Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
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: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 65 of 316
Found at i:19130318 original size:85 final size:85
Alignment explanation
Indices: 19130220--19130426 Score: 351
Period size: 85 Copynumber: 2.4 Consensus size: 85
19130210 GTAACATGTA
* * * *
19130220 TAACCATGGCATATTCACTTAGCACCACGTTACATGTTTAACCGTGGTATATCCACTTAGCACCA
1 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTTTAACCGTGGTATATCCACTGAACACCA
19130285 CGCTAATGAATCAATATATG
66 CGCTAATGAATCAATATATG
* *
19130305 TAACCGTGGCATATCCACTCAGCCCCACGTTACATGTTTAACCGTGGTATATCCACTGAACACCA
1 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTTTAACCGTGGTATATCCACTGAACACCA
*
19130370 CGTTAATGAATCAATATATG
66 CGCTAATGAATCAATATATG
19130390 TAACCGTGGCATATCCACTTAGCACCACGTTACATGT
1 TAACCGTGGCATATCCACTTAGCACCACGTTACATGT
19130427 ATCAATTTGT
Statistics
Matches: 113, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
85 113 1.00
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (85 bp):
TAACCGTGGCATATCCACTTAGCACCACGTTACATGTTTAACCGTGGTATATCCACTGAACACCA
CGCTAATGAATCAATATATG
Found at i:19130452 original size:48 final size:48
Alignment explanation
Indices: 19130343--19130476 Score: 189
Period size: 48 Copynumber: 2.8 Consensus size: 48
19130333 GTTACATGTT
* * *
19130343 TAACCGTGGTATATCCACTGAACACCACGTTA-ATGAATCAATATATG
1 TAACCGTGGTATATCCACTTAGCACCACGTTACATGTATCAATATATG
* * *
19130390 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTATCAATTTGTG
1 TAACCGTGGTATATCCACTTAGCACCACGTTACATGTATCAATATATG
* *
19130438 TAATCGTGGTATATCCACTTAGCACCACGTTACACGTAT
1 TAACCGTGGTATATCCACTTAGCACCACGTTACATGTAT
19130477 AACCGTGGTA
Statistics
Matches: 77, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
47 29 0.38
48 48 0.62
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.30
Consensus pattern (48 bp):
TAACCGTGGTATATCCACTTAGCACCACGTTACATGTATCAATATATG
Found at i:19130502 original size:133 final size:132
Alignment explanation
Indices: 19130258--19130506 Score: 372
Period size: 133 Copynumber: 1.9 Consensus size: 132
19130248 GTTACATGTT
*
19130258 TAACCGTGGTATATCCACTTAGCACCACGCTAATGAATCAATATATGTAACCGTGGCATATCCAC
1 TAACCGTGGCATATCCACTTAGCACCACGCTAATGAATCAATATATGTAACCGTGGCATATCCAC
* * *
19130323 TCAGCCCCACGTTACATGTTTAACCGTGGTATATCCACTGAACACCACGTTAATGAATCAATATA
66 TCAGCACCACGTTACACGTATAACCGTGGTATATCCACTGAACACCACGTTAATGAATCAATATA
19130388 TG
131 TG
* * * * * *
19130390 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTATCAATTTGTGTAATCGTGGTATATCCA
1 TAACCGTGGCATATCCACTTAGCACCACGCTA-ATGAATCAATATATGTAACCGTGGCATATCCA
* * *
19130455 CTTAGCACCACGTTACACGTATAACCGTGGTATATCCACTTAGCACCACGTT
65 CTCAGCACCACGTTACACGTATAACCGTGGTATATCCACTGAACACCACGTT
19130507 TTCATTCTGA
Statistics
Matches: 103, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
132 30 0.29
133 73 0.71
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.29
Consensus pattern (132 bp):
TAACCGTGGCATATCCACTTAGCACCACGCTAATGAATCAATATATGTAACCGTGGCATATCCAC
TCAGCACCACGTTACACGTATAACCGTGGTATATCCACTGAACACCACGTTAATGAATCAATATA
TG
Found at i:19131736 original size:52 final size:52
Alignment explanation
Indices: 19131658--19131761 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
19131648 GCAACACAAT
19131658 GCTTAGTAAGTTCGTACGGAATTTAACACAACTTACCCGAAATTAATATATC
1 GCTTAGTAAGTTCGTACGGAATTTAACACAACTTACCCGAAATTAATATATC
19131710 GCTTAGTAAGTTCGTACGGAATTTAACACAACTTACCCGAAATTAATATATC
1 GCTTAGTAAGTTCGTACGGAATTTAACACAACTTACCCGAAATTAATATATC
19131762 TTAAGCATTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (52 bp):
GCTTAGTAAGTTCGTACGGAATTTAACACAACTTACCCGAAATTAATATATC
Found at i:19141068 original size:19 final size:19
Alignment explanation
Indices: 19141044--19141080 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
19141034 TATATTATTA
*
19141044 TTATTATTATTATTGTTAC
1 TTATTATTATTACTGTTAC
19141063 TTATTATTATTACTGTTA
1 TTATTATTATTACTGTTA
19141081 TGTACATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.62
Consensus pattern (19 bp):
TTATTATTATTACTGTTAC
Found at i:19141093 original size:3 final size:3
Alignment explanation
Indices: 19140854--19141074 Score: 106
Period size: 3 Copynumber: 72.7 Consensus size: 3
19140844 TGAATTTCTA
* * *
19140854 TAT TAT TAT TAT TAT TAT TAT TGT TACT TAT TAT TAT TAC TGT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
* * * *
19140900 GTACA TAT TAT T-T ATAC TA- TACT TAA TAT TAT TAT TAT CAT TAT TAT
1 -TA-T TAT TAT TAT -TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
* * *
19140947 TAT TAT TA- TATT TAC TAT TAT TATT TAT AAA TAT TAGT GTA- TAT T-T
1 TAT TAT TAT TA-T TAT TAT TAT TA-T TAT TAT TAT TA-T -TAT TAT TAT
* *
19140993 TAT T-T TAA TAT CAT T-T TAT TAT GT-T TACT T-T T-T TGAAT T-T CTA-
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA-T TAT TAT T--AT TAT -TAT
*
19141036 TAT TAT TAT TAT TAT TAT TAT TGT TACT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TA
19141075 CTGTTATGTA
Statistics
Matches: 167, Mismatches: 25, Indels: 52
0.68 0.10 0.21
Matches are distributed among these distances:
2 21 0.13
3 121 0.72
4 21 0.13
5 4 0.02
ACGTcount: A:0.31, C:0.05, G:0.04, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:19153741 original size:68 final size:70
Alignment explanation
Indices: 19153662--19154371 Score: 398
Period size: 68 Copynumber: 9.7 Consensus size: 70
19153652 GTATTTGATA
*
19153662 TTTTATTTCTA-TTTCAAAATTC-ACTCATATTACGAGAATGAGTTGAGCCTCAAGACACGTTAG
1 TTTTATTTCTATTTTCAAAATTCAACTCATATTGCGAGAATGAGTTGAGCCTCAAGACACGTTAG
19153725 GTAAT
66 GTAAT
19153730 TTTTATTTCTATTTTC-AAATTCAACTCATATTGCGA-AATGAGTTGAGCCTCAAGACACGTTGA
1 TTTTATTTCTATTTTCAAAATTCAACTCATATTGCGAGAATGAGTTGAGCCTCAAGACACGTT-A
19153793 GGTAA-
65 GGTAAT
* * *
19153798 TTTTATTTCTATTTTCAAAATTCAACTCAGATTGCGAGAAATGAGTTGAG-CTCAA-ACATGCTG
1 TTTTATTTCTATTTTCAAAATTCAACTCATATTGCGAG-AATGAGTTGAGCCTCAAGACACG-TT
19153861 AGGT-AT
64 AGGTAAT
* * * * ** *
19153867 TTTCAATTCTATTTTTCAAAAAAAAAATCGACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGAC
1 TTTTATTTCTA-TTTTC-----AAAATTCAACTCATATTGCGAGA-ATGAGTTGAGCCTCAAGAC
*
19153932 ACGCTGAGGT-AT
59 ACG-TTAGGTAAT
** * *
19153944 TTCAATTTCTATTTTCAAAATTCAACTTATATTGCGAGTAATGAGTTGAACCTCAAGACACGTTG
1 TTTTATTTCTATTTTCAAAATTCAACTCATATTGCGAG-AATGAGTTGAGCCTCAAGACACGTT-
19154009 AGGT-A-
64 AGGTAAT
* * * * * * * *
19154014 TTTCAATTATGTTTT-AAAA-TCAACTCATATTGCGAGAGGTGAGTTAAG-CTC-GGTTCACATG
1 TTTTATTTCTATTTTCAAAATTCAACTCATATTGCGAGA-ATGAGTTGAGCCTCAAG---ACACG
*
19154075 CT-GAGT-A-
62 TTAG-GTAAT
* * * * ** *
19154082 TTTCAATTCTATCTTTCAAAAAAAAATT-AACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGGC
1 TTTTATTTCTAT-TTTC-----AAAATTCAACTCATATTGCGAGA-ATGAGTTGAGCCTCAAGAC
19154146 ACGTTGAGGTATTGGCAAT
59 ACGTT-AGG---T---AAT
* ** *
19154165 TTTTGTTTCTTAATTTATGTTTCAAAATTCAACTCATATTGTGAGAAATGAGTTGAGCCTCAAGA
1 TTTTATTTC-T-A--T-T-TTCAAA-ATTCAACTCATATTGCGAG-AATGAGTTGAGCCTCAAGA
19154230 CACGTTGAGGTAAT
58 CACGTT-AGGTAAT
** * * * * * *
19154244 TTCAATTTTTGTTTTCAAAATTCAACTCAGATAGCGAGAAATGAGTTGAGCCTCAAGACATGCTG
1 TTTTATTTCTATTTTCAAAATTCAACTCATATTGCGAG-AATGAGTTGAGCCTCAAGACACG-TT
19154309 AGGT-AT
64 AGGTAAT
* * * * *
19154315 TTTCATTTCTGTTTTTCAAAAAAAATCGACTCATATTGCGAGAGGTGAGTTAGAGCC
1 TTTTATTTCT-ATTTTC---AAAATTCAACTCATATTGCGAGA-ATGAGTT-GAGCC
19154372 ATCATNNNNN
Statistics
Matches: 507, Mismatches: 76, Indels: 110
0.73 0.11 0.16
Matches are distributed among these distances:
66 1 0.00
67 5 0.01
68 95 0.19
69 70 0.14
70 22 0.04
71 62 0.12
72 49 0.10
73 5 0.01
74 7 0.01
75 82 0.16
76 19 0.04
77 23 0.05
78 2 0.00
79 8 0.02
82 2 0.00
83 8 0.02
84 4 0.01
85 38 0.07
86 1 0.00
87 2 0.00
88 2 0.00
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (70 bp):
TTTTATTTCTATTTTCAAAATTCAACTCATATTGCGAGAATGAGTTGAGCCTCAAGACACGTTAG
GTAAT
Found at i:19153799 original size:69 final size:70
Alignment explanation
Indices: 19153662--19154050 Score: 429
Period size: 68 Copynumber: 5.6 Consensus size: 70
19153652 GTATTTGATA
*
19153662 TTTTATTTCTA-TTTCAAAATTC-ACTCATATTACGAGAATGAGTTGAGCCTCAAGACACGTT-A
1 TTTTATTTCTATTTTCAAAATTCAACTCATATTGCGAGAATGAGTTGAGCCTCAAGACACGTTGA
19153724 GGTAAT
66 GGT-AT
19153730 TTTTATTTCTATTTTC-AAATTCAACTCATATTGCGA-AATGAGTTGAGCCTCAAGACACGTTGA
1 TTTTATTTCTATTTTCAAAATTCAACTCATATTGCGAGAATGAGTTGAGCCTCAAGACACGTTGA
*
19153793 GGTAA
66 GGTAT
* * *
19153798 TTTTATTTCTATTTTCAAAATTCAACTCAGATTGCGAGAAATGAGTTGAG-CTCAA-ACATGCTG
1 TTTTATTTCTATTTTCAAAATTCAACTCATATTGCGAG-AATGAGTTGAGCCTCAAGACACGTTG
19153861 AGGTAT
65 AGGTAT
* * * * ** *
19153867 TTTCAATTCTATTTTTCAAAAAAAAAATCGACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGAC
1 TTTTATTTCTA-TTTTC-----AAAATTCAACTCATATTGCGAGA-ATGAGTTGAGCCTCAAGAC
*
19153932 ACGCTGAGGTAT
59 ACGTTGAGGTAT
** * *
19153944 TTCAATTTCTATTTTCAAAATTCAACTTATATTGCGAGTAATGAGTTGAACCTCAAGACACGTTG
1 TTTTATTTCTATTTTCAAAATTCAACTCATATTGCGAG-AATGAGTTGAGCCTCAAGACACGTTG
19154009 AGGTA-
65 AGGTAT
* * * *
19154014 TTTCAATTATGTTTT-AAAA-TCAACTCATATTGCGAGA
1 TTTTATTTCTATTTTCAAAATTCAACTCATATTGCGAGA
19154051 GGTGAGTTAA
Statistics
Matches: 273, Mismatches: 32, Indels: 33
0.81 0.09 0.10
Matches are distributed among these distances:
67 1 0.00
68 75 0.27
69 63 0.23
70 20 0.07
71 55 0.20
72 1 0.00
74 1 0.00
75 27 0.10
76 9 0.03
77 21 0.08
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (70 bp):
TTTTATTTCTATTTTCAAAATTCAACTCATATTGCGAGAATGAGTTGAGCCTCAAGACACGTTGA
GGTAT
Found at i:19154105 original size:214 final size:213
Alignment explanation
Indices: 19153684--19154371 Score: 773
Period size: 214 Copynumber: 3.1 Consensus size: 213
19153674 TTCAAAATTC
* * * * **
19153684 ACTCATATTACGAGA-ATGAGTTGAGCCTCAAGACACGTTAGGTAATTTTTATTTCTATTTTC-A
1 ACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGTGAGGT-ATTTCAATTTCTATTTTCAA
* * * *
19153747 AATTCAACTCATATTGCGA-AATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTTATTTCTATT
65 AATTCAACTCATATTGCGAGAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTATGTT
*
19153811 TTCAAAATTCAACTCAGATTGCGAGAAATGAGTTGAGCTCAAACATGCTGAGGTATTTTCAATTC
130 TTCAAAATTCAACTCAGATTGCGAGAAATGAGTTGAGCTC-GACATGCTGAGGTATTTTCAATTC
19153876 TATTTTTCAAAAAAAAAATCG
194 TATTTTTC-AAAAAAAAATCG
*
19153897 ACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGACACGCTGAGGTATTTCAATTTCTATTTTCAA
1 ACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG-TGAGGTATTTCAATTTCTATTTTCAA
* *
19153962 AATTCAACTTATATTGCGAGTAATGAGTTGAACCTCAAGACACGTTGAGGT-ATTTCAATTATGT
65 AATTCAACTCATATTGCGAG-AATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTATGT
* ** *
19154026 TTT-AAAA-TCAACTCATATTGCGAGAGGTGAGTTAAGCTCGGTTCACATGCTGA-GTA-TTTCA
129 TTTCAAAATTCAACTCAGATTGCGAGAAATGAGTTGAGCTC-G---ACATGCTGAGGTATTTTCA
* **
19154087 ATTCTATCTTTCAAAAAAAAATTA
190 ATTCTATTTTTCAAAAAAAAATCG
* * * *
