Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold11
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: 5230303
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 140504 characters in sequence are not A, C, G, or T
File 8 of 29
Found at i:1077848 original size:43 final size:42
Alignment explanation
Indices: 1077777--1077892 Score: 119
Period size: 43 Copynumber: 2.7 Consensus size: 42
1077767 AAATGGAGAG
* * * * *
1077777 TGTCCTGCTCTTTGAGGACCAAAG-AAAAAGGGAAAATG-AAA
1 TGTCCTGCTCCTTGAGGA-TAAAGAAAAAAAGAAAAAAGAAAA
*
1077818 TCGGTCCTGATCCTTGAGGATAAAGAAAAAAAGAAAAAAGAAAA
1 T--GTCCTGCTCCTTGAGGATAAAGAAAAAAAGAAAAAAGAAAA
*
1077862 TGTCCTGCTCCTTGGGGATAAAGGAAAAAAA
1 TGTCCTGCTCCTTGAGGATAAA-GAAAAAAA
1077893 AAATGAAGTG
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
41 1 0.02
42 23 0.37
43 34 0.55
44 4 0.06
ACGTcount: A:0.44, C:0.14, G:0.23, T:0.19
Consensus pattern (42 bp):
TGTCCTGCTCCTTGAGGATAAAGAAAAAAAGAAAAAAGAAAA
Found at i:1077930 original size:42 final size:41
Alignment explanation
Indices: 1077864--1078089 Score: 193
Period size: 42 Copynumber: 5.4 Consensus size: 41
1077854 AAAGAAAATG
* * * * ** *
1077864 TCCTGCTCCTTGGGGATAAAGGAAAAAAAAAATGAAGTGCA
1 TCCTGCTCTTTGAGGACAAAAGAAAAAGGAAATAAAGTGCA
* * * **
1077905 TCCTACTCTTTGAGGACAAAGGGAAAATAAGGAAATGAAGTGTG
1 TCCTGCTCTTTGAGGACAAA-AG-AAA-AAGGAAATAAAGTGCA
** * *
1077949 TTATGCTCTTTGAGGACAAAAGAGAAAAGGAAATAGAGTGCG
1 TCCTGCTCTTTGAGGACAAAAGA-AAAAGGAAATAAAGTGCA
* * *
1077991 TCTTGCCCTTCGAGGAC-AAAGAAGAAAGGAAATAAAGTGCA
1 TCCTGCTCTTTGAGGACAAAAGAA-AAAGGAAATAAAGTGCA
* *
1078032 TCTTGCTCTTTGAGGACAAAAGAGAAAAGAAAATAAAGTGCA
1 TCCTGCTCTTTGAGGACAAAAGA-AAAAGGAAATAAAGTGCA
*
1078074 TCCTGTTCTTTGAGGA
1 TCCTGCTCTTTGAGGA
1078090 TTAAAGGGTG
Statistics
Matches: 152, Mismatches: 26, Indels: 13
0.80 0.14 0.07
Matches are distributed among these distances:
40 1 0.01
41 51 0.34
42 64 0.42
43 7 0.05
44 29 0.19
ACGTcount: A:0.39, C:0.13, G:0.25, T:0.22
Consensus pattern (41 bp):
TCCTGCTCTTTGAGGACAAAAGAAAAAGGAAATAAAGTGCA
Found at i:1078089 original size:83 final size:85
Alignment explanation
Indices: 1077887--1078089 Score: 241
Period size: 83 Copynumber: 2.4 Consensus size: 85
1077877 GGATAAAGGA
* * * * **
1077887 AAAAAAAAATGAAGTGCATCCTACTCTTTGAGGACAAAGGGAAAATAAGGAAATGAAGTGTGTTA
1 AAAAGAAAATAAAGTGCATCCTGCTCTTTGAGGACAAA-GGAAAATAAGGAAATAAAGTGCATTA
1077952 TGCTCTTTGAGGACAAAAGAG
65 TGCTCTTTGAGGACAAAAGAG
* * * * * * *
1077973 AAAAGGAAATAGAGTGCGTCTTGCCCTTCGAGGACAAA-GAAGA-AAGGAAATAAAGTGCATCT-
1 AAAAGAAAATAAAGTGCATCCTGCTCTTTGAGGACAAAGGAAAATAAGGAAATAAAGTGCAT-TA
1078035 TGCTCTTTGAGGACAAAAGAG
65 TGCTCTTTGAGGACAAAAGAG
*
1078056 AAAAGAAAATAAAGTGCATCCTGTTCTTTGAGGA
1 AAAAGAAAATAAAGTGCATCCTGCTCTTTGAGGA
1078090 TTAAAGGGTG
Statistics
Matches: 96, Mismatches: 20, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
83 62 0.65
84 5 0.05
86 29 0.30
ACGTcount: A:0.41, C:0.12, G:0.25, T:0.22
Consensus pattern (85 bp):
AAAAGAAAATAAAGTGCATCCTGCTCTTTGAGGACAAAGGAAAATAAGGAAATAAAGTGCATTAT
GCTCTTTGAGGACAAAAGAG
Found at i:1078213 original size:62 final size:62
Alignment explanation
Indices: 1078074--1078798 Score: 797
Period size: 62 Copynumber: 11.9 Consensus size: 62
1078064 ATAAAGTGCA
* * * * * * *
1078074 TCCTGTTCTTTGAGGATTAAAGGGTGCCACTAATTCGTGTGGGCTTTGAAAA--AAAAAGCA
1 TCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGGAAAAGGCG
* ** * *
1078134 TCCTGATCTTTGAGGACTAAATAGTGCCACCAACTCATATGGGCTTTGACAAGGAAAAGGCG
1 TCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGGAAAAGGCG
* * *
1078196 TCCTGCTCTTTGAGGACTAAAGGAG-GCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGACA
1 TCCTGCTCTTTGAGGACTAAAGG-GTGCCACCAACTCATGTGGGCTTTGAAAAGGAAAAGG-CG
**
1078259 TCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGCGTGGGCTTTGAAAAGGAAAAGGCG
1 TCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGGAAAAGGCG
* * * *
1078321 TCCTGCTTTTTGAAGACTAAAGGGTGCCACCAACTCATGT-GGCTTTGAAAAGGAAAATGCA
1 TCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGGAAAAGGCG
* **
1078382 TCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACT-AGTATGGGCTTTGAAAAGGAAAAGATG
1 TCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCA-TGTGGGCTTTGAAAAGGAAAAGGCG
* *
1078444 TCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACT-AGTGTGGACTTTGAAAA-GAAAAAGCG
1 TCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCA-TGTGGGCTTTGAAAAGGAAAAGGCG
** * *
1078505 TTTTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGAGCTTTGAAAAGGAAAAGGCG
1 TCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGGAAAAGGCG
* * * * *
1078567 TCATGCTCTTTGAGGAC-------T---A--AACTCATGTAGGCTTTGAAAAAGAAAATGAG
1 TCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGGAAAAGGCG
* * * *
1078617 TCTTGCTCTTTGAGGACTGAATGGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGGCG
1 TCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGGAAAAGGCG
* * * * * * * *
1078679 TCCTACTCTTTGAGAACTGAATGGTGCCACTAACTCGTGTGGGCTTTGAAAAGAAAAAGGCA
1 TCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGGAAAAGGCG
** * * *
1078741 TTATGCTCTTTGAGGACCAAAGGGTGCCACCAACTC-TAGTGGGCTTTAAAAAGAAAAA
1 TCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCAT-GTGGGCTTTGAAAAGGAAAA
1078799 AATGTCTTGC
Statistics
Matches: 568, Mismatches: 75, Indels: 42
0.83 0.11 0.06
Matches are distributed among these distances:
50 41 0.07
52 1 0.00
55 1 0.00
57 1 0.00
60 45 0.08
61 107 0.19
62 314 0.55
63 58 0.10
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (62 bp):
TCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGGAAAAGGCG
Found at i:1078303 original size:185 final size:185
Alignment explanation
Indices: 1078072--1078798 Score: 833
Period size: 185 Copynumber: 4.0 Consensus size: 185
1078062 AAATAAAGTG
* * * * *
1078072 CATCCTGTTCTTTGAGGATTAAAGGGTGCCACTAATTCGTGTGGGCTTTGAAAA-AAAAAGCATC
1 CATCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGCGTC
** * * * *
1078136 CTGATCTTTGAGGACTAAATAGTGCCACCAACTCATATGGGCTTTGACAAGGAAAAGGCGTCCTG
66 CTGATCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGGAAAAGGCATCATG
1078201 CTCTTTGAGGACTAAAGGAG-GCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGA
131 CTCTTTGAGGACTAAAGG-GTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAA-GA
* *
1078257 CATCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGCGTGGGCTTTGAAAAGGAAAAGGCGT
1 CATCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAA-GAAAAAGCGT
* * * * *
1078322 CCTGCTTTTTGAAGACTAAAGGGTGCCACCAACTCATGT-GGCTTTGAAAAGGAAAATGCATCCT
65 CCTGATCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGGAAAAGGCATCAT
* * *
1078386 GCTCTTTGAGGACTAAAGGGTGCCACCAACTAGTATGGGCTTTGAAAAGGAAAAGA
130 GCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGA
** * * *
1078442 TGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTAGTGTGGACTTTGAAAAGAAAAAGCGTT
1 CATCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGCGTC
* * * * *
1078507 TTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGAGCTTTGAAAAGGAAAAGGCGTCATG
66 CTGATCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGGAAAAGGCATCATG
* * *
1078572 CTCTTTGAGGAC-------T---A--AACTCATGTAGGCTTTGAAAAAGAAAATGA
131 CTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTG-AAAAGAAAAAGA
* * * * *
1078616 -GTCTTGCTCTTTGAGGACTGAATGGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGGCGT
1 CATCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAA-GCGT
* * * * * * *
1078680 CCT-ACTCTTTGAGAACTGAATGGTGCCACTAACTCGTGTGGGCTTTGAAAAGAAAAAGGCATTA
65 CCTGA-TCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGGAAAAGGCATCA
* *
1078744 TGCTCTTTGAGGACCAAAGGGTGCCACCAACTC-TAGTGGGCTTTAAAAAGAAAAA
129 TGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGT-GTGGGCTTTGAAAAGAAAAA
1078799 AATGTCTTGC
Statistics
Matches: 462, Mismatches: 60, Indels: 40
0.82 0.11 0.07
Matches are distributed among these distances:
173 66 0.14
174 80 0.17
175 1 0.00
178 1 0.00
181 1 0.00
184 44 0.10
185 145 0.31
186 84 0.18
187 40 0.09
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.25
Consensus pattern (185 bp):
CATCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGCGTC
CTGATCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGGAAAAGGCATCATG
CTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGA
Found at i:1078437 original size:123 final size:124
Alignment explanation
Indices: 1078074--1078798 Score: 787
Period size: 123 Copynumber: 6.0 Consensus size: 124
1078064 ATAAAGTGCA
* * * * *
1078074 TCCTGTTCTTTGAGGATTAAAGGGTGCCACTAATTCGTGTGGGCTTTGAAAA--AAAAAGCATCC
1 TCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGGAAAAAGCATCC
* ** *
1078137 TGATCTTTGAGGACTAAATAGTGCCACCAACTCA-TATGGGCTTTGACAAGGAAAAGGCG
66 TGCTCTTTGAGGACTAAAGGGTGCCACCAACT-AGTATGGGCTTTGAAAAGGAAAAGGCG
*
1078196 TCCTGCTCTTTGAGGACTAAAGGAG-GCCACCAACTCGTGTGGGCTTTGAAAA-GAAAAAGGACA
1 TCCTGCTCTTTGAGGACTAAAGG-GTGCCACCAACTCATGTGGGCTTTGAAAAGGAAAAA-G-CA
* **
1078259 TCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGCGTGGGCTTTGAAAAGGAAAAGGCG
63 TCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTAGTATGGGCTTTGAAAAGGAAAAGGCG
* * *
1078321 TCCTGCTTTTTGAAGACTAAAGGGTGCCACCAACTCATGT-GGCTTTGAAAAGGAAAATGCATCC
1 TCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGGAAAAAGCATCC
**
1078385 TGCTCTTTGAGGACTAAAGGGTGCCACCAACTAGTATGGGCTTTGAAAAGGAAAAGATG
66 TGCTCTTTGAGGACTAAAGGGTGCCACCAACTAGTATGGGCTTTGAAAAGGAAAAGGCG
* * *
1078444 TCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACT-AGTGTGGACTTTGAAAA-GAAAAAGCGTT
1 TCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCA-TGTGGGCTTTGAAAAGGAAAAAGCATC
* * * *
1078507 TTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGAGCTTTGAAAAGGAAAAGGCG
65 CTGCTCTTTGAGGACTAAAGGGTGCCACCAACTAGTATGGGCTTTGAAAAGGAAAAGGCG
* * * *
