Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold365
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: 425848
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.31
Warning! 31381 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:901 original size:64 final size:64
Alignment explanation
Indices: 828--948 Score: 233
Period size: 64 Copynumber: 1.9 Consensus size: 64
818 ATAATAACAA
*
828 TGAATATTTGTTTTTTAATCAAGTTGTTTACTTGATTATATCTAATGATCCAATTTTAATATAT
1 TGAATATTTGTTTTTTAATCAAGTTGTTTACTTGATTATATCTAATGATCAAATTTTAATATAT
892 TGAATATTTGTTTTTTAATCAAGTTGTTTACTTGATTATATCTAATGATCAAATTTT
1 TGAATATTTGTTTTTTAATCAAGTTGTTTACTTGATTATATCTAATGATCAAATTTT
949 TATTTTATTT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 56 1.00
ACGTcount: A:0.31, C:0.07, G:0.10, T:0.52
Consensus pattern (64 bp):
TGAATATTTGTTTTTTAATCAAGTTGTTTACTTGATTATATCTAATGATCAAATTTTAATATAT
Found at i:8203 original size:9 final size:9
Alignment explanation
Indices: 8189--8225 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
8179 TATAGTTTGA
8189 TATTCGAAT
1 TATTCGAAT
8198 TATTCGAAT
1 TATTCGAAT
*
8207 TATTCGAGT
1 TATTCGAAT
8216 TATTCGAAT
1 TATTCGAAT
8225 T
1 T
8226 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:9096 original size:106 final size:105
Alignment explanation
Indices: 8923--9502 Score: 619
Period size: 106 Copynumber: 5.5 Consensus size: 105
8913 TGATTAATTA
* ** * *
8923 TTATAAATTGTTTGTGTTTAGTGTTTA-TGGTTTAATGTTTTTTTATAAATGTAAATTTTTTGTT
1 TTATAAATTGTTAGTGTTTA--GTTTAGT-GTTTTGTGATTTTTTATTAATGT-AATTTTTT-TT
* *
8987 TTTTTAATTATTTTATAGTTATTTTGTTAATAATTTATTATTAGG
61 TTTTAAATTATTTTATAGTTATTTTGTTAATAATTTATGATTAGG
* * *
9032 TTATAAATT-CT-GTCTTTTAGGTTTAGTG-TTTGTGAATTTTTATTAATGTAATTTTTTTGTTT
1 TTATAAATTGTTAGT-GTTTA-GTTTAGTGTTTTGTGATTTTTTATTAATGTAA-TTTTTT-TTT
* *
9094 TTTTAATTATTTTATAGTTATTTTGTTAATAATTTATTATTAGG
62 TTTAAATTATTTTATAGTTATTTTGTTAATAATTTATGATTAGG
* * *
9138 TTATAAATTGAT-GTGTTTAGTTTTGTGTTTTGGGATTTTTTATTAATGTAA------TTTTTTA
1 TTATAAATTGTTAGTGTTTAGTTTAGTGTTTTGTGATTTTTTATTAATGTAATTTTTTTTTTTTA
* * * *
9196 AATAATTTTAAAGTTATTTTGTTAGTAATTTATAATTAGG
66 AATTATTTTATAGTTATTTTGTTAATAATTTATGATTAGG
* * * * * ***
9236 TTATAACTTGTTAGTATTTAGTTTAGTGTTTTGTGGTTTTTTAGTAATTTAA-TTTTTTTTAAAA
1 TTATAAATTGTTAGTGTTTAGTTTAGTGTTTTGTGATTTTTTATTAATGTAATTTTTTTTTTTTA
* * *
9300 ACATAATTTTGTAGTTATTTTGTTAATAATTTACGATTAGG
66 A-ATTATTTTATAGTTATTTTGTTAATAATTTATGATTAGG
* * * * ***
9341 TTATAAATTGTTAGTGGTTAGTTTAGTGTTTTGTGATTTTTTAGTGATGTAAATGTTTTTTTAAA
1 TTATAAATTGTTAGTGTTTAGTTTAGTGTTTTGTGATTTTTTATTAATGT-AATTTTTTTTTTTT
* *
9406 AAATTATTTTATAATTATTTTGTTAGTAATTTATGATTAGG
65 AAATTATTTTATAGTTATTTTGTTAATAATTTATGATTAGG
9447 TTAT-AATTGTTAGTGTTTAGTTTAGTGTTTTGTGATTTTTTATTAATGTAATTTTT
1 TTATAAATTGTTAGTGTTTAGTTTAGTGTTTTGTGATTTTTTATTAATGTAATTTTT
9503 ATAATGTAAT
Statistics
Matches: 407, Mismatches: 50, Indels: 33
0.83 0.10 0.07
Matches are distributed among these distances:
98 52 0.13
99 33 0.08
104 11 0.03
105 129 0.32
106 144 0.35
107 23 0.06
108 6 0.01
109 9 0.02
ACGTcount: A:0.26, C:0.01, G:0.14, T:0.58
Consensus pattern (105 bp):
TTATAAATTGTTAGTGTTTAGTTTAGTGTTTTGTGATTTTTTATTAATGTAATTTTTTTTTTTTA
AATTATTTTATAGTTATTTTGTTAATAATTTATGATTAGG
Found at i:9330 original size:105 final size:104
Alignment explanation
Indices: 8996--9502 Score: 611
Period size: 105 Copynumber: 4.9 Consensus size: 104
8986 TTTTTTAATT
* * *
8996 ATTTTATAGTTATTTTGTTAATAATTTATTATTAGGTTATAAATT-CT-GTCTTTTAGGTTTAGT
1 ATTTTATAGTTATTTTGTTAATAATTTATGATTAGGTTATAAATTGTTAGT-GTTTA-GTTTAGT
* **** *
9059 G-TTTGTGAATTTTTATTAATGTAATTTTTTTGTTTTTTTAATT
64 GTTTTGTGATTTTTTATTAATGTAA--TTTTT-TTTAAAAAATA
* * *
9102 ATTTTATAGTTATTTTGTTAATAATTTATTATTAGGTTATAAATTGAT-GTGTTTAGTTTTGTGT
1 ATTTTATAGTTATTTTGTTAATAATTTATGATTAGGTTATAAATTGTTAGTGTTTAGTTTAGTGT
*
9166 TTTGGGATTTTTTATTAATGTAA--TTTTTT---AAATA
66 TTTGTGATTTTTTATTAATGTAATTTTTTTTAAAAAATA
* * * * *
9200 ATTTTAAAGTTATTTTGTTAGTAATTTATAATTAGGTTATAACTTGTTAGTATTTAGTTTAGTGT
1 ATTTTATAGTTATTTTGTTAATAATTTATGATTAGGTTATAAATTGTTAGTGTTTAGTTTAGTGT
* * *
9265 TTTGTGGTTTTTTAGTAATTTAATTTTTTTTAAAAACATA
66 TTTGTGATTTTTTATTAATGTAATTTTTTTTAAAAA-ATA
* * *
9305 ATTTTGTAGTTATTTTGTTAATAATTTACGATTAGGTTATAAATTGTTAGTGGTTAGTTTAGTGT
1 ATTTTATAGTTATTTTGTTAATAATTTATGATTAGGTTATAAATTGTTAGTGTTTAGTTTAGTGT
* * *
9370 TTTGTGATTTTTTAGTGATGTAAATGTTTTTTTAAAAAATT
66 TTTGTGATTTTTTATTAATGT-AAT-TTTTTTTAAAAAATA
* *
9411 ATTTTATAATTATTTTGTTAGTAATTTATGATTAGGTTAT-AATTGTTAGTGTTTAGTTTAGTGT
1 ATTTTATAGTTATTTTGTTAATAATTTATGATTAGGTTATAAATTGTTAGTGTTTAGTTTAGTGT
9475 TTTGTGATTTTTTATTAATGTAATTTTT
66 TTTGTGATTTTTTATTAATGTAATTTTT
9503 ATAATGTAAT
Statistics
Matches: 353, Mismatches: 37, Indels: 25
0.85 0.09 0.06
Matches are distributed among these distances:
98 46 0.13
99 33 0.09
101 9 0.03
102 3 0.01
103 4 0.01
104 5 0.01
105 127 0.36
106 111 0.31
107 15 0.04
ACGTcount: A:0.27, C:0.01, G:0.15, T:0.58
Consensus pattern (104 bp):
ATTTTATAGTTATTTTGTTAATAATTTATGATTAGGTTATAAATTGTTAGTGTTTAGTTTAGTGT
TTTGTGATTTTTTATTAATGTAATTTTTTTTAAAAAATA
Found at i:9507 original size:14 final size:15
Alignment explanation
Indices: 9483--9515 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
9473 GTTTTGTGAT
9483 TTTTTATTAATGTAA
1 TTTTTATTAATGTAA
9498 TTTTTA-TAATGTAA
1 TTTTTATTAATGTAA
9512 TTTT
1 TTTT
9516 ATTTGATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (15 bp):
TTTTTATTAATGTAA
Found at i:13968 original size:22 final size:22
Alignment explanation
Indices: 13934--13986 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
13924 TGTCCCTGGC
* *
13934 TCACACGGGCGTGTGCCTCTCT
1 TCACATGGGCGTGTGCCTATCT
*
13956 TTACATGGGCGTGTGCCTATCT
1 TCACATGGGCGTGTGCCTATCT
13978 TCACATGGG
1 TCACATGGG
13987 TGTTTTGACC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.13, C:0.28, G:0.28, T:0.30
Consensus pattern (22 bp):
TCACATGGGCGTGTGCCTATCT
Found at i:19057 original size:37 final size:37
Alignment explanation
Indices: 19010--19085 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
19000 AATAATTTAT
*
19010 AATAGTAACTAACAAAATAACTCTAAAATAAATTAAA
1 AATAATAACTAACAAAATAACTCTAAAATAAATTAAA
19047 AATAATAACTAACAAAATAACTCTAAAATAAATTAAA
1 AATAATAACTAACAAAATAACTCTAAAATAAATTAAA
19084 AA
1 AA
19086 CAACATAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.64, C:0.11, G:0.01, T:0.24
Consensus pattern (37 bp):
AATAATAACTAACAAAATAACTCTAAAATAAATTAAA
Found at i:24659 original size:21 final size:21
Alignment explanation
Indices: 24622--24661 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
24612 GGTCTATAAG
*
24622 CAGCAGCACTAGACCCAAAAC
1 CAGCAGCACCAGACCCAAAAC
24643 CAGCAGCACGCAG-CCCAAA
1 CAGCAGCAC-CAGACCCAAA
24662 CAATGAGTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.40, C:0.40, G:0.17, T:0.03
Consensus pattern (21 bp):
CAGCAGCACCAGACCCAAAAC
Found at i:38679 original size:44 final size:44
Alignment explanation
Indices: 38524--39004 Score: 260
Period size: 44 Copynumber: 10.7 Consensus size: 44
38514 AATTGTAAAC
* * * * *
38524 CTTATCTCCTTGAAGTTGCAGTGGAGTAGGTTGAAGTTA-CTAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTATC-AAT
* * * * * *
38568 CTTATCTCCCTGAATTTGCTA-TGGAACAGACTAAAGATAACGAAT
1 CTTATCTCCCTGAAGTTGC-AGTGGAGCAGATTGAAGCTATC-AAT
* * * *
38613 CTTATCTCCATGAAGTTACAGTGGAGCAAATTGAAGCTATTAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTATCAAT
* * * * * *
38657 CCTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAACAATGAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTATCAAT
* * * * * * *
38701 CCTATAC-CTCTGAGGTTGCAGTAGG-TCGGATTAAATCTACCATAGCAATT
1 CTTAT-CTCCCTGAAGTTGCAGT-GGAGCAGATTGAAGCT---AT--CAA-T
* * * * * *
38751 TTTATCTCCTTGAAGTTGTAGTGGAGCAGACTGAAGATAACCAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCT-ATCAAT
* * * *
38796 CTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCCA-CAAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTATC-AAT
* * *
38840 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACCAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTATCAAT
* * * *
38884 CTTATCTCCCTGAAGTTACAGTGGAACAAATTGAAGCTATAAGTTATTGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGC--T-A-TCA---AT
* * *
38935 CTTATCTCTCTGAAGTTGCAGTAGAGCAGA-TCATAGC-A--AAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA-AGCTATCAAT
* *
38976 GTTATCTCCCTGAAGTTGCAGTAGAGCAG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAG
39005 TTACAGTAGA
Statistics
Matches: 335, Mismatches: 79, Indels: 49
0.72 0.17 0.11
Matches are distributed among these distances:
41 29 0.09
43 1 0.00
44 168 0.50
45 68 0.20
46 4 0.01
47 4 0.01
48 2 0.01
49 5 0.01
50 24 0.07
51 30 0.09
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.30
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTATCAAT
Found at i:38863 original size:89 final size:90
Alignment explanation
Indices: 38524--38908 Score: 284
Period size: 89 Copynumber: 4.3 Consensus size: 90
38514 AATTGTAAAC
* * * ** * *
38524 CTTATCTCCTTGAAGTTGCAGTGGAGTAGGTTGAAGTTA-CTAGT-CTTATCTCCCTGAATTTGC
1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCCAGC-AATCCTTATCTCCCTGAAGTTGC
* * *
38587 TA-TGGAACAGACTAAAGATAACGAAT
65 -AGTGGAGCAGACTGAAGATAACCAAT
* * * * * * ** *
38613 CTTATCTCCATGAAGTTACAGTGGAGCAAATTGAAGCTATTAATCC-TATCTCTCTGAAGTTGCA
1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCCAGCAATCCTTATCTCCCTGAAGTTGCA
* * * **
38677 GTGGAGCAGA-TTAAAACAATGAAT
66 GTGGAGCAGACTGAAGATAACCAAT
* * * * * * ** *
38701 CCTATAC-CTCTGAGGTTGCAGTAG-GTCGGATTAAATCTACCATAGCAATTTTTATCTCCTTGA
1 CTTAT-CTCCCTGAAGTTGCAGTGGAGT-AGATTAAA---GCC--AGCAATCCTTATCTCCCTGA
*
38764 AGTTGTAGTGGAGCAGACTGAAGATAACCAAT
59 AGTTGCAGTGGAGCAGACTGAAGATAACCAAT
*
38796 CTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCCA-CAAACCTTATCTCCCTGAAGTTGCA
1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCCAGCAATCCTTATCTCCCTGAAGTTGCA
**
38860 GTGGAGCAGGTTGAAGAT-ACCAAT
66 GTGGAGCAGACTGAAGATAACCAAT
*
38884 CTTATCTCCCTGAAGTTACAGTGGA
1 CTTATCTCCCTGAAGTTGCAGTGGA
38909 ACAAATTGAA
Statistics
Matches: 229, Mismatches: 53, Indels: 29
0.74 0.17 0.09
Matches are distributed among these distances:
87 1 0.00
88 62 0.27
89 95 0.41
90 2 0.01
91 1 0.00
92 2 0.01
93 4 0.02
94 26 0.11
95 34 0.15
96 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (90 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCCAGCAATCCTTATCTCCCTGAAGTTGCA
GTGGAGCAGACTGAAGATAACCAAT
Found at i:39011 original size:14 final size:14
Alignment explanation
Indices: 38989--39018 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
38979 ATCTCCCTGA
*
38989 AGTTGCAGTAGAGC
1 AGTTACAGTAGAGC
39003 AGTTACAGTAGAGC
1 AGTTACAGTAGAGC
39017 AG
1 AG
39019 ATTGAAGCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.20
Consensus pattern (14 bp):
AGTTACAGTAGAGC
Found at i:40347 original size:143 final size:143
Alignment explanation
Indices: 40192--40476 Score: 552
Period size: 143 Copynumber: 2.0 Consensus size: 143
40182 CTTCTCCTTT
40192 TAGAGAGAGAAAATATCATACCCAATGAGTTAGGGCATGATTTTTCACCTCCTCAAAAATGAGCT
1 TAGAGAGAGAAAATATCATACCCAATGAGTTAGGGCATGATTTTTCACCTCCTCAAAAATGAGCT
*
40257 TTGTCTAAAAACTCATGCAATAAAATTTAAAAAGATATTCAATTGTTTATGTCAGATGAAAAAAT
66 TTATCTAAAAACTCATGCAATAAAATTTAAAAAGATATTCAATTGTTTATGTCAGATGAAAAAAT
40322 TGCAGCCCAATAA
131 TGCAGCCCAATAA
40335 TAGAGAGAGAAAATATCATACCCAATGAGTTAGGGCATGATTTTTCACCTCCTCAAAAATGAGCT
1 TAGAGAGAGAAAATATCATACCCAATGAGTTAGGGCATGATTTTTCACCTCCTCAAAAATGAGCT
*
