTA
*
29496023 TATATGTATATGTATATATATTTATATATAGTATTATTTTTTATTACTTTATTTTAATACTTTTA
1 TATATGTATATGTATATATATTTATATATAGTATTATTTTTTATTACTTTATTTTAATATTTTTA
* * *
29496088 TTATATTTACTTTTTTTGTATTTCAATATGATTACTATTATTATTATCATTATTATATATTA-TA
66 TTATATTTGC--TTTTTGTATTTCAATATTATTACTATTATTATTATTATTATTATATATTAGT-
29496152 GTATATTTTTTTATTA
128 GTATA-TTTTTTATTA
* *
29496168 TATATGTATATGTATATATATTTATATATAGTATTATTTTTTATTATTTTGTTTTAATATTTTTA
1 TATATGTATATGTATATATATTTATATATAGTATTATTTTTTATTACTTTATTTTAATATTTTTA
*
29496233 TTATATTGGCTTTTTGTATTTCAATATTATTACTATTATTATTATTATTATTATATATTAGTGTA
66 TTATATTTGCTTTTTGTATTTCAATATTATTACTATTATTATTATTATTATTATATATTAGTGTA
*
29496298 TACTTTTTATTA
131 TATTTTTTATTA
* * * * * *
29496310 TATACGTATACGTAAATGTATATTTATATATAATATT-TTTATTATTATTTTATTTTAATATTTT
1 TATATGTATATGT--ATATATATTTATATATAGTATTATTTTTTATTACTTTATTTTAATATTTT
*
29496374 TATTATATTTGCTTTTTGTATTTCAATATTATTACTATTATCATTATTATTATTA-ATATTAGTG
64 TATTATATTTGCTTTTTGTATTTCAATATTATTACTATTATTATTATTATTATTATATATTAGTG
29496438 TATA-TTTTTATTA
129 TATATTTTTTATTA
* * * **
29496451 TATATGTATGTATACGTATATATATTTATACATAGTACTATTTTTAATTACTTTATTTTAACGTT
1 TATATGTA--TAT--GTATATATATTTATATATAGTATTATTTTTTATTACTTTATTTTAATATT
* * * *
29496516 ATTATTAT-TTT--TTTTTGTATTTCATTATTATTGCTAGTT-TTATTATCATTAT
62 TTTATTATATTTGCTTTTTGTATTTCAATATTATTACTA-TTATTATTATTATTAT
29496568 CATCATTATT
Statistics
Matches: 493, Mismatches: 39, Indels: 31
0.88 0.07 0.06
Matches are distributed among these distances:
141 50 0.10
142 35 0.07
143 155 0.31
144 82 0.17
145 81 0.16
146 36 0.07
147 24 0.05
148 30 0.06
ACGTcount: A:0.30, C:0.04, G:0.05, T:0.60
Consensus pattern (142 bp):
TATATGTATATGTATATATATTTATATATAGTATTATTTTTTATTACTTTATTTTAATATTTTTA
TTATATTTGCTTTTTGTATTTCAATATTATTACTATTATTATTATTATTATTATATATTAGTGTA
TATTTTTTATTA
Found at i:29496373 original size:13 final size:12
Alignment explanation
Indices: 29496329--29496383 Score: 58
Period size: 13 Copynumber: 4.5 Consensus size: 12
29496319 ACGTAAATGT
*
29496329 ATATTTATATATA
1 ATATTTTTAT-TA
29496342 ATATTTTTATTA
1 ATATTTTTATTA
* *
29496354 TTATTTTATTTTA
1 ATATTTT-TATTA
29496367 ATATTTTTATT-
1 ATATTTTTATTA
29496378 ATATTT
1 ATATTT
29496384 GCTTTTTGTA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
11 6 0.17
12 11 0.31
13 19 0.53
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTTTTATTA
Found at i:29496396 original size:24 final size:25
Alignment explanation
Indices: 29496340--29496389 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
29496330 TATTTATATA
*
29496340 TAATATTTTTATTATTATTTTATTT
1 TAATATTTTTATTATTATTTGATTT
*
29496365 TAATATTTTTATTA-TATTTGCTTT
1 TAATATTTTTATTATTATTTGATTT
29496389 T
1 T
29496390 TGTATTTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (25 bp):
TAATATTTTTATTATTATTTGATTT
Found at i:29496495 original size:287 final size:287
Alignment explanation
Indices: 29495809--29496567 Score: 955
Period size: 287 Copynumber: 2.6 Consensus size: 287
29495799 TAATATTATT
*
29495809 AATATTATCACTATTATTATTATTATTATTATATATTAGTGTATATTTTTTTATTGTATATGTAT
1 AATATTATTACTATTATTATTATTATTATTATATATTAGTGTATA--TTTTTA---T-TA--TAT
29495874 ATGTATATGTATATGTATATATATTTATATATAGTATTA-TTTTT-TTACTTTATTTTAATATTT
58 ATG--TATGTATATGTATATATATTTATATATAGTATTATTTTTTATTACTTTATTTTAATATTT
* *
29495937 TTATTATATTTGCTTTTTTTTGTATTTCAATATGATCACTATTATTATTATTATTATTATTATAT
121 TTATTATA-TTGC---TTTTTGTATTTCAATAT--T-ATTACTATTATTATTATTATTATTATAT
* * * * * *
29496002 ATTAATGTATATTTTTTATTGTATATGTATATGTATATATATTTATATATAGTATTATTTTTTAT
179 ATTAATGTATACTTTTTATTATATACGTATACGTATATATATTTATATATAATATTATTTATTAT
29496067 TACTTTATTTTAATACTTTTATTATATTTACTTTTTTTGTATTTC
244 TACTTTATTTTAATACTTTTATTATATTTAC-TTTTTTGTATTTC
* * *
29496112 AATATGATTACTATTATTATTATCATTATTATATATTA-TAGTATATTTTT-TTAT-TATATATG
1 AATATTATTACTATTATTATTATTATTATTATATATTAGT-GTATATTTTTATTATATATGTATG
* *
29496174 TATATGTATATATATTTATATATAGTATTATTTTTTATTATTTTGTTTTAATATTTTTATTATAT
65 TATATGTATATATATTTATATATAGTATTATTTTTTATTACTTTATTTTAATATTTTTATTATAT
*
29496239 TGGCTTTTTGTATTTCAATATTATTACTATTATTATTATTATTATTATATATTAGTGTATACTTT
130 T-GCTTTTTGTATTTCAATATTATTACTATTATTATTATTATTATTATATATTAATGTATACTTT
* *
29496304 TTATTATATACGTATACGTAAATGTATATTTATATATAATATT-TTTATTATTATTTTATTTTAA
194 TTATTATATACGTATACGT--ATATATATTTATATATAATATTATTTATTATTACTTTATTTTAA
* *
29496368 TATTTTTATTATATTTGC-TTTTTGTATTTC
257 TACTTTTATTATATTTACTTTTTTGTATTTC
*
29496398 AATATTATTACTATTATCATTATTATTATTA-ATATTAGTGTATATTTTTATTATATATGTATGT
1 AATATTATTACTATTATTATTATTATTATTATATATTAGTGTATATTTTTATTATATATGTATGT
* * * * ** *
29496462 ATACGTATATATATTTATACATAGTACTATTTTTAATTACTTTATTTTAACGTTATTATTAT-TT
66 ATATGTATATATATTTATATATAGTATTATTTTTTATTACTTTATTTTAATATTTTTATTATATT
* * * *
29496526 -TTTTTTGTATTTCATTATTATTGCTAGTT-TTATTATCATTAT
131 GCTTTTTGTATTTCAATATTATTACTA-TTATTATTATTATTAT
29496568 CATCATTATT
Statistics
Matches: 410, Mismatches: 36, Indels: 39
0.85 0.07 0.08
Matches are distributed among these distances:
284 35 0.09
285 18 0.04
286 47 0.11
287 116 0.28
288 36 0.09
289 20 0.05
290 17 0.04
291 34 0.08
292 7 0.02
293 30 0.07
294 1 0.00
296 2 0.00
297 1 0.00
301 5 0.01
302 1 0.00
303 40 0.10
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (287 bp):
AATATTATTACTATTATTATTATTATTATTATATATTAGTGTATATTTTTATTATATATGTATGT
ATATGTATATATATTTATATATAGTATTATTTTTTATTACTTTATTTTAATATTTTTATTATATT
GCTTTTTGTATTTCAATATTATTACTATTATTATTATTATTATTATATATTAATGTATACTTTTT
ATTATATACGTATACGTATATATATTTATATATAATATTATTTATTATTACTTTATTTTAATACT
TTTATTATATTTACTTTTTTGTATTTC
Found at i:29498062 original size:22 final size:22
Alignment explanation
Indices: 29498015--29498056 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
29498005 ATTTGAATTC
29498015 TAAAATTTAAAAAATAAAAAAT
1 TAAAATTTAAAAAATAAAAAAT
* *
29498037 TAAATTTTTAAAAATAAAAA
1 TAAAATTTAAAAAATAAAAA
29498057 TATAAAAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATTTAAAAAATAAAAAAT
Found at i:29504201 original size:18 final size:20
Alignment explanation
Indices: 29504161--29504203 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
29504151 TTTCAGGATG
* *
29504161 TTAACATTTTTAAATTTACA
1 TTAACATTTTTAAATTAAAA
29504181 TTAACA-TTTT-AATTAAAA
1 TTAACATTTTTAAATTAAAA
29504199 TTAAC
1 TTAAC
29504204 TAATAATATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 11 0.52
19 4 0.19
20 6 0.29
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (20 bp):
TTAACATTTTTAAATTAAAA
Found at i:29511584 original size:68 final size:68
Alignment explanation
Indices: 29511475--29511611 Score: 265
Period size: 68 Copynumber: 2.0 Consensus size: 68
29511465 ACCGCGATAC
*
29511475 CTGCAATGACCGCAATAGCATCCGTTATGTCCGCAACCGCGATAAACGCACTGCGACCGAAAACG
1 CTGCAATGACCGCAATAGCATCCGTTATGTCCGCAACCGCGATAAACGCAATGCGACCGAAAACG
29511540 CGA
66 CGA
29511543 CTGCAATGACCGCAATAGCATCCGTTATGTCCGCAACCGCGATAAACGCAATGCGACCGAAAACG
1 CTGCAATGACCGCAATAGCATCCGTTATGTCCGCAACCGCGATAAACGCAATGCGACCGAAAACG
29511608 CGA
66 CGA
29511611 C
1 C
29511612 CGCGACCGCA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.31, C:0.32, G:0.22, T:0.15
Consensus pattern (68 bp):