1078567 TCATGCTCTTTGAGGAC-------T---A--AACTCATGTAGGCTTTGAAAAAGAAAATG-AGTC
1 TCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGGAAAAAGCA-TC
* * * * *
1078619 TTGCTCTTTGAGGACTGAATGGTGCCACCAACTCA-TGTGGGCTTTGAAAAGAAAAAGGCG
65 CTGCTCTTTGAGGACTAAAGGGTGCCACCAACT-AGTATGGGCTTTGAAAAGGAAAAGGCG
* * * * * * *
1078679 TCCTACTCTTTGAGAACTGAATGGTGCCACTAACTCGTGTGGGCTTTGAAAA-GAAAAAGGCATT
1 TCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGGAAAAA-GCATC
* * * * *
1078743 ATGCTCTTTGAGGACCAAAGGGTGCCACCAACT-CTAGTGGGCTTTAAAAAGAAAAA
65 CTGCTCTTTGAGGACTAAAGGGTGCCACCAACTAGTA-TGGGCTTTGAAAAGGAAAA
1078799 AATGTCTTGC
Statistics
Matches: 518, Mismatches: 56, Indels: 56
0.82 0.09 0.09
Matches are distributed among these distances:
111 17 0.03
112 76 0.15
113 1 0.00
116 1 0.00
119 1 0.00
122 48 0.09
123 185 0.36
124 92 0.18
125 97 0.19
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (124 bp):
TCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGGGCTTTGAAAAGGAAAAAGCATCC
TGCTCTTTGAGGACTAAAGGGTGCCACCAACTAGTATGGGCTTTGAAAAGGAAAAGGCG
Found at i:1078643 original size:112 final size:111
Alignment explanation
Indices: 1078487--1078692 Score: 313
Period size: 112 Copynumber: 1.8 Consensus size: 111
1078477 CTAGTGTGGA
* * *
1078487 CTTTGAAAAGAAAAAGCGTTTTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGAGCTTT
1 CTTTGAAAAGAAAAAGAGTCTTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGAGCTTT
* *
1078552 GAAAAGGAAAAGGCGTCATGCTCTTTGAGGACTAAACTCATGTAGG
66 GAAAAGAAAAAGGCGTCATACTCTTTGAGGACTAAACTCATGTAGG
* * * *
1078598 CTTTGAAAAAGAAAATGAGTCTTGCTCTTTGAGGACTGAATGGTGCCACCAACTCATGTGGGCTT
1 CTTTG-AAAAGAAAAAGAGTCTTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGAGCTT
*
1078663 TGAAAAGAAAAAGGCGTCCTACTCTTTGAG
65 TGAAAAGAAAAAGGCGTCATACTCTTTGAG
1078693 AACTGAATGG
Statistics
Matches: 84, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
111 5 0.06
112 79 0.94
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (111 bp):
CTTTGAAAAGAAAAAGAGTCTTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTGAGCTTT
GAAAAGAAAAAGGCGTCATACTCTTTGAGGACTAAACTCATGTAGG
Found at i:1078752 original size:174 final size:173
Alignment explanation
Indices: 1078423--1078757 Score: 485
Period size: 174 Copynumber: 1.9 Consensus size: 173
1078413 AACTAGTATG
*
1078423 GGCTTTGAAAAGGAAAAGATGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTAGTGTGGAC
1 GGCTTTGAAAAAGAAAAGATGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTAGTGTGGAC
** * *
1078488 TTTGAAAAGAAAAAGCGTTTTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGAGCTTTG
66 TTTGAAAAGAAAAAGCGTCCTACTCTTTGAGAACTAAAGGGTGCCACCAACTCGTGTGAGCTTTG
* *
1078553 AAAAGGAAAAGGCGTCATGCTCTTTGAGGACTAAACTCATGTA
131 AAAAGAAAAAGGCATCATGCTCTTTGAGGACTAAACTCATGTA
* * *
1078596 GGCTTTGAAAAAGAAAATGA-GTCTTGCTCTTTGAGGACTGAATGGTGCCACCAACTCA-TGTGG
1 GGCTTTGAAAAAGAAAA-GATGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACT-AGTGTGG
* * * * *
1078659 GCTTTGAAAAGAAAAAGGCGTCCTACTCTTTGAGAACTGAATGGTGCCACTAACTCGTGTGGGCT
64 ACTTTGAAAAGAAAAA-GCGTCCTACTCTTTGAGAACTAAAGGGTGCCACCAACTCGTGTGAGCT
*
1078724 TTGAAAAGAAAAAGGCATTATGCTCTTTGAGGAC
128 TTGAAAAGAAAAAGGCATCATGCTCTTTGAGGAC
1078758 CAAAGGGTGC
Statistics
Matches: 143, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
173 69 0.48
174 74 0.52
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (173 bp):
GGCTTTGAAAAAGAAAAGATGTCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTAGTGTGGAC
TTTGAAAAGAAAAAGCGTCCTACTCTTTGAGAACTAAAGGGTGCCACCAACTCGTGTGAGCTTTG
AAAAGAAAAAGGCATCATGCTCTTTGAGGACTAAACTCATGTA
Found at i:1078868 original size:82 final size:82
Alignment explanation
Indices: 1078746--1078897 Score: 216
Period size: 82 Copynumber: 1.9 Consensus size: 82
1078736 AGGCATTATG
* * * *
1078746 CTCTTTGAGGACCAAAGGGTGCCACCAACTCTAGTGGGCTTTAAAAAGAAAAAAATGTCTTGCTC
1 CTCTTTAAGGACCAAAGGGTGCCACCAACTATAGTAGGCTTTAAAAAGAAAAAAACGTCTTGCTC
1078811 TTTGAAAAGACGTCTTA
66 TTTGAAAAGACGTCTTA
* * **
1078828 CTCTTTAAGGACTAAAGGGTGCCACCAACTA-ATGTAGGCTTTGAAAAGAAAAAGGCGTCTTGCT
1 CTCTTTAAGGACCAAAGGGTGCCACCAACTATA-GTAGGCTTTAAAAAGAAAAAAACGTCTTGCT
1078892 CTTTGA
65 CTTTGA
1078898 GGACTAAAGG
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
81 1 0.02
82 60 0.98
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (82 bp):
CTCTTTAAGGACCAAAGGGTGCCACCAACTATAGTAGGCTTTAAAAAGAAAAAAACGTCTTGCTC
TTTGAAAAGACGTCTTA
Found at i:1078931 original size:144 final size:144
Alignment explanation
Indices: 1078671--1078931 Score: 364
Period size: 144 Copynumber: 1.8 Consensus size: 144
1078661 TTTGAAAAGA
* * * * * ** *
1078671 AAAAGGCGTCCTACTCTTTGAGAACTGAATGGTGCCACTAACTCGTGTGGGCTTTGAAAAGAAAA
1 AAAAGACGTCCTACTCTTTAAGAACTAAAGGGTGCCACCAACTAATGTAGGCTTTGAAAAGAAAA
**
1078736 AGGCATTATGCTCTTTGAGGACCAAAGGGTGCCACCAACTCTAGTGGGCTTTAAAAAGAAAAAAA
66 AGGCATTATGCTCTTTGAGGACCAAAGGGTGCCACCAACTCTAGTAAGCTTTAAAAAGAAAAAAA
1078801 TGTCTTGCTCTTTG
131 TGTCTTGCTCTTTG
* *
1078815 AAAAGACGTCTTACTCTTTAAGGACTAAAGGGTGCCACCAACTAATGTAGGCTTTGAAAAGAAAA
1 AAAAGACGTCCTACTCTTTAAGAACTAAAGGGTGCCACCAACTAATGTAGGCTTTGAAAAGAAAA
* *
1078880 AGGCGTCT-TGCTCTTTGAGGACTAAAGGGTGCCACCAACTC-ATGTAAGCTTT
66 AGGCAT-TATGCTCTTTGAGGACCAAAGGGTGCCACCAACTCTA-GTAAGCTTT
1078932 GAAGAAAAAA
Statistics
Matches: 101, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
143 1 0.01
144 99 0.98
145 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (144 bp):
AAAAGACGTCCTACTCTTTAAGAACTAAAGGGTGCCACCAACTAATGTAGGCTTTGAAAAGAAAA
AGGCATTATGCTCTTTGAGGACCAAAGGGTGCCACCAACTCTAGTAAGCTTTAAAAAGAAAAAAA
TGTCTTGCTCTTTG
Found at i:1078971 original size:61 final size:62
Alignment explanation
Indices: 1078815--1078976 Score: 247
Period size: 62 Copynumber: 2.6 Consensus size: 62
1078805 TTGCTCTTTG
* * *
1078815 AAAAGACGTCTTACTCTTTAAGGACTAAAGGGTGCCACCAACTAATGTAGGCTTTGAAAAGA
1 AAAAGACGTCTTGCTCTTTGAGGACTAAAGGGTGCCACCAACTAATGTAAGCTTTGAAAAGA
* * *
1078877 AAAAGGCGTCTTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCATGTAAGCTTTGAAGA-A
1 AAAAGACGTCTTGCTCTTTGAGGACTAAAGGGTGCCACCAACTAATGTAAGCTTTGAAAAGA
1078938 AAAAGACGT-TCTGCTCTTTGAGGACTAAAGGGTGCCACC
1 AAAAGACGTCT-TGCTCTTTGAGGACTAAAGGGTGCCACC
1078977 TGTAGACACC
Statistics
Matches: 92, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
60 1 0.01
61 37 0.40
62 54 0.59
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (62 bp):
AAAAGACGTCTTGCTCTTTGAGGACTAAAGGGTGCCACCAACTAATGTAAGCTTTGAAAAGA
Found at i:1079250 original size:10 final size:10
Alignment explanation
Indices: 1079235--1079281 Score: 53
Period size: 9 Copynumber: 4.7 Consensus size: 10
1079225 ATTTAACATG
1079235 AATAATAAAA
1 AATAATAAAA
1079245 AATAAT-AAA
1 AATAATAAAA
1079254 AATAA-AAAA
1 AATAATAAAA
*
1079263 TAAAAATAAATA
1 -AATAATAAA-A
1079275 AATAATA
1 AATAATA
1079282 TACATAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
9 11 0.35
10 10 0.32
11 9 0.29
12 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
AATAATAAAA
Found at i:1079261 original size:7 final size:7
Alignment explanation
Indices: 1079238--1079279 Score: 50
Period size: 7 Copynumber: 5.7 Consensus size: 7
1079228 TAACATGAAT
1079238 AATAAAA
1 AATAAAA
1079245 AATAATAAA
1 AAT-A-AAA
1079254 AATAAAA
1 AATAAAA
1079261 AAT-AAA
1 AATAAAA
1079267 AATAAATA
1 AATAAA-A
1079275 AATAA
1 AATAA
1079280 TATACATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
6 6 0.19
7 11 0.35
8 8 0.26
9 6 0.19
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (7 bp):
AATAAAA
Found at i:1079288 original size:17 final size:14
Alignment explanation
Indices: 1079235--1079296 Score: 58
Period size: 13 Copynumber: 4.4 Consensus size: 14
1079225 ATTTAACATG
*
1079235 AATAATAAA-AAAT
1 AATAATAAATAAAA
1079248 AATAA-AAATAAAA
1 AATAATAAATAAAA
1079261 AATAA-AAATAAATA
1 AATAATAAATAAA-A
1079275 AATAATATACATAAAA
1 AATAATA-A-ATAAAA
1079291 TAATAA
1 -AATAA
1079297 CAATAATTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
12 3 0.07
13 20 0.48
14 6 0.14
15 1 0.02
16 2 0.05
17 10 0.24
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.23
Consensus pattern (14 bp):
AATAATAAATAAAA
Found at i:1079313 original size:23 final size:22
Alignment explanation
Indices: 1079237--1079313 Score: 54
Period size: 22 Copynumber: 3.5 Consensus size: 22
1079227 TTAACATGAA
*
1079237 TAATAAAAAATAATAAAAATAA-
1 TAATTAAAAATAAT-AAAATAAT
* *
1079259 AAAATAAAAATAA-ATAAATAAT
1 TAATTAAAAATAATA-AAATAAT
1079281 ATACA-T-AAAATAATAACAATAAT
1 -TA-ATTAAAAATAATAA-AATAAT
1079304 TAATTAAAAA
1 TAATTAAAAA
1079314 ATTAAAACAG
Statistics
Matches: 43, Mismatches: 4, Indels: 15
0.69 0.06 0.24
Matches are distributed among these distances:
20 1 0.02
21 7 0.16
22 21 0.49
23 13 0.30
24 1 0.02
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.25
Consensus pattern (22 bp):
TAATTAAAAATAATAAAATAAT
Found at i:1082849 original size:62 final size:61
Alignment explanation
Indices: 1082726--1082880 Score: 186
Period size: 62 Copynumber: 2.5 Consensus size: 61
1082716 TGTCGCGACA
* * * *
1082726 CCACCAACTCGTGTGGGATTTGAAAA-AAAAAACGCCCTGCTCTTTGAGGACTAAAATGTG
1 CCACCAACTCGTGTGGGCTTTAAAAAGAAAAAACGCCCTGCTCTTTAAGGACTAAAAGGTG
** * * *
1082786 CCATTAACTCGTGTGGGCTTTAAAAAGAAAAAGACGTCTTGCTTTTTAAGGACTAAAAGGTG
1 CCACCAACTCGTGTGGGCTTTAAAAAGAAAAA-ACGCCCTGCTCTTTAAGGACTAAAAGGTG
** *
1082848 CCACCAACTCGCATGAGCTTTAAAAAGAAAAAA
1 CCACCAACTCGTGTGGGCTTTAAAAAGAAAAAA
1082881 GTGTCGTACT
Statistics
Matches: 79, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
60 22 0.28
61 6 0.08
62 51 0.65
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (61 bp):
CCACCAACTCGTGTGGGCTTTAAAAAGAAAAAACGCCCTGCTCTTTAAGGACTAAAAGGTG
Found at i:1082893 original size:62 final size:61
Alignment explanation
Indices: 1082726--1082939 Score: 177
Period size: 62 Copynumber: 3.5 Consensus size: 61
1082716 TGTCGCGACA
