Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr10
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: 57797951
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1092422 characters in sequence are not A, C, G, or T
File 104 of 187
Found at i:30443522 original size:44 final size:43
Alignment explanation
Indices: 30443455--30444015 Score: 411
Period size: 44 Copynumber: 12.8 Consensus size: 43
30443445 GATTTGTGGC
*
30443455 TTTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAG
1 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GTAG
* * ** *
30443499 CTTCAATCTGCTCCACTATAACTTCAGGGAGATAAGGTTTGTTA-
1 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA-GATTG-TAG
* * *
30443543 TTTTCAGTCTGTTCCACTGCAACTTCAGGGAGATAAAACTTGTTATG
1 TTTT-AATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTG-TA-G
* * * * * * *
30443590 GTGTGATCTGCTCTACTACAACTTCAGAGAGATAAGATTTGTTAT
1 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTG-TAG
* * *
30443635 TTTTAGTCTGTTCCACTGCAACTTCAGGGAGATAAGACTTCTTATG
1 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TT-GTA-G
* * * * *
30443681 GTGTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGT-G
1 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TGTAG
* * *
30443724 ATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGT-T
1 -TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GTAG
** * * *
30443768 TCTTTCGTCTACTCCACTGCAACATCAGGGAGATAAGACTG--G
1 T-TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTAG
* * * * * *
30443810 ATGTGATCTGCTCTATTGCAACTTCAGAGAGATAAGATTTGT-G
1 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGTAG
* * *
30443853 TTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGT-T
1 -TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GTAG
*
30443897 TCTTTTATCTGCTCCACTGCAACTTCAGGGAGATAAGATTG--G
1 T-TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTAG
* * * * * * *
30443939 ATGTGATCTGCTCTACTGCAACTTCAGAGACATAAGATCTATAG
1 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TGTAG
* *
30443983 TTTTAATCTACTCCACTGTAACTTCAGGGAGAT
1 TTTTAATCTGCTCCACTGCAACTTCAGGGAGAT
30444016 CGGATTGGCT
Statistics
Matches: 399, Mismatches: 98, Indels: 40
0.74 0.18 0.07
Matches are distributed among these distances:
41 60 0.15
42 3 0.01
43 9 0.02
44 189 0.47
45 73 0.18
46 63 0.16
47 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (43 bp):
TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTAG
Found at i:30443632 original size:91 final size:90
Alignment explanation
Indices: 30443455--30444015 Score: 462
Period size: 91 Copynumber: 6.4 Consensus size: 90
30443445 GATTTGTGGC
* * *
30443455 TTTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTAG-TA-GCT-TCAATCTGCTCCACT
1 TTTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GTTATGGTGT-GATCTGCTCTACT
* * *
30443516 ATAACTTCAGGGAGATAAGGTTTGTTA
64 ACAACTTCAGAGAGATAAGATTTGTTA
* *
30443543 TTTTCAGTCTGTTCCACTGCAACTTCAGGGAGATAAAACTTGTTATGGTGTGATCTGCTCTACTA
1 TTTT-AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTATGGTGTGATCTGCTCTACTA
30443608 CAACTTCAGAGAGATAAGATTTGTTA
65 CAACTTCAGAGAGATAAGATTTGTTA
* * *
30443634 TTTTTAGTCTGTTCCACTGCAACTTCAGGGAGATAAGACTTCTTATGGTGTGATCTGCTCTACTG
1 -TTTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTATGGTGTGATCTGCTCTACTA
* *
30443699 CAACTTCAGAGAGATAAGATCTGTGA
65 CAACTTCAGAGAGATAAGATTTGTTA
* * * * * * *
30443725 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGA-TTGGTT-T-CTTTCG-TCTACTCCACT
1 TTTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GTTATGGTGT-GATCTGCTCTACT
* * * * *
30443786 GCAACATCAGGGAGATAAGA-CTG-GA
64 ACAACTTCAGAGAGATAAGATTTGTTA
* * * * * * * * * * *
30443811 TGTGA-TCTGCTCTATTGCAACTTCAGAGAGATAAGATTTGTGT-T--TTTAATCCGCTCCACTG
1 TTTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGT-TATGGTGTGATCTGCTCTACTA
* * * *
30443872 CAACTTCAGGGAGATAGGATTGGTTTC
65 CAACTTCAGAGAGATAAGATTTG-TTA
* *
30443899 TTTTA-TCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTG----GATGTGATCTGCTCTACTGC
1 TTTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTATGGTGTGATCTGCTCTACTAC
* * *
30443958 AACTTCAGAGACATAAGATCT-ATA
66 AACTTCAGAGAGATAAGATTTGTTA
* * *
30443982 GTTTTAATCTACTCCACTGTAACTTCAGGGAGAT
1 -TTTTAGTCTGCTCCACTGCAACTTCAGGGAGAT
30444016 CGGATTGGCT
Statistics
Matches: 397, Mismatches: 58, Indels: 39
0.80 0.12 0.08
Matches are distributed among these distances:
83 1 0.00
84 5 0.01
85 113 0.28
86 10 0.03
87 6 0.02
88 64 0.16
89 36 0.09
90 39 0.10
91 118 0.30
92 5 0.01
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (90 bp):
TTTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTATGGTGTGATCTGCTCTACTAC
AACTTCAGAGAGATAAGATTTGTTA
Found at i:30443868 original size:85 final size:88
Alignment explanation
Indices: 30443464--30444029 Score: 283
Period size: 85 Copynumber: 6.4 Consensus size: 88
30443454 CTTTTAGTCT
* * ** * * **
30443464 GCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTCAATCTGCTCCACTATAACTTCAGGGA
1 GCTCCACTGCAACTTCAGAGAGATAAGATTGGTTTCTTTAATCCGCTCCACTGCAACTTCAGGGA
* * * * * *
30443529 GATAAGGTTTGTTATTTTCAGTCT
66 GATAAGATCTGTGATTGT-AATCC
* * * * * * * * *
30443553 GTTCCACTGCAACTTCAGGGAGATAAAACTT-GTTATGGTGTGATCTGCTCTACTACAACTTCAG
1 GCTCCACTGCAACTTCAGAGAGATAAGA-TTGGTT-T-CTTTAATCCGCTCCACTGCAACTTCAG
* * * * * *
30443617 AGAGATAAGATTTGTTATTTTTAGTCT
63 GGAGATAAGATCTGTGA-TTGTAATCC
* * * * * * * *
30443644 GTTCCACTGCAACTTCAGGGAGATAAGACTT-CTTATGGTGTGATCTGCTCTACTGCAACTTCAG
1 GCTCCACTGCAACTTCAGAGAGATAAGA-TTGGTT-T-CTTTAATCCGCTCCACTGCAACTTCAG
* *
30443708 AGAGATAAGATCTGTGATTTTAATCC
63 GGAGATAAGATCTGTGATTGTAATCC
* * ** ** *
30443734 GCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTTCGTCTACTCCACTGCAACATCAGGGA
1 GCTCCACTGCAACTTCAGAGAGATAAGATTGGTTTCTTTAATCCGCTCCACTGCAACTTCAGGGA
* *
30443799 GATAAGA-CTG-GA-TGTGATCT
66 GATAAGATCTGTGATTGTAATCC
* * *
30443819 GCTCTATTGCAACTTCAGAGAGATAAGATTTGTGTT-TTTAATCCGCTCCACTGCAACTTCAGGG
1 GCTCCACTGCAACTTCAGAGAGATAAGATTGGT-TTCTTTAATCCGCTCCACTGCAACTTCAGGG
* * * * *
30443883 AGATAGGAT-TG-GTTTCTTTTATCT
65 AGATAAGATCTGTG-AT-TGTAATCC
* * * * * * *
30443907 GCTCCACTGCAACTTCAGGGAGATAAGATTGG---ATGTGATCTGCTCTACTGCAACTTCAGAGA
1 GCTCCACTGCAACTTCAGAGAGATAAGATTGGTTTCTTTAATCCGCTCCACTGCAACTTCAGGGA
* * * *
30443969 CATAAGATCTAT-AGTTTTAATCT
66 GATAAGATCTGTGA-TTGTAATCC
* * * ** *
30443992 ACTCCACTGTAACTTCAGGGAGATCGGATTGGCTTCTT
1 GCTCCACTGCAACTTCAGAGAGATAAGATTGGTTTCTT
30444030 CTATCTAACT
Statistics
Matches: 393, Mismatches: 67, Indels: 35
0.79 0.14 0.07
Matches are distributed among these distances:
85 131 0.33
86 6 0.02
87 3 0.01
88 64 0.16
89 31 0.08
90 37 0.09
91 117 0.30
92 4 0.01
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (88 bp):
GCTCCACTGCAACTTCAGAGAGATAAGATTGGTTTCTTTAATCCGCTCCACTGCAACTTCAGGGA
GATAAGATCTGTGATTGTAATCC
Found at i:30444035 original size:129 final size:128
Alignment explanation
Indices: 30443455--30444035 Score: 583
Period size: 129 Copynumber: 4.4 Consensus size: 128
30443445 GATTTGTGGC
* * * * ** * **
30443455 TTTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTCAATCTGCTCCACTATAA
1 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTT-TATCTGCTCCACTGCAA
* * * * * * * *
30443520 CTTCAGGGAGATAAGGTTTGTTATTTTCAGTCTGTTCCACTGCAACTTCAGGGAGATAA-AACTT
65 CTTCAGGGAGATAA-GATTG-GA-TGTGA-TCTGCTCTACTGCAACTTCAGAGAGATAAGATC-T
*
30443584 GTTA
125 GTGA
* * * * * * * * * *
30443588 TGGTGTGATCTGCTCTACTACAACTTCAGAGAGATAAGATTTGTTATTTTTAGTCTGTTCCACTG
1 T--TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTT-TCTTTA-TCTGCTCCACTG
30443653 CAACTTCAGGGAGATAAGACTTCTTATGG-TGTGATCTGCTCTACTGCAACTTCAGAGAGATAAG
62 CAACTTCAGGGAGATAAGA-----T-TGGATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAG
30443717 ATCTGTGA
121 ATCTGTGA
* *
30443725 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTTCGTCTACTCCACTGCAA
1 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTT-ATCTGCTCCACTGCAA
* * * * *
30443790 CATCAGGGAGATAAGACTGGATGTGATCTGCTCTATTGCAACTTCAGAGAGATAAGATTTGTGT
65 CTTCAGGGAGATAAGATTGGATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGA
30443854 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTTTATCTGCTCCACTGCAA
1 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTC-TTTATCTGCTCCACTGCAA
* *
30443919 CTTCAGGGAGATAAGATTGGATGTGATCTGCTCTACTGCAACTTCAGAGACATAAGATCTAT-A
65 CTTCAGGGAGATAAGATTGGATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGA
** * * *
30443982 GTTTTAATCTACTCCACTGTAACTTCAGGGAGATCGGATTGGCTTCTTCTATCT
1 -TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTT-TATCT
30444036 AACTACAATT
Statistics
Matches: 378, Mismatches: 54, Indels: 36
0.81 0.12 0.08
Matches are distributed among these distances:
128 5 0.01
129 200 0.53
130 3 0.01
133 1 0.00
134 32 0.08
135 70 0.19
136 28 0.07
137 31 0.08
138 5 0.01
140 1 0.00
141 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.34
Consensus pattern (128 bp):
TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTTATCTGCTCCACTGCAAC
TTCAGGGAGATAAGATTGGATGTGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGA
Found at i:30444180 original size:49 final size:49
Alignment explanation
Indices: 30444109--30444477 Score: 220
Period size: 49 Copynumber: 7.5 Consensus size: 49
30444099 GGGAAGTAAA
* *
30444109 ATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAACAAG
1 ATTCACCGTTGCAGCTTCAATCTTTTAAATTGCAATGTCGGGGAACAAG
* * * ** * ** * *
30444158 ATTCACCGTTGTAGCTTTAATCTATTCCACTGCACCG-CTAGGGAAGTAAG
1 ATTCACCGTTGCAGCTTCAATCTTTTAAATTGCAATGTC-GGGGAA-CAAG
** * * *
30444208 ATTTGCCATTGCGGCTTCAATCTTTTAAATTGCAATGTTGGGGAACAAG
1 ATTCACCGTTGCAGCTTCAATCTTTTAAATTGCAATGTCGGGGAACAAG
* * * ** * ** * ** *
30444257 ATTCACCGTTGTATCTTCAATCTGTTCCACTGCACCGCCAAGGAAGTAAG
1 ATTCACCGTTGCAGCTTCAATCTTTTAAATTGCAATGTCGGGGAA-CAAG
** * *
30444307 ATTCGTCGTTGCAGCTTCAATATTTTAAATTGCAATTTCGGGGAACAAG
1 ATTCACCGTTGCAGCTTCAATCTTTTAAATTGCAATGTCGGGGAACAAG
** * ** * * * * *
30444356 ATTCACCGTTTTAGCTTCAATCTATTCCACTGCACTG-CTAGGAAAGTAAG
1 ATTCACCGTTGCAGCTTCAATCTTTTAAATTGCAATGTC-GGGGAA-CAAG
**** *
30444406 ATTTGTTGTTGCGGCTTCAATCTTTTAAATTGCAATGTCGGGGAACAAG
1 ATTCACCGTTGCAGCTTCAATCTTTTAAATTGCAATGTCGGGGAACAAG
** *
30444455 ATTTGCCGTTGTAGCTTCAATCT
1 ATTCACCGTTGCAGCTTCAATCT
30444478 GTTCCACTGC
Statistics
Matches: 221, Mismatches: 92, Indels: 14
0.68 0.28 0.04
Matches are distributed among these distances:
48 2 0.01
49 120 0.54
50 98 0.44
51 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (49 bp):
ATTCACCGTTGCAGCTTCAATCTTTTAAATTGCAATGTCGGGGAACAAG
Found at i:30444201 original size:99 final size:99
