Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 98 of 356
Found at i:30986738 original size:7 final size:7
Alignment explanation
Indices: 30986726--30986750 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
30986716 ACTTAATAAA
30986726 TTTAGAT
1 TTTAGAT
30986733 TTTAGAT
1 TTTAGAT
30986740 TTTAGAT
1 TTTAGAT
30986747 TTTA
1 TTTA
30986751 TACTTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TTTAGAT
Found at i:30987174 original size:43 final size:43
Alignment explanation
Indices: 30987113--30987195 Score: 148
Period size: 43 Copynumber: 1.9 Consensus size: 43
30987103 ATAGTTCGGA
*
30987113 AAAATTAAGGGAAAATGTTGATTTAAAGTAAAAATTAAGGGGC
1 AAAATTAAGGGAAAATGTTGATTTAAAATAAAAATTAAGGGGC
*
30987156 AAAATTAGGGGAAAATGTTGATTTAAAATAAAAATTAAGG
1 AAAATTAAGGGAAAATGTTGATTTAAAATAAAAATTAAGG
30987196 AATTGAGACT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.51, C:0.01, G:0.22, T:0.27
Consensus pattern (43 bp):
AAAATTAAGGGAAAATGTTGATTTAAAATAAAAATTAAGGGGC
Found at i:30987853 original size:23 final size:24
Alignment explanation
Indices: 30987826--30987876 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
30987816 TAATGTTATA
*
30987826 AAATTTTAATTTTTT-TATT-CATT
1 AAATTTAAATTTTTTATATTGCA-T
30987849 AAA-TTAAATTTTTTATATTGCAT
1 AAATTTAAATTTTTTATATTGCAT
30987872 AAATT
1 AAATT
30987877 AATTTGATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
22 10 0.42
23 11 0.46
24 3 0.12
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (24 bp):
AAATTTAAATTTTTTATATTGCAT
Found at i:30987859 original size:22 final size:23
Alignment explanation
Indices: 30987833--30987878 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
30987823 ATAAAATTTT
30987833 AATTTTTT-TATT-CATTAAATTA
1 AATTTTTTATATTGCA-TAAATTA
30987855 AATTTTTTATATTGCATAAATTA
1 AATTTTTTATATTGCATAAATTA
30987878 A
1 A
30987879 TTTGATAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.36
23 12 0.55
24 2 0.09
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.54
Consensus pattern (23 bp):
AATTTTTTATATTGCATAAATTA
Found at i:30987880 original size:22 final size:21
Alignment explanation
Indices: 30987831--30987881 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 21
30987821 TTATAAAATT
30987831 TTAATTTTTTTATTCATTAAA
1 TTAATTTTTTTATTCATTAAA
30987852 TTAAATTTTTTATATTGCA-TAAA
1 TT-AATTTTTT-TATT-CATTAAA
30987875 TTAATTT
1 TTAATTT
30987882 GATAAACGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
21 2 0.07
22 13 0.48
23 10 0.37
24 2 0.07
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (21 bp):
TTAATTTTTTTATTCATTAAA
Found at i:30993446 original size:47 final size:47
Alignment explanation
Indices: 30993377--30993598 Score: 187
Period size: 47 Copynumber: 4.6 Consensus size: 47
30993367 TATGGCAACA
* *
30993377 TGTGATATGTGATTTCCGTATAAGACCATACCTAGGATATGACATCTG
1 TGTGATATGTG-CTTCCGTATAAGACCATACCTGGGATATGACATCTG
* * * * *
30993425 TGTGATATGTGCTCCCATATAAGACCATAGCTGGGCTATGGCATCGGTGTG
1 TGTGATATGTGCTTCCGTATAAGACCATACCTGGGATATGACATC----TG
* *
30993476 ATGTGATTATGTGCTTCCGTATAAGACCATATCTGGGATATGACATCAG
1 -TGTGA-TATGTGCTTCCGTATAAGACCATACCTGGGATATGACATCTG
** * * * * *
30993525 TGAT-ATATGTGCTTTTGTGTAAGACAATATCTGGGATATGGCATCAG
1 TG-TGATATGTGCTTCCGTATAAGACCATACCTGGGATATGACATCTG
* * *
30993572 AGTGATATGTG-ATCCGTGTAAGACCAT
1 TGTGATATGTGCTTCCGTATAAGACCAT
30993599 GTCTGGGCTA
Statistics
Matches: 143, Mismatches: 23, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
46 13 0.09
47 72 0.50
48 14 0.10
49 2 0.01
51 2 0.01
52 5 0.03
53 35 0.24
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (47 bp):
TGTGATATGTGCTTCCGTATAAGACCATACCTGGGATATGACATCTG
Found at i:30993549 original size:100 final size:100
Alignment explanation
Indices: 30993376--30993569 Score: 248
Period size: 100 Copynumber: 1.9 Consensus size: 100
30993366 CTATGGCAAC
* *
30993376 ATGTGATATGTGATTTCCGTATAAGACCATACCTAGGATATGACATCTGTGTGATATGTGCTCCC
1 ATGTGATATGTGACTTCCGTATAAGACCATACCTAGGATATGACATCAGTGTGATATGTGCTCCC
* *
30993441 ATATAAGACCATAGCTGGGCTATGGCATCGGTGTG
66 ATATAAGACAATAGCTGGGATATGGCATCGGTGTG
* * *
30993476 ATGTGATTATGTG-CTTCCGTATAAGACCATATCTGGGATATGACATCAGTGAT-ATATGTGCTT
1 ATGTGA-TATGTGACTTCCGTATAAGACCATACCTAGGATATGACATCAGTG-TGATATGTGCTC
*** * *
30993539 TTGTGTAAGACAATATCTGGGATATGGCATC
64 CCATATAAGACAATAGCTGGGATATGGCATC
30993570 AGAGTGATAT
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
100 73 0.91
101 7 0.09
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (100 bp):
ATGTGATATGTGACTTCCGTATAAGACCATACCTAGGATATGACATCAGTGTGATATGTGCTCCC
ATATAAGACAATAGCTGGGATATGGCATCGGTGTG
Found at i:30997294 original size:34 final size:34
Alignment explanation
Indices: 30997234--30997299 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
30997224 GTTTCATTTA
* *
30997234 GGGCCTTAGCCCACTACAGTATCAGTATCAGTGT
1 GGGCCTTAGCCCACTACAATATCAGTAACAGTGT
* *
30997268 GGGCCTTAGCCCATTTCAATGA-CAGTAACAGT
1 GGGCCTTAGCCCACTACAAT-ATCAGTAACAGT
30997300 ACAGATATGC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 26 0.96
35 1 0.04
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (34 bp):
GGGCCTTAGCCCACTACAATATCAGTAACAGTGT
Found at i:30999026 original size:12 final size:12
Alignment explanation
Indices: 30998993--30999026 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
30998983 AACCTCTCTT
30998993 AATTCTCTCCTC
1 AATTCTCTCCTC
*
30999005 AAATCTCTCCTC
1 AATTCTCTCCTC
*
30999017 AATTCACTCC
1 AATTCTCTCC
30999027 AACCGATCCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.24, C:0.41, G:0.00, T:0.35
Consensus pattern (12 bp):
AATTCTCTCCTC
Found at i:31002816 original size:37 final size:37
Alignment explanation
Indices: 31002757--31002865 Score: 191
Period size: 37 Copynumber: 2.9 Consensus size: 37
31002747 AGCTCAGACG
* *
31002757 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
31002794 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
31002831 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
31002866 ATATATTTCC
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:31003135 original size:48 final size:49
Alignment explanation
Indices: 31003011--31003147 Score: 215
Period size: 50 Copynumber: 2.8 Consensus size: 49
31003001 GCACATCGCC
*
31003011 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA-A
* *
31003061 TATATATTTCACATT-GACCATTCGGCTTTACCACATATGCATATCTC-A
1 TACATATTTCACATTAG-CCATTCGGCTTTACCACATATACATATCTCAA
31003109 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
31003148 TGCATGTTCA
Statistics
Matches: 80, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
48 36 0.45
49 2 0.03
50 42 0.52
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36
Consensus pattern (49 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCAA
Found at i:31003149 original size:50 final size:50
Alignment explanation
Indices: 31003011--31003246 Score: 210
Period size: 47 Copynumber: 4.9 Consensus size: 50
31003001 GCACATCGCC
*
31003011 TACATATTTCACACTAGCCATTCGGCTTTACCACATATA--CATATCTCATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATATGCATATCTC--A
*
31003061 TATATATTTCACATT-GACCATTCGGCTTTACCAC--ATATGCATATCTCA
1 TACATATTTCACATTAG-CCATTCGGCTTTACCACATATATGCATATCTCA
*
31003109 TACATATTTCACATTAGCCATTCGGCTTTACCACATATATGCATGT-TCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATATGCATATCTCA
** * * * * *
31003158 T--AT-TCACCACATTGGCCATTCGGCCTTATCACACATATGCA-AGCTC-
1 TACATAT-TTCACATTAGCCATTCGGCTTTACCACATATATGCATATCTCA
* * * *
31003204 -ACAT-TCATCACATTGGCCATTCGGCCTTATCACATATATGCAT
1 TACATAT-TTCACATTAGCCATTCGGCTTTACCACATATATGCAT
31003247 GTTCACATTC
Statistics
Matches: 161, Mismatches: 14, Indels: 24
0.81 0.07 0.12
Matches are distributed among these distances:
46 1 0.01
47 72 0.45
48 35 0.22
49 6 0.04
50 47 0.29
ACGTcount: A:0.29, C:0.28, G:0.10, T:0.34
Consensus pattern (50 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATATGCATATCTCA
Found at i:31003196 original size:47 final size:47
Alignment explanation
Indices: 31003117--31003310 Score: 280
Period size: 47 Copynumber: 4.1 Consensus size: 47
31003107 CATACATATT
* * * *
31003117 TCACATTAGCCATTCGGCTTTACCACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * * *
31003164 CCACATTGGCCATTCGGCCTTATCACACATATGCAAGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
31003211 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * **
31003258 TCACATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
31003305 TCACAT
1 TCACAT
31003311 AAAATCCTAA
Statistics
Matches: 131, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 131 1.00
ACGTcount: A:0.27, C:0.29, G:0.11, T:0.32
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
Found at i:31003237 original size:22 final size:22
Alignment explanation
Indices: 31003210--31003281 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
31003200 GCTCACATTC
31003210 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * *
31003232 ATCACATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
31003256 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
31003279 ATC
1 ATC
31003282 TCATATATAC
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
22 13 0.35
23 7 0.19
24 7 0.19
25 10 0.27
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:31003241 original size:94 final size:93
Alignment explanation
Indices: 31003070--31003310 Score: 290
Period size: 94 Copynumber: 2.5 Consensus size: 93
31003060 ATATATATTT
* * * *
31003070 CACATTGACCATTCGGCTTTA-CCACATATGCATATCTCATACATAT-TTCACATTAGCCATTCG
1 CACATTGGCCATTCGGCCTTATCCACATATGCACA-CTC--ACAT-TCATCACATTAGCCATTCG
* *
31003133 GCTTTACCACATATATGCATGTTCATATTCAC
62 GCCTTACCACATATATGCATGTTCACATTCAC
*
31003165 CACATTGGCCATTCGGCCTTATCACACATATGCA-AGCTCACATTCATCACATTGGCCATTCGGC
1 CACATTGGCCATTCGGCCTTATC-CACATATGCACA-CTCACATTCATCACATTAGCCATTCGGC
* *
31003229 CTTATCACATATATGCATGTTCACATTCAT
64 CTTACCACATATATGCATGTTCACATTCAC
* * *
31003259 CACATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCATCACAT
1 CACATTGGCCATTCGGCCTTATC-CACATATGCACACTCACATTCATCACAT
31003311 AAAATCCTAA
Statistics
Matches: 129, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
93 1 0.01
94 93 0.72
95 20 0.16
96 5 0.04
97 10 0.08
ACGTcount: A:0.28, C:0.29, G:0.10, T:0.33
Consensus pattern (93 bp):
CACATTGGCCATTCGGCCTTATCCACATATGCACACTCACATTCATCACATTAGCCATTCGGCCT
TACCACATATATGCATGTTCACATTCAC
Found at i:31008200 original size:46 final size:45
Alignment explanation
Indices: 31008108--31008272 Score: 156
Period size: 46 Copynumber: 3.6 Consensus size: 45