* * * * * * * *
1082726 CCACCAACTCGTGTGGGATTTGAAAA-AAAAA-ACGCCCTGCTCTTTGAGGACTAAAATGTG
1 CCACCAACTCGTGTGAGCTTTAAAAAGAAAAAGACGTCGTACT-TTTTAGGACTAAAAGGTG
** * * *
1082786 CCATTAACTCGTGTGGGCTTTAAAAAGAAAAAGACGTCTTGCTTTTTAAGGACTAAAAGGTG
1 CCACCAACTCGTGTGAGCTTTAAAAAGAAAAAGACGTCGTACTTTTT-AGGACTAAAAGGTG
** * *
1082848 CCACCAACTCGCATGAGCTTTAAAAAGAAAAA-AGTGTCGTACTTTTT--GACTAAAAGATG
1 CCACCAACTCGTGTGAGCTTTAAAAAGAAAAAGA-CGTCGTACTTTTTAGGACTAAAAGGTG
* * *
1082907 CCACCTAGCTCGTGTGAGCTTTGAAAAGGAAAA
1 CCACC-AACTCGTGTGAGCTTTAAAAAGAAAAA
1082940 TATGTGGCTC
Statistics
Matches: 127, Mismatches: 22, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
59 16 0.13
60 44 0.35
61 9 0.07
62 58 0.46
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (61 bp):
CCACCAACTCGTGTGAGCTTTAAAAAGAAAAAGACGTCGTACTTTTTAGGACTAAAAGGTG
Found at i:1083058 original size:32 final size:32
Alignment explanation
Indices: 1083017--1083096 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 32
1083007 TGTCACTATA
* * * *
1083017 TCGTGGACTTTAAAAAAAAAGATGCCATTGAG
1 TCGTAGACTTTGAAAAAAAAGATACCACTGAG
* *
1083049 TCGTAGACTTTGAAGAAAGAGATACCACTGAG
1 TCGTAGACTTTGAAAAAAAAGATACCACTGAG
*
1083081 TCATAGACTTTGAAAA
1 TCGTAGACTTTGAAAA
1083097 TGTTGCTTTA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (32 bp):
TCGTAGACTTTGAAAAAAAAGATACCACTGAG
Found at i:1084318 original size:20 final size:20
Alignment explanation
Indices: 1084295--1084333 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1084285 TATCGTTCCC
**
1084295 CTTTTATTTCTTTTTTTTGT
1 CTTTTATTTAATTTTTTTGT
*
1084315 CTTTTTTTTAATTTTTTTG
1 CTTTTATTTAATTTTTTTG
1084334 ATTTTTGTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.08, C:0.08, G:0.05, T:0.79
Consensus pattern (20 bp):
CTTTTATTTAATTTTTTTGT
Found at i:1085826 original size:21 final size:21
Alignment explanation
Indices: 1085783--1085826 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1085773 GATGCATTGG
* **
1085783 TTGGATGAAAGAATATATTTT
1 TTGGATGAAAAAATATAACTT
1085804 TTGGATGAAAAAATATAACTT
1 TTGGATGAAAAAATATAACTT
1085825 TT
1 TT
1085827 ATGACCAAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.02, G:0.16, T:0.41
Consensus pattern (21 bp):
TTGGATGAAAAAATATAACTT
Found at i:1087366 original size:24 final size:24
Alignment explanation
Indices: 1087320--1087369 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1087310 TTTGGTAAGA
*
1087320 TTGATTTTCATTTAACTTGATAAT
1 TTGATTTTCATTTAACTTAATAAT
*
1087344 TTGATTTTTATTTATA-TTAATAAT
1 TTGATTTTCATTTA-ACTTAATAAT
1087368 TT
1 TT
1087370 TGCTTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 22 0.96
25 1 0.04
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (24 bp):
TTGATTTTCATTTAACTTAATAAT
Found at i:1095843 original size:24 final size:24
Alignment explanation
Indices: 1095797--1095846 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1095787 TTTGGTAAGA
*
1095797 TTGATTTTCATTTAACTTGATAAT
1 TTGATTTTCATTTAACTTAATAAT
*
1095821 TTGATTTTTATTTATA-TTAATAAT
1 TTGATTTTCATTTA-ACTTAATAAT
1095845 TT
1 TT
1095847 TGCTTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 22 0.96
25 1 0.04
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (24 bp):
TTGATTTTCATTTAACTTAATAAT
Found at i:1100006 original size:12 final size:12
Alignment explanation
Indices: 1099989--1100015 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1099979 ACAAAAATCT
1099989 ATGTATCGATAC
1 ATGTATCGATAC
1100001 ATGTATCGATAC
1 ATGTATCGATAC
1100013 ATG
1 ATG
1100016 GAATAATGTA
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:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:1100006 original size:32 final size:32
Alignment explanation
Indices: 1099970--1100134 Score: 124
Period size: 32 Copynumber: 5.2 Consensus size: 32
1099960 AATTCCCAAA
1099970 TGTATCAATACAAAAATCTATGTATCGATACA-
1 TGTATCAATACAAAAAT-TATGTATCGATACAT
* ** * *
1100002 TGTATCGATACATGGAATAATGTATCGATATAT
1 TGTATCAATACA-AAAATTATGTATCGATACAT
* * * ** *
1100035 T-T-TC-TTGGCAGTAGCTT-TGTAGCGATACAT
1 TGTATCAAT-ACA-AAAATTATGTATCGATACAT
*
1100065 TGTATCAATACAAAACTTATGTATCGATACAT
1 TGTATCAATACAAAAATTATGTATCGATACAT
* * *
1100097 TGTATCGATACAACACTTATGTATCGATACAT
1 TGTATCAATACAAAAATTATGTATCGATACAT
1100129 TGTATC
1 TGTATC
1100135 GATAATTGTT
Statistics
Matches: 104, Mismatches: 22, Indels: 14
0.74 0.16 0.10
Matches are distributed among these distances:
30 13 0.12
31 10 0.10
32 76 0.73
33 5 0.05
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (32 bp):
TGTATCAATACAAAAATTATGTATCGATACAT
Found at i:1100102 original size:13 final size:13
Alignment explanation
Indices: 1100084--1100143 Score: 59
Period size: 13 Copynumber: 4.2 Consensus size: 13
1100074 ACAAAACTTA
1100084 TGTATCGATACAT
1 TGTATCGATACAT
1100097 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
1100115 ATGTATCGATACAT
1 -TGTATCGATACAT
1100129 TGTATCGATA-AT
1 TGTATCGATACAT
1100141 TGT
1 TGT
1100144 TGAAATTTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
12 5 0.12
13 19 0.46
14 1 0.02
16 6 0.15
18 1 0.02
19 9 0.22
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1100121 original size:19 final size:19
Alignment explanation
Indices: 1100065--1100127 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
1100055 AGCGATACAT
* *
1100065 TGTATCAATACAAAACTTA
1 TGTATCGATACAACACTTA
1100084 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
1100097 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1100116 TGTATCGATACA
1 TGTATCGATACA
1100128 TTGTATCGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 9 0.25
14 1 0.03
16 5 0.14
18 1 0.03
19 20 0.56
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:1100135 original size:32 final size:32
Alignment explanation
Indices: 1100052--1100138 Score: 147
Period size: 32 Copynumber: 2.7 Consensus size: 32
1100042 GCAGTAGCTT
* *
1100052 TGTAGCGATACATTGTATCAATACAAAACTTA
1 TGTATCGATACATTGTATCGATACAAAACTTA
*
1100084 TGTATCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAAAACTTA
1100116 TGTATCGATACATTGTATCGATA
1 TGTATCGATACATTGTATCGATA
1100139 ATTGTTGAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACAAAACTTA
Found at i:1101127 original size:13 final size:13
Alignment explanation
Indices: 1101109--1101133 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1101099 AAATTGCACA
1101109 GTATCGATACATT
1 GTATCGATACATT
1101122 GTATCGATACAT
1 GTATCGATACAT
1101134 GACCAAATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1101146 original size:20 final size:21
Alignment explanation
Indices: 1101121--1101173 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
1101111 ATCGATACAT
**
1101121 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGAAAAGAA
*
1101141 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAAGAA
1101162 TGTATCGATACA
1 TGTATCGATACA
1101174 GGTCATTGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGAAAAGAA
Found at i:1107638 original size:30 final size:29
Alignment explanation
Indices: 1107604--1107684 Score: 103
Period size: 29 Copynumber: 2.8 Consensus size: 29
1107594 ATTTATCATG
*
1107604 TATTATTAAAATTAAAAATATTAT-TTTATA
1 TATTATTAAAA-TATAAATATTATATTTA-A
1107634 TATTATTAAAATATAAATA-TATATTTAA
1 TATTATTAAAATATAAATATTATATTTAA
*
1107662 TAATATTTAAAATATAAATATTA
1 TATTA-TTAAAATATAAATATTA
1107685 AAAATTATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
28 8 0.17
29 25 0.54
30 13 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
TATTATTAAAATATAAATATTATATTTAA
Found at i:1107671 original size:29 final size:31
Alignment explanation
Indices: 1107604--1107682 Score: 103
Period size: 30 Copynumber: 2.6 Consensus size: 31
1107594 ATTTATCATG
* *
1107604 TATTATTAAAAT-TAAAAATATTATTTTATA
1 TATTATTAAAATATAAATATATTATTTAATA
1107634 TATTATTAAAATATAAATATA-TATTTAATA
1 TATTATTAAAATATAAATATATTATTTAATA
1107664 -A-TATTTAAAATATAAATAT
1 TATTA-TTAAAATATAAATAT
1107683 TAAAAATTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
28 2 0.04
29 16 0.36
30 20 0.44
31 7 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (31 bp):
TATTATTAAAATATAAATATATTATTTAATA
Found at i:1110402 original size:14 final size:14
Alignment explanation
Indices: 1110368--1110421 Score: 53
Period size: 13 Copynumber: 4.1 Consensus size: 14
1110358 TTTTTATAAA
1110368 AAAT-TTTTATATT
1 AAATATTTTATATT
*
1110381 -ATTA-TTTATATT
1 AAATATTTTATATT
*
1110393 AAATATTTTAAATT
1 AAATATTTTATATT
*
1110407 AAA-ATATTATATT
1 AAATATTTTATATT
1110420 AA
1 AA
1110422 CAATTTATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
12 10 0.30
13 13 0.39
14 10 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
AAATATTTTATATT
Found at i:1110429 original size:13 final size:12
Alignment explanation
Indices: 1110373--1110429 Score: 51
Period size: 13 Copynumber: 4.4 Consensus size: 12
1110363 ATAAAAAATT
**
1110373 TTTATATTATTA
1 TTTATATTAAAA
1110385 TTTATATTAAATA
1 TTTATATTAAA-A
*
1110398 TTTTAAATTAAAA
1 -TTTATATTAAAA
1110411 TATTATATTAACAA
1 T-TTATATTAA-AA
1110425 TTTAT
1 TTTAT
1110430 TAATAGTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
12 10 0.27
13 14 0.38
14 13 0.35
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (12 bp):
TTTATATTAAAA
Found at i:1110455 original size:28 final size:27
Alignment explanation
Indices: 1110386--1110459 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 27
1110376 ATATTATTAT
*
1110386 TTATATTAAATATTTTAAATTAAAATA
1 TTATATTAAATATTTTTAATTAAAATA
*
1110413 TTATATTAACA-ATTTATTAA-TAGTAATA
1 TTATATTAA-ATATTT-TTAATTA-AAATA
1110441 TTATATTAAATATTTTTAA
1 TTATATTAAATATTTTTAA
1110460 ATCACAAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
27 20 0.49
28 21 0.51
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (27 bp):
TTATATTAAATATTTTTAATTAAAATA
Found at i:1110891 original size:116 final size:115
Alignment explanation
Indices: 1110682--1110910 Score: 379
Period size: 116 Copynumber: 2.0 Consensus size: 115
1110672 TGTGCAAAGG
* **
1110682 ACTGGCGGCTCTGGACAGATTTTCCGACCTTGTAGTACAATGTCTGTGACCAGGAACCGAGGACC
1 ACTGGCGGCTCTGGACAGATTTTCCGACCTTGTACTACAATGTCTGCCACCAGGAACCGAGGACC
1110747 AGTGGCTACGAAGCCGCGAATGTTTGACACCGACGTGGCAACGTTAAATT
66 AGTGGCTACGAAGCCGCGAATGTTTGACACCGACGTGGCAACGTTAAATT
* *
1110797 ACTGGACGGCTCTGGACTGATTTTCCGACCTTGTACTACAATGTCTGCCACCAGGAACCTAGGAC
1 ACTGG-CGGCTCTGGACAGATTTTCCGACCTTGTACTACAATGTCTGCCACCAGGAACCGAGGAC
*
1110862 CAGTGGCTGCGAAGCCGC-AAGTGTTTGACACCGACGTGGCAACGTTAAA
65 CAGTGGCTACGAAGCCGCGAA-TGTTTGACACCGACGTGGCAACGTTAAA
1110911 ATATGCCACA
Statistics
Matches: 106, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
115 7 0.07
116 99 0.93
ACGTcount: A:0.25, C:0.26, G:0.27, T:0.22
Consensus pattern (115 bp):
ACTGGCGGCTCTGGACAGATTTTCCGACCTTGTACTACAATGTCTGCCACCAGGAACCGAGGACC
AGTGGCTACGAAGCCGCGAATGTTTGACACCGACGTGGCAACGTTAAATT
Found at i:1111236 original size:15 final size:16
Alignment explanation
Indices: 1111218--1111258 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
1111208 AGTAATTGAG
1111218 TTTAAATT-ATTTAAT
1 TTTAAATTAATTTAAT
1111233 TTT-AATTAATTTAAT
1 TTTAAATTAATTTAAT
*
1111248 ATTAAAATTAA
1 -TTTAAATTAA
1111259 AATTATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 4 0.18
15 10 0.45
16 2 0.09
17 6 0.27
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTTAAATTAATTTAAT
Found at i:1111852 original size:37 final size:37
Alignment explanation
Indices: 1111793--1111897 Score: 165
Period size: 37 Copynumber: 2.8 Consensus size: 37
1111783 TTTATTTACA
1111793 ATATTATATGATTATATAAATTTTAATATATTAATAATTT
1 ATATTATAT--TT-TATAAATTTTAATATATTAATAATTT
*
1111833 ATATTATATTTTATAAATTTTAATATATTAATAGTTT
1 ATATTATATTTTATAAATTTTAATATATTAATAATTT
*
1111870 ATATTATATTTTATACATTTTAATATAT
1 ATATTATATTTTATAAATTTTAATATAT
1111898 CTTTATATTT
Statistics
Matches: 63, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
37 52 0.83
38 2 0.03
40 9 0.14
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (37 bp):
ATATTATATTTTATAAATTTTAATATATTAATAATTT
Found at i:1112845 original size:29 final size:29
Alignment explanation
Indices: 1112812--1112908 Score: 78
Period size: 28 Copynumber: 3.4 Consensus size: 29
1112802 TTAGTTTATC
1112812 TATATTTTGATATATTTGTATATTCGTAT
1 TATATTTTGATATATTTGTATATTCGTAT
* *
1112841 TATA--TTCATATTATTTTTCATATTGCGTAT
1 TATATTTTGATA-TATTTGT-ATATT-CGTAT
* *
1112871 TA-ATTTTTATATATATTG-A-GTTCGTAT
1 TATATTTTGATATAT-TTGTATATTCGTAT
*
1112898 TATATCTTGAT
1 TATATTTTGAT
1112909 CATCTTATAT
Statistics
Matches: 54, Mismatches: 7, Indels: 15
0.71 0.09 0.20
Matches are distributed among these distances:
27 12 0.22
28 14 0.26
29 11 0.20
30 10 0.19
31 7 0.13
ACGTcount: A:0.28, C:0.06, G:0.09, T:0.57
Consensus pattern (29 bp):
TATATTTTGATATATTTGTATATTCGTAT
Found at i:1113307 original size:27 final size:28
Alignment explanation
Indices: 1113264--1113322 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 28
1113254 TTTTCATATT
*
1113264 ATTTTTTCAAAAGTTTTAAATAT-TATA
1 ATTTTTTCAAAAGTTTTAAATATAAATA
* *
1113291 ATTTTTT-ATAAATTTTTACATATAAATA
1 ATTTTTTCA-AAAGTTTTAAATATAAATA
1113319 ATTT
1 ATTT
1113323 ATTTTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 1 0.04
27 19 0.70
28 7 0.26
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (28 bp):
ATTTTTTCAAAAGTTTTAAATATAAATA
Found at i:1113540 original size:18 final size:19
Alignment explanation
Indices: 1113517--1113552 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1113507 TGTATTCGTA
1113517 TCATGTT-TATATTATTTT
1 TCATGTTGTATATTATTTT
*
1113535 TCATGTTGTATTTTATTT
1 TCATGTTGTATATTATTT
1113553 ATATATATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.19, C:0.06, G:0.08, T:0.67
Consensus pattern (19 bp):
TCATGTTGTATATTATTTT
Found at i:1113863 original size:23 final size:23
Alignment explanation
Indices: 1113828--1113871 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1113818 TTATATTCAT
* * *
1113828 ATTATTTTTTATGTTGTGTTTTA
1 ATTATTCTCTATGTTATGTTTTA
1113851 ATTATTCTCTATGTTATGTTT
1 ATTATTCTCTATGTTATGTTT
1113872 ATTTTGTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.18, C:0.05, G:0.11, T:0.66
Consensus pattern (23 bp):
ATTATTCTCTATGTTATGTTTTA
Found at i:1114131 original size:32 final size:32
Alignment explanation
Indices: 1114094--1114165 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 32
1114084 GTGTTATTTT
*
1114094 TATTTATACA-AAATATTTTAAAT-TTATATAAA
1 TATTTATACATAAATA-ATT-AATGTTATATAAA
* *
1114126 TATTTATACATTAATAATTCATGTTATATAAA
1 TATTTATACATAAATAATTAATGTTATATAAA
1114158 TATTTATA
1 TATTTATA
1114166 TATTCGTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 2 0.06
32 29 0.83
33 4 0.11
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.49
Consensus pattern (32 bp):
TATTTATACATAAATAATTAATGTTATATAAA
Found at i:1114295 original size:15 final size:15
Alignment explanation
Indices: 1114272--1114380 Score: 63
Period size: 13 Copynumber: 7.4 Consensus size: 15
1114262 TATATTCTAC
*
1114272 TTAATTTTTATATAA
1 TTAAATTTTATATAA
*
1114287 TTAAATTTTA-AT-T
1 TTAAATTTTATATAA
1114300 TTAAATTTGT-T-T-A
1 TTAAATTT-TATATAA
1114313 TTAAATATTT-TA-AA
1 TTAAAT-TTTATATAA
*
1114327 ATAAATTTTAT-TAA
1 TTAAATTTTATATAA
*
1114341 TTATAATTTTATTTAA
1 TTA-AATTTTATATAA
*
1114357 TTATAAATTTTATAAATA
1 -T-TAAATTTTATATA-A
1114375 TTAAAT
1 TTAAAT
1114381 CTTCCAAACA
Statistics
Matches: 75, Mismatches: 7, Indels: 23
0.71 0.07 0.22
Matches are distributed among these distances:
13 20 0.27
14 16 0.21
15 17 0.23
16 8 0.11
17 11 0.15
18 3 0.04
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (15 bp):
TTAAATTTTATATAA
Found at i:1114349 original size:27 final size:27
Alignment explanation
Indices: 1114277--1114351 Score: 66
Period size: 27 Copynumber: 2.7 Consensus size: 27
1114267 TCTACTTAAT
**
1114277 TTTTATATAATTAAATTTTAATTTTAAA
1 TTTTAT-TAATTAAATTTTAATAATAAA
1114305 TTTGT-TT-ATTAAATATTTTAA-AATAAA
1 TTT-TATTAATT-AA-ATTTTAATAATAAA
1114332 TTTTATTAATTATAATTTTA
1 TTTTATTAATTA-AATTTTA
1114352 TTTAATTATA
Statistics
Matches: 39, Mismatches: 2, Indels: 13
0.72 0.04 0.24
Matches are distributed among these distances:
26 4 0.10
27 19 0.49
28 15 0.38
29 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (27 bp):
TTTTATTAATTAAATTTTAATAATAAA
Found at i:1116554 original size:3 final size:3
Alignment explanation
Indices: 1116548--1116578 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1116538 AATAATTTTA
*
1116548 TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1116579 TGTAATCTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1117092 original size:13 final size:14
Alignment explanation
Indices: 1117063--1117096 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
1117053 TTTTAAAAAT
1117063 AATTATAAATATTAA
1 AATT-TAAATATTAA
1117078 AATTTAAAT-TTAA
1 AATTTAAATATTAA
1117091 AATTTA
1 AATTTA
1117097 TTAAAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.53
14 5 0.26
15 4 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AATTTAAATATTAA
Found at i:1119700 original size:18 final size:18
Alignment explanation
Indices: 1119670--1119710 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
1119660 TATATTTTGG
1119670 AATATATTTAAAAATAAA
1 AATATATTTAAAAATAAA
1119688 AATAT-TTTAAAAAT-AA
1 AATATATTTAAAAATAAA
1119704 AATATAT
1 AATATAT
1119711 AATAATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.32
17 10 0.45
18 5 0.23
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AATATATTTAAAAATAAA
Found at i:1120842 original size:18 final size:18
Alignment explanation
Indices: 1120819--1120859 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1120809 AGCTTAATAT
*
1120819 ATTTTTTAAATAAACTTA
1 ATTTTTTAAATAAACTCA
**
1120837 ATTTTTTATTTAAACTCA
1 ATTTTTTAAATAAACTCA
1120855 ATTTT
1 ATTTT
1120860 CAAGTAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTTTTAAATAAACTCA
Found at i:1121208 original size:2 final size:2
Alignment explanation
Indices: 1121201--1121227 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1121191 TTTTTGCGTT
1121201 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1121228 TTCATAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1122913 original size:13 final size:13
Alignment explanation
Indices: 1122889--1122928 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
1122879 ACCTTTTTTA
1122889 AATATAATTAATAT
1 AATAT-ATTAATAT
1122903 AATATATTAATAT
1 AATATATTAATAT
* *
1122916 ATTATATTTATAT
1 AATATATTAATAT
1122929 TTAAAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 19 0.79
14 5 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AATATATTAATAT
Found at i:1123417 original size:27 final size:25
Alignment explanation
Indices: 1123387--1123444 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
1123377 TTGTAGATTT
1123387 ATATTTTTATTAAAAATATTTAAAAAA
1 ATATTTTTA-TAAAAATATTT-AAAAA
** *
1123414 ATATTTTTATATTAATATTTATAAA
1 ATATTTTTATAAAAATATTTAAAAA
1123439 ATATTT
1 ATATTT
1123445 AATTAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 10 0.36
26 9 0.32
27 9 0.32
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
ATATTTTTATAAAAATATTTAAAAA
Found at i:1123420 original size:26 final size:25
Alignment explanation
Indices: 1123391--1123451 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
1123381 AGATTTATAT
1123391 TTTTATTAAAAATATTTAAAAAAATA
1 TTTTATTAAAAATATTT-AAAAAATA
** *
1123417 TTTT-TATATTAATATTTATAAAATA
1 TTTTAT-TAAAAATATTTAAAAAATA
*
1123442 TTTAATTAAA
1 TTTTATTAAA
1123452 TTTAAAATAA
Statistics
Matches: 27, Mismatches: 6, Indels: 5
0.71 0.16 0.13
Matches are distributed among these distances:
25 13 0.48
26 14 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TTTTATTAAAAATATTTAAAAAATA
Found at i:1123496 original size:17 final size:17
Alignment explanation
Indices: 1123474--1123533 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 17
1123464 TTATTTTTTA
1123474 TAAATTAAATAATAATT
1 TAAATTAAATAATAATT
1123491 TAAATTAAATTAAAATAATT
1 TAAATTAAA-T--AATAATT
1123511 TAAA-TAAA-AATTATATT
1 TAAATTAAATAA-TA-ATT
1123528 TAAATT
1 TAAATT
1123534 TAATTCACTT
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
15 2 0.05
16 2 0.05
17 16 0.43
18 2 0.05
19 4 0.11
20 11 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATTAAATAATAATT
Found at i:1123509 original size:20 final size:22
Alignment explanation
Indices: 1123474--1123515 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
1123464 TTATTTTTTA
1123474 TAAATTAAATAATAATTTAAAT
1 TAAATTAAATAATAATTTAAAT
1123496 TAAATT-AA-AATAATTTAAAT
1 TAAATTAAATAATAATTTAAAT
1123516 AAAAATTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 12 0.60
21 2 0.10
22 6 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATTAAATAATAATTTAAAT
Found at i:1123515 original size:15 final size:17
Alignment explanation
Indices: 1123495--1123533 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
1123485 ATAATTTAAA
1123495 TTAAATTAAAA-TA-AT
1 TTAAATTAAAATTATAT
*
1123510 TTAAATAAAAATTATAT
1 TTAAATTAAAATTATAT
1123527 TTAAATT
1 TTAAATT
1123534 TAATTCACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 10 0.50
16 2 0.10
17 8 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAATTAAAATTATAT
Found at i:1125931 original size:42 final size:40
Alignment explanation
Indices: 1125853--1125931 Score: 113
Period size: 42 Copynumber: 1.9 Consensus size: 40
1125843 ATTTCTCAGG
**
1125853 AAAAAAAAAAAAAAAAGGAACATTAGAGATGGCTGTTGAA
1 AAAAAAAAAAAAAAAAGGAACATTAGAGATACCTGTTGAA
*
1125893 AAAAAAAAGAAAAAAAGAGGAACATTAGAGCTACCTGTT
1 AAAAAAAA-AAAAAAA-AGGAACATTAGAGATACCTGTT
1125932 TTCCACTAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 8 0.24
41 7 0.21
42 19 0.56
ACGTcount: A:0.58, C:0.08, G:0.19, T:0.15
Consensus pattern (40 bp):
AAAAAAAAAAAAAAAAGGAACATTAGAGATACCTGTTGAA
Found at i:1126512 original size:2 final size:2
Alignment explanation
Indices: 1126505--1126539 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1126495 AACATATGTG
1126505 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1126540 GTACACACAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1131167 original size:22 final size:22
Alignment explanation
Indices: 1131135--1131176 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1131125 AATTATTATT
*
1131135 AAATAATTTAAATTATAAAATC
1 AAATAAATTAAATTATAAAATC
*
1131157 AAATAAATTAAATTTTAAAA
1 AAATAAATTAAATTATAAAA
1131177 ATTAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
AAATAAATTAAATTATAAAATC
Found at i:1131200 original size:14 final size:15
Alignment explanation
Indices: 1131161--1131191 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1131151 AAAATCAAAT
1131161 AAATT-AAATTTTAA
1 AAATTAAAATTTTAA
1131175 AAATTAAAATTTTAA
1 AAATTAAAATTTTAA
1131190 AA
1 AA
1131192 TAATAATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAATTAAAATTTTAA
Found at i:1132019 original size:20 final size:20
Alignment explanation
Indices: 1131978--1132020 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
1131968 AAAAAAGAAA
1131978 AAAAAATTTTATTTTTAAATT
1 AAAAAATTTTATTTTT-AATT
1131999 AAAAAATTATTATTTTT-ATT
1 AAAAAATT-TTATTTTTAATT
1132019 AA
1 AA
1132021 TACAAACAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AAAAAATTTTATTTTTAATT
Found at i:1133136 original size:28 final size:28
Alignment explanation
Indices: 1133091--1133149 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
1133081 TTATTTATTG
*
1133091 TATTTATATCATATTTA-TATAATAATTA
1 TATTTATATCATAGTTATTA-AATAATTA
*
1133119 TATTTATATTCA-AGTTATTAAATATTTA
1 TATTTATA-TCATAGTTATTAAATAATTA
1133147 TAT
1 TAT
1133150 AAAATTTAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 22 0.81
29 5 0.19
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (28 bp):
TATTTATATCATAGTTATTAAATAATTA
Found at i:1133229 original size:18 final size:19
Alignment explanation
Indices: 1133195--1133230 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1133185 TTGTGACATA
*
1133195 TTTATTTATTTATGTCATG
1 TTTATTTATTTACGTCATG
1133214 TTTATTT-TTTACGTCAT
1 TTTATTTATTTACGTCAT
1133231 ATCATGTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.19, C:0.08, G:0.08, T:0.64
Consensus pattern (19 bp):
TTTATTTATTTACGTCATG
Found at i:1133835 original size:26 final size:26
Alignment explanation
Indices: 1133806--1133855 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1133796 TTTATTTGTT
*
1133806 ATTTGC-TTTCTAATTATTATGTATAA
1 ATTTGCATTTCT-ATGATTATGTATAA
*
1133832 ATTTTCATTTCTATGATTATGTAT
1 ATTTGCATTTCTATGATTATGTAT
1133856 TTATTTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (26 bp):
ATTTGCATTTCTATGATTATGTATAA
Found at i:1133861 original size:26 final size:26
Alignment explanation
Indices: 1133804--1133861 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
1133794 ATTTTATTTG
*
1133804 TTATTTGCTTTCTAATTATTATGTAT
1 TTATTTGCTTTCTAATGATTATGTAT
** *
1133830 AAATTTTCATTTCT-ATGATTATGTAT
1 TTATTTGC-TTTCTAATGATTATGTAT
1133856 TTATTT
1 TTATTT
1133862 ATAATAATAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
26 20 0.80
27 5 0.20
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.60
Consensus pattern (26 bp):
TTATTTGCTTTCTAATGATTATGTAT
Found at i:1135267 original size:26 final size:26
Alignment explanation
Indices: 1135225--1135274 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 26
1135215 ATTTTATAAA
1135225 AATATTAATTAATAAT-AATTTTACT
1 AATATTAATTAATAATAAATTTTACT
1135250 AATATTATATT-ATGAATAAATTTTA
1 AATATTA-ATTAAT-AATAAATTTTA
1135275 TTTTATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 9 0.41
26 6 0.27
27 7 0.32
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (26 bp):
AATATTAATTAATAATAAATTTTACT
Found at i:1137077 original size:18 final size:18
Alignment explanation
Indices: 1137054--1137110 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
1137044 AATCTAAAAA
* * *
1137054 AAAAATTTATAAAAATTT
1 AAAAATTCAAAAAAATAT
1137072 AAAAATTCAAAAAAATAT
1 AAAAATTCAAAAAAATAT
*
1137090 -AAAATT-AGAAAAAAAAT
1 AAAAATTCA-AAAAAATAT
1137107 AAAA
1 AAAA
1137111 GTATAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 1 0.03
17 14 0.42
18 18 0.55
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (18 bp):
AAAAATTCAAAAAAATAT
Found at i:1137093 original size:17 final size:17
Alignment explanation
Indices: 1137080--1137120 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1137070 TTAAAAATTC
1137080 AAAAAAATATAAAATTAG
1 AAAAAAA-ATAAAATTAG
* *
1137098 AAAAAAAATAAAAGTAT
1 AAAAAAAATAAAATTAG
1137115 AAAAAA
1 AAAAAA
1137121 TTCAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (17 bp):
AAAAAAAATAAAATTAG
Found at i:1137120 original size:19 final size:17
Alignment explanation
Indices: 1137073--1137120 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
1137063 TAAAAATTTA
* *
1137073 AAAATTCAAAAAAATAT
1 AAAATTAAAAAAAAAAT
*
1137090 AAAATTAGAAAAAAAAT
1 AAAATTAAAAAAAAAAT
*
1137107 AAAAGTATAAAAAA
1 AAAATTA-AAAAAA
1137121 TTCAAAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 20 0.80
18 5 0.20
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.19
Consensus pattern (17 bp):
AAAATTAAAAAAAAAAT
Found at i:1137155 original size:82 final size:83
Alignment explanation
Indices: 1137054--1137230 Score: 195
Period size: 82 Copynumber: 2.2 Consensus size: 83
1137044 AATCTAAAAA
*
1137054 AAAAATTTATAAAAATTTAAAAATTCA-A-AAAAATATAAAATTAGAAAAAAAATAAAAGTATAA
1 AAAAATTTATAAAAATTTAAAAATACACATAAAAATA-AAAA-TAGAAAAAAAATAAAAGTATAA
1137117 AAAATTCAAAAAATTATTTG
64 AAAATTCAAAAAATTATTTG
** ** * * *
1137137 AAAAA-TTATAAATTTTTAAAAATACACATAAAAATAAAAATATCAAAAAATTAAAATTTTAAAA
1 AAAAATTTATAAAAATTTAAAAATACACATAAAAATAAAAATAGAAAAAAAATAAAAGTATAAAA
* *
1137201 AATTGAAAATA-TA-TT-
66 AATTCAAAAAATTATTTG
*
1137216 AAAAATTTGTAAAAA
1 AAAAATTTATAAAAA
1137231 AGAAACTTAG
Statistics
Matches: 78, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
79 5 0.06
80 8 0.10
81 2 0.03
82 46 0.59
83 10 0.13
84 7 0.09
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (83 bp):
AAAAATTTATAAAAATTTAAAAATACACATAAAAATAAAAATAGAAAAAAAATAAAAGTATAAAA
AATTCAAAAAATTATTTG
Found at i:1137191 original size:17 final size:17
Alignment explanation
Indices: 1137152--1137212 Score: 54
Period size: 16 Copynumber: 3.6 Consensus size: 17
1137142 TTATAAATTT
1137152 TTAAAAATA-CACATAAAA
1 TTAAAAATATCA-A-AAAA
*
1137170 ATAAAAATATCAAAAAA
1 TTAAAAATATCAAAAAA
* *
1137187 TT-AAAATTTTAAAAAA
1 TTAAAAATATCAAAAAA
*
1137203 TTGAAAATAT
1 TTAAAAATAT
1137213 ATTAAAAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
16 14 0.39
17 11 0.31
18 9 0.25
19 2 0.06
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.28
Consensus pattern (17 bp):
TTAAAAATATCAAAAAA
Found at i:1137222 original size:18 final size:16
Alignment explanation
Indices: 1137166--1137220 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
1137156 AAATACACAT
* * *
1137166 AAAAATAAAAATATCA
1 AAAAATTAAAATTTTA
1137182 AAAAATTAAAATTTTA
1 AAAAATTAAAATTTTA
1137198 AAAAATTGAAAATATATTA
1 AAAAATT-AAAAT-T-TTA
1137217 AAAA
1 AAAA
1137221 TTTGTAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
16 20 0.61
17 5 0.15
18 1 0.03
19 7 0.21
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (16 bp):
AAAAATTAAAATTTTA
Found at i:1141523 original size:2 final size:2
Alignment explanation
Indices: 1141498--1141537 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
1141488 CCATAAATCA
* * *
1141498 AG AG AG AA AG AG AA AG AG AA AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1141538 GTCTTTGAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.57, C:0.00, G:0.42, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1141535 original size:12 final size:12
Alignment explanation
Indices: 1141498--1141537 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
1141488 CCATAAATCA
1141498 AGAGAGAAAGAG
1 AGAGAGAAAGAG
*
1141510 AAAGAGAAAGAG
1 AGAGAGAAAGAG
*
1141522 AGAGAGAGAGAG
1 AGAGAGAAAGAG
1141534 AGAG
1 AGAG
1141538 GTCTTTGAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.57, C:0.00, G:0.42, T:0.00
Consensus pattern (12 bp):
AGAGAGAAAGAG
Found at i:1141771 original size:6 final size:6
Alignment explanation
Indices: 1141760--1141809 Score: 57
Period size: 6 Copynumber: 8.3 Consensus size: 6
1141750 AGAATAATTT
** *
1141760 TAAATA TAAATA TAAATA TTTA-A TAAATA TAAAAA TAAATA TAATATA
1 TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA TAA-ATA
1141808 TA
1 TA
1141810 TTAATTTATA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
5 3 0.08
6 28 0.78
7 5 0.14
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
TAAATA
Found at i:1141805 original size:17 final size:18
Alignment explanation
Indices: 1141760--1141807 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
1141750 AGAATAATTT
*
1141760 TAAATATAAATATAAATAT
1 TAAATAT-AATATAAATAA
*
1141779 TTAATA-AATATAAA-AA
1 TAAATATAATATAAATAA
1141795 TAAATATAATATA
1 TAAATATAATATA
1141808 TATTAATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
16 6 0.24
17 14 0.56
19 5 0.20
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAATATAATATAAATAA
Found at i:1141969 original size:18 final size:19
Alignment explanation
Indices: 1141930--1141988 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
1141920 AATAAAAATT
* *
1141930 TATTTAAAATTAATTATAAA
1 TATTTAATA-TAATTTTAAA
*
1141950 TA-TTAATATAATTTTTAA
1 TATTTAATATAATTTTAAA
*
1141968 TATTTAATATTATTTTAAA
1 TATTTAATATAATTTTAAA
1141987 TA
1 TA
1141989 ATATTTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
18 10 0.30
19 21 0.64
20 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TATTTAATATAATTTTAAA
Found at i:1141989 original size:29 final size:30
Alignment explanation
Indices: 1141930--1142008 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 30
1141920 AATAAAAATT
* *
1141930 TATTTAAAA-TTAATTATAAATATTAATATAA
1 TATTTAAAATTTAA-TAT-TATTTTAATATAA
* *
1141961 TTTTTAATATTTAATATTATTTTAA-ATAA
1 TATTTAAAATTTAATATTATTTTAATATAA
*
1141990 TATTTAAAATTTTATATTA
1 TATTTAAAATTTAATATTA
1142009 ATATGATATA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
29 20 0.50
30 6 0.15
31 10 0.25
32 4 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (30 bp):
TATTTAAAATTTAATATTATTTTAATATAA
Found at i:1143099 original size:32 final size:31
Alignment explanation
Indices: 1143041--1143100 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 31
1143031 TTCGGATTTA
*
1143041 TTTAATTTTATATTAAATTATTTTGTTGTAT
1 TTTAATTTTATATTAAATTATCTTGTTGTAT
* * *
1143072 TTTAATTTTGTGATTAATTTGTCTTGTTG
1 TTTAATTTTAT-ATTAAATTATCTTGTTG
1143101 AGTAATTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 10 0.42
32 14 0.58
ACGTcount: A:0.23, C:0.02, G:0.12, T:0.63
Consensus pattern (31 bp):
TTTAATTTTATATTAAATTATCTTGTTGTAT
Found at i:1144907 original size:12 final size:12
Alignment explanation
Indices: 1144869--1144905 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
1144859 AAAAAATAAT
*
1144869 AAATAT-TTTTA
1 AAATATATTTAA
1144880 AAATATATTTAA
1 AAATATATTTAA
1144892 AAAT-TATTTAA
1 AAATATATTTAA
1144903 AAA
1 AAA
1144906 ATCAAATTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 16 0.67
12 8 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
AAATATATTTAA
Found at i:1145295 original size:34 final size:34
Alignment explanation
Indices: 1145250--1145467 Score: 247
Period size: 34 Copynumber: 6.4 Consensus size: 34
1145240 GGTTTGGTAA
* * *
1145250 AAACCATCAAATCACCCATTTATTCAACAATGGC
1 AAACCACCAAATCACCCATTTAGTCAACAATGAC
* * * *
1145284 AAACTACCAAATCTCCCATTTAGTAAACAATGGC
1 AAACCACCAAATCACCCATTTAGTCAACAATGAC
* * *
1145318 AAACCATCAAATTACCCATTTAATCAACAATGAC
1 AAACCACCAAATCACCCATTTAGTCAACAATGAC
* * * *
1145352 AAACTACCAAATCTCCTATTTAGTCAACAATGAT
1 AAACCACCAAATCACCCATTTAGTCAACAATGAC
* * **
1145386 AAACCACCAAATCACCCATTTAATTAACAATGGT
1 AAACCACCAAATCACCCATTTAGTCAACAATGAC
* * *
1145420 AAACTACCAAATCTCCCATTTAGTCAATAATGAC
1 AAACCACCAAATCACCCATTTAGTCAACAATGAC
1145454 AAACCACCAAATCA
1 AAACCACCAAATCA
1145468 ATGGCAAACT
Statistics
Matches: 150, Mismatches: 34, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 150 1.00
ACGTcount: A:0.44, C:0.27, G:0.06, T:0.24
Consensus pattern (34 bp):
AAACCACCAAATCACCCATTTAGTCAACAATGAC
Found at i:1145325 original size:68 final size:68
Alignment explanation
Indices: 1145250--1145467 Score: 321
Period size: 68 Copynumber: 3.2 Consensus size: 68
1145240 GGTTTGGTAA
* *
1145250 AAACCATCAAATCACCCATTTATTCAACAATGGCAAACTACCAAATCTCCCATTTAGTAAACAAT
1 AAACCACCAAATCACCCATTTATTCAACAATGGCAAACTACCAAATCTCCCATTTAGTCAACAAT
*
1145315 GGC
66 GAC
* * * * *
1145318 AAACCATCAAATTACCCATTTAATCAACAATGACAAACTACCAAATCTCCTATTTAGTCAACAAT
1 AAACCACCAAATCACCCATTTATTCAACAATGGCAAACTACCAAATCTCCCATTTAGTCAACAAT
*
1145383 GAT
66 GAC
* *
1145386 AAACCACCAAATCACCCATTTAATT-AACAATGGTAAACTACCAAATCTCCCATTTAGTCAATAA
1 AAACCACCAAATCACCCATTT-ATTCAACAATGGCAAACTACCAAATCTCCCATTTAGTCAACAA
1145450 TGAC
65 TGAC
1145454 AAACCACCAAATCA
1 AAACCACCAAATCA
1145468 ATGGCAAACT
Statistics
Matches: 134, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
68 132 0.99
69 2 0.01
ACGTcount: A:0.44, C:0.27, G:0.06, T:0.24
Consensus pattern (68 bp):
AAACCACCAAATCACCCATTTATTCAACAATGGCAAACTACCAAATCTCCCATTTAGTCAACAAT
GAC
Found at i:1145383 original size:102 final size:102
Alignment explanation
Indices: 1145250--1145467 Score: 276
Period size: 102 Copynumber: 2.1 Consensus size: 102
1145240 GGTTTGGTAA
* * * * * *
1145250 AAACCATCAAATCACCCATTTATTCAACAATGGCAAACTACCAAATCTCCCATTTAGTAAACAAT
1 AAACCACCAAATCACCCATTTAGTCAACAATGACAAACCACCAAATCACCCATTTAATAAACAAT
*
1145315 GGCAAACCATCAAAT-TACCCATTTAATCAACAATGAC
66 GGCAAACCACCAAATCT-CCCATTTAATCAACAATGAC
* * * * *
1145352 AAACTACCAAATCTCCTATTTAGTCAACAATGATAAACCACCAAATCACCCATTTAATTAACAAT
1 AAACCACCAAATCACCCATTTAGTCAACAATGACAAACCACCAAATCACCCATTTAATAAACAAT
* * * *
1145417 GGTAAACTACCAAATCTCCCATTTAGTCAATAATGAC
66 GGCAAACCACCAAATCTCCCATTTAATCAACAATGAC
1145454 AAACCACCAAATCA
1 AAACCACCAAATCA
1145468 ATGGCAAACT
Statistics
Matches: 97, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
102 96 0.99
103 1 0.01
ACGTcount: A:0.44, C:0.27, G:0.06, T:0.24
Consensus pattern (102 bp):
AAACCACCAAATCACCCATTTAGTCAACAATGACAAACCACCAAATCACCCATTTAATAAACAAT
GGCAAACCACCAAATCTCCCATTTAATCAACAATGAC
Found at i:1148591 original size:19 final size:19
Alignment explanation
Indices: 1148564--1148618 Score: 74
Period size: 19 Copynumber: 2.9 Consensus size: 19
1148554 CACAGTACTG
1148564 TATACGTGAATAGTACCCA
1 TATACGTGAATAGTACCCA
* **
1148583 TATATGTGAATAGTACATA
1 TATACGTGAATAGTACCCA
*
1148602 TATACGTAAATAGTACC
1 TATACGTGAATAGTACC
1148619 TTGACAACCA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (19 bp):
TATACGTGAATAGTACCCA
Found at i:1148970 original size:34 final size:34
Alignment explanation
Indices: 1148918--1149201 Score: 336
Period size: 34 Copynumber: 8.4 Consensus size: 34
1148908 AGTTTGGTAA
* * *
1148918 AAACCACCAAATCACCCATTTATTCAACAATGGC
1 AAACTACCAAATCTCCCATTTAGTCAACAATGGC
* *
1148952 AAACTACCAAATCTCCCATTTAGTCAATAATGAC
1 AAACTACCAAATCTCCCATTTAGTCAACAATGGC
* * *
1148986 AAACTACCAAATC-ACCATTTAATCAACAATAGC
1 AAACTACCAAATCTCCCATTTAGTCAACAATGGC
*
1149019 AAACTACCAAATCTCCCATTTAGTCAACAATGGT
1 AAACTACCAAATCTCCCATTTAGTCAACAATGGC
* * *
1149053 AAACCACCAAATCACCCATTTAATCAACAATGGC
1 AAACTACCAAATCTCCCATTTAGTCAACAATGGC
** ** * *
1149087 AAACTACCAAAAATCTTATTTAGTCAATAATGGT
1 AAACTACCAAATCTCCCATTTAGTCAACAATGGC
* * * *
1149121 AAACCACCAAATCACCCATTTAATCAACAATGAC
1 AAACTACCAAATCTCCCATTTAGTCAACAATGGC
* * *
1149155 AAACTACCAAATCTCTCATCTAGTCAATAATGGC
1 AAACTACCAAATCTCCCATTTAGTCAACAATGGC
1149189 AAACTACCAAATC
1 AAACTACCAAATC
1149202 AATGACAAAC
Statistics
Matches: 205, Mismatches: 44, Indels: 2
0.82 0.18 0.01
Matches are distributed among these distances:
33 28 0.14
34 177 0.86
ACGTcount: A:0.43, C:0.27, G:0.06, T:0.23
Consensus pattern (34 bp):
AAACTACCAAATCTCCCATTTAGTCAACAATGGC
Found at i:1149109 original size:68 final size:68
Alignment explanation
Indices: 1148918--1149202 Score: 428
Period size: 68 Copynumber: 4.2 Consensus size: 68
1148908 AGTTTGGTAA
*
1148918 AAACCACCAAATCACCCATTTATTCAACAATGGCAAACTACCAAATCTCCCATTTAGTCAATAAT
1 AAACCACCAAATCACCCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAGTCAATAAT
*
1148983 GAC
66 GGC
* * *
1148986 AAACTACCAAATCA-CCATTTAATCAACAATAGCAAACTACCAAATCTCCCATTTAGTCAACAAT
1 AAACCACCAAATCACCCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAGTCAATAAT
*
1149050 GGT
66 GGC
** **
1149053 AAACCACCAAATCACCCATTTAATCAACAATGGCAAACTACCAAAAATCTTATTTAGTCAATAAT
1 AAACCACCAAATCACCCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAGTCAATAAT
*
1149118 GGT
66 GGC
* * *
1149121 AAACCACCAAATCACCCATTTAATCAACAATGACAAACTACCAAATCTCTCATCTAGTCAATAAT
1 AAACCACCAAATCACCCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAGTCAATAAT
1149186 GGC
66 GGC
*
1149189 AAACTACCAAATCA
1 AAACCACCAAATCA
1149203 ATGACAAACT
Statistics
Matches: 196, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
67 61 0.31
68 135 0.69
ACGTcount: A:0.44, C:0.27, G:0.06, T:0.23
Consensus pattern (68 bp):
AAACCACCAAATCACCCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAGTCAATAAT
GGC
Found at i:1150853 original size:3 final size:3
Alignment explanation
Indices: 1150801--1150837 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1150791 AGTCCTCTAC