40400 TTATCTAAAAACTCGTGCAATAAAATTTAAAAAGATATTCAATTGTTTATGTCAGATGAAAAAAT
66 TTATCTAAAAACTCATGCAATAAAATTTAAAAAGATATTCAATTGTTTATGTCAGATGAAAAAAT
40465 TGCAGCCCAATA
131 TGCAGCCCAATA
40477 TATTAGAGCA
Statistics
Matches: 140, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
143 140 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (143 bp):
TAGAGAGAGAAAATATCATACCCAATGAGTTAGGGCATGATTTTTCACCTCCTCAAAAATGAGCT
TTATCTAAAAACTCATGCAATAAAATTTAAAAAGATATTCAATTGTTTATGTCAGATGAAAAAAT
TGCAGCCCAATAA
Found at i:41310 original size:57 final size:55
Alignment explanation
Indices: 41215--41321 Score: 124
Period size: 57 Copynumber: 1.9 Consensus size: 55
41205 AATATGTAAG
* * *
41215 TATATATATATATGAAAATAAAATACATTTATAGACATATATGTAGATATATATA
1 TATATATATATATGAAAAAAAAATACATATAGAGACATATATGTAGATATATATA
** * * *
41270 TATATATATAATTATGAAAAAAAAATGTATATAGATACATATTTGTATATAT
1 TATATATAT-A-TATGAAAAAAAAATACATATAGAGACATATATGTAGATAT
41322 GGATAAATTA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
55 9 0.21
56 1 0.02
57 32 0.76
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.39
Consensus pattern (55 bp):
TATATATATATATGAAAAAAAAATACATATAGAGACATATATGTAGATATATATA
Found at i:57155 original size:21 final size:21
Alignment explanation
Indices: 57130--57171 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
57120 CTGTTAAGCA
*
57130 GATGGCACCATTGAAAGCACC
1 GATGGCACCATTGAAAACACC
57151 GATGGCACCATTGAAAACACC
1 GATGGCACCATTGAAAACACC
57172 CGGAGTGGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.29, G:0.21, T:0.14
Consensus pattern (21 bp):
GATGGCACCATTGAAAACACC
Found at i:61799 original size:32 final size:32
Alignment explanation
Indices: 61734--61793 Score: 97
Period size: 30 Copynumber: 1.9 Consensus size: 32
61724 GAAATGGGCA
*
61734 AAAAAAATATTAATTAGTTGGGTGAACAAATT
1 AAAAAAATATTAATTAGTTGGGTGAAAAAATT
61766 AAAAAAAT-TTAA-TAGTTGGGTGAAAAAA
1 AAAAAAATATTAATTAGTTGGGTGAAAAAA
61794 AATTAAGTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 15 0.56
31 4 0.15
32 8 0.30
ACGTcount: A:0.53, C:0.02, G:0.17, T:0.28
Consensus pattern (32 bp):
AAAAAAATATTAATTAGTTGGGTGAAAAAATT
Found at i:63977 original size:17 final size:19
Alignment explanation
Indices: 63920--63979 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 19
63910 CAATTTGTTG
*
63920 TAAAAAATAAATCACGATGA
1 TAAAAAATAAATCA-GATAA
* *
63940 TAATAAAATAAATGAGTTAA
1 TAA-AAAATAAATCAGATAA
63960 TAAAAAATAAAT-A-ATAA
1 TAAAAAATAAATCAGATAA
63977 TAA
1 TAA
63980 TAATAAAGAC
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 6 0.17
18 1 0.03
19 9 0.26
20 9 0.26
21 10 0.29
ACGTcount: A:0.65, C:0.03, G:0.07, T:0.25
Consensus pattern (19 bp):
TAAAAAATAAATCAGATAA
Found at i:64722 original size:23 final size:23
Alignment explanation
Indices: 64696--64741 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
64686 GTTTGAAATT
* *
64696 ATAAAAGGATATAAGTAAATATA
1 ATAAAAGGATAAAAATAAATATA
*
64719 ATAAAATGATAAAAATAAATATA
1 ATAAAAGGATAAAAATAAATATA
64742 TTTACAGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (23 bp):
ATAAAAGGATAAAAATAAATATA
Found at i:74159 original size:12 final size:13
Alignment explanation
Indices: 74142--74170 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
74132 GCCTGACACA
74142 AAAAAAATTGAT-
1 AAAAAAATTGATG
74154 AAAAAAATTGATG
1 AAAAAAATTGATG
74167 AAAA
1 AAAA
74171 CAAAAATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (13 bp):
AAAAAAATTGATG
Found at i:76487 original size:14 final size:14
Alignment explanation
Indices: 76468--76502 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
76458 TTAACATTTT
*
76468 TTCTAATGATACTA
1 TTCTAACGATACTA
*
76482 TTCTAACGATTCTA
1 TTCTAACGATACTA
76496 TTCTAAC
1 TTCTAAC
76503 ATGTAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.31, C:0.20, G:0.06, T:0.43
Consensus pattern (14 bp):
TTCTAACGATACTA
Found at i:77745 original size:62 final size:64
Alignment explanation
Indices: 77593--77757 Score: 203
Period size: 62 Copynumber: 2.6 Consensus size: 64
77583 AGATTAATTG
* * *
77593 CAACATTAAAACTTGGAACAAACTTTGTAGTCATAAA-TTAGATTAATTGTAACATTACAACATT
1 CAACATTAAAACTTGGAACAAACTTTGTA-ACATAAATTTAGA-TAATTATAACATTAAAACATT
77657 A
64 A
* *
77658 CAACATTAAAACTTGGAACATACTTTGTAACATAAATTTTG-TAA-TATAA-ATTAAATACATTA
1 CAACATTAAAACTTGGAACAAACTTTGTAACATAAATTTAGATAATTATAACATTAAA-ACATTA
* * *
77720 CAACATTAAAAATTGGAATAAACTTTGTAATATAAATT
1 CAACATTAAAACTTGGAACAAACTTTGTAACATAAATT
77758 AGGTACATTG
Statistics
Matches: 89, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
61 5 0.06
62 44 0.49
63 3 0.03
64 6 0.07
65 31 0.35
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.34
Consensus pattern (64 bp):
CAACATTAAAACTTGGAACAAACTTTGTAACATAAATTTAGATAATTATAACATTAAAACATTA
Found at i:80899 original size:9 final size:9
Alignment explanation
Indices: 80887--80921 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
80877 ATAATAATAC
80887 CTTCTCTTT
1 CTTCTCTTT
80896 CTTCTCTTTT
1 CTTCTC-TTT
80906 CTT-TCTTT
1 CTTCTCTTT
80914 CTTCTCTT
1 CTTCTCTT
80922 CTCCCTATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 6 0.25
9 12 0.50
10 6 0.25
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (9 bp):
CTTCTCTTT
Found at i:81072 original size:9 final size:9
Alignment explanation
Indices: 81060--81094 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
81050 ATAATAATAC
81060 CTTCTCTTT
1 CTTCTCTTT
81069 CTTCTCTTTT
1 CTTCTC-TTT
81079 CTT-TCTTT
1 CTTCTCTTT
81087 CTTCTCTT
1 CTTCTCTT
81095 CTCCCTATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 6 0.25
9 12 0.50
10 6 0.25
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (9 bp):
CTTCTCTTT
Found at i:81143 original size:173 final size:174
Alignment explanation
Indices: 80844--81190 Score: 687
Period size: 173 Copynumber: 2.0 Consensus size: 174
80834 TTTTTCTTAT
80844 CATAATCTATTCTATTTGAAAATAACAATAAAAATAATAATACCTTCTCTTTCTTCTCTTTTCTT
1 CATAATCTATTCTATTTGAAAATAACAATAAAAATAATAATACCTTCTCTTTCTTCTCTTTTCTT
80909 TCTTTCTTCTCTTCTCCCTATCTTCTCCTGCTATTTTTTTAATTGATACTTTAAAATAGAGCCAG
66 TCTTTCTTCTCTTCTCCCTATCTTCTCCTGCTATTTTTTTAATTGATACTTTAAAATAGAGCCAG
80974 ATGGAGGAGGGGGAAAAAAGCTACCGATGCCGCCTATGGAGAAG
131 ATGGAGGAGGGGGAAAAAAGCTACCGATGCCGCCTATGGAGAAG
81018 CATAATCTA-TCTATTTGAAAATAACAATAAAAATAATAATACCTTCTCTTTCTTCTCTTTTCTT
1 CATAATCTATTCTATTTGAAAATAACAATAAAAATAATAATACCTTCTCTTTCTTCTCTTTTCTT
81082 TCTTTCTTCTCTTCTCCCTATCTTCTCCTGCTATTTTTTTAATTGATACTTTAAAATAGAGCCAG
66 TCTTTCTTCTCTTCTCCCTATCTTCTCCTGCTATTTTTTTAATTGATACTTTAAAATAGAGCCAG
81147 ATGGAGGAGGGGGAAAAAAGCTACCGATGCCGCCTATGGAGAAG
131 ATGGAGGAGGGGGAAAAAAGCTACCGATGCCGCCTATGGAGAAG
81191 ATGTGATTGA
Statistics
Matches: 173, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
173 164 0.95
174 9 0.05
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.37
Consensus pattern (174 bp):
CATAATCTATTCTATTTGAAAATAACAATAAAAATAATAATACCTTCTCTTTCTTCTCTTTTCTT
TCTTTCTTCTCTTCTCCCTATCTTCTCCTGCTATTTTTTTAATTGATACTTTAAAATAGAGCCAG
ATGGAGGAGGGGGAAAAAAGCTACCGATGCCGCCTATGGAGAAG
Found at i:81223 original size:27 final size:27
Alignment explanation
Indices: 81172--81223 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
81162 AAAAGCTACC
*
81172 GATGCCGCCTATGGAGAAGATGTGATT
1 GATGCCGCCTATGGAGAAGACGTGATT
* *
81199 GATGCCGCCTATGGGGAAGGCGTGA
1 GATGCCGCCTATGGAGAAGACGTGA
81224 CCGGTGTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.23, C:0.17, G:0.38, T:0.21
Consensus pattern (27 bp):
GATGCCGCCTATGGAGAAGACGTGATT
Found at i:81306 original size:13 final size:15
Alignment explanation
Indices: 81276--81312 Score: 51
Period size: 13 Copynumber: 2.5 Consensus size: 15
81266 TCAGTTTAAT
81276 TTTTGTTTTCATCAAG
1 TTTT-TTTTCATCAAG
81292 TTTTTTTT-ATC-AG
1 TTTTTTTTCATCAAG
81305 TTTTTTTT
1 TTTTTTTT
81313 TTTTTTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 10 0.48
14 3 0.14
15 4 0.19
16 4 0.19
ACGTcount: A:0.14, C:0.08, G:0.08, T:0.70
Consensus pattern (15 bp):
TTTTTTTTCATCAAG
Found at i:82227 original size:75 final size:75
Alignment explanation
Indices: 82099--82242 Score: 270
Period size: 75 Copynumber: 1.9 Consensus size: 75
82089 AAAAAAAAAT
82099 AATTCTTAGTGATGACATTGGACTGAAGTGTGATTATATAAAACGTTCAGAAACATGATGAAGTA
1 AATTCTTAGTGATGACATTGGACTGAAGTGTGATTATATAAAACGTTCAGAAACATGATGAAGTA
82164 ATTAAATTTA
66 ATTAAATTTA
* *
82174 AATTTTTAGTGATGACATTGGACTGAAGTGTGATTATATAAAATGTTCAGAAACATGATGAAGTA
1 AATTCTTAGTGATGACATTGGACTGAAGTGTGATTATATAAAACGTTCAGAAACATGATGAAGTA
82239 ATTA
66 ATTA
82243 CCCTTTAGAT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 67 1.00
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.34
Consensus pattern (75 bp):
AATTCTTAGTGATGACATTGGACTGAAGTGTGATTATATAAAACGTTCAGAAACATGATGAAGTA
ATTAAATTTA
Found at i:87707 original size:45 final size:46
Alignment explanation
Indices: 87620--87710 Score: 125
Period size: 45 Copynumber: 2.0 Consensus size: 46
87610 GGATGGTGGG
87620 GGAGAGGGAAAGAATCAGAGTAAGAGGAAGGATGGTGAGGAAGAGGC
1 GGAGAGGGAAAGAATCAGAGTAAGAGG-AGGATGGTGAGGAAGAGGC
*
87667 GGAGAGGGAGAGAGAATCAGAGT-AG-GG-GGATGGTGGGGAAGAGG
1 GGAGAGGGA-A-AGAATCAGAGTAAGAGGAGGATGGTGAGGAAGAGG
87711 GTGAGGGATG
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
45 16 0.39
47 11 0.27
48 3 0.07
49 11 0.27
ACGTcount: A:0.36, C:0.03, G:0.52, T:0.09
Consensus pattern (46 bp):
GGAGAGGGAAAGAATCAGAGTAAGAGGAGGATGGTGAGGAAGAGGC
Found at i:87849 original size:71 final size:71
Alignment explanation
Indices: 87731--87883 Score: 243
Period size: 71 Copynumber: 2.2 Consensus size: 71
87721 GGAGGGGGAT
* * * *
87731 GGAAAATGGTAGTTTAGTTAAGTCTGTAGTGGAACTATAACGGAAAATGGTAGCTCCGTTACGTT
1 GGAAAATGGTAGTTTAGTTAAGTATGTAGTGGAACTATAACGAAAAATGATAGCTCCGTTACGTC
87796 TGTAAC
66 TGTAAC
* * *
87802 GGAAAATGGTAGTTTGGTTAAGTATGTAGTGGAACTGTAACGAAAAATGATAGCTTCGTTACGTC
1 GGAAAATGGTAGTTTAGTTAAGTATGTAGTGGAACTATAACGAAAAATGATAGCTCCGTTACGTC
87867 TGTAAC
66 TGTAAC
87873 GGAAAATGGTA
1 GGAAAATGGTA
87884 ACTCCGTTAC
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
71 75 1.00
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.30
Consensus pattern (71 bp):
GGAAAATGGTAGTTTAGTTAAGTATGTAGTGGAACTATAACGAAAAATGATAGCTCCGTTACGTC
TGTAAC
Found at i:87911 original size:30 final size:30
Alignment explanation
Indices: 87836--87912 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 30
87826 TGTAGTGGAA
* * *
87836 CTGTAACGAAAAATGATAGCTTCGTTACGT
1 CTGTAACGAAAAATGGTAACTCCGTTACGT
* *
87866 CTGTAACGGAAAATGGTAACTCCGTTACTT
1 CTGTAACGAAAAATGGTAACTCCGTTACGT
*
87896 CTGTAATGAAAAATGGT
1 CTGTAACGAAAAATGGT
87913 TAGTGGTAAC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.30
Consensus pattern (30 bp):
CTGTAACGAAAAATGGTAACTCCGTTACGT
Found at i:92981 original size:16 final size:17
Alignment explanation
Indices: 92956--92996 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
92946 ATTTATTTTC
* *
92956 TTTAAATTAA-GTATTT
1 TTTAATTTAATGTATTA
92972 TTTAATTTAATGTATTA
1 TTTAATTTAATGTATTA
92989 TTT-ATTTA
1 TTTAATTTA
92997 TTTTATCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (17 bp):
TTTAATTTAATGTATTA
Found at i:95324 original size:8 final size:8
Alignment explanation
Indices: 95311--95336 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
95301 TCATTCAACA
95311 CATACATG
1 CATACATG
95319 CATACATG
1 CATACATG
95327 CATACATG
1 CATACATG
95335 CA
1 CA
95337 GGCACCATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.27, G:0.12, T:0.23
Consensus pattern (8 bp):
CATACATG
Found at i:101173 original size:15 final size:14
Alignment explanation