31008098 GACGAGGGCT
* * * * *
31008108 AGTGTAAGACATGTCTGGGACATGCATC-AGCCACAATATGAGAGCC
1 AGTGTAAGACATGTCTAGGACATGCATCGA-CCTCGAGATG-TAGCC
*
31008154 AGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGATGTTAGCC
1 AGTGTAAGACATGTCTAGGACATGCATCGACCTCGAGATG-TAGCC
* * ** * *
31008200 AATGTTAGACATGTCTAGGACATGGGTCG-GCTACGAGATGT-GCT
1 AGTGTAAGACATGTCTAGGACATGCATCGACCT-CGAGATGTAGCC
*
31008244 AGTGTAAGACATGTTTAGGACATGCATCG
1 AGTGTAAGACATGTCTAGGACATGCATCG
31008273 GCACAGTTAC
Statistics
Matches: 100, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
44 26 0.26
45 3 0.03
46 70 0.70
47 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.24
Consensus pattern (45 bp):
AGTGTAAGACATGTCTAGGACATGCATCGACCTCGAGATGTAGCC
Found at i:31017331 original size:47 final size:47
Alignment explanation
Indices: 31017279--31017509 Score: 191
Period size: 47 Copynumber: 4.8 Consensus size: 47
31017269 TGGTTAAACC
* *
31017279 ATGGCAAC-ATGTGATATGTGATTTCCATATAAGACCATATCTAGGAT
1 ATGGCATCGATGTGATATGTG-CTTCCATATAAGACCATATCTAGGAT
* * * * *
31017326 ATGGCATCGGTGTGATATGTGCTCCCATATAAGACCATAGCTGGGCT
1 ATGGCATCGATGTGATATGTGCTTCCATATAAGACCATATCTAGGAT
* * * * *
31017373 ATGGCATCGGTGTGATGGGATTATGTGCTTCCGTATAAGATCATTTCTGGGAT
1 ATGGCATC-----GATGTGA-TATGTGCTTCCATATAAGACCATATCTAGGAT
* ** *
31017426 ATGGCATCAATGAT-ATATGTGCTTCTGTGTAAGACCATATCTAGGAT
1 ATGGCATCGATG-TGATATGTGCTTCCATATAAGACCATATCTAGGAT
* *
31017473 ATGGCATCAGA-GTGATATGTG-ATCCATGTAAGACCAT
1 ATGGCATC-GATGTGATATGTGCTTCCATATAAGACCAT
31017510 GGCTGGGCTA
Statistics
Matches: 148, Mismatches: 26, Indels: 21
0.76 0.13 0.11
Matches are distributed among these distances:
46 14 0.09
47 79 0.53
48 16 0.11
52 5 0.03
53 34 0.23
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.32
Consensus pattern (47 bp):
ATGGCATCGATGTGATATGTGCTTCCATATAAGACCATATCTAGGAT
Found at i:31017399 original size:53 final size:47
Alignment explanation
Indices: 31017288--31017541 Score: 188
Period size: 47 Copynumber: 5.2 Consensus size: 47
31017278 CATGGCAACA
* * *
31017288 TGTGATATGTGATTTCCATATAAGACCATATCTAGGATATGGCATCGG
1 TGTGATATGTG-CTCCCATATAAGACCATATCTGGGATATGGCATCGG
* *
31017336 TGTGATATGTGCTCCCATATAAGACCATAGCTGGGCTATGGCATCGGTG
1 TGTGATATGTGCTCCCATATAAGACCATATCTGGGATATGGCATC-G-G
* * * * **
31017385 TGATGGGATTATGTGCTTCCGTATAAGATCATTTCTGGGATATGGCATCAA
1 TG-T--GA-TATGTGCTCCCATATAAGACCATATCTGGGATATGGCATCGG
* ** * * *
31017436 TGAT-ATATGTGCTTCTGTGTAAGACCATATCTAGGATATGGCATCAG
1 TG-TGATATGTGCTCCCATATAAGACCATATCTGGGATATGGCATCGG
* * * ** * *
31017483 AGTGATATGTGAT-CCATGTAAGACCATGGCTGGGCTATGGCTTCGGTG
1 TGTGATATGTGCTCCCATATAAGACCATATCTGGGATATGGCATC-G-G
31017531 TGTGATATGTG
1 TGTGATATGTG
31017542 ACTATGTGCA
Statistics
Matches: 167, Mismatches: 30, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
46 25 0.15
47 74 0.44
48 24 0.14
49 3 0.02
50 1 0.01
51 4 0.02
52 2 0.01
53 34 0.20
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (47 bp):
TGTGATATGTGCTCCCATATAAGACCATATCTGGGATATGGCATCGG
Found at i:31017444 original size:100 final size:100
Alignment explanation
Indices: 31017301--31017480 Score: 227
Period size: 100 Copynumber: 1.8 Consensus size: 100
31017291 GATATGTGAT
**
31017301 TTCCATATAAGACCATATCTAGGATATGGCATCGGTGTGATATGTGCTCCCATATAAGACCATAG
1 TTCCATATAAGACCATATCTAGGATATGGCATCAATGTGATATGTGCTCCCATATAAGACCATAG
* *
31017366 CTGGGCTATGGCATCGGTGTGATGGGATTATGTGC
66 CTAGGATATGGCATCGGTGTGATGGGATTATGTGC
* * * * * ** *
31017401 TTCCGTATAAGATCATTTCTGGGATATGGCATCAATGAT-ATATGTGCTTCTGTGTAAGACCATA
1 TTCCATATAAGACCATATCTAGGATATGGCATCAATG-TGATATGTGCTCCCATATAAGACCATA
*
31017465 TCTAGGATATGGCATC
65 GCTAGGATATGGCATC
31017481 AGAGTGATAT
Statistics
Matches: 66, Mismatches: 13, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
100 65 0.98
101 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.32
Consensus pattern (100 bp):
TTCCATATAAGACCATATCTAGGATATGGCATCAATGTGATATGTGCTCCCATATAAGACCATAG
CTAGGATATGGCATCGGTGTGATGGGATTATGTGC
Found at i:31019888 original size:13 final size:15
Alignment explanation
Indices: 31019870--31019901 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
31019860 CTACAGGGGA
31019870 CACATGG-C-TGTGT
1 CACATGGCCGTGTGT
31019883 CACATGGCCGTGTGT
1 CACATGGCCGTGTGT
31019898 CACA
1 CACA
31019902 CACGGCTGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 1 0.06
15 9 0.53
ACGTcount: A:0.19, C:0.28, G:0.28, T:0.25
Consensus pattern (15 bp):
CACATGGCCGTGTGT
Found at i:31020820 original size:33 final size:33
Alignment explanation
Indices: 31020778--31020954 Score: 255
Period size: 33 Copynumber: 5.4 Consensus size: 33
31020768 GCCAATTCAT
* *
31020778 CCATTACACCAATGCTTATAAGAGCTAATCCAA
1 CCATCACACCAATGCTCATAAGAGCTAATCCAA
31020811 CCATCACACCAATGCTCATAAGAGCTAATCCAA
1 CCATCACACCAATGCTCATAAGAGCTAATCCAA
* **
31020844 CCATCACACCAATGCTCATAAGAGGTAATTGAA
1 CCATCACACCAATGCTCATAAGAGCTAATCCAA
* * *
31020877 CCATCACACTAATGTTCATAAGAGCTAAACCAA
1 CCATCACACCAATGCTCATAAGAGCTAATCCAA
*
31020910 CCATCACACCAATGCTCATAAGAACTAATCCAA
1 CCATCACACCAATGCTCATAAGAGCTAATCCAA
* *
31020943 CTAGCACACCAA
1 CCATCACACCAA
31020955 ATAGAGAGTA
Statistics
Matches: 127, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 127 1.00
ACGTcount: A:0.41, C:0.30, G:0.10, T:0.20
Consensus pattern (33 bp):
CCATCACACCAATGCTCATAAGAGCTAATCCAA
Found at i:31022943 original size:26 final size:24
Alignment explanation
Indices: 31022861--31022953 Score: 82
Period size: 24 Copynumber: 3.8 Consensus size: 24
31022851 GAGCTTATAG
*
31022861 ACAGTAAGGTC-TATTGAGCTG-AA
1 ACAGTAAGCTCTTA-TGAGCTGAAA
** *
31022884 ATGGTAAGCTCTGATGAGCTGAAA
1 ACAGTAAGCTCTTATGAGCTGAAA
31022908 ACAGTAAGCTCTTATGAGCTGATATA
1 ACAGTAAGCTCTTATGAGCTGA-A-A
* * *
31022934 TCAGTAAGCTCATACGAGCT
1 ACAGTAAGCTCTTATGAGCT
31022954 ATTGTGAGTC
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
23 15 0.27
24 22 0.39
25 1 0.02
26 18 0.32
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (24 bp):
ACAGTAAGCTCTTATGAGCTGAAA
Found at i:31030167 original size:29 final size:29
Alignment explanation
Indices: 31030125--31030182 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
31030115 TCCGTCCATT
31030125 TTAGGAAAAACCCCTTTTGTTTTAAGGAA
1 TTAGGAAAAACCCCTTTTGTTTTAAGGAA
*
31030154 TTAGGAAAAACCCCTTTTGTTTTAGGGAA
1 TTAGGAAAAACCCCTTTTGTTTTAAGGAA
31030183 AACCGTTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (29 bp):
TTAGGAAAAACCCCTTTTGTTTTAAGGAA
Found at i:31032641 original size:23 final size:24
Alignment explanation
Indices: 31032601--31032694 Score: 84
Period size: 24 Copynumber: 3.8 Consensus size: 24
31032591 AGCTCCTCCT
* *
31032601 GAGCTGATAGACAGTAAGCTCT-ATT
1 GAGCTGA-AAACAGTAAGCTCTGA-C
*
31032626 GAGGTG-AAACAGTAAGCTCTGAC
1 GAGCTGAAAACAGTAAGCTCTGAC
*
31032649 GAGCTGAAAACAGTAAGCTCTTAC
1 GAGCTGAAAACAGTAAGCTCTGAC
* *
31032673 GAGATGATATATCAGTAAGCTC
1 GAGCTGA-A-AACAGTAAGCTC
31032695 ATATGAGCTG
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
23 18 0.31
24 23 0.40
25 6 0.10
26 11 0.19
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.23
Consensus pattern (24 bp):
GAGCTGAAAACAGTAAGCTCTGAC
Found at i:31032664 original size:24 final size:24
Alignment explanation
Indices: 31032587--31032704 Score: 89
Period size: 26 Copynumber: 4.8 Consensus size: 24
31032577 AGCTATGATT
* *
31032587 AGTAAGCTCCTCCTGAGCTGATAGAC
1 AGTAAGCT-CTAC-GAGCTGATAAAC
* *
31032613 AGTAAGCTCTATTGAGGTG--AAAC
1 AGTAAGCTCTA-CGAGCTGATAAAC
31032636 AGTAAGCTCTGACGAGCTGA-AAAC
1 AGTAAGCTCT-ACGAGCTGATAAAC
* *
31032660 AGTAAGCTCTTACGAGATGATATATC
1 AGTAAGCTC-TACGAGCTGATA-AAC
*
31032686 AGTAAGCTCATATGAGCTG
1 AGTAAGCTC-TACGAGCTG
31032705 TTGTGAGTCC
Statistics
Matches: 75, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
23 18 0.24
24 22 0.29
25 9 0.12
26 26 0.35
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.25
Consensus pattern (24 bp):
AGTAAGCTCTACGAGCTGATAAAC
Found at i:31035604 original size:40 final size:40
Alignment explanation
Indices: 31035567--31035752 Score: 268
Period size: 40 Copynumber: 4.7 Consensus size: 40
31035557 GCTACTCGTT
* *
31035567 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
* *
31035607 CAATTGCCTTCGGGACTTCACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
31035647 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
31035687 CAAATGCCTTCGGGACTTAACCCGGATTTAGTCACTTAGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAAC-TCGCA
*
31035728 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
31035753 CATCATTCAA
Statistics
Matches: 133, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
40 124 0.93
41 9 0.07
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:31039127 original size:51 final size:51
Alignment explanation
Indices: 31039067--31039176 Score: 193
Period size: 51 Copynumber: 2.1 Consensus size: 51
31039057 TCATTCATGC
*
31039067 CATCTTAAAACTGGATACACATTTCTTCTTTAGTAGGTACAATCCCTCGGG
1 CATCTTAAAACTAGATACACATTTCTTCTTTAGTAGGTACAATCCCTCGGG
*
31039118 CATCTTAAAACTAGATACACATTTCTTCTTTAGTAGGTACAATCTCTCGGG
1 CATCTTAAAACTAGATACACATTTCTTCTTTAGTAGGTACAATCCCTCGGG
31039169 CATACTTA
1 CAT-CTTA
31039177 CTAAGATATA
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
51 52 0.93
52 4 0.07
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.35
Consensus pattern (51 bp):
CATCTTAAAACTAGATACACATTTCTTCTTTAGTAGGTACAATCCCTCGGG
Found at i:31041064 original size:28 final size:28
Alignment explanation
Indices: 31041024--31041077 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
31041014 ACAATTCAAA
31041024 AAGTAATATACAACCATGAAAGTTTCCT
1 AAGTAATATACAACCATGAAAGTTTCCT
31041052 AAGTAATATACAACCATGAAAGTTTC
1 AAGTAATATACAACCATGAAAGTTTC
31041078 TCGTCATCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (28 bp):
AAGTAATATACAACCATGAAAGTTTCCT
Found at i:31041295 original size:33 final size:33
Alignment explanation
Indices: 31041253--31041375 Score: 158
Period size: 33 Copynumber: 3.7 Consensus size: 33
31041243 ATGCTCACTT
* *
31041253 GAGCCAATCCATCCATCACACCAATGCTTATAA
1 GAGCTAATCCAACCATCACACCAATGCTTATAA
* * *
31041286 GAGCTAATCCAACTATCACACCAGTGCTCATAA
1 GAGCTAATCCAACCATCACACCAATGCTTATAA
*
31041319 GAGCTAAACCAACCATCACACCAATG-TTCATAA
1 GAGCTAATCCAACCATCACACCAATGCTT-ATAA
* *
31041352 GAGCTAATCCAACTAGCACACCAA
1 GAGCTAATCCAACCATCACACCAA
31041376 ATAGAGATTA
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
32 1 0.01
33 76 0.99
ACGTcount: A:0.39, C:0.32, G:0.11, T:0.19
Consensus pattern (33 bp):
GAGCTAATCCAACCATCACACCAATGCTTATAA
Found at i:31043926 original size:18 final size:18