CTGCAATGACCGCAATAGCATCCGTTATGTCCGCAACCGCGATAAACGCAATGCGACCGAAAACG
CGA
Found at i:29511615 original size:32 final size:32
Alignment explanation
Indices: 29511510--29511616 Score: 81
Period size: 32 Copynumber: 3.2 Consensus size: 32
29511500 TATGTCCGCA
*
29511510 ACCGCGATAAACGCACTGCGACCGAAAACGCG
1 ACCGCGATAAACGCAATGCGACCGAAAACGCG
* * * * *** *
29511542 ACTGCAATGACCGCAATAGC-ATCCGTTATGTCCGCA
1 ACCGCGATAAACGCAAT-GCGA-CCG--A-AAACGCG
29511578 ACCGCGATAAACGCAATGCGACCGAAAACGCG
1 ACCGCGATAAACGCAATGCGACCGAAAACGCG
29511610 ACCGCGA
1 ACCGCGA
29511617 CCGCAATTTA
Statistics
Matches: 52, Mismatches: 17, Indels: 12
0.64 0.21 0.15
Matches are distributed among these distances:
32 23 0.44
33 6 0.12
35 6 0.12
36 17 0.33
ACGTcount: A:0.33, C:0.33, G:0.23, T:0.11
Consensus pattern (32 bp):
ACCGCGATAAACGCAATGCGACCGAAAACGCG
Found at i:29518928 original size:6 final size:6
Alignment explanation
Indices: 29518912--29518959 Score: 87
Period size: 6 Copynumber: 7.8 Consensus size: 6
29518902 AGTTGATAAC
29518912 GATTGAG GATTAG GATTAG GATTAG GATTAG GATTAG GATTAG GATTA
1 GATT-AG GATTAG GATTAG GATTAG GATTAG GATTAG GATTAG GATTA
29518960 AAGAGAAGCA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
6 37 0.90
7 4 0.10
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (6 bp):
GATTAG
Found at i:29519977 original size:59 final size:59
Alignment explanation
Indices: 29519797--29519977 Score: 142
Period size: 59 Copynumber: 3.1 Consensus size: 59
29519787 ACCCAGATTA
29519797 GCAGTTCTCCTAGCTTCAAAGCATCCACCATTTCTTCTTTTTCTTACTCTCTAACATCG
1 GCAGTTCTCCTAGCTTCAAAGCATCCACCATTTCTTCTTTTTCTTACTCTCTAACATCG
*** ** ** * * *** * * **
29519856 GCAGTTCTGGAAG--T-AAAAAAAGCAACATTTGTGTCAATGCATATTAC-C-C--AGATTA
1 GCAGTTCTCCTAGCTTCAAAGCATCCACCATTTCT-TC--TTTTTCTTACTCTCTAACATCG
29519911 GCAGTTCTCCTAGCTTCAAAGCATCCACCATTTCTTCTTTTTCTTACTCTCTAACATCG
1 GCAGTTCTCCTAGCTTCAAAGCATCCACCATTTCTTCTTTTTCTTACTCTCTAACATCG
29519970 GCAGTTCT
1 GCAGTTCT
29519978 GGAAGTAAAA
Statistics
Matches: 80, Mismatches: 32, Indels: 20
0.61 0.24 0.15
Matches are distributed among these distances:
55 19 0.24
56 13 0.16
57 8 0.10
58 13 0.16
59 27 0.34
ACGTcount: A:0.25, C:0.27, G:0.12, T:0.35
Consensus pattern (59 bp):
GCAGTTCTCCTAGCTTCAAAGCATCCACCATTTCTTCTTTTTCTTACTCTCTAACATCG
Found at i:29519987 original size:114 final size:114
Alignment explanation
Indices: 29519787--29520007 Score: 442
Period size: 114 Copynumber: 1.9 Consensus size: 114
29519777 ATTTATGGCC
29519787 ACCCAGATTAGCAGTTCTCCTAGCTTCAAAGCATCCACCATTTCTTCTTTTTCTTACTCTCTAAC
1 ACCCAGATTAGCAGTTCTCCTAGCTTCAAAGCATCCACCATTTCTTCTTTTTCTTACTCTCTAAC
29519852 ATCGGCAGTTCTGGAAGTAAAAAAAGCAACATTTGTGTCAATGCATATT
66 ATCGGCAGTTCTGGAAGTAAAAAAAGCAACATTTGTGTCAATGCATATT
29519901 ACCCAGATTAGCAGTTCTCCTAGCTTCAAAGCATCCACCATTTCTTCTTTTTCTTACTCTCTAAC
1 ACCCAGATTAGCAGTTCTCCTAGCTTCAAAGCATCCACCATTTCTTCTTTTTCTTACTCTCTAAC
29519966 ATCGGCAGTTCTGGAAGTAAAAAAAGCAACATTTGTGTCAAT
66 ATCGGCAGTTCTGGAAGTAAAAAAAGCAACATTTGTGTCAAT
29520008 ACAAATATGC
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 107 1.00
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (114 bp):
ACCCAGATTAGCAGTTCTCCTAGCTTCAAAGCATCCACCATTTCTTCTTTTTCTTACTCTCTAAC
ATCGGCAGTTCTGGAAGTAAAAAAAGCAACATTTGTGTCAATGCATATT
Found at i:29526614 original size:29 final size:29
Alignment explanation
Indices: 29526582--29526640 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
29526572 TTTTAGTTGT
*
29526582 AAATAAATTATATTTATTAAATTCATTAA
1 AAATAAATGATATTTATTAAATTCATTAA
* *
29526611 AAATAAATGGTCTTTATTAAATTCATTAA
1 AAATAAATGATATTTATTAAATTCATTAA
29526640 A
1 A
29526641 TTAAGTTACA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.42
Consensus pattern (29 bp):
AAATAAATGATATTTATTAAATTCATTAA
Found at i:29530123 original size:24 final size:24
Alignment explanation
Indices: 29530108--29530157 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
29530098 AATCAAATTC
29530108 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
* * *
29530132 AAATATATTATACTCATAAATACT
1 AAATATATTATGCTAATAAATGCT
29530156 AA
1 AA
29530158 CTCTTCTAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.36
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATGCT
Found at i:29531242 original size:20 final size:19
Alignment explanation
Indices: 29531200--29531245 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
29531190 TAAAAATTAG
* *
29531200 AAAAATTATTAGAAATTGT
1 AAAAATTATTAGAAATAGC
29531219 AAAATATTATTAGAAATAGC
1 AAAA-ATTATTAGAAATAGC
29531239 AAAAATT
1 AAAAATT
29531246 GTTATTGGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.57, C:0.02, G:0.09, T:0.33
Consensus pattern (19 bp):
AAAAATTATTAGAAATAGC
Found at i:29532996 original size:26 final size:26
Alignment explanation
Indices: 29532967--29533049 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
29532957 ATACAATACT
29532967 AACTATCTTCATCTT-AATACCATTCA
1 AACTATCTTCAT-TTCAATACCATTCA
* * * * * *
29532993 AACTTTAATT-ATTTTCATTACAATACT
1 AACTAT-CTTCA-TTTCAATACCATTCA
*
29533020 AACTATCTTCATTTGAATACCATTCA
1 AACTATCTTCATTTCAATACCATTCA
29533046 AACT
1 AACT
29533050 TTAACTATTT
Statistics
Matches: 40, Mismatches: 13, Indels: 8
0.66 0.21 0.13
Matches are distributed among these distances:
26 24 0.60
27 16 0.40
ACGTcount: A:0.36, C:0.22, G:0.01, T:0.41
Consensus pattern (26 bp):
AACTATCTTCATTTCAATACCATTCA
Found at i:29533069 original size:32 final size:32
Alignment explanation
Indices: 29533019--29533082 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
29533009 ATTACAATAC
29533019 TAACTATCTTCATTTGAATACCATTCAAACTT
1 TAACTATCTTCATTTGAATACCATTCAAACTT
*
29533051 TAACTATTTTC-TTCTGAATACCATTCAAACTT
1 TAACTATCTTCATT-TGAATACCATTCAAACTT
29533083 GAACAAAGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 2 0.07
32 28 0.93
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (32 bp):
TAACTATCTTCATTTGAATACCATTCAAACTT
Found at i:29533071 original size:53 final size:53
Alignment explanation
Indices: 29532958--29533061 Score: 183
Period size: 53 Copynumber: 2.0 Consensus size: 53
29532948 TAGCTATCAA
*
29532958 TACAATACTAACTATCTTCATCTTAATACCATTCAAACTTTAATTATTTTCAT
1 TACAATACTAACTATCTTCATCTTAATACCATTCAAACTTTAACTATTTTCAT
29533011 TACAATACTAACTATCTTCAT-TTGAATACCATTCAAACTTTAACTATTTTC
1 TACAATACTAACTATCTTCATCTT-AATACCATTCAAACTTTAACTATTTTC
29533062 TTCTGAATAC
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
52 2 0.04
53 47 0.96
ACGTcount: A:0.36, C:0.21, G:0.01, T:0.42
Consensus pattern (53 bp):
TACAATACTAACTATCTTCATCTTAATACCATTCAAACTTTAACTATTTTCAT
Found at i:29543780 original size:35 final size:37
Alignment explanation
Indices: 29543703--29543783 Score: 98
Period size: 35 Copynumber: 2.2 Consensus size: 37
29543693 TGGTAATATA
* *
29543703 ATTTTTTAAAAATAAAAAATAATTTAAAGTCATTAAAT
1 ATTTTTTAAAAAT-AAAAATAATTTAAAATCATAAAAT
29543741 -TTTTTTAAAAAT-AAAATAA-TTAAAATC-TAAAAGT
1 ATTTTTTAAAAATAAAAATAATTTAAAATCATAAAA-T
29543775 ATTTTTTAA
1 ATTTTTTAA
29543784 TATTTTTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
33 4 0.10
34 8 0.21
35 15 0.38
37 12 0.31