Alignment explanation
Indices: 30444056--30444539 Score: 680
Period size: 99 Copynumber: 4.9 Consensus size: 99
30444046 TTTGGGAAGT
* * * * * * *
30444056 AAGATTCGCCGTCGTAGCTTCAACCTATTCCACTACACTGCCAGGGAAGTAAAATTCACCGTTGC
1 AAGATTCACCGTTGTAGCTTCAATCTATTCCACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGC
*
30444121 GGCTTCAATCTTTTTAATTGCAATGTCGGGGAAC
66 GGCTTCAATCTTTTAAATTGCAATGTCGGGGAAC
* * * *
30444155 AAGATTCACCGTTGTAGCTTTAATCTATTCCACTGCACCGCTAGGGAAGTAAGATTTGCCATTGC
1 AAGATTCACCGTTGTAGCTTCAATCTATTCCACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGC
*
30444220 GGCTTCAATCTTTTAAATTGCAATGTTGGGGAAC
66 GGCTTCAATCTTTTAAATTGCAATGTCGGGGAAC
* * * *
30444254 AAGATTCACCGTTGTATCTTCAATCTGTTCCACTGCACCGCCAAGGAAGTAAGATTCGTCGTTGC
1 AAGATTCACCGTTGTAGCTTCAATCTATTCCACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGC
* * *
30444319 AGCTTCAATATTTTAAATTGCAATTTCGGGGAAC
66 GGCTTCAATCTTTTAAATTGCAATGTCGGGGAAC
* * * * * **
30444353 AAGATTCACCGTTTTAGCTTCAATCTATTCCACTGCACTGCTAGGAAAGTAAGATTTGTTGTTGC
1 AAGATTCACCGTTGTAGCTTCAATCTATTCCACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGC
30444418 GGCTTCAATCTTTTAAATTGCAATGTCGGGGAAC
66 GGCTTCAATCTTTTAAATTGCAATGTCGGGGAAC
** * * *
30444452 AAGATTTGCCGTTGTAGCTTCAATCTGTTCCACTGCACCACCAGGGAAGTAAGATTCGCCGTTAC
1 AAGATTCACCGTTGTAGCTTCAATCTATTCCACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGC
30444517 GGCTTCAATCTTTTAAATTGCAA
66 GGCTTCAATCTTTTAAATTGCAA
30444540 CCTCAGGGGT
Statistics
Matches: 336, Mismatches: 49, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
99 336 1.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.31
Consensus pattern (99 bp):
AAGATTCACCGTTGTAGCTTCAATCTATTCCACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGC
GGCTTCAATCTTTTAAATTGCAATGTCGGGGAAC
Found at i:30445470 original size:16 final size:16
Alignment explanation
Indices: 30445451--30445484 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
30445441 TTTTTTGTTC
30445451 TTCTTTTCT-TTTCTTT
1 TTCTTTT-TGTTTCTTT
30445467 TTCTTTTTGTTTCTTT
1 TTCTTTTTGTTTCTTT
30445483 TT
1 TT
30445485 TTCAAGTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 1 0.06
16 16 0.94
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (16 bp):
TTCTTTTTGTTTCTTT
Found at i:30445470 original size:19 final size:19
Alignment explanation
Indices: 30445435--30445485 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
30445425 AGCCTCTCCT
30445435 TTTTCCTTTTTTGTTCTTC
1 TTTTCCTTTTTTGTTCTTC
* *
30445454 TTTT-CTTTTCTTTTTCTTT
1 TTTTCCTTTT-TTGTTCTTC
*
30445473 TTGTTTCTTTTTT
1 TT-TTCCTTTTTT
30445486 TCAAGTGAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 5 0.19
19 13 0.48
20 4 0.15
21 5 0.19
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (19 bp):
TTTTCCTTTTTTGTTCTTC
Found at i:30448009 original size:22 final size:23
Alignment explanation
Indices: 30447955--30448029 Score: 125
Period size: 23 Copynumber: 3.3 Consensus size: 23
30447945 AGTGTTATTG
30447955 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
30447978 ATCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
30448001 CT-AGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
30448023 ATCAGTG
1 ATCAGTG
30448030 TGGCACTTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
22 20 0.43
23 27 0.57
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:30448201 original size:38 final size:37
Alignment explanation
Indices: 30448159--30448231 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 37
30448149 ATGCGTGGAA
* *
30448159 TTGAATTGAATATTGACTTGAAAA-TGGAAAAGTGAATT
1 TTGAATTGAATAGTGA-TT-AAAAGTGAAAAAGTGAATT
30448197 TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAA
1 TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAA
30448232 ATTATGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 4 0.12
37 13 0.41
38 15 0.47
ACGTcount: A:0.45, C:0.01, G:0.22, T:0.32
Consensus pattern (37 bp):
TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAATT
Found at i:30458262 original size:23 final size:24
Alignment explanation
Indices: 30458225--30458271 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
30458215 GAATATTTTT
30458225 AATCTTAGTAGATTTGATTCTGTA
1 AATCTTAGTAGATTTGATTCTGTA
*
30458249 AATCTTA-TAGATTTGATTTTGTA
1 AATCTTAGTAGATTTGATTCTGTA
30458272 GATTGCTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.30, C:0.06, G:0.15, T:0.49
Consensus pattern (24 bp):
AATCTTAGTAGATTTGATTCTGTA
Found at i:30468248 original size:75 final size:74
Alignment explanation
Indices: 30468125--30468262 Score: 213
Period size: 75 Copynumber: 1.9 Consensus size: 74
30468115 AGAAAAAAAA
* * *
30468125 AGAGATTATCAATTCTGTTTTACTTTCTCTTCCCTATTAAAACTTGTTATCCATATGAATCATAC
1 AGAGATTATCAATTCTGTTTTACTTTCTCTTCCCTATCAAAACGTGTTATCCAAATGAATCATAC
30468190 AAAGTAGGG
66 AAAGTAGGG
* * *
30468199 AGAGATTATTAATTCTTTTCTTACTTTCTCTTCCCTATCCAAACGTGTTATCCAAATGAATCAT
1 AGAGATTATCAATTCTGTT-TTACTTTCTCTTCCCTATCAAAACGTGTTATCCAAATGAATCAT
30468263 TCCCTATTAC
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
74 17 0.30
75 40 0.70
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.41
Consensus pattern (74 bp):
AGAGATTATCAATTCTGTTTTACTTTCTCTTCCCTATCAAAACGTGTTATCCAAATGAATCATAC
AAAGTAGGG
Found at i:30470824 original size:24 final size:25
Alignment explanation
Indices: 30470792--30470846 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
30470782 CACTATTTTA
* * *
30470792 AATATAAAATATTCATT-TTTATAT
1 AATAAAAAATATACATTAATTATAT
30470816 AATAAAAAATATACATTAATTATAT
1 AATAAAAAATATACATTAATTATAT
*
30470841 ATTAAA
1 AATAAA
30470847 TAAAAATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 15 0.58
25 11 0.42
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (25 bp):
AATAAAAAATATACATTAATTATAT
Found at i:30471223 original size:7 final size:7
Alignment explanation
Indices: 30471213--30471239 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
30471203 ATTATAGATT
30471213 ATAAATG
1 ATAAATG
30471220 ATAAATG
1 ATAAATG
30471227 ATAAATG
1 ATAAATG
30471234 ATAAAT
1 ATAAAT
30471240 ATGGTTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (7 bp):
ATAAATG
Found at i:30471647 original size:20 final size:20
Alignment explanation
Indices: 30471619--30471659 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
30471609 CTTAATTACC
* *
30471619 AAATTTAAACATGAAAATGA
1 AAATATAAACATCAAAATGA
*
30471639 AAATATAAATATCAAAATGA
1 AAATATAAACATCAAAATGA
30471659 A
1 A
30471660 TTTAATTTCC
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:0.63, C:0.05, G:0.07, T:0.24
Consensus pattern (20 bp):
AAATATAAACATCAAAATGA
Found at i:30481784 original size:21 final size:21
Alignment explanation
Indices: 30481758--30481798 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
30481748 ATCTGCTCAA
* *
30481758 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
30481779 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
30481799 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:30488071 original size:16 final size:16
Alignment explanation
Indices: 30488050--30488085 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
30488040 TTTGGTTCGC
30488050 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
30488066 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
30488082 TGTA
1 TGTA
30488086 ATAGCTAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:30488150 original size:44 final size:45
Alignment explanation
Indices: 30488066--30488156 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
30488056 GGATTAGAGG
* * *
30488066 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
30488111 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
30488155 TG
1 TG
30488157 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:30488338 original size:16 final size:16
Alignment explanation
Indices: 30488301--30488342 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
30488291 TTAATCATAT
*
30488301 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
30488317 TT-AAATATATTATAA
1 TTAAAATATATTATAA
30488332 TTAAAATATAT
1 TTAAAATATAT
30488343 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:30488349 original size:14 final size:15
Alignment explanation
Indices: 30488310--30488351 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
30488300 TTTAAACATA
*
30488310 ATTATTATTAAATAT
1 ATTATAATTAAATAT
30488325 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
30488339 A-TATAATTTAATA
1 ATTATAATTAAATA
30488352 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:30488462 original size:18 final size:17
Alignment explanation
Indices: 30488441--30488475 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
30488431 TTATTATTAA
*
30488441 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
30488459 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
30488476 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:30488558 original size:66 final size:66
Alignment explanation
Indices: 30488480--30488678 Score: 235
Period size: 66 Copynumber: 3.2 Consensus size: 66
30488470 TAAAATTCTT
30488480 AATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTG
1 AATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTG
30488545 A
66 A
** * * * *
30488546 AATAATTAATATT-AAATAT--ATTT--T--AAT--TAAAATAT-ATAATTTAATA-A-AATTCT
1 AATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATT-T
*
30488599 -T
65 GA
30488600 AATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTG
1 AATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTG
30488665 A
66 A
30488666 AATAATTAATATT
1 AATAATTAATATT
30488679 AAATATATTT
Statistics
Matches: 105, Mismatches: 14, Indels: 28
0.71 0.10 0.19
Matches are distributed among these distances:
54 17 0.16
55 6 0.06
56 8 0.08
57 11 0.10
59 4 0.04
61 4 0.04
63 11 0.10
64 8 0.08
65 6 0.06
66 30 0.29
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.42
Consensus pattern (66 bp):
AATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTG
A
Found at i:30488588 original size:18 final size:17
Alignment explanation
Indices: 30488561--30488595 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
30488551 TTAATATTAA
*
30488561 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
30488579 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
30488596 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:30488727 original size:120 final size:120
Alignment explanation
Indices: 30488307--30488716 Score: 723
Period size: 120 Copynumber: 3.4 Consensus size: 120
30488297 ATATTTAAAC
* *
30488307 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
