Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 202 of 206
Found at i:61135801 original size:15 final size:16
Alignment explanation
Indices: 61135769--61135808 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
61135759 GCAAACAAAG
*
61135769 AAGAAA-AAAAGAGCA
1 AAGAAAGAAAAGAGAA
61135784 AAGAAAGAAAAGA-AA
1 AAGAAAGAAAAGAGAA
61135799 AAG-AAGAAAA
1 AAGAAAGAAAA
61135809 TAGGGGAGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 7 0.30
15 10 0.43
16 6 0.26
ACGTcount: A:0.78, C:0.03, G:0.20, T:0.00
Consensus pattern (16 bp):
AAGAAAGAAAAGAGAA
Found at i:61135893 original size:4 final size:4
Alignment explanation
Indices: 61135884--61135939 Score: 55
Period size: 4 Copynumber: 14.2 Consensus size: 4
61135874 GGGCTGATCG
* *
61135884 AGAA AGAA AGAA AGGAA GGAA AG-A AG-A AGAA AGAA AGAA GAAAA AGAA
1 AGAA AGAA AGAA A-GAA AGAA AGAA AGAA AGAA AGAA AGAA -AGAA AGAA
61135932 AG-A AGAA A
1 AGAA AGAA A
61135940 ATGGGAAGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
3 9 0.20
4 29 0.66
5 6 0.14
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:61135926 original size:21 final size:20
Alignment explanation
Indices: 61135887--61135982 Score: 69
Period size: 18 Copynumber: 4.9 Consensus size: 20
61135877 CTGATCGAGA
61135887 AAGAAAGAAAGGAAGGAAAGAAG
1 AAGAAAGAAA-GAA-GAAA-AAG
61135910 AAGAAAGAAAGAAGAAAAAG
1 AAGAAAGAAAGAAGAAAAAG
* **
61135930 AA-AGAAGAAA-ATG-GGAAG
1 AAGA-AAGAAAGAAGAAAAAG
*
61135948 AAG-AAGGAAGAA-AAAAAG
1 AAGAAAGAAAGAAGAAAAAG
*
61135966 AA-AAAGAAAAAAGAAAA
1 AAGAAAGAAAGAAGAAAA
61135983 TAATTTTTTT
Statistics
Matches: 58, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
17 5 0.09
18 18 0.31
19 7 0.12
20 11 0.19
21 4 0.07
22 3 0.05
23 10 0.17
ACGTcount: A:0.72, C:0.00, G:0.27, T:0.01
Consensus pattern (20 bp):
AAGAAAGAAAGAAGAAAAAG
Found at i:61136903 original size:18 final size:18
Alignment explanation
Indices: 61136880--61136922 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
61136870 CAAAAAAAAA
*
61136880 TTCGTGTTTTCACAAATT
1 TTCGTGTTTTCAAAAATT
61136898 TTCGTGTTTTCAAAAATT
1 TTCGTGTTTTCAAAAATT
61136916 TTCGTGT
1 TTCGTGT
61136923 AAAAAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.51
Consensus pattern (18 bp):
TTCGTGTTTTCAAAAATT
Found at i:61146246 original size:74 final size:73
Alignment explanation
Indices: 61146068--61147126 Score: 1130
Period size: 74 Copynumber: 14.0 Consensus size: 73
61146058 TTTTCAAAAA
* * * * **
61146068 AAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTTATGCCGTTGTATTTCTTTTAAAT
1 AAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA--T-TTTT-AAT
* * **
61146133 TTT-TGTTCTTCA
61 TTTGTCTTTTTTT
61146145 AAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTTGG
1 AAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTT-G
61146210 TCTTTTTTT
65 TCTTTTTTT
* *
61146219 AAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACACTGAGGTATTTTTAATTTCGG
1 AAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTT-TG
61146284 T-TTTTTTT
65 TCTTTTTTT
* * *
61146292 TAAATCAACTCATAATACAGAAGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTCGG
1 AAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTT-TG
61146357 TCTTTTTTT
65 TCTTTTTTT
*
61146366 AAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTCGG
1 AAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTT-TG
61146431 TCTTTTTTT
65 TCTTTTTTT
61146440 AAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTCTG
1 AAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTT-TG
61146505 TC-TTTTTT
65 TCTTTTTTT
*
61146513 AAAATCAACTCATAATACAGAGATGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTATG
1 AAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTT-TG
61146578 TCTTTTTTTT
65 TC-TTTTTTT
* **
61146588 TAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAAATATTTTTAATTTATG
1 AAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTT-TG
61146653 TC-TTTTTT
65 TCTTTTTTT
*
61146661 -AAATCAACTCATAATACAGAGGTGAGTTGAGCCTTGGGTCACGCTGAGGTATTTTTAATTTATG
1 AAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTT-TG
61146725 TCTTTTTTT
65 TCTTTTTTT
* *
61146734 -AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACG-TCGAGGTATTTCTTTTA
1 AAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGT--CACGCT-GAGGTA--T-TTTT-
* **
61146797 AATTTT-TGTTTTTCA
58 AATTTTGTCTTTTTTT
* * * *
61146812 AAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAGGTCATACGCTGAGGTATTTTTTTAAT
1 AAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTC--ACGCTGAGGTA--TTTTTAAT
**
61146877 TTCTGT-TTTTTCAAA
61 TT-TGTCTTTTT--TT
* * *
61146892 AAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGTCACATGCCGAGGTATTTCTTTTAA
1 AAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCAC--GCTGAGGTA--T-TTTTAA
* * * **
61146957 ATTTCTATTTTTCAAAAAAA
60 TTTTGTCTTTTT------TT
* * *
61146977 AAAACTCAACTCATATTACAGATGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTCTTTTAAAT
1 AAAA-TCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA--T-TTTTAATT
* * **
61147042 TTCTGTTTTTCA
62 TTGTCTTTTTTT
* * * * *
61147054 AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGCCACACGCCGAGGTATTTTCAATTT
1 AAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGG--TCACGCTGAGGTATTTTTAATTT
61147119 CTGT-TTTT
63 -TGTCTTTT
61147127 CAAATAAAAA
Statistics
Matches: 890, Mismatches: 56, Indels: 73
0.87 0.05 0.07
Matches are distributed among these distances:
72 69 0.08
73 172 0.19
74 235 0.26
75 70 0.08
76 63 0.07
77 51 0.06
78 19 0.02
79 67 0.08
80 60 0.07
81 13 0.01
83 29 0.03
85 30 0.03
86 12 0.01
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (73 bp):
AAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTTGT
CTTTTTTT
Found at i:61146318 original size:147 final size:146
Alignment explanation
Indices: 61146068--61147126 Score: 1128
Period size: 147 Copynumber: 7.0 Consensus size: 146
61146058 TTTTCAAAAA
* * * * **
61146068 AAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTTATGCCGTTGTATTTCTTTTAAAT
1 AAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA--T-TTTT-AAT
** * **
61146133 TTTTG-TTCTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA
61 TTCGGTTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA
61146197 TTTTTAATTTTGGTCTTTTTTT
126 TTTTTAATTTT-GTCTTTTTTT
*
61146219 AAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACACTGAGGTATTTTTAATTTCGG
1 AAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTCGG
* *
61146284 TTTTTTTTTAAATCAACTCATAATACAGAAGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTT
66 TTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTT
*
61146349 AATTTCGGTCTTTTTTT
131 AATTT-TGTCTTTTTTT
61146366 AAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTCGG
1 AAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTCGG
61146431 TCTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTT
66 T-TTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTT
61146496 TAATTTCTGTC-TTTTTT
130 TAATTT-TGTCTTTTTTT
* *
61146513 AAAATCAACTCATAATACAGAGATGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTATG
1 AAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTT-CG
* * **
61146578 TCTTTTTTTTTAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAAATATTT
65 -GTTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
61146643 TTAATTTATGTC-TTTTTT
129 TTAATTT-TGTCTTTTTTT
* **
61146661 -AAATCAACTCATAATACAGAGGTGAGTTGAGCCTTGGGTCACGCTGAGGTATTTTTAATTTATG
1 AAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTCGG
* *
61146725 TCTTTTTTT-AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACG-TCGAGGTA
66 T-TTTTTTTAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGT--CACGCT-GAGGTA
* **
61146788 TTTCTTTTAAATTTT-TGTTTTTCA
126 --T-TTTT-AATTTTGTCTTTTTTT
* * * *
61146812 AAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAGGTCATACGCTGAGGTATTTTTTTAAT
1 AAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTC--ACGCTGAGGTA--TTTTTAAT
* ** * * *
61146877 TTCTGTTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGTCACATGCCG
61 TTCGGTTTTTT--TTAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCAC--GCTG
* * * **
61146942 AGGTATTTCTTTTAAATTTCTATTTTTCAAAAAAA
121 AGGTA--T-TTTTAATTTTGTCTTTTT------TT
* *
61146977 AAAACTCAACTCATATTACAGATGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTCTTTTAAAT
1 AAAA-TCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA--T-TTTT-AAT
* ** * * * *
61147042 TTCTG-TTTTTCAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGCCACACGCCGAG
61 TTCGGTTTTTTTTAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGG--TCACGCTGAG
*
61147106 GTATTTTCAATTTCTGT-TTTT
123 GTATTTTTAATTT-TGTCTTTT
61147127 CAAATAAAAA
Statistics
Matches: 804, Mismatches: 64, Indels: 72
0.86 0.07 0.08
Matches are distributed among these distances:
145 16 0.02
146 35 0.04
147 270 0.34
148 157 0.20
149 1 0.00
150 30 0.04
151 26 0.03
152 20 0.02
153 20 0.02
155 11 0.01
156 5 0.01
157 16 0.02
158 5 0.01
159 70 0.09
160 3 0.00
162 47 0.06
163 14 0.02
164 12 0.01
165 33 0.04
166 13 0.02
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (146 bp):
AAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAATTTCGG
TTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTT
AATTTTGTCTTTTTTT
Found at i:61146528 original size:221 final size:223
Alignment explanation
Indices: 61146068--61147119 Score: 1189
Period size: 221 Copynumber: 4.6 Consensus size: 223
61146058 TTTTCAAAAA
* * * * * **
61146068 AAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTTATGCCGTTGTATTTCTTTTAAAT
1 AAAATCAACTCATAATAC-AGAAGTGAGTTGAGCCTCGGGTCACGCTGAGGTA-TTCTTTTAAAT
* * *
61146133 TT-TTGTTCTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA
64 TTCGTCTTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA
*
61146197 TTTTTAATTTTGGTCTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCAC
129 TTTTTAATTTCGGTCTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCAC
* * *
61146262 ACTGAGGTATTTTTAATTTCGGTTTTTTTT
194 GCTGAGGTATTTTTAATTTCTGTCTTTTTT
*
61146292 TAAATCAACTCATAATACAGAAGTGAGTTGAGCCTCGGGTCACGCTGAGGTA-T-TTTT-AATTT
1 AAAATCAACTCATAATACAGAAGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTCTTTTAAATTT
**
61146354 CGGTCTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTAT
66 C-GTCTTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTAT
61146419 TTTTAATTTCGGTCTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACG
130 TTTTAATTTCGGTCTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACG
61146484 CTGAGGTATTTTTAATTTCTGTCTTTTTT
195 CTGAGGTATTTTTAATTTCTGTCTTTTTT
61146513 AAAATCAACTCATAATACAG-AGATGAGTTGAGCCTCGGGTCACGCTGAGGTA-T-TTTT-AATT
1 AAAATCAACTCATAATACAGAAG-TGAGTTGAGCCTCGGGTCACGCTGAGGTATTCTTTTAAATT
* *** **
61146574 TATGTCTTTTTTTTTAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAAAT
65 T-CGTC-TTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGT
** *
61146639 ATTTTTAATTTATGTC-TTTTTT-AAATCAACTCATAATACAGAGGTGAGTTGAGCCTTGGGTCA
128 ATTTTTAATTTCGGTCTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCA
*
61146702 CGCTGAGGTATTTTTAATTTATGTCTTTTTT
193 CGCTGAGGTATTTTTAATTTCTGTCTTTTTT
* * * *
61146733 TAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACG-TCGAGGTATTTCTTTTA
1 AAAATCAACTCATAATAC-AGAAGTGAGTTGAGCCTCGGGT--CACGCT-GAGGTA-TTCTTTTA
* * * * * *
61146797 AATTT-TTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAGGTCATACGCT
61 AATTTCGTCTTTTTCAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTC--ACGCT
* ** *
61146861 GAGGTATTTTTTTAATTTCTGT-TTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAG
123 GAGGTA--TTTTTAATTTCGGTCTTTTT--TTAAAATCAACTCATAATAC-AGAGGTGAGTTGAG
* * * **
61146925 CCTCAGGTCACATGCCGAGGTATTTCTTTTAAATTTCTAT-TTTTCAAAAAAA
183 CCTCGGGTCAC--GCTGAGGTA--T-TTTT-AATTTCTGTCTTTT------TT
* *
61146977 AAAACTCAACTCATATTACAGATGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTCTTTTAAAT
1 AAAA-TCAACTCATAATACAGAAGTGAGTTGAGCCTCGGGTCACGCTGAGGTA-TTCTTTTAAAT
* * * * *
61147042 TTC-TGTTTTTCAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGCCACACGCCGAG
64 TTCGTCTTTTTCAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGG--TCACGCTGAG
*
61147106 GTATTTTCAATTTC
126 GTATTTTTAATTTC
61147120 TGTTTTTCAA
Statistics
Matches: 726, Mismatches: 61, Indels: 66
0.85 0.07 0.08
Matches are distributed among these distances:
219 5 0.01
220 91 0.13
221 235 0.32
222 71 0.10
223 38 0.05
224 36 0.05
225 23 0.03
226 4 0.01
227 14 0.02
229 17 0.02
232 16 0.02
233 23 0.03
235 8 0.01
237 1 0.00
238 8 0.01
239 7 0.01
240 10 0.01
242 80 0.11
243 1 0.00
244 25 0.03
245 13 0.02
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (223 bp):
AAAATCAACTCATAATACAGAAGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTCTTTTAAATTT
CGTCTTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
TTTAATTTCGGTCTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGC
TGAGGTATTTTTAATTTCTGTCTTTTTT
Found at i:61147324 original size:29 final size:28
Alignment explanation
Indices: 61147290--61147374 Score: 100
Period size: 29 Copynumber: 3.0 Consensus size: 28
61147280 ACAAAAATAA
61147290 AAAATTACATTTTGACCCCTAAAATTTTT
1 AAAATTACATTTTGACCCCT-AAATTTTT
* * * * *
61147319 GAAATTTCACTTTAACCCCTCAACTTTTT
1 AAAATTACATTTTGACCCCT-AAATTTTT
61147348 AAAATTACATTTTGA-CCCTAAATTTTT
1 AAAATTACATTTTGACCCCTAAATTTTT
61147375 CTCAAAATTA
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
27 7 0.16
28 4 0.09
29 34 0.76
ACGTcount: A:0.34, C:0.20, G:0.04, T:0.42
Consensus pattern (28 bp):
AAAATTACATTTTGACCCCTAAATTTTT
Found at i:61147760 original size:22 final size:21
Alignment explanation
Indices: 61147724--61147787 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 21
61147714 AGCAAAGATA
*
61147724 CAAA-AAAGTAAAAAAAAATAG
1 CAAACAAAG-AAAAAAAAAGAG
61147745 CAAACAAAGAAGAAAAAAAGAG
1 CAAACAAAGAA-AAAAAAAGAG
*
61147767 CAAAGAAAGAAAAGAAAAAGA
1 CAAACAAAGAAAA-AAAAAGA
61147788 AGAAAATAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
21 8 0.21
22 30 0.79
ACGTcount: A:0.75, C:0.06, G:0.16, T:0.03
Consensus pattern (21 bp):
CAAACAAAGAAAAAAAAAGAG
Found at i:61147786 original size:15 final size:16
Alignment explanation
Indices: 61147754--61147793 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
61147744 GCAAACAAAG
*
61147754 AAGAAA-AAAAGAGCA
1 AAGAAAGAAAAGAGAA
61147769 AAGAAAGAAAAGA-AA
1 AAGAAAGAAAAGAGAA
61147784 AAG-AAGAAAA
1 AAGAAAGAAAA
61147794 TAGGGGAGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 7 0.30
15 10 0.43
16 6 0.26
ACGTcount: A:0.78, C:0.03, G:0.20, T:0.00
Consensus pattern (16 bp):
AAGAAAGAAAAGAGAA
Found at i:61147879 original size:4 final size:4
Alignment explanation
Indices: 61147870--61147924 Score: 53
Period size: 4 Copynumber: 14.0 Consensus size: 4
61147860 GGCTGATCGG
* *
61147870 GAAA GAAA GAAA GGAAG GAAA G-AA G-AA GAAA GAAA GAAGA AAAA GAAA
1 GAAA GAAA GAAA -GAAA GAAA GAAA GAAA GAAA GAAA GAA-A GAAA GAAA
61147918 G-AA GAAA
1 GAAA GAAA
61147925 ATGGGAAGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
3 9 0.21
4 28 0.65
5 6 0.14
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:61147919 original size:21 final size:22
Alignment explanation
Indices: 61147870--61147966 Score: 75
Period size: 24 Copynumber: 4.5 Consensus size: 22
61147860 GGCTGATCGG
61147870 GAAAGAAAGAAAGGAAGGAAAGAA
1 GAAAGAAAGAAAGGAA-GAAA-AA
61147894 G-AAGAAAGAAA-GAAGAAAAA
1 GAAAGAAAGAAAGGAAGAAAAA
*
61147914 GAAAG-AAGAAAATGGGAAGAAGAA
1 GAAAGAAAG-AAA--GGAAGAAAAA
*
61147938 GGAAG-AA-AAA--AAGAAAAA
1 GAAAGAAAGAAAGGAAGAAAAA
61147956 GAAA-AAAGAAA
1 GAAAGAAAGAAA
61147967 ATAATTTTTT
Statistics
Matches: 62, Mismatches: 4, Indels: 19
0.73 0.05 0.22
Matches are distributed among these distances:
18 12 0.19
19 3 0.05
20 6 0.10
21 10 0.16
22 6 0.10
23 10 0.16
24 15 0.24
ACGTcount: A:0.71, C:0.00, G:0.28, T:0.01
Consensus pattern (22 bp):
GAAAGAAAGAAAGGAAGAAAAA
Found at i:61147967 original size:21 final size:21
Alignment explanation
Indices: 61147887--61147967 Score: 65
Period size: 21 Copynumber: 3.9 Consensus size: 21
61147877 AGAAAGGAAG
* *
61147887 GAAAGAAGAAGAAAG-AAAGAA
1 GAAA-AAGAAAAAAGAAAAAAA
* ***
61147908 GAAAAAGAAAGAAGAAAATGG
1 GAAAAAGAAAAAAGAAAAAAA
* **
61147929 GAAGAAGAAGGAAGAAAAAAA
1 GAAAAAGAAAAAAGAAAAAAA
61147950 GAAAAAGAAAAAAGAAAA
1 GAAAAAGAAAAAAGAAAA
61147968 TAATTTTTTT
Statistics
Matches: 46, Mismatches: 13, Indels: 2
0.75 0.21 0.03
Matches are distributed among these distances:
20 8 0.17
21 38 0.83
ACGTcount: A:0.73, C:0.00, G:0.26, T:0.01
Consensus pattern (21 bp):
GAAAAAGAAAAAAGAAAAAAA
Found at i:61148316 original size:16 final size:16
Alignment explanation
Indices: 61148295--61148338 Score: 65
Period size: 14 Copynumber: 2.9 Consensus size: 16
61148285 CCAACCAGAA
61148295 AAAAAAAAGAAGAAAG
1 AAAAAAAAGAAGAAAG
61148311 AAAAAAAAG-A-AAAG
1 AAAAAAAAGAAGAAAG
*
61148325 GAAAAAAAGAAGAA
1 AAAAAAAAGAAGAA
61148339 GAAGAGGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 12 0.48
15 2 0.08
16 11 0.44
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AAAAAAAAGAAGAAAG
Found at i:61148891 original size:18 final size:18
Alignment explanation
Indices: 61148829--61148912 Score: 84
Period size: 18 Copynumber: 4.8 Consensus size: 18
61148819 CGTCATTCAG
**
61148829 AAAAATTTTTATGTTTTC
1 AAAAATTTTCGTGTTTTC
*
61148847 AACAA--TTCGTG-TTTC
1 AAAAATTTTCGTGTTTTC
**
61148862 AAAAAAAATTCGTGTTTTC
1 -AAAAATTTTCGTGTTTTC
*
61148881 ACAAATTTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
61148899 AAAAATTTTCGTGT
1 AAAAATTTTCGTGT
61148913 AAAAAAAAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
15 4 0.07
16 8 0.15
18 38 0.70
19 4 0.07
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (18 bp):
AAAAATTTTCGTGTTTTC
Found at i:61151058 original size:42 final size:42
Alignment explanation
Indices: 61151005--61151202 Score: 270
Period size: 42 Copynumber: 4.7 Consensus size: 42
61150995 TTATACAAAG
* * *
61151005 CGCCGTTAAAGAACATGTTCTTTAGCGGCGCTTATAGAAAAA
1 CGCCGCTAAAGAACATGTTCTTCAGCGGCGCTTAGAGAAAAA
* *
61151047 CGCTGCTAAAGAACATGTTCTTCAGCGGCGCTTAAAGAAAAA
1 CGCCGCTAAAGAACATGTTCTTCAGCGGCGCTTAGAGAAAAA
* *
61151089 CGCCGCTTAAGAACATGTTCTTCAGCGGCGCTTAGAAAAAAA
1 CGCCGCTAAAGAACATGTTCTTCAGCGGCGCTTAGAGAAAAA
* * * *
61151131 CGCCACTAAAGACCATGTTCTTTAGCGGCGCTTAGATAAAAA
1 CGCCGCTAAAGAACATGTTCTTCAGCGGCGCTTAGAGAAAAA
* * *
61151173 CACCGCTAAAGACCATGTTCTTCAGTGGCG
1 CGCCGCTAAAGAACATGTTCTTCAGCGGCG
61151203 TTTTTTTCTA
Statistics
Matches: 139, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 139 1.00
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.23
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGTTCTTCAGCGGCGCTTAGAGAAAAA
Found at i:61151116 original size:84 final size:84
Alignment explanation
Indices: 61151005--61151244 Score: 275
Period size: 84 Copynumber: 2.9 Consensus size: 84
61150995 TTATACAAAG
* *
61151005 CGCCG-TTAAAGAACATGTTCTTTAGCGGCGCTTATAGAAAAACGCTGCTAAAGAACATGTTCTT
1 CGCCGCTT-AAGAACATGTTCTTCAGCGGCGCTTATAAAAAAACGCTGCTAAAGAACATGTTCTT
*
61151069 CAGCGGCGCTTAAAGAAAAA
65 TAGCGGCGCTTAAAGAAAAA
* ** *
61151089 CGCCGCTTAAGAACATGTTCTTCAGCGGCGCTTAGAAAAAAACGCCACTAAAGACCATGTTCTTT
1 CGCCGCTTAAGAACATGTTCTTCAGCGGCGCTTATAAAAAAACGCTGCTAAAGAACATGTTCTTT
* *
61151154 AGCGGCGCTTAGATAAAAA
66 AGCGGCGCTTAAAGAAAAA
* * * * * * **** * *
61151173 CACCGCTAAAGACCATGTTCTTCAGTGGCGTTTTTTTCTAAGCGCTGCTAAAGAACATGATCTTT
1 CGCCGCTTAAGAACATGTTCTTCAGCGGCGCTTATAAAAAAACGCTGCTAAAGAACATGTTCTTT
61151238 AGCGGCG
66 AGCGGCG
61151245 TTTTTGGTTG
Statistics
Matches: 130, Mismatches: 25, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
84 128 0.98
85 2 0.02
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (84 bp):
CGCCGCTTAAGAACATGTTCTTCAGCGGCGCTTATAAAAAAACGCTGCTAAAGAACATGTTCTTT
AGCGGCGCTTAAAGAAAAA
Found at i:61154088 original size:36 final size:36
Alignment explanation
Indices: 61154005--61154105 Score: 112
