Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 130 of 318
Found at i:40227105 original size:48 final size:49
Alignment explanation
Indices: 40227014--40227112 Score: 146
Period size: 48 Copynumber: 2.0 Consensus size: 49
40227004 ATAAAATTAA
**
40227014 AATTAAAATTGCATAAATGAAAAAAAATATTAAATTGTATTGAAAAATT
1 AATTAAAATTGCATAAATGAAAAAAAATATTAAATACTATTGAAAAATT
* * *
40227063 AATTAAAATTGCATAAAT-TAAAAAGATATTAAATACTATTGAAATATT
1 AATTAAAATTGCATAAATGAAAAAAAATATTAAATACTATTGAAAAATT
40227111 AA
1 AA
40227113 AATTATCACT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
48 27 0.60
49 18 0.40
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (49 bp):
AATTAAAATTGCATAAATGAAAAAAAATATTAAATACTATTGAAAAATT
Found at i:40235523 original size:206 final size:206
Alignment explanation
Indices: 40234980--40235536 Score: 907
Period size: 207 Copynumber: 2.7 Consensus size: 206
40234970 GCAGATCTGG
*
40234980 CTGAAGCAAAATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
1 CTGAAGC-AGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
*
40235045 GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
65 GATTTGGTTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
* * **
40235110 AGAACAAATCAAAGTTTGGCGTCTCCATATTCGACAGAGAGCAGACACATAGCAGATCTGGCCTT
130 AGAACAAATCGAAGTTTGGCATCTCCATATTCGACAGAGAGCAGACACATAGCAGATCTAACCTT
* *
40235175 CAGATGTTTATA
195 CAGATGATTAGA
* *
40235187 CTGAAGTAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
1 CTGAAG-CAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
**
40235252 GATTTGGTTTTCACGTGCTTACGATGAAAAAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
65 GATTTGGTTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
* *
40235317 AGAACAAATCGAAGTTTGGCATCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTAACCTT
130 AGAACAAATCGAAGTTTGGCATCTCCATATTCGACAGAGAGCAGACACATAGCAGATCTAACCTT
40235382 CAGATGATTAGA
195 CAGATGATTAGA
* *
40235394 CTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTG
1 CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTG
** ** *
40235459 ATTTGGTTTTTGCGTGCTTACCCTGAAGCAAATCTAAGATAATTTGGCATCTCTGTATTGTCAGA
66 ATTTGGTTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
40235524 GAACAAATCGAAG
131 GAACAAATCGAAG
40235537 AAGCAGATTT
Statistics
Matches: 324, Mismatches: 25, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
206 126 0.39
207 198 0.61
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (206 bp):
CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTG
ATTTGGTTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
GAACAAATCGAAGTTTGGCATCTCCATATTCGACAGAGAGCAGACACATAGCAGATCTAACCTTC
AGATGATTAGA
Found at i:40239729 original size:44 final size:44
Alignment explanation
Indices: 40239664--40240077 Score: 261
Period size: 44 Copynumber: 9.5 Consensus size: 44
40239654 CAGCCTGTTA
*
40239664 CCCTACTGCTTTGGGGGTTAAGGCCCTTCGTCTTCGATCTCTTT
1 CCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTCTTT
* * ** *** *
40239708 CCCTGCTGCTTAGGGCGTTAA-GATCTAT-AAATTC-AGC-CTGTT
1 CCCTACTGCTTAGGGGGTTAAGGCCCT-TCGTCTTCGATCTCT-TT
*
40239750 ACCCTACTGCTTAGGGGGTTAAGGCCCTTCATCTTCGATCTCTTT
1 -CCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTCTTT
** * * * * *
40239795 CCCTACTGCTTAGGGGGTTAA-GATC-T-GTAAATT-TAGCATGTTA
1 CCCTACTGCTTAGGGGGTTAAGGCCCTTCGT--CTTCGATC-TCTTT
*
40239838 CCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTATTT
1 CCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTCTTT
* ** * *
40239882 CCCTACTGCTTAGGGGGCTAA-GATC-T-GTAAATTC-AGC-CTGTT
1 CCCTACTGCTTAGGGGGTTAAGGCCCTTCGT--CTTCGATCTCT-TT
* *
40239924 ACCCTACTGCTTAGGGGCTTAAGGCCCTTCGTCTTCGATCTGTTT
1 -CCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTCTTT
* * *** * *
40239969 CCCTACTGCTTAGGGAGCTAA-AATC-T-GTAAATTC-AGC-CTGTT
1 CCCTACTGCTTAGGGGGTTAAGGCCCTTCGT--CTTCGATCTCT-TT
*
40240011 ACCCTACTACTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTCTTT
1 -CCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTCTTT
* *
40240056 CCCTACTACTTAGGGGGCTAAG
1 CCCTACTGCTTAGGGGGTTAAG
40240078 ATCTGTAAAT
Statistics
Matches: 276, Mismatches: 62, Indels: 64
0.69 0.15 0.16
Matches are distributed among these distances:
41 9 0.03
42 17 0.06
43 100 0.36
44 122 0.44
45 17 0.06
46 11 0.04
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34
Consensus pattern (44 bp):
CCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTCTTT
Found at i:40239775 original size:87 final size:87
Alignment explanation
Indices: 40239621--40240111 Score: 793
Period size: 87 Copynumber: 5.6 Consensus size: 87
40239611 CAGCCTGTTA
* * * * *
40239621 CCCTACTACTTAGAGGGTTAAGATTTGTAAATTCAGCCTGTTACCCTACTGCTTTGGGGGTTAAG
1 CCCTACTGCTTAGGGGGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAG
40239686 GCCCTTCGTCTTCGATCTCTTT
66 GCCCTTCGTCTTCGATCTCTTT
* * * *
40239708 CCCTGCTGCTTAGGGCGTTAAGATCTATAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAG
1 CCCTACTGCTTAGGGGGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAG
*
40239773 GCCCTTCATCTTCGATCTCTTT
66 GCCCTTCGTCTTCGATCTCTTT
* * *
40239795 CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTTAGCATGTTACCCTACTGCTTAGGGGGTTAAG
1 CCCTACTGCTTAGGGGGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAG
*
40239860 GCCCTTCGTCTTCGATCTATTT
66 GCCCTTCGTCTTCGATCTCTTT
*
40239882 CCCTACTGCTTAGGGGGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGCTTAAG
1 CCCTACTGCTTAGGGGGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAG
*
40239947 GCCCTTCGTCTTCGATCTGTTT
66 GCCCTTCGTCTTCGATCTCTTT
* * *
40239969 CCCTACTGCTTAGGGAGCTAAAATCTGTAAATTCAGCCTGTTACCCTACTACTTAGGGGGTTAAG
1 CCCTACTGCTTAGGGGGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAG
40240034 GCCCTTCGTCTTCGATCTCTTT
66 GCCCTTCGTCTTCGATCTCTTT
* *
40240056 CCCTACTACTTAGGGGGCTAAGATCTGTAAATTCAGCTTGTTACCCTACTGCTTAG
1 CCCTACTGCTTAGGGGGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAG
40240112 AGGGCTGTTA
Statistics
Matches: 374, Mismatches: 30, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 374 1.00
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.34
Consensus pattern (87 bp):
CCCTACTGCTTAGGGGGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAG
GCCCTTCGTCTTCGATCTCTTT
Found at i:40240085 original size:261 final size:271
Alignment explanation
Indices: 40239621--40240251 Score: 879
Period size: 261 Copynumber: 2.3 Consensus size: 271
40239611 CAGCCTGTTA
* * * * *
40239621 CCCTACTACTTAGAGGGTTAAGATTTGTAAATTCAGCCTGTTACCCTACTGCTTTGGGGGTTAAG
1 CCCTACTGCTTAGGGGGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGC-TTAGGGGTTAAG
* * * * *
40239686 GCCCTTCGTCTTCGATCTCTTTCCCTGCTGCTTAGGGCGTTAAGATCTATAAATTCAGCCTGTTA
65 GCCCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGGAGCTAAAATCTATAAATTCAGCCTGTTA
* * *
40239751 CCCTACTGCTTAGGGGGTTAAGGCCCTTCATCTTCGATCTCTTTCCCTACTGCTTAGGGGGTTAA
130 CCCTACTACTTAGGGGGTTAAGGCCCTTCATCTTCGATCTCTTTCCCTACTACTTAGGGGGCTAA
* *
40239816 GATCTGT-AA-A-T-TTA-GC-A-TG-TT-A-C-CCTACTGCTTAGGGGGTTAAGGCCCTTCGTC
195 GATCTGTAAATACTGTTACCCTACTGCTTAAGCTCCTACTACTTAGGGGGTTAAGGCCCTTCGTC
40239870 TTCGATCTATTT
260 TTCGATCTATTT
40239882 CCCTACTGCTTAGGGGGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGCTTAAG
1 CCCTACTGCTTAGGGGGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGG-TTAAG
*
40239947 GCCCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGGAGCTAAAATCTGTAAATTCAGCCTGTTA
65 GCCCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGGAGCTAAAATCTATAAATTCAGCCTGTTA
*
40240012 CCCTACTACTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTCTTTCCCTACTACTTAGGGGGCTAA
130 CCCTACTACTTAGGGGGTTAAGGCCCTTCATCTTCGATCTCTTTCCCTACTACTTAGGGGGCTAA
40240077 GATCTGTAAATTCAGCTTGTTACCCTACTGCTTAGAGGGCTGTTACCCTACTACTTAGGGGGTTA
195 GATCTGTAAA-T-A-C-TGTTACCCTACTGCTTA-A--GC---T--CCTACTACTTAGGGGGTTA
*
40240142 AGGCCCTTCGTCTTCGATCTCTTT
248 AGGCCCTTCGTCTTCGATCTATTT
*
40240166 CCCTACTGTTTAGGGGGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAAGGGGTTAAG
1 CCCTACTGCTTAGGGGGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTT-AGGGGTTAAG
40240231 GCCCTTCGTCTTCGATCTGTT
65 GCCCTTCGTCTTCGATCTGTT
40240252 ACACCATTCT
Statistics
Matches: 326, Mismatches: 19, Indels: 27
0.88 0.05 0.07
Matches are distributed among these distances:
260 6 0.02
261 180 0.55
262 2 0.01
265 1 0.00
268 1 0.00
269 3 0.01
270 1 0.00
271 1 0.00
272 2 0.01
273 2 0.01
275 1 0.00
278 1 0.00
284 120 0.37
285 5 0.02
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (271 bp):
CCCTACTGCTTAGGGGGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTAAGG
CCCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGGAGCTAAAATCTATAAATTCAGCCTGTTAC
CCTACTACTTAGGGGGTTAAGGCCCTTCATCTTCGATCTCTTTCCCTACTACTTAGGGGGCTAAG
ATCTGTAAATACTGTTACCCTACTGCTTAAGCTCCTACTACTTAGGGGGTTAAGGCCCTTCGTCT
TCGATCTATTT
Found at i:40240199 original size:110 final size:109
Alignment explanation
Indices: 40240006--40240224 Score: 402
Period size: 110 Copynumber: 2.0 Consensus size: 109
40239996 TAAATTCAGC
40240006 CTGTTACCCTACTACTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTCTTTCCCTACTACTTAGGG
1 CTGTTACCCTACTACTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTCTTTCCCTACTACTTAGGG
*
40240071 GGCTAAGATCTGTAAATTCAGCTTGTTACCCTACTGCTTAGAGGG
66 GGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTA-AGGG
**
40240116 CTGTTACCCTACTACTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTCTTTCCCTACTGTTTAGGG
1 CTGTTACCCTACTACTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTCTTTCCCTACTACTTAGGG
40240181 GGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAAGGG
66 GGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAAGGG
40240225 GTTAAGGCCC
Statistics
Matches: 106, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
109 4 0.04
110 102 0.96
ACGTcount: A:0.19, C:0.26, G:0.22, T:0.34
Consensus pattern (109 bp):
CTGTTACCCTACTACTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTCTTTCCCTACTACTTAGGG
GGCTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAAGGG
Found at i:40240251 original size:44 final size:44
Alignment explanation
Indices: 40240116--40240253 Score: 131
Period size: 44 Copynumber: 3.2 Consensus size: 44
40240106 GCTTAGAGGG
*
40240116 CTGTTACCCTACTACTTAGGGGGTTAAGGCCCTTCGTCTTCGAT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGAT
* * * * ** * *
40240160 CTCTTTCCCTACTGTTTAGGGGGCTAA-GATC-T-GTAAATTC-AGC
1 CTGTTACCCTACTGCTTAGGGGGTTAAGGCCCTTCGT--CTTCGA-T
*
40240203 CTGTTACCCTACTGCTTAAGGGGTTAAGGCCCTTCGTCTTCGAT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGAT
40240247 CTGTTAC
1 CTGTTAC
40240254 ACCATTCTTT
Statistics
Matches: 69, Mismatches: 18, Indels: 14
0.68 0.18 0.14
Matches are distributed among these distances:
41 2 0.03
42 2 0.03
43 27 0.39
44 34 0.49
45 2 0.03
46 2 0.03
ACGTcount: A:0.17, C:0.26, G:0.22, T:0.35
Consensus pattern (44 bp):
CTGTTACCCTACTGCTTAGGGGGTTAAGGCCCTTCGTCTTCGAT
Found at i:40240286 original size:87 final size:87
Alignment explanation
Indices: 40240116--40240279 Score: 206
Period size: 87 Copynumber: 1.9 Consensus size: 87
