Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 16 of 213
Found at i:4443698 original size:26 final size:26
Alignment explanation
Indices: 4443661--4443724 Score: 112
Period size: 26 Copynumber: 2.5 Consensus size: 26
4443651 TATAAATATC
4443661 AAAAAATG-TGAGTACTACATGGATA
1 AAAAAATGATGAGTACTACATGGATA
*
4443686 AAAAAATGATGAGTACTACATGGATC
1 AAAAAATGATGAGTACTACATGGATA
4443712 AAAAAATGATGAG
1 AAAAAATGATGAG
4443725 ATCGTTATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
25 8 0.22
26 29 0.78
ACGTcount: A:0.50, C:0.08, G:0.20, T:0.22
Consensus pattern (26 bp):
AAAAAATGATGAGTACTACATGGATA
Found at i:4444882 original size:69 final size:68
Alignment explanation
Indices: 4444765--4444921 Score: 226
Period size: 69 Copynumber: 2.3 Consensus size: 68
4444755 TTTTTGCTTC
* * * * *
4444765 GTGTGTTCTAAATTAATATTGTTTATTTTTATTTGATAATGTGTAATTGCAGCTTTAATTCTTTG
1 GTGTGTTCTAAATTAATATTGTATATTTTTATTGGATAATGTGTAATTGAAACTTCAATTCTTTG
4444830 ATA
66 ATA
4444833 GTGTGTTCTAAATTAATATTGTATATTTTT-TTAGGTATAATGTGTAATTGAAACTTCAATTCTT
1 GTGTGTTCTAAATTAATATTGTATATTTTTATT-GG-ATAATGTGTAATTGAAACTTCAATTCTT
4444897 TGATA
64 TGATA
*
4444902 GTGTGTTCTAATTTTAATAT
1 GTGTGTTCTAA-ATTAATAT
4444922 GTTGCAGTAA
Statistics
Matches: 80, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
67 2 0.03
68 30 0.38
69 41 0.51
70 7 0.09
ACGTcount: A:0.28, C:0.06, G:0.15, T:0.52
Consensus pattern (68 bp):
GTGTGTTCTAAATTAATATTGTATATTTTTATTGGATAATGTGTAATTGAAACTTCAATTCTTTG
ATA
Found at i:4447953 original size:90 final size:90
Alignment explanation
Indices: 4447808--4448013 Score: 306
Period size: 90 Copynumber: 2.3 Consensus size: 90
4447798 CTGATTTTAG
* *
4447808 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAATTATATATCATTATTAAATTATA
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAATTATATATCATTATTAAATTATA
* * *
4447873 TTTAATATTAATTA-TTTAAATTGTA
65 TGTAATAATAATTATTTTAAATTATA
* *
4447898 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTTTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATG-AATTATATATCATTATTAAATTATA
4447963 TGTAATAATAATTATTTTAAATTATA
65 TGTAATAATAATTATTTTAAATTATA
* *
4447989 CAAATTCATATAAGATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
4448014 GTTATAATTA
Statistics
Matches: 105, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
89 21 0.20
90 51 0.49
91 33 0.31
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.47
Consensus pattern (90 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAATTATATATCATTATTAAATTATAT
GTAATAATAATTATTTTAAATTATA
Found at i:4447962 original size:28 final size:26
Alignment explanation
Indices: 4447928--4447985 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 26
4447918 TATTATCAAG
*
4447928 AATTTTATGAAATTATATATTATTATTA
1 AATTTTATGAAATAATA-ATTATT-TTA
*
4447956 AATTTTATGTAATAATAATTATTTTA
1 AATTTTATGAAATAATAATTATTTTA
4447982 AATT
1 AATT
4447986 ATACAAATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 7 0.25
27 6 0.21
28 15 0.54
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (26 bp):
AATTTTATGAAATAATAATTATTTTA
Found at i:4448166 original size:37 final size:39
Alignment explanation
Indices: 4448101--4448285 Score: 98
Period size: 38 Copynumber: 4.7 Consensus size: 39
4448091 TTATAGTATC
* * *
4448101 ATATATTATG-ATTTGAGTAAATTCATATAAGAATAT-TA
1 ATATATTAAGAATTTTATTAAATT-ATATAAGAATATATA
**
4448139 AT-TATTAAGAATTTTATTAAATTATATATTTTAAT-TATA
1 ATATATTAAGAATTTTATTAAATTATATA--AGAATATATA
* * * *** *
4448178 ATATATTTAATAATAATTATGTTAATT-TATATTTATAGTATC
1 ATATA-TTAAGAAT-TTTAT-TAAATTATATAAGAATA-TATA
* * * *
4448220 ATATATTATG-ATTTGAGTAAATTCATATAAGAATAT-TG
1 ATATATTAAGAATTTTATTAAATT-ATATAAGAATATATA
4448258 AT-TATTAAGAATTTTATTAAATTATATA
1 ATATATTAAGAATTTTATTAAATTATATA
4448286 TTTTAATTAT
Statistics
Matches: 111, Mismatches: 23, Indels: 27
0.69 0.14 0.17
Matches are distributed among these distances:
37 22 0.20
38 33 0.30
39 10 0.09
40 15 0.14
41 10 0.09
42 16 0.14
43 5 0.05
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (39 bp):
ATATATTAAGAATTTTATTAAATTATATAAGAATATATA
Found at i:4448188 original size:15 final size:15
Alignment explanation
Indices: 4448153--4448204 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
4448143 TTAAGAATTT
*
4448153 TATTAAATTAT-ATA
1 TATTTAATTATAATA
4448167 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
4448181 TATTTAATAATAAT-
1 TATTTAATTATAATA
4448195 TATGTTAATT
1 TAT-TTAATT
4448205 TATATTTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:4448247 original size:119 final size:121
Alignment explanation
Indices: 4448018--4448324 Score: 514
Period size: 119 Copynumber: 2.6 Consensus size: 121
4448008 TTATTAGTTA
* * * *
4448018 TAATTATTTA-AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTC
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTC
*
4448081 AAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATAT
66 AAATTATCATTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATAT
4448137 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTC
*
4448201 AATTTAT-ATTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATAT
66 AAATTATCATTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATAT
* *
4448256 TGATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTC
4448321 AAAT
66 AAAT
4448325 ATGATTAAAT
Statistics
Matches: 177, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
119 119 0.67
120 56 0.32
121 2 0.01
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (121 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTC
AAATTATCATTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATAT
Found at i:4448302 original size:16 final size:16
Alignment explanation
Indices: 4448281--4448322 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
4448271 TTATTAAATT
*
4448281 ATATATTTTAATTATA
1 ATATATTTTAATAATA
4448297 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
4448312 AT-TATGTTTAA
1 ATATAT-TTTAA
4448323 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:4448307 original size:15 final size:15
Alignment explanation
Indices: 4448272--4448313 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
4448262 TTAAGAATTT
*
4448272 TATTAAATTAT-ATA
1 TATTTAATTATAATA
4448286 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
4448300 TATTTAATAATAAT
1 TATTTAATTATAAT
4448314 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:4448560 original size:16 final size:16
Alignment explanation
Indices: 4448539--4448608 Score: 113
Period size: 16 Copynumber: 4.4 Consensus size: 16
4448529 TTGATTTGCT
4448539 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
4448555 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
4448571 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
*
4448587 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
*
4448603 AATACA
1 ATTACA
4448609 ACGAACCAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.26, C:0.36, G:0.03, T:0.36
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:4449747 original size:152 final size:151
Alignment explanation
Indices: 4448896--4450004 Score: 1033
Period size: 152 Copynumber: 7.4 Consensus size: 151
4448886 AACATGTTCG
* *
4448896 TATTTCAGCCATTTGTTCGT-TTTTTTCCCCT-GATTTTATTACTTT--TAAAAACTATACTATT
1 TATTTCGGCCATTTGTTCGTATTTTTT--CCTGGATTTTATTACTTTAATAAAAA-TATATTATT
*
4448957 TTCTAATTTTATTATTTTACATTATTTTTGTACATTATGTTTGAAATGTATTCATTT-A-GTGTG
63 TT-TAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAACGTGT-
** * * *
4449020 TTTTTATTTAAATTAAAAAAAATCTT
126 TTTTTAAATAAATTTAAAAAAACCCT
* * * * *
4449046 TATTTCGGCCATTTATTCAT-TTTTTTTCAGGATTTTATTATTTTCAATAAAAATATATTATTTT
1 TATTTCGGCCATTTGTTCGTATTTTTTCCTGGATTTTATTACTTT-AATAAAAATATATTATTTT
*
4449110 CGT-ATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTT-ACTGTGTT
65 --TAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAAC-GTGTT
4449173 TTTTAAATAAATTTTAAAAAAACCCT
127 TTTTAAATAAA-TTTAAAAAAACCCT
* * * *** *
4449199 TATTTTGGCTC-TTTATTCTTATTTTTTCCCCAATATTTTATTACTTTAA-AAAAA-CTA-T-TT
1 TATTTCGGC-CATTTGTTCGTATTTTTT--CCTGGATTTTATTACTTTAATAAAAATATATTATT
* * **
4449259 TCTAATTTTATTATTTTACATTATTTTAGTACATTATGTCTGAAATGTATTCATTTAGTGTGTTT
63 TTTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAACGTGTTT
** * *
4449324 TTTATTTAAAATTTTTAAAAAACCCA
128 TTTAAAT-AAA-TTTAAAAAAACCCT
* * * * * * *
4449350 TATTCCGTCCCTTTGTTTGTATTTTTTCC-CGAGTTTTATTATTTTCAATGAAAATATATTA---
1 TATTTCGGCCATTTGTTCGTATTTTTTCCTGGA-TTTTATTACTTT-AATAAAAATATATTATTT
* * * * *
4449411 -T--TTTT-TTATTTT--ATTA-TTT--TACATTTTTTTTGAAGTGTATTAATTT-ACTATGTTT
64 TTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAAC-GTGTTT
*
4449466 TTTAAATAAATTTTAAAAAACCCT
128 TTTAAATAAATTTAAAAAAACCCT
* * * * * *
4449490 TATTTTGACCCTTTGTTCGTATTTTTTTCCCGGAATTTATTACTTTAA-AAAAATATACTATTTT
1 TATTTCGGCCATTTGTTCGTA-TTTTTTCCTGGATTTTATTACTTTAATAAAAATATATTATTTT
* *
4449554 CTAATTTTATTATTTTTACATTATTTTAGTTCATTATGTTTGAAATCTATTCATTTAACGTGTTT
65 -TAATTTTATTA-TTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAACGTGTTT
** *
4449619 TTTATTTAAA-TTAAAAAAACTCT
128 TTTAAATAAATTTAAAAAAACCCT
* * *
4449642 TATTTTGGCCATTTGTTTGTATTTTTTCCTGGATTTTATTCCTTTCAATAAAAATATATTATTTT
1 TATTTCGGCCATTTGTTCGTATTTTTTCCTGGATTTTATTACTTT-AATAAAAATATATTATTTT
* * * *** *
4449707 TGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATATATTAATTTATTTTATTTT
65 T-AATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAACGTGTTTT
4449772 TTAAATAAATTTAAAAAAACCCT
129 TTAAATAAATTTAAAAAAACCCT
* *
4449795 TATTTCGGTCC-TTTGTTCGTATTTTTTTCCTGGATTTTATTACTTTTA-AAAAATATAATATTT
1 TATTTCGG-CCATTTGTTCGTA-TTTTTTCCTGGATTTTATTACTTTAATAAAAATATATTATTT
**
4449858 TATAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTT
64 T-TAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAACGTGTTT
* *
4449923 TTTAAATAATTTTTTTTAAAAAAAACTCT
128 TTTAAATAA----ATTT-AAAAAAACCCT
* * * * *
4449952 TATTTCCGCCCTTTGCTC-TATTTTTTTCGGGATTTTATTACTTTCAATAAAAA
1 TATTTCGGCCATTTGTTCGTATTTTTTCCTGGATTTTATTACTTT-AATAAAAA
4450005 ACAAACTAAA
Statistics
Matches: 795, Mismatches: 109, Indels: 103
0.79 0.11 0.10
Matches are distributed among these distances:
139 10 0.01
140 32 0.04
141 21 0.03
142 34 0.04
144 4 0.01
145 4 0.01
146 4 0.01
147 10 0.01
148 10 0.01
149 27 0.03
150 92 0.12
151 127 0.16
152 185 0.23
153 122 0.15
154 39 0.05
155 24 0.03
156 22 0.03
157 28 0.04
ACGTcount: A:0.29, C:0.10, G:0.07, T:0.54
Consensus pattern (151 bp):
TATTTCGGCCATTTGTTCGTATTTTTTCCTGGATTTTATTACTTTAATAAAAATATATTATTTTT
AATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAACGTGTTTTTT
AAATAAATTTAAAAAAACCCT
Found at i:4449810 original size:305 final size:302
Alignment explanation
Indices: 4448907--4450004 Score: 1347
Period size: 305 Copynumber: 3.6 Consensus size: 302
4448897 ATTTCAGCCA
* * * *
4448907 TTTGTTCGT-TTTTTTCCCCTGATTTTATTACTTTTAAAAACTATACTATTTTCTAATTTTATTA
1 TTTGTTCGTATTTTTTTCCCGGAATTTATTACTTTTAAAAAATATACTATTTTCTAATTTTATTA
* *
4448971 TTTTACATTATTTTTGTACATTATGTTTGAAATGTATTCATTTAGTGTG-TTTTTATTTAAATTA
66 TTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAATGTGTTTTTTATTTAAATTA
* * ** * *
4449035 AAAAAAATCTTTATTTCGGCCATTTATTCATTTTTTTTCAGGATTTTATTATTTTCAATAAAAAT
131 AAAAAACTC-TTATTTCGGCCATTTGTTTGTATTTTTTCCGGATTTTATTATTTTCAATAAAAAT
*
4449100 ATATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTT
195 ATATTATTTTTGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTT
*
4449165 ACTGTGTTTTTTAAATAAATTTTAAAAAAACCCTTATTTTGGCTC
260 ACTATGTTTTTTAAATAAA-TTTAAAAAAACCCTTATTTTGGC-C
* * **
4449210 TTTATTCTTA-TTTTTTCCCCAATATTTTATTAC-TTT-AAAAA-A-ACTATTTTCTAATTTTAT
1 TTTGTTCGTATTTTTTTCCCGGA-A-TTTATTACTTTTAAAAAATATACTATTTTCTAATTTTAT
* *
4449270 TATTTTACATTATTTTAGTACATTATGTCTGAAATGTATTCATTTAGTGTGTTTTTTATTTAAAA
64 TATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAATGTGTTTTTTATTT-AAA
* * * * * * * *
4449335 TTTTTAAAAAACCCATATTCCGTCCCTTTGTTTGTATTTTTTCCCGAGTTTTATTATTTTCAATG
128 --TTAAAAAAACTCTTATTTCGGCCATTTGTTTGTATTTTTTCCGGA-TTTTATTATTTTCAATA
* *
4449400 AAAATATATTATTTTTTTATTTTATTATTTTAC---A---T--T---TT-T-TTTGAAGTGTATT
190 AAAATATATTATTTTTGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATT
* *
4449452 AATTTACTATGTTTTTTAAATAAATTTTAAAAAACCCTTATTTTGACCC
