Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A01
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 115637255
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5450143 characters in sequence are not A, C, G, or T
File 43 of 349
Found at i:12099129 original size:24 final size:24
Alignment explanation
Indices: 12099101--12099185 Score: 127
Period size: 24 Copynumber: 3.5 Consensus size: 24
12099091 CCCTCCTCGT
12099101 CCATTCCCTCCTCACCCACCGCGA
1 CCATTCCCTCCTCACCCACCGCGA
*
12099125 CCATTCCCTCCTCACCCGCCGCGA
1 CCATTCCCTCCTCACCCACCGCGA
* *
12099149 CCGA-TCCCTCCTCATCCACCACGA
1 CC-ATTCCCTCCTCACCCACCGCGA
12099173 CCATTCCCTCCTC
1 CCATTCCCTCCTC
12099186 CTCATCCTCA
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
23 1 0.02
24 53 0.96
25 1 0.02
ACGTcount: A:0.15, C:0.58, G:0.08, T:0.19
Consensus pattern (24 bp):
CCATTCCCTCCTCACCCACCGCGA
Found at i:12101577 original size:18 final size:18
Alignment explanation
Indices: 12101535--12101578 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
12101525 CCTTTTTTTC
12101535 TTTATT-TTTATTTTAGT
1 TTTATTATTTATTTTAGT
*
12101552 TTTTTTATTTATTTTA-T
1 TTTATTATTTATTTTAGT
12101569 TCTTATTATT
1 T-TTATTATT
12101579 ACTATTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.77
Consensus pattern (18 bp):
TTTATTATTTATTTTAGT
Found at i:12102337 original size:34 final size:34
Alignment explanation
Indices: 12102298--12102362 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
12102288 ATTTAAAGGC
12102298 AAACTTGTTCTCGAATGTTCGAATGTCGCATCCT
1 AAACTTGTTCTCGAATGTTCGAATGTCGCATCCT
*
12102332 AAACTTGTTCTCGAATGTTTGAATGTCGCAT
1 AAACTTGTTCTCGAATGTTCGAATGTCGCAT
12102363 TTCGTTATCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (34 bp):
AAACTTGTTCTCGAATGTTCGAATGTCGCATCCT
Found at i:12102649 original size:154 final size:155
Alignment explanation
Indices: 12102354--12102659 Score: 569
Period size: 154 Copynumber: 2.0 Consensus size: 155
12102344 GAATGTTTGA
12102354 ATGTCGCATTTCGTTATCTCAGGACGAATGGGCCTTTGATGTTCGTTTCAACTTAATTCAAGCTT
1 ATGTCGCATTTCGTTATCTCAGGACGAATGGGCCTTTGATGTTCGTTTCAACTTAATTCAAGC-T
**
12102419 TTTTTTTAAAAAAAAAAGCTTTAATAAAAAGGGATCGTATTTTAAATCTTTTCAAAATTTCAACT
65 TTTTTAAAAAAAAAAAAGCTTTAATAAAAAGGGATCGTATTTTAAATCTTTTCAAAATTTCAACT
12102484 TTCGCCATTAAGACATTAATTACGGG
130 TTCGCCATTAAGACATTAATTACGGG
*
12102510 ATGTCGCATTTCGTTATCTCAGGACGAGTGGGCCTTTGATGTTCGTTTCAACTTAATTCAAGC-T
1 ATGTCGCATTTCGTTATCTCAGGACGAATGGGCCTTTGATGTTCGTTTCAACTTAATTCAAGCTT
12102574 TTTTAAAAAAAAAAAAGCTTTAATAAAAAGGGATCGTATTTTAAATCTTTTCAAAATTTCAACTT
66 TTTTAAAAAAAAAAAAGCTTTAATAAAAAGGGATCGTATTTTAAATCTTTTCAAAATTTCAACTT
12102639 TCGCCATTAAGACATTAATTA
131 TCGCCATTAAGACATTAATTA
12102660 ATTAATTGGG
Statistics
Matches: 147, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
154 85 0.58
156 62 0.42
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.37
Consensus pattern (155 bp):
ATGTCGCATTTCGTTATCTCAGGACGAATGGGCCTTTGATGTTCGTTTCAACTTAATTCAAGCTT
TTTTAAAAAAAAAAAAGCTTTAATAAAAAGGGATCGTATTTTAAATCTTTTCAAAATTTCAACTT
TCGCCATTAAGACATTAATTACGGG
Found at i:12109431 original size:37 final size:37
Alignment explanation
Indices: 12109363--12109434 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
12109353 TCTGTGCAAG
*
12109363 TATTCTTTTATTATTTTCATTCTATTCATAACCAAAA
1 TATTCTTTTATTATTTCCATTCTATTCATAACCAAAA
* * *
12109400 TATTCTTTTATTCTTTCCATTTTATTTATAACCAA
1 TATTCTTTTATTATTTCCATTCTATTCATAACCAA
12109435 TCATATGGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (37 bp):
TATTCTTTTATTATTTCCATTCTATTCATAACCAAAA
Found at i:12113896 original size:44 final size:44
Alignment explanation
Indices: 12113833--12113967 Score: 135
Period size: 44 Copynumber: 3.0 Consensus size: 44
12113823 CCATGGCGAA
* *
12113833 TCTTATTTCCCTGAAGTTGCAGCGGAGTAGATTAAAGCCACAAG
1 TCTTATTTCCCTGAAGTTGCAGAGGAGTAGATTAAAGCAACAAG
* * * * * ** * *
12113877 TCTTATCTCCTTGAAGTTGCGGTGGAGCAGATTGGAGATAACAAA
1 TCTTATTTCCCTGAAGTTGCAGAGGAGTAGATTAAAG-CAACAAG
* * *
12113922 TCTTATTTCCCTGAAGTTGCAGAGGAATAGATTACAGCTACAAG
1 TCTTATTTCCCTGAAGTTGCAGAGGAGTAGATTAAAGCAACAAG
12113966 TC
1 TC
12113968 ACAAATCCTA
Statistics
Matches: 69, Mismatches: 21, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
44 36 0.52
45 33 0.48
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.29
Consensus pattern (44 bp):
TCTTATTTCCCTGAAGTTGCAGAGGAGTAGATTAAAGCAACAAG
Found at i:12114087 original size:44 final size:45
Alignment explanation
Indices: 12114021--12114357 Score: 190
Period size: 44 Copynumber: 7.5 Consensus size: 45
12114011 TACCATGGCG
* *
12114021 AATCTTATCTCCCTGAAGTTGCAGTAGAGTAGATAGAAACCA-CT
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGTAGATAGAAAACAGCA
* * ** * *
12114065 AGTCTTATCTCCCTGAAATTGCAG-AGGAACAGATTGAAAATAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTA-GAGTAGATAGAAAACAGCA
* * *
12114110 AATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATTAAAACTATAAACAACA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGTAGA-T---A-GA-AAACAGCA
* * * * * * * **
12114161 AACCCTATCTCCCTAAAGTTACAGTAGAGCAGGTTGAAATTA-CA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGTAGATAGAAAACAGCA
* * * *
12114205 AATCTAATTTCCCTGAAGTT---GTGGAGTAGATAGAAACCA-CA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGTAGATAGAAAACAGCA
* * * * *
12114246 AATCTTATCTCCAT-AATGTTGCAATGGAGTAGATTGAAAAAAGCA
1 AATCTTATCTCCCTGAA-GTTGCAGTAGAGTAGATAGAAAACAGCA
* * * * * *
12114291 AGTCTTATCTCCTTGAAGTT-CAGTGGAGTAGACT-GAAGATAGCG
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGTAGA-TAGAAAACAGCA
* *
12114335 AATATTATTTCCCTGAAGTTGCA
1 AATCTTATCTCCCTGAAGTTGCA
12114358 ATGGAACAGA
Statistics
Matches: 220, Mismatches: 56, Indels: 33
0.71 0.18 0.11
Matches are distributed among these distances:
40 2 0.01
41 29 0.13
43 1 0.00
44 99 0.45
45 50 0.23
46 5 0.02
50 2 0.01
51 32 0.15
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (45 bp):
AATCTTATCTCCCTGAAGTTGCAGTAGAGTAGATAGAAAACAGCA
Found at i:12116192 original size:18 final size:19
Alignment explanation
Indices: 12116151--12116193 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
12116141 CTTTTTTTCT
12116151 TTATT-TTTATTTTAGTTA
1 TTATTATTTATTTTAGTTA
*
12116169 TT-TTATTTATTTTA-TTC
1 TTATTATTTATTTTAGTTA
12116186 TTATTATT
1 TTATTATT
12116194 ACTATTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (19 bp):
TTATTATTTATTTTAGTTA
Found at i:12116199 original size:24 final size:24
Alignment explanation
Indices: 12116150--12116201 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
12116140 CCTTTTTTTC
*
12116150 TTTATTTTTATTTTAGTTATTTTA
1 TTTATTTTTATTTTAGTTATTCTA
12116174 TTTA-TTTTATTCTTA-TTATTACTA
1 TTTATTTTTATT-TTAGTTATT-CTA
12116198 TTTA
1 TTTA
12116202 AAATTGTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (24 bp):
TTTATTTTTATTTTAGTTATTCTA
Found at i:12116357 original size:13 final size:14
Alignment explanation
Indices: 12116339--12116380 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
12116329 ATTTTCAATA
12116339 TTTTATA-AATTAT
1 TTTTATATAATTAT
*
12116352 TTTTATATATTTA-
1 TTTTATATAATTAT
*
12116365 TTTTATATATTTAT
1 TTTTATATAATTAT
12116379 TT
1 TT
12116381 AATTACTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 20 0.77
14 6 0.23
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTATATAATTAT
Found at i:12116373 original size:15 final size:14
Alignment explanation
Indices: 12116337--12116380 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 14
12116327 TTATTTTCAA
12116337 TATTTTATA-A-AT
1 TATTTTATATATAT
12116349 TATTTT-TATATATT
1 TATTTTATATATA-T
12116363 TATTTTATATAT-T
1 TATTTTATATATAT
12116376 TATTT
1 TATTT
12116381 AATTACTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
11 2 0.07
12 7 0.25
13 7 0.25
14 7 0.25
15 5 0.18
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTTTATATATAT
Found at i:12118756 original size:24 final size:25
Alignment explanation
Indices: 12118709--12118764 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
12118699 TATTCAATAC
** *
12118709 AATATATTATTTATATATTTTTTAA
1 AATATATTAAATATATATTGTTTAA
12118734 AATATATTAAATAT-TATTGTTTAA
1 AATATATTAAATATATATTGTTTAA
*
12118758 TATATAT
1 AATATAT
12118765 ATGCTTGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 15 0.56
25 12 0.44
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (25 bp):
AATATATTAAATATATATTGTTTAA
Found at i:12122816 original size:18 final size:18
Alignment explanation
Indices: 12122793--12122848 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
12122783 CCACCACCAA
12122793 CTCCACTAGCCACAATTG
1 CTCCACTAGCCACAATTG
*
12122811 CTCCACCA--C-CAA---
1 CTCCACTAGCCACAATTG
*
12122823 CTCCACTAGCCACACTTG
1 CTCCACTAGCCACAATTG
12122841 CTCCACTA
1 CTCCACTA
12122849 CCTACTCCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 12
0.66 0.07 0.27
Matches are distributed among these distances:
12 7 0.24
14 1 0.03
15 5 0.17
16 1 0.03
18 15 0.52
ACGTcount: A:0.27, C:0.46, G:0.07, T:0.20
Consensus pattern (18 bp):
CTCCACTAGCCACAATTG
Found at i:12122819 original size:30 final size:30
Alignment explanation
Indices: 12122783--12122881 Score: 171
Period size: 30 Copynumber: 3.3 Consensus size: 30
12122773 TTAGCATTTG
*
12122783 CCACCACCAACTCCACTAGCCACAATTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
12122813 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
* *
12122843 CCACTACCTACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
12122873 CCACCACCA
1 CCACCACCA
12122882 CTTGTACCTA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 64 1.00
ACGTcount: A:0.27, C:0.49, G:0.06, T:0.17
Consensus pattern (30 bp):
CCACCACCAACTCCACTAGCCACACTTGCT
Found at i:12122876 original size:18 final size:18
Alignment explanation
Indices: 12122823--12122876 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
12122813 CCACCACCAA
12122823 CTCCACTAGCCACACTTG
1 CTCCACTAGCCACACTTG
*
12122841 CTCCACT----AC-C-TA
1 CTCCACTAGCCACACTTG
12122853 CTCCACTAGCCACACTTG
1 CTCCACTAGCCACACTTG
12122871 CTCCAC
1 CTCCAC
12122877 CACCACTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
12 8 0.29
13 1 0.04
14 2 0.07
16 2 0.07
17 1 0.04
18 14 0.50
ACGTcount: A:0.22, C:0.48, G:0.07, T:0.22
Consensus pattern (18 bp):
CTCCACTAGCCACACTTG
Found at i:12130624 original size:162 final size:163
Alignment explanation
Indices: 12130331--12131336 Score: 816
Period size: 164 Copynumber: 6.0 Consensus size: 163
12130321 TTTATTTATA
* * * *
12130331 TTTTCAAAAAAATCTACTCATATTGCGAGAGATGAGTTGAGCCTCGG-GCAC--GCTGAGGTATT
1 TTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGGCTCACGTGCTGAGGTATT
** * * *
12130393 TTCAAAATCTATTTTTCAA-ATTCTGTTTTCAAA-AATCAACTCATATTGCAAGGAGGTGAGTTG
66 TTCAATTTCTA-TTTTCAATA-TCTATTTTTAAAGAATCAACTCATATTGCGA-GAGGTGAGTTG
*
12130456 AGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGT
128 AGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGT
* * * * * *
12130492 CTTTT-AAAAAAATCAATTCATATTTCGAGAAGTGAGTTGAACCTTGGCTCACGTGCTGAGCTAT
1 -TTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGGCTCACGTGCTGAGGTAT
* * * * *
12130556 GTTCAATTTCTATTTT-AATGTCTGTTTTTAAAGAATCAACTCATATTGTGAGTGGTGAGTTGAG
65 TTTCAATTTCTATTTTCAATATCTATTTTTAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAG
*
12130620 CCTCAAGACACGCTGAGGTAATTTT-AATTTCTAT
130 CCTCAAGACACGCTGAGGT-ATTTTCAATTTCTGT
* *
12130654 TTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG-ACACGT--TGAGGTA
1 TTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-AGGCTCACGTGCTGAGGTA
*** ** ** * *
12130716 TTTTCAATTTCTATCTTTCAA-AAAAAAATAAAAAAAATCAACTTATATTGCGAGAGGTGAGTTG
64 TTTTCAATTTCTAT-TTTCAATATCTATTTTTAAAGAATCAACTCATATTGCGAGAGGTGAGTTG
* **
12130780 AGCCTCAAG--ACGCTGAGGCATTTTCAATTTCTAC
128 AGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGT
*
12130814 TTTTCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGGCTCACGTGCTGAGGTATT
1 TTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGGCTCACGTGCTGAGGTATT
* * *
12130879 TTAAATTTCTACTTTTCAATTTCTATTTTTCAAAAGAATCAACTTATATTGCGAGAGGTGAGTTG
66 TTCAATTTCTA-TTTTCAATATCTATTTTT--AAAGAATCAACTCATATTGCGAGAGGTGAGTTG
* *
12130944 AGCCTCAGGACACGCTGAGGTAATTTCAATTTCTG-
128 AGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGT
* ** * * *** * *
12130979 TTGTC-AAAAAATCAACTTGTATTGCGAGAGGTGAGTTGAGTCTCGGGC-CATACGCCGAGGTCT
1 TTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-AGGCTCACGTGCTGAGGTAT
* ** *
12131042 TTTCAAATTCCGTTTTCAATTTCCATTTTTTCAATTTATGCTTTTGAAAAAATCAACTCATATTG
65 TTTCAATTTCTATTTTCAA--T--A-----TC----TAT--TTTT-AAAGAATCAACTCATATTG
* * * *
12131107 CGA-ATGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTATGC
114 CGAGA-GGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGT
* * ** **
12131157 TTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGCTGAGCCTCGGGGCAC--GCCAAGGTATT
1 TTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGGCTCACGTGCTGAGGTATT
* *
12131218 TTTAATTTCTATTTTTCAATTTCTGCTTTTAATTTCTGTTTTTCAAA-AATCAACTCATATTGCG
66 TTCAATTTCTA-TTTTCAA----------T-A--TCTATTTTT-AAAGAATCAACTCATATTGCG
* * *
12131282 AGAGGTGAGTTGAGCCTCAGGGCACGCTGAGATATTTTCAATTTCTGT
116 AGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGT
12131330 TTTTCAA
1 TTTTCAA
12131337 TTTTTGCCTT
Statistics
Matches: 690, Mismatches: 102, Indels: 91
0.78 0.12 0.10
Matches are distributed among these distances:
158 2 0.00
159 48 0.07
160 22 0.03
161 83 0.12
162 103 0.15
163 74 0.11
164 111 0.16
165 8 0.01
166 21 0.03
172 2 0.00
173 63 0.09
174 8 0.01
175 16 0.02
176 15 0.02
177 98 0.14
178 8 0.01
180 4 0.01
183 1 0.00
184 3 0.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (163 bp):
TTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGGCTCACGTGCTGAGGTATT
TTCAATTTCTATTTTCAATATCTATTTTTAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGC
CTCAAGACACGCTGAGGTATTTTCAATTTCTGT
Found at i:12130690 original size:76 final size:76
Alignment explanation
Indices: 12130589--12131018 Score: 390
Period size: 73 Copynumber: 5.4 Consensus size: 76
12130579 GTTTTTAAAG
* *
12130589 AATCAACTCATATTGTGAGTGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTT-AATTTCTA
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGT-ATTTTCAATTTCTA
12130653 TTTTTCAAAAAA
65 TTTTTCAAAAAA
*
12130665 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTAT
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTAT
*
12130730 CTTTCAAAAAAAAATAAAAAA
66 TTTTC----------AAAAAA
* * *
12130751 AATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAAG--ACGCTGAGGCATTTTCAATTTCTAC
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTAT
*
12130814 TTTTC-AAAAG
66 TTTTCAAAAAA
* * *
12130824 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-AGGCTCACGTGCTGAGGTATTTTAAATTTC
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG-ACAC--GCTGAGGTATTTTCAATTTC
*
12130888 TACTTTTCAATTTCTATTTTTCAAAAG
63 TA---TT---TTTC-A------AAAAA
* * * *
12130915 AATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT-G
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTAT
*
12130979 TTGTC--AAAA
66 TTTTCAAAAAA
**
12130988 AATCAACTTGTATTGCGAGAGGTGAGTTGAG
1 AATCAACTCATATTGCGAGAGGTGAGTTGAG
12131019 TCTCGGGCCA
Statistics
Matches: 300, Mismatches: 23, Indels: 65
0.77 0.06 0.17
Matches are distributed among these distances:
72 2 0.01
73 70 0.23
75 7 0.02
76 60 0.20
77 20 0.07
80 1 0.00
82 3 0.01
83 4 0.01
84 26 0.09
85 1 0.00
86 43 0.14
89 19 0.06
91 41 0.14
92 3 0.01
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (76 bp):
AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTAT
TTTTCAAAAAA
Found at i:12130755 original size:86 final size:79
Alignment explanation
Indices: 12130423--12130977 Score: 374
Period size: 76 Copynumber: 6.8 Consensus size: 79
12130413 TTCTGTTTTC
* *
12130423 AAAAATCAACTCATATTGCAAGGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTT
1 AAAAATCAACTCATATTGCGA-GAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTT
*
12130488 CTGTCTTT----T-AA
65 CT-ACTTTCAAATAAA
* * * * ** * * *
12130499 AAAAATCAATTCATATTTCGAGAAGTGAGTTGAACCT-TGGCTCACGTGCTGAGCTATGTTCAAT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG-ACAC--GCTGAGGTATTTTCAAT
* * **
12130563 TTCTA-TTTTAATGTCTGTTTTTA
63 TTCTACTTTCAA-------ATAAA
* * *
12130586 AAGAATCAACTCATATTGTGAGTGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTT-AATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGT-ATTTTCAATTT
*
12130650 CTA-TTT---TTCAAA
65 CTACTTTCAAAT-AAA
*
12130662 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTC
12130727 TATCTTTCAAAAAAAAATAAA
66 TA-CTTTC------AAATAAA
* *
12130748 AAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAAG--ACGCTGAGGCATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTC
*
12130811 TACTTT----TCAA
66 TACTTTCAAATAAA
* * * *
12130821 AAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-AGGCTCACGTGCTGAGGTATTTTAAAT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG-ACAC--GCTGAGGTATTTTCAAT
*
12130885 TTCTACTTTTCAATTTCTATTTTTCAA
63 TTCTAC-TTTCAA-----A----TAAA
* * * *
12130912 AAGAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTC
12130977 T
66 T
12130978 GTTGTCAAAA
Statistics
Matches: 384, Mismatches: 45, Indels: 87
0.74 0.09 0.17
Matches are distributed among these distances:
72 2 0.01
73 38 0.10
74 1 0.00
75 29 0.08
76 76 0.20
77 39 0.10
78 6 0.02
83 4 0.01
84 22 0.06
85 18 0.05
86 48 0.12
87 35 0.09
88 1 0.00
89 19 0.05
91 43 0.11
92 3 0.01
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (79 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTC
TACTTTCAAATAAA
Found at i:12130820 original size:84 final size:85
Alignment explanation
Indices: 12130659--12130822 Score: 269
Period size: 86 Copynumber: 1.9 Consensus size: 85
12130649 TCTATTTTTC
* *
12130659 AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAAT
1 AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGA-ACGCTGAGGCATTTTCAAT
12130724 TTCTATCTTTCAAAAAAAAAT
65 TTCTATCTTTCAAAAAAAAAT
*
12130745 AAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAAG-ACGCTGAGGCATTTTCAATT
1 AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGAACGCTGAGGCATTTTCAATT
12130809 TCTA-CTTTTCAAAA
66 TCTATC-TTTCAAAA
12130823 GAATCAACTC
Statistics
Matches: 74, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
83 1 0.01
84 30 0.41
86 43 0.58
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (85 bp):
AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGAACGCTGAGGCATTTTCAATT
TCTATCTTTCAAAAAAAAAT
Found at i:12130899 original size:14 final size:14
Alignment explanation
Indices: 12130877--12130911 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
12130867 TGCTGAGGTA
*
12130877 TTTTAAATTTCTAC
1 TTTTCAATTTCTAC
*
12130891 TTTTCAATTTCTAT
1 TTTTCAATTTCTAC
12130905 TTTTCAA
1 TTTTCAA
12130912 AAGAATCAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.26, C:0.14, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTTCAATTTCTAC
Found at i:12130994 original size:164 final size:161
Alignment explanation
Indices: 12130331--12131332 Score: 809
Period size: 162 Copynumber: 6.0 Consensus size: 161
12130321 TTTATTTATA
* * *
12130331 TTTTCAAAAAAATCTACTCATATTGCGAGAGATGAGTTGAGCCTCGG-GCAC--GCTGAGGTATT
1 TTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGGCGCACGTGCTGAGGTATT
* * *
12130393 TTCAAA-ATCTATTTTTCAAATTCTG-TTTTCAAAAATCAACTCATATTGCAAGGAGGTGAGTTG
65 TT-AAATTTCTA-TTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGA-GAGGTGAGTTG
* * *
12130456 AGCCTCAAGACACGTTGAGGTATTTTCAATTTCTG
127 AGCCTCAGGACACGCTGAGGTAATTTCAATTTCTG
* * * * * * * *
12130491 TCTTTTAAAAAAATCAATTCATATTTCGAGAAGTGAGTTGAACCTTGGCTCACGTGCTGAGCTAT
1 --TTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGGCGCACGTGCTGAGGTAT
* * * * *
12130556 GTTCAATTTCTATTTT-AATGTCTGTTTTT-AAAGAATCAACTCATATTGTGAGTGGTGAGTTGA
64 TTTAAATTTCTATTTTCAATTTCTGTTTTTCAAA-AATCAACTCATATTGCGAGAGGTGAGTTGA
* * *
12130619 GCCTCAAGACACGCTGAGGTAATTTTAATTTCTAT
128 GCCTCAGGACACGCTGAGGTAATTTCAATTTCT-G
* *
12130654 TTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG-ACACGT--TGAGGTA
1 TTTTC--AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-AGGCGCACGTGCTGAGGTA
* ******* *** *
12130716 TTTTCAATTTCTATCTTTCAA-AAAAAAATAAAAAAAATCAACTTATATTGCGAGAGGTGAGTTG
63 TTTTAAATTTCTAT-TTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTG
* * * *
12130780 AGCCTCA--AGACGCTGAGGCATTTTCAATTTCTAC
127 AGCCTCAGGACACGCTGAGGTAATTTCAATTTCT-G
*
12130814 TTTTCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGGCTCACGTGCTGAGGTATT
1 TTTTCAAAA-AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGGCGCACGTGCTGAGGTATT
* *
12130879 TTAAATTTCTACTTTTCAATTTCTATTTTTCAAAAGAATCAACTTATATTGCGAGAGGTGAGTTG
65 TTAAATTTCTA-TTTTCAATTTCTGTTTTTC-AAA-AATCAACTCATATTGCGAGAGGTGAGTTG
12130944 AGCCTCAGGACACGCTGAGGTAATTTCAATTTCTG
127 AGCCTCAGGACACGCTGAGGTAATTTCAATTTCTG
* ** * * * * *
12130979 TTGTCAAAAAATCAACTTGTATTGCGAGAGGTGAGTTGAGTCTCGG-GC-CATACGCCGAGGTCT
1 TTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGGCGCACGT--GCTGAGGTAT
* **
12131042 TTTCAAATTCCGTTTTCAATTTCCATTTTTTCAATTTATGCTTTTGAAAAAATCAACTCATATTG
64 TTT-AAA------TTTC----T--A--TTTTCAATTTCTG-TTTTTCAAAAATCAACTCATATTG
*
12131107 CGA-ATGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTATG
113 CGAGA-GGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTG
* * * **
12131156 CTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGCTGAGCCTCGGGGCAC--GCCAAGGTATT
1 -TTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGGCGCACGTGCTGAGGTA-T
*
12131218 TTTAATTTCTATTTTTCAATTTCTGCTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGA
64 TTTAA-----A--TTTCTATTT-T-C----AATTTCTGTTTTTCAAAAATCAACTCATATTGCGA
* * *
12131283 GAGGTGAGTTGAGCCTCAGGGCACGCTGAGATATTTTCAATTTCTG
116 GAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTG
12131329 TTTT
1 TTTT
12131333 TCAATTTTTG
Statistics
Matches: 686, Mismatches: 97, Indels: 104
0.77 0.11 0.12
Matches are distributed among these distances:
158 6 0.01
159 39 0.06
160 27 0.04
161 82 0.12
162 99 0.14
163 74 0.11
164 96 0.14
165 11 0.02
166 22 0.03
168 3 0.00
169 1 0.00
170 2 0.00
171 4 0.01
172 4 0.01
173 65 0.09
174 8 0.01
175 10 0.01
176 10 0.01
177 97 0.14
178 20 0.03
179 5 0.01
180 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (161 bp):
TTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGGCGCACGTGCTGAGGTATTT
TAAATTTCTATTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
TCAGGACACGCTGAGGTAATTTCAATTTCTG
Found at i:12131188 original size:177 final size:173
Alignment explanation
Indices: 12130877--12131332 Score: 571
Period size: 177 Copynumber: 2.6 Consensus size: 173
12130867 TGCTGAGGTA
* * * *
12130877 TTTTAAATTTCTACTTTTCAATTTCTATTTTTCAAAAGAATCAACTTATATTGCGAGAGGTGAGT
1 TTTTCAATTTCTGCTTTTCAATTTCT-GTTTTCAAAA-AATCAACTCATATTGCGAGAGGTGAGT
* **
12130942 TGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTGTCAAAAAATCAACTTGTATTGCGAG
64 TGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTTC-AAAAATCAACTCATATTGCGAG
* * * * *
12131007 AGGTGAGTTGAGTCTCGGGCCATACGCCGAGGTCTTTTCAAATTC-CG
128 AGGTGAGCTGAGCCTCGGGCC--ACGCCAAGGTATTTTCAAATTCTAG
* * *
12131054 TTTTCAATTTCCAT-TTTTTCAATTTATGCTTTTGAAAAAATCAACTCATATTGCGA-ATGGTGA
1 TTTTCAATTT-C-TGCTTTTCAATTTCTG-TTTTCAAAAAATCAACTCATATTGCGAGA-GGTGA
*
12131117 GTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTATGCTTTTCAAAAATCAACTCATATTGCG
62 GTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTG-TTTTCAAAAATCAACTCATATTGCG
* * * *
12131182 AGAGGTGAGCTGAGCCTCGGGGCACGCCAAGGTATTTTTAATTTCTAT
126 AGAGGTGAGCTGAGCCTCGGGCCACGCCAAGGTATTTTCAAATTCTAG
12131230 TTTTCAATTTCTGCTTTT-AATTTCTGTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTT
1 TTTTCAATTTCTGCTTTTCAATTTCTG-TTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTT
* * *
12131293 GAGCCTCAGGGCACGCTGAGATATTTTCAATTTCTGTTTT
