Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009344.1 Hibiscus syriacus cultivar Beakdansim tig00113124_pilon, whole genome shotgun sequence
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: 4287485
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 24
Found at i:1999228 original size:27 final size:28
Alignment explanation
Indices: 1999190--1999252 Score: 119
Period size: 28 Copynumber: 2.3 Consensus size: 28
1999180 CTTTATTTTG
1999190 TTCGGGTCGGG-TTTTTTAAGTGTGATA
1 TTCGGGTCGGGTTTTTTTAAGTGTGATA
1999217 TTCGGGTCGGGTTTTTTTAAGTGTGATA
1 TTCGGGTCGGGTTTTTTTAAGTGTGATA
1999245 TTCGGGTC
1 TTCGGGTC
1999253 AGGTCGGGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 11 0.31
28 24 0.69
ACGTcount: A:0.13, C:0.10, G:0.33, T:0.44
Consensus pattern (28 bp):
TTCGGGTCGGGTTTTTTTAAGTGTGATA
Found at i:2005711 original size:21 final size:21
Alignment explanation
Indices: 2005686--2005751 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
2005676 GCGTCTGACC
2005686 CGGCTGCGATACCATCTGAAA
1 CGGCTGCGATACCATCTGAAA
* * *
2005707 TGGCTGC-AGTGCCATCTGATA
1 CGGCTGCGA-TACCATCTGAAA
* * *
2005728 CGACTGCGATACCATTTAAAA
1 CGGCTGCGATACCATCTGAAA
2005749 CGG
1 CGG
2005752 TTGTAGAATG
Statistics
Matches: 33, Mismatches: 10, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
20 1 0.03
21 31 0.94
22 1 0.03
ACGTcount: A:0.27, C:0.26, G:0.24, T:0.23
Consensus pattern (21 bp):
CGGCTGCGATACCATCTGAAA
Found at i:2006383 original size:20 final size:20
Alignment explanation
Indices: 2006347--2006384 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2006337 ATATTCTAAT
*
2006347 TAAATAATGATAATTAAAAG
1 TAAATAATGAAAATTAAAAG
2006367 TAAATAAT-AAAACTTAAA
1 TAAATAATGAAAA-TTAAA
2006385 TACATACCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAATAATGAAAATTAAAAG
Found at i:2008617 original size:229 final size:228
Alignment explanation
Indices: 2008217--2008707 Score: 883
Period size: 229 Copynumber: 2.1 Consensus size: 228
2008207 TATTGTAAAT
* * * *
2008217 TATATATCCTTTTTATAAAAGTGTCCATACTTATTTCATTGTGAAAATATATTTATTATTATCTT
1 TATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATT
2008282 TAGTTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAT
66 TAGTTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAT
*
2008347 TTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAA
131 ATTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAA
2008412 ATTGAAACATAAATTACATAACTTTCAAAAAAG
196 ATTGAAACATAAATTACATAACTTTCAAAAAAG
2008445 TATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATAT
1 TATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATAT
* *
2008510 TTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAA
65 TTAGTTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAA
* *
2008575 TATTTTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATA
130 TATTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAA
*
2008640 AATTGAAACATAAATTACATAACTTTCAAAGAAG
195 AATTGAAACATAAATTACATAACTTTCAAAAAAG
2008674 TATATATCATTTTTATAAAAGTGTCCATACTTAT
1 TATATATCATTTTTATAAAAGTGTCCATACTTAT
2008708 AAAAGTAGGT
Statistics
Matches: 252, Mismatches: 10, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
228 39 0.15
229 213 0.85
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (228 bp):
TATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATT
TAGTTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAT
ATTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAA
ATTGAAACATAAATTACATAACTTTCAAAAAAG
Found at i:2009009 original size:20 final size:19
Alignment explanation
Indices: 2008986--2009032 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
2008976 CGATATACCA
2008986 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
2009006 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
2009026 GGTAAAA
1 GGTAAAA
2009033 CGTTACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:2009120 original size:181 final size:182
Alignment explanation
Indices: 2008774--2009246 Score: 698
Period size: 181 Copynumber: 2.6 Consensus size: 182
2008764 GATCCAAATT
* * * *
2008774 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGAAAAAACCGGTATA-GAAATGAT
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTA-ACAAAATGAT
* * * * * *
2008838 AAAACCGGTCAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTT
65 AAAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTT
* * * *
2008903 CGTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTTA
130 CGTGAATTTAAAAAAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAA
*
2008956 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
* *
2009021 AAACCGGTAAAACGTTACCGGATATATTAAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
** *
2009085 GTGAATTTAAAAAAGAAGCAGTTATAGCGCCTATAATGTGTCGATACTTTAA
131 GTGAATTTAAAAAAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAA
* * *
2009137 AAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
* *
2009202 AAACCGGTAAAATGATACCGGATATATTGAAAGTGTCGATACTTT
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTT
2009247 CGTAAGTACG
Statistics
Matches: 264, Mismatches: 26, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
181 167 0.63
182 97 0.37
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (182 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAAAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAA
Found at i:2009190 original size:20 final size:19
Alignment explanation
Indices: 2009167--2009213 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
2009157 CGATATAACA
2009167 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
2009187 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
2009207 GGTAAAA
1 GGTAAAA
2009214 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:2009215 original size:17 final size:19
Alignment explanation
Indices: 2009176--2009218 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
2009166 AGGTAAAAAT
2009176 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
2009196 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
2009213 ATGATA
1 ATGATA
2009219 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:2011422 original size:21 final size:21
Alignment explanation
Indices: 2011395--2011459 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
2011385 AAGACAATCA
*
2011395 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
* * *
2011416 CGAGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
2011437 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
2011458 AG
1 AG
2011460 GCATAAGGGG
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.38, C:0.14, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:2011535 original size:33 final size:33
Alignment explanation
Indices: 2011493--2011558 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
2011483 AAATAGATGG
*
2011493 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
2011526 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
2011559 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:2013371 original size:19 final size:19
Alignment explanation
Indices: 2013347--2013395 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
2013337 AATGTAGGCT
2013347 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
2013366 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
2013385 TATTTTTGTAT
1 TAATTTTGTAT
2013396 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:2015099 original size:6 final size:6
Alignment explanation
Indices: 2015075--2015166 Score: 60
Period size: 6 Copynumber: 15.3 Consensus size: 6
2015065 AGCGGTCGCA
* * * * * *
2015075 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GACGAT GAAGCT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
** * * * *
2015123 GGCGAT GAAGAT -AATGAC GATGAT GATGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAA-GAT GAAGAT GAAGAT GAAGAT GAAGAT GA
2015167 TGATCCAAAC
Statistics
Matches: 66, Mismatches: 18, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
5 2 0.03
6 63 0.95
7 1 0.02
ACGTcount: A:0.38, C:0.08, G:0.34, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:2015110 original size:3 final size:3
Alignment explanation
Indices: 2015090--2015170 Score: 63
Period size: 3 Copynumber: 27.0 Consensus size: 3
2015080 TGAAGCTGAC
* * * * * ** * *
2015090 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT AAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
2015138 GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
2015171 CCAAACAAGT
Statistics
Matches: 57, Mismatches: 21, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.37, C:0.06, G:0.33, T:0.23
Consensus pattern (3 bp):
GAT
Found at i:2015129 original size:36 final size:37
Alignment explanation
Indices: 2015078--2015157 Score: 117
Period size: 39 Copynumber: 2.1 Consensus size: 37
2015068 GGTCGCAGAA
2015078 GATGAAGCTGACGATGAAG-ATGACGATGATGATGAC
1 GATGAAGCTGACGATGAAGAATGACGATGATGATGAC
* *
2015114 GATGAAGCTGGCGATGAAGATAATGACGATGATGATGAT
1 GATGAAGCTGACGATGAAG--AATGACGATGATGATGAC
2015153 GATGA
1 GATGA
2015158 TGAAGATGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
36 18 0.46
39 21 0.54
ACGTcount: A:0.36, C:0.09, G:0.34, T:0.21
Consensus pattern (37 bp):
GATGAAGCTGACGATGAAGAATGACGATGATGATGAC
Found at i:2015158 original size:12 final size:12
Alignment explanation
Indices: 2015086--2015170 Score: 80
Period size: 12 Copynumber: 7.1 Consensus size: 12
2015076 AAGATGAAGC
*
2015086 TGACGATGAAGA
1 TGACGATGATGA
2015098 TGACGATGATGA
1 TGACGATGATGA
* *
2015110 TGACGATGAAGC
1 TGACGATGATGA
* *
2015122 TGGCGATGAAGA
1 TGACGATGATGA
* * *
2015134 TAATGACGATGA
1 TGACGATGATGA
*
2015146 TGATGATGATGA
1 TGACGATGATGA
*
2015158 TGAAGATGATGA
1 TGACGATGATGA
2015170 T
1 T
2015171 CCAAACAAGT
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 60 1.00
ACGTcount: A:0.36, C:0.07, G:0.33, T:0.24
Consensus pattern (12 bp):
TGACGATGATGA
Found at i:2016953 original size:183 final size:182
