Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold76
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: 1973630
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 106294 characters in sequence are not A, C, G, or T
File 3 of 5
Found at i:829836 original size:30 final size:30
Alignment explanation
Indices: 829802--829861 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
829792 CATTACATAG
*
829802 CTATTATCAAATTGATGTCAAACGGTGTAT
1 CTATTATCAAATTGATGTCAAACAGTGTAT
829832 CTATTATCAAATTGATGTCAAACAGTGTAT
1 CTATTATCAAATTGATGTCAAACAGTGTAT
829862 GAGCATGGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (30 bp):
CTATTATCAAATTGATGTCAAACAGTGTAT
Found at i:830144 original size:23 final size:22
Alignment explanation
Indices: 830118--830161 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
830108 ATTTTACCAA
*
830118 TAAAAATGTAGACAAGTTGCCAG
1 TAAAAACG-AGACAAGTTGCCAG
*
830141 TAAAAACGAGATAAGTTGCCA
1 TAAAAACGAGACAAGTTGCCA
830162 TTCCCCTCGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.45, C:0.14, G:0.20, T:0.20
Consensus pattern (22 bp):
TAAAAACGAGACAAGTTGCCAG
Found at i:832276 original size:20 final size:19
Alignment explanation
Indices: 832250--832300 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 19
832240 TTGGAGTAGG
*
832250 AATATCGATACCTTAGGAA
1 AATATCGATACCTTAAGAA
832269 ATATATCGATACCTTAAGAA
1 A-ATATCGATACCTTAAGAA
832289 AAGTATCGATAC
1 AA-TATCGATAC
832301 TAGATCAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 2 0.07
20 27 0.93
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.27
Consensus pattern (19 bp):
AATATCGATACCTTAAGAA
Found at i:839189 original size:3 final size:3
Alignment explanation
Indices: 839181--839263 Score: 157
Period size: 3 Copynumber: 27.7 Consensus size: 3
839171 AGGATCCTAA
*
839181 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAA AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
839229 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
839264 AGTGAGGATC
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:843325 original size:37 final size:37
Alignment explanation
Indices: 843282--843356 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
843272 ATGAAATGCT
* *
843282 TAAGTCATATGCTTTGAAATCAATGCTTGTAGCATAC
1 TAAGTCATATACTCTGAAATCAATGCTTGTAGCATAC
*
843319 TAAGTCATATACTCTGAAATCAGTGCTTGTAGCATAC
1 TAAGTCATATACTCTGAAATCAATGCTTGTAGCATAC
843356 T
1 T
843357 TTATCAATGG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (37 bp):
TAAGTCATATACTCTGAAATCAATGCTTGTAGCATAC
Found at i:849126 original size:20 final size:20
Alignment explanation
Indices: 849079--849130 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
849069 GACAATCATT
* *
849079 TTAAAATGATTTTGACTTGA
1 TTAAAATCATTTTGACATGA
** *
849099 TTGGAATCATTTTGACATGG
1 TTAAAATCATTTTGACATGA
849119 TTAAAATCATTT
1 TTAAAATCATTT
849131 GCTCTTGATT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44
Consensus pattern (20 bp):
TTAAAATCATTTTGACATGA
Found at i:849378 original size:30 final size:29
Alignment explanation
Indices: 849342--849412 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
849332 TCCTCTTGAC
* *
849342 TTAGATAGCCACAGAGGTG-TCTACACATCA
1 TTAGATAGCCACA-AGG-GATCCAAACATCA
*
849372 TTAGATAGCCATAAGGGCATCCAAACATCA
1 TTAGATAGCCACAAGGG-ATCCAAACATCA
849402 TTAGATAGCCA
1 TTAGATAGCCA
849413 TAAAGGCGTC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 1 0.03
29 3 0.08
30 32 0.89
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.23
Consensus pattern (29 bp):
TTAGATAGCCACAAGGGATCCAAACATCA
Found at i:849413 original size:30 final size:30
Alignment explanation
Indices: 849366--849424 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
849356 AGGTGTCTAC
*
849366 ACATCATTAGATAGCCATAAGGGCATCCAA
1 ACATCATTAGATAGCCATAAAGGCATCCAA
*
849396 ACATCATTAGATAGCCATAAAGGCGTCCA
1 ACATCATTAGATAGCCATAAAGGCATCCA
849425 TACACATACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (30 bp):
ACATCATTAGATAGCCATAAAGGCATCCAA
Found at i:850461 original size:32 final size:32
Alignment explanation
Indices: 850420--850548 Score: 258
Period size: 32 Copynumber: 4.0 Consensus size: 32
850410 ACGTCAATGC
850420 TGCTGTCCAAAAACTGTTCCATTCCAAATTTT
1 TGCTGTCCAAAAACTGTTCCATTCCAAATTTT
850452 TGCTGTCCAAAAACTGTTCCATTCCAAATTTT
1 TGCTGTCCAAAAACTGTTCCATTCCAAATTTT
850484 TGCTGTCCAAAAACTGTTCCATTCCAAATTTT
1 TGCTGTCCAAAAACTGTTCCATTCCAAATTTT
850516 TGCTGTCCAAAAACTGTTCCATTCCAAATTTT
1 TGCTGTCCAAAAACTGTTCCATTCCAAATTTT
850548 T
1 T
850549 ACTCTTTTAT
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 97 1.00
ACGTcount: A:0.28, C:0.25, G:0.09, T:0.38
Consensus pattern (32 bp):
TGCTGTCCAAAAACTGTTCCATTCCAAATTTT
Found at i:850976 original size:20 final size:20
Alignment explanation
Indices: 850951--850989 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
850941 TACTTTCTTC
850951 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