40240106 GCTTAGAGGG
* * * *
40240116 CTGTTACCCTACTACTTAGGGGGTTAAGGCCCTTCGTCTTCGATCTCTTTCCCTACTGTTTAGGG
1 CTGTTACCCTACTACTTAAGGGGTTAAGGCCCTTCGTCTTCGATCTCTTACCCTACTCTTTAGAG
** *
40240181 GGCTAAGATCTGTAAATTCAGC
66 AACTAAGACCTGTAAATTCAGC
* * *
40240203 CTGTTACCCTACTGCTTAAGGGGTTAAGGCCCTTCGTCTTCGATCTGTTACACC-ATTCTTTAGA
1 CTGTTACCCTACTACTTAAGGGGTTAAGGCCCTTCGTCTTCGATCTCTTAC-CCTACTCTTTAGA
*
40240267 GAAC-ATGACCTGT
65 GAACTAAGACCTGT
40240280 TGAATTCGTT
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
86 7 0.11
87 56 0.86
88 2 0.03
ACGTcount: A:0.20, C:0.26, G:0.21, T:0.34
Consensus pattern (87 bp):
CTGTTACCCTACTACTTAAGGGGTTAAGGCCCTTCGTCTTCGATCTCTTACCCTACTCTTTAGAG
AACTAAGACCTGTAAATTCAGC
Found at i:40240982 original size:14 final size:14
Alignment explanation
Indices: 40240963--40240991 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
40240953 TGTTAATTCA
40240963 GAGAAGACAAAACT
1 GAGAAGACAAAACT
40240977 GAGAAGACAAAACT
1 GAGAAGACAAAACT
40240991 G
1 G
40240992 CCGCATGCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.14, G:0.24, T:0.07
Consensus pattern (14 bp):
GAGAAGACAAAACT
Found at i:40248339 original size:19 final size:20
Alignment explanation
Indices: 40248315--40248357 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
40248305 GGTCTTTTCG
* *
40248315 TGAAATTTAATGCACATG-A
1 TGAAATGTAATGCAAATGAA
40248334 TGAAATGTAATGCAAATGAA
1 TGAAATGTAATGCAAATGAA
40248354 TGAA
1 TGAA
40248358 TGCAAAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.47, C:0.07, G:0.19, T:0.28
Consensus pattern (20 bp):
TGAAATGTAATGCAAATGAA
Found at i:40254892 original size:5 final size:5
Alignment explanation
Indices: 40254884--40254935 Score: 54
Period size: 5 Copynumber: 10.4 Consensus size: 5
40254874 AAATTACACA
* *
40254884 TATAT TATA- TATTT TATAT TATTAT T-TACT TATAT TTTAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TA-TAT TATA-T TATAT TATAT TATAT TATAT
40254934 TA
1 TA
40254936 CTTCATATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 5 0.13
5 28 0.72
6 6 0.15
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (5 bp):
TATAT
Found at i:40254921 original size:23 final size:24
Alignment explanation
Indices: 40254884--40255049 Score: 92
Period size: 23 Copynumber: 7.3 Consensus size: 24
40254874 AAATTACACA
40254884 TATATTA--TATATTTTATATTAT
1 TATATTACTTATATTTTATATTAT
40254906 TAT-TTACTTATATTTTAT-TATAT
1 TATATTACTTATATTTTATAT-TAT
*
40254929 TATATTACTTCATATTTTTCTATTAT
1 TATATTACTT-ATA-TTTTATATTAT
* * *
40254955 CATATTAATATATATTTTA-A-CA-
1 TATATTACT-TATATTTTATATTAT
*
40254977 TATATCA-TTAT-TTATTAT-TTAT
1 TATATTACTTATATT-TTATATTAT
*
40254999 TATATTA--TAT-TTTT-TATCA-
1 TATATTACTTATATTTTATATTAT
* * *
40255018 CATAATATTTATATTTTTATATTAT
1 TATATTACTTATA-TTTTATATTAT
40255043 TATATTA
1 TATATTA
40255050 TTTTACATTT
Statistics
Matches: 110, Mismatches: 15, Indels: 35
0.69 0.09 0.22
Matches are distributed among these distances:
19 8 0.07
20 10 0.09
21 13 0.12
22 15 0.14
23 21 0.19
24 11 0.10
25 12 0.11
26 18 0.16
27 2 0.02
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.60
Consensus pattern (24 bp):
TATATTACTTATATTTTATATTAT
Found at i:40255008 original size:41 final size:41
Alignment explanation
Indices: 40254884--40255118 Score: 126
Period size: 44 Copynumber: 5.7 Consensus size: 41
40254874 AAATTACACA
40254884 TATATTATATATTTT---ATAT-TATTATTTACTTATATTTTAT
1 TATATTATATATTTTAACATATATATTATTTA-TTATA--TTAT
* *
40254924 TATATTATAT-TACTT--CATAT-T-TT-TCTATTATCA-TAT
1 TATATTATATAT-TTTAACATATATATTATTTATTAT-ATTAT
40254960 TA-A-TATATATTTTAACATATATCATTATTTATTAT-TTAT
1 TATATTATATATTTTAACATATAT-ATTATTTATTATATTAT
* *
40254999 TATATTATATTTTTTATCACATA-ATATTTATATTTTTATATTAT
1 TATATTATATATTTTA--ACATATATA-TTAT-TTATTATATTAT
*
40255043 TATATTATTTTACATTTTAACA-ATATATTATTTCA-TATTATTAT
1 TATATTA---TATATTTTAACATATATATTATTT-ATTA-TATTAT
** *
40255087 TATCCATTATATATTTTTTCATGTATATTATT
1 TAT--ATTATATATTTTAACATATATATTATT
40255119 ATTCACATTA
Statistics
Matches: 155, Mismatches: 13, Indels: 50
0.71 0.06 0.23
Matches are distributed among these distances:
34 7 0.05
35 2 0.01
36 10 0.06
37 1 0.01
38 4 0.03
39 12 0.08
40 22 0.14
41 16 0.10
42 6 0.04
43 24 0.15
44 34 0.22
45 6 0.04
46 4 0.03
47 7 0.05
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (41 bp):
TATATTATATATTTTAACATATATATTATTTATTATATTAT
Found at i:40255119 original size:31 final size:32
Alignment explanation
Indices: 40255065--40255142 Score: 94
Period size: 30 Copynumber: 2.6 Consensus size: 32
40255055 CATTTTAACA
40255065 ATATATTATTTCATATTATTATTA-TC-CATT
1 ATATATTATTTCATATTATTATTATTCACATT
* *
40255095 ATATATTTTTTCATGTATATTATTATTCACATT
1 ATATATTATTTCATAT-TATTATTATTCACATT
40255128 AT-T-TT-TTTCATATTA
1 ATATATTATTTCATATTA
40255143 AATTGATATT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
29 2 0.05
30 21 0.50
31 10 0.24
32 3 0.07
33 6 0.14
ACGTcount: A:0.31, C:0.09, G:0.01, T:0.59
Consensus pattern (32 bp):
ATATATTATTTCATATTATTATTATTCACATT
Found at i:40261822 original size:101 final size:102
Alignment explanation
Indices: 40261660--40261873 Score: 340
Period size: 101 Copynumber: 2.1 Consensus size: 102
40261650 ACTTCTGATC
* * *
40261660 AGTGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGATAAGTGACAAGTGATA
1 AGTGATAAATGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGATA
40261725 AGTAGTAGCTTTAGCTACACTTATCTGATCAGTGACA
66 AGTAGTAGCTTTAGCTACACTTATCTGATCAGTGACA
** * *
40261762 AGTGATAAATGATAAGTGGTAGTGT-AGCTACACTTGTCTGATCAGTGACAAGTGATAAGTGATA
1 AGTGATAAATGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGATA
* *
40261826 AGTGGTAGCTTTAGCTACACTTATCTGATCAGTGATA
66 AGTAGTAGCTTTAGCTACACTTATCTGATCAGTGACA
40261863 AGTGATAAATG
1 AGTGATAAATG
40261874 TGATCAGTGT
Statistics
Matches: 103, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
101 82 0.80
102 21 0.20
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.30
Consensus pattern (102 bp):
AGTGATAAATGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGATA
AGTAGTAGCTTTAGCTACACTTATCTGATCAGTGACA
Found at i:40261868 original size:51 final size:51
Alignment explanation
Indices: 40261655--40261870 Score: 326
Period size: 51 Copynumber: 4.3 Consensus size: 51
40261645 TGAGTACTTC
* * * *
40261655 TGATCAGTGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAG
1 TGATAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
* *
40261706 TGATAAGTGACAAGTGATAAGTAGTAGCTTTAGCTACACTTATCTGATCAG
1 TGATAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
* * * *
40261757 TGACAAGTGATAAATGATAAGTGGTAG-TGTAGCTACACTTGTCTGATCAG
1 TGATAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
*
40261807 TGACAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
1 TGATAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
40261858 TGATAAGTGATAA
1 TGATAAGTGATAA
40261871 ATGTGATCAG
Statistics
Matches: 150, Mismatches: 14, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
50 47 0.31
51 103 0.69
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (51 bp):
TGATAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
Found at i:40268846 original size:21 final size:21
Alignment explanation
Indices: 40268820--40268860 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
40268810 AGACGAGCAA
*
40268820 TACTCCAAAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
40268841 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
40268861 TTGAGCAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.20, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:40272228 original size:14 final size:14
Alignment explanation
Indices: 40272209--40272235 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40272199 TAATGACCTT
40272209 AATTGAGAATGCCC
1 AATTGAGAATGCCC
40272223 AATTGAGAATGCC
1 AATTGAGAATGCC
40272236 TAGAGAATAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (14 bp):
AATTGAGAATGCCC
Found at i:40274651 original size:40 final size:40
Alignment explanation
Indices: 40274569--40274651 Score: 105
Period size: 40 Copynumber: 2.1 Consensus size: 40
40274559 TTCATGCACA
* * * * *
40274569 CAAGAATTCATGCACATAATTTGTCCGGGTAAAGTACGTG
1 CAAGAATCCATGCACATAATTTGCCCGGCTAAAATACATG
40274609 CAAGAATCCATGCACATAAGTTT-CCCGGCTAAAATACATG
1 CAAGAATCCATGCACATAA-TTTGCCCGGCTAAAATACATG
40274649 CAA
1 CAA
40274652 CAGGAGATGT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 34 0.92
41 3 0.08
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (40 bp):
CAAGAATCCATGCACATAATTTGCCCGGCTAAAATACATG
Found at i:40276685 original size:12 final size:13
Alignment explanation
Indices: 40276667--40276715 Score: 57
Period size: 14 Copynumber: 3.8 Consensus size: 13
40276657 AAAAAATATG
40276667 ATATTTAATAATA
1 ATATTTAATAATA
40276680 AT-TTTAA-AATA
1 ATATTTAATAATA
*
40276691 GTATTTAATATATA
1 ATATTTAATA-ATA
*
40276705 ATATATAATAA
1 ATATTTAATAA
40276716 AAAAATTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
11 5 0.17
12 10 0.33
13 4 0.13
14 11 0.37
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (13 bp):
ATATTTAATAATA
Found at i:40276714 original size:24 final size:24
Alignment explanation
Indices: 40276659--40276712 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 24
40276649 TACTTATAAA
*
40276659 AAAATATGATATTTAATAATAATTTT
1 AAAATA-G-TATTTAATAATAATTAT
40276685 AAAATAGTATTTAATATATAATATAT
1 AAAATAGTATTTAATA-ATAAT-TAT
40276711 AA
1 AA
40276713 TAAAAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 9 0.36
25 6 0.24
26 10 0.40
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (24 bp):
AAAATAGTATTTAATAATAATTAT
Found at i:40277052 original size:22 final size:21
Alignment explanation
Indices: 40276995--40277081 Score: 79
Period size: 22 Copynumber: 4.0 Consensus size: 21
40276985 AACTTTTGAT
*
40276995 AATA-ATAATATAGATAAAA-A
1 AATACATAATA-ATATAAAATA
* *
40277015 AATATATAATAGTATAAAATA
1 AATACATAATAATATAAAATA
40277036 AATGACATAATAATATAAAATA
1 AAT-ACATAATAATATAAAATA
*
40277058 AATATAATATATAATATGAAAATA
1 AATA-CATA-ATAATAT-AAAATA
40277082 TATATGTAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
20 10 0.18
21 11 0.20
22 22 0.39
23 7 0.12
24 6 0.11
ACGTcount: A:0.64, C:0.01, G:0.05, T:0.30
Consensus pattern (21 bp):
AATACATAATAATATAAAATA
Found at i:40277137 original size:45 final size:41
Alignment explanation
Indices: 40276995--40277160 Score: 109
Period size: 45 Copynumber: 3.8 Consensus size: 41
40276985 AACTTTTGAT
* * * * *
40276995 AATAATAATATAGATAAAAAAATATATAATAGTAT-AAAATA
1 AATAATAAAATA-ATATAAATATATAAAATAATATGAAAATA
* * *
40277036 AATGACATAATAATATAAAATAAATATAATATATAATATGAAAATA
1 AATAATAAAATAATAT-AAAT--ATATAA-A-ATAATATGAAAATA
* *
40277082 TATATGTAAAAATAATATATAATATATATAAATAATATGAATAATA
1 AATA-AT-AAAATAATATA-AATATATA-AAATAATATGAA-AATA
*
40277128 AATAATAAAATAATTATATAATATATAATATAA
1 AATAATAAAATAA-TATA-AATATATAAAATAA
40277161 GAATAAGATT
Statistics
Matches: 97, Mismatches: 16, Indels: 21
0.72 0.12 0.16
Matches are distributed among these distances:
40 3 0.03
41 11 0.11
43 5 0.05
44 13 0.13
45 30 0.31
46 21 0.22