1 ATAATTAATATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
* * * * *
30488372 TCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT-AA
66 TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTGAA
*
30488426 CATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATA
1 -ATAATTAATATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATA
30488491 TTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTGAA
65 TTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTGAA
30488547 ATAATTAATATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
1 ATAATTAATATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
30488612 TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTGAA
66 TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTGAA
*
30488667 ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATAATTAATATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
30488717 TAAAATAATT
Statistics
Matches: 281, Mismatches: 8, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
120 279 0.99
121 2 0.01
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.43
Consensus pattern (120 bp):
ATAATTAATATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTGAA
Found at i:30488763 original size:101 final size:93
Alignment explanation
Indices: 30488657--30488940 Score: 317
Period size: 91 Copynumber: 3.0 Consensus size: 93
30488647 ACTATAAAAG
* * * *
30488657 ATAATTTGAAATAATTAATATTAAATATATTTTAATTAA-AATATATGATTTAATAAAATTTAAA
1 ATAATTTAAAATAATTAATATTAAATATAATTTAA-TAATAATATATAATTTCATAAAATTT---
*
30488721 ATAATTACAACTAATAAATTATCTTATATGAATTTGT
62 -T-ATT--AA-TAATAAATTATCTTATATGAATTTAT
* * *
30488758 ATAATTTAAAATAATTATTATTACATATAATTTAATAATAATATATAATTTCATAAAA--TTCTT
1 ATAATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTTTATT
* *
30488821 GATAATAAATTTTCTTATATGAATTTAT
66 AATAATAAATTATCTTATATGAATTTAT
* * *
30488849 ACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCATAAAA--TTCTT
1 ATAATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTTTATT
* *
30488912 GATAATAAATTTTCTTATATGAATTTAT
66 AATAATAAATTATCTTATATGAATTTAT
30488940 A
1 A
30488941 CAATAGATAT
Statistics
Matches: 168, Mismatches: 14, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
91 112 0.67
92 1 0.01
94 2 0.01
95 1 0.01
99 1 0.01
100 3 0.02
101 48 0.29
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (93 bp):
ATAATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTTTATT
AATAATAAATTATCTTATATGAATTTAT
Found at i:30488786 original size:26 final size:28
Alignment explanation
Indices: 30488757--30488817 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
30488747 TATGAATTTG
*
30488757 TATAATTTAA-AATAAT-TATTATTACA
1 TATAATTTAATAATAATATATAATTACA
*
30488783 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTACA
*
30488811 TAAAATT
1 TATAATT
30488818 CTTGATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTACA
Found at i:30488815 original size:47 final size:46
Alignment explanation
Indices: 30488764--30488907 Score: 113
Period size: 47 Copynumber: 3.1 Consensus size: 46
30488754 TTGTATAATT
30488764 TAAAATAATTATTATTACATATAATTTAATAATAATATATAATTTCA
1 TAAAATAATTATTATTA-ATATAATTTAATAATAATATATAATTTCA
* ** * *
30488811 TAAAAT--TCT-TGA-TAATA-AATTTTCTTATATGAATTTATACAATT--
1 TAAAATAAT-TATTATTAATATAA-TTTAATA-AT-AATATATA-ATTTCA
* *
30488855 TAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCA
1 TAAAATAATTATTATT-AATATAATTTAATAATAATATATAATTTCA
30488902 TAAAAT
1 TAAAAT
30488908 TCTTGATAAT
Statistics
Matches: 72, Mismatches: 12, Indels: 26
0.65 0.11 0.24
Matches are distributed among these distances:
42 2 0.03
43 8 0.11
44 10 0.14
45 14 0.19
46 12 0.17
47 15 0.21
48 9 0.12
49 2 0.03
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (46 bp):
TAAAATAATTATTATTAATATAATTTAATAATAATATATAATTTCA
Found at i:30488827 original size:91 final size:91
Alignment explanation
Indices: 30488732--30488944 Score: 372
Period size: 91 Copynumber: 2.3 Consensus size: 91
30488722 TAATTACAAC
* * * * *
30488732 TAATAAATTATCTTATATGAATTTGTATAATTTAAAATAATTATTATTACATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
30488797 AATATATAATTTCATAAAATTCTTGA
66 AATATATAATTTCATAAAATTCTTGA
30488823 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
30488888 GATATATAATTTCATAAAATTCTTGA
66 AATATATAATTTCATAAAATTCTTGA
30488914 TAATAAATTTTCTTATATGAATTTATACAAT
1 TAATAAATTTTCTTATATGAATTTATACAAT
30488945 AGATATTTAA
Statistics
Matches: 116, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 116 1.00
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (91 bp):
TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
AATATATAATTTCATAAAATTCTTGA
Found at i:30488921 original size:47 final size:47
Alignment explanation
Indices: 30488782--30488921 Score: 139
Period size: 47 Copynumber: 3.0 Consensus size: 47
30488772 TTATTATTAC
*
30488782 ATATAATTTAATAATAATATATAATTTCATAAAATTCTTGATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTGATAATAA
* * * ** * *
30488829 AT-T--TTCTTAT-ATGAATTTATACAATT--TAAAATAATTAATATTAA
1 ATATAATT-TAATAATG-ATATATA-ATTTCATAAAATTCTTGATAATAA
30488873 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTGATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTGATAATAA
30488920 AT
1 AT
30488922 TTTCTTATAT
Statistics
Matches: 69, Mismatches: 15, Indels: 18
0.68 0.15 0.18
Matches are distributed among these distances:
44 20 0.29
45 13 0.19
46 13 0.19
47 23 0.33
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (47 bp):
ATATAATTTAATAATGATATATAATTTCATAAAATTCTTGATAATAA
Found at i:30502575 original size:41 final size:41
Alignment explanation
Indices: 30502456--30502613 Score: 156
Period size: 41 Copynumber: 3.9 Consensus size: 41
30502446 GGAGTGAAAC
** * * * *
30502456 AACAATTTAAGCTTGTATTTAGGAGCCTCATTTTTTGGATA
1 AACAATTTAAGCTCATGTTTAGGAGCATCATATTTTGGATG
* ** * *
30502497 AACAATTTAAGTTTGTGCTTAAGAG-ATCATATTTTGGATG
1 AACAATTTAAGCTCATGTTTAGGAGCATCATATTTTGGATG
*
30502537 ACCAATTTAAGCTCATGTTTAGGAGCATCATATTTTGGATG
1 AACAATTTAAGCTCATGTTTAGGAGCATCATATTTTGGATG
* * * * *
30502578 AATAGTTTAAGTTCATGTTAAGGAGCATCATTTTTT
1 AACAATTTAAGCTCATGTTTAGGAGCATCATATTTT
30502614 TTTCTTTGAG
Statistics
Matches: 97, Mismatches: 19, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
40 31 0.32
41 66 0.68
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.41
Consensus pattern (41 bp):
AACAATTTAAGCTCATGTTTAGGAGCATCATATTTTGGATG
Found at i:30513799 original size:21 final size:21
Alignment explanation
Indices: 30513773--30513828 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
30513763 AACAGCGGTG
*
30513773 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
* *
30513794 GCGGTGAGATTGGATATTGTA
1 GCGGTGAGATTAGATACTGTA
30513815 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
30513829 AACAATGGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.07, G:0.38, T:0.30
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:30514260 original size:17 final size:17
Alignment explanation
Indices: 30514240--30514284 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
30514230 TATTACTAGA
30514240 AATTTTTAATTATAAAT
1 AATTTTTAATTATAAAT
** *
30514257 AATTTAAAATAATAAAT
1 AATTTTTAATTATAAAT
30514274 AATTTTTAATT
1 AATTTTTAATT
30514285 TTTAATTATA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AATTTTTAATTATAAAT
Found at i:30519182 original size:6 final size:6
Alignment explanation
Indices: 30519168--30519209 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
30519158 GGTTTTATCA
* *
30519168 AAATTG AAATGG AAATGG AAATGG AAATGA AAATGAG AAATG
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATG-G AAATG
30519210 ATTTATTTGC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
6 27 0.84
7 5 0.16
ACGTcount: A:0.55, C:0.00, G:0.26, T:0.19
Consensus pattern (6 bp):
AAATGG
Found at i:30527281 original size:25 final size:24
Alignment explanation
Indices: 30527253--30527312 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
30527243 TTCTTTTCTT
* *
30527253 TTTTCTTTTTCATTTTTAGATTAGG
1 TTTTCTTTTTC-TTTTTAGAATAGA
*
30527278 TTTTCCCTTTTCTTTTTAGAATAGA
1 TTTT-CTTTTTCTTTTTAGAATAGA
*
30527303 TTTTATTTTT
1 TTTTCTTTTT
30527313 GTTGCTTTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 4 0.14
25 19 0.66
26 6 0.21
ACGTcount: A:0.17, C:0.10, G:0.08, T:0.65
Consensus pattern (24 bp):
TTTTCTTTTTCTTTTTAGAATAGA
Found at i:30534705 original size:14 final size:15
Alignment explanation
Indices: 30534686--30534719 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
30534676 CAATTTAGTC
30534686 TAATTTTTTCATT-T
1 TAATTTTTTCATTAT
30534700 TAATTTTTTCATTAT
1 TAATTTTTTCATTAT
30534715 TAATT
1 TAATT
30534720 AGATCTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (15 bp):
TAATTTTTTCATTAT
Found at i:30536286 original size:29 final size:31
Alignment explanation
Indices: 30536246--30536308 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 31
30536236 CCTTTTAATA
*
30536246 TTTTTTAAAAA-TCTTATTAAAT-TCTAAAT
1 TTTTTTAAAAATTCTAATTAAATCTCTAAAT
* *
30536275 TTTTTTGAAAATTCTAATTAAATCTTTAAAT
1 TTTTTTAAAAATTCTAATTAAATCTCTAAAT
30536306 TTT
1 TTT
30536309 CTAAAAGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 10 0.34
30 10 0.34
31 9 0.31
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (31 bp):
TTTTTTAAAAATTCTAATTAAATCTCTAAAT
Found at i:30536295 original size:30 final size:30
Alignment explanation
Indices: 30536246--30536308 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
30536236 CCTTTTAATA
*
30536246 TTTTTTAAAAATCTTATTAAAT-TCTAAAT
1 TTTTTTAAAAATCTAATTAAATCTCTAAAT
* *
30536275 TTTTTTGAAAATTCTAATTAAATCTTTAAAT
1 TTTTTT-AAAAATCTAATTAAATCTCTAAAT
30536306 TTT
1 TTT
30536309 CTAAAAGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 6 0.21
30 14 0.48
31 9 0.31
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (30 bp):
TTTTTTAAAAATCTAATTAAATCTCTAAAT
Found at i:30536314 original size:29 final size:28
Alignment explanation
Indices: 30536238--30536314 Score: 82
Period size: 30 Copynumber: 2.6 Consensus size: 28
30536228 TCAATAATCC
*
30536238 TTTTAATATTTTTTAAAAATCTTATTAAA
1 TTTTAA-ATTTTTTAAAAATCTAATTAAA
* *
30536267 TTCTAAATTTTTTTGAAAATTCTAATTAAA
1 TTTTAAA-TTTTTT-AAAAATCTAATTAAA
*
30536297 TCTTTAAATTTTCTAAAA
1 T-TTTAAATTTTTTAAAA
30536315 GTTTTGATTG
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
28 1 0.03
29 15 0.38
30 19 0.47
31 5 0.12
ACGTcount: A:0.40, C:0.06, G:0.01, T:0.52
Consensus pattern (28 bp):
TTTTAAATTTTTTAAAAATCTAATTAAA
Found at i:30537305 original size:13 final size:13
Alignment explanation
