Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008136.1 Hibiscus syriacus cultivar Beakdansim tig00110691_pilon, whole genome shotgun sequence
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: 1585607
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 9
Found at i:1125562 original size:17 final size:17
Alignment explanation
Indices: 1125539--1125590 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
1125529 TGGGTCTGTA
1125539 ATAATAAATAAAATTAT
1 ATAATAAATAAAATTAT
* *
1125556 TTAAT-AATAATAATAAT
1 ATAATAAATAA-AATTAT
* *
1125573 ATAATAATTATAATTAT
1 ATAATAAATAAAATTAT
1125590 A
1 A
1125591 ATTATAATTA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
16 5 0.19
17 19 0.70
18 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATAATAAATAAAATTAT
Found at i:1125563 original size:3 final size:3
Alignment explanation
Indices: 1125557--1125637 Score: 78
Period size: 3 Copynumber: 27.7 Consensus size: 3
1125547 TAAAATTATT
* * * *
1125557 TAA TAA TAA TAA TAA T-A TAA TAA TTA TAA TTA TAA TTA TAA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
1125604 TTA TAA TTA TAA TAA TAA TAA -AA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA
1125638 TTCAAATGAA
Statistics
Matches: 62, Mismatches: 12, Indels: 8
0.76 0.15 0.10
Matches are distributed among these distances:
2 6 0.10
3 54 0.87
4 2 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:1125591 original size:12 final size:12
Alignment explanation
Indices: 1125557--1125622 Score: 87
Period size: 12 Copynumber: 5.3 Consensus size: 12
1125547 TAAAATTATT
* *
1125557 TAATAATAATAA
1 TAATTATAATTA
1125569 TAATATAATAATTA
1 TAAT-T-ATAATTA
1125583 TAATTATAATTA
1 TAATTATAATTA
1125595 TAATTATAATTA
1 TAATTATAATTA
*
1125607 TAATTATAATAA
1 TAATTATAATTA
1125619 TAAT
1 TAAT
1125623 AAAATATAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
12 38 0.78
13 1 0.02
14 10 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAATTATAATTA
Found at i:1125978 original size:120 final size:120
Alignment explanation
Indices: 1125854--1126136 Score: 530
Period size: 120 Copynumber: 2.4 Consensus size: 120
1125844 ATGTAATCTA
* **
1125854 GCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTA
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTA
1125919 TGAACTCCTTCTGGAAATGCTGATGATGATATATCTCTTTATGTGATAGAGTTAT
66 TGAACTCCTTCTGGAAATGCTGATGATGATATATCTCTTTATGTGATAGAGTTAT
1125974 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTA
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTA
*
1126039 TGAACTCCTTCTGGAAATGCTGATGATGATATATCTCTTTCTGTGATAGAGTTAT
66 TGAACTCCTTCTGGAAATGCTGATGATGATATATCTCTTTATGTGATAGAGTTAT
1126094 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTC
1126137 CTTCTTCAGA
Statistics
Matches: 159, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 159 1.00
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (120 bp):
GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTCCTTCTGGAAATGCTGATGATGATATATCTCTTTATGTGATAGAGTTAT
Found at i:1126563 original size:113 final size:113
Alignment explanation
Indices: 1126364--1127624 Score: 1895
Period size: 113 Copynumber: 11.2 Consensus size: 113
1126354 CTTCAGATGA
* * * * * *
1126364 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAAGCAAAAGGTTGAACAAA
1 ATTATGAACTCTATCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAG
* * *
1126429 TTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGAGTTCTTCTC
66 CTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * ** *
1126477 ATTATGAACTCTAACTTGCACTGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAG
1 ATTATGAACTCTATCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAG
1126542 CTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG---TTCTC
66 CTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * ** * *
1126587 ATTATGATCTTTCTCTGGAAAAAGCTGATCCATCAAGTGATGGATTCAAGTAAAAAGTTGAACAA
1 ATTATGAACTCTATCTGG-AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAA
* *
1126652 GTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTT
65 GCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * *
1126701 ATTATAAACTCTACCTGGAAATGCTGATCCATCAAATGATGGATTTGAGAAAAAGGTTGAACAAG
1 ATTATGAACTCTATCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAG
*
1126766 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
66 CTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
1126814 ATTATGAACTCTACCTGGAAATGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAG
1 ATTATGAACTCTATCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAG
* *
1126879 CTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCGC
66 CTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * ** *
1126927 ATTATGAACTTTCTCTGGAAAAAGTTGATCCATCAAGTGATAGATTCAAGCAAAAAGTTGAACAA
1 ATTATGAACTCTATCTGG-AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAA
*
1126992 GTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
65 GCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
1127041 ATTATAAACTCTACCTGGAAATGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAG
1 ATTATGAACTCTATCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAG
1127106 CTCTTCTCATTATGAACTTCTT-TTCCTTCTTCAGATGAGTTCTTCTC
66 CTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
1127153 ATTATGAACTCTACCTGGAAATGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAG
1 ATTATGAACTCTATCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAG
1127218 CTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
66 CTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * **
1127266 ATTATGAACTTTCTCTGGAAAAAGCTGATCCATCAAGTGATGGATTCAAGCAAAAGGTTGAACAA
1 ATTATGAACTCTATCTGG-AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAA
*
1127331 GCTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTC
65 GCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
1127380 A-TATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAG
1 ATTATGAACTCTATCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAG
1127444 CTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
66 CTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * *
1127492 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGGATTTTAGCAAAAGGTTGAACAAG
1 ATTATGAACTCTATCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAG
* *
1127557 CTCTTCTCATTATGAACTTCTTCTTCATTCTTCATATGAGTTCTTCTC
66 CTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
1127605 ATTATGAACCCT-TCTGGAAA
1 ATTATGAACTCTATCTGGAAA
1127625 TGTTTTAAGA
Statistics
Matches: 1053, Mismatches: 87, Indels: 17
0.91 0.08 0.01
Matches are distributed among these distances:
110 18 0.02
111 78 0.07
112 212 0.20
113 536 0.51
114 209 0.20
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.37
Consensus pattern (113 bp):
ATTATGAACTCTATCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAG
CTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
Found at i:1126947 original size:226 final size:226
Alignment explanation
Indices: 1126150--1127626 Score: 2143
Period size: 226 Copynumber: 6.6 Consensus size: 226
1126140 CTTCAGATGA
* * *
1126150 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAAGCAAAAGGTTGAACAAA
1 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTAAGCAAAAGGTTGAACAAG
* * *
1126215 TTCTTCTCATTA-GAATTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAAC--TCTCTG
66 CTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * ** * * *
1126277 GCACTGTTGATCCACCGGGTGATGAATTTAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
131 GAAATGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
1126342 TTCTTCTTCCTTCTTCAGATGA---------
196 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
1126364 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAAGCAAAAGGTTGAACAAA
1 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTAAGCAAAAGGTTGAACAAG
* * * * ** *
1126429 TTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTT
66 CTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * *
1126494 GCACTGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
131 GAAATGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
1126559 TTCTTCTTCCTTCTTCAGATGAG---TTCTC
196 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
1126587 ATTATGATCTTTCTCTGGAAAAAGCTGATCCATCAAGTGATGGATTCAAGTAAAAAGTTGAACAA
1 ATTATGAACTTTCTCTGG-AAAAGCTGATCCATCAAGTGATGGATTTAAGCAAAAGGTTGAACAA
* * * *
1126652 GTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATAAACTCTAC-C
65 GCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTC
* * *
1126716 TGGAAATGCTGATCCATCAAATGATGGATTTGAGAAAAAGGTTGAACAAGTTCTTCTCATTATGA
129 TGGAAATGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGA
1126781 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
194 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
1126814 ATTATGAACTCTAC-CTGGAAATGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAA
1 ATTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTAAGCAAAAGGTTGAACAA
* *
1126878 GCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCGCATTATGAACTTTCTCT
65 GCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
* * * ** * *
1126943 GGAAAAAGTTGATCCATCAAGTGATAGATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGA
130 GG-AAATGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGA
1127008 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
194 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
1127041 ATTATAAACTCTAC-CTGGAAATGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAA
1 ATTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTAAGCAAAAGGTTGAACAA
*
1127105 GCTCTTCTCATTATGAACTTCTT-TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-C
65 GCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTC
1127168 TGGAAATGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGA
129 TGGAAATGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGA
1127233 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
194 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
1127266 ATTATGAACTTTCTCTGGAAAAAGCTGATCCATCAAGTGATGGATTCAAGCAAAAGGTTGAACAA
1 ATTATGAACTTTCTCTGG-AAAAGCTGATCCATCAAGTGATGGATTTAAGCAAAAGGTTGAACAA
*
1127331 GCTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCA-TATGAACTTTCTCT
65 GCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
*
1127395 GGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAA
130 GGAAATGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAA
1127460 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
195 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
1127492 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGGATTTTAGCAAAAGGTTGAACAAG
1 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTAAGCAAAAGGTTGAACAAG
* * **
1127557 CTCTTCTCATTATGAACTTCTTCTTCATTCTTCATATGAGTTCTTCTCATTATGAACCCT-TCTG
66 CTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1127621 GAAATG
131 GAAATG
1127627 TTTTAAGAAA
Statistics
Matches: 1162, Mismatches: 78, Indels: 35
0.91 0.06 0.03
Matches are distributed among these distances:
214 77 0.07
215 44 0.04
217 84 0.07
223 17 0.01
224 181 0.16
225 205 0.18
226 334 0.29
227 218 0.19
228 2 0.00
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.37
Consensus pattern (226 bp):
ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTAAGCAAAAGGTTGAACAAG
CTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAATGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
Found at i:1127300 original size:339 final size:340
Alignment explanation
Indices: 1126094--1127613 Score: 2283
Period size: 339 Copynumber: 4.5 Consensus size: 340
1126084 ATAGAGTTAT
1126094 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA---------
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
1126150 ATTATGAACT-TTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAAGCAAAAGGTTGAACAA
66 ATTATGAACTCTAC-CTGGAAATGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAA
** * *
1126214 ATTCTTCTCATTA-GAATTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAAC--TCTCT
130 GCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
* ** * * ** * * *
1126276 GG-CACTGTTGATCCACCGGGTGATGAATTTAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGA
195 GGAAAAAGCTGATCCATCAAGTGATGGATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGA
* * *
1126340 ACTTCTTCTTCCTTCTTCAGATGA---------ATTATGAACTTTCTCTGGAAAAGTTGATCCAT
260 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATAAACTTACTCTGGAAAAGCTGATCCAT
* *
1126396 CAAGTGATGAATTTAA
325 CAAGTGATGGATTTGA
** * *
1126412 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
1126477 ATTATGAACTCTAACTTGCACTGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAG
66 ATTATGAACTCTACCTGGAAATGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAG
*
1126542 CTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG---TTCTCATTATGATCTTTCTCTG
131 CTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*
1126604 GAAAAAGCTGATCCATCAAGTGATGGATTCAAGTAAAAAGTTGAACAAGTTCTTCTCATTATGAA
196 GAAAAAGCTGATCCATCAAGTGATGGATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAA
* *
1126669 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATAAACTCTAC-CTGGAAATGCTGATCCAT
261 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATAAACT-TACTCTGGAAAAGCTGATCCAT
*
1126733 CAAATGATGGATTTGA
325 CAAGTGATGGATTTGA
* *
1126749 GAAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
1126814 ATTATGAACTCTACCTGGAAATGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAG
66 ATTATGAACTCTACCTGGAAATGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAG
* *
1126879 CTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCGCATTATGAACTTTCTCTG
131 CTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
1126944 GAAAAAGTTGATCCATCAAGTGATAGATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAA
196 GAAAAAGCTGATCCATCAAGTGATGGATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAA
*
1127009 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATAAACTCTAC-CTGGAAATGCTGATCCAT
261 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATAAACT-TACTCTGGAAAAGCTGATCCAT
1127073 CAAGTGATGGATTTGA
325 CAAGTGATGGATTTGA
1127089 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTT-TTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
1127153 ATTATGAACTCTACCTGGAAATGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAG
66 ATTATGAACTCTACCTGGAAATGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAG
1127218 CTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
131 CTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
1127283 GAAAAAGCTGATCCATCAAGTGATGGATTCAAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAA
196 GAAAAAGCTGATCCATCAAGTGATGGATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAA
* * *
1127348 CTTCTTCTTCATTCTTCAGATGAGTTCTTCTCA-TATGAACTTTCTCTGGAAAAGCTGATCCATC
261 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATAAACTTACTCTGGAAAAGCTGATCCATC
1127412 AAGTGATGGATTTGA
326 AAGTGATGGATTTGA
1127427 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
1127492 ATTATGAACT-TTCTCTGGAAAAGTTGATCCATCGAGTGATGGATTTTAGCAAAAGGTTGAACAA
66 ATTATGAACTCTAC-CTGGAAATGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAA
* *
1127556 GCTCTTCTCATTATGAACTTCTTCTTCATTCTTCATATGAGTTCTTCTCATTATGAAC
130 GCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
1127614 CCTTCTGGAA
Statistics
Matches: 1101, Mismatches: 71, Indels: 39
0.91 0.06 0.03
Matches are distributed among these distances:
318 52 0.05
325 13 0.01
327 72 0.07
328 101 0.09
337 200 0.18
338 83 0.08
339 383 0.35
340 197 0.18
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.37
Consensus pattern (340 bp):
GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTCTACCTGGAAATGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAG
CTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAAAAGCTGATCCATCAAGTGATGGATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAA
CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATAAACTTACTCTGGAAAAGCTGATCCATC
AAGTGATGGATTTGA
Found at i:1128383 original size:22 final size:22
Alignment explanation
Indices: 1128358--1128412 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
1128348 AATAAAGCTT
1128358 TCATCTTTGAAAAGAAAATCTA
1 TCATCTTTGAAAAGAAAATCTA
* *
1128380 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAAAATCTA
1128402 TCATCTTTGAA
1 TCATCTTTGAA
1128413 GAGTGTGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAAAATCTA
Found at i:1129946 original size:76 final size:75
Alignment explanation
Indices: 1129732--1129985 Score: 321
Period size: 75 Copynumber: 3.4 Consensus size: 75
1129722 AGGATGATAT
* * * *
1129732 GGGCCTTCAGCATGCCCCAACAATTGCTGATACGAACGTTCAAAATACATCAACATTCTTGATTT
1 GGGCTTTCAGCATGCCCCAGCAATTGCTGATACGAACGTTCAAAATACATCAACATTCTTCATTC
*
1129797 TGATTGAAAT
66 TGATTGAAAG
* * *
1129807 AGGCTTTCAGTATGCCCCATCAATTGCTGATACGAACGTTCAAAATACATCAACATTCTTCATTC
1 GGGCTTTCAGCATGCCCCAGCAATTGCTGATACGAACGTTCAAAATACATCAACATTCTTCATTC
*
1129872 TGATTAAAAG
66 TGATTGAAAG
* * ** * ** *
1129882 GGGCTTTCAGCATGCCCCAGTATTTTGCTGATATAAACATTCAGGATACATCAACATTCCTCATT
1 GGGCTTTCAGCATGCCCCAGCA-ATTGCTGATACGAACGTTCAAAATACATCAACATTCTTCATT
1129947 CTGATTGAAAG
65 CTGATTGAAAG
*
1129958 GGG-TTTCCAGCATGCCCCAGCATTTGCT
1 GGGCTTT-CAGCATGCCCCAGCAATTGCT
1129986 TCTTGTTAAT
Statistics
Matches: 156, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
75 94 0.60
76 62 0.40
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30
Consensus pattern (75 bp):
GGGCTTTCAGCATGCCCCAGCAATTGCTGATACGAACGTTCAAAATACATCAACATTCTTCATTC
TGATTGAAAG
Found at i:1131283 original size:114 final size:114
Alignment explanation
Indices: 1131083--1131303 Score: 397
Period size: 114 Copynumber: 1.9 Consensus size: 114
1131073 TCATGCATTC
* *
1131083 ATCTTTCAATTCCAATGATTGGTTCTGGGGTTCCTACCAAACCAGATCAGATAACTCAAAGAACA
1 ATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACA
1131148 CTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAATTA
66 CTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAATTA
* * *
1131197 ATCTTTCAAATCTAATGATTGGTTTTGGGGTTCATACCAAACTAGATCAGATAACTCAAAGAACA
1 ATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACA
1131262 CTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAG
66 CTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAG
1131304 AACGTGGCAC
Statistics
Matches: 102, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 102 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (114 bp):
ATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACA
CTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAATTA
Found at i:1135426 original size:7 final size:7
Alignment explanation
Indices: 1135416--1135446 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
1135406 TAAAAATGAA
1135416 AAAATGC
1 AAAATGC
1135423 AAAATGC
1 AAAATGC
1135430 AAAATGC
1 AAAATGC
1135437 AAAATGC
1 AAAATGC
1135444 AAA
1 AAA
1135447 TTTAAATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.61, C:0.13, G:0.13, T:0.13
Consensus pattern (7 bp):
AAAATGC
Found at i:1137900 original size:21 final size:22
Alignment explanation
Indices: 1137876--1137916 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1137866 TTCTTTGATA
*
1137876 AAAAATAAAT-AAATTATAATG
1 AAAAATAAATCAAATAATAATG
*
1137897 AAAAATTAATCAAATAATAA
1 AAAAATAAATCAAATAATAA
1137917 ATATTAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (22 bp):
AAAAATAAATCAAATAATAATG
Found at i:1139165 original size:3 final size:3
Alignment explanation
Indices: 1139157--1139248 Score: 75
Period size: 3 Copynumber: 30.7 Consensus size: 3
1139147 GTTGGGTCTG
*
1139157 TAA TAA TAAA TAA -AA TTAA TTAA TAA TAA TAA TAA T-A TAA TAA TTA
1 TAA TAA T-AA TAA TAA -TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
1139203 TAA TTA TAA TTA TAA TTA TAA TTA TAA TAA TAA -AA T-A TAAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
1139247 TA
1 TA
1139249 TTCAAATGAA
Statistics
Matches: 72, Mismatches: 10, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
2 8 0.11
3 53 0.74
4 11 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:1139182 original size:17 final size:18
Alignment explanation
Indices: 1139159--1139248 Score: 62
Period size: 17 Copynumber: 4.9 Consensus size: 18
1139149 TGGGTCTGTA
1139159 ATAATAAATAA-AATTAAT
1 ATAATAAATAATAA-TAAT
1139177 -TAAT-AATAATAATAAT
1 ATAATAAATAATAATAAT
*
1139193 ATAATAATTATAATTATAATT
1 ATAATAA--ATAATAATAA-T
*
1139214 ATAATTATAATTATAATAAT
1 ATAA-TA-AATAATAATAAT
* *
1139234 AAAATATA-AATAATA
1 ATAATAAATAATAATA
1139249 TTCAAATGAA
Statistics
Matches: 58, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
16 9 0.16
17 16 0.28
18 2 0.03
19 2 0.03
20 13 0.22
21 13 0.22
22 2 0.03
23 1 0.02
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAATAAATAATAATAAT
Found at i:1139211 original size:12 final size:12
Alignment explanation
Indices: 1139157--1139235 Score: 85
Period size: 12 Copynumber: 6.8 Consensus size: 12
1139147 GTTGGGTCTG
1139157 TAATAATAA--A
1 TAATAATAATTA
1139167 TAA-AATTAATTAA
1 TAATAA-TAATT-A
*
1139180 TAATAATAATAA
1 TAATAATAATTA
1139192 T-ATAATAATTA
1 TAATAATAATTA
*
1139203 TAATTATAATTA
1 TAATAATAATTA
*
1139215 TAATTATAATTA
1 TAATAATAATTA
1139227 TAATAATAA
1 TAATAATAA
1139236 AATATAAATA
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
9 2 0.03
10 6 0.10
11 10 0.17
12 31 0.53
13 8 0.14
14 2 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAATAATAATTA
Found at i:1140288 original size:2 final size:2
Alignment explanation
Indices: 1140281--1140323 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1140271 AATATTTTTA
1140281 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
1140323 A
1 A
1140324 CCCCCATCCC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1145619 original size:11 final size:11
Alignment explanation
Indices: 1145603--1145628 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1145593 TATGAAATTG
1145603 TGACCGATCGA
1 TGACCGATCGA
1145614 TGACCGATCGA
1 TGACCGATCGA
1145625 TGAC
1 TGAC
1145629 GAATCAACAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (11 bp):
TGACCGATCGA
Found at i:1148720 original size:26 final size:26
Alignment explanation
Indices: 1148690--1148741 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
1148680 CTTTCCTGTT
1148690 TGGCCCATCTCTCGCTGAATTTTCTG
1 TGGCCCATCTCTCGCTGAATTTTCTG
* *
1148716 TGGCCCATTTCTCGCTGAGTTTTCTG
1 TGGCCCATCTCTCGCTGAATTTTCTG
1148742 AGGCTTGTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.10, C:0.29, G:0.21, T:0.40
Consensus pattern (26 bp):
TGGCCCATCTCTCGCTGAATTTTCTG
Found at i:1166745 original size:2 final size:2
Alignment explanation
Indices: 1166738--1166802 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
1166728 AATCATTGTT
1166738 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1166780 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
1166803 GATTAATAAG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1170523 original size:2 final size:2
Alignment explanation
Indices: 1170516--1170546 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1170506 GTGGTTTTAA
1170516 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1170547 AGTTCATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1170890 original size:18 final size:17
Alignment explanation
Indices: 1170869--1170902 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1170859 CTTCAACAAC
*
1170869 TGAAGCAACAACAACTGG
1 TGAAACAACAA-AACTGG
1170887 TGAAACAACAAAACTG
1 TGAAACAACAAAACTG
1170903 ATCAGCTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.21, G:0.18, T:0.12
Consensus pattern (17 bp):
TGAAACAACAAAACTGG
Found at i:1173284 original size:24 final size:24
Alignment explanation
Indices: 1173222--1173339 Score: 150
Period size: 24 Copynumber: 5.0 Consensus size: 24
1173212 AAACATAAAT
* * *
1173222 CATGTCAAGTAACATATCGGAAT-
1 CATGTCAAGTATCAGATCAGAATC
* *
1173245 CAGGTCAAGTAACAGATCAGAATC
1 CATGTCAAGTATCAGATCAGAATC
*
1173269 CAAGTCAAGTATCAGATCAGAATC
1 CATGTCAAGTATCAGATCAGAATC
*
1173293 TATGTC-AGATATCAGATCAGAATC
1 CATGTCAAG-TATCAGATCAGAATC
1173317 CATGTCAAGTATCAGATCAGAAT
1 CATGTCAAGTATCAGATCAGAAT
1173340 TCAAATCGAA
Statistics
Matches: 84, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
23 22 0.26
24 60 0.71
25 2 0.02
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.24
Consensus pattern (24 bp):
CATGTCAAGTATCAGATCAGAATC
Found at i:1173355 original size:48 final size:48
Alignment explanation
Indices: 1173257--1173357 Score: 134
Period size: 48 Copynumber: 2.1 Consensus size: 48
1173247 GGTCAAGTAA
** *
1173257 CAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCTATGTCAGATAT
1 CAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCTAAATCAGAAAT
*
1173305 CAGATCAGAATCCATGTCAAGTATCAGATCAGAAT-TCAAATC-GAAAAT
1 CAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCT-AAATCAG-AAAT
1173353 CAGAT
1 CAGAT
1173358 AAAATATTCA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
47 2 0.04
48 45 0.96
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.24
Consensus pattern (48 bp):
CAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCTAAATCAGAAAT
Found at i:1174469 original size:18 final size:18
Alignment explanation
Indices: 1174446--1174483 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1174436 TTCCATCCGG
*
1174446 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
1174464 TCTTATCATTTACTTCAA
1 TCTTATCATTTAATTCAA
1174482 TC
1 TC
1174484 CTTTCGAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.53