19154111 ACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGGCACGTTGAGGTATTGGCAATTTTTGTTTCTT
1 ACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG-TGAGGTATT-TCAA------TTTC--
*
19154176 AATTTATGTTTCAAAATTCAACTCATATTGTGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGT
56 ----TAT-TTTCAAAATTCAACTCATATTGCGAG-AATGAGTTGAGCCTCAAGACACGTTGAGGT
* *
19154241 AATTTCAATTTTTGTTTTCAAAATTCAACTCAGATAGCGAGAAATGAGTTGAGCCTCAAGACATG
115 AATTTCAA-TTATGTTTTCAAAATTCAACTCAGATTGCGAGAAATGAGTTGAG-CTC--GACATG
* *
19154306 CTGAGGTATTTTCATTTCTGTTTTTC-AAAAAAAATCG
176 CTGAGGTATTTTCAATTCTATTTTTCAAAAAAAAATCG
19154343 ACTCATATTGCGAGAGGTGAGTTAGAGCC
1 ACTCATATTGCGAGAGGTGAGTT-GAGCC
19154372 ATCATNNNNN
Statistics
Matches: 399, Mismatches: 45, Indels: 42
0.82 0.09 0.09
Matches are distributed among these distances:
213 14 0.04
214 116 0.29
215 47 0.12
216 15 0.04
217 38 0.10
221 4 0.01
227 3 0.01
228 53 0.13
229 7 0.02
230 8 0.02
231 13 0.03
232 58 0.15
233 22 0.06
234 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34
Consensus pattern (213 bp):
ACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGTGAGGTATTTCAATTTCTATTTTCAAA
ATTCAACTCATATTGCGAGAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTATGTTT
TCAAAATTCAACTCAGATTGCGAGAAATGAGTTGAGCTCGACATGCTGAGGTATTTTCAATTCTA
TTTTTCAAAAAAAAATCG
Found at i:19154292 original size:72 final size:72
Alignment explanation
Indices: 19154176--19154335 Score: 225
Period size: 72 Copynumber: 2.2 Consensus size: 72
19154166 TTTGTTTCTT
* * * *
19154176 AATTTATG-TTTCAAAATTCAACTCATATTGTGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTATGTTTTCAAAATTCAACTCAGATAGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGG
19154240 TAATTTC
66 TAATTTC
* *
19154247 AATTTTTGTTTTCAAAATTCAACTCAGATAGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGG
1 AATTTATGTTTTCAAAATTCAACTCAGATAGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGG
*
19154312 TATTTTC
66 TAATTTC
*
19154319 -ATTTCTGTTTTTCAAAA
1 AATTTATG-TTTTCAAAA
19154336 AAAATCGACT
Statistics
Matches: 79, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
71 13 0.16
72 66 0.84
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (72 bp):
AATTTATGTTTTCAAAATTCAACTCAGATAGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGG
TAATTTC
Found at i:19170953 original size:21 final size:21
Alignment explanation
Indices: 19170927--19170968 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
19170917 AAAATTAGCG
*
19170927 CTTCTTGTTCTGCTCTTCTTA
1 CTTCTTGTTCCGCTCTTCTTA
19170948 CTTCTTGTTCCGCTCTTCTTA
1 CTTCTTGTTCCGCTCTTCTTA
19170969 GGTTTGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.05, C:0.31, G:0.10, T:0.55
Consensus pattern (21 bp):
CTTCTTGTTCCGCTCTTCTTA
Found at i:19174956 original size:39 final size:38
Alignment explanation
Indices: 19174833--19174957 Score: 119
Period size: 39 Copynumber: 3.3 Consensus size: 38
19174823 TCTATAAAGA
*
19174833 TGATT-TA-GAGTATTGTGGTATATGCTTGAATGTTATG
1 TGATTATATGAGTA-TGTGATATATGCTTGAATGTTATG
* * * * *
19174870 TGATTTTACGAGTACTATGACATATGCTTAAATGTTATG
1 TGATTATATGAGTA-TGTGATATATGCTTGAATGTTATG
* * *
19174909 AGATTATATGAGTATGGTGATATATGCTTGTATGTTAGG
1 TGATTATATGAGTAT-GTGATATATGCTTGAATGTTATG
*
19174948 TGACTATATG
1 TGATTATATG
19174958 TGAAATATGC
Statistics
Matches: 70, Mismatches: 15, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
37 5 0.07
38 3 0.04
39 62 0.89
ACGTcount: A:0.28, C:0.06, G:0.24, T:0.42
Consensus pattern (38 bp):
TGATTATATGAGTATGTGATATATGCTTGAATGTTATG
Found at i:19179798 original size:69 final size:68
Alignment explanation
Indices: 19179605--19180083 Score: 257
Period size: 69 Copynumber: 6.9 Consensus size: 68
19179595 TAGTGAAAAT
* * * * * * * * *
19179605 TAGGAGCTTTGCTCTCGCTAACTATATTGGAAGCTGTGGCTTTTCAC-CTGCAAGCTTTAATATA
1 TAGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTCGCTATG--AGCCTTAATATG
* **
19179669 ATAGT
64 ACAAC
* * * * * * * **
19179674 TTGGAGCTTTCCTCTCGTTAATTGTGTTGGAAGTTGCGACTCTTCGCCTGCGAGCCTTAATATGA
1 TAGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTCG-CTATGAGCCTTAATATGA
19179739 CAAC
65 CAAC
* *
19179743 TAGGAGCTTTGCTCTTGCTAACTGTGTTGGAGGCTGCGGCTCTTCGCTAATGAGCCTTAATATAA
1 TAGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTCGCT-ATGAGCCTTAATATGA
*
19179808 TAGA-
65 CA-AC
* * ** ** *** **
19179812 TGGGAGCTTTGTTCTCAATAACTGCATTGGAGGCTGCAATTCTTTAC-CTACAAGCCTTAATATG
1 TAGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGCTGCGGCTC-TT-CGCTATGAGCCTTAATATG
* *
19179876 ATAGC
64 ACAAC
* *** * ** * *
19179881 TGGGAGCTTTGCTCTCGCTAACTACATTGGAAGCTGTAGCTCGTCGCCTACGAGCCTTAATATGA
1 TAGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTCG-CTATGAGCCTTAATATGA
19179946 CAA-
65 CAAC
* * * ** * * * *
19179949 TTGAGAGCTTTACTCTTGCTAACTGTGTCAGAGGTTGTGGCTCTTC-TTTTGCTAGCCTTAATAT
1 TAG-GAGCTTTGCTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTCGCTATG--AGCCTTAATAT
*
19180013 GACAGC
63 GACAAC
* * ** * *
19180019 TAGGAGCTTTGTTCTCGCTGACTGTGTTGGAGGCTATGGCTCTTCTCCTGTGAGCCTTAATATGA
1 TAGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTC-GCTATGAGCCTTAATATGA
19180084 TATGAATTTT
Statistics
Matches: 312, Mismatches: 83, Indels: 30
0.73 0.20 0.07
Matches are distributed among these distances:
67 3 0.01
68 5 0.02
69 291 0.93
70 8 0.03
71 5 0.02
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.34
Consensus pattern (68 bp):
TAGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGCTGCGGCTCTTCGCTATGAGCCTTAATATGAC
AAC
Found at i:19182834 original size:23 final size:23
Alignment explanation
Indices: 19182808--19182855 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
19182798 GCACATGCTC
19182808 ACCTATGGATGTACTTTTCACTA
1 ACCTATGGATGTACTTTTCACTA
19182831 ACCTATGGATGTACTTTTCACTA
1 ACCTATGGATGTACTTTTCACTA
19182854 AC
1 AC
19182856 ATGTCATCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (23 bp):
ACCTATGGATGTACTTTTCACTA
Found at i:19188427 original size:21 final size:21
Alignment explanation
Indices: 19188403--19188442 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
19188393 CAAAATGACG
19188403 TAGTTTT-ACCTTTTAACTTAA
1 TAGTTTTGA-CTTTTAACTTAA
19188424 TAGTTTTGACTTTTAACTT
1 TAGTTTTGACTTTTAACTT
19188443 TAAAAAAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.25, C:0.12, G:0.07, T:0.55
Consensus pattern (21 bp):
TAGTTTTGACTTTTAACTTAA
Found at i:19198784 original size:22 final size:22
Alignment explanation
Indices: 19198757--19198799 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
19198747 ACTAGTTGTT
*
19198757 TAATTTTGAATAATTTTTTTAA
1 TAATTTTAAATAATTTTTTTAA
*
19198779 TAATTTTAAATATTTTTTTTA
1 TAATTTTAAATAATTTTTTTA
19198800 TTGTTTAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (22 bp):
TAATTTTAAATAATTTTTTTAA
Found at i:19199050 original size:33 final size:34
Alignment explanation
Indices: 19199013--19199103 Score: 98
Period size: 33 Copynumber: 2.7 Consensus size: 34
19199003 AATTTTGAAA
*
19199013 TTTTTATATTTTAAAAAACTTA-TATTTTAT-ATCT
1 TTTTTATATTTTAAAAAA-TTATTATTTT-TCATAT
*
19199047 TTTTTA-ATTTTAAAGAATTATTATTTTTCATAT
1 TTTTTATATTTTAAAAAATTATTATTTTTCATAT
* *
19199080 TTTTTAATTTTTTTAAAAATTATT
1 TTTTT-ATATTTTAAAAAATTATT
19199104 TAAAATATGA
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
32 4 0.08
33 24 0.50
34 7 0.15
35 13 0.27
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (34 bp):
TTTTTATATTTTAAAAAATTATTATTTTTCATAT
Found at i:19211377 original size:87 final size:86
Alignment explanation
Indices: 19211192--19211572 Score: 563
Period size: 87 Copynumber: 4.4 Consensus size: 86
19211182 GTTTATTGGA
* * * *
19211192 AAAAGACGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGG-GAAAGCGCCGTTAAAGGTCAA
1 AAAAG-CGCCGCTAAACGTCAAGGCTTTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAACGTCAA
*
19211256 GGCTTTTAGCGGCGTTTGTGGG
65 GGCTTTTAGCGGCGTTTGTGGT
* *
19211278 GAAAGCGCCGCTAAACGTCAAGGCTTTTAACGGCGTTTGTGGTAAAAGCGCCGCTAAACGTCAAG
1 AAAAGCGCCGCTAAACGTCAAGGCTTTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAACGTCAAG
19211343 GCTTTTTAGCGGCGTTTGTGGT
66 GC-TTTTAGCGGCGTTTGTGGT
* *
19211365 AAAAGCGTCGCTAAA-GATCAAGGCTTTTAGCAGCGTTTGTGCGT-AAAGCGCCGCTAAACGTCA
1 AAAAGCGCCGCTAAACG-TCAAGGCTTTTAGCGGCGTTTGTG-GTAAAAGCGCCGCTAAACGTCA
*
19211428 AGGCTTTTAACGGCGTTTGTGGT
64 AGGCTTTTAGCGGCGTTTGTGGT
* *
19211451 AAAAGCGCCGCTAAACGTCAAGGCTTTTTAACGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCAA
1 AAAAGCGCCGCTAAACGTCAAGGC-TTTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAACGTCAA
19211516 GGCTTTTAGCGGCGTTTGTGCGT
65 GGCTTTTAGCGGCGTTTGTG-GT
*
19211539 -AAAGCACCGCTAAACGTCAAGGCTTTTAGCGGCG
1 AAAAGCGCCGCTAAACGTCAAGGCTTTTAGCGGCG
19211573 CTTTTTTTAC
Statistics
Matches: 268, Mismatches: 19, Indels: 16
0.88 0.06 0.05
Matches are distributed among these distances:
85 35 0.13
86 77 0.29
87 152 0.57
88 4 0.01
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.25
Consensus pattern (86 bp):
AAAAGCGCCGCTAAACGTCAAGGCTTTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAACGTCAAG
GCTTTTAGCGGCGTTTGTGGT
Found at i:19211595 original size:43 final size:43
Alignment explanation
Indices: 19211192--19211572 Score: 563
Period size: 43 Copynumber: 8.8 Consensus size: 43
19211182 GTTTATTGGA
*
19211192 AAAAGACGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGG-
1 AAAAG-CGCCGCTAAACGTCAAGGCTTTTAGCGGCGTTTGTGGT
* * * *
19211235 GAAAGCGCCGTTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
1 AAAAGCGCCGCTAAACGTCAAGGCTTTTAGCGGCGTTTGTGGT
* *
19211278 GAAAGCGCCGCTAAACGTCAAGGCTTTTAACGGCGTTTGTGGT
1 AAAAGCGCCGCTAAACGTCAAGGCTTTTAGCGGCGTTTGTGGT
19211321 AAAAGCGCCGCTAAACGTCAAGGCTTTTTAGCGGCGTTTGTGGT
1 AAAAGCGCCGCTAAACGTCAAGGC-TTTTAGCGGCGTTTGTGGT
* *
19211365 AAAAGCGTCGCTAAA-GATCAAGGCTTTTAGCAGCGTTTGTGCGT
1 AAAAGCGCCGCTAAACG-TCAAGGCTTTTAGCGGCGTTTGTG-GT
*
19211409 -AAAGCGCCGCTAAACGTCAAGGCTTTTAACGGCGTTTGTGGT
1 AAAAGCGCCGCTAAACGTCAAGGCTTTTAGCGGCGTTTGTGGT
*
19211451 AAAAGCGCCGCTAAACGTCAAGGCTTTTTAACGGCGTTTGTGGT
1 AAAAGCGCCGCTAAACGTCAAGGC-TTTTAGCGGCGTTTGTGGT
*
19211495 AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGCGT
1 AAAAGCGCCGCTAAACGTCAAGGCTTTTAGCGGCGTTTGTG-GT
*
19211539 -AAAGCACCGCTAAACGTCAAGGCTTTTAGCGGCG
1 AAAAGCGCCGCTAAACGTCAAGGCTTTTAGCGGCG
19211573 CTTTTTTTAC
Statistics
Matches: 313, Mismatches: 17, Indels: 16
0.90 0.05 0.05
Matches are distributed among these distances:
42 38 0.12
43 189 0.60
44 86 0.27
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.25
Consensus pattern (43 bp):
AAAAGCGCCGCTAAACGTCAAGGCTTTTAGCGGCGTTTGTGGT
Found at i:19211595 original size:130 final size:130
Alignment explanation
Indices: 19211192--19211572 Score: 640
Period size: 130 Copynumber: 2.9 Consensus size: 130
19211182 GTTTATTGGA
* * *
19211192 AAAAGACGCCGCTAAAGGTCAAGGC-TTTTAGCGGCGTTTGTGG-GAAAGCGCCGTTAAAGGTCA
1 AAAAG-CGCCGCTAAACGTCAAGGCTTTTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCA
* *
19211255 AGGCTTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAACGTCAAGGCTTTTAACGGCGTTTGTGG
65 AGGCTTTTAGCGGCGTTTGTGCGTAAAGCGCCGCTAAACGTCAAGGCTTTTAACGGCGTTTGTGG
19211320 T
130 T
* *
19211321 AAAAGCGCCGCTAAACGTCAAGGCTTTTTAGCGGCGTTTGTGGTAAAAGCGTCGCTAAAGATCAA
1 AAAAGCGCCGCTAAACGTCAAGGCTTTTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCAA
*
19211386 GGCTTTTAGCAGCGTTTGTGCGTAAAGCGCCGCTAAACGTCAAGGCTTTTAACGGCGTTTGTGGT
66 GGCTTTTAGCGGCGTTTGTGCGTAAAGCGCCGCTAAACGTCAAGGCTTTTAACGGCGTTTGTGGT
*
19211451 AAAAGCGCCGCTAAACGTCAAGGCTTTTTAACGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCAA
1 AAAAGCGCCGCTAAACGTCAAGGCTTTTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCAA
* *
19211516 GGCTTTTAGCGGCGTTTGTGCGTAAAGCACCGCTAAACGTCAAGGCTTTTAGCGGCG
66 GGCTTTTAGCGGCGTTTGTGCGTAAAGCGCCGCTAAACGTCAAGGCTTTTAACGGCG
19211573 CTTTTTTTAC
Statistics
Matches: 236, Mismatches: 14, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
128 18 0.08
129 23 0.10
130 195 0.83
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.25
Consensus pattern (130 bp):
AAAAGCGCCGCTAAACGTCAAGGCTTTTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCAA
GGCTTTTAGCGGCGTTTGTGCGTAAAGCGCCGCTAAACGTCAAGGCTTTTAACGGCGTTTGTGGT
Found at i:19211682 original size:31 final size:31
Alignment explanation
Indices: 19211647--19211727 Score: 81
Period size: 31 Copynumber: 2.5 Consensus size: 31
19211637 CTTCCTGCAT
* *
19211647 TAAAATCCAACCAAATACAACAAATATAATA
1 TAAAATCCAACCAAAAACAACAAATATAACA
* * * *
19211678 TAAAATGCAGCCAAAAACAGCAAATTTAACA
1 TAAAATCCAACCAAAAACAACAAATATAACA
*
19211709 TAAAAAATACAACCAAAAA
1 T--AAAATCCAACCAAAAA
19211728 TATTAATTCT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
31 26 0.65
33 14 0.35
ACGTcount: A:0.62, C:0.19, G:0.04, T:0.16
Consensus pattern (31 bp):
TAAAATCCAACCAAAAACAACAAATATAACA
Found at i:19211997 original size:21 final size:21
Alignment explanation
Indices: 19211973--19212018 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
19211963 GCTCGTGCCT
*
19211973 CTGCCTCTCTCGCTGCAGCCG
1 CTGCCTCCCTCGCTGCAGCCG
* * *
19211994 CTGCCTCCCTCTCTGCTGCCT
1 CTGCCTCCCTCGCTGCAGCCG
19212015 CTGC
1 CTGC
19212019 TCTAAGTTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.02, C:0.50, G:0.20, T:0.28
Consensus pattern (21 bp):
CTGCCTCCCTCGCTGCAGCCG
Found at i:19217637 original size:9 final size:9
Alignment explanation
Indices: 19217623--19217750 Score: 121
Period size: 9 Copynumber: 13.6 Consensus size: 9
19217613 ATGTATTAGT
19217623 TAAGTTATG
1 TAAGTTATG
19217632 TAAGTTGTTATG
1 TAA---GTTATG
*
19217644 TACGTTATG
1 TAAGTTATG
*
19217653 TGAGTTATG
1 TAAGTTATG
*
19217662 TAAATTATG
1 TAAGTTATG
19217671 TAAGTTATG
1 TAAGTTATG
*
19217680 TGAGTTATG
1 TAAGTTATG
19217689 TAAGTTGCTATG
1 TAAG-T--TATG
*
19217701 TAAATTATG
1 TAAGTTATG
*
19217710 TAAGTTATA
1 TAAGTTATG
*
19217719 TGAGTTATG
1 TAAGTTATG
19217728 TAAGTTATG
1 TAAGTTATG
* *
19217737 TAATTTATT
1 TAAGTTATG
19217746 TAAGT
1 TAAGT
19217751 AATGATCAAT
Statistics
Matches: 96, Mismatches: 17, Indels: 12
0.77 0.14 0.10
Matches are distributed among these distances:
9 79 0.82
10 1 0.01
11 1 0.01
12 15 0.16
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.46
Consensus pattern (9 bp):
TAAGTTATG
Found at i:19217750 original size:57 final size:57
Alignment explanation
Indices: 19217623--19217750 Score: 166
Period size: 57 Copynumber: 2.2 Consensus size: 57
19217613 ATGTATTAGT
* ** * *
19217623 TAAGTTATGTAAGTTGTTATGTACGTTATGTGAGTTATGTAAATTATGTAAGTTATG
1 TAAGTTATGTAAGTTGCTATGTAAATTATGTAAGTTATATAAATTATGTAAGTTATG
* * *
19217680 TGAGTTATGTAAGTTGCTATGTAAATTATGTAAGTTATATGAGTTATGTAAGTTATG
1 TAAGTTATGTAAGTTGCTATGTAAATTATGTAAGTTATATAAATTATGTAAGTTATG
* *
19217737 TAATTTATTTAAGT
1 TAAGTTATGTAAGT
19217751 AATGATCAAT
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.46
Consensus pattern (57 bp):
TAAGTTATGTAAGTTGCTATGTAAATTATGTAAGTTATATAAATTATGTAAGTTATG
Found at i:19219181 original size:189 final size:190
Alignment explanation
Indices: 19218913--19219338 Score: 748
Period size: 189 Copynumber: 2.2 Consensus size: 190
19218903 GATTTTATTG
*
19218913 ATATTATATTAATAAATAAATTTATT-AAAATCGTGATAGAAATATTTGTATATTAGATGGGACA
1 ATATTATATTAATAAATAAATTTATTAAAAATCGTGATAGAAATATTTGTATATTAGATGAGACA
* * *
19218977 TATTATATTAATAAATAAATTTATTAAAAATCATGATAGAAATATTTGTATATTAGATGGGACAT
66 TATTATATCAATAAATAAATTTATTAAAAATCATGATAGAAATATTTATATATTAGATGAGACAT
*
19219042 ATTATATTAATAAATAAATTTATTAAAAATCGTGATAGAAATATTTGTATATTAGAT-AC
131 ATTATATCAATAAATAAATTTATTAAAAATCGTGATAGAAATATTTGTATATTAGATGAC
19219101 ATATTATATTAATAAATAAATTTATTAAAAATCGTGATAGAAATATTTGTATATTAGATGAGACA
1 ATATTATATTAATAAATAAATTTATTAAAAATCGTGATAGAAATATTTGTATATTAGATGAGACA
*
19219166 TATTATATCAATAAATAAATTTATTAAAAATCGTGATAGAAATATTTATATATTAGATGAGACAT
66 TATTATATCAATAAATAAATTTATTAAAAATCATGATAGAAATATTTATATATTAGATGAGACAT
19219231 ATTATATCAATAAATAAATTTATTAAAAATCGTGATAGAAATATTTGTATATTAGATGGGAC
131 ATTATATCAATAAATAAATTTATTAAAAATCGTGATAGAAATATTTGTATATTAGAT--GAC
* *
19219293 ATATTATATCAATAAATAAATTTATTAAAAATTGTGATAGAAATAT
1 ATATTATATTAATAAATAAATTTATTAAAAATCGTGATAGAAATAT
19219339 AGAAATATTA
Statistics
Matches: 226, Mismatches: 8, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
188 26 0.12
189 154 0.68
192 46 0.20
ACGTcount: A:0.47, C:0.04, G:0.10, T:0.39
Consensus pattern (190 bp):
ATATTATATTAATAAATAAATTTATTAAAAATCGTGATAGAAATATTTGTATATTAGATGAGACA
TATTATATCAATAAATAAATTTATTAAAAATCATGATAGAAATATTTATATATTAGATGAGACAT
ATTATATCAATAAATAAATTTATTAAAAATCGTGATAGAAATATTTGTATATTAGATGAC
Found at i:19219348 original size:64 final size:64
Alignment explanation
Indices: 19218913--19219338 Score: 752
Period size: 64 Copynumber: 6.7 Consensus size: 64
19218903 GATTTTATTG
19218913 ATATTATATTAATAAATAAATTTATT-AAAATCGTGATAGAAATATTTGTATATTAGATGGGAC
1 ATATTATATTAATAAATAAATTTATTAAAAATCGTGATAGAAATATTTGTATATTAGATGGGAC
*
19218976 ATATTATATTAATAAATAAATTTATTAAAAATCATGATAGAAATATTTGTATATTAGATGGGAC
1 ATATTATATTAATAAATAAATTTATTAAAAATCGTGATAGAAATATTTGTATATTAGATGGGAC
19219040 ATATTATATTAATAAATAAATTTATTAAAAATCGTGATAGAAATATTTGTATATTAGAT---AC
1 ATATTATATTAATAAATAAATTTATTAAAAATCGTGATAGAAATATTTGTATATTAGATGGGAC
*
19219101 ATATTATATTAATAAATAAATTTATTAAAAATCGTGATAGAAATATTTGTATATTAGATGAGAC
1 ATATTATATTAATAAATAAATTTATTAAAAATCGTGATAGAAATATTTGTATATTAGATGGGAC
* * *
19219165 ATATTATATCAATAAATAAATTTATTAAAAATCGTGATAGAAATATTTATATATTAGATGAGAC
1 ATATTATATTAATAAATAAATTTATTAAAAATCGTGATAGAAATATTTGTATATTAGATGGGAC
*
19219229 ATATTATATCAATAAATAAATTTATTAAAAATCGTGATAGAAATATTTGTATATTAGATGGGAC
1 ATATTATATTAATAAATAAATTTATTAAAAATCGTGATAGAAATATTTGTATATTAGATGGGAC
* *
19219293 ATATTATATCAATAAATAAATTTATTAAAAATTGTGATAGAAATAT
1 ATATTATATTAATAAATAAATTTATTAAAAATCGTGATAGAAATAT
19219339 AGAAATATTA
Statistics
Matches: 352, Mismatches: 7, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
61 61 0.17
63 26 0.07
64 265 0.75
ACGTcount: A:0.47, C:0.04, G:0.10, T:0.39
Consensus pattern (64 bp):
ATATTATATTAATAAATAAATTTATTAAAAATCGTGATAGAAATATTTGTATATTAGATGGGAC
Found at i:19222272 original size:16 final size:17
Alignment explanation
Indices: 19222251--19222286 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
19222241 AAATTATTTT
19222251 ATATAAA-TAAAAAACA
1 ATATAAATTAAAAAACA
19222267 ATATAAATTAAAAAACA
1 ATATAAATTAAAAAACA
19222284 ATA
1 ATA
19222287 AGTTATATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (17 bp):
ATATAAATTAAAAAACA
Found at i:19222696 original size:29 final size:28
Alignment explanation
Indices: 19222657--19222730 Score: 69
Period size: 29 Copynumber: 2.6 Consensus size: 28
19222647 AATCATGTCC
* *
19222657 CATTAACCCCTAAACCCTTGAACCTTAAA
1 CATTAAACCCTAAACCC-TAAACCTTAAA
* *
19222686 CCA-TAAACCCTTAATCCCTAAACTTTAAA
1 -CATTAAACCC-TAAACCCTAAACCTTAAA
*
19222715 CATTAATCCCTAAACC
1 CATTAAACCCTAAACC
19222731 ATATCCCCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
28 7 0.19
29 21 0.58
30 8 0.22
ACGTcount: A:0.39, C:0.34, G:0.01, T:0.26
Consensus pattern (28 bp):
CATTAAACCCTAAACCCTAAACCTTAAA
Found at i:19222707 original size:22 final size:22
Alignment explanation
Indices: 19222667--19222750 Score: 82
Period size: 22 Copynumber: 3.9 Consensus size: 22
19222657 CATTAACCCC
*
19222667 TAAACCCTTGAA-CCTTAAACCA
1 TAAACCCTT-AATCCCTAAACCA
**
19222689 TAAACCCTTAATCCCTAAACTT
1 TAAACCCTTAATCCCTAAACCA
*
19222711 TAAA-CATTAATCCCTAAACCA
1 TAAACCCTTAATCCCTAAACCA
** *
19222732 TATCCCCTTAACCCCTAAA
1 TAAACCCTTAATCCCTAAA
19222751 GCCTCAACCT
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
21 18 0.36
22 32 0.64
ACGTcount: A:0.39, C:0.33, G:0.01, T:0.26
Consensus pattern (22 bp):
TAAACCCTTAATCCCTAAACCA
Found at i:19222765 original size:80 final size:79
Alignment explanation
Indices: 19222550--19222761 Score: 262
Period size: 80 Copynumber: 2.6 Consensus size: 79
19222540 TAACTTTTTT
* * * *
19222550 AACACTAATTACCCTTAACCCATGTCCCCTTAATCCCTAAACCCCTCAACCCTAAACCATTAACC
1 AACACTAA--ACCC-TAAACCATGTCCCCTTAACCCCTAAA-CCCTCAACCTTAAACCATAAACC
19222615 ATTAATCCCTAAAATTTA
62 ATTAATCCCTAAAATTTA
* * * *
19222633 AACACTAAACCCTAAATCATGTCCCATTAACCCCTAAACCCTTGAACCTTAAACCATAAACCCTT
1 AACACTAAACCCTAAACCATGTCCCCTTAACCCCTAAACCC-TCAACCTTAAACCATAAACCATT
*
19222698 AATCCCTAAACTTTA
65 AATCCCTAAAATTTA
* * * *
19222713 AACATTAATCCCTAAACCATATCCCCTTAACCCCTAAAGCCTCAACCTT
1 AACACTAAACCCTAAACCATGTCCCCTTAACCCCTAAACCCTCAACCTT
19222762 TAAATGTTAA
Statistics
Matches: 112, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
79 10 0.09
80 90 0.80
81 4 0.04
83 8 0.07
ACGTcount: A:0.37, C:0.36, G:0.02, T:0.25
Consensus pattern (79 bp):
AACACTAAACCCTAAACCATGTCCCCTTAACCCCTAAACCCTCAACCTTAAACCATAAACCATTA
ATCCCTAAAATTTA
Found at i:19223253 original size:14 final size:14
Alignment explanation
Indices: 19223234--19223287 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
19223224 GTGTCATTAA
19223234 TTTAGGGTTTATAG
1 TTTAGGGTTTATAG
*
19223248 TTTAGGGTTTCA-AA
1 TTTAGGGTTT-ATAG
* *
19223262 TTTAAGGTCTATAG
1 TTTAGGGTTTATAG
19223276 TTTATGGGTTTA
1 TTTA-GGGTTTA
19223288 GGGGTTAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
13 1 0.03
14 24 0.77
15 6 0.19
ACGTcount: A:0.24, C:0.04, G:0.24, T:0.48
Consensus pattern (14 bp):
TTTAGGGTTTATAG
Found at i:19223274 original size:28 final size:29
Alignment explanation
Indices: 19223232--19223286 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
19223222 ATGTGTCATT
* *
19223232 AATTTAGGGTTTATAGTTTA-GGGTTTCA
1 AATTTAAGGTCTATAGTTTATGGGTTTCA
19223260 AATTTAAGGTCTATAGTTTATGGGTTT
1 AATTTAAGGTCTATAGTTTATGGGTTT
19223287 AGGGGTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 18 0.75
29 6 0.25
ACGTcount: A:0.25, C:0.04, G:0.24, T:0.47
Consensus pattern (29 bp):
AATTTAAGGTCTATAGTTTATGGGTTTCA
Found at i:19223888 original size:43 final size:42
Alignment explanation
Indices: 19223809--19223966 Score: 135