Indices: 30537284--30537324 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
30537274 CTCTTGCTTC
30537284 TTCCGTTTTCTTT
1 TTCCGTTTTCTTT
*
30537297 TTCCTTTTTTCTTT
1 TTCC-GTTTTCTTT
*
30537311 TTCGGTTTTCTTT
1 TTCCGTTTTCTTT
30537324 T
1 T
30537325 CGGTTTTGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.00, C:0.20, G:0.07, T:0.73
Consensus pattern (13 bp):
TTCCGTTTTCTTT
Found at i:30537319 original size:14 final size:14
Alignment explanation
Indices: 30537289--30537331 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
30537279 GCTTCTTCCG
**
30537289 TTTTCTTTTTCCTT
1 TTTTCTTTTTCGGT
30537303 TTTTCTTTTTCGG-
1 TTTTCTTTTTCGGT
30537316 TTTTC-TTTTCGGT
1 TTTTCTTTTTCGGT
30537329 TTT
1 TTT
30537332 GGTTTTGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 7 0.27
13 8 0.31
14 11 0.42
ACGTcount: A:0.00, C:0.16, G:0.09, T:0.74
Consensus pattern (14 bp):
TTTTCTTTTTCGGT
Found at i:30537326 original size:12 final size:13
Alignment explanation
Indices: 30537288--30537331 Score: 54
Period size: 12 Copynumber: 3.4 Consensus size: 13
30537278 TGCTTCTTCC
*
30537288 GTTTTCTTTTTCCT
1 GTTTTCTTTTT-CG
*
30537302 TTTTTCTTTTTCG
1 GTTTTCTTTTTCG
30537315 GTTTTC-TTTTCG
1 GTTTTCTTTTTCG
30537327 GTTTT
1 GTTTT
30537332 GGTTTTGATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 11 0.41
13 6 0.22
14 10 0.37
ACGTcount: A:0.00, C:0.16, G:0.11, T:0.73
Consensus pattern (13 bp):
GTTTTCTTTTTCG
Found at i:30538121 original size:15 final size:16
Alignment explanation
Indices: 30538086--30538128 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
30538076 ATTTTATATG
*
30538086 TTATTTTAAAATTAGT
1 TTATTTTAAAATTAAT
*
30538102 TTATTTT-AATTTAAT
1 TTATTTTAAAATTAAT
30538117 TTA-TTTAAAATT
1 TTATTTTAAAATT
30538129 TCCCGTGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 3 0.13
15 13 0.57
16 7 0.30
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
TTATTTTAAAATTAAT
Found at i:30542781 original size:13 final size:13
Alignment explanation
Indices: 30542763--30542789 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
30542753 TAGCGACTAT
30542763 GGCATCTAACAAG
1 GGCATCTAACAAG
30542776 GGCATCTAACAAG
1 GGCATCTAACAAG
30542789 G
1 G
30542790 AGATCGGAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (13 bp):
GGCATCTAACAAG
Found at i:30545743 original size:158 final size:158
Alignment explanation
Indices: 30545516--30546474 Score: 1580
Period size: 158 Copynumber: 6.0 Consensus size: 158
30545506 GAAATGTACT
* *
30545516 AACAAATGGCTAAAATAAGGGTTTTTTTACTAAATTTATATAAAAAAAAACACACTAAATTAATA
1 AACAAAGGGCCAAAATAAGGG-TTTTTTACTAAATTTATAT---AAAAAACACACTAAATTAATA
*
30545581 CATTTCAAACTTTATGTACTAAAATAATATAAAATAATAAAATACAAAAATAGTATATTTTTTGA
62 CATTTCAAACTTTATGTACTAAAATAATATAAAATAATAAAATACGAAAATAGTATATTTTTTGA
**
30545646 AAGTAATAAAATATGAAAATAAGAAAAATACG
127 AAGTAATAAAATCCGAAAATAAGAAAAATACG
* *
30545678 AACAAAGGGCTAAAATAAGGGTTTTTTACTAAATTTATATAAAAAATACACTAAATTAATACATT
1 AACAAAGGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACACTAAATTAATACATT
30545743 TCAAACTTTATGTACTAAAATAATATAAAATAATAAAATACGAAAATAGTATATTTTTTGAAAGT
66 TCAAACTTTATGTACTAAAATAATATAAAATAATAAAATACGAAAATAGTATATTTTTTGAAAGT
* *
30545808 AATAAAATCCGAAAAAAAGAAAAATACA
131 AATAAAATCCGAAAATAAGAAAAATACG
*
30545836 AACAAAGGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAACACACACTAAATTAATACATT
1 AACAAAGGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACACTAAATTAATACATT
* * * *
30545901 TCAAAATTTATGTACTAAAATCATATAAAATAAGAAAATAAGAAAATAGTATATTTTTTGAAAGT
66 TCAAACTTTATGTACTAAAATAATATAAAATAATAAAATACGAAAATAGTATATTTTTTGAAAGT
*
30545966 AATAAAATCCGAAAATAAGAAAAATATG
131 AATAAAATCCGAAAATAAGAAAAATACG
* * *
30545994 AATAAAGGGCCAAAATAAGGGTTTTTTTACTAAATTTATA-AAAAAACACAATAAATTAATATAT
1 AACAAAGGGCCAAAATAAGGG-TTTTTTACTAAATTTATATAAAAAACACACTAAATTAATACAT
30546058 TTCAAACTTTATGTACTAAAATAATATAAAATAATAAAATACGAAAATAGTATATTTTTTGAAAG
65 TTCAAACTTTATGTACTAAAATAATATAAAATAATAAAATACGAAAATAGTATATTTTTTGAAAG
*
30546123 TAATAAAATCCAAAAATAAGAAAAATACG
130 TAATAAAATCCGAAAATAAGAAAAATACG
* * * *
30546152 AATAAAGGGCCAAAATAAGGATTTTTTACTAAATTTATAAAAAAAACACAATAAATTAATACATT
1 AACAAAGGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACACTAAATTAATACATT
*
30546217 TCAAACTTTATGTACTAAAATAATATAAAATAATAAAATACGAAAATAATATATTTTTTGAAAGT
66 TCAAACTTTATGTACTAAAATAATATAAAATAATAAAATACGAAAATAGTATATTTTTTGAAAGT
*
30546282 AATAAAATCCGAAAAAAAGAAAAATACG
131 AATAAAATCCGAAAATAAGAAAAATACG
* * *
30546310 AACAAAGGGCCAAAATAAAGGGTTTTCTACTAAATTTATATAAAAAATACACTAAAATAATACAT
1 AACAAAGGGCCAAAAT-AAGGGTTTTTTACTAAATTTATATAAAAAACACACTAAATTAATACAT
*
30546375 TTCAAACATTATGTACTAAAATAATATAAAATAA-ATAAATACGAAAATAGTATATTTTTTGAAA
65 TTCAAACTTTATGTACTAAAATAATATAAAATAATA-AAATACGAAAATAGTATATTTTTTGAAA
30546439 GTAATAAAATCCGAAAATAAGAAAAATACG
129 GTAATAAAATCCGAAAATAAGAAAAATACG
30546469 AACAAA
1 AACAAA
30546475 TGGGGTGCCG
Statistics
Matches: 751, Mismatches: 42, Indels: 11
0.93 0.05 0.01
Matches are distributed among these distances:
157 18 0.02
158 539 0.72
159 155 0.21
161 19 0.03
162 20 0.03
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.29
Consensus pattern (158 bp):
AACAAAGGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACACTAAATTAATACATT
TCAAACTTTATGTACTAAAATAATATAAAATAATAAAATACGAAAATAGTATATTTTTTGAAAGT
AATAAAATCCGAAAATAAGAAAAATACG
Found at i:30548660 original size:22 final size:22
Alignment explanation
Indices: 30548617--30548676 Score: 90
Period size: 22 Copynumber: 2.8 Consensus size: 22
30548607 GTACGGGATC
30548617 GCACTTCGGTGCCTC--TATTT
1 GCACTTCGGTGCCTCTGTATTT
30548637 GCACTTCGGTGCCTCTGTATTT
1 GCACTTCGGTGCCTCTGTATTT
30548659 GCACTAT-GGTGCCTCTGT
1 GCACT-TCGGTGCCTCTGT
30548677 TAGCATTTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.41
22 21 0.57
23 1 0.03
ACGTcount: A:0.10, C:0.28, G:0.23, T:0.38
Consensus pattern (22 bp):
GCACTTCGGTGCCTCTGTATTT
Found at i:30556044 original size:14 final size:15
Alignment explanation
Indices: 30556015--30556047 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
30556005 TTTCCTTTTA
*
30556015 TTCTCTTTTTTTCTT
1 TTCTCTTTTCTTCTT
30556030 TTCTC-TTTCTTCTT
1 TTCTCTTTTCTTCTT
30556044 TTCT
1 TTCT
30556048 TGCCTTCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (15 bp):
TTCTCTTTTCTTCTT
Found at i:30556678 original size:62 final size:62
Alignment explanation
Indices: 30556612--30556755 Score: 159
Period size: 63 Copynumber: 2.3 Consensus size: 62
30556602 GGAGACAAAT
* * * *
30556612 GTGTGTCCAAGCCGTGTAACTTATTGTTTGTA-ATTTTA-GTCACACGAGCT-AGAGATACGGGC
1 GTGTGTCCAGGCCGTGTAACTCACTGTTT-TAGA-TTTAGGTCACACG-GCTCAGAGACACGGGC
* * * *
30556674 GTGTGTCCAGGCCGTATAACTCACTGTTTTAGATTTAGGGTCATACGGGTCAGGGACACGGGC
1 GTGTGTCCAGGCCGTGTAACTCACTGTTTTAGATTTA-GGTCACACGGCTCAGAGACACGGGC
30556737 GTGTGTCCAGGCCGTGTAA
1 GTGTGTCCAGGCCGTGTAA
30556756 GGGCTTGTGA
Statistics
Matches: 69, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
61 6 0.09
62 28 0.41
63 35 0.51
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (62 bp):
GTGTGTCCAGGCCGTGTAACTCACTGTTTTAGATTTAGGTCACACGGCTCAGAGACACGGGC
Found at i:30564138 original size:43 final size:44
Alignment explanation
Indices: 30564081--30564163 Score: 132
Period size: 43 Copynumber: 1.9 Consensus size: 44
30564071 TCTCAATTCA
* * *
30564081 TCATTTCATAATTCATTTCTCATCTTTTCCATTTCAATATTTTC
1 TCATCTCATAATTCATTTCTCATCTTTGCAATTTCAATATTTTC
30564125 TCATCTCAT-ATTCATTTCTCATCTTTGCAATTTCAATAT
1 TCATCTCATAATTCATTTCTCATCTTTGCAATTTCAATAT
30564164 CAATCACATA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
43 28 0.78
44 8 0.22
ACGTcount: A:0.24, C:0.23, G:0.01, T:0.52
Consensus pattern (44 bp):
TCATCTCATAATTCATTTCTCATCTTTGCAATTTCAATATTTTC
Found at i:30564856 original size:19 final size:18
Alignment explanation
Indices: 30564816--30564856 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
30564806 AATATTATAC
*
30564816 ATTTCAATTTCACATTAA
1 ATTTCAATTTCACACTAA
*
30564834 ATTTCAATTTTCACACTAT
1 ATTTCAA-TTTCACACTAA
30564853 ATTT
1 ATTT
30564857 TGCTTATTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTTCAATTTCACACTAA
Found at i:30575911 original size:13 final size:15
Alignment explanation
Indices: 30575881--30575912 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
30575871 CCATTTCATG
30575881 CATTTCATCAATAAT
1 CATTTCATCAATAAT
30575896 CATTTCAT-AA-AAT
1 CATTTCATCAATAAT
30575909 CATT
1 CATT
30575913 ATTTCATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 2 0.12
15 8 0.47
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (15 bp):
CATTTCATCAATAAT
Found at i:30576189 original size:20 final size:20
Alignment explanation
Indices: 30576164--30576225 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 20
30576154 TCAATTAAAA
30576164 TTCAAATATTATTTCACTAT
1 TTCAAATATTATTTCACTAT
*
30576184 TTCAAATCA--CTTT-A--A-
1 TTCAAAT-ATTATTTCACTAT
*
30576199 TTCAAGTATTATTTCACTAT
1 TTCAAATATTATTTCACTAT
30576219 TTCAAAT
1 TTCAAAT
30576226 CACTTTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 14
0.63 0.08 0.29
Matches are distributed among these distances:
14 1 0.03
15 6 0.19
16 4 0.13
17 1 0.03
18 1 0.03
19 4 0.13
20 13 0.42
21 1 0.03
ACGTcount: A:0.35, C:0.16, G:0.02, T:0.47
Consensus pattern (20 bp):
TTCAAATATTATTTCACTAT
Found at i:30576201 original size:35 final size:35
Alignment explanation
Indices: 30576162--30576232 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
30576152 ATTCAATTAA
30576162 AATTCAAATATTATTTCACTATTTCAAATCACTTT
1 AATTCAAATATTATTTCACTATTTCAAATCACTTT
*
30576197 AATTCAAGTATTATTTCACTATTTCAAATCACTTT
1 AATTCAAATATTATTTCACTATTTCAAATCACTTT
30576232 A
1 A
30576233 TTTTCACTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.37, C:0.17, G:0.01, T:0.45
Consensus pattern (35 bp):
AATTCAAATATTATTTCACTATTTCAAATCACTTT
Found at i:30576856 original size:18 final size:18
Alignment explanation
Indices: 30576788--30576856 Score: 56
Period size: 18 Copynumber: 4.0 Consensus size: 18
30576778 TTAGTAGGGT
*
30576788 ATTCAAATT-ATTTTTCTA
1 ATTCAAATTCACTTTTC-A
* *
30576806 TTTCAAATTCAC-TTTCT
1 ATTCAAATTCACTTTTCA
**
30576823 ATTC-AA-TCACAATTCA
1 ATTCAAATTCACTTTTCA
30576839 ATTCAAATTCACTTTTCA
1 ATTCAAATTCACTTTTCA
30576857 CTTTATAATC
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
15 4 0.10
16 9 0.23
17 5 0.13
18 20 0.51
19 1 0.03
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTCAAATTCACTTTTCA
Found at i:30576897 original size:41 final size:40
Alignment explanation
Indices: 30576813--30576890 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 40
30576803 CTATTTCAAA
* * * *