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (37 bp):
ATTTTTTAAAAATAAAAATAATTTAAAATCATAAAAT
Found at i:29547702 original size:19 final size:20
Alignment explanation
Indices: 29547680--29547719 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
29547670 TTATGTTTTT
*
29547680 AAAAATTTTAAATAT-ATTA
1 AAAAATGTTAAATATAATTA
*
29547699 AAAAATGTTAAGTATAATTA
1 AAAAATGTTAAATATAATTA
29547719 A
1 A
29547720 TTTTAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (20 bp):
AAAAATGTTAAATATAATTA
Found at i:29547827 original size:17 final size:17
Alignment explanation
Indices: 29547807--29547847 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
29547797 TAAAAAATTT
29547807 AAAAAATAAATATATTA
1 AAAAAATAAATATATTA
** *
29547824 AAAATTTAAATATGTTA
1 AAAAAATAAATATATTA
29547841 AAAAAAT
1 AAAAAAT
29547848 GTTGATTATA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (17 bp):
AAAAAATAAATATATTA
Found at i:29557635 original size:26 final size:26
Alignment explanation
Indices: 29557599--29557649 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
29557589 TTAAAATTTA
*
29557599 TAAATGACTATTATGCCACTATGAGG
1 TAAATAACTATTATGCCACTATGAGG
*
29557625 TAAATAACTATTATGCCCCTATGAG
1 TAAATAACTATTATGCCACTATGAG
29557650 ATGTATGACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (26 bp):
TAAATAACTATTATGCCACTATGAGG
Found at i:29560837 original size:27 final size:26
Alignment explanation
Indices: 29560772--29560855 Score: 96
Period size: 27 Copynumber: 3.2 Consensus size: 26
29560762 ACCCCTTAAT
* *
29560772 TGATAAAATGACTGATATACCCCATT
1 TGATAAAATGACTGTTATACCCCATG
**
29560798 TGATAAAATGACTGTTATACCTTTATG
1 TGATAAAATGACTGTTATACC-CCATG
* *
29560825 TGGTAAAATGACTGTTATGCCCCTATG
1 TGATAAAATGACTGTTATACCCC-ATG
29560852 TGAT
1 TGAT
29560856 GTATGATTGT
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
26 20 0.43
27 27 0.57
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (26 bp):
TGATAAAATGACTGTTATACCCCATG
Found at i:29566457 original size:45 final size:44
Alignment explanation
Indices: 29566377--29566683 Score: 162
Period size: 44 Copynumber: 6.8 Consensus size: 44
29566367 TTATTTATAG
* * * * * *
29566377 CTTCAATCTGTTCCACTGCAACTT-TGAGGAAATAAGATTCGCTAT
1 CTTCAGTCTGCTCCACTACAACTTCAG-GGAGATAAGATTTG-TAT
* *
29566422 CTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGATCCAACATGGTAGAT
1 CTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGAT------TTGT--AT
* * * * *
29566474 -TTGA-TCTGAC-CTACTACAACTTCAGAGG-TATAGGATTTGTAA
1 CTTCAGTCTG-CTCCACTACAACTTCAG-GGAGATAAGATTTGTAT
* * *
29566516 CTTTAATCTGC-CCTACTACAACTTCAGAGAGATAAGATTTGCTAT
1 CTTCAGTCTGCTCC-ACTACAACTTCAGGGAGATAAGATTTG-TAT
* * * * *
29566561 CTTCAGGCTGGTCCACTGCAACTTCAGGGAGATAAGACTTGTAA
1 CTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGATTTGTAT
* * * **
29566605 CTTC-GACCTGCCCCACTACAACTTCAAGGGA-ATAAGGTTTGTGG
1 CTTCAG-TCTGCTCCACTACAACTTC-AGGGAGATAAGATTTGTAT
* *
29566649 CTTCAATCTACTCCACTACAACTTCAGGGAGATAA
1 CTTCAGTCTGCTCCACTACAACTTCAGGGAGATAA
29566684 ACTCCACCAT
Statistics
Matches: 203, Mismatches: 38, Indels: 43
0.71 0.13 0.15
Matches are distributed among these distances:
42 1 0.00
43 12 0.06
44 83 0.41
45 70 0.34
46 3 0.01
50 24 0.12
51 8 0.04
52 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (44 bp):
CTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGATTTGTAT
Found at i:29566555 original size:44 final size:44
Alignment explanation
Indices: 29566477--29566792 Score: 160
Period size: 44 Copynumber: 7.0 Consensus size: 44
29566467 GGTAGATTTG
* *
29566477 ATCTGACCTACTACAACTTCAGAG-GTATAGGATTTGTAACTTTA
1 ATCTGCCCTACTACAACTTCAGAGAG-ATAAGATTTGTAACTTTA
* *
29566521 ATCTGCCCTACTACAACTTCAGAGAGATAAGATTTGCTATCTTCA
1 ATCTGCCCTACTACAACTTCAGAGAGATAAGATTTG-TAACTTTA
** * * * * **
29566566 GGCTGGTCC-ACTGCAACTTCAGGGAGATAAGACTTGTAACTTCG
1 ATCT-GCCCTACTACAACTTCAGAGAGATAAGATTTGTAACTTTA
* * * * ** *
29566610 ACCTGCCCCACTACAACTTCA-AGGGAATAAGGTTTGTGGCTTCA
1 ATCTGCCCTACTACAACTTCAGAGAG-ATAAGATTTGTAACTTTA
* * * *
29566654 ATCTACTCC-ACTACAACTTCAGGGAGATAA-ACTCCACCATGGTAGA-TTTG
1 ATCTGC-CCTACTACAACTTCAGAGAGATAAGA-T------TTGTA-ACTTTA
* * * *
29566704 ATCTGTCCTACTGCAACTTCAGAG-GTATAGGATTTGTAGCTTTA
1 ATCTGCCCTACTACAACTTCAGAGAG-ATAAGATTTGTAACTTTA
* * * * *
29566748 ATCTACTCTACTGCAGCTTCAGAGAGATAAGATTTGCTATCTTTA
1 ATCTGCCCTACTACAACTTCAGAGAGATAAGATTTG-TAACTTTA
29566793 GTTTACTCCA
Statistics
Matches: 204, Mismatches: 47, Indels: 41
0.70 0.16 0.14
Matches are distributed among these distances:
43 5 0.02
44 121 0.59
45 45 0.22
46 3 0.01
49 3 0.01
50 26 0.13
51 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.30
Consensus pattern (44 bp):
ATCTGCCCTACTACAACTTCAGAGAGATAAGATTTGTAACTTTA
Found at i:29566938 original size:132 final size:132
Alignment explanation
Indices: 29566796--29567441 Score: 845
Period size: 132 Copynumber: 4.9 Consensus size: 132
29566786 ATCTTTAGTT
*
29566796 TACTCCACTACCGCTTAGGGAGATAGGATGGTGGCTTAAATCTGCTCTACTGCAACTTCA-GAGA
1 TACTCCACTACTGCTTAGGGAGATAGGATGGTGGCTTAAATCTGCTCTACTGCAACTTCAGGA-A
* * * * **
29566860 GACAAGATTCGTCGTCTTCGATCTGTTCCACTGCAACCTCAGGGAAGCAAGATCTGTAATCTTCA
65 GACAAGATTCGCCGTCTTCGATCTGCTCCACTGCAACTTCAGGGAGGCAAGATCTACAATCTTCA
29566925 GCC
130 GCC
* * * *
29566928 TACTCCACTACTTCTTAGGGAGATAGGATGGTAGCTTAAATCTGCGCTCCTGCAACTTCAGGAAG
1 TACTCCACTACTGCTTAGGGAGATAGGATGGTGGCTTAAATCTGCTCTACTGCAACTTCAGGAAG
* ** *
29566993 ACAAGATTTGCCGTCTTCGATCTAATCCACTGCAACTTCAGAGAGGCAAGATCTACAATCTTCAG
66 ACAAGATTCGCCGTCTTCGATCTGCTCCACTGCAACTTCAGGGAGGCAAGATCTACAATCTTCAG
29567058 CC
131 CC
* *
29567060 TACTCCACTACTACTTAGGGAGATAGGATGGTGG-TTCAATTCTGCT-TCACTGCAACTTCAGGA
1 TACTCCACTACTGCTTAGGGAGATAGGATGGTGGCTT-AAATCTGCTCT-ACTGCAACTTCAGGA
* * *
29567123 AGACAAGATTCGCCATCTTCGATCTGCTCCACTGCAACTTGAGGGAGACAAGATCTA-AATCTTC
64 AGACAAGATTCGCCGTCTTCGATCTGCTCCACTGCAACTTCAGGGAGGCAAGATCTACAATCTTC
29567187 AGCC
129 AGCC
* * * *
29567191 TACTCCACTACTGTTTTGGGAGATAGGATGGTGGCTTAAATCTGCTCCACTGCAACTTCA-AAGA
1 TACTCCACTACTGCTTAGGGAGATAGGATGGTGGCTTAAATCTGCTCTACTGCAACTTCAGGA-A
* * ** *
29567255 GACAAGATTCGCCGTCTTCGATCTACTCCACTACAACTTCAAAGAGGAAAGATCTACAATCTTCA
65 GACAAGATTCGCCGTCTTCGATCTGCTCCACTGCAACTTCAGGGAGGCAAGATCTACAATCTTCA
*
29567320 ACC
130 GCC
* * * *
29567323 TACACCACTACTGCTTAGGAAGATAGGATGGTGGCTTAAATTTGCT-TCACTGTAACTTCAGGAA
1 TACTCCACTACTGCTTAGGGAGATAGGATGGTGGCTTAAATCTGCTCT-ACTGCAACTTCAGGAA
* * * * * *
29567387 GACAAGTTTCACCTTCTTCGATCTGTTCTACTGTAACTTCAGGGAGGCAAGATCT
65 GACAAGATTCGCCGTCTTCGATCTGCTCCACTGCAACTTCAGGGAGGCAAGATCT
29567442 GTAGAATTGG
Statistics
Matches: 445, Mismatches: 60, Indels: 18
0.85 0.11 0.03
Matches are distributed among these distances:
130 1 0.00
131 114 0.26
132 327 0.73
133 3 0.01
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (132 bp):
TACTCCACTACTGCTTAGGGAGATAGGATGGTGGCTTAAATCTGCTCTACTGCAACTTCAGGAAG
ACAAGATTCGCCGTCTTCGATCTGCTCCACTGCAACTTCAGGGAGGCAAGATCTACAATCTTCAG
CC
Found at i:29567309 original size:263 final size:264
Alignment explanation
Indices: 29566796--29567442 Score: 907
Period size: 263 Copynumber: 2.5 Consensus size: 264
29566786 ATCTTTAGTT
* *