Period size: 40 Copynumber: 3.8 Consensus size: 42
19223799 AATAGTTTAC
* ** * *
19223809 ATCTATAGCGGCGTTTTTCCAATAAGCGCCGCTAAAACTCAA
1 ATCTATAGCGGCCTTTTTTGAAAAAACGCCGCTAAAACTCAA
* * * *
19223851 ATCTATTGCGGCCTTTTTTTATAAAAACGCCACTAAAACCCAA
1 ATCTATAGCGGCCTTTTTTGA-AAAAACGCCGCTAAAACTCAA
* * *
19223894 ATCCT-TAGCGG-CGTTTTTGAAAAAGCGCCGCTAATACTC-A
1 AT-CTATAGCGGCCTTTTTTGAAAAAACGCCGCTAAAACTCAA
* **
19223934 ATCTATAGCGG-CGTTTTTGAGGAAACGCCGCTA
1 ATCTATAGCGGCCTTTTTTGAAAAAACGCCGCTA
19223967 TTGCCACTGA
Statistics
Matches: 95, Mismatches: 18, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
39 2 0.02
40 28 0.29
41 15 0.16
42 24 0.25
43 24 0.25
44 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.28
Consensus pattern (42 bp):
ATCTATAGCGGCCTTTTTTGAAAAAACGCCGCTAAAACTCAA
Found at i:19223943 original size:40 final size:42
Alignment explanation
Indices: 19223809--19223966 Score: 155
Period size: 43 Copynumber: 3.8 Consensus size: 42
19223799 AATAGTTTAC
* *
19223809 ATCTATAGCGGCGTTTTTCCA-ATAAGCGCCGCTAAAACTCAA
1 ATCTATAGCGGCGTTTTT-GAGAAAAGCGCCGCTAAAACTCAA
* * * * * * *
19223851 ATCTATTGCGGCCTTTTTTTATAAAAACGCCACTAAAACCCAA
1 ATCTATAGCGG-CGTTTTTGAGAAAAGCGCCGCTAAAACTCAA
*
19223894 ATCCT-TAGCGGCGTTTTTGA-AAAAGCGCCGCTAATACTC-A
1 AT-CTATAGCGGCGTTTTTGAGAAAAGCGCCGCTAAAACTCAA
*
19223934 ATCTATAGCGGCGTTTTTGAGGAAA-CGCCGCTA
1 ATCTATAGCGGCGTTTTTGAGAAAAGCGCCGCTA
19223967 TTGCCACTGA
Statistics
Matches: 96, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
39 2 0.02
40 26 0.27
41 18 0.19
42 18 0.19
43 30 0.31
44 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.28
Consensus pattern (42 bp):
ATCTATAGCGGCGTTTTTGAGAAAAGCGCCGCTAAAACTCAA
Found at i:19224086 original size:154 final size:146
Alignment explanation
Indices: 19223913--19224265 Score: 419
Period size: 146 Copynumber: 2.4 Consensus size: 146
19223903 GGCGTTTTTG
*
19223913 AAAAAGCGCCGCTAATACTCAATCTATAGCGGCGTTTTTGAGGAAACGCCGCTATTGCCACTGAA
1 AAAAA-CGCCGCTAATACTCAATCTATAGCGGCGTTTTTGAGGAAACGCCGCTATTGCCACCGAA
* * *
19223978 GCTCAG-AATAAACGACGCCGTTCTGCTTAATCTTTTAGCAGCGTTTTTGTACAAACGCCGCTAT
65 GCTC-GCAAT-----ACG--GTTCGGCTTAATC-TTTAGCAGCGTTTTTATAAAAACGCCGCTAT
* *
19224042 A-AGTCGACCTATAGCGGCGCTTCCTT
121 AGA-TAGACCTATAGCGGCGCTTCCAT
* *
19224068 AAAAACGCCGCTAATACTCAAACCTATAGCGGCG-TTTTG-GTGAAGCGCCGCTATTGCCACCGA
1 AAAAACGCCGCTAATACTC-AATCTATAGCGGCGTTTTTGAG-GAAACGCCGCTATTGCCACCGA
* **
19224131 AGCTCGCAATATGGTTCGGCTTAATCTTTAGTGGCGTTTTTATAAAAACGCCGCTATAGATAGAC
64 AGCTCGCAATACGGTTCGGCTTAATCTTTAGCAGCGTTTTTATAAAAACGCCGCTATAGATAGAC
*
19224196 CTATAGCGGCGCTTTCAT
129 CTATAGCGGCGCTTCCAT
* * *
19224214 AAAAACGCCGCTAATACTCAATTTATAGCGGCATTTTTGA-AAAACGCCGCTA
1 AAAAACGCCGCTAATACTCAATCTATAGCGGCGTTTTTGAGGAAACGCCGCTA
19224266 ATACCCGATT
Statistics
Matches: 175, Mismatches: 17, Indels: 22
0.82 0.08 0.10
Matches are distributed among these distances:
145 21 0.12
146 72 0.41
147 13 0.07
149 2 0.01
153 2 0.01
154 47 0.27
155 18 0.10
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (146 bp):
AAAAACGCCGCTAATACTCAATCTATAGCGGCGTTTTTGAGGAAACGCCGCTATTGCCACCGAAG
CTCGCAATACGGTTCGGCTTAATCTTTAGCAGCGTTTTTATAAAAACGCCGCTATAGATAGACCT
ATAGCGGCGCTTCCAT
Found at i:19224241 original size:40 final size:39
Alignment explanation
Indices: 19224197--19224278 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 39
19224187 TAGATAGACC
* *
19224197 TATAGCGGCGCTTTCAT-AAAAACGCCGCTAATACTCAATT
1 TATAGCGGC-ATTT-ATGAAAAACGCCGCTAATACCCAATT
* *
19224237 TATAGCGGCATTTTTGAAAAACGCCGCTAATACCCGATT
1 TATAGCGGCATTTATGAAAAACGCCGCTAATACCCAATT
19224276 TAT
1 TAT
19224279 TCAATTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
38 1 0.03
39 27 0.73
40 9 0.24
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (39 bp):
TATAGCGGCATTTATGAAAAACGCCGCTAATACCCAATT
Found at i:19224392 original size:19 final size:20
Alignment explanation
Indices: 19224353--19224394 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
19224343 GTAGTGATTA
19224353 TAAATAATTAAGTTTTTAAAAG
1 TAAATAATTAAG--TTTAAAAG
*
19224375 TAAATAATTAAGTTAAAAAG
1 TAAATAATTAAGTTTAAAAG
19224395 ACAAAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
22 12 0.63
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.36
Consensus pattern (20 bp):
TAAATAATTAAGTTTAAAAG
Found at i:19225004 original size:7 final size:7
Alignment explanation
Indices: 19224992--19225016 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
19224982 TATGTTTAAT
19224992 AAATATA
1 AAATATA
19224999 AAATATA
1 AAATATA
19225006 AAATATA
1 AAATATA
19225013 AAAT
1 AAAT
19225017 CATGCGTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AAATATA
Found at i:19225945 original size:25 final size:23
Alignment explanation
Indices: 19225917--19225975 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 23
19225907 AATATAATTA
*
19225917 AAAATATTTTATATTAATATTAAAT
1 AAAA-ATTTTATATCAAT-TTAAAT
*
19225942 AAAAATAATTATATCAATTTAAAT
1 AAAAAT-TTTATATCAATTTAAAT
*
19225966 AAAAAATTTA
1 AAAAATTTTA
19225976 CGTCTCCCCC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 3 0.10
24 13 0.45
25 13 0.45
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
AAAAATTTTATATCAATTTAAAT
Found at i:19225968 original size:24 final size:26
Alignment explanation
Indices: 19225907--19225970 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 26
19225897 ACACCATTAA
* * *
19225907 AATA-TAATTAAAAATATTTTATATT
1 AATATTAAATAAAAATATATTATATC
19225932 AATATTAAATAAAAATA-ATTATATC
1 AATATTAAATAAAAATATATTATATC
19225957 AAT-TTAAATAAAAA
1 AATATTAAATAAAAA
19225971 ATTTACGTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
24 11 0.31
25 13 0.37
26 11 0.31
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (26 bp):
AATATTAAATAAAAATATATTATATC
Found at i:19230912 original size:53 final size:53
Alignment explanation
Indices: 19230846--19230961 Score: 214
Period size: 53 Copynumber: 2.2 Consensus size: 53
19230836 CACAGGTGTG
* *
19230846 TAGCATGGCCGTGTGCATAATTCAAAGAGTTGCACGGGGTTGAACACGACCTC
1 TAGCATGGGCGTGTGCATAATTCAAAGAGTTACACGGGGTTGAACACGACCTC
19230899 TAGCATGGGCGTGTGCATAATTCAAAGAGTTACACGGGGTTGAACACGACCTC
1 TAGCATGGGCGTGTGCATAATTCAAAGAGTTACACGGGGTTGAACACGACCTC
19230952 TAGCATGGGC
1 TAGCATGGGC
19230962 ATGTCCCAGG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
53 61 1.00
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (53 bp):
TAGCATGGGCGTGTGCATAATTCAAAGAGTTACACGGGGTTGAACACGACCTC
Found at i:19235053 original size:37 final size:37
Alignment explanation
Indices: 19235012--19235089 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
19235002 GCCATTGGTG
* *
19235012 TGTTATCAGGTGGATCGA-CTCTTATGTGCATTTGGCA
1 TGTTATCAGGTGGAT-GAGCTCTTACGAGCATTTGGCA
* * *
19235049 TGTTATCGGGTGGATTAGCTCTTACGAGCATTTGGCG
1 TGTTATCAGGTGGATGAGCTCTTACGAGCATTTGGCA
19235086 TGTT
1 TGTT
19235090 TCAATTGGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
36 1 0.03
37 34 0.97
ACGTcount: A:0.17, C:0.15, G:0.29, T:0.38
Consensus pattern (37 bp):
TGTTATCAGGTGGATGAGCTCTTACGAGCATTTGGCA
Found at i:19241750 original size:24 final size:24
Alignment explanation
Indices: 19241718--19241814 Score: 131
Period size: 24 Copynumber: 3.9 Consensus size: 24
19241708 CATTGTGCTC
19241718 AGTGAAATAAGACCATGGCATCTA
1 AGTGAAATAAGACCATGGCATCTA
* *
19241742 AGTGAAATAAGTCCGTGGCAATGTGCTA
1 AGTGAAATAAGACCATGGC-A--T-CTA
19241770 AGTGAAATAAGACCATGGCATCTA
1 AGTGAAATAAGACCATGGCATCTA
*
19241794 AGTGAAATAAGTCCATGGCAT
1 AGTGAAATAAGACCATGGCAT
19241815 GGTGCAAAGT
Statistics
Matches: 64, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
24 40 0.62
25 2 0.03
27 2 0.03
28 20 0.31
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (24 bp):
AGTGAAATAAGACCATGGCATCTA
Found at i:19241774 original size:52 final size:51
Alignment explanation
Indices: 19241711--19241826 Score: 187
Period size: 52 Copynumber: 2.2 Consensus size: 51
19241701 GATATGACAT
* *
19241711 TGTGCTCAGTGAAATAAGACCATGGCATCTAAGTGAAATAAGTCCGTGGCAA
1 TGTGCTAAGTGAAATAAGACCATGGCATCTAAGTGAAATAAGTCCATGGC-A
19241763 TGTGCTAAGTGAAATAAGACCATGGCATCTAAGTGAAATAAGTCCATGGCA
1 TGTGCTAAGTGAAATAAGACCATGGCATCTAAGTGAAATAAGTCCATGGCA
*
19241814 TGGTGCAAAGTGA
1 T-GTGCTAAGTGA
19241827 GAAATTTCCC
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
51 2 0.03
52 58 0.97
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.23
Consensus pattern (51 bp):
TGTGCTAAGTGAAATAAGACCATGGCATCTAAGTGAAATAAGTCCATGGCA
Found at i:19241779 original size:28 final size:27
Alignment explanation
Indices: 19241711--19241826 Score: 127
Period size: 24 Copynumber: 4.4 Consensus size: 27
19241701 GATATGACAT
*
19241711 TGTGCTCAGTGAAATAAGACCATGGCA
1 TGTGCTAAGTGAAATAAGACCATGGCA
* *
19241738 --T-CTAAGTGAAATAAGTCCGTGGCAA
1 TGTGCTAAGTGAAATAAGACCATGGC-A
19241763 TGTGCTAAGTGAAATAAGACCATGGCA
1 TGTGCTAAGTGAAATAAGACCATGGCA
*
19241790 --T-CTAAGTGAAATAAGTCCATGGCA
1 TGTGCTAAGTGAAATAAGACCATGGCA
*
19241814 TGGTGCAAAGTGA
1 T-GTGCTAAGTGA
19241827 GAAATTTCCC
Statistics
Matches: 74, Mismatches: 7, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
24 41 0.55
25 3 0.04
27 3 0.04
28 27 0.36
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.23
Consensus pattern (27 bp):
TGTGCTAAGTGAAATAAGACCATGGCA
Found at i:19241905 original size:51 final size:51
Alignment explanation
Indices: 19241850--19241998 Score: 219
Period size: 51 Copynumber: 2.9 Consensus size: 51
19241840 TGAACCTTAG
19241850 GAATAAAATAGCTTTGGGCACAAGTGTGGTACTATGTGAAGGCCACTTTGT
1 GAATAAAATAGCTTTGGGCACAAGTGTGGTACTATGTGAAGGCCACTTTGT
* * * * *
19241901 GAATATAATAGCTTTGGACACAAGTGTGGCACTATGTGAAGACCATTTTGT
1 GAATAAAATAGCTTTGGGCACAAGTGTGGTACTATGTGAAGGCCACTTTGT
* *
19241952 GAATAAAATAACTTT-GGCTACAAGGGTGGTACTATGTGAAGGCCACT
1 GAATAAAATAGCTTTGGGC-ACAAGTGTGGTACTATGTGAAGGCCACT
19241999 GGGTATCTGT
Statistics
Matches: 85, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
50 2 0.02
51 83 0.98
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.29
Consensus pattern (51 bp):
GAATAAAATAGCTTTGGGCACAAGTGTGGTACTATGTGAAGGCCACTTTGT
Found at i:19245118 original size:17 final size:17
Alignment explanation
Indices: 19245083--19245132 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
19245073 CCCACATACT
* *
19245083 CGTGTGGACCCATAAGCC
1 CGTGTGG-CCCACACGCC
19245101 CGTGTGGCCCACACGCC
1 CGTGTGGCCCACACGCC
19245118 CGTGTGGCCCACACG
1 CGTGTGGCCCACACG
19245133 TCCCAATTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 23 0.77
18 7 0.23
ACGTcount: A:0.16, C:0.40, G:0.30, T:0.14
Consensus pattern (17 bp):
CGTGTGGCCCACACGCC
Found at i:19255087 original size:12 final size:12
Alignment explanation
Indices: 19255072--19255112 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
19255062 CAGTCAGAAG
*
19255072 CAGATACAAATT
1 CAGATTCAAATT
*
19255084 CAGATTCAGATT
1 CAGATTCAAATT
19255096 CAGATTCAAATT
1 CAGATTCAAATT
19255108 ACAGA
1 -CAGA
