Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 92 of 187
Found at i:27486353 original size:81 final size:82
Alignment explanation
Indices: 27486110--27486357 Score: 308
Period size: 81 Copynumber: 3.1 Consensus size: 82
27486100 AAAATAGTCA
* ** * * *
27486110 TTTACCCT-CTAGGGGAATTACGGTCATTTTACTTTACAGG-GGTATTTCGATCATTTAACCCTA
1 TTTACCCTAC-AGGGGCATTACGGTCATTTTACCCTATAGGAGGTTTTTCGATCATTTTACCCTA
*
27486173 TAGGGGTATTACGGTCAT
65 TAGGGGTATTACGGTTAT
* * * *
27486191 TTTACCCTACAGGGGCATTACGGTCATTTTACCCTATGGGGGGTTTTT-GATTATTTTACCCTAC
1 TTTACCCTACAGGGGCATTACGGTCATTTTACCCTATAGGAGGTTTTTCGATCATTTTACCCTAT
27486255 AGGGGTATTACGGTTAT
66 AGGGGTATTACGGTTAT
* *
27486272 TTTACCCTACGGGGGCATTATGGAT-ATTTTACCCTATAGGAGGTTTTTCGATCATTTTACCCTA
1 TTTACCCTACAGGGGCATTACGG-TCATTTTACCCTATAGGAGGTTTTTCGATCATTTTACCCTA
* *
27486336 TA-GGGTATTATGATTAT
65 TAGGGGTATTACGGTTAT
27486353 TTTAC
1 TTTAC
27486358 AAATATTGGG
Statistics
Matches: 145, Mismatches: 18, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
81 122 0.84
82 23 0.16
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.39
Consensus pattern (82 bp):
TTTACCCTACAGGGGCATTACGGTCATTTTACCCTATAGGAGGTTTTTCGATCATTTTACCCTAT
AGGGGTATTACGGTTAT
Found at i:27492146 original size:28 final size:28
Alignment explanation
Indices: 27492111--27492165 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
27492101 AAAATTGTCA
*
27492111 TTAAACTA-TTCAGAATTTTTCATTTAAG
1 TTAAACTATTTCAAAATTTTT-ATTTAAG
*
27492139 TTAAACTATTTGAAAATTTTTATTTAA
1 TTAAACTATTTCAAAATTTTTATTTAA
27492166 ATAATTGAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.49
Consensus pattern (28 bp):
TTAAACTATTTCAAAATTTTTATTTAAG
Found at i:27492775 original size:18 final size:19
Alignment explanation
Indices: 27492740--27492779 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
27492730 ACTTCTATTT
27492740 ATTAAATAAAATTTAAATA
1 ATTAAATAAAATTTAAATA
*
27492759 ATTAAATTAAA-TTAAATA
1 ATTAAATAAAATTTAAATA
27492777 ATT
1 ATT
27492780 TATCTATTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
ATTAAATAAAATTTAAATA
Found at i:27493113 original size:23 final size:24
Alignment explanation
Indices: 27493084--27493131 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 24
27493074 TTGTGAAACG
* *
27493084 TTATAAAATAAAAAT-AA-TATTT
1 TTATTAAACAAAAATAAAGTATTT
27493106 TTATTAAACAAAAATAAAGTATTT
1 TTATTAAACAAAAATAAAGTATTT
27493130 TT
1 TT
27493132 TTCCGCATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 13 0.59
23 2 0.09
24 7 0.32
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (24 bp):
TTATTAAACAAAAATAAAGTATTT
Found at i:27496442 original size:17 final size:17
Alignment explanation
Indices: 27496422--27496502 Score: 90
Period size: 17 Copynumber: 4.4 Consensus size: 17
27496412 TATCTCTCTA
27496422 CTTTGCTTATTGCATTT
1 CTTTGCTTATTGCATTT
*
27496439 CTTTGCTTATTAGTTATCTCTTT
1 CTTTGCTTATT-G----C-ATTT
27496462 ACTTTGCTTATTGCATTT
1 -CTTTGCTTATTGCATTT
27496480 CTTTGCTTATTGCATTT
1 CTTTGCTTATTGCATTT
27496497 CTTTGC
1 CTTTGC
27496503 ATTTAATCTA
Statistics
Matches: 55, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
17 34 0.62
18 4 0.07
19 1 0.02
22 1 0.02
23 4 0.07
24 11 0.20
ACGTcount: A:0.12, C:0.19, G:0.11, T:0.58
Consensus pattern (17 bp):
CTTTGCTTATTGCATTT
Found at i:27496465 original size:41 final size:41
Alignment explanation
Indices: 27496407--27496490 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
27496397 ATATCAAGTG
27496407 TTAGTTATCTCTCTACTTTGCTTATTGCATTTCTTTGCTTA
1 TTAGTTATCTCTCTACTTTGCTTATTGCATTTCTTTGCTTA
*
27496448 TTAGTTATCTCTTTACTTTGCTTATTGCATTTCTTTGCTTA
1 TTAGTTATCTCTCTACTTTGCTTATTGCATTTCTTTGCTTA
27496489 TT
1 TT
27496491 GCATTTCTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.14, C:0.18, G:0.10, T:0.58
Consensus pattern (41 bp):
TTAGTTATCTCTCTACTTTGCTTATTGCATTTCTTTGCTTA
Found at i:27499045 original size:66 final size:66
Alignment explanation
Indices: 27498959--27499111 Score: 218
Period size: 66 Copynumber: 2.3 Consensus size: 66
27498949 GTTATACCGA
* *
27498959 TGAGGCACTAGGTGTCAAACTATGTGATAAGCATTCGACCCAACTATTTGCTTCGGATTTATCTA
1 TGAGGCATTGGGTGTCAAACTATGTGATAAGCATTCGACCCAACTATTTGCTTCGGATTTATC-A
27499024 G-
65 GC
* * * ** *
27499025 TGAGGCTTTGGGTGTCAAACTATTTGATAAGCGTTCGATGCAACTATTTGCTTCGGATTTATCCG
1 TGAGGCATTGGGTGTCAAACTATGTGATAAGCATTCGACCCAACTATTTGCTTCGGATTTATCAG
27499090 C
66 C
27499091 TGAGGCATTGGGTGTCAAACT
1 TGAGGCATTGGGTGTCAAACT
27499112 GGTGTATTGG
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
65 1 0.01
66 76 0.99
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (66 bp):
TGAGGCATTGGGTGTCAAACTATGTGATAAGCATTCGACCCAACTATTTGCTTCGGATTTATCAG
C
Found at i:27509424 original size:43 final size:43
Alignment explanation
Indices: 27509375--27509486 Score: 138
Period size: 43 Copynumber: 2.6 Consensus size: 43
27509365 TGTTATCGTG
* *
27509375 TAAGACCACGTCTGAGACGTTGGCATCGACT-TGTGTTTACATC
1 TAAGACCACGTCTGGGACGTTGGCATCG-CTATGTGATTACATC
** * *
27509418 TAAGACCTTGTCTGGGACAG-TGGCATCGTTATGTGATTACATG
1 TAAGACCACGTCTGGGAC-GTTGGCATCGCTATGTGATTACATC
27509461 TAAGACCACGTCTGGGACGTTGGCAT
1 TAAGACCACGTCTGGGACGTTGGCAT
27509487 TGTACGAAAT
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
42 2 0.03
43 55 0.95
44 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (43 bp):
TAAGACCACGTCTGGGACGTTGGCATCGCTATGTGATTACATC
Found at i:27512745 original size:24 final size:24
Alignment explanation
Indices: 27512718--27512769 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
27512708 TGCGTTTATG
27512718 ATTTCAGAATA-AAATACAGAAGCA
1 ATTTCA-AATATAAATACAGAAGCA
* * *
27512742 ATTTCAATTATAGATACAGAGGCA
1 ATTTCAAATATAAATACAGAAGCA
27512766 ATTT
1 ATTT
27512770 TAGATACAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.29
Consensus pattern (24 bp):
ATTTCAAATATAAATACAGAAGCA
Found at i:27526048 original size:14 final size:15
Alignment explanation
Indices: 27526029--27526061 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
27526019 TAATAGTAAG
27526029 AATAATACTAAAAA-
1 AATAATACTAAAAAT
27526043 AATAATACTAAAAAT
1 AATAATACTAAAAAT
27526058 AATA
1 AATA
27526062 GAAATATAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (15 bp):
AATAATACTAAAAAT
Found at i:27526057 original size:12 final size:12
Alignment explanation
Indices: 27526013--27526061 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
27526003 CCAGTAAAAT
* *
27526013 TAAAGATAATAG
1 TAAAAATAATAC
*
27526025 TAAGAATAATAC
1 TAAAAATAATAC
27526037 TAAAAAAATAATAC
1 T--AAAAATAATAC
27526051 TAAAAATAATA
1 TAAAAATAATA
27526062 GAAATATAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
12 20 0.65
14 11 0.35
ACGTcount: A:0.65, C:0.04, G:0.06, T:0.24
Consensus pattern (12 bp):
TAAAAATAATAC
Found at i:27533253 original size:34 final size:33
Alignment explanation
Indices: 27533213--27533294 Score: 112
Period size: 34 Copynumber: 2.5 Consensus size: 33
27533203 TCTGATATGG
27533213 TATGACATTTTGATACGA-TATATGTTTCTGAAAA
1 TATGACATTTTGAT-CGAGTATATGTTT-TGAAAA
* * *
27533247 TATGACATTATGATCTAGTATATGTTTTGGAAA
1 TATGACATTTTGATCGAGTATATGTTTTGAAAA
27533280 TATGACATTTTGATC
1 TATGACATTTTGATC
27533295 TGACATACAT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
33 21 0.49
34 22 0.51
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.43
Consensus pattern (33 bp):
TATGACATTTTGATCGAGTATATGTTTTGAAAA
Found at i:27533286 original size:33 final size:33
Alignment explanation
Indices: 27533213--27533295 Score: 114
Period size: 33 Copynumber: 2.5 Consensus size: 33
27533203 TCTGATATGG
*
27533213 TATGACATTTTGATACGATATATGTTTCTGAAAA
1 TATGACATTTTGAT-CTATATATGTTTCTGAAAA
* *
27533247 TATGACATTATGATCTAGTATATGTTT-TGGAAA
1 TATGACATTTTGATCTA-TATATGTTTCTGAAAA
27533280 TATGACATTTTGATCT
1 TATGACATTTTGATCT
27533296 GACATACATT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
33 22 0.50
34 22 0.50
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (33 bp):
TATGACATTTTGATCTATATATGTTTCTGAAAA
Found at i:27533559 original size:19 final size:18
Alignment explanation
Indices: 27533535--27533575 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
27533525 TTTTCTCGAC
27533535 TTTTGGGACTGTAATTTGT
1 TTTTGGG-CTGTAATTTGT
* *
27533554 TTTTGGGCTTTGATTTGT
1 TTTTGGGCTGTAATTTGT
27533572 TTTT
1 TTTT
27533576 TTTTGTCGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.10, C:0.05, G:0.24, T:0.61
Consensus pattern (18 bp):
TTTTGGGCTGTAATTTGT
Found at i:27537501 original size:21 final size:20
Alignment explanation
Indices: 27537477--27537520 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
27537467 TATTTTTATC
27537477 ATTTTAATCA-AAATTTTATTT
1 ATTTTAAT-ATAAA-TTTATTT
*
27537498 ATTTTTATATAAATTTATTT
1 ATTTTAATATAAATTTATTT
27537518 ATT
1 ATT
27537521 AAATATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTTTAATATAAATTTATTT
Found at i:27540794 original size:20 final size:20
Alignment explanation
Indices: 27540769--27540809 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
27540759 AATTAATTGT
27540769 ATATATTAATAAAATATTAA
1 ATATATTAATAAAATATTAA
** *
27540789 ATATATTTTTAAAATTTTAA
1 ATATATTAATAAAATATTAA
27540809 A
1 A
27540810 ACAATTTGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATATATTAATAAAATATTAA
Found at i:27548144 original size:47 final size:47
