Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 3 of 189
Found at i:794989 original size:20 final size:20
Alignment explanation
Indices: 794964--795408 Score: 150
Period size: 27 Copynumber: 20.1 Consensus size: 20
794954 TTTAGATTAG
*
794964 AATTTTGTATGAATATTTTA
1 AATTTTGTATGAATATTGTA
*
794984 AATTTTTTGTATGAATATTATA
1 AA--TTTTGTATGAATATTGTA
* *
795006 ATTTTTTTATGAATATTGT-
1 AATTTTGTATGAATATTGTA
*
795025 AATGTTGTATGAATATTGTA
1 AATTTTGTATGAATATTGTA
* *
795045 ATTATTTTATAATTAA-ATTTGT-
1 A--ATTTTGT-ATGAATA-TTGTA
* * *
795067 -ATTTATAGTTTTGGAT-TAGTA
1 AATTT-T-G-TATGAATATTGTA
*
795088 ATTTTTTGTATGAATATTGT-
1 A-ATTTTGTATGAATATTGTA
*
795108 AATTTTGTATGAATATTATA
1 AATTTTGTATGAATATTGTA
795128 AATTTTTGTATGAATATTGTAATA
1 AA-TTTTGTATGAATATTG---TA
*
795152 TTATAGTTTTGTATGAATATTGCA
1 --A-A-TTTTGTATGAATATTGTA
*
795176 ATTTTTTTGTATGAATATTGTAA
1 A--ATTTTGTATGAATATTGT-A
*
795199 TTTTGTAATTTTGTATGAATATTATA
1 ------AATTTTGTATGAATATTGTA
**
795225 TTTTTTTGTATGAATATTGTAATATTA
1 -AATTTTGTATGAATATTG------TA
*
795252 TAATTTTGTATGAATATTGCA
1 -AATTTTGTATGAATATTGTA
*
795273 ATTTTTTTGTATGAATATTGTA
1 A--ATTTTGTATGAATATTGTA
*
795295 GTTTTGTAATTTTGTATGAATATTAT-
1 -------AATTTTGTATGAATATTGTA
*
795321 AATTTTTTATGAATATTGT-
1 AATTTTGTATGAATATTGTA
*
795340 AATGTTGTATGAATATTGTAATATTA
1 AATTTTGTATGAATATTG------TA
*
795366 TAATTTTGTATGAATATTGCA
1 -AATTTTGTATGAATATTGTA
*
795387 ATTTTTTGTATGAATATTGTA
1 A-ATTTTGTATGAATATTGTA
795408 A
1 A
795409 TATTGTAATT
Statistics
Matches: 324, Mismatches: 46, Indels: 109
0.68 0.10 0.23
Matches are distributed among these distances:
19 69 0.21
20 32 0.10
21 57 0.18
22 60 0.19
23 13 0.04
24 3 0.01
25 1 0.00
26 2 0.01
27 85 0.26
29 2 0.01
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.54
Consensus pattern (20 bp):
AATTTTGTATGAATATTGTA
Found at i:795038 original size:61 final size:60
Alignment explanation
Indices: 794968--795491 Score: 175
Period size: 70 Copynumber: 7.8 Consensus size: 60
794958 GATTAGAATT
*
794968 TTGTATGAATATTTTAAATTTTTTGTATGAATATTATAATTTTTTTATGAATATTGTAATG
1 TTGTATGAATATTGT-AATTTTTTGTATGAATATTATAATTTTTTTATGAATATTGTAATG
* **
795029 TTGTATGAATATTGTAATTATTT-TAT--A-ATTA-AATTTGTATTTATAGTTTTGGATTAGTAA
1 TTGTATGAATATTGTAATTTTTTGTATGAATATTATAATTT-T-TTTAT-G-AAT--ATT-GTAA
*
795089 TTTT
59 --TG
*
795093 TTGTATGAATATTGTAA--TTTTGTATGAATATTATAAATTTTTGTATGAATATTGTAATATTAT
1 TTGTATGAATATTGTAATTTTTTGTATGAATATTAT-AATTTTTTTATGAATATTG---TA--AT
795156 AG
60 -G
* * *
795158 TTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATTTTGTAATTTTGTATGAATATTA
1 --TTGTATGAATATTGTAA-TTTTTTGTATGAATATTATAA---T-T--TTTT-TATGAATATTG
* *
795223 TATTTTT
56 TA--ATG
**
795230 TTGTATGAATATTGTAATATTATAATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTA
1 TTGTATGAATATTGT-A-A-T-T--TTTTGTATGAATATTATAA-TTTTTT-TATG-A-A---TA
*
795295 GTTTTGTAATT
53 ---TTGTAATG
* * * *
795306 TTGTATGAATATTATAA-TTTTT-TATGAATATTGTAATGTTGTATGAATATTGTAATATTATAA
1 TTGTATGAATATTGTAATTTTTTGTATGAATATTATAAT-TT-T-T--TTA-TG-AATATTGTAA
*
795369 TT
59 TG
* *
795371 TTGTATGAATATTGCAATTTTTTGTATGAATATTGTAATATTGTAATTTTATATGAATATTGTAA
1 TTGTATGAATATTGTAATTTTTTGTATGAATA-T-T-ATAAT-T--TTTT-TATGAATATTGTAA
795436 TG
59 TG
* * *
795438 TGGGGATATATTGTAATATTGTAATTTTTTGTATGAATATTGTAATTATTTTAT
1 T-----TGTA-TG-AATATTGTAATTTTTTGTATGAATATTATAATTTTTTTAT
795492 AATTAATTTG
Statistics
Matches: 359, Mismatches: 37, Indels: 128
0.69 0.07 0.24
Matches are distributed among these distances:
55 5 0.01
56 5 0.01
57 6 0.02
58 1 0.00
59 4 0.01
60 7 0.02
61 18 0.05
62 10 0.03
63 3 0.01
64 22 0.06
65 24 0.07
66 14 0.04
67 40 0.11
68 28 0.08
69 10 0.03
70 47 0.13
71 10 0.03
72 14 0.04
73 12 0.03
74 25 0.07
75 24 0.07
76 26 0.07
78 4 0.01
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.54
Consensus pattern (60 bp):
TTGTATGAATATTGTAATTTTTTGTATGAATATTATAATTTTTTTATGAATATTGTAATG
Found at i:795166 original size:27 final size:25
Alignment explanation
Indices: 795110--795436 Score: 228
Period size: 27 Copynumber: 13.8 Consensus size: 25
795100 AATATTGTAA
*
795110 TTTTGTATGAATA-T-T-ATA-AAT
1 TTTTGTATGAATATTGTAATATTAT
795131 TTTTGTATGAATATTGTAATATTAT
1 TTTTGTATGAATATTGTAATATTAT
*
795156 AGTTTTGTATGAATATTG-CA-ATT-T
1 --TTTTGTATGAATATTGTAATATTAT
* *
795180 TTTTGTATGAATATTGTAATTTTGTAA
1 TTTTGTATGAATATTGTAA-TAT-TAT
795207 TTTTGTATGAATA-T-T-ATATT-T
1 TTTTGTATGAATATTGTAATATTAT
795228 TTTTGTATGAATATTGTAATATTAT
1 TTTTGTATGAATATTGTAATATTAT
*
795253 AATTTTGTATGAATATTG-CA-ATT-T
1 --TTTTGTATGAATATTGTAATATTAT
* * *
795277 TTTTGTATGAATATTGTAGTTTTGTAA
1 TTTTGTATGAATATTGTA-ATAT-TAT
795304 TTTTGTATGAATA-T-T-ATA--AT
1 TTTTGTATGAATATTGTAATATTAT
795324 TTTT-TATGAATATTGT---A--A-
1 TTTTGTATGAATATTGTAATATTAT
*
795342 TGTTGTATGAATATTGTAATATTAT
1 TTTTGTATGAATATTGTAATATTAT
*
795367 AATTTTGTATGAATATTG-CA-A-T-T
1 --TTTTGTATGAATATTGTAATATTAT
*
795390 TTTTGTATGAATATTGTAATATTGTAA
1 TTTTGTATGAATATTGTAATA-T-TAT
*
795417 TTTTATATGAATATTGTAAT
1 TTTTGTATGAATATTGTAAT
795437 GTGGGGATAT
Statistics
Matches: 246, Mismatches: 21, Indels: 72
0.73 0.06 0.21
Matches are distributed among these distances:
18 3 0.01
19 22 0.09
20 6 0.02
21 43 0.17
22 37 0.15
23 8 0.03
24 13 0.05
25 14 0.06
26 8 0.03
27 92 0.37
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.54
Consensus pattern (25 bp):
TTTTGTATGAATATTGTAATATTAT
Found at i:795211 original size:49 final size:49
Alignment explanation
Indices: 795100--795348 Score: 346
Period size: 49 Copynumber: 5.2 Consensus size: 49
795090 TTTTTGTATG
* *
795100 AATATTGTAATTTTGTATGAATATTATAA-ATTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTACAATTTTTTTGTATGAATATTGT
* * *
795148 AATATTATAGTTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTACAATTTTTTTGTATGAATATTGT
* *
795197 AATTTTGTAATTTTGTATGAATATTA-TATTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTACAATTTTTTTGTATGAATATTGT
* *
795245 AATATTATAATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTACAATTTTTTTGTATGAATATTGT
* * *
795294 AGTTTTGTAATTTTGTATGAATATTATAA--TTTTT-TATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTACAATTTTTTTGTATGAATATTGT
*
795340 AATGTTGTA
1 AATATTGTA
795349 TGAATATTGT
Statistics
Matches: 178, Mismatches: 21, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
46 19 0.11
47 5 0.03
48 69 0.39
49 85 0.48
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.54
Consensus pattern (49 bp):
AATATTGTAATTTTGTATGAATATTACAATTTTTTTGTATGAATATTGT
Found at i:795211 original size:97 final size:97
Alignment explanation
Indices: 795104--795342 Score: 428
Period size: 97 Copynumber: 2.5 Consensus size: 97
795094 TGTATGAATA
*
795104 TTGTAATTTTGTATGAATATTATAAATTTTTGTATGAATATTGTAATATTATAGTTTTGTATGAA
1 TTGTAATTTTGTATGAATATTATAAATTTTTGTATGAATATTGTAATATTATAATTTTGTATGAA
795169 TATTGCAATTTTTTTGTATGAATATTGTAATT
66 TATTGCAATTTTTTTGTATGAATATTGTAATT
**
795201 TTGTAATTTTGTATGAATATTATATTTTTTTGTATGAATATTGTAATATTATAATTTTGTATGAA
1 TTGTAATTTTGTATGAATATTATAAATTTTTGTATGAATATTGTAATATTATAATTTTGTATGAA
*
795266 TATTGCAATTTTTTTGTATGAATATTGTAGTT
66 TATTGCAATTTTTTTGTATGAATATTGTAATT
795298 TTGTAATTTTGTATGAATATTAT-AATTTTT-TATGAATATTGTAAT
1 TTGTAATTTTGTATGAATATTATAAATTTTTGTATGAATATTGTAAT
795343 GTTGTATGAA
Statistics
Matches: 136, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
95 15 0.11
96 5 0.04
97 116 0.85
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.55
Consensus pattern (97 bp):
TTGTAATTTTGTATGAATATTATAAATTTTTGTATGAATATTGTAATATTATAATTTTGTATGAA
TATTGCAATTTTTTTGTATGAATATTGTAATT
Found at i:795373 original size:114 final size:113
Alignment explanation
Indices: 795230--795436 Score: 369
Period size: 113 Copynumber: 1.8 Consensus size: 113
795220 TTATATTTTT
795230 TTGTATGAATATTGTAATATTATAATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTA
1 TTGTATGAATATTGTAATATTATAATTTTGTATGAATATTGCAA-TTTTTTGTATGAATATTGTA
* * *
795295 GTTTTGTAATTTTGTATGAATATTATAATTTTTTATGAATATTGTAATG
65 ATATTGTAATTTTATATGAATATTATAATTTTTTATGAATATTGTAATG
795344 TTGTATGAATATTGTAATATTATAATTTTGTATGAATATTGCAATTTTTTGTATGAATATTGTAA
1 TTGTATGAATATTGTAATATTATAATTTTGTATGAATATTGCAATTTTTTGTATGAATATTGTAA
*
795409 TATTGTAATTTTATATGAATATTGTAAT
66 TATTGTAATTTTATATGAATATTATAAT
795437 GTGGGGATAT
Statistics
Matches: 89, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
113 45 0.51
114 44 0.49
ACGTcount: A:0.33, C:0.01, G:0.14, T:0.53
Consensus pattern (113 bp):
TTGTATGAATATTGTAATATTATAATTTTGTATGAATATTGCAATTTTTTGTATGAATATTGTAA
TATTGTAATTTTATATGAATATTATAATTTTTTATGAATATTGTAATG
Found at i:795429 original size:19 final size:19
Alignment explanation
Indices: 794964--795361 Score: 168
Period size: 19 Copynumber: 21.2 Consensus size: 19
794954 TTTAGATTAG
*
794964 AATTTTGTATGAATATTTT
1 AATTTTGTATGAATATTGT
*
794983 AAATTTTTTGTATGAATATTAT
1 -AA--TTTTGTATGAATATTGT
*
795005 AATTTTTTTATGAATATTGT
1 AA-TTTTGTATGAATATTGT
*
795025 AATGTTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
*
795044 AATTATTTTAT-AATTAAATTTGT
1 AATT-TTGTATGAA-T--A-TTGT
* * *
795067 -ATTTATAGTTTTGGAT-TAGT
1 AATTT-T-G-TATGAATATTGT
795087 AATTTTTTGTATGAATATTGT
1 AA--TTTTGTATGAATATTGT
*
795108 AATTTTGTATGAATATTAT
1 AATTTTGTATGAATATTGT
795127 AAATTTTTGTATGAATATTGTAATATT
1 -AA-TTTTGTATGAATATTG------T
*
795154 ATAGTTTTGTATGAATATTGC
1 A-A-TTTTGTATGAATATTGT
*
795175 AATTTT-TTTG--TA-TG-
1 AATTTTGTATGAATATTGT
* *
795189 AATATTG--T-AATTTTGT
1 AATTTTGTATGAATATTGT
*
795205 AATTTTGTATGAATATTAT
1 AATTTTGTATGAATATTGT
*
795224 -ATTTT-TTTG--TA-TG-
1 AATTTTGTATGAATATTGT
* *
795237 AATATTG--T-AATATTAT
1 AATTTTGTATGAATATTGT
*
795253 AATTTTGTATGAATATTGC
1 AATTTTGTATGAATATTGT
*
795272 AATTTT-TTTG--TA-TG-
1 AATTTTGTATGAATATTGT
* *
795286 AATATTGTA-G--TTTTGT
1 AATTTTGTATGAATATTGT
*
795302 AATTTTGTATGAATATTAT
1 AATTTTGTATGAATATTGT
*
795321 AATTTTTTATGAATATTGT
1 AATTTTGTATGAATATTGT
*
795340 AATGTTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
795359 AAT
1 AAT
795362 ATTATAATTT
Statistics
Matches: 289, Mismatches: 42, Indels: 95
0.68 0.10 0.22
Matches are distributed among these distances:
13 2 0.01
14 20 0.07
15 12 0.04
16 24 0.08
17 4 0.01
18 13 0.04
19 99 0.34
20 37 0.13
21 26 0.09
22 22 0.08
23 7 0.02
24 3 0.01
25 1 0.00
26 1 0.00
27 18 0.06
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.55
Consensus pattern (19 bp):
AATTTTGTATGAATATTGT
Found at i:795683 original size:38 final size:37
Alignment explanation
Indices: 795632--795712 Score: 135
Period size: 38 Copynumber: 2.2 Consensus size: 37
795622 CATATAAAGT
*
795632 TTATAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
1 TTATAAAAAATTAAAAATCATTTCATTAAAAATTTAA
*
795669 TTATAAATAAATTAAAAATCATTTTATTAAAAATTTAA
1 TTATAAA-AAATTAAAAATCATTTCATTAAAAATTTAA
795707 TTATAA
1 TTATAA
795713 CTGACTTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
37 7 0.17
38 34 0.83
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (37 bp):
TTATAAAAAATTAAAAATCATTTCATTAAAAATTTAA
Found at i:799576 original size:27 final size:26
Alignment explanation
Indices: 799527--799629 Score: 107
Period size: 27 Copynumber: 3.8 Consensus size: 26
799517 AAAATCACAG
* *
799527 CATTGGCACCTTCTAATATGGCACCAC
1 CATTGGCGCCTCCTAATA-GGCACCAC
*
799554 CATTGGCGCCTGCTACATAGGCACCAC
1 CATTGGCGCCTCCTA-ATAGGCACCAC
* *
799581 CATTGGTGCCTCCCAAATAGGCACCAC
1 CATTGGCGCCT-CCTAATAGGCACCAC
* *
799608 CATTGGAGCCTTCCAAATAGGC
1 CATTGGCGCC-TCCTAATAGGC
799630 GCCAATACTA
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
27 61 0.91
28 6 0.09
ACGTcount: A:0.25, C:0.34, G:0.19, T:0.21
Consensus pattern (26 bp):
CATTGGCGCCTCCTAATAGGCACCAC
Found at i:807761 original size:22 final size:22
Alignment explanation
Indices: 807732--807789 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
807722 CCTCTGAATA
*
807732 TTTAAAAATCTTAATTAAAATT
1 TTTAAAAATTTTAATTAAAATT
* * **
807754 TTTGAAAATTTTTATTAATCTT
1 TTTAAAAATTTTAATTAAAATT
807776 TTTAAAAATTTTAA
1 TTTAAAAATTTTAA
807790 AAGTTTTAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (22 bp):
TTTAAAAATTTTAATTAAAATT
Found at i:808362 original size:16 final size:16
Alignment explanation
Indices: 808341--808389 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 16
808331 TGTCAAAATA
808341 TAATTTTATCATTTAT
1 TAATTTTATCATTTAT
*
808357 TAA-TTTATTAATTTA-
1 TAATTTTA-TCATTTAT
*
808372 TAATTTCATCATTT-T
1 TAATTTTATCATTTAT
808387 TAA
1 TAA
808390 GGGACTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
15 15 0.56
16 12 0.44
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTTATCATTTAT
Found at i:812999 original size:29 final size:29
Alignment explanation
Indices: 812965--813020 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
812955 TTTGATTCTT
*
812965 TTTAATTGTACAAGAACTAAATTGATCCA
1 TTTAATTATACAAGAACTAAATTGATCCA
* *
812994 TTTAATTATAGAAGAACTAATTTGATC
1 TTTAATTATACAAGAACTAAATTGATC
813021 AAATCCTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.38
Consensus pattern (29 bp):
TTTAATTATACAAGAACTAAATTGATCCA
Found at i:814871 original size:22 final size:21
Alignment explanation
Indices: 814835--814890 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
814825 GGCCCGACCC
*
814835 ATTT-TTTTAATAAATATCAAAA
1 ATTTATTTTAA-AAAT-TAAAAA
814857 ATTTATTTTAAAAATTAAAAA
1 ATTTATTTTAAAAATTAAAAA
**
814878 AAGTATTTTAAAA
1 ATTTATTTTAAAA
814891 GTATTTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 16 0.53
22 8 0.27
23 6 0.20
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (21 bp):
ATTTATTTTAAAAATTAAAAA
Found at i:814892 original size:11 final size:11
Alignment explanation
Indices: 814875--814970 Score: 66
Period size: 11 Copynumber: 9.4 Consensus size: 11
814865 TAAAAATTAA
814875 AAAAAGTATTTT
1 AAAAA-TATTTT
*
814887 AAAAGTATTTT
1 AAAAATATTTT
814898 --AAA-A--TT
1 AAAAATATTTT
814904 AAAAATATTTT
1 AAAAATATTTT
814915 AAAAATATTTT
1 AAAAATATTTT
*
814926 --AAA-A-TTA
1 AAAAATATTTT
* **
814933 AAAAATAATAA
1 AAAAATATTTT
814944 AAAAAGTATTTT
1 AAAAA-TATTTT
814956 AAAAATATTTT
1 AAAAATATTTT
814967 AAAA
1 AAAA
814971 TTTAAAAAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 21
0.71 0.07 0.22
Matches are distributed among these distances:
6 2 0.03
7 2 0.03
8 5 0.07
9 9 0.13
10 1 0.01
11 36 0.54
12 12 0.18
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:814930 original size:28 final size:29
Alignment explanation
Indices: 814860--814959 Score: 121
Period size: 28 Copynumber: 3.3 Consensus size: 29
814850 ATCAAAAATT
*
814860 TATTTTAAAAATTAAAAAAAGTATTTTAAAAG
1 TATTTT-AAAATT-AAAAAA-TATTTTAAAAA
814892 TATTTTAAAATT-AAAAATATTTTAAAAA
1 TATTTTAAAATTAAAAAATATTTTAAAAA
* **
814920 TATTTTAAAATTAAAAAATAATAAAAAAA
1 TATTTTAAAATTAAAAAATATTTTAAAAA
814949 GTATTTTAAAA
1 -TATTTTAAAA
814960 ATATTTTAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
28 22 0.35
29 18 0.29
30 10 0.16
31 6 0.10
32 6 0.10
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (29 bp):
TATTTTAAAATTAAAAAATATTTTAAAAA
Found at i:814936 original size:17 final size:17
Alignment explanation
Indices: 814885--814918 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
814875 AAAAAGTATT
*
814885 TTAAAAGTATTTTAAAA
1 TTAAAAATATTTTAAAA
814902 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
814919 ATATTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:814954 original size:41 final size:39
Alignment explanation
Indices: 814904--814987 Score: 132
Period size: 41 Copynumber: 2.1 Consensus size: 39
814894 TTTTAAAATT
814904 AAAAATATTTTAAAAATATTTTAAAATTAAAAAATAATAA
1 AAAAATATTTTAAAAATATTTTAAAATTAAAAAA-AATAA
* *
814944 AAAAAGTATTTTAAAAATATTTTAAAATTTAAAAAAATTA
1 AAAAA-TATTTTAAAAATATTTTAAAATTAAAAAAAATAA
814984 AAAA
1 AAAA
814988 TAAATATATT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
40 13 0.32
41 28 0.68
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (39 bp):
AAAAATATTTTAAAAATATTTTAAAATTAAAAAAAATAA
Found at i:828158 original size:29 final size:29
Alignment explanation
Indices: 828098--828157 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
828088 GATTTCGCGG
828098 AAAAT-GGCCCATTCCGGTAAATAATTAA
1 AAAATCGGCCCATTCCGGTAAATAATTAA
* *
828126 AAAATCGGCCCATTTCGGTAAAT-TTTAA
1 AAAATCGGCCCATTCCGGTAAATAATTAA
828154 AAAA
1 AAAA
828158 AACGGCCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 13 0.45
29 16 0.55
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (29 bp):
AAAATCGGCCCATTCCGGTAAATAATTAA
Found at i:828163 original size:29 final size:29
Alignment explanation
Indices: 828098--828164 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
828088 GATTTCGCGG
*
828098 AAAATGGCCCATTCCGGTAAATAATTAAA
1 AAAACGGCCCATTCCGGTAAATAATTAAA
* * *
828127 AAATCGGCCCATTTCGGTAAAT-TTTAAAA
1 AAAACGGCCCATTCCGGTAAATAATT-AAA
828156 AAAACGGCC
1 AAAACGGCC
828165 TTTTTTGGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 2 0.06
29 30 0.94
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (29 bp):
AAAACGGCCCATTCCGGTAAATAATTAAA
Found at i:852961 original size:29 final size:29
Alignment explanation
Indices: 852916--852971 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
852906 ATATAAGGGC
* *
852916 TAGATCAAATTAGTCCATTTACTATTATA
1 TAGATCAAATTAATCCATGTACTATTATA
*
852945 TAGAT-AAATTGAATCCATGTATTATTA
1 TAGATCAAATT-AATCCATGTACTATTA
852972 AAAAGAATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 5 0.22
29 18 0.78
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (29 bp):
TAGATCAAATTAATCCATGTACTATTATA
Found at i:855903 original size:15 final size:15
Alignment explanation
Indices: 855885--855931 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
855875 AAATTTAAAC
855885 TTTAATTTTTATATT
1 TTTAATTTTTATATT
**
855900 TTT-ATTTTTA-AGAA
1 TTTAATTTTTATA-TT
855914 TTTAATTTTTATATT
1 TTTAATTTTTATATT
855929 TTT
1 TTT
855932 CAGATTTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
13 1 0.04
14 10 0.40
15 13 0.52
16 1 0.04
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (15 bp):
TTTAATTTTTATATT
Found at i:855906 original size:14 final size:14
Alignment explanation
Indices: 855889--855931 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
855879 TTAAACTTTA
855889 ATTTTTATATTTTT
1 ATTTTTATATTTTT
* * *
855903 ATTTTTAAGAATTTA
1 ATTTTT-ATATTTTT
855918 ATTTTTATATTTTT
1 ATTTTTATATTTTT
855932 CAGATTTTAA
Statistics
Matches: 22, Mismatches: 6, Indels: 2
0.73 0.20 0.07
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (14 bp):
ATTTTTATATTTTT
Found at i:855940 original size:23 final size:23
Alignment explanation
Indices: 855889--855946 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
855879 TTAAACTTTA
*
855889 ATTTTTATATTTTTATTTTTAAG
1 ATTTTAATATTTTTATTTTTAAG
* *
855912 AATTTAAT-TTTTATATTTTTCAG
1 ATTTTAATATTTT-TATTTTTAAG
*
855935 ATTTTAACATTT
1 ATTTTAATATTT
855947 AAGTTCGATT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
22 4 0.14
23 21 0.75
24 3 0.11
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.64
Consensus pattern (23 bp):
ATTTTAATATTTTTATTTTTAAG
Found at i:856884 original size:22 final size:22
Alignment explanation
Indices: 856851--856895 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
856841 ATTTAATCAT
*
856851 ATTTAATTTATATAATTTTAAA
1 ATTTAATTTATAAAATTTTAAA
856873 ATTT-ATTGTATAAAATTTTAAA
1 ATTTAATT-TATAAAATTTTAAA
856895 A
1 A
856896 ATAACAGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
ATTTAATTTATAAAATTTTAAA
Found at i:874135 original size:21 final size:21
Alignment explanation
Indices: 874109--874149 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
874099 AGACGAGCAA
* *
874109 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
874130 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
874150 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:879304 original size:16 final size:16
Alignment explanation
Indices: 879253--879306 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
879243 CTTCGAGATT
*
879253 TTTTAAGTTTGAGTCAA
1 TTTTAAGTTTAAGTC-A
* * *
879270 TTTTAAGTTAAAATTA
1 TTTTAAGTTTAAGTCA
*
879286 TTTTAGGTTTAAGTCA
1 TTTTAAGTTTAAGTCA
879302 TTTTA
1 TTTTA
879307 TGTTCGAATC
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
16 18 0.62
17 11 0.38
ACGTcount: A:0.31, C:0.04, G:0.13, T:0.52
Consensus pattern (16 bp):
TTTTAAGTTTAAGTCA
Found at i:880738 original size:27 final size:27
Alignment explanation
Indices: 880708--880772 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
880698 CCTGTCAAGT
* * *
880708 AGGCGCCAATGAATGTGCCTCGTAGAG
1 AGGCGCCAATAAAAGTGCCTCATAGAG
* * *
880735 AGGCGCCATTAAAAGTGTCTCATAGGG
1 AGGCGCCAATAAAAGTGCCTCATAGAG
880762 AGGCGCCAATA
1 AGGCGCCAATA
880773 GGTAATTTTG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.29, C:0.22, G:0.31, T:0.18
Consensus pattern (27 bp):
AGGCGCCAATAAAAGTGCCTCATAGAG
Found at i:905187 original size:52 final size:49
Alignment explanation
Indices: 905102--905468 Score: 440
Period size: 46 Copynumber: 7.6 Consensus size: 49
905092 TTTGAGTACT
* **
905102 TCTGATCAAGTG---ATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
* *
905148 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTAATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAA-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
905200 TCTGATCAAGTG---ATAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
905246 TCTGATCAAGTGAC---AAAGTGATAAGTGATAGCTTCAGCTACACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
905292 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTA
1 TCTGATCAAGTGACAA-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
905344 TCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAA-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTA
* **
905396 TCTGATCAAGAGAC---AAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
905442 TCTGATCAAGAGAC---AAAGTGATAAGTG
1 TCTGATCAAGTGACAATAAAGTGATAAGTG
905469 GCTACACTTA
Statistics
Matches: 292, Mismatches: 15, Indels: 28
0.87 0.04 0.08
Matches are distributed among these distances:
46 155 0.53
48 1 0.00
49 2 0.01
50 1 0.00
52 133 0.46
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (49 bp):
TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
Found at i:905222 original size:98 final size:97
Alignment explanation
Indices: 905102--905468 Score: 501
Period size: 98 Copynumber: 3.7 Consensus size: 97
905092 TTTGAGTACT
* *
905102 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGT-
*
905167 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
65 GAAAGTGATAAGTGATAGCTTCGGCTATACTTA
* *
905200 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGAC-----
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
* *
905260 AAAGTGATAAGTGATAGCTTCAGCTACACTTA
66 AAAGTGATAAGTGATAGCTTCGGCTATACTTA
*
905292 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
1 TCTGATCAAGTG---A-T--AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGA
905357 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
60 CAAGTG-AAAGTGATAAGTGATAGCTTCGGCTATACTTA
* * * *
905396 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC-AAGT
905461 GATAAGTG
65 GA-AAGTG
905469 GCTACACTTA
Statistics
Matches: 240, Mismatches: 15, Indels: 27
0.85 0.05 0.10
Matches are distributed among these distances:
92 41 0.17
95 1 0.00
96 1 0.00
98 145 0.60
99 10 0.04
101 1 0.00
104 41 0.17
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (97 bp):
TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
AAAGTGATAAGTGATAGCTTCGGCTATACTTA
Found at i:905450 original size:196 final size:196
Alignment explanation
Indices: 905116--905468 Score: 607
Period size: 196 Copynumber: 1.8 Consensus size: 196
905106 ATCAAGTGAT
* * *
905116 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTA
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
* * * *
905181 ATAGCTTCGGCTATACTTATCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
*
905246 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
131 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
905311 G
196 G
* *
905312 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
*
905377 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
66 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
905442 TCTGATCAAGAGACAAAGTGATAAGTG
131 TCTGATCAAGAGACAAAGTGATAAGTG
905469 GCTACACTTA
Statistics
Matches: 146, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
196 146 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (196 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
G
Found at i:905476 original size:37 final size:37
Alignment explanation
Indices: 905432--905540 Score: 177
Period size: 37 Copynumber: 3.0 Consensus size: 37
905422 GATAGCTTTA
905432 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
* *
905469 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
905506 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
905541 ATCATACGTA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
35 11 0.16
36 4 0.06
37 52 0.78
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:906856 original size:49 final size:49
Alignment explanation
Indices: 906795--906987 Score: 323
Period size: 49 Copynumber: 3.9 Consensus size: 49
906785 ATGTGAACAT
906795 GTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
1 GTGA-TATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
906845 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
1 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* *
906894 GTGATATGTGATTTCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAT
1 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* * * *
906943 GTGATTTGTGATTACGTGTAAGACCATAGTTGGACTATGGCATCG
1 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCG
906988 AGAAAACGAA
Statistics
Matches: 137, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
49 133 0.97
50 4 0.03
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.31
Consensus pattern (49 bp):
GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
Found at i:910198 original size:52 final size:49
Alignment explanation
Indices: 910113--910479 Score: 440
Period size: 46 Copynumber: 7.6 Consensus size: 49
910103 TTTGAGTACT
* **
910113 TCTGATCAAGTG---ATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
* *
910159 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTAATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAA-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
910211 TCTGATCAAGTG---ATAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
910257 TCTGATCAAGTGAC---AAAGTGATAAGTGATAGCTTCAGCTACACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
910303 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTA
1 TCTGATCAAGTGACAA-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
910355 TCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAA-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTA
* **
910407 TCTGATCAAGAGAC---AAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
910453 TCTGATCAAGAGAC---AAAGTGATAAGTG
1 TCTGATCAAGTGACAATAAAGTGATAAGTG
910480 GCTACACTTA
Statistics
Matches: 292, Mismatches: 15, Indels: 28
0.87 0.04 0.08
Matches are distributed among these distances:
46 155 0.53
48 1 0.00
49 2 0.01
50 1 0.00
52 133 0.46
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (49 bp):
TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
Found at i:910233 original size:98 final size:97
Alignment explanation
Indices: 910113--910479 Score: 501
Period size: 98 Copynumber: 3.7 Consensus size: 97
910103 TTTGAGTACT
* *
910113 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGT-
*
910178 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
65 GAAAGTGATAAGTGATAGCTTCGGCTATACTTA
* *
910211 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGAC-----
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
* *
910271 AAAGTGATAAGTGATAGCTTCAGCTACACTTA
66 AAAGTGATAAGTGATAGCTTCGGCTATACTTA
*
910303 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
1 TCTGATCAAGTG---A-T--AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGA
910368 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
60 CAAGTG-AAAGTGATAAGTGATAGCTTCGGCTATACTTA
* * * *
910407 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC-AAGT
910472 GATAAGTG
65 GA-AAGTG
910480 GCTACACTTA
Statistics
Matches: 240, Mismatches: 15, Indels: 27
0.85 0.05 0.10
Matches are distributed among these distances:
92 41 0.17
95 1 0.00
96 1 0.00
98 145 0.60
99 10 0.04
101 1 0.00
104 41 0.17
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (97 bp):
TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
AAAGTGATAAGTGATAGCTTCGGCTATACTTA
Found at i:910461 original size:196 final size:196
Alignment explanation
Indices: 910127--910479 Score: 607
Period size: 196 Copynumber: 1.8 Consensus size: 196
910117 ATCAAGTGAT
* * *
910127 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTA
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
* * * *
910192 ATAGCTTCGGCTATACTTATCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
*
910257 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
131 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
910322 G
196 G
* *
910323 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
*
910388 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
66 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
910453 TCTGATCAAGAGACAAAGTGATAAGTG
131 TCTGATCAAGAGACAAAGTGATAAGTG
910480 GCTACACTTA
Statistics
Matches: 146, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
196 146 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (196 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
G
Found at i:910487 original size:37 final size:37
Alignment explanation
Indices: 910443--910551 Score: 177
Period size: 37 Copynumber: 3.0 Consensus size: 37
910433 GATAGCTTTA
910443 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
* *
910480 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
910517 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
910552 ATCATACGTA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
35 11 0.16
36 4 0.06
37 52 0.78
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:918508 original size:22 final size:22
Alignment explanation
Indices: 918482--918558 Score: 66
Period size: 22 Copynumber: 3.2 Consensus size: 22
918472 AATGTATTAA
918482 ATATTAATCTTAAAATAAATAT
1 ATATTAATCTTAAAATAAATAT
* *
918504 ATATTTTAATTGTTATAAGTGTAAA-AT
1 ATA--TTAA-TCTTA-AA--ATAAATAT
918531 AATATTAATCTTAAAATAAATAT
1 -ATATTAATCTTAAAATAAATAT
918554 ATATT
1 ATATT
918559 TTAATTGTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 16
0.68 0.06 0.25
Matches are distributed among these distances:
22 12 0.28
23 2 0.05
24 6 0.14
25 8 0.19
26 6 0.14
27 2 0.05
28 7 0.16
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (22 bp):
ATATTAATCTTAAAATAAATAT
Found at i:918536 original size:28 final size:29
Alignment explanation
Indices: 918498--918581 Score: 94
Period size: 29 Copynumber: 3.2 Consensus size: 29
918488 ATCTTAAAAT
918498 AAATATATATTTTAATTGTTATAAGTGTA
1 AAATATATATTTTAATTGTTATAAGTGTA
* *
918527 AAATA-ATA--TTAA-TCTTA-AA--AT-
1 AAATATATATTTTAATTGTTATAAGTGTA
918548 AAATATATATTTTAATTGTTATAAGTGTA
1 AAATATATATTTTAATTGTTATAAGTGTA
918577 AAATA
1 AAATA
918582 ATAATATTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 16
0.68 0.06 0.25
Matches are distributed among these distances:
21 5 0.12
22 4 0.09
24 6 0.14
25 8 0.19
26 6 0.14
28 4 0.09
29 10 0.23
ACGTcount: A:0.48, C:0.01, G:0.07, T:0.44
Consensus pattern (29 bp):
AAATATATATTTTAATTGTTATAAGTGTA
Found at i:918536 original size:50 final size:50
Alignment explanation
Indices: 918481--918584 Score: 208
Period size: 50 Copynumber: 2.1 Consensus size: 50
918471 CAATGTATTA
918481 AATATTAATCTTAAAATAAATATATATTTTAATTGTTATAAGTGTAAAAT
1 AATATTAATCTTAAAATAAATATATATTTTAATTGTTATAAGTGTAAAAT
918531 AATATTAATCTTAAAATAAATATATATTTTAATTGTTATAAGTGTAAAAT
1 AATATTAATCTTAAAATAAATATATATTTTAATTGTTATAAGTGTAAAAT
918581 AATA
1 AATA
918585 ATATTATTTG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (50 bp):
AATATTAATCTTAAAATAAATATATATTTTAATTGTTATAAGTGTAAAAT
Found at i:921218 original size:20 final size:20
Alignment explanation
Indices: 921193--921242 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
921183 TGGCTTAAAA
921193 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
921213 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
921230 GTGGTAGTGGATT
1 TTGGTAGTGGATT
921243 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:925857 original size:20 final size:20
Alignment explanation
Indices: 925832--925881 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
925822 TGGCTTAAAA
925832 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
925852 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
925869 GTGGTAGTGGATT
1 TTGGTAGTGGATT
925882 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:930264 original size:21 final size:21
Alignment explanation
Indices: 930236--930278 Score: 54
Period size: 20 Copynumber: 2.0 Consensus size: 21
930226 TACATTTTTT
930236 ATTCGAAAAGTAAA-AA-AAAA
1 ATTCGAAAA-TAAAGAATAAAA
930256 ATTCTGAAAATAAAGAATAAAA
1 ATTC-GAAAATAAAGAATAAAA
930278 A
1 A
930279 CTAAATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 8 0.40
21 7 0.35
22 5 0.25
ACGTcount: A:0.67, C:0.05, G:0.09, T:0.19
Consensus pattern (21 bp):
ATTCGAAAATAAAGAATAAAA
Found at i:933607 original size:23 final size:23
Alignment explanation
Indices: 933581--933629 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
933571 GGTTTTACAC
933581 TTCTTTGAAACCATGAATTTGTT
1 TTCTTTGAAACCATGAATTTGTT
*
933604 TTCTTTGAAACCATGGATTTGTT
1 TTCTTTGAAACCATGAATTTGTT
933627 TTC
1 TTC
933630 ATTTTAGTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.49
Consensus pattern (23 bp):
TTCTTTGAAACCATGAATTTGTT
Found at i:936205 original size:25 final size:25
Alignment explanation
Indices: 936177--936226 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
936167 TAAATAGAAA
*
936177 AAGGAGAGAAA-AAAACGAAACAAAG
1 AAGGAAAGAAAGAAAA-GAAACAAAG
*
936202 AAGGAAAGAAAGAAAAGAAAGAAAG
1 AAGGAAAGAAAGAAAAGAAACAAAG
936227 GAGAAAAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.70, C:0.04, G:0.26, T:0.00
Consensus pattern (25 bp):
AAGGAAAGAAAGAAAAGAAACAAAG
Found at i:936234 original size:25 final size:25
Alignment explanation
Indices: 936183--936234 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
936173 GAAAAAGGAG
*
936183 AGAAAAAAACGAAACAAAGAAGGAA
1 AGAAAAAAACGAAACAAAGAAGAAA
* *
936208 AGAAAGAAAA-GAAAGAAAGGAGAAA
1 AGAAA-AAAACGAAACAAAGAAGAAA
936233 AG
1 AG
936235 TTAGGGTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.71, C:0.04, G:0.25, T:0.00
Consensus pattern (25 bp):
AGAAAAAAACGAAACAAAGAAGAAA
Found at i:937141 original size:37 final size:39
Alignment explanation
Indices: 937050--937152 Score: 122
Period size: 41 Copynumber: 2.6 Consensus size: 39
937040 GATTTCGACT
*
937050 CGATGAGACACTGGGTGTCAATTTACTATTTCGGATTAATT
1 CGATGAGACACTGGGTGTCAATTTAC--TTTCGGATTAATC
* * *
937091 CGATGAGGCACTGGTTG-CTAATTTAC-TTCGGTTTAA-C
1 CGATGAGACACTGGGTGTC-AATTTACTTTCGGATTAATC
937128 CGATGAGACACTGGGTGTCAATTTA
1 CGATGAGACACTGGGTGTCAATTTA
937153 TTACTTCGAA
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
37 21 0.39
38 10 0.19
40 1 0.02
41 22 0.41
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAATTTACTTTCGGATTAATC
Found at i:944632 original size:17 final size:17
Alignment explanation
Indices: 944610--944647 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
944600 GTTGTTTGTG
944610 TGTATTTATATATACTA
1 TGTATTTATATATACTA
*
944627 TGTATTTATATCTACTA
1 TGTATTTATATATACTA
944644 TGTA
1 TGTA
944648 GTTTGAAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.53
Consensus pattern (17 bp):
TGTATTTATATATACTA
Found at i:946789 original size:54 final size:54
Alignment explanation
Indices: 946707--946813 Score: 214
Period size: 54 Copynumber: 2.0 Consensus size: 54
946697 TGATGAAATA
946707 CTATAATCATCCCTTTGATTAATAAAGTACATTCTCTATTACTTTCATATTTTT
1 CTATAATCATCCCTTTGATTAATAAAGTACATTCTCTATTACTTTCATATTTTT
946761 CTATAATCATCCCTTTGATTAATAAAGTACATTCTCTATTACTTTCATATTTT
1 CTATAATCATCCCTTTGATTAATAAAGTACATTCTCTATTACTTTCATATTTT
946814 CTTTGTTCTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.30, C:0.19, G:0.04, T:0.48
Consensus pattern (54 bp):
CTATAATCATCCCTTTGATTAATAAAGTACATTCTCTATTACTTTCATATTTTT
Found at i:952310 original size:15 final size:15
Alignment explanation
Indices: 952290--952339 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
952280 TTAAAATTTA
952290 AATTTAAATTATATT
1 AATTTAAATTATATT
*
952305 AATTTAATTTA-ATAT
1 AATTTAAATTATAT-T
*
952320 AA-TTAATATTATTTT
1 AATTTAA-ATTATATT
952335 AATTT
1 AATTT
952340 TTTACATGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
14 6 0.21
15 19 0.68
16 3 0.11
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
AATTTAAATTATATT
Found at i:960068 original size:39 final size:37
Alignment explanation
Indices: 960001--960093 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
959991 ACCAGAATGG
* *
960001 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
960040 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
960077 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
960094 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:960494 original size:18 final size:18
Alignment explanation
Indices: 960452--960495 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
960442 CCCACTACTC
*
960452 ATAATAATAATACTAATA
1 ATAATACTAATACTAATA
960470 ATAATACTAATACTAATA
1 ATAATACTAATACTAATA
*
960488 TTAATACT
1 ATAATACT
960496 TACCTCACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (18 bp):
ATAATACTAATACTAATA
Found at i:960495 original size:12 final size:12
Alignment explanation
Indices: 960453--960493 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
960443 CCACTACTCA
960453 TAATAATAATAC
1 TAATAATAATAC
960465 TAATAATAATAC
1 TAATAATAATAC
* *
960477 TAATACTAATAT
1 TAATAATAATAC
960489 TAATA
1 TAATA
960494 CTTACCTCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (12 bp):
TAATAATAATAC
Found at i:961172 original size:11 final size:11
Alignment explanation
Indices: 961156--961181 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
961146 CTTTTTCTTC
961156 TTTCTCCCCTG
1 TTTCTCCCCTG
961167 TTTCTCCCCTG
1 TTTCTCCCCTG
961178 TTTC
1 TTTC
961182 GTCTCTTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.42, G:0.08, T:0.50
Consensus pattern (11 bp):
TTTCTCCCCTG
Found at i:961567 original size:21 final size:21
Alignment explanation
Indices: 961543--961585 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
961533 AATAATAACT
961543 AATAACTAATAATAAATAATA
1 AATAACTAATAATAAATAATA
* * * *
961564 AATATCTTATACTAATTAATA
1 AATAACTAATAATAAATAATA
961585 A
1 A
961586 GCAAATTAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (21 bp):
AATAACTAATAATAAATAATA
Found at i:964963 original size:30 final size:30
Alignment explanation
Indices: 964929--965040 Score: 197
Period size: 30 Copynumber: 3.7 Consensus size: 30
964919 CCAATATCTC
964929 GATACCCATATCTTTGACTTTCTAATATTT
1 GATACCCATATCTTTGACTTTCTAATATTT
*
964959 GATACCCATATCTTTGACTTTCCAATATTT
1 GATACCCATATCTTTGACTTTCTAATATTT
*
964989 GATACCCATATCTTTGACTTTCTATTATTT
1 GATACCCATATCTTTGACTTTCTAATATTT
*
965019 GATACCCATATCTTTGATTTTC
1 GATACCCATATCTTTGACTTTC
965041 CATAAATATG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 78 1.00
ACGTcount: A:0.25, C:0.21, G:0.07, T:0.46
Consensus pattern (30 bp):
GATACCCATATCTTTGACTTTCTAATATTT
Found at i:964974 original size:15 final size:15
Alignment explanation
Indices: 964929--965036 Score: 69
Period size: 15 Copynumber: 7.2 Consensus size: 15
964919 CCAATATCTC
964929 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
964944 GACTTTCTA-ATATTT
1 GA-TACCCATATCTTT
964959 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
964974 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
964989 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
965004 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
965019 GATACCCATATCTTT
1 GATACCCATATCTTT
965034 GAT
1 GAT
965037 TTTCCATAAA
Statistics
Matches: 65, Mismatches: 22, Indels: 12
0.66 0.22 0.12
Matches are distributed among these distances:
14 11 0.17
15 43 0.66
16 11 0.17
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.45
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:969654 original size:30 final size:30
Alignment explanation
Indices: 969620--969731 Score: 197
Period size: 30 Copynumber: 3.7 Consensus size: 30
969610 CCAATATCTC
969620 GATACCCATATCTTTGACTTTCTAATATTT
1 GATACCCATATCTTTGACTTTCTAATATTT
*
969650 GATACCCATATCTTTGACTTTCCAATATTT
1 GATACCCATATCTTTGACTTTCTAATATTT
*
969680 GATACCCATATCTTTGACTTTCTATTATTT
1 GATACCCATATCTTTGACTTTCTAATATTT
*
969710 GATACCCATATCTTTGATTTTC
1 GATACCCATATCTTTGACTTTC
969732 CATAAATATG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 78 1.00
ACGTcount: A:0.25, C:0.21, G:0.07, T:0.46
Consensus pattern (30 bp):
GATACCCATATCTTTGACTTTCTAATATTT
Found at i:969665 original size:15 final size:15
Alignment explanation
Indices: 969620--969727 Score: 69
Period size: 15 Copynumber: 7.2 Consensus size: 15
969610 CCAATATCTC
969620 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
969635 GACTTTCTA-ATATTT
1 GA-TACCCATATCTTT
969650 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
969665 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
969680 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
969695 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
969710 GATACCCATATCTTT
1 GATACCCATATCTTT
969725 GAT
1 GAT
969728 TTTCCATAAA
Statistics
Matches: 65, Mismatches: 22, Indels: 12
0.66 0.22 0.12
Matches are distributed among these distances:
14 11 0.17
15 43 0.66
16 11 0.17
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.45
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:974266 original size:21 final size:18
Alignment explanation
Indices: 974230--974268 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 18
974220 AAATTTATTT
974230 AAATTATATAAAATTTTA
1 AAATTATATAAAATTTTA
974248 AAATTAGTAATAAATATTTTA
1 AAATTA-T-ATAAA-ATTTTA
974269 CATTTTGGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 1 0.06
20 5 0.28
21 6 0.33
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
AAATTATATAAAATTTTA
Found at i:976602 original size:18 final size:20
Alignment explanation
Indices: 976548--976593 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
976538 ATTTTAATAC
*
976548 ATTTTTGTAAA-AGTATTGGA
1 ATTTTTATAAATA-TATTGGA
976568 ATTTTTATAAATATATT-GA
1 ATTTTTATAAATATATTGGA
976587 ATTTTTA
1 ATTTTTA
976594 AATATTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 9 0.38
20 14 0.58
21 1 0.04
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (20 bp):
ATTTTTATAAATATATTGGA
Found at i:981350 original size:4 final size:4
Alignment explanation
Indices: 981335--981364 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
981325 TATTATATAT
*
981335 ATAG ATAA ATAG ATAG ATAG ATAG ATAG AT
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG AT
981365 TGTGTGTCGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.20, T:0.27
Consensus pattern (4 bp):
ATAG
Found at i:990221 original size:23 final size:22
Alignment explanation
Indices: 990179--990221 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
990169 TTTATGATCC
*
990179 AGTCATTTCAAAATTGGGTTCA
1 AGTCATTTCAAAATTAGGTTCA
*
990201 AGTCATTTTCAAATTTAGGTT
1 AGTCA-TTTCAAAATTAGGTT
990222 GAATGAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (22 bp):
AGTCATTTCAAAATTAGGTTCA
Found at i:993189 original size:13 final size:14
Alignment explanation
Indices: 993164--993192 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
993154 ATAATCTCAG
993164 CTCAAAAACAAACC
1 CTCAAAAACAAACC
993178 CTCAAAAA-AAACC
1 CTCAAAAACAAACC
993191 CT
1 CT
993193 TTGATCATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.55, C:0.34, G:0.00, T:0.10
Consensus pattern (14 bp):
CTCAAAAACAAACC
Found at i:1003834 original size:20 final size:18
Alignment explanation
Indices: 1003809--1003855 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 18
1003799 TCGAGCTTTT
1003809 AAATTAAATCATTTATAATA
1 AAATTAAATCATTT-TAA-A
1003829 AAATTAAA--ATTTTAAA
1 AAATTAAATCATTTTAAA
*
1003845 AAATCAAATCA
1 AAATTAAATCA
1003856 ATTAAACTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
16 8 0.33
17 3 0.12
18 5 0.21
20 8 0.33
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATTAAATCATTTTAAA
Found at i:1005513 original size:16 final size:16
Alignment explanation
Indices: 1005471--1005513 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1005461 ATCTTGAACT
* *
1005471 AACCCAAACTTGTAATT
1 AACCCAAA-TTGAAATG
*
1005488 AACTCAAATTGAAATG
1 AACCCAAATTGAAATG
1005504 AACCCAAATT
1 AACCCAAATT
1005514 TTAAAATTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.47, C:0.21, G:0.07, T:0.26
Consensus pattern (16 bp):
AACCCAAATTGAAATG
Found at i:1007975 original size:6 final size:6
Alignment explanation
Indices: 1007964--1007993 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
1007954 TTTTACAATA
1007964 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
1007994 GCCATGCACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTCT
Found at i:1008284 original size:22 final size:24
Alignment explanation
Indices: 1008253--1008300 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
1008243 TAGGGTTTTT
1008253 TTTTTAC-TTTGGGCTTGTAATAA
1 TTTTTACTTTTGGGCTTGTAATAA
*
1008276 TTTTT-CTTTTGGGTTTGTAATAA
1 TTTTTACTTTTGGGCTTGTAATAA
1008299 TT
1 TT
1008301 ATTTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.19, C:0.06, G:0.17, T:0.58
Consensus pattern (24 bp):
TTTTTACTTTTGGGCTTGTAATAA
Found at i:1008652 original size:44 final size:44
Alignment explanation
Indices: 1008567--1008653 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 44
1008557 GGTTTGTAAC
*
1008567 TTGTAGCTTCAATCTATTCGACTACAACTTTAGGAAAATAAGAT
1 TTGTAGCTTCAATCTATTCGACTACAACTTCAGGAAAATAAGAT
* * * *
1008611 TTGTAGCTTCAATTTACTTC-ACTGCAACTTCAGGGAGATAAGA
1 TTGTAGCTTCAATCTA-TTCGACTACAACTTCAGGAAAATAAGA
1008654 CTCGCCACAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
44 34 0.92
45 3 0.08
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Consensus pattern (44 bp):
TTGTAGCTTCAATCTATTCGACTACAACTTCAGGAAAATAAGAT
Found at i:1008747 original size:145 final size:145
Alignment explanation
Indices: 1008526--1009084 Score: 748
Period size: 145 Copynumber: 3.9 Consensus size: 145
1008516 TTGTCGCTTT
* * ** * *
1008526 AATCTGCTCCACTACAACTTCAGGGAGCTA-AGG-TTTGTAACTTGTAG-CTTCAATCTATTCGA
1 AATCTGTTCCACTACAATTTCAGGG-G-TATAGGATTTGCGACTTGTAGCCTT-AATCTAATCCA
* * * *
1008588 CTACAACTTTAGGAAAATAAGATTTGTAGCTTCAATTTACTTCACTGCAACTTCAGGGAGATAAG
63 CTGCAACTTTAGGAAAATAAGATTTGTAACTTCAATTTGCTTCACTACAACTTCAGGGAGATAAG
1008653 ACTCGCCACAATGACTTC
128 ACTCGCCACAATGACTTC
*
1008671 AATTTGTTCCACTACAATTTCAGGGGTATAGGATTTGCGACTTGTAGCCTTAATCTAATCCACTG
1 AATCTGTTCCACTACAATTTCAGGGGTATAGGATTTGCGACTTGTAGCCTTAATCTAATCCACTG
* * *
1008736 CAACTTCAGGAAAATAAGATTTGTAACTTCAATCTGCTTCACTACAACTTTAGGGAGATAAGACT
66 CAACTTTAGGAAAATAAGATTTGTAACTTCAATTTGCTTCACTACAACTTCAGGGAGATAAGACT
* *
1008801 TGGCACAATGACTTC
131 CGCCACAATGACTTC
* * *
1008816 AATCTGTTCCACTGCAATTTCAGGGGTATAGGATTTGCGACTTGTAGCTTTAATCTAATCTACTG
1 AATCTGTTCCACTACAATTTCAGGGGTATAGGATTTGCGACTTGTAGCCTTAATCTAATCCACTG
*
1008881 CAACTTTAGGAAAATAAGATTTGTAACTTCAATTTGCTCCACTACAACTTCAGGGAGATAAGACT
66 CAACTTTAGGAAAATAAGATTTGTAACTTCAATTTGCTTCACTACAACTTCAGGGAGATAAGACT
1008946 CGCCACAATGACTTC
131 CGCCACAATGACTTC
* * ** * *
1008961 AATCCGTTCCATTGTAATTTCAGGGGTATATGATTTGCGACTTGTAGCTTTAATC-AATTCCACT
1 AATCTGTTCCACTACAATTTCAGGGGTATAGGATTTGCGACTTGTAGCCTTAATCTAA-TCCACT
* * * ** * * *
1009025 GCAACTTTAGGGAAATAAGATTCGCATTTTCAACTTGCTACACTGCAACTTCAGGGAGAT
65 GCAACTTTAGGAAAATAAGATTTGTAACTTCAATTTGCTTCACTACAACTTCAGGGAGAT
1009085 TAGATTTGTA
Statistics
Matches: 371, Mismatches: 39, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
143 2 0.01
144 6 0.02
145 360 0.97
146 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (145 bp):
AATCTGTTCCACTACAATTTCAGGGGTATAGGATTTGCGACTTGTAGCCTTAATCTAATCCACTG
CAACTTTAGGAAAATAAGATTTGTAACTTCAATTTGCTTCACTACAACTTCAGGGAGATAAGACT
CGCCACAATGACTTC
Found at i:1009108 original size:95 final size:92
Alignment explanation
Indices: 1009009--1009186 Score: 252
Period size: 95 Copynumber: 1.9 Consensus size: 92
1008999 GACTTGTAGC
* *
1009009 TTTAATCA-ATTCCACTGCAACTTTAGGGAAATAAGATTCGCATTTTCAA-CTTGCTACACTGCA
1 TTTAAT-ATATTCCACTGCAACTTCAGGGAAATAAGATTCGCATATTCAATC-TGCTACACT---
*
1009072 ACTTCAGGGAGATTAGATTTGTAACTTATATT
61 ACTTCAGGGAGATAAGATTTGTAACTTATATT
* *
1009104 TTTAATATGTTCCACTGCAACTTCAGGGAAATAAGATTCGCATATTCAATCTGCTCCACTACTTC
1 TTTAATATATTCCACTGCAACTTCAGGGAAATAAGATTCGCATATTCAATCTGCTACACTACTTC
1009169 AGGGAGATAAGATTTGTA
66 AGGGAGATAAGATTTGTA
1009187 TTTTCAATCT
Statistics
Matches: 76, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
92 22 0.29
94 1 0.01
95 52 0.68
96 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (92 bp):
TTTAATATATTCCACTGCAACTTCAGGGAAATAAGATTCGCATATTCAATCTGCTACACTACTTC
AGGGAGATAAGATTTGTAACTTATATT
Found at i:1009223 original size:44 final size:44
Alignment explanation
Indices: 1009019--1009833 Score: 662
Period size: 44 Copynumber: 18.4 Consensus size: 44
1009009 TTTAATCAAT
* * *
1009019 TCCACTGCAACTTTAGGGAAATAAGATTCGCATTTTCAA-CTTGC
1 TCCACTGCAACTTTAGGGAGATAAGATTTGTATTTTCAATC-TGC
* * * * * *
1009063 TACACTGCAACTTCAGGGAGATTAGATTTGTAACTTATATTTTTAATATGT
1 TCCACTGCAACTTTAGGGAGATAAGATTTG-------TATTTTCAATCTGC
* * * * *
1009114 TCCACTGCAACTTCAGGGAAATAAGATTCGCATATTCAATCTGC
1 TCCACTGCAACTTTAGGGAGATAAGATTTGTATTTTCAATCTGC
* **
1009158 TCCACT---ACTTCAGGGAGATAAGATTTGTATTTTCAATCTTT
1 TCCACTGCAACTTTAGGGAGATAAGATTTGTATTTTCAATCTGC
* * *
1009199 TCTACTGCAACTTTAGGGAGATAAGATTTATAGCTTT-AATCTGC
1 TCCACTGCAACTTTAGGGAGATAAGATTTGTA-TTTTCAATCTGC
* * * *
1009243 TCTACTGCAACTTCTTA--GAGACAAGATTTGCTATCTTCAATATGC
1 TCCACTGCAAC-T-TTAGGGAGATAAGATTTG-TATTTTCAATCTGC
* * * * **
1009288 TCTACTACAACTTCAGGGAGATAAGATTTATGGCTTT-AATCTGC
1 TCCACTGCAACTTTAGGGAGATAAGATTTGT-ATTTTCAATCTGC
* * *
1009332 TCCTCTACAATTTTA-GGAGATAAGATTTGCTATCTTT-AATCTGC
1 TCCACTGCAACTTTAGGGAGATAAGATTTG-TAT-TTTCAATCTGC
* * * **
1009376 TCCACTGCAACTTCAAGGAGATAATATTTGTGGCTTT-AATCTGC
1 TCCACTGCAACTTTAGGGAGATAAGATTTGT-ATTTTCAATCTGC
* *
1009420 TCCACTGCAACTTCA-GGAGATAAGATTTGCTATTTTCAATTTGC
1 TCCACTGCAACTTTAGGGAGATAAGATTTG-TATTTTCAATCTGC
* * * **
1009464 TTCACTACAACTTTAGGAAGATAAGATTTGTGGCTTT-AATCTGC
1 TCCACTGCAACTTTAGGGAGATAAGATTTGT-ATTTTCAATCTGC
* *
1009508 TCCACTGCAACTTTA-GGAGATAAGATTTGCTATCTTCAATCCGC
1 TCCACTGCAACTTTAGGGAGATAAGATTTG-TATTTTCAATCTGC
* *
1009552 TCCACTGCAGCTTTAGGGAGATAAGATTTGTGACTTT-AATCTGC
1 TCCACTGCAACTTTAGGGAGATAAGATTTGT-ATTTTCAATCTGC
* * *
1009596 TCCACTACAACTTTA-GGAGATAAGATTTGCTATCTTCAATCCGC
1 TCCACTGCAACTTTAGGGAGATAAGATTTG-TATTTTCAATCTGC
*
1009640 TCCACTGCAACTTTAGGG-GATAAGATTTG-AGCCTTTCAATCTGC
1 TCCACTGCAACTTTAGGGAGATAAGATTTGTA--TTTTCAATCTGC
* * * ** *
1009684 TCCACTGCAACTTCAGGGGGATAAGATTTATGGCTTT-AACCTGC
1 TCCACTGCAACTTTAGGGAGATAAGATTTGT-ATTTTCAATCTGC
* * * * *
1009728 TCCACTACAACTTCA-AGAGATAAGATTTGCTATGTTCAATCTAC
1 TCCACTGCAACTTTAGGGAGATAAGATTTG-TATTTTCAATCTGC
* *
1009772 TCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAATCTGC
1 TCCACTGCAACTTTAGGGAGATAAGATTTG-TATTTTCAATCTGC
1009817 TCCACTGCAACTTTAGG
1 TCCACTGCAACTTTAGG
1009834 TTTTTGCCAT
Statistics
Matches: 623, Mismatches: 106, Indels: 83
0.77 0.13 0.10
Matches are distributed among these distances:
41 34 0.05
42 1 0.00
43 76 0.12
44 335 0.54
45 139 0.22
46 3 0.00
51 35 0.06
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (44 bp):
TCCACTGCAACTTTAGGGAGATAAGATTTGTATTTTCAATCTGC
Found at i:1009396 original size:88 final size:88
Alignment explanation
Indices: 1009151--1009829 Score: 734
Period size: 88 Copynumber: 7.7 Consensus size: 88
1009141 TCGCATATTC
* * ** *
1009151 AATCTGCTCCACT---ACTTCAGGGAGATAAGATTTG-TATTTTCAATCTTTTCTACTGCAACTT
1 AATCTGCTCCACTGCAACTTTA-GGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTT
* * *
1009212 TAGGGAGATAAGATTTATAGCTTT
65 CAAGGAGATAAGATTTATGGCTTT
* * * * *
1009236 AATCTGCTCTACTGCAACTTCTTA-GAGACAAGATTTGCTATCTTCAATATGCTCTACTACAACT
1 AATCTGCTCCACTGCAAC-T-TTAGGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACT
*
1009300 TCAGGGAGATAAGATTTATGGCTTT
64 TCAAGGAGATAAGATTTATGGCTTT
* * * *
1009325 AATCTGCTCCTCTACAATTTTAGGAGATAAGATTTGCTATCTTTAATCTGCTCCACTGCAACTTC
1 AATCTGCTCCACTGCAACTTTAGGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTC
* *
1009390 AAGGAGATAATATTTGTGGCTTT
66 AAGGAGATAAGATTTATGGCTTT
* * * * *
1009413 AATCTGCTCCACTGCAACTTCAGGAGATAAGATTTGCTATTTTCAATTTGCTTCACTACAACTT-
1 AATCTGCTCCACTGCAACTTTAGGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTC
* *
1009477 TAGGAAGATAAGATTTGTGGCTTT
66 AAGG-AGATAAGATTTATGGCTTT
* * *
1009501 AATCTGCTCCACTGCAACTTTAGGAGATAAGATTTGCTATCTTCAATCCGCTCCACTGCAGCTTT
1 AATCTGCTCCACTGCAACTTTAGGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTC
* * *
1009566 AGGGAGATAAGATTTGTGACTTT
66 AAGGAGATAAGATTTATGGCTTT
* *
1009589 AATCTGCTCCACTACAACTTTAGGAGATAAGATTTGCTATCTTCAATCCGCTCCACTGCAACTT-
1 AATCTGCTCCACTGCAACTTTAGGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTC
* * *
1009653 TAGGGGATAAGATTTGA-GCCTTT
66 AAGGAGATAAGATTT-ATGGCTTT
* * * ** * * *
1009676 CAATCTGCTCCACTGCAACTTCAGGGGGATAAGATTT-ATGGCTTTAACCTGCTCCACTACAACT
1 -AATCTGCTCCACTGCAACTTTA-GGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACT
*
1009740 TCAA-GAGATAAGATTTGCTAT-G-TTC
64 TCAAGGAGATAAGA-TT--TATGGCTTT
* *
1009765 AATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTT
1 AATCTGCTCCACTGCAACTTTA-GGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTT
1009830 TAGGTTTTTG
Statistics
Matches: 504, Mismatches: 72, Indels: 32
0.83 0.12 0.05
Matches are distributed among these distances:
85 12 0.02
87 23 0.05
88 365 0.72
89 100 0.20
90 3 0.01
91 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (88 bp):
AATCTGCTCCACTGCAACTTTAGGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTC
AAGGAGATAAGATTTATGGCTTT
Found at i:1012069 original size:20 final size:21
Alignment explanation
Indices: 1012027--1012072 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
1012017 TTTTTTTTGC
1012027 TTTGGGCTTGTAATAATTTTTAT
1 TTTGGGCTTGTAATAA--TTTAT
*
1012050 TTTGGGTTTGTAATAA-TTAT
1 TTTGGGCTTGTAATAATTTAT
1012070 TTT
1 TTT
1012073 TATTTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 7 0.32
23 15 0.68
ACGTcount: A:0.22, C:0.02, G:0.17, T:0.59
Consensus pattern (21 bp):
TTTGGGCTTGTAATAATTTAT
Found at i:1017820 original size:14 final size:15
Alignment explanation
Indices: 1017793--1017821 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1017783 TTCTTTCTTT
1017793 CCTCTTTATTTTCAA
1 CCTCTTTATTTTCAA
1017808 CCTCTTT-TTTTCAA
1 CCTCTTTATTTTCAA
1017822 TTATTGCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.17, C:0.28, G:0.00, T:0.55
Consensus pattern (15 bp):
CCTCTTTATTTTCAA
Found at i:1018309 original size:20 final size:21
Alignment explanation
Indices: 1018279--1018318 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
1018269 ACCAAAATTT
1018279 TATTTTAAAAATTAAAAAAAG
1 TATTTTAAAAATTAAAAAAAG
1018300 TATTTT-AAAATTAAAAAAA
1 TATTTTAAAAATTAAAAAAA
1018319 TAAAAAAAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (21 bp):
TATTTTAAAAATTAAAAAAAG
Found at i:1018316 original size:28 final size:30
Alignment explanation
Indices: 1018280--1018349 Score: 99
Period size: 28 Copynumber: 2.4 Consensus size: 30
1018270 CCAAAATTTT
* *
1018280 ATTTTAAAAATTAAAAAAAGTA-TTTTAAA
1 ATTTAAAAAATTAAAAAAAGCATTTTTAAA
*
1018309 A-TTAAAAAAATAAAAAAAGCATTTTTAAA
1 ATTTAAAAAATTAAAAAAAGCATTTTTAAA
1018338 ATTTAAAAAATT
1 ATTTAAAAAATT
1018350 TTAAAATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 17 0.49
29 9 0.26
30 9 0.26
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.34
Consensus pattern (30 bp):
ATTTAAAAAATTAAAAAAAGCATTTTTAAA
Found at i:1018318 original size:29 final size:30
Alignment explanation
Indices: 1018285--1018349 Score: 98
Period size: 29 Copynumber: 2.2 Consensus size: 30
1018275 ATTTTATTTT
*
1018285 AAAAATTAAAAAAAGTA-TTTTAAAATTAA
1 AAAAATTAAAAAAAGCATTTTTAAAATTAA
*
1018314 AAAAA-TAAAAAAAGCATTTTTAAAATTTA
1 AAAAATTAAAAAAAGCATTTTTAAAATTAA
1018343 AAAAATT
1 AAAAATT
1018350 TTAAAATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
28 10 0.31
29 21 0.66
30 1 0.03
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.31
Consensus pattern (30 bp):
AAAAATTAAAAAAAGCATTTTTAAAATTAA
Found at i:1030027 original size:17 final size:19
Alignment explanation
Indices: 1030005--1030046 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
1029995 AAATAAATTT
1030005 ATTTTAAAAT-TTTTTT-A
1 ATTTTAAAATATTTTTTAA
1030022 ATTTTAAAATACTTTTTTAA
1 ATTTTAAAATA-TTTTTTAA
1030042 ATTTT
1 ATTTT
1030047 TTATTTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.45
19 6 0.27
20 6 0.27
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTTAAAATATTTTTTAA
Found at i:1030037 original size:28 final size:29
Alignment explanation
Indices: 1030006--1030090 Score: 136
Period size: 28 Copynumber: 2.9 Consensus size: 29
1029996 AATAAATTTA
1030006 TTTTAAAATTTTTTTAATTTTAAAATACT
1 TTTTAAAATTTTTTTAATTTTAAAATACT
* *
1030035 TTTTTAAA-TTTTTTATTTTTAAAATACT
1 TTTTAAAATTTTTTTAATTTTAAAATACT
1030063 TTTTAAAATTTTTTTAATTTTTAAAATA
1 TTTTAAAATTTTTTTAA-TTTTAAAATA
1030091 AATTTTTAGT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
28 26 0.52
29 14 0.28
30 10 0.20
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (29 bp):
TTTTAAAATTTTTTTAATTTTAAAATACT
Found at i:1031773 original size:22 final size:22
Alignment explanation
Indices: 1031750--1031790 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1031740 TAATATTTTA
1031750 AAAAAT-ATTTTTTAAATAAAT
1 AAAAATAATTTTTTAAATAAAT
* *
1031771 AAAGATAATTTTTTATATAA
1 AAAAATAATTTTTTAAATAA
1031791 CATTTTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
AAAAATAATTTTTTAAATAAAT
Found at i:1032931 original size:24 final size:24
Alignment explanation
Indices: 1032899--1032947 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
1032889 TCTATGACAT
1032899 TTATAAATTTAGATTATCATCGTA
1 TTATAAATTTAGATTATCATCGTA
*
1032923 TTATAAATTTAGATTATTATCGTA
1 TTATAAATTTAGATTATCATCGTA
1032947 T
1 T
1032948 GATTTAGGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.06, G:0.08, T:0.49
Consensus pattern (24 bp):
TTATAAATTTAGATTATCATCGTA
Found at i:1034131 original size:13 final size:13
Alignment explanation
Indices: 1034101--1034130 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1034091 TTTATTATAG
1034101 TTTTTCTTTTCTT
1 TTTTTCTTTTCTT
1034114 TTTTTCTTTT-TT
1 TTTTTCTTTTCTT
1034126 TTTTT
1 TTTTT
1034131 TTTAATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTTCTTTTCTT
Found at i:1040673 original size:25 final size:25
Alignment explanation
Indices: 1040644--1040747 Score: 114
Period size: 25 Copynumber: 4.4 Consensus size: 25
1040634 GAACCTTAGC
*
1040644 GTGCTCTCTGATTATTAGCACGTTA
1 GTGCTCTCTGATTATTAGCACATTA
1040669 GTGCTCTCTGATTATTAGCACATTA
1 GTGCTCTCTGATTATTAGCACATTA
*
1040694 GTGCTCTCCG--T-TTAGCACATTTA
1 GTGCTCTCTGATTATTAGCACA-TTA
* *
1040717 -TGCTCTCTG--TA-TAGTACTTTA
1 GTGCTCTCTGATTATTAGCACATTA
1040738 GTGCTCTCTG
1 GTGCTCTCTG
1040748 TTTAATAGTG
Statistics
Matches: 71, Mismatches: 5, Indels: 9
0.84 0.06 0.11
Matches are distributed among these distances:
21 3 0.04
22 31 0.44
23 4 0.06
25 33 0.46
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.41
Consensus pattern (25 bp):
GTGCTCTCTGATTATTAGCACATTA
Found at i:1040711 original size:22 final size:22
Alignment explanation
Indices: 1040644--1040751 Score: 101
Period size: 22 Copynumber: 4.6 Consensus size: 22
1040634 GAACCTTAGC
*
1040644 GTGCTCTCTGATTATTAGCACGTTA
1 GTGCTCTCTG--T-TTAGCACATTA
1040669 GTGCTCTCTGATTATTAGCACATTA
1 GTGCTCTCTG--T-TTAGCACATTA
*
1040694 GTGCTCTCCGTTTAGCACATTTA
1 GTGCTCTCTGTTTAGCACA-TTA
* * *
1040717 -TGCTCTCTGTATAGTACTTTA
1 GTGCTCTCTGTTTAGCACATTA
1040738 GTGCTCTCTGTTTA
1 GTGCTCTCTGTTTA
1040752 ATAGTGTAGA
Statistics
Matches: 74, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.04
22 34 0.46
23 4 0.05
25 33 0.45
ACGTcount: A:0.19, C:0.21, G:0.18, T:0.43
Consensus pattern (22 bp):
GTGCTCTCTGTTTAGCACATTA
Found at i:1043486 original size:27 final size:26
Alignment explanation
Indices: 1043427--1043487 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
1043417 TTCACATGTT
1043427 TTTTTATATATATATTCATATTTTCA
1 TTTTTATATATATATTCATATTTTCA
*
1043453 TAATTTACTA-ATATATT-ATATTTATACA
1 T-TTTTA-TATATATATTCATATTT-T-CA
1043481 TTTTTAT
1 TTTTTAT
1043488 GTTTATTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
26 8 0.28
27 16 0.55
28 5 0.17
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (26 bp):
TTTTTATATATATATTCATATTTTCA
Found at i:1049778 original size:51 final size:51
Alignment explanation
Indices: 1049723--1049829 Score: 160
Period size: 51 Copynumber: 2.1 Consensus size: 51
1049713 AACATTGCTA
* * **
1049723 GCATGCTGATCTGTCTAATAATTAGTCTTAATTGTTTGTTTAACCTTGTTG
1 GCATGCTGACCTGTCTAATAATTAGTCTTAATTGTTTGGTTAACCTTACTG
* *
1049774 GCATGCTGACCTGTGTAATAATTAGTTTTAATTGTTTGGTTAACCTTACTG
1 GCATGCTGACCTGTCTAATAATTAGTCTTAATTGTTTGGTTAACCTTACTG
1049825 GCATG
1 GCATG
1049830 TCTAAAAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.22, C:0.14, G:0.20, T:0.44
Consensus pattern (51 bp):
GCATGCTGACCTGTCTAATAATTAGTCTTAATTGTTTGGTTAACCTTACTG
Found at i:1060443 original size:127 final size:127
Alignment explanation
Indices: 1060280--1060535 Score: 363
Period size: 127 Copynumber: 2.0 Consensus size: 127
1060270 TATTAAAAGG
* * *
1060280 AACATTTTAGTCCCTATACATTTCAAAAGCTAACATTTTAATCCTTGCATGTTAAGTTTGTCGTT
1 AACATTTTAGTCCCCATACATGTCAAAAGCTAACATTTTAATCCTTGCACGTTAAGTTTGTCGTT
* * * *
1060345 AAAT-GAATGACATGACTTAACTA-TTATTGACGTAACATTAAATCAAATATTAAATCAAATTA
66 -AATGGAATGACATGACTTAAC-AGTGACTGACATAACATTAAATCAAACATTAAATCAAATTA
* * *
1060407 AACATTTTAGTCCCCATACATGTGAAAAGCTGACATTTTAATCCTTGCACGTTAAGTTTGTTGTT