19255113 AATAGATATG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
12 21 0.84
13 4 0.16
ACGTcount: A:0.44, C:0.17, G:0.12, T:0.27
Consensus pattern (12 bp):
CAGATTCAAATT
Found at i:19257303 original size:15 final size:16
Alignment explanation
Indices: 19257283--19257316 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
19257273 AATCTTTTAA
19257283 AAATTATAAAAAT-AT
1 AAATTATAAAAATAAT
*
19257298 AAATTATTAAAATAAT
1 AAATTATAAAAATAAT
19257314 AAA
1 AAA
19257317 ATTACATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATTATAAAAATAAT
Found at i:19260054 original size:31 final size:31
Alignment explanation
Indices: 19260019--19260079 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
19260009 TTAATAGCCC
*
19260019 AGTGACTTAAATAAAAACTTTCAAATAGTTT
1 AGTGACATAAATAAAAACTTTCAAATAGTTT
* * *
19260050 AGTGACATAAATGAAAATTTTTAAATAGTT
1 AGTGACATAAATAAAAACTTTCAAATAGTT
19260080 CAGCAACCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.36
Consensus pattern (31 bp):
AGTGACATAAATAAAAACTTTCAAATAGTTT
Found at i:19262418 original size:47 final size:45
Alignment explanation
Indices: 19262361--19262470 Score: 123
Period size: 47 Copynumber: 2.4 Consensus size: 45
19262351 AAAATCTTGC
* * * *
19262361 AGATGAAATCTGCTTCTAGAT-GTGGATTTCACAGCAAATAACCCGCA
1 AGATGGAATCTGCCTCT-GATCGTGGATAT-ACAACAAATAACCCG-A
* * *
19262408 AGATGGAATCTGCCTCTGGTCGTGGATATACAACAAATAACTCGT
1 AGATGGAATCTGCCTCTGATCGTGGATATACAACAAATAACCCGA
19262453 AGATGGAATCTGCCTCTG
1 AGATGGAATCTGCCTCTG
19262471 GCTGTGGGTA
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
45 18 0.33
46 15 0.27
47 22 0.40
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (45 bp):
AGATGGAATCTGCCTCTGATCGTGGATATACAACAAATAACCCGA
Found at i:19262647 original size:34 final size:34
Alignment explanation
Indices: 19262586--19262665 Score: 106
Period size: 34 Copynumber: 2.4 Consensus size: 34
19262576 CCAGTAGTAT
*
19262586 TTAATATGCTTTTAATAAAACAATATAGTAGCAA
1 TTAATATGCTTATAATAAAACAATATAGTAGCAA
** ** *
19262620 TTAATATGCTTATAATAATTCGTTATAGTAGCCA
1 TTAATATGCTTATAATAAAACAATATAGTAGCAA
19262654 TTAATATGCTTA
1 TTAATATGCTTA
19262666 CAAGAGATCA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (34 bp):
TTAATATGCTTATAATAAAACAATATAGTAGCAA
Found at i:19263528 original size:23 final size:22
Alignment explanation
Indices: 19263485--19263528 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
19263475 ATAATAATGT
* **
19263485 AATAAAATAAGTAAAGTTAAAA
1 AATAAAATAAGAAAACATAAAA
19263507 AATAATAATAAGAAAACATAAA
1 AATAA-AATAAGAAAACATAAA
19263529 GCATTGTCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.20
Consensus pattern (22 bp):
AATAAAATAAGAAAACATAAAA
Found at i:19264953 original size:30 final size:30
Alignment explanation
Indices: 19264887--19264955 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
19264877 GTGTACTAGT
*
19264887 CATGTGTCTCACACGGCCCAATCACACTCC
1 CATGTGTCTCACACGGCCCAATCACACACC
* * * *
19264917 CGTGTGTCTCACACGGCTCAGTCACACACT
1 CATGTGTCTCACACGGCCCAATCACACACC
*
19264947 TATGTGTCT
1 CATGTGTCT
19264956 AGCCGTATGG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.20, C:0.36, G:0.17, T:0.26
Consensus pattern (30 bp):
CATGTGTCTCACACGGCCCAATCACACACC
Found at i:19265932 original size:40 final size:41
Alignment explanation
Indices: 19265872--19265975 Score: 122
Period size: 41 Copynumber: 2.6 Consensus size: 41
19265862 AACACACCAG
* *
19265872 TTTGGCACCCAGTGCCTCATCGGA-TAAT-TCAAAGTAATAA
1 TTTGACACCCAGTGCCTCATCGAATTAATAT-AAAGTAATAA
* * *
19265912 TTTGACACCCAGTGCCTCATCAAATTAATATGAAGTATTAA
1 TTTGACACCCAGTGCCTCATCGAATTAATATAAAGTAATAA
* *
19265953 ATTGACACCCAGTGTCTCATCGA
1 TTTGACACCCAGTGCCTCATCGA
19265976 CTCGAAGTCG
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
40 21 0.39
41 32 0.59
42 1 0.02
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (41 bp):
TTTGACACCCAGTGCCTCATCGAATTAATATAAAGTAATAA
Found at i:19266817 original size:20 final size:19
Alignment explanation
Indices: 19266784--19266822 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
19266774 CATCGTCTCC
19266784 TTCTTTCTCCCTTTTCTTTT
1 TTCTTTCTCCC-TTTCTTTT
**
19266804 TTCTTTCTTTCTTTCTTTT
1 TTCTTTCTCCCTTTCTTTT
19266823 CTGTTTCGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (19 bp):
TTCTTTCTCCCTTTCTTTT
Found at i:19273154 original size:40 final size:40
Alignment explanation
Indices: 19273101--19273239 Score: 113
Period size: 40 Copynumber: 3.5 Consensus size: 40
19273091 AACACACCAG
* **
19273101 TTTGGCACCTAGTGCCTCATCGGATAATTCGAAGTAATAA
1 TTTGACACCTAGTGCCTCATCGGATAAACCGAAGTAATAA
* * *
19273141 TTTGACACTTAGTGTCTCATCGGCTAAACCGAAGT-A-AA
1 TTTGACACCTAGTGCCTCATCGGATAAACCGAAGTAATAA
* * * * * *
19273179 -TTGGCACCCAGTGCCTCATCGAATTAATCTGAAGTAGTAA
1 TTTGACACCTAGTGCCTCATCGGA-TAAACCGAAGTAATAA
* * *
19273219 ATTGACACCCAGTGTCTCATC
1 TTTGACACCTAGTGCCTCATC
19273240 AACTCGAAGT
Statistics
Matches: 78, Mismatches: 17, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
37 17 0.22
38 11 0.14
39 1 0.01
40 31 0.40
41 18 0.23
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (40 bp):
TTTGACACCTAGTGCCTCATCGGATAAACCGAAGTAATAA
Found at i:19278236 original size:22 final size:22
Alignment explanation
Indices: 19278211--19278303 Score: 79
Period size: 19 Copynumber: 4.2 Consensus size: 22
19278201 ATGTTGTATG
19278211 TATTTTCATTATATATAT-TATT
1 TATTTT-ATTATATATATATATT
*
19278233 TATTTTACTATAT-T-T-TATT
1 TATTTTATTATATATATATATT
* *
19278252 TATTATATTAT-TATATATGTT
1 TATTTTATTATATATATATATT
19278273 TAATTTTTATTATATATTATATATAT
1 T-A-TTTTATTATATA-TATATAT-T
19278299 TATTT
1 TATTT
19278304 ATGTCTATAT
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
18 1 0.02
19 15 0.26
20 2 0.04
21 10 0.18
22 7 0.12
23 8 0.14
24 5 0.09
25 7 0.12
26 2 0.04
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (22 bp):
TATTTTATTATATATATATATT
Found at i:19278237 original size:43 final size:40
Alignment explanation
Indices: 19278174--19278269 Score: 108
Period size: 41 Copynumber: 2.4 Consensus size: 40
19278164 TTTTTCATCA
19278174 TATATT-TT-TATATTTGTATTTTACTATATGTTGTATGTAT
1 TATATTATTATATATTTGTATTTTACTATAT-TT-TATGTAT
* * *
19278214 TTTCATTA-TATATATTATTTATTTTACTATATTTTATTTAT
1 TAT-ATTATTATATATT-TGTATTTTACTATATTTTATGTAT
19278255 TATATTATTATATAT
1 TATATTATTATATAT
19278270 GTTTAATTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
40 6 0.13
41 19 0.40
42 8 0.17
43 14 0.30
ACGTcount: A:0.29, C:0.03, G:0.04, T:0.64
Consensus pattern (40 bp):
TATATTATTATATATTTGTATTTTACTATATTTTATGTAT
Found at i:19278250 original size:19 final size:20
Alignment explanation
Indices: 19278190--19278255 Score: 71
Period size: 22 Copynumber: 3.2 Consensus size: 20
19278180 TTTATATTTG
* *
19278190 TATTTTACTATATGTTGTATG
1 TATTTTACTATATATT-TATT
*
19278211 TATTTTCATTATATATATTATT
1 TATTTT-ACTATATAT-TTATT
19278233 TATTTTACTATAT-TTTATT
1 TATTTTACTATATATTTATT
19278252 TATT
1 TATT
19278256 ATATTATTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
19 9 0.23
20 1 0.03
21 12 0.31
22 16 0.41
23 1 0.03
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.64
Consensus pattern (20 bp):
TATTTTACTATATATTTATT
Found at i:19278290 original size:7 final size:7
Alignment explanation
Indices: 19278222--19278362 Score: 62
Period size: 7 Copynumber: 20.4 Consensus size: 7
19278212 ATTTTCATTA
19278222 TATATAT
1 TATATAT
*
19278229 TATTTAT
1 TATATAT
*
19278236 T-T-TAC
1 TATATAT
*
19278241 TATATTT
1 TATATAT
*
19278248 TATTTAT
1 TATATAT
19278255 TATATTAT
1 TATA-TAT
19278263 TATATAT
1 TATATAT
*
19278270 GTTTA-AT
1 -TATATAT
*
19278277 T-TTTAT
1 TATATAT
19278283 TATATATT
1 TATATA-T
19278291 ATATATAT
1 -TATATAT
*
19278299 TATTTAT
1 TATATAT
*
19278306 GTCTATAT
1 -TATATAT
*
19278314 TATATGT
1 TATATAT
*
19278321 T-T-TAG
1 TATATAT
* *
19278326 TACATGT
1 TATATAT
*
19278333 TAT-TTT
1 TATATAT
19278339 TATATAT
1 TATATAT
19278346 TATATAT
1 TATATAT
*
19278353 GATATAT
1 TATATAT
19278360 TAT
1 TAT
19278363 TCATATTATT
Statistics
Matches: 97, Mismatches: 25, Indels: 24
0.66 0.17 0.16
Matches are distributed among these distances:
5 6 0.06
6 12 0.12
7 56 0.58
8 17 0.18
9 6 0.06
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (7 bp):
TATATAT
Found at i:19278300 original size:9 final size:9
Alignment explanation
Indices: 19278218--19278301 Score: 61
Period size: 9 Copynumber: 9.6 Consensus size: 9
19278208 ATGTATTTTC
19278218 ATTATATAT
1 ATTATATAT
19278227 ATTAT-T-T
1 ATTATATAT
*
19278234 ATTTTACTAT
1 ATTATA-TAT
* *
19278244 ATTTTATTT
1 ATTATATAT
19278253 ATTATAT-T
1 ATTATATAT
19278261 ATTATATAT
1 ATTATATAT
*
19278270 GTT-TA-ATT
1 ATTATATA-T
*
19278278 TTTATTATAT
1 ATTA-TATAT
19278288 ATTATATAT
1 ATTATATAT
19278297 ATTAT
1 ATTAT
19278302 TTATGTCTAT
Statistics
Matches: 61, Mismatches: 6, Indels: 16
0.73 0.07 0.19
Matches are distributed among these distances:
7 6 0.10
8 14 0.23
9 27 0.44
10 13 0.21
11 1 0.02
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (9 bp):
ATTATATAT
Found at i:19278493 original size:23 final size:22
Alignment explanation
Indices: 19278467--19278526 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
19278457 TTAGATTATT
*
19278467 ATTATTTTATATATTCTTCTTAC
1 ATTATTTTATATATT-TTATTAC
*
19278490 ATTATATTATATATTTTATTAC
1 ATTATTTTATATATTTTATTAC
19278512 ATATATTTTAT-TATT
1 AT-TATTTTATATATT
19278527 ATATGATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 12 0.36
23 21 0.64
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.62
Consensus pattern (22 bp):
ATTATTTTATATATTTTATTAC
Found at i:19278515 original size:14 final size:14
Alignment explanation
Indices: 19278498--19278524 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19278488 ACATTATATT
19278498 ATATATTTTATTAC
1 ATATATTTTATTAC
19278512 ATATATTTTATTA
1 ATATATTTTATTA
19278525 TTATATGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (14 bp):
ATATATTTTATTAC
Found at i:19278525 original size:17 final size:17
Alignment explanation
Indices: 19278505--19278556 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
19278495 ATTATATATT
19278505 TTATTACATATATTTTA
1 TTATTACATATATTTTA
19278522 TTATT--ATATGATTTATA
1 TTATTACATAT-ATTT-TA
19278539 TTATTACATAT-TTTTA
1 TTATTACATATATTTTA
19278555 TT
1 TT
19278557 TGTAAATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
15 4 0.13
16 8 0.26
17 15 0.48
19 4 0.13
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (17 bp):
TTATTACATATATTTTA
Found at i:19278528 original size:34 final size:33
Alignment explanation
Indices: 19278490--19278556 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 33
19278480 TTCTTCTTAC
* *
19278490 ATTATATTATATATTTTATTACATATATTTTATT
1 ATTATATGATATATATTATTACATAT-TTTTATT
*
19278524 ATTATATGATTTATATTATTACATATTTTTATT
1 ATTATATGATATATATTATTACATATTTTTATT
19278557 TGTAAATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 7 0.23
34 23 0.77
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.61