47 2 0.02
48 12 0.12
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.33
Consensus pattern (41 bp):
AATAATAAAATAATATAAATATATAAAATAATATGAAAATA
Found at i:40277188 original size:52 final size:50
Alignment explanation
Indices: 40277093--40277208 Score: 119
Period size: 52 Copynumber: 2.3 Consensus size: 50
40277083 ATATGTAAAA
* * *
40277093 ATAATATATAATATATATAAATAATATGAATAATAAATAATAAAATAATTAT
1 ATAATATATAATATATATAAATAAGATGAAAAATAAACAATAAAA-AATT-T
* *
40277145 ATAATATATAATATA-A-GAATAAGATTAAAAATAAAACAGATAAAAAATTT
1 ATAATATATAATATATATAAATAAGATGAAAAAT-AAACA-ATAAAAAATTT
*
40277195 ATATTTATATAATA
1 ATA-ATATATAATA
40277209 ACAACAGAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
50 16 0.29
51 18 0.33
52 21 0.38
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.34
Consensus pattern (50 bp):
ATAATATATAATATATATAAATAAGATGAAAAATAAACAATAAAAAATTT
Found at i:40289293 original size:25 final size:26
Alignment explanation
Indices: 40289260--40289320 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 26
40289250 TATTATTTTG
40289260 AAAT-TTAAAATATATAAAATCTA-AA
1 AAATATTAAAATATAT-AAATCTACAA
* *
40289285 AAA-ATTAAAATTTATAAATTTACAA
1 AAATATTAAAATATATAAATCTACAA
40289310 AAATATTAAAA
1 AAATATTAAAA
40289321 ATAATTTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 6 0.19
25 18 0.58
26 7 0.23
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (26 bp):
AAATATTAAAATATATAAATCTACAA
Found at i:40289521 original size:26 final size:24
Alignment explanation
Indices: 40289492--40289540 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
40289482 AAAATCTGAT
40289492 ATTTTATAATATTTTACATTTTATAC
1 ATTTT-TAATATTTT-CATTTTATAC
* *
40289518 ATTTTTTATATTTTTATTTTATA
1 ATTTTTAATATTTTCATTTTATA
40289541 TAAATTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 8 0.38
25 8 0.38
26 5 0.24
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (24 bp):
ATTTTTAATATTTTCATTTTATAC
Found at i:40289530 original size:18 final size:17
Alignment explanation
Indices: 40289490--40289531 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
40289480 ATAAAATCTG
40289490 ATATTTTATAATATTTT
1 ATATTTTATAATATTTT
* *
40289507 ACATTTTATACATTTTTT
1 ATATTTTATA-ATATTTT
40289525 ATATTTT
1 ATATTTT
40289532 TATTTTATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (17 bp):
ATATTTTATAATATTTT
Found at i:40292723 original size:40 final size:40
Alignment explanation
Indices: 40292687--40292765 Score: 124
Period size: 39 Copynumber: 2.0 Consensus size: 40
40292677 CACTAAAGAT
*
40292687 TGAGCATTAGTGGCGTTTTT-AAAAAAATGCCGCTAAAAA
1 TGAGCATTAGCGGCGTTTTTCAAAAAAATGCCGCTAAAAA
* *
40292726 TGAGCATTAGCGGCGTTTTTCAAAAAAACGCCGCAAAAAA
1 TGAGCATTAGCGGCGTTTTTCAAAAAAATGCCGCTAAAAA
40292766 CCTTAGCCCA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 19 0.53
40 17 0.47
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.24
Consensus pattern (40 bp):
TGAGCATTAGCGGCGTTTTTCAAAAAAATGCCGCTAAAAA
Found at i:40292741 original size:39 final size:39
Alignment explanation
Indices: 40292612--40292765 Score: 139
Period size: 40 Copynumber: 3.8 Consensus size: 39
40292602 AGCGGCACTT
** * *
40292612 TTAGCGGCGTTTGGACAAAAAACGCCGGTAAAAATCAAGCA
1 TTAGCGGCGTTTTTA-AAAAAACGCCGCTAAAAAT-GAGCA
* ** * * *
40292653 TTAGCGGCGCTTTCT-GGAAATCGCCACTAAAGATTGAGCA
1 TTAGCGGCG-TTTTTAAAAAAACGCCGCTAAA-AATGAGCA
* *
40292693 TTAGTGGCGTTTTTAAAAAAATGCCGCTAAAAATGAGCA
1 TTAGCGGCGTTTTTAAAAAAACGCCGCTAAAAATGAGCA
*
40292732 TTAGCGGCGTTTTTCAAAAAAACGCCGCAAAAAA
1 TTAGCGGCGTTTTT-AAAAAAACGCCGCTAAAAA
40292766 CCTTAGCCCA
Statistics
Matches: 89, Mismatches: 20, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
39 24 0.27
40 51 0.57
41 11 0.12
42 3 0.03
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (39 bp):
TTAGCGGCGTTTTTAAAAAAACGCCGCTAAAAATGAGCA
Found at i:40292857 original size:40 final size:40
Alignment explanation
Indices: 40292804--40292902 Score: 130
Period size: 40 Copynumber: 2.5 Consensus size: 40
40292794 ATTTCGTGGC
* *
40292804 TTTGAAAAACGCCGCTAATGCCT-GGGTCTTTAGCGGC-TT
1 TTTGAAAAGCGCCGCTAATG-CTAGGGGCTTTAGCGGCGTT
*
40292843 TTTGGAAAAGCGCCGCTAATGGTAGGGGCTTTAGCGGCGTT
1 TTT-GAAAAGCGCCGCTAATGCTAGGGGCTTTAGCGGCGTT
40292884 TTTGATAAAGCGCCGCTAA
1 TTTGA-AAAGCGCCGCTAA
40292903 AAACATTTTA
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
39 4 0.08
40 31 0.58
41 18 0.34
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.28
Consensus pattern (40 bp):
TTTGAAAAGCGCCGCTAATGCTAGGGGCTTTAGCGGCGTT
Found at i:40293154 original size:15 final size:14
Alignment explanation
Indices: 40293143--40293176 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
40293133 GAGTATGTAT
40293143 TTAAGGATTATGGA
1 TTAAGGATTATGGA
* *
40293157 TTAGGGATTATGGT
1 TTAAGGATTATGGA
40293171 TTAAGG
1 TTAAGG
40293177 GTTGAGATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.38
Consensus pattern (14 bp):
TTAAGGATTATGGA
Found at i:40293230 original size:22 final size:22
Alignment explanation
Indices: 40293168--40293251 Score: 73
Period size: 22 Copynumber: 3.9 Consensus size: 22
40293158 TAGGGATTAT
* * *
40293168 GGTTTAAGGGTTGAGATTTAA-
1 GGTTTAGGGGTTAAGAGTTAAG
* *
40293189 GGTTTAGGGGTT-AGTGGTTAGG
1 GGTTTAGGGGTTAAG-AGTTAAG
40293211 GGTTTAGGGGTTAAGAGTTAAG
1 GGTTTAGGGGTTAAGAGTTAAG
* * *
40293233 GATTTAGGGTTTATGAGTT
1 GGTTTAGGGGTTAAGAGTT
40293252 CATGGGTCAA
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
20 2 0.04
21 14 0.27
22 33 0.65
23 2 0.04
ACGTcount: A:0.23, C:0.00, G:0.39, T:0.38
Consensus pattern (22 bp):
GGTTTAGGGGTTAAGAGTTAAG
Found at i:40293321 original size:23 final size:23
Alignment explanation
Indices: 40293281--40293334 Score: 74
Period size: 22 Copynumber: 2.3 Consensus size: 23
40293271 TTGGGTTTAG
*
40293281 ATTAATTATTTTTTAATTTAT-T
1 ATTAAATATTTTTTAATTTATAT
*
40293303 TTTAAATATTTTTTAAATTTATAT
1 ATTAAATATTTTTT-AATTTATAT
40293327 ATTAAATA
1 ATTAAATA
40293335 ATTTCATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 12 0.44
23 7 0.26
24 8 0.30
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
ATTAAATATTTTTTAATTTATAT
Found at i:40293556 original size:21 final size:21
Alignment explanation
Indices: 40293532--40293572 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
40293522 GATTTAAGGT
40293532 TTAGGGATTAAGAGTTAGGGG
1 TTAGGGATTAAGAGTTAGGGG
*
40293553 TTAGGGGTTAAGAGTTAGGG
1 TTAGGGATTAAGAGTTAGGG
40293573 ATTTAGGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.44, T:0.29
Consensus pattern (21 bp):
TTAGGGATTAAGAGTTAGGGG
Found at i:40293581 original size:21 final size:20
Alignment explanation
Indices: 40293529--40293582 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 20
40293519 TAGGATTTAA
40293529 GGTTTAGGGATTAAGAGTTAG
1 GGTTTAGGG-TTAAGAGTTAG
*
40293550 GGGTTAGGGGTTAAGAGTTAG
1 GGTTTA-GGGTTAAGAGTTAG
40293571 GGATTTAGGGTT
1 GG-TTTAGGGTT
40293583 TCAATGGTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 23 0.79
22 6 0.21
ACGTcount: A:0.24, C:0.00, G:0.43, T:0.33
Consensus pattern (20 bp):
GGTTTAGGGTTAAGAGTTAG
Found at i:40298175 original size:43 final size:43
Alignment explanation
Indices: 40298128--40298373 Score: 278
Period size: 43 Copynumber: 5.7 Consensus size: 43
40298118 ATGGCACTTT
* * * * *
40298128 TAGCGGCGTTTGCGAAAAAAACGTCGCTAAAAGTCATGATCTA
1 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCCTGATCTA
* * * *
40298171 TAGCGGCATTTATAAAAAAAGCGCCGCTAAAGGTCTTGATCTA
1 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCCTGATCTA
* *
40298214 TAGCGGCGTTTGTG-TAAAAGTGCCGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCCTGATCTA
* ** * * *
40298256 TAGCGGCATTTGTGGGAAAAGTGTCGCTAAAGGTTCTGATCTA
1 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCCTGATCTA
** * *
40298299 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTCTT
1 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCCTGATCTA
**
40298342 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAG
1 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAG
40298374 TTAGCGACGC
Statistics
Matches: 178, Mismatches: 24, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
42 38 0.21
43 140 0.79
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (43 bp):
TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCCTGATCTA
Found at i:40298253 original size:85 final size:86
Alignment explanation
Indices: 40298128--40298373 Score: 307
Period size: 85 Copynumber: 2.9 Consensus size: 86
40298118 ATGGCACTTT
* ** * * * * * ***
40298128 TAGCGGCGTTTGCGAAAAAAACGTCGCTAAAAGTCATGATCTATAGCGGCATTTATAAAAAAAGC
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCATTTGTGGGAAAAGC
40298193 GCCGCTAAAGG-TCTTGATCTA
66 GCCGCTAAAGGTTC-TGATCTA
* * *
40298214 TAGCGGCGTTTGT-GTAAAAGTGCCGCTAAAGGTCCTGATCTATAGCGGCATTTGTGGGAAAAGT
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCATTTGTGGGAAAAGC
*
40298278 GTCGCTAAAGGTTCTGATCTA
66 GCCGCTAAAGGTTCTGATCTA
* * *
40298299 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGGAAAAGC
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCATTTGTGGGAAAAGC
40298364 GCCGCTAAAG
66 GCCGCTAAAG
40298374 TTAGCGACGC
Statistics
Matches: 137, Mismatches: 21, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
85 69 0.50
86 68 0.50
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (86 bp):
TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCATTTGTGGGAAAAGC
GCCGCTAAAGGTTCTGATCTA
Found at i:40298473 original size:22 final size:22
Alignment explanation
Indices: 40298445--40298487 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
40298435 CAGTGGCGCT
*
40298445 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
40298467 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
40298488 GTTTTGGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.28, G:0.21, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:40303838 original size:43 final size:44
Alignment explanation
Indices: 40303741--40303893 Score: 145
Period size: 43 Copynumber: 3.5 Consensus size: 44
40303731 ATCGATATGT
* * *
40303741 GATTATATGTAAGACCATGTTTGGGACATTGGCAT-TGTATTGA
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATCTGTAATGA
*
40303784 GATTACATGTAAGACCATGTCTGGGACATTGGCATCAT-TAAT-C
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATC-TGTAATGA
*** * * *
40303827 GATTTTGTGTAAGACCCTGTCTGGGACAGTGGCATC-G-ATATGT
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATCTGTA-ATGA
* *
40303870 GATAACATGTAAGACCATATCTGG
1 GATTACATGTAAGACCATGTCTGG
40303894 AATATGATAT
Statistics
Matches: 89, Mismatches: 16, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
41 1 0.01
42 2 0.02
43 82 0.92
44 3 0.03
45 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (44 bp):
GATTACATGTAAGACCATGTCTGGGACATTGGCATCTGTAATGA
Found at i:40308159 original size:42 final size:42
Alignment explanation
Indices: 40308111--40308228 Score: 139
Period size: 43 Copynumber: 2.8 Consensus size: 42
40308101 TTAGGGTTAT
* *
40308111 TGAGACTTCGTGTAAGACCATATTTGGGATATGACATCGATA
1 TGAGACTTCGTGTAAGACCATATCTGGGATATGACATCAATA
* * * *
40308153 TGAGACTTCGTATAAGACCATAGCTGGGCTATTGGCATCAATA
