Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 59 of 150
Found at i:17595539 original size:178 final size:178
Alignment explanation
Indices: 17595061--17595817 Score: 824
Period size: 178 Copynumber: 4.2 Consensus size: 178
17595051 CTTGTTATGG
* * ** * *
17595061 TCTGCTCTACTGCAACTTCAGAGAGATAAGACCCGCTATCTTCAGTCTGCTCCACTGCAACTTCA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATCTTCAGTCTGCCCCACTGCAACTTCA
* * * * * * * * ** * * * **
17595126 GAGAGATAAGA-GTGGTGTCTTCAATCCGCTCCACTACAACTTCAAGGAGAT-AGAATTATTTGC
66 GGGGGATAAGACTTGCTTTCTTTAGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTT-GTAAC
* * * * ** *
17595189 TGTAATCTGCTCCACTGTAACTTCAGGGAGATAAGA-T-TT-GCCATGA
130 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAA
* * * ** * * ** *
17595235 TCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGATTTATAGCTTTAATCTGTTCCACTACA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGAT-T-CG--CCAT--CTTCAGTCTGCCCCACTGCA
* ** * * **
17595300 ACTTCAGAGAAATAAGA-TTCGCTATCTTTAATCTGCTCCACTACAACTTCAGGGAGATAAGACT
60 ACTTCAGGGGGATAAGACTT-GCTTTCTTTAGTCTGCTCCACTGTAACTTCAGGGAGATAAGACT
*
17595364 TGTCACTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAA
124 TGTAACTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAA
* * * * * *
17595419 TTTACTCCACTGCAACTTCAAGGAGATAAGATTCACCATCTTCATTCTGCCCCACTGCAACTTTA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATCTTCAGTCTGCCCCACTGCAACTTCA
* *
17595484 GGGGGATAAGACTTGTTTTCTTTAGTCTGCTCCACTGTAACTTCAAGGAGATAAGACTTGTAACT
66 GGGGGATAAGACTTGCTTTCTTTAGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTTGTAACT
* * * *
17595549 TTAACCCGCTCCACTGTAACTTCAGGGAGATATGATTACTGGCTTTAA
131 TTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAA
*
17595597 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATCTTCAGTCTGTCCCACTGCAACTTCA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATCTTCAGTCTGCCCCACTGCAACTTCA
*
17595662 GGGGGATAAGACTTGCTTTCTTCAGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTTGTAACT
66 GGGGGATAAGACTTGCTTTCTTTAGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTTGTAACT
* * *
17595727 TTAATTCGCTCCACTACAACTTCAGGGAGATAGTATTATTGGCTTTAA
131 TTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAA
*
17595775 TCTGCTCCACTACAACTTCAGGGAGATAAGATTCGCCATCTTC
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATCTTC
17595818 TTCAATCCAT
Statistics
Matches: 498, Mismatches: 73, Indels: 20
0.84 0.12 0.03
Matches are distributed among these distances:
174 31 0.06
176 1 0.00
178 322 0.65
179 2 0.00
180 35 0.07
181 67 0.13
182 6 0.01
183 3 0.01
184 31 0.06
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (178 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATCTTCAGTCTGCCCCACTGCAACTTCA
GGGGGATAAGACTTGCTTTCTTTAGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTTGTAACT
TTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAA
Found at i:17595784 original size:222 final size:221
Alignment explanation
Indices: 17595015--17595808 Score: 588
Period size: 225 Copynumber: 3.6 Consensus size: 221
17595005 ATTTGCTATA
* * * * * * *
17595015 TTCAGTCTGCCCTACTGCAACTTTAGGGGGATAGGACTTGTT-A---TGGTCTGCTCTACTGCAA
1 TTCAGTCTGCCCCACTGCAACTTCAGGGAGATAAGACTTGTTAACTTTAGTCTGCTCCACTACAA
** * * * * * *
17595076 CTTC-AGAGAGATAAGACCCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGAGAGATAAGAGTG
66 CTTCAAG-GAGATAAGACTTG-TAACTTTAATCTGCTCCACTACAACTTCAGGGAGATAAGA-TT
* ** * * * * * * *
17595140 GTGTCTTCAATCCGCTCCACTACAACTTCAAGGAGAT-AGAATTATTTG-CTGTAATCTGCTCCA
128 CTCACTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAG-ATTA-TCGCCTTTAATTTACTCCA
* * **
17595203 CTGTAACTTCAGGGAGATAAGATTTGCCA--
191 CTGCAACTTCAAGGAGATAAGATTCACCATC
* * * * * *
17595232 -TGA-TCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGATTTATAGCTTTAATCTGTTCCA
1 TTCAGTCTGCCCCACTGCAACTTCAGGGAGATAAGA-CT-TG--TTA-A-CTTTAGTCTGCTCCA
* *
17595295 CTACAACTTC-AGAGAAATAAGA-TTCGCTATCTTTAATCTGCTCCACTACAACTTCAGGGAGAT
60 CTACAACTTCAAG-GAGATAAGACTT-G-TAACTTTAATCTGCTCCACTACAACTTCAGGGAGAT
* * * *
17595358 AAGACTTGTCACTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATTTA
122 AAGA-TTCTCACTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGATTATCGCCTTTAATTTA
17595423 CTCCACTGCAACTTCAAGGAGATAAGATTCACCATC
186 CTCCACTGCAACTTCAAGGAGATAAGATTCACCATC
* * * ** **
17595459 TTCATTCTGCCCCACTGCAACTTTAGGGGGATAAGACTTGTTTTCTTTAGTCTGCTCCACTGTAA
1 TTCAGTCTGCCCCACTGCAACTTCAGGGAGATAAGACTTGTTAACTTTAGTCTGCTCCACTACAA
* * ** *
17595524 CTTCAAGGAGATAAGACTTGTAACTTTAACCCGCTCCACTGTAACTTCAGGGAGATATGATTACT
66 CTTCAAGGAGATAAGACTTGTAACTTTAATCTGCTCCACTACAACTTCAGGGAGATAAGATT-CT
** * *
17595589 GGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-T-TCGCCATCTTCAGTCTGT-C-CC
130 CACTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGATTATCGCC-T-TT-AAT-T-TACTCC
* * * **
17595650 ACTGCAACTTCAGGGGGATAAGACTT-GCTTTC
190 ACTGCAACTTCAAGGAGATAAGA-TTCACCATC
* * *
17595682 TTCAGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTTG-TAACTTTAAT-TCGCTCCACTACA
1 TTCAGTCTGCCCCACTGCAACTTCAGGGAGATAAGACTTGTTAACTTTAGTCT-GCTCCACTACA
* * **
17595745 ACTTCAGGGAGAT-AGTA-TTATTGGCTTTAATCTGCTCCACTACAACTTCAGGGAGATAAGATT
65 ACTTCAAGGAGATAAG-ACTT-GTAACTTTAATCTGCTCCACTACAACTTCAGGGAGATAAGATT
17595808 C
128 C
17595809 GCCATCTTCT
Statistics
Matches: 464, Mismatches: 84, Indels: 54
0.77 0.14 0.09
Matches are distributed among these distances:
215 26 0.06
216 4 0.01
217 2 0.00
219 2 0.00
220 3 0.01
221 11 0.02
222 136 0.29
223 93 0.20
224 11 0.02
225 143 0.31
226 1 0.00
227 2 0.00
228 4 0.01
229 26 0.06
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (221 bp):
TTCAGTCTGCCCCACTGCAACTTCAGGGAGATAAGACTTGTTAACTTTAGTCTGCTCCACTACAA
CTTCAAGGAGATAAGACTTGTAACTTTAATCTGCTCCACTACAACTTCAGGGAGATAAGATTCTC
ACTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGATTATCGCCTTTAATTTACTCCACTGCA
ACTTCAAGGAGATAAGATTCACCATC
Found at i:17596161 original size:24 final size:24
Alignment explanation
Indices: 17596134--17596194 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
17596124 CAGATTACCC
17596134 CCACTGTAATTTTCAAGATTCAAT
1 CCACTGTAATTTTCAAGATTCAAT
* *
17596158 CCACTGTAATCTTCAAGGTTCAAT
1 CCACTGTAATTTTCAAGATTCAAT
*
17596182 CCACTGTACTTTT
1 CCACTGTAATTTT
17596195 GAGACATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.28, C:0.25, G:0.10, T:0.38
Consensus pattern (24 bp):
CCACTGTAATTTTCAAGATTCAAT
Found at i:17598018 original size:6 final size:6
Alignment explanation
Indices: 17598007--17598051 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
17597997 TGGCCTCTCA
* *
17598007 TTTTTC TTTTTC -TTTTC TTTTTC CTTCTC -TTTTC TTTTT- TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
17598052 ATCATTTTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
5 14 0.42
6 19 0.58
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:17598022 original size:11 final size:11
Alignment explanation
Indices: 17598008--17598051 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
17597998 GGCCTCTCAT
17598008 TTTTCTTTTTC
1 TTTTCTTTTTC
17598019 TTTTCTTTTTC
1 TTTTCTTTTTC
*
17598030 -CTTCTCTTTTC
1 TTTTCT-TTTTC
*
17598041 TTTTTTTTTTC
1 TTTTCTTTTTC
17598052 ATCATTTTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
10 4 0.14
11 21 0.75
12 3 0.11
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:17598029 original size:17 final size:17
Alignment explanation
Indices: 17598007--17598051 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
17597997 TGGCCTCTCA
17598007 TTTTTCTTTTTCTTTTC
1 TTTTTCTTTTTCTTTTC
* *
17598024 TTTTTCCTTCTCTTTTC
1 TTTTTCTTTTTCTTTTC
17598041 TTTTT-TTTTTC
1 TTTTTCTTTTTC
17598052 ATCATTTTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 4 0.17
17 20 0.83
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTTTCTTTTTCTTTTC
Found at i:17598079 original size:29 final size:29
Alignment explanation
Indices: 17598045--17598103 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
17598035 CTTTTCTTTT
17598045 TTTTTTCATCATTTTCATTTTTTTGAAATA
1 TTTTTTCAT-ATTTTCATTTTTTTGAAATA
* * *
17598075 TTTTTTGATTTTTTGATTTTTTTGAAATA
1 TTTTTTCATATTTTCATTTTTTTGAAATA
17598104 CTCTTTTGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.22, C:0.05, G:0.07, T:0.66
Consensus pattern (29 bp):
TTTTTTCATATTTTCATTTTTTTGAAATA
Found at i:17602371 original size:13 final size:13
Alignment explanation
Indices: 17602355--17602379 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17602345 ATGAAATTAA
17602355 ATAATAATATAAG
1 ATAATAATATAAG
17602368 ATAATAATATAA
1 ATAATAATATAA
17602380 AAAAAACTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (13 bp):
ATAATAATATAAG
Found at i:17603591 original size:47 final size:46
Alignment explanation
Indices: 17603522--17603615 Score: 152
Period size: 47 Copynumber: 2.0 Consensus size: 46
17603512 CACCACTAGA
* *
17603522 GTTAGAATCAGATGTAAAGATCAAAGGGTTTTTGTTAGGTTGTAACG
1 GTTAGAATCAGATGCAAAGATCAAAGGG-TTTTGTTAGGTTATAACG
*
17603569 GTTAGAATCGGATGCAAAGATCAAAGGGTTTTGTTAGGTTATAACG
1 GTTAGAATCAGATGCAAAGATCAAAGGGTTTTGTTAGGTTATAACG
17603615 G
1 G
17603616 GGCTTGGGTC
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
46 18 0.41
47 26 0.59
ACGTcount: A:0.32, C:0.07, G:0.29, T:0.32
Consensus pattern (46 bp):
GTTAGAATCAGATGCAAAGATCAAAGGGTTTTGTTAGGTTATAACG
Found at i:17614183 original size:16 final size:16
Alignment explanation
Indices: 17614162--17614192 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17614152 CCACTACAGA
17614162 AAATATTACAATTTCT
1 AAATATTACAATTTCT
*
17614178 AAATATTGCAATTTC
1 AAATATTACAATTTC
17614193 ATTATTCGAT
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:0.42, C:0.13, G:0.03, T:0.42
Consensus pattern (16 bp):
AAATATTACAATTTCT