Alignment explanation
Indices: 31043889--31043927 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
31043879 TTGGAAATCA
*
31043889 AAATTATTAAAAGATGAT
1 AAATTATTAAAAGATAAT
31043907 AAATTATTAAATAGA-AAT
1 AAATTATTAAA-AGATAAT
31043925 AAA
1 AAA
31043928 AATCATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (18 bp):
AAATTATTAAAAGATAAT
Found at i:31046079 original size:17 final size:19
Alignment explanation
Indices: 31046037--31046080 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
31046027 ATGAAATTTT
*
31046037 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
31046056 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
31046074 AA-TATTA
1 AATTATTA
31046081 CTGTATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:31062517 original size:42 final size:42
Alignment explanation
Indices: 31062424--31062573 Score: 169
Period size: 42 Copynumber: 3.5 Consensus size: 42
31062414 GTTACAAATG
* * * *
31062424 TGGTCTTACATGTAATCAAATATCGATACCACTATCCCAGACA
1 TGGTCTTACACGAAATCAAATA-CGATGCCAATATCCCAGACA
* *
31062467 GGGTCTTACACGAAATCAAATACGATGCCAATGTCCCAGACA
1 TGGTCTTACACGAAATCAAATACGATGCCAATATCCCAGACA
* *
31062509 TGGTCTTACACGTAAATCTCAAAT-CGATGCCAACATCCCAGACG
1 TGGTCTTACACG-AAA--TCAAATACGATGCCAATATCCCAGACA
*
31062553 TGGTCTTAAACG-AATCAAATA
1 TGGTCTTACACGAAATCAAATA
31062574 TAAAAAATTC
Statistics
Matches: 92, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
40 6 0.07
42 30 0.33
43 22 0.24
44 28 0.30
45 6 0.07
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.24
Consensus pattern (42 bp):
TGGTCTTACACGAAATCAAATACGATGCCAATATCCCAGACA
Found at i:31067988 original size:33 final size:33
Alignment explanation
Indices: 31067941--31068005 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
31067931 AAATCTTAGG
* *
31067941 TAACTCATTCTCTCGGAACCACATATATCAACA
1 TAACTCATTCTCTCGAAACCACAGATATCAACA
* *
31067974 TAACTCATTTTCTCGAAACCATAGATATCAAC
1 TAACTCATTCTCTCGAAACCACAGATATCAAC
31068006 GTCTTCTACT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.37, C:0.28, G:0.06, T:0.29
Consensus pattern (33 bp):
TAACTCATTCTCTCGAAACCACAGATATCAACA
Found at i:31068841 original size:41 final size:41
Alignment explanation
Indices: 31068796--31068877 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
31068786 CGTATAAAAG
31068796 TTTCCAGACACTTAGAAAAATTTCTTGTAATCACAGGTCAC
1 TTTCCAGACACTTAGAAAAATTTCTTGTAATCACAGGTCAC
*
31068837 TTTCCAGACACTTAGAAAAATTTCTTGTAATCATAGGTCAC
1 TTTCCAGACACTTAGAAAAATTTCTTGTAATCACAGGTCAC
31068878 ACACCTGTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.33
Consensus pattern (41 bp):
TTTCCAGACACTTAGAAAAATTTCTTGTAATCACAGGTCAC
Found at i:31070196 original size:42 final size:44
Alignment explanation
Indices: 31070131--31070215 Score: 122
Period size: 42 Copynumber: 2.0 Consensus size: 44
31070121 ACATGTAATC
31070131 AAATATCGATGCCACTGTCCCAGAAAGGGTCTTACACA-AAATA
1 AAATATCGATGCCACTGTCCCAGAAAGGGTCTTACACATAAATA
* *
31070174 AAATA-CGATGCCGA-TGTCCCAGACATGGTCTTACACATAAAT
1 AAATATCGATGCC-ACTGTCCCAGAAAGGGTCTTACACATAAAT
31070216 CTCAAATCGA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
42 28 0.74
43 10 0.26
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.22
Consensus pattern (44 bp):
AAATATCGATGCCACTGTCCCAGAAAGGGTCTTACACATAAATA
Found at i:31070562 original size:15 final size:17
Alignment explanation
Indices: 31070542--31070581 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 17
31070532 ATCTATATAA
*
31070542 ATTCAAATCTGAC-TT-
1 ATTCAAATCTCACATTC
31070557 ATTC-AATCTCACATTC
1 ATTCAAATCTCACATTC
31070573 ATTCAAATC
1 ATTCAAATC
31070582 AATCCATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 7 0.33
15 6 0.29
16 4 0.19
17 4 0.19
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.38
Consensus pattern (17 bp):
ATTCAAATCTCACATTC
Found at i:31072282 original size:22 final size:22
Alignment explanation
Indices: 31072256--31072300 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
31072246 ATTATGTGTA
31072256 TTAATTAATAATATAAT-TAATT
1 TTAATT-ATAATATAATCTAATT
*
31072278 TTAATTATAATCTAATCTAATT
1 TTAATTATAATATAATCTAATT
31072300 T
1 T
31072301 GGGTCAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (22 bp):
TTAATTATAATATAATCTAATT
Found at i:31072695 original size:20 final size:20
Alignment explanation
Indices: 31072657--31072696 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
31072647 TTTTGGGTTA
*
31072657 TTATTCTATTTTATATTATT
1 TTATTCTATTTGATATTATT
* *
31072677 TTATTCTCTTTGATTTTATT
1 TTATTCTATTTGATATTATT
31072697 GTACTTTGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.20, C:0.07, G:0.03, T:0.70
Consensus pattern (20 bp):
TTATTCTATTTGATATTATT
Found at i:31084267 original size:3 final size:3
Alignment explanation
Indices: 31084259--31084293 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
31084249 GGATTCCGAT
*
31084259 GAA GAA GAA GAA GAA AAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
31084294 TCTCATAGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:31086486 original size:16 final size:16
Alignment explanation
Indices: 31086467--31086499 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
31086457 TAATTCATAA
31086467 TATAAT-CAATTTTAAT
1 TATAATCCAA-TTTAAT
31086483 TATAATCCAATTTAAT
1 TATAATCCAATTTAAT
31086499 T
1 T
31086500 TGGGTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (16 bp):
TATAATCCAATTTAAT
Found at i:31097263 original size:52 final size:51
Alignment explanation
Indices: 31097145--31097322 Score: 204
Period size: 52 Copynumber: 3.5 Consensus size: 51
31097135 ATTAGTGCCT
*
31097145 CAAGTGTGTTACTATGTGAAGGCCAC-TTTG-AGAAGAGATAGCTTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTTGAAGAAGAGATAGCTTGGTCA
* *
31097194 CAAGTGTGGTACTATGTGAAGGTCACTTTATGAAGAA-AGATAGTTTTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTT-TGAAGAAGAGATAG-CTTGGTCA
* * * *
31097246 CAAGTGCGGTACTATGTGAAGGCCACTTTGTGAATAAG-G-TAGCTTTGACTA
1 CAAGTGTGGTACTATGTGAAGGCCACTTT-TGAAGAAGAGATAGCTTGGTC-A
* *
31097297 CAAGGGTGGTACTATGTGCAGGCCAC
1 CAAGTGTGGTACTATGTGAAGGCCAC
31097323 CGGGAATCCG
Statistics
Matches: 110, Mismatches: 13, Indels: 10
0.83 0.10 0.08
Matches are distributed among these distances:
49 24 0.22
50 6 0.05
51 35 0.32
52 45 0.41
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.29
Consensus pattern (51 bp):
CAAGTGTGGTACTATGTGAAGGCCACTTTTGAAGAAGAGATAGCTTGGTCA
Found at i:31097320 original size:51 final size:49
Alignment explanation
Indices: 31097145--31097322 Score: 187
Period size: 51 Copynumber: 3.5 Consensus size: 49
31097135 ATTAGTGCCT
* * * *
31097145 CAAGTGTGTTACTATGTGAAGGCCACTTTGAGAAGAGATAGC-TTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAAAGATAGCTTTGCT-A
* * * *
31097194 CAAGTGTGGTACTATGTGAAGGTCACTTTATGAAGAAAGATAGTTTTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTG-A-AAAGATAGCTTTGCT-A
* *
31097246 CAAGTGCGGTACTATGTGAAGGCCACTTTGTGAATAAGGTAGCTTTGACTA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAA-AAGATAGCTTTG-CTA
* *
31097297 CAAGGGTGGTACTATGTGCAGGCCAC
1 CAAGTGTGGTACTATGTGAAGGCCAC
31097323 CGGGAATCCG
Statistics
Matches: 109, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
49 28 0.26
50 2 0.02
51 42 0.39
52 37 0.34
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.29
Consensus pattern (49 bp):
CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAAAGATAGCTTTGCTA
Found at i:31102817 original size:15 final size:14
Alignment explanation
Indices: 31102797--31102842 Score: 56
Period size: 16 Copynumber: 3.1 Consensus size: 14
31102787 AATAATAAAT
31102797 AAATAACAATAACTA
1 AAATAACAATAA-TA
31102812 AAATAACAAATTAATA
1 AAATAAC-AA-TAATA
*
31102828 AAATAATAATAATA
1 AAATAACAATAATA
31102842 A
1 A
31102843 CAAAATAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.21
15 9 0.32
16 10 0.36
17 3 0.11
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.24
Consensus pattern (14 bp):
AAATAACAATAATA
Found at i:31102841 original size:25 final size:26
Alignment explanation
Indices: 31102787--31102851 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
31102777 ACAAGTAAAG
*
31102787 AATAATAAATAAATAACAATAACTAA
1 AATAACAAATAAATAACAATAACTAA
*
31102813 AATAACAAATTAATAA-AATAA-TAA
1 AATAACAAATAAATAACAATAACTAA
31102837 TAATAACAAAATAAA
1 -AATAAC-AAATAAA
31102852 GTAAAATGGG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 3 0.09
25 11 0.32
26 20 0.59
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (26 bp):
AATAACAAATAAATAACAATAACTAA
Found at i:31128218 original size:47 final size:47
Alignment explanation
Indices: 31128152--31128441 Score: 445
Period size: 47 Copynumber: 6.1 Consensus size: 47
31128142 GAAATGATAG
*
31128152 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
31128199 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
31128246 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG----TATATATGTGA
*
31128297 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
31128344 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * *
31128391 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
31128438 TAAG
1 TAAG
31128442 TCCCGAAGGG
Statistics
Matches: 226, Mismatches: 13, Indels: 8
0.91 0.05 0.03
Matches are distributed among these distances:
47 181 0.80
51 45 0.20
ACGTcount: A:0.32, C:0.10, G:0.31, T:0.28
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:31128420 original size:145 final size:145
Alignment explanation
Indices: 31128155--31128430 Score: 471
Period size: 145 Copynumber: 1.9 Consensus size: 145
31128145 ATGATAGTAA
31128155 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTG
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTG
* * * *
31128220 ATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
66 ATGAATGTGAAAGTGTATATACGTGACAAGGCCGAATGGCCAACGTGATGAATGTGAAAGTGTAT
31128285 ATATATATGTGATAG
131 ATATATATGTGATAG
*
31128300 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTG
* * * *
31128365 ATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTAT
66 ATGAATGTGAAAGTGTATATACGTGACAAGGCCGAATGGCCAACGTGATGAATGTGAAAGTGTAT
31128430 A
131 A
31128431 AATGTGATAA
Statistics
Matches: 122, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
145 122 1.00
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.28
Consensus pattern (145 bp):
GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTG
ATGAATGTGAAAGTGTATATACGTGACAAGGCCGAATGGCCAACGTGATGAATGTGAAAGTGTAT
ATATATATGTGATAG
Found at i:31128616 original size:37 final size:37
Alignment explanation
Indices: 31128560--31128638 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
31128550 CCGAGCTCTA
* * *
31128560 AAGACCCAATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCAATAACTACGTGTGGAGATTATGTCCGGGT
* * *
31128597 AAGACCCGATAACTTCGTGTGGAGATTATGTTCGGGT
1 AAGACCCAATAACTACGTGTGGAGATTATGTCCGGGT
31128634 AAGAC
1 AAGAC
31128639 TTCGTAATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (37 bp):
AAGACCCAATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:31131961 original size:25 final size:25
Alignment explanation
Indices: 31131925--31131972 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
31131915 ATCGTTCATC
31131925 TAATGACAAGATTCAAGAACAAACA
1 TAATGACAAGATTCAAGAACAAACA
*
31131950 TAATGATC-AGATTCAATAACAAA
1 TAATGA-CAAGATTCAAGAACAAA
31131973 ACACAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 20 0.95
26 1 0.05
ACGTcount: A:0.54, C:0.15, G:0.10, T:0.21
Consensus pattern (25 bp):
TAATGACAAGATTCAAGAACAAACA
Found at i:31134340 original size:20 final size:19
Alignment explanation
Indices: 31134298--31134340 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
31134288 ATTAAACTTT
*
31134298 AAAATTGGACCTGAGATCC
1 AAAATTGGACCTGAGACCC
31134317 AAAATTGGACCTGAGAACCC
1 AAAATTGGACCTGAG-ACCC
31134337 AAAA
1 AAAA
31134341 CCGAGATCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.44, C:0.21, G:0.19, T:0.16
Consensus pattern (19 bp):
AAAATTGGACCTGAGACCC
Found at i:31140385 original size:25 final size:25
Alignment explanation
Indices: 31140348--31140409 Score: 90
Period size: 25 Copynumber: 2.5 Consensus size: 25
31140338 ATGCTAATTT
31140348 GAGCTA-AAGATCGATATGCTCTCAC
1 GAGCTATAA-ATCGATATGCTCTCAC
* *
31140373 GAGTTATAAATCGGTATGCTCTCAC
1 GAGCTATAAATCGATATGCTCTCAC
31140398 GAGCTATAAATC
1 GAGCTATAAATC
31140410 AGTAACCCTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
25 31 0.94
26 2 0.06
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.27
Consensus pattern (25 bp):
GAGCTATAAATCGATATGCTCTCAC
Found at i:31145138 original size:3 final size:3
Alignment explanation
Indices: 31145130--31145175 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
31145120 TATAGTGGCT
31145130 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
31145176 TGTAACACCC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:31147523 original size:27 final size:26
Alignment explanation
Indices: 31147478--31147591 Score: 84
Period size: 27 Copynumber: 4.2 Consensus size: 26
31147468 CCCTGTTTAG
* * *
31147478 AATACTTTAGTTTACTAAAATTACCGA
1 AATACCTTAGTTT-GTAAAATTACCAA
* *
31147505 AATACGCTTAGTTTGTAAAAATACTAA
1 AATAC-CTTAGTTTGTAAAATTACCAA
* * *
31147532 AATACCCTCGATTTGTAAAATTACTAA
1 AATACCTTAG-TTTGTAAAATTACCAA
* * *
31147559 AGTACCTTCGACTTGTAAAATTACCAA
1 AATACCTTAG-TTTGTAAAATTACCAA
*
31147586 AGTACC
1 AATACC
31147592 CCCGATTTAC
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
26 3 0.04
27 63 0.86
28 7 0.10
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (26 bp):
AATACCTTAGTTTGTAAAATTACCAA
Found at i:31147607 original size:27 final size:27
Alignment explanation
Indices: 31147577--31147638 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
31147567 CGACTTGTAA
31147577 AATTACCAAAGTACCCCCGATTTACAG
1 AATTACCAAAGTACCCCCGATTTACAG
*** *
31147604 AATTACCATTTTACCCCCGATTTACAT
1 AATTACCAAAGTACCCCCGATTTACAG
31147631 AATTACCA
1 AATTACCA
31147639 TTTTACCCCC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.35, C:0.29, G:0.06, T:0.29
Consensus pattern (27 bp):
AATTACCAAAGTACCCCCGATTTACAG
Found at i:31147639 original size:27 final size:27
Alignment explanation
Indices: 31147588--31147781 Score: 129
Period size: 27 Copynumber: 6.8 Consensus size: 27
31147578 ATTACCAAAG
31147588 TACCCCCGATTTACAGAATTACCATTT
1 TACCCCCGATTTACAGAATTACCATTT
*
31147615 TACCCCCGATTTACATAATTACCATTT
1 TACCCCCGATTTACAGAATTACCATTT
* *
31147642 TACCCCC-ATTTTACCTCAACTTACAGAATTACCGTTT
1 TACCCCCGA--TT---T--AC--AG--AATTACCATTT
* * *
31147679 TACCCTCGATTTACAGAAGTACCGTTT
1 TACCCCCGATTTACAGAATTACCATTT
* ** * **
31147706 TATCCTTGATTTATAGAATTACTGTTT
1 TACCCCCGATTTACAGAATTACCATTT
** *
31147733 TACCCTTGATTTACAGAATTACTATTT
1 TACCCCCGATTTACAGAATTACCATTT
* *
31147760 TACCCTCGATTTACAAAATTAC
1 TACCCCCGATTTACAGAATTAC
31147782 TAGAATACCC
Statistics
Matches: 139, Mismatches: 16, Indels: 24
0.78 0.09 0.13
Matches are distributed among these distances:
26 1 0.01
27 109 0.78
28 2 0.01
29 1 0.01
31 3 0.02
33 3 0.02
35 1 0.01
36 2 0.01
37 16 0.12
38 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.38
Consensus pattern (27 bp):
TACCCCCGATTTACAGAATTACCATTT
Found at i:31147646 original size:54 final size:54
Alignment explanation
Indices: 31147588--31147781 Score: 163
Period size: 54 Copynumber: 3.4 Consensus size: 54
31147578 ATTACCAAAG
* * *
31147588 TACCCCCGATTTACAGAATTACCATTTTACCCCCGATTTACATAATTACCATTT
1 TACCCCCGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACCATTT
* * *
31147642 TACCCCCATTTTACCTCAACTTACAGAATTACCGTTTTACCCTCGATTTACAGAAGTACCGTTT
1 TACCCCC----GA--T----TTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACCATTT
* ** * * * *
31147706 TATCCTTGATTTATAGAATTACTGTTTTACCCTTGATTTACAGAATTACTATTT
1 TACCCCCGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACCATTT
* *
31147760 TACCCTCGATTTACAAAATTAC
1 TACCCCCGATTTACAGAATTAC
31147782 TAGAATACCC
Statistics
Matches: 110, Mismatches: 20, Indels: 20
0.73 0.13 0.13
Matches are distributed among these distances:
54 63 0.57
58 2 0.02
60 2 0.02
64 43 0.39
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.38
Consensus pattern (54 bp):
TACCCCCGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACCATTT
Found at i:31147782 original size:27 final size:27
Alignment explanation
Indices: 31147649--31147783 Score: 146
Period size: 27 Copynumber: 5.0 Consensus size: 27
31147639 TTTTACCCCC
* * *
31147649 ATTTTA-CCTCAACTTACAGAATTACC
1 ATTTTACCCTCGATTTACAGAATTACT
* * *
31147675 GTTTTACCCTCGATTTACAGAAGTACC
1 ATTTTACCCTCGATTTACAGAATTACT
* * * *
31147702 GTTTTATCCTTGATTTATAGAATTACT
1 ATTTTACCCTCGATTTACAGAATTACT
* *
31147729 GTTTTACCCTTGATTTACAGAATTACT
1 ATTTTACCCTCGATTTACAGAATTACT
*
31147756 ATTTTACCCTCGATTTACAAAATTACT
1 ATTTTACCCTCGATTTACAGAATTACT
31147783 A
1 A
31147784 GAATACCCTA
Statistics
Matches: 94, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
26 5 0.05
27 89 0.95
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.41
Consensus pattern (27 bp):
ATTTTACCCTCGATTTACAGAATTACT
Found at i:31147782 original size:54 final size:53
Alignment explanation
Indices: 31147647--31147782 Score: 164
Period size: 54 Copynumber: 2.5 Consensus size: 53
31147637 CATTTTACCC
* * *
31147647 CCATTTTACCTCAACTTACAGAATTACCGTTTTACCCTCGATTTACAGAAGTA
1 CCATTTTACCTCGATTTACAGAATTACTGTTTTACCCTCGATTTACAGAAGTA
* * * * *
31147700 CCGTTTTATCCTTGATTTATAGAATTACTGTTTTACCCTTGATTTACAGAATTA
1 CCATTTTA-CCTCGATTTACAGAATTACTGTTTTACCCTCGATTTACAGAAGTA
* *
31147754 CTATTTTACCCTCGATTTACAAAATTACT
1 CCATTTTA-CCTCGATTTACAGAATTACT
31147783 AGAATACCCT
Statistics
Matches: 68, Mismatches: 14, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
53 7 0.10
54 61 0.90
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (53 bp):
CCATTTTACCTCGATTTACAGAATTACTGTTTTACCCTCGATTTACAGAAGTA
Found at i:31147790 original size:27 final size:27
Alignment explanation
Indices: 31147760--31148063 Score: 183
Period size: 27 Copynumber: 11.2 Consensus size: 27
31147750 ATTACTATTT
** *
31147760 TACCCTCGATTTACAAAATTACTAGAA
1 TACCCTCGATTTGTAAAATTACTAAAA
* *
31147787 TACCCTAG-TCTGTAAAATTACTAAAA
1 TACCCTCGATTTGTAAAATTACTAAAA
* *
31147813 TACCCTTGGTTTGTAAAATTAC-AGAAA
1 TACCCTCGATTTGTAAAATTACTA-AAA
* *
31147840 TACCCTCAATTTGTAAAATTACAAAAA
1 TACCCTCGATTTGTAAAATTACTAAAA
* *
31147867 TACCC-CTAGTTTGTAAAATTACCAAAA
1 TACCCTCGA-TTTGTAAAATTACTAAAA
* * **
31147894 TACCACT-GGTTTGTGAAATTACCGAAA
1 TACC-CTCGATTTGTAAAATTACTAAAA
*
31147921 TACCCTC-ATTTTGTAAAATTACCAAAA
1 TACCCTCGA-TTTGTAAAATTACTAAAA
** *
31147948 TACCC-CTGATTTACAAAGTTAC-AGAAA
1 TACCCTC-GATTTGTAAAATTACTA-AAA
* *
31147975 TACCCTTGACTTTCTAAAAATTA-TAGAAA
1 TACCCTCGA-TTTGT-AAAATTACTA-AAA
* * * **
31148004 TACCATTGGTTTACAAAATTACTAAAA
1 TACCCTCGATTTGTAAAATTACTAAAA
* * * * *
31148031 TACCCTTGGTTTGTAGATTTACCAAAA
1 TACCCTCGATTTGTAAAATTACTAAAA
*
31148058 CACCCT
1 TACCCT
31148064 TGTAGGATGA
Statistics
Matches: 224, Mismatches: 37, Indels: 32
0.76 0.13 0.11
Matches are distributed among these distances:
26 28 0.12
27 167 0.75
28 11 0.05
29 18 0.08
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.31
Consensus pattern (27 bp):
TACCCTCGATTTGTAAAATTACTAAAA
Found at i:31147871 original size:54 final size:53
Alignment explanation
Indices: 31147774--31148045 Score: 217
Period size: 54 Copynumber: 5.0 Consensus size: 53
31147764 CTCGATTTAC
* * *
31147774 AAAATTACTAG-AATACCCTAGTCTGTAAAATTACTAAAATACCCTTGGTTTGT
1 AAAATTAC-AGAAATACCCTGGTTTGTAAAATTACAAAAATACCCTTGGTTTGT
** * *
31147827 AAAATTACAGAAATACCCTCAATTTGTAAAATTACAAAAATACCCCTAGTTTGT
1 AAAATTACAGAAATACCCT-GGTTTGTAAAATTACAAAAATACCCTTGGTTTGT
* ** ***
31147881 AAAATTACCA-AAATACCACTGGTTTGTGAAATTACCGAAATACCCTCATTTTGT
1 AAAATTA-CAGAAATACC-CTGGTTTGTAAAATTACAAAAATACCCTTGGTTTGT
* ** * * * *
31147935 AAAATTACCA-AAATACCCCTGATTTACAAAGTTACAGAAATACCCTTGACTTTCT
1 AAAATTA-CAGAAATA-CCCTGGTTTGTAAAATTACAAAAATACCCTTG-GTTTGT
* * ** *
31147990 AAAAATTATAGAAATACCATTGGTTTACAAAATTACTAAAATACCCTTGGTTTGT
1 -AAAATTACAGAAATACC-CTGGTTTGTAAAATTACAAAAATACCCTTGGTTTGT
31148045 A
1 A
31148046 GATTTACCAA
Statistics
Matches: 179, Mismatches: 31, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
52 2 0.01
53 16 0.09
54 107 0.60
55 17 0.09
56 37 0.21
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (53 bp):
AAAATTACAGAAATACCCTGGTTTGTAAAATTACAAAAATACCCTTGGTTTGT
Found at i:31147904 original size:81 final size:81
Alignment explanation
Indices: 31147760--31147954 Score: 268
Period size: 81 Copynumber: 2.4 Consensus size: 81
31147750 ATTACTATTT
* ** * * *
31147760 TACCCTCGATTTACAAAATTACTAGAATA-CCCTAGTCTGTAAAATTACTAAAATACCCTTGGTT
1 TACCCTCAATTTGTAAAATTACAAAAATACCCCTAGTCTGTAAAATTACCAAAATACCCTTGGTT
31147824 TGTAAAATTACAGAAA
66 TGTAAAATTACAGAAA
*
31147840 TACCCTCAATTTGTAAAATTACAAAAATACCCCTAGTTTGTAAAATTACCAAAATACCAC-TGGT
1 TACCCTCAATTTGTAAAATTACAAAAATACCCCTAGTCTGTAAAATTACCAAAATACC-CTTGGT
* *
31147904 TTGTGAAATTACCGAAA
65 TTGTAAAATTACAGAAA
* *
31147921 TACCCTCATTTTGTAAAATTACCAAAATACCCCT
1 TACCCTCAATTTGTAAAATTACAAAAATACCCCT
31147955 GATTTACAAA
Statistics
Matches: 102, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
80 24 0.24
81 77 0.75
82 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (81 bp):
TACCCTCAATTTGTAAAATTACAAAAATACCCCTAGTCTGTAAAATTACCAAAATACCCTTGGTT
TGTAAAATTACAGAAA
Found at i:31147976 original size:81 final size:81
Alignment explanation
Indices: 31147760--31148007 Score: 265
Period size: 81 Copynumber: 3.0 Consensus size: 81
31147750 ATTACTATTT
* ** * * *
31147760 TACCCTCGATTTACAAAATTACTAGAATA-CCCTAG-TCTGTAAAATTACTAAAATACCCTTGGT
1 TACCCTCAATTTGTAAAATTACAAAAATACCCCTAGAT-TGTAAAATTACCAAAATACCCTTGGT
31147823 TTGTAAAATTACAGAAA
65 TTGTAAAATTACAGAAA
*
31147840 TACCCTCAATTTGTAAAATTACAAAAATACCCCTAGTTTGTAAAATTACCAAAATACCAC-TGGT
1 TACCCTCAATTTGTAAAATTACAAAAATACCCCTAGATTGTAAAATTACCAAAATACC-CTTGGT
* *
31147904 TTGTGAAATTACCGAAA
65 TTGTAAAATTACAGAAA
* *
31147921 TACCCTCATTTTGTAAAATTACCAAAATACCCCT-GATT-TACAAAGTTA-CAGAAATACCCTTG
1 TACCCTCAATTTGTAAAATTACAAAAATACCCCTAGATTGTA-AAA-TTACCA-AAATACCCTTG
* * *
31147983 ACTTTCTAAAAATTATAGAAA
63 -GTTTGT-AAAATTACAGAAA
31148004 TACC
1 TACC
31148008 ATTGGTTTAC
Statistics
Matches: 143, Mismatches: 16, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
79 2 0.01
80 33 0.23
81 88 0.62
82 6 0.04
83 14 0.10
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (81 bp):
TACCCTCAATTTGTAAAATTACAAAAATACCCCTAGATTGTAAAATTACCAAAATACCCTTGGTT
TGTAAAATTACAGAAA
Found at i:31148160 original size:27 final size:27
Alignment explanation
Indices: 31148083--31148160 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
31148073 AAATGACTAA
* * *
31148083 AATACCCCTAT-TAGGTAAAAAGATCGT
1 AATACCCCTGTAT-GGTAAAATGACCGT
* *
31148110 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTATGGTAAAATGACCGT
31148137 AATACCCCTGTATGGTAAAATGAC
1 AATACCCCTGTATGGTAAAATGAC
31148161 GAATATGCCC
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
26 1 0.02
27 39 0.95
28 1 0.02
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.23
Consensus pattern (27 bp):
AATACCCCTGTATGGTAAAATGACCGT
Found at i:31149559 original size:25 final size:24
Alignment explanation
Indices: 31149480--31149673 Score: 252
Period size: 25 Copynumber: 8.0 Consensus size: 24
31149470 AGGAAGTGCA
*
31149480 AAAGGGCTTATGCCCTAGTTAT-T
1 AAAGGGCTTATGCCCCAGTTATAT
*
31149503 AAAGGGCTTATGCCCCAATTAT-T
1 AAAGGGCTTATGCCCCAGTTATAT
31149526 AAAGGGCTTATGCCCCAGTTATGAT
1 AAAGGGCTTATGCCCCAGTTAT-AT
31149551 AAAGGGCTTATGCCCCAGTTATGAT
1 AAAGGGCTTATGCCCCAGTTAT-AT
*
31149576 GAAGGGCTTATGCCCCAGTTATGAT
1 AAAGGGCTTATGCCCCAGTTAT-AT
*
31149601 AAAGGGCTTATGCCCCAGTTATAA
1 AAAGGGCTTATGCCCCAGTTATAT
*
31149625 AAAGGGCTTTTGCCCCAGTTACTA-
1 AAAGGGCTTATGCCCCAGTTA-TAT
*
31149649 AAAGAGGC-TAGGCCTCCAGTTATAT
1 AAAG-GGCTTATGCC-CCAGTTATAT
31149674 GATAAAGCAG
Statistics
Matches: 156, Mismatches: 9, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
23 42 0.27
24 31 0.20
25 83 0.53
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (24 bp):
AAAGGGCTTATGCCCCAGTTATAT
Found at i:31152211 original size:42 final size:42
Alignment explanation
Indices: 31152100--31152254 Score: 202
Period size: 42 Copynumber: 3.7 Consensus size: 42
31152090 TACTAAACCA
* * * *
31152100 ATGCCATATCCCATATATGGTCTTACATGTAATCTCATATCG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATTG
* * *
31152142 ATGCCAATAGCCTAGCTATGGTCTTACACGAAATCTCATATTG
1 ATGCC-ATATCCCAGATATGGTCTTACACGAAATCTCATATTG
* * *
31152185 ATGCCATATCCTAGATATGGTCTTACACGAAGTCTCATACTG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATTG
*
31152227 ATGTCATATCCCAGATATGGTCTTACAC
1 ATGCCATATCCCAGATATGGTCTTACAC
31152255 ATAAACTTAG
Statistics
Matches: 99, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
42 64 0.65
43 35 0.35
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATTG
Found at i:31152544 original size:39 final size:39
Alignment explanation
Indices: 31152494--31152572 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
31152484 TCCCCAAATC
31152494 TAGGTCCGAACCTCGTTTCTCTTGATCTATAATAGCAAA
1 TAGGTCCGAACCTCGTTTCTCTTGATCTATAATAGCAAA
*
31152533 TAGGTCCGAACCTTGTTTCTCTTGATCTATAATAGCAAA
1 TAGGTCCGAACCTCGTTTCTCTTGATCTATAATAGCAAA
31152572 T
1 T
31152573 TAAACTCATT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (39 bp):
TAGGTCCGAACCTCGTTTCTCTTGATCTATAATAGCAAA
Found at i:31162772 original size:43 final size:42
Alignment explanation
Indices: 31162665--31162778 Score: 124
Period size: 43 Copynumber: 2.6 Consensus size: 42
31162655 ACATTAGGTT
* *
31162665 ATCGATATGTGATTACATGTAAAACCATGTCTGGGACATTGGC
1 ATCGATATGTG-TTACATGTAAGACCATGTCTGGGACAGTGGC
* * *
31162708 ATCGTTAATCGAT-TT-CGTGTAAGACCCTGTCTGGGACAGTGGC
1 ATCGAT-AT-G-TGTTACATGTAAGACCATGTCTGGGACAGTGGC
31162751 ATCGATATGTGTTAACATGTAAGACCAT
1 ATCGATATGTGTT-ACATGTAAGACCAT
31162779 ATCTAGGATA
Statistics
Matches: 57, Mismatches: 8, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
40 1 0.02
41 3 0.05
42 2 0.04
43 45 0.79
44 4 0.07
45 1 0.02
46 1 0.02
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.31
Consensus pattern (42 bp):
ATCGATATGTGTTACATGTAAGACCATGTCTGGGACAGTGGC
Found at i:31178150 original size:20 final size:20
Alignment explanation
Indices: 31178116--31178153 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
31178106 TCAACATCCC
31178116 ATATTTAAACTATCACATGA
1 ATATTTAAACTATCACATGA
31178136 ATATTATAAAC-ATCACAT
1 ATATT-TAAACTATCACAT
31178154 TTCTTACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.47, C:0.16, G:0.03, T:0.34
Consensus pattern (20 bp):
ATATTTAAACTATCACATGA
Found at i:31178776 original size:40 final size:41
Alignment explanation
Indices: 31178729--31178825 Score: 119
Period size: 40 Copynumber: 2.4 Consensus size: 41
31178719 TATCTTGGTA
* *
31178729 TCGCACACTTAGTGCC-TCATATAGTCGAAGCTA-TTTCAAC
1 TCGCACACTTAGTGCCAT-ATATAGCCAAAGCTATTTTCAAC
* * *
31178769 TCGCACACTTAGTGCCATTTGTAGCCAAAGCTATTTTGAAC
1 TCGCACACTTAGTGCCATATATAGCCAAAGCTATTTTCAAC
31178810 -CGCACACTTAGTGCCA
1 TCGCACACTTAGTGCCA
31178826 AACATAGTCG
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
40 43 0.86
41 7 0.14
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (41 bp):
TCGCACACTTAGTGCCATATATAGCCAAAGCTATTTTCAAC
Found at i:31179065 original size:18 final size:18
Alignment explanation
Indices: 31179042--31179079 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
31179032 TTCAAAATTA
31179042 ACCCTTTTAATCACCAAC
1 ACCCTTTTAATCACCAAC
31179060 ACCCTTTTAATCACCAAC
1 ACCCTTTTAATCACCAAC
31179078 AC
1 AC
31179080 ATTCAATACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.39, G:0.00, T:0.26
Consensus pattern (18 bp):
ACCCTTTTAATCACCAAC
Found at i:31192130 original size:30 final size:31
Alignment explanation
Indices: 31192054--31192136 Score: 143
Period size: 31 Copynumber: 2.7 Consensus size: 31
31192044 TAAGTCTCGA
31192054 CATAT-ACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
31192084 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
*
31192115 CATATCA-TTGGCCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
31192137 ACTGTAAGCG
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
30 19 0.37
31 32 0.63
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATAAAT
Found at i:31192383 original size:25 final size:25
Alignment explanation
Indices: 31192355--31192424 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 25
31192345 CTCTTTTAAT
* *
31192355 AACTGGGACAAATCCCTTTTTGATA
1 AACTGGGACAAAGCCCTTTTCGATA
* *
31192380 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGACAAAGCCCTTTTCGATA
* *
31192405 AACTGGGGCATAGCCCTTTT
1 AACTGGGACAAAGCCCTTTT
31192425 AGTACTTCCT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.29
Consensus pattern (25 bp):
AACTGGGACAAAGCCCTTTTCGATA
Found at i:31193441 original size:81 final size:81
Alignment explanation
Indices: 31193341--31193536 Score: 218
Period size: 81 Copynumber: 2.4 Consensus size: 81
31193331 GGGTGTTTTG
* *** **
31193341 TCTACAAACTAAGGGTATTTCAGTAATTTTGTAAACCAATGGTATTTCT-ATAATTTTGTAAA-T
1 TCTACAAATTAAGGGTATTTCAGTAATTTCACAAACCAATGGTATTT-TGATAATTTTACAAACT
*
31193404 CAGGGGTATTTTGGTAAT
65 -AAGGGTATTTTGGTAAT
* * * *
31193422 TTTACAAATTAAGGGTATTTCGGTAATTTCACAAACCAGTGGTATTTTGGTAATTTTACAAACTA
1 TCTACAAATTAAGGGTATTTCAGTAATTTCACAAACCAATGGTATTTTGATAATTTTACAAACTA
31193487 AGGGTATTTTGGTAAT
66 AGGGTATTTTGGTAAT
** *
31193503 TCTAC-CCTATAGGGGTATTTCAGTAATTTCACAA
1 TCTACAAAT-TAAGGGTATTTCAGTAATTTCACAA
31193537 TCGAGGGTAA
Statistics
Matches: 96, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
80 2 0.02
81 93 0.97
82 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (81 bp):
TCTACAAATTAAGGGTATTTCAGTAATTTCACAAACCAATGGTATTTTGATAATTTTACAAACTA
AGGGTATTTTGGTAAT
Found at i:31193496 original size:27 final size:27
Alignment explanation
Indices: 31193343--31193503 Score: 148
Period size: 27 Copynumber: 6.0 Consensus size: 27
31193333 GTGTTTTGTC
**
31193343 TACAAACTAAGGGTATTTCAGTAATTT
1 TACAAACTAAGGGTATTTTGGTAATTT
** * * *
31193370 TGTAAACCAATGGTATTTCT-ATAATTT
1 TACAAACTAAGGGTATTT-TGGTAATTT
** *
31193397 TGTAAA-TCAGGGGTATTTTGGTAATTT
1 TACAAACT-AAGGGTATTTTGGTAATTT
* *
31193424 TACAAATTAAGGGTATTTCGGTAATTT
1 TACAAACTAAGGGTATTTTGGTAATTT
* *
31193451 CACAAAC-CAGTGGTATTTTGGTAATTT
1 TACAAACTAAG-GGTATTTTGGTAATTT
31193478 TACAAACTAAGGGTATTTTGGTAATT
1 TACAAACTAAGGGTATTTTGGTAATT
31193504 CTACCCTATA
Statistics
Matches: 108, Mismatches: 20, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
26 3 0.03
27 102 0.94
28 3 0.03
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.40
Consensus pattern (27 bp):
TACAAACTAAGGGTATTTTGGTAATTT
Found at i:31193543 original size:27 final size:26
Alignment explanation
Indices: 31193404--31193536 Score: 97
Period size: 27 Copynumber: 5.0 Consensus size: 26
31193394 TTTTGTAAAT
* *
31193404 CAGGGGTATTTTGGTAATTTTACAAA
1 CAGGGGTATTTCGGTAATTTCACAAA
* *
31193430 TTAAGGGTATTTCGGTAATTTCACAAA
1 -CAGGGGTATTTCGGTAATTTCACAAA
* * *
31193457 CCAGTGGTATTTTGGTAATTTTACAAA
1 -CAGGGGTATTTCGGTAATTTCACAAA
* * **
31193484 CTAAGGGTATTTTGGTAA-TTCTACCCTA
1 C-AGGGGTATTTCGGTAATTTC-A-CAAA
* *
31193512 TAGGGGTATTTCAGTAATTTCACAA
1 CAGGGGTATTTCGGTAATTTCACAA
31193537 TCGAGGGTAA
Statistics
Matches: 81, Mismatches: 21, Indels: 9
0.73 0.19 0.08
Matches are distributed among these distances:
26 4 0.05
27 72 0.89
28 5 0.06
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (26 bp):
CAGGGGTATTTCGGTAATTTCACAAA
Found at i:31193565 original size:27 final size:27
Alignment explanation
Indices: 31193535--31193599 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
31193525 GTAATTTCAC
* * *
31193535 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACAGTAATTCTATA
* *
31193562 AATCGATGGTAAAACAGTGATTCTATA
1 AATCGAGGGTAAAACAGTAATTCTATA
*
31193589 AATCTAGGGTA
1 AATCGAGGGTA
31193600 CATTGGTAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.29
Consensus pattern (27 bp):
AATCGAGGGTAAAACAGTAATTCTATA
Found at i:31195825 original size:31 final size:31
Alignment explanation
Indices: 31195776--31195843 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
31195766 TCAGTCTCGA
*
31195776 CATAT-ACTCGGCCGAAGCCTTTTCATAAAT
1 CATATCACTCGGCCAAAGCCTTTTCATAAAT
* *
31195806 TATATCACTGGGCCAAAGCCTTTTCATAAAT
1 CATATCACTCGGCCAAAGCCTTTTCATAAAT
31195837 CATATCA
1 CATATCA
31195844 TTAGTCGAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
30 4 0.12
31 29 0.88
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.31
Consensus pattern (31 bp):
CATATCACTCGGCCAAAGCCTTTTCATAAAT
Found at i:31195857 original size:30 final size:31
Alignment explanation
Indices: 31195786--31195858 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
31195776 CATATACTCG
* *
31195786 GCCGAAGCCTTTTCATAAATTATATCACTGG
1 GCCGAAGCCTTTTCATAAATCATATCACTGA
* *
31195817 GCCAAAGCCTTTTCATAAATCATATCA-TTA
1 GCCGAAGCCTTTTCATAAATCATATCACTGA
*
31195847 GTCGAAGCCTTT
1 GCCGAAGCCTTT
31195859 ACTGTAAGCG
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 11 0.31
31 25 0.69
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (31 bp):
GCCGAAGCCTTTTCATAAATCATATCACTGA
Found at i:31196097 original size:25 final size:24
Alignment explanation
Indices: 31196069--31196147 Score: 88
Period size: 25 Copynumber: 3.2 Consensus size: 24
31196059 AGGCCTAGCT
31196069 TTTTTTAATAACTGGGGCAAAGCCC
1 TTTTTT-ATAACTGGGGCAAAGCCC
*
31196094 TTTTTGATAAACTGGGGCAAAGCCC
1 TTTTTTAT-AACTGGGGCAAAGCCC
* *
31196119 TTTTCGGTA-AACTGGGGCATAGCCC
1 TTTT--TTATAACTGGGGCAAAGCCC
31196144 TTTT
1 TTTT
31196148 AGCATTTCCT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
24 2 0.04
25 44 0.94
27 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (24 bp):
TTTTTTATAACTGGGGCAAAGCCC
Found at i:31196986 original size:27 final size:27
Alignment explanation
Indices: 31196956--31197020 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
31196946 GGGCATATTC
*
31196956 GTCATTTTATCATACAAGGG-TATTACG
1 GTCATTTTACCATACAAGGGCT-TTACG
* * *
31196983 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCATTTTACCATACAAGGGCTTTACG
*
31197010 GTCTTTTTACC
1 GTCATTTTACC
31197021 TATTAGGGGT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
27 30 0.97
28 1 0.03
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (27 bp):
GTCATTTTACCATACAAGGGCTTTACG
Found at i:31197104 original size:27 final size:27
Alignment explanation
Indices: 31197074--31197159 Score: 86
Period size: 27 Copynumber: 3.1 Consensus size: 27
31197064 GTAAATCTAC
31197074 AAACCAAAGGTATTTCAGTAATTTTGT
1 AAACCAAAGGTATTTCAGTAATTTTGT
*
31197101 AAACCAATGGTATTTCTA-TAATTTT-T
1 AAACCAAAGGTATTTC-AGTAATTTTGT
* * *
31197127 AGAAAGTCAAGGGTATTTCTGTAATTTTGT
1 --AAA-CCAAAGGTATTTCAGTAATTTTGT
31197157 AAA
1 AAA
31197160 TTATGGGTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
26 1 0.02
27 22 0.45
28 7 0.14
29 18 0.37
30 1 0.02
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (27 bp):
AAACCAAAGGTATTTCAGTAATTTTGT
Found at i:31197177 original size:27 final size:26
Alignment explanation
Indices: 31197136--31197260 Score: 117
Period size: 27 Copynumber: 4.7 Consensus size: 26
31197126 TAGAAAGTCA
**
31197136 AGGGTATTTCT-GTAATTTTGTAAATT
1 AGGGTATTT-TGGTAATTTTACAAATT
*
31197162 ATGGGTATTTTGGTAATTTTACATATT
1 A-GGGTATTTTGGTAATTTTACAAATT
* * * **
31197189 AAGGGTAGTTCGGTAATTTCACAAACC
1 -AGGGTATTTTGGTAATTTTACAAATT
*
31197216 AGTGGTATTTTGGTAATTTTACAAAAT
1 AG-GGTATTTTGGTAATTTTACAAATT
31197243 AGGGGTATTTTGGTAATT
1 A-GGGTATTTTGGTAATT
31197261 CTACCCTATA
Statistics
Matches: 80, Mismatches: 14, Indels: 9
0.78 0.14 0.09
Matches are distributed among these distances:
26 4 0.05
27 74 0.93
28 2 0.03
ACGTcount: A:0.29, C:0.06, G:0.22, T:0.43
Consensus pattern (26 bp):
AGGGTATTTTGGTAATTTTACAAATT
Found at i:31197250 original size:81 final size:81
Alignment explanation
Indices: 31197138--31197293 Score: 199
Period size: 81 Copynumber: 1.9 Consensus size: 81
31197128 GAAAGTCAAG
** * * * *
31197138 GGTATTTCTGTAATTTTGTAAATTATGGGTATTTTGGTAATTTTA-CATATTAAGGGTAGTTCGG
1 GGTATTTCTGTAATTTTACAAAATAGGGGTATTTTGGTAATTCTACCATA-TAAGGGTAGTTCAG
31197202 TAATTTCACAAACCAGT
65 TAATTTCACAAACCAGT
* * *
31197219 GGTATTT-TGGTAATTTTACAAAATAGGGGTATTTTGGTAATTCTACCCTATAGGGGTATTTCAG
1 GGTATTTCT-GTAATTTTACAAAATAGGGGTATTTTGGTAATTCTACCATATAAGGGTAGTTCAG
31197283 TAATTTCACAA
65 TAATTTCACAA
31197294 TCGATGGTAA
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
80 1 0.02
81 60 0.94
82 3 0.05
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.42
Consensus pattern (81 bp):
GGTATTTCTGTAATTTTACAAAATAGGGGTATTTTGGTAATTCTACCATATAAGGGTAGTTCAGT
AATTTCACAAACCAGT
Found at i:31197271 original size:27 final size:27
Alignment explanation
Indices: 31197164--31197279 Score: 99
Period size: 27 Copynumber: 4.3 Consensus size: 27
31197154 TGTAAATTAT
* * * *
31197164 GGGTATTTTGGTAATTTTACATATTAA
1 GGGTATTTTGGTAATTCTACAAAATAG
* * **
31197191 GGGTAGTTCGGTAATT-TCACAAACCAG
1 GGGTATTTTGGTAATTCT-ACAAAATAG
* *
31197218 TGGTATTTTGGTAATTTTACAAAATAG
1 GGGTATTTTGGTAATTCTACAAAATAG
***
31197245 GGGTATTTTGGTAATTCTACCCTATAG
1 GGGTATTTTGGTAATTCTACAAAATAG
31197272 GGGTATTT
1 GGGTATTT
31197280 CAGTAATTTC
Statistics
Matches: 71, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
26 1 0.01
27 69 0.97
28 1 0.01
ACGTcount: A:0.28, C:0.09, G:0.22, T:0.41
Consensus pattern (27 bp):
GGGTATTTTGGTAATTCTACAAAATAG
Found at i:31197329 original size:27 final size:27
Alignment explanation
Indices: 31197292--31197356 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
31197282 GTAATTTCAC
* ** * *
31197292 AATCGATGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAACAGTAATTCTATA
*
31197319 AATCGAGGGTAAAACAGTGATTCTATA
1 AATCGAGGGTAAAACAGTAATTCTATA
31197346 AATCGAGGGTA
1 AATCGAGGGTA
31197357 CTTTGGTAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.29
Consensus pattern (27 bp):
AATCGAGGGTAAAACAGTAATTCTATA
Found at i:31216981 original size:33 final size:32
Alignment explanation
Indices: 31216908--31216985 Score: 84
Period size: 33 Copynumber: 2.4 Consensus size: 32
31216898 CAGTATTTAT
* * * *
31216908 ATGTAAGACCATAGCTGGGCTATATCATTCTA
1 ATGTAAGACCATAACTGGGCTATAGCATACGA
* *
31216940 ATGATAAGACCATAACTGGGTTATGGCACTACGA
1 ATG-TAAGACCATAACTGGGCTATAGCA-TACGA
31216974 ATGTAAGACCAT
1 ATGTAAGACCAT
31216986 GGCAGGGCCA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
32 3 0.08
33 29 0.76
34 6 0.16
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.27
Consensus pattern (32 bp):
ATGTAAGACCATAACTGGGCTATAGCATACGA
Found at i:31219539 original size:40 final size:40
Alignment explanation
Indices: 31219348--31219532 Score: 198
Period size: 40 Copynumber: 4.7 Consensus size: 40
31219338 TTGAATGATG
* * * * *
31219348 TCCGGGCTAAGTCCTGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
31219388 TCCGGACTAAGAT-CCGAAGGCATTTGTGTGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
31219428 TCCGGGCTAAG-CCCAAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
31219467 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
31219508 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
31219533 AACGAGTAGC
Statistics
Matches: 120, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
39 33 0.28
40 78 0.65
41 9 0.08
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:31219554 original size:79 final size:79
Alignment explanation
Indices: 31219401--31219565 Score: 183
Period size: 79 Copynumber: 2.1 Consensus size: 79
31219391 GGACTAAGAT
* * * **
31219401 CCGAAGGCATTTGTGTGAGATACTAATTCCGGGCTAAGCCCAAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCAAAGGCATTTGAACGAGTTACTAA
*
31219466 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* * *
31219480 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCAAAGGCATTTGAACGAGTTA-C
* *
31219543 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
31219559 CCGAAGG
1 CCGAAGG
31219566 TACGTGATTT
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
78 2 0.03
79 46 0.64
80 24 0.33
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCAAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:31227441 original size:79 final size:81
Alignment explanation
Indices: 31227305--31227489 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
31227295 TTGAATGATG
* *
31227305 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
31227369 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
31227384 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
31227446 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
31227464 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
31227490 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:31227503 original size:40 final size:40
Alignment explanation
Indices: 31227306--31227489 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
31227296 TGAATGATGT
* * * *
31227306 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
31227346 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
31227386 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
31227424 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
31227465 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
31227490 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:31227511 original size:79 final size:79
Alignment explanation
Indices: 31227358--31227522 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
31227348 GGACTAAGAT
* * **
31227358 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
31227423 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
31227437 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
31227500 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
31227516 CCGAAGG
1 CCGAAGG
31227523 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:31234988 original size:40 final size:39
Alignment explanation
Indices: 31234904--31235088 Score: 194
Period size: 40 Copynumber: 4.6 Consensus size: 39
31234894 TTGAATGATG
* * * *
31234904 TCCGGGCTAAGTCCTGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCC-GAAGGCATTTGTGC-GAGTTACTAAA
* * *
31234944 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
* *
31234984 TCCGGGCTAAGCCCAAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
* *
31235023 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
31235064 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
31235089 AACGAGTAGC
Statistics
Matches: 122, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
39 34 0.28
40 76 0.62
41 12 0.10
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:31235110 original size:79 final size:79
Alignment explanation
Indices: 31234957--31235121 Score: 192
Period size: 79 Copynumber: 2.1 Consensus size: 79
31234947 GGACTAAGAT
* * **
31234957 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCAAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCAAAGGCATTTGAACGAGTTACTAA
*
31235022 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* * *
31235036 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCAAAGGCATTTGAACGAGTTA-C
* *
31235099 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
31235115 CCGAAGG
1 CCGAAGG
31235122 TACGTGATTT
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 24 0.33
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCAAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:31242289 original size:79 final size:81
Alignment explanation
Indices: 31242152--31242335 Score: 216
Period size: 79 Copynumber: 2.3 Consensus size: 81
31242142 TGAATGATGT
* *
31242152 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAATT
*
31242216 GTGCGAGATACTA-ATT
66 GTGCGAGATACTATA-A
* * * * **
31242232 TCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCTGAAGGCAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCC-GAAGGCAAT
*
31242294 TGTGCGAGTTACTATAA
65 TGTGCGAGATACTATAA
*
31242311 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
31242336 AACGAGTAGC
Statistics
Matches: 88, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.61
80 31 0.35
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (81 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAATT
GTGCGAGATACTATAA
Found at i:31242342 original size:40 final size:40
Alignment explanation
Indices: 31242151--31242335 Score: 207
Period size: 40 Copynumber: 4.7 Consensus size: 40
31242141 TTGAATGATG
* * * *
31242151 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
31242191 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
31242231 TTCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
31242270 TCCGGGTTAAGTCCTGAAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
31242311 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
31242336 AACGAGTAGC
Statistics
Matches: 121, Mismatches: 19, Indels: 10
0.81 0.13 0.07
Matches are distributed among these distances:
39 34 0.28
40 77 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:31242357 original size:79 final size:78
Alignment explanation
Indices: 31242152--31242368 Score: 192
Period size: 79 Copynumber: 2.7 Consensus size: 78
31242142 TGAATGATGT
** * * * * *
31242152 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 CCGGGCTAAG-CCCGAAGGCATTTGAAC-GAGTTACTATATCCGG-TTAAGATCCGAAGGCAATT
*
31242216 GTGCGAGATACTAATT
63 GTGCGAGATACTAATA
* ** *
31242232 TCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAG-TCCTGAAGGCAATTG
1 CCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTATATCC-GGTTAAGATCC-GAAGGCAATTG
*
31242296 TGCGAGTTACT-ATAA
64 TGCGAGATACTAAT-A
*
31242311 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATATCCGGTTAA-ATTCCGAAGG
1 CCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-CTATATCCGGTTAAGA-TCCGAAGG
31242369 TACGTGATTT
Statistics
Matches: 115, Mismatches: 14, Indels: 17
0.79 0.10 0.12
Matches are distributed among these distances:
78 5 0.04
79 64 0.56
80 46 0.40
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (78 bp):
CCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTATATCCGGTTAAGATCCGAAGGCAATTGTG
CGAGATACTAATA
Found at i:31246653 original size:44 final size:45
Alignment explanation
Indices: 31246597--31246688 Score: 159
Period size: 44 Copynumber: 2.1 Consensus size: 45
31246587 ATGTATGAGG
31246597 CATCCGAACTCGTTGAGTTGGTCCGAGTTCATTATGGATGCGA-A
1 CATCCGAACTCGTTGAGTTGGTCCGAGTTCATTATGGATGCGATA
* *
31246641 CATCCGAGCTCGTTGAGTTGGTCGGAGTTCATTATGGATGCGATA
1 CATCCGAACTCGTTGAGTTGGTCCGAGTTCATTATGGATGCGATA
31246686 CAT
1 CAT
31246689 GTACTTGGGT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 41 0.91
45 4 0.09
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (45 bp):
CATCCGAACTCGTTGAGTTGGTCCGAGTTCATTATGGATGCGATA
Found at i:31252327 original size:18 final size:18
Alignment explanation
Indices: 31252301--31252337 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
31252291 ACTTGATAAG
*
31252301 TTAGTTGAATAGTATATT
1 TTAGCTGAATAGTATATT
*
31252319 TTAGCTGAATTGTATATT
1 TTAGCTGAATAGTATATT
31252337 T
1 T
31252338 CTGAGTTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.03, G:0.16, T:0.51
Consensus pattern (18 bp):
TTAGCTGAATAGTATATT
Found at i:31254619 original size:44 final size:43
Alignment explanation
Indices: 31254519--31254633 Score: 133
Period size: 44 Copynumber: 2.6 Consensus size: 43
31254509 AAAATCTGAA
* *
31254519 CTCGTTGAGTTGGTCC-AGGTTCGTGATATGTATGAGGCATCCAAG
1 CTCGTTGAGTTGGTCCGA-GTTCAT--TATGGATGAGGCATCCAAG
* * * *
31254564 CTCGTTAAGTTGGTCCGAGTTCATTATGGATGCGAGCATTCGAG
1 CTCGTTGAGTTGGTCCGAGTTCATTATGGATGAG-GCATCCAAG
31254608 CTCGTTGAGTTGGTCCGAGTTCATTA
1 CTCGTTGAGTTGGTCCGAGTTCATTA
31254634 CGAATGTGAT
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
43 8 0.13
44 32 0.52
45 20 0.33
46 1 0.02
ACGTcount: A:0.19, C:0.18, G:0.30, T:0.33
Consensus pattern (43 bp):
CTCGTTGAGTTGGTCCGAGTTCATTATGGATGAGGCATCCAAG
Found at i:31257365 original size:31 final size:31
Alignment explanation
Indices: 31257327--31257391 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
31257317 ACTTTCATTG
31257327 CTTACAATTTTCGATTGAATTGGTATTTTTT
1 CTTACAATTTTCGATTGAATTGGTATTTTTT
31257358 CTTACAATTTTCGATTGAATTGGTATTTTTT
1 CTTACAATTTTCGATTGAATTGGTATTTTTT
31257389 CTT
1 CTT
31257392 TCTTTCTTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.22, C:0.11, G:0.12, T:0.55
Consensus pattern (31 bp):
CTTACAATTTTCGATTGAATTGGTATTTTTT
Found at i:31257572 original size:29 final size:29
Alignment explanation
Indices: 31257530--31257589 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
31257520 AGGTTCTCGG
*
31257530 TTACCTCTTGGATTGCGGTTTATATTTTC
1 TTACCTCTTGGATTGCGATTTATATTTTC
*
31257559 TTACCTCTTGGATTGCGATTTATCTTTTC
1 TTACCTCTTGGATTGCGATTTATATTTTC
31257588 TT
1 TT
31257590 GATCGATTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.13, C:0.18, G:0.15, T:0.53
Consensus pattern (29 bp):
TTACCTCTTGGATTGCGATTTATATTTTC
Found at i:31259409 original size:20 final size:20
Alignment explanation
Indices: 31259381--31259421 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
31259371 GTACACAACT
31259381 TAACAATTTAGTATGGGTCA
1 TAACAATTTAGTATGGGTCA
*
31259401 TAACGATTTAGTATGGGTCA
1 TAACAATTTAGTATGGGTCA
31259421 T
1 T
31259422 GTTTTGCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.10, G:0.22, T:0.37
Consensus pattern (20 bp):
TAACAATTTAGTATGGGTCA
Found at i:31266285 original size:15 final size:15
Alignment explanation
Indices: 31266267--31266295 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
31266257 AATATCTTCA
31266267 TCATAATTGAAGTCT
1 TCATAATTGAAGTCT
31266282 TCATAATTGAAGTC
1 TCATAATTGAAGTC
31266296 ATACATGACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (15 bp):
TCATAATTGAAGTCT
Found at i:31268411 original size:26 final size:26
Alignment explanation
Indices: 31268382--31268474 Score: 123
Period size: 26 Copynumber: 3.5 Consensus size: 26
31268372 AATGTTCTAG
*
31268382 AAATTTTGCTAAGGGCAAAATTATCA
1 AAATTTTACTAAGGGCAAAATTATCA
31268408 AAATTTTACTAAGGGCAAAATTATCA
1 AAATTTTACTAAGGGCAAAATTATCA
* * * *
31268434 AAATTTTACTAAGAGTAAAATTGTAAA
1 AAATTTTACTAAGGGCAAAATTAT-CA
*
31268461 AAAATTTACTAAGG
1 AAATTTTACTAAGG
31268475 TAAAATTGAG
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
26 46 0.78
27 13 0.22
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.31
Consensus pattern (26 bp):
AAATTTTACTAAGGGCAAAATTATCA
Found at i:31270713 original size:30 final size:29
Alignment explanation
Indices: 31270658--31270714 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
31270648 ATGTATATTT
* *
31270658 TTTTATTAAATTGAATGTTATTATATGAA
1 TTTTATTAAAATGAATGATATTATATGAA
31270687 TTTTATTGAAAATGAATCGATA-TATATG
1 TTTTATT-AAAATGAAT-GATATTATATG
31270715 TTATCATACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.29
30 14 0.58
31 3 0.12
ACGTcount: A:0.39, C:0.02, G:0.12, T:0.47
Consensus pattern (29 bp):
TTTTATTAAAATGAATGATATTATATGAA
Found at i:31274088 original size:27 final size:27
Alignment explanation
Indices: 31274055--31274478 Score: 264
Period size: 27 Copynumber: 15.7 Consensus size: 27
31274045 CCTCAAATTG
*
31274055 TAAAATTACCAAAGTACCCTCGATTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* ***
31274082 TAGAATTACCATTTTACCCTCGATTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* * * ****
31274109 CAGAATTATCGTTTTACCCTCGATTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* ** *** *
31274136 TAGAATTATTATTTTACCCTTGATTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* *****
31274163 CAAAATTACTGTTTTACCCTCGATTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* * *
31274190 TAAAATTACTAAAATACCCTTGGTTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* **
31274217 CAAAATTACCAAAATACCCTCGA-CCA
1 TAAAATTACCAAAATACCCTCGATTTA
* * *
31274243 GTAAAATTACCAAAATACCCTAG-TCTG
1 -TAAAATTACCAAAATACCCTCGATTTA
* * *
31274270 TAAAATTGCTAAAATACCC-CTAGTTTA
1 TAAAATTACCAAAATACCCTCGA-TTTA
* * *
31274297 TAAAATTACCGAAATACCCTCAATTTG
1 TAAAATTACCAAAATACCCTCGATTTA
* *
31274324 TAAAATTACCAAAATACCC-CTAGTTTG
1 TAAAATTACCAAAATACCCTCGA-TTTA
* * * *
31274351 TAAAATTACCAAAATACCATTGGTTTG
1 TAAAATTACCAAAATACCCTCGATTTA
* * * *
31274378 TGAAATTACCGAAATACCCTCAATTTG
1 TAAAATTACCAAAATACCCTCGATTTA
*
31274405 TAAAATTACCAAAATACCCTTGATTTA
1 TAAAATTACCAAAATACCCTCGATTTA
* * *
31274432 CAAAATTA-CAGAAATACCCTTGATTTG
1 TAAAATTACCA-AAATACCCTCGATTTA
* * *
31274459 TAGATTTACCAAAACACCCT
1 TAAAATTACCAAAATACCCT
31274479 TGTAGGATGA
Statistics
Matches: 321, Mismatches: 67, Indels: 18
0.79 0.17 0.04
Matches are distributed among these distances:
26 22 0.07
27 295 0.92
28 4 0.01
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (27 bp):
TAAAATTACCAAAATACCCTCGATTTA
