Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 138 of 175
Found at i:42662453 original size:264 final size:264
Alignment explanation
Indices: 42662067--42662666 Score: 914
Period size: 264 Copynumber: 2.3 Consensus size: 264
42662057 ACCACAGCTT
* * *
42662067 TATCTCCCTAAGCAGTAGTAGAGTAGGTTGAAGATTGTAGATCCTATCTCCCTAAGCAGTAGTGG
1 TATCTCCCTAAGCAATAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGG
* *
42662132 AGCAGATCAAAAACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGGTTTAAGCCACCAGT
66 AGCAGATCAAAAACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAAT
* * * * * * * *
42662197 CCTATCTCCCTTACCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGT
131 CCTATCTCCCTAAACAGCAATGGAGTAGGTTGAAGAATGCAGATCCCGTATCCCTAAGCAATAGT
* * * *
42662262 GGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAATGTAGTAGGGAAGCATG-TTTAAGCTACC
196 GGAGCAGATCAAAGACGGTGAATCTTATATTCCCAAGGTAGTAGGGAAGCA-GATTTAAACCACC
* **
42662326 AGTTT
260 AATCC
* * * *
42662331 TGTCTCCCTGAGCAACAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTTCCTAAGCAGTAGTGG
1 TATCTCCCTAAGCAATAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGG
*
42662396 AGCAGATCAAAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAAT
66 AGCAGATCAAAAACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAAT
42662461 CCTATCTCCCTAAACAGCAATGGAGTAGGTTGAAGAATGCAGATCCCGTATCCCTAAGCAATAGT
131 CCTATCTCCCTAAACAGCAATGGAGTAGGTTGAAGAATGCAGATCCCGTATCCCTAAGCAATAGT
* *
42662526 GGAGCAGATCAAAGACGGTGAATTTTATATTCCCAAGGTAGTAGGGAATCAGATTTAAACCACCA
196 GGAGCAGATCAAAGACGGTGAATCTTATATTCCCAAGGTAGTAGGGAAGCAGATTTAAACCACCA
42662591 ATCC
261 ATCC
* *
42662595 TATCTCCCTAAGCAATAGTGGAGTAAGTTGAAGATTGTAGATCATGTCTCCCTAAGCAGTAGTGG
1 TATCTCCCTAAGCAATAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGG
*
42662660 AGAAGAT
66 AGCAGAT
42662667 AGAAGGCAGC
Statistics
Matches: 301, Mismatches: 34, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
263 1 0.00
264 300 1.00
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (264 bp):
TATCTCCCTAAGCAATAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGG
AGCAGATCAAAAACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAAT
CCTATCTCCCTAAACAGCAATGGAGTAGGTTGAAGAATGCAGATCCCGTATCCCTAAGCAATAGT
GGAGCAGATCAAAGACGGTGAATCTTATATTCCCAAGGTAGTAGGGAAGCAGATTTAAACCACCA
ATCC
Found at i:42665907 original size:89 final size:89
Alignment explanation
Indices: 42665750--42666041 Score: 354
Period size: 89 Copynumber: 3.3 Consensus size: 89
42665740 ACTATAAGCT
* * * * * * *
42665750 TTGCCTCCCTGAGTTTGCAGTGAAGCAAACTAAAGATAACAGATCATGCCTTCCTATACTGACT-
1 TTGCCTCCCTGAGTTTGTAGTGGAGCAGACTAAAGATAACAGATCTTGTCTTCCTGTACTG-GTA
* *
42665814 GTGAAGCATATCGAAGACACTAGCC
65 GTGAAGCAGATCGAAGACACCAGCC
* * * *
42665839 TTGCCTCTCTGAGTTTGTAGCGGAGCAGACTAAAGATAGCAGATCTTGTCTTCCTGTATTGGTAG
1 TTGCCTCCCTGAGTTTGTAGTGGAGCAGACTAAAGATAACAGATCTTGTCTTCCTGTACTGGTAG
*
42665904 TGAAACAGATCGAAGACACCAGCC
66 TGAAGCAGATCGAAGACACCAGCC
* * * * *
42665928 TTGCCTCCCTGAGTTTGTAGTAGAGCAGACTGAAA-ACAACAAATCTTGTCTTCTTGTACTGGCA
1 TTGCCTCCCTGAGTTTGTAGTGGAGCAGACT-AAAGATAACAGATCTTGTCTTCCTGTACTGGTA
*
42665992 GTGAAGCAGATCGAAAACACCAGCC
65 GTGAAGCAGATCGAAGACACCAGCC
* *
42666017 TTGCCTCTCTGAGTTTGCAGTGGAG
1 TTGCCTCCCTGAGTTTGTAGTGGAG
42666042 TAGGTTGAAG
Statistics
Matches: 173, Mismatches: 28, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
88 1 0.01
89 169 0.98
90 3 0.02
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (89 bp):
TTGCCTCCCTGAGTTTGTAGTGGAGCAGACTAAAGATAACAGATCTTGTCTTCCTGTACTGGTAG
TGAAGCAGATCGAAGACACCAGCC
Found at i:42666338 original size:85 final size:84
Alignment explanation
Indices: 42666233--42666482 Score: 250
Period size: 85 Copynumber: 2.9 Consensus size: 84
42666223 TTAAAACCAC
*
42666233 AGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCCAGTCTTATCTCTCTGAAGTTGTAG
1 AGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGTAG
* *
42666298 TGGGGCAGACTAAAGACGGT
66 TGGAGCAGACTAAAG-CGCT
* * * * * * * * *
42666318 -GAATCTTATCTCCCTAAAGTTGCAACAGAGTAGATTGAAGCCAATAATCCTATCTCCCTGAAGT
1 AG-ATCTTATCTCTCTGAAGTTGC-AGAGAGCAGATCGCATCC---AGTCTTATCTCCCTGAAGT
* *
42666382 TGTAGTGGAGCAGATTAAAGTGCT
61 TGTAGTGGAGCAGACTAAAGCGCT
* * * **
42666406 AGATATTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCTAGTCTTATCTCCCTAAAGTTACA
1 AGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGTA
*
42666471 GTAGAGCAGACT
65 GTGGAGCAGACT
42666483 GAATAAACCA
Statistics
Matches: 128, Mismatches: 30, Indels: 14
0.74 0.17 0.08
Matches are distributed among these distances:
84 1 0.01
85 47 0.37
86 13 0.10
87 1 0.01
88 31 0.24
89 35 0.27
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (84 bp):
AGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGTAG
TGGAGCAGACTAAAGCGCT
Found at i:42666397 original size:44 final size:45
Alignment explanation
Indices: 42666279--42666401 Score: 113
Period size: 44 Copynumber: 2.8 Consensus size: 45
42666269 CATCCAGTCT
* * * ** *
42666279 TATCTCTCTGAAGTTGTAGTGGGGCAGACTAAAGACGGTGAATCT
1 TATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGACAATGAATCC
* * *** * * *
42666324 TATCTCCCTAAAGTTGCAACAGAGTAGATTGAAGCCAAT-AATCC
1 TATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGACAATGAATCC
42666368 TATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAG
1 TATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAG
42666402 TGCTAGATAT
Statistics
Matches: 57, Mismatches: 21, Indels: 1
0.72 0.27 0.01
Matches are distributed among these distances:
44 31 0.54
45 26 0.46
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.28
Consensus pattern (45 bp):
TATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGACAATGAATCC
Found at i:42666498 original size:173 final size:170
Alignment explanation
Indices: 42666190--42666658 Score: 507
Period size: 173 Copynumber: 2.7 Consensus size: 170
42666180 TGAAGAAACC
* ** *
42666190 AATCCTATCTCCCCGAAGTTGCAGTAGAGCGAATTAAAACCACAGATCTTATCTCTCTGAAGTTG
1 AATCCTATCTCCCTGAAGTTGCAGTAGAGCG-ATTAAATGC-TAGATCTTATCTCTCTGAAGTTG
* * * * * *
42666255 CAGAGAGCAGATCGCATCCAGTCTTATCTCTCTGAAGTTGTAGTGGGGCAGACT-AAAGACGGTG
64 CAGAGAGCAGATCGCATCAAGTCTTATCTCCCTGAAGTTGTAGTAGAGCAGACTGAAAAAC-G-C
* * *
42666319 AATCTTATCTCCCTAAAGTTGCAACAGAGTAGATTGAAGCCAAT
127 AATCTTATCTCCCTAAAGTAGCAACAGAGTAGATTAAAACCAAT
* * *
42666363 AATCCTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGTGCTAGATATTATCTCTCTGAAGTTG
1 AATCCTATCTCCCTGAAGTTGCAGTAGAGC-GATTAAA-TGCTAGATCTTATCTCTCTGAAGTTG
* * **
42666428 CAGTAGAGCAGATCGCATCTAGTCTTATCTCCCTAAAGTTACAGTAGAGCAGACTGAATAAAC-C
64 CAG-AGAGCAGATCGCATCAAGTCTTATCTCCCTGAAGTTGTAGTAGAGCAGACTGAA-AAACGC
* * ****
42666492 AATCTTATCTCCTTGAAGTAGTTGTAGAGTAGATTAAAACCAAT
127 AATCTTATCTCCCTAAAGTAGCAACAGAGTAGATTAAAACCAAT
* * *
42666536 AATCCTATCTCTCTGAAGTTGCAGTTA-ATTGC-ATTAAAATGATGGATCTTATCTCTCTGAAGT
1 AATCCTATCTCCCTGAAGTTGCAG-TAGA--GCGATT-AAATGCTAGATCTTATCTCTCTGAAGT
*
42666599 TGCAGCAGAGCAGATCGC-TACAAGTCTTATCTCCCTGAAGTTGTAGTAAAGCAGACTGAA
62 TGCAG-AGAGCAGATCGCAT-CAAGTCTTATCTCCCTGAAGTTGTAGTAGAGCAGACTGAA
42666659 GATAGCAAAT
Statistics
Matches: 249, Mismatches: 37, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
172 1 0.00
173 191 0.77
174 50 0.20
175 4 0.02
176 3 0.01
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (170 bp):
AATCCTATCTCCCTGAAGTTGCAGTAGAGCGATTAAATGCTAGATCTTATCTCTCTGAAGTTGCA
GAGAGCAGATCGCATCAAGTCTTATCTCCCTGAAGTTGTAGTAGAGCAGACTGAAAAACGCAATC
TTATCTCCCTAAAGTAGCAACAGAGTAGATTAAAACCAAT
Found at i:42668112 original size:23 final size:22
Alignment explanation
Indices: 42668048--42668194 Score: 79
Period size: 23 Copynumber: 6.5 Consensus size: 22
42668038 AGTGTATTGT
* *
42668048 ATATTATTATTTTAGATTTATC
1 ATATTACTATTTTAAATTTATC
* *
42668070 ATGTTGTATTATTTGT-AATTTATC
1 AT-AT-TACTATTT-TAAATTTATC
*
42668094 AATATTACTATTTTAAATTCATC
1 -ATATTACTATTTTAAATTTATC
* *
42668117 GT-TAACATTATTTTAAATTTATC
1 ATATTAC--TATTTTAAATTTATC
* *
42668140 ATGTATATCTATTTCAAATTTAT-
1 ATAT-TA-CTATTTTAAATTTATC
* *
42668163 -TATTAATATTTTCAAATTTATT
1 ATATTACTATTTT-AAATTTATC
42668185 ATA-TACTATT
1 ATATTACTATT
42668195 ATTTTTGGAT
Statistics
Matches: 97, Mismatches: 15, Indels: 26
0.70 0.11 0.19
Matches are distributed among these distances:
20 5 0.05
21 13 0.13
22 12 0.12
23 32 0.33
24 30 0.31
25 4 0.04
26 1 0.01
ACGTcount: A:0.34, C:0.07, G:0.04, T:0.54
Consensus pattern (22 bp):
ATATTACTATTTTAAATTTATC
Found at i:42668177 original size:21 final size:23
Alignment explanation
Indices: 42668125--42668186 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 23
42668115 TCGTTAACAT
*
42668125 TATTTT-AAATTTATCATGTATA
1 TATTTTCAAATTTATTATGTATA
*
42668147 TCTATTTCAAATTTATTAT-TA-A
1 TAT-TTTCAAATTTATTATGTATA
42668169 TATTTTCAAATTTATTAT
1 TATTTTCAAATTTATTAT
42668187 ATACTATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 15 0.43
22 5 0.14
23 5 0.14
24 10 0.29
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.56
Consensus pattern (23 bp):
TATTTTCAAATTTATTATGTATA
Found at i:42668196 original size:115 final size:116
Alignment explanation
Indices: 42668076--42668289 Score: 251
Period size: 115 Copynumber: 1.9 Consensus size: 116
42668066 TATCATGTTG
* * * * *
42668076 TATTATTTGT-AATTTATCA-ATATTACTATTTTA-AATTCATCGTTAACATTATTTTAAA-TTT
1 TATTATTTGTGAATTTATCACATATGACTATTCTAGAATT-ATCATCAA-AAT-TTTTAAATTTT
42668137 ATCATGTA-TATCTATTTCAAATTTATTAT-TAATATTTTCAAATTTATTATATAC
63 AT-ATGTATTAT-TATTTCAAATTTATTATATAATATTTTCAAATTTATTATATAC
* * * *
42668191 TATTATTTTTGGATTTATCACGTATGATTATTCTAGAATTATCATCAAAATTTTTAAATTTTATA
1 TATTATTTGTGAATTTATCACATATGACTATTCTAGAATTATCATCAAAATTTTTAAATTTTATA
*
42668256 TGTATTATTATTTCAAATTTATTATATATTATTT
66 TGTATTATTATTTCAAATTTATTATATAATATTT
42668290 ATTGTAAATT
Statistics
Matches: 83, Mismatches: 10, Indels: 11
0.80 0.10 0.11
Matches are distributed among these distances:
115 38 0.46
116 25 0.30
117 16 0.19
118 4 0.05
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (116 bp):
TATTATTTGTGAATTTATCACATATGACTATTCTAGAATTATCATCAAAATTTTTAAATTTTATA
TGTATTATTATTTCAAATTTATTATATAATATTTTCAAATTTATTATATAC
Found at i:42668301 original size:24 final size:23
Alignment explanation
Indices: 42668243--42668301 Score: 59
Period size: 24 Copynumber: 2.4 Consensus size: 23
42668233 CATCAAAATT
42668243 TTTAAATT-TTATATGTATTATTA
1 TTTAAATTATTATA-GTATTATTA
42668266 TTTCAAATTTATTATA-TATTATTTA
1 TTT-AAA-TTATTATAGTATTA-TTA
42668291 TTGTAAATTAT
1 TT-TAAATTAT
42668302 CCAATTCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
23 3 0.10
24 12 0.39
25 10 0.32
26 6 0.19
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (23 bp):
TTTAAATTATTATAGTATTATTA
Found at i:42668440 original size:3 final size:3
Alignment explanation
Indices: 42668432--42668458 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
42668422 TACATATTAC
42668432 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
42668459 CTATATAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:42668915 original size:20 final size:20
Alignment explanation
Indices: 42668890--42668927 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
42668880 TTTATATCAT
42668890 TGTTAATATTGCATTAAACC
1 TGTTAATATTGCATTAAACC
42668910 TGTTAATATTGCATTAAA
1 TGTTAATATTGCATTAAA
42668928 ACTTCGCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.42
Consensus pattern (20 bp):
TGTTAATATTGCATTAAACC
Found at i:42673653 original size:14 final size:14
Alignment explanation
Indices: 42673634--42673661 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