850971 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
850990 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:852620 original size:50 final size:50
Alignment explanation
Indices: 852556--852785 Score: 325
Period size: 50 Copynumber: 4.6 Consensus size: 50
852546 GAGCCAATGT
* * * * * *
852556 CATGTCCCAGACATGGTCTTACACAGACTCTTCTCTGTCTGTGCCGATGG
1 CATGTCCCAGACATGGTCTTACACTGGCACTCCTCGGTCTGTGCCGATGC
* *
852606 CATGTCCTAAACATGGTCTTACACTGGCACTCCTCGGTCTGTGCCGATGC
1 CATGTCCCAGACATGGTCTTACACTGGCACTCCTCGGTCTGTGCCGATGC
*
852656 CATGTCCCAGACATGGTCTTACACTGGCACTCCTCAGTCTGTGCCGATGC
1 CATGTCCCAGACATGGTCTTACACTGGCACTCCTCGGTCTGTGCCGATGC
* * * **
852706 CATGTCCTAGACATGGTCTTACATTGGCACTTCTCGGTCTGTGTTGATGC
1 CATGTCCCAGACATGGTCTTACACTGGCACTCCTCGGTCTGTGCCGATGC
*
852756 CATGTCCCAGACATGGTCTTACACTAGCAC
1 CATGTCCCAGACATGGTCTTACACTGGCAC
852786 ACTTACTGCC
Statistics
Matches: 160, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 160 1.00
ACGTcount: A:0.19, C:0.30, G:0.22, T:0.29
Consensus pattern (50 bp):
CATGTCCCAGACATGGTCTTACACTGGCACTCCTCGGTCTGTGCCGATGC
Found at i:852773 original size:150 final size:147
Alignment explanation
Indices: 852500--852785 Score: 349
Period size: 150 Copynumber: 1.9 Consensus size: 147
852490 CTTGGTAGGA
* * *
852500 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCATATCTCGAGCCAATGTCATGTCCCA
1 TGCCAATGCCATATCCCAGACATGGTCTTACATGGCATCATATCTCGAGCCAATGCCATGTCCCA
* * * *
852565 GACATGGTCTTACACAGACTCTTCTCTGTCTGTGCCGATGGCATGTCCTAAACATGGTCTTACAC
66 GACATGGTCTTACACAGACACTTCTCGGTCTGTGCCGATGCCATGTCCCAAACATGGTCTTACAC
*
852630 TGGCACTCCTCGGTCTG
131 TAGCACTCCTCGGTCTG
* * * * *
852647 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCCTCAGTCT-GTGCCGATGCCATGT
1 TGCCAATGCCATATCCCAGACATGGTCTTACA-TGGCA-TCAT-A-TCTCGAGCCAATGCCATGT
* ** * ** *
852711 CCTAGACATGGTCTTACATTGGCACTTCTCGGTCTGTGTTGATGCCATGTCCCAGACATGGTCTT
62 CCCAGACATGGTCTTACACAGACACTTCTCGGTCTGTGCCGATGCCATGTCCCAAACATGGTCTT
852776 ACACTAGCAC
127 ACACTAGCAC
852786 ACTTACTGCC
Statistics
Matches: 115, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
147 29 0.25
148 4 0.03
149 3 0.03
150 76 0.66
151 3 0.03
ACGTcount: A:0.20, C:0.29, G:0.21, T:0.29
Consensus pattern (147 bp):
TGCCAATGCCATATCCCAGACATGGTCTTACATGGCATCATATCTCGAGCCAATGCCATGTCCCA
GACATGGTCTTACACAGACACTTCTCGGTCTGTGCCGATGCCATGTCCCAAACATGGTCTTACAC
TAGCACTCCTCGGTCTG
Found at i:852866 original size:44 final size:44
Alignment explanation
Indices: 852813--852900 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 44
852803 AACCATGGTA
* * *
852813 TTTTTCGTCAATTTTTTCTTAATTGCCATGTTATAAACATGGAC
1 TTTTCCGTCAATTCTTCCTTAATTGCCATGTTATAAACATGGAC
852857 TTTTCCGTCAATTCTTCCTTAATTGCCATGTTATAAACATGGAC
1 TTTTCCGTCAATTCTTCCTTAATTGCCATGTTATAAACATGGAC
852901 CTTGAGATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.44
Consensus pattern (44 bp):
TTTTCCGTCAATTCTTCCTTAATTGCCATGTTATAAACATGGAC
Found at i:854580 original size:56 final size:52
Alignment explanation
Indices: 854450--854587 Score: 163
Period size: 50 Copynumber: 2.6 Consensus size: 52
854440 TCTCATATCG
* * *
854450 ATGCCCATGCCATGTCCTAGACATGGTCTTACGGGGGACCTCTCATCTCAGT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCAAT
* *
854502 A--CCAACGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATAACCTCAAT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCAT---CTCAAT
* *
854555 AATGCCAATGCCATGTCCCAAACATGGTGTTAC
1 -ATGCCAATGCCATGTCCCAGACATGGTCTTAC
854588 ATGATGTCTC
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
50 39 0.54
52 1 0.01
53 5 0.07
54 1 0.01
56 26 0.36
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.25
Consensus pattern (52 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCAAT
Found at i:855682 original size:50 final size:50
Alignment explanation
Indices: 855611--855740 Score: 143
Period size: 50 Copynumber: 2.6 Consensus size: 50
855601 CTGTACTGCA
* * * ** * *
855611 AATGTCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATCGGTGCC
1 AATGACATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCAGTACC
* * *** *
855661 CATGCCATGTCCCAGACATGGTCTTATGGGAGACCTCTCATCTCAGTACC
1 AATGACATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCAGTACC
855711 AATGACATGTCCCAGACATGGTCTTACATG
1 AATGACATGTCCCAGACATGGTCTTACATG
855741 GGGTCTCATC
Statistics
Matches: 63, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
50 63 1.00
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.28
Consensus pattern (50 bp):
AATGACATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCAGTACC
Found at i:858926 original size:49 final size:49
Alignment explanation
Indices: 858869--858966 Score: 178
Period size: 49 Copynumber: 2.0 Consensus size: 49
858859 CTAATCCAAG
*
858869 AAAACTTCTAACCTCTGACACATTTCTGGGTGGTTTCCACTCAACAATT
1 AAAACTTCTAACCTCTCACACATTTCTGGGTGGTTTCCACTCAACAATT
*
858918 AAAACTTCTAACCTCTCACACATTTTTGGGTGGTTTCCACTCAACAATT