Found at i:31274386 original size:81 final size:81
Alignment explanation
Indices: 31274190--31274423 Score: 335
Period size: 81 Copynumber: 2.9 Consensus size: 81
31274180 CCTCGATTTA
* * * ***
31274190 TAAAATTACTAAAATACCCTTGGTTTACAAAATTACCAAAATACCCTCGACCAGTAAAATTACCA
1 TAAAATTACTAAAATACCCTTGGTTTATAAAATTACCGAAATACCCTCAATTTGTAAAATTACCA
31274255 AAATA-CCCTAGTCTG
66 AAATACCCCTAGTCTG
* * *
31274270 TAAAATTGCTAAAATACCCCTAGTTTATAAAATTACCGAAATACCCTCAATTTGTAAAATTACCA
1 TAAAATTACTAAAATACCCTTGGTTTATAAAATTACCGAAATACCCTCAATTTGTAAAATTACCA
*
31274335 AAATACCCCTAGTTTG
66 AAATACCCCTAGTCTG
* * * *
31274351 TAAAATTACCAAAATACCATTGGTTTGTGAAATTACCGAAATACCCTCAATTTGTAAAATTACCA
1 TAAAATTACTAAAATACCCTTGGTTTATAAAATTACCGAAATACCCTCAATTTGTAAAATTACCA
31274416 AAATACCC
66 AAATACCC
31274424 TTGATTTACA
Statistics
Matches: 136, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
80 61 0.45
81 75 0.55
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.29
Consensus pattern (81 bp):
TAAAATTACTAAAATACCCTTGGTTTATAAAATTACCGAAATACCCTCAATTTGTAAAATTACCA
AAATACCCCTAGTCTG
Found at i:31274437 original size:81 final size:81
Alignment explanation
Indices: 31274177--31274453 Score: 326
Period size: 81 Copynumber: 3.4 Consensus size: 81
31274167 ATTACTGTTT
* * * * * **
31274177 TACCCTCGATTTATAAAATTACTAAAATACCCTTGGTTTACAAAATTACCAAAATACCCTCGACC
1 TACCCTTGATTTATAAAATTACCAAAATACCCTTGGTTTATAAAATTACCGAAATACCCTCAATT
*
31274242 AGTAAAATTACCAAAA
66 TGTAAAATTACCAAAA
* * * * * * *
31274258 TACCCTAG-TCTGTAAAATTGCTAAAATACCCCTAGTTTATAAAATTACCGAAATACCCTCAATT
1 TACCCTTGATTTATAAAATTACCAAAATACCCTTGGTTTATAAAATTACCGAAATACCCTCAATT
31274322 TGTAAAATTACCAAAA
66 TGTAAAATTACCAAAA
* * * * *
31274338 TACCCCT-AGTTTGTAAAATTACCAAAATACCATTGGTTTGTGAAATTACCGAAATACCCTCAAT
1 TACCCTTGA-TTTATAAAATTACCAAAATACCCTTGGTTTATAAAATTACCGAAATACCCTCAAT
31274402 TTGTAAAATTACCAAAA
65 TTGTAAAATTACCAAAA
*
31274419 TACCCTTGATTTACAAAATTA-CAGAAATACCCTTG
1 TACCCTTGATTTATAAAATTACCA-AAATACCCTTG
31274454 ATTTGTAGAT
Statistics
Matches: 166, Mismatches: 26, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
80 68 0.41
81 97 0.58
82 1 0.01
ACGTcount: A:0.41, C:0.22, G:0.08, T:0.30
Consensus pattern (81 bp):
TACCCTTGATTTATAAAATTACCAAAATACCCTTGGTTTATAAAATTACCGAAATACCCTCAATT
TGTAAAATTACCAAAA
Found at i:31274479 original size:27 final size:27
Alignment explanation
Indices: 31274177--31274480 Score: 274
Period size: 27 Copynumber: 11.3 Consensus size: 27
31274167 ATTACTGTTT
* * *
31274177 TACCCTCGATTTATAAAATTACTAAAA
1 TACCCTTGATTTGTAAAATTACCAAAA
* **
31274204 TACCCTTGGTTTACAAAATTACCAAAA
1 TACCCTTGATTTGTAAAATTACCAAAA
* ***
31274231 TACCCTCGACCAGTAAAATTACCAAAA
1 TACCCTTGATTTGTAAAATTACCAAAA
* * * *
31274258 TACCCTAG-TCTGTAAAATTGCTAAAA
1 TACCCTTGATTTGTAAAATTACCAAAA
* * *
31274284 TACCCCT-AGTTTATAAAATTACCGAAA
1 TACCCTTGA-TTTGTAAAATTACCAAAA
**
31274311 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTTGATTTGTAAAATTACCAAAA
*
31274338 TACCCCT-AGTTTGTAAAATTACCAAAA
1 TACCCTTGA-TTTGTAAAATTACCAAAA
* * * *
31274365 TACCATTGGTTTGTGAAATTACCGAAA
1 TACCCTTGATTTGTAAAATTACCAAAA
**
31274392 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTTGATTTGTAAAATTACCAAAA
**
31274419 TACCCTTGATTTACAAAATTA-CAGAAA
1 TACCCTTGATTTGTAAAATTACCA-AAA
* *
31274446 TACCCTTGATTTGTAGATTTACCAAAA
1 TACCCTTGATTTGTAAAATTACCAAAA
*
31274473 CACCCTTG
1 TACCCTTG
31274481 TAGGATGAAA
Statistics
Matches: 221, Mismatches: 49, Indels: 14
0.78 0.17 0.05
Matches are distributed among these distances:
26 22 0.10
27 196 0.89
28 3 0.01
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.30
Consensus pattern (27 bp):
TACCCTTGATTTGTAAAATTACCAAAA
Found at i:31275448 original size:25 final size:26
Alignment explanation
Indices: 31275377--31275473 Score: 126
Period size: 26 Copynumber: 3.8 Consensus size: 26
31275367 GAGGAAGTGC
* *
31275377 AAAAGGCCTTATGCCCTAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
**
31275403 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
31275429 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
* *
31275454 AAAATGGCTT-TACCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
31275474 ATTAAAGAGG
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
25 31 0.49
26 32 0.51
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.28
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:31275454 original size:51 final size:51
Alignment explanation
Indices: 31275377--31275473 Score: 142
Period size: 51 Copynumber: 1.9 Consensus size: 51
31275367 GAGGAAGTGC
* *
31275377 AAAAGGCCTTATGCCCTAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGCCTTATGCCCCAGTTTACCGAAAAGGGCTT-TACCCCAGTTTATTG
* *
31275429 AAAAGGGCTT-TGCCCCAGTTTACCGAAAATGGCTTTACCCCAGTT
1 AAAAGGCCTTATGCCCCAGTTTACCGAAAAGGGCTTTACCCCAGTT
31275474 ATTAAAGAGG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
50 9 0.22
51 23 0.56
52 9 0.22
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.28
Consensus pattern (51 bp):
AAAAGGCCTTATGCCCCAGTTTACCGAAAAGGGCTTTACCCCAGTTTATTG
Found at i:31275677 original size:42 final size:42
Alignment explanation
Indices: 31275618--31275709 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 42
31275608 TAGTCTCCCC
* * *** *
31275618 AAATGGGCTTGCTTACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATCCATTAACATTACATGTGATATTG
31275660 AAATGGGCTTGCATACATCCATTAACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTAACATTACATGTGATATTG
31275702 AAATGGGC
1 AAATGGGC
31275710 CTAAGGGCCA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTAACATTACATGTGATATTG
Found at i:31275768 original size:31 final size:31
Alignment explanation
Indices: 31275733--31275809 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
31275723 CGTTTACAGT
31275733 AAAGGCTTCGGCCCAATGATATGATTTATGA
1 AAAGGCTTCGGCCCAATGATATGATTTATGA
* * *
31275764 AAAGGCTTCGACCTAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAATGATATGATTTATGA
*
31275795 AAAGGCTTCAGCCCA
1 AAAGGCTTCGGCCCA
31275810 GTAACCGTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAATGATATGATTTATGA
Found at i:31285598 original size:13 final size:13
Alignment explanation
Indices: 31285580--31285604 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31285570 ATTTTACCTC
31285580 TTTTTCTTCTTCA
1 TTTTTCTTCTTCA
31285593 TTTTTCTTCTTC
1 TTTTTCTTCTTC
31285605 CCCTTTTTAT
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:0.04, C:0.24, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTCTTCTTCA
Found at i:31287637 original size:34 final size:34
Alignment explanation
Indices: 31287590--31287663 Score: 141
Period size: 34 Copynumber: 2.2 Consensus size: 34
31287580 GAGATAGACT
31287590 CAAT-TCCCAAATCAACTAAAATAGAATTATTGA
1 CAATATCCCAAATCAACTAAAATAGAATTATTGA
31287623 CAATATCCCAAATCAACTAAAATAGAATTATTGA
1 CAATATCCCAAATCAACTAAAATAGAATTATTGA
31287657 CAATATC
1 CAATATC
31287664 TATGGCAACA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 4 0.10
34 36 0.90
ACGTcount: A:0.49, C:0.19, G:0.05, T:0.27
Consensus pattern (34 bp):
CAATATCCCAAATCAACTAAAATAGAATTATTGA
Found at i:31298354 original size:20 final size:21
Alignment explanation
Indices: 31298320--31298360 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
31298310 CCAGGGGAAG
31298320 GAAAGAAAGAAAAAGAGAAAA
1 GAAAGAAAGAAAAAGAGAAAA
*
31298341 GAAAGAAA-AAAAAGGGAAAA
1 GAAAGAAAGAAAAAGAGAAAA
31298361 TCAAAGATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (21 bp):
GAAAGAAAGAAAAAGAGAAAA
Found at i:31298366 original size:21 final size:21
Alignment explanation
Indices: 31298321--31298367 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
31298311 CAGGGGAAGG
*
31298321 AAAGAAAGAAAAAGAGAAAAG
1 AAAGAAAGAAAAAGAGAAAAC
*
31298342 AAAGAAA-AAAAAGGGAAAATC
1 AAAGAAAGAAAAAGAGAAAA-C
31298363 AAAGA
1 AAAGA
31298368 TGTGAAGCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.74, C:0.02, G:0.21, T:0.02
Consensus pattern (21 bp):
AAAGAAAGAAAAAGAGAAAAC
Found at i:31300340 original size:46 final size:46
Alignment explanation
Indices: 31300288--31300515 Score: 296
Period size: 46 Copynumber: 5.0 Consensus size: 46
31300278 AGTGTGCTCT
*
31300288 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACTATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
31300334 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
31300380 CTGATATGAAATGTGTAAAACCATGGTTGAAAGATAACATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * **
31300426 GTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * ** * *
31300472 ATGACA-GAAAATGAGTAAGACCATAATTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
31300516 TCATGTCAAA
Statistics
Matches: 164, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
45 1 0.01
46 163 0.99
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:31309166 original size:28 final size:29
Alignment explanation
Indices: 31309129--31309253 Score: 144
Period size: 29 Copynumber: 4.3 Consensus size: 29
31309119 AAGTCTACAT
* *
31309129 ACATGCATATGGCCCACTAGGCCC-AATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
* * *
31309157 TCATTCATATGGCCCTTTAGGCCTAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
** * *
31309186 ACATTTGTGTGGTCCATTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
* *
31309215 ACATTCATACGGCCTATTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
31309244 ACATTCATAT
1 ACATTCATAT
31309254 ACATGCTTTC
Statistics
Matches: 77, Mismatches: 19, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
28 19 0.25
29 58 0.75
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (29 bp):
ACATTCATATGGCCCATTAGGCCCAAATC
Found at i:31309485 original size:16 final size:16
Alignment explanation
Indices: 31309464--31309499 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
31309454 GTAGCCAAAC
*
31309464 TTTCAGCTTTTCGGCA
1 TTTCAGCTTTTCGACA
31309480 TTTCAGCTTTTCGACA
1 TTTCAGCTTTTCGACA
31309496 TTTC
1 TTTC
31309500 GGGATTTGCC
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:0.14, C:0.25, G:0.14, T:0.47
Consensus pattern (16 bp):
TTTCAGCTTTTCGACA
Found at i:31310853 original size:18 final size:17
Alignment explanation
Indices: 31310812--31310853 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
31310802 AAATTAGGCC
31310812 GTGTGGGCCACATGGGA
1 GTGTGGGCCACATGGGA
* *
31310829 GTATGGGCCCACATGGGT
1 GTGTGGG-CCACATGGGA
31310847 GTGTGGG
1 GTGTGGG
31310854 AAAATAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.14, C:0.17, G:0.48, T:0.21
Consensus pattern (17 bp):
GTGTGGGCCACATGGGA
Done.