30576813 TTCACTTTCTATTCAATCACAATTCAATTCAAATTCACTT
1 TTCACTTTATAATCAATCACAATTCAATACAAATACACTT
*
30576853 TTCACTTTATAATCAATACACAATTCAATACCAATACA
1 TTCACTTTATAATCAAT-CACAATTCAATACAAATACA
30576891 TATTTCAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
40 15 0.47
41 17 0.53
ACGTcount: A:0.38, C:0.24, G:0.00, T:0.37
Consensus pattern (40 bp):
TTCACTTTATAATCAATCACAATTCAATACAAATACACTT
Found at i:30577454 original size:11 final size:11
Alignment explanation
Indices: 30577438--30577462 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
30577428 TTAAATTTTC
30577438 CTATTCAATTT
1 CTATTCAATTT
30577449 CTATTCAATTT
1 CTATTCAATTT
30577460 CTA
1 CTA
30577463 CCGTAAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.20, G:0.00, T:0.52
Consensus pattern (11 bp):
CTATTCAATTT
Found at i:30577992 original size:3 final size:3
Alignment explanation
Indices: 30577984--30578009 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
30577974 TATATTAGTT
30577984 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
30578010 TAATATAATA
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:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:30579663 original size:13 final size:13
Alignment explanation
Indices: 30579645--30579681 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
30579635 ATAGGGGACA
30579645 CATGGTCGTGTCG
1 CATGGTCGTGTCG
30579658 CATGGTCGTGTCG
1 CATGGTCGTGTCG
30579671 CATGGTCGTGT
1 CATGGTCGTGT
30579682 GTCACACACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.08, C:0.22, G:0.38, T:0.32
Consensus pattern (13 bp):
CATGGTCGTGTCG
Found at i:30579888 original size:91 final size:91
Alignment explanation
Indices: 30579742--30579926 Score: 334
Period size: 91 Copynumber: 2.0 Consensus size: 91
30579732 AATTGGCCAA
* **
30579742 AATCAAGCCATTTATTTCACCCATTCAAGCATGAACCTACAAGAAACTTGTACATATAACCAAGA
1 AATCAAGCCATTTATTTCACCCATTCAAGCATGAACCTACAAAAAACTTACACATATAACCAAGA
30579807 CCTTAAAATATTCCCAAATTATGTAT
66 CCTTAAAATATTCCCAAATTATGTAT
*
30579833 AATCAAGCCATTTCTTTCACCCATTCAAGCATGAACCTACAAAAAACTTACACATATAACCAAGA
1 AATCAAGCCATTTATTTCACCCATTCAAGCATGAACCTACAAAAAACTTACACATATAACCAAGA
30579898 CCTTAAAATATTCCCAAATTATGTAT
66 CCTTAAAATATTCCCAAATTATGTAT
30579924 AAT
1 AAT
30579927 AAGACCAATT
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
91 90 1.00
ACGTcount: A:0.42, C:0.24, G:0.06, T:0.28
Consensus pattern (91 bp):
AATCAAGCCATTTATTTCACCCATTCAAGCATGAACCTACAAAAAACTTACACATATAACCAAGA
CCTTAAAATATTCCCAAATTATGTAT
Found at i:30594725 original size:22 final size:22
Alignment explanation
Indices: 30594697--30594741 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
30594687 GGACTGAGCA
* *
30594697 ATTAGGCTAAAGAATTCCAAAG
1 ATTAGGCCAAAGAAATCCAAAG
30594719 ATTAGGCCAAAGAAATCCAAAG
1 ATTAGGCCAAAGAAATCCAAAG
30594741 A
1 A
30594742 GAAGCACACG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.16, G:0.18, T:0.18
Consensus pattern (22 bp):
ATTAGGCCAAAGAAATCCAAAG
Found at i:30597116 original size:16 final size:15
Alignment explanation
Indices: 30597091--30597120 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
30597081 ATTAAATTAA
30597091 TTAACTAAATGCAAG
1 TTAACTAAATGCAAG
30597106 TTAACCTAAATGCAA
1 TTAA-CTAAATGCAA
30597121 ATGAAATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.27
Consensus pattern (15 bp):
TTAACTAAATGCAAG
Found at i:30600246 original size:50 final size:50
Alignment explanation
Indices: 30600178--30600367 Score: 191
Period size: 50 Copynumber: 3.7 Consensus size: 50
30600168 TTTTTTGTAC
* **
30600178 TGCCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATCGG
1 TGCCAATGCCATATCCCAGACATGGTCTTACATGAGACCTCTCATATCGG
* ** * *
30600228 TGCCCATGCCATATCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATATCCCAGACATGGTCTTACATGAGACCTCTCATATCGG
* * * * *
30600278 TGCCAAAGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAGTCTCAATGA
1 TGCCAATGCCATATCCCAGACATGGTCTTACATGAGACCTCTCATA---TC---GG
* *
30600334 TGCCAATGCCATGTCCCAAACATGGTCTTACATG
1 TGCCAATGCCATATCCCAGACATGGTCTTACATG
30600368 GGATCTCTTT
Statistics
Matches: 115, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
50 81 0.70
53 2 0.02
56 32 0.28
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATATCCCAGACATGGTCTTACATGAGACCTCTCATATCGG
Found at i:30601184 original size:17 final size:17
Alignment explanation
Indices: 30601162--30601199 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
30601152 TGGCTTCCTT
30601162 CAAATTTCGGCAGCAAG
1 CAAATTTCGGCAGCAAG
* *
30601179 CAAATTTTGGTAGCAAG
1 CAAATTTCGGCAGCAAG
30601196 CAAA
1 CAAA
30601200 GATGATGAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.21
Consensus pattern (17 bp):
CAAATTTCGGCAGCAAG
Found at i:30607876 original size:50 final size:50
Alignment explanation
Indices: 30607690--30607936 Score: 201
Period size: 50 Copynumber: 4.8 Consensus size: 50
30607680 GATAATAACA
* * ** * ** *
30607690 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGAGATGTTTTTTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGG
* * * ** * *
30607739 TGCCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * **
30607789 TGCCCATGCCATATCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
30607839 TGCCAAAGTCATGTCCCAGACATGGTCTTACATGGGACCTTTCATAGTCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC--A-TCTC---GG
*
30607895 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
30607937 TCACCCAAAT
Statistics
Matches: 159, Mismatches: 31, Indels: 9
0.80 0.16 0.05
Matches are distributed among these distances:
49 38 0.24
50 77 0.48
52 1 0.01
53 4 0.03
56 39 0.25
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.29
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:30610338 original size:138 final size:137
Alignment explanation
Indices: 30610155--30610434 Score: 409
Period size: 138 Copynumber: 2.0 Consensus size: 137
30610145 GAGAACATAT
* * * *
30610155 ATATAATTAATATATGAATTTGATTCATATAATATATTAATTGTATATGTTTTACCAAATTTAGT
1 ATATAATTAACATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTAGT
* * *
30610220 AATATAAATAATTATATTAATTAATTTCGATCC-AAATATAAAAGACATGAAAATTAACATTCTT
66 AATATAAACAATTATATTAATTAATTTCG-GCCAAAATATAAAAGACATG-AAATTAACATTATT
*
30610284 TTGGAAAGA
129 TTGAAAAGA
* *
30610293 ATATAATTAACATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATCAAATTTATT
1 ATATAATTAACATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTAGT
* * * *
30610358 AATATAAACAATTATATTAATTAATTTTGGCCAAAATATAAAAGATATGGAATTAATATTATTTT
66 AATATAAACAATTATATTAATTAATTTCGGCCAAAATATAAAAGACATGAAATTAACATTATTTT
30610423 GAAAAGA
131 GAAAAGA
30610430 ATATA
1 ATATA
30610435 CTTCCTGTTT
Statistics
Matches: 127, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
137 26 0.20
138 101 0.80
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (137 bp):
ATATAATTAACATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTAGT
AATATAAACAATTATATTAATTAATTTCGGCCAAAATATAAAAGACATGAAATTAACATTATTTT
GAAAAGA
Found at i:30610573 original size:74 final size:75
Alignment explanation
Indices: 30610452--30610619 Score: 232
Period size: 74 Copynumber: 2.3 Consensus size: 75
30610442 TTTTTAACTT
* * * *
30610452 TCTATTAATAAGAGAATAATCTTATATTCTTTTAGAAAATATATAATTCTTTTTTCTAACTTTCC
1 TCTATTAATAAGAGAATAATCCTACATTATTTTAGAAAATATATAATTCATTTTTCTAACTTTCC
30610517 ATTT-CATTC
66 ATTTGCATTC
* * *
30610526 TCTATTAATAAGGGAATAATCCTACATTATTTTCGAAAGA-ATATAATTCATTTTTCTAACTTTT
1 TCTATTAATAAGAGAATAATCCTACATTATTTTAGAAA-ATATATAATTCATTTTTCTAACTTTC
*
30610590 CATTTGCCTTC
65 CATTTGCATTC
*
30610601 TCTATTAATAAGAGGATAA
1 TCTATTAATAAGAGAATAA
30610620 AAGAGGATAA
Statistics
Matches: 82, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
74 60 0.73
75 22 0.27
ACGTcount: A:0.35, C:0.14, G:0.07, T:0.45
Consensus pattern (75 bp):
TCTATTAATAAGAGAATAATCCTACATTATTTTAGAAAATATATAATTCATTTTTCTAACTTTCC
ATTTGCATTC
Found at i:30613078 original size:20 final size:20
Alignment explanation
Indices: 30613053--30613091 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
30613043 TTGCTTGTTC
30613053 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
30613073 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
30613092 AAATAACTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:30613436 original size:50 final size:50
Alignment explanation
Indices: 30613382--30613488 Score: 133
Period size: 50 Copynumber: 2.1 Consensus size: 50
30613372 ACATGAGAGT
* ***
30613382 TCTCATATCGGTGCCCTTGCCATGTCCAAGACATGGTCTTACGGGGGACC
1 TCTCATATAGGTGCCAACGCCATGTCCAAGACATGGTCTTACGGGGGACC
* * * *
30613432 TCTCATCTAGGTGCCAACGCCATGTCCCAGACATGGTCTTATGTGGGACC
1 TCTCATATAGGTGCCAACGCCATGTCCAAGACATGGTCTTACGGGGGACC
*
30613482 TTTCATA
1 TCTCATA
30613489 ACCTCAATAA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.20, C:0.29, G:0.23, T:0.28
Consensus pattern (50 bp):
TCTCATATAGGTGCCAACGCCATGTCCAAGACATGGTCTTACGGGGGACC
Found at i:30622498 original size:23 final size:20
Alignment explanation
Indices: 30622471--30622513 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
30622461 TAAACATAAG
30622471 CATTTTAGTTAAAGTTTTAGTTA
1 CATTTTAG-T-AAG-TTTAGTTA
30622494 CATTTTAGTAAGTTTAGTTA
1 CATTTTAGTAAGTTTAGTTA
30622514 AGTTTAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 8 0.40
21 3 0.15
22 1 0.05
23 8 0.40
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.51
Consensus pattern (20 bp):
CATTTTAGTAAGTTTAGTTA
Found at i:30624393 original size:167 final size:165
Alignment explanation
Indices: 30624095--30624428 Score: 623
Period size: 167 Copynumber: 2.0 Consensus size: 165
30624085 GACCCGAAAC
30624095 AACTAGATTCTGAAGAAATAAAAGACACTTTTGTTGACGAGAAATTGTTCAGAGTCGATATCCAC
1 AACTAGATTCTGAAGAAATAAAAGACACTTTTGTTGACGAGAAATTGTTCAGAGTCGATATCCAC
30624160 AAAAAAAGGTTAAGAAATAATGGCACTCTATGGTATGTTGATTATGTAAACTATATTGCTAAAGG
66 AAAAAAAGGTTAAGAAATAATGGCACTCTATGGTATGTTGATTATGTAAACTATATTGCTAAAGG
30624225 TGTCTTTCCACCACAATTATCATGGAAACAAAAGA
131 TGTCTTTCCACCACAATTATCATGGAAACAAAAGA
* *
30624260 AACTGGATTCTGAAGAAATAAAAGAGACTTTTGTTGACGAGAAATTGTTCAGAGTCGATATCCAC
1 AACTAGATTCTGAAGAAATAAAAGACACTTTTGTTGACGAGAAATTGTTCAGAGTCGATATCCAC
*
30624325 AAAAAAAAAGGTTAAGAAATAATGGCACTCTATGGTATGTTGATTATGTAAACTATATTGTTAAA
66 --AAAAAAAGGTTAAGAAATAATGGCACTCTATGGTATGTTGATTATGTAAACTATATTGCTAAA
30624390 GGTGTCTTTCCACCACAATTATCATGGAAACAAAAGA
129 GGTGTCTTTCCACCACAATTATCATGGAAACAAAAGA
30624427 AA
1 AA
30624429 ATGATCATAA
Statistics
Matches: 164, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
165 63 0.38
167 101 0.62
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.28
Consensus pattern (165 bp):
