Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008727.1 Hibiscus syriacus cultivar Beakdansim tig00111794_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: 1388410
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 8
Found at i:390460 original size:87 final size:87
Alignment explanation
Indices: 390353--390514 Score: 270
Period size: 87 Copynumber: 1.9 Consensus size: 87
390343 AAATAGGTCA
* *
390353 ATATAAGCGCTACCTATTACATTATATAAGCGTTACCTAATTTGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
*
390418 CCGGTTAAATACCTATTTTATT
66 CCAGTTAAATACCTATTTTATT
* * *
390440 ATATTAGCGCTACCTATTACATTATATAAGCGCTGCCTAATATGTTATTGTGCTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
390505 CCAGTTAAAT
66 CCAGTTAAAT
390515 GATATAATAT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 69 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
CCAGTTAAATACCTATTTTATT
Found at i:391069 original size:182 final size:182
Alignment explanation
Indices: 390779--391733 Score: 1447
Period size: 182 Copynumber: 5.3 Consensus size: 182
390769 TACAAATGAA
* * * * * *
390779 AAATGTATCAATCCATAGCAATATAACAGGTAAAAATATGATAAAACCGGTGTC-ATTATGATAA
1 AAATGTATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCGA-AATGATAA
** **
390843 AACCGGTAAACTGCTACCGGATATATTGAAAGTGTAAATAAATTAATATAAGTATCGACACTTTT
65 AACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTT
*
390908 GTAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTATAC
130 GTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATAC
* * * *
390961 AAATGTATCGATCCATAGCAATATAACATGTAATAATATGACAAAACCGGTGTC-ATTATGATAA
1 AAATGTATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCGA-AATGATAA
** * *
391025 AACCGGTAAACCGCTACCGGATATATTGAAAGTGTCAATAAATTAATATAAGTATCGACAATTTT
65 AACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTT
*
391090 ATAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATAC
130 GTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATAC
*
391143 AAATATATCGATCCATAGCAATATAACA-GTAATAATATGAC-AAACAGGTCTCGAAATGATAAA
1 AAATGTATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCGAAATGATAAA
*
391206 ACCGGTAAAAAGCTACCGGATATATTGAAAGTATCGATAAATTAATATAAGTATCGACACTTTTG
66 ACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTTG
*
391271 -ATATTTAAAAGAGAAGAAGTTATAGCGCTTAAAAAGTGTCGATACTTTATAC
131 TA-ATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATAC
* * *
391323 AAATGTATCGATCCATATCAATATAACAGGTAATAATATGAAAAAATAGGTCTCGAAATGATAAA
1 AAATGTATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCGAAATGATAAA
* * *
391388 ATCGGTAAAAAGCTAACGGATATATTGAAAGTGTCGATAAATTAATATAATTATCGACACTTTT-
66 ACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTTG
391452 TATATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATAC
131 TA-ATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATAC
* * *
391505 AAATGTATCGATCCATATCAATATAACAGGTAATAGTATGAAAAAACAGGTCTCGAAATGATAAA
1 AAATGTATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCGAAATGATAAA
*
391570 ACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTCG
66 ACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTTG
* * * * *
391635 TAATTTCAAAGAGAATAAATTATAGAGACTAAAAAGTGTCGATACTTTATGA-
131 TAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTAT-AC
* * *
391687 AAATGTATCGATCCATAACAATATAATAGGTAAAAATATGACAAAAC
1 AAATGTATCGATCCATAGCAATATAACAGGTAATAATATGACAAAAC
391734 CGGTAAAGCG
Statistics
Matches: 721, Mismatches: 45, Indels: 14
0.92 0.06 0.02
Matches are distributed among these distances:
179 1 0.00
180 151 0.21
181 26 0.04
182 540 0.75
183 3 0.00
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.28
Consensus pattern (182 bp):
AAATGTATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCGAAATGATAAA
ACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTTG
TAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATAC
Found at i:391501 original size:362 final size:362
Alignment explanation
Indices: 390779--391733 Score: 1445
Period size: 362 Copynumber: 2.6 Consensus size: 362
390769 TACAAATGAA
* * * * *
390779 AAATGTATCAATCCATAGCAATATAACAGGTAAAAATATGATAAAACCGGTGTC-ATTATGATAA
1 AAATGTATCGATCCATAGCAATATAACAGGTAATAATATGA-AAAACAGGTCTCGA-AATGATAA
** **
390843 AACCGGTAAACTGCTACCGGATATATTGAAAGTGTAAATAAATTAATATAAGTATCGACACTTTT
64 AACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTT
*
390908 GTAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTATACAAATGTATCGAT
129 GTAATTTAAAAGAGAAGAAGTTATAGCG-CTAAAAAGTGTCGATACTTTATACAAATGTATCGAT
* * * * * **
390973 CCATAGCAATATAACATGTAATAATATGACAAAACCGGTGTCATTATGATAAAACCGGTAAACCG
193 CCATAACAATATAACAGGTAATAATATGACAAAACAGGTCTCATAATGATAAAACCGGTAAAAAG
*
391038 CTACCGGATATATTGAAAGTGTCAATAAATTAATATAAGTATCGACAATTTTATAATTTAAAAGA
258 CTAACGGATATATTGAAAGTGTCAATAAATTAATATAAGTATCGACAATTTTATAATTTAAAAGA
391103 GAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATAC
323 GAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATAC
* *
391143 AAATATATCGATCCATAGCAATATAACA-GTAATAATATGACAAACAGGTCTCGAAATGATAAAA
1 AAATGTATCGATCCATAGCAATATAACAGGTAATAATATGAAAAACAGGTCTCGAAATGATAAAA
*
391207 CCGGTAAAAAGCTACCGGATATATTGAAAGTATCGATAAATTAATATAAGTATCGACACTTTTG-
66 CCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTTGT
391271 ATATTTAAAAGAGAAGAAGTTATAGCGCTTAAAAAGTGTCGATACTTTATACAAATGTATCGATC
131 A-ATTTAAAAGAGAAGAAGTTATAGCGC-TAAAAAGTGTCGATACTTTATACAAATGTATCGATC
* * * *
391336 CATATCAATATAACAGGTAATAATATGAAAAAATAGGTCTCGA-AATGATAAAATCGGTAAAAAG
194 CATAACAATATAACAGGTAATAATATGACAAAACAGGTCTC-ATAATGATAAAACCGGTAAAAAG
* * *
391400 CTAACGGATATATTGAAAGTGTCGATAAATTAATATAATTATCGACACTTTT-TATATTTAAAAG
258 CTAACGGATATATTGAAAGTGTCAATAAATTAATATAAGTATCGACAATTTTATA-ATTTAAAAG
391464 AGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATAC
322 AGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATAC
* *
391505 AAATGTATCGATCCATATCAATATAACAGGTAATAGTATGAAAAAACAGGTCTCGAAATGATAAA
1 AAATGTATCGATCCATAGCAATATAACAGGTAATAATATG-AAAAACAGGTCTCGAAATGATAAA
*
391570 ACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTCG
65 ACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTTG
* * * *
391635 TAATTTCAAAGAGAATAAATTATAGAGACTAAAAAGTGTCGATACTTTATGA-AAATGTATCGAT
130 TAATTTAAAAGAGAAGAAGTTATAGCG-CTAAAAAGTGTCGATACTTTAT-ACAAATGTATCGAT
* *
391699 CCATAACAATATAATAGGTAAAAATATGACAAAAC
193 CCATAACAATATAACAGGTAATAATATGACAAAAC
391734 CGGTAAAGCG
Statistics
Matches: 539, Mismatches: 42, Indels: 20
0.90 0.07 0.03
Matches are distributed among these distances:
361 4 0.01
362 313 0.58
363 23 0.04
364 196 0.36
365 3 0.01
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.28
Consensus pattern (362 bp):
AAATGTATCGATCCATAGCAATATAACAGGTAATAATATGAAAAACAGGTCTCGAAATGATAAAA
CCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTTGT
AATTTAAAAGAGAAGAAGTTATAGCGCTAAAAAGTGTCGATACTTTATACAAATGTATCGATCCA
TAACAATATAACAGGTAATAATATGACAAAACAGGTCTCATAATGATAAAACCGGTAAAAAGCTA
ACGGATATATTGAAAGTGTCAATAAATTAATATAAGTATCGACAATTTTATAATTTAAAAGAGAA
GAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATAC
Found at i:392372 original size:19 final size:19
Alignment explanation
Indices: 392311--392373 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
392301 ATTATATTAT
392311 ATAATATTATAGGTAGAAA
1 ATAATATTATAGGTAGAAA
* ** * *
392330 ATAAATATGGATACAT-GTAT
1 AT-AATAT-TATAGGTAGAAA
392350 ATAATATTATAGGTAGAAA
1 ATAATATTATAGGTAGAAA
392369 ATAAT
1 ATAAT
392374 TTTTTAGGTT
Statistics
Matches: 31, Mismatches: 10, Indels: 6
0.66 0.21 0.13
Matches are distributed among these distances:
18 4 0.13
19 14 0.45
20 9 0.29
21 4 0.13
ACGTcount: A:0.51, C:0.02, G:0.14, T:0.33
Consensus pattern (19 bp):
ATAATATTATAGGTAGAAA
Found at i:394471 original size:23 final size:23
Alignment explanation
Indices: 394421--394465 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
394411 TGCCTATTTT
*
394421 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
394444 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
394466 TGTTATTGTG
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:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:394483 original size:87 final size:87
Alignment explanation
Indices: 394337--394498 Score: 279
Period size: 87 Copynumber: 1.9 Consensus size: 87
394327 AAATATGTCA
* *
394337 ATATAAGCGCTACATATTACATTATATAAGCGCTACCTACTTTGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACATATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
394402 CCGGTTAAATGCCTATTTTATT
66 CCGGTTAAATGCCTATTTTATT
* *
394424 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATATTT
1 ATATAAGCGCTACATATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
*
394489 TCGGTTAAAT
66 CCGGTTAAAT
394499 AATATAATAT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 70 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.41
Consensus pattern (87 bp):
ATATAAGCGCTACATATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
CCGGTTAAATGCCTATTTTATT
Found at i:397273 original size:2 final size:2
Alignment explanation
Indices: 397266--397297 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
397256 ACCAAAATTC
397266 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
397298 TACTTTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:404794 original size:11 final size:11
Alignment explanation
Indices: 404767--404795 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
404757 AATTGGATGA
404767 TTAAATTTATT
1 TTAAATTTATT
404778 TT-AATTTATT
1 TTAAATTTATT
404788 TTAAATTT
1 TTAAATTT
404796 GATATATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TTAAATTTATT
Found at i:405179 original size:31 final size:30
Alignment explanation
Indices: 405098--405204 Score: 90
Period size: 31 Copynumber: 3.5 Consensus size: 30
405088 TTAACTTATT
* **
405098 AAATATATTTTATTCTTAT-TTTAATTTAA
1 AAATATATTTTATTCTTATCTTAAATAAAA
* * *
405127 AAATATATTTTAATATCATCTTAAACTAAAA
1 AAATATATTTTATTCTTATCTTAAA-TAAAA
* * *
405158 AAATATAATTTATTCTTATCTTAACTTAAAT
1 AAATATATTTTATTCTTATCTTAA-ATAAAA
**
405189 ATTTATATTTTATTCT
1 AAATATATTTTATTCT
405205 GATAATATTT
Statistics
Matches: 60, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
29 16 0.27
30 4 0.07
31 40 0.67
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.51
Consensus pattern (30 bp):
AAATATATTTTATTCTTATCTTAAATAAAA
Found at i:405254 original size:30 final size:30
Alignment explanation
Indices: 405218--405295 Score: 113
Period size: 30 Copynumber: 2.6 Consensus size: 30
405208 AATATTTTCA
405218 ATTTAAGA-AAAAATATAATATATTTTTTGT
1 ATTTAAGATAAAAATATAATATA-TTTTTGT
*
405248 ATTTAAGATAAAAATAAAATATATTTTTGT
1 ATTTAAGATAAAAATATAATATATTTTTGT
* *
405278 AGTTAAAATAAAAATATA
1 ATTTAAGATAAAAATATA
405296 TTTTTAAGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
30 30 0.70
31 13 0.30
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (30 bp):
ATTTAAGATAAAAATATAATATATTTTTGT
Found at i:405286 original size:24 final size:23
Alignment explanation
Indices: 405249--405317 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 23
405239 ATTTTTTGTA
*
405249 TTTAAGATAAAAATAAAATATATT
1 TTTAAG-TTAAAATAAAATATATT
*
405273 TTTGTAGTTAAAATAAAAATATATT
1 TTT-AAGTTAAAAT-AAAATATATT
*
405298 TTTAAGTTAAGATAAGAATA
1 TTTAAGTTAAAATAA-AATA
405318 AAAGATATGG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
23 2 0.05
24 21 0.55
25 15 0.39
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (23 bp):
TTTAAGTTAAAATAAAATATATT
Found at i:405318 original size:30 final size:29
Alignment explanation
Indices: 405250--405440 Score: 117
Period size: 30 Copynumber: 6.6 Consensus size: 29
405240 TTTTTTGTAT
* *
405250 TTAAGATAAAAATAAAATATATTT-T-TG
1 TTAAGATAAGAATAAAATATATTTATAAG
* *
405277 -T-AGTTAA-AATAAAAATATATTTTTAAG
1 TTAAGATAAGAAT-AAAATATATTTATAAG
*
405304 TTAAGATAAGAATAAAAGATATGGTT-TAAG
1 TTAAGATAAGAATAAAATATAT--TTATAAG
* * * *
405334 TTAAAATAAGAATTAATTATATTTAATAAT
1 TTAAGATAAGAATAAAATATATTT-ATAAG
* * * *
405364 TTAAGGTGAGAATAGAATATATTTAATAAT
1 TTAAGATAAGAATAAAATATATTT-ATAAG
* * * *
405394 TTAAGTTAAGAATATAATTTATGTAATAAG
1 TTAAGATAAGAATAAAATATAT-TTATAAG
*
405424 TTAAGATAA-AAAAAAAT
1 TTAAGATAAGAATAAAAT
405441 GGATGTCCCT
Statistics
Matches: 129, Mismatches: 24, Indels: 20
0.75 0.14 0.12
Matches are distributed among these distances:
24 3 0.02
25 16 0.12
26 2 0.02
27 1 0.01
28 3 0.02
29 19 0.15
30 82 0.64
31 3 0.02
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (29 bp):
TTAAGATAAGAATAAAATATATTTATAAG
Found at i:405601 original size:29 final size:29
Alignment explanation
Indices: 405563--405630 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
405553 ATAAAGACTA
*
405563 AAAAAATATTCTTAAGTT-A-AAATAGGAAT
1 AAAATATATTCTTAAGTTGAGAAA-A-GAAT
* *
405592 AAAATATATTTTTAGGTTGAGAAAAGAAT
1 AAAATATATTCTTAAGTTGAGAAAAGAAT
405621 AAAATATATT
1 AAAATATATT
405631 TAATAGGTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 29 0.85
30 2 0.06
31 3 0.09
ACGTcount: A:0.53, C:0.01, G:0.12, T:0.34
Consensus pattern (29 bp):
AAAATATATTCTTAAGTTGAGAAAAGAAT
Found at i:405631 original size:29 final size:29
Alignment explanation
Indices: 405547--405673 Score: 103
Period size: 30 Copynumber: 4.2 Consensus size: 29
405537 CGAATTATGA
* * * *
405547 GTTAAGATAAAGACTAAAAAAATATTCTTAA
1 GTTAAGA-AAAGAAT-AAAATATATTTTTAG
*
405578 GTTAA-AATAGGAATAAAATATATTTTTAG
1 GTTAAGAA-AAGAATAAAATATATTTTTAG
* *
405607 GTTGAGAAAAGAATAAAATATATTTAATAG
1 GTTAAGAAAAGAATAAAATATATTT-TTAG
* * * *
405637 GTTAATAAAAAAATAAAATACATTTTTAAT
1 GTTAAGAAAAGAATAAAATATATTTTT-AG
405667 GTTAAGA
1 GTTAAGA
405674 TGTAAAATTA
Statistics
Matches: 77, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
29 34 0.44
30 38 0.49
31 5 0.06
ACGTcount: A:0.53, C:0.02, G:0.12, T:0.33
Consensus pattern (29 bp):
GTTAAGAAAAGAATAAAATATATTTTTAG
Found at i:406818 original size:41 final size:41
Alignment explanation
Indices: 406747--406848 Score: 143
Period size: 41 Copynumber: 2.5 Consensus size: 41
406737 TCTAATTCGT
*
406747 TTAACTTGTGCTTTTCA-TATTTAAACCATATAAAGTCACA
1 TTAACTTGTACTTTTCATTATTTAAACCATATAAAGTCACA
* * *
406787 TTAATTTGTACTTTTCATTATTTAAATCATATAAATTCACA
1 TTAACTTGTACTTTTCATTATTTAAACCATATAAAGTCACA
* *
406828 TTAACTCGTATTTTTCATTAT
1 TTAACTTGTACTTTTCATTAT
406849 AGCCAAATGT
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 15 0.28
41 39 0.72
ACGTcount: A:0.33, C:0.15, G:0.05, T:0.47
Consensus pattern (41 bp):
TTAACTTGTACTTTTCATTATTTAAACCATATAAAGTCACA
Found at i:424943 original size:15 final size:15
Alignment explanation
Indices: 424921--424961 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
424911 TTCGCACCTC
424921 TGAATGATTCAGTGT
1 TGAATGATTCAGTGT
* *
424936 TTAATGATTTAGTGT
1 TGAATGATTCAGTGT
424951 TGAATGATTCA
1 TGAATGATTCA
424962 ACACAGAAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.29, C:0.05, G:0.22, T:0.44
Consensus pattern (15 bp):
TGAATGATTCAGTGT
Found at i:426295 original size:8 final size:7
Alignment explanation
Indices: 426269--426293 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
426259 TCACATCTAT
426269 TTTTAAA
1 TTTTAAA
426276 TTTTAAA
1 TTTTAAA
426283 TTTTAAA
1 TTTTAAA
426290 TTTT
1 TTTT
426294 TAGGTTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
TTTTAAA
Found at i:436307 original size:46 final size:46
Alignment explanation
Indices: 436227--436371 Score: 218
Period size: 46 Copynumber: 3.2 Consensus size: 46
436217 ACCATTAATA
** *
436227 CACTGTTATGTATTTTCATTTGTGGCATCCTTTCATGCCAATTATG
1 CACTGTTATACATTTTCATTTATGGCATCCTTTCATGCCAATTATG
* * *
436273 CACTGTTATACATTTTCATTTATGACATCATTTCATGCAAATTATG
1 CACTGTTATACATTTTCATTTATGGCATCCTTTCATGCCAATTATG
* *
436319 CATTGTTATACATTTTCATTGATGGCATCCTTTCATGCCAATTATG
1 CACTGTTATACATTTTCATTTATGGCATCCTTTCATGCCAATTATG
436365 CACTGTT
1 CACTGTT
436372 CTTCATCTAA
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 87 1.00
ACGTcount: A:0.24, C:0.19, G:0.12, T:0.44
Consensus pattern (46 bp):
CACTGTTATACATTTTCATTTATGGCATCCTTTCATGCCAATTATG
Found at i:436576 original size:81 final size:81
Alignment explanation
Indices: 436423--436981 Score: 751
Period size: 81 Copynumber: 6.9 Consensus size: 81
436413 GCACTGTTAT
* * * * * * *
436423 GCATCTAACTTTTCATCTAACTTGCATTAATGGTACCTTTCTGCCAAAAAGCATAGTTAGACATT
1 GCATTTAACCTTTCATCTAACTTGCATTATTGGCACATTTCTGCC-AAATGCACAGTTAGACATT
*
436488 TAGTCTTTCGTCCAAAG
65 TAGTCTTTCATCCAAAG
* * * * * * *
436505 GCATTTAACCTTTCATCTAACTCGTATTATTGACATATTTTTGCCAAATACAGAGTTAGACATTT
1 GCATTTAACCTTTCATCTAACTTGCATTATTGGCACATTTCTGCCAAATGCACAGTTAGACATTT
*
436570 AGTCTTTCATCCCAAG
66 AGTCTTTCATCCAAAG
* * **
436586 GCATTTAACATTT-ATTCTAGCTTGCATTATTGGCACATTTCTGATAAATGCACAGTTAGACATT
1 GCATTTAACCTTTCA-TCTAACTTGCATTATTGGCACATTTCTGCCAAATGCACAGTTAGACATT
* *
436650 TAGTCTTTTATTCAAAG
65 TAGTCTTTCATCCAAAG
* *
436667 GCATTTAACCTTTTATCTATCTTGCATTATTGGCACATTTCTGCCAAATGCACAGTTAGACATTT
1 GCATTTAACCTTTCATCTAACTTGCATTATTGGCACATTTCTGCCAAATGCACAGTTAGACATTT
* *
436732 AGTCGTTCATCCAAAC
66 AGTCTTTCATCCAAAG
* * *
436748 GCATTTACCCATTCATCTAACTTGCATTATTGGCACATTTCTGCCAAATGCACAGTTAGATATTT
1 GCATTTAACCTTTCATCTAACTTGCATTATTGGCACATTTCTGCCAAATGCACAGTTAGACATTT
* *
436813 AGTCTTTTATTCAAAG
66 AGTCTTTCATCCAAAG
* * * * * *
436829 ACATTTAACCTTTCATCTAACTTGCATTATTGACACCTTTTTTCCAAATGCACAATTAGACATTT
1 GCATTTAACCTTTCATCTAACTTGCATTATTGGCACATTTCTGCCAAATGCACAGTTAGACATTT
436894 AGTCTTTCATCCAAAG
66 AGTCTTTCATCCAAAG
*
436910 GCATTTAACCTTTCATCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGACATTT
1 GCATTTAACCTTTCATCTAACTTGCATTATTGGCACATTTCTGCCAAATGCACAGTTAGACATTT
436975 AGTCTTT
66 AGTCTTT
436982 TATTTTAGAA
Statistics
Matches: 413, Mismatches: 62, Indels: 5
0.86 0.13 0.01
Matches are distributed among these distances:
80 1 0.00
81 376 0.91
82 36 0.09
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (81 bp):
GCATTTAACCTTTCATCTAACTTGCATTATTGGCACATTTCTGCCAAATGCACAGTTAGACATTT
AGTCTTTCATCCAAAG
Found at i:437351 original size:18 final size:19
Alignment explanation
Indices: 437330--437370 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
437320 GTACTATTAT
*
437330 TTTCAAT-TTCTATTACAA
1 TTTCAATCTTATATTACAA
*
437348 TTTC-ATCTTATCTTACAA
1 TTTCAATCTTATATTACAA
437366 TTTCA
1 TTTCA
437371 GACTCAATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.29, C:0.20, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTCAATCTTATATTACAA
Found at i:441771 original size:21 final size:21
Alignment explanation
Indices: 441726--441771 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
441716 AAAAGAGGTA
*
441726 ATAA-AAACAAATAAAATAAG
1 ATAACAAACAAATAAAAGAAG
441746 A-AACAAACGAAAT-AAAGAAG
1 ATAACAAAC-AAATAAAAGAAG
441766 ATAACA
1 ATAACA
441772 TAAAAGGAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 2 0.09
20 12 0.55
21 8 0.36
ACGTcount: A:0.72, C:0.09, G:0.09, T:0.11
Consensus pattern (21 bp):
ATAACAAACAAATAAAAGAAG
Found at i:441861 original size:22 final size:19
Alignment explanation
Indices: 441825--441887 Score: 56
Period size: 22 Copynumber: 3.1 Consensus size: 19
441815 AAATAAAGAT
441825 AAGAA-ATAAACAAAATAAA
1 AAGAACATAAA-AAAATAAA
* *
441844 AGGAAACATAACTAAAAAAAATA
1 AAG-AACATAA--AAAAATAA-A
441867 AAGAACATAAAAAAATAAA
1 AAGAACATAAAAAAATAAA
441886 AA
1 AA
441888 TAAAAAAGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
19 5 0.14
20 9 0.26
21 4 0.11
22 13 0.37
23 4 0.11
ACGTcount: A:0.76, C:0.06, G:0.06, T:0.11
Consensus pattern (19 bp):
AAGAACATAAAAAAATAAA
Found at i:441865 original size:25 final size:23
Alignment explanation
Indices: 441828--441900 Score: 69
Period size: 23 Copynumber: 3.1 Consensus size: 23
441818 TAAAGATAAG
*
441828 AAATAAACAAAATAAAAGGAAACAT
1 AAATAAAAAAAATAAAA-G-AACAT
*
441853 AACTAAAAAAAAT-AAAGAACAT
1 AAATAAAAAAAATAAAAGAACAT
* *
441875 AAAAAAATAAAAATAAAA-AAGAT
1 AAATAAA-AAAAATAAAAGAACAT
441898 AAA
1 AAA
441901 AAATGACATA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
22 10 0.24
23 14 0.34
24 6 0.15
25 11 0.27
ACGTcount: A:0.77, C:0.05, G:0.05, T:0.12
Consensus pattern (23 bp):
AAATAAAAAAAATAAAAGAACAT
Found at i:441890 original size:23 final size:23
Alignment explanation
Indices: 441847--441903 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
441837 AAATAAAAGG
**
441847 AAACATAACTAAA-AAAAATAAA
1 AAACATAAAAAAATAAAAATAAA
*
441869 GAACATAAAAAAATAAAAATAAA
1 AAACATAAAAAAATAAAAATAAA
*
441892 AAAGATAAAAAA
1 AAACATAAAAAA
441904 TGACATAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 10 0.34
23 19 0.66
ACGTcount: A:0.79, C:0.05, G:0.04, T:0.12
Consensus pattern (23 bp):
AAACATAAAAAAATAAAAATAAA
Found at i:442127 original size:15 final size:16
Alignment explanation
Indices: 442098--442129 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
442088 ACAAAAATGT
442098 AAATAAAAAATAATAA
1 AAATAAAAAATAATAA
442114 AAATAAAAAA-AATAA
1 AAATAAAAAATAATAA
442129 A
1 A
442130 TGAATATATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (16 bp):
AAATAAAAAATAATAA
Found at i:444150 original size:124 final size:122
Alignment explanation
Indices: 443927--444245 Score: 390
Period size: 124 Copynumber: 2.6 Consensus size: 122
443917 GTTGAAATCC
* * * **
443927 AATGTTGTTTGTGAGCACGATATCCATTGTCGTGAAGTTGAAATCATGGATGGCCCCTTCGTTTT
1 AATGTTG-TTGTGGGCACGATATCCTTTGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTCGT
* * * *
443992 GAAGTTGAGCCTTGAATTATATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATG
65 GAAGTTGAGCCTTGAATTAGATATCCTTCATCGTGAAGTTGAAATCAAATCTAAAG-TA
* * * *
444051 AATGTTGATGGTGGGCACGATATCCTTTGTCATGAAGTTGAAATCGTGGATGACACCTTCGTCGT
1 AATGTTG-TTGTGGGCACGATATCCTTTGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTCGT
* * **
444116 CAAGTTGAGCCTTGAATTGGATATCCTTCATCGTGAAGTTGAAATCAAATCTTGAGTA
65 GAAGTTGAGCCTTGAATTAGATATCCTTCATCGTGAAGTTGAAATCAAATCTAAAGTA
* ** *
444174 AAT-TTGTTGTGGGCATGATA-CCATTCATTGTGAAGTTGAAATCGTGGATGGCCCCTTCGTTCG
1 AATGTTGTTGTGGGCACGATATCC-TTTGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCG-TCG
444237 TGAAGTTGA
64 TGAAGTTGA
444246 AATCCATGTG
Statistics
Matches: 166, Mismatches: 27, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
120 2 0.01
121 42 0.25
122 14 0.08
123 4 0.02
124 104 0.63
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (122 bp):
AATGTTGTTGTGGGCACGATATCCTTTGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTCGTG
AAGTTGAGCCTTGAATTAGATATCCTTCATCGTGAAGTTGAAATCAAATCTAAAGTA
Found at i:445154 original size:7 final size:6
Alignment explanation
Indices: 445134--445192 Score: 64
Period size: 6 Copynumber: 9.0 Consensus size: 6
445124 ACCCATCTTA
*
445134 TTTTTC TTTTTC TTTTCTC TTTTCTC TTTTCTC TTTTGTTC TTTTTC TTTTTT
1 TTTTTC TTTTTC TTTT-TC TTTT-TC TTTT-TC -TTT-TTC TTTTTC TTTTTC
445187 TTTTTC
1 TTTTTC
445193 AATTTAGGGC
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
6 23 0.48
7 19 0.40
8 5 0.10
9 1 0.02
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:455496 original size:30 final size:27
Alignment explanation
Indices: 455460--455515 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
455450 AAGAGTAAAG
455460 AAAGATAAAGAAAAATAACAATAATAAAAT
1 AAAGAT-AAGAAAAA-AACAA-AATAAAAT
*
455490 AAAGATAAGAAATAAACAAAATAAAA
1 AAAGATAAGAAAAAAACAAAATAAAA
455516 GGAAACATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 7 0.28
28 5 0.20
29 7 0.28
30 6 0.24
ACGTcount: A:0.75, C:0.04, G:0.07, T:0.14
Consensus pattern (27 bp):
AAAGATAAGAAAAAAACAAAATAAAAT
Found at i:455525 original size:28 final size:27
Alignment explanation
Indices: 455472--455525 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
455462 AGATAAAGAA
* *
455472 AAATAACAATAATAAAATAAAGATAAG
1 AAATAACAATAATAAAAGAAACATAAG
455499 AAATAAACAA-AATAAAAGGAAACATAA
1 AAAT-AACAATAATAAAA-GAAACATAA
455526 CTAAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.72, C:0.06, G:0.07, T:0.15
Consensus pattern (27 bp):
AAATAACAATAATAAAAGAAACATAAG
Found at i:458579 original size:18 final size:18
Alignment explanation
Indices: 458556--458590 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
458546 AGAAAAAGGC
*
458556 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
458574 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
458591 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:458902 original size:140 final size:140
Alignment explanation
Indices: 458650--458919 Score: 513
Period size: 140 Copynumber: 1.9 Consensus size: 140
458640 AAACGTTGTA
*
458650 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTGTTAGTAACTTGAGTTTAAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTAAACATTGCTA
*
458715 TGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
458780 TATGTGTATT
131 TATGTGTATT
*
458790 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTAAACATTGCTA
458855 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
458920 CGTAACGCAA
Statistics
Matches: 127, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 127 1.00
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.42
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTAAACATTGCTA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
TATGTGTATT
Found at i:458915 original size:20 final size:20
Alignment explanation
Indices: 458890--459114 Score: 213
Period size: 20 Copynumber: 11.8 Consensus size: 20
458880 TTACACATTC
*
458890 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
458910 ATTTGACTATCGTAACGCAA
1 ATTTGACTATCGCAACGCGA
* *
458930 ATTTGATTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
* *
458949 A----A-AATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
* *
458964 ATTTAACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
*
458984 ATATGACTATCGCAACGC-A
1 ATTTGACTATCGCAACGCGA
* *
459003 A----A-AATCTCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
459018 ATTTGTCTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
459038 ATTTGACTATCGCAACTCGA
1 ATTTGACTATCGCAACGCGA
459058 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
459078 ATTTGATTATCGCAACGGGT
1 ATTTGACTATCGCAACGCGA
459098 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
459115 AGAAAATCGC
Statistics
Matches: 166, Mismatches: 27, Indels: 24
0.76 0.12 0.11
Matches are distributed among these distances:
14 17 0.10
15 6 0.04
19 5 0.03
20 138 0.83
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.27
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:458995 original size:54 final size:54
Alignment explanation
Indices: 458898--459163 Score: 275
Period size: 54 Copynumber: 4.8 Consensus size: 54
458888 TCATTTGAAT
* * *
458898 ATCGCAACGCGAATTTGACTATCGTAACGCAAATTTGATTATCGCAACTCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACTCAAAA
* * * * *
458952 ATCGCAATGCGAATTTAACTATCGCAACACGAATATGACTATCGCAACGCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACTCAAAA
* * *
459006 ATCTCAACGCGAATTTGTCTATCGCAACGCGAATTTGACTATCGCAACTCGAATTTGACT
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACTC-AA----A-A
* * * *
459066 ATCGCAACGCGAATTTGATTATCGCAACGGGTATTTGACTATCGCAAC-GAGAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACTCA-AAA
* * * * *
459120 ATCGCAAAGCGTATTAGACTATCGCAACGTGAA-TTGACTTTCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGC
459164 GTTGCGATTT
Statistics
Matches: 175, Mismatches: 30, Indels: 15
0.80 0.14 0.07
Matches are distributed among these distances:
53 10 0.06
54 116 0.66
55 3 0.02
58 1 0.01
59 2 0.01
60 43 0.25
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.26
Consensus pattern (54 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACTCAAAA
Found at i:459182 original size:20 final size:20
Alignment explanation
Indices: 459157--459194 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
459147 CGTGAATTGA
*
459157 CTTTCGCGTTGCGATTTTAT
1 CTTTCGCATTGCGATTTTAT
459177 CTTTCGCATTGCGATTTT
1 CTTTCGCATTGCGATTTT
459195 GAGTTTAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.11, C:0.21, G:0.18, T:0.50
Consensus pattern (20 bp):
CTTTCGCATTGCGATTTTAT
Found at i:459369 original size:14 final size:14
Alignment explanation
Indices: 459332--459370 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
459322 TCGATATTAA
*
459332 ACAAATCAACTTTT
1 ACAAATCAATTTTT
459346 ACAAATCAATTTTT
1 ACAAATCAATTTTT
*
459360 ATAAATCAATT
1 ACAAATCAATT
459371 AAACAAGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (14 bp):
ACAAATCAATTTTT
Found at i:460879 original size:42 final size:42
Alignment explanation
Indices: 460772--460883 Score: 104
Period size: 42 Copynumber: 2.7 Consensus size: 42
460762 TCTAGAATGT
* * *
460772 TGGG-AGGGACCTCTTCAACGATAACAGTGGCCTCTTGAACAG
1 TGGGAAGGG-CCTCTTGAACGATGACAGGGGCCTCTTGAACAG
* ** *
460814 TGGGAAGGGACTCTTGAGGGATGATAGGGGCCTCTTGAAC-G
1 TGGGAAGGGCCTCTTGAACGATGACAGGGGCCTCTTGAACAG
*
460855 ATAGGGGA-GGCCTCTTGAACGATGACAGG
1 -T-GGGAAGGGCCTCTTGAACGATGACAGG
460884 TGAGTCAGAC
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
41 1 0.02
42 46 0.84
43 8 0.15
ACGTcount: A:0.25, C:0.19, G:0.36, T:0.21
Consensus pattern (42 bp):
TGGGAAGGGCCTCTTGAACGATGACAGGGGCCTCTTGAACAG
Found at i:461392 original size:18 final size:18
Alignment explanation
Indices: 461369--461415 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 18
461359 GAAACTTAAA
461369 ATCGCAAC-AAGAATGACT
1 ATCGCAACGAA-AATGACT
461387 ATCGCAACGCGAAAATGACT
1 ATCGCAA--CGAAAATGACT
461407 ATCGCAACG
1 ATCGCAACG
461416 CGAATTTGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 9 0.35
20 15 0.58
21 2 0.08
ACGTcount: A:0.40, C:0.26, G:0.19, T:0.15
Consensus pattern (18 bp):
ATCGCAACGAAAATGACT
Found at i:461405 original size:20 final size:20
Alignment explanation
Indices: 461380--461435 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
461370 TCGCAACAAG
461380 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
461400 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
** *
461420 TTTGACTATTGCAACG
1 AATGACTATCGCAACG
461436 AGAGAATCGC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:461503 original size:20 final size:20
Alignment explanation
Indices: 461478--461545 Score: 118
Period size: 20 Copynumber: 3.4 Consensus size: 20
461468 GTGATTCTTT
**
461478 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
461498 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
461518 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
461538 CGTTGCGA
1 CGTTGCGA
461546 AAGTAAACTA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:461716 original size:18 final size:18
Alignment explanation
Indices: 461693--461742 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
461683 TTTACTAAGC
461693 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
461711 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
461729 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
461743 TACGAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (18 bp):
AATCTAAGTGAAATGGTT
Found at i:467625 original size:22 final size:22
Alignment explanation
Indices: 467600--467641 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
467590 CAATTCATTT
467600 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
467622 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
467642 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:469150 original size:20 final size:20
Alignment explanation
Indices: 469127--469233 Score: 119
Period size: 20 Copynumber: 5.5 Consensus size: 20
469117 TCTGAAACTT
*
469127 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
*
469147 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
** **
469167 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACGCGAAAATG
**
469187 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACGCGAAAATG
*
469206 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACGCGAAAATG
469225 AAAATCGCA
1 AAAATCGCA
469234 TTGCGATTCT
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
19 24 0.32
20 52 0.68
ACGTcount: A:0.46, C:0.23, G:0.17, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:469843 original size:20 final size:20
Alignment explanation
Indices: 469820--469871 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
469810 GAAAATCGCA
*
469820 TTGCGATAGTCAGCATCGTG
1 TTGCGATAGTCAGAATCGTG
*
469840 TTGCGATAGTCAGAATCTTG
1 TTGCGATAGTCAGAATCGTG
469860 TTGCGATAGTCA
1 TTGCGATAGTCA
469872 TACTCGCATT
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:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGTG
Found at i:469883 original size:20 final size:20
Alignment explanation
Indices: 469815--469910 Score: 70
Period size: 20 Copynumber: 4.8 Consensus size: 20
469805 GCTTTGAAAA
*
469815 TCGCATTGCGATAGTCA-GC
1 TCGCATTGCGATAGTCATAC
** * *
469834 ATCGTGTTGCGATAGTCAGAA
1 -TCGCATTGCGATAGTCATAC
***
469855 TCTTGTTGCGATAGTCATAC
1 TCGCATTGCGATAGTCATAC
* *
469875 TCGCATTGCGAT-TTACATAT
1 TCGCATTGCGATAGT-CATAC
469895 TCGCATTGCGATAGTC
1 TCGCATTGCGATAGTC
469911 GGAAAATCGC
Statistics
Matches: 60, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
19 1 0.02
20 58 0.97
21 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (20 bp):
TCGCATTGCGATAGTCATAC
Found at i:482101 original size:64 final size:64
Alignment explanation
Indices: 482027--482169 Score: 193
Period size: 64 Copynumber: 2.2 Consensus size: 64
482017 AATTGTTAAG
*
482027 GTGCATCGATGCAT-GAATTTAAATAGAAAACATCGAATAGGATTTATGCATCGATGCATAAG-G
1 GTGCATCGATGCATCCAA-TTAAATA-AAAACATCGAATAGGATTTATGCATCGATGCAT-AGTG
482090 -A
63 TA
* * *
482091 GTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTATGCATCGATGCATGGTGTA
1 GTGCATCGATGCAT-CCAATTAAATAAAAACATCGAATAGGATTTATGCATCGATGCATAGTGTA
482156 GTGCATCGATGCAT
1 GTGCATCGATGCAT
482170 ACCTTCATTA
Statistics
Matches: 71, Mismatches: 4, Indels: 7
0.87 0.05 0.09
Matches are distributed among these distances:
63 1 0.01
64 47 0.66
65 22 0.31
66 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (64 bp):
GTGCATCGATGCATCCAATTAAATAAAAACATCGAATAGGATTTATGCATCGATGCATAGTGTA
Found at i:482169 original size:65 final size:65
Alignment explanation
Indices: 482045--482169 Score: 200
Period size: 64 Copynumber: 1.9 Consensus size: 65
482035 ATGCATGAAT
482045 TTAAATAGAAAACATCGAATAGGATTTATGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA
1 TTAAATAGAAAACATCGAATAGGATTTATGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA
* *
482110 TTAAATA-CAAACATCGAATAGGATTTATGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TTAAATAGAAAACATCGAATAGGATTTATGCATCGATGCATAAG-G-AGTGCATCGATGCAT
482170 ACCTTCATTA
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
63 1 0.02
64 33 0.59
65 22 0.39
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (65 bp):
TTAAATAGAAAACATCGAATAGGATTTATGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA
Found at i:482684 original size:18 final size:18
Alignment explanation
Indices: 482661--482695 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
482651 CTAGGAGATT
482661 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
482679 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
482696 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:482826 original size:2 final size:2
Alignment explanation
Indices: 482814--482859 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
482804 GTAAACAAAT
*
482814 TA TA T- TA TA TA TA -A TA TA TA TA TA TC TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
482854 TA TA TA
1 TA TA TA
482860 AAGAAATAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:483783 original size:146 final size:148
Alignment explanation
Indices: 483589--483900 Score: 506
Period size: 147 Copynumber: 2.1 Consensus size: 148
483579 GAGTCGAGGG
* **
483589 TCTACGCGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACAT
1 TCTACGCGGTCCTTCGGGA-ATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
483654 A-TAT-ATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCTTTATAGACATCATT
65 ACT-TGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATAGACATCATT
483717 ATATGGCACTACGGTGCAAT
129 ATATGGCACTACGGTGCAAT
*
483737 TCTACGCGGTCCTTCGGG-ATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATA
1 TCTACGCGGTCCTTCGGGAATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACATA
* *
483801 CTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTAT
66 CTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATAGACATCATTAT
483866 ATGGCACTACGGTGCAAT
131 ATGGCACTACGGTGCAAT
483884 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
483901 TGCAATTATA
Statistics
Matches: 154, Mismatches: 7, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
146 44 0.29
147 92 0.60
148 18 0.12
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.35
Consensus pattern (148 bp):
TCTACGCGGTCCTTCGGGAATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACATA
CTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATAGACATCATTAT
ATGGCACTACGGTGCAAT
Found at i:483901 original size:23 final size:23
Alignment explanation
Indices: 483868--483912 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
483858 ATTATTATAT
*
483868 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
483891 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
483913 AGCTGTGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:487167 original size:64 final size:64
Alignment explanation
Indices: 487082--487242 Score: 204
Period size: 64 Copynumber: 2.5 Consensus size: 64
487072 ATTGTTAAGG
* *
487082 TGCATCGATGCACA-TGTAGTGCATCGATGCAT-GAATTTAAATAGAAAACATCGAATAGGATTT
1 TGCATCGATGCATAGTGTAGTGCATCGATGCATCCAA-TTAAATA-AAAACATCGAATAGGATTT
487145 A
64 A
* * *
487146 TGCATTGATGCATAAG-G-AGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTT
1 TGCATCGATGCAT-AGTGTAGTGCATCGATGCAT-CCAATTAAATAAAAACATCGAATAGGATTT
487209 A
64 A
*
487210 TGCATCGATGCATGGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAGTGTAGTGCATCGATGCAT
487243 ACCTTCATTA
Statistics
Matches: 84, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
63 1 0.01
64 58 0.69
65 24 0.29
66 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.28
Consensus pattern (64 bp):
TGCATCGATGCATAGTGTAGTGCATCGATGCATCCAATTAAATAAAAACATCGAATAGGATTTA
Found at i:487751 original size:18 final size:18
Alignment explanation
Indices: 487728--487762 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
487718 CTAGGAGATC
487728 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
487746 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
487763 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:488957 original size:23 final size:23
Alignment explanation
Indices: 488924--488969 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
488914 ATTATTATAT
*
488924 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
488947 GGCACTTCGGTGCAATTATACGC
1 GGCACTACGGTGCAATTATACGC
488970 TGTGTGACAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.28, G:0.26, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:497935 original size:27 final size:27
Alignment explanation
Indices: 497899--497951 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
497889 CTAAAAATTC
* *
497899 GAGTCGGGTGAAGAATATATATTTTTT
1 GAGTCAGGTGAAGAATATATAATTTTT
* *
497926 GAGTCAGGTGGAGGATATATAATTTT
1 GAGTCAGGTGAAGAATATATAATTTT
497952 CGGGTCGGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.30, C:0.04, G:0.28, T:0.38
Consensus pattern (27 bp):
GAGTCAGGTGAAGAATATATAATTTTT
Found at i:499102 original size:17 final size:18
Alignment explanation
Indices: 499064--499103 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
499054 AACATATAAT
*
499064 ATATATATATATTATTTC
1 ATATATATATATTATTTA
*
499082 ATAT-TATATATTGTTTA
1 ATATATATATATTATTTA
499099 ATATA
1 ATATA
499104 CCAAATATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (18 bp):
ATATATATATATTATTTA
Found at i:503533 original size:12 final size:13
Alignment explanation
Indices: 503506--503538 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
503496 CGTCCCTCAA
503506 TATAATTATTTAAT
1 TATAATTA-TTAAT
503520 TATAATTA-TAAT
1 TATAATTATTAAT
503532 TATAATT
1 TATAATT
503539 TAAATTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 11 0.58
14 8 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TATAATTATTAAT
Found at i:515666 original size:28 final size:28
Alignment explanation
Indices: 515626--515679 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
515616 TGATATTAAT
515626 ATAAAAATTTGATAACAAATTCTAACCC
1 ATAAAAATTTGATAACAAATTCTAACCC
* *
515654 ATAAAATTTTGATAATAAATTCTAAC
1 ATAAAAATTTGATAACAAATTCTAAC
515680 ACGTATTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.50, C:0.13, G:0.04, T:0.33
Consensus pattern (28 bp):
ATAAAAATTTGATAACAAATTCTAACCC
Found at i:523608 original size:5 final size:5
Alignment explanation
Indices: 523564--523624 Score: 59
Period size: 5 Copynumber: 11.8 Consensus size: 5
523554 AGGCAACCCA
* * * **
523564 ATTTT TTTTT TTTTT TTTTT AATTTCT ATTTT CGTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT -ATTT-T ATTTT ATTTT ATTTT ATTTT ATTTT
523616 ATTTT ATTT
1 ATTTT ATTT
523625 ACTTGATTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
5 40 0.83
6 7 0.15
7 1 0.02
ACGTcount: A:0.15, C:0.03, G:0.02, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:529111 original size:20 final size:20
Alignment explanation
Indices: 529086--529139 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
529076 GAACAACAAA
529086 TTCGCAACGCGAATTCCAAT
1 TTCGCAACGCGAATTCCAAT
* *
529106 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGA-ATTCCAAT
529126 TTCGCAACGCGAAT
1 TTCGCAACGCGAAT
529140 ATGTAAATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.07
20 24 0.86
21 2 0.07
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.26
Consensus pattern (20 bp):
TTCGCAACGCGAATTCCAAT
Found at i:529176 original size:21 final size:21
Alignment explanation
Indices: 529147--529193 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
529137 AATATGTAAA
529147 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
*
529168 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
529189 TCGCA
1 TCGCA
529194 ACGCGATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:529209 original size:20 final size:20
Alignment explanation
Indices: 529184--529251 Score: 111
Period size: 20 Copynumber: 3.4 Consensus size: 20
529174 TGCGATTTTC
529184 CAAATTCGCAACGCGATAAT
1 CAAATTCGCAACGCGATAAT
*
529204 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGATAAT
529224 CAAATTCGCAACGCGA-AAGT
1 CAAATTCGCAACGCGATAA-T
529244 CAAATTCG
1 CAAATTCG
529252 TAACTGAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
19 1 0.02
20 44 0.98
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
CAAATTCGCAACGCGATAAT
Found at i:529267 original size:19 final size:19
Alignment explanation
Indices: 529243--529293 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
529233 AACGCGAAAG
* *
529243 TCAAATTCGTAACTGAATT
1 TCAAATTCGCAACTAAATT
529262 TCAAATTCGCAACTAAATT
1 TCAAATTCGCAACTAAATT
*
529281 TCAAATTCACAAC
1 TCAAATTCGCAAC
529294 GCGAATTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.41, C:0.22, G:0.06, T:0.31
Consensus pattern (19 bp):
TCAAATTCGCAACTAAATT
Found at i:530294 original size:24 final size:24
Alignment explanation
Indices: 530212--530282 Score: 124
Period size: 24 Copynumber: 3.0 Consensus size: 24
530202 AGTCAGTATT
*
530212 CGAAATTTGATCTTGGTCAATACC
1 CGAACTTTGATCTTGGTCAATACC
530236 CGAACTTTGATCTTGGTCAATACC
1 CGAACTTTGATCTTGGTCAATACC
*
530260 CAAACTTTGATCTTGGTCAATAC
1 CGAACTTTGATCTTGGTCAATAC
530283 TCGGATTTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (24 bp):
CGAACTTTGATCTTGGTCAATACC
Found at i:530486 original size:12 final size:12
Alignment explanation
Indices: 530469--530493 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
530459 ATATAACCCT
530469 GAAGAAGAAAAA
1 GAAGAAGAAAAA
530481 GAAGAAGAAAAA
1 GAAGAAGAAAAA
530493 G
1 G
530494 TCCCCAAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:532590 original size:18 final size:18
Alignment explanation
Indices: 532557--532592 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
532547 AAGCAAAAGG
**
532557 AAATCAAAATTGCAATCA
1 AAATCAAAATCCCAATCA
532575 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
532593 CAACCGACTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:532903 original size:20 final size:20
Alignment explanation
Indices: 532878--533000 Score: 91
Period size: 20 Copynumber: 6.5 Consensus size: 20
532868 ATGTTGCGAT
532878 CAACGCGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
*
532898 CAACGC-AAAGGACAAATT-G
1 CAACGCGAAA-GTCAAATTCG
*
532917 CAATGCGAAA-T--AA---G
1 CAACGCGAAAGTCAAATTCG
*** *
532931 CGTTGCGATAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
*
532951 CAACGCGAAAGACAAATTCG
1 CAACGCGAAAGTCAAATTCG
* * *
532971 CAACACGATAGTCAAATTCA
1 CAACGCGAAAGTCAAATTCG
532991 CAACGCGAAA
1 CAACGCGAAA
533001 TCGCAAACCG
Statistics
Matches: 78, Mismatches: 17, Indels: 16
0.70 0.15 0.14
Matches are distributed among these distances:
14 8 0.10
15 1 0.01
16 2 0.03
17 2 0.03
19 9 0.12
20 56 0.72
ACGTcount: A:0.42, C:0.23, G:0.20, T:0.15
Consensus pattern (20 bp):
CAACGCGAAAGTCAAATTCG
Found at i:533173 original size:25 final size:25
Alignment explanation
Indices: 533135--533184 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
533125 AAATCAATTA
*
533135 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
533160 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
533185 GAAAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:533591 original size:18 final size:18
Alignment explanation
Indices: 533570--533606 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
533560 GTAATTGGAG
533570 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
533588 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
533606 T
1 T
533607 ATAAATTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:533613 original size:24 final size:24
Alignment explanation
Indices: 533562--533614 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
533552 TTTCATATGT
* * *
533562 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
533586 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
533610 AATTT
1 AATTT
533615 TGGCTCCAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:533959 original size:39 final size:39
Alignment explanation
Indices: 533916--534041 Score: 234
Period size: 39 Copynumber: 3.2 Consensus size: 39
533906 TCCGATGCTC
533916 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
533955 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
* *
533994 ATCAAAATCCAAATCTCATATGGTTCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
534033 ATCAAAATC
1 ATCAAAATC
534042 TACAACTTGA
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 85 1.00
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:535919 original size:21 final size:20
Alignment explanation
Indices: 535860--535920 Score: 50
Period size: 21 Copynumber: 2.9 Consensus size: 20
535850 GCATCGGGCT
* * *
535860 CTTGAACGGCGGGCGGGACCT
1 CTTGAACGGTGGG-GGGGCCA
* *
535881 CTTGAACGATGACGGGGGCCA
1 CTTGAACGGTG-GGGGGGCCA
535902 CTTGAACGGTGGGAGGGGC
1 CTTGAACGGTGGG-GGGGC
535921 TTCTTCGATG
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.18, C:0.23, G:0.44, T:0.15
Consensus pattern (20 bp):
CTTGAACGGTGGGGGGGCCA
Found at i:535974 original size:42 final size:42
Alignment explanation
Indices: 535878--535976 Score: 103
Period size: 42 Copynumber: 2.4 Consensus size: 42
535868 GCGGGCGGGA
* * * **
535878 CCTCTTGAACGATGACGGGGGCCACTTGAACGGTGGGAGGGG
1 CCTCTTGAATGATGACGGGGGCCACTTGAACGATAGGAGACG
* *
535920 CTTCTTCG-ATGATGA-GAGGGGCCTCTTGAACGATAGGAGACG
1 CCTCTT-GAATGATGACG-GGGGCCACTTGAACGATAGGAGACG
535962 CCTCTTGAATGATGA
1 CCTCTTGAATGATGA
535977 TAGGTGTATC
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
41 2 0.04
42 43 0.93
43 1 0.02
ACGTcount: A:0.22, C:0.20, G:0.35, T:0.22
Consensus pattern (42 bp):
CCTCTTGAATGATGACGGGGGCCACTTGAACGATAGGAGACG
Found at i:538156 original size:19 final size:20
Alignment explanation
Indices: 538132--538181 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
538122 AAACTTAAAT
*
538132 TCGCAACGCGAAAATG-ATA
1 TCGCAACGCGAAAATGAAAA
538151 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
538171 TTGCAACGCGA
1 TCGCAACGCGA
538182 TTTTAGTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.42, C:0.22, G:0.22, T:0.14
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:538489 original size:22 final size:22
Alignment explanation
Indices: 538461--538511 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
538451 GATGGAGATA
538461 GACGGATTTCGTCGGAAATGGG
1 GACGGATTTCGTCGGAAATGGG
*
538483 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAAATGGG
538505 GACGGAT
1 GACGGAT
538512 GTCGCCGTAG
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:0.22, C:0.14, G:0.43, T:0.22
Consensus pattern (22 bp):
GACGGATTTCGTCGGAAATGGG
Found at i:538664 original size:20 final size:20
Alignment explanation
Indices: 538639--538779 Score: 130
Period size: 20 Copynumber: 7.0 Consensus size: 20
538629 CCGTAAAAAC
538639 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
538659 ATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* *
538679 ATTTAAC-TTCTGTGTTGCG-
1 ATTTGACTTTC-GCGTTGCGA
* **
538698 ATTT-ACAAATTCGCAATGCGA
1 ATTTGAC--TTTCGCGTTGCGA
538719 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* *
538739 ATTTGACTATCGCGTTGTG-
1 ATTTGACTTTCGCGTTGCGA
538758 ATTT-ACATATTCGCGTTGCGA
1 ATTTGAC-T-TTCGCGTTGCGA
538779 A
1 A
538780 ATTAGAAACT
Statistics
Matches: 98, Mismatches: 14, Indels: 17
0.76 0.11 0.13
Matches are distributed among these distances:
18 4 0.04
19 11 0.11
20 73 0.74
21 8 0.08
22 2 0.02
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:538778 original size:60 final size:60
Alignment explanation
Indices: 538647--538779 Score: 187
Period size: 60 Copynumber: 2.2 Consensus size: 60
538637 ACATTTGACT
*
538647 TTCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTAACTTCTGTGTTGCGATTTACAAA
1 TTCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTAACTTCTGCGTTGCGATTTACAAA
** * * * *
538707 TTCGCAATGCGAATTTGACTTTCGCGTTGCGAATTTGACTATC-GCGTTGTGATTTACATA
1 TTCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTAACT-TCTGCGTTGCGATTTACAAA
538767 TTCGCGTTGCGAA
1 TTCGCGTTGCGAA
538780 ATTAGAAACT
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
60 61 0.97
61 2 0.03
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.38
Consensus pattern (60 bp):
TTCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTAACTTCTGCGTTGCGATTTACAAA
Found at i:538798 original size:80 final size:81
Alignment explanation
Indices: 538639--538841 Score: 206
Period size: 80 Copynumber: 2.5 Consensus size: 81
538629 CCGTAAAAAC
* * *
538639 ATTTGACTTTCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTAACTTCTGTGTTGCGATTTAC
1 ATTTGACTTTCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTAAATTCTGCGTTGCGAATTAC
*
538704 AAATTCGCAATGCG-A
66 AAACTCGCAATGCGAA
*
538719 ATTTGACTTTCGCGTTGCGAATTTGACTATCGCGTTGTG-ATTTACATATTC-GCGTTGCGAAAT
1 ATTTGACTTTCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTA-A-ATTCTGCGTTGCG-AAT
* *
538782 TAGAAACT-G-AGTTGCGAA
63 TACAAACTCGCA-ATGCGAA
* * * *
538800 ATTGGAATTAT--CGTTGCGAATTTGA-GATCGCTTTGCGAATTT
1 ATTTGACTT-TCGCGTTGCGAATTTGACTATCGCGTTGCGAATTT
538842 GTTGGTCATT
Statistics
Matches: 104, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
79 15 0.14
80 69 0.66
81 19 0.18
82 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.37
Consensus pattern (81 bp):
ATTTGACTTTCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTAAATTCTGCGTTGCGAATTAC
AAACTCGCAATGCGAA
Found at i:538976 original size:28 final size:29
Alignment explanation
Indices: 538927--538982 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
538917 TTTTCTCTTT
538927 ATTTTTTAAGTTATTTATTGAT-TTATTG
1 ATTTTTTAAGTTATTTATTGATGTTATTG
*
538955 ATTTTTTAA-TTTTTTATATGATGTTATT
1 ATTTTTTAAGTTATTTAT-TGATGTTATT
538983 TAGAAGAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 7 0.28
28 13 0.52
29 5 0.20
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66
Consensus pattern (29 bp):
ATTTTTTAAGTTATTTATTGATGTTATTG
Found at i:539115 original size:20 final size:20
Alignment explanation
Indices: 539090--539268 Score: 125
Period size: 20 Copynumber: 8.8 Consensus size: 20
539080 ATGCGAAACA
*
539090 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* * *
539110 AAAATCGCAATGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
*
539130 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TAAG
***
539150 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
*
539171 AAGAATCGCAATGCGATTCAA-
1 AA-AATCGCAACGCGATT-AAG
* *
539192 AGAATCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTAAG
*
539212 AAAATCGCAACGCGATTCCAG
1 AAAATCGCAACGCGATT-AAG
* * *
539233 -GAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTAAG
539252 AAAATCGCAACGCGATT
1 AAAATCGCAACGCGATT
539269 CCAAGAATCG
Statistics
Matches: 125, Mismatches: 23, Indels: 22
0.74 0.14 0.13
Matches are distributed among these distances:
18 1 0.01
19 3 0.02
20 98 0.78
21 9 0.07
22 14 0.11
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:539228 original size:40 final size:40
Alignment explanation
Indices: 539174--539281 Score: 180
Period size: 40 Copynumber: 2.7 Consensus size: 40
539164 ATCTTCCAAG
* *
539174 AATCGCAATGCGATTCAAAGAATCGCAACGCGATTGAGAA
1 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTGAGAA
* *
539214 AATCGCAACGCGATTCCAGGAATCGCAATGCGATTGAGAA
1 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTGAGAA
539254 AATCGCAACGCGATTCCAAGAATCGCAA
1 AATCGCAACGCGATTCCAAGAATCGCAA
539282 AACGGCAAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 63 1.00
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (40 bp):
AATCGCAACGCGATTCCAAGAATCGCAACGCGATTGAGAA
Found at i:539260 original size:60 final size:61
Alignment explanation
Indices: 539148--539268 Score: 192
Period size: 60 Copynumber: 2.0 Consensus size: 61
539138 AACGGTCAAA
539148 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAATGCGATTCAAAGAATCGCAACGCGATTG
1 AGAAAATCGCAACGCGA-CTTCCAAGAATCGCAATGCGATTCAAAGAATCGCAACGCGATTG
* *
539210 AGAAAATCGCAACGCGA-TTCCAGGAATCGCAATGCGATTGAGAA-AATCGCAACGCGATT
1 AGAAAATCGCAACGCGACTTCCAAGAATCGCAATGCGATTCA-AAGAATCGCAACGCGATT
539269 CCAAGAATCG
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
60 37 0.66
61 2 0.04
62 17 0.30
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.17
Consensus pattern (61 bp):
AGAAAATCGCAACGCGACTTCCAAGAATCGCAATGCGATTCAAAGAATCGCAACGCGATTG
Found at i:539277 original size:20 final size:20
Alignment explanation
Indices: 539152--539281 Score: 138
Period size: 20 Copynumber: 6.4 Consensus size: 20
539142 GTCAAAAGAA
539152 AATCGCAACGCGATCTTCCAAG
1 AATCGCAACGCGA--TTCCAAG
* *
539174 AATCGCAATGCGATTCAAAG
1 AATCGCAACGCGATTCCAAG
* *
539194 AATCGCAACGCGATT-GAGAA
1 AATCGCAACGCGATTCCA-AG
*
539214 AATCGCAACGCGATTCCAGG
1 AATCGCAACGCGATTCCAAG
* * *
539234 AATCGCAATGCGATT-GAGAA
1 AATCGCAACGCGATTCCA-AG
539254 AATCGCAACGCGATTCCAAG
1 AATCGCAACGCGATTCCAAG
539274 AATCGCAA
1 AATCGCAA
539282 AACGGCAAAA
Statistics
Matches: 89, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
19 2 0.02
20 73 0.82
21 2 0.02
22 12 0.13
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.17
Consensus pattern (20 bp):
AATCGCAACGCGATTCCAAG
Found at i:539403 original size:6 final size:6
Alignment explanation
Indices: 539392--539440 Score: 98
Period size: 6 Copynumber: 8.2 Consensus size: 6
539382 GACACGTATT
539392 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
539440 A
1 A
539441 GACGGCGGCG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.35, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:540209 original size:6 final size:6
Alignment explanation
Indices: 540198--540236 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
540188 TCTCGTCTCG
540198 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
540237 AATACGTGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.00, C:0.15, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:540372 original size:20 final size:20
Alignment explanation
Indices: 540347--540516 Score: 159
Period size: 20 Copynumber: 8.4 Consensus size: 20
540337 TTTTGCCGTT
*
540347 TTGCGATTCTTGGAATCGCA
1 TTGCGATTCTTGGAATCGCG
**
540367 TTGCGATT-TTCTCAATCGCG
1 TTGCGATTCTT-GGAATCGCG
540387 TTGCGATTCTTGGAATCGCG
1 TTGCGATTCTTGGAATCGCG
**
540407 TTGCGATT-TTCTCAATCGCG
1 TTGCGATTCTT-GGAATCGCG
*
540427 TTGCGATTATTGGAATCGCG
1 TTGCGATTCTTGGAATCGCG
**
540447 TTGCGATT-TTCTCAATCGCG
1 TTGCGATTCTT-GGAATCGCG
* *
540467 TTGCGATTCTTTGG-CTCGCA
1 TTGCGATTC-TTGGAATCGCG
540487 TTGCGATTCTTGGAAGATCGCG
1 TTGCGATTCTTGG-A-ATCGCG
*
540509 TTGTGATT
1 TTGCGATT
540517 TTCTTTTGAC
Statistics
Matches: 122, Mismatches: 18, Indels: 18
0.77 0.11 0.11
Matches are distributed among these distances:
19 10 0.08
20 95 0.78
21 4 0.03
22 13 0.11
ACGTcount: A:0.16, C:0.21, G:0.25, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTTGGAATCGCG
Found at i:540394 original size:40 final size:40
Alignment explanation
Indices: 540347--540494 Score: 244
Period size: 40 Copynumber: 3.7 Consensus size: 40
540337 TTTTGCCGTT
540347 TTGCGATTCTTGGAATCGCATTGCGATTTTCTCAATCGCG
1 TTGCGATTCTTGGAATCGCATTGCGATTTTCTCAATCGCG
*
540387 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCG
1 TTGCGATTCTTGGAATCGCATTGCGATTTTCTCAATCGCG
* *
540427 TTGCGATTATTGGAATCGCGTTGCGATTTTCTCAATCGCG
1 TTGCGATTCTTGGAATCGCATTGCGATTTTCTCAATCGCG
*
540467 TTGCGATTCTTTGG-CTCGCATTGCGATT
1 TTGCGATTC-TTGGAATCGCATTGCGATT
540495 CTTGGAAGAT
Statistics
Matches: 102, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
40 98 0.96
41 4 0.04
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.39
Consensus pattern (40 bp):
TTGCGATTCTTGGAATCGCATTGCGATTTTCTCAATCGCG
Found at i:540570 original size:20 final size:20
Alignment explanation
Indices: 540360--540597 Score: 157
Period size: 20 Copynumber: 11.8 Consensus size: 20
540350 CGATTCTTGG
* *
540360 AATCGCATTGCGATTTTCTC
1 AATCGCGTTGCGATTTTCTA
**
540380 AATCGCGTTGCGATTCTT-GG
1 AATCGCGTTGCGATT-TTCTA
*
540400 AATCGCGTTGCGATTTTCTC
1 AATCGCGTTGCGATTTTCTA
**
540420 AATCGCGTTGCGATTATT-GG
1 AATCGCGTTGCGATT-TTCTA
*
540440 AATCGCGTTGCGATTTTCTC
1 AATCGCGTTGCGATTTTCTA
*
540460 AATCGCGTTGCGATTCTT-TG
1 AATCGCGTTGCGATT-TTCTA
** * **
540480 GCTCGCATTGCGATTCTTGGA
1 AATCGCGTTGCGATT-TTCTA
*
540501 AGATCGCGTTGTGATTTTCT-
1 A-ATCGCGTTGCGATTTTCTA
* *
540521 -TTTGACCGTTGCGATTTTCT-
1 AATCG--CGTTGCGATTTTCTA
** *
540541 TTTCAACGTTGCGATTTTCTA
1 AATC-GCGTTGCGATTTTCTA
*
540562 AATCGCGTTGCGATTTT-GA
1 AATCGCGTTGCGATTTTCTA
*
540581 TATCGCGTTGCGATTTT
1 AATCGCGTTGCGATTTT
540598 GTTGGTCATT
Statistics
Matches: 175, Mismatches: 31, Indels: 25
0.76 0.13 0.11
Matches are distributed among these distances:
18 2 0.01
19 21 0.12
20 129 0.74
21 12 0.07
22 11 0.06
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.41
Consensus pattern (20 bp):
AATCGCGTTGCGATTTTCTA
Found at i:545486 original size:31 final size:31
Alignment explanation
Indices: 545451--545535 Score: 116
Period size: 31 Copynumber: 2.7 Consensus size: 31
545441 AACTACTACA
* * *
545451 CATTATCTAAATGCGAACCTGACAGATTGTG
1 CATTATCTGAATGCAAACCTGACAGACTGTG
* * *
545482 CATTATTTGAATGCAAACCTGCCATACTGTG
1 CATTATCTGAATGCAAACCTGACAGACTGTG
545513 CATTATCTGAATGCAAACCTGAC
1 CATTATCTGAATGCAAACCTGAC
545536 TAGTATCTGG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.29
Consensus pattern (31 bp):
CATTATCTGAATGCAAACCTGACAGACTGTG
Found at i:547284 original size:14 final size:14
Alignment explanation
Indices: 547249--547294 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
547239 AGCTACTTAG
547249 AGAAGATGAAGGAAGA
1 AGAA-ATGAA-GAAGA
547265 TA-AAATGAAGAAGA
1 -AGAAATGAAGAAGA
547279 AGAAATGAAG-AGA
1 AGAAATGAAGAAGA
547292 AGA
1 AGA
547295 GAAATAGGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 7 0.25
14 13 0.46
15 5 0.18
16 2 0.07
17 1 0.04
ACGTcount: A:0.61, C:0.00, G:0.30, T:0.09
Consensus pattern (14 bp):
AGAAATGAAGAAGA
Found at i:554425 original size:22 final size:21
Alignment explanation
Indices: 554400--554456 Score: 89
Period size: 20 Copynumber: 2.7 Consensus size: 21
554390 ATTAAGCTAA
554400 TTCTATAGAAGATTGTGAACCC
1 TTCTATA-AAGATTGTGAACCC
554422 TTCTAT-AAGATTGTGAACCC
1 TTCTATAAAGATTGTGAACCC
554442 TTCTATAAAGGATTG
1 TTCTATAAA-GATTG
554457 GTCTCAACGC
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 20 0.61
21 2 0.06
22 11 0.33
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (21 bp):
TTCTATAAAGATTGTGAACCC
Found at i:557584 original size:19 final size:19
Alignment explanation
Indices: 557560--557598 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
557550 CCTTAGAAAT
557560 TTTTTTACACTTAGGTGTA
1 TTTTTTACACTTAGGTGTA
557579 TTTTTTACACTTAGGTGTA
1 TTTTTTACACTTAGGTGTA
557598 T
1 T
557599 GTTTACAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.10, G:0.15, T:0.54
Consensus pattern (19 bp):
TTTTTTACACTTAGGTGTA
Found at i:557605 original size:18 final size:19
Alignment explanation
Indices: 557563--557605 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
557553 TAGAAATTTT
*
557563 TTTACACTTAGGTGTATTT
1 TTTACACTTAGGTGTATTG
557582 TTTACACTTAGGTGTA-TG
1 TTTACACTTAGGTGTATTG
557600 TTTACA
1 TTTACA
557606 ATACTTAGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.23, C:0.12, G:0.16, T:0.49
Consensus pattern (19 bp):
TTTACACTTAGGTGTATTG
Found at i:566565 original size:65 final size:65
Alignment explanation
Indices: 566449--566841 Score: 606
Period size: 65 Copynumber: 6.0 Consensus size: 65
566439 GGTTGAGTGA
* * *
566449 ACAAGTACATATCACTTATATGACTCATGTACCTTTGTCGTGCATGAGGTGGAGTGATAATTGAA
1 ACAA-TACAAATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAA
566514 T
65 T
* *
566515 ACATTACAAATCACTCATATGACTCATGTACCTTTGTGGTGCATGGGGTGGAGTGATAATTGAAT
1 ACAATACAAATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAAT
* *
566580 ACAGTACATATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAAT
1 ACAATACAAATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAAT
* * * * * *
566645 ACTATACATATCAATCATATGACTCATGTACCTTTGTGGTGCGTGAGGTGGGGTGATAATTGTAT
1 ACAATACAAATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAAT
* * *
566710 ACAATACAAATCACACATATAACTCATGTACCTTTGTGGTGCATAAGGTGGAGTGATAATTGAAT
1 ACAATACAAATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAAT
* * *
566775 ACAATACAAATCACTCATATGACTCATATAACTTTGTGGTGCATGAGGTGGATTGATAATTGAAT
1 ACAATACAAATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAAT
566840 AC
1 AC
566842 TGCAAAGATC
Statistics
Matches: 298, Mismatches: 29, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
65 295 0.99
66 3 0.01
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.32
Consensus pattern (65 bp):
ACAATACAAATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAAT
Found at i:568939 original size:22 final size:24
Alignment explanation
Indices: 568891--568941 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
568881 TGCATAGAAT
*
568891 TTTTAATTTATTATTATATAGGAA
1 TTTTAATATATTATTATATAGGAA
568915 TTTTAATAT-TTATTA-ATGAGG-A
1 TTTTAATATATTATTATAT-AGGAA
568937 TTTTA
1 TTTTA
568942 GTTTGTTAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 8 0.32
23 9 0.36
24 8 0.32
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (24 bp):
TTTTAATATATTATTATATAGGAA
Found at i:576139 original size:31 final size:32
Alignment explanation
Indices: 576071--576148 Score: 92
Period size: 32 Copynumber: 2.6 Consensus size: 32
576061 AACATACAAA
*
576071 AAAAAAACAGAAATTGAGAAAAATAACGCAAC
1 AAAAAAACAGAAATTGAGAAAAATAACGAAAC
*
576103 AAAAAACCAGAAATTGAG-AAAATAA-GAAAC
1 AAAAAAACAGAAATTGAGAAAAATAACGAAAC
**
576133 GCAAAAA-A-AAATTGAG
1 AAAAAAACAGAAATTGAG
576149 GCTTACTTGA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
28 8 0.20
29 1 0.02
30 8 0.20
31 7 0.17
32 17 0.41
ACGTcount: A:0.65, C:0.10, G:0.14, T:0.10
Consensus pattern (32 bp):
AAAAAAACAGAAATTGAGAAAAATAACGAAAC
Found at i:576222 original size:16 final size:16
Alignment explanation
Indices: 576203--576255 Score: 97
Period size: 16 Copynumber: 3.3 Consensus size: 16
576193 AGAAATGCAA
*
576203 AAAACCAGAAATTGAG
1 AAAACCAGAAATTTAG
576219 AAAACCAGAAATTTAG
1 AAAACCAGAAATTTAG
576235 AAAACCAGAAATTTAG
1 AAAACCAGAAATTTAG
576251 AAAAC
1 AAAAC
576256 ATAAAACAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.58, C:0.13, G:0.13, T:0.15
Consensus pattern (16 bp):
AAAACCAGAAATTTAG
Found at i:576223 original size:32 final size:32
Alignment explanation
Indices: 576187--576256 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
576177 AGAAAACCTT
576187 AAAACAAGAAATGCAAAAAACCAGAAATTGAG
1 AAAACAAGAAATGCAAAAAACCAGAAATTGAG
* ** * *
576219 AAAACCAGAAATTTAGAAAACCAGAAATTTAG
1 AAAACAAGAAATGCAAAAAACCAGAAATTGAG
576251 AAAACA
1 AAAACA
576257 TAAAACAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.61, C:0.13, G:0.13, T:0.13
Consensus pattern (32 bp):
AAAACAAGAAATGCAAAAAACCAGAAATTGAG
Found at i:576312 original size:14 final size:14
Alignment explanation
Indices: 576289--576322 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
576279 AAAGAAACAA
*
576289 AAAACACAAAAGAG
1 AAAACCCAAAAGAG
576303 AAAACCCAAAAGAG
1 AAAACCCAAAAGAG
576317 AAAACC
1 AAAACC
576323 AGAAATTGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.68, C:0.21, G:0.12, T:0.00
Consensus pattern (14 bp):
AAAACCCAAAAGAG
Found at i:576467 original size:22 final size:22
Alignment explanation
Indices: 576422--576467 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
576412 GGTTGGCTTT
*
576422 TGACGGCCAGAAGGACAGCGTG
1 TGACGGCCAGAAGGACAACGTG
* * *
576444 TGACGGCTAGAAGGGCAACTTG
1 TGACGGCCAGAAGGACAACGTG
576466 TG
1 TG
576468 GCGGAGAGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.26, C:0.20, G:0.39, T:0.15
Consensus pattern (22 bp):
TGACGGCCAGAAGGACAACGTG
Found at i:579238 original size:17 final size:17
Alignment explanation
Indices: 579216--579249 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
579206 ACTTTGACCC
579216 AAAAGTCAAATTTTATG
1 AAAAGTCAAATTTTATG
*
579233 AAAAGTCATATTTTATG
1 AAAAGTCAAATTTTATG
579250 TTTTTCAACG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (17 bp):
AAAAGTCAAATTTTATG
Found at i:581084 original size:36 final size:38
Alignment explanation
Indices: 581035--581110 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 38
581025 ATATCTTTTA
* **
581035 TTTTTCAAGTTATTTGGTTAAACTTTTTATGTATTTCC
1 TTTTTCAAGTTATTTGGCTAAACTTTTTAACTATTTCC
* *
581073 TTTTT-AA-TTATTTGGCTGAATTTTTTAACTATTTCC
1 TTTTTCAAGTTATTTGGCTAAACTTTTTAACTATTTCC
581109 TT
1 TT
581111 GTATTATTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
36 26 0.79
37 2 0.06
38 5 0.15
ACGTcount: A:0.21, C:0.11, G:0.09, T:0.59
Consensus pattern (38 bp):
TTTTTCAAGTTATTTGGCTAAACTTTTTAACTATTTCC
Found at i:596322 original size:2 final size:2
Alignment explanation
Indices: 596310--596345 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
596300 TGTAATATTA
596310 AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
596346 ATGAATGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:601226 original size:3 final size:3
Alignment explanation
Indices: 601218--601248 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
601208 AATCAGAGTT
601218 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
601249 GATATATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:604881 original size:19 final size:21
Alignment explanation
Indices: 604857--604898 Score: 70
Period size: 19 Copynumber: 2.1 Consensus size: 21
604847 GGAATTTTAT
604857 TTCTTCATTTT-ATAGG-TCA
1 TTCTTCATTTTAATAGGTTCA
604876 TTCTTCATTTTAATAGGTTCA
1 TTCTTCATTTTAATAGGTTCA
604897 TT
1 TT
604899 TCAAGCCCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 11 0.52
20 5 0.24
21 5 0.24
ACGTcount: A:0.21, C:0.14, G:0.10, T:0.55
Consensus pattern (21 bp):
TTCTTCATTTTAATAGGTTCA
Found at i:612610 original size:21 final size:21
Alignment explanation
Indices: 612584--612655 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
612574 TCTAGATTCA
* *
612584 CAACGCAAACTTCGACTATCG
1 CAACGCGAACTTGGACTATCG
612605 CAACGCGAACTTGGACTATCG
1 CAACGCGAACTTGGACTATCG
612626 CAACGCGAACTTGGACTATCG
1 CAACGCGAACTTGGACTATCG
*
612647 CAATGCGAA
1 CAACGCGAA
612656 TATGTAAATC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.32, C:0.29, G:0.21, T:0.18
Consensus pattern (21 bp):
CAACGCGAACTTGGACTATCG
Found at i:612775 original size:90 final size:92
Alignment explanation
Indices: 612618--612800 Score: 241
Period size: 90 Copynumber: 2.0 Consensus size: 92
612608 CGCGAACTTG
* * *
612618 GACTATCGCAACGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAA
1 GACTATCGCAACGCGAACTTGAACTATCACAATGCGAATATGTAAATCGCAATGCGATAGTCCAA
612683 GTTCGCGTTGCAATTT-TT-CAAATTC
66 GTTCGCGTTGCAATTTATTCCAAATTC
* * *
612708 GACTATCGCAACGCGAACTTTAACTATCACATTGCG-AT-T-TACATATTCGCATTGCGATAGTC
1 GACTATCGCAACGCGAACTTGAACTATCACAATGCGAATATGTA-A-A-TCGCAATGCGATAGTC
*
612770 CAAGTTCGCGTTGCGATTTATTCCAAATTC
63 CAAGTTCGCGTTGCAATTTATTCCAAATTC
612800 G
1 G
612801 TTACGATAGT
Statistics
Matches: 81, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
87 2 0.02
88 2 0.02
89 3 0.04
90 64 0.79
91 2 0.02
92 8 0.10
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.30
Consensus pattern (92 bp):
GACTATCGCAACGCGAACTTGAACTATCACAATGCGAATATGTAAATCGCAATGCGATAGTCCAA
GTTCGCGTTGCAATTTATTCCAAATTC
Found at i:612783 original size:21 final size:21
Alignment explanation
Indices: 612752--612857 Score: 85
Period size: 21 Copynumber: 5.0 Consensus size: 21
612742 CGATTTACAT
*
612752 ATTCGCATTGCGATAGTCCAA
1 ATTCGCGTTGCGATAGTCCAA
* *
612773 GTTCGCGTTGCGATTTATTCCAA
1 ATTCGCGTTGCGA--TAGTCCAA
* *
612796 ATT--CGTTACGATAGTCGAA
1 ATTCGCGTTGCGATAGTCCAA
* *
612815 GTTCGCGTTGCGATTTATTCCAA
1 ATTCGCGTTGCGA--TAGTCCAA
612838 ATT--CGTTGCGATAGTCCAA
1 ATTCGCGTTGCGATAGTCCAA
612857 A
1 A
612858 ATCGTAACGA
Statistics
Matches: 66, Mismatches: 13, Indels: 14
0.71 0.14 0.15
Matches are distributed among these distances:
19 16 0.24
21 33 0.50
23 17 0.26
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.34
Consensus pattern (21 bp):
ATTCGCGTTGCGATAGTCCAA
Found at i:612817 original size:42 final size:42
Alignment explanation
Indices: 612762--612856 Score: 172
Period size: 42 Copynumber: 2.3 Consensus size: 42
612752 ATTCGCATTG
612762 CGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTA
1 CGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTA
* *
612804 CGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTG
1 CGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTA
612846 CGATAGTCCAA
1 CGATAGTCCAA
612857 AATCGTAACG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (42 bp):
CGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTA
Found at i:612938 original size:6 final size:6
Alignment explanation
Indices: 612927--612966 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
612917 TTCGCGCGGA
612927 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACC
612967 CGAGACGAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.33, C:0.50, G:0.17, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:612977 original size:5 final size:5
Alignment explanation
Indices: 612967--612997 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
612957 GACCACGACC
612967 CGAGA CGAGA CGAGA CGAGA CGAGA CG-GA CG
1 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG
612998 GCGGCGGCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.35, C:0.23, G:0.42, T:0.00
Consensus pattern (5 bp):
CGAGA
Found at i:613696 original size:117 final size:117
Alignment explanation
Indices: 613490--613720 Score: 417
Period size: 117 Copynumber: 2.0 Consensus size: 117
613480 ACGTGTCTTC
*
613490 GACACGGCCGCGCGAATACTATTTTTTTAGAGAAAATTCTTAAGAAACAAATGCAATACTATCGC
1 GACACGGCCGCGCGAATACTATCTTTTTAGAGAAAATTCTTAAGAAACAAATGCAATACTATCGC
613555 AACGAATTTGGAATAAATCGCAACGCAAACTTCGACTATCGCAATGCGAATA
66 AACGAATTTGGAATAAATCGCAACGCAAACTTCGACTATCGCAATGCGAATA
*
613607 GACACGTCCGCGCGAATACTATCTTTTTAGAGAAAATTCTTAAGAAACAAATGCAATACTATCGC
1 GACACGGCCGCGCGAATACTATCTTTTTAGAGAAAATTCTTAAGAAACAAATGCAATACTATCGC
* * *
613672 AACGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCATTGCGA
66 AACGAATTTGGAATAAATCGCAACGCAAACTTCGACTATCGCAATGCGA
613721 TAGTCCAAGT
Statistics
Matches: 109, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
117 109 1.00
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.24
Consensus pattern (117 bp):
GACACGGCCGCGCGAATACTATCTTTTTAGAGAAAATTCTTAAGAAACAAATGCAATACTATCGC
AACGAATTTGGAATAAATCGCAACGCAAACTTCGACTATCGCAATGCGAATA
Found at i:613734 original size:21 final size:21
Alignment explanation
Indices: 613710--613762 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
613700 ACTTGGACTA
613710 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
*
613731 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAGT
* *
613752 TCACGTTGCGA
1 TCGCATTGCGA
613763 ATCTGGAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:614023 original size:18 final size:17
Alignment explanation
Indices: 614002--614047 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
613992 TTATTAAGTA
614002 AAAGAATATTATATTTTT
1 AAAG-ATATTATATTTTT
614020 AAAG-TATTATATTTTT
1 AAAGATATTATATTTTT
614036 AAAG-TA-TATATT
1 AAAGATATTATATT
614048 AAAATTTGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.21
16 18 0.64
18 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (17 bp):
AAAGATATTATATTTTT
Found at i:614045 original size:15 final size:16
Alignment explanation
Indices: 614008--614047 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
613998 AGTAAAAGAA
614008 TATTATATTTTTAAAG
1 TATTATATTTTTAAAG
614024 TATTATATTTTTAAAG
1 TATTATATTTTTAAAG
614040 TA-TATATT
1 TATTATATT
614048 AAAATTTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 6 0.25
16 18 0.75
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (16 bp):
TATTATATTTTTAAAG
Found at i:614894 original size:23 final size:23
Alignment explanation
Indices: 614845--614894 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
614835 ATGATGAATT
***
614845 TATAAAATTTTAAAGGACAATTT
1 TATAAAATTTTAAAGGACAAAAA
614868 TATAAAATTTTAAAGGA-AGAAAA
1 TATAAAATTTTAAAGGACA-AAAA
614891 TATA
1 TATA
614895 TTGTCGATAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.54, C:0.02, G:0.10, T:0.34
Consensus pattern (23 bp):
TATAAAATTTTAAAGGACAAAAA
Found at i:621929 original size:26 final size:26
Alignment explanation
Indices: 621893--621942 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
621883 TGGTATGATC
*
621893 CATAAGTAAATTATCTGTAAAAAATG
1 CATAAGTAAATTATCAGTAAAAAATG
621919 CATAAGTAAATTATCAGTAAAAAA
1 CATAAGTAAATTATCAGTAAAAAA
621943 CTATCATTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.54, C:0.08, G:0.10, T:0.28
Consensus pattern (26 bp):
CATAAGTAAATTATCAGTAAAAAATG
Found at i:623527 original size:43 final size:42
Alignment explanation
Indices: 623418--623543 Score: 162
Period size: 42 Copynumber: 2.9 Consensus size: 42
623408 CTGTACAACA
* * * *
623418 CAAAGATATATAAGAATTAACCACATGCAATAACAAGCTTCCT
1 CAAA-ATATATAAGCATTAACAATATGCAATAACAAGTTTCCT
*
623461 CAAAATATATAAGCATTAGCAATATGCAATAACAAGTTTCCT
1 CAAAATATATAAGCATTAACAATATGCAATAACAAGTTTCCT
*
623503 GAAGAATATATAAGCATTAACAATATGCACACTAACAAGTT
1 CAA-AATATATAAGCATTAACAATATGCA-A-TAACAAGTT
623544 ATACCTATTT
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
42 35 0.48
43 28 0.38
44 1 0.01
45 9 0.12
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.25
Consensus pattern (42 bp):
CAAAATATATAAGCATTAACAATATGCAATAACAAGTTTCCT
Found at i:628607 original size:23 final size:23
Alignment explanation
Indices: 628576--628635 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
628566 ATTATTATAT
*
628576 GGCATTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
628599 GGCACTACGGTGCAATTCTATGT
1 GGCACTACGGTGCAATTCTACGC
*
628622 GGCACTTCGGTGCA
1 GGCACTACGGTGCA
628636 TTTATATAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:636583 original size:21 final size:22
Alignment explanation
Indices: 636557--636665 Score: 109
Period size: 21 Copynumber: 5.0 Consensus size: 22
636547 CACATAGAAC
636557 GTCCCGAAGGA-CAATATATAT
1 GTCCCGAAGGACCAATATATAT
* * *
636578 GTCCCGAATGACCACAAAGA-ATT
1 GTCCCGAAGGACCA-ATATATA-T
636601 GTCCCGAAGGACC-ATATATAT
1 GTCCCGAAGGACCAATATATAT
* *
636622 GTTCCAAAGGACCAA-ATATAT
1 GTCCCGAAGGACCAATATATAT
*
636643 GTCCCAAAGGACCACATATATAT
1 GTCCCGAAGGACCA-ATATATAT
636666 TCCAAAGGAT
Statistics
Matches: 72, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
21 44 0.61
22 6 0.08
23 22 0.31
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.22
Consensus pattern (22 bp):
GTCCCGAAGGACCAATATATAT
Found at i:636593 original size:43 final size:44
Alignment explanation
Indices: 636538--636623 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
636528 ATCATATGCA
*
636538 CCGAAGTGCCACATAGAA-CGTCCCGAAGGACAATATATATGTC
1 CCGAAGTGCCACAAAGAATCGTCCCGAAGGACAATATATATGTC
* *
636581 CCGAA-TGACCACAAAGAATTGTCCCGAAGGACCATATATATGT
1 CCGAAGTG-CCACAAAGAATCGTCCCGAAGGACAATATATATGT
636624 TCCAAAGGAC
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
42 2 0.05
43 14 0.37
44 22 0.58
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (44 bp):
CCGAAGTGCCACAAAGAATCGTCCCGAAGGACAATATATATGTC
Done.