Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009001.1 Hibiscus syriacus cultivar Beakdansim tig00112383_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: 4740655
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 24
Found at i:2490924 original size:25 final size:24
Alignment explanation
Indices: 2490865--2490924 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 24
2490855 GCACATGACT
*
2490865 TTTATCTGATTTGAAGTATGATTG
1 TTTATCTGATTTGAAGTATGAATG
* *
2490889 TCTGATTTGATTTGAA-TATTGAATG
1 T-TTATCTGATTTGAAGTA-TGAATG
2490914 ATTTATCTGAT
1 -TTTATCTGAT
2490925 CTAAAAGCCT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
24 3 0.11
25 24 0.86
26 1 0.04
ACGTcount: A:0.27, C:0.05, G:0.18, T:0.50
Consensus pattern (24 bp):
TTTATCTGATTTGAAGTATGAATG
Found at i:2499178 original size:24 final size:24
Alignment explanation
Indices: 2499146--2499270 Score: 146
Period size: 24 Copynumber: 5.2 Consensus size: 24
2499136 TTTTCGATTT
2499146 GATTACTGATCTGATACTTGACATG
1 GATT-CTGATCTGATACTTGACATG
*
2499171 GATTCTGATATGATA-TCTGACATG
1 GATTCTGATCTGATACT-TGACATG
* *
2499195 GATTCTGATCTAATACTTGACTTG
1 GATTCTGATCTGATACTTGACATG
*
2499219 GATTCTGATC-GAATACTTGACCTG
1 GATTCTGATCTG-ATACTTGACATG
* * *
2499243 GATTTTGATATGATACTTGACCTG
1 GATTCTGATCTGATACTTGACATG
2499267 GATT
1 GATT
2499271 ATGTTTTGAT
Statistics
Matches: 88, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
23 1 0.01
24 81 0.92
25 6 0.07
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.38
Consensus pattern (24 bp):
GATTCTGATCTGATACTTGACATG
Found at i:2499201 original size:12 final size:12
Alignment explanation
Indices: 2499164--2499202 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
2499154 ATCTGATACT
2499164 TGACATGGATTC
1 TGACATGGATTC
*
2499176 TGATAT-GATATC
1 TGACATGGAT-TC
2499188 TGACATGGATTC
1 TGACATGGATTC
2499200 TGA
1 TGA
2499203 TCTAATACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 3 0.13
12 17 0.74
13 3 0.13
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:2500619 original size:2 final size:2
Alignment explanation
Indices: 2500612--2500636 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2500602 AGATCTTTTA
2500612 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 A
2500637 CCCCCATCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2500862 original size:24 final size:24
Alignment explanation
Indices: 2500835--2500884 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
2500825 CATATCAAAA
*
2500835 ATCAAAACATAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* *
2500859 ATCATATCAAAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
2500883 AT
1 AT
2500885 TCGATCAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.44, C:0.20, G:0.12, T:0.24
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:2500891 original size:24 final size:25
Alignment explanation
Indices: 2500845--2500969 Score: 145
Period size: 24 Copynumber: 5.2 Consensus size: 25
2500835 ATCAAAACAT
* *
2500845 AATCCAGGTCAAGTA-TCATATCAA
1 AATCCAGGTCAAGTATTCAGATCAG
2500869 AATCCAGGTCAAGTATTC-GATCAG
1 AATCCAGGTCAAGTATTCAGATCAG
*
2500893 AATCCAAGTCAAGTATT-AGATCAG
1 AATCCAGGTCAAGTATTCAGATCAG
*
2500917 AATCCATGTC-AG-ATATCAGATCAG
1 AATCCAGGTCAAGTAT-TCAGATCAG
*
2500941 AATCCATGTCAAGTA-TCAGATCAG
1 AATCCAGGTCAAGTATTCAGATCAG
2500965 TAATC
1 -AATC
2500970 AAATAAAAAA
Statistics
Matches: 90, Mismatches: 4, Indels: 13
0.84 0.04 0.12
Matches are distributed among these distances:
22 2 0.02
23 3 0.03
24 76 0.84
25 8 0.09
26 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (25 bp):
AATCCAGGTCAAGTATTCAGATCAG
Found at i:2500983 original size:48 final size:48
Alignment explanation
Indices: 2500887--2500983 Score: 115
Period size: 48 Copynumber: 2.0 Consensus size: 48
2500877 TCAAGTATTC
* ** * * *
2500887 GATCAGAATCCAAGTCAAGTATTAGATCAGAATCCATGTCAGATATCA
1 GATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATAAAAAATCA
*
2500935 GATCAGAATCCATGTCAAGTATCAGATCAGTAAT-CAAATAAAAAATCA
1 GATCAGAATCCAAGTCAAGTATCAGATCAG-AATCCAAATAAAAAATCA
2500983 G
1 G
2500984 GTAAAATATT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
48 38 0.93
49 3 0.07
ACGTcount: A:0.43, C:0.18, G:0.15, T:0.24
Consensus pattern (48 bp):
GATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATAAAAAATCA
Found at i:2503460 original size:18 final size:18
Alignment explanation
Indices: 2503437--2503475 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
2503427 AACAATCAAC
*
2503437 GGTCAACGGATCGGGTCG
1 GGTCAACGGATCAGGTCG
2503455 GGTCAACGGATCAGGTCG
1 GGTCAACGGATCAGGTCG
2503473 GGT
1 GGT
2503476 TGTGACCGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.18, C:0.21, G:0.44, T:0.18
Consensus pattern (18 bp):
GGTCAACGGATCAGGTCG
Found at i:2513328 original size:20 final size:20
Alignment explanation
Indices: 2513303--2513347 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
2513293 AGCGTGACAT
2513303 AAAGGAAGAGAACATGTCAC
1 AAAGGAAGAGAACATGTCAC
2513323 AAAGGAAGAGAACATGTCAC
1 AAAGGAAGAGAACATGTCAC
2513343 AAAGG
1 AAAGG
2513348 CATAATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.51, C:0.13, G:0.27, T:0.09
Consensus pattern (20 bp):
AAAGGAAGAGAACATGTCAC
Found at i:2515123 original size:13 final size:13
Alignment explanation
Indices: 2515100--2515136 Score: 56
Period size: 14 Copynumber: 2.7 Consensus size: 13
2515090 TGTTTGATAA
2515100 ATTTTTCTAAAAAT
1 ATTTTT-TAAAAAT
2515114 ATTTTTTAAAAAT
1 ATTTTTTAAAAAT
2515127 ATGTTTTTAA
1 AT-TTTTTAA
2515137 TGAAACATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (13 bp):
ATTTTTTAAAAAT
Found at i:2515453 original size:87 final size:88
Alignment explanation
Indices: 2515346--2515506 Score: 288
Period size: 87 Copynumber: 1.8 Consensus size: 88
2515336 TATGTTATGT
*
2515346 TATATTATTTAACCGGAAATATTATCAAGTATAATAACATATTAGATAACGCTTATATAATGTAA
1 TATATTATTTAACCGGAAATATTATCAAGTACAATAACATATTAGATAACGCTTATATAATGTAA
2515411 TAGGTAGCGCTTACATAATAAAA
66 TAGGTAGCGCTTACATAATAAAA
* *
2515434 TATA-TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAA
1 TATATTATTTAACCGGAAATATTATCAAGTACAATAACATATTAGATAACGCTTATATAATGTAA
2515498 TAGGTAGCG
66 TAGGTAGCG
2515507 TTTATATTGA
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
87 66 0.94
88 4 0.06
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.34
Consensus pattern (88 bp):
TATATTATTTAACCGGAAATATTATCAAGTACAATAACATATTAGATAACGCTTATATAATGTAA
TAGGTAGCGCTTACATAATAAAA
Found at i:2516215 original size:200 final size:198
Alignment explanation
Indices: 2515508--2516230 Score: 773
Period size: 199 Copynumber: 3.6 Consensus size: 198
2515498 TAGGTAGCGT
* * * *
2515508 TTATATTGACCTATTTTATAAGT-AAACCGATATATTTATATCAGTAACATTGTAAATTTACCTA
1 TTATGTTGACCTATTTTCTAA-TAAAACCGATATATTTATACCAGTTACATTGTAAATTTACCTA
* *
2515572 TTACATTATAATTATTGGTTTCAATATTTTTT-GGATCGATACATTTTTATAAATGTATCGACAC
65 TTACATTATAATTATTGGTTTCGAT-TTTTTTGGGATCGATACA-TTTTAAAAATGTATCGACAC
* * * * * **
2515636 TATATGCGTTCACCCTTTTGGGCATTCATTCTGGAAAAAAATATTTACACAACATTAAAAAGTGT
128 TTTATGAGTGCACCCGTTTGGGCATTCATTCTGGACAAAAATATCGACACAA-ATTAAAAAGTGT
*
2515701 CGACACA
192 CGATACA
* * * ** * * * ** *
2515708 TTATGTAGACCTATTCTC-ACATAAAACCGGTATAAATATATC-GATTATACTACAAAATTACCT
1 TTATGTTGACCTATTTTCTA-ATAAAACCGATATATTTATACCAG-TTACATTGTAAATTTACCT
* *
2515771 ATTACATTATAATTA-TGAGTTTCGATATTTTTGGGATCGATACTTTTTAAAAATGTATCGACAC
64 ATTACATTATAATTATTG-GTTTCGATTTTTTTGGGATCGATACATTTTAAAAATGTATCGACAC
* * *
2515835 TTTATGAGTGCACCCGTCT-GGCATTCATTATGGACAAAATATATCGACACAAATTTAATAAGTG
128 TTTATGAGTGCACCCGTTTGGGCATTCATTCTGGACAAAA-ATATCGACACAAA-TTAAAAAGTG
* *
2515899 TCGATGCT
191 TCGATACA
* * * * *
2515907 TTATGATGACCTATTTTCTCATAAAACTGATATATTTATACCGGTTACATTGTAAATTTACATAT
1 TTATGTTGACCTATTTTCTAATAAAACCGATATATTTATACCAGTTACATTGTAAATTTACCTAT
* * * *
2515972 TACATTATAATTATCGGTTTCGATTTTATTGGGATCAATAC-TTTTAATAATTGTATCGACACTT
66 TACATTATAATTATTGGTTTCGATTTTTTTGGGATCGATACATTTTAA-AAATGTATCGACACTT
* * * *
2516036 TATGTGTGCACCCCGTTTGGGCATTGATTCTGGACAATAAGTATCGACACAAATTACACAAGTGT
130 TATGAGTGCA-CCCGTTTGGGCATTCATTCTGGACAA-AAATATCGACACAAATTA-AAAAGTGT
2516101 CGATACA
192 CGATACA
* * * * * *
2516108 TTATGTTGACATGTTTTCTAAT-TAACCGGTATATTTATGCCAGTTACATTGTTAATTTACCTAT
1 TTATGTTGACCTATTTTCTAATAAAACCGATATATTTATACCAGTTACATTGTAAATTTACCTAT
*
2516172 TACATTATAATTATTGGTTTTGATGTTTTTTGGG-TCGATAC-TTTTAGAAAATGTATCGA
66 TACATTATAATTATTGGTTTCGAT-TTTTTTGGGATCGATACATTTTA-AAAATGTATCGA
2516231 TACATATTTA
Statistics
Matches: 432, Mismatches: 74, Indels: 34
0.80 0.14 0.06
Matches are distributed among these distances:
198 25 0.06
199 173 0.40
200 165 0.38
201 67 0.16
202 2 0.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (198 bp):
TTATGTTGACCTATTTTCTAATAAAACCGATATATTTATACCAGTTACATTGTAAATTTACCTAT
TACATTATAATTATTGGTTTCGATTTTTTTGGGATCGATACATTTTAAAAATGTATCGACACTTT
ATGAGTGCACCCGTTTGGGCATTCATTCTGGACAAAAATATCGACACAAATTAAAAAGTGTCGAT
ACA
Found at i:2519875 original size:199 final size:197
Alignment explanation
Indices: 2519526--2520687 Score: 1242
Period size: 199 Copynumber: 5.8 Consensus size: 197
2519516 TATTTACAAA
* * * * * ** * * *
2519526 TATCGACACAAATCTAAAACATGTCGATACACTATGTTCACCTAATT-TCTCATAAAACCGGAAC
1 TATCGACACACATTTAAAA-GTGTCGACACATTATGTAGACCT-ATTCTCACATAAAACCGGTAT
** * * *
2519590 ATTTATACTAGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGG
64 ATTTATACCGGTTATATTATAAAATTACCTATTACATTATAATTATCGGTTTCGATG-TTTTGGG
* * *
2519655 ATCGATACTTTTTATAAATGTATCGATACTTTTTGCGTTCACCCTTTTGGGCATTCATTCTGGCA
128 ATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTTCACCCTTTTGGGCATTCATTCTGGCA
2519720 AAAAG
193 AAAAG
* * *
2519725 TATCGACACATCATTTAAAAGTGTCGACAAATTATGTAGACCTATTCTGACATAAAACCCGTATA
1 TATCGACACA-CATTTAAAAGTGTCGACACATTATGTAGACCTATTCTCACATAAAACCGGTATA
* *
2519790 TTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTAGGGA
65 TTTATACCGGTTATATTATAAAATTACCTATTACATTATAATTATCGGTTTCGATGTTTT-GGGA
* * * * * * *
2519855 TCGATACTGTTTAAAAATGTATCGACACTTTATGGGTGCAACCTTTTTGG-ATTTTCCTTGTGGA
129 TCGATACTTTTTAAAAATGTATCGACACTTTATGCGTTCACCCTTTTGGGCA--TTCATTCTGG-
*
2519919 CCAAAAG
191 CAAAAAG
* * * * * ** * * * *
2519926 TATCGACACAAATCTACAACGTGTCAATACATTATGTTCACCTATTTTCTCAAAAAACCGGTACA
1 TATCGACACACATTTA-AAAGTGTCGACACATTATGTAGACCTATTCTCACATAAAACCGGTATA
** * * * * *
2519991 TTTATATTGGTTACATTGTAAATTTACTTATTACATTATAATTATCGGCTTCGATGCTTTTGGGA
65 TTTATACCGGTTATATTATAAAATTACCTATTACATTATAATTATCGGTTTCGATG-TTTTGGGA
* *
2520056 TCGATACTTTTTATAAATGTATCGACATTTTATGCGTTCACCCTTTTGGGCATTCATTCTGGCAA
129 TCGATACTTTTTAAAAATGTATCGACACTTTATGCGTTCACCCTTTTGGGCATTCATTCTGGCAA
2520121 AAAG
194 AAAG
* * * *
2520125 TATCGACACAACATTCAAAAGTGTCGACACATTATGTAGAACTATTCTAACATAAAACTGGTATA
1 TATCGACAC-ACATTTAAAAGTGTCGACACATTATGTAGACCTATTCTCACATAAAACCGGTATA
*
2520190 TTTATACCGGTTATATTATAAAATTACCTATTACATTATATTTAT-GGATTTCGATGTTTCTGGG
65 TTTATACCGGTTATATTATAAAATTACCTATTACATTATAATTATCGG-TTTCGATGTTT-TGGG
* * * * * * *
2520254 ATCAATACTGTTTAAAAATGTATCGACACTTTATGGGTGCACCCTTTTTGG-ATTTTCCTTGTGG
128 ATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTTCACCCTTTTGGGCA--TTCATTCTGG
2520318 ACCAAAAA-
191 --CAAAAAG
* * * * * * * * * *
2520326 TATTGATACAAATTCTACAAGTGTCGATACATTATGTATATCTATTTTCTA-A-AAAAACGGTTT
1 TATCGACACACATT-TAAAAGTGTCGACACATTATGTAGACCTATTCTC-ACATAAAACCGGTAT
* * * *
2520389 ATTTATACCGGTTACATTGTAAATTTACCCATTACATTATAATTATCGGTTTCGATGTTTTTGGG
64 ATTTATACCGGTTATATTATAAAATTACCTATTACATTATAATTATCGGTTTCGATG-TTTTGGG
* * * *
2520454 ATCGATACTTTTTATAATTATATCGACACTTTATGCGTTCACCCTTTTGGGCATTCATTATGGCA
128 ATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTTCACCCTTTTGGGCATTCATTCTGGCA