29566796 TACTCCACTACCGCTTAGGGAGATAGGATGGTGGCTTAAATCTGC-TCTACTGCAACTTCA-GAG
1 TACTCCACTACTGCTTAGGGAGATAGGATGGTGGCTTAATTCTGCTTC-ACTGCAACTTCAGGA-
* * * *
29566859 AGACAAGATTCGTCGTCTTCGATCTGTTCCACTGCAACCTCAGGGA-AGCAAGATCTGTAATCTT
64 AGACAAGATTCGCCATCTTCGATCTGTTCCACTGCAACTTCAGGGAGA-CAAGATCTGAAATCTT
29566923 CAGCCTACTCCACTACTTCTTAGGGAGATAGGATGGTAGCTTAAATCTGCGCTCCTGCAACTTCA
128 CAGCCTACTCCACTACTTCTTAGGGAGATAGGATGGTAGCTTAAATCTGCGCTCCTGCAACTTCA
* * * * *
29566988 GGAAGACAAGATTTGCCGTCTTCGATCTAATCCACTGCAACTTCAGAGAGGCAAGATCTACAATC
193 AGAAGACAAGATTCGCCGTCTTCGATCTAATCCACTACAACTTCAAAGAGGAAAGATCTACAATC
*
29567053 TTCAGCC
258 TTCAACC
*
29567060 TACTCCACTACTACTTAGGGAGATAGGATGGTGG-TTCAATTCTGCTTCACTGCAACTTCAGGAA
1 TACTCCACTACTGCTTAGGGAGATAGGATGGTGGCTT-AATTCTGCTTCACTGCAACTTCAGGAA
* *
29567124 GACAAGATTCGCCATCTTCGATCTGCTCCACTGCAACTTGAGGGAGACAAGATCT-AAATCTTCA
65 GACAAGATTCGCCATCTTCGATCTGTTCCACTGCAACTTCAGGGAGACAAGATCTGAAATCTTCA
* * *
29567188 GCCTACTCCACTACTGT-TTTGGGAGATAGGATGGTGGCTTAAATCTGCTC-CACTGCAACTTCA
130 GCCTACTCCACTACT-TCTTAGGGAGATAGGATGGTAGCTTAAATCTGCGCTC-CTGCAACTTCA
*
29567251 A-AGAGACAAGATTCGCCGTCTTCGATCTACTCCACTACAACTTCAAAGAGGAAAGATCTACAAT
193 AGA-AGACAAGATTCGCCGTCTTCGATCTAATCCACTACAACTTCAAAGAGGAAAGATCTACAAT
29567315 CTTCAACC
257 CTTCAACC
* * *
29567323 TACACCACTACTGCTTAGGAAGATAGGATGGTGGCTTAAATT-TGCTTCACTGTAACTTCAGGAA
1 TACTCCACTACTGCTTAGGGAGATAGGATGGTGGCTT-AATTCTGCTTCACTGCAACTTCAGGAA
* * * * * *
29567387 GACAAGTTTCACCTTCTTCGATCTGTTCTACTGTAACTTCAGGGAGGCAAGATCTG
65 GACAAGATTCGCCATCTTCGATCTGTTCCACTGCAACTTCAGGGAGACAAGATCTG
29567443 TAGAATTGGT
Statistics
Matches: 342, Mismatches: 32, Indels: 18
0.87 0.08 0.05
Matches are distributed among these distances:
262 2 0.01
263 228 0.67
264 107 0.31
265 5 0.01
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (264 bp):
TACTCCACTACTGCTTAGGGAGATAGGATGGTGGCTTAATTCTGCTTCACTGCAACTTCAGGAAG
ACAAGATTCGCCATCTTCGATCTGTTCCACTGCAACTTCAGGGAGACAAGATCTGAAATCTTCAG
CCTACTCCACTACTTCTTAGGGAGATAGGATGGTAGCTTAAATCTGCGCTCCTGCAACTTCAAGA
AGACAAGATTCGCCGTCTTCGATCTAATCCACTACAACTTCAAAGAGGAAAGATCTACAATCTTC
AACC
Found at i:29567318 original size:45 final size:45
Alignment explanation
Indices: 29567229--29567333 Score: 106
Period size: 45 Copynumber: 2.3 Consensus size: 45
29567219 TGGTGGCTTA
* * * **
29567229 AATCTGCTCCACTGCAACTTCAAAGAGACAAGATTCGCCGTCTTC
1 AATCTACTCCACTACAACTTCAAAGAGACAAGATTCACAATCTTC
*
29567274 GATCTACTCCACTACAACTTCAAAGAGGA-AAGA-TCTACAATCTTC
1 AATCTACTCCACTACAACTTCAAAGA-GACAAGATTC-ACAATCTTC
* *
29567319 AACCTACACCACTAC
1 AATCTACTCCACTAC
29567334 TGCTTAGGAA
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
44 2 0.04
45 45 0.92
46 2 0.04
ACGTcount: A:0.34, C:0.31, G:0.11, T:0.23
Consensus pattern (45 bp):
AATCTACTCCACTACAACTTCAAAGAGACAAGATTCACAATCTTC
Found at i:29575490 original size:3 final size:3
Alignment explanation
Indices: 29575482--29575612 Score: 74
Period size: 3 Copynumber: 44.7 Consensus size: 3
29575472 ATTCATTAAT
** * * *
29575482 TTA TTA TTA TTA ACA -TA TTA TTA TTC TTAA TGTA TTA TCA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A T-TA TTA TTA TTA TTA
* * * * * * *
29575528 TTA TTT TTA TTT TTA TTA CTA TTA TCA TT- TTT TTA -AA TTA TTG TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
29575574 CTA TTA TTA TTA -TA TTG TTA TTA TTA CTA TTA -TA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
29575613 GTATTATCTT
Statistics
Matches: 93, Mismatches: 28, Indels: 14
0.69 0.21 0.10
Matches are distributed among these distances:
2 8 0.09
3 81 0.87
4 3 0.03
5 1 0.01
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:29575591 original size:20 final size:20
Alignment explanation
Indices: 29575566--29575609 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
29575556 TTTTTTAAAT
*
29575566 TATTGTTACTATTATTATTA
1 TATTGTTACTATTACTATTA
*
29575586 TATTGTTATTATTACTATTA
1 TATTGTTACTATTACTATTA
29575606 TATT
1 TATT
29575610 ATTGTATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.61
Consensus pattern (20 bp):
TATTGTTACTATTACTATTA
Found at i:29575594 original size:11 final size:11
Alignment explanation
Indices: 29575486--29575612 Score: 59
Period size: 11 Copynumber: 11.6 Consensus size: 11
29575476 ATTAATTTAT
**
29575486 TATTATTAACA
1 TATTATTATTA
*
29575497 TATTATTATTC
1 TATTATTATTA
*
29575508 T-TAATGTATTA
1 TATTAT-TATTA
*
29575519 TCATTACTATTA
1 T-ATTATTATTA
*
29575531 T-TT-TTATTTT
1 TATTATTA-TTA
*
29575541 TATTACTATTA
1 TATTATTATTA
*
29575552 TCATT-TTTTTA
1 T-ATTATTATTA
* *
29575563 AATTATTGTTA
1 TATTATTATTA
29575574 CTATTATTATTA
1 -TATTATTATTA
*
29575586 TATTGTTA-T-
1 TATTATTATTA
*
29575595 TATTACTATTA
1 TATTATTATTA
29575606 TATTATT
1 TATTATT
29575613 GTATTATCTT
Statistics
Matches: 84, Mismatches: 21, Indels: 22
0.66 0.17 0.17
Matches are distributed among these distances:
9 8 0.10
10 13 0.15
11 41 0.49
12 20 0.24
13 2 0.02
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (11 bp):
TATTATTATTA
Found at i:29575614 original size:23 final size:26
Alignment explanation
Indices: 29575516--29575611 Score: 78
Period size: 28 Copynumber: 3.8 Consensus size: 26
29575506 TCTTAATGTA
*
29575516 TTATCATTACTATTATT-TT-TA-T-
1 TTATTATTACTATTATTATTATATTG
* * * *
29575538 TT-TTATTACTATTATCATTTTTTTAAA
1 TTATTATTACTATTATTATTATATT--G
*
29575565 TTATTGTTACTATTATTATTATATTG
1 TTATTATTACTATTATTATTATATTG
29575591 TTATTATTACTATTA-TATTAT
1 TTATTATTACTATTATTATTAT
29575612 TGTATTATCT
Statistics
Matches: 58, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
21 12 0.21
22 4 0.07
23 1 0.02
24 1 0.02
25 6 0.10
26 14 0.24
27 2 0.03
28 18 0.31
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.62
Consensus pattern (26 bp):
TTATTATTACTATTATTATTATATTG
Found at i:29584514 original size:28 final size:29
Alignment explanation
Indices: 29584474--29584546 Score: 76
Period size: 28 Copynumber: 2.5 Consensus size: 29
29584464 TTTTACCTTT
* *
29584474 TTTTTTAAATTTTTTAAATATATTTTATA-
1 TTTTTT-AGTTTTATAAATATATTTTATAG
** *
29584503 TTTTTTAGTTTTATATTTATATTTTTTAG
1 TTTTTTAGTTTTATAAATATATTTTATAG
29584532 TTTTTATAGTTTTAT
1 TTTTT-TAGTTTTAT
29584547 TTTATTTAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 17 0.46
29 11 0.30
30 9 0.24
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (29 bp):
TTTTTTAGTTTTATAAATATATTTTATAG
Found at i:29584516 original size:15 final size:15
Alignment explanation
Indices: 29584496--29584546 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
29584486 TTTAAATATA
29584496 TTTTATATTTTTTAG
1 TTTTATATTTTTTAG
*
29584511 TTTTATA-TTTATA-
1 TTTTATATTTTTTAG
*
29584524 TTTTTTAGTTTTTATAG
1 TTTTATA-TTTTT-TAG
29584541 TTTTAT
1 TTTTAT
29584547 TTTATTTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
13 6 0.21
14 5 0.18
15 10 0.36
16 2 0.07
17 5 0.18
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.73
Consensus pattern (15 bp):
TTTTATATTTTTTAG
Found at i:29584517 original size:22 final size:23
Alignment explanation
Indices: 29584492--29584554 Score: 87
Period size: 21 Copynumber: 2.8 Consensus size: 23
29584482 ATTTTTTAAA
29584492 TATATTTTATATTTTTTAG-TTT