Consensus pattern (33 bp):
ATTATATGATATATATTATTACATATTTTTATT
Found at i:19278540 original size:14 final size:13
Alignment explanation
Indices: 19278491--19278542 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 13
19278481 TCTTCTTACA
19278491 TTATATTATATAT
1 TTATATTATATAT
19278504 TT-TATTACATATATT
1 TTATATT--ATATA-T
19278519 TTATTATTATATGAT
1 TTA-TATTATAT-AT
19278534 TTATATTAT
1 TTATATTAT
19278543 TACATATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
12 4 0.12
13 2 0.06
14 11 0.33
15 11 0.33
16 1 0.03
17 4 0.12
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (13 bp):
TTATATTATATAT
Found at i:19282493 original size:26 final size:26
Alignment explanation
Indices: 19282455--19282512 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
19282445 CATGAAATTC
19282455 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
19282481 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
19282507 TTATCA
1 TTATCA
19282513 ATTTGTATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:19293713 original size:283 final size:285
Alignment explanation
Indices: 19293200--19293872 Score: 940
Period size: 283 Copynumber: 2.4 Consensus size: 285
19293190 CTGAAGCTAG
* *
19293200 ATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAACCGAAGACATAACTGATTTGGTTT
1 ATCCAAGATGATTTGGTATCCTTGTGCTTACAAGGAACAAACCGAAGACATAACTGATTTGGTAT
*
19293265 TCACGTGTTTACGTTGAAGCAAGTCTAAAATGATTTGGCATCTCTGTATTGACAGAGAACAAATC
66 TCACGTGTTTACGTTGAAGCAAGTCTAAAATGATTTGGCATATCTGTATTGACA-AG---AAATC
* ** **
19293330 AAAGTTTGGCGTCTCCATATTTGACGGAGGGCAGACACATAACAGACCTAACCTTCAGATGTTTA
127 AAAGTTTGGCATCTCCATATTCAACAAAGGGCAGACACATAACAGACCTAACCTTCAGATGTTTA
* *
19293395 TACTGAAGCAGATCCAAGATGATTTGGCATTCTTGTGTTTACAATGAACAAATCGAGGACATAGC
192 TACTGAAGAAGATCCAAGATGATTTGGCATTCTTGTGTTTACAAGGAACAAATCGAGGACATAGC
*
19293460 AGATTTGACTCTTAGATGTTCTCAAACAA
257 AGATTTGACTCTCAGATGTTCTCAAACAA
* * * * *
19293489 ATCCAAGATGATTTGGTATTCTTGTGTTTACAAGGAACAAATCGGAA-CCATAGCTGATTTGGTA
1 ATCCAAGATGATTTGGTATCCTTGTGCTTACAAGGAACAAA-CCGAAGACATAACTGATTTGGTA
* * * *
19293553 TTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGTCATATCTGTATTGTC-AG-AATCGAA
65 TTCACGTGTTTACGTTGAAGCAAGTCTAAAATGATTTGGCATATCTGTATTGACAAGAAATCAAA
* * *
19293616 GTTTGGCATCTCCATATTCAACAAAGGGCAGACACATAGCATATCTAACCTTCAGATGTTTATAC
130 GTTTGGCATCTCCATATTCAACAAAGGGCAGACACATAACAGACCTAACCTTCAGATGTTTATAC
19293681 TGAAGAAGATCCAAGATGATTTGGCATTCTTGTGTTTACAAGGAACAAATCGAGGACATAGCAGA
195 TGAAGAAGATCCAAGATGATTTGGCATTCTTGTGTTTACAAGGAACAAATCGAGGACATAGCAGA
19293746 TTTGACTCTCAGATGTTCTCAAACAA
260 TTTGACTCTCAGATGTTCTCAAACAA
* ** * * * *
19293772 ATCCAAGATGATTTGATATCCTTGTGCTTACAAGGAGTAAATCGAAGGCATAATTGATATGGCT-
1 ATCCAAGATGATTTGGTATCCTTGTGCTTACAAGGAACAAACCGAAGACATAACTGATTTGG-TA
* * * * * *
19293836 TTTACGTGCTTACGCTGAATCAAATCTAAGATGATTT
65 TTCACGTGTTTACGTTGAAGCAAGTCTAAAATGATTT
19293873 TGTATCCCTG
Statistics
Matches: 342, Mismatches: 39, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
282 3 0.01
283 230 0.67
284 1 0.00
287 2 0.01
289 102 0.30
290 4 0.01
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (285 bp):
ATCCAAGATGATTTGGTATCCTTGTGCTTACAAGGAACAAACCGAAGACATAACTGATTTGGTAT
TCACGTGTTTACGTTGAAGCAAGTCTAAAATGATTTGGCATATCTGTATTGACAAGAAATCAAAG
TTTGGCATCTCCATATTCAACAAAGGGCAGACACATAACAGACCTAACCTTCAGATGTTTATACT
GAAGAAGATCCAAGATGATTTGGCATTCTTGTGTTTACAAGGAACAAATCGAGGACATAGCAGAT
TTGACTCTCAGATGTTCTCAAACAA
Found at i:19295770 original size:22 final size:21
Alignment explanation
Indices: 19295745--19295832 Score: 83
Period size: 22 Copynumber: 4.1 Consensus size: 21
19295735 ATGTTGTATG
19295745 TATTTTCATTATATATATTATT
1 TATTTT-ATTATATATATTATT
*
19295767 TATTTTACTATAT-T-TTATT
1 TATTTTATTATATATATTATT
*
19295786 TATTATATTATTATATATGT-TT
1 TATTTTATTA-TATATAT-TATT
* *
19295808 AATTTTTATTATATATATTAGT
1 TA-TTTTATTATATATATTATT
19295830 TAT
1 TAT
19295833 ATCTATATTA
Statistics
Matches: 53, Mismatches: 7, Indels: 13
0.73 0.10 0.18
Matches are distributed among these distances:
19 13 0.25
20 4 0.08
21 9 0.17
22 19 0.36
23 8 0.15
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (21 bp):
TATTTTATTATATATATTATT
Found at i:19295782 original size:32 final size:31
Alignment explanation
Indices: 19295745--19295834 Score: 89
Period size: 32 Copynumber: 2.8 Consensus size: 31
19295735 ATGTTGTATG
19295745 TATTTTCATTATATATATTATTTAT-T-TTACTA
1 TATTTT-ATTATATATATTATTTATATGTT--TA
19295777 TATTTTATT-TATTATATTATTATATATGTTTA
1 TATTTTATTATA-TATATTATT-TATATGTTTA
*
19295809 -ATTTTTATTATATATATTAGTTATAT
1 TA-TTTTATTATATATATTATTTATAT
19295835 CTATATTATA
Statistics
Matches: 51, Mismatches: 1, Indels: 13
0.78 0.02 0.20
Matches are distributed among these distances:
30 2 0.04
31 18 0.35
32 26 0.51
33 3 0.06
34 2 0.04
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (31 bp):
TATTTTATTATATATATTATTTATATGTTTA
Found at i:19295784 original size:19 final size:20
Alignment explanation
Indices: 19295725--19295789 Score: 69
Period size: 22 Copynumber: 3.1 Consensus size: 20
19295715 TTATATTTGC
* *
19295725 ATTTTACTATATGTTGTATGT
1 ATTTTACTATATATT-TATTT
*
19295746 ATTTTCATTATATATATTATTT
1 ATTTT-ACTATATAT-TTATTT
19295768 ATTTTACTATAT-TTTATTT
1 ATTTTACTATATATTTATTT
19295787 ATT
1 ATT
19295790 ATATTATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
19 9 0.24
20 1 0.03
21 11 0.29
22 16 0.42
23 1 0.03
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.63
Consensus pattern (20 bp):
ATTTTACTATATATTTATTT
Found at i:19296020 original size:23 final size:22
Alignment explanation
Indices: 19295994--19296053 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
19295984 TTAGATTATT
*
19295994 ATTATTTTATATATTCTTCTTAC
1 ATTATTTTATATATT-TTATTAC
*
19296017 ATTATATTATATATTTTATTAC
1 ATTATTTTATATATTTTATTAC
19296039 ATATATTTTAT-TATT
1 AT-TATTTTATATATT
19296054 ATATGATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 12 0.36
23 21 0.64
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.62
Consensus pattern (22 bp):
ATTATTTTATATATTTTATTAC
Found at i:19296042 original size:14 final size:14
Alignment explanation
Indices: 19296025--19296051 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19296015 ACATTATATT
19296025 ATATATTTTATTAC
1 ATATATTTTATTAC
19296039 ATATATTTTATTA
1 ATATATTTTATTA
19296052 TTATATGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (14 bp):
ATATATTTTATTAC
Found at i:19296052 original size:17 final size:17
Alignment explanation
Indices: 19296032--19296083 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
19296022 ATTATATATT
19296032 TTATTACATATATTTTA
1 TTATTACATATATTTTA
19296049 TTATT--ATATGATTTATA
1 TTATTACATAT-ATTT-TA
19296066 TTATTACATAT-TTTTA
1 TTATTACATATATTTTA
19296082 TT
1 TT
19296084 TGTAAATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
15 4 0.13
16 8 0.26
17 15 0.48
19 4 0.13
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (17 bp):
TTATTACATATATTTTA
Found at i:19296055 original size:34 final size:33
Alignment explanation
Indices: 19296017--19296083 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 33
19296007 TTCTTCTTAC
* *
19296017 ATTATATTATATATTTTATTACATATATTTTATT
1 ATTATATGATATATATTATTACATAT-TTTTATT
*
19296051 ATTATATGATTTATATTATTACATATTTTTATT
1 ATTATATGATATATATTATTACATATTTTTATT
19296084 TGTAAATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 7 0.23
34 23 0.77
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.61
Consensus pattern (33 bp):
ATTATATGATATATATTATTACATATTTTTATT
Found at i:19296067 original size:14 final size:13
Alignment explanation
Indices: 19296018--19296069 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 13
19296008 TCTTCTTACA
19296018 TTATATTATATAT
1 TTATATTATATAT
19296031 TT-TATTACATATATT
1 TTATATT--ATATA-T
19296046 TTATTATTATATGAT
1 TTA-TATTATAT-AT
19296061 TTATATTAT
1 TTATATTAT
19296070 TACATATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
12 4 0.12
13 2 0.06
14 11 0.33
15 11 0.33
16 1 0.03
17 4 0.12
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (13 bp):
TTATATTATATAT
Found at i:19297963 original size:4 final size:4
Alignment explanation
Indices: 19297954--19297985 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
19297944 AATAAAGAAT
19297954 AATA AATA AAT- AATA AATA AAT- AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AATA AA
19297986 AATGATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 6 0.23
4 20 0.77
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:19297965 original size:11 final size:11
Alignment explanation
Indices: 19297951--19297985 Score: 70
Period size: 11 Copynumber: 3.2 Consensus size: 11
19297941 AAGAATAAAG
19297951 AATAATAAATA
1 AATAATAAATA
19297962 AATAATAAATA
1 AATAATAAATA
19297973 AATAATAAATA
1 AATAATAAATA
19297984 AA
1 AA
19297986 AATGATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AATAATAAATA
Found at i:19300713 original size:24 final size:24
Alignment explanation
Indices: 19300686--19300734 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
19300676 GACATTTGGC
19300686 TATCACACATAGTCCTCACTAAAT
1 TATCACACATAGTCCTCACTAAAT
19300710 TATCACACATAGTCCTCACTAAAT
1 TATCACACATAGTCCTCACTAAAT
19300734 T
1 T
19300735 CATACTCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.29, G:0.04, T:0.31
Consensus pattern (24 bp):
TATCACACATAGTCCTCACTAAAT
Found at i:19302919 original size:305 final size:307
Alignment explanation
Indices: 19302330--19302942 Score: 1095
Period size: 305 Copynumber: 2.0 Consensus size: 307
19302320 GCGACTCGGT
* *
19302330 TTAGCGGTCCCGAAATCACTTCCCGACTAGGGTCAGAATAGGGTTATCTCACACACAATTACTAT
1 TTAGCGGTCCCGAAATCACTTCCCGACTAGGGTCAGAATAGGGCTATCACACACACAATTACTAT
* *
19302395 ACTCTTAATCAAAACATCGAAACATTCAAAACCAAACCTGCCTCAAAGTCGTCGAGGACACTCTC
66 ACTCTTAATCAAAACATCAAAACATTCAAAACCAAACCTGCCTCAAAGTCGTCGAGGACACTCCC
* * *
19302460 TGACCTGATGTTATGTGTATCCACATCGAAAACATGCTCCATGCATTTTTCCAGCAATTGGCCGG
131 CGACCTGATGTTATGTGGATCCACATCGAAAACATGCTCCATGCATTTTTCCAGCAATTGCCCGG
*
19302525 ATGGCGATTTTTACAGTGCTCACAAAATGGAGTGCTCGCACTACTACCAACACCCTCCTCAAAAC
196 ATGGCGATTTTTACAGTGCTCACAAAATGGAGCGCTCGCACTACTACCAACACCCTCCTCAAAAC
19302590 CACTATTACCACTCAAATGCGTTCTAACACTTTTCGAAAAATAAGGC
261 CACTATTACCACTCAAATGCGTTCTAACACTTTTCGAAAAATAAGGC
19302637 TTAGCGGTCCCGAAATCACTTCCCGACTAGGGTCAGAATAGGGCTATCACACACACAATTACTAT
1 TTAGCGGTCCCGAAATCACTTCCCGACTAGGGTCAGAATAGGGCTATCACACACACAATTACTAT
*
19302702 ACTCTTAATCAAAACATCAAAACATTCACAACCAAACCTGCCTCAAAGTCGTCGAGGACACTCCC
66 ACTCTTAATCAAAACATCAAAACATTCAAAACCAAACCTGCCTCAAAGTCGTCGAGGACACTCCC
**
19302767 CGA-CTGATGTTATGTGGATCCACATCGAAAACATGCT-TTTGCATTTTTCCAGCAATTGCCCGG
131 CGACCTGATGTTATGTGGATCCACATCGAAAACATGCTCCATGCATTTTTCCAGCAATTGCCCGG
19302830 ATGGCGATTTTTACAGTGCTCACAAAATGGAGCGCTCGCACTACTACCAACACCCTCCTCAAAAC
196 ATGGCGATTTTTACAGTGCTCACAAAATGGAGCGCTCGCACTACTACCAACACCCTCCTCAAAAC