Found at i:17614268 original size:114 final size:114
Alignment explanation
Indices: 17614068--17614312 Score: 411
Period size: 114 Copynumber: 2.1 Consensus size: 114
17614058 TACAGAAAAA
*
17614068 ATTGCAATTCCATTATTTAATATTTCAGTCTCAAACAATGTGTACATCTTTGATTTGATAAAGTA
1 ATTGCAATTCCATTATTCAATATTTCAGTCTCAAACAATGTGTACATCTTTGATTTGATAAAGTA
17614133 GATATTATTTAACATCCATCCA-CTACAGAAAATATTACAATTTCTAAAT
66 GATATTATTTAACATCCATCCATC-ACAGAAAATATTACAATTTCTAAAT
* * * *
17614182 ATTGCAATTTCATTATTCGATATTTTAGTCTCAATCAATGTGTACATCTTTGATTTGATAAAGTA
1 ATTGCAATTCCATTATTCAATATTTCAGTCTCAAACAATGTGTACATCTTTGATTTGATAAAGTA
* *
17614247 GATATTATTTGACATCCATCCATCATAGAAAATATTACAATTTCTAAAT
66 GATATTATTTAACATCCATCCATCACAGAAAATATTACAATTTCTAAAT
17614296 ATTGCAATTCCATTATT
1 ATTGCAATTCCATTATT
17614313 AAAACTTAAG
Statistics
Matches: 122, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
114 121 0.99
115 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (114 bp):
ATTGCAATTCCATTATTCAATATTTCAGTCTCAAACAATGTGTACATCTTTGATTTGATAAAGTA
GATATTATTTAACATCCATCCATCACAGAAAATATTACAATTTCTAAAT
Found at i:17622470 original size:16 final size:16
Alignment explanation
Indices: 17622451--17622482 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
17622441 GCAAGGACAT
*
17622451 ATCGATGCATATTTTA
1 ATCGATGCACATTTTA
17622467 ATCGATGCACATTTTA
1 ATCGATGCACATTTTA
17622483 TAAAGTTCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (16 bp):
ATCGATGCACATTTTA
Found at i:17629216 original size:16 final size:16
Alignment explanation
Indices: 17629179--17629209 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17629169 TGAGAGCTAA
*
17629179 GAGAGTTGAGAGAATT
1 GAGAGATGAGAGAATT
17629195 GAGAGATGAGAGAAT
1 GAGAGATGAGAGAAT
17629210 GATGAGAAGT
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:0.42, C:0.00, G:0.39, T:0.19
Consensus pattern (16 bp):
GAGAGATGAGAGAATT
Found at i:17639027 original size:14 final size:14
Alignment explanation
Indices: 17639008--17639037 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
17638998 ACACAGTCGT
17639008 TATCAAGTAATAAG
1 TATCAAGTAATAAG
17639022 TATCAAGTAATAAG
1 TATCAAGTAATAAG
17639036 TA
1 TA
17639038 AGTATCGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.07, G:0.13, T:0.30
Consensus pattern (14 bp):
TATCAAGTAATAAG
Found at i:17647377 original size:16 final size:16
Alignment explanation
Indices: 17647356--17647388 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
17647346 GTGGCAGAAG
17647356 GAAAGCGCACCACGTA
1 GAAAGCGCACCACGTA
17647372 GAAAGCGCACCACGTA
1 GAAAGCGCACCACGTA
17647388 G
1 G
17647389 GACGAGCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.30, G:0.27, T:0.06
Consensus pattern (16 bp):
GAAAGCGCACCACGTA
Found at i:17651577 original size:20 final size:20
Alignment explanation
Indices: 17651552--17651592 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
17651542 AATGACATAC
17651552 TTTTATGTGTTAATTGTATA
1 TTTTATGTGTTAATTGTATA
17651572 TTTTATGTGTTAATTGTATA
1 TTTTATGTGTTAATTGTATA
17651592 T
1 T
17651593 ATATTTTGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.15, T:0.61
Consensus pattern (20 bp):
TTTTATGTGTTAATTGTATA
Found at i:17652042 original size:20 final size:20
Alignment explanation
Indices: 17652017--17652083 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
17652007 TGTTCCTTTT
* *
17652017 ATTTATTCAGTAAAATTCTA
1 ATTTATTCAATAAAATTCCA
* *
17652037 ATTTATTCAATGAATTTCCA
1 ATTTATTCAATAAAATTCCA
*
17652057 ATTTATTCAATAAATTTCCA
1 ATTTATTCAATAAAATTCCA
*
17652077 TTTTATT
1 ATTTATT
17652084 AAACTTATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.36, C:0.12, G:0.03, T:0.49
Consensus pattern (20 bp):
ATTTATTCAATAAAATTCCA
Found at i:17658022 original size:17 final size:18
Alignment explanation
Indices: 17657990--17658025 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
17657980 TAAGTAAACA
*
17657990 AAAATATTCATTAAAAAT
1 AAAATATTCATCAAAAAT
17658008 AAAATATTCA-CAAAAAT
1 AAAATATTCATCAAAAAT
17658025 A
1 A
17658026 GTCAAACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAATATTCATCAAAAAT
Found at i:17668182 original size:3 final size:3
Alignment explanation
Indices: 17668176--17668202 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
17668166 AATAATAATA
17668176 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
17668203 CATTCACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:17673402 original size:43 final size:43
Alignment explanation
Indices: 17673333--17673437 Score: 113
Period size: 43 Copynumber: 2.4 Consensus size: 43
17673323 AATACCAACA
** * ** *
17673333 TCCCACACGTGGTCTTACATGTAATTACGTAGCGATGCCGCTG
1 TCCCACACAAGGTCTTACATGCAATTACAAAGCGATGCCACTG
* **
17673376 TCCCACACAAGGTCTTAC-TCGCAATTATAAATTGATGCCACTG
1 TCCCACACAAGGTCTTACAT-GCAATTACAAAGCGATGCCACTG
17673419 TCCCACACAAGGTCTTACA
1 TCCCACACAAGGTCTTACA
17673438 CTGTAACATT
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
42 1 0.02
43 50 0.98
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.27
Consensus pattern (43 bp):
TCCCACACAAGGTCTTACATGCAATTACAAAGCGATGCCACTG
Found at i:17673942 original size:29 final size:29
Alignment explanation
Indices: 17673909--17673976 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
17673899 AGCTTATATA
*
17673909 AGTCCTCAC-ATTTCATT-TTTTCACATTTT
1 AGTCC-CACAATTT-ATTATTTTCACAATTT
*
17673938 AGTCCCCCAATTTATTATTTTCACAATTT
1 AGTCCCACAATTTATTATTTTCACAATTT
17673967 AG-CCCA-AATT
1 AGTCCCACAATT
17673977 ACTCAAATTC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 4 0.12
28 8 0.24
29 22 0.65
ACGTcount: A:0.26, C:0.25, G:0.04, T:0.44
Consensus pattern (29 bp):
AGTCCCACAATTTATTATTTTCACAATTT
Found at i:17679840 original size:67 final size:67
Alignment explanation
Indices: 17679740--17680025 Score: 267
Period size: 67 Copynumber: 4.3 Consensus size: 67
17679730 CCATCGTAGC
* * * *
17679740 CGAGCTATGGTCTTACACAACAT--ACCATGTGTTTATTGTCCTGGC-GAAATTTTTATGCTGCC
1 CGAGCTATGGTCTTACACAACATACACCA--TGTTTACTGTCCTGGCAG-ACTCTCTATGCTGCC
17679802 ATAGT
63 ATAGT
*
17679807 CGAGCTATGGTCTTACACAACATACACCATGTTTACTGTCCCT-GCAGACTCTCTATGTTGCCAT
1 CGAGCTATGGTCTTACACAACATACACCATGTTTACTGT-CCTGGCAGACTCTCTATGCTGCCAT
17679871 AGT
65 AGT
* * * * * * * * *
17679874 CAAGCTTTGGTCTTACGCAACATACCCCGTGTTTACTCTCCCGACAGACTCTCTGTGCTGCCATA
1 CGAGCTATGGTCTTACACAACATACACCATGTTTACTGTCCTGGCAGACTCTCTATGCTGCCATA
*
17679939 GC
66 GT
* * * * * * ** *
17679941 CGAACTATGATCATACATAACATAC-CTCATGTTTACTATCTTGGTGGACTCTTTATGCTGCCAT
1 CGAGCTATGGTCTTACACAACATACAC-CATGTTTACTGTCCTGGCAGACTCTCTATGCTGCCAT
17680005 AGT
65 AGT
*
17680008 CGAGTTATGGTCTTACAC
1 CGAGCTATGGTCTTACAC
17680026 CTTATACCTC
Statistics
Matches: 175, Mismatches: 38, Indels: 12
0.78 0.17 0.05
Matches are distributed among these distances:
66 3 0.02
67 164 0.94
68 4 0.02
69 4 0.02
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.33
Consensus pattern (67 bp):
CGAGCTATGGTCTTACACAACATACACCATGTTTACTGTCCTGGCAGACTCTCTATGCTGCCATA
GT
Found at i:17682635 original size:37 final size:37
Alignment explanation
Indices: 17682585--17682656 Score: 144
Period size: 37 Copynumber: 1.9 Consensus size: 37
17682575 TTGGAACGCC
17682585 CAAAGGAAAATACACCTAGTGCTTATCGACATATAGT
1 CAAAGGAAAATACACCTAGTGCTTATCGACATATAGT
17682622 CAAAGGAAAATACACCTAGTGCTTATCGACATATA
1 CAAAGGAAAATACACCTAGTGCTTATCGACATATA
17682657 ATACTTAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (37 bp):
CAAAGGAAAATACACCTAGTGCTTATCGACATATAGT
Found at i:17689354 original size:32 final size:33
Alignment explanation
Indices: 17689318--17689426 Score: 79
Period size: 32 Copynumber: 3.5 Consensus size: 33
17689308 TAATAACTCA
17689318 CATATATATA-TGTATATATATACAACCCCACT
1 CATATATATACTGTATATATATACAACCCCACT
* * * * *
17689350 CATATGTA-AATGCATAT-TA-CCAACCCCTC-
1 CATATATATACTGTATATATATACAACCCCACT
* * *
17689379 CATTTATATATTTTATATATATAGC-A-CCCACT
1 CATATATATACTGTATATATATA-CAACCCCACT
*
17689411 AATATATATACTGTAT
1 CATATATATACTGTAT
17689427 GCACAATAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 12
0.67 0.18 0.14
Matches are distributed among these distances:
29 6 0.11
30 14 0.25
31 9 0.16
32 26 0.46
33 1 0.02
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (33 bp):
CATATATATACTGTATATATATACAACCCCACT
Found at i:17689873 original size:32 final size:32
Alignment explanation
Indices: 17689829--17689897 Score: 113
Period size: 32 Copynumber: 2.2 Consensus size: 32
17689819 GAAATTCTAT
17689829 TTTTACGAATTGATTAGGATTTTATGGGATA-
1 TTTTACGAATTGATTAGGATTTTATGGGATAC
*
17689860 TTTTATGAGATTGATTAGGATTTTATGGGATAC
1 TTTTACGA-ATTGATTAGGATTTTATGGGATAC
17689893 TTTTA
1 TTTTA
17689898 AAAGGGGTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 7 0.20
32 23 0.66
33 5 0.14
ACGTcount: A:0.28, C:0.03, G:0.22, T:0.48
Consensus pattern (32 bp):
TTTTACGAATTGATTAGGATTTTATGGGATAC
Found at i:17690739 original size:21 final size:21
Alignment explanation
Indices: 17690713--17690761 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
17690703 AAATGTAACT
17690713 GACTGGACTAACAGGACATTA
1 GACTGGACTAACAGGACATTA
** * *
17690734 GACTGGACTGGCAGGATATTG
1 GACTGGACTAACAGGACATTA
17690755 GACTGGA
1 GACTGGA
17690762 TCCAAGTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.31, C:0.16, G:0.33, T:0.20
Consensus pattern (21 bp):
GACTGGACTAACAGGACATTA
Found at i:17692609 original size:78 final size:78
Alignment explanation
Indices: 17692522--17692677 Score: 276
Period size: 78 Copynumber: 2.0 Consensus size: 78
17692512 ACAGCTTCTA
* * *
17692522 AAAGAAACTCAAGAGCAATTCTTGAAGAAAAATTCAAAGAGAATTATTATTAACTCAATAAAACA
1 AAAGAAACTCAAGAGCAATTCTTGAAGAAAAACTCAAAGAGAATTATTATTAACTAAAAAAAACA
*
17692587 TAAATCAATTGTG
66 TAAATAAATTGTG
17692600 AAAGAAACTCAAGAGCAATTCTTGAAGAAAAACTCAAAGAGAATTATTATTAACTAAAAAAAACA