Indices: 101155--101199 Score: 63
Period size: 15 Copynumber: 3.1 Consensus size: 14
101145 AATTTCAAAC
101155 TTTAAATATAAAAAA
1 TTTAAA-ATAAAAAA
*
101170 TTTAAAATAAAAAG
1 TTTAAAATAAAAAA
101184 TTCTAAAATAAAAAA
1 TT-TAAAATAAAAAA
101199 T
1 T
101200 CTCAATTAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 9 0.33
15 18 0.67
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (14 bp):
TTTAAAATAAAAAA
Found at i:107280 original size:11 final size:11
Alignment explanation
Indices: 107266--107292 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
107256 AGATAAATAT
107266 TATTTAATTAA
1 TATTTAATTAA
107277 TATTTAATTAA
1 TATTTAATTAA
107288 TATTT
1 TATTT
107293 TTAGTATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TATTTAATTAA
Found at i:107286 original size:19 final size:20
Alignment explanation
Indices: 107241--107288 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
107231 TTGTGATATT
107241 TTTAATTAATTAATTAGATA
1 TTTAATTAATTAATTAGATA
** *
107261 AAT-ATTATTTAATTA-ATA
1 TTTAATTAATTAATTAGATA
107279 TTTAATTAAT
1 TTTAATTAAT
107289 ATTTTTAGTA
Statistics
Matches: 21, Mismatches: 6, Indels: 3
0.70 0.20 0.10
Matches are distributed among these distances:
18 4 0.19
19 16 0.76
20 1 0.05
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TTTAATTAATTAATTAGATA
Found at i:114498 original size:23 final size:22
Alignment explanation
Indices: 114389--114497 Score: 118
Period size: 23 Copynumber: 5.0 Consensus size: 22
114379 CCAGATCAGT
114389 ATACGACACAT-AAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
** *
114410 A-ACGACACACGAGGTGCCTG-
1 ATACGACACATAAAGTGCCTGA
*
114430 ATACGACACA-AGAGGTGCCTGA
1 ATACGACACATA-AAGTGCCTGA
114452 AGTACGACACATAAAGTGCCTGA
1 A-TACGACACATAAAGTGCCTGA
*
114475 TATACGACACATAAAGTGTCTGA
1 -ATACGACACATAAAGTGCCTGA
114498 TCGACAAAGC
Statistics
Matches: 76, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
20 9 0.12
21 26 0.34
22 1 0.01
23 38 0.50
24 2 0.03
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (22 bp):
ATACGACACATAAAGTGCCTGA
Found at i:115164 original size:26 final size:27
Alignment explanation
Indices: 115119--115170 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
115109 AAATCCCAAA
*
115119 TTTTCTTCCTTTCCTTCCCT-TTTTCT
1 TTTTCTTCCTTTCCTCCCCTGTTTTCT
115145 TTTTCTTTCCTTT-CTCCCCTGTTTTC
1 TTTTC-TTCCTTTCCTCCCCTGTTTTC
115171 GTTTGCCTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.00, C:0.35, G:0.02, T:0.63
Consensus pattern (27 bp):
TTTTCTTCCTTTCCTCCCCTGTTTTCT
Found at i:118735 original size:21 final size:21
Alignment explanation
Indices: 118711--118750 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
118701 GAAAAGTTCG
118711 TGTTAAGTGATAAAGGGTACC
1 TGTTAAGTGATAAAGGGTACC
118732 TGTTAAGTGATAAAGGGTA
1 TGTTAAGTGATAAAGGGTA
118751 AGTATGGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.05, G:0.30, T:0.30
Consensus pattern (21 bp):
TGTTAAGTGATAAAGGGTACC
Found at i:119796 original size:14 final size:14
Alignment explanation
Indices: 119774--119804 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
119764 GAACAAGGTA
119774 CATGAATATAATTG
1 CATGAATATAATTG
*
119788 CATGTATATAATTG
1 CATGAATATAATTG
119802 CAT
1 CAT
119805 CAAATCAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.39
Consensus pattern (14 bp):
CATGAATATAATTG
Found at i:122160 original size:16 final size:16
Alignment explanation
Indices: 122112--122166 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
122102 TATTATTTTT
*
122112 AATTAAAATATATAAA
1 AATTAAAATATAGAAA
*
122128 TATTGAAAATA-AGAAA
1 AATT-AAAATATAGAAA
122144 AATTAATAATATA-AAA
1 AATTAA-AATATAGAAA
*
122160 ATTTAAA
1 AATTAAA
122167 GTTATTTTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
15 3 0.09
16 22 0.69
17 7 0.22
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (16 bp):
AATTAAAATATAGAAA
Found at i:132679 original size:18 final size:20
Alignment explanation
Indices: 132642--132689 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
132632 GTACGTGCTC
132642 TATTTT-AATTTTGTTGATA
1 TATTTTAAATTTTGTTGATA
*
132661 T-TTTTAAATTTT-TTTATA
1 TATTTTAAATTTTGTTGATA
132679 TATTTATAAAT
1 TATTT-TAAAT
132690 AAAAATATAG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 10 0.40
19 10 0.40
20 5 0.20
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (20 bp):
TATTTTAAATTTTGTTGATA
Found at i:132697 original size:18 final size:17
Alignment explanation
Indices: 132676--132722 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
132666 AAATTTTTTT
132676 ATATATTTATAAATAAAA
1 ATATATTTATAAAT-AAA
*
132694 ATATAGTTT-TTAATAAA
1 ATATA-TTTATAAATAAA
132711 ATATATTATATA
1 ATATATT-TATA
132723 TGTAACTAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
16 2 0.08
17 9 0.38
18 10 0.42
19 3 0.12
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (17 bp):
ATATATTTATAAATAAA
Found at i:136839 original size:333 final size:333
Alignment explanation
Indices: 136233--137240 Score: 1890
Period size: 333 Copynumber: 3.0 Consensus size: 333
136223 CATTTTTTGT
* * *
136233 TAATCTATACTAACAAGTTTTAGGGAGCAGAACGCAAATAGGAAATTAGTAAGTAGCACCAAGAT
1 TAATCTATACTGACAAGTTTTAGGGAGCAGAACGCGAATAGGAAATTAGTAAGTAGCAACAAGAT
*
136298 GAGCCTTGGCTTGGAGTTTGATCTAGGGTATTCAAGTTTAAGATTGAGGCAAACATGGTATTCGT
66 GAGCCTTGGCTTGGAGTTTGATCTAGGGTATTCAAGTTTAAGATCGAGGCAAACATGGTATTCGT
** * *
136363 GATCTAAAATAATGGCTAGTGTTTTGTTGAAACAAGTGTGGAAAGACACAAGGGCATGCATTGAT
131 GATCTAAAATAATGGCTACAGTTTTGTTGAAAGAAGTGTGGACAGACACAAGGGCATGCATTGAT
136428 TTTGCTACTAGTTTCTTCATTTGTTGGTTTACTCCATTTGTCAATATTTTGATTAAAATGGGACC
196 TTTGCTACTAGTTTCTTCATTTGTTGGTTTACTCCATTTGTCAATATTTTGATTAAAATGGGACC
136493 ATATTCATTTGCTATTTGGAGTGACCCATTTTTGGAAAGTAAAGATGTTTGATATGAATAAAATA
261 ATATTCATTTGCTATTTGGAGTGACCCATTTTTGGAAAGTAAAGATGTTTGATATGAATAAAATA
136558 TAATAATA
326 TAATAATA
136566 TAATCTATACTGACAAGTTTTAGGGAGCAGAACGCGAATAGGAAATTAGTAAGTAGCAACAAGAT
1 TAATCTATACTGACAAGTTTTAGGGAGCAGAACGCGAATAGGAAATTAGTAAGTAGCAACAAGAT
136631 GAGCCTTGGCTTGGAGTTTGATCTAGGGTATTCAAGTTTAAGATCGAGGCAAACATGGTATTCGT
66 GAGCCTTGGCTTGGAGTTTGATCTAGGGTATTCAAGTTTAAGATCGAGGCAAACATGGTATTCGT
136696 GATCTAAAATAATGGCTACAGTTTTGTTGAAAGAAGTGTGGACAGACACAAGGGCATGCATTGAT
131 GATCTAAAATAATGGCTACAGTTTTGTTGAAAGAAGTGTGGACAGACACAAGGGCATGCATTGAT
136761 TTTGCTACTAGTTTCTTCATTTGTTGGTTTACTCCATTTGTCAATATTTTGATTAAAATGGGACC
196 TTTGCTACTAGTTTCTTCATTTGTTGGTTTACTCCATTTGTCAATATTTTGATTAAAATGGGACC
136826 ATATTCATTTGCTATTTGGAGTGACCCATTTTTGGAAAGTAAAGATGTTTGATATGAATAAAATA
261 ATATTCATTTGCTATTTGGAGTGACCCATTTTTGGAAAGTAAAGATGTTTGATATGAATAAAATA
136891 TAATAATA
326 TAATAATA
136899 TAATCTATACTGACAAGTTTTAGGGAGCAGAACGCGAATAGGAAATTAGTAAGTAGCAACAAGAT
1 TAATCTATACTGACAAGTTTTAGGGAGCAGAACGCGAATAGGAAATTAGTAAGTAGCAACAAGAT
*
136964 GAGCCTTGGCTTGGAGTTTGATCTAGGGTATTCAAGTTTAAGATCGAGGCAAACATGGTATTCAT
66 GAGCCTTGGCTTGGAGTTTGATCTAGGGTATTCAAGTTTAAGATCGAGGCAAACATGGTATTCGT
* *
137029 GATCTAAAATAATGGCTACAGTTTTGTTGAAAGAATTATGGACAGACACAAGGGCATGCATTGAT
131 GATCTAAAATAATGGCTACAGTTTTGTTGAAAGAAGTGTGGACAGACACAAGGGCATGCATTGAT
137094 TTTGCTACTAGTTTCTTCATTTGTTGGTTTACTCCATTTGTCAATATTTTGATTAAAAATGGGAC
196 TTTGCTACTAGTTTCTTCATTTGTTGGTTTACTCCATTTGTCAATATTTTGATT-AAAATGGGAC
*
137159 CATATTCATTTGCTATTTGGAGTGACCCATTTTTGGAAAATAAAGATGTTTGATATGAATAAAAT
260 CATATTCATTTGCTATTTGGAGTGACCCATTTTTGGAAAGTAAAGATGTTTGATATGAATAAAAT
*
137224 GTAATAATA
325 ATAATAATA
137233 TAATCTAT
1 TAATCTAT
137241 CTTACTTCTT
Statistics
Matches: 661, Mismatches: 13, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
333 571 0.86
334 90 0.14
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.34
Consensus pattern (333 bp):
TAATCTATACTGACAAGTTTTAGGGAGCAGAACGCGAATAGGAAATTAGTAAGTAGCAACAAGAT
GAGCCTTGGCTTGGAGTTTGATCTAGGGTATTCAAGTTTAAGATCGAGGCAAACATGGTATTCGT
GATCTAAAATAATGGCTACAGTTTTGTTGAAAGAAGTGTGGACAGACACAAGGGCATGCATTGAT
TTTGCTACTAGTTTCTTCATTTGTTGGTTTACTCCATTTGTCAATATTTTGATTAAAATGGGACC
ATATTCATTTGCTATTTGGAGTGACCCATTTTTGGAAAGTAAAGATGTTTGATATGAATAAAATA
TAATAATA
Found at i:139074 original size:6 final size:6
Alignment explanation
Indices: 139065--139097 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
139055 CCCCCCCAAA
139065 AAAAAG AAAAA- AAAAAG AAAAAAG AAAAAG AAA
1 AAAAAG AAAAAG AAAAAG -AAAAAG AAAAAG AAA
139098 TACTCCCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.20
6 14 0.56
7 6 0.24
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:139078 original size:11 final size:11
Alignment explanation
Indices: 139062--139097 Score: 54
Period size: 11 Copynumber: 3.1 Consensus size: 11
139052 CCCCCCCCCC
139062 AAAAAAAAGAA
1 AAAAAAAAGAA
139073 AAAAAAAAGAAA
1 AAAAAAAAG-AA
139085 AAAGAAAAAGAA
1 AAA-AAAAAGAA
139097 A
1 A
139098 TACTCCCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 9 0.39
12 8 0.35
13 6 0.26
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:148485 original size:50 final size:50
Alignment explanation
Indices: 148431--148532 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
148421 GTTAATCCTT
148431 GTATCTTGGCAACATTATATGTTGTTGGTTGACTATCTGACTACACTTCA
1 GTATCTTGGCAACATTATATGTTGTTGGTTGACTATCTGACTACACTTCA
148481 GTATCTTGGCAACATTATATGTTGTTGGTTGACTATCTGACTACACTTCA
1 GTATCTTGGCAACATTATATGTTGTTGGTTGACTATCTGACTACACTTCA
148531 GT
1 GT
148533 GCTGTAATCT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.40
Consensus pattern (50 bp):
GTATCTTGGCAACATTATATGTTGTTGGTTGACTATCTGACTACACTTCA
Found at i:154190 original size:45 final size:45
Alignment explanation
Indices: 154139--154226 Score: 167
Period size: 45 Copynumber: 2.0 Consensus size: 45
154129 AAGTAGAATG
154139 CTAATAAATGATATAGATTATGGTTATGGATGTAATCTTTTATTT
1 CTAATAAATGATATAGATTATGGTTATGGATGTAATCTTTTATTT
*
154184 CTAATAAATGATTTAGATTATGGTTATGGATGTAATCTTTTAT
1 CTAATAAATGATATAGATTATGGTTATGGATGTAATCTTTTAT
154227 GTAAGGTATA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.33, C:0.05, G:0.16, T:0.47
Consensus pattern (45 bp):
CTAATAAATGATATAGATTATGGTTATGGATGTAATCTTTTATTT
Found at i:163777 original size:2 final size:2
Alignment explanation
Indices: 163687--163762 Score: 134
Period size: 2 Copynumber: 38.0 Consensus size: 2
163677 GATAAGGAAT
* *
163687 AG AG AG AG AG AG AG TG AG TG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
163729 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
163763 TGGGTGAAAG
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.47, C:0.00, G:0.50, T:0.03
Consensus pattern (2 bp):
AG
Found at i:180270 original size:2 final size:2
Alignment explanation
Indices: 180263--180849 Score: 1156
Period size: 2 Copynumber: 293.5 Consensus size: 2
180253 GATAAGGAAT
* *
180263 AG AG AG AG AG AG AG TG AG TG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
180305 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
180347 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
180389 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
180431 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
180473 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
180515 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
180557 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
180599 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
180641 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
180683 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
180725 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
180767 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