1 TGAGACTTCGTGTAAGACCATATCTGGGATA-TGACATCAATA
* *
40308196 TGAGA-TCCCATGTAAGACCATATCTGGGATATG
1 TGAGACT-TCGTGTAAGACCATATCTGGGATATG
40308229 GCATTGGTAT
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
42 30 0.48
43 33 0.52
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.29
Consensus pattern (42 bp):
TGAGACTTCGTGTAAGACCATATCTGGGATATGACATCAATA
Found at i:40309033 original size:47 final size:46
Alignment explanation
Indices: 40308974--40309066 Score: 159
Period size: 47 Copynumber: 2.0 Consensus size: 46
40308964 TATGTGAACG
*
40308974 GAAGGGTGACAAAATGGCTTGGTAAATAGCCTTATTTTATGTGCATA
1 GAAGGGTGACAAAATGGCTTGGTAAATAGCCTTATTTT-TGTCCATA
*
40309021 GAAGGGTGACAAAATGGCTTGGTAAATAGCCTTGTTTTTGTCCATA
1 GAAGGGTGACAAAATGGCTTGGTAAATAGCCTTATTTTTGTCCATA
40309067 TGGGTAGACA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
46 7 0.16
47 37 0.84
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.32
Consensus pattern (46 bp):
GAAGGGTGACAAAATGGCTTGGTAAATAGCCTTATTTTTGTCCATA
Found at i:40328662 original size:18 final size:17
Alignment explanation
Indices: 40328626--40328668 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
40328616 AGGCCAAGTT
*
40328626 GGGCATGTAGGCTACAC
1 GGGCATGTAGGCCACAC
*
40328643 GGGCATGTGGGACCACAC
1 GGGCATGTAGG-CCACAC
*
40328661 GGCCATGT
1 GGGCATGT
40328669 CACACGGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.21, C:0.26, G:0.37, T:0.16
Consensus pattern (17 bp):
GGGCATGTAGGCCACAC
Found at i:40336290 original size:37 final size:37
Alignment explanation
Indices: 40336193--40336290 Score: 151
Period size: 37 Copynumber: 2.6 Consensus size: 37
40336183 AGCGCTATAT
* * *
40336193 AAATTGACACCTAGTGTCTCATCAGTTAAACGGAAGC
1 AAATTGACACCCAGTGCCTCATCGGTTAAACGGAAGC
* *
40336230 AAATTGATACCCAGTGCCTCATCGGTTAAACTGAAGC
1 AAATTGACACCCAGTGCCTCATCGGTTAAACGGAAGC
40336267 AAATTGACACCCAGTGCCTCATCG
1 AAATTGACACCCAGTGCCTCATCG
40336291 AATTCACGTT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (37 bp):
AAATTGACACCCAGTGCCTCATCGGTTAAACGGAAGC
Found at i:40341645 original size:80 final size:80
Alignment explanation
Indices: 40341543--40341719 Score: 239
Period size: 80 Copynumber: 2.2 Consensus size: 80
40341533 AATACATCTG
* *
40341543 AAACACACGAAAAAAAGCCTCATAAGAGTTGATCCAATCGAAACACCCCAAACAGAAACTCATAA
1 AAACACACCAAAAAAAGCCTCATAAGAGCTGATCCAATCGAAACACCCCAAACAGAAACTCATAA
*
40341608 GGGCTGATCCAACAA
66 GAGCTGATCCAACAA
* * * *
40341623 AAACACACCAAACAAAAG-CTCATGAGAGCTGATCCAATCGAAACACGCCAAATAGAAGCTCATA
1 AAACACACCAAA-AAAAGCCTCATAAGAGCTGATCCAATCGAAACACCCCAAACAGAAACTCATA
**
40341687 AGAGCTGATCCAACCG
65 AGAGCTGATCCAACAA
* *
40341703 AAACACGCCAAATAAAG
1 AAACACACCAAAAAAAG
40341720 AGTATAACAC
Statistics
Matches: 85, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
79 4 0.05
80 76 0.89
81 5 0.06
ACGTcount: A:0.47, C:0.27, G:0.15, T:0.12
Consensus pattern (80 bp):
AAACACACCAAAAAAAGCCTCATAAGAGCTGATCCAATCGAAACACCCCAAACAGAAACTCATAA
GAGCTGATCCAACAA
Found at i:40341715 original size:40 final size:40
Alignment explanation
Indices: 40341503--40341716 Score: 205
Period size: 40 Copynumber: 5.3 Consensus size: 40
40341493 TAGATCAACT
* * * * * * *
40341503 AAACAGACCAGATAGAAGCTCGTAAGAGCTAATACATCTG
1 AAACACACCAAATAGAAGCTCATAAGAGCTGATCCAACCG
* * * *
40341543 AAACACACGAAA-AAAAGCCTCATAAGAGTTGATCCAATCG
1 AAACACACCAAATAGAAG-CTCATAAGAGCTGATCCAACCG
* * * * **
40341583 AAACACCCCAAACAGAAACTCATAAGGGCTGATCCAACAA
1 AAACACACCAAATAGAAGCTCATAAGAGCTGATCCAACCG
* * * *
40341623 AAACACACCAAACAAAAGCTCATGAGAGCTGATCCAATCG
1 AAACACACCAAATAGAAGCTCATAAGAGCTGATCCAACCG
*
40341663 AAACACGCCAAATAGAAGCTCATAAGAGCTGATCCAACCG
1 AAACACACCAAATAGAAGCTCATAAGAGCTGATCCAACCG
*
40341703 AAACACGCCAAATA
1 AAACACACCAAATA
40341717 AAGAGTATAA
Statistics
Matches: 139, Mismatches: 33, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
39 4 0.03
40 132 0.95
41 3 0.02
ACGTcount: A:0.46, C:0.26, G:0.15, T:0.13
Consensus pattern (40 bp):
AAACACACCAAATAGAAGCTCATAAGAGCTGATCCAACCG
Found at i:40343250 original size:23 final size:23
Alignment explanation
Indices: 40343168--40343254 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
40343158 CCTGATCAGT
*
40343168 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* *
40343190 A-ACGACACACGAGGTGCCTG--
1 ATACGACACACAAAGTGCCTGAA
* *
40343210 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
*
40343233 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
40343255 TCAGTAAAGC
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
20 1 0.02
21 34 0.62
22 1 0.02
23 19 0.35
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.15
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:40351078 original size:21 final size:21
Alignment explanation
Indices: 40351052--40351134 Score: 76
Period size: 21 Copynumber: 3.9 Consensus size: 21
40351042 TGATCAGTAT
*
40351052 ACGACACATAAAGTGCCTAAA
1 ACGACACACAAAGTGCCTAAA
* * * *
40351073 ACGACACACGAGGTGCCTGAT
1 ACGACACACAAAGTGCCTAAA
* *
40351094 ACGACACACGAGGTGCCTAAAA
1 ACGACACACAAAGTGCCT-AAA
*
40351116 TACGACACATAAAGTGCCT
1 -ACGACACACAAAGTGCCT
40351135 GATCAGTAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
21 34 0.68
22 1 0.02
23 15 0.30
ACGTcount: A:0.39, C:0.27, G:0.20, T:0.14
Consensus pattern (21 bp):
ACGACACACAAAGTGCCTAAA
Found at i:40351118 original size:23 final size:22
Alignment explanation
Indices: 40351050--40351124 Score: 91
Period size: 21 Copynumber: 3.5 Consensus size: 22
40351040 CCTGATCAGT
** *
40351050 ATACGACACATAAAGTGCCTAA
1 ATACGACACACGAGGTGCCTAA
*
40351072 A-ACGACACACGAGGTGCCT-G
1 ATACGACACACGAGGTGCCTAA
40351092 ATACGACACACGAGGTGCCTAAA
1 ATACGACACACGAGGTGCCT-AA
40351115 ATACGACACA
1 ATACGACACA
40351125 TAAAGTGCCT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.02
21 33 0.73
22 1 0.02
23 10 0.22
ACGTcount: A:0.40, C:0.27, G:0.20, T:0.13
Consensus pattern (22 bp):
ATACGACACACGAGGTGCCTAA
Found at i:40355223 original size:86 final size:85
Alignment explanation
Indices: 40355120--40355281 Score: 227
Period size: 86 Copynumber: 1.9 Consensus size: 85
40355110 ACGTTTATTA
* * **
40355120 AAAAAACGTCGCTAAAAGTGCTGGCTTTTAGCGACGTTTGTTAAAAAAGCACAGCTAAAAGTGCA
1 AAAAAACGCCGCTAAAAGTGCTGCCTTTTAGCGACGTTTCCTAAAAAAGCACAGCTAAAAGT-CA
40355185 -GGCTTTTTAGCGTCGTTTGCT
65 TGGC-TTTTAGCGTCGTTTGCT
* * * *
40355206 AAAAAATGCCGCTAAAAGTGCTGCCTTTTAGCGGCGTTTCCTAAAAAAGCGCCGCTAAAAGTCAT
1 AAAAAACGCCGCTAAAAGTGCTGCCTTTTAGCGACGTTTCCTAAAAAAGCACAGCTAAAAGTCAT
40355271 GGCTTTTAGCG
66 GGCTTTTAGCG
40355282 GCGCTTTTCC
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
85 10 0.15
86 57 0.85
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (85 bp):
AAAAAACGCCGCTAAAAGTGCTGCCTTTTAGCGACGTTTCCTAAAAAAGCACAGCTAAAAGTCAT
GGCTTTTAGCGTCGTTTGCT
Found at i:40355282 original size:43 final size:43
Alignment explanation
Indices: 40355118--40355284 Score: 203
Period size: 43 Copynumber: 3.9 Consensus size: 43
40355108 AAACGTTTAT
* * * *
40355118 TAAAAAAACGTCGCTAAAAGTGCTGGCTTTTAGCGACGTTTGT
1 TAAAAAAGCGCCGCTAAAAGTGCTGGCTTTTAGCGGCGTTTGC
* * * *
40355161 TAAAAAAGCACAGCTAAAAGTGCAGGCTTTTTAGCGTCGTTTGC
1 TAAAAAAGCGCCGCTAAAAGTGCTGGC-TTTTAGCGGCGTTTGC
* * *
40355205 TAAAAAA-TGCCGCTAAAAGTGCTGCCTTTTAGCGGCGTTTCC
1 TAAAAAAGCGCCGCTAAAAGTGCTGGCTTTTAGCGGCGTTTGC
40355247 TAAAAAAGCGCCGCTAAAAGT-CATGGCTTTTAGCGGCG
1 TAAAAAAGCGCCGCTAAAAGTGC-TGGCTTTTAGCGGCG
40355285 CTTTTCCCAC
Statistics
Matches: 105, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
42 22 0.21
43 62 0.59
44 21 0.20
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (43 bp):
TAAAAAAGCGCCGCTAAAAGTGCTGGCTTTTAGCGGCGTTTGC
Found at i:40355303 original size:86 final size:86
Alignment explanation
Indices: 40355120--40355306 Score: 225
Period size: 86 Copynumber: 2.2 Consensus size: 86
40355110 ACGTTTATTA
* * **
40355120 AAAAAACGTCGCTAAAAGTGCTGGCTTTTAGCGACGTTTGTTAAAAAAGCACAGCTAAAAGTGCA
1 AAAAAACGCCGCTAAAAGTGCTGCCTTTTAGCGACGTTTCCTAAAAAAGCACAGCTAAAAGTGCA
* *
40355185 GGCTTTTTAGCGTCGTTTGCT
66 GGCTTTTTAGCGGCGTTTGCC
* * * *
40355206 AAAAAATGCCGCTAAAAGTGCTGCCTTTTAGCGGCGTTTCCTAAAAAAGCGCCGCTAAAAGT-CA
1 AAAAAACGCCGCTAAAAGTGCTGCCTTTTAGCGACGTTTCCTAAAAAAGCACAGCTAAAAGTGCA
*
40355270 TGGC-TTTTAGCGGCGCTTTTCC
66 -GGCTTTTTAGCGGCG-TTTGCC
* *
40355292 CACAAACGCCGCTAA
1 AAAAAACGCCGCTAA
40355307 TTTTGACAGA
Statistics
Matches: 85, Mismatches: 14, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
85 12 0.14
86 73 0.86
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (86 bp):
AAAAAACGCCGCTAAAAGTGCTGCCTTTTAGCGACGTTTCCTAAAAAAGCACAGCTAAAAGTGCA
GGCTTTTTAGCGGCGTTTGCC
Found at i:40361323 original size:9 final size:9
Alignment explanation
Indices: 40361311--40361369 Score: 82
Period size: 9 Copynumber: 6.6 Consensus size: 9
40361301 TCCGTCAGTT
*
40361311 GTTATGTAC
1 GTTATGTAA
*
40361320 GTTATGTGA
1 GTTATGTAA
40361329 GTTATGTAA
1 GTTATGTAA
*
40361338 ATTATGTAA
1 GTTATGTAA
*
40361347 GTTATGTGA
1 GTTATGTAA
40361356 GTTATGTAA
1 GTTATGTAA
40361365 GTTAT
1 GTTAT
40361370 TTTTTAAGAT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 43 1.00
ACGTcount: A:0.29, C:0.02, G:0.24, T:0.46
Consensus pattern (9 bp):
GTTATGTAA
Found at i:40361343 original size:27 final size:27
Alignment explanation
Indices: 40361312--40361369 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
40361302 CCGTCAGTTG
*
40361312 TTATGTACGTTATGTGAGTTATGTAAA
1 TTATGTAAGTTATGTGAGTTATGTAAA
*
40361339 TTATGTAAGTTATGTGAGTTATGTAAG
1 TTATGTAAGTTATGTGAGTTATGTAAA
40361366 TTAT
1 TTAT
40361370 TTTTTAAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.22, T:0.47
Consensus pattern (27 bp):
TTATGTAAGTTATGTGAGTTATGTAAA
Found at i:40363883 original size:25 final size:25
Alignment explanation
Indices: 40363855--40363919 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
40363845 GAGAAGCAGC
*
40363855 AGAGGGATGCCGACGGAGATGTAAA
1 AGAGGGATGCCGACGGAGAAGTAAA
* * **
40363880 AGAGGGATGCCAATGGAGAAGTAGC
1 AGAGGGATGCCGACGGAGAAGTAAA
*
40363905 AGAGGGCTGCCGACG
1 AGAGGGATGCCGACG
40363920 ATGATGCAGA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.32, C:0.15, G:0.42, T:0.11
Consensus pattern (25 bp):
AGAGGGATGCCGACGGAGAAGTAAA
Found at i:40365935 original size:19 final size:19
Alignment explanation
Indices: 40365911--40365949 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
40365901 GAAAGGCTGA
*
40365911 GAAAGAAAAGGGAATTGGG
1 GAAAGAAAAGGGAATCGGG
40365930 GAAAGAAAAGGGAATCGGG
1 GAAAGAAAAGGGAATCGGG
40365949 G
1 G
40365950 GAGAGAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.46, C:0.03, G:0.44, T:0.08
Consensus pattern (19 bp):
GAAAGAAAAGGGAATCGGG
Found at i:40365956 original size:20 final size:19
Alignment explanation
Indices: 40365911--40365957 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
40365901 GAAAGGCTGA
*
40365911 GAAAGAAAAGGGAATTGGG
1 GAAAGAAAAGGGAATGGGG
40365930 GAAAGAAAAGGGAATCGGGG
1 GAAAGAAAAGGGAAT-GGGG
*
40365950 GAGAGAAA
1 GAAAGAAA
40365958 TAGAAGTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.49, C:0.02, G:0.43, T:0.06
Consensus pattern (19 bp):