1 AAAACTTCTAACCTCTCACACATTTCTGGGTGGTTTCCACTCAACAATT
858967 GCTAAAATTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.34
Consensus pattern (49 bp):
AAAACTTCTAACCTCTCACACATTTCTGGGTGGTTTCCACTCAACAATT
Found at i:867284 original size:20 final size:18
Alignment explanation
Indices: 867259--867295 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 18
867249 CTACCTAATA
867259 AAAGAAGGAGAGAGAAGAAG
1 AAAGAA-GA-AGAGAAGAAG
867279 AAAGAAGAAGAGAAGAA
1 AAAGAAGAAGAGAAGAA
867296 TTTGTGTGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 2 0.12
20 6 0.35
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (18 bp):
AAAGAAGAAGAGAAGAAG
Found at i:875319 original size:27 final size:27
Alignment explanation
Indices: 875262--875323 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
875252 TTAAGAGTGT
* *
875262 GCCACGAAGGCATTCCTTACAAAGTTT
1 GCCACAAAGGCATTCCTTACAAAGTTC
* *
875289 GCCACAAAGGCATTCCTTCCATA-TTAC
1 GCCACAAAGGCATTCCTTACAAAGTT-C
875316 GCCACAAA
1 GCCACAAA
875324 CGTTTTCTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 2 0.07
27 28 0.93
ACGTcount: A:0.32, C:0.31, G:0.15, T:0.23
Consensus pattern (27 bp):
GCCACAAAGGCATTCCTTACAAAGTTC
Found at i:880190 original size:41 final size:43
Alignment explanation
Indices: 880132--880213 Score: 116
Period size: 41 Copynumber: 2.0 Consensus size: 43
880122 ATTTCCATGT
* *
880132 CATTTTCATTTTTCATTTTTG-AGAAAACGACA-TTCATTTCTC
1 CATTCTCATTTTTCA-TTTTGCAGAAAACCACATTTCATTTCTC
880174 CATTCTCA-TTTTCATTTTGCAGAAAACCACATTTCATTTC
1 CATTCTCATTTTTCATTTTGCAGAAAACCACATTTCATTTC
880214 CAAATGTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
40 5 0.14
41 16 0.44
42 15 0.42
ACGTcount: A:0.27, C:0.22, G:0.06, T:0.45
Consensus pattern (43 bp):
CATTCTCATTTTTCATTTTGCAGAAAACCACATTTCATTTCTC
Found at i:884566 original size:42 final size:42
Alignment explanation
Indices: 884485--884611 Score: 148
Period size: 43 Copynumber: 3.0 Consensus size: 42
884475 TTCCAATATT
* * * ** *
884485 GATTTGAGATCCCGTATAATACCATATATGGGATA-TGGCATC
1 GATTTGAGAT-TCGTGTAAGACCATAGCTGGGCTATTGGCATC
*
884527 GATTTGAGATTCGTGTAAGACCATAGCTGGGCTATTGGCATT
1 GATTTGAGATTCGTGTAAGACCATAGCTGGGCTATTGGCATC
* *
884569 GATTTAAGATTTTGTGTAAGACCATAGCTGGGCTATTGGCATC
1 GATTTGAGA-TTCGTGTAAGACCATAGCTGGGCTATTGGCATC
884612 AATACGAGAT
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
41 18 0.25
42 24 0.33
43 31 0.42
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (42 bp):
GATTTGAGATTCGTGTAAGACCATAGCTGGGCTATTGGCATC
Found at i:884622 original size:43 final size:44
Alignment explanation
Indices: 884538--884637 Score: 130
Period size: 43 Copynumber: 2.3 Consensus size: 44
884528 ATTTGAGATT
** **
884538 CGTGTAAGACCATAGCTGGGCTATTGGCATTGATTTAAGATTT-
1 CGTGTAAGACCATAGCTGGGCTATTGGCATCAATACAAGATTTC
* *
884581 TGTGTAAGACCATAGCTGGGCTATTGGCATCAATACGAGATTTC
1 CGTGTAAGACCATAGCTGGGCTATTGGCATCAATACAAGATTTC
*
884625 CATGTAAGACCAT
1 CGTGTAAGACCAT
884638 GTCTGGGACA
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 37 0.77
44 11 0.23
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (44 bp):
CGTGTAAGACCATAGCTGGGCTATTGGCATCAATACAAGATTTC
Found at i:888015 original size:18 final size:17
Alignment explanation
Indices: 887990--888023 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
887980 TATATATTAT
887990 TTAATAAATTAATTTAA
1 TTAATAAATTAATTTAA
888007 TTAACTAAATTAATTTA
1 TTAA-TAAATTAATTTA
888024 TCAATTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAATAAATTAATTTAA
Found at i:889791 original size:10 final size:10
Alignment explanation
Indices: 889776--889817 Score: 61
Period size: 10 Copynumber: 4.3 Consensus size: 10
889766 AACTTCAATT
889776 ATTTCTATTC
1 ATTTCTATTC
889786 ATTTCTA-TC
1 ATTTCTATTC
889795 ATTTGC-ATTC
1 ATTT-CTATTC
889805 ATTTCTATTC
1 ATTTCTATTC
889815 ATT
1 ATT
889818 GGTTCTACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.28
10 21 0.72
ACGTcount: A:0.21, C:0.19, G:0.02, T:0.57
Consensus pattern (10 bp):
ATTTCTATTC
Found at i:900444 original size:42 final size:42
Alignment explanation
Indices: 900377--900474 Score: 153
Period size: 42 Copynumber: 2.4 Consensus size: 42
900367 TACTTAGTGA
* * *
900377 GTTACACAGC-TAGGACACGACCGTGTGTCCCTTGTTTGAAT
1 GTTACACAGCTTGGGACACAACCGTGTGTCCCTTGTTCGAAT
*
900418 GTTACACAGGTTGGGACACAACCGTGTGTCCCTTGTTCGAAT
1 GTTACACAGCTTGGGACACAACCGTGTGTCCCTTGTTCGAAT
900460 GTTACACAGCTTGGG
1 GTTACACAGCTTGGG
900475 GAGATATTAC
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 9 0.18
42 42 0.82
ACGTcount: A:0.21, C:0.23, G:0.27, T:0.29
Consensus pattern (42 bp):
GTTACACAGCTTGGGACACAACCGTGTGTCCCTTGTTCGAAT
Found at i:900571 original size:21 final size:21
Alignment explanation
Indices: 900545--900584 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
900535 TTTTCTTAAA
*
900545 AGTTCTCATTTGCTTCAAATT
1 AGTTCTCAATTGCTTCAAATT
*
900566 AGTTCTGAATTGCTTCAAA
1 AGTTCTCAATTGCTTCAAA