Alignment explanation
Indices: 27548091--27548235 Score: 133
Period size: 47 Copynumber: 3.1 Consensus size: 47
27548081 TCATATAAAA
*
27548091 ATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATT
1 ATATTTATTATTAAGAATTTTATGAAATTATATATAATTATTAAATT
** * *
27548138 ATATTTA--A-TAATTATTATT-TTAAATTATACA-AATTCATATAAGA--
1 ATATTTATTATTAAGAATT-TTATGAAATTATATATAATT-AT-TAA-ATT
* * *
27548182 AAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATT
1 ATATTTATTATTAAGAATTTTATGAAATTATATATAATTATTAAATT
27548229 ATATTTA
1 ATATTTA
27548236 ATAATATTTA
Statistics
Matches: 74, Mismatches: 13, Indels: 22
0.68 0.12 0.20
Matches are distributed among these distances:
43 3 0.04
44 24 0.32
45 7 0.09
46 7 0.09
47 30 0.41
48 3 0.04
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (47 bp):
ATATTTATTATTAAGAATTTTATGAAATTATATATAATTATTAAATT
Found at i:27548188 original size:44 final size:43
Alignment explanation
Indices: 27548140--27548279 Score: 117
Period size: 44 Copynumber: 3.1 Consensus size: 43
27548130 ATTAAATTAT
27548140 ATTTAATAATTATTATTTTAAATTATACAAATTCATATAAGAAA
1 ATTTAATAA-TATTATTTTAAATTATACAAATTCATATAAGAAA
* * * * *
27548184 ATTTATTATCAAGAATT-TTATGAAATTATATATTATT-AT-TAA-ATTAT
1 ATTTA--AT-AA-TATTATT-TTAAATTATACA-AATTCATATAAGA--AA
27548231 ATTTAATAATATTTATTTTAAATTATACAAATTCATATAAGAAA
1 ATTTAATAATA-TTATTTTAAATTATACAAATTCATATAAGAAA
27548275 ATTTA
1 ATTTA
27548280 TTAGTAAGAG
Statistics
Matches: 73, Mismatches: 11, Indels: 24
0.68 0.10 0.22
Matches are distributed among these distances:
43 4 0.05
44 27 0.37
45 8 0.11
46 8 0.11
47 23 0.32
48 3 0.04
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (43 bp):
ATTTAATAATATTATTTTAAATTATACAAATTCATATAAGAAA
Found at i:27548212 original size:91 final size:90
Alignment explanation
Indices: 27548077--27548340 Score: 406
Period size: 91 Copynumber: 2.8 Consensus size: 90
27548067 TGATTTTAGT
*
27548077 AAATTCATATAA-AAATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1 AAATTCATATAAGAAA-ATTTATTA-TAAGAATTTTATGAAATTATATATTATTATTAAATTATA
27548141 TTTAATAATTATTATTTTAAATTATAC
64 TTTAATAATTATTATTTTAAATTATAC
27548168 AAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATAT
1 AAATTCATATAAGAAAATTTATTAT-AAGAATTTTATGAAATTATATATTATTATTAAATTATAT
27548233 TTAATAA-TATTTATTTTAAATTATAC
65 TTAATAATTA-TTATTTTAAATTATAC
*
27548259 AAATTCATATAAGAAAATTTATTAGTAAGAGTTTTTATGAAATTATATATTTATTATTAAAATTT
1 AAATTCATATAAGAAAATTTATTA-TAAGA-ATTTTATGAAATTATATA-TTATTATT-AAA-TT
27548324 ATATTTTAATAATTATT
61 ATA-TTTAATAATTATT
27548341 TTNNNNNNNN
Statistics
Matches: 161, Mismatches: 2, Indels: 15
0.90 0.01 0.08
Matches are distributed among these distances:
90 3 0.02
91 109 0.68
92 21 0.13
93 8 0.05
94 3 0.02
95 5 0.03
96 10 0.06
97 2 0.01
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (90 bp):
AAATTCATATAAGAAAATTTATTATAAGAATTTTATGAAATTATATATTATTATTAAATTATATT
TAATAATTATTATTTTAAATTATAC
Found at i:27548249 original size:47 final size:47
Alignment explanation
Indices: 27548107--27548250 Score: 115
Period size: 47 Copynumber: 3.1 Consensus size: 47
27548097 ATTATTAAGA
*
27548107 ATTTTATGAAATTATATATCATTATTAAATTATATTTAATAAT-TATT
1 ATTTTATGAAATTATATATAATTATTAAATTATATTTAATAATAT-TT
* * * ***
27548154 A-TTT-T-AAATTATACA-AATTCATATAAGA--AAATTT-ATTATCAAGA
1 ATTTTATGAAATTATATATAATT-AT-TAA-ATTATATTTAATAAT-ATTT
*
27548198 ATTTTATGAAATTATATATTATTATTAAATTATATTTAATAATATTT
1 ATTTTATGAAATTATATATAATTATTAAATTATATTTAATAATATTT
27548245 ATTTTA
1 ATTTTA
27548251 AATTATACAA
Statistics
Matches: 71, Mismatches: 14, Indels: 24
0.65 0.13 0.22
Matches are distributed among these distances:
43 7 0.10
44 17 0.24
45 8 0.11
46 8 0.11
47 24 0.34
48 7 0.10
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (47 bp):
ATTTTATGAAATTATATATAATTATTAAATTATATTTAATAATATTT
Found at i:27548592 original size:18 final size:17
Alignment explanation
Indices: 27548564--27548598 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
27548554 ATTATTAAGA
*
27548564 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
27548581 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
27548599 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:27548656 original size:120 final size:120
Alignment explanation
Indices: 27548443--27548972 Score: 988
Period size: 120 Copynumber: 4.4 Consensus size: 120
27548433 NNNNNNNNNN
* *
27548443 AATTTTATTAAATCATATATTTTAATTAAAATGTATTTAATAATAATTATTTCAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
27548508 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
*
27548563 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTG
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
27548628 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
*
27548683 AATTTTATTAAATAATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
27548748 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
* *
27548803 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATTATTATTTCAAATCATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
*
27548868 ATAGTATCATATAATATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
*
27548923 AATTTTATTAAATTATATGTTTTAATTAAAATATATTTAATAATAATTAT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTAT
27548973 GTTAAAATAT
Statistics
Matches: 399, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 399 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
Found at i:27548733 original size:14 final size:16
Alignment explanation
Indices: 27548693--27548734 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 16
27548683 AATTTTATTA
27548693 AATAATATATTTTAATT
1 AATAATATA-TTTAATT
27548710 AA-AATATATTTAA-T
1 AATAATATATTTAATT
27548724 AATAAT-TATTT
1 AATAATATATTT
27548735 CAAATTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 8 0.33
15 8 0.33
16 6 0.25
17 2 0.08
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AATAATATATTTAATT
Found at i:27548832 original size:18 final size:17
Alignment explanation
Indices: 27548804--27548838 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
27548794 ATTATTAAGA
*
27548804 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
27548821 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
27548839 TTAATAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:27548952 original size:18 final size:17
Alignment explanation
Indices: 27548925--27548958 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
27548915 TTATTAAGAA
*
27548925 TTTTATTAAATTATATG
1 TTTTATTAAAATATATG
27548942 TTTTAATTAAAATATAT
1 TTTT-ATTAAAATATAT
27548959 TTAATAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
TTTTATTAAAATATATG
Found at i:27549173 original size:44 final size:46
Alignment explanation
Indices: 27549110--27549205 Score: 169
Period size: 44 Copynumber: 2.1 Consensus size: 46
27549100 CTATTACACC
*
27549110 TCCATTCCATTCAACCAAACACAAGAA-TA-CTATTACGCCTCTAT
1 TCCATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTAT
27549154 TCCATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTAT
1 TCCATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTAT
27549200 TCCATT
1 TCCATT
27549206 ACACCTCTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 26 0.53
45 2 0.04
46 21 0.43
ACGTcount: A:0.35, C:0.31, G:0.04, T:0.29
Consensus pattern (46 bp):
TCCATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTAT
Found at i:27549212 original size:16 final size:16
Alignment explanation
Indices: 27549187--27549240 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
27549177 AGAATTACCT
*
27549187 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
*
27549203 ATTACACCTCTATTTC
1 ATTACACCTCTATTCC
27549219 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
27549235 ATTACA
1 ATTACA
27549241 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.26, C:0.33, G:0.02, T:0.39
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:27553240 original size:10 final size:10
Alignment explanation
Indices: 27553219--27553276 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
27553209 GAATCTGTCG
*
27553219 AAAATAAATC
1 AAAATTAATC
*
27553229 AAGATTAATC
1 AAAATTAATC
*
27553239 AAAATTAATTAT
1 AAAATTAA-T-C
*
27553251 AAAATTAATT
1 AAAATTAATC
*
27553261 AAAATTAATT
1 AAAATTAATC
27553271 AAAATT
1 AAAATT
27553277 CAACATGTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
10 32 0.76
11 2 0.05
12 8 0.19
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.34
Consensus pattern (10 bp):
AAAATTAATC
Found at i:27554360 original size:21 final size:21
Alignment explanation
Indices: 27554321--27554360 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
27554311 TTGTTTCTAA
*
27554321 AGAAAAATCCAGTTTCACAGC
1 AGAAAAATCCAGTTCCACAGC
27554342 AGAAAAAT-CAGTGTCCACA
1 AGAAAAATCCAGT-TCCACA
27554361 ACCATAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.45, C:0.23, G:0.15, T:0.17
Consensus pattern (21 bp):
AGAAAAATCCAGTTCCACAGC
Found at i:27554845 original size:25 final size:25
Alignment explanation
Indices: 27554817--27554898 Score: 119
Period size: 25 Copynumber: 3.3 Consensus size: 25
27554807 CAGCTCGAGA
* **
27554817 GAGCTTACCGATATTCAATTCGTAT
1 GAGCTTACCGTTATTCAGCTCGTAT
*
27554842 GAGCTTACCGTTATTCAGGTCGTAT
1 GAGCTTACCGTTATTCAGCTCGTAT
*
27554867 GAGCTTACCGTTATTCAGCTCATAT
1 GAGCTTACCGTTATTCAGCTCGTAT
