Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002616.1 Hibiscus syriacus cultivar Beakdansim tig00005294_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: 1287628
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 7
Found at i:542810 original size:201 final size:200
Alignment explanation
Indices: 542355--543243 Score: 930
Period size: 201 Copynumber: 4.4 Consensus size: 200
542345 AAGTAAACAT
* * *
542355 GTATATTTATACCGGTAACATTGCAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
1 GTATATTTATATCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
* * * *
542420 TTAGATCGATACAATTT--TAAATATATCGACACTTTATGTGTGCACCTCGTTGGGCATTCATTC
66 TGAGATCGATACATTTTAATAAATATATCGACACTTTATGCGTGCACCTCGTTTGGCATTCATTC
* * * * * *
542483 TGGA-AACAAGTATCGACATAAACTTAAAGTGTGTCGATACATTAT-TTAGACCTATTTTTTTCT
131 TGGACAAAAAATATCGACACAAATTTAAA-AGTGTCGATACATTATGTT-GA-C-A---TATT-T
542546 TCTTCATAAAACCG
188 TC-TCATAAAACCG
* * * * * *
542560 GTATATTTCTATCGGGTACATTGTAAATTTACCTATCACATTGTAATTATCGATTTTGATGTTTT
1 GTATATTTATATCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
* * * * *
542625 TGAGATTGATA-GTTTTAATAAATGTATCGACACTTTATGCGTGCACC-CGTTTGACATTCATTA
66 TGAGATCGATACATTTTAATAAATATATCGACACTTTATGCGTGCACCTCGTTTGGCATTCATTC
* * *
542688 TGGACAAAATATATATTGACACAAATTTAATAAGTGTCGATACTTTATGATGACATATTTTCTCA
131 TGGACAAAA-A-ATATCGACACAAATTTAA-AAGTGTCGATACATTATGTTGACATATTTTCTCA
*
542753 TAAAACTG
193 TAAAACCG
* *
542761 GTATATCTATATCGGTTACATTGTAAATTTACATATTACATTATAATTATCGGTTTCGATGTTTT
1 GTATATTTATATCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATG-TTT
* * *
542826 TTG-GATCGATACTTTTTAA-AACATATATCGACACTTTATGCGCGCATCC-CTTTTGGCATTCA
65 TTGAGATCGATACATTTTAATAA-ATATATCGACACTTTATGCGTGCA-CCTCGTTTGGCATTCA
* * * * * * **
542888 TTTTAGACAAAAAGTATCGACACAAATATAAAACGTGTCGATACATTATGTTCACCTATTTTAAC
128 TTCTGGACAAAAAATATCGACACAAATTTAAAA-GTGTCGATACATTATGTTGACATATTTTCTC
542953 ATAAAACCG
192 ATAAAACCG
*
542962 GTATATTTAT-TCTGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTTGAT-TTT
1 GTATATTTATATC-GGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
* * * * *
543025 ATTGGGATCAATAC-TTTTAATAATTGTATCGACACTTTATGTGTGCACCTCGTTTGGGCATTCA
65 -TTGAGATCGATACATTTTAATAAATATATCGACACTTTATGCGTGCACCTCGTTT-GGCATTCA
* * * *
543089 TTCTGGACAATAAGTATCGACACAAA-TTACACAAGTGTCGATACATTATGTTGACCTGTTTTCT
128 TTCTGGACAAAAAATATCGACACAAATTTA-A-AAGTGTCGATACATTATGTTGACATATTTTCT
* *
543153 -A-AGTAACTG
191 CATA-AAACCG
* * * *
543162 GTATATTTATACCGGTTACATTGTTAATTTACCTATTACATTATAATTATTGATTTCGATGTTTT
1 GTATATTTATATCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATG-TTT
*
543227 TTG-GGTCGATAC-TTTTA
65 TTGAGATCGATACATTTTA
543244 GAAAATGTAT
Statistics
Matches: 580, Mismatches: 80, Indels: 53
0.81 0.11 0.07
Matches are distributed among these distances:
199 6 0.01
200 109 0.19
201 246 0.42
202 43 0.07
203 26 0.04
204 3 0.01
205 82 0.14
206 31 0.05
207 2 0.00
208 30 0.05
209 2 0.00
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (200 bp):
GTATATTTATATCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
TGAGATCGATACATTTTAATAAATATATCGACACTTTATGCGTGCACCTCGTTTGGCATTCATTC
TGGACAAAAAATATCGACACAAATTTAAAAGTGTCGATACATTATGTTGACATATTTTCTCATAA
AACCG
Found at i:543127 original size:402 final size:399
Alignment explanation
Indices: 542332--543242 Score: 1110
Period size: 402 Copynumber: 2.3 Consensus size: 399
542322 GCGCTTATAT
* * * *
542332 TGACCTATTTTATAAGTAAACAT-GTATATTTATACCGGTAACATTGCAAATTTACCTATTACAT
1 TGACATATTTTCTAAG-AAAC-TGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACAT
* * * *
542396 TATAATTATCGGTTTCGATGTTTTTTAGATCGATACAATTTTAAATATATCGACACTTTATGTGT
64 TATAATTATCGGTTTCGATGTTTTTTGGATCGATAC-TTTTTAAATATATCGACACTTTATGCGC
* * * **
542461 GCACCTCGTTGGGCATTCATTCTGGAAACAAGTATCGACATAAACTTAAAGTGTGTCGATACATT
128 GCACCTCGTTGGGCATTCATTCTAGAAAAAAGTATCGACACAAACTTAAAACGTGTCGATACATT
* ** *
542526 ATTTAGACCTATTTTTTTCTTCTTCATAAAACCGGTATATTTCTATCGGGTACATTGTAAATTTA
193 ATTTACACCTA----TTTCTTCAACATAAAACCGGTATATTTATATCGGGTACATTGTAAATTTA
* ** *
542591 CCTATCACATTGTAATTATCGATTTTGATGTTTTTGAGATTGATAGTTTTAATAAATGTATCGAC
254 CCTATCACATTATAATTATCGATTTTGATGTTTTTGAGATCAATACTTTTAATAAATGTATCGAC
* *
542656 ACTTTATGCGTGCACCCGTTTGACATTCATTATGGACAAAATATATATTGACACAAATTTAATAA
319 ACTTTATGCGTGCACCCGTTTGACATTCATTATGGAC-AAATATATATCGACACAAATTTAACAA
*
542721 GTGTCGATACTTTATGA
383 GTGTCGATACATTATGA
* * *
542738 TGACATATTTTCTCATA-AAACTGGTATATCTATATCGGTTACATTGTAAATTTACATATTACAT
1 TGACATATTTTCT-A-AGAAACTGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACAT
542802 TATAATTATCGGTTTCGATGTTTTTTGGATCGATACTTTTTAAAACATATATCGACACTTTATGC
64 TATAATTATCGGTTTCGATGTTTTTTGGATCGATACTTTTT--AA-ATATATCGACACTTTATGC
* * *
542867 GCGCATCC-CTTTTGGCATTCATTTTAGACAAAAAGTATCGACACAAA-TATAAAACGTGTCGAT
126 GCGCA-CCTCGTTGGGCATTCATTCTAGA-AAAAAGTATCGACACAAACT-TAAAACGTGTCGAT
*
542930 ACATTATGTT-CACCTA-TT-TT-AACATAAAACCGGTATATTTAT-TCTGGTTACATTGTAAAT
188 ACATTAT-TTACACCTATTTCTTCAACATAAAACCGGTATATTTATATC-GGGTACATTGTAAAT
* * * *
542990 TTACCTATTACATTATAATTATCGGTTTTGAT-TTTATTGGGATCAATACTTTTAATAATTGTAT
251 TTACCTATCACATTATAATTATCGATTTTGATGTTT-TTGAGATCAATACTTTTAATAAATGTAT
* * *
543054 CGACACTTTATGTGTGCACCTCGTTTGGGCATTCATTCTGGAC-AATA-AGTATCGACACAAA-T
315 CGACACTTTATGCGTGCACC-CGTTT-GACATTCATTATGGACAAATATA-TATCGACACAAATT
*
543116 TACACAAGTGTCGATACATTATGT
377 TA-ACAAGTGTCGATACATTATGA
* * * *
543140 TGACCTGTTTTCTAAGTAACTGGTATATTTATACCGGTTACATTGTTAATTTACCTATTACATTA
1 TGACATATTTTCTAAGAAACTGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTA
* * *
543205 TAATTATTGATTTCGATGTTTTTTGGGTCGATACTTTT
66 TAATTATCGGTTTCGATGTTTTTTGGATCGATACTTTT
543243 AGAAAATGTA
Statistics
Matches: 439, Mismatches: 49, Indels: 39
0.83 0.09 0.07
Matches are distributed among these distances:
400 1 0.00
401 89 0.20
402 148 0.34
403 7 0.02
404 16 0.04
405 5 0.01
406 86 0.20
407 3 0.01
408 40 0.09
409 42 0.10
410 2 0.00
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.41
Consensus pattern (399 bp):
TGACATATTTTCTAAGAAACTGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTA
TAATTATCGGTTTCGATGTTTTTTGGATCGATACTTTTTAAATATATCGACACTTTATGCGCGCA
CCTCGTTGGGCATTCATTCTAGAAAAAAGTATCGACACAAACTTAAAACGTGTCGATACATTATT
TACACCTATTTCTTCAACATAAAACCGGTATATTTATATCGGGTACATTGTAAATTTACCTATCA
CATTATAATTATCGATTTTGATGTTTTTGAGATCAATACTTTTAATAAATGTATCGACACTTTAT
GCGTGCACCCGTTTGACATTCATTATGGACAAATATATATCGACACAAATTTAACAAGTGTCGAT
ACATTATGA
Found at i:547739 original size:200 final size:201
Alignment explanation
Indices: 547271--547743 Score: 666
Period size: 200 Copynumber: 2.4 Consensus size: 201
547261 GTTATTATAT
* * ** * *
547271 GTATCGACACAAATCTAAAACGTGTCGATACATTATGTTCACCTATTTTCTCATAAAACCGGTAC
1 GTATCGACACAAATCTAAAAAGTGTCGACACATTATGTAGACCTATTTTCACATAAAACCGGTAT
* *
547336 ATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTTGG
66 ATTTATACAGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGG
* *
547401 ATCGATACTTTTTAAAACATGTATCGACACTTTATGCGTGCAACCCTTTTGACATTCATTTTGGA
131 ATCGATACTTTTTAAAACATGTATCGACACTTTATACGTGCAACCCTTTTGACATTCATTCTGGA
547466 CAAAAA
196 CAAAAA
* * ** *
547472 GTATCGACACAAATCTAAAACGTGTCGATACATTATGTTTACCTATTTTAACATAAAA-CGGTAT
1 GTATCGACACAAATCTAAAAAGTGTCGACACATTATGTAGACCTATTTTCACATAAAACCGGTAT
547536 ATTTATACAGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGG
66 ATTTATACAGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGG
* * * *
547601 ATCGATACTTTTTATAA-ATGTATCGACACTTTATACGTTC-ACCCTTTTGGGCATTCATTCTGT
131 ATCGATACTTTTTAAAACATGTATCGACACTTTATACGTGCAACCCTTTT-GACATTCATTCTGG
*
547664 TCAAAAA
195 ACAAAAA
* * ** * *
547671 GTATCGACACAACAT-TAAAAAGTGTTGACATATTATGTAGGTCTATTCTCACATAAAACCGATA
1 GTATCGACACAA-ATCTAAAAAGTGTCGACACATTATGTAGACCTATTTTCACATAAAACCGGTA
547735 TATTTATAC
65 TATTTATAC
547744 CGGTCGATAC
Statistics
Matches: 245, Mismatches: 24, Indels: 7
0.89 0.09 0.03
Matches are distributed among these distances:
198 8 0.03
199 83 0.34
200 99 0.40
201 55 0.22
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (201 bp):
GTATCGACACAAATCTAAAAAGTGTCGACACATTATGTAGACCTATTTTCACATAAAACCGGTAT
ATTTATACAGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGG
ATCGATACTTTTTAAAACATGTATCGACACTTTATACGTGCAACCCTTTTGACATTCATTCTGGA
CAAAAA
Found at i:547939 original size:252 final size:251
Alignment explanation
Indices: 547495--547999 Score: 850
Period size: 252 Copynumber: 2.0 Consensus size: 251
547485 TCTAAAACGT
* *
547495 GTCGATACATTATGTTTACCTATTTTAACATAAAACGGTATATTTATACAGGTTACATTGTAAAT
1 GTCGATACATTATGTTCACCTATTTTAACATAAAACAGTATATTTATACAGGTTACATTGTAAAT
* *
547560 TTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTTATAAATGTATC
66 TTACATATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCAATACTTTTTATAAATGTATC
* *
547625 GACACTTTATACGTTCACCCTTTTGGGCATTCATTCTGTTCAAAAAGTATCGACACAACATTAAA
131 GACACTTTATACGTTCACCCTTTTGGGCATTCATTATGTACAAAAAGTATCGACACAACATTAAA
* **
547690 AAGTGTTGACATATTATGTAGGTCTATTCTCACATAAAACCGATATATTTATACCG
196 AAGTGTCGACATATTATGTAGACCTATTCTCACATAAAACCGATATATTTATACCG
* *
547746 GTCGATACATTATGTTCACCTATTTTAACATAAAATCAGTATATTTATACCGTTTACATTGTAAA
1 GTCGATACATTATGTTCACCTATTTTAACATAAAA-CAGTATATTTATACAGGTTACATTGTAAA
547811 TTTACATATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCAATACTTTTTATAAATGTAT
65 TTTACATATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCAATACTTTTTATAAATGTAT
* *
547876 CGACACTTTATGCGTTCACCCTTTTGGGCATTCATTATGTACAAAATA-TATCGATACAACATTA
130 CGACACTTTATACGTTCACCCTTTTGGGCATTCATTATGTACAAAA-AGTATCGACACAACATTA
* *
547940 AAAAGTGTCGACATATTATGTAGACCTATTCTCACATAAAACTGATATATTTATATCG
194 AAAAGTGTCGACATATTATGTAGACCTATTCTCACATAAAACCGATATATTTATACCG
547998 GT
1 GT
548000 TATATTAAAA
Statistics
Matches: 237, Mismatches: 15, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
251 34 0.14
252 202 0.85
253 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.39
Consensus pattern (251 bp):
GTCGATACATTATGTTCACCTATTTTAACATAAAACAGTATATTTATACAGGTTACATTGTAAAT
TTACATATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCAATACTTTTTATAAATGTATC
GACACTTTATACGTTCACCCTTTTGGGCATTCATTATGTACAAAAAGTATCGACACAACATTAAA
AAGTGTCGACATATTATGTAGACCTATTCTCACATAAAACCGATATATTTATACCG
Found at i:548023 original size:200 final size:198
Alignment explanation
Indices: 547754--548288 Score: 644
Period size: 201 Copynumber: 2.7 Consensus size: 198
547744 CGGTCGATAC
** * * * * *
547754 ATTATGTTCACCTATTTTAACATAAAATCAGTATATTTATACCGTTTACATTGTAAATTTACATA
1 ATTATGTAGACCTATTCTCACATAAAATGA-TATATTTATATCGGTTACATTGTAAATTTACATA
*
547819 TTACATTATAATTATCGGTTTCGATGTTTTTGGGATCAATACTTTTTATAAATGTATCGACACTT
65 TTACATTATAATTAT-GGTTTCGATGTTTTTGGGATCGATACTTTTTA-AAATGTATCGACACTT
* * * * *
547884 TATGCGTTCA-CCCTTTTGGGCATTCATTATGTACAAA-ATATATCGATACAACATT-AAAAAGT
128 TATGAGTGCACCCCTTATGGGCATTCATTATGGACAAACA-ATATCGACACAA-ATTCAAAAAGT
*
547946 GTCGACAT
191 GTCGACAA
* ** * *
547954 ATTATGTAGACCTATTCTCACATAAAACTGATATATTTATATCGGTTATATTAAAAAATTACCTA
1 ATTATGTAGACCTATTCTCACATAAAA-TGATATATTTATATCGGTTACATTGTAAATTTACATA
* * * *
548019 TTACATTATAATTATAGATTTCGATGTTTTTGGGATCGATACGTTTTAAAAATATTTCGACACTT
65 TTACATTATAATTAT-GGTTTCGATGTTTTTGGGATCGATAC-TTTTTAAAATGTATCGACACTT
* * * *
548084 TATGAGTGCACCCCTTATGGGCATTCTTTCTGGACAAACAATATCGACACAAATTCCAGAAGTGT
128 TATGAGTGCACCCCTTATGGGCATTCATTATGGACAAACAATATCGACACAAATTCAAAAAGTGT
*
548149 CGATAA
193 CGACAA
* * * *
548155 ATTATGTAGACCTATTCTCTCATAAAATCGGTTTAGTTATATCGGTTACATTGTAAATTTACATA
1 ATTATGTAGACCTATTCTCACATAAAAT-GATATATTTATATCGGTTACATTGTAAATTTACATA
* *
548220 TTACATTATATTTATGGATTTCGATGTTTCTGGGATCGATACTTTTTAAAATTGTATCGACACTT
65 TTACATTATAATTATGG-TTTCGATGTTTTTGGGATCGATACTTTTTAAAA-TGTATCGACACTT
548285 TATG
128 TATG
548289 TGAAACTTTA
Statistics
Matches: 283, Mismatches: 44, Indels: 15
0.83 0.13 0.04
Matches are distributed among these distances:
200 124 0.44
201 158 0.56
202 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.40
Consensus pattern (198 bp):
ATTATGTAGACCTATTCTCACATAAAATGATATATTTATATCGGTTACATTGTAAATTTACATAT
TACATTATAATTATGGTTTCGATGTTTTTGGGATCGATACTTTTTAAAATGTATCGACACTTTAT
GAGTGCACCCCTTATGGGCATTCATTATGGACAAACAATATCGACACAAATTCAAAAAGTGTCGA
CAA
Found at i:548310 original size:15 final size:15
Alignment explanation
Indices: 548285--548327 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
548275 ATCGACACTT
548285 TATGTGAAACTTTAAG
1 TATG-GAAACTTTAAG
* *
548301 TTTGGAAACTTTATG
1 TATGGAAACTTTAAG
*
548316 TATGAAAACTTT
1 TATGGAAACTTT
548328 GTTGTGGAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 20 0.87
16 3 0.13
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.42
Consensus pattern (15 bp):
TATGGAAACTTTAAG
Found at i:548609 original size:11 final size:11
Alignment explanation
Indices: 548593--548652 Score: 75
Period size: 11 Copynumber: 5.2 Consensus size: 11
548583 TATACATAAA
548593 AATGTTCAAAT
1 AATGTTCAAAT
548604 AATGTTCAAAT
1 AATGTTCAAAT
* *
548615 AATTTATACATAAC
1 AATGT-T-CA-AAT
548629 AATGTTCAAAT
1 AATGTTCAAAT
548640 AATGTTCAAAT
1 AATGTTCAAAT
548651 AA
1 AA
548653 CGTACCCACA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
11 30 0.71
12 3 0.07
13 3 0.07
14 6 0.14
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.35
Consensus pattern (11 bp):
AATGTTCAAAT
Found at i:548626 original size:36 final size:36
Alignment explanation
Indices: 548579--548652 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
548569 GTACACAAGA
548579 AATTTATACATAAAAATGTTCAAATAATGTTCAAAT
1 AATTTATACATAAAAATGTTCAAATAATGTTCAAAT
*
548615 AATTTATACATAACAATGTTCAAATAATGTTCAAAT
1 AATTTATACATAAAAATGTTCAAATAATGTTCAAAT
548651 AA
1 AA
548653 CGTACCCACA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.35
Consensus pattern (36 bp):
AATTTATACATAAAAATGTTCAAATAATGTTCAAAT
Found at i:548652 original size:25 final size:25
Alignment explanation
Indices: 548593--548653 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
548583 TATACATAAA
548593 AATGTTCAAAT---AATGTTCAAAT
1 AATGTTCAAATAACAATGTTCAAAT
548615 AAT-TT-ATACATAACAATGTTCAAAT
1 AATGTTCA-A-ATAACAATGTTCAAAT
548640 AATGTTCAAATAAC
1 AATGTTCAAATAAC
548654 GTACCCACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
20 1 0.03
21 3 0.09
22 5 0.16
25 19 0.59
26 3 0.09
27 1 0.03
ACGTcount: A:0.48, C:0.11, G:0.07, T:0.34
Consensus pattern (25 bp):
AATGTTCAAATAACAATGTTCAAAT
Found at i:549653 original size:6 final size:6
Alignment explanation
Indices: 549635--549687 Score: 52
Period size: 6 Copynumber: 8.8 Consensus size: 6
549625 ACTTGTTTGG
* * * * *
549635 ATCATC ATAATC ATCATC ATCATC TTCATC TTCATC GTCATC TTCATC
1 ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC
*
549683 TTCAT
1 ATCAT
549688 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:0.26, C:0.30, G:0.02, T:0.42
Consensus pattern (6 bp):
ATCATC
Found at i:549669 original size:12 final size:12
Alignment explanation
Indices: 549648--549687 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
549638 ATCATAATCA
*
549648 TCATCATCATCT
1 TCATCTTCATCT
*
549660 TCATCTTCATCG
1 TCATCTTCATCT
549672 TCATCTTCATCT
1 TCATCTTCATCT
549684 TCAT
1 TCAT
549688 TGACCTCTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.20, C:0.33, G:0.03, T:0.45
Consensus pattern (12 bp):
TCATCTTCATCT
Found at i:549669 original size:18 final size:18
Alignment explanation
Indices: 549648--549687 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
549638 ATCATAATCA
549648 TCATCATCATCTTCATCT
1 TCATCATCATCTTCATCT
*
549666 TCATCGTCATCTTCATCT
1 TCATCATCATCTTCATCT
549684 TCAT
1 TCAT
549688 TGACCTCTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.20, C:0.33, G:0.03, T:0.45
Consensus pattern (18 bp):
TCATCATCATCTTCATCT
Found at i:550958 original size:200 final size:197
Alignment explanation
Indices: 550466--551821 Score: 1507
Period size: 200 Copynumber: 6.8 Consensus size: 197
550456 ATTTAAAATG
* * * * * ** *
550466 GTATCGACTCAAATTTA-ATAATTGTCGATACTTTATG-ATGACCTATTTTCTCATAAAAAAGAT
1 GTATCGACACAAA-TTACAAAAGTGTCGATACATTATGTA-GACCTATTCTCTCATAAAACCGGT
* * * *
550529 ATATTTATACCAGTTACATTGAAAATTTACCTATTACATTATAATTATCGATTTCGATGTTCTTT
64 ATATTTATACCGGTTACATT-AAAAATTACCTATTACATTATAATTATGGGTTTCGATGTT-TTT
* * * * * * *
550594 GGATCGACACTTTTTAAAAAAGTATCGACACTTTATACATACAACC-CTTT-GTCATTCCTTCTG
127 GGATCGACACTTTTTATAAATGTATCGACACTTTATGCGTAC-ACCATTTTGGGCATTCATTCTG
550657 GAC-AAA
191 GACAAAA
* * *
550663 GTATCGACACCAATTCCACAAGTGTCGATACATGT-TGTAGACCTATTCTCTCATAAAACCGGTA
1 GTATCGACACAAATTACAAAAGTGTCGATACAT-TATGTAGACCTATTCTCTCATAAAACCGGTA
* * * * *
550727 TAGTTATACCGGTTACATTGTAAATTTACCTATTACATTATATTTATGGGTTTCGATGTTTCTGG
65 TATTTATACCGGTTACATT-AAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGG
* * * *
550792 TATCGACACTTTTTATAAATATATCGACACTTTATGCGTTCATCATTTTGGGCATTCATTTTGGA
129 -ATCGACACTTTTTATAAATGTATCGACACTTTATGCGTACACCATTTTGGGCATTCATTCTGGA
550857 CAAAA
193 CAAAA
* * * **
550862 CGTATCGACACAAAATAAAAAAGTGTCGATACATTATGTAGACCTATTCTCGCATAAAACCTTTA
1 -GTATCGACACAAATTACAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTA
* * *
550927 TTTTTACACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTAG
65 TATTTATACCGGTTACATTA-AAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTT-G
* * * * *
550992 GATCGATACTTTGTATAAATGTATCGACAC-TTAGTG-GTACACCCTTTTTGGGTATTCCTTCTG
128 GATCGACACTTTTTATAAATGTATCGACACTTTA-TGCGTACA-CCATTTTGGGCATTCATTCTG
551055 GACCAAAA
191 GA-CAAAA
* *
551063 GTATCGACACAAATTACACAAGTGTCGATACA-TATTGTACACCTATTCTCTCATAAAACCGGTA
1 GTATCGACACAAATTACAAAAGTGTCGATACATTA-TGTAGACCTATTCTCTCATAAAACCGGTA
** * * *
551127 TAAGTATATCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTTGATGTTTCTGG
65 TATTTATACCGGTTACATT-AAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTT-TTG
* * * *
551192 GATCGACACTTCTTATAAATGTATCGACAC-TTAGTG-GTGCACCCTTTTTGGGCATTCCTTCTG
128 GATCGACACTTTTTATAAATGTATCGACACTTTA-TGCGTACA-CCATTTTGGGCATTCATTCTG
551255 GACCAAAA
191 GA-CAAAA
* * * *
551263 GTATCGACACAAATTACACAAGTATCGATACA-TATTGTACACCTATTCTCTCATAAAATCGGTA
1 GTATCGACACAAATTACAAAAGTGTCGATACATTA-TGTAGACCTATTCTCTCATAAAACCGGTA
* * *
551327 TATGTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCAATGTTTCTGG
65 TATTTATACCGGTTACATT-AAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGG
* * * *
551392 AATCGATACTTGTTTATAAATGTATCGACACTTTTTGCGTGCACCCTTTTGGGCATTCATTCTGG
129 -ATCGACACTT-TTTATAAATGTATCGACACTTTATGCGTACACCATTTTGGGCATTCATTCTGG
551457 ACAAACA
192 ACAAA-A
* * * *
551464 GTATGGACACAAATTCCAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACTGGTTT
1 GTATCGACACAAATTACAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTAT
* **
551529 AGTTATACATGTTACATTTAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGG
66 ATTTATACCGGTTACA-TTAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTT-GG
** * * * * * * **
551594 ATCGACACTTTCAATAAATGTATTGACACATTATGCATTCATCATTTTGGGAATTCATTCTAAAC
129 ATCGACACTTTTTATAAATGTATCGACACTTTATGCGTACACCATTTTGGGCATTCATTCTGGAC
551659 AAAAA
194 -AAAA
* * * * * *
551664 GTATTGACGCATAATGA-AAAAATGTCGATACATTATGTAGA-CTATTCTCACATAAAACCAGTA
1 GTATCGACACA-AATTACAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTA
* *
551727 TATTTATACCGGTTATATTACAAAATTACCTATAACATTATAATTATGGGTTTCGATGTTTTTGG
65 TATTTATACCGGTTACATTA-AAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGG
*
551792 TATCGACACTTTTTATAAACGTATCGACAC
129 -ATCGACACTTTTTATAAATGTATCGACAC
551822 ATATGCTTAC
Statistics
Matches: 999, Mismatches: 131, Indels: 56
0.84 0.11 0.05
Matches are distributed among these distances:
196 8 0.01
197 138 0.14
198 20 0.02
199 112 0.11
200 535 0.54
201 173 0.17
202 13 0.01
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (197 bp):
GTATCGACACAAATTACAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTAT
ATTTATACCGGTTACATTAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGAT
CGACACTTTTTATAAATGTATCGACACTTTATGCGTACACCATTTTGGGCATTCATTCTGGACAA
AA
Found at i:551810 original size:600 final size:595
Alignment explanation
Indices: 550488--551821 Score: 1708
Period size: 600 Copynumber: 2.2 Consensus size: 595
550478 ATTTAATAAT
* * * *
550488 TGTCGATACTTTATG-ATGACCTATTTTCTCATAAAA-AAGATATATTTATACCAGTTACATTGA
1 TGTCGATACATTATGTA-GACCTATTCTCTCATAAAACCAG-TATATTTATACCGGTTACATTGA
* * * *
550551 AAATTTACCTATTACATTATAATTATCGATTTCGATGTTCTTTGGATCGACACTTTTTAAAAAAG
64 AAAATTACCTATTACATTATAATTATGGGTTTCGATGTT-TTTGGATCGACACTTTTTATAAAAG
* * *
550616 TATCGACACTTTATACATACAACCCTTTGTCATTCCTTCTGGACAAAGTATCGACACCAATTCCA
128 TATCGACACTTTATACATACAACCCTTTGGCATTCCTTCTGGACAAAGTATCGACACAAATTACA
* * *
550681 CAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGTATAGTTATACCGGTTACATT
193 CAAGTATCGATACATATTGTACACCTATTCTCTCATAAAACCGGTATAGTTATACCGGTTACATT
* * * * *
550746 GTAAATTTACCTATTACATTATATTTATGGGTTTCGATGTTTCTGGTATCGACACTTTTTATAAA
258 GAAAAATTACCTATTACATTATAATTATGGGTTTCAATGTTTCTGGAATCGACACTTTTTATAAA
* * *
550811 TATATCGACACTTTATGCGTTCATCATTTTGGGCATTCATTTTGGACAAAACGTATCGACACAAA
323 TATATCGACACTTTATGCGTGCACCATTTTGGGCATTCATTCTGGACAAAACGTATCGACACAAA
* *
550876 ATAAAAAAGTGTCGATACATTATGTAGACCTATTCTCGCATAAAACCTTTATTTTTACACCGGTT
388 ATAAAAAAGTGTCGATACATTATGTAGACCTATTCTCGCATAAAACCTTTAGTTATACA-CGGTT
* * **
550941 ATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTAGGATCGATACTTTGT
452 ACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTAGGATCGACACTTTCA
* * * * ** *
551006 ATAAATGTATCGACACTTAGTGGTACACCCTTTTTGGGTATTCCTTCTGGACCAAAAGTATCGAC
517 ATAAATGTATCGACACTTAGTGATACACCCATTTTGGGAATTCATTCTAAACAAAAAGTATCGAC
* * *
551071 ACAAATTACACAAG
582 ACAAATGACAAAAA
* * ** *
551085 TGTCGATACA-TATTGTACACCTATTCTCTCATAAAACCGGTATAAGTATATCGGTTACATTGAA
1 TGTCGATACATTA-TGTAGACCTATTCTCTCATAAAACCAGTATATTTATACCGGTTACATTGAA
* * * *
551149 AAATTACCTATTACATTATAATTATGGGTTTTGATGTTTCTGGGATCGACACTTCTTATAAATGT
65 AAATTACCTATTACATTATAATTATGGGTTTCGATGTTT-TTGGATCGACACTTTTTATAAAAGT
** *
551214 ATCGACAC-TTAGT-GGTGC-ACCCTTTTTGGGCATTCCTTCTGGACCAAAAGTATCGACACAAA
129 ATCGACACTTTA-TACATACAACCC--TTT-GGCATTCCTTCTGGA-C-AAAGTATCGACACAAA
*
551276 TTACACAAGTATCGATACATATTGTACACCTATTCTCTCATAAAATCGGTATA-TGTATACCGGT
188 TTACACAAGTATCGATACATATTGTACACCTATTCTCTCATAAAACCGGTATAGT-TATACCGGT
*
551340 TACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCAATGTTTCTGGAATCGATACTTGT
252 TACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCAATGTTTCTGGAATCGACACTT-T
* * * *
551405 TTATAAATGTATCGACACTTTTTGCGTGCACCCTTTTGGGCATTCATTCTGGAC-AAACAGTATG
316 TTATAAATATATCGACACTTTATGCGTGCACCATTTTGGGCATTCATTCTGGACAAAAC-GTATC
* ** * *
551469 GACACAAATTCCAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACTGGTTTAGTTA
380 GACACAAAATAAAAAAGTGTCGATACATTATGTAGACCTATTCTCGCATAAAAC--CTTTAGTTA
* *
551534 TACA-TGTTACATTTA-AAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATC
443 TACACGGTTACA-TTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTAGGATC
* * *
551597 GACACTTTCAATAAATGTATTGACACATTA-TGCATTCA-TCATTTTGGGAATTCATTCTAAACA
507 GACACTTTCAATAAATGTATCGACAC-TTAGTG-ATACACCCATTTTGGGAATTCATTCTAAACA
* *
551660 AAAAGTATTGACGCATAATGA-AAAAA
570 AAAAGTATCGACACA-AATGACAAAAA
* *
551686 TGTCGATACATTATGTAGA-CTATTCTCACATAAAACCAGTATATTTATACCGGTTATATT-ACA
1 TGTCGATACATTATGTAGACCTATTCTCTCATAAAACCAGTATATTTATACCGGTTACATTGA-A
* *
551749 AAATTACCTATAACATTATAATTATGGGTTTCGATGTTTTTGGTATCGACACTTTTTATAAACGT
65 AAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGG-ATCGACACTTTTTATAAAAGT
551814 ATCGACAC
129 ATCGACAC
551822 ATATGCTTAC
Statistics
Matches: 635, Mismatches: 80, Indels: 41
0.84 0.11 0.05
Matches are distributed among these distances:
595 4 0.01
596 8 0.01
597 115 0.18
598 16 0.03
599 6 0.01
600 233 0.37
601 228 0.36
602 15 0.02
603 10 0.02
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (595 bp):
TGTCGATACATTATGTAGACCTATTCTCTCATAAAACCAGTATATTTATACCGGTTACATTGAAA
AATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGATCGACACTTTTTATAAAAGTAT
CGACACTTTATACATACAACCCTTTGGCATTCCTTCTGGACAAAGTATCGACACAAATTACACAA
GTATCGATACATATTGTACACCTATTCTCTCATAAAACCGGTATAGTTATACCGGTTACATTGAA
AAATTACCTATTACATTATAATTATGGGTTTCAATGTTTCTGGAATCGACACTTTTTATAAATAT
ATCGACACTTTATGCGTGCACCATTTTGGGCATTCATTCTGGACAAAACGTATCGACACAAAATA
AAAAAGTGTCGATACATTATGTAGACCTATTCTCGCATAAAACCTTTAGTTATACACGGTTACAT
TACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTAGGATCGACACTTTCAATAA
ATGTATCGACACTTAGTGATACACCCATTTTGGGAATTCATTCTAAACAAAAAGTATCGACACAA
ATGACAAAAA
Found at i:552196 original size:19 final size:19
Alignment explanation
Indices: 552172--552220 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
552162 TTACATCCAC
552172 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
552191 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
552210 ATACAAAATTA
1 ATACAAAATTA
552221 ACTCTACATT
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:553797 original size:18 final size:18
Alignment explanation
Indices: 553774--553812 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
553764 TCCTCCTCAT
553774 TTCCTCCATCTTTTCTTC
1 TTCCTCCATCTTTTCTTC
*
553792 TTCCTCCCTCTTTTCTTC
1 TTCCTCCATCTTTTCTTC
553810 TTC
1 TTC
553813 ATATTTTTTC
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:0.03, C:0.41, G:0.00, T:0.56
Consensus pattern (18 bp):
TTCCTCCATCTTTTCTTC
Found at i:554103 original size:21 final size:21
Alignment explanation
Indices: 554078--554138 Score: 95
Period size: 21 Copynumber: 2.9 Consensus size: 21
554068 CCCCTTATGC
*
554078 CTCTCAAGTGTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
554099 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
* *
554120 CTCGCAAGTTTCTATTCGA
1 CTCTCAAGTTTCTCTTCGA
554139 ATCTTTATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.16, C:0.31, G:0.13, T:0.39
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:554247 original size:15 final size:15
Alignment explanation
Indices: 554224--554255 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
554214 ACTCTGTTTT
554224 CCTCACCGTCATCCC
1 CCTCACCGTCATCCC
*
554239 CCTCTCCGTCATCCC
1 CCTCACCGTCATCCC
554254 CC
1 CC
554256 AATACAACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.09, C:0.62, G:0.06, T:0.22
Consensus pattern (15 bp):
CCTCACCGTCATCCC
Found at i:554562 original size:22 final size:23
Alignment explanation
Indices: 554534--554592 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 23
554524 AACCTGCATT
554534 TATAATAAAAT-TTATAATTTTA
1 TATAATAAAATATTATAATTTTA
* *
554556 TATAATAACTATATTATCATTTTA
1 TATAATAA-AATATTATAATTTTA
*
554580 GATAA-AAAATATT
1 TATAATAAAATATT
554593 CTTCAACTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
22 13 0.42
23 4 0.13
24 14 0.45
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (23 bp):
TATAATAAAATATTATAATTTTA
Found at i:556867 original size:182 final size:181
Alignment explanation
Indices: 556552--556942 Score: 593
Period size: 182 Copynumber: 2.2 Consensus size: 181
556542 TACGCGTACT
* ** *
556552 TATTAAAGTATCAACACTTTCAATATATTTGGTAGCGCTTTACCGGTTTTATCATTTAGAGACCG
1 TATTAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTATCATTTACAGACCG
* * *
556617 GTTTTATCATATTTTACCTTTTATATCGTTATGGATCGATATATTTTTATAAAGAATCGACACTT
66 GTTTTATCATATTTTACCTGTTATATCGTTATGGATCGATACATATTTATAAAGAATCGACACTT
556682 TATAGGAGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
131 TATAGGAGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
* * * * * * * *
556733 TATTAAAGTATTGACACTTTCAATATATCCGGTATCTCTTTATCGGTTTTTTCTTTTCCTGACCG
1 TATTAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTATCATTTACAGACCG
* *
556798 GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACT
66 GTTTTATCATA-TTTTACCTGTTATATCGTTATGGATCGATACATATTTATAAAGAATCGACACT
* * *
556863 TTATAGGCGTTAAAACTGCTTCTCCTTTAAATTCACTATGTGTCGATACTTA
130 TTATAGGAGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
556915 TATTAAAGTATCGACACTTTCAATATAT
1 TATTAAAGTATCGACACTTTCAATATAT
556943 TCAATATCTT
Statistics
Matches: 188, Mismatches: 21, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
181 63 0.34
182 125 0.66
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (181 bp):
TATTAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTATCATTTACAGACCG
GTTTTATCATATTTTACCTGTTATATCGTTATGGATCGATACATATTTATAAAGAATCGACACTT
TATAGGAGCTAAAACTGCTTCTCCTTTAAATTCACAATGTGTCGATACTTA
Found at i:556971 original size:160 final size:160
Alignment explanation
Indices: 556801--557102 Score: 541
Period size: 160 Copynumber: 1.9 Consensus size: 160
556791 CTGACCGGTT
*
556801 TTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACTTTA
1 TTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACTTTA
* * *
556866 TAGGCGTTAAAACTGCTTCTCCTTTAAATTCACTATGTGTCGATACTTATATTAAAGTATCGACA
66 CAGGCGCTAAAACTGCTTCTCCTTTAAATTCACTATGTGTCGATACTTATATTAAAGTAGCGACA
*
556931 CTTTCAATATATTCAATATCTTTTTACCGG
131 CTTGCAATATATTCAATATCTTTTTACCGG
556961 TTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACTTTA
1 TTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACTTTA
* *
557026 CAGGCGCTAAAACTGCTTCTCCTTTAAATTCACTATGTGTCGATATTTATATTAAAGTAGCGATA
66 CAGGCGCTAAAACTGCTTCTCCTTTAAATTCACTATGTGTCGATACTTATATTAAAGTAGCGACA
557091 CTTGCAATATAT
131 CTTGCAATATAT
557103 CCGGTAGCGC
Statistics
Matches: 135, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
160 135 1.00
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.40
Consensus pattern (160 bp):
TTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACTTTA
CAGGCGCTAAAACTGCTTCTCCTTTAAATTCACTATGTGTCGATACTTATATTAAAGTAGCGACA
CTTGCAATATATTCAATATCTTTTTACCGG
Found at i:557774 original size:115 final size:115
Alignment explanation
Indices: 557572--557808 Score: 467
Period size: 115 Copynumber: 2.1 Consensus size: 115
557562 AACCTTTTTC
557572 AACTTTTACCTTCTTTTTTTTCTCCCTAACAATAAATACCTTTAAATTATTCTATAAAACGTTAA
1 AACTTTTACCTTCTTTTTTTTCTCCCTAACAATAAATACCTTTAAATTATTCTATAAAACGTTAA
557637 AATTATAAAATATTCAAATATAATTATATTTTAGTTGAAAATCTAATTGT
66 AATTATAAAATATTCAAATATAATTATATTTTAGTTGAAAATCTAATTGT
557687 AACTTTTACCTTCTTTTTTTTCTCCCTAACAATAAATACCTTTAAATTATTCTATAAAACGTTAA
1 AACTTTTACCTTCTTTTTTTTCTCCCTAACAATAAATACCTTTAAATTATTCTATAAAACGTTAA
557752 AATTATAAAATATTCAAATATAATTATATTTTAGTTGAAAATCTAATTGT
66 AATTATAAAATATTCAAATATAATTATATTTTAGTTGAAAATCTAATTGT
557802 AA-TTTTA
1 AACTTTTA
557809 AATAAATTAT
Statistics
Matches: 122, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
114 5 0.04
115 117 0.96
ACGTcount: A:0.39, C:0.13, G:0.03, T:0.45
Consensus pattern (115 bp):
AACTTTTACCTTCTTTTTTTTCTCCCTAACAATAAATACCTTTAAATTATTCTATAAAACGTTAA
AATTATAAAATATTCAAATATAATTATATTTTAGTTGAAAATCTAATTGT
Found at i:560553 original size:20 final size:20
Alignment explanation
Indices: 560528--560597 Score: 113
Period size: 20 Copynumber: 3.5 Consensus size: 20
560518 TTCACAAGAA
560528 CTTTTAGGATGAATAATTAT
1 CTTTTAGGATGAATAATTAT
*
560548 CTTTTACGATGAATAATTAT
1 CTTTTAGGATGAATAATTAT
* *
560568 CTTATAGGATAAATAATTAT
1 CTTTTAGGATGAATAATTAT
560588 CTTTTAGGAT
1 CTTTTAGGAT
560598 CAGATTTATT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (20 bp):
CTTTTAGGATGAATAATTAT
Found at i:561408 original size:10 final size:10
Alignment explanation
Indices: 561393--561435 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
561383 CTATTTTTTC
561393 AAAAAAAACA
1 AAAAAAAACA
561403 AAAAAAAAC-
1 AAAAAAAACA
**
561412 AAAAAAGGCA
1 AAAAAAAACA
561422 AAAAAAAACA
1 AAAAAAAACA
561432 AAAA
1 AAAA
561436 TGCCAAAACT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 7 0.25
10 21 0.75
ACGTcount: A:0.86, C:0.09, G:0.05, T:0.00
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:561416 original size:19 final size:19
Alignment explanation
Indices: 561392--561435 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
561382 GCTATTTTTT
561392 CAAAAAAAACAAAAAAAAA
1 CAAAAAAAACAAAAAAAAA
**
561411 CAAAAAAGGCAAAAAAAAA
1 CAAAAAAAACAAAAAAAAA
561430 CAAAAA
1 CAAAAA
561436 TGCCAAAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.84, C:0.11, G:0.05, T:0.00
Consensus pattern (19 bp):
CAAAAAAAACAAAAAAAAA
Found at i:561442 original size:19 final size:19
Alignment explanation
Indices: 561401--561443 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
561391 TCAAAAAAAA
*
561401 CAAAAAAAAACAAAAAAGG
1 CAAAAAAAAACAAAAAAGC
*
561420 CAAAAAAAAACAAAAATGC
1 CAAAAAAAAACAAAAAAGC
561439 CAAAA
1 CAAAA
561444 CTTCAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.77, C:0.14, G:0.07, T:0.02
Consensus pattern (19 bp):
CAAAAAAAAACAAAAAAGC
Found at i:570054 original size:19 final size:19
Alignment explanation
Indices: 570030--570073 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
570020 CCGACTCCAT
570030 GGAGCATATTACAGGCCAA
1 GGAGCATATTACAGGCCAA
570049 GGAGCATATTACAGGCCAA
1 GGAGCATATTACAGGCCAA
*
570068 GTAGCA
1 GGAGCA
570074 CCCATCAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.36, C:0.20, G:0.27, T:0.16
Consensus pattern (19 bp):
GGAGCATATTACAGGCCAA
Found at i:571115 original size:20 final size:20
Alignment explanation
Indices: 571092--571143 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
571082 AACGCGATCC
571092 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
571112 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
571132 CCAAAATCGCAA
1 CCAGAATCGCAA
571144 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:571224 original size:20 final size:20
Alignment explanation
Indices: 571199--571392 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
571189 GATTTTCCAT
* *
571199 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
571219 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
571239 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
571259 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
571279 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
571299 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
571319 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
571339 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
571360 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
571380 AATCGCAACGCGA
1 AATCGCAACGCGA
571393 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:571244 original size:40 final size:39
Alignment explanation
Indices: 571195--571392 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
571185 TTGCGATTTT
* ** *
571195 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
571233 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
571274 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
571314 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
571353 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
571393 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:571282 original size:60 final size:60
Alignment explanation
Indices: 571199--571391 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
571189 GATTTTCCAT
* ** * *
571199 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
571259 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
571319 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
571380 AATCGCAACGCG
1 AATCGCAACGCG
571392 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:571812 original size:33 final size:33
Alignment explanation
Indices: 571773--571843 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
571763 TTCACTTAGA
*
571773 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
571806 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
571839 TTTCA
1 TTTCA
571844 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:571983 original size:14 final size:14
Alignment explanation
Indices: 571964--572018 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
571954 AGAATGACTG
571964 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
571978 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
571997 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
572011 TCGCAACG
1 TCGCAACG
572019 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:572001 original size:33 final size:33
Alignment explanation
Indices: 571964--572034 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
571954 AGAATGACTG
**
571964 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
571997 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
572030 TCGCA
1 TCGCA
572035 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:574013 original size:185 final size:186
Alignment explanation
Indices: 573782--574248 Score: 909
Period size: 185 Copynumber: 2.5 Consensus size: 186
573772 TAGATTGCTT
*
573782 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
573847 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
573912 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
573967 AGTAAATTTGTTCGGTTGATGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
574032 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
574097 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
574153 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
574218 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGT
574249 TTCAATTTGC
Statistics
Matches: 278, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
185 153 0.55
186 125 0.45
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:574076 original size:93 final size:93
Alignment explanation
Indices: 573782--574248 Score: 909
Period size: 93 Copynumber: 5.0 Consensus size: 93
573772 TAGATTGCTT
*
573782 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
573847 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
573875 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
573939 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
573967 AGTAAATTTGTTCGGTTGATGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
574032 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
574060 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
574125 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
574153 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
574218 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
574246 AGT
1 AGT
574249 TTCAATTTGC
Statistics
Matches: 370, Mismatches: 3, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
92 91 0.25
93 279 0.75
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:574320 original size:19 final size:19
Alignment explanation
Indices: 574280--574408 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
574270 TAGTTTACTT
* *
574280 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
574300 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
574319 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
574338 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
574352 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
574371 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
574385 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
574404 TCGCA
1 TCGCA
574409 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:574359 original size:33 final size:32
Alignment explanation
Indices: 574316--574408 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
574306 CGCGAAACCA
**
574316 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
574348 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
574381 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
574409 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:574406 original size:52 final size:52
Alignment explanation
Indices: 574280--574408 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
574270 TAGTTTACTT
**
574280 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
574332 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
574385 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
574409 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:574426 original size:19 final size:19
Alignment explanation
Indices: 574404--574521 Score: 121
Period size: 19 Copynumber: 6.7 Consensus size: 19
574394 GAAACCAAAA
*
574404 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
574423 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
574439 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
574456 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
574472 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
574489 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
574508 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
574522 AAGTTTCGTG
Statistics
Matches: 82, Mismatches: 7, Indels: 20
0.75 0.06 0.18
Matches are distributed among these distances:
14 15 0.18
16 11 0.13
17 11 0.13
19 45 0.55
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:574445 original size:14 final size:14
Alignment explanation
Indices: 574426--574482 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
574416 TTTCATTTCG
574426 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
574440 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
574457 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
574473 CGTTGCGATT
1 CGTTGCGATT
574483 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:574451 original size:33 final size:33
Alignment explanation
Indices: 574409--574501 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
574399 CAAAATCGCA
*
574409 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
574442 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
574475 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
574502 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:574527 original size:19 final size:19
Alignment explanation
Indices: 574473--574537 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
574463 GCGATTCTGT
*
574473 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGA-TTTAAGTTTCG
**
574492 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTAAGTTTCG
574511 CGTTGCGATTTAAGTTTCG
1 CGTTGCGATTTAAGTTTCG
*
574530 TGTTGCGA
1 CGTTGCGA
574538 AAGTAAACTA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
18 3 0.08
19 37 0.93
ACGTcount: A:0.11, C:0.17, G:0.28, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTAAGTTTCG
Found at i:576482 original size:14 final size:14
Alignment explanation
Indices: 576463--576498 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
576453 ATTGTTTAAT
576463 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
576477 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
576491 TGATTTGT
1 TGATTTGT
576499 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:576621 original size:19 final size:19
Alignment explanation
Indices: 576605--576706 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
576595 AAAAATGACT
576605 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
576624 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
576643 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
576657 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
576676 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
576696 ATCGCAATGCG
1 ATCGCAATGCG
576707 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:576755 original size:33 final size:33
Alignment explanation
Indices: 576713--576964 Score: 183
Period size: 33 Copynumber: 7.5 Consensus size: 33
576703 TGCGTTTATA
*
576713 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATTTCGTTGCGATTTTC
576746 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTC
576782 -TTTCG--TTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTC
*
576815 -TTTCG--TTGCGATTCTTTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATTTCGTTGCGATTTTC
*
576845 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATTTCGTTGCGATTTTC
576878 ATTTCGCATTGCGATTTTAATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTC
*
576914 -TGTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTC
576949 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
576965 TTCATTTCGC
Statistics
Matches: 193, Mismatches: 6, Indels: 37
0.82 0.03 0.16
Matches are distributed among these distances:
28 6 0.03
30 8 0.04
31 7 0.04
33 116 0.60
35 16 0.08
36 22 0.11
38 18 0.09
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
ATTTCGCATTGCGATTATTTCGTTGCGATTTTC
Found at i:576759 original size:19 final size:19
Alignment explanation
Indices: 576735--577050 Score: 333
Period size: 19 Copynumber: 18.4 Consensus size: 19
576725 GATTATCTCG
576735 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
576754 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
576773 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
576787 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
576806 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
576820 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
576834 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
576853 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
576867 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
576886 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
576905 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
576919 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
576938 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
576957 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
576976 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
576990 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
577010 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
577024 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
577043 TTGCGATT
1 TTGCGATT
577051 GTATTTTCCG
Statistics
Matches: 258, Mismatches: 8, Indels: 62
0.79 0.02 0.19
Matches are distributed among these distances:
14 55 0.21
16 40 0.16
17 36 0.14
18 3 0.01
19 112 0.43
20 12 0.05
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:576775 original size:52 final size:51
Alignment explanation
Indices: 576713--577022 Score: 352
Period size: 52 Copynumber: 6.0 Consensus size: 51
576703 TGCGTTTATA
*
576713 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCG-ATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
576765 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCG-ATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
576815 -TTTCG-TTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
576862 -TTTCG-TTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGATTCTGTC
1 ATTTCGATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATT-T-TC
* * * * *
576918 GTTGCGATTTTC-ATT-TCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGA-TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
576968 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCG-ATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
577021 AT
1 AT
577023 GTTGGGATTT
Statistics
Matches: 228, Mismatches: 14, Indels: 31
0.84 0.05 0.11
Matches are distributed among these distances:
47 53 0.23
49 8 0.04
50 17 0.07
51 5 0.02
52 113 0.50
53 17 0.07
54 2 0.01
55 1 0.00
56 4 0.02
57 4 0.02
58 1 0.00
59 3 0.01
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (51 bp):
ATTTCGATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:576792 original size:14 final size:14
Alignment explanation
Indices: 576773--576874 Score: 114
Period size: 14 Copynumber: 6.6 Consensus size: 14
576763 TCATTTCGCA
576773 TTGCGATTCTTTCG
1 TTGCGATTCTTTCG
576787 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TTTCG
576804 CATTGCGATTCTTTCG
1 --TTGCGATTCTTTCG
576820 TTGCGATTCTTTCG
1 TTGCGATTCTTTCG
576834 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TTTCG
576851 CATTGCGATTCTTTCG
1 --TTGCGATTCTTTCG
576867 TTGCGATT
1 TTGCGATT
576875 TTCATTTCGC
Statistics
Matches: 78, Mismatches: 0, Indels: 20
0.80 0.00 0.20
Matches are distributed among these distances:
14 34 0.44
16 16 0.21
17 16 0.21
19 12 0.15
ACGTcount: A:0.11, C:0.21, G:0.20, T:0.49
Consensus pattern (14 bp):
TTGCGATTCTTTCG
Found at i:576999 original size:33 final size:33
Alignment explanation
Indices: 576754--577050 Score: 303
Period size: 33 Copynumber: 8.8 Consensus size: 33
576744 TCATTTCGCA
576754 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
576787 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
576820 TTGCGA--TTC-TTTCG--TTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG
576851 CATTGCGA--TTC-TTTCG--TTGCGATTTTCATTTCG
1 --TTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG
* *
576884 CATTGCGATTTTAATTTCGCATTGCGATTCTGTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
576919 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG
*
576955 CATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
576990 TTGCGATTTTCATTTCCGCATTGCGA-T-TTTCATG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTTTC--G
* *
577024 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
577051 GTATTTTCCG
Statistics
Matches: 237, Mismatches: 8, Indels: 37
0.84 0.03 0.13
Matches are distributed among these distances:
28 6 0.03
30 8 0.03
31 8 0.03
32 3 0.01
33 127 0.54
34 26 0.11
35 13 0.05
36 15 0.06
38 31 0.13
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
Found at i:579350 original size:12 final size:12
Alignment explanation
Indices: 579333--579357 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
579323 TCTTCGGGGA
579333 CTTTTTCTTCTT
1 CTTTTTCTTCTT
579345 CTTTTTCTTCTT
1 CTTTTTCTTCTT
579357 C
1 C
579358 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:579566 original size:24 final size:24
Alignment explanation
Indices: 579532--579578 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
579522 CTGAAACATC
579532 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
579556 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
579579 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:580289 original size:20 final size:20
Alignment explanation
Indices: 580261--580629 Score: 440
Period size: 20 Copynumber: 18.4 Consensus size: 20
580251 AAATTTCAGT
* * * *
580261 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
580281 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
580301 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
580321 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
580341 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
580361 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
580381 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
580401 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
580421 ATTGCGATTTACGAATACGC
1 GTTGCGATTTACGGATACGC
*
580441 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
580461 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
580481 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
580501 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
580521 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
* *
580541 GTTGCGATTTACAGATACAC
1 GTTGCGATTTACGGATACGC
580561 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
580581 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
580601 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
580621 GTTGCGATT
1 GTTGCGATT
580630 ATGGAAAATC
Statistics
Matches: 306, Mismatches: 35, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
19 5 0.02
20 296 0.97
21 5 0.02
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:580710 original size:20 final size:20
Alignment explanation
Indices: 580685--580736 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
580675 AAGAATCGCG
*
580685 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
580705 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
580725 TTGCGATTCTGG
1 TTGCGATTCTGG
580737 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:583475 original size:18 final size:18
Alignment explanation
Indices: 583426--583538 Score: 118
Period size: 18 Copynumber: 5.8 Consensus size: 18
583416 GTTCTTAAGG
583426 AGTGGTCCTTCGGGACATAT
1 AGTGGTCCTTCGGGAC--AT
*
583446 ACAGTTGTCCTTCGGGACAT
1 --AGTGGTCCTTCGGGACAT
583466 AGTGGTCCTTCGGGACGTATAT
1 AGTGGTCCTTCGGGAC----AT
583488 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
583506 AGTGATCCTTCGGGAAAT
1 AGTGGTCCTTCGGGACAT
*
583524 AGTGATCCTTCGGGA
1 AGTGGTCCTTCGGGA
583539 TAAATATTCA
Statistics
Matches: 83, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
18 48 0.58
20 2 0.02
22 33 0.40
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:583481 original size:40 final size:40
Alignment explanation
Indices: 583426--583520 Score: 154
Period size: 40 Copynumber: 2.4 Consensus size: 40
583416 GTTCTTAAGG
*
583426 AGTGGTCCTTCGGGACATATACAGTTGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACATATACAGTGGTCCTTCGGGACAT
* *
583466 AGTGGTCCTTCGGGACGTATATAGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACATATACAGTGGTCCTTCGGGACAT
*
583506 AGTGATCCTTCGGGA
1 AGTGGTCCTTCGGGA
583521 AATAGTGATC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.19, C:0.21, G:0.31, T:0.29
Consensus pattern (40 bp):
AGTGGTCCTTCGGGACATATACAGTGGTCCTTCGGGACAT
Found at i:584265 original size:20 final size:20
Alignment explanation
Indices: 584240--584288 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
584230 TGAAAGCTTA
584240 TATTTTTACGAGTTTATACG
1 TATTTTTACGAGTTTATACG
*
584260 TATTTTTATGAGTTTATACG
1 TATTTTTACGAGTTTATACG
584280 TATTTTTAC
1 TATTTTTAC
584289 TAAAGTTACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.08, G:0.12, T:0.55
Consensus pattern (20 bp):
TATTTTTACGAGTTTATACG
Found at i:584322 original size:21 final size:21
Alignment explanation
Indices: 584296--584335 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
584286 TACTAAAGTT
584296 ACTGTAGCAGTGCATCGATGC
1 ACTGTAGCAGTGCATCGATGC
*
584317 ACTGTAGGAGTGCATCGAT
1 ACTGTAGCAGTGCATCGAT
584336 ACACAATTTA
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:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (21 bp):
ACTGTAGCAGTGCATCGATGC
Found at i:585126 original size:18 final size:19
Alignment explanation
Indices: 585111--585166 Score: 58
Period size: 23 Copynumber: 2.7 Consensus size: 19
585101 ATATAATTTT
585111 TTTTAAAAAAATAATTTAA
1 TTTTAAAAAAATAATTTAA
*
585130 TTTTAAAAATATTAAAATTTTAA
1 TTTTAAAAA-A--ATAA-TTTAA
*
585153 TTTTAAAAATATAA
1 TTTTAAAAAAATAA
585167 AAAATGAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
19 9 0.30
20 4 0.13
22 3 0.10
23 14 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTTTAAAAAAATAATTTAA
Found at i:585151 original size:23 final size:23
Alignment explanation
Indices: 585125--585169 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
585115 AAAAAAATAA
*
585125 TTTAATTTTAAAAATATTAAAAT
1 TTTAATTTTAAAAATATAAAAAT
585148 TTTAATTTTAAAAATATAAAAA
1 TTTAATTTTAAAAATATAAAAA
585170 ATGAGAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TTTAATTTTAAAAATATAAAAAT
Found at i:586177 original size:18 final size:19
Alignment explanation
Indices: 586154--586189 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
586144 CAGAGGTCAG
586154 GATTCAACAAT-ACAATGT
1 GATTCAACAATGACAATGT
*
586172 GATTCATCAATGACAATG
1 GATTCAACAATGACAATG
586190 CTATTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (19 bp):
GATTCAACAATGACAATGT
Found at i:590609 original size:31 final size:31
Alignment explanation
Indices: 590571--590649 Score: 151
Period size: 30 Copynumber: 2.6 Consensus size: 31
590561 TCATTTGATT
590571 TTTACCCTTAAATTAATAAAAAAAAATATTA
1 TTTACCCTTAAATTAATAAAAAAAAATATTA
590602 TTTACCCTTAAATTAAT-AAAAAAAATATTA
1 TTTACCCTTAAATTAATAAAAAAAAATATTA
590632 TTTACCCTTAAATTAATA
1 TTTACCCTTAAATTAATA
590650 TTTAAGTTAC
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
30 30 0.64
31 17 0.36
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (31 bp):
TTTACCCTTAAATTAATAAAAAAAAATATTA
Found at i:594045 original size:21 final size:21
Alignment explanation
Indices: 594015--594059 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
594005 AAGTAAATAT
594015 ATATATATTT-TT-TTTTATAA
1 ATATATATTTATTATTTTA-AA
594035 ATATGATATTTATTATTTTAAA
1 ATAT-ATATTTATTATTTTAAA
594057 ATA
1 ATA
594060 CCAGAATATG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.18
21 6 0.27
22 7 0.32
23 5 0.23
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
ATATATATTTATTATTTTAAA
Found at i:594239 original size:22 final size:22
Alignment explanation
Indices: 594212--594262 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
594202 ATAAATAGAA
* *
594212 TAAAATTGCATTAAATAATGAC
1 TAAAATAGCATTAAACAATGAC
594234 TAAAATAGCATTAAACAATGAC
1 TAAAATAGCATTAAACAATGAC
594256 TAAAATA
1 TAAAATA
594263 AAAGGAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (22 bp):
TAAAATAGCATTAAACAATGAC
Found at i:596100 original size:123 final size:121
Alignment explanation
Indices: 595943--596798 Score: 536
Period size: 112 Copynumber: 7.3 Consensus size: 121
595933 TGAGTCGAGT
* * ** * * *
595943 AAAAGGCTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTATACAGATGAGTTCTTCTTATT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
596008 ATGAACTCTTTCTGGAAATATTGATGTTGATTTATCTCATTCTGTGATAGAATTGATC
66 ATGAACTCTTTCTGGAAA-ATTGATGTTGA-TTATCTCATTCTGTGATAGAATTGATC
* * * * * *
596066 AAAAGGTTGAACAAATTCTTCTCATTATGTACTTCTTTTTCCTCTTCAGATAAGTTTTTCTTATT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
* * * *
596131 ATGAACT-TCTTCTGGAAAAGTTGATGCTGATATATCTCTTTCTGTGATAG-AGTCATGC
66 ATGAACTCT-TTCTGGAAAA-TTGATGTTGAT-TATCTCATTCTGTGATAGAATTGAT-C
*
596189 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC--CTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
** * * *
596252 ATGAACTCTACCTGG--CA---ATGTTG---ATC-CA-TCGAGTGAT-GAATTCGAGC
66 ATGAACTCTTTCTGGAAAATTGATGTTGATTATCTCATTC-TGTGATAGAATT-GATC
*
596299 GAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
** * * * * *
596364 ATGAACTCTACCTGG-----TAATGTTG---ATC-CA-TCAAGTGAT-GTATTCAAGC
66 ATGAACTCTTTCTGGAAAATTGATGTTGATTATCTCATTC-TGTGATAGAATT-GATC
* * * *
596411 GAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTCATTATGAATTTTTCTTCATCTACATATG
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAAC-T-TC-----------TTCTTCCTCTTCAGATG
* * * *
596476 AGTTCTTCTCATTATGAACTC-ATCTGG----GTAATGTTG---ATC-CA-TCAAGTGAT-GAAT
53 AGTTCTTCTCATTATGAACTCTTTCTGGAAAATTGATGTTGATTATCTCATTC-TGTGATAGAAT
*
596530 TCGAGC
117 T-GATC
* * * *
596536 GAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTCTTTAGATGAGTTATTCTCATT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
** * *
596601 ATGAACTCTACCTGG-----TGATGTTG---ATC-CA-TCAAGTGAT-GAATTCGAGC
66 ATGAACTCTTTCTGGAAAATTGATGTTGATTATCTCATTC-TGTGATAGAATT-GATC
* * *
596648 GAAAGGTTGAACAAGTTCTTATCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-CTCTTCAGATGAGTTCTTCTCAT
* *
596713 TATGAACTCTTT-TGG--AA---ATGTTG---ATC-CA-TCAAGTGAT-GAATTCGAGC
65 TATGAACTCTTTCTGGAAAATTGATGTTGATTATCTCATTC-TGTGATAGAATT-GATC
*
596760 GAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT
596799 CCTTATGTTG
Statistics
Matches: 645, Mismatches: 58, Indels: 71
0.83 0.07 0.09
Matches are distributed among these distances:
109 3 0.00
110 46 0.07
111 4 0.01
112 271 0.42
113 36 0.06
114 2 0.00
115 5 0.01
119 1 0.00
121 32 0.05
122 8 0.01
123 134 0.21
124 6 0.01
125 97 0.15
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (121 bp):
AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
ATGAACTCTTTCTGGAAAATTGATGTTGATTATCTCATTCTGTGATAGAATTGATC
Found at i:596384 original size:112 final size:110
Alignment explanation
Indices: 596190--596797 Score: 620
Period size: 112 Copynumber: 5.3 Consensus size: 110
596180 GAGTCATGCA
*
596190 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATG
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCCCTCTTCAGATGAGTTCTTCTCATTATG
* *
596255 AACTCTACCTGGCAATGTTGATCCATCGAGTGATGAATTCGAGCG
66 AACTCTACCTGGCAATGTTGATCCATCAAGTGATGAATTCAAGCG
596300 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTA
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC--CCTCTTCAGATGAGTTCTTCTCATTA
* *
596365 TGAACTCTACCTGGTAATGTTGATCCATCAAGTGATGTATTCAAGCG
64 TGAACTCTACCTGGCAATGTTGATCCATCAAGTGATGAATTCAAGCG
* * ** *
596412 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTC-T-CAT-TATGA-AT-TTTTCTTCATCTACA
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCCCTCT-TCAGATGAGTTCTTC-TC-A-T
** * * * ** * *
596472 TATGAGTTCTTCTCATTATG-AACTCATCTGGGTAATGTTGATCCA-TCAAGTGATGAATTCGAG
62 TATGAACTCTAC-C--T-GGCAA-T-GT-T--G--A--TCCATCAAGT---G--ATGAATTCAAG
596535 CG
109 CG
* * *
596537 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTCTTTAGATGAGTTATTCTCATTA
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC--CCTCTTCAGATGAGTTCTTCTCATTA
** *
596602 TGAACTCTACCTGGTGATGTTGATCCATCAAGTGATGAATTCGAGCG
64 TGAACTCTACCTGGCAATGTTGATCCATCAAGTGATGAATTCAAGCG
* *
596649 AAAGGTTGAACAAGTTCTTATCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC--C-CTCTTCAGATGAGTTCTTCTCATT
** * *
596714 ATGAACTCT-TTTGGAAATGTTGATCCATCAAGTGATGAATTCGAGCG
63 ATGAACTCTACCTGGCAATGTTGATCCATCAAGTGATGAATTCAAGCG
596761 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC
596798 TCCTTATGTT
Statistics
Matches: 418, Mismatches: 46, Indels: 66
0.79 0.09 0.12
Matches are distributed among these distances:
106 6 0.01
107 5 0.01
108 5 0.01
109 9 0.02
110 38 0.09
111 1 0.00
112 226 0.54
113 32 0.08
114 2 0.00
115 1 0.00
116 5 0.01
117 2 0.00
118 1 0.00
119 1 0.00
120 2 0.00
121 5 0.01
122 1 0.00
123 2 0.00
124 2 0.00
125 47 0.11
126 1 0.00
127 1 0.00
128 9 0.02
129 4 0.01
130 5 0.01
131 5 0.01
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.38
Consensus pattern (110 bp):
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCCCTCTTCAGATGAGTTCTTCTCATTATG
AACTCTACCTGGCAATGTTGATCCATCAAGTGATGAATTCAAGCG
Found at i:596447 original size:14 final size:14
Alignment explanation
Indices: 596428--596455 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
596418 TGAACAAGTT
596428 CTTCTCATTATGAA
1 CTTCTCATTATGAA
596442 CTTCTCATTATGAA
1 CTTCTCATTATGAA
596456 TTTTTCTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (14 bp):
CTTCTCATTATGAA
Found at i:596538 original size:237 final size:234
Alignment explanation
Indices: 596206--596798 Score: 902
Period size: 237 Copynumber: 2.6 Consensus size: 234
596196 TGAACAAGTT
* * *
596206 CTTCTCATTATGAACTTCTTCCTTCT-TCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAA
1 CTTCTCATTATGAA-TT-TTTCTTCTCTCAGATGAGTTCTTCTCATTATGAACTC-ATCTGGAAA
*
596270 TGTTGATCCATCGAGTGATGAATTCGAGCGAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCT
63 TGTTGATCCATCAAGTGATGAATTCGAGCGAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCT
*
596335 TCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGTAATGTTGATCCATCAAGTGA
128 TCTTCCTCTTCAGATGAGTTATTCTCATTATGAACTCTACCTGGTAATGTTGATCCATCAAGTGA
* *
596400 TGTATTCAAGCGAAAGGTTGAACAAGTTCTTCTCATTATGAA
193 TGAATTCAAGCGAAAGGTTGAACAAGTTCTTATCATTATGAA
* *
596442 CTTCTCATTATGAATTTTTCTTCATCTACATATGAGTTCTTCTCATTATGAACTCATCTGGGTAA
1 CTTCTCATTATGAATTTTTCTTC-TCT-CAGATGAGTTCTTCTCATTATGAACTCATCT-GGAAA
596507 TGTTGATCCATCAAGTGATGAATTCGAGCGAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCT
63 TGTTGATCCATCAAGTGATGAATTCGAGCGAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCT
* * *
596572 TCTTTCTCTTTAGATGAGTTATTCTCATTATGAACTCTACCTGGTGATGTTGATCCATCAAGTGA
128 TCTTCCTCTTCAGATGAGTTATTCTCATTATGAACTCTACCTGGTAATGTTGATCCATCAAGTGA
*
596637 TGAATTCGAGCGAAAGGTTGAACAAGTTCTTATCATTATGAA
193 TGAATTCAAGCGAAAGGTTGAACAAGTTCTTATCATTATGAA
* * * *
596679 C-T-TC--T-T---CTTCT-TTCT-TCAGATGAGTTCTTCTCATTATGAACTCTTTTGGAAATGT
1 CTTCTCATTATGAATTTTTCTTCTCTCAGATGAGTTCTTCTCATTATGAACTCATCTGGAAATGT
596734 TGATCCATCAAGTGATGAATTCGAGCGAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT
66 TGATCCATCAAGTGATGAATTCGAGCGAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT
596799 CCTTATGTTG
Statistics
Matches: 335, Mismatches: 18, Indels: 20
0.90 0.05 0.05
Matches are distributed among these distances:
224 72 0.21
225 28 0.08
226 1 0.00
227 1 0.00
228 3 0.01
229 3 0.01
232 1 0.00
233 1 0.00
234 6 0.02
235 5 0.01
236 19 0.06
237 195 0.58
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (234 bp):
CTTCTCATTATGAATTTTTCTTCTCTCAGATGAGTTCTTCTCATTATGAACTCATCTGGAAATGT
TGATCCATCAAGTGATGAATTCGAGCGAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT
TCCTCTTCAGATGAGTTATTCTCATTATGAACTCTACCTGGTAATGTTGATCCATCAAGTGATGA
ATTCAAGCGAAAGGTTGAACAAGTTCTTATCATTATGAA
Found at i:597145 original size:75 final size:74
Alignment explanation
Indices: 596987--597151 Score: 240
Period size: 75 Copynumber: 2.2 Consensus size: 74
596977 CATCTTGCAC
* * * *
596987 TGTAGGTCTTATAAATTACCCGGAGGCTTTAAATATCAAAAAGCTCCCAAAGACTTCTTGAAAAC
1 TGTAGGTCTTATAGATAACCCGGAGGCTTTAAATATAAAAAAACTCCCAAAGACTTCTTGAAAAC
* *
597052 ATCATGCAC
66 ATCAGGCAA
* * *
597061 TGTAGGTCTTACAGATAACCCGGAGGCTTTAAATATAAAAAAAACTCCCGAAGGCTTCTTGAAAA
1 TGTAGGTCTTATAGATAACCCGGAGGCTTTAAATAT-AAAAAAACTCCCAAAGACTTCTTGAAAA
597126 CATCAGGCAA
65 CATCAGGCAA
597136 TGTAGGTCTTATAGAT
1 TGTAGGTCTTATAGAT
597152 GTGGGAAATA
Statistics
Matches: 80, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
74 33 0.41
75 47 0.59
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (74 bp):
TGTAGGTCTTATAGATAACCCGGAGGCTTTAAATATAAAAAAACTCCCAAAGACTTCTTGAAAAC
ATCAGGCAA
Found at i:597839 original size:22 final size:22
Alignment explanation
Indices: 597811--597861 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
597801 TAAAGCTTTC
597811 ATCTTTGCAAAGAGAATCTATT
1 ATCTTTGCAAAGAGAATCTATT
597833 ATCTTTGCAAAGAGAATCTATT
1 ATCTTTGCAAAGAGAATCTATT
597855 ATCTTTG
1 ATCTTTG
597862 AAGAATGTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (22 bp):
ATCTTTGCAAAGAGAATCTATT
Found at i:598336 original size:54 final size:54
Alignment explanation
Indices: 598233--598336 Score: 136
Period size: 54 Copynumber: 1.9 Consensus size: 54
598223 TAATTGGTTT
* * * * *
598233 GTAAAATATTTGACAACACATTCATCATTTCCTGTAGTTTCTGCTCAGATGTTC
1 GTAAAACATTTGACAACACATTCATCATTTCATGTAGCTTCTACACAGATGTTC
** *
598287 GTAAAACATTTGACAACGTATTCATCATTTCATGTGGCTTCTACACAGAT
1 GTAAAACATTTGACAACACATTCATCATTTCATGTAGCTTCTACACAGAT
598337 TTCTGGTCAG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 42 1.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (54 bp):
GTAAAACATTTGACAACACATTCATCATTTCATGTAGCTTCTACACAGATGTTC
Found at i:600441 original size:53 final size:54
Alignment explanation
Indices: 600361--600468 Score: 209
Period size: 54 Copynumber: 2.0 Consensus size: 54
600351 ACAAGAAAAG
600361 GCGAAACTCGGGCTATGATTTTTTT-AAAAAAAAAGAAGAAGCAGAGGAAGCTT
1 GCGAAACTCGGGCTATGATTTTTTTAAAAAAAAAAGAAGAAGCAGAGGAAGCTT
600414 GCGAAACTCGGGCTATGATTTTTTTAAAAAAAAAAGAAGAAGCAGAGGAAGCTT
1 GCGAAACTCGGGCTATGATTTTTTTAAAAAAAAAAGAAGAAGCAGAGGAAGCTT
600468 G
1 G
600469 AAAAGAAGCT
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
53 25 0.46
54 29 0.54
ACGTcount: A:0.42, C:0.11, G:0.25, T:0.22
Consensus pattern (54 bp):
GCGAAACTCGGGCTATGATTTTTTTAAAAAAAAAAGAAGAAGCAGAGGAAGCTT
Found at i:605892 original size:36 final size:36
Alignment explanation
Indices: 605832--605903 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
605822 TTTTGCCGTA
* * *
605832 GAATGCTTTTGGTATCAATCTAACAGTATCTTTGTG
1 GAATACTTTTGGTATCAATATAACAGGATCTTTGTG
*
605868 GAATACTTTTGGTATTAATATAACAGGATCTTTGTG
1 GAATACTTTTGGTATCAATATAACAGGATCTTTGTG
605904 TGTATAGCTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (36 bp):
GAATACTTTTGGTATCAATATAACAGGATCTTTGTG
Found at i:606756 original size:25 final size:26
Alignment explanation
Indices: 606728--606779 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
606718 AAATAACTTA
*
606728 ATACTTAAAAATATTA-AAAAATAAT
1 ATACATAAAAATATTATAAAAATAAT
* *
606753 ATACATATAAATATTATGAAAATAAT
1 ATACATAAAAATATTATAAAAATAAT
606779 A
1 A
606780 AATATATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.33
Consensus pattern (26 bp):
ATACATAAAAATATTATAAAAATAAT
Found at i:606774 original size:28 final size:29
Alignment explanation
Indices: 606743--606829 Score: 76
Period size: 28 Copynumber: 3.1 Consensus size: 29
606733 TAAAAATATT
*
606743 AAAA-AATAATATACATATAAATATTATG
1 AAAAGAATAATATAAATATAAATATTATG
* * *
606771 AAAATAATAA-ATATATATAAAAAATT-TG
1 AAAAGAATAATATAAATAT-AAATATTATG
606799 AAAAGAATGAATTATAAAT-TAAATA-TATG
1 AAAAGAAT-AA-TATAAATATAAATATTATG
606828 AA
1 AA
606830 TTTTTAATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
28 21 0.44
29 21 0.44
30 1 0.02
31 5 0.10
ACGTcount: A:0.62, C:0.01, G:0.06, T:0.31
Consensus pattern (29 bp):
AAAAGAATAATATAAATATAAATATTATG
Found at i:606786 original size:26 final size:25
Alignment explanation
Indices: 606736--606787 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
606726 TAATACTTAA
*
606736 AAATATTAAAAAATAATATACATAT
1 AAATATTAAAAAATAATAAACATAT
* *
606761 AAATATTATGAAAATAATAAATATAT
1 AAATATTA-AAAAATAATAAACATAT
606787 A
1 A
606788 TAAAAAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (25 bp):
AAATATTAAAAAATAATAAACATAT
Found at i:606829 original size:29 final size:28
Alignment explanation
Indices: 606732--606829 Score: 74
Period size: 29 Copynumber: 3.5 Consensus size: 28
606722 AACTTAATAC
* * *
606732 TTAAAAATATTAAAA-AAT-AATATACA
1 TTAAATATATGAAAAGAATAAATATAAA
* *
606758 TATAAATATTATGAAAATAATAAATATATA
1 T-TAAATA-TATGAAAAGAATAAATATAAA
* * * *
606788 TAAAAAATTTGAAAAGAATGAATTATAAA
1 TTAAATATATGAAAAGAAT-AAATATAAA
606817 TTAAATATATGAA
1 TTAAATATATGAA
606830 TTTTTAATTT
Statistics
Matches: 55, Mismatches: 12, Indels: 7
0.74 0.16 0.09
Matches are distributed among these distances:
26 1 0.02
27 5 0.09
28 17 0.31
29 24 0.44
30 8 0.15
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.33
Consensus pattern (28 bp):
TTAAATATATGAAAAGAATAAATATAAA
Found at i:607337 original size:23 final size:23
Alignment explanation
Indices: 607292--607338 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
607282 TAATTTTAAG
* *
607292 AAAATATTTATATTTTTATAAAT
1 AAAATATTTATATTCTTAGAAAT
607315 AAAATATTTAT-TTACTTAGAAAT
1 AAAATATTTATATT-CTTAGAAAT
607338 A
1 A
607339 TCAGAAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 2 0.10
23 19 0.90
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
AAAATATTTATATTCTTAGAAAT
Found at i:607625 original size:146 final size:144
Alignment explanation
Indices: 607293--607690 Score: 371
Period size: 146 Copynumber: 2.8 Consensus size: 144
607283 AATTTTAAGA
* ** * * *
607293 AAATATTTATA-TTTTTATAAATAAAATATTTATTTACTT-AGAAATATCAGAAAATGACTTCTC
1 AAATATATATATTTTTTATAAATATGATATTTATTTATTTAAG-AATATCAGAAAAGGACTTCTA
* * *
607356 GGTGCTTTAAGACAACCCATTTCTTAATATTAAAAAATAAATAAATATTAATAAAACATTTCTCT
65 GGTGCTTTAAGACAACCCATTTCTTAATATTAAAAAATAAATAAATATGAATAAAACAATTCTAT
*
607421 AAAAATAATTAAAAT
130 AAAAATAATTAAAAC
** * * *
607436 AAAT-TAATATATAATTTATAAAAATAGAATATTTATTTATTTAAGAATATCATAAAAGGATTTC
1 AAATAT-ATATATTTTTTATAAATAT-G-ATATTTATTTATTTAAGAATATCAGAAAAGGACTTC
* * *
607500 TAGGTGCTTTAAGACAACCCTTTTCTTAATATTAAAAAATACATATTAAAATATGATTAAAATAA
63 TAGGTGCTTTAAGACAACCCATTTCTTAATATTAAAAAATA-A-A-T-AAATATGAATAAAACAA
* *
607565 TT-TAT-ATAA-AATTAAAGC
124 TTCTATAAAAATAATTAAAAC
* * * * *
607583 AAATATATATATTTTTTATAAATATGATATTTATTATTTTTAA-AATACCAGAATATGACATCTA
1 AAATATATATATTTTTTATAAATATGATATTTATT-TATTTAAGAATATCAGAAAAGGACTTCTA
* ** *** *
607647 GTTATTTTAAGACTGTCC-TTTCTTAATATTTAAAAATAAATAAA
65 GGTGCTTTAAGACAACCCATTTCTTAATATTAAAAAATAAATAAA
607691 GATTATTATT
Statistics
Matches: 207, Mismatches: 37, Indels: 25
0.77 0.14 0.09
Matches are distributed among these distances:
140 3 0.01
141 1 0.00
142 2 0.01
143 9 0.04
144 28 0.14
145 36 0.17
146 75 0.36
147 30 0.14
148 5 0.02
149 3 0.01
150 15 0.07
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.40
Consensus pattern (144 bp):
AAATATATATATTTTTTATAAATATGATATTTATTTATTTAAGAATATCAGAAAAGGACTTCTAG
GTGCTTTAAGACAACCCATTTCTTAATATTAAAAAATAAATAAATATGAATAAAACAATTCTATA
AAAATAATTAAAAC
Found at i:607809 original size:22 final size:22
Alignment explanation
Indices: 607782--607832 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
607772 ATAAATAGAA
*
607782 TAAAATTGCATTAAATAATGAC
1 TAAAATAGCATTAAATAATGAC
607804 TAAAATAGCATTAAATAATGAC
1 TAAAATAGCATTAAATAATGAC
607826 TAAAATA
1 TAAAATA
607833 AAAGGAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.29
Consensus pattern (22 bp):
TAAAATAGCATTAAATAATGAC
Found at i:608567 original size:23 final size:22
Alignment explanation
Indices: 608535--608583 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
608525 CCAAAACTAA
* *
608535 AAAATTAAAATATCCTAATATATT
1 AAAATTAAAAAAACCTAA-A-ATT
608559 AAAA-TAAAAAAACCTAAAATT
1 AAAATTAAAAAAACCTAAAATT
608580 AAAA
1 AAAA
608584 CCTAAAAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 7 0.30
22 1 0.04
23 11 0.48
24 4 0.17
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (22 bp):
AAAATTAAAAAAACCTAAAATT
Found at i:611266 original size:24 final size:23
Alignment explanation
Indices: 611237--611281 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
611227 TGAAAGATTT
611237 AATCGAAAATAAACTTGAAAATCA
1 AATCGAAAATAAACTT-AAAATCA
*
611261 AATCGAAAATAATCTTAAAAT
1 AATCGAAAATAAACTTAAAAT
611282 TTCTTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.58, C:0.11, G:0.07, T:0.24
Consensus pattern (23 bp):
AATCGAAAATAAACTTAAAATCA
Found at i:618079 original size:59 final size:58
Alignment explanation
Indices: 618006--618152 Score: 165
Period size: 59 Copynumber: 2.5 Consensus size: 58
617996 AAATTTAGCA
* *
618006 ACTAATTTAGAATGAAGATCATATTTGGGGATGAAATTAAAA-TGTTCAAAAGTTTGA-TG
1 ACTAATTTAGAATGAAGATCATATTTGAGGATGAAATTAAAACT-TT-AAAAG-TTGAGGG
*
618065 ACTAATTTAGAATGATA-ATCATAATTTAAGGATGAAATTAAAACTTTAAAAGTTGAGGG
1 ACTAATTTAGAATGA-AGATCAT-ATTTGAGGATGAAATTAAAACTTTAAAAGTTGAGGG
* * *
618124 ACTAATTTAAAAAGAGGATCATACTTTGA
1 ACTAATTTAGAATGAAGATCATA-TTTGA
618153 TGATATGTGA
Statistics
Matches: 75, Mismatches: 7, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
58 5 0.07
59 48 0.64
60 21 0.28
61 1 0.01
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.33
Consensus pattern (58 bp):
ACTAATTTAGAATGAAGATCATATTTGAGGATGAAATTAAAACTTTAAAAGTTGAGGG
Found at i:620997 original size:20 final size:20
Alignment explanation
Indices: 620972--621125 Score: 114
Period size: 20 Copynumber: 7.6 Consensus size: 20
620962 AATGACCAAT
620972 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
**
620992 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
621012 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
621033 AAGTTCGCAACGCGATTTAGG
1 AAAATCGCAACGCGATTTA-G
* * * *
621054 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * * *
621074 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
*
621094 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
621114 AAAATCGCAACG
1 AAAATCGCAACG
621126 TTGAAAATAA
Statistics
Matches: 106, Mismatches: 22, Indels: 12
0.76 0.16 0.09
Matches are distributed among these distances:
18 1 0.01
19 1 0.01
20 77 0.73
21 27 0.25
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:621152 original size:20 final size:20
Alignment explanation
Indices: 621114--621152 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
621104 CGCGATTTAG
* *
621114 AAAATCGCAACGTTGAAAAT
1 AAAATCGCAACGGTCAAAAT
621134 AAAATCGCAACGGTCAAAA
1 AAAATCGCAACGGTCAAAA
621153 GAATAGTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.18, G:0.15, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACGGTCAAAAT
Found at i:621244 original size:6 final size:6
Alignment explanation
Indices: 621233--621335 Score: 206
Period size: 6 Copynumber: 17.2 Consensus size: 6
621223 GACACGTATT
621233 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
621281 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
621329 ACCACG A
1 ACCACG A
621336 GACGAGACGG
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 97 1.00
ACGTcount: A:0.34, C:0.50, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:622041 original size:6 final size:6
Alignment explanation
Indices: 622030--622152 Score: 246
Period size: 6 Copynumber: 20.5 Consensus size: 6
622020 TCTCGTCTCG
622030 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
622078 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
622126 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
622153 AATACGTGTC
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 117 1.00
ACGTcount: A:0.00, C:0.16, G:0.50, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:622285 original size:20 final size:20
Alignment explanation
Indices: 622262--622412 Score: 140
Period size: 20 Copynumber: 7.4 Consensus size: 20
622252 ATTTTCAACG
* *
622262 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTCAATCGCA
* *
622282 TTGCGATTCTCTCAGTCGCG
1 TTGCGATTCTCTCAATCGCA
* * *
622302 TTGTGATTTTCTTCTAAATCGCG
1 TTGCGA--TTC-TCTCAATCGCA
* * *
622325 TTGCGACTCTCTCAAACGCG
1 TTGCGATTCTCTCAATCGCA
* *
622345 CTGCGACTCTCTCAATCGCA
1 TTGCGATTCTCTCAATCGCA
* *
622365 TTGCGATTATATCAATCGCA
1 TTGCGATTCTCTCAATCGCA
*
622385 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTCTCAATCGCA
622405 TTGCGATT
1 TTGCGATT
622413 TTCTTCTAAA
Statistics
Matches: 109, Mismatches: 19, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
20 90 0.83
21 2 0.02
22 3 0.03
23 14 0.13
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.35
Consensus pattern (20 bp):
TTGCGATTCTCTCAATCGCA
Found at i:622304 original size:40 final size:40
Alignment explanation
Indices: 622260--622433 Score: 159
Period size: 40 Copynumber: 4.2 Consensus size: 40
622250 TTATTTTCAA
*
622260 CGTTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCG
1 CGTTGCGATTCTATAAATCGCATTGCGATTCTCTCAATCG
* * * * *
622300 CGTTGTGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAAACG
1 CGTTGCGA--TTC-TATAAATCGCATTGCGATTCTCTCAATCG
* * * * * *
622343 CGCTGCGACTCTCTCAATCGCATTGCGATTATATCAATCG
1 CGTTGCGATTCTATAAATCGCATTGCGATTCTCTCAATCG
* * *
622383 CATTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCG
1 CGTTGCGATTCTATAAATCGCATTGCGA--TTC-TCTCAATCG
622426 CGTTGCGA
1 CGTTGCGA
622434 ACTTGGAAGC
Statistics
Matches: 105, Mismatches: 23, Indels: 9
0.77 0.17 0.07
Matches are distributed among these distances:
40 54 0.51
41 2 0.02
42 5 0.05
43 44 0.42
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.35
Consensus pattern (40 bp):
CGTTGCGATTCTATAAATCGCATTGCGATTCTCTCAATCG
Found at i:622474 original size:20 final size:20
Alignment explanation
Indices: 622449--622500 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
622439 GAAGCTCGCA
*
622449 TTGCGATTTTCTTTTGACCG
1 TTGCGATTTTCTTTTGAACG
*
622469 TTGCGATTTTCTTTTTAACG
1 TTGCGATTTTCTTTTGAACG
622489 TTGCGATTTTCT
1 TTGCGATTTTCT
622501 AAATCGCGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.12, C:0.17, G:0.17, T:0.54
Consensus pattern (20 bp):
TTGCGATTTTCTTTTGAACG
Found at i:622683 original size:22 final size:22
Alignment explanation
Indices: 622649--622691 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
622639 GATCCATTCT
*
622649 AATATTAACAATTTTAACTATA
1 AATATTAACAATTTAAACTATA
* *
622671 AATATTTATAATTTAAACTAT
1 AATATTAACAATTTAAACTAT
622692 TCCTTAAACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (22 bp):
AATATTAACAATTTAAACTATA
Found at i:627904 original size:33 final size:33
Alignment explanation
Indices: 627866--627969 Score: 87
Period size: 33 Copynumber: 3.4 Consensus size: 33
627856 TTAGCGAAGC
627866 CGAAAGAAACCCGAACCAAATTTTAATCCGATT
1 CGAAAGAAACCCGAACCAAATTTTAATCCGATT
* * **
627899 CGAAAGCAACCCAAACTGAA-TTTAA--C----
1 CGAAAGAAACCCGAACCAAATTTTAATCCGATT
* **
627925 CGAATGAAATTCGAACCAAATTTTAATCCGATT
1 CGAAAGAAACCCGAACCAAATTTTAATCCGATT
*
627958 CGAAAGCAACCC
1 CGAAAGAAACCC
627970 AAACTGAATT
Statistics
Matches: 49, Mismatches: 15, Indels: 14
0.63 0.19 0.18
Matches are distributed among these distances:
26 13 0.27
27 5 0.10
29 1 0.02
30 1 0.02
32 5 0.10
33 24 0.49
ACGTcount: A:0.42, C:0.25, G:0.12, T:0.20
Consensus pattern (33 bp):
CGAAAGAAACCCGAACCAAATTTTAATCCGATT
Found at i:627982 original size:32 final size:32
Alignment explanation
Indices: 627887--627987 Score: 108
Period size: 32 Copynumber: 3.3 Consensus size: 32
627877 CGAACCAAAT
627887 TTTAATCCGATTCGAAAGCAACCCAAACTGAA
1 TTTAATCCGATTCGAAAGCAACCCAAACTGAA
* *
627919 TTTAA-CCGAAT-GAAATTCGAA-CCAAA-T---
1 TTTAATCCGATTCGAAA-GC-AACCCAAACTGAA
627946 TTTAATCCGATTCGAAAGCAACCCAAACTGAA
1 TTTAATCCGATTCGAAAGCAACCCAAACTGAA
*
627978 TTTAACCCGA
1 TTTAATCCGA
627988 CCCAAATTTA
Statistics
Matches: 55, Mismatches: 5, Indels: 18
0.71 0.06 0.23
Matches are distributed among these distances:
27 7 0.13
28 11 0.20
29 5 0.09
30 5 0.09
31 11 0.20
32 16 0.29
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.24
Consensus pattern (32 bp):
TTTAATCCGATTCGAAAGCAACCCAAACTGAA
Found at i:627995 original size:16 final size:16
Alignment explanation
Indices: 627976--628019 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
627966 ACCCAAACTG
627976 AATTTAACCCGACCCA
1 AATTTAACCCGACCCA
627992 AATTTAACCCGACCCA
1 AATTTAACCCGACCCA
**
628008 AAAGTAACCCGA
1 AATTTAACCCGA
628020 ATAAAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.41, C:0.34, G:0.09, T:0.16
Consensus pattern (16 bp):
AATTTAACCCGACCCA
Found at i:628236 original size:23 final size:23
Alignment explanation
Indices: 628210--628290 Score: 63
Period size: 23 Copynumber: 3.3 Consensus size: 23
628200 CTTGTAATAA
628210 AATATTAGATTTATAATAAAAAT
1 AATATTAGATTTATAATAAAAAT
** * * * *
628233 AATAGAAAATAACTAAAACAAAGGAAAT
1 AATATTAGAT--TTATAATAAA--AA-T
628261 AATATTAGATTTATAATAAAAAT
1 AATATTAGATTTATAATAAAAAT
628284 AATATTA
1 AATATTA
628291 AGTTTATTTA
Statistics
Matches: 41, Mismatches: 12, Indels: 10
0.65 0.19 0.16
Matches are distributed among these distances:
23 15 0.37
24 2 0.05
25 7 0.17
26 7 0.17
27 2 0.05
28 8 0.20
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.31
Consensus pattern (23 bp):
AATATTAGATTTATAATAAAAAT
Found at i:628640 original size:2 final size:2
Alignment explanation
Indices: 628635--628663 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
628625 TCAATAATTT
628635 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 T
628664 GATTAAATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:628771 original size:16 final size:15
Alignment explanation
Indices: 628729--628791 Score: 54
Period size: 16 Copynumber: 4.0 Consensus size: 15
628719 ACTGAAAATC
*
628729 AACCGATCCGATATT
1 AACCGATCCAATATT
* *
628744 GACTCGACCCAATATT
1 AAC-CGATCCAATATT
*
628760 AACCTGATCCAAAATCT
1 AACC-GATCCAATAT-T
*
628777 AACCGATACAATATT
1 AACCGATCCAATATT
628792 GGACCGACCC
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
15 4 0.11
16 28 0.76
17 5 0.14
ACGTcount: A:0.38, C:0.27, G:0.10, T:0.25
Consensus pattern (15 bp):
AACCGATCCAATATT
Found at i:637610 original size:20 final size:20
Alignment explanation
Indices: 637587--637660 Score: 55
Period size: 20 Copynumber: 3.7 Consensus size: 20
637577 TCTACAAGCT
637587 TCTAGAAAGTTCTACACTTC
1 TCTAGAAAGTTCTACACTTC
* *
637607 TCTAG--AGTTCTCCAAAATGT-
1 TCTAGAAAGTTCT--ACACT-TC
*
637627 TCTAGAAATTTCTACACTTC
1 TCTAGAAAGTTCTACACTTC
* *
637647 TCCAGAAAGCTCTA
1 TCTAGAAAGTTCTA
637661 GAAATTTCTA
Statistics
Matches: 40, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
18 6 0.15
19 1 0.03
20 27 0.68
21 1 0.03
22 5 0.12
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.34
Consensus pattern (20 bp):
TCTAGAAAGTTCTACACTTC
Found at i:637648 original size:30 final size:30
Alignment explanation
Indices: 637614--637670 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
637604 TTCTCTAGAG
*
637614 TTCTCCA-AAATGTTCTAGAAATTTCTACAC
1 TTCTCCAGAAA-GCTCTAGAAATTTCTACAC
637644 TTCTCCAGAAAGCTCTAGAAATTTCTA
1 TTCTCCAGAAAGCTCTAGAAATTTCTA
637671 GAACTCTCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 22 0.88
31 3 0.12
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.35
Consensus pattern (30 bp):
TTCTCCAGAAAGCTCTAGAAATTTCTACAC
Found at i:637670 original size:40 final size:40
Alignment explanation
Indices: 637586--637673 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 40
637576 TTCTACAAGC
* ***
637586 TTCTAGAAAGTTCTACACTTCTCTAGAGTTCTCCAAAATG
1 TTCTAGAAAGTTCTACACTTCTCCAGAAAGCTCCAAAATG
* *
637626 TTCTAGAAATTTCTACACTTCTCCAGAAAGCTCTAGAAAT-
1 TTCTAGAAAGTTCTACACTTCTCCAGAAAGCTCCA-AAATG
637666 TTCTAGAA
1 TTCTAGAA
637674 CTCTCCAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
40 37 0.90
41 4 0.10
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.34
Consensus pattern (40 bp):
TTCTAGAAAGTTCTACACTTCTCCAGAAAGCTCCAAAATG
Found at i:646753 original size:12 final size:12
Alignment explanation
Indices: 646732--646762 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
646722 ATTAAATATA
*
646732 TTTATATTTATT
1 TTTATTTTTATT
646744 TTTATTTTTATT
1 TTTATTTTTATT
646756 TTTATTT
1 TTTATTT
646763 AAATATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTATTTTTATT
Found at i:651402 original size:16 final size:16
Alignment explanation
Indices: 651360--651407 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
651350 TTTTTTAGTA
651360 ATTTATTTAATTATTTT
1 ATTTATTTAA-TATTTT
* *
651377 AATTGTTTAATATTTT
1 ATTTATTTAATATTTT
*
651393 ATTTAATTAA-ATTTT
1 ATTTATTTAATATTTT
651408 TTTGCATATA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 5 0.19
16 13 0.50
17 8 0.31
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (16 bp):
ATTTATTTAATATTTT
Found at i:652819 original size:15 final size:15
Alignment explanation
Indices: 652799--652829 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
652789 GCTGCTCAGA
652799 ACGACGACGATGATG
1 ACGACGACGATGATG
652814 ACGACGACGATGATG
1 ACGACGACGATGATG
652829 A
1 A
652830 TGGTGATGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.19, G:0.32, T:0.13
Consensus pattern (15 bp):
ACGACGACGATGATG
Found at i:652985 original size:26 final size:25
Alignment explanation
Indices: 652956--653015 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 25
652946 TTTTTTATAC
* *
652956 TTGTATTTAGTACTTTTTTATTGTAG
1 TTGT-TTTAGGACTTTTTTATTGTAA
*
652982 TTGTTTATTGGACTTTTTTATTGTAA
1 TTGTTT-TAGGACTTTTTTATTGTAA
653008 TTGTTTTA
1 TTGTTTTA
653016 TTAATTATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 3 0.10
26 26 0.90
ACGTcount: A:0.18, C:0.03, G:0.15, T:0.63
Consensus pattern (25 bp):
TTGTTTTAGGACTTTTTTATTGTAA
Found at i:653581 original size:16 final size:16
Alignment explanation
Indices: 653560--653596 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
653550 CTATCACATG
653560 AGAGCATGGATACTTC
1 AGAGCATGGATACTTC
653576 AGAGCATGGATACTTC
1 AGAGCATGGATACTTC
653592 AGAGC
1 AGAGC
653597 TTGAAAAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.32, C:0.19, G:0.27, T:0.22
Consensus pattern (16 bp):
AGAGCATGGATACTTC
Found at i:659280 original size:26 final size:26
Alignment explanation
Indices: 659251--659327 Score: 60
Period size: 26 Copynumber: 3.2 Consensus size: 26
659241 ATATTTATAT
659251 TATAGTTTAAATTGATATAATTCATA
1 TATAGTTTAAATTGATATAATTCATA
* *
659277 TATA--AT-AATT--TTTGAA-T-ATA
1 TATAGTTTAAATTGATAT-AATTCATA
*
659297 TTATAGTTTAAATTGATATGATTCATA
1 -TATAGTTTAAATTGATATAATTCATA
659324 TATA
1 TATA
659328 AGTGTAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 18
0.62 0.08 0.30
Matches are distributed among these distances:
20 3 0.08
21 7 0.19
22 2 0.05
23 5 0.14
24 5 0.14
25 1 0.03
26 11 0.30
27 3 0.08
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.48
Consensus pattern (26 bp):
TATAGTTTAAATTGATATAATTCATA
Found at i:659617 original size:18 final size:17
Alignment explanation
Indices: 659594--659627 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
659584 TTTCTTTAAA
*
659594 ATTTTAATTTTATTATAT
1 ATTTTAACTTT-TTATAT
659612 ATTTTAACTTTTTATA
1 ATTTTAACTTTTTATA
659628 CTTTCTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTTTAACTTTTTATAT
Found at i:662967 original size:17 final size:17
Alignment explanation
Indices: 662954--662986 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
662944 CGAATGCATT
662954 CCATGCATCGATGCACA
1 CCATGCATCGATGCACA
*
662971 CCATGCACCGATGCAC
1 CCATGCATCGATGCAC
662987 TGAGGATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.39, G:0.18, T:0.15
Consensus pattern (17 bp):
CCATGCATCGATGCACA
Found at i:663031 original size:46 final size:45
Alignment explanation
Indices: 662973--663079 Score: 119
Period size: 45 Copynumber: 2.4 Consensus size: 45
662963 GATGCACACC
* *
662973 ATGCACCGATGCACT-GAGGAT-TTTATAAGAACATCAAATGCATTTG
1 ATGCATCGATGCACTCGA-GATATTT-TAA-AACATCAAATGCACTTG
* **
663019 ATGCATCGATGCACTCGAGCTATTTTAAAACATTGAATGCACTTG
1 ATGCATCGATGCACTCGAGATATTTTAAAACATCAAATGCACTTG
*
663064 ATGCATCGTTGCACTC
1 ATGCATCGATGCACTC
663080 TTAGTGCACC
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
45 29 0.55
46 19 0.36
47 5 0.09
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.30
Consensus pattern (45 bp):
ATGCATCGATGCACTCGAGATATTTTAAAACATCAAATGCACTTG
Found at i:663321 original size:17 final size:16
Alignment explanation
Indices: 663291--663324 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
663281 GAAGCCATTG
663291 ATCAACAACAAGAATC
1 ATCAACAACAAGAATC
*
663307 ATCAAGCAACTAGAATC
1 ATCAA-CAACAAGAATC
663324 A
1 A
663325 AGAGAGAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.53, C:0.24, G:0.09, T:0.15
Consensus pattern (16 bp):
ATCAACAACAAGAATC
Found at i:670506 original size:21 final size:21
Alignment explanation
Indices: 670477--670528 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
670467 ACTTCGGGAG
* *
670477 CTAGTTCCTCTCGAGCTGCTC
1 CTAGCTCCTCTCGAGCTCCTC
*
670498 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCTCGAGCTCCTC
*
670519 CT-CCTCCTCT
1 CTAGCTCCTCT
670529 TTCGGCTCCG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 7 0.26
21 20 0.74
ACGTcount: A:0.06, C:0.46, G:0.13, T:0.35
Consensus pattern (21 bp):
CTAGCTCCTCTCGAGCTCCTC
Found at i:671792 original size:64 final size:63
Alignment explanation
Indices: 671646--671804 Score: 182
Period size: 64 Copynumber: 2.5 Consensus size: 63
671636 GAATTAAATT
* *
671646 GAACATCAAATGCATTCCATGCATCGATGCA-CACCATGCACCAATGCACTGAGGATTTTATAA
1 GAACATCGAATGCATT-GATGCATCGATGCACCACCATGCACCAATGCACTGAGGATTTTATAA
* * *
671709 GAACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCG-GGCTATTT-T
1 GAACATCGAATGCA-TTGATGCATCGATGCACCA-CCATGCACCAATGCACT-GAGGAT-TTTAT
671772 AA
62 AA
*
671774 -AACATCGAATGCACTTGATGCATCGGTGCAC
1 GAACATCGAATGCA-TTGATGCATCGATGCAC
671805 TCTTAGTGCA
Statistics
Matches: 84, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
63 26 0.31
64 33 0.39
65 21 0.25
66 4 0.05
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (63 bp):
GAACATCGAATGCATTGATGCATCGATGCACCACCATGCACCAATGCACTGAGGATTTTATAA
Found at i:672048 original size:17 final size:16
Alignment explanation
Indices: 672018--672051 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
672008 GAAGCCATTG
672018 ATCAACAACAAGAATC
1 ATCAACAACAAGAATC
*
672034 ATCAAGCAACTAGAATC
1 ATCAA-CAACAAGAATC
672051 A
1 A
672052 AGAGAGAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.53, C:0.24, G:0.09, T:0.15
Consensus pattern (16 bp):
ATCAACAACAAGAATC
Found at i:679138 original size:26 final size:26
Alignment explanation
Indices: 679109--679170 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
679099 AATTTTTTAG
*
679109 CTTATATTATTTTTTTCACATAACAT
1 CTTATATTAATTTTTTCACATAACAT
*
679135 CTTATATTAATTTTTTCGCATAACAT
1 CTTATATTAATTTTTTCACATAACAT
679161 CTTATATTAA
1 CTTATATTAA
679171 ATTATAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.32, C:0.15, G:0.02, T:0.52
Consensus pattern (26 bp):
CTTATATTAATTTTTTCACATAACAT
Found at i:680550 original size:21 final size:21
Alignment explanation
Indices: 680526--680566 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
680516 ATATCAAGCT
680526 GCTTACCACTTGATTCAACCC
1 GCTTACCACTTGATTCAACCC
680547 GCTTACCACTTGATTCAACC
1 GCTTACCACTTGATTCAACC
680567 TCGTTGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.37, G:0.10, T:0.29
Consensus pattern (21 bp):
GCTTACCACTTGATTCAACCC
Found at i:681215 original size:16 final size:19
Alignment explanation
Indices: 681194--681235 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
681184 CGATAAGTTT
681194 TAATTT-TTTT-TCT-AAA
1 TAATTTATTTTATCTCAAA
681210 TAATTTATTTTATCTCAAA
1 TAATTTATTTTATCTCAAA
*
681229 CAATTTA
1 TAATTTA
681236 AACTTAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 6 0.27
17 4 0.18
18 3 0.14
19 9 0.41
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.55
Consensus pattern (19 bp):
TAATTTATTTTATCTCAAA
Found at i:683895 original size:10 final size:10
Alignment explanation
Indices: 683868--683906 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
683858 AAAATCTATT
683868 TTCATTTATG
1 TTCATTTATG
* * *
683878 TCCGTTTACG
1 TTCATTTATG
683888 TTCATTTATG
1 TTCATTTATG
683898 TTCATTTAT
1 TTCATTTAT
683907 TGTGTTCGTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.18, C:0.15, G:0.10, T:0.56
Consensus pattern (10 bp):
TTCATTTATG
Found at i:683905 original size:20 final size:20
Alignment explanation
Indices: 683868--683905 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
683858 AAAATCTATT
*
683868 TTCATTTATGTCCGTTTACG
1 TTCATTTATGTCCATTTACG
*
683888 TTCATTTATGTTCATTTA
1 TTCATTTATGTCCATTTA
683906 TTGTGTTCGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.16, G:0.11, T:0.55
Consensus pattern (20 bp):
TTCATTTATGTCCATTTACG
Found at i:690854 original size:18 final size:18
Alignment explanation
Indices: 690828--690862 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
690818 AAATAGTGGT
* *
690828 GAAATTAAATAAAATCAA
1 GAAAATAAAAAAAATCAA
690846 GAAAATAAAAAAAATCA
1 GAAAATAAAAAAAATCA
690863 GATATCATAA
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:0.71, C:0.06, G:0.06, T:0.17
Consensus pattern (18 bp):
GAAAATAAAAAAAATCAA
Found at i:691091 original size:23 final size:21
Alignment explanation
Indices: 691048--691205 Score: 67
Period size: 22 Copynumber: 7.1 Consensus size: 21
691038 ATGAAATAAA
691048 ATAAAATAAAATACAAAATAT
1 ATAAAATAAAATACAAAATAT
691069 ATAATAATAACAATA-AAACATAT
1 ATAA-AATAA-AATACAAA-ATAT
* * *
691092 ATAAAA-AAATTAGTAACAATAC
1 ATAAAATAAAATA-CAA-AATAT
*
691114 ATTAAAAATGAAATAC-AAATAAT
1 A-T-AAAATAAAATACAAAAT-AT
* *
691137 ATAATATAATAGTA-ATAAATAT
1 ATAAAATAA-AATACA-AAATAT
* *
691159 AAAAAATTAAAGATAAAAAGATAT
1 ATAAAA-TAAA-ATACAAA-ATAT
*
691183 ATAAAAT-GAATA-AAATATAT
1 ATAAAATAAAATACAAA-ATAT
691203 ATA
1 ATA
691206 TATAACAAAA
Statistics
Matches: 105, Mismatches: 15, Indels: 35
0.68 0.10 0.23
Matches are distributed among these distances:
20 13 0.12
21 14 0.13
22 31 0.30
23 29 0.28
24 14 0.13
25 4 0.04
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.27
Consensus pattern (21 bp):
ATAAAATAAAATACAAAATAT
Done.