Alignment explanation
Indices: 2016643--2017128 Score: 857
Period size: 183 Copynumber: 2.7 Consensus size: 182
2016633 TTCAACATAT
* *
2016643 TATAAATATACCGGTTTTTTGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATCTTGTG
1 TATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTG
* * *
2016708 TCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATTGTTAAAAAGTGTCGACATTT
66 TCGGTACTTTATGTCCAAATTGGAAGAAAAATGTGTCGATACATT-TAAAAAAGTATCGACATTT
2016773 ACACATCGGAACCCATAA-TTATAATGTAATAGATAATTTTGTAATATAACCGG
130 ACACATCGGAACCCA-AATTTATAATGTAATAGATAATTTTGTAATATAACCGG
2016826 TATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTG
1 TATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTG
*
2016891 TCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTATCGACATTT
66 TCGGTACTTTATGTCCAAATTGGAAGAAAAATGTGTCGATAC-ATTTAAAAAAGTATCGACATTT
2016956 ACACATCGGAACCCAAATTTATAATGTAATAGATAATTTTGTAATATAACCGG
130 ACACATCGGAACCCAAATTTATAATGTAATAGATAATTTTGTAATATAACCGG
* *
2017009 TATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTATAATATTGTG
1 TATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTG
2017074 TCGGTACTTTATGTCCAAATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGT
66 TCGGTACTTTATGTCCAAATTGGAAGAAAAATGTGTCGATA-CATTTAAAAAAGT
2017129 GTCGGTAATT
Statistics
Matches: 292, Mismatches: 8, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
182 2 0.01
183 286 0.98
184 4 0.01
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (182 bp):
TATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTG
TCGGTACTTTATGTCCAAATTGGAAGAAAAATGTGTCGATACATTTAAAAAAGTATCGACATTTA
CACATCGGAACCCAAATTTATAATGTAATAGATAATTTTGTAATATAACCGG
Found at i:2019631 original size:25 final size:25
Alignment explanation
Indices: 2019603--2019667 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
2019593 TTATCATTAA
2019603 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
2019628 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
2019653 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
2019668 TCTTTTGAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:2020045 original size:23 final size:23
Alignment explanation
Indices: 2020014--2020073 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
2020004 ATAGGTAAAC
*
2020014 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* * *
2020037 ATATAATGTAATATGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
2020060 ATATAATGTAATAG
1 ATATAATGTAATAG
2020074 ATAGTGGTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.37, C:0.05, G:0.18, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:2020084 original size:23 final size:22
Alignment explanation
Indices: 2020014--2020086 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 22
2020004 ATAGGTAAAC
* *
2020014 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATA-GTAGTGCTT
*
2020037 ATATAATGTAATATGTA-TCGTTT
1 ATATAATGTAATA-GTAGT-GCTT
*
2020060 ATATAATGTAATAGATAGTGGTT
1 ATATAATGTAATAG-TAGTGCTT
2020083 ATAT
1 ATAT
2020087 TGTAAAGTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
22 1 0.02
23 40 0.95
24 1 0.02
ACGTcount: A:0.36, C:0.04, G:0.19, T:0.41
Consensus pattern (22 bp):
ATATAATGTAATAGTAGTGCTT
Found at i:2020535 original size:18 final size:18
Alignment explanation
Indices: 2020514--2020550 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2020504 GTAATTGGAG
2020514 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
2020532 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
2020550 T
1 T
2020551 ATATATTTCG
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:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:2020558 original size:24 final size:24
Alignment explanation
Indices: 2020506--2020552 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2020496 TTTCATATGT
* *
2020506 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
2020530 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
2020553 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:2020851 original size:39 final size:39
Alignment explanation
Indices: 2020808--2020894 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
2020798 TCCGATGCTC
*
2020808 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
* *
2020847 ATCAAAATTCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
2020886 ATCAAAATC
1 ATCAAAATC
2020895 TACAACTTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.48, C:0.20, G:0.14, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:2021345 original size:23 final size:23
Alignment explanation
Indices: 2021314--2021386 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
2021304 ATAGGTAAAC
*
2021314 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
2021337 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
2021360 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
2021383 ATAT
1 ATAT
2021387 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:2021591 original size:30 final size:29
Alignment explanation
Indices: 2021532--2021598 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
2021522 GTTACGATAT
* *
2021532 ATATTATTATTAAATTAAAAATTCTAAATA
1 ATATT-TTATAAAATTAAAAAATCTAAATA
2021562 ATATTTTATAAAATATCAAAAAATC-AAATA
1 ATATTTTATAAAAT-T-AAAAAATCTAAATA
*
2021592 ATTTTTT
1 ATATTTT
2021599 GTGCAAATGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 8 0.25
30 17 0.53
31 7 0.22
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (29 bp):
ATATTTTATAAAATTAAAAAATCTAAATA
Found at i:2029614 original size:24 final size:22
Alignment explanation
Indices: 2029574--2029617 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
2029564 TAAGTATAAT
*
2029574 TTAAAAAAACATAATTAAATGA
1 TTAAAAAAAAATAATTAAATGA
2029596 TTAAAATAAAAATATATTAAAT
1 TTAAAA-AAAAATA-ATTAAAT
2029618 ACATAGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 6 0.32
24 7 0.37
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (22 bp):
TTAAAAAAAAATAATTAAATGA
Found at i:2033556 original size:18 final size:20
Alignment explanation
Indices: 2033535--2033578 Score: 65
Period size: 18 Copynumber: 2.2 Consensus size: 20
2033525 AAATATCTAA
2033535 AATTATAAAAA-AAAT-TAT
1 AATTATAAAAATAAATATAT
2033553 AATTATAAAAATTAAATATAT
1 AATTATAAAAA-TAAATATAT
2033574 AATTA
1 AATTA
2033579 GGAAAATTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 11 0.48
20 4 0.17
21 8 0.35
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AATTATAAAAATAAATATAT
Found at i:2033584 original size:21 final size:20
Alignment explanation
Indices: 2033546--2033586 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
2033536 ATTATAAAAA
*
2033546 AAATTATAATTATAAAAATT
1 AAATTATAATTAGAAAAATT
*
2033566 AAATATATAATTAGGAAAATT
1 AAAT-TATAATTAGAAAAATT
2033587 CCTAATATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.37
Consensus pattern (20 bp):
AAATTATAATTAGAAAAATT
Found at i:2033829 original size:162 final size:162
Alignment explanation
Indices: 2033655--2033987 Score: 623
Period size: 162 Copynumber: 2.1 Consensus size: 162
2033645 AAAATATTAA
*
2033655 AAATAC-ATCAAAAAATTTAAACAAAATATAAATACGAATGTGTCTAATTGTATTGGCAAACGAA
1 AAATACAATCAAAAAATTTAAACAAAATATAAATACGAATGTGTCTAACTGTATTGGCAAACGAA
2033719 CCAAATCAAAGGGTCAAACTACTGAAAGATCACCGACATCTACATATCAGATTCGAGCATCACAA
66 CCAAATCAAAGGGTCAAACTACTGAAAGATCACCGACATCTACATATCAGATTCGAGCATCACAA
2033784 GAAAATTATCTCTAAACGCAAACAAAATATCC
131 GAAAATTATCTCTAAACGCAAACAAAATATCC
2033816 AAATACAATCAAAAAATTTAAACAAAATATAAATACGAATGTGTCTAACTGTATTGGCAAACGAA
1 AAATACAATCAAAAAATTTAAACAAAATATAAATACGAATGTGTCTAACTGTATTGGCAAACGAA
*
2033881 CCAAATCAAAGGGTCAAACTACTGAAAGATCACCGACATCTACATATCATATTCGAGCATCACAA
66 CCAAATCAAAGGGTCAAACTACTGAAAGATCACCGACATCTACATATCAGATTCGAGCATCACAA
*
2033946 GAAAATTATCTCTAAACGCAAACAACATATCC
131 GAAAATTATCTCTAAACGCAAACAAAATATCC
*
2033978 AAGTACAATC
1 AAATACAATC
2033988 TGATGGTCCA
Statistics
Matches: 167, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
161 6 0.04
162 161 0.96
ACGTcount: A:0.47, C:0.20, G:0.11, T:0.22
Consensus pattern (162 bp):
AAATACAATCAAAAAATTTAAACAAAATATAAATACGAATGTGTCTAACTGTATTGGCAAACGAA
CCAAATCAAAGGGTCAAACTACTGAAAGATCACCGACATCTACATATCAGATTCGAGCATCACAA
GAAAATTATCTCTAAACGCAAACAAAATATCC
Found at i:2039315 original size:55 final size:54
Alignment explanation
Indices: 2039195--2039629 Score: 606
Period size: 55 Copynumber: 8.0 Consensus size: 54
2039185 TGCTTCCACG
* * * *
2039195 ATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGAC-CTACAATCTTCATCA
1 ATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCAACAATCTTCAACA
*
2039248 ATCGCGTCTGCCCCCCATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACA
1 ATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTC-AACAATCTTCAACA
* * * *
2039303 ATCGCGTCTGCCCCCTATATGTTCAGAGAGTATAAGAC-CCACAATCTTCATCA
1 ATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCAACAATCTTCAACA
*
2039356 ATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACG
1 ATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTC-AACAATCTTCAACA
* * * *
2039411 ATTGCGTCTGCCCCCTATTTCTTTAGAGAGTATAAGAC-CCACAATCTTCATCA
1 ATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCAACAATCTTCAACA
* * *
2039464 ATCGCGTCTCCCCCCTATTTCTTTAGAGAGTATAAGACTCGAACAATCTTCAACG
1 ATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTC-AACAATCTTCAACA
* * * * *
2039519 ATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACTCAATATTTCTTCAACG
1 ATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCAACA-ATCTTCAACA
2039574 ATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACA
1 ATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTC-AACAATCTTCAACA
2039629 A
1 A
2039630 ATGGGTTCGC
Statistics
Matches: 338, Mismatches: 36, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
53 130 0.38
54 8 0.02
55 197 0.58
56 3 0.01
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (54 bp):
ATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCAACAATCTTCAACA
Found at i:2039389 original size:108 final size:108
Alignment explanation
Indices: 2039195--2039629 Score: 701
Period size: 108 Copynumber: 4.0 Consensus size: 108
2039185 TGCTTCCACG
* *
2039195 ATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCTACAATCTTCATCAATCGCGTCTGCC
1 ATCGCGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCC
*
2039260 CCCCATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACA
66 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACA
*
2039303 ATCGCGTCTGCCCCCTATATGTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCC
1 ATCGCGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCC
*
2039368 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACG
66 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACA
* * * *
2039411 ATTGCGTCTGCCCCCTATTTCTTTAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTCCC
1 ATCGCGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCC
* *
2039476 CCCTATTTCTTTAGAGAGTATAAGACTCGAACAATCTTCAACG
66 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACA
* * * *
2039519 ATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACTCA-ATATTTCTTCAACGATCGCGTCT
1 ATCGCGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCCACA-A--TCTTCATCAATCGCGTCT
2039583 GCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACA
63 GCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACA
2039629 A
1 A
2039630 ATGGGTTCGC
Statistics
Matches: 303, Mismatches: 21, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
107 1 0.00
108 242 0.80
110 60 0.20
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (108 bp):
ATCGCGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCC
CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACA
Found at i:2039512 original size:163 final size:164
Alignment explanation
Indices: 2039195--2039673 Score: 650
Period size: 163 Copynumber: 2.9 Consensus size: 164
2039185 TGCTTCCACG
* * *
2039195 ATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGAC-CTACAATCTTCATCAATCGCGTCTGC
1 ATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACTCAACAATCTTCAACGATCGCGTCTGC
* * * *
2039259 CCCCCATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATATG
66 CCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTCCCCCCTATTTC
* * *
2039324 TTCAGAGAGTATAAGAC-C-CACAATCTTCATCA
131 TTTAGAGAGTATAAGACTCGAACAATCTTCAACA
* * *
2039356 ATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTG
1 ATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACTC-AACAATCTTCAACGATCGCGTCTG
* * *
2039421 CCCCCTATTTCTTTAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTCCCCCCTATTT
65 CCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTCCCCCCTATTT
*
2039484 CTTTAGAGAGTATAAGACTCGAACAATCTTCAACG
130 CTTTAGAGAGTATAAGACTCGAACAATCTTCAACA
* *
2039519 ATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACTCAATATTTCTTCAACGATCGCGTCTG
1 ATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACTCAACA-ATCTTCAACGATCGCGTCTG
* * *
2039584 CCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAAT-GGGT-TCGCTCCCTCT
65 CCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC-AATCGCGTCTC-CCCCCTAT
*
2039647 TTCTTTAGGGAGTAT-AGAACTCGAACA
128 TTCTTTAGAGAGTATAAG-ACTCGAACA
2039674 TCTCTTCACG
Statistics
Matches: 279, Mismatches: 29, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
161 82 0.29
162 6 0.02
163 140 0.50
164 5 0.02
165 43 0.15
166 3 0.01
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (164 bp):
ATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACTCAACAATCTTCAACGATCGCGTCTGC
CCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTCCCCCCTATTTC
TTTAGAGAGTATAAGACTCGAACAATCTTCAACA
Found at i:2039707 original size:51 final size:50
Alignment explanation
Indices: 2039601--2039883 Score: 320
Period size: 51 Copynumber: 5.5 Consensus size: 50
2039591 TTTCTTCAGA
* * *
2039601 GAGTATA-AGACTCGAACAATCTTCAACAAATGGGTTCGCTCCCTCTTTCTTTAGG
1 GAGTATAGA-ACTCGAAC-ATCTTCAAC----GGGTTCGCTCCTTCTTTCTCTAAG
* *
2039656 GAGTATAGAACTCGAACATCTCTTC-ACGGGTTCGCTCCCTCTTTCTCTAGG
1 GAGTATAGAACTCGAACA--TCTTCAACGGGTTCGCTCCTTCTTTCTCTAAG
* *
2039707 GAGTATGGAACTCGAACATCTTCAAATGGGTTCGCTCCTTCTTTCAT-TAAG
1 GAGTATAGAACTCGAACATCTTC-AACGGGTTCGCTCCTTCTTTC-TCTAAG
* * * *
2039758 GAGTATGGAACTCGGATATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
1 GAGTATAGAACTCGAACATCTTC-AACGGGTTCGCTCCTTCTTTCTCTAAG
2039809 GAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTCTAAG
1 GAGTATAGAACTCGAACATCTTC-AACGGGTTCGCTCCTTCTTTCTCTAAG
* *
2039860 GAGTATAGAACTCGCATATCTTCA
1 GAGTATAGAACTCGAACATCTTCA
2039884 TTTGCTTCAC
Statistics
Matches: 207, Mismatches: 14, Indels: 19
0.86 0.06 0.08
Matches are distributed among these distances:
49 5 0.02
50 2 0.01
51 175 0.85
52 1 0.00
54 1 0.00
55 17 0.08
56 6 0.03
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (50 bp):
GAGTATAGAACTCGAACATCTTCAACGGGTTCGCTCCTTCTTTCTCTAAG
Found at i:2039771 original size:102 final size:100
Alignment explanation
Indices: 2039601--2039883 Score: 363
Period size: 102 Copynumber: 2.7 Consensus size: 100
2039591 TTTCTTCAGA
* *
2039601 GAGTATA-AGACTCGAACAATCTTCAACAAATGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGA
1 GAGTATAGA-ACTCGAAC-ATCTT---CAAATGGGTTCGCTCCTTCTTTC-TTAAGGAGTATAGA
* *
2039665 ACTCGAACATCTCTTC-ACGGGTTCGCTCCCTCTTTCTCTAGG
60 ACTCG--CATATCTTCAACGGGTTCGCTCCCTCTTTCTCTAAG
* *
2039707 GAGTATGGAACTCGAACATCTTCAAATGGGTTCGCTCCTTCTTTCATTAAGGAGTATGGAACTCG
1 GAGTATAGAACTCGAACATCTTCAAATGGGTTCGCTCCTTCTTTC-TTAAGGAGTATAGAACTCG
* * *
2039772 GATATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
65 CATATCTTC-AACGGGTTCGCTCCCTCTTTCTCTAAG
*
2039809 GAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTCTAAGGAGTATAGAACTCG
1 GAGTATAGAACTCGAACATCTTCAAATGGGTTCGCTCCTTCTTTCT-TAAGGAGTATAGAACTCG
2039874 CATATCTTCA
65 CATATCTTCA
2039884 TTTGCTTCAC
Statistics
Matches: 159, Mismatches: 14, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
100 7 0.04
101 2 0.01
102 130 0.82
105 5 0.03
106 14 0.09
107 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (100 bp):
GAGTATAGAACTCGAACATCTTCAAATGGGTTCGCTCCTTCTTTCTTAAGGAGTATAGAACTCGC
ATATCTTCAACGGGTTCGCTCCCTCTTTCTCTAAG
Found at i:2040311 original size:36 final size:35
Alignment explanation
Indices: 2040253--2040440 Score: 205
Period size: 35 Copynumber: 5.3 Consensus size: 35
2040243 ACTCTTCTGA
* * ***
2040253 GAAGGCTTAAAATGGATCTGCTTCACTACTTTTTGGT
1 GAAGGCTTAAGATGG-TTTGCTTCACTA-TTCCCGGT
* * *
2040290 GAAGACTTAAGATGGTTTGCTTCACTACTCTCTGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTC-CCGGT
* * *
2040326 GAAGACTTATGATGGTTTGCTTCACTATTCTCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCCCGGT
* * *
2040361 GAAGGCTTCAGATTGATTGCTTCACTATTCCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCCCGGT
*
2040396 GAAGGCTTCAGATGGTTTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTC-CCGGT
2040432 GAAGGCTTA
1 GAAGGCTTA
2040441 GGATTGACTT
Statistics
Matches: 130, Mismatches: 19, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
35 61 0.47
36 56 0.43
37 13 0.10
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (35 bp):
GAAGGCTTAAGATGGTTTGCTTCACTATTCCCGGT
Found at i:2041840 original size:124 final size:124
Alignment explanation
Indices: 2041618--2041993 Score: 504
Period size: 124 Copynumber: 3.0 Consensus size: 124
2041608 ACTAATGTCG
* * * * *
2041618 CAACATTATTTTATTCTGGTACGGGCCTTCAAAATGCCTCAAT-ATCTCAAATTATAAGGCTCAT
1 CAACATTATCTTATACTGGTACGGGCCTTCAAAATGCC-CCATCACCTCAAATTGTAAGGCTCAT
* * * * *
2041682 TCTCAATGCCTTCTTGGTCTGAATCTTGTAATTTCATCATGAT-GTGGTTCAGTCGCGCCC
65 TCTCAATGCCTTCTTCGTCTGAATCTTGTCATTTCA-AATGATGGGGGTTCAGTCGTGCCC
*
2041742 CAACATTATCTCATACTGGTACGGGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGGCTCATT
1 CAACATTATCTTATACTGGTACGGGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGGCTCATT
** * *
2041807 CTTGATGCCTTCTTTGTCTGAATCTTGTCATTTCAAATGATGGGGGTTCAATCGTGCCC
66 CTCAATGCCTTCTTCGTCTGAATCTTGTCATTTCAAATGATGGGGGTTCAGTCGTGCCC
** * * * *
2041866 CAACATTATCTTATAAAGGTACGGGTCTTCAAAATACCCCAACACCTCAAATTGTAAGGCTTATT
1 CAACATTATCTTATACTGGTACGGGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGGCTCATT
* *
2041931 CTCAATGCCTTCTTCGTCTGGATCTTGTCATTTCAAAATGATGGGGGTTCAGTCATGCCC
66 CTCAATGCCTTCTTCGTCTGAATCTTGTCATTTC-AAATGATGGGGGTTCAGTCGTGCCC
2041991 CAA
1 CAA
2041994 TATGGGTATT
Statistics
Matches: 222, Mismatches: 27, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
123 8 0.04
124 188 0.85
125 26 0.12
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (124 bp):
CAACATTATCTTATACTGGTACGGGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGGCTCATT
CTCAATGCCTTCTTCGTCTGAATCTTGTCATTTCAAATGATGGGGGTTCAGTCGTGCCC
Found at i:2051655 original size:18 final size:18
Alignment explanation
Indices: 2051626--2051663 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
2051616 ATTTGGGGAT
2051626 AAAATTAAAAT-ATTTAA
1 AAAATTAAAATAATTTAA
2051643 AAAATTCAAAATAATTTAA
1 AAAATT-AAAATAATTTAA
2051662 AA
1 AA
2051664 TAGAAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.32
18 5 0.26
19 8 0.42
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAATTAAAATAATTTAA
Found at i:2054780 original size:23 final size:24
Alignment explanation
Indices: 2054750--2054795 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
2054740 CAAACTGTTA
2054750 ACCGTTGATCGCCATTGA-TTTTG
1 ACCGTTGATCGCCATTGACTTTTG
* *
2054773 ACCGTTGATTGTCATTGACTTTT
1 ACCGTTGATCGCCATTGACTTTT
2054796 TTCGAAAGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.17, C:0.20, G:0.20, T:0.43
Consensus pattern (24 bp):
ACCGTTGATCGCCATTGACTTTTG
Found at i:2054891 original size:36 final size:37
Alignment explanation
Indices: 2054850--2054922 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
2054840 GATGTATGTT
2054850 TCATTAAAATTTGA-CCCAAAGTCCCGAAATAAGCCC
1 TCATTAAAATTTGACCCCAAAGTCCCGAAATAAGCCC
* *
2054886 TCATTAAATTTTGACCCCAAAGTCCTGAAATAAGCCC
1 TCATTAAAATTTGACCCCAAAGTCCCGAAATAAGCCC