27554892 GAGCTTA
1 GAGCTTA
27554899 TCAATTACAG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 52 1.00
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (25 bp):
GAGCTTACCGTTATTCAGCTCGTAT
Found at i:27556114 original size:25 final size:25
Alignment explanation
Indices: 27556085--27556137 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
27556075 GTAGTTGACC
27556085 GCAAATTGTAATTGGCAGCTTT-TCT
1 GCAAATTGTAATTGGCAG-TTTATCT
*
27556110 GCAAATTGTTATTGGCAGTTTATCT
1 GCAAATTGTAATTGGCAGTTTATCT
27556135 GCA
1 GCA
27556138 TTTCTGGTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 3 0.12
25 23 0.88
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.40
Consensus pattern (25 bp):
GCAAATTGTAATTGGCAGTTTATCT
Found at i:27563561 original size:20 final size:20
Alignment explanation
Indices: 27563472--27563561 Score: 58
Period size: 20 Copynumber: 4.4 Consensus size: 20
27563462 TTTTCTACCT
* ** *
27563472 AAAAAACATGAGGGAGTACA
1 AAAAAAAATGAGAAAGTATA
*
27563492 AAAAAATATGAGGAAA-TATA
1 AAAAAAAATGA-GAAAGTATA
* * *
27563512 AAAAAAATTGTGAGAATGTGCT-
1 AAAAAAA--ATGAGAAAGT-ATA
27563534 AAAAAAAATGAGAAAGTATA
1 AAAAAAAATGAGAAAGTATA
27563554 AAAAAAAA
1 AAAAAAAA
27563562 AAAAGTAAAA
Statistics
Matches: 53, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
19 1 0.02
20 35 0.66
21 5 0.09
22 11 0.21
23 1 0.02
ACGTcount: A:0.62, C:0.03, G:0.18, T:0.17
Consensus pattern (20 bp):
AAAAAAAATGAGAAAGTATA
Found at i:27569017 original size:44 final size:44
Alignment explanation
Indices: 27568954--27569042 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
27568944 GCCAGAAAGT
27568954 AAACACATTTAAACAACAAAATTGCCACAGAAAGGCAATACGAG
1 AAACACATTTAAACAACAAAATTGCCACAGAAAGGCAATACGAG
27568998 AAACACATTTAAACAACAAAATTGCCACAGAAAGGCAATACGAG
1 AAACACATTTAAACAACAAAATTGCCACAGAAAGGCAATACGAG
27569042 A
1 A
27569043 GTTTTAAAGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.53, C:0.20, G:0.13, T:0.13
Consensus pattern (44 bp):
AAACACATTTAAACAACAAAATTGCCACAGAAAGGCAATACGAG
Found at i:27573377 original size:37 final size:37
Alignment explanation
Indices: 27573327--27573399 Score: 146
Period size: 37 Copynumber: 2.0 Consensus size: 37
27573317 TGGCCTGAGA
27573327 AGAAAACACCATTTTTGTTAGGTTTGAAGCTTTTGGT
1 AGAAAACACCATTTTTGTTAGGTTTGAAGCTTTTGGT
27573364 AGAAAACACCATTTTTGTTAGGTTTGAAGCTTTTGG
1 AGAAAACACCATTTTTGTTAGGTTTGAAGCTTTTGG
27573400 CTCTAATTCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.40
Consensus pattern (37 bp):
AGAAAACACCATTTTTGTTAGGTTTGAAGCTTTTGGT
Found at i:27574921 original size:2 final size:2
Alignment explanation
Indices: 27574914--27574958 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
27574904 TGCTAAGTGT
27574914 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27574956 TA T
1 TA T
27574959 TAGGTCTTGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:27575556 original size:24 final size:25
Alignment explanation
Indices: 27575529--27575579 Score: 86
Period size: 24 Copynumber: 2.1 Consensus size: 25
27575519 GGTGAGTTCG
27575529 ATTTAGTCTTTTT-TTATAATTTTT
1 ATTTAGTCTTTTTCTTATAATTTTT
*
27575553 ATTTAGTCTTTTTCTTGTAATTTTT
1 ATTTAGTCTTTTTCTTATAATTTTT
27575578 AT
1 AT
27575580 GTTTTTGAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 13 0.52
25 12 0.48
ACGTcount: A:0.20, C:0.06, G:0.06, T:0.69
Consensus pattern (25 bp):
ATTTAGTCTTTTTCTTATAATTTTT
Found at i:27584341 original size:39 final size:39
Alignment explanation
Indices: 27584298--27584438 Score: 237
Period size: 39 Copynumber: 3.6 Consensus size: 39
27584288 CATATTCACT
* * *
27584298 TTTAAGCATATATCGCATTACACATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
*
27584337 TTTAAGCATGTATCACAATACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
*
27584376 TTCAAGCATATATCACAATACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
27584415 TTTAAGCATATATCACAATACTCA
1 TTTAAGCATATATCACAATACTCA
27584439 AAAACATGTT
Statistics
Matches: 95, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 95 1.00
ACGTcount: A:0.44, C:0.21, G:0.04, T:0.30
Consensus pattern (39 bp):
TTTAAGCATATATCACAATACTCATATAATCACATAACA
Found at i:27584370 original size:17 final size:17
Alignment explanation
Indices: 27584348--27584409 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 17
27584338 TTAAGCATGT
27584348 ATCACAATACTCATATA
1 ATCACAATACTCATATA
*
27584365 ATCAC-ATAACATTCAAGCATA
1 ATCACAAT-AC--TC-A-TATA
27584386 TATCACAATACTCATATA
1 -ATCACAATACTCATATA
27584404 ATCACA
1 ATCACA
27584410 TAACATTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
16 2 0.06
17 13 0.36
18 3 0.08
19 3 0.08
20 3 0.08
21 3 0.08
22 7 0.19
23 2 0.06
ACGTcount: A:0.47, C:0.24, G:0.02, T:0.27
Consensus pattern (17 bp):
ATCACAATACTCATATA
Found at i:27587619 original size:20 final size:20
Alignment explanation
Indices: 27587559--27587631 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
27587549 CTCCAAAAGT
* * *
27587559 TTTGTTGTTTGAATCGATTA
1 TTTGTTGTTTAAATCAATTC
* * * *
27587579 TCTTGCTATTTGAATCGATTC
1 T-TTGTTGTTTAAATCAATTC
*
27587600 TTTTTTGTTTAAATCAATTC
1 TTTGTTGTTTAAATCAATTC
27587620 TTTGTTGTTTAA
1 TTTGTTGTTTAA
27587632 CTCGATTTAA
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
20 26 0.60
21 17 0.40
ACGTcount: A:0.21, C:0.10, G:0.14, T:0.56
Consensus pattern (20 bp):
TTTGTTGTTTAAATCAATTC
Found at i:27590673 original size:18 final size:18
Alignment explanation
Indices: 27590650--27590686 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
27590640 ACTGAATAGT
*
27590650 CAAAATAAGTACATGTGA
1 CAAAATAAGTAAATGTGA
27590668 CAAAATAAGTAAATGTGA
1 CAAAATAAGTAAATGTGA
27590686 C
1 C
27590687 GAGTGAGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.11, G:0.16, T:0.22
Consensus pattern (18 bp):
CAAAATAAGTAAATGTGA
Found at i:27600086 original size:16 final size:16
Alignment explanation
Indices: 27600067--27600105 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
27600057 TAGAATAAAT
27600067 GCGTAATGAAATAGAG
1 GCGTAATGAAATAGAG
*
27600083 GCGTAATGGAATAGAG
1 GCGTAATGAAATAGAG
27600099 GCGTAAT
1 GCGTAAT
27600106 AGATAATCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.38, C:0.08, G:0.33, T:0.21
Consensus pattern (16 bp):
GCGTAATGAAATAGAG
Found at i:27600166 original size:44 final size:43
Alignment explanation
Indices: 27600091--27600177 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 43
27600081 AGGCGTAATG
*
27600091 GAATAGAGGCGTAATAGATAATCTTTTTTTGGTTGAATGGAATA
1 GAATAGAGGCGTAATAGAT-ATCTTTGTTTGGTTGAATGGAATA
27600135 GAATAGAGGCGTAATAGCAT-TCTTGTGTTTGGTTGAATGGAAT
1 GAATAGAGGCGTAATAG-ATATCTT-TGTTTGGTTGAATGGAAT
27600178 GATGTTATAA
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
43 4 0.10
44 34 0.85
45 2 0.05
ACGTcount: A:0.31, C:0.06, G:0.28, T:0.36
Consensus pattern (43 bp):
GAATAGAGGCGTAATAGATATCTTTGTTTGGTTGAATGGAATA
Found at i:27600302 original size:32 final size:32
Alignment explanation
Indices: 27600266--27600326 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
27600256 TGTTATTGTT
*
27600266 ATTAA-ATTTTAATAAGATTATTAATATAAATA
1 ATTAATATTTTAATAAGATT-TTAAAATAAATA
*
27600298 ATTAATATTTTAATAATATTTTAAAATAA
1 ATTAATATTTTAATAAGATTTTAAAATAA
27600327 TTATTATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
32 13 0.50
33 13 0.50
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (32 bp):
ATTAATATTTTAATAAGATTTTAAAATAAATA
Found at i:27600479 original size:17 final size:17
Alignment explanation
Indices: 27600457--27600490 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
27600447 TTATTATTAA
27600457 ATATAATTTAAAAAAAT
1 ATATAATTTAAAAAAAT
*
27600474 ATATAATTTAATAAAAT
1 ATATAATTTAAAAAAAT
27600491 TCTTAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATATAATTTAAAAAAAT
Found at i:27600510 original size:119 final size:120
Alignment explanation
Indices: 27600317--27600720 Score: 785
Period size: 119 Copynumber: 3.4 Consensus size: 120
27600307 TTAATAATAT
27600317 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
*
27600382 AAATATTCTTATATAAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
27600437 TTTAAAATAATTATTATTAAATATAATTTAA-AAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
27600501 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
27600556 TTTAAAATAATTATTATTAAATATAATTTAA-AAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
27600620 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
27600675 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATT
27600721 CGCCCCACGT
Statistics
Matches: 282, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
119 237 0.84
120 45 0.16
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (120 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
Found at i:27600598 original size:17 final size:17
Alignment explanation
Indices: 27600576--27600609 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
27600566 TTATTATTAA
27600576 ATATAATTTAAAAAAAT
1 ATATAATTTAAAAAAAT
*
27600593 ATATAATTTAATAAAAT
1 ATATAATTTAAAAAAAT
27600610 TCTTAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATATAATTTAAAAAAAT
Found at i:27605848 original size:14 final size:14
Alignment explanation
Indices: 27605831--27605879 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
27605821 TCTCTGGGTT