AACTAGATTCTGAAGAAATAAAAGACACTTTTGTTGACGAGAAATTGTTCAGAGTCGATATCCAC
AAAAAAAGGTTAAGAAATAATGGCACTCTATGGTATGTTGATTATGTAAACTATATTGCTAAAGG
TGTCTTTCCACCACAATTATCATGGAAACAAAAGA
Found at i:30627882 original size:14 final size:13
Alignment explanation
Indices: 30627863--30627896 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
30627853 TAAACAATGT
30627863 TAAAGAAATAGATA
1 TAAAGAAATAGA-A
30627877 TAAAG-AATAGAA
1 TAAAGAAATAGAA
30627889 TAAAGAAA
1 TAAAGAAA
30627897 AAGAGATGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.32
13 8 0.42
14 5 0.26
ACGTcount: A:0.68, C:0.00, G:0.15, T:0.18
Consensus pattern (13 bp):
TAAAGAAATAGAA
Found at i:30627893 original size:12 final size:13
Alignment explanation
Indices: 30627863--30627895 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
30627853 TAAACAATGT
30627863 TAAAGAAATAGATA
1 TAAAG-AATAGATA
30627877 TAAAGAATAGA-A
1 TAAAGAATAGATA
30627889 TAAAGAA
1 TAAAGAA
30627896 AAAGAGATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
13 6 0.32
14 5 0.26
ACGTcount: A:0.67, C:0.00, G:0.15, T:0.18
Consensus pattern (13 bp):
TAAAGAATAGATA
Found at i:30635492 original size:50 final size:48
Alignment explanation
Indices: 30635385--30635779 Score: 234
Period size: 56 Copynumber: 7.6 Consensus size: 48
30635375 TGCGAAAGCT
* * * * *
30635385 ATGTCCCAGACATAGTCTTACATGGGATGTTTCTTGTA-CTGCCAATGCC
1 ATGTCCCAGACATGGTCTTACATGGGAT-TCTCATCTAGGTGCC-ATGCC
* * * *
30635434 ATATCCCAGATATGGTCTTACATGAGAGTTCTCATATAGGTGTCCATGCC
1 ATGTCCCAGACATGGTCTTACATGGGA-TTCTCATCTAGGTG-CCATGCC
** * * * **
30635484 ATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTTGGTGCGAACACC
1 ATGTCCCAGACATGGTCTTACATGGGA-TTCTCATCTAGGTGC-CATGCC
*
30635534 ATGTCCCAGACATGGTCTTACATGGGATCTCTCATCTCGGTGCCAATGCC
1 ATGTCCCAGACATGGTCTTACATGGGAT-TCTCATCTAGGTGCC-ATGCC
** * *
30635584 ATGTCCTTGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATGCCAATGCC
1 ATGTCCCAGACATGGTCTTACATGGGA--T-TC-TCATCT--A-GGTGCC-ATGCC
** * *
30635640 ATGTCCTTGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATGCCAATGCC
1 ATGTCCCAGACATGGTCTTACATGGGA--T-TC-TCATCT--A-GGTGCC-ATGCC
* *
30635696 ATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATGCCAATGCC
1 ATGTCCCAGACATGGTCTTACATGGGA--T-TC-TCATCT--A-GGTGCC-ATGCC
**
30635752 ATGTCCCAGACATATTCTTACATGGGAT
1 ATGTCCCAGACATGGTCTTACATGGGAT
30635780 CTCTTTACCC
Statistics
Matches: 298, Mismatches: 36, Indels: 19
0.84 0.10 0.05
Matches are distributed among these distances:
49 30 0.10
50 110 0.37
51 2 0.01
52 4 0.01
53 5 0.02
54 1 0.00
56 146 0.49
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (48 bp):
ATGTCCCAGACATGGTCTTACATGGGATTCTCATCTAGGTGCCATGCC
Found at i:30635552 original size:100 final size:100
Alignment explanation
Indices: 30635432--30635730 Score: 278
Period size: 100 Copynumber: 2.9 Consensus size: 100
30635422 ACTGCCAATG
*
30635432 CCATATCCCAGATATGGTCTTACATGAGAGT-TCTCATATAGGTGTCC-ATGCCATGTCCCAGAC
1 CCATATCCCAGACATGGTCTTACATGAGA-TCTCTCATATAGGTG-CCAATGCCATGTCCCAGAC
*
30635495 ATGGTCTTACGGGGGACCTCTCATCTTGGTGCGAACA
64 ATGGTCTTACAGGGGACCTCTCATCTTGGTGCGAACA
* * * * **
30635532 CCATGTCCCAGACATGGTCTTACATGGGATCTCTCATCTCGGTGCCAATGCCATGTCCTTGACAT
1 CCATATCCCAGACATGGTCTTACATGAGATCTCTCATATAGGTGCCAATGCCATGTCCCAGACAT
* * * **
30635597 GGTCTTACATGGGACCTCTCATAATCTCAATGATGCCAATG
66 GGTCTTACAGGGGACCTCTC---ATCT---TGGTGCGAACA
* ** * * *
30635638 CCATGTCCTTGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATGCCAATGCCATGTCCC
1 CCATATCCCAGACATGGTCTTACATGAGATCTCTCAT-A--T--A-GGTGCCAATGCCATGTCCC
*
30635703 AGACATGGTCTTACATGGGACCTCTCAT
60 AGACATGGTCTTACAGGGGACCTCTCAT
30635731 AATCTCAATG
Statistics
Matches: 164, Mismatches: 21, Indels: 19
0.80 0.10 0.09
Matches are distributed among these distances:
99 3 0.02
100 71 0.43
103 4 0.02
106 41 0.25
109 3 0.02
112 42 0.26
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (100 bp):
CCATATCCCAGACATGGTCTTACATGAGATCTCTCATATAGGTGCCAATGCCATGTCCCAGACAT
GGTCTTACAGGGGACCTCTCATCTTGGTGCGAACA
Found at i:30635640 original size:56 final size:56
Alignment explanation
Indices: 30635574--30635783 Score: 357
Period size: 56 Copynumber: 3.8 Consensus size: 56
30635564 CTCATCTCGG
**
30635574 TGCCAATGCCATGTCCTTGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
**
30635630 TGCCAATGCCATGTCCTTGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
30635686 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
** *
30635742 TGCCAATGCCATGTCCCAGACATATTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
30635784 TTACCCAAAT
Statistics
Matches: 149, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 149 1.00
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.30
Consensus pattern (56 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
Found at i:30644865 original size:17 final size:17
Alignment explanation
Indices: 30644843--30644875 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
30644833 ATAAGTATAC
30644843 ATTGTCATTACATTTTT
1 ATTGTCATTACATTTTT
*
30644860 ATTGTCATTACCTTTT
1 ATTGTCATTACATTTT
30644876 AGTGTTAGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.15, G:0.06, T:0.58
Consensus pattern (17 bp):
ATTGTCATTACATTTTT
Found at i:30652627 original size:24 final size:20
Alignment explanation
Indices: 30652582--30652622 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
30652572 CAAGACAAGC
30652582 ATACAAATCAAATATTCCTT
1 ATACAAATCAAATATTCCTT
30652602 ATACAAATCAAATATTCCTT
1 ATACAAATCAAATATTCCTT
30652622 A
1 A
30652623 CTTATTCAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (20 bp):
ATACAAATCAAATATTCCTT
Found at i:30656911 original size:42 final size:42
Alignment explanation
Indices: 30656814--30656911 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 42
30656804 GAAATGGGCA
* * *
30656814 TACTCACACGAGATGTGGGTCAAAATGTGAGCTGCACGATAC
1 TACTCACACGAGCTGTGGGTCAAAATGTAAGCTACACGATAC
** * * *
30656856 TGTTAACACGAGCTGTGGGTCAAAATGTAAGCTACATGATGC
1 TACTCACACGAGCTGTGGGTCAAAATGTAAGCTACACGATAC
*
30656898 TACTCACATGAGCT
1 TACTCACACGAGCT
30656912 ATTGAGTATC
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (42 bp):
TACTCACACGAGCTGTGGGTCAAAATGTAAGCTACACGATAC
Found at i:30660787 original size:23 final size:23
Alignment explanation
Indices: 30660758--30660806 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
30660748 ACCTTAGGAC
30660758 TGGATGATGAACTAAAGTGAGAT
1 TGGATGATGAACTAAAGTGAGAT
30660781 TGGATGATGAACTAAAGTGAGAT
1 TGGATGATGAACTAAAGTGAGAT
30660804 TGG
1 TGG
30660807 TTAACTTAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.37, C:0.04, G:0.33, T:0.27
Consensus pattern (23 bp):
TGGATGATGAACTAAAGTGAGAT
Found at i:30668313 original size:20 final size:20
Alignment explanation
Indices: 30668261--30668315 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
30668251 ATATGTATGA
* *
30668261 ATACCCTGAATGAAGTATCG
1 ATACCTTGACTGAAGTATCG
* *
30668281 ATACTTTGGCTGAAGTATCG
1 ATACCTTGACTGAAGTATCG
*
30668301 ATGCCTTGACTGAAG
1 ATACCTTGACTGAAG
30668316 CATCAATACA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (20 bp):
ATACCTTGACTGAAGTATCG
Found at i:30671192 original size:18 final size:18
Alignment explanation
Indices: 30671162--30671209 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
30671152 TTTCTATCAC
*
30671162 TTTT-AATACTTTTTAAT
1 TTTTAAATAATTTTTAAT
*
30671179 TTTTAAATAATTTTTTATT
1 TTTTAAATAA-TTTTTAAT
30671198 TTTTAAA-AATTT
1 TTTTAAATAATTT
30671210 AAAAATTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 7 0.26
18 6 0.22
19 14 0.52
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTAAATAATTTTTAAT
Found at i:30671195 original size:19 final size:18
Alignment explanation
Indices: 30671171--30671209 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
30671161 CTTTTAATAC
30671171 TTTTTAATTTTTAAATAAT
1 TTTTTAATTTTTAAA-AAT
*
30671190 TTTTTATTTTTTAAAAAT
1 TTTTTAATTTTTAAAAAT
30671208 TT
1 TT
30671210 AAAAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTTAATTTTTAAAAAT
Found at i:30673944 original size:88 final size:90
Alignment explanation
Indices: 30673841--30674022 Score: 260
Period size: 88 Copynumber: 2.0 Consensus size: 90
30673831 TCCTCTTTTT
* * *
30673841 TTTTTTTGCACTCAATTGAGCACTTAAACTTTCAAAATGTATCAAAAAGGCCCTTAAAC-CTTTT
1 TTTTTTTGCACTCAATTGAGCACTTAAACTTTCAAAATATATCAAAAAGACCCTCAAACTCTTTT
*
30673905 C-AAAAAAAGCAATTAAGCCCCTAC
66 CAAAAAAAAACAATTAAGCCCCTAC
* * * * *
30673929 TTTTTTTGCATTCAATTGGGTACTTGAACTTTCAAAATATATCAAAAAGACCCTCAAACTTTTTT
1 TTTTTTTGCACTCAATTGAGCACTTAAACTTTCAAAATATATCAAAAAGACCCTCAAACTCTTTT
*
30673994 CAAAAAAAAATAATTAAGCCCCTAC
66 CAAAAAAAAACAATTAAGCCCCTAC
30674019 TTTT
1 TTTT
30674023 ATTAAAAATT
Statistics
Matches: 82, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
88 52 0.63
89 5 0.06
90 25 0.30
ACGTcount: A:0.37, C:0.20, G:0.08, T:0.34
Consensus pattern (90 bp):
TTTTTTTGCACTCAATTGAGCACTTAAACTTTCAAAATATATCAAAAAGACCCTCAAACTCTTTT
CAAAAAAAAACAATTAAGCCCCTAC
Found at i:30674049 original size:9 final size:9
Alignment explanation
Indices: 30674037--30674147 Score: 86
Period size: 9 Copynumber: 12.1 Consensus size: 9
30674027 AAAATTAGAA
30674037 AAAATATAT
1 AAAATATAT
30674046 AAAA-ATATT
1 AAAATATA-T
*
30674055 AAAAAATAT
1 AAAATATAT
30674064 AAAA-ATAT
1 AAAATATAT
* *
30674072 AAAAATTTGT
1 -AAAATATAT
*
30674082 AAAATTTTAT
1 AAAA-TATAT
30674092 AAAA-ATCAT
1 AAAATAT-AT
30674101 AAAATATTAT
1 AAAATA-TAT
30674111 AAAATATAT
1 AAAATATAT
*
30674120 AGAAATATAA
1 A-AAATATAT
30674130 AAAAT-TAT
1 AAAATATAT
*
30674138 AAAATTTAT
1 AAAATATAT
30674147 A
1 A
30674148 GTCATTAGAA
Statistics
Matches: 86, Mismatches: 6, Indels: 20
0.77 0.05 0.18
Matches are distributed among these distances:
8 15 0.17
9 40 0.47
10 30 0.35
11 1 0.01
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (9 bp):
AAAATATAT
Found at i:30674050 original size:20 final size:19
Alignment explanation
Indices: 30674025--30674069 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
30674015 CTACTTTTAT
30674025 TAAAAATTAGAAAAAATATA
1 TAAAAATTAGAAAAAA-ATA
**
30674045 TAAAAA-TATTAAAAAATA
1 TAAAAATTAGAAAAAAATA
30674063 TAAAAAT
1 TAAAAAT
30674070 ATAAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 9 0.41
19 7 0.32
20 6 0.27
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (19 bp):
TAAAAATTAGAAAAAAATA
Found at i:30674061 original size:10 final size:9
Alignment explanation
Indices: 30674025--30674141 Score: 69
Period size: 10 Copynumber: 12.6 Consensus size: 9
30674015 CTACTTTTAT
*
30674025 TAAAAATTA
1 TAAAAAATA
*
30674034 GAAAAAATA
1 TAAAAAATA
30674043 TATAAAAATA
1 TA-AAAAATA
30674053 TTAAAAAATA
1 -TAAAAAATA