180809 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
180850 TTGGTTGAAC
Statistics
Matches: 581, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
2 581 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:182277 original size:16 final size:15
Alignment explanation
Indices: 182250--182289 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
182240 AATACAAGAA
182250 AAATAAAGAAATAGAT
1 AAATAAA-AAATAGAT
*
182266 AAATGAAAAAATATAT
1 AAAT-AAAAAATAGAT
182282 AAATAAAA
1 AAATAAAA
182290 CAGAACAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 4 0.18
16 15 0.68
17 3 0.14
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.20
Consensus pattern (15 bp):
AAATAAAAAATAGAT
Found at i:184357 original size:6 final size:7
Alignment explanation
Indices: 184340--184365 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
184330 GGAAGTAGAT
184340 AAAAAAG
1 AAAAAAG
184347 AAAAAAG
1 AAAAAAG
184354 AAAAAAG
1 AAAAAAG
184361 AAAAA
1 AAAAA
184366 CATTCCGGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:185496 original size:2 final size:2
Alignment explanation
Indices: 185491--185530 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
185481 TTTTAAAGCG
185491 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
185531 TATGATATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:191187 original size:13 final size:12
Alignment explanation
Indices: 191153--191218 Score: 55
Period size: 13 Copynumber: 5.3 Consensus size: 12
191143 AAAGAATGTT
*
191153 AAAAA-AAAACA
1 AAAAAGAAAAGA
*
191164 AACAAAAAAAAGA
1 AA-AAAGAAAAGA
191177 AGAAAAGAAAAGA
1 A-AAAAGAAAAGA
191190 AAAGAAGAAAAGGA
1 AAA-AAGAAAA-GA
*
191204 AAATA-AAAAGA
1 AAAAAGAAAAGA
191215 AAAA
1 AAAA
191219 GGAGAGGCCA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
11 7 0.15
12 9 0.20
13 24 0.52
14 6 0.13
ACGTcount: A:0.82, C:0.03, G:0.14, T:0.02
Consensus pattern (12 bp):
AAAAAGAAAAGA
Found at i:191192 original size:18 final size:18
Alignment explanation
Indices: 191167--191217 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
191157 AAAAACAAAC
191167 AAAAAAAAGAAGAAAA-G
1 AAAAAAAAGAAGAAAAGG
191184 AAAAGAAAAGAAGAAAAGG
1 AAAA-AAAAGAAGAAAAGG
*
191203 AAAATAAA-AAGAAAA
1 AAAAAAAAGAAGAAAA
191218 AGGAGAGGCC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 11 0.35
18 15 0.48
19 5 0.16
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (18 bp):
AAAAAAAAGAAGAAAAGG
Found at i:191688 original size:108 final size:103
Alignment explanation
Indices: 191482--191697 Score: 281
Period size: 108 Copynumber: 2.0 Consensus size: 103
191472 GGGCACATGC
* * * * * **
191482 TTTCATCTTATTCATTTTGTATTTTAGCAAAATTTGCTATCTTGATTATTTATTTCGAGCTTTTT
1 TTTCATCTTATTCATTTTGAATCTTAGCAAAATTTGCTATCCTGATTATTTATTTAGAGCTCTGC
191547 TCTCAATAAAATTCCATCTTGTCCATTGTGATAATCCT
66 TCTCAATAAAATTCCATCTTGTCCATTGTGATAATCCT
*
191585 TTTCATCTTATTCATTTTGAATCTTAGCAAAATTTTCTATCCTGATTAATTTATTTGTTTAGAGC
1 TTTCATCTTATTCATTTTGAATCTTAGCAAAATTTGCTATCCTGATT-ATTTA----TTTAGAGC
* *
191650 TCTGCTCTCAATAAAATTTCATCTT-TCCCATTGTGATAATCTT
61 TCTGCTCTCAATAAAATTCCATCTTGT-CCATTGTGATAATCCT
191693 TTTCA
1 TTTCA
191698 AGCATTTTTC
Statistics
Matches: 97, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
103 43 0.44
104 5 0.05
107 1 0.01
108 48 0.49
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.50
Consensus pattern (103 bp):
TTTCATCTTATTCATTTTGAATCTTAGCAAAATTTGCTATCCTGATTATTTATTTAGAGCTCTGC
TCTCAATAAAATTCCATCTTGTCCATTGTGATAATCCT
Found at i:192604 original size:44 final size:44
Alignment explanation
Indices: 192537--192649 Score: 138
Period size: 44 Copynumber: 2.6 Consensus size: 44
192527 TCATATCAAG
* * *
192537 TCCTATCTCCCTGAGCAGCAGTGGAATAGGTT-GAAGATTACAGA
1 TCCTATCTCCCTAAGCAGTAGTGGAATAGGTTAG-AGATAACAGA
* *
192581 TCCTATCTCCTTAAGCAGTAGTGGAGTAGGTTAGAGATAACAGA
1 TCCTATCTCCCTAAGCAGTAGTGGAATAGGTTAGAGATAACAGA
* **
192625 TCTTATCTCCCTAAATAGTAGTGGA
1 TCCTATCTCCCTAAGCAGTAGTGGA
192650 GCAGATCGAA
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
44 58 0.98
45 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (44 bp):
TCCTATCTCCCTAAGCAGTAGTGGAATAGGTTAGAGATAACAGA
Found at i:192807 original size:44 final size:44
Alignment explanation
Indices: 192759--193346 Score: 372
Period size: 44 Copynumber: 13.7 Consensus size: 44
192749 TTGTAAATCC
* **
192759 TATCTCCCTGAACTTGCAGTGGAGTGGATTAAAACCACAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCT
* * * *** *
192803 TATCTCTCTGAAGTTGCAGTAGATCAGA-TCGCATC-CAG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCT
** * *
192844 TATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGA-AATCA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA-ACCA-CAGATCT
* * * *
192888 TATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACAACATATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCT
* * * *** *
192932 TATCTCTCTGAAGTTGCAGTAGAGGAGA-TCGCATC-CAG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCT
* ** *
192973 TATCTCCCTGAAGTTGCAGTGGAGCAGA-CAAAAGAAACTA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAA-CCAC-AGATCT
* *
193017 TATCTCTCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCT
** * ** * * * *
193061 TATCTCTTTGAAGTTACAGTAAAGCATA-TCACATC-CA-ATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCT
** * *
193102 TATCTCCCTGAAGTTGCAGTGGAGCAGACGAAATA-AACTA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA-ACCAC-AGATCT
* * *
193146 TATCTCCCTGAAATTGAAGTGGAGCAGATTAAAGCCACAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCT
* * * *** *
193190 TATCTCTCTGAAGTTGCAGTAGAACAGA-TCGCATCA-AG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCT
** * ** * *
193231 TATCTCCCT-AAGCAGTAGTGGAGCAGACAGAAGAAAC-CA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAA-AACCACAGATCT
**
193274 TATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCACAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCT
* *
193318 TATCTCTCTGAAGTTGCAGTAGAGCAGAT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGAT
193347 CGCATCCAAT
Statistics
Matches: 404, Mismatches: 113, Indels: 54
0.71 0.20 0.09
Matches are distributed among these distances:
40 13 0.03
41 94 0.23
42 13 0.03
43 39 0.10
44 241 0.60
45 4 0.01
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.26
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCT
Found at i:192854 original size:85 final size:85
Alignment explanation
Indices: 192754--193402 Score: 385
Period size: 85 Copynumber: 7.6 Consensus size: 85
192744 GAAGATTGTA
* * * * *
192754 AATCCTATCTCCCTGAACTTGCAGTGGAGTGGATTAAAACCACAGATCTTATCTCTCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGACTAAAACCACAGATCTTATCTCCCTGAAGTTG
* * *
192819 CAGTAGATCAGATCGCATCC
66 CAGTAGAGCAGATCGAAACC
* * * * * *
192839 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGA-AATCA-ATCCTATCTCCCTAAAGT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGACTAAA-ACCA-CAGATCTTATCTCCCTGAAGT
* * **
192902 TGCAGTGGAGCGGATTAAAACAAC
64 TGCAGTAGAGCAGATCGAAAC--C
* * *** *
192926 ATATCTTATCTCTCTGAAGTTGCAGTAGAG-GAGA-TCGCATC-CAG-TCTTATCTCCCTGAAGT
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCG-GACTAAAACCACAGATCTTATCTCCCTGAAGT
* *
192987 TGCAGTGGAGCAGA-CAAAAGAAACT
64 TGCAGTAGAGCAGATC----GAAACC
* * * ** *
193012 AATCCTATCTCTCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTTTGAAGTTA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGACTAAAACCACAGATCTTATCTCCCTGAAGTTG
* * *
193077 CAGTAAAGCATATC-ACATCC
66 CAGTAGAGCAGATCGA-AACC
* * * * *
193097 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAATA-AACTA-ATCCTATCTCCCTGAAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGACTAAA-ACCAC-AGATCTTATCTCCCTGAAGT
* * *
193160 TGAAGTGGAGCAGAT-TAAAGCCAC
64 TGCAGTAGAGCAGATCGAAA--C-C
* * * * *** * **
193184 AGATCTTATCTCTCTGAAGTTGCAGTAGAACAGA-TCGCATCA-AG-TCTTATCTCCCT-AAGCA
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCGGACTAAAACCACAGATCTTATCTCCCTGAAGTT
* *
193245 GTAGTGGAGCAGACAGA-AGAAACC
65 GCAGT--AG-AG-CAGATCGAAACC
* * * *
193269 AATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCACAGATCTTATCTCTCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGACTAAAACCACAGATCTTATCTCCCTGAAGTTG
* *
193334 CAGTAGAGCAGATCGCATCC
66 CAGTAGAGCAGATCGAAACC
* * * * * * *
193354 AATCCTATCTCTCTGAGGATGTAGTGGAGTGGACTAAAACCACAAATCT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGACTAAAACCACAGATCT
193403 CGTCCTCCTA
Statistics
Matches: 426, Mismatches: 101, Indels: 74
0.71 0.17 0.12
Matches are distributed among these distances:
84 38 0.09
85 248 0.58
86 19 0.04
87 21 0.05
88 99 0.23
89 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.26
Consensus pattern (85 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGACTAAAACCACAGATCTTATCTCCCTGAAGTTG
CAGTAGAGCAGATCGAAACC
Found at i:192888 original size:129 final size:129
Alignment explanation
Indices: 192754--193369 Score: 923
Period size: 129 Copynumber: 4.8 Consensus size: 129
192744 GAAGATTGTA
* *
192754 AATCCTATCTCCCTGAACTTGCAGTGGAGTGGATTAAAACCACAGATCTTATCTCTCTGAAGTTG
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTG
*
192819 CAGTAGATCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGAAA-T
66 CAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGAAACT
* * *
192882 CAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACAACATATCTTATCTCTCTGAAGTT
1 -AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTT
* *
192947 GCAGTAGAGGAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACT
65 GCAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGAAACT
* * *
193012 AATCCTATCTCTCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTTTGAAGTTA
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTG
* * * * *
193077 CAGTAAAGCATATCACATCCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAATAAACT
66 CAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGAAACT
* * * *
193141 AATCCTATCTCCCTGAAATTGAAGTGGAGCAGATTAAAGCCACAGATCTTATCTCTCTGAAGTTG
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTG
* * ** * *
193206 CAGTAGAACAGATCGCATCAAGTCTTATCTCCCT-AAGCAGTAGTGGAGCAGAC-AGAAGAAACC
66 CAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGA-AAGAAACT
*
193269 AATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCACAGATCTTATCTCTCTGAAGTTG
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTG
* * *
193334 CAGTAGAGCAGATCGCATCCAATCCTATCTCTCTGA
66 CAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGA
193370 GGATGTAGTG
Statistics
Matches: 435, Mismatches: 49, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
127 1 0.00
128 111 0.26
129 322 0.74
130 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (129 bp):
AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTG
CAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGAAACT
Found at i:193433 original size:85 final size:85
Alignment explanation
Indices: 193267--193426 Score: 214
Period size: 85 Copynumber: 1.9 Consensus size: 85
193257 ACAGAAGAAA
* * * * *
193267 CCAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCACAGATCTTATCTCTCTGAAGT
1 CCAATCCTATCTCCCTGAAGATGCAGTGGAGTGGACTAAAACCACAAATCTCATCTCTCTAAAGT
*
193332 TGCAGTAGAGCAGATCGCAT
66 TGCAGCAGAGCAGATCGCAT
* * * *
193352 CCAATCCTATCTCTCTGAGGATGTAGTGGAGTGGACTAAAACCACAAATCTCGTC-CTCCTAAAG
1 CCAATCCTATCTCCCTGAAGATGCAGTGGAGTGGACTAAAACCACAAATCTCATCTCT-CTAAAG
193416 TTGCAGCAGAG
65 TTGCAGCAGAG
193427 TGGATCGAAG
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
84 2 0.03
85 62 0.97
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (85 bp):
CCAATCCTATCTCCCTGAAGATGCAGTGGAGTGGACTAAAACCACAAATCTCATCTCTCTAAAGT
TGCAGCAGAGCAGATCGCAT
Found at i:194118 original size:2 final size:2
Alignment explanation
Indices: 194113--194156 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
194103 TTTTTTAAAG
*
194113 CA CA CA CA CA CA CA TA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
194155 CA
1 CA
194157 NNNNNNNNNN
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.48, G:0.00, T:0.02
Consensus pattern (2 bp):
CA
Found at i:200477 original size:9 final size:9
Alignment explanation
Indices: 200458--200488 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
200448 TGTTATGTGT
200458 TTATT-TTA
1 TTATTGTTA
200466 TTATTGTTA
1 TTATTGTTA
200475 TTATTGTTA
1 TTATTGTTA
200484 TTATT
1 TTATT
200489 CATTAATGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 5 0.23
9 17 0.77
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (9 bp):
TTATTGTTA
Found at i:202973 original size:29 final size:30
Alignment explanation
Indices: 202930--202988 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
202920 GCTTTTTAAG
* *
202930 GATTTTTTTA-TTTTTTATTTTATTATCATC
1 GATTTTTTTAGTTTTTT-TATAATTATCATC
202960 GATTTTTTT-GTTTTTTTATAATTATCATC
1 GATTTTTTTAGTTTTTTTATAATTATCATC
202989 ATCATCATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.20, C:0.07, G:0.05, T:0.68
Consensus pattern (30 bp):
GATTTTTTTAGTTTTTTTATAATTATCATC
Found at i:202990 original size:32 final size:30
Alignment explanation
Indices: 202930--202991 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 30
202920 GCTTTTTAAG
* *
202930 GATTTTTTTATTTTTTATTTTATTATCATC
1 GATTTTTTTATTTTTTATATTATCATCATC
*
202960 GATTTTTTTGTTTTTTTATAATTATCATCATC
1 GATTTTTTT-ATTTTTTAT-ATTATCATCATC
202992 ATCATCATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 9 0.33
31 8 0.30
32 10 0.37
ACGTcount: A:0.21, C:0.08, G:0.05, T:0.66
Consensus pattern (30 bp):
GATTTTTTTATTTTTTATATTATCATCATC
Found at i:203007 original size:3 final size:3
Alignment explanation
Indices: 203001--203031 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
202991 CATCATCATC
203001 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
203032 CAGCCTCAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:209667 original size:16 final size:16
Alignment explanation
Indices: 209646--209717 Score: 108
Period size: 16 Copynumber: 4.5 Consensus size: 16
209636 CGTTTGGTTT
209646 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
209662 GCTGTAATTGAATAGA
1 GCTGTAATGGAATAGA
*
209678 GCTGTAATTGAATAGA
1 GCTGTAATGGAATAGA
*
209694 GCTATAATGGAATAGA
1 GCTGTAATGGAATAGA
*
209710 ACTGTAAT
1 GCTGTAAT
209718 AGTAATTCAA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.29
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:209757 original size:45 final size:44
Alignment explanation
Indices: 209699--209791 Score: 143
Period size: 44 Copynumber: 2.1 Consensus size: 44
209689 ATAGAGCTAT
209699 AATGGAATAGAACTGTAATAGTAATTCAAT-TGTTTGGTTGAATGA
1 AATGGAATAGAACTGTAATAGT-ATTC-ATGTGTTTGGTTGAATGA
* *
209744 AATGGAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGTATTCATGTGTTTGGTTGAATGA
209788 AATG
1 AATG
209792 ATGTCGTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
43 1 0.02
44 22 0.49
45 22 0.49
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.37
Consensus pattern (44 bp):
AATGGAATAGAACTGTAATAGTATTCATGTGTTTGGTTGAATGA
Found at i:209972 original size:18 final size:18
Alignment explanation
Indices: 209949--210080 Score: 111
Period size: 18 Copynumber: 7.8 Consensus size: 18
209939 TTATTATTAA
209949 ATATAATTTAATAATAAT
1 ATATAATTTAATAATAAT
209967 ATATAATTTAATAA-AAT
1 ATATAATTTAATAATAAT
*
209984 ATATGAATTTACTAA-AAT
1 ATAT-AATTTAATAATAAT
* * *
210002 -CATAATAT-ATAATACT
1 ATATAATTTAATAATAAT
* * *
210018 ATAAAATATAAT-TTAA-
1 ATATAATTTAATAATAAT
* *
210034 A-ATAA-TTATTATTAA-
1 ATATAATTTAATAATAAT
210049 ATATAATTTAATAATAAT
1 ATATAATTTAATAATAAT
210067 ATATAATTTAATAA
1 ATATAATTTAATAA
210081 AATTCAATAT
Statistics
Matches: 92, Mismatches: 14, Indels: 16
0.75 0.11 0.13
Matches are distributed among these distances:
14 3 0.03
15 11 0.12
16 11 0.12
17 25 0.27
18 42 0.46
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (18 bp):
ATATAATTTAATAATAAT
Found at i:211497 original size:38 final size:38
Alignment explanation
Indices: 211438--211512 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
211428 GGTTGAGGAA
*
211438 AGGGAAAAAAAGGCAATTACTTTACCAAAATGGATCCC
1 AGGGAAAAAAAGGCAACTACTTTACCAAAATGGATCCC
*
211476 AGGG-AAAAAAGAGTAACTACTTTACCAAAATGGATCC
1 AGGGAAAAAAAG-GCAACTACTTTACCAAAATGGATCC
211513 TAATACAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
37 7 0.21
38 27 0.79
ACGTcount: A:0.45, C:0.17, G:0.19, T:0.19
Consensus pattern (38 bp):
AGGGAAAAAAAGGCAACTACTTTACCAAAATGGATCCC
Found at i:213302 original size:88 final size:88
Alignment explanation
Indices: 212969--213277 Score: 618
Period size: 88 Copynumber: 3.5 Consensus size: 88
212959 AGAGTAGTTA
212969 AATACACAAACTTGTAGGTCTTGGAGACCCCATCGAACAACATCAGGATCTAAATCACATGTAAG
1 AATACACAAACTTGTAGGTCTTGGAGACCCCATCGAACAACATCAGGATCTAAATCACATGTAAG
213034 CATTATTAAAACTTCAAAGGTTT
66 CATTATTAAAACTTCAAAGGTTT
213057 AATACACAAACTTGTAGGTCTTGGAGACCCCATCGAACAACATCAGGATCTAAATCACATGTAAG
1 AATACACAAACTTGTAGGTCTTGGAGACCCCATCGAACAACATCAGGATCTAAATCACATGTAAG
213122 CATTATTAAAACTTCAAAGGTTT
66 CATTATTAAAACTTCAAAGGTTT
213145 AATACACAAACTTGTAGGTCTTGGAGACCCCATCGAACAACATCAGGATCTAAATCACATGTAAG
1 AATACACAAACTTGTAGGTCTTGGAGACCCCATCGAACAACATCAGGATCTAAATCACATGTAAG
213210 CATTATTAAAACTTCAAAGGTTT
66 CATTATTAAAACTTCAAAGGTTT
213233 AATACACAAACTTGTAGGTCTTGGAGACCCCATCGAACAACATCA
1 AATACACAAACTTGTAGGTCTTGGAGACCCCATCGAACAACATCA
213278 CAGATTATTG
Statistics
Matches: 221, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 221 1.00
ACGTcount: A:0.39, C:0.21, G:0.15, T:0.25
Consensus pattern (88 bp):
AATACACAAACTTGTAGGTCTTGGAGACCCCATCGAACAACATCAGGATCTAAATCACATGTAAG
CATTATTAAAACTTCAAAGGTTT
Found at i:217394 original size:44 final size:45
Alignment explanation
Indices: 217345--217435 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
217335 ACCTCTATTC
*
217345 CATTCAACCAAACACAAGA-TTACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTTACTATTACACCTCTATTCCATTA
*** * *
217389 CATTCAACCAAACAGTTGATTTGCTATTATACCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTTACTATTACACCTCTATTCCATTA
217434 CA
1 CA
217436 CCTCTATTCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 16 0.40
45 24 0.60
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.33
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTTACTATTACACCTCTATTCCATTA
Found at i:217475 original size:16 final size:16
Alignment explanation
Indices: 217419--217483 Score: 85
Period size: 16 Copynumber: 4.1 Consensus size: 16
217409 TTGCTATTAT
* *
217419 ACCTCTATTCCATTAC
1 ACCTCTAATCCAATAC
* *
217435 ACCTCTATTCCAGTAC
1 ACCTCTAATCCAATAC
217451 ACCTCTAATCCAATAC
1 ACCTCTAATCCAATAC
*
217467 ACCTATAATCCAATAC
1 ACCTCTAATCCAATAC
217483 A
1 A
217484 GCGAACCAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.34, C:0.35, G:0.02, T:0.29
Consensus pattern (16 bp):
ACCTCTAATCCAATAC
Found at i:219538 original size:109 final size:107
Alignment explanation
Indices: 219349--219677 Score: 471
Period size: 109 Copynumber: 3.0 Consensus size: 107
219339 TGGATTAAGA
* * *
219349 TTTAAGAGGATATTCGGCTATTTGGTCCAACGAG-AAATCGAAACCCAGCACATTAGGGCACGTT
1 TTTAAAAGGATATTTGGC-ATTTGGTCGAACGAGAAAATCGAAACCCAGCACATTAGGGCACGTT
*
219413 TTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATT
65 TTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAAT
* * *
219456 TTTAAAAGGATATTTGGCAATTTGATCGGACGAGAAAAATCGAAACCCAGCACATTAGGGCACAT
1 TTTAAAAGGATATTTGGC-ATTTGGTCGAACGAG-AAAATCGAAACCCAGCACATTAGGGCACGT
*
219521 TTTCTCGAATTTCCAAACGCAAAACATTGTCTTATTTTGAAAAT
64 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAAT
* *
219565 TTTAAAAGGATATTTGGTCATTTGGTCGAATGAGAGAAATCGAAACCCAGCATATTAGGGCACGT
1 TTTAAAAGGATATTTGG-CATTTGGTCGAACGAGA-AAATCGAAACCCAGCACATTAGGGCACGT
* * * *
219630 TTTCTCGAATTTTCAAACGCAAAATATTGCCTTACTTAGAAAAAT
64 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTG-AAAAT
219675 TTT
1 TTT
219678 CCTTTTTGAA
Statistics
Matches: 198, Mismatches: 19, Indels: 7
0.88 0.08 0.03
Matches are distributed among these distances:
107 28 0.14
108 1 0.01
109 160 0.81
110 9 0.05
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (107 bp):
TTTAAAAGGATATTTGGCATTTGGTCGAACGAGAAAATCGAAACCCAGCACATTAGGGCACGTTT
TCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAAT
Found at i:220128 original size:18 final size:18
Alignment explanation
Indices: 220092--220130 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
220082 ATGTATGTAG
* *
220092 ATATATATAGATTATAAA
1 ATATATATAGATAAAAAA
*
220110 ATATATATATATAAAAAA
1 ATATATATAGATAAAAAA
220128 ATA
1 ATA
220131 CAATTATGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
ATATATATAGATAAAAAA
Found at i:220247 original size:16 final size:17
Alignment explanation
Indices: 220226--220261 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
220216 ATAACGTATA
*
220226 TATATAAATTATA-AAG
1 TATATAAAGTATAGAAG
220242 TATATAAAGTATAGAAG
1 TATATAAAGTATAGAAG
220259 TAT
1 TAT
220262 GCATATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.36
Consensus pattern (17 bp):
TATATAAAGTATAGAAG
Found at i:220290 original size:29 final size:29
Alignment explanation
Indices: 220258--220313 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
220248 AAGTATAGAA
220258 GTATGCATATAT-ATATAAATCAAAAATAT
1 GTATGCATATATAAT-TAAATCAAAAATAT
* *
220287 GTATGTATATATAATTAAATCTAAAAT
1 GTATGCATATATAATTAAATCAAAAAT
220314 TTAAAAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 22 0.92
30 2 0.08
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (29 bp):
GTATGCATATATAATTAAATCAAAAATAT
Found at i:221871 original size:18 final size:18
Alignment explanation
Indices: 221830--221877 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
221820 TACGAAAAAT
* * *
221830 ATAATAATAATGGTATTG
1 ATAATAATAATAGTAATA
*
221848 ACAATAATAATAGTAATA
1 ATAATAATAATAGTAATA
221866 ATAATAATAATA
1 ATAATAATAATA
221878 TTTTGAAAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.56, C:0.02, G:0.08, T:0.33
Consensus pattern (18 bp):
ATAATAATAATAGTAATA
Found at i:222520 original size:17 final size:18
Alignment explanation
Indices: 222498--222532 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
222488 GGGTCAGGCC
222498 TTTTTTG-CTATTTTCTT
1 TTTTTTGCCTATTTTCTT
*
222515 TTTTTTGCCTCTTTTCTT
1 TTTTTTGCCTATTTTCTT
222533 GGGTTGCCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.03, C:0.17, G:0.06, T:0.74
Consensus pattern (18 bp):
TTTTTTGCCTATTTTCTT
Found at i:223094 original size:30 final size:30
Alignment explanation
Indices: 223048--223127 Score: 101
Period size: 29 Copynumber: 2.7 Consensus size: 30
223038 TAGGAATTTT
*
223048 AGGATCAAAATGTAATTTTAAATAAGTTGAG
1 AGGATCAAAATATAATTTTAAA-AAGTTGAG
* * *
223079 -GGATTAAAATATAATTTTAAAAATTTTAG
1 AGGATCAAAATATAATTTTAAAAAGTTGAG
223108 AGG-TCAAAATATAATTTTAA
1 AGGATCAAAATATAATTTTAA
223128 GAAAATTAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
29 22 0.51
30 21 0.49
ACGTcount: A:0.47, C:0.03, G:0.14, T:0.36
Consensus pattern (30 bp):
AGGATCAAAATATAATTTTAAAAAGTTGAG
Found at i:223153 original size:30 final size:29
Alignment explanation