2054923 GTTAATATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
36 13 0.38
37 21 0.62
ACGTcount: A:0.37, C:0.27, G:0.11, T:0.25
Consensus pattern (37 bp):
TCATTAAAATTTGACCCCAAAGTCCCGAAATAAGCCC
Found at i:2056719 original size:106 final size:106
Alignment explanation
Indices: 2056502--2056719 Score: 359
Period size: 106 Copynumber: 2.1 Consensus size: 106
2056492 CGATTTGATC
* * *
2056502 ATTTATGTTATTGATTTTCTTTATTTTGATCATCGAATTGTTAACTCGATGATATGACAAATTAG
1 ATTTATGTTATTGATTTTCTTTATTTTGATCACCGAACTATTAACTCGATGATATGACAAATTAG
* *
2056567 TAAAAATGTTAATTTCTAATTTAACCCCTTGAACTTTTAAA
66 TAAAAAAGTTAATTTCTAATTTAACCCCATGAACTTTTAAA
2056608 ATTTATGTTATTGATTTTCTTTATTTTGATCACCGAACTATTAACTCGATGATATGACAAATTAG
1 ATTTATGTTATTGATTTTCTTTATTTTGATCACCGAACTATTAACTCGATGATATGACAAATTAG
2056673 TAAAAAAGATTAATTTCTAATTTAA-CCCATG-ACTTTTAAA
66 TAAAAAAG-TTAATTTCTAATTTAACCCCATGAACTTTTAAA
2056713 AGTTTAT
1 A-TTTAT
2056720 TTTTTTCACG
Statistics
Matches: 105, Mismatches: 5, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
105 10 0.10
106 79 0.75
107 16 0.15
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.44
Consensus pattern (106 bp):
ATTTATGTTATTGATTTTCTTTATTTTGATCACCGAACTATTAACTCGATGATATGACAAATTAG
TAAAAAAGTTAATTTCTAATTTAACCCCATGAACTTTTAAA
Found at i:2059056 original size:25 final size:23
Alignment explanation
Indices: 2059004--2059049 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
2058994 AAGAGCAGAC
*
2059004 AAAATCATATATCATTTTTTATA
1 AAAATCATATATCATTTTTCATA
2059027 AAAATCATATATCATTTTTCATA
1 AAAATCATATATCATTTTTCATA
2059050 CGAAAATAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (23 bp):
AAAATCATATATCATTTTTCATA
Found at i:2067624 original size:17 final size:18
Alignment explanation
Indices: 2067597--2067630 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2067587 AAATAATATA
2067597 ATAATTAATAAAATTTAC
1 ATAATTAATAAAATTTAC
*
2067615 ATAA-TAATAAATTTTA
1 ATAATTAATAAAATTTA
2067631 TACTTAAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (18 bp):
ATAATTAATAAAATTTAC
Found at i:2069567 original size:19 final size:20
Alignment explanation
Indices: 2069527--2069567 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
2069517 AGGTAAACAA
*
2069527 AAACAATGGCAAAAAATCGT
1 AAACAACGGCAAAAAATCGT
2069547 AAACAACGGCAAAAAAT-GT
1 AAACAACGGCAAAAAATCGT
2069566 AA
1 AA
2069568 TTACCATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.59, C:0.15, G:0.15, T:0.12
Consensus pattern (20 bp):
AAACAACGGCAAAAAATCGT
Found at i:2070075 original size:12 final size:14
Alignment explanation
Indices: 2070057--2070095 Score: 55
Period size: 12 Copynumber: 2.9 Consensus size: 14
2070047 ATAGCATAAG
2070057 TTTTATTTATTT-A
1 TTTTATTTATTTCA
2070070 -TTTATTTATTTCA
1 TTTTATTTATTTCA
2070083 TTTTATATTATTT
1 TTTTAT-TTATTT
2070096 TCGAAGCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 11 0.48
13 1 0.04
14 5 0.22
15 6 0.26
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTATTTATTTCA
Found at i:2072657 original size:23 final size:23
Alignment explanation
Indices: 2072631--2072680 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
2072621 TGAGCTACCA
*
2072631 AAAGACAGAGAAAAATATGTCAT
1 AAAGACAGAGAAAAACATGTCAT
* * * *
2072654 AAAGGCATAGATAAACGTGTCAT
1 AAAGACAGAGAAAAACATGTCAT
2072677 AAAG
1 AAAG
2072681 GCATAGAACA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.52, C:0.10, G:0.20, T:0.18
Consensus pattern (23 bp):
AAAGACAGAGAAAAACATGTCAT
Found at i:2072700 original size:20 final size:21
Alignment explanation
Indices: 2072647--2072705 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
2072637 AGAGAAAAAT
2072647 ATGTCATAAAGGCATAGATAAAC
1 ATGTCATAAAGGCATAG--AAAC
*
2072670 GTGTCATAAAGGCATAG-AAC
1 ATGTCATAAAGGCATAGAAAC
* *
2072690 ATGTCACAAAGACATA
1 ATGTCATAAAGGCATA
2072706 ATTATTGTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 16 0.50
23 16 0.50
ACGTcount: A:0.46, C:0.15, G:0.19, T:0.20
Consensus pattern (21 bp):
ATGTCATAAAGGCATAGAAAC
Found at i:2073837 original size:35 final size:35
Alignment explanation
Indices: 2073764--2073842 Score: 106
Period size: 35 Copynumber: 2.3 Consensus size: 35
2073754 ATATAAAATT
* * **
2073764 TAAAATTTAAAAGTTTATAATACATAATTAACTCA
1 TAAAATTTAAAAATTTAAAATACATAATTAACAAA
2073799 TAAAATTTAAAAATTTAAAATACATAATTGAA-AAA
1 TAAAATTTAAAAATTTAAAATACATAATT-AACAAA
2073834 TAAAATTTA
1 TAAAATTTA
2073843 TTAAACATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 37 0.95
36 2 0.05
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (35 bp):
TAAAATTTAAAAATTTAAAATACATAATTAACAAA
Found at i:2075973 original size:22 final size:22
Alignment explanation
Indices: 2075926--2075991 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
2075916 TCGAGGGTTA
* * **
2075926 CATAGATCCTTCGGGATATAGA
1 CATAGGTCCTTCGGGACATATT
2075948 CATAGGTCCTTCGGGACATATT
1 CATAGGTCCTTCGGGACATATT
*
2075970 CATAGGTCATTCGGGACATATT
1 CATAGGTCCTTCGGGACATATT
2075992 TCACATGCCA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (22 bp):
CATAGGTCCTTCGGGACATATT
Found at i:2079128 original size:23 final size:23
Alignment explanation
Indices: 2079092--2079148 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
2079082 GTTTTTGAAT
*
2079092 AAATGATTTGTATATTG-TTATA
1 AAATGATTTTTATATTGATTATA
*
2079114 AAATGTATTTTTATATTGATTTATT
1 AAATG-ATTTTTATATTGA-TTATA
2079139 AAATGATTTT
1 AAATGATTTT
2079149 GTTATGATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 5 0.17
23 11 0.37
24 5 0.17
25 9 0.30
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (23 bp):
AAATGATTTTTATATTGATTATA
Found at i:2079572 original size:23 final size:23
Alignment explanation
Indices: 2079546--2079617 Score: 92
Period size: 23 Copynumber: 3.1 Consensus size: 23
2079536 GGTTCTACGC
*
2079546 GGTCATTCGGGATAATTCTATGT
1 GGTCATTCGGGACAATTCTATGT
*
2079569 GGTCATTAGGGACAATTCTACT-T
1 GGTCATTCGGGACAATTCTA-TGT
* *
2079592 GGTCCTTCGGGACAAATCTATGT
1 GGTCATTCGGGACAATTCTATGT
2079615 GGT
1 GGT
2079618 ACTTCGGTGC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
22 1 0.02
23 40 0.95
24 1 0.02
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (23 bp):
GGTCATTCGGGACAATTCTATGT
Found at i:2083240 original size:12 final size:13
Alignment explanation
Indices: 2083211--2083240 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2083201 CTTATTAAAA
2083211 AAAAAACAAAGAG
1 AAAAAACAAAGAG
*
2083224 AAAAAATAAAGAG
1 AAAAAACAAAGAG
2083237 AAAA
1 AAAA
2083241 GAAAACCAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.80, C:0.03, G:0.13, T:0.03
Consensus pattern (13 bp):
AAAAAACAAAGAG
Found at i:2084387 original size:30 final size:30
Alignment explanation
Indices: 2084347--2084412 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
2084337 GAATCCTTAT
* * *
2084347 TAAAAAAATC-TTAATAAATAAAATTAATCA
1 TAAAATAATCTTTAAGAAATAAAATT-ATAA
*
2084377 TAAAATAATCTTTAAGCAATAAAATTATAA
1 TAAAATAATCTTTAAGAAATAAAATTATAA
2084407 TAAAAT
1 TAAAAT
2084413 CGAACTTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 18 0.58
31 13 0.42
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.32
Consensus pattern (30 bp):
TAAAATAATCTTTAAGAAATAAAATTATAA
Found at i:2089417 original size:7 final size:7
Alignment explanation
Indices: 2089402--2089444 Score: 77
Period size: 7 Copynumber: 6.1 Consensus size: 7
2089392 CCGAAATTTA
2089402 TAAATAT
1 TAAATAT
*
2089409 TATATAT
1 TAAATAT
2089416 TAAATAT
1 TAAATAT
2089423 TAAATAT
1 TAAATAT
2089430 TAAATAT
1 TAAATAT
2089437 TAAATAT
1 TAAATAT
2089444 T
1 T
2089445 TTTTGATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
TAAATAT
Found at i:2092433 original size:20 final size:20
Alignment explanation
Indices: 2092400--2092449 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
2092390 AGACTATTTC
**
2092400 AAAATTTTTGTTTTT-AATA
1 AAAATTTTAATTTTTAAATA
*
2092419 TATAATTTTAATTTTTAAATA
1 -AAAATTTTAATTTTTAAATA
2092440 AAAATTTTAA
1 AAAATTTTAA
2092450 AATTATCAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
AAAATTTTAATTTTTAAATA
Found at i:2093979 original size:14 final size:14
Alignment explanation
Indices: 2093960--2093988 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2093950 TGTAATGCAA
2093960 CTTTTATTCATTAT
1 CTTTTATTCATTAT
2093974 CTTTTATTCATTAT
1 CTTTTATTCATTAT
2093988 C
1 C
2093989 CGGCTACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.17, G:0.00, T:0.62
Consensus pattern (14 bp):
CTTTTATTCATTAT
Found at i:2101364 original size:14 final size:15
Alignment explanation
Indices: 2101342--2101388 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
2101332 TATAAGGTAA
*
2101342 TTTTGTTATAATT-T
1 TTTTATTATAATTAT
*
2101356 TTTTATTATACTTAT
1 TTTTATTATAATTAT
*
2101371 TGTTTATTATGATTAT
1 T-TTTATTATAATTAT
2101387 TT
1 TT
2101389 GAAAAAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 11 0.41
15 3 0.11
16 13 0.48
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTATAATTAT
Found at i:2101409 original size:23 final size:24
Alignment explanation
Indices: 2101374--2101436 Score: 74
Period size: 23 Copynumber: 2.6 Consensus size: 24
2101364 TACTTATTGT
*
2101374 TTATTATGATTATTTGAAAAAATA
1 TTATTATGTTTATTTGAAAAAATA
* * *
2101398 TTA-TATGTTTATGTGTAAAAATT
1 TTATTATGTTTATTTGAAAAAATA
2101421 TTATTATGTTATATTT
1 TTATTATGTT-TATTT
2101437 TCGTTCATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
23 19 0.59
24 9 0.28
25 4 0.12
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.54
Consensus pattern (24 bp):
TTATTATGTTTATTTGAAAAAATA
Found at i:2105818 original size:17 final size:17
Alignment explanation
Indices: 2105792--2105829 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
2105782 AATTAAATAC
*
2105792 AATA-TTAAATAATTTA
1 AATACTTAAATAAATTA
2105808 AATACTTAAATAAATTA
1 AATACTTAAATAAATTA
2105825 AATAC
1 AATAC
2105830 AAAATATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (17 bp):
AATACTTAAATAAATTA
Found at i:2105834 original size:24 final size:24
Alignment explanation