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:1175806 original size:15 final size:15
Alignment explanation
Indices: 1175786--1175818 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1175776 TGGTCAACGC
1175786 CGGTCAACGGGTCAA
1 CGGTCAACGGGTCAA
1175801 CGGTCAACGGGTCAA
1 CGGTCAACGGGTCAA
1175816 CGG
1 CGG
1175819 GTCGGGTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.27, G:0.36, T:0.12
Consensus pattern (15 bp):
CGGTCAACGGGTCAA
Found at i:1175826 original size:13 final size:13
Alignment explanation
Indices: 1175808--1175839 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1175798 CAACGGTCAA
*
1175808 CGGGTCAACGGGT
1 CGGGTCAACAGGT
1175821 CGGGTCAACAGGT
1 CGGGTCAACAGGT
1175834 CGGGTC
1 CGGGTC
1175840 GGGTAAACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.25, G:0.44, T:0.16
Consensus pattern (13 bp):
CGGGTCAACAGGT
Found at i:1175834 original size:8 final size:8
Alignment explanation
Indices: 1175777--1175821 Score: 65
Period size: 8 Copynumber: 5.5 Consensus size: 8
1175767 GATCAACAGT
1175777 GGTCAACG
1 GGTCAACG
1175785 CCGGTCAACG
1 --GGTCAACG
1175795 GGTCAAC-
1 GGTCAACG
1175802 GGTCAACG
1 GGTCAACG
1175810 GGTCAACG
1 GGTCAACG
1175818 GGTC
1 GGTC
1175822 GGGTCAACAG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 7 0.21
8 19 0.56
10 8 0.24
ACGTcount: A:0.22, C:0.29, G:0.36, T:0.13
Consensus pattern (8 bp):
GGTCAACG
Found at i:1175839 original size:18 final size:18
Alignment explanation
Indices: 1175816--1175856 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1175806 AACGGGTCAA
*
1175816 CGGGTCGGGTCAACAGGT
1 CGGGTCGGGTAAACAGGT
*
1175834 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACAGGT
1175852 CGGGT
1 CGGGT
1175857 AAACGGGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.15, C:0.20, G:0.49, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTAAACAGGT
Found at i:1175849 original size:31 final size:31
Alignment explanation
Indices: 1175808--1175874 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
1175798 CAACGGTCAA
* * *
1175808 CGGGTCAACGGGTCGGGTCAACAGGTCGGGT
1 CGGGTAAACGGGTCGGGTAAACAGGTCAGGT
*
1175839 CGGGTAAACGGGTCGGGTAAACGGGTCAGGT
1 CGGGTAAACGGGTCGGGTAAACAGGTCAGGT
1175870 CGGGT
1 CGGGT
1175875 TATGACCGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.18, C:0.19, G:0.46, T:0.16
Consensus pattern (31 bp):
CGGGTAAACGGGTCGGGTAAACAGGTCAGGT
Found at i:1175850 original size:13 final size:13
Alignment explanation
Indices: 1175834--1175865 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
1175824 GTCAACAGGT
1175834 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
1175847 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
1175860 CGGGTC
1 CGGGTC
1175866 AGGTCGGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.19, C:0.19, G:0.47, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:1177995 original size:24 final size:24
Alignment explanation
Indices: 1177936--1178050 Score: 153
Period size: 24 Copynumber: 4.8 Consensus size: 24
1177926 CATAAATCAG
* * *
1177936 GTCAAGTAACAGATCGGAAT-CAG
1 GTCAAGTATCAGATCAGAATCCAT
* *
1177959 GTCAAGTAACAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
*
1177983 GTCAAGTATCAGATCAGAATCTAT
1 GTCAAGTATCAGATCAGAATCCAT
1178007 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
1178031 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
1178051 TCAAATCGAA
Statistics
Matches: 83, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
23 21 0.25
24 60 0.72
25 2 0.02
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:1178066 original size:48 final size:48
Alignment explanation
Indices: 1177968--1178068 Score: 134
Period size: 48 Copynumber: 2.1 Consensus size: 48
1177958 GGTCAAGTAA
** *
1177968 CAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCTATGTCAGATAT
1 CAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCTAAATCAGAAAT
*
1178016 CAGATCAGAATCCATGTCAAGTATCAGATCAGAAT-TCAAATC-GAAAAT
1 CAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCT-AAATCAG-AAAT
1178064 CAGAT
1 CAGAT
1178069 AAAATATTCA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
47 2 0.04
48 45 0.96
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.24
Consensus pattern (48 bp):
CAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCTAAATCAGAAAT
Found at i:1179182 original size:18 final size:18
Alignment explanation
Indices: 1179159--1179193 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1179149 TTCCATCCGG
*
1179159 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
1179177 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
1179194 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:1180519 original size:15 final size:15
Alignment explanation
Indices: 1180499--1180531 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1180489 TGGTCAACGC
1180499 CGGTCAACGGGTCAA
1 CGGTCAACGGGTCAA
1180514 CGGTCAACGGGTCAA
1 CGGTCAACGGGTCAA
1180529 CGG
1 CGG
1180532 GTCGGGTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.27, G:0.36, T:0.12
Consensus pattern (15 bp):
CGGTCAACGGGTCAA
Found at i:1180543 original size:13 final size:13
Alignment explanation
Indices: 1180521--1180564 Score: 70
Period size: 13 Copynumber: 3.4 Consensus size: 13
1180511 CAACGGTCAA
*
1180521 CGGGTCAACGGGT
1 CGGGTAAACGGGT
1180534 CGGGTAAACGGGT
1 CGGGTAAACGGGT
*
1180547 CAGGTAAACGGGT
1 CGGGTAAACGGGT
1180560 CGGGT
1 CGGGT
1180565 CGGGTTATGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.20, C:0.18, G:0.45, T:0.16
Consensus pattern (13 bp):
CGGGTAAACGGGT
Found at i:1180546 original size:8 final size:8
Alignment explanation
Indices: 1180480--1180534 Score: 67
Period size: 8 Copynumber: 6.5 Consensus size: 8
1180470 TCAAAGTTTT
1180480 GGTCAACAG
1 GGTCAAC-G
1180489 TGGTCAACG
1 -GGTCAACG
1180498 CCGGTCAACG
1 --GGTCAACG
1180508 GGTCAAC-
1 GGTCAACG
1180515 GGTCAACG
1 GGTCAACG
1180523 GGTCAACG
1 GGTCAACG
1180531 GGTC
1 GGTC
1180535 GGGTAAACGG
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
7 7 0.17
8 19 0.45
9 1 0.02
10 15 0.36
ACGTcount: A:0.24, C:0.27, G:0.35, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:1183009 original size:25 final size:25
Alignment explanation
Indices: 1182978--1183088 Score: 204
Period size: 25 Copynumber: 4.4 Consensus size: 25
1182968 TGACTCTATC
* *
1182978 CGAGTTGACTCAACAGGTTGACTAA
1 CGAGTTGACTCAACGGGTTAACTAA
1183003 CGAGTTGACTCAACGGGTTAACTAA
1 CGAGTTGACTCAACGGGTTAACTAA
1183028 CGAGTTGACTCAACGGGTTAACTAA
1 CGAGTTGACTCAACGGGTTAACTAA
1183053 CGAGTTGACTCAACGGGTTAACTAA
1 CGAGTTGACTCAACGGGTTAACTAA
1183078 CGAGTTGACTC
1 CGAGTTGACTC
1183089 GACTGACTCG
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 84 1.00
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (25 bp):
CGAGTTGACTCAACGGGTTAACTAA
Found at i:1193783 original size:12 final size:13
Alignment explanation
Indices: 1193752--1193789 Score: 60
Period size: 12 Copynumber: 3.0 Consensus size: 13
1193742 TTCCTTCTAA
*
1193752 CTATTAAGATAAT
1 CTATTAAAATAAT
1193765 CTATTAAAATAAT
1 CTATTAAAATAAT
1193778 -TATTAAAATAAT
1 CTATTAAAATAAT
1193790 AATAAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 12 0.50
13 12 0.50
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (13 bp):
CTATTAAAATAAT
Found at i:1195966 original size:40 final size:40
Alignment explanation
Indices: 1195868--1195959 Score: 125
Period size: 38 Copynumber: 2.4 Consensus size: 40
1195858 TCGATACTCC
**
1195868 TATACATGTATATTGCATAT-AAAAAAATATGAATTAGGA
1 TATACATGTATATTGCATATGAAAAAAATATGAAGAAGGA
* *
1195907 -GTACATGTATATTGCATATGAAAAAAATATGAAGAAGTA
1 TATACATGTATATTGCATATGAAAAAAATATGAAGAAGGA
*
1195946 TATATATGTATATT
1 TATACATGTATATT
1195960 ATATATGGTT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
38 18 0.40
39 16 0.36
40 11 0.24
ACGTcount: A:0.47, C:0.04, G:0.14, T:0.35
Consensus pattern (40 bp):
TATACATGTATATTGCATATGAAAAAAATATGAAGAAGGA
Found at i:1198811 original size:3 final size:3
Alignment explanation
Indices: 1198803--1198831 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1198793 TTATATAAAT
1198803 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1198832 GTTTAATAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1203758 original size:21 final size:21
Alignment explanation
Indices: 1203729--1203768 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1203719 TATTAACATA
*
1203729 AAGATATTTAATACTAATACG
1 AAGAGATTTAATACTAATACG
*
1203750 AAGAGATTTAATATTAATA
1 AAGAGATTTAATACTAATA
1203769 TGAATATATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (21 bp):
AAGAGATTTAATACTAATACG
Found at i:1204815 original size:60 final size:59
Alignment explanation
Indices: 1204711--1204822 Score: 145
Period size: 60 Copynumber: 1.9 Consensus size: 59
1204701 ATTTGGATGG
** * *
1204711 ATTTGGGGATGAAATTGAAAGATTCAAAAGCTTGGGTACCAATTTAGAATGAGGGTTAT
1 ATTTGGGGATGAAATTGAAAGATTCAAAAGCTTAAGAACCAATTTAAAATGAGGGTTAT
* *
1204770 ATTTCGGGGATGAAATTGAAATGA-TCAAAAGTTTAAGAACTAATTTAAAATGA
1 ATTT-GGGGATGAAATTGAAA-GATTCAAAAGCTTAAGAACCAATTTAAAATGA
1204823 TTATTATAGT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
59 4 0.09
60 39 0.87
61 2 0.04
ACGTcount: A:0.40, C:0.06, G:0.23, T:0.30
Consensus pattern (59 bp):
ATTTGGGGATGAAATTGAAAGATTCAAAAGCTTAAGAACCAATTTAAAATGAGGGTTAT
Found at i:1211478 original size:34 final size:34
Alignment explanation
Indices: 1211329--1211498 Score: 109
Period size: 34 Copynumber: 4.9 Consensus size: 34
1211319 ATTTACATAT
*
1211329 ATATATATTATATAGTTTTGAAATCA-TTTTAAAA
1 ATATATATTATATAGTTTTAAAAT-ATTTTTAAAA
* * * *
1211363 ACATATAATATATAGTTTTAAAAACATTTTTGAAA
1 ATATATATTATATAGTTTT-AAAATATTTTTAAAA
* * * *
1211398 A-CTATA-TA-AT--TTTGAAAACATTTTAAAAAAAAA
1 ATATATATTATATAGTTTTAAAATATTTT----TAAAA
* *
1211431 AGTATATAATATATAATTTTAAAATATTTTTAAAA
1 A-TATATATTATATAGTTTTAAAATATTTTTAAAA
1211466 ATATATATTATATAGGTTTTGGAAAATATTTTT
1 ATATATATTATATA-GTTTT--AAAATATTTTT
1211499 TTACATATAA
Statistics
Matches: 106, Mismatches: 15, Indels: 27
0.72 0.10 0.18
Matches are distributed among these distances:
29 10 0.09
30 3 0.03
32 2 0.02
33 6 0.06
34 34 0.32
35 24 0.23
36 2 0.02
37 13 0.12
39 12 0.11
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.44
Consensus pattern (34 bp):
ATATATATTATATAGTTTTAAAATATTTTTAAAA
Found at i:1211751 original size:33 final size:33
Alignment explanation
Indices: 1211714--1211777 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
1211704 AGAATCTCTG
*
1211714 GACTGACCTATCCCGAGATGGCCGATATCACGA
1 GACTGACCCATCCCGAGATGGCCGATATCACGA
* *
1211747 GACTGACCCATCCCGGGATGGCCGGTATCAC
1 GACTGACCCATCCCGAGATGGCCGATATCAC
1211778 AAACAACATG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.23, C:0.33, G:0.27, T:0.17
Consensus pattern (33 bp):
GACTGACCCATCCCGAGATGGCCGATATCACGA
Found at i:1213108 original size:12 final size:12
Alignment explanation
Indices: 1213091--1213117 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1213081 ATCGAATACT
1213091 TTTAATTTTTAA
1 TTTAATTTTTAA
1213103 TTTAATTTTTAA
1 TTTAATTTTTAA
1213115 TTT
1 TTT
1213118 TCGTAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTAATTTTTAA
Found at i:1216562 original size:95 final size:94
Alignment explanation
Indices: 1216428--1216671 Score: 296
Period size: 95 Copynumber: 2.7 Consensus size: 94
1216418 TATAATATTA
* * *
1216428 TATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCTGACTTTATGGA
1 TATATATACAATAAAGCTTGAGCTATCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTATGGA
* *
1216493 TAATATTCAGCTAGCCTGATAAAGGTAAT
66 TAAGATTCAGCTAACCTGATAAAGGTAAT
*
1216522 TATACTATACAATAAAGCTTGAGCTATCCCTCTA-AGGCAATTGGTTAAACGCCCCGGCTTTATG
1 TATA-TATACAATAAAGCTTGAGCTATCCCTCTAGA-GCAATTGGTTAAACGCCCCGACTTTATG
*
1216586 GATAAGATTCAGCTAACCTGATAAAGGT-GT
64 GATAAGATTCAGCTAACCTGATAAAGGTAAT
* * *
1216616 T-TATAT---ATTAAG-TT--G---TCTCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGA
1 TATATATACAATAAAGCTTGAGCTATCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTATGGA
1216671 T
66 T
1216672 CCACTAGCCA
Statistics
Matches: 138, Mismatches: 9, Indels: 17
0.84 0.05 0.10
Matches are distributed among these distances:
83 38 0.28
84 1 0.01
86 1 0.01
88 2 0.01
89 5 0.04
92 3 0.02
93 2 0.01
94 7 0.05
95 79 0.57
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (94 bp):
TATATATACAATAAAGCTTGAGCTATCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTATGGA
TAAGATTCAGCTAACCTGATAAAGGTAAT
Found at i:1218966 original size:250 final size:250
Alignment explanation
Indices: 1217779--1219772 Score: 2323
Period size: 250 Copynumber: 8.0 Consensus size: 250
1217769 ATGTTTTAGG
* * * * * * ** *
1217779 ACATCATTTACAACATAACTCAAATCTAGAAGGGTTATTTG-TGACCAAAATACCTTCGAGTTCG
1 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCG
* * * * * * * * * *