Period size: 36 Copynumber: 2.8 Consensus size: 36
61153995 TAAGCCATCT
* * * * * *
61154005 ATTGACAATATAAAATGCAAGAGGTGTGCAAATTGTTT
1 ATTGACGATATAAAATGTAA-A-ATGTGCAAACTATTC
*
61154043 ATTGACGATATGAAATGTAAAATGTGCAAACTATTC
1 ATTGACGATATAAAATGTAAAATGTGCAAACTATTC
*
61154079 ATTGGCGATATAAAATGTAAAATGTGC
1 ATTGACGATATAAAATGTAAAATGTGC
61154106 TATCGTTGGC
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
36 36 0.67
37 1 0.02
38 17 0.31
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.31
Consensus pattern (36 bp):
ATTGACGATATAAAATGTAAAATGTGCAAACTATTC
Found at i:61154118 original size:31 final size:33
Alignment explanation
Indices: 61154043--61154134 Score: 107
Period size: 31 Copynumber: 2.8 Consensus size: 33
61154033 CAAATTGTTT
* *
61154043 ATTGACGATATGAAATGTAAAATGTGCAAACTATTC
1 ATTGGCGATATAAAATGTAAAATGTG---ACTATTC
61154079 ATTGGCGATATAAAATGTAAAATGTG-CTA-TC
1 ATTGGCGATATAAAATGTAAAATGTGACTATTC
* *
61154110 GTTGGCGATGTAAAATGTAAAATGT
1 ATTGGCGATATAAAATGTAAAATGT
61154135 AAAATGTGTG
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
31 25 0.48
32 3 0.06
36 24 0.46
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.32
Consensus pattern (33 bp):
ATTGGCGATATAAAATGTAAAATGTGACTATTC
Found at i:61154129 original size:7 final size:7
Alignment explanation
Indices: 61154117--61154141 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
61154107 ATCGTTGGCG
61154117 ATGTAAA
1 ATGTAAA
61154124 ATGTAAA
1 ATGTAAA
61154131 ATGTAAA
1 ATGTAAA
61154138 ATGT
1 ATGT
61154142 GTGATCATTG
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:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (7 bp):
ATGTAAA
Found at i:61154140 original size:38 final size:38
Alignment explanation
Indices: 61154089--61154169 Score: 128
Period size: 38 Copynumber: 2.1 Consensus size: 38
61154079 ATTGGCGATA
*
61154089 TAAAATGTAAAATGTGCT-ATCGTTGGCGATGTAAAATG
1 TAAAATGTAAAATGTG-TGATCATTGGCGATGTAAAATG
*
61154127 TAAAATGTAAAATGTGTGATCATTGGTGATGTAAAATG
1 TAAAATGTAAAATGTGTGATCATTGGCGATGTAAAATG
61154165 TAAAA
1 TAAAA
61154170 GGTGCAAACT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
37 1 0.03
38 39 0.98
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (38 bp):
TAAAATGTAAAATGTGTGATCATTGGCGATGTAAAATG
Found at i:61154500 original size:60 final size:59
Alignment explanation
Indices: 61154388--61154502 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 59
61154378 TCACTTTCGT
* * * **
61154388 GGAGAGCCACAAAGAGTTCACGGAGGAGCCCGAATATTGAATATATGCCTCACCTCCAC
1 GGAGAGCCACAAAAAGTTCACGGAGGAGCCCGAATACTGAAGATACACCTCACCTCCAC
* * * *
61154447 GGAGAGCCATAAAAAGGTTCACGGAGGGGCCTGAATACTGAAGATACATCTCACCT
1 GGAGAGCCACAAAAA-GTTCACGGAGGAGCCCGAATACTGAAGATACACCTCACCT
61154503 ATGTGGAGAG
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
59 13 0.28
60 33 0.72
ACGTcount: A:0.33, C:0.24, G:0.25, T:0.17
Consensus pattern (59 bp):
GGAGAGCCACAAAAAGTTCACGGAGGAGCCCGAATACTGAAGATACACCTCACCTCCAC
Found at i:61156110 original size:35 final size:34
Alignment explanation
Indices: 61156023--61156110 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
61156013 AGTAACAAAT
*
61156023 GTCCTACTCCCACATATGGGGGTAGGCTTACGAG
1 GTCCTACTCCCACACATGGGGGTAGGCTTACGAG
* *
61156057 GTTCTTGCTCCCACACATGGGGG-AGGCTTACGGGAG
1 G-TCCTACTCCCACACATGGGGGTAGGCTTAC--GAG
* *
61156093 GTCCTACTCTCATACATG
1 GTCCTACTCCCACACATG
61156111 AAGAGTAACG
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
34 9 0.20
35 31 0.70
36 4 0.09
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (34 bp):
GTCCTACTCCCACACATGGGGGTAGGCTTACGAG
Found at i:61158507 original size:18 final size:18
Alignment explanation
Indices: 61158484--61158519 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
61158474 GTTTTATTCA
61158484 AAGATTTCTAGGTTTTCT
1 AAGATTTCTAGGTTTTCT
* *
61158502 AAGATTTTTGGGTTTTCT
1 AAGATTTCTAGGTTTTCT
61158520 CATTCAGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.19, T:0.53
Consensus pattern (18 bp):
AAGATTTCTAGGTTTTCT
Found at i:61158798 original size:20 final size:18
Alignment explanation
Indices: 61158766--61158809 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
61158756 TAATTATTTC
*
61158766 TTATATATATTTTAGAGT
1 TTATATATATTTTAGAAT
*
61158784 TTATATATAATTTTTATAAT
1 TTATATAT-A-TTTTAGAAT
61158804 TTATAT
1 TTATAT
61158810 TTAGATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 8 0.36
19 1 0.05
20 13 0.59
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (18 bp):
TTATATATATTTTAGAAT
Found at i:61158876 original size:2 final size:2
Alignment explanation
Indices: 61158869--61158895 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
61158859 TAGAGTTTAC
61158869 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
61158896 CTTTTTATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:61158931 original size:81 final size:81
Alignment explanation
Indices: 61158776--61158927 Score: 186
Period size: 81 Copynumber: 1.9 Consensus size: 81
61158766 TTATATATAT
* * * * * * *
61158776 TTTAGAGTTTATATATAATTTTTATAATTTATATTTAGATTTTATATAGTTTTTTTTCTCAATTT
1 TTTAGAGTTTACATATAATATATATAATATATATATAGATTTTATATAGTTTGTTTCCTCAATTT
61158841 TTATATATTTAATTAG
66 TTATATATTTAATTAG
*
61158857 TTTAGAGTTTACATATATATATATATATATATATATATA-CTTTT-TATAGTTTGTTTCCT--AT
1 TTTAGAGTTTACATATA-ATATATATA-ATATATATATAGATTTTATATAGTTTGTTTCCTCAAT
61158918 TTTTATATAT
64 TTTTATATAT
61158928 ATTTTTAGAT
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
79 12 0.20
81 29 0.48
82 11 0.18
83 9 0.15
ACGTcount: A:0.32, C:0.04, G:0.06, T:0.59
Consensus pattern (81 bp):
TTTAGAGTTTACATATAATATATATAATATATATATAGATTTTATATAGTTTGTTTCCTCAATTT
TTATATATTTAATTAG
Found at i:61159653 original size:21 final size:22
Alignment explanation
Indices: 61159613--61159667 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
61159603 TAGTGAGATG
61159613 ACAACAAAACAATGGAAAAATA
1 ACAACAAAACAATGGAAAAATA
* * *
61159635 GCAGCAAAATAAT-GAAAAATA
1 ACAACAAAACAATGGAAAAATA
61159656 ACAACAAAACAA
1 ACAACAAAACAA
61159668 CAAGTTTTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.67, C:0.15, G:0.09, T:0.09
Consensus pattern (22 bp):
ACAACAAAACAATGGAAAAATA
Found at i:61160528 original size:19 final size:18
Alignment explanation
Indices: 61160483--61160528 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
61160473 TTTTTTATTA
*
61160483 TATTTTTTTCTATTTTCT
1 TATTTTTTTCCATTTTCT
*
61160501 AATTATTTTTCCATTTTCCT
1 TATT-TTTTTCCATTTT-CT
61160521 TATTTTTT
1 TATTTTTT
61160529 GAATTTATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 3 0.13
19 15 0.65
20 5 0.22
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (18 bp):
TATTTTTTTCCATTTTCT
Found at i:61161407 original size:2 final size:2
Alignment explanation
Indices: 61161400--61161428 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
61161390 AAACTTTCTT
61161400 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
61161429 TGCAGCCCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:61166061 original size:14 final size:14
Alignment explanation
Indices: 61166042--61166078 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
61166032 CAGCAAAAAG
61166042 AAACAGAAGTTGCA
1 AAACAGAAGTTGCA
*
61166056 AAACAGAATTTGCA
1 AAACAGAAGTTGCA
*
61166070 AAACTGAAG
1 AAACAGAAG
61166079 CAAGAAGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.51, C:0.14, G:0.19, T:0.16
Consensus pattern (14 bp):
AAACAGAAGTTGCA
Found at i:61170692 original size:14 final size:14
Alignment explanation
Indices: 61170673--61170709 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
61170663 CAGCAAAAAG
61170673 AAACAGAAGTTGCA
1 AAACAGAAGTTGCA
*
61170687 AAACAGAATTTGCA
1 AAACAGAAGTTGCA
*
61170701 AAACTGAAG
1 AAACAGAAG
61170710 CAAGAAGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.51, C:0.14, G:0.19, T:0.16
Consensus pattern (14 bp):
AAACAGAAGTTGCA
Found at i:61177741 original size:11 final size:11
Alignment explanation
Indices: 61177725--61177750 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
61177715 ATATTTGTCT
61177725 TTATATTGATA
1 TTATATTGATA
61177736 TTATATTGATA
1 TTATATTGATA
61177747 TTAT
1 TTAT
61177751 TTATATCCTT
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:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (11 bp):
TTATATTGATA
Found at i:61178011 original size:4 final size:4
Alignment explanation
Indices: 61178004--61178034 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
61177994 TTATGAATAT
61178004 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
61178035 TTTTTATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:61178069 original size:16 final size:15
Alignment explanation
Indices: 61178028--61178069 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
61178018 ACATACATAC
61178028 ATAC-ATATTTTTAT
1 ATACTATATTTTTAT
*
61178042 ATTCTATAATTTTTAT
1 ATACTAT-ATTTTTAT
61178058 ATACATATATTT
1 ATAC-TATATTT
61178070 GCACATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 3 0.13
15 2 0.09
16 15 0.65
17 3 0.13
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (15 bp):
ATACTATATTTTTAT
Found at i:61182555 original size:18 final size:17
Alignment explanation
Indices: 61182529--61182565 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
61182519 ACTTAGGGGT
*
61182529 CCCTCGCCTCTGCCACTG
1 CCCTAGCCTCTGCCA-TG
61182547 CCCTAGCCTCTGCCATG
1 CCCTAGCCTCTGCCATG
61182564 CC
1 CC
61182566 AGCACCGCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.08, C:0.54, G:0.16, T:0.22
Consensus pattern (17 bp):
CCCTAGCCTCTGCCATG
Found at i:61185246 original size:23 final size:23
Alignment explanation
Indices: 61185186--61185248 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
61185176 TTCATGCTAT
* *
61185186 TTCATCATAAACTTCCAGCACATA
1 TTCAT-ATCAACTTTCAGCACATA
61185210 TTCATATCAACTTTCAGCACATA
1 TTCATATCAACTTTCAGCACATA
61185233 TTCATATCAACTTTCA
1 TTCATATCAACTTTCA
61185249 CTTTCATTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
23 32 0.86
24 5 0.14
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (23 bp):
TTCATATCAACTTTCAGCACATA
Found at i:61194655 original size:15 final size:15
Alignment explanation
Indices: 61194635--61194664 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
61194625 GGGCAGAAAA
61194635 ATGAAAACAGTGCAT
1 ATGAAAACAGTGCAT
61194650 ATGAAAACAGTGCAT
1 ATGAAAACAGTGCAT
61194665 TCTAGATGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.20, T:0.20
Consensus pattern (15 bp):
ATGAAAACAGTGCAT
Found at i:61196492 original size:11 final size:11
Alignment explanation
Indices: 61196476--61196501 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
61196466 ACTGAACTGG
61196476 TTTAATGATTT
1 TTTAATGATTT
61196487 TTTAATGATTT
1 TTTAATGATTT
61196498 TTTA
1 TTTA
61196502 TCGGAGCGGT
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:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (11 bp):
TTTAATGATTT
Found at i:61196754 original size:161 final size:162
Alignment explanation
Indices: 61196439--61196761 Score: 603
Period size: 161 Copynumber: 2.0 Consensus size: 162
61196429 TAAAACCATG
* *
61196439 GTTTTCAGAACTAGACCAGATGGTTGGACTGAACTGGTTTAATGATTTTTTAATGATTTTTTATC
1 GTTTTCAGAACTAGACCAGATGATTGGACTGAACTGGTTTAATGAGTTTTTAATGATTTTTTATC
* *
61196504 GGAGCGGTGAGCTGGAGGTCTGACCGGTTCGACCACCGGTCCAGTTCTGAAAACCTTGGTTAAAA
66 GGAGCGGTGAGCTGGAGGTCTGACCAGTTCAACCACCGGTCCAGTTCTGAAAACCTTGGTTAAAA
61196569 CATTAGATGTAAGGAAATGGTTTTTAAAAATC
131 CATTAGATGTAAGGAAATGGTTTTTAAAAATC
61196601 GTTTTCAGAACTAGACCAGATGATTGGACTGAACTGGTTTAATGAGTTTTTAATGATTTTTTATC
1 GTTTTCAGAACTAGACCAGATGATTGGACTGAACTGGTTTAATGAGTTTTTAATGATTTTTTATC
61196666 GGAGCGGTGA-CTGGAGGTCTGACCAGTTCAACCACCGGTCCAGTTCTGAAAACCTTGGTTAAAA
66 GGAGCGGTGAGCTGGAGGTCTGACCAGTTCAACCACCGGTCCAGTTCTGAAAACCTTGGTTAAAA
61196730 CATTAGATGTAAGGAAATGGTTTTTAAAAATC
131 CATTAGATGTAAGGAAATGGTTTTTAAAAATC
61196762 TTCACTGCCT
Statistics
Matches: 157, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
161 84 0.54
162 73 0.46
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.33
Consensus pattern (162 bp):
GTTTTCAGAACTAGACCAGATGATTGGACTGAACTGGTTTAATGAGTTTTTAATGATTTTTTATC
GGAGCGGTGAGCTGGAGGTCTGACCAGTTCAACCACCGGTCCAGTTCTGAAAACCTTGGTTAAAA
CATTAGATGTAAGGAAATGGTTTTTAAAAATC
Found at i:61198545 original size:23 final size:23
Alignment explanation
Indices: 61198500--61198545 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
61198490 CTTGTTTCCT
* * *
61198500 TTTGCCTTCTCTTTTGCTGGAAA
1 TTTGCCTTCTCGTTTGATAGAAA
*
61198523 TTTGTCTTCTCGTTTGATAGAAA
1 TTTGCCTTCTCGTTTGATAGAAA
61198546 ATGCCTCTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.48
Consensus pattern (23 bp):
TTTGCCTTCTCGTTTGATAGAAA
Found at i:61203706 original size:23 final size:23
Alignment explanation
Indices: 61203651--61203717 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 23
61203641 AGATGCTTAT
*
61203651 ATATAAAATTTTAATAAATA-AAA
1 ATATAAAATATT-ATAAATATAAA
* *
61203674 ATATATAATATTATTAAATATTAA
1 ATATAAAATATTA-TAAATATAAA
*
61203698 AT-TAAAATAATATAAATATA
1 ATATAAAATATTATAAATATA
61203718 CATTTTTTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
22 8 0.22
23 24 0.67
24 4 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
ATATAAAATATTATAAATATAAA
Found at i:61216909 original size:21 final size:20
Alignment explanation
Indices: 61216861--61216910 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
61216851 TATATATTAT
61216861 TTCAAAAAATAATTTAAAAA
1 TTCAAAAAATAATTTAAAAA
61216881 TT-ATAAAAAT-ATTCATAAAAA
1 TTCA-AAAAATAATT--TAAAAA
61216902 TTCAAAAAA
1 TTCAAAAAA
61216911 AAAGCATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 4 0.15
20 8 0.31
21 13 0.50
22 1 0.04
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (20 bp):
TTCAAAAAATAATTTAAAAA
Found at i:61222697 original size:31 final size:32
Alignment explanation
Indices: 61222627--61222697 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 32
61222617 AAAAACTTAT
* *
61222627 GTACCAAACTAAACATTAAAATCAAACTCAAA
1 GTACCAAATTAAACATTAAAACCAAACTCAAA
* *
61222659 -TATCAAATTAGACATTAAAACCAAA-T-ATAA
1 GTACCAAATTAAACATTAAAACCAAACTCA-AA
61222689 GTACCAAAT
1 GTACCAAAT
61222698 AACGTATTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
29 1 0.03
30 3 0.09
31 28 0.88
ACGTcount: A:0.55, C:0.18, G:0.04, T:0.23
Consensus pattern (32 bp):
GTACCAAATTAAACATTAAAACCAAACTCAAA
Found at i:61227379 original size:17 final size:16
Alignment explanation
Indices: 61227357--61227400 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
61227347 AGAGAGAATG
*
61227357 AAAAGAAAAAGATAGTA
1 AAAAGAAAAAGAAAG-A
*
61227374 AAAAGAAGTAAGAAAGA
1 AAAAGAA-AAAGAAAGA
61227391 AAAAGAAAAA
1 AAAAGAAAAA
61227401 AGGAGATGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 2 0.09
17 15 0.65
18 6 0.26
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.07
Consensus pattern (16 bp):
AAAAGAAAAAGAAAGA
Found at i:61234358 original size:5 final size:5
Alignment explanation
Indices: 61234348--61234379 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
61234338 CCATGAACTA
61234348 TGTCG TGTCG TGTCG TGTCG TGTCG TGTCG TG
1 TGTCG TGTCG TGTCG TGTCG TGTCG TGTCG TG
61234380 AAAGTATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.00, C:0.19, G:0.41, T:0.41
Consensus pattern (5 bp):
TGTCG
Found at i:61241547 original size:15 final size:15
Alignment explanation
Indices: 61241518--61241546 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
61241508 TACCATAAAG
61241518 CTCTGTTTCTTTTTT
1 CTCTGTTTCTTTTTT
61241533 CTCTGTTT-TTTTTT
1 CTCTGTTTCTTTTTT
61241547 TTTTTTGGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.17, G:0.07, T:0.76
Consensus pattern (15 bp):
CTCTGTTTCTTTTTT
Found at i:61249187 original size:22 final size:22
Alignment explanation
Indices: 61249162--61249203 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
61249152 GGGGTCAAAA
61249162 TATAAATTTAT-TATTATTAATT
1 TATAAATTTATATATT-TTAATT
*
61249184 TATAATTTTATATATTTTAA
1 TATAAATTTATATATTTTAA
61249204 AAATAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TATAAATTTATATATTTTAATT
Found at i:61250758 original size:17 final size:17
Alignment explanation
Indices: 61250736--61250770 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
61250726 AGAAGAACAT
*
61250736 ACTTTAGATCTAAATTA
1 ACTTTAGATCCAAATTA
61250753 ACTTTAGATCCAAATTA
1 ACTTTAGATCCAAATTA
61250770 A
1 A
61250771 TCTGACGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.37
Consensus pattern (17 bp):
ACTTTAGATCCAAATTA
Found at i:61260283 original size:22 final size:22
Alignment explanation
Indices: 61260240--61260280 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
61260230 TTATTTTTAT
*
61260240 TTTTATGATGTAAAAATAAATA
1 TTTTATGATCTAAAAATAAATA
*
61260262 TTTTAT-ATCTAAAATTAAA
1 TTTTATGATCTAAAAATAAA
61260281 ATAACTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (22 bp):
TTTTATGATCTAAAAATAAATA
Found at i:61269852 original size:24 final size:24
Alignment explanation
Indices: 61269820--61269870 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
61269810 TAAACATTTT
*
61269820 TATATATTTAGGATTTTTTAAAAA
1 TATAAATTTAGGATTTTTTAAAAA
* *
61269844 TATAAATTTTGGATTTTTTATAAA
1 TATAAATTTAGGATTTTTTAAAAA
61269868 TAT
1 TAT
61269871 TTGAATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (24 bp):
TATAAATTTAGGATTTTTTAAAAA
Found at i:61269867 original size:18 final size:19
Alignment explanation
Indices: 61269844--61269881 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
61269834 TTTTTAAAAA
*
61269844 TATAAAT-TTTGGATTTTT
1 TATAAATATTTGAATTTTT
61269862 TATAAATATTTGAATTTTT
1 TATAAATATTTGAATTTTT
61269881 T
1 T
61269882 TGAGACTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.61
Consensus pattern (19 bp):
TATAAATATTTGAATTTTT
Found at i:61272498 original size:6 final size:7
Alignment explanation
Indices: 61272479--61272508 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
61272469 TTAGGGCATT
61272479 ATAAAAA
1 ATAAAAA
61272486 ATAAAAA
1 ATAAAAA
61272493 ATAAAAA
1 ATAAAAA
61272500 ATAAAAA
1 ATAAAAA
61272507 AT
1 AT
61272509 TATTTAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (7 bp):
ATAAAAA
Found at i:61275946 original size:3 final size:3
Alignment explanation
Indices: 61275940--61275976 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
61275930 GGTGGCCTTT
61275940 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
61275977 CTTTTTCATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:61291157 original size:22 final size:20
Alignment explanation
Indices: 61291120--61291187 Score: 86
Period size: 22 Copynumber: 3.4 Consensus size: 20
61291110 TTATCAAGTG
61291120 TATATAAAAATTGAAAAATA
1 TATATAAAAATTGAAAAATA
61291140 TATATAAAAATATGGAAATAA-A
1 TATATAAAAAT-T-GAAA-AATA
*
61291162 TATATAAAAATT-CAAAATA
1 TATATAAAAATTGAAAAATA
61291181 TATATAA
1 TATATAA
61291188 TCAAGAAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
18 2 0.05
19 10 0.23
20 11 0.26
21 2 0.05
22 16 0.37
23 2 0.05
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.31
Consensus pattern (20 bp):
TATATAAAAATTGAAAAATA
Found at i:61291329 original size:20 final size:20
Alignment explanation
Indices: 61291303--61291356 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
61291293 AACTATTATA
*
61291303 AAAATTTGTAAAAATTATTTT
1 AAAATTTATAAAAATT-TTTT
* *
61291324 -AAATTTTTTAAAATTTTTT
1 AAAATTTATAAAAATTTTTT
61291343 AAAATTTATAAAAA
1 AAAATTTATAAAAA
61291357 ATAAAAAGCT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
AAAATTTATAAAAATTTTTT
Found at i:61291346 original size:10 final size:10
Alignment explanation
Indices: 61291303--61291349 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
61291293 AACTATTATA
* *
61291303 AAAATTTGTA
1 AAAATTTTTT
61291313 AAAATTATTTT
1 AAAATT-TTTT
61291324 -AAATTTTTT
1 AAAATTTTTT
61291333 AAAATTTTTT
1 AAAATTTTTT
61291343 AAAATTT
1 AAAATTT
61291350 ATAAAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 4 0.12
10 27 0.82
11 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (10 bp):
AAAATTTTTT
Found at i:61293434 original size:14 final size:13
Alignment explanation
Indices: 61293397--61293435 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
61293387 TTAACATATA
61293397 TAATTAATATAAT
1 TAATTAATATAAT
**
61293410 TAATTTTTATAACT
1 TAATTAATATAA-T
61293424 TAATTAATATAA
1 TAATTAATATAA
61293436 ATATGTATAG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (13 bp):
TAATTAATATAAT
Found at i:61303262 original size:27 final size:27
Alignment explanation
Indices: 61303177--61303262 Score: 100
Period size: 27 Copynumber: 3.2 Consensus size: 27
61303167 AAGGGGGTGG
* *
61303177 GGTGCCCATTTGATAGGCGGCACCAGT
1 GGTGCCTATTTGATAGGCGGCACTAGT
*** *
61303204 GACCCCTATTTGATAGGCGGCACTGGT
1 GGTGCCTATTTGATAGGCGGCACTAGT
* *
61303231 TGTGCCTATCTGATAGGCGGCACTAGT
1 GGTGCCTATTTGATAGGCGGCACTAGT
61303258 GGTGC
1 GGTGC
61303263 AATTATTCTT
Statistics
Matches: 46, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.17, C:0.24, G:0.33, T:0.26
Consensus pattern (27 bp):
GGTGCCTATTTGATAGGCGGCACTAGT
Found at i:61304958 original size:6 final size:6
Alignment explanation
Indices: 61304930--61304972 Score: 59
Period size: 6 Copynumber: 6.8 Consensus size: 6
61304920 CCAAACACAC
*
61304930 CAGTATA CAGTAA TCAATAA CAGTAA CAGTAA CAGTAA CAGTA
1 CAGTA-A CAGTAA -CAGTAA CAGTAA CAGTAA CAGTAA CAGTA
61304973 TTCAACACAC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
6 23 0.70
7 10 0.30
ACGTcount: A:0.49, C:0.16, G:0.14, T:0.21
Consensus pattern (6 bp):
CAGTAA
Found at i:61304970 original size:18 final size:20
Alignment explanation
Indices: 61304930--61304973 Score: 65
Period size: 18 Copynumber: 2.3 Consensus size: 20
61304920 CCAAACACAC
61304930 CAGTATACAGTAATCAATAA
1 CAGTATACAGTAATCAATAA
*
61304950 CAGTA-ACAGTAA-CAGTAA
1 CAGTATACAGTAATCAATAA
61304968 CAGTAT
1 CAGTAT
61304974 TCAACACACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 10 0.45
19 7 0.32
20 5 0.23
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.23
Consensus pattern (20 bp):
CAGTATACAGTAATCAATAA
Found at i:61305016 original size:45 final size:45
Alignment explanation
Indices: 61304950--61305191 Score: 412
Period size: 45 Copynumber: 5.4 Consensus size: 45
61304940 TAATCAATAA
* ** *
61304950 CAGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGTTGAAC
1 CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
* ** *
61304995 CTGTAACAGTAATGGTAACAGTATTCGACACACAAAGTGCCGAGT
1 CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
61305040 CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
1 CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
61305085 CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
1 CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
61305130 CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
1 CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
61305175 CAGTAACAGTAACAGTA
1 CAGTAACAGTAACAGTA
61305192 GTCGGCACAT
Statistics
Matches: 185, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 185 1.00
ACGTcount: A:0.42, C:0.21, G:0.18, T:0.19
Consensus pattern (45 bp):
CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
Found at i:61305044 original size:39 final size:39
Alignment explanation
Indices: 61304956--61305218 Score: 206
Period size: 45 Copynumber: 6.2 Consensus size: 39
61304946 ATAACAGTAA
* **
61304956 CAGTAACAGTAACAGTATTCAACACACAAAGTGTTGAACCTGT
1 CAGTAACAGTAACAGTATTCGACACACAAAGTGCCG-A---GT
**
61304999 AACAGTAATGGTAACAGTATTCGACACACAAAGTGCCGAGTCAGT
1 --CAGTAACAGTAACAGTATTCGACACACAAAGTGCC--G--AGT
61305044 AACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCAGT
1 --CAGTAACAGTAACAGTATTCGACACACAAAGTGCCG----AGT
61305089 AACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCAGT
1 --CAGTAACAGTAACAGTATTCGACACACAAAGTGCCG----AGT
*
61305134 AACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
1 --CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAGT
* * *
61305175 CAGTAACAGTAACAGTAGTCGGCACA-TAAGTGCCTGA-T
1 CAGTAACAGTAACAGTATTCGACACACAAAGTGCC-GAGT
61305213 CAGTAA
1 CAGTAA
61305219 GCCGGCAAAT
Statistics
Matches: 200, Mismatches: 12, Indels: 19
0.87 0.05 0.08
Matches are distributed among these distances:
38 14 0.07
39 26 0.13
41 2 0.01
43 1 0.00
45 155 0.77
47 1 0.00
48 1 0.00
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.19
Consensus pattern (39 bp):
CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAGT
Found at i:61305479 original size:39 final size:40
Alignment explanation
Indices: 61305395--61305479 Score: 93
Period size: 40 Copynumber: 2.1 Consensus size: 40
61305385 TTCTTTACTT
* * * *
61305395 CAGTAATTTCACAATTCAATGCATTATACATAACAATATT
1 CAGTATTTTCACAATTCAATGCATAATACAAAACAATATC
* *
61305435 TAGTATTTTCACAATTCACT-CAGTAAT-CAAAACAATATC
1 CAGTATTTTCACAATTCAATGCA-TAATACAAAACAATATC
61305474 CAGTAT
1 CAGTAT
61305480 CCCATAATTC
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
39 17 0.46
40 20 0.54
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.34
Consensus pattern (40 bp):
CAGTATTTTCACAATTCAATGCATAATACAAAACAATATC
Found at i:61308095 original size:23 final size:23
Alignment explanation
Indices: 61308069--61308144 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
61308059 ATAAGTGCCA
61308069 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
61308092 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
61308115 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
61308138 CACTGAT
1 CACTGAT
61308145 CAATAACACT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:61309365 original size:19 final size:19
Alignment explanation
Indices: 61309337--61309373 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
61309327 CTCCTTCTCC
*
61309337 TTTTCTTCTTCTTCTCTTA
1 TTTTCATCTTCTTCTCTTA
*
61309356 TTTTCATCTTTTTCTCTT
1 TTTTCATCTTCTTCTCTT
61309374 TCTTCCCCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.05, C:0.24, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTCATCTTCTTCTCTTA
Found at i:61314491 original size:11 final size:12
Alignment explanation
Indices: 61314475--61314503 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
61314465 ATGTTAATGG
61314475 TGAATG-ATATT
1 TGAATGAATATT
61314486 TGAATGAATATT
1 TGAATGAATATT
61314498 TGAATG
1 TGAATG
61314504 TTCTTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 6 0.35
12 11 0.65
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (12 bp):
TGAATGAATATT
Found at i:61318748 original size:16 final size:16
Alignment explanation
Indices: 61318727--61318759 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
61318717 AAAAGATAAA
*
61318727 TGTAAATTTATTTAAT
1 TGTAAATTTAATTAAT
61318743 TGTAAATTTAATTAAT
1 TGTAAATTTAATTAAT
61318759 T
1 T
61318760 AATTAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (16 bp):
TGTAAATTTAATTAAT
Found at i:61320788 original size:13 final size:13
Alignment explanation
Indices: 61320772--61320813 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
61320762 TAAAAACATT
61320772 ATTATAAAATATA
1 ATTATAAAATATA
*
61320785 ATTATCGAAAT-T-
1 ATTAT-AAAATATA
61320797 ATTATAAAATATA
1 ATTATAAAATATA
61320810 ATTA
1 ATTA
61320814 ATTAATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
11 4 0.17
12 6 0.25
13 10 0.42
14 4 0.17
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (13 bp):
ATTATAAAATATA
Found at i:61326311 original size:19 final size:20
Alignment explanation
Indices: 61326269--61326315 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
61326259 TCCAAACTTT
* * *
61326269 AATTAATATTTTTAAAATTG
1 AATTAATATTTATAAAAATA
61326289 AATTAATA-TTATAAAAATA
1 AATTAATATTTATAAAAATA
61326308 AATTAATA
1 AATTAATA
61326316 AAAAATAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
AATTAATATTTATAAAAATA
Found at i:61327064 original size:19 final size:19
Alignment explanation
Indices: 61327036--61327073 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
61327026 TGAATTAAAA
*
61327036 TTTTAGTAATTTATATAAT
1 TTTTAATAATTTATATAAT
*
61327055 TTTTAATAATTTATTTAAT
1 TTTTAATAATTTATATAAT
61327074 CAAATTAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (19 bp):
TTTTAATAATTTATATAAT
Found at i:61330160 original size:19 final size:18
Alignment explanation
Indices: 61330135--61330184 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
61330125 CATTATTTTT
*
61330135 AATTAATTTTTTTTATAAT
1 AATTAATTTTTTTTA-AAG
* *
61330154 CATTAATTTTTTATAAAG
1 AATTAATTTTTTTTAAAG
61330172 AATTAATTTTTTT
1 AATTAATTTTTTT
61330185 AATGAAAATG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 13 0.50
19 13 0.50
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (18 bp):
AATTAATTTTTTTTAAAG
Found at i:61330185 original size:19 final size:20
Alignment explanation
Indices: 61330135--61330185 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
61330125 CATTATTTTT
*
61330135 AATTAATTTTTTT-TATAAT
1 AATTAATTTTTTTATATAAG
*
61330154 CATTAA-TTTTTTATA-AAG
1 AATTAATTTTTTTATATAAG
61330172 AATTAATTTTTTTA
1 AATTAATTTTTTTA
61330186 ATGAAAATGT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (20 bp):
AATTAATTTTTTTATATAAG
Found at i:61337974 original size:19 final size:17
Alignment explanation
Indices: 61337947--61337990 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
61337937 AATTTTGTAT
*
61337947 TCATATTAAATTACACTTA
1 TCATTTTAAATTA-AC-TA
61337966 TCATTTTAAATTAACTA
1 TCATTTTAAATTAACTA
*
61337983 TCACTTTA
1 TCATTTTA
61337991 TTATTATTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 9 0.39
18 2 0.09
19 12 0.52
ACGTcount: A:0.39, C:0.16, G:0.00, T:0.45
Consensus pattern (17 bp):
TCATTTTAAATTAACTA
Found at i:61337990 original size:17 final size:19
Alignment explanation
Indices: 61337952--61337990 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
61337942 TGTATTCATA
*
61337952 TTAAATTACACTTATCATT
1 TTAAATTACACTTATCACT
61337971 TTAAATTA-AC-TATCACT
1 TTAAATTACACTTATCACT
61337988 TTA
1 TTA
61337991 TTATTATTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 2 0.11
19 8 0.42
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (19 bp):
TTAAATTACACTTATCACT
Found at i:61345968 original size:2 final size:2
Alignment explanation
Indices: 61345961--61345993 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
61345951 TGAAAAATGA
61345961 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
61345994 AACTTACACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:61347429 original size:29 final size:29
Alignment explanation
Indices: 61347365--61347445 Score: 90
Period size: 31 Copynumber: 2.7 Consensus size: 29
61347355 AATATCAAAA
* *
61347365 TTATACATGAACTTTGATCTAATGTGTAATG
1 TTATACATGAACTTTGAT-T-TTGTGGAATG
*
61347396 TTATACATGAACTTTGATTTTGTGGAATT
1 TTATACATGAACTTTGATTTTGTGGAATG
* *
61347425 TTATATATGAAATTTTGATTT
1 TTATACATG-AACTTTGATTT
61347446 GATTCAATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
29 15 0.34
30 11 0.25
31 18 0.41
ACGTcount: A:0.31, C:0.06, G:0.15, T:0.48
Consensus pattern (29 bp):
TTATACATGAACTTTGATTTTGTGGAATG
Found at i:61351867 original size:21 final size:21
Alignment explanation
Indices: 61351826--61351867 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
61351816 TATATTGTAA
*
61351826 TTGGTAACTGTTTTCGGTTGT
1 TTGGTAACTGTTTTCGATTGT
*
61351847 TTGG-AACTGATTTTTGATTGT
1 TTGGTAACTG-TTTTCGATTGT
61351868 CATTTGGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.14, C:0.07, G:0.26, T:0.52
Consensus pattern (21 bp):
TTGGTAACTGTTTTCGATTGT
Found at i:61358977 original size:16 final size:16
Alignment explanation
Indices: 61358940--61358979 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
61358930 TTAATAAAAT
* *
61358940 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
61358956 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
61358972 TAAAATTA
1 TAAAATTA
61358980 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:61358979 original size:22 final size:22
Alignment explanation
Indices: 61358912--61358964 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
61358902 TAATTAAAAT
* * *
61358912 TAAAATTAAAATTATTTTTTAA
1 TAAAATTAAAACTAATTGTTAA
*
61358934 TAAAATTAAAACTAATTGTTAT
1 TAAAATTAAAACTAATTGTTAA
61358956 TAAAATTAA
1 TAAAATTAA
61358965 TTGTTAGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
TAAAATTAAAACTAATTGTTAA
Found at i:61359058 original size:59 final size:59
Alignment explanation
Indices: 61358990--61359129 Score: 271
Period size: 59 Copynumber: 2.4 Consensus size: 59
61358980 TCAAATTATT
*
61358990 AATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
61359049 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
61359108 AATTATTAATTGTATTAATTGT
1 AATTATTAATTGTATTAATTGT
61359130 ATTAATTGTT
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
59 80 1.00
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.47
Consensus pattern (59 bp):
AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
Found at i:61359123 original size:9 final size:9
Alignment explanation
Indices: 61359111--61359138 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
61359101 TTTATCAAAT
61359111 TATTAATTG
1 TATTAATTG
61359120 TATTAATTG
1 TATTAATTG
61359129 TATTAATTG
1 TATTAATTG
61359138 T
1 T
61359139 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:61359268 original size:24 final size:25
Alignment explanation
Indices: 61359235--61359281 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
61359225 AAATAAACTT
61359235 AAAATAAAAAAACTAT-TATATTTTA
1 AAAATAAAAAAA-TATATATATTTTA
61359260 AAAAT-AAAAAATATATATATTT
1 AAAATAAAAAAATATATATATTT
61359282 AATATTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (25 bp):
AAAATAAAAAAATATATATATTTTA
Found at i:61362626 original size:22 final size:23
Alignment explanation
Indices: 61362573--61362628 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
61362563 TTTAATTAAA
* * *
61362573 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
61362596 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
61362618 ATTAAAATTAA
1 ATTAAAATTAA
61362629 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:61362641 original size:16 final size:16
Alignment explanation
Indices: 61362604--61362643 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
61362594 TTAATAAAAT
* *
61362604 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
61362620 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
61362636 TAAAATTA
1 TAAAATTA
61362644 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:61362722 original size:59 final size:59
Alignment explanation
Indices: 61362654--61362793 Score: 271
Period size: 59 Copynumber: 2.4 Consensus size: 59
61362644 TCAAATTATT
*
61362654 AATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
61362713 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
61362772 AATTATTAATTGTATTAATTGT
1 AATTATTAATTGTATTAATTGT
61362794 ATTAATTGTT
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
59 80 1.00
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.47
Consensus pattern (59 bp):
AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
Found at i:61362787 original size:9 final size:9
Alignment explanation
Indices: 61362775--61362802 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
61362765 TTTATCAAAT
61362775 TATTAATTG
1 TATTAATTG
61362784 TATTAATTG
1 TATTAATTG
61362793 TATTAATTG
1 TATTAATTG
61362802 T
1 T
61362803 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:61362939 original size:22 final size:24
Alignment explanation
Indices: 61362899--61362942 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
61362889 AAATAAACTT
61362899 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
61362923 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
61362943 AATATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:61367567 original size:29 final size:29
Alignment explanation
Indices: 61367516--61367574 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 29
61367506 TGTATATGAG
*
61367516 TGCATCTAAATTAAAGCTTATGTATTAAAT
1 TGCATCTAAATCAAAGCTTATGTA-TAAAT
61367546 TGCAT-TAAATCAAAG-TTCATGTATAAAT
1 TGCATCTAAATCAAAGCTT-ATGTATAAAT
61367574 T
1 T
61367575 TTAAAATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 8 0.30
29 14 0.52
30 5 0.19
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (29 bp):
TGCATCTAAATCAAAGCTTATGTATAAAT
Found at i:61369256 original size:114 final size:112
Alignment explanation
Indices: 61369042--61369256 Score: 322
Period size: 114 Copynumber: 1.9 Consensus size: 112
61369032 ACAAAGGCTG
* * * *
61369042 TATTGCTTTGGGTTCTTTGAATATATTTACCTTAGTTTTCTTCCGGCCATTGCACCTTGTCTCGC
1 TATTGCTTTGGGTTATTTGAATACATTTACCTTAGTTCTCTTCCGGCCATTGCACCTTGTATCGC
* ***
61369107 AAGCAATTTCATCTAAACAATGTTCTTTTGTGAGCTTTTGCTTCGGT
66 AAACAATTTCATCTAAACAATGTTCTTTCACGAGCTTTTGCTTCGGT
*
61369154 TATTGCATTTAGGGTTATTTGAATACATTTACCTTAGTTCTCTTCTGGCCATTGCACCTTGTATC
1 TATTGC-TTT-GGGTTATTTGAATACATTTACCTTAGTTCTCTTCCGGCCATTGCACCTTGTATC
*
61369219 GTAAACAATTTCATCTAAACAATGTTCTTTCACGAGCT
64 GCAAACAATTTCATCTAAACAATGTTCTTTCACGAGCT
61369257 ACGCATGAAC
Statistics
Matches: 91, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
112 6 0.07
113 3 0.03
114 82 0.90
ACGTcount: A:0.21, C:0.20, G:0.15, T:0.43
Consensus pattern (112 bp):
TATTGCTTTGGGTTATTTGAATACATTTACCTTAGTTCTCTTCCGGCCATTGCACCTTGTATCGC
AAACAATTTCATCTAAACAATGTTCTTTCACGAGCTTTTGCTTCGGT
Found at i:61370905 original size:20 final size:21
Alignment explanation
Indices: 61370868--61370907 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
61370858 TAATATTAAA
61370868 TAATTAAAAACCAATTAATTTT
1 TAATTAAAAA-CAATTAATTTT
61370890 TAATTAAAAA-AATTAATT
1 TAATTAAAAACAATTAATT
61370908 ATGTTCTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
22 10 0.56
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (21 bp):
TAATTAAAAACAATTAATTTT
Found at i:61371873 original size:30 final size:30
Alignment explanation
Indices: 61371818--61371918 Score: 83
Period size: 30 Copynumber: 3.6 Consensus size: 30
61371808 AAGTTTAGTA
*
61371818 CAAGTTTAGTACCAAATTAAGAAAAAGTGT
1 CAAGTTCAGTACCAAATTAAGAAAAAGTGT
*
61371848 CAAGTTCAGGTACTAAATTAA-AAAAA--GT
1 CAAGTTCA-GTACCAAATTAAGAAAAAGTGT
* * *
61371876 ----TTAAGTACCAAATT-AGGAAAAGGGT
1 CAAGTTCAGTACCAAATTAAGAAAAAGTGT
61371901 CAAGTTCAGGTACCAAAT
1 CAAGTTCA-GTACCAAAT
61371919 GTTATATTAA
Statistics
Matches: 56, Mismatches: 6, Indels: 18
0.70 0.08 0.22
Matches are distributed among these distances:
22 1 0.02
23 13 0.23
24 3 0.05
25 2 0.04
28 2 0.04
29 3 0.05
30 21 0.38
31 11 0.20
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.25
Consensus pattern (30 bp):
CAAGTTCAGTACCAAATTAAGAAAAAGTGT
Found at i:61380387 original size:21 final size:20
Alignment explanation
Indices: 61380363--61380409 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
61380353 TAGTAAGTTT
61380363 TAATTTTAAA-AAGTTATAAAA
1 TAATTTTAAATAA--TATAAAA
61380384 TAATTATTAAATAATATAAAA
1 TAATT-TTAAATAATATAAAA
61380405 -AATTT
1 TAATTT
61380410 ATTTAAGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 12 0.50
22 5 0.21
23 2 0.08
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
TAATTTTAAATAATATAAAA
Found at i:61381532 original size:3 final size:3
Alignment explanation
Indices: 61381524--61381563 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
61381514 GTTCAAAAAT
61381524 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
61381564 AATTCAAGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:61384165 original size:2 final size:2
Alignment explanation
Indices: 61384158--61384182 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
61384148 TTTCAGTTAC
61384158 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
61384183 GGGTTGGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:61385603 original size:29 final size:29
Alignment explanation