1150801 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1150838 GAGACAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1151380 original size:11 final size:11
Alignment explanation
Indices: 1151364--1151530 Score: 88
Period size: 11 Copynumber: 15.7 Consensus size: 11
1151354 TGATCATTCA
1151364 TATATTTATAT
1 TATATTTATAT
1151375 TATATTCGTATAT
1 TATATT--TATAT
1151388 T-T-TTATATAT
1 TATATT-TATAT
*
1151398 TATAATTATAT
1 TATATTTATAT
*
1151409 TA-A--AATAT
1 TATATTTATAT
*
1151417 TATATTAATA-
1 TATATTTATAT
**
1151427 TATAAATA-AT
1 TATATTTATAT
1151437 TA-ATATTATAT
1 TATAT-TTATAT
* * *
1151448 AAAATTT-TAA
1 TATATTTATAT
1151458 TATA-TT-TA-
1 TATATTTATAT
1151466 TATATTTATAT
1 TATATTTATAT
*
1151477 TATATTTATTT
1 TATATTTATAT
*
1151488 TATTTTTATAT
1 TATATTTATAT
1151499 TATATTTATAT
1 TATATTTATAT
*
1151510 CATATAATTATAT
1 --TATATTTATAT
*
1151523 TTTATTTA
1 TATATTTA
1151531 AAATTATTTG
Statistics
Matches: 121, Mismatches: 19, Indels: 32
0.70 0.11 0.19
Matches are distributed among these distances:
8 10 0.08
9 9 0.07
10 22 0.18
11 60 0.50
12 4 0.03
13 16 0.13
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1151428 original size:8 final size:8
Alignment explanation
Indices: 1151417--1151476 Score: 50
Period size: 8 Copynumber: 7.4 Consensus size: 8
1151407 ATTAAAATAT
1151417 TATATTAA
1 TATATTAA
*
1151425 TATATAAA
1 TATATTAA
1151433 TA-ATTAA
1 TATATTAA
1151440 TATTATATAA
1 TA-TAT-TAA
* *
1151450 AATTTTAA
1 TATATTAA
*
1151458 TATATTTA
1 TATATTAA
*
1151466 TATATTTA
1 TATATTAA
1151474 TAT
1 TAT
1151477 TATATTTATT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
7 6 0.14
8 28 0.67
9 4 0.10
10 4 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TATATTAA
Found at i:1151457 original size:18 final size:18
Alignment explanation
Indices: 1151402--1151481 Score: 67
Period size: 18 Copynumber: 4.4 Consensus size: 18
1151392 ATATATTATA
1151402 ATTATATTAAAATATT-AT
1 ATTATA-TAAAATATTAAT
1151420 ATTAATATATAAATAATTAAT
1 ATT-ATATA-AAAT-ATTAAT
*
1151441 ATTATATAAAATTTTAAT
1 ATTATATAAAATATTAAT
* * *
1151459 A-TAT-TTATATATTTAT
1 ATTATATAAAATATTAAT
1151475 ATTATAT
1 ATTATAT
1151482 TTATTTTATT
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
16 9 0.18
17 6 0.12
18 12 0.24
19 11 0.22
20 8 0.16
21 5 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTATATAAAATATTAAT
Found at i:1151483 original size:19 final size:19
Alignment explanation
Indices: 1151363--1151524 Score: 87
Period size: 19 Copynumber: 8.0 Consensus size: 19
1151353 ATGATCATTC
1151363 ATATATTTATATTATATTCGT
1 ATATATTTATATTATATT--T
* *
1151384 ATATTTTTATATATTATAATT
1 ATA-TATT-TATATTATATTT
** *
1151405 ATAT-TAAAATATTATATTA
1 ATATAT-TTATATTATATTT
**
1151424 ATATATAAATAATTAATATTAT
1 ATATATTTAT-ATT-ATATT-T
* *
1151446 ATAAAATTT-TAATATATTT
1 AT-ATATTTATATTATATTT
1151465 ATATATTTATATTATATTT
1 ATATATTTATATTATATTT
*
1151484 ATTTTATTTTTATATTATATTT
1 A---TATATTTATATTATATTT
*
1151506 ATATCATATA-ATTATATTT
1 ATAT-ATTTATATTATATTT
1151525 TATTTAAAAT
Statistics
Matches: 112, Mismatches: 16, Indels: 28
0.72 0.10 0.18
Matches are distributed among these distances:
18 5 0.04
19 43 0.38
20 13 0.12
21 14 0.12
22 24 0.21
23 13 0.12
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (19 bp):
ATATATTTATATTATATTT
Found at i:1153083 original size:21 final size:20
Alignment explanation
Indices: 1153037--1153088 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1153027 ATTATTTATT
1153037 TATATTTTTTAAATAATAAAA
1 TATATTTTTTAAATAA-AAAA
* *
1153058 TAT-TTATTTCAATAAAAAA
1 TATATTTTTTAAATAAAAAA
1153077 TATATTTTTTAA
1 TATATTTTTTAA
1153089 CTACATCTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.27
20 16 0.62
21 3 0.12
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TATATTTTTTAAATAAAAAA
Found at i:1153679 original size:19 final size:18
Alignment explanation
Indices: 1153619--1153680 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 18
1153609 ACTATTCTTA
*
1153619 AAAAAGATCGATCATTTTT
1 AAAAAGATCGAT-TTTTTT
* *
1153638 AAAAAGTATAGTTTTTTTAT
1 AAAAAG-ATCGATTTTTT-T
1153658 AAAAAGATCGATTTGTTTT
1 AAAAAGATCGATTT-TTTT
1153677 AAAA
1 AAAA
1153681 TTTTATATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
19 21 0.60
20 14 0.40
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.40
Consensus pattern (18 bp):
AAAAAGATCGATTTTTTT
Found at i:1156652 original size:20 final size:20
Alignment explanation
Indices: 1156629--1156705 Score: 109
Period size: 20 Copynumber: 3.9 Consensus size: 20
1156619 AAGTACCTAG
1156629 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1156649 ATGTATCGATATATGTATGA
1 ATGTATCGATACATTTTTCA
*
1156669 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
1156689 ATGTATCGATACATTTT
1 ATGTATCGATACATTTT
1156706 GTTTTTTTAC
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1157634 original size:20 final size:21
Alignment explanation
Indices: 1157602--1157640 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1157592 AGCCTTTGAC
*
1157602 CATGCATTTTTTATTATGTTT
1 CATGCATTTTTTAATATGTTT
1157623 CATGCA-TTTTTAATATGT
1 CATGCATTTTTTAATATGT
1157641 CCAGCATCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.23, C:0.10, G:0.10, T:0.56
Consensus pattern (21 bp):
CATGCATTTTTTAATATGTTT
Found at i:1168878 original size:15 final size:15
Alignment explanation
Indices: 1168858--1168887 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1168848 ATGTATAAAT
1168858 ATAAAACATAAAGCA
1 ATAAAACATAAAGCA
*
1168873 ATAAAACATTAAGCA
1 ATAAAACATAAAGCA
1168888 TACATTACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.13, G:0.07, T:0.17
Consensus pattern (15 bp):
ATAAAACATAAAGCA
Found at i:1169586 original size:19 final size:20
Alignment explanation
Indices: 1169545--1169586 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1169535 TATTTTTACT
* *
1169545 AAAAACCTTTTGAAATATTG
1 AAAAACCTTTTGAAACATAG
*
1169565 AAAAGCCTTTT-AAACATAG
1 AAAAACCTTTTGAAACATAG
1169584 AAA
1 AAA
1169587 TGATTGAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.29
Consensus pattern (20 bp):
AAAAACCTTTTGAAACATAG
Found at i:1169866 original size:21 final size:21
Alignment explanation
Indices: 1169841--1169891 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
1169831 AATTAGTTGA
*
1169841 AAATTGATAT-AATTTTTAATT
1 AAATTAATATCAATTTTT-ATT
1169862 AAATTAATATCAATTTTTATT
1 AAATTAATATCAATTTTTATT
*
1169883 AATTTAATA
1 AAATTAATA
1169892 AAAATTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 20 0.74
22 7 0.26
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
AAATTAATATCAATTTTTATT
Found at i:1169897 original size:21 final size:21
Alignment explanation
Indices: 1169851--1169922 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
1169841 AAATTGATAT
**
1169851 AATTTTTAATTAAATTAATATC
1 AATTTTT-ATTAAATTAATAAA
*
1169873 AATTTTTATTAATTTAATAAA
1 AATTTTTATTAAATTAATAAA
* * *
1169894 AATTATTATAAAAATTAAAATAA
1 AATTTTTAT-TAAATTAATA-AA
1169917 AATTTT
1 AATTTT
1169923 AATATCAAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
21 19 0.47
22 14 0.35
23 7 0.17
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (21 bp):
AATTTTTATTAAATTAATAAA
Found at i:1170315 original size:13 final size:13
Alignment explanation
Indices: 1170278--1170320 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1170268 TATTTATAAA
*
1170278 ATTTAAAAATTTAA
1 ATTTAAAAA-TTAT
*
1170292 ATTTAATAATTAT
1 ATTTAAAAATTAT
*
1170305 CTTTAAAAATTAT
1 ATTTAAAAATTAT
1170318 ATT
1 ATT
1170321 ATTATAAATA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 16 0.67
14 8 0.33
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (13 bp):
ATTTAAAAATTAT
Found at i:1171678 original size:20 final size:20
Alignment explanation
Indices: 1171647--1171721 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
1171637 TCATACCCTG
*
1171647 ATGTATCAATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1171667 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
1171687 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
1171707 ATGTATCGATACATT
1 ATGTATCGATACATT
1171722 ATGTCTTTTT
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1171714 original size:40 final size:39
Alignment explanation
Indices: 1171647--1171724 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
1171637 TCATACCCTG
* *
1171647 ATGTATCAATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCAATACATTCTACAATATATCGATACAT-TATGA
* * *
1171687 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCAATACATTCTACAATATATCGATACATTATG
1171725 TCTTTTTACC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.40
Consensus pattern (39 bp):
ATGTATCAATACATTCTACAATATATCGATACATTATGA
Found at i:1172664 original size:24 final size:24
Alignment explanation
Indices: 1172632--1172688 Score: 100
Period size: 22 Copynumber: 2.5 Consensus size: 24
1172622 AGCCTTTGAC
1172632 CATGCATTTTTTTTTATTATGTTT
1 CATGCATTTTTTTTTATTATGTTT
1172656 CATGCA--TTTTTTTATTATGTTT
1 CATGCATTTTTTTTTATTATGTTT
1172678 CATGCATTTTT
1 CATGCATTTTT
1172689 AACATGTCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
22 22 0.71
24 9 0.29
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.63
Consensus pattern (24 bp):
CATGCATTTTTTTTTATTATGTTT
Found at i:1172695 original size:20 final size:21
Alignment explanation
Indices: 1172641--1172695 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
1172631 CCATGCATTT
**
1172641 TTTTTTATTATGTTTCATGCA
1 TTTTTTAACATGTTTCATGCA
**
1172662 TTTTTTTATTATGTTTCATGCA
1 -TTTTTTAACATGTTTCATGCA
1172684 -TTTTTAACATGT
1 TTTTTTAACATGT
1172696 CCAGCATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 10 0.32
22 21 0.68
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.62
Consensus pattern (21 bp):
TTTTTTAACATGTTTCATGCA
Found at i:1179619 original size:20 final size:20
Alignment explanation
Indices: 1179591--1179687 Score: 113
Period size: 20 Copynumber: 4.7 Consensus size: 20
1179581 CTTTTCCCAG
1179591 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* *
1179611 ATATATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
**
1179631 ATGTATCGATACATTCTACCCA
1 ATGTATCGATACATT-T-TTCA
* *
1179653 GATGTGTCGATACATTGTTCA
1 -ATGTATCGATACATTTTTCA
1179674 ATGTATCGATACAT
1 ATGTATCGATACAT
1179688 CTAGTTAAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 6
0.79 0.14 0.08
Matches are distributed among these distances:
20 45 0.71
21 2 0.03
22 2 0.03
23 14 0.22
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1190437 original size:35 final size:35
Alignment explanation
Indices: 1190391--1190460 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
1190381 GAGCTGTTTC
1190391 ATCGTCTCAAACTACTCTAGGGCTATGGAAACAAG
1 ATCGTCTCAAACTACTCTAGGGCTATGGAAACAAG
*
1190426 ATCGTCTCAAACTATTCTAGGGCTATGGAAACAAG
1 ATCGTCTCAAACTACTCTAGGGCTATGGAAACAAG
1190461 TTCATGACAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.24
Consensus pattern (35 bp):
ATCGTCTCAAACTACTCTAGGGCTATGGAAACAAG
Found at i:1191558 original size:98 final size:96
Alignment explanation
Indices: 1191344--1191558 Score: 245
Period size: 98 Copynumber: 2.2 Consensus size: 96
1191334 ATTCTGAAGG
* * *
1191344 GATACTCCAACCCCA-TTTTTAAACTTGTCAAGATTTAAATCTTATTTTCATCTGAATTATCACA
1 GATACTCTAACCCCATTTTTTAAACTTATCAAGATTTAAATCTTATTTTCAACTGAATTATCACA
* * *
1191408 TCGGGGACACCCCAACCCTATTCTTCCAAGA
66 TCAGGGACACCCCAACCCCATTCCTCCAAGA
* * * *
1191439 GAATACTTTAACTCCATTTTTTTAAACTTATCAAGATTTAAATCTTATTTTCAACT-AGATTGTT
1 G-ATACTCTAACCCCA-TTTTTTAAACTTATCAAGATTTAAATCTTATTTTCAACTGA-ATTATC
* ** *
1191503 ATCGTCAGGGACACTTCAACCCCATTCCTCTAAGAA
63 A-CATCAGGGACACCCCAACCCCATTCCTCCAAG-A
1191539 GATACTCTAACCCCATTTTT
1 GATACTCTAACCCCATTTTT
1191559 CAACCAAAAT
Statistics
Matches: 98, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
95 1 0.01
96 11 0.11
97 1 0.01
98 46 0.47
99 37 0.38
100 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.09, T:0.36
Consensus pattern (96 bp):
GATACTCTAACCCCATTTTTTAAACTTATCAAGATTTAAATCTTATTTTCAACTGAATTATCACA
TCAGGGACACCCCAACCCCATTCCTCCAAGA
Found at i:1196463 original size:34 final size:36
Alignment explanation
Indices: 1196420--1196487 Score: 113
Period size: 34 Copynumber: 1.9 Consensus size: 36
1196410 AAGTCATTTG
*
1196420 TCCTCTTTCTTATTTGA-CAT-TATGTTTTAATTAA
1 TCCTCTTTCTTATTTGATAATATATGTTTTAATTAA
1196454 TCCTCTTTCTTATTTGATAATATATGTTTTAATT
1 TCCTCTTTCTTATTTGATAATATATGTTTTAATT
1196488 TAACACACTC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 17 0.55
35 2 0.06
36 12 0.39
ACGTcount: A:0.24, C:0.13, G:0.06, T:0.57
Consensus pattern (36 bp):
TCCTCTTTCTTATTTGATAATATATGTTTTAATTAA
Found at i:1198463 original size:86 final size:86
Alignment explanation
Indices: 1198317--1198489 Score: 328
Period size: 86 Copynumber: 2.0 Consensus size: 86
1198307 TTAATCAGTT
1198317 ACATGAAACTTTTTAATGGCTTAAAACATCAAAGTAACAGGACATCCTGGGTCCAAACCCATAAT
1 ACATGAAACTTTTTAATGGCTTAAAACATCAAAGTAACAGGACATCCTGGGTCCAAACCCATAAT
1198382 ATGGAAGCAAGAATCACATAG
66 ATGGAAGCAAGAATCACATAG
* *
1198403 ACATGAATCTTTTTAATGGCTTAAAACATCAAAGTAACAGGACATCCTGGGTCCAGACCCATAAT
1 ACATGAAACTTTTTAATGGCTTAAAACATCAAAGTAACAGGACATCCTGGGTCCAAACCCATAAT
1198468 ATGGAAGCAAGAATCACATAG
66 ATGGAAGCAAGAATCACATAG
1198489 A
1 A
1198490 AGACGTAAAA
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
86 85 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.23
Consensus pattern (86 bp):
ACATGAAACTTTTTAATGGCTTAAAACATCAAAGTAACAGGACATCCTGGGTCCAAACCCATAAT
ATGGAAGCAAGAATCACATAG
Found at i:1209619 original size:13 final size:13
Alignment explanation
Indices: 1209601--1209626 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1209591 CTGAATCCAA
1209601 ATTGAAGAAAGGG
1 ATTGAAGAAAGGG
1209614 ATTGAAGAAAGGG
1 ATTGAAGAAAGGG
1209627 TTCATATGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.38, T:0.15
Consensus pattern (13 bp):
ATTGAAGAAAGGG
Found at i:1210387 original size:2 final size:2
Alignment explanation
Indices: 1210380--1210410 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1210370 TCAAGTTTCT
*
1210380 TA TA TA TA TT TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1210411 CATTTTCTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:1211471 original size:2 final size:2
Alignment explanation
Indices: 1211466--1211519 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
1211456 ACACACACAC
1211466 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
*
1211508 AT AT AT GT AT AT
1 AT AT AT AT AT AT
1211520 TGTATGTTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1212542 original size:2 final size:2
Alignment explanation
Indices: 1212535--1212565 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1212525 CAAAATAATC
1212535 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1212566 TACGTAAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1213728 original size:22 final size:21
Alignment explanation
Indices: 1213678--1213728 Score: 50
Period size: 22 Copynumber: 2.3 Consensus size: 21
1213668 TCAAATATTA
*
1213678 AATATAAGTAAAAATTATATC
1 AATATAAGTAAAAATTATAAC
*
1213699 TATAATAAGTAAAAATCT-TCAAC
1 AAT-ATAAGTAAAAAT-TAT-AAC
1213722 AATATAA
1 AATATAA
1213729 AACTTCAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
21 2 0.08
22 17 0.71
23 5 0.21
ACGTcount: A:0.57, C:0.08, G:0.04, T:0.31
Consensus pattern (21 bp):
AATATAAGTAAAAATTATAAC
Found at i:1215741 original size:26 final size:25
Alignment explanation
Indices: 1215712--1215763 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
1215702 TGTTATTTCC
* **
1215712 TTTCTTTCTTTTTTTTTCCCTTTCTT
1 TTTCTCTCTTTTACTTTCCC-TTCTT
1215738 TTTCTCTCTTTTACTTTCCCTTCTT
1 TTTCTCTCTTTTACTTTCCCTTCTT
1215763 T
1 T
1215764 CTTTTTTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 6 0.26
26 17 0.74
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (25 bp):
TTTCTCTCTTTTACTTTCCCTTCTT
Found at i:1215778 original size:15 final size:15
Alignment explanation
Indices: 1215715--1215782 Score: 50
Period size: 15 Copynumber: 4.5 Consensus size: 15
1215705 TATTTCCTTT
* *
1215715 CTTTCTTTTTTTTTCC
1 CTTTCTTTTTCTCT-C
1215731 CTTTCTTTTTCTCT-
1 CTTTCTTTTTCTCTC
* * *
1215745 CTTT-TACTTTCCCTT
1 CTTTCT-TTTTCTCTC
*
1215760 CTTTCTTTTTTTCTC
1 CTTTCTTTTTCTCTC
1215775 CTTTCTTT
1 CTTTCTTT
1215783 CCTTATGTTG
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
13 1 0.02
14 10 0.24
15 17 0.41
16 13 0.32
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (15 bp):
CTTTCTTTTTCTCTC
Found at i:1216279 original size:15 final size:15
Alignment explanation
Indices: 1216259--1216288 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1216249 TATCAAACGT
1216259 TCTAAAAAAATAGAC
1 TCTAAAAAAATAGAC
*
1216274 TCTAAAAAAGTAGAC
1 TCTAAAAAAATAGAC
1216289 AAAGTTTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.13, G:0.10, T:0.20
Consensus pattern (15 bp):
TCTAAAAAAATAGAC
Found at i:1217549 original size:65 final size:65
Alignment explanation
Indices: 1217473--1217604 Score: 214
Period size: 65 Copynumber: 2.0 Consensus size: 65
1217463 ATACTATAAA
* *
1217473 TAAAAATTAAAATTTTGTATTATTTTTATTTTAATTGA-TATTTATCATTAAA-TATTTGAATTA
1 TAAAAAATAAAATTTTATATTATTTTTATTTTAATT-ATTATTTATCATTAAACT-TTTGAATTA
1217536 AT
64 AT
1217538 TAAAAAATAAAATTTTATATTATTTTTATTTTAATTATTATTTATCATTAAACTTTTGAATTAAT
1 TAAAAAATAAAATTTTATATTATTTTTATTTTAATTATTATTTATCATTAAACTTTTGAATTAAT
1217603 TA
1 TA
1217605 TAAATTTATC
Statistics
Matches: 63, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
64 1 0.02
65 61 0.97
66 1 0.02
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (65 bp):
TAAAAAATAAAATTTTATATTATTTTTATTTTAATTATTATTTATCATTAAACTTTTGAATTAAT
Found at i:1217570 original size:16 final size:16
Alignment explanation
Indices: 1217549--1217582 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1217539 AAAAAATAAA
1217549 ATTTTATATTATT-TTT
1 ATTTTA-ATTATTATTT
1217565 ATTTTAATTATTATTT
1 ATTTTAATTATTATTT
1217581 AT
1 AT
1217583 CATTAAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
ATTTTAATTATTATTT
Found at i:1217875 original size:28 final size:28
Alignment explanation
Indices: 1217822--1217875 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
1217812 AACTTTTGTT
**
1217822 TTTTATTTTTTAAAGTTTTATGAATTAA
1 TTTTATTTTTTAAAGTTTTAAAAATTAA
*
1217850 TTTTA-TTTTTAAATTTTTTAAAAATT
1 TTTTATTTTTTAAA-GTTTTAAAAATT
1217876 GAGTAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 8 0.36
28 14 0.64
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (28 bp):
TTTTATTTTTTAAAGTTTTAAAAATTAA
Found at i:1218292 original size:11 final size:10
Alignment explanation
Indices: 1218269--1218428 Score: 53
Period size: 9 Copynumber: 16.6 Consensus size: 10
1218259 TTAAATAATT
*
1218269 TATATATTAA
1 TATATATTTA
1218279 TATCATATTTA
1 TAT-ATATTTA
*
1218290 TATAT-TTTT
1 TATATATTTA
1218299 TATATA-TT-
1 TATATATTTA
1218307 T-TATATTTA
1 TATATATTTA
*
1218316 TA-A-ATTTT
1 TATATATTTA
* *
1218324 TATACATTAA
1 TATATATTTA
*
1218334 TA-ATTTTTA
1 TATATATTTA
1218343 TGATATAAATTT-
1 T-ATAT--ATTTA
*
1218355 TA-A-A-ATA
1 TATATATTTA
*
1218362 TATGTATTTA
1 TATATATTTA
1218372 TAT-TATTT-
1 TATATATTTA
1218380 T-TATATTATA
1 TATATATT-TA
*
1218390 TAATTATTTTTA
1 T-A-TATATTTA
1218402 TATCATATTTA
1 TAT-ATATTTA
1218413 TATTATATTTA
1 TA-TATATTTA
1218424 -ATATA
1 TATATA
1218429 ATTAAATAAA
Statistics
Matches: 113, Mismatches: 14, Indels: 47
0.65 0.08 0.27
Matches are distributed among these distances:
6 1 0.01
7 8 0.07
8 14 0.12
9 29 0.26
10 20 0.18
11 28 0.25
12 5 0.04
13 8 0.07
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (10 bp):
TATATATTTA
Done.