900585 GTTATTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
AGTTCTCAATTGCTTCAAATT
Found at i:913111 original size:558 final size:558
Alignment explanation
Indices: 912057--913177 Score: 2039
Period size: 558 Copynumber: 2.0 Consensus size: 558
912047 CCCAAAAAAT
*
912057 AGAGACATAGATGTGACTGACTAGACTAGCAATACATTGGACTGGACCTAAGAAGAATAGATCAT
1 AGAGACATAGATGTGACTGACTAGACTAGCAATACATTGGACTGGACCTAAGAAAAATAGATCAT
*
912122 GAATCCATTTATGTATTTATTCACTTGTGATGTTCATAGTGTGGTATACCTAAATCCTGAGTGGA
66 GAATCCATTTATGTATTTATTCACTTGTGATGTTCATAGTGTGGCATACCTAAATCCTGAGTGGA
912187 TGACGGGCTATGTATGCATGACTCGTACACTTTTATGTAAGTAAAAGCTTAAGTTTGAATAGATA
131 TGACGGGCTATGTATGCATGACTCGTACACTTTTATGTAAGTAAAAGCTTAAGTTTGAATAGATA
*
912252 AGGAACCTAAAGCTGGTGTGTTGGATGTACAACTTCTACAATATGTAGCTTAATTTACAATAATG
196 AGGAACCGAAAGCTGGTGTGTTGGATGTACAACTTCTACAATATGTAGCTTAATTTACAATAATG
912317 GAATTCATAGCCCAAGACATGGGTAAATAATATCCTCTCATTTACATTACACAGTTGATGAAAAG
261 GAATTCATAGCCCAAGACATGGGTAAATAATATCCTCTCATTTACATTACACAGTTGATGAAAAG
*
912382 TAAACGTGGTCACAGGTTGTTTGTCTTTGTGATGAATGACTTGATTACTATTGGTTAGTAACTGA
326 TAAACGTGGTCACAGGTTGTTTGTCTTTGTGATGAATGACTTGATTACTATTAGTTAGTAACTGA
912447 CTTCTTATGAAAGAAAATGTAATGGTTACCATGAGATAAAATACGATCATATTGGGAGAACAAAT
391 CTTCTTATGAAAGAAAATGTAATGGTTACCATGAGATAAAATACGATCATATTGGGAGAACAAAT
912512 ATTATCCCAAAGAGATTAAGGATATCATATTAGGGTAACACACATATGACAAGGTCATTGGACGA
456 ATTATCCCAAAGAGATTAAGGATATCATATTAGGGTAACACACATATGACAAGGTCATTGGACGA
*
912577 GCATTGGTAGAGTTGATTTTGCAATGGTATGCCATTGG
521 GCATTGGTAGAGTTGATTTCGCAATGGTATGCCATTGG
*
912615 AGAGACATAGATGTGACTGACTAGACTAGCAATACATTGGACTGGACCTAAGAAAAATAGATCCT
1 AGAGACATAGATGTGACTGACTAGACTAGCAATACATTGGACTGGACCTAAGAAAAATAGATCAT
*
912680 GAATCCATTTATGTCTTTATTCACTTGTGATGTTCATAGTGTGGCATACCTAAATCCTGAGTGGA
66 GAATCCATTTATGTATTTATTCACTTGTGATGTTCATAGTGTGGCATACCTAAATCCTGAGTGGA
**
912745 TGACGGGCTATGTATGCATGACTCGTACACTTTTATGTAAGTAAAAGCTTGCGTTTGAATAGATA
131 TGACGGGCTATGTATGCATGACTCGTACACTTTTATGTAAGTAAAAGCTTAAGTTTGAATAGATA
912810 AGGAACCGAAAGCTGGTGTGTTGGATGTACGAA-TTCTACAATATGTAGCTTAATTTACAATAAT
196 AGGAACCGAAAGCTGGTGTGTTGGATGTAC-AACTTCTACAATATGTAGCTTAATTTACAATAAT
* *
912874 GGAATTCATAGCCTAAGACATGGGTAAATAATATCCTCTCATTTACATTACACAGTTGATGATAA
260 GGAATTCATAGCCCAAGACATGGGTAAATAATATCCTCTCATTTACATTACACAGTTGATGAAAA
* * *
912939 GTAAACGTGGTCATAGGTTGTTTGTGTTTGTGATGAATGACTTGATTACTATTAGTTAGTAATTG
325 GTAAACGTGGTCACAGGTTGTTTGTCTTTGTGATGAATGACTTGATTACTATTAGTTAGTAACTG
*
913004 ACTT-TTCATGAAAGAAAATGTAATGGTTACCATGAGATAAAATAGGATCATATTGGGAGAACAA
390 ACTTCTT-ATGAAAGAAAATGTAATGGTTACCATGAGATAAAATACGATCATATTGGGAGAACAA
* *
913068 ATATTATCCCAAAGAGATTAAGGATATCCTATTAGGGTAACACATATATGACAAGGTCATTGGAC
454 ATATTATCCCAAAGAGATTAAGGATATCATATTAGGGTAACACACATATGACAAGGTCATTGGAC
* *
913133 GAGTATTGGTAGAGTTGATTTCGTAATGGTATGCCATTGG
519 GAGCATTGGTAGAGTTGATTTCGCAATGGTATGCCATTGG
913173 AGAGA
1 AGAGA
913178 GCTCAGTCTG
Statistics
Matches: 542, Mismatches: 19, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
557 2 0.00
558 538 0.99
559 2 0.00
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (558 bp):
AGAGACATAGATGTGACTGACTAGACTAGCAATACATTGGACTGGACCTAAGAAAAATAGATCAT
GAATCCATTTATGTATTTATTCACTTGTGATGTTCATAGTGTGGCATACCTAAATCCTGAGTGGA
TGACGGGCTATGTATGCATGACTCGTACACTTTTATGTAAGTAAAAGCTTAAGTTTGAATAGATA
AGGAACCGAAAGCTGGTGTGTTGGATGTACAACTTCTACAATATGTAGCTTAATTTACAATAATG
GAATTCATAGCCCAAGACATGGGTAAATAATATCCTCTCATTTACATTACACAGTTGATGAAAAG
TAAACGTGGTCACAGGTTGTTTGTCTTTGTGATGAATGACTTGATTACTATTAGTTAGTAACTGA
CTTCTTATGAAAGAAAATGTAATGGTTACCATGAGATAAAATACGATCATATTGGGAGAACAAAT
ATTATCCCAAAGAGATTAAGGATATCATATTAGGGTAACACACATATGACAAGGTCATTGGACGA
GCATTGGTAGAGTTGATTTCGCAATGGTATGCCATTGG
Found at i:914463 original size:50 final size:50
Alignment explanation
Indices: 914398--914529 Score: 147
Period size: 50 Copynumber: 2.6 Consensus size: 50
914388 GGAACGAGAT
* ***
914398 CCCATGTAAGACCATGTCTGGGACATGGCATTACCACCGAGATGAGAGGT
1 CCCACGTAAGACCATGTCTGGGACATGGCATTACCACCGAGATGAGAACA
* * *** *
914448 CCCCCGTAAGACCATGTTTGGGACATGGCATGGGCACCGATATGAGAACA
1 CCCACGTAAGACCATGTCTGGGACATGGCATTACCACCGAGATGAGAACA
* * *
914498 CCCATGTAAGACCATATCTGGGATATGGCATT
1 CCCACGTAAGACCATGTCTGGGACATGGCATT
914530 GGCAGTACAG
Statistics
Matches: 66, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
50 66 1.00
ACGTcount: A:0.28, C:0.24, G:0.27, T:0.21
Consensus pattern (50 bp):
CCCACGTAAGACCATGTCTGGGACATGGCATTACCACCGAGATGAGAACA
Found at i:926794 original size:3 final size:3
Alignment explanation
Indices: 926786--926813 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
926776 ATGTGTATGT
926786 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
926814 CTTCATAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:926856 original size:7 final size:7
Alignment explanation
Indices: 926837--926871 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
926827 AAATCAAATT
926837 TAATAAA
1 TAATAAA
926844 -AATAAA
1 TAATAAA
926850 TAATAAA