*
27605831 TTTCTTTTGAAGAA
1 TTTCTCTTGAAGAA
27605845 TTTCTCTTG-AG--
1 TTTCTCTTGAAGAA
*
27605856 TTTCTTTTGAAGAA
1 TTTCTCTTGAAGAA
27605870 TTTCTCTTGA
1 TTTCTCTTGA
27605880 GTTTCTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
11 8 0.28
12 2 0.07
13 2 0.07
14 17 0.59
ACGTcount: A:0.20, C:0.12, G:0.14, T:0.53
Consensus pattern (14 bp):
TTTCTCTTGAAGAA
Found at i:27605863 original size:25 final size:25
Alignment explanation
Indices: 27605831--27605894 Score: 119
Period size: 25 Copynumber: 2.5 Consensus size: 25
27605821 TCTCTGGGTT
27605831 TTTCTTTTGAAGAATTTCTCTTGAG
1 TTTCTTTTGAAGAATTTCTCTTGAG
27605856 TTTCTTTTGAAGAATTTCTCTTGAG
1 TTTCTTTTGAAGAATTTCTCTTGAG
27605881 TTTCTTTTAGAAGA
1 TTTCTTTT-GAAGA
27605895 GTTTTAACAA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 33 0.87
26 5 0.13
ACGTcount: A:0.22, C:0.11, G:0.16, T:0.52
Consensus pattern (25 bp):
TTTCTTTTGAAGAATTTCTCTTGAG
Found at i:27605865 original size:11 final size:13
Alignment explanation
Indices: 27605831--27605894 Score: 55
Period size: 14 Copynumber: 5.0 Consensus size: 13
27605821 TCTCTGGGTT
27605831 TTTCTTTTGAAGAA
1 TTTCTTTTGAAG-A
*
27605845 TTTCTCTTG-AG-
1 TTTCTTTTGAAGA
27605856 TTTCTTTTGAAGAA
1 TTTCTTTTGAAG-A
*
27605870 TTTCTCTTG-AG-
1 TTTCTTTTGAAGA
27605881 TTTCTTTTAGAAGA
1 TTTCTTTT-GAAGA
27605895 GTTTTAACAA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
11 15 0.38
12 3 0.08
13 6 0.15
14 16 0.40
ACGTcount: A:0.22, C:0.11, G:0.16, T:0.52
Consensus pattern (13 bp):
TTTCTTTTGAAGA
Found at i:27608265 original size:120 final size:119
Alignment explanation
Indices: 27608126--27608367 Score: 439
Period size: 120 Copynumber: 2.0 Consensus size: 119
27608116 AAGAAAAAGA
27608126 TGAAAAAAGAAAAGAGAGAAGAAATAGGGATAGGAGAGCAAAAATTCTAATTGGAATGGAAAAAA
1 TGAAAAAAGAAAAGAGAGAAGAAATAGGGATAGGAGAGCAAAAATTCTAATTGGAATGGAAAAAA
*
27608191 AAACATAATCCTAATGTAATTAGGGGGGAAAGGGACTAAATAGCTAGTGGTTGCG
66 AAACATAATCCTAATGTAATTA-GGGGAAAAGGGACTAAATAGCTAGTGGTTGCG
*
27608246 TGAAAAAAGAAAAGAGAGAAGAAATAGGGATAGGAGAGCAAAAATTCTAATTGGAATGGAAAAAG
1 TGAAAAAAGAAAAGAGAGAAGAAATAGGGATAGGAGAGCAAAAATTCTAATTGGAATGGAAAAAA
* *
27608311 AAACATAATCTTAATGTAATTAGGGGAAAAGGGACTAAATAGCTAGTGGTTGTG
66 AAACATAATCCTAATGTAATTAGGGGAAAAGGGACTAAATAGCTAGTGGTTGCG
27608365 TGA
1 TGA
27608368 TAATTTGCCC
Statistics
Matches: 118, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
119 33 0.28
120 85 0.72
ACGTcount: A:0.48, C:0.06, G:0.27, T:0.19
Consensus pattern (119 bp):
TGAAAAAAGAAAAGAGAGAAGAAATAGGGATAGGAGAGCAAAAATTCTAATTGGAATGGAAAAAA
AAACATAATCCTAATGTAATTAGGGGAAAAGGGACTAAATAGCTAGTGGTTGCG
Found at i:27609378 original size:42 final size:42
Alignment explanation
Indices: 27609332--27609422 Score: 123
Period size: 41 Copynumber: 2.2 Consensus size: 42
27609322 GTTTAGTCCC
* * * *
27609332 TAGGGTTTTTTGGTTTAGGGTTTTGTTAAAATAATTT-AGGTT
1 TAGGGTTTGTAGGGTTAGGGTTTTGTTAAAAGAATTTAAGG-T
27609374 TAGGG-TTGTAGGGTTAGGGTTTTGTTAAAAGAATTTAAGGT
1 TAGGGTTTGTAGGGTTAGGGTTTTGTTAAAAGAATTTAAGGT
27609415 TAGGGTTT
1 TAGGGTTT
27609423 AAAAATTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
41 33 0.77
42 10 0.23
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (42 bp):
TAGGGTTTGTAGGGTTAGGGTTTTGTTAAAAGAATTTAAGGT
Found at i:27609459 original size:28 final size:27
Alignment explanation
Indices: 27609414--27609471 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
27609404 GAATTTAAGG
27609414 TTAGGGTTTAAAAATTTTAAAAAATAAA
1 TTAGGGTTTAAAAATTTTAAAAAA-AAA
* ** *
27609442 TTAGGGTTTAGATTTTTTTAAAAAAAA
1 TTAGGGTTTAAAAATTTTAAAAAAAAA
27609469 TTA
1 TTA
27609472 ATTATATTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 6 0.23
28 20 0.77
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (27 bp):
TTAGGGTTTAAAAATTTTAAAAAAAAA
Found at i:27609542 original size:33 final size:33
Alignment explanation
Indices: 27609438--27609572 Score: 139
Period size: 34 Copynumber: 4.0 Consensus size: 33
27609428 TTTTAAAAAA
*
27609438 TAAATTAGGGTTTAGATTTTTTTAAAAAAAATTAAT
1 TAAATTAGGGTTTAGAGTTTTTT---AAAAATTAAT
* * * * **
27609474 TATATTAGGTTTTAGGGGTTTAAAATAAATTAAT
1 TAAATTAGGGTTTAGAGTTTTTTAA-AAATTAAT
*
27609508 TAAATTAGGGTTTATAGTTTTTTAAAAATTAAT
1 TAAATTAGGGTTTAGAGTTTTTTAAAAATTAAT
*
27609541 TAAATTAGGGTTTAG-TTTTTTTAAAAA-TAAT
1 TAAATTAGGGTTTAGAGTTTTTTAAAAATTAAT
27609572 T
1 T
27609573 TTGTGTTTAG
Statistics
Matches: 82, Mismatches: 16, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
31 5 0.06
32 11 0.13
33 24 0.29
34 26 0.32
36 16 0.20
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (33 bp):
TAAATTAGGGTTTAGAGTTTTTTAAAAATTAAT
Found at i:27609694 original size:12 final size:12
Alignment explanation
Indices: 27609677--27609703 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
27609667 ACAGTTCTGA
27609677 AAAGATAATGTC
1 AAAGATAATGTC
27609689 AAAGATAATGTC
1 AAAGATAATGTC
27609701 AAA
1 AAA
27609704 ATAGTTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.07, G:0.15, T:0.22
Consensus pattern (12 bp):
AAAGATAATGTC
Found at i:27609819 original size:24 final size:23
Alignment explanation
Indices: 27609763--27609819 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 23
27609753 AAGAACTTCT
27609763 ATTTTATTAAAAATATAAAAATA
1 ATTTTATTAAAAATATAAAAATA
27609786 ATTTACTATT-AAAATATTAAAAATAA
1 ATTT--TATTAAAAATA-TAAAAAT-A
27609812 ATTTTATT
1 ATTTTATT
27609820 TTATTAAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
23 4 0.13
24 10 0.33
25 11 0.37
26 5 0.17
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
ATTTTATTAAAAATATAAAAATA
Found at i:27624941 original size:108 final size:109
Alignment explanation
Indices: 27624800--27625029 Score: 277
Period size: 108 Copynumber: 2.1 Consensus size: 109
27624790 TTGAACAATT
* * *
27624800 AATTGTATAATTCAATTGATTACGTTCGTAATTAGAGAT-AAGCATATACGAGTAATGCCATTAC
1 AATTGTATAATTCAATTGATCACGTTCATAATTAAAG-TCAAGCATATACGAGTAATGCCATTAC
* *
27624864 ATTTGTACATA-AAAGATTCAATTAGATCAATGATAGTATTTATC
65 ATTTGTACATAGAAAGATTCAATTAGATCAATGATAGTACTTACC
* * ** * * *
27624908 AATTGTATAATTC-ATTCGATCAGGTTCATAATTAAAGTCATGTGTTTACGAGTAATGTCATTAT
1 AATTGTATAATTCAATT-GATCACGTTCATAATTAAAGTCAAGCATATACGAGTAATGCCATTAC
** * *
27624972 ATTTGTACATAGATTGATTCAATTGGATCAATGATCGTACTTACC
65 ATTTGTACATAGAAAGATTCAATTAGATCAATGATAGTACTTACC
27625017 AATTGTATAATTC
1 AATTGTATAATTC
27625030 CTCCAATTAC
Statistics
Matches: 103, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
107 4 0.04
108 59 0.57
109 40 0.39
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (109 bp):
AATTGTATAATTCAATTGATCACGTTCATAATTAAAGTCAAGCATATACGAGTAATGCCATTACA
TTTGTACATAGAAAGATTCAATTAGATCAATGATAGTACTTACC
Found at i:27625044 original size:109 final size:108
Alignment explanation
Indices: 27624846--27625054 Score: 283
Period size: 109 Copynumber: 1.9 Consensus size: 108
27624836 GATAAGCATA
* *
27624846 TACGAGTAATGCCATTACATTTGTACATAAAAGATTCAATTAGATCAATGATAGTATTTATCAAT
1 TACGAGTAATGCCATTACATTTGTACATAAAAGATTCAATTAGATCAATGATAGTACTTACCAAT
* * * *
27624911 TGTATAATTCATTCGATCAGGTTCATAATTAAAGTCATGTGTT
66 TGTATAATTCATCCAATCACGTTCATAATAAAAGTCATGTGTT
* * ** * *
27624954 TACGAGTAATGTCATTATATTTGTACATAGATTGATTCAATTGGATCAATGATCGTACTTACCAA
1 TACGAGTAATGCCATTACATTTGTACATA-AAAGATTCAATTAGATCAATGATAGTACTTACCAA
* *
27625019 TTGTATAATTCCTCCAATTACGTTCATAATAAAAGT
65 TTGTATAATTCATCCAATCACGTTCATAATAAAAGT
27625055 TGCGCGTTGA
Statistics
Matches: 86, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
108 27 0.31
109 59 0.69
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.38
Consensus pattern (108 bp):
TACGAGTAATGCCATTACATTTGTACATAAAAGATTCAATTAGATCAATGATAGTACTTACCAAT
TGTATAATTCATCCAATCACGTTCATAATAAAAGTCATGTGTT
Found at i:27625425 original size:73 final size:73
Alignment explanation
Indices: 27625306--27625451 Score: 292
Period size: 73 Copynumber: 2.0 Consensus size: 73
27625296 GCACTAAGCC
27625306 TAAAATTGAACCAAGATGATGAGTGACAGTCCAATGCTCAAAGATTCAAAATTTTTAATTTGGAC
1 TAAAATTGAACCAAGATGATGAGTGACAGTCCAATGCTCAAAGATTCAAAATTTTTAATTTGGAC
27625371 ACATTCAA
66 ACATTCAA
27625379 TAAAATTGAACCAAGATGATGAGTGACAGTCCAATGCTCAAAGATTCAAAATTTTTAATTTGGAC
1 TAAAATTGAACCAAGATGATGAGTGACAGTCCAATGCTCAAAGATTCAAAATTTTTAATTTGGAC
27625444 ACATTCAA
66 ACATTCAA
27625452 AACTTCTAGC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (73 bp):
TAAAATTGAACCAAGATGATGAGTGACAGTCCAATGCTCAAAGATTCAAAATTTTTAATTTGGAC
ACATTCAA
Found at i:27627057 original size:51 final size:51
Alignment explanation
Indices: 27627000--27627336 Score: 408
Period size: 51 Copynumber: 6.6 Consensus size: 51
27626990 CATATAATAT
* * * * *
27627000 TTTACATAACCAATAAGCACATACTTTGCATAGACTGTTCACACATAGAAA
1 TTTACATAATCAGTACGCACACACTTTGCATAGACAGTTCACACATAGAAA
* * *
27627051 TATACATAATCAGTACGTACACACTTTGCATAGACAGTTCACACATAGAAC
1 TTTACATAATCAGTACGCACACACTTTGCATAGACAGTTCACACATAGAAA
* *
27627102 TTTACATAATCAGTACGCACACACTTTGCATAGATAGTTAACACATA-AAA
1 TTTACATAATCAGTACGCACACACTTTGCATAGACAGTTCACACATAGAAA
* * * *
27627152 CTTTACATAATCAGTTCACACACACTTTGCATGGATAGTTCACACATA-AAA
1 -TTTACATAATCAGTACGCACACACTTTGCATAGACAGTTCACACATAGAAA
* * * * * * *
27627203 CTTTACAAAATCATTATGCACACACTTTGCATGGACAATTCACGCATAGAAC
1 -TTTACATAATCAGTACGCACACACTTTGCATAGACAGTTCACACATAGAAA
* * * *
27627255 TTTACATAATCAGTATGCACATACTTTGCATAGACAGTTCACACATAGGAC