GAAAGAAAAGGGAATGGGG
Found at i:40366015 original size:16 final size:19
Alignment explanation
Indices: 40365984--40366020 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
40365974 GAATGGCTGA
40365984 GAAAGAAAGTGGAATT-GG
1 GAAAGAAAGTGGAATTAGG
40366002 GAAAG-AAG-GGAATTAGG
1 GAAAGAAAGTGGAATTAGG
40366019 GA
1 GA
40366021 GGGGAGAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.33
17 7 0.39
18 5 0.28
ACGTcount: A:0.46, C:0.00, G:0.41, T:0.14
Consensus pattern (19 bp):
GAAAGAAAGTGGAATTAGG
Found at i:40366224 original size:22 final size:20
Alignment explanation
Indices: 40366197--40366253 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 20
40366187 ATGTTTGATT
40366197 TTTTATAATTTTTATATTGAA
1 TTTTATAATTTTTATATT-AA
40366218 TTATTAT-ATCTTTTATATTAA
1 TT-TTATAAT-TTTTATATTAA
40366239 TTTTAAATAATTTTT
1 TTTT--ATAATTTTT
40366254 TTTAAAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
20 2 0.06
21 8 0.26
22 19 0.61
23 2 0.06
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTTATAATTTTTATATTAA
Found at i:40366682 original size:7 final size:7
Alignment explanation
Indices: 40366581--40366726 Score: 53
Period size: 7 Copynumber: 20.6 Consensus size: 7
40366571 TTTTATCTCC
*
40366581 TAAACCC
1 TAAACCA
*
40366588 TAAATCA
1 TAAACCA
40366595 TACAA-CA
1 TA-AACCA
* *
40366602 TAACCCT
1 TAAACCA
40366609 TAAACCCA
1 TAAA-CCA
*
40366617 TAACCCA
1 TAAACCA
* *
40366624 TAACCCC
1 TAAACCA
* *
40366631 TAATCCC
1 TAAACCA
40366638 TAACACC-
1 TAA-ACCA
*
40366645 TAAACCT
1 TAAACCA
*
40366652 TAAACCC
1 TAAACCA
* * *
40366659 CAACCCT
1 TAAACCA
40366666 TAAACCA
1 TAAACCA
*
40366673 TAAACTA
1 TAAACCA
*
40366680 TAAATCA
1 TAAACCA
*
40366687 TAATCCA
1 TAAACCA
40366694 TAAACCCA
1 TAAA-CCA
*
40366702 TAATCCA
1 TAAACCA
**
40366709 TAATTCA
1 TAAACCA
*
40366716 TAAACCT
1 TAAACCA
40366723 TAAA
1 TAAA
40366727 ATAGTAACTC
Statistics
Matches: 105, Mismatches: 28, Indels: 12
0.72 0.19 0.08
Matches are distributed among these distances:
6 4 0.04
7 86 0.82
8 15 0.14
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.22
Consensus pattern (7 bp):
TAAACCA
Found at i:40366726 original size:29 final size:28
Alignment explanation
Indices: 40366663--40366726 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
40366653 AAACCCCAAC
* *
40366663 CCTTAAACCATAAACTATAAATCATAAT
1 CCTTAAACCATAAACCATAAATCATAAA
* * *
40366691 CCATAAACCCATAATCCATAATTCATAAA
1 CCTTAAA-CCATAAACCATAAATCATAAA
40366720 CCTTAAA
1 CCTTAAA
40366727 ATAGTAACTC
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
28 6 0.21
29 23 0.79
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27
Consensus pattern (28 bp):
CCTTAAACCATAAACCATAAATCATAAA
Found at i:40367037 original size:24 final size:24
Alignment explanation
Indices: 40367009--40367058 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
40366999 ACCAAAATAA
*
40367009 AAATTAATTTTTATATAGACTTTT
1 AAATTAATTTTTATATAAACTTTT
*
40367033 AAATTAATTTTTTTATAAACTTTT
1 AAATTAATTTTTATATAAACTTTT
40367057 AA
1 AA
40367059 TAAATATACG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (24 bp):
AAATTAATTTTTATATAAACTTTT
Found at i:40367613 original size:16 final size:16
Alignment explanation
Indices: 40367580--40367615 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
40367570 CTTGTTAGGA
**
40367580 TTTAGGGGTTTACTAT
1 TTTAGGGGTTTAAGAT
40367596 TTTAGGGGTTTAAGAT
1 TTTAGGGGTTTAAGAT
40367612 TTTA
1 TTTA
40367616 AGAGTTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.22, C:0.03, G:0.25, T:0.50
Consensus pattern (16 bp):
TTTAGGGGTTTAAGAT
Found at i:40367673 original size:41 final size:41
Alignment explanation
Indices: 40367628--40367900 Score: 371
Period size: 41 Copynumber: 6.8 Consensus size: 41
40367618 AGTTATATGA
* *
40367628 CTTTTAGCGGTGTTTTACCAAAAGCGTCGCTAATGCTCTGT
1 CTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGT
* * * *
40367669 CTTTTAGTGGCGTTTTACCAAAAGTGTCGCTACTGCTCTGT
1 CTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGT
*
40367710 CTTTTAGCAGCGTTTTACCAAAAGCGCCGCTAATGCTCTGT
1 CTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGT
*
40367751 CTTTTAGCGGCGTTTTACCAAAAGCGCCGCT-ACGTCTCTGT
1 CTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATG-CTCTGT
* * *
40367792 CTTTTAGTGGCGTTTTACCAAAAGCACTGCTAATGCTCTGT
1 CTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGT
*
40367833 CTTTTA---GCG--TT-CCAAAAGCGCCGCTAGTGCTCTGT
1 CTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGT
*
40367868 CTTTTAGCGGCGTTTTACTAAAAGCGCCGCTAA
1 CTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAA
40367901 AGCCCTATTT
Statistics
Matches: 204, Mismatches: 20, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
35 27 0.13
36 2 0.01
38 6 0.03
40 4 0.02
41 163 0.80
42 2 0.01
ACGTcount: A:0.20, C:0.25, G:0.21, T:0.34
Consensus pattern (41 bp):
CTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGT
Found at i:40379015 original size:49 final size:47
Alignment explanation
Indices: 40378931--40379435 Score: 803
Period size: 47 Copynumber: 10.6 Consensus size: 47
40378921 TATTTGAATA
* *
40378931 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
40378978 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
40379027 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
40379074 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
40379123 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
40379172 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
40379219 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
40379268 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
40379315 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * * *
40379362 AATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
40379409 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
40379436 TCCCGAAGGG
Statistics
Matches: 430, Mismatches: 22, Indels: 12
0.93 0.05 0.03
Matches are distributed among these distances:
47 246 0.57
49 184 0.43
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:40379039 original size:96 final size:94
Alignment explanation
Indices: 40378931--40379435 Score: 803
Period size: 96 Copynumber: 5.3 Consensus size: 94
40378921 TATTTGAATA
* *
40378931 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATA
40378996 TATGTGATAAGGCCTAATGGCCGATGTGATG
64 TATGTGATAAGGCCTAATGGCCGATGTGATG
* *
40379027 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATA
40379092 TATGTGATAAGGCCTAATGGCCGATGTGATG
64 TATGTGATAAGGCCTAATGGCCGATGTGATG
40379123 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
* *
40379188 TATGTGATAAGGCCGAATGGCCAATGTGATG
64 TATGTGATAAGGCCTAATGGCCGATGTGATG
40379219 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
*
40379284 TATGTGATAAGGCCTAATAGCCGATGTGATG
64 TATGTGATAAGGCCTAATGGCCGATGTGATG
40379315 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* * * * * *
40379380 TGTGACAGGGCCGAGTGGCCAACGTGATG
66 TGTGATAAGGCCTAATGGCCGATGTGATG
* *
40379409 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
40379436 TCCCGAAGGG
Statistics
Matches: 391, Mismatches: 16, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
94 100 0.26
96 246 0.63
98 45 0.12
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (94 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
TGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:40390409 original size:20 final size:20
Alignment explanation
Indices: 40390386--40390446 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
40390376 ATTTTTTATA
40390386 TTTTA-AATTTATTATAATTT
1 TTTTACAATTT-TTATAATTT
*
40390406 TTTTACAATTTTTATAAATT
1 TTTTACAATTTTTATAATTT
*
40390426 TTTAACAATTTTT-TAATTT
1 TTTTACAATTTTTATAATTT
40390445 TT
1 TT
40390447 AAACAACTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.19
20 25 0.68
21 5 0.14
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTACAATTTTTATAATTT
Found at i:40390417 original size:10 final size:9
Alignment explanation
Indices: 40390386--40390551 Score: 63
Period size: 10 Copynumber: 17.6 Consensus size: 9
40390376 ATTTTTTATA
40390386 TTTTAAATT
1 TTTTAAATT
*
40390395 TATTATAATTT
1 T-TT-TAAATT
40390406 TTTTACAATT
1 TTTTA-AATT
40390416 TTTATAAATT
1 TTT-TAAATT
*
40390426 TTTAACAATT
1 TTTTA-AATT
40390436 TTTT-AA-T
1 TTTTAAATT
**
40390443 TTTTAAACA
1 TTTTAAATT
**
40390452 ACTTAAATT
1 TTTTAAATT
*
40390461 TTTTATATAT
1 TTTTAAAT-T
*
40390471 TTTTAAATAAA
1 TTTTAAAT--T
40390482 TTTTAAATT
1 TTTTAAATT
*
40390491 TTCTAAATAAT
1 TTTTAAAT--T
*
40390502 TTTGGAAATT
1 TTT-TAAATT
*
40390512 TTAT-AA-T
1 TTTTAAATT
40390519 TTTTACAATT
1 TTTTA-AATT
**
40390529 TTTTTCA-T
1 TTTTAAATT
40390537 TTTTAAATAT
1 TTTTAAAT-T
40390547 TTTTA
1 TTTTA
40390552 TGATTTTCGA
Statistics
Matches: 115, Mismatches: 25, Indels: 33
0.66 0.14 0.19
Matches are distributed among these distances:
7 9 0.08
8 12 0.10
9 24 0.21
10 46 0.40
11 20 0.17
12 4 0.03
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.58
Consensus pattern (9 bp):
TTTTAAATT
Found at i:40390451 original size:19 final size:19
Alignment explanation
Indices: 40390391--40390558 Score: 77
Period size: 20 Copynumber: 8.8 Consensus size: 19
40390381 TTATATTTTA
*
40390391 AATTTATTATAATTTTTTTAC
1 AATTT-TTATAA-TTTTTAAC
40390412 AATTTTTATAAATTTTTAAC
1 AATTTTTAT-AATTTTTAAC
40390432 AATTTTT-TAATTTTTAAAC
1 AATTTTTATAATTTTT-AAC
* * *
40390451 AA--CTTA-AATTTTTTAT
1 AATTTTTATAATTTTTAAC
*
40390467 ATATTTTTAAATAAATTTT-A-
1 A-ATTTTT--ATAATTTTTAAC
**
40390487 AATTTTCTAAATAATTTTGGA-
1 AATTTT-T--ATAATTTTTAAC
40390508 AA-TTTTATAATTTTT-AC
1 AATTTTTATAATTTTTAAC
* *
40390525 AATTTTTTTCATTTTTAA-
1 AATTTTTATAATTTTTAAC
*
40390543 ATATTTTTATGATTTT
1 A-ATTTTTATAATTTT
40390559 CGAATGATTT
Statistics
Matches: 119, Mismatches: 13, Indels: 32
0.73 0.08 0.20
Matches are distributed among these distances:
16 3 0.03
17 20 0.17
18 19 0.16
19 27 0.23
20 32 0.27
21 12 0.10
22 6 0.05
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (19 bp):
AATTTTTATAATTTTTAAC
Found at i:40398089 original size:3 final size:3
Alignment explanation
Indices: 40398081--40398122 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
40398071 AATTGAGCAT
40398081 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
40398123 AACCTTAATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:40403444 original size:21 final size:21
Alignment explanation
Indices: 40403418--40403459 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
40403408 AGACACGGGC
40403418 ATGTGTCTTAGCTGTGTGTGA
1 ATGTGTCTTAGCTGTGTGTGA
40403439 ATGTGTCTTAGCTGTGTGTGA
1 ATGTGTCTTAGCTGTGTGTGA
40403460 CACACGGCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.10, G:0.33, T:0.43
Consensus pattern (21 bp):
ATGTGTCTTAGCTGTGTGTGA
Found at i:40409824 original size:94 final size:94
Alignment explanation
Indices: 40409659--40409830 Score: 211
Period size: 94 Copynumber: 1.8 Consensus size: 94
40409649 AATGTTTAAA
* * * * **
40409659 TGTAAGACCATAGCTGGGCTATGACATTTTAGTGAAAAGACCATAATTGGGATATGGCACCGTGA
1 TGTAAGACCATAGCTGGGCTATGACATCTGAGTGAAAAGACCATAACTAGGATATGGCACCACGA