1 TATATTTTATATTTTTTAGTTTT
29584514 TATA-TTTATATTTTTTAGTTTT
1 TATATTTTATATTTTTTAGTTTT
29584536 TATAGTTTTAT-TTTATTTA
1 TATA-TTTTATATTT-TTTA
29584555 ATAAAAATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
21 14 0.38
22 11 0.30
23 3 0.08
24 9 0.24
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (23 bp):
TATATTTTATATTTTTTAGTTTT
Found at i:29584530 original size:30 final size:29
Alignment explanation
Indices: 29584491--29584551 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 29
29584481 AATTTTTTAA
*
29584491 ATATATTTTA-TATTTTTTAGTTTTATATTT
1 ATATATTTTAGT-TTTTATAGTTTTAT-TTT
*
29584521 ATATTTTTTAGTTTTTATAGTTTTATTTT
1 ATATATTTTAGTTTTTATAGTTTTATTTT
29584550 AT
1 AT
29584552 TTAATAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 5 0.18
30 22 0.79
31 1 0.04
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (29 bp):
ATATATTTTAGTTTTTATAGTTTTATTTT
Found at i:29584547 original size:28 final size:28
Alignment explanation
Indices: 29584492--29584551 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
29584482 ATTTTTTAAA
29584492 TATATTTTATATTTTTTAGTTTTATATT
1 TATATTTTATATTTTTTAGTTTTATATT
*
29584520 TATATTTTTTAGTTTTTATAGTTTTAT-TT
1 TATATTTTATA-TTTTT-TAGTTTTATATT
29584549 TAT
1 TAT
29584552 TTAATAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 10 0.34
29 10 0.34
30 9 0.31
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (28 bp):
TATATTTTATATTTTTTAGTTTTATATT
Found at i:29585287 original size:20 final size:22
Alignment explanation
Indices: 29585262--29585303 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
29585252 TTTTTATTAA
29585262 ATAAATA-AAAACT-ATAAAAT
1 ATAAATATAAAACTAATAAAAT
29585282 ATAAATATAAAACTAATAAAAT
1 ATAAATATAAAACTAATAAAAT
29585304 TTTATAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.35
21 6 0.30
22 7 0.35
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (22 bp):
ATAAATATAAAACTAATAAAAT
Found at i:29589211 original size:4 final size:4
Alignment explanation
Indices: 29589202--29589227 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
29589192 CATTGGCATC
29589202 TTGT TTGT TTGT TTGT TTGT TTGT TT
1 TTGT TTGT TTGT TTGT TTGT TTGT TT
29589228 TTTTAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (4 bp):
TTGT
Found at i:29592718 original size:38 final size:38
Alignment explanation
Indices: 29592670--29592745 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
29592660 AATCAAAATC
* *
29592670 AAAGTTTCATGTATATAATTGCATCCATTTAAAGTTCA
1 AAAGTTTCATGTATATAATTGCACCCAATTAAAGTTCA
29592708 AAAGTTTCATGTATATAATTGCACCCAATTAAAGTTCA
1 AAAGTTTCATGTATATAATTGCACCCAATTAAAGTTCA
29592746 TATAACAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (38 bp):
AAAGTTTCATGTATATAATTGCACCCAATTAAAGTTCA
Found at i:29594228 original size:30 final size:30
Alignment explanation
Indices: 29594193--29594255 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
29594183 AAAATATTAT
29594193 AAACTATTTTAAAAAAAGGGTAAATTATCA
1 AAACTATTTTAAAAAAAGGGTAAATTATCA
29594223 AAACTATTTTAAAAAAAGGGTAAATTATCA
1 AAACTATTTTAAAAAAAGGGTAAATTATCA
29594253 AAA
1 AAA
29594256 TAAACACTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.56, C:0.06, G:0.10, T:0.29
Consensus pattern (30 bp):
AAACTATTTTAAAAAAAGGGTAAATTATCA
Found at i:29597467 original size:21 final size:21
Alignment explanation
Indices: 29597428--29597499 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 21
29597418 ATATATATAA
*
29597428 ATATATATAATGGTATTAGAAAT
1 ATATATATAATAG--TTAGAAAT
29597451 ATATATAGTAAT-GTTAGAAAT
1 ATATATA-TAATAGTTAGAAAT
* *
29597472 ATACATATAATAGTTCA-AAAG
1 ATATATATAATAGTT-AGAAAT
29597493 ATATATA
1 ATATATA
29597500 ACTAACAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
20 4 0.09
21 26 0.60
22 1 0.02
23 8 0.19
24 4 0.09
ACGTcount: A:0.50, C:0.03, G:0.11, T:0.36
Consensus pattern (21 bp):
ATATATATAATAGTTAGAAAT
Found at i:29597689 original size:10 final size:10
Alignment explanation
Indices: 29597674--29597699 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
29597664 ATATATTAAG
29597674 TACATATACA
1 TACATATACA
29597684 TACATATACA
1 TACATATACA
29597694 TACATA
1 TACATA
29597700 CATGTACGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (10 bp):
TACATATACA
Found at i:29599114 original size:41 final size:41
Alignment explanation
Indices: 29599027--29599115 Score: 110
Period size: 41 Copynumber: 2.2 Consensus size: 41
29599017 GGGTTAGGTA
* * *
29599027 TTGGGCTAGTTATTGGGCTAGGTTGGTTTAGGTTAGTGGGT
1 TTGGGTTAGTTATTGGGCTAGGTAGGTTTAGGGTAGTGGGT
*
29599068 GTGGGTTAG-TATTGGGCTGAGGGTAGGTTT-GGGTAGTGGGT
1 TTGGGTTAGTTATTGGGCT-A-GGTAGGTTTAGGGTAGTGGGT
29599109 TTGGGTT
1 TTGGGTT
29599116 TTGTAAAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
40 9 0.22
41 24 0.59
42 8 0.20
ACGTcount: A:0.11, C:0.03, G:0.46, T:0.39
Consensus pattern (41 bp):
TTGGGTTAGTTATTGGGCTAGGTAGGTTTAGGGTAGTGGGT
Found at i:29600815 original size:33 final size:32
Alignment explanation
Indices: 29600768--29600842 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 32
29600758 CACAATTATA
** *
29600768 AATATAATTTTTTTTAAAATTAAATTTATCCC
1 AATATAATTTTTTTTAAAACGAAAATTATCCC
* *
29600800 AATATACTTTATTTTTTAAACGAAAATTATCCC
1 AATATAATTT-TTTTTAAAACGAAAATTATCCC
29600833 AA-ATAATTTT
1 AATATAATTTT
29600843 AAACAGAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
31 1 0.03
32 15 0.42
33 20 0.56
ACGTcount: A:0.41, C:0.11, G:0.01, T:0.47
Consensus pattern (32 bp):
AATATAATTTTTTTTAAAACGAAAATTATCCC
Found at i:29601532 original size:17 final size:17
Alignment explanation
Indices: 29601510--29601543 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
29601500 TTTAACATAT
29601510 TGTTAAAATACTATTTA
1 TGTTAAAATACTATTTA
* *
29601527 TGTTAAACTAGTATTTA
1 TGTTAAAATACTATTTA
29601544 AACAATATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (17 bp):
TGTTAAAATACTATTTA
Found at i:29608612 original size:53 final size:53
Alignment explanation
Indices: 29608532--29608637 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
29608522 CAACTCACTA
29608532 AGTGAATAAATCTACAGTATCACTTATACATATAATTCCTAGCATAGTAAGAT
1 AGTGAATAAATCTACAGTATCACTTATACATATAATTCCTAGCATAGTAAGAT
29608585 AGTGAATAAATCTACAGTATCACTTATACATATAATTCCTAGCATAGTAAGAT
1 AGTGAATAAATCTACAGTATCACTTATACATATAATTCCTAGCATAGTAAGAT
29608638 TTTAAACAAC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (53 bp):
AGTGAATAAATCTACAGTATCACTTATACATATAATTCCTAGCATAGTAAGAT
Found at i:29608619 original size:26 final size:26
Alignment explanation
Indices: 29608537--29608619 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
29608527 CACTAAGTGA
29608537 ATAAATCTACAGTATCACTTATACAT
1 ATAAATCTACAGTATCACTTATACAT
* * ** *
29608563 ATAATTCCTAGCA-TAGTAAGATAGT-GA-
1 ATAAAT-CTA-CAGTA-TCACTTA-TACAT
29608590 ATAAATCTACAGTATCACTTATACAT
1 ATAAATCTACAGTATCACTTATACAT
29608616 ATAA
1 ATAA
29608620 TTCCTAGCAT
Statistics
Matches: 40, Mismatches: 10, Indels: 14
0.62 0.16 0.22
Matches are distributed among these distances:
24 1 0.03
25 7 0.17
26 14 0.35
27 10 0.25
28 7 0.17
29 1 0.03
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.33