Indices: 223082--223156 Score: 96
Period size: 30 Copynumber: 2.6 Consensus size: 29
223072 AGTTGAGGGA
* * *
223082 TTAAAATATAATTTTAAAAATTTTAGAGG
1 TTAAAATATAATTTTAAAAAATTAAAAGG
*
223111 TCAAAATATAATTTTAAGAAAATTAAAAGG
1 TTAAAATATAATTTTAA-AAAATTAAAAGG
*
223141 TTAAAATGTAATTTTA
1 TTAAAATATAATTTTA
223157 TATTTTTGGA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 16 0.41
30 23 0.59
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.39
Consensus pattern (29 bp):
TTAAAATATAATTTTAAAAAATTAAAAGG
Found at i:224133 original size:7 final size:7
Alignment explanation
Indices: 224122--224188 Score: 98
Period size: 7 Copynumber: 9.6 Consensus size: 7
224112 ATAAATATAT
*
224122 ATTTTTT
1 ATTTTTA
224129 ATTTTTA
1 ATTTTTA
*
224136 TTTTTTA
1 ATTTTTA
224143 ATTTTTA
1 ATTTTTA
224150 ATTTTTA
1 ATTTTTA
*
224157 TTTTTTA
1 ATTTTTA
224164 ATTTTTA
1 ATTTTTA
224171 ATTTTTA
1 ATTTTTA
*
224178 ATTTTAA
1 ATTTTTA
224185 ATTT
1 ATTT
224189 CGGGCTTGTT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 54 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (7 bp):
ATTTTTA
Found at i:226127 original size:5 final size:5
Alignment explanation
Indices: 226117--226141 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
226107 TAAAGCAAAT
226117 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
226142 ATTTAAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:230376 original size:16 final size:17
Alignment explanation
Indices: 230344--230378 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
230334 TTAGGAGAAA
*
230344 AATAAAATGTTTTAGGG
1 AATAAAATGTTTGAGGG
230361 AATAAAA-GTTTGAGGG
1 AATAAAATGTTTGAGGG
230377 AA
1 AA
230379 AGTAAATAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.46, C:0.00, G:0.26, T:0.29
Consensus pattern (17 bp):
AATAAAATGTTTGAGGG
Found at i:230745 original size:9 final size:9
Alignment explanation
Indices: 230731--230767 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
230721 TATAGTTTGA
230731 TATTCGAAT
1 TATTCGAAT
230740 TATTCGAAT
1 TATTCGAAT
*
230749 TATTCGAGT
1 TATTCGAAT
230758 TATTCGAAT
1 TATTCGAAT
230767 T
1 T
230768 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:233887 original size:34 final size:34
Alignment explanation
Indices: 233849--233916 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
233839 TAATAAAAAA
233849 AACTGAAATTTGTATGGAGCAATGCTTAAAGGGT
1 AACTGAAATTTGTATGGAGCAATGCTTAAAGGGT
233883 AACTGAAATTTGTATGGAGCAATGCTTAAAGGGT
1 AACTGAAATTTGTATGGAGCAATGCTTAAAGGGT
233917 TTTTTTTTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.35, C:0.09, G:0.26, T:0.29
Consensus pattern (34 bp):
AACTGAAATTTGTATGGAGCAATGCTTAAAGGGT
Found at i:234621 original size:74 final size:75
Alignment explanation
Indices: 234515--234661 Score: 260
Period size: 74 Copynumber: 2.0 Consensus size: 75
234505 ATTGGATTTT
* * *
234515 AAAAGAAAGAGATCATGCCCAGTAAGTTAGGACACGATCTTTTCTTAATTCCCGAGATCATTTAA
1 AAAAAAAAGAGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTAAATTCCCGAGATCATTTAA
234580 AACTTGAGGA
66 AACTTGAGGA
234590 AAAAAAAAG-GATCATGCCCAGTAAGTTAGGACACGATCTCTTCTAAATTCCCGAGATCATTTAA
1 AAAAAAAAGAGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTAAATTCCCGAGATCATTTAA
234654 AACTTGAG
66 AACTTGAG
234662 CTTGAAAAGA
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
74 61 0.88
75 8 0.12
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (75 bp):
AAAAAAAAGAGATCATGCCCAGTAAGTTAGGACACGATCTCTTCTAAATTCCCGAGATCATTTAA
AACTTGAGGA
Found at i:235220 original size:23 final size:25
Alignment explanation
Indices: 235176--235227 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 25
235166 TTACAAAAGT
*
235176 TAAAAATATGTTCGTATATATATTA
1 TAAAAATATGTTCATATATATATTA
235201 TAAAAATATG-T-ATATATATATTA
1 TAAAAATATGTTCATATATATATTA
235224 TAAA
1 TAAA
235228 GTACAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 15 0.58
24 1 0.04
25 10 0.38
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (25 bp):
TAAAAATATGTTCATATATATATTA
Found at i:235306 original size:12 final size:12
Alignment explanation
Indices: 235291--235399 Score: 50
Period size: 12 Copynumber: 9.2 Consensus size: 12
235281 TAAACGGGTA
235291 AATAAAAATAAT
1 AATAAAAATAAT
**
235303 AAT-AAGGTAAGT
1 AATAAAAATAA-T
235315 AATACTAAAA-AAT
1 AATA--AAAATAAT
*
235328 -ACAAAAATAAT
1 AATAAAAATAAT
** *
235339 GCTAATAATAAT
1 AATAAAAATAAT
235351 AAT---AATAAT
1 AATAAAAATAAT
* *
235360 AATAATAGTAAT
1 AATAAAAATAAT
*
235372 AATAAAACTAAT
1 AATAAAAATAAT
*
235384 TATAAATAATAAT
1 AATAAA-AATAAT
235397 AAT
1 AAT
235400 GATAATGGGA
Statistics
Matches: 71, Mismatches: 16, Indels: 19
0.67 0.15 0.18
Matches are distributed among these distances:
9 9 0.13
10 4 0.06
11 8 0.11
12 38 0.54
13 8 0.11
14 2 0.03
15 2 0.03
ACGTcount: A:0.63, C:0.04, G:0.05, T:0.28
Consensus pattern (12 bp):
AATAAAAATAAT
Found at i:235349 original size:3 final size:3
Alignment explanation
Indices: 235341--235405 Score: 78
Period size: 3 Copynumber: 21.3 Consensus size: 3
235331 AAAATAATGC
* *
235341 TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA -AA CTAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA
*
235386 TAAA TAA TAA TAA TGA TAA T
1 T-AA TAA TAA TAA TAA TAA T
235406 GGGACTAAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.04
3 47 0.89
4 4 0.08
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:236081 original size:13 final size:14
Alignment explanation
Indices: 236063--236091 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
236053 TTGCTATTAC
236063 AAAAC-AAAATAGA
1 AAAACAAAAATAGA
236076 AAAACAAAAATAGA
1 AAAACAAAAATAGA
236090 AA
1 AA
236092 TAGAAATGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.79, C:0.07, G:0.07, T:0.07
Consensus pattern (14 bp):
AAAACAAAAATAGA
Found at i:237522 original size:89 final size:89
Alignment explanation
Indices: 237365--238073 Score: 920
Period size: 89 Copynumber: 8.0 Consensus size: 89
237355 CTGCAGACTA
* * * *
237365 TGGTGTCTTCAATCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTGCTATCTTCAGTCTGTTTC
1 TGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCC
237430 GCTGTCAGTACAGGAAGGCAAGGC
66 GCTGTCAGTACAGGAAGGCAAGGC
* * * * *
237454 TGGTGTCTTCGATCTGCTTCGCTGTCAGTACAAGAAGGCAAGATCTACTATTTTTAGTCTTCTCC
1 TGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCC
*
237519 GCTGTCAGTACAGGAAGGCAAAGC
66 GCTGTCAGTACAGGAAGGCAAGGC
* * * *
237543 TGGTGTATTCGATCTACTTCGCTGTAAGTACAGGAAGGCAATATCTGCTATCTTCAGTCTGCTCC
1 TGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCC
* *
237608 GCTATCAGTACAGGAAGGCAAGAC
66 GCTGTCAGTACAGGAAGGCAAGGC
** * *
237632 TGGTGTCTTCGATCTGCTTCGCCATCAGTATAGGAAGGCAAGATCTGTTATCTTCAGTCTGCTCC
1 TGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCC
237697 GCTGTCAGTACAGGAAGGCAAGGC
66 GCTGTCAGTACAGGAAGGCAAGGC
* * * * * **
237721 TGATGTTTTCGATTTACTTCGCCGTCAGTACAGGAAGGCAAGATCTATTATCTTCAGTCTGCTCC
1 TGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCC
*
237786 GCTGTCAGTAAAGGAAGGCAAGGC
66 GCTGTCAGTACAGGAAGGCAAGGC
* *
237810 TGGTGTCTTCGATCTGCTTCACCGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCC
1 TGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCC
*
237875 GCTGTCAGTACAGGAAGACAAGGC
66 GCTGTCAGTACAGGAAGGCAAGGC
* * * * *
237899 TGGTGTCTTTGATCTTCTTCGTTGTCAATACAGGAATGCAAGATCTGCTATCTTCAGTCTGCTCC
1 TGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCC
* * **
237964 ACTATCAGTACAGGAAGGCAATATC
66 GCTGTCAGTACAGGAAGGCAA-GGC
* * * * * * * * *
237989 TGCTATCTTC-AGTCTGCTCCGCTGTCAGTA-AGGAAGGCAAG-GCTGGTGTCTTTAATCTGCTT
1 TGGTGTCTTCGA-TCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTC
* *
238051 CACTGTCAGTACATGAAGGCAAG
65 CGCTGTCAGTACAGGAAGGCAAG
238074 ATCTGCTATC
Statistics
Matches: 540, Mismatches: 78, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
88 35 0.06
89 483 0.89
90 22 0.04
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (89 bp):
TGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCC
GCTGTCAGTACAGGAAGGCAAGGC
Found at i:239324 original size:6 final size:6
Alignment explanation
Indices: 239315--239400 Score: 108
Period size: 6 Copynumber: 14.7 Consensus size: 6
239305 TGACCTCTCC
239315 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT-T TTCTT-T
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TT-TTCT
* *
239362 TCTTCAT CTTT-T TTTTCT TTTTCT TTTT-T TTTTCT TTTT
1 TTTTC-T TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
239401 TCTCTTTTTT
Statistics
Matches: 71, Mismatches: 4, Indels: 10
0.84 0.05 0.12
Matches are distributed among these distances:
5 14 0.20
6 54 0.76
7 3 0.04
ACGTcount: A:0.01, C:0.15, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTCT
Found at i:239336 original size:18 final size:17
Alignment explanation
Indices: 239314--239411 Score: 117
Period size: 18 Copynumber: 5.5 Consensus size: 17
239304 TTGACCTCTC
*
239314 CTTTTCTTTTTCTTTTT
1 CTTTTTTTTTTCTTTTT
239331 CTTTTTCTTTTTCTTTTT
1 CTTTTT-TTTTTCTTTTT
*
239349 CTTTTTTTTCTT-TTCTT
1 CTTTTTTTT-TTCTTTTT
*
239366 CATCTTTTTTTTCTTTTT
1 C-TTTTTTTTTTCTTTTT
239384 CTTTTTTTTTTCTTTTTT
1 CTTTTTTTTTTC-TTTTT
239402 CTCTTTTTTT
1 CT-TTTTTTT
239412 AAACATTTTT
Statistics
Matches: 70, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
17 25 0.36
18 38 0.54
19 7 0.10
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.83
Consensus pattern (17 bp):
CTTTTTTTTTTCTTTTT
Found at i:239401 original size:12 final size:12
Alignment explanation
Indices: 239315--239411 Score: 90
Period size: 12 Copynumber: 8.0 Consensus size: 12
239305 TGACCTCTCC
*
239315 TTTTCTTTTTCT
1 TTTTCTTTTTTT
*
239327 TTTTCTTTTTCT
1 TTTTCTTTTTTT
*
239339 TTTTCTTTTTCT
1 TTTTCTTTTTTT
*
239351 TTTT-TTTCTTT
1 TTTTCTTTTTTT
* * *
239362 TCTTCATCTTTT
1 TTTTCTTTTTTT
239374 TTTTCTTTTTCTT
1 TTTTCTTTTT-TT
239387 TTTT-TTTTCTTT
1 TTTTCTTTT-TTT
239399 TTTCTCTTTTTTT
1 TTT-TCTTTTTTT
239412 AAACATTTTT
Statistics
Matches: 71, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
11 8 0.11
12 48 0.68
13 11 0.15
14 4 0.06
ACGTcount: A:0.01, C:0.15, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTCTTTTTTT
Found at i:239421 original size:1 final size:1
Alignment explanation
Indices: 239315--239411 Score: 50
Period size: 1 Copynumber: 97.0 Consensus size: 1
239305 TGACCTCTCC
* * * * * * * * ** * *
239315 TTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTTTTCTTTTCTTCATCTTTTTTTTCT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * *
239380 TTTTCTTTTTTTTTTCTTTTTTCTCTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
239412 AAACATTTTT
Statistics
Matches: 65, Mismatches: 31, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
1 65 1.00
ACGTcount: A:0.01, C:0.15, G:0.00, T:0.84
Consensus pattern (1 bp):
T
Found at i:239421 original size:46 final size:47
Alignment explanation
Indices: 239326--239421 Score: 140
Period size: 46 Copynumber: 2.1 Consensus size: 47
239316 TTTCTTTTTC
* * * *
239326 TTTTTCTTTTTCTTTTTCTTTTTCTTTTTTTTCTTTTCTTCATCTTT
1 TTTTTCTTTTTCTTTTTCTTTTTCTTTTTTCTCTTTTCTTAAACATT
*
239373 TTTTTCTTTTTCTTTTT-TTTTTCTTTTTTCTCTTTTTTTAAACATT
1 TTTTTCTTTTTCTTTTTCTTTTTCTTTTTTCTCTTTTCTTAAACATT
239419 TTT
1 TTT
239422 ATTAAATTTG
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
46 27 0.61
47 17 0.39
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (47 bp):
TTTTTCTTTTTCTTTTTCTTTTTCTTTTTTCTCTTTTCTTAAACATT
Found at i:240322 original size:8 final size:8
Alignment explanation
Indices: 240309--240356 Score: 53