255 AATTTACTATGTTTTTTAAATAAATTTAAAAAAACCCTTATTTTG-GCC
*
4449501 TTTGTTCGTATTTTTTTCCCGGAATTTATTACTTTAAAAAAATATACTATTTTCTAATTTTATTA
1 TTTGTTCGTATTTTTTTCCCGGAATTTATTACTTTTAAAAAATATACTATTTTCTAATTTTATTA
* * *
4449566 TTTTTACATTATTTTAGTTCATTATGTTTGAAATCTATTCATTTAACGTGTTTTTTATTTAAATT
66 -TTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAATGTGTTTTTTATTTAAATT
* **
4449631 AAAAAAACTCTTATTTTGGCCATTTGTTTGTATTTTTTCCTGGATTTTATTCCTTTCAATAAAAA
130 AAAAAAACTCTTATTTCGGCCATTTGTTTGTATTTTTTCC-GGATTTTATTATTTTCAATAAAAA
*
4449696 TATATTATTTTTGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATATATTAATT
194 TATATTATTTTTGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATT
* * * *
4449761 TATTTTATTTTTTAAATAAATTTAAAAAAACCCTTATTTCGGTCC
259 TACTATGTTTTTTAAATAAATTTAAAAAAACCCTTATTTTGG-CC
* * * *
4449806 TTTGTTCGTATTTTTTTCCTGGATTTTATTACTTTTAAAAAATATAATATTTTATAATTTTATTA
1 TTTGTTCGTATTTTTTTCCCGGAATTTATTACTTTTAAAAAATATACTATTTTCTAATTTTATTA
* *
4449871 TTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTTAAATAATTTT
66 TTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAATGTG-TTTTT---T-ATTTA
** * * * * * *
4449936 TTTTAAAAAAAACTCTTATTTCCGCCCTTTG-CTCTATTTTTTTCGGGATTTTATTACTTTCAAT
126 AATT-AAAAAAACTCTTATTTCGGCCATTTGTTTGTA-TTTTTTCCGGATTTTATTATTTTCAAT
4450000 AAAAA
189 AAAAA
4450005 ACAAACTAAA
Statistics
Matches: 680, Mismatches: 78, Indels: 68
0.82 0.09 0.08
Matches are distributed among these distances:
290 8 0.01
291 32 0.05
292 132 0.19
293 4 0.01
294 25 0.04
295 55 0.08
297 1 0.00
298 1 0.00
299 1 0.00
300 1 0.00
301 67 0.10
302 11 0.02
303 25 0.04
304 72 0.11
305 182 0.27
308 1 0.00
309 32 0.05
310 30 0.04
ACGTcount: A:0.29, C:0.10, G:0.07, T:0.54
Consensus pattern (302 bp):
TTTGTTCGTATTTTTTTCCCGGAATTTATTACTTTTAAAAAATATACTATTTTCTAATTTTATTA
TTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAATGTGTTTTTTATTTAAATTA
AAAAAACTCTTATTTCGGCCATTTGTTTGTATTTTTTCCGGATTTTATTATTTTCAATAAAAATA
TATTATTTTTGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTA
CTATGTTTTTTAAATAAATTTAAAAAAACCCTTATTTTGGCC
Found at i:4450461 original size:126 final size:125
Alignment explanation
Indices: 4450195--4450618 Score: 627
Period size: 125 Copynumber: 3.4 Consensus size: 125
4450185 TTGACGTGCT
* * * *
4450195 AAGAATTTTTGAAATCGCACCCTCGTGGACGCGCTTTTGCTACAATAGGTCTTGGAAAAAATAAT
1 AAGAATTTGTGAAATCGCACCCTCGTGGACGCGCTTTTGCTACAGTAGGTCCTAGAAAAAATAAT
4450260 TTCGAGTTGACGTTTCTAAGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTTTATCAG
66 TTCGAGTTGACGTTTCTAAGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTTTATCAG
* * *
4450320 AAGAATTTGTGAAATCGCGCCCACGTGGACGCGCGTTTGCTACAGTAGGTCCT-GAAAAAATAAT
1 AAGAATTTGTGAAATCGCACCCTCGTGGACGCGCTTTTGCTACAGTAGGTCCTAGAAAAAATAAT
* * * *
4450384 TTTGAGTTGATGTTTCTAAGTAAATAGTATAAAAAAACGCTTCAAGCAGGATGCTTTATGAG
66 TTCGAGTTGACGTTTCTAAGCAAATAGTAT--AAAAACGCTTCAAGCAGGATGCTTTATCAG
* * * *
4450446 AAGAATTTGTGAAATCGCGCCCTCGTGGACACGCTTTTGCTTCAGTAGGTTCTAGAAAAAATAAT
1 AAGAATTTGTGAAATCGCACCCTCGTGGACGCGCTTTTGCTACAGTAGGTCCTAGAAAAAATAAT
* * *
4450511 TTCGAGTTAACGTTTCTGAA-CAAATAGTATAAAAACGCTTCAAGAAGGATGCTTTATTAG
66 TTCGAGTTGACGTTTCT-AAGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTTTATCAG
* *
4450571 AAGAATTTGTGAAATCGCACCCCCGTGGATGCGCTTTTGCTACAGTAG
1 AAGAATTTGTGAAATCGCACCCTCGTGGACGCGCTTTTGCTACAGTAG
4450619 CATGTTTGGG
Statistics
Matches: 269, Mismatches: 26, Indels: 8
0.89 0.09 0.03
Matches are distributed among these distances:
124 38 0.14
125 118 0.44
126 77 0.29
127 34 0.13
128 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.29
Consensus pattern (125 bp):
AAGAATTTGTGAAATCGCACCCTCGTGGACGCGCTTTTGCTACAGTAGGTCCTAGAAAAAATAAT
TTCGAGTTGACGTTTCTAAGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTTTATCAG
Found at i:4453614 original size:9 final size:9
Alignment explanation
Indices: 4453600--4453630 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
4453590 GTTAAACGAA
4453600 TCGAGTTAT
1 TCGAGTTAT
*
4453609 TCGAGTTAA
1 TCGAGTTAT
4453618 TCGAGTTAT
1 TCGAGTTAT
4453627 TCGA
1 TCGA
4453631 ATCAACTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:4453701 original size:9 final size:9
Alignment explanation
Indices: 4453684--4453720 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
4453674 TGAGTTTTCG
4453684 AATTCGAAT
1 AATTCGAAT
*
4453693 AACTCGAAT
1 AATTCGAAT
4453702 AATTCGAAT
1 AATTCGAAT
4453711 AATTCGAAT
1 AATTCGAAT
4453720 A
1 A
4453721 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:4454467 original size:114 final size:114
Alignment explanation
Indices: 4454295--4454563 Score: 450
Period size: 114 Copynumber: 2.4 Consensus size: 114
4454285 ATATTTTTTC
* *
4454295 AATTATTAATTGATAATTGTATTAATTGTTAGTAAAACTATCAAATTATATCAAATTATTAATTG
1 AATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATTATCAAATTATATCAAATTATTAATTG
* *
4454360 TTAGTACCAGTCAAAACA-TTTTGTAAAATCTAACTTTTTGTGAATGTAA
66 TTAGTACCAGT-AAAAAATTTTTGTAAAATCTAACATTTTGTGAATGTAA
*
4454409 AATTATTAATTGTTAATTGTATTAATTATTAGTAAAATTATCAAATTATATCAAATTATTAATTG
1 AATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATTATCAAATTATATCAAATTATTAATTG
** *
4454474 TTAGTGGCAGTAAAAAATTTTTGTAAAATTTAACATTTTGTGAATGTAA
66 TTAGTACCAGTAAAAAATTTTTGTAAAATCTAACATTTTGTGAATGTAA
4454523 AATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATTAT
1 AATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATTAT
4454564 TAATTGTTAA
Statistics
Matches: 145, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
113 5 0.03
114 140 0.97
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.45
Consensus pattern (114 bp):
AATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATTATCAAATTATATCAAATTATTAATTG
TTAGTACCAGTAAAAAATTTTTGTAAAATCTAACATTTTGTGAATGTAA
Found at i:4454478 original size:37 final size:38
Alignment explanation
Indices: 4454314--4454478 Score: 92
Period size: 37 Copynumber: 4.4 Consensus size: 38
4454304 TTGATAATTG
*
4454314 TATTAATTGTTAGTAAAACTATCAAATTATATCAAAT-
1 TATTAATTGTTAGTAAAATTATCAAATTATATCAAATC
* * * * * * *
4454351 TATTAATTGTTAGTACCAGTCA-AAACATTTTGTAAAATC
1 TATTAATTGTTAGTA-AAATTATCAA-ATTATATCAAATC
* * * * * *
4454390 TAACTT-TTTGTGAATGTAAAATTAT-TAATTGT-T-AATTG
1 T-A-TTAATTGT-TA-GTAAAATTATCAAATTATATCAAATC
*
4454428 TATTAATTATTAGTAAAATTATCAAATTATATCAAAT-
1 TATTAATTGTTAGTAAAATTATCAAATTATATCAAATC
4454465 TATTAATTGTTAGT
1 TATTAATTGTTAGT
4454479 GGCAGTAAAA
Statistics
Matches: 92, Mismatches: 24, Indels: 24
0.66 0.17 0.17
Matches are distributed among these distances:
35 10 0.11
36 8 0.09
37 35 0.38
38 18 0.20
39 2 0.02
40 9 0.10
41 7 0.08
42 3 0.03
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (38 bp):
TATTAATTGTTAGTAAAATTATCAAATTATATCAAATC
Found at i:4456798 original size:22 final size:22
Alignment explanation
Indices: 4456751--4456804 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
4456741 AAATATGGAT
*
4456751 TTGAGAGAAATTTGGAAGGAAT
1 TTGAGAGAAATTTGGAAGGAAG
4456773 TTGAGAGCAAA-TT-GAGAGGAAG
1 TTGAGAG-AAATTTGGA-AGGAAG
4456795 TTGAGA-AAAT
1 TTGAGAGAAAT
4456805 AATTGAGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 3 0.11
21 2 0.07
22 20 0.71
23 3 0.11
ACGTcount: A:0.43, C:0.02, G:0.31, T:0.24
Consensus pattern (22 bp):
TTGAGAGAAATTTGGAAGGAAG
Found at i:4457545 original size:42 final size:42
Alignment explanation
Indices: 4457466--4457545 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 42
4457456 GTAAAATACC
*
4457466 ATATAATAATATATTATAATTAAAACATAAAATATCTTTGTT
1 ATATAATAATATATAATAATTAAAACATAAAATATCTTTGTT
4457508 ATATAATAATATAATAATATATT-AAACATAAAA-ATCTT
1 ATATAATAATAT-ATAATA-ATTAAAACATAAAATATCTT
4457546 AGATTTTCCT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
42 17 0.49
43 15 0.43
44 3 0.09
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.40
Consensus pattern (42 bp):
ATATAATAATATATAATAATTAAAACATAAAATATCTTTGTT
Found at i:4459711 original size:50 final size:50
Alignment explanation
Indices: 4459636--4459735 Score: 173
Period size: 50 Copynumber: 2.0 Consensus size: 50
4459626 AAGAATATGA
* *
4459636 GTTAAAAAGTTGAAATGATTTAACATAACGACTCCGTTTTCAAAACCCAT
1 GTTAAAAAGCTGAAAGGATTTAACATAACGACTCCGTTTTCAAAACCCAT
*
4459686 GTTAATAAGCTGAAAGGATTTAACATAACGACTCCGTTTTCAAAACCCAT
1 GTTAAAAAGCTGAAAGGATTTAACATAACGACTCCGTTTTCAAAACCCAT
4459736 TCTTTGTGAC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.29
Consensus pattern (50 bp):
GTTAAAAAGCTGAAAGGATTTAACATAACGACTCCGTTTTCAAAACCCAT
Found at i:4461377 original size:30 final size:28
Alignment explanation
Indices: 4461331--4461391 Score: 86
Period size: 30 Copynumber: 2.1 Consensus size: 28
4461321 ACATATTTTA
4461331 TTGTTAATTTTTATTATTTTAAAGACAT
1 TTGTTAATTTTTATTATTTTAAAGACAT
* *
4461359 TTGTTAATTTTGTTATTATTTTAGAGATAT
1 TTGTTAA-TTT-TTATTATTTTAAAGACAT
4461389 TTG
1 TTG
4461392 ATTGTTAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 7 0.24
29 3 0.10
30 19 0.66
ACGTcount: A:0.28, C:0.02, G:0.11, T:0.59
Consensus pattern (28 bp):
TTGTTAATTTTTATTATTTTAAAGACAT
Found at i:4464248 original size:16 final size:17
Alignment explanation
Indices: 4464197--4464248 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 17
4464187 AAAATGAAAT
4464197 AATTATTTCAAATATAA
1 AATTATTTCAAATATAA
* * *
4464214 TAATTATTTTATATGTAA
1 -AATTATTTCAAATATAA
*
4464232 AA-TATTTCACATATAA
1 AATTATTTCAAATATAA
4464248 A
1 A
4464249 CATAGTAATA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
16 12 0.43
17 2 0.07
18 14 0.50
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (17 bp):
AATTATTTCAAATATAA
Found at i:4464445 original size:13 final size:13
Alignment explanation
Indices: 4464412--4464452 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
4464402 AATAAAAGAG
4464412 ATATTAATTAAAA
1 ATATTAATTAAAA
4464425 A-ATTAATTAAAA
1 ATATTAATTAAAA
*
4464437 ATATGAATTAAAA
1 ATATTAATTAAAA
4464450 ATA
1 ATA
4464453 AAAAATTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 12 0.46
13 14 0.54
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (13 bp):
ATATTAATTAAAA
Found at i:4469993 original size:63 final size:63
Alignment explanation
Indices: 4469889--4470009 Score: 188
Period size: 63 Copynumber: 1.9 Consensus size: 63
4469879 ATCAAAATGC
* * * *
4469889 AGAGGCACGGGCGTGCGTCTAGGCCGTGTGACTCACTGTTTACGATTTAGGACCACACGGACT
1 AGAGACACGGGCGTGCGTCCAGGCCGTGTGACTCACTGTTTACAAATTAGGACCACACGGACT
* *
4469952 AGAGACACGGGCGTGTGTCCAGGCCGTGTGACTCACTGTTTACAAATTAGGATCACAC
1 AGAGACACGGGCGTGCGTCCAGGCCGTGTGACTCACTGTTTACAAATTAGGACCACAC
4470010 AAGCAGACGA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 52 1.00
ACGTcount: A:0.23, C:0.25, G:0.30, T:0.22
Consensus pattern (63 bp):
AGAGACACGGGCGTGCGTCCAGGCCGTGTGACTCACTGTTTACAAATTAGGACCACACGGACT
Found at i:4475360 original size:7 final size:7
Alignment explanation
Indices: 4475348--4475372 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
4475338 AGTCGATTGA
4475348 TATTTAG
1 TATTTAG
4475355 TATTTAG
1 TATTTAG
4475362 TATTTAG
1 TATTTAG
4475369 TATT
1 TATT
4475373 ATGTATATAA
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:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:4476496 original size:25 final size:25
Alignment explanation
Indices: 4476462--4476584 Score: 141
Period size: 25 Copynumber: 5.1 Consensus size: 25
4476452 TGAGTATTTT
4476462 GAAGTTTATTTGATGTAATAAAATA
1 GAAGTTTATTTGATGTAATAAAATA
4476487 GAAGTTTATTTGATGTAATAAAAATA
1 GAAGTTTATTTGATGTAAT-AAAATA
* * ***
4476513 GAAATTT-TTTGA-GTTAT-TTTTA
1 GAAGTTTATTTGATGTAATAAAATA
*
4476535 -TA--TTATTTGATGTAATAAAATA
1 GAAGTTTATTTGATGTAATAAAATA
4476557 GAAGTTTATTTGATGTAATAAAATA
1 GAAGTTTATTTGATGTAATAAAATA
4476582 GAA
1 GAA
4476585 ATTTTTGAAT
Statistics
Matches: 80, Mismatches: 11, Indels: 14
0.76 0.10 0.13
Matches are distributed among these distances:
19 2 0.03
20 5 0.06
21 5 0.06
22 4 0.05
23 1 0.01
24 4 0.05
25 47 0.59
26 12 0.15
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.43
Consensus pattern (25 bp):
GAAGTTTATTTGATGTAATAAAATA
Found at i:4476601 original size:9 final size:9
Alignment explanation
Indices: 4476587--4476623 Score: 67
Period size: 9 Copynumber: 4.2 Consensus size: 9
4476577 AAATAGAAAT
4476587 TTTTGAATA
1 TTTTGAATA
4476596 TTTTGAATA
1 TTTTGAATA
4476605 TTTTGAATA
1 TTTTGAATA
