Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008613.1 Hibiscus syriacus cultivar Beakdansim tig00111569_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: 647085
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:516158 original size:24 final size:23
Alignment explanation
Indices: 516106--516173 Score: 93
Period size: 23 Copynumber: 2.9 Consensus size: 23
516096 GTGTTTGTGT
516106 TGTTCGTTTATGTTCATTTATTG
1 TGTTCGTTTATGTTCATTTATTG
516129 TGTTCGTTTATGTTCATTCGT-TTG
1 TGTTCGTTTATGTTCATT--TATTG
* *
516153 TGTTCGTTTACGTTCGTTTAT
1 TGTTCGTTTATGTTCATTTAT
516174 CATTTAAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
22 1 0.03
23 19 0.47
24 19 0.47
25 1 0.03
ACGTcount: A:0.10, C:0.12, G:0.19, T:0.59
Consensus pattern (23 bp):
TGTTCGTTTATGTTCATTTATTG
Found at i:536126 original size:23 final size:23
Alignment explanation
Indices: 536079--536128 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
536069 AATAGCATAT
**
536079 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
536102 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
536125 TAGG
1 TAGG
536129 CATTTAACCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:536189 original size:87 final size:87
Alignment explanation
Indices: 536043--536204 Score: 288
Period size: 87 Copynumber: 1.9 Consensus size: 87
536033 ATATTATATT
* *
536043 ATTTAACCAGAAATATTATCAAGCACAATAGCATATTAGGTAGCGCTTATATAATGTAATAGGTA
1 ATTTAACCAGAAATATTATCAAGCACAATAACATATTAGGTAGAGCTTATATAATGTAATAGGTA
536108 GCGCTTATATAATAAAATAGGC
66 GCGCTTATATAATAAAATAGGC
* *
536130 ATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGAGCTTATATAATGTAATAGGTA
1 ATTTAACCAGAAATATTATCAAGCACAATAACATATTAGGTAGAGCTTATATAATGTAATAGGTA
536195 GCGCTTATAT
66 GCGCTTATAT
536205 TGACATATTT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (87 bp):
ATTTAACCAGAAATATTATCAAGCACAATAACATATTAGGTAGAGCTTATATAATGTAATAGGTA
GCGCTTATATAATAAAATAGGC
Found at i:541062 original size:199 final size:200
Alignment explanation
Indices: 540251--541602 Score: 1415
Period size: 200 Copynumber: 6.8 Consensus size: 200
540241 TTCTATTTAC
* * * * * * *
540251 ACCGGTAAATTTCA-ACCGGTTACATTGTAAATTGACCTATTACATTATAATTTTTGGTCTCGAT
1 ACCGGTATATTT-AGACCAGTTACATTGTTAATTTACCTATTACATTATAATTATAGGTTTCGAT
* * * * * * * * *
540315 GTATTTGGGGTCGATACTTTTTATAAATGTATCGAAACTTTATGCGTGGACATT-GTTTGG--CA
65 GTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTGT-TGTGCAC-TTGGTTTGGAAAA
* * * * * *** * * * *
540377 TTCATTATGGACATAAAGTATCGACAC-AGATAT-AAAAAGTATCGATACATTATGTAGACCTGT
128 TACATTCTGGACAAAAAGTATCGACACTTG-T-TGGATTTGTGTCGATACTTTATGTATACATGT
*
540440 TTGCTCATAAA
191 TTTCTCAT-AA
* * * * * * * * * *
540451 ACCAGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTTTTGGTCTCGATG
1 ACCGGTATATTTAGACCAGTTACATTGTTAATTTACCTATTACATTATAATTATAGGTTTCGATG
* * * * * * *
540516 TATTTGGGGTCGATACTT-TTAATAAATGTATCGACACTTTAAG-CGTGCACATAGTTTGG-GAA
66 TTTTTGGGATCGACACTTGTT-ATAAATGTATCGACACTTT--GTTGTGCACTTGGTTTGGAAAA
* * * * * *** ** ** * * * * **
540578 TTCATTATTGATAAAAAGTATCGACGC-AAATAAATAAAGTGTCGATACATTATTTAGACTTACT
128 TACATTCTGGACAAAAAGTATCGACACTTGTTGGAT-TTGTGTCGATACTTTATGTATACATGTT
540642 TTCTCATAAA
192 TTCTCAT-AA
* * ** * * *
540652 ACCGGTAAATTTAAACCAACTACATTGTAAAGTGACCTATTACATTATAATTATAGGTTTCGATG
1 ACCGGTATATTTAGACCAGTTACATTGTTAATTTACCTATTACATTATAATTATAGGTTTCGATG
* * *
540717 TATTTGGGATCGACACATGTTATAAATGTATCGACACTTTTTTGTGCACTTGGTTTGGAAAATAC
66 TTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTGTTGTGCACTTGGTTTGGAAAATAC
* ** *
540782 ATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTATGTATACTTGTTTTCT
131 ATTCTGGACAAAAAGTATCGACACTTGTTGGATTTGTGTCGATACTTTATGTATACATGTTTTCT
540847 CATAA
196 CATAA
* **
540852 ACCGGTATATTTAGACCAATTACATTGTTAATTTACCTATTACATTATAATTATAGGTTTCGACA
1 ACCGGTATATTTAGACCAGTTACATTGTTAATTTACCTATTACATTATAATTATAGGTTTCGATG
* * **
540917 TTTTTGGGATCGATACTTGTTATAAATGTATCGACACTTTGTTGTACACTTGG-TTAAAAAATAC
66 TTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTGTTGTGCACTTGGTTTGGAAAATAC
* *
540981 ACTCTGGACAAAAAGTATCGACACTTGTTGGATTTGTGTCGATACTTTATGTATACCTGTTTTCT
131 ATTCTGGACAAAAAGTATCGACACTTGTTGGATTTGTGTCGATACTTTATGTATACATGTTTTCT
541046 CATAA
196 CATAA
* * *
541051 ACCGATATATTTAGACCGGTTAAATTGTTAATTTACCTATTACATTATAATTATAGGTTTCGATG
1 ACCGGTATATTTAGACCAGTTACATTGTTAATTTACCTATTACATTATAATTATAGGTTTCGATG
**
541116 TTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTGTTGTGCACTTGGTTTTTAAAATAC
66 TTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTGTTGTGCACTTGGTTTGGAAAATAC
* * *
541181 ACTCTGGACAAAAAGTATCGACACTTATTGGATTTGTGTCGATACTTTATATATACATGTTTTCT
131 ATTCTGGACAAAAAGTATCGACACTTGTTGGATTTGTGTCGATACTTTATGTATACATGTTTTCT
541246 CATAA
196 CATAA
* * *
541251 ACTGATATATTTAGACCGGTTACATTGTTAATTTACCTATTACATT-TAATTAT-GGATTTCGAT
1 ACCGGTATATTTAGACCAGTTACATTGTTAATTTACCTATTACATTATAATTATAGG-TTTCGAT
*
541314 GTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTT-TTAGTGCACTTGGTTTTG-AAAT
65 GTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTGTT-GTGCACTTGGTTTGGAAAAT
* * ** * * *
541377 ATATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACATATGTTTT
129 ACATTCTGGACAAAAAGTATCGACACTTGTTGGATTTGTGTCGATACTTTATGTATACATGTTTT
*
541442 CTCAAAA
194 CTCATAA
* * *
541449 ATCGGTATATTTAGGCCAGTTACATTGTTATTTTACCTATTACATTAT-ATCTAT-GTGTTTCGA
1 ACCGGTATATTTAGACCAGTTACATTGTTAATTTACCTATTACATTATAAT-TATAG-GTTTCGA
* * *
541512 TGTTTTTAGTATCGACACTTGTTATAAATGTATCGACACTTTGTCGTGCACTTGGTTTGGAAAAT
64 TGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTGTTGTGCACTTGGTTTGGAAAAT
* *
541577 ACATTCTGGACAACATGTATCGACAC
129 ACATTCTGGACAAAAAGTATCGACAC
541603 GAATGAATAA
Statistics
Matches: 1018, Mismatches: 114, Indels: 40
0.87 0.10 0.03
Matches are distributed among these distances:
198 111 0.11
199 323 0.32
200 379 0.37
201 200 0.20
202 5 0.00
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (200 bp):
ACCGGTATATTTAGACCAGTTACATTGTTAATTTACCTATTACATTATAATTATAGGTTTCGATG
TTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTGTTGTGCACTTGGTTTGGAAAATAC
ATTCTGGACAAAAAGTATCGACACTTGTTGGATTTGTGTCGATACTTTATGTATACATGTTTTCT
CATAA
Found at i:541518 original size:398 final size:399
Alignment explanation
Indices: 540641--541602 Score: 1367
Period size: 398 Copynumber: 2.4 Consensus size: 399
540631 TTAGACTTAC
* * * ** * * * *
540641 TTTCTCATAAAACCGGTAAATTTAAACCAACTACATTGTAAAGTGACCTATTACATTATAATTAT
1 TTTCTCA-AAAACCGATATATTTAGACCAGTTAAATTGTTAATTTACCTATTACATTATAATTAT
* * *
540706 AGGTTTCGATGTATTTGGGATCGACACATGTTATAAATGTATCGACACTTTTTTGTGCACTTGGT
65 AGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTGTTGTGCACTTGGT
* * ** *
540771 TTGGAAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTATGTAT
130 TTGGAAAATACATTCTGGACAAAAAGTATCGACACTTATTGGATTTGTGTCGATACTTTATATAT
* *
540836 ACTTGTTTTCTCATAAACCGGTATATTTAGACCAATTACATTGTTAATTTACCTATTACATTATA
195 ACATGTTTTCTCATAAACCGATATATTTAGACCAATTACATTGTTAATTTACCTATTACATTATA
*
540901 ATTATAGGTTTCGACATTTTTGGGATCGATACTTGTTATAAATGTATCGACACTTTGTTGTACAC
260 ATTATAGGTTTCGACATTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTGTTGTACAC
540966 TTGGTTAAAAAATACACTCTGGACAAAAAGTATCGACACTTGTTGGATTTGTGTCGATACTTTAT
325 TTGGTTAAAAAATACACTCTGGACAAAAAGTATCGACACTTGTTGGATTTGTGTCGATACTTTAT
* *
541031 GTATACCTGT
390 GTACACATGT
* *
541041 TTTCTCATAAACCGATATATTTAGACCGGTTAAATTGTTAATTTACCTATTACATTATAATTATA
1 TTTCTCAAAAACCGATATATTTAGACCAGTTAAATTGTTAATTTACCTATTACATTATAATTATA
541106 GGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTGTTGTGCACTTGGTT
66 GGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTGTTGTGCACTTGGTT
** *
541171 TTTAAAATACACTCTGGACAAAAAGTATCGACACTTATTGGATTTGTGTCGATACTTTATATATA
131 TGGAAAATACATTCTGGACAAAAAGTATCGACACTTATTGGATTTGTGTCGATACTTTATATATA
* **
541236 CATGTTTTCTCATAAACTGATATATTTAGACCGGTTACATTGTTAATTTACCTATTACATT-TAA
196 CATGTTTTCTCATAAACCGATATATTTAGACCAATTACATTGTTAATTTACCTATTACATTATAA
** *
541300 TTAT-GGATTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTT-TTAGTGCA
261 TTATAGG-TTTCGACATTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTGTT-GTACA
*** * * * ** *
541363 CTTGGTTTTGAAATATATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTT
324 CTTGGTTAAAAAATACACTCTGGACAAAAAGTATCGACACTTGTTGGATTTGTGTCGATACTTTA
*
541428 TGTACATATGT
389 TGTACACATGT
* * * * *
541439 TTTCTCAAAAATCGGTATATTTAGGCCAGTTACATTGTTATTTTACCTATTACATTAT-ATCTAT
1 TTTCTCAAAAACCGATATATTTAGACCAGTTAAATTGTTAATTTACCTATTACATTATAAT-TAT
* * *
541503 -GTGTTTCGATGTTTTTAGTATCGACACTTGTTATAAATGTATCGACACTTTGTCGTGCACTTGG
65 AG-GTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTGTTGTGCACTTGG
* *
541567 TTTGGAAAATACATTCTGGACAACATGTATCGACAC
129 TTTGGAAAATACATTCTGGACAAAAAGTATCGACAC
541603 GAATGAATAA
Statistics
Matches: 500, Mismatches: 58, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
397 7 0.01
398 264 0.53
399 222 0.44
400 7 0.01
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.41
Consensus pattern (399 bp):
TTTCTCAAAAACCGATATATTTAGACCAGTTAAATTGTTAATTTACCTATTACATTATAATTATA
GGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTGTTGTGCACTTGGTT
TGGAAAATACATTCTGGACAAAAAGTATCGACACTTATTGGATTTGTGTCGATACTTTATATATA
CATGTTTTCTCATAAACCGATATATTTAGACCAATTACATTGTTAATTTACCTATTACATTATAA
TTATAGGTTTCGACATTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTGTTGTACACT
TGGTTAAAAAATACACTCTGGACAAAAAGTATCGACACTTGTTGGATTTGTGTCGATACTTTATG
TACACATGT
Found at i:541838 original size:24 final size:24
Alignment explanation
Indices: 541787--541838 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
541777 ATTTATATTT
* *
541787 AAATTCAAACTCAAATTGAAATTT
1 AAATTCAAACTCAAATTGAAAATG
*
541811 AAATTCAAACTCTAATT-ATAAATG
1 AAATTCAAACTCAAATTGA-AAATG
541835 AAAT
1 AAAT
541839 GAAAATGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.52, C:0.12, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATTCAAACTCAAATTGAAAATG
Found at i:542539 original size:13 final size:13
Alignment explanation
Indices: 542521--542551 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
542511 CTGTTTAACT
542521 ATGAAAATATGGC
1 ATGAAAATATGGC
542534 ATGAAAATATGGC
1 ATGAAAATATGGC
542547 ATGAA
1 ATGAA
542552 TGTAACTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.48, C:0.06, G:0.23, T:0.23
Consensus pattern (13 bp):
ATGAAAATATGGC
Found at i:543202 original size:3 final size:3
Alignment explanation
Indices: 543194--543240 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
543184 ACTTGTTTGG
* * *
543194 ATC ATC ATC ATC ATC ATC ATC AT- ATTC ATC TTC ATC GTC ATC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC A-TC ATC ATC ATC ATC ATC ATC
543239 AT
1 AT
543241 TGACCGCTTG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
2 1 0.03
3 34 0.94
4 1 0.03
ACGTcount: A:0.28, C:0.30, G:0.02, T:0.40
Consensus pattern (3 bp):
ATC
Found at i:544431 original size:15 final size:15
Alignment explanation
Indices: 544395--544452 Score: 89
Period size: 15 Copynumber: 3.7 Consensus size: 15
544385 AGGCGATTGT
544395 TTGAGAATGAGGTTGTGG
1 TTGAGAA-GAGG-TG-GG
544413 TTGAGAAGAGGTGGG
1 TTGAGAAGAGGTGGG
544428 TTGAGAAGAGGTGGG
1 TTGAGAAGAGGTGGG
544443 TTGAGAAGAG
1 TTGAGAAGAG
544453 CTTTGAGACC
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
15 27 0.68
16 2 0.05
17 4 0.10
18 7 0.17
ACGTcount: A:0.28, C:0.00, G:0.48, T:0.24
Consensus pattern (15 bp):
TTGAGAAGAGGTGGG
Found at i:545239 original size:199 final size:199
Alignment explanation
Indices: 544795--546076 Score: 1783
Period size: 199 Copynumber: 6.5 Consensus size: 199
544785 TTTTCAAATT
* * * ** * * * *
544795 AAACTGGTATATTTATACCAGTTACATTGCAAAATGACCTATTACATTAAAATTTTGGGTTTCGA
1 AAACCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
* * * ** *
544860 TGTTCTTAGGATCGATACTTGTTATAAATGTATCGACACTTTTTCTTGCACTTGGTTTTTAAAAT
66 TGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGCACTTGG-TTTTGAAAT
* * ** * *
544925 ACACTCTGGACAAAAAGTATCGACACTTGTTGGATTTGTGTCGATACTTTATGTATACCTGTTTT
130 ACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTT
*
544990 CTCAT
195 CTCAA
*
544995 AAACCGGTATATTAAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
1 AAACCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
* * **
545060 TGTTTTTGGGATCGACACTTATTATAAATGTATTGACACTTTTCCGTGCACTTGGTTTAT-AAAT
66 TGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTT-TGAAAT
* * *
545124 ACATTCTGGACCAAAAGTATCGACAATTGTTTTATTTGTGTCGATACTTTTTGTACACTTGTTCT
130 ACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTT
545189 CTCAA
195 CTCAA
* * * * *
545194 AAACCGATATATTTAGACTGGTTACATTGCTAATTTACTTATTACATTCTAATTATGGGTTTCGA
1 AAACCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
* * * ** *
545259 TGTTTTTGGGATCGATACTTTTTATAAATGTATTGACACTTTTCCGTGCACTTGGTTTGGAAAAT
66 TGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTG-AAAT
* *
545324 ACATTCTGGACCAAAAGTATCGACATTTGTTTTATTTGTGTCGATACTTTTTGTACACATGTTTT
130 ACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTT
545389 CTCAA
195 CTCAA
* * *
545394 AAACTGGTATATTTAGATCGGTTACATTGTTAATTTATCTATTACATTATAATTATGGGTTTCGA
1 AAACCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
*
545459 TGTTTTTGGGATCGACACTTGTTATAAATGTATCGACATTTTTTAGTGCACTTGGTTTTGAAATA
66 TGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATA
* * *
545524 CATTATGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTGTTGTACACCTATTTTC
131 CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTC
545589 TCAA
196 TCAA
* * *
545593 AAACTGGTACATTTAGACCGTTTACATTGTTAATTTA-C-----C--------TA----TTTCGA
1 AAACCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
*
545640 TGTTTTTGGGATCGACACTTGTTATAAATGTATCAACACTTTTTAGTGCACTTGGTTTTGAAATA
66 TGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATA
* * *
545705 CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCAATACTTGTTGTACACCTATTTTC
131 CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTC
*
545770 TAAA
196 TCAA
* * * * * *
545774 AAACTGGTACATTTAGACCGTTTACATTGTTAATTTACCTATTACATTATAAATATGTGTTTCAA
1 AAACCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
545839 TGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATA
66 TGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATA
545904 CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTC
131 CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTC
*
545969 TAAA
196 TCAA
***
545973 AAACCGGTATATTTAGATATGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
1 AAACCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
*
546038 TGTTTTTGGGATCGATACTTGTTATAAATGTATCGACAC
66 TGTTTTTGGGATCGACACTTGTTATAAATGTATCGACAC
546077 ATAAGTTTAC
Statistics
Matches: 979, Mismatches: 82, Indels: 43
0.89 0.07 0.04
Matches are distributed among these distances:
181 172 0.18
182 1 0.00
185 2 0.00
187 1 0.00
193 1 0.00
195 2 0.00
198 1 0.00
199 514 0.53
200 285 0.29
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.42
Consensus pattern (199 bp):
AAACCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
TGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATA
CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTC
TCAA
Found at i:545540 original size:399 final size:399
Alignment explanation
Indices: 544795--546076 Score: 1823
Period size: 399 Copynumber: 3.3 Consensus size: 399
544785 TTTTCAAATT
* * ** * * * * *
544795 AAACTGGTATATTTATACCAGTTACATTGCAAAATGACCTATTACATTAAAATTTTGGGTTTCGA
1 AAACCGGTATATTTAGACTGGTTACATTGCTAATTTACCTATTACATTATAATTATGGGTTTCGA
* * * *
544860 TGTTCTTAGGATCGATACTTGTTATAAATGTATCGACACTTTTTCTTGCACTTGGTTTTTAAAAT
66 TGTTTTTGGGATCGATACTTGTTATAAATGTATCGACACTTTTTCGTGCACTTGGTTTTGAAAAT
* * ** * *
544925 ACACTCTGGACAAAAAGTATCGACACTTGTTGGATTTGTGTCGATACTTTATGTATACCTGTTTT
131 ACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTT
* * *
544990 CTCATAAACCGGTATATTAAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGT
196 CTCAAAAACTGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGT
* * **
545055 TTCGATGTTTTTGGGATCGACACTTATTATAAATGTATTGACACTTTTCCGTGCACTTGGTTTAT
261 TTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTT-T
* *
545120 -AAATACATTCTGGACCAAAAGTATCGACAATTGTTTTATTTGTGTCGATACTTTTTGTACACTT
325 GAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCT
*
545184 GTTCTCTCAA
390 GTTTTCTCAA
* * *
545194 AAACCGATATATTTAGACTGGTTACATTGCTAATTTACTTATTACATTCTAATTATGGGTTTCGA
1 AAACCGGTATATTTAGACTGGTTACATTGCTAATTTACCTATTACATTATAATTATGGGTTTCGA
* * * *
545259 TGTTTTTGGGATCGATACTTTTTATAAATGTATTGACACTTTTCCGTGCACTTGGTTTGGAAAAT
66 TGTTTTTGGGATCGATACTTGTTATAAATGTATCGACACTTTTTCGTGCACTTGGTTTTGAAAAT
* *
545324 ACATTCTGGACCAAAAGTATCGACATTTGTTTTATTTGTGTCGATACTTTTTGTACACATGTTTT
131 ACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTT
* *
545389 CTCAAAAACTGGTATATTTAGATCGGTTACATTGTTAATTTATCTATTACATTATAATTATGGGT
196 CTCAAAAACTGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGT
*
545454 TTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACATTTTTTAGTGCACTTGGTTTTG
261 TTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTG
* * *
545519 AAATACATTATGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTGTTGTACACCTA
326 AAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTG
545584 TTTTCTCAA
391 TTTTCTCAA
* * * * *
545593 AAACTGGTACATTTAGACCGTTTACATTGTTAATTTA-C-----C--------TA----TTTCGA
1 AAACCGGTATATTTAGACTGGTTACATTGCTAATTTACCTATTACATTATAATTATGGGTTTCGA
* * *
545640 TGTTTTTGGGATCGACACTTGTTATAAATGTATCAACACTTTTTAGTGCACTTGGTTTTG-AAAT
66 TGTTTTTGGGATCGATACTTGTTATAAATGTATCGACACTTTTTCGTGCACTTGGTTTTGAAAAT
* * *
545704 ACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCAATACTTGTTGTACACCTATTTT
131 ACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTT
* * * * *
545769 CTAAAAAACTGGTACATTTAGACCGTTTACATTGTTAATTTACCTATTACATTATAAATATGTGT
196 CTCAAAAACTGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGT
*
545834 TTCAATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTG
261 TTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTG
545899 AAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTG
326 AAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTG
*
545964 TTTTCTAAA
391 TTTTCTCAA
* *
545973 AAACCGGTATATTTAGA-TATGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCG
1 AAACCGGTATATTTAGACT-GGTTACATTGCTAATTTACCTATTACATTATAATTATGGGTTTCG
546037 ATGTTTTTGGGATCGATACTTGTTATAAATGTATCGACAC
65 ATGTTTTTGGGATCGATACTTGTTATAAATGTATCGACAC
546077 ATAAGTTTAC
Statistics
Matches: 780, Mismatches: 83, Indels: 41
0.86 0.09 0.05
Matches are distributed among these distances:
380 286 0.37
381 60 0.08
385 2 0.00
386 1 0.00
393 1 0.00
394 2 0.00
398 44 0.06
399 384 0.49
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.42
Consensus pattern (399 bp):
AAACCGGTATATTTAGACTGGTTACATTGCTAATTTACCTATTACATTATAATTATGGGTTTCGA
TGTTTTTGGGATCGATACTTGTTATAAATGTATCGACACTTTTTCGTGCACTTGGTTTTGAAAAT
ACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTT
CTCAAAAACTGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGT
TTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTG
AAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTG
TTTTCTCAA
Found at i:545757 original size:181 final size:181
Alignment explanation
Indices: 545453--546015 Score: 840
Period size: 181 Copynumber: 3.0 Consensus size: 181
545443 TAATTATGGG
*
545453 TTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACATTTTTTAGTGCACTTGGTTTT
1 TTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTT
*
545518 GAAATACATTATGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTGTTGTACACCT
66 GAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTGTTGTACACCT
*
545583 ATTTTCTCAAAAACTGGTACATTTAGACCGTTTACATTGTTAATTTACCTA
131 ATTTTCTAAAAAACTGGTACATTTAGACCGTTTACATTGTTAATTTACCTA
*
545634 TTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCAACACTTTTTAGTGCACTTGGTTTT
1 TTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTT
*
545699 GAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCAATACTTGTTGTACACCT
66 GAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTGTTGTACACCT
545764 ATTTTCTAAAAAACTGGTACATTTAGACCGTTTACATTGTTAATTTACCTATTACATTATAAATA
131 ATTTTCTAAAAAACTGGTACATTTAGACCGTTTACATTGTTAATTTA-C-----C--------TA
*
545829 TGTGTTTCAATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGCACTTGG
1 ----TTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGCACTTGG
*
545894 TTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTAC
62 TTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTGTTGTAC
* * * **
545959 ACCTGTTTTCTAAAAAACCGGTATATTTAGA-TATGTTACATTGTTAATTTACCTA
127 ACCTATTTTCTAAAAAACTGGTACATTTAGACCGT-TTACATTGTTAATTTACCTA
546014 TT
1 TT
546016 ACATTATAAT
Statistics
Matches: 349, Mismatches: 14, Indels: 38
0.87 0.03 0.09
Matches are distributed among these distances:
181 174 0.50
182 1 0.00
185 2 0.01
187 1 0.00
193 1 0.00
195 2 0.01
198 2 0.01
199 166 0.48
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (181 bp):
TTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTT
GAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTGTTGTACACCT
ATTTTCTAAAAAACTGGTACATTTAGACCGTTTACATTGTTAATTTACCTA
Found at i:546473 original size:19 final size:19
Alignment explanation
Indices: 546449--546497 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
546439 TTACATTCAC
546449 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
546468 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
546487 ATACAAAATTA
1 ATACAAAATTA
546498 ACCCTACATT
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:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:548706 original size:22 final size:23
Alignment explanation
Indices: 548678--548728 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 23
548668 AACCTGCATT
548678 TATAATAA-TAGT-TATCATTTTA
1 TATAATAACTA-TATATCATTTTA
548700 TATAATAACTATACTATCATTTTA
1 TATAATAACTATA-TATCATTTTA
548724 TATAA
1 TATAA
548729 AAAAAACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 9 0.35
23 2 0.08
24 15 0.58
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (23 bp):
TATAATAACTATATATCATTTTA
Found at i:550985 original size:182 final size:182
Alignment explanation
Indices: 550450--551288 Score: 1093
Period size: 182 Copynumber: 4.6 Consensus size: 182
550440 TACGCATACT
* *
550450 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGATCG
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCA
* * * *
550515 GTTTTATCATATTTTTACATGTTATATTGTTATGGATCGATATATTTTTTAAAAGTATCGACACT
66 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTATAAAAGTATCGACACT
* *
550580 TTATAGGCGTTATAACTTCTTCTCTTTTAAATTCCAAAAATGTCGATACTTA
131 TTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* * * ** *
550632 TATTAAATTATCGACACTTTTAACATATCCGATATAGTTTTACCGGTTTTGTCATTTTTGA-AAC
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCA-TTTTGAGACC
* * ** *
550696 ATGTTTTGTCATATTTTTACCTGTTATATTATTATAGATTAATACATTTTTTAAAAGTATCGACA
65 A-GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTATAAAAGTATCGACA
* *
550761 CTTTATAGGTGCTATAAATTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
129 CTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* *
550815 TATTAAAGTATCGACACTTTCAACATATTCGGTAGCGCTTTACCGGTTTTGTCATTTTGAGACCA
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCA
* * *
550880 GTTTTGTCATATTTTTAGCTGTTATATTGTTATGGATCGATACATTTTCAT-AGAGTGTCGACAC
66 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTT-ATAAAAGTATCGACAC
* * * *
550944 TTTTTAGGCACTATAACTTATTCTCTTTTAAATTACAAAAGTGTCGATACTTA
130 TTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* * *
550997 TATT-AAGTTATCGACACTTTCAACATATCTGGTAG-TTATTTACCTGTTTTGTCATTTTGAGAC
1 TATTAAAG-TATCGACACTTTCAACATATCCGGTAGCGT-TTTACCGGTTTTGTCATTTTGAGAC
* * * * * *
551060 CGGTTTTATCAAATTTTTAGCTGTTATATTATTATGGATCGATACATTTTCAT-AAAGTGTCGAC
64 CAGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTT-ATAAAAGTATCGAC
*
551124 ACTTTTTAGGCGCTAT-AC--CTTCTCTTTTAAATT-CAGAAAGTGTCGATACTTA
128 ACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCA-AAAGTGTCGATACTTA
* * * * * * * *
551176 TATTCAATTATCGACACTTTCAACATATACGGTAACATTTTACCGGTTTTGTTATTTCGAGACCC
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCA
* * *
551241 GTTTTGTCATATTTTTACCTGTAATATTGCTATGGAGCGATACATTTT
66 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTT
551289 TCATTTGTAT
Statistics
Matches: 580, Mismatches: 68, Indels: 21
0.87 0.10 0.03
Matches are distributed among these distances:
178 2 0.00
179 122 0.21
180 3 0.01
181 5 0.01
182 285 0.49
183 163 0.28
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (182 bp):
TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCA
GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTATAAAAGTATCGACACT
TTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
Found at i:559519 original size:21 final size:21
Alignment explanation
Indices: 559493--559560 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 21
559483 GAAGTATCCA
*
559493 TGCTCTCATGTGACATCAGCT
1 TGCTCTCATGTGACAGCAGCT
* *
559514 TGCTCTCATTTGAGAGCAGCT
1 TGCTCTCATGTGACAGCAGCT
*
559535 TGCTCTCATGTGATAGCAGCT
1 TGCTCTCATGTGACAGCAGCT
559556 TGCTC
1 TGCTC
559561 GCATATACGT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34
Consensus pattern (21 bp):
TGCTCTCATGTGACAGCAGCT
Found at i:562526 original size:17 final size:17
Alignment explanation
Indices: 562501--562539 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
562491 AAATAAGTAA
562501 AAATA-TTAAATAAATT
1 AAATACTTAAATAAATT
562517 AAATACTTAAATAAATT
1 AAATACTTAAATAAATT
562534 AAATAC
1 AAATAC
562540 AAAATATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATACTTAAATAAATT
Found at i:562527 original size:26 final size:24
Alignment explanation
Indices: 562483--562555 Score: 78
Period size: 26 Copynumber: 3.0 Consensus size: 24
562473 ATATCTGCAA
*
562483 AAATAAATAAATAAGTAAAAATATT
1 AAATAAATAAAT-ATTAAAAATATT
562508 AAATAAATTAAATACTTAAATAA-ATT
1 AAATAAA-TAAATA-TTAAA-AATATT
*
562534 AAATACA-AAATATTAAAAATAT
1 AAATAAATAAATATTAAAAATAT
562556 AATAAAATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
22 2 0.05
23 7 0.17
24 5 0.12
25 8 0.19
26 18 0.43
27 2 0.05
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (24 bp):
AAATAAATAAATATTAAAAATATT
Found at i:563634 original size:2 final size:2
Alignment explanation
Indices: 563627--563661 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
563617 AATTGAAAAT
563627 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
563662 GTGACCAACC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:571328 original size:6 final size:6
Alignment explanation
Indices: 571309--571395 Score: 56
Period size: 6 Copynumber: 14.8 Consensus size: 6
571299 GTAAAAAAAG
* * * *
571309 AAATAT -AATAAT AAATAT AAAGA- AATATAT ATATAT ATATAT ATATAT
1 AAATAT AAAT-AT AAATAT AAATAT AA-ATAT AAATAT AAATAT AAATAT
* * * *
571357 ATATAT ATATAT ATATAT AAA-AT AAA-AT ATATAT AAATA
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATA
571396 ATAGTAATGA
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
5 14 0.20
6 52 0.74
7 4 0.06
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (6 bp):
AAATAT
Found at i:571332 original size:22 final size:24
Alignment explanation
Indices: 571305--571395 Score: 93
Period size: 24 Copynumber: 4.0 Consensus size: 24
571295 ATGTGTAAAA
571305 AAAGAAATATA-ATA-ATAAATAT
1 AAAGAAATATATATATATAAATAT
*
571327 AAAGAAATATATATATATATATAT
1 AAAGAAATATATATATATAAATAT
* * * *
571351 ATATATATATATATATATATATAT
1 AAAGAAATATATATATATAAATAT
571375 AAA-ATAA-A-ATATATATAAATA
1 AAAGA-AATATATATATATAAATA
571396 ATAGTAATGA
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
22 23 0.39
23 5 0.08
24 31 0.53
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (24 bp):
AAAGAAATATATATATATAAATAT
Found at i:571386 original size:16 final size:17
Alignment explanation
Indices: 571331--571393 Score: 67
Period size: 16 Copynumber: 3.8 Consensus size: 17
571321 AAATATAAAG
*
571331 AAATATATAT-ATATAT
1 AAATATATATAAAATAT
* *
571347 ATATATATATATATATAT
1 AAATATATATA-AAATAT
*
571365 ATATATATATAAAATA-
1 AAATATATATAAAATAT
571381 AAATATATATAAA
1 AAATATATATAAA
571394 TAATAGTAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
16 21 0.50
17 4 0.10
18 17 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATATATAAAATAT
Found at i:571391 original size:2 final size:2
Alignment explanation
Indices: 571333--571375 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
571323 ATATAAAGAA
571333 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
571375 A
1 A
571376 AAATAAAATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:575074 original size:8 final size:7
Alignment explanation
Indices: 575055--575106 Score: 61
Period size: 8 Copynumber: 7.1 Consensus size: 7
575045 ATTTTTCTTC
575055 TCTTTTT
1 TCTTTTT
575062 TCTTTTGT
1 TCTTTT-T
575070 TCTTTTT
1 TCTTTTT
*
575077 CTCTTTTCC
1 -TCTTTT-T
575086 TCTTTTT
1 TCTTTTT
575093 TC-TTTT
1 TCTTTTT
575099 TCTTTTT
1 TCTTTTT
575106 T
1 T
575107 TAATTTAGGG
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
6 6 0.15
7 14 0.36
8 19 0.49
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (7 bp):
TCTTTTT
Found at i:575081 original size:16 final size:15
Alignment explanation
Indices: 575054--575106 Score: 65
Period size: 15 Copynumber: 3.6 Consensus size: 15
575044 TATTTTTCTT
*
575054 CTCTTTTTTCTTTTG
1 CTCTTTTTTCTTTTC
*
575069 TTCTTTTTCTCTTTTC
1 CTCTTTTT-TCTTTTC
575085 CTCTTTTTTCTTTT-
1 CTCTTTTTTCTTTTC
575099 -TCTTTTTT
1 CTCTTTTTT
575107 TAATTTAGGG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.24
15 13 0.38
16 13 0.38
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (15 bp):
CTCTTTTTTCTTTTC
Found at i:575082 original size:23 final size:22
Alignment explanation
Indices: 575052--575107 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 22
575042 CTTATTTTTC
575052 TTCTCTTTTTTCTTTTGTTCTTT
1 TTCTCTTTTTTCTTTT-TTCTTT
*
575075 TTCTCTTTTCCTCTTTTTTCTTT
1 TTCTCTTTT-TTCTTTTTTCTTT
575098 TTCT-TTTTTT
1 TTCTCTTTTTT
575108 AATTTAGGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 1 0.03
22 4 0.13
23 19 0.63
24 6 0.20
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (22 bp):
TTCTCTTTTTTCTTTTTTCTTT
Found at i:584359 original size:12 final size:12
Alignment explanation
Indices: 584334--584426 Score: 55
Period size: 12 Copynumber: 7.8 Consensus size: 12
584324 ACGGAGATAT
* *
584334 CAGAAATCAAAA
1 CAGAATTCAGAA
584346 CAGAATTCAGAA
1 CAGAATTCAGAA
*
584358 CATGTA-TCAGAA
1 CA-GAATTCAGAA
* * *
584370 CAGAATCCATAT
1 CAGAATTCAGAA
*
584382 CAGAAATCAGAA
1 CAGAATTCAGAA
* **
584394 CATAATTCAGGC
1 CAGAATTCAGAA
*
584406 CATGTA-TCAGAA
1 CA-GAATTCAGAA
584418 CAGAATTCA
1 CAGAATTCA
584427 AGTCGAAAAT
Statistics
Matches: 57, Mismatches: 20, Indels: 8
0.67 0.24 0.09
Matches are distributed among these distances:
11 4 0.07
12 50 0.88
13 3 0.05
ACGTcount: A:0.47, C:0.19, G:0.14, T:0.19
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:584366 original size:24 final size:24
Alignment explanation
Indices: 584339--584426 Score: 88
Period size: 24 Copynumber: 3.7 Consensus size: 24
584329 GATATCAGAA
*
584339 ATCAAAACAGAATTCAGAACATGT
1 ATCAGAACAGAATTCAGAACATGT
* * * *
584363 ATCAGAACAGAATCCATATCA-GAA
1 ATCAGAACAGAATTCAGAACATG-T
* **
584387 ATCAGAACATAATTCAGGCCATGT
1 ATCAGAACAGAATTCAGAACATGT
584411 ATCAGAACAGAATTCA
1 ATCAGAACAGAATTCA
584427 AGTCGAAAAT
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
23 1 0.02
24 48 0.96
25 1 0.02
ACGTcount: A:0.47, C:0.19, G:0.14, T:0.20
Consensus pattern (24 bp):
ATCAGAACAGAATTCAGAACATGT
Found at i:584440 original size:48 final size:48
Alignment explanation
Indices: 584330--584423 Score: 152
Period size: 48 Copynumber: 2.0 Consensus size: 48
584320 TTAAACGGAG
*
584330 ATATCAGAAATCAAAACAGAATTCAGAACATGTATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTCAGAACATGTATCAGAACAGAATCC
* **
584378 ATATCAGAAATCAGAACATAATTCAGGCCATGTATCAGAACAGAAT
1 ATATCAGAAATCAGAACAGAATTCAGAACATGTATCAGAACAGAAT
584424 TCAAGTCGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.20
Consensus pattern (48 bp):
ATATCAGAAATCAGAACAGAATTCAGAACATGTATCAGAACAGAATCC
Found at i:588227 original size:14 final size:13
Alignment explanation
Indices: 588205--588249 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
588195 GAAATATAAT
*
588205 AATAAATATAAAGA
1 AATATATATAAA-A
588219 AATATATATAATAA
1 AATATATATAA-AA
*
588233 AATATATATAAAT
1 AATATATATAAAA
588246 AATA
1 AATA
588250 GTAATGATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 5 0.18
14 22 0.79
15 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (13 bp):
AATATATATAAAA
Found at i:588246 original size:24 final size:23
Alignment explanation
Indices: 588192--588238 Score: 78
Period size: 22 Copynumber: 2.0 Consensus size: 23
588182 GTAAGAAAAA
588192 AAAGAAATATA-ATAATAAATAT
1 AAAGAAATATATATAATAAATAT
588214 AAAGAAATATATATAATAAAATAT
1 AAAGAAATATATATAAT-AAATAT
588238 A
1 A
588239 TATAAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 11 0.48
23 5 0.22
24 7 0.30
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (23 bp):
AAAGAAATATATATAATAAATAT
Found at i:588254 original size:24 final size:22
Alignment explanation
Indices: 588203--588254 Score: 52
Period size: 24 Copynumber: 2.2 Consensus size: 22
588193 AAGAAATATA
588203 ATAATAAATATA-AAGAAATATAT
1 ATAATAAATATATAA-AAATA-AT
*
588226 ATAATAAAATATATATAAATAAT
1 ATAAT-AAATATATAAAAATAAT
588249 AGTAAT
1 A-TAAT
588255 GATGAGGACT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
23 8 0.32
24 16 0.64
25 1 0.04
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (22 bp):
ATAATAAATATATAAAAATAAT
Found at i:588464 original size:2 final size:2
Alignment explanation
Indices: 588457--588484 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
588447 ATTAAATGTG
588457 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
588485 AATACTAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:594208 original size:14 final size:15
Alignment explanation
Indices: 594186--594214 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
594176 TTTTATTTAA
594186 ATTATTTTTAATTTT
1 ATTATTTTTAATTTT
594201 ATTA-TTTTAATTTT
1 ATTATTTTTAATTTT
594215 CTAATATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
ATTATTTTTAATTTT
Found at i:595036 original size:26 final size:26
Alignment explanation
Indices: 595007--595057 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
594997 TAAGCAAAGA
595007 TTAAAACTTTATAATTTTATAAGCTT
1 TTAAAACTTTATAATTTTATAAGCTT
595033 TTAAAACTTTATAATTTTATAAGCT
1 TTAAAACTTTATAATTTTATAAGCT
595058 CTGTCCGGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.49
Consensus pattern (26 bp):
TTAAAACTTTATAATTTTATAAGCTT
Found at i:595192 original size:18 final size:19
Alignment explanation
Indices: 595169--595204 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
595159 TTGCTTAATA
595169 AATTTTTT-TAAATTTTTT
1 AATTTTTTATAAATTTTTT
*
595187 AATTTTTTATAAGTTTTT
1 AATTTTTTATAAATTTTT
595205 AACCGATGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (19 bp):
AATTTTTTATAAATTTTTT
Found at i:597196 original size:87 final size:87
Alignment explanation
Indices: 597050--597214 Score: 255
Period size: 87 Copynumber: 1.9 Consensus size: 87
597040 GAGATCCAAC
597050 AGAAGTTGAGATATCACAGCATTCCTCGGAACTAGAATCGGAATATGTTAGCCAAGCCGAAGATG
1 AGAAGTTGAGATATCACAGCATTCCTCGGAACTAGAATCGGAATATGTTAGCCAAGCCGAAGATG
597115 ATCAATCATCAATTCTCACATT
66 ATCAATCATCAATTCTCACATT
* * *
597137 AGAAGTTGAGATATCAGAGCATT-CTCCGGAA-TCAGAATCGGAACT-TGTTATCGAAGCCGAAG
1 AGAAGTTGAGATATCACAGCATTCCT-CGGAACT-AGAATCGGAA-TATGTTAGCCAAGCCGAAG
597199 ATGATCAATCATCAAT
63 ATGATCAATCATCAAT
597215 ACTAATGGCG
Statistics
Matches: 72, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
86 3 0.04
87 68 0.94
88 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (87 bp):
AGAAGTTGAGATATCACAGCATTCCTCGGAACTAGAATCGGAATATGTTAGCCAAGCCGAAGATG
ATCAATCATCAATTCTCACATT
Found at i:597229 original size:87 final size:87
Alignment explanation
Indices: 597049--597246 Score: 253
Period size: 87 Copynumber: 2.3 Consensus size: 87
597039 AGAGATCCAA
597049 CAGAAGTTGAGATATCACAGCATTCCTCGGAACTAGAATCGGAATATGTTAGCCAAGCCGAAGAT
1 CAGAAGTTGAGATATCACAGCATTCCTCGGAACTAGAATCGGAATATGTTAGCCAAGCCGAAGAT
*
597114 GATCAATCATCAATTCTCACAT
66 GATCAATCATCAATACTCACAT
* * * *
597136 TAGAAGTTGAGATATCAGAGCATT-CTCCGGAA-TCAGAATCGGAACT-TGTTATCGAAGCCGAA
1 CAGAAGTTGAGATATCACAGCATTCCT-CGGAACT-AGAATCGGAA-TATGTTAGCCAAGCCGAA
597198 GATGATCAATCATCAATACT-A-AT
63 GATGATCAATCATCAATACTCACAT
* *
597221 GGCGGAAGTTGAGTTATCACAGCATT
1 --CAGAAGTTGAGATATCACAGCATT
597247 TCCAACCTCA
Statistics
Matches: 97, Mismatches: 9, Indels: 10
0.84 0.08 0.09
Matches are distributed among these distances:
85 2 0.02
86 4 0.04
87 90 0.93
88 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (87 bp):
CAGAAGTTGAGATATCACAGCATTCCTCGGAACTAGAATCGGAATATGTTAGCCAAGCCGAAGAT
GATCAATCATCAATACTCACAT
Found at i:598016 original size:31 final size:31
Alignment explanation
Indices: 597974--598046 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
597964 TTAAAACTTG
* ***
597974 CAATATAGTCCCCCAACATTTAGTTTGTTTA
1 CAATATGGTCCCCCAACATTTAGTCCATTTA
*
598005 CAATATGGTCCCCCAACATTTAGTCCATTTG
1 CAATATGGTCCCCCAACATTTAGTCCATTTA
598036 CAATATGGTCC
1 CAATATGGTCC
598047 TCGACGTAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.34
Consensus pattern (31 bp):
CAATATGGTCCCCCAACATTTAGTCCATTTA
Found at i:598432 original size:16 final size:16
Alignment explanation
Indices: 598411--598441 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
598401 AAAAAAAATT
598411 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
598427 TGTTCGTTTATGTTC
1 TGTTCGTTTATGTTC
598442 ATTTATTTAT
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:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:602208 original size:54 final size:54
Alignment explanation
Indices: 602149--602258 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
602139 ATTTTGTTGC
602149 TACGTTTATGTGACAATCTCGTAATATTCAAACCTTCATCATCAATATTGTTAT
1 TACGTTTATGTGACAATCTCGTAATATTCAAACCTTCATCATCAATATTGTTAT
602203 TACGTTTATGTGACAATCTCGTAATATTCAAACCTTCATCATCAATATTGTTAT
1 TACGTTTATGTGACAATCTCGTAATATTCAAACCTTCATCATCAATATTGTTAT
602257 TA
1 TA
602259 TTTCCTGCAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (54 bp):
TACGTTTATGTGACAATCTCGTAATATTCAAACCTTCATCATCAATATTGTTAT
Found at i:605568 original size:3 final size:3
Alignment explanation
Indices: 605560--605627 Score: 84
Period size: 3 Copynumber: 22.0 Consensus size: 3
605550 ATTTATTTAT
* *
605560 TTA TTA TTA TTA TAA TAA TTA TTA TTA TTAA TTA TTA TATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA T-TA TTA TTA
605607 -TA TATA TTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA
605628 AAAAAAATAA
Statistics
Matches: 59, Mismatches: 2, Indels: 8
0.86 0.03 0.12
Matches are distributed among these distances:
2 2 0.03
3 48 0.81
4 9 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:605588 original size:32 final size:36
Alignment explanation
Indices: 605548--605623 Score: 104
Period size: 35 Copynumber: 2.1 Consensus size: 36
605538 TTTACCCATT
*
605548 TTATTTATTTATT-TATTATTATTATA-ATAATTATTA
1 TTATTTAATTATTATA-TATTATTATATAT-ATTATTA
605584 TTA-TTAATTATTATATATTATTATATATATTATTA
1 TTATTTAATTATTATATATTATTATATATATTATTA
605619 TTATT
1 TTATT
605624 ATTAAAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
35 28 0.78
36 8 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (36 bp):
TTATTTAATTATTATATATTATTATATATATTATTA
Found at i:605619 original size:38 final size:38
Alignment explanation
Indices: 605556--605628 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
605546 TTTTATTTAT
*
605556 TTATTTATTATTATTATAATAATTATTATTATTAATTA
1 TTATATATTATTATTATAATAATTATTATTATTAATTA
*
605594 TTATATATTATTA-TATATATTATTATTATTATTAA
1 TTATATATTATTATTATA-ATAATTATTATTATTAA
605629 AAAAAATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
37 4 0.12
38 28 0.88
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (38 bp):
TTATATATTATTATTATAATAATTATTATTATTAATTA
Found at i:606754 original size:22 final size:22
Alignment explanation
Indices: 606729--606784 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
606719 CAATTATAAA
606729 TATTTTTATATAGTTCTAATTG
1 TATTTTTATATAGTTCTAATTG
* *
606751 TATTTTTAT-T-GTTTTAATTT
1 TATTTTTATATAGTTCTAATTG
606771 TACTTGTTTATATA
1 TA-TT-TTTATATA
606785 TTTAAATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 10 0.36
21 3 0.11
22 14 0.50
23 1 0.04
ACGTcount: A:0.25, C:0.04, G:0.07, T:0.64
Consensus pattern (22 bp):
TATTTTTATATAGTTCTAATTG
Found at i:609123 original size:14 final size:14
Alignment explanation
Indices: 609103--609138 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
609093 ATTTTAAATA
609103 ATTTACATTTACAT
1 ATTTACATTTACAT
* *
609117 TTTTACATTTGCAT
1 ATTTACATTTACAT
609131 ATTTACAT
1 ATTTACAT
609139 CTGGCATCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.31, C:0.14, G:0.03, T:0.53
Consensus pattern (14 bp):
ATTTACATTTACAT
Found at i:610981 original size:22 final size:22
Alignment explanation
Indices: 610950--611007 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
610940 TACATCTACA
*
610950 TTTTTCAAAGATGATAGATT-TCC
1 TTTTT-AAAGATGACAGATTCT-C
*
610973 TTTTTAAAGATGGCAGATTCTC
1 TTTTTAAAGATGACAGATTCTC
*
610995 TTTTCAAAGATGA
1 TTTTTAAAGATGA
611008 AAGCTTTATC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 24 0.80
23 6 0.20
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (22 bp):
TTTTTAAAGATGACAGATTCTC
Found at i:611605 original size:113 final size:113
Alignment explanation
Indices: 611407--612051 Score: 1204
Period size: 113 Copynumber: 5.7 Consensus size: 113
611397 TTAGCAAAGA
*
611407 TTCAAATCCATCACCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
1 TTCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
611472 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG
611520 TTCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
1 TTCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
611585 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG
*
611633 TTCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTG
1 TTCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
611698 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG
611746 TTCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
1 TTCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
611811 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG
* *
611859 CTCAAATACATCA-CTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCT
1 TTCAAATCCATCATC-TGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCT
611923 GAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG
65 GAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG
*
611972 CTCAAATCCATC-TCTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCT
1 TTCAAATCCATCATC-TGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCT
*
612036 GAAGAAAGAAGAAGAA
65 GAAGAAGGAAGAAGAA
612052 TTTATTCAAC
Statistics
Matches: 523, Mismatches: 7, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
112 1 0.00
113 522 1.00
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.27
Consensus pattern (113 bp):
TTCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG
Found at i:612170 original size:206 final size:202
Alignment explanation
Indices: 611867--612254 Score: 523
Period size: 206 Copynumber: 1.9 Consensus size: 202
611857 TGCTCAAATA
* * * *
611867 CATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCACTTGATGGATCAACATTGCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
* * * * *
611932 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTT-GCTCA-AATCCATCTCTTGATGGAT
66 AGAAGAAATTCATAATAAGAAGAACTTGTTCAA-CTTTTCGCT-AGAATCAATCACTCGATGGAT
*
611995 CAGCTTTTCCAGAA-A-AAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAATTTATT
129 CAACTTTTCCA-AAGAGAA-TTCATAATGAGAAGAACTCATCTGAAG-AAGAAGAAGAATTTATT
612058 CAACATTTTTTT
191 CAACATTTTTTT
* ** *
612070 CATCATTTGATGGATCAACATTGCCAGGTAAAGTTTATAATGAGAAGAACTCGTCATCTGAAGAA
1 CATCACTTGATGGATCAACATTGCCAGAAAAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAA
* *
612135 AGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTCGCTAGAATTAATCACTCGATGGA
63 AGAAGAAGAAATTCATAATAAGAAGAACTTGTTCAACTTTTCGCTAGAATCAATCACTCGATGGA
*
612200 TCAACTTTTCCAAAGAGAATTCATCATGAGAAGAACTCATCTGAAGAAGAAGAAG
128 TCAACTTTTCCAAAGAGAATTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAG
612255 TTCACAATGA
Statistics
Matches: 161, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
203 42 0.26
205 18 0.11
206 99 0.61
207 2 0.01
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (202 bp):
CATCACTTGATGGATCAACATTGCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
AGAAGAAATTCATAATAAGAAGAACTTGTTCAACTTTTCGCTAGAATCAATCACTCGATGGATCA
ACTTTTCCAAAGAGAATTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAATTTATTCAACA
TTTTTTT
Found at i:612524 original size:3 final size:3
Alignment explanation
Indices: 612516--612587 Score: 94
Period size: 3 Copynumber: 24.0 Consensus size: 3
612506 ATTTATTTAT
* *
612516 TTA TTA TTA TTA TAA TTA TTA TTA TTA TTA TAA TTA TTA -TA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
612561 TTA TTA -TA TATA TTA TTA TTA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA
612588 AAAATAATAA
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.07
3 51 0.84
4 6 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:613717 original size:22 final size:22
Alignment explanation
Indices: 613692--613747 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
613682 CAATTTTAAA
613692 TATTTTTATATAGTTCTAATTG
1 TATTTTTATATAGTTCTAATTG
* *
613714 TATTTTTAT-T-GTTTTAATTT
1 TATTTTTATATAGTTCTAATTG
613734 TACTTGTTTATATA
1 TA-TT-TTTATATA
613748 TTTAAATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 10 0.36
21 3 0.11
22 14 0.50
23 1 0.04
ACGTcount: A:0.25, C:0.04, G:0.07, T:0.64
Consensus pattern (22 bp):
TATTTTTATATAGTTCTAATTG
Found at i:615149 original size:25 final size:24
Alignment explanation
Indices: 615116--615162 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 24
615106 ATTAGTTAAT
615116 TGATCTAAATCATATTTTTAAATATG
1 TGATCTAAAT-A-ATTTTTAAATATG
615142 TGAT-TAAATAATTTTTAAATA
1 TGATCTAAATAATTTTTAAATA
615163 ATAATTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 11 0.52
24 1 0.05
25 5 0.24
26 4 0.19
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (24 bp):
TGATCTAAATAATTTTTAAATATG
Found at i:617324 original size:43 final size:42
Alignment explanation
Indices: 617258--617424 Score: 194
Period size: 43 Copynumber: 3.9 Consensus size: 42
617248 TTTTTTAACA
* *
617258 AAAAACGCCGCAATATGTATTGATATTTAGCGGCGTTTGTGTG
1 AAAAACGCCGCAATAGGT-TTGATATTTAGCGGCGTTTGTATG
* *
617301 ACAAACGTCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAT-
1 AAAAACGCCGCAATAGGT-TTGATATTTAGCGGCGTTTGT-ATG
* *
617344 AAAAACGCCGCAATAGGTTTTGATAATTAGCGGCGTTT-TTTAG
1 AAAAACGCCGCAATAGG-TTTGATATTTAGCGGCGTTTGTAT-G
* *
617387 AAAAATGCCGCAATAGGTTATGATGTTTAGCGGCGTTT
1 AAAAACGCCGCAATAGGTT-TGATATTTAGCGGCGTTT
617425 TTCCACAAAC
Statistics
Matches: 107, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
41 1 0.01
42 3 0.03
43 101 0.94
44 2 0.02
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.32
Consensus pattern (42 bp):
AAAAACGCCGCAATAGGTTTGATATTTAGCGGCGTTTGTATG
Found at i:617403 original size:86 final size:85
Alignment explanation
Indices: 617258--617452 Score: 232
Period size: 86 Copynumber: 2.3 Consensus size: 85
617248 TTTTTTAACA
* * * * *
617258 AAAAACGCCGCAATATGTATTGATATTTAGCGGCGTTTGTGTGACAAACGTCGCAATAGGTGT-T
1 AAAAACGCCGCAATAGGTTTTGATAATTAGCGGCGTTTGTGTGAAAAACGCCGCAATAGGT-TAT
*
617322 GATATTTAGCGGCGTTTGTCAT
65 GATATTTAGCGGCGTTTGTC-C
* *
617344 AAAAACGCCGCAATAGGTTTTGATAATTAGCGGCGTTT-TTTAGAAAAATGCCGCAATAGGTTAT
1 AAAAACGCCGCAATAGGTTTTGATAATTAGCGGCGTTTGTGT-GAAAAACGCCGCAATAGGTTAT
* *
617408 GATGTTTAGCGGCGTTTTTCC
65 GATATTTAGCGGCGTTTGTCC
* * *
617429 ACAAACGCCGCAGTGGGTTTTGAT
1 AAAAACGCCGCAATAGGTTTTGAT
617453 GTTTTGCGGT
Statistics
Matches: 94, Mismatches: 13, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
85 24 0.26
86 70 0.74
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (85 bp):
AAAAACGCCGCAATAGGTTTTGATAATTAGCGGCGTTTGTGTGAAAAACGCCGCAATAGGTTATG
ATATTTAGCGGCGTTTGTCC
Found at i:617468 original size:85 final size:86
Alignment explanation
Indices: 617249--617511 Score: 210
Period size: 86 Copynumber: 3.1 Consensus size: 86
617239 TTCGCGGTGT
* * * * * * * * * * *
617249 TTTTTAACAAAAAACGCCGCAATATGTATTGATATTTAGCGGCGTTTGTGTGACAAACGTCGCAA
1 TTTTTCAC-AAAAACGCCGCAATAGGTTTTGATAATTAGCGGCATTTTTCTCAAAAATGCCGCAA
*
617314 TAGGTGT-TGATATTTAGCGGCG
65 TAGGT-TATGATGTTTAGCGGCG
* * * *
617336 TTTGTCATAAAAACGCCGCAATAGGTTTTGATAATTAGCGGCGTTTTT-TAGAAAAATGCCGCAA
1 TTTTTCACAAAAACGCCGCAATAGGTTTTGATAATTAGCGGCATTTTTCT-CAAAAATGCCGCAA
617400 TAGGTTATGATGTTTAGCGGCG
65 TAGGTTATGATGTTTAGCGGCG
* * * ** * * * * * *
617422 TTTTTC-CACAAACGCCGCAGTGGGTTTTGATGTTTTGCGGTATTTTTCTCACAAATGTCGTAGT
1 TTTTTCACAAAAACGCCGCAATAGGTTTTGATAATTAGCGGCATTTTTCTCAAAAATGCCGCAAT
*
617486 AGG-TATTGATGTTTTGCGGCG
66 AGGTTA-TGATGTTTAGCGGCG
617507 TTTTT
1 TTTTT
617512 GCTAAAAACG
Statistics
Matches: 145, Mismatches: 27, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
84 2 0.01
85 66 0.46
86 72 0.50
87 5 0.03
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (86 bp):
TTTTTCACAAAAACGCCGCAATAGGTTTTGATAATTAGCGGCATTTTTCTCAAAAATGCCGCAAT
AGGTTATGATGTTTAGCGGCG
Found at i:617495 original size:43 final size:42
Alignment explanation
Indices: 617393--617511 Score: 123
Period size: 43 Copynumber: 2.8 Consensus size: 42
617383 TTAGAAAAAT
* * *
617393 GCCGCAATAGGT-TATGATGTTTAGCGGCGTTTTTCCACAAAC
1 GCCGCAGTAGGTAT-TGATGTTTTGCGGCATTTTTCCACAAAC
* * * *
617435 GCCGCAGTGGGTTTTGATGTTTTGCGGTATTTTTCTCACAAAT
1 GCCGCAGTAGGTATTGATGTTTTGCGGCATTTTTC-CACAAAC
* * *
617478 GTCGTAGTAGGTATTGATGTTTTGCGGCGTTTTT
1 GCCGCAGTAGGTATTGATGTTTTGCGGCATTTTT
617512 GCTAAAAACG
Statistics
Matches: 63, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
42 28 0.44
43 35 0.56
ACGTcount: A:0.18, C:0.16, G:0.27, T:0.39
Consensus pattern (42 bp):
GCCGCAGTAGGTATTGATGTTTTGCGGCATTTTTCCACAAAC
Found at i:617953 original size:21 final size:21
Alignment explanation
Indices: 617929--617979 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
617919 GCTAATATGT
*
617929 TGCTTCTCTCTGTGCTGCCGC
1 TGCTTCTCTCTGTACTGCCGC
* * *
617950 TGCTTCTTTCTTTACTTCCGC
1 TGCTTCTCTCTGTACTGCCGC
*
617971 TGCTGCTCT
1 TGCTTCTCT
617980 GGCTGCTTCT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.02, C:0.35, G:0.18, T:0.45
Consensus pattern (21 bp):
TGCTTCTCTCTGTACTGCCGC
Found at i:627502 original size:190 final size:188
Alignment explanation
Indices: 627120--627579 Score: 624
Period size: 190 Copynumber: 2.4 Consensus size: 188
627110 CAACTAATGT
* * *
627120 TAAAAACATTTGCGGCGTTTTTTGTCAAAACGCCA-TAAATGTATCG-TTAATTTACGGCGTTTG
1 TAAAAACATTTGCGGCGTTTTTTGTCTAAACGCCACT-AATGTA-CGAATCATTTAC-GCGTTTG
* * * *
627183 TTACTACAACGCCGCTATATGTGCAACCTATTGCAGCGTTTTTATCAAAACGCTACTAAAGTACT
63 TTACCAAAACGCCGCTATATGTGCAACCTATTGAAGCATTTTTATCAAAACGCTACTAAAGTACT
627248 AATTTATTGCGGCGTTTATTAAAAAAACGCCGCTATATGTCTAAAGTTAATGACGTTTAAA
128 AATTTATTGCGGCGTTTATTAAAAAAACGCCGCTATATGTCTAAAGTTAATGACGTTTAAA
* *
627309 TAAAATACATTTACGGCGTTTTTTGTCTAAACGCCACTAATGTACGAAATCATTTGCAGCGTTTG
1 TAAAA-ACATTTGCGGCGTTTTTTGTCTAAACGCCACTAATGTACG-AATCATTTAC-GCGTTTG
* * *
627374 TTACCAAAACGTCGCTATATGTG-AACCCTATT-AAGGCATTTTTGTCAAAACGCTGCTAAAGTA
63 TTACCAAAACGCCGCTATATGTGCAA-CCTATTGAA-GCATTTTTATCAAAACGCTACTAAAGTA
* * * *
627437 CTAGTTTATTGCGGCGTTTATT-AAAAAATGCTGTTATATGTCTAAAGTTAATGACGTTTAAA
126 CTAATTTATTGCGGCGTTTATTAAAAAAACGCCGCTATATGTCTAAAGTTAATGACGTTTAAA
* *
627499 TAAAAAACATTTGCTGCATTTTTTGTCTAAACGCCACTAATGTACGAATCATTTACGACGTTTGT
1 T-AAAAACATTTGCGGCGTTTTTTGTCTAAACGCCACTAATGTACGAATCATTTACG-CGTTTGT
*
627564 TATCAAAACGCCGCTA
64 TACCAAAACGCCGCTA
627580 AAGTACTAAT
Statistics
Matches: 240, Mismatches: 23, Indels: 16
0.86 0.08 0.06
Matches are distributed among these distances:
188 1 0.00
189 37 0.15
190 112 0.47
191 90 0.38
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (188 bp):
TAAAAACATTTGCGGCGTTTTTTGTCTAAACGCCACTAATGTACGAATCATTTACGCGTTTGTTA
CCAAAACGCCGCTATATGTGCAACCTATTGAAGCATTTTTATCAAAACGCTACTAAAGTACTAAT
TTATTGCGGCGTTTATTAAAAAAACGCCGCTATATGTCTAAAGTTAATGACGTTTAAA
Found at i:627583 original size:148 final size:148
Alignment explanation
Indices: 627418--627727 Score: 449
Period size: 148 Copynumber: 2.1 Consensus size: 148
627408 GGCATTTTTG
* * * * * * *
627418 TCAAAACGCTGCTAAAGTACTAGTTTATTGCGGCGTTTATTAAAAAATGCTGTTATATGTCTAAA
1 TCAAAACGCCGCTAAAGTACTAATATATTGCGACGTTTATTAAAAAACGCCGCTATATGTCTAAA
* * * * *
627483 GTTAATGACGTTTAAATAAAAAACATTTGCTGCATTTTTTGTCTAAACGCCACTAATGTACGAAT
66 GTTAATGACGTTTAAATAAAAAACATTTGCGGCATTTTCTATCAAAACGCCACTAAAGTACGAAT
*
627548 CATTTACGACGTTTGTTA
131 CATTTACGACGTTTGATA
627566 TCAAAACGCCGCTAAAGTACTAATATATTGCGACGTTTATTAAAAAACGCCGCTATATGTCTAAA
1 TCAAAACGCCGCTAAAGTACTAATATATTGCGACGTTTATTAAAAAACGCCGCTATATGTCTAAA
*
627631 GTTAATGACGTTTAAATAAAAAACATTTGCGGCATTTTCTATCAAAACGCCACTAAAGTCCGAAT
66 GTTAATGACGTTTAAATAAAAAACATTTGCGGCATTTTCTATCAAAACGCCACTAAAGTACGAAT
** *
627696 CATTTGTGGCGTTTGATA
131 CATTTACGACGTTTGATA
* *
627714 CCAAAACGTCGCTA
1 TCAAAACGCCGCTA
627728 TGTGTTAACC
Statistics
Matches: 143, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
148 143 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (148 bp):
TCAAAACGCCGCTAAAGTACTAATATATTGCGACGTTTATTAAAAAACGCCGCTATATGTCTAAA
GTTAATGACGTTTAAATAAAAAACATTTGCGGCATTTTCTATCAAAACGCCACTAAAGTACGAAT
CATTTACGACGTTTGATA
Found at i:627617 original size:41 final size:42
Alignment explanation
Indices: 627527--627620 Score: 111
Period size: 42 Copynumber: 2.3 Consensus size: 42
627517 TTTTTTGTCT
* * * *
627527 AAACGCCACTAATGTACGAATCATTTACGACGTTTGTTATCA
1 AAACGCCGCTAAAGTACGAATCATTTACGACGTTTATTATAA
* *
627569 AAACGCCGCTAAAGTACTAAT-ATATTGCGACGTTTATTA-AA
1 AAACGCCGCTAAAGTACGAATCAT-TTACGACGTTTATTATAA
627610 AAACGCCGCTA
1 AAACGCCGCTA
627621 TATGTCTAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
41 14 0.31
42 31 0.69
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (42 bp):
AAACGCCGCTAAAGTACGAATCATTTACGACGTTTATTATAA
Found at i:629670 original size:20 final size:20
Alignment explanation
Indices: 629647--629691 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
629637 AATTAGCGTT
* *
629647 GCGAAAATGAAATTTGCAAC
1 GCGAAAATCAAATTCGCAAC
*
629667 GCGAAAGTCAAATTCGCAAC
1 GCGAAAATCAAATTCGCAAC
629687 GCGAA
1 GCGAA
629692 TAGTTAAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.16
Consensus pattern (20 bp):
GCGAAAATCAAATTCGCAAC
Found at i:629703 original size:20 final size:21
Alignment explanation
Indices: 629656--629712 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
629646 TGCGAAAATG
*
629656 AAATTTGCAACGCGAA-AGTC
1 AAATTCGCAACGCGAATAGTC
*
629676 AAATTCGCAACGCGAATAGTT
1 AAATTCGCAACGCGAATAGTC
*
629697 AAA-TCGCAACGTGAAT
1 AAATTCGCAACGCGAAT
629713 TTCGTTTTCG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 27 0.82
21 6 0.18
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.21
Consensus pattern (21 bp):
AAATTCGCAACGCGAATAGTC
Found at i:629840 original size:20 final size:20
Alignment explanation
Indices: 629817--629878 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 20
629807 TCATTACGAT
*
629817 TTACCTATTCGCGTTGAGAA
1 TTACCTATTCGCGTTGCGAA
* ** *
629837 TTACATATTATCGTTGCGAT
1 TTACCTATTCGCGTTGCGAA
* *
629857 TTAACTATTCGCATTGCGAA
1 TTACCTATTCGCGTTGCGAA
629877 TT
1 TT
629879 TGACTTTCGT
Statistics
Matches: 31, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (20 bp):
TTACCTATTCGCGTTGCGAA
Found at i:629845 original size:40 final size:40
Alignment explanation
Indices: 629783--629878 Score: 129
Period size: 40 Copynumber: 2.4 Consensus size: 40
629773 AATTTGGAGA
* * *
629783 ATTCGCGTTGCGATTTATATATTATCATTACGATTTACCT
1 ATTCGCGTTGCGAATTACATATTATCATTACGATTTAACT
* * *
629823 ATTCGCGTTGAGAATTACATATTATCGTTGCGATTTAACT
1 ATTCGCGTTGCGAATTACATATTATCATTACGATTTAACT
*
629863 ATTCGCATTGCGAATT
1 ATTCGCGTTGCGAATT
629879 TGACTTTCGT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.42
Consensus pattern (40 bp):
ATTCGCGTTGCGAATTACATATTATCATTACGATTTAACT
Found at i:629887 original size:20 final size:20
Alignment explanation
Indices: 629783--629875 Score: 55
Period size: 20 Copynumber: 4.7 Consensus size: 20
629773 AATTTGGAGA
*
629783 ATTCGCGTTGCGATTTATA-T
1 ATTCGCATTGCGATTTA-ACT
** * *
629803 ATTATCATTACGATTTACCT
1 ATTCGCATTGCGATTTAACT
* * *
629823 ATTCGCGTTGAGAATT-ACAT
1 ATTCGCATTGCGATTTAAC-T
** *
629843 ATTATCGTTGCGATTTAACT
1 ATTCGCATTGCGATTTAACT
629863 ATTCGCATTGCGA
1 ATTCGCATTGCGA
629876 ATTTGACTTT
Statistics
Matches: 51, Mismatches: 19, Indels: 6
0.67 0.25 0.08
Matches are distributed among these distances:
19 1 0.02
20 48 0.94
21 2 0.04
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTAACT
Found at i:629940 original size:21 final size:21
Alignment explanation
Indices: 629894--629933 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
629884 TTCGTGTTGT
*
629894 GAATTTGGAAAATCGCAACAC
1 GAATTCGGAAAATCGCAACAC
629915 GAATTCGGAAAATCGCAAC
1 GAATTCGGAAAATCGCAAC
629934 GCTAATTACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.17
Consensus pattern (21 bp):
GAATTCGGAAAATCGCAACAC
Found at i:630004 original size:20 final size:20
Alignment explanation
Indices: 629962--630007 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
629952 TAATTAACTA
* *
629962 TTCGTGTTGCGAATTTGACT
1 TTCGCGTTGCGAATTTCACT
*
629982 TTCGCGTTGCGAATTTCATT
1 TTCGCGTTGCGAATTTCACT
630002 TTCGCG
1 TTCGCG
630008 CTAATTACCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.13, C:0.20, G:0.24, T:0.43
Consensus pattern (20 bp):
TTCGCGTTGCGAATTTCACT
Found at i:630216 original size:20 final size:20
Alignment explanation
Indices: 630167--630287 Score: 106
Period size: 20 Copynumber: 6.0 Consensus size: 20
630157 AATTTGGAGA
630167 ATTCGCGTTGCGATTT-ACAT
1 ATTCGCGTTGCGATTTGAC-T
** *
630187 ATTATCGTTGCGATTTAACT
1 ATTCGCGTTGCGATTTGACT
*
630207 ATTCGTGTTGCGAATTTGACT
1 ATTCGCGTTGCG-ATTTGACT
*
630228 -TTCGCGTTGTGAATTTGACT
1 ATTCGCGTTGCG-ATTTGACT
630248 -TTCGCGTTGCGATTTTGA-T
1 ATTCGCGTTGCGA-TTTGACT
* *
630267 TTTCACGTTGCGAATTTGACT
1 ATTCGCGTTGCG-ATTTGACT
630288 TTCATGTTGA
Statistics
Matches: 85, Mismatches: 10, Indels: 11
0.80 0.09 0.10
Matches are distributed among these distances:
19 2 0.02
20 72 0.85
21 11 0.13
ACGTcount: A:0.18, C:0.17, G:0.21, T:0.44
Consensus pattern (20 bp):
ATTCGCGTTGCGATTTGACT
Found at i:630236 original size:40 final size:40
Alignment explanation
Indices: 630192--630296 Score: 131
Period size: 40 Copynumber: 2.6 Consensus size: 40
630182 TACATATTAT
* *
630192 CGTTGCG-ATTTAACTATTCGTGTTGCGAATTTGACTTTCG
1 CGTTGCGAATTTGACT-TTCGTGTTGCGAATTTGACTTTCA
* * * *
630232 CGTTGTGAATTTGACTTTCGCGTTGCGATTTTGATTTTCA
1 CGTTGCGAATTTGACTTTCGTGTTGCGAATTTGACTTTCA
*
630272 CGTTGCGAATTTGACTTTCATGTTG
1 CGTTGCGAATTTGACTTTCGTGTTG
630297 AGAACAATTA
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
40 48 0.87
41 7 0.13
ACGTcount: A:0.16, C:0.16, G:0.23, T:0.45
Consensus pattern (40 bp):
CGTTGCGAATTTGACTTTCGTGTTGCGAATTTGACTTTCA
Found at i:630290 original size:20 final size:20
Alignment explanation
Indices: 630213--630296 Score: 114
Period size: 20 Copynumber: 4.2 Consensus size: 20
630203 AACTATTCGT
*
630213 GTTGCGAATTTGACTTTCGC
1 GTTGCGAATTTGACTTTCAC
* *
630233 GTTGTGAATTTGACTTTCGC
1 GTTGCGAATTTGACTTTCAC
* *
630253 GTTGCGATTTTGATTTTCAC
1 GTTGCGAATTTGACTTTCAC
*
630273 GTTGCGAATTTGACTTTCAT
1 GTTGCGAATTTGACTTTCAC
630293 GTTG
1 GTTG
630297 AGAACAATTA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.15, C:0.15, G:0.24, T:0.45
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTCAC
Found at i:633011 original size:13 final size:13
Alignment explanation
Indices: 633008--633083 Score: 62
Period size: 13 Copynumber: 5.3 Consensus size: 13
632998 CCGTTGACCC
633008 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
633021 TACCTGACCCGTT
1 GACCCGACCCGTT
633034 GACCCGACCCGACCCGTT
1 G-----ACCCGACCCGTT
633052 GACCCGACCCGTT
1 GACCCGACCCGTT
*
633065 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
633080 GACC
1 GACC
633084 ATTGACCGGA
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
13 27 0.53
15 12 0.24
18 12 0.24
ACGTcount: A:0.16, C:0.43, G:0.22, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:633016 original size:18 final size:18
Alignment explanation
Indices: 632987--633062 Score: 92
Period size: 18 Copynumber: 4.6 Consensus size: 18
632977 ACCGGTCACA
632987 ACCCGA-CCGACCCGTTG
1 ACCCGACCCGACCCGTTG
633004 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
* *
633021 ----TACCTGACCCGTTG
1 ACCCGACCCGACCCGTTG
633035 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
633053 ACCCGACCCG
1 ACCCGACCCG
633063 TTGACCGTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
13 11 0.22
17 6 0.12
18 32 0.65
ACGTcount: A:0.17, C:0.49, G:0.21, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:633033 original size:31 final size:31
Alignment explanation
Indices: 632993--633068 Score: 134
Period size: 31 Copynumber: 2.5 Consensus size: 31
632983 CACAACCCGA
*
632993 CCGACCCGTTGACCCGACCCGACCCGTTTAC
1 CCGACCCGTTGACCCGACCCGACCCGTTGAC
*
633024 CTGACCCGTTGACCCGACCCGACCCGTTGAC
1 CCGACCCGTTGACCCGACCCGACCCGTTGAC
633055 CCGACCCGTTGACC
1 CCGACCCGTTGACC
633069 GTTGACCCGT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.16, C:0.47, G:0.21, T:0.16
Consensus pattern (31 bp):
CCGACCCGTTGACCCGACCCGACCCGTTGAC
Found at i:633038 original size:8 final size:8
Alignment explanation
Indices: 633025--633083 Score: 54
Period size: 8 Copynumber: 7.6 Consensus size: 8
633015 CCCGTTTACC
633025 TGACCCGT
1 TGACCCGT
*
633033 TGACCCGACC
1 TGACCCG--T
*
633043 CGACCCGT
1 TGACCCGT
633051 TGACCC--
1 TGACCCGT
633057 -GACCCGT
1 TGACCCGT
633064 TGA-CCGT
1 TGACCCGT
633071 TGACCCGT
1 TGACCCGT
633079 TGACC
1 TGACC
633084 ATTGACCGGA
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
5 5 0.12
7 7 0.17
8 23 0.56
10 6 0.15
ACGTcount: A:0.15, C:0.42, G:0.24, T:0.19
Consensus pattern (8 bp):
TGACCCGT
Found at i:633077 original size:15 final size:14
Alignment explanation
Indices: 633044--633090 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
633034 GACCCGACCC
*
633044 GACCCGTTGACC-C
1 GACCCGTTGACCTT
633057 GACCCGTTGACCGTT
1 GACCCGTTGACC-TT
633072 GACCCGTTGACCATT
1 GACCCGTTGACC-TT
633087 GACC
1 GACC
633091 GGAGTTGACC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 12 0.40
15 18 0.60
ACGTcount: A:0.17, C:0.38, G:0.23, T:0.21
Consensus pattern (14 bp):
GACCCGTTGACCTT
Found at i:634405 original size:18 final size:18
Alignment explanation
Indices: 634379--634413 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
634369 TCGAAAGGAC
*
634379 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
634397 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
634414 CCGGATGGAA
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:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:638212 original size:18 final size:18
Alignment explanation
Indices: 638183--638227 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
638173 ACCGGTCACA
638183 ACCCGA-CCGACCCGTTG
1 ACCCGACCCGACCCGTTG
638200 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
638218 ACCTGACCCG
1 ACCCGACCCG
638228 TTGACCCGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 6 0.23
18 20 0.77
ACGTcount: A:0.18, C:0.49, G:0.22, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:638220 original size:8 final size:8
Alignment explanation
Indices: 638209--638261 Score: 57
Period size: 8 Copynumber: 7.5 Consensus size: 8
638199 GACCCGACCC
638209 GACCCGTT
1 GACCCGTT
638217 GA-CC--T
1 GACCCGTT
638222 GACCCGTT
1 GACCCGTT
638230 GACCC---
1 GACCCGTT
638235 GACCCGTT
1 GACCCGTT
638243 GA-CCGTT
1 GACCCGTT
638250 GACCCGTT
1 GACCCGTT
638258 GACC
1 GACC
638262 ATTGACCGGA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
5 8 0.21
6 2 0.05
7 9 0.24
8 19 0.50
ACGTcount: A:0.15, C:0.40, G:0.25, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:638233 original size:26 final size:27
Alignment explanation
Indices: 638204--638261 Score: 100
Period size: 26 Copynumber: 2.1 Consensus size: 27
638194 CCGTTGACCC
638204 GACCCGACCCGTTGACC-TGACCCGTT
1 GACCCGACCCGTTGACCGTGACCCGTT
638230 GACCCGACCCGTTGACCGTTGACCCGTT
1 GACCCGACCCGTTGACCG-TGACCCGTT
638258 GACC
1 GACC
638262 ATTGACCGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 17 0.57
28 13 0.43
ACGTcount: A:0.16, C:0.41, G:0.24, T:0.19
Consensus pattern (27 bp):
GACCCGACCCGTTGACCGTGACCCGTT
Found at i:638268 original size:15 final size:13
Alignment explanation
Indices: 638204--638261 Score: 80
Period size: 13 Copynumber: 4.3 Consensus size: 13
638194 CCGTTGACCC
*
638204 GACCCGACCCGTT
1 GACCTGACCCGTT
638217 GACCTGACCCGTT
1 GACCTGACCCGTT
*
638230 GACCCGACCCGTT
1 GACCTGACCCGTT
638243 GACCGTTGACCCGTT
1 GACC--TGACCCGTT
638258 GACC
1 GACC
638262 ATTGACCGGA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
13 28 0.70
15 12 0.30
ACGTcount: A:0.16, C:0.41, G:0.24, T:0.19
Consensus pattern (13 bp):
GACCTGACCCGTT
Found at i:639580 original size:18 final size:18
Alignment explanation
Indices: 639554--639588 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
639544 TCGAAAGGAC
*
639554 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
639572 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
639589 CCGGATGGAA
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:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:645437 original size:16 final size:16
Alignment explanation
Indices: 645412--645442 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
645402 AAGTAAAAAG
645412 TATAAAAGTCACTACT
1 TATAAAAGTCACTACT
*
645428 TATAAGAGTCACTAC
1 TATAAAAGTCACTAC
645443 ATCCAACTCG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (16 bp):
TATAAAAGTCACTACT
Found at i:646319 original size:71 final size:71
Alignment explanation
Indices: 646214--646345 Score: 180
Period size: 71 Copynumber: 1.9 Consensus size: 71
646204 TATAATTTTT
* *
646214 AAATTAAAAAAATATTTAAAACAAGAGAATAAAAC-AACACATCCATAATGTTGCTCATAAATTT
1 AAATAAAAAAAATATTTAAAACAAGAGAAGAAAACAAAC-CATCCATAATGTTGCTCATAAATTT
646278 GATTTAA
65 GATTTAA
* *
646285 AAATAAAAAAAATATTAATAAAA-AA-AGAAGAAAACAAACCATCCATAATGTTTCTTATAAA
1 AAATAAAAAAAATATT--TAAAACAAGAGAAGAAAACAAACCATCCATAATGTTGCTCATAAA
646346 ATGGTTGAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
71 44 0.81
72 5 0.09
73 5 0.09
ACGTcount: A:0.58, C:0.11, G:0.06, T:0.26
Consensus pattern (71 bp):
AAATAAAAAAAATATTTAAAACAAGAGAAGAAAACAAACCATCCATAATGTTGCTCATAAATTTG
ATTTAA
Done.