1 TTTACATAATCAGTACGCACACACTTTGCATAGACAGTTCACACATAGAAA
*
27627306 TTTACATAATCAATACGCACACACTTTGCAT
1 TTTACATAATCAGTACGCACACACTTTGCAT
27627337 TGATAGTTAT
Statistics
Matches: 248, Mismatches: 36, Indels: 4
0.86 0.12 0.01
Matches are distributed among these distances:
50 2 0.01
51 244 0.98
52 2 0.01
ACGTcount: A:0.38, C:0.23, G:0.11, T:0.28
Consensus pattern (51 bp):
TTTACATAATCAGTACGCACACACTTTGCATAGACAGTTCACACATAGAAA
Found at i:27627082 original size:24 final size:24
Alignment explanation
Indices: 27627055--27627133 Score: 63
Period size: 24 Copynumber: 3.2 Consensus size: 24
27627045 TAGAAATATA
27627055 CATAATCAGTACGTACACACTTTG
1 CATAATCAGTACGTACACACTTTG
* * *
27627079 CATAGA-CAGTTCACACATAGA-ACTTTA
1 CATA-ATCAG-T---ACGTACACACTTTG
*
27627106 CATAATCAGTACGCACACACTTTG
1 CATAATCAGTACGTACACACTTTG
27627130 CATA
1 CATA
27627134 GATAGTTAAC
Statistics
Matches: 41, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
23 4 0.10
24 16 0.39
25 2 0.05
26 2 0.05
27 12 0.29
28 5 0.12
ACGTcount: A:0.37, C:0.25, G:0.11, T:0.27
Consensus pattern (24 bp):
CATAATCAGTACGTACACACTTTG
Found at i:27627146 original size:24 final size:24
Alignment explanation
Indices: 27627069--27627197 Score: 91
Period size: 24 Copynumber: 5.1 Consensus size: 24
27627059 ATCAGTACGT
*
27627069 ACACACTTTGCATAGACAGTTCAC
1 ACACACTTTGCATAGATAGTTCAC
* * * *
27627093 ACATAGAACTTTACATA-ATCAGTACGC
1 AC--A-CACTTTGCATAGAT-AGTTCAC
27627120 ACACACTTTGCATAGATAGTTAACAC
1 ACACACTTTGCATAGATAGTT--CAC
* * *
27627146 ATAAAACTTTACATA-ATCAGTTCAC
1 A-CACACTTTGCATAGAT-AGTTCAC
*
27627171 ACACACTTTGCATGGATAGTTCAC
1 ACACACTTTGCATAGATAGTTCAC
27627195 ACA
1 ACA
27627198 TAAAACTTTA
Statistics
Matches: 79, Mismatches: 16, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
24 33 0.42
25 9 0.11
26 7 0.09
27 30 0.38
ACGTcount: A:0.38, C:0.24, G:0.11, T:0.27
Consensus pattern (24 bp):
ACACACTTTGCATAGATAGTTCAC
Found at i:27627245 original size:153 final size:153
Alignment explanation
Indices: 27627000--27627344 Score: 453
Period size: 153 Copynumber: 2.3 Consensus size: 153
27626990 CATATAATAT
* * *
27627000 TTTACATAACCAATA-AGCACATACTTTGCATAGACT-GTTCACACATAGAAATATACATAATCA
1 TTTACATAATCAATACA-CACACACTTTGCATAGA-TAGTTCACACATAGAAATATACAAAATCA
* *
27627063 GTACGTACACACTTTGCATAGACAGTTCACACATAGAACTTTACATAATCAGTACGCACACACTT
64 GTACGCACACACTTTGCATAGACAATTCACACATAGAACTTTACATAATCAGTACGCACACACTT
*
27627128 TGCATAGATAGTTAACACATAAAAC
129 TGCATAGACAGTTAACACATAAAAC
* * * * *
27627153 TTTACATAATCAGTTCACACACACTTTGCATGGATAGTTCACACATA-AAACTTTACAAAATCAT
1 TTTACATAATCAATACACACACACTTTGCATAGATAGTTCACACATAGAAA-TATACAAAATCAG
* * * * *
27627217 TATGCACACACTTTGCATGGACAATTCACGCATAGAACTTTACATAATCAGTATGCACATACTTT
65 TACGCACACACTTTGCATAGACAATTCACACATAGAACTTTACATAATCAGTACGCACACACTTT
* **
27627282 GCATAGACAGTTCACACATAGGAC
130 GCATAGACAGTTAACACATAAAAC
* *
27627306 TTTACATAATCAATACGCACACACTTTGCATTGATAGTT
1 TTTACATAATCAATACACACACACTTTGCATAGATAGTT
27627345 ATGTTGGATC
Statistics
Matches: 166, Mismatches: 23, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
152 4 0.02
153 161 0.97
154 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.29
Consensus pattern (153 bp):
TTTACATAATCAATACACACACACTTTGCATAGATAGTTCACACATAGAAATATACAAAATCAGT
ACGCACACACTTTGCATAGACAATTCACACATAGAACTTTACATAATCAGTACGCACACACTTTG
CATAGACAGTTAACACATAAAAC
Found at i:27631080 original size:21 final size:21
Alignment explanation
Indices: 27631055--27631100 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
27631045 CAAACAAACG
*
27631055 AAAATATTAAAATATTAAAAT
1 AAAATATTAAAAAATTAAAAT
* *
27631076 AAAATTTTAAAAAATTAAATT
1 AAAATATTAAAAAATTAAAAT
27631097 AAAA
1 AAAA
27631101 AATGGCTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAATATTAAAAAATTAAAAT
Found at i:27633951 original size:27 final size:26
Alignment explanation
Indices: 27633886--27633952 Score: 109
Period size: 25 Copynumber: 2.5 Consensus size: 26
27633876 CAACCCATAT
27633886 TAAATATATATATTTGATTAAAAATAA
1 TAAA-ATATATATTTGATTAAAAATAA
27633913 -AAAATATATATTTGATTAAAAATAA
1 TAAAATATATATTTGATTAAAAATAA
27633938 GTAAAATATATATTT
1 -TAAAATATATATTT
27633953 AATATATAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
25 22 0.58
26 3 0.08
27 13 0.34
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.40
Consensus pattern (26 bp):
TAAAATATATATTTGATTAAAAATAA
Found at i:27634141 original size:90 final size:90
Alignment explanation
Indices: 27634035--27634217 Score: 366
Period size: 90 Copynumber: 2.0 Consensus size: 90
27634025 AATTTTTTGC
27634035 TCAAACCCATATTTCGAGCCTATATTTTTACCCGAACCCTCCCATTTTTTGGACAGGTCGTCGGG
1 TCAAACCCATATTTCGAGCCTATATTTTTACCCGAACCCTCCCATTTTTTGGACAGGTCGTCGGG
27634100 CCGGGCCAGATAACCCAACCCATGA
66 CCGGGCCAGATAACCCAACCCATGA
27634125 TCAAACCCATATTTCGAGCCTATATTTTTACCCGAACCCTCCCATTTTTTGGACAGGTCGTCGGG
1 TCAAACCCATATTTCGAGCCTATATTTTTACCCGAACCCTCCCATTTTTTGGACAGGTCGTCGGG
27634190 CCGGGCCAGATAACCCAACCCATGA
66 CCGGGCCAGATAACCCAACCCATGA
27634215 TCA
1 TCA
27634218 CCTCTAAGTG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 93 1.00
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.26
Consensus pattern (90 bp):
TCAAACCCATATTTCGAGCCTATATTTTTACCCGAACCCTCCCATTTTTTGGACAGGTCGTCGGG
CCGGGCCAGATAACCCAACCCATGA
Found at i:27635384 original size:9 final size:9
Alignment explanation
Indices: 27635372--27635406 Score: 70
Period size: 9 Copynumber: 3.9 Consensus size: 9
27635362 ATCATCATCC
27635372 TCATCGTCG
1 TCATCGTCG
27635381 TCATCGTCG
1 TCATCGTCG
27635390 TCATCGTCG
1 TCATCGTCG
27635399 TCATCGTC
1 TCATCGTC
27635407 CTTTTTGCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.11, C:0.34, G:0.20, T:0.34
Consensus pattern (9 bp):
TCATCGTCG
Found at i:27637965 original size:16 final size:16
Alignment explanation
Indices: 27637944--27637980 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
27637934 GAACTCTTTA
*
27637944 ATTAACTTGCTGTTAT
1 ATTAACTTACTGTTAT
27637960 ATTAACTTACTGTTAT
1 ATTAACTTACTGTTAT
27637976 ATTAA
1 ATTAA
27637981 TTTGTTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.49
Consensus pattern (16 bp):
ATTAACTTACTGTTAT
Found at i:27637988 original size:13 final size:15
Alignment explanation
Indices: 27637944--27637989 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
27637934 GAACTCTTTA
*
27637944 ATTAACTTGCTGTTAT
1 ATTAACTT-ATGTTAT
27637960 ATTAACTTACTGTTAT
1 ATTAACTTA-TGTTAT
27637976 ATTAA-TT-TGTTAT
1 ATTAACTTATGTTAT
27637989 A
1 A
27637990 AATATATAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 7 0.25
15 2 0.07
16 19 0.68
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (15 bp):
ATTAACTTATGTTAT
Found at i:27661341 original size:82 final size:81
Alignment explanation
Indices: 27661197--27661349 Score: 218
Period size: 82 Copynumber: 1.9 Consensus size: 81
27661187 ATGTGTTCTG
* *
27661197 AACTACAATTCCTAATCACCTTCCCAAGAAATTACATGGTTATTGCTAGTCTAGTCTCCATGGAA
1 AACTACAATTCCTAATCACATTCCCAAGAAATTACATGGATATTGCTAGTCTAGTCTCCATGGAA
27661262 TCATTGTCTTGGTTAA
66 TCATTGTCTTGGTTAA
* * * *
27661278 AACTACAGTTCCTAATCACATTTCCAAGTCAATTTCATGGATATTGCTAGTCTAGTC-CTCATGG
1 AACTACAATTCCTAATCACATTCCCAAG-AAATTACATGGATATTGCTAGTCTAGTCTC-CATGG
*
27661342 AATTATTG
64 AATCATTG
27661350 AAAGATCAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
81 26 0.41
82 37 0.59
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (81 bp):
AACTACAATTCCTAATCACATTCCCAAGAAATTACATGGATATTGCTAGTCTAGTCTCCATGGAA
TCATTGTCTTGGTTAA
Found at i:27681459 original size:23 final size:23
Alignment explanation
Indices: 27681433--27681478 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
27681423 GCGTAACTGC
27681433 TGTATAGTAATAGGGTGCCCGAA
1 TGTATAGTAATAGGGTGCCCGAA
* *
27681456 TGTATAGTTATAGGGTGCGCGAA
1 TGTATAGTAATAGGGTGCCCGAA
27681479 GCCCACCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.11, G:0.33, T:0.28
Consensus pattern (23 bp):
TGTATAGTAATAGGGTGCCCGAA
Found at i:27689678 original size:18 final size:18
Alignment explanation
Indices: 27689655--27689694 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
27689645 CATAAACAAT
27689655 AAGAATAATAAGAATACA
1 AAGAATAATAAGAATACA
27689673 AAGAATAATAAGAATACA
1 AAGAATAATAAGAATACA
27689691 AAGA
1 AAGA
27689695 CATGATACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.68, C:0.05, G:0.12, T:0.15
Consensus pattern (18 bp):
AAGAATAATAAGAATACA
Found at i:27689694 original size:9 final size:9
Alignment explanation
Indices: 27689652--27689688 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
27689642 AACCATAAAC
27689652 AATAAGAAT
1 AATAAGAAT
27689661 AATAAGAAT
1 AATAAGAAT
27689670 ACA-AAGAAT
1 A-ATAAGAAT
27689679 AATAAGAAT
1 AATAAGAAT
27689688 A
1 A
27689689 CAAAGACATG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 1 0.04
9 24 0.92
10 1 0.04
ACGTcount: A:0.68, C:0.03, G:0.11, T:0.19
Consensus pattern (9 bp):
AATAAGAAT
Found at i:27693058 original size:41 final size:40
Alignment explanation
Indices: 27692932--27693067 Score: 111
Period size: 41 Copynumber: 3.5 Consensus size: 40
27692922 ATCAGTTTGG
* * *
27692932 CACCTAGTGCCTCATC-AGAT-AATTCGGAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGA-ATAAATCCGAAGTA-TAAATTGA
* * * ** * *
27692972 CACGCTGTGTCTCATCGGTTAAA-CCGAAG--TAAGTTGG
1 CACCCAGTGCCTCATCGAATAAATCCGAAGTATAAATTGA