1217843 ACTACGCTCAGC-TCCAAGGCATATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCTA
65 ATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG-TG
* * * * *
1217907 ACCAAAAGACCTTCGAGTTTGACTACGCTCAGCTCAAAGGAATATCATTTGCAACATAGCTTAAG
129 ACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAG
* * * * * * * * *
1217972 TCAAGAAGGGCTATCTGCCAACCAAAAACCTTCGAGTTTGACTACGCTCAAC-TCTAAGGC
194 TCGAGAAGGGCTATCTG----CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGC
* * * * *
1218032 ATATCATTTTCAGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGACTTTCTAGTTCGA
1 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGA
* ** * * ** * * * * * * *
1218097 CTATGCTCAGC-TCCAAGGCGTATCATTTGCAACATAGCTTAAGTCGAGAAGGGCTATC--TG-C
66 TTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGAC
* * * * * * * * * *
1218158 C-AAAGACCCTCGAGTTC-AATAACACTCAACTTCGAGGGAACATCATTTACAGCATAACTCAAG
131 CAAAAGACCTTCGAGTTCGACT-ACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAG
* * * * * * * *
1218221 GCTAGAAGGGTTATCTGTAACTAAAAGACCTTCGAGTTCGACTACGA-TCAGC-TCCAAGGC
194 TCGAGAAGGGCTATCTG---C-CAAAGACCCTCGAGTTCGATTAC-ACTCAGCTTCGAGGGC
* * * * * *
1218281 ATATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCT----TCCAAAGACCCTCGAGTTCGA
1 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGA
* *
1218342 TTACACTCAGCTTCGAGGGAACATCATTTACATCATAACTCAAGGCTAGAAGGGTTATCTGTGAC
66 TTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGAC
1218407 CAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
131 CAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
* * * *
1218472 GAGAAGGGCTATCTACCAAATACCCTGGAGTTCGATTACACTCATCTTCGAGGGC
196 GAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGC
** *
1218527 ACATCATTTGCAGCATAGTTTAAGTCGAGAAGGGTTATCT----ACCAAAGACCCTCGAGTTCGA
1 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGA
* *
1218588 TTACACTCAGCTTCGAGGGTACATCATTTACTGCATAACTCAAGGCTAGAAGGGTTATCTGTGAC
66 TTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGAC
*
1218653 CAAAAGACCTTCAAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
131 CAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
*
1218718 GAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGTTTCGAGGGC
196 GAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGC
** *
1218773 ACATCATTTGCAATATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGA
1 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGA
* *
1218838 TTACACTCAGCTTCTG-GGGCACATAATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTATGA
66 TTACACTCAGCTTC-GAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGA
* * *
1218902 CCAAAAGACCTTCGTGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGTAGCATAGCTTAAGT
130 CCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGT
* * * *
1218967 CGAGAAGTGTTATCTGCCAAAGGCCCTCTAGTTCGATTACACTCAGCTTCGAGGGC
195 CGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGC
* *
1219023 ACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGA
1 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGA
* *
1219088 TTACACTCAGCTTCGAGGGTACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATTTGTGAC
66 TTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGAC
* * * *
1219153 CAAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGTACATCATTTGCAACAAAGCTTAAGTC
131 CAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
* * * * *
1219218 GAGAAGGGCTATCTGTCAAAGACCCTCGAGTTTGATTGCACTCAACTTCAAGGGC
196 GAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGC
* * *
1219273 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGATATCTGCCAACCAAAGACCTTTGAGTTCAA
1 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGA
*
1219338 TGACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGAC
66 TTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGAC
* * * * * * *
1219403 AAAAAAACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCATATCATTTGCAGTATAACTTAAATC
131 CAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
* * * * * * * *
1219468 GAGAAGGGTTATCTGTCAACCAGAGACCTTCGAGTTCGACTACGCTCAAC-TCTAAGGC
196 GAGAAGGGCTATCTG----CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGC
* * * *
1219526 GCATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCC-A--AACGCCCTT-GAGTTCGA
1 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGA
* * *
1219587 TTACACTTAGCTTCGAGGGCACATCATTTATAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAC
66 TTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGAC
* * *
1219652 C--AAGACTTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGTAGCATAGCTTAAGTC
131 CAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
* * *
1219715 AAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCCATTACACTCAGCTTCGAGAGC
196 GAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGC
1219770 ACA
1 ACA
1219773 CCAAATTTAC
Statistics
Matches: 1515, Mismatches: 202, Indels: 57
0.85 0.11 0.03
Matches are distributed among these distances:
243 25 0.02
244 8 0.01
245 47 0.03
246 310 0.20
247 68 0.04
248 26 0.02
249 217 0.14
250 634 0.42
251 3 0.00
252 1 0.00
253 149 0.10
254 27 0.02
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.26
Consensus pattern (250 bp):
ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGA
TTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGAC
CAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
GAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGC
Found at i:1219814 original size:165 final size:165
Alignment explanation
Indices: 1217779--1219815 Score: 1580
Period size: 165 Copynumber: 12.3 Consensus size: 165
1217769 ATGTTTTAGG
* * * * * *
1217779 ACATCATTTACAACATAACTCAAATCTAGAAGGGTTATTTGTGACCAAAATACCTTCGAGTTCGA
1 ACATCATTTACAGCATAACTCAAGTCGAGAAGGGTTATCTGTCACC-AAAGACCTTCGAGTTCGA
* * * *
1217844 CTACGCTCAGC-TCCAAGGCATATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCTAA
65 CTACACTCAGCTTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG----
* * * * * * *
1217908 CCAAAAGACCTTCGAGTTTGACTACGCTCAGC-TCAAAGGA
126 CC-AAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGC
* * * * * * * * * *
1217948 ATATCATTTGCAACATAGCTTAAGTCAAGAAGGGCTATCTGCCAACCAAAAACCTTCGAGTTTGA
1 ACATCATTTACAGCATAACTCAAGTCGAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCGA
* * * * * * *
1218013 CTACGCTCAAC-TCTAAGGCATATCATTTTCAGCATAACTTAAATCGAGAAGGGTTATCTGCCAA
65 CTACACTCAGCTTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG----
** * * ** * *
1218077 CCAAAGACTTTCTAGTTCGACTATGCTCAGC-TCCAAGGC
126 CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGC
** * * * * * * *
1218116 GTATCATTTGCAACATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAGACCCTCGAGTTC-AA
1 ACATCATTTACAGCATAACTCAAGTCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGAC
* * * * * * * * *
1218177 TAACACTCAACTTCGAGGGAACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAAC
66 T-ACACTCAGCTTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG---C
* * * * *
1218242 TAAAAGACCTTCGAGTTCGACTACGA-TCAGC-TCCAAGGC
127 -CAAAGACCCTCGAGTTCGATTAC-ACTCAGCTTCGAGGGC
* * * * * * * *
1218281 ATATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCT-T--CCAAAGACCCTCGAGTTCGAT
1 ACATCATTTACAGCATAACTCAAGTCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGAC
* * * * * * * * *
1218343 TACACTCAGCTTCGAGGGAACATCATTTACATCATAACTCAAGGCTAGAAGGGTTATCTGTGACC
66 TACACTCAGCTTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATC--TG-CC
* * * * *
1218408 AAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGC
128 -AAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGC
* * * * * * * *
1218446 ACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATC--T-ACCAAATACCCTGGAGTTCGAT
1 ACATCATTTACAGCATAACTCAAGTCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGAC
* * * ** * *
1218508 TACACTCATCTTCGAGGGCACATCATTTGCAGCATAGTTTAAGTCGAGAAGGGTTATCTACCAAA
66 TACACTCAGCTTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAA
*
1218573 GACCCTCGAGTTCGATTACACTCAGCTTCGAGGGT
131 GACCCTCGAGTTCGATTACACTCAGCTTCGAGGGC
* * * * *
1218608 ACATCATTTACTGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCAAGTTCGA
1 ACATCATTTACAGCATAACTCAAGTCGAGAAGGGTTATCTGTCACC-AAAGACCTTCGAGTTCGA
* *
1218673 CTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAA
65 CTACACTCAGCTTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAA
*
1218737 AGACCCTCGAGTTCGATTACACTCAGTTTCGAGGGC
130 AGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGC
* ** * * *
1218773 ACATCATTTGCAATATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGA
1 ACATCATTTACAGCATAACTCAAGTCGAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCGA
* *** * * * * * *
1218838 TTACACTCAGCTTCTGGGGCACATAATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTATGAC
65 CTACACTCAGCTTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATC--TG-C
* * * * * *
1218903 CAAAAGACCTTCGTGTTCGACTACGCTCAGC-TCCAAGGC
127 C-AAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGC
* ** * * * * * * *
1218942 ATATCATTTGTAGCATAGCTTAAGTCGAGAAGTGTTATCTG---CCAAAGGCCCTCTAGTTCGAT
1 ACATCATTTACAGCATAACTCAAGTCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGAC
* * * * *
1219004 TACACTCAGCTTCGAGGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAAC
66 TACACTCAGCTTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG----C
* *
1219069 CAAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGT
127 CAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGC
* * * *
1219108 ACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATTTGTGACCAAAAGACCTTCGAGTTCGA
1 ACATCATTTACAGCATAACTCAAGTCGAGAAGGGTTATCTGTCACC-AAAGACCTTCGAGTTCGA
* * * * *
1219173 CTACGCTCAAC-TCCAAGGTACATCATTTGCAACA-AAGCTTAAGTCGAGAAGGGCTATCTGTCA
65 CTACACTCAGCTTCCAAGGCACATCATTTGCAGCATAA-CTTAAGTCGAGAAGGGCTATCTGCCA
* * * *
1219236 AAGACCCTCGAGTTTGATTGCACTCAACTTCAAGGGC
129 AAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGC
* * * * *
1219273 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGATATCTGCCAACCAAAGACCTTTGAGTTC-A
1 ACATCATTTACAGCATAACTCAAGTCGAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCGA
* * * * * * * *
1219337 ATGACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGA
65 CT-ACACTCAGCTTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATC--TG-
* * * * * * * *
1219402 CAAAAAAACCTTCGAGTTTGACTACGCTCAGC-TCCAAGGC
126 C-CAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGC
* * * * * *
1219442 ATATCATTTGCAGTATAACTTAAATCGAGAAGGGTTATCTGTCAACCAGAGACCTTCGAGTTCGA
1 ACATCATTTACAGCATAACTCAAGTCGAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCGA
* * * *
1219507 CTACGCTCAAC-TCTAAGGCGCATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAA
65 CTACACTCAGCTTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAA
* *
1219571 ACG-CCCTTGAGTTCGATTACACTTAGCTTCGAGGGC
130 A-GACCCTCGAGTTCGATTACACTCAGCTTCGAGGGC
* * * *
1219607 ACATCATTTATAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACC-AAGACTTTCGAGTTCGAC
1 ACATCATTTACAGCATAACTCAAGTCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGAC
* * *
1219671 TACACTCAGC-TCCAAGGCACATCATTTGTAGCATAGCTTAAGTCAAGAAGGGCTATCTGCCAAA
66 TACACTCAGCTTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAA
* *
1219735 GACCCTCGAGTTCCATTACACTCAGCTTCGAGAGC
131 GACCCTCGAGTTCGATTACACTCAGCTTCGAGGGC
* ** *
1219770 ACACCAAATTTACATAATAACTCAAGGT-AAGAAGGGTTATCTGTCA
1 ACATC--ATTTACAGCATAACTCAA-GTCGAGAAGGGTTATCTGTCA
1219816 ATAAATTGTT
Statistics
Matches: 1557, Mismatches: 264, Indels: 98
0.81 0.14 0.05
Matches are distributed among these distances:
161 26 0.02
162 40 0.03
163 111 0.07
164 54 0.03
165 725 0.47
166 145 0.09
167 4 0.00
168 115 0.07
169 262 0.17
170 75 0.05
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.26
Consensus pattern (165 bp):
ACATCATTTACAGCATAACTCAAGTCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGAC
TACACTCAGCTTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAA
GACCCTCGAGTTCGATTACACTCAGCTTCGAGGGC
Found at i:1220258 original size:36 final size:37
Alignment explanation
Indices: 1220211--1220413 Score: 218
Period size: 39 Copynumber: 5.4 Consensus size: 37
1220201 CATATATATA
**
1220211 TATATATAATATGCAG-TTTGAAAACATTTT-AAAAT
1 TATATATAATATATAGTTTTGAAAACATTTTGAAAAT
*
1220246 GTATATATAATATATAGTTTTGAAAACATGTTTCAAAACAT
1 -TATATATAATATATAGTTTTGAAAACAT-TTT-GAAA-AT
* *
1220287 T-TATATATTATATAGTTTTTAAAACATTTTGAAAAT
1 TATATATAATATATAGTTTTGAAAACATTTTGAAAAT
*
1220323 TA-ATATAATATATAGTTTTCAAAACATTTTTGAAAAT
1 TATATATAATATATAGTTTTGAAAACA-TTTTGAAAAT
* * *
1220360 ATATATATATTATATAGTTTTTAAAAACATTTTGAGAAT
1 -TATATATAATATATAG-TTTTGAAAACATTTTGAAAAT
*
1220399 TA-ATATAATTTATAG
1 TATATATAATATATAG
1220414 ATTCTTTTAT
Statistics
Matches: 145, Mismatches: 12, Indels: 19
