Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 16 of 187
Found at i:5630784 original size:46 final size:45
Alignment explanation
Indices: 5630177--5630809 Score: 228
Period size: 44 Copynumber: 14.5 Consensus size: 45
5630167 AGCACGATAA
* ** *
5630177 CTGAGGTTACAGTAGAGCAGATTGAAGCA-A-GAGATCTTATCTCC
1 CTGAGGTTACAGTGGAGCAGA-TGAAAAATATCAGATCTTATCTCC
* * ** * * *
5630221 TTGAGATTACAGTGGAGCAGATCCAAGACAT-A-ATCCTATCTCC
1 CTGAGGTTACAGTGGAGCAGATGAAAAATATCAGATCTTATCTCC
* * * * ** * *
5630264 CTAAGATTACAGTGGAGCGGAT-TAAAATAAAAGTTCTTATCTCT
1 CTGAGGTTACAGTGGAGCAGATGAAAAATATCAGATCTTATCTCC
* * * * *
5630308 CTGAAGTTACAGTAGAGTAGATCG-----CATCAGGTCTTATCTCC
1 CTGAGGTTACAGTGGAGCAGAT-GAAAAATATCAGATCTTATCTCC
* * * * * *
5630349 CTAAGGTTACAGTGGAGTAAACCGAATAATTTCAGATCTTATCTCC
1 CTGAGGTTACAGTGGAGCAGA-TGAAAAATATCAGATCTTATCTCC
* * ** * *
5630395 CTGAGGTCATAGTGGAGCAGATTGAAGCA-A-GAGATCTTATCTCA
1 CTGAGGTTACAGTGGAGCAGA-TGAAAAATATCAGATCTTATCTCC
* * ** * * * *
5630439 TTGAGATTACAGTGGAGCAGATCCAAGACA-CA-ATCCTATCTCT
1 CTGAGGTTACAGTGGAGCAGATGAAAAATATCAGATCTTATCTCC
* * ** *
5630482 CTG-GGATTACAGTGGAGCGGAT-TAAAATAAAAGATCTTATCTCT
1 CTGAGG-TTACAGTGGAGCAGATGAAAAATATCAGATCTTATCTCC
* ** * * *
5630526 CTGAAGTTACAGCAGAGTAGATCG-----CATCAGGTCTTATCTCC
1 CTGAGGTTACAGTGGAGCAGAT-GAAAAATATCAGATCTTATCTCC
* * * *
5630567 CTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCC
1 CTGAGGTTACAGTGGAGCAGA-TGAAAAATATCAGATCTTATCTCC
* * ** *
5630613 CTGAGGTTATAGCGGAGCAGATTG-AAGCTAGT-A-ATCATATCTCC
1 CTGAGGTTACAGTGGAGCAGA-TGAAAAATA-TCAGATCTTATCTCC
** * * * ** *
5630657 CTGATATTACAGTGAAGCGGAT-TAAAATAAAAGATCTTATCTCT
1 CTGAGGTTACAGTGGAGCAGATGAAAAATATCAGATCTTATCTCC
* * * * * *
5630701 CTGAAGTTATAGTAGAGTAGATCG-----CATCAGGTCTTATCTCC
1 CTGAGGTTACAGTGGAGCAGAT-GAAAAATATCAGATCTTATCTCC
* * *
5630742 CTGAGGTTACAGTGGAGTAGACTGAAAAATTTTAGATCTTATCTCC
1 CTGAGGTTACAGTGGAGCAGA-TGAAAAATATCAGATCTTATCTCC
5630788 CTGAGGTTACAGTGGAGCAGAT
1 CTGAGGTTACAGTGGAGCAGAT
5630810 TGAAGCCAGA
Statistics
Matches: 426, Mismatches: 126, Indels: 73
0.68 0.20 0.12
Matches are distributed among these distances:
41 92 0.22
42 10 0.02
43 69 0.16
44 149 0.35
45 5 0.01
46 101 0.24
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.28
Consensus pattern (45 bp):
CTGAGGTTACAGTGGAGCAGATGAAAAATATCAGATCTTATCTCC
Found at i:5630835 original size:175 final size:174
Alignment explanation
Indices: 5630426--5630840 Score: 614
Period size: 175 Copynumber: 2.4 Consensus size: 174
5630416 TTGAAGCAAG
** * ** * * * * *
5630426 AGATCTTATCTCATTGAGATTACAGTGGAGCAGATCCAAGACACAATCCTATCTCTCTGGGATTA
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAATCATATCTCCCTGAGATTA
*
5630491 CAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAG
66 CAGTGAAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAG
*
5630556 GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTC
131 GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAAAATTTC
* * * *
5630600 AGATCTTATCTCCCTGAGGTTATAGCGGAGCAGATTGAAGCTAGTAATCATATCTCCCTGATATT
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG-AATCATATCTCCCTGAGATT
* *
5630665 ACAGTGAAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTATAGTAGAGTAGATCGCATCA
65 ACAGTGAAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCA
* *
5630730 GGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACTGAAAAATTTT
130 GGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAAAATTTC
* *
5630775 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATTTCCCTGAGATT
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGA-ATCATATCTCCCTGAGATT
5630840 A
65 A
5630841 TAACGGAGTA
Statistics
Matches: 213, Mismatches: 26, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
174 35 0.16
175 178 0.84
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (174 bp):
AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAATCATATCTCCCTGAGATTA
CAGTGAAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCAG
GTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAAAATTTC
Found at i:5630854 original size:44 final size:44
Alignment explanation
Indices: 5630775--5630859 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
5630765 GAAAAATTTT
* **
5630775 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG
1 AGATCTTATCTCCCTGAGATTACAACGGAGCAGATTGAAGCCAG
* * *
5630819 AGATCTTATTTCCCTGAGATTATAACGGAGTAGATTGAAGC
1 AGATCTTATCTCCCTGAGATTACAACGGAGCAGATTGAAGC
5630860 TAGTAATCCT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (44 bp):
AGATCTTATCTCCCTGAGATTACAACGGAGCAGATTGAAGCCAG
Found at i:5630878 original size:175 final size:175
Alignment explanation
Indices: 5630426--5630893 Score: 528
Period size: 175 Copynumber: 2.7 Consensus size: 175
5630416 TTGAAGCAAG
** * * ** * * * * *
5630426 AGATCTTATCTCATTGAGATTACAGTGGAGCAGATCCAAGACA-CAATCCTATCTCTCTGGGATT
1 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATTGAAGCCAGTAATCATATCTCCCTGAGATT
** * * * * *
5630490 ACAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCA
66 ACAACGAAGCAGATTAAAATAAAAGATCCTAACTCTCTGAAGTTACAGTAGAGTAGATCGCATCA
*
5630555 GGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTC
131 GGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAAAATTTC
* * *
5630600 AGATCTTATCTCCCTGAGGTTATAGCGGAGCAGATTGAAGCTAGTAATCATATCTCCCTGATATT
1 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATTGAAGCCAGTAATCATATCTCCCTGAGATT
** * * * *
5630665 ACAGTGAAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTATAGTAGAGTAGATCGCATCA
66 ACAACGAAGCAGATTAAAATAAAAGATCCTAACTCTCTGAAGTTACAGTAGAGTAGATCGCATCA
* *
5630730 GGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACTGAAAAATTTT
131 GGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAAAATTTC
* * *
5630775 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG-AGATCTTATTTCCCTGAGAT
1 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATTGAAGCCAGTA-ATCATATCTCCCTGAGAT
* * * ** ** *
5630839 TATAACGGAGTAGATTGAAGCTAGTA-ATCCTAACTCTCTGAAGTTACAGTGGAGT
65 TACAACGAAGCAGATT-AAAATAAAAGATCCTAACTCTCTGAAGTTACAGTAGAGT
5630894 GGATTAAAAT
Statistics
Matches: 251, Mismatches: 40, Indels: 5
0.85 0.14 0.02
Matches are distributed among these distances:
174 35 0.14
175 211 0.84
176 5 0.02
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (175 bp):
AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATTGAAGCCAGTAATCATATCTCCCTGAGATT
ACAACGAAGCAGATTAAAATAAAAGATCCTAACTCTCTGAAGTTACAGTAGAGTAGATCGCATCA
GGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAAAATTTC
Found at i:5632543 original size:3 final size:3
Alignment explanation
Indices: 5632535--5632632 Score: 99
Period size: 3 Copynumber: 32.7 Consensus size: 3
5632525 TATTTTTAAC
* *
5632535 ATT ATT ATT TTT AAT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * * *
5632583 ATC ATCT -TT ACT GTT ATT ATT AAT ATT AAT GTT ATT ATT ATT ATC
1 ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5632628 ATT AT
1 ATT AT
5632633 ATTTCTATTT
Statistics
Matches: 75, Mismatches: 18, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
2 1 0.01
3 74 0.99
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:5632543 original size:15 final size:15
Alignment explanation
Indices: 5632523--5632603 Score: 81
Period size: 15 Copynumber: 5.4 Consensus size: 15
5632513 TATTTAGCTA
*
5632523 ATTATTTTTAACATT
1 ATTATTTTTAATATT
5632538 ATTATTTTTAATATT
1 ATTATTTTTAATATT
* *
5632553 ATTATTATTATTATT
1 ATTATTTTTAATATT
* *
5632568 ATTATTATTATTATT
1 ATTATTTTTAATATT
* * * *
5632583 ATCATCTTTACTGTT
1 ATTATTTTTAATATT
5632598 ATTATT
1 ATTATT
5632604 AATATTAATG
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 56 1.00
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.63
Consensus pattern (15 bp):
ATTATTTTTAATATT
Found at i:5634325 original size:18 final size:18
Alignment explanation
Indices: 5634304--5634349 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
5634294 TCATATGTCC
5634304 ATTTTTATGT-TTTAGTTT
1 ATTTTTATGTATTTA-TTT
*
5634322 ATTTTTATTTATTTATTT
1 ATTTTTATGTATTTATTT
5634340 ATTTGTTATG
1 ATTT-TTATG
5634350 ATATATACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.72
Consensus pattern (18 bp):
ATTTTTATGTATTTATTT
Found at i:5634686 original size:110 final size:110
Alignment explanation
Indices: 5634469--5634864 Score: 584
Period size: 110 Copynumber: 3.6 Consensus size: 110
5634459 ATATTTTTCT
* * * *
5634469 AAATGAGGCAATGTTTTGC-TTTTAGAAATTCAAGAAAACATGCCCTAAGGTGCTGGGTGTCGAT
1 AAATAAGGCAATGTTTTGCGTTTGAGAAATCCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGAT
*
5634533 TTTTCTCGTTAAACCAAATGGCTTAATATCCTTTTAAAAATTTTA
66 TTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTA
* *
5634578 AAATAAAGCAATGTTTTGCGTTTGGGAAATCCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGAT
1 AAATAAGGCAATGTTTTGCGTTTGAGAAATCCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGAT
5634643 TTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTA
66 TTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTA
* * *
5634688 AAATAAGGCAATGTTTTGTGTTTG-GAAAATTCGAGAAAACATGCCCTAAGGTGTTGGGTGTCGA
1 AAATAAGGCAATGTTTTGCGTTTGAG-AAATCCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGA
* * *
5634752 TTTTTCTCATTCAACCAAATGGCTAAATATCCTTTTAAAAAAATTTCA
65 TTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTT--AAAAATTTTA
* * * *
5634800 AAATAAGGCAATGTTTTGCGTTT-AGAAATCCGAG-AAACGTGCCCTAATGTGTTGGGTTTCGAT
1 AAATAAGGCAATGTTTTGCGTTTGAGAAATCCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGAT
5634863 TT
66 TT
5634865 CTCGATTGAT
Statistics
Matches: 263, Mismatches: 19, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
109 18 0.07
110 205 0.78
111 8 0.03
112 32 0.12
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (110 bp):
AAATAAGGCAATGTTTTGCGTTTGAGAAATCCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGAT
TTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTA
Found at i:5638215 original size:59 final size:59
Alignment explanation
Indices: 5638152--5638335 Score: 173
Period size: 59 Copynumber: 3.1 Consensus size: 59
5638142 TATAGTATCA
5638152 TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
1 TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
* * * * * * * * *
5638211 TATATATTTTAATTGTAATAAATTTA-ATAATAATTATGTTAA-T-TT-A-TATTTTA-CAGTAT
1 TATAT-TATGATTTG-AGTAAATTCATATAAGAA-TA--TTAATTATTAAGAATTTTATTA-AAT
5638270 CATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
1 --TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
5638331 TATAT
1 TATAT
5638336 ATTTTAATTA
Statistics
Matches: 93, Mismatches: 18, Indels: 28
0.67 0.13 0.20
Matches are distributed among these distances:
57 4 0.04
58 2 0.02
59 30 0.32
60 26 0.28
61 25 0.27
62 2 0.02
63 4 0.04
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (59 bp):
TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
Found at i:5638216 original size:61 final size:61
Alignment explanation
Indices: 5638151--5638338 Score: 201
Period size: 61 Copynumber: 3.1 Consensus size: 61
5638141 TTATAGTATC
5638151 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
* * * * * * * *
5638212 ATATATT-TTAATTGTAATAAATTTA-ATAATAATTATGTTAA-T-TT-A-TATTTTA-CAGTAT
1 ATATATTATGATTTG-AGTAAATTCATATAAGAA-TA--TTAATTATTAAGAATTTTATTA-AAT
*
5638270 C
61 T
5638271 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
5638332 ATATATT
1 ATATATT
5638339 TTAATTATAA
Statistics
Matches: 97, Mismatches: 18, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
57 4 0.04
58 2 0.02
59 27 0.28
60 24 0.25
61 34 0.35
62 2 0.02
63 4 0.04
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
Found at i:5638246 original size:54 final size:53
Alignment explanation
Indices: 5638182--5638367 Score: 133
Period size: 54 Copynumber: 3.2 Consensus size: 53
5638172 TTCATATAAG
*
5638182 AATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTGTAATAAATTT
1 AATAATAATTATTAAGAATTTTATTAAATTATATATTTTAATT-TAATAAATTT
* * * * *
5638236 AATAATAATTATGT--TAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATAT
1 AATAATAATTAT-TAAGAATTT-TA--TTA-A--ATTATATATTTTAATTT-AATAAA-T--T-T
* *
5638299 AAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTT
1 ---AATAATAATTATTAAGAATTTTATTAAATTATATATTTTAATT-TAATAAATTT
5638356 AATAATAATTAT
1 AATAATAATTAT
5638368 GTTTAAATAT
Statistics
Matches: 100, Mismatches: 14, Indels: 36
0.67 0.09 0.24
Matches are distributed among these distances:
53 5 0.05
54 24 0.24
55 1 0.01
56 3 0.03
57 2 0.02
58 2 0.02
59 18 0.18
60 2 0.02
61 17 0.17
62 2 0.02
63 2 0.02
64 3 0.03
65 1 0.01
66 13 0.13
67 5 0.05
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (53 bp):
AATAATAATTATTAAGAATTTTATTAAATTATATATTTTAATTTAATAAATTT
Found at i:5638286 original size:120 final size:120
Alignment explanation
Indices: 5638140--5638370 Score: 435
Period size: 120 Copynumber: 1.9 Consensus size: 120
5638130 GCTACCACAG
*
5638140 TTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
1 TTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
*
5638205 TTAAATTATATATTTTAATTGTAATAAATTTAATAATAATTATGTTAATTTATAT
66 TTAAATTATATATTTTAATTATAATAAATTTAATAATAATTATGTTAATTTATAT
5638260 TTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
1 TTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
*
5638325 TTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
66 TTAAATTATATATTTTAATTATAATAAATTTAATAATAATTATGTT
5638371 TAAATATGAT
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 108 1.00
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.49
Consensus pattern (120 bp):
TTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
TTAAATTATATATTTTAATTATAATAAATTTAATAATAATTATGTTAATTTATAT
Found at i:5638353 original size:16 final size:16
Alignment explanation
Indices: 5638332--5638373 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
5638322 TTATTAAATT
*
5638332 ATATATTTTAATTATA
1 ATATATTTTAATAATA
5638348 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
5638363 AT-TATGTTTAA
1 ATATAT-TTTAA
5638374 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:5638358 original size:15 final size:15
Alignment explanation
Indices: 5638323--5638364 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
5638313 TTAAGAATTT
*
5638323 TATTAAATTAT-ATA
1 TATTTAATTATAATA
5638337 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
5638351 TATTTAATAATAAT
1 TATTTAATTATAAT
5638365 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:5638485 original size:157 final size:157
Alignment explanation
Indices: 5638307--5638623 Score: 589
Period size: 157 Copynumber: 2.0 Consensus size: 157
5638297 ATAAGAATAT
*
5638307 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTGATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
*
5638372 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
5638437 TAATAATTTACCAAAACAAATTTCTGC
131 TAATAATTTACCAAAACAAATTTATGC
5638464 TAATTATTAAGAATTTGATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTGATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
5638529 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
* *
5638594 TAATCATTTACCAAAATAAATTTATGC
131 TAATAATTTACCAAAACAAATTTATGC
5638621 TAA
1 TAA
5638624 GGGTATTCTA
Statistics
Matches: 155, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 155 1.00
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (157 bp):
TAATTATTAAGAATTTGATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTATGC
Found at i:5638510 original size:16 final size:16
Alignment explanation
Indices: 5638489--5638530 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
5638479 TGATTAAATT
*
5638489 ATATATTTTAATTATA
1 ATATATTTTAATAATA
5638505 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
5638520 AT-TATGTTTAA
1 ATATAT-TTTAA
5638531 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:5638701 original size:39 final size:40
Alignment explanation
Indices: 5638658--5638762 Score: 113
Period size: 44 Copynumber: 2.5 Consensus size: 40
5638648 TTCCATTATG
5638658 CTATTACACCTCTATTCCATTCAACCAAACACAAGA-TTA
1 CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
* *** *
5638697 CTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATTTG
1 CTATTACACCTCTATT-C----CATTCAACCAAACACAAGATTTA
5638742 CTATTACACCTCTATTCCATT
1 CTATTACACCTCTATTCCATT
5638763 ACACCTCTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
39 15 0.28
40 5 0.09
44 17 0.31
45 17 0.31
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.34
Consensus pattern (40 bp):
CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
Found at i:5638756 original size:45 final size:44
Alignment explanation
Indices: 5638656--5638765 Score: 131
Period size: 45 Copynumber: 2.6 Consensus size: 44
5638646 TTTTCCATTA
5638656 TGCTATTACACCTCTATT-C----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* * ***
5638695 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T
5638740 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTCCATTACA
5638766 CCTCTAATCC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 25 0.43
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:5638765 original size:16 final size:16
Alignment explanation
Indices: 5638744--5638781 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
5638734 TTGATTTGCT
*
5638744 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
5638760 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
5638776 AATACA
1 ATTACA
5638782 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:5645261 original size:17 final size:18
Alignment explanation
Indices: 5645235--5645268 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5645225 AATGAACACA
*
5645235 AATAATCAAT-CAATACC
1 AATAAGCAATACAATACC
5645252 AATAAGCAATACAATAC
1 AATAAGCAATACAATAC
5645269 ACATGAGGGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.56, C:0.21, G:0.03, T:0.21
Consensus pattern (18 bp):
AATAAGCAATACAATACC
Found at i:5647408 original size:15 final size:15
Alignment explanation
Indices: 5647388--5647422 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5647378 ATCATGCCAT
*
5647388 AGAAGGTGAAGTACA
1 AGAAGGTAAAGTACA
5647403 AGAAGGTAAAGTACA
1 AGAAGGTAAAGTACA
*
5647418 TGAAG
1 AGAAG
5647423 AAGAGATACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.49, C:0.06, G:0.31, T:0.14
Consensus pattern (15 bp):
AGAAGGTAAAGTACA
Found at i:5653360 original size:8 final size:8
Alignment explanation
Indices: 5653321--5653347 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
5653311 TAGATTTTTT
5653321 AATTTTAA
1 AATTTTAA
5653329 AATTTTAA
1 AATTTTAA
5653337 AATTTTAA
1 AATTTTAA
5653345 AAT
1 AAT
5653348 GAATTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
AATTTTAA
Found at i:5655431 original size:17 final size:16
Alignment explanation
Indices: 5655411--5655442 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
5655401 AGAAATTATG
5655411 ATAATTATATATTTAAA
1 ATAATTATA-ATTTAAA
5655428 ATAATTATAATTTAA
1 ATAATTATAATTTAA
5655443 TAGAAGTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAATTATAATTTAAA
Found at i:5657676 original size:22 final size:21
Alignment explanation
Indices: 5657611--5657678 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 21
5657601 TAATATTAAA
5657611 TATTTCAGTTTAAATCATATTTT
1 TATTT-AGTTTAAATCAT-TTTT
* *
5657634 TATTCT-GTGTAAA-CA--TAT
1 TATT-TAGTTTAAATCATTTTT
5657652 TATTTAGTTTAAATCATTTTTT
1 TATTTAGTTTAAATCA-TTTTT
5657674 TATTT
1 TATTT
5657679 TATTGTAAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 13
0.67 0.08 0.25
Matches are distributed among these distances:
17 1 0.03
18 12 0.34
19 2 0.06
21 2 0.06
22 13 0.37
23 4 0.11
24 1 0.03
ACGTcount: A:0.29, C:0.07, G:0.06, T:0.57
Consensus pattern (21 bp):
TATTTAGTTTAAATCATTTTT
Found at i:5659390 original size:14 final size:13
Alignment explanation
Indices: 5659350--5659400 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
5659340 TTAAGTATAT
*
5659350 TATTATTTTATTA
1 TATTATTATATTA
* *
5659363 TATT-GTAAATTA
1 TATTATTATATTA
5659375 TATTAATTATATTA
1 TATT-ATTATATTA
5659389 TATTATTATATT
1 TATTATTATATT
5659401 TCAAATAAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
12 9 0.29
13 12 0.39
14 10 0.32
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (13 bp):
TATTATTATATTA
Found at i:5659662 original size:19 final size:18
Alignment explanation
Indices: 5659609--5659662 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
5659599 ACGAAACAGA
*
5659609 GAAGGAAAGAAGGAAAGG
1 GAAGGAAAGAAGAAAAGG
* * *
5659627 AAAGAAAAAGAAAAAAAGG
1 GAAG-GAAAGAAGAAAAGG
5659646 GAAGGAAAGGAAGAAAA
1 GAAGGAAA-GAAGAAAA
5659663 TTTGGGATTT
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
18 6 0.22
19 21 0.78
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (18 bp):
GAAGGAAAGAAGAAAAGG
Found at i:5662520 original size:84 final size:84
Alignment explanation
Indices: 5662415--5662584 Score: 286
Period size: 84 Copynumber: 2.0 Consensus size: 84
5662405 TCACTAATTT
* *
5662415 ACATAATAAATCATCCAAAAACGCATCAAGAATGGGATTAAAAACATGAAACTTTTATGGCTTGT
1 ACATAATAAATCATCCAAAAACGCATCAAAAATGGGATTAAAAACATGAAACTTTTATGGCTTAT
5662480 CAGACATCGGGATCAATAA
66 CAGACATCGGGATCAATAA
**
5662499 ACATAATAAATCATCCAAAAACGCATCAAAAATGGGATTAAAAACATGTTACTTTTATGGCTTAT
1 ACATAATAAATCATCCAAAAACGCATCAAAAATGGGATTAAAAACATGAAACTTTTATGGCTTAT
**
5662564 TGGACATCGGGATCAATAA
66 CAGACATCGGGATCAATAA
5662583 AC
1 AC
5662585 CCTAAACCTA
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 80 1.00
ACGTcount: A:0.44, C:0.16, G:0.15, T:0.25
Consensus pattern (84 bp):
ACATAATAAATCATCCAAAAACGCATCAAAAATGGGATTAAAAACATGAAACTTTTATGGCTTAT
CAGACATCGGGATCAATAA
Found at i:5663374 original size:17 final size:18
Alignment explanation
Indices: 5663342--5663375 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5663332 CATCTTTGTG
*
5663342 ATAATTACACATTTAAAA
1 ATAATTACAAATTTAAAA
5663360 ATAATTA-AAATTTAAA
1 ATAATTACAAATTTAAA
5663376 TTACAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (18 bp):
ATAATTACAAATTTAAAA
Found at i:5671127 original size:22 final size:23
Alignment explanation
Indices: 5671083--5671129 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
5671073 GATCTAAGAA
*
5671083 AAAAATTTAACCCATATTTTTTC
1 AAAAATTTAACCCATATTATTTC
* *
5671106 AAAAATTTCACCTA-ATTATTTC
1 AAAAATTTAACCCATATTATTTC
5671128 AA
1 AA
5671130 TTTTATTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (23 bp):
AAAAATTTAACCCATATTATTTC
Found at i:5672040 original size:16 final size:17
Alignment explanation
Indices: 5672009--5672049 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
5671999 AAGTGTTGTT
5672009 TGTTAAAAAAATATTAAA
1 TGTT-AAAAAATATTAAA
5672027 TGTTAAAAAA-ATTAAA
1 TGTTAAAAAATATTAAA
*
5672043 TATTAAA
1 TGTTAAA
5672050 TTTAAGTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 12 0.55
17 6 0.27
18 4 0.18
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (17 bp):
TGTTAAAAAATATTAAA
Found at i:5684065 original size:19 final size:19
Alignment explanation
Indices: 5684032--5684070 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
5684022 TCAAATTATG
*
5684032 TCTCAAATTTTAAAT-TCA
1 TCTCAAATTTAAAATATCA
5684050 TCTCAAACTTTAAAATATCA
1 TCTCAAA-TTTAAAATATCA
5684070 T
1 T
5684071 TAGAATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 7 0.39
20 4 0.22
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (19 bp):
TCTCAAATTTAAAATATCA
Found at i:5703869 original size:13 final size:13
Alignment explanation
Indices: 5703851--5703875 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5703841 TGTGCACCAG
5703851 ATTATTAGATAAA
1 ATTATTAGATAAA
5703864 ATTATTAGATAA
1 ATTATTAGATAA
5703876 TGCGAAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (13 bp):
ATTATTAGATAAA
Found at i:5707873 original size:13 final size:13
Alignment explanation
Indices: 5707852--5707886 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
5707842 TTCTGATTAT
*
5707852 GTACCGCATTTCG
1 GTACAGCATTTCG
5707865 GTACAGCATTTCG
1 GTACAGCATTTCG
5707878 GTACAGCAT
1 GTACAGCAT
5707887 GGTATGTAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.29
Consensus pattern (13 bp):
GTACAGCATTTCG
Found at i:5714152 original size:21 final size:21
Alignment explanation
Indices: 5714126--5714171 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
5714116 TTTACATTCG
5714126 AAAAATACAAA-AAATAATTTT
1 AAAAATACAAATAAA-AATTTT
*
5714147 AAAAATATAAATAAAAATTTT
1 AAAAATACAAATAAAAATTTT
5714168 AAAA
1 AAAA
5714172 TTTAATGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (21 bp):
AAAAATACAAATAAAAATTTT
Found at i:5716507 original size:72 final size:73
Alignment explanation
Indices: 5716429--5716568 Score: 167
Period size: 72 Copynumber: 1.9 Consensus size: 73
5716419 AGCTCATAAG
* * * *
5716429 AGCCATAT-TTAGAAAGCTCATGCGAGCCAATAAGGGGTAGCTCCGAAGAGCCATTAA-CAGGAA
1 AGCCATATATCAGAAAGCTCAAGCGAGCC-ATAACGGGAAGCTCCGAAGAGCCATTAATCAGGAA
5716492 GCTCCGGAT
65 GCTCCGGAT
* * * ** *
5716501 AGCCATATATCAGGAAGTTTAAGCGAGCCATCTCGGGAAGCTCCGGAGAGCCATTAATCAGGAAG
1 AGCCATATATCAGAAAGCTCAAGCGAGCCATAACGGGAAGCTCCGAAGAGCCATTAATCAGGAAG
5716566 CTC
66 CTC
5716569 ACAAAGAGCC
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
72 31 0.55
73 25 0.45
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (73 bp):
AGCCATATATCAGAAAGCTCAAGCGAGCCATAACGGGAAGCTCCGAAGAGCCATTAATCAGGAAG
CTCCGGAT
Found at i:5716567 original size:25 final size:25
Alignment explanation
Indices: 5716467--5716606 Score: 94
Period size: 26 Copynumber: 5.6 Consensus size: 25
5716457 AATAAGGGGT
5716467 AGCTCCGAAGAGCCATTAA-CAGGA
1 AGCTCCGAAGAGCCATTAATCAGGA
* *
5716491 AGCTCCGGATAGCCA-TATATCAGGA
1 AGCTCCGAAGAGCCATTA-ATCAGGA
** * *
5716516 AG-T-TTAAGCGAGCCA-T-CTCGGGA
1 AGCTCCGAA--GAGCCATTAATCAGGA
*
5716539 AGCTCCGGAGAGCCATTAATCAGGA
1 AGCTCCGAAGAGCCATTAATCAGGA
* * **
5716564 AGCTCACAAAGAGCCTTTAATTGGGA
1 AGCTC-CGAAGAGCCATTAATCAGGA
5716590 AGCTCACGAAGAGCCAT
1 AGCTC-CGAAGAGCCAT
5716607 ATATCGGGGC
Statistics
Matches: 87, Mismatches: 20, Indels: 16
0.71 0.16 0.13
Matches are distributed among these distances:
23 16 0.18
24 17 0.20
25 24 0.28
26 30 0.34
ACGTcount: A:0.33, C:0.24, G:0.26, T:0.18
Consensus pattern (25 bp):
AGCTCCGAAGAGCCATTAATCAGGA
Found at i:5720590 original size:80 final size:80
Alignment explanation
Indices: 5720457--5720618 Score: 324
Period size: 80 Copynumber: 2.0 Consensus size: 80
5720447 GAAAATCAAA
5720457 AGGCAATCAAATATTTATTCCCAGGGACTTCTTGAGCTTCTCAACTTCCAAATATACTGTTGAGT
1 AGGCAATCAAATATTTATTCCCAGGGACTTCTTGAGCTTCTCAACTTCCAAATATACTGTTGAGT
5720522 ATGGAAGGAACTCCG
66 ATGGAAGGAACTCCG
5720537 AGGCAATCAAATATTTATTCCCAGGGACTTCTTGAGCTTCTCAACTTCCAAATATACTGTTGAGT
1 AGGCAATCAAATATTTATTCCCAGGGACTTCTTGAGCTTCTCAACTTCCAAATATACTGTTGAGT
5720602 ATGGAAGGAACTCCG
66 ATGGAAGGAACTCCG
5720617 AG
1 AG
5720619 AAATGTTCTT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 82 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (80 bp):
AGGCAATCAAATATTTATTCCCAGGGACTTCTTGAGCTTCTCAACTTCCAAATATACTGTTGAGT
ATGGAAGGAACTCCG
Found at i:5723228 original size:31 final size:30
Alignment explanation
Indices: 5723152--5723236 Score: 82
Period size: 31 Copynumber: 2.7 Consensus size: 30
5723142 CATTTACCAT
*
5723152 AAATACTAATATGGACCAAAAAATCAAGTTC
1 AAATACTAAT-TGAACCAAAAAATCAAGTTC
* * *
5723183 AGATA-TCAATTTGAACCAATAAGTCAAGTTC
1 AAATACT-AA-TTGAACCAAAAAATCAAGTTC
*
5723214 AAATACCTAATTGAAGCAAAAAA
1 AAATA-CTAATTGAACCAAAAAA
5723237 AAAAAAACTT
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
30 1 0.02
31 37 0.88
32 3 0.07
33 1 0.02
ACGTcount: A:0.51, C:0.15, G:0.11, T:0.24
Consensus pattern (30 bp):
AAATACTAATTGAACCAAAAAATCAAGTTC
Found at i:5726246 original size:40 final size:40
Alignment explanation
Indices: 5726154--5726268 Score: 119
Period size: 40 Copynumber: 2.9 Consensus size: 40
5726144 GTTTGGACAA
* * *
5726154 AAAATGCCACTAAAAATCGAGCATTAGCGGC-TCTTTATGT
1 AAAACGCCGCTAAAAATCGAGCATTAGCGGCGT-TTTATGG
* * *
5726194 AAAACGCTGCTAAAGATCGAGCATTAGCAGCGTTTCTA-GG
1 AAAACGCCGCTAAAAATCGAGCATTAGCGGCGTTT-TATGG
* *
5726234 AAAGCGCCGCTAAAAAT-TAGCATTAGCGGCGTTTT
1 AAAACGCCGCTAAAAATCGAGCATTAGCGGCGTTTT
5726269 TCCAAAAAAC
Statistics
Matches: 62, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
38 1 0.02
39 15 0.24
40 43 0.69
41 3 0.05
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (40 bp):
AAAACGCCGCTAAAAATCGAGCATTAGCGGCGTTTTATGG
Found at i:5727084 original size:74 final size:77
Alignment explanation
Indices: 5726958--5727116 Score: 227
Period size: 74 Copynumber: 2.1 Consensus size: 77
5726948 ATTTGATAGT
*
5726958 AAAATAATTTTACTTTAAACAAATAGCGTCATTTCATATAGCAAAACATTTAGCGGCGTTTTTAT
1 AAAATAATTTTACTTTAAACAAATAGCG-CATTTCATATAGCAAAACATTTAGCGGCGTTTTCAT
5727023 AAAAAAAGCCACAA
65 -AAAAAAGCCACAA
* *
5727037 AAAATAA-TTTACTTT-AA-AAATAGC-CATTTTATATAGCAAAACATTTAGTGGCGTTTTCATA
1 AAAATAATTTTACTTTAAACAAATAGCGCATTTCATATAGCAAAACATTTAGCGGCGTTTTCATA
* *
5727098 AAAACGCCGCAA
66 AAAAAGCCACAA
5727110 AAAATAA
1 AAAATAA
5727117 ATCAATTTAT
Statistics
Matches: 75, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
73 18 0.24
74 33 0.44
76 7 0.09
77 2 0.03
78 8 0.11
79 7 0.09
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.30
Consensus pattern (77 bp):
AAAATAATTTTACTTTAAACAAATAGCGCATTTCATATAGCAAAACATTTAGCGGCGTTTTCATA
AAAAAGCCACAA
Found at i:5729272 original size:53 final size:53
Alignment explanation
Indices: 5729191--5729305 Score: 221
Period size: 53 Copynumber: 2.2 Consensus size: 53
5729181 AAGGGATAAT
5729191 TTTCAGTTTAAATCAGAACTTTTAGGTCAAGTCATCATGCTATTGCATTCTCC
1 TTTCAGTTTAAATCAGAACTTTTAGGTCAAGTCATCATGCTATTGCATTCTCC
*
5729244 TTTCAGTTTAAATCAGAACTTTTGGGTCAAGTCATCATGCTATTGCATTCTCC
1 TTTCAGTTTAAATCAGAACTTTTAGGTCAAGTCATCATGCTATTGCATTCTCC
5729297 TTTCAGTTT
1 TTTCAGTTT
5729306 TATTAATTCT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 61 1.00
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (53 bp):
TTTCAGTTTAAATCAGAACTTTTAGGTCAAGTCATCATGCTATTGCATTCTCC
Found at i:5729995 original size:19 final size:20
Alignment explanation
Indices: 5729967--5730008 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
5729957 GTATTATTTA
5729967 TTTTAGTTTTGA-TTCTAATT
1 TTTTAGTTTTGACTT-TAATT
*
5729987 TTTTA-TTTTTACTTTAATT
1 TTTTAGTTTTGACTTTAATT
5730006 TTT
1 TTT
5730009 ACGACAACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.71
Consensus pattern (20 bp):
TTTTAGTTTTGACTTTAATT
Found at i:5729996 original size:20 final size:19
Alignment explanation
Indices: 5729967--5730008 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
5729957 GTATTATTTA
5729967 TTTTAGTTTTGA-TTCTAATT
1 TTTTAGTTTT-ACTT-TAATT
*
5729987 TTTTATTTTTACTTTAATT
1 TTTTAGTTTTACTTTAATT
5730006 TTT
1 TTT
5730009 ACGACAACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTTAGTTTTACTTTAATT
Found at i:5730305 original size:43 final size:43
Alignment explanation
Indices: 5730242--5730342 Score: 148
Period size: 43 Copynumber: 2.3 Consensus size: 43
5730232 TAATTTTTTT
* * *
5730242 TAAAGGTCATGGTTTTTAGCGGCCTTTATGGGAAAAGCGCCGC
1 TAAAGGTCTTGGTCTATAGCGGCCTTTATGGGAAAAGCGCCGC
** *
5730285 TAAAGGTCTTGGTCTATAGCGGTGTTTGTGGGAAAAGCGCCGC
1 TAAAGGTCTTGGTCTATAGCGGCCTTTATGGGAAAAGCGCCGC
5730328 TAAAGGTCTTGGTCT
1 TAAAGGTCTTGGTCT
5730343 TTAGTGGCGT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.30
Consensus pattern (43 bp):
TAAAGGTCTTGGTCTATAGCGGCCTTTATGGGAAAAGCGCCGC
Found at i:5730447 original size:22 final size:22
Alignment explanation
Indices: 5730419--5730460 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
5730409 GGCGCTTATC
*
5730419 AAAGCGCCGCTAAAGGCCTAAA
1 AAAGCGCCGCTAAAAGCCTAAA
5730441 AAAGCGCCGCTAAAAGCCTA
1 AAAGCGCCGCTAAAAGCCTA
5730461 TTTTGGTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.29, G:0.21, T:0.10
Consensus pattern (22 bp):
AAAGCGCCGCTAAAAGCCTAAA
Found at i:5731574 original size:11 final size:11
Alignment explanation
Indices: 5731558--5731588 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
5731548 TATATATATT
5731558 TAAAAATTATA
1 TAAAAATTATA
*
5731569 TAAAAATAATA
1 TAAAAATTATA
5731580 TAAAAATTA
1 TAAAAATTA
5731589 ATACGAGCGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:5736614 original size:34 final size:34
Alignment explanation
Indices: 5736554--5736644 Score: 98
Period size: 34 Copynumber: 2.7 Consensus size: 34
5736544 TATCTATATA
* *
5736554 TATATATATATATATACACATA--TTTTTATTTTC
1 TATA-ATATATATATACATATATTTTTTTATATTC
*
5736587 -ATGAATATATACATACATATATTTTTTTATATTC
1 TAT-AATATATATATACATATATTTTTTTATATTC
* *
5736621 TATAATTTTTATATACATATATTT
1 TATAATATATATATACATATATTT
5736645 GCACATTTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
32 17 0.35
33 1 0.02
34 28 0.58
35 2 0.04
ACGTcount: A:0.37, C:0.08, G:0.01, T:0.54
Consensus pattern (34 bp):
TATAATATATATATACATATATTTTTTTATATTC
Found at i:5736641 original size:17 final size:18
Alignment explanation
Indices: 5736599--5736642 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 18
5736589 GAATATATAC
*
5736599 ATACATATATTTTTTTAT
1 ATACATATATATTTTTAT
*
5736617 ATTC-TATA-ATTTTTAT
1 ATACATATATATTTTTAT
5736633 ATACATATAT
1 ATACATATAT
5736643 TTGCACATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
16 10 0.48
17 8 0.38
18 3 0.14
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (18 bp):
ATACATATATATTTTTAT
Found at i:5736770 original size:2 final size:2
Alignment explanation
Indices: 5736723--5736759 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
5736713 GTACACCTTT
5736723 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5736760 CACGCATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5743126 original size:27 final size:27
Alignment explanation
Indices: 5743096--5743148 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
5743086 TTCAGGAACC
5743096 TAAATCCTCAAGTTGAGTGTAGTATAT
1 TAAATCCTCAAGTTGAGTGTAGTATAT
5743123 TAAATCCTCAAGTTGAGTGTAGTATA
1 TAAATCCTCAAGTTGAGTGTAGTATA
5743149 CCATGCATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (27 bp):
TAAATCCTCAAGTTGAGTGTAGTATAT
Found at i:5747316 original size:2 final size:2
Alignment explanation
Indices: 5747309--5747343 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5747299 ATTTAAGTTG
5747309 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5747344 TTAAAATTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5749573 original size:5 final size:6
Alignment explanation
Indices: 5749558--5749582 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5749548 GAAATACTTA
5749558 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
5749583 TTAAACAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:5750026 original size:23 final size:23
Alignment explanation
Indices: 5749999--5750074 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
5749989 ATAAGTGCCA
5749999 CACTGATATGTAGCAGAAGCTAC
1 CACTGATATGTAGCAGAAGCTAC
* *
5750022 CACTGATATGCAGCCA-TAGCTAC
1 CACTGATATGTAG-CAGAAGCTAC
*
5750045 CACTGA-ATTGTAGCCGAAGCTAC
1 CACTGATA-TGTAGCAGAAGCTAC
*
5750068 CATTGAT
1 CACTGAT
5750075 CAATAACACT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
22 2 0.05
23 39 0.91
24 2 0.05
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.24
Consensus pattern (23 bp):
CACTGATATGTAGCAGAAGCTAC
Found at i:5750326 original size:18 final size:17
Alignment explanation
Indices: 5750300--5750338 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
5750290 ATTTTCCTTC
5750300 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
5750317 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
5750335 CACA
1 CACA
5750339 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:5752966 original size:7 final size:7
Alignment explanation
Indices: 5752954--5752979 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
5752944 CTAAATCTAC
5752954 CAAAATA
1 CAAAATA
5752961 CAAAATA
1 CAAAATA
5752968 CAAAATA
1 CAAAATA
5752975 CAAAA
1 CAAAA
5752980 ACCTTGCACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.73, C:0.15, G:0.00, T:0.12
Consensus pattern (7 bp):
CAAAATA
Found at i:5771563 original size:60 final size:61
Alignment explanation
Indices: 5771498--5771625 Score: 138
Period size: 61 Copynumber: 2.1 Consensus size: 61
5771488 CAGCTGGTAA
*
5771498 CAAAAAAAGACAAAATTA-AATAGTTAGAT-A-TCATTTTGTAACTTTTCATAGTTGGGTGAC
1 CAAAAAAAGAC-AAATTACAATAGTTAGATGACT-ATTTTGTAACTTTTCATAGTTAGGTGAC
** * * * *
5771558 C-AAAAAAGACATTTTACTAGTAGTTAGGTGACTATTTTGTAACTTTTTATAGTTAGGTGAT
1 CAAAAAAAGACAAATTAC-AATAGTTAGATGACTATTTTGTAACTTTTCATAGTTAGGTGAC
5771619 CAAAAAA
1 CAAAAAA
5771626 GTAATTTACT
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
58 4 0.07
59 9 0.16
60 10 0.18
61 27 0.48
62 6 0.11
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (61 bp):
CAAAAAAAGACAAATTACAATAGTTAGATGACTATTTTGTAACTTTTCATAGTTAGGTGAC
Found at i:5771636 original size:60 final size:61
Alignment explanation
Indices: 5771530--5771651 Score: 169
Period size: 61 Copynumber: 2.0 Consensus size: 61
5771520 GTTAGATATC
* *
5771530 ATTTTGTAACTTTTCATAGTTGGGTGACCAAAAAAGACATTTTACTAGTAGTT-AGGTGACT
1 ATTTTGTAACTTTTCATAGTTAGGTGACCAAAAAAGACATTTTACTAATAGTTGA-GTGACT
* *
5771591 ATTTTGTAACTTTTTATAGTTAGGTGATCAAAAAAGTA-A-TTTACTAATAGTTGAGTGACT
1 ATTTTGTAACTTTTCATAGTTAGGTGACCAAAAAAG-ACATTTTACTAATAGTTGAGTGACT
5771651 A
1 A
5771652 CTAGTGCAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
60 19 0.35
61 35 0.64
62 1 0.02
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.39
Consensus pattern (61 bp):
ATTTTGTAACTTTTCATAGTTAGGTGACCAAAAAAGACATTTTACTAATAGTTGAGTGACT
Found at i:5785528 original size:18 final size:18
Alignment explanation
Indices: 5785491--5785529 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5785481 AATTAAAATT
*
5785491 TATTTTATAATAATATAA
1 TATTTTATAATAATACAA
5785509 TATTTTATAAATAAT-CAA
1 TATTTTAT-AATAATACAA
5785527 TAT
1 TAT
5785530 CATATTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
TATTTTATAATAATACAA
Found at i:5785572 original size:6 final size:6
Alignment explanation
Indices: 5785561--5785588 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
5785551 AACAATGTCT
5785561 AATTTA AATTTA AATTTA AATTTA AATT
1 AATTTA AATTTA AATTTA AATTTA AATT
5785589 ATATATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
AATTTA
Found at i:5785726 original size:24 final size:23
Alignment explanation
Indices: 5785667--5785722 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
5785657 TGATTTAAAC
*
5785667 AAATATTCATATTTATATAATTA
1 AAATATTTATATTTATATAATTA
* *
5785690 AAATGTTTATATTT-TATACTATA
1 AAATATTTATATTTATATAAT-TA
5785713 AAATATTTAT
1 AAATATTTAT
5785723 TATTAAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 5 0.18
23 23 0.82
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.50
Consensus pattern (23 bp):
AAATATTTATATTTATATAATTA
Found at i:5791271 original size:28 final size:28
Alignment explanation
Indices: 5791231--5791286 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
5791221 AACAAAAGAA
*
5791231 TACTTCTTGATTATTGAACCGTCAGCTT
1 TACTTCTTGATTATTCAACCGTCAGCTT
5791259 TACTTCTTGATTATTCAACCGTCAGCTT
1 TACTTCTTGATTATTCAACCGTCAGCTT
5791287 CCCTGCAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.43
Consensus pattern (28 bp):
TACTTCTTGATTATTCAACCGTCAGCTT
Found at i:5799660 original size:43 final size:41
Alignment explanation
Indices: 5799599--5799681 Score: 112
Period size: 43 Copynumber: 2.0 Consensus size: 41
5799589 TGTAAATGTT
*
5799599 AAAATTAAAAGTTAATATATGGTAAAATTATACTTTGAACCA
1 AAAATTAAAAGTTAATATATGATAAAATTATA-TTTGAACCA
* * *
5799641 AAAATTTATAAGTTCATATATGATAAAATTATATTTTAACC
1 AAAA-TTAAAAGTTAATATATGATAAAATTATATTTGAACC
5799682 TCCCAATGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
42 11 0.31
43 25 0.69
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.37
Consensus pattern (41 bp):
AAAATTAAAAGTTAATATATGATAAAATTATATTTGAACCA
Found at i:5803893 original size:2 final size:2
Alignment explanation
Indices: 5803888--5803926 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5803878 TACACACTGC
5803888 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5803927 NNNNNNNNNN
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5806637 original size:23 final size:24
Alignment explanation
Indices: 5806598--5806642 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
5806588 TAATTTAATC
*
5806598 CTTTAAAAATTATAAAAATATAAG
1 CTTTAAAAATTAAAAAAATATAAG
*
5806622 CTTT-AAAATTAAAAAATTATA
1 CTTTAAAAATTAAAAAAATATA
5806643 TTTTAACTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (24 bp):
CTTTAAAAATTAAAAAAATATAAG
Found at i:5809592 original size:16 final size:16
Alignment explanation
Indices: 5809571--5809606 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
5809561 ATTTTTTAAA
* *
5809571 AAATATTTAATATATT
1 AAATATTAAATATATC
5809587 AAATATTAAATATATC
1 AAATATTAAATATATC
5809603 AAAT
1 AAAT
5809607 GAATTAGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATATTAAATATATC
Found at i:5810770 original size:2 final size:2
Alignment explanation
Indices: 5810763--5810820 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
5810753 NNNNNNTGTG
5810763 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5810805 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
5810821 GAATTCACAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5810860 original size:16 final size:18
Alignment explanation
Indices: 5810839--5810884 Score: 60
Period size: 16 Copynumber: 2.6 Consensus size: 18
5810829 ACACTATATG
5810839 TGAAAAATAAT-CT-TTT
1 TGAAAAATAATACTCTTT
5810855 TGAAAAATAATACTCTTT
1 TGAAAAATAATACTCTTT
*
5810873 TCTAAAAATAAT
1 T-GAAAAATAAT
5810885 TATATTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 11 0.42
17 2 0.08
18 4 0.15
19 9 0.35
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.39
Consensus pattern (18 bp):
TGAAAAATAATACTCTTT
Found at i:5810871 original size:19 final size:19
Alignment explanation
Indices: 5810844--5810884 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
5810834 ATATGTGAAA
5810844 AATAATCTTTT-TGAAAAAT
1 AATAATCTTTTCT-AAAAAT
*
5810863 AATACTCTTTTCTAAAAAT
1 AATAATCTTTTCTAAAAAT
5810882 AAT
1 AAT
5810885 TATATTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.41
Consensus pattern (19 bp):
AATAATCTTTTCTAAAAAT
Found at i:5821626 original size:23 final size:25
Alignment explanation
Indices: 5821580--5821627 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
5821570 AAAACGCCTC
* *
5821580 TTTTAATTTTATAACTATTTTTAAT
1 TTTTAATTATATAACTATTCTTAAT
5821605 TTTTAATTATATAA-T-TTCTTAAT
1 TTTTAATTATATAACTATTCTTAAT
5821628 CTTATAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 7 0.33
24 1 0.05
25 13 0.62
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (25 bp):
TTTTAATTATATAACTATTCTTAAT
Found at i:5823530 original size:21 final size:21
Alignment explanation
Indices: 5823500--5823542 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
5823490 TTTGGTGGAG
*
5823500 CCATAGAGAATGACGCCACCA
1 CCATAAAGAATGACGCCACCA
*
5823521 CCATAAAGAATGGCGCCACCA
1 CCATAAAGAATGACGCCACCA
5823542 C
1 C
5823543 TAAGTAGCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.37, C:0.35, G:0.19, T:0.09
Consensus pattern (21 bp):
CCATAAAGAATGACGCCACCA
Found at i:5831901 original size:31 final size:30
Alignment explanation
Indices: 5831866--5831964 Score: 110
Period size: 31 Copynumber: 3.2 Consensus size: 30
5831856 ATTTCAAAAA
5831866 TAATATTTATCTTGATAGTATTTTATTTATT
1 TAATATTTATCTTGATA-TATTTTATTTATT
* * * **
5831897 TAATATTAAT-GTGAGATATTAAATTTAATT
1 TAATATTTATCTTGATATATTTTATTT-ATT
*
5831927 TAATATTTATCTTGATAATATTTTATTAATT
1 TAATATTTATCTTGAT-ATATTTTATTTATT
5831958 TAATATT
1 TAATATT
5831965 AATATGATTA
Statistics
Matches: 54, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
29 8 0.15
30 16 0.30
31 22 0.41
32 8 0.15
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.56
Consensus pattern (30 bp):
TAATATTTATCTTGATATATTTTATTTATT
Found at i:5832984 original size:26 final size:26
Alignment explanation
Indices: 5832955--5833006 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
5832945 CACGTAACAG
*
5832955 TTAATAGAATCAGTTGGTCAAATCAA
1 TTAATACAATCAGTTGGTCAAATCAA
*
5832981 TTAATACAATCAGTTGGTTAAATCAA
1 TTAATACAATCAGTTGGTCAAATCAA
5833007 CCATTGCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (26 bp):
TTAATACAATCAGTTGGTCAAATCAA
Found at i:5833016 original size:26 final size:26
Alignment explanation
Indices: 5832957--5833018 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 26
5832947 CGTAACAGTT
* **
5832957 AATAGAATCAGTTGGTCAAATCAATT
1 AATACAATCAGTTGGTCAAATCAACC
*
5832983 AATACAATCAGTTGGTTAAATCAACC
1 AATACAATCAGTTGGTCAAATCAACC
* *
5833009 ATTGCAATCA
1 AATACAATCA
5833019 ATTATTAGCC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (26 bp):
AATACAATCAGTTGGTCAAATCAACC
Found at i:5834024 original size:6 final size:6
Alignment explanation
Indices: 5833994--5834023 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
5833984 TTTTTTCCTG
5833994 TCATTT TCATTT TCATTT TCATTT T-ATTT T
1 TCATTT TCATTT TCATTT TCATTT TCATTT T
5834024 TCTGAATGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (6 bp):
TCATTT
Found at i:5836618 original size:2 final size:2
Alignment explanation
Indices: 5836611--5836635 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5836601 ATAAAAAGAA
5836611 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5836636 ACTAGATGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5842539 original size:198 final size:198
Alignment explanation
Indices: 5842197--5842986 Score: 943
Period size: 198 Copynumber: 4.0 Consensus size: 198
5842187 ACCTTTTAAG
* * *
5842197 CTAAACATCACAATCACGGATGCTTGATCATAAAAACTAAGAAATAAAGATTAAAATCTA-C-CA
1 CTAAACATCACAATCACGGATGCATGATCATAAAAACTAAGAAATAAAGATTAAATTCTATCATA
* * * *
5842260 --TCTCCTTTAGCATGCTATTTTCCAATTCCATGGCGGCTGAATGAGATGTTATCGAGCTACTAT
66 TTTCTTCTTCAGCATGCTATTTTCCAATTCCATGGTGGATGAATGAGATGTTATCGAGCTACTAT
5842323 TCGATATTTTCCTCAATAGAAAAGAAGCTTATAGAGAAAAGAGATCGTACA-TGGTTTCAATTTT
131 TCGATATTTTCCTCAATAGAAAAGAAGCTTATAGAGAAAAGAGATCGTA-AGTGGTTTCAATTTT
**
5842387 GGAC
195 CAAC
* *
5842391 CTAAACATCACAATCATGGATGCATGATCATAAAAACTAAGAAATAAAGATTAAATTCTATTATA
1 CTAAACATCACAATCACGGATGCATGATCATAAAAACTAAGAAATAAAGATTAAATTCTATCATA
* * * * *
5842456 TTTCTTCATT-AGCATGCTATTTTCTGAA-TCCATGGAGGATTAATGGGATGTTATCGAGCAACT
66 TTTCTTC-TTCAGCATGCTATTTTC-CAATTCCATGGTGGATGAATGAGATGTTATCGAGCTACT
* * * * *
5842519 ATTTGATATTTTCATCAATAGAAAAGAAGCTTATAGAGAAAAGAAACCTTAAGTGGTTTCAATTT
129 ATTCGATATTTTCCTCAATAGAAAAGAAGCTTATAGAGAAAAGAGATCGTAAGTGGTTTCAATTT
5842584 TCAAC
194 TCAAC
* * ** *
5842589 CTAAACATCATAATCATGGATGCATGATTGTAAAAACTAAGAAATAAAGATCAAATTCTATCATA
1 CTAAACATCACAATCACGGATGCATGATCATAAAAACTAAGAAATAAAGATTAAATTCTATCATA
* * * * * **
5842654 TTTCTTCTTCAACATGCTAGTTTCCAAATCCATGGTGAATGAATGAGATGTTATCTAGCTTTTAT
66 TTTCTTCTTCAGCATGCTATTTTCCAATTCCATGGTGGATGAATGAGATGTTATCGAGCTACTAT
* * * *
5842719 TCGATATTTTCCTCATTAGAAAAGAAGCTTGTCGAGAAACA-AGATCGTAAGAGGTTTCAATTTT
131 TCGATATTTTCCTCAATAGAAAAGAAGCTTATAGAGAAA-AGAGATCGTAAGTGGTTTCAATTTT
5842783 CAAC
195 CAAC
* * * * * * * * *
5842787 CTAAATAACATAATCACGGATGCATTATCTTAGAAGCTAAGAACTAAATATTAAATTCTATCATA
1 CTAAACATCACAATCACGGATGCATGATCATAAAAACTAAGAAATAAAGATTAAATTCTATCATA
* * *
5842852 TTTCTTCTTCAGCATGCTATTTTCCAATTCCATGGTGGATGAATGAGATATTATTGAGCTGCTAT
66 TTTCTTCTTCAGCATGCTATTTTCCAATTCCATGGTGGATGAATGAGATGTTATCGAGCTACTAT
* * ** * * *
5842917 TTGTTATTACCCTCGAGA-AAATAGAAGCTTATAGAGAAAAGAGATCGTAAAG-GGTTTCGATTT
131 TCGATATTTTCCTCAATAGAAA-AGAAGCTTATAGAGAAAAGAGATCGT-AAGTGGTTTCAATTT
*
5842980 TGAAC
194 TCAAC
5842985 CT
1 CT
5842987 GTTGGAGAAT
Statistics
Matches: 508, Mismatches: 75, Indels: 22
0.84 0.12 0.04
Matches are distributed among these distances:
194 57 0.11
196 1 0.00
197 9 0.02
198 433 0.85
199 8 0.02
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (198 bp):
CTAAACATCACAATCACGGATGCATGATCATAAAAACTAAGAAATAAAGATTAAATTCTATCATA
TTTCTTCTTCAGCATGCTATTTTCCAATTCCATGGTGGATGAATGAGATGTTATCGAGCTACTAT
TCGATATTTTCCTCAATAGAAAAGAAGCTTATAGAGAAAAGAGATCGTAAGTGGTTTCAATTTTC
AAC
Found at i:5844813 original size:23 final size:23
Alignment explanation
Indices: 5844763--5844822 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
5844753 CTTTTTAAAG
* * *
5844763 TTTATAATATTATATTTTTTATTT
1 TTTAT-ATATTATATATTATATTA
*
5844787 TTTATATATTATATATTATGTTA
1 TTTATATATTATATATTATATTA
5844810 TTTATA-A-TATATA
1 TTTATATATTATATA
5844823 AAAATTAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 6 0.19
22 1 0.03
23 20 0.62
24 5 0.16
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (23 bp):
TTTATATATTATATATTATATTA
Found at i:5847306 original size:19 final size:19
Alignment explanation
Indices: 5847282--5847321 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
5847272 TGCCAAAATT
5847282 GAGCTTGACT-TAAAATTGA
1 GAGCTTGA-TATAAAATTGA
5847301 GAGCTTGATACTAAAATTGA
1 GAGCTTGATA-TAAAATTGA
5847321 G
1 G
5847322 CTCGATTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 1 0.05
19 8 0.42
20 10 0.53
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.30
Consensus pattern (19 bp):
GAGCTTGATATAAAATTGA
Found at i:5851655 original size:18 final size:18
Alignment explanation
Indices: 5851634--5851668 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5851624 ACACAAAACT
* *
5851634 AAAATCTAACCTAAAAAA
1 AAAACCTAAACTAAAAAA
5851652 AAAACCTAAACTAAAAA
1 AAAACCTAAACTAAAAA
5851669 TGAAATGAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.17, G:0.00, T:0.14
Consensus pattern (18 bp):
AAAACCTAAACTAAAAAA
Found at i:5853513 original size:35 final size:35
Alignment explanation
Indices: 5853474--5853548 Score: 150
Period size: 35 Copynumber: 2.1 Consensus size: 35
5853464 ACATATATGT
5853474 ATGTATAAATTATATTCGAATATACATGTGTATAC
1 ATGTATAAATTATATTCGAATATACATGTGTATAC
5853509 ATGTATAAATTATATTCGAATATACATGTGTATAC
1 ATGTATAAATTATATTCGAATATACATGTGTATAC
5853544 ATGTA
1 ATGTA
5853549 AATTTTGTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (35 bp):
ATGTATAAATTATATTCGAATATACATGTGTATAC
Found at i:5853792 original size:27 final size:27
Alignment explanation
Indices: 5853761--5853812 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
5853751 GAATATGTAC
5853761 GAGTATATAGGTATATGTTCTTGTTAT
1 GAGTATATAGGTATATGTTCTTGTTAT
5853788 GAGTATATAGGTATATGTTCTTGTT
1 GAGTATATAGGTATATGTTCTTGTT
5853813 TCGAATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.25, C:0.04, G:0.23, T:0.48
Consensus pattern (27 bp):
GAGTATATAGGTATATGTTCTTGTTAT
Found at i:5853821 original size:27 final size:27
Alignment explanation
Indices: 5853764--5853821 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 27
5853754 TATGTACGAG
*
5853764 TATATAGGTATATGTTCTTGTTATGAG
1 TATATAGGTATATGTTCTTGTTATGAA
5853791 TATATAGGTATATGTTCTTGTT-TCGAA
1 TATATAGGTATATGTTCTTGTTAT-GAA
5853818 TATA
1 TATA
5853822 AGCATAGAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 1 0.03
27 28 0.97
ACGTcount: A:0.28, C:0.05, G:0.19, T:0.48
Consensus pattern (27 bp):
TATATAGGTATATGTTCTTGTTATGAA
Found at i:5854289 original size:41 final size:41
Alignment explanation
Indices: 5854232--5854463 Score: 392
Period size: 41 Copynumber: 5.6 Consensus size: 41
5854222 GACTATACGT
*
5854232 CTAGCAGGCTAAGTGCCGATGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
*
5854273 CTAGCAGGCTAAGTGCCAGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
5854314 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
*
5854355 CTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* * *
5854396 CTAGCAAGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
*
5854437 CTAGCAAGCTAAGTGCCGGTGAATCTG
1 CTAGCAGGCTAAGTGCCGGTG-ATCTG
5854464 TTAAATTAAG
Statistics
Matches: 182, Mismatches: 8, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
41 177 0.97
42 5 0.03
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:5854497 original size:2 final size:2
Alignment explanation
Indices: 5854490--5854523 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5854480 TATGCATTTG
5854490 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
5854524 GATTTTGGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5856631 original size:15 final size:15
Alignment explanation
Indices: 5856611--5856640 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5856601 GTTTTCCAAA
5856611 ATTATAATATATCAT
1 ATTATAATATATCAT
*
5856626 ATTATATTATATCAT
1 ATTATAATATATCAT
5856641 GCAATTTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTATAATATATCAT
Found at i:5856890 original size:15 final size:15
Alignment explanation
Indices: 5856867--5856906 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
5856857 TAATTCACAA
5856867 AAAAAAATATAAAAT
1 AAAAAAATATAAAAT
*
5856882 AAAATAATATAAAAAT
1 AAAAAAATAT-AAAAT
*
5856898 TAAAAAATA
1 AAAAAAATA
5856907 AAATGGGTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAAAAATATAAAAT
Found at i:5857802 original size:14 final size:14
Alignment explanation
Indices: 5857783--5857810 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5857773 TACAATATCC
5857783 AAATAATAACAACA
1 AAATAATAACAACA
5857797 AAATAATAACAACA
1 AAATAATAACAACA
5857811 TAATTGTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.14, G:0.00, T:0.14
Consensus pattern (14 bp):
AAATAATAACAACA
Found at i:5857893 original size:18 final size:18
Alignment explanation
Indices: 5857855--5857896 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
5857845 AAAAGAAGAG
*
5857855 AAAATAGCAATAAAATAAT
1 AAAA-AGCAATAAAACAAT
*
5857874 AAAAAGCAATAAAACGAT
1 AAAAAGCAATAAAACAAT
5857892 AAAAA
1 AAAAA
5857897 AACAACACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.71, C:0.07, G:0.07, T:0.14
Consensus pattern (18 bp):
AAAAAGCAATAAAACAAT
Found at i:5861742 original size:52 final size:51
Alignment explanation
Indices: 5861641--5861843 Score: 244
Period size: 52 Copynumber: 4.1 Consensus size: 51
5861631 GATTAAGTGA
* *
5861641 CAAGTGGAAAGTGATAAGTGAT-A--GATAGTTTCGGCTACACTTATCTGAT
1 CAAGT-GAAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGAT
* *
5861690 CAAGTGATAAGTGGAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGAT
1 CAAGTGA-AAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGAT
*
5861742 CAA--G--A--GACAAAGTGATAAGTGATAGTTTCGGCTACACTTATCTGAT
1 CAAGTGAAAGTGA-AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGAT
**
5861788 CAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGAT
1 CAAGTGA-AAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGAT
5861840 CAAG
1 CAAG
5861844 AGACAAAGTG
Statistics
Matches: 132, Mismatches: 10, Indels: 21
0.81 0.06 0.13
Matches are distributed among these distances:
45 1 0.01
46 39 0.30
47 1 0.01
48 3 0.02
49 17 0.13
50 2 0.02
51 1 0.01
52 66 0.50
53 2 0.02
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.29
Consensus pattern (51 bp):
CAAGTGAAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGAT
Found at i:5861757 original size:46 final size:46
Alignment explanation
Indices: 5861704--5861897 Score: 217
Period size: 46 Copynumber: 4.3 Consensus size: 46
5861694 TGATAAGTGG
*
5861704 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGAC
* *
5861750 AAAGTGATAAGTGATAGTTTCGGCTACACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGAC
**
5861796 AAGTGAAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC
1 ------AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGAC
*
5861848 AAAGTG---A-T-A-AG--T-GGCTACACTTATCTGATCAAGAAAC
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGAC
5861885 AAAGTGATAAGTG
1 AAAGTGATAAGTG
5861898 GCTACACTTA
Statistics
Matches: 128, Mismatches: 9, Indels: 26
0.79 0.06 0.16
Matches are distributed among these distances:
37 29 0.23
38 1 0.01
40 3 0.02
41 2 0.02
42 1 0.01
43 1 0.01
46 49 0.38
52 42 0.33
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (46 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGAC
Found at i:5861821 original size:98 final size:98
Alignment explanation
Indices: 5861664--5861860 Score: 349
Period size: 98 Copynumber: 2.0 Consensus size: 98
5861654 ATAAGTGATA
* * *
5861664 GATAGTTTCGGCTACACTTATCTGATCAAGTGATAAGTGGAAAGTGATAAGTGATAGCTTCGGCT
1 GATAGTTTCGGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCAGCT
*
5861729 ATACTTATCTGATCAAGAGACAAAGTGATAAGT
66 ACACTTATCTGATCAAGAGACAAAGTGATAAGT
*
5861762 GATAGTTTCGGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTTAGCT
1 GATAGTTTCGGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCAGCT
5861827 ACACTTATCTGATCAAGAGACAAAGTGATAAGT
66 ACACTTATCTGATCAAGAGACAAAGTGATAAGT
5861860 G
1 G
5861861 GCTACACTTA
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.29
Consensus pattern (98 bp):
GATAGTTTCGGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCAGCT
ACACTTATCTGATCAAGAGACAAAGTGATAAGT
Found at i:5861849 original size:52 final size:53
Alignment explanation
Indices: 5861750--5861860 Score: 172
Period size: 52 Copynumber: 2.1 Consensus size: 53
5861740 ATCAAGAGAC
* *
5861750 AAAGTGATAAGTGATAGTTTCGGCTACACTTATCTGATCAAGTGAC-AAGTGA
1 AAAGTGATAAGTGATAGTTTCAGCTACACTTATCTGATCAAGAGACAAAGTGA
5861802 AAAGTGATAAGTGATAGCTTT-AGCTACACTTATCTGATCAAGAGACAAAGTGA
1 AAAGTGATAAGTGATAG-TTTCAGCTACACTTATCTGATCAAGAGACAAAGTGA
*
5861855 TAAGTG
1 AAAGTG
5861861 GCTACACTTA
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
52 40 0.74
53 14 0.26
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.28
Consensus pattern (53 bp):
AAAGTGATAAGTGATAGTTTCAGCTACACTTATCTGATCAAGAGACAAAGTGA
Found at i:5861868 original size:37 final size:37
Alignment explanation
Indices: 5861824--5861932 Score: 186
Period size: 37 Copynumber: 3.0 Consensus size: 37
5861814 GATAGCTTTA
5861824 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
5861861 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
5861898 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
5861933 ATCATATGTA
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
35 12 0.17
36 4 0.06
37 53 0.77
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:5863803 original size:41 final size:41
Alignment explanation
Indices: 5863758--5863914 Score: 242
Period size: 41 Copynumber: 3.8 Consensus size: 41
5863748 TTGTATATAA
* ** * * *
5863758 CACCGGCATAAAGCCTGCTAGGCACCAAGCCCGATACATTT
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
* *
5863799 CACCGGCACAAAGCCTGCTAGACATAAAGTCTGATATAATT
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
5863840 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
5863881 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGA
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGA
5863915 ACTTACAAAA
Statistics
Matches: 106, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 106 1.00
ACGTcount: A:0.33, C:0.29, G:0.20, T:0.18
Consensus pattern (41 bp):
CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
Found at i:5865167 original size:42 final size:42
Alignment explanation
Indices: 5865104--5865202 Score: 135
Period size: 42 Copynumber: 2.4 Consensus size: 42
5865094 CACTCGGTAT
* *
5865104 CGCACACTTAGTGCCCGTTATTCAACATCATTATTATAATTC
1 CGCACACTTAGTGCCCATTATTCAACATCATCATTATAATTC
* * *
5865146 CGCACACTTAGTGCCTATTATTCAACATCATCATTTTAATTT
1 CGCACACTTAGTGCCCATTATTCAACATCATCATTATAATTC
**
5865188 TACACACTTAGTGCC
1 CGCACACTTAGTGCC
5865203 ATTCATATAG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.28, C:0.26, G:0.09, T:0.36
Consensus pattern (42 bp):
CGCACACTTAGTGCCCATTATTCAACATCATCATTATAATTC
Found at i:5866573 original size:32 final size:32
Alignment explanation
Indices: 5866532--5866595 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
5866522 CTGTATGTAT
5866532 TGTGGGCACACTACAGCTCTTATGAGCGTCCC
1 TGTGGGCACACTACAGCTCTTATGAGCGTCCC
5866564 TGTGGGCACACTACAGCTCTTATGAGCGTCCC
1 TGTGGGCACACTACAGCTCTTATGAGCGTCCC
5866596 GTTATATGGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.19, C:0.31, G:0.25, T:0.25
Consensus pattern (32 bp):
TGTGGGCACACTACAGCTCTTATGAGCGTCCC
Found at i:5866632 original size:26 final size:26
Alignment explanation
Indices: 5866603--5866671 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
5866593 CCCGTTATAT
*
5866603 GGCTTTCCATGAGCTTCCTGATTAAA
1 GGCTTTCTATGAGCTTCCTGATTAAA
* * *
5866629 GGCTCTT-TGTGAGCTTTCTGATTAAT
1 GGCT-TTCTATGAGCTTCCTGATTAAA
5866655 GGCTTTCTA-GAGCTTCC
1 GGCTTTCTATGAGCTTCC
5866672 CGATATGGCT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
25 9 0.26
26 24 0.69
27 2 0.06
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (26 bp):
GGCTTTCTATGAGCTTCCTGATTAAA
Found at i:5866681 original size:23 final size:23
Alignment explanation
Indices: 5866653--5866731 Score: 59
Period size: 23 Copynumber: 3.3 Consensus size: 23
5866643 TTTCTGATTA
5866653 ATGGCTTTCTAGAGCTTCCCGAT
1 ATGGCTTTCTAGAGCTTCCCGAT
** * **
5866676 ATGGCTCGCTTGAATTTCCCGATCT
1 ATGGCTTTCTAGAGCTTCCCGA--T
* * *
5866701 ATGGCTATCTGGAGCTTCCCGTT
1 ATGGCTTTCTAGAGCTTCCCGAT
5866724 ATTGGCTT
1 A-TGGCTT
5866732 GCATGAGCTT
Statistics
Matches: 41, Mismatches: 12, Indels: 5
0.71 0.21 0.09
Matches are distributed among these distances:
23 19 0.46
24 5 0.12
25 17 0.41
ACGTcount: A:0.15, C:0.25, G:0.23, T:0.37
Consensus pattern (23 bp):
ATGGCTTTCTAGAGCTTCCCGAT
Found at i:5870392 original size:20 final size:20
Alignment explanation
Indices: 5870367--5870405 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5870357 AATTTTAAAA
5870367 TATTTTTAAAATACTTTTTT
1 TATTTTTAAAATACTTTTTT
**
5870387 TATTTTTAATTTACTTTTT
1 TATTTTTAAAATACTTTTT
5870406 AAAAATATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (20 bp):
TATTTTTAAAATACTTTTTT
Found at i:5870439 original size:20 final size:21
Alignment explanation
Indices: 5870396--5870454 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 21
5870386 TTATTTTTAA
* *
5870396 TTTACTTTTTAAAAATATACT
1 TTTAATTTTTAAAAATAAACT
*
5870417 TTTAATTTTT-AAAATAAATT
1 TTTAATTTTTAAAAATAAACT
5870437 TTTAGTATTTATTAAAAA
1 TTTA--ATTT-TTAAAAA
5870455 AAGGGCCGGG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 12 0.39
21 9 0.29
22 4 0.13
23 2 0.06
24 4 0.13
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (21 bp):
TTTAATTTTTAAAAATAAACT
Found at i:5877918 original size:64 final size:64
Alignment explanation
Indices: 5877817--5877945 Score: 258
Period size: 64 Copynumber: 2.0 Consensus size: 64
5877807 AGGAAGTTAA
5877817 TTGTGTTAATGACAAAAGAAATGCCGTTCTTCAGATAACTGCTTATTGTCTTTTAGTTGTTACG
1 TTGTGTTAATGACAAAAGAAATGCCGTTCTTCAGATAACTGCTTATTGTCTTTTAGTTGTTACG
5877881 TTGTGTTAATGACAAAAGAAATGCCGTTCTTCAGATAACTGCTTATTGTCTTTTAGTTGTTACG
1 TTGTGTTAATGACAAAAGAAATGCCGTTCTTCAGATAACTGCTTATTGTCTTTTAGTTGTTACG
5877945 T
1 T
5877946 AGGCAATCTC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.41
Consensus pattern (64 bp):
TTGTGTTAATGACAAAAGAAATGCCGTTCTTCAGATAACTGCTTATTGTCTTTTAGTTGTTACG
Found at i:5878138 original size:29 final size:29
Alignment explanation
Indices: 5878096--5878158 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
5878086 GTTAAGAGTA
5878096 TGTTTACATTTCTTAGTCATTATTTTAAG
1 TGTTTACATTTCTTAGTCATTATTTTAAG
5878125 TGTTTACATTTCTTAGTCATTATTTTAAG
1 TGTTTACATTTCTTAGTCATTATTTTAAG
*
5878154 GGTTT
1 TGTTT
5878159 GCTCAGGAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.22, C:0.10, G:0.13, T:0.56
Consensus pattern (29 bp):
TGTTTACATTTCTTAGTCATTATTTTAAG
Found at i:5879663 original size:161 final size:162
Alignment explanation
Indices: 5879390--5879714 Score: 456
Period size: 161 Copynumber: 2.0 Consensus size: 162
5879380 AAATAAAATT
* * * *
5879390 ACCACGTTAGAGGCTGTTTTCTAGGTCATTGTTAACTTAATGGGTGTAATGTTTTGATATTTCAG
1 ACCACGTTAGAGGCTATTGTATAGGTCATTGTTAACTTAAGGGGTGTAATGTTTTGATATTTCAG
* * * **
5879455 GGTAGTTTTGGTAGGTTGCGTGACAGGGGGAAGGAAGTTCAGAAGGCTACTTAAATTTT-ACTAA
66 GATAGCTTTGGTAGGTTGCATGACAGGGGGAAGGAAGTTCAGAAGGCTACAAAAATTTTGACTAA
*
5879519 GCATTTTCCAAATAAA-ACCATTCATATGCCA
131 GCATTTTCCAAATAAATACCATTCACATGCCA
* * * * *
5879550 ACCATGTTAGAGGCTATTGTATAGGTTATTGTTAATTTAAGGGGTGTGATGTTTTGCTATTTTCA
1 ACCACGTTAGAGGCTATTGTATAGGTCATTGTTAACTTAAGGGGTGTAATGTTTTGATA-TTTCA
*
5879615 GGATAGCTTTGGTAGGTTGCATGACAGGGGGAAGGAAGTTCCGAAGGCTACAAAAATTTTGACTA
65 GGATAGCTTTGGTAGGTTGCATGACAGGGGGAAGGAAGTTCAGAAGGCTACAAAAATTTTGACTA
*
5879680 AGCTTTTTCCAAATAAAGTTACCATTCACATGCCA
130 AGCATTTTCCAAATAAA--TACCATTCACATGCCA
5879715 CAGGTCCGTA
Statistics
Matches: 143, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
160 50 0.35
161 59 0.41
162 20 0.14
165 14 0.10
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (162 bp):
ACCACGTTAGAGGCTATTGTATAGGTCATTGTTAACTTAAGGGGTGTAATGTTTTGATATTTCAG
GATAGCTTTGGTAGGTTGCATGACAGGGGGAAGGAAGTTCAGAAGGCTACAAAAATTTTGACTAA
GCATTTTCCAAATAAATACCATTCACATGCCA
Found at i:5882511 original size:15 final size:16
Alignment explanation
Indices: 5882493--5882525 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
5882483 CAAAAAACTA
*
5882493 TTTTCTTT-TTTCCTT
1 TTTTCTTTACTTCCTT
5882508 TTTTCTTTACTTCCTT
1 TTTTCTTTACTTCCTT
5882524 TT
1 TT
5882526 GTTGCAGTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTCTTTACTTCCTT
Found at i:5895393 original size:7 final size:7
Alignment explanation
Indices: 5895381--5895411 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
5895371 AGAAATGGTC
5895381 AAACTTA
1 AAACTTA
5895388 AAACTTA
1 AAACTTA
5895395 AAACTTA
1 AAACTTA
5895402 AAACTTA
1 AAACTTA
5895409 AAA
1 AAA
5895412 GAAGAGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.61, C:0.13, G:0.00, T:0.26
Consensus pattern (7 bp):
AAACTTA
Found at i:5899411 original size:15 final size:14
Alignment explanation
Indices: 5899391--5899421 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
5899381 CACCTGCTTC
5899391 TTTTTCTTTTTCTTT
1 TTTTTCTTTTT-TTT
5899406 TTTTTCTTTTTTTT
1 TTTTTCTTTTTTTT
5899420 TT
1 TT
5899422 CCATATGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (14 bp):
TTTTTCTTTTTTTT
Found at i:5901846 original size:37 final size:37
Alignment explanation
Indices: 5901805--5901990 Score: 293
Period size: 37 Copynumber: 5.0 Consensus size: 37
5901795 GCTGAAGCTA
*
5901805 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
* *
5901842 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAA
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
** *
5901879 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAA
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
*
5901916 CCACTTATCACTTTGTTTA-TTGATCAGATAAGTGTAG
1 CCACTTATCACTTTG-TCACTTGATCAGATAAGTGTAG
5901953 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
5901990 C
1 C
5901991 TAAAACTACC
Statistics
Matches: 140, Mismatches: 7, Indels: 4
0.93 0.05 0.03
Matches are distributed among these distances:
36 2 0.01
37 136 0.97
38 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (37 bp):
CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
Found at i:5909597 original size:2 final size:2
Alignment explanation
Indices: 5909590--5909618 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5909580 CTTTTACCAA
5909590 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5909619 GAGAGAGAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5916475 original size:2 final size:2
Alignment explanation
Indices: 5916463--5916494 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
5916453 AAATATAAAA
*
5916463 AT AT GT 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
5916495 TTACAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5918335 original size:44 final size:44
Alignment explanation
Indices: 5918260--5918619 Score: 220
Period size: 44 Copynumber: 8.2 Consensus size: 44
5918250 TCATTACTGG
* * **
5918260 CTTCAATGTATTCCACTGCAACTTCAGGGAGGTAAAATCTGCCAT
1 CTTCAATCTACTCCACTGCTGCTT-AGGGAGGTAAAATCTGCCAT
* * * * * **
5918305 CTTCGATCTGCTCCACTACTGCTTAGGGAGGCAAGATCTGAAAT
1 CTTCAATCTACTCCACTGCTGCTTAGGGAGGTAAAATCTGCCAT
* ** * * * ***
5918349 CTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAAT-TACTGG
1 CTTCAATCTACTCCACTGCTGCTTAGGGAGGTAAAATCTGCCAT
* ** *
5918392 CTTCAATGTACTCCACTGCAACTTTAGGGAGGTAAAATCCGCCAT
1 CTTCAATCTACTCCACTGCTGC-TTAGGGAGGTAAAATCTGCCAT
* * ** * * **
5918437 CTTCGATCTGCTCCACTATTGCTTAGGGAGGCAAGATCTGAAAT
1 CTTCAATCTACTCCACTGCTGCTTAGGGAGGTAAAATCTGCCAT
* ** * * * ***
5918481 CTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAAT-TACTGG
1 CTTCAATCTACTCCACTGCTGCTTAGGGAGGTAAAATCTGCCAT
* ** *
5918524 CTTCAATGTACTCCACTGCAACTTCAGGGAGGTAAAATCCGCCAT
1 CTTCAATCTACTCCACTGCTGCTT-AGGGAGGTAAAATCTGCCAT
* * * * **
5918569 CTTCGATCTGCTCCACTACTGCTTAGGGAGGTAAGATCTGTAAT
1 CTTCAATCTACTCCACTGCTGCTTAGGGAGGTAAAATCTGCCAT
5918613 CTTCAAT
1 CTTCAAT
5918620 TTGTTCAACT
Statistics
Matches: 220, Mismatches: 91, Indels: 9
0.69 0.28 0.03
Matches are distributed among these distances:
43 38 0.17
44 130 0.59
45 52 0.24
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.28
Consensus pattern (44 bp):
CTTCAATCTACTCCACTGCTGCTTAGGGAGGTAAAATCTGCCAT
Found at i:5918631 original size:132 final size:132
Alignment explanation
Indices: 5918178--5918619 Score: 731
Period size: 132 Copynumber: 3.3 Consensus size: 132
5918168 TATACTTCTG
* ** ** * *
5918178 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAG
1 TCTGCTCCACTACTGCTT-AGGGAGGCAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAG
* ** * *
5918243 GGAAATATCATTACTGGCTTCAATGTATTCCACTGCAACTTCAGGGAGGTAAAATCTGCCATCTT
65 GGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACTTCAGGGAGGTAAAATCCGCCATCTT
5918308 CGA
130 CGA
5918311 TCTGCTCCACTACTGCTTAGGGAGGCAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGG
1 TCTGCTCCACTACTGCTTAGGGAGGCAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGG
*
5918376 GAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACTTTAGGGAGGTAAAATCCGCCATCTTC
66 GAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACTTCAGGGAGGTAAAATCCGCCATCTTC
5918441 GA
131 GA
*
5918443 TCTGCTCCACTATTGCTTAGGGAGGCAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGG
1 TCTGCTCCACTACTGCTTAGGGAGGCAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGG
5918508 GAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACTTCAGGGAGGTAAAATCCGCCATCTTC
66 GAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACTTCAGGGAGGTAAAATCCGCCATCTTC
5918573 GA
131 GA
* *
5918575 TCTGCTCCACTACTGCTTAGGGAGGTAAGATCTGTAATCTTCAAT
1 TCTGCTCCACTACTGCTTAGGGAGGCAAGATCTGAAATCTTCAAT
5918620 TTGTTCAACT
Statistics
Matches: 291, Mismatches: 18, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
132 276 0.95
133 15 0.05
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (132 bp):
TCTGCTCCACTACTGCTTAGGGAGGCAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGG
GAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACTTCAGGGAGGTAAAATCCGCCATCTTC
GA
Found at i:5918675 original size:50 final size:50
Alignment explanation
Indices: 5918613--5918882 Score: 211
Period size: 50 Copynumber: 5.4 Consensus size: 50
5918603 GATCTGTAAT
* * * * *
5918613 CTTCAATTTGTTCAACTGCAATGTCGGGGAAACCAGATCTGTCGTCGTAG
1 CTTCAATCTGTTCAACTGCAATGTCAGGGAAACCAGATCCGCCGTTGTAG
* * * * * *** *
5918663 CTTCAATCTGTTCCACCGTACTG-CTAAGGAAGTAAGATCCGCCGTTGTGG
1 CTTCAATCTGTTCAACTGCAATGTC-AGGGAAACCAGATCCGCCGTTGTAG
* * * * * *
5918713 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGTCGTCGTAG
1 CTTCAATCTGTTCAACTGCAATGTCAGGGAAACCAGATCCGCCGTTGTAG
* * * * *** *
5918763 CTTTAATCTGTTCCACTGCACTG-CTAAGGAAGTAAGATCCGCCGTTGTGG
1 CTTCAATCTGTTCAACTGCAATGTC-AGGGAAACCAGATCCGCCGTTGTAG
* * * *
5918813 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTTGTAG
1 CTTCAATCTGTTCAACTGCAATGTCAGGGAAACCAGATCCGCCGTTGTAG
*
5918863 CTTCAATCTGTTCCACTGCA
1 CTTCAATCTGTTCAACTGCA
5918883 CTGCTAAGGA
Statistics
Matches: 157, Mismatches: 59, Indels: 8
0.70 0.26 0.04
Matches are distributed among these distances:
49 2 0.01
50 153 0.97
51 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (50 bp):
CTTCAATCTGTTCAACTGCAATGTCAGGGAAACCAGATCCGCCGTTGTAG
Found at i:5918743 original size:100 final size:100
Alignment explanation
Indices: 5918629--5918908 Score: 470
Period size: 100 Copynumber: 2.8 Consensus size: 100
5918619 TTTGTTCAAC
* * * * *
5918629 TGCAATGTCGGGGAAACCAGATCTGTCGTCGTAGCTTCAATCTGTTCCACCGTACTGCTAAGGAA
1 TGCAATATCAGGGAAACCAGATCCGTCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
5918694 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
*
5918729 TGCAATATCAGGGAAACCAGATCCGTCGTCGTAGCTTTAATCTGTTCCACTGCACTGCTAAGGAA
1 TGCAATATCAGGGAAACCAGATCCGTCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
5918794 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
* *
5918829 TGCAATATCAGGGAAACCAGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
1 TGCAATATCAGGGAAACCAGATCCGTCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
* *
5918894 ATAAGATTCGCCGTT
66 GTAAGATCCGCCGTT
5918909 TCACCGGTTT
Statistics
Matches: 169, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
100 169 1.00
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.30
Consensus pattern (100 bp):
TGCAATATCAGGGAAACCAGATCCGTCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
Found at i:5920158 original size:14 final size:15
Alignment explanation
Indices: 5920139--5920176 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
5920129 AGCCTCTCCA
5920139 TTTTATTTTTCAT-T
1 TTTTATTTTTCATCT
5920153 TTTTA-TTTTCATCT
1 TTTTATTTTTCATCT
*
5920167 TTTCATTTTT
1 TTTTATTTTT
5920177 TCACATCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 7 0.33
14 10 0.48
15 4 0.19
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTATTTTTCATCT
Found at i:5920170 original size:21 final size:19
Alignment explanation
Indices: 5920138--5920177 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 19
5920128 TAGCCTCTCC
5920138 ATTTTATTTTTCATTTTTT
1 ATTTTATTTTTCATTTTTT
5920157 ATTTTCATCTTTTCATTTTTT
1 ATTTT-AT-TTTTCATTTTTT
5920178 CACATCATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.26
20 2 0.11
21 12 0.63
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (19 bp):
ATTTTATTTTTCATTTTTT
Found at i:5927832 original size:25 final size:25
Alignment explanation
Indices: 5927781--5927832 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
5927771 ATTGTTTTAA
* *
5927781 TATCATAATTTTTTAAATTATTATT
1 TATCATAATATTTTAAATAATTATT
*
5927806 TATCA-AATATTTTAATATAATTTTT
1 TATCATAATATTTTAA-ATAATTATT
5927831 TA
1 TA
5927833 CTAAGATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (25 bp):
TATCATAATATTTTAAATAATTATT
Found at i:5928348 original size:21 final size:22
Alignment explanation
Indices: 5928304--5928348 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
5928294 TTAAATATTG
*
5928304 TTAAAATATAATGATTGTAAAT
1 TTAAAATATAATGATTATAAAT
* *
5928326 TTAAATTATAATG-TTATATAT
1 TTAAAATATAATGATTATAAAT
5928347 TT
1 TT
5928349 GAAACAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (22 bp):
TTAAAATATAATGATTATAAAT
Found at i:5929387 original size:12 final size:13
Alignment explanation
Indices: 5929356--5929405 Score: 57
Period size: 12 Copynumber: 3.8 Consensus size: 13
5929346 ATTATATGTT
*
5929356 TTTTATTTTTAGA
1 TTTTAGTTTTAGA
*
5929369 CTTTAGTTTTAG-
1 TTTTAGTTTTAGA
5929381 TTTTAGTTTTAGAA
1 TTTTAGTTTTAG-A
*
5929395 TTTTATTTTTA
1 TTTTAGTTTTA
5929406 TTTATTAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
12 11 0.35
13 10 0.32
14 10 0.32
ACGTcount: A:0.22, C:0.02, G:0.10, T:0.66
Consensus pattern (13 bp):
TTTTAGTTTTAGA
Found at i:5930303 original size:33 final size:32
Alignment explanation
Indices: 5930237--5930357 Score: 107
Period size: 33 Copynumber: 3.7 Consensus size: 32
5930227 TTTTTGTGCT
* * ** *
5930237 ATAGTCCAACTATGGTCTTACACATGCATTGCC
1 ATAGCCCAGCTATGGTCTTACATTTG-AATGCC
* * * *
5930270 ATGGCCCTGCCATGGTCTTACATTTGTAGTGCC
1 ATAGCCCAGCTATGGTCTTACATTTG-AATGCC
* * *
5930303 ATAACCCAGTTATGGTCTTATCATTAGAATGCC
1 ATAGCCCAGCTATGGTCTTA-CATTTGAATGCC
5930336 ATAGCCCAGCTATGGTCTTACA
1 ATAGCCCAGCTATGGTCTTACA
5930358 CATGTAACTA
Statistics
Matches: 69, Mismatches: 18, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
32 2 0.03
33 62 0.90
34 5 0.07
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (32 bp):
ATAGCCCAGCTATGGTCTTACATTTGAATGCC
Found at i:5930422 original size:105 final size:101
Alignment explanation
Indices: 5930302--5930495 Score: 291
Period size: 105 Copynumber: 1.9 Consensus size: 101
5930292 TTTGTAGTGC
* *
5930302 CATAACCCAGTTATGGTCTTATCATTAGAATGCCATAGCCCAGCTATGGTCTTACACATGT-AAC
1 CATAACCCAATTATGGTCTTATCATTAAAATGCCATAGCCCAGCTATGGTCTT--ACATGTAAAC
*
5930366 TATACTGCCATGGTCCAACCATGGTCTTACGTTCAAGGTGT
64 -AT--TCCCATGGTCCAACCATGGTCTTACGTTCAAGGTGT
* *
5930407 CATAACCCAATTATGGTCTTTTCATTAAAATGCCATAGCCCAGCTATGGTCTTACATTTAAACAT
1 CATAACCCAATTATGGTCTTATCATTAAAATGCCATAGCCCAGCTATGGTCTTACATGTAAACAT
5930472 TCCCATGGTCCAACCATGGTCTTA
66 TCCCATGGTCCAACCATGGTCTTA
5930496 TCCGTCAATT
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
101 23 0.28
103 7 0.08
104 3 0.04
105 50 0.60
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.31
Consensus pattern (101 bp):
CATAACCCAATTATGGTCTTATCATTAAAATGCCATAGCCCAGCTATGGTCTTACATGTAAACAT
TCCCATGGTCCAACCATGGTCTTACGTTCAAGGTGT
Done.