* *
19302895 TACTATTACCACTCAAATGCGTTCTAACACTTTTCGAAAAATGAGGC
261 CACTATTACCACTCAAATGCGTTCTAACACTTTTCGAAAAATAAGGC
19302942 T
1 T
19302943 CCAACATCGT
Statistics
Matches: 293, Mismatches: 13, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
305 133 0.45
306 33 0.11
307 127 0.43
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.25
Consensus pattern (307 bp):
TTAGCGGTCCCGAAATCACTTCCCGACTAGGGTCAGAATAGGGCTATCACACACACAATTACTAT
ACTCTTAATCAAAACATCAAAACATTCAAAACCAAACCTGCCTCAAAGTCGTCGAGGACACTCCC
CGACCTGATGTTATGTGGATCCACATCGAAAACATGCTCCATGCATTTTTCCAGCAATTGCCCGG
ATGGCGATTTTTACAGTGCTCACAAAATGGAGCGCTCGCACTACTACCAACACCCTCCTCAAAAC
CACTATTACCACTCAAATGCGTTCTAACACTTTTCGAAAAATAAGGC
Found at i:19305273 original size:19 final size:20
Alignment explanation
Indices: 19305245--19305283 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
19305235 TCCCATTATT
19305245 TATTTATTTTT-TGTTTTAA
1 TATTTATTTTTATGTTTTAA
*
19305264 TATTTGTTTTTATGTTTTAA
1 TATTTATTTTTATGTTTTAA
19305284 ATATATTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.72
Consensus pattern (20 bp):
TATTTATTTTTATGTTTTAA
Found at i:19305289 original size:23 final size:25
Alignment explanation
Indices: 19305263--19305309 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
19305253 TTTTGTTTTA
*
19305263 ATATTTG-TTT-TTATGTTTTAAAT
1 ATATTTGATTTATTATATTTTAAAT
19305286 ATATTTGATTTATTATATTTTAAA
1 ATATTTGATTTATTATATTTTAAA
19305310 GTTTTTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.33
24 3 0.14
25 11 0.52
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (25 bp):
ATATTTGATTTATTATATTTTAAAT
Found at i:19306337 original size:34 final size:30
Alignment explanation
Indices: 19306279--19306339 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 30
19306269 TGAAAAGAAT
*
19306279 AAATAATAATAAATAAAAATCAAATAAATA
1 AAATAATAAAAAATAAAAATCAAATAAATA
19306309 AAATAAATAAAAAATAATAACATACAAATAA
1 AAAT-AATAAAAAATAA-AA-AT-CAAATAA
19306340 GACTAAACAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 4 0.15
31 11 0.42
32 2 0.08
33 2 0.08
34 7 0.27
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (30 bp):
AAATAATAAAAAATAAAAATCAAATAAATA
Found at i:19307785 original size:21 final size:21
Alignment explanation
Indices: 19307759--19307807 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
19307749 AATCATAGCA
19307759 CTGAGGAGGCCACGTGGGAGC
1 CTGAGGAGGCCACGTGGGAGC
*
19307780 CTGAGGAGGCCATGTGGGAGC
1 CTGAGGAGGCCACGTGGGAGC
19307801 CTGAGGA
1 CTGAGGA
19307808 TGCGATGCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.20, C:0.20, G:0.47, T:0.12
Consensus pattern (21 bp):
CTGAGGAGGCCACGTGGGAGC
Found at i:19313182 original size:25 final size:25
Alignment explanation
Indices: 19313154--19313222 Score: 66
Period size: 25 Copynumber: 2.8 Consensus size: 25
19313144 CTGTCAACAA
*
19313154 TCCTCTGTTGCATCATCATCGACAG
1 TCCTCTGTTGCATCACCATCGACAG
** * * * *
19313179 TCCTCTACTGCATCGCCGTTGATAG
1 TCCTCTGTTGCATCACCATCGACAG
*
19313204 TCCTCTGTTGCATCGCCAT
1 TCCTCTGTTGCATCACCAT
19313223 GTAAGTTTTT
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.16, C:0.33, G:0.17, T:0.33
Consensus pattern (25 bp):
TCCTCTGTTGCATCACCATCGACAG
Found at i:19315986 original size:21 final size:23
Alignment explanation
Indices: 19315960--19316005 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
19315950 CTTATCTATA
* *
19315960 AATTTAA-ATGGAT-TAAATTAC
1 AATTTAAGATGAATATAAAGTAC
19315981 AATTTAAGATGAATATAAAGTAC
1 AATTTAAGATGAATATAAAGTAC
19316004 AA
1 AA
19316006 ATCAATCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.33
22 5 0.24
23 9 0.43
ACGTcount: A:0.52, C:0.04, G:0.11, T:0.33
Consensus pattern (23 bp):
AATTTAAGATGAATATAAAGTAC
Found at i:19327944 original size:27 final size:27
Alignment explanation
Indices: 19327913--19327967 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
19327903 AGTAGTTTTG
19327913 TAGTTAATTAGGTTTTGGTTAAGTGAA
1 TAGTTAATTAGGTTTTGGTTAAGTGAA
19327940 TAGTTAATTAGGTTTTGGTTAAGTGAA
1 TAGTTAATTAGGTTTTGGTTAAGTGAA
19327967 T
1 T
19327968 TTGCATGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.25, T:0.45
Consensus pattern (27 bp):
TAGTTAATTAGGTTTTGGTTAAGTGAA
Found at i:19334792 original size:42 final size:42
Alignment explanation
Indices: 19334698--19334792 Score: 127
Period size: 42 Copynumber: 2.3 Consensus size: 42
19334688 TAGACACATG
* * *
19334698 CCCATGTCCTTGTCCGTGTGGCTCACACAGCCTGAACATACA
1 CCCATGTCCTTGTCCATATGGCTCACACAGCCTGAACACACA
* * *
19334740 TCCATGTCCTTGTCCATATGGCTCACACAGCCTGGATACACA
1 CCCATGTCCTTGTCCATATGGCTCACACAGCCTGAACACACA
*
19334782 CCCATATCCTT
1 CCCATGTCCTT
19334793 ACCCGTGTGA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.22, C:0.36, G:0.16, T:0.26
Consensus pattern (42 bp):
CCCATGTCCTTGTCCATATGGCTCACACAGCCTGAACACACA
Found at i:19335564 original size:26 final size:27
Alignment explanation
Indices: 19335512--19335564 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
19335502 GATCAGAAAA
*
19335512 AATAAAAAGAAAAGAAAAAGAATGAAG
1 AATAAAAAGAAAAGAAAAAGAACGAAG
19335539 AATAAAAAG-AAAG-AAAAGTAACGAAG
1 AATAAAAAGAAAAGAAAAAG-AACGAAG
19335565 GAGAAAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 5 0.21
26 10 0.42
27 9 0.38
ACGTcount: A:0.72, C:0.02, G:0.19, T:0.08
Consensus pattern (27 bp):
AATAAAAAGAAAAGAAAAAGAACGAAG
Found at i:19335571 original size:26 final size:25
Alignment explanation
Indices: 19335515--19335579 Score: 62
Period size: 26 Copynumber: 2.6 Consensus size: 25
19335505 CAGAAAAAAT
* *
19335515 AAAAAGAAAAGAAAAAGAATGAAGAAT
1 AAAAAG-AAAG-AAAAGAACGAAGAAG
*
19335542 AAAAAGAAAGAAAAGTAACGAAGGAG
1 AAAAAGAAAGAAAAG-AACGAAGAAG
19335568 -AAAAG-AAGAAAA
1 AAAAAGAAAGAAAA
19335580 CTTAAGAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
24 7 0.21
25 10 0.29
26 11 0.32
27 6 0.18
ACGTcount: A:0.72, C:0.02, G:0.22, T:0.05
Consensus pattern (25 bp):
AAAAAGAAAGAAAAGAACGAAGAAG
Found at i:19339892 original size:15 final size:15
Alignment explanation
Indices: 19339874--19339902 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
19339864 AAAGTTACGA
19339874 AATGCAAAATATTTT
1 AATGCAAAATATTTT
19339889 AATGCAAAATATTT
1 AATGCAAAATATTT
19339903 ATAGACTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (15 bp):
AATGCAAAATATTTT
Found at i:19342523 original size:74 final size:74
Alignment explanation
Indices: 19342402--19342557 Score: 303
Period size: 74 Copynumber: 2.1 Consensus size: 74
19342392 TAGATAACAT
19342402 TAAAAACTATAAGGAATTGAATCATTACCTTAGATGAAGAAAATCTATGCGTTTGATCGAAAATT
1 TAAAAACTATAAGGAATTGAATCATTACCTTAGATGAAGAAAATCTATGCGTTTGATCGAAAATT
19342467 CGAAAAATC
66 CGAAAAATC
19342476 TAAAAACTATAAGGAATTGAATCATTACCTTAGATGAAGAAAATCTATGCGTTTGATCGAAAATT
1 TAAAAACTATAAGGAATTGAATCATTACCTTAGATGAAGAAAATCTATGCGTTTGATCGAAAATT
19342541 CGAAAAATC
66 CGAAAAATC
*
19342550 CAAAAACT
1 TAAAAACT
19342558 TGACAATGGA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 81 1.00
ACGTcount: A:0.46, C:0.13, G:0.14, T:0.28
Consensus pattern (74 bp):
TAAAAACTATAAGGAATTGAATCATTACCTTAGATGAAGAAAATCTATGCGTTTGATCGAAAATT
CGAAAAATC
Found at i:19346533 original size:6 final size:6
Alignment explanation
Indices: 19346522--19346552 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
19346512 TCATTAGTGC
19346522 CAGCGG CAGCGG CAGCGG CAGCGG CAGCGG C
1 CAGCGG CAGCGG CAGCGG CAGCGG CAGCGG C
19346553 TTCAGGCATT
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:0.16, C:0.35, G:0.48, T:0.00
Consensus pattern (6 bp):
CAGCGG
Found at i:19361019 original size:12 final size:11
Alignment explanation
Indices: 19361004--19361029 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
19360994 TTTTCCTTTC
19361004 TTTTTTTTTTA
1 TTTTTTTTTTA
19361015 TTTTTTTTTTA
1 TTTTTTTTTTA
19361026 TTTT
1 TTTT
19361030 GAGGAAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTTTTA
Found at i:19364150 original size:37 final size:37
Alignment explanation
Indices: 19364100--19364175 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
19364090 ATGCAAAAGT
19364100 ATGGAAGTTGCCATAGACTAGAAGCTACTAAGCTTAA
1 ATGGAAGTTGCCATAGACTAGAAGCTACTAAGCTTAA
19364137 ATGGAAGTTGCCATAGACTAGAAGCTACTAAGCTTAA
1 ATGGAAGTTGCCATAGACTAGAAGCTACTAAGCTTAA
19364174 AT
1 AT
19364176 CAAAAGAATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (37 bp):
ATGGAAGTTGCCATAGACTAGAAGCTACTAAGCTTAA
Found at i:19370753 original size:30 final size:31
Alignment explanation
Indices: 19370713--19370789 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
19370703 GCAATGTAAT
*
19370713 ACAC-AAACTTTAATTT-GATACAATAATAC
1 ACACGAAACTTTGATTTGGATACAATAATAC
* * *
19370742 ACATGAAACTTTGATTTGGATTCAATCATAC
1 ACACGAAACTTTGATTTGGATACAATAATAC
*
19370773 ACACGAAAATTTGATTT
1 ACACGAAACTTTGATTT
19370790 TGATTTTGAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
29 3 0.08
30 11 0.28
31 26 0.65
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.34
Consensus pattern (31 bp):
ACACGAAACTTTGATTTGGATACAATAATAC
Found at i:19370816 original size:21 final size:21
Alignment explanation
Indices: 19370786--19370825 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
19370776 CGAAAATTTG
19370786 ATTTTGATTTTG-ATTCAATAA
1 ATTTTGA-TTTGAATTCAATAA
*
19370807 ATTTTTATTTGAATTCAAT
1 ATTTTGATTTGAATTCAAT
19370826 TATACACATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (21 bp):
ATTTTGATTTGAATTCAATAA
Found at i:19374043 original size:45 final size:45
Alignment explanation
Indices: 19373992--19374081 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
19373982 AAGAACAACA
19373992 CAATCCTATATATGAAAATTTATATACTAAATTCACTAAAATCTT
1 CAATCCTATATATGAAAATTTATATACTAAATTCACTAAAATCTT
19374037 CAATCCTATATATGAAAATTTATATACTAAATTCACTAAAATCTT
1 CAATCCTATATATGAAAATTTATATACTAAATTCACTAAAATCTT
19374082 ACTTCTAAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.44, C:0.16, G:0.02, T:0.38
Consensus pattern (45 bp):
CAATCCTATATATGAAAATTTATATACTAAATTCACTAAAATCTT
Found at i:19376867 original size:11 final size:11
Alignment explanation
Indices: 19376853--19376892 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
19376843 TTATTTTTCA
19376853 TATTTTACTAC
1 TATTTTACTAC
*
19376864 TATTTTACTAT
1 TATTTTACTAC
* *
19376875 TATGTTGCTAC
1 TATTTTACTAC
19376886 TATTTTA
1 TATTTTA
19376893 TTGGTATTAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.25, C:0.12, G:0.05, T:0.57
Consensus pattern (11 bp):
TATTTTACTAC
Found at i:19376971 original size:18 final size:20
Alignment explanation
Indices: 19376948--19376988 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
19376938 TTTATTGATA
*
19376948 TTTTGATGT-TTTTA-ATAT
1 TTTTGATGTATTATATATAT
19376966 TTTTGATGTATTATATATAT
1 TTTTGATGTATTATATATAT
19376986 TTT
1 TTT
19376989 ACAATTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 4 0.20
20 7 0.35
ACGTcount: A:0.24, C:0.00, G:0.10, T:0.66
Consensus pattern (20 bp):