4476614 TTTTG-ATA
1 TTTTGAATA
4476622 TT
1 TT
4476624 ATTTGAGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 5 0.18
9 23 0.82
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (9 bp):
TTTTGAATA
Found at i:4476676 original size:23 final size:23
Alignment explanation
Indices: 4476650--4476953 Score: 317
Period size: 23 Copynumber: 13.3 Consensus size: 23
4476640 AACCTAATTA
4476650 AATTGAAA-AGAAAACCCTAACCT
1 AATT-AAATAGAAAACCCTAACCT
*
4476673 AATTAAATTGAAAACCCTAACCT
1 AATTAAATAGAAAACCCTAACCT
4476696 AATTAAATTA-AAAACCCTAACCT
1 AATTAAA-TAGAAAACCCTAACCT
4476719 AATTAAATTA-AAAACCCTAACCT
1 AATTAAA-TAGAAAACCCTAACCT
*
4476742 AATTAAAAAGAAAACCCTAACCT
1 AATTAAATAGAAAACCCTAACCT
**** *
4476765 AATTAAACCCTAAACCATAACCT
1 AATTAAATAGAAAACCCTAACCT
4476788 AATTAAATTA-AAAACCCTAACCT
1 AATTAAA-TAGAAAACCCTAACCT
4476811 AATTAAATTGAAAAGAAAACCCTAACCT
1 AATTAAA-T----AGAAAACCCTAACCT
* *
4476839 AAGTAAATTGAAAACCCTAACCT
1 AATTAAATAGAAAACCCTAACCT
*
4476862 AATTAAATTA-AAAACCATAACCT
1 AATTAAA-TAGAAAACCCTAACCT
* *
4476885 AATTAAAAAGAAAACCTTAACCT
1 AATTAAATAGAAAACCCTAACCT
4476908 AA-T---T---AAACCCTAACCT
1 AATTAAATAGAAAACCCTAACCT
*
4476924 AATTAAATTGAAAACCCTAACCT
1 AATTAAATAGAAAACCCTAACCT
4476947 AATTAAA
1 AATTAAA
4476954 CCCTAAACCC
Statistics
Matches: 242, Mismatches: 21, Indels: 36
0.81 0.07 0.12
Matches are distributed among these distances:
16 13 0.05
17 1 0.00
20 1 0.00
22 6 0.02
23 198 0.82
24 2 0.01
27 2 0.01
28 19 0.08
ACGTcount: A:0.52, C:0.21, G:0.03, T:0.23
Consensus pattern (23 bp):
AATTAAATAGAAAACCCTAACCT
Found at i:4476739 original size:69 final size:68
Alignment explanation
Indices: 4476660--4476953 Score: 386
Period size: 69 Copynumber: 4.3 Consensus size: 68
4476650 AATTGAAAAG
**
4476660 AAAACCCTAACCTAATTAAATTGAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAA
1 AAAACCCTAACCTAATTAAAAAGAAAACCCTAACCTAATTAAATT-AAAACCCTAACCTAATTAA
4476725 ATTA
65 ATTA
* *
4476729 AAAACCCTAACCTAATTAAAAAGAAAACCCTAACCTAATTAAACCCT-AAACCATAACCTAATTA
1 AAAACCCTAACCTAATTAAAAAGAAAACCCTAACCTAATTAAA--TTAAAACCCTAACCTAATTA
4476793 AATTA
64 AATTA
*
4476798 AAAACCCTAACCTAATTAAATTGAAAAGAAAACCCTAACCTAAGTAAATTGAAAACCCTAACCTA
1 AAAACCCTAACCTAATT--A---AAAAGAAAACCCTAACCTAATTAAATT-AAAACCCTAACCTA
4476863 ATTAAATTA
60 ATTAAATTA
* *
4476872 AAAACCATAACCTAATTAAAAAGAAAACCTTAACC----T-AATT-AAACCCTAACCTAATTAAA
1 AAAACCCTAACCTAATTAAAAAGAAAACCCTAACCTAATTAAATTAAAACCCTAACCTAATTAAA
*
4476931 TTG
66 TTA
4476934 AAAACCCTAACCTAATTAAA
1 AAAACCCTAACCTAATTAAA
4476954 CCCTAAACCC
Statistics
Matches: 205, Mismatches: 11, Indels: 25
0.85 0.05 0.10
Matches are distributed among these distances:
62 40 0.20
64 4 0.02
65 1 0.00
69 95 0.46
71 2 0.01
72 2 0.01
74 61 0.30
ACGTcount: A:0.52, C:0.22, G:0.03, T:0.23
Consensus pattern (68 bp):
AAAACCCTAACCTAATTAAAAAGAAAACCCTAACCTAATTAAATTAAAACCCTAACCTAATTAAA
TTA
Found at i:4476956 original size:39 final size:39
Alignment explanation
Indices: 4476827--4476959 Score: 158
Period size: 39 Copynumber: 3.2 Consensus size: 39
4476817 ATTGAAAAGA
*
4476827 AAACCCTAACCTAAGTAAATTGAAAACCCTAACCTAATTAAATT
1 AAACCCTAACCTAATTAAATTGAAAACCCTAACC----T-AATT
* ** *
4476871 AAAAACCATAACCTAATTAAAAAGAAAACCTTAACCTAATT
1 --AAACCCTAACCTAATTAAATTGAAAACCCTAACCTAATT
4476912 AAACCCTAACCTAATTAAATTGAAAACCCTAACCTAATT
1 AAACCCTAACCTAATTAAATTGAAAACCCTAACCTAATT
4476951 AAACCCTAA
1 AAACCCTAA
4476960 ACCCTAACCT
Statistics
Matches: 78, Mismatches: 9, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
39 44 0.56
41 4 0.05
42 1 0.01
46 29 0.37
ACGTcount: A:0.50, C:0.23, G:0.03, T:0.23
Consensus pattern (39 bp):
AAACCCTAACCTAATTAAATTGAAAACCCTAACCTAATT
Found at i:4476959 original size:16 final size:16
Alignment explanation
Indices: 4476896--4476930 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
4476886 ATTAAAAAGA
*
4476896 AAACCTTAACCTAATT
1 AAACCCTAACCTAATT
4476912 AAACCCTAACCTAATT
1 AAACCCTAACCTAATT
4476928 AAA
1 AAA
4476931 TTGAAAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (16 bp):
AAACCCTAACCTAATT
Found at i:4476961 original size:23 final size:23
Alignment explanation
Indices: 4476911--4476969 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
4476901 TTAACCTAAT
***
4476911 TAAACCCTAACCTAATTAAATTG
1 TAAACCCTAACCTAATTAAACCC
*
4476934 AAAACCCTAACCTAATTAAACCC
1 TAAACCCTAACCTAATTAAACCC
4476957 TAAACCCTAACCT
1 TAAACCCTAACCT
4476970 TTGTACTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.44, C:0.31, G:0.02, T:0.24
Consensus pattern (23 bp):
TAAACCCTAACCTAATTAAACCC
Found at i:4476962 original size:62 final size:62
Alignment explanation
Indices: 4476707--4476969 Score: 256
Period size: 62 Copynumber: 3.9 Consensus size: 62
4476697 ATTAAATTAA
* *
4476707 AAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAAAAGAAAACCCTAACCTAATT
1 AAACCCTAACCTAATTAAATTAAAAACCATAACCTAATTAAAAACAAAACCCTAACCTAATT
* *
4476769 AAACCCTAAACCATAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTGAAAAGAAAACCCT
1 AAA--C----CC-TAACCTAATTAAATTAAAAACCATAACCTAATT--A---AAAACAAAACCCT
4476834 AACCTAAGTAAATT
54 AACC----T-AATT
* *
4476848 GAAAACCCTAACCTAATTAAATTAAAAACCATAACCTAATTAAAAAGAAAACCTTAACCTAATT
1 --AAACCCTAACCTAATTAAATTAAAAACCATAACCTAATTAAAAACAAAACCCTAACCTAATT
* * ** *
4476912 AAACCCTAACCTAATTAAATTGAAAACCCTAACCTAATTAAACCCTAAACCCTAACCT
1 AAACCCTAACCTAATTAAATTAAAAACCATAACCTAATTAAAAACAAAACCCTAACCT
4476970 TTGTACTTTT
Statistics
Matches: 173, Mismatches: 9, Indels: 38
0.79 0.04 0.17
Matches are distributed among these distances:
62 54 0.31
64 5 0.03
65 1 0.01
68 2 0.01
69 49 0.28
71 1 0.01
72 1 0.01
74 49 0.28
75 2 0.01
78 1 0.01
79 5 0.03
81 3 0.02
ACGTcount: A:0.51, C:0.24, G:0.03, T:0.23
Consensus pattern (62 bp):
AAACCCTAACCTAATTAAATTAAAAACCATAACCTAATTAAAAACAAAACCCTAACCTAATT
Found at i:4476969 original size:46 final size:46
Alignment explanation
Indices: 4476659--4476953 Score: 361
Period size: 46 Copynumber: 6.5 Consensus size: 46
4476649 AAATTGAAAA
*
4476659 GAAAACCCTAACCTAATTAAATTGAAAACCCTAACCTAATTAAATT
1 GAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATT
* **
4476705 AAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAAAA
1 GAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATT
**** *
4476751 GAAAACCCTAACCTAATTAAACCCTAAACCATAACCTAATTAAATT
1 GAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATT
* *
4476797 AAAAACCCTAACCTAATTAAATTGAAAAGAAAACCCTAACCTAAGTAAATT
1 GAAAACCCTAACCTAATTAAATT----A-AAAACCCTAACCTAATTAAATT
* **
4476848 GAAAACCCTAACCTAATTAAATTAAAAACCATAACCTAATTAAAAA
1 GAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATT
*
4476894 GAAAACCTTAACC----T-AATT--AAACCCTAACCTAATTAAATT
1 GAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATT
4476933 GAAAACCCTAACCTAATTAAA
1 GAAAACCCTAACCTAATTAAA
4476954 CCCTAAACCC
Statistics
Matches: 210, Mismatches: 29, Indels: 22
0.80 0.11 0.08
Matches are distributed among these distances:
39 30 0.14
41 4 0.02
42 1 0.00
43 1 0.00
44 2 0.01
46 130 0.62
47 1 0.00
51 41 0.20
ACGTcount: A:0.52, C:0.22, G:0.03, T:0.23
Consensus pattern (46 bp):
GAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATT
Found at i:4478434 original size:124 final size:124
Alignment explanation
Indices: 4478210--4478549 Score: 538
Period size: 124 Copynumber: 2.7 Consensus size: 124
4478200 AACATGCTAC
* *
4478210 TGTAGCAAAAGCGCGTCTACGAGGGCGAGATTTTCACAAATTCTTCTCAAATAGCATCCTGCTAG
1 TGTAGCAAAAGCGCGTCCACGAGGGCGCGA-TTTCACAAATTCTTCTCAAATAGCATCCTGCTAG
4478275 AAGCGATTTTATACTATTTGCTCAGAAACGCCAAAAAAAATTATTTCATCCATGACCTAA
65 AAGCGATTTTATACTATTTGCTCAGAAACGCCAAAAAAAATTATTTCATCCATGACCTAA
*
4478335 TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTGT-ACAAATTATTCTCAAATAGCATCCTGCTAG
1 TGTAGCAAAAGCGCGTCCACGAGGGCGCGATT-TCACAAATTCTTCTCAAATAGCATCCTGCTAG
* * * * *
4478399 AAGTGATTTTATACTATTTGCTCAGAAAGGTCAAAAAAATTTATTTCATCCATGACCTAC
65 AAGCGATTTTATACTATTTGCTCAGAAACGCCAAAAAAAATTATTTCATCCATGACCTAA
* * *
4478459 TGTTGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTTAAATAGCATCTTGCTAGA
1 TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTAGA
* *
4478524 AGCGGTTTTATACTATTTGATCAGAA
66 AGCGATTTTATACTATTTGCTCAGAA
4478550 GCATCAACTC
Statistics
Matches: 198, Mismatches: 15, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
123 1 0.01
124 168 0.85
125 29 0.15
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (124 bp):
TGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTAGA
AGCGATTTTATACTATTTGCTCAGAAACGCCAAAAAAAATTATTTCATCCATGACCTAA
Found at i:4479251 original size:18 final size:16
Alignment explanation
Indices: 4479217--4479259 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
4479207 TAATCTTTTT
4479217 ATTTTTATAAAAATTG
1 ATTTTTATAAAAATTG
**
4479233 AAATTTTTATAAATCTTG
1 --ATTTTTATAAAAATTG
4479251 ATTTTTATA
1 ATTTTTATA
4479260 TATTTTTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 9 0.39
18 14 0.61
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (16 bp):
ATTTTTATAAAAATTG
Found at i:4491293 original size:17 final size:18
Alignment explanation
Indices: 4491266--4491299 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4491256 TAGTGAAACA
*
4491266 ATAACTTTTTATGATTTC
1 ATAACTTTTTATCATTTC
4491284 ATAA-TTTTTATCATTT
1 ATAACTTTTTATCATTT
4491300 TAATAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.29, C:0.09, G:0.03, T:0.59
Consensus pattern (18 bp):
ATAACTTTTTATCATTTC
Found at i:4491305 original size:18 final size:18
Alignment explanation
Indices: 4491265--4491331 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 18
4491255 ATAGTGAAAC
*
4491265 AATAACTTTTTATGA-TTT
1 AATAA-TTTTTATCATTTT
*
4491283 CATAATTTTTATCATTTT
1 AATAATTTTTATCATTTT
*
4491301 AATAATTATTAATACATTTT
1 AATAATT-TTTAT-CATTTT
* *
4491321 TATAAATTTTA
1 AATAATTTTTA
4491332 ATAATTTATT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
17 8 0.21
18 13 0.33
19 7 0.18
20 11 0.28
ACGTcount: A:0.37, C:0.06, G:0.01, T:0.55
Consensus pattern (18 bp):
AATAATTTTTATCATTTT
Found at i:4491314 original size:10 final size:9
Alignment explanation
Indices: 4491284--4491338 Score: 56
Period size: 9 Copynumber: 5.8 Consensus size: 9
4491274 TTATGATTTC
*
4491284 ATAATTTTT
1 ATAATTTTA
*
4491293 ATCATTTTA
1 ATAATTTTA
4491302 ATAATTATTA
1 ATAATT-TTA
*
4491312 ATACATTTTT
1 ATA-ATTTTA
4491322 ATAAATTTTA
1 AT-AATTTTA
4491332 ATAATTT
1 ATAATTT
4491339 ATTATTATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
9 17 0.45
10 17 0.45
11 4 0.11
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (9 bp):
ATAATTTTA
Found at i:4491320 original size:20 final size:20
Alignment explanation
Indices: 4491286--4491338 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
4491276 ATGATTTCAT
*
4491286 AATTTTTAT-CATTTTAAT-
1 AATTTTAATACATTTTAATA
*
4491304 AATTATTAATACATTTTTATA
1 AATT-TTAATACATTTTAATA
4491325 AATTTTAATA-ATTT
1 AATTTTAATACATTT
4491339 ATTATTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 4 0.13
19 8 0.27
20 14 0.47
21 4 0.13
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.57
Consensus pattern (20 bp):
AATTTTAATACATTTTAATA
Found at i:4491343 original size:20 final size:21
Alignment explanation
Indices: 4491295--4491343 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
4491285 TAATTTTTAT
*
4491295 CATTTTAAT-AATTATTAATA
1 CATTTTTATAAATTATTAATA
4491315 CATTTTTATAAATT-TTAATA
1 CATTTTTATAAATTATTAATA
4491335 -ATTTATTAT
1 CATTT-TTAT
4491344 TATTACAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 4 0.15
20 18 0.69
21 4 0.15
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (21 bp):
CATTTTTATAAATTATTAATA
Found at i:4491555 original size:10 final size:9
Alignment explanation
Indices: 4491494--4491575 Score: 60
Period size: 9 Copynumber: 8.8 Consensus size: 9
4491484 CTTTTTAGTT
4491494 ATTTTTATTA
1 ATTTTTA-TA
**
4491504 ATTTTTAGG
1 ATTTTTATA
*
4491513 ATTTTTAAA
1 ATTTTTATA
4491522 ATTTTTATA
1 ATTTTTATA
4491531 TAGTTTTT-TA
1 -A-TTTTTATA
4491541 TATTTTTATA
1 -ATTTTTATA
*
4491551 GA-TTTGATA
1 -ATTTTTATA
*
4491560 ATTTCTATA
1 ATTTTTATA
4491569 ATTTTTA
1 ATTTTTA
4491576 AAATATTCTA
Statistics
Matches: 58, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
8 1 0.02
9 37 0.64
10 15 0.26
11 5 0.09
ACGTcount: A:0.30, C:0.01, G:0.06, T:0.62