Consensus pattern (26 bp):
ATAAATCTACAGTATCACTTATACAT
Found at i:29609289 original size:21 final size:21
Alignment explanation
Indices: 29609265--29609328 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
29609255 TAAAAACCCG
29609265 TAAGGGTTGAAAAGAAGCTCA
1 TAAGGGTTGAAAAGAAGCTCA
* * ** *
29609286 TAAGAGCTGAACGGAAGCCCA
1 TAAGGGTTGAAAAGAAGCTCA
*
29609307 TAAGGGTT-AAACAGAAACTCA
1 TAAGGGTTGAAA-AGAAGCTCA
29609328 T
1 T
29609329 GTGAGTTAAA
Statistics
Matches: 31, Mismatches: 11, Indels: 2
0.70 0.25 0.05
Matches are distributed among these distances:
20 2 0.06
21 29 0.94
ACGTcount: A:0.42, C:0.16, G:0.25, T:0.17
Consensus pattern (21 bp):
TAAGGGTTGAAAAGAAGCTCA
Found at i:29609577 original size:45 final size:45
Alignment explanation
Indices: 29609522--29609614 Score: 143
Period size: 45 Copynumber: 2.1 Consensus size: 45
29609512 ATTCAATTTC
* *
29609522 ATAATTTAACAATATTCCATTTTTCAACAAC-ATGCTATATACATA
1 ATAATTTAACAATATTCCATTTTTCAAC-ACTATACTAAATACATA
*
29609567 ATAATTTAACAATATTCTATTTTTCAACACTATACTAAATACATA
1 ATAATTTAACAATATTCCATTTTTCAACACTATACTAAATACATA
29609612 ATA
1 ATA
29609615 TCATTCATCA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 2 0.05
45 42 0.95
ACGTcount: A:0.44, C:0.16, G:0.01, T:0.39
Consensus pattern (45 bp):
ATAATTTAACAATATTCCATTTTTCAACACTATACTAAATACATA
Found at i:29616155 original size:27 final size:27
Alignment explanation
Indices: 29616112--29616185 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
29616102 AAATGACTAA
*
29616112 AATACCCCTAATA-GGTAAAAAGACCGT
1 AATACCCCT-GTAGGGTAAAAAGACCGT
**
29616139 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTAGGGTAAAAAGACCGT
* *
29616166 AATACCCTTGTATGGTAAAA
1 AATACCCCTGTAGGGTAAAA
29616186 TGACGAATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
26 3 0.08
27 34 0.89
28 1 0.03
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (27 bp):
AATACCCCTGTAGGGTAAAAAGACCGT
Found at i:29616189 original size:27 final size:27
Alignment explanation
Indices: 29616125--29616189 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
29616115 ACCCCTAATA
*
29616125 GGTAAAAAGACCGTAAAGCCCCTGTAG
1 GGTAAAATGACCGTAAAGCCCCTGTAG
* * *
29616152 GGTAAAGTGACCGTAATA-CCCTTGTAT
1 GGTAAAATGACCGTAA-AGCCCCTGTAG
29616179 GGTAAAATGAC
1 GGTAAAATGAC
29616190 GAATATGCCC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (27 bp):
GGTAAAATGACCGTAAAGCCCCTGTAG
Found at i:29617013 original size:25 final size:25
Alignment explanation
Indices: 29616975--29617044 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
29616965 AGGAAGTGCT
* *
29616975 AAAAGGGCTATGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCA
* *
29617000 AAAAGGGCTTTGCCCTAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
29617025 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
29617045 ATTAAAAGAG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:29617057 original size:24 final size:24
Alignment explanation
Indices: 29616974--29617069 Score: 86
Period size: 25 Copynumber: 3.9 Consensus size: 24
29616964 GAGGAAGTGC
*
29616974 TAAAAGGGCTATGCCCCAGTTTACC
1 TAAAAGGGCTATGCCCCAGTTTA-T
* * *
29616999 GAAAAGGGCTTTGCCCTAGTTTAT
1 TAAAAGGGCTATGCCCCAGTTTAT
* *
29617023 CAAAAAGGGCTTTGCCCCAG-TTAT
1 -TAAAAGGGCTATGCCCCAGTTTAT
*
29617047 TAAAAGAGGCTAGGCCTCCAGTT
1 TAAAAG-GGCTATGCC-CCAGTT
29617070 ATATGATAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
23 5 0.09
24 11 0.19
25 41 0.71
26 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (24 bp):
TAAAAGGGCTATGCCCCAGTTTAT
Found at i:29617313 original size:31 final size:31
Alignment explanation
Indices: 29617264--29617376 Score: 178
Period size: 30 Copynumber: 3.7 Consensus size: 31
29617254 TGCTTACAGT
*
29617264 AAAGGCTTCAG-CCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
29617294 AAAGGCTTCGGCCCAGTGATATGA-TTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
* *
29617324 AAAGGCTTCGGCCTAGTGATATGATTTATGG
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
29617355 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
29617377 TCAAAATTAA
Statistics
Matches: 77, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
30 44 0.57
31 33 0.43
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:29617351 original size:61 final size:59
Alignment explanation
Indices: 29617264--29617376 Score: 190
Period size: 61 Copynumber: 1.9 Consensus size: 59
29617254 TGCTTACAGT
29617264 AAAGGCTTCAGCCAGTGATATGATTTATGAAAAGGCTTCGGCCCAGTGATATGATTATGA
1 AAAGGCTTCAGCCAGTGATATGATTTATGAAAAGGCTTCGGCCCAGT-ATATGATTATGA
* *
29617324 AAAGGCTTCGGCCTAGTGATATGATTTATGGAAAGGCTTCGGCCCAGTATATG
1 AAAGGCTTCAGCC-AGTGATATGATTTATGAAAAGGCTTCGGCCCAGTATATG
29617377 TCAAAATTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
60 17 0.34
61 33 0.66
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (59 bp):
AAAGGCTTCAGCCAGTGATATGATTTATGAAAAGGCTTCGGCCCAGTATATGATTATGA
Found at i:29626143 original size:14 final size:14
Alignment explanation
Indices: 29626126--29626155 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29626116 TAAATTTTAC
*
29626126 AAATAATTAATATA
1 AAATAATAAATATA
29626140 AAATAATAAATATA
1 AAATAATAAATATA
29626154 AA
1 AA
29626156 TTCTTGATAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAATAATAAATATA
Found at i:29626528 original size:12 final size:12
Alignment explanation
Indices: 29626507--29626545 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
29626497 TGACGTGGCA
*
29626507 GAGGAGGACGAT
1 GAGGACGACGAT
*
29626519 GAGGACGACGAA
1 GAGGACGACGAT
*
29626531 GAGGATGACGAT
1 GAGGACGACGAT
29626543 GAG
1 GAG
29626546 CTTTATGGCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.36, C:0.10, G:0.46, T:0.08
Consensus pattern (12 bp):
GAGGACGACGAT
Found at i:29629788 original size:55 final size:55
Alignment explanation
Indices: 29629723--29629832 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 55
29629713 TTGTTTTTCG
*
29629723 TTGCACTAGCATAGCAGTTGCACTTTTGATGTATATTAATGATGATTCTTTTCAT
1 TTGCACTAGCATAGCAGTTGCACTTTTGATGTATACTAATGATGATTCTTTTCAT
*
29629778 TTGCACTAGCATAGCGGTTGCACTTTTGATGTATACTAATGATGATTCTTTTCAT
1 TTGCACTAGCATAGCAGTTGCACTTTTGATGTATACTAATGATGATTCTTTTCAT
29629833 ACTTACGCAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.43
Consensus pattern (55 bp):
TTGCACTAGCATAGCAGTTGCACTTTTGATGTATACTAATGATGATTCTTTTCAT
Found at i:29629946 original size:125 final size:125
Alignment explanation
Indices: 29629773--29630168 Score: 456
Period size: 125 Copynumber: 3.2 Consensus size: 125
29629763 GATGATTCTT
*
29629773 TTCATTTGCACTAGCATAGCGGTTGCACTTTTGATGTATACTAATGATGATTCTTTTCATACTTA
1 TTCA-TTGCACTAGCATAGCGGTTGCACTTTTGATGTATACTAATGATGATTCTTTTCATTCTTA
* * * * * * *
29629838 CGCAATTTGTTGCATATGTTGTTATTCATTTCCATTTCTCGATTTTAATGTTGACATATTC
65 CGCAATTTGTTGCATATATTGTTATTCGTTTGCATATCTCGAGTTTAATGTTGATATGTTC
* * * * * *
29629899 TTCATTGCAATAGAATAGTGGTTGCACTTTTGATGTATACTAGTGATGATTCTTTCCGGTTCTTA
1 TTCATTGCACTAGCATAGCGGTTGCACTTTTGATGTATACTAATGATGATTCTTTTC-ATTCTTA
* * * * * * *
29629964 CACAATTTGTTGCATTTATGGTTATTCGTTTGTATATCTTGAGTTTAATGTCGATACGTTC