1 TAATAAA
926857 TAATAAA
1 TAATAAA
926864 TAAATAAA
1 T-AATAAA
926872 AAGACTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 6 0.23
7 14 0.54
8 6 0.23
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
TAATAAA
Found at i:927049 original size:88 final size:88
Alignment explanation
Indices: 926891--927655 Score: 822
Period size: 88 Copynumber: 8.7 Consensus size: 88
926881 TCGAGGCAAT
* * * * * **
926891 AAGACTGATGTCTTCGATCTGCTTCACTGCCAGTACAGAAAGGCAAGATCTACTATTTTCAACCT
1 AAGACTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAGTCT
* ** **
926956 ACTCCACTGC-TGCTCAGGGAGAT
66 GCTCCACTGCAACCT-AGGGAGGC
* * * * ** * *
926979 AAGGCCGGAT-TTTTCGATTTGCTTCGCTACCGGTACAGGAAGGCAAGATCTGCTATCTTCAGTC
1 AAGACTGG-TGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAGTC
* *
927043 TGCTCCACTACAACCTAAGGAGGC
65 TGCTCCACTGCAACCTAGGGAGGC
* * * * * **
927067 AAGACTGGCGTCTTCAATCTGCTTCGCTGTCAGTACAAGAAGCCAAGATCTACTATTTTCAACCT
1 AAGACTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAGTCT
* *
927132 GCTCCGCTACAATCC-AGGGAGGC
66 GCTCCACTGCAA-CCTAGGGAGGC
* * * ** * *
927155 AAGGCTGGTGTCTTTGATCTGCTTTGCTACCAGTATAGGAAGGTAAGATCTGCTATCTTT-AGTC
1 AAGACTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTAT-TTTCAGTC
*
927219 TGCTCCACTGCACCCTAGGGAGGC
65 TGCTCCACTGCAACCTAGGGAGGC
* * *
927243 AAGACTGGTGTCTTCGATCTGCTTCACCGTCAGTACAGGAAGGCAAGATCTGCTATTTTCA-ACG
1 AAGACTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAGTC-
* *
927307 TGCTCCGCTGCAACCCAGGGAGGC
65 TGCTCCACTGCAACCTAGGGAGGC
* * * * * * *
927331 AAGGCTGGTGTCCTT-GATATGCTTCACTGTCGGTACAGGAAGGCAAGATCTACTGTCTTCAGTC
1 AAGACTGGTGT-CTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAGTC
927395 TGCTCCACTGCAACCTAGGGAGGC
65 TGCTCCACTGCAACCTAGGGAGGC
* * * *
927419 AAGACTGGTATCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTACTGTCTTCAGTCT
1 AAGACTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAGTCT
927484 GCTCCACTGCAACCTAGGGAGGC
66 GCTCCACTGCAACCTAGGGAGGC
* * * **
927507 AAGACTGGTATCTTCGATCTGCTTCACTGTCAGTACAGGAAGGCAATATCTGCTATTTTCAACCT
1 AAGACTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAGTCT
* *
927572 GCTCCGCTGCAACCCAGGGAGGC
66 GCTCCACTGCAACCTAGGGAGGC
* ** * * *
927595 AAGGCTGGTGTCTTTAATCTGCTTCGCTGCCGGTATAGGAAGGCAAGATCTGCTATTTTCA
1 AAGACTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCA
927656 ATGATCTGTT
Statistics
Matches: 566, Mismatches: 100, Indels: 22
0.82 0.15 0.03
Matches are distributed among these distances:
87 9 0.02
88 545 0.96
89 12 0.02
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27
Consensus pattern (88 bp):
AAGACTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAGTCT
GCTCCACTGCAACCTAGGGAGGC
Found at i:927288 original size:44 final size:44
Alignment explanation
Indices: 927063--927552 Score: 227
Period size: 44 Copynumber: 11.1 Consensus size: 44
927053 CAACCTAAGG
* * * *
927063 AGGCAAGACTGGCGTCTTCAATCTGCTTCGCTGTCAGTACAAGA
1 AGGCAAGACTGGTGTCTTCGATCTGCTTCACTGTCAGTACAGGA
* ** * * * * * * * * * *
927107 AGCCAAGATCTACTATTTTCAACCTGCTCCGCT-ACAATCCAGGG
1 AGGCAAGA-CTGGTGTCTTCGATCTGCTTCACTGTCAGTACAGGA
* * ** ** *
927151 AGGCAAGGCTGGTGTCTTTGATCTGCTTTGCTACCAGTATAGGA
1 AGGCAAGACTGGTGTCTTCGATCTGCTTCACTGTCAGTACAGGA
* * * * * ** *
927195 AGGTAAGATCTGCTATCTT-TAGTCTGCTCCACTG-CA-CCCTAGGG
1 AGGCAAGA-CTGGTGTCTTCGA-TCTGCTTCACTGTCAGTAC-AGGA
*
927239 AGGCAAGACTGGTGTCTTCGATCTGCTTCACCGTCAGTACAGGA
1 AGGCAAGACTGGTGTCTTCGATCTGCTTCACTGTCAGTACAGGA
* * * * * * *** *
927283 AGGCAAGATCTGCTATTTTC-AACGTGCTCCGCTG-CAACCCAGGG
1 AGGCAAGA-CTGGTGTCTTCGATC-TGCTTCACTGTCAGTACAGGA
* * *
927327 AGGCAAGGCTGGTGTCCTT-GATATGCTTCACTGTCGGTACAGGA
1 AGGCAAGACTGGTGT-CTTCGATCTGCTTCACTGTCAGTACAGGA
** * *
927371 AGGCAAGATCTACTGTCTTC-AGTCTGCTCCACTG-CA--ACCTAGGG
1 AGGCAAGA-CTGGTGTCTTCGA-TCTGCTTCACTGTCAGTA-C-AGGA
* *
927415 AGGCAAGACTGGTATCTTCGATCTGCTTCGCTGTCAGTACAGGA
1 AGGCAAGACTGGTGTCTTCGATCTGCTTCACTGTCAGTACAGGA
** * *
927459 AGGCAAGATCTACTGTCTTC-AGTCTGCTCCACTG-CA--ACCTAGGG
1 AGGCAAGA-CTGGTGTCTTCGA-TCTGCTTCACTGTCAGTA-C-AGGA
*
927503 AGGCAAGACTGGTATCTTCGATCTGCTTCACTGTCAGTACAGGA
1 AGGCAAGACTGGTGTCTTCGATCTGCTTCACTGTCAGTACAGGA
927547 AGGCAA
1 AGGCAA
927553 TATCTGCTAT
Statistics
Matches: 317, Mismatches: 99, Indels: 60
0.67 0.21 0.13
Matches are distributed among these distances:
42 2 0.01
43 85 0.27
44 144 0.45
45 84 0.26
46 2 0.01
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (44 bp):
AGGCAAGACTGGTGTCTTCGATCTGCTTCACTGTCAGTACAGGA
Found at i:928902 original size:11 final size:11
Alignment explanation
Indices: 928886--928923 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
928876 CTTTCCTTTT
928886 TTTTTTTGCTA
1 TTTTTTTGCTA
928897 TTTTTTTGCTA
1 TTTTTTTGCTA
*
928908 TTTTTTT-ATA
1 TTTTTTTGCTA
928918 TTTTTT
1 TTTTTT
928924 ATATTTTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.11, C:0.05, G:0.05, T:0.79
Consensus pattern (11 bp):
TTTTTTTGCTA