Consensus pattern (9 bp):
ATTTTTATA
Found at i:4495009 original size:15 final size:16
Alignment explanation
Indices: 4494975--4495011 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
4494965 TTTCATGCAT
*
4494975 TTTTATTTTTTAAGTA
1 TTTTATTTTATAAGTA
4494991 -TTTATTTTAT-AGTA
1 TTTTATTTTATAAGTA
4495005 TTTTATT
1 TTTTATT
4495012 ATACTTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.70
Consensus pattern (16 bp):
TTTTATTTTATAAGTA
Found at i:4495660 original size:21 final size:22
Alignment explanation
Indices: 4495635--4495687 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 22
4495625 TTATTTTTTA
4495635 TTTTTATAAAATTTCAAATA-G
1 TTTTTATAAAATTTCAAATATG
* * *
4495656 TTTTT-CAAAATTTTAAATATT
1 TTTTTATAAAATTTCAAATATG
4495677 TTTTTATAAAA
1 TTTTTATAAAA
4495688 ATTTTATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 12 0.46
21 10 0.38
22 4 0.15
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTTTATAAAATTTCAAATATG
Found at i:4499317 original size:8 final size:8
Alignment explanation
Indices: 4499304--4499337 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
4499294 ATAATAAATA
4499304 TTTTATTT
1 TTTTATTT
4499312 TTTTATTT
1 TTTTATTT
4499320 TTTTAATTT
1 TTTT-ATTT
*
4499329 TTTAATTT
1 TTTTATTT
4499337 T
1 T
4499338 AAAATACTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTATTT
Found at i:4499329 original size:16 final size:17
Alignment explanation
Indices: 4499304--4499337 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4499294 ATAATAAATA
*
4499304 TTTT-ATTTTTTTATTT
1 TTTTAATTTTTTAATTT
4499320 TTTTAATTTTTTAATTT
1 TTTTAATTTTTTAATTT
4499337 T
1 T
4499338 AAAATACTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTAATTTTTTAATTT
Found at i:4499434 original size:11 final size:11
Alignment explanation
Indices: 4499334--4499461 Score: 71
Period size: 11 Copynumber: 12.4 Consensus size: 11
4499324 AATTTTTTAA
*
4499334 TTTTAAAATAC
1 TTTTAAAATAT
4499345 TTTTAAAATACT
1 TTTTAAAATA-T
*
4499357 TTTTTAAAT-T
1 TTTTAAAATAT
*
4499367 TTTT----TAA
1 TTTTAAAATAT
4499374 TTTTAAAATAT
1 TTTTAAAATAT
4499385 TTTTAAAATACT
1 TTTTAAAATA-T
*
4499397 TTGTAAAAT-T
1 TTTTAAAATAT
*
4499407 TTTT----TAA
1 TTTTAAAATAT
*
4499414 TTTAAAAATAT
1 TTTTAAAATAT
4499425 TTTTAAAATAT
1 TTTTAAAATAT
***
4499436 TTTT-TTTTAT
1 TTTTAAAATAT
4499446 TTTTAAAATAAT
1 TTTTAAAAT-AT
4499458 TTTT
1 TTTT
4499462 TGGTATTTAT
Statistics
Matches: 87, Mismatches: 16, Indels: 27
0.67 0.12 0.21
Matches are distributed among these distances:
6 2 0.02
7 7 0.08
10 16 0.18
11 39 0.45
12 23 0.26
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:4499449 original size:40 final size:40
Alignment explanation
Indices: 4499317--4499441 Score: 189
Period size: 40 Copynumber: 3.1 Consensus size: 40
4499307 TATTTTTTTA
* *
4499317 TTTTTTTAA-TTTTTTAATTTTAAAATACTTTTAAAATAC
1 TTTTTTAAATTTTTTTAATTTTAAAATATTTTTAAAATAC
4499356 TTTTTTAAATTTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTAAATTTTTTTAATTTTAAAATATTTTTAAAATAC
* * * *
4499396 TTTGTAAAATTTTTTTAATTTAAAAATATTTTTAAAATAT
1 TTTTTTAAATTTTTTTAATTTTAAAATATTTTTAAAATAC
4499436 TTTTTT
1 TTTTTT
4499442 TTATTTTTAA
Statistics
Matches: 77, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 8 0.10
40 69 0.90
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (40 bp):
TTTTTTAAATTTTTTTAATTTTAAAATATTTTTAAAATAC
Found at i:4499459 original size:22 final size:21
Alignment explanation
Indices: 4499422--4499462 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
4499412 AATTTAAAAA
4499422 TATTTTTAAAATATTTTTTTT
1 TATTTTTAAAATATTTTTTTT
*
4499443 TATTTTTAAAATAATTTTTT
1 TATTTTTAAAATATTTTTTT
4499463 GGTATTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TATTTTTAAAATATTTTTTTT
Found at i:4499468 original size:22 final size:21
Alignment explanation
Indices: 4499422--4499469 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
4499412 AATTTAAAAA
**
4499422 TATTTTTAAAATATTTTTTTT
1 TATTTTTAAAATATTTTTTGG
4499443 TATTTTTAAAATAATTTTTTGG
1 TATTTTTAAAAT-ATTTTTTGG
4499465 TATTT
1 TATTT
4499470 ATTTAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (21 bp):
TATTTTTAAAATATTTTTTGG
Found at i:4502775 original size:12 final size:12
Alignment explanation
Indices: 4502758--4502788 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
4502748 TATTAGGTTC
4502758 TATTTTTTT-TA
1 TATTTTTTTATA
4502769 TATTTTTTTATA
1 TATTTTTTTATA
4502781 TATTTTTT
1 TATTTTTT
4502789 AGTTTTTACC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (12 bp):
TATTTTTTTATA
Found at i:4503649 original size:18 final size:19
Alignment explanation
Indices: 4503613--4503650 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
4503603 TTGTAATGTA
4503613 TAATTTTTCTTTCATTTTT
1 TAATTTTTCTTTCATTTTT
4503632 TAATTTATT-TTT-ATTTTT
1 TAATTT-TTCTTTCATTTTT
4503650 T
1 T
4503651 CCAGAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 9 0.50
20 2 0.11
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (19 bp):
TAATTTTTCTTTCATTTTT
Found at i:4517093 original size:21 final size:21
Alignment explanation
Indices: 4517047--4517093 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
4517037 TGGCCTGCTT
* *
4517047 TGCTTCTCTCGCTGCAGCTTC
1 TGCTTCCCTCGCTGCAGCCTC
* *
4517068 CGCTTCCCTCGCTGCCGCCTC
1 TGCTTCCCTCGCTGCAGCCTC
4517089 TGCTT
1 TGCTT
4517094 TAAGTTGTAG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.02, C:0.45, G:0.19, T:0.34
Consensus pattern (21 bp):
TGCTTCCCTCGCTGCAGCCTC
Found at i:4520268 original size:9 final size:9
Alignment explanation
Indices: 4520251--4520501 Score: 175
Period size: 9 Copynumber: 28.8 Consensus size: 9
4520241 TATGTATTAA
*
4520251 GTAAATTAT
1 GTAAGTTAT
4520260 GTAAGTTAT
1 GTAAGTTAT
*
4520269 GTACGTGTA-
1 GTAAGT-TAT
4520278 -TAAGTTAT
1 GTAAGTTAT
*
4520286 GTAAGTTTT
1 GTAAGTTAT
*
4520295 GT-A-TTAA
1 GTAAGTTAT
**
4520302 GTAAACTAT
1 GTAAGTTAT
*
4520311 GTAAGTTGT
1 GTAAGTTAT
4520320 GT-A-TTAT
1 GTAAGTTAT
*
4520327 GTAACTTAT
1 GTAAGTTAT
4520336 GTAAGTTAT
1 GTAAGTTAT
** *
4520345 CAAAGTAAT
1 GTAAGTTAT
*
4520354 GTATGTTAT
1 GTAAGTTAT
4520363 GTAAG-T-T
1 GTAAGTTAT
4520370 GTAAGTTAT
1 GTAAGTTAT
*
4520379 -TATGTATTAT
1 GTAAG--TTAT
* * *
4520389 ATAACTTCT
1 GTAAGTTAT
4520398 GTAAGTTAT
1 GTAAGTTAT
4520407 GTAAGTTAT
1 GTAAGTTAT
*
4520416 GTAAGTTGT
1 GTAAGTTAT
*
4520425 GTAAGCTAT
1 GTAAGTTAT
* *
4520434 TTTAGTTAT
1 GTAAGTTAT
4520443 GTAAGCTT-T
1 GTAAG-TTAT
4520452 GT-A-TTAT
1 GTAAGTTAT
4520459 GTAAGTTAT
1 GTAAGTTAT
*
4520468 GTAGGTTAT
1 GTAAGTTAT
*
4520477 GTAAGTTGT
1 GTAAGTTAT
*
4520486 GTAAATTAT
1 GTAAGTTAT
4520495 GTAAGTT
1 GTAAGTT
4520502 CTTGTACATA
Statistics
Matches: 184, Mismatches: 42, Indels: 32
0.71 0.16 0.12
Matches are distributed among these distances:
6 2 0.01
7 20 0.11
8 15 0.08
9 137 0.74
10 8 0.04
11 2 0.01
ACGTcount: A:0.31, C:0.03, G:0.20, T:0.45
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:4520271 original size:25 final size:25
Alignment explanation
Indices: 4520240--4520344 Score: 115
Period size: 25 Copynumber: 4.2 Consensus size: 25
4520230 TAATATATAT
4520240 TTATGTATTAAGTAAATTATGTAAG
1 TTATGTATTAAGTAAATTATGTAAG
*
4520265 TTATGTACGTGT-A-TAAGTTATGTAAG
1 TTATGTA--T-TAAGTAAATTATGTAAG
* *
4520291 TTTTGTATTAAGTAAACTATGTAAG
1 TTATGTATTAAGTAAATTATGTAAG
* * *
4520316 TTGTGTATTATGTAACTTATGTAAG
1 TTATGTATTAAGTAAATTATGTAAG
4520341 TTAT
1 TTAT
4520345 CAAAGTAATG
Statistics
Matches: 66, Mismatches: 9, Indels: 10
0.78 0.11 0.12
Matches are distributed among these distances:
23 1 0.02
24 2 0.03
25 42 0.64
26 18 0.27
27 2 0.03
28 1 0.02
ACGTcount: A:0.33, C:0.03, G:0.18, T:0.46
Consensus pattern (25 bp):
TTATGTATTAAGTAAATTATGTAAG
Found at i:4520768 original size:13 final size:13
Alignment explanation
Indices: 4520750--4520801 Score: 77
Period size: 13 Copynumber: 4.0 Consensus size: 13
4520740 GAAATTTTAG
*
4520750 TAAGTAATGTATT
1 TAAGTAATATATT
*
4520763 TAAGTAATTTATT
1 TAAGTAATATATT
4520776 TAAGTAATATATT
1 TAAGTAATATATT
*
4520789 CAAGTAATATATT
1 TAAGTAATATATT
4520802 AAGAGTAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (13 bp):
TAAGTAATATATT
Found at i:4520776 original size:53 final size:53
Alignment explanation
Indices: 4520647--4520782 Score: 191
Period size: 53 Copynumber: 2.6 Consensus size: 53
4520637 TTTATAGCGG
* *
4520647 GTAATATATTCAAGTAACATATTTAAGTAAAAAATTTAACCAAATTTTAGTAA
1 GTAATGTATTTAAGTAACATATTTAAGTAAAAAATTTAACCAAATTTTAGTAA
* * ** *
4520700 TTAATGTATCTGCGTAACATATTTAAGTAAAAAATTTAACGAAATTTTAGTAA
1 GTAATGTATTTAAGTAACATATTTAAGTAAAAAATTTAACCAAATTTTAGTAA
**
4520753 GTAATGTATTTAAGTAATTTATTTAAGTAA
1 GTAATGTATTTAAGTAACATATTTAAGTAA
4520783 TATATTCAAG
Statistics
Matches: 70, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
53 70 1.00
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (53 bp):
GTAATGTATTTAAGTAACATATTTAAGTAAAAAATTTAACCAAATTTTAGTAA
Found at i:4532501 original size:17 final size:17
Alignment explanation
Indices: 4532479--4532519 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
4532469 CAGAAATTTC
*
4532479 TGTTTCTCTAGCATGTA
1 TGTTTCTCTACCATGTA
* *
4532496 TGTTTCTGTACCATTTA
1 TGTTTCTCTACCATGTA
4532513 TGTTTCT
1 TGTTTCT
4532520 TTATTTTCTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.15, C:0.17, G:0.15, T:0.54
Consensus pattern (17 bp):
TGTTTCTCTACCATGTA
Found at i:4532544 original size:7 final size:7
Alignment explanation
Indices: 4532523--4532608 Score: 111
Period size: 7 Copynumber: 12.3 Consensus size: 7
4532513 TGTTTCTTTA
4532523 TTTTCTG
1 TTTTCTG
4532530 TTTT-TG
1 TTTTCTG
4532536 TTTTCTG
1 TTTTCTG
4532543 TTTTCTG
1 TTTTCTG
4532550 TTTTCTG
1 TTTTCTG
**
4532557 CATTCTG
1 TTTTCTG
4532564 TTTTCTG
1 TTTTCTG
*
4532571 TTTTCTA
1 TTTTCTG
*
4532578 TTTTTTG
1 TTTTCTG
4532585 TTTTCTG
1 TTTTCTG
*
4532592 TTTTGCTA
1 TTTT-CTG
4532600 TTTTCTG
1 TTTTCTG
4532607 TT
1 TT
4532609 GAATGAAGTG
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
6 6 0.09
7 55 0.82
8 6 0.09
ACGTcount: A:0.03, C:0.13, G:0.13, T:0.71
Consensus pattern (7 bp):
TTTTCTG
Found at i:4533335 original size:192 final size:193
Alignment explanation
Indices: 4533003--4533535 Score: 783
Period size: 192 Copynumber: 2.8 Consensus size: 193
4532993 ATATTAAAAG
*
4533003 TATATATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATATTGTTCGAATA
1 TATAAATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATATTGTTCGAATA
* *
4533068 TATTTTTTAAAATTTATATATTACATTA-TGGGAATATATATATGTTAATA-TTTTACAATTTAA
66 TAATTTTTAAAATTTATAT-TTACATTACT--TAATATATATATGTTAATATTTTTACAATTTAA
*
4533131 TTTAACTTATTACTAATACATATATTGTTCG-A-ATAATTTTTAAATTTATATATTACATGACT-
128 TTTAACTTATTACTAATACATATATTGTTCGAATATAATTTTTAAAATTATAT-TTACATGA-TG
*
4533193 TAA
191 GAA
4533196 -ATAAATATGTTAATATTTTTACAATTTAATTTAAC-TATTACTAATACATATATT-TTCGAATA
1 TATAAATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATATTGTTCGAATA
4533258 TAATTTTTCAAAATTTATATGTTACATTACTTAAATATATATATGTTAATATTTTTACAATTTAA
66 TAATTTTT-AAAATTTATAT-TTACATTACTT-AATATATATATGTTAATATTTTTACAATTTAA
*
4533323 TTTAACTTATTACTAATACATATATTGTTCGAATATAATTTTTAAAATTATATTTACATTATGGG
128 TTTAACTTATTACTAATACATATATTGTTCGAATATAATTTTTAAAATTATATTTACATGAT-GG
4533388 AA
192 AA
* *
4533390 TATATATGTGTTAATATTTTTACAA-TTAATTTAACTTATTACTAATACATATATTGTTCGAATA
1 TATAAATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATATTGTTCGAATA
* *
4533454 TAATTTTT-AAATTT-TATATACATGAC-T--TATATATATGTTAATATTTTTACAATTTAATTT
66 TAATTTTTAAAATTTATATTTACATTACTTAATATATATATGTTAATATTTTTACAATTTAATTT
4533514 -ACTTATTACTAATA-ATATATTG
131 AACTTATTACTAATACATATATTG
4533536 AGTAAGAACA
Statistics
Matches: 318, Mismatches: 11, Indels: 29
0.89 0.03 0.08
Matches are distributed among these distances:
186 8 0.03
187 14 0.04
188 33 0.10
190 15 0.05
191 57 0.18
192 87 0.27
193 11 0.03
194 36 0.11
195 41 0.13
196 16 0.05
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.49
Consensus pattern (193 bp):
TATAAATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATATTGTTCGAATA
TAATTTTTAAAATTTATATTTACATTACTTAATATATATATGTTAATATTTTTACAATTTAATTT
AACTTATTACTAATACATATATTGTTCGAATATAATTTTTAAAATTATATTTACATGATGGAA
Found at i:4533551 original size:290 final size:289
Alignment explanation
Indices: 4533003--4533567 Score: 921
Period size: 290 Copynumber: 1.9 Consensus size: 289
4532993 ATATTAAAAG
4533003 TATATATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATATTGTTCGAATA
1 TATATATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATATTGTTCGAATA
*
4533068 TATTTTTTAAAATTTATATATTACATTATGGGAATATATATATGTTAATATTTTACAATTTAATT
66 TAATTTTTAAAATTTATATATTACATTATGGGAATATATATATGTTAATATTTTACAATTTAATT
4533133 TAACTTATTACTAATACATATATTGTTCGAATAATTTTTAAATTTATATATTACATGACTTAAAT
131 TAACTTATTACTAATACATATATTGTTCGAATAATTTTTAAATTTATATATTACATGACTT-AAT
**
4533198 AAATATGTTAATATTTTTACAATTTAATTTAACTATTACTAATACATATATTTTCGAATATAATT
195 AAATATGTTAATATTTTTACAATTTAATTTAACTATTACTAATACATATATTTAAGAATATAATT
* *
4533263 TTTCAAAATTTATATGTTACATTACTTAAA
260 TTTAAAAATATATATGTTACATTACTTAAA
4533293 TATATATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATATTGTTCGAATA
1 TATATATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATATTGTTCGAATA
*
4533358 TAATTTTTAAAA-TTATAT-TTACATTATGGGAATATATATGTGTTAATATTTTTACAA-TTAAT
66 TAATTTTTAAAATTTATATATTACATTATGGGAATATATATATGTTAATA-TTTTACAATTTAAT
4533420 TTAACTTATTACTAATACATATATTGTTCGAATATAATTTTTAAATTT-TATA-TACATGACTT-
130 TTAACTTATTACTAATACATATATTGTTCG-A-ATAATTTTTAAATTTATATATTACATGACTTA
*
4533482 ATATATATGTTAATATTTTTACAATTTAATTT-ACTTATTACTAATA-ATATATTGAGTAAGAAC
193 ATAAATATGTTAATATTTTTACAATTTAATTTAAC-TATTACTAATACATATATT---TAAG-A-
4533545 ATATAATTTTTAAAAATATATAT
252 ATATAATTTTTAAAAATATATAT
4533568 ATTTAAGTAA
Statistics
Matches: 259, Mismatches: 7, Indels: 18
0.91 0.02 0.06
Matches are distributed among these distances:
285 9 0.03
286 42 0.16
288 76 0.29
289 20 0.08
290 112 0.43
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (289 bp):
TATATATATGTTAATATTTTTACAATTTAATTTAACTTATTACTAATACATATATTGTTCGAATA
TAATTTTTAAAATTTATATATTACATTATGGGAATATATATATGTTAATATTTTACAATTTAATT
TAACTTATTACTAATACATATATTGTTCGAATAATTTTTAAATTTATATATTACATGACTTAATA
AATATGTTAATATTTTTACAATTTAATTTAACTATTACTAATACATATATTTAAGAATATAATTT
TTAAAAATATATATGTTACATTACTTAAA
Found at i:4533677 original size:48 final size:48
Alignment explanation
Indices: 4533625--4533776 Score: 188
Period size: 48 Copynumber: 3.1 Consensus size: 48
4533615 TATATGTATT
4533625 AGTAATAAGTTAAATTAAATTGTAAAAATATTAACATATATATATTTA
1 AGTAATAAGTTAAATTAAATTGTAAAAATATTAACATATATATATTTA
* *
4533673 AGTAAT--G-TAATATATAAATTTTAAAAATTATATTGAACA-ATATATGTATT-
1 AGTAATAAGTTAA-AT-TAAATTGT-AAAA--ATATT-AACATATATATAT-TTA
4533723 AGTAATAAGTTAAATTAAATTGTAAAAATATTAACATATATATATTTA
1 AGTAATAAGTTAAATTAAATTGTAAAAATATTAACATATATATATTTA
4533771 AGTAAT
1 AGTAAT
4533777 GTAATATATA
Statistics
Matches: 88, Mismatches: 4, Indels: 24
0.76 0.03 0.21
Matches are distributed among these distances:
45 3 0.03
46 3 0.03
47 13 0.15
48 28 0.32
50 22 0.25
51 13 0.15
52 3 0.03
53 3 0.03
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.40
Consensus pattern (48 bp):
AGTAATAAGTTAAATTAAATTGTAAAAATATTAACATATATATATTTA
Found at i:4533868 original size:100 final size:100
Alignment explanation
Indices: 4533560--4533859 Score: 540
Period size: 98 Copynumber: 3.1 Consensus size: 100
4533550 ATTTTTAAAA
4533560 ATATATATATTTAAGTAATGTAATATATAAATTTTAAAAAATTATATTCGAACAATATATGTATT
1 ATATATATATTTAAGTAATGTAATATATAAATTTTAAAAAATTATATTCGAACAATATATGTATT
4533625 AGTAATAAGTTAAATTAAATTGTAAAAATATTAAC
66 AGTAATAAGTTAAATTAAATTGTAAAAATATTAAC
4533660 ATATATATATTTAAGTAATGTAATATATAAATTTT-AAAAATTATATT-GAACAATATATGTATT
1 ATATATATATTTAAGTAATGTAATATATAAATTTTAAAAAATTATATTCGAACAATATATGTATT
4533723 AGTAATAAGTTAAATTAAATTGTAAAAATATTAAC
66 AGTAATAAGTTAAATTAAATTGTAAAAATATTAAC
*
4533758 ATATATATATTTAAGTAATGTAATATATAAATTTTAAAAAAATATATTCGAACAATATATGTATT
1 ATATATATATTTAAGTAATGTAATATATAAATTTTAAAAAATTATATTCGAACAATATATGTATT
*
4533823 AGTAATAAGTT-AA-TAAATTGT-AAAATA-TAAT
66 AGTAATAAGTTAAATTAAATTGTAAAAATATTAAC
4533854 ATATAT
1 ATATAT
4533860 TTTAATATTA
Statistics
Matches: 196, Mismatches: 2, Indels: 8
0.95 0.01 0.04
Matches are distributed among these distances:
96 9 0.05
97 6 0.03
98 94 0.48
99 25 0.13
100 62 0.32
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.40
Consensus pattern (100 bp):
ATATATATATTTAAGTAATGTAATATATAAATTTTAAAAAATTATATTCGAACAATATATGTATT
AGTAATAAGTTAAATTAAATTGTAAAAATATTAAC
Found at i:4534283 original size:7 final size:7
Alignment explanation
Indices: 4534258--4534330 Score: 83
Period size: 7 Copynumber: 10.3 Consensus size: 7
4534248 CACTTCATTC
4534258 AACAGAA
1 AACAGAA
*
4534265 AATAGCAA
1 AACAG-AA
4534273 AACAGAA
1 AACAGAA
*
4534280 AACAAAA
1 AACAGAA
*
4534287 AATAGAA
1 AACAGAA
4534294 AACAGAA
1 AACAGAA
4534301 AACAGAA
1 AACAGAA
**
4534308 TGCAGAA
1 AACAGAA
*
4534315 AATAGAA
1 AACAGAA
4534322 AACAGAA
1 AACAGAA
4534329 AA
1 AA
4534331 TAAAGAAACA
Statistics
Matches: 53, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
7 47 0.89
8 6 0.11
ACGTcount: A:0.70, C:0.11, G:0.14, T:0.05
Consensus pattern (7 bp):
AACAGAA
Found at i:4534287 original size:21 final size:21
Alignment explanation
Indices: 4534258--4534332 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
4534248 CACTTCATTC
4534258 AACAGAAAATAGCAAAACAGAA
1 AACAGAAAATAG-AAAACAGAA
*
4534280 AACAAAAAATAGAAAACAGAA
1 AACAGAAAATAGAAAACAGAA
*** *
4534301 AACAGAATGCAGAAAATAGAA
1 AACAGAAAATAGAAAACAGAA
4534322 AACAGAAAATA
1 AACAGAAAATA
4534333 AAGAAACATA
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
21 33 0.75
22 11 0.25
ACGTcount: A:0.69, C:0.11, G:0.13, T:0.07
Consensus pattern (21 bp):
AACAGAAAATAGAAAACAGAA
Found at i:4534376 original size:18 final size:19
Alignment explanation
Indices: 4534334--4534377 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
4534324 CAGAAAATAA
*
4534334 AGAAACATAAAAATGGTAC
1 AGAAACATAAAAATGCTAC
* *
4534353 AGAAACAT-AACATGCTAG
1 AGAAACATAAAAATGCTAC
4534371 AGAAACA
1 AGAAACA
4534378 GAAATTTCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.57, C:0.14, G:0.16, T:0.14
Consensus pattern (19 bp):
AGAAACATAAAAATGCTAC
Found at i:4535978 original size:198 final size:198
Alignment explanation
Indices: 4535639--4536050 Score: 637
Period size: 198 Copynumber: 2.1 Consensus size: 198
4535629 TAATTAACCC
* *
4535639 ATTTGCGGCGTTTATATACCAGCGCCACTAGTAATGTGATCAAACGCTGTCGTTTCCCGATCAGT
1 ATTTGCGGCGTTTATATACCAGCGCCACTAGTAATATGATCAAACGCTGTCGTTCCCCGATCAGT
* * * * * * *
4535704 TAACTCAAAGTCATTGCGTTTTAGAGAAAACGGCATCGTCTCCATAAAAATTAAAACATTTTTGC
66 AAACTAAAACTCATGGCGTTTTAGACAAAACGGAATCGTCTCCATAAAAATTAAAACAATTTTGC
* *
4535769 GGTGTTTACTAAAAGCGCCACTAAA-AGTAAATAAGAAAACGAAGCCGTTTTCCTAAACAATTTC
131 AGCGTTTACTAAAAGCGCCACTAAAGA-TAAATAAGAAAACGAAGCCGTTTTCCTAAACAATTTC
4535833 TATA
195 TATA
* * *
4535837 CTTTGCGGCGTTTATATACTAGCGCCACTAGTAATATGATCAAACGCTGTCGTTCCCCGATTAGT
1 ATTTGCGGCGTTTATATACCAGCGCCACTAGTAATATGATCAAACGCTGTCGTTCCCCGATCAGT
4535902 AAACTAAAACTCATGGCGTTTTAGACAAAACGGAATCGTCTCCATAAAAATTAAAACAATTTTGC
66 AAACTAAAACTCATGGCGTTTTAGACAAAACGGAATCGTCTCCATAAAAATTAAAACAATTTTGC
* * *
4535967 AGCGTTTACTAAAAGCGCCACTAATGATAAATAAGAAAACGGAGCCGTTTTCGTAAACAATTTCT
131 AGCGTTTACTAAAAGCGCCACTAAAGATAAATAAGAAAACGAAGCCGTTTTCCTAAACAATTTCT
*
4536032 GTA
196 ATA
*
4536035 AATTGCGGCGTTTATA
1 ATTTGCGGCGTTTATA
4536051 CATAAACGCC
Statistics
Matches: 193, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
198 192 0.99
199 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (198 bp):
ATTTGCGGCGTTTATATACCAGCGCCACTAGTAATATGATCAAACGCTGTCGTTCCCCGATCAGT
AAACTAAAACTCATGGCGTTTTAGACAAAACGGAATCGTCTCCATAAAAATTAAAACAATTTTGC
AGCGTTTACTAAAAGCGCCACTAAAGATAAATAAGAAAACGAAGCCGTTTTCCTAAACAATTTCT
ATA
Found at i:4536538 original size:18 final size:19
Alignment explanation
Indices: 4536516--4536564 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
4536506 TAAAATAAAA
4536516 ATTTTAGTTTTTTTA-TTTC
1 ATTTTA-TTTTTTTATTTTC
*
4536535 TTTTTA-TTTTTTATTTTC
1 ATTTTATTTTTTTATTTTC
4536553 ATTTTATTTTTT
1 ATTTTATTTTTT
4536565 GTAATTTGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 7 0.27
18 9 0.35
19 10 0.38
ACGTcount: A:0.14, C:0.04, G:0.02, T:0.80
Consensus pattern (19 bp):
ATTTTATTTTTTTATTTTC
Found at i:4536546 original size:17 final size:18
Alignment explanation
Indices: 4536524--4536564 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
4536514 AAATTTTAGT
*
4536524 TTTTTTA-TTTCTTTTTA
1 TTTTTTATTTTCATTTTA
4536541 TTTTTTATTTTCATTTTA
1 TTTTTTATTTTCATTTTA
4536559 TTTTTT
1 TTTTTT
4536565 GTAATTTGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.12, C:0.05, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTTTTATTTTCATTTTA
Found at i:4536629 original size:16 final size:14
Alignment explanation
Indices: 4536600--4536626 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4536590 TTTACAATTC
4536600 CAAATTATTATATT
1 CAAATTATTATATT
4536614 CAAATTATTATAT
1 CAAATTATTATAT
4536627 ATTGCATATC
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:0.44, C:0.07, G:0.00, T:0.48
Consensus pattern (14 bp):
CAAATTATTATATT
Found at i:4536779 original size:13 final size:13
Alignment explanation
Indices: 4536761--4536785 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4536751 CCCGACTCCA
4536761 AACCCCTAACCCT
1 AACCCCTAACCCT
4536774 AACCCCTAACCC
1 AACCCCTAACCC
4536786 CTAAACTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.56, G:0.00, T:0.12
Consensus pattern (13 bp):
AACCCCTAACCCT
Found at i:4536780 original size:7 final size:7
Alignment explanation
Indices: 4536761--4536789 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
4536751 CCCGACTCCA
4536761 AACCCCT
1 AACCCCT
4536768 AA-CCCT
1 AACCCCT
4536774 AACCCCT
1 AACCCCT
4536781 AACCCCT
1 AACCCCT
4536788 AA
1 AA
4536790 ACTTTATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.34, C:0.52, G:0.00, T:0.14
Consensus pattern (7 bp):
AACCCCT
Found at i:4536860 original size:95 final size:97
Alignment explanation
Indices: 4536697--4536873 Score: 225
Period size: 95 Copynumber: 1.8 Consensus size: 97
4536687 TATAAAGAAC
* * ** * * * *
4536697 TTATTTAATATGTTAATTAAATAAGTACTAATTAATCCAAATCTTAATCCCTAACCCGACTCCAA
1 TTATTTAATATATAAATTAAATAAACACTAATTAATCCAAACCTTAAACCATAACCCGAATCCAA
4536762 ACCCCTAACCC-TAACCCCTAACCCCTAAACT
66 ACCCCTAACCCTTAACCCCTAACCCCTAAACT
* *
4536793 TTATTTAATATATAAATTAAA-AAACACTAATTAATCTAAACCTTAAACCATAACCC-AATCCTT
1 TTATTTAATATATAAATTAAATAAACACTAATTAATCCAAACCTTAAACCATAACCCGAATCC-A
*
4536856 AACCCTTAACCCTTAACC
65 AACCCCTAACCCTTAACC
4536874 TTTAACCCTT
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
94 4 0.06
95 40 0.59
96 24 0.35
ACGTcount: A:0.41, C:0.28, G:0.02, T:0.30
Consensus pattern (97 bp):
TTATTTAATATATAAATTAAATAAACACTAATTAATCCAAACCTTAAACCATAACCCGAATCCAA
ACCCCTAACCCTTAACCCCTAACCCCTAAACT
Found at i:4536914 original size:7 final size:7
Alignment explanation
Indices: 4536852--4536895 Score: 79
Period size: 7 Copynumber: 6.3 Consensus size: 7
4536842 ATAACCCAAT
4536852 CCTTAAC
1 CCTTAAC
4536859 CCTTAAC
1 CCTTAAC
4536866 CCTTAAC
1 CCTTAAC
*
4536873 CTTTAAC
1 CCTTAAC
4536880 CCTTAAC
1 CCTTAAC
4536887 CCTTAAC
1 CCTTAAC
4536894 CC
1 CC
4536896 ATGACTTCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.27, C:0.43, G:0.00, T:0.30
Consensus pattern (7 bp):
CCTTAAC
Found at i:4537036 original size:12 final size:12
Alignment explanation
Indices: 4537019--4537057 Score: 60
Period size: 12 Copynumber: 3.1 Consensus size: 12
4537009 CTCTTAACAT
4537019 CTAACCCCTAAC
1 CTAACCCCTAAC
4537031 CTAACCCCTAACC
1 CTAACCCCTAA-C
4537044 CATAACCCCTAAC
1 C-TAACCCCTAAC
4537057 C
1 C
4537058 CCTAATCCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 11 0.44
13 4 0.16
14 10 0.40
ACGTcount: A:0.33, C:0.51, G:0.00, T:0.15
Consensus pattern (12 bp):
CTAACCCCTAAC
Found at i:4537056 original size:21 final size:21
Alignment explanation
Indices: 4537030--4537069 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
4537020 TAACCCCTAA
4537030 CCTAACCCCTAACCCATAACC
1 CCTAACCCCTAACCCATAACC
*
4537051 CCTAACCCCTAATCCATAA
1 CCTAACCCCTAACCCATAA
4537070 ACCTTAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.47, G:0.00, T:0.17
Consensus pattern (21 bp):
CCTAACCCCTAACCCATAACC
Found at i:4537058 original size:14 final size:13
Alignment explanation
Indices: 4536996--4537058 Score: 65
Period size: 14 Copynumber: 4.7 Consensus size: 13
4536986 ATTTTATAAA
4536996 CCCTAAACCCTAAC
1 CCCT-AACCCTAAC
* * *
4537010 TCTTAACATCTAAC
1 CCCTAAC-CCTAAC
4537024 CCCTAA-CCTAAC
1 CCCTAACCCTAAC
4537036 CCCTAACCCATAAC
1 CCCTAACCC-TAAC
4537050 CCCTAACCC
1 CCCTAACCC
4537059 CTAATCCATA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
12 11 0.28
13 5 0.12
14 24 0.60
ACGTcount: A:0.33, C:0.48, G:0.00, T:0.19
Consensus pattern (13 bp):
CCCTAACCCTAAC
Found at i:4537122 original size:14 final size:15
Alignment explanation
Indices: 4537100--4537133 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
4537090 CTTAAACCAG
*
4537100 AATCCCTAA-TCCAT
1 AATCTCTAATTCCAT
4537114 AATCTCTAATTCCAT
1 AATCTCTAATTCCAT
4537129 AATCT
1 AATCT
4537134 ATAAAACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.35
Consensus pattern (15 bp):
AATCTCTAATTCCAT
Found at i:4537593 original size:114 final size:112
Alignment explanation
Indices: 4537467--4537683 Score: 253
Period size: 113 Copynumber: 1.9 Consensus size: 112
4537457 GCTTTACCGA
* * *
4537467 AAACGCCGCTAA-TACTATTC-TTTAGCGGCGTTTTACCATAAACGCCACTAAT-TCTAATATAC
1 AAACGCCACTAATTA-TATTCTTTTA-CGGCGTTTT-CCAAAAACACCACTAATAT-TAATATAC
*
4537529 ATCAAAACCAAACGCTGCGTTTTGGTTAAGGCAT-TTTGCGGCGCTTCCAAAT
62 ATCAAAACCAAACGCTGCGTTTTCGTTAA-G-ATATTTGCGGCGCTTCCAAAT
* ** * *
4537581 AAACGCCACTAATTATGTTCTTTTACGGCGTTTTTTAAAAACACCACTAATATTAATCTACCTCA
1 AAACGCCACTAATTATATTCTTTTACGGCGTTTTCCAAAAACACCACTAATATTAATATACATCA
* *
4537646 AGACCAAACGGTGCGTTTTCGTTAAGATATTTGCGGCG
66 AAACCAAACGCTGCGTTTTCGTTAAGATATTTGCGGCG
4537684 TTTTATCGTA
Statistics
Matches: 88, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
111 2 0.02
112 10 0.11
113 45 0.51
114 25 0.28
115 6 0.07
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (112 bp):
AAACGCCACTAATTATATTCTTTTACGGCGTTTTCCAAAAACACCACTAATATTAATATACATCA
AAACCAAACGCTGCGTTTTCGTTAAGATATTTGCGGCGCTTCCAAAT
Found at i:4537702 original size:74 final size:75
Alignment explanation
Indices: 4537619--4537758 Score: 203
Period size: 74 Copynumber: 1.9 Consensus size: 75
4537609 CGTTTTTTAA
* * *
4537619 AAACACCACTAATAT-TAATCTACCTCAAGACCAAACGGTGCGTTTTCGTTAAGATA-TTTGCGG
1 AAACACCACTAAT-TCTAATATACCTCAAAACCAAACGCTGCGTTTTCGTTAAGATATTTTGCGG
4537682 CGTTTTATCGT
65 CGTTTTATCGT
* * *
4537693 AAACGCCACTAATTCTAATATACCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGC
1 AAACACCACTAATTCTAATATACCTCAAAACCAAACGCTGCGTTTTCGTTAAGATATTTTGCGGC
4537758 G
66 G
4537759 CATAAAAATA
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
73 1 0.02
74 48 0.83
75 9 0.16
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (75 bp):
AAACACCACTAATTCTAATATACCTCAAAACCAAACGCTGCGTTTTCGTTAAGATATTTTGCGGC
GTTTTATCGT
Found at i:4537709 original size:187 final size:188
Alignment explanation
Indices: 4537491--4537893 Score: 657
Period size: 187 Copynumber: 2.1 Consensus size: 188
4537481 CTATTCTTTA
*
4537491 GCGGCGTTTTACCATAAACGCCACTAATTCTAATATACATCAAAACCAAACGCTGCGTTTTGGTT
1 GCGGCGTTTTACCGTAAACGCCACTAATTCTAATATACATCAAAACCAAACGCTGCGTTTTGGTT
* **
4537556 AAGGCATTTTGCGGCGCTTCCAAATAAACGCCACTAATTATGTTCTTTTACGGCGTTTTT-TAAA
66 AAGGCATTTTGCGGCGCATAAAAATAAACGCCACTAATTATGTTCTTTTACGGCGTTTTTCTAAA
* *
4537620 AACACCACTAATATTAATCTACCTCAAGACCAAACGGTGCGTTTTCGTTAAGATATTT
131 AACACCACTAATACTAATCTACCTCAAGACCAAACGGTGCGTTTTCATTAAGATATTT
* *
4537678 GCGGCGTTTTATCGTAAACGCCACTAATTCTAATATACCTCAAAACCAAACGCTGCGTTTTGGTT
1 GCGGCGTTTTACCGTAAACGCCACTAATTCTAATATACATCAAAACCAAACGCTGCGTTTTGGTT
* *
4537743 AAGGTATTTTGCGGCGCATAAAAATAAACGCCACTAATTATGTTCTTTTACGGTGTTTTTCTAAA
66 AAGGCATTTTGCGGCGCATAAAAATAAACGCCACTAATTATGTTCTTTTACGGCGTTTTTCTAAA
* *
4537808 AACGCCACTAATACTAATCTACCTCAAGACGAAACGGTGCGTTTTCATTAAGATATTT
131 AACACCACTAATACTAATCTACCTCAAGACCAAACGGTGCGTTTTCATTAAGATATTT
* *
4537866 GCGGCGCTTTACCG-ACAACGCCGCTAAT
1 GCGGCGTTTTACCGTA-AACGCCACTAAT
4537894 ACTATTCTTT
Statistics
Matches: 199, Mismatches: 15, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
187 118 0.59
188 81 0.41
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (188 bp):
GCGGCGTTTTACCGTAAACGCCACTAATTCTAATATACATCAAAACCAAACGCTGCGTTTTGGTT
AAGGCATTTTGCGGCGCATAAAAATAAACGCCACTAATTATGTTCTTTTACGGCGTTTTTCTAAA
AACACCACTAATACTAATCTACCTCAAGACCAAACGGTGCGTTTTCATTAAGATATTT
Found at i:4537938 original size:113 final size:111
Alignment explanation
Indices: 4537675--4538270 Score: 434
Period size: 114 Copynumber: 5.2 Consensus size: 111
4537665 CGTTAAGATA
** * * *
4537675 TTTGCGGCGTTTTATCGTAAACGCCACTAATTCTAATATACCTCAAAACCAAACGCTGCGTTTTG
1 TTTGCGGCGTTTTAT-AAAAACGCCAC-AAATCTAATATACCTCAAGACCAAACGCTGCGTTTTC
* **** *
4537740 GTTAAGGTATTTTGCGGCGCATAAAAATAAACGCCACTAATTATGTTCT
64 GTTAAGATATTTTGCGGCGC-TTCCGATAAACGCCACTAATTATATTCT
* * * * * * *
4537789 TTTACGGTGTTTTTCTAAAAACGCCACTAATACTAATCTACCTCAAGACGAAACGGTGCGTTTTC
1 TTTGCGGCG-TTTTATAAAAACGCCACAAAT-CTAATATACCTCAAGACCAAACGCTGCGTTTTC
* * *
4537854 ATTAAGATA-TTTGCGGCGCTTTACCGA-CAACGCCGCTAA-TACTATTCT
64 GTTAAGATATTTTGCGGCGC-TT-CCGATAAACGCCACTAATTA-TATTCT
* **
4537902 TTTGCGGCGTTTTATAGAAAACGCCACAAAGTCTAATATACAATTGA-ACCAAACGCTGCGTTTT
1 TTTGCGGCGTTTTATA-AAAACGCCACAAA-TCTAATATAC-CTCAAGACCAAACGCTGCGTTTT
* * * *
4537966 GGTTAAGGTATTTTGCGGCGCCTCCTGATAAACGCCACTAATTATGTTCT
63 CGTTAAGATATTTTGCGGCGCTTCC-GATAAACGCCACTAATTATATTCT
* * * * * * *
4538016 TTTACAGCATTATTTTAAAAACGCCACTAATAT-TAATCTACCTCAAGACAAAACGGTGCGTTTT
1 TTTGCGGCGTT-TTATAAAAACGCCAC-AA-ATCTAATATACCTCAAGACCAAACGCTGCGTTTT
* ** * *
4538080 CCTTAAGATA-TTTGCGGCGCTTTTTGTTAAACGCCGCTAA-TACTATTCT
63 CGTTAAGATATTTTGCGGCGC-TTCCGATAAACGCCACTAATTA-TATTCT
* * * * **
4538129 TTAGCGGCGTTTTTTATAAAAAACGCCATGAATTCTAATATACAATTGA-ACCAAACGCTGCGTT
1 TTTGCGGCG--TTTTAT-AAAAACGCCA-CAAATCTAATATAC-CTCAAGACCAAACGCTGCGTT
* * * * *
4538193 TTGGTTAAGGTATTTTGCGGCGCTTACAATAAACGCCACTAATTATGTTCT
61 TTCGTTAAGATATTTTGCGGCGCTTCCGATAAACGCCACTAATTATATTCT
* * * *
4538244 TTTACGACGTTTTTTTAGAAACGCCAC
1 TTTGCGGCG-TTTTATAAAAACGCCAC
4538271 TAGTTCTTCA
Statistics
Matches: 371, Mismatches: 86, Indels: 52
0.73 0.17 0.10
Matches are distributed among these distances:
112 12 0.03
113 124 0.33
114 138 0.37
115 82 0.22
116 15 0.04
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.33
Consensus pattern (111 bp):
TTTGCGGCGTTTTATAAAAACGCCACAAATCTAATATACCTCAAGACCAAACGCTGCGTTTTCGT
TAAGATATTTTGCGGCGCTTCCGATAAACGCCACTAATTATATTCT
Found at i:4538041 original size:114 final size:110
Alignment explanation
Indices: 4537693--4538270 Score: 477
Period size: 113 Copynumber: 5.1 Consensus size: 110
4537683 GTTTTATCGT
* *
4537693 AAACGCCACTAATTCTAATATACCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGC
1 AAACGCCAC-AAATCTAATATACATC-AAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGC
* ** *
4537758 GCATAAAAATAAACGCCACTAATTATGTTCTTTTACGGTGTTTTTCTAA
64 GC-TTACGATAAACGCCACTAATTATGTTCTTTTACGGCGTTTTT-TAA
* * * * * ** *
4537807 AAACGCCACTAATACTAATCTACCTCAAGACGAAACGGTGCGTTTTCATTAAGATA-TTTGCGGC
1 AAACGCCACAAAT-CTAATATACATCAA-ACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGC
* * * * *
4537871 GCTTTACCGA-CAACGCCGCTAA-TACTATTCTTTTGCGGCGTTTTATAGA
64 GC-TTA-CGATAAACGCCACTAATTA-TGTTCTTTTACGGCGTTTTTTA-A
**
4537920 AAACGCCACAAAGTCTAATATACAATTGAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGC
1 AAACGCCACAAA-TCTAATATAC-ATCAAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGC
* * * *
4537985 GCCTCCTGATAAACGCCACTAATTATGTTCTTTTACAGCATTATTTTAA
64 GCTTAC-GATAAACGCCACTAATTATGTTCTTTTACGGCGTT-TTTTAA
* * * * ** *
4538034 AAACGCCACTAATAT-TAATCTACCTCAAGACAAAACGGTGCGTTTTCCTTAAGATA-TTTGCGG
1 AAACGCCAC-AA-ATCTAATATACATCAA-ACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGG
** * * *
4538097 CGCTTTTTGTTAAACGCCGCTAA-TACTATTC-TTTAGCGGCGTTTTTTATAAA
63 CGC-TTACGATAAACGCCACTAATTA-TGTTCTTTTA-CGGCG-TTTTT-T-AA
* * **
4538149 AAACGCCATGAATTCTAATATACAATTGAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGC
1 AAACGCCA-CAAATCTAATATAC-ATCAAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGC
* * *
4538214 GCTTACAATAAACGCCACTAATTATGTTCTTTTACGACGTTTTTTTAG
64 GCTTACGATAAACGCCACTAATTATGTTCTTTTACGGCG-TTTTTTAA
4538262 AAACGCCAC
1 AAACGCCAC
4538271 TAGTTCTTCA
Statistics
Matches: 363, Mismatches: 74, Indels: 56
0.74 0.15 0.11
Matches are distributed among these distances:
112 11 0.03
113 131 0.36
114 124 0.34
115 78 0.21
116 19 0.05
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (110 bp):
AAACGCCACAAATCTAATATACATCAAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGCGC
TTACGATAAACGCCACTAATTATGTTCTTTTACGGCGTTTTTTAA
Found at i:4538072 original size:227 final size:223
Alignment explanation
Indices: 4537675--4538272 Score: 840
Period size: 227 Copynumber: 2.6 Consensus size: 223
4537665 CGTTAAGATA
* * * * **
4537675 TTTGCGGCGTTTTATCGTAAACGCCACTAATTCTAATATAC-CTCAAAACCAAACGCTGCGTTTT
1 TTTGCGGCGTTTTATAGAAAACGCCACAAATTCTAATATACAAT-TGAACCAAACGCTGCGTTTT
* *
4537739 GGTTAAGGTATTTTGCGGCGCATAAAAATAAACGCCACTAATTATGTTCTTTTACGGTGTTTTTC
65 GGTTAAGGTATTTTGCGGCGCAT-ACAATAAACGCCACTAATTATGTTCTTTTAC-GCGTTTTT-
*
4537804 TAAAAACGCCACTAATACTAATCTACCTCAAGACGAAACGGTGCGTTTTCATTAAGATATTTGCG
127 TAAAAACGCCACTAATACTAATCTACCTCAAGACAAAACGGTGCGTTTTCATTAAGATATTTGCG
4537869 GCGCTTTACCG-ACAACGCCGCTAATACTATTCT
192 GCGCTTT-CCGTA-AACGCCGCTAATACTATTCT
*
4537902 TTTGCGGCGTTTTATAGAAAACGCCACAAAGTCTAATATACAATTGAACCAAACGCTGCGTTTTG
1 TTTGCGGCGTTTTATAGAAAACGCCACAAATTCTAATATACAATTGAACCAAACGCTGCGTTTTG
* * * *
4537967 GTTAAGGTATTTTGCGGCGCCTCCTGATAAACGCCACTAATTATGTTCTTTTACAGCATTATTTT
66 GTTAAGGTATTTTGCGGCGCATAC-AATAAACGCCACTAATTATGTTCTTTTAC-GCGTT-TTTT
* *
4538032 AAAAACGCCACTAATATTAATCTACCTCAAGACAAAACGGTGCGTTTTCCTTAAGATATTTGCGG
128 AAAAACGCCACTAATACTAATCTACCTCAAGACAAAACGGTGCGTTTTCATTAAGATATTTGCGG
**
4538097 CGCTTTTTGTTAAACGCCGCTAATACTATTCT
193 CGCTTTCCG-TAAACGCCGCTAATACTATTCT
* * **
4538129 TTAGCGGCGTTTTTTATAAAAAACGCCATGAATTCTAATATACAATTGAACCAAACGCTGCGTTT
1 TTTGCGGCG--TTTTATAGAAAACGCCACAAATTCTAATATACAATTGAACCAAACGCTGCGTTT
*
4538194 TGGTTAAGGTATTTTGCGGCGCTTACAATAAACGCCACTAATTATGTTCTTTTACGACGTTTTTT
64 TGGTTAAGGTATTTTGCGGCGCATACAATAAACGCCACTAATTATGTTCTTTTACG-CG-TTTTT
*
4538259 TAGAAACGCCACTA
127 TAAAAACGCCACTA
4538273 GTTCTTCAGG
Statistics
Matches: 333, Mismatches: 29, Indels: 17
0.88 0.08 0.04
Matches are distributed among these distances:
226 1 0.00
227 206 0.62
228 50 0.15
229 76 0.23
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.33
Consensus pattern (223 bp):
TTTGCGGCGTTTTATAGAAAACGCCACAAATTCTAATATACAATTGAACCAAACGCTGCGTTTTG
GTTAAGGTATTTTGCGGCGCATACAATAAACGCCACTAATTATGTTCTTTTACGCGTTTTTTAAA
AACGCCACTAATACTAATCTACCTCAAGACAAAACGGTGCGTTTTCATTAAGATATTTGCGGCGC
TTTCCGTAAACGCCGCTAATACTATTCT
Found at i:4539288 original size:20 final size:19
Alignment explanation
Indices: 4539263--4539328 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
4539253 CTTGTTTACA
4539263 TTGATTTGATTCTCAATCTT
1 TTGATTTGATTCTCAATC-T
** * *
4539283 TTGATTTCTTTC-CATTACA
1 TTGATTTGATTCTCAAT-CT
4539302 TTGATTTGATTCTCAATCCT
1 TTGATTTGATTCTCAAT-CT
4539322 TTGATTT
1 TTGATTT
4539329 CTTTCCATTA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
19 13 0.37
20 22 0.63
ACGTcount: A:0.20, C:0.17, G:0.09, T:0.55
Consensus pattern (19 bp):
TTGATTTGATTCTCAATCT
Found at i:4539307 original size:19 final size:19
Alignment explanation
Indices: 4539283--4539339 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
4539273 TCTCAATCTT
4539283 TTGATTTCTTTCCATTACA
1 TTGATTTCTTTCCATTACA
** * * *
4539302 TTGATTTGATTCTCAATCCT
1 TTGATTTCTTTC-CATTACA
4539322 TTGATTTCTTTCCATTAC
1 TTGATTTCTTTCCATTAC
4539340 TGTTTTGATT
Statistics
Matches: 28, Mismatches: 9, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.19, C:0.21, G:0.07, T:0.53
Consensus pattern (19 bp):
TTGATTTCTTTCCATTACA
Found at i:4539312 original size:39 final size:39
Alignment explanation
Indices: 4539258--4539376 Score: 206
Period size: 39 Copynumber: 3.1 Consensus size: 39
4539248 AAAATCTTGT
*
4539258 TTACATTGATTTGATTCTCAATCTTTTGATTTCTTTCCA
1 TTACATTGATTTGATTCTCAATCCTTTGATTTCTTTCCA
4539297 TTACATTGATTTGATTCTCAATCCTTTGATTTCTTTCCA
1 TTACATTGATTTGATTCTCAATCCTTTGATTTCTTTCCA
*
4539336 TTAC--TGTTTTGATTCTCAATCCTTTGATTTCTTTCCA
1 TTACATTGATTTGATTCTCAATCCTTTGATTTCTTTCCA
4539373 TTAC
1 TTAC
4539377 TGTTTTGCTT