65 CGCAATTTGTTGCATATATTGTTATTCGTTTGCATATCTCGAGTTTAATGTTGATATGTTC
* * * * ** *
29630025 TTCATTGTATTAGCTTAGCGATTGCAC-TTCAATATATACTAATGATGATTCTTTAT-AGTTCTT
1 TTCATTGCACTAGCATAGCGGTTGCACTTTTGATGTATACTAATGATGATTCTTT-TCA-TTCTT
*
29630088 ACGCAATTT-TCTGCATATATTGTTATTTGTTTGCATATCTCGAGTTTAATGTTGATATGTTC
64 ACGCAATTTGT-TGCATATATTGTTATTCGTTTGCATATCTCGAGTTTAATGTTGATATGTTC
*
29630150 TTCAATGCACTAGCATAGC
1 TTCATTGCACTAGCATAGC
29630169 ATAGTAAGCT
Statistics
Matches: 221, Mismatches: 45, Indels: 9
0.80 0.16 0.03
Matches are distributed among these distances:
124 1 0.00
125 143 0.65
126 77 0.35
ACGTcount: A:0.24, C:0.15, G:0.16, T:0.45
Consensus pattern (125 bp):
TTCATTGCACTAGCATAGCGGTTGCACTTTTGATGTATACTAATGATGATTCTTTTCATTCTTAC
GCAATTTGTTGCATATATTGTTATTCGTTTGCATATCTCGAGTTTAATGTTGATATGTTC
Found at i:29630795 original size:9 final size:9
Alignment explanation
Indices: 29630775--29630811 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
29630765 GTGAATGGTT
29630775 AAATTTATTA
1 AAATTTA-TA
29630785 AAATTTATA
1 AAATTTATA
*
29630794 AAATTAATA
1 AAATTTATA
29630803 AAATTTATA
1 AAATTTATA
29630812 TTAGAATCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 18 0.72
10 7 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
AAATTTATA
Found at i:29632282 original size:69 final size:69
Alignment explanation
Indices: 29632186--29632381 Score: 302
Period size: 69 Copynumber: 2.8 Consensus size: 69
29632176 TCTCGAATGC
* * * *
29632186 ACAAATGAGAAAGAGAGGGAGGGAGCATGTTTGGCGGCATGGATTGGAGCTTGGGACAATTACAG
1 ACAAATAAGAAAGAGAGTGAGGAAGCATGTTTGGAGGCATGGATTGGAGCTTGGGACAATTACAG
29632251 ATAG
66 ATAG
* *
29632255 ACAAATAAGAAAGAGAGTGAGGAAGCATGTTTGGGGGCATGGATTGGAGCTTGGGACAATTCCAG
1 ACAAATAAGAAAGAGAGTGAGGAAGCATGTTTGGAGGCATGGATTGGAGCTTGGGACAATTACAG
29632320 ATAG
66 ATAG
* * * *
29632324 ACAAATAAGAAAGAGAGTGTGGAAGCATGCTTGGAGGCACGGATTGGAGGTTGGGACA
1 ACAAATAAGAAAGAGAGTGAGGAAGCATGTTTGGAGGCATGGATTGGAGCTTGGGACA
29632382 GTCAAGGATA
Statistics
Matches: 117, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 117 1.00
ACGTcount: A:0.34, C:0.10, G:0.37, T:0.19
Consensus pattern (69 bp):
ACAAATAAGAAAGAGAGTGAGGAAGCATGTTTGGAGGCATGGATTGGAGCTTGGGACAATTACAG
ATAG
Found at i:29635124 original size:19 final size:18
Alignment explanation
Indices: 29635087--29635127 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
29635077 ATATTAAAAC
*
29635087 ATATACATGACATACATA
1 ATATACATGACAAACATA
*
29635105 ATATACATGATAGAACATA
1 ATATACATGACA-AACATA
29635124 ATAT
1 ATAT
29635128 GATATTTACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.51, C:0.12, G:0.07, T:0.29
Consensus pattern (18 bp):
ATATACATGACAAACATA
Found at i:29640773 original size:15 final size:15
Alignment explanation
Indices: 29640743--29640771 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
29640733 ACTATTAGTG
29640743 ATTTTTTAAATATTT
1 ATTTTTTAAATATTT
29640758 ATTTTTT-AATATTT
1 ATTTTTTAAATATTT
29640772 TACCATACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTTTTAAATATTT
Found at i:29641968 original size:26 final size:26
Alignment explanation
Indices: 29641904--29641956 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
29641894 TTAATTTCAG
29641904 TATTGTTAATTTTTTTTAATTTGAAA
1 TATTGTTAATTTTTTTTAATTTGAAA
29641930 TATTGTTAATTTTTTTTAATTTGAAA
1 TATTGTTAATTTTTTTTAATTTGAAA
29641956 T
1 T
29641957 TGTTTTCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (26 bp):
TATTGTTAATTTTTTTTAATTTGAAA
Found at i:29657933 original size:16 final size:16
Alignment explanation
Indices: 29657909--29657951 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
29657899 ATTTTATTAC
29657909 TATTA-TTATTATATT
1 TATTATTTATTATATT
*
29657924 TATTATTTATTGTATT
1 TATTATTTATTATATT
29657940 TATTATTTATTA
1 TATTATTTATTA
29657952 GCATTAGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 5 0.20
16 20 0.80
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (16 bp):
TATTATTTATTATATT
Found at i:29657962 original size:19 final size:16
Alignment explanation
Indices: 29657921--29657966 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 16
29657911 TTATTATTAT
*
29657921 ATTTATTATTTATTGT
1 ATTTATTATTTATTGC
29657937 ATTTATTATTTATTAGC
1 ATTTATTATTTATT-GC
29657954 ATTAGTATTATTT
1 ATT--TATTATTT
29657967 TTACTTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 14 0.54
17 4 0.15
19 8 0.31
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.63
Consensus pattern (16 bp):
ATTTATTATTTATTGC
Found at i:29658547 original size:25 final size:26
Alignment explanation
Indices: 29658497--29658569 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 26
29658487 TTTTTAATAC
29658497 TATATTTTTAATACCATATATATTG-TG
1 TATATTTTTAATA-C-TATATATTGATG
*
29658524 TATATTCTTAATACTATATATTGTATG
1 TATATTTTTAATACTATATATTG-ATG
29658551 TAT-TTTTTAATAACTATAT
1 TATATTTTTAAT-ACTATAT
29658570 TATATGTATA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
25 9 0.22
26 8 0.20
27 24 0.59
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.53
Consensus pattern (26 bp):
TATATTTTTAATACTATATATTGATG
Found at i:29658724 original size:20 final size:21
Alignment explanation
Indices: 29658699--29658742 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
29658689 ATGTATGTAT
29658699 TATGTATATA-TTTTTAATAC
1 TATGTATATATTTTTTAATAC
29658719 TATGTATATATTTTTTAATAC
1 TATGTATATATTTTTTAATAC
29658740 TAT
1 TAT
29658743 TATTATGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.57
Consensus pattern (21 bp):
TATGTATATATTTTTTAATAC
Found at i:29658756 original size:47 final size:46
Alignment explanation
Indices: 29658663--29658763 Score: 118
Period size: 46 Copynumber: 2.2 Consensus size: 46
29658653 TTAATAGTTG
* *
29658663 TTTTTAATATTATTATTATTTCTAATATGTATGTATTATGTATATA
1 TTTTTAATACTATTATTATTTCTAATATCTATGTATTATGTATATA
* *
29658709 TTTTTAATACTATGTATATATTTTTTAATA-CTAT-TATTATGTTTATA
1 TTTTTAATACTAT-TAT-TA-TTTCTAATATCTATGTATTATGTATATA
29658756 -TTTTAATA
1 TTTTTAATA
29658764 TATATACATA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
46 20 0.42
47 15 0.31
48 5 0.10
49 8 0.17
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (46 bp):
TTTTTAATACTATTATTATTTCTAATATCTATGTATTATGTATATA
Found at i:29666827 original size:242 final size:243
Alignment explanation
Indices: 29666401--29666891 Score: 795
Period size: 242 Copynumber: 2.0 Consensus size: 243
29666391 TACCGTAAAT
* * * *
29666401 AAATTCTAAAAATAAGCCCGTGCAATATCTTCCATTTCCCAAAAGTCTTCCGTTTCCCCTCCACT
1 AAATTCTAAAAATAAGCACGTGCAATACCCTCAATTTCCCAAAAGTCTTCCGTTTCCCCTCCACT
*
29666466 TTCATTCTGTAACTTATTAATATAGTTTCTCCTCCGTCTTTATGTTGCTTGGCTATGAAAAAAAA
66 TTCATTCTGTAACTTATTAATATAGTTTCTCCTCCGTCTTTATGTTACTTGGCTATGAAAAAAAA
* **
29666531 CCGTATTCCTGTCATGGAATTTCAACCAGTTCAGTGGCGCCCTTTGCTCCCAGTAATATTCATCA
131 CCGTATTCCTATCACCGAATTTCAACCAGTTCAGTGGCGCCCTTTGCTCCCAGTAATATTCATCA
29666596 TTTTCAATCTCAAAGTTTAGCTGAATCTTTGTGTCAATTATCTCAGCC
196 TTTTCAATCTCAAAGTTTAGCTGAATCTTTGTGTCAATTATCTCAGCC
*
29666644 AAATTCTAAAAATAAGCACGTGCAATACCCTCAATTTCCCAAAA-TTTTCCGTTTCCCCTCCACT
1 AAATTCTAAAAATAAGCACGTGCAATACCCTCAATTTCCCAAAAGTCTTCCGTTTCCCCTCCACT