27693009 CACCCAGTGCCTCATCGAATAAATCCGAAGTAATAAATTGA
1 CACCCAGTGCCTCATCGAATAAATCCGAAGT-ATAAATTGA
*
27693050 CACCCAGTGTCTCATCGA
1 CACCCAGTGCCTCATCGA
27693068 CTCGAAGTCG
Statistics
Matches: 72, Mismatches: 18, Indels: 11
0.71 0.18 0.11
Matches are distributed among these distances:
37 24 0.33
38 6 0.08
40 17 0.24
41 25 0.35
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (40 bp):
CACCCAGTGCCTCATCGAATAAATCCGAAGTATAAATTGA
Found at i:27696072 original size:20 final size:20
Alignment explanation
Indices: 27696049--27696100 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
27696039 AAACATATTC
27696049 AAAAAATGAAAAAAAAA-TT
1 AAAAAATGAAAAAAAAATTT
* *
27696068 AAAAACTTACAAAAAAAATTAT
1 AAAAAATGA-AAAAAAAATT-T
27696090 AAAAAATGAAA
1 AAAAAATGAAA
27696101 TCATAAACAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 7 0.27
20 8 0.31
21 3 0.12
22 8 0.31
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.17
Consensus pattern (20 bp):
AAAAAATGAAAAAAAAATTT
Found at i:27697185 original size:34 final size:34
Alignment explanation
Indices: 27697147--27697214 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
27697137 TCAATTGACA
*
27697147 AAGTTGGAAATATCAAATGTCATGGCCTTGACTT
1 AAGTTGGAAATATCAAATGCCATGGCCTTGACTT
*
27697181 AAGTTGGAAATATCAAATGCCATGGTCTTGACTT
1 AAGTTGGAAATATCAAATGCCATGGCCTTGACTT
27697215 GCAATCTCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (34 bp):
AAGTTGGAAATATCAAATGCCATGGCCTTGACTT
Found at i:27697547 original size:15 final size:15
Alignment explanation
Indices: 27697519--27697554 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
27697509 GAGAAAAAAT
27697519 AAATATAAATTATAA
1 AAATATAAATTATAA
27697534 AAATAGTAAA-TATAA
1 AAATA-TAAATTATAA
27697549 AAATAT
1 AAATAT
27697555 TTTAAAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 1 0.05
15 15 0.75
16 4 0.20
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (15 bp):
AAATATAAATTATAA
Found at i:27697588 original size:10 final size:11
Alignment explanation
Indices: 27697554--27697580 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
27697544 TATAAAAATA
27697554 TTTTAAAGATT
1 TTTTAAAGATT
27697565 TTTTAAAGATT
1 TTTTAAAGATT
27697576 TTTTA
1 TTTTA
27697581 TAATTTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.59
Consensus pattern (11 bp):
TTTTAAAGATT
Found at i:27698148 original size:22 final size:22
Alignment explanation
Indices: 27698120--27698165 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
27698110 CTTCTTTAGT
27698120 TTTCAAGTAACAAAATATGGGC
1 TTTCAAGTAACAAAATATGGGC
27698142 TTTCAAGTAACAAAATATGGGC
1 TTTCAAGTAACAAAATATGGGC
27698164 TT
1 TT
27698166 ACAACACTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.30
Consensus pattern (22 bp):
TTTCAAGTAACAAAATATGGGC
Found at i:27698660 original size:15 final size:16
Alignment explanation
Indices: 27698640--27698674 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
27698630 AAGAGAGCTT
*
27698640 AAAACAACAA-AGCAA
1 AAAACAACAACAACAA
27698655 AAAACAACAACAACAA
1 AAAACAACAACAACAA
27698671 AAAA
1 AAAA
27698675 AACGATTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.77, C:0.20, G:0.03, T:0.00
Consensus pattern (16 bp):
AAAACAACAACAACAA
Found at i:27708677 original size:63 final size:63
Alignment explanation
Indices: 27708552--27708681 Score: 152
Period size: 63 Copynumber: 2.1 Consensus size: 63
27708542 GTGTCAAGTT
* * * * * **
27708552 GTGTAACTCACTATTTGTGATTTAGGGTCACATGGGACAGAGGCACGGGTGTGTGTTTAGGCC
1 GTGTAACTCACTATTTGTGATTAAGGGTCACACGGGACAGAGACACGGGCGTGTATCCAGGCC
* * * * *
27708615 GTGTAACTCTCTATTTGTGATTAAGTGTCACACGGGCCATAGACACGTGCGTGTATCCAGGCC
1 GTGTAACTCACTATTTGTGATTAAGGGTCACACGGGACAGAGACACGGGCGTGTATCCAGGCC
27708678 GTGT
1 GTGT
27708682 GAGAGTTATT
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (63 bp):
GTGTAACTCACTATTTGTGATTAAGGGTCACACGGGACAGAGACACGGGCGTGTATCCAGGCC
Found at i:27726423 original size:30 final size:32
Alignment explanation
Indices: 27726384--27726444 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 32
27726374 GGAGGTGGGA
*
27726384 TGGGAAGGGAATAAAAGTTTT-AGGGGAAATG
1 TGGGAAGGGAATAAAAATTTTGAGGGGAAATG
* *
27726415 TGGG-AGGGAGTAAAAATTTTGGGGGGAAAT
1 TGGGAAGGGAATAAAAATTTTGAGGGGAAAT
27726445 AAAAAGTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 14 0.54
31 12 0.46
ACGTcount: A:0.36, C:0.00, G:0.41, T:0.23
Consensus pattern (32 bp):
TGGGAAGGGAATAAAAATTTTGAGGGGAAATG
Found at i:27726670 original size:9 final size:9
Alignment explanation
Indices: 27726656--27726692 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
27726646 TATAGTTTGA
27726656 TATTCGAAT
1 TATTCGAAT
27726665 TATTCGAAT
1 TATTCGAAT
*
27726674 TATTCGAGT
1 TATTCGAAT
*
27726683 TATTCAAAT
1 TATTCGAAT
27726692 T
1 T
27726693 CGAAAACTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:27727709 original size:34 final size:34
Alignment explanation
Indices: 27727654--27727725 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
27727644 GGATCTAGAC
*
27727654 CTTTTATTTTCCTTAGTTTTTACT-TTCATTTGGG
1 CTTTTATTTTCCTTAGTTTTTA-TATTCAATTGGG
**
27727688 CTTTTATTTTGTTTA-TATTTTATATTCAATTGGG
1 CTTTTATTTTCCTTAGT-TTTTATATTCAATTGGG
27727722 CTTT
1 CTTT
27727726 CCGGTTTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 2 0.06
34 31 0.94
ACGTcount: A:0.15, C:0.11, G:0.11, T:0.62
Consensus pattern (34 bp):
CTTTTATTTTCCTTAGTTTTTATATTCAATTGGG
Found at i:27729517 original size:25 final size:26
Alignment explanation
Indices: 27729489--27729603 Score: 112
Period size: 25 Copynumber: 4.6 Consensus size: 26
27729479 CAAGATTAGA
*
27729489 CACAAAGGCTTTTCATAAGAATA-AC
1 CACAAAGGCTTTCCATAAGAATACAC
* **
27729514 CACAAAGGCTTTCCAT-ATAATATGC
1 CACAAAGGCTTTCCATAAGAATACAC
*
27729539 CACAAAGGCTTTCCAGAA-AATACAC
1 CACAAAGGCTTTCCATAAGAATACAC
* * * *
27729564 CACAAAAGCTTTTCATAAGATTA-GC
1 CACAAAGGCTTTCCATAAGAATACAC
*
27729589 CACAAAGGCTATCCA
1 CACAAAGGCTTTCCA
27729604 GATAACATGC
Statistics
Matches: 73, Mismatches: 14, Indels: 6
0.78 0.15 0.06
Matches are distributed among these distances:
24 5 0.07
25 64 0.88
26 4 0.05
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.23
Consensus pattern (26 bp):
CACAAAGGCTTTCCATAAGAATACAC
Found at i:27729543 original size:50 final size:50
Alignment explanation
Indices: 27729480--27729654 Score: 160
Period size: 50 Copynumber: 3.5 Consensus size: 50
27729470 GGTTTTTCAC
* * * *
27729480 AAGATTAGACACAAAGGCTTTTCATAAGAATA-ACCACAAAGGCTTTCCAT
1 AAGATTAGCCACAAAGGCTTTCCAGAA-AATACACCACAAAAGCTTTCCAT
*
27729530 ATA-A-TATGCCACAAAGGCTTTCCAGAAAATACACCACAAAAGCTTTTCAT
1 A-AGATTA-GCCACAAAGGCTTTCCAGAAAATACACCACAAAAGCTTTCCAT
* * * ** * *
27729580 AAGATTAGCCACAAAGGCTATCCAGATAACATGCCA-AAAGGCTTTTCAT
1 AAGATTAGCCACAAAGGCTTTCCAGAAAATACACCACAAAAGCTTTCCAT
* * *
27729629 AAGATTACCCATAAAGGTTTTCCAGA
1 AAGATTAGCCACAAAGGCTTTCCAGA
27729655 TAATCCATTT
Statistics
Matches: 105, Mismatches: 15, Indels: 11
0.80 0.11 0.08
Matches are distributed among these distances:
49 41 0.39
50 61 0.58
51 3 0.03
ACGTcount: A:0.41, C:0.22, G:0.14, T:0.24
Consensus pattern (50 bp):
AAGATTAGCCACAAAGGCTTTCCAGAAAATACACCACAAAAGCTTTCCAT
Found at i:27729615 original size:25 final size:25
Alignment explanation
Indices: 27729513--27729624 Score: 104
Period size: 25 Copynumber: 4.5 Consensus size: 25
27729503 ATAAGAATAA
*
27729513 CCACAAAGGCTTTCCATATAATATG
1 CCACAAAGGCTTTCCAGATAATATG
* **
27729538 CCACAAAGGCTTTCCAGAAAATACA
1 CCACAAAGGCTTTCCAGATAATATG
* * *
27729563 CCACAAAAGCTTTTC--ATAAGATTAG
1 CCACAAAGGCTTTCCAGATAATA-T-G
* *
27729588 CCACAAAGGCTATCCAGATAACATG
1 CCACAAAGGCTTTCCAGATAATATG
27729613 CCA-AAAGGCTTT
1 CCACAAAGGCTTT
27729625 TCATAAGATT
Statistics
Matches: 68, Mismatches: 15, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
23 4 0.06
24 8 0.12
25 50 0.74
26 1 0.01
27 5 0.07
ACGTcount: A:0.39, C:0.25, G:0.13, T:0.22
Consensus pattern (25 bp):
CCACAAAGGCTTTCCAGATAATATG
Found at i:27736974 original size:33 final size:32
Alignment explanation
Indices: 27736931--27737000 Score: 104
Period size: 33 Copynumber: 2.2 Consensus size: 32
27736921 CATGGGCCAG
* *
27736931 CACACGGGCAAGACCAATTTAGGCGTGTGGGTC
1 CACACAGGCAAGACCAATTTAGGCGTATGGG-C
*
27736964 CACACAGGCAAGGCCAATTTAGGCGTATGGGC
1 CACACAGGCAAGACCAATTTAGGCGTATGGGC
27736996 CACAC
1 CACAC
27737001 GGGTGTATGA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 6 0.18
33 28 0.82
ACGTcount: A:0.27, C:0.27, G:0.30, T:0.16
Consensus pattern (32 bp):
CACACAGGCAAGACCAATTTAGGCGTATGGGC
Found at i:27740450 original size:26 final size:26
Alignment explanation
Indices: 27740405--27740498 Score: 65
Period size: 26 Copynumber: 3.7 Consensus size: 26
27740395 ACACACCGCA
*
27740405 GCTCTT-ATGAG-TGTCTCGATATATG
1 GCTCTTCATGAGCT-TCCCGATATATG
*
27740430 GCTCTTCATGAGCTTCCCGAT-TAAAG
1 GCTCTTCATGAGCTTCCCGATAT-ATG
** * *
27740456 GCTCTTTGTGAGCTTCTCGTTA-ATG
1 GCTCTTCATGAGCTTCCCGATATATG
27740481 GCTC-TC-TGGAGCTTCCCG
1 GCTCTTCAT-GAGCTTCCCG
27740499 GTATGGCTAG
Statistics
Matches: 55, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
23 1 0.02
24 10 0.18
25 13 0.24
26 30 0.55
27 1 0.02
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.36
Consensus pattern (26 bp):
GCTCTTCATGAGCTTCCCGATATATG
Found at i:27742456 original size:25 final size:25