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
37 36 0.46
39 42 0.54
ACGTcount: A:0.19, C:0.20, G:0.08, T:0.53
Consensus pattern (39 bp):
TTACATTGATTTGATTCTCAATCCTTTGATTTCTTTCCA
Found at i:4539349 original size:22 final size:22
Alignment explanation
Indices: 4539321--4539383 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 22
4539311 TTCTCAATCC
4539321 TTTGATTTCTTTCCATTACTGT
1 TTTGATTTCTTTCCATTACTGT
**
4539343 TTTGA-TTC--T-CA--A-TCC
1 TTTGATTTCTTTCCATTACTGT
4539358 TTTGATTTCTTTCCATTACTGT
1 TTTGATTTCTTTCCATTACTGT
4539380 TTTG
1 TTTG
4539384 CTTCCTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 14
0.62 0.08 0.29
Matches are distributed among these distances:
15 6 0.20
16 4 0.13
18 3 0.10
19 3 0.10
21 4 0.13
22 10 0.33
ACGTcount: A:0.14, C:0.19, G:0.10, T:0.57
Consensus pattern (22 bp):
TTTGATTTCTTTCCATTACTGT
Found at i:4539356 original size:37 final size:37
Alignment explanation
Indices: 4539267--4539383 Score: 198
Period size: 37 Copynumber: 3.1 Consensus size: 37
4539257 TTTACATTGA
* *
4539267 TTTGATTCTCAATCTTTTGATTTCTTTCCATTACATTGA
1 TTTGATTCTCAATCCTTTGATTTCTTTCCATTAC--TGT
4539306 TTTGATTCTCAATCCTTTGATTTCTTTCCATTACTGT
1 TTTGATTCTCAATCCTTTGATTTCTTTCCATTACTGT
4539343 TTTGATTCTCAATCCTTTGATTTCTTTCCATTACTGT
1 TTTGATTCTCAATCCTTTGATTTCTTTCCATTACTGT
4539380 TTTG
1 TTTG
4539384 CTTCCTTTTT
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
37 43 0.57
39 33 0.43
ACGTcount: A:0.17, C:0.20, G:0.09, T:0.55
Consensus pattern (37 bp):
TTTGATTCTCAATCCTTTGATTTCTTTCCATTACTGT
Found at i:4545707 original size:12 final size:12
Alignment explanation
Indices: 4545692--4545721 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4545682 ACAATAATAC
4545692 TATATATAAATG
1 TATATATAAATG
*
4545704 TATATATATATG
1 TATATATAAATG
4545716 TATATA
1 TATATA
4545722 ATAGAAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (12 bp):
TATATATAAATG
Found at i:4545822 original size:18 final size:19
Alignment explanation
Indices: 4545799--4545857 Score: 70
Period size: 18 Copynumber: 3.2 Consensus size: 19
4545789 AATTAAAGTA
4545799 ATAAAAATA-ATACTATAT
1 ATAAAAATATATACTATAT
*
4545817 AT-AAAATATATA-TATAC
1 ATAAAAATATATACTATAT
*
4545834 ATAAAAATATACACTAATAT
1 ATAAAAATATATACT-ATAT
4545854 ATAA
1 ATAA
4545858 TAGTAATAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 12 0.35
18 14 0.41
19 1 0.03
20 7 0.21
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (19 bp):
ATAAAAATATATACTATAT
Found at i:4545824 original size:17 final size:17
Alignment explanation
Indices: 4545802--4545844 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
4545792 TAAAGTAATA
*
4545802 AAAATA-ATACTATATAT
1 AAAATATATA-TATACAT
4545819 AAAATATATATATACAT
1 AAAATATATATATACAT
4545836 AAAA-ATATA
1 AAAATATATA
4545845 CACTAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 5 0.21
17 16 0.67
18 3 0.12
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATATATATATACAT
Found at i:4546075 original size:3 final size:3
Alignment explanation
Indices: 4546062--4546146 Score: 63
Period size: 3 Copynumber: 28.3 Consensus size: 3
4546052 GAGGGTATAT
*
4546062 ATA AT- ATA ATA ATA AT- ATA AAA ATA ATA TATA CATGA GA-A ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA -AT-A -ATA ATA ATA
* *
4546108 ATA ATA AT- ATAA ATA ATA GTA AAA ATA ATA A-A ATA ATA A
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
4546147 AACAAAGCTC
Statistics
Matches: 66, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
2 9 0.14
3 48 0.73
4 7 0.11
5 2 0.03
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:4546078 original size:11 final size:11
Alignment explanation
Indices: 4546062--4546146 Score: 66
Period size: 11 Copynumber: 7.4 Consensus size: 11
4546052 GAGGGTATAT
4546062 ATAATATAATA
1 ATAATATAATA
*
4546073 ATAATATAAAA
1 ATAATATAATA
4546084 ATAATAT-ATA
1 ATAATATAATA
*
4546094 CATGAGAAATAATA
1 -AT-A-ATATAATA
4546108 ATAATA-ATATAA
1 ATAATATA-AT-A
*
4546120 ATAATAGTAAAA
1 ATAATA-TAATA
*
4546132 ATAATAAAATA
1 ATAATATAATA
4546143 ATAA
1 ATAA
4546147 AACAAAGCTC
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
10 3 0.05
11 30 0.51
12 16 0.27
13 6 0.10
14 4 0.07
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (11 bp):
ATAATATAATA
Found at i:4546134 original size:24 final size:23
Alignment explanation
Indices: 4546062--4546143 Score: 76
Period size: 24 Copynumber: 3.4 Consensus size: 23
4546052 GAGGGTATAT
4546062 ATAATATAATAATAATATAAAAATA
1 ATAATAT-A-AATAATATAAAAATA
* * *
4546087 AT-ATATACATGAGAAATAATAATA
1 ATAATATAAAT-A-ATATAAAAATA
4546111 ATAATATAAATAATAGTAAAAATA
1 ATAATATAAATAATA-TAAAAATA
*
4546135 ATAAAATAA
1 ATAATATAA
4546144 TAAAACAAAG
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
22 2 0.04
23 4 0.09
24 31 0.67
25 9 0.20
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (23 bp):
ATAATATAAATAATATAAAAATA
Found at i:4546142 original size:38 final size:36
Alignment explanation
Indices: 4546062--4546146 Score: 91
Period size: 35 Copynumber: 2.3 Consensus size: 36
4546052 GAGGGTATAT
* * * *
4546062 ATAATATAATAATAATATAAAAATAATATATACATG
1 ATAAAATAATAATAATATAAAAATAATATAAAAATA
* *
4546098 A-GAAATAATAATAATAATATAAATAATAGTAAAAATA
1 ATAAAATAATAATAAT-ATAAAAATAATA-TAAAAATA
4546135 ATAAAATAATAA
1 ATAAAATAATAA
4546147 AACAAAGCTC
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
35 12 0.31
36 12 0.31
37 6 0.15
38 9 0.23
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (36 bp):
ATAAAATAATAATAATATAAAAATAATATAAAAATA
Found at i:4546507 original size:23 final size:23
Alignment explanation
Indices: 4546472--4546544 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
4546462 CCTTTTTTAC
*
4546472 AAAAAAA-CACCTCCAAAAAACA
1 AAAAAAACCTCCTCCAAAAAACA
4546494 AAAAAAACCTCCTCC--AAAACA
1 AAAAAAACCTCCTCCAAAAAACA
* * *
4546515 AAGAACAATCCTTCTCCAAAAAACC
1 AA-AA-AAACCTCCTCCAAAAAACA
4546540 AAAAA
1 AAAAA
4546545 CCCACCCCTA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
21 8 0.19
22 9 0.21
23 16 0.38
24 2 0.05
25 7 0.17
ACGTcount: A:0.60, C:0.29, G:0.01, T:0.10
Consensus pattern (23 bp):
AAAAAAACCTCCTCCAAAAAACA
Found at i:4546512 original size:21 final size:21
Alignment explanation
Indices: 4546470--4546535 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
4546460 AACCTTTTTT
**
4546470 ACAAAAAAACACCTCC-AAAAA
1 ACAAAAAAA-ACCTCCTCCAAA
4546491 ACAAAAAAAACCTCCTCCAAA
1 ACAAAAAAAACCTCCTCCAAA
* *
4546512 ACAAAGAACAATCCTTCTCCAAA
1 ACAAA-AA-AAACCTCCTCCAAA
4546535 A
1 A
4546536 AACCAAAAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.16
21 17 0.45
22 2 0.05
23 13 0.34
ACGTcount: A:0.58, C:0.30, G:0.02, T:0.11
Consensus pattern (21 bp):
ACAAAAAAAACCTCCTCCAAA
Found at i:4547047 original size:40 final size:40
Alignment explanation
Indices: 4547003--4547154 Score: 196
Period size: 40 Copynumber: 3.8 Consensus size: 40
4546993 GTGTTTTTAG
*
4547003 TCTGCTCCACTACTACTTAGGGAGATAAGACTTGATGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
* * * * ***
4547043 TCTGCTTCACTATTGCTTAGGGAAATAAGATCTGTGGTTTTA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGATGCGA
*
4547085 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTAATGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
*
4547125 TCTACTCCACTACTGCTTAGGGAGATAAGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA
4547155 TTGTAATCTT
Statistics
Matches: 93, Mismatches: 17, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
40 58 0.62
41 4 0.04
42 31 0.33
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (40 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
Found at i:4547094 original size:82 final size:83
Alignment explanation
Indices: 4546987--4547155 Score: 259
Period size: 82 Copynumber: 2.0 Consensus size: 83
4546977 CCATGGGGAG
* * * * *
4546987 AGATTTGTGTTTTTAGTCTGCTCCACTACTACTTAGGGAGATAAGACTTGATGCGATCTGCTTCA
1 AGATCTGTGGTTTTAGTCTGCTCCACTACTACTTAGGGAGATAAGACTTAATGCGATCTACTCCA
*
4547052 CTATTGCTTAGGGAAATA
66 CTACTGCTTAGGGAAATA
*
4547070 AGATCTGTGGTTTTA-TCTGCTCCACTACTGCTTAGGGAGATAAGACTTAATGCGATCTACTCCA
1 AGATCTGTGGTTTTAGTCTGCTCCACTACTACTTAGGGAGATAAGACTTAATGCGATCTACTCCA
*
4547134 CTACTGCTTAGGGAGATA
66 CTACTGCTTAGGGAAATA
4547152 AGAT
1 AGAT
4547156 TGTAATCTTC
Statistics
Matches: 78, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
82 65 0.83
83 13 0.17
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (83 bp):
AGATCTGTGGTTTTAGTCTGCTCCACTACTACTTAGGGAGATAAGACTTAATGCGATCTACTCCA
CTACTGCTTAGGGAAATA
Found at i:4547494 original size:46 final size:45
Alignment explanation
Indices: 4547315--4547504 Score: 127
Period size: 46 Copynumber: 4.2 Consensus size: 45
4547305 CCACTTCCTA
* *
4547315 CCAATATAGGAAGGCAGGATCTGCAATCTTCAATCTATTCCACTG
1 CCAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTG
* *** * * ** * *
4547360 CCAGATACAGGGAGATGAGTTAT-C-GGCTTCAATGTACTCCACTG
1 CCA-ATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTG
* * * * * * * *
4547404 -TAGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTT-CACTG
1 CCAAT-ACAGGAAGGCAAGATCTGCAATCTTCAATCT-ATTCCACTG
4547449 CCTAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTG
1 CC-AATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTG
4547495 CCAGATACAG
1 CCA-ATACAG
4547505 TGAGATAGAG
Statistics
Matches: 103, Mismatches: 33, Indels: 17
0.67 0.22 0.11
Matches are distributed among these distances:
42 1 0.01
43 13 0.13
44 17 0.17
45 19 0.18
46 51 0.50
47 2 0.02
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (45 bp):
CCAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTG
Found at i:4547600 original size:134 final size:134
Alignment explanation
Indices: 4547317--4547620 Score: 502
Period size: 134 Copynumber: 2.3 Consensus size: 134
4547307 ACTTCCTACC
* *
4547317 AATATAGGAAGGCAGGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATGAGTTA
1 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATGAGTTA
4547382 TCGGCTTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCAC
66 TCGGCTTCAATGTACTCCACTGTAGT-ACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCAC
*
4547447 TGCCT
130 TGCCA
*
4547452 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGTGAGATAGAGTT
1 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGAT-GAGTT
* * * * *
4547517 ATCGGCTTCAATGTACTCCACTGTGGT-CAGGGAGGTAAAATCTGTCATCTTTGATCTGTTTCGC
65 ATCGGCTTCAATGTACTCCACTGTAGTACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCAC
4547581 TGCCA
130 TGCCA
4547586 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTA
1 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTA
4547621 CTTCACCACC
Statistics
Matches: 159, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
134 72 0.45
135 56 0.35
136 31 0.19
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (134 bp):
AATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATGAGTTA
TCGGCTTCAATGTACTCCACTGTAGTACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCACT
GCCA
Found at i:4547701 original size:44 final size:45
Alignment explanation
Indices: 4547586--4548133 Score: 415
Period size: 44 Copynumber: 12.4 Consensus size: 45
4547576 TTCGCTGCCA
* * * ** *
4547586 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTACTTCACCACC
1 AATATAGGAAGACAAGATCTGCTATCTTGGATCTACTTCACTACC
* * * *
4547631 AGTATGGGAAGACAAGATCTGC-ATCTTGGATCCACTTC-CTATC
1 AATATAGGAAGACAAGATCTGCTATCTTGGATCTACTTCACTACC
* * * * *
4547674 AATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCAC-GCC
1 AATATAGGAAGACAAGATCTGCTATCTTGGATCTACTTCACTACC
* * * * * *
4547718 AATACATGAAGGCAAGATCTGCTTTC-TGCGATCTACTTCGCCACC
1 AATATAGGAAGACAAGATCTGCTATCTTG-GATCTACTTCACTACC
* * * *
4547763 AATATGGGAAGACAAGATCTGC-ATATTGGATCCACTTC-CTATC
1 AATATAGGAAGACAAGATCTGCTATCTTGGATCTACTTCACTACC
* * * *
4547806 AATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCAC-ACC
1 AATATAGGAAGACAAGATCTGCTATCTTGGATCTACTTCACTACC
* * * * *
4547850 AATACATGAAGACAAGATCTGCTTTC-TGCGATCTACTTCGCCACC
1 AATATAGGAAGACAAGATCTGCTATCTTG-GATCTACTTCACTACC
* * *
4547895 AATATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTC-CTACC
1 AATATAGGAAGACAAGATCTGCTATCTTGGATCTACTTCACTACC
* * * * * *
4547938 AATATAGAAAGATAGGATCTGCTACCTTCGATCTACTTCAC-GCC
1 AATATAGGAAGACAAGATCTGCTATCTTGGATCTACTTCACTACC