1 AACATTTTAGTCCCCATACATGTCAAAAGCTAACATTTTAATCCTTGCACGTTAAGTTTGTCGTT
** *
1060472 AATGGAATGACATGACTTAACAGTGACTGACATCGCATTAAATCAAACATTAAATTAAATTA
66 AATGGAATGACATGACTTAACAGTGACTGACATAACATTAAATCAAACATTAAATCAAATTA
1060534 AA
1 AA
1060536 AGGCTAAAAA
Statistics
Matches: 114, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
126 4 0.04
127 110 0.96
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.35
Consensus pattern (127 bp):
AACATTTTAGTCCCCATACATGTCAAAAGCTAACATTTTAATCCTTGCACGTTAAGTTTGTCGTT
AATGGAATGACATGACTTAACAGTGACTGACATAACATTAAATCAAACATTAAATCAAATTA
Found at i:1064056 original size:5 final size:5
Alignment explanation
Indices: 1064048--1064101 Score: 58
Period size: 5 Copynumber: 10.8 Consensus size: 5
1064038 TTTACTTTAT
* *
1064048 ATATA ATATA ATATA ATAATA ATATA ATAT- ATAATA ATAAA ACATA ATA-A
1 ATATA ATATA ATATA AT-ATA ATATA ATATA AT-ATA ATATA ATATA ATATA
1064098 ATAT
1 ATAT
1064102 CTTTATTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
4 6 0.15
5 28 0.68
6 7 0.17
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (5 bp):
ATATA
Found at i:1068137 original size:563 final size:563
Alignment explanation
Indices: 1067071--1068204 Score: 2268
Period size: 563 Copynumber: 2.0 Consensus size: 563
1067061 AAAAGATTAG
1067071 TTAAATTTTATAATAACATCTAATTTACAAAATTTTGAAATATTAAAATATAATGCCGTTGTCGA
1 TTAAATTTTATAATAACATCTAATTTACAAAATTTTGAAATATTAAAATATAATGCCGTTGTCGA
1067136 ATTTGACGTTTATTCTGTGTAAATATCATTGTGTGAATTCTTATCAAGATATATTATAATTTTTA
66 ATTTGACGTTTATTCTGTGTAAATATCATTGTGTGAATTCTTATCAAGATATATTATAATTTTTA
1067201 ATTTATCATGTTTTGTATTGAATTTATTCTAATTTTAGTAGATCGAGTATATATTATTTATGATT
131 ATTTATCATGTTTTGTATTGAATTTATTCTAATTTTAGTAGATCGAGTATATATTATTTATGATT
1067266 TTTGTTGTACTTATAATTGTATTTATATTTGTAAATTCTTTTATATTAATTAAATTACGAATGAA
196 TTTGTTGTACTTATAATTGTATTTATATTTGTAAATTCTTTTATATTAATTAAATTACGAATGAA
1067331 GTCTTAATAGCAAAGTTAAAGATCATTGGAACTTTAAAATCTCATCTTATATTGATCGTGTATGA
261 GTCTTAATAGCAAAGTTAAAGATCATTGGAACTTTAAAATCTCATCTTATATTGATCGTGTATGA
1067396 ATTATCTCCATATTTACTTTTTTAATCCATTATTTTATTCTAGGTATGAATGTATTTTGATTTTC
326 ATTATCTCCATATTTACTTTTTTAATCCATTATTTTATTCTAGGTATGAATGTATTTTGATTTTC
1067461 AATTAAACTTTTTCTCTATAATTGATTAACTTTAATTATTGTTATTTGAATTAATTATTTATAAT
391 AATTAAACTTTTTCTCTATAATTGATTAACTTTAATTATTGTTATTTGAATTAATTATTTATAAT
1067526 TACAATGGTAATTATTTATAATTTTACATTGTTATTTAAAAAGGTTGATTGAATCGATGTCATCT
456 TACAATGGTAATTATTTATAATTTTACATTGTTATTTAAAAAGGTTGATTGAATCGATGTCATCT
1067591 ATTTTTTTATCCAATTTTATATTTTATGTGAATTATAGTAAAT
521 ATTTTTTTATCCAATTTTATATTTTATGTGAATTATAGTAAAT
1067634 TTAAATTTTATAATAACATCTAATTTACAAAATTTTGAAATATTAAAATATAATGCCGTTGTCGA
1 TTAAATTTTATAATAACATCTAATTTACAAAATTTTGAAATATTAAAATATAATGCCGTTGTCGA
1067699 ATTTGACGTTTATTCTGTGTAAATATCATTGTGTGAATTCTTATCAAGATATATTATAATTTTTA
66 ATTTGACGTTTATTCTGTGTAAATATCATTGTGTGAATTCTTATCAAGATATATTATAATTTTTA
1067764 ATTTATCATGTTTTGTATTGAATTTATTCTAATTTTAGTAGATCGAGTATATATTATTTATGATT
131 ATTTATCATGTTTTGTATTGAATTTATTCTAATTTTAGTAGATCGAGTATATATTATTTATGATT
1067829 TTTGTTGTACTTATAATTGTATTTATATTTGTAAATTCTTTTATATTAATTAAATTACGAATGAA
196 TTTGTTGTACTTATAATTGTATTTATATTTGTAAATTCTTTTATATTAATTAAATTACGAATGAA
1067894 GTCTTAATAGCAAAGTTAAAGATCATTGGAACTTTAAAATCTCATCTTATATTGATCGTGTATGA
261 GTCTTAATAGCAAAGTTAAAGATCATTGGAACTTTAAAATCTCATCTTATATTGATCGTGTATGA
1067959 ATTATCTCCATATTTACTTTTTTAATCCATTATTTTATTCTAGGTATGAATGTATTTTGATTTTC
326 ATTATCTCCATATTTACTTTTTTAATCCATTATTTTATTCTAGGTATGAATGTATTTTGATTTTC
1068024 AATTAAACTTTTTCTCTATAATTGATTAACTTTAATTATTGTTATTTGAATTAATTATTTATAAT
391 AATTAAACTTTTTCTCTATAATTGATTAACTTTAATTATTGTTATTTGAATTAATTATTTATAAT
1068089 TACAATGGTAATTATTTATAATTTTACATTGTTATTTAAAAAGGTTGATTGAATCGATGTCATCT
456 TACAATGGTAATTATTTATAATTTTACATTGTTATTTAAAAAGGTTGATTGAATCGATGTCATCT
1068154 ATTTTTTTATCCAATTTTATATTTTATGTGAATTATAGTAAAT
521 ATTTTTTTATCCAATTTTATATTTTATGTGAATTATAGTAAAT
1068197 TTAAATTT
1 TTAAATTT
1068205 AAATTTAAAT
Statistics
Matches: 571, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
563 571 1.00
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.49
Consensus pattern (563 bp):
TTAAATTTTATAATAACATCTAATTTACAAAATTTTGAAATATTAAAATATAATGCCGTTGTCGA
ATTTGACGTTTATTCTGTGTAAATATCATTGTGTGAATTCTTATCAAGATATATTATAATTTTTA
ATTTATCATGTTTTGTATTGAATTTATTCTAATTTTAGTAGATCGAGTATATATTATTTATGATT
TTTGTTGTACTTATAATTGTATTTATATTTGTAAATTCTTTTATATTAATTAAATTACGAATGAA
GTCTTAATAGCAAAGTTAAAGATCATTGGAACTTTAAAATCTCATCTTATATTGATCGTGTATGA
ATTATCTCCATATTTACTTTTTTAATCCATTATTTTATTCTAGGTATGAATGTATTTTGATTTTC
AATTAAACTTTTTCTCTATAATTGATTAACTTTAATTATTGTTATTTGAATTAATTATTTATAAT
TACAATGGTAATTATTTATAATTTTACATTGTTATTTAAAAAGGTTGATTGAATCGATGTCATCT
ATTTTTTTATCCAATTTTATATTTTATGTGAATTATAGTAAAT
Found at i:1068203 original size:6 final size:6
Alignment explanation
Indices: 1068192--1068216 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1068182 TGAATTATAG
1068192 TAAATT TAAATT TAAATT TAAATT T
1 TAAATT TAAATT TAAATT TAAATT T
1068217 TACCATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAAATT
Found at i:1071513 original size:5 final size:5
Alignment explanation
Indices: 1071503--1071532 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
1071493 TTCTTTGGGG
1071503 TTATT TTATT TTATT TTATT TTATT ATTAT
1 TTATT TTATT TTATT TTATT TTATT -TTAT
1071533 AAAAGAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.83
6 4 0.17
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
TTATT
Found at i:1075535 original size:39 final size:40
Alignment explanation
Indices: 1075438--1075538 Score: 125
Period size: 39 Copynumber: 2.6 Consensus size: 40
1075428 CAATTTTGAG
* * * *
1075438 TTTAAATTATTTCGAATATA-ATAATTTTAAATTTTATTA
1 TTTAAATTATTTTGAATTTAGATAATTTTAAATTATATCA
* *
1075477 TTTTAATTATTATGAATTTAGATAATTTTAAATTATA-CA
1 TTTAAATTATTTTGAATTTAGATAATTTTAAATTATATCA
*
1075516 TTTAAATTATTTTAAATTTAGAT
1 TTTAAATTATTTTGAATTTAGAT
1075539 TGAATGAATA
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
39 37 0.71
40 15 0.29
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (40 bp):
TTTAAATTATTTTGAATTTAGATAATTTTAAATTATATCA
Found at i:1077666 original size:17 final size:17
Alignment explanation
Indices: 1077625--1077657 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1077615 GGTAAATGAT
*
1077625 ATTTTTCAAATATTAAA
1 ATTTTTAAAATATTAAA
1077642 ATTTTTAAAAT-TTAAA
1 ATTTTTAAAATATTAAA
1077658 CTTATTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (17 bp):
ATTTTTAAAATATTAAA
Found at i:1081786 original size:23 final size:24
Alignment explanation
Indices: 1081760--1081805 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1081750 ATAAAATTTA
1081760 AATTTT-AAAAAATAAAAAATAAT
1 AATTTTCAAAAAATAAAAAATAAT
* *
1081783 AATTTTCTAAAAATAAAATATAA
1 AATTTTCAAAAAATAAAAAATAA
1081806 AGACTAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (24 bp):
AATTTTCAAAAAATAAAAAATAAT
Found at i:1083153 original size:4 final size:4
Alignment explanation
Indices: 1083144--1083178 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
1083134 GGTTTCTTAC
* *
1083144 CATA CATA CATG CATA CATA CACA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CATA CATA CAT
1083179 GCATGCATGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.46, C:0.29, G:0.03, T:0.23
Consensus pattern (4 bp):
CATA
Found at i:1083161 original size:12 final size:12
Alignment explanation
Indices: 1083144--1083199 Score: 67
Period size: 12 Copynumber: 4.7 Consensus size: 12
1083134 GGTTTCTTAC
1083144 CATACATACATG
1 CATACATACATG
**
1083156 CATACATACACA
1 CATACATACATG
1083168 CATACATACATG
1 CATACATACATG
* * *
1083180 CATGCATGCTTG
1 CATACATACATG
1083192 CATACATA
1 CATACATA
1083200 ATGATGATGA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.39, C:0.27, G:0.09, T:0.25
Consensus pattern (12 bp):
CATACATACATG
Found at i:1088364 original size:26 final size:26
Alignment explanation
Indices: 1088330--1088380 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
1088320 TTGTAGACAA
*
1088330 AAATTAGTATAAATCAATAGTTCAAC
1 AAATTAGTAAAAATCAATAGTTCAAC
*
1088356 AAATTAGTAAAAATCAATGGTTCAA
1 AAATTAGTAAAAATCAATAGTTCAA
1088381 AATCATTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.29
Consensus pattern (26 bp):
AAATTAGTAAAAATCAATAGTTCAAC
Found at i:1096845 original size:21 final size:20
Alignment explanation
Indices: 1096796--1096848 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1096786 TACAAAATCA
1096796 AAAGTATCGATACCCTTAAC
1 AAAGTATCGATACCCTTAAC
* *
1096816 AAAGTATCGATACCTTTCAC
1 AAAGTATCGATACCCTTAAC
1096836 AAAGGTATCGATA
1 AAA-GTATCGATA
1096849 TCATTTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 21 0.70
21 9 0.30
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (20 bp):
AAAGTATCGATACCCTTAAC
Found at i:1111828 original size:22 final size:22
Alignment explanation
Indices: 1111803--1111844 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1111793 GCAACTGTGA
*
1111803 TTTCAGTCGAAGAAACGAGGTC
1 TTTCAGTCGAAGAAAAGAGGTC
* *
1111825 TTTCATTGGAAGAAAAGAGG
1 TTTCAGTCGAAGAAAAGAGG
1111845 GAGAAAATTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.29, T:0.24
Consensus pattern (22 bp):
TTTCAGTCGAAGAAAAGAGGTC
Found at i:1119697 original size:8 final size:9
Alignment explanation
Indices: 1119677--1119701 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1119667 TAAAATATAT
1119677 AAAATTACA
1 AAAATTACA
1119686 AAAATTACA
1 AAAATTACA
1119695 AAAATTA
1 AAAATTA
1119702 TTTAAAAACG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (9 bp):
AAAATTACA
Found at i:1120412 original size:11 final size:11
Alignment explanation
Indices: 1120398--1120426 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1120388 AAAAAATAAA
1120398 AAAATTATTTT
1 AAAATTATTTT
1120409 AAAATTATTTT
1 AAAATTATTTT
1120420 AAAATTA
1 AAAATTA
1120427 AAAAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
AAAATTATTTT
Found at i:1126875 original size:32 final size:31
Alignment explanation
Indices: 1126839--1126899 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
1126829 ATCTTTATGG
*
1126839 TTTTTTAGAAGGACTAAATTAAAATTTTAGCA
1 TTTTTT-GAAGGACTAAACTAAAATTTTAGCA
* *
1126871 TTTTTTGAAGGTCTAAACTATAATTTTAG
1 TTTTTTGAAGGACTAAACTAAAATTTTAG
1126900 ATGTAACCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 20 0.77
32 6 0.23
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (31 bp):
TTTTTTGAAGGACTAAACTAAAATTTTAGCA
Found at i:1149455 original size:2 final size:2
Alignment explanation
Indices: 1149448--1149480 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
1149438 CATGTTCTTC
1149448 AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
1149481 TTGATGTCGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1158858 original size:18 final size:18
Alignment explanation
Indices: 1158835--1158872 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1158825 CATGAGTTAG
1158835 CATAATAAGATTAATGGT
1 CATAATAAGATTAATGGT
1158853 CATAATAAGATTAATGGT
1 CATAATAAGATTAATGGT
1158871 CA
1 CA
1158873 AAAATATCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.32
Consensus pattern (18 bp):
CATAATAAGATTAATGGT
Found at i:1160901 original size:20 final size:20
Alignment explanation
Indices: 1160869--1160911 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
1160859 TTCAAAATAA
1160869 TTATTTTAGGTTGATA-TTAT
1 TTATTTTAGGTTGA-AGTTAT
1160889 TTATTTT-GAGTTGAAGTTAT
1 TTATTTTAG-GTTGAAGTTAT
1160909 TTA
1 TTA
1160912 AATTTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.26, C:0.00, G:0.16, T:0.58
Consensus pattern (20 bp):
TTATTTTAGGTTGAAGTTAT
Found at i:1163001 original size:4 final size:4
Alignment explanation
Indices: 1162992--1163075 Score: 141
Period size: 4 Copynumber: 21.0 Consensus size: 4
1162982 ATGTAGCTTA
* * *
1162992 GTAT GTAT GTAT ATAT GCAT GCAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1163040 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1163076 ATTTTCTCTT
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 76 1.00
ACGTcount: A:0.26, C:0.02, G:0.24, T:0.48
Consensus pattern (4 bp):
GTAT
Found at i:1170264 original size:20 final size:20
Alignment explanation
Indices: 1170239--1170277 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1170229 TGGTGAATAT
1170239 GCCAAGAGTTAAGTGGAGAC
1 GCCAAGAGTTAAGTGGAGAC
1170259 GCCAAGAGTTAAGTGGAGA
1 GCCAAGAGTTAAGTGGAGA
1170278 ACCGTCTGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.13, G:0.36, T:0.15
Consensus pattern (20 bp):
GCCAAGAGTTAAGTGGAGAC
Found at i:1170770 original size:3 final size:3
Alignment explanation
Indices: 1170762--1170787 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1170752 AATAATTCAA
1170762 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
1170788 TCGCTTGATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1173555 original size:19 final size:18
Alignment explanation
Indices: 1173518--1173561 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1173508 TTCTTTTACA
* *
1173518 TTTTGCTTTTGATTCCTT
1 TTTTTCTTTGGATTCCTT
1173536 TTTTTCTTTGGATTCACTT
1 TTTTTCTTTGGATTC-CTT
*
1173555 TATTTCT
1 TTTTTCT
1173562 ACGGCATGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.09, C:0.16, G:0.09, T:0.66
Consensus pattern (18 bp):
TTTTTCTTTGGATTCCTT
Found at i:1176951 original size:17 final size:17
Alignment explanation
Indices: 1176931--1176964 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1176921 AATAAAAGGG
*
1176931 AAAGAAAGGAAAAAGAA
1 AAAGAAAAGAAAAAGAA
*
1176948 AAAGAAAAGAAGAAGAA
1 AAAGAAAAGAAAAAGAA
1176965 GAACGATTAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (17 bp):
AAAGAAAAGAAAAAGAA
Found at i:1193668 original size:31 final size:32
Alignment explanation
Indices: 1193633--1193696 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
1193623 AAATACAAAG
*
1193633 TAAACA-TTTTTTTCAAATGCCCTTTGTACAT
1 TAAACATTTTTTTTCAAATACCCTTTGTACAT
1193664 TAAACATTTTTTTTCAAATACCCTTTGTACAT
1 TAAACATTTTTTTTCAAATACCCTTTGTACAT
1193696 T
1 T
1193697 TTTTTATAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 6 0.19
32 25 0.81
ACGTcount: A:0.30, C:0.19, G:0.05, T:0.47
Consensus pattern (32 bp):
TAAACATTTTTTTTCAAATACCCTTTGTACAT
Found at i:1193975 original size:177 final size:171
Alignment explanation
Indices: 1193674--1194311 Score: 727
Period size: 178 Copynumber: 3.7 Consensus size: 171
1193664 TAAACATTTT
* * * * * *
1193674 TTTTCAAATACCCTTTGTACATTTTTTTATAAACCTTATTAATTTTTTCAACTTTACCCAGTACT
1 TTTTCAAATA-CCTTTGCACA-ATTTTTATAAACCTTATTAATTTGTACAACTTTCCCCACTACT
*
1193739 TTCTCAGGAAACAAACACCAAGTAATGGTGGGTAATTAAAGAGTACCTCAAAGCTGCCAAAAAAA
64 TTCTCAGCAAACAAACACCAAGTAATGGTGGGTAATTAAAGAGTACCTCAAAGCTGCCAAAAAAA
*
1193804 TGACCCAATTTCTAAATTAAAACACAGAGAAAATACAAAGCAAGTA
129 TGACCCAATTTCTAAATTAAAACACATAGAAAAT-CAAA-CAA-TA
* * *
1193850 CTTCTTCAAATACCGTTTGCAGAATATTTTATAAACCTTACTAATTTGTACAAC-TTCCCCTCTA
1 -TT-TTCAAATACC-TTTGCACAAT-TTTTATAAACCTTATTAATTTGTACAACTTTCCCCACTA
* * *
1193914 CTTTCTCAGCAAACAAACACCAAGTAATGGTGGGTAATTAGAGAGTACCACAAAACTGCCAAAAA
62 CTTTCTCAGCAAACAAACACCAAGTAATGGTGGGTAATTAAAGAGTACCTCAAAGCTGCCAAAAA
* * * * *
1193979 AACGACCCAATTTCTAATTTAAACCACATAAAAAATGCAAACTAAACATTT
127 AATGACCCAATTTCTAAATTAAAACACATAGAAAAT-CAAAC---A-A-TA
* * ** * *
1194030 TTTTCAAATACCTTTGTATAATTTTTATTAAACCTTATTAATTTCAACAA-ATTCTCCGACTACT
1 TTTTCAAATACCTTTGCACAATTTTTA-TAAACCTTATTAATTTGTACAACTTTC-CCCACTACT
* *
1194094 TTCTCAGCAAACAAACACCAAGTAATGGTGAGTAATTAAAAAGTACCTCAAAGCTGCCAAAAAAA
64 TTCTCAGCAAACAAACACCAAGTAATGGTGGGTAATTAAAGAGTACCTCAAAGCTGCCAAAAAAA
*
1194159 TGACCCAATTTCTAAATTCAAACACATAGAAAAT---AC--T-
129 TGACCCAATTTCTAAATTAAAACACATAGAAAATCAAACAATA
* * * * *
1194196 TTTTCAAATACCCTTTGCTCATTTTTTTATAAACCTTATTAAATTGT-TAACTTTTCCCACTACT
1 TTTTCAAATA-CCTTTGCACA-ATTTTTATAAACCTTATTAATTTGTACAACTTTCCCCACTACT
* *
1194260 TTCTCAGCAAACAAACACCAAGTAATGATGGGTAACTAAAGAGTACCTCAAA
64 TTCTCAGCAAACAAACACCAAGTAATGGTGGGTAATTAAAGAGTACCTCAAA
1194312 CAAGGCCATC
Statistics
Matches: 395, Mismatches: 53, Indels: 37
0.81 0.11 0.08
Matches are distributed among these distances:
166 68 0.17
167 25 0.06
168 6 0.02
174 2 0.01
176 6 0.02
177 138 0.35
178 145 0.37
179 3 0.01
180 2 0.01
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (171 bp):
TTTTCAAATACCTTTGCACAATTTTTATAAACCTTATTAATTTGTACAACTTTCCCCACTACTTT
CTCAGCAAACAAACACCAAGTAATGGTGGGTAATTAAAGAGTACCTCAAAGCTGCCAAAAAAATG
ACCCAATTTCTAAATTAAAACACATAGAAAATCAAACAATA
Found at i:1238904 original size:30 final size:28
Alignment explanation
Indices: 1238851--1238906 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
1238841 TGAAATTTAA
* *
1238851 TTTTTATATTTTCTTTAAGAATTTAGTC
1 TTTTTATATTTTATTTAAAAATTTAGTC
1238879 TTTTTATATTTTATATTTAAAAATTTAG
1 TTTTTATA-TTT-TATTTAAAAATTTAG
1238907 ATTTATTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 8 0.33
29 3 0.12
30 13 0.54
ACGTcount: A:0.30, C:0.04, G:0.05, T:0.61
Consensus pattern (28 bp):
TTTTTATATTTTATTTAAAAATTTAGTC
Found at i:1240901 original size:20 final size:21
Alignment explanation
Indices: 1240862--1240901 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1240852 AAATATTTGA
1240862 TATTAAATATAATGATTAATT
1 TATTAAATATAATGATTAATT
1240883 TATTAAA-AT-ATGTATTAAT
1 TATTAAATATAATG-ATTAAT
1240902 GATTCACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.17
20 8 0.44
21 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (21 bp):
TATTAAATATAATGATTAATT
Found at i:1241308 original size:31 final size:31
Alignment explanation
Indices: 1241273--1241332 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
1241263 AAAGTTCAAA
*
1241273 CCTTAAAATGAAAATAATTGTCAAGTTTAGG
1 CCTTAAAATGAAAATAATTGCCAAGTTTAGG
* ** *
1241304 CCTTAATATGGGAATTATTGCCAAGTTTA
1 CCTTAAAATGAAAATAATTGCCAAGTTTA
1241333 AGAATTAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.35
Consensus pattern (31 bp):
CCTTAAAATGAAAATAATTGCCAAGTTTAGG
Found at i:1243504 original size:18 final size:18
Alignment explanation
Indices: 1243468--1243506 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
1243458 ATTATATCAG
1243468 TAAAATTTAATTCGAATT
1 TAAAATTTAATTCGAATT
*
1243486 TAAATATTTAATTCGATTT
1 TAAA-ATTTAATTCGAATT
1243505 TA
1 TA
1243507 TTATAAAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (18 bp):
TAAAATTTAATTCGAATT
Found at i:1248512 original size:39 final size:40
Alignment explanation
Indices: 1248468--1248550 Score: 100
Period size: 39 Copynumber: 2.1 Consensus size: 40
1248458 TTTACATATT
1248468 TTTTAAAAA-AATTTTAAAAATTTTTATAAAT-ATTTTAAA-
1 TTTTAAAAATAATTTT-AAAATTTTTA-AAATGATTTTAAAC
* * *
1248507 TTTTAAAAATGATTTTGAATTTTTTAAAATGATTTTAAAC
1 TTTTAAAAATAATTTTAAAATTTTTAAAATGATTTTAAAC
1248547 TTTT
1 TTTT
1248551 GTTAAATGCG
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
38 4 0.11
39 25 0.66
40 9 0.24
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (40 bp):
TTTTAAAAATAATTTTAAAATTTTTAAAATGATTTTAAAC
Found at i:1248531 original size:28 final size:28
Alignment explanation
Indices: 1248476--1248534 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
1248466 TTTTTTAAAA
*
1248476 AAATTTTAAAAATTTTTATAAATATTTT
1 AAATTTTAAAAATATTTATAAATATTTT
* *
1248504 AAATTTTAAAAATGATTT-TGAATTTTTT
1 AAATTTTAAAAAT-ATTTATAAATATTTT
1248532 AAA
1 AAA
1248535 ATGATTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 24 0.89
29 3 0.11
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AAATTTTAAAAATATTTATAAATATTTT
Found at i:1248533 original size:21 final size:21
Alignment explanation
Indices: 1248465--1248556 Score: 86
Period size: 21 Copynumber: 4.5 Consensus size: 21
1248455 TTCTTTACAT
*
1248465 ATTTTTTAAAAA-AATTTTAAA
1 ATTTTTTAAAAATGATTTT-AA
* *
1248486 AATTTTTATAAAT-ATTTTAA
1 ATTTTTTAAAAATGATTTTAA
*
1248506 A--TTTTAAAAATGATTTTGA
1 ATTTTTTAAAAATGATTTTAA
1248525 ATTTTTT-AAAATGATTTTAA
1 ATTTTTTAAAAATGATTTTAA
1248545 ACTTTTGTTAAA
1 A-TTTT-TTAAA
1248557 TGCGATACTA
Statistics
Matches: 59, Mismatches: 5, Indels: 12
0.78 0.07 0.16
Matches are distributed among these distances:
18 9 0.15
19 7 0.12
20 16 0.27
21 23 0.39
22 2 0.03
23 2 0.03
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (21 bp):
ATTTTTTAAAAATGATTTTAA
Found at i:1248535 original size:20 final size:20
Alignment explanation
Indices: 1248465--1248556 Score: 89
Period size: 20 Copynumber: 4.5 Consensus size: 20
1248455 TTCTTTACAT
**
1248465 ATTTTTTAAAAAAATTTTAAA
1 ATTTTTTAAAATGATTTT-AA
*
1248486 AATTTTTATAAAT-ATTTTAA
1 ATTTTTTA-AAATGATTTTAA
* *
1248506 A-TTTTAAAAATGATTTTGA
1 ATTTTTTAAAATGATTTTAA
1248525 ATTTTTTAAAATGATTTTAA
1 ATTTTTTAAAATGATTTTAA
1248545 ACTTTTGTTAAA
1 A-TTTT-TTAAA
1248557 TGCGATACTA
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
18 4 0.07
19 12 0.20
20 20 0.33
21 16 0.27
22 8 0.13
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (20 bp):
ATTTTTTAAAATGATTTTAA
Done.