Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 104 of 198
Found at i:33363854 original size:28 final size:28
Alignment explanation
Indices: 33363818--33363884 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 28
33363808 AGAGTGCACT
* * *
33363818 ACAAGGGCTTTTATTTCAAATTATTTCC
1 ACAAAGGCTATTACTTCAAATTATTTCC
* * * *
33363846 ATAAAGGCTATTCCTTCAGATTTTTTCC
1 ACAAAGGCTATTACTTCAAATTATTTCC
33363874 ACAAAGGCTAT
1 ACAAAGGCTAT
33363885 CATGTCAAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (28 bp):
ACAAAGGCTATTACTTCAAATTATTTCC
Found at i:33368385 original size:42 final size:42
Alignment explanation
Indices: 33368337--33368417 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
33368327 ACGGCCTGGA
*
33368337 GACATGACCATGTGACCTTATTTCGAATCACACACGGTCTAC
1 GACATGACCATGTGACCCTATTTCGAATCACACACGGTCTAC
* *
33368379 GACATGACCATGTGACCCTATTTCGAATTACACATGGTC
1 GACATGACCATGTGACCCTATTTCGAATCACACACGGTC
33368418 GGGCACATGG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.27
Consensus pattern (42 bp):
GACATGACCATGTGACCCTATTTCGAATCACACACGGTCTAC
Found at i:33381302 original size:111 final size:111
Alignment explanation
Indices: 33381183--33381405 Score: 369
Period size: 111 Copynumber: 2.0 Consensus size: 111
33381173 CACCTATTTA
*
33381183 TAGCTAAAATTTTCTGAA-CTAATTAAGTTAATTACAGCCTAAAAAATGATAAATGTTTATTGTG
1 TAGCTAAAATTTTCT-AATCTAATTAAGTTAATTACAACCTAAAAAATGATAAATGTTTATTGTG
* *
33381247 CTGACAGAAACACTCCTAACTTAATTATTTATGTTT-GTCGTTTGGTG
65 CTGACAGAAACACCCCTAACTTAATTATTTAT-TTTCGTCGTTCGGTG
* *
33381294 TAGCTAAAATTTTCTAATCTAATTAAGTTAATTACAACTTAAAAATTGATAAATGTTTATTGTGC
1 TAGCTAAAATTTTCTAATCTAATTAAGTTAATTACAACCTAAAAAATGATAAATGTTTATTGTGC
33381359 TGACAGAAACACCCCTAACTTAATTATTTATTTTCGTCGTTCGGTG
66 TGACAGAAACACCCCTAACTTAATTATTTATTTTCGTCGTTCGGTG
33381405 T
1 T
33381406 CACGGCATCA
Statistics
Matches: 105, Mismatches: 5, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
110 5 0.05
111 100 0.95
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.39
Consensus pattern (111 bp):
TAGCTAAAATTTTCTAATCTAATTAAGTTAATTACAACCTAAAAAATGATAAATGTTTATTGTGC
TGACAGAAACACCCCTAACTTAATTATTTATTTTCGTCGTTCGGTG
Found at i:33383184 original size:16 final size:17
Alignment explanation
Indices: 33383163--33383195 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
33383153 AATTGGATTG
*
33383163 AGAAAA-TAATTTAATT
1 AGAAAATTAATTAAATT
33383179 AGAAAATTAATTAAATT
1 AGAAAATTAATTAAATT
33383196 TATTTTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (17 bp):
AGAAAATTAATTAAATT
Found at i:33388953 original size:18 final size:17
Alignment explanation
Indices: 33388920--33388958 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
33388910 TTTTATAAAT
33388920 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
33388938 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
33388955 TGTG
1 TGTG
33388959 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:33389219 original size:23 final size:23
Alignment explanation
Indices: 33389188--33389263 Score: 107
Period size: 23 Copynumber: 3.3 Consensus size: 23
33389178 AGTGTTATTG
33389188 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * * * *
33389211 TTCAGTGGTAGGTACGACTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
33389234 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
33389257 ATCAGTG
1 ATCAGTG
33389264 TGACACTTAT
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:33395572 original size:31 final size:31
Alignment explanation
Indices: 33395529--33395624 Score: 104
Period size: 31 Copynumber: 3.1 Consensus size: 31
33395519 TATATAAAAC
* *
33395529 TTAAATTAATTTAAATTTTATGT-ATTATTATA
1 TTAAATT-ATTTAAATATAAT-TAATTATTATA
* * * *
33395561 TTAGATTATTTAAATAGAATTGATCATTATA
1 TTAAATTATTTAAATATAATTAATTATTATA
*
33395592 TTAAATTATTTAAATGTAATTAATTATTATA
1 TTAAATTATTTAAATATAATTAATTATTATA
33395623 TT
1 TT
33395625 TAAAAATTTT
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
30 1 0.02
31 46 0.87
32 6 0.11
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (31 bp):
TTAAATTATTTAAATATAATTAATTATTATA
Found at i:33398884 original size:18 final size:20
Alignment explanation
Indices: 33398863--33398908 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
33398853 TTTTTTCTAT
33398863 AATTATAATTTT-AAAA-AA
1 AATTATAATTTTGAAAATAA
* *
33398881 AATTAGAATTTTGAAAATTA
1 AATTATAATTTTGAAAATAA
33398901 AATTATAA
1 AATTATAA
33398909 ATTTCAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 11 0.48
19 4 0.17
20 8 0.35
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (20 bp):
AATTATAATTTTGAAAATAA
Found at i:33400135 original size:22 final size:20
Alignment explanation
Indices: 33400083--33400136 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 20
33400073 TTAAAATTTT
*
33400083 AAAATTATAAAAAATATATA
1 AAAATTATAAAAAATAAATA
*
33400103 CAAATTATAAAAATATGAAATA
1 AAAATTATAAAAA-AT-AAATA
*
33400125 AAAATTTTAAAA
1 AAAATTATAAAA
33400137 TTAAAAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 12 0.43
21 2 0.07
22 14 0.50
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (20 bp):
AAAATTATAAAAAATAAATA
Found at i:33403884 original size:29 final size:28
Alignment explanation
Indices: 33403805--33403902 Score: 164
Period size: 28 Copynumber: 3.5 Consensus size: 28
33403795 AAAAATAAAA
33403805 ATTTACCAAAATATTACAAC-TTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTT
33403832 ATTTACCAAAATATTACAACTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTT
33403860 ATTTACCAAAATATTTA-AACTTTTTTATT
1 ATTTACCAAAATA-TTACAACTTTTTT-TT
33403889 ATTTACCAAAATAT
1 ATTTACCAAAATAT
33403903 ATTTAAAAAA
Statistics
Matches: 68, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
27 20 0.29
28 30 0.44
29 18 0.26
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (28 bp):
ATTTACCAAAATATTACAACTTTTTTTT
Found at i:33404042 original size:27 final size:27
Alignment explanation
Indices: 33403974--33404044 Score: 124
Period size: 27 Copynumber: 2.6 Consensus size: 27
33403964 CCCCAATAGT
*
33403974 ATTGGCGGCACCAAAGGTGCCAAAACC
1 ATTGGCGGCACCAATGGTGCCAAAACC
*
33404001 ATTGGCGGCACCAATGGTGCCAATACC
1 ATTGGCGGCACCAATGGTGCCAAAACC
33404028 ATTGGCGGCACCAATGG
1 ATTGGCGGCACCAATGG
33404045 GTTTTATGGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.15
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAAAACC
Found at i:33404110 original size:18 final size:19
Alignment explanation
Indices: 33404083--33404231 Score: 112
Period size: 20 Copynumber: 7.6 Consensus size: 19
33404073 AGAAGAGAAA
33404083 AAAGGA-AAGAAAGAAAGG
1 AAAGGAGAAGAAAGAAAGG
*
33404101 AGAGGGAAGAAAGAAAGAAAGG
1 A-AAGG-AG-AAGAAAGAAAGG
*
33404123 AGAGGA-AAGAAAGAAAAGG
1 AAAGGAGAAGAAAG-AAAGG
*
33404142 AAAGGAGAAGAGAAAAAAGG
1 AAAGGAGAAGA-AAGAAAGG
*
33404162 AAAGAAAGAAG-AAGAAAAGG
1 AAAG-GAGAAGAAAG-AAAGG
33404182 AGAA-GAGAAGAAA-AAA-G
1 A-AAGGAGAAGAAAGAAAGG
*
33404199 AAAGAAAGAAGGAAAGAAAGGG
1 AAAG-GAGAA-GAAAGAAA-GG
33404221 AAAGGAGAAGA
1 AAAGGAGAAGA
33404232 GAAAAAAAAA
Statistics
Matches: 104, Mismatches: 10, Indels: 32
0.71 0.07 0.22
Matches are distributed among these distances:
16 2 0.02
17 2 0.02
18 15 0.14
19 24 0.23
20 28 0.27
21 15 0.14
22 18 0.17
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (19 bp):
AAAGGAGAAGAAAGAAAGG
Found at i:33404112 original size:22 final size:22
Alignment explanation
Indices: 33404087--33404169 Score: 103
Period size: 22 Copynumber: 3.6 Consensus size: 22
33404077 GAGAAAAAAG
33404087 GAAAGAAAGAAAGGAGAGGGAA
1 GAAAGAAAGAAAGGAGAGGGAA
*
33404109 GAAAGAAAGAAAGGAGAGGAAA
1 GAAAGAAAGAAAGGAGAGGGAA
*
33404131 GAAAGAAAAGGAAAGGAGAAGAGAA
1 GAAAG-AAA-GAAAGGAG-AGGGAA
*
33404156 AAAAGGAAAGAAAG
1 GAAA-GAAAGAAAG
33404170 AAGAAGAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
22 26 0.49
23 3 0.06
24 13 0.25
25 10 0.19
26 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (22 bp):
GAAAGAAAGAAAGGAGAGGGAA
Found at i:33404130 original size:14 final size:14
Alignment explanation
Indices: 33404082--33404218 Score: 85
Period size: 12 Copynumber: 10.0 Consensus size: 14
33404072 CAGAAGAGAA
33404082 AAAAGGAAAGAAAG
1 AAAAGGAAAGAAAG
* *
33404096 -AAAGGAGAGGGAAG
1 AAAAGGA-AAGAAAG
33404110 -AAA-GAAAGAAAG
1 AAAAGGAAAGAAAG
* *
33404122 GAGAGGAAAGAAAG
1 AAAAGGAAAGAAAG
*
33404136 AAAAGGAAAG-GAG
1 AAAAGGAAAGAAAG
*
33404149 AAGA-GAAA-AAAG
1 AAAAGGAAAGAAAG
*
33404161 GAAA-GAAAGAAGAAG
1 AAAAGGAAAG-A-AAG
33404176 AAAAGGAGAAGAGAAG
1 AAAAGGA-AAGA-AAG
*
33404192 AAAAAAGAAAGAAAG
1 -AAAAGGAAAGAAAG
33404207 --AAGGAAAGAAAG
1 AAAAGGAAAGAAAG
33404219 GGAAAGGAGA
Statistics
Matches: 98, Mismatches: 15, Indels: 22
0.73 0.11 0.16
Matches are distributed among these distances:
12 28 0.29
13 15 0.15
14 26 0.27
15 9 0.09
16 11 0.11
17 9 0.09
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (14 bp):
AAAAGGAAAGAAAG
Found at i:33404250 original size:79 final size:80
Alignment explanation
Indices: 33404073--33404252 Score: 229
Period size: 79 Copynumber: 2.4 Consensus size: 80
33404063 GTGGTGGGGC
* *
33404073 AGAAGAGAAAAAAG---GAAAG-A-AAG-AAAGGAGAGGGAAGAAAGAAAGAAAGGAGAGGAAAG
1 AGAAGAGAAAAAAGAAAGAAAGAAGAAGAAAAGGAGAGAGAAGAAAGAAAGAAAGGAGAAGAAAG
33404132 AAAGAAAAGGAAAGG
66 AAAGAAAAGGAAAGG
33404147 AGAAGAGAAAAAAGGAAAGAAAGAAGAAGAAAAGGAGAAGAGAAGAAA-AAAGAAA-GA-AAGAA
1 AGAAGAGAAAAAA-GAAAGAAAGAAGAAGAAAAGGAG-AGAGAAGAAAGAAAGAAAGGAGAAGAA
* *
33404209 GGAAAGAAAGGGAAAGG
64 AGAAAGAAAAGGAAAGG
33404226 AGAAGAGAAAAAA-AAAG-AAGAAGAAGA
1 AGAAGAGAAAAAAGAAAGAAAGAAGAAGA
33404253 GGGAAGAAAG
Statistics
Matches: 94, Mismatches: 4, Indels: 14
0.84 0.04 0.12
Matches are distributed among these distances:
74 13 0.14
75 1 0.01
76 10 0.11
77 4 0.04
78 5 0.05
79 33 0.35
80 5 0.05
81 14 0.15
82 9 0.10
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (80 bp):
AGAAGAGAAAAAAGAAAGAAAGAAGAAGAAAAGGAGAGAGAAGAAAGAAAGAAAGGAGAAGAAAG
AAAGAAAAGGAAAGG
Found at i:33404263 original size:44 final size:44
Alignment explanation
Indices: 33404073--33404251 Score: 152
Period size: 44 Copynumber: 4.3 Consensus size: 44
33404063 GTGGTGGGGC
* * *
33404073 AGAAGAGAAAAAAGGAAAGAAA--GAAAGGAG-AGGGAAGAAAGAA
1 AGAA-AGAAAGAAGGAAAGAAAGGGAAAGGAGAAGAGAA-AAAAAA
* * *
33404116 AGAAAGGAGAGGAAAGAAAGAAAAGGAAAGGAGAAGAG--AAAAAA
1 AGAAA-GA-AAGAAGGAAAGAAAGGGAAAGGAGAAGAGAAAAAAAA
* *
33404160 GGAAAGAAAGAA-G-AAG--A---AAAGGAGAAGAGAAGAAAAA
1 AGAAAGAAAGAAGGAAAGAAAGGGAAAGGAGAAGAGAAAAAAAA
33404197 AGAAAGAAAGAAGGAAAGAAAGGGAAAGGAGAAGAGAAAAAAAA
1 AGAAAGAAAGAAGGAAAGAAAGGGAAAGGAGAAGAGAAAAAAAA
33404241 AG-AAG-AAGAAG
1 AGAAAGAAAGAAG
33404252 AGGGAAGAAA
Statistics
Matches: 112, Mismatches: 10, Indels: 29
0.74 0.07 0.19
Matches are distributed among these distances:
35 12 0.11
37 16 0.14
38 2 0.02
39 3 0.03
40 3 0.03
41 2 0.02
42 11 0.10
43 11 0.10
44 41 0.37
46 8 0.07
47 3 0.03
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (44 bp):
AGAAAGAAAGAAGGAAAGAAAGGGAAAGGAGAAGAGAAAAAAAA
Found at i:33410576 original size:26 final size:26
Alignment explanation
Indices: 33410527--33410579 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
33410517 ACACACTAAA
* *
33410527 ATTATTAATTTTATACTACGAATAAT
1 ATTAATAATTTTATACTACAAATAAT
33410553 ATTAATAATTTTATACT-CAAAATAAT
1 ATTAATAATTTTATACTAC-AAATAAT
33410579 A
1 A
33410580 CACACTANNN
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 23 0.96
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (26 bp):
ATTAATAATTTTATACTACAAATAAT
Found at i:33410874 original size:3 final size:3
Alignment explanation
Indices: 33410866--33410915 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
33410856 TCTTCATACT
33410866 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
33410914 AA
1 AA
33410916 TAATAATAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:33410920 original size:3 final size:3
Alignment explanation
Indices: 33410914--33410978 Score: 112
Period size: 3 Copynumber: 21.3 Consensus size: 3
33410904 CAACAACAAC
33410914 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
33410962 AAT AAT ACT AACT AAT A
1 AAT AAT AAT AA-T AAT A
33410979 CTTTTATTTT
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
3 56 0.95
4 3 0.05
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:33411063 original size:12 final size:12
Alignment explanation
Indices: 33411020--33411049 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
33411010 CTAAACTACA
33411020 ACAAAAAATATT
1 ACAAAAAATATT
33411032 ACAAAAAATATT
1 ACAAAAAATATT
33411044 ACAAAA
1 ACAAAA
33411050 TATACAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.70, C:0.10, G:0.00, T:0.20
Consensus pattern (12 bp):
ACAAAAAATATT
Found at i:33411072 original size:21 final size:20
Alignment explanation
Indices: 33411024--33411074 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 20
33411014 ACTACAACAA
33411024 AAAATATTACAAAAAATATTAC
1 AAAATA-TACAAAAAATA-TAC
33411046 AAAATATACAAAATAATA-AC
1 AAAATATACAAAA-AATATAC
33411066 AATAATATA
1 AA-AATATA
33411075 ATCAATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 4 0.15
21 13 0.48
22 10 0.37
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (20 bp):
AAAATATACAAAAAATATAC
Found at i:33411320 original size:27 final size:27
Alignment explanation
Indices: 33411214--33411312 Score: 162
Period size: 27 Copynumber: 3.7 Consensus size: 27
33411204 TATAAATAAT
*
33411214 ACCAGTGGTGCCGCCAATGGTATTGGC
1 ACCATTGGTGCCGCCAATGGTATTGGC
*
33411241 ACAATTGGTGCCGCCAATGGTATTGGC
1 ACCATTGGTGCCGCCAATGGTATTGGC
*
33411268 ACCATTGGTGCCGCCAATGGTTTTGGC
1 ACCATTGGTGCCGCCAATGGTATTGGC
*
33411295 ACCTTTGGTGCCGCCAAT
1 ACCATTGGTGCCGCCAAT
33411313 ACCATTGGGG
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 67 1.00
ACGTcount: A:0.18, C:0.26, G:0.29, T:0.26
Consensus pattern (27 bp):
ACCATTGGTGCCGCCAATGGTATTGGC
Found at i:33411418 original size:29 final size:29
Alignment explanation
Indices: 33411386--33411486 Score: 152
Period size: 29 Copynumber: 3.5 Consensus size: 29
33411376 TTTTTTTGAT
33411386 ATATTTTGGTAAATAATAAAAAAGTTTAA
1 ATATTTTGGTAAATAATAAAAAAGTTTAA
*
33411415 ATATTTTGGTAAATAAAAAAAAAG-TTATA
1 ATATTTTGGTAAATAATAAAAAAGTTTA-A
*
33411444 ATATTTTGATAAATAATAAAAAAGTTGT-A
1 ATATTTTGGTAAATAATAAAAAAGTT-TAA
33411473 ATATTTTGGTAAAT
1 ATATTTTGGTAAAT
33411487 TTTTATTTTT
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
28 3 0.05
29 60 0.92
30 1 0.02
31 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (29 bp):
ATATTTTGGTAAATAATAAAAAAGTTTAA
Found at i:33412543 original size:37 final size:36
Alignment explanation
Indices: 33412502--33412571 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
33412492 AAAATGCGAG
* * * *
33412502 AAATGCATATTATCTGTTTGGTGATATGAAATGTTAT
1 AAATGCATACTATC-GTTGGGCGATATAAAATGTTAT
*
33412539 AAATGTATACTATCGTTGGGCGATATAAAATGT
1 AAATGCATACTATCGTTGGGCGATATAAAATGT
33412572 AAGAAAGTCG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
36 16 0.57
37 12 0.43
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.39
Consensus pattern (36 bp):
AAATGCATACTATCGTTGGGCGATATAAAATGTTAT
Found at i:33415831 original size:114 final size:113
Alignment explanation
Indices: 33415659--33415975 Score: 463
Period size: 114 Copynumber: 2.8 Consensus size: 113
33415649 AAAGCGCGTC
* * * * * *
33415659 AAAATACCTAAGCCCAACGATGCCGTTTTCGGAGCTTTCAGGGATTTAGTGGCGTTTCTAAGAAA
1 AAAATACCTAAGACCAACGACGCCGTTTTCTGAGCTGTCGGGGATTTAGTGGCGTTTCTAGGAAA
* *
33415724 GTGCAGCTAATGCTCAGTGATTTAGCGGCGTTTTTGGGAAAGCGCCACA
66 GCGCCGCTAATGCTCAG-GATTTAGCGGCGTTTTTGGGAAAGCGCCACA
* *
33415773 AAAATACCTAAGGCCAACGACGCCGTTTTCTGAGCTGTCGGGGATTTAGTGGCGTTTCTAGGTAA
1 AAAATACCTAAGACCAACGACGCCGTTTTCTGAGCTGTCGGGGATTTAGTGGCGTTTCTAGGAAA
* * *
33415838 GCGCCGCTAACGCTCAGGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCA
66 GCGCCGCTAATGCTCA-GGATTTAGCGGCGTTTTTGGGAAAGCGCCACA
* *
33415887 AAAATACCTAAGACCAACGACGCCGTTTTCTGAGCTGTCGGGGATTTAGCGGCGTTTTTAGGAAA
1 AAAATACCTAAGACCAACGACGCCGTTTTCTGAGCTGTCGGGGATTTAGTGGCGTTTCTAGGAAA
*
33415952 GCGCCGTTAATGCTCAAGGATTTA
66 GCGCCGCTAATGCTC-AGGATTTA
33415976 AAATAATTTA
Statistics
Matches: 182, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
114 180 0.99
115 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (113 bp):
AAAATACCTAAGACCAACGACGCCGTTTTCTGAGCTGTCGGGGATTTAGTGGCGTTTCTAGGAAA
GCGCCGCTAATGCTCAGGATTTAGCGGCGTTTTTGGGAAAGCGCCACA
Found at i:33416272 original size:38 final size:39
Alignment explanation
Indices: 33416163--33416270 Score: 114
Period size: 38 Copynumber: 2.8 Consensus size: 39
33416153 GTCGGGGTAT
** *
33416163 GAATTTA-GGGTTTGGGATTTAATGTTTAGGGGTTAGGG
1 GAATTTAGGGGTTAAGGATTTAAGGTTTAGGGGTTAGGG
* * *
33416201 GAATTTAGGGGTTAAGG-GTTATGCTTTAGGGGTTAGGG
1 GAATTTAGGGGTTAAGGATTTAAGGTTTAGGGGTTAGGG
* *
33416239 G-ATTTAGGGGGTTATGGATTTAGGGTTTAGGG
1 GAATTTA-GGGGTTAAGGATTTAAGGTTTAGGG
33416271 TTTCAACGGT
Statistics
Matches: 57, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
37 5 0.09
38 34 0.60
39 18 0.32
ACGTcount: A:0.20, C:0.01, G:0.42, T:0.37
Consensus pattern (39 bp):
GAATTTAGGGGTTAAGGATTTAAGGTTTAGGGGTTAGGG
Found at i:33418984 original size:18 final size:18
Alignment explanation
Indices: 33418952--33419040 Score: 110
Period size: 18 Copynumber: 4.8 Consensus size: 18
33418942 TATATATTAC
*
33418952 ATTAC-TTACTAAAATAT
1 ATTACATTACTTAAATAT
33418969 ATTACATTACTTAAATAT
1 ATTACATTACTTAAATAT
*
33418987 ATTAC-TTACTAAAATTTAT
1 ATTACATTACTTAAA--TAT
33419006 AACTTACATTACTTAAATAT
1 -A-TTACATTACTTAAATAT
33419026 ATTACATTACTTAAA
1 ATTACATTACTTAAA
33419041 ATTTATATAT
Statistics
Matches: 63, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
17 13 0.21
18 30 0.48
19 4 0.06
20 4 0.06
21 4 0.06
22 8 0.13
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTACATTACTTAAATAT
Found at i:33418996 original size:39 final size:41
Alignment explanation
Indices: 33418943--33419069 Score: 147
Period size: 39 Copynumber: 3.1 Consensus size: 41
33418933 AAATTACAGT
33418943 ATATATTACATTACTTACTAAA-ATAT-A-TTACATTACTTAA
1 ATATATTACATTACTTA--AAATATATAACTTACATTACTTAA
*
33418983 ATATATTAC-TTAC-TAAAATTTATAACTTACATTACTTAA
1 ATATATTACATTACTTAAAATATATAACTTACATTACTTAA
*
33419022 ATATATTACATTACTTAAAATTTATATATATATTACATTACTTAA
1 ATATATTACATTACTTAAAA--TATATA-A-CTTACATTACTTAA
33419067 ATA
1 ATA
33419070 AAATTTAGCT
Statistics
Matches: 75, Mismatches: 3, Indels: 13
0.82 0.03 0.14
Matches are distributed among these distances:
36 3 0.04
37 3 0.04
38 3 0.04
39 26 0.35
40 13 0.17
41 5 0.07
43 5 0.07
44 1 0.01
45 16 0.21
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.44
Consensus pattern (41 bp):
ATATATTACATTACTTAAAATATATAACTTACATTACTTAA
Found at i:33419861 original size:22 final size:21
Alignment explanation
Indices: 33419803--33419878 Score: 95
Period size: 22 Copynumber: 3.6 Consensus size: 21
33419793 NNNNNNNNNN
33419803 TACATAAGTTACATTAATA-TA
1 TACATAA-TTACATTAATATTA
*
33419824 -ACTTAATTA-ATTAATATTA
1 TACATAATTACATTAATATTA
33419843 TACATAACTTACATTAATATTA
1 TACATAA-TTACATTAATATTA
33419865 TACATAAATTACAT
1 TACAT-AATTACAT
33419879 AACTTAATTA
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
18 7 0.15
19 5 0.10
20 10 0.21
21 3 0.06
22 21 0.44
23 2 0.04
ACGTcount: A:0.47, C:0.11, G:0.01, T:0.41
Consensus pattern (21 bp):
TACATAATTACATTAATATTA
Found at i:33419879 original size:9 final size:9
Alignment explanation
Indices: 33419865--33420222 Score: 132
Period size: 9 Copynumber: 42.2 Consensus size: 9
33419855 ATTAATATTA
*
33419865 TACATAAAT
1 TACATAACT
33419874 TACATAACT
1 TACATAACT
33419883 TA-ATTAA-T
1 TACA-TAACT
*
33419891 TA-AT-ATT
1 TACATAACT
33419898 ATACATAACT
1 -TACATAACT
33419908 TACATAACT
1 TACATAACT
33419917 TAC--AACT
1 TACATAACT
***
33419924 TACATTTTTT
1 TACA-TAACT
*
33419934 TA-ATTA-T
1 TACATAACT
*
33419941 T-CATAAAT
1 TACATAACT
33419949 TACATAACT
1 TACATAACT
*
33419958 TACATTAATATT
1 TACA-T-A-ACT
*
33419970 ATACATAAAT
1 -TACATAACT
33419980 TACATAACT
1 TACATAACT
33419989 TA-ATTAA-T
1 TACA-TAACT
*
33419997 TA-AT-ATT
1 TACATAACT
33420004 ATACATAACT
1 -TACATAACT
33420014 TACATAACT
1 TACATAACT
33420023 TAC--AACT
1 TACATAACT
33420030 TACATAACT
1 TACATAACT
***
33420039 TACATTTTTT
1 TACA-TAACT
*
33420049 TA-ATTA-T
1 TACATAACT
*
33420056 T-CATAAAT
1 TACATAACT
33420064 TACATAACT
1 TACATAACT
* *
33420073 TACTTAATT
1 TACATAACT
*
33420082 TTCATAA--
1 TACATAACT
*
33420089 TAAATAACT
1 TACATAACT
*
33420098 TGCATAACT
1 TACATAACT
33420107 TACATAA--
1 TACATAACT
33420114 TACATAACT
1 TACATAACT
* *
33420123 TATATGACT
1 TACATAACT
33420132 TACATAACT
1 TACATAACT
33420141 TACAT-A--
1 TACATAACT
* *
33420147 -GCATAATT
1 TACATAACT
*
33420155 TTCATAA--
1 TACATAACT
*
33420162 TACACAACT
1 TACATAACT
*
33420171 TACATAATT
1 TACATAACT
*
33420180 TTCATAA--
1 TACATAACT
*
33420187 TAAATAACT
1 TACATAACT
33420196 TACATAA--
1 TACATAACT
33420203 TACATAACT
1 TACATAACT
*
33420212 TACATAGCT
1 TACATAACT
33420221 TA
1 TA
33420223 ATTATACTTA
Statistics
Matches: 267, Mismatches: 42, Indels: 80
0.69 0.11 0.21
Matches are distributed among these distances:
5 3 0.01
6 3 0.01
7 57 0.21
8 23 0.09
9 158 0.59
10 14 0.05
11 2 0.01
12 3 0.01
13 4 0.01
ACGTcount: A:0.44, C:0.15, G:0.01, T:0.40
Consensus pattern (9 bp):
TACATAACT
Found at i:33419895 original size:56 final size:56
Alignment explanation
Indices: 33419821--33420018 Score: 259
Period size: 56 Copynumber: 3.6 Consensus size: 56
33419811 TTACATTAAT
33419821 ATAACTTAATTAATTAATATTATACATAACTTACATTAATATTATACATAAATTAC
1 ATAACTTAATTAATTAATATTATACATAACTTACATTAATATTATACATAAATTAC
* *
33419877 ATAACTTAATTAATTAATATTATACATAACTTACA-T-A-ACT-TAC--AACTTAC
1 ATAACTTAATTAATTAATATTATACATAACTTACATTAATATTATACATAAATTAC
*** * *
33419927 ATTTTTTTAATT-ATTCATA-AATTACATAACTTACATTAATATTATACATAAATTAC
1 A-TAACTTAATTAATTAATATTA-TACATAACTTACATTAATATTATACATAAATTAC
33419983 ATAACTTAATTAATTAATATTATACATAACTTACAT
1 ATAACTTAATTAATTAATATTATACATAACTTACAT
33420019 AACTTACAAC
Statistics
Matches: 118, Mismatches: 14, Indels: 20
0.78 0.09 0.13
Matches are distributed among these distances:
49 1 0.01
50 26 0.22
51 8 0.07
52 4 0.03
53 4 0.03
54 4 0.03
55 8 0.07
56 62 0.53
57 1 0.01
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (56 bp):
ATAACTTAATTAATTAATATTATACATAACTTACATTAATATTATACATAAATTAC
Found at i:33419898 original size:34 final size:34
Alignment explanation
Indices: 33419855--33420024 Score: 202
Period size: 34 Copynumber: 4.9 Consensus size: 34
33419845 CATAACTTAC
33419855 ATTAATATTATACATAAATTACATAACTTAATTA
1 ATTAATATTATACATAAATTACATAACTTAATTA
*
33419889 ATTAATATTATACATAACTTACATAACTTACAACTTA
1 ATTAATATTATACATAAATTACATAACTT--AA-TTA
** * *
33419926 CATTTTTTTAATTATTCATAAATTACATAACTT-A--C
1 -A--TTAAT-ATTATACATAAATTACATAACTTAATTA
33419961 ATTAATATTATACATAAATTACATAACTTAATTA
1 ATTAATATTATACATAAATTACATAACTTAATTA
*
33419995 ATTAATATTATACATAACTTACATAACTTA
1 ATTAATATTATACATAAATTACATAACTTA
33420025 CAACTTACAT
Statistics
Matches: 115, Mismatches: 11, Indels: 20
0.79 0.08 0.14
Matches are distributed among these distances:
31 22 0.19
32 4 0.03
34 58 0.50
36 2 0.02
37 3 0.03
38 2 0.02
40 3 0.03
41 21 0.18
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (34 bp):
ATTAATATTATACATAAATTACATAACTTAATTA
Found at i:33419964 original size:25 final size:24
Alignment explanation
Indices: 33419861--33419994 Score: 65
Period size: 25 Copynumber: 5.2 Consensus size: 24
33419851 TTACATTAAT
*
33419861 ATTATACATAAATTACATAACTTA
1 ATTATTCATAAATTACATAACTTA
* *
33419885 ATTAATTAAT-ATTATACATAACTTA
1 ATT-ATTCATAAAT-TACATAACTTA
* * * ***
33419910 CATAACTT-ACAACTTACATTTTTTTA
1 -ATTA-TTCATAAATTACA-TAACTTA
33419936 ATTATTCATAAATTACATAACTTA
1 ATTATTCATAAATTACATAACTTA
33419960 CATTAATATTATACATAAATTACATAACTTA
1 -A-T--TA-T-T-CATAAATTACATAACTTA
33419991 ATTA
1 ATTA
33419995 ATTAATATTA
Statistics
Matches: 81, Mismatches: 15, Indels: 25
0.67 0.12 0.21
Matches are distributed among these distances:
24 11 0.14
25 33 0.41
26 11 0.14
27 2 0.02
28 2 0.02
29 2 0.02
30 2 0.02
31 18 0.22
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.42
Consensus pattern (24 bp):
ATTATTCATAAATTACATAACTTA
Found at i:33420028 original size:106 final size:110
Alignment explanation
Indices: 33419843--33420093 Score: 397
Period size: 106 Copynumber: 2.3 Consensus size: 110
33419833 ATTAATATTA
33419843 TACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACT
1 TACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACT
33419908 TAC-A-T-AACTTAC-AACTTACATTTTTTTAATTATTCATAAAT
66 TACAACTAAACTTACAAACTTACATTTTTTTAATTATTCATAAAT
33419949 TACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACT
1 TACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACT
33420014 TACATAACTTACAACTTACATAACTTACATTTTTTTAATTATTCATAAAT
66 TAC--AAC-TA-AACTTACA-AACTTACATTTTTTTAATTATTCATAAAT
*
33420064 TACATAACTTAC-TTAATTTTCATA-ATAAAT
1 TACATAACTTACATTAATATT-ATACATAAAT
33420094 AACTTGCATA
Statistics
Matches: 134, Mismatches: 1, Indels: 12
0.91 0.01 0.08
Matches are distributed among these distances:
106 68 0.51
109 1 0.01
111 1 0.01
113 7 0.05
114 13 0.10
115 44 0.33
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (110 bp):
TACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACT
TACAACTAAACTTACAAACTTACATTTTTTTAATTATTCATAAAT
Found at i:33420031 original size:16 final size:16
Alignment explanation
Indices: 33420010--33420042 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
33420000 TATTATACAT
33420010 AACTTACATAACTTAC
1 AACTTACATAACTTAC
33420026 AACTTACATAACTTAC
1 AACTTACATAACTTAC
33420042 A
1 A
33420043 TTTTTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.30
Consensus pattern (16 bp):
AACTTACATAACTTAC
Found at i:33420033 original size:25 final size:25
Alignment explanation
Indices: 33420005--33420146 Score: 98
Period size: 25 Copynumber: 5.6 Consensus size: 25
33419995 ATTAATATTA
*
33420005 TACATAACTTACATAACTTACAACT
1 TACATAACTTACATAACTTATAACT
** *
33420030 TACATAACTTACAT-TTTTTTAA-T
1 TACATAACTTACATAACTTATAACT
* *
33420053 TATTCATAAATTACATAACTTACTTAATT
1 TA--CATAACTTACATAACTTA--TAACT
* *
33420082 TTCATAA--TAAATAACTTGCATAACT
1 TACATAACTTACATAACTT--ATAACT
33420107 TACATAA--TACATAACTTATATGACT
1 TACATAACTTACATAACTTATA--ACT
33420132 TACATAACTTACATA
1 TACATAACTTACATA
33420147 GCATAATTTT
Statistics
Matches: 92, Mismatches: 13, Indels: 22
0.72 0.10 0.17
Matches are distributed among these distances:
23 6 0.07
24 4 0.04
25 63 0.68
26 2 0.02
27 12 0.13
28 3 0.03
29 2 0.02
ACGTcount: A:0.42, C:0.17, G:0.01, T:0.39
Consensus pattern (25 bp):
TACATAACTTACATAACTTATAACT
Found at i:33420043 original size:34 final size:33
Alignment explanation
Indices: 33420005--33420217 Score: 120
Period size: 34 Copynumber: 6.5 Consensus size: 33
33419995 ATTAATATTA
* *
33420005 TACATAACTTACATAACTTACAACTTACATAACT
1 TACATAATTTACATAA-TTATAACTTACATAACT
** * *
33420039 TACATTTTTTTA-ATTATTCATAAATTACATAACT
1 TACA-TAATTTACATAATT-ATAACTTACATAACT
* * * *
33420073 TACTTAATTTTCATAATAAATAACTTGCATAACT
1 TACATAATTTACATAAT-TATAACTTACATAACT
33420107 TACATAA--TACATAACTTATATGACTTACATAACT
1 TACATAATTTACATAA-TTATA--ACTTACATAACT
*** * *
33420141 TACATAGCATA-AT-TTTCATAA--TACACAACT
1 TACATAATTTACATAATT-ATAACTTACATAACT
* *
33420171 TACATAATTTTCATAATAAATAACTTACATAA--
1 TACATAATTTACATAAT-TATAACTTACATAACT
*
33420203 TACATAACTTACATA
1 TACATAATTTACATA
33420218 GCTTAATTAT
Statistics
Matches: 134, Mismatches: 30, Indels: 32
0.68 0.15 0.16
Matches are distributed among these distances:
30 15 0.11
31 2 0.01
32 28 0.21
33 9 0.07
34 72 0.54
35 6 0.04
36 2 0.01
ACGTcount: A:0.44, C:0.17, G:0.01, T:0.38
Consensus pattern (33 bp):
TACATAATTTACATAATTATAACTTACATAACT
Found at i:33420072 original size:84 final size:84
Alignment explanation
Indices: 33419967--33420124 Score: 221
Period size: 84 Copynumber: 1.9 Consensus size: 84
33419957 TTACATTAAT
* * *
33419967 ATTATACATAAATTACATAACTTAATTAATTAAT-ATTATACATAACTTACATAACTTACA-ACT
1 ATTATACATAAATTACATAACTTAATTAATT-ATCATAATAAATAACTTACATAACTTACATA-A
33420030 TACATAACTTACATTTTTTTA
64 TACATAACTTACATTTTTTTA
* * * *
33420051 ATTATTCATAAATTACATAACTTACTTAATTTTCATAATAAATAACTTGCATAACTTACATAATA
1 ATTATACATAAATTACATAACTTAATTAATTATCATAATAAATAACTTACATAACTTACATAATA
33420116 CATAACTTA
66 CATAACTTA
33420125 TATGACTTAC
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
83 1 0.02
84 63 0.97
85 1 0.02
ACGTcount: A:0.44, C:0.15, G:0.01, T:0.41
Consensus pattern (84 bp):
ATTATACATAAATTACATAACTTAATTAATTATCATAATAAATAACTTACATAACTTACATAATA
CATAACTTACATTTTTTTA
Found at i:33420119 original size:16 final size:16
Alignment explanation
Indices: 33420100--33420217 Score: 92
Period size: 16 Copynumber: 7.8 Consensus size: 16
33420090 AAATAACTTG
33420100 CATAACTTACATAATA
1 CATAACTTACATAATA
* *
33420116 CATAACTTATATGACTTA
1 CATAACTTACAT-A-ATA
*
33420134 CATAACTTACAT-A-G
1 CATAACTTACATAATA
* *
33420148 CATAATTTTCATAATA
1 CATAACTTACATAATA
*
33420164 CACAACTTACATAAT-
1 CATAACTTACATAATA
33420179 --T---TT-CATAATA
1 CATAACTTACATAATA
*
33420189 AATAACTTACATAATA
1 CATAACTTACATAATA
33420205 CATAACTTACATA
1 CATAACTTACATA
33420218 GCTTAATTAT
Statistics
Matches: 78, Mismatches: 13, Indels: 22
0.69 0.12 0.19
Matches are distributed among these distances:
9 6 0.08
10 2 0.03
12 1 0.01
14 10 0.13
15 3 0.04
16 42 0.54
17 1 0.01
18 13 0.17
ACGTcount: A:0.46, C:0.18, G:0.02, T:0.35
Consensus pattern (16 bp):
CATAACTTACATAATA
Found at i:33420177 original size:25 final size:25
Alignment explanation
Indices: 33420064--33420203 Score: 133
Period size: 25 Copynumber: 5.7 Consensus size: 25
33420054 ATTCATAAAT
*
33420064 TACATAACTTACTTAATTTTCATAA
1 TACATAACTTACATAATTTTCATAA
* * * *
33420089 TAAATAACTTGCATAACTTACATAA
1 TACATAACTTACATAATTTTCATAA
* * * *
33420114 TACATAACTTATATGACTTACAT-A
1 TACATAACTTACATAATTTTCATAA
* *
33420138 -AC-TTACATAGCATAATTTTCATAA
1 TACATAACTTA-CATAATTTTCATAA
*
33420162 TACACAACTTACATAATTTTCATAA
1 TACATAACTTACATAATTTTCATAA
*
33420187 TAAATAACTTACATAAT
1 TACATAACTTACATAAT
33420204 ACATAACTTA
Statistics
Matches: 91, Mismatches: 20, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
22 5 0.05
23 10 0.11
24 2 0.02
25 70 0.77
26 4 0.04
ACGTcount: A:0.44, C:0.16, G:0.02, T:0.37
Consensus pattern (25 bp):
TACATAACTTACATAATTTTCATAA
Found at i:33425714 original size:21 final size:21
Alignment explanation
Indices: 33425688--33425759 Score: 92
Period size: 21 Copynumber: 3.4 Consensus size: 21
33425678 CAACAACTTA
*
33425688 AAGCAGAGGCGACAGCGAGGG
1 AAGCAGAGGCGACAGCGAGAG
*
33425709 AAGCAGAGGCTACAGCGAGAG
1 AAGCAGAGGCGACAGCGAGAG
**
33425730 AAGCGAGAGAAG-CAGCGAGAG
1 AAGC-AGAGGCGACAGCGAGAG
33425751 AAGCAGAGG
1 AAGCAGAGG
33425760 TTCAAAAGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
20 4 0.09
21 36 0.82
22 4 0.09
ACGTcount: A:0.39, C:0.17, G:0.43, T:0.01
Consensus pattern (21 bp):
AAGCAGAGGCGACAGCGAGAG
Found at i:33425748 original size:12 final size:12
Alignment explanation
Indices: 33425731--33425756 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
33425721 CAGCGAGAGA
33425731 AGCGAGAGAAGC
1 AGCGAGAGAAGC
33425743 AGCGAGAGAAGC
1 AGCGAGAGAAGC
33425755 AG
1 AG
33425757 AGGTTCAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.42, T:0.00
Consensus pattern (12 bp):
AGCGAGAGAAGC
Found at i:33426241 original size:42 final size:42
Alignment explanation
Indices: 33426192--33426443 Score: 341
Period size: 42 Copynumber: 6.0 Consensus size: 42
33426182 ATTTGTGAAA
*
33426192 TAAGCGCCGCTAAAGAACACT-A-CTTTTAGCGGCGTTTTTGACC
1 TAAGCGCCGCTAAAGAACA-TGATC-TTTAGCGGCGTTTTT-TCC
* *
33426235 -AAGCGCCGCTATAGAACATTA-CTTTTAGCGGCGTTTTTTCC
1 TAAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTTTTTCC
* *
33426276 CAAGCGCCGCTAAAGAACATGATCGTTAGCGGCGTTTTCTTCC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTT-TTCC
*
33426319 TAAGCGACGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCC
* *
33426361 AAAGCGCCGCTAAAGAACATGATCTTTAGCGGCATTTTTTCC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCC
* *
33426403 TAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCTTTTTTTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTC
33426444 TATAAGCACC
Statistics
Matches: 191, Mismatches: 14, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
41 3 0.02
42 148 0.77
43 40 0.21
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.31
Consensus pattern (42 bp):
TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCC
Found at i:33426367 original size:127 final size:127
Alignment explanation
Indices: 33426192--33426440 Score: 353
Period size: 127 Copynumber: 2.0 Consensus size: 127
33426182 ATTTGTGAAA
* * *
33426192 TAAGCGCCGCTAAAGAACACTACTTTTAGCGGCGTTTTTGACCAAGCGCCGCTATAGAACATTA-
1 TAAGCGACGCTAAAGAACACTACTTTTAGCGGCGTTTTTGACCAAGCGCCGCTAAAGAACATGAT
*
33426256 CTTTTAGCGGCGTTTTTTCCCAAGCGCCGCTAAAGAACATGATCGTTAGCGGCGTTTTCTTCC
66 C-TTTAGCGGCATTTTTTCCCAAGCGCCGCTAAAGAACATGATCGTTAGCGGCGTTTTCTTCC
*
33426319 TAAGCGACGCTAAAGAACA-TGA-TCTTTAGCGGCGTTTTT-TCCAAAGCGCCGCTAAAGAACAT
1 TAAGCGACGCTAAAGAACACT-ACT-TTTAGCGGCGTTTTTGACC-AAGCGCCGCTAAAGAACAT
* * * *
33426381 GATCTTTAGCGGCATTTTTTCCTAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCTTTTT
63 GATCTTTAGCGGCATTTTTTCCCAAGCGCCGCTAAAGAACATGATCGTTAGCGGCGTTTT
33426441 TTCTATAAGC
Statistics
Matches: 109, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
126 4 0.04
127 104 0.95
128 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (127 bp):
TAAGCGACGCTAAAGAACACTACTTTTAGCGGCGTTTTTGACCAAGCGCCGCTAAAGAACATGAT
CTTTAGCGGCATTTTTTCCCAAGCGCCGCTAAAGAACATGATCGTTAGCGGCGTTTTCTTCC
Found at i:33437085 original size:31 final size:31
Alignment explanation
Indices: 33437025--33437085 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
33437015 TGTGTTGAAA
* *
33437025 TTTAAACTTGACAATTGTTCTCACGTTGGGG
1 TTTAAACTAGACAATTGTTCTCACATTGGGG
*
33437056 TTTAAACTAGACAATTGTTCTCATATTGGG
1 TTTAAACTAGACAATTGTTCTCACATTGGG
33437086 ACCTTAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (31 bp):
TTTAAACTAGACAATTGTTCTCACATTGGGG
Found at i:33438342 original size:37 final size:37
Alignment explanation
Indices: 33438270--33438357 Score: 104
Period size: 37 Copynumber: 2.4 Consensus size: 37
33438260 TGGGAGAATT
* * *
33438270 TTTGTAGAGAATCGTTATTGTTCATCTTCATCTTTTC
1 TTTGTAGAGAATCATCATTGTTCATCTTCACCTTTTC
** *
33438307 TTTGTAGAGAATCATCATTGTTCATCTTTGCCTTTTG
1 TTTGTAGAGAATCATCATTGTTCATCTTCACCTTTTC
*
33438344 TCTTCTAGAGAATC
1 T-TTGTAGAGAATC
33438358 TTTACTATTT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
37 32 0.74
38 11 0.26
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.48
Consensus pattern (37 bp):
TTTGTAGAGAATCATCATTGTTCATCTTCACCTTTTC
Found at i:33446706 original size:23 final size:21
Alignment explanation
Indices: 33446640--33446707 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 21
33446630 TGTGGAAGAT
* *
33446640 CACATGCCTGTGTGA-GAGGA
1 CACACGCCTGTGTGACGATGA
*
33446660 GGCACACGCCTGTGTGACTATGA
1 --CACACGCCTGTGTGACGATGA
33446683 CACACGCCTGTGTGACCGAGTGA
1 CACACGCCTGTGTGA-CGA-TGA
33446706 CA
1 CA
33446708 TGGCCGTGTG
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
21 15 0.38
22 16 0.41
23 8 0.21
ACGTcount: A:0.24, C:0.26, G:0.31, T:0.19
Consensus pattern (21 bp):
CACACGCCTGTGTGACGATGA
Found at i:33450948 original size:15 final size:16
Alignment explanation
Indices: 33450928--33450964 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
33450918 AAGTATAATA
*
33450928 AAATATTTTTA-AAAT
1 AAATATTTTTAGAAAG
33450943 AAATATTTTTAGAAAG
1 AAATATTTTTAGAAAG
33450959 AAATAT
1 AAATAT
33450965 GTGATAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (16 bp):
AAATATTTTTAGAAAG
Found at i:33464671 original size:44 final size:44
Alignment explanation
Indices: 33464608--33464694 Score: 165
Period size: 44 Copynumber: 2.0 Consensus size: 44
33464598 CATCAAACTG
33464608 GCAAGTAAGCTCTTGTACCCTCTATTATTCTTTTAATATACCTA
1 GCAAGTAAGCTCTTGTACCCTCTATTATTCTTTTAATATACCTA
*
33464652 GCAAGTAAGCTCTTGTACCCTCTATTCTTCTTTTAATATACCT
1 GCAAGTAAGCTCTTGTACCCTCTATTATTCTTTTAATATACCT
33464695 TGTTAGAGTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.25, C:0.24, G:0.09, T:0.41
Consensus pattern (44 bp):
GCAAGTAAGCTCTTGTACCCTCTATTATTCTTTTAATATACCTA
Found at i:33466100 original size:11 final size:11
Alignment explanation
Indices: 33466084--33466110 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
33466074 TAAATAAGTT
33466084 AAGAACACTTC
1 AAGAACACTTC
33466095 AAGAACACTTC
1 AAGAACACTTC
33466106 AAGAA
1 AAGAA
33466111 TAATAATAAG
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:0.52, C:0.22, G:0.11, T:0.15
Consensus pattern (11 bp):
AAGAACACTTC
Found at i:33466134 original size:2 final size:2
Alignment explanation
Indices: 33466127--33466155 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
33466117 TAAGAAATAA
33466127 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 A
33466156 TGAAAGATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:33471306 original size:12 final size:12
Alignment explanation
Indices: 33471279--33471311 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
33471269 AACTAAATGA
*
33471279 TTTTTTTTTCTC
1 TTTTTGTTTCTC
33471291 -TTTTGTTTCTC
1 TTTTTGTTTCTC
33471302 TTTTTGTTTC
1 TTTTTGTTTC
33471312 GTTTGTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (12 bp):
TTTTTGTTTCTC
Found at i:33472461 original size:27 final size:28
Alignment explanation
Indices: 33472425--33472478 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
33472415 GTAACAGTAC
* *
33472425 AGTGTGGGC-TTATCCCAATATAGTAAT
1 AGTGTAGGCTTTAGCCCAATATAGTAAT
33472452 AGTGTAGGCTTTAGCCCAATATAGTAA
1 AGTGTAGGCTTTAGCCCAATATAGTAA
33472479 CAGTACTGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.31
Consensus pattern (28 bp):
AGTGTAGGCTTTAGCCCAATATAGTAAT
Found at i:33472614 original size:26 final size:26
Alignment explanation
Indices: 33472585--33472691 Score: 180
Period size: 26 Copynumber: 4.1 Consensus size: 26
33472575 AACACTCTAA
33472585 TATCGCTA-CAAAGCTGCCAGTAACAG
1 TATCGC-AGCAAAGCTGCCAGTAACAG
33472611 TATCGCAGCAAAGCTGCCAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
*
33472637 TATTGCAGCAAAGCTGCCAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
*
33472663 TATCGCAGCAAAGCTTCCAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
33472689 TAT
1 TAT
33472692 ACTTCCTCCA
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
25 1 0.01
26 76 0.99
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.20
Consensus pattern (26 bp):
TATCGCAGCAAAGCTGCCAGTAACAG
Found at i:33472888 original size:27 final size:27
Alignment explanation
Indices: 33472857--33472996 Score: 172
Period size: 27 Copynumber: 5.2 Consensus size: 27
33472847 GTATAACAAA
33472857 CATTTTACCCTATAGGGGTATTTCGGT
1 CATTTTACCCTATAGGGGTATTTCGGT
* * * *
33472884 TATTTTACCATGTAGGGGTATTCCGGT
1 CATTTTACCCTATAGGGGTATTTCGGT
*
33472911 CATTTTACCCTATAGAGGTATTTCGGT
1 CATTTTACCCTATAGGGGTATTTCGGT
* * * **
33472938 TATTTTATCATATAGGATTATTTCGGT
1 CATTTTACCCTATAGGGGTATTTCGGT
* *
33472965 CATTGTACCCTATAGGGGTATTTCAGT
1 CATTTTACCCTATAGGGGTATTTCGGT
33472992 CATTT
1 CATTT
33472997 ATTAACCTCT
Statistics
Matches: 90, Mismatches: 23, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 90 1.00
ACGTcount: A:0.21, C:0.16, G:0.20, T:0.43
Consensus pattern (27 bp):
CATTTTACCCTATAGGGGTATTTCGGT
Found at i:33472915 original size:54 final size:54
Alignment explanation
Indices: 33472857--33472988 Score: 201
Period size: 54 Copynumber: 2.4 Consensus size: 54
33472847 GTATAACAAA
* *
33472857 CATTTTACCCTATAGGGGTATTTCGGTTATTTTACCATGTAGGGGTATTCCGGT
1 CATTTTACCCTATAGGGGTATTTCGGTTATTTTACCATATAGGAGTATTCCGGT
* * * *
33472911 CATTTTACCCTATAGAGGTATTTCGGTTATTTTATCATATAGGATTATTTCGGT
1 CATTTTACCCTATAGGGGTATTTCGGTTATTTTACCATATAGGAGTATTCCGGT
*
33472965 CATTGTACCCTATAGGGGTATTTC
1 CATTTTACCCTATAGGGGTATTTC
33472989 AGTCATTTAT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 70 1.00
ACGTcount: A:0.21, C:0.16, G:0.20, T:0.42
Consensus pattern (54 bp):
CATTTTACCCTATAGGGGTATTTCGGTTATTTTACCATATAGGAGTATTCCGGT
Found at i:33474743 original size:50 final size:50
Alignment explanation
Indices: 33474681--33474776 Score: 149
Period size: 50 Copynumber: 1.9 Consensus size: 50
33474671 ACCTTATTCT
*
33474681 AATCAATGTCAAATAAAAGGAA-AGAAGTTTTATACGGATTCTACTTGTAC
1 AATCAATATCAAATAAAA-GAAGAGAAGTTTTATACGGATTCTACTTGTAC
* *
33474731 AATCAATATCAAATAGAAGAAGAGTAGTTTTATACGGATTCTACTT
1 AATCAATATCAAATAAAAGAAGAGAAGTTTTATACGGATTCTACTT
33474777 ATGCCACTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
49 3 0.07
50 39 0.93
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (50 bp):
AATCAATATCAAATAAAAGAAGAGAAGTTTTATACGGATTCTACTTGTAC
Found at i:33476311 original size:13 final size:13
Alignment explanation
Indices: 33476293--33476332 Score: 80
Period size: 13 Copynumber: 3.1 Consensus size: 13
33476283 TTAATTTATA
33476293 TGTGTGAAAATTT
1 TGTGTGAAAATTT
33476306 TGTGTGAAAATTT
1 TGTGTGAAAATTT
33476319 TGTGTGAAAATTT
1 TGTGTGAAAATTT
33476332 T
1 T
33476333 ATCGTTTGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (13 bp):
TGTGTGAAAATTT
Found at i:33477571 original size:43 final size:42
Alignment explanation
Indices: 33477467--33477579 Score: 106
Period size: 43 Copynumber: 2.7 Consensus size: 42
33477457 GAGATTTACG
* ** * *
33477467 TGTAAGACCATGTCTGGGACA-TAGGCATCGTATATGTTTTCG
1 TGTAAGACCACGTCTGGGACAGT-GGCATCGTATATGGATACA
* *
33477509 TGTAAGACC-CTGTCCGGGACAGTGGCATCGTTATTTGGATACA
1 TGTAAGACCAC-GTCTGGGACAGTGGCATCG-TATATGGATACA
33477552 TGTAAGACCACGTCTGGGAC-GTTGGCAT
1 TGTAAGACCACGTCTGGGACAG-TGGCAT
33477580 TGTACGAGCT
Statistics
Matches: 58, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
42 26 0.45
43 31 0.53
44 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.29
Consensus pattern (42 bp):
TGTAAGACCACGTCTGGGACAGTGGCATCGTATATGGATACA
Found at i:33478527 original size:2 final size:2
Alignment explanation
Indices: 33478520--33478550 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
33478510 ATTGGTCGTG
33478520 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
33478551 GGAGCTTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33480395 original size:32 final size:33
Alignment explanation
Indices: 33480359--33480432 Score: 82
Period size: 32 Copynumber: 2.3 Consensus size: 33
33480349 TCATAAACTT
33480359 ATAAATTGATT-ACTTGAATTT-AGTAACTCA-TG
1 ATAAATTGATTCA-TTGAATTTGA-TAACTCATTG
* *
33480391 ATAAATTAATTCATTTAATTTGATAACTCATTG
1 ATAAATTGATTCATTGAATTTGATAACTCATTG
*
33480424 ATTAATTGA
1 ATAAATTGA
33480433 ACTTGTTAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
32 24 0.69
33 11 0.31
ACGTcount: A:0.39, C:0.08, G:0.09, T:0.43
Consensus pattern (33 bp):
ATAAATTGATTCATTGAATTTGATAACTCATTG
Found at i:33483701 original size:19 final size:19
Alignment explanation
Indices: 33483677--33483715 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
33483667 CAACATACAT
33483677 AGAATTATTATTAGGAATC
1 AGAATTATTATTAGGAATC
33483696 AGAATTATTATTAGGAATC
1 AGAATTATTATTAGGAATC
33483715 A
1 A
33483716 AAATCTAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.36
Consensus pattern (19 bp):
AGAATTATTATTAGGAATC
Found at i:33494714 original size:25 final size:25
Alignment explanation
Indices: 33494685--33494735 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
33494675 TGTTTGGGTG
33494685 ATCTGAAGAGGGGGAACAAGAAGCT
1 ATCTGAAGAGGGGGAACAAGAAGCT
33494710 ATCTGAAGAGGGGGAACAAGAAGCT
1 ATCTGAAGAGGGGGAACAAGAAGCT
33494735 A
1 A
33494736 ACTAACCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.41, C:0.12, G:0.35, T:0.12
Consensus pattern (25 bp):
ATCTGAAGAGGGGGAACAAGAAGCT
Found at i:33502987 original size:12 final size:12
Alignment explanation
Indices: 33502957--33502989 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
33502947 TATATATTTT
33502957 AAAATT-ATATA
1 AAAATTAATATA
33502968 AAAA-TAATATA
1 AAAATTAATATA
33502979 AAAATTAATAT
1 AAAATTAATAT
33502990 GGGCGGGTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:33507703 original size:3 final size:3
Alignment explanation
Indices: 33507697--33507749 Score: 52
Period size: 3 Copynumber: 17.7 Consensus size: 3
33507687 GATATAAAAA
* ** * * *
33507697 AAT AAT AAT AAT ACT AAT AAT AAT AGC AGT AGT AGT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
33507745 AAT AA
1 AAT AA
33507750 GAGTATTAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.58, C:0.04, G:0.08, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:33511256 original size:43 final size:44
Alignment explanation
Indices: 33511191--33511281 Score: 107
Period size: 43 Copynumber: 2.1 Consensus size: 44
33511181 TACATGTAAT
* *
33511191 CACATATCGATGCCACTATCCCAGACAG-GATCTTACAC-ATAAA
1 CACAAATCGATGCCACTATCCCAGAC-GTGATCTTACACTAAAAA
* *
33511234 CACAAATCGATGCCAAC-GTCCCAGACGTGGTCTTACACTAAAAA
1 CACAAATCGATGCC-ACTATCCCAGACGTGATCTTACACTAAAAA
33511278 CACA
1 CACA
33511282 TATTAGAGGT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
42 1 0.02
43 30 0.73
44 10 0.24
ACGTcount: A:0.37, C:0.31, G:0.13, T:0.19
Consensus pattern (44 bp):
CACAAATCGATGCCACTATCCCAGACGTGATCTTACACTAAAAA
Found at i:33513063 original size:41 final size:41
Alignment explanation
Indices: 33513005--33513095 Score: 146
Period size: 41 Copynumber: 2.2 Consensus size: 41
33512995 GCATGTAGTC
*
33513005 ACCACTACTAAAGATTCTTTGAAATTCTTTGGTATGTAATT
1 ACCACTATTAAAGATTCTTTGAAATTCTTTGGTATGTAATT
* *
33513046 ACTACTATTAAATATTCTTTGAAATTCTTTGGTATGTAATT
1 ACCACTATTAAAGATTCTTTGAAATTCTTTGGTATGTAATT
*
33513087 GCCACTATT
1 ACCACTATT
33513096 CACTTCTTTC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (41 bp):
ACCACTATTAAAGATTCTTTGAAATTCTTTGGTATGTAATT
Found at i:33516409 original size:20 final size:20
Alignment explanation
Indices: 33516387--33516423 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
33516377 TAGTTCCAAA
*
33516387 AAAATA-ATTTTATAATTTT
1 AAAATATATTTTAAAATTTT
33516406 AAAATATATTTTAAAATT
1 AAAATATATTTTAAAATT
33516424 AAATTAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AAAATATATTTTAAAATTTT
Found at i:33516940 original size:18 final size:18
Alignment explanation
Indices: 33516912--33516949 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
33516902 AAAAGTGTTT
33516912 AATATATTATT-ATAAAA
1 AATATATTATTCATAAAA
33516929 AATATAATTATTCATAAAA
1 AATAT-ATTATTCATAAAA
33516948 AA
1 AA
33516950 ATGTTATAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.26
18 6 0.32
19 8 0.42
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (18 bp):
AATATATTATTCATAAAA
Found at i:33517791 original size:18 final size:17
Alignment explanation
Indices: 33517751--33517794 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
33517741 ATTTAGAAAT
33517751 TATTTTTATAATACTAA
1 TATTTTTATAATACTAA
* *
33517768 TAATTTTTATAGTAATTAA
1 T-ATTTTTATAAT-ACTAA
33517787 TATTTTTA
1 TATTTTTA
33517795 AAAATATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.04
18 17 0.74
19 5 0.22
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (17 bp):
TATTTTTATAATACTAA
Found at i:33518194 original size:19 final size:18
Alignment explanation
Indices: 33518163--33518200 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
33518153 TTTTTATGAG
33518163 TATTTTATATTTGAGATT
1 TATTTTATATTTGAGATT
*
33518181 TATTTTATTATTTGATATT
1 TATTTTA-TATTTGAGATT
33518200 T
1 T
33518201 GTAAATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.66
Consensus pattern (18 bp):
TATTTTATATTTGAGATT
Found at i:33518917 original size:16 final size:17
Alignment explanation
Indices: 33518889--33518920 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
33518879 GAAATAAATT
33518889 TATAAATATATTTTTAA
1 TATAAATATATTTTTAA
33518906 TATAAA-ATATTTTTA
1 TATAAATATATTTTTA
33518921 TTCACTCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATAAATATATTTTTAA
Found at i:33518969 original size:15 final size:16
Alignment explanation
Indices: 33518942--33518971 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
33518932 CGTGGGTGTG
33518942 ATAAAATCTAGTATTA
1 ATAAAATCTAGTATTA
33518958 ATAAAA-CTAGTATT
1 ATAAAATCTAGTATT
33518972 CGTCCAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.37
Consensus pattern (16 bp):
ATAAAATCTAGTATTA
Found at i:33522207 original size:24 final size:25
Alignment explanation
Indices: 33522180--33522227 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
33522170 TCCGGTAATT
33522180 GCTCTTTG-GAACTACCCGTTATAG
1 GCTCTTTGTGAACTACCCGTTATAG
* *
33522204 GCTCTTTGTGAGCTTCCCGTTATA
1 GCTCTTTGTGAACTACCCGTTATA
33522228 TTGCCCGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.17, C:0.25, G:0.21, T:0.38
Consensus pattern (25 bp):
GCTCTTTGTGAACTACCCGTTATAG
Found at i:33526511 original size:109 final size:109
Alignment explanation
Indices: 33526318--33526759 Score: 762
Period size: 109 Copynumber: 4.1 Consensus size: 109
33526308 TACGCATACT
*
33526318 AATATCCTTTTAAAAATTTCAAAATAAGGCAATGTTTTGCTTTTGGAAATTCGAGAAAACGTGCC
1 AATATCCTTTTAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
* *
33526383 CTAATGTGTTGGGTATCGATTTTTCTCGTTCGACCAAATAGCCA
66 CTAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
33526427 AATATCCTTTTAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
1 AATATCCTTTTAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
*
33526492 CTAATGTGCTGGGTTTCGATTTTTCTCGTTTGACCAAATAGCCA
66 CTAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
*
33526536 AATATCTTTTTAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
1 AATATCCTTTTAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
* * *
33526601 CTAATGTGTTGGGTTTCAATTTTTCTCGTTCGACCAAATAGCAA
66 CTAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
* *
33526645 AATATCCTTTTAAAAATTTCAAAATAAGGCAATGTTTTGCGCTTGAAAATTCGAGAAAACGTGCC
1 AATATCCTTTTAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
* *
33526710 CTAATGTGCTAGGTTTCGA--TTTCTCGTTCGATCAAATAGCCA
66 CTAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
33526752 AATATCCT
1 AATATCCT
33526760 CCTAAATCTT
Statistics
Matches: 316, Mismatches: 17, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
107 29 0.09
109 287 0.91
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Consensus pattern (109 bp):
AATATCCTTTTAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
CTAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
Found at i:33527697 original size:16 final size:16
Alignment explanation
Indices: 33527676--33527711 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
33527666 TTGTTGTTTT
*
33527676 ATTTTGACTGCATGGC
1 ATTTTGACTACATGGC
33527692 ATTTTGACTACATGGC
1 ATTTTGACTACATGGC
33527708 ATTT
1 ATTT
33527712 CATTAAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (16 bp):
ATTTTGACTACATGGC
Found at i:33535052 original size:21 final size:21
Alignment explanation
Indices: 33535028--33535071 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
33535018 GCGAGACGAG
33535028 ATATTCGCCAATTGAGAAACT
1 ATATTCGCCAATTGAGAAACT
33535049 ATATTCGCCAATTGAGAAACT
1 ATATTCGCCAATTGAGAAACT
33535070 AT
1 AT
33535072 GTTGTGCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.30
Consensus pattern (21 bp):
ATATTCGCCAATTGAGAAACT
Found at i:33537594 original size:108 final size:108
Alignment explanation
Indices: 33537391--33537587 Score: 254
Period size: 108 Copynumber: 1.8 Consensus size: 108
33537381 GGGGCACCTG
* * * *
33537391 TATTCATCTTTGTATCTTAGCAAAATTTGCTATCTTGATTAATTTGTTCATTAGAGCTTTGCTCT
1 TATTCATCTTCGTATCTCAGCAAAATTTGCTATCTTGATTAATTTGTTCATTAGAGATCTGCTCT
* *
33537456 CAATAAATTCTCATCTTATCCATTGCGATAACCTTGTTTATCT
66 CAATAAATTCTCATCGTATCAATTGCGATAACCTTGTTTATCT
* * * **
33537499 TATTCAT-TTCGTATGTCAGCAAAATTTGCTATCTTGATTGATTTATTTGTTTAGAGATCTGCTC
1 TATTCATCTTCGTATCTCAGCAAAATTTGCTATCTTGATTAATTT-GTTCATTAGAGATCTGCTC
*
33537563 TCAATAAAATT-TCATCGTGTCAATT
65 TCAAT-AAATTCTCATCGTATCAATT
33537588 TTGATAATCT
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
107 33 0.44
108 37 0.49
109 5 0.07
ACGTcount: A:0.26, C:0.17, G:0.12, T:0.46
Consensus pattern (108 bp):
TATTCATCTTCGTATCTCAGCAAAATTTGCTATCTTGATTAATTTGTTCATTAGAGATCTGCTCT
CAATAAATTCTCATCGTATCAATTGCGATAACCTTGTTTATCT
Found at i:33538219 original size:45 final size:43
Alignment explanation
Indices: 33538039--33538385 Score: 254
Period size: 40 Copynumber: 8.2 Consensus size: 43
33538029 GAAGTTACCC
*
33538039 ATCTCCCTAAAGTTGCAGT-GGAGCAGATTAAAAACACAGATCTT
1 ATCTCCCTGAAGTTGCAGTAGGAGCAGA-TAAAAAC-CAGATCTT
* * *** *
33538083 ATCTCTCTGAAGTTACAGTA-GAGCAGATCGCATCCAG-TCTT
1 ATCTCCCTGAAGTTGCAGTAGGAGCAGATAAAAACCAGATCTT
* ** * *
33538124 ACCTCCCT-AAGCAGTAGT-GGAGCAGA-AAAAAGCCA-ATCCT
1 ATCTCCCTGAAGTTGCAGTAGGAGCAGATAAAAA-CCAGATCTT
33538164 ATCTCCCTGAAGTTGCAGTAGGAGCAGATTAAAAACACAGATCTT
1 ATCTCCCTGAAGTTGCAGTAGGAGCAGA-TAAAAAC-CAGATCTT
* *** *
33538209 ATCTCTCTGAAGTTGCAGTA-GAGCAGATCGCATCCAG-TCTT
1 ATCTCCCTGAAGTTGCAGTAGGAGCAGATAAAAACCAGATCTT
* ** * * * *
33538250 ACCTCCCT-AAGCAGTAGT-GGAGCAGACAAAAGCCA-ATCCT
1 ATCTCCCTGAAGTTGCAGTAGGAGCAGATAAAAACCAGATCTT
*
33538290 ATCTCCCTGAAGTTGCAGTAGGAGCGGATTAAAAACACAGATCTT
1 ATCTCCCTGAAGTTGCAGTAGGAGCAGA-TAAAAAC-CAGATCTT
* * *** *
33538335 ATCTCTCTGAAGTTGTAGTA-GAGCAGATCGCATCCAG-TCTT
1 ATCTCCCTGAAGTTGCAGTAGGAGCAGATAAAAACCAGATCTT
33538376 ATCTCCCTGA
1 ATCTCCCTGA
33538386 CGACACAGTG
Statistics
Matches: 231, Mismatches: 55, Indels: 37
0.72 0.17 0.11
Matches are distributed among these distances:
39 1 0.00
40 54 0.23
41 47 0.20
42 24 0.10
43 15 0.06
44 45 0.19
45 45 0.19
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (43 bp):
ATCTCCCTGAAGTTGCAGTAGGAGCAGATAAAAACCAGATCTT
Found at i:33538263 original size:126 final size:126
Alignment explanation
Indices: 33538039--33538383 Score: 629
Period size: 126 Copynumber: 2.7 Consensus size: 126
33538029 GAAGTTACCC
* *
33538039 ATCTCCCTAAAGTTGCAGT-GGAGCAGATTAAAAACACAGATCTTATCTCTCTGAAGTTACAGTA
1 ATCTCCCTGAAGTTGCAGTAGGAGCAGATTAAAAACACAGATCTTATCTCTCTGAAGTTGCAGTA
33538103 GAGCAGATCGCATCCAGTCTTACCTCCCTAAGCAGTAGTGGAGCAGAAAAAAGCCAATCCT
66 GAGCAGATCGCATCCAGTCTTACCTCCCTAAGCAGTAGTGGAGCAGAAAAAAGCCAATCCT
33538164 ATCTCCCTGAAGTTGCAGTAGGAGCAGATTAAAAACACAGATCTTATCTCTCTGAAGTTGCAGTA
1 ATCTCCCTGAAGTTGCAGTAGGAGCAGATTAAAAACACAGATCTTATCTCTCTGAAGTTGCAGTA
*
33538229 GAGCAGATCGCATCCAGTCTTACCTCCCTAAGCAGTAGTGGAGCAGACAAAAGCCAATCCT
66 GAGCAGATCGCATCCAGTCTTACCTCCCTAAGCAGTAGTGGAGCAGAAAAAAGCCAATCCT
* *
33538290 ATCTCCCTGAAGTTGCAGTAGGAGCGGATTAAAAACACAGATCTTATCTCTCTGAAGTTGTAGTA
1 ATCTCCCTGAAGTTGCAGTAGGAGCAGATTAAAAACACAGATCTTATCTCTCTGAAGTTGCAGTA
*
33538355 GAGCAGATCGCATCCAGTCTTATCTCCCT
66 GAGCAGATCGCATCCAGTCTTACCTCCCT
33538384 GACGACACAG
Statistics
Matches: 213, Mismatches: 6, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
125 18 0.08
126 195 0.92
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (126 bp):
ATCTCCCTGAAGTTGCAGTAGGAGCAGATTAAAAACACAGATCTTATCTCTCTGAAGTTGCAGTA
GAGCAGATCGCATCCAGTCTTACCTCCCTAAGCAGTAGTGGAGCAGAAAAAAGCCAATCCT
Found at i:33541019 original size:109 final size:107
Alignment explanation
Indices: 33540662--33541093 Score: 642
Period size: 109 Copynumber: 4.0 Consensus size: 107
33540652 TACGCATACT
* * *
33540662 AATATCCTTTTAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTTGAGAAAACGTACC
1 AATATCCTTTTAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACGTGCC
* *
33540727 CTAATGTGCTGGGTATC-ATTTTTCTCGTTCGACCAAATAGCGA
66 CTAATGTGCTGGGTTTCGA--TTTCTCGTTCGACCAAATAGCCA
*
33540770 AATATCCTTTTAAAAATTTCAAAATAGGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACGTGCC
1 AATATCCTTTTAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACGTGCC
*
33540835 CTAATGTGCTGGGTTTCGA----TCGTTTGACCAAATAGCCA
66 CTAATGTGCTGGGTTTCGATTTCTCGTTCGACCAAATAGCCA
* * *
33540873 AATATCCTTTTAAAAATTTCAAAACAAGACAATGTTTTGCGTTTTG-AAATTTGAGAAAACGTGC
1 AATATCCTTTTAAAAATTTCAAAATAAGGCAATGTTTTGCG-TTTGAAAATTCGAGAAAACGTGC
* *
33540937 CTTAATGTGCTGGGTTTCGATTTTTCTCATTCGACCAAATAGCCA
65 CCTAATGTGCTGGGTTTCGA--TTTCTCGTTCGACCAAATAGCCA
* *
33540982 AATATCCTTTTAAAAATTTCAAAATAAGGCAATGTTTTGTGCTTGAAAATTCGAGAAAACGTGCC
1 AATATCCTTTTAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACGTGCC
*
33541047 CTAATGTGCTGGGTTTCGATTTCTCGTTCGGCCAAATAGCCA
66 CTAATGTGCTGGGTTTCGATTTCTCGTTCGACCAAATAGCCA
33541089 AATAT
1 AATAT
33541094 GCTCCTAAAT
Statistics
Matches: 293, Mismatches: 22, Indels: 19
0.88 0.07 0.06
Matches are distributed among these distances:
103 91 0.31
104 4 0.01
107 26 0.09
108 80 0.27
109 92 0.31
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (107 bp):
AATATCCTTTTAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACGTGCC
CTAATGTGCTGGGTTTCGATTTCTCGTTCGACCAAATAGCCA
Found at i:33541030 original size:212 final size:212
Alignment explanation
Indices: 33540662--33541093 Score: 704
Period size: 212 Copynumber: 2.0 Consensus size: 212
33540652 TACGCATACT
* *
33540662 AATATCCTTTTAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTTGAGAAAACGTACC
1 AATATCCTTTTAAAAATTTCAAAACAAGACAATGTTTTGCGTTTGGAAATTTGAGAAAACGTACC
* *
33540727 CTAATGTGCTGGGTATCATTTTTCTCGTTCGACCAAATAGCGAAATATCCTTTTAAAAATTTCAA
66 CTAATGTGCTGGGTATCATTTTTCTCATTCGACCAAATAGCCAAATATCCTTTTAAAAATTTCAA
* *
33540792 AATAGGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGA-TC
131 AATAAGGCAATGTTTTGCGCTTGAAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTC
*
33540856 GTTTGACCAAATAGCCA
196 GTTCGACCAAATAGCCA
* *
33540873 AATATCCTTTTAAAAATTTCAAAACAAGACAATGTTTTGCGTTTTGAAATTTGAGAAAACGTGCC
1 AATATCCTTTTAAAAATTTCAAAACAAGACAATGTTTTGCGTTTGGAAATTTGAGAAAACGTACC
* *
33540938 TTAATGTGCTGGGTTTCGATTTTTCTCATTCGACCAAATAGCCAAATATCCTTTTAAAAATTTCA
66 CTAATGTGCTGGGTATC-ATTTTTCTCATTCGACCAAATAGCCAAATATCCTTTTAAAAATTTCA
*
33541003 AAATAAGGCAATGTTTTGTGCTTGAAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATT
130 AAATAAGGCAATGTTTTGCGCTTGAAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGA--
*
33541068 TCTCGTTCGGCCAAATAGCCA
193 T-TCGTTCGACCAAATAGCCA
33541089 AATAT
1 AATAT
33541094 GCTCCTAAAT
Statistics
Matches: 203, Mismatches: 13, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
211 76 0.37
212 105 0.52
216 22 0.11
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (212 bp):
AATATCCTTTTAAAAATTTCAAAACAAGACAATGTTTTGCGTTTGGAAATTTGAGAAAACGTACC
CTAATGTGCTGGGTATCATTTTTCTCATTCGACCAAATAGCCAAATATCCTTTTAAAAATTTCAA
AATAAGGCAATGTTTTGCGCTTGAAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTC
GTTCGACCAAATAGCCA
Found at i:33545689 original size:12 final size:12
Alignment explanation
Indices: 33545672--33545706 Score: 56
Period size: 11 Copynumber: 3.1 Consensus size: 12
33545662 TAGCCCGCTC
33545672 ATATTAATTTTT
1 ATATTAATTTTT
33545684 ATATT-ATTTTT
1 ATATTAATTTTT
33545695 ATA-TAATTTTT
1 ATATTAATTTTT
33545706 A
1 A
33545707 AATATATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.05
11 16 0.73
12 5 0.23
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:33548459 original size:17 final size:17
Alignment explanation
Indices: 33548415--33548460 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 17
33548405 GAAATACATG
*
33548415 GAAATG-ATGGTAT-AT
1 GAAATGAATGATATAAT
*
33548430 GAAAT-ATTGATATAAT
1 GAAATGAATGATATAAT
33548446 GAAATGAATGATATA
1 GAAATGAATGATATA
33548461 TGTTTATGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
15 10 0.40
16 7 0.28
17 8 0.32
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.33
Consensus pattern (17 bp):
GAAATGAATGATATAAT
Found at i:33561865 original size:24 final size:23
Alignment explanation
Indices: 33561838--33561884 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
33561828 AGTTTAGTTG
33561838 TCGAC-TTAAAAATGAAAATTGGGA
1 TCGACTTTAAAAAT-AAAA-TGGGA
*
33561862 TCGACTTTGAAAATAAAATGGGA
1 TCGACTTTAAAAATAAAATGGGA
33561885 GTCGCCACCG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 5 0.24
24 9 0.43
25 7 0.33
ACGTcount: A:0.45, C:0.09, G:0.21, T:0.26
Consensus pattern (23 bp):
TCGACTTTAAAAATAAAATGGGA
Found at i:33568487 original size:24 final size:24
Alignment explanation
Indices: 33568455--33568514 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
33568445 GTCGTGATCA
* *
33568455 TCATCTTCATCTTCACCTCGACTC
1 TCATATTCATCTTCACCTCGACCC
* *
33568479 TCGTATTCATCTTCATCTCGACCC
1 TCATATTCATCTTCACCTCGACCC
*
33568503 TCATCTTCATCT
1 TCATATTCATCT
33568515 CTACCTCTGT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.17, C:0.38, G:0.05, T:0.40
Consensus pattern (24 bp):
TCATATTCATCTTCACCTCGACCC
Found at i:33571615 original size:22 final size:22
Alignment explanation
Indices: 33571587--33571629 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
33571577 TTTATTGTTC
33571587 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
33571609 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
33571630 TAACCAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:33576779 original size:38 final size:38
Alignment explanation
Indices: 33576728--33576804 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
33576718 GTGCAAAAGA
33576728 TAGTTTATAATCTAAAGAAAATGATACAGAACATACAG
1 TAGTTTATAATCTAAAGAAAATGATACAGAACATACAG
33576766 TAGTTTATAATCTAAAGAAAATGATACAGAACATACAG
1 TAGTTTATAATCTAAAGAAAATGATACAGAACATACAG
33576804 T
1 T
33576805 TTGAGAGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.27
Consensus pattern (38 bp):
TAGTTTATAATCTAAAGAAAATGATACAGAACATACAG
Found at i:33582106 original size:32 final size:32
Alignment explanation
Indices: 33582070--33582135 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
33582060 CCATATCTGA
33582070 ATATGAAAGAGAATTCGTCCGATTAAGTAAGT
1 ATATGAAAGAGAATTCGTCCGATTAAGTAAGT
33582102 ATATGAAAGAGAATTCGTCCGATTAAGTAAGT
1 ATATGAAAGAGAATTCGTCCGATTAAGTAAGT
33582134 AT
1 AT
33582136 GCCCGAGAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.41, C:0.09, G:0.21, T:0.29
Consensus pattern (32 bp):
ATATGAAAGAGAATTCGTCCGATTAAGTAAGT
Found at i:33587394 original size:25 final size:25
Alignment explanation
Indices: 33587333--33587396 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
33587323 ACCACAGCTT
33587333 GTATGAGCTTACCGATTTACAACTC
1 GTATGAGCTTACCGATTTACAACTC
*
33587358 GTGA-GAGTTTACCGATTCT-CAACTC
1 GT-ATGAGCTTACCGATT-TACAACTC
33587383 GTATGAGCTTACCG
1 GTATGAGCTTACCG
33587397 TTGTTTAGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
24 1 0.03
25 31 0.91
26 2 0.06
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.31
Consensus pattern (25 bp):
GTATGAGCTTACCGATTTACAACTC
Found at i:33592800 original size:41 final size:41
Alignment explanation
Indices: 33592739--33592852 Score: 174
Period size: 41 Copynumber: 2.8 Consensus size: 41
33592729 TTAATTTAAA
* * *
33592739 CAGATTCAACGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGA-TCACCGGCACGTAGCCTGCTAGGCTTATAACCTGATT
*
33592781 CAGATCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACGTAGCCTGCTAGGCTTATAACCTGATT
*
33592822 CAGATCACCGGCACGTAGCCTGCTAGACTTA
1 CAGATCACCGGCACGTAGCCTGCTAGGCTTA
33592853 AAGTCTGAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
41 62 0.94
42 4 0.06
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (41 bp):
CAGATCACCGGCACGTAGCCTGCTAGGCTTATAACCTGATT
Found at i:33593351 original size:25 final size:26
Alignment explanation
Indices: 33593297--33593364 Score: 102
Period size: 25 Copynumber: 2.6 Consensus size: 26
33593287 AAAAATAAAA
*
33593297 ATTTACCAAAATATTTTAACTTTTTTT
1 ATTTACCAAAATA-TATAACTTTTTTT
*
33593324 ATTTACAAAAATATATAA-TTTTTTT
1 ATTTACCAAAATATATAACTTTTTTT
33593349 ATTTACCAAAATATAT
1 ATTTACCAAAATATAT
33593365 CATAAAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
25 22 0.58
26 4 0.11
27 12 0.32
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (26 bp):
ATTTACCAAAATATATAACTTTTTTT
Found at i:33593462 original size:27 final size:27
Alignment explanation
Indices: 33593432--33593525 Score: 118
Period size: 27 Copynumber: 3.5 Consensus size: 27
33593422 CGCCAATGGT
* *
33593432 ATTGGCGGCACCAAAGGTGCCAAAACC
1 ATTGGCGGCACCAATGGTGCCAATACC
*
33593459 ATTGGCGGCACCAATGGTGCCAATGCC
1 ATTGGCGGCACCAATGGTGCCAATACC
* * *
33593486 AATGGTGGCACCAATGGTGCC-ATACTA
1 ATTGGCGGCACCAATGGTGCCAATAC-C
33593513 ATTGGCGGCACCA
1 ATTGGCGGCACCA
33593526 CTCGTATTAT
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
26 3 0.05
27 54 0.95
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.17
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAATACC
Found at i:33593622 original size:11 final size:11
Alignment explanation
Indices: 33593606--33593642 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
33593596 GTTGGCGCAG
33593606 AAAAGAAGAGA
1 AAAAGAAGAGA
33593617 AAAAG-AGAGA
1 AAAAGAAGAGA
*
33593627 AAAAGAGGAGA
1 AAAAGAAGAGA
33593638 AAAAG
1 AAAAG
33593643 GAGGTATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 10 0.42
11 14 0.58
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAGA
Found at i:33593708 original size:19 final size:21
Alignment explanation
Indices: 33593670--33593708 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
33593660 AATAATTGAT
*
33593670 TATATTGTTGTTATTATTTTG
1 TATATTGTTGTTAATATTTTG
33593691 TATATT-TTG-TAATATTTT
1 TATATTGTTGTTAATATTTT
33593709 TTGTTTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (21 bp):
TATATTGTTGTTAATATTTTG
Found at i:33593770 original size:3 final size:3
Alignment explanation
Indices: 33593754--33593788 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
33593744 AAAATAATAG
*
33593754 TAT TAGT TAG TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT T
33593789 GTTGTTGTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:33593793 original size:3 final size:3
Alignment explanation
Indices: 33593787--33593866 Score: 160
Period size: 3 Copynumber: 26.7 Consensus size: 3
33593777 ATTATTATTA
33593787 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
33593835 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
33593867 AGTATTAAGA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:33594085 original size:26 final size:26
Alignment explanation
Indices: 33594056--33594108 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
33594046 TTTTAGTGTG
*
33594056 TATTATTTTGAGTATAAAATTATTAA
1 TATTATTTTGAGTATAAAATTAATAA
33594082 TATTATTTTGAGTATAAAATTAATAA
1 TATTATTTTGAGTATAAAATTAATAA
33594108 T
1 T
33594109 TTTAGTGTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (26 bp):
TATTATTTTGAGTATAAAATTAATAA
Found at i:33594131 original size:12 final size:12
Alignment explanation
Indices: 33594114--33594144 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
33594104 ATAATTTTAG
33594114 TGTGTATTATTT
1 TGTGTATTATTT
33594126 TGTGTATTATTT
1 TGTGTATTATTT
*
33594138 TGAGTAT
1 TGTGTAT
33594145 AAAATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.61
Consensus pattern (12 bp):
TGTGTATTATTT
Found at i:33594152 original size:26 final size:25
Alignment explanation
Indices: 33594054--33594153 Score: 73
Period size: 26 Copynumber: 4.0 Consensus size: 25
33594044 AATTTTAGTG
33594054 TGTATTATTTTGAGTATAAAATTATT
1 TGTATTATTTTGAGTATAAAATT-TT
**
33594080 AATATTATTTTGAGTATAAAA---T
1 TGTATTATTTTGAGTATAAAATTTT
* * * * **
33594102 T-AATAATTTTAGTGTGTATTATTTT
1 TGTATTATTTT-GAGTATAAAATTTT
33594127 GTGTATTATTTTGAGTATAAAATTTT
1 -TGTATTATTTTGAGTATAAAATTTT
33594153 T
1 T
33594154 TTTAAGTAAT
Statistics
Matches: 53, Mismatches: 15, Indels: 13
0.65 0.19 0.16
Matches are distributed among these distances:
21 7 0.13
22 7 0.13
25 2 0.04
26 30 0.57
27 7 0.13
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.54
Consensus pattern (25 bp):
TGTATTATTTTGAGTATAAAATTTT
Found at i:33603495 original size:29 final size:28
Alignment explanation
Indices: 33603462--33603536 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 28
33603452 TTTTTGGTTT
*
33603462 TTTTATATATTTTGGTAGTAAATAAAAAA
1 TTTTATATATTTTGGTAATAAA-AAAAAA
*
33603491 TTTTATATATTTTGGTAAATAAAAAAAAG
1 TTTTATATATTTTGGT-AATAAAAAAAAA
*
33603520 TTATA-ATATTTTGGTAA
1 TTTTATATATTTTGGTAA
33603537 ATTTTTATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
27 2 0.05
28 10 0.24
29 25 0.60
30 5 0.12
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.45
Consensus pattern (28 bp):
TTTTATATATTTTGGTAATAAAAAAAAA
Found at i:33604282 original size:16 final size:17
Alignment explanation
Indices: 33604261--33604307 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 17
33604251 TTCAAAATTA
33604261 TTTTAAA-ATTTTTAAT
1 TTTTAAACATTTTTAAT
*
33604277 TTTTAAAGA-TTTT-A-
1 TTTTAAACATTTTTAAT
33604291 TTTTAAACATTTTTAAT
1 TTTTAAACATTTTTAAT
33604308 ACATTTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
14 8 0.31
15 5 0.19
16 12 0.46
17 1 0.04
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (17 bp):
TTTTAAACATTTTTAAT
Found at i:33612895 original size:32 final size:33
Alignment explanation
Indices: 33612828--33612899 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 33
33612818 TGTAAACATT
*
33612828 AATATTTTTTGGTGTTTGGATAAATCTGTGTAA
1 AATATTTTTTGGTGTTTGGATAAATCTCTGTAA
* * *
33612861 AATATTTTTTGTTGTTT-GATAGATTTCT-TAAA
1 AATATTTTTTGGTGTTTGGATAAATCTCTGT-AA
33612893 AATATTT
1 AATATTT
33612900 CATAAAAGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 1 0.03
32 17 0.50
33 16 0.47
ACGTcount: A:0.29, C:0.03, G:0.15, T:0.53
Consensus pattern (33 bp):
AATATTTTTTGGTGTTTGGATAAATCTCTGTAA
Found at i:33614727 original size:28 final size:28
Alignment explanation
Indices: 33614670--33614727 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
33614660 TACAAACGAA
* *
33614670 AATAATAATTTATTACATTTTAAACTAT
1 AATAATAATTTATAACATTTTAAACAAT
33614698 AATAATAAATTTA-AACATTATTAAA-AAT
1 AATAAT-AATTTATAACATT-TTAAACAAT
33614726 AA
1 AA
33614728 ATATTACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 15 0.58
29 11 0.42
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (28 bp):
AATAATAATTTATAACATTTTAAACAAT
Found at i:33614730 original size:29 final size:27
Alignment explanation
Indices: 33614669--33614730 Score: 63
Period size: 29 Copynumber: 2.2 Consensus size: 27
33614659 ATACAAACGA
* *
33614669 AAATAATAATTTATTACATTTTAAACT
1 AAATAATAATTTATAACATTTTAAAAT
33614696 ATAATAATAAATTTA-AACATTATTAAAAAT
1 A-AATAAT-AATTTATAACATT-TT-AAAAT
33614726 AAATA
1 AAATA
33614731 TTACAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
27 1 0.03
28 11 0.38
29 12 0.41
30 5 0.17
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (27 bp):
AAATAATAATTTATAACATTTTAAAAT
Found at i:33616025 original size:25 final size:25
Alignment explanation
Indices: 33615987--33616035 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
33615977 ATGTTTCTGT
33615987 ATTTTTGGACTTTTAATTTATTTTTA
1 ATTTTTGGACTTTT-ATTTATTTTTA
* *
33616013 ATTTTTTGA-TTTTATTTGTTTTT
1 ATTTTTGGACTTTTATTTATTTTT
33616036 GTAAGGGCCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 9 0.43
25 4 0.19
26 8 0.38
ACGTcount: A:0.18, C:0.02, G:0.08, T:0.71
Consensus pattern (25 bp):
ATTTTTGGACTTTTATTTATTTTTA
Found at i:33616403 original size:100 final size:100
Alignment explanation
Indices: 33616298--33616945 Score: 798
Period size: 100 Copynumber: 6.5 Consensus size: 100
33616288 TCGGAGAAAT
* * * * * * *
33616298 AAGATTCGTAGTTGTAGCTTCAATCGGTTCCACTACACCGCTTGGGAAGTAAGATTCGCTATTGT
1 AAGATTCGCAGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTGGGAAGTAAGATTCGCTGTTGT
* * *
33616363 AGGTTTAATCTTTTTAACTACAATGTCAGGGAAGC
66 AGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC
* * * *
33616398 AAGATTCGTC-GTTGTGGCGTTAATCTGTTCCACTGCACCGCTTGAGAAGTAAGATTTGCTGTTG
1 AAGATTCG-CAGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTGGGAAGTAAGATTCGCTGTTG
*
33616462 TAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGA
65 TAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC
* * * * *
33616498 AAGATTCGCCGTTGTGGCGTTAATCTGTTCCACTGCACCACTTGAGAAGTAAGATTCGCTGTTGT
1 AAGATTCGCAGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTGGGAAGTAAGATTCGCTGTTGT
*
33616563 AGCTTTAATCTTTTTAACTGCAATGTCGGGGAACC
66 AGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC
* * * * *
33616598 AAGGTTCGCCA-TTGTGGCTTTAATCTGTTCCACTGCACTGCCAGGGAAATAAGATTCGTTGTTG
1 AAGATTCG-CAGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTGGGAAGTAAGATTCGCTGTTG
* *
33616662 TATCTTTAATCTTTTTAACTGCAATGTCGGGAAAGC
65 TAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC
* * * * * ** * * *
33616698 AAGATTCACCGATGTGACTTTAATCTGTTCCACTCCGTCGCCTGGGGAGTAAGATTTGTTGTTGT
1 AAGATTCGCAGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTGGGAAGTAAGATTCGCTGTTGT
* *
33616763 AGCTTTAATCTTTTTAATTGCAATGTCGGGGAAGT
66 AGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC
* * * *
33616798 AAGATTCAACA-ATGTGGCTTTAATCTGTTCCACTGCACCGCCTGGGGAGTAAGATTTGCTGTTG
1 AAGATTC-GCAGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTGGGAAGTAAGATTCGCTGTTG
33616862 TAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC
65 TAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC
* * * * * *
33616898 AAGATTCACCGATGTGGCTTTAATCTGTTCCACAGCATCACCTGGGAA
1 AAGATTCGCAGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTGGGAA
33616946 TTAAAATTGG
Statistics
Matches: 482, Mismatches: 60, Indels: 12
0.87 0.11 0.02
Matches are distributed among these distances:
99 4 0.01
100 475 0.99
101 3 0.01
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (100 bp):
AAGATTCGCAGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTGGGAAGTAAGATTCGCTGTTGT
AGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC
Found at i:33616883 original size:50 final size:50
Alignment explanation
Indices: 33616340--33616923 Score: 368
Period size: 50 Copynumber: 11.7 Consensus size: 50
33616330 CTACACCGCT
* * * *
33616340 TGGGAAGTAAGATTCGCTATTGTAGGTTTAATCTTTTTAACTACAATGTC
1 TGGGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGCC
* * * * * ** ** *
33616390 AGGGAAGCAAGATTCG-TCGTTGTGGCGTTAATCTGTTCCACTGCACCGCT
1 TGGGAAGTAAGATTCGCT-GTTGTAGCTTTAATCTTTTTAACTGCAATGCC
* * *
33616440 TGAGAAGTAAGATTTGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTC
1 TGGGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGCC
* * * * * * ** *** *
33616490 GGGGAAGAAAGATTCGCCGTTGTGGCGTTAATCTGTTCCACTGCACCACT
1 TGGGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGCC
* *
33616540 TGAGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTC
1 TGGGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGCC
* ** * ** * * ** *
33616590 GGGGAACCAAGGTTCGCCATTGTGGCTTTAATCTGTTCCACTGCACTGCC
1 TGGGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGCC
* * * * *
33616640 AGGGAAATAAGATTCGTTGTTGTATCTTTAATCTTTTTAACTGCAATGTC
1 TGGGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGCC
* * * * * ** **
33616690 -GGGAAAGCAAGATTCACCGATGT-GACTTTAATCTGTTCCACT-CCGTCGCC
1 TGGG-AAGTAAGATTCGCTGTTGTAG-CTTTAATCTTTTTAACTGCAAT-GCC
* * * * *
33616740 TGGGGAGTAAGATTTGTTGTTGTAGCTTTAATCTTTTTAATTGCAATGTC
1 TGGGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGCC
* * ** * * ** **
33616790 GGGGAAGTAAGATTCAAC-AATGTGGCTTTAATCTGTTCCACTGCACCGCC
1 TGGGAAGTAAGATTC-GCTGTTGTAGCTTTAATCTTTTTAACTGCAATGCC
* * *
33616840 TGGGGAGTAAGATTTGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTC
1 TGGGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGCC
* * * * * *
33616890 GGGGAAGCAAGATTCACCGATGTGGCTTTAATCT
1 TGGGAAGTAAGATTCGCTGTTGTAGCTTTAATCT
33616924 GTTCCACAGC
Statistics
Matches: 378, Mismatches: 146, Indels: 20
0.69 0.27 0.04
Matches are distributed among these distances:
49 7 0.02
50 364 0.96
51 7 0.02
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (50 bp):
TGGGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGCC
Found at i:33618243 original size:7 final size:7
Alignment explanation
Indices: 33618224--33618273 Score: 50
Period size: 7 Copynumber: 7.0 Consensus size: 7
33618214 TTAGCCTCTC
33618224 CATTTTT
1 CATTTTT
33618231 -ACTTTTT
1 CA-TTTTT
33618238 CATTTTT
1 CATTTTT
*
33618245 TA-TTTT
1 CATTTTT
33618251 CATTTTTT
1 CA-TTTTT
33618259 CATTTTT
1 CATTTTT
33618266 CATATTTT
1 CAT-TTTT
33618274 TTTTCTGACT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
6 6 0.17
7 19 0.53
8 11 0.31
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (7 bp):
CATTTTT
Found at i:33618246 original size:15 final size:15
Alignment explanation
Indices: 33618226--33618274 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
33618216 AGCCTCTCCA
33618226 TTTTTACTTTTTCAT
1 TTTTTACTTTTTCAT
33618241 TTTTTA--TTTTCAT
1 TTTTTACTTTTTCAT
33618254 TTTTT-CATTTTTCAT
1 TTTTTAC-TTTTTCAT
33618269 ATTTTT
1 -TTTTT
33618275 TTTCTGACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
13 12 0.40
15 13 0.43
16 5 0.17
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTACTTTTTCAT
Found at i:33618249 original size:21 final size:22
Alignment explanation
Indices: 33618225--33618274 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
33618215 TAGCCTCTCC
33618225 ATTTTTACTTTTTCATTTTT-T
1 ATTTTTACTTTTTCATTTTTAT
* *
33618246 ATTTTCATTTTTTCATTTTTCAT
1 ATTTTTACTTTTTCATTTTT-AT
33618269 ATTTTT
1 ATTTTT
33618275 TTTCTGACTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 18 0.75
23 6 0.25
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.74
Consensus pattern (22 bp):
ATTTTTACTTTTTCATTTTTAT
Found at i:33618250 original size:13 final size:13
Alignment explanation
Indices: 33618234--33618278 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
33618224 CATTTTTACT
33618234 TTTTCATTTTTTA
1 TTTTCATTTTTTA
33618247 TTTTCATTTTTTCA
1 TTTTCATTTTTT-A
*
33618261 TTTTTCATATTTT-
1 -TTTTCATTTTTTA
33618274 TTTTC
1 TTTTC
33618279 TGACTTAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 5 0.17
13 12 0.41
14 1 0.03
15 11 0.38
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTCATTTTTTA
Found at i:33618257 original size:28 final size:27
Alignment explanation
Indices: 33618224--33618278 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
33618214 TTAGCCTCTC
* *
33618224 CATTTTTAC-TTTTTCATTTTTTATTTT
1 CATTTTTTCATTTTTCATATTTT-TTTT
33618251 CATTTTTTCATTTTTCATATTTTTTTT
1 CATTTTTTCATTTTTCATATTTTTTTT
33618278 C
1 C
33618279 TGACTTAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 13 0.52
28 12 0.48
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.73
Consensus pattern (27 bp):
CATTTTTTCATTTTTCATATTTTTTTT
Found at i:33621383 original size:109 final size:109
Alignment explanation
Indices: 33621201--33621593 Score: 520
Period size: 109 Copynumber: 3.6 Consensus size: 109
33621191 TGATACAAAA
* * * * * *
33621201 CGTAGTGACGGCTGAGATCCAGCATATGTTGTAGATTCTCTACAAG-TTGTATGAGCAGCATCAT
1 CGTAGCGATGGCTGAGATCCTGCATATGTTGCAGATTCTCTAC-AGCTTGTGTGAGCAGCATCGT
* * *
33621265 GAGATGGTGATTATTTAGCAGGTACTATGTACCGATGATATAGGC
65 GAGACGGTGATTATTTAGCAGGTACTATGTACCGGTGATATAGAC
* * *
33621310 CGTAGCAATGGCTGAGATCCTGCATATATTGCGGATTCTCTACAGCTTGTGTGAGCAGCATCGTG
1 CGTAGCGATGGCTGAGATCCTGCATATGTTGCAGATTCTCTACAGCTTGTGTGAGCAGCATCGTG
*
33621375 AGACGGTGATTATTTAGCAGGTACTATGTACAGGTGATATAGAC
66 AGACGGTGATTATTTAGCAGGTACTATGTACCGGTGATATAGAC
* ** * * * * * *
33621419 TGTATTGATGGTTGAGATCTTGTATATGTTGCGGGTTCTCTACAGCTTGTGTAAGCAGCATCGTG
1 CGTAGCGATGGCTGAGATCCTGCATATGTTGCAGATTCTCTACAGCTTGTGTGAGCAGCATCGTG
* * *
33621484 AGACAGTGATTATTTAGTAGGTACTATGTA-CGGTGATACAGAC
66 AGACGGTGATTATTTAGCAGGTACTATGTACCGGTGATATAGAC
* *
33621527 CGTAGCGATGGCTGAGATACTGCATATGTTGCAGATTCTCTGCAGCTTGTGTGAGCAGCATCGTG
1 CGTAGCGATGGCTGAGATCCTGCATATGTTGCAGATTCTCTACAGCTTGTGTGAGCAGCATCGTG
33621592 AG
66 AG
33621594 CTGGTCAAAA
Statistics
Matches: 245, Mismatches: 38, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
108 69 0.28
109 176 0.72
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (109 bp):
CGTAGCGATGGCTGAGATCCTGCATATGTTGCAGATTCTCTACAGCTTGTGTGAGCAGCATCGTG
AGACGGTGATTATTTAGCAGGTACTATGTACCGGTGATATAGAC
Found at i:33623108 original size:22 final size:20
Alignment explanation
Indices: 33623041--33623117 Score: 91
Period size: 20 Copynumber: 3.7 Consensus size: 20
33623031 TGGGGGGTAT
*
33623041 ACACGCCCATGTGAATGAGGC
1 ACACGCCCGTGTGAA-GAGGC
* *
33623062 ACACGCCCGTGCGAAGAAGC
1 ACACGCCCGTGTGAAGAGGC
33623082 ACACGCCCGTGTGAAAGGAGGC
1 ACACGCCCGTGTG-AA-GAGGC
*
33623104 ACACGGCCGTGTGA
1 ACACGCCCGTGTGA
33623118 CTCTGACACA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
20 16 0.33
21 16 0.33
22 16 0.33
ACGTcount: A:0.27, C:0.30, G:0.32, T:0.10
Consensus pattern (20 bp):
ACACGCCCGTGTGAAGAGGC
Found at i:33642634 original size:24 final size:24
Alignment explanation
Indices: 33642604--33642665 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
33642594 AGTAGAAGAC
33642604 GCTCCAAAAGCTGGAGTGCTAGAT
1 GCTCCAAAAGCTGGAGTGCTAGAT
* * *
33642628 G-TGCCAAAAGCAGGTGTGCTTGAT
1 GCT-CCAAAAGCTGGAGTGCTAGAT
*
33642652 GCTCCAAATGCTGG
1 GCTCCAAAAGCTGG
33642666 GGCATTAGAC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
23 1 0.03
24 29 0.94
25 1 0.03
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.23
Consensus pattern (24 bp):
GCTCCAAAAGCTGGAGTGCTAGAT
Found at i:33642750 original size:24 final size:24
Alignment explanation
Indices: 33642720--33642922 Score: 266
Period size: 24 Copynumber: 8.5 Consensus size: 24
33642710 TTCCAGTTGA
* *
33642720 ACCAAAGGCAGGGCTGCTTGTGGA
1 ACCAAAGGCAGGGGTGCTTGTGGC
* * *
33642744 ACCAAAGGCTGGGGTACTAGTGGC
1 ACCAAAGGCAGGGGTGCTTGTGGC
33642768 ACCGAAA-GCAGGGGTGCTTGTGGC
1 ACC-AAAGGCAGGGGTGCTTGTGGC
33642792 ACCGAAA-GCAGGGGTGCTTGTGGC
1 ACC-AAAGGCAGGGGTGCTTGTGGC
* * *
33642816 ACCGAAGGCAGGGGTACTGGTGGC
1 ACCAAAGGCAGGGGTGCTTGTGGC
*
33642840 ACCGAAGGCAGGGGTGCTTGTGGC
1 ACCAAAGGCAGGGGTGCTTGTGGC
33642864 ACCAAAGGCAGGGGTGCTTGTGGC
1 ACCAAAGGCAGGGGTGCTTGTGGC
* *
33642888 ACCAAACGCAGCGGTGCTTGTGGC
1 ACCAAAGGCAGGGGTGCTTGTGGC
*
33642912 ACCAAATGCAG
1 ACCAAAGGCAG
33642923 ACTGTGTTGA
Statistics
Matches: 160, Mismatches: 17, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
23 2 0.01
24 155 0.97
25 3 0.02
ACGTcount: A:0.23, C:0.22, G:0.39, T:0.16
Consensus pattern (24 bp):
ACCAAAGGCAGGGGTGCTTGTGGC
Found at i:33649755 original size:91 final size:92
Alignment explanation
Indices: 33649634--33649846 Score: 229
Period size: 91 Copynumber: 2.3 Consensus size: 92
33649624 ATGGTTGAAG
* * * * * *
33649634 GATGCCAT-GGTGTCTTTCAACCATGGTCTTAATCA-TACCCGACTTGATT-CGATAGTTTCTTT
1 GATGCCATAGCTGTCTTTCAGCTATGGTCTTAATCATTACCCGACGTG-TTGCCATAGTGTCTTT
*
33649696 CAACCATGGTCTTATTCATTTTACGTCGT
65 CAACCATGGTCTTATTCATTTGA-GTCGT
* * * ** *
33649725 GTTGCCATA-CTGTCTTTCAGCTATGGTCTTATTTATTTTCCGTCGTGTTGCCATAGTGTCTTTC
1 GATGCCATAGCTGTCTTTCAGCTATGGTCTTAATCATTACCCGACGTGTTGCCATAGTGTCTTTC
* *
33649789 AACTATGGTCTTATTCGTTTGAGTCGT
66 AACCATGGTCTTATTCATTTGAGTCGT
*
33649816 GATGCCGTAGC-GTCTTTCAGCTATGGTCTTA
1 GATGCCATAGCTGTCTTTCAGCTATGGTCTTA
33649847 TTTGATAGAA
Statistics
Matches: 101, Mismatches: 17, Indels: 8
0.80 0.13 0.06
Matches are distributed among these distances:
91 62 0.61
92 39 0.39
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (92 bp):
GATGCCATAGCTGTCTTTCAGCTATGGTCTTAATCATTACCCGACGTGTTGCCATAGTGTCTTTC
AACCATGGTCTTATTCATTTGAGTCGT
Found at i:33649763 original size:46 final size:46
Alignment explanation
Indices: 33649691--33649848 Score: 203
Period size: 46 Copynumber: 3.5 Consensus size: 46
33649681 TTCGATAGTT
*
33649691 TCTTTCAACCATGGTCTTATTCATTTTACGTCGTGTTGCCATACTG
1 TCTTTCAACTATGGTCTTATTCATTTTACGTCGTGTTGCCATACTG
* * * *
33649737 TCTTTCAGCTATGGTCTTATTTATTTTCCGTCGTGTTGCCATAGTG
1 TCTTTCAACTATGGTCTTATTCATTTTACGTCGTGTTGCCATACTG
* * * *
33649783 TCTTTCAACTATGGTCTTATTCGTTTGA-GTCGTGATGCCGTAGC-G
1 TCTTTCAACTATGGTCTTATTCATTTTACGTCGTGTTGCCATA-CTG
*
33649828 TCTTTCAGCTATGGTCTTATT
1 TCTTTCAACTATGGTCTTATT
33649849 TGATAGAATC
Statistics
Matches: 97, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
45 33 0.34
46 64 0.66
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.45
Consensus pattern (46 bp):
TCTTTCAACTATGGTCTTATTCATTTTACGTCGTGTTGCCATACTG
Found at i:33649832 original size:45 final size:45
Alignment explanation
Indices: 33649691--33649891 Score: 170
Period size: 45 Copynumber: 4.4 Consensus size: 45
33649681 TTCGATAGTT
* * * *
33649691 TCTTTCAACCATGGTCTTATTCATTTTACGTCGTGTTGCCATA-CTG
1 TCTTTCAACTATGGTCTTATTCGTTTGA-GTCGTGATGCCATAGC-G
* ** ** * *
33649737 TCTTTCAGCTATGGTCTTATTTATTTTCCGTCGTGTTGCCATAGTG
1 TCTTTCAACTATGGTCTTA-TTCGTTTGAGTCGTGATGCCATAGCG
*
33649783 TCTTTCAACTATGGTCTTATTCGTTTGAGTCGTGATGCCGTAGCG
1 TCTTTCAACTATGGTCTTATTCGTTTGAGTCGTGATGCCATAGCG
* * * * * * * *
33649828 TCTTTCAGCTATGGTCTTATTTGATAGAATCGTGATGCCACAACA
1 TCTTTCAACTATGGTCTTATTCGTTTGAGTCGTGATGCCATAGCG
* *
33649873 TCTTTCAGCTATTGTCTTA
1 TCTTTCAACTATGGTCTTA
33649892 CTCGCTTCTA
Statistics
Matches: 128, Mismatches: 25, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
45 73 0.57
46 50 0.39
47 5 0.04
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.43
Consensus pattern (45 bp):
TCTTTCAACTATGGTCTTATTCGTTTGAGTCGTGATGCCATAGCG
Done.