65 GAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTT
12131333 TCAATTTTTG
Statistics
Matches: 244, Mismatches: 27, Indels: 21
0.84 0.09 0.07
Matches are distributed among these distances:
172 4 0.02
173 61 0.25
174 13 0.05
175 23 0.09
176 11 0.05
177 107 0.44
178 24 0.10
179 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (173 bp):
TTTTCAATTTCTGCTTTTCAATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTG
AGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGG
TGAGCTGAGCCTCGGGCCACGCCAAGGTATTTTCAAATTCTAG
Found at i:12131190 original size:73 final size:74
Alignment explanation
Indices: 12131070--12131208 Score: 219
Period size: 73 Copynumber: 1.9 Consensus size: 74
12131060 ATTTCCATTT
*
12131070 TTTCAATTTATGCTTTTGAAAAAATCAACTCATATTGCGAATGGTGAGTTGAGCCTCAGGACACG
1 TTTCAATTTATGCTTTTGAAAAAATCAACTCATATTGCGAATGGTGAGCTGAGCCTCAGGACACG
12131135 CTGAGGTAA
66 CTGAGGTAA
* * *
12131144 TTTCAATTTATGCTTTT-CAAAAATCAACTCATATTGCGAGA-GGTGAGCTGAGCCTCGGGGCAC
1 TTTCAATTTATGCTTTTGAAAAAATCAACTCATATTGCGA-ATGGTGAGCTGAGCCTCAGGACAC
12131207 GC
65 GC
12131209 CAAGGTATTT
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
73 42 0.70
74 18 0.30
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (74 bp):
TTTCAATTTATGCTTTTGAAAAAATCAACTCATATTGCGAATGGTGAGCTGAGCCTCAGGACACG
CTGAGGTAA
Found at i:12131215 original size:73 final size:74
Alignment explanation
Indices: 12131070--12131225 Score: 217
Period size: 73 Copynumber: 2.1 Consensus size: 74
12131060 ATTTCCATTT
*
12131070 TTTCAATTTATGCTTTTGAAAAAATCAACTCATATTGCGAATGGTGAGTTGAGCCTCAGGACACG
1 TTTCAATTTATGCTTTTGAAAAAATCAACTCATATTGCGAATGGTGAGCTGAGCCTCAGGACACG
**
12131135 CTGAGGTAA
66 CCAAGGTAA
* * *
12131144 TTTCAATTTATGCTTTT-CAAAAATCAACTCATATTGCGAGA-GGTGAGCTGAGCCTCGGGGCAC
1 TTTCAATTTATGCTTTTGAAAAAATCAACTCATATTGCGA-ATGGTGAGCTGAGCCTCAGGACAC
*
12131207 GCCAAGGTAT
65 GCCAAGGTAA
*
12131217 TTTTAATTT
1 TTTCAATTT
12131226 CTATTTTTCA
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
73 55 0.75
74 18 0.25
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (74 bp):
TTTCAATTTATGCTTTTGAAAAAATCAACTCATATTGCGAATGGTGAGCTGAGCCTCAGGACACG
CCAAGGTAA
Found at i:12131238 original size:14 final size:13
Alignment explanation
Indices: 12131214--12131260 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
12131204 CACGCCAAGG
12131214 TATTTTTAATTTC
1 TATTTTTAATTTC
12131227 TATTTTTCAATTTC
1 TATTTTT-AATTTC
**
12131241 TGCTTTTAATTTC
1 TATTTTTAATTTC
*
12131254 TGTTTTT
1 TATTTTT
12131261 CAAAAATCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
13 19 0.63
14 11 0.37
ACGTcount: A:0.17, C:0.11, G:0.04, T:0.68
Consensus pattern (13 bp):
TATTTTTAATTTC
Found at i:12131325 original size:100 final size:99
Alignment explanation
Indices: 12131148--12131514 Score: 404
Period size: 100 Copynumber: 3.8 Consensus size: 99
12131138 AGGTAATTTC
* * * **
12131148 AATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGCTGAGCCTCGGGGCACGCCAAG
1 AATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
*
12131213 GTATTTTTAATTTCTATTTTTCAATTTCTGCTTTT
66 GTATTTTCAATTTCTATTTTTCAATTT-TGCTTTT
* * *
12131248 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAG
1 AATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
* * **
12131313 ATATTTTCAATTTCTGTTTTTCAATTTTTGCCTTAC
66 GTATTTTCAATTTCTATTTTTCAA-TTTTG-CTTTT
* *
12131349 AAATTCTGCTTTTC--AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
1 AATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
12131412 GTATTTTC-A-----A-TTTTC-A-TTT--TTTT
66 GTATTTTCAATTTCTATTTTTCAATTTTGCTTTT
* *
12131435 AATTTATG--TTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGT
1 AATTTATGCTTTTC----AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
*
12131498 TGAGTTATTTTCAATTT
62 TGAGGTATTTTCAATTT
12131515 TTGTCTTCCA
Statistics
Matches: 232, Mismatches: 23, Indels: 30
0.81 0.08 0.11
Matches are distributed among these distances:
84 4 0.02
86 8 0.03
89 3 0.01
90 54 0.23
91 2 0.01
92 5 0.02
98 1 0.00
99 55 0.24
100 82 0.35
101 18 0.08
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (99 bp):
AATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
GTATTTTCAATTTCTATTTTTCAATTTTGCTTTT
Found at i:12131552 original size:75 final size:75
Alignment explanation
Indices: 12131449--12131737 Score: 396
Period size: 75 Copynumber: 3.9 Consensus size: 75
12131439 TATGTTTCAA
* *
12131449 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGTTATTTTCAATT
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACGTTGAGGTATTTTCAATT
*
12131514 TTTGTCTTCC
66 TTTGTCTTTC
* * *
12131524 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAG--ACGCTGAGGTAATTTCAATT
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACGTTGAGGTATTTTCAATT
12131587 TTTGT-TTGTC
66 TTTGTCTT-TC
* *
12131597 --AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACGTTGAGGTATTTTCAATT
12131660 TCTT-TCTTTC
66 T-TTGTCTTTC
* * * *
12131670 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAG--ACGCTGAGGTGTTTTCCATT
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACGTTGAGGTATTTTCAATT
12131733 TTTGT
66 TTTGT
12131738 TCTTCAATTT
Statistics
Matches: 189, Mismatches: 17, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
71 38 0.20
72 4 0.02
73 64 0.34
74 4 0.02
75 79 0.42
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (75 bp):
AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACGTTGAGGTATTTTCAATT
TTTGTCTTTC
Found at i:12131611 original size:146 final size:146
Alignment explanation
Indices: 12131451--12131738 Score: 506
Period size: 146 Copynumber: 2.0 Consensus size: 146
12131441 TGTTTCAAAA
* *
12131451 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGTTATTTTCAATTT-
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
12131515 TTGTCTTCCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTAAT
66 TT-TCTTCCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTAAT
12131580 TTCAATTTTTGTTTGTC
130 TTCAATTTTTGTTTGTC
12131597 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
* **
12131662 TTTCTTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTGTTT
66 TTTCTTCCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTAATT
*
12131727 TCCATTTTTGTT
131 TCAATTTTTGTT
12131739 CTTCAATTTC
Statistics
Matches: 135, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
146 133 0.99
147 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (146 bp):
AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
TTTCTTCCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTAATT
TCAATTTTTGTTTGTC
Found at i:12131867 original size:92 final size:92
Alignment explanation
Indices: 12131743--12132242 Score: 406
Period size: 92 Copynumber: 5.6 Consensus size: 92
12131733 TTTGTTCTTC
* * * *
12131743 AATTTCTGTATTTCAAAAAAATCAGCTCATATTGCGAGTGGTGAGTTGAGCCTTGACTCACACGC
1 AATTTATGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGACTCACACGC
12131808 TGAGGTATTTTCAAATTCTGTTTTTTA
66 TGAGGTATTTTCAAATTCTGTTTTTTA
* * **
12131835 AATTT-TGTTTTTCCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTCAGCC-TCA-GGACACG
1 AATTTATGTTTTT-CAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGACTCACACG
* * *
12131897 CTGAGGTATTTTCAATTTCTTTTTTTTTTC
65 CTGAGGTATTTTCAAATTC--TGTTTTTTA
* * *
12131927 AATTTATGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC-TCAGGTCACACG
1 AATTTATGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGA-CTCACACG
* * *
12131991 CCGAGGTATTTTC-AATTGATGTTTTTTTC
65 CTGAGGTATTTTCAAATT-CTG-TTTTTTA
* * * * * ** **
12132020 AATTTATGCTTTGC--AAAAATTAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACA-TA
1 AATTTATGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGACTCACACGC
* * **
12132082 TCGAGGTATATTCAAAATCTGTTTTACA
66 T-GAGGTATTTTCAAATTCTGTTTTTTA
* * **
12132110 AATTT-TG-TTTT---AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGC
1 AATTTATGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGACTCACACGC
* * * *
12132170 TGAGCTATGTTC-AATT-TCTATTTT-
66 TGAGGTATTTTCAAATTCTGTTTTTTA
* * * * * **
12132194 AATGTCTGTTTTT--AAAGAGTCAATTCATATTGCGAGAAATGAGTTGAGC
1 AATTTATGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
12132243 TCAGGATCAC
Statistics
Matches: 337, Mismatches: 56, Indels: 35
0.79 0.13 0.08
Matches are distributed among these distances:
84 4 0.01
85 6 0.02
86 7 0.02
87 80 0.24
88 4 0.01
89 2 0.01
90 32 0.09
91 60 0.18
92 98 0.29
93 27 0.08
94 17 0.05
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (92 bp):
AATTTATGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGACTCACACGC
TGAGGTATTTTCAAATTCTGTTTTTTA
Found at i:12132065 original size:91 final size:89
Alignment explanation
Indices: 12131671--12132157 Score: 417
Period size: 92 Copynumber: 5.4 Consensus size: 89
12131661 CTTTCTTTCA
* * * * * *
12131671 AAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCA----AGACGCTGAGGTGTTTTCCAT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAAT
* *
12131732 T-T-TTGTTCTTCAATTTCTGTATTTC
66 TATGTT-TTTTTCAATTT-TGT-TTGC
* * * * *
12131757 AAAAAAATCAGCTCATATTGCGAGTGGTGAGTTGAGCCT-TGACTCACACGCTGAGGTATTTTCA
1 -AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG-GTCACACGCCGAGGTATTTTC-
* * *
12131821 AATTCTG-TTTTTTAAATTTTGTTTTTCC
63 AATTATGTTTTTTTCAATTTTG--TTTGC
* *
12131849 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTCAGCCTCAGG--ACACGCTGAGGTATTTTCAA
1 -AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAA
* *
12131912 TTTCTTTTTTTTTTCAATTTATGTTTGTC
65 -TT-ATGTTTTTTTCAATTT-TGTTTG-C
12131941 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAA
1 -AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAA
12132006 TTGATGTTTTTTTCAATTTATGCTTTGC
65 TT-ATGTTTTTTTCAATTT-TG-TTTGC
* * * *** *
12132034 -AAAAATTAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACATATCGAGGTATATTCAA-
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAAT
* * * *
12132097 AATCTGTTTTACAAATTTTGTTT--
66 TATGTTTTTTTC-AATTTTGTTTGC
* *
12132120 TAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
12132158 TGGCTCACGT
Statistics
Matches: 342, Mismatches: 37, Indels: 42
0.81 0.09 0.10
Matches are distributed among these distances:
87 70 0.20
88 3 0.01
89 12 0.04
90 25 0.07
91 78 0.23
92 105 0.31
93 26 0.08
94 23 0.07
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (89 bp):
AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAAT
TATGTTTTTTTCAATTTTGTTTGC
Found at i:12132183 original size:87 final size:86
Alignment explanation
Indices: 12131672--12132242 Score: 399
Period size: 87 Copynumber: 6.4 Consensus size: 86
12131662 TTTCTTTCAA
* * * * * *
12131672 AAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACC----TCAAGACGCTGAGGTGTTTTCCATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGGTC-ACACGCTGAGGTATTTTCAAAT
* * *
12131733 TTTGTTCTTCAATTTCTGTATTTCAA
65 TCTGTTTTTCAATTT-TGT-TTT--T
* * * *
12131759 AAAAATCAGCTCATATTGCGAGTGGTGAGTTGAGCCTTGACTCACACGCTGAGGTATTTTCAAAT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAG-GTCACACGCTGAGGTATTTTCAAAT
*
12131824 TCTGTTTTTTAAATTTTGTTTTT
65 TCTG-TTTTTCAATTTTGTTTTT
*
12131847 CCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTCAGCCTCAGG--ACACGCTGAGGTATTTTC
1 ----AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-AGGTCACACGCTGAGGTATTTTC
* * *
12131910 AATTTCTTTTTTTTTTCAATTTATGTTTGTCAA
61 AAATTC---TGTTTTTCAATTT-TGTTT-T--T
*
12131943 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTC-AAT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-AGGTCACACGCTGAGGTATTTTCAAAT
* **
12132007 TGATGTTTTTTTCAATTTATGCTTTGC
65 T-CTG--TTTTTCAATTT-TG-TTTTT
* * * ** *
12132034 AAAAATTAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACA-TATCGAGGTATATTCAAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-AGGTCACACGCT-GAGGTATTTTCAAA
* *
12132098 ATCTGTTTTACAAATTTTG-TTTT
64 TTCTGTTTTTC-AATTTTGTTTTT
* * ** * * *