30674063 T-AAAAATA
1 TAAAAAATA
*
30674071 T-AAAAATT
1 TAAAAAATA
* * *
30674079 TGTAAAATTT
1 T-AAAAAATA
30674089 TATAAAAATCA
1 TA-AAAAAT-A
*
30674100 TAAAATAT-
1 TAAAAAATA
*
30674108 TATAAAATA
1 TAAAAAATA
*
30674117 TATAGAAATA
1 TA-AAAAATA
30674127 TAAAAAATTA
1 TAAAAAA-TA
30674137 TAAAA
1 TAAAA
30674142 TTTATAGTCA
Statistics
Matches: 85, Mismatches: 14, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
8 21 0.25
9 15 0.18
10 45 0.53
11 4 0.05
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.31
Consensus pattern (9 bp):
TAAAAAATA
Found at i:30674075 original size:46 final size:47
Alignment explanation
Indices: 30674025--30674141 Score: 125
Period size: 46 Copynumber: 2.5 Consensus size: 47
30674015 CTACTTTTAT
30674025 TAAAAATTAGAAAAAATATATAAAAAT-ATTAAAA-AATATAAAA-ATA
1 TAAAAATTAGAAAAAAT-TATAAAAATCA-TAAAATAATATAAAATATA
* ** *
30674071 TAAAAATTTGTAAAATTTTATAAAAATCATAAAATATTATAAAATATA
1 TAAAAATTAG-AAAAAATTATAAAAATCATAAAATAATATAAAATATA
* *
30674119 TAGAAA-TATAAAAAATTATAAAA
1 TAAAAATTAGAAAAAATTATAAAA
30674142 TTTATAGTCA
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
46 35 0.60
47 15 0.26
48 8 0.14
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.31
Consensus pattern (47 bp):
TAAAAATTAGAAAAAATTATAAAAATCATAAAATAATATAAAATATA
Found at i:30674171 original size:56 final size:55
Alignment explanation
Indices: 30674047--30674186 Score: 149
Period size: 56 Copynumber: 2.5 Consensus size: 55
30674037 AAAATATATA
* * *
30674047 AAAATATTAAAAAATATAA-AAATATAAAAATTTGTAAAATTTTATAAAAATCAT
1 AAAATATTAAAAAATATAAGAAATATAAAAAATTATAAAATTTTATAAAAATCAG
* *** *
30674101 AAAATATTATAAAATATATAGAAATATAAAAAATTATAAAA-TTTATAGTCATTAG
1 AAAATATTAAAAAATATA-AGAAATATAAAAAATTATAAAATTTTATAAAAATCAG
* *
30674156 AAAATTATAAAAAAATGTAAAGAAATATAAA
1 AAAA-TATTAAAAAATAT-AAGAAATATAAA
30674187 TTTCGTAAAA
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
54 17 0.24
55 14 0.20
56 39 0.55
57 1 0.01
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.31
Consensus pattern (55 bp):
AAAATATTAAAAAATATAAGAAATATAAAAAATTATAAAATTTTATAAAAATCAG
Found at i:30674374 original size:10 final size:10
Alignment explanation
Indices: 30674361--30674386 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
30674351 TTTTTCTAAT
30674361 TTTTATAAAA
1 TTTTATAAAA
30674371 TTTTATAAAA
1 TTTTATAAAA
30674381 TTTTAT
1 TTTTAT
30674387 TTTTTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
TTTTATAAAA
Found at i:30674449 original size:20 final size:20
Alignment explanation
Indices: 30674426--30674486 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
30674416 TTAATAAATT
30674426 TTAAATTTTTTATATTTTTA
1 TTAAATTTTTTATATTTTTA
* * *
30674446 TTAAA-ATTTAATAATTTTTC
1 TTAAATTTTTTAT-ATTTTTA
* *
30674466 TAAAATTTATTAT-TTTTTA
1 TTAAATTTTTTATATTTTTA
30674485 TT
1 TT
30674487 TTTATAAAAA
Statistics
Matches: 30, Mismatches: 9, Indels: 5
0.68 0.20 0.11
Matches are distributed among these distances:
19 11 0.37
20 15 0.50
21 4 0.13
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (20 bp):
TTAAATTTTTTATATTTTTA
Found at i:30674461 original size:47 final size:47
Alignment explanation
Indices: 30674371--30674517 Score: 155
Period size: 46 Copynumber: 3.2 Consensus size: 47
30674361 TTTTATAAAA
*
30674371 TTTT-ATAAAATTT-T-ATTTTTTATTTTTAT-AAAAAAATTCTAAT
1 TTTTAATAAAATTTATAATTTTTTATTTTTATAAAAAAAATTATAAT
* ** *
30674414 TTTTAATAAATTTTA-AATTTTTTATATTTT-TATTAAAATTTAATAAT
1 TTTTAATAAAATTTATAATTTTTTAT-TTTTATAAAAAAAATT-ATAAT
* * *
30674461 TTTT-CTAAAATTTATTATTTTTTATTTTTATAAAAAAAATTCTAAT
1 TTTTAATAAAATTTATAATTTTTTATTTTTATAAAAAAAATTATAAT
30674507 TTTTAATAAAA
1 TTTTAATAAAA
30674518 GTAGGGGCTT
Statistics
Matches: 82, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
43 4 0.05
44 8 0.10
45 10 0.12
46 30 0.37
47 30 0.37
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (47 bp):
TTTTAATAAAATTTATAATTTTTTATTTTTATAAAAAAAATTATAAT
Found at i:30674482 original size:18 final size:19
Alignment explanation
Indices: 30674434--30674482 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
30674424 TTTTAAATTT
*
30674434 TTTA-TATTTTTATTAAAA
1 TTTATTATTTTTACTAAAA
*
30674452 TTTAATAATTTTT-CTAAAA
1 TTT-ATTATTTTTACTAAAA
30674471 TTTATTATTTTT
1 TTTATTATTTTT
30674483 TATTTTTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 11 0.42
19 9 0.35
20 6 0.23
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTATTATTTTTACTAAAA
Found at i:30674482 original size:19 final size:17
Alignment explanation
Indices: 30674434--30674483 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 17
30674424 TTTTAAATTT
30674434 TTTATATTTTTATTAAAA
1 TTTATATTTTT-TTAAAA
*
30674452 TTTAATAATTTTTCTAAAA
1 TTT-AT-ATTTTTTTAAAA
30674471 TTTATTATTTTTT
1 TTTA-TATTTTTT
30674484 ATTTTTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
18 10 0.37
19 11 0.41
20 6 0.22
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTATATTTTTTTAAAA
Found at i:30678685 original size:3 final size:3
Alignment explanation
Indices: 30678671--30678710 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
30678661 ACAAAATTTA
*
30678671 AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
30678711 CTATCAACTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:30680056 original size:187 final size:184
Alignment explanation
Indices: 30679797--30680341 Score: 869
Period size: 187 Copynumber: 2.9 Consensus size: 184
30679787 AAAAAGGCGG
** *
30679797 AACCAAATTAGTGAAAAAAATTAAGTAACAATAGAATATTTAAGTAGAGCAAATCTGCAATTAGA
1 AACCAAATTAGTGAAAAAAA-CGAGT-A-AATAGAATATTTAAGTAGAGCAAATCTGCAATGAGA
*
30679862 ACAGAGATCTTCAACATCAACTAAACAGCTT-ATGCATTTTCTCTTCACATTGATCTACTCTTTC
63 ACAGAGATCTTCAACATCAACTAAACAGCTTAATGCA-TTTCTCTTCACATTGATCTACTCTTAC
30679926 CTAAAATCAAACATGAAATTCTCACTCTTTCTCAGGAAACAAACAAACAATAAACACT
127 CTAAAATCAAACATGAAATTCTCACTCTTTCTCAGGAAACAAACAAACAATAAACACT
* * *
30679984 AACCAAATTAGTGAAAAGAAACGAGTAAGACTAGAAGATTTAAGTAGAGCACATCTGCAACGAGA
1 AACCAAATTAGTGAAAA-AAACGAGTAA-A-TAGAATATTTAAGTAGAGCAAATCTGCAATGAGA
* * *
30680049 ACAGAGATCTTCAACATCAACTAAACAGCTTAACGCATTTCTTTTCACATTGATCTACTATTACC
63 ACAGAGATCTTCAACATCAACTAAACAGCTTAATGCATTTCTCTTCACATTGATCTACTCTTACC
* *
30680114 TAAAATCAAACATGAAATTCCCACTCTTTCTCAGGAAACAAACAAACACTAAACACT
128 TAAAATCAAACATGAAATTCTCACTCTTTCTCAGGAAACAAACAAACAATAAACACT
* *
30680171 AACCAAAGTAGTGAAAAAAACGAGT-AATAGATTATTTAAGTAGAGCAAATCTGCAATGAGAACA
1 AACCAAATTAGTGAAAAAAACGAGTAAATAGAATATTTAAGTAGAGCAAATCTGCAATGAGAACA
*
30680235 GAGATCTTCAACATCAACTAAGCAGCTTAATGCATTTCTCTTCACATTGATCTACTCTTACCTAA
66 GAGATCTTCAACATCAACTAAACAGCTTAATGCATTTCTCTTCACATTGATCTACTCTTACCTAA
*
30680300 AATCAAACATGAAATTCTCACTCTTTCTCAGGAAACAGACAA
131 AATCAAACATGAAATTCTCACTCTTTCTCAGGAAACAAACAA
30680342 GCAACAATTT
Statistics
Matches: 331, Mismatches: 23, Indels: 12
0.90 0.06 0.03
Matches are distributed among these distances:
183 134 0.40
184 1 0.00
185 2 0.01
186 10 0.03
187 177 0.53
188 7 0.02
ACGTcount: A:0.42, C:0.21, G:0.11, T:0.26
Consensus pattern (184 bp):
AACCAAATTAGTGAAAAAAACGAGTAAATAGAATATTTAAGTAGAGCAAATCTGCAATGAGAACA
GAGATCTTCAACATCAACTAAACAGCTTAATGCATTTCTCTTCACATTGATCTACTCTTACCTAA
AATCAAACATGAAATTCTCACTCTTTCTCAGGAAACAAACAAACAATAAACACT
Found at i:30683243 original size:10 final size:10
Alignment explanation
Indices: 30683228--30683254 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
30683218 AAAGTGAATA
30683228 ATTCAAATTT
1 ATTCAAATTT
30683238 ATTCAAATTT
1 ATTCAAATTT
30683248 ATTCAAA
1 ATTCAAA
30683255 CCAAATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (10 bp):
ATTCAAATTT
Found at i:30687571 original size:50 final size:50
Alignment explanation
Indices: 30687508--30687637 Score: 152
Period size: 50 Copynumber: 2.6 Consensus size: 50
30687498 AGGTCCCATG
* * ** *
30687508 TAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCA
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGAAGAGAACTCCCACA
* * * **
30687558 TAAGACCATGTCTGAGACATGGCATGGGCACCGATAAGAGAACTCCCATG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGAAGAGAACTCCCACA
* *
30687608 TAAGACCATATCTGGGATATGGCATTGGCA
1 TAAGACCATGTCTGGGACATGGCATTGGCA
30687638 GTACAGAAAA
Statistics
Matches: 66, Mismatches: 14, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
50 66 1.00
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.20
Consensus pattern (50 bp):
TAAGACCATGTCTGGGACATGGCATTGGCACCGAGAAGAGAACTCCCACA
Found at i:30689972 original size:25 final size:25
Alignment explanation
Indices: 30689923--30689972 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
30689913 TTCATACTAT
* *
30689923 TTTTTGAAATTTTTTATAATTTTTA
1 TTTTTAAAATTTTTTATAATATTTA
30689948 TTTTTAAAATATTTTTATAA-ATTTA
1 TTTTTAAAAT-TTTTTATAATATTTA
30689973 ATATTTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (25 bp):
TTTTTAAAATTTTTTATAATATTTA
Found at i:30691014 original size:30 final size:30
Alignment explanation
Indices: 30690980--30691039 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
30690970 ACTTAACAAG
*
30690980 TAAATGTCTCTAAAATAATAACAAAATTAA
1 TAAATGCCTCTAAAATAATAACAAAATTAA
* *
30691010 TAAATGCCTTTAAAATAATAATAAAATTAA
1 TAAATGCCTCTAAAATAATAACAAAATTAA
30691040 CAATAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.57, C:0.08, G:0.03, T:0.32
Consensus pattern (30 bp):
TAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:30691049 original size:17 final size:17
Alignment explanation
Indices: 30691019--30691051 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
30691009 ATAAATGCCT
30691019 TTAAAATAATAATAAAA
1 TTAAAATAATAATAAAA
30691036 TTAACAATAA-AATAAA
1 TTAA-AATAATAATAAA
30691052 TTTTATACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (17 bp):
TTAAAATAATAATAAAA
Found at i:30691097 original size:22 final size:22
Alignment explanation
Indices: 30691072--30691114 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
30691062 TATCCAAACA
30691072 ATAACAATAAAATAGTAGCAAC
1 ATAACAATAAAATAGTAGCAAC
* * *
30691094 ATAATAGTAAAATGGTAGCAA
1 ATAACAATAAAATAGTAGCAA
30691115 AATAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.56, C:0.09, G:0.14, T:0.21
Consensus pattern (22 bp):
ATAACAATAAAATAGTAGCAAC
Found at i:30692554 original size:25 final size:23
Alignment explanation
Indices: 30692507--30692554 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
30692497 ATACTTTTAC
* *
30692507 ATATTCATATTTTTTATTTTTTT
1 ATATTCATATTTTTAATTATTTT
30692530 ATATTCATATTTTTGCAATTATTTT
1 ATATTCATATTTTT--AATTATTTT
30692555 TAACCTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 14 0.67
25 7 0.33
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (23 bp):