Found at i:929020 original size:14 final size:15
Alignment explanation
Indices: 928997--929029 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
928987 ATCGACGCTT
928997 TTCCAAATAAGG-CC
1 TTCCAAATAAGGTCC
*
929011 TTCCACATAAGGTCC
1 TTCCAAATAAGGTCC
929026 TTCC
1 TTCC
929030 CAGCTTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.33, G:0.12, T:0.27
Consensus pattern (15 bp):
TTCCAAATAAGGTCC
Found at i:929903 original size:25 final size:26
Alignment explanation
Indices: 929852--929912 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
929842 AAGAAAATCC
* **
929852 AAAAGAATGAAAGAATAATTATTTCA
1 AAAAGAATGAAAAAATAATTAGCTCA
*
929878 AAAAGAATGAAAAAAT-ATTGGCTCA
1 AAAAGAATGAAAAAATAATTAGCTCA
929903 AAAATGAATG
1 AAAA-GAATG
929913 CAAAGATGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 10 0.33
26 20 0.67
ACGTcount: A:0.57, C:0.05, G:0.15, T:0.23
Consensus pattern (26 bp):
AAAAGAATGAAAAAATAATTAGCTCA
Found at i:934194 original size:17 final size:17
Alignment explanation
Indices: 934172--934215 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
934162 TAGGAAATAA
*
934172 AAAATGTATATGTCTAT
1 AAAATGTATATGTATAT
*
934189 AAAATGTAAATGTATAT
1 AAAATGTATATGTATAT
*
934206 -ATATGTATAT
1 AAAATGTATAT
934216 AAAAGTTATG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.41
Consensus pattern (17 bp):
AAAATGTATATGTATAT
Found at i:934317 original size:3 final size:3
Alignment explanation
Indices: 934309--934353 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
934299 ATATATATAG
* *
934309 TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA CAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
934354 CTTAATAACA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:934733 original size:21 final size:20
Alignment explanation
Indices: 934692--934743 Score: 79
Period size: 21 Copynumber: 2.6 Consensus size: 20
934682 AATCACATCT
*
934692 TCTAAGATTGC-ATATCGTA
1 TCTAAGATTGCAATATCATA
934711 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCA-ATATCATA
934732 TCTAAGATTGCA
1 TCTAAGATTGCA
934744 CATCCTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
21 19 0.63
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (20 bp):
TCTAAGATTGCAATATCATA
Found at i:937030 original size:18 final size:18
Alignment explanation
Indices: 936996--937041 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
936986 TAACCGGTTC
*
936996 AAATAAAAAATTATTAAA
1 AAATAAAAAAATATTAAA
*
937014 ACATTAAAAAAAT-TTAAA
1 A-AATAAAAAAATATTAAA
937032 AAATAAAAAA
1 AAATAAAAAA
937042 TCTAATTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 8 0.33
18 7 0.29
19 9 0.38
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (18 bp):
AAATAAAAAAATATTAAA
Found at i:940474 original size:43 final size:42
Alignment explanation
Indices: 940427--940605 Score: 186
Period size: 43 Copynumber: 4.2 Consensus size: 42
940417 AAGGAAATAC
940427 ACGCCACT-AAAGATCA-TGTTCTTTAGCGGCGCTTTTTCATAAA
1 ACGCCACTAAAAG-T-AGTGTTCTTTAGCGGCGCTTTTTCA-AAA
* * ***
940470 ACGCCGCT-AAAGATCA-TGTTCTTTAGTGGCGCTTTGGAAGAAA
1 ACGCCACTAAAAG-T-AGTGTTCTTTAGCGGCGCTTTTTCA-AAA
* *
940513 ACGCCTCTAAAAGTAGTGTTCTTTAGCGGCGCTTGTTCAAAA
1 ACGCCACTAAAAGTAGTGTTCTTTAGCGGCGCTTTTTCAAAA
* *
940555 ACGCCGCTAAAAGTAGTGTTCTTTAGCGGCGCTTGTTTCACAA
1 ACGCCACTAAAAGTAGTGTTCTTTAGCGGCGCTT-TTTCAAAA
940598 ACGCCACT
1 ACGCCACT
940606 GTTTTGATAT
Statistics
Matches: 117, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
42 37 0.32
43 76 0.65
44 4 0.03
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (42 bp):
ACGCCACTAAAAGTAGTGTTCTTTAGCGGCGCTTTTTCAAAA
Found at i:940569 original size:42 final size:43
Alignment explanation
Indices: 940443--940591 Score: 189
Period size: 43 Copynumber: 3.5 Consensus size: 43
940433 CTAAAGATCA
* *
940443 TGTTCTTTAGCGGCGCTTTTTCATAAAACGCCGCT-AAAGATCA-
1 TGTTCTTTAGCGGCGCTTGTTCAGAAAACGCCGCTAAAAG-T-AG
* ** *
940486 TGTTCTTTAGTGGCGCTT-TGGAAGAAAACGCCTCTAAAAGTAG
1 TGTTCTTTAGCGGCGCTTGT-TCAGAAAACGCCGCTAAAAGTAG
940529 TGTTCTTTAGCGGCGCTTGTTCA-AAAACGCCGCTAAAAGTAG
1 TGTTCTTTAGCGGCGCTTGTTCAGAAAACGCCGCTAAAAGTAG
940571 TGTTCTTTAGCGGCGCTTGTT
1 TGTTCTTTAGCGGCGCTTGTT
940592 TCACAAACGC
Statistics
Matches: 93, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
42 41 0.44
43 47 0.51
44 5 0.05
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.33
Consensus pattern (43 bp):
TGTTCTTTAGCGGCGCTTGTTCAGAAAACGCCGCTAAAAGTAG
Found at i:940602 original size:85 final size:86
Alignment explanation
Indices: 940381--940588 Score: 257
Period size: 86 Copynumber: 2.4 Consensus size: 86
940371 CTTACAGAAA
* * ** * *
940381 AAAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTAAGGAA-ATACACGCCACT-AAAGATCA-
1 AAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTGGAAGA-AAACGCCTCTAAAAG-T-AG
*
940443 TGTTCTTTAGCGGCGCTTTTTCAT
63 TGTTCTTTAGCGGCGCTTGTTCAT
*
940467 AAAACGCCGCTAAAGATCATGTTCTTTAGTGGCGCTTTGGAAGAAAACGCCTCTAAAAGTAGTGT