12132121 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATGTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGG-TCACACGCTGAGGTATTTTCAAAT
* *
12132186 TCT-ATTTT-AATGTCTGTTTTT
65 TCTGTTTTTCAAT-TTTGTTTTT
* * **
12132207 AAAGAGTCAATTCATATTGCGAGAAATGAGTTGAGC
1 AAA-AATCAACTCATATTGCGAGAGGTGAGTTGAGC
12132243 TCAGGATCAC
Statistics
Matches: 397, Mismatches: 55, Indels: 64
0.77 0.11 0.12
Matches are distributed among these distances:
84 3 0.01
85 3 0.01
86 12 0.03
87 117 0.29
88 1 0.00
89 7 0.02
90 31 0.08
91 80 0.20
92 98 0.25
93 24 0.06
94 21 0.05
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (86 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGGTCACACGCTGAGGTATTTTCAAATT
CTGTTTTTCAATTTTGTTTTT
Found at i:12132956 original size:30 final size:30
Alignment explanation
Indices: 12132896--12132993 Score: 153
Period size: 30 Copynumber: 3.3 Consensus size: 30
12132886 CTAGCCTTTG
*
12132896 CCACCACCAACTCCACTAGCCA-AATTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
*
12132925 CCACCACAAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
* *
12132955 CCACTACCTACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
12132985 CCACCACCA
1 CCACCACCA
12132994 CTTTTACCTA
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
29 21 0.34
30 40 0.66
ACGTcount: A:0.29, C:0.48, G:0.06, T:0.17
Consensus pattern (30 bp):
CCACCACCAACTCCACTAGCCACACTTGCT
Found at i:12132958 original size:18 final size:18
Alignment explanation
Indices: 12132935--12132988 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
12132925 CCACCACAAA
12132935 CTCCACTAGCCACACTTG
1 CTCCACTAGCCACACTTG
*
12132953 CTCCACT----AC-C-TA
1 CTCCACTAGCCACACTTG
12132965 CTCCACTAGCCACACTTG
1 CTCCACTAGCCACACTTG
12132983 CTCCAC
1 CTCCAC
12132989 CACCACTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
12 8 0.29
13 1 0.04
14 2 0.07
16 2 0.07
17 1 0.04
18 14 0.50
ACGTcount: A:0.22, C:0.48, G:0.07, T:0.22
Consensus pattern (18 bp):
CTCCACTAGCCACACTTG
Found at i:12141036 original size:11 final size:11
Alignment explanation
Indices: 12140993--12141044 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
12140983 TTAATTAAAT
12140993 TTTATATTTTAA
1 TTTA-ATTTTAA
12141005 TATTACATTTTAA
1 T-TTA-ATTTTAA
*
12141018 -TTATTTTTAA
1 TTTAATTTTAA
*
12141028 TTTAATTTTTA
1 TTTAATTTTAA
12141039 TTTAAT
1 TTTAAT
12141045 GTTCAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
10 6 0.18
11 17 0.50
12 1 0.03
13 10 0.29
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (11 bp):
TTTAATTTTAA
Found at i:12141038 original size:22 final size:24
Alignment explanation
Indices: 12140994--12141036 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
12140984 TAATTAAATT
12140994 TTATATTTTAATATTACATTTTAA
1 TTATATTTTAATATTACATTTTAA
12141018 TTAT-TTTTAAT-TTA-ATTTT
1 TTATATTTTAATATTACATTTT
12141037 TATTTAATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 3 0.16
23 7 0.37
24 4 0.21
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (24 bp):
TTATATTTTAATATTACATTTTAA
Found at i:12141290 original size:60 final size:60
Alignment explanation
Indices: 12141219--12141334 Score: 223
Period size: 60 Copynumber: 1.9 Consensus size: 60
12141209 TTATTTTTTT
12141219 AAATTTAAAAAATAATTTGATAAATACAAATAAAAATATGTTTTCAATGAAATATGAAAA
1 AAATTTAAAAAATAATTTGATAAATACAAATAAAAATATGTTTTCAATGAAATATGAAAA
*
12141279 AAATTTAAAAAATCATTTGATAAATACAAATAAAAATATGTTTTCAATGAAATATG
1 AAATTTAAAAAATAATTTGATAAATACAAATAAAAATATGTTTTCAATGAAATATG
12141335 TTTCGTACAT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.56, C:0.04, G:0.07, T:0.33
Consensus pattern (60 bp):
AAATTTAAAAAATAATTTGATAAATACAAATAAAAATATGTTTTCAATGAAATATGAAAA
Found at i:12145739 original size:50 final size:51
Alignment explanation
Indices: 12145625--12145868 Score: 269
Period size: 50 Copynumber: 4.7 Consensus size: 51
12145615 GATAATAACA
* * ** * *
12145625 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTTCTCAT-CTCGG
* *
12145676 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGA-CTTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTTCTCATCTCGG
* * * *
12145726 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACC-TCTCGTCTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTTCTCATCTCGG
* * *
12145776 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCT-TC-TCATC-T-CGG
*
12145831 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA
12145869 TCTCTTTTCC
Statistics
Matches: 163, Mismatches: 22, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
49 1 0.01
50 86 0.53
51 34 0.21
52 2 0.01
53 3 0.02
54 1 0.01
55 1 0.01
56 35 0.21
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (51 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTTCTCATCTCGG
Found at i:12145804 original size:100 final size:106
Alignment explanation
Indices: 12145624--12145873 Score: 343
Period size: 100 Copynumber: 2.4 Consensus size: 106
12145614 TGATAATAAC
** *
12145624 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATAGTGCCCATGCCATG
* *
12145689 TCCCAGACATGGTCTTATAGGGGA-CT-TC-TCATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCATCATCTTAAGG
* *
12145726 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCAGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-AGTGCCCATGCCATG
*
12145789 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCATCATCTTAAGG
* *
12145831 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
12145874 TTTCCCAAAT
Statistics
Matches: 131, Mismatches: 10, Indels: 10
0.87 0.07 0.07
Matches are distributed among these distances:
99 1 0.01
100 43 0.33
101 38 0.29
102 2 0.02
103 4 0.03
104 1 0.01
105 2 0.02
106 40 0.31
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (106 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATAGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCATCATCTTAAGG
Found at i:12145990 original size:11 final size:11
Alignment explanation
Indices: 12145974--12145998 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12145964 ATCATCATCA
12145974 AATAAATTCAT
1 AATAAATTCAT
12145985 AATAAATTCAT
1 AATAAATTCAT
12145996 AAT
1 AAT
12145999 TGCTGGAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (11 bp):
AATAAATTCAT
Found at i:12146244 original size:30 final size:30
Alignment explanation
Indices: 12146209--12146266 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
12146199 CCTCGACTCT
*
12146209 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
12146239 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
12146267 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:12148278 original size:16 final size:16
Alignment explanation
Indices: 12148253--12148283 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12148243 CCTTCAACTC
*
12148253 TTATATGTAAAAAAAT
1 TTATAAGTAAAAAAAT
12148269 TTATAAGTAAAAAAA
1 TTATAAGTAAAAAAA
12148284 AAAAAAAACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.32
Consensus pattern (16 bp):
TTATAAGTAAAAAAAT
Found at i:12153993 original size:10 final size:10
Alignment explanation
Indices: 12153967--12154032 Score: 52
Period size: 10 Copynumber: 7.0 Consensus size: 10
12153957 CAAATTTTCG
12153967 ATAATATTTT
1 ATAATATTTT
12153977 -T-ATATTTT
1 ATAATATTTT
12153985 ATAATATTTT
1 ATAATATTTT
*
12153995 AT-CTATCTTT
1 ATAATAT-TTT
12154005 -TAATA-TTT
1 ATAATATTTT
* *
12154013 AAAACATTTT
1 ATAATATTTT
*
12154023 ATGATATTTT
1 ATAATATTTT
12154033 GTAGTTTGTT
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
8 10 0.23
9 9 0.21
10 24 0.56
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.59
Consensus pattern (10 bp):
ATAATATTTT
Found at i:12154010 original size:19 final size:18
Alignment explanation
Indices: 12153967--12154012 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
12153957 CAAATTTTCG
12153967 ATAATATTTTTATATTTT
1 ATAATATTTTTATATTTT
*
12153985 ATAATATTTTATCTATCTTT
1 ATAATATTTT-TATAT-TTT
12154005 -TAATATTT
1 ATAATATTT
12154013 AAAACATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 10 0.40
19 12 0.48
20 3 0.12
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (18 bp):
ATAATATTTTTATATTTT
Found at i:12157343 original size:42 final size:42
Alignment explanation
Indices: 12157284--12157370 Score: 147
Period size: 42 Copynumber: 2.1 Consensus size: 42
12157274 TATCACTTTA
* * *
12157284 TTGATGAAGCAGGGATGACGTTTAATGACTTCTCTGAATTCT
1 TTGATGAAGCAAGGATGACATTTAATGACTTCTCTGAATTAT
12157326 TTGATGAAGCAAGGATGACATTTAATGACTTCTCTGAATTAT
1 TTGATGAAGCAAGGATGACATTTAATGACTTCTCTGAATTAT
12157368 TTG
1 TTG
12157371 TTTACACGTG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.37
Consensus pattern (42 bp):
TTGATGAAGCAAGGATGACATTTAATGACTTCTCTGAATTAT
Found at i:12161321 original size:26 final size:26
Alignment explanation
Indices: 12161292--12161344 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
12161282 GATGTGCCAT
12161292 TACCCCTTAAGCCTATGTCATCACAA
1 TACCCCTTAAGCCTATGTCATCACAA
12161318 TACCCCTTAAGCCTATGTCATCACAA
1 TACCCCTTAAGCCTATGTCATCACAA
12161344 T
1 T
12161345 CTTCTTTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.34, G:0.08, T:0.28
Consensus pattern (26 bp):
TACCCCTTAAGCCTATGTCATCACAA
Found at i:12165943 original size:22 final size:22
Alignment explanation
Indices: 12165918--12165981 Score: 57
Period size: 22 Copynumber: 3.0 Consensus size: 22
12165908 AATTTTAGCT
12165918 ATTAATGTTTAATTT-TTTATTA
1 ATTAAT-TTTAATTTATTTATTA
* *
12165940 ATTAGTTTTTATTTATTTATT-
1 ATTAATTTTAATTTATTTATTA
12165961 -TTAA-TTTAATTTAATTT-TTA
1 ATTAATTTTAATTT-ATTTATTA
12165981 A
1 A
12165982 CTTTTTGAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
19 9 0.26
20 7 0.21
21 7 0.21
22 11 0.32
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (22 bp):
ATTAATTTTAATTTATTTATTA
Found at i:12167941 original size:19 final size:19
Alignment explanation
Indices: 12167913--12167949 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12167903 TAGAAAAAAT
12167913 AAATTATAAAAATCGTAAA
1 AAATTATAAAAATCGTAAA
* *
12167932 AAATTTTAAAAATTGTAA
1 AAATTATAAAAATCGTAA
12167950 GATTTTATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.32
Consensus pattern (19 bp):
AAATTATAAAAATCGTAAA
Found at i:12168244 original size:19 final size:18
Alignment explanation
Indices: 12168213--12168374 Score: 80
Period size: 18 Copynumber: 8.8 Consensus size: 18
12168203 TAAAGGGTCT
*
12168213 TTTTTATACATTTTATAA
1 TTTTTATAAATTTTATAA
*
12168231 TTTTTATAAAATTTTACAA
1 TTTTTAT-AAATTTTATAA
*
12168250 TTTTT-TAAATTTTTTACGA
1 TTTTTATAAATTTTATA--A
* *
12168269 TTTTTATAATTTTTCTAA
1 TTTTTATAAATTTTATAA
* *
12168287 TTTTAACAAAATTTTA-ATA
1 TTTTTA-TAAATTTTATA-A
* *
12168306 TAATTTAT-ATTTTTATTAAA
1 T-TTTTATAAATTTTA-T-AA
* * *
12168326 ATTTAATAAATTTAATAA
1 TTTTTATAAATTTTATAA
* ** *
12168344 ATTTTATTGATTTT-TAT
1 TTTTTATAAATTTTATAA
12168361 TTTTTATAAATTTT
1 TTTTTATAAATTTT
12168375 TTTACCACAT
Statistics
Matches: 106, Mismatches: 27, Indels: 23
0.68 0.17 0.15
Matches are distributed among these distances:
17 21 0.20
18 33 0.31
19 33 0.31
20 18 0.17
21 1 0.01
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.59
Consensus pattern (18 bp):
TTTTTATAAATTTTATAA
Found at i:12168256 original size:29 final size:28
Alignment explanation
Indices: 12168223--12168338 Score: 78
Period size: 28 Copynumber: 4.0 Consensus size: 28
12168213 TTTTTATACA
12168223 TTTTATAATTTTTATAAAATTTTACAATT
1 TTTTATAATTTTTATAAAATTTTA-AATT
* *
12168252 TTTTA-AATTTTT-TACGATTTTTATAA-T
1 TTTTATAATTTTTATA-AAATTTTA-AATT
* * * *
12168279 TTTTCTAATTTTAACAAAATTTTAATATA
1 TTTTATAATTTTTATAAAATTTTAA-ATT
*
12168308 ATTTAT-ATTTTTATTAAAATTTAATAAATT
1 TTTTATAATTTTTA-TAAAATTT--TAAATT
12168338 T
1 T
12168339 AATAAATTTT
Statistics
Matches: 64, Mismatches: 15, Indels: 15
0.68 0.16 0.16
Matches are distributed among these distances:
27 8 0.12
28 34 0.53
29 17 0.27
30 2 0.03
31 3 0.05
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (28 bp):
TTTTATAATTTTTATAAAATTTTAAATT
Found at i:12168318 original size:56 final size:56