ATATTCATATTTTTAATTATTTT
Found at i:30705418 original size:25 final size:24
Alignment explanation
Indices: 30705368--30705418 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 24
30705358 GGGTATCAAC
*
30705368 AAAAAAAATATCAAATTAAAATAT
1 AAAAAAAATATCAAATTAAAACAT
* **
30705392 AAAAATAAATATTAAATTTTAACAT
1 AAAAA-AAATATCAAATTAAAACAT
30705417 AA
1 AA
30705419 TTCACTAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (24 bp):
AAAAAAAATATCAAATTAAAACAT
Found at i:30705513 original size:74 final size:73
Alignment explanation
Indices: 30705375--30705513 Score: 224
Period size: 74 Copynumber: 1.9 Consensus size: 73
30705365 AACAAAAAAA
* * * **
30705375 ATATCAAATTAAAATATAAAAATAAATATTAAATTTTAACATAATTCACTAATAATTAGTCAAAA
1 ATATCAAATTAAAATATAAAAATAAATATTAAAATTTAACATAATCCACTAATAATAACCCAAAA
30705440 ATTTATAT
66 ATTTATAT
30705448 ATATCAAATTAAAATATAAAAAATAAATATTAAAATTTAACATAATCCACTAATAATAACCCAAA
1 ATATCAAATTAAAATAT-AAAAATAAATATTAAAATTTAACATAATCCACTAATAATAACCCAAA
30705513 A
65 A
30705514 GCTAATCTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
73 17 0.28
74 43 0.72
ACGTcount: A:0.58, C:0.09, G:0.01, T:0.32
Consensus pattern (73 bp):
ATATCAAATTAAAATATAAAAATAAATATTAAAATTTAACATAATCCACTAATAATAACCCAAAA
ATTTATAT
Found at i:30713377 original size:3 final size:3
Alignment explanation
Indices: 30713369--30713393 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
30713359 GGCCCCGCCA
30713369 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
30713394 TCTCTACTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:30715564 original size:34 final size:34
Alignment explanation
Indices: 30715521--30715588 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
30715511 TTTTTCGAGT
30715521 TAGTTCACACACACTTGATGATAATTCTAATAAC
1 TAGTTCACACACACTTGATGATAATTCTAATAAC
30715555 TAGTTCACACACACTTGATGATAATTCTAATAAC
1 TAGTTCACACACACTTGATGATAATTCTAATAAC
30715589 CCACACATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (34 bp):
TAGTTCACACACACTTGATGATAATTCTAATAAC
Found at i:30716072 original size:15 final size:17
Alignment explanation
Indices: 30716043--30716074 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
30716033 AGAAAATTGT
30716043 GAAAAGAAAACAAAAGA
1 GAAAAGAAAACAAAAGA
30716060 GAAAA-AAAA-AAAAGA
1 GAAAAGAAAACAAAAGA
30716075 AAACGTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (17 bp):
GAAAAGAAAACAAAAGA
Found at i:30718348 original size:25 final size:25
Alignment explanation
Indices: 30718312--30718393 Score: 103
Period size: 25 Copynumber: 3.3 Consensus size: 25
30718302 CGAGTTGAAT
* * *
30718312 TCGAGCTGAATATCAGTAAGCTCATG
1 TCGAGCTAAATATCGGTAAGCTC-TC
30718338 T-GAGCTAAATATCGGTAAGCTCTC
1 TCGAGCTAAATATCGGTAAGCTCTC
*
30718362 TCGAGCTAAATATCGGTAACCTCTC
1 TCGAGCTAAATATCGGTAAGCTCTC
*
30718387 TTGAGCT
1 TCGAGCT
30718394 GAGAATCAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
24 2 0.04
25 47 0.94
26 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (25 bp):
TCGAGCTAAATATCGGTAAGCTCTC
Found at i:30721752 original size:42 final size:43
Alignment explanation
Indices: 30721705--30721813 Score: 139
Period size: 42 Copynumber: 2.6 Consensus size: 43
30721695 ATATTCGTAT
* *
30721705 ACAAGCTACCATGTAGGTTGTGGATAAACGA-AAAATTTGCAG
1 ACAAGCTACCATGTAGGTTGTGGATAAACCACAAAATTTGCAA
* * * *
30721747 ACAAGCTACCTTGTAGGTTATGGATAAACCACCAATTTTGCAA
1 ACAAGCTACCATGTAGGTTGTGGATAAACCACAAAATTTGCAA
* *
30721790 AGAAGCTGCCATGTAGGTTGTGGA
1 ACAAGCTACCATGTAGGTTGTGGA
30721814 CGAAGCCACA
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
42 28 0.50
43 28 0.50
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.26
Consensus pattern (43 bp):
ACAAGCTACCATGTAGGTTGTGGATAAACCACAAAATTTGCAA
Found at i:30728258 original size:41 final size:41
Alignment explanation
Indices: 30728199--30728284 Score: 95
Period size: 41 Copynumber: 2.1 Consensus size: 41
30728189 CATGTTATCA
** * *
30728199 CATATCGATGCCTCTGTCCTAGACA-GGGTCTTACAC-GAAT
1 CATATCGATGCCAATGTCCCAGA-ATGGGTCTTACACAAAAT
*
30728239 CATATACGATGCCAATGTCCCAGAATTGGTCTTACACAAAAT
1 CATAT-CGATGCCAATGTCCCAGAATGGGTCTTACACAAAAT
30728281 CATA
1 CATA
30728285 CCTCAAAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
40 6 0.16
41 25 0.66
42 7 0.18
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (41 bp):
CATATCGATGCCAATGTCCCAGAATGGGTCTTACACAAAAT
Found at i:30737038 original size:39 final size:39
Alignment explanation
Indices: 30736949--30737220 Score: 270
Period size: 39 Copynumber: 7.1 Consensus size: 39
30736939 TGCTATTGGA
*
30736949 GTATCGAAGTACAACCA--GGCACGTAAGTGCAATTAGGG
1 GTATCGAAGTACAA-CAGGGGCACGTAAGTGCAATCAGGG
* * ** *
30736987 GTA-CCAAGGTACAACAAGGGCATATAAGTGCAATTAGGG
1 GTATCGAA-GTACAACAGGGGCACGTAAGTGCAATCAGGG
* * * **
30737026 GTATTGAAGTACAATAGGGGCACGTAAGAGTGATCAGGG
1 GTATCGAAGTACAACAGGGGCACGTAAGTGCAATCAGGG
* *
30737065 GTATCAAAGTACAACAGGGGCACGTAAGTGCGATCAGGG
1 GTATCGAAGTACAACAGGGGCACGTAAGTGCAATCAGGG
* * * *
30737104 GTACCGAAGTAAAATAGGGGCACGTAAGTGC-GTCAGGG
1 GTATCGAAGTACAACAGGGGCACGTAAGTGCAATCAGGG
* * *
30737142 GTATCGAAGTACAACAGGGGCACGTAGGTGCGATCAAGG
1 GTATCGAAGTACAACAGGGGCACGTAAGTGCAATCAGGG
* * *
30737181 GTACCAAAGTAC-A-A-GGGCACGTAAGTGCCATCAGGG
1 GTATCGAAGTACAACAGGGGCACGTAAGTGCAATCAGGG
30737217 GTAT
1 GTAT
30737221 AATTATATAA
Statistics
Matches: 194, Mismatches: 35, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
36 22 0.11
37 6 0.03
38 43 0.22
39 121 0.62
40 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.33, T:0.17
Consensus pattern (39 bp):
GTATCGAAGTACAACAGGGGCACGTAAGTGCAATCAGGG
Found at i:30737093 original size:19 final size:19
Alignment explanation
Indices: 30737071--30737167 Score: 72
Period size: 19 Copynumber: 5.1 Consensus size: 19
30737061 AGGGGTATCA
30737071 AAGTACAACAGGGGCACGT
1 AAGTACAACAGGGGCACGT
* * *
30737090 AAGTGCGATCAGGGGTACCG-
1 AAGTAC-AACAGGGGCA-CGT
* *
30737110 AAGTAAAATAGGGGCACGT
1 AAGTACAACAGGGGCACGT
* ** *
30737129 AAGTGCGTCAGGGGTATCG-
1 AAGTACAACAGGGGCA-CGT
30737148 AAGTACAACAGGGGCACGT
1 AAGTACAACAGGGGCACGT
30737167 A
1 A
30737168 GGTGCGATCA
Statistics
Matches: 55, Mismatches: 18, Indels: 10
0.66 0.22 0.12
Matches are distributed among these distances:
18 4 0.07
19 35 0.64
20 14 0.25
21 2 0.04
ACGTcount: A:0.33, C:0.18, G:0.35, T:0.14
Consensus pattern (19 bp):
AAGTACAACAGGGGCACGT
Found at i:30738830 original size:16 final size:17
Alignment explanation
Indices: 30738799--30738831 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
30738789 AAAAATAATT
30738799 TAATTTGATATAATTTA
1 TAATTTGATATAATTTA
*
30738816 TAATTT-ATTTAATTTA
1 TAATTTGATATAATTTA
30738832 ATTGTCGTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
TAATTTGATATAATTTA
Found at i:30739883 original size:24 final size:22
Alignment explanation
Indices: 30739851--30739900 Score: 55
Period size: 24 Copynumber: 2.2 Consensus size: 22
30739841 ATCTTAAAAT
*
30739851 AAAATCATTAATTAAAAATTAATA
1 AAAAACATTAATT-AAAA-TAATA
**
30739875 AAAAACATTTCTTAAAATAATA
1 AAAAACATTAATTAAAATAATA
30739897 AAAA
1 AAAA
30739901 TGTGTTAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 9 0.39
23 4 0.17
24 10 0.43
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (22 bp):
AAAAACATTAATTAAAATAATA
Found at i:30739977 original size:23 final size:23
Alignment explanation
Indices: 30739950--30739994 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
30739940 ATATATTTTA
30739950 ATTAAATT-TTAAAAATAATTAAT
1 ATTAAATTCTTAAAAAT-ATTAAT
*
30739973 ATTAATTTCTTAAAAATATTAA
1 ATTAAATTCTTAAAAATATTAA
30739995 AAAATTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
ATTAAATTCTTAAAAATATTAAT
Found at i:30740225 original size:26 final size:26
Alignment explanation
Indices: 30740196--30740247 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
30740186 AAACCAAACA
*
30740196 TTTCAAAAGTACTTCT-CAAAAGCAAT
1 TTTCAAAAGCACTT-TGCAAAAGCAAT
* *
30740222 TTTCCATAGCACTTTGCAAAAGCAAT
1 TTTCAAAAGCACTTTGCAAAAGCAAT
30740248 GCTAAACTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (26 bp):
TTTCAAAAGCACTTTGCAAAAGCAAT
Found at i:30743313 original size:16 final size:15
Alignment explanation
Indices: 30743294--30743327 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
30743284 AAAGTTGATA
*
30743294 ATAATTAATATATATT
1 ATAATAAATATA-ATT
30743310 ATAATAAATATAATT
1 ATAATAAATATAATT
30743325 ATA
1 ATA
30743328 TACTATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:30751061 original size:10 final size:10
Alignment explanation
Indices: 30751042--30751089 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
30751032 GAATTTGTCA
*
30751042 AAAATAAATC
1 AAAATTAATC
30751052 AAAATTAATC
1 AAAATTAATC
*
30751062 AAAATTTAATAT
1 AAAA-TTAAT-C
*
30751074 AAAATTAATT
1 AAAATTAATC
30751084 AAAATT
1 AAAATT
30751090 CAACATGTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
10 20 0.59
11 10 0.29
12 4 0.12
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (10 bp):
AAAATTAATC
Found at i:30754483 original size:47 final size:46
Alignment explanation
Indices: 30754415--30754503 Score: 133
Period size: 47 Copynumber: 1.9 Consensus size: 46
30754405 TTGTAATGGT
* *
30754415 ATGTCGTTGGGAGAGCTCAATCACAATATTATAGTGAAATGATTTG
1 ATGTCATTGGGAGAGCTCAATCACAATACTATAGTGAAATGATTTG
* *
30754461 ATGTCATTGGGGAGAGCTCAATCACAATGCTATAGTGGAATGA
1 ATGTCATT-GGGAGAGCTCAATCACAATACTATAGTGAAATGA
30754504 CTTGGTGACT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
46 7 0.18
47 31 0.82
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (46 bp):
ATGTCATTGGGAGAGCTCAATCACAATACTATAGTGAAATGATTTG
Found at i:30756010 original size:25 final size:25
Alignment explanation
Indices: 30755976--30756053 Score: 138
Period size: 25 Copynumber: 3.1 Consensus size: 25
30755966 TAGGACATAA
*
30755976 ATGTAATTTTTCCAAAAAAGATTCC
1 ATGTAATTTTTCCAAAAAGGATTCC
*
30756001 ATGTAATTTTTCTAAAAAGGATTCC
1 ATGTAATTTTTCCAAAAAGGATTCC
30756026 ATGTAATTTTTCCAAAAAGGATTCC
1 ATGTAATTTTTCCAAAAAGGATTCC
30756051 ATG
1 ATG
30756054 GCGAAGAGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 50 1.00
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (25 bp):
ATGTAATTTTTCCAAAAAGGATTCC
Found at i:30765388 original size:26 final size:26
Alignment explanation
Indices: 30765359--30765416 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
30765349 AATTTTCTTG
*
30765359 AAATTTTATCGAGGGTAAAATTGTCA
1 AAATTTTACCGAGGGTAAAATTGTCA
* *
30765385 AAATTTTACCGTGTGTAAAATTGTCA
1 AAATTTTACCGAGGGTAAAATTGTCA
30765411 AAATTT
1 AAATTT
30765417 AACTGGGGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (26 bp):
AAATTTTACCGAGGGTAAAATTGTCA
Done.