1 AAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTGGAAGAAAACGCCTCTAAAAGTAGTGT
940532 TCTTTAGCGGCGCTTGTTCA-
66 TCTTTAGCGGCGCTTGTTCAT
940552 AAAACGCCGCTAAA-AGT-AGTGTTCTTTAGCGGCGCTT
1 AAAACGCCGCTAAAGA-TCA-TGTTCTTTAGCGGCGCTT
940589 GTTTCACAAA
Statistics
Matches: 108, Mismatches: 9, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
84 2 0.02
85 33 0.31
86 68 0.63
87 5 0.05
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (86 bp):
AAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTGGAAGAAAACGCCTCTAAAAGTAGTGT
TCTTTAGCGGCGCTTGTTCAT
Found at i:940667 original size:44 final size:44
Alignment explanation
Indices: 940576--940660 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
940566 AGTAGTGTTC
* * * *
940576 TTTAGCGGCGCTTGTTTCACAAACGCCACTGTTTTGATATGACT
1 TTTAGCGGCGCTTGTTTAAAAAACGCCACTATTTTGAGATGACT
*
940620 TTTAGCGGCGCTTTTTTAAAAAACGCCACTAATTTTGAGAT
1 TTTAGCGGCGCTTGTTTAAAAAACGCCACT-ATTTTGAGAT
940661 TTTTTTAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
44 27 0.77
45 8 0.23
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (44 bp):
TTTAGCGGCGCTTGTTTAAAAAACGCCACTATTTTGAGATGACT
Found at i:941047 original size:21 final size:21
Alignment explanation
Indices: 941023--941080 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
941013 ACTTCTATCG
*
941023 CTGCTTCTCTCGCTGCGGCCT
1 CTGCTTCTCTCGCTGCAGCCT
*
941044 CTGCTTCTCTCGCTGTAGCCT
1 CTGCTTCTCTCGCTGCAGCCT
*
941065 CTGCTTCCCTCGCTGC
1 CTGCTTCTCTCGCTGC
941081 CACCTGTGCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.02, C:0.43, G:0.21, T:0.34
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCAGCCT
Found at i:941090 original size:21 final size:21
Alignment explanation
Indices: 941023--941091 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
941013 ACTTCTATCG
**
941023 CTGCTTCTCTCGCTGCGGCCT
1 CTGCTTCTCTCGCTGCCACCT
*
941044 CTGCTTCTCTCGCTG-TAGCCT
1 CTGCTTCTCTCGCTGCCA-CCT
*
941065 CTGCTTCCCTCGCTGCCACCT
1 CTGCTTCTCTCGCTGCCACCT
*
941086 GTGCTT
1 CTGCTT
941092 TAAGTTGTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
21 40 0.98
22 1 0.02
ACGTcount: A:0.03, C:0.42, G:0.20, T:0.35
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCCACCT
Found at i:947166 original size:9 final size:9
Alignment explanation
Indices: 947152--947352 Score: 158
Period size: 9 Copynumber: 23.8 Consensus size: 9
947142 AAGTTATTTA
947152 TTATGTAAG
1 TTATGTAAG
947161 TTATGTAAG
1 TTATGTAAG
*
947170 TTGTGTAAG
1 TTATGTAAG
947179 TTATGTAAG
1 TTATGTAAG
*
947188 CTATGTAAG
1 TTATGTAAG
*
947197 TTGTGT-A-
1 TTATGTAAG
* *
947204 TTATGAAAC
1 TTATGTAAG
947213 TTATGTAAG
1 TTATGTAAG
*
947222 TTATGT--C
1 TTATGTAAG
947229 TTATGTAAG
1 TTATGTAAG
*
947238 TTATGTAAA
1 TTATGTAAG
*
947247 ATATGT-A-
1 TTATGTAAG
947254 TTATGTAAG
1 TTATGTAAG
*
947263 TTATGTCAG
1 TTATGTAAG
*
947272 TTGTGTAA-
1 TTATGTAAG
947280 TTATGTAA-
1 TTATGTAAG
*
947288 ATATGT-A-
1 TTATGTAAG
*
947295 TTTTGTAAG
1 TTATGTAAG
*
947304 TTATGTAAT
1 TTATGTAAG
*
947313 TTGTGTAA-
1 TTATGTAAG
*
947321 -TATGTAAC
1 TTATGTAAG
* *
947329 TTATTTAAT
1 TTATGTAAG
947338 TTATGTAAG
1 TTATGTAAG
947347 -TATGTA
1 TTATGTA
947353 TTATTATGTA
Statistics
Matches: 153, Mismatches: 29, Indels: 21
0.75 0.14 0.10
Matches are distributed among these distances:
7 26 0.17
8 23 0.15
9 104 0.68
ACGTcount: A:0.32, C:0.02, G:0.19, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:947170 original size:25 final size:25
Alignment explanation
Indices: 947141--947399 Score: 174
Period size: 25 Copynumber: 10.2 Consensus size: 25
947131 GATTTAGGAA
*
947141 TAAGTTATTTATTATGTAAGTTATG
1 TAAGTTATGTATTATGTAAGTTATG
* *
947166 TAAGTTGTGTAAGTTATGTAAGCTATG
1 TAAGTTATGT-A-TTATGTAAGTTATG
* * *
947193 TAAGTTGTGTATTATGAAACTTATG
1 TAAGTTATGTATTATGTAAGTTATG
*
947218 TAAGTTATGTCTTATGTAAGTTATG
1 TAAGTTATGTATTATGTAAGTTATG
**
947243 TAAAATATGTATTATGTAAGTTATG
1 TAAGTTATGTATTATGTAAGTTATG
* * *
947268 TCAGTTGTGTAATTATGTAA-ATATG
1 TAAGTTATGT-ATTATGTAAGTTATG
* * *
947293 T-A-TTTTGTAAGTTATGTAATTTGTG
1 TAAGTTATGT-A-TTATGTAAGTTATG
* *
947318 TAA--TATGTAACTTATTTAATTTATG
1 TAAGTTATGT-A-TTATGTAAGTTATG
*
947343 TAAG-TATGTATTATTATGTAATTTAT-
1 TAAGTTATG---TATTATGTAAGTTATG
* * *
947369 TATG-TAGGATATTATCTAAGTTATG
1 TAAGTTATG-TATTATGTAAGTTATG
947394 TAAGTT
1 TAAGTT
947400 TTTTTTTTGG
Statistics
Matches: 190, Mismatches: 32, Indels: 23
0.78 0.13 0.09
Matches are distributed among these distances:
23 7 0.04
24 22 0.12
25 101 0.53
26 23 0.12
27 35 0.18
28 1 0.01
29 1 0.01
ACGTcount: A:0.32, C:0.02, G:0.18, T:0.48
Consensus pattern (25 bp):
TAAGTTATGTATTATGTAAGTTATG
Found at i:947242 original size:34 final size:35
Alignment explanation
Indices: 947161--947342 Score: 80
Period size: 34 Copynumber: 5.4 Consensus size: 35
947151 ATTATGTAAG
* * * *
947161 TTATGTAAGTTGTGTAAGTTATGTAAGCTATGTAAG
1 TTATGTAAGTTATGAAACTTATGTAAGCTATGT-AC
* *
947197 TTGTGT-A-TTATGAAACTTATGTAAGTTATGT-C
1 TTATGTAAGTTATGAAACTTATGTAAGCTATGTAC