Indices: 61385569--61385624 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
61385559 ATAAAAACTT
*
61385569 GATCAAATTAGTCTCTCTATTATTAAATG
1 GATCAAATTAGTCTCTATATTATTAAATG
*
61385598 GATCAATTTAGTCTCTATATTATTAAA
1 GATCAAATTAGTCTCTATATTATTAAA
61385625 AAGAATCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.43
Consensus pattern (29 bp):
GATCAAATTAGTCTCTATATTATTAAATG
Found at i:61385641 original size:30 final size:29
Alignment explanation
Indices: 61385570--61385641 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
61385560 TAAAAACTTG
* * *
61385570 ATCAAATTAGTCTCTCTATTATTAAATGG
1 ATCAAATTAGTCTCTATATTATTAAAAGA
*
61385599 ATCAATTTAGTCTCTATATTATTAAAAAGA
1 ATCAAATTAGTCTCTATATTATT-AAAAGA
*
61385629 ATCAAATAAGTCT
1 ATCAAATTAGTCT
61385642 AAATTGTAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 21 0.58
30 15 0.42
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.39
Consensus pattern (29 bp):
ATCAAATTAGTCTCTATATTATTAAAAGA
Found at i:61385854 original size:29 final size:29
Alignment explanation
Indices: 61385820--61385875 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
61385810 TTTGATTCTT
*
61385820 TTTAATAATATAGAGACTAAATTGATCCA
1 TTTAATAATAGAGAGACTAAATTGATCCA
* *
61385849 TTTAATAATAGAGGGACTAATTTGATC
1 TTTAATAATAGAGAGACTAAATTGATC
61385876 AGGTTACTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (29 bp):
TTTAATAATAGAGAGACTAAATTGATCCA
Found at i:61400464 original size:6 final size:6
Alignment explanation
Indices: 61400450--61400514 Score: 121
Period size: 6 Copynumber: 10.8 Consensus size: 6
61400440 TCTGGTTTTA
*
61400450 CATCTT CATCCT CATCCT CATCCT CATCCT CATCCT CATCCT CATCCT
1 CATCCT CATCCT CATCCT CATCCT CATCCT CATCCT CATCCT CATCCT
61400498 CATCCT CATCCT CATCC
1 CATCCT CATCCT CATCC
61400515 GTGCTTGTAC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.17, C:0.49, G:0.00, T:0.34
Consensus pattern (6 bp):
CATCCT
Found at i:61402345 original size:3 final size:3
Alignment explanation
Indices: 61402270--61402334 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
61402260 AAATGTATAT
61402270 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
61402318 ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA AT
61402335 TAGTATAATA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:61405664 original size:45 final size:44
Alignment explanation
Indices: 61405582--61405672 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 44
61405572 AAACTCCTAC
61405582 GTGTGAAAAGAATACATACAGTGTTCAATTAGAGTTGTTCATGG
1 GTGTGAAAAGAATACATACAGTGTTCAATTAGAGTTGTTCATGG
*
61405626 GTGTGAAAAGAATACATACCAGTGTTCAGTTAGAGTTGTTCATGG
1 GTGTGAAAAGAATACATA-CAGTGTTCAATTAGAGTTGTTCATGG
61405671 GT
1 GT
61405673 CGGGTTGGTT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.32, C:0.10, G:0.26, T:0.32
Consensus pattern (44 bp):
GTGTGAAAAGAATACATACAGTGTTCAATTAGAGTTGTTCATGG
Found at i:61406063 original size:21 final size:20
Alignment explanation
Indices: 61406039--61406096 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
61406029 AAATGGTAGC
*
61406039 AAAACAGTGGCAAAAAGTGGA
1 AAAACAGTAGCAAAAA-TGGA
*
61406060 AAAACTA-CAGCAAAACATGGA
1 AAAAC-AGTAGCAAAA-ATGGA
61406081 AAAACAGTAGCAAAAA
1 AAAACAGTAGCAAAAA
61406097 CAATAGATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.59, C:0.14, G:0.19, T:0.09
Consensus pattern (20 bp):
AAAACAGTAGCAAAAATGGA
Found at i:61410300 original size:4 final size:4
Alignment explanation
Indices: 61410291--61410324 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
61410281 TAAGGTTGCA
*
61410291 TATG TATG TATG TATG CATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TATG TA
61410325 ATAGGTGGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.26, C:0.03, G:0.24, T:0.47
Consensus pattern (4 bp):
TATG
Found at i:61421009 original size:2 final size:2
Alignment explanation
Indices: 61421002--61421043 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
61420992 AAATTGGACA
61421002 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61421044 GTAGTAGTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61434598 original size:17 final size:19
Alignment explanation
Indices: 61434566--61434601 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
61434556 AAATCGATAG
61434566 GCATCAAAATTCAACATCT
1 GCATCAAAATTCAACATCT
61434585 GCATC-AAA-TCAACATCT
1 GCATCAAAATTCAACATCT
61434602 TCCTACAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 3 0.18
19 5 0.29
ACGTcount: A:0.42, C:0.28, G:0.06, T:0.25
Consensus pattern (19 bp):
GCATCAAAATTCAACATCT
Found at i:61453766 original size:6 final size:6
Alignment explanation
Indices: 61453755--61453789 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
61453745 CAATTTTGGG
61453755 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
61453790 CAATAATAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:61453797 original size:18 final size:18
Alignment explanation
Indices: 61453755--61453797 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
61453745 CAATTTTGGG
*
61453755 AAAAATAAAAATAAAAAT
1 AAAAATAAAAATAAAAAC
61453773 AAAAATAAAAATAAAAAC
1 AAAAATAAAAATAAAAAC
*
61453791 AATAATA
1 AAAAATA
61453798 GGAAAAGAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.16
Consensus pattern (18 bp):
AAAAATAAAAATAAAAAC
Found at i:61454450 original size:3 final size:3
Alignment explanation
Indices: 61454442--61454478 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
61454432 GAATTAAGTA
61454442 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
61454479 TACATAAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:61456820 original size:113 final size:112
Alignment explanation
Indices: 61456663--61456949 Score: 285
Period size: 112 Copynumber: 2.6 Consensus size: 112
61456653 TGGTTTTACG
* * * *
61456663 CCGCAAAATCTCA-AGACCAAAACGCATCGTTTTTGTCTTGATGTATACAATAATTAGTGGCGAT
1 CCGCAAAATATCATA-ACCAAAACGCATCGTTTTGGTATTGATGTATACAAGAATTAGTGGCGAT
* * * * * * *
61456727 TATGATAAAACGCC-GCTAAAGCAAGTATTAGCGGCGCATTGCGGGAAGCG
65 TA-CAAAAAAAGCCAG-TAAAACAAGTATTAGCGGCGC-TTACGGAAAGCA
* * ** *
61456777 CCGCAAAA-ATCTTAACGAAAACGCATCGTTTTGGTATCT-ATGTATATTAGAATTAGTGGCGTT
1 CCGCAAAATATCATAACCAAAACGCATCGTTTTGGTAT-TGATGTATACAAGAATTAGTGGCGAT
*
61456840 TACAAAAAAAGCCAGTAAAACAAGTCTTAGCGGCGCTTACGGAAAGCA
65 TACAAAAAAAGCCAGTAAAACAAGTATTAGCGGCGCTTACGGAAAGCA
* ** * * **
61456888 CCGCAAAATATGATAACCAAAACGCAGAGTTTTGATCTTGATGTATATTAGAATTAGTGGCG
1 CCGCAAAATATCATAACCAAAACGCATCGTTTTGGTATTGATGTATACAAGAATTAGTGGCG
61456950 CTTCATAGTA
Statistics
Matches: 144, Mismatches: 24, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
111 18 0.12
112 71 0.49
113 45 0.31
114 10 0.07
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (112 bp):
CCGCAAAATATCATAACCAAAACGCATCGTTTTGGTATTGATGTATACAAGAATTAGTGGCGATT
ACAAAAAAAGCCAGTAAAACAAGTATTAGCGGCGCTTACGGAAAGCA
Found at i:61457006 original size:75 final size:75
Alignment explanation
Indices: 61456884--61457024 Score: 210
Period size: 75 Copynumber: 1.9 Consensus size: 75
61456874 GCTTACGGAA
* * * * *
61456884 AGCACCGCAAAATATGATAACCAAAACGCAGAGTTTTGATCTTGATGTATATTAGAATTAGTGGC
1 AGCACCGCAAAAAATGATAACCAAAACGCAGAGGTTTGATCTCGATGTATAATACAATTAGTGGC
61456949 GCTTCATAGT
66 GCTTCATAGT
* * *
61456959 AGCACCGCAAAAAATGTTAACCAAAACGCAGCGGTTTGGTCTCGATGTATAATACAATTAGTGGC
1 AGCACCGCAAAAAATGATAACCAAAACGCAGAGGTTTGATCTCGATGTATAATACAATTAGTGGC
61457024 G
66 G
61457025 TTAGGGAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
75 58 1.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (75 bp):
AGCACCGCAAAAAATGATAACCAAAACGCAGAGGTTTGATCTCGATGTATAATACAATTAGTGGC
GCTTCATAGT
Found at i:61457157 original size:114 final size:112
Alignment explanation
Indices: 61456978--61457405 Score: 379
Period size: 114 Copynumber: 3.8 Consensus size: 112
61456968 AAAAATGTTA
* * * * * ** **
61456978 ACCAAAACGCAGCGGTTTGGTCTCGATGTATAATACAATTAGTGGCG-TTAGGGAAAAACGCCGC
1 ACCAAAACGTAG-AGTTTGGTCTTGAGGTATATTAGGATTAGTGGCGCTTACTG-AAAACGCCGC
* *
61457042 TAAAGCATAAC-ATTAGCGGCGATTTTCTAGAATCGCCGCAAGATATTCAC
64 TAAAGCAT-ACTATTAGCGGCGATTTT-GAGAACCGCCGCAAGATATTCAC
*
61457092 ACCAAAACGTAGAGTTTGGTGTTGAGGTATATTAGGATTAGTGGCGCTTACTGTAAAACGCCGCT
1 ACCAAAACGTAGAGTTTGGTCTTGAGGTATATTAGGATTAGTGGCGCTTACTG-AAAACGCCGCT
* * * *
61457157 AAAGCGTACTATTAGCGGCGCTTCTGGAGAAGCGCCGCTAA-AT-TTCTTA-
65 AAAGCATACTATTAGCGGCGATT-TTGAGAACCGCCGC-AAGATATTC--AC
* * * *
61457206 ACCAAAAC-TCAGCGTTTTGGTCTTGATGTATACTATA-G-TTAGTGGCACTTACGAGAAAACGC
1 ACCAAAACGT-AGAG-TTTGGTCTTGAGGTATA-T-TAGGATTAGTGGCGCTTAC-TGAAAACGC
** * *
61457268 CGCTAAATAATAGTATTAGCGGCGA-TTTGAGTTAACCGCCGCAAGATATGCAC
61 CGCTAAAGCATACTATTAGCGGCGATTTTGAG--AACCGCCGCAAGATATTCAC
* * * *
61457321 ACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTGATTAGAAAACGCCGCT
1 ACCAAAACGTAGAGTTTGGTCTTGAGGTATATTAGGATTAGTGGCGCTTACT-GAAAACGCCGCT
*
61457386 AAAGTATACTATTAGCGGCG
65 AAAGCATACTATTAGCGGCG
61457406 CGTTTTTAGA
Statistics
Matches: 254, Mismatches: 40, Indels: 40
0.76 0.12 0.12
Matches are distributed among these distances:
112 2 0.01
113 38 0.15
114 127 0.50
115 80 0.31
116 5 0.02
117 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (112 bp):
ACCAAAACGTAGAGTTTGGTCTTGAGGTATATTAGGATTAGTGGCGCTTACTGAAAACGCCGCTA
AAGCATACTATTAGCGGCGATTTTGAGAACCGCCGCAAGATATTCAC
Found at i:61457285 original size:115 final size:112
Alignment explanation
Indices: 61456975--61457573 Score: 405
Period size: 115 Copynumber: 5.2 Consensus size: 112
61456965 GCAAAAAATG
* * * * * *
61456975 TTAACCAAAACGCAGCGGTTTGGTCTCGATGTATAATACAATTAGTGGCGTTA-GGGAAAAACGC
1 TTAACCAAAACGCAGCGTTTTGGTCTTGATGTATACTAGAATTAGTGGCCTTACGAG-AAAACGC
* ** *
61457039 CGCTAAAGCATAAC-ATTAGCGGCGATTTTCTAGAATCGCCGCAAGATATTC
65 CGCTAAAGCAT-ACTATTAGCGGCG-CTTTGGAGAAGCGCCGCAA-AT-TTC
* * * * * * *
61457090 --ACACCAAAACGTAGAG-TTTGGTGTTGAGGTATATTAGGATTAGTGGCGCTTACTG-TAAAAC
1 TTA-ACCAAAACGCAGCGTTTTGGTCTTGATGTATACTAGAATTAGTGGC-CTTAC-GAGAAAAC
*
61457151 GCCGCTAAAGCGTACTATTAGCGGCGCTTCTGGAGAAGCGCCGCTAAATTTC