Alignment explanation
Indices: 12168213--12168319 Score: 128
Period size: 56 Copynumber: 1.9 Consensus size: 56
12168203 TAAAGGGTCT
* * **
12168213 TTTTTATACATTTTATAATTTTTATAAAATTTTACAATTTTTTAAATTTTTTACGA
1 TTTTTATACATTTTATAATTTTAACAAAATTTTACAATAATTTAAATTTTTTACGA
* *
12168269 TTTTTATA-ATTTTTCTAATTTTAACAAAATTTTA-ATATAATTTATATTTTT
1 TTTTTATACA-TTTTATAATTTTAACAAAATTTTACA-ATAATTTAAATTTTT
12168320 ATTAAAATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
55 2 0.05
56 41 0.95
ACGTcount: A:0.35, C:0.05, G:0.01, T:0.60
Consensus pattern (56 bp):
TTTTTATACATTTTATAATTTTAACAAAATTTTACAATAATTTAAATTTTTTACGA
Found at i:12168348 original size:29 final size:29
Alignment explanation
Indices: 12168284--12168351 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
12168274 ATAATTTTTC
**
12168284 TAATTTTAACAAAATTTTAATATAATTTA
1 TAATTTTATTAAAATTTTAATATAATTTA
*
12168313 TATTTTTATTAAAA-TTTAATA-AATTTAA
1 TAATTTTATTAAAATTTTAATATAATTT-A
12168341 TAAATTTTATT
1 T-AATTTTATT
12168352 GATTTTTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 5 0.15
28 9 0.27
29 19 0.58
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (29 bp):
TAATTTTATTAAAATTTTAATATAATTTA
Found at i:12168374 original size:9 final size:9
Alignment explanation
Indices: 12168214--12168374 Score: 62
Period size: 9 Copynumber: 17.4 Consensus size: 9
12168204 AAAGGGTCTT
*
12168214 TTTTATACA
1 TTTTATAAA
*
12168223 TTTTATAAT
1 TTTTATAAA
12168232 TTTTATAAAA
1 TTTTAT-AAA
*
12168242 TTTTA-CAA
1 TTTTATAAA
*
12168250 TTTTTTAAA
1 TTTTATAAA
* *
12168259 TTTTTTACGAT
1 TTTTATA--AA
*
12168270 TTTTATAAT
1 TTTTATAAA
*
12168279 TTTTCT-AA
1 TTTTATAAA
*
12168287 TTTTAACAAAA
1 TTTT-A-TAAA
12168298 TTTTAATATAA
1 TTTT-ATA-AA
*
12168309 -TTTAT-AT
1 TTTTATAAA
12168316 TTTTATTAAAA
1 TTTTA-T-AAA
*
12168327 TTTAATAAA
1 TTTTATAAA
*
12168336 TTTAATAAA
1 TTTTATAAA
**
12168345 TTTTATTGA
1 TTTTATAAA
**
12168354 TTTT-TATT
1 TTTTATAAA
12168362 TTTTATAAA
1 TTTTATAAA
12168371 TTTT
1 TTTT
12168375 TTTACCACAT
Statistics
Matches: 115, Mismatches: 24, Indels: 26
0.70 0.15 0.16
Matches are distributed among these distances:
7 1 0.01
8 20 0.17
9 60 0.52
10 12 0.10
11 22 0.19
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (9 bp):
TTTTATAAA
Found at i:12171510 original size:20 final size:19
Alignment explanation
Indices: 12171485--12171525 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
12171475 CGTTCCCACT
*
12171485 TTCTTTTTCTTTATTCTTTA
1 TTCTTTTTCTTT-TTATTTA
*
12171505 TTCTTTTTGTTTTTATTTA
1 TTCTTTTTCTTTTTATTTA
12171524 TT
1 TT
12171526 TATTTTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.10, C:0.10, G:0.02, T:0.78
Consensus pattern (19 bp):
TTCTTTTTCTTTTTATTTA
Found at i:12173255 original size:53 final size:53
Alignment explanation
Indices: 12173161--12173297 Score: 150
Period size: 53 Copynumber: 2.6 Consensus size: 53
12173151 TATAAGCCCG
* * * * *
12173161 TAACTGGTTGGTTATGGAATCATATTGAAAAAAGACAATATCGTGCAAGACCGA
1 TAACTGGTGGGTTATGAAATCATATGGAAAAAAGACAATATCATACAAGACC-A
* * * *
12173215 -AACTGGTGGGTTATGAAATCATATGGAAAGAATACCATATCATATAAGACCA
1 TAACTGGTGGGTTATGAAATCATATGGAAAAAAGACAATATCATACAAGACCA
* * *
12173267 TAATTGGTGGATTATGACATCATATGGAAAA
1 TAACTGGTGGGTTATGAAATCATATGGAAAA
12173298 GTTAAGGAAG
Statistics
Matches: 69, Mismatches: 13, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
52 1 0.01
53 68 0.99
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (53 bp):
TAACTGGTGGGTTATGAAATCATATGGAAAAAAGACAATATCATACAAGACCA
Found at i:12174580 original size:35 final size:35
Alignment explanation
Indices: 12174534--12174604 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
12174524 TTAGTGACTA
12174534 GTTTAGATTTTTTACTAAAGTAAGTTGTTTTTCTC
1 GTTTAGATTTTTTACTAAAGTAAGTTGTTTTTCTC
12174569 GTTTAGATTTTTTACTAAAGTAAGTTGTTTTTCTC
1 GTTTAGATTTTTTACTAAAGTAAGTTGTTTTTCTC
12174604 G
1 G
12174605 CAATGTAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.23, C:0.08, G:0.15, T:0.54
Consensus pattern (35 bp):
GTTTAGATTTTTTACTAAAGTAAGTTGTTTTTCTC
Found at i:12174961 original size:21 final size:21
Alignment explanation
Indices: 12174937--12174978 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12174927 TCTTATAGCT
12174937 TTAAA-AAATTTTATATAATAA
1 TTAAACAAATTTT-TATAATAA
*
12174958 TTAAACATATTTTTATAATAA
1 TTAAACAAATTTTTATAATAA
12174979 AATTAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
TTAAACAAATTTTTATAATAA
Found at i:12175737 original size:30 final size:30
Alignment explanation
Indices: 12175701--12175762 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
12175691 ACTTATTTTA
*
12175701 TTATTAATTTTGTTATTATTTTAAAGGCAT
1 TTATTAATTTTATTATTATTTTAAAGGCAT
* *
12175731 TTATTAATTTTATTATTATTTTAGAGGTAT
1 TTATTAATTTTATTATTATTTTAAAGGCAT
12175761 TT
1 TT
12175763 GCTTGTTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.60
Consensus pattern (30 bp):
TTATTAATTTTATTATTATTTTAAAGGCAT
Found at i:12181460 original size:11 final size:11
Alignment explanation
Indices: 12181444--12181469 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
12181434 TTAATATGAC
12181444 TTTTTTTTTCT
1 TTTTTTTTTCT
12181455 TTTTTTTTTCT
1 TTTTTTTTTCT
12181466 TTTT
1 TTTT
12181470 GTTATAGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTTTCT
Found at i:12182469 original size:6 final size:5
Alignment explanation
Indices: 12182417--12182467 Score: 54
Period size: 5 Copynumber: 10.4 Consensus size: 5
12182407 AATAATAACT
*
12182417 AATAA AAT-- AATAA GAA-AA AATAA AATAA ACTAA AATAA AATAAA AATAA
1 AATAA AATAA AATAA -AATAA AATAA AATAA AATAA AATAA AAT-AA AATAA
12182466 AA
1 AA
12182468 ATTGGGTTGC
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
3 3 0.08
4 2 0.05
5 27 0.69
6 7 0.18
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (5 bp):
AATAA
Found at i:12205626 original size:3 final size:3
Alignment explanation
Indices: 12205618--12205698 Score: 62
Period size: 3 Copynumber: 26.3 Consensus size: 3
12205608 CATATACAAT
12205618 ATA ATA ATA AT- ATAA ATA ATA ATA TATA CATGA GA-A ATA ATA ATA
1 ATA ATA ATA ATA AT-A ATA ATA ATA -ATA -AT-A -ATA ATA ATA ATA
* *
12205663 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
12205699 AACAAAGCTC
Statistics
Matches: 64, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
2 7 0.11
3 46 0.72
4 9 0.14
5 2 0.03
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:12205637 original size:12 final size:12
Alignment explanation
Indices: 12205615--12205695 Score: 69
Period size: 12 Copynumber: 6.6 Consensus size: 12
12205605 GGGCATATAC
12205615 AATAT-AATAAT
1 AATATAAATAAT
12205626 AATATAAATAAT
1 AATATAAATAAT
12205638 AATATATACATGAGA-
1 AATATA-A-AT-A-AT
12205653 AATA-ATAATAAT
1 AATATA-AATAAT
12205665 AATATAAATAAT
1 AATATAAATAAT
* *
12205677 AGTAAAAATAAT
1 AATATAAATAAT
*
12205689 AAAATAA
1 AATATAA
12205696 TAAAACAAAG
Statistics
Matches: 58, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
11 6 0.10
12 37 0.64
13 4 0.07
14 5 0.09
15 5 0.09
16 1 0.02
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (12 bp):
AATATAAATAAT
Found at i:12205657 original size:21 final size:18
Alignment explanation
Indices: 12205618--12205698 Score: 76
Period size: 18 Copynumber: 4.4 Consensus size: 18
12205608 CATATACAAT
*
12205618 ATAATAATAATATAAATA
1 ATAATAATAATAGAAATA
12205636 ATAATATATACATGAGAAATA
1 ATAATA-ATA-AT-AGAAATA
*
12205657 ATAATAATAATATAAATA
1 ATAATAATAATAGAAATA
* *
12205675 ATAGTAAAAATA-ATAA-A
1 ATAATAATAATAGA-AATA
12205692 ATAATAA
1 ATAATAA
12205699 AACAAAGCTC
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
17 8 0.15
18 24 0.44
19 5 0.09
20 5 0.09
21 12 0.22
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (18 bp):
ATAATAATAATAGAAATA
Found at i:12206054 original size:21 final size:22
Alignment explanation
Indices: 12206030--12206127 Score: 78
Period size: 22 Copynumber: 4.5 Consensus size: 22
12206020 CTTCTTTCCA
12206030 AAAAAACAAAAAAA-CACCTCC
1 AAAAAACAAAAAAACCACCTCC
*
12206051 AAAAAACAAAAAAACCTCCTCC
1 AAAAAACAAAAAAACCACCTCC
**
12206073 --AAAACAAAGAACAATCCTTCTCC
1 AAAAAACAAA-AA-AA-CCACCTCC
* *
12206096 AAAAAACCAAAAACCCACAC-CC
1 AAAAAACAAAAAAACCAC-CTCC
*
12206118 TAAAAACAAA
1 AAAAAACAAA
12206128 GTCTTGAATG
Statistics
Matches: 62, Mismatches: 8, Indels: 13
0.75 0.10 0.16
Matches are distributed among these distances:
20 8 0.13
21 16 0.26
22 20 0.32
23 9 0.15
24 2 0.03
25 7 0.11
ACGTcount: A:0.60, C:0.31, G:0.01, T:0.08
Consensus pattern (22 bp):
AAAAAACAAAAAAACCACCTCC
Found at i:12206054 original size:22 final size:23
Alignment explanation
Indices: 12206026--12206076 Score: 79
Period size: 21 Copynumber: 2.3 Consensus size: 23
12206016 TAACCTTCTT
12206026 TCCAAAAAAACAAAAAAA-CACC
1 TCCAAAAAAACAAAAAAACCACC
*
12206048 TCC-AAAAAACAAAAAAACCTCC
1 TCCAAAAAAACAAAAAAACCACC
12206070 TCCAAAA
1 TCCAAAA
12206077 CAAAGAACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 14 0.54
22 9 0.35
23 3 0.12
ACGTcount: A:0.63, C:0.29, G:0.00, T:0.08
Consensus pattern (23 bp):
TCCAAAAAAACAAAAAAACCACC
Found at i:12206099 original size:23 final size:20
Alignment explanation
Indices: 12206032--12206099 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
12206022 TCTTTCCAAA
*
12206032 AAAACAAAAAAA-CACCTCC
1 AAAACAAAAAAACCTCCTCC
12206051 AAAAAACAAAAAAACCTCCTCC
1 --AAAACAAAAAAACCTCCTCC
*
12206073 AAAACAAAGAACAATCCTTCTCC
1 AAAACAAA-AA-AA-CCTCCTCC
12206096 AAAA
1 AAAA
12206100 AACCAAAAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
20 8 0.20
21 14 0.34
22 8 0.20
23 11 0.27
ACGTcount: A:0.59, C:0.29, G:0.01, T:0.10
Consensus pattern (20 bp):
AAAACAAAAAAACCTCCTCC
Found at i:12207725 original size:11 final size:12
Alignment explanation
Indices: 12207685--12207728 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
12207675 CCTTGTTTCC
12207685 CTTTCCCTTCCTT
1 CTTT-CCTTCCTT
*
12207698 CTTTCTTTCCTT
1 CTTTCCTTCCTT
12207710 CTTTCCTTCC-T
1 CTTTCCTTCCTT
12207721 CTTTCCTT
1 CTTTCCTT
12207729 TGTCTTCTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 9 0.31
12 16 0.55
13 4 0.14
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (12 bp):
CTTTCCTTCCTT
Found at i:12219779 original size:21 final size:21
Alignment explanation
Indices: 12219753--12219793 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
12219743 ATCTGCTCAA
* *
12219753 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
12219774 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
12219794 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:12246529 original size:183 final size:183
Alignment explanation
Indices: 12246221--12246587 Score: 734
Period size: 183 Copynumber: 2.0 Consensus size: 183
12246211 AAAACCAGAC
12246221 AGACGAGATTAATAAAGACAATAATCAAGCCTGTAAGAGAACGGCGTCGGTTCAGTTTGTACTTG
1 AGACGAGATTAATAAAGACAATAATCAAGCCTGTAAGAGAACGGCGTCGGTTCAGTTTGTACTTG
12246286 TGATTAGGCCGGTAATAAATTAATTAAGTCCACGTGTTAAGCAAACATAAAACAAAGTTTAATGA
66 TGATTAGGCCGGTAATAAATTAATTAAGTCCACGTGTTAAGCAAACATAAAACAAAGTTTAATGA
12246351 AAGAGAAAAAATTTAAAATTATACATTAATTTTGATTTAATGTAAAATTTTAT
131 AAGAGAAAAAATTTAAAATTATACATTAATTTTGATTTAATGTAAAATTTTAT
12246404 AGACGAGATTAATAAAGACAATAATCAAGCCTGTAAGAGAACGGCGTCGGTTCAGTTTGTACTTG
1 AGACGAGATTAATAAAGACAATAATCAAGCCTGTAAGAGAACGGCGTCGGTTCAGTTTGTACTTG
12246469 TGATTAGGCCGGTAATAAATTAATTAAGTCCACGTGTTAAGCAAACATAAAACAAAGTTTAATGA
66 TGATTAGGCCGGTAATAAATTAATTAAGTCCACGTGTTAAGCAAACATAAAACAAAGTTTAATGA
12246534 AAGAGAAAAAATTTAAAATTATACATTAATTTTGATTTAATGTAAAATTTTAT
131 AAGAGAAAAAATTTAAAATTATACATTAATTTTGATTTAATGTAAAATTTTAT
12246587 A
1 A
12246588 TATAAAATTT
Statistics
Matches: 184, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
183 184 1.00
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.31
Consensus pattern (183 bp):
AGACGAGATTAATAAAGACAATAATCAAGCCTGTAAGAGAACGGCGTCGGTTCAGTTTGTACTTG
TGATTAGGCCGGTAATAAATTAATTAAGTCCACGTGTTAAGCAAACATAAAACAAAGTTTAATGA
AAGAGAAAAAATTTAAAATTATACATTAATTTTGATTTAATGTAAAATTTTAT