Period size: 8 Copynumber: 5.8 Consensus size: 8
240299 CAGTATGATT
240309 ATGAAAGA
1 ATGAAAGA
240317 ATGAAAGA
1 ATGAAAGA
*
240325 ATGATTTAGA
1 ATGA--AAGA
240335 A-GAAAGA
1 ATGAAAGA
240342 ATGAAAGA
1 ATGAAAGA
240350 ATAGAAA
1 AT-GAAA
240357 TAATTATTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
7 4 0.12
8 20 0.59
9 6 0.18
10 4 0.12
ACGTcount: A:0.60, C:0.00, G:0.23, T:0.17
Consensus pattern (8 bp):
ATGAAAGA
Found at i:247773 original size:23 final size:25
Alignment explanation
Indices: 247729--247780 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 25
247719 TTACAAAAGT
*
247729 TAAAAATATGTTCGTATATATATTA
1 TAAAAATATGTTCATATATATATTA
247754 TAAAAATATG-T-ATATATATATTA
1 TAAAAATATGTTCATATATATATTA
247777 TAAA
1 TAAA
247781 GTACAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 15 0.58
24 1 0.04
25 10 0.38
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (25 bp):
TAAAAATATGTTCATATATATATTA
Found at i:251959 original size:45 final size:45
Alignment explanation
Indices: 251866--251973 Score: 132
Period size: 45 Copynumber: 2.4 Consensus size: 45
251856 ATCACCCTAT
* *
251866 GTTGCTCGACAATGATGACGCTAACTTGTACATACTACCACCTCGG
1 GTTGCCCGACAACGATGACGCTAAC-TGTACATACTACCACCTCGG
*
251912 GTTGCCCGACAACGATGACTCTAGA-TGTACA-ATCTACCACC-CTGG
1 GTTGCCCGACAACGATGACGCTA-ACTGTACATA-CTACCACCTC-GG
251957 GTTGCCCGACAACGATG
1 GTTGCCCGACAACGATG
251974 GTTTTCAATC
Statistics
Matches: 56, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
44 2 0.04
45 33 0.59
46 20 0.36
47 1 0.02
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (45 bp):
GTTGCCCGACAACGATGACGCTAACTGTACATACTACCACCTCGG
Found at i:252209 original size:45 final size:45
Alignment explanation
Indices: 252116--252223 Score: 141
Period size: 45 Copynumber: 2.4 Consensus size: 45
252106 ATCACCCTAT
*
252116 GTTGCTCGACAACGATGACGCTAACTTGTACATACTACCACCTCGG
1 GTTGCCCGACAACGATGACGCTAAC-TGTACATACTACCACCTCGG
*
252162 GTTGCCCGACAACGATGACTCTAGA-TGTACA-ATCTACCACC-CTGG
1 GTTGCCCGACAACGATGACGCTA-ACTGTACATA-CTACCACCTC-GG
252207 GTTGCCCGACAACGATG
1 GTTGCCCGACAACGATG
252224 GTTTTCAATC
Statistics
Matches: 57, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
44 2 0.04
45 33 0.58
46 21 0.37
47 1 0.02
ACGTcount: A:0.26, C:0.31, G:0.21, T:0.22
Consensus pattern (45 bp):
GTTGCCCGACAACGATGACGCTAACTGTACATACTACCACCTCGG
Found at i:252227 original size:250 final size:250
Alignment explanation
Indices: 251786--252277 Score: 957
Period size: 250 Copynumber: 2.0 Consensus size: 250
251776 TATTTCACAC
*
251786 ATCATTTAGCCAATTCGTCTGTTTATAACCCTATTAACCAAACACGGACTCAGAACGGATACATG
1 ATCATTTAACCAATTCGTCTGTTTATAACCCTATTAACCAAACACGGACTCAGAACGGATACATG
*
251851 GATCCATCACCCTATGTTGCTCGACAATGATGACGCTAACTTGTACATACTACCACCTCGGGTTG
66 GATCCATCACCCTATGTTGCTCGACAACGATGACGCTAACTTGTACATACTACCACCTCGGGTTG
251916 CCCGACAACGATGACTCTAGATGTACAATCTACCACCCTGGGTTGCCCGACAACGATGGTTTTCA
131 CCCGACAACGATGACTCTAGATGTACAATCTACCACCCTGGGTTGCCCGACAACGATGGTTTTCA
251981 ATCAATATCCTAACCCTATGGCATGCCAACTATATCCAACTCGATCCATCACTAT
196 ATCAATATCCTAACCCTATGGCATGCCAACTATATCCAACTCGATCCATCACTAT
252036 ATCATTTAACCAATTCGTCTGTTTATAACCCTATTAACCAAACACGGACTCAGAACGGATACATG
1 ATCATTTAACCAATTCGTCTGTTTATAACCCTATTAACCAAACACGGACTCAGAACGGATACATG
252101 GATCCATCACCCTATGTTGCTCGACAACGATGACGCTAACTTGTACATACTACCACCTCGGGTTG
66 GATCCATCACCCTATGTTGCTCGACAACGATGACGCTAACTTGTACATACTACCACCTCGGGTTG
252166 CCCGACAACGATGACTCTAGATGTACAATCTACCACCCTGGGTTGCCCGACAACGATGGTTTTCA
131 CCCGACAACGATGACTCTAGATGTACAATCTACCACCCTGGGTTGCCCGACAACGATGGTTTTCA
*
252231 ATCAATATTCTAACCCTATGGCATGCCAACTATATCCAACTCGATCC
196 ATCAATATCCTAACCCTATGGCATGCCAACTATATCCAACTCGATCC
252278 GAACAACTAA
Statistics
Matches: 239, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
250 239 1.00
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (250 bp):
ATCATTTAACCAATTCGTCTGTTTATAACCCTATTAACCAAACACGGACTCAGAACGGATACATG
GATCCATCACCCTATGTTGCTCGACAACGATGACGCTAACTTGTACATACTACCACCTCGGGTTG
CCCGACAACGATGACTCTAGATGTACAATCTACCACCCTGGGTTGCCCGACAACGATGGTTTTCA
ATCAATATCCTAACCCTATGGCATGCCAACTATATCCAACTCGATCCATCACTAT
Found at i:258896 original size:10 final size:10
Alignment explanation
Indices: 258881--258914 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
258871 TAATGGTTTT
*
258881 TTTTTTACAA
1 TTTTTTATAA
*
258891 TTTTTTATAT
1 TTTTTTATAA
258901 TTTTTTATAA
1 TTTTTTATAA
258911 TTTT
1 TTTT
258915 AAAATGAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:259279 original size:144 final size:145
Alignment explanation
Indices: 259086--259366 Score: 514
Period size: 144 Copynumber: 1.9 Consensus size: 145
259076 CATGTCAACA
259086 TTGTCATTAATTTTTAATGGTTAACATTGATCAAAAGATCTCACTAATCTATTTAGGAGCTTAAT
1 TTGTCATTAA-TTTTAATGGTTAACATTGATCAAAAGATCTCACTAATCTATTTAGGAGCTTAAT
259151 TCAGTGCAAAAAATTGAGAGGAGCTTA-A-CTAATTTTTTTTTAATTCTTTAAAGATTTTTATCC
65 TCAGTGCAAAAAATTGAGAGGAGCTTATATCT--TTTTTTTTTAATTCTTTAAAGATTTTTATCC
259214 ATTAAGCCTTATATATAT
128 ATTAAGCCTTATATATAT
259232 TTGTCATTAA-TTTAATGGTTAACATTGATCAAAAGATCTCACTAATCTATTTAGGAGCTTAATT
1 TTGTCATTAATTTTAATGGTTAACATTGATCAAAAGATCTCACTAATCTATTTAGGAGCTTAATT
259296 CAGTGCAAAAAATTGAGAGGAGCTTATATCTTTTTTTTTTAATTCTTTAAAGATTTTTATCCATT
66 CAGTGCAAAAAATTGAGAGGAGCTTATATCTTTTTTTTTTAATTCTTTAAAGATTTTTATCCATT
259361 AAGCCT
131 AAGCCT
259367 NNNNNNNNNN
Statistics
Matches: 133, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
144 120 0.90
145 1 0.01
146 12 0.09
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (145 bp):
TTGTCATTAATTTTAATGGTTAACATTGATCAAAAGATCTCACTAATCTATTTAGGAGCTTAATT
CAGTGCAAAAAATTGAGAGGAGCTTATATCTTTTTTTTTTAATTCTTTAAAGATTTTTATCCATT
AAGCCTTATATATAT
Found at i:261405 original size:21 final size:20
Alignment explanation
Indices: 261358--261412 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
261348 ACCATTGTTT
*
261358 CTAATCTCACTGCTACAGTA
1 CTAATCTCACCGCTACAGTA
* *
261378 TTCAATCTCACCGTTACAGTAA
1 CT-AATCTCACCGCTACAGT-A
261400 CTAATCTCACCGC
1 CTAATCTCACCGC
261413 CACCGCTGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 1 0.04
21 25 0.89
22 2 0.07
ACGTcount: A:0.29, C:0.33, G:0.09, T:0.29
Consensus pattern (20 bp):
CTAATCTCACCGCTACAGTA
Found at i:264201 original size:7 final size:7
Alignment explanation
Indices: 264186--264228 Score: 59
Period size: 7 Copynumber: 6.1 Consensus size: 7
264176 AACGTAGTCG
*
264186 ATTTCGT
1 ATTTAGT
264193 ATTTAGT
1 ATTTAGT
264200 ATTTAGT
1 ATTTAGT
264207 ATTTAGT
1 ATTTAGT
*
264214 ATTTAAT
1 ATTTAGT
*
264221 AATTAGT
1 ATTTAGT
264228 A
1 A
264229 GTATATATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (7 bp):
ATTTAGT
Found at i:267751 original size:13 final size:14
Alignment explanation
Indices: 267724--267755 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
267714 CTTAATTTCA
267724 TAAATCTTAAACCC
1 TAAATCTTAAACCC
267738 TAAATCTT-AACCC
1 TAAATCTTAAACCC
267751 TAAAT
1 TAAAT
267756 AATTAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (14 bp):
TAAATCTTAAACCC
Found at i:268485 original size:6 final size:6
Alignment explanation
Indices: 268474--268503 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
268464 GTGGTCCTAC
268474 TCACCA TCACCA TCACCA TCACCA TCACCA
1 TCACCA TCACCA TCACCA TCACCA TCACCA
268504 AACAAGCAGT
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:0.33, C:0.50, G:0.00, T:0.17
Consensus pattern (6 bp):
TCACCA
Found at i:268891 original size:124 final size:125
Alignment explanation
Indices: 268665--268914 Score: 484
Period size: 124 Copynumber: 2.0 Consensus size: 125
268655 AAAATAATAA
268665 ATTAATTCCTTTTTTAATAGTTAAACAATATCAATTTTATGAAATAGATTTAGTTAAATTACTAA
1 ATTAATTCCTTTTTTAATAGTTAAACAATATCAATTTTATGAAATAGATTTAGTTAAATTACTAA
*
268730 CATGGTCTAATAATACGGCTGTGTGACTATTGGTGAACAAGGTCGATTTTGTGCCACATG
66 CAAGGTCTAATAATACGGCTGTGTGACTATTGGTGAACAAGGTCGATTTTGTGCCACATG
268790 ATTAA-TCCTTTTTTAATAGTTAAACAATATCAATTTTATGAAATAGATTTAGTTAAATTACTAA
1 ATTAATTCCTTTTTTAATAGTTAAACAATATCAATTTTATGAAATAGATTTAGTTAAATTACTAA
268854 CAAGGTCTAATAATACGGCTGTGTGACTATTGGTGAACAAGGTCGATTTTGTGCCACATG
66 CAAGGTCTAATAATACGGCTGTGTGACTATTGGTGAACAAGGTCGATTTTGTGCCACATG
268914 A
1 A
268915 CCTCCGTGAG
Statistics
Matches: 124, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
124 119 0.96
125 5 0.04
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (125 bp):
ATTAATTCCTTTTTTAATAGTTAAACAATATCAATTTTATGAAATAGATTTAGTTAAATTACTAA
CAAGGTCTAATAATACGGCTGTGTGACTATTGGTGAACAAGGTCGATTTTGTGCCACATG
Found at i:275525 original size:23 final size:24
Alignment explanation
Indices: 275481--275529 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
275471 GTTATCTGTT
**
275481 ATGTTTGATTTTTATTATTATTTG
1 ATGTTTGATACTTATTATTATTTG
275505 ATGTTTGATACTT-TTATTATTTG
1 ATGTTTGATACTTATTATTATTTG
275528 AT
1 AT
275530 TTTTAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.22, C:0.02, G:0.12, T:0.63
Consensus pattern (24 bp):
ATGTTTGATACTTATTATTATTTG
Found at i:275547 original size:26 final size:24
Alignment explanation
Indices: 275492--275549 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
275482 TGTTTGATTT
* *
275492 TTATTATTATTTGATGTTTGATAC
1 TTATTATTATTTGATGTTTAATAA
*
275516 TT-TTATTATTTGATTTTTAATAA
1 TTATTATTATTTGATGTTTAATAA
*
275539 -TAATATTATTT
1 TTATTATTATTT
275550 ATTATATCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 1 0.03
23 26 0.90
24 2 0.07
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.62
Consensus pattern (24 bp):
TTATTATTATTTGATGTTTAATAA
Found at i:276026 original size:14 final size:14
Alignment explanation
Indices: 275987--276028 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
275977 CCAATTGCTG
*
275987 AAAATTCTAAAT-T
1 AAAATTTTAAATAT
*
276000 AAAGTTTTGAAATAT
1 AAAATTTT-AAATAT
276015 AAAATTTTAAATAT
1 AAAATTTTAAATAT
276029 TAAGATTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 6 0.25
14 10 0.42
15 8 0.33
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.40
Consensus pattern (14 bp):
AAAATTTTAAATAT
Found at i:276734 original size:16 final size:15
Alignment explanation
Indices: 276709--276757 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
276699 TATTTTTTGG
276709 GTGACCAAAATGAAA
1 GTGACCAAAATGAAA
* *
276724 GTGACCCAAAA-GTTAG
1 GTGA-CCAAAATG-AAA
276740 GTGACCAAAATGAAA
1 GTGACCAAAATGAAA
276755 GTG
1 GTG
276758 TAAATATGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
15 15 0.56
16 12 0.44
ACGTcount: A:0.45, C:0.14, G:0.24, T:0.16
Consensus pattern (15 bp):
GTGACCAAAATGAAA
Found at i:282705 original size:9 final size:9
Alignment explanation
Indices: 282693--282755 Score: 62
Period size: 9 Copynumber: 7.2 Consensus size: 9
282683 TTTACATACG
282693 TTTTATATT
1 TTTTATATT
282702 TTTTATATAT
1 TTTTATAT-T
282712 TTTT-TATT
1 TTTTATATT
282720 TTTT-TATCT
1 TTTTATAT-T
*
282729 TTTTA-A-C
1 TTTTATATT
*
282736 TTTTATATA
1 TTTTATATT
282745 TTTTATATT
1 TTTTATATT
282754 TT
1 TT
282756 ATTGATATAT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
7 5 0.11
8 9 0.20
9 27 0.59
10 5 0.11
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTATATT
Found at i:282706 original size:20 final size:19
Alignment explanation
Indices: 282683--282725 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
282673 ATGCATATAC
282683 TTTACATACGTTTTATATTT
1 TTTACATACGTTTTAT-TTT
* **
282703 TTTATATATTTTTTATTTT
1 TTTACATACGTTTTATTTT
282722 TTTA
1 TTTA
282726 TCTTTTTAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (19 bp):
TTTACATACGTTTTATTTT