Alignment explanation
Indices: 27742420--27742656 Score: 135
Period size: 25 Copynumber: 9.6 Consensus size: 25
27742410 CAGACAATAC
*
27742420 GCCATAAA-GCTTTTCATAAGATTA
1 GCCACAAAGGCTTTTCATAAGATTA
*
27742444 GCCACAAAGGCTTTCCCGAT-A-A-TA
1 GCCACAAAGGCTTT-TC-ATAAGATTA
27742468 CGCCACAACA-GC-TTTC-T-AGATAATA
1 -GCCACAA-AGGCTTTTCATAAGAT--TA
* * *
27742493 TGTCACAAAAGTTTTTCATAAGATTA
1 -GCCACAAAGGCTTTTCATAAGATTA
* *
27742519 GCCATAAAAGC-TTTC-T-AGATAATA
1 GCCACAAAGGCTTTTCATAAGAT--TA
*
27742543 CGTCACAAAGGCTTTTCATAAGATTA
1 -GCCACAAAGGCTTTTCATAAGATTA
*
27742569 ACCACAAA-G-TTTTC-T-AGATAATA
1 GCCACAAAGGCTTTTCATAAGAT--TA
* *
27742592 TGCCACAAAGGCTTTTTATAAAATTA
1 -GCCACAAAGGCTTTTCATAAGATTA
* *
27742618 GCCACAAAGGCTTTTTATAAAATTA
1 GCCACAAAGGCTTTTCATAAGATTA
27742643 GCCACAAAGGCTTT
1 GCCACAAAGGCTTT
27742657 CCAGATAATT
Statistics
Matches: 170, Mismatches: 17, Indels: 51
0.71 0.07 0.21
Matches are distributed among these distances:
21 6 0.04
22 6 0.04
23 9 0.05
24 26 0.15
25 86 0.51
26 21 0.12
27 5 0.03
28 11 0.06
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (25 bp):
GCCACAAAGGCTTTTCATAAGATTA
Found at i:27742531 original size:50 final size:49
Alignment explanation
Indices: 27742477--27742631 Score: 195
Period size: 50 Copynumber: 3.1 Consensus size: 49
27742467 ACGCCACAAC
*
27742477 AGCTTTCTAGATAATATGTCACAAAAGTTTTTCATAAGATTAGCCATAAA
1 AGCTTTCTAGATAATATGTCACAAAGGTTTTTCATAAGATTAGCCA-AAA
* * * *
27742527 AGCTTTCTAGATAATACGTCACAAAGGCTTTTCATAAGATTAACCACAA
1 AGCTTTCTAGATAATATGTCACAAAGGTTTTTCATAAGATTAGCCAAAA
* * *
27742576 AGTTTTCTAGATAATATGCCACAAAGGCTTTTT-ATAAAATTAGCCACAAA
1 AGCTTTCTAGATAATATGTCACAAAGG-TTTTTCATAAGATTAGCCA-AAA
*
27742626 GGCTTT
1 AGCTTT
27742632 TTATAAAATT
Statistics
Matches: 89, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
49 37 0.42
50 52 0.58
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (49 bp):
AGCTTTCTAGATAATATGTCACAAAGGTTTTTCATAAGATTAGCCAAAA
Found at i:27742575 original size:75 final size:73
Alignment explanation
Indices: 27742425--27742581 Score: 167
Period size: 75 Copynumber: 2.1 Consensus size: 73
27742415 AATACGCCAT
* * *
27742425 AAAGCTTTTCATAAGATTAGCCACAAAGGCTTTCCCGATAATACGCCACAACAGCTTTCTAGATA
1 AAAGTTTTTCATAAGATTAGCCACAAAAGCTTTCCAGATAATACGCCACAACAGCTTTCTAGAT-
**
27742490 ATATGTCAC
65 ATATACCAC
* * *
27742499 AAAAGTTTTTCATAAGATTAGCCATAAAAGCTTTCTAGATAATACGTCACAA-AGGCTTTTCATA
1 -AAAGTTTTTCATAAGATTAGCCACAAAAGCTTTCCAGATAATACGCCACAACA-GC-TTTC-T-
27742563 AGAT-TA-ACCAC
61 AGATATATACCAC
27742574 AAAGTTTT
1 AAAGTTTT
27742582 CTAGATAATA
Statistics
Matches: 70, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
74 9 0.13
75 50 0.71
76 6 0.09
77 1 0.01
78 4 0.06
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.30
Consensus pattern (73 bp):
AAAGTTTTTCATAAGATTAGCCACAAAAGCTTTCCAGATAATACGCCACAACAGCTTTCTAGATA
TATACCAC
Found at i:27742606 original size:124 final size:124
Alignment explanation
Indices: 27742406--27742665 Score: 303
Period size: 124 Copynumber: 2.1 Consensus size: 124
27742396 TACCATAAGT
* * * *
27742406 TTTCCAGACAATACGCCATAAAGCTTTTCATAAGATTAGCCACAAAGGCTTTCCCGATAATACGC
1 TTTCCAGATAATACGCCACAAAGCTTTTCATAAGATTAACCACAAAGGCTTTCCAGATAATACGC
* * * *
27742471 CACAACAGCTTTCTAGATAA-TATGTCACAAAAG-TTTTTCATAAGATTAGCCATAAAAGC
66 CACAACAGCTTTCTAGAAAATTA-GCCACAAAAGCTTTTT-ATAAAATTAGCCACAAAAGC
* * * * *
27742530 TTTCTAGATAATACGTCACAAAGGCTTTTCATAAGATTAACCACAAA-GTTTTCTAGATAATATG
1 TTTCCAGATAATACGCCACAAA-GCTTTTCATAAGATTAACCACAAAGGCTTTCCAGATAATACG
* * * *
27742594 CCACAA-AGGCTTTTTATAAAATTAGCCACAAAGGCTTTTTATAAAATTAGCCACAAAGGC
65 CCACAACA-GCTTTCTAGAAAATTAGCCACAAAAGCTTTTTATAAAATTAGCCACAAAAGC
27742654 TTTCCAGATAAT
1 TTTCCAGATAAT
27742666 TCGTTTTTAC
Statistics
Matches: 114, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
123 1 0.01
124 83 0.73
125 30 0.26
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.30
Consensus pattern (124 bp):
TTTCCAGATAATACGCCACAAAGCTTTTCATAAGATTAACCACAAAGGCTTTCCAGATAATACGC
CACAACAGCTTTCTAGAAAATTAGCCACAAAAGCTTTTTATAAAATTAGCCACAAAAGC
Found at i:27742649 original size:99 final size:99
Alignment explanation
Indices: 27742420--27742665 Score: 261
Period size: 99 Copynumber: 2.5 Consensus size: 99
27742410 CAGACAATAC
* * *
27742420 GCCATAAAGCTTTTCATAAGATTAGCCACAAAGGCTTTCCCGATAATACGCCACAACAGCTTTCT
1 GCCATAAAGCTTTTTATAAAATTAGCCACAAAGGCTTTCCCGATAATACACCACAACAGCTTTCT
* *
27742485 AGATAATATGTCACAAAAGTTTTTCATAAGATTA
66 AGATAATATGCCACAAAAGTTTTTCATAAAATTA
* * * * * *
27742519 GCCATAAAAGCTTTCTAGATAA-TACGTCACAAAGGCTTT-TC-ATAAGATTA-ACCACAA-AGT
1 GCCAT-AAAGCTTTTTATAAAATTA-GCCACAAAGGCTTTCCCGAT-A-A-TACACCACAACAGC
*
27742579 TTTCTAGATAATATGCCACAAAGGCTTTTT-ATAAAATTA
61 TTTCTAGATAATATGCCACAAAAG-TTTTTCATAAAATTA
* *
27742618 GCCACAAAGGCTTTTTATAAAATTAGCCACAAAGGCTTTCCAGATAAT
1 GCCATAAA-GCTTTTTATAAAATTAGCCACAAAGGCTTTCCCGATAAT
27742666 TCGTTTTTAC
Statistics
Matches: 118, Mismatches: 19, Indels: 21
0.75 0.12 0.13
Matches are distributed among these distances:
98 6 0.05
99 69 0.58
100 39 0.33
101 4 0.03
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.30
Consensus pattern (99 bp):
GCCATAAAGCTTTTTATAAAATTAGCCACAAAGGCTTTCCCGATAATACACCACAACAGCTTTCT
AGATAATATGCCACAAAAGTTTTTCATAAAATTA
Found at i:27744643 original size:16 final size:16
Alignment explanation
Indices: 27744601--27744645 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
27744591 AACTAAAGCC
*
27744601 TTGTTCTGAAC-ATAG
1 TTGTTCTGAACAATAA
*
27744616 TTATTCTCGAACAATAA
1 TTGTTCT-GAACAATAA
27744633 TTGTTCTGAACAA
1 TTGTTCTGAACAA
27744646 CAACAATTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 6 0.24
16 10 0.40
17 9 0.36
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (16 bp):
TTGTTCTGAACAATAA
Found at i:27746281 original size:12 final size:14
Alignment explanation
Indices: 27746241--27746291 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 14
27746231 TAAAATTTTA
*
27746241 ATAAATAAAAAGTAT
1 ATAAATTAAAA-TAT
27746256 ATAAATTTATTAAATAT
1 ATAAA-TTA--AAATAT
27746273 -TAAATTAAAATAT
1 ATAAATTAAAATAT
27746286 ATAAAT
1 ATAAAT
27746292 ATTTTTTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
13 6 0.19
14 5 0.16
15 8 0.26
16 6 0.19
17 3 0.10
18 3 0.10
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (14 bp):
ATAAATTAAAATAT
Found at i:27746539 original size:18 final size:17
Alignment explanation
Indices: 27746506--27746538 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
27746496 TAAAATTAAA
27746506 AATAAAAATCCTAAAAC
1 AATAAAAATCCTAAAAC
27746523 AATAATAAAT-CTAAAA
1 AATAA-AAATCCTAAAA
27746539 AAAAAAGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.67, C:0.12, G:0.00, T:0.21
Consensus pattern (17 bp):
AATAAAAATCCTAAAAC
Found at i:27746647 original size:17 final size:16
Alignment explanation
Indices: 27746604--27746659 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
27746594 AATAAACATA
27746604 AAATTATAAAAATTAT
1 AAATTATAAAAATTAT
* *
27746620 TAATTATTAAAAATTCT
1 AAATTA-TAAAAATTAT
*
27746637 AAA-TATATAAA-TAT
1 AAATTATAAAAATTAT
27746651 ATAATTATA
1 A-AATTATA
27746660 TGTGGTGAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
14 3 0.09
15 7 0.22
16 11 0.34
17 11 0.34
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATTATAAAAATTAT
Found at i:27749314 original size:3 final size:3
Alignment explanation
Indices: 27749306--27749331 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
27749296 AAAGTACAGA
27749306 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
27749332 AATGTTTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:27753696 original size:42 final size:42
Alignment explanation
Indices: 27753650--27753732 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
27753640 AAAACACCTT
* **
27753650 AAATGTGCAAAGCACAATATTATACCCTCC-AATCACACCAAA
1 AAATGTACAAAGCACAATAAAATACCCTCCTAA-CACACCAAA
* *
27753692 AAATGTATAAAGCACAATAAAATATCCTCCTAACACACCAA
1 AAATGTACAAAGCACAATAAAATACCCTCCTAACACACCAA
27753733 TACTCTCATG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.48, C:0.27, G:0.06, T:0.19
Consensus pattern (42 bp):
AAATGTACAAAGCACAATAAAATACCCTCCTAACACACCAAA
Found at i:27755277 original size:30 final size:30
Alignment explanation
Indices: 27755243--27755305 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
27755233 ACTTATTTTA
27755243 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
* *
27755273 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
27755303 TTG
1 TTG
27755306 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.03, G:0.14, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:27757556 original size:5 final size:5
Alignment explanation
Indices: 27757546--27757616 Score: 62
Period size: 5 Copynumber: 14.6 Consensus size: 5
27757536 AAAAAAATAT
* *
27757546 TATTA TATTA TAGTAA TGATTA TGTT- T-TTA TATTA TATTA TTATTA
1 TATTA TATTA TA-TTA T-ATTA TATTA TATTA TATTA TATTA -TATTA
27757592 -A-TA TATTA TATTA TATTA TA-TA TAT
1 TATTA TATTA TATTA TATTA TATTA TAT
27757617 ACATAAAACA
Statistics
Matches: 55, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
3 4 0.07
4 8 0.15
5 31 0.56
6 11 0.20
7 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (5 bp):
TATTA
Found at i:27757598 original size:19 final size:19
Alignment explanation