1 AAAGAAACTCAAGAGCAATTCTTGAAGAAAAACTCAAAGAGAATTATTATTAACTAAAAAAAACA
17692665 TAAATAAATTGTG
66 TAAATAAATTGTG
17692678 TGTATAACAG
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 74 1.00
ACGTcount: A:0.53, C:0.11, G:0.12, T:0.24
Consensus pattern (78 bp):
AAAGAAACTCAAGAGCAATTCTTGAAGAAAAACTCAAAGAGAATTATTATTAACTAAAAAAAACA
TAAATAAATTGTG
Found at i:17705329 original size:28 final size:28
Alignment explanation
Indices: 17705298--17705354 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
17705288 ACTAAGACAT
17705298 TGGATCAAAACACTAGGCAAGTAAAATG
1 TGGATCAAAACACTAGGCAAGTAAAATG
*
17705326 TGGATCAAAACATTAGGCAAGTAAAATG
1 TGGATCAAAACACTAGGCAAGTAAAATG
17705354 T
1 T
17705355 AAGTATATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.46, C:0.12, G:0.21, T:0.21
Consensus pattern (28 bp):
TGGATCAAAACACTAGGCAAGTAAAATG
Found at i:17710960 original size:21 final size:21
Alignment explanation
Indices: 17710922--17711004 Score: 89
Period size: 21 Copynumber: 4.0 Consensus size: 21
17710912 CAAATATGTC
*
17710922 AACAGAAGCT--TGAAAGCTA
1 AACAGAAGCTCGTAAAAGCTA
* *
17710941 AACAAAAGCTCGTAAAAGCTG
1 AACAGAAGCTCGTAAAAGCTA
* *
17710962 AACAGTAGCTCGTAAGAGCTA
1 AACAGAAGCTCGTAAAAGCTA
* *
17710983 AACAGAAGCTCATAAGAGCTA
1 AACAGAAGCTCGTAAAAGCTA
17711004 A
1 A
17711005 TTCACCCAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
19 9 0.17
21 44 0.83
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.16
Consensus pattern (21 bp):
AACAGAAGCTCGTAAAAGCTA
Found at i:17713451 original size:15 final size:15
Alignment explanation
Indices: 17713431--17713485 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
17713421 ATAAAACAAC
17713431 AAATTTAAAGATAAA
1 AAATTTAAAGATAAA
* *
17713446 AAATTTGAGGA-AGAA
1 AAATTTAAAGATA-AA
17713461 AATATTATAAAGAT-AA
1 AA-ATT-TAAAGATAAA
17713477 AAATTTAAA
1 AAATTTAAA
17713486 TAAAATGTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
14 5 0.16
15 16 0.50
16 7 0.22
17 4 0.12
ACGTcount: A:0.62, C:0.00, G:0.11, T:0.27
Consensus pattern (15 bp):
AAATTTAAAGATAAA
Found at i:17713936 original size:2 final size:2
Alignment explanation
Indices: 17713929--17713955 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17713919 CAAGAAGATA
17713929 GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT G
17713956 CGCGCGCGCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:17715425 original size:51 final size:51
Alignment explanation
Indices: 17715308--17715438 Score: 136
Period size: 51 Copynumber: 2.6 Consensus size: 51
17715298 GTATATGGCA
* * * * * *
17715308 TAAGACTATGGATGAAAAATGCTATGGTAGTCTAGTATAAGGTATATAGTG
1 TAAGACCATGGATGAAAGACGCTATGGCAATCTAGTATAAGGTACATAGTG
** * * * *
17715359 TAAGACCATATATGAAAGACGCTATGGCAATTTGGTATGAGGTACGTAGTG
1 TAAGACCATGGATGAAAGACGCTATGGCAATCTAGTATAAGGTACATAGTG
* *
17715410 TAAGACCATGGATGAAAGACACCATGGCA
1 TAAGACCATGGATGAAAGACGCTATGGCA
17715439 GCATGGTACA
Statistics
Matches: 64, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
51 64 1.00
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.26
Consensus pattern (51 bp):
TAAGACCATGGATGAAAGACGCTATGGCAATCTAGTATAAGGTACATAGTG
Found at i:17715453 original size:51 final size:51
Alignment explanation
Indices: 17715354--17715453 Score: 119
Period size: 51 Copynumber: 2.0 Consensus size: 51
17715344 ATAAGGTATA
* * * ** **
17715354 TAGTGTAAGACCATATATGAAAGACGCTATGGCAATTTGGTATGAGGTACG
1 TAGTGTAAGACCATAGATGAAAGACACCATGGCAACATGGTACAAGGTACG
* *
17715405 TAGTGTAAGACCATGGATGAAAGACACCATGGCAGCATGGTACAAGGTA
1 TAGTGTAAGACCATAGATGAAAGACACCATGGCAACATGGTACAAGGTA
17715454 TAAGGTATAC
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
51 40 1.00
ACGTcount: A:0.35, C:0.14, G:0.28, T:0.23
Consensus pattern (51 bp):
TAGTGTAAGACCATAGATGAAAGACACCATGGCAACATGGTACAAGGTACG
Found at i:17718425 original size:23 final size:23
Alignment explanation
Indices: 17718348--17718435 Score: 65
Period size: 23 Copynumber: 3.9 Consensus size: 23
17718338 GATATTTTAT
* * *
17718348 TGTTGT-AATTGAGGTGTATAAA
1 TGTTGTAAATTAAAGTGTTTAAA
*
17718370 TGTTGTTAA-TAAAGATG-TTAAA
1 TGTTGTAAATTAAAG-TGTTTAAA
* **
17718392 GTGCTACAAATTAAAGTGTTTAAA
1 -TGTTGTAAATTAAAGTGTTTAAA
*
17718416 TGTTGTAAATTGAAGTGTTT
1 TGTTGTAAATTAAAGTGTTT
17718436 TAAGTATCGC
Statistics
Matches: 50, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
22 13 0.26
23 27 0.54
24 10 0.20
ACGTcount: A:0.35, C:0.02, G:0.22, T:0.41
Consensus pattern (23 bp):
TGTTGTAAATTAAAGTGTTTAAA
Found at i:17718527 original size:138 final size:138
Alignment explanation
Indices: 17718279--17718542 Score: 449
Period size: 138 Copynumber: 1.9 Consensus size: 138
17718269 TCTGTCTTAA
17718279 GTTGTAAATTGAAGTGTTTTAAGTACTGCAAATTGAATTATTTAGTTGCTGGAAATTGAGATATT
1 GTTGTAAATTGAAGTGTTTTAAGTACTGCAAATTGAATTATTTAGTTGCTGGAAATTGAGATATT
*
17718344 TTATTGTTGTAATTGAGGTGTATAAATGTTGTTAATAAAGATGTTAAAGTGCTACAAATTAAAGT
66 TTATTGTTGTAACTGAGGTGTATAAATGTTGTTAATAAAGATGTTAAAGTGCTACAAATTAAAGT
17718409 GTTTAAAT
131 GTTTAAAT
* * *
17718417 GTTGTAAATTGAAGTGTTTTAAGTA-TCGCAAATTGAATTGTTTAGTTTCTGGAAATTGAGATGT
1 GTTGTAAATTGAAGTGTTTTAAGTACT-GCAAATTGAATTATTTAGTTGCTGGAAATTGAGATAT
* * *
17718481 TTTATTGTTGTAACTGAGGTGTATAAATGTTGTTAATAGAGATGTTAAAGTGTTGCAAATTA
65 TTTATTGTTGTAACTGAGGTGTATAAATGTTGTTAATAAAGATGTTAAAGTGCTACAAATTA
17718543 CTGAAGCTCT
Statistics
Matches: 118, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
137 1 0.01
138 117 0.99
ACGTcount: A:0.33, C:0.04, G:0.22, T:0.42
Consensus pattern (138 bp):
GTTGTAAATTGAAGTGTTTTAAGTACTGCAAATTGAATTATTTAGTTGCTGGAAATTGAGATATT
TTATTGTTGTAACTGAGGTGTATAAATGTTGTTAATAAAGATGTTAAAGTGCTACAAATTAAAGT
GTTTAAAT
Found at i:17720286 original size:58 final size:56
Alignment explanation
Indices: 17720223--17720387 Score: 174
Period size: 58 Copynumber: 2.9 Consensus size: 56
17720213 TTTTTATAGT
* * *
17720223 ATTATATATTATGATTT-TTTAATTCATA-TAATAATAATTATATTAAGAATTTTATTAA
1 ATTATATATTAT--TTTATTAAATT-ATATTAATAATAATTATATTAA-AATATGATTAA
* *
17720281 ATTATATATTATTTTATTAAATTATATTTAATAATAATTATGTTAAAATATGGTTAA
1 ATTATATATTATTTTATTAAATTATA-TTAATAATAATTATATTAAAATATGATTAA
* *
17720338 ATTATTTATTATTTTTATTAAATTATTTTTAATAATAATCT-TATTAAAAT
1 ATTATATATTA-TTTTATTAAATTA-TATTAATAATAAT-TATATTAAAAT
17720388 TTAATACCAA
Statistics
Matches: 93, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
56 6 0.06
57 24 0.26
58 61 0.66
59 2 0.02
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.53
Consensus pattern (56 bp):
ATTATATATTATTTTATTAAATTATATTAATAATAATTATATTAAAATATGATTAA
Found at i:17720566 original size:16 final size:16
Alignment explanation
Indices: 17720545--17720609 Score: 70
Period size: 16 Copynumber: 4.4 Consensus size: 16
17720535 TGAGTTACTG
*
17720545 ATTACAGCTTTATTCC
1 ATTACAGCTCTATTCC
17720561 ATTACAGCTC---T--
1 ATTACAGCTCTATTCC
*
17720572 ATT-CAGCTCTATTCA
1 ATTACAGCTCTATTCC
17720587 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
17720603 ATTACAG
1 ATTACAG
17720610 TGAACCAAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
10 6 0.15
11 3 0.07
13 2 0.05
15 3 0.07
16 27 0.66
ACGTcount: A:0.28, C:0.26, G:0.08, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:17720578 original size:26 final size:26
Alignment explanation
Indices: 17720549--17720601 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
17720539 TTACTGATTA
* *
17720549 CAGCTTTATTCCATTACAGCTCTATT
1 CAGCTCTATTCAATTACAGCTCTATT
17720575 CAGCTCTATTCAATTACAGCTCTATT
1 CAGCTCTATTCAATTACAGCTCTATT
17720601 C
1 C
17720602 CATTACAGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.25, C:0.28, G:0.08, T:0.40
Consensus pattern (26 bp):
CAGCTCTATTCAATTACAGCTCTATT
Found at i:17728019 original size:9 final size:9
Alignment explanation
Indices: 17728002--17728038 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
17727992 TGAGTTTTCG
17728002 AATTCGAAT
1 AATTCGAAT
*
17728011 AACTCGAAT
1 AATTCGAAT
17728020 AATTCGAAT
1 AATTCGAAT
17728029 AATTCGAAT
1 AATTCGAAT
17728038 A
1 A
17728039 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:17728429 original size:19 final size:19
Alignment explanation
Indices: 17728397--17728433 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
17728387 TTTTTAATAT
17728397 TTTCCCTCCAAACTATTTAC
1 TTTCCCTCCAAACT-TTTAC
17728417 TTTCCCT-CAAACTTTTA
1 TTTCCCTCCAAACTTTTA
17728434 TTCTCCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 6 0.35
20 7 0.41
ACGTcount: A:0.24, C:0.32, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTCCCTCCAAACTTTTAC
Found at i:17728456 original size:35 final size:36
Alignment explanation
Indices: 17728402--17728475 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 36
17728392 AATATTTTCC
*
17728402 CTCCAAACTATTTACTTTCCCTC-AAACTTTTA-TT
1 CTCCAAACTATTTACTTTCCCCCTAAACTTTTACTT
* * *
17728436 CTCCAAAACTTTTTATTTTCCCCCTACACTTTTACTT
1 CTCC-AAACTATTTACTTTCCCCCTAAACTTTTACTT
17728473 CTC
1 CTC
17728476 ACCATTTACT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
34 4 0.12
35 16 0.48
36 8 0.24
37 5 0.15
ACGTcount: A:0.23, C:0.32, G:0.00, T:0.45
Consensus pattern (36 bp):
CTCCAAACTATTTACTTTCCCCCTAAACTTTTACTT
Found at i:17729463 original size:14 final size:14
Alignment explanation
Indices: 17729440--17729473 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
17729430 TACAATCTCC
17729440 AAATAATAACAATA
1 AAATAATAACAATA
*
17729454 AAATAGTAACAATA
1 AAATAATAACAATA
*
17729468 TAATAA
1 AAATAA
17729474 CGAAACGATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.24
Consensus pattern (14 bp):
AAATAATAACAATA
Found at i:17732742 original size:12 final size:11
Alignment explanation
Indices: 17732714--17732743 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
17732704 AATTTTTTAA
17732714 TTTTTAAGAAT
1 TTTTTAAGAAT