63 GCCGCTAAAGCATACTATTAGCGGCGCTT-TGGAGAAGCGCCGC-AAATTTC
* * *
61457203 TTAACCAAAACTCAGCGTTTTGGTCTTGATGTATACTATAGTTAGTGGCACTTACGAGAAAACGC
1 TTAACCAAAACGCAGCGTTTTGGTCTTGATGTATACTAGAATTAGTGGC-CTTACGAGAAAACGC
** * * * *
61457268 CGCTAAATAATAGTATTAGCGGCGATTT-GAGTTAACCGCCGCAAGATATGC
65 CGCTAAAGCATACTATTAGCGGCGCTTTGGAG--AAGCGCCGCAA-AT-TTC
* * * * **
61457319 --ACACCAAAACGCAGAG-TTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTGATTAGAAAACG
1 TTA-ACCAAAACGCAGCGTTTTGGTCTTGATGTATACTAGAATTAGTGGC-CTTACGAGAAAACG
* ** * * * * *
61457381 CCGCTAAAGTATACTATTAGCGGCGCGTTTTTAGATGCTCCGTAGAATATA
64 CCGCTAAAGCATACTATTAGCGGCGC-TTTGGAGAAGCGCCGCA-AATTTC
* *** * * * *
61457432 TTAACCGAAACGCTA-CGTTTAAATCTTGATGTATACTGGAATTAGTGGCGTTCACGATAAATCG
1 TTAACCAAAACGC-AGCGTTTTGGTCTTGATGTATACTAGAATTAGTGGCCTT-ACGAGAAAACG
* * *
61457496 CCGCTAAAGCATATTATTAGCGGCGCTTTTTGG-TAAGCGCCGCAAAATATC
64 CCGCTAAAGCATACTATTAGCGGCGC--TTTGGAGAAGCGCCGC-AAATTTC
*
61457547 TTAACCAAAACACA-CAGTTTTGGTCTT
1 TTAACCAAAACGCAGC-GTTTTGGTCTT
61457574 AACCATGCAT
Statistics
Matches: 373, Mismatches: 84, Indels: 54
0.73 0.16 0.11
Matches are distributed among these distances:
113 36 0.10
114 152 0.41
115 176 0.47
116 9 0.02
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (112 bp):
TTAACCAAAACGCAGCGTTTTGGTCTTGATGTATACTAGAATTAGTGGCCTTACGAGAAAACGCC
GCTAAAGCATACTATTAGCGGCGCTTTGGAGAAGCGCCGCAAATTTC
Found at i:61457443 original size:114 final size:113
Alignment explanation
Indices: 61456975--61457525 Score: 370
Period size: 114 Copynumber: 4.8 Consensus size: 113
61456965 GCAAAAAATG
* * * * * *
61456975 TTAACCAAAACGCAGCGGTTTGGTCTCGATGTATAATACAATTAGTGGCG-TTA-GGGAAAAACG
1 TTAACCAAAACGCAG-AGTTTGGTCTTGAGGTATACTAGAATTAGTGGCGCTTACGAG-AAAACG
* * * *
61457038 CCGCTAAAGCATAAC-ATTAGCGGCGATTTTCTAGAAT-CGCCGCA-AGATAT-
64 CCGCTAAAGCAT-ACTATTAGCGGCGCTTTT-GAG-ATGCACCGTAGA-ATATA
* * * * * *
61457088 TCACACCAAAACGTAGAGTTTGGTGTTGAGGTATATTAGGATTAGTGGCGCTTACTG-TAAAACG
1 TTA-ACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGAATTAGTGGCGCTTAC-GAGAAAACG
* * * * * *
61457152 CCGCTAAAGCGTACTATTAGCGGCGCTTCTGGAGAAGCGCCGCTA-AATTTC
64 CCGCTAAAGCATACTATTAGCGGCGCTT-TTGAGATGCACCG-TAGAATATA
* * * * * *
61457203 TTAACCAAAACTCAGCGTTTTGGTCTTGATGTATACTATAGTTAGTGGCACTTACGAGAAAACGC
1 TTAACCAAAACGCAGAG-TTTGGTCTTGAGGTATACTAGAATTAGTGGCGCTTACGAGAAAACGC
** * * ** ** *
61457268 CGCTAAATAATAGTATTAGCGGCG-ATTTGAG-TTAACCGCCGCAAGATA
65 CGCTAAAGCATACTATTAGCGGCGCTTTTGAGATGCACCGTAG-AATATA
* * * **
61457316 TGCACACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTGATTAGAAAACG
1 T-TA-ACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGAATTAGTGGCGCTTACGAGAAAACG
* * *
61457381 CCGCTAAAGTATACTATTAGCGGCGCGTTTTTAGATGCTCCGTAGAATATA
64 CCGCTAAAGCATACTATTAGCGGCGC-TTTTGAGATGCACCGTAGAATATA
* * ** * * * *
61457432 TTAACCGAAACGCTA-CGTTTAAATCTTGATGTATACTGGAATTAGTGGCG-TTCACGATAAATC
1 TTAACCAAAACGC-AGAGTTT-GGTCTTGAGGTATACTAGAATTAGTGGCGCTT-ACGAGAAAAC
*
61457495 GCCGCTAAAGCATATTATTAGCGGCGCTTTT
63 GCCGCTAAAGCATACTATTAGCGGCGCTTTT
61457526 TGGTAAGCGC
Statistics
Matches: 336, Mismatches: 81, Indels: 41
0.73 0.18 0.09
Matches are distributed among these distances:
112 3 0.01
113 40 0.12
114 145 0.43
115 131 0.39
116 12 0.04
117 5 0.01
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (113 bp):
TTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGAATTAGTGGCGCTTACGAGAAAACGCC
GCTAAAGCATACTATTAGCGGCGCTTTTGAGATGCACCGTAGAATATA
Found at i:61457539 original size:229 final size:227
Alignment explanation
Indices: 61456975--61457545 Score: 614
Period size: 229 Copynumber: 2.5 Consensus size: 227
61456965 GCAAAAAATG
** * * * *
61456975 TTAACCAAAACGCAGCGGTTT-GGTCTCGATGTATAATACAATTAGTGGCGTTAGGGAAAAACGC
1 TTAACCAAAACGCAGC-GTTTAAATCTTGATGTATACTAGAATTAGTGGCGTTA-CGAAAAACGC
* * * * *
61457039 CGCTAAAGCATAACATTAGCGGCGATTTTCTAG-AATCGCCGCAAGATATTCACACCAAAACGTA
64 CGCTAAAGCATAATATTAGCGGCGATTTT-TGGTAACCGCCGCAAGATATGCACACCAAAACGCA
* * * *
61457103 GAGTTTGGTGTTGAGGTATATTAGGATTAGTGGCGCTTACTGTAAAACGCCGCTAAAGCGTACTA
128 GAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTGACTGTAAAACGCCGCTAAAGCATACTA
* *
61457168 TTAGCGGCGCTTCTGGAGAAGCGCCGCTAAATTTC
193 TTAGCGGCGCTTCTGGAGAAGCGCCGCTAAATATA
* *** * * *
61457203 TTAACCAAAACTCAGCGTTTTGGTCTTGATGTATACTATAGTTAGTGGCACTTACGAGAAAACGC
1 TTAACCAAAACGCAGCGTTTAAATCTTGATGTATACTAGAATTAGTGGC-GTTACGA-AAAACGC
** * ** *
61457268 CGCTAAATAATAGTATTAGCGGCGATTTGAGTTAACCGCCGCAAGATATGCACACCAAAACGCAG
64 CGCTAAAGCATAATATTAGCGGCGATTTTTGGTAACCGCCGCAAGATATGCACACCAAAACGCAG
* *
61457333 AGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTGATTAG-AAAACGCCGCTAAAGTATACTA
129 AGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTGACT-GTAAAACGCCGCTAAAGCATACTA
** * *
61457397 TTAGCGGCGCGTT-TTTAGATGCTCCG-TAGAATATA
193 TTAGCGGCGC-TTCTGGAGAAGCGCCGCTA-AATATA
* * *
61457432 TTAACCGAAACGCTA-CGTTTAAATCTTGATGTATACTGGAATTAGTGGCGTTCACGATAAATCG
1 TTAACCAAAACGC-AGCGTTTAAATCTTGATGTATACTAGAATTAGTGGCGTT-ACGA-AAAACG
* * * *
61457496 CCGCTAAAGCATATTATTAGCGGCGCTTTTTGGTAAGCGCCGCAAAATAT
63 CCGCTAAAGCATAATATTAGCGGCGATTTTTGGTAACCGCCGCAAGATAT
61457546 CTTAACCAAA
Statistics
Matches: 284, Mismatches: 50, Indels: 17
0.81 0.14 0.05
Matches are distributed among these distances:
227 4 0.01
228 45 0.16
229 231 0.81
230 4 0.01
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (227 bp):
TTAACCAAAACGCAGCGTTTAAATCTTGATGTATACTAGAATTAGTGGCGTTACGAAAAACGCCG
CTAAAGCATAATATTAGCGGCGATTTTTGGTAACCGCCGCAAGATATGCACACCAAAACGCAGAG
TTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTGACTGTAAAACGCCGCTAAAGCATACTATTA
GCGGCGCTTCTGGAGAAGCGCCGCTAAATATA
Found at i:61458355 original size:23 final size:24
Alignment explanation
Indices: 61458297--61458369 Score: 62
Period size: 24 Copynumber: 3.0 Consensus size: 24
61458287 TTTTAAAATT
* *
61458297 ATAATACATTAATTTAATAA-TATAA
1 ATAATTCA-TAATTT-ATAATTTTAA
*
61458322 ATAATTTATAATTTATAATTTTAA
1 ATAATTCATAATTTATAATTTTAA
61458346 AT-ATTCATAATATT-TAAATTTTAA
1 ATAATTCATAAT-TTAT-AATTTTAA
61458370 TGTATGAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
23 13 0.32
24 22 0.54
25 6 0.15
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (24 bp):
ATAATTCATAATTTATAATTTTAA
Found at i:61459241 original size:111 final size:110
Alignment explanation
Indices: 61459078--61459391 Score: 495
Period size: 111 Copynumber: 2.8 Consensus size: 110
61459068 GAAATTCGAG
* * * *
61459078 AGGATATTTGGCTATTTGGTTAAACGAGAAAAATCGACACCCAGCACCTTAGGGCACATTTTCTC
1 AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
* *
61459143 AAATTTCCCAAATGCAAAACATTGCCTTATTTCGAAAATTTTTAAA
66 GAATTTCCCAAACGCAAAACATTGCCTTATTT-GAAAATTTTTAAA
*
61459189 AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTCTCTC
1 AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
61459254 GAATTTCCCAAACGCAAAACATTGCCTTATTTGAAAATTTTTAAA
66 GAATTTCCCAAACGCAAAACATTGCCTTATTTGAAAATTTTTAAA
* *
61459299 AGGATATTTAGCCATTTGGTTGAACGAGAAAAAAATCGAAACCCAGCACATTAGGGCACGTTTTC
1 AGGATATTTAGCCATTTGGTTGAACGAG--AAAAATCGACACCCAGCACCTTAGGGCACGTTTTC
* *
61459364 TCGAATTT-CCAAACGCTAAATATTGCCT
64 TCGAATTTCCCAAACGCAAAACATTGCCT
61459392 CAATTAGAAA
Statistics
Matches: 189, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
110 41 0.22
111 108 0.57
112 40 0.21
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (110 bp):
AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
GAATTTCCCAAACGCAAAACATTGCCTTATTTGAAAATTTTTAAA
Found at i:61460025 original size:3 final size:3
Alignment explanation
Indices: 61460010--61460060 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
61460000 TAAAAATTGT
* * * *
61460010 TAA TAA TAG TAA TAA TAA TGA TAA TAA CAC TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
61460058 TAA
1 TAA
61460061 ACTAAATAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:61463401 original size:16 final size:17
Alignment explanation
Indices: 61463340--61463401 Score: 58
Period size: 17 Copynumber: 3.7 Consensus size: 17
61463330 TAAATATTTT
61463340 ATTTTATTTTAATCACA
1 ATTTTATTTTAATCACA
* **
61463357 ATTTT-TTTAAAT-ATTTT
1 ATTTTATTTTAATCA--CA
61463374 ATTTTATTTTAATCACA
1 ATTTTATTTTAATCACA
61463391 ATTTT-TTTTAA
1 ATTTTATTTTAA
61463402 ATATTTTATT
Statistics
Matches: 35, Mismatches: 6, Indels: 9
0.70 0.12 0.18
Matches are distributed among these distances:
15 1 0.03
16 12 0.34
17 15 0.43
18 6 0.17
19 1 0.03
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTTATTTTAATCACA
Found at i:61463464 original size:34 final size:34
Alignment explanation
Indices: 61463327--61463448 Score: 217
Period size: 35 Copynumber: 3.5 Consensus size: 34
61463317 TAAAGTTATA
61463327 TTTTAAATATTTTATTTTATTTTAATCACAATTT
1 TTTTAAATATTTTATTTTATTTTAATCACAATTT
61463361 TTTTAAATATTTTATTTTATTTTAATCACAATTTT
1 TTTTAAATATTTTATTTTATTTTAATCACAA-TTT
61463396 TTTTAAATATTTTATTTTATTTTAATCACGAATTT
1 TTTTAAATATTTTATTTTATTTTAATCAC-AATTT
*
61463431 TTTTAAATATTTAATTTT
1 TTTTAAATATTTTATTTT
61463449 TTTAAAGTTC
Statistics
Matches: 85, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
34 31 0.36
35 52 0.61
36 2 0.02
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.62
Consensus pattern (34 bp):
TTTTAAATATTTTATTTTATTTTAATCACAATTT
Found at i:61463492 original size:9 final size:9
Alignment explanation
Indices: 61463468--61463545 Score: 63
Period size: 9 Copynumber: 8.7 Consensus size: 9
61463458 CAAATTTCAC
*
61463468 AACTTACGT
1 AACTTACAT
*
61463477 AATTTACAT
1 AACTTACAT
61463486 AACTTACAT
1 AACTTACAT
61463495 AA-TT-CAT
1 AACTTACAT
61463502 AACTTACAT
1 AACTTACAT
* *
61463511 AATTTAAATTT
1 AACTTACA--T
*
61463522 ATA-ATACAT
1 A-ACTTACAT
61463531 AACTTACAT
1 AACTTACAT
61463540 AACTTA
1 AACTTA
61463546 TTAATATTTA
Statistics
Matches: 55, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
7 5 0.09
8 5 0.09
9 39 0.71
11 5 0.09
12 1 0.02
ACGTcount: A:0.45, C:0.15, G:0.01, T:0.38
Consensus pattern (9 bp):
AACTTACAT
Done.