42673624 CGTCTTAGTA
42673634 AATCTATTACATTC
1 AATCTATTACATTC
42673648 AATCTATTACATTC
1 AATCTATTACATTC
42673662 CCCGAAGTGA
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:0.36, C:0.21, G:0.00, T:0.43
Consensus pattern (14 bp):
AATCTATTACATTC
Found at i:42680341 original size:18 final size:18
Alignment explanation
Indices: 42680311--42680362 Score: 77
Period size: 18 Copynumber: 2.8 Consensus size: 18
42680301 TAAATGATTT
42680311 TTTTAATTAAGTAATAATA
1 TTTTAA-TAAGTAATAATA
42680330 TTTTAATAAGTAATAATA
1 TTTTAATAAGTAATAATA
* *
42680348 TTTTATTAATTAATA
1 TTTTAATAAGTAATA
42680363 TTATAATACA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 25 0.81
19 6 0.19
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (18 bp):
TTTTAATAAGTAATAATA
Found at i:42681365 original size:16 final size:17
Alignment explanation
Indices: 42681348--42681380 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
42681338 AACAGAATTG
42681348 AAATGAGAATT-AAATGA
1 AAAT-AGAATTGAAATGA
42681365 AAATAGAATTGAAATG
1 AAATAGAATTGAAATG
42681381 GATCATGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.58, C:0.00, G:0.18, T:0.24
Consensus pattern (17 bp):
AAATAGAATTGAAATGA
Found at i:42686049 original size:33 final size:33
Alignment explanation
Indices: 42685998--42686062 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
42685988 ATCATTCTCA
42685998 TAAATAATTCTTAACTCAACCTATTTTTGTAAG
1 TAAATAATTCTTAACTCAACCTATTTTTGTAAG
* *
42686031 TAAATAATTGTTATCTCAACCTATTTTTGTAA
1 TAAATAATTCTTAACTCAACCTATTTTTGTAA
42686063 ATAATTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.35, C:0.14, G:0.06, T:0.45
Consensus pattern (33 bp):
TAAATAATTCTTAACTCAACCTATTTTTGTAAG
Found at i:42686272 original size:16 final size:16
Alignment explanation
Indices: 42686251--42686286 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
42686241 CTATTAAAAT
* *
42686251 AAAAATTACAAACACA
1 AAAAATAACAAAAACA
42686267 AAAAATAACAAAAACA
1 AAAAATAACAAAAACA
42686283 AAAA
1 AAAA
42686287 CTTCAATCAC
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:0.78, C:0.14, G:0.00, T:0.08
Consensus pattern (16 bp):
AAAAATAACAAAAACA
Found at i:42701562 original size:32 final size:32
Alignment explanation
Indices: 42701526--42701586 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
42701516 AAATAAACAC
42701526 ATAATTATTCATTT-AATA-TTATAACTATTCAA
1 ATAA-TATT-ATTTAAATAGTTATAACTATTCAA
*
42701558 ATAATATTATTTAAATAGTTATAATTATT
1 ATAATATTATTTAAATAGTTATAACTATT
42701587 TTTCAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 4 0.15
31 8 0.31
32 14 0.54
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (32 bp):
ATAATATTATTTAAATAGTTATAACTATTCAA
Found at i:42701748 original size:32 final size:32
Alignment explanation
Indices: 42701706--42701766 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
42701696 TTTTTTGAAA
42701706 AATAATTATAACTATTTAAAT-AAT-ATTATTTG
1 AATAATTATAA-TA-TTAAATGAATAATTATTTG
*
42701738 AATAGTTATAATATTAAATGAATAATTAT
1 AATAATTATAATATTAAATGAATAATTAT
42701767 GTGTTTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 6 0.23
31 5 0.19
32 15 0.58
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (32 bp):
AATAATTATAATATTAAATGAATAATTATTTG
Found at i:42701759 original size:20 final size:20
Alignment explanation
Indices: 42701725--42701766 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
42701715 AACTATTTAA
** *
42701725 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
42701745 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
42701765 AT
1 AT
42701767 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:42701896 original size:25 final size:25
Alignment explanation
Indices: 42701864--42701916 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
42701854 GGAATGGAAT
42701864 TTCATCTAGAAAACACACCAACAAA
1 TTCATCTAGAAAACACACCAACAAA
42701889 TTCATCTAGAAAACACACCAACAAA
1 TTCATCTAGAAAACACACCAACAAA
42701914 TTC
1 TTC
42701917 TAATATTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.49, C:0.28, G:0.04, T:0.19
Consensus pattern (25 bp):
TTCATCTAGAAAACACACCAACAAA
Found at i:42705987 original size:27 final size:27
Alignment explanation
Indices: 42705957--42706326 Score: 185
Period size: 27 Copynumber: 13.7 Consensus size: 27
42705947 ATCTCCTAGA
42705957 GGTATAAT-AATCATTTTACCCTATGAG
1 GGTAT-ATCAATCATTTTACCCTATGAG
* * *
42705984 GGTAT-TTAGGTCATTTTACCCTATGGG
1 GGTATATCA-ATCATTTTACCCTATGAG
* * * *
42706011 GGTATTTCGATCATTCTACCCTATGGG
1 GGTATATCAATCATTTTACCCTATGAG
** * *
42706038 GGTATATCGGTTACTTTACCCTATGAG
1 GGTATATCAATCATTTTACCCTATGAG
* * * *
42706065 GGTATTTCAGTCATTTTATCCTAT-AA
1 GGTATATCAATCATTTTACCCTATGAG
* * ** * *
42706091 GATATTTCGGTCATTTTATCCTATGGG
1 GGTATATCAATCATTTTACCCTATGAG
* ** * * *
42706118 GGTATTTCGGTTATTCTACCCTATGGG
1 GGTATATCAATCATTTTACCCTATGAG
* *
42706145 GGTATTTCGATCATTTTACCCTAT-AGG
1 GGTATATCAATCATTTTACCCTATGA-G
* * * * *
42706172 GGTATTTCAGTCATTATATCCTATGGG
1 GGTATATCAATCATTTTACCCTATGAG
* ** * * * *
42706199 GGTATTTCGGTCATTCTATCGTATGGG
1 GGTATATCAATCATTTTACCCTATGAG
* *
42706226 GGTATTTCAATCATTCTACCCTAT-AGG
1 GGTATATCAATCATTTTACCCTATGA-G
* * *
42706253 GGTATTTCGATCATTTTACCCTATGGG
1 GGTATATCAATCATTTTACCCTATGAG
* * *
42706280 GGTATTTCGATCATTCTACCCTATG-G
1 GGTATATCAATCATTTTACCCTATGAG
* * *
42706306 GGATATTTCGATTATTTTACC
1 GG-TATATCAATCATTTTACC
42706327 TATTTTAGGG
Statistics
Matches: 285, Mismatches: 49, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
25 1 0.00
26 27 0.09
27 256 0.90
28 1 0.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.41
Consensus pattern (27 bp):
GGTATATCAATCATTTTACCCTATGAG
Found at i:42706015 original size:54 final size:54
Alignment explanation
Indices: 42705965--42706326 Score: 406
Period size: 54 Copynumber: 6.7 Consensus size: 54
42705955 GAGGTATAAT
* *
42705965 AATCATTTTACCCTATGAGGGTATTTAGGTCATTTTACCCTATGGGGGTATTTC
1 AATCATTCTACCCTATGAGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTC
* * * * * *
42706019 GATCATTCTACCCTATGGGGGTATATCGGTTACTTTACCCTATGAGGGTATTTC
1 AATCATTCTACCCTATGAGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTC
* * * * * *
42706073 AGTCATTTTATCCTAT-AAGATATTTCGGTCATTTTATCCTATGGGGGTATTTC
1 AATCATTCTACCCTATGAGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTC
** * * * *
42706126 GGTTATTCTACCCTATGGGGGTATTTCGATCATTTTACCCTATAGGGGTATTTC
1 AATCATTCTACCCTATGAGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTC
* * * * * * *
42706180 AGTCATTATATCCTATGGGGGTATTTCGGTCATTCTATCGTATGGGGGTATTTC
1 AATCATTCTACCCTATGAGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTC
*
42706234 AATCATTCTACCCTAT-AGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTC
1 AATCATTCTACCCTATGA-GGGTATTTCGGTCATTTTACCCTATGGGGGTATTTC
* * *
42706288 GATCATTCTACCCTATG-GGGATATTTCGATTATTTTACC
1 AATCATTCTACCCTATGAGGG-TATTTCGGTCATTTTACC
42706327 TATTTTAGGG
Statistics
Matches: 255, Mismatches: 49, Indels: 8
0.82 0.16 0.03
Matches are distributed among these distances:
53 44 0.17
54 211 0.83
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41
Consensus pattern (54 bp):
AATCATTCTACCCTATGAGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTC
Found at i:42706078 original size:81 final size:81
Alignment explanation
Indices: 42705967--42706314 Score: 429
Period size: 81 Copynumber: 4.3 Consensus size: 81
42705957 GGTATAATAA
* * *
42705967 TCATTTTACCCTATGAGGGTATTT-AGGTCATTTTACCCTATGGGGGTATTTCGATCATTCTACC
1 TCATTCTACCCTATGAGGGTATTTCA-GTCATTTTACCCTATAGGGGTATTTCGATCATTTTACC
*
42706031 CTATGGGGGTATATCGG
65 CTATGGGGGTATTTCGG
* * * * * *
42706048 TTACTT-TACCCTATGAGGGTATTTCAGTCATTTTATCCTATA-AGATATTTCGGTCATTTTATC
1 TCA-TTCTACCCTATGAGGGTATTTCAGTCATTTTACCCTATAGGGGTATTTCGATCATTTTACC
42706111 CTATGGGGGTATTTCGG
65 CTATGGGGGTATTTCGG
* * * *
42706128 TTATTCTACCCTATGGGGGTATTTC-GATCATTTTACCCTATAGGGGTATTTC-AGTCATTATAT
1 TCATTCTACCCTATGAGGGTATTTCAG-TCATTTTACCCTATAGGGGTATTTCGA-TCATTTTAC
42706191 CCTATGGGGGTATTTCGG
64 CCTATGGGGGTATTTCGG
* * * * *
42706209 TCATTCTATCGTATGGGGGTATTTCAATCATTCTACCCTATAGGGGTATTTCGATCATTTTACCC
1 TCATTCTACCCTATGAGGGTATTTCAGTCATTTTACCCTATAGGGGTATTTCGATCATTTTACCC
*
42706274 TATGGGGGTATTTCGA
66 TATGGGGGTATTTCGG
42706290 TCATTCTACCCTATG-GGGATATTTC
1 TCATTCTACCCTATGAGGG-TATTTC
42706315 GATTATTTTA
Statistics
Matches: 233, Mismatches: 25, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
79 3 0.01
80 70 0.30
81 156 0.67
82 4 0.02
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.41
Consensus pattern (81 bp):
TCATTCTACCCTATGAGGGTATTTCAGTCATTTTACCCTATAGGGGTATTTCGATCATTTTACCC
TATGGGGGTATTTCGG
Found at i:42710456 original size:23 final size:22
Alignment explanation
Indices: 42710413--42710456 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
42710403 TTCTAAGTCG
42710413 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
42710436 ATATTCACTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
42710457 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.27, G:0.00, T:0.36
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:42710658 original size:51 final size:50
Alignment explanation
Indices: 42710600--42710786 Score: 196
Period size: 51 Copynumber: 3.7 Consensus size: 50
42710590 TCGGTTCACA
* * *
42710600 TAGTAGCCTACACATAGTACTATACATGTGACCATTACCATCTGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCA-TACCATCTGGTACACG
* * * * ** *
42710651 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATCTGGTATGCA
1 TAGTAGCCTGCACATAGTACTACACATGTGA-CCATACCATCTGGTACACG
* * * * *
42710702 TAGTAGCCTGTACATGGTACTACACATGCGACC-TATCATTCCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATACCA-TCTGGTACACG
*
42710752 TAGTAGCCCGCACATAGTACTACACATGTGACCAT
1 TAGTAGCCTGCACATAGTACTACACATGTGACCAT
42710787 CACTTTCACT
Statistics
Matches: 107, Mismatches: 26, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
49 2 0.02
50 37 0.35
51 66 0.62
52 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCATACCATCTGGTACACG
Found at i:42713413 original size:20 final size:20
Alignment explanation
Indices: 42713379--42713420 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
42713369 AACTATTTAA
** *
42713379 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
42713399 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
42713419 AT
1 AT
42713421 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:42714983 original size:32 final size:32
Alignment explanation
Indices: 42714922--42715156 Score: 269
Period size: 32 Copynumber: 7.4 Consensus size: 32
42714912 GAATGTCTAC
** *
42714922 AAGCCATAAGT-ACAATAATATGATTGGCACA
1 AAGCCATAAGTAACGGTAATATGATCGGCACA
* * *
42714953 AAGCCATAAGTAGCAGTGATATGATCGGCACA
1 AAGCCATAAGTAACGGTAATATGATCGGCACA
* *
42714985 CAGCCATCAGTAACGGTAATATGATCGGCACA
1 AAGCCATAAGTAACGGTAATATGATCGGCACA
42715017 AAGCCATCAA-TAACGGTAATATGATCGGCACA
1 AAGCCAT-AAGTAACGGTAATATGATCGGCACA
* * *
42715049 AAGCCATCAA-TAATGGTAATATGACCGGTACA
1 AAGCCAT-AAGTAACGGTAATATGATCGGCACA
* **
42715081 AAGCCATTAGTAACGGTAATATGATCGATACA
1 AAGCCATAAGTAACGGTAATATGATCGGCACA
* * *
42715113 AAGCCATCAGTAACGGTAATATGATCGGTATA
1 AAGCCATAAGTAACGGTAATATGATCGGCACA
*
42715145 AAGCCATCAGTA
1 AAGCCATAAGTA
42715157 GCATCGCAGC
Statistics
Matches: 180, Mismatches: 21, Indels: 5
0.87 0.10 0.02
Matches are distributed among these distances:
31 12 0.07
32 167 0.93
33 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.21
Consensus pattern (32 bp):
AAGCCATAAGTAACGGTAATATGATCGGCACA
Found at i:42715176 original size:26 final size:26
Alignment explanation