Indices: 27757574--27757616 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
27757564 ATTATGTTTT
27757574 TATATTATATTATTATTA-A
1 TATATTATATTA-TATTATA
27757593 TATATTATATTATATTATA
1 TATATTATATTATATTATA
27757612 TATAT
1 TATAT
27757617 ACATAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:27757646 original size:15 final size:15
Alignment explanation
Indices: 27757626--27757667 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
27757616 TACATAAAAC
*
27757626 AAAAGAAAGAATAGA
1 AAAAGAAAGAAAAGA
27757641 AAAAGAAAGAAAAGA
1 AAAAGAAAGAAAAGA
*
27757656 AACAGAATAGAA
1 AAAAGAA-AGAA
27757668 GAGACGAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 20 0.83
16 4 0.17
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.05
Consensus pattern (15 bp):
AAAAGAAAGAAAAGA
Found at i:27759651 original size:17 final size:17
Alignment explanation
Indices: 27759629--27759662 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
27759619 ATGTGGCATG
*
27759629 TACCTAGGTAATGTATA
1 TACCTAAGTAATGTATA
*
27759646 TACCTAAGTGATGTATA
1 TACCTAAGTAATGTATA
27759663 GGGATTAGTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (17 bp):
TACCTAAGTAATGTATA
Found at i:27763543 original size:2 final size:2
Alignment explanation
Indices: 27763536--27763563 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
27763526 AAATTAGTCC
27763536 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27763564 CTTAGATCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27770495 original size:30 final size:30
Alignment explanation
Indices: 27770455--27770511 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
27770445 AATAAACATT
*
27770455 ACCCATCCCAATACAAATAAACATTTAAAA
1 ACCCAACCCAATACAAATAAACATTTAAAA
*
27770485 ACCCAACCCAATTCAAATAAACATTTA
1 ACCCAACCCAATACAAATAAACATTTA
27770512 TTACCCAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.21
Consensus pattern (30 bp):
ACCCAACCCAATACAAATAAACATTTAAAA
Found at i:27773059 original size:19 final size:19
Alignment explanation
Indices: 27773032--27773069 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
27773022 TGGGTGTCAA
* *
27773032 ATTGGTGTGTTGGTTGGAT
1 ATTGATGTGTTGGCTGGAT
27773051 ATTGATGTGTTGGCTGGAT
1 ATTGATGTGTTGGCTGGAT
27773070 TTGCGTATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.13, C:0.03, G:0.39, T:0.45
Consensus pattern (19 bp):
ATTGATGTGTTGGCTGGAT
Found at i:27778109 original size:19 final size:19
Alignment explanation
Indices: 27778074--27778132 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
27778064 ATTTTTTAAA
*
27778074 TATAAAT-TTTGGAATTTT
1 TATAAATATTTTGAATTTT
27778092 TATAAATATTTTGAATTTT
1 TATAAATATTTTGAATTTT
*
27778111 TGA-AAATTATTTTGATTTTT
1 T-ATAAA-TATTTTGAATTTT
27778131 TA
1 TA
27778133 AAAAGTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
18 7 0.19
19 15 0.42
20 14 0.39
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:27778135 original size:19 final size:19
Alignment explanation
Indices: 27778064--27778135 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 19
27778054 TTTTTTTAGA
*
27778064 ATTTTTTAAATATAAATTTTGG
1 ATTTTTTAAA-AT-TATTTT-G
*
27778086 AATTTTTATAAA-TATTTTG
1 ATTTTTTA-AAATTATTTTG
*
27778105 AATTTTTGAAAATTATTTTG
1 -ATTTTTTAAAATTATTTTG
27778125 ATTTTTTAAAA
1 ATTTTTTAAAA
27778136 AGTTTTTTAG
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
19 14 0.33
20 18 0.43
22 8 0.19
23 2 0.05
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.56
Consensus pattern (19 bp):
ATTTTTTAAAATTATTTTG
Found at i:27778143 original size:20 final size:20
Alignment explanation
Indices: 27778079--27778136 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
27778069 TTAAATATAA
*
27778079 ATTTTGGAATTTTTATAAA-T
1 ATTTT-GAATTTTTAAAAATT
*
27778099 ATTTTGAATTTTTGAAAATT
1 ATTTTGAATTTTTAAAAATT
*
27778119 ATTTTGATTTTTTAAAAA
1 ATTTTGAATTTTTAAAAA
27778137 GTTTTTTAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.33
20 22 0.67
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (20 bp):
ATTTTGAATTTTTAAAAATT
Found at i:27778298 original size:23 final size:23
Alignment explanation
Indices: 27778248--27778301 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
27778238 CTCGACTCGA
*
27778248 AACTCGAATTACTTGTTCGAGTT
1 AACTCGAATAACTTGTTCGAGTT
* *
27778271 GACTCGAATAACTTGATTC-ATTT
1 AACTCGAATAACTTG-TTCGAGTT
27778294 AACTCGAA
1 AACTCGAA
27778302 ATTTGAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 23 0.88
24 3 0.12
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (23 bp):
AACTCGAATAACTTGTTCGAGTT
Found at i:27780373 original size:27 final size:26
Alignment explanation
Indices: 27780338--27780401 Score: 78
Period size: 25 Copynumber: 2.5 Consensus size: 26
27780328 TTAAGGAACC
* *
27780338 TTAGCGCTCTCTCTGATTATTAGCACGA
1 TTAGTGCTCTCTC-AATTATTAGCAC-A
27780366 -TAGTGCTCTC-CAATTATTAGCACA
1 TTAGTGCTCTCTCAATTATTAGCACA
27780390 TTAGTGCTCTCT
1 TTAGTGCTCTCT
27780402 GTTTAATAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 1 0.03
25 21 0.66
26 1 0.03
27 9 0.28
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.38
Consensus pattern (26 bp):
TTAGTGCTCTCTCAATTATTAGCACA
Found at i:27780374 original size:25 final size:25
Alignment explanation
Indices: 27780346--27780402 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
27780336 CCTTAGCGCT
27780346 CTCTCTGATTATTAGCACGA-TAGTG
1 CTCTCTGATTATTAGCAC-ATTAGTG
**
27780371 CTCTCCAATTATTAGCACATTAGTG
1 CTCTCTGATTATTAGCACATTAGTG
27780396 CTCTCTG
1 CTCTCTG
27780403 TTTAATAGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 1 0.04
25 26 0.96
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.37
Consensus pattern (25 bp):
CTCTCTGATTATTAGCACATTAGTG
Found at i:27783026 original size:31 final size:31
Alignment explanation
Indices: 27782940--27783026 Score: 102
Period size: 31 Copynumber: 2.8 Consensus size: 31
27782930 AGGGTTTAAA
* * *
27782940 GTATCAGGTACTATGTACCGGTGATTATGTT
1 GTATCAAGTACTATGTACCGGTGTTTATATT
* * * *
27782971 ATAACAAGTACTTTGTACCAGTGTTTATATT
1 GTATCAAGTACTATGTACCGGTGTTTATATT
*
27783002 GTATCAAGTACTATATACCGGTGTT
1 GTATCAAGTACTATGTACCGGTGTT
27783027 GGATACCTTA
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.39
Consensus pattern (31 bp):
GTATCAAGTACTATGTACCGGTGTTTATATT
Found at i:27788853 original size:50 final size:50
Alignment explanation
Indices: 27788778--27788876 Score: 189
Period size: 50 Copynumber: 2.0 Consensus size: 50
27788768 CCGTGATGCC
*
27788778 ATATCGCATGTGCTATTTAAATCAGTGATATGTTGCCTAGTTAATATCTT
1 ATATCGCATGTGCTATTTAAATCAGTGATATGTTGCCTAATTAATATCTT
27788828 ATATCGCATGTGCTATTTAAATCAGTGATATGTTGCCTAATTAATATCT
1 ATATCGCATGTGCTATTTAAATCAGTGATATGTTGCCTAATTAATATCT
27788877 AATTTTTTTC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.41
Consensus pattern (50 bp):
ATATCGCATGTGCTATTTAAATCAGTGATATGTTGCCTAATTAATATCTT
Found at i:27788858 original size:27 final size:27
Alignment explanation
Indices: 27788778--27788858 Score: 84
Period size: 27 Copynumber: 3.1 Consensus size: 27
27788768 CCGTGATGCC
27788778 ATATCGCATGTGCTATTTAAATCAGTG
1 ATATCGCATGTGCTATTTAAATCAGTG
* *
27788805 ATAT-G--T-TGCCTAGTTAATATC--TT
1 ATATCGCATGTG-CTATTTAA-ATCAGTG
27788828 ATATCGCATGTGCTATTTAAATCAGTG
1 ATATCGCATGTGCTATTTAAATCAGTG
27788855 ATAT
1 ATAT
27788859 GTTGCCTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 16
0.68 0.06 0.26
Matches are distributed among these distances:
23 7 0.17
24 9 0.21
25 6 0.14
26 9 0.21
27 11 0.26
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.41
Consensus pattern (27 bp):
ATATCGCATGTGCTATTTAAATCAGTG
Found at i:27808117 original size:14 final size:14
Alignment explanation
Indices: 27808098--27808137 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
27808088 TTGATTGCCA
27808098 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
27808112 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
27808126 GGAAAATGTTTT
1 GTAAAATGTTTT
27808138 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:27808146 original size:20 final size:20
Alignment explanation
Indices: 27808121--27808160 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
27808111 CGTAAAATGA
*
27808121 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
27808141 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
27808161 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:27808150 original size:34 final size:35
Alignment explanation
Indices: 27808106--27808172 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
27808096 CAGTAAAATG
*
27808106 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
27808140 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
27808173 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:27808176 original size:14 final size:15
Alignment explanation
Indices: 27808100--27808176 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
27808090 GATTGCCAGT
* *
27808100 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
27808114 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
27808128 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
27808148 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
27808163 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
27808177 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Done.