2520519 AAAAG
193 AAAAG
*
2520524 TATCGACACAACA-TTAACAAGTGTCGACACATTATGTAGACCTATTCTCACATAAAACCAGTAT
1 TATCGACAC-ACATTTAA-AAGTGTCGACACATTATGTAGACCTATTCTCACATAAAACCGGTAT
* * * * * *
2520588 ATTTATACCGGTTATATTACAAAATTATCTATTACATTATATTTATTGATTTCTATGTTTCTGGG
64 ATTTATACCGGTTATATTATAAAATTACCTATTACATTATAATTATCGGTTTCGATGTTT-TGGG
* * *
2520653 ATAGATACTTTTTAAAACTCTATCGACACTTTATG
128 ATCGATACTTTTTAAAAATGTATCGACACTTTATG
2520688 GGAAACTTTA
Statistics
Matches: 787, Mismatches: 149, Indels: 54
0.79 0.15 0.05
Matches are distributed among these distances:
197 9 0.01
198 53 0.07
199 379 0.48
200 147 0.19
201 187 0.24
202 12 0.02
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (197 bp):
TATCGACACACATTTAAAAGTGTCGACACATTATGTAGACCTATTCTCACATAAAACCGGTATAT
TTATACCGGTTATATTATAAAATTACCTATTACATTATAATTATCGGTTTCGATGTTTTGGGATC
GATACTTTTTAAAAATGTATCGACACTTTATGCGTTCACCCTTTTGGGCATTCATTCTGGCAAAA
AG
Found at i:2520266 original size:400 final size:399
Alignment explanation
Indices: 2519523--2520689 Score: 1815
Period size: 400 Copynumber: 2.9 Consensus size: 399
2519513 CGTTATTTAC
* * * * * *
2519523 AAATATCGACACAAATCTAAAACATGTCGATACACTATGTTCACCTAATTTCTCATAAAACCGGA
1 AAATATCGACACAAATCTACAACGTGTCGATACATTATGTTCACCTATTTTCTCAAAAAACCGGT
*
2519588 ACATTTATACTAGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTG
66 ACATTTATACTGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTG
*
2519653 GGATCGATACTTTTTATAAATGTATCGATACTTTT-TGCGTTCACCCTTTTGGGCATTCATTCTG
131 GGATCGATACTTTTTATAAATGTATCGACA-TTTTATGCGTTCACCCTTTTGGGCATTCATTCTG
* * *
2519717 GCAAAAAGTATCGACACATCATTTAAAAGTGTCGACAAATTATGTAGACCTATTCTGACATAAAA
195 GCAAAAAGTATCGACACAACA-TTAAAAGTGTCGACACATTATGTAGACCTATTCTAACATAAAA
* * *
2519782 CCCGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGT
259 CCAGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATATTTATGGATTTCGATGT
*
2519847 TT-TAGGGATCGATACTGTTTAAAAATGTATCGACACTTTATGGGTGCAACCTTTTTGGATTTTC
324 TTCT-GGGATCAATACTGTTTAAAAATGTATCGACACTTTATGGGTGCAACCTTTTTGGATTTTC
2519911 CTTGTGGACCAA
388 CTTGTGGACCAA
* *
2519923 AAGTATCGACACAAATCTACAACGTGTCAATACATTATGTTCACCTATTTTCTCAAAAAACCGGT
1 AAATATCGACACAAATCTACAACGTGTCGATACATTATGTTCACCTATTTTCTCAAAAAACCGGT
* * * *
2519988 ACATTTATATTGGTTACATTGTAAATTTACTTATTACATTATAATTATCGGCTTCGATGCTTTTG
66 ACATTTATACTGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTG
2520053 GGATCGATACTTTTTATAAATGTATCGACATTTTATGCGTTCACCCTTTTGGGCATTCATTCTGG
131 GGATCGATACTTTTTATAAATGTATCGACATTTTATGCGTTCACCCTTTTGGGCATTCATTCTGG
*
2520118 CAAAAAGTATCGACACAACATTCAAAAGTGTCGACACATTATGTAGAACTATTCTAACATAAAAC
196 CAAAAAGTATCGACACAACATT-AAAAGTGTCGACACATTATGTAGACCTATTCTAACATAAAAC
** *
2520183 TGGTATATTTATACCGGTTATATTATAAAATTACCTATTACATTATATTTATGGATTTCGATGTT
260 CAGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATATTTATGGATTTCGATGTT
*
2520248 TCTGGGATCAATACTGTTTAAAAATGTATCGACACTTTATGGGTGCACCCTTTTTGGATTTTCCT
325 TCTGGGATCAATACTGTTTAAAAATGTATCGACACTTTATGGGTGCAACCTTTTTGGATTTTCCT
2520313 TGTGGACCAA
390 TGTGGACCAA
* * * *
2520323 AAATATTGATACAAATTCTACAA-GTGTCGATACATTATGTAT-ATCTATTTTCT-AAAAAAACG
1 AAATATCGACACAAA-TCTACAACGTGTCGATACATTATGT-TCACCTATTTTCTCAAAAAACCG
** * *
2520385 GTTTATTTATACCGGTTACATTGTAAATTTACCCATTACATTATAATTATCGGTTTCGATGTTTT
64 GTACATTTATACTGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
* * * *
2520450 TGGGATCGATACTTTTTATAATTATATCGACACTTTATGCGTTCACCCTTTTGGGCATTCATTAT
129 TGGGATCGATACTTTTTATAAATGTATCGACATTTTATGCGTTCACCCTTTTGGGCATTCATTCT
*
2520515 GGCAAAAAGTATCGACACAACATTAACAAGTGTCGACACATTATGTAGACCTATTCTCACATAAA
194 GGCAAAAAGTATCGACACAACATTAA-AAGTGTCGACACATTATGTAGACCTATTCTAACATAAA
* * *
2520580 ACCAGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATATTTATTGATTTCTATG
258 ACCAGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATATTTATGGATTTCGATG
* * *
2520645 TTTCTGGGAT-AGATACTTTTTAAAACTCTATCGACACTTTATGGG
323 TTTCTGGGATCA-ATACTGTTTAAAAATGTATCGACACTTTATGGG
2520690 AAACTTTAAG
Statistics
Matches: 706, Mismatches: 54, Indels: 15
0.91 0.07 0.02
Matches are distributed among these distances:
398 3 0.00
399 291 0.41
400 403 0.57
401 9 0.01
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.38
Consensus pattern (399 bp):
AAATATCGACACAAATCTACAACGTGTCGATACATTATGTTCACCTATTTTCTCAAAAAACCGGT
ACATTTATACTGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTG
GGATCGATACTTTTTATAAATGTATCGACATTTTATGCGTTCACCCTTTTGGGCATTCATTCTGG
CAAAAAGTATCGACACAACATTAAAAGTGTCGACACATTATGTAGACCTATTCTAACATAAAACC
AGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATATTTATGGATTTCGATGTTT
CTGGGATCAATACTGTTTAAAAATGTATCGACACTTTATGGGTGCAACCTTTTTGGATTTTCCTT
GTGGACCAA
Found at i:2520708 original size:15 final size:15
Alignment explanation
Indices: 2520688--2520726 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
2520678 ACACTTTATG
*
2520688 GGAAACTTTAAGTTT
1 GGAAACTTTAAGTGT
*
2520703 GGAAACTTTATGTGT
1 GGAAACTTTAAGTGT
*
2520718 GAAAACTTT
1 GGAAACTTT
2520727 GTTGTGGAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (15 bp):
GGAAACTTTAAGTGT
Found at i:2521048 original size:11 final size:11
Alignment explanation
Indices: 2520998--2521049 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
2520988 TATACATAAC
2520998 AATGTTCAAAT
1 AATGTTCAAAT
*
2521009 AGTGTTCAAAT
1 AATGTTCAAAT
* *
2521020 AATTTATGCATAAC
1 AATGT-T-CA-AAT
2521034 AATGTTCAAAT
1 AATGTTCAAAT
2521045 AATGT
1 AATGT
2521050 ACCCACAACG
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
11 20 0.62
12 3 0.09
13 3 0.09
14 6 0.19
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.37
Consensus pattern (11 bp):
AATGTTCAAAT
Found at i:2522067 original size:6 final size:6
Alignment explanation
Indices: 2522038--2522090 Score: 52
Period size: 6 Copynumber: 8.8 Consensus size: 6
2522028 GATCATTATA
* * * * *
2522038 ATCATA ATCATA ATCATC ATCATC ATCATC GTCATC TTCATC GTCATC
1 ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC
*
2522086 TTCAT
1 ATCAT
2522091 TGACCTCTTG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.30, C:0.28, G:0.04, T:0.38
Consensus pattern (6 bp):
ATCATC
Found at i:2522360 original size:18 final size:18
Alignment explanation
Indices: 2522337--2522371 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2522327 TCTCCAACTG
*
2522337 GAGCTTATGGAGCTTCTA
1 GAGCTTACGGAGCTTCTA
*
2522355 GAGCTTCCGGAGCTTCT
1 GAGCTTACGGAGCTTCT
2522372 TCCATCATTG
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:0.17, C:0.23, G:0.29, T:0.31
Consensus pattern (18 bp):
GAGCTTACGGAGCTTCTA
Found at i:2522922 original size:2 final size:2
Alignment explanation
Indices: 2522915--2523002 Score: 176
Period size: 2 Copynumber: 44.0 Consensus size: 2
2522905 TAGTTTTCAG
2522915 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
2522957 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
2522999 AT AT
1 AT AT
2523003 TCCCCATGAA
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 86 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2524002 original size:198 final size:199
Alignment explanation
Indices: 2523662--2524618 Score: 1142
Period size: 200 Copynumber: 4.8 Consensus size: 199
2523652 ATTTAAAATG
* * * * * * *
2523662 GTATCGACACAAATTTAACAATTGTCGATACTTTATG-ATGACCTATTTTCTCATAAAAGCGGTA
1 GTATCGACACAAATTAAAAAAGTGTCGATACATTATGTA-GACATATTCTCTCATAAAACCGGTA
* ** * * *
2523726 TATTTATACCGGTTACATTGGAAATTTACCTATTATATTATAATTATCGGTTTCGATGTTATTGG
65 TATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGG
* * * * *
2523791 GATCGACACTTTTTAAAAATGTATCGACACTTTATGCGTGCA-ACTTTTGG-ATTTCCTTCTGGA
130 GATCGACACTTTTTATAAATGTATCGACACTTTATTCGTTCACATTTTTGGCA-TTCATTCTGGA
*
2523854 TAAAAA
194 CAAAAA
** * * *
2523860 GTATCGACACAAATTCCACAAGTGTTGATACATGT-TGTAGACATATTCTCTCATAAAACCAGTA
1 GTATCGACACAAATTAAAAAAGTGTCGATACAT-TATGTAGACATATTCTCTCATAAAACCGGTA
* * ** * * * * *
2523924 T-TGTTATACTGGTTACATTGTAAATTTACCTATTATATTATATTTATGGGTTTCGATGTTTCTG
65 TAT-TTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATCGGTTTCGATGTTTTTG
* *
2523988 GTATCGAAACTTTTTATAAATGTATCGACACTTTATTCGTTCATCATTTTTGGCATTCATTCTGG
129 GGATCGACACTTTTTATAAATGTATCGACACTTTATTCGTTCA-CATTTTTGGCATTCATTCTGG
2524053 ACAAAAA
193 ACAAAAA
* * * * *
2524060 GTATCGACACAAAATAAAAAAGTGTCGATATATTATGTAGACCTATTCT-TACATACAACTGGTA
1 GTATCGACACAAATTAAAAAAGTGTCGATACATTATGTAGACATATTCTCT-CATAAAACCGGTA
* * **
2524124 TATTTATACCGGTTGTATTACAAAATTACCTAGTACATTATAATTATTTGTTTCGATGTTTTTGG
65 TATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGG
* *
2524189 GATTGATACTTTTTATAAATGTATCGACACTTTATTCGTTCATCATTTTTGGCATTCATTCTGGA
130 GATCGACACTTTTTATAAATGTATCGACACTTTATTCGTTCA-CATTTTTGGCATTCATTCTGGA
2524254 CAAAAA
194 CAAAAA
* *
2524260 GTATCGACACAACATT-AAAAAGTGTCGATACATTATGTAGATC-TATTCTCACATAAAACTGGT
1 GTATCGACACAA-ATTAAAAAAGTGTCGATACATTATGTAGA-CATATTCTCTCATAAAACCGGT
* * * *
2524323 ATATTTATACCGATTATATTACAAAATTACTTATTACATTATATTTAT-GGATTTTGATGTTTTT
64 ATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATCGG-TTTCGATGTTTTT
2524387 GGGATCGACACTTTTTA-AAACTGTATCGACACTTTATTCGTTCATCATTTTTGGCATTCATTCT
128 GGGATCGACACTTTTTATAAA-TGTATCGACACTTTATTCGTTCA-CATTTTTGGCATTCATTCT
2524451 GGACAAAAA
191 GGACAAAAA
* * ** * * * *
2524460 GTATCGACACAAAATAAAAAAGTATAAATATATTATGTAGACATATTCTCACATAAAATCGATAT
1 GTATCGACACAAATTAAAAAAGTGTCGATACATTATGTAGACATATTCTCTCATAAAACCGGTAT
** * *
2524525 ATTTATACATGTTATATTACAAAATTACCTATTACATTATAATTATCTGTTTCGATTTTTTTGGG
66 ATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGG
* *
2524590 ATCGACACGTTTTATAAATGTATCAACAC
131 ATCGACACTTTTTATAAATGTATCGACAC
2524619 ATATGCTTAC
Statistics
Matches: 662, Mismatches: 79, Indels: 34
0.85 0.10 0.04
Matches are distributed among these distances:
197 1 0.00
198 145 0.22
199 11 0.02
200 496 0.75
201 9 0.01
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (199 bp):
GTATCGACACAAATTAAAAAAGTGTCGATACATTATGTAGACATATTCTCTCATAAAACCGGTAT
ATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGG
ATCGACACTTTTTATAAATGTATCGACACTTTATTCGTTCACATTTTTGGCATTCATTCTGGACA
AAAA
Found at i:2524899 original size:19 final size:19
Alignment explanation
Indices: 2524875--2524923 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
2524865 TTACATCCAC
2524875 ATACAAAATTATAAAT-TGT
1 ATACAAAATTATAAATCT-T
2524894 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCTT
2524913 ATACAAAATTA
1 ATACAAAATTA
2524924 ACTCTACATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 28 0.97
20 1 0.03
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.35
Consensus pattern (19 bp):
ATACAAAATTATAAATCTT
Found at i:2526512 original size:18 final size:18
Alignment explanation
Indices: 2526489--2526555 Score: 134
Period size: 18 Copynumber: 3.7 Consensus size: 18
2526479 ATTTCCTTTG
2526489 TCTTTTCTTCTTCGTCCC
1 TCTTTTCTTCTTCGTCCC
2526507 TCTTTTCTTCTTCGTCCC
1 TCTTTTCTTCTTCGTCCC
2526525 TCTTTTCTTCTTCGTCCC
1 TCTTTTCTTCTTCGTCCC
2526543 TCTTTTCTTCTTC
1 TCTTTTCTTCTTC
2526556 ATATTTTTTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 49 1.00
ACGTcount: A:0.00, C:0.37, G:0.04, T:0.58
Consensus pattern (18 bp):
TCTTTTCTTCTTCGTCCC
Found at i:2526821 original size:21 final size:21
Alignment explanation
Indices: 2526796--2526860 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
2526786 CCCATTACGC
*
2526796 CTCTCAAGTGTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
2526817 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
2526838 CTCTCAAGTTTCTCTTCTACT
1 CTCTCAAGTTTCTCTTCGACT
2526859 CT
1 CT
2526861 TGATTGTCTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.14, C:0.34, G:0.09, T:0.43
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:2529525 original size:181 final size:182
Alignment explanation
Indices: 2529201--2529996 Score: 1112
Period size: 182 Copynumber: 4.4 Consensus size: 182
2529191 TACGCGTACC
** * * * * *
2529201 TATTAAAGTATTAACACTTTCAATATATCCGGTAGCGCTTTACCAGTTTTGTCATTTAGAGACCG
1 TATTAAAGTATCGACACTTGCAATATATCCGGTAGCGCTTTACCGGTTTTGTCTTTTCGTGACCG
* * * * *
2529266 G-TTTATCATATTTTTACCTGTTATATCATTATGGATCGATATATTTTTATAAAGTATCGACACT
66 GTTTTATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACT
* * *
2529330 TTATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
131 TTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
* * * * *
2529382 TATTAAATTATCGACACTTTCAATATATCCGATAGCGCTTTATCGGTTTTGTCTATTT-GAGACC
1 TATTAAAGTATCGACACTTGCAATATATCCGGTAGCGCTTTACCGGTTTTGTCT-TTTCGTGACC
* *
2529446 GGTGTTATCATATTTTTACCTGTTATATCGTTGTAGATCGATACATATTTATAAAGAATCGACAC
65 GGTTTTATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACAC
* *
2529511 TTTATA-GTGCTAAAATTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
130 TTTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
* * * * * * * *
2529563 TATTAAAATATCGACACTTGCAATATATTCGATATCTCTTTATCGGTTTTGTCTTTTCCTGACTG
1 TATTAAAGTATCGACACTTGCAATATATCCGGTAGCGCTTTACCGGTTTTGTCTTTTCGTGACCG
*
2529628 GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACT
66 GTTTTATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACT
* * *
2529693 TTATAGACGCTAAAACTGTTTATCCTTTAAATTCACAATGTGTCGATACTTA
131 TTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
* ** * *
2529745 TATTAAAGTATCGACACTTGCAATATATCCGGTATCTTTTTACCGGTTTTATCTTTTCCTGACCG
1 TATTAAAGTATCGACACTTGCAATATATCCGGTAGCGCTTTACCGGTTTTGTCTTTTCGTGACCG
* * *
2529810 GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATTGAAACATATTTATAAAGAATCGACACT
66 GTTTTATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACT
*
2529875 TTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACCATGTGTCGATACTTA
131 TTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
* * * * *
2529927 TTTTAAAGTATCGACACGTGCAATATATCTGGTAGTGCTTTACCGGTTTTATCTTTTCGTGACCG
1 TATTAAAGTATCGACACTTGCAATATATCCGGTAGCGCTTTACCGGTTTTGTCTTTTCGTGACCG
2529992 GTTTT
66 GTTTT
2529997 GTATACATTT
Statistics
Matches: 556, Mismatches: 55, Indels: 7
0.90 0.09 0.01
Matches are distributed among these distances:
180 3 0.01
181 217 0.39
182 336 0.60
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (182 bp):
TATTAAAGTATCGACACTTGCAATATATCCGGTAGCGCTTTACCGGTTTTGTCTTTTCGTGACCG
GTTTTATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACT
TTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
Found at i:2530158 original size:150 final size:150
Alignment explanation
Indices: 2529851--2530148 Score: 488
Period size: 150 Copynumber: 2.0 Consensus size: 150
2529841 GTGGATTGAA
* * * *
2529851 ACATATTTATAAAGAATCGACACTTTATAGGCGCTAAAACTGCTTCTCCTTTAAATTCACCATGT
1 ACATTTTTATAAAGAATCGACACTTTATAGGCGCTAAAACTGCTTCTCCTTTAAACTCAACATAT
* * *
2529916 GTCGATACTTATTTTAAAGTATCGACACGTGCAATATATCTGGTAGTGCTTTACCGGTTTTATCT
66 GTCGATACTTATATTAAAGTATCGACACGTGCAATATATCCGGTAGCGCTTTACCGGTTTTATCT
2529981 TTTCGTGACCGGTTTTGTAT
131 TTTCGTGACCGGTTTTGTAT
* *
2530001 ACATTTTTATAAAGTATCGACACTTTATAGGCGCTAAAACTGCTTCTCCTTTAAACTCAATATAT
1 ACATTTTTATAAAGAATCGACACTTTATAGGCGCTAAAACTGCTTCTCCTTTAAACTCAACATAT
* *
2530066 GTCGATACTTATATTAAAGTATCGGCACGTGCAATATATCCGGTAGCGCTTTACCGGTTTTGTCT
66 GTCGATACTTATATTAAAGTATCGACACGTGCAATATATCCGGTAGCGCTTTACCGGTTTTATCT
*
2530131 TTTCGTGACTGGTTTTGT
131 TTTCGTGACCGGTTTTGT
2530149 CATATTTTTT
Statistics
Matches: 136, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
150 136 1.00
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (150 bp):
ACATTTTTATAAAGAATCGACACTTTATAGGCGCTAAAACTGCTTCTCCTTTAAACTCAACATAT
GTCGATACTTATATTAAAGTATCGACACGTGCAATATATCCGGTAGCGCTTTACCGGTTTTATCT
TTTCGTGACCGGTTTTGTAT
Found at i:2532304 original size:16 final size:18
Alignment explanation
Indices: 2532269--2532305 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
2532259 CTTATTGGAC
*
2532269 AAAAATAATATATTAAAT
1 AAAAATAATATATAAAAT
2532287 AAAAAT-AT-TATAAAAT
1 AAAAATAATATATAAAAT
2532303 AAA
1 AAA
2532306 TCATGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 10 0.56
17 2 0.11
18 6 0.33
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAAATAATATATAAAAT
Found at i:2533716 original size:20 final size:19
Alignment explanation
Indices: 2533693--2533739 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
2533683 CGATATACCA
2533693 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
2533713 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
2533733 GGTAAAA
1 GGTAAAA
2533740 CGTTACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:2533816 original size:181 final size:181
Alignment explanation
Indices: 2533481--2533953 Score: 716
Period size: 181 Copynumber: 2.6 Consensus size: 181
2533471 GATCCAAATT
* * * * **
2533481 AAAAATGTGTCGATCTAAAACGATATAACAGGTAAAACTATGACAAAACCGGTATTGAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * * *
2533546 AAACCGGTAAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTC
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
*
2533611 GTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAA-AGTGTCGATACTTTTA
131 GTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAATA-TGTCGATAC-TTTA
* *
2533663 AAAAATGTATTGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* *
2533728 AAACCGGTAAAACGTTACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
**
2533792 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATATGTCGATACTTTA
131 GTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAATATGTCGATACTTTA
* *
2533843 AAAATATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGAT
1 AAAA-ATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGAT
*
2533908 AAAATCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
65 AAAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
2533954 CGTAAGTACG
Statistics
Matches: 266, Mismatches: 23, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
180 8 0.03
181 160 0.60
182 98 0.37
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (181 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAATATGTCGATACTTTA
Found at i:2533897 original size:20 final size:19
Alignment explanation
Indices: 2533874--2533920 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
2533864 CGATATAACA
2533874 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
* *
2533894 GGTATCAAAATGATAAAATC
1 GGTA-AAAAATGATAAAACC
2533914 GGTAAAA
1 GGTAAAA
2533921 CGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.53, C:0.09, G:0.17, T:0.21
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:2536167 original size:21 final size:21
Alignment explanation
Indices: 2536141--2536205 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
2536131 AAGACAATCA
*
2536141 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
2536162 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
2536183 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
2536204 AG
1 AG
2536206 GCATAAAGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.42, C:0.11, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:2536281 original size:33 final size:33
Alignment explanation
Indices: 2536239--2536304 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
2536229 AAATAGATGG
*
2536239 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
2536272 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
2536305 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:2538118 original size:19 final size:19
Alignment explanation
Indices: 2538094--2538142 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
2538084 AATGTAGGGT
2538094 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
2538113 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
2538132 TAATTTTGTAT
1 TAATTTTGTAT
2538143 GTGAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:2538724 original size:200 final size:200
Alignment explanation
Indices: 2538379--2539139 Score: 1274
Period size: 200 Copynumber: 3.8 Consensus size: 200
2538369 TTACAATATT
*
2538379 GCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGA
1 GCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGA
* *
2538444 AACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAATCGGTACAAGTATACCGGTTTTATG
66 AACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGATTTTATG
2538509 AGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAAT
131 AGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAAT
2538574 GAATG
196 GAATG
*
2538579 GCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCGATAAACATCGA
1 GCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGA
**
2538644 AACCCCTAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGATTTTATG
66 AACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGATTTTATG
* *
2538709 AGAGAATATGTCTAAATAATGTATCGACATTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAAT
131 AGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAAT
2538774 GAATG
196 GAATG
*
2538779 GCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAATATCGA
1 GCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGA
*
2538844 AACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACC-AGTTTTAT
66 AACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGA-TTTTAT
*
2538908 GAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTTGATATTTTTGGTCCAGAA
130 GAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAA
2538973 TGAATG
195 TGAATG
* * * * * * *
2538979 GAAAACAGGGTACAACCATAAAGTATCGATCCATATATAAAAAGTGTTGATCCCATAAATATCAA
1 GCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGA
* * *
2539044 AACCCAAAAGTATAATGTATTAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTTATG
66 AACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGATTTTATG
* * *
2539109 GGAGAATTGGTATATAAT-ATGTATCGACACT
131 AGAGAATAGGTCTA-AATAATGTATCGACACT
2539140 GTTTAATGTT
Statistics
Matches: 531, Mismatches: 27, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
199 1 0.00
200 527 0.99
201 3 0.01
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (200 bp):
GCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGA
AACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGATTTTATG
AGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAAT
GAATG
Found at i:2540617 original size:6 final size:6
Alignment explanation
Indices: 2540606--2540657 Score: 59
Period size: 6 Copynumber: 8.7 Consensus size: 6
2540596 CAAGCGGTCA
* * * * *
2540606 ATGAAG ATGAAG CTGACG ATGAAG ATGATG ATGAAG ATGACG ATGATG
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG
2540654 ATGA
1 ATGA
2540658 TCCAAACAAG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.40, C:0.06, G:0.33, T:0.21
Consensus pattern (6 bp):
ATGAAG
Found at i:2540628 original size:12 final size:12
Alignment explanation
Indices: 2540606--2540657 Score: 68
Period size: 12 Copynumber: 4.3 Consensus size: 12
2540596 CAAGCGGTCA
*
2540606 ATGAAGATGAAG
1 ATGACGATGAAG
*
2540618 CTGACGATGAAG
1 ATGACGATGAAG
*
2540630 ATGATGATGAAG
1 ATGACGATGAAG
*
2540642 ATGACGATGATG
1 ATGACGATGAAG
2540654 ATGA
1 ATGA
2540658 TCCAAACAAG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.40, C:0.06, G:0.33, T:0.21
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:2540644 original size:18 final size:18
Alignment explanation
Indices: 2540606--2540657 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
2540596 CAAGCGGTCA
* * *
2540606 ATGAAGATGAAGCTGACG
1 ATGAAGATGATGATGAAG
2540624 ATGAAGATGATGATGAAG
1 ATGAAGATGATGATGAAG
*
2540642 ATGACGATGATGATGA
1 ATGAAGATGATGATGA
2540658 TCCAAACAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.40, C:0.06, G:0.33, T:0.21
Consensus pattern (18 bp):
ATGAAGATGATGATGAAG
Found at i:2542216 original size:183 final size:183
Alignment explanation
Indices: 2541868--2542456 Score: 1029
Period size: 183 Copynumber: 3.2 Consensus size: 183
2541858 CAAAGTTTTC
*
2541868 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTTT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
* * *
2541933 CAAAAAGTGTCG--ATTGAAAAAACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAA
66 CAAAAAGTGTCGACATT---TACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAA
* * *
2541996 TATAATCTGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCA
128 TATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
2542052 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATAGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
2542117 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
*
2542182 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACTTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
2542235 ACACTTTTTAATTTTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
2542300 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
*
2542365 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAATCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
2542418 ACACTTTTTAATTTTGTGTCGGTACTTTATGTCCAGAAT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAAT
2542457 TATAATGTAC
Statistics
Matches: 390, Mismatches: 13, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
183 312 0.80
184 75 0.19
186 3 0.01
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (183 bp):
ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:2542543 original size:120 final size:120
Alignment explanation
Indices: 2542330--2542576 Score: 440
Period size: 120 Copynumber: 2.1 Consensus size: 120
2542320 ACATCGGAAC
2542330 CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGC
1 CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGC
* *
2542395 GAATAGGTCTACAATCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGT
66 GAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
* * *
2542450 CCAGAATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGC
1 CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGC
*
2542515 GAATAGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGT
66 GAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
2542570 CCAGAAT
1 CCAGAAT
2542577 GGAAGAAAAA
Statistics
Matches: 121, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
120 121 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (120 bp):
CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGC
GAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
Found at i:2542694 original size:303 final size:302
Alignment explanation
Indices: 2542147--2543044 Score: 1598
Period size: 303 Copynumber: 3.0 Consensus size: 302
2542137 ACATCGGAAC
* * *
2542147 CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGC
1 CCAGAATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGC
* * *
2542212 GAATAGGTCTACAACTTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGTCCAGAATGGA
66 GAATAGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGA
2542277 AGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAA
131 AGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAA
2542342 TGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTAC
196 TGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTAC
2542407 AATCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGT
261 AA-CTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGT
2542450 CCAGAATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGC
1 CCAGAATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGC
2542515 GAATAGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGA
66 GAATAGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGA
*
2542580 AGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACATATACACATCGGAACCCAGAATTATAA
131 AGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAA
* * * *
2542645 TGTAATATATAATGTTGTAATATAACCAGTATAAATATACCGGTTTTATGAGAGAATAGGTCTAC
196 TGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTAC
2542710 AACTTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGT
261 AAC-TATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGT
2542753 CCAGAATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGC
1 CCAGAATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGC
* *
2542818 GAATAGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTATTTTATGTCCAGAATGAA
66 GAATAGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGA
* * *
2542883 AGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTATACATCGGCACCTAGAATTATAA
131 AGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAA
* *
2542948 TGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGAACGAATAGGTCTAC
196 TGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTAC
*
2543013 AACCTATATCGACACTTTTTAATATTGTGTCG
261 AA-CTATATCGACACTTTTTAATTTTGTGTCG
2543045 CTAATTTTAA
Statistics
Matches: 569, Mismatches: 24, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
302 1 0.00
303 567 1.00
304 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (302 bp):
CCAGAATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGC
GAATAGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGA
AGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAA
TGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTAC
AACTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGT
Found at i:2542846 original size:120 final size:120
Alignment explanation
Indices: 2542633--2542879 Score: 395
Period size: 120 Copynumber: 2.1 Consensus size: 120
2542623 ACATCGGAAC
*
2542633 CCAGAATTATAATGTAATATATAATGTTGTAATATAACCAGTATAAATATACCGGTTTTATGAGA
1 CCAGAATTATAATGTAATAGATAATGTTGTAATATAACCAGTATAAATATACCGGTTTTATGAGA
* *
2542698 GAATAGGTCTACAACTTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGT
66 GAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
* * * * * *
2542753 CCAGAATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGC
1 CCAGAATTATAATGTAATAGATAATGTTGTAATATAACCAGTATAAATATACCGGTTTTATGAGA
* *
2542818 GAATAGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTATTTTATGT
66 GAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
2542873 CCAGAAT
1 CCAGAAT
2542880 GAAAGAAAAA
Statistics
Matches: 116, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
120 116 1.00
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (120 bp):
CCAGAATTATAATGTAATAGATAATGTTGTAATATAACCAGTATAAATATACCGGTTTTATGAGA
GAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
Found at i:2542944 original size:486 final size:475
Alignment explanation
Indices: 2541868--2543044 Score: 1304
Period size: 486 Copynumber: 2.4 Consensus size: 475
2541858 CAAAGTTTTC
* *
2541868 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTTT
1 ACACTTTTTAATATTGTGTCGGTATTTTATGTCCAGAATGAAAGAAAAATGTGTCGATACCTTTT
* * *
2541933 CAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATA
66 CAAAAAGTGTCGATT---TATACATCGG-A-CCAGAATTATAATGTAATAGATAATTTTGTAATA
* * *
2541998 TAATCTGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCAACACTTTTTAA
126 TAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAA
2542063 TATTGTGTCGGTACTTTATGTCCAGAATAGAAGAAAAATGTGTCGATACCTTGTCAAAAAGTGTC
191 TATTGTGTCGGTACTTTATGTCCAGAATAGAAGAAAAATGTGTCGATACCTTGTCAAAAAGTGTC
* * *
2542128 GACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAA
256 GACATATACACATCGGAACCCAGAATTATAATGTAATAGATAATGTTGTAATATAACCAGTATAA
*
2542193 ATATACCGGTTTTATGAGCGAATAGGTCTACAACTTATATCGACACTTTTTAATTTTGTGTCGGT
321 ATATACCGGTTTTATGAGAGAATAGGTCTACAACTTATATCGACACTTTTTAATTTTGTGTCGGT
* * * *
2542258 ACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACA
386 ACTTTATGTCCAGAATAGAAGAAAAATGTGTAGATACCTGGT-AAAAAGTATCGACATTTACACA
* * **
2542323 TCGGAACCCAGAATTATAATGTAATAG
450 GCGGAA-CCAGAATTACAACCTAATAG
* * *** * * ** ** ** *
2542350 ATAATTTTGTAATA-T-AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAATCTA
1 ACACTTTT-TAATATTGTGTCGGTAT---TTTA--TG-TCCA-GAATGAA-A-G---A-AAAATG
* * * *** * * *
2542413 TATCGACA-CTTTTTAATTTTGTGTCGGTACTT-T--AT--GTCCAGAATTATAATGTACTAGAT
52 TGTCGATACCTTTTCAA-AAAGTGTC-G-ATTTATACATCGGACCAGAATTATAATGTAATAGAT
* * *
2542472 AATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGCGAATAGGTCTACAACCTATGTC
114 AATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATC
*
2542537 GACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTG
179 GACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATAGAAGAAAAATGTGTCGATACCTTG
*
2542602 TCAAAAAGTGTCGACATATACACATCGGAACCCAGAATTATAATGTAATATATAATGTTGTAATA
244 TCAAAAAGTGTCGACATATACACATCGGAACCCAGAATTATAATGTAATAGATAATGTTGTAATA
2542667 TAACCAGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACTTATATCGACACTTTTTAA
309 TAACCAGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACTTATATCGACACTTTTTAA
* * *
2542732 TTTTGTGTCGGTACTTTATGTCCAGAATTATAATGTACTAGATAATTTTGTAATATAACC-GGT-
374 TTTTGTGTCGGTACTTTATGTCCAGAA-TAGAA-G-A--A-A-AA-TGTGT-AGAT-ACCTGGTA
* ** ** * * * *
2542795 ATAAGTATACCG-GTTTTA-TTAGC-GAA-TAG-GTCTACAACCTATGTCG
429 AAAAGTAT--CGACATTTACACAGCGGAACCAGAAT-TACAACCTA-ATAG
*
2542841 ACACTTTTTAATATTGTGTCGGTATTTTATGTCCAGAATGAAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTATTTTATGTCCAGAATGAAAGAAAAATGTGTCGATACCTTTT
2542906 CAAAAAGTGTCGACATTTATACATCGGCACCTAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCG--ATTTATACATCGG-ACC-AGAATTATAATGTAATAGATAATTTTGTAATAT
* *
2542971 AACCGGTATAAATATACCGATTTTATGAACGAATAGGTCTACAACCTATATCGACACTTTTTAAT
127 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAAT
2543036 ATTGTGTCG
192 ATTGTGTCG
2543045 CTAATTTTAA
Statistics
Matches: 563, Mismatches: 90, Indels: 80
0.77 0.12 0.11
Matches are distributed among these distances:
478 1 0.00
479 17 0.03
480 8 0.01
481 5 0.01
482 9 0.02
483 6 0.01
484 5 0.01
485 7 0.01
486 399 0.71
487 6 0.01
488 6 0.01
489 6 0.01
490 16 0.03
491 10 0.02
492 10 0.02
493 18 0.03
494 22 0.04
495 7 0.01
496 5 0.01
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (475 bp):
ACACTTTTTAATATTGTGTCGGTATTTTATGTCCAGAATGAAAGAAAAATGTGTCGATACCTTTT
CAAAAAGTGTCGATTTATACATCGGACCAGAATTATAATGTAATAGATAATTTTGTAATATAACC
GGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTG
TGTCGGTACTTTATGTCCAGAATAGAAGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACAT
ATACACATCGGAACCCAGAATTATAATGTAATAGATAATGTTGTAATATAACCAGTATAAATATA
CCGGTTTTATGAGAGAATAGGTCTACAACTTATATCGACACTTTTTAATTTTGTGTCGGTACTTT
ATGTCCAGAATAGAAGAAAAATGTGTAGATACCTGGTAAAAAGTATCGACATTTACACAGCGGAA
CCAGAATTACAACCTAATAG
Found at i:2546511 original size:21 final size:22
Alignment explanation
Indices: 2546466--2546511 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
2546456 TACCTATTTT
*
2546466 ATTATATAAGCGCTATCTATTAC
1 ATTATATAAGCGCTACCTA-TAC
*
2546489 ATTATATAAGCGTTACCTA-AC
1 ATTATATAAGCGCTACCTATAC
2546510 AT
1 AT
2546512 GTTATTGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
23 17 0.81
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (22 bp):
ATTATATAAGCGCTACCTATAC
Found at i:2546528 original size:87 final size:87
Alignment explanation
Indices: 2546382--2546630 Score: 412
Period size: 87 Copynumber: 2.9 Consensus size: 87
2546372 AAATAGATCA
* *
2546382 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
2546447 CCCGTTAAATACCTATTTTATT
66 CCCGTTAAATACCTATTTTATT
*
2546469 ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAACATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
2546534 CCCGTTAAATACCTATTTTATT
66 CCCGTTAAATACCTATTTTATT
* * * *
2546556 ATATAAACACTATCTATTGCATTATATAAGCGTTACCTAATATGTTATTATAC-TGATAATATTT
1 ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
2546620 -CCGATTAAATA
66 CCCG-TTAAATA
2546631 ATATAACATA
Statistics
Matches: 153, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
85 3 0.02
86 18 0.12
87 132 0.86
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (87 bp):
ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
CCCGTTAAATACCTATTTTATT
Found at i:2546806 original size:16 final size:16
Alignment explanation
Indices: 2546785--2546815 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2546775 ATTAATACTC
2546785 AACTCAAACTCAAAAA
1 AACTCAAACTCAAAAA
*
2546801 AACTCAAATTCAAAA
1 AACTCAAACTCAAAA
2546816 GTAAATTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.23, G:0.00, T:0.16
Consensus pattern (16 bp):
AACTCAAACTCAAAAA
Found at i:2546870 original size:22 final size:22
Alignment explanation
Indices: 2546826--2546872 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
2546816 GTAAATTCAA
*
2546826 AAACTCAATTAAAACGAGTCTC
1 AAACTCAATTAAAACGAGACTC
**
2546848 AAACTCAATTAAAACTCGACTC
1 AAACTCAATTAAAACGAGACTC
2546870 AAA
1 AAA
2546873 AAAACTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.49, C:0.23, G:0.06, T:0.21
Consensus pattern (22 bp):
AAACTCAATTAAAACGAGACTC
Found at i:2546929 original size:22 final size:22
Alignment explanation
Indices: 2546886--2546944 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
2546876 ACTTAAAGAG
*
2546886 CTCAATTAAAGCTTGAGATTCAAA
1 CTCAATTAAAAC-T-AGATTCAAA
* *
2546910 CTCAATTATAACTAGATTCAAG
1 CTCAATTAAAACTAGATTCAAA
*
2546932 CTTAATTAAAACT
1 CTCAATTAAAACT
2546945 GAATACTAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 19 0.63
23 1 0.03
24 10 0.33
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.32
Consensus pattern (22 bp):
CTCAATTAAAACTAGATTCAAA
Found at i:2548359 original size:36 final size:36
Alignment explanation
Indices: 2548261--2548367 Score: 132
Period size: 36 Copynumber: 3.1 Consensus size: 36
2548251 TAATTCCCTG
2548261 AAGGGACCATCATTGGACTTCTTTGGTGTTCCTGTC
1 AAGGGACCATCATTGGACTTCTTTGGTGTTCCTGTC
* * *
2548297 AAGGCA-AATGATCT-G--TTCTTTGGTGTTCCTGTC
1 AAGGGACCATCAT-TGGACTTCTTTGGTGTTCCTGTC
* *
2548330 AAGGGACCATTATTGGACTTCTTTAGTGTTCCTGTC
1 AAGGGACCATCATTGGACTTCTTTGGTGTTCCTGTC
2548366 AA
1 AA
2548368 AGCCTTTAGG
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
33 24 0.41
34 5 0.08
35 5 0.08
36 25 0.42
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (36 bp):
AAGGGACCATCATTGGACTTCTTTGGTGTTCCTGTC
Found at i:2548556 original size:11 final size:11
Alignment explanation
Indices: 2548540--2548602 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
2548530 GTATTATAGA
2548540 ATTTTTAATAT
1 ATTTTTAATAT
2548551 ATTTTTAA-A-
1 ATTTTTAATAT
2548560 ATTTTATAAT-T
1 ATTTT-TAATAT
*** * *
2548571 ATCAATAGTGT
1 ATTTTTAATAT
2548582 ATTTTTAATAT
1 ATTTTTAATAT
2548593 ATTTTTAATA
1 ATTTTTAATA
2548603 ATGTAATTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 5 0.13
10 7 0.18
11 27 0.69
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:2553829 original size:21 final size:21
Alignment explanation
Indices: 2553715--2553852 Score: 165
Period size: 21 Copynumber: 6.6 Consensus size: 21
2553705 TCATACCAAG
*
2553715 GACGAGAAGAGCATTCATCAA
1 GACGAGAAGACCATTCATCAA
*
2553736 GACGAGAATG-TCATTCATCAA
1 GACGAGAA-GACCATTCATCAA
2553757 GACGAGAATG-CCATTCATCAA
1 GACGAGAA-GACCATTCATCAA
*
2553778 GACGAGAAGGCCATTCATCAA
1 GACGAGAAGACCATTCATCAA
* *
2553799 GACGAGAAGACCCTTCATAAA
1 GACGAGAAGACCATTCATCAA
* *
2553820 GACGAGAAGACC-TTCGTAAA
1 GACGAGAAGACCATTCATCAA
*
2553840 GATGAGAAGACCA
1 GACGAGAAGACCA
2553853 CATCGCATGG
Statistics
Matches: 107, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
20 19 0.18
21 87 0.81
22 1 0.01
ACGTcount: A:0.41, C:0.21, G:0.22, T:0.16
Consensus pattern (21 bp):
GACGAGAAGACCATTCATCAA
Found at i:2556201 original size:2 final size:2
Alignment explanation
Indices: 2556194--2556282 Score: 178
Period size: 2 Copynumber: 44.5 Consensus size: 2
2556184 CATTTATCCT
2556194 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
2556236 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
2556278 TA TA T
1 TA TA T
2556283 CCCTTGTGGT
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 87 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2556530 original size:11 final size:11
Alignment explanation
Indices: 2556510--2556550 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
2556500 AGAGAAATGT
*
2556510 AGAAAGAGAAA
1 AGAAAAAGAAA
2556521 AGAAAAAGAAA
1 AGAAAAAGAAA
2556532 AGAAAAAAGAAA
1 AG-AAAAAGAAA
2556544 AGAAAAA
1 AGAAAAA
2556551 ATTGAAAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
11 17 0.61
12 11 0.39
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (11 bp):
AGAAAAAGAAA
Found at i:2556540 original size:12 final size:12
Alignment explanation
Indices: 2556516--2556551 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
2556506 ATGTAGAAAG
2556516 AGAAAAG-AAAA
1 AGAAAAGAAAAA
2556527 AGAAAAGAAAAA
1 AGAAAAGAAAAA
2556539 AGAAAAGAAAAA
1 AGAAAAGAAAAA
2556551 A
1 A
2556552 TTGAAAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 7 0.29
12 17 0.71
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
AGAAAAGAAAAA
Found at i:2559525 original size:36 final size:36
Alignment explanation
Indices: 2559242--2559509 Score: 385
Period size: 36 Copynumber: 7.4 Consensus size: 36
2559232 ACCAAAGTCA
* * * **
2559242 ATCTTAAGCCTTCACTGAAGAGGAGTGAAGCAAACC
1 ATCTGAAGCCTTCACCGGAGAATAGTGAAGCAAACC
* *
2559278 ATCTGAATCCTTCACTGGAGAATAGTGAAGCAAACC
1 ATCTGAAGCCTTCACCGGAGAATAGTGAAGCAAACC
2559314 ATCCT-AAGCCTTCACCGGAGAATAGTGAAGCAAACC
1 AT-CTGAAGCCTTCACCGGAGAATAGTGAAGCAAACC
* *
2559350 ATCTGAAGCCTTCACCGGAGAATAGTGAAGCAATCA
1 ATCTGAAGCCTTCACCGGAGAATAGTGAAGCAAACC
*
2559386 ATCTGAAGCCTTCACCTGAGAATAGTGAAGCAAACC
1 ATCTGAAGCCTTCACCGGAGAATAGTGAAGCAAACC
*
2559422 ATCTGAAGCCTTCACCGGAGAATAGTGAAGCAATCC
1 ATCTGAAGCCTTCACCGGAGAATAGTGAAGCAAACC
* *
2559458 ATCTGAAGCCTTCACCAGAGAGTAGTGAAGCAAACC
1 ATCTGAAGCCTTCACCGGAGAATAGTGAAGCAAACC
* *
2559494 ATCTTAAGTCTTCACC
1 ATCTGAAGCCTTCACC
2559510 AAAAAGTAGT
Statistics
Matches: 211, Mismatches: 19, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
35 2 0.01
36 207 0.98
37 2 0.01
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (36 bp):
ATCTGAAGCCTTCACCGGAGAATAGTGAAGCAAACC
Found at i:2560096 original size:54 final size:55
Alignment explanation
Indices: 2559870--2560470 Score: 672
Period size: 54 Copynumber: 11.3 Consensus size: 55
2559860 TCGACATTTC
* * * *
2559870 AAGAAGATATCCGAGTTCCATACT-CCTA-TAGAAAGAGAGAGCGAACCCGTTTG
1 AAGAAGATGTTCGAGTTCCATACTCCCTAGAAGAAAGAGGGAGCGAACCCGTTTG
* *
2559923 AAG-A-TTGTTCGAGTTCCATACTCCCT-GAAGAAAGAAGGAGCGAACCCGTTTG
1 AAGAAGATGTTCGAGTTCCATACTCCCTAGAAGAAAGAGGGAGCGAACCCGTTTG
* * * * *
2559975 AAG-A-TTGTTCGAGTTCTATACTTCCT-GAAAGAAAGAGGAAGCGAAACCGTTTG
1 AAGAAGATGTTCGAGTTCCATACTCCCTAG-AAGAAAGAGGGAGCGAACCCGTTTG
* **
2560028 AAG-A-TTGTTCGAGTTCCATACTCCCTAGAA-AAAGAGGGAGCGAACCCGTAAG
1 AAGAAGATGTTCGAGTTCCATACTCCCTAGAAGAAAGAGGGAGCGAACCCGTTTG
*
2560080 AAGAAGATGTTCGAGTTCTATACTCCCT-GAAGAAAGAGGGAGCGAACCCGTTT-
1 AAGAAGATGTTCGAGTTCCATACTCCCTAGAAGAAAGAGGGAGCGAACCCGTTTG
* *
2560133 --GAAGATGTTCGAGTTCCATACTCCTTA-AAGAAAGAAGGAGCGAACCCGTTTG
1 AAGAAGATGTTCGAGTTCCATACTCCCTAGAAGAAAGAGGGAGCGAACCCGTTTG
* * * *
2560185 AAG-AGATGTTCGAGTTCCATACTCCTTA-AAGAAAGAAGGAGAGAACCCGGTAAT-
1 AAGAAGATGTTCGAGTTCCATACTCCCTAGAAGAAAGAGGGAGCGAACCC-GT-TTG
* * * **
2560239 AAGAAAATTTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCTGTAAG
1 AAGAAGATGTTCGAGTTCCATACTCCCTAGAAGAAAGAGGGAGCGAACCCGTTTG
* * * * *
2560293 AAGAAGATTTTCGAGTTCTATACTTCCTAG-AGAAAGAGAGAGCGAACCTGTTTG
1 AAGAAGATGTTCGAGTTCCATACTCCCTAGAAGAAAGAGGGAGCGAACCCGTTTG
**
2560347 AAGAAGATGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTAAG
1 AAGAAGATGTTCGAGTTCCATACTCCCTAGAAGAAAGAGGGAGCGAACCCGTTTG
* * ** *
2560401 AAGAATATGTTCGAGTTCTATACTCCCT-GAAGAGGGAGAGAGCGAACCCGTTTG
1 AAGAAGATGTTCGAGTTCCATACTCCCTAGAAGAAAGAGGGAGCGAACCCGTTTG
2560455 AAGAAGATGTTCGAGT
1 AAGAAGATGTTCGAGT
2560471 CTTATACTCT
Statistics
Matches: 477, Mismatches: 54, Indels: 33
0.85 0.10 0.06
Matches are distributed among these distances:
51 62 0.13
52 72 0.15
53 101 0.21
54 203 0.43
55 39 0.08
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.22
Consensus pattern (55 bp):
AAGAAGATGTTCGAGTTCCATACTCCCTAGAAGAAAGAGGGAGCGAACCCGTTTG
Found at i:2560586 original size:55 final size:55
Alignment explanation
Indices: 2560467--2560595 Score: 134
Period size: 55 Copynumber: 2.3 Consensus size: 55
2560457 GAAGATGTTC
* * * *
2560467 GAGTCTTATACTCTCTGAACAAATAGAGAGCAGACAAGATTATTGAAGATTGTCC
1 GAGTCTCATACTCTCTGAACAAATAAAGAGCAGACAAGATTATTGAAGATTATCA
* * * * *
2560522 GTGTCTCATACTCTCTGAAGAAATAAAGAGCAGACACGATTCTT-AGAGATTATTA
1 GAGTCTCATACTCTCTGAACAAATAAAGAGCAGACAAGATTATTGA-AGATTATCA
* * *
2560577 GAGTTTCATATTCCCTGAA
1 GAGTCTCATACTCTCTGAA
2560596 AGCAATAGGG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
54 1 0.02
55 59 0.98
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (55 bp):
GAGTCTCATACTCTCTGAACAAATAAAGAGCAGACAAGATTATTGAAGATTATCA
Found at i:2565089 original size:26 final size:26
Alignment explanation
Indices: 2565045--2565094 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
2565035 TATGTTTTGG
* **
2565045 GTGAATTTATAAATTTTTAAGGGAAT
1 GTGAACTTATAAAACTTTAAGGGAAT
*
2565071 GTGAACTTATAAAACTTTAGGGGA
1 GTGAACTTATAAAACTTTAAGGGA
2565095 TGAAAATAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.38, C:0.04, G:0.22, T:0.36
Consensus pattern (26 bp):
GTGAACTTATAAAACTTTAAGGGAAT
Found at i:2566359 original size:18 final size:18
Alignment explanation
Indices: 2566336--2566382 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
2566326 ATGCAATTTG
2566336 GGTATCGATACCGAGGTC
1 GGTATCGATACCGAGGTC
2566354 GGTATCGATACCGAGGTC
1 GGTATCGATACCGAGGTC
2566372 GGTATCGATAC
1 GGTATCGATAC
2566383 TATAGAAGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.23
Consensus pattern (18 bp):
GGTATCGATACCGAGGTC
Found at i:2567106 original size:23 final size:23
Alignment explanation
Indices: 2567071--2567192 Score: 90
Period size: 23 Copynumber: 5.2 Consensus size: 23
2567061 GAGTCGAGGG
*
2567071 TTCTATATGGTCCTTCGGGACAA
1 TTCTATGTGGTCCTTCGGGACAA
* *
2567094 TTCTATGTAGTCCTTCGAGACAA
1 TTCTATGTGGTCCTTCGGGACAA
* * *
2567117 TTCTACGCGGTCATTCGGGACGAA
1 TTCTATGTGGTCCTTCGGGAC-AA
2567141 -TCTATGTGG-CACTTCGGTG-CATA
1 TTCTATGTGGTC-CTTCGG-GACA-A
* *
2567164 TTCTACGTGG-CACTTCGGTACAAA
1 TTCTATGTGGTC-CTTCGGGAC-AA
2567188 TTCTA
1 TTCTA
2567193 CGCAGAAGTT
Statistics
Matches: 79, Mismatches: 13, Indels: 13
0.75 0.12 0.12
Matches are distributed among these distances:
22 2 0.03
23 50 0.63
24 26 0.33
25 1 0.01
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.33
Consensus pattern (23 bp):
TTCTATGTGGTCCTTCGGGACAA
Found at i:2567173 original size:24 final size:24
Alignment explanation
Indices: 2567115--2567194 Score: 83
Period size: 24 Copynumber: 3.4 Consensus size: 24
2567105 CCTTCGAGAC
* * *
2567115 AATTCTACGCGGTCA-TTCGGGACG
1 AATTCTACGTGG-CACTTCGGTACA
* *
2567139 AA-TCTATGTGGCACTTCGGTGCA
1 AATTCTACGTGGCACTTCGGTACA
*
2567162 TATTCTACGTGGCACTTCGGTACA
1 AATTCTACGTGGCACTTCGGTACA
2567186 AATTCTACG
1 AATTCTACG
2567195 CAGAAGTTTC
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
22 2 0.04
23 14 0.31
24 29 0.64
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.30
Consensus pattern (24 bp):
AATTCTACGTGGCACTTCGGTACA
Found at i:2568488 original size:22 final size:22
Alignment explanation
Indices: 2568460--2568560 Score: 184
Period size: 22 Copynumber: 4.6 Consensus size: 22
2568450 AGTGTTATGA
*
2568460 CACTTTTGTATCAATGTGAATG
1 CACTTTTGTATCAATGCGAATG
2568482 CACTTTTGTATCAATGCGAATG
1 CACTTTTGTATCAATGCGAATG
*
2568504 CACTTTTGTATCAATGTGAATG
1 CACTTTTGTATCAATGCGAATG
2568526 CACTTTTGTATCAATGCGAATG
1 CACTTTTGTATCAATGCGAATG
2568548 CACTTTTGTATCA
1 CACTTTTGTATCA
2568561 GTGCTGAGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 76 1.00
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.40
Consensus pattern (22 bp):
CACTTTTGTATCAATGCGAATG
Found at i:2568572 original size:22 final size:23
Alignment explanation
Indices: 2568460--2568575 Score: 179
Period size: 22 Copynumber: 5.3 Consensus size: 23
2568450 AGTGTTATGA
2568460 CACTTTTGTATCAATG-TGAATG
1 CACTTTTGTATCAATGCTGAATG
2568482 CACTTTTGTATCAATGC-GAATG
1 CACTTTTGTATCAATGCTGAATG
2568504 CACTTTTGTATCAATG-TGAATG
1 CACTTTTGTATCAATGCTGAATG
2568526 CACTTTTGTATCAATGC-GAATG
1 CACTTTTGTATCAATGCTGAATG
* *
2568548 CACTTTTGTATCAGTGCTG-AGG
1 CACTTTTGTATCAATGCTGAATG
2568570 CACTTT
1 CACTTT
2568576 AATATTACTG
Statistics
Matches: 88, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
22 87 0.99
23 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39
Consensus pattern (23 bp):
CACTTTTGTATCAATGCTGAATG
Found at i:2568595 original size:44 final size:44
Alignment explanation
Indices: 2568460--2568600 Score: 158
Period size: 44 Copynumber: 3.2 Consensus size: 44
2568450 AGTGTTATGA
* ** *
2568460 CACTTTTGTATCAATGTGAATGCACTTTTGTATCAATGCGAATG
1 CACTTTTGTATCAATGTGAAGGCACTTTAATATCAATGCGAAGG
* ** *
2568504 CACTTTTGTATCAATGTGAATGCACTTTTGTATCAATGCGAATG
1 CACTTTTGTATCAATGTGAAGGCACTTTAATATCAATGCGAAGG
* * * *
2568548 CACTTTTGTATCAGTGCTG-AGGCACTTTAATATTACTGCTAAGG
1 CACTTTTGTATCAATG-TGAAGGCACTTTAATATCAATGCGAAGG
2568592 CACTTTTGT
1 CACTTTTGT
2568601 GATTTATTGG
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
44 86 0.98
45 2 0.02
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.39
Consensus pattern (44 bp):
CACTTTTGTATCAATGTGAAGGCACTTTAATATCAATGCGAAGG
Found at i:2568595 original size:66 final size:66
Alignment explanation
Indices: 2568460--2568600 Score: 178
Period size: 66 Copynumber: 2.1 Consensus size: 66
2568450 AGTGTTATGA
* * ** *
2568460 CACTTTTGTATCAATGTGAATGCACTTTTGTATCAATGCGAATGCACTTTTGTATCAATGTGAAT
1 CACTTTTGTATCAATGCGAATGCACTTTTGTATCAATGCGAAGGCACTTTAATATCAATGTGAAG
2568525 G
66 G
* * *
2568526 CACTTTTGTATCAATGCGAATGCACTTTTGTATCAGTGCTG-AGGCACTTTAATATTACTGCT-A
1 CACTTTTGTATCAATGCGAATGCACTTTTGTATCAATGC-GAAGGCACTTTAATATCAATG-TGA
2568589 AGG
64 AGG
2568592 CACTTTTGT
1 CACTTTTGT
2568601 GATTTATTGG
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
66 63 0.97
67 2 0.03
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.39
Consensus pattern (66 bp):
CACTTTTGTATCAATGCGAATGCACTTTTGTATCAATGCGAAGGCACTTTAATATCAATGTGAAG
G
Found at i:2569508 original size:30 final size:29
Alignment explanation
Indices: 2569474--2569535 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 29
2569464 AAAAAAATTA
*
2569474 ATTCTTATTTTAACGTAAAACATATCTTTT
1 ATTCTTATCTTAACGTAAAACATAT-TTTT
* *
2569504 ATTCTTATCTTAACTTAAAATATATTTTT
1 ATTCTTATCTTAACGTAAAACATATTTTT
2569533 ATT
1 ATT
2569536 TTAACCACAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 7 0.24
30 22 0.76
ACGTcount: A:0.34, C:0.11, G:0.02, T:0.53
Consensus pattern (29 bp):
ATTCTTATCTTAACGTAAAACATATTTTT
Found at i:2569554 original size:25 final size:25
Alignment explanation
Indices: 2569520--2569567 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
2569510 ATCTTAACTT
2569520 AAAATATATTTTTATTTTAACCACA
1 AAAATATATTTTTATTTTAACCACA
2569545 AAAATATATTTTTATTTTAACCA
1 AAAATATATTTTTATTTTAACCA
2569568 TAATTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (25 bp):
AAAATATATTTTTATTTTAACCACA
Found at i:2569704 original size:29 final size:29
Alignment explanation
Indices: 2569611--2569756 Score: 125
Period size: 30 Copynumber: 4.9 Consensus size: 29
2569601 TTAAAATATT
* *
2569611 ATAAGAATAAAATATAATTATTTAAGTTAAT
1 ATAAGAATAAAATAT-ATT-TTTAAATTAAA
* * *
2569642 ATAAGAATAAATTATATTTTTTAATTTAAG
1 ATAAGAATAAAATATA-TTTTTAAATTAAA
*
2569672 ATAAGATTAAAATATATTTTTAAATTAAA
1 ATAAGAATAAAATATATTTTTAAATTAAA
* * ** *
2569701 ATAAGAATAAAA-AAAATTTTAGGTTACGA
1 ATAAGAATAAAATATATTTTTAAATTA-AA
*
2569730 A-AAGAATAAAATATATTTAATAAATTA
1 ATAAGAATAAAATATATTT-TTAAATTA
2569757 CGTTAAAAAA
Statistics
Matches: 93, Mismatches: 18, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
28 20 0.22
29 28 0.30
30 29 0.31
31 16 0.17
ACGTcount: A:0.55, C:0.01, G:0.07, T:0.38
Consensus pattern (29 bp):
ATAAGAATAAAATATATTTTTAAATTAAA
Found at i:2569813 original size:18 final size:18
Alignment explanation
Indices: 2569772--2569818 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
2569762 AAAAATATTT
2569772 TTTAATGTTAATATGTAAA
1 TTTAAT-TTAATATGTAAA
* *
2569791 ATTAATTTAATATGTGAA
1 TTTAATTTAATATGTAAA
*
2569809 TTTAAGTTAA
1 TTTAATTTAA
2569819 AATATATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.47
Consensus pattern (18 bp):
TTTAATTTAATATGTAAA
Found at i:2570038 original size:22 final size:22
Alignment explanation
Indices: 2570008--2570051 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2569998 AGAGGGTGAC
*
2570008 ACATGTTAAAAATAAATTAAAA
1 ACATATTAAAAATAAATTAAAA
2570030 ACATATTAAAAATAAATTAAAA
1 ACATATTAAAAATAAATTAAAA
2570052 TAAATTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (22 bp):
ACATATTAAAAATAAATTAAAA
Found at i:2570051 original size:10 final size:10
Alignment explanation
Indices: 2570016--2570057 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
2570006 ACACATGTTA
2570016 AAAATAAATT
1 AAAATAAATT
2570026 AAAA-ACATATT
1 AAAATA-A-ATT
2570037 AAAAATAAATT
1 -AAAATAAATT
2570048 AAAATAAATT
1 AAAATAAATT
2570058 TAATCGTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
9 1 0.04
10 15 0.54
11 6 0.21
12 5 0.18
13 1 0.04
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (10 bp):
AAAATAAATT
Found at i:2570060 original size:11 final size:11
Alignment explanation
Indices: 2570013--2570057 Score: 65
Period size: 11 Copynumber: 4.2 Consensus size: 11
2570003 GTGACACATG
2570013 TTAAAAATAAA
1 TTAAAAATAAA
* *
2570024 TTAAAAACATA
1 TTAAAAATAAA
2570035 TTAAAAATAAA
1 TTAAAAATAAA
2570046 TT-AAAATAAA
1 TTAAAAATAAA
2570056 TT
1 TT
2570058 TAATCGTTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
10 10 0.33
11 20 0.67
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (11 bp):
TTAAAAATAAA
Found at i:2571606 original size:57 final size:58
Alignment explanation
Indices: 2571517--2571652 Score: 204
Period size: 58 Copynumber: 2.3 Consensus size: 58
2571507 TTTAATATTT
*
2571517 AAAATTAATTGTCCCTCTCATCTTACCACTAATCTTCTCATCTT-CCCGAACAAAATAA
1 AAAATAAATT-TCCCTCTCATCTTACCACTAATCTTCTCATCTTCCCCGAACAAAATAA
*
2571575 AATAA-AAATTTCCCTCTCATCTTACCGCTAATCTTCTCATCTTCCCCGAACAAAATAA
1 AA-AATAAATTTCCCTCTCATCTTACCACTAATCTTCTCATCTTCCCCGAACAAAATAA
* *
2571633 AAAATGATTTTCCCTCTCAT
1 AAAATAAATTTCCCTCTCAT
2571653 GTTCACTGTG
Statistics
Matches: 71, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
57 34 0.48
58 35 0.49
59 2 0.03
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (58 bp):
AAAATAAATTTCCCTCTCATCTTACCACTAATCTTCTCATCTTCCCCGAACAAAATAA
Found at i:2571651 original size:58 final size:57
Alignment explanation
Indices: 2571523--2571652 Score: 199
Period size: 57 Copynumber: 2.2 Consensus size: 57
2571513 ATTTAAAATT
2571523 AATTGTCCCTCTCATCTTACCACTAATCTTCTCATCTTCCCGAACAAAATAAAATAAA
1 AATT-TCCCTCTCATCTTACCACTAATCTTCTCATCTTCCCGAACAAAATAAAATAAA
* *
2571581 AATTTCCCTCTCATCTTACCGCTAATCTTCTCATCTTCCCCGAACAAAATAAAA-AATG
1 AATTTCCCTCTCATCTTACCACTAATCTTCTCATCTT-CCCGAACAAAATAAAATAA-A
*
2571639 ATTTTCCCTCTCAT
1 AATTTCCCTCTCAT
2571653 GTTCACTGTG
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
57 34 0.51
58 33 0.49
ACGTcount: A:0.32, C:0.31, G:0.04, T:0.33
Consensus pattern (57 bp):
AATTTCCCTCTCATCTTACCACTAATCTTCTCATCTTCCCGAACAAAATAAAATAAA
Found at i:2573155 original size:19 final size:19
Alignment explanation
Indices: 2573127--2573163 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2573117 CCTAGTGTTT
*
2573127 TTCTCTATCTTTTAATATG
1 TTCTCAATCTTTTAATATG
*
2573146 TTCTCAATCTTTTTATAT
1 TTCTCAATCTTTTAATAT
2573164 TTCGTTTGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.16, G:0.03, T:0.59
Consensus pattern (19 bp):
TTCTCAATCTTTTAATATG
Found at i:2573788 original size:20 final size:21
Alignment explanation
Indices: 2573763--2573801 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2573753 ACTATTAATA
2573763 ATACTAAT-TGATAGTTTATT
1 ATACTAATATGATAGTTTATT
*
2573783 ATACTAATATGATGGTTTA
1 ATACTAATATGATAGTTTA
2573802 GATATTAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.46
Consensus pattern (21 bp):
ATACTAATATGATAGTTTATT
Found at i:2577543 original size:2 final size:2
Alignment explanation
Indices: 2577536--2577569 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2577526 ACTCACACGA
2577536 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2577570 GAATAGGGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2579548 original size:20 final size:22
Alignment explanation
Indices: 2579519--2579569 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
2579509 AAAACCTTAG
*
2579519 GTATCAATACTCTTAT-AG-GA
1 GTATCGATACTCTTATGAGAGA
* *
2579539 GTATCGATACTTTTATGAGAGG
1 GTATCGATACTCTTATGAGAGA
2579561 GTATCGATA
1 GTATCGATA
2579570 TTATCTAGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 14 0.54
21 2 0.08
22 10 0.38
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.35
Consensus pattern (22 bp):
GTATCGATACTCTTATGAGAGA
Found at i:2582626 original size:11 final size:10
Alignment explanation
Indices: 2582601--2582634 Score: 59
Period size: 10 Copynumber: 3.3 Consensus size: 10
2582591 TCTTAGAGTT
2582601 TTAAGCTTTC
1 TTAAGCTTTC
2582611 TTAAGCTTTGC
1 TTAAGCTTT-C
2582622 TTAAGCTTTC
1 TTAAGCTTTC
2582632 TTA
1 TTA
2582635 TCATCTCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.21, C:0.18, G:0.12, T:0.50
Consensus pattern (10 bp):
TTAAGCTTTC
Found at i:2583712 original size:18 final size:18
Alignment explanation
Indices: 2583682--2583716 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2583672 TTAGCATTAC
2583682 TTGCATAAACCTTATTCT
1 TTGCATAAACCTTATTCT
2583700 TTGCA-AAATCCTTATTC
1 TTGCATAAA-CCTTATTC
2583717 ATATTACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.29, C:0.23, G:0.06, T:0.43
Consensus pattern (18 bp):
TTGCATAAACCTTATTCT
Found at i:2585576 original size:2 final size:2
Alignment explanation
Indices: 2585569--2585627 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
2585559 TAACAAATGC
2585569 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
2585611 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
2585628 AATACTAATA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2585945 original size:23 final size:23
Alignment explanation
Indices: 2585902--2585946 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2585892 ATATAAACTT
* * *
2585902 TGTCTCGAAGGACCGCGTATAAA
1 TGTCACGAAGGACCACATATAAA
2585925 TGTCACGAAGGACCACATATAA
1 TGTCACGAAGGACCACATATAA
2585947 CACATATGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (23 bp):
TGTCACGAAGGACCACATATAAA
Found at i:2587776 original size:25 final size:25
Alignment explanation
Indices: 2587748--2587798 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
2587738 ACTAACTCTT
2587748 TTCCAAGATTTCACTTATAACCCTC
1 TTCCAAGATTTCACTTATAACCCTC
2587773 TTCCAAGATTTCACTTATAACCCTC
1 TTCCAAGATTTCACTTATAACCCTC
2587798 T
1 T
2587799 CATCTTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.31, G:0.04, T:0.37
Consensus pattern (25 bp):
TTCCAAGATTTCACTTATAACCCTC
Found at i:2587858 original size:11 final size:10
Alignment explanation
Indices: 2587836--2587869 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
2587826 TCTTAGAGTT
2587836 TTAAGCTTTC
1 TTAAGCTTTC
2587846 TTAAGCTTTTC
1 TTAAGC-TTTC
*
2587857 TTAAACTTTC
1 TTAAGCTTTC
2587867 TTA
1 TTA
2587870 TCATCTGAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.53
Consensus pattern (10 bp):
TTAAGCTTTC
Found at i:2589712 original size:29 final size:30
Alignment explanation
Indices: 2589643--2589701 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
2589633 CAATTTAAGG
2589643 CAAAATATTTTTGGACTTGAATTGAATTTA
1 CAAAATATTTTTGGACTTGAATTGAATTTA
2589673 CAAAATATTTTTGGACTT-AATTGAATTTA
1 CAAAATATTTTTGGACTTGAATTGAATTTA
2589702 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.38
30 18 0.62
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (30 bp):
CAAAATATTTTTGGACTTGAATTGAATTTA
Found at i:2589810 original size:20 final size:21
Alignment explanation
Indices: 2589785--2589835 Score: 86
Period size: 20 Copynumber: 2.5 Consensus size: 21
2589775 TGTCAAAGTG
2589785 CATCCATGCATCCCTG-AGTA
1 CATCCATGCATCCCTGCAGTA
*
2589805 CATCCATGCATCCCTGCAGTG
1 CATCCATGCATCCCTGCAGTA
2589826 CATCCATGCA
1 CATCCATGCA
2589836 CCTGTACTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.24, C:0.37, G:0.16, T:0.24
Consensus pattern (21 bp):
CATCCATGCATCCCTGCAGTA
Found at i:2590337 original size:34 final size:32
Alignment explanation
Indices: 2590298--2590367 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
2590288 TTTTGTAAAG
* *
2590298 GGGAAACGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAACGTTCTAGCTTAGCCCG-G-AAAAACTA
* *
2590332 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAACGTTCTAGCTTAGCCCGGAAAAACTA
2590364 GGGA
1 GGGA
2590368 GTTTGTAAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 20 0.62
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (32 bp):
GGGAAACGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:2591253 original size:19 final size:20
Alignment explanation
Indices: 2591229--2591276 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
2591219 AACGATTTTC
*
2591229 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
2591248 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
2591268 TTTTGAAAA
1 TTTTGAAAA
2591277 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:2592425 original size:42 final size:42
Alignment explanation
Indices: 2592372--2592458 Score: 156
Period size: 42 Copynumber: 2.1 Consensus size: 42
2592362 TCAATTTTTA
2592372 AATGAAAAAGGGGGAACTTAACATTTTCATTTATTTTCCAAC
1 AATGAAAAAGGGGGAACTTAACATTTTCATTTATTTTCCAAC
* *
2592414 AATGATAAAGGGGGAGCTTAACATTTTCATTTATTTTCCAAC
1 AATGAAAAAGGGGGAACTTAACATTTTCATTTATTTTCCAAC
2592456 AAT
1 AAT
2592459 TGTTAACAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (42 bp):
AATGAAAAAGGGGGAACTTAACATTTTCATTTATTTTCCAAC
Found at i:2592660 original size:29 final size:30
Alignment explanation
Indices: 2592591--2592649 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
2592581 CAATTTAAGG
2592591 CAAAATGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
*
2592621 CAAAATATTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
2592650 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.44
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:2592781 original size:14 final size:14
Alignment explanation
Indices: 2592762--2592791 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2592752 TGCATCCATA
2592762 CACCTGAACTAATG
1 CACCTGAACTAATG
*
2592776 CACCTGCACTAATG
1 CACCTGAACTAATG
2592790 CA
1 CA
2592792 TCGATGCATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.33, G:0.13, T:0.20
Consensus pattern (14 bp):
CACCTGAACTAATG
Found at i:2592811 original size:20 final size:18
Alignment explanation
Indices: 2592786--2592875 Score: 60
Period size: 20 Copynumber: 4.9 Consensus size: 18
2592776 CACCTGCACT
2592786 AATGCATCGATGCATCATGC
1 AATGCATCGATGCATC-T-C
*
2592806 AATGCATCCATGCA-CTC
1 AATGCATCGATGCATCTC
* *
2592823 AA-ACATCGAATGCA-CTT
1 AATGCATCG-ATGCATCTC
*
2592840 AGTGCATCGATGCATCCTGC
1 AATGCATCGATGCAT-CT-C
* *
2592860 CATGCATCCATGCATC
1 AATGCATCGATGCATC
2592876 AAGGCTGCAA
Statistics
Matches: 55, Mismatches: 10, Indels: 11
0.72 0.13 0.14
Matches are distributed among these distances:
16 4 0.07
17 16 0.29
18 6 0.11
19 4 0.07
20 25 0.45
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (18 bp):
AATGCATCGATGCATCTC
Found at i:2593279 original size:34 final size:32
Alignment explanation
Indices: 2593240--2593309 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
2593230 TTTTGTAAAG
* * *
2593240 GGGAAATGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
2593274 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
2593306 GGGA
1 GGGA
2593310 GCTTGTAAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 20 0.62
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:2596046 original size:30 final size:30
Alignment explanation
Indices: 2596012--2596084 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 30
2596002 AAACACGATT
* *
2596012 AACAGAAATTTAAAGGA-CTGAAATGACAAA
1 AACAGAAATTTAAAGGATC-AAAATAACAAA
*
2596042 AACAGAAAATTAAAGGATCAAAATAACAAA
1 AACAGAAATTTAAAGGATCAAAATAACAAA
2596072 AACAGAAAATTTA
1 AACAG-AAATTTA
2596085 GGGGCTAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 30 0.81
31 7 0.19
ACGTcount: A:0.62, C:0.10, G:0.12, T:0.16
Consensus pattern (30 bp):
AACAGAAATTTAAAGGATCAAAATAACAAA
Found at i:2596095 original size:30 final size:29
Alignment explanation
Indices: 2596012--2596107 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 29
2596002 AAACACGATT
* *
2596012 AACAGAAATTTAAAGGA-CTGAAATGACAAA
1 AACAGAAAATTAAAGGATC-AAAAT-ACAAA
2596042 AACAGAAAATTAAAGGATCAAAATAACAAA
1 AACAGAAAATTAAAGGATCAAAAT-ACAAA
* **
2596072 AACAGAAAATT-TAGGGGCTAAAATA-AAA
1 AACAGAAAATTAAAGGATC-AAAATACAAA
2596100 AACAGAAA
1 AACAGAAA
2596108 CTTCATGGAC
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
28 11 0.19
29 5 0.09
30 41 0.71
31 1 0.02
ACGTcount: A:0.61, C:0.09, G:0.15, T:0.15
Consensus pattern (29 bp):
AACAGAAAATTAAAGGATCAAAATACAAA
Found at i:2597716 original size:13 final size:13
Alignment explanation
Indices: 2597712--2597742 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2597702 ATTAATAAAC
2597712 ATAATAATAATAA
1 ATAATAATAATAA
2597725 ATAATAATAAT-A
1 ATAATAATAATAA
2597737 ATAATA
1 ATAATA
2597743 TTAAAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
ATAATAATAATAA
Found at i:2597720 original size:3 final size:3
Alignment explanation
Indices: 2597712--2597742 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
2597702 ATTAATAAAC
2597712 ATA ATA ATA ATAA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA
2597743 TTAAAATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2597737 original size:22 final size:22
Alignment explanation
Indices: 2597704--2597747 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2597694 AATATGTAAT
2597704 TAATAAACATAATAATAATAAA
1 TAATAAACATAATAATAATAAA
*
2597726 TAATAATA-ATAATAATATTAAA
1 TAATAA-ACATAATAATAATAAA
2597748 ATTAAATAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (22 bp):
TAATAAACATAATAATAATAAA
Found at i:2598009 original size:40 final size:42
Alignment explanation
Indices: 2597946--2598150 Score: 154
Period size: 40 Copynumber: 4.8 Consensus size: 42
2597936 GGGTCGTCTA
* *
2597946 AGGG-TGACTCGGTTCCTATGTGATGAGGA-GATCTGG-TCG
1 AGGGATGACACGGTTCCTACGTGATGAGGACGATCTGGATCG
* *
2597985 AGGGATGACACGGTTCCTACGTGATGTGGACG-GCTGGCCATCTTTAGG
1 AGGGATGACACGGTTCCTACGTGATGAGGACGATCTGG--ATC-----G
* * *
2598033 AGTGGTGATAACTCGGTTCCTACGTGATGAGGACGA-CTGGTTATCT
1 A--GG-GATGACACGGTTCCTACGTGATGAGGACGATCTGG--ATCG
* * * *
2598079 AAGGTTGACGCGGCTCCTACGTGATGAGGA-GATCTGG-TCG
1 AGGGATGACACGGTTCCTACGTGATGAGGACGATCTGGATCG
2598119 AGGGATGACACGGTTCCTACGTGATGAGGACG
1 AGGGATGACACGGTTCCTACGTGATGAGGACG
2598151 GTTGGCCATC
Statistics
Matches: 130, Mismatches: 20, Indels: 30
0.72 0.11 0.17
Matches are distributed among these distances:
39 4 0.03
40 54 0.42
41 2 0.02
42 2 0.02
43 29 0.22
44 1 0.01
46 1 0.01
48 2 0.02
50 2 0.02
51 33 0.25
ACGTcount: A:0.20, C:0.19, G:0.36, T:0.25
Consensus pattern (42 bp):
AGGGATGACACGGTTCCTACGTGATGAGGACGATCTGGATCG
Found at i:2598159 original size:134 final size:134
Alignment explanation
Indices: 2597942--2598433 Score: 774
Period size: 134 Copynumber: 3.7 Consensus size: 134
2597932 GTTCGGGTCG
* * * * ** *
2597942 TCTAAGGGTGACTCGGTTCCTATGTGATGAGGAGATCTGGTC-GAGGGATGACACGGTTCCTACG
1 TCTAAGGTTGACGCGGCTCCTACGTGATGAGGAGATCTGGTCAG-GGGATGACACGACTCATACG
* *
2598006 TGATGTGGACGGCTGGCCATCTTTAGGAGTGGTGATAACTCGGTTCCTACGTGATGAGGACGACT
65 TGATGAGGACGGTTGGCCATCTTTAGGAGTGGTGATAACTCGGTTCCTACGTGATGAGGACGACT
2598071 GGTTA
130 GGTTA
** *
2598076 TCTAAGGTTGACGCGGCTCCTACGTGATGAGGAGATCTGGTC-GAGGGATGACACGGTTCCTACG
1 TCTAAGGTTGACGCGGCTCCTACGTGATGAGGAGATCTGGTCAG-GGGATGACACGACTCATACG
* *
2598140 TGATGAGGACGGTTGGCCATCTTTAGGAGTGGTGATAACTCGGTTCCTACGTAATGAGGACGGCT
65 TGATGAGGACGGTTGGCCATCTTTAGGAGTGGTGATAACTCGGTTCCTACGTGATGAGGACGACT
2598205 GGTTA
130 GGTTA
2598210 TCTAAGGTTGACGCGGCTCCTACGTGATGAGGAGATCTGGTCAGGGGATGACACGACTCATACGT
1 TCTAAGGTTGACGCGGCTCCTACGTGATGAGGAGATCTGGTCAGGGGATGACACGACTCATACGT
*
2598275 GATGAGGACGGTTGGCCATCTTTAGGAGTGGTGATAACTTGGTTCCTACGTGATGAGGACGACTG
66 GATGAGGACGGTTGGCCATCTTTAGGAGTGGTGATAACTCGGTTCCTACGTGATGAGGACGACTG
2598340 GTTA
131 GTTA
*
2598344 TCTAAGGTTGACGCGGCTCCTACGTGATGAGGAGATCTGGTCAGGGGATGACACGACTCATACTT
1 TCTAAGGTTGACGCGGCTCCTACGTGATGAGGAGATCTGGTCAGGGGATGACACGACTCATACGT
* *
2598409 GATGAAGA-GTTTTGGCCATCTTTAG
66 GATGAGGACG-GTTGGCCATCTTTAG
2598434 TGATTATGGT
Statistics
Matches: 339, Mismatches: 17, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
133 1 0.00
134 337 0.99
135 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.33, T:0.27
Consensus pattern (134 bp):
TCTAAGGTTGACGCGGCTCCTACGTGATGAGGAGATCTGGTCAGGGGATGACACGACTCATACGT
GATGAGGACGGTTGGCCATCTTTAGGAGTGGTGATAACTCGGTTCCTACGTGATGAGGACGACTG
GTTA
Found at i:2598250 original size:43 final size:45
Alignment explanation
Indices: 2598050--2598384 Score: 195
Period size: 43 Copynumber: 7.6 Consensus size: 45
2598040 ATAACTCGGT
2598050 TCCTACGTGATGAGGACGA-CTGGTTATCTA-AGGTTGACGCGGC
1 TCCTACGTGATGAGGACGATCTGGTTATCTAGAGGTTGACGCGGC
* * * *
2598093 TCCTACGTGATGAGGA-GATCTGG---TCGAG-GGATGACACGGT
1 TCCTACGTGATGAGGACGATCTGGTTATCTAGAGGTTGACGCGGC
* ** * * *
2598133 TCCTACGTGATGAGGACGGT-TGGCCATCTTTAGGAGTGGTGATAACTCGGT
1 TCCTACGTGATGAGGACGATCTGGTTATC--TA-GA--GGT--TGACGCGGC
* *
2598184 TCCTACGTAATGAGGACG-GCTGGTTATCTA-AGGTTGACGCGGC
1 TCCTACGTGATGAGGACGATCTGGTTATCTAGAGGTTGACGCGGC
* * * *
2598227 TCCTACGTGATGAGGA-GATCTGG---TC-AGGGGATGACACGAC
1 TCCTACGTGATGAGGACGATCTGGTTATCTAGAGGTTGACGCGGC
* * ** * ** *
2598267 TCATACGTGATGAGGACGGT-TGGCCATCTTTAGGAGTGGTGATAACTTGGT
1 TCCTACGTGATGAGGACGATCTGGTTATC--TA-GA--GGT--TGACGCGGC
2598318 TCCTACGTGATGAGGACGA-CTGGTTATCTA-AGGTTGACGCGGC
1 TCCTACGTGATGAGGACGATCTGGTTATCTAGAGGTTGACGCGGC
2598361 TCCTACGTGATGAGGA-GATCTGGT
1 TCCTACGTGATGAGGACGATCTGGT
2598385 CAGGGGATGA
Statistics
Matches: 222, Mismatches: 39, Indels: 62
0.69 0.12 0.19
Matches are distributed among these distances:
39 1 0.00
40 60 0.27
41 4 0.02
42 5 0.02
43 75 0.34
45 7 0.03
46 2 0.01
47 3 0.01
49 8 0.04
51 57 0.26
ACGTcount: A:0.21, C:0.19, G:0.34, T:0.26
Consensus pattern (45 bp):
TCCTACGTGATGAGGACGATCTGGTTATCTAGAGGTTGACGCGGC
Found at i:2598482 original size:28 final size:28
Alignment explanation
Indices: 2598442--2598521 Score: 90
Period size: 28 Copynumber: 2.9 Consensus size: 28
2598432 AGTGATTATG
** *
2598442 GTTTCAAGGGAAACCGACTAAAAGATTT
1 GTTTCAAAAGAAACAGACTAAAAGATTT
*
2598470 GTTTCAAAAGAAACAGACTCAAAGATTT
1 GTTTCAAAAGAAACAGACTAAAAGATTT
* *
2598498 GTTTCAAGAA-AAACAAACTCAAAG
1 GTTTCAA-AAGAAACAGACTAAAAG
2598522 GTGATGTGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 44 0.96
29 2 0.04
ACGTcount: A:0.46, C:0.15, G:0.16, T:0.23
Consensus pattern (28 bp):
GTTTCAAAAGAAACAGACTAAAAGATTT
Found at i:2598793 original size:74 final size:70
Alignment explanation
Indices: 2598658--2598793 Score: 157
Period size: 74 Copynumber: 1.9 Consensus size: 70
2598648 CAAAGATCGG
* * * *
2598658 TGTTTCGAGAGAAACAAACTCAAAGTTGTTTTTGTTTCAAGAAAAACATACTCAAGGATTTTGTT
1 TGTTTCAAGAGAAACAAACTCAAAGTGGTTTTTGTTTCAAGAAAAACAGACTCAAAGATTTTGTT
2598723 TGTTT
66 TGTTT
* * *
2598728 TGTTTCAAGGGAAACAAACTCAAAGATGGTAAATTTTGTTTCCAA-AGAAAGAGACTCAAAGATT
1 TGTTTCAAGAGAAACAAACTCAAAG-TGGT---TTTTGTTT-CAAGAAAAACAGACTCAAAGATT
2598792 TT
61 TT
2598794 CTCAAAGAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
70 23 0.43
71 3 0.06
74 25 0.46
75 3 0.06
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.34
Consensus pattern (70 bp):
TGTTTCAAGAGAAACAAACTCAAAGTGGTTTTTGTTTCAAGAAAAACAGACTCAAAGATTTTGTT
TGTTT
Found at i:2599138 original size:31 final size:31
Alignment explanation
Indices: 2599056--2599130 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 31
2599046 GTCAAATTCG
* *
2599056 TTTCAAGGGAAAC-GACTCAAAGATGGTTTTA
1 TTTCAAGAGAAACAAACTCAAAGAT-GTTTTA
2599087 TTTCAAGAGAAACAAACTCAAAGAT-TTTGTA
1 TTTCAAGAGAAACAAACTCAAAGATGTTT-TA
*
2599118 TTTCTAGAGAAAC
1 TTTCAAGAGAAAC
2599131 TGTCTCAAGG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
30 3 0.08
31 26 0.67
32 10 0.26
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.29
Consensus pattern (31 bp):
TTTCAAGAGAAACAAACTCAAAGATGTTTTA
Found at i:2599215 original size:30 final size:29
Alignment explanation
Indices: 2599181--2599237 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
2599171 TCAAAGGTGT
*
2599181 GTGTTTCAAGAGAAACTAACTCAAAGATAG
1 GTGTTTCAAAAGAAA-TAACTCAAAGATAG
*
2599211 GTGTTTCAAAAGAAATGACTCAAAGAT
1 GTGTTTCAAAAGAAATAACTCAAAGAT
2599238 TTTTCACGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (29 bp):
GTGTTTCAAAAGAAATAACTCAAAGATAG
Found at i:2599333 original size:15 final size:15
Alignment explanation
Indices: 2599313--2599343 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2599303 GTTTTGTTTT
2599313 AAGTGAAACAGACTC
1 AAGTGAAACAGACTC
2599328 AAGTGAAACAGACTC
1 AAGTGAAACAGACTC
2599343 A
1 A
2599344 CAATTGGCAA
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:0.48, C:0.19, G:0.19, T:0.13
Consensus pattern (15 bp):
AAGTGAAACAGACTC
Found at i:2599462 original size:16 final size:16
Alignment explanation
Indices: 2599441--2599471 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2599431 AACATACTCA
2599441 AAGATTTTTCATTTTT
1 AAGATTTTTCATTTTT
2599457 AAGATTTTTCATTTT
1 AAGATTTTTCATTTT
2599472 GTTTCAAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.61
Consensus pattern (16 bp):
AAGATTTTTCATTTTT
Found at i:2599714 original size:36 final size:34
Alignment explanation
Indices: 2599671--2599804 Score: 124
Period size: 36 Copynumber: 3.7 Consensus size: 34
2599661 AAAGAAAAAG
*
2599671 TGTCTCAAGTGAGACGAAATTTGTTTTTCAAGAAAT
1 TGTCTCAAGCGAGAC-AAATTTGTTTTT-AAGAAAT
* * *
2599707 TGTCTCAAACGACACAAAAATTGTTTTTACAGAAAT
1 TGTCTCAAGCGAGAC-AAATTTGTTTTTA-AGAAAT
* *
2599743 TGTCTCAAGCGAGACAACATTTGTTTTTGAGAAAA
1 TGTCTCAAGCGAGACAA-ATTTGTTTTTAAGAAAT
* * *
2599778 CGATCTCAAGTGAGATCAACTTTGTTT
1 TG-TCTCAAGCGAGA-CAAATTTGTTT
2599805 AATATGAAAA
Statistics
Matches: 81, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
35 9 0.11
36 69 0.85
37 3 0.04
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (34 bp):
TGTCTCAAGCGAGACAAATTTGTTTTTAAGAAAT
Found at i:2601635 original size:13 final size:13
Alignment explanation
Indices: 2601619--2601648 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2601609 TTTGATTTTC
2601619 TTTTTACTTTATT
1 TTTTTACTTTATT
*
2601632 TTTTTGCTTTATT
1 TTTTTACTTTATT
2601645 TTTT
1 TTTT
2601649 CTTTGCTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.10, C:0.07, G:0.03, T:0.80
Consensus pattern (13 bp):
TTTTTACTTTATT
Found at i:2601661 original size:15 final size:16
Alignment explanation
Indices: 2601630--2601689 Score: 52
Period size: 15 Copynumber: 3.8 Consensus size: 16
2601620 TTTTACTTTA
2601630 TTTT-TTTGCTTTATT
1 TTTTCTTTGCTTTATT
*
2601645 TTTTCTTTGC-TTCTT
1 TTTTCTTTGCTTTATT
* * *
2601660 TTCTCTTTGTTTTTTT
1 TTTTCTTTGCTTTATT
*
2601676 GTTTTCTTCGCTTT
1 -TTTTCTTTGCTTT
2601690 GATATGATCT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
15 16 0.46
16 9 0.26
17 10 0.29
ACGTcount: A:0.02, C:0.15, G:0.08, T:0.75
Consensus pattern (16 bp):
TTTTCTTTGCTTTATT
Found at i:2604483 original size:23 final size:22
Alignment explanation
Indices: 2604445--2604527 Score: 86
Period size: 22 Copynumber: 3.9 Consensus size: 22
2604435 GTTGTTTAAT
2604445 TTTAAA-A-AAAATATAAATTA
1 TTTAAATATAAAATATAAATTA
2604465 TTTTAAAT-TATAAATATAAATTA
1 -TTTAAATATA-AAATATAAATTA
*
2604488 TTTAAATATAAAATATAAAATA
1 TTTAAATATAAAATATAAATTA
*
2604510 -TAAAATATTAAAA-ATAAA
1 TTTAAATA-TAAAATATAAA
2604528 AATTAAATTA
Statistics
Matches: 55, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
21 17 0.31
22 24 0.44
23 14 0.25
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAATATAAAATATAAATTA
Found at i:2604494 original size:22 final size:23
Alignment explanation
Indices: 2604443--2604506 Score: 91
Period size: 22 Copynumber: 2.9 Consensus size: 23
2604433 GAGTTGTTTA
2604443 ATTTTAAA-A-AAAATATAAATT
1 ATTTTAAATATAAAATATAAATT
2604464 ATTTTAAAT-TATAAATATAAATT
1 ATTTTAAATATA-AAATATAAATT
2604487 A-TTTAAATATAAAATATAAA
1 ATTTTAAATATAAAATATAAA
2604507 ATATAAAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
21 8 0.21
22 17 0.44
23 14 0.36
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
ATTTTAAATATAAAATATAAATT
Found at i:2604510 original size:14 final size:15
Alignment explanation
Indices: 2604471--2604534 Score: 80
Period size: 14 Copynumber: 4.4 Consensus size: 15
2604461 ATTATTTTAA
*
2604471 ATTATAAATATAAATT
1 ATTA-AAATATAAAAT
*
2604487 ATTTAAATATAAAAT
1 ATTAAAATATAAAAT
2604502 A-TAAAATATAAAAT
1 ATTAAAATATAAAAT
2604516 ATTAAAA-ATAAAA-
1 ATTAAAATATAAAAT
2604529 ATTAAA
1 ATTAAA
2604535 TTACTGGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
13 6 0.14
14 19 0.43
15 16 0.36
16 3 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
ATTAAAATATAAAAT
Found at i:2604529 original size:7 final size:7
Alignment explanation
Indices: 2604476--2604528 Score: 63
Period size: 7 Copynumber: 7.4 Consensus size: 7
2604466 TTTAAATTAT
2604476 AAATATA
1 AAATATA
* *
2604483 AATTATTT
1 AAATA-TA
2604491 AAATATA
1 AAATATA
2604498 AAATATA
1 AAATATA
2604505 AAATATA
1 AAATATA
2604512 AAATATTA
1 AAATA-TA
2604520 AAA-ATA
1 AAATATA
2604526 AAA
1 AAA
2604529 ATTAAATTAC
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
6 5 0.12
7 25 0.62
8 10 0.25
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
AAATATA
Found at i:2604529 original size:29 final size:28
Alignment explanation
Indices: 2604469--2604534 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 28
2604459 AAATTATTTT
* *
2604469 AAATTATAAATATAAATTATTTAAATATA
1 AAATTA-AAATATAAAATATTAAAATATA
2604498 AAATATAAAATATAAAATATTAAAA-ATAA
1 AAAT-TAAAATATAAAATATTAAAATAT-A
2604527 AAATTAAA
1 AAATTAAA
2604535 TTACTGGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 6 0.18
29 25 0.76
30 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (28 bp):
AAATTAAAATATAAAATATTAAAATATA
Found at i:2605190 original size:6 final size:7
Alignment explanation
Indices: 2605175--2605199 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2605165 GCACCTCATT
2605175 AAAAGAA
1 AAAAGAA
2605182 AAAAGAA
1 AAAAGAA
2605189 AAAAGAA
1 AAAAGAA
2605196 AAAA
1 AAAA
2605200 TAATTTGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:2612965 original size:6 final size:6
Alignment explanation
Indices: 2612954--2613029 Score: 116
Period size: 6 Copynumber: 12.7 Consensus size: 6
2612944 CAGTCAAGGT
2612954 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
* * * *
2613002 ATACAC ACATAC ATATAT ATATAT ATAT
1 ATATAC ATATAC ATATAC ATATAC ATAT
2613030 TGATGGTCAT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 65 1.00
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAC
Found at i:2615500 original size:3 final size:3
Alignment explanation
Indices: 2615486--2615546 Score: 52
Period size: 3 Copynumber: 20.7 Consensus size: 3
2615476 GTGACATATA
* * * * * *
2615486 AAG AAG ACG AAG AAG AAG AAG AAG ATG GAG AAT CA- AAG AAG ATG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
*
2615533 AAG AAG ATG AAG AA
1 AAG AAG AAG AAG AA
2615547 AACTGGGGCA
Statistics
Matches: 44, Mismatches: 13, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
2 1 0.02
3 43 0.98
ACGTcount: A:0.59, C:0.03, G:0.31, T:0.07
Consensus pattern (3 bp):
AAG
Found at i:2615640 original size:2 final size:2
Alignment explanation
Indices: 2615633--2615671 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2615623 TGCTATTGAA
2615633 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2615672 AGAATTTTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2626504 original size:59 final size:59
Alignment explanation
Indices: 2626408--2626530 Score: 239
Period size: 59 Copynumber: 2.1 Consensus size: 59
2626398 AAGCTCTCTA
2626408 TTTA-TAGGCTTCACATCAGGGGTAAAATGGTCCAACAAAAATCATTTTAAAGTCTGAT
1 TTTATTAGGCTTCACATCAGGGGTAAAATGGTCCAACAAAAATCATTTTAAAGTCTGAT
2626466 TTTATTAGGCTTCACATCAGGGGTAAAATGGTCCAACAAAAATCATTTTAAAGTCTGAT
1 TTTATTAGGCTTCACATCAGGGGTAAAATGGTCCAACAAAAATCATTTTAAAGTCTGAT
2626525 TTTATT
1 TTTATT
2626531 TCCTGGAATT
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
58 4 0.06
59 60 0.94
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (59 bp):
TTTATTAGGCTTCACATCAGGGGTAAAATGGTCCAACAAAAATCATTTTAAAGTCTGAT
Found at i:2628333 original size:3 final size:3
Alignment explanation
Indices: 2628321--2628369 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
2628311 CATAATAATA
* * *
2628321 ATT ATA ATT ATT ATT AAT ATA ATAT ATT ATT ATT ATT ATTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT A-TT ATT ATT
2628368 AT
1 AT
2628370 ATATATATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
3 33 0.87
4 5 0.13
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:2628338 original size:22 final size:22
Alignment explanation
Indices: 2628313--2628358 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
2628303 ATTTTTTTCA
2628313 TAATAATAAT-TATAATTATTAT
1 TAAT-ATAATATATAATTATTAT
*
2628335 TAATATAATATATTATTATTAT
1 TAATATAATATATAATTATTAT
2628357 TA
1 TA
2628359 TTTATTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TAATATAATATATAATTATTAT
Done.