0.82 0.07 0.11
Matches are distributed among these distances:
36 39 0.27
37 35 0.24
38 10 0.07
39 45 0.31
40 14 0.10
41 2 0.01
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (37 bp):
TATATATAATATATAGTTTTGAAAACATTTTGAAAAT
Found at i:1220293 original size:75 final size:75
Alignment explanation
Indices: 1220210--1220413 Score: 241
Period size: 75 Copynumber: 2.7 Consensus size: 75
1220200 ACATATATAT
* *
1220210 ATATATATAATATGCAG-TTTGAAAACATTTT-AAAATGTATATATAATATATAGTTTTGAAAAC
1 ATATATATAATATACAGTTTTGAAAACATTTTGAAAAT-TA-ATATAATATATAGTTTTCAAAAC
1220273 ATGTTTCAAAAC
64 ATGTTTCAAAAC
* * * *
1220285 ATTTATATATTATATAGTTTTTAAAACATTTTGAAAATTAATATAATATATAGTTTTCAAAACAT
1 ATATATATAATATACAGTTTTGAAAACATTTTGAAAATTAATATAATATATAGTTTTCAAAACAT
* * *
1220350 TTTTGAAAAT
66 GTTTCAAAAC
* * * * *
1220360 ATATATATATTATATAGTTTTTAAAAACATTTTGAGAATTAATATAATTTATAG
1 ATATATATAATATACAG-TTTTGAAAACATTTTGAAAATTAATATAATATATAG
1220414 ATTCTTTTAT
Statistics
Matches: 113, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
75 60 0.53
76 48 0.42
77 5 0.04
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (75 bp):
ATATATATAATATACAGTTTTGAAAACATTTTGAAAATTAATATAATATATAGTTTTCAAAACAT
GTTTCAAAAC
Found at i:1220430 original size:126 final size:123
Alignment explanation
Indices: 1220294--1220534 Score: 292
Period size: 126 Copynumber: 1.9 Consensus size: 123
1220284 CATTTATATA
* *
1220294 TTATATAGTTTTT-AAAACATTTTGAAAA-TTA-ATATAATATATAGTTTTCAAAACATTTTTGA
1 TTATATAGTTTTTAAAAACATTTCGAAAACATATATATAATATATAGTTTTCAAAACA-TTTTG-
* * *
1220356 AAATATATATATATTATATAGTTTTTAAAAACA-TTTTGAGAATTAATATAATTTATAGATTCTT
64 AAA-ACATATA-A-TATATAG-TTTTAAAAACATTTTTGAAAACT-ATATAATTTATAGATTCTT
** * *
1220420 TTATATAGTTTTTAAAAAAACATTTCGAAAACATATATATGTTATATAGTTTTGAAATCATTTTG
1 TTATATAGTTTTT--AAAAACATTTCGAAAACATATATATAATATATAGTTTTCAAAACATTTTG
1220485 AAAACATATAATATATAGTTTTAAAAACATTTTTGAAAACTATATAATTT
64 AAAACATATAATATATAGTTTTAAAAACATTTTTGAAAACTATATAATTT
1220535 TGAAAATATT
Statistics
Matches: 100, Mismatches: 9, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
125 20 0.20
126 29 0.29
127 1 0.01
128 6 0.06
129 17 0.17
130 7 0.07
131 20 0.20
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.45
Consensus pattern (123 bp):
TTATATAGTTTTTAAAAACATTTCGAAAACATATATATAATATATAGTTTTCAAAACATTTTGAA
AACATATAATATATAGTTTTAAAAACATTTTTGAAAACTATATAATTTATAGATTCTT
Found at i:1220505 original size:34 final size:36
Alignment explanation
Indices: 1220421--1220532 Score: 113
Period size: 34 Copynumber: 3.0 Consensus size: 36
1220411 TAGATTCTTT
* *
1220421 TATATAGTTTTTAAAAAAACA-TTTCGAAAACATATATATGT
1 TATATAG-TTTT--AAAAACATTTTTGAAAAC-TATATA--A
* *
1220462 TATATAGTTTTGAAATCA-TTTTGAAAAC-ATATAA
1 TATATAGTTTTAAAAACATTTTTGAAAACTATATAA
1220496 TATATAGTTTTAAAAACATTTTTGAAAACTATATAA
1 TATATAGTTTTAAAAACATTTTTGAAAACTATATAA
1220532 T
1 T
1220533 TTTGAAAATA
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
34 16 0.25
35 10 0.16
36 12 0.19
38 14 0.22
40 4 0.06
41 7 0.11
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (36 bp):
TATATAGTTTTAAAAACATTTTTGAAAACTATATAA
Found at i:1220597 original size:36 final size:38
Alignment explanation
Indices: 1220525--1220603 Score: 103
Period size: 34 Copynumber: 2.2 Consensus size: 38
1220515 TTTTGAAAAC
*
1220525 TATATAATTTTGAAAATATTTTTTTAAAAAAGTATATAA
1 TATATAATTTT-AAAATATGTTTTTAAAAAAGTATATAA
*
1220564 TATATAATTTT-AAA-ATGTTTTT-AAAAA-TATATAT
1 TATATAATTTTAAAATATGTTTTTAAAAAAGTATATAA
1220598 TATATA
1 TATATA
1220604 GGTTTTGGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
34 12 0.32
35 5 0.13
36 7 0.18
37 3 0.08
39 11 0.29
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (38 bp):
TATATAATTTTAAAATATGTTTTTAAAAAAGTATATAA
Found at i:1220608 original size:25 final size:25
Alignment explanation
Indices: 1220580--1220628 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
1220570 ATTTTAAAAT
*
1220580 GTTTTTAAAAATATATATTATATAG
1 GTTTTGAAAAATATATATTATATAG
* * *
1220605 GTTTTGGAAAATATTTTTTATATA
1 GTTTTGAAAAATATATATTATATA
1220629 TAATATATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (25 bp):
GTTTTGAAAAATATATATTATATAG
Found at i:1223166 original size:3 final size:3
Alignment explanation
Indices: 1223158--1223197 Score: 71
Period size: 3 Copynumber: 13.0 Consensus size: 3
1223148 GAGGTATTAA
1223158 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
1223198 TTAAAAAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1228786 original size:2 final size:2
Alignment explanation
Indices: 1228779--1228809 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1228769 TCAATCTACA
1228779 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1228810 ATTTACAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1228977 original size:85 final size:85
Alignment explanation
Indices: 1228829--1229018 Score: 224
Period size: 85 Copynumber: 2.2 Consensus size: 85
1228819 ATAGAATCAC
* * * *
1228829 GACACACGAATGTGTGTCATCTTTTCTAATGGCGTGTGCTTCAATGACACGCAATGTAAGTCATA
1 GACACACAAATGTGTGTCATCTTTTCTAATGACGGGGGCTTCAATGACACGCAATGTAAGTCATA
** *
1228894 AATGCGTGTCATAAATTTAT
66 AATGCGCATCATAAATTCAT
* *
1228914 GACACACAAATGTGTGTCATCTTCATT-T-ATGACGGGGGCTTCAATGACGCGCAATG-AGCGTC
1 GACACACAAATGTGTGTCATCTT--TTCTAATGACGGGGGCTTCAATGACACGCAATGTA-AGTC
1228976 ATAAATGCGCATCATAAATTCAT
63 ATAAATGCGCATCATAAATTCAT
* * *
1228999 GACGCACAATTGCGTGTCAT
1 GACACACAAATGTGTGTCAT
1229019 ATGAGTTTCA
Statistics
Matches: 90, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
84 1 0.01
85 86 0.96
86 1 0.01
87 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.29
Consensus pattern (85 bp):
GACACACAAATGTGTGTCATCTTTTCTAATGACGGGGGCTTCAATGACACGCAATGTAAGTCATA
AATGCGCATCATAAATTCAT
Found at i:1231488 original size:3 final size:3
Alignment explanation
Indices: 1231480--1231515 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
1231470 AAGGTATTAA
* *
1231480 AAT AAT AAT AAT AGT AGT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1231516 TTAAAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1232313 original size:19 final size:19
Alignment explanation
Indices: 1232289--1232338 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 19
1232279 CCCTTATTAA
1232289 GGTTTGTTTAGTGATTTTG
1 GGTTTGTTTAGTGATTTTG
1232308 GGTTTGTTTTTAGTGATTTTG
1 GGTTTG--TTTAGTGATTTTG
*
1232329 GGGTTGTTTA
1 GGTTTGTTTA
1232339 TCCCTATTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 10 0.36
21 18 0.64
ACGTcount: A:0.10, C:0.00, G:0.32, T:0.58
Consensus pattern (19 bp):
GGTTTGTTTAGTGATTTTG
Found at i:1232321 original size:21 final size:21
Alignment explanation
Indices: 1232295--1232337 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1232285 TTAAGGTTTG
*
1232295 TTTAGTGATTTTGGGTTTGTT
1 TTTAGTGATTTTGGGGTTGTT
1232316 TTTAGTGATTTTGGGGTTGTT
1 TTTAGTGATTTTGGGGTTGTT
1232337 T
1 T
1232338 ATCCCTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.09, C:0.00, G:0.30, T:0.60
Consensus pattern (21 bp):
TTTAGTGATTTTGGGGTTGTT
Found at i:1233370 original size:20 final size:22
Alignment explanation
Indices: 1233325--1233382 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
1233315 ATATGGGTAG
1233325 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
1233349 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
1233369 TGCATCGATGCACT
1 TGCATCGATGCACT
1233383 TCAAGGGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.53
22 1 0.03
23 2 0.06
24 13 0.38
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:1235200 original size:71 final size:72
Alignment explanation
Indices: 1235096--1235285 Score: 242
Period size: 71 Copynumber: 2.6 Consensus size: 72
1235086 TCATATATTA
* * * *
1235096 TATATATTTTCAAAAATGTTTTCTAAA-TTTATATTATATGTTTTTTC-ATAAGCATTTTTAAAA
1 TATATATTTTCAAAAATGTTTTCAAAACTATATATTATATGTTTTTTCGAAAAG-ATTTTCAAAA
* *
1235159 TTATACAT
65 CTATACAC
* * *
1235167 TATATATTTTC-AAAATGTTTTCAAAACTATATATTATATATGTTTTCGAAAAGGTTTTCAAAAC
1 TATATATTTTCAAAAATGTTTTCAAAACTATATATTATATGTTTTTTCGAAAAGATTTTCAAAAC
*
1235231 TATATAC
66 TATACAC
1235238 TATATATTTTCAAAAATGTTTTCAAAACTATATAGTATATATGTTTTT
1 TATATATTTTCAAAAATGTTTTCAAAACTATATA-T-TATATGTTTTT
1235286 AAAAATGTTT
Statistics
Matches: 102, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
70 14 0.14
71 52 0.51
72 26 0.25
73 1 0.01
74 9 0.09
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.48
Consensus pattern (72 bp):
TATATATTTTCAAAAATGTTTTCAAAACTATATATTATATGTTTTTTCGAAAAGATTTTCAAAAC
TATACAC
Found at i:1235242 original size:35 final size:36
Alignment explanation
Indices: 1235053--1235312 Score: 241
Period size: 37 Copynumber: 7.3 Consensus size: 36
1235043 TATTTAAAAA
* * *
1235053 ATAT-TATATATATTTTCTAAAATATTTCCAAAA-T
1 ATATATATATATATTTTCAAAAATGTTTTCAAAACT
*
1235087 CATATATTATATATATTTTCAAAAATGTTTTCTAAA-T
1 -ATATA-TATATATATTTTCAAAAATGTTTTCAAAACT
* * * * *
1235124 TTATATTATATGTTTTTTCATAAGCAT-TTTT-AAAATT
1 ATATA-TATATATATTTTCA-AA-AATGTTTTCAAAACT
*
1235161 ATACAT-TATATATTTTC-AAAATGTTTTCAAAACT
1 ATATATATATATATTTTCAAAAATGTTTTCAAAACT
* * *
1235195 ATATATTATATATGTTTTCGAAAAGGTTTTCAAAACT
1 ATATA-TATATATATTTTCAAAAATGTTTTCAAAACT
*
1235232 ATATA-CTATATATTTTCAAAAATGTTTTCAAAACT
1 ATATATATATATATTTTCAAAAATGTTTTCAAAACT
* * *
1235267 ATATAGTATATATGTTTTTAAAAATGTTTT-TAAACT
1 ATATA-TATATATATTTTCAAAAATGTTTTCAAAACT
1235303 ATATATATAT
1 ATATATATAT
1235313 TTTCAAAATT
Statistics
Matches: 187, Mismatches: 26, Indels: 24
0.79 0.11 0.10
Matches are distributed among these distances:
32 2 0.01
33 6 0.03
34 9 0.05
35 50 0.27
36 41 0.22
37 77 0.41
38 2 0.01
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.48
Consensus pattern (36 bp):
ATATATATATATATTTTCAAAAATGTTTTCAAAACT
Found at i:1235306 original size:71 final size:68
Alignment explanation
Indices: 1235096--1235320 Score: 244
Period size: 72 Copynumber: 3.2 Consensus size: 68
1235086 TCATATATTA
* * * * *
1235096 TATATATTTTCAAAAATGTTTTCTAAA-TTTATAT-TATATGTTTTTTCATAAGCATTTTTAAAA
1 TATATATTTTCAAAAATGTTTTCAAAACTATATATATATATG-TTTTTAAAAAG--TTTTTAAAC
1235159 TTATAC
63 TTATAC
* * *
1235165 ATTATATATTTTC-AAAATGTTTTCAAAACTATATATTATATATGTTTTCGAAAAGGTTTTCAAA
1 --TATATATTTTCAAAAATGTTTTCAAAACTATATA-TATATATGTTTT-TAAAAAGTTTT-TAA
1235229 ACTATATAC
61 ACT-TATAC
1235238 TATATATTTTCAAAAATGTTTTCAAAACTATATAGTATATATGTTTTTAAAAATGTTTTTAAAC-
1 TATATATTTTCAAAAATGTTTTCAAAACTATATA-TATATATGTTTTTAAAAA-GTTTTTAAACT
1235302 TATA-
64 TATAC
1235306 TATATATTTTCAAAA
1 TATATATTTTCAAAA
1235321 TTATATATTA
Statistics
Matches: 134, Mismatches: 12, Indels: 19
0.81 0.07 0.12
Matches are distributed among these distances:
68 15 0.11
69 4 0.03
70 14 0.10
71 39 0.29
72 48 0.36
73 14 0.10
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.48
Consensus pattern (68 bp):
TATATATTTTCAAAAATGTTTTCAAAACTATATATATATATGTTTTTAAAAAGTTTTTAAACTTA
TAC
Found at i:1235326 original size:56 final size:60
Alignment explanation
Indices: 1235256--1235374 Score: 156
Period size: 56 Copynumber: 2.0 Consensus size: 60
1235246 TTCAAAAATG
* *
1235256 TTTTCAAAACTATATAGTATATATGTTTT-TAAA-AATGTTTTTAAA-CTATATA-TATA
1 TTTTCAAAACTATATAGTATATATATTTTAAAAATAATGTTTTTAAAGCTATATATTATA
* *
1235312 TTTTCAAAATTATATATTATATATATTTTCAAAAAATAATGTTTTTAAAGCTATATATTATA
1 TTTTCAAAACTATATAGTATATATATTTT--AAAAATAATGTTTTTAAAGCTATATATTATA
1235374 T
1 T
1235375 ATGTTATATG
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
56 26 0.49
59 3 0.06
60 12 0.23
61 7 0.13
62 5 0.09
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (60 bp):
TTTTCAAAACTATATAGTATATATATTTTAAAAATAATGTTTTTAAAGCTATATATTATA
Found at i:1236495 original size:13 final size:13
Alignment explanation
Indices: 1236477--1236512 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 13
1236467 CGTACTTTAC
1236477 ACATGCATGAGAT
1 ACATGCATGAGAT
1236490 ACATGCATATGAGAT
1 ACATGC--ATGAGAT
1236505 ACATGCAT
1 ACATGCAT
1236513 ACATCACATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 8 0.38
15 13 0.62
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (13 bp):
ACATGCATGAGAT
Found at i:1236501 original size:15 final size:15
Alignment explanation
Indices: 1236483--1236513 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1236473 TTACACATGC
1236483 ATGAGATACATGCAT
1 ATGAGATACATGCAT
1236498 ATGAGATACATGCAT
1 ATGAGATACATGCAT
1236513 A
1 A
1236514 CATCACATAC
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:0.42, C:0.13, G:0.19, T:0.26
Consensus pattern (15 bp):
ATGAGATACATGCAT
Found at i:1247853 original size:21 final size:21
Alignment explanation
Indices: 1247829--1247871 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1247819 ATAAAAAGGC
1247829 AAAAAAACATAAAATAAAAAT
1 AAAAAAACATAAAATAAAAAT
** *
1247850 AAAAAAGTATATAATAAAAAT
1 AAAAAAACATAAAATAAAAAT
1247871 A
1 A
1247872 TATATAAAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (21 bp):
AAAAAAACATAAAATAAAAAT
Found at i:1247924 original size:19 final size:19
Alignment explanation
Indices: 1247902--1247947 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1247892 ATGAAAAAAG
*
1247902 AAATAAAGACTAA-AAAATA
1 AAATAAA-ACAAAGAAAATA
*
1247921 AAATAAATCAAAGAAAATA
1 AAATAAAACAAAGAAAATA
1247940 AAATAAAA
1 AAATAAAA
1247948 TATTATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 3 0.13
19 20 0.87
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.15
Consensus pattern (19 bp):
AAATAAAACAAAGAAAATA
Found at i:1247933 original size:24 final size:23
Alignment explanation
Indices: 1247897--1247949 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
1247887 ATCAAATGAA
* *
1247897 AAAAGAAATAAAGACTAA-AAAAT
1 AAAATAAATAAAGA-AAATAAAAT
1247920 AAAATAAATCAAAGAAAATAAAAT
1 AAAATAAAT-AAAGAAAATAAAAT
1247944 AAAATA
1 AAAATA
1247950 TTATTTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 10 0.38
24 16 0.62
ACGTcount: A:0.75, C:0.04, G:0.06, T:0.15
Consensus pattern (23 bp):
AAAATAAATAAAGAAAATAAAAT
Found at i:1249024 original size:3 final size:3
Alignment explanation
Indices: 1249016--1249050 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
1249006 TAAAATAAAA
1249016 AAT AAT AAT AAT AAT AAAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT A
1249051 TAAAAAAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1249034 original size:16 final size:16
Alignment explanation
Indices: 1249009--1249053 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
1248999 TTAGACCTAA
*
1249009 AATAAAAAATAATAAT
1 AATAATAAATAATAAT
1249025 AATAATAAATAATAAT
1 AATAATAAATAATAAT
1249041 AATAATAATATAA
1 AATAATAA-ATAA
1249054 AAAAGTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
16 23 0.85
17 4 0.15
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AATAATAAATAATAAT
Found at i:1249158 original size:41 final size:38
Alignment explanation
Indices: 1249062--1249190 Score: 137
Period size: 37 Copynumber: 3.5 Consensus size: 38
1249052 AAAAAAGTAT
1249062 TTTTTTAAAAAACTATA-TAATATAAATTTTAAAAATG
1 TTTTTTAAAAAACTATATTAATATAAATTTTAAAAATG
*
1249099 TTTTTTAAAAAACTTATATTATATATATATTTTAAAAAATG
1 TTTTTTAAAAAAC-TATATTA-ATATAAATTTT-AAAAATG
* **
1249140 CTTTTTAAAAAAACTATA-TAAT-T---TTCAAAAAATG
1 -TTTTTTAAAAAACTATATTAATATAAATTTTAAAAATG
1249174 TTTTTT-AAAAACTATAT
1 TTTTTTAAAAAACTATAT
1249191 ATTTTCAAAA
Statistics
Matches: 81, Mismatches: 5, Indels: 16
0.79 0.05 0.16
Matches are distributed among these distances:
32 10 0.12
33 5 0.06
34 7 0.09
35 2 0.02
37 13 0.16
38 5 0.06
39 4 0.05
40 12 0.15
41 11 0.14
42 12 0.15
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (38 bp):
TTTTTTAAAAAACTATATTAATATAAATTTTAAAAATG
Found at i:1249184 original size:32 final size:32
Alignment explanation
Indices: 1249120--1249259 Score: 126
Period size: 32 Copynumber: 4.2 Consensus size: 32
1249110 ACTTATATTA
1249120 TATATATATTTT-AAAAAATGCTTTTTAAAAAAAC
1 TATATA-ATTTTCAAAAAATG-TTTTT-AAAAAAC
*
1249154 TATATAATTTTCAAAAAATGTTTTTTAAAAAC
1 TATATAATTTTCAAAAAATGTTTTTAAAAAAC
* *
1249186 TATAT-ATTTTC-AAAAATGTTTTCAAAAATTATATAT
1 TATATAATTTTCAAAAAATGTTTT--TAAA--A-A-AC
*
1249222 TATATAAGTTTTCAAAAAATG-TTTTCAAAAAC
1 TATATAA-TTTTCAAAAAATGTTTTTAAAAAAC
1249254 TATATA
1 TATATA
1249260 TTATATTATA
Statistics
Matches: 89, Mismatches: 7, Indels: 22
0.75 0.06 0.19
Matches are distributed among these distances:
30 11 0.12
31 6 0.07
32 20 0.22
33 11 0.12
34 16 0.18
35 1 0.01
36 8 0.09
37 1 0.01
38 8 0.09
39 7 0.08
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (32 bp):
TATATAATTTTCAAAAAATGTTTTTAAAAAAC
Found at i:1249245 original size:39 final size:37
Alignment explanation
Indices: 1249064--1249437 Score: 230
Period size: 36 Copynumber: 9.9 Consensus size: 37
1249054 AAAAGTATTT
*
1249064 TTTTAAAAAACTATATA--ATATAAATTTT-AAAAATG
1 TTTT-AAAAACTATATATTATATAAGTTTTCAAAAATG
* *
1249099 TTTTTTAAAAAACT-TATATTATATATATATTTTAAAAAATG
1 --TTTT-AAAAACTATATATTATATA-A-GTTTTCAAAAATG
* *
1249140 CTTTTTAAAA--A-A-ACTATATAA-TTTTCAAAAAATG
1 -TTTTAAAAACTATATATTATATAAGTTTTC-AAAAATG
** *
1249174 TTTT-TTAA--A-A-ACTATAT-A-TTTTCAAAAATG
1 TTTTAAAAACTATATATTATATAAGTTTTCAAAAATG
*
1249204 TTTTCAAAAATTATATATTATATAAGTTTTCAAAAAATG
1 TTTT-AAAAACTATATATTATATAAGTTTTC-AAAAATG
* *
1249243 TTTTCAAAAACTATATATTATATTATATTATATATACTTTCTAAAATG
1 TTTT-AAAAAC----TA-TATATTATA-TA-A-GT--TTTCAAAAATG
*
1249291 TTTTAAAAACTATATATTATAT-AGTTTTCAAAAGTG
1 TTTTAAAAACTATATATTATATAAGTTTTCAAAAATG
*
1249327 TTTTAAAAACTATATATTATAT-AGTTTTCAAAAGTG
1 TTTTAAAAACTATATATTATATAAGTTTTCAAAAATG
*
1249363 TTTTAAAAAATTATATATTATATACA-TTTTC-AAAATG
1 TTTT-AAAAACTATATATTATATA-AGTTTTCAAAAATG
* *
1249400 TTTTTAGAAACTATATATTATATACGTATTTTCAAAAA
1 -TTTTAAAAACTATATATTATATAAG--TTTTCAAAAA
1249438 CCATTTGCAA
Statistics
Matches: 283, Mismatches: 20, Indels: 65
0.77 0.05 0.18
Matches are distributed among these distances:
30 11 0.04
31 6 0.02
32 13 0.05
33 8 0.03
34 8 0.03
35 2 0.01
36 66 0.23
37 53 0.19
38 20 0.07
39 29 0.10
40 13 0.05
41 8 0.03
42 9 0.03
43 4 0.01
44 9 0.03
45 2 0.01
46 1 0.00
47 7 0.02
48 10 0.04
49 4 0.01
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (37 bp):
TTTTAAAAACTATATATTATATAAGTTTTCAAAAATG
Found at i:1249381 original size:37 final size:35
Alignment explanation
Indices: 1249266--1249423 Score: 210
Period size: 37 Copynumber: 4.3 Consensus size: 35
1249256 TATATTATAT
1249266 TATATTATATA-TACTTTCTAAAATGTTTTAAAAACTA
1 TATATTATATAGT--TTTC-AAAATGTTTTAAAAACTA
1249303 TATATTATATAGTTTTCAAAAGTGTTTTAAAAACTA
1 TATATTATATAGTTTTCAAAA-TGTTTTAAAAACTA
*
1249339 TATATTATATAGTTTTCAAAAGTGTTTTAAAAAATTA
1 TATATTATATAGTTTTCAAAA-TGTTTT-AAAAACTA
* *
1249376 TATATTATATACATTTTCAAAATGTTTTTAGAAACTA
1 TATATTATATA-GTTTTCAAAATG-TTTTAAAAACTA
1249413 TATATTATATA
1 TATATTATATA
1249424 CGTATTTTCA
Statistics
Matches: 112, Mismatches: 4, Indels: 10
0.89 0.03 0.08
Matches are distributed among these distances:
35 4 0.04
36 46 0.41
37 48 0.43
38 14 0.12
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (35 bp):
TATATTATATAGTTTTCAAAATGTTTTAAAAACTA
Found at i:1249450 original size:39 final size:37
Alignment explanation
Indices: 1249292--1249464 Score: 109
Period size: 36 Copynumber: 4.6 Consensus size: 37
1249282 TCTAAAATGT
* * ****
1249292 TTTAAAAACTATATATTATATA-GTTTTCAAAAGTGT
1 TTTAGAAACTATATATTATATACATTTTCAAAAACCA
* * ****
1249328 TTTAAAAACTATATATTATATA-GTTTTCAAAAGTGT
1 TTTAGAAACTATATATTATATACATTTTCAAAAACCA
* * ****
1249364 TTTAAAAAATTATATATTATATACATTTTCAAAATGTT
1 TTT-AGAAACTATATATTATATACATTTTCAAAAACCA
1249402 TTTAGAAACTATATATTATATACGTATTTTCAAAAACCA
1 TTTAGAAACTATATATTATATAC--ATTTTCAAAAACCA
1249441 TTT-GCAAACTATAATATATATATA
1 TTTAG-AAACTAT-ATAT-TATATA
1249465 TGTGTGTGTG
Statistics
Matches: 119, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
36 39 0.33
37 36 0.30
38 14 0.12
39 20 0.17
40 4 0.03
41 6 0.05
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (37 bp):
TTTAGAAACTATATATTATATACATTTTCAAAAACCA
Found at i:1250300 original size:84 final size:84
Alignment explanation
Indices: 1250195--1251059 Score: 1136
Period size: 84 Copynumber: 10.4 Consensus size: 84
1250185 TTTTTATTGA
* ** * * * * * *
1250195 CAGATAGCCCTTCTTTCCTTGAGCTAAGTTGTAAATGATATGCCTTTGAGCTGAGTGTAGTCAAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAA
*
1250260 CTGGAAGGTCTTTTGGTGG
66 CTCGAAGGTCTTTTGGTGG
1250279 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAA
* *
1250344 CTCGAAGGTATTTTGTTGG
66 CTCGAAGGTCTTTTGGTGG
* * * * * *
1250363 CAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAA
1250428 CTCGAAGG--TTTTGGTCGG
66 CTCGAAGGTCTTTTGGT-GG
* * *
1250446 CAAATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAACGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAA
1250511 CTCGAAGGTCTTTTGGTGG
66 CTCGAAGGTCTTTTGGTGG
* *
1250530 CAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAA
*
1250595 CTCGAAGGTCTTTTGTTGG
66 CTCGAAGGTCTTTTGGTGG
* * * * * * *
1250614 CAAATAACCCTTCTTGTCTTGAGCTATGTTGCAAATGATGTGCCTTGAAGCTGAGTGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAA
* *
1250679 CTTGAAGGTC-TTCGGTCGG
66 CTCGAAGGTCTTTTGGT-GG
* * * *
1250698 CAGATAACCCTTCTAGCCTTGAGTTATACTGCAAATGATATGCCTTGGAGCTGAACTTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAA
*
1250763 CTCAAAGGTCTTTTGGTGG
66 CTCGAAGGTCTTTTGGTGG
* * **
1250782 CAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTTAAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAA
*
1250847 CTCAAAGGTCTTTTGGTGG
66 CTCGAAGGTCTTTTGGTGG
* * *
1250866 CATATAACCCTTCTAGCCTTGAGCTATGTTGCAAATGATATGCCTTGGAGCTGAGCGCAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAA
* *
1250931 CTCGAAGGTC-TTTGATGA
66 CTCGAAGGTCTTTTGGTGG
* * **
1250949 CAGATAGCCTTTCTTTCCTTGAGCTATGCTGCAAATG--ATGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAA
*
1251012 CTCGAAGGTC--TTGGCTGA
66 CTCGAAGGTCTTTTGG-TGG
* *
1251030 CAGATAACGCC-TCTCGCCTTGAGTTATGCT
1 CAGATAAC-CCTTCTAGCCTTGAGCTATGCT
1251060 ACCGATAGTT
Statistics
Matches: 687, Mismatches: 87, Indels: 17
0.87 0.11 0.02
Matches are distributed among these distances:
80 3 0.00
81 61 0.09
82 7 0.01
83 109 0.16
84 495 0.72
85 12 0.02
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.31
Consensus pattern (84 bp):
CAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAA
CTCGAAGGTCTTTTGGTGG
Found at i:1250819 original size:252 final size:252
Alignment explanation
Indices: 1250195--1251023 Score: 1261
Period size: 251 Copynumber: 3.3 Consensus size: 252
1250185 TTTTTATTGA
* ** * * * * * ** *
1250195 CAGATAGCCCTTCTTTCCTTGAGCTAAGTTGTAAATGATATGCCTTTGAGCTGAGTGTAGTCAAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAACGTAGTCGAA
* * *
1250260 CTGGAAGGTCTTTTGGTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATATGCCTT
66 CTCGAAGGTCTTTTGGTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTT
* *
1250325 GGAGCTGAGCGTAGTCGAACTCGAAGGTATTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTAT
131 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTAT
1250390 GTTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGAACTCGAAGGT-TTTGGTCGG
196 GTTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTCGG
*
1250446 CAAATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAACGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAACGTAGTCGAA
1250511 CTCGAAGGTCTTTTGGTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTT
66 CTCGAAGGTCTTTTGGTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTT
*
1250576 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGTCTTGAGCTAT
131 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTAT
* * *
1250641 GTTGCAAATGATGTGCCTTGAAGCTGAGTGTAGTCGAACTTGAAGGTCTTCGGTCGG
196 GTTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTCGG
* *
1250698 CAGATAACCCTTCTAGCCTTGAGTTATACTGCAAATGATATGCCTTGGAGCTGAACTTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAACGTAGTCGAA
*
1250763 CTCAAAGGTCTTTTGGTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTT
66 CTCGAAGGTCTTTTGGTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTT
** * * * *
1250828 GGAGCTGAGCGTAGTTAAACTCAAAGGTCTTTTGGTGGCATATAACCCTTCTAGCCTTGAGCTAT
131 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTAT
* * * * *
1250893 GTTGCAAATGATATGCCTTGGAGCTGAGCGCAGTCGAACTCGAAGGTCTTTGAT-GA
196 GTTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTCGG
* * ** * *
1250949 CAGATAGCCTTTCTTTCCTTGAGCTATGCTGCAAATG--ATGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAACGTAGTCGAA
1251012 CTCGAAGGTCTT
66 CTCGAAGGTCTT
1251024 GGCTGACAGA
Statistics
Matches: 528, Mismatches: 49, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
249 35 0.07
251 254 0.48
252 239 0.45
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (252 bp):
CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAACGTAGTCGAA
CTCGAAGGTCTTTTGGTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTT
GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTAT
GTTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTCGG
Found at i:1252447 original size:3 final size:3
Alignment explanation
Indices: 1252439--1252471 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1252429 AATAAGAAAT
1252439 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1252472 ATATAAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1252513 original size:37 final size:37
Alignment explanation
Indices: 1252472--1252622 Score: 99
Period size: 37 Copynumber: 4.3 Consensus size: 37
1252462 ATAATAATAA
*
1252472 ATATAA-AT-AAA-TATAAAAATGTATTTTTAAAAAAACT
1 ATATAATATAAAATTATAAAAAAGT-TTTTT--AAAAACT
*
1252509 ATATAATATAAAATTTTAAAAAAGTTTTTTAAAAACT
1 ATATAATATAAAATTATAAAAAAGTTTTTTAAAAACT
* *
1252546 ATATAAT-T----TT-TAAAAATG-TTTTCAAAAACT
1 ATATAATATAAAATTATAAAAAAGTTTTTTAAAAACT
* * * * *
1252576 ATATATTATATAAGTTTTAAAAAA-TGTTTTCAAAACT
1 ATATAATATA-AAATTATAAAAAAGTTTTTTAAAAACT
*
1252613 ATATATTATA
1 ATATAATATA
1252623 TAAGTTTTCA
Statistics
Matches: 94, Mismatches: 9, Indels: 22
0.75 0.07 0.18
Matches are distributed among these distances:
30 17 0.18
31 8 0.09
32 2 0.02
36 3 0.03
37 45 0.48
38 2 0.02
39 8 0.09
40 9 0.10
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (37 bp):
ATATAATATAAAATTATAAAAAAGTTTTTTAAAAACT
Found at i:1252555 original size:30 final size:30
Alignment explanation
Indices: 1252515--1252580 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
1252505 AACTATATAA
* *
1252515 TATAAAATTTTAAAAAA-GTTTTTTAAAAAC
1 TATATAATTTTAAAAAATG-TTTTCAAAAAC
*
1252545 TATATAATTTTTAAAAATGTTTTCAAAAAC
1 TATATAATTTTAAAAAATGTTTTCAAAAAC
1252575 TATATA
1 TATATA
1252581 TTATATAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 31 0.97
31 1 0.03
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (30 bp):
TATATAATTTTAAAAAATGTTTTCAAAAAC
Found at i:1252623 original size:37 final size:36
Alignment explanation
Indices: 1252545--1252774 Score: 236
Period size: 37 Copynumber: 6.2 Consensus size: 36
1252535 TTTTAAAAAC
*
1252545 TATATAATTTTTAAAAATGTTTTCAAAAACTATATAT
1 TATATAAGTTTTAAAAATGTTTTC-AAAACTATATAT
1252582 TATATAAGTTTTAAAAAATGTTTTCAAAACTATATAT
1 TATATAAGTTTT-AAAAATGTTTTCAAAACTATATAT
*
1252619 TATATAAGTTTTCAAAATGATTTT-AAAACCTATATAT
1 TATATAAGTTTTAAAAATG-TTTTCAAAA-CTATATAT
* *
1252656 TATATATACTTTCT-AAAATGTTTTAAAAACTATATAT
1 TATATA-AGTTT-TAAAAATGTTTTCAAAACTATATAT
* * *
1252693 TATAT-AGTTTTCAAAAGTATTTTAAAAAACTATATAT
1 TATATAAGTTTT-AAAAATGTTTT-CAAAACTATATAT
*
1252730 TATATACA-TTTTCAAAAATCGTTTGC-AAACTATAATAT
1 TATATA-AGTTTT-AAAAAT-GTTTTCAAAACTAT-ATAT
1252768 ATATATA
1 -TATATA
1252775 TATATAGATA
Statistics
Matches: 169, Mismatches: 10, Indels: 26
0.82 0.05 0.13
Matches are distributed among these distances:
34 1 0.01
35 4 0.02
36 18 0.11
37 95 0.56
38 40 0.24
39 11 0.07
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.43
Consensus pattern (36 bp):
TATATAAGTTTTAAAAATGTTTTCAAAACTATATAT
Found at i:1252652 original size:74 final size:74
Alignment explanation
Indices: 1252545--1252774 Score: 267
Period size: 74 Copynumber: 3.1 Consensus size: 74
1252535 TTTTAAAAAC
* * *
1252545 TATATAATTTTTAAAAATG-TTTTCAAAAACTATATATTATATA-AGTTTTAAAAAATGTTTTCA
1 TATATAAGTTTTCAAAATGATTTTAAAAAACTATATATTATATACA-TTTT-AAAAATGTTTTCA
1252608 AAACTATATAT
64 AAACTATATAT
* * *
1252619 TATATAAGTTTTCAAAATGATTTT-AAAACCTATATATTATATATACTTTCT-AAAATGTTTTAA
1 TATATAAGTTTTCAAAATGATTTTAAAAAACTATATATTATATACA-TTT-TAAAAATGTTTTCA
1252682 AAACTATATAT
64 AAACTATATAT
*
1252693 TATAT-AGTTTTCAAAA-GTATTTTAAAAAACTATATATTATATACATTTTCAAAAATCGTTTGC
1 TATATAAGTTTTCAAAATG-ATTTTAAAAAACTATATATTATATACATTTT-AAAAAT-GTTTTC
1252756 -AAACTATAATAT
63 AAAACTAT-ATAT
1252768 ATATATA
1 -TATATA
1252775 TATATAGATA
Statistics
Matches: 136, Mismatches: 9, Indels: 19
0.83 0.05 0.12
Matches are distributed among these distances:
72 2 0.01
73 19 0.14
74 93 0.68
75 16 0.12
76 6 0.04
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.43
Consensus pattern (74 bp):
TATATAAGTTTTCAAAATGATTTTAAAAAACTATATATTATATACATTTTAAAAATGTTTTCAAA
ACTATATAT
Found at i:1252763 original size:111 final size:114
Alignment explanation
Indices: 1252558--1252776 Score: 299
Period size: 111 Copynumber: 1.9 Consensus size: 114
1252548 ATAATTTTTA
* *
1252558 AAAATGTTTTCAAAAACTATATATTATATAAGTTTTAAAAAATGTTTTCAAAACTATATATTATA
1 AAAATGTTTTCAAAAACTATATATTATATAAGTTTTAAAAAATATTTTAAAAACTATATATTATA
*
1252623 TAAGTTTTCAAAATGATTTTAAAACCTAT-ATAT-TATATATACTTTCT
66 TAAGTTTTCAAAATGATTTGAAAACCTATAATATATATATATACTTTCT
* *
1252670 AAAATGTTTT-AAAAACTATATATTATAT-AGTTTTCAAAAGTATTTTAAAAAACTATATATTAT
1 AAAATGTTTTCAAAAACTATATATTATATAAGTTTTAAAAAATATTTT-AAAAACTATATATTAT
*
1252733 ATACA-TTTTCAAAAATCG-TTTGCAAA-CTATAATATATATATATA
65 ATA-AGTTTTC-AAAAT-GATTTGAAAACCTATAATATATATATATA
1252777 TATAGATAGA
Statistics
Matches: 95, Mismatches: 6, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
110 15 0.16
111 45 0.47
112 26 0.27
113 9 0.09
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (114 bp):
AAAATGTTTTCAAAAACTATATATTATATAAGTTTTAAAAAATATTTTAAAAACTATATATTATA
TAAGTTTTCAAAATGATTTGAAAACCTATAATATATATATATACTTTCT
Found at i:1254050 original size:24 final size:26
Alignment explanation
Indices: 1254023--1254075 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
1254013 CTGATAATTT
*
1254023 ATTTAT-AT-TTTTAAAATATTATAA
1 ATTTATCATCTTTTAAAATATTAAAA
*
1254047 ATTTATCTTCTTTTAAAATATTAAAA
1 ATTTATCATCTTTTAAAATATTAAAA
1254073 ATT
1 ATT
1254076 CGTTGTCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 6 0.24
25 1 0.04
26 18 0.72
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (26 bp):
ATTTATCATCTTTTAAAATATTAAAA
Found at i:1255554 original size:20 final size:20
Alignment explanation
Indices: 1255529--1255566 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1255519 CAAAGAAAAT
1255529 ATAATTCCTAAAAATAATAG
1 ATAATTCCTAAAAATAATAG
*
1255549 ATAATTCCTAAAGATAAT
1 ATAATTCCTAAAAATAAT
1255567 TCTCAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.32
Consensus pattern (20 bp):
ATAATTCCTAAAAATAATAG
Found at i:1259617 original size:24 final size:24
Alignment explanation
Indices: 1259590--1259675 Score: 91
Period size: 24 Copynumber: 3.6 Consensus size: 24
1259580 CTGATTTGAA
* *
1259590 TTCTGATACCTAACCTGGATTCTG
1 TTCTGATATCTAATCTGGATTCTG
* *
1259614 TTCTGATTTCTGATCTGGATTCTG
1 TTCTGATATCTAATCTGGATTCTG
* * *
1259638 TTATGATATCTTATCTGAATTCTG
1 TTCTGATATCTAATCTGGATTCTG
* *
1259662 TTTTGATTTCTAAT
1 TTCTGATATCTAAT
1259676 ATATCCGTTA
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.20, C:0.16, G:0.15, T:0.49
Consensus pattern (24 bp):
TTCTGATATCTAATCTGGATTCTG
Found at i:1259630 original size:12 final size:12
Alignment explanation
Indices: 1259609--1259672 Score: 51
Period size: 12 Copynumber: 5.3 Consensus size: 12
1259599 CTAACCTGGA
1259609 TTCTGTTCTGAT
1 TTCTGTTCTGAT
*
1259621 TTCTGATCTGGA-
1 TTCTGTTCT-GAT
*
1259633 TTCTGTTATGAT
1 TTCTGTTCTGAT
* *
1259645 ATCT-TATCTGAA
1 TTCTGT-TCTGAT
*
1259657 TTCTGTTTTGAT
1 TTCTGTTCTGAT
1259669 TTCT
1 TTCT
1259673 AATATATCCG
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
11 3 0.08
12 33 0.85
13 3 0.08
ACGTcount: A:0.16, C:0.14, G:0.16, T:0.55
Consensus pattern (12 bp):
TTCTGTTCTGAT
Found at i:1261624 original size:2 final size:2
Alignment explanation
Indices: 1261617--1261646 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1261607 TCAAATTTTG
1261617 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
1261647 CAAGTTTGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1263996 original size:2 final size:2
Alignment explanation
Indices: 1263989--1264027 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1263979 ACTAAAAATG
1263989 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1264028 TATTTGTATA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1268266 original size:37 final size:38
Alignment explanation
Indices: 1268180--1268268 Score: 110
Period size: 38 Copynumber: 2.3 Consensus size: 38
1268170 TTTTCACCCT
* * *
1268180 AAACCCGAACCCG-ACCTGACCCGAATATTACGCTTAAAA
1 AAACCCG-ACCCGAATC-GACCCGAATATCACACTTAAAA
1268219 AAACCCGACCCGAATCGACCCGAATATCACACTT-AAA
1 AAACCCGACCCGAATCGACCCGAATATCACACTTAAAA
*
1268256 AAACTCGACCCGA
1 AAACCCGACCCGA
1268269 CCCGAACAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
37 15 0.33
38 21 0.47
39 9 0.20
ACGTcount: A:0.39, C:0.35, G:0.12, T:0.13
Consensus pattern (38 bp):
AAACCCGACCCGAATCGACCCGAATATCACACTTAAAA
Found at i:1269670 original size:2 final size:2
Alignment explanation
Indices: 1269661--1269702 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1269651 AAAATATAAA
1269661 AT AT -T 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
1269702 A
1 A
1269703 ATCGGGGCGG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1270026 original size:19 final size:19
Alignment explanation
Indices: 1270002--1270062 Score: 77
Period size: 19 Copynumber: 3.1 Consensus size: 19
1269992 TCGTGTTCAA
1270002 ATTTAATATTATTATTATT
1 ATTTAATATTATTATTATT
* *
1270021 ATTTAACATTACTATTATT
1 ATTTAATATTATTATTATT
1270040 ATTACTAATATTTATTATTATT
1 ATT--TAATA-TTATTATTATT
1270062 A
1 A
1270063 CATATTTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 20 0.57
21 4 0.11
22 11 0.31
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTAATATTATTATTATT
Found at i:1270054 original size:16 final size:17
Alignment explanation
Indices: 1270035--1270069 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1270025 AACATTACTA
1270035 TTATTATTACTA-ATAT
1 TTATTATTACTACATAT
*
1270051 TTATTATTATTACATAT
1 TTATTATTACTACATAT
1270068 TT
1 TT
1270070 TTACAGGCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (17 bp):
TTATTATTACTACATAT
Found at i:1271646 original size:2 final size:2
Alignment explanation
Indices: 1271641--1271680 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1271631 ATTTTTTTTA
1271641 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
1271681 GTTAAATAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1276018 original size:15 final size:17
Alignment explanation
Indices: 1275998--1276030 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
1275988 TTTTATTTTT
1275998 TTAAATT-CAAG-TAGA
1 TTAAATTACAAGATAGA
1276013 TTAAATTACAAGATAGA
1 TTAAATTACAAGATAGA
1276030 T
1 T
1276031 AAAAATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 4 0.25
17 5 0.31
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.33
Consensus pattern (17 bp):
TTAAATTACAAGATAGA
Found at i:1276118 original size:19 final size:19
Alignment explanation
Indices: 1276069--1276112 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
1276059 CATACTAATT
1276069 TTTTTTGTAATTTTTCTGA
1 TTTTTTGTAATTTTTCTGA
1276088 TTTTTTGTAATTTTTCTGA
1 TTTTTTGTAATTTTTCTGA
1276107 TTTTTT
1 TTTTTT
1276113 TAAATTCAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.14, C:0.05, G:0.09, T:0.73
Consensus pattern (19 bp):
TTTTTTGTAATTTTTCTGA
Found at i:1276120 original size:114 final size:114
Alignment explanation
Indices: 1275972--1276212 Score: 369
Period size: 114 Copynumber: 2.1 Consensus size: 114
1275962 TTTTCTCTTT
* * *
1275972 TTTTTTGTAATTTTTTTTTTATTTTTTTAAATTCAAGTAGATTAAATTACAAGATAGATAAAAAT
1 TTTTTTGTAA--TTTTTCTGATTTTTTTAAATTCAAGTAGATCAAATTACAAGATAGATAAAAAT
1276037 AAATTAAAATTAGATAAATAAACATACTAATTTT-TTTTGTAATTTTTCTGA
64 AAATTAAAATTAGATAAATAAACATACT-ATTTTGTTTTGTAATTTTTCTGA
* * **
1276088 TTTTTTGTAATTTTTCTGATTTTTTTAAATTCAAGTAGATCAATTTGCAAGATAGATAAAAATGT
1 TTTTTTGTAATTTTTCTGATTTTTTTAAATTCAAGTAGATCAAATTACAAGATAGATAAAAATAA
*
1276153 ATTGAAATTAGATAAATAAACATACTATTTTGTTTTGTAATTTTTCTGA
66 ATTAAAATTAGATAAATAAACATACTATTTTGTTTTGTAATTTTTCTGA
1276202 TTTTTT-TAATT
1 TTTTTTGTAATT
1276213 CAAGTAGATA
Statistics
Matches: 116, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
113 10 0.09
114 96 0.83
116 10 0.09
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.50
Consensus pattern (114 bp):
TTTTTTGTAATTTTTCTGATTTTTTTAAATTCAAGTAGATCAAATTACAAGATAGATAAAAATAA
ATTAAAATTAGATAAATAAACATACTATTTTGTTTTGTAATTTTTCTGA
Found at i:1276282 original size:93 final size:95
Alignment explanation
Indices: 1276090--1276300 Score: 333
Period size: 94 Copynumber: 2.3 Consensus size: 95
1276080 TTTTCTGATT
* * **
1276090 TTTTGTAATTTTTCTGATTTTTTTAAATTCAAGTAGATCAATTTGCAAGATAGATAAAAATGTAT
1 TTTTGTAATTTTTCTGATTTTTTTAAATTCAAGTAGATCAAATTGAAAGATAGATAAAAATACAT
1276155 TGAAATTAGATAAATAAACATACTATTTTG
66 TGAAATTAGATAAATAAACATACTATTTTG
1276185 TTTTGTAATTTTTCTGATTTTTTT-AATTCAAGTAGAT-AAATTGAAAGATAGATAAAAAATACA
1 TTTTGTAATTTTTCTGATTTTTTTAAATTCAAGTAGATCAAATTGAAAGATAGAT-AAAAATACA
1276248 TTGAAATTAGATAAATAAA-ATACTATTTTG
65 TTGAAATTAGATAAATAAACATACTATTTTG
1276278 TTTTGT-ATGTTTTCT-ATTTTTTT
1 TTTTGTAAT-TTTTCTGATTTTTTT
1276301 GTAATTTGTC
Statistics
Matches: 110, Mismatches: 4, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
92 10 0.09
93 37 0.34
94 39 0.35
95 24 0.22
ACGTcount: A:0.37, C:0.05, G:0.11, T:0.46
Consensus pattern (95 bp):
TTTTGTAATTTTTCTGATTTTTTTAAATTCAAGTAGATCAAATTGAAAGATAGATAAAAATACAT
TGAAATTAGATAAATAAACATACTATTTTG
Found at i:1276333 original size:115 final size:114
Alignment explanation
Indices: 1276185--1276393 Score: 334
Period size: 115 Copynumber: 1.8 Consensus size: 114
1276175 TACTATTTTG
*
1276185 TTTTGTAATTTTTCTGATTTTTTTAATTCAAGTAGA-TAAATTGAAAGATAGATAAAAAATACAT
1 TTTTGTAATTTGTCTGATTTTTTTAATTCAAGTAGATTAAATTGAAAGATAGAT-AAAAATACAT
1276249 TGAAATTAGATAAATAAA-ATACT-ATTTTGTTTTGTATGTTTTCTATTT
65 TGAAATTAGATAAATAAACATACTAATTTTGTTTTGTATGTTTTCTATTT
* *
1276297 TTTTGTAATTTGTCTGATTTTTTTTAAAATTCAAGTAGATTAAATTGTAATATAGATAAAAATAC
1 TTTTGTAATTTGTCTGA-TTTTTTT--AATTCAAGTAGATTAAATTGAAAGATAGATAAAAATAC
1276362 ATTGAAATTAGATAAATAAACATACTAATTTT
63 ATTGAAATTAGATAAATAAACATACTAATTTT
1276394 TTAAAACATA
Statistics
Matches: 88, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
112 16 0.18
113 7 0.08
115 40 0.45
116 20 0.23
117 5 0.06
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (114 bp):
TTTTGTAATTTGTCTGATTTTTTTAATTCAAGTAGATTAAATTGAAAGATAGATAAAAATACATT
GAAATTAGATAAATAAACATACTAATTTTGTTTTGTATGTTTTCTATTT
Found at i:1276371 original size:209 final size:211
Alignment explanation
Indices: 1275969--1276393 Score: 607
Period size: 209 Copynumber: 2.0 Consensus size: 211
1275959 TTTTTTTCTC
* * *
1275969 TTTTTTTTTGTAATTTTTTTTTTATTTTTTTAAATTCAAGTAGATTAAATTACAAGATAGATAAA
1 TTTTGTTTTGTAA-TTTTTTCTGATTTTTTTAAATTCAAGTAGATTAAATTACAAGATAGATAAA
1276034 AATAAATTAAAATTAGATAAATAAACATACTAATTTTTTTTGTAATTTTTCTGATTTTTTGTAAT
65 AATAAATTAAAATTAGATAAATAAACATACTAATTTTTTTTGTAATTTTTCTGATTTTTTGTAAT
* * **
1276099 TTTTCTGATTTTTTTAAATTCAAGTAGATCAATTTGCAAGATAGATAAAAATGTATTGAAATTAG
130 TTGTCTGATTTTTTTAAATTCAAGTAGATCAAATTGCAAGATAGATAAAAATACATTGAAATTAG
1276164 ATAAATAAACATACT-A
195 ATAAATAAACATACTAA
1276180 TTTTGTTTTGTAA-TTTTTCTGATTTTTTT-AATTCAAGTAGA-TAAATTGA-AAGATAGATAAA
1 TTTTGTTTTGTAATTTTTTCTGATTTTTTTAAATTCAAGTAGATTAAATT-ACAAGATAGAT-AA
* *
1276241 AAATACATTGAAATTAGATAAATAAA-ATACT-ATTTTGTTTTGT-ATGTTTTCT-ATTTTTTTG
64 AAATAAATTAAAATTAGATAAATAAACATACTAATTTT-TTTTGTAAT-TTTTCTGA-TTTTTTG
* * *
1276302 TAATTTGTCTGATTTTTTTTAAAATTCAAGTAGATTAAATTGTAATATAGATAAAAATACATTGA
126 TAATTTGTCTGA-TTTTTTT-AAATTCAAGTAGATCAAATTGCAAGATAGATAAAAATACATTGA
1276367 AATTAGATAAATAAACATACTAA
189 AATTAGATAAATAAACATACTAA
1276390 TTTT
1 TTTT
1276394 TTAAAACATA
Statistics
Matches: 194, Mismatches: 12, Indels: 17
0.87 0.05 0.08
Matches are distributed among these distances:
206 8 0.04
207 50 0.26
208 46 0.24
209 73 0.38
210 5 0.03
211 12 0.06
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.47
Consensus pattern (211 bp):
TTTTGTTTTGTAATTTTTTCTGATTTTTTTAAATTCAAGTAGATTAAATTACAAGATAGATAAAA
ATAAATTAAAATTAGATAAATAAACATACTAATTTTTTTTGTAATTTTTCTGATTTTTTGTAATT
TGTCTGATTTTTTTAAATTCAAGTAGATCAAATTGCAAGATAGATAAAAATACATTGAAATTAGA
TAAATAAACATACTAA
Found at i:1280699 original size:14 final size:15
Alignment explanation
Indices: 1280670--1280712 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 15
1280660 TTTTTAGTAG
1280670 ATATTT-ATAATATT
1 ATATTTAATAATATT
*
1280684 ATTTTTAATAAT-TT
1 ATATTTAATAATATT
1280698 ATATTTAAT-ATATT
1 ATATTTAATAATATT
1280712 A
1 A
1280713 AATACTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 2 0.08
14 18 0.72
15 5 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATATTTAATAATATT
Found at i:1285600 original size:20 final size:20
Alignment explanation
Indices: 1285563--1285601 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1285553 TTCACCAATT
**
1285563 TAAATCAAAATATGATACAA
1 TAAATCAAAATAAAATACAA
1285583 TAAATCAAAATAAAATACA
1 TAAATCAAAATAAAATACA
1285602 TAATTTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.64, C:0.10, G:0.03, T:0.23
Consensus pattern (20 bp):
TAAATCAAAATAAAATACAA
Found at i:1290334 original size:21 final size:21
Alignment explanation
Indices: 1290308--1290361 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
1290298 GATGAAGGAT
1290308 TACCTTGGTAAGAGGATGAAG
1 TACCTTGGTAAGAGGATGAAG
1290329 TACCTTGGTAAGAGGATGAAG
1 TACCTTGGTAAGAGGATGAAG
1290350 TACCTTGGTAAG
1 TACCTTGGTAAG
1290362 GTTCTCTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.31, C:0.11, G:0.31, T:0.26
Consensus pattern (21 bp):
TACCTTGGTAAGAGGATGAAG
Found at i:1291775 original size:59 final size:59
Alignment explanation
Indices: 1291698--1291818 Score: 190
Period size: 59 Copynumber: 2.1 Consensus size: 59
1291688 AATAGATGGA
* * * *
1291698 TAAGTTTCCTATCTAACCCTCCTAGTCGCAATGAAAAGGCAAACTCGATAATATGGCTC
1 TAAGTTTCCTATCGAACCCTCATAGTCGCAATGAAAAGACAAACTCGATAATATGACTC
1291757 TAAGTGTT-CTATCGAACCCTCATAGTCGCAATGAAAAGACAAACTCGATAATATGACTC
1 TAAGT-TTCCTATCGAACCCTCATAGTCGCAATGAAAAGACAAACTCGATAATATGACTC
1291816 TAA
1 TAA
1291819 CCAACCCTCC
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
59 55 0.96
60 2 0.04
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (59 bp):
TAAGTTTCCTATCGAACCCTCATAGTCGCAATGAAAAGACAAACTCGATAATATGACTC
Found at i:1296142 original size:23 final size:23
Alignment explanation
Indices: 1296108--1296165 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
1296098 ACGACCGAAT
* * *
1296108 ATGTGTCA-AAAGGCATAGGAAA
1 ATGTGCCATAAAGGCAAAGAAAA
1296130 ATGT-CCTATAAAGGCAAAGAAAA
1 ATGTGCC-ATAAAGGCAAAGAAAA
1296153 ATGTGCCATAAAG
1 ATGTGCCATAAAG
1296166 CCGAGATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 1 0.03
22 5 0.17
23 22 0.73
24 2 0.07
ACGTcount: A:0.47, C:0.12, G:0.22, T:0.19
Consensus pattern (23 bp):
ATGTGCCATAAAGGCAAAGAAAA
Found at i:1298203 original size:17 final size:17
Alignment explanation
Indices: 1298183--1298215 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1298173 AATATCTTGA
*
1298183 ATGAGCTAATGAATTGT
1 ATGAGCTAACGAATTGT
1298200 ATGAGCTAACGAATTG
1 ATGAGCTAACGAATTG
1298216 AGGACTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.09, G:0.24, T:0.30
Consensus pattern (17 bp):
ATGAGCTAACGAATTGT
Found at i:1299261 original size:43 final size:43
Alignment explanation
Indices: 1299213--1299388 Score: 271
Period size: 43 Copynumber: 4.1 Consensus size: 43
1299203 TGGTAACAAA
* * * *
1299213 AAACGCCGCAATAGGTGTTGATATTTGGCGGCATTTTTCCAAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
* *
1299256 GAACGCCGTAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
* *
1299299 AAACGCCGTAATAGGTGTTGATATTTAGCGGCGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
*
1299342 AAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
1299385 AAAC
1 AAAC
1299389 ACCACAAAAG
Statistics
Matches: 122, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 122 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (43 bp):
AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
Found at i:1299422 original size:43 final size:43
Alignment explanation
Indices: 1299273--1299422 Score: 115
Period size: 43 Copynumber: 3.5 Consensus size: 43
1299263 GTAATAGGTG
* * * ** * * *
1299273 TTGAGATTTAGCGGCGTTTTTCCCACAAACGCCGTAATAGGTG
1 TTGAGATATAACGGCGTTTTTCCCACAAACACCACAAAAGATC
* * * * * * *
1299316 TTGATATTTAGCGGCGTTTTTCCCACAAACGCCGCAATAGGTC
1 TTGAGATATAACGGCGTTTTTCCCACAAACACCACAAAAGATC
* *
1299359 TTGAGATTTAGCGGCGTTTTTCCCACAAACACCACAAAAGATC
1 TTGAGATATAACGGCGTTTTTCCCACAAACACCACAAAAGATC
1299402 -TG-GTATATAACGGCGCTTTTT
1 TTGAG-ATATAACGGCG-TTTTT
1299423 AGAATAAACA
Statistics
Matches: 95, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
41 1 0.01
42 11 0.12
43 83 0.87
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (43 bp):
TTGAGATATAACGGCGTTTTTCCCACAAACACCACAAAAGATC
Found at i:1299422 original size:86 final size:86
Alignment explanation
Indices: 1299241--1299422 Score: 222
Period size: 86 Copynumber: 2.1 Consensus size: 86
1299231 TGATATTTGG
* * * * *
1299241 CGGCATTTTTCCAACGAACGCCGTAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCACAAACGCC
1 CGGCGTTTTTCCAACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCCACAAACACC
** * * * * *
1299306 GTAATAGGTGTTGATATTTAG
66 ACAAAAGATGCTGATATATAA
*
1299327 CGGCGTTTTTCCCACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCCACAAACACC
1 CGGCGTTTTTCCAACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCCACAAACACC
*
1299392 ACAAAAGAT-CTGGTATATAA
66 ACAAAAGATGCTGATATATAA
1299412 CGGCGCTTTTT
1 CGGCG-TTTTT
1299423 AGAATAAACA
Statistics
Matches: 81, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
85 12 0.15
86 69 0.85
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (86 bp):
CGGCGTTTTTCCAACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCCACAAACACC
ACAAAAGATGCTGATATATAA
Found at i:1299617 original size:21 final size:21
Alignment explanation
Indices: 1299591--1299649 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
1299581 ATTTTCCAAT
*
1299591 AAACTTGACATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
* *
1299612 AAACTTAAAATCCATAACAAG
1 AAACTTGAAATCCATAACAAC
**
1299633 AAAAATGAAATCCATAA
1 AAACTTGAAATCCATAA
1299650 TAATAAATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.56, C:0.20, G:0.05, T:0.19
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:1310342 original size:7 final size:7
Alignment explanation
Indices: 1310332--1310364 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
1310322 TTAGAACTTG
1310332 TTTAGGA
1 TTTAGGA
1310339 TTTAGGA
1 TTTAGGA
1310346 TTTAGG-
1 TTTAGGA
*
1310352 TTTAGGG
1 TTTAGGA
1310359 TTTAGG
1 TTTAGG
1310365 CCGGTTTAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.45
Consensus pattern (7 bp):
TTTAGGA
Found at i:1310357 original size:13 final size:14
Alignment explanation
Indices: 1310332--1310364 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1310322 TTAGAACTTG
1310332 TTTAGGATTTAGGA
1 TTTAGGATTTAGGA
*
1310346 TTTAGG-TTTAGGG
1 TTTAGGATTTAGGA
1310359 TTTAGG
1 TTTAGG
1310365 CCGGTTTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.45
Consensus pattern (14 bp):
TTTAGGATTTAGGA
Found at i:1310434 original size:29 final size:30
Alignment explanation
Indices: 1310402--1310466 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
1310392 TTCAGATCGA
* **
1310402 GCTTAGGGTTTAGGTTGGGTTTAAA-CCGG
1 GCTTAGGGTTCAGGCCGGGTTTAAATCCGG
*
1310431 GCTTAGGGTTCAGGCCGGGTTTAAATCGGG
1 GCTTAGGGTTCAGGCCGGGTTTAAATCCGG
1310461 GCTTAG
1 GCTTAG
1310467 ATTGCAAACC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 22 0.71
30 9 0.29
ACGTcount: A:0.17, C:0.14, G:0.38, T:0.31
Consensus pattern (30 bp):
GCTTAGGGTTCAGGCCGGGTTTAAATCCGG
Found at i:1310513 original size:18 final size:18
Alignment explanation
Indices: 1310480--1310540 Score: 88
Period size: 18 Copynumber: 3.4 Consensus size: 18
1310470 GCAAACCTGG
*
1310480 TTAGGG-TCAGACCGGGT
1 TTAGGGTTCAGATCGGGT
1310497 TTAGGGTTCAGATCGGGT
1 TTAGGGTTCAGATCGGGT
*
1310515 TTAGGGTTCAGATCGGAT
1 TTAGGGTTCAGATCGGGT
*
1310533 TCAGGGTT
1 TTAGGGTT
1310541 TGTATACAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
17 6 0.15
18 34 0.85
ACGTcount: A:0.18, C:0.13, G:0.38, T:0.31
Consensus pattern (18 bp):
TTAGGGTTCAGATCGGGT
Found at i:1313818 original size:5 final size:5
Alignment explanation
Indices: 1313808--1313832 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1313798 CATGGGACTG
1313808 AAATA AAATA AAATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA
1313833 GAATGCAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:1313930 original size:71 final size:71
Alignment explanation
Indices: 1313842--1313976 Score: 198
Period size: 71 Copynumber: 1.9 Consensus size: 71
1313832 AGAATGCAAT
* * *
1313842 AATTAAAGGACTGAAATTAAATTACTAAAAAGTAGAGGACAGAAATAAAAGGCAGAAAATTAAAA
1 AATTAAAGGACTCAAATTAAATCACTAAAAAGTAAAGGACAGAAATAAAAGGCAGAAAATTAAAA
1313907 TCATAA
66 TCATAA
* * * * *
1313913 AATTTAAGGACTCAAATTAAATCACTGAAAAGTAAAGGACATAAATAGAAGGCAGCAAATTAAA
1 AATTAAAGGACTCAAATTAAATCACTAAAAAGTAAAGGACAGAAATAAAAGGCAGAAAATTAAA
1313977 GTAATGTAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
71 56 1.00
ACGTcount: A:0.56, C:0.09, G:0.16, T:0.20
Consensus pattern (71 bp):
AATTAAAGGACTCAAATTAAATCACTAAAAAGTAAAGGACAGAAATAAAAGGCAGAAAATTAAAA
TCATAA
Found at i:1313988 original size:71 final size:71
Alignment explanation
Indices: 1313840--1314006 Score: 190
Period size: 71 Copynumber: 2.3 Consensus size: 71
1313830 ATAGAATGCA
* * * *
1313840 ATAATTAAAGGACTGAAATTAAATTACTAAAAAGTAGAGGACAGAAATAAAAGGCAGAAAATTAA
1 ATAATTTAAGGACTAAAATTAAATCACTAAAAAGTAAAGGACAGAAATAAAAGGCAGAAAATTAA
*
1313905 AATCAT
66 AATAAT
* * * * * *
1313911 AAAATTTAAGGACTCAAATTAAATCACTGAAAAGTAAAGGACATAAATAGAAGGCAGCAAATTAA
1 ATAATTTAAGGACTAAAATTAAATCACTAAAAAGTAAAGGACAGAAATAAAAGGCAGAAAATTAA
*
1313976 AGTAAT
66 AATAAT
* * *
1313982 GTAATTTTATGGACTAAAATAAAAT
1 ATAA-TTTAAGGACTAAAATTAAAT
1314007 AAAGGAAAAT
Statistics
Matches: 79, Mismatches: 16, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
71 62 0.78
72 17 0.22
ACGTcount: A:0.54, C:0.08, G:0.15, T:0.23
Consensus pattern (71 bp):
ATAATTTAAGGACTAAAATTAAATCACTAAAAAGTAAAGGACAGAAATAAAAGGCAGAAAATTAA
AATAAT
Found at i:1314225 original size:23 final size:23
Alignment explanation
Indices: 1314199--1314246 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
1314189 AAAATTAGTT
*
1314199 GTTAGTAGTTAGAAGTTAGAAAA
1 GTTAGTAGTTAGAAATTAGAAAA
* * *
1314222 GTTAGTTGTTATAAATTAGTAAA
1 GTTAGTAGTTAGAAATTAGAAAA
1314245 GT
1 GT
1314247 CATGATCATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.38
Consensus pattern (23 bp):
GTTAGTAGTTAGAAATTAGAAAA
Done.