17732725 TTTTTAAGAAT
1 TTTTTAAGAAT
17732736 TTATTTAA
1 TT-TTTAA
17732744 TTAAAATTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (11 bp):
TTTTTAAGAAT
Found at i:17743054 original size:21 final size:21
Alignment explanation
Indices: 17743028--17743072 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
17743018 AATGGAGGAA
*
17743028 GTTGAGTAGTTTATCTACACC
1 GTTGAGTAGTTTATCCACACC
* *
17743049 GTTGAGTGGTTTATCCATACC
1 GTTGAGTAGTTTATCCACACC
17743070 GTT
1 GTT
17743073 TGAATAACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.40
Consensus pattern (21 bp):
GTTGAGTAGTTTATCCACACC
Found at i:17750696 original size:18 final size:20
Alignment explanation
Indices: 17750656--17750697 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
17750646 TGTTAAAAAC
*
17750656 AAATTGAGCTAAAAAAATTT
1 AAATTGAGCTAAAAAAATAT
*
17750676 AAATTGA-C-AAAAATATAT
1 AAATTGAGCTAAAAAAATAT
17750694 AAAT
1 AAAT
17750698 ATGGGTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 12 0.60
19 1 0.05
20 7 0.35
ACGTcount: A:0.60, C:0.05, G:0.07, T:0.29
Consensus pattern (20 bp):
AAATTGAGCTAAAAAAATAT
Found at i:17750982 original size:30 final size:32
Alignment explanation
Indices: 17750948--17751011 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 32
17750938 TCATTTTCTG
* *
17750948 TTTTTTTAATAAATGGCTCAATAT-TTT-TAC
1 TTTTTTGAATAAATGGCCCAATATGTTTATAC
**
17750978 TTTTTTGCTTAAATGGCCCAATATGTTTATAC
1 TTTTTTGAATAAATGGCCCAATATGTTTATAC
17751010 TT
1 TT
17751012 CTTCTTTTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 20 0.71
31 3 0.11
32 5 0.18
ACGTcount: A:0.27, C:0.12, G:0.09, T:0.52
Consensus pattern (32 bp):
TTTTTTGAATAAATGGCCCAATATGTTTATAC
Found at i:17775130 original size:22 final size:22
Alignment explanation
Indices: 17775101--17775154 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
17775091 GAAATAGAAG
* *
17775101 CATA-GCATAATATGTTAGTTA
1 CATATGCATAATATGATAGATA
*
17775122 CATATGCATATTATGATAGATA
1 CATATGCATAATATGATAGATA
*
17775144 CAGAATGCATA
1 CA-TATGCATA
17775155 TTTCCTACCC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 4 0.15
22 16 0.59
23 7 0.26
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (22 bp):
CATATGCATAATATGATAGATA
Found at i:17775321 original size:22 final size:22
Alignment explanation
Indices: 17775291--17775358 Score: 100
Period size: 22 Copynumber: 3.0 Consensus size: 22
17775281 TAACTGTCCA
*
17775291 TATGTTAGTTACATATGCATAT
1 TATGATAGTTACATATGCATAT
17775313 TATGATAGTTACATATGCATAT
1 TATGATAGTTACATATGCATAT
* *
17775335 TATGATAGATACAGAATGCATAT
1 TATGATAGTTACA-TATGCATAT
17775358 T
1 T
17775359 TCCTACCCCC
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 33 0.79
23 9 0.21
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.40
Consensus pattern (22 bp):
TATGATAGTTACATATGCATAT
Found at i:17775462 original size:202 final size:201
Alignment explanation
Indices: 17775101--17775490 Score: 744
Period size: 202 Copynumber: 1.9 Consensus size: 201
17775091 GAAATAGAAG
*
17775101 CATAGCATAATATGTTAGTTACATATGCATATTATGATAGATACAGAATGCATATTTCCTACCCC
1 CATAGCATAATATGATAGTTACATATGCATATTATGATAGATACAGAATGCATATTTCCTACCCC
17775166 CCATCAGCTACACACCATCTCCGTCCAGCCCTACACATCAAAAAGGGTATCGAGTACCCATCCAT
66 CCATCAGCTACACACCATCTCCGTCCAGCCCTACACATCAAAAAGGGTATCGAGTACCCATCCAT
*
17775231 CCCTGCAAACCACATAGTGATTGTATGTCACGTTCAAAACTACTGCAGACTAACTGTCCATATGT
131 CCCTGCAAACCACATAATGATTGTATGTCACGTTCAAAACTACTGCAGACTAACTGTCCATATGT
17775296 TAGTTA
196 TAGTTA
*
17775302 CATATGCATATTATGATAGTTACATATGCATATTATGATAGATACAGAATGCATATTTCCTACCC
1 CATA-GCATAATATGATAGTTACATATGCATATTATGATAGATACAGAATGCATATTTCCTACCC
17775367 CCCATCAGCTACACACCATCTCCGTCCAGCCCTACACATCAAAAAGGGTATCGAGTACCCATCCA
65 CCCATCAGCTACACACCATCTCCGTCCAGCCCTACACATCAAAAAGGGTATCGAGTACCCATCCA
17775432 TCCCTGCAAACCACATAATGATTGTATGTCACGTTCAAAACTACTGCAGACTAACTGTC
130 TCCCTGCAAACCACATAATGATTGTATGTCACGTTCAAAACTACTGCAGACTAACTGTC
17775491 AGAACAGAAT
Statistics
Matches: 185, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
201 4 0.02
202 181 0.98
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (201 bp):
CATAGCATAATATGATAGTTACATATGCATATTATGATAGATACAGAATGCATATTTCCTACCCC
CCATCAGCTACACACCATCTCCGTCCAGCCCTACACATCAAAAAGGGTATCGAGTACCCATCCAT
CCCTGCAAACCACATAATGATTGTATGTCACGTTCAAAACTACTGCAGACTAACTGTCCATATGT
TAGTTA
Found at i:17789694 original size:31 final size:29
Alignment explanation
Indices: 17789624--17789697 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
17789614 GGCTCAGGTT
* *
17789624 ACATTTTAGTCACTTATGTTTGAAATGTT
1 ACATTTTAGTCACTTATGTTTCAAATGTA
* **
17789653 ACGTTTTAGTCACTTATGTTATCACGTTGTA
1 ACATTTTAGTCACTTATGTT-TCA-AATGTA
17789684 ACATTTTAGTCACT
1 ACATTTTAGTCACT
17789698 AAGCCGTTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 19 0.51
30 2 0.05
31 16 0.43
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.46
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTCAAATGTA
Found at i:17791285 original size:42 final size:43
Alignment explanation
Indices: 17791154--17791288 Score: 191
Period size: 43 Copynumber: 3.2 Consensus size: 43
17791144 ACGTCGCTAA
* *
17791154 CTTTAGCGGCGCTTCTCCCACGAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTATCCCACAAACGCCGCTAAAGACCAAGAC
* *
17791197 CTTTAGCGGCGCGTATACCACAAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTATCCCACAAACGCCGCTAAAGACCAAGAC
* * * *
17791240 CTTTAGCGTCGCTTTTCCCAC-AACGCCGCTAAAGACCAGGTC
1 CTTTAGCGGCGCTTATCCCACAAACGCCGCTAAAGACCAAGAC
17791282 CTTTAGC
1 CTTTAGC
17791289 AGCACCGCTA
Statistics
Matches: 82, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
42 26 0.32
43 56 0.68
ACGTcount: A:0.26, C:0.35, G:0.20, T:0.19
Consensus pattern (43 bp):
CTTTAGCGGCGCTTATCCCACAAACGCCGCTAAAGACCAAGAC
Found at i:17791354 original size:43 final size:43
Alignment explanation
Indices: 17791293--17791473 Score: 254
Period size: 43 Copynumber: 4.2 Consensus size: 43
17791283 TTTAGCAGCA
* ** ** *
17791293 CCGCTAAAGACCAGGACCTTTAGCGGTACTTTTTTCAAAAACG
1 CCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCACAAACG
* *
17791336 CCGCTAAAGACCAAGACCTTTAGCGGCGCTTATACCACGAACG
1 CCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCACAAACG
*
17791379 CCGCTAAAGACTAAGACCTTTAGCGGCGCTTTTACCACAAACG
1 CCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCACAAACG
* *
17791422 CCGCTAAAGACCAAAACCTTTAGCGGCGCTTTTTATCACAAACG
1 CCGCTAAAGACCAAGACCTTTAGCGGCGC-TTTTACCACAAACG
17791466 CCGCTAAA
1 CCGCTAAA
17791474 AACATAATCT
Statistics
Matches: 123, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
43 102 0.83
44 21 0.17
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.21
Consensus pattern (43 bp):
CCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCACAAACG
Found at i:17791677 original size:46 final size:46
Alignment explanation
Indices: 17791626--17791723 Score: 196
Period size: 46 Copynumber: 2.1 Consensus size: 46
17791616 GAATTTAGTT
17791626 TTAGAATTTAGGGCCGTAAATTAATAAGACAATTAAAATCCAAAAG
1 TTAGAATTTAGGGCCGTAAATTAATAAGACAATTAAAATCCAAAAG
17791672 TTAGAATTTAGGGCCGTAAATTAATAAGACAATTAAAATCCAAAAG
1 TTAGAATTTAGGGCCGTAAATTAATAAGACAATTAAAATCCAAAAG
17791718 TTAGAA
1 TTAGAA
17791724 CTCAAGTTGT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 52 1.00
ACGTcount: A:0.48, C:0.10, G:0.15, T:0.27
Consensus pattern (46 bp):
TTAGAATTTAGGGCCGTAAATTAATAAGACAATTAAAATCCAAAAG
Found at i:17791873 original size:37 final size:37
Alignment explanation
Indices: 17791823--17791898 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
17791813 TTTATCAAAC
17791823 TAGTTAAGAAATACATGGTGCAGCCATGCAATATAAA
1 TAGTTAAGAAATACATGGTGCAGCCATGCAATATAAA
17791860 TAGTTAAGAAATACATGGTGCAGCCATGCAATATAAA
1 TAGTTAAGAAATACATGGTGCAGCCATGCAATATAAA
17791897 TA
1 TA
17791899 CAATAGAATC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.25
Consensus pattern (37 bp):
TAGTTAAGAAATACATGGTGCAGCCATGCAATATAAA
Found at i:17792229 original size:23 final size:23
Alignment explanation
Indices: 17792179--17792230 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
17792169 GTTAGGTGTC
* *
17792179 AGTATAAAGACATGTCAGATATG
1 AGTATGAAGACATGTCAGAGATG
* * *
17792202 GGTATGAAGGCATGTCTGAGATG
1 AGTATGAAGACATGTCAGAGATG
17792225 AGTATG
1 AGTATG
17792231 TTCAATTTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.08, G:0.31, T:0.27
Consensus pattern (23 bp):
AGTATGAAGACATGTCAGAGATG
Found at i:17792708 original size:12 final size:12
Alignment explanation
Indices: 17792691--17792720 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
17792681 CAAGACAGAT
17792691 CAAATTTTAAAG
1 CAAATTTTAAAG
17792703 CAAATTTTAAAG
1 CAAATTTTAAAG
17792715 CAAATT
1 CAAATT
17792721 GCTGATGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (12 bp):
CAAATTTTAAAG
Found at i:17794907 original size:21 final size:21
Alignment explanation
Indices: 17794881--17794926 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
17794871 TCTTGGATGT
17794881 GGGAAA-TTAGGGATTTTAGGG
1 GGGAAAGTTAGGGA-TTTAGGG
* *
17794902 GGGAAAGTTGGGGATTTCGGG
1 GGGAAAGTTAGGGATTTAGGG
17794923 GGGA
1 GGGA
17794927 GGGGGTAGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.24, C:0.02, G:0.50, T:0.24
Consensus pattern (21 bp):
GGGAAAGTTAGGGATTTAGGG
Found at i:17801918 original size:12 final size:12
Alignment explanation
Indices: 17801898--17801978 Score: 58
Period size: 11 Copynumber: 6.4 Consensus size: 12
17801888 AAAATTAAAA
17801898 AAAAGTATTTTTT
1 AAAA-TATTTTTT
17801911 AAAATATTTTTT
1 AAAATATTTTTT
17801923 -AAATATTTTAAAATT
1 AAAATATTTT----TT
* *
17801938 AAAAAAATTTTT
1 AAAATATTTTTT
*
17801950 AAAA-ATATTTT
1 AAAATATTTTTT
*
17801961 AAAAAATATTTTT
1 AAAATAT-TTTTT
17801974 AAAAT
1 AAAAT
17801979 TTAAAAAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
11 18 0.33
12 16 0.29
13 12 0.22
15 2 0.04
16 7 0.13
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (12 bp):
AAAATATTTTTT
Found at i:17801920 original size:11 final size:11
Alignment explanation
Indices: 17801906--17801978 Score: 57
Period size: 12 Copynumber: 6.9 Consensus size: 11
17801896 AAAAAAGTAT
17801906 TTTTTAAAATA
1 TTTTTAAAATA
*
17801917 TTTTTTAAATA
1 TTTTTAAAATA
17801928 -TTTT-AAA-A
1 TTTTTAAAATA
* *
17801936 --TTAAAAAAA
1 TTTTTAAAATA
17801945 TTTTTAAAAATA
1 TTTTT-AAAATA
*
17801957 TTTTAAAAAATA
1 TTTT-TAAAATA
17801969 TTTTTAAAAT
1 TTTTTAAAAT
17801979 TTAAAAAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
7 2 0.04
8 4 0.08
9 4 0.08
10 4 0.08
11 17 0.34
12 19 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
TTTTTAAAATA
Found at i:17801993 original size:12 final size:12
Alignment explanation
Indices: 17801936--17802019 Score: 81
Period size: 12 Copynumber: 7.5 Consensus size: 12
17801926 TATTTTAAAA
17801936 TTAAAAAA-ATT
1 TTAAAAAATATT
*
17801947 TTTAAAAATATT
1 TTAAAAAATATT
17801959 TTAAAAAATATT
1 TTAAAAAATATT
*
17801971 TT--TAAA-A-T
1 TTAAAAAATATT
*
17801979 TTAAAAAAAATT
1 TTAAAAAATATT
*
17801991 TTAAAAAGTA-T
1 TTAAAAAATATT
*
17802002 GTAAAAAATATT
1 TTAAAAAATATT
17802014 TTAAAA
1 TTAAAA
17802020 TTAAAAAAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
8 3 0.05
9 1 0.02
10 6 0.10
11 17 0.29
12 31 0.53
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.39
Consensus pattern (12 bp):
TTAAAAAATATT
Found at i:17802029 original size:42 final size:41
Alignment explanation
Indices: 17801923--17802030 Score: 164
Period size: 43 Copynumber: 2.6 Consensus size: 41
17801913 AATATTTTTT
* *
17801923 AAATATTTTAAAATTAAAAAAATTTTTAAAAATATTTTAAA
1 AAATATTTTAAAATTAAAAAAAATTTTAAAAATATTGTAAA
17801964 AAATATTTTTAAAATTTAAAAAAAATTTTAAAAAGTA-TGTAAA
1 AAATA-TTTTAAAA-TTAAAAAAAATTTTAAAAA-TATTGTAAA
17802007 AAATATTTTAAAATTAAAAAAAAT
1 AAATATTTTAAAATTAAAAAAAAT
17802031 AAATATATTT
Statistics
Matches: 62, Mismatches: 2, Indels: 6
0.89 0.03 0.09
Matches are distributed among these distances:
41 16 0.26
42 16 0.26
43 28 0.45
44 2 0.03
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (41 bp):
AAATATTTTAAAATTAAAAAAAATTTTAAAAATATTGTAAA
Found at i:17802491 original size:31 final size:31
Alignment explanation
Indices: 17802453--17802520 Score: 106
Period size: 28 Copynumber: 2.3 Consensus size: 31
17802443 TTTAATAGAA
17802453 GACTAATTTTTTCTTTAATCCAATGTGCAAG
1 GACTAATTTTTTCTTTAATCCAATGTGCAAG
*
17802484 GACTAA---TTTGTTTAATCCAATGTGCAAG
1 GACTAATTTTTTCTTTAATCCAATGTGCAAG
17802512 GACTAATTT
1 GACTAATTT
17802521 GTCTAACTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
28 27 0.82
31 6 0.18
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.40
Consensus pattern (31 bp):
GACTAATTTTTTCTTTAATCCAATGTGCAAG
Found at i:17802502 original size:28 final size:28
Alignment explanation
Indices: 17802466--17802522 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
17802456 TAATTTTTTC
17802466 TTTAATCCAATGTGCAAGGACTAATTTG
1 TTTAATCCAATGTGCAAGGACTAATTTG
17802494 TTTAATCCAATGTGCAAGGACTAATTTG
1 TTTAATCCAATGTGCAAGGACTAATTTG
17802522 T
1 T
17802523 CTAACTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.37
Consensus pattern (28 bp):
TTTAATCCAATGTGCAAGGACTAATTTG
Found at i:17805806 original size:15 final size:15
Alignment explanation
Indices: 17805786--17805816 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
17805776 CCAACCTTCA
17805786 AATTTTACCTCAATT
1 AATTTTACCTCAATT
17805801 AATTTTACCTCAATT
1 AATTTTACCTCAATT
17805816 A
1 A
17805817 TACATAATAT
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:0.35, C:0.19, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTTTACCTCAATT
Found at i:17809260 original size:93 final size:92
Alignment explanation
Indices: 17809128--17809322 Score: 286
Period size: 93 Copynumber: 2.1 Consensus size: 92
17809118 TTGATTTTAG
* *
17809128 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTA-TATAATTA
1 TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTA-AATTA
* *
17809192 TATTTAAT-ATTAATTATTTTAAATTGTA
65 TATGTAATAATT-ATTATTTTAAATTATA
* *
17809220 TAAATTCATATAAGAAAATTTTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTA
1 TAAATTCATATAAGAAAA-TTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTA
17809285 TATGTAATAATTATTATTTTAAATTATA
65 TATGTAATAATTATTATTTTAAATTATA
*
17809313 CAAATTCATA
1 TAAATTCATA
17809323 AACTATAATC
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
92 17 0.18
93 71 0.76
94 5 0.05
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (92 bp):
TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTAT
ATGTAATAATTATTATTTTAAATTATA
Found at i:17809380 original size:17 final size:17
Alignment explanation
Indices: 17809355--17809388 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
17809345 ATAATTTTAA
*
17809355 ATTTTATTAAATCATAT
1 ATTTAATTAAATCATAT
17809372 ATTTAATTAAATCATAT
1 ATTTAATTAAATCATAT
17809389 TTAATATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATTAAATCATAT
Found at i:17809390 original size:15 final size:16
Alignment explanation
Indices: 17809355--17809393 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
17809345 ATAATTTTAA
*
17809355 ATTTTATTAAATCATAT
1 ATTTAATTAAATCA-AT
17809372 ATTTAATTAAATC-AT
1 ATTTAATTAAATCAAT
17809387 ATTTAAT
1 ATTTAAT
17809394 ATTAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.43
17 12 0.57
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTTAATTAAATCAAT
Found at i:17809397 original size:17 final size:18
Alignment explanation
Indices: 17809359--17809398 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
17809349 TTTTAAATTT
*
17809359 TATTAAATCATATATTTA
1 TATTAAATCATATATTAA
17809377 -ATTAAATCATAT-TTAA
1 TATTAAATCATATATTAA
17809393 TATTAA
1 TATTAA
17809399 TTATTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTAAATCATATATTAA
Found at i:17809513 original size:15 final size:15
Alignment explanation
Indices: 17809478--17809612 Score: 70
Period size: 15 Copynumber: 8.9 Consensus size: 15
17809468 TTAAGAATTT
*
17809478 TATTAAATTAT-ATA
1 TATTTAATTATAATA
17809492 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
17809506 TATTTAATAATAAT-
1 TATTTAATTATAATA
17809520 TATGTTAATT-T-ATA
1 TAT-TTAATTATAATA
* *
17809534 T-TTTACAGTATCATA
1 TATTTA-ATTATAATA
*
17809549 TATTATGATTTGAGTAAATTCA
1 TATT-T-AATT-A-T-AA-T-A
*
17809571 TATTAAATTAT-ATA
1 TATTTAATTATAATA
17809585 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
17809599 TATTTAATAATAAT
1 TATTTAATTATAAT
17809613 TATGTTTAAA
Statistics
Matches: 93, Mismatches: 11, Indels: 33
0.68 0.08 0.24
Matches are distributed among these distances:
12 3 0.03
13 21 0.23
14 17 0.18
15 32 0.34
16 3 0.03
17 2 0.02
18 3 0.03
19 2 0.02
20 4 0.04
21 1 0.01
22 5 0.05
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:17809520 original size:120 final size:119
Alignment explanation
Indices: 17809354--17809572 Score: 345
Period size: 120 Copynumber: 1.8 Consensus size: 119
17809344 AATAATTTTA
* *
17809354 AATTTTATTAAATCATATATTTAATTAAATCATATTTAATATTAATTAT-TTAAAATTT-TCTTT
1 AATTTTATTAAATCATATATTTAATTAAATCATATTTAATAATAATTATGTT--AATTTATATTT
*
17809417 TATAGTATCATATATTATGATTTGAGTAAATTCATAGAAGAATTTTATTTATTAAG
64 TACAGTATCATATATTATGATTTGAGTAAATTCATAGAAGAATTTTATTTATTAAG
*
17809473 AATTTTATTAAATTATATATTTTAATTATAAT-ATATTTAATAATAATTATGTTAATTTATATTT
1 AATTTTATTAAATCATATA-TTTAATTA-AATCATATTTAATAATAATTATGTTAATTTATATTT
17809537 TACAGTATCATATATTATGATTTGAGTAAATTCATA
64 TACAGTATCATATATTATGATTTGAGTAAATTCATA
17809573 TTAAATTATA
Statistics
Matches: 92, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
119 23 0.25
120 64 0.70
121 5 0.05
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (119 bp):
AATTTTATTAAATCATATATTTAATTAAATCATATTTAATAATAATTATGTTAATTTATATTTTA
CAGTATCATATATTATGATTTGAGTAAATTCATAGAAGAATTTTATTTATTAAG
Found at i:17809601 original size:16 final size:16
Alignment explanation
Indices: 17809580--17809621 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
17809570 ATATTAAATT
*
17809580 ATATATTTTAATTATA
1 ATATATTTTAATAATA
17809596 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
17809611 AT-TATGTTTAA
1 ATATAT-TTTAA
17809622 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:17809729 original size:154 final size:156
Alignment explanation
Indices: 17809571--17809868 Score: 537
Period size: 154 Copynumber: 1.9 Consensus size: 156
17809561 AGTAAATTCA
*
17809571 TATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
1 TATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
17809636 TTTATTATTGAT-AT-TAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAAC
66 TTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAAC
17809699 AAATTTATGCTAATTATTAAGAATTT
131 AAATTTATGCTAATTATTAAGAATTT
17809725 TATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
1 TATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
* *
17809790 TTTATTATTGATAATAATAATCTTATTAAAATTTAAATAATAATAACAATAATCATTTACCAAAA
66 TTTATTATTGATAAT-ATAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAA
*
17809855 CAAATTTCTGCTAA
130 CAAATTTATGCTAA
17809869 GGGTATTCTA
Statistics
Matches: 137, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
154 76 0.55
155 2 0.01
157 59 0.43
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (156 bp):
TATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
TTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAAC
AAATTTATGCTAATTATTAAGAATTT
Found at i:17809749 original size:18 final size:17
Alignment explanation
Indices: 17809721--17809755 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
17809711 ATTATTAAGA
*
17809721 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