40409724 ACGTAAGACCATGGCAGTATATGTATATG
66 ACGTAAGACCATGGCAGTATATGTATATG
* * * **
40409753 TGTAAGACCATAGCTGGGCTATGGCATCCTGA-TGATAAGACCATAACTAGGTTATGGCATTACG
1 TGTAAGACCATAGCTGGGCTATGACAT-CTGAGTGAAAAGACCATAACTAGGATATGGCACCACG
**
40409817 AGTGTAAGACCATG
65 AACGTAAGACCATG
40409831 TCAGCGGCAT
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
94 62 0.97
95 2 0.03
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (94 bp):
TGTAAGACCATAGCTGGGCTATGACATCTGAGTGAAAAGACCATAACTAGGATATGGCACCACGA
ACGTAAGACCATGGCAGTATATGTATATG
Found at i:40409825 original size:33 final size:33
Alignment explanation
Indices: 40409752--40409829 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 33
40409742 ATATGTATAT
* * *
40409752 GTGTAAGACCATAGCTGGGCTATGGCATCCTGA
1 GTGTAAGACCATAACTAGGCTATGGCATACTGA
*
40409785 -TGATAAGACCATAACTAGGTTATGGCATTAC-GA
1 GTG-TAAGACCATAACTAGGCTATGGCA-TACTGA
40409818 GTGTAAGACCAT
1 GTGTAAGACCAT
40409830 GTCAGCGGCA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
32 2 0.05
33 32 0.84
34 4 0.11
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.26
Consensus pattern (33 bp):
GTGTAAGACCATAACTAGGCTATGGCATACTGA
Found at i:40411609 original size:18 final size:18
Alignment explanation
Indices: 40411588--40411651 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 18
40411578 TAGCAATTGG
*
40411588 TTATTCAGTAACGGTCAA
1 TTATTCAGTAACAGTCAA
* *
40411606 TTATTCGGTAACAGTCAG
1 TTATTCAGTAACAGTCAA
*
40411624 TCT-TTCAGTAATAGTCAA
1 T-TATTCAGTAACAGTCAA
40411642 TTATTCAGTA
1 TTATTCAGTA
40411652 CATTTATTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
17 1 0.03
18 36 0.95
19 1 0.03
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.38
Consensus pattern (18 bp):
TTATTCAGTAACAGTCAA
Found at i:40411774 original size:6 final size:6
Alignment explanation
Indices: 40411763--40411797 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
40411753 TACACTGTAT
* *
40411763 CAGTAA CAGTAA CGGTAA CAGTAA CAGTAG CAGTA
1 CAGTAA CAGTAA CAGTAA CAGTAA CAGTAA CAGTA
40411798 CACAAAGTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.43, C:0.17, G:0.23, T:0.17
Consensus pattern (6 bp):
CAGTAA
Found at i:40412068 original size:18 final size:19
Alignment explanation
Indices: 40412045--40412081 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
40412035 TAAGCTAATC
*
40412045 ATATATAT-TTTCAGTTCA
1 ATATATATATTTCAATTCA
40412063 ATATATATATTTCAATTCA
1 ATATATATATTTCAATTCA
40412082 CTTTACATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.38, C:0.11, G:0.03, T:0.49
Consensus pattern (19 bp):
ATATATATATTTCAATTCA
Found at i:40414506 original size:50 final size:51
Alignment explanation
Indices: 40414429--40414557 Score: 206
Period size: 50 Copynumber: 2.5 Consensus size: 51
40414419 GACCATGGCA
* *
40414429 ACAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGGACAAGTG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
*
40414480 A-AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAATG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
* *
40414530 ACAAGTGAGAAGTGGTAGCTTCGGCTAC
1 ACAAGTGATAAGTGATAGCTTCGGCTAC
40414558 CTGATCAGTG
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
50 47 0.65
51 25 0.35
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (51 bp):
ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
Found at i:40414574 original size:31 final size:31
Alignment explanation
Indices: 40414533--40414681 Score: 244
Period size: 31 Copynumber: 4.8 Consensus size: 31
40414523 ACAAATGACA
*
40414533 AGTGAGAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
40414564 AGTGAAAAGTGGTAGCTTCTGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
40414595 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
40414626 AGTGAAAAATGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
40414657 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
40414682 AAGTGACAAG
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 110 1.00
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.26
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:40414852 original size:48 final size:48
Alignment explanation
Indices: 40414781--40414885 Score: 167
Period size: 49 Copynumber: 2.2 Consensus size: 48
40414771 GCATCAGTGA
*
40414781 GATATGTGATTCGTGTAAAACCATAGCT-GACTATGGCATCGATATGT
1 GATATGTGATTCGTGTAAAACCATAGCTGGACTATGGCATCGATATAT
*
40414828 GATATGTGATTACGTGTAAGACCATAGCTGGACTATGGCATCGATATAT
1 GATATGTGATT-CGTGTAAAACCATAGCTGGACTATGGCATCGATATAT
40414877 GAATATGTG
1 G-ATATGTG
40414886 TAAGACCATA
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
47 11 0.21
48 16 0.30
49 19 0.36
50 7 0.13
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.31
Consensus pattern (48 bp):
GATATGTGATTCGTGTAAAACCATAGCTGGACTATGGCATCGATATAT
Found at i:40414887 original size:42 final size:43
Alignment explanation
Indices: 40414793--40414955 Score: 163
Period size: 42 Copynumber: 3.7 Consensus size: 43
40414783 TATGTGATTC
* *
40414793 GTGTAAAACCATAGCT-GACTATGGCATCGATATGTGATATG-TGATT
1 GTGTAAGACCATAGCTGGACTATGGCATCG--AT-T-ATATGAAGA-T
*
40414839 ACGTGTAAGACCATAGCTGGACTATGGCATCGA-TATATGAATAT
1 --GTGTAAGACCATAGCTGGACTATGGCATCGATTATATGAAGAT
** *
40414883 GTGTAAGACCATAGCTGGGTTATGGCATC-ATTATGTGAAGAT
1 GTGTAAGACCATAGCTGGACTATGGCATCGATTATATGAAGAT
* *
40414925 GTGTAAGACCATAGTTGAACTATGGCATCGA
1 GTGTAAGACCATAGCTGGACTATGGCATCGA
40414956 GAAAACGAAG
Statistics
Matches: 100, Mismatches: 11, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
41 1 0.01
42 61 0.61
43 1 0.01
44 6 0.06
45 2 0.02
47 1 0.01
48 15 0.15
49 13 0.13
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.29
Consensus pattern (43 bp):
GTGTAAGACCATAGCTGGACTATGGCATCGATTATATGAAGAT
Found at i:40416239 original size:20 final size:18
Alignment explanation
Indices: 40416203--40416247 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
40416193 AAACATTCAA
40416203 TTTTCCCTTTCTTCTTTC
1 TTTTCCCTTTCTTCTTTC
40416221 TTTTCTCCTTTCTTTCTTTC
1 TTTTC-CCTTTC-TTCTTTC
40416241 -TTTCCCT
1 TTTTCCCT
40416248 GCTTTTCGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.32
19 10 0.40
20 7 0.28
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTCCCTTTCTTCTTTC
Found at i:40418539 original size:26 final size:26
Alignment explanation
Indices: 40418510--40418619 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
40418500 TGGTACAAAT
*
40418510 TGATAATAGGTTAGGTAAATGTTCAA
1 TGATAATAGGTTAGGTAAATGTTCCA
40418536 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
40418562 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
40418588 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
40418614 TGATAA
1 TGATAA
40418620 GAATTTCATG
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 81 1.00
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:40420101 original size:28 final size:26
Alignment explanation
Indices: 40420070--40420134 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 26
40420060 AATTACTATA
40420070 ATACCCCTATGTATGGAAAATT-CCTGTT
1 ATACCCCTA-G-ATGGAAAATTACC-GTT
* *
40420098 ATACCCCCTAGGTGTAAAATTACCGTT
1 ATA-CCCCTAGATGGAAAATTACCGTT
40420125 ATACCCCTAG
1 ATACCCCTAG
40420135 GGTTAATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 7 0.21
27 14 0.42
28 6 0.18
29 6 0.18
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (26 bp):
ATACCCCTAGATGGAAAATTACCGTT
Found at i:40420279 original size:27 final size:26
Alignment explanation
Indices: 40420238--40420323 Score: 91
Period size: 27 Copynumber: 3.2 Consensus size: 26
40420228 GAGGAAGCGT
* *
40420238 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCAC-ATTATCTGA
40420265 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCAC-ATTATCTG-A
* * * *
40420293 TTTGGTGACTCTGTCACATTATCTGT
1 TCTGGTGGCTCTGCCACATTATCTGA
40420319 TCTGG
1 TCTGG
40420324 CAGTCATGCT
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
26 4 0.08
27 31 0.62
28 15 0.30
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.37
Consensus pattern (26 bp):
TCTGGTGGCTCTGCCACATTATCTGA
Found at i:40424031 original size:26 final size:26
Alignment explanation
Indices: 40424000--40424107 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
40423990 TGAAATGCCC
*
40424000 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
40424026 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
40424052 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
40424078 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
40424104 ATCA
1 ATCA
40424108 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:40428581 original size:27 final size:27
Alignment explanation
Indices: 40428551--40428728 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
40428541 ATATTGAGTC
* * * *
40428551 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
40428578 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40428605 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
40428633 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
40428660 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
40428687 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40428714 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40428729 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:40428690 original size:82 final size:81
Alignment explanation
Indices: 40428572--40428727 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
40428562 TGCTATATAA
* *
40428572 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
40428637 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
40428654 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
40428718 CACTTAGTGC
65 CACTTAGTGC
40428728 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:40434316 original size:26 final size:26
Alignment explanation
Indices: 40434280--40434388 Score: 168
Period size: 26 Copynumber: 4.2 Consensus size: 26
40434270 ATGAAAGGCC
40434280 TATCATGGAACATTTACCTAAACCAT
1 TATCATGGAACATTTACCTAAACCAT
40434306 TATCATGGAACATTTACCT-AACTCAT
1 TATCATGGAACATTTACCTAAAC-CAT
*
40434332 TATCATGGAATATTTACCTAATA-CAT
1 TATCATGGAACATTTACCTAA-ACCAT
*
40434358 TATCATGGAACATTTACCTAACCCAT
1 TATCATGGAACATTTACCTAAACCAT
40434384 TATCA
1 TATCA
40434389 ATTTGTACCA
Statistics
Matches: 76, Mismatches: 3, Indels: 8
0.87 0.03 0.09
Matches are distributed among these distances:
25 3 0.04
26 71 0.93
27 1 0.01
28 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.34
Consensus pattern (26 bp):
TATCATGGAACATTTACCTAAACCAT
Found at i:40435038 original size:11 final size:11
Alignment explanation
Indices: 40435024--40435064 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
40435014 TGTTTTCTCC
40435024 CTATTTTGCTA
1 CTATTTTGCTA
*
40435035 CTATTTTACTA
1 CTATTTTGCTA
* *
40435046 TTATGTTGCTA
1 CTATTTTGCTA
40435057 CTATTTTG
1 CTATTTTG
40435065 TTGTTATTGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:40436705 original size:13 final size:13
Alignment explanation
Indices: 40436689--40436713 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40436679 AATATTAAAT