* * *
947229 TTATGTAAGTTATGTAAA-ATATGT-A-TTATGTAAG
1 TTATGTAAGTTATG-AAACTTATGTAAGCTATGT-AC
* * * *
947263 TTATGTCAGTTGTGTAA-TTATGTAA-ATATGTA-
1 TTATGTAAGTTATGAAACTTATGTAAGCTATGTAC
* * * *
947295 TTTTGTAAGTTATGTAATTTGTGTAA--TATGTAAC
1 TTATGTAAGTTATGAAACTTATGTAAGCTATGT-AC
* *
947329 TTATTTAATTTATG
1 TTATGTAAGTTATG
947343 TAAGTATGTA
Statistics
Matches: 116, Mismatches: 21, Indels: 20
0.74 0.13 0.13
Matches are distributed among these distances:
32 30 0.26
33 18 0.16
34 59 0.51
35 4 0.03
36 5 0.04
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.47
Consensus pattern (35 bp):
TTATGTAAGTTATGAAACTTATGTAAGCTATGTAC
Found at i:947258 original size:41 final size:40
Alignment explanation
Indices: 947213--947327 Score: 144
Period size: 41 Copynumber: 2.8 Consensus size: 40
947203 ATTATGAAAC
947213 TTATGTAAGTTATGTC-TTATGTAAGTTATGTAAAATATGTA
1 TTATGTAAGTTATGTCATTATGTAA-TTATGT-AAATATGTA
*
947254 TTATGTAAGTTATGTCAGTTGTGTAATTATGTAAATATGTA
1 TTATGTAAGTTATGTCA-TTATGTAATTATGTAAATATGTA
* * *
947295 TTTTGTAAGTTATGTAATTTGTGTAA-TATGTAA
1 TTATGTAAGTTATGTCA-TTATGTAATTATGTAA
947328 CTTATTTAAT
Statistics
Matches: 68, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
40 7 0.10
41 48 0.71
42 6 0.09
43 7 0.10
ACGTcount: A:0.32, C:0.02, G:0.18, T:0.48
Consensus pattern (40 bp):
TTATGTAAGTTATGTCATTATGTAATTATGTAAATATGTA
Found at i:947267 original size:16 final size:18
Alignment explanation
Indices: 947152--947352 Score: 158
Period size: 16 Copynumber: 11.9 Consensus size: 18
947142 AAGTTATTTA
947152 TTATGTAAGTTATGTAAG
1 TTATGTAAGTTATGTAAG
*
947170 TTGTGTAAGTTATGTAAG
1 TTATGTAAGTTATGTAAG
* *
947188 CTATGTAAGTTGTGT-A-
1 TTATGTAAGTTATGTAAG
* *
947204 TTATGAAACTTATGTAAG
1 TTATGTAAGTTATGTAAG
*
947222 TTATGT--CTTATGTAAG
1 TTATGTAAGTTATGTAAG
**
947238 TTATGTAAAATATGT-A-
1 TTATGTAAGTTATGTAAG
*
947254 TTATGTAAGTTATGTCAG
1 TTATGTAAGTTATGTAAG
*
947272 TTGTGTAA-TTATGTAA-
1 TTATGTAAGTTATGTAAG
* *
947288 ATATGT-A-TTTTGTAAG
1 TTATGTAAGTTATGTAAG
* *
947304 TTATGTAATTTGTGTAA-
1 TTATGTAAGTTATGTAAG
* * *
947321 -TATGTAACTTATTTAAT
1 TTATGTAAGTTATGTAAG
947338 TTATGTAAG-TATGTA
1 TTATGTAAGTTATGTA
947353 TTATTATGTA
Statistics
Matches: 147, Mismatches: 25, Indels: 23
0.75 0.13 0.12
Matches are distributed among these distances:
15 8 0.05
16 62 0.42
17 17 0.12
18 60 0.41
ACGTcount: A:0.32, C:0.02, G:0.19, T:0.47
Consensus pattern (18 bp):
TTATGTAAGTTATGTAAG
Found at i:947663 original size:15 final size:15
Alignment explanation
Indices: 947643--947675 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
947633 AGAATTTTTT
*
947643 ATAAATTTAATAGTA
1 ATAAATTTAATACTA
947658 ATAAATTTAATACTA
1 ATAAATTTAATACTA
947673 ATA
1 ATA
947676 TAGAAACCTT
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:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (15 bp):
ATAAATTTAATACTA
Found at i:948907 original size:16 final size:16
Alignment explanation
Indices: 948874--948907 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
948864 CGGGGAAACT
*
948874 GGGGGAATAAGAATTG
1 GGGGGAATAAGAAATG
*
948890 GGGGGAATACGAAATG
1 GGGGGAATAAGAAATG
948906 GG
1 GG
948908 AAATTAGGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.47, T:0.15
Consensus pattern (16 bp):
GGGGGAATAAGAAATG
Found at i:950683 original size:257 final size:263
Alignment explanation
Indices: 950071--950869 Score: 1297
Period size: 257 Copynumber: 3.0 Consensus size: 263
950061 GTATTTTGCT
* *
950071 TTTTTGCGGTGTTTTAACGTCAGCGCCACTAATTGAAGTATACATCGAGACCAAAATGGTGCGTT
1 TTTTTGCGGCGTTTTAACGTCAGCGCCACTAATTGAAGTATACATCGAGACCAAAACGGTGCGTT
* * *
950136 TTGGTTCAGATATTTTGTGGCATTTTCCTATAAGCGCCACTAAATGTAACACAGCTTAAGACAAA
66 TTGGTTCAGATATTTTGTGGCGTTTTCCTATAAGCGCCACTAAATGTAACATAGCTTAAGACCAA
* * * *
950201 ACATTACGTTTTGTTAAGATACATTGCGGCGCTTTGGATCAAGCGCCGCTAAAGCTATTCTTTAA
131 ACACTGCGTTTTGTTAAGATACGTTGCGGCGCTTTGGCTCAAGCGCCGCTAAAGCTATTCTTTAA
950266 CGGCGTTTTCTAGTAAGCGCCACTAATATAAGTATACATCAAAATTAAAACTACGCGTTTTAGTT
196 CGGCG-TTTCTAGTAAGCGCCACTAATATAAGTAT--ATCAAAATTAAAACTACGCGTTTTAGTT
950331 AAGATA
258 AAGATA
*
950337 TTTTTGCGGCGTTTTAACGTCAGCGCCACTAATTGAAGTATACATCGAGACCAAAACGGTGTGTT
1 TTTTTGCGGCGTTTTAACGTCAGCGCCACTAATTGAAGTATACATCGAGACCAAAACGGTGCGTT
* * *
950402 TTGGTTCAGAAATTTTGCGGCGTTTTCCTATAAGCACCACTAAATGTAACATAGCTTAAGACCAA
66 TTGGTTCAGATATTTTGTGGCGTTTTCCTATAAGCGCCACTAAATGTAACATAGCTTAAGACCAA
*
950467 ACACTGCGTTTTGTTAAGATACGTTGCGGCACTTTGGCTCAAGCGCCGCTAAAGCTATTCTTTAA
131 ACACTGCGTTTTGTTAAGATACGTTGCGGCGCTTTGGCTCAAGCGCCGCTAAAGCTATTCTTTAA
*
950532 CGGC-ATTCTAGTAAGCGCCACT-A-AT-A-TAT-TCAAAATTAAAACTACGCGTTTTAGTTAAG
196 CGGCGTTTCTAGTAAGCGCCACTAATATAAGTATATCAAAATTAAAACTACGCGTTTTAGTTAAG
950591 ATA
261 ATA
* * *
950594 TTTTTGCGGCGTTTTAACTTCAGCGCCTCTAATTGAAGTATACATCGAGACCAAAACGATGCGTT
1 TTTTTGCGGCGTTTTAACGTCAGCGCCACTAATTGAAGTATACATCGAGACCAAAACGGTGCGTT
* *
950659 TTGGTTTAGATTTTTTGTGGCGTTTTCCTATAAGCGCCACTAAATGTAACATAGCTTAