Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 69 of 190
Found at i:20066000 original size:18 final size:18
Alignment explanation
Indices: 20065977--20066013 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
20065967 TGAGTTTTCA
*
20065977 AATTCGAATAACCCGAAT
1 AATTCGAATAAACCGAAT
20065995 AATTCGAATAAACCGAAT
1 AATTCGAATAAACCGAAT
20066013 A
1 A
20066014 CCAAACTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.19, G:0.11, T:0.22
Consensus pattern (18 bp):
AATTCGAATAAACCGAAT
Found at i:20066324 original size:17 final size:17
Alignment explanation
Indices: 20066268--20066326 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
20066258 TATATTCTAC
*
20066268 TATTTATATTATTAAAT
1 TATTTATATTATTGAAT
* *
20066285 TAAATTTCATATT-TTGTAC
1 T--ATTT-ATATTATTGAAT
20066304 TATTTATATTATTGAAT
1 TATTTATATTATTGAAT
20066321 TATTTA
1 TATTTA
20066327 ATCATATTGG
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 5 0.15
17 15 0.45
19 8 0.24
20 5 0.15
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (17 bp):
TATTTATATTATTGAAT
Found at i:20066399 original size:19 final size:19
Alignment explanation
Indices: 20066351--20066399 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
20066341 TTATAAATTT
* *
20066351 ATGTTAAAATTGAATTATTG
1 ATGTTAAAA-TAAATTATTC
* *
20066371 ATGATGAAATAAATTATTC
1 ATGTTAAAATAAATTATTC
20066390 ATGTTAAAAT
1 ATGTTAAAAT
20066400 TTTATACTGG
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.45, C:0.02, G:0.12, T:0.41
Consensus pattern (19 bp):
ATGTTAAAATAAATTATTC
Found at i:20067825 original size:3 final size:3
Alignment explanation
Indices: 20067817--20067877 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
20067807 AGGATAAATG
20067817 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
20067865 AGA AGA AGA AGA A
1 AGA AGA AGA AGA A
20067878 AGAGATTTTC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:20068929 original size:18 final size:18
Alignment explanation
Indices: 20068902--20068939 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
20068892 GCAAGGCTTT
20068902 AAGAGCCCTTGAAAAGTG
1 AAGAGCCCTTGAAAAGTG
* *
20068920 AAGAGTCCTTGAAATGTG
1 AAGAGCCCTTGAAAAGTG
20068938 AA
1 AA
20068940 TTCCCTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.21
Consensus pattern (18 bp):
AAGAGCCCTTGAAAAGTG
Found at i:20072930 original size:17 final size:18
Alignment explanation
Indices: 20072897--20072937 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
20072887 CATACCATAG
20072897 CCAGATACAAGTAGAATA
1 CCAGATACAAGTAGAATA
*
20072915 CCAGATATAA-TAGAATA
1 CCAGATACAAGTAGAATA
*
20072932 ACAGAT
1 CCAGAT
20072938 TCCAGAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.51, C:0.15, G:0.15, T:0.20
Consensus pattern (18 bp):
CCAGATACAAGTAGAATA
Found at i:20085137 original size:102 final size:102
Alignment explanation
Indices: 20085016--20085317 Score: 487
Period size: 102 Copynumber: 3.0 Consensus size: 102
20085006 CAATGAGTCA
* * ** *
20085016 GGGAATCAACACTTAGCAACCCCTTTCACATTTAAGATACGGTGGGTTCAGCACTTAGCAACCAC
1 GGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAACACTTAGCAACCAC
* * *
20085081 CAATGATTCGGGGAATCAGTACTTAGCAACCCCTCGG
66 CAATGAATAGGGGAATCAGCACTTAGCAACCCCTCGG
20085118 GGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAACACTTAGCAACCAC
1 GGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAACACTTAGCAACCAC
* *
20085183 CAATGAATAGGGGAATCAACACTTAGCAACCCCTTGG
66 CAATGAATAGGGGAATCAGCACTTAGCAACCCCTCGG
* * *
20085220 GGGAATCAGCACTTAGCAACCCCCTTCAAATTTAAAATACGATGGAATCAACACTTAGCAACCAC
1 GGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAACACTTAGCAACCAC
20085285 CAATGAATAGGGGAATCAGCACTTAGCAACCCC
66 CAATGAATAGGGGAATCAGCACTTAGCAACCCC
20085318 CTCTTTATTC
Statistics
Matches: 186, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
102 186 1.00
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (102 bp):
GGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAACACTTAGCAACCAC
CAATGAATAGGGGAATCAGCACTTAGCAACCCCTCGG
Found at i:20085203 original size:33 final size:33
Alignment explanation
Indices: 20085161--20085315 Score: 133
Period size: 33 Copynumber: 4.6 Consensus size: 33
20085151 AAGATACGGT
20085161 GGAATCAACACTTAGCAACCACCAATGAATAGG
1 GGAATCAACACTTAGCAACCACCAATGAATAGG
*
20085194 GGAATCAACACTTAGCAACC-CC--T---TGGG
1 GGAATCAACACTTAGCAACCACCAATGAATAGG
* * * *
20085221 GGAATCAGCACTTAGCAACCCCCTTCAAATTTAAAATACGAT
1 GGAATCAACACTTAGCAA-CCAC--C-AA--T-GAATA-G-G
20085263 GGAATCAACACTTAGCAACCACCAATGAATAGG
1 GGAATCAACACTTAGCAACCACCAATGAATAGG
*
20085296 GGAATCAGCACTTAGCAACC
1 GGAATCAACACTTAGCAACC
20085316 CCCTCTTTAT
Statistics
Matches: 98, Mismatches: 9, Indels: 30
0.72 0.07 0.22
Matches are distributed among these distances:
27 20 0.20
28 2 0.02
29 1 0.01
30 1 0.01
31 1 0.01
32 2 0.02
33 39 0.40
34 1 0.01
35 4 0.04
36 2 0.02
38 2 0.02
39 1 0.01
40 1 0.01
41 4 0.04
42 17 0.17
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.18
Consensus pattern (33 bp):
GGAATCAACACTTAGCAACCACCAATGAATAGG
Found at i:20086913 original size:18 final size:18
Alignment explanation
Indices: 20086890--20086932 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
20086880 TGCCCCATAG
20086890 CTAGATACAAAAAGAATA
1 CTAGATACAAAAAGAATA
*
20086908 CTAGATA-TAAAAGAATA
1 CTAGATACAAAAAGAATA
*
20086925 ATAGATAC
1 CTAGATAC
20086933 CAGAATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (18 bp):
CTAGATACAAAAAGAATA
Found at i:20089580 original size:21 final size:20
Alignment explanation
Indices: 20089539--20089587 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
20089529 ATAAATAAAA
*
20089539 TCATTCATGTCAATTCCCTG
1 TCATTCATGACAATTCCCTG
**
20089559 TCATTCACTGACAATTTTCTG
1 TCATTCA-TGACAATTCCCTG
20089580 TCATTCAT
1 TCATTCAT
20089588 AACTTCTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.22, C:0.27, G:0.08, T:0.43
Consensus pattern (20 bp):
TCATTCATGACAATTCCCTG
Found at i:20089805 original size:21 final size:21
Alignment explanation
Indices: 20089760--20089817 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
20089750 TGAATATGCC
* *
20089760 AACAGAAGCTCG-AA-AACTG
1 AACAGAAGCTCGTAAGAGCTA
20089779 AACAGAAGCTCGTAAGAGCTA
1 AACAGAAGCTCGTAAGAGCTA
20089800 AACAGAAGCTCGTAAGAG
1 AACAGAAGCTCGTAAGAG
20089818 TGATCCATCC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.34
20 2 0.06
21 21 0.60
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.12
Consensus pattern (21 bp):
AACAGAAGCTCGTAAGAGCTA
Found at i:20090021 original size:39 final size:39
Alignment explanation
Indices: 20089967--20090045 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
20089957 CGTTCAATTC
20089967 AAATCAAACATCCAATTCAATATTACAATTCCAACAATA
1 AAATCAAACATCCAATTCAATATTACAATTCCAACAATA
* * *
20090006 AAATCGAATATCCAATTCAATATTATAATTCCAACAATA
1 AAATCAAACATCCAATTCAATATTACAATTCCAACAATA
20090045 A
1 A
20090046 TTCATTTCTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.51, C:0.20, G:0.01, T:0.28
Consensus pattern (39 bp):
AAATCAAACATCCAATTCAATATTACAATTCCAACAATA
Found at i:20091726 original size:30 final size:30
Alignment explanation
Indices: 20091690--20091766 Score: 136
Period size: 30 Copynumber: 2.6 Consensus size: 30
20091680 TCTTCATATG
20091690 AAAACTTGATGTATGTGCCTGGCATAACAA
1 AAAACTTGATGTATGTGCCTGGCATAACAA
*
20091720 AAAACTTGATGTATGTGCCTGGTATAACAA
1 AAAACTTGATGTATGTGCCTGGCATAACAA
*
20091750 AAAACTTGATGTCTGTG
1 AAAACTTGATGTATGTG
20091767 TCACAATTCT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (30 bp):
AAAACTTGATGTATGTGCCTGGCATAACAA
Found at i:20094888 original size:14 final size:15
Alignment explanation
Indices: 20094855--20094888 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
20094845 TTAAGACTGT
20094855 TAGTTAGTTAGCTAG
1 TAGTTAGTTAGCTAG
20094870 T-GTTAGTTAGCTA-
1 TAGTTAGTTAGCTAG
20094883 TAGTTA
1 TAGTTA
20094889 TTTATTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.06
14 16 0.89
15 1 0.06
ACGTcount: A:0.26, C:0.06, G:0.24, T:0.44
Consensus pattern (15 bp):
TAGTTAGTTAGCTAG
Found at i:20095276 original size:3 final size:3
Alignment explanation
Indices: 20095268--20095328 Score: 104
Period size: 3 Copynumber: 20.3 Consensus size: 3
20095258 AACACATAGT
*
20095268 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAT AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
*
20095316 AAA AAC AAC AAC A
1 AAC AAC AAC AAC A
20095329 CACCCATGCC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.69, C:0.30, G:0.00, T:0.02
Consensus pattern (3 bp):
AAC
Found at i:20097444 original size:34 final size:35
Alignment explanation
Indices: 20097381--20097447 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
20097371 CAAAATCTAA
* *
20097381 AACAATAGTAATAAATAATTAAATTAAACTAAAAT
1 AACAATAATAATAAATAATTAAATAAAACTAAAAT
* *
20097416 AACAATAATAA-AATTAATTAACTAAAACTAAA
1 AACAATAATAATAAATAATTAAATAAAACTAAA
20097448 CCTAAGTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 18 0.64
35 10 0.36
ACGTcount: A:0.64, C:0.07, G:0.01, T:0.27
Consensus pattern (35 bp):
AACAATAATAATAAATAATTAAATAAAACTAAAAT
Found at i:20099880 original size:13 final size:14
Alignment explanation
Indices: 20099859--20099940 Score: 69
Period size: 13 Copynumber: 5.6 Consensus size: 14
20099849 CCCTGAATGG
20099859 TTTATTTTTAGTGT
1 TTTATTTTTAGTGT
*
20099873 TTTA-TTTTAGAGT
1 TTTATTTTTAGTGT
20099886 TTTACAATTTTTAGTGT
1 TTT---ATTTTTAGTGT
*
20099903 TTTA-TGTTAGTGT
1 TTTATTTTTAGTGT
*
20099916 TTTACAATTTTTAGTAT
1 TTT---ATTTTTAGTGT
20099933 TTTATTTT
1 TTTATTTT
20099941 AGTCCCTGAA
Statistics
Matches: 55, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
13 22 0.40
14 10 0.18
16 2 0.04
17 21 0.38
ACGTcount: A:0.21, C:0.02, G:0.12, T:0.65
Consensus pattern (14 bp):
TTTATTTTTAGTGT
Found at i:20099943 original size:30 final size:30
Alignment explanation
Indices: 20099862--20099943 Score: 137
Period size: 30 Copynumber: 2.7 Consensus size: 30
20099852 TGAATGGTTT
*
20099862 ATTTTTAGTGTTTTATTTTAGAGTTTTACA
1 ATTTTTAGTGTTTTATTTTAGTGTTTTACA
*
20099892 ATTTTTAGTGTTTTATGTTAGTGTTTTACA
1 ATTTTTAGTGTTTTATTTTAGTGTTTTACA
*
20099922 ATTTTTAGTATTTTATTTTAGT
1 ATTTTTAGTGTTTTATTTTAGT
20099944 CCCTGAATGA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.22, C:0.02, G:0.13, T:0.62
Consensus pattern (30 bp):
ATTTTTAGTGTTTTATTTTAGTGTTTTACA
Found at i:20101989 original size:45 final size:45
Alignment explanation
Indices: 20101925--20102047 Score: 165
Period size: 45 Copynumber: 2.7 Consensus size: 45
20101915 TACTGAGTAT
**
20101925 CATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACTGGGCAC
1 CATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACTGGAAAC
** * *
20101970 CATTGATTATAAAGGTGGTTGCTATGTGAGGACTCCACTGGAAAT
1 CATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACTGGAAAC
** *
20102015 CATTGAAAATAAATGTGGTTGCTATGTGCTGAT
1 CATTGATTATAAAGGTGGTTGCTATGTGCTGAT
20102048 CGACCGTGTA
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 66 1.00
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (45 bp):
CATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACTGGAAAC
Found at i:20105549 original size:3 final size:3
Alignment explanation
Indices: 20105541--20105578 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
20105531 TGGATGTATG
20105541 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
20105579 AGTCCAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:20106102 original size:18 final size:18
Alignment explanation
Indices: 20106067--20106106 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
20106057 ATAAATGGTA
*
20106067 CTTTTCATATTATCTCCT
1 CTTTTCATATCATCTCCT
20106085 CTTTTCATATCA-CTTCCT
1 CTTTTCATATCATC-TCCT
20106103 CTTT
1 CTTT
20106107 GGTCCTTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 1 0.05
18 19 0.95
ACGTcount: A:0.15, C:0.30, G:0.00, T:0.55
Consensus pattern (18 bp):
CTTTTCATATCATCTCCT
Found at i:20106883 original size:2 final size:2
Alignment explanation
Indices: 20106876--20106935 Score: 93
Period size: 2 Copynumber: 29.0 Consensus size: 2
20106866 GTTATTGCGC
20106876 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
20106918 ACT AC ACT AT AT AT AT AT
1 A-T AT A-T AT AT AT AT AT
20106936 TAGTAGNNNN
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
2 51 0.94
3 3 0.06
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:20108149 original size:13 final size:13
Alignment explanation
Indices: 20108131--20108155 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20108121 TTTAAAAATA
20108131 TTTTTATTTTTAT
1 TTTTTATTTTTAT
20108144 TTTTTATTTTTA
1 TTTTTATTTTTA
20108156 AAAAATATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTATTTTTAT
Found at i:20108577 original size:19 final size:19
Alignment explanation
Indices: 20108553--20108601 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
20108543 TGAGAGTTTC
* *
20108553 TTTTATATTTCTTCTTCTG
1 TTTTATATTTCCTATTCTG
*
20108572 TTTTATTAGTTCCTATTCTG
1 TTTTA-TATTTCCTATTCTG
*
20108592 TTTAATATTT
1 TTTTATATTT
20108602 TGAAGCTGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.16, C:0.12, G:0.06, T:0.65
Consensus pattern (19 bp):
TTTTATATTTCCTATTCTG
Found at i:20109389 original size:17 final size:17
Alignment explanation
Indices: 20109367--20109401 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
20109357 GTTTGGTTTA
20109367 TGTAATTTTAATCCTTC
1 TGTAATTTTAATCCTTC
20109384 TGTAATTTTAATCCTTC
1 TGTAATTTTAATCCTTC
20109401 T
1 T
20109402 ATATAATCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (17 bp):
TGTAATTTTAATCCTTC
Found at i:20110199 original size:13 final size:13
Alignment explanation
Indices: 20110181--20110205 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20110171 ACACTCAAAT
20110181 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
20110194 TTCTCAAAAGCA
1 TTCTCAAAAGCA
20110206 ATAAAGAACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.28, G:0.08, T:0.24
Consensus pattern (13 bp):
TTCTCAAAAGCAC
Found at i:20113150 original size:21 final size:21
Alignment explanation
Indices: 20113116--20113155 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
20113106 ACGGTGGTGA
* *
20113116 TGAGATTAGTTACTGTAACAG
1 TGAGATTAGATACTATAACAG
*
20113137 TGAGATTGGATACTATAAC
1 TGAGATTAGATACTATAAC
20113156 GATGAAATTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.33
Consensus pattern (21 bp):
TGAGATTAGATACTATAACAG
Found at i:20115319 original size:14 final size:15
Alignment explanation
Indices: 20115297--20115373 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
20115287 CAATCAAACA
20115297 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
20115311 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
20115326 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
20115346 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
20115360 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
20115374 ACTAACAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:20115338 original size:20 final size:20
Alignment explanation
Indices: 20115313--20115352 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
20115303 AATATTTTCC
*
20115313 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
20115333 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
20115353 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:20115358 original size:34 final size:35
Alignment explanation
Indices: 20115301--20115367 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
20115291 CAAACACCAG
*
20115301 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
20115336 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
20115368 TATTTTACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:20117402 original size:52 final size:50
Alignment explanation
Indices: 20117341--20117451 Score: 131
Period size: 49 Copynumber: 2.2 Consensus size: 50
20117331 ACAGTGTTTC
20117341 AGGTGTGTTTC-AAGGGCGGATGTAAAGCATAC-AGGCTTGGCACTTGGTG-CCG
1 AGGTGTGTTTCGAA--G-GGATGTAAAGC-TACGA-GCTTGGCACTTGGTGCCCG
* *
20117393 AGGTGTGTTTCGAAGGGATGTTAGGCTACGAGCTTGGCACTTGGTGCCCG
1 AGGTGTGTTTCGAAGGGATGTAAAGCTACGAGCTTGGCACTTGGTGCCCG
20117443 -GGTGTGTTT
1 AGGTGTGTTT
20117452 TTGGATGGTT
Statistics
Matches: 54, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
49 27 0.50
50 13 0.24
51 1 0.02
52 11 0.20
53 2 0.04
ACGTcount: A:0.17, C:0.16, G:0.38, T:0.29
Consensus pattern (50 bp):
AGGTGTGTTTCGAAGGGATGTAAAGCTACGAGCTTGGCACTTGGTGCCCG
Found at i:20119248 original size:40 final size:40
Alignment explanation
Indices: 20119182--20119435 Score: 295
Period size: 40 Copynumber: 6.4 Consensus size: 40
20119172 ATGCTCGTTT
* *
20119182 GAGCA-AC-TTTCAGTAGAATT-AATAGGTATGGCTCGATA
1 GAGCATACATTTCAGTA-AATTCAGTAGGTATGGCTCAATA
* * *
20119220 GAGCATACTTTTCAGTAAATTCTGTAGGTATGGCTCGATA
1 GAGCATACATTTCAGTAAATTCAGTAGGTATGGCTCAATA
* *
20119260 GTGCATACATTTCAGTAAATTCAATAGGTATGGCTCAATA
1 GAGCATACATTTCAGTAAATTCAGTAGGTATGGCTCAATA
* * *
20119300 GAGCATAC-TTTCAGTAGAA-TCAATAAGTATGGCTCGATA
1 GAGCATACATTTCAGTA-AATTCAGTAGGTATGGCTCAATA
*
20119339 TCA-CATACATTTCAGTAAATTCAGTAGGTATGGCTCAATA
1 -GAGCATACATTTCAGTAAATTCAGTAGGTATGGCTCAATA
* * *
20119379 GCGCATACATATCAGTAGATTCAGTAGGTATGGCTCAATA
1 GAGCATACATTTCAGTAAATTCAGTAGGTATGGCTCAATA
* *
20119419 GCGCATACGTTTCAGTA
1 GAGCATACATTTCAGTA
20119436 GGTAATGCTC
Statistics
Matches: 188, Mismatches: 20, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
38 5 0.03
39 39 0.21
40 144 0.77
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (40 bp):
GAGCATACATTTCAGTAAATTCAGTAGGTATGGCTCAATA
Found at i:20119401 original size:119 final size:119
Alignment explanation
Indices: 20119182--20119436 Score: 379
Period size: 119 Copynumber: 2.1 Consensus size: 119
20119172 ATGCTCGTTT
* * * * *
20119182 GAGCA-ACTTTCAGTAGAATTAATAGGTATGGCTCGATAGAGCATACTTTTCAGTAAATTCTGTA
1 GAGCATACTTTCAGTAGAATCAATAAGTATGGCTCGATACAGCATACATTTCAGTAAATTCAGTA
* * *
20119246 GGTATGGCTCGATAGTGCATACATTTCAGTAAATTCAATAGGTATGGCTCAATA
66 GGTATGGCTCAATAGCGCATACATATCAGTAAATTCAATAGGTATGGCTCAATA
20119300 GAGCATACTTTCAGTAGAATCAATAAGTATGGCTCGATATCA-CATACATTTCAGTAAATTCAGT
1 GAGCATACTTTCAGTAGAATCAATAAGTATGGCTCGATA-CAGCATACATTTCAGTAAATTCAGT
* *
20119364 AGGTATGGCTCAATAGCGCATACATATCAGTAGATTCAGTAGGTATGGCTCAATA
65 AGGTATGGCTCAATAGCGCATACATATCAGTAAATTCAATAGGTATGGCTCAATA
*
20119419 GCGCATACGTTTCAGTAG
1 GAGCATAC-TTTCAGTAG
20119437 GTAATGCTCA
Statistics
Matches: 123, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
118 5 0.04
119 108 0.88
120 10 0.08
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.31
Consensus pattern (119 bp):
GAGCATACTTTCAGTAGAATCAATAAGTATGGCTCGATACAGCATACATTTCAGTAAATTCAGTA
GGTATGGCTCAATAGCGCATACATATCAGTAAATTCAATAGGTATGGCTCAATA
Found at i:20120208 original size:47 final size:47
Alignment explanation
Indices: 20120129--20120319 Score: 285
Period size: 47 Copynumber: 4.0 Consensus size: 47
20120119 CAACCCTGTT
* * * *
20120129 TTGGACAGCAATTATTCATCAAATTGGACAGCAAT-AATATGCTCAAAA
1 TTGGACAGC-ATTATACATTAAAATGGACAGC-ATCAATATACTCAAAA
* * *
20120177 TTTGACAACATTATACATTAAAATGGACAGCATCAATATACTTAAAA
1 TTGGACAGCATTATACATTAAAATGGACAGCATCAATATACTCAAAA
*
20120224 TTGGACAGCATTATACATTAAAATGGACGGCATCAATATACTCAAAA
1 TTGGACAGCATTATACATTAAAATGGACAGCATCAATATACTCAAAA
20120271 TTGGACAGCATTATACATTAAAATGGACAGCATCAATATACTCAAAA
1 TTGGACAGCATTATACATTAAAATGGACAGCATCAATATACTCAAAA
20120318 TT
1 TT
20120320 ATAACACAAA
Statistics
Matches: 130, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
46 2 0.02
47 121 0.93
48 7 0.05
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.28
Consensus pattern (47 bp):
TTGGACAGCATTATACATTAAAATGGACAGCATCAATATACTCAAAA
Found at i:20120217 original size:25 final size:25
Alignment explanation
Indices: 20120188--20120311 Score: 156
Period size: 25 Copynumber: 5.2 Consensus size: 25
20120178 TTGACAACAT
20120188 TATACATTAAAATGGACAGCATCAA
1 TATACATTAAAATGGACAGCATCAA
20120213 TATAC-TTAAAATTGGACAGCAT---
1 TATACATTAAAA-TGGACAGCATCAA
*
20120235 TATACATTAAAATGGACGGCATCAA
1 TATACATTAAAATGGACAGCATCAA
*
20120260 TATAC-TCAAAATTGGACAGCAT---
1 TATACATTAAAA-TGGACAGCATCAA
20120282 TATACATTAAAATGGACAGCATCAA
1 TATACATTAAAATGGACAGCATCAA
20120307 TATAC
1 TATAC
20120312 TCAAAATTAT
Statistics
Matches: 85, Mismatches: 4, Indels: 20
0.78 0.04 0.18
Matches are distributed among these distances:
22 29 0.34
23 11 0.13
24 11 0.13
25 34 0.40
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.27
Consensus pattern (25 bp):
TATACATTAAAATGGACAGCATCAA
Found at i:20120250 original size:22 final size:22
Alignment explanation
Indices: 20120180--20120303 Score: 135
Period size: 22 Copynumber: 5.4 Consensus size: 22
20120170 CTCAAAATTT
*
20120180 GACAACATTATACATTAAAATG
1 GACAGCATTATACATTAAAATG
20120202 GACAGCATCAATATAC-TTAAAATTG
1 GACAGCAT---TATACATTAAAA-TG
20120227 GACAGCATTATACATTAAAATG
1 GACAGCATTATACATTAAAATG
* *
20120249 GACGGCATCAATATAC-TCAAAATTG
1 GACAGCAT---TATACATTAAAA-TG
20120274 GACAGCATTATACATTAAAATG
1 GACAGCATTATACATTAAAATG
20120296 GACAGCAT
1 GACAGCAT
20120304 CAATATACTC
Statistics
Matches: 87, Mismatches: 5, Indels: 20
0.78 0.04 0.18
Matches are distributed among these distances:
22 36 0.41
23 11 0.13
24 11 0.13
25 29 0.33
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.26
Consensus pattern (22 bp):
GACAGCATTATACATTAAAATG
Found at i:20121310 original size:28 final size:27
Alignment explanation
Indices: 20121254--20121352 Score: 110
Period size: 28 Copynumber: 3.6 Consensus size: 27
20121244 TTAATAAGTA
*
20121254 CGCACACTTAGTGCTTAAT-AATCAAACT
1 CGCACACTTAGTGCTT--TCAATTAAACT
* ** *
20121282 CACACACTTAGTGCTTTACCCTTATACT
1 CGCACACTTAGTGCTTT-CAATTAAACT
20121310 CGCACACTTAGTGCATTTCAATTAAACT
1 CGCACACTTAGTGC-TTTCAATTAAACT
20121338 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
20121353 AATCTCATTA
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
26 1 0.02
27 1 0.02
28 54 0.92
29 3 0.05
ACGTcount: A:0.29, C:0.28, G:0.11, T:0.31
Consensus pattern (27 bp):
CGCACACTTAGTGCTTTCAATTAAACT
Found at i:20126398 original size:32 final size:35
Alignment explanation
Indices: 20126345--20126436 Score: 88
Period size: 32 Copynumber: 2.8 Consensus size: 35
20126335 TAAATACTTA
***
20126345 AAAATAA-ATAAAATAAAATAAACATAAT-ATTT-
1 AAAATAATATAAAATTTTATAAACATAATAATTTG
* *
20126377 AAAATAAT-TAATATTTTATAAATA-AATAATTTG
1 AAAATAATATAAAATTTTATAAACATAATAATTTG
20126410 AAAATAATATAAAATTTTA-AAATCATA
1 AAAATAATATAAAATTTTATAAA-CATA
20126437 TTAGAAAGTA
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
31 3 0.06
32 22 0.47
33 11 0.23
34 10 0.21
35 1 0.02
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (35 bp):
AAAATAATATAAAATTTTATAAACATAATAATTTG
Found at i:20126399 original size:18 final size:16
Alignment explanation
Indices: 20126345--20126432 Score: 65
Period size: 18 Copynumber: 5.3 Consensus size: 16
20126335 TAAATACTTA
*
20126345 AAAATAAATAA-A-AT
1 AAAATAAATAATATTT
20126359 AAAATAAACATAATATTT
1 AAAAT-AA-ATAATATTT
*
20126377 AAAATAATTAATATTTT
1 AAAATAAATAATA-TTT
*
20126394 ATAAATAAATAAT-TTG
1 A-AAATAAATAATATTT
*
20126410 AAAATAATATAAAATTTT
1 AAAATAA-ATAATA-TTT
20126428 AAAAT
1 AAAAT
20126433 CATATTAGAA
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
14 5 0.08
15 8 0.14
16 16 0.27
17 7 0.12
18 23 0.39
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (16 bp):
AAAATAAATAATATTT
Found at i:20126659 original size:3 final size:3
Alignment explanation
Indices: 20126651--20126698 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
20126641 AATTTCACCT
20126651 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
20126699 GAATAAAAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:20127290 original size:22 final size:25
Alignment explanation
Indices: 20127237--20127294 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
20127227 AATCACAACT
20127237 TATTTTTAAA-TAAAGTTATAACTAA
1 TATTTTTAAATTAAAGTTATAAC-AA
*
20127262 TAATTTTAAATTAAA-TTAT-A-AA
1 TATTTTTAAATTAAAGTTATAACAA
20127284 TATTTTTAAAT
1 TATTTTTAAAT
20127295 GTTAATTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 12 0.40
24 1 0.03
25 13 0.43
26 4 0.13
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (25 bp):
TATTTTTAAATTAAAGTTATAACAA
Found at i:20141336 original size:23 final size:23
Alignment explanation
Indices: 20141283--20141336 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
20141273 ACCATCTACT
*
20141283 GGCAAATCTAAGAACTGTGCTAA
1 GGCAAATCTAAGAACAGTGCTAA
*
20141306 GTCAAATCTAAGAACAGTGCTAA
1 GGCAAATCTAAGAACAGTGCTAA
*
20141329 GGCTAATC
1 GGCAAATC
20141337 CATTCACAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (23 bp):
GGCAAATCTAAGAACAGTGCTAA
Found at i:20146094 original size:5 final size:5
Alignment explanation
Indices: 20146084--20146108 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
20146074 TGTCATATCC
20146084 AATCT AATCT AATCT AATCT AATCT
1 AATCT AATCT AATCT AATCT AATCT
20146109 TTACAAGATA
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:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
AATCT
Found at i:20156581 original size:23 final size:23
Alignment explanation
Indices: 20156547--20156593 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
20156537 ATATATAATC
20156547 ACTCAACACTTCATTAATTTTTA
1 ACTCAACACTTCATTAATTTTTA
*
20156570 ACTCAACTCTTCATTAATTTTTA
1 ACTCAACACTTCATTAATTTTTA
20156593 A
1 A
20156594 TTGGCCATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (23 bp):
ACTCAACACTTCATTAATTTTTA
Found at i:20156824 original size:9 final size:9
Alignment explanation
Indices: 20156810--20156840 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
20156800 GTTAAACGAA
20156810 TCGAGTTAT
1 TCGAGTTAT
*
20156819 TCGAGTTAA
1 TCGAGTTAT
20156828 TCGAGTTAT
1 TCGAGTTAT
20156837 TCGA
1 TCGA
20156841 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:20156910 original size:9 final size:9
Alignment explanation
Indices: 20156893--20156929 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
20156883 TGAGTTTTCG
20156893 AATTCGAAT
1 AATTCGAAT
*
20156902 AACTCGAAT
1 AATTCGAAT
20156911 AATTCGAAT
1 AATTCGAAT
20156920 AATTCGAAT
1 AATTCGAAT
20156929 A
1 A
20156930 TCAAACTATA
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:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:20157692 original size:5 final size:5
Alignment explanation
Indices: 20157682--20157708 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
20157672 CTCGAAAATT
20157682 TTCGA TTCGA TTCGA TTCGA TTCGA TT
1 TTCGA TTCGA TTCGA TTCGA TTCGA TT
20157709 GAATGCTCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (5 bp):
TTCGA
Found at i:20157848 original size:18 final size:17
Alignment explanation
Indices: 20157822--20157855 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
20157812 TTGTAAAATT
*
20157822 TTTATAAATTTATATAAC
1 TTTAAAAATTT-TATAAC
20157840 TTTAAAAATTTTATAA
1 TTTAAAAATTTTATAA
20157856 TTTGGTCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTAAAAATTTTATAAC
Found at i:20160084 original size:25 final size:25
Alignment explanation
Indices: 20160044--20160098 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
20160034 CACAAGTCCA
* * *
20160044 CCTTCAACTGGGCTATATGTAAAGG
1 CCTTCAACTAGACTATATGAAAAGG
*
20160069 CCTTCAACTAGACTATATGAAAAGT
1 CCTTCAACTAGACTATATGAAAAGG
20160094 CCTTC
1 CCTTC
20160099 TCTTTTTTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (25 bp):
CCTTCAACTAGACTATATGAAAAGG
Found at i:20161817 original size:20 final size:20
Alignment explanation
Indices: 20161788--20161826 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
20161778 ATGGGATTGC
20161788 ACTTTAGTGCCTCTGTTTGA
1 ACTTTAGTGCCTCTGTTTGA
*
20161808 ACTTTGGTGCCTCTGTTTG
1 ACTTTAGTGCCTCTGTTTG
20161827 CACTACGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.10, C:0.21, G:0.23, T:0.46
Consensus pattern (20 bp):
ACTTTAGTGCCTCTGTTTGA
Found at i:20161838 original size:20 final size:20
Alignment explanation
Indices: 20161795--20161881 Score: 77
Period size: 20 Copynumber: 4.3 Consensus size: 20
20161785 TGCACTTTAG
* ** *
20161795 TGCCTCTGTTTGAACTTTGG
1 TGCCTCTGTTTGCACTACGA
20161815 TGCCTCTGTTTGCACTACGA
1 TGCCTCTGTTTGCACTACGA
* *
20161835 TGCCTTTGATTGCACTATCG-
1 TGCCTCTGTTTGCACTA-CGA
* * *
20161855 TGTCTTTGTTTGCACTATGA
1 TGCCTCTGTTTGCACTACGA
20161875 TGCCTCT
1 TGCCTCT
20161882 ATATAGCATT
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
19 1 0.02
20 51 0.94
21 2 0.04
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.43
Consensus pattern (20 bp):
TGCCTCTGTTTGCACTACGA
Found at i:20161839 original size:40 final size:40
Alignment explanation
Indices: 20161795--20161881 Score: 102
Period size: 40 Copynumber: 2.2 Consensus size: 40
20161785 TGCACTTTAG
* * *
20161795 TGCCTCTGTTTGAACTTTGGTGCCTCTGTTTGCACTACGA
1 TGCCTCTGATTGAACTATCGTGCCTCTGTTTGCACTACGA
* * * * *
20161835 TGCCTTTGATTGCACTATCGTGTCTTTGTTTGCACTATGA
1 TGCCTCTGATTGAACTATCGTGCCTCTGTTTGCACTACGA
20161875 TGCCTCT
1 TGCCTCT
20161882 ATATAGCATT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.43
Consensus pattern (40 bp):
TGCCTCTGATTGAACTATCGTGCCTCTGTTTGCACTACGA
Found at i:20162099 original size:26 final size:24
Alignment explanation
Indices: 20162036--20162090 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
20162026 AGACTTAAAT
*
20162036 GAATATACATGAATGTTTTCAATC
1 GAATATACATGAATGATTTCAATC
*
20162060 GAATATACATGAATGATTTCAATG
1 GAATATACATGAATGATTTCAATC
20162084 GAATATA
1 GAATATA
20162091 TATATGAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.35
Consensus pattern (24 bp):
GAATATACATGAATGATTTCAATC
Found at i:20163913 original size:17 final size:17
Alignment explanation
Indices: 20163891--20163925 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
20163881 AACGTCAAAC
20163891 TTAAATTCACATACACA
1 TTAAATTCACATACACA
20163908 TTAAATTCACATACACA
1 TTAAATTCACATACACA
20163925 T
1 T
20163926 CACAAGCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (17 bp):
TTAAATTCACATACACA
Found at i:20165726 original size:22 final size:21
Alignment explanation
Indices: 20165698--20165742 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
20165688 TGCATTCACT
20165698 TTTTCTTTCCACTATGTTTCTA
1 TTTTCTTT-CACTATGTTTCTA
* *
20165720 TTTTCTTTTATTATGTTTCTA
1 TTTTCTTTCACTATGTTTCTA
20165741 TT
1 TT
20165743 ATAATATCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.13, C:0.16, G:0.04, T:0.67
Consensus pattern (21 bp):
TTTTCTTTCACTATGTTTCTA
Found at i:20166280 original size:19 final size:18
Alignment explanation
Indices: 20166223--20166292 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 18
20166213 ATAAAAATTG
20166223 AAATTTATAAAATTGTAA
1 AAATTTATAAAATTGTAA
* *
20166241 AAAATTATAAAAGTAGATAA
1 AAATTTATAAAA-TTG-TAA
*
20166261 AAATTTATTAAATTGTTAA
1 AAATTTATAAAATTG-TAA
*
20166280 AAATTTAAAAAAT
1 AAATTTATAAAAT
20166293 AAAATTATTA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
18 11 0.26
19 18 0.43
20 13 0.31
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.36
Consensus pattern (18 bp):
AAATTTATAAAATTGTAA
Found at i:20168983 original size:9 final size:9
Alignment explanation
Indices: 20168969--20168999 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
20168959 GTTAAACGAA
20168969 TCGAGTTAT
1 TCGAGTTAT
*
20168978 TCGAGTTAA
1 TCGAGTTAT
20168987 TCGAGTTAT
1 TCGAGTTAT
20168996 TCGA
1 TCGA
20169000 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:20169070 original size:9 final size:9
Alignment explanation
Indices: 20169053--20169089 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
20169043 TGAGTTTTCG
20169053 AATTCGAAT
1 AATTCGAAT
*
20169062 AACTCGAAT
1 AATTCGAAT
20169071 AATTCGAAT
1 AATTCGAAT
20169080 AATTCGAAT
1 AATTCGAAT
20169089 A
1 A
20169090 TCAAACTATA
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:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:20169447 original size:19 final size:19
Alignment explanation
Indices: 20169415--20169451 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
20169405 TTTTTAATAT
20169415 TTTCCCTCCAAACTATTTAC
1 TTTCCCTCCAAACT-TTTAC
20169435 TTTCCCT-CAAACTTTTA
1 TTTCCCTCCAAACTTTTA
20169452 TTCTCCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 6 0.35
20 7 0.41
ACGTcount: A:0.24, C:0.32, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTCCCTCCAAACTTTTAC
Found at i:20169499 original size:21 final size:20
Alignment explanation
Indices: 20169424--20169499 Score: 56
Period size: 20 Copynumber: 4.0 Consensus size: 20
20169414 TTTTCCCTCC
*
20169424 AAACTATTTACTT-T-CCCT
1 AAACTTTTTACTTCTCCCCT
*
20169442 CAAAC-TTTTA-TTCT--CCA
1 -AAACTTTTTACTTCTCCCCT
* *
20169459 AAACTTTTTATTTTTCCCCT
1 AAACTTTTTACTTCTCCCCT
20169479 AAACTTTTTACTTCTCACCCT
1 AAACTTTTTACTTCTC-CCCT
20169500 TTACTCTTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
16 4 0.09
17 9 0.20
18 8 0.18
19 4 0.09
20 16 0.36
21 4 0.09
ACGTcount: A:0.25, C:0.29, G:0.00, T:0.46
Consensus pattern (20 bp):
AAACTTTTTACTTCTCCCCT
Found at i:20169631 original size:17 final size:17
Alignment explanation
Indices: 20169577--20169657 Score: 69
Period size: 17 Copynumber: 4.6 Consensus size: 17
20169567 TTATATCTAC
20169577 TATTTATATTATTAAAT
1 TATTTATATTATTAAAT
* *
20169594 TAAATTTCACATT-TTATAT
1 T--ATTT-ATATTATTAAAT
20169613 TATTTATATTATTAAAT
1 TATTTATATTATTAAAT
*
20169630 TATTTAGTCA-TATTGAA-
1 TATTTA-T-ATTATTAAAT
20169647 TATTTATATTA
1 TATTTATATTA
20169658 AAATTGAATT
Statistics
Matches: 52, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
15 1 0.02
16 7 0.13
17 22 0.42
18 7 0.13
19 11 0.21
20 4 0.08
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (17 bp):
TATTTATATTATTAAAT
Found at i:20170114 original size:5 final size:5
Alignment explanation
Indices: 20170104--20170129 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
20170094 CTCGAAAATT
20170104 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
20170130 CAAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:20172978 original size:23 final size:19
Alignment explanation
Indices: 20172946--20173002 Score: 51
Period size: 19 Copynumber: 2.8 Consensus size: 19
20172936 CTCTATTTAG
*
20172946 TTATTATTTTGAATATTTATCC
1 TTATT-TTTTTAAT-TTT-TCC
*
20172968 TTTATTTTTTTAATTTTTTC
1 -TTATTTTTTTAATTTTTCC
*
20172988 TTATTTTTTTTATTT
1 TTATTTTTTTAATTT
20173003 CCTTTGTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 14 0.45
20 2 0.06
21 3 0.10
22 7 0.23
23 5 0.16
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (19 bp):
TTATTTTTTTAATTTTTCC
Found at i:20172985 original size:9 final size:9
Alignment explanation
Indices: 20172968--20173017 Score: 55
Period size: 9 Copynumber: 5.1 Consensus size: 9
20172958 ATATTTATCC
20172968 TTTATTTTT
1 TTTATTTTT
*
20172977 TTAATTTTT
1 TTTATTTTT
20172986 TCTTATTTTT
1 T-TTATTTTT
20172996 TTTATTTCCTT
1 TTTATTT--TT
20173007 TGTTATTTTT
1 T-TTATTTTT
20173017 T
1 T
20173018 AAATTTATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
9 15 0.43
10 11 0.31
11 3 0.09
12 6 0.17
ACGTcount: A:0.12, C:0.06, G:0.02, T:0.80
Consensus pattern (9 bp):
TTTATTTTT
Found at i:20173012 original size:21 final size:19
Alignment explanation
Indices: 20172969--20173023 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 19
20172959 TATTTATCCT
20172969 TTATTTTTTTAATTTTTTC
1 TTATTTTTTTAATTTTTTC
* *
20172988 TTATTTTTTTTATTTCCTTTG
1 TTATTTTTTTAATTT--TTTC
*
20173009 TTATTTTTTAAATTT
1 TTATTTTTTTAATTT
20173024 ATTTGGTTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 14 0.47
21 16 0.53
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.76
Consensus pattern (19 bp):
TTATTTTTTTAATTTTTTC
Found at i:20176075 original size:14 final size:14
Alignment explanation
Indices: 20176056--20176083 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
20176046 TGATAAAAGA
20176056 TGATAATATGAAAT
1 TGATAATATGAAAT
20176070 TGATAATATGAAAT
1 TGATAATATGAAAT
20176084 GAATTATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (14 bp):
TGATAATATGAAAT
Found at i:20185356 original size:15 final size:14
Alignment explanation
Indices: 20185333--20185368 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
20185323 TACACGTCAT
*
20185333 TTAAAAATCAATTC
1 TTAAAAATCAAATC
20185347 TTAGAAAATCAAATC
1 TTA-AAAATCAAATC
20185362 TTAAAAA
1 TTAAAAA
20185369 CCCAAATCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.56, C:0.11, G:0.03, T:0.31
Consensus pattern (14 bp):
TTAAAAATCAAATC
Found at i:20196518 original size:6 final size:6
Alignment explanation
Indices: 20196507--20196541 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
20196497 CTATTAACGT
20196507 GACTCG GACTCG GACTCG GACTCG GACTCG GACTC
1 GACTCG GACTCG GACTCG GACTCG GACTCG GACTC
20196542 AGATACGCGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.34, G:0.31, T:0.17
Consensus pattern (6 bp):
GACTCG
Found at i:20205871 original size:13 final size:13
Alignment explanation
Indices: 20205855--20205879 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20205845 TCTCCCTTCC
20205855 TCTCTGTCCATCA
1 TCTCTGTCCATCA
20205868 TCTCTGTCCATC
1 TCTCTGTCCATC
20205880 GTCCCTTCTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.40, G:0.08, T:0.40
Consensus pattern (13 bp):
TCTCTGTCCATCA
Found at i:20210144 original size:32 final size:32
Alignment explanation
Indices: 20210103--20210186 Score: 91
Period size: 33 Copynumber: 2.6 Consensus size: 32
20210093 AACTTTTTCG
*
20210103 GAAAATATTTTCAGGAAATT-TGCCAAACAACA
1 GAAAATATTTTCAGCAAATTAT-CCAAACAACA
* *
20210135 GAAAATATTTTACA-CAGATTCATCCAAACACCA
1 GAAAATATTTT-CAGCAAATT-ATCCAAACAACA
*
20210168 GAAAATATTTTCAGTAAAT
1 GAAAATATTTTCAGCAAAT
20210187 CATTTTCCAA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
32 17 0.40
33 25 0.58
34 1 0.02
ACGTcount: A:0.46, C:0.17, G:0.10, T:0.27
Consensus pattern (32 bp):
GAAAATATTTTCAGCAAATTATCCAAACAACA
Found at i:20210205 original size:20 final size:20
Alignment explanation
Indices: 20210180--20210219 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
20210170 AAATATTTTC
20210180 AGTAAATCATTTTCCAAAAA
1 AGTAAATCATTTTCCAAAAA
20210200 AGTAAATCATTTTCCAAAAA
1 AGTAAATCATTTTCCAAAAA
20210220 TCATTTTCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.05, T:0.30
Consensus pattern (20 bp):
AGTAAATCATTTTCCAAAAA
Found at i:20210499 original size:14 final size:14
Alignment explanation
Indices: 20210480--20210517 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
20210470 GTTTGCCAAT
* *
20210480 AAAATGTTTTTTGG
1 AAAATGATTTCTGG
20210494 AAAATGATTTCTGG
1 AAAATGATTTCTGG
20210508 AAAATGATTT
1 AAAATGATTT
20210518 ACTTTTCTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.37, C:0.03, G:0.18, T:0.42
Consensus pattern (14 bp):
AAAATGATTTCTGG
Found at i:20210526 original size:20 final size:20
Alignment explanation
Indices: 20210501--20210540 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
20210491 TGGAAAATGA
20210501 TTTCTGGAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
20210521 TTTCTGGAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
20210541 GAAAATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.10, G:0.15, T:0.45
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:20210534 original size:34 final size:33
Alignment explanation
Indices: 20210486--20210550 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 33
20210476 CAATAAAATG
*
20210486 TTTTTTGGAAAATGATTT-CTGGAAAATGATTTAC
1 TTTTCTGGAAAATGATTTACT-GAAAAT-ATTTAC
20210520 TTTTCTGGAAAATGATTTACTGAAAATATTT
1 TTTTCTGGAAAATGATTTACTGAAAATATTT
20210551 TATGGTGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 4 0.14
34 23 0.79
35 2 0.07
ACGTcount: A:0.34, C:0.06, G:0.15, T:0.45
Consensus pattern (33 bp):
TTTTCTGGAAAATGATTTACTGAAAATATTTAC
Found at i:20210661 original size:20 final size:20
Alignment explanation
Indices: 20210638--20210676 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
20210628 ATTTTTACAT
20210638 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
20210658 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
20210677 TTTTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:20211974 original size:32 final size:32
Alignment explanation
Indices: 20211928--20211988 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
20211918 TGTCAATCAT
20211928 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCCAACAAGCTTAAAACATAATAAA
*
20211960 TTCAATATCTAACAAGCTTAAAACATAAT
1 TTCAATATCCAACAAGCTTAAAACATAAT
20211989 CAATATCTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.51, C:0.18, G:0.03, T:0.28
Consensus pattern (32 bp):
TTCAATATCCAACAAGCTTAAAACATAATAAA
Found at i:20211995 original size:27 final size:30
Alignment explanation
Indices: 20211928--20212001 Score: 100
Period size: 32 Copynumber: 2.5 Consensus size: 30
20211918 TGTCAATCAT
*
20211928 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCTAACAAGCTTAAAAC--AATAAA
20211960 TTCAATATCTAACAAGCTTAAAAC-AT-AA
1 TTCAATATCTAACAAGCTTAAAACAATAAA
20211988 -TCAATATCTAACAA
1 TTCAATATCTAACAA
20212002 ATTCAATACA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
27 14 0.34
28 2 0.05
29 2 0.05
32 23 0.56
ACGTcount: A:0.51, C:0.19, G:0.03, T:0.27
Consensus pattern (30 bp):
TTCAATATCTAACAAGCTTAAAACAATAAA
Found at i:20212012 original size:27 final size:27
Alignment explanation
Indices: 20211929--20212015 Score: 77
Period size: 27 Copynumber: 3.0 Consensus size: 27
20211919 GTCAATCATT
* *
20211929 TCAATATCCAACAAGCTTAAAACATAATAAA
1 TCAATATCTAACAAGATTAAAAC---AT-AA
*
20211960 TTCAATATCTAACAAGCTTAAAACATAA
1 -TCAATATCTAACAAGATTAAAACATAA
*
20211988 TCAATATCTAACAA-ATTCAATACATAA
1 TCAATATCTAACAAGATT-AAAACATAA
20212015 T
1 T
20212016 AATTTCAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
26 2 0.04
27 23 0.45
28 2 0.04
29 2 0.04
32 22 0.43
ACGTcount: A:0.52, C:0.18, G:0.02, T:0.28
Consensus pattern (27 bp):
TCAATATCTAACAAGATTAAAACATAA
Found at i:20215900 original size:51 final size:51
Alignment explanation
Indices: 20215819--20216037 Score: 368
Period size: 51 Copynumber: 4.3 Consensus size: 51
20215809 ACTTCTGATT
* *
20215819 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
20215870 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
20215921 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
* * * *
20215972 AGTAACAAGTGATAAATGATAGCTTTAGCTACACTTATCTGATCAGGGAC-
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
20216022 AGTGGACAAGTGATAA
1 AGT-GACAAGTGATAA
20216038 ATGTGATCCG
Statistics
Matches: 160, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
50 3 0.02
51 157 0.98
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.28
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
Found at i:20218197 original size:59 final size:59
Alignment explanation
Indices: 20218127--20218244 Score: 184
Period size: 59 Copynumber: 2.0 Consensus size: 59
20218117 GAAGTGAAAG
20218127 TTATTAAAAAATGTGATAAAATGCAT-ACTTATTAGTCATTGGATGACATAATAATGTAA
1 TTATTAAAAAATGTGATAAAATGCATGA-TTATTAGTCATTGGATGACATAATAATGTAA
* * * *
20218186 TTATTATAAAATGTGATCACATGCATGATTATTAGTCATTGGATGGCATAATAATGTAA
1 TTATTAAAAAATGTGATAAAATGCATGATTATTAGTCATTGGATGACATAATAATGTAA
20218245 CAATATTTAT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
59 53 0.98
60 1 0.02
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (59 bp):
TTATTAAAAAATGTGATAAAATGCATGATTATTAGTCATTGGATGACATAATAATGTAA
Found at i:20220253 original size:17 final size:17
Alignment explanation
Indices: 20220231--20220267 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
20220221 ATAGTAGTAG
20220231 TAAACTATTCATAATAA
1 TAAACTATTCATAATAA
*
20220248 TAAACTTTTCATAATAA
1 TAAACTATTCATAATAA
20220265 TAA
1 TAA
20220268 TAATAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAACTATTCATAATAA
Found at i:20221018 original size:30 final size:30
Alignment explanation
Indices: 20220982--20221045 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
20220972 AACAAATATG
20220982 TATGTTGAAAACTCTAACTAGGAAGTTACA
1 TATGTTGAAAACTCTAACTAGGAAGTTACA
20221012 TATGTTGAAAACTCTAACTAGGAAGTTACA
1 TATGTTGAAAACTCTAACTAGGAAGTTACA
20221042 TATG
1 TATG
20221046 AAGCAACACC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.31
Consensus pattern (30 bp):
TATGTTGAAAACTCTAACTAGGAAGTTACA
Found at i:20230279 original size:33 final size:33
Alignment explanation
Indices: 20230237--20230306 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
20230227 ATTTAATAAA
20230237 ATTATTCATGAATTACGTTAATACCATTTGTAC
1 ATTATTCATGAATTACGTTAATACCATTTGTAC
20230270 ATTATTCATGAATTACGTTAATACCATTTGTAC
1 ATTATTCATGAATTACGTTAATACCATTTGTAC
20230303 ATTA
1 ATTA
20230307 CCCTCAATGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (33 bp):
ATTATTCATGAATTACGTTAATACCATTTGTAC
Found at i:20233663 original size:20 final size:20
Alignment explanation
Indices: 20233640--20233724 Score: 66
Period size: 20 Copynumber: 4.2 Consensus size: 20
20233630 TAAGTCCAGT
*
20233640 CAGGGGCACCAAAGTGTGAA
1 CAGGGGCACCAAAGTGCGAA
*
20233660 CAGGGGCA-CAAACGTGCAAA
1 CAGGGGCACCAAA-GTGCGAA
* * *
20233680 CAGGGACACCGAAGTG-TATA
1 CAGGGGCACCAAAGTGCGA-A
* * *
20233700 CAAGGGCATCGAAGTGCGAA
1 CAGGGGCACCAAAGTGCGAA
20233720 CAGGG
1 CAGGG
20233725 TCACATAGGT
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
19 5 0.10
20 42 0.82
21 4 0.08
ACGTcount: A:0.35, C:0.21, G:0.34, T:0.09
Consensus pattern (20 bp):
CAGGGGCACCAAAGTGCGAA
Found at i:20233707 original size:40 final size:40
Alignment explanation
Indices: 20233640--20233724 Score: 93
Period size: 40 Copynumber: 2.1 Consensus size: 40
20233630 TAAGTCCAGT
* *
20233640 CAGGGGCACCAAAGTGTGAACAGGGGCA-CAAACGTGCAAA
1 CAGGGACACCAAAGTGTGAACAAGGGCATCAAA-GTGCAAA
* * *
20233680 CAGGGACACCGAAGTGT-ATACAAGGGCATCGAAGTGCGAA
1 CAGGGACACCAAAGTGTGA-ACAAGGGCATCAAAGTGCAAA
20233720 CAGGG
1 CAGGG
20233725 TCACATAGGT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
39 1 0.03
40 34 0.89
41 3 0.08
ACGTcount: A:0.35, C:0.21, G:0.34, T:0.09
Consensus pattern (40 bp):
CAGGGACACCAAAGTGTGAACAAGGGCATCAAAGTGCAAA
Found at i:20233774 original size:61 final size:60
Alignment explanation
Indices: 20233640--20233790 Score: 185
Period size: 61 Copynumber: 2.5 Consensus size: 60
20233630 TAAGTCCAGT
* * * *
20233640 CAGGGGCACCAAAGTGTGAACAGGGGCACAAACGTGCAAACAGGGACACCGAAGTGTATA
1 CAGGGGCACCGAAGTGCGAACAGGGGCACAAACGTGCAAACAGAGACAACGAAGTGTATA
* * * * * * *
20233700 CAAGGGCATCGAAGTGCGAACAGGGTCACATAGGTGCAAATTAGAGACAATGAAGTGTATA
1 CAGGGGCACCGAAGTGCGAACAGGGGCACAAACGTGCAAA-CAGAGACAACGAAGTGTATA
*
20233761 CAGGGGCACCGAAGTGCGAACAGAGGCACA
1 CAGGGGCACCGAAGTGCGAACAGGGGCACA
20233791 GTTGTGCAAA
Statistics
Matches: 75, Mismatches: 15, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
60 33 0.44
61 42 0.56
ACGTcount: A:0.36, C:0.20, G:0.32, T:0.12
Consensus pattern (60 bp):
CAGGGGCACCGAAGTGCGAACAGGGGCACAAACGTGCAAACAGAGACAACGAAGTGTATA
Found at i:20240785 original size:62 final size:59
Alignment explanation
Indices: 20240716--20240832 Score: 153
Period size: 59 Copynumber: 1.9 Consensus size: 59
20240706 AGTGATTATC
* * *
20240716 TTAATATTAAATTAAATTTAATGTTTATTTTGTAGATAAATATTCTATTAATTAAATAATAT
1 TTAATATTAAATTAAATATAATATTTA---TGTAGATAAATATTATATTAATTAAATAATAT
* * *
20240778 TTAATATTAAATTTAATATAATATTTATGTTGATAAATATTATATTAATTTAATA
1 TTAATATTAAATTAAATATAATATTTATGTAGATAAATATTATATTAATTAAATA
20240833 TTAAAGTGAT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
59 25 0.51
62 24 0.49
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.50
Consensus pattern (59 bp):
TTAATATTAAATTAAATATAATATTTATGTAGATAAATATTATATTAATTAAATAATAT
Found at i:20240803 original size:12 final size:12
Alignment explanation
Indices: 20240767--20240804 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
20240757 ATTCTATTAA
20240767 TTAA-ATAATAT
1 TTAATATAATAT
20240778 TTAATATTAA-AT
1 TTAATA-TAATAT
20240790 TTAATATAATAT
1 TTAATATAATAT
20240802 TTA
1 TTA
20240805 TGTTGATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 7 0.29
12 14 0.58
13 3 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TTAATATAATAT
Found at i:20242716 original size:21 final size:22
Alignment explanation
Indices: 20242692--20242734 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
20242682 GTGTTATAAG
*
20242692 TTAAAATTAAATA-AATAAAAC
1 TTAAAATAAAATACAATAAAAC
20242713 TTAAAATAAAATACAATAAAAC
1 TTAAAATAAAATACAATAAAAC
20242735 ATAATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (22 bp):
TTAAAATAAAATACAATAAAAC
Found at i:20244351 original size:18 final size:17
Alignment explanation
Indices: 20244324--20244358 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
20244314 ATTTATACAA
20244324 GTTATATTTTGAATTAT
1 GTTATATTTTGAATTAT
*
20244341 GTTAGTATTTTGAGTTAT
1 GTTA-TATTTTGAATTAT
20244359 CATTTGTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.26, C:0.00, G:0.17, T:0.57
Consensus pattern (17 bp):
GTTATATTTTGAATTAT
Found at i:20246812 original size:16 final size:16
Alignment explanation
Indices: 20246791--20246826 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
20246781 TTTGGTTCGC
20246791 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
20246807 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
20246823 TGTA
1 TGTA
20246827 ATAGCAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:20247150 original size:157 final size:157
Alignment explanation
Indices: 20246949--20247265 Score: 580
Period size: 157 Copynumber: 2.0 Consensus size: 157
20246939 TAGAATACCC
*
20246949 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* * *
20247014 TTATCAATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
20247079 TATATAATTGAATAAAATTCTTAATAA
131 TATATAATTGAATAAAATTCTTAATAA
*
20247106 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
20247171 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
*
20247236 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTGAATAAAATTCTTAATAA
20247263 TTA
1 TTA
20247266 ATATTCTTAT
Statistics
Matches: 154, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
157 154 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.47
Consensus pattern (157 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
TATATAATTGAATAAAATTCTTAATAA
Found at i:20247236 original size:16 final size:16
Alignment explanation
Indices: 20247199--20247240 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
20247189 TTAATCATAT
*
20247199 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
20247215 TT-AAATATATTATAA
1 TTAAAATATATTATAA
20247230 TTAAAATATAT
1 TTAAAATATAT
20247241 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:20247247 original size:14 final size:15
Alignment explanation
Indices: 20247208--20247249 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
20247198 TTTAAACATA
*
20247208 ATTATTATTAAATAT
1 ATTATAATTAAATAT
20247223 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
20247237 A-TATAATTTAATA
1 ATTATAATTAAATA
20247250 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:20247337 original size:120 final size:121
Alignment explanation
Indices: 20247197--20247493 Score: 505
Period size: 120 Copynumber: 2.5 Consensus size: 121
20247187 ATTTAATCAT
*
20247197 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
*
20247262 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAAT-ATAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTAT-AAATGA-AA
20247319 A-TT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
20247382 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
* *
20247438 ATTTGAA-ATAATTA-TATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
20247494 TAAAATAATT
Statistics
Matches: 169, Mismatches: 3, Indels: 9
0.93 0.02 0.05
Matches are distributed among these distances:
119 47 0.28
120 117 0.69
121 4 0.02
122 1 0.01
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (121 bp):
ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
Found at i:20247367 original size:14 final size:15
Alignment explanation
Indices: 20247318--20247369 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
20247308 GTAAAATATA
20247318 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
20247333 TATTAAATATATTAT
1 AATTAAATATATTAT
20247348 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
20247361 AATTTAATA
1 AATTAAATA
20247370 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:20247580 original size:24 final size:25
Alignment explanation
Indices: 20247534--20247581 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
20247524 TATGAATTTG
20247534 TATAATTTAAAATAATAATTATTACA
1 TATAATTTAAAAT-ATAATTATTACA
20247560 TATAATTTAATAAT-TAA-TATTA
1 TATAATTTAA-AATATAATTATTA
20247582 AATTTCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 10 0.48
27 3 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAATTTAAAATATAATTATTACA
Found at i:20247606 original size:92 final size:91
Alignment explanation
Indices: 20247509--20247717 Score: 262
Period size: 92 Copynumber: 2.3 Consensus size: 91
20247499 TAATTATAAC
* * * *
20247509 TAATAAATTATATTTTATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATTTAATAA
1 TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTTAAT-A
* *
20247573 TTAATAT-TAAATTTCATAAAATTCTTGA
64 GTAATATAT-AATTTCATAAAATTCTTAA
* *
20247601 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAGT
1 TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAGT
*
20247666 GATATATAATTTCATAAAATTCTTAA
66 AATATATAATTTCATAAAATTCTTAA
*
20247692 TAATAAAATGT-TCTTATATGAATTTA
1 TAAT-AAAT-TATATTATATGAATTTA
20247718 CTAAAATCAA
Statistics
Matches: 104, Mismatches: 9, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
91 28 0.27
92 72 0.69
93 4 0.04
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAGT
AATATATAATTTCATAAAATTCTTAA
Found at i:20252859 original size:7 final size:7
Alignment explanation
Indices: 20252847--20252873 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
20252837 GAAAAAGAAA
20252847 AGAAGGT
1 AGAAGGT
20252854 AGAAGGT
1 AGAAGGT
20252861 AGAAGGT
1 AGAAGGT
20252868 AGAAGG
1 AGAAGG
20252874 AAATCGGTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.44, T:0.11
Consensus pattern (7 bp):
AGAAGGT
Found at i:20256193 original size:22 final size:22
Alignment explanation
Indices: 20256141--20256193 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
20256131 AGTGAAGATG
20256141 CCCTTCAGTGGTATTGCGATATT
1 CCCTTC-GTGGTATTGCGATATT
* *
20256164 CTCATCGTGGTATTGCGATA-T
1 CCCTTCGTGGTATTGCGATATT
20256185 CACCTTCGT
1 C-CCTTCGT
20256194 TAGGGGCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
21 2 0.08
22 19 0.76
23 4 0.16
ACGTcount: A:0.17, C:0.25, G:0.21, T:0.38
Consensus pattern (22 bp):
CCCTTCGTGGTATTGCGATATT
Found at i:20267325 original size:19 final size:18
Alignment explanation
Indices: 20267301--20267345 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
20267291 TATCAAGATA
20267301 AGTATTAATTTATTAAAAT
1 AGTATTAATTT-TTAAAAT
*
20267320 AGTATT-ATTTTTGAAAT
1 AGTATTAATTTTTAAAAT
20267337 A--ATTAATTT
1 AGTATTAATTT
20267346 GAAATCAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 3 0.12
16 4 0.17
17 7 0.29
18 4 0.17
19 6 0.25
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (18 bp):
AGTATTAATTTTTAAAAT
Found at i:20277742 original size:23 final size:23
Alignment explanation
Indices: 20277716--20277813 Score: 171
Period size: 23 Copynumber: 4.3 Consensus size: 23
20277706 ATAAGTGCCA
20277716 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
20277739 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
20277762 CACTGA-ATGTAGCCGAACCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
20277784 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
20277807 CACTGAT
1 CACTGAT
20277814 CAATAACACT
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
22 21 0.30
23 50 0.70
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:20277784 original size:45 final size:46
Alignment explanation
Indices: 20277716--20277813 Score: 171
Period size: 45 Copynumber: 2.2 Consensus size: 46
20277706 ATAAGTGCCA
* *
20277716 CACTGATATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAACCTACCACTGAAATGTAGCCGAAGCTAC
20277762 CACTGA-ATGTAGCCGAACCTACCACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAACCTACCACTGAAATGTAGCCGAAGCTAC
20277807 CACTGAT
1 CACTGAT
20277814 CAATAACACT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
45 43 0.88
46 6 0.12
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.20
Consensus pattern (46 bp):
CACTGATATGTAGCCGAACCTACCACTGAAATGTAGCCGAAGCTAC
Found at i:20285348 original size:20 final size:20
Alignment explanation
Indices: 20285323--20285369 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
20285313 CTGAGAAAGA
20285323 CAAAACAAAAGAAGAATTGC
1 CAAAACAAAAGAAGAATTGC
*
20285343 CAAAACAAAAGAAGAATTGT
1 CAAAACAAAAGAAGAATTGC
20285363 CAAAACA
1 CAAAACA
20285370 GTTAGAAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.62, C:0.15, G:0.13, T:0.11
Consensus pattern (20 bp):
CAAAACAAAAGAAGAATTGC
Found at i:20288112 original size:59 final size:59
Alignment explanation
Indices: 20287957--20288157 Score: 341
Period size: 58 Copynumber: 3.4 Consensus size: 59
20287947 GAGAAGGGAA
*
20287957 CAAGGTAAAAACCCGCAAAGGGCGCTTTGAAAATAAAAATAAAAAAATAAAATGGAGAGGC
1 CAAGGTGAAAACCCGCAAAGGGCGCTTTG-AAA-AAAAATAAAAAAATAAAATGGAGAGGC
* *
20288018 CAAGGTGAAAACCCGCAAAGGGCACTTTGAAAAAAAAT-AAAAAAGAAAATGGAGAGGC
1 CAAGGTGAAAACCCGCAAAGGGCGCTTTGAAAAAAAATAAAAAAATAAAATGGAGAGGC
*
20288076 CAAGGTGAAAACCCGCAAAGGGTGCTTTGAAAAAAAATAAAAAAATAAAATGGAGAGGC
1 CAAGGTGAAAACCCGCAAAGGGCGCTTTGAAAAAAAATAAAAAAATAAAATGGAGAGGC
20288135 CAAGGTGAAAACCCGCAAAGGGC
1 CAAGGTGAAAACCCGCAAAGGGC
20288158 ACCTTGAGAC
Statistics
Matches: 132, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
58 55 0.42
59 47 0.36
60 3 0.02
61 27 0.20
ACGTcount: A:0.50, C:0.14, G:0.24, T:0.11
Consensus pattern (59 bp):
CAAGGTGAAAACCCGCAAAGGGCGCTTTGAAAAAAAATAAAAAAATAAAATGGAGAGGC
Found at i:20289150 original size:26 final size:26
Alignment explanation
Indices: 20289114--20289166 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
20289104 TTGGATAAAA
20289114 AGGGGTTGCTAAGTGCAGATTCCCCG
1 AGGGGTTGCTAAGTGCAGATTCCCCG
**
20289140 AGGGGTTGCTAAGTGTTGATTCCCCG
1 AGGGGTTGCTAAGTGCAGATTCCCCG
20289166 A
1 A
20289167 ATTATTGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.19, C:0.21, G:0.34, T:0.26
Consensus pattern (26 bp):
AGGGGTTGCTAAGTGCAGATTCCCCG
Found at i:20289232 original size:43 final size:41
Alignment explanation
Indices: 20289140--20289420 Score: 264
Period size: 43 Copynumber: 6.6 Consensus size: 41
20289130 AGATTCCCCG
* * *
20289140 AGGGGTTGCTAAGTGTTGATTCCCCGAAT-TATTGATTCTAA
1 AGGGGTTGCTAAGTGCTGATTCCCCGTATAT-TTGATTGTAA
20289181 AGGTGGTTGCTAAGTGCTGATTCCACCGTATATTTGATTGTGAA
1 AGG-GGTTGCTAAGTGCTGATTCC-CCGTATATTTGATTGT-AA
* * * *
20289225 AGGGGTTGCTATGTGCTGATTCCCCGTATCA-CTGAATATAA
1 AGGGGTTGCTAAGTGCTGATTCCCCGTAT-ATTTGATTGTAA
*
20289266 AGGTGGTTGCTAAGTGCTGATTCCACCGTATATTTGAGTGTGAA
1 AGG-GGTTGCTAAGTGCTGATTCC-CCGTATATTTGATTGT-AA
* * * * *
20289310 AGGGGTTGCTATA-TGTTGATTCCCCGTATCA-CTAAATATAA
1 AGGGGTTGCTA-AGTGCTGATTCCCCGTAT-ATTTGATTGTAA
* *
20289351 AGGTGGTTGCTAAGTGCTGATTTCACCGTATGTTTGATTGTGAA
1 AGG-GGTTGCTAAGTGCTGA-TTCCCCGTATATTTGATTGT-AA
**
20289395 AGGGGTTGCTGTGTGCTGATTCCCCG
1 AGGGGTTGCTAAGTGCTGATTCCCCG
20289421 CTGACCAATT
Statistics
Matches: 198, Mismatches: 26, Indels: 31
0.78 0.10 0.12
Matches are distributed among these distances:
41 14 0.07
42 79 0.40
43 88 0.44
44 17 0.09
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.35
Consensus pattern (41 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGTATATTTGATTGTAA
Found at i:20289283 original size:85 final size:85
Alignment explanation
Indices: 20289140--20289420 Score: 436
Period size: 85 Copynumber: 3.3 Consensus size: 85
20289130 AGATTCCCCG
* * * * * * *
20289140 AGGGGTTGCTAAGTGTTGATTCCCCGAATTATTGATTCTAAAGGTGGTTGCTAAGTGCTGATTCC
1 AGGGGTTGCTATGTGCTGATTCCCCGTATCACTGAATATAAAGGTGGTTGCTAAGTGCTGATTCC
20289205 ACCGTATATTTGATTGTGAA
66 ACCGTATATTTGATTGTGAA
20289225 AGGGGTTGCTATGTGCTGATTCCCCGTATCACTGAATATAAAGGTGGTTGCTAAGTGCTGATTCC
1 AGGGGTTGCTATGTGCTGATTCCCCGTATCACTGAATATAAAGGTGGTTGCTAAGTGCTGATTCC
*
20289290 ACCGTATATTTGAGTGTGAA
66 ACCGTATATTTGATTGTGAA
* * * *
20289310 AGGGGTTGCTATATGTTGATTCCCCGTATCACTAAATATAAAGGTGGTTGCTAAGTGCTGATTTC
1 AGGGGTTGCTATGTGCTGATTCCCCGTATCACTGAATATAAAGGTGGTTGCTAAGTGCTGATTCC
*
20289375 ACCGTATGTTTGATTGTGAA
66 ACCGTATATTTGATTGTGAA
*
20289395 AGGGGTTGCTGTGTGCTGATTCCCCG
1 AGGGGTTGCTATGTGCTGATTCCCCG
20289421 CTGACCAATT
Statistics
Matches: 179, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
85 179 1.00
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.35
Consensus pattern (85 bp):
AGGGGTTGCTATGTGCTGATTCCCCGTATCACTGAATATAAAGGTGGTTGCTAAGTGCTGATTCC
ACCGTATATTTGATTGTGAA
Found at i:20291499 original size:6 final size:6
Alignment explanation
Indices: 20291488--20291532 Score: 54
Period size: 6 Copynumber: 6.8 Consensus size: 6
20291478 AGTTGTAAAG
20291488 TTTTAT TTTTAT TTTTAT TTTTAT TTACTTATT TATTTAT TTTTA
1 TTTTAT TTTTAT TTTTAT TTTTAT TT--TTA-T T-TTTAT TTTTA
20291533 CTTAGTTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
6 24 0.69
7 2 0.06
8 6 0.17
9 2 0.06
10 1 0.03
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTTAT
Found at i:20291548 original size:22 final size:21
Alignment explanation
Indices: 20291498--20291549 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
20291488 TTTTATTTTT
*
20291498 ATTTTTATTTTTATTTACTTA
1 ATTTTTATTTTTACTTACTTA
* *
20291519 TTTATTTATTTTTACTTAGTTTA
1 ATT-TTTATTTTTACTTA-CTTA
20291542 ATTTTTAT
1 ATTTTTAT
20291550 GTAAATATTC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
21 2 0.08
22 18 0.72
23 5 0.20
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (21 bp):
ATTTTTATTTTTACTTACTTA
Found at i:20292403 original size:13 final size:13
Alignment explanation
Indices: 20292385--20292409 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20292375 CTTCTCTTCC
20292385 TTTTCTTTTTTCT
1 TTTTCTTTTTTCT
20292398 TTTTCTTTTTTC
1 TTTTCTTTTTTC
20292410 CATAAGATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTCTTTTTTCT
Found at i:20311103 original size:14 final size:14
Alignment explanation
Indices: 20311084--20311116 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
20311074 CTACAAAAAT
*
20311084 AAAATAAAATAGTA
1 AAAATAAAATAATA
20311098 AAAAT-AAATAATA
1 AAAATAAAATAATA
20311111 AAAATA
1 AAAATA
20311117 GGAAAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (14 bp):
AAAATAAAATAATA
Found at i:20311112 original size:21 final size:21
Alignment explanation
Indices: 20311078--20311130 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
20311068 GTTTTCCTAC
*
20311078 AAAAAT-AAAAT-AAAATAGT
1 AAAAATAAAAATAAAAATAGG
20311097 AAAAATAAATAATAAAAATAGG
1 AAAAATAAA-AATAAAAATAGG
*
20311119 AAAATTAAAAAT
1 AAAAATAAAAAT
20311131 TTTTTTCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 6 0.21
20 2 0.07
21 6 0.21
22 15 0.52
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (21 bp):
AAAAATAAAAATAAAAATAGG
Found at i:20321013 original size:114 final size:114
Alignment explanation
Indices: 20320882--20321285 Score: 492
Period size: 114 Copynumber: 3.5 Consensus size: 114
20320872 TTTAGTAAAC
* * * *
20320882 GCCGCAAAATATCTTAACCAAAACGCATCATTTGGTCTTGAGGTATATAAGAATTAGTAGCGGTT
1 GCCGCAAAATATCTTAACCAAAACGTAGCGTTTGGTCTTGAGGTATATAAGAATTAGTGGCGGTT
** *
20320947 ACAAAAAAACGCCGCTAAAGGAGAGTATTAGAGGCGCTTTGTAACAAAT
66 ACGGAAAAACGCCGCTAAAGCAGAGTATTAGAGGCGCTTTGTAACAAAT
* * * * * * *
20320996 GCCAC-TAATCATCTTAACCAAAACGTAGCGTTTTGTCTTCATGTATATTAGAATTAGTGGCGCT
1 GCCGCAAAAT-ATCTTAACCAAAACGTAGCGTTTGGTCTTGAGGTATATAAGAATTAGTGGCGGT
** * *
20321060 TGTGGAAAAACGCCGCTATAGCACAGTATTAGCA-GCG-TTT-TATACGAAAT
65 TACGGAAAAACGCCGCTAAAGCAGAGTATTAG-AGGCGCTTTGTA-AC-AAAT
* *
20321110 GCCGCAAAATATCTTAACCAAAACGTATCGTTTTGTCTTGAGGTATATAAGAATTAGTGGCGGTT
1 GCCGCAAAATATCTTAACCAAAACGTAGCGTTTGGTCTTGAGGTATATAAGAATTAGTGGCGGTT
* ** * *
20321175 ACGGAAAAACGCAGCTAAAGCAGAGTATTAGAGATGCTTTGTAAGAATT
66 ACGGAAAAACGCCGCTAAAGCAGAGTATTAGAGGCGCTTTGTAACAAAT
* * *
20321224 GCCGCAAAATATATTAACCAAAACGTAGCGTTTGGTCTTGATGTATATTAGAATTAGTGGCG
1 GCCGCAAAATATCTTAACCAAAACGTAGCGTTTGGTCTTGAGGTATATAAGAATTAGTGGCG
20321286 CTCATGTAAA
Statistics
Matches: 243, Mismatches: 39, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
112 2 0.01
113 9 0.04
114 222 0.91
115 8 0.03
116 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.28
Consensus pattern (114 bp):
GCCGCAAAATATCTTAACCAAAACGTAGCGTTTGGTCTTGAGGTATATAAGAATTAGTGGCGGTT
ACGGAAAAACGCCGCTAAAGCAGAGTATTAGAGGCGCTTTGTAACAAAT
Found at i:20321119 original size:228 final size:227
Alignment explanation
Indices: 20320811--20321300 Score: 653
Period size: 228 Copynumber: 2.1 Consensus size: 227
20320801 TGTTCCCGAG
* * * * * * * * *
20320811 GTATATTAGACTTGGTGGCGTTTATGATAAATGCCGCTATAGTATATTATTAGCGGCGTTCTTTA
1 GTATATTAGAATTAGTGGCGCTTATGAAAAACGCCGCTATAGCACAGTATTAGCAGCGTTCTTTA
20320876 GTAAACGCCGCAAAATATCTTAACCAAAACGCATCATTTGGTCTTGAGGTATATAAGAATTAGTA
66 GTAAACGCCGCAAAATATCTTAACCAAAACGCATCATTTGGTCTTGAGGTATATAAGAATTAGTA
* * * *
20320941 GCGGTTACAAAAAAACGCCGCTAAAGGAGAGTATTAGAGGCGCTTTGTAACAAATGCCAC-TAAT
131 GCGGTTACAAAAAAACGCAGCTAAAGCAGAGTATTAGAGACGCTTTGTAACAAATGCCACAAAAT
* *
20321005 CATCTTAACCAAAACGTAGCGTTTTGTCTTCAT
196 -ATATTAACCAAAACGTAGCGTTTGGTCTTCAT
*
20321038 GTATATTAGAATTAGTGGCGCTTGTGGAAAAACGCCGCTATAGCACAGTATTAGCAGCGTT-TTA
1 GTATATTAGAATTAGTGGCGCTTAT-GAAAAACGCCGCTATAGCACAGTATTAGCAGCGTTCTT-
* * * *
20321102 TACG-AAATGCCGCAAAATATCTTAACCAAAACGTATCGTTTTGTCTTGAGGTATATAAGAATTA
64 TA-GTAAACGCCGCAAAATATCTTAACCAAAACGCATCATTTGGTCTTGAGGTATATAAGAATTA
* ** * * * *
20321166 GTGGCGGTTACGGAAAAACGCAGCTAAAGCAGAGTATTAGAGATGCTTTGTAAGAATTGCCGCAA
128 GTAGCGGTTACAAAAAAACGCAGCTAAAGCAGAGTATTAGAGACGCTTTGTAACAAATGCCACAA
*
20321231 AATATATTAACCAAAACGTAGCGTTTGGTCTTGAT
193 AATATATTAACCAAAACGTAGCGTTTGGTCTTCAT
*
20321266 GTATATTAGAATTAGTGGCGCTCATGTAAAAACGC
1 GTATATTAGAATTAGTGGCGCTTATG-AAAAACGC
20321301 ATGTAGGTTT
Statistics
Matches: 228, Mismatches: 30, Indels: 9
0.85 0.11 0.03
Matches are distributed among these distances:
227 24 0.11
228 200 0.88
229 4 0.02
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.29
Consensus pattern (227 bp):
GTATATTAGAATTAGTGGCGCTTATGAAAAACGCCGCTATAGCACAGTATTAGCAGCGTTCTTTA
GTAAACGCCGCAAAATATCTTAACCAAAACGCATCATTTGGTCTTGAGGTATATAAGAATTAGTA
GCGGTTACAAAAAAACGCAGCTAAAGCAGAGTATTAGAGACGCTTTGTAACAAATGCCACAAAAT
ATATTAACCAAAACGTAGCGTTTGGTCTTCAT
Found at i:20322182 original size:12 final size:12
Alignment explanation
Indices: 20322165--20322191 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
20322155 AAATTTTTTA
20322165 AATAATATTAAT
1 AATAATATTAAT
20322177 AATAATATTAAT
1 AATAATATTAAT
20322189 AAT
1 AAT
20322192 GTCATAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
AATAATATTAAT
Found at i:20323562 original size:14 final size:15
Alignment explanation
Indices: 20323543--20323571 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20323533 GGCACATTAC
20323543 TTGGTATTCT-TTTT
1 TTGGTATTCTGTTTT
20323557 TTGGTATTCTGTTTT
1 TTGGTATTCTGTTTT
20323572 GGCACAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.07, C:0.07, G:0.17, T:0.69
Consensus pattern (15 bp):
TTGGTATTCTGTTTT
Found at i:20323570 original size:39 final size:38
Alignment explanation
Indices: 20323499--20323577 Score: 106
Period size: 39 Copynumber: 2.0 Consensus size: 38
20323489 GACTTTGTGG
20323499 ATTACTTGGTATTCTGTTTTGGTAGGATTGTTTTGGCAC
1 ATTACTTGGTATTCTGTTTTGGTA-GATTGTTTTGGCAC
* *
20323538 ATTACTTGGTATTCTTTTTTTGGTA-TTCTGTTTTGGCAC
1 ATTACTTGGTATTC-TGTTTTGGTAGAT-TGTTTTGGCAC
20323577 A
1 A
20323578 GTTTCTTTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
38 1 0.03
39 26 0.72
40 9 0.25
ACGTcount: A:0.15, C:0.11, G:0.22, T:0.52
Consensus pattern (38 bp):
ATTACTTGGTATTCTGTTTTGGTAGATTGTTTTGGCAC
Found at i:20324296 original size:44 final size:44
Alignment explanation
Indices: 20324229--20324316 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
20324219 GTTTTCTATA
20324229 ATTAAAATCAATTATAATCATTGAAGAGACTGATGAGTTTCAAC
1 ATTAAAATCAATTATAATCATTGAAGAGACTGATGAGTTTCAAC
*
20324273 ATTAAAATCAATTATAATTATTGAAGAGACTGATGAGTTTCAAC
1 ATTAAAATCAATTATAATCATTGAAGAGACTGATGAGTTTCAAC
20324317 TCTCTAAAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (44 bp):
ATTAAAATCAATTATAATCATTGAAGAGACTGATGAGTTTCAAC
Found at i:20324916 original size:25 final size:24
Alignment explanation
Indices: 20324832--20324916 Score: 71
Period size: 25 Copynumber: 3.3 Consensus size: 24
20324822 ACTTTTTTAG
20324832 ATTTTCATAGTACATAACTTACATA
1 ATTTTCA-AGTACATAACTTACATA
* * * * *
20324857 ATATTGAACTTACTTAACTTTAATAATA
1 ATTTTCAA-GTACATAAC-TT-A-CATA
20324885 ATTTTCACAGTACATAACTTACATA
1 ATTTTCA-AGTACATAACTTACATA
20324910 ATTTTCA
1 ATTTTCA
20324917 TAACCTACAT
Statistics
Matches: 45, Mismatches: 10, Indels: 10
0.69 0.15 0.15
Matches are distributed among these distances:
24 1 0.02
25 22 0.49
26 3 0.07
27 3 0.07
28 15 0.33
29 1 0.02
ACGTcount: A:0.40, C:0.15, G:0.04, T:0.41
Consensus pattern (24 bp):
ATTTTCAAGTACATAACTTACATA
Done.