TTTTGATGTATTATATATAT
Found at i:19405001 original size:30 final size:32
Alignment explanation
Indices: 19404957--19405042 Score: 97
Period size: 30 Copynumber: 2.8 Consensus size: 32
19404947 TGTGCCTTTG
*
19404957 TGAAATGATAACAAATATCAACTTTAATTTTT
1 TGAAATGATAACAAATACCAACTTTAATTTTT
* *
19404989 TGAAAT-A-AACAAATACCAACTTTAATTATG
1 TGAAATGATAACAAATACCAACTTTAATTTTT
* *
19405019 TAAAATGGTAA-AACATACCAACTT
1 TGAAATGATAACAA-ATACCAACTT
19405043 GGATGAAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
30 25 0.54
31 3 0.07
32 18 0.39
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.33
Consensus pattern (32 bp):
TGAAATGATAACAAATACCAACTTTAATTTTT
Found at i:19405725 original size:11 final size:11
Alignment explanation
Indices: 19405709--19405742 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
19405699 ATGTCAAATC
19405709 ATTAAGAATAA
1 ATTAAGAATAA
**
19405720 ATTAAGAGCAA
1 ATTAAGAATAA
19405731 ATTAAGAATAA
1 ATTAAGAATAA
19405742 A
1 A
19405743 ACTAGATGCG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.62, C:0.03, G:0.12, T:0.24
Consensus pattern (11 bp):
ATTAAGAATAA
Found at i:19426796 original size:3 final size:3
Alignment explanation
Indices: 19426783--19426812 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
19426773 AATTTCCACT
*
19426783 TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
19426813 GACATATCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:19428273 original size:39 final size:39
Alignment explanation
Indices: 19428219--19428296 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
19428209 CCCCACACCA
19428219 TTTATCATGTTGGATCATCAAGAACAAAAACTAGATGTG
1 TTTATCATGTTGGATCATCAAGAACAAAAACTAGATGTG
19428258 TTTATCATGTTGGATCATCAAGAACAAAAACTAGATGTG
1 TTTATCATGTTGGATCATCAAGAACAAAAACTAGATGTG
19428297 AAAGTGTACC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (39 bp):
TTTATCATGTTGGATCATCAAGAACAAAAACTAGATGTG
Found at i:19430574 original size:4 final size:4
Alignment explanation
Indices: 19430567--19430647 Score: 72
Period size: 4 Copynumber: 19.8 Consensus size: 4
19430557 AAGTTAAAAA
* *** * * **
19430567 AAAG AAAG AAAG AAAG AAAG ATAG AAAG AGTT ACAG AGAG CAAACG TGAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG -AAA-G AAAG
19430617 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
19430648 TAGAAAAGGG
Statistics
Matches: 61, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
4 57 0.93
5 3 0.05
6 1 0.02
ACGTcount: A:0.65, C:0.04, G:0.26, T:0.05
Consensus pattern (4 bp):
AAAG
Found at i:19437434 original size:4 final size:4
Alignment explanation
Indices: 19437427--19437503 Score: 64
Period size: 4 Copynumber: 18.8 Consensus size: 4
19437417 AAGTTAAAAA
* *** * * **
19437427 AAAG AAAG AAAG AAAG AAAG ATAG AAAG AGTT ACAG AGAG CAAACG TGAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG -AAA-G AAAG
19437477 AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAA
19437504 TAGAAAAGGG
Statistics
Matches: 57, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
4 53 0.93
5 3 0.05
6 1 0.02
ACGTcount: A:0.65, C:0.04, G:0.26, T:0.05
Consensus pattern (4 bp):
AAAG
Found at i:19440847 original size:13 final size:13
Alignment explanation
Indices: 19440817--19440859 Score: 68
Period size: 13 Copynumber: 3.2 Consensus size: 13
19440807 TTGGGTTGAG
19440817 AAATTAATTAAGTT
1 AAATTAATTAA-TT
19440831 AAATTAATTAATT
1 AAATTAATTAATT
*
19440844 AAATTAATTGATT
1 AAATTAATTAATT
19440857 AAA
1 AAA
19440860 AAATAATGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
13 17 0.61
14 11 0.39
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (13 bp):
AAATTAATTAATT
Found at i:19443962 original size:4 final size:4
Alignment explanation
Indices: 19443953--19443978 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
19443943 TTAACTACAT
19443953 CCAG CCAG CCAG CCAG CCAG CCAG CC
1 CCAG CCAG CCAG CCAG CCAG CCAG CC
19443979 CCAACAATAC
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:0.23, C:0.54, G:0.23, T:0.00
Consensus pattern (4 bp):
CCAG
Found at i:19446751 original size:12 final size:12
Alignment explanation
Indices: 19446736--19446763 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
19446726 GTGGGGGGCA
19446736 AAGTGCATGTGC
1 AAGTGCATGTGC
19446748 AAGTGCATGTGC
1 AAGTGCATGTGC
19446760 AAGT
1 AAGT
19446764 TCAAGTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.14, G:0.32, T:0.25
Consensus pattern (12 bp):
AAGTGCATGTGC
Found at i:19450703 original size:18 final size:18
Alignment explanation
Indices: 19450680--19450735 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
19450670 CCACCACCAA
19450680 CTCCACTAACCACACTTG
1 CTCCACTAACCACACTTG
*
19450698 CTCCAC-CACCA-A----
1 CTCCACTAACCACACTTG
*
19450710 CTCCACTAGCCACACTTG
1 CTCCACTAACCACACTTG
19450728 CTCCACTA
1 CTCCACTA
19450736 CCTACTCCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 12
0.66 0.07 0.27
Matches are distributed among these distances:
12 6 0.21
13 3 0.10
14 1 0.03
16 1 0.03
17 4 0.14
18 14 0.48
ACGTcount: A:0.27, C:0.48, G:0.05, T:0.20
Consensus pattern (18 bp):
CTCCACTAACCACACTTG
Found at i:19450704 original size:30 final size:30
Alignment explanation
Indices: 19450670--19450768 Score: 171
Period size: 30 Copynumber: 3.3 Consensus size: 30
19450660 CTAGCCTTTG
*
19450670 CCACCACCAACTCCACTAACCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
19450700 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
* *
19450730 CCACTACCTACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
19450760 CCACCACCA
1 CCACCACCA
19450769 CTTGTACCTA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 64 1.00
ACGTcount: A:0.27, C:0.51, G:0.05, T:0.17
Consensus pattern (30 bp):
CCACCACCAACTCCACTAGCCACACTTGCT
Found at i:19450763 original size:18 final size:18
Alignment explanation
Indices: 19450710--19450763 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
19450700 CCACCACCAA
19450710 CTCCACTAGCCACACTTG
1 CTCCACTAGCCACACTTG
*
19450728 CTCCACT----AC-C-TA
1 CTCCACTAGCCACACTTG
19450740 CTCCACTAGCCACACTTG
1 CTCCACTAGCCACACTTG
19450758 CTCCAC
1 CTCCAC
19450764 CACCACTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
12 8 0.29
13 1 0.04
14 2 0.07
16 2 0.07
17 1 0.04
18 14 0.50
ACGTcount: A:0.22, C:0.48, G:0.07, T:0.22
Consensus pattern (18 bp):
CTCCACTAGCCACACTTG
Found at i:19454186 original size:51 final size:51
Alignment explanation
Indices: 19454105--19454207 Score: 154
Period size: 51 Copynumber: 2.0 Consensus size: 51
19454095 TACTGATTTC
* * *
19454105 AGAATGGAAATGAGAGCGAGTTATAATGGATTTTGTATCAGGATTGCCGTT
1 AGAAGGGAAATGAGAGCGAGTTACAATGGATTTTATATCAGGATTGCCGTT
*
19454156 AGAAGGGAAAT-AGGAGCGAGTTACAATGGATTTTATATTAGGATTGCCGTT
1 AGAAGGGAAATGA-GAGCGAGTTACAATGGATTTTATATCAGGATTGCCGTT
19454207 A
1 A
19454208 ACTCCGAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
50 1 0.02
51 46 0.98
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (51 bp):
AGAAGGGAAATGAGAGCGAGTTACAATGGATTTTATATCAGGATTGCCGTT
Found at i:19459776 original size:27 final size:27
Alignment explanation
Indices: 19459704--19459776 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
19459694 TAGGTCTAGC
* *
19459704 GAGATGGTATACGCTAGCAAGCCTGGA
1 GAGATGGTGTACGCTAGTAAGCCTGGA
* * * *
19459731 GAGACGATGTATGCCAGTAAGCCTGGCA
1 GAGATGGTGTACGCTAGTAAGCCTGG-A
19459759 -AGATGGTGTACGCTAGTA
1 GAGATGGTGTACGCTAGTA
19459777 GGTCTGGCGA
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
27 34 0.97
28 1 0.03
ACGTcount: A:0.29, C:0.18, G:0.33, T:0.21
Consensus pattern (27 bp):
GAGATGGTGTACGCTAGTAAGCCTGGA
Found at i:19460839 original size:27 final size:26
Alignment explanation
Indices: 19460809--19460859 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
19460799 CACAAAGGCG
*
19460809 ATATATATAGAGTATGAACACAAAGTT
1 ATATATACAGAGTAT-AACACAAAGTT
*
19460836 ATATATACAGAGTATACCACAAAG
1 ATATATACAGAGTATAACACAAAG
19460860 GTGATTCATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.25
Consensus pattern (26 bp):
ATATATACAGAGTATAACACAAAGTT
Found at i:19466091 original size:20 final size:20
Alignment explanation
Indices: 19466068--19466109 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
19466058 GATTCCATAA
19466068 TTAT-TATTTTATTAAATTTT
1 TTATATATTTT-TTAAATTTT
*
19466088 TTATATATTTTTTAGATTTT
1 TTATATATTTTTTAAATTTT
19466108 TT
1 TT
19466110 TAAAAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (20 bp):
TTATATATTTTTTAAATTTT
Found at i:19468395 original size:52 final size:51
Alignment explanation
Indices: 19468338--19468487 Score: 124
Period size: 47 Copynumber: 3.1 Consensus size: 51
19468328 AAAATATTTG
19468338 GAAAATAACCAATAGTAAATTAGTAAATAATTAGATAAAATATGAATTTTAA
1 GAAAATAACCAATAGTAAATTA-TAAATAATTAGATAAAATATGAATTTTAA
* * * * * *
19468390 GAAAATAA--ATTA-TAAATTA-AATTGAA-AAAATAAAA-A--AA-ATT-G
1 GAAAATAACCAATAGTAAATTATAAAT-AATTAGATAAAATATGAATTTTAA
*
19468432 GAAAACAACCAATAGTAAATTAATAAA-AAGTTAGATAAAATATGAATTTTAA
1 GAAAATAACCAATAGTAAATT-ATAAATAA-TTAGATAAAATATGAATTTTAA
19468484 GAAA
1 GAAA
19468488 GTAGATTATA
Statistics
Matches: 72, Mismatches: 13, Indels: 26
0.65 0.12 0.23
Matches are distributed among these distances:
42 7 0.10
43 2 0.03
44 5 0.07
45 8 0.11
46 2 0.03
47 19 0.26
48 3 0.04
49 7 0.10
50 5 0.07
51 2 0.03
52 12 0.17
ACGTcount: A:0.60, C:0.03, G:0.09, T:0.27
Consensus pattern (51 bp):
GAAAATAACCAATAGTAAATTATAAATAATTAGATAAAATATGAATTTTAA
Found at i:19468436 original size:94 final size:97
Alignment explanation
Indices: 19468325--19468514 Score: 307
Period size: 94 Copynumber: 2.0 Consensus size: 97
19468315 TTAGAAACTC
* *
19468325 AAAAAAATATTTGGAAAATAACCAATAGTAAATTAGTAAATAA-TTAGATAAAATATGAATTTTA
1 AAAAAAATATTTGGAAAACAACCAATAGTAAATTAATAAA-AAGTTAGATAAAATATGAATTTTA
19468389 AGAAAATAAATTATAA-ATTAAATTGAAAAAAT
65 AGAAAATAAATTATAATATTAAATTGAAAAAAT
19468421 AAAAAAA-A-TTGGAAAACAACCAATAGTAAATTAATAAAAAGTTAGATAAAATATGAATTTTAA
1 AAAAAAATATTTGGAAAACAACCAATAGTAAATTAATAAAAAGTTAGATAAAATATGAATTTTAA
* *
19468484 GAAAGTAGATTATAATATTAAATTGAAAAAA
66 GAAAATAAATTATAATATTAAATTGAAAAAA
19468515 AAAGTAAAGT
Statistics
Matches: 88, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
93 2 0.02
94 63 0.72
95 16 0.18
96 7 0.08
ACGTcount: A:0.59, C:0.03, G:0.09, T:0.28
Consensus pattern (97 bp):
AAAAAAATATTTGGAAAACAACCAATAGTAAATTAATAAAAAGTTAGATAAAATATGAATTTTAA
GAAAATAAATTATAATATTAAATTGAAAAAAT
Found at i:19470792 original size:36 final size:36
Alignment explanation
Indices: 19470752--19470823 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
19470742 AAAATTAAAA
*
19470752 GTATAACTTTTAAATTGAAATAATGAAAAATTATTT
1 GTATAACTTCTAAATTGAAATAATGAAAAATTATTT
19470788 GTATAACTTCTAAATTGAAATAATGAAAAATTATTT
1 GTATAACTTCTAAATTGAAATAATGAAAAATTATTT
19470824 TAAAAAATAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.40
Consensus pattern (36 bp):
GTATAACTTCTAAATTGAAATAATGAAAAATTATTT
Done.