Indices: 2105807--2105852 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
2105797 TAAATAATTT
*
2105807 AAATACTTAAATA-AATTAAATACA
1 AAATA-TTAAATATAATAAAATACA
2105831 AAATATTAAATATAATAAAATA
1 AAATATTAAATATAATAAAATA
2105853 TACCTTAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.30
Consensus pattern (24 bp):
AAATATTAAATATAATAAAATACA
Found at i:2112633 original size:18 final size:19
Alignment explanation
Indices: 2112610--2112647 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
2112600 TATTTAAGTG
*
2112610 ATAAAAGCGA-TTAAATAA
1 ATAAAAGCAATTTAAATAA
2112628 ATAAAAGCAATTTAAATAA
1 ATAAAAGCAATTTAAATAA
2112647 A
1 A
2112648 AATAAGAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.63, C:0.05, G:0.08, T:0.24
Consensus pattern (19 bp):
ATAAAAGCAATTTAAATAA
Found at i:2114679 original size:2 final size:2
Alignment explanation
Indices: 2114674--2114702 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2114664 AATCAATTTG
2114674 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
2114703 GAGACAGGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2120905 original size:43 final size:42
Alignment explanation
Indices: 2120865--2121003 Score: 135
Period size: 42 Copynumber: 3.3 Consensus size: 42
2120855 TTTTAAAAGT
2120865 ATTTTATTTATTTAAAAGAACGTTTTTATAATAACATAAAAC
1 ATTTTATTTATTTAAAAGAACGTTTTTATAATAACATAAAAC
* * * * * *
2120907 ATTTTTTTTA-TTAATTA-TA--TTTTTAAAAATAATATTTTAAAAGT
1 ATTTTATTTATTTAA-AAGAACGTTTTT-ATAATAACA---TAAAA-C
2120951 ATTTTATTTATTTAAAAGAACGTTTTTATAATAACATAAAAC
1 ATTTTATTTATTTAAAAGAACGTTTTTATAATAACATAAAAC
2120993 ATTTT-TTTATT
1 ATTTTATTTATT
2121004 AATTTGGGGT
Statistics
Matches: 75, Mismatches: 12, Indels: 21
0.69 0.11 0.19
Matches are distributed among these distances:
39 5 0.07
40 7 0.09
41 11 0.15
42 15 0.20
43 10 0.13
44 10 0.13
45 5 0.07
46 7 0.09
47 5 0.07
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (42 bp):
ATTTTATTTATTTAAAAGAACGTTTTTATAATAACATAAAAC
Found at i:2120924 original size:86 final size:85
Alignment explanation
Indices: 2120834--2121007 Score: 330
Period size: 86 Copynumber: 2.0 Consensus size: 85
2120824 CATCAATTCT
*
2120834 ATTATATTTTTTAAAATAATATTTTAAAAGTATTTTATTTATTTAAAAGAACGTTTTTATAATAA
1 ATTATATTTTTAAAAATAATATTTTAAAAGTATTTTATTTATTTAAAAGAACGTTTTTATAATAA
2120899 CATAAAACATTTTTTTTATTA
66 CATAAAACA-TTTTTTTATTA
2120920 ATTATATTTTTAAAAATAATATTTTAAAAGTATTTTATTTATTTAAAAGAACGTTTTTATAATAA
1 ATTATATTTTTAAAAATAATATTTTAAAAGTATTTTATTTATTTAAAAGAACGTTTTTATAATAA
2120985 CATAAAACATTTTTTTATTA
66 CATAAAACATTTTTTTATTA
2121005 ATT
1 ATT
2121008 TGGGGTGACA
Statistics
Matches: 87, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
85 14 0.16
86 73 0.84
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (85 bp):
ATTATATTTTTAAAAATAATATTTTAAAAGTATTTTATTTATTTAAAAGAACGTTTTTATAATAA
CATAAAACATTTTTTTATTA
Found at i:2127376 original size:22 final size:23
Alignment explanation
Indices: 2127328--2127377 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
2127318 GAGCAACACT
2127328 AGATGATTTTAGTTTCAAATGTC
1 AGATGATTTTAGTTTCAAATGTC
2127351 -GATGA-TTTAGTTTTCAAATG-C
1 AGATGATTTTAG-TTTCAAATGTC
2127372 AGATGA
1 AGATGA
2127378 GGAGAAATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 6 0.24
22 19 0.76
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (23 bp):
AGATGATTTTAGTTTCAAATGTC
Found at i:2135022 original size:16 final size:17
Alignment explanation
Indices: 2135001--2135052 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 17
2134991 TTTTTAATTT
2135001 AATTACT-TAACTTTCA
1 AATTACTCTAACTTTCA
2135017 AATTACTCCTAA-TTT--
1 AATTACT-CTAACTTTCA
*
2135032 AATCACTCTAACTTTCA
1 AATTACTCTAACTTTCA
2135049 AATT
1 AATT
2135053 TATTTTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 4 0.14
15 9 0.31
16 7 0.24
17 6 0.21
18 3 0.10
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTACTCTAACTTTCA
Found at i:2139107 original size:50 final size:50
Alignment explanation
Indices: 2139032--2139166 Score: 261
Period size: 50 Copynumber: 2.7 Consensus size: 50
2139022 ATGGGTAAGT
*
2139032 GAAAGCAAGTTAGTAAGTTATACATTTTTTGATCATTTTAATTTTGCAAA
1 GAAAGCAATTTAGTAAGTTATACATTTTTTGATCATTTTAATTTTGCAAA
2139082 GAAAGCAATTTAGTAAGTTATACATTTTTTGATCATTTTAATTTTGCAAA
1 GAAAGCAATTTAGTAAGTTATACATTTTTTGATCATTTTAATTTTGCAAA
2139132 GAAAGCAATTTAGTAAGTTATACATTTTTTGATCA
1 GAAAGCAATTTAGTAAGTTATACATTTTTTGATCA
2139167 GGTTACGAAC
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 84 1.00
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.42
Consensus pattern (50 bp):
GAAAGCAATTTAGTAAGTTATACATTTTTTGATCATTTTAATTTTGCAAA
Found at i:2140290 original size:24 final size:24
Alignment explanation
Indices: 2140216--2140291 Score: 64
Period size: 25 Copynumber: 3.1 Consensus size: 24
2140206 AAGTCCAACA
* *
2140216 AATTTAACAAAATAAAGTAAGTATT
1 AATTTAACAAAATAAAGTAAATA-C
* * * *
2140241 AAATGAAAAATAATAAA-AAAATTAC
1 AATTTAACAA-AATAAAGTAAA-TAC
2140266 AATTTAACAAAATAAAGTAAATAC
1 AATTTAACAAAATAAAGTAAATAC
2140290 AA
1 AA
2140292 ATATAATAAA
Statistics
Matches: 38, Mismatches: 10, Indels: 7
0.69 0.18 0.13
Matches are distributed among these distances:
24 11 0.29
25 19 0.50
26 8 0.21
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.25
Consensus pattern (24 bp):
AATTTAACAAAATAAAGTAAATAC
Found at i:2142536 original size:17 final size:18
Alignment explanation
Indices: 2142516--2142556 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2142506 GAATTATATT
*
2142516 AGTAAAATA-TTAAATAA
1 AGTAAAATACCTAAATAA
2142533 AGTAAAATACCTAAATAA
1 AGTAAAATACCTAAATAA
*
2142551 ATTAAA
1 AGTAAA
2142557 TACATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.27
Consensus pattern (18 bp):
AGTAAAATACCTAAATAA
Found at i:2142826 original size:42 final size:43
Alignment explanation
Indices: 2142778--2142859 Score: 112
Period size: 42 Copynumber: 1.9 Consensus size: 43
2142768 CCTCTATGTG
* *
2142778 GCGTATAGCGCGGATCAGGGGCCGCGCTATA-CCCACGTGTCA
1 GCGTATAGCGCGGAGCAGGGGCCGCACTATACCCCACGTGTCA
* **
2142820 GCGTATAGCGCGGGGCAGGGGGTGCACTATACCCCACGTG
1 GCGTATAGCGCGGAGCAGGGGCCGCACTATACCCCACGTG
2142860 GCGCCAAATC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
42 26 0.76
43 8 0.24
ACGTcount: A:0.18, C:0.29, G:0.37, T:0.16
Consensus pattern (43 bp):
GCGTATAGCGCGGAGCAGGGGCCGCACTATACCCCACGTGTCA
Found at i:2144260 original size:2 final size:2
Alignment explanation
Indices: 2144255--2144289 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2144245 ATTAAAATTT
2144255 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
2144290 TTAAAAGAAA
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:2144705 original size:2 final size:2
Alignment explanation
Indices: 2144700--2144727 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2144690 TGTTTTTTCT
2144700 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2144728 ATTTTAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2151620 original size:31 final size:30
Alignment explanation
Indices: 2151561--2151630 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 30
2151551 ACAAGCCTTA
* ** *
2151561 GAAAAATTAGGGGACCATTTTGTAATTTTT
1 GAAAAGTTAGGGGACCATTCGGTAATTTTG
2151591 GAAAAGTTAGGGGACCAATTCGGTAATTTTG
1 GAAAAGTTAGGGGACC-ATTCGGTAATTTTG
2151622 GAAAAGTTA
1 GAAAAGTTA
2151631 TGAATGATTG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
30 15 0.43
31 20 0.57
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.33
Consensus pattern (30 bp):
GAAAAGTTAGGGGACCATTCGGTAATTTTG
Found at i:2152443 original size:26 final size:26
Alignment explanation
Indices: 2152414--2152466 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
2152404 GAAAATGGGT
*
2152414 ATATGTGTCATATGTTATTATATGTG
1 ATATGTGTCACATGTTATTATATGTG
* * *
2152440 ATATGTTTGACATGTTATTTTATGTG
1 ATATGTGTCACATGTTATTATATGTG
2152466 A
1 A
2152467 CATGATTGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.26, C:0.04, G:0.19, T:0.51
Consensus pattern (26 bp):
ATATGTGTCACATGTTATTATATGTG
Found at i:2152475 original size:26 final size:26
Alignment explanation
Indices: 2152425--2152475 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
2152415 TATGTGTCAT
* *
2152425 ATGTTATTATATGTGATATGTTTGAC
1 ATGTTATTATATGTGACATGATTGAC
*
2152451 ATGTTATTTTATGTGACATGATTGA
1 ATGTTATTATATGTGACATGATTGA
2152476 TGTGAACATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.27, C:0.04, G:0.20, T:0.49
Consensus pattern (26 bp):
ATGTTATTATATGTGACATGATTGAC
Found at i:2152900 original size:20 final size:20
Alignment explanation
Indices: 2152872--2152917 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
2152862 TTGGGATAAT
*
2152872 TTTACATGCCTTAATGGGAA
1 TTTATATGCCTTAATGGGAA
*
2152892 TTTATATGCCTTAGTGGGAA
1 TTTATATGCCTTAATGGGAA
2152912 TTTATA
1 TTTATA
2152918 CGAGCTGTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41
Consensus pattern (20 bp):
TTTATATGCCTTAATGGGAA
Found at i:2153009 original size:30 final size:30
Alignment explanation
Indices: 2152975--2153037 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
2152965 CCTTGAGTTC
* *
2152975 TCAGTAATGTATATGGGCTTATAAAAGATA
1 TCAGTAATGTATATGGGCCTACAAAAGATA
*
2153005 TCAGTACTGTATATGGGCCTACAAAAGATA
1 TCAGTAATGTATATGGGCCTACAAAAGATA
2153035 TCA
1 TCA
2153038 AAAGTATGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (30 bp):
TCAGTAATGTATATGGGCCTACAAAAGATA
Found at i:2162233 original size:23 final size:23
Alignment explanation
Indices: 2162159--2162233 Score: 71
Period size: 23 Copynumber: 3.1 Consensus size: 23
2162149 AAGATGAGTA
* *
2162159 AAAGAGAGAGAAAAAGTAAAAGTT
1 AAAGAAAGAG-AAAAGAAAAAGTT
* *
2162183 AACATGAAAGAGAAAA-AAAATGAAT
1 AA-A-GAAAGAGAAAAGAAAAAG-TT
2162208 AAAGAAAGAGAAAAGAAAAAGTT
1 AAAGAAAGAGAAAAGAAAAAGTT
2162231 AAA
1 AAA
2162234 AATTTGGGAG
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
23 15 0.37
24 12 0.29
25 8 0.20
26 6 0.15
ACGTcount: A:0.68, C:0.01, G:0.20, T:0.11
Consensus pattern (23 bp):
AAAGAAAGAGAAAAGAAAAAGTT
Found at i:2168535 original size:21 final size:22