Found at i:290861 original size:88 final size:88
Alignment explanation
Indices: 290675--291430 Score: 742
Period size: 88 Copynumber: 8.5 Consensus size: 88
290665 TTGTAGATTT
* * *
290675 CAGATATTGTCTTCATGTACTAGCGTGAAGTAGATTAAAGATAGCAGATCT-TGCCTTCCCATAC
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGCAGATCTAT--CTTCCCATAC
*
290739 TGGTGGCGAAGCAGATCGAAGAAAA
64 TGGTGGCGAAGCAGATCAAAGAAAA
*
290764 TAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGCAGATCTATCTTCCCATACTG
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGCAGATCTATCTTCCCATACTG
290829 GTGGCGAAGCAGATCAAAGAAAA
66 GTGGCGAAGCAGATCAAAGAAAA
*
290852 CAGATCTTGTCTTCATGTACTGGCATGAAGTAGATCAAAGATAGCAGATCTATCTTCCCATACTG
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGCAGATCTATCTTCCCATACTG
290917 GTGGCGAAGCAGATCAAAGAAAA
66 GTGGCGAAGCAGATCAAAGAAAA
290940 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGCAGATCTATCTTCCCATACTG
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGCAGATCTATCTTCCCATACTG
*
291005 GTGGCGAAGCAGATCAAAGAAAG
66 GTGGCGAAGCAGATCAAAGAAAA
* * * * * * * * * * *
291028 CAGATCCTGTCTTCCTATATTGGTAGCGGAGTGGATCATAGATAACAGATCTTATCTCCCCATAC
1 CAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGATAGCAGATC-TATCTTCCCATAC
* * * * *
291093 TGGTCGTGGAGTAGATCAAAGATAA
64 TGGTGGCGAAGCAGATCAAAGAAAA
*** * * * * *
291118 CAGATCTTGTCTTCCCATACTCGTG-GTGAAGTAGATCGAAGAAAGTAAATCCTATCTTCCTATA
1 CAGATCTTGTCTTCATGTACT-G-GCGTGAAGTAGATCAAAGATAGCAGAT-CTATCTTCCCATA
* * * ** * *
291182 TTGGTAGCGGAGGGGATCATAGATAA
63 CTGGTGGCGAAGCAGATCAAAGAAAA
* * * *** *
291208 CTGATCTTATCTCCCCATACTGGTCGTGGAGTAGATCAAAGATAGCAGATCTATCTTCCCATACT
1 CAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGATAGCAGATCTATCTTCCCATACT
* * * * *
291273 GGTAGTGAAGTAGATCGAAGAAAG
65 GGTGGCGAAGCAGATCAAAGAAAA
* * * * * * * * * * ** * * * *
291297 TAAATCCTATCTTCCTATATTGGTAGCGGAGGGGATCATAGATAACTGATCTTATCTCCCCATAC
1 CAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGATAGCAGATC-TATCTTCCCATAC
* * * * *
291362 TGGTCGTGGAGTAGATCAAAGATAA
64 TGGTGGCGAAGCAGATCAAAGAAAA
* * *
291387 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAAATCAAATATAG
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAG
291431 TAGGTCTTAT
Statistics
Matches: 559, Mismatches: 99, Indels: 18
0.83 0.15 0.03
Matches are distributed among these distances:
88 226 0.40
89 147 0.26
90 183 0.33
91 2 0.00
92 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (88 bp):
CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGCAGATCTATCTTCCCATACTG
GTGGCGAAGCAGATCAAAGAAAA
Found at i:291077 original size:45 final size:45
Alignment explanation
Indices: 290703--291400 Score: 507
Period size: 45 Copynumber: 15.7 Consensus size: 45
290693 ACTAGCGTGA
* * ** * * *
290703 AGTAGATTAAAGATAGCAGATCTTGCCTTCCCATACTGGTGGCGA
1 AGTAGATCAAAGATAACAGATCTTATCTTCCCATACTGGTAGTGG
* * * * * *** * *
290748 AGCAGATCGAAGAAAATAGATCTTGTCTTCATGTACTGG-CGTGA
1 AGTAGATCAAAGATAACAGATCTTATCTTCCCATACTGGTAGTGG
* * * *
290792 AGTAGATCAAAGATAGCAGATC-TATCTTCCCATACTGGTGGCGA
1 AGTAGATCAAAGATAACAGATCTTATCTTCCCATACTGGTAGTGG
* * * *** * *
290836 AGCAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCA-TGA
1 AGTAGATCAAAGATAACAGATCTTATCTTCCCATACTGGTAGTGG
* * * *
290880 AGTAGATCAAAGATAGCAGATC-TATCTTCCCATACTGGTGGCGA
1 AGTAGATCAAAGATAACAGATCTTATCTTCCCATACTGGTAGTGG
* * * *** * *
290924 AGCAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGG-CGTGA
1 AGTAGATCAAAGATAACAGATCTTATCTTCCCATACTGGTAGTGG
* * * *
290968 AGTAGATCAAAGATAGCAGATC-TATCTTCCCATACTGGTGGCGA
1 AGTAGATCAAAGATAACAGATCTTATCTTCCCATACTGGTAGTGG
* * * * * *
291012 AGCAGATCAAAGA-AAGCAGATCCTGTCTTCCTATATTGGTAGCGG
1 AGTAGATCAAAGATAA-CAGATCTTATCTTCCCATACTGGTAGTGG
* * * *
291057 AGTGGATCATAGATAACAGATCTTATCTCCCCATACTGGTCGTGG
1 AGTAGATCAAAGATAACAGATCTTATCTTCCCATACTGGTAGTGG
* * * *
291102 AGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTCGTGGTGA
1 AGTAGATCAAAGATAACAGATCTTATCTTCCCATACTGGTAGTGG
* * * * * * *
291147 AGTAGATCGAAGA-AAGTAAATCCTATCTTCCTATATTGGTAGCGG
1 AGTAGATCAAAGATAA-CAGATCTTATCTTCCCATACTGGTAGTGG
** * * * *
291192 AGGGGATCATAGATAACTGATCTTATCTCCCCATACTGGTCGTGG
1 AGTAGATCAAAGATAACAGATCTTATCTTCCCATACTGGTAGTGG
* *
291237 AGTAGATCAAAGATAGCAGATC-TATCTTCCCATACTGGTAGTGA
1 AGTAGATCAAAGATAACAGATCTTATCTTCCCATACTGGTAGTGG
* * * * * * *
291281 AGTAGATCGAAGA-AAGTAAATCCTATCTTCCTATATTGGTAGCGG
1 AGTAGATCAAAGATAA-CAGATCTTATCTTCCCATACTGGTAGTGG
** * * * *
291326 AGGGGATCATAGATAACTGATCTTATCTCCCCATACTGGTCGTGG
1 AGTAGATCAAAGATAACAGATCTTATCTTCCCATACTGGTAGTGG
*
291371 AGTAGATCAAAGATAACAGATCTTGTCTTC
1 AGTAGATCAAAGATAACAGATCTTATCTTC
291401 ATGTATTGGC
Statistics
Matches: 496, Mismatches: 144, Indels: 26
0.74 0.22 0.04
Matches are distributed among these distances:
43 38 0.08
44 164 0.33
45 288 0.58
46 6 0.01
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.27
Consensus pattern (45 bp):
AGTAGATCAAAGATAACAGATCTTATCTTCCCATACTGGTAGTGG
Found at i:291273 original size:269 final size:266
Alignment explanation
Indices: 290692--291425 Score: 882
Period size: 269 Copynumber: 2.8 Consensus size: 266
290682 TGTCTTCATG
* *
290692 TACTAGCGTGAAGTAGATTAAAGATAGCAGATCT-TGCCTTCCCATACTGGTGGCGAAGCAGATC
1 TACTGGCGTGAAGTAGATCAAAGATAGCAGATCTAT--CTTCCCATACTGGTGGCGAAGCAGATC
* * * * * * * * * * *
290756 GAAGAAAATAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGATAGCAGATC-TATCT
64 GAAGAAAGTAGATCCTGTCTTCCTATATTGGTAGCGGAGTGGATCATAGATAACAGATCTTATCT
* * * * * * **
290819 TCCCATACTGGTGGCGAAGCAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCATGAAGTA
129 CCCCATACTGGTCGTGGAGTAGATCAAAGATAACAGATCTTGTCTTCACATACTGGCATGAAGTA
* * * *
290884 GATCAAAGATAGCAGATCTATCTTCCCATACTGGTGGCGAAGCAGATCAAAGAAAACAGATCTTG
194 GATCAAAGAAAGCAAATCTATCTTCCCATACTGGTAGCGAAGCAGATCAAAGAAAACAGATCTTA
* **
290949 TCTTCATG
259 TCTCCACA
*
290957 TACTGGCGTGAAGTAGATCAAAGATAGCAGATCTATCTTCCCATACTGGTGGCGAAGCAGATCAA
1 TACTGGCGTGAAGTAGATCAAAGATAGCAGATCTATCTTCCCATACTGGTGGCGAAGCAGATCGA
*
291022 AGAAAGCAGATCCTGTCTTCCTATATTGGTAGCGGAGTGGATCATAGATAACAGATCTTATCTCC
66 AGAAAGTAGATCCTGTCTTCCTATATTGGTAGCGGAGTGGATCATAGATAACAGATCTTATCTCC
* *
291087 CCATACTGGTCGTGGAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTCGTG-GTGAAGTA
131 CCATACTGGTCGTGGAGTAGATCAAAGATAACAGATCTTGTCTTCACATACT-G-GCATGAAGTA
* * * * * ** * * *
291151 GATCGAAGAAAGTAAATCCTATCTTCCTATATTGGTAGCGGAGGGGATCATAGATAACTGATCTT
194 GATCAAAGAAAGCAAAT-CTATCTTCCCATACTGGTAGCGAAGCAGATCAAAGAAAACAGATCTT
*
291216 ATCTCCCCA
258 ATCTCCACA
* * * *
291225 TACTGGTCGTGGAGTAGATCAAAGATAGCAGATCTATCTTCCCATACTGGTAGTGAAGTAGATCG
1 TACTGG-CGTGAAGTAGATCAAAGATAGCAGATCTATCTTCCCATACTGGTGGCGAAGCAGATCG
* * * *
291290 AAGAAAGTAAATCCTATCTTCCTATATTGGTAGCGGAGGGGATCATAGATAACTGATCTTATCTC
65 AAGAAAGTAGATCCTGTCTTCCTATATTGGTAGCGGAGTGGATCATAGATAACAGATCTTATCTC
** * * *
291355 CCCATACTGGTCGTGGAGTAGATCAAAGATAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAA
130 CCCATACTGGTCGTGGAGTAGATCAAAGATAACAGATCTTGTCTTCACATACTGGCATGAAGTAG
291420 ATCAAA
195 ATCAAA
291426 TATAGTAGGT
Statistics
Matches: 402, Mismatches: 59, Indels: 13
0.85 0.12 0.03
Matches are distributed among these distances:
264 51 0.13
265 53 0.13
266 51 0.13
267 22 0.05
268 63 0.16
269 162 0.40
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (266 bp):
TACTGGCGTGAAGTAGATCAAAGATAGCAGATCTATCTTCCCATACTGGTGGCGAAGCAGATCGA
AGAAAGTAGATCCTGTCTTCCTATATTGGTAGCGGAGTGGATCATAGATAACAGATCTTATCTCC
CCATACTGGTCGTGGAGTAGATCAAAGATAACAGATCTTGTCTTCACATACTGGCATGAAGTAGA
TCAAAGAAAGCAAATCTATCTTCCCATACTGGTAGCGAAGCAGATCAAAGAAAACAGATCTTATC
TCCACA
Found at i:291415 original size:134 final size:134
Alignment explanation
Indices: 290796--291425 Score: 732
Period size: 134 Copynumber: 4.7 Consensus size: 134
290786 GCGTGAAGTA
* * * * * * * *
290796 GATCAAAGATAGCAGATC-TATCTTCCCATACTGGTGGCGAAGCAGATCAAAGAAAACAGATCTT
1 GATCATAGATAACAGATCTTATCTCCCCATACTGGTCGTGGAGTAGATCAAAGATAACAGATCTT
*** * * * * * * *
290860 GTCTTCATGTACTGGCATGAAGTAGATCAAAGATAGCAGAT-CTATCTTCCCATACTGGTGGCGA
66 GTCTTCCCATACTGGCGTGAAGTAGATCAAAGAAAGCAAATCCTATCTTCCTATATTGGTAGCGG
**
290924 AGCA
131 AGGG
* * * * *** * *
290928 GATCAAAGAAAACAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGATAGCAGATC-T
1 GATCATAGATAACAGATCTTATCTCCCCATACTGGTCGTGGAGTAGATCAAAGATAACAGATCTT
* * * * * *
290991 ATCTTCCCATACTGGTGGCGAAGCAGATCAAAGAAAGCAGATCCTGTCTTCCTATATTGGTAGCG
66 GTCTTCCCATACTGG-CGTGAAGTAGATCAAAGAAAGCAAATCCTATCTTCCTATATTGGTAGCG
*
291056 GAGTG
130 GAGGG
291061 GATCATAGATAACAGATCTTATCTCCCCATACTGGTCGTGGAGTAGATCAAAGATAACAGATCTT
1 GATCATAGATAACAGATCTTATCTCCCCATACTGGTCGTGGAGTAGATCAAAGATAACAGATCTT
* *
291126 GTCTTCCCATACTCGTG-GTGAAGTAGATCGAAGAAAGTAAATCCTATCTTCCTATATTGGTAGC
66 GTCTTCCCATACT-G-GCGTGAAGTAGATCAAAGAAAGCAAATCCTATCTTCCTATATTGGTAGC
291190 GGAGGG
129 GGAGGG
* *
291196 GATCATAGATAACTGATCTTATCTCCCCATACTGGTCGTGGAGTAGATCAAAGATAGCAGATC-T
1 GATCATAGATAACAGATCTTATCTCCCCATACTGGTCGTGGAGTAGATCAAAGATAACAGATCTT
* * * *
291260 ATCTTCCCATACTGGTAGTGAAGTAGATCGAAGAAAGTAAATCCTATCTTCCTATATTGGTAGCG
66 GTCTTCCCATACTGG-CGTGAAGTAGATCAAAGAAAGCAAATCCTATCTTCCTATATTGGTAGCG
291325 GAGGG
130 GAGGG
*
291330 GATCATAGATAACTGATCTTATCTCCCCATACTGGTCGTGGAGTAGATCAAAGATAACAGATCTT
1 GATCATAGATAACAGATCTTATCTCCCCATACTGGTCGTGGAGTAGATCAAAGATAACAGATCTT
*** * *
291395 GTCTTCATGTATTGGCGTGAAGTAAATCAAA
66 GTCTTCCCATACTGGCGTGAAGTAGATCAAA
291426 TATAGTAGGT
Statistics
Matches: 432, Mismatches: 56, Indels: 18
0.85 0.11 0.04
Matches are distributed among these distances:
131 12 0.03
132 60 0.14
133 61 0.14
134 166 0.38
135 131 0.30
136 1 0.00
137 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (134 bp):
GATCATAGATAACAGATCTTATCTCCCCATACTGGTCGTGGAGTAGATCAAAGATAACAGATCTT
GTCTTCCCATACTGGCGTGAAGTAGATCAAAGAAAGCAAATCCTATCTTCCTATATTGGTAGCGG
AGGG
Found at i:292680 original size:63 final size:62
Alignment explanation
Indices: 292600--292724 Score: 232
Period size: 63 Copynumber: 2.0 Consensus size: 62
292590 AATGATTTTA
292600 TTTTTTTCTTTTTTTCAATTTTGTTTCATTTATGCAGCACATGAAACGGCGCCATTTTAAAT
1 TTTTTTTCTTTTTTTCAATTTTGTTTCATTTATGCAGCACATGAAACGGCGCCATTTTAAAT
*
292662 TTTTTTTCTTTTTTTTCAATTTTGTTTCATTTATGCAGCACATGAAACGGCGCCGTTTTAAAT
1 TTTTTTTC-TTTTTTTCAATTTTGTTTCATTTATGCAGCACATGAAACGGCGCCATTTTAAAT
292725 AGCCAAACCC
Statistics
Matches: 61, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
62 8 0.13
63 53 0.87
ACGTcount: A:0.22, C:0.16, G:0.12, T:0.50
Consensus pattern (62 bp):
TTTTTTTCTTTTTTTCAATTTTGTTTCATTTATGCAGCACATGAAACGGCGCCATTTTAAAT
Found at i:293166 original size:9 final size:9
Alignment explanation
Indices: 293154--293216 Score: 62
Period size: 9 Copynumber: 7.2 Consensus size: 9
293144 TTTACATACG
293154 TTTTATATT
1 TTTTATATT
293163 TTTTATATAT
1 TTTTATAT-T
293173 TTTT-TATT
1 TTTTATATT
293181 TTTT-TATCT
1 TTTTATAT-T
*
293190 TTTTA-A-C
1 TTTTATATT
*
293197 TTTTATATA
1 TTTTATATT
293206 TTTTATATT
1 TTTTATATT
293215 TT
1 TT
293217 ATTGATATAT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
7 5 0.11
8 9 0.20
9 27 0.59
10 5 0.11
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTATATT
Found at i:293167 original size:20 final size:19
Alignment explanation
Indices: 293144--293186 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
293134 ATGCATATAC
293144 TTTACATACGTTTTATATTT
1 TTTACATACGTTTTAT-TTT
* **
293164 TTTATATATTTTTTATTTT
1 TTTACATACGTTTTATTTT
293183 TTTA
1 TTTA
293187 TCTTTTTAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (19 bp):
TTTACATACGTTTTATTTT
Done.