* * * *
29666708 TTCATTCTGTAGCTTATTAATCTGGTTTCTCCTCCGTCTTTATGTTACTTGGCTATGAAAAAAAG
66 TTCATTCTGTAACTTATTAATATAGTTTCTCCTCCGTCTTTATGTTACTTGGCTATGAAAAAAAA
** * *
29666773 TTGTATTCCTATCACCGAATTTCAACCAGTTCAGTTGCGCCCTTTGCTCCCAGTAATATTCATCC
131 CCGTATTCCTATCACCGAATTTCAACCAGTTCAGTGGCGCCCTTTGCTCCCAGTAATATTCATCA
* * *
29666838 TTTTCAATCTCAAAGTTTCGCTGAATCTTTGTGTCAATTATTTTAGCC
196 TTTTCAATCTCAAAGTTTAGCTGAATCTTTGTGTCAATTATCTCAGCC
29666886 AAATTC
1 AAATTC
29666892 GTATCATCCC
Statistics
Matches: 228, Mismatches: 20, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
242 188 0.82
243 40 0.18
ACGTcount: A:0.26, C:0.25, G:0.12, T:0.37
Consensus pattern (243 bp):
AAATTCTAAAAATAAGCACGTGCAATACCCTCAATTTCCCAAAAGTCTTCCGTTTCCCCTCCACT
TTCATTCTGTAACTTATTAATATAGTTTCTCCTCCGTCTTTATGTTACTTGGCTATGAAAAAAAA
CCGTATTCCTATCACCGAATTTCAACCAGTTCAGTGGCGCCCTTTGCTCCCAGTAATATTCATCA
TTTTCAATCTCAAAGTTTAGCTGAATCTTTGTGTCAATTATCTCAGCC
Found at i:29670486 original size:27 final size:27
Alignment explanation
Indices: 29670455--29670527 Score: 65
Period size: 29 Copynumber: 2.6 Consensus size: 27
29670445 TTTAGGGTTT
29670455 TTAGGGTTAGAGTTTTGCTAAAATAAG
1 TTAGGGTTAGAGTTTTGCTAAAATAAG
* * ** *
29670482 TTAGGTTTAGTGGTTTTTTTTAAAATATG
1 TTAGGGTTAG-AG-TTTTGCTAAAATAAG
*
29670511 TTAGGGTTTAAAGTTTT
1 TTAGGG-TTAGAGTTTT
29670528 AGTAGATTTT
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
27 9 0.26
28 5 0.14
29 18 0.51
30 3 0.09
ACGTcount: A:0.27, C:0.01, G:0.23, T:0.48
Consensus pattern (27 bp):
TTAGGGTTAGAGTTTTGCTAAAATAAG
Found at i:29670652 original size:22 final size:22
Alignment explanation
Indices: 29670625--29670677 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
29670615 AATTAGAGTT
*
29670625 CTAGGGTTTTGAATAAATAAAA
1 CTAGGGTTTTAAATAAATAAAA
* *
29670647 TTAGGGTTTTAAATAAATTAAA
1 CTAGGGTTTTAAATAAATAAAA
29670669 CTAGGGTTT
1 CTAGGGTTT
29670678 ATGGTGTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.38
Consensus pattern (22 bp):
CTAGGGTTTTAAATAAATAAAA
Found at i:29670681 original size:86 final size:86
Alignment explanation
Indices: 29670578--29670741 Score: 247
Period size: 86 Copynumber: 1.9 Consensus size: 86
29670568 TAAAAATTAT
* * * *
29670578 TTAAATTAGCGTTTATGGTTTTTAAATAAATTTAGTAAATTAGAGTTCTAGGGTTTTGAATAAAT
1 TTAAACTAGCGTTTATGGTGTTTAAATAAATTAAGTAAATTAGAGTTCTAGGGTTTTAAATAAAT
29670643 AAAATTAGGGTTTTAAATAAA
66 AAAATTAGGGTTTTAAATAAA
* * *
29670664 TTAAACTAGGGTTTATGGTGTTTAAATAAATTAATTAAATTAGGGTTCTAGGGTTTTAAATAAAT
1 TTAAACTAGCGTTTATGGTGTTTAAATAAATTAAGTAAATTAGAGTTCTAGGGTTTTAAATAAAT
* *
29670729 TAAATTATGGTTT
66 AAAATTAGGGTTT
29670742 AGGGTTAAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
86 69 1.00
ACGTcount: A:0.38, C:0.02, G:0.17, T:0.43
Consensus pattern (86 bp):
TTAAACTAGCGTTTATGGTGTTTAAATAAATTAAGTAAATTAGAGTTCTAGGGTTTTAAATAAAT
AAAATTAGGGTTTTAAATAAA
Found at i:29670700 original size:34 final size:34
Alignment explanation
Indices: 29670656--29670731 Score: 109
Period size: 34 Copynumber: 2.2 Consensus size: 34
29670646 ATTAGGGTTT
* *
29670656 TAAATAAATTAAACTAGGGTT-TATGGTGTTTAAA
1 TAAATTAATTAAACTAGGGTTCTAGGGT-TTTAAA
*
29670690 TAAATTAATTAAATTAGGGTTCTAGGGTTTTAAA
1 TAAATTAATTAAACTAGGGTTCTAGGGTTTTAAA
29670724 TAAATTAA
1 TAAATTAA
29670732 ATTATGGTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 33 0.87
35 5 0.13
ACGTcount: A:0.42, C:0.03, G:0.16, T:0.39
Consensus pattern (34 bp):
TAAATTAATTAAACTAGGGTTCTAGGGTTTTAAA
Found at i:29670717 original size:64 final size:58
Alignment explanation
Indices: 29670648--29670768 Score: 170
Period size: 64 Copynumber: 2.0 Consensus size: 58
29670638 TAAATAAAAT
29670648 TAGGGTTTTAAATAAATTAAACTAGGGTTTATGGTGTTTAAATAAATTAATTAAATTAGGGTTC
1 TAGGGTTTTAAATAAATTAAACTAGGGTTTA-GG-G-TT--A-AAATTAATTAAATTAGGGTTC
* *
29670712 TAGGGTTTTAAATAAATTAAATTATGGTTTAGGGTTAAAATTAATTAAATTAGGGTT
1 TAGGGTTTTAAATAAATTAAACTAGGGTTTAGGGTTAAAATTAATTAAATTAGGGTT
29670769 TAGTTATTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
58 20 0.36
59 1 0.02
61 2 0.04
62 1 0.02
63 2 0.04
64 29 0.53
ACGTcount: A:0.38, C:0.02, G:0.19, T:0.41
Consensus pattern (58 bp):
TAGGGTTTTAAATAAATTAAACTAGGGTTTAGGGTTAAAATTAATTAAATTAGGGTTC
Found at i:29670759 original size:28 final size:29
Alignment explanation
Indices: 29670647--29670771 Score: 135
Period size: 28 Copynumber: 4.1 Consensus size: 29
29670637 ATAAATAAAA
* * *
29670647 TTAGGGTTTTAAATAAATTAAACTAGGGT
1 TTAGGGTTTAAAATTAATTAAATTAGGGT
29670676 TTATGGTGTTTAAATAAATTAATTAAATTAGGGT
1 TTA-GG-GTTT--A-AAATTAATTAAATTAGGGT
* * *
29670710 TCTAGGGTTTTAAATAAATTAAATTATGGT
1 T-TAGGGTTTAAAATTAATTAAATTAGGGT
29670740 TTAGGG-TTAAAATTAATTAAATTAGGGT
1 TTAGGGTTTAAAATTAATTAAATTAGGGT
29670768 TTAG
1 TTAG
29670772 TTATTTTAAA
Statistics
Matches: 81, Mismatches: 9, Indels: 13
0.79 0.09 0.13
Matches are distributed among these distances:
28 23 0.28
29 8 0.10
30 20 0.25
31 4 0.05
33 4 0.05
34 20 0.25
35 2 0.02
ACGTcount: A:0.38, C:0.02, G:0.19, T:0.42
Consensus pattern (29 bp):
TTAGGGTTTAAAATTAATTAAATTAGGGT
Found at i:29671045 original size:125 final size:124
Alignment explanation
Indices: 29670825--29671074 Score: 369
Period size: 125 Copynumber: 2.0 Consensus size: 124
29670815 CTATTTTGAC
*
29670825 CCTAAAAAAATAATTTTGAGAATACATTTCTAACAAATAGTGTAAAAAAACTTCAAGAAGGATGT
1 CCTAAAAAAATAATTTTGAGAATACATTTCTAACAAATAGTGTAAAAAAACTTCAAGAAGGATGC
** * *
29670890 ACTGTCAGCAAAATTATAGAAAAAAGCTCCCATGTGGACG-TTTTTTTCTACAGTAGTT
66 ACTGTCAGCAAAATTATAGAAAAAAGCTCCCACATGGACGCTCTTTTTCCACAGTAGTT
* ** *
29670948 CCTAAAAAAATAATTTTGAGAATACGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGAT
1 CCTAAAAAAATAATTTTGAGAATACATTTCT-AACAAATAGTGT-AAAAAAACTTCAAGAAGGAT
*
29671013 GCACTGTCAGCAAAATT-TCTGAAAAAAGCTCCCACATGGACGCTCTTTTTCCACAGTAGTT
64 GCACTGTCAGCAAAATTAT-AGAAAAAAGCTCCCACATGGACGCTCTTTTTCCACAGTAGTT
29671074 C
1 C
29671075 ATGCTTGGCC
Statistics
Matches: 113, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
123 30 0.27
124 13 0.12
125 53 0.47
126 17 0.15
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (124 bp):
CCTAAAAAAATAATTTTGAGAATACATTTCTAACAAATAGTGTAAAAAAACTTCAAGAAGGATGC
ACTGTCAGCAAAATTATAGAAAAAAGCTCCCACATGGACGCTCTTTTTCCACAGTAGTT
Found at i:29674563 original size:18 final size:18
Alignment explanation
Indices: 29674537--29674579 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
29674527 GACTGGAAAA
*
29674537 AGGAAACATATAAGGGTT
1 AGGATACATATAAGGGTT
29674555 AGGATACATATAAGGGTT
1 AGGATACATATAAGGGTT
29674573 AGGATAC
1 AGGATAC
29674580 GCACCTGGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.42, C:0.07, G:0.28, T:0.23
Consensus pattern (18 bp):
AGGATACATATAAGGGTT
Found at i:29676129 original size:14 final size:16
Alignment explanation
Indices: 29676110--29676141 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
29676100 GACTGTTATA
29676110 AAAAATT-A-TAAAAT
1 AAAAATTAATTAAAAT
29676124 AAAAATTAATTAAAAT
1 AAAAATTAATTAAAAT
29676140 AA
1 AA
29676142 CATAAATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 1 0.06
16 8 0.50
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAAATTAATTAAAAT
Done.