Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008016.1 Hibiscus syriacus cultivar Beakdansim tig00110482_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: 5469637
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 25
Found at i:1450631 original size:479 final size:479
Alignment explanation
Indices: 1449557--1451410 Score: 2923
Period size: 479 Copynumber: 3.8 Consensus size: 479
1449547 TTTTTACCTG
* * * * * *
1449557 TTATATTGTAAAATATTTATCCTTTTTATAAAAGTGTTCATACTTTTTTCAATGTGTAAAATATT
1 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATT
* *
1449622 AATTTAAGGTTATTTTTTAAGTGAGTTTTAAGAAATTAATTTAGTAATTATAGGCGTCTAATAAT
66 AATTTAAGG-------TT-A-TGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGAT
1449687 TTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATAT
122 TTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATAT
1449752 TTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAA
187 TTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAA
1449817 ACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAA
252 ACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAA
1449882 CACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAA
317 CACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAA
1449947 AAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTA
382 AAGTAT-GACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTA
*
1450012 ATAGGTAGCGTTTATATAATATAATAGGTAGTGC
446 ATAGGTAGCGTTTATATAATGTAATAGGTAGTGC
* * *
1450046 TTATATTGTAAAGTATCTATCATTTTTATAAAAATGTCCATACTTTTTTCATTGTGGAAAACATT
1 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATT
*
1450111 AATTTAAGG-T-T-AGTTTTAAGATATTAATTTAGTAATTATAGGCGCCTAATGATTTATTTTTT
66 AATTTAAGGTTATGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTT
*
1450173 ACGGTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTA
131 ACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTA
1450238 TCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAA
196 TCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAA
* * *
1450303 TAATTTTTGGTGTAAATGAAATTATTAAATTAATATTGTAGGTGTAAAACATGAAACATTATTAA
261 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-A
*
1450368 AAAAAATTGAAACATAAATTACATAACTTTTAAAAAAAATATCGATCATTTTTATAAAAAGTATG
325 AAAAAATTGAAACATAAATTACATAAC-TTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATG
* *
1450433 AACACTTTCAATATAATAGGTAAAAGTATGATGTAATAAGTAGCGCTTATATAATGTAATAGGTA
389 -ACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTA
*
1450498 GCGTTTATATAATGTAATAGGTAGTAC
453 GCGTTTATATAATGTAATAGGTAGTGC
* * *
1450525 TTATATTGTAAAGTATTTATCCTTTTTATAAAATTGTCCATACTTTTTTCACTGTGGAAAATATT
1 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATT
1450590 AATTTAAGG-T-T-AGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTT
66 AATTTAAGGTTATGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTT
* ** *
1450652 ATGTTACTATATTTATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTA
131 ACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTA
* *
1450717 TCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATTAAAACAATTAAA
196 TCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAA
*
1450782 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAA
261 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
* * * *
1450847 AAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCTATCCTTTTAATAAAAAGGATCGA
326 AAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTAT-GA
*
1450912 TACTTTACAATAT-ATCAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTA
390 CACTTT-CAATATAAT-AGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTA
* * *
1450976 GCGCTTATATAATGTAATAGGTAGCGT
453 GCGTTTATATAATGTAATAGGTAGTGC
* * * *
1451003 TTATATTGTAAATTATCTATCCTTTTTATATAAGTGTCCATACTTATATCACTGTGGAAAACATT
1 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATT
* **
1451068 AATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATATGTATCTAATGAT
66 AATTTAAGG-------TT-A-TGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGAT
* * *
1451133 TTATTTTTTATGTTACGGTATATATTATCATTAAATTAAAAACGATAAACATATATATTACATAT
122 TTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATAT
* *
1451198 TTATTATTATCTTTGGTTAATATTATTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAA
187 TTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATC-AA
*
1451263 AACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAA
251 AACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAA
*
1451328 ACACTATT-AAAAAATTAAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAA
316 ACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAA
*
1451392 AAAGTATAGACAATTTCAA
381 AAAGTAT-GACACTTTCAA
1451411 CATATTATAA
Statistics
Matches: 1268, Mismatches: 78, Indels: 38
0.92 0.06 0.03
Matches are distributed among these distances:
477 276 0.22
478 201 0.16
479 425 0.34
481 1 0.00
486 1 0.00
489 70 0.06
490 222 0.18
491 72 0.06
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.41
Consensus pattern (479 bp):
TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATT
AATTTAAGGTTATGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTT
ACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTA
TCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAA
TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
AAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGAC
ACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCG
TTTATATAATGTAATAGGTAGTGC
Found at i:1450917 original size:22 final size:21
Alignment explanation
Indices: 1450873--1450917 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
1450863 ATTACATAAC
* * *
1450873 TTTAAAAAAAGTATCTATCCT
1 TTTAAAAAAAGGATCGATACT
1450894 TTTAATAAAAAGGATCGATACT
1 TTTAA-AAAAAGGATCGATACT
1450916 TT
1 TT
1450918 ACAATATATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (21 bp):
TTTAAAAAAAGGATCGATACT
Found at i:1451013 original size:21 final size:23
Alignment explanation
Indices: 1450936--1451008 Score: 128
Period size: 23 Copynumber: 3.2 Consensus size: 23
1450926 TCAGGTAAAA
*
1450936 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
1450959 ATATAATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
1450982 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
1451005 ATAT
1 ATAT
1451009 TGTAAATTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.34, C:0.07, G:0.22, T:0.37
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1456269 original size:4 final size:4
Alignment explanation
Indices: 1456262--1456293 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
1456252 CAATGAATGT
*
1456262 ATAA ATAA ATAA ATAA ATAA ATAA ATAC ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
1456294 TTGGCAGAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:1457281 original size:22 final size:21
Alignment explanation
Indices: 1457208--1457295 Score: 67
Period size: 19 Copynumber: 4.2 Consensus size: 21
1457198 CGCGATTTTG
1457208 AAAAATGTGTTGCGATAGT--
1 AAAAATGTGTTGCGATAGTGA
* * *
1457227 TAAAATGTATTGCGAGAGTTTGA
1 AAAAATGTGTTGCGATAG--TGA
*
1457250 AAAACGTGTTGTTGCGATAGTGA
1 AAAA-ATG-TGTTGCGATAGTGA
*
1457273 AAAAA--TGTTACGATAGTGA
1 AAAAATGTGTTGCGATAGTGA
1457292 AAAA
1 AAAA
1457296 TCCAAAATAA
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
19 32 0.59
21 1 0.02
23 10 0.19
24 2 0.04
25 9 0.17
ACGTcount: A:0.40, C:0.06, G:0.25, T:0.30
Consensus pattern (21 bp):
AAAAATGTGTTGCGATAGTGA
Found at i:1461447 original size:22 final size:22
Alignment explanation
Indices: 1461422--1461463 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1461412 GAATTTTTTC
* *
1461422 TTAACTTATTTTTATATATTAT
1 TTAACTTATTCTAATATATTAT
*
1461444 TTAATTTATTCTAATATATT
1 TTAACTTATTCTAATATATT
1461464 TAAACTGTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (22 bp):
TTAACTTATTCTAATATATTAT
Found at i:1474135 original size:55 final size:55
Alignment explanation
Indices: 1474069--1474233 Score: 276
Period size: 55 Copynumber: 3.0 Consensus size: 55
1474059 AGGCGTTCAG
* *
1474069 ATGATTCATGAAGAATGAAATCCGATGAATAAAGAAATTTGAACCTGACTGAAGA
1 ATGATTCATGAAGAATGACATCCGATGAATGAAGAAATTTGAACCTGACTGAAGA
*
1474124 ATGATTCATGAAGAATGGCATCCGATGAATGAAGAAATTTGAACCTGACTGAAGA
1 ATGATTCATGAAGAATGACATCCGATGAATGAAGAAATTTGAACCTGACTGAAGA
* * *
1474179 ACGATTCATGAAGAATGACATCCGATGAATGAAGAAATTTGAAACTGATTGAAGA
1 ATGATTCATGAAGAATGACATCCGATGAATGAAGAAATTTGAACCTGACTGAAGA
1474234 CAGATCCACA
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 103 1.00
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.24
Consensus pattern (55 bp):
ATGATTCATGAAGAATGACATCCGATGAATGAAGAAATTTGAACCTGACTGAAGA
Found at i:1475035 original size:72 final size:72
Alignment explanation
Indices: 1474915--1475065 Score: 257
Period size: 72 Copynumber: 2.1 Consensus size: 72
1474905 CCCTATTACA
* * *
1474915 CAAGAAAATATGAAGACTTCGGGTGAGAATCTGAATGTTAGTGATGCAGCCAATGTGATGATAGC
1 CAAGAACAGATGAAGACTTCGAGTGAGAATCTGAATGTTAGTGATGCAGCCAATGTGATGATAGC
1474980 AAATGAT
66 AAATGAT
*
1474987 CAAGAACAGATGAAGACTTCGAGTGAGAATCTGAATGTTAGTGGTGCAGCCAATGTGATGATAGC
1 CAAGAACAGATGAAGACTTCGAGTGAGAATCTGAATGTTAGTGATGCAGCCAATGTGATGATAGC
*
1475052 AACTGAT
66 AAATGAT
1475059 CAAGAAC
1 CAAGAAC
1475066 CTGTTAGGGG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.23
Consensus pattern (72 bp):
CAAGAACAGATGAAGACTTCGAGTGAGAATCTGAATGTTAGTGATGCAGCCAATGTGATGATAGC
AAATGAT
Found at i:1478682 original size:125 final size:125
Alignment explanation
Indices: 1478460--1478708 Score: 335
Period size: 125 Copynumber: 2.0 Consensus size: 125
1478450 TACCCACATT
* * *
1478460 GGGGCATGACTAAACCCACATCATGTTGAGATGACAAGATTTGAACCAAGGAGTCATGAAGAATG
1 GGGGCACGACTAAACCCACATCATGTTGAGATGACAAGATTAGAACCAAGGAGGCATGAAGAATG
* *
1478525 AGCCTTACAAATTGAGGTGATTGGGCATTTTGAAGGCTCGTACCAGTATGAGATAATGTC
66 AGCCTTACAAATTGAGGTGATTGGGCATTTTGAAGGCTCGTACCAGAATAAGATAATGTC
* *
1478585 GGGGCACGACTGAACCCACATCATGTTGAGATGATAAGATTCAG-ACCAA-GATGGCATTGAA-A
1 GGGGCACGACTAAACCCACATCATGTTGAGATGACAAGATT-AGAACCAAGGA-GGCA-TGAAGA
* * * *
1478647 ATGAGCCTTATAATTTGAGGTG-TTGGGGCATTTTGAAGGCTCTTACCTGAATAAGATAATGT
63 ATGAGCCTTACAAATTGAGGTGATT-GGGCATTTTGAAGGCTCGTACCAGAATAAGATAATGT
1478709 TGCGGCATTA
Statistics
Matches: 109, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
124 4 0.04
125 100 0.92
126 5 0.05
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (125 bp):
GGGGCACGACTAAACCCACATCATGTTGAGATGACAAGATTAGAACCAAGGAGGCATGAAGAATG
AGCCTTACAAATTGAGGTGATTGGGCATTTTGAAGGCTCGTACCAGAATAAGATAATGTC
Found at i:1480000 original size:36 final size:36
Alignment explanation
Indices: 1479921--1480008 Score: 124
Period size: 36 Copynumber: 2.4 Consensus size: 36
1479911 GTCTTCACCA
* * *
1479921 AAGAGTAGTGAAGCAAATCCATTTTGAGCCTTCACT
1 AAGAGTAGTGAAGCAAATCCATCTTAAGCCTTCACG
1479957 AACGAGTAGTGAAGCAAA-CCATCTTAAGCCTTCATCG
1 AA-GAGTAGTGAAGCAAATCCATCTTAAGCCTTCA-CG
1479994 AAGAGTAGTGAAGCA
1 AAGAGTAGTGAAGCA
1480009 TATCTTTTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
36 29 0.62
37 18 0.38
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (36 bp):
AAGAGTAGTGAAGCAAATCCATCTTAAGCCTTCACG
Found at i:1480494 original size:54 final size:54
Alignment explanation
Indices: 1480413--1480570 Score: 289
Period size: 54 Copynumber: 2.9 Consensus size: 54
1480403 GTAGTAAAGC
*
1480413 AGAAGAAAATGTTCGAGTTTCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
1 AGAAGAAAATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
*
1480467 AGAAGAAAATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCAAACCTGTA
1 AGAAGAAAATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
*
1480521 AGAAGAATATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACC
1 AGAAGAAAATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACC
1480571 CGTTTGTTGA
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 100 1.00
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.19
Consensus pattern (54 bp):
AGAAGAAAATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
Found at i:1480621 original size:55 final size:55
Alignment explanation
Indices: 1480542--1480966 Score: 433
Period size: 55 Copynumber: 7.8 Consensus size: 55
1480532 TTCGAGTTCC
* *
1480542 ATACTCCCT-AGAGAAAGAGGGAGC-GAACCCGTTTGTTGAAGATTGTTCGAGT-TCT
1 ATACTCCCTGA-AGGAATAGGGAGCAG-ACCCGTTTGTTGAAGATTGTTCGAGTCT-T
* * *
1480597 ATACTCTCTGAAGGAATAGAGAGCGGACCCGTTT-TATGAAGATTGTTCGAGT-TCT
1 ATACTCCCTGAAGGAATAGGGAGCAGACCCGTTTGT-TGAAGATTGTTCGAGTCT-T
* *
1480652 ATACTCCCTGAACGG-ATAGGGAGCAGACCTGTTT-TATGAAGATTGTTCGAGTCCT
1 ATACTCCCTGAA-GGAATAGGGAGCAGACCCGTTTGT-TGAAGATTGTTCGAGTCTT
* ** ** * *
1480707 ATACTCTCTGAATAAATAGGGAGCAGACATGTTTATTGAA-A---ATCGAGTCTT
1 ATACTCCCTGAAGGAATAGGGAGCAGACCCGTTTGTTGAAGATTGTTCGAGTCTT
* * *
1480758 ATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGTTGAAGATTATTCGAGTCTT
1 ATACTCCCTGAAGGAATAGGGAGCAGACCCGTTTGTTGAAGATTGTTCGAGTCTT
* * *
1480813 ATACTCCCTGAACGAATAGGGAGCAGACACGTTTGTTGAAGATTGTTTGAGTCTT
1 ATACTCCCTGAAGGAATAGGGAGCAGACCCGTTTGTTGAAGATTGTTCGAGTCTT
* * ***
1480868 ATACTCCCTGAATGAATAGGGAGCAGACACGTTTGCCAAAGATTGTTCGAGTCTT
1 ATACTCCCTGAAGGAATAGGGAGCAGACCCGTTTGTTGAAGATTGTTCGAGTCTT
* * * *
1480923 ATACTCCTTGAAAGAAAAGGGAGCAAACCCGTTAT-TTGAAGATT
1 ATACTCCCTGAAGGAATAGGGAGCAGACCCGTT-TGTTGAAGATT
1480967 TTTCAAGTAT
Statistics
Matches: 317, Mismatches: 41, Indels: 24
0.83 0.11 0.06
Matches are distributed among these distances:
51 42 0.13
52 1 0.00
54 2 0.01
55 266 0.84
56 6 0.02
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.29
Consensus pattern (55 bp):
ATACTCCCTGAAGGAATAGGGAGCAGACCCGTTTGTTGAAGATTGTTCGAGTCTT
Found at i:1480785 original size:161 final size:161
Alignment explanation
Indices: 1480588--1480901 Score: 476
Period size: 161 Copynumber: 2.0 Consensus size: 161
1480578 TGAAGATTGT
*
1480588 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTT-TATGAAGATTGTTCGAGT-TC
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGT-TGAAGATTATTCGAGTCT-
* *
1480651 TATACTCCCTGAACGGATAGGGAGCAGAC-CTGTTT-TATGAAGATTGTTCGAGTCCTATACTCT
64 TATACTCCCTGAACGAATAGGGAGCAGACAC-GTTTGT-TGAAGATTGTTCGAGTCCTATACTCC
*
1480714 CTGAATAAATAGGGAGCAGACATGTTTATTGAAAA
127 CTGAATAAATAGGGAGCAGACACGTTTATTGAAAA
*
1480749 TCGAG-TCTTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGTTGAAGATTATTCGAGTCTT
1 TCGAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTATTCGAGTCTT
* *
1480813 ATACTCCCTGAACGAATAGGGAGCAGACACGTTTGTTGAAGATTGTTTGAGTCTTATACTCCCTG
65 ATACTCCCTGAACGAATAGGGAGCAGACACGTTTGTTGAAGATTGTTCGAGTCCTATACTCCCTG
*
1480878 AATGAATAGGGAGCAGACACGTTT
130 AATAAATAGGGAGCAGACACGTTT
1480902 GCCAAAGATT
Statistics
Matches: 140, Mismatches: 8, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
160 2 0.01
161 134 0.96
162 4 0.03
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (161 bp):
TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTATTCGAGTCTTA
TACTCCCTGAACGAATAGGGAGCAGACACGTTTGTTGAAGATTGTTCGAGTCCTATACTCCCTGA
ATAAATAGGGAGCAGACACGTTTATTGAAAA
Found at i:1489299 original size:2 final size:2
Alignment explanation
Indices: 1489292--1489339 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1489282 ATATCTTTAA
1489292 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1489334 AT AT AT
1 AT AT AT
1489340 TCGATATCCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1492750 original size:17 final size:18
Alignment explanation
Indices: 1492715--1492755 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1492705 ATATTATGTA
*
1492715 TTTAATTTATTTAATTAT
1 TTTACTTTATTTAATTAT
1492733 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAATTAT
1492750 TTTACT
1 TTTACT
1492756 AATATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTACTTTATTTAATTAT
Found at i:1494459 original size:18 final size:18
Alignment explanation
Indices: 1494432--1494468 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1494422 ACAGTAGCCA
* *
1494432 CCGCAGCCATTTATGATG
1 CCGCAACCATATATGATG
1494450 CCGCAACCATATATGATG
1 CCGCAACCATATATGATG
1494468 C
1 C
1494469 TGTCATCGCC
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:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (18 bp):
CCGCAACCATATATGATG
Found at i:1498829 original size:51 final size:50
Alignment explanation
Indices: 1498770--1498899 Score: 147
Period size: 51 Copynumber: 2.5 Consensus size: 50
1498760 CCCCTACGTG
** *
1498770 GCGTATAGCGCGGATTAGGGGGCGCGCTATA-CACACGTGTAAC-CCATGTCT
1 GCGTATAGCGCGG-TTAGGGGGCGCGCTATACCACACGTG--ACGCCAAATCA
* *
1498821 GCGTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGACGCCAAATCA
1 GCGTATAGCGCGGT-TAGGGGGCGCGCTATACCACACGTGACGCCAAATCA
*
1498872 GCATATAGCGCGGTTCAGGGGGCGCGCT
1 GCGTATAGCGCGGTT-AGGGGGCGCGCT
1498900 TTACTGCTAC
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
50 3 0.04
51 58 0.85
52 7 0.10
ACGTcount: A:0.20, C:0.28, G:0.35, T:0.18
Consensus pattern (50 bp):
GCGTATAGCGCGGTTAGGGGGCGCGCTATACCACACGTGACGCCAAATCA
Found at i:1498973 original size:30 final size:29
Alignment explanation
Indices: 1498911--1498973 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
1498901 TACTGCTACG
* * *
1498911 GGTGTTAGATCGGGAAATATAATATGACC
1 GGTGTTAGATCAGGAAATATAAGATCACC
* *
1498940 GGTGTTAGATCAGTAAATATACCGATCACC
1 GGTGTTAGATCAGGAAATATA-AGATCACC
1498970 GGTG
1 GGTG
1498974 ATTTTTCGAG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 19 0.68
30 9 0.32
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (29 bp):
GGTGTTAGATCAGGAAATATAAGATCACC
Found at i:1500156 original size:21 final size:21
Alignment explanation
Indices: 1500109--1500149 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1500099 TAGTTTGATA
*
1500109 ATTCACGATATTGATATGACG
1 ATTCATGATATTGATATGACG
*
1500130 ATTCATGATATTGATGTGAC
1 ATTCATGATATTGATATGAC
1500150 ACTTCATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.37
Consensus pattern (21 bp):
ATTCATGATATTGATATGACG
Found at i:1511290 original size:35 final size:35
Alignment explanation
Indices: 1511216--1511324 Score: 155
Period size: 35 Copynumber: 3.0 Consensus size: 35
1511206 ATATTTCAAC
* *
1511216 AAACATCTACCAAACTTTGAAAAACTATTTTTCAAAG
1 AAACATTTACCAAACTTTG-AAAACCA-TTTTCAAAG
*
1511253 AAACATTTACCTAACTTTGAAAACCATTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCATTTTCAAAG
1511288 AAACATTTACCAAACTTTGAAAACCAAATTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACC--ATTTTCAAAG
1511325 TTGGTTGCCA
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
35 33 0.50
36 6 0.09
37 27 0.41
ACGTcount: A:0.46, C:0.19, G:0.06, T:0.29
Consensus pattern (35 bp):
AAACATTTACCAAACTTTGAAAACCATTTTCAAAG
Found at i:1515909 original size:35 final size:35
Alignment explanation
Indices: 1515822--1515937 Score: 153
Period size: 35 Copynumber: 3.2 Consensus size: 35
1515812 TTATCCCATT
* *
1515822 ACAATATTTC-AACAAACATCTACCAAACTTTGAAAA
1 ACAAT-TTTCAAAGAAACATTTACCAAACTTTG-AAA
*
1515858 ACTATTTTTCAAAGAAACATTTACCAAACTTTGAAA
1 AC-AATTTTCAAAGAAACATTTACCAAACTTTGAAA
*
1515894 ACAATTTTCAAAGAAACATTTATCAAACTTTGAAA
1 ACAATTTTCAAAGAAACATTTACCAAACTTTGAAA
1515929 ACCAATTTT
1 A-CAATTTT
1515938 TAAAAGTTGG
Statistics
Matches: 72, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
35 32 0.44
36 18 0.25
37 22 0.31
ACGTcount: A:0.47, C:0.18, G:0.04, T:0.31
Consensus pattern (35 bp):
ACAATTTTCAAAGAAACATTTACCAAACTTTGAAA
Found at i:1515965 original size:34 final size:34
Alignment explanation
Indices: 1515917--1516007 Score: 148
Period size: 34 Copynumber: 2.7 Consensus size: 34
1515907 AAACATTTAT
*
1515917 CAAACTTTGAAAACCAATTTTTAAAAGTTGGTTGC
1 CAAAC-TTGAAAACCAATTTTTAAAAGTTGATTGC
1515952 CAAACTTGAAAACCAATTTTTAAAAGTTGATTGC
1 CAAACTTGAAAACCAATTTTTAAAAGTTGATTGC
*
1515986 CAAACTTAAAAACC-ATTTTTAA
1 CAAACTTGAAAACCAATTTTTAA
1516008 CAATACTTTC
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 8 0.15
34 41 0.76
35 5 0.09
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (34 bp):
CAAACTTGAAAACCAATTTTTAAAAGTTGATTGC
Found at i:1521024 original size:96 final size:97
Alignment explanation
Indices: 1520898--1521090 Score: 379
Period size: 96 Copynumber: 2.0 Consensus size: 97
1520888 TTTTATTATT
1520898 TTGGGTCGGGTCGGGTTTCTAATTCATATATTCAGGTCGGGTCGGGTCGGGTGAAACTTTATTTT
1 TTGGGTCGGGTCGGGTTTCTAATTCATATATTCAGGTCGGGTCGGGTCGGGTGAAACTTTATTTT
1520963 GGTCGGTTCGGGTTCGGG-TTAGGGTAAAAAA
66 GGTCGGTTCGGGTTCGGGTTTAGGGTAAAAAA
1520994 TTGGGTCGGGTCGGGTTTCTAATTCATATATTCAGGTCGGGTCGGGTCGGGTGAAACTTTATTTT
1 TTGGGTCGGGTCGGGTTTCTAATTCATATATTCAGGTCGGGTCGGGTCGGGTGAAACTTTATTTT
1521059 GGTCGGTTCGGGTTCGGGTTTAGGGTAAAAAA
66 GGTCGGTTCGGGTTCGGGTTTAGGGTAAAAAA
1521091 CCGGACCGAC
Statistics
Matches: 96, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
96 83 0.86
97 13 0.14
ACGTcount: A:0.18, C:0.12, G:0.35, T:0.35
Consensus pattern (97 bp):
TTGGGTCGGGTCGGGTTTCTAATTCATATATTCAGGTCGGGTCGGGTCGGGTGAAACTTTATTTT
GGTCGGTTCGGGTTCGGGTTTAGGGTAAAAAA
Found at i:1521255 original size:147 final size:149
Alignment explanation
Indices: 1521059--1521372 Score: 474
Period size: 152 Copynumber: 2.1 Consensus size: 149
1521049 ACTTTATTTT
*
1521059 GGTCGGTTCGGGTTCGGGTTTAGGGTAAAAAACCGGACCGACCTAAAAATATATATAA-T-TCGG
1 GGTCGGGTC-GGTTCGGGTTTAGGGTAAAAAACCGGACCGACCTAAAAATATATATAATTGTCGG
*
1521122 GTCGGATTAAGTCACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCAGG-C-CGG
65 GTCGGATTAAGTAACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCAGGTCGCGG
*
1521185 ATTTCTAATTCATATATTCG
130 ATTTCTAATTCACATATTCG
*
1521205 GGTCGGGTCGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCTGAAAATATATATAATTCGGG
1 GGTCGGGTCGGTTCGGGTTTAGGGT--AAAAAACCGGACCGACCTAAAAATATATATAATT---G
*
1521270 TCGGGTCGGATTAAGTAACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTC
61 TCGGGTCGGATTAAGTAACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCAGGTC
1521335 GGGTCGGATTTCTAATTCACATATTCG
126 --G-CGGATTTCTAATTCACATATTCG
1521362 GGTCGGGTCGG
1 GGTCGGGTCGG
1521373 ATGAAATTTT
Statistics
Matches: 151, Mismatches: 5, Indels: 13
0.89 0.03 0.08
Matches are distributed among these distances:
145 16 0.11
146 8 0.05
147 31 0.21
148 1 0.01
152 61 0.40
153 1 0.01
157 33 0.22
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (149 bp):
GGTCGGGTCGGTTCGGGTTTAGGGTAAAAAACCGGACCGACCTAAAAATATATATAATTGTCGGG
TCGGATTAAGTAACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCAGGTCGCGGA
TTTCTAATTCACATATTCG
Found at i:1521432 original size:37 final size:38
Alignment explanation
Indices: 1521388--1521470 Score: 150
Period size: 37 Copynumber: 2.2 Consensus size: 38
1521378 ATTTTATTTT
1521388 GTTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
1 GTTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
*
1521426 G-TCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGG
1 GTTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
1521463 GTTCGGGT
1 GTTCGGGT
1521471 TTAGGGTGAA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
37 36 0.84
38 7 0.16
ACGTcount: A:0.11, C:0.11, G:0.40, T:0.39
Consensus pattern (38 bp):
GTTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
Found at i:1521480 original size:248 final size:246
Alignment explanation
Indices: 1521207--1521768 Score: 826
Period size: 248 Copynumber: 2.2 Consensus size: 246
1521197 TATATTCGGG
* * *
1521207 TCGGGTC-GGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCTGAAAATATATATAATTCGGGT
1 TCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACAGGACCGACCCGAAAATATATATAATTCGAGT
1521271 CGGGTCGGATTAAGTAACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCG
66 CGGGTCGGATTAAGTAACTGTTTTTATTAAATAAAAATAATTTTTTATTATTT----T-GGGTCG
*
1521336 GGTCGGATTTCTAATTCACATATTCGGGTCGGGTCGGATGAAATTTTATTTTGTTCGGGTC-G-G
126 GGTCGGATTTCTAATTCACATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGAG
* *
1521399 GTTTTTTAAGTGTGATATTCGGGTCGAGTCGGGTCG-GGTTTTTTAAGTGTGATAT
191 GTTTTTTAAGTGTGATATTCGGGTCGAGTCGAGTAGAGGTTTTTTAAGTGTGATAT
* *
1521454 TCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACTGGACTGACCCGAAAATATATATAATTCGAGT
1 TCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACAGGACCGACCCGAAAATATATATAATTCGAGT
*
1521519 CGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTTGGGTCGGGTCG
66 CGGGTCGGATTAAGTAACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTTGGGTCGGGTCG
* * *
1521584 GATTTCTAATTCATATATTCGGGTTGGGTCGGATGAAACTTTCTTTTGTTCGGGTCGGGTCAGGT
131 GATTTCTAATTCACATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTC-GG--AGGT
*
1521649 TTTTTAAGTGTGATATTCGGGTCGAGTCGAGTAGAGTTTTTTTAAGTGTGATAT
193 TTTTTAAGTGTGATATTCGGGTCGAGTCGAGTAGAGGTTTTTTAAGTGTGATAT
* * *
1521703 TCGGGTCAGGTCGGGTTCGAGTTTAGGGTGAAAAAAACAGGACCGACCCCAAAAAAATATATAAT
1 TC--G---GGTCGGGTTCGGGTTTAGGGTGAAAAAAACAGGACCGA-CCCGAAAATATATATAAT
1521768 T
60 T
1521769 TTACCTTATA
Statistics
Matches: 285, Mismatches: 17, Indels: 18
0.89 0.05 0.06
Matches are distributed among these distances:
243 63 0.22
244 1 0.00
245 1 0.00
247 7 0.02
248 140 0.49
249 20 0.07
251 1 0.00
254 35 0.12
255 17 0.06
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.36
Consensus pattern (246 bp):
TCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACAGGACCGACCCGAAAATATATATAATTCGAGT
CGGGTCGGATTAAGTAACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTTGGGTCGGGTCG
GATTTCTAATTCACATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGAGGTTTT
TTAAGTGTGATATTCGGGTCGAGTCGAGTAGAGGTTTTTTAAGTGTGATAT
Found at i:1522313 original size:16 final size:18
Alignment explanation
Indices: 1522289--1522334 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
1522279 TATGGAATTG
1522289 GATTCCAATTCC-T-ACA
1 GATTCCAATTCCTTCACA
*
1522305 GATTTCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
1522323 GATTCCAATTCC
1 GATTCCAATTCC
1522335 CTCATAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 11 0.42
17 1 0.04
18 14 0.54
ACGTcount: A:0.28, C:0.30, G:0.07, T:0.35
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:1530051 original size:29 final size:30
Alignment explanation
Indices: 1530019--1530084 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
1530009 AATGATGTAA
1530019 TAATTA-ATAATA-TTTATATAATTA-TAAAT
1 TAATTATA-AATATTTTATAT-ATTATTAAAT
1530048 TAATTATAAATATTTTATATATTATTAAAT
1 TAATTATAAATATTTTATATATTATTAAAT
1530078 T-ATTATA
1 TAATTATA
1530085 GTATAATCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 20 0.59
30 14 0.41
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
TAATTATAAATATTTTATATATTATTAAAT
Found at i:1531174 original size:276 final size:276
Alignment explanation
Indices: 1530681--1531236 Score: 1094
Period size: 276 Copynumber: 2.0 Consensus size: 276
1530671 TAAATGAGTT
*
1530681 AGTAACTCATTCCATTGTTTATTCTAGTGAGAGAAGTTGGTGAAGGCTCCAAAAGTAAAAATAAA
1 AGTAACTCATTCCATTGTTTATTCTAGTGAGAGAAGTTGGTGAAGGCTCCAAAAGTAAAAACAAA
1530746 GGGAAAGAGGTGCTTGATTGAGCCTTGGGTTATTTCTTCAGCCTCTAAGTGAAAGGTAACAATAC
66 GGGAAAGAGGTGCTTGATTGAGCCTTGGGTTATTTCTTCAGCCTCTAAGTGAAAGGTAACAATAC
1530811 TTCTAACCTTTCATTACTGCTTGTAGATTAGCATATGAAGTTTTCATGCATGTTTATGAGCCATT
131 TTCTAACCTTTCATTACTGCTTGTAGATTAGCATATGAAGTTTTCATGCATGTTTATGAGCCATT
1530876 TGTGTGCACTTGGGGGTTTTAAACATGAAAACGAGAATTGATGTTATTCATGCAAAAAGTAATGA
196 TGTGTGCACTTGGGGGTTTTAAACATGAAAACGAGAATTGATGTTATTCATGCAAAAAGTAATGA
1530941 CCTTTCATATTCCTTA
261 CCTTTCATATTCCTTA
1530957 AGTAACTCATTCCATTGTTTATTCTAGTGAGAGAAGTTGGTGAAGGCTCCAAAAGTAAAAACAAA
1 AGTAACTCATTCCATTGTTTATTCTAGTGAGAGAAGTTGGTGAAGGCTCCAAAAGTAAAAACAAA
1531022 GGGAAAGAGGTGCTTGATTGAGCCTTGGGTTATTTCTTCAGCCTCTAAGTGAAAGGTAACAATAC
66 GGGAAAGAGGTGCTTGATTGAGCCTTGGGTTATTTCTTCAGCCTCTAAGTGAAAGGTAACAATAC
*
1531087 TTCTAGCCTTTCATTACTGCTTGTAGATTAGCATATGAAGTTTTCATGCATGTTTATGAGCCATT
131 TTCTAACCTTTCATTACTGCTTGTAGATTAGCATATGAAGTTTTCATGCATGTTTATGAGCCATT
1531152 TGTGTGCACTTGGGGGTTTTAAACATGAAAACGAGAATTGATGTTATTCATGCAAAAAGTAATGA
196 TGTGTGCACTTGGGGGTTTTAAACATGAAAACGAGAATTGATGTTATTCATGCAAAAAGTAATGA
1531217 CCTTTCATATTCCTTA
261 CCTTTCATATTCCTTA
1531233 AGTA
1 AGTA
1531237 CTAAATAGTC
Statistics
Matches: 278, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
276 278 1.00
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.34
Consensus pattern (276 bp):
AGTAACTCATTCCATTGTTTATTCTAGTGAGAGAAGTTGGTGAAGGCTCCAAAAGTAAAAACAAA
GGGAAAGAGGTGCTTGATTGAGCCTTGGGTTATTTCTTCAGCCTCTAAGTGAAAGGTAACAATAC
TTCTAACCTTTCATTACTGCTTGTAGATTAGCATATGAAGTTTTCATGCATGTTTATGAGCCATT
TGTGTGCACTTGGGGGTTTTAAACATGAAAACGAGAATTGATGTTATTCATGCAAAAAGTAATGA
CCTTTCATATTCCTTA
Found at i:1533955 original size:24 final size:26
Alignment explanation
Indices: 1533903--1533957 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
1533893 TATTAAGAAT
* *
1533903 TTTAAAATTATGTTTGTGCTCATTTA
1 TTTAAAATTATGTGTGTGCTCATTCA
*
1533929 TTTAAAATTATGTGTGT-C-CGTTCA
1 TTTAAAATTATGTGTGTGCTCATTCA
1533953 TTTAA
1 TTTAA
1533958 TCTTTGGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 9 0.35
25 1 0.04
26 16 0.62
ACGTcount: A:0.27, C:0.09, G:0.13, T:0.51
Consensus pattern (26 bp):
TTTAAAATTATGTGTGTGCTCATTCA
Found at i:1534829 original size:6 final size:6
Alignment explanation
Indices: 1534818--1534849 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
1534808 AATAAACTTC
1534818 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT AT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT AT
1534850 ATTTAACTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
ATTTAT
Found at i:1535264 original size:2 final size:2
Alignment explanation
Indices: 1535257--1535486 Score: 117
Period size: 2 Copynumber: 117.0 Consensus size: 2
1535247 GCACCAAACA
1535257 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * * * * *
1535299 TC TC TC CC TC CC GC TC TC TC TC TC CC CC TC CC TC CC TC CC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * * * * * *
1535341 CC CC CC TC TC TC TC TC TC TC -C CC CC TC CC TC -C CC CC CC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * * *
1535381 TC TC TC TC TC TC TC -C CC CC TC CC TC CC CC CC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * * * * * *
1535422 TC TC CC CC TC TC CC CC CC CC CC CC CC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * *
1535464 -C CC CC TC TC TC TC CC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC
1535487 CGTATATAGA
Statistics
Matches: 193, Mismatches: 31, Indels: 8
0.83 0.13 0.03
Matches are distributed among these distances:
1 4 0.02
2 189 0.98
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (2 bp):
TC
Found at i:1537145 original size:26 final size:28
Alignment explanation
Indices: 1537116--1537185 Score: 71
Period size: 26 Copynumber: 2.7 Consensus size: 28
1537106 GATGATGATG
1537116 ATAAATATTT-TATA-ATTT-AAAAAATT
1 ATAAAT-TTTATATATATTTGAAAAAATT
*
1537142 ATAAATTTTATATATTTTTGAAAAAATT
1 ATAAATTTTATATATATTTGAAAAAATT
*
1537170 -TGAA-TTTATAT-TATTT
1 ATAAATTTTATATATATTT
1537186 TTGTATTGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
25 7 0.18
26 17 0.45
27 6 0.16
28 8 0.21
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
ATAAATTTTATATATATTTGAAAAAATT
Found at i:1537187 original size:28 final size:28
Alignment explanation
Indices: 1537134--1537188 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
1537124 TTTATAATTT
1537134 AAAAAATTATAAATTTTATATATTTTTG
1 AAAAAATTATAAATTTTATATATTTTTG
*
1537162 AAAAAATT-TGAA-TTTATATTATTTTTG
1 AAAAAATTATAAATTTTATA-TATTTTTG
1537189 TATTGAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 6 0.24
27 11 0.44
28 8 0.32
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (28 bp):
AAAAAATTATAAATTTTATATATTTTTG
Found at i:1537658 original size:10 final size:10
Alignment explanation
Indices: 1537628--1537691 Score: 56
Period size: 10 Copynumber: 6.2 Consensus size: 10
1537618 TTTAGCTTTA
*
1537628 TATTCTTTTT
1 TATTCATTTT
* *
1537638 TATTGAATTT
1 TATTCATTTT
1537648 TATTCACTTTT
1 TATTCA-TTTT
* *
1537659 AATTCTTTTT
1 TATTCATTTT
1537669 TATTACATTTT
1 TATT-CATTTT
*
1537680 TATTGATTTT
1 TATTCATTTT
1537690 TA
1 TA
1537692 AAAAAATAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
10 26 0.62
11 16 0.38
ACGTcount: A:0.22, C:0.08, G:0.03, T:0.67
Consensus pattern (10 bp):
TATTCATTTT
Found at i:1537658 original size:21 final size:21
Alignment explanation
Indices: 1537634--1537691 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
1537624 TTTATATTCT
*
1537634 TTTTTATTGAATTTTATT-CA
1 TTTTTATTGATTTTTATTACA
* **
1537654 CTTTTAATTCTTTTTTATTACA
1 -TTTTTATTGATTTTTATTACA
1537676 TTTTTATTGATTTTTA
1 TTTTTATTGATTTTTA
1537692 AAAAAATAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
21 27 0.93
22 2 0.07
ACGTcount: A:0.22, C:0.07, G:0.03, T:0.67
Consensus pattern (21 bp):
TTTTTATTGATTTTTATTACA
Found at i:1537767 original size:22 final size:22
Alignment explanation
Indices: 1537733--1537777 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1537723 AATTGTAATT
*
1537733 AAAAGTATAAAAA-TGTAATAAA
1 AAAAGAATAAAAAGTG-AATAAA
*
1537755 AAAAGAATTAAAAGTGAATAAA
1 AAAAGAATAAAAAGTGAATAAA
1537777 A
1 A
1537778 TTTAATACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.69, C:0.00, G:0.11, T:0.20
Consensus pattern (22 bp):
AAAAGAATAAAAAGTGAATAAA
Found at i:1537784 original size:32 final size:31
Alignment explanation
Indices: 1537729--1537799 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 31
1537719 TATCAATTGT
1537729 AATTAAAAGTATAAAAATGTAATAAAAAAAG
1 AATTAAAAGTATAAAAATGTAATAAAAAAAG
* *
1537760 AATTAAAAGTGA-ATAAAATTTAATACAAAAAG
1 AATTAAAAGT-ATA-AAAATGTAATAAAAAAAG
1537792 AATATAAA
1 AAT-TAAA
1537800 GTCACTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 11 0.31
32 20 0.57
33 4 0.11
ACGTcount: A:0.66, C:0.01, G:0.08, T:0.24
Consensus pattern (31 bp):
AATTAAAAGTATAAAAATGTAATAAAAAAAG
Found at i:1537837 original size:26 final size:26
Alignment explanation
Indices: 1537808--1537857 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1537798 AAGTCACTTT
1537808 TTTTTAAAAATATATAAA-ATTTATAA
1 TTTTTAAAAATATA-AAATATTTATAA
* *
1537834 TTTTTTAAATTATAAAATATTTAT
1 TTTTTAAAAATATAAAATATTTAT
1537858 TATCATCATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 18 0.86
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
TTTTTAAAAATATAAAATATTTATAA
Found at i:1539234 original size:24 final size:24
Alignment explanation
Indices: 1539202--1539249 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1539192 TGGTCAATGG
1539202 TTCGAGTTCCCAGAGTCGTCGGTA
1 TTCGAGTTCCCAGAGTCGTCGGTA
1539226 TTCGAGTTCCCAGAGTCGTCGGTA
1 TTCGAGTTCCCAGAGTCGTCGGTA
1539250 CGTTTATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.25, G:0.29, T:0.29
Consensus pattern (24 bp):
TTCGAGTTCCCAGAGTCGTCGGTA
Found at i:1540712 original size:26 final size:25
Alignment explanation
Indices: 1540659--1540720 Score: 58
Period size: 26 Copynumber: 2.5 Consensus size: 25
1540649 TTTAGATCCT
* *
1540659 TATACATT-ATTTTTAATTTTTAAG
1 TATACATTAATTTTTAATTTATAAA
1540683 TATACATTAATTTTT-ATTTAAATAAA
1 TATACATTAATTTTTAATTT--ATAAA
1540709 TATA-ATTTAATT
1 TATACA-TTAATT
1540721 AAATTTTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 12 0.38
25 7 0.22
26 13 0.41
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (25 bp):
TATACATTAATTTTTAATTTATAAA
Found at i:1543349 original size:20 final size:20
Alignment explanation
Indices: 1543299--1543349 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
1543289 CGTGTAATTT
*
1543299 TAATTATA-CAAAAAAATGA
1 TAATTATATTAAAAAAATGA
*
1543318 TGAATTTATATTAAAAGAATGA
1 T-AA-TTATATTAAAAAAATGA
1543340 TAATTATATT
1 TAATTATATT
1543350 TCTTTTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 1 0.04
20 9 0.33
21 7 0.26
22 10 0.37
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (20 bp):
TAATTATATTAAAAAAATGA
Found at i:1545250 original size:33 final size:31
Alignment explanation
Indices: 1545213--1545277 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 31
1545203 AGTTCTCGCC
*
1545213 ATCCATAAATCCAAACAAATT-CAAAATCAATCA
1 ATCCACAAATCCAAAC--ATTCCAAAAT-AATCA
*
1545246 ATCCACAAATTCAAACATTCCAAAATAATCA
1 ATCCACAAATCCAAACATTCCAAAATAATCA
1545277 A
1 A
1545278 AATGCTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 9 0.31
32 6 0.21
33 14 0.48
ACGTcount: A:0.54, C:0.25, G:0.00, T:0.22
Consensus pattern (31 bp):
ATCCACAAATCCAAACATTCCAAAATAATCA
Found at i:1545839 original size:108 final size:108
Alignment explanation
Indices: 1545650--1545865 Score: 432
Period size: 108 Copynumber: 2.0 Consensus size: 108
1545640 GAAGCTCGGG
1545650 ATCGTCATCAGCTTCTGGTTGAGCTCGTGAAGAACTAGCTCCCGGAGTATTTTCAGACGATCGAG
1 ATCGTCATCAGCTTCTGGTTGAGCTCGTGAAGAACTAGCTCCCGGAGTATTTTCAGACGATCGAG
1545715 CCCATTCACCGGTTTCCTTATCCTTTATCCATCCCGCTCTTGT
66 CCCATTCACCGGTTTCCTTATCCTTTATCCATCCCGCTCTTGT
1545758 ATCGTCATCAGCTTCTGGTTGAGCTCGTGAAGAACTAGCTCCCGGAGTATTTTCAGACGATCGAG
1 ATCGTCATCAGCTTCTGGTTGAGCTCGTGAAGAACTAGCTCCCGGAGTATTTTCAGACGATCGAG
1545823 CCCATTCACCGGTTTCCTTATCCTTTATCCATCCCGCTCTTGT
66 CCCATTCACCGGTTTCCTTATCCTTTATCCATCCCGCTCTTGT
1545866 TAAAGAAAGA
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
108 108 1.00
ACGTcount: A:0.19, C:0.30, G:0.19, T:0.32
Consensus pattern (108 bp):
ATCGTCATCAGCTTCTGGTTGAGCTCGTGAAGAACTAGCTCCCGGAGTATTTTCAGACGATCGAG
CCCATTCACCGGTTTCCTTATCCTTTATCCATCCCGCTCTTGT
Found at i:1547370 original size:19 final size:20
Alignment explanation
Indices: 1547346--1547424 Score: 63
Period size: 19 Copynumber: 3.9 Consensus size: 20
1547336 CCAAAACCCC
*
1547346 AGGGGGTATCGATTCCCCT-
1 AGGGGGAATCGATTCCCCTA
*
1547365 AGGGGGAATCGGTTCCCCTTTAA
1 AGGGGGAATCGATTCCCC--T-A
*
1547388 AGGGGGAATCGGTT-CCCTCA
1 AGGGGGAATCGATTCCCCT-A
* *
1547408 TGGGGGTATCGATTCCC
1 AGGGGGAATCGATTCCC
1547425 TCTGCACCAA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
19 16 0.33
20 13 0.27
21 3 0.06
22 3 0.06
23 14 0.29
ACGTcount: A:0.18, C:0.24, G:0.33, T:0.25
Consensus pattern (20 bp):
AGGGGGAATCGATTCCCCTA
Found at i:1547418 original size:20 final size:20
Alignment explanation
Indices: 1547389--1547426 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1547379 CCCCTTTAAA
*
1547389 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
1547409 GGGGGTATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
1547427 TGCACCAAAA
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:0.13, C:0.26, G:0.34, T:0.26
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:1551255 original size:22 final size:21
Alignment explanation
Indices: 1551213--1551252 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1551203 GAGTTTATTT
*
1551213 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1551234 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1551253 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1559285 original size:12 final size:12
Alignment explanation
Indices: 1559270--1559298 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1559260 CAAGGCCATG
1559270 CATCGATGCATC
1 CATCGATGCATC
1559282 CATCGATGCATC
1 CATCGATGCATC
1559294 CATCG
1 CATCG
1559299 GGTTTTGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.24, C:0.34, G:0.17, T:0.24
Consensus pattern (12 bp):
CATCGATGCATC
Found at i:1560788 original size:3 final size:3
Alignment explanation
Indices: 1560780--1560804 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1560770 TCTTCTCGTG
1560780 CTC CTC CTC CTC CTC CTC CTC CTC C
1 CTC CTC CTC CTC CTC CTC CTC CTC C
1560805 GGCACCGGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (3 bp):
CTC
Found at i:1561981 original size:65 final size:64
Alignment explanation
Indices: 1561904--1562057 Score: 213
Period size: 65 Copynumber: 2.4 Consensus size: 64
1561894 GAATAAATTG
* *
1561904 AACATCGAATGCATTTTATGCATCGATACACATA-CCATGCATCGATGCACTCAGGGT-TTTATG
1 AACATCGAATGCATTTCATGCATCGATACACA-AGCCATGCATCGATGCACTCAGGCTATTT-TG
1561967 AA
64 -A
* * * *
1561969 AACATCGAATGCATTTGATACATCGATGCACAAGCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTCATGCATCGATACACAAGCCATGCATCGATGCACTCAGGCTATTTTGA
1562033 AACATCGAATGCATTTCATGCATCG
1 AACATCGAATGCATTTCATGCATCG
1562058 GTGTACTAAG
Statistics
Matches: 80, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
64 25 0.31
65 52 0.65
66 3 0.04
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.29
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATACACAAGCCATGCATCGATGCACTCAGGCTATTTTGA
Found at i:1562079 original size:64 final size:63
Alignment explanation
Indices: 1561876--1562083 Score: 190
Period size: 65 Copynumber: 3.3 Consensus size: 63
1561866 TTTTCAAAGT
** * * *
1561876 GATGCACCGATGCAC-CTGGAATAAATTG-AACATCGAATGCATTTTATGCATCGATACACATAC
1 GATGCACCGATGCACTCTGG-ATATTTTGAAACATCGAATGCATTTCATGCATCGATGCAC-TAA
* * * * * *
1561939 CATGCATCGATGCACTCAGGGT-TTTATGAAAACATCGAATGCATTTGATACATCGATGCAC-AA
1 GATGCACCGATGCACTCTGGATATTT-TG-AAACATCGAATGCATTTCATGCATCGATGCACTAA
* * * *
1562002 GCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCATTTCATGCATCGGTGTACTAA
1 G--ATGCACCGATGCACTCTGGATATTTTGAAACATCGAATGCATTTCATGCATCGATGCACTAA
1562067 GAGTGCACCGATGCACT
1 GA-TGCACCGATGCACT
1562084 AAGTGTAACA
Statistics
Matches: 118, Mismatches: 18, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
62 1 0.01
63 18 0.15
64 44 0.37
65 52 0.44
66 3 0.03
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.27
Consensus pattern (63 bp):
GATGCACCGATGCACTCTGGATATTTTGAAACATCGAATGCATTTCATGCATCGATGCACTAA
Found at i:1562821 original size:21 final size:21
Alignment explanation
Indices: 1562795--1562839 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1562785 GATTTATGGG
* *
1562795 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1562816 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1562837 CAA
1 CAA
1562840 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1564709 original size:105 final size:104
Alignment explanation
Indices: 1564538--1564753 Score: 335
Period size: 105 Copynumber: 2.1 Consensus size: 104
1564528 CCTTTGGGAC
* * ** *
1564538 ATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCTTGGCATATGTAT
1 ATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAACATATATAT
* *
1564603 ATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATAT
66 ATGATTCTTAAGGAATGATATGTAGTCCTTAGGGACAT-T
*
1564643 ATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAATATATATAT
1 ATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAACATATATAT
*
1564708 ATGATTCTTAAGGAATGATATGTAGTCCTTATGGACATT
66 ATGATTCTTAAGGAATGATATGTAGTCCTTAGGGACATT
1564747 AT-TATAT
1 ATATATAT
1564754 GGCACTACGA
Statistics
Matches: 102, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
103 5 0.05
104 3 0.03
105 94 0.92
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (104 bp):
ATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAACATATATAT
ATGATTCTTAAGGAATGATATGTAGTCCTTAGGGACATT
Found at i:1564790 original size:23 final size:23
Alignment explanation
Indices: 1564754--1564821 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
1564744 ATTATTATAT
*
1564754 GGCACTACGATGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* **
1564777 GGCACTCCGGTGCAATTCTACAT
1 GGCACTACGGTGCAATTCTACGC
* * *
1564800 TGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
1564822 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:1568661 original size:20 final size:23
Alignment explanation
Indices: 1568604--1568661 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 23
1568594 GCATGGGTAG
*
1568604 TGCATCGATGCACATGTTAAGGGA
1 TGCATCGATGCAC-TGTTAAGGAA
* *
1568628 TGCATCGGTACACTG-T-A-GAA
1 TGCATCGATGCACTGTTAAGGAA
1568648 TGCATCGATGCACT
1 TGCATCGATGCACT
1568662 TCAAGGGGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 14 0.48
21 1 0.03
22 1 0.03
23 2 0.07
24 11 0.38
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (23 bp):
TGCATCGATGCACTGTTAAGGAA
Found at i:1572282 original size:23 final size:23
Alignment explanation
Indices: 1572222--1572285 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
1572212 CATCTAATAT
1572222 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACGTAG
* * * *
1572245 AATTGCACTGTAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCACGTAG
1572268 AAATGCACC-AGAGTGCCA
1 AAATGCACCGA-AGTGCCA
1572286 TGTAAGATTG
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.31, C:0.25, G:0.27, T:0.17
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGTAG
Found at i:1573975 original size:64 final size:62
Alignment explanation
Indices: 1573866--1574026 Score: 187
Period size: 64 Copynumber: 2.5 Consensus size: 62
1573856 TCTTTAACAT
* * * * * *
1573866 GTGCATCGATGCACTACCCATGCATCGATACACAAATTACCTTCGATGTTTTCATTTTAAGGG
1 GTGCATCGATGCACT-CCTATGCATCGATACACTAACTACATTCGATATTTCCATTTTAAGGG
* * * *
1573929 GATGTATCGATGCACTCCTTATGCATCGATGCACTAACTGCATTCGATATTTCCATTTTAATGG
1 G-TGCATCGATGCACTCC-TATGCATCGATACACTAACTACATTCGATATTTCCATTTTAAGGG
*
1573993 GTGCATCGATGCACTTCCTGTGCATCGATACACT
1 GTGCATCGATGCAC-TCCTATGCATCGATACACT
1574027 CTGAACAATT
Statistics
Matches: 82, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
63 29 0.35
64 53 0.65
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (62 bp):
GTGCATCGATGCACTCCTATGCATCGATACACTAACTACATTCGATATTTCCATTTTAAGGG
Found at i:1575132 original size:23 final size:23
Alignment explanation
Indices: 1575078--1575132 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
1575068 GAGTATATAG
1575078 ATATAT-AAAATATCATATAAACC
1 ATATATAAAAATATCATATAAA-C
*
1575101 ATACA-AAAAATATCATATAATA-
1 ATATATAAAAATATCATATAA-AC
1575123 ATATATAAAA
1 ATATATAAAA
1575133 TACGTAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
22 4 0.15
23 22 0.81
24 1 0.04
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (23 bp):
ATATATAAAAATATCATATAAAC
Found at i:1581754 original size:11 final size:11
Alignment explanation
Indices: 1581738--1581775 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
1581728 TTTAGATTTT
1581738 TTATTTTTAAA
1 TTATTTTTAAA
1581749 TTATTTTT---
1 TTATTTTTAAA
1581757 TTATTTTTAAA
1 TTATTTTTAAA
1581768 TTATTTTT
1 TTATTTTT
1581776 TATATAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
8 8 0.33
11 16 0.67
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTATTTTTAAA
Found at i:1581758 original size:19 final size:19
Alignment explanation
Indices: 1581734--1581776 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
1581724 AAAATTTAGA
1581734 TTTTTTATTTTTAAATTAT
1 TTTTTTATTTTTAAATTAT
1581753 TTTTTTATTTTTAAATTAT
1 TTTTTTATTTTTAAATTAT
1581772 TTTTT
1 TTTTT
1581777 ATATAATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTTTATTTTTAAATTAT
Found at i:1583472 original size:4 final size:4
Alignment explanation
Indices: 1583463--1583488 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1583453 TTCTCTTTTC
1583463 TATT TATT TATT TATT TATT TATT TA
1 TATT TATT TATT TATT TATT TATT TA
1583489 ACTTACTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:1583794 original size:28 final size:28
Alignment explanation
Indices: 1583757--1583829 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 28
1583747 ATTTGTTGTG
* *
1583757 GTGGAGGGGGCTGCTGGGTTACTTGAAAT
1 GTGGA-GGGGTTGCTGGGTTACTTGAAAC
**
1583786 GTGGAGGGGTTGCTGGGTTGTTTGAAAC
1 GTGGAGGGGTTGCTGGGTTACTTGAAAC
1583814 GTGGAGGGGTTGCTGG
1 GTGGAGGGGTTGCTGG
1583830 TTATGAAAGG
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 35 0.88
29 5 0.12
ACGTcount: A:0.14, C:0.08, G:0.49, T:0.29
Consensus pattern (28 bp):
GTGGAGGGGTTGCTGGGTTACTTGAAAC
Found at i:1584440 original size:48 final size:48
Alignment explanation
Indices: 1584378--1584615 Score: 349
Period size: 48 Copynumber: 5.0 Consensus size: 48
1584368 TAAAATCTCA
*
1584378 TTTG-AAAACATCATGCACTGAAGGTCTTATGGATGACCCGAAGGCTT
1 TTTGAAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGGCTT
* * *
1584425 CTTGAAAAACTTCATGCACTGAAGGTCTTATGGATGACCCGAAGGCTT
1 TTTGAAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGGCTT
* *
1584473 TTTGAAAAACATCCTCCACTAAAGGTCTTATGGATGACCCGAAGGCTT
1 TTTGAAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGGCTT
* *
1584521 TTTAAAAAAAATCCTGCACTGAAGGTCTTAT-GATGACCCGAAGGCTT
1 TTTGAAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGGCTT
* * *
1584568 TTTG-AAAGCATCCTGCACTGAAGGTCTTATAGATGATCCGAAGG-TT
1 TTTGAAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGGCTT
1584614 TT
1 TT
1584616 ACAAATTACC
Statistics
Matches: 174, Mismatches: 15, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
46 28 0.16
47 34 0.20
48 112 0.64
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (48 bp):
TTTGAAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGGCTT
Found at i:1584812 original size:42 final size:42
Alignment explanation
Indices: 1584747--1584828 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
1584737 AAGGACTTAT
* * * * *
1584747 CATCTTGCTCGAAAGACTGACAGATGACCCGGAGGTTTTAAG
1 CATCATGCTCAAAAGACTAACAGATGACCCGAAGGATTTAAG
1584789 CATCATGCTCAAAAGACTAACAGATGACCCGAAGGATTTA
1 CATCATGCTCAAAAGACTAACAGATGACCCGAAGGATTTA
1584829 CAAAGTTATG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (42 bp):
CATCATGCTCAAAAGACTAACAGATGACCCGAAGGATTTAAG
Found at i:1585061 original size:42 final size:42
Alignment explanation
Indices: 1584996--1585077 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
1584986 AAGGACTTAT
* * * *
1584996 CATCTTGCTCGAAAAACTGACAGATGACCCGAAGGTTTTAAG
1 CATCATGCTCGAAAAACTAACAGATAACCCGAAGGATTTAAG
*
1585038 CATCATGCTCGAAAGACTAACAGATAACCCGAAGGATTTA
1 CATCATGCTCGAAAAACTAACAGATAACCCGAAGGATTTA
1585078 CAAATTTGTG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (42 bp):
CATCATGCTCGAAAAACTAACAGATAACCCGAAGGATTTAAG
Found at i:1585080 original size:249 final size:249
Alignment explanation
Indices: 1584637--1585660 Score: 1692
Period size: 249 Copynumber: 4.1 Consensus size: 249
1584627 GGAGGTTTTA
* * * *
1584637 ATTTTCTAGAACATTAAATGAGAAACTTTGATAATCGTTTTCTCATTTTCATGTGAAAATCATAT
1 ATTTTCTAGAACATTAAATGAGAAACTTTGAAAATCGCTATCTCATTTTCATGCGAAAATCATAT
*
1584702 GTGAACAT-CTACCTAAAGGCTTTACGGATGGCCCTAAGGACTTATCATCTTGCTCGAAAGACTG
66 GTGAACATCCTACCCAAAGGCTTTACGGATGGCCCTAAGGACTTATCATCTTGCTCGAAAGACTG
*
1584766 ACAGATGACCCGGAGGTTTTAAGCATCATGCTCAAAAGACTAACAGATGACCCGAAGGATTTACA
131 ACAGATGACCCGAAGGTTTTAAGCATCATGCTCAAAAGACTAACAGATGACCCGAAGGATTTACA
* * *
1584831 AAGTTATGGGAAATACTTTACTGGGTAAGAAACTTCTTACTTTTCAAGAATTTG
196 AATTTGTGGGAAATACTTTACTAGGTAAGAAACTTCTTACTTTTCAAGAATTTG
* *
1584885 ATTTTGTAGAACATTAAATGAGAAACTTTGAAAACCGCTATCTCATTTTCATGCGAAAATCATAT
1 ATTTTCTAGAACATTAAATGAGAAACTTTGAAAATCGCTATCTCATTTTCATGCGAAAATCATAT
* * *
1584950 GTGAACATCCTACCCAAAGACTTTACGGATGGGCCTAAGGACTTATCATCTTGCTCGAAAAACTG
66 GTGAACATCCTACCCAAAGGCTTTACGGATGGCCCTAAGGACTTATCATCTTGCTCGAAAGACTG
* *
1585015 ACAGATGACCCGAAGGTTTTAAGCATCATGCTCGAAAGACTAACAGATAACCCGAAGGATTTACA
131 ACAGATGACCCGAAGGTTTTAAGCATCATGCTCAAAAGACTAACAGATGACCCGAAGGATTTACA
1585080 AATTTGTGGGAAATACTTTACTAGGTAAGAAACTTCTTACTTTTCAAGAATTTG
196 AATTTGTGGGAAATACTTTACTAGGTAAGAAACTTCTTACTTTTCAAGAATTTG
* *
1585134 ATTTTCTAGAACATTAAATGATAAACTTTGAAAATCGTTATCTCATTTTCATGCGAAAATCATAT
1 ATTTTCTAGAACATTAAATGAGAAACTTTGAAAATCGCTATCTCATTTTCATGCGAAAATCATAT
* *
1585199 GTGAACATCCTACCCAAAGGCTTTACGGGTGGCCCTAAGGACTTATCATCTTGCTTGAAAGACTG
66 GTGAACATCCTACCCAAAGGCTTTACGGATGGCCCTAAGGACTTATCATCTTGCTCGAAAGACTG
* * * *
1585264 ACAGATGACCCGGAGGTTTTAAGCATCATACTCAAAAGACTAACAGATTACCCGAAGGATTTAAA
131 ACAGATGACCCGAAGGTTTTAAGCATCATGCTCAAAAGACTAACAGATGACCCGAAGGATTTACA
*
1585329 AATTTGTGGGAAATACTTTACTAGGTAAAAAACTTCTTACTTTTCAAGAATTTG
196 AATTTGTGGGAAATACTTTACTAGGTAAGAAACTTCTTACTTTTCAAGAATTTG
*
1585383 ATTTTCTAGAACATTAAATGAGAAACTTTGAAAATTGCTATCTCATTTTCATGCGAAAATCATAT
1 ATTTTCTAGAACATTAAATGAGAAACTTTGAAAATCGCTATCTCATTTTCATGCGAAAATCATAT
* *
1585448 GTGAACATCCTACCCAAAGGCTTTACGGATGGCCCTAAGGACTTAT-ATCTTGCTTGAAAGACTA
66 GTGAACATCCTACCCAAAGGCTTTACGGATGGCCCTAAGGACTTATCATCTTGCTCGAAAGACTG
* * *
1585512 ACAGATGACCTGATGGTTTTAAGCATCATGCTCGAAAGACTAACAGATGACCCGAAGGATTTACA
131 ACAGATGACCCGAAGGTTTTAAGCATCATGCTCAAAAGACTAACAGATGACCCGAAGGATTTACA
* * *
1585577 AATTTGTGGGAAATACTTTACTGGGTAAGAAACTTATTACTTTTCAAGAATTTC
196 AATTTGTGGGAAATACTTTACTAGGTAAGAAACTTCTTACTTTTCAAGAATTTG
* *
1585631 ATTTTCTAAAAAAGATTAAATGAGAAACTT
1 ATTTTCT--AGAACATTAAATGAGAAACTT
1585661 ATTGGTTGGG
Statistics
Matches: 724, Mismatches: 49, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
248 199 0.27
249 506 0.70
250 19 0.03
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (249 bp):
ATTTTCTAGAACATTAAATGAGAAACTTTGAAAATCGCTATCTCATTTTCATGCGAAAATCATAT
GTGAACATCCTACCCAAAGGCTTTACGGATGGCCCTAAGGACTTATCATCTTGCTCGAAAGACTG
ACAGATGACCCGAAGGTTTTAAGCATCATGCTCAAAAGACTAACAGATGACCCGAAGGATTTACA
AATTTGTGGGAAATACTTTACTAGGTAAGAAACTTCTTACTTTTCAAGAATTTG
Found at i:1586845 original size:51 final size:50
Alignment explanation
Indices: 1586753--1586900 Score: 197
Period size: 52 Copynumber: 2.9 Consensus size: 50
1586743 ATATTTCAAC
* * *
1586753 CTTTTTATGCTGGTGTGAGCCTTTAAGATGCCTCACATGGATTACTTCTGT
1 CTTTTTATGCTGATGTGAGCCTTTAAGATGCC-CACATGGATAACTTATGT
1586804 CTTTTTCATGCTGATGTGAGCCTTTAAGATGCCCACATGGATAACTTATGT
1 CTTTTT-ATGCTGATGTGAGCCTTTAAGATGCCCACATGGATAACTTATGT
* * *
1586855 CTTTTTTTATGCTGATGTGAGCCTTCAATATGCCCTAGATGGATAA
1 C--TTTTTATGCTGATGTGAGCCTTTAAGATGCCC-ACATGGATAA
1586901 TATAGACCTT
Statistics
Matches: 87, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
51 23 0.26
52 50 0.57
53 14 0.16
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (50 bp):
CTTTTTATGCTGATGTGAGCCTTTAAGATGCCCACATGGATAACTTATGT
Found at i:1588383 original size:6 final size:6
Alignment explanation
Indices: 1588364--1588444 Score: 69
Period size: 6 Copynumber: 13.2 Consensus size: 6
1588354 GAGTCACCCA
* *
1588364 TCTTGTT TCATTT TCTTTTT TCTTTT T-TTTT TCCTTTT TCTCTTT TC--CT
1 TCTT-TT TCTTTT TC-TTTT TCTTTT TCTTTT T-CTTTT TCT-TTT TCTTTT
*
1588413 TCTTTT TCTTTT TCTTTT TTTCTTT TCTTTT T
1 TCTTTT TCTTTT TCTTTT TCT-TTT TCTTTT T
1588445 TTCTCTTTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 15
0.74 0.07 0.18
Matches are distributed among these distances:
4 3 0.05
5 5 0.08
6 30 0.49
7 23 0.38
ACGTcount: A:0.01, C:0.19, G:0.01, T:0.79
Consensus pattern (6 bp):
TCTTTT
Found at i:1588392 original size:8 final size:8
Alignment explanation
Indices: 1588374--1588456 Score: 66
Period size: 8 Copynumber: 10.5 Consensus size: 8
1588364 TCTTGTTTCA
1588374 TTTTC-TT
1 TTTTCTTT
1588381 TTTTCTTT
1 TTTTCTTT
*
1588389 TTTTTTTCCT
1 TTTTCTT--T
*
1588399 TTTTCTCT
1 TTTTCTTT
*
1588407 TTTCCTTCT
1 TTTTCTT-T
1588416 TTTTC--T
1 TTTTCTTT
1588422 TTTTCTTT
1 TTTTCTTT
1588430 TTTTCTTT
1 TTTTCTTT
*
1588438 TCTT-TTT
1 TTTTCTTT
*
1588445 TTCTCTTT
1 TTTTCTTT
1588453 TTTT
1 TTTT
1588457 ATGATGGATG
Statistics
Matches: 59, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
6 6 0.10
7 10 0.17
8 32 0.54
9 5 0.08
10 6 0.10
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTCTTT
Found at i:1588417 original size:29 final size:28
Alignment explanation
Indices: 1588377--1588454 Score: 97
Period size: 29 Copynumber: 2.8 Consensus size: 28
1588367 TGTTTCATTT
1588377 TCTTTT-TTCTTTTT-TTTTTCCTTTTTC
1 TCTTTTCTTCTTTTTCTTTTT-CTTTTTC
*
1588404 TCTTTTCCTTCTTTTTCTTTTTCTTTTTT
1 TCTTTT-CTTCTTTTTCTTTTTCTTTTTC
*
1588433 TCTTTTCTTTTTTTCTCTTTTT
1 TCTTTTCTTCTTTT-TCTTTTT
1588455 TTATGATGGA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
27 6 0.13
28 7 0.16
29 27 0.60
30 5 0.11
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (28 bp):
TCTTTTCTTCTTTTTCTTTTTCTTTTTC
Found at i:1588455 original size:36 final size:35
Alignment explanation
Indices: 1588377--1588455 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 35
1588367 TGTTTCATTT
1588377 TCTTTTTTCTTTTTTTTTTCCTTTTTCTCTTTTCC
1 TCTTTTTTCTTTTTTTTTTCCTTTTTCTCTTTTCC
* * *
1588412 T-TCTTTTTCTTTTTCTTTTT-TTCTTTTCTTTTTTTC
1 TCT-TTTTTCTTTTT-TTTTTCCT-TTTTCTCTTTTCC
1588448 TCTTTTTT
1 TCTTTTTT
1588456 TATGATGGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
34 1 0.03
35 13 0.35
36 22 0.59
37 1 0.03
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (35 bp):
TCTTTTTTCTTTTTTTTTTCCTTTTTCTCTTTTCC
Found at i:1592426 original size:18 final size:18
Alignment explanation
Indices: 1592395--1592432 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1592385 GATCATCGGT
*
1592395 CTCTTCAGCGTCAGTAGG
1 CTCTTCAGCGTCAGCAGG
1592413 CTCTTCAG-GTTCAGCAGG
1 CTCTTCAGCG-TCAGCAGG
1592431 CT
1 CT
1592433 GGGGACTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.16, C:0.29, G:0.26, T:0.29
Consensus pattern (18 bp):
CTCTTCAGCGTCAGCAGG
Found at i:1600504 original size:21 final size:21
Alignment explanation
Indices: 1600462--1600504 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1600452 TTTATGGGCT
* *
1600462 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
1600483 AGGGGAATCGATCCCCCCTCA
1 AGGGGAATCGATACCCACTCA
1600504 A
1 A
1600505 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:1601357 original size:103 final size:103
Alignment explanation
Indices: 1601029--1601345 Score: 571
Period size: 103 Copynumber: 3.1 Consensus size: 103
1601019 GTAGAGGGTC
* * *
1601029 TATGTGGTCATTCGGGATATATATGTATTCTTTGGAACATGTGTAAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1601094 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
1601132 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
1601197 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1601235 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
1601300 TTGATCTTTGGCATATATATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1601338 TATGTGGT
1 TATGTGGT
1601346 TCTTATGGAC
Statistics
Matches: 205, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 205 1.00
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:1601399 original size:23 final size:23
Alignment explanation
Indices: 1601366--1601428 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
1601356 ATTATTATAT
*
1601366 GGCACTACGGTGTAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
1601389 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
1601412 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
1601429 ATATGAGCTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 34 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.25, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:1608261 original size:103 final size:103
Alignment explanation
Indices: 1607933--1608253 Score: 579
Period size: 103 Copynumber: 3.1 Consensus size: 103
1607923 GTAGAGGGTC
* * *
1607933 TATGTGGTCATTCGGGATATATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1607998 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
1608036 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
1608101 TTGATCCTTGGTATATGTATATGGTTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
1608139 TATGTGGTTCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1608204 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1608242 TATGTGGTCCTT
1 TATGTGGTCCTT
1608254 ATGGACATTA
Statistics
Matches: 207, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 207 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:1608305 original size:23 final size:23
Alignment explanation
Indices: 1608270--1608321 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
1608260 ATTATTATAT
1608270 GGCACTACAGTGTAATTCTACGC
1 GGCACTACAGTGTAATTCTACGC
* * *
1608293 GGCACTCCGGTGTAATTCTACGT
1 GGCACTACAGTGTAATTCTACGC
1608316 GGCACT
1 GGCACT
1608322 TAGGTGCAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27
Consensus pattern (23 bp):
GGCACTACAGTGTAATTCTACGC
Found at i:1608327 original size:23 final size:23
Alignment explanation
Indices: 1608270--1608332 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
1608260 ATTATTATAT
1608270 GGCACTACA-GTGTAATTCTACGC
1 GGCACT-CAGGTGTAATTCTACGC
* *
1608293 GGCACTCCGGTGTAATTCTACGT
1 GGCACTCAGGTGTAATTCTACGC
* *
1608316 GGCACTTAGGTGCAATT
1 GGCACTCAGGTGTAATT
1608333 ATATGAGCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
22 1 0.03
23 33 0.97
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (23 bp):
GGCACTCAGGTGTAATTCTACGC
Found at i:1615053 original size:28 final size:28
Alignment explanation
Indices: 1615022--1615091 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
1615012 TTGTGGCGGA
* *
1615022 AGGGGCTGCTGGTTTACTTGAAACTTGG
1 AGGGGCTGCTGGGTTACTTGAAACGTGG
* **
1615050 AGGGGATGCTGGGTTGTTTGAAACGTGG
1 AGGGGCTGCTGGGTTACTTGAAACGTGG
1615078 AGGGGCTGCTGGGT
1 AGGGGCTGCTGGGT
1615092 ATGAAAGGTA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.16, C:0.11, G:0.44, T:0.29
Consensus pattern (28 bp):
AGGGGCTGCTGGGTTACTTGAAACGTGG
Found at i:1616755 original size:26 final size:26
Alignment explanation
Indices: 1616721--1616793 Score: 103
Period size: 30 Copynumber: 2.7 Consensus size: 26
1616711 AATTTTAATA
1616721 ATATTTGTAATATGTTTTTTTATCAT
1 ATATTTGTAATATGTTTTTTTATCAT
1616747 ATATTTGTAATAGTTTTGTTTTTTTATCAT
1 ATATTTGTAATA----TGTTTTTTTATCAT
1616777 ATATTTGTAATA-GTTTT
1 ATATTTGTAATATGTTTT
1616794 GTTTTTTTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
25 5 0.12
26 12 0.28
30 26 0.60
ACGTcount: A:0.26, C:0.03, G:0.10, T:0.62
Consensus pattern (26 bp):
ATATTTGTAATATGTTTTTTTATCAT
Found at i:1616769 original size:30 final size:30
Alignment explanation
Indices: 1616733--1616803 Score: 142
Period size: 30 Copynumber: 2.4 Consensus size: 30
1616723 ATTTGTAATA
1616733 TGTTTTTTTATCATATATTTGTAATAGTTT
1 TGTTTTTTTATCATATATTTGTAATAGTTT
1616763 TGTTTTTTTATCATATATTTGTAATAGTTT
1 TGTTTTTTTATCATATATTTGTAATAGTTT
1616793 TGTTTTTTTAT
1 TGTTTTTTTAT
1616804 AGATAAGTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.21, C:0.03, G:0.10, T:0.66
Consensus pattern (30 bp):
TGTTTTTTTATCATATATTTGTAATAGTTT
Found at i:1636509 original size:398 final size:397
Alignment explanation
Indices: 1635767--1636566 Score: 1591
Period size: 398 Copynumber: 2.0 Consensus size: 397
1635757 AAGAAGCCAA
1635767 GGAAGTGAGCCAAAAGAAGAATCAAAAGCTCTTAGGTGCTGCAAAAGAAGTCTCCGAGAAGGACC
1 GGAAGTGAGCCAAAAGAAGAATCAAAAGCTCTTAGGTGCTGCAAAAGAAGTCTCCGAGAAGGACC
1635832 ATCATTGTTGCCATAAATAGCAGTGATGACAAAAGGATCACTATTGAATTGGCATTTGACAGTGA
66 ATCATTGTTGCCATAAATAGCAGTGATGACAAAAGGATCACTATTGAATTGGCATTTGACAGTGA
1635897 TGCTTTGAGAAGAAGAATGACAGAAAGAGATATATATTCTTTTTTTCCAAAGAAGCCAGATTCTA
131 TGCTTTGAGAAGAAGAATGACAGAAAGAGATATATATTCTTTTTTTCCAAAGAAGCCAGATTCTA
1635962 CCATTGGTAGCAGAGTCATAATTGGTAAAAACATTCTAATTCCCAAATCTAGAGTGCAAGATATT
196 CCATTGGTAGCAGAGTCATAATTGGTAAAAACATTCTAATTCCCAAATCTAGAGTGCAAGATATT
1636027 ATAAGATTTATCAGCTTTGACACGAGTCTCCATCAAACAAAGAACATCAACATTATAAAGATTAG
261 ATAAGATTTATCAGCTTTGACACGAGTCTCCATCAAACAAAGAACATCAACATTATAAAGATTAG
1636092 CCCTATGAAGCACTTTATTCTGTTTTTTAGGATTGTTTAATCCTCTTATAATCCAGAAGCAAATG
326 CCCTATGAAGCACTTTATTCTGTTTTTTAGGATTGTTTAATCCTCTTATAATCCAGAAGCAAATG
1636157 ATCATTG
391 ATCATTG
1636164 GGAAGTGAGCCAAAAGAAGAATCAAAAGCTCTTAGGTGCTGCAAAAGAAGTCTCCGAGAAGGACC
1 GGAAGTGAGCCAAAAGAAGAATCAAAAGCTCTTAGGTGCTGCAAAAGAAGTCTCCGAGAAGGACC
1636229 ATCATTGTTGCCATAAATAGCAGTGATGACAAAAGGATCACTATTGAATTGGCATTTGACAGTGA
66 ATCATTGTTGCCATAAATAGCAGTGATGACAAAAGGATCACTATTGAATTGGCATTTGACAGTGA
1636294 TGCTTTGAGAAGAAGAATGACAGAAAGAGATATATATTCTTTTTTTTCCAAAGAAGCCAGATTCT
131 TGCTTTGAGAAGAAGAATGACAGAAAGAGATATATATTC-TTTTTTTCCAAAGAAGCCAGATTCT
1636359 ACCATTGGTAGCAGAGTCATAATTGGTAAAAACATTCTAATTCCCAAATCTAGAGTGCAAGATAT
195 ACCATTGGTAGCAGAGTCATAATTGGTAAAAACATTCTAATTCCCAAATCTAGAGTGCAAGATAT
1636424 TATAAGATTTATCAGCTTTGACACGAGTCTCCATCAAACAAAGAACATCAACATTATAAAGATTA
260 TATAAGATTTATCAGCTTTGACACGAGTCTCCATCAAACAAAGAACATCAACATTATAAAGATTA
1636489 GCCCTATGAAGCACTTTATTCTGTTTTTTAGGATTGTTTAATCCTCTTATAATCCAGAAGCAAAT
325 GCCCTATGAAGCACTTTATTCTGTTTTTTAGGATTGTTTAATCCTCTTATAATCCAGAAGCAAAT
1636554 GATCATTG
390 GATCATTG
1636562 GGAAG
1 GGAAG
1636567 GAGATATGGT
Statistics
Matches: 402, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
397 169 0.42
398 233 0.58
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (397 bp):
GGAAGTGAGCCAAAAGAAGAATCAAAAGCTCTTAGGTGCTGCAAAAGAAGTCTCCGAGAAGGACC
ATCATTGTTGCCATAAATAGCAGTGATGACAAAAGGATCACTATTGAATTGGCATTTGACAGTGA
TGCTTTGAGAAGAAGAATGACAGAAAGAGATATATATTCTTTTTTTCCAAAGAAGCCAGATTCTA
CCATTGGTAGCAGAGTCATAATTGGTAAAAACATTCTAATTCCCAAATCTAGAGTGCAAGATATT
ATAAGATTTATCAGCTTTGACACGAGTCTCCATCAAACAAAGAACATCAACATTATAAAGATTAG
CCCTATGAAGCACTTTATTCTGTTTTTTAGGATTGTTTAATCCTCTTATAATCCAGAAGCAAATG
ATCATTG
Found at i:1637859 original size:161 final size:160
Alignment explanation
Indices: 1637592--1637989 Score: 582
Period size: 161 Copynumber: 2.5 Consensus size: 160
1637582 AGTGCTCCGG
* * **
1637592 GGGACATGAGTGACATAATAGGGCAATGATAATATATTCTCTGACAAAATAATGGAAGGCACGCC
1 GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGAAAGGTGC-CC
* * *
1637657 CCCGAGAACGCGCTTTCACCACTTTGGGTACTGATATGAATAGTGCCCCCAAAGGACATGACTGA
65 CCCGAGAACGCGCTTTCACCACTTTAGGTACTGACATGAATAGTGCCCCCAAAGGACATGACTAA
* *
1637722 CATAATAGGGTAATGATAACATAGCTCTCGA
130 CATAATAGGGTAATGATAACATAGCCCCCGA
*
1637753 GGGACATGAGTGACATAGTAGGGCAATGATAACATATTCTCTGACAAAATAATGAAAGGTGCCCA
1 GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGAAAGGTGCCC-
* * * * * * *
1637818 CCCGTGAACGTGTTTTCACCACTTTAGGTACTGACATGAATAGTTCCCCCGAGGGACATGAGTAA
65 CCCGAGAACGCGCTTTCACCACTTTAGGTACTGACATGAATAGTGCCCCCAAAGGACATGACTAA
1637883 CATAATAGGGTAATGATAACATAGCCCCCGA
130 CATAATAGGGTAATGATAACATAGCCCCCGA
* *
1637914 GGGACATGAGTGACATAATAGGGCACTGATAACATATTCTCTGAGAAAATAAT-AGAAGGTGCCC
1 GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGA-AAGGTGCCC
*
1637978 CCCGATAACGCG
65 CCCGAGAACGCG
1637990 TCTTCATGTG
Statistics
Matches: 212, Mismatches: 23, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
160 12 0.06
161 200 0.94
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.22
Consensus pattern (160 bp):
GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGAAAGGTGCCCC
CCGAGAACGCGCTTTCACCACTTTAGGTACTGACATGAATAGTGCCCCCAAAGGACATGACTAAC
ATAATAGGGTAATGATAACATAGCCCCCGA
Found at i:1637930 original size:44 final size:44
Alignment explanation
Indices: 1637863--1637949 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 44
1637853 ATGAATAGTT
*
1637863 CCCCCGAGGGACATGAGTAACATAATAGGGTAATGATAACATAG
1 CCCCCGAGGGACATGAGTAACATAATAGGGCAATGATAACATAG
* *
1637907 CCCCCGAGGGACATGAGTGACATAATAGGGCACTGATAACATA
1 CCCCCGAGGGACATGAGTAACATAATAGGGCAATGATAACATA
1637950 TTCTCTGAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.37, C:0.21, G:0.25, T:0.17
Consensus pattern (44 bp):
CCCCCGAGGGACATGAGTAACATAATAGGGCAATGATAACATAG
Found at i:1639815 original size:31 final size:31
Alignment explanation
Indices: 1639777--1639841 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
1639767 ATGGAAACCA
1639777 CAATATTCTTCCTGTTGCGTTTGCCCTCGTT
1 CAATATTCTTCCTGTTGCGTTTGCCCTCGTT
1639808 CAATATTCTTCCTGTTGCGTTTGCCCTCGTT
1 CAATATTCTTCCTGTTGCGTTTGCCCTCGTT
1639839 CAA
1 CAA
1639842 GGAGAAGACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.12, C:0.29, G:0.15, T:0.43
Consensus pattern (31 bp):
CAATATTCTTCCTGTTGCGTTTGCCCTCGTT
Found at i:1641155 original size:28 final size:29
Alignment explanation
Indices: 1641123--1641207 Score: 81
Period size: 28 Copynumber: 3.1 Consensus size: 29
1641113 AAAAATTATT
1641123 TTATTATATTTATTTAATATAATAATTAA
1 TTATTATATTTATTTAATATAATAATTAA
* * *
1641152 -TATTAT-TATTATTTATTATAAAAAATAA
1 TTATTATAT-TTATTTAATATAATAATTAA
* *
1641180 TTATTA-ATTT-TTAAATATTATAA-TAA
1 TTATTATATTTATTTAATATAATAATTAA
1641206 TT
1 TT
1641208 CCACCTTCTA
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
26 5 0.11
27 10 0.22
28 25 0.54
29 6 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (29 bp):
TTATTATATTTATTTAATATAATAATTAA
Found at i:1641179 original size:32 final size:30
Alignment explanation
Indices: 1641107--1641182 Score: 93
Period size: 32 Copynumber: 2.5 Consensus size: 30
1641097 CTAAATAATT
*
1641107 TTTAAAAAA-AATT-ATTTTATTATATTTA
1 TTTAAAAAATAATTAATATTATTATATTTA
*
1641135 TTTAATATAATAATTAATATTATTATTATTTA
1 TTTAA-AAAATAATTAATATTATTA-TATTTA
1641167 TTATAAAAAATAATTA
1 TT-TAAAAAATAATTA
1641183 TTAATTTTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 5 0.12
29 3 0.08
30 4 0.10
31 8 0.20
32 17 0.43
33 3 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (30 bp):
TTTAAAAAATAATTAATATTATTATATTTA
Found at i:1641447 original size:19 final size:19
Alignment explanation
Indices: 1641423--1641471 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
1641413 TTCGTTAAAT
1641423 ATTGATAACATATGACTAG
1 ATTGATAACATATGACTAG
1641442 ATTGATAACATATGACTAG
1 ATTGATAACATATGACTAG
1641461 ATTGATAACAT
1 ATTGATAACAT
1641472 TTAAATAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (19 bp):
ATTGATAACATATGACTAG
Found at i:1642559 original size:93 final size:95
Alignment explanation
Indices: 1642452--1642627 Score: 268
Period size: 94 Copynumber: 1.9 Consensus size: 95
1642442 CGCTACAATT
* *
1642452 TTTTTTTTAAATTCAAGTAGATTAAATTATAAGA-A-ATATAAAAATACATTAAAATTATATATA
1 TTTTTTTTAAATTCAAGTAGATTAAATTACAAGATAGATA-AAAAATACATTAAAATTATATAAA
1642515 TAAACATACTAATTTTTTGTAATTTTTCTGA
65 TAAACATACTAATTTTTTGTAATTTTTCTGA
* * *
1642546 TTTTTTTT-AATTCAAGTAGATTAATTTGCAAGATAGATAAAAAATACATTGAAATTATATAAAT
1 TTTTTTTTAAATTCAAGTAGATTAAATTACAAGATAGATAAAAAATACATTAAAATTATATAAAT
*
1642610 AAACATATTAATTTTTTG
66 AAACATACTAATTTTTTG
1642628 AAACATAAAA
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
93 22 0.30
94 49 0.66
95 3 0.04
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (95 bp):
TTTTTTTTAAATTCAAGTAGATTAAATTACAAGATAGATAAAAAATACATTAAAATTATATAAAT
AAACATACTAATTTTTTGTAATTTTTCTGA
Found at i:1645313 original size:3 final size:3
Alignment explanation
Indices: 1645305--1645393 Score: 142
Period size: 3 Copynumber: 29.7 Consensus size: 3
1645295 TTTTTATCCA
*
1645305 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TTT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
1645353 TTT TAT TAT TAT TAT TAT TAT TAT TTT TAC TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1645394 AATATATTAA
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:1645916 original size:16 final size:16
Alignment explanation
Indices: 1645892--1645923 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1645882 ACAGAAACAG
*
1645892 AAAACGAAAAAAAAAA
1 AAAAAGAAAAAAAAAA
1645908 AAAAAGAAAAAAAAAA
1 AAAAAGAAAAAAAAAA
1645924 CAAACTAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.91, C:0.03, G:0.06, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAAAAAAA
Found at i:1647624 original size:18 final size:18
Alignment explanation
Indices: 1647577--1647625 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
1647567 CTTTTCAATT
1647577 TTTTTA-TTTATTTATTA
1 TTTTTATTTTATTTATTA
**
1647594 TTTTTATAATATTTA-TA
1 TTTTTATTTTATTTATTA
1647611 TGTTTTATTTTATTT
1 T-TTTTATTTTATTT
1647626 GCAAGTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 9 0.35
18 17 0.65
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (18 bp):
TTTTTATTTTATTTATTA
Found at i:1647647 original size:13 final size:15
Alignment explanation
Indices: 1647616--1647652 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
1647606 TTATATGTTT
1647616 TATTTTATTTGCAAG
1 TATTTTATTTGCAAG
1647631 TATTTTATTT-C-AG
1 TATTTTATTTGCAAG
1647644 TA-TTTATTT
1 TATTTTATTT
1647653 TTATGTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
14 1 0.05
15 10 0.45
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62
Consensus pattern (15 bp):
TATTTTATTTGCAAG
Found at i:1658237 original size:18 final size:18
Alignment explanation
Indices: 1658216--1658251 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1658206 GCTTGAAGAG
* *
1658216 AATAGAAAAAAAATAGAA
1 AATAAAAAAAAAAGAGAA
1658234 AATAAAAAAAAAAGAGAA
1 AATAAAAAAAAAAGAGAA
1658252 GAAAAAGAAA
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:0.81, C:0.00, G:0.11, T:0.08
Consensus pattern (18 bp):
AATAAAAAAAAAAGAGAA
Found at i:1658256 original size:16 final size:16
Alignment explanation
Indices: 1658214--1658257 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
1658204 ATGCTTGAAG
* *
1658214 AGAATAGAAAAAAAAT
1 AGAAAAGAAAAAAAAA
*
1658230 AGAAAATAAAAAAAAA
1 AGAAAAGAAAAAAAAA
*
1658246 AGAGAAGAAAAA
1 AGAAAAGAAAAA
1658258 GAAAGGGGGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.07
Consensus pattern (16 bp):
AGAAAAGAAAAAAAAA
Found at i:1658626 original size:19 final size:18
Alignment explanation
Indices: 1658587--1658632 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
1658577 CTATTTCAAG
1658587 TTCAATTTA--TTTGAAA
1 TTCAATTTATTTTTGAAA
*
1658603 GTCAATTTATTTTTGGAAA
1 TTCAATTTATTTTT-GAAA
1658622 TTCAATTTATT
1 TTCAATTTATT
1658633 CTTTTCTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 8 0.32
18 3 0.12
19 14 0.56
ACGTcount: A:0.33, C:0.07, G:0.09, T:0.52
Consensus pattern (18 bp):
TTCAATTTATTTTTGAAA
Found at i:1659511 original size:83 final size:83
Alignment explanation
Indices: 1659367--1659972 Score: 1002
Period size: 83 Copynumber: 7.3 Consensus size: 83
1659357 ATATCCCAGT
* *
1659367 TCAAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 TCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1659432 TGATCTGATTGGACAGAA
66 TGATCTGATTGGACAGAA
*
1659450 TCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATA
1 TCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1659515 TGATCTGATTGGACAGAA
66 TGATCTGATTGGACAGAA
1659533 TCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 TCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1659598 TGATCTGATTGGACAGAA
66 TGATCTGATTGGACAGAA
* *
1659616 TCAAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 TCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1659681 TGATCTGATTGGACAGAA
66 TGATCTGATTGGACAGAA
*
1659699 TCAATCATTGAATTTAGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 TCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
* * *
1659764 TGACCTGGTTTGACAGAA
66 TGATCTGATTGGACAGAA
* * *
1659782 CCAAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 TCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
* * *
1659847 TGACCTGGTT-TAGCAGAA
66 TGATCTGATTGGA-CAGAA
*
1659865 -CAATCATCGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 TCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
* *
1659929 TGATTTGGTTGGACAGAA
66 TGATCTGATTGGACAGAA
* *
1659947 -CAATCATTGAATTTGGAAGATAAATT
1 TCAATCATTGAATTTAGAAGATGAATT
1659973 GGCTCATAGT
Statistics
Matches: 495, Mismatches: 26, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
82 98 0.20
83 397 0.80
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.35
Consensus pattern (83 bp):
TCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
TGATCTGATTGGACAGAA
Found at i:1660826 original size:113 final size:113
Alignment explanation
Indices: 1660601--1661155 Score: 878
Period size: 113 Copynumber: 4.9 Consensus size: 113
1660591 TCAAATCCAC
1660601 TTGATGGATCATTCATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 TTGATGGATCA-TCATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
*
1660666 AAGTTCATAATGAGAAGAACTTATTCAACTTTTTGTTTAAATTCATCAT
65 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
* * *
1660715 TTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCATCATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* * *** * *
1660780 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
* * *
1660828 TTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCATCATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1660893 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
* * * *
1660941 TTGATGGATCAACATTACCAGAGAAGGTTCGTAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCATCATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
*
1661006 GGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
* *
1661054 TTGATGGATCAACATTGCCAGAGAAAGTTCATGAATGAAAAGAACTCATCTGAAGAAGGAAGAAG
1 TTGATGGATCATCATTGCCAGAGAAAGTTCAT-AATGAGAAGAACTCATCTGAAGAAGGAAGAAG
* *
1661119 AAGTTCATAATGAGAAGAGCTTGTTCAAC-CTTTGTTT
65 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTT
1661156 GATATTATCT
Statistics
Matches: 408, Mismatches: 32, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
113 340 0.83
114 68 0.17
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (113 bp):
TTGATGGATCATCATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
Found at i:1661454 original size:3 final size:3
Alignment explanation
Indices: 1661446--1661519 Score: 112
Period size: 3 Copynumber: 24.7 Consensus size: 3
1661436 TTTTTATCCA
* *
1661446 TAT TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT TTT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
1661494 TAT TAT TAT TTT TAC TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
1661520 AATATATTAA
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1662034 original size:19 final size:19
Alignment explanation
Indices: 1662012--1662048 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1662002 AGAGACAGAA
1662012 ACAGA-AAACGAAAAAAAAT
1 ACAGAGAAA-GAAAAAAAAT
1662031 ACAGAGAAAGAAAAAAAA
1 ACAGAGAAAGAAAAAAAA
1662049 CAAACTAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.76, C:0.08, G:0.14, T:0.03
Consensus pattern (19 bp):
ACAGAGAAAGAAAAAAAAT
Found at i:1673338 original size:147 final size:147
Alignment explanation
Indices: 1673071--1673358 Score: 504
Period size: 147 Copynumber: 2.0 Consensus size: 147
1673061 AAACAAAAGT
* * *
1673071 CCAGAAATCAATGGATTGTAGAAGGTGATGGAAACACTGGCTTTTTTCACTTGATGGCCTCGGAT
1 CCAGAAATCAATGGATTCTAGAAGGTGATAGAAACACTGGCTTTTTTCACATGATGGCCTCGGAT
* *
1673136 AGAAGAAATAAAAATTTGATAAGTAGGCTTAAGGTGGATTGATGACGTGCAAGGCATTAGAGATT
66 AGAAGAAATAAAAACTGGATAAGTAGGCTTAAGGTGGATTGATGACGTGCAAGGCATTAGAGATT
1673201 TAGTTATAAAACATTTC
131 TAGTTATAAAACATTTC
* *
1673218 CCAGAAATCAATGGATTCTGGAAGTTGATAGAAACACTGGCTTTTTTCACATGATGGCCTCGGAT
1 CCAGAAATCAATGGATTCTAGAAGGTGATAGAAACACTGGCTTTTTTCACATGATGGCCTCGGAT
*
1673283 AGAAGAAATAAAAACTGGATAAGTAGGCTTAAGGTGGCTTGATGACGTGCAAGGCATTAGAGATT
66 AGAAGAAATAAAAACTGGATAAGTAGGCTTAAGGTGGATTGATGACGTGCAAGGCATTAGAGATT
1673348 TAGTTATAAAA
131 TAGTTATAAAA
1673359 TTCCATTTGC
Statistics
Matches: 133, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
147 133 1.00
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (147 bp):
CCAGAAATCAATGGATTCTAGAAGGTGATAGAAACACTGGCTTTTTTCACATGATGGCCTCGGAT
AGAAGAAATAAAAACTGGATAAGTAGGCTTAAGGTGGATTGATGACGTGCAAGGCATTAGAGATT
TAGTTATAAAACATTTC
Found at i:1673442 original size:29 final size:29
Alignment explanation
Indices: 1673410--1673467 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
1673400 GGCTTAATAA
*
1673410 ATATACACACTAAAGCCCTATCTAAATGT
1 ATATACACACTAAACCCCTATCTAAATGT
*
1673439 ATATATACACTAAACCCCTATCTAAATGT
1 ATATACACACTAAACCCCTATCTAAATGT
1673468 GTGTGCACGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.41, C:0.24, G:0.05, T:0.29
Consensus pattern (29 bp):
ATATACACACTAAACCCCTATCTAAATGT
Found at i:1681286 original size:13 final size:14
Alignment explanation
Indices: 1681270--1681301 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
1681260 TTATATTTTT
1681270 ATTTTATAATTA-A
1 ATTTTATAATTATA
1681283 ATTTTATAATTATA
1 ATTTTATAATTATA
1681297 ATTTT
1 ATTTT
1681302 TATCTTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTTTATAATTATA
Found at i:1681304 original size:15 final size:15
Alignment explanation
Indices: 1681271--1681314 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
1681261 TATATTTTTA
1681271 TTTTATAATTA-AA-
1 TTTTATAATTATAAT
1681284 TTTTATAATTATAAT
1 TTTTATAATTATAAT
**
1681299 TTTTATCTTTATAAT
1 TTTTATAATTATAAT
1681314 T
1 T
1681315 GAGGTTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
13 11 0.41
14 2 0.07
15 14 0.52
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTTATAATTATAAT
Found at i:1681496 original size:41 final size:41
Alignment explanation
Indices: 1681412--1681498 Score: 97
Period size: 41 Copynumber: 2.1 Consensus size: 41
1681402 TGATCTAAAA
* * *
1681412 TTTTTAATTATACTTTTTACTTTTATAATTTAGTTCATGAT
1 TTTTTAATTATACTTTTTACCTTTATAATTGAGTTCATAAT
* *
1681453 TTTTTAATTTTA-TTTTATACCTTTATAATTGAGGTT-TTAAT
1 TTTTTAATTATACTTTT-TACCTTTATAATTGA-GTTCATAAT
1681494 TTTTT
1 TTTTT
1681499 TTTAATATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
40 4 0.10
41 32 0.82
42 3 0.08
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.63
Consensus pattern (41 bp):
TTTTTAATTATACTTTTTACCTTTATAATTGAGTTCATAAT
Found at i:1681522 original size:42 final size:41
Alignment explanation
Indices: 1681452--1681585 Score: 99
Period size: 43 Copynumber: 3.1 Consensus size: 41
1681442 TAGTTCATGA
* *
1681452 TTTTTTAATTTTATTTTATACCTTTATAATTGAGGTTTTAATTT
1 TTTTTTAATATT-TTTT-TACCTATATAATT-AGGTTTTAATTT
* * *
1681496 TTTTTTAATATTTTTTTACGTATATAATTAAGTCTTTGA-TT
1 TTTTTTAATATTTTTTTACCTATATAATTAGGT-TTTAATTT
* * * * *
1681537 TTTTTCAATCTCATTTTTTACTTATATAATTTAAGCTCTTAATTT
1 TTTTTTAATAT--TTTTTTACCTATATAA-TT-AGGTTTTAATTT
1681582 TTTT
1 TTTT
1681586 CAATTTCACT
Statistics
Matches: 72, Mismatches: 12, Indels: 11
0.76 0.13 0.12
Matches are distributed among these distances:
41 14 0.19
42 15 0.21
43 19 0.26
44 16 0.22
45 8 0.11
ACGTcount: A:0.25, C:0.07, G:0.05, T:0.62
Consensus pattern (41 bp):
TTTTTTAATATTTTTTTACCTATATAATTAGGTTTTAATTT
Found at i:1681554 original size:43 final size:42
Alignment explanation
Indices: 1681507--1681655 Score: 149
Period size: 43 Copynumber: 3.5 Consensus size: 42
1681497 TTTTTAATAT
*
1681507 TTTTTTACGTATATAATTAAGTCTTTGATTTTTTTCAATCTCA
1 TTTTTTACTTATATAATTAAGTCTTT-ATTTTTTTCAATCTCA
* *
1681550 TTTTTTACTTATATAATTTAAGCTCTTAATTTTTTTCAATTTCA
1 TTTTTTACTTATATAA-TTAAG-TCTTTATTTTTTTCAATCTCA
* * * * * *
1681594 CTTTTTACTTTTAAAATTGAGATCTCTAATTTTTT-AATCTCA
1 TTTTTTACTTATATAATTAAG-TCTTTATTTTTTTCAATCTCA
*
1681636 TTTTTTTA-TTTTATAATTAA
1 -TTTTTTACTTATATAATTAA
1681656 AGTCCCTAAT
Statistics
Matches: 88, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
42 16 0.18
43 35 0.40
44 33 0.38
45 4 0.05
ACGTcount: A:0.28, C:0.11, G:0.04, T:0.58
Consensus pattern (42 bp):
TTTTTTACTTATATAATTAAGTCTTTATTTTTTTCAATCTCA
Found at i:1681665 original size:42 final size:42
Alignment explanation
Indices: 1681507--1681696 Score: 136
Period size: 43 Copynumber: 4.4 Consensus size: 42
1681497 TTTTTAATAT
* * ** *
1681507 TTTTTTACGTATATAATTAAGTCTTTGATTTTTTTCAATCTCA
1 TTTTTTACTTTTATAATTAAGTCCCT-AATTTTTTCAATCTCA
* * *
1681550 TTTTTTACTTATATAATTTAAG-CTCTTAATTTTTTTCAATTTCA
1 TTTTTTACTTTTATAA-TTAAGTC-CCTAA-TTTTTTCAATCTCA
* * * *
1681594 CTTTTTACTTTTAAAATTGAGATCTCTAATTTTTT-AATCTCA
1 TTTTTTACTTTTATAATTAAG-TCCCTAATTTTTTCAATCTCA
* *
1681636 TTTTTTTA-TTTTATAATTAAAGTCCCTAATATTTTCAATAAT-A
1 -TTTTTTACTTTTATAATT-AAGTCCCTAATTTTTTCAAT-CTCA
* *
1681679 ATTTCTACTTTTATAATT
1 TTTTTTACTTTTATAATT
1681697 TAAACATTAA
Statistics
Matches: 118, Mismatches: 19, Indels: 20
0.75 0.12 0.13
Matches are distributed among these distances:
42 31 0.26
43 49 0.42
44 37 0.31
45 1 0.01
ACGTcount: A:0.29, C:0.12, G:0.04, T:0.56
Consensus pattern (42 bp):
TTTTTTACTTTTATAATTAAGTCCCTAATTTTTTCAATCTCA
Found at i:1681954 original size:17 final size:18
Alignment explanation
Indices: 1681915--1681960 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
1681905 TGTTTATGAG
*
1681915 GGAATTGGAATCTGTGAA
1 GGAATTAGAATCTGTGAA
*
1681933 GGAATTAGAATCTGT-CA
1 GGAATTAGAATCTGTGAA
1681950 GGAATTAGAAT
1 GGAATTAGAAT
1681961 TCAATTTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.37, C:0.07, G:0.28, T:0.28
Consensus pattern (18 bp):
GGAATTAGAATCTGTGAA
Found at i:1682582 original size:33 final size:33
Alignment explanation
Indices: 1682540--1682656 Score: 202
Period size: 33 Copynumber: 3.6 Consensus size: 33
1682530 CCTAAACCCG
1682540 AACCCGACCCGACCCGAATATCACACTTAAAAA
1 AACCCGACCCGACCCGAATATCACACTTAAAAA
1682573 AACCCGACCCGACCCGAATATCACACTTAAAAA
1 AACCCGACCCGACCCGAATATCACACTTAAAAA
* *
1682606 AACCCGACTCGACCTGAATATCACACTT--AAA
1 AACCCGACCCGACCCGAATATCACACTTAAAAA
1682637 AACCCGACCCGACCCGAATA
1 AACCCGACCCGACCCGAATA
1682657 AAATAAAGTT
Statistics
Matches: 80, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 21 0.26
33 59 0.74
ACGTcount: A:0.40, C:0.37, G:0.10, T:0.13
Consensus pattern (33 bp):
AACCCGACCCGACCCGAATATCACACTTAAAAA
Found at i:1687184 original size:82 final size:83
Alignment explanation
Indices: 1687061--1687307 Score: 354
Period size: 82 Copynumber: 3.0 Consensus size: 83
1687051 AAATTTCGAG
** *
1687061 AGAGTTTTACTCAAATTAAAATTCTTTTAATATCTAAATTTAAACATATAATAATATCTTTTAAA
1 AGAGTTTTACTCAAACCAAAACTCTTTTAATATCTAAATTTAAACATATAATAATATCTTTTAAA
1687126 TTTAAAATATTAAACATA
66 TTTAAAATATTAAACATA
* * * * * * * *
1687144 AGAGTTTTACTCCAACC-AAGCTCTTTTAATATTTAGATTTAAACAAATAAAAATATATTCTAAA
1 AGAGTTTTACTCAAACCAAAACTCTTTTAATATCTAAATTTAAACATATAATAATATCTTTTAAA
* *
1687208 TTTAAAATATTAAACCTG
66 TTTAAAATATTAAACATA
*
1687226 AGAGTTTTATTCAAACCAAAACTCTTTTAATATCTAAATTTAAACATATAATAATATCTTTTAAA
1 AGAGTTTTACTCAAACCAAAACTCTTTTAATATCTAAATTTAAACATATAATAATATCTTTTAAA
1687291 TTT-AAATATTAAACATA
66 TTTAAAATATTAAACATA
1687308 TATTTCCTCT
Statistics
Matches: 139, Mismatches: 24, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
82 82 0.59
83 57 0.41
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.40
Consensus pattern (83 bp):
AGAGTTTTACTCAAACCAAAACTCTTTTAATATCTAAATTTAAACATATAATAATATCTTTTAAA
TTTAAAATATTAAACATA
Found at i:1690463 original size:24 final size:22
Alignment explanation
Indices: 1690436--1690485 Score: 55
Period size: 24 Copynumber: 2.2 Consensus size: 22
1690426 AACTATTTAA
1690436 ATTATAATAATTAATTATAAATGT
1 ATTATAATAATT-ATTATAAA-GT
** *
1690460 ATTATTTTAATTATTTTAAAGT
1 ATTATAATAATTATTATAAAGT
1690482 ATTA
1 ATTA
1690486 ACACATTCGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 6 0.26
23 7 0.30
24 10 0.43
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (22 bp):
ATTATAATAATTATTATAAAGT
Found at i:1697752 original size:20 final size:19
Alignment explanation
Indices: 1697712--1697755 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1697702 TCGATTACAA
1697712 ATTTATTAATTTTTATAAT
1 ATTTATTAATTTTTATAAT
*
1697731 ATTTATCTACATTTTT-TTAT
1 ATTTAT-TA-ATTTTTATAAT
1697751 ATTTA
1 ATTTA
1697756 AATAATTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 6 0.27
20 10 0.45
21 6 0.27
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTTATTAATTTTTATAAT
Found at i:1701306 original size:45 final size:43
Alignment explanation
Indices: 1701242--1701368 Score: 132
Period size: 43 Copynumber: 2.9 Consensus size: 43
1701232 GAAGTGAACT
* * *
1701242 TTTAATGTGGTGTACTACTATTTATGAATTAGACAATATTTAAGC
1 TTTAATGTGTTGTAGTACTAATTATGAATTAGACAATATTT--GC
* * *
1701287 TTTAATGTGTTCTAGTACTAATTATAGACTTTAG-CAATA-TTGG
1 TTTAATGTGTTGTAGTACTAATTAT-GA-ATTAGACAATATTTGC
* *
1701330 TTTGATGTGTTGTAGCACTAATTATGAATTAGACAATAT
1 TTTAATGTGTTGTAGTACTAATTATGAATTAGACAATAT
1701369 CTTTGTAAAT
Statistics
Matches: 68, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
41 4 0.06
42 7 0.10
43 23 0.34
45 23 0.34
46 7 0.10
47 4 0.06
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.43
Consensus pattern (43 bp):
TTTAATGTGTTGTAGTACTAATTATGAATTAGACAATATTTGC
Found at i:1702034 original size:35 final size:35
Alignment explanation
Indices: 1701964--1702035 Score: 83
Period size: 35 Copynumber: 2.1 Consensus size: 35
1701954 TAAATAGACC
* * *
1701964 TTTAATTTTATATTTGGATTATGCAATTTGAATTT
1 TTTAACTTTATATTTGAATTATGCAATTAGAATTT
* *
1701999 TTTAACTTTATGTTTGAATTATGTAATTCAG-ATTT
1 TTTAACTTTATATTTGAATTATGCAATT-AGAATTT
1702034 TT
1 TT
1702036 AAGCGTCCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
35 30 0.97
36 1 0.03
ACGTcount: A:0.28, C:0.04, G:0.11, T:0.57
Consensus pattern (35 bp):
TTTAACTTTATATTTGAATTATGCAATTAGAATTT
Found at i:1702112 original size:22 final size:22
Alignment explanation
Indices: 1702073--1702117 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1702063 TACAGAAAAG
*
1702073 TTAGTGCATAATCATTTATTGT
1 TTAGTGCATAATCATTTACTGT
* **
1702095 TTAGTGCATTATTGTTTACTGT
1 TTAGTGCATAATCATTTACTGT
1702117 T
1 T
1702118 AGTACAAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.22, C:0.09, G:0.16, T:0.53
Consensus pattern (22 bp):
TTAGTGCATAATCATTTACTGT
Found at i:1702826 original size:2 final size:2
Alignment explanation
Indices: 1702819--1702847 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1702809 AATAAAATAG
1702819 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
1702848 GACAAGAATA
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:1702907 original size:10 final size:9
Alignment explanation
Indices: 1702891--1702940 Score: 55
Period size: 10 Copynumber: 5.2 Consensus size: 9
1702881 AAAGGAAAAT
1702891 AATAAATAA
1 AATAAATAA
*
1702900 GGATAAATAA
1 -AATAAATAA
1702910 AAGTAAATAGA
1 AA-TAAATA-A
*
1702921 GATAAATAA
1 AATAAATAA
1702930 AATAAATAA
1 AATAAATAA
1702939 AA
1 AA
1702941 AATATGTATA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
9 12 0.35
10 20 0.59
11 2 0.06
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (9 bp):
AATAAATAA
Found at i:1702918 original size:20 final size:20
Alignment explanation
Indices: 1702891--1702938 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1702881 AAAGGAAAAT
1702891 AATAAATAAG-GATAAATAA
1 AATAAATAAGAGATAAATAA
1702910 AAGTAAAT-AGAGATAAATAA
1 AA-TAAATAAGAGATAAATAA
1702930 AATAAATAA
1 AATAAATAA
1702939 AAAATATGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (20 bp):
AATAAATAAGAGATAAATAA
Found at i:1703135 original size:3 final size:3
Alignment explanation
Indices: 1703123--1703182 Score: 57
Period size: 3 Copynumber: 19.0 Consensus size: 3
1703113 TTTGGTTTTT
* * * *
1703123 TTA TTT TTA TTA TTA TTA TTTA TTA GTA TTA TTA TTA ATA ATA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
1703169 TTTA TTA TATA TTA
1 -TTA TTA T-TA TTA
1703183 CAGGCCCAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
3 39 0.81
4 9 0.19
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Done.