Indices: 42715147--42715203 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
42715137 TCGGTATAAA
* *
42715147 GCCATCAGTAGCATCGCAGCAAAACT
1 GCCAGCAGAAGCATCGCAGCAAAACT
* * *
42715173 GCCAGCAGAAGTATTGCAGCAAAGCT
1 GCCAGCAGAAGCATCGCAGCAAAACT
42715199 GCCAG
1 GCCAG
42715204 TAATAGTATA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.33, C:0.28, G:0.25, T:0.14
Consensus pattern (26 bp):
GCCAGCAGAAGCATCGCAGCAAAACT
Found at i:42715355 original size:24 final size:24
Alignment explanation
Indices: 42715328--42715385 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
42715318 CCATGCTCAG
*
42715328 AATCAGTCA-ATCAAATCACAGACA
1 AATCAGTCATACCAAA-CACAGACA
*
42715352 AATCAGTCATACCAAACACAGATA
1 AATCAGTCATACCAAACACAGACA
42715376 AATCAGTCAT
1 AATCAGTCAT
42715386 TTAACCACAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 26 0.84
25 5 0.16
ACGTcount: A:0.48, C:0.24, G:0.09, T:0.19
Consensus pattern (24 bp):
AATCAGTCATACCAAACACAGACA
Found at i:42715480 original size:27 final size:27
Alignment explanation
Indices: 42715445--42715583 Score: 181
Period size: 27 Copynumber: 5.1 Consensus size: 27
42715435 TTCACCCACT
42715445 AGGGCATTACGATCATTTTACCCTACA
1 AGGGCATTACGATCATTTTACCCTACA
* * *
42715472 AGGGTATTACGGTTATTTTACCCTACA
1 AGGGCATTACGATCATTTTACCCTACA
*
42715499 GGGGCATTACGATCATTTTACCCTACA
1 AGGGCATTACGATCATTTTACCCTACA
* * *
42715526 TGGGTATTACGTTCATTTTA-CCTCACA
1 AGGGCATTACGATCATTTTACCCT-ACA
* *
42715553 AGGGCATTACGGTCATTTTACCCTATA
1 AGGGCATTACGATCATTTTACCCTACA
42715580 AGGG
1 AGGG
42715584 TATTTTAGTC
Statistics
Matches: 96, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
26 3 0.03
27 90 0.94
28 3 0.03
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (27 bp):
AGGGCATTACGATCATTTTACCCTACA
Found at i:42715511 original size:54 final size:54
Alignment explanation
Indices: 42715445--42715587 Score: 218
Period size: 54 Copynumber: 2.6 Consensus size: 54
42715435 TTCACCCACT
42715445 AGGGCATTACGATCATTTTACCCTACAAGGGTATTACGGTT-ATTTTACC-CTACA
1 AGGGCATTACGATCATTTTACCCTACAAGGGTATTAC-GTTCATTTTACCTC-ACA
* *
42715499 GGGGCATTACGATCATTTTACCCTACATGGGTATTACGTTCATTTTACCTCACA
1 AGGGCATTACGATCATTTTACCCTACAAGGGTATTACGTTCATTTTACCTCACA
* *
42715553 AGGGCATTACGGTCATTTTACCCTATAAGGGTATT
1 AGGGCATTACGATCATTTTACCCTACAAGGGTATT
42715588 TTAGTCATTT
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
53 3 0.04
54 77 0.95
55 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (54 bp):
AGGGCATTACGATCATTTTACCCTACAAGGGTATTACGTTCATTTTACCTCACA
Found at i:42715643 original size:27 final size:27
Alignment explanation
Indices: 42715527--42715647 Score: 93
Period size: 27 Copynumber: 4.5 Consensus size: 27
42715517 TACCCTACAT
* * * *
42715527 GGGTATTACGTTCATTTTACCTCA-CAA
1 GGGTATTTCGGTCATTCTACC-CATCGA
* * * *
42715554 GGGCATTACGGTCATTTTACCCTAT-AA
1 GGGTATTTCGGTCATTCTACCC-ATCGA
** *
42715581 GGGTATTTTAGTCATTTTACCCATCGA
1 GGGTATTTCGGTCATTCTACCCATCGA
* *
42715608 GGGTATTTCGGTTATTCTACCCTTCGA
1 GGGTATTTCGGTCATTCTACCCATCGA
42715635 GGGTATTTCGGTC
1 GGGTATTTCGGTC
42715648 TAGATATCGA
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
26 3 0.04
27 75 0.96
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (27 bp):
GGGTATTTCGGTCATTCTACCCATCGA
Found at i:42723305 original size:16 final size:16
Alignment explanation
Indices: 42723274--42723310 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
42723264 AAGTGAAGAA
42723274 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
42723290 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
42723306 TATTA
1 TATTA
42723311 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:42723394 original size:26 final size:25
Alignment explanation
Indices: 42723322--42723396 Score: 64
Period size: 26 Copynumber: 2.9 Consensus size: 25
42723312 AATAAAATTG
*
42723322 AAATATTAAAT-ATTAAAT-TATATT
1 AAATA-TAAATAATTAAATATATACT
* * *
42723346 AATTATACTAATAATTTATTATATGACT
1 AAATATA--AATAATTAAATATAT-ACT
42723374 AAATATAAATAATTAAATATATA
1 AAATATAAATAATTAAATATATA
42723397 TGTTTAATAA
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
23 2 0.05
24 4 0.10
25 4 0.10
26 18 0.46
27 3 0.08
28 8 0.21
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (25 bp):
AAATATAAATAATTAAATATATACT
Found at i:42723465 original size:5 final size:6
Alignment explanation
Indices: 42723449--42723473 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
42723439 TTAATATTTT
42723449 TAAAAA TAAAAA TAAAAA TAAAAA T
1 TAAAAA TAAAAA TAAAAA TAAAAA T
42723474 TATTATCAAT
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
TAAAAA
Found at i:42732277 original size:20 final size:21
Alignment explanation
Indices: 42732241--42732283 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
42732231 GTTATTAAAT
42732241 ATTATGTTATTATAAAA-TAA
1 ATTATGTTATTATAAAACTAA
*
42732261 ATTATGTT-TTGTCAAAACTAA
1 ATTATGTTATTAT-AAAACTAA
42732282 AT
1 AT
42732284 GCTACTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 3 0.15
20 12 0.60
21 5 0.25
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (21 bp):
ATTATGTTATTATAAAACTAA
Found at i:42736064 original size:16 final size:19
Alignment explanation
Indices: 42736043--42736082 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 19
42736033 TTTATGAACA
42736043 AATTTTTA-CTT-AGTT-T
1 AATTTTTACCTTCAGTTGT
42736059 AA-TTTTACCTTCAGTTGT
1 AATTTTTACCTTCAGTTGT
42736077 AATTTT
1 AATTTT
42736083 GATTTCCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
15 5 0.25
16 5 0.25
17 4 0.20
18 3 0.15
19 3 0.15
ACGTcount: A:0.25, C:0.10, G:0.07, T:0.57
Consensus pattern (19 bp):
AATTTTTACCTTCAGTTGT
Found at i:42736097 original size:23 final size:23
Alignment explanation
Indices: 42736071--42736116 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
42736061 TTTTACCTTC
*
42736071 AGTTGTAATTTTGATTTCCTTTT
1 AGTTATAATTTTGATTTCCTTTT
* * *
42736094 AGTTATAGTTTTTATTTCGTTTT
1 AGTTATAATTTTGATTTCCTTTT
42736117 TTCTATTTTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.17, C:0.07, G:0.13, T:0.63
Consensus pattern (23 bp):
AGTTATAATTTTGATTTCCTTTT
Found at i:42740171 original size:15 final size:14
Alignment explanation
Indices: 42740128--42740172 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
42740118 TAATTCTATT
42740128 TTTATTTTTATTTA
1 TTTATTTTTATTTA
*
42740142 TTATATATTTATTTA
1 TT-TATTTTTATTTA
*
42740157 CTTTATTTTTCTTTA
1 -TTTATTTTTATTTA
42740172 T
1 T
42740173 CAACTAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 3 0.12
15 21 0.81
16 2 0.08
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTATTTTTATTTA
Found at i:42749307 original size:23 final size:23
Alignment explanation
Indices: 42749281--42749388 Score: 65
Period size: 23 Copynumber: 4.4 Consensus size: 23
42749271 CAACAATTTG
42749281 GACAGCATTTATATACCAAACTA
1 GACAGCATTTATATACCAAACTA
* * * *
42749304 GACATCATTT-TCACACCAAAATTTG
1 GACAGCATTTAT-ATACC-AAA-CTA
** *
42749329 GACAGCATATATATATACAACAATTTG
1 GACAGCAT-T-TATATAC--CAAACTA
* *
42749356 GGCAGCATTTATATACCTAACTA
1 GACAGCATTTATATACCAAACTA
42749379 GACAGCATTT
1 GACAGCATTT
42749389 TCACACCAAA
Statistics
Matches: 64, Mismatches: 13, Indels: 16
0.69 0.14 0.17
Matches are distributed among these distances:
22 1 0.02
23 25 0.39
24 3 0.05
25 15 0.23
26 2 0.03
27 14 0.22
28 3 0.05
29 1 0.02
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (23 bp):
GACAGCATTTATATACCAAACTA
Found at i:42749433 original size:23 final size:23
Alignment explanation
Indices: 42749401--42749902 Score: 360
Period size: 23 Copynumber: 21.5 Consensus size: 23
42749391 ACACCAAAAT
* *
42749401 TTGGACAGCATATATACAACAAT
1 TTGGGCAGCATATATACAACAAA
* * * *
42749424 TTGGGTAGCATTTATATACCAAA
1 TTGGGCAGCATATATACAACAAA
* * *
42749447 CTAGGCAGCATATATACAAAAAA
1 TTGGGCAGCATATATACAACAAA
* * * *
42749470 TTGAGCAGCATTTTTACACAAAAAA
1 TTGGGCAGCA--TATATACAACAAA
*
42749495 TTGGACAGCATATATACAACAAA
1 TTGGGCAGCATATATACAACAAA
* * *
42749518 TTGGGCAGAATATATATACCAAA
1 TTGGGCAGCATATATACAACAAA
* * * * *
42749541 TTGAGCCGCATTTTTACATCAAAA
1 TTGGGCAGCATATATACAAC-AAA
* * *
42749565 TTGGACAGCATATATACAACCAT
1 TTGGGCAGCATATATACAACAAA
*
42749588 TTGGGCAGCATAAATACAACAAA
1 TTGGGCAGCATATATACAACAAA
* * * * *
42749611 TTGAGTAGCATTTTTACACCAAAAA
1 TTGGGCAGCATATATACA--ACAAA
*
42749636 TTGGACAGCATATATACAACAAA
1 TTGGGCAGCATATATACAACAAA
* *
42749659 TTGGGCAGCATATATATACCAAA
1 TTGGGCAGCATATATACAACAAA
* * * * *
42749682 TTGAGCCGCATTTTTACATCAAAA
1 TTGGGCAGCATATATACAAC-AAA
* *
42749706 TTGGACAGCATATATACTACAAA
1 TTGGGCAGCATATATACAACAAA
* * *
42749729 TTGGGCAGGATATATATACCAAA
1 TTGGGCAGCATATATACAACAAA
* * * * *
42749752 TTGAGCCGCATTTTTACATCAAAA
1 TTGGGCAGCATATATACAAC-AAA
* *
42749776 TTGGACAGCATATATACAACAAT
1 TTGGGCAGCATATATACAACAAA
*
42749799 TTGGGCAGCATAAATACAACAAA
1 TTGGGCAGCATATATACAACAAA
* * *
42749822 TTGAGCAGCACT-TTTACACCAAAAA
1 TTGGGCAGCA-TATATACA--ACAAA
* * *
42749847 TTGGACAGCCTATATGCAACAAA
1 TTGGGCAGCATATATACAACAAA
* *
42749870 TTGAGCAGTATATATACAACAAA
1 TTGGGCAGCATATATACAACAAA
42749893 TT-GGCAGCAT
1 TTGGGCAGCAT
42749903 TTAAGCATCA
Statistics
Matches: 355, Mismatches: 113, Indels: 23
0.72 0.23 0.05
Matches are distributed among these distances:
22 6 0.02
23 246 0.69
24 52 0.15
25 51 0.14
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (23 bp):
TTGGGCAGCATATATACAACAAA
Found at i:42749456 original size:71 final size:71
Alignment explanation
Indices: 42749264--42749457 Score: 300
Period size: 75 Copynumber: 2.7 Consensus size: 71
42749254 AACTATACTA
* *
42749264 CATAT-TACAACAATTTGGACAGCATTTATATACCAAACTAGACATCATTTTCACACCAAAATTT
1 CATATATACAACAATTTGGGCAGCATTTATATACCAAACTAGACAGCATTTTCACACCAAAATTT
42749328 GGACAG
66 GGACAG
*
42749334 CATATATATATACAACAATTTGGGCAGCATTTATATACCTAACTAGACAGCATTTTCACACCAAA
1 C----ATATATACAACAATTTGGGCAGCATTTATATACCAAACTAGACAGCATTTTCACACCAAA
42749399 ATTTGGACAG
62 ATTTGGACAG
* *
42749409 CATATATACAACAATTTGGGTAGCATTTATATACCAAACTAGGCAGCAT
1 CATATATACAACAATTTGGGCAGCATTTATATACCAAACTAGACAGCAT
42749458 ATATACAAAA
Statistics
Matches: 113, Mismatches: 6, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
70 1 0.01
71 45 0.40
74 4 0.04
75 63 0.56
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (71 bp):
CATATATACAACAATTTGGGCAGCATTTATATACCAAACTAGACAGCATTTTCACACCAAAATTT
GGACAG
Found at i:42749595 original size:70 final size:71
Alignment explanation
Indices: 42749450--42749904 Score: 632
Period size: 70 Copynumber: 6.5 Consensus size: 71
42749440 TACCAAACTA
*
42749450 GGCAGCATATATACAAAAAATTGAGCAGCATTTTTACA-CAAAAAATTGGACAGCATATATACAA
1 GGCAGCATATATACAACAAATTGAGCAGCATTTTTACATC-AAAAATTGGACAGCATATATACAA
42749514 CAAATTG
65 CAAATTG
* * * *
42749521 GGCAGAATATATATACCAAATTGAGCCGCATTTTTACATC-AAAATTGGACAGCATATATACAAC
1 GGCAGCATATATACAACAAATTGAGCAGCATTTTTACATCAAAAATTGGACAGCATATATACAAC
* *
42749585 CATTTG
66 AAATTG
* * *
42749591 GGCAGCATAAATACAACAAATTGAGTAGCATTTTTACACCAAAAATTGGACAGCATATATACAAC
1 GGCAGCATATATACAACAAATTGAGCAGCATTTTTACATCAAAAATTGGACAGCATATATACAAC
42749656 AAATTG
66 AAATTG
* * * *
42749662 GGCAGCATATATATACCAAATTGAGCCGCATTTTTACATC-AAAATTGGACAGCATATATACTAC
1 GGCAGCATATATACAACAAATTGAGCAGCATTTTTACATCAAAAATTGGACAGCATATATACAAC
42749726 AAATTG
66 AAATTG
* * * *
42749732 GGCAGGATATATATACCAAATTGAGCCGCATTTTTACATC-AAAATTGGACAGCATATATACAAC
1 GGCAGCATATATACAACAAATTGAGCAGCATTTTTACATCAAAAATTGGACAGCATATATACAAC
*
42749796 AATTTG
66 AAATTG
* * * * *
42749802 GGCAGCATAAATACAACAAATTGAGCAGCACTTTTACACCAAAAATTGGACAGCCTATATGCAAC
1 GGCAGCATATATACAACAAATTGAGCAGCATTTTTACATCAAAAATTGGACAGCATATATACAAC
42749867 AAATTG
66 AAATTG
* *
42749873 AGCAGTATATATACAACAAATTG-GCAGCATTT
1 GGCAGCATATATACAACAAATTGAGCAGCATTT
42749905 AAGCATCAAA
Statistics
Matches: 341, Mismatches: 40, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
70 198 0.58
71 142 0.42
72 1 0.00
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.26
Consensus pattern (71 bp):
GGCAGCATATATACAACAAATTGAGCAGCATTTTTACATCAAAAATTGGACAGCATATATACAAC
AAATTG
Found at i:42749596 original size:141 final size:140
Alignment explanation
Indices: 42749450--42749904 Score: 662
Period size: 141 Copynumber: 3.2 Consensus size: 140
42749440 TACCAAACTA
*
42749450 GGCAGCATATATACAAAAAATTGAGCAGCATTTTTACACAAAAAATTGGACAGCATATATACAAC
1 GGCAGCATATATACAACAAATTGAGCAGCATTTTTACAC-AAAAATTGGACAGCATATATACAAC
*
42749515 AAATTGGGCAGAATATATATACCAAATTGAGCCGCATTTTTACATCAAAATTGGACAGCATATAT
65 AAATTGGGCAGCATATATATACCAAATTGAGCCGCATTTTTACATCAAAATTGGACAGCATATAT
* *
42749580 ACAACCATTTG
130 ACAACAAATTG
* *
42749591 GGCAGCATAAATACAACAAATTGAGTAGCATTTTTACACCAAAAATTGGACAGCATATATACAAC
1 GGCAGCATATATACAACAAATTGAGCAGCATTTTTACA-CAAAAATTGGACAGCATATATACAAC
42749656 AAATTGGGCAGCATATATATACCAAATTGAGCCGCATTTTTACATCAAAATTGGACAGCATATAT
65 AAATTGGGCAGCATATATATACCAAATTGAGCCGCATTTTTACATCAAAATTGGACAGCATATAT
*
42749721 ACTACAAATTG
130 ACAACAAATTG
* * * *
42749732 GGCAGGATATATATACCAAATTGAGCCGCATTTTTACATC-AAAATTGGACAGCATATATACAAC
1 GGCAGCATATATACAACAAATTGAGCAGCATTTTTACA-CAAAAATTGGACAGCATATATACAAC
* * * * * * * *
42749796 AATTTGGGCAGCATAAATACAACAAATTGAGCAGCACTTTTACACCAAAAATTGGACAGCCTATA
65 AAATTGGGCAGCATATATATACCAAATTGAGCCGCATTTTTACATC-AAAATTGGACAGCATATA
*
42749861 TGCAACAAATTG
129 TACAACAAATTG
* *
42749873 AGCAGTATATATACAACAAATTG-GCAGCATTT
1 GGCAGCATATATACAACAAATTGAGCAGCATTT
42749905 AAGCATCAAA
Statistics
Matches: 283, Mismatches: 29, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
140 71 0.25
141 211 0.75
142 1 0.00
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.26
Consensus pattern (140 bp):
GGCAGCATATATACAACAAATTGAGCAGCATTTTTACACAAAAATTGGACAGCATATATACAACA
AATTGGGCAGCATATATATACCAAATTGAGCCGCATTTTTACATCAAAATTGGACAGCATATATA
CAACAAATTG
Found at i:42749735 original size:211 final size:211
Alignment explanation
Indices: 42749450--42749904 Score: 761
Period size: 211 Copynumber: 2.2 Consensus size: 211
42749440 TACCAAACTA
*
42749450 GGCAGCATATATACAAAAAATTGAGCAGCATTTTTACACAAAAAATTGGACAGCATATATACAAC
1 GGCAGCATATATACAACAAATTGAGCAGCATTTTTACAC-AAAAATTGGACAGCATATATACAAC
42749515 AAATTGGGCAGAATATATATACCAAATTGAGCCGCATTTTTACATCAAAATTGGACAGCATATAT
65 AAATTGGGCAGAATATATATACCAAATTGAGCCGCATTTTTACATCAAAATTGGACAGCATATAT
* * *
42749580 ACAACCATTTGGGCAGCATAAATACAACAAATTGAGTAGCATTTTTACACCAAAAATTGGACAGC
130 ACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCACTTTTACACCAAAAATTGGACAGC
42749645 ATATATACAACAAATTG
195 ATATATACAACAAATTG
* * * *
42749662 GGCAGCATATATATACCAAATTGAGCCGCATTTTTACATC-AAAATTGGACAGCATATATACTAC
1 GGCAGCATATATACAACAAATTGAGCAGCATTTTTACA-CAAAAATTGGACAGCATATATACAAC
*
42749726 AAATTGGGCAGGATATATATACCAAATTGAGCCGCATTTTTACATCAAAATTGGACAGCATATAT
65 AAATTGGGCAGAATATATATACCAAATTGAGCCGCATTTTTACATCAAAATTGGACAGCATATAT
42749791 ACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCACTTTTACACCAAAAATTGGACAGC
130 ACAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCACTTTTACACCAAAAATTGGACAGC
* *
42749856 CTATATGCAACAAATTG
195 ATATATACAACAAATTG
* *
42749873 AGCAGTATATATACAACAAATTG-GCAGCATTT
1 GGCAGCATATATACAACAAATTGAGCAGCATTT
42749905 AAGCATCAAA
Statistics
Matches: 226, Mismatches: 16, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
210 8 0.04
211 183 0.81
212 34 0.15
213 1 0.00
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.26
Consensus pattern (211 bp):
GGCAGCATATATACAACAAATTGAGCAGCATTTTTACACAAAAATTGGACAGCATATATACAACA
AATTGGGCAGAATATATATACCAAATTGAGCCGCATTTTTACATCAAAATTGGACAGCATATATA
CAACAATTTGGGCAGCATAAATACAACAAATTGAGCAGCACTTTTACACCAAAAATTGGACAGCA
TATATACAACAAATTG
Found at i:42750660 original size:28 final size:28
Alignment explanation
Indices: 42750628--42750725 Score: 160
Period size: 28 Copynumber: 3.5 Consensus size: 28
42750618 TAATAAGTTT
42750628 GCACACTTAGTGCTTAATAATCAATCTC
1 GCACACTTAGTGCTTAATAATCAATCTC
42750656 GCACACTTAGTGCTTAATAATCAATCTC
1 GCACACTTAGTGCTTAATAATCAATCTC
* * * *
42750684 GCACACTTAGTGCTTTACAATTAAACTC
1 GCACACTTAGTGCTTAATAATCAATCTC
42750712 GCACACTTAGTGCT
1 GCACACTTAGTGCT
42750726 AATCTCATTA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 66 1.00
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.32
Consensus pattern (28 bp):
GCACACTTAGTGCTTAATAATCAATCTC
Found at i:42776529 original size:34 final size:31
Alignment explanation
Indices: 42776491--42776613 Score: 95
Period size: 34 Copynumber: 3.7 Consensus size: 31
42776481 GCTACCGAAT
*
42776491 TGATCTGTTATAAGCATGCTTATTGCTATCGTAA
1 TGATCTATTATAAGCATG-TTATTGCTA-C-TAA
* * *
42776525 TGATCTATTATAAGTATGATAATTTCTACTATA
1 TGATCTATTATAAGCATG-TTATTGCTACTA-A
* * *
42776558 TCGA-CTTGTTATAAGTATGTTATTGCTACCTTAT
1 T-GATC-TATTATAAGCATGTTATTGCTA-C-TAA
42776592 TGATCTATTATAAGCATGTTAT
1 TGATCTATTATAAGCATGTTAT
42776614 GTTACATTGC
Statistics
Matches: 72, Mismatches: 11, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
32 2 0.03
33 28 0.39
34 40 0.56
35 2 0.03
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (31 bp):
TGATCTATTATAAGCATGTTATTGCTACTAA
Found at i:42776631 original size:17 final size:17
Alignment explanation
Indices: 42776609--42776641 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
42776599 TTATAAGCAT
42776609 GTTATGTTACATTGCAC
1 GTTATGTTACATTGCAC
42776626 GTTATGTTACATTGCA
1 GTTATGTTACATTGCA
42776642 TGGGGTGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.42
Consensus pattern (17 bp):
GTTATGTTACATTGCAC
Found at i:42778919 original size:14 final size:15
Alignment explanation
Indices: 42778895--42778923 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
42778885 GAAACTAGAG
42778895 AAAGAATAAAAGATA
1 AAAGAATAAAAGATA
42778910 AAAG-ATAAAAGATA
1 AAAGAATAAAAGATA
42778924 GGCTAGGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (15 bp):
AAAGAATAAAAGATA
Found at i:42779688 original size:28 final size:28
Alignment explanation
Indices: 42779656--42779787 Score: 176
Period size: 28 Copynumber: 4.7 Consensus size: 28
42779646 TGACTTTCGA
42779656 CACTAAGTGTGCGAATTTAATTGTAAAG
1 CACTAAGTGTGCGAATTTAATTGTAAAG
*
42779684 CACTAAGTGTGCGAGTTTAATTTGTAAAG
1 CACTAAGTGTGCGAATTTAA-TTGTAAAG
*
42779713 CACTAAGTGTGC-AAGTTTAATGGTAAAG
1 CACTAAGTGTGCGAA-TTTAATTGTAAAG
* * * **
42779741 CACTAAGTGTGCGAGTTTGATTATTGAG
1 CACTAAGTGTGCGAATTTAATTGTAAAG
42779769 CACTAAGTGTGCGAATTTA
1 CACTAAGTGTGCGAATTTA
42779788 TTAAATATTT
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
28 64 0.71
29 26 0.29
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (28 bp):
CACTAAGTGTGCGAATTTAATTGTAAAG
Found at i:42779744 original size:57 final size:56
Alignment explanation
Indices: 42779656--42779787 Score: 196
Period size: 57 Copynumber: 2.3 Consensus size: 56
42779646 TGACTTTCGA
*
42779656 CACTAAGTGTGCGAATTTAATTGTAAAGCACTAAGTGTGCGAGTTTAATT-TGTAAAG
1 CACTAAGTGTGCGAATTTAATGGTAAAGCACTAAGTGTGCGAGTTTAATTAT-T-AAG
* *
42779713 CACTAAGTGTGC-AAGTTTAATGGTAAAGCACTAAGTGTGCGAGTTTGATTATTGAG
1 CACTAAGTGTGCGAA-TTTAATGGTAAAGCACTAAGTGTGCGAGTTTAATTATTAAG
42779769 CACTAAGTGTGCGAATTTA
1 CACTAAGTGTGCGAATTTA
42779788 TTAAATATTT
Statistics
Matches: 69, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
56 20 0.29
57 48 0.70
58 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (56 bp):
CACTAAGTGTGCGAATTTAATGGTAAAGCACTAAGTGTGCGAGTTTAATTATTAAG
Found at i:42780560 original size:23 final size:23
Alignment explanation
Indices: 42780513--42780571 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
42780503 TTATGCTTAA
* *
42780513 ATGCTGCCC-AATTGATGTATTT
1 ATGCTGCCCAAATTGATATATAT
42780535 ATGCTGCCCAAATTG-TCATATAT
1 ATGCTGCCCAAATTGAT-ATATAT
*
42780558 ATGCTGTCCAAATT
1 ATGCTGCCCAAATT
42780572 TTTGATGTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 10 0.31
23 22 0.69
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.37
Consensus pattern (23 bp):
ATGCTGCCCAAATTGATATATAT
Found at i:42780619 original size:23 final size:22
Alignment explanation
Indices: 42780547--42780831 Score: 137
Period size: 23 Copynumber: 12.0 Consensus size: 22
42780537 GCTGCCCAAA
42780547 TTGTCATATATATGCTGTCCAAATTT
1 TTGT-ATATA-ATGCTGT-CAAA-TT
* * *
42780573 TTGATGTAAAAATGCTGTCCAATT
1 TTG-TAT-ATAATGCTGTCAAATT
*
42780597 TTGTATATACATGCTGTTAAATT
1 TTGTATATA-ATGCTGTCAAATT
*
42780620 TTGTGTATAAGTGCTGTCCAAATT
1 TTGTATATAA-TGCTGT-CAAATT
* * * *
42780644 GGTGTATGT-ATGCTGCCTAATTT
1 -TTGTATATAATGCTGTC-AAATT
*
42780667 TTGGTGA-ATCAATGCTGTCCAATT
1 TT-GT-ATAT-AATGCTGTCAAATT
*
42780691 TTGTATATACATGCTGTTAAATT
1 TTGTATATA-ATGCTGTCAAATT
*
42780714 TTGTGTATAAGTGCTGTCCAAATT
1 TTGTATATAA-TGCTGT-CAAATT
* * * *
42780738 GGTGTATGT-ATGCTGCCTAATTT
1 -TTGTATATAATGCTGTC-AAATT
*
42780761 TTGGTGA-ATCAATGCTGTCCAATT
1 TT-GT-ATAT-AATGCTGTCAAATT
* *
42780785 TTGTATACACATGCTGTTAAATT
1 TTGTATATA-ATGCTGTCAAATT
*
42780808 TTGTGTATAAGTGCTGTCCAAATT
1 TTGTATATAA-TGCTGT-CAAATT
42780832 GGTATATGTA
Statistics
Matches: 195, Mismatches: 39, Indels: 52
0.68 0.14 0.18
Matches are distributed among these distances:
22 13 0.07
23 107 0.55
24 34 0.17
25 27 0.14
26 11 0.06
27 3 0.02
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (22 bp):
TTGTATATAATGCTGTCAAATT
Found at i:42780693 original size:94 final size:95
Alignment explanation
Indices: 42780557--42780927 Score: 568
Period size: 94 Copynumber: 3.9 Consensus size: 95
42780547 TTGTCATATA
* * *
42780557 TATGCTGTCCAAATTTTTGATGTAA-AAATGCTGTCCAATTTTGTATATACATGCTGTTAAATTT
1 TATGCTG-CCTAATTTTTGGTGAAATAAATGCTGTCCAATTTTGTATATACATGCTGTTAAATTT
42780621 TGTGTATAAGTGCTGTCCAAATTGGTGTATG
65 TGTGTATAAGTGCTGTCCAAATTGGTGTATG
*
42780652 TATGCTGCCTAATTTTTGGTG-AATCAATGCTGTCCAATTTTGTATATACATGCTGTTAAATTTT
1 TATGCTGCCTAATTTTTGGTGAAATAAATGCTGTCCAATTTTGTATATACATGCTGTTAAATTTT
42780716 GTGTATAAGTGCTGTCCAAATTGGTGTATG
66 GTGTATAAGTGCTGTCCAAATTGGTGTATG
* *
42780746 TATGCTGCCTAATTTTTGGTG-AATCAATGCTGTCCAATTTTGTATACACATGCTGTTAAATTTT
1 TATGCTGCCTAATTTTTGGTGAAATAAATGCTGTCCAATTTTGTATATACATGCTGTTAAATTTT
*
42780810 GTGTATAAGTGCTGTCCAAATTGGTATATG
66 GTGTATAAGTGCTGTCCAAATTGGTGTATG
* * * * *
42780840 TATGCTGCCTAATTTTTGGTGAAAAAAAATGCTGTCCAATTTTATATATATATGCTGCTCAATTT
1 TATGCTGCCTAATTTTTGGTG-AAATAAATGCTGTCCAATTTTGTATATACATGCTG-TTAAATT
*
42780905 TTGATGTATAAGAGCTGTCCAAA
64 TTG-TGTATAAGTGCTGTCCAAA
42780928 CAGGGTAGAT
Statistics
Matches: 258, Mismatches: 13, Indels: 7
0.93 0.05 0.03
Matches are distributed among these distances:
93 2 0.01
94 194 0.75
95 7 0.03
96 29 0.11
97 8 0.03
98 18 0.07
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (95 bp):
TATGCTGCCTAATTTTTGGTGAAATAAATGCTGTCCAATTTTGTATATACATGCTGTTAAATTTT
GTGTATAAGTGCTGTCCAAATTGGTGTATG
Found at i:42787253 original size:28 final size:28
Alignment explanation
Indices: 42787221--42787352 Score: 192
Period size: 28 Copynumber: 4.7 Consensus size: 28
42787211 TGACTTTCGA
*
42787221 CACTAAGTGTGCGAATTTAATTGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
42787249 CACTAAGTGTGCGAGTTTAATTTGTAAAG
1 CACTAAGTGTGCGAGTTTAA-TTGTAAAG
*
42787278 CACTAAGTGTGCGAGTTTAATGGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
* * **
42787306 CACTAAGTGTGCGAGTTTGATTATTGAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
*
42787334 CACTAAGTGTGCGAATTTA
1 CACTAAGTGTGCGAGTTTA
42787353 TTAAATATTT
Statistics
Matches: 94, Mismatches: 9, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
28 66 0.70
29 28 0.30
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (28 bp):
CACTAAGTGTGCGAGTTTAATTGTAAAG
Found at i:42787309 original size:57 final size:56
Alignment explanation
Indices: 42787221--42787352 Score: 203
Period size: 57 Copynumber: 2.3 Consensus size: 56
42787211 TGACTTTCGA
*
42787221 CACTAAGTGTGCGAATTTAATTGTAAAGCACTAAGTGTGCGAGTTTAATT-TGTAAAG
1 CACTAAGTGTGCGAATTTAATGGTAAAGCACTAAGTGTGCGAGTTTAATTAT-T-AAG
* * *
42787278 CACTAAGTGTGCGAGTTTAATGGTAAAGCACTAAGTGTGCGAGTTTGATTATTGAG
1 CACTAAGTGTGCGAATTTAATGGTAAAGCACTAAGTGTGCGAGTTTAATTATTAAG
42787334 CACTAAGTGTGCGAATTTA
1 CACTAAGTGTGCGAATTTA
42787353 TTAAATATTT
Statistics
Matches: 69, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
56 20 0.29
57 48 0.70
58 1 0.01
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (56 bp):
CACTAAGTGTGCGAATTTAATGGTAAAGCACTAAGTGTGCGAGTTTAATTATTAAG
Found at i:42788134 original size:23 final size:23
Alignment explanation
Indices: 42788087--42788145 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
42788077 TTATGCTTAA
* *
42788087 ATGCTGCCC-AATTGATGTATTT
1 ATGCTGCCCAAATTGATATATAT
42788109 ATGCTGCCCAAATTG-TCATATAT
1 ATGCTGCCCAAATTGAT-ATATAT
*
42788132 ATGCTGTCCAAATT
1 ATGCTGCCCAAATT
42788146 TTTGATGTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 10 0.31
23 22 0.69
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.37
Consensus pattern (23 bp):
ATGCTGCCCAAATTGATATATAT
Found at i:42788193 original size:23 final size:22
Alignment explanation
Indices: 42788121--42788499 Score: 176
Period size: 23 Copynumber: 16.0 Consensus size: 22
42788111 GCTGCCCAAA
42788121 TTGTCATATATATGCTGTCCAAATTT
1 TTGT-ATATA-ATGCTGT-CAAA-TT
* * *
42788147 TTGATGTAAAAATGCTGTCCAATT
1 TTG-TAT-ATAATGCTGTCAAATT
*
42788171 TTGTATATACATGCTGTTAAATT
1 TTGTATATA-ATGCTGTCAAATT
*
42788194 TTGTGTATAAGTGCTGTCCAAATT
1 TTGTATATAA-TGCTGT-CAAATT
* * * *
42788218 GGTGTATGT-ATGCTGCCTAATTT
1 -TTGTATATAATGCTGTC-AAATT
*
42788241 TTGGTGA-ATCAATGCTGTCCAATT
1 TT-GT-ATAT-AATGCTGTCAAATT
*
42788265 TTGTATATACATGCTGTTAAATT
1 TTGTATATA-ATGCTGTCAAATT
*
42788288 TTGTGTATAAGTGCTGTCCAAATT
1 TTGTATATAA-TGCTGT-CAAATT
* * * *
42788312 GGTGTATGT-ATGCTGCCTAATTT
1 -TTGTATATAATGCTGTC-AAATT
*
42788335 TTGGTGA-ATCAATGCTGTCCAATT
1 TT-GT-ATAT-AATGCTGTCAAATT
*
42788359 TTGTATATACATGCTGTTAAATT
1 TTGTATATA-ATGCTGTCAAATT
*
42788382 TTGTGTATAAGTGCTGTCCAAATT
1 TTGTATATAA-TGCTGT-CAAATT
* * * *
42788406 GGTGTATGT-ATGCTGCCTAATTT
1 -TTGTATATAATGCTGTC-AAATT
*
42788429 TTGGTGA-ATCAATGCTGTCCAATT
1 TT-GT-ATAT-AATGCTGTCAAATT
* *
42788453 TTGTATACACATGCTGTTAAATT
1 TTGTATATA-ATGCTGTCAAATT
*
42788476 TTGTGTATAAGTGCTGTCCAAATT
1 TTGTATATAA-TGCTGT-CAAATT
42788500 GGTATATGTA
Statistics
Matches: 265, Mismatches: 53, Indels: 72
0.68 0.14 0.18
Matches are distributed among these distances:
22 18 0.07
23 148 0.56
24 46 0.17
25 39 0.15
26 11 0.04
27 3 0.01
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (22 bp):
TTGTATATAATGCTGTCAAATT
Found at i:42788267 original size:94 final size:94
Alignment explanation
Indices: 42788131--42788595 Score: 761
Period size: 94 Copynumber: 4.9 Consensus size: 94
42788121 TTGTCATATA
* * *
42788131 TATGCTGTCCAAATTTTTGATGTAA-AAATGCTGTCCAATTTTGTATATACATGCTGTTAAATTT
1 TATGCTG-CCTAATTTTTGGTG-AATCAATGCTGTCCAATTTTGTATATACATGCTGTTAAATTT
42788195 TGTGTATAAGTGCTGTCCAAATTGGTGTATG
64 TGTGTATAAGTGCTGTCCAAATTGGTGTATG
42788226 TATGCTGCCTAATTTTTGGTGAATCAATGCTGTCCAATTTTGTATATACATGCTGTTAAATTTTG
1 TATGCTGCCTAATTTTTGGTGAATCAATGCTGTCCAATTTTGTATATACATGCTGTTAAATTTTG
42788291 TGTATAAGTGCTGTCCAAATTGGTGTATG
66 TGTATAAGTGCTGTCCAAATTGGTGTATG
42788320 TATGCTGCCTAATTTTTGGTGAATCAATGCTGTCCAATTTTGTATATACATGCTGTTAAATTTTG
1 TATGCTGCCTAATTTTTGGTGAATCAATGCTGTCCAATTTTGTATATACATGCTGTTAAATTTTG
42788385 TGTATAAGTGCTGTCCAAATTGGTGTATG
66 TGTATAAGTGCTGTCCAAATTGGTGTATG
*
42788414 TATGCTGCCTAATTTTTGGTGAATCAATGCTGTCCAATTTTGTATACACATGCTGTTAAATTTTG
1 TATGCTGCCTAATTTTTGGTGAATCAATGCTGTCCAATTTTGTATATACATGCTGTTAAATTTTG
*
42788479 TGTATAAGTGCTGTCCAAATTGGTATATG
66 TGTATAAGTGCTGTCCAAATTGGTGTATG
** * * * *
42788508 TATGCTGCCTAATTTTTGGTGAAAAAAAATGCTGTCCAATTTTATATATATATGCTGCTCAATTT
1 TATGCTGCCTAATTTTTGGTG--AATCAATGCTGTCCAATTTTGTATATACATGCTG-TTAAATT
*
42788573 TTGATGTATAAGAGCTGTCCAAA
63 TTG-TGTATAAGTGCTGTCCAAA
42788596 CAGGGTAGAT
Statistics
Matches: 352, Mismatches: 13, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
93 2 0.01
94 288 0.82
95 7 0.02
96 29 0.08
97 8 0.02
98 18 0.05
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.42
Consensus pattern (94 bp):
TATGCTGCCTAATTTTTGGTGAATCAATGCTGTCCAATTTTGTATATACATGCTGTTAAATTTTG
TGTATAAGTGCTGTCCAAATTGGTGTATG
Found at i:42813742 original size:20 final size:20
Alignment explanation
Indices: 42813706--42813744 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
42813696 CGACGCCAAT
42813706 TCTGTAAGTATTCTGAAAAC
1 TCTGTAAGTATTCTGAAAAC
*
42813726 TCTGATAAGT-TTTTGAAAA
1 TCTG-TAAGTATTCTGAAAA
42813745 TATGAGTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.38
Consensus pattern (20 bp):
TCTGTAAGTATTCTGAAAAC
Found at i:42815335 original size:18 final size:18
Alignment explanation
Indices: 42815312--42815347 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
42815302 CATCATATGT
42815312 CAGTTTGGGATGTGTGCC
1 CAGTTTGGGATGTGTGCC
42815330 CAGTTTGGGATGTGTGCC
1 CAGTTTGGGATGTGTGCC
42815348 GATACAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.17, G:0.39, T:0.33
Consensus pattern (18 bp):
CAGTTTGGGATGTGTGCC
Found at i:42819729 original size:9 final size:9
Alignment explanation
Indices: 42819715--42819750 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
42819705 GATAAAGTAA
42819715 AATTAAATT
1 AATTAAATT
42819724 AATTAAATT
1 AATTAAATT
*
42819733 AATCAAATT
1 AATTAAATT
42819742 AATTAAATT
1 AATTAAATT
42819751 TAATATGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (9 bp):
AATTAAATT
Found at i:42822689 original size:16 final size:16
Alignment explanation
Indices: 42822668--42822726 Score: 66
Period size: 16 Copynumber: 3.7 Consensus size: 16
42822658 TTAATCACTT
42822668 TAATATTAAATTAATA
1 TAATATTAAATTAATA
**
42822684 TAATATTTATCTTAATA
1 TAATA-TTAAATTAATA
* *
42822701 -AATATTATATTAATT
1 TAATATTAAATTAATA
42822716 TAATATTAAAT
1 TAATATTAAAT
42822727 CTTATTAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
15 9 0.25
16 18 0.50
17 9 0.25
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
TAATATTAAATTAATA
Found at i:42822704 original size:21 final size:20
Alignment explanation
Indices: 42822680--42822720 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
42822670 ATATTAAATT
*
42822680 AATATAATATTTATCTTAATA
1 AATATAATATTAAT-TTAATA
*
42822701 AATATTATATTAATTTAATA
1 AATATAATATTAATTTAATA
42822721 TTAAATCTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
AATATAATATTAATTTAATA
Found at i:42822706 original size:32 final size:32
Alignment explanation
Indices: 42822669--42822782 Score: 98
Period size: 32 Copynumber: 3.7 Consensus size: 32
42822659 TAATCACTTT
42822669 AATATTAAATTAATATAATATTTATCTTAATA
1 AATATTAAATTAATATAATATTTATCTTAATA
* * *
42822701 AATATTATATTAATTTAATATTAAATCTT-AT-
1 AATATTAAATTAATATAATATT-TATCTTAATA
*
42822732 --TA--AAA-TAATAGAATATTTATCTTAGATA
1 AATATTAAATTAATATAATATTTATCTTA-ATA
* *
42822760 AACATTAAATTAAATTTAATATT
1 AATATTAAATT-AATATAATATT
42822783 AAACTATTAA
Statistics
Matches: 62, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
25 5 0.08
26 10 0.16
27 4 0.06
29 2 0.03
30 1 0.02
32 25 0.40
33 6 0.10
34 9 0.15
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.46
Consensus pattern (32 bp):
AATATTAAATTAATATAATATTTATCTTAATA
Found at i:42822718 original size:5 final size:6
Alignment explanation
Indices: 42822667--42822724 Score: 56
Period size: 5 Copynumber: 10.7 Consensus size: 6
42822657 CTTAATCACT
* *
42822667 TTAATA TTAA-A TTAATA -TAATA TTTATC TTAATA --AATA TT-ATA
1 TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA
42822710 TTAAT- TTAATA TTAA
1 TTAATA TTAATA TTAA
42822725 ATCTTATTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
4 4 0.10
5 20 0.48
6 18 0.43
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (6 bp):
TTAATA
Found at i:42822733 original size:58 final size:58
Alignment explanation
Indices: 42822671--42822800 Score: 192
Period size: 58 Copynumber: 2.2 Consensus size: 58
42822661 ATCACTTTAA
* * *
42822671 TATTAAATTAATATAATATTTATCTTA-ATAAATATTATATT-AATTTAATATTAAATC
1 TATTAAAATAATATAATATTTATCTTAGATAAACATTAAATTAAATTTAATATTAAA-C
*
42822728 TTATTAAAATAATAGAATATTTATCTTAGATAAACATTAAATTAAATTTAATATTAAAC
1 -TATTAAAATAATATAATATTTATCTTAGATAAACATTAAATTAAATTTAATATTAAAC
42822787 TATTAAAATAATAT
1 TATTAAAATAATAT
42822801 TATTTTTGAA
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
58 38 0.58
59 13 0.20
60 14 0.22
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.45
Consensus pattern (58 bp):
TATTAAAATAATATAATATTTATCTTAGATAAACATTAAATTAAATTTAATATTAAAC
Found at i:42834793 original size:58 final size:56
Alignment explanation
Indices: 42834717--42834870 Score: 181
Period size: 57 Copynumber: 2.7 Consensus size: 56
42834707 GAATTTTTTG
*
42834717 TTTGAAAACACGAGAATTTTG-AGACACAATAACTCTTTTTTATTGAAAACACAAAAATT
1 TTTGAAAACACGAGAATTTTGAAAACACAA-AA-T-TTTTTT-TTGAAAACACAAAAATT
*
42834776 TTT-AAAACACGAGAATTTTTTGAAAACACGAAATTTTTTTTTGAAAACACAAAAATT
1 TTTGAAAACACGAGAA--TTTTGAAAACACAAAATTTTTTTTTGAAAACACAAAAATT
42834833 TTTGAAATAC-CG-GAATTTTTGAAAACACAAAGATTTTT
1 TTTGAAA-ACACGAGAA-TTTTGAAAACACAAA-ATTTTT
42834871 GAAACACGAA
Statistics
Matches: 86, Mismatches: 3, Indels: 14
0.83 0.03 0.14
Matches are distributed among these distances:
56 15 0.17
57 29 0.34
58 23 0.27
59 6 0.07
60 7 0.08
61 6 0.07
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (56 bp):
TTTGAAAACACGAGAATTTTGAAAACACAAAATTTTTTTTTGAAAACACAAAAATT
Found at i:42834823 original size:40 final size:38
Alignment explanation
Indices: 42834774--42834887 Score: 105
Period size: 35 Copynumber: 3.1 Consensus size: 38
42834764 AACACAAAAA
* *
42834774 TTTTTAAAACACGAGAATTTTTTGAAA-ACACGAAATTTT
1 TTTTTAAAACAC-AAAAATTTTTGAAATAC-CGAAATTTT
*
42834813 TTTTTGAAAACACAAAAATTTTTGAAATACCGGAA---T
1 TTTTT-AAAACACAAAAATTTTTGAAATACCGAAATTTT
* * *
42834849 TTTTGAAAACACAAAGATTTTTGAAACA-CG-AATTTT
1 TTTTTAAAACACAAAAATTTTTGAAATACCGAAATTTT
42834885 TTT
1 TTT
42834888 AATTTTTCCT
Statistics
Matches: 64, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
33 2 0.03
34 2 0.03
35 21 0.33
36 9 0.14
39 21 0.33
40 9 0.14
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.38
Consensus pattern (38 bp):
TTTTTAAAACACAAAAATTTTTGAAATACCGAAATTTT
Found at i:42834887 original size:17 final size:18
Alignment explanation
Indices: 42834754--42834886 Score: 107
Period size: 18 Copynumber: 7.3 Consensus size: 18
42834744 AATAACTCTT
*
42834754 TTTTATTGAAAACACAAAA
1 TTTT-TTGAAAACACGAAA
*
42834773 ATTTTT-AAAACACGAGAA
1 TTTTTTGAAAACACGA-AA
42834791 TTTTTTGAAAACACGAAA
1 TTTTTTGAAAACACGAAA
*
42834809 TTTTTTTTTGAAAACACAAAA
1 ---TTTTTTGAAAACACGAAA
* *
42834830 ATTTTTGAAATAC-CGGAA
1 TTTTTTGAAA-ACACGAAA
42834848 -TTTTTGAAAACAC-AAA
1 TTTTTTGAAAACACGAAA
*
42834864 GATTTTTG-AAACACG-AA
1 -TTTTTTGAAAACACGAAA
42834881 TTTTTT
1 TTTTTT
42834887 TAATTTTTCC
Statistics
Matches: 95, Mismatches: 9, Indels: 23
0.75 0.07 0.18
Matches are distributed among these distances:
16 9 0.09
17 26 0.27
18 29 0.31
19 14 0.15
21 17 0.18
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.36
Consensus pattern (18 bp):
TTTTTTGAAAACACGAAA
Found at i:42835397 original size:7 final size:7
Alignment explanation
Indices: 42835385--42835426 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
42835375 CTTTCCCCTC
42835385 CCTTTTT
1 CCTTTTT
42835392 CCTTTTT
1 CCTTTTT
42835399 -CTTTTT
1 CCTTTTT
* *
42835405 TCTTCTT
1 CCTTTTT
42835412 CCTTTCTT
1 CCTTT-TT
42835420 CCTTTTT
1 CCTTTTT
42835427 TTTCTTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
6 6 0.20
7 17 0.57
8 7 0.23
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (7 bp):
CCTTTTT
Found at i:42835431 original size:21 final size:20
Alignment explanation
Indices: 42835390--42835432 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
42835380 CCCTCCCTTT
42835390 TTCCTTTTTCTTTTTTCTTC
1 TTCCTTTTTCTTTTTTCTTC
42835410 TTCCTTTCTTCCTTTTTT-TTC
1 TTCCTTT-TT-CTTTTTTCTTC
42835431 TT
1 TT
42835433 TTTTCGGCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.33
21 7 0.33
22 7 0.33
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (20 bp):
TTCCTTTTTCTTTTTTCTTC
Found at i:42835734 original size:15 final size:15
Alignment explanation
Indices: 42835716--42835753 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
42835706 GATTTTTTTA
42835716 TTTTTTCTCTTTCCT
1 TTTTTTCTCTTTCCT
*
42835731 TTTTTTTTCTTTCCT
1 TTTTTTCTCTTTCCT
*
42835746 TTTCTTCT
1 TTTTTTCT
42835754 TTCTTTTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTTCTCTTTCCT
Found at i:42835735 original size:21 final size:20
Alignment explanation
Indices: 42835709--42835779 Score: 56
Period size: 21 Copynumber: 3.5 Consensus size: 20
42835699 TATTTTAGAT
42835709 TTTTTTATTTTTTCTCTTTCC
1 TTTTTTATTTTTTCTCTTT-C
42835730 TTTTTT-TTTCTTTC-CTTTTC
1 TTTTTTATTT-TTTCTC-TTTC
* * *
42835750 TTCTTTCTTTTTCTTTCTTTC
1 TTTTTTATTTTT-TCTCTTTC
*
42835771 TTTCTTATT
1 TTTTTTATT
42835780 CCATTTTTCT
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
20 12 0.30
21 27 0.68
22 1 0.03
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTTTATTTTTTCTCTTTC
Found at i:42835736 original size:17 final size:18
Alignment explanation
Indices: 42835719--42835790 Score: 64
Period size: 18 Copynumber: 4.1 Consensus size: 18
42835709 TTTTTTATTT
42835719 TTTCTCTTTCC-TTTTT-
1 TTTCTCTTTCCTTTTTTC
42835735 TTT-TCTTTCCTTTTCTTC
1 TTTCTCTTTCCTTTT-TTC
*
42835753 TTTCT-TTTTCTTTCTTTC
1 TTTCTCTTTCCTTT-TTTC
*
42835771 TTTCT-TATTCCATTTTTC
1 TTTCTCT-TTCCTTTTTTC
42835789 TT
1 TT
42835791 CCTTCTCCGT
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
15 7 0.15
16 6 0.13
17 2 0.04
18 25 0.53
19 7 0.15
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTCTCTTTCCTTTTTTC
Found at i:42835748 original size:27 final size:27
Alignment explanation
Indices: 42835718--42835770 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
42835708 TTTTTTTATT
*
42835718 TTTTC-TCTTTCCTTTTTTTTTCTTTCC
1 TTTTCTTCTTT-CTTTTTCTTTCTTTCC
42835745 TTTTCTTCTTTCTTTTTCTTTCTTTC
1 TTTTCTTCTTTCTTTTTCTTTCTTTC
42835771 TTTCTTATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 19 0.79
28 5 0.21
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (27 bp):
TTTTCTTCTTTCTTTTTCTTTCTTTCC
Found at i:42836425 original size:60 final size:60
Alignment explanation
Indices: 42836338--42836494 Score: 147
Period size: 59 Copynumber: 2.6 Consensus size: 60
42836328 AATATGGGGC
* * *
42836338 CAAAATGTAATTTTTAGAAAAGTTTAGGGGCCCAAATGAAAATTTAAGAAAGTTAAAAGGT
1 CAAAATGTAATATGTAGAAAAGTTTAGGGGCCAAAATGAAAATTTAA-AAAGTTAAAAGGT
* * * * * *
42836399 CAAAATGTAA-ATGTAGGAAAGTTTAGGGTCCAAAATGCAATTTTGAAAAGTTAAAGGGT
1 CAAAATGTAATATGTAGAAAAGTTTAGGGGCCAAAATGAAAATTTAAAAAGTTAAAAGGT
* ** * * * *
42836458 TAAAAAATAAT-TTTAAAAAAGTTTAAGGGTCAAAATG
1 CAAAATGTAATATGTAGAAAAGTTTAGGGGCCAAAATG
42836495 TAATTTTTTA
Statistics
Matches: 77, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
59 39 0.51
60 28 0.36
61 10 0.13
ACGTcount: A:0.46, C:0.06, G:0.20, T:0.28
Consensus pattern (60 bp):
CAAAATGTAATATGTAGAAAAGTTTAGGGGCCAAAATGAAAATTTAAAAAGTTAAAAGGT
Found at i:42836499 original size:30 final size:30
Alignment explanation
Indices: 42836310--42836501 Score: 142
Period size: 30 Copynumber: 6.4 Consensus size: 30
42836300 TTTTTTGGGA
* * *
42836310 AAAATGTAATTTTAGGAAAA-TAT-GGGGCC
1 AAAATGTAATTTTA-GAAAAGTTTAAGGGTC
* *
42836339 AAAATGTAATTTTTAGAAAAGTTTAGGGGCC
1 AAAATGTAA-TTTTAGAAAAGTTTAAGGGTC
* * * * *
42836370 CAAATGAAAATTTA-AGAAAGTTAAAAGGTC
1 AAAATGTAATTTTAGA-AAAGTTTAAGGGTC
* * *
42836400 AAAATGTAAATGTAGGAAAGTTT-AGGGTCC
1 AAAATGTAATTTTAGAAAAGTTTAAGGGT-C
* * *
42836430 AAAATGCAATTTT-GAAAAGTTAAAGGGTT
1 AAAATGTAATTTTAGAAAAGTTTAAGGGTC
** *
42836459 AAAAAATAATTTTAAAAAAGTTTAAGGGTC
1 AAAATGTAATTTTAGAAAAGTTTAAGGGTC
42836489 AAAATGTAATTTT
1 AAAATGTAATTTT
42836502 TTATTTTAAA
Statistics
Matches: 127, Mismatches: 28, Indels: 15
0.75 0.16 0.09
Matches are distributed among these distances:
29 36 0.28
30 78 0.61
31 13 0.10
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (30 bp):
AAAATGTAATTTTAGAAAAGTTTAAGGGTC
Found at i:42836953 original size:81 final size:78
Alignment explanation
Indices: 42836689--42837295 Score: 552
Period size: 76 Copynumber: 7.8 Consensus size: 78
42836679 GCGACCCAAA
**
42836689 GCTCAACTCACCTCTCG-AATCATGAGTTGA--TTTTTTGAAAAACAGAAATTGAAAAGAATACC
1 GCTCAACTCACCTCTCGCAAT-ATGAGTTGATTTTTTTTGAAAAGTAGAAATTG-AAA-AATACC
*
42836751 TC-AGCATGCGACCCGAG
63 TCGA-CGTG-GACCCGAG
* * * *
42836768 GCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTTT-AAAAGCAAAAATTGAAAAATACCTTG
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAGTAGAAATTGAAAAATACCTCG
*
42836832 ACGT-GACTCGAG
66 ACGTGGACCCGAG
* * * *
42836844 ACTCAACTCACCTCTTGCAATATGAGTTGATTTTTTTTTTGAAAAGTAGTAATTGAAAATTACCT
1 GCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTTTGAAAAGTAGAAATTGAAAAATACCT
42836909 CGACGTGCGACCCGAG
64 CGACGTG-GACCCGAG
* * *
42836925 GCTCAACTCACCCCTCGCAATATGAGTTGATTTTTTATTTGAAAAATAGAAATTTAAAAGAAATA
1 GCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTT-TTTGAAAAGTAGAAA-TT-GAA-AAATA
* * * *
42836990 CCTTGGCATGTGACTCGAG
61 CCTCGACGTG-GACCCGAG
* * * *
42837009 ACTCAACTCACCTCTCACAATATAAGTTGA-TTTTTTTGAAAAGTAGTAATTGAAAAATACCTCG
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAGTAGAAATTGAAAAATACCTCG
* *
42837073 ACGT-GACTCAAG
66 ACGTGGACCCGAG
* *
42837085 GCTCAACTTCACCTCTTGCAATATGAGTTGATTTTTTTTGCAGAAATTTA-AAA--G--AAATAC
1 GCTCAAC-TCACCTCTCGCAATATGAGTTGATTTTTTTTG-A-AAA-GTAGAAATTGAAAAATAC
* * *
42837145 CTCGGCATGTAACCCGAG
62 CTCGACGTG-GACCCGAG
* *
42837163 GCTCAACTCACATCTCGCGATATGAGTTGA-TTTTTTTGAAAAGTAGAAATTG-AAAATACCTC-
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAGTAGAAATTGAAAAATACCTCG
*
42837225 AGCGT-GACCTGAG
66 A-CGTGGACCCGAG
* * * *
42837238 GCTCAACTCACTTTTCGCATTATGAGTTGA---TTTTTGAAAAATAGAAATTGCAAAAATA
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAGTAGAAATTG-AAAAATA
42837296 TAATTCTTGA
Statistics
Matches: 440, Mismatches: 61, Indels: 58
0.79 0.11 0.10
Matches are distributed among these distances:
73 21 0.05
74 6 0.01
75 39 0.09
76 68 0.15
77 51 0.12
78 49 0.11
79 58 0.13
80 28 0.06
81 68 0.15
82 6 0.01
83 2 0.00
84 44 0.10
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (78 bp):
GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAGTAGAAATTGAAAAATACCTCG
ACGTGGACCCGAG
Found at i:42837122 original size:241 final size:234
Alignment explanation
Indices: 42836677--42837272 Score: 681
Period size: 241 Copynumber: 2.5 Consensus size: 234
42836667 ATAGCTTGGT
* * *
42836677 GTGCGACCCAAAGCTCAACTCACCTCTCG-AATCATGAGTTGA-TTTTTTGAAAAACAGAAATTG
1 GTGCGACCCGAGGCTCAACTCACCTCTCGCAAT-ATGAGTTGATTTTTTTGAAAAATAGAAATTG
* ** *
42836740 AAAAGAATACCTCAGCATGCGACCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTT
65 AAAAGAATACCTCAGCATGCGACCCGAGACTCAACTCACCTCTCACAATATAAGTTGATTTTTTT
* * *
42836805 TAAAAGCAAAAATTGAAAAATACCTTGACGTGACTCGAGACTCAACTCACCTCTTGCAATATGAG
130 GAAAAGCAAAAATTGAAAAATACCTCGACGTGACTCAAGACTCAACTCACCTCTTGCAATATGAG
**
42836870 TTGATTTTTTTTTTG-A-AAAGTAGTAATTGAAAATTACCTCGAC
195 TTGA-TTTTTTTTTGCAGAAA-T-GTAAAAG-AAA-TACCTCGAC
*
42836913 GTGCGACCCGAGGCTCAACTCACCCCTCGCAATATGAGTTGATTTTTTATTTGAAAAATAGAAAT
1 GTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTT-TTTGAAAAATAGAAAT
* ** * *
42836978 TTAAAAGAAATACCTTGGCATGTGACTCGAGACTCAACTCACCTCTCACAATATAAGTTGATTTT
63 TGAAAAG-AATACCTCAGCATGCGACCCGAGACTCAACTCACCTCTCACAATATAAGTTGATTTT
* ** *
42837043 TTTGAAAAGTAGTAATTGAAAAATACCTCGACGTGACTCAAGGCTCAACTTCACCTCTTGCAATA
127 TTTGAAAAGCAAAAATTGAAAAATACCTCGACGTGACTCAAGACTCAAC-TCACCTCTTGCAATA
* *
42837108 TGAGTTGA-TTTTTTTTGCAGAAATTTAAAAGAAATACCTCGGC
191 TGAGTTGATTTTTTTTTGCAGAAATGTAAAAGAAATACCTCGAC
* ** * * *
42837151 ATGTAACCCGAGGCTCAACTCACATCTCGCGATATGAGTTGATTTTTTTGAAAAGTAGAAATTG-
1 GTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAATAGAAATTGA
* * * * * * * *
42837215 -AA-AATACCTCAGC--GTGACCTGAGGCTCAACTCACTTTTCGCATTATGAGTTGATTTTT
66 AAAGAATACCTCAGCATGCGACCCGAGACTCAACTCACCTCTCACAATATAAGTTGATTTTT
42837273 GAAAAATAGA
Statistics
Matches: 309, Mismatches: 42, Indels: 25
0.82 0.11 0.07
Matches are distributed among these distances:
229 37 0.12
231 9 0.03
233 2 0.01
235 16 0.05
236 39 0.13
237 3 0.01
238 44 0.14
239 6 0.02
240 34 0.11
241 93 0.30
242 26 0.08
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.31
Consensus pattern (234 bp):
GTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAATAGAAATTGA
AAAGAATACCTCAGCATGCGACCCGAGACTCAACTCACCTCTCACAATATAAGTTGATTTTTTTG
AAAAGCAAAAATTGAAAAATACCTCGACGTGACTCAAGACTCAACTCACCTCTTGCAATATGAGT
TGATTTTTTTTTGCAGAAATGTAAAAGAAATACCTCGAC
Found at i:42837173 original size:154 final size:152
Alignment explanation
Indices: 42836690--42837272 Score: 624
Period size: 154 Copynumber: 3.7 Consensus size: 152
42836680 CGACCCAAAG
**
42836690 CTCAACTCACCTCTCG-AATCATGAGTTGA-TTTTTTGAAAAACAGAAATTGAAAAGAATACCTC
1 CTCAACTCACCTCTCGCAAT-ATGAGTTGATTTTTTTGAAAAGTAGAAATTG-AAA-AATACCTC
* * * *
42836753 AGCATGCGACCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTTTAAAAGCA-AAAA
63 -G-ACGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTT----GCAGAAAT
* * *
42836817 TT-GAA-AAATACCTTG-ACGTGACTCGAGA
122 TTAAAAGAAATACCTGGCATGTGACTCGAGA
* * *
42836845 CTCAACTCACCTCTTGCAATATGAGTTGATTTTTTTTTTGAAAAGTAGTAATTGAAAATTACCTC
1 CTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTTTGAAAAGTAGAAATTGAAAAATACCTC
* *
42836910 GACGTGCGACCCGAGGCTCAACTCACCCCTCGCAATATGAGTTGATTTTTTATTTGAAAAATAGA
63 GACGT--GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTT-TTTG-----CAGA
42836975 AATTTAAAAGAAATACCTTGGCATGTGACTCGAGA
119 AATTTAAAAGAAATACC-TGGCATGTGACTCGAGA
* * *
42837010 CTCAACTCACCTCTCACAATATAAGTTGATTTTTTTGAAAAGTAGTAATTGAAAAATACCTCGAC
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGTAGAAATTGAAAAATACCTCGAC
* * *
42837075 GTGACTCAAGGCTCAACTTCACCTCTTGCAATATGAGTTGATTTTTTTTGCAGAAATTTAAAAGA
66 GTGACCCGAGGCTCAAC-TCACCTCTCGCAATATGAGTTGATTTTTTTTGCAGAAATTTAAAAGA
* * *
42837140 AATACCTCGGCATGTAACCCGAGG
130 AATACCT-GGCATGTGACTCGAGA
* *
42837164 CTCAACTCACATCTCGCGATATGAGTTGATTTTTTTGAAAAGTAGAAATTG-AAAATACCTC-AG
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGTAGAAATTGAAAAATACCTCGA-
* * * *
42837227 CGTGACCTGAGGCTCAACTCACTTTTCGCATTATGAGTTGATTTTT
65 CGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
42837273 GAAAAATAGA
Statistics
Matches: 368, Mismatches: 38, Indels: 47
0.81 0.08 0.10
Matches are distributed among these distances:
152 25 0.07
153 26 0.07
154 79 0.21
155 27 0.07
156 4 0.01
157 43 0.12
158 8 0.02
159 25 0.07
160 19 0.05
161 26 0.07
162 39 0.11
163 7 0.02
164 2 0.01
165 38 0.10
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (152 bp):
CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGTAGAAATTGAAAAATACCTCGAC
GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGCAGAAATTTAAAAGAA
ATACCTGGCATGTGACTCGAGA
Found at i:42849227 original size:17 final size:17
Alignment explanation
Indices: 42849154--42849220 Score: 91
Period size: 17 Copynumber: 3.9 Consensus size: 17
42849144 AATAACTCTT
42849154 TTTTTGAAAACACGAAAA
1 TTTTT-AAAACACGAAAA
* *
42849172 TTTGTAAAACACGAGAA
1 TTTTTAAAACACGAAAA
42849189 -TTTTAGAAACACGAAAA
1 TTTTTA-AAACACGAAAA
42849206 TTTTTAAAACACGAA
1 TTTTTAAAACACGAA
42849221 TTTTTTTTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
16 4 0.09
17 30 0.70
18 9 0.21
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.27
Consensus pattern (17 bp):
TTTTTAAAACACGAAAA
Found at i:42849753 original size:28 final size:28
Alignment explanation
Indices: 42849715--42849775 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
42849705 ATTTTGGGCA
* *
42849715 TTTTCTCCCTTT-TTCTTTTTTCTTTTTT
1 TTTTCTCCCTTTCTTCCTTTTT-TTTCTT
*
42849743 TTTTCTTCCTTTCTTCCTTTTTTTTCTT
1 TTTTCTCCCTTTCTTCCTTTTTTTTCTT
42849771 TTTTC
1 TTTTC
42849776 GGTTGGGCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 21 0.72
29 8 0.28
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (28 bp):
TTTTCTCCCTTTCTTCCTTTTTTTTCTT
Found at i:42850062 original size:14 final size:14
Alignment explanation
Indices: 42850039--42850103 Score: 52
Period size: 13 Copynumber: 5.0 Consensus size: 14
42850029 GATTTTTTAT
42850039 TTTTTC-TCTTTCC
1 TTTTTCTTCTTTCC
42850052 TTTTTCTTCTTT-C
1 TTTTTCTTCTTTCC
*
42850065 ---TTCTTCTTTCT
1 TTTTTCTTCTTTCC
*
42850076 TTCTTTCTT-ATTCC
1 TT-TTTCTTCTTTCC
*
42850090 ATTTTCTTCTTTCC
1 TTTTTCTTCTTTCC
42850104 CGTTCAGCCC
Statistics
Matches: 40, Mismatches: 5, Indels: 13
0.69 0.09 0.22
Matches are distributed among these distances:
10 9 0.22
13 13 0.32
14 13 0.32
15 5 0.12
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTTCTTCTTTCC
Found at i:42850272 original size:26 final size:26
Alignment explanation
Indices: 42850227--42850281 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
42850217 TGCTCTTTCG
42850227 TTTTTTCTCTTTTTTACTT-GTTGTT
1 TTTTTTCTCTTTTTTACTTGGTTGTT
*
42850252 TTTTTTC-CTTTTTGCTTCTTGGTTGTT
1 TTTTTTCTCTTTTT--TACTTGGTTGTT
42850279 TTT
1 TTT
42850282 GCTAGGTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 6 0.23
25 7 0.27
26 4 0.15
27 9 0.35
ACGTcount: A:0.02, C:0.13, G:0.11, T:0.75
Consensus pattern (26 bp):
TTTTTTCTCTTTTTTACTTGGTTGTT
Found at i:42853751 original size:3 final size:3
Alignment explanation
Indices: 42853743--42853805 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
42853733 GCAAATCACT
42853743 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
42853791 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
42853806 AAGTTATTGC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:42858825 original size:6 final size:6
Alignment explanation
Indices: 42858808--42858840 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
42858798 AAATTATATA
42858808 ATTAAC -TTAAC ATTAAC ATTAAC ATTAAC ATTA
1 ATTAAC ATTAAC ATTAAC ATTAAC ATTAAC ATTA
42858841 TTAAAACAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.36
Consensus pattern (6 bp):
ATTAAC
Found at i:42861074 original size:27 final size:26
Alignment explanation
Indices: 42861016--42861076 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
42861006 GACATTACGG
* * * *
42861016 TCATTTTACCCTATGGGGTTTTTTGG
1 TCATTTTACCCTAAGGGGTATTATGA
*
42861042 TAATTTTACCCTACAGGGGTATTATGA
1 TCATTTTACCCTA-AGGGGTATTATGA
42861069 TCATTTTA
1 TCATTTTA
42861077 AAAATATTAG
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
26 12 0.43
27 16 0.57
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.46
Consensus pattern (26 bp):
TCATTTTACCCTAAGGGGTATTATGA
Found at i:42864493 original size:16 final size:16
Alignment explanation
Indices: 42864472--42864503 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
42864462 AATTAATTTA
*
42864472 AATTAATTAATTTTCT
1 AATTAAATAATTTTCT
42864488 AATTAAATAATTTTCT
1 AATTAAATAATTTTCT
42864504 CAATCCTATT
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:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (16 bp):
AATTAAATAATTTTCT
Found at i:42872027 original size:81 final size:81
Alignment explanation
Indices: 42871889--42872050 Score: 245
Period size: 81 Copynumber: 2.0 Consensus size: 81
42871879 GATTCCGAAG
* * *
42871889 ATAAGGCATCTCCCTAATTAGATCTAATAAATAGCATATTAGTCTTCCAATCAGTTTGATCA-TT
1 ATAAGGCATCTCCCCAATTAGATATAATAAATAGCATATTAGTCCTCCAATCAGTTTGATCATTT
42871953 TCTGATTAGACTAAGGA
66 TC-GATTAGACTAAGGA
* * * *
42871970 ATAAGGCATCTCCCCAATTGGATATGATAAATAGCATATTAGTCCTCCAATCGGTTTGATCGTTT
1 ATAAGGCATCTCCCCAATTAGATATAATAAATAGCATATTAGTCCTCCAATCAGTTTGATCATTT
42872035 TCGATTAGACTAAGGA
66 TCGATTAGACTAAGGA
42872051 CATATTTAGG
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
81 69 0.95
82 4 0.05
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (81 bp):
ATAAGGCATCTCCCCAATTAGATATAATAAATAGCATATTAGTCCTCCAATCAGTTTGATCATTT
TCGATTAGACTAAGGA
Found at i:42874629 original size:17 final size:17
Alignment explanation
Indices: 42874607--42874645 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
42874597 AATGGTGAGA
*
42874607 ATCTTAAATTAGTTTCC
1 ATCTTAAATTAGTTACC
42874624 ATCTT-AATTAGTTACC
1 ATCTTAAATTAGTTACC
42874640 ATCTTA
1 ATCTTA
42874646 GTTGCACCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.31, C:0.18, G:0.05, T:0.46
Consensus pattern (17 bp):
ATCTTAAATTAGTTACC
Found at i:42883895 original size:30 final size:30
Alignment explanation
Indices: 42883859--42883920 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
42883849 CTCCATCTAA
42883859 ACTCAATCCCATCGAATCCAAGAATTTACG
1 ACTCAATCCCATCGAATCCAAGAATTTACG
42883889 ACTCAATCCCATCGAATCCAAGAATTTACG
1 ACTCAATCCCATCGAATCCAAGAATTTACG
42883919 AC
1 AC
42883921 GCCGTTCCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.37, C:0.31, G:0.10, T:0.23
Consensus pattern (30 bp):
ACTCAATCCCATCGAATCCAAGAATTTACG
Found at i:42884733 original size:2 final size:2
Alignment explanation
Indices: 42884726--42884756 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
42884716 GCATTTTGAA
42884726 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
42884757 CCTTGGGGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:42896495 original size:24 final size:24
Alignment explanation
Indices: 42896466--42896514 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
42896456 TAGCTAAAGG
42896466 ACAAATGTGACAATAGGAAATACA
1 ACAAATGTGACAATAGGAAATACA
*
42896490 ACAAATGTGACAATGGGAAATACA
1 ACAAATGTGACAATAGGAAATACA
42896514 A
1 A
42896515 TCATTGTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.53, C:0.12, G:0.18, T:0.16
Consensus pattern (24 bp):
ACAAATGTGACAATAGGAAATACA
Found at i:42900378 original size:13 final size:13
Alignment explanation
Indices: 42900360--42900385 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42900350 TAATTTTTAA
42900360 AAAATTGATTTTT
1 AAAATTGATTTTT
42900373 AAAATTGATTTTT
1 AAAATTGATTTTT
42900386 CTTTCAGTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
AAAATTGATTTTT
Found at i:42900780 original size:27 final size:27
Alignment explanation
Indices: 42900717--42900780 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
42900707 AATTGTAATG
*
42900717 AATAAAAATATATTAAATTATTAAATT
1 AATAAAAATATATTAAATTATTAAAAT
*
42900744 AA-AAACAATATATTATATTATTAAAAT
1 AATAAA-AATATATTAAATTATTAAAAT
*
42900771 AATAATAATA
1 AATAAAAATA
42900781 GAAGAAGAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 3 0.09
27 27 0.84
28 2 0.06
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (27 bp):
AATAAAAATATATTAAATTATTAAAAT
Found at i:42905744 original size:24 final size:24
Alignment explanation
Indices: 42905698--42905744 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
42905688 ACACCAGATG
*
42905698 AAAATAATTACATAGTAAATTTAT
1 AAAATAATTAAATAGTAAATTTAT
*
42905722 AAAATAAATTAAATA-TAATTTTA
1 AAAAT-AATTAAATAGTAAATTTA
42905745 GTTAGAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (24 bp):
AAAATAATTAAATAGTAAATTTAT
Found at i:42906017 original size:12 final size:12
Alignment explanation
Indices: 42906000--42906025 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42905990 AGGATATGCA
42906000 ATCTTAGATATG
1 ATCTTAGATATG
42906012 ATCTTAGATATG
1 ATCTTAGATATG
42906024 AT
1 AT
42906026 ATATGCAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (12 bp):
ATCTTAGATATG
Found at i:42906048 original size:19 final size:20
Alignment explanation
Indices: 42906012--42906059 Score: 71
Period size: 19 Copynumber: 2.4 Consensus size: 20
42906002 CTTAGATATG
*
42906012 ATCTTAGATATGATATATGCA
1 ATCTTAGATACGA-ATATGCA
42906033 ATCTTAGATACG-ATATGCA
1 ATCTTAGATACGAATATGCA
42906052 ATCTTAGA
1 ATCTTAGA
42906060 AGATACGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 15 0.58
21 11 0.42
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (20 bp):
ATCTTAGATACGAATATGCA
Found at i:42906406 original size:3 final size:3
Alignment explanation
Indices: 42906398--42906433 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
42906388 AGTTATTAAG
* *
42906398 TTA TTA TTA TTG TTA TTA TTA TCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
42906434 CTATATATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:42906583 original size:17 final size:17
Alignment explanation
Indices: 42906552--42906595 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
42906542 CATAACTTTT
*
42906552 ATATACA-TATATATAC
1 ATATACATTTTATATAC
*
42906568 ATTTACATTTTATATAC
1 ATATACATTTTATATAC
42906585 ATATACATTTT
1 ATATACATTTT
42906596 TTATTTCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATACATTTTATATAC
Found at i:42906799 original size:30 final size:31
Alignment explanation
Indices: 42906747--42906804 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
42906737 ATTATTTGTT
*
42906747 TATATATATGTAATTATCTTTTT-TATAATC
1 TATATATATGTAATAATCTTTTTATATAATC
42906777 TATATATATGTATATAAT-TTTTTATATA
1 TATATATATGTA-ATAATCTTTTTATATA
42906805 TGTACATGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.57
Consensus pattern (31 bp):
TATATATATGTAATAATCTTTTTATATAATC
Found at i:42909933 original size:20 final size:19
Alignment explanation
Indices: 42909897--42909939 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
42909887 CCATATTTGT
*
42909897 ATTATTTTCTCAAAATTTTA
1 ATTATTTTCT-AAAAATTTA
42909917 ATTATTTT-TAAATAATTTA
1 ATTATTTTCTAAA-AATTTA
42909936 ATTA
1 ATTA
42909940 AAAGTGATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 10 0.48
20 8 0.38
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTATTTTCTAAAAATTTA
Found at i:42914684 original size:117 final size:117
Alignment explanation
Indices: 42914476--42914947 Score: 822
Period size: 117 Copynumber: 4.0 Consensus size: 117
42914466 GAAACGTTTA
42914476 TAATAGAAGAAGAAAAGGTTAATTATAAGGTTGATATTTCCATTGGACTAACCCTCGACTCCACT
1 TAATAGAAGAAGAAAAGGTTAATTATAAGGTTGATATTTCCATTGGACTAACCCTCGACTCCACT
* *
42914541 AGCTAGACAGGTCATAACAACCACAACATGATACGTTTATACTCCTTAACCT
66 AGCTAGACAAGTCATAACAACCACAACATGATACATTTATACTCCTTAACCT
*
42914593 TAATAGAAGAAGAAAAGGTTAATTATAAGGTTGATATTTCCATTGGACTAACCCTTGACTCCACT
1 TAATAGAAGAAGAAAAGGTTAATTATAAGGTTGATATTTCCATTGGACTAACCCTCGACTCCACT
*
42914658 AGCTAGACAAGTCATAACAACGACAACATGATACATTTATACTCCTTAACCT
66 AGCTAGACAAGTCATAACAACCACAACATGATACATTTATACTCCTTAACCT
*
42914710 TAATAG-AGAAGAAAGGGTTAATTATAAGGTTGATATTTCCATTGGACTAACCCTCGACTCCACT
1 TAATAGAAGAAGAAAAGGTTAATTATAAGGTTGATATTTCCATTGGACTAACCCTCGACTCCACT
* *
42914774 AGCTAGACAGGTCATAACAACGACAACATGATACATTTATACTCCTTAACCT
66 AGCTAGACAAGTCATAACAACCACAACATGATACATTTATACTCCTTAACCT
* * *
42914826 TAATAGAAGAAGAAAGGGTTAATTATAAGATTGATATTTCCATTAGACTAACCCTCGACTCCACT
1 TAATAGAAGAAGAAAAGGTTAATTATAAGGTTGATATTTCCATTGGACTAACCCTCGACTCCACT
*
42914891 AGCTAGAC-AGATCATAACAACCACAACATGATACATTTATACTTCTTAACCT
66 AGCTAGACAAG-TCATAACAACCACAACATGATACATTTATACTCCTTAACCT
42914943 TAATA
1 TAATA
42914948 AGATAAATCT
Statistics
Matches: 341, Mismatches: 12, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
116 114 0.33
117 227 0.67
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (117 bp):
TAATAGAAGAAGAAAAGGTTAATTATAAGGTTGATATTTCCATTGGACTAACCCTCGACTCCACT
AGCTAGACAAGTCATAACAACCACAACATGATACATTTATACTCCTTAACCT
Found at i:42914890 original size:233 final size:234
Alignment explanation
Indices: 42914476--42914947 Score: 840
Period size: 233 Copynumber: 2.0 Consensus size: 234
42914466 GAAACGTTTA
42914476 TAATAGAAGAAGAAAAGGTTAATTATAAGGTTGATATTTCCATTGGACTAACCCTCGACTCCACT
1 TAATAGAAGAAGAAAAGGTTAATTATAAGGTTGATATTTCCATTGGACTAACCCTCGACTCCACT
*
42914541 AGCTAGACAGGTCATAACAACCACAACATGATACGTTTATACTCCTTAACCTTAATAGAAGAAGA
66 AGCTAGACAGGTCATAACAACCACAACATGATACATTTATACTCCTTAACCTTAATAGAAGAAGA
* * *
42914606 AAAGGTTAATTATAAGGTTGATATTTCCATTGGACTAACCCTTGACTCCACTAGCTAGACA-AGT
131 AAAGGTTAATTATAAGATTGATATTTCCATTAGACTAACCCTCGACTCCACTAGCTAGACAGA-T
*
42914670 CATAACAACGACAACATGATACATTTATACTCCTTAACCT
195 CATAACAACCACAACATGATACATTTATACTCCTTAACCT
*
42914710 TAATAG-AGAAGAAAGGGTTAATTATAAGGTTGATATTTCCATTGGACTAACCCTCGACTCCACT
1 TAATAGAAGAAGAAAAGGTTAATTATAAGGTTGATATTTCCATTGGACTAACCCTCGACTCCACT
*
42914774 AGCTAGACAGGTCATAACAACGACAACATGATACATTTATACTCCTTAACCTTAATAGAAGAAGA
66 AGCTAGACAGGTCATAACAACCACAACATGATACATTTATACTCCTTAACCTTAATAGAAGAAGA
*
42914839 AAGGGTTAATTATAAGATTGATATTTCCATTAGACTAACCCTCGACTCCACTAGCTAGACAGATC
131 AAAGGTTAATTATAAGATTGATATTTCCATTAGACTAACCCTCGACTCCACTAGCTAGACAGATC
*
42914904 ATAACAACCACAACATGATACATTTATACTTCTTAACCT
196 ATAACAACCACAACATGATACATTTATACTCCTTAACCT
42914943 TAATA
1 TAATA
42914948 AGATAAATCT
Statistics
Matches: 228, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
233 221 0.97
234 7 0.03
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (234 bp):
TAATAGAAGAAGAAAAGGTTAATTATAAGGTTGATATTTCCATTGGACTAACCCTCGACTCCACT
AGCTAGACAGGTCATAACAACCACAACATGATACATTTATACTCCTTAACCTTAATAGAAGAAGA
AAAGGTTAATTATAAGATTGATATTTCCATTAGACTAACCCTCGACTCCACTAGCTAGACAGATC
ATAACAACCACAACATGATACATTTATACTCCTTAACCT
Found at i:42915725 original size:6 final size:6
Alignment explanation
Indices: 42915714--42915745 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
42915704 CTTTTTCAGA
42915714 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TT
42915746 CAATCACTCA
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:42916740 original size:10 final size:9
Alignment explanation
Indices: 42916718--42916788 Score: 81
Period size: 9 Copynumber: 7.7 Consensus size: 9
42916708 AAAATTTATT
42916718 TTAAAAA-A
1 TTAAAAATA
42916726 TTAAAAATCA
1 TTAAAAAT-A
42916736 TTAAAAATA
1 TTAAAAATA
42916745 TTAAAAATA
1 TTAAAAATA
42916754 TATAAAAATTA
1 T-TAAAAA-TA
*
42916765 TTGAAAATA
1 TTAAAAATA
* *
42916774 GTGAAAATA
1 TTAAAAATA
42916783 TTAAAA
1 TTAAAA
42916789 TTTTAATCAA
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
8 7 0.13
9 25 0.45
10 20 0.36
11 3 0.05
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.31
Consensus pattern (9 bp):
TTAAAAATA
Found at i:42916747 original size:19 final size:18
Alignment explanation
Indices: 42916718--42916788 Score: 81
Period size: 19 Copynumber: 3.8 Consensus size: 18
42916708 AAAATTTATT
42916718 TTAAAAA-ATTAAAAATCA
1 TTAAAAATATTAAAAAT-A
42916736 TTAAAAATATTAAAAATA
1 TTAAAAATATTAAAAATA
*
42916754 TATAAAAATTATTGAAAATA
1 T-TAAAAA-TATTAAAAATA
* *
42916774 GTGAAAATATTAAAA
1 TTAAAAATATTAAAA
42916789 TTTTAATCAA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
18 16 0.35
19 20 0.43
20 10 0.22
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.31
Consensus pattern (18 bp):
TTAAAAATATTAAAAATA
Found at i:42916780 original size:29 final size:28
Alignment explanation
Indices: 42916719--42916788 Score: 88
Period size: 29 Copynumber: 2.5 Consensus size: 28
42916709 AAATTTATTT
*
42916719 TAAAAA-ATTAAAAATCATTAAAAATAT
1 TAAAAATATTAAAAATCATTAAAAATAG
* *
42916746 TAAAAATATATAAAAATTATTGAAAATAG
1 TAAAAATAT-TAAAAATCATTAAAAATAG
*
42916775 TGAAAATATTAAAA
1 TAAAAATATTAAAA
42916789 TTTTAATCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 6 0.16
28 7 0.19
29 24 0.65
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.30
Consensus pattern (28 bp):
TAAAAATATTAAAAATCATTAAAAATAG
Found at i:42917649 original size:40 final size:40
Alignment explanation
Indices: 42917592--42917695 Score: 138
Period size: 40 Copynumber: 2.6 Consensus size: 40
42917582 ATACGCATCA
* *
42917592 TGTTAGCACTACGGTGCTCCTGATAGTACT-TTTGTACTCC
1 TGTTAGCACTACAGTGCTCCTGATAGCA-TATTTGTACTCC
*
42917632 TGTTAGCATTACAGTGCTCCTGATAGCATATTTGTACTCC
1 TGTTAGCACTACAGTGCTCCTGATAGCATATTTGTACTCC
* * *
42917672 TGTTTGCACTAGAGTGCCCCTGAT
1 TGTTAGCACTACAGTGCTCCTGAT
42917696 TGCACATATG
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
39 1 0.02
40 55 0.98
ACGTcount: A:0.19, C:0.24, G:0.20, T:0.37
Consensus pattern (40 bp):
TGTTAGCACTACAGTGCTCCTGATAGCATATTTGTACTCC
Found at i:42917671 original size:20 final size:19
Alignment explanation
Indices: 42917608--42917673 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
42917598 CACTACGGTG
*
42917608 CTCCTGATAGTACTTTTGTA
1 CTCCTGATAGCA-TTTTGTA
* ** *
42917628 CTCCTGTTAGCATTACAGTG
1 CTCCTGATAGCATT-TTGTA
42917648 CTCCTGATAGCATATTTGTA
1 CTCCTGATAGCAT-TTTGTA
42917668 CTCCTG
1 CTCCTG
42917674 TTTGCACTAG
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
19 2 0.06
20 32 0.91
21 1 0.03
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.39
Consensus pattern (19 bp):
CTCCTGATAGCATTTTGTA
Found at i:42924736 original size:5 final size:5
Alignment explanation
Indices: 42924728--42924756 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
42924718 TATTTTTATT
42924728 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
42924757 TACTTAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:42941807 original size:13 final size:13
Alignment explanation
Indices: 42941786--42941820 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
42941776 ATAGTAAATA
42941786 TTCAAAAATATTT
1 TTCAAAAATATTT
*
42941799 TTCATAAATATTT
1 TTCAAAAATATTT
42941812 TT-AAAAATA
1 TTCAAAAATA
42941821 AATCTTTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (13 bp):
TTCAAAAATATTT
Found at i:42942276 original size:26 final size:26
Alignment explanation
Indices: 42942247--42942296 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
42942237 TTTCGTCCGC
* * * *
42942247 CCAACAAAACCAAACAAACCAAAAGA
1 CCAAAAAAACAAAAAAAAACAAAAGA
42942273 CCAAAAAAACAAAAAAAAACAAAA
1 CCAAAAAAACAAAAAAAAACAAAA
42942297 AATAAAAACA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.74, C:0.24, G:0.02, T:0.00
Consensus pattern (26 bp):
CCAAAAAAACAAAAAAAAACAAAAGA
Found at i:42947032 original size:11 final size:11
Alignment explanation
Indices: 42947016--42947053 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
42947006 TAAATAATAA
42947016 TCAATATTTTT
1 TCAATATTTTT
42947027 TCAATATTTTT
1 TCAATATTTTT
*
42947038 TTAAT-TTTTT
1 TCAATATTTTT
*
42947048 ACAATA
1 TCAATA
42947054 ATAGATAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.61
Consensus pattern (11 bp):
TCAATATTTTT
Found at i:42948011 original size:13 final size:13
Alignment explanation
Indices: 42947995--42948068 Score: 60
Period size: 13 Copynumber: 5.4 Consensus size: 13
42947985 AAAGTTTAAG
42947995 AAAATAAAAAAAT
1 AAAATAAAAAAAT
* * *
42948008 AAAACAATTAAAAC
1 AAAATAA-AAAAAT
*
42948022 AAAATTAAAAAGAAAG
1 AAAA-T-AAAA-AAAT
42948038 ATAAAT-AAAAAAT
1 A-AAATAAAAAAAT
42948051 AAAATAAAAAAAT
1 AAAATAAAAAAAT
42948064 AAAAT
1 AAAAT
42948069 GATAATAATA
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
12 4 0.08
13 22 0.46
14 11 0.23
15 1 0.02
16 7 0.15
17 3 0.06
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.16
Consensus pattern (13 bp):
AAAATAAAAAAAT
Found at i:42948028 original size:48 final size:47
Alignment explanation
Indices: 42947976--42948067 Score: 114
Period size: 48 Copynumber: 1.9 Consensus size: 47
42947966 AAAAGATAAT
* * *
42947976 AATTAAAAA-AAAGTTTAAGAAAATAAAAAAATAAAACAATTAAAACAA
1 AATTAAAAAGAAAGATAAAGAAAA-AAAAAAATAAAA-AAATAAAACAA
* *
42948024 AATTAAAAAGAAAGATAAATAAAAAATAAAATAAAAAAATAAAA
1 AATTAAAAAGAAAGATAAAGAAAAAAAAAAATAAAAAAATAAAA
42948068 TGATAATAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
47 7 0.18
48 20 0.53
49 11 0.29
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.17
Consensus pattern (47 bp):
AATTAAAAAGAAAGATAAAGAAAAAAAAAAATAAAAAAATAAAACAA
Found at i:42948210 original size:12 final size:12
Alignment explanation
Indices: 42948195--42948233 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
42948185 AATTAGTAAA
42948195 ATAATAAATAAT
1 ATAATAAATAAT
*
42948207 ATAATAAAGAAT
1 ATAATAAATAAT
*
42948219 A-AATAAATAAA
1 ATAATAAATAAT
42948230 ATAA
1 ATAA
42948234 AAGAGGTAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (12 bp):
ATAATAAATAAT
Found at i:42948221 original size:19 final size:20
Alignment explanation
Indices: 42948197--42948234 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
42948187 TTAGTAAAAT
*
42948197 AATAAAT-AATATAATAAAG
1 AATAAATAAATAAAATAAAG
42948216 AATAAATAAATAAAATAAA
1 AATAAATAAATAAAATAAA
42948235 AGAGGTAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (20 bp):
AATAAATAAATAAAATAAAG
Found at i:42948787 original size:178 final size:178
Alignment explanation
Indices: 42948485--42948845 Score: 553
Period size: 178 Copynumber: 2.0 Consensus size: 178
42948475 TGGCCTGGGC
*
42948485 GCCGTGTCTCTCACACGACCGTGTCCCTTGCCCGTGTAACTCTCTGACGTGATTTAAAATTGAAA
1 GCCGTGTCTCTCACACGACCGTGTCCCTTGCCCGTGTAACTCTCTGACGTGATTTAAAACTGAAA
*
42948550 AAAATTAGCTCATGGTTTCACACGGCCTAAGACACACCCGTATGCCCAGGCCGTGTGTGTTTTCC
66 AAAATTAGCTCATGGTTTCACACGGCCTAAGACACACCCGTATGCCCAGGCCATGTGTGTTTTCC
*
42948615 TTCACTTCTCCCACGCCCATGTGAGATCTCATACGCTCGTGTGGCCAG
131 TTCACTTCTCCCACGCCCATGTGAGATCCCATACGCTCGTGTGGCCAG
* * * * *
42948663 GCCGTGTCTCTCACACGGCTGTGTGCCTTGCTCGTGTAACTCTCTGACTTGATTTAAAACTGAAA
1 GCCGTGTCTCTCACACGACCGTGTCCCTTGCCCGTGTAACTCTCTGACGTGATTTAAAACTGAAA
* * * * *
42948728 AAAATTAGCTCCA-GGTTTCACACGGCCTAGGACACGCCCGTGTGTCTAGGCCATGTGTGTTTTC
66 AAAATTAGCT-CATGGTTTCACACGGCCTAAGACACACCCGTATGCCCAGGCCATGTGTGTTTTC
* * * *
42948792 CTTCGCTTCTCTCACGCTCATGTGAGATCCCATATGCTCGTGTGGCCAG
130 CTTCACTTCTCCCACGCCCATGTGAGATCCCATACGCTCGTGTGGCCAG
42948841 GCCGT
1 GCCGT
42948846 ATAGGTCACA
Statistics
Matches: 165, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
178 163 0.99
179 2 0.01
ACGTcount: A:0.19, C:0.30, G:0.22, T:0.29
Consensus pattern (178 bp):
GCCGTGTCTCTCACACGACCGTGTCCCTTGCCCGTGTAACTCTCTGACGTGATTTAAAACTGAAA
AAAATTAGCTCATGGTTTCACACGGCCTAAGACACACCCGTATGCCCAGGCCATGTGTGTTTTCC
TTCACTTCTCCCACGCCCATGTGAGATCCCATACGCTCGTGTGGCCAG
Done.