Found at i:12246762 original size:31 final size:32
Alignment explanation
Indices: 12246727--12246796 Score: 83
Period size: 31 Copynumber: 2.2 Consensus size: 32
12246717 ATTTATTTAA
*
12246727 ATATATATGA-TTGAA-TCAAAATTAAAATTTT
1 ATATATATCATTTGAACT-AAAATTAAAATTTT
**
12246758 ATATATA-CATTTGAACTGGAATTAAAATTTT
1 ATATATATCATTTGAACTAAAATTAAAATTTT
12246789 ATATATAT
1 ATATATAT
12246797 AGTTACATCA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
30 1 0.03
31 31 0.94
32 1 0.03
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (32 bp):
ATATATATCATTTGAACTAAAATTAAAATTTT
Found at i:12261639 original size:32 final size:32
Alignment explanation
Indices: 12261594--12261662 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
12261584 TAAAAGAACA
12261594 ATTT-TACCCTTTATTAATTAATCATTATTCT
1 ATTTATACCCTTTATTAATTAATCATTATTCT
12261625 ATTTATACCCTTTATTAATTAATCATTATTCT
1 ATTTATACCCTTTATTAATTAATCATTATTCT
12261657 ATTTAT
1 ATTTAT
12261663 TTTTGTTATC
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 4 0.11
32 33 0.89
ACGTcount: A:0.30, C:0.14, G:0.00, T:0.55
Consensus pattern (32 bp):
ATTTATACCCTTTATTAATTAATCATTATTCT
Found at i:12268360 original size:8 final size:8
Alignment explanation
Indices: 12268341--12268370 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
12268331 GATATTAGAT
12268341 TTATTATTA
1 TTATT-TTA
12268350 TTATTTTA
1 TTATTTTA
12268358 TTATTTTA
1 TTATTTTA
12268366 TTATT
1 TTATT
12268371 CTCAAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 16 0.76
9 5 0.24
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (8 bp):
TTATTTTA
Found at i:12269478 original size:2 final size:2
Alignment explanation
Indices: 12269471--12269511 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
12269461 AAAGGTCTGT
12269471 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
12269512 TTAATGATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:12277516 original size:3 final size:3
Alignment explanation
Indices: 12277508--12277535 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
12277498 CAGTATTAAA
12277508 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
12277536 CCTGAGCTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:12287989 original size:20 final size:21
Alignment explanation
Indices: 12287946--12287994 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
12287936 AAGGTTGTAA
*
12287946 ATTTATATAAATATATAATAT
1 ATTTATATAAATATAAAATAT
*
12287967 ATTT-TATATAAT-TAAAATTT
1 ATTTATATA-AATATAAAATAT
12287987 ATTTATAT
1 ATTTATAT
12287995 GGACACGTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTATATAAATATAAAATAT
Found at i:12292499 original size:19 final size:19
Alignment explanation
Indices: 12292454--12292503 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
12292444 GTATAATTAG
12292454 AATTATTTTATAATTGTTT
1 AATTATTTTATAATTGTTT
*
12292473 -ATAAATTTTATAATAT-TTT
1 AAT-TATTTTATAAT-TGTTT
12292492 AATTATTTTATA
1 AATTATTTTATA
12292504 CTTTTATAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 2 0.08
19 21 0.81
20 3 0.12
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
AATTATTTTATAATTGTTT
Found at i:12295708 original size:115 final size:115
Alignment explanation
Indices: 12295506--12295736 Score: 426
Period size: 115 Copynumber: 2.0 Consensus size: 115
12295496 TACTTCATGC
*
12295506 AACCAATATCAAACATGTCAAACTCACTTTTCATTGAACTTTTGAACTTTCCAAACATCTGCTTA
1 AACCAAGATCAAACATGTCAAACTCACTTTTCATTGAACTTTTGAACTTTCCAAACATCTGCTTA
* *
12295571 TTGTTTCCTGTAAAAATAATATCAATGACGTATAAACTTACTATGAGAAT
66 TTGTTTCCTGTAAAAATAATATCAACGACATATAAACTTACTATGAGAAT
*
12295621 AACCAAGATCAAACATGTCAAACTCACTTTTCATTGAACTTTTGAACTTTCCAAATATCTGCTTA
1 AACCAAGATCAAACATGTCAAACTCACTTTTCATTGAACTTTTGAACTTTCCAAACATCTGCTTA
12295686 TTGTTTCCTGTAAAAATAATATCAACGACATATAAACTTACTATGAGAAT
66 TTGTTTCCTGTAAAAATAATATCAACGACATATAAACTTACTATGAGAAT
12295736 A
1 A
12295737 CCTCCATATT
Statistics
Matches: 112, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
115 112 1.00
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (115 bp):
AACCAAGATCAAACATGTCAAACTCACTTTTCATTGAACTTTTGAACTTTCCAAACATCTGCTTA
TTGTTTCCTGTAAAAATAATATCAACGACATATAAACTTACTATGAGAAT
Found at i:12302473 original size:35 final size:35
Alignment explanation
Indices: 12302296--12302473 Score: 250
Period size: 35 Copynumber: 5.1 Consensus size: 35
12302286 GGAAAAGTGC
12302296 GAAATGTAGGTATGGTATTATCCATACCGAGTTGT
1 GAAATGTAGGTATGGTATTATCCATACCGAGTTGT
* *
12302331 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
1 GAAATGTAGGTATGGTATTATCCATACCGAGTTGT
* * **
12302366 GAAATATAGGTATGGTATTATCCATACTGAGTTAA
1 GAAATGTAGGTATGGTATTATCCATACCGAGTTGT
*
12302401 GAAATGTAGGTATGGCATT-TCCCATACCGAGTTGT
1 GAAATGTAGGTATGGTATTAT-CCATACCGAGTTGT
* * *
12302436 GAAACGTAGGTATGGTATTTTCCATACCGAGTGGT
1 GAAATGTAGGTATGGTATTATCCATACCGAGTTGT
12302471 GAA
1 GAA
12302474 TCGTGGCACT
Statistics
Matches: 127, Mismatches: 14, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
34 1 0.01
35 125 0.98
36 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.31
Consensus pattern (35 bp):
GAAATGTAGGTATGGTATTATCCATACCGAGTTGT
Found at i:12303695 original size:27 final size:27
Alignment explanation
Indices: 12303671--12303725 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
12303661 GCTACCACAC
*
12303671 GACCCCGACGACGCTCGACCACCACGA
1 GACCCCGACGACGCTCAACCACCACGA
*
12303698 GACCCTGACGACGCTCAACCACCACGA
1 GACCCCGACGACGCTCAACCACCACGA
12303725 G
1 G
12303726 CACTACGAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.27, C:0.45, G:0.22, T:0.05
Consensus pattern (27 bp):
GACCCCGACGACGCTCAACCACCACGA
Found at i:12308238 original size:46 final size:44
Alignment explanation
Indices: 12308134--12308238 Score: 138
Period size: 44 Copynumber: 2.3 Consensus size: 44
12308124 TGTCTTTGAC
** * * *
12308134 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
12308178 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
12308224 ATGGACTTACATGGC
1 ATGGACTTACATGGC
12308239 GCATTTCTGT
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
44 33 0.62
46 20 0.38
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:12315610 original size:46 final size:44
Alignment explanation
Indices: 12315506--12315613 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
12315496 TGTCTTTGAC
** * * *
12315506 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
12315550 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
12315596 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
12315614 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:12323880 original size:31 final size:32
Alignment explanation
Indices: 12323842--12323906 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
12323832 TCGTGGGTTC
* *
12323842 TTCTTTCTTTTTC-TTTCT-CTTTTTTTTTTCT
1 TTCTTTCTATTTCGTTT-TGCTTTTTTCTTTCT
12323873 TTCTTTCTATTTCGTTTTGCTTTTTTCTTTCT
1 TTCTTTCTATTTCGTTTTGCTTTTTTCTTTCT
12323905 TT
1 TT
12323907 TTTTTTCTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.02, C:0.18, G:0.03, T:0.77
Consensus pattern (32 bp):
TTCTTTCTATTTCGTTTTGCTTTTTTCTTTCT
Found at i:12323917 original size:21 final size:22
Alignment explanation
Indices: 12323845--12323917 Score: 80
Period size: 21 Copynumber: 3.4 Consensus size: 22
12323835 TGGGTTCTTC
*
12323845 TTTC-TTTTTCTTTCTCTTTTT
1 TTTCTTTTTTCTTTCTATTTTT
*
12323866 TTT-TTCTTTCTTTCTATTTCGTT
1 TTTCTTTTTTCTTTCTATTT--TT
*
12323889 TTGCTTTTTTCTTTCT-TTTTT
1 TTTCTTTTTTCTTTCTATTTTT
12323910 TTTCTTTT
1 TTTCTTTT
12323918 ATTACTATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
21 25 0.58
23 7 0.16
24 11 0.26
ACGTcount: A:0.01, C:0.16, G:0.03, T:0.79
Consensus pattern (22 bp):
TTTCTTTTTTCTTTCTATTTTT
Found at i:12328589 original size:8 final size:8
Alignment explanation
Indices: 12328576--12328605 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
12328566 AATTATTTCA
*
12328576 AATTCATC
1 AATTCAAC
12328584 AATTCAAC
1 AATTCAAC
12328592 AATTCAAC
1 AATTCAAC
12328600 AATTCA
1 AATTCA
12328606 TATATTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (8 bp):
AATTCAAC
Found at i:12329626 original size:25 final size:25
Alignment explanation
Indices: 12329567--12329645 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 25
12329557 ATACATGTTT
* * * *
12329567 GCTCATACGAGCTATA-AACTATAA
1 GCTCATCCGAGCTAAATAACGAGAA
*
12329591 GCTCTTCCGAGCTAAATAACG-GAAA
1 GCTCATCCGAGCTAAATAACGAG-AA
* *
12329616 GCTCATGCGAGCTGAATAACGAGAA
1 GCTCATCCGAGCTAAATAACGAGAA
12329641 GCTCA
1 GCTCA
12329646 GAAGAGTTGA
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
24 13 0.30
25 30 0.68
26 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (25 bp):
GCTCATCCGAGCTAAATAACGAGAA
Found at i:12333693 original size:9 final size:9
Alignment explanation
Indices: 12333679--12333707 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
12333669 TCTATTAAAA
12333679 TAAATCTAT
1 TAAATCTAT
12333688 TAAATCTAT
1 TAAATCTAT
12333697 TAAATCTAT
1 TAAATCTAT
12333706 TA
1 TA
12333708 CCATCATGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (9 bp):
TAAATCTAT
Found at i:12339878 original size:52 final size:52
Alignment explanation
Indices: 12339807--12340056 Score: 368
Period size: 52 Copynumber: 4.9 Consensus size: 52
12339797 ATCAAGTGAT
* *
12339807 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGG
*
12339859 AAAGTGATAAGTAATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGG
* *
12339911 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGG
* * *
12339963 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC------
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGG
* *
12340009 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAA
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAA
12340057 AGTGATAAGT
Statistics
Matches: 185, Mismatches: 11, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
46 43 0.23
52 142 0.77
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.28
Consensus pattern (52 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGG
Found at i:12340057 original size:46 final size:44
Alignment explanation
Indices: 12339963--12340178 Score: 190
Period size: 37 Copynumber: 5.3 Consensus size: 44
12339953 TGACAAGTGA
*
12339963 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
1 AAAGTGATAAGTGATAGCTT--GCTACACTTATCTGATCAAGAGAC
12340009 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC
1 AAAGTGATAAGTGATAGC-TT-GCTACACTTATCTGATCAAGAGAC
*
12340055 AAAGTGATAA--G-T-G---GCTACACTTATCTGATCAAGAAAC
1 AAAGTGATAAGTGATAGCTTGCTACACTTATCTGATCAAGAGAC
* *
12340092 AAAGTGATAA--G-T-G---GCTACACTTATGTGATCAAGAAAC
1 AAAGTGATAAGTGATAGCTTGCTACACTTATCTGATCAAGAGAC
*
12340129 AAAGTGAT-AG-G-T-G---GCTACACTTATCTGATC-AGGGAC
1 AAAGTGATAAGTGATAGCTTGCTACACTTATCTGATCAAGAGAC
12340165 -AAGTGATAAGTGAT
1 AAAGTGATAAGTGAT
12340179 CATACGTAAG
Statistics
Matches: 158, Mismatches: 7, Indels: 18
0.86 0.04 0.10
Matches are distributed among these distances:
35 7 0.04
36 7 0.04
37 87 0.55
38 1 0.01
42 1 0.01
43 1 0.01
44 1 0.01
46 51 0.32
47 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.26
Consensus pattern (44 bp):
AAAGTGATAAGTGATAGCTTGCTACACTTATCTGATCAAGAGAC
Found at i:12340075 original size:37 final size:37
Alignment explanation
Indices: 12340031--12340176 Score: 233
Period size: 37 Copynumber: 4.0 Consensus size: 37
12340021 GATAGCTTTA
*
12340031 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
12340068 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
* *
12340105 GCTACACTTATGTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
12340142 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
12340177 ATCATACGTA
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 87 0.85
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:12349653 original size:37 final size:38
Alignment explanation
Indices: 12349611--12349691 Score: 94
Period size: 39 Copynumber: 2.2 Consensus size: 38
12349601 AATTAATACA
*
12349611 ATTTTTT-AACTAATAATTAT-AATTTAATTTATTTTT
1 ATTTTTTAAACTAATAATTATAAATCTAATTTATTTTT
* ** *
12349647 ATTTTTTAAATTTGTAATTATCAAATCTATTTTATTTTT
1 ATTTTTTAAACTAATAATTAT-AAATCTAATTTATTTTT
12349686 ATTTTT
1 ATTTTT
12349692 AAATGTGAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
36 7 0.19
37 10 0.27
39 20 0.54
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (38 bp):
ATTTTTTAAACTAATAATTATAAATCTAATTTATTTTT
Found at i:12350458 original size:18 final size:18
Alignment explanation
Indices: 12350435--12350484 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
12350425 AAGTAGATTT
12350435 TTATATCATGTATACTTC
1 TTATATCATGTATACTTC
*
12350453 TTATATCTATGAATA-TTC
1 TTATATC-ATGTATACTTC
12350471 TT-TATCATGTATAC
1 TTATATCATGTATAC
12350485 CATGGTTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
16 6 0.21
17 4 0.14
18 12 0.43
19 6 0.21
ACGTcount: A:0.30, C:0.14, G:0.06, T:0.50
Consensus pattern (18 bp):
TTATATCATGTATACTTC
Found at i:12353197 original size:58 final size:58
Alignment explanation
Indices: 12353133--12353307 Score: 208
Period size: 52 Copynumber: 3.1 Consensus size: 58
12353123 ATAGAAATTG
*
12353133 TGAAAATGGAGAAATTGAAATCATTTGGAAATTATTATGATTTTCTCCAAAATGAAAA
1 TGAAAATGGAGAAATTGAAATCATTTGGAAATGATTATGATTTTCTCCAAAATGAAAA
* * *
12353191 TGAAAATGGAGAAATGGAAA-CATTTGGAAATGATTATGGGTTTTTTCC------AAAA
1 TGAAAATGGAGAAATTGAAATCATTTGGAAATGATTAT-GATTTTCTCCAAAATGAAAA
*
12353243 TGAAAATGGAGAAA-TGGAATCATTTGGAAATGA--ATGTAGTTTTCTCCAAAATGAAAA
1 TGAAAATGGAGAAATTGAAATCATTTGGAAATGATTATG-A-TTTTCTCCAAAATGAAAA
12353300 TGAAAATG
1 TGAAAATG
12353308 AAAATGAAAA
Statistics
Matches: 99, Mismatches: 8, Indels: 21
0.77 0.06 0.16
Matches are distributed among these distances:
49 1 0.01
50 2 0.02
51 10 0.10
52 31 0.31
57 28 0.28
58 27 0.27
ACGTcount: A:0.43, C:0.06, G:0.20, T:0.30
Consensus pattern (58 bp):
TGAAAATGGAGAAATTGAAATCATTTGGAAATGATTATGATTTTCTCCAAAATGAAAA
Found at i:12353320 original size:13 final size:13
Alignment explanation
Indices: 12353290--12353327 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
12353280 AGTTTTCTCC
12353290 AAAATGAAAATG-
1 AAAATGAAAATGA
12353302 AAAATGAAAATGA
1 AAAATGAAAATGA
12353315 AAAATGAAAATGA
1 AAAATGAAAATGA
12353328 CCTGAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 12 0.48
13 13 0.52
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (13 bp):
AAAATGAAAATGA
Found at i:12353326 original size:52 final size:52
Alignment explanation
Indices: 12353157--12353327 Score: 145
Period size: 51 Copynumber: 3.2 Consensus size: 52
12353147 TTGAAATCAT
*
12353157 TTGGAAATTATTATGA-TTTTCTCCAAAATGAAAATGAAAATGGAGAAATGGAAACA
1 TTGGAAATGA-TATGAGTTTTCTCCAAAATGAAAATGAAAAT-GA-AAAT-GAAA-A
* * * * *
12353213 TTTGGAAATGATTATGGGTTTTTTCCAAAATGAAAATGGAGAAATG-GAAT--CAT
1 -TTGGAAATGA-TATGAGTTTTCTCCAAAATGAAAAT-GA-AAATGAAAATGAAAA
12353266 TTGGAAATGA-ATGTAGTTTTCTCCAAAATGAAAATGAAAATGAAAATGAAAA
1 TTGGAAATGATATG-AGTTTTCTCCAAAATGAAAATGAAAATGAAAATGAAAA
* *
12353318 ATGAAAATGA
1 TTGGAAATGA
12353328 CCTGAAAAAT
Statistics
Matches: 94, Mismatches: 13, Indels: 19
0.75 0.10 0.15
Matches are distributed among these distances:
49 5 0.05
50 8 0.09
51 19 0.20
52 19 0.20
54 1 0.01
57 17 0.18
58 18 0.19
59 3 0.03
60 4 0.04
ACGTcount: A:0.46, C:0.06, G:0.19, T:0.29
Consensus pattern (52 bp):
TTGGAAATGATATGAGTTTTCTCCAAAATGAAAATGAAAATGAAAATGAAAA
Found at i:12353340 original size:7 final size:6
Alignment explanation
Indices: 12353290--12353327 Score: 67
Period size: 6 Copynumber: 6.2 Consensus size: 6
12353280 AGTTTTCTCC
12353290 AAAATG AAAATG AAAATG AAAATG AAAAATG AAAATG A
1 AAAATG AAAATG AAAATG AAAATG -AAAATG AAAATG A
12353328 CCTGAAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:12355932 original size:21 final size:21
Alignment explanation
Indices: 12355864--12355935 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
12355854 AGGTCAAACG
* *
12355864 CCCGTATGACTGAGGTACACA
1 CCCGTGTGACTGAGGCACACA
** *
12355885 CCCGTGTGAAGGGAGGCACATGA
1 CCCGTGTG-ACTGAGGCACA-CA
12355908 -CCGTGTGACTGAGGCACACA
1 CCCGTGTGACTGAGGCACACA
12355928 CCCGTGTG
1 CCCGTGTG
12355936 GACCAAGGAC
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
20 1 0.03
21 23 0.57
22 15 0.38
23 1 0.03
ACGTcount: A:0.24, C:0.28, G:0.32, T:0.17
Consensus pattern (21 bp):
CCCGTGTGACTGAGGCACACA
Found at i:12360027 original size:48 final size:48
Alignment explanation
Indices: 12359927--12360197 Score: 192
Period size: 46 Copynumber: 5.8 Consensus size: 48
12359917 ATTTGTTTAT
* * * * * *
12359927 GAGCTAGTGTAAGAAATGTTTGAGACAT-GCATCGGCCAC-ATTA-TGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGGCATCAGCCTCGA-GACTGA
* *
12359973 GAGCTAGTGTAAGACCATGT-TCGGGACATGGCATCAGCGTTGAGAC-GA
1 GAGCTAGTGTAAGA-CATGTCT-GGGACATGGCATCAGCCTCGAGACTGA
* *
12360021 GAGCTAGGGTAAGACATGTCTGGGACAT-GCATCAGCCTCGAGACTTA
1 GAGCTAGTGTAAGACATGTCTGGGACATGGCATCAGCCTCGAGACTGA
* * * *
12360068 -AGCCAGTGTAAGACATGTCTGGGACAT-GCAT-TGGCTACAAGA-TGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGGCATCAGCCT-CGAGACTGA
* * * *
12360113 TAG-TCAGTGTAAGACCATGTCTGAGACATGGCATC-GACTTGAGA-T-A
1 GAGCT-AGTGTAAGA-CATGTCTGGGACATGGCATCAGCCTCGAGACTGA
* *
12360159 TGAGCCAGTGTAAGAACATGTCTGGTACATGGCATCAGC
1 -GAGCTAGTGTAAG-ACATGTCTGGGACATGGCATCAGC
12360198 ACCTTACCAA
Statistics
Matches: 181, Mismatches: 27, Indels: 32
0.75 0.11 0.13
Matches are distributed among these distances:
45 5 0.03
46 74 0.41
47 68 0.38
48 33 0.18
49 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.29, T:0.23
Consensus pattern (48 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGGCATCAGCCTCGAGACTGA
Found at i:12360079 original size:46 final size:47
Alignment explanation
Indices: 12359969--12360197 Score: 202
Period size: 46 Copynumber: 4.9 Consensus size: 47
12359959 CGGCCACATT
* * *
12359969 ATGAGAGCTAGTGTAAGACCATGT-TCGGGACATGGCATCAGCGTTGAG
1 ATGAGAGCCAGTGTAAGA-CATGTCT-GGGACATGGCATCAGCCTCGAG
* * *
12360017 ACGAGAGCTAGGGTAAGACATGTCTGGGACAT-GCATCAGCCTCGAG
1 ATGAGAGCCAGTGTAAGACATGTCTGGGACATGGCATCAGCCTCGAG
* * * *
12360063 ACTTA-AGCCAGTGTAAGACATGTCTGGGACAT-GCAT-TGGCTACAAG
1 A-TGAGAGCCAGTGTAAGACATGTCTGGGACATGGCATCAGCCT-CGAG
* * * * *
12360109 ATGATAGTCAGTGTAAGACCATGTCTGAGACATGGCATC-GACTTGAG
1 ATGAGAGCCAGTGTAAGA-CATGTCTGGGACATGGCATCAGCCTCGAG
*
12360156 AT-ATGAGCCAGTGTAAGAACATGTCTGGTACATGGCATCAGC
1 ATGA-GAGCCAGTGTAAG-ACATGTCTGGGACATGGCATCAGC
12360198 ACCTTACCAA
Statistics
Matches: 149, Mismatches: 22, Indels: 20
0.78 0.12 0.10
Matches are distributed among these distances:
45 5 0.03
46 59 0.40
47 59 0.40
48 26 0.17
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (47 bp):
ATGAGAGCCAGTGTAAGACATGTCTGGGACATGGCATCAGCCTCGAG
Found at i:12360168 original size:47 final size:47
Alignment explanation
Indices: 12359973--12360194 Score: 174
Period size: 47 Copynumber: 4.7 Consensus size: 47
12359963 CACATTATGA
* * *
12359973 GAGCTAGTGTAAGACCATGT-TCGGGACATGGCATC-AGCGTTGAGACGA-
1 GAGCCAGTGTAAGA-CATGTCT-GGGACATGGCATCGA-C-TCGAGACTAT
* * *
12360021 GAGCTAGGGTAAGACATGTCTGGGACAT-GCATCAGCCTCGAGACT-T
1 GAGCCAGTGTAAGACATGTCTGGGACATGGCATC-GACTCGAGACTAT
* * * *
12360067 AAGCCAGTGTAAGACATGTCTGGGACAT-GCATTGGCTACAAGA-TGAT
1 GAGCCAGTGTAAGACATGTCTGGGACATGGCATCGACT-CGAGACT-AT
* * *
12360114 -AGTCAGTGTAAGACCATGTCTGAGACATGGCATCGACTTGAGA-TAT
1 GAGCCAGTGTAAGA-CATGTCTGGGACATGGCATCGACTCGAGACTAT
*
12360160 GAGCCAGTGTAAGAACATGTCTGGTACATGGCATC
1 GAGCCAGTGTAAG-ACATGTCTGGGACATGGCATC
12360195 AGCACCTTAC
Statistics
Matches: 144, Mismatches: 19, Indels: 23
0.77 0.10 0.12
Matches are distributed among these distances:
45 4 0.03
46 58 0.40
47 60 0.42
48 22 0.15
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (47 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGGCATCGACTCGAGACTAT
Found at i:12360189 original size:140 final size:141
Alignment explanation
Indices: 12359932--12360197 Score: 328
Period size: 140 Copynumber: 1.9 Consensus size: 141
12359922 TTTATGAGCT
* ** *
12359932 AGTGTAAGAAATGTTTGAGACATGCATCGGCCACATTATGAGAGCTAGTGTAAGACCATGTTCGG
1 AGTGTAAGAAATGTCTGAGACATGCATCGGCCACAAGATGAGAGCTAGTGTAAGACCATGTTCGA
*
12359997 GACATGGCATCAGCGTTGAGACGAGAGCTAGGGTAAGACATGTCTGGGACAT-GCATCAGCCTCG
66 GACATGGCATCAGCGTTGAGACGAGAGCCAGGGTAAGACATGTCTGGGACATGGCATCAGCCTCG
12360061 AGACTTAAGCC
131 AGACTTAAGCC
* * * * *
12360072 AGTGTAAGACATGTCTGGGACATGCATTGGCTACAAGATGATAG-TCAGTGTAAGACCATG-TCT
1 AGTGTAAGAAATGTCTGAGACATGCATCGGCCACAAGATGAGAGCT-AGTGTAAGACCATGTTC-
* * *
12360135 GAGACATGGCATC-GAC-TTGAGA-TATGAGCCAGTGTAAGAACATGTCTGGTACATGGCATCAG
64 GAGACATGGCATCAG-CGTTGAGACGA-GAGCCAGGGTAAG-ACATGTCTGGGACATGGCATCAG
12360197 C
126 C
12360198 ACCTTACCAA
Statistics
Matches: 107, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
138 1 0.01
139 21 0.20
140 77 0.72
141 8 0.07
ACGTcount: A:0.30, C:0.18, G:0.29, T:0.23
Consensus pattern (141 bp):
AGTGTAAGAAATGTCTGAGACATGCATCGGCCACAAGATGAGAGCTAGTGTAAGACCATGTTCGA
GACATGGCATCAGCGTTGAGACGAGAGCCAGGGTAAGACATGTCTGGGACATGGCATCAGCCTCG
AGACTTAAGCC
Found at i:12366788 original size:47 final size:47
Alignment explanation
Indices: 12366600--12366826 Score: 202
Period size: 47 Copynumber: 4.8 Consensus size: 47
12366590 CGGCCACATT
* * * *
12366600 ATGAGAGCTAGTGTAAGACCATGT-TCGGGACATGGCATC-AGCGTTGAG
1 ATGATAGCCAGTGTAAGA-CATGTCT-GGGACATGGCATCGA-CCTCGAG
* * * *
12366648 ACGAGAGCTAGGGTAAGACATGTCTGGGACAT-GCATC-ACCCTCGAG
1 ATGATAGCCAGTGTAAGACATGTCTGGGACATGGCATCGA-CCTCGAG
* *
12366694 ACTTA-AGCCAGTGTAAGACATGTCTGGGACAT-GCATCG-GCTACGAG
1 A-TGATAGCCAGTGTAAGACATGTCTGGGACATGGCATCGACCT-CGAG
* *
12366740 ATGATAGTCAGTGTAAGATCATGTCTGGGACATGGCATCGA-CTTGAG
1 ATGATAGCCAGTGTAAGA-CATGTCTGGGACATGGCATCGACCTCGAG
12366787 AT-ATGAGCCAGTGTAAGACTATGTCTGGGACATGGCATCG
1 ATGAT-AGCCAGTGTAAGAC-ATGTCTGGGACATGGCATCG
12366827 GCACCTTACC
Statistics
Matches: 155, Mismatches: 14, Indels: 21
0.82 0.07 0.11
Matches are distributed among these distances:
45 4 0.03
46 62 0.40
47 64 0.41
48 25 0.16
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (47 bp):
ATGATAGCCAGTGTAAGACATGTCTGGGACATGGCATCGACCTCGAG
Found at i:12366815 original size:140 final size:141
Alignment explanation
Indices: 12366563--12366825 Score: 333
Period size: 140 Copynumber: 1.9 Consensus size: 141
12366553 TTTATGAGCT
* *
12366563 AGTGTAAGAAATGTTTGAGACATGCATCGGCCACATTATGAGAGCTAGTGTAAGACCATGTTCGG
1 AGTGTAAGAAATGTCTGAGACATGCATCGGCCACATGATGAGAGCTAGTGTAAGACCATGTTCGG
*
12366628 GACATGGCATCAGCGTTGAGACGAGAGCTAGGGTAAGACATGTCTGGGACAT-GCATCACCCTCG
66 GACATGGCATCAGCGTTGAGACGAGAGCCAGGGTAAGACATGTCTGGGACATGGCATCACCCTCG
12366692 AGACTTAAGCC
131 AGACTTAAGCC
* * * * *
12366703 AGTGTAAGACATGTCTGGGACATGCATCGGCTACGA-GATGATAG-TCAGTGTAAGATCATG-TC
1 AGTGTAAGAAATGTCTGAGACATGCATCGGCCAC-ATGATGAGAGCT-AGTGTAAGACCATGTTC
* *
12366765 TGGGACATGGCATC-GAC-TTGAGA-TATGAGCCAGTGTAAGACTATGTCTGGGACATGGCATC
64 -GGGACATGGCATCAG-CGTTGAGACGA-GAGCCAGGGTAAGAC-ATGTCTGGGACATGGCATC
12366826 GGCACCTTAC
Statistics
Matches: 106, Mismatches: 10, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
138 1 0.01
139 23 0.22
140 76 0.72
141 6 0.06
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.24
Consensus pattern (141 bp):
AGTGTAAGAAATGTCTGAGACATGCATCGGCCACATGATGAGAGCTAGTGTAAGACCATGTTCGG
GACATGGCATCAGCGTTGAGACGAGAGCCAGGGTAAGACATGTCTGGGACATGGCATCACCCTCG
AGACTTAAGCC
Found at i:12373275 original size:16 final size:16
Alignment explanation
Indices: 12373256--12373286 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12373246 CTTCTTCACT
12373256 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
12373272 TACTTACTTACTTAA
1 TACTCACTTACTTAA
12373287 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:12373292 original size:20 final size:20
Alignment explanation
Indices: 12373253--12373292 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
12373243 GAACTTCTTC
* *