17809738 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
17809756 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:17810009 original size:16 final size:16
Alignment explanation
Indices: 17809988--17810026 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
17809978 TTGATTTGCT
*
17809988 ATTACACAGCTTTTCC
1 ATTACACAGCTATTCC
**
17810004 ATTACACCTCTATTCC
1 ATTACACAGCTATTCC
17810020 ATTACAC
1 ATTACAC
17810027 CTCTAATCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.33, G:0.03, T:0.36
Consensus pattern (16 bp):
ATTACACAGCTATTCC
Found at i:17810027 original size:16 final size:16
Alignment explanation
Indices: 17810001--17810057 Score: 78
Period size: 16 Copynumber: 3.6 Consensus size: 16
17809991 ACACAGCTTT
* *
17810001 TCCATTACACCTCTAT
1 TCCAATACACCTCTAA
*
17810017 TCCATTACACCTCTAA
1 TCCAATACACCTCTAA
*
17810033 TCTAATACACCTCTAA
1 TCCAATACACCTCTAA
17810049 TCCAATACA
1 TCCAATACA
17810058 GCGAACCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.33, C:0.35, G:0.00, T:0.32
Consensus pattern (16 bp):
TCCAATACACCTCTAA
Found at i:17810826 original size:25 final size:25
Alignment explanation
Indices: 17810792--17810841 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
17810782 AAGCCCAACT
17810792 CCTCAGCCACCGTCACTGCTTGGAG
1 CCTCAGCCACCGTCACTGCTTGGAG
17810817 CCTCAGCCACCGTCACTGCTTGGAG
1 CCTCAGCCACCGTCACTGCTTGGAG
17810842 GCACGCTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.16, C:0.40, G:0.24, T:0.20
Consensus pattern (25 bp):
CCTCAGCCACCGTCACTGCTTGGAG
Found at i:17815834 original size:19 final size:18
Alignment explanation
Indices: 17815806--17815854 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
17815796 AAATCTGACA
* *
17815806 ATTTATATATTTATATTAT
1 ATTTAAATATTTA-AATAT
17815825 ATTTAAATATTTAAATAT
1 ATTTAAATATTTAAATAT
*
17815843 AGTT-AATATTTA
1 ATTTAAATATTTA
17815855 CATAGCTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 8 0.30
18 7 0.26
19 12 0.44
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
ATTTAAATATTTAAATAT
Found at i:17819901 original size:5 final size:5
Alignment explanation
Indices: 17819887--17819917 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
17819877 ATGAATGACA
*
17819887 TATGG GATGG TATGG TATGG TATGG TATGG T
1 TATGG TATGG TATGG TATGG TATGG TATGG T
17819918 TAAGTTGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.19, C:0.00, G:0.42, T:0.39
Consensus pattern (5 bp):
TATGG
Found at i:17832329 original size:18 final size:18
Alignment explanation
Indices: 17832294--17832345 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
17832284 ACATAGCTTT
*
17832294 TAAAAATAAAAACTAAAA
1 TAAAAATAAAAACAAAAA
*
17832312 TAAAAATAAAACCAAAAA
1 TAAAAATAAAAACAAAAA
* *
17832330 GAAAAAAAATAAACAA
1 TAAAAATAA-AAACAA
17832346 TAAAGTTTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 23 0.82
19 5 0.18
ACGTcount: A:0.79, C:0.08, G:0.02, T:0.12
Consensus pattern (18 bp):
TAAAAATAAAAACAAAAA
Found at i:17834688 original size:104 final size:103
Alignment explanation
Indices: 17834393--17834762 Score: 600
Period size: 103 Copynumber: 3.6 Consensus size: 103
17834383 TAGCCGTTAT
** * *
17834393 TGGTGGATCCCGCACTTAGCACCACCACTGAATCGGGGAATCAACACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
*
17834458 AATCAGCACATAGCAACCCCCTTTTTATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
17834496 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
17834561 AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
17834599 TGGTGGATATCGCACTTAGCACCACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATG-AATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
*
17834664 GAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
65 GAATCAGCACATAGCAACCCCCTTT-TCATTTCAAAGATA
* * **
17834704 TGGTGGATCA-CGCACATAGCACCATCC-ATAAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCA-CCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
17834763 TTTATATACA
Statistics
Matches: 253, Mismatches: 10, Indels: 7
0.94 0.04 0.03
Matches are distributed among these distances:
103 128 0.51
104 86 0.34
105 36 0.14
106 3 0.01
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.20
Consensus pattern (103 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
Found at i:17839392 original size:25 final size:24
Alignment explanation
Indices: 17839364--17839455 Score: 105
Period size: 25 Copynumber: 3.7 Consensus size: 24
17839354 TCCGACCCAC
17839364 AGCTCGTGTGAGCATACCGATTCA
1 AGCTCGTGTGAGCATACCGATTCA
*
17839388 TAGCTCGTGAGAGCATACCGATCTACA
1 -AGCTCGTGTGAGCATACCGAT-T-CA
* *
17839415 A-CTCGAGTGAGCATACCAATTCA
1 AGCTCGTGTGAGCATACCGATTCA
*
17839438 CAGCTCGTTTGAGCATAC
1 -AGCTCGTGTGAGCATAC
17839456 ATGTACATGA
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
23 2 0.04
24 2 0.04
25 49 0.86
26 2 0.04
27 2 0.04
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (24 bp):
AGCTCGTGTGAGCATACCGATTCA
Found at i:17847196 original size:25 final size:25
Alignment explanation
Indices: 17847163--17847236 Score: 87
Period size: 25 Copynumber: 3.0 Consensus size: 25
17847153 GCTACGCTTT
*
17847163 GATCCACAGCTCGTGTGAGCATACC
1 GATCTACAGCTCGTGTGAGCATACC
* *
17847188 GATCTACAGCTCGAGTGAGCAAACC
1 GATCTACAGCTCGTGTGAGCATACC
* *
17847213 GAT-TCACAGCTTGTATGAGCATAC
1 GATCT-ACAGCTCGTGTGAGCATAC
17847237 ATGTACATGA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
24 1 0.02
25 40 0.98
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.22
Consensus pattern (25 bp):
GATCTACAGCTCGTGTGAGCATACC
Found at i:17849829 original size:16 final size:17
Alignment explanation
Indices: 17849805--17849840 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
17849795 AACCATAATT
*
17849805 TTTTTAATTT-ATTTAA
1 TTTTGAATTTAATTTAA
17849821 TTTTGAATTTAATTTAA
1 TTTTGAATTTAATTTAA
17849838 TTT
1 TTT
17849841 ATGTTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (17 bp):
TTTTGAATTTAATTTAA
Found at i:17853225 original size:85 final size:84
Alignment explanation
Indices: 17853082--17853296 Score: 261
Period size: 85 Copynumber: 2.5 Consensus size: 84
17853072 ATGCCGTTAT
* *
17853082 AGAACATGACCTTTAGCGGCACCTTTCCCACAAACGCCACTAAAGAATTGACCTTTAGCGGCA-C
1 AGAACATGACCTTTAGCGGC-GCTTTCCCACAAACGCCACTAAAGAAATGACCTTTAGCGG-AGC
17853146 TTTCCCCACAAACGCTGCTAA
64 TTTCCCCACAAACGCTGCTAA
* * *** *
17853167 AGAACATGACCTTTGGCGGCGCTTTCCCACAAATGTTGCTATAGAACATGACCTTTAGCGGAGCT
1 AGAACATGACCTTTAGCGGCGCTTTCCCACAAACGCCACTAAAGAA-ATGACCTTTAGCGGAGCT
**
17853232 TTTTCCACAAACGCTGCTAA
65 TTCCCCACAAACGCTGCTAA
* * * *
17853252 AGATCATGACCTTTAGCAGCGCTTTCCCCAGAAACGCCGCTAAAG
1 AGAACATGACCTTTAGCGGCGCTTT-CCCACAAACGCCACTAAAG
17853297 GTCATGTTCT
Statistics
Matches: 109, Mismatches: 18, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
84 21 0.19
85 74 0.68
86 14 0.13
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (84 bp):
AGAACATGACCTTTAGCGGCGCTTTCCCACAAACGCCACTAAAGAAATGACCTTTAGCGGAGCTT
TCCCCACAAACGCTGCTAA
Found at i:17853302 original size:43 final size:42
Alignment explanation
Indices: 17853082--17853296 Score: 252
Period size: 43 Copynumber: 5.0 Consensus size: 42
17853072 ATGCCGTTAT
* **
17853082 AGAACATGACCTTTAGCGGCACCTTTCCCACAAACGCCACTAA
1 AGAACATGACCTTTAGCGGC-GCTTTCCCACAAACGCTGCTAA
* *
17853125 AGAA-TTGACCTTTAGCGGCACTTTCCCCACAAACGCTGCTAA
1 AGAACATGACCTTTAGCGGCGCTTT-CCCACAAACGCTGCTAA
* * * *
17853167 AGAACATGACCTTTGGCGGCGCTTTCCCACAAATGTTGCTAT
1 AGAACATGACCTTTAGCGGCGCTTTCCCACAAACGCTGCTAA
* *
17853209 AGAACATGACCTTTAGCGGAGCTTTTTCCACAAACGCTGCTAA
1 AGAACATGACCTTTAGCGGCGC-TTTCCCACAAACGCTGCTAA
* * * *
17853252 AGATCATGACCTTTAGCAGCGCTTTCCCCAGAAACGCCGCTAA
1 AGAACATGACCTTTAGCGGCGCTTT-CCCACAAACGCTGCTAA
17853295 AG
1 AG
17853297 GTCATGTTCT
Statistics
Matches: 146, Mismatches: 22, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
41 4 0.03
42 70 0.48
43 72 0.49
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (42 bp):
AGAACATGACCTTTAGCGGCGCTTTCCCACAAACGCTGCTAA
Found at i:17853671 original size:21 final size:21
Alignment explanation
Indices: 17853646--17853686 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
17853636 TGCTTTGCTC
* *
17853646 TGCTTCTCTTGCTGCTGCCTT
1 TGCTTCCCTCGCTGCTGCCTT
17853667 TGCTTCCCTCGCTGCTGCCT
1 TGCTTCCCTCGCTGCTGCCT
17853687 CCGCTTTAAG
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:0.00, C:0.39, G:0.20, T:0.41
Consensus pattern (21 bp):
TGCTTCCCTCGCTGCTGCCTT
Found at i:17853692 original size:21 final size:21
Alignment explanation
Indices: 17853647--17853692 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
17853637 GCTTTGCTCT
* * **
17853647 GCTTCTCTTGCTGCTGCCTTT
1 GCTTCCCTCGCTGCTGCCTCC
17853668 GCTTCCCTCGCTGCTGCCTCC
1 GCTTCCCTCGCTGCTGCCTCC
17853689 GCTT
1 GCTT
17853693 TAAGTTCTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.00, C:0.41, G:0.20, T:0.39
Consensus pattern (21 bp):
GCTTCCCTCGCTGCTGCCTCC
Found at i:17859254 original size:21 final size:22
Alignment explanation
Indices: 17859216--17859256 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
17859206 TTAATTATAC
**
17859216 TTTTTTAATTTATAAATTTATG
1 TTTTTTAATAAATAAATTTATG
17859238 TTTTTTAATAAAT-AATTTA
1 TTTTTTAATAAATAAATTTA
17859257 AATAATTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTTTTAATAAATAAATTTATG
Found at i:17860200 original size:2 final size:2
Alignment explanation
Indices: 17860193--17860243 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
17860183 AAGCATAAGA
17860193 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17860235 AT AT AT AT A
1 AT AT AT AT A
17860244 ACACTGTTCA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17860448 original size:24 final size:24
Alignment explanation
Indices: 17860416--17860468 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
17860406 AGTATTTTAT
17860416 AATATAATATTAATTTTAGATACA
1 AATATAATATTAATTTTAGATACA
*
17860440 AATATAATATTAATTTTAGTTACA
1 AATATAATATTAATTTTAGATACA
17860464 AATAT
1 AATAT
17860469 TATACAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (24 bp):
AATATAATATTAATTTTAGATACA
Found at i:17860914 original size:17 final size:17
Alignment explanation
Indices: 17860894--17860931 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
17860884 TTAAAGTTCA
17860894 CAAGGAAGTAAAGGCTG
1 CAAGGAAGTAAAGGCTG
*
17860911 CAAGGAAGTAGAGGCTG
1 CAAGGAAGTAAAGGCTG
17860928 CAAG
1 CAAG
17860932 TTCCTGGGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.39, C:0.13, G:0.37, T:0.11
Consensus pattern (17 bp):
CAAGGAAGTAAAGGCTG
Found at i:17861219 original size:33 final size:33
Alignment explanation
Indices: 17861172--17861239 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
17861162 ATATACATGT
*
17861172 ATTCATACCTAACACTAATCTCATTTAACTCGA
1 ATTCATACCCAACACTAATCTCATTTAACTCGA
*
17861205 ATTCATACCCAACACTTATCTCATTTAACTCGA
1 ATTCATACCCAACACTAATCTCATTTAACTCGA
17861238 AT
1 AT
17861240 AACATAGATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (33 bp):
ATTCATACCCAACACTAATCTCATTTAACTCGA
Found at i:17861893 original size:15 final size:14
Alignment explanation
Indices: 17861861--17861900 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
17861851 AATTGGGAAA
*
17861861 TTGGGGAAAATAAT
1 TTGGGGAAAATAAC
17861875 TTGGGGAAGAATAAC
1 TTGGGGAA-AATAAC
*
17861890 TTGGGGGAAAT
1 TTGGGGAAAAT
17861901 TGGGGGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.38, C:0.03, G:0.35, T:0.25
Consensus pattern (14 bp):
TTGGGGAAAATAAC
Found at i:17861904 original size:25 final size:22
Alignment explanation
Indices: 17861875--17861931 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 22
17861865 GGAAAATAAT
*
17861875 TTGGGGAAGAATAACTTGGGGGAAA
1 TTGGGGAA-AAGAACTT--GGGAAA
*
17861900 TTGGGGGAAAAGAAGTTGGGAAA
1 TT-GGGGAAAAGAACTTGGGAAA
17861923 TTGGGGAAA
1 TTGGGGAAA
17861932 TGAAATCGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 7 0.24
23 8 0.28
25 8 0.28
26 6 0.21
ACGTcount: A:0.37, C:0.02, G:0.42, T:0.19
Consensus pattern (22 bp):
TTGGGGAAAAGAACTTGGGAAA
Found at i:17861944 original size:23 final size:23
Alignment explanation
Indices: 17861894--17861947 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
17861884 AATAACTTGG
* *
17861894 GGGAAATTGGGGGAAAAGAAGTT
1 GGGAAATTGGGGGAAAAGAAATC
*
17861917 GGGAAATT-GGGGAAATGAAATC
1 GGGAAATTGGGGGAAAAGAAATC
17861939 GTGGAAATT
1 G-GGAAATT
17861948 TGACTTGGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 12 0.44
23 15 0.56
ACGTcount: A:0.39, C:0.02, G:0.39, T:0.20
Consensus pattern (23 bp):
GGGAAATTGGGGGAAAAGAAATC
Found at i:17862171 original size:12 final size:11
Alignment explanation
Indices: 17862154--17862187 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
17862144 ACAGCATTTT
17862154 AGTAAAAACGCC
1 AGTAAAAACG-C
17862166 AGTAAAAACGC
1 AGTAAAAACGC
17862177 AGATAAAAACG
1 AG-TAAAAACG
17862188 TCAAATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 3 0.14
12 18 0.86
ACGTcount: A:0.56, C:0.18, G:0.18, T:0.09
Consensus pattern (11 bp):
AGTAAAAACGC
Found at i:17862429 original size:116 final size:113
Alignment explanation
Indices: 17862051--17862459 Score: 374
Period size: 116 Copynumber: 3.5 Consensus size: 113
17862041 CACTAATGCA
* * * * *
17862051 ACTAAAAATGCAGCTTAAAACGACAACATTTTGCAAACTCTTAAAACATATTTGCAGTGTTTTTT
1 ACTAAAAACGCAGC-TAAAACGACAACGTTTTGCAAACTCTTAATACATATTCGCAGCG-TTTTT
** * *
17862116 TGTGAAAA-CCACTAACTTATATCCTTTTACAGCATTTTAGTAAAAACGCC
64 TGTGAAAAGCCACTAACGCATATCCTTTTGCGGCATTTTAGT-AAAACGCC
* * * ** * * *
17862166 AGTAAAAACGCAGATAAAAACGTCAAATTTTTGCAAACTCTTAA-ACCAAATTCGCGGCATTTTT
1 ACTAAAAACGCAGCT-AAAACGACAACGTTTTGCAAACTCTTAATA-CATATTCGCAGCGTTTTT
* ** *
17862230 TGTGAAAAGGCCACTAACGCATATCCTTTTGTGGTTTTTTAGTAAAAGTGCC
64 TGTGAAAA-GCCACTAACGCATATCCTTTTGCGGCATTTTAGTAAAA-CGCC
* ** *
17862282 ACCAAAAGTGCAGCTGAAAACGAC-ACTGTTTTGCAAACTCTTAATACATATTTGCAGCGTTTTT
1 ACTAAAAACGCAGCT-AAAACGACAAC-GTTTTGCAAACTCTTAATACATATTCGCAGCGTTTTT
* * *
17862346 GGTGAAAACGCCACTAACGCATAACCTTTTGCGGCGTTTTAGTCAAAACGCC
64 TGTGAAAA-GCCACTAACGCATATCCTTTTGCGGCATTTTAGT-AAAACGCC
** * ** * *
17862398 ACTAAAAACATAGCTACAAATGACAACGTTTTGCATTCTTTTAATACATATTCGCCGCGTTT
1 ACTAAAAACGCAGCTA-AAACGACAACGTTTTGCAAACTCTTAATACATATTCGCAGCGTTT
17862460 GGACCAAAAA
Statistics
Matches: 234, Mismatches: 50, Indels: 19
0.77 0.17 0.06
Matches are distributed among these distances:
114 15 0.06
115 50 0.21
116 162 0.69
117 7 0.03
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (113 bp):
ACTAAAAACGCAGCTAAAACGACAACGTTTTGCAAACTCTTAATACATATTCGCAGCGTTTTTTG
TGAAAAGCCACTAACGCATATCCTTTTGCGGCATTTTAGTAAAACGCC
Found at i:17862991 original size:7 final size:7
Alignment explanation
Indices: 17862981--17863043 Score: 54
Period size: 7 Copynumber: 8.7 Consensus size: 7
17862971 AAATTTATTT
17862981 TTTAGGG
1 TTTAGGG
*
17862988 TTTATGG
1 TTTAGGG
* *
17862995 TATATGGT
1 TTTA-GGG
17863003 TTTAGGG
1 TTTAGGG
17863010 TTTAGGG
1 TTTAGGG
*
17863017 TTTAAGG
1 TTTAGGG
* *
17863024 TCTAAAGG
1 T-TTAGGG
17863032 TTTAGGG
1 TTTAGGG
17863039 TTTAG
1 TTTAG
17863044 AGAAAGCCAT
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
7 34 0.77
8 10 0.23
ACGTcount: A:0.21, C:0.02, G:0.33, T:0.44
Consensus pattern (7 bp):
TTTAGGG
Found at i:17863013 original size:29 final size:29
Alignment explanation
Indices: 17862981--17863043 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
17862971 AAATTTATTT
* *
17862981 TTTAGGGTTTATGGTAT-ATGGTTTTAGGG
1 TTTAGGGTTTAAGGTATAAAGG-TTTAGGG
*
17863010 TTTAGGGTTTAAGGTCTAAAGGTTTAGGG
1 TTTAGGGTTTAAGGTATAAAGGTTTAGGG
17863039 TTTAG
1 TTTAG
17863044 AGAAAGCCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 27 0.90
30 3 0.10
ACGTcount: A:0.21, C:0.02, G:0.33, T:0.44
Consensus pattern (29 bp):
TTTAGGGTTTAAGGTATAAAGGTTTAGGG
Found at i:17863501 original size:41 final size:41
Alignment explanation
Indices: 17863444--17863603 Score: 212
Period size: 41 Copynumber: 3.9 Consensus size: 41
17863434 CATATTCGCG
* * * *
17863444 GCGTTTGGACCCAAAACGCTATTATTGCTCAACGTTTTGCA
1 GCGTTTGGACCAAAAACGCCACTATTGCTCAACTTTTTGCA
* * *
17863485 GCGTTTGGACCAAAAACACCACTATTGCTCAAATTTTTGCG
1 GCGTTTGGACCAAAAACGCCACTATTGCTCAACTTTTTGCA
* * *
17863526 GCGTTTGGACAAAAAATGCCACTATTGCTCAACTTTTTGCT
1 GCGTTTGGACCAAAAACGCCACTATTGCTCAACTTTTTGCA
* *
17863567 GCGTTTGGACCAAAAATGCCACTATTGCTCACCTTTT
1 GCGTTTGGACCAAAAACGCCACTATTGCTCAACTTTT
17863604 ACAGTGTTTT
Statistics
Matches: 105, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 105 1.00
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.32
Consensus pattern (41 bp):
GCGTTTGGACCAAAAACGCCACTATTGCTCAACTTTTTGCA
Found at i:17865417 original size:25 final size:26
Alignment explanation
Indices: 17865380--17865430 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
17865370 GTTGTAAATA
17865380 AGAAAAATATCTTTAGA-AATTTTCT
1 AGAAAAATATCTTTAGAGAATTTTCT
* *
17865405 AGAATAATCTCTTTAGAGAATTTTCT
1 AGAAAAATATCTTTAGAGAATTTTCT
17865431 CTCTACAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (26 bp):
AGAAAAATATCTTTAGAGAATTTTCT
Found at i:17865588 original size:38 final size:38
Alignment explanation
Indices: 17865546--17865646 Score: 168
Period size: 38 Copynumber: 2.6 Consensus size: 38
17865536 TAATATTATA
17865546 TTAATATAATATTTATTAAGATAAATATTAGATTAAAT
1 TTAATATAATATTTATTAAGATAAATATTAGATTAAAT
17865584 TTAATATAATATTTATTAAGATAAATATTAGATTAAAT
1 TTAATATAATATTTATTAAGATAAATATTAGATTAAAT
*
17865622 TTAATATTAA-ATCTTATTAAAATAA
1 TTAATA-TAATAT-TTATTAAGATAA
17865647 TAGAATGTTT
Statistics
Matches: 60, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
38 46 0.77
39 14 0.23
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.45
Consensus pattern (38 bp):
TTAATATAATATTTATTAAGATAAATATTAGATTAAAT
Found at i:17865719 original size:20 final size:18
Alignment explanation
Indices: 17865667--17865778 Score: 70
Period size: 20 Copynumber: 6.1 Consensus size: 18
17865657 ATCTACAAGA
17865667 TTAATATTAAATTAA-AT
1 TTAATATTAAATTAATAT
17865684 TTAATATTAAGA-TAATCACT
1 TTAATATTAA-ATTAAT-A-T
*
17865704 TTAATATTAAATTAATAAA
1 TTAATATTAAATTAAT-AT
* * *
17865723 CTACTATTAAGATAAATA-
1 TTAATATTAA-ATTAATAT
*
17865741 TTAA-ATTAAATCAAATAT
1 TTAATATTAAAT-TAATAT
* *
17865759 TAAACTATTAAAATAATAT
1 TTAA-TATTAAATTAATAT
17865778 T
1 T
17865779 ATTTTTGGAA
Statistics
Matches: 75, Mismatches: 10, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
16 2 0.03
17 23 0.31
18 6 0.08
19 17 0.23
20 27 0.36
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (18 bp):
TTAATATTAAATTAATAT
Found at i:17869730 original size:24 final size:24
Alignment explanation
Indices: 17869693--17869743 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
17869683 TATCTCATTA
*
17869693 AATATCTATTTTAT-AAATGTTTAT
1 AATATCTATATTATGAAATG-TTAT
* *
17869717 AATATTTATATTATGTAATGTTAT
1 AATATCTATATTATGAAATGTTAT
17869741 AAT
1 AAT
17869744 TGTGATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (24 bp):
AATATCTATATTATGAAATGTTAT
Found at i:17873097 original size:34 final size:35
Alignment explanation
Indices: 17873039--17873105 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
17873029 CAAACACCAG
* *
17873039 AAAATATTTTCCAGTAAATGATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
17873074 AAAACATTTTTCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
17873106 TATTTTACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:17876386 original size:12 final size:12
Alignment explanation
Indices: 17876371--17876409 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
17876361 TGCCAGGCCG
17876371 TGTGCTAAGCCA
1 TGTGCTAAGCCA
17876383 TGTGCTAAGCCA
1 TGTGCTAAGCCA
*
17876395 TGTGCTAGGCCA
1 TGTGCTAAGCCA
17876407 TGT
1 TGT
17876410 AACGGCCTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.21, C:0.23, G:0.28, T:0.28
Consensus pattern (12 bp):
TGTGCTAAGCCA
Found at i:17876518 original size:70 final size:68
Alignment explanation
Indices: 17876395--17876533 Score: 188
Period size: 70 Copynumber: 2.0 Consensus size: 68
17876385 TGCTAAGCCA
* * *
17876395 TGTGCTAGGCCATGTAACGGCCTGACTTGCAGCTCTTTGAAAGCTACAGGGGACACATGGCTATG
1 TGTGCTAGGCCATGTAACAGCCTGACTTGCAACTCTTTGAAAGCTACAAGGGACACATGG--ATG
17876460 TGTTG
64 TGTTG
* * * * *
17876465 TGTGCTAGGCCGTGTAACAGCTTGACTTGCAACTCTTTTAAAGTTATAAGGGACACATGGATGTG
1 TGTGCTAGGCCATGTAACAGCCTGACTTGCAACTCTTTGAAAGCTACAAGGGACACATGGATGTG
17876530 TTG
66 TTG
17876533 T
1 T
17876534 CTGACCATGT
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
68 9 0.15
70 52 0.85
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (68 bp):
TGTGCTAGGCCATGTAACAGCCTGACTTGCAACTCTTTGAAAGCTACAAGGGACACATGGATGTG
TTG
Found at i:17881742 original size:51 final size:50
Alignment explanation
Indices: 17881623--17881855 Score: 270
Period size: 51 Copynumber: 4.6 Consensus size: 50
17881613 TCGATAAACG
* * * *
17881623 TAGTAGCCTTCACGTAGTACTACACACGTGATCAAG-TTTTACGGTTCACG
1 TAGTAGCCTTCACATAGTACTACACACGTGACCAAGATTTT-CGGTACACA
17881673 TAGTAGCCTTCACATAGTACTACACACGTGACCAAAGATTTTCGGTACACA
1 TAGTAGCCTTCACATAGTACTACACACGTGACC-AAGATTTTCGGTACACA
* * ** * * *
17881724 TAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACG
1 TAGTAGCCTTCACATAGTACTACACACGTGACCAAGATTT-TCGGTACACA
* * * *
17881775 TAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTTGGTACATA
1 TAGTAGCCTTCACATAGTACTACACACGTGACC-AAGATTTTCGGTACACA
* *
17881826 TTGTAGCCTTCACACAGTACTACACACGTG
1 TAGTAGCCTTCACATAGTACTACACACGTG
17881856 TTCATCGATA
Statistics
Matches: 156, Mismatches: 23, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
50 36 0.23
51 112 0.72
52 8 0.05
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (50 bp):
TAGTAGCCTTCACATAGTACTACACACGTGACCAAGATTTTCGGTACACA
Found at i:17881798 original size:102 final size:101
Alignment explanation
Indices: 17881623--17881855 Score: 331
Period size: 102 Copynumber: 2.3 Consensus size: 101
17881613 TCGATAAACG
* * ** * *
17881623 TAGTAGCCTTCACGTAGTACTACACACGTGATCAAGTTTTACGGTTCACGTAGTAGCCTTCACAT
1 TAGTAGCCTTCACATAGTACTACACACGTGACCAACATTTACGATTCACGTAGTAGCCTTCACAC
17881688 AGTACTACACACGTGACCAAAGATTTTCGGTACACA
66 AGTACTACACACGTGACCAAAGATTTTCGGTACACA
* * *
17881724 TAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCCTTCACA
1 TAGTAGCCTTCACATAGTACTACACACGTGACCAACATTTA-CGATTCACGTAGTAGCCTTCACA
* * *
17881789 CAGTACTACACACGTGACCAAAGCTTTTTGGTACATA
65 CAGTACTACACACGTGACCAAAGATTTTCGGTACACA
* *
17881826 TTGTAGCCTTCACACAGTACTACACACGTG
1 TAGTAGCCTTCACATAGTACTACACACGTG
17881856 TTCATCGATA
Statistics
Matches: 116, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
101 35 0.30
102 81 0.70
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (101 bp):
TAGTAGCCTTCACATAGTACTACACACGTGACCAACATTTACGATTCACGTAGTAGCCTTCACAC
AGTACTACACACGTGACCAAAGATTTTCGGTACACA
Found at i:17882376 original size:30 final size:31
Alignment explanation
Indices: 17882322--17882386 Score: 89
Period size: 30 Copynumber: 2.1 Consensus size: 31
17882312 GCTTCGACTC
*
17882322 AACTTTTGTCAAAATTACGATTTTGTCCCTA
1 AACTTTTGTCAAAATTACGATTTTGTCCCCA
*
17882353 AACTTTTG-CATAATTAC-ATTTTTGTCCCCA
1 AACTTTTGTCAAAATTACGA-TTTTGTCCCCA
17882383 AACT
1 AACT
17882387 CGAAAATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 1 0.03
30 22 0.71
31 8 0.26
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.42
Consensus pattern (31 bp):
AACTTTTGTCAAAATTACGATTTTGTCCCCA
Found at i:17886715 original size:39 final size:39
Alignment explanation
Indices: 17886672--17886747 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
17886662 GCTATCAAGA
17886672 GTACCAAAGTACAACAGGGGCACGTAAGTGCGATTAGGG
1 GTACCAAAGTACAACAGGGGCACGTAAGTGCGATTAGGG
* *
17886711 GTACCGAAGTACAATAGGGGCACGTAAGTGCGATTAG
1 GTACCAAAGTACAACAGGGGCACGTAAGTGCGATTAG
17886748 AGATATAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.33, C:0.17, G:0.33, T:0.17
Consensus pattern (39 bp):
GTACCAAAGTACAACAGGGGCACGTAAGTGCGATTAGGG
Found at i:17886720 original size:20 final size:20
Alignment explanation
Indices: 17886687--17886747 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
17886677 AAAGTACAAC
17886687 AGGGGCACGTAAGTGCGATT
1 AGGGGCACGTAAGTGCGATT
* * *
17886707 AGGGGTACCG-AAGTAC-AAT
1 AGGGGCA-CGTAAGTGCGATT
17886726 AGGGGCACGTAAGTGCGATT
1 AGGGGCACGTAAGTGCGATT
17886746 AG
1 AG
17886748 AGATATAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
18 2 0.06
19 13 0.41
20 15 0.47
21 2 0.06
ACGTcount: A:0.30, C:0.15, G:0.38, T:0.18
Consensus pattern (20 bp):
AGGGGCACGTAAGTGCGATT
Found at i:17886739 original size:19 final size:19
Alignment explanation
Indices: 17886678--17886739 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
17886668 AAGAGTACCA
*
17886678 AAGTACAACAGGGGCACGT
1 AAGTACAATAGGGGCACGT
* * *
17886697 AAGTGCGATTAGGGGTACCG-
1 AAGTAC-AATAGGGGCA-CGT
17886717 AAGTACAATAGGGGCACGT
1 AAGTACAATAGGGGCACGT
17886736 AAGT
1 AAGT
17886740 GCGATTAGAG
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
18 2 0.06
19 17 0.52
20 12 0.36
21 2 0.06
ACGTcount: A:0.34, C:0.16, G:0.34, T:0.16
Consensus pattern (19 bp):
AAGTACAATAGGGGCACGT
Found at i:17892018 original size:11 final size:11
Alignment explanation
Indices: 17892002--17892026 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
17891992 TAGTCCCATA
17892002 AAAAATAAAAT
1 AAAAATAAAAT
17892013 AAAAATAAAAT
1 AAAAATAAAAT
17892024 AAA
1 AAA
17892027 TATTTTCATG
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:17892617 original size:46 final size:45
Alignment explanation
Indices: 17892567--17892656 Score: 101
Period size: 45 Copynumber: 2.0 Consensus size: 45
17892557 AGAATGAATA
*
17892567 GAAATAAAGAAATGAAAAACATTT-AGAAATGATTATGGTTTTCTCC
1 GAAATAAAGAAATG-AAAACATTTGA-AAATGAATATGGTTTTCTCC
** * * *
17892613 GAAATGGAGAAATGGAATCATTTGAAAATGAATGTGGTTTTCTC
1 GAAATAAAGAAATGAAAACATTTGAAAATGAATATGGTTTTCTC
17892657 AAAAATGGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
45 24 0.65
46 13 0.35
ACGTcount: A:0.41, C:0.08, G:0.20, T:0.31
Consensus pattern (45 bp):
GAAATAAAGAAATGAAAACATTTGAAAATGAATATGGTTTTCTCC
Found at i:17894729 original size:25 final size:24
Alignment explanation
Indices: 17894683--17894729 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
17894673 TGAGCATCCT
* *
17894683 GATATTGGCTCTCTTGAGCTTCTC
1 GATATTGGCTCTCATGAACTTCTC
*
17894707 GATATTTGGCTTTCATGAACTTC
1 GATA-TTGGCTCTCATGAACTTC
17894730 CCGTCATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 4 0.21
25 15 0.79
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.43
Consensus pattern (24 bp):
GATATTGGCTCTCATGAACTTCTC
Found at i:17894820 original size:26 final size:27
Alignment explanation
Indices: 17894766--17894821 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
17894756 CGACATATGG
*
17894766 CTCTAACGAGCTTCCTTATTTAAGGCT
1 CTCTAACGAGCTTCCTCATTTAAGGCT
* * *
17894793 CTCTAATGAGCTTCC-CGTTTATGGCT
1 CTCTAACGAGCTTCCTCATTTAAGGCT
17894819 CTC
1 CTC
17894822 CGGAGCTTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.18, C:0.29, G:0.16, T:0.38
Consensus pattern (27 bp):
CTCTAACGAGCTTCCTCATTTAAGGCT
Found at i:17894875 original size:24 final size:24
Alignment explanation
Indices: 17894824--17894876 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
17894814 TGGCTCTCCG
* *
17894824 GAGCTTCCTGATATTGGCTTGCAT
1 GAGCTTCCTGATATTGGCTTGAAA
*
17894848 GAGCTT-CTCGATTTTGGCTTGAAA
1 GAGCTTCCT-GATATTGGCTTGAAA
17894872 GAGCT
1 GAGCT
17894877 ACCCGTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 2 0.08
24 23 0.92
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (24 bp):
GAGCTTCCTGATATTGGCTTGAAA
Found at i:17901872 original size:24 final size:24
Alignment explanation
Indices: 17901836--17901952 Score: 83
Period size: 25 Copynumber: 4.8 Consensus size: 24
17901826 GACACACTGC
* * * *
17901836 AGCTCACAAGAGCGTCCCGTTTTT
1 AGCTCTCATGAGCATCCCGTATTT
17901860 AGCTCTCATGAGCATCCCG-ATATT
1 AGCTCTCATGAGCATCCCGTAT-TT
* * * *
17901884 GGCTCTCTTGAGCTTCTCGATATTT
1 AGCTCTCATGAGCATCCCG-TATTT
* * * *
17901909 GGCTCTCACGAGCTTCCCATCATTT
1 AGCTCTCATGAGCATCCCGT-ATTT
*
17901934 AGCTCTTATGAGCATCCCG
1 AGCTCTCATGAGCATCCCG
17901953 ACATATGGCT
Statistics
Matches: 72, Mismatches: 17, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
23 1 0.01
24 34 0.47
25 35 0.49
26 2 0.03
ACGTcount: A:0.19, C:0.30, G:0.19, T:0.32
Consensus pattern (24 bp):
AGCTCTCATGAGCATCCCGTATTT
Found at i:17901921 original size:25 final size:25
Alignment explanation
Indices: 17901861--17902026 Score: 124
Period size: 25 Copynumber: 6.6 Consensus size: 25
17901851 CCCGTTTTTA
*
17901861 GCTCTCATGAGCATCCCGATA-TTG
1 GCTCTCATGAGCTTCCCGATATTTG
* *
17901885 GCTCTCTTGAGCTTCTCGATATTTG
1 GCTCTCATGAGCTTCCCGATATTTG
* *
17901910 GCTCTCACGAGCTTCCC-ATCATTTA
1 GCTCTCATGAGCTTCCCGAT-ATTTG
* * * *
17901935 GCTCTTATGAGCATCCCGACATATG
1 GCTCTCATGAGCTTCCCGATATTTG
* * * *
17901960 GCTCTTACGAGCTTCCTGAT-TTAAG
1 GCTCTCATGAGCTTCCCGATATT-TG
* *
17901985 GCTCTCTCATTAGCTTCCTGATA-TTG
1 G--CTCTCATGAGCTTCCCGATATTTG
*
17902011 GCTCACATGAGCTTCC
1 GCTCTCATGAGCTTCC
17902027 TGAGTATGGC
Statistics
Matches: 110, Mismatches: 25, Indels: 14
0.74 0.17 0.09
Matches are distributed among these distances:
24 34 0.31
25 56 0.51
26 3 0.03
27 17 0.15
ACGTcount: A:0.19, C:0.29, G:0.18, T:0.34
Consensus pattern (25 bp):
GCTCTCATGAGCTTCCCGATATTTG
Done.