Alignment explanation
Indices: 2168505--2168551 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
2168495 CAAGGCAATG
*
2168505 AAAAATGATAAA-AACAGTAAAT
1 AAAAATGATAAATAA-AATAAAT
2168527 AAAAA-GATAAATAAAATAAAT
1 AAAAATGATAAATAAAATAAAT
2168548 AAAA
1 AAAA
2168552 TAAGAAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.17
Consensus pattern (22 bp):
AAAAATGATAAATAAAATAAAT
Found at i:2194980 original size:22 final size:21
Alignment explanation
Indices: 2194941--2194996 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
2194931 ATTCTGACTA
*
2194941 TCGCATTACGA-TTTCCTAAAT
1 TCGCATTGCGATTTTCCT-AAT
*
2194962 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCTAAT
2194983 TCGCATTGCGATTT
1 TCGCATTGCGATTT
2194997 ACGTAATCGC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 25 0.81
22 6 0.19
ACGTcount: A:0.20, C:0.23, G:0.16, T:0.41
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCTAAT
Found at i:2195885 original size:24 final size:24
Alignment explanation
Indices: 2195858--2195911 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2195848 GTATTCAAAA
2195858 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
2195882 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
2195906 TTTGAT
1 TTTGAT
2195912 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:2198043 original size:21 final size:21
Alignment explanation
Indices: 2197977--2198043 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2197967 TGTGAATCGG
*
2197977 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
2197997 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
2198019 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
2198040 CTCT
1 CTCT
2198044 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:2198062 original size:42 final size:41
Alignment explanation
Indices: 2197977--2198099 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
2197967 TGTGAATCGG
* * * *
2197977 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
2198019 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
2198061 CTCTTTAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
2198100 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:2198579 original size:19 final size:19
Alignment explanation
Indices: 2198496--2198586 Score: 92
Period size: 19 Copynumber: 4.6 Consensus size: 19
2198486 TCTGGAACTT
*
2198496 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAACGCG--AAATG
**
2198517 ACTATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
**
2198536 AAAATCGCAACAAGAGAATG
1 AAAATCGCAACGCGA-AATG
* *
2198556 AAAATCACAACGCGAAACG
1 AAAATCGCAACGCGAAATG
2198575 AAAATCGCAACG
1 AAAATCGCAACG
2198587 AGAGAATCGC
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
19 30 0.53
20 16 0.28
21 11 0.19
ACGTcount: A:0.49, C:0.21, G:0.19, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:2198697 original size:58 final size:58
Alignment explanation
Indices: 2198600--2198710 Score: 152
Period size: 58 Copynumber: 1.9 Consensus size: 58
2198590 GAATCGCAAC
* **
2198600 GCGATTATAGTTTCGCGTTGCGGTTTTTGGTTTCGCGTTGCGATTTTCATTTCGCGTT
1 GCGATTATAGTTTCGCGTTGCGGATTTTCATTTCGCGTTGCGATTTTCATTTCGCGTT
* * *
2198658 GCGATTTTCGTTTCGCGTTGC-GATTTTCATTCTCTCGTTGCGATTTTCATTTC
1 GCGATTATAGTTTCGCGTTGCGGATTTTCATT-TCGCGTTGCGATTTTCATTTC
2198711 AACCAAAAGA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
57 7 0.15
58 39 0.85
ACGTcount: A:0.09, C:0.20, G:0.23, T:0.48
Consensus pattern (58 bp):
GCGATTATAGTTTCGCGTTGCGGATTTTCATTTCGCGTTGCGATTTTCATTTCGCGTT
Found at i:2198698 original size:20 final size:19
Alignment explanation
Indices: 2198610--2198710 Score: 139
Period size: 19 Copynumber: 5.2 Consensus size: 19
2198600 GCGATTATAG
* **
2198610 TTTCGCGTTGCGGTTTTTGG
1 TTTCGCGTTGC-GATTTTCA
2198630 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
2198649 TTTCGCGTTGCGATTTTCG
1 TTTCGCGTTGCGATTTTCA
2198668 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
2198687 TTCTCTCGTTGCGATTTTCA
1 TT-TCGCGTTGCGATTTTCA
2198707 TTTC
1 TTTC
2198711 AACCAAAAGA
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
19 45 0.61
20 29 0.39
ACGTcount: A:0.07, C:0.21, G:0.23, T:0.50
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:2198913 original size:94 final size:94
Alignment explanation
Indices: 2198801--2199176 Score: 606
Period size: 94 Copynumber: 4.1 Consensus size: 94
2198791 ATGGATTGCA
* *
2198801 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
2198865 TTAGCAGAATTGGCAGCAAACGAACAAAT
66 TTAGCAGAATTGGCAGCAAACGAACAAAT
2198894 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
2198959 TTAGCAGAATTGGCAG-AAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAAA-CGAACAAAT
2198988 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
2199053 TTAGCAGAATTGGCAGCAACCG-ACTAAAT
66 TTAGCAGAATTGGCAGCAAACGAAC-AAAT
*
2199082 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTT----AATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* * *
2199142 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAAACGAACAAAT
2199172 TTACT
1 TTACT
2199177 AAGCAATCTA
Statistics
Matches: 270, Mismatches: 6, Indels: 16
0.92 0.02 0.05
Matches are distributed among these distances:
90 38 0.14
91 1 0.00
93 28 0.10
94 201 0.74
95 2 0.01
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.21
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAAACGAACAAAT
Found at i:2200015 original size:21 final size:22
Alignment explanation
Indices: 2199973--2200015 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
2199963 AATAAACAAC
*
2199973 ATTAGTAATTGTTAAATAATTA
1 ATTAGTAATTGTTAAAAAATTA
2199995 ATTA-TAATT-TTAAAAACATTA
1 ATTAGTAATTGTTAAAAA-ATTA
2200016 TATAGAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 9 0.47
22 4 0.21
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (22 bp):
ATTAGTAATTGTTAAAAAATTA
Found at i:2200887 original size:20 final size:20
Alignment explanation
Indices: 2200862--2200924 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
2200852 TTTTGGTTGA
2200862 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
2200882 AATGAAAATCGCAACGCG-G
1 AATGAAAATCGCAACGAGAG
**
2200901 AAATGACTATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
2200922 AAT
1 AAT
2200925 CACAACGCGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.03
20 35 0.95
21 1 0.03
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:2200939 original size:33 final size:33
Alignment explanation
Indices: 2200860--2200981 Score: 154
Period size: 33 Copynumber: 3.5 Consensus size: 33
2200850 TCTTTTGGTT
2200860 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAAC--GAG-A-G--AATCGCAACGC
** *
2200899 GGAAATGACTATCGCAACGAGAGAATCACAACGC
1 -GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2200933 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2200966 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
2200982 TGCGATTTTG
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
33 46 0.61
34 10 0.13
36 1 0.01
37 1 0.01
38 3 0.04
40 15 0.20
ACGTcount: A:0.47, C:0.20, G:0.23, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:2207288 original size:22 final size:21
Alignment explanation
Indices: 2207263--2207320 Score: 57
Period size: 23 Copynumber: 2.7 Consensus size: 21
2207253 AACAAAAAGG
2207263 GCAAAAAGAAAAAAGAAACGAA
1 GCAAAAAGAAAAAAGAAA-GAA
*
2207285 GCAAAAAAGGAAAAAA-CAAGAA
1 GC-AAAAA-GAAAAAAGAAAGAA
*
2207307 -CAAAAATAAAAAAG
1 GCAAAAAGAAAAAAG
2207321 GGAACAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
19 6 0.19
20 5 0.16
21 1 0.03
22 5 0.16
23 7 0.23
24 7 0.23
ACGTcount: A:0.74, C:0.09, G:0.16, T:0.02
Consensus pattern (21 bp):
GCAAAAAGAAAAAAGAAAGAA
Found at i:2208222 original size:105 final size:102
Alignment explanation
Indices: 2207901--2208406 Score: 717
Period size: 100 Copynumber: 5.0 Consensus size: 102
2207891 CTTCCAGTAG
* **
2207901 AGACAATGCAAGTTCAACTTCACGACGAAATGACCGCTGCTTGTCAACAACAACTTTCCAATCTC
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAA-TTTCC-AT-TC
*
2207966 AGAGCCAATTTCAACTTCACAACGAATGATATTGGACTCC
63 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*
2208006 AGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGCTTGTCAACAA-AATTT-CATTCAGA
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAATTTCCATTCAGA
*
2208069 GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*
2208106 AGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAATCTC
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAA-TTTCC-AT-TC
* *
2208171 AGAGCTAATTTCAACTTCACAACGAAAGATATTGGACTCC
63 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
2208211 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AATTT-CATTCAGA
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAATTTCCATTCAGA
** *
2208274 TTCAATTTCAACTTCACAACGAAGGATATTGGACTCG
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* * * *
2208311 AGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAA--T---TTCG
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGCTTGTCAAC-AACAATTTCCATTCA
*
2208370 GAGCCAATCTCAACTTCACAACGAAGGATATTGGACT
64 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
2208407 TGGAACAATG
Statistics
Matches: 369, Mismatches: 24, Indels: 23
0.89 0.06 0.06
Matches are distributed among these distances:
98 37 0.10
99 2 0.01
100 168 0.46
101 8 0.02
102 7 0.02
103 7 0.02
104 6 0.02
105 134 0.36
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (102 bp):
AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAATTTCCATTCAGA
GCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
Found at i:2208253 original size:205 final size:205
Alignment explanation
Indices: 2207901--2208406 Score: 794
Period size: 205 Copynumber: 2.5 Consensus size: 205
2207891 CTTCCAGTAG
**
2207901 AGACAATGCAAGTTCAACTTCACGACGAAATGACCGCTGCTTGTCAACAACAACTTTCCAATCTC
1 AGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAATCTC
*