40436689 AATAATATTTACG
1 AATAATATTTACG
40436702 AATAATATTTAC
1 AATAATATTTAC
40436714 ATACTTACTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (13 bp):
AATAATATTTACG
Found at i:40436942 original size:19 final size:18
Alignment explanation
Indices: 40436892--40436945 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
40436882 TATGAAAAAT
40436892 AATATTTATTTTAATTATAA
1 AATATTTA-TTT-ATTATAA
*
40436912 AATATATAATTTATTATAAA
1 AATAT-TTATTTATTAT-AA
40436932 AATATTTATTTATT
1 AATATTTATTTATT
40436946 TTTAACATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 13 0.43
20 15 0.50
21 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AATATTTATTTATTATAA
Found at i:40445236 original size:22 final size:23
Alignment explanation
Indices: 40445183--40445237 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
40445173 ACACTTCAAT
40445183 AATATAAATAATATAAAATGTGA
1 AATATAAATAATATAAAATGTGA
*
40445206 AAT-TTAATAATAT-AAATAGT-A
1 AATATAAATAATATAAAAT-GTGA
*
40445227 TATATAAATAA
1 AATATAAATAA
40445238 AATTATTACT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
21 7 0.26
22 17 0.63
23 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (23 bp):
AATATAAATAATATAAAATGTGA
Found at i:40448862 original size:63 final size:63
Alignment explanation
Indices: 40448756--40448881 Score: 198
Period size: 63 Copynumber: 2.0 Consensus size: 63
40448746 TCCCTTTGGT
*** *
40448756 TATGCACTAGTTGATGGTCTGAGAGTCAATCGATTGTAGAAGTTGGGTAGAATCCGTCTAAAA
1 TATGCACTAGTTGATGGTCTGAGAGTCAATCGACCATAGAAGTTGGGTAGAATCCGACTAAAA
* *
40448819 TATGCACTAGTTGATGGTCTGAGAGTCAATCGACCATATAAGTTGGGTAGAATCTGACTAAAA
1 TATGCACTAGTTGATGGTCTGAGAGTCAATCGACCATAGAAGTTGGGTAGAATCCGACTAAAA
40448882 CAGAAAGGAC
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.29
Consensus pattern (63 bp):
TATGCACTAGTTGATGGTCTGAGAGTCAATCGACCATAGAAGTTGGGTAGAATCCGACTAAAA
Found at i:40450147 original size:19 final size:19
Alignment explanation
Indices: 40450123--40450171 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
40450113 TAGCTGTAGC
40450123 CGTAAAAGGCT-GCTATAGA
1 CGTAAAAGGCTAGCTATA-A
*
40450142 CGTAAAAGGTTAGCTATAA
1 CGTAAAAGGCTAGCTATAA
40450161 CTGTAAAAGGC
1 C-GTAAAAGGC
40450172 AAGTTTGCGC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.22
Consensus pattern (19 bp):
CGTAAAAGGCTAGCTATAA
Found at i:40450159 original size:20 final size:20
Alignment explanation
Indices: 40450111--40450171 Score: 72
Period size: 19 Copynumber: 3.1 Consensus size: 20
40450101 AGTTGAATAA
* *
40450111 GCTAGCTGTAGCCGTAAAAG
1 GCTAGCTATAGACGTAAAAG
40450131 GCT-GCTATAGACGTAAAAG
1 GCTAGCTATAGACGTAAAAG
*
40450150 GTTAGCTATA-ACTGTAAAAG
1 GCTAGCTATAGAC-GTAAAAG
40450170 GC
1 GC
40450172 AAGTTTGCGC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
19 18 0.51
20 17 0.49
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.23
Consensus pattern (20 bp):
GCTAGCTATAGACGTAAAAG
Found at i:40458006 original size:19 final size:19
Alignment explanation
Indices: 40457982--40458018 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
40457972 ATCACTATCA
40457982 CCACTGTAATCAAATTTGT
1 CCACTGTAATCAAATTTGT
40458001 CCACTGTAATCAAATTTG
1 CCACTGTAATCAAATTTG
40458019 AATAATTCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (19 bp):
CCACTGTAATCAAATTTGT
Found at i:40458058 original size:18 final size:18
Alignment explanation
Indices: 40458013--40458067 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
40458003 ACTGTAATCA
*
40458013 AATTTGAATAATTCGAGTT
1 AATTCGAATAATTCGA-TT
* *
40458032 GACTCGAATAATTCGATT
1 AATTCGAATAATTCGATT
*
40458050 AATTCGAATAACTCGATT
1 AATTCGAATAATTCGATT
40458068 CGTCTAACTC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 17 0.57
19 13 0.43
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (18 bp):
AATTCGAATAATTCGATT
Found at i:40460730 original size:124 final size:124
Alignment explanation
Indices: 40460501--40460962 Score: 504
Period size: 124 Copynumber: 3.8 Consensus size: 124
40460491 AACCTTGGTC
* * * * *
40460501 TCTGCTCATAATTTGGCAATATGCCTCTCATTCGACTCAATGTAAGAGGTGAGTTGATCAATCAT
1 TCTGCTCGTAATTTGGCAACATGCCTCTCATTCGACTCATTATAGGAGGTGAGTTGATCAATCAT
* * *
40460566 TCGTTCTTGAATGCTTGTGGGAATAGACTTGGGGCTTGAGCTAGTGAGCACTCATTGAG
66 TCGTTCTTGAATGCTTGTGGGAATAGCCTTGGGACCTGAGCTAGTGAGCACTCATTGAG
40460625 TCTGCTCGTAATTTGGCAACATGCCTCTCATTCGACTCATTATAGGAGGTGAGTTGATCAATCAT
1 TCTGCTCGTAATTTGGCAACATGCCTCTCATTCGACTCATTATAGGAGGTGAGTTGATCAATCAT
* * * * ** *
40460690 TCGTTCTTGAATACTTGTGGGAGTAGCCTTTGGACCTGAGCTAGTGGGCTTTCCTTGAG
66 TCGTTCTTGAATGCTTGTGGGAATAGCCTTGGGACCTGAGCTAGTGAGCACTCATTGAG
* * * * * * *
40460749 TCTGCTCGTAATCTGGAAACATGCCTCTTATTCTACTCATTATAGAAGGTGAGTAGATTAATCAT
1 TCTGCTCGTAATTTGGCAACATGCCTCTCATTCGACTCATTATAGGAGGTGAGTTGATCAATCAT
* *
40460814 TCGTTCTTGAATGCTTGTGGGAATAGCCTT-GG----G-GC-------CACTCCTTAAG
66 TCGTTCTTGAATGCTTGTGGGAATAGCCTTGGGACCTGAGCTAGTGAGCACTCATTGAG
* * * * * * *
40460860 GCT-ATCGTAATTTGGAAACATGCCTCTCATTTGAATCACTT-TAAGAGGTGAGTTGACCAATCA
1 TCTGCTCGTAATTTGGCAACATGCCTCTCATTCGACTCA-TTATAGGAGGTGAGTTGATCAATCA
* * *
40460923 TTCATTCTTGAATGCCTGTGGGAATAGCCTTGGGGCCTGA
65 TTCGTTCTTGAATGCTTGTGGGAATAGCCTTGGGACCTGA
40460963 AGTAATGGGC
Statistics
Matches: 290, Mismatches: 41, Indels: 22
0.82 0.12 0.06
Matches are distributed among these distances:
110 75 0.26
111 14 0.05
115 1 0.00
118 2 0.01
119 1 0.00
123 2 0.01
124 195 0.67
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (124 bp):
TCTGCTCGTAATTTGGCAACATGCCTCTCATTCGACTCATTATAGGAGGTGAGTTGATCAATCAT
TCGTTCTTGAATGCTTGTGGGAATAGCCTTGGGACCTGAGCTAGTGAGCACTCATTGAG
Found at i:40460947 original size:110 final size:110
Alignment explanation
Indices: 40460754--40460959 Score: 292
Period size: 110 Copynumber: 1.9 Consensus size: 110
40460744 TTGAGTCTGC
* * ** *
40460754 TCGTAATCTGGAAACATGCCTCTTATTCTACTCATTATAGAAGGTGAGTAGATTAATCATTCGTT
1 TCGTAATCTGGAAACATGCCTCTCATTCTAATCATTATAGAAGGTGAGTAGACCAATCATTCATT
*
40460819 CTTGAATGCTTGTGGGAATAGCCTTGGGGCCACTCCTTAAGGCTA
66 CTTGAATGCCTGTGGGAATAGCCTTGGGGCCACTCCTTAAGGCTA
* *
40460864 TCGTAATTTGGAAACATGCCTCTCATT-TGAATCACTT-TA-AGAGGTGAGTTGACCAATCATTC
1 TCGTAATCTGGAAACATGCCTCTCATTCT-AATCA-TTATAGA-AGGTGAGTAGACCAATCATTC
40460926 ATTCTTGAATGCCTGTGGGAATAGCCTTGGGGCC
63 ATTCTTGAATGCCTGTGGGAATAGCCTTGGGGCC
40460960 TGAAGTAATG
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
109 2 0.02
110 81 0.95
111 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.33
Consensus pattern (110 bp):
TCGTAATCTGGAAACATGCCTCTCATTCTAATCATTATAGAAGGTGAGTAGACCAATCATTCATT
CTTGAATGCCTGTGGGAATAGCCTTGGGGCCACTCCTTAAGGCTA
Found at i:40465385 original size:29 final size:29
Alignment explanation
Indices: 40465342--40465429 Score: 104
Period size: 29 Copynumber: 3.0 Consensus size: 29
40465332 GTACATAGTA
* *
40465342 CCTGATAATTATAACACTGGCACAAAGTG
1 CCTGATAACTGTAACACTGGCACAAAGTG
* *
40465371 CCTGATAACTGTAACACTAGCACAAAGTA
1 CCTGATAACTGTAACACTGGCACAAAGTG
* * *
40465400 CCTAATAACTGTAATCACCGGCACATAGTG
1 CCTGATAACTGTAA-CACTGGCACAAAGTG
40465430 TCTCATAAAC
Statistics
Matches: 49, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 38 0.78
30 11 0.22
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.23
Consensus pattern (29 bp):
CCTGATAACTGTAACACTGGCACAAAGTG
Found at i:40469459 original size:24 final size:24
Alignment explanation
Indices: 40469432--40469535 Score: 86
Period size: 24 Copynumber: 4.3 Consensus size: 24
40469422 TGGCTCTTCG
* *
40469432 GAGCTACCTGTTATTGGCTCGCAT
1 GAGCTTCCTGTTATAGGCTCGCAT
**
40469456 GAGCTTCCTGATT-TAGGCTCTTAT
1 GAGCTTCCTG-TTATAGGCTCGCAT
* *
40469480 GAGCTTCCTGTTATA-GCCCGAAT
1 GAGCTTCCTGTTATAGGCTCGCAT
* * * *
40469503 AAGCTTCCTGTTACATGGCTCACTT
1 GAGCTTCCTGTTATA-GGCTCGCAT
40469528 GAGCTTCC
1 GAGCTTCC
40469536 CATTAAATGG
Statistics
Matches: 62, Mismatches: 14, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
23 20 0.32
24 29 0.47
25 13 0.21
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.35
Consensus pattern (24 bp):
GAGCTTCCTGTTATAGGCTCGCAT
Found at i:40477251 original size:35 final size:35
Alignment explanation
Indices: 40477205--40477274 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
40477195 GCCTGAAGAC
40477205 CCAATTGGGCAAAGAGAATCACATTAGTTGTCGAA
1 CCAATTGGGCAAAGAGAATCACATTAGTTGTCGAA
40477240 CCAATTGGGCAAAGAGAATCACATTAGTTGTCGAA
1 CCAATTGGGCAAAGAGAATCACATTAGTTGTCGAA
40477275 ATGATGACAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (35 bp):
CCAATTGGGCAAAGAGAATCACATTAGTTGTCGAA
Found at i:40490616 original size:38 final size:38
Alignment explanation
Indices: 40490505--40490623 Score: 159
Period size: 38 Copynumber: 3.1 Consensus size: 38
40490495 ATTTGATGTG
* *
40490505 TATCCGGGCTTAAAGACCCGCAGGCTTCA-TGCTGGTAATA
1 TATCCGGG-TTAAA-TCCCGCAGGCTT-AGTGCTGGTATTA
*
40490545 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGTATTA
* *
40490583 TATCCGGGTTAAATCCCGCAGGCCTAGTACTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGTATTA
40490621 TAT
1 TAT
40490624 TCAGGCCTTT
Statistics
Matches: 72, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
38 59 0.82
39 5 0.07
40 8 0.11
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.29
Consensus pattern (38 bp):
TATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGTATTA
Found at i:40490676 original size:45 final size:45
Alignment explanation
Indices: 40490620--40490751 Score: 148
Period size: 45 Copynumber: 3.0 Consensus size: 45
40490610 TACTGGTATT
* * *
40490620 ATATTCAGGCCTTTGAGCCTAGCAGGCTATTATGCCGGTGAGAT-
1 ATATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGACATG
* *
40490664 ACTATTCGGGCCTTTGAGCCTAGTAGGCTATAATGTCGGTGACATG
1 A-TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGACATG
* * *
40490710 ATA-TCGAGCC-TTGAGCCTAGCAGGCGA-AATACCGGTGA-ATG
1 ATATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGACATG
40490751 A
1 A
40490752 ATAAAAGTCT
Statistics
Matches: 76, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
41 4 0.05
42 9 0.12
43 15 0.20
44 7 0.09
45 40 0.53
46 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (45 bp):
ATATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGACATG
Found at i:40491863 original size:34 final size:35
Alignment explanation
Indices: 40491817--40491894 Score: 99
Period size: 34 Copynumber: 2.3 Consensus size: 35
40491807 ATCTCAATAC
*
40491817 AGTATCAATATGT-TGTAGGGCCTTAGCCCATCA-A
1 AGTATCAGTATGTAT-TAGGGCCTTAGCCCATCACA
* *
40491851 AGTATCAGTATGTATTAGGGCTTTAGCTCATCACA
1 AGTATCAGTATGTATTAGGGCCTTAGCCCATCACA
40491886 A-TATCAGTA
1 AGTATCAGTA
40491895 GCAGTCATGC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
34 36 0.92
35 3 0.08
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (35 bp):
AGTATCAGTATGTATTAGGGCCTTAGCCCATCACA
Found at i:40493548 original size:22 final size:22
Alignment explanation
Indices: 40493520--40493570 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
40493510 CACAATGAAT
40493520 AATGTGACTAATTATTAAGCTA
1 AATGTGACTAATTATTAAGCTA
40493542 AATGTGACTAATTATTAAGCTA
1 AATGTGACTAATTATTAAGCTA
40493564 AATGTGA
1 AATGTGA
40493571 TGTTATAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (22 bp):
AATGTGACTAATTATTAAGCTA
Found at i:40498827 original size:26 final size:26
Alignment explanation
Indices: 40498791--40498844 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
40498781 CCCTAGCCAC
40498791 CAATATAACTCACGAAGGTCTTGGTA
1 CAATATAACTCACGAAGGTCTTGGTA
*
40498817 CAATATAACTCATGAAGGTCTTGGTA
1 CAATATAACTCACGAAGGTCTTGGTA
40498843 CA
1 CA
40498845 TCTTATTTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (26 bp):
CAATATAACTCACGAAGGTCTTGGTA
Found at i:40502333 original size:25 final size:23
Alignment explanation
Indices: 40502303--40502358 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
40502293 TTAACTATAG
40502303 TTTTCAGTATGTACTAACTAGAGTA
1 TTTTCAGTA--TACTAACTAGAGTA
*
40502328 TTTTCACAGTATACTAACTATAGTA
1 TTTT--CAGTATACTAACTAGAGTA
*
40502353 GTTTCA
1 TTTTCA
40502359 AAATAGCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
23 2 0.07
25 20 0.74
27 5 0.19
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.41
Consensus pattern (23 bp):
TTTTCAGTATACTAACTAGAGTA
Found at i:40511159 original size:19 final size:19
Alignment explanation
Indices: 40511122--40511221 Score: 168
Period size: 19 Copynumber: 5.3 Consensus size: 19
40511112 CAAGATTACA
40511122 ATATCATATCTTCAAGATTGC
1 ATATCATATC-T-AAGATTGC
40511143 ATATCATATCTAAGATTGC
1 ATATCATATCTAAGATTGC
40511162 ATATCATATCTAAGATTG-
1 ATATCATATCTAAGATTGC
40511180 -TATCATATCTAAGATTGC
1 ATATCATATCTAAGATTGC
40511198 ATATCATATCTAAGATTGC
1 ATATCATATCTAAGATTGC
40511217 ATATC
1 ATATC
40511222 CCTAAAGATT
Statistics
Matches: 77, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
17 17 0.22
19 49 0.64
20 1 0.01
21 10 0.13
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (19 bp):
ATATCATATCTAAGATTGC
Found at i:40511190 original size:36 final size:37
Alignment explanation
Indices: 40511113--40511221 Score: 157
Period size: 36 Copynumber: 2.8 Consensus size: 37
40511103 TTAAATCTCC
*
40511113 AAGATTACAATATCATATCTTCAAGATTGCATATCATATCT
1 AAGATTGC-ATATCATATC-T-AAGATTG-ATATCATATCT
40511154 AAGATTGCATATCATATCTAAGATTG-TATCATATCT
1 AAGATTGCATATCATATCTAAGATTGATATCATATCT
40511190 AAGATTGCATATCATATCTAAGATTGCATATC
1 AAGATTGCATATCATATCTAAGATTG-ATATC
40511222 CCTAAAGATT
Statistics
Matches: 65, Mismatches: 1, Indels: 7
0.89 0.01 0.10
Matches are distributed among these distances:
36 36 0.55
38 11 0.17
39 1 0.02
40 10 0.15
41 7 0.11
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.37
Consensus pattern (37 bp):
AAGATTGCATATCATATCTAAGATTGATATCATATCT
Found at i:40511452 original size:28 final size:29
Alignment explanation
Indices: 40511420--40511492 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 29
40511410 GATTAGGCCT
*
40511420 AATGGGCCATATGAATGTGATTGGGCCCG
1 AATGGGCCATATGAATGAGATTGGGCCCG
*
40511449 -ATGGGCCATATGAATGAGATTGGGCCTG
1 AATGGGCCATATGAATGAGATTGGGCCCG
* *
40511477 AAGGGGCCAAATGAAT
1 AATGGGCCATATGAAT
40511493 AAGTATGGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 26 0.67
29 13 0.33
ACGTcount: A:0.29, C:0.15, G:0.34, T:0.22
Consensus pattern (29 bp):
AATGGGCCATATGAATGAGATTGGGCCCG
Found at i:40520347 original size:16 final size:16
Alignment explanation
Indices: 40520326--40520362 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
40520316 CGGTAAATTT
*
40520326 TGAAATGCCGAAAAGC
1 TGAAATACCGAAAAGC
40520342 TGAAATACCGAAAAGC
1 TGAAATACCGAAAAGC
*
40520358 CGAAA
1 TGAAA
40520363 GTTTGGCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.49, C:0.19, G:0.22, T:0.11
Consensus pattern (16 bp):
TGAAATACCGAAAAGC
Found at i:40520589 original size:28 final size:28
Alignment explanation
Indices: 40520556--40520675 Score: 150
Period size: 28 Copynumber: 4.2 Consensus size: 28
40520546 ATTGCATGAC
*
40520556 TATGAATGTGATTGGGCCTGACGGGCCA
1 TATGAATGTGATTGGGCCTGATGGGCCA
* *
40520584 TATGAAAGTGATTGGGCCTAATGGGCCA
1 TATGAATGTGATTGGGCCTGATGGGCCA
* *
40520612 TATGAATTTGATTGGGCCCGATGGGCCA
1 TATGAATGTGATTGGGCCTGATGGGCCA
* * *
40520640 TACGAATGAGATTGGGCCTGAAAGGGCCA
1 TATGAATGTGATTGGGCCTG-ATGGGCCA
*
40520669 AATGAAT
1 TATGAAT
40520676 AAGTATGGAT
Statistics
Matches: 77, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
28 65 0.84
29 12 0.16
ACGTcount: A:0.28, C:0.16, G:0.33, T:0.24
Consensus pattern (28 bp):
TATGAATGTGATTGGGCCTGATGGGCCA
Found at i:40521977 original size:26 final size:26
Alignment explanation
Indices: 40521948--40522001 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
40521938 TTGGTATAGG
40521948 TATGTTTTGACCATGTTTAAAATACT
1 TATGTTTTGACCATGTTTAAAATACT
40521974 TATGTTTTGACCATGTTTAAAATACT
1 TATGTTTTGACCATGTTTAAAATACT
40522000 TA
1 TA
40522002 GATAGGTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.46
Consensus pattern (26 bp):
TATGTTTTGACCATGTTTAAAATACT
Found at i:40545152 original size:24 final size:25
Alignment explanation
Indices: 40545125--40545178 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
40545115 TAGACAAGTC
40545125 ACATTTTCG-TATAATATTTTAACA
1 ACATTTTCGTTATAATATTTTAACA
* * * *
40545149 ACA-TCTCGTTATCATATTTTTACT
1 ACATTTTCGTTATAATATTTTAACA
40545173 ACATTT
1 ACATTT
40545179 CCCTTTTTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
23 4 0.17
24 18 0.78
25 1 0.04
ACGTcount: A:0.31, C:0.17, G:0.04, T:0.48
Consensus pattern (25 bp):
ACATTTTCGTTATAATATTTTAACA
Found at i:40548507 original size:11 final size:11
Alignment explanation
Indices: 40548491--40548526 Score: 54
Period size: 11 Copynumber: 3.1 Consensus size: 11
40548481 GATTGGTTAG
40548491 AATATTTTATT
1 AATATTTTATT
40548502 AATATTTTATCAT
1 AATATTTTAT--T
40548515 AATATTTTATT
1 AATATTTTATT
40548526 A
1 A
40548527 TAAGAATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 12 0.52
13 11 0.48
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (11 bp):
AATATTTTATT
Found at i:40548519 original size:13 final size:12
Alignment explanation
Indices: 40548491--40548529 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
40548481 GATTGGTTAG
40548491 AATATTTTAT-T
1 AATATTTTATAT
40548502 AATATTTTATCAT
1 AATATTTTAT-AT
40548515 AATATTTTATTAT
1 AATATTTTA-TAT
40548528 AA
1 AA
40548530 GAATTTGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 10 0.40
13 14 0.56
14 1 0.04
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (12 bp):
AATATTTTATAT
Found at i:40551816 original size:48 final size:48
Alignment explanation
Indices: 40551660--40551875 Score: 269
Period size: 48 Copynumber: 4.5 Consensus size: 48
40551650 TATGTGTGCT
* * * *
40551660 AGTGTAAGACATGTCTGGGACATGCATTGGCCAC-A-TTATGA-GAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATAT-ACAAGCC
* *
40551706 AGTATAAGACATGTTTGGGACATGCATCGGCCTCGAGATATATACAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAG--ATATACAAGCC
40551756 AGTGTAAGACATGTCTGGGACATGCATCGGCC-CTGAGATATACAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTC-GAGATATACAAGCC
* * *
40551804 AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAAATATACAAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATACAAGCC
* *
40551852 AGTGTAAGACCTGTCTAGGACATG
1 AGTGTAAGACATGTCTGGGACATG
40551876 GCATTAGCTT
Statistics
Matches: 150, Mismatches: 13, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
46 30 0.20
47 1 0.01
48 76 0.51
49 3 0.02
50 40 0.27
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (48 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATACAAGCC
Found at i:40551955 original size:49 final size:49
Alignment explanation
Indices: 40551660--40552067 Score: 233
Period size: 48 Copynumber: 8.5 Consensus size: 49
40551650 TATGTGTGCT
* * * * * *
40551660 AGTGTAAGACATGTCTGGGACAT-GCATTGGCCAC-AT-TATGAGAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAGATGAAAGCC
* * * * *
40551706 AGTATAAGACATGTTTGGGACAT-GCATCGGCCTCGAGATATAT-ACAAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACCTC--GATAGATGA-AAGCC
* * * *
40551756 AGTGTAAGACATGTCTGGGACAT-GCATCGGCC-CTGAGATAT-ACAAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACCTC-GATAGATGA-AAGCC
* * * *
40551804 AGTGTAAGACATGTCTGGGACAT-GCATC-AGCCTCGAAATAT-ACAAGCT
1 AGTGTAAGACCTGTCTGGGACATGGCATCGA-CCTCGATAGATGA-AAGCC
* * * * * * *
40551852 AGTGTAAGACCTGTCTAGGACATGGCAT-TAGCTTG-TTG-TG--TGTC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAGATGAAAGCC
*
40551896 AGTGTAAGACCTGTCTGGGACATGGCATCGACAC-CGATAGATGAGAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGAC-CTCGATAGATGAAAGCC
* * * * * * **
40551945 AGTGTAAGACCTATCTGGGACATGACATTGGCCTTGATATATGAAATTC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAGATGAAAGCC
* * **
40551994 AGTGTAAGACCTGTCTGGGACATGGCATCGACTTTGAT-G-TGCTAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAGATGAAAGCC
* *
40552041 AGTGTAAGACCATGTTTGGAACATGGC
1 AGTGTAAGACC-TGTCTGGGACATGGC
40552068 GTCGGCATCT
Statistics
Matches: 294, Mismatches: 50, Indels: 34
0.78 0.13 0.09
Matches are distributed among these distances:
44 28 0.10
45 2 0.01
46 34 0.12
47 17 0.06
48 93 0.32
49 83 0.28
50 37 0.13
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (49 bp):
AGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAGATGAAAGCC
Found at i:40552010 original size:98 final size:97
Alignment explanation
Indices: 40551660--40552025 Score: 319
Period size: 98 Copynumber: 3.8 Consensus size: 97
40551650 TATGTGTGCT
* ** * ** * * *
40551660 AGTGTAAGACATGTCTGGGACATGCATTGGCC-ACAT-TATGAGAGCCAGTATAAGACATGTTTG
1 AGTGTAAGACCTGTCTGGGACATGCATTGGCCTTGATATATGAAATTCAGTGTAAGACCTGTCTG
* *
40551723 GGACAT-GCATCGGCCTCGAGATATATACAAGCC
66 GGACATGGCATCGACCTCGA-A-AGATACAAGCC
* * * * ** *
40551756 AGTGTAAGACATGTCTGGGACATGCATCGGCCCTGAGATAT-ACAAGCCAGTGTAAGACATGTCT
1 AGTGTAAGACCTGTCTGGGACATGCATTGGCCTTGATATATGA-AATTCAGTGTAAGACCTGTCT
* *
40551820 GGGACAT-GCATC-AGCCTCGAAATATACAAGCT
65 GGGACATGGCATCGA-CCTCGAAAGATACAAGCC
* * *
40551852 AGTGTAAGACCTGTCTAGGACATGGCATTAG-CTTG-T-TGTG---TGTCAGTGTAAGACCTGTC
1 AGTGTAAGACCTGTCTGGGACAT-GCATTGGCCTTGATATATGAAAT-TCAGTGTAAGACCTGTC
* *
40551911 TGGGACATGGCATCGACAC-CGATAGATGA-GAGCC
64 TGGGACATGGCATCGAC-CTCGAAAGAT-ACAAGCC
*
40551945 AGTGTAAGACCTATCTGGGACATGACATTGGCCTTGATATATGAAATTCAGTGTAAGACCTGTCT
1 AGTGTAAGACCTGTCTGGGACATG-CATTGGCCTTGATATATGAAATTCAGTGTAAGACCTGTCT
40552010 GGGACATGGCATCGAC
65 GGGACATGGCATCGAC
40552026 TTTGATGTGC
Statistics
Matches: 225, Mismatches: 27, Indels: 34
0.79 0.09 0.12
Matches are distributed among these distances:
92 24 0.11
93 41 0.18
94 9 0.04
95 1 0.00
96 68 0.30
97 8 0.04
98 73 0.32
99 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.25
Consensus pattern (97 bp):
AGTGTAAGACCTGTCTGGGACATGCATTGGCCTTGATATATGAAATTCAGTGTAAGACCTGTCTG
GGACATGGCATCGACCTCGAAAGATACAAGCC
Found at i:40554745 original size:22 final size:22
Alignment explanation
Indices: 40554720--40554761 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
40554710 ATGATTATGG
*
40554720 TTGCTCATACAAGCTAACATAT
1 TTGCTCACACAAGCTAACATAT
*
40554742 TTGCTCACACAAGCTGACAT
1 TTGCTCACACAAGCTAACAT
40554762 TATAACCTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (22 bp):
TTGCTCACACAAGCTAACATAT
Done.