12373253 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
12373273 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
12373293 TTATTAATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:12373561 original size:48 final size:48
Alignment explanation
Indices: 12373476--12373620 Score: 141
Period size: 53 Copynumber: 2.9 Consensus size: 48
12373466 ATACGGGTAC
* * *
12373476 CTTACCATTGCATGACTTGTCATGGTCATTACGTGGTATCCTTTGA-AA
1 CTTACCATTGCATGTCTTGACATGGTC-TTACATGGTATCCTTTGAGAA
*
12373524 CTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAA
1 CTTACCATTG-CATGTCTTGACATGGTCTTACATGGTATCCTT---TGA-GAA
* * * *
12373577 CTCACCAATGTCATGTCTTGGCATGGTCTTACATGGGA-CCTTTG
1 CTTACCATTG-CATGTCTTGACATGGTCTTACATGGTATCCTTTG
12373621 CCTTATAGTA
Statistics
Matches: 81, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
48 24 0.30
49 16 0.20
51 2 0.02
52 4 0.05
53 35 0.43
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (48 bp):
CTTACCATTGCATGTCTTGACATGGTCTTACATGGTATCCTTTGAGAA
Found at i:12373677 original size:55 final size:54
Alignment explanation
Indices: 12373524--12373727 Score: 223
Period size: 55 Copynumber: 3.8 Consensus size: 54
12373514 TCCTTTGAAA
* * *
12373524 CTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-GAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTATAGAC
* * * **
12373577 CTCACCAATGTCATGTCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAC
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCC-TTGCCTTATAG-AC
** * * *
12373632 CTTATGAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTAGAAAC
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTATAGAC
* * *
12373686 CTTACCAATTTCCATGCCTTGGCATGGTCTTACATGATATCC
1 CTTACCAA-TGCCATGTCTTGACATGGTCTTACATGATATCC
12373728 AAAAACCCTA
Statistics
Matches: 124, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
52 2 0.02
53 42 0.34
54 9 0.07
55 69 0.56
56 2 0.02
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (54 bp):
CTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTATAGAC
Found at i:12380852 original size:16 final size:16
Alignment explanation
Indices: 12380833--12380863 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12380823 CTTCTTCACT
12380833 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
12380849 TACTTACTTACTTAA
1 TACTCACTTACTTAA
12380864 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:12380869 original size:20 final size:20
Alignment explanation
Indices: 12380830--12380869 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
12380820 GAACTTCTTC
* *
12380830 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
12380850 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
12380870 TTATTAATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:12381310 original size:55 final size:54
Alignment explanation
Indices: 12381065--12381310 Score: 204
Period size: 55 Copynumber: 4.6 Consensus size: 54
12381055 CTTACCGTTG
* * * *
12381065 CCATGACTTGTCATGGTCTTACGTGGTATCC-T---TT-TGAAACTTACCATTT
1 CCATGCCTTGACATGGTCTTACATGGTATCCTTACCTTATGAAACTTACCAATT
* * *
12381114 CCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AACTCACCAATGT
1 CCATGCCTTGACATGGTCTTACATGGTATCCTTACCTTATGAAACTTACCAAT-T
* * * * * * *
12381168 -CATGCATTGGCATGGTCTTACATGGGA-CCTTTGCCTTATTGTAACTTATCAATG
1 CCATGCCTTGACATGGTCTTACATGGTATCC-TTACCTTA-TGAAACTTACCAATT
* * *
12381222 CTATGCCTTGACATGGTCTTACATGATTTCCTTACCTTA-GAAACCTTACCAATT
1 CCATGCCTTGACATGGTCTTACATGGTATCCTTACCTTATGAAA-CTTACCAATT
* * *
12381276 ACCATGCCTCGGCATGGTCTTACATGGCATCCTTA
1 -CCATGCCTTGACATGGTCTTACATGGTATCCTTA
12381311 AACCCTAAAG
Statistics
Matches: 156, Mismatches: 28, Indels: 20
0.76 0.14 0.10
Matches are distributed among these distances:
49 28 0.18
50 1 0.01
52 2 0.01
53 45 0.29
54 13 0.08
55 65 0.42
56 2 0.01
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (54 bp):
CCATGCCTTGACATGGTCTTACATGGTATCCTTACCTTATGAAACTTACCAATT
Found at i:12388924 original size:14 final size:14
Alignment explanation
Indices: 12388905--12388937 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
12388895 CATAACTTAT
12388905 ATTATATACATTTC
1 ATTATATACATTTC
12388919 ATTATATACATTTC
1 ATTATATACATTTC
12388933 ATTAT
1 ATTAT
12388938 TATAACATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTATATACATTTC
Found at i:12394670 original size:13 final size:13
Alignment explanation
Indices: 12394652--12394679 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
12394642 ACAAACGATA
12394652 AAAATTTTCACAC
1 AAAATTTTCACAC
12394665 AAAATTTTCACAC
1 AAAATTTTCACAC
12394678 AA
1 AA
12394680 GTCACATATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (13 bp):
AAAATTTTCACAC
Found at i:12396103 original size:4 final size:4
Alignment explanation
Indices: 12396091--12396137 Score: 51
Period size: 4 Copynumber: 11.8 Consensus size: 4
12396081 CTCTTTTACG
* * *
12396091 TTTC CTTC TTTC TTTC TTTC TTTC TTTT TTTGC TTTC TCT- TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT-C TTTC TTTC TTTC TTT
12396138 TCTACTTTTG
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
3 2 0.06
4 30 0.86
5 3 0.09
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.74
Consensus pattern (4 bp):
TTTC
Found at i:12398536 original size:21 final size:21
Alignment explanation
Indices: 12398511--12398552 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
12398501 GACATGAAAG
12398511 AAGAAAGACTAGTGAAATTTC
1 AAGAAAGACTAGTGAAATTTC
12398532 AAGAAAGACTAGTGAAATTTC
1 AAGAAAGACTAGTGAAATTTC
12398553 TATGTTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.10, G:0.19, T:0.24
Consensus pattern (21 bp):
AAGAAAGACTAGTGAAATTTC
Found at i:12401264 original size:23 final size:23
Alignment explanation
Indices: 12401238--12401361 Score: 117
Period size: 23 Copynumber: 5.4 Consensus size: 23
12401228 CTGCTCATTT
* *
12401238 GAGCTTACCGATTCAGCTCGTAA
1 GAGCTTACTGATTCAGCTCATAA
* * **
12401261 GAGCTTAATGTTTCAGCTCATTG
1 GAGCTTACTGATTCAGCTCATAA
*
12401284 GAGCTTACTGATTCAGCTCGTAA
1 GAGCTTACTGATTCAGCTCATAA
**
12401307 GAGCTTACTG-TTCAGCTCATTG
1 GAGCTTACTGATTCAGCTCATAA
* * *
12401329 GAACTTACCGTTTCAGCTCA-ATA
1 GAGCTTACTGATTCAGCTCATA-A
12401352 GAGCTTACTG
1 GAGCTTACTG
12401362 TCCATCAACT
Statistics
Matches: 79, Mismatches: 20, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
22 17 0.22
23 62 0.78
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (23 bp):
GAGCTTACTGATTCAGCTCATAA
Found at i:12401297 original size:46 final size:45
Alignment explanation
Indices: 12401230--12401347 Score: 182
Period size: 46 Copynumber: 2.6 Consensus size: 45
12401220 ACTCACCACT
*
12401230 GCTCATTTGAGCTTACCGATTCAGCTCGTAAGAGCTTAATGTTTCA
1 GCTCATTGGAGCTTACCGATTCAGCTCGTAAGAGCTTAATG-TTCA
* *
12401276 GCTCATTGGAGCTTACTGATTCAGCTCGTAAGAGCTTACTGTTCA
1 GCTCATTGGAGCTTACCGATTCAGCTCGTAAGAGCTTAATGTTCA
* *
12401321 GCTCATTGGAACTTACCGTTTCAGCTC
1 GCTCATTGGAGCTTACCGATTCAGCTC
12401348 AATAGAGCTT
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
45 28 0.42
46 38 0.58
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (45 bp):
GCTCATTGGAGCTTACCGATTCAGCTCGTAAGAGCTTAATGTTCA
Found at i:12401336 original size:45 final size:45
Alignment explanation
Indices: 12401230--12401362 Score: 187
Period size: 45 Copynumber: 2.9 Consensus size: 45
12401220 ACTCACCACT
* *
12401230 GCTCATTTGAGCTTACCGATTCAGCTCGTAAGAGCTTAATGTTTCA
1 GCTCATTGGAGCTTACCGATTCAGCTCGTAAGAGCTTACTG-TTCA
*
12401276 GCTCATTGGAGCTTACTGATTCAGCTCGTAAGAGCTTACTGTTCA
1 GCTCATTGGAGCTTACCGATTCAGCTCGTAAGAGCTTACTGTTCA
* * *
12401321 GCTCATTGGAACTTACCGTTTCAGCTC-AATAGAGCTTACTGT
1 GCTCATTGGAGCTTACCGATTCAGCTCGTA-AGAGCTTACTGT
12401363 CCATCAACTC
Statistics
Matches: 79, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
44 1 0.01
45 40 0.51
46 38 0.48
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (45 bp):
GCTCATTGGAGCTTACCGATTCAGCTCGTAAGAGCTTACTGTTCA
Found at i:12412429 original size:58 final size:56
Alignment explanation
Indices: 12412327--12412435 Score: 128
Period size: 58 Copynumber: 1.9 Consensus size: 56
12412317 CAATAATGGA
* * * * *
12412327 TTTTTTTTATTACCCTACTATGAAAAGTTAGAAAATAATTACTCAATTATTAGTAT
1 TTTTTTTTATTAACCTACTATAAAAAGTTACAAAATAATCACTCAACTATTAGTAT
* **
12412383 TTTTTTTTTTGTAACCTAACTATAAAAAGTTACAAAATGGTCACTCAACTATT
1 TTTTTTTTAT-TAACCT-ACTATAAAAAGTTACAAAATAATCACTCAACTATT
12412436 CAATTGTCTT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
56 9 0.21
57 5 0.12
58 29 0.67
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (56 bp):
TTTTTTTTATTAACCTACTATAAAAAGTTACAAAATAATCACTCAACTATTAGTAT
Found at i:12415374 original size:150 final size:149
Alignment explanation
Indices: 12415056--12415644 Score: 844
Period size: 150 Copynumber: 3.9 Consensus size: 149
12415046 TAGGCGATCT
* * * *
12415056 GGAGGCACATTCCACTGAGGATCTAATACTACCCATCACATTGGATGGAGAAGAGTGCGGAATTC
1 GGAGGCACCTTCCACTGAGGATCTACTACTACCCATCACATTGGACGGAGAAGAGTGAGGAATTC
** * *
12415121 CACTGTATGTCTCACTTCTAGGAGTCC-T--TCCACTCTTCTTATTAGTTTTCCTTCCAAGATTT
66 CACCATGTGTCTCACTTCTAGGAGTCCTTCCTCCACTCTT-TTATCAGTTTTCCTTCCAAGATTT
**
12415183 TCTTCAGAGTGCAATTTGGA
130 TCTTCACTGTGCAATTTGGA
* * * *
12415203 AGAGGCACCTTCCACTGAGGATCTACTACTACCCATCACGTTGTACGGAGAAGAGTGGGGAATTC
1 GGAGGCACCTTCCACTGAGGATCTACTACTACCCATCACATTGGACGGAGAAGAGTGAGGAATTC
*
12415268 CACCGTGTGTCTCACTTCTAGGAGTCCTTCCTCCACTCATTTTATCAGTTTTCCTTCCAAGATTT
66 CACCATGTGTCTCACTTCTAGGAGTCCTTCCTCCACTC-TTTTATCAGTTTTCCTTCCAAGATTT
*
12415333 TCTTCACTGTGCAATTTGGG
130 TCTTCACTGTGCAATTTGGA
*
12415353 GGAGGCACCTTTCACTGAGGATCTACTACTACCCATCACATTGGACGGAGAAGAGTGAGGAATTC
1 GGAGGCACCTTCCACTGAGGATCTACTACTACCCATCACATTGGACGGAGAAGAGTGAGGAATTC
* ** * *
12415418 CACTATGCATCTCACTTCTAGGAGTCCTTCCTCCACCCTTTATATCAGTTTTCCTTACAAGATTT
66 CACCATGTGTCTCACTTCTAGGAGTCCTTCCTCCACTCTTT-TATCAGTTTTCCTTCCAAGATTT
12415483 TCTTCACTGTGCAATTTGGA
130 TCTTCACTGTGCAATTTGGA
* * *
12415503 GGAGGCACCTTCCACCGAGGATCTACTACTACCCATCACATTGAATGGAGAAGAGTGAGGAATTC
1 GGAGGCACCTTCCACTGAGGATCTACTACTACCCATCACATTGGACGGAGAAGAGTGAGGAATTC
* * **
12415568 CATCATGTGTCTCGCTTCTAGGAGT-CTGTCCTCCACTCTTTTTATCAGTTTTCCTTCCATCATT
66 CACCATGTGTCTCACTTCTAGGAGTCCT-TCCTCCACTC-TTTTATCAGTTTTCCTTCCAAGATT
12415632 TTCTTCACTGTGC
129 TTCTTCACTGTGC
12415645 TTTCTCTTCT
Statistics
Matches: 397, Mismatches: 38, Indels: 11
0.89 0.09 0.02
Matches are distributed among these distances:
147 83 0.21
148 1 0.00
149 5 0.01
150 303 0.76
151 5 0.01
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (149 bp):
GGAGGCACCTTCCACTGAGGATCTACTACTACCCATCACATTGGACGGAGAAGAGTGAGGAATTC
CACCATGTGTCTCACTTCTAGGAGTCCTTCCTCCACTCTTTTATCAGTTTTCCTTCCAAGATTTT
CTTCACTGTGCAATTTGGA
Found at i:12417912 original size:36 final size:36
Alignment explanation
Indices: 12417872--12417945 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
12417862 AGAAATAGGA
*
12417872 CAAAGCATTGTTTTTGCAATGACACAAAAATAAAAT
1 CAAAGCATTGTTTTTGCAATGAAACAAAAATAAAAT
12417908 CAAAGCATTGTTTTTGCAATGAAACAAAAATAAAAT
1 CAAAGCATTGTTTTTGCAATGAAACAAAAATAAAAT
12417944 CA
1 CA
12417946 TACTCCCTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.27
Consensus pattern (36 bp):
CAAAGCATTGTTTTTGCAATGAAACAAAAATAAAAT
Found at i:12420260 original size:3 final size:3
Alignment explanation
Indices: 12420246--12420279 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
12420236 ATCATACAAG
* *
12420246 TCA TCT TCA TCA TCA TCA TTA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
12420280 TATTGGAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.41
Consensus pattern (3 bp):
TCA
Found at i:12420280 original size:15 final size:15
Alignment explanation
Indices: 12420252--12420282 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
12420242 CAAGTCATCT
12420252 TCATCATCATCATTA
1 TCATCATCATCATTA
12420267 TCATCATCATCATTA
1 TCATCATCATCATTA
12420282 T
1 T
12420283 TGGAATCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.26, G:0.00, T:0.42
Consensus pattern (15 bp):
TCATCATCATCATTA
Done.