2207966 AGAGCCAATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
66 AGAGCCAATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
2208031 TGAAGGGACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAGCGAAGGAT
131 CGAAGGGACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGAT
2208096 ATTGGACTCC
196 ATTGGACTCC
2208106 AGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAATCTC
1 AGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAATCTC
*
2208171 AGAGCTAATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
66 AGAGCCAATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
**
2208236 CGAAGGGACCGCTGCTTGTCAACAAAATTTCATTCAGATTCAATTTCAACTTCACAACGAAGGAT
131 CGAAGGGACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGAT
*
2208301 ATTGGACTCG
196 ATTGGACTCC
** * * *
2208311 AGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAAC-A-AA-----CAATTT
1 AGACAATGCAAGTTCAACTTCACGACGAAGGGACCG-CTGCTTGTCAACAACAACTTTCCAATCT
* * *
2208368 CGGAGCCAATCTCAACTTCACAACGAAGGATATTGGACT
65 CAGAGCCAATTTCAACTTCACAACGAAAGATATTGGACT
2208407 TGGAACAATG
Statistics
Matches: 282, Mismatches: 18, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
198 40 0.14
203 2 0.01
204 3 0.01
205 237 0.84
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (205 bp):
AGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAATCTC
AGAGCCAATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGAT
ATTGGACTCC
Found at i:2208977 original size:34 final size:33
Alignment explanation
Indices: 2208934--2209055 Score: 117
Period size: 34 Copynumber: 3.7 Consensus size: 33
2208924 GTCCTACTAG
2208934 GATTCAAACTCCTAAAAATAGGATAGAATTTTAA
1 GATTCAAACTCCTAAAAATAGGATAGAATTTT-A
* *
2208968 GATTCAAACTCCTAAAGATATGATAGAATTTT-
1 GATTCAAACTCCTAAAAATAGGATAGAATTTTA
* * * *
2209000 G-CT-AGGA-TTCAAAAAATAGGATAGAATTTTA
1 GATTCA-AACTCCTAAAAATAGGATAGAATTTTA
* *
2209031 TGATTTAAACTCCTAAAGATAGGAT
1 -GATTCAAACTCCTAAAAATAGGAT
2209056 CCACAAGCAC
Statistics
Matches: 69, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
30 20 0.29
31 2 0.03
32 2 0.03
33 2 0.03
34 43 0.62
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (33 bp):
GATTCAAACTCCTAAAAATAGGATAGAATTTTA
Found at i:2210829 original size:19 final size:19
Alignment explanation
Indices: 2210775--2210829 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
2210765 ATAAACTATA
*
2210775 TATTTAGTTATTCA-ATTAT
1 TATTTAATTATT-ATATTAT
2210794 TATTTTAATT-TTATATTAGT
1 TA-TTTAATTATTATATTA-T
2210814 TATTTAATTATT-TATT
1 TATTTAATTATTATATT
2210830 TTTAAATCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
18 1 0.03
19 19 0.61
20 11 0.35
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.64
Consensus pattern (19 bp):
TATTTAATTATTATATTAT
Found at i:2210919 original size:23 final size:23
Alignment explanation
Indices: 2210889--2210934 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
2210879 TCCAAATACT
2210889 CTCAACCATTTAACAATGAACGC
1 CTCAACCATTTAACAATGAACGC
*
2210912 CTCAACCATTTAACAGTGAACGC
1 CTCAACCATTTAACAATGAACGC
2210935 TTAATCACCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.30, G:0.11, T:0.22
Consensus pattern (23 bp):
CTCAACCATTTAACAATGAACGC
Found at i:2212219 original size:14 final size:14
Alignment explanation
Indices: 2212200--2212288 Score: 65
Period size: 14 Copynumber: 6.0 Consensus size: 14
2212190 ATTGTCATTA
2212200 TATTTTTTATTATT
1 TATTTTTTATTATT
* *
2212214 TATTTTTTCTTTTT
1 TATTTTTTATTATT
2212228 TATTTATTTATTA-T
1 TATTT-TTTATTATT
*
2212242 TA-TTATTATTATAT
1 TATTTTTTATTAT-T
*
2212256 TATTATTATTACTTTTT
1 TATT-TT-TTA-TTATT
2212273 TCATTTTATTATTATT
1 T-ATTTT-TTATTATT
2212289 CCTTTTTTTA
Statistics
Matches: 59, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
12 6 0.10
13 2 0.03
14 23 0.39
15 6 0.10
16 5 0.08
17 11 0.19
18 6 0.10
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (14 bp):
TATTTTTTATTATT
Found at i:2212237 original size:8 final size:8
Alignment explanation
Indices: 2212200--2212348 Score: 53
Period size: 8 Copynumber: 20.0 Consensus size: 8
2212190 ATTGTCATTA
2212200 TATTT-TT
1 TATTTATT
2212207 TA-TTATT
1 TATTTATT
2212214 TATTT-TT
1 TATTTATT
*
2212221 TCTTT-TT
1 TATTTATT
2212228 TATTTATT
1 TATTTATT
2212236 TA-TTA-T
1 TATTTATT
2212242 TA-TTA-T
1 TATTTATT
2212248 TA-TTATAT
1 TATTTAT-T
2212256 TA-TTA-T
1 TATTTATT
2212262 TA-TTACTT
1 TATTTA-TT
2212270 T-TTTCATT
1 TATTT-ATT
2212278 T-TATTA-T
1 TAT-TTATT
**
2212285 TATTCCTT
1 TATTTATT
*
2212293 TTTTTATT
1 TATTTATT
*
2212301 TGCTTT-TAT
1 T-ATTTAT-T
*
2212310 T-TTTACT
1 TATTTATT
2212317 TATTTATT
1 TATTTATT
*
2212325 TACTTATT
1 TATTTATT
*
2212333 TACTTATT
1 TATTTATT
2212341 TATTTATT
1 TATTTATT
2212349 ACTTGTTTTT
Statistics
Matches: 114, Mismatches: 12, Indels: 31
0.73 0.08 0.20
Matches are distributed among these distances:
6 20 0.18
7 29 0.25
8 57 0.50
9 8 0.07
ACGTcount: A:0.21, C:0.06, G:0.01, T:0.72
Consensus pattern (8 bp):
TATTTATT
Found at i:2212243 original size:3 final size:3
Alignment explanation
Indices: 2212235--2212288 Score: 62
Period size: 3 Copynumber: 18.7 Consensus size: 3
2212225 TTTTATTTAT
2212235 TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA CTT- TT- TTCA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TT-A TTA
2212278 TTA TTA TTA TT
1 TTA TTA TTA TT
2212289 CCTTTTTTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
2 8 0.17
3 34 0.74
4 4 0.09
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2212261 original size:23 final size:21
Alignment explanation
Indices: 2212202--2212349 Score: 97
Period size: 23 Copynumber: 6.7 Consensus size: 21
2212192 TGTCATTATA
* *
2212202 TTTTTTA-TTATTTATTTTTTC
1 TTTTTTATTTA-TTATTATTAC
2212223 TTTTTTATTTATTTATTATTA-
1 TTTTTTATTTA-TTATTATTAC
2212244 TTATTATTATATTATTATTATTAC
1 TT-TT-TTAT-TTATTATTATTAC
*
2212268 TTTTTTCATTTTATTATTATTCC
1 TTTTTT-A-TTTATTATTATTAC
* *
2212291 TTTTTTTATTTGCTTTTATTTTTAC
1 -TTTTTTA-TT--TATTATTATTAC
*
2212316 TTATTTATTTACTTA-T-TTAC
1 TTTTTTATTTA-TTATTATTAC
*
2212336 TTATTTATTTATTA
1 TTTTTTATTTATTA
2212350 CTTGTTTTTC
Statistics
Matches: 108, Mismatches: 8, Indels: 24
0.77 0.06 0.17
Matches are distributed among these distances:
19 3 0.03
20 15 0.14
21 11 0.10
22 18 0.17
23 34 0.31
24 18 0.17
25 9 0.08
ACGTcount: A:0.22, C:0.06, G:0.01, T:0.72
Consensus pattern (21 bp):
TTTTTTATTTATTATTATTAC
Found at i:2212326 original size:12 final size:12
Alignment explanation
Indices: 2212311--2212352 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
2212301 TGCTTTTATT
2212311 TTTACTTATTTA
1 TTTACTTATTTA
2212323 TTTACTTATTTA
1 TTTACTTATTTA
* *
2212335 CTTATTTATTTA
1 TTTACTTATTTA
2212347 -TTACTT
1 TTTACTT
2212353 GTTTTTCTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
11 5 0.19
12 22 0.81
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTACTTATTTA
Found at i:2212521 original size:3 final size:3
Alignment explanation
Indices: 2212513--2212538 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2212503 ATTTAGTTAT
2212513 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
2212539 TCTTCTTGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2216408 original size:24 final size:24
Alignment explanation
Indices: 2216354--2216415 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
2216344 GAAAGGAACA
*
2216354 ATATTTTCAAAACTTTTGATTAAAC
1 ATATTTTCAAAACTCTT-ATTAAAC
*
2216379 AT-TTTTCAAAACTCTT-TTAAATG
1 ATATTTTCAAAACTCTTATTAAA-C
*
2216402 ATATTTTCAGAACT
1 ATATTTTCAAAACT
2216416 TTGAAAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
22 5 0.16
23 2 0.06
24 23 0.72
25 2 0.06
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.45
Consensus pattern (24 bp):
ATATTTTCAAAACTCTTATTAAAC
Found at i:2217312 original size:36 final size:36
Alignment explanation
Indices: 2217264--2217350 Score: 111
Period size: 36 Copynumber: 2.4 Consensus size: 36
2217254 CATTGAAAAC
* ** * *
2217264 ATTTCCCCTGAAATGAATTTTGTCTCTCTTGAGATA
1 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
*
2217300 GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
1 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
*
2217336 ATTTCTCTTGAAACA
1 ATTTCCCTTGAAACA
2217351 TAAACATTGA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39
Consensus pattern (36 bp):
ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
Found at i:2217359 original size:101 final size:101
Alignment explanation
Indices: 2217208--2217579 Score: 654
Period size: 101 Copynumber: 3.7 Consensus size: 101
2217198 AATTTACTCA
* *
2217208 AAACAAAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAACATAAACATTGAAAACATTTCCCCT
1 AAACAAA-TTTTGTCTCCCTTGAGACAATTTCTCTTGAAACATAAACATTGAAAACATTTCCCTT
2217273 GAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTG
65 GAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTG
2217310 AAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTG
1 AAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTG
* *
2217375 AAATGAATTTTATCTCTCTTGAGATAGTTTCCATTG
66 AAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTG
* *
2217411 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAACATTTCCCTTG
1 AAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTG
*
2217476 AAATGAATTTTGTCTTTCTTGAGATAGTTTCCCTTG
66 AAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTG
* *
2217512 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAACATTTCCCTTG
1 AAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTG
2217577 AAA
66 AAA
2217580 AACAAAATAT
Statistics
Matches: 261, Mismatches: 9, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
101 254 0.97
102 7 0.03
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.37
Consensus pattern (101 bp):
AAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTG
AAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTG
Found at i:2217413 original size:36 final size:35
Alignment explanation
Indices: 2217370--2217451 Score: 101
Period size: 36 Copynumber: 2.3 Consensus size: 35
2217360 AAAACATTTC
** * *
2217370 CCTTGAAATGAATTTTATCTCTCTTGAGATAGTTT
1 CCTTGAAACAAATTTTATCTCCCTTGAGACAGTTT
*
2217405 CCATTGAAACAAATTTTGTCTCCCTTGAGACAGTTT
1 CC-TTGAAACAAATTTTATCTCCCTTGAGACAGTTT
2217441 CTCTTGAAACA
1 C-CTTGAAACA
2217452 TAAACTTTGA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
35 2 0.05
36 37 0.93
37 1 0.03
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (35 bp):
CCTTGAAACAAATTTTATCTCCCTTGAGACAGTTT
Found at i:2217514 original size:36 final size:36
Alignment explanation
Indices: 2217467--2217552 Score: 118
Period size: 36 Copynumber: 2.4 Consensus size: 36
2217457 TTTGAAAACA
** ** *
2217467 TTTCCCTTGAAATGAATTTTGTCTTTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
2217503 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
*
2217539 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
2217553 TAAACTTTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
Found at i:2217719 original size:30 final size:30
Alignment explanation
Indices: 2217683--2217765 Score: 112
Period size: 30 Copynumber: 2.8 Consensus size: 30
2217673 TTTATCTCTC
*
2217683 TTGAGACAGTTTCTCTTGAAAGACCAACCT
1 TTGAGACAGTTTCTCTTGAAACACCAACCT
*
2217713 TTGAGACATTTTCTCTTGAAACACCAACCT
1 TTGAGACAGTTTCTCTTGAAACACCAACCT
* ** *
2217743 TTAAGATTGTTTCCCTTGAAACA
1 TTGAGACAGTTTCTCTTGAAACA
2217766 AATTTTGTCT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (30 bp):
TTGAGACAGTTTCTCTTGAAACACCAACCT
Found at i:2217786 original size:96 final size:97
Alignment explanation
Indices: 2217616--2217800 Score: 228
Period size: 96 Copynumber: 1.9 Consensus size: 97
2217606 TGAAACGAGT
* * * **
2217616 TTTGAGATAGTTTCCCTTGAAACACCCACATTTGAGATTGTTTCCCTTAAAACATGTTTTATCTC
1 TTTGAGACAGTTTCCCTTGAAACACCAACATTTAAGATTGTTTCCCTTAAAACAAATTTTATCTC
* * * *
2217681 TCTTGAGAC-AGTTTCTCTTGAAAGACCAACC
66 GCATAAGACAAGTTTCCCTTGAAAGACCAACC
* * * * *
2217712 TTTGAGACATTTTCTCTTGAAACACCAACCTTTAAGATTGTTTCCCTTGAAACAAATTTTGTCTC
1 TTTGAGACAGTTTCCCTTGAAACACCAACATTTAAGATTGTTTCCCTTAAAACAAATTTTATCTC
*
2217777 GCATAAGACAATTTTCCCTTGAAA
66 GCATAAGACAAGTTTCCCTTGAAA
2217801 CAATAAATTT
Statistics
Matches: 73, Mismatches: 15, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
96 61 0.84
97 12 0.16
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (97 bp):
TTTGAGACAGTTTCCCTTGAAACACCAACATTTAAGATTGTTTCCCTTAAAACAAATTTTATCTC
GCATAAGACAAGTTTCCCTTGAAAGACCAACC
Found at i:2219682 original size:15 final size:15
Alignment explanation
Indices: 2219659--2219705 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
2219649 TCCCCTGTTA
2219659 TTATATTTTTTATTAT
1 TTAT-TTTTTTATTAT
*
2219675 TTATTTTTTTATTTT
1 TTATTTTTTTATTAT
*
2219690 TTATTTATTTATTAT
1 TTATTTTTTTATTAT
2219705 T
1 T
2219706 ATTATTACTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
15 24 0.86
16 4 0.14
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
TTATTTTTTTATTAT
Found at i:2219710 original size:24 final size:24
Alignment explanation
Indices: 2219656--2219803 Score: 106
Period size: 28 Copynumber: 5.8 Consensus size: 24
2219646 TGATCCCCTG
2219656 TTATTA-TATTTTTTA-TTATTTA
1 TTATTATTATTTTTTATTTATTTA
*
2219678 TT-TTTTTATTTTTTATTTATTTA
1 TTATTATTATTTTTTATTTATTTA
2219701 TTATTATTATTACTTTT-TTTCATTTTA
1 TTATTATTATT--TTTTATTT-A-TTTA
*
2219728 TTATTATTCCTTTTTTATTTTGATTTTA
1 TTATTATT-ATTTTTTA-TTT-A-TTTA
* *
2219756 TTTTTACTTATTTACTTATTTATTTA
1 TTATTA-TTATTT-TTTATTTATTTA
2219782 CTTATTAACTTATTTATTTATT
1 -TTATT-A-TTATTT-TTTATT
2219804 GTTTGTTTTT
Statistics
Matches: 103, Mismatches: 9, Indels: 22
0.77 0.07 0.16
Matches are distributed among these distances:
21 2 0.02
22 11 0.11
23 9 0.09
24 7 0.07
25 3 0.03
26 13 0.13
27 17 0.17
28 36 0.35
29 5 0.05
ACGTcount: A:0.22, C:0.05, G:0.01, T:0.72
Consensus pattern (24 bp):
TTATTATTATTTTTTATTTATTTA
Found at i:2219778 original size:12 final size:12
Alignment explanation
Indices: 2219763--2219803 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
2219753 TTATTTTTAC
2219763 TTATTTACTTAT
1 TTATTTACTTAT
2219775 TTATTTACTTAT
1 TTATTTACTTAT
* * *
2219787 TAACTTATTTAT
1 TTATTTACTTAT
2219799 TTATT
1 TTATT
2219804 GTTTGTTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (12 bp):
TTATTTACTTAT
Found at i:2219783 original size:20 final size:20
Alignment explanation
Indices: 2219758--2219801 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
2219748 TGATTTTATT
*
2219758 TTTACTTATTTACTTATTTA
1 TTTACTTATTAACTTATTTA
2219778 TTTACTTATTAACTTATTTA
1 TTTACTTATTAACTTATTTA
2219798 TTTA
1 TTTA
2219802 TTGTTTGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTACTTATTAACTTATTTA
Found at i:2219928 original size:20 final size:19
Alignment explanation
Indices: 2219874--2219937 Score: 58
Period size: 21 Copynumber: 3.2 Consensus size: 19
2219864 CTTTTTTATT
2219874 TTTTTATTTTCTTTATTTTCC
1 TTTTTATTTT-TTTATTTT-C
* * *
2219895 TTTTGACTTCTTTTATTTTA
1 TTTTTA-TTTTTTTATTTTC
2219915 TTTTTATTTATTTT-TTTTC
1 TTTTTATTT-TTTTATTTTC
2219934 TTTT
1 TTTT
2219938 CTTCTTTTGT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
19 10 0.29
20 9 0.26
21 13 0.37
22 3 0.09
ACGTcount: A:0.11, C:0.09, G:0.02, T:0.78
Consensus pattern (19 bp):
TTTTTATTTTTTTATTTTC
Found at i:2219951 original size:36 final size:40
Alignment explanation
Indices: 2219874--2219952 Score: 96
Period size: 41 Copynumber: 2.0 Consensus size: 40
2219864 CTTTTTTATT
*
2219874 TTTTTATTTTCTTTATTTTCCTTTTGACTTCTTTTATTTTA
1 TTTTTATTTTCTTTATTTTCCTTTT-ACTTCTTTTAGTTTA
2219915 TTTTTATTTAT-TTT-TTTT-CTTTT-CTTCTTTT-GTTTA
1 TTTTTATTT-TCTTTATTTTCCTTTTACTTCTTTTAGTTTA
2219951 TT
1 TT
2219953 ATGTTAGTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
36 6 0.17
37 8 0.22
39 5 0.14
40 4 0.11
41 12 0.33
42 1 0.03
ACGTcount: A:0.10, C:0.10, G:0.03, T:0.77
Consensus pattern (40 bp):
TTTTTATTTTCTTTATTTTCCTTTTACTTCTTTTAGTTTA
Found at i:2223039 original size:15 final size:15
Alignment explanation
Indices: 2223019--2223051 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2223009 TTAGCTGGGT
*
2223019 GGGCGGATGTGGGGC
1 GGGCGGATGCGGGGC
2223034 GGGCGGATGCGGGGC
1 GGGCGGATGCGGGGC
2223049 GGG
1 GGG
2223052 TAATGTCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.15, G:0.70, T:0.09
Consensus pattern (15 bp):
GGGCGGATGCGGGGC
Found at i:2224753 original size:24 final size:24
Alignment explanation
Indices: 2224710--2224758 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
2224700 ATATTATTTA
* *
2224710 TATTCTTTATATTATTATAATTAT
1 TATTATTTATATTATTATAAATAT
2224734 TATTATTT-TATTATTAATAAATAT
1 TATTATTTATATTATT-ATAAATAT
2224758 T
1 T
2224759 TTTACAGGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (24 bp):
TATTATTTATATTATTATAAATAT
Found at i:2226889 original size:26 final size:27
Alignment explanation
Indices: 2226837--2226894 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
2226827 TAATTCTTTC
*
2226837 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATATTTATATATAC-TATTA
* *
2226865 TTTTCATAATATTTATATGTA-TATTA
1 TTTTCAAAATATTTATATATACTATTA
2226891 TTTT
1 TTTT
2226895 ATTAATGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 9 0.33
28 18 0.67
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATACTATTA
Found at i:2230199 original size:15 final size:15
Alignment explanation
Indices: 2230181--2230212 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2230171 GATCAATACC
2230181 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
2230196 TTTTGCATACATTCA
1 TTTTGCATACATGCA
2230211 TT
1 TT
2230213 ATTCATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:2237531 original size:7 final size:7
Alignment explanation
Indices: 2237519--2237631 Score: 88
Period size: 7 Copynumber: 15.6 Consensus size: 7
2237509 ATGCTTGAAG
2237519 AAAGAAA
1 AAAGAAA
2237526 AAAGAAAA
1 AAAG-AAA
*
2237534 AAAAAAGA
1 AAAGAA-A
2237542 GAAAGACAA
1 -AAAGA-AA
*
2237551 AAGGAAA
1 AAAGAAA
*
2237558 AAA-AGAG
1 AAAGA-AA
2237565 AAAGAAA
1 AAAGAAA
2237572 AAAGGAAA
1 AAA-GAAA
*
2237580 AAGGAAA
1 AAAGAAA
*
2237587 AAAG-AG
1 AAAGAAA
2237593 AAAGAAAA
1 AAAG-AAA
*
2237601 AAAGAGA
1 AAAGAAA
2237608 AAAGAAA
1 AAAGAAA
2237615 AAAG-AA
1 AAAGAAA
2237621 AAAGAAA
1 AAAGAAA
2237628 AAAG
1 AAAG
2237632 GGGGTCAAGA
Statistics
Matches: 84, Mismatches: 12, Indels: 20
0.72 0.10 0.17
Matches are distributed among these distances:
6 12 0.14
7 43 0.51
8 23 0.27
9 5 0.06
10 1 0.01
ACGTcount: A:0.79, C:0.01, G:0.20, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:2237547 original size:28 final size:29
Alignment explanation
Indices: 2237519--2237631 Score: 53
Period size: 22 Copynumber: 4.4 Consensus size: 29
2237509 ATGCTTGAAG
2237519 AAAGAAAAAAGA-AAA-AAAAAAGAG---
1 AAAGAAAAAAGAGAAAGAAAAAAGAGAAA
*
2237543 AAAGACAAAAG-G--A-AAAAAAGAG--A
1 AAAGAAAAAAGAGAAAGAAAAAAGAGAAA
*
2237566 -AAGAAAAAAGGAAAAAGGAAAAAAGAG-AA
1 AAAGAAAAAA-GAGAAA-GAAAAAAGAGAAA
*
2237595 AGA-AAAAAAGAGAAA-AGAAAAA-AG-AA
1 AAAGAAAAAAGAGAAAGA-AAAAAGAGAAA
2237621 AAAGAAAAAAG
1 AAAGAAAAAAG
2237632 GGGGTCAAGA
Statistics
Matches: 71, Mismatches: 6, Indels: 21
0.72 0.06 0.21
Matches are distributed among these distances:
22 18 0.25
23 1 0.01
24 10 0.14
26 8 0.11
27 12 0.17
28 14 0.20
29 7 0.10
30 1 0.01
ACGTcount: A:0.79, C:0.01, G:0.20, T:0.00
Consensus pattern (29 bp):
AAAGAAAAAAGAGAAAGAAAAAAGAGAAA
Found at i:2237558 original size:22 final size:21
Alignment explanation
Indices: 2237533--2237623 Score: 98
Period size: 22 Copynumber: 4.2 Consensus size: 21
2237523 AAAAAAGAAA
2237533 AAAAAAAGAGAAAGACAAAAGG
1 AAAAAAAGAGAAAGA-AAAAGG
2237555 AAAAAAAGAGAAAGAAAAAAGG
1 AAAAAAAGAGAAAG-AAAAAGG
*
2237577 AAAAAGGAA-A-AAAGAGAAA-G
1 AAAAA--AAGAGAAAGAAAAAGG
*
2237597 AAAAAAAGAGAAAAGAAAAAAG
1 AAAAAAAGAG-AAAGAAAAAGG
2237619 AAAAA
1 AAAAA
2237624 GAAAAAAGGG
Statistics
Matches: 60, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
18 2 0.03
19 1 0.02
20 6 0.10
21 12 0.20
22 35 0.58
23 2 0.03
24 2 0.03
ACGTcount: A:0.78, C:0.01, G:0.21, T:0.00
Consensus pattern (21 bp):
AAAAAAAGAGAAAGAAAAAGG
Done.