* * * * *
4547982 AATACATGAAGACAAGATCTGCTTTC-TGCGATCTACTTCGCCACC
1 AATATAGGAAGACAAGATCTGCTATCTTG-GATCTACTTCACTACC
* * * * *
4548027 AATATGGGAAGACAAGCTCTGC-ATCCTGGATCCACTTC-CTATC
1 AATATAGGAAGACAAGATCTGCTATCTTGGATCTACTTCACTACC
* * * * * *
4548070 AATATAGGAAGATAGGACCTGCTATCTTCGATCTGCTTCAC-GCC
1 AATATAGGAAGACAAGATCTGCTATCTTGGATCTACTTCACTACC
* *
4548114 AATACATGAAGACAAGATCT
1 AATATAGGAAGACAAGATCT
4548134 ACTTTAATGA
Statistics
Matches: 385, Mismatches: 101, Indels: 35
0.74 0.19 0.07
Matches are distributed among these distances:
43 86 0.22
44 210 0.55
45 89 0.23
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (45 bp):
AATATAGGAAGACAAGATCTGCTATCTTGGATCTACTTCACTACC
Found at i:4547823 original size:132 final size:132
Alignment explanation
Indices: 4547586--4548138 Score: 926
Period size: 132 Copynumber: 4.2 Consensus size: 132
4547576 TTCGCTGCCA
* * ** * * * *
4547586 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTACTTCACCACCAGTATGGGAAGACAAGATCT
1 AATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCT
4547651 GCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACG
66 GCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACG
4547716 CC
131 CC
*
4547718 AATACATGAAGGCAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCT
1 AATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCT
* *
4547783 GCATATTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACA
66 GCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACG
4547848 CC
131 CC
4547850 AATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCT
1 AATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCT
* * * * *
4547915 GCATCTTCGATCCACTTCCTACCAATATAGAAAGATAGGATCTGCTACCTTCGATCTACTTCACG
66 GCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACG
4547980 CC
131 CC
*
4547982 AATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGCTCT
1 AATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCT
* *
4548047 GCATCCTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTGCTTCACG
66 GCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACG
4548112 CC
131 CC
*
4548114 AATACATGAAGACAAGATCTACTTT
1 AATACATGAAGACAAGATCTGCTTT
4548139 AATGACTTCA
Statistics
Matches: 395, Mismatches: 26, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 395 1.00
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.27
Consensus pattern (132 bp):
AATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCT
GCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACG
CC
Found at i:4560381 original size:15 final size:16
Alignment explanation
Indices: 4560349--4560388 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
4560339 TAAAGTAATA
*
4560349 AAAATATACTATATAT
1 AAAATATACTATACAT
4560365 AAAATATA-TATACAT
1 AAAATATACTATACAT
4560380 AAAATATAC
1 AAAATATAC
4560389 ACTAATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAATATACTATACAT
Found at i:4560609 original size:3 final size:3
Alignment explanation
Indices: 4560596--4560677 Score: 57
Period size: 3 Copynumber: 27.3 Consensus size: 3
4560586 GAGGGCATAT
*
4560596 ATA AT- ATA ATA ATA AT- ATA AAA ATA ATA TATA CATGA GA-A ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA -AT-A -ATA ATA ATA
* *
4560642 ATA AT- ATAA ATA ATA GTA AAA ATA ATA A-A ATA ATA A
1 ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
4560678 ACAAAGCTCT
Statistics
Matches: 63, Mismatches: 8, Indels: 16
0.72 0.09 0.18
Matches are distributed among these distances:
2 9 0.14
3 45 0.71
4 7 0.11
5 2 0.03
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:4560612 original size:11 final size:11
Alignment explanation
Indices: 4560596--4560677 Score: 71
Period size: 11 Copynumber: 7.4 Consensus size: 11
4560586 GAGGGCATAT
4560596 ATAATATAATA
1 ATAATATAATA
*
4560607 ATAATATAAAA
1 ATAATATAATA
4560618 ATAATAT-ATA
1 ATAATATAATA
*
4560628 CATGAGAAATAATA
1 -AT-A-ATATAATA
4560642 ATAATAT-A-A
1 ATAATATAATA
*
4560651 ATAATAGTAAAA
1 ATAATA-TAATA
*
4560663 ATAATAAAATA
1 ATAATATAATA
4560674 ATAA
1 ATAA
4560678 ACAAAGCTCT
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
9 7 0.12
10 4 0.07
11 30 0.52
12 9 0.16
13 5 0.09
14 3 0.05
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (11 bp):
ATAATATAATA
Found at i:4560642 original size:27 final size:28
Alignment explanation
Indices: 4560612--4560678 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 28
4560602 TAATAATAAT
* *
4560612 ATAAAAATAATATATACAT-G-AGAAATA
1 ATAAAAATAATAAATA-ATAGTAAAAATA
*
4560639 ATAATAAT-ATAAATAATAGTAAAAATA
1 ATAAAAATAATAAATAATAGTAAAAATA
4560666 AT-AAAATAATAAA
1 ATAAAAATAATAAA
4560679 CAAAGCTCTC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
25 2 0.06
26 11 0.33
27 20 0.61
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.27
Consensus pattern (28 bp):
ATAAAAATAATAAATAATAGTAAAAATA
Found at i:4560665 original size:24 final size:24
Alignment explanation
Indices: 4560596--4560674 Score: 69
Period size: 24 Copynumber: 3.4 Consensus size: 24
4560586 GAGGGCATAT
4560596 ATAATATAATAATAATA-TAAAAATA
1 ATAATAT-A-AATAATAGTAAAAATA
* *
4560621 AT-ATATACAT--GAG-AAATAATA
1 ATAATATAAATAATAGTAAA-AATA
4560642 ATAATATAAATAATAGTAAAAATA
1 ATAATATAAATAATAGTAAAAATA
*
4560666 ATAAAATAA
1 ATAATATAA
4560675 TAAACAAAGC
Statistics
Matches: 43, Mismatches: 5, Indels: 13
0.70 0.08 0.21
Matches are distributed among these distances:
20 4 0.09
21 6 0.14
22 9 0.21
23 1 0.02
24 18 0.42
25 5 0.12
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (24 bp):
ATAATATAAATAATAGTAAAAATA
Found at i:4561031 original size:23 final size:23
Alignment explanation
Indices: 4560997--4561068 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 23
4560987 ACCTTTTTAC
*
4560997 AAAAAA-CACCTCCAAAAAACAA
1 AAAAAACCTCCTCCAAAAAACAA
4561019 AAAAAACCTCCTCC--AAAACAA
1 AAAAAACCTCCTCCAAAAAACAA
* * *
4561040 AGAACAATCCTTCTCCAAAAAACCA
1 A-AA-AAACCTCCTCCAAAAAACAA
4561065 AAAA
1 AAAA
4561069 CCCACCCCTA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
21 8 0.20
22 8 0.20
23 16 0.39
24 2 0.05
25 7 0.17
ACGTcount: A:0.60, C:0.29, G:0.01, T:0.10
Consensus pattern (23 bp):
AAAAAACCTCCTCCAAAAAACAA
Found at i:4561036 original size:21 final size:21
Alignment explanation
Indices: 4560995--4561059 Score: 60
Period size: 20 Copynumber: 3.0 Consensus size: 21
4560985 TAACCTTTTT
* **
4560995 ACAAAAAACACCTCC-AAAAA
1 ACAAAAAAAACCTCCTCCAAA
4561015 ACAAAAAAAACCTCCTCCAAA
1 ACAAAAAAAACCTCCTCCAAA
* *
4561036 ACAAAGAACAATCCTTCTCCAAA
1 ACAAA-AA-AAACCTCCTCCAAA
4561059 A
1 A
4561060 AACCAAAAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
20 14 0.38
21 8 0.22
22 2 0.05
23 13 0.35
ACGTcount: A:0.57, C:0.31, G:0.02, T:0.11
Consensus pattern (21 bp):
ACAAAAAAAACCTCCTCCAAA
Found at i:4561190 original size:23 final size:23
Alignment explanation
Indices: 4561142--4561205 Score: 87
Period size: 23 Copynumber: 2.8 Consensus size: 23
4561132 GGGTGGTTTA
*
4561142 GGTGGCCAAGG-GTGGTGG-AGTT
1 GGTGGCTAAGGTG-GGTGGCAGTT
4561164 GGTGGCTAAGGTGGGTGGCAGTT
1 GGTGGCTAAGGTGGGTGGCAGTT
*
4561187 GGTGGGTAAGGTGGGTGGC
1 GGTGGCTAAGGTGGGTGGC
4561206 CAACAAAGGT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
22 15 0.39
23 23 0.61
ACGTcount: A:0.12, C:0.08, G:0.56, T:0.23
Consensus pattern (23 bp):
GGTGGCTAAGGTGGGTGGCAGTT
Found at i:4574591 original size:6 final size:6
Alignment explanation
Indices: 4574580--4574604 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4574570 GAAAAATGAT
4574580 AAATAA AAATAA AAATAA AAATAA A
1 AAATAA AAATAA AAATAA AAATAA A
4574605 TAAAAGTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:4574799 original size:30 final size:30
Alignment explanation
Indices: 4574765--4574890 Score: 84
Period size: 30 Copynumber: 4.2 Consensus size: 30
4574755 TTTTTTACGA
*
4574765 TTTTTATAAAATTTTACAATTATTTATATT
1 TTTTTATAAAATTTTATAATTATTTATATT
* * * *
4574795 TTTTTAT-GATTTTTATAATCTTTTTATAAT
1 TTTTTATAAAATTTTATAAT-TATTTATATT
* * *
4574825 TTTTAATAAAA-ATTA-AA-TATTTCTTATAT
1 TTTTTATAAAATTTTATAATTATTT-ATAT-T
*
4574854 TTTTTATTAAAATTTAATAATT-TTTAT-TT
1 TTTTTA-TAAAATTTTATAATTATTTATATT
4574883 ATTTTTAT
1 -TTTTTAT
4574891 CATTTTTTGC
Statistics
Matches: 71, Mismatches: 16, Indels: 19
0.67 0.15 0.18
Matches are distributed among these distances:
27 4 0.06
28 2 0.03
29 19 0.27
30 36 0.51
31 4 0.06
32 5 0.07
33 1 0.01
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (30 bp):
TTTTTATAAAATTTTATAATTATTTATATT
Found at i:4574818 original size:11 final size:10
Alignment explanation
Indices: 4574765--4574833 Score: 59
Period size: 10 Copynumber: 6.9 Consensus size: 10
4574755 TTTTTTACGA
*
4574765 TTTTTATAAA
1 TTTTTATAAT
* *
4574775 ATTTTACAAT
1 TTTTTATAAT
* *
4574785 TATTTATATT
1 TTTTTATAAT
*
4574795 TTTTTATGA-
1 TTTTTATAAT
4574804 TTTTTATAAT
1 TTTTTATAAT
4574814 CTTTTTATAAT
1 -TTTTTATAAT
*
4574825 TTTTAATAA
1 TTTTTATAA
4574834 AAATTAAATA
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
9 8 0.18
10 27 0.60
11 10 0.22
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.62
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:4574833 original size:10 final size:9
Alignment explanation
Indices: 4574764--4574897 Score: 52
Period size: 10 Copynumber: 13.7 Consensus size: 9
4574754 TTTTTTTACG
4574764 ATTTTTATAA
1 ATTTTTAT-A
* *
4574774 AATTTTACA
1 ATTTTTATA
4574783 ATTATTTATA
1 ATT-TTTATA
* *
4574793 TTTTTTTATG
1 -ATTTTTATA
4574803 ATTTTTATA
1 ATTTTTATA
4574812 ATCTTTTTATA
1 A--TTTTTATA
4574823 ATTTTTAATA
1 ATTTTT-ATA
*** *
4574833 AAAATTAAA
1 ATTTTTATA
4574842 TATTTCTTATA
1 -ATTT-TTATA
*
4574853 TTTTTTATTAA
1 ATTTTTA-T-A
* *
4574864 AATTTAATA
1 ATTTTTATA
*
4574873 ATTTTTATTT
1 ATTTTTA-TA
*
4574883 ATTTTTATC
1 ATTTTTATA
4574892 ATTTTT
1 ATTTTT
4574898 TGCTACATCT
Statistics
Matches: 90, Mismatches: 24, Indels: 21
0.67 0.18 0.16
Matches are distributed among these distances:
9 34 0.38
10 36 0.40
11 20 0.22
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (9 bp):
ATTTTTATA
Found at i:4580887 original size:13 final size:13
Alignment explanation
Indices: 4580869--4580929 Score: 52
Period size: 13 Copynumber: 4.3 Consensus size: 13
4580859 TCAAATTAAG
4580869 ATATTTTATATTT
1 ATATTTTATATTT
4580882 ATATTTTAT-TTAT
1 ATATTTTATATT-T
4580895 ATATTTTCAGGTATATT
1 ATATTTT-A--TAT-TT
*
4580912 ATAATTATATATTT
1 AT-ATTTTATATTT
4580926 ATAT
1 ATAT
4580930 AATTTGACAA
Statistics
Matches: 40, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
12 2 0.05
13 19 0.47
14 5 0.12
15 3 0.08
16 1 0.03
17 5 0.12
18 5 0.12
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (13 bp):
ATATTTTATATTT
Found at i:4587847 original size:52 final size:54
Alignment explanation
Indices: 4587767--4587871 Score: 135
Period size: 52 Copynumber: 2.0 Consensus size: 54
4587757 GTATCAAATT
* *
4587767 AAAAAAATGACAAGTTCAACTGTAAAATTAAA-AAAAATTAAGTACCAAATTAG
1 AAAAAAATGACAAGTTCAACTATAAAATTAAACAAAAATTAAATACCAAATTAG
* *
4587820 AAAAAAAT-ACAAGTTCAGA-TATTAAATTAAACCAAAACTTAAATACCAAATT
1 AAAAAAATGACAAGTTCA-ACTATAAAATTAAA-CAAAAATTAAATACCAAATT
4587872 TTGTAAACAT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
52 19 0.42
53 9 0.20
54 17 0.38
ACGTcount: A:0.58, C:0.11, G:0.07, T:0.24
Consensus pattern (54 bp):
AAAAAAATGACAAGTTCAACTATAAAATTAAACAAAAATTAAATACCAAATTAG
Found at i:4590086 original size:25 final size:24
Alignment explanation
Indices: 4590032--4590092 Score: 59
Period size: 25 Copynumber: 2.5 Consensus size: 24
4590022 AATTTTATAT
*
4590032 TATATATATATATAATTTAACAAA
1 TATATATATATATAATCTAACAAA
* * *
4590056 TAATATATTTGTATAATCTAATCTAA
1 T-ATATATATATATAATCTAA-CAAA
*
4590082 TATATTTATAT
1 TATATATATAT
4590093 TATATTTATA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
24 1 0.04
25 23 0.82
26 4 0.14
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.48
Consensus pattern (24 bp):
TATATATATATATAATCTAACAAA
Found at i:4590098 original size:11 final size:11
Alignment explanation
Indices: 4590082--4590109 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
4590072 TCTAATCTAA
4590082 TATATTTATAT
1 TATATTTATAT
4590093 TATATTTATAT
1 TATATTTATAT
4590104 TATATT
1 TATATT
4590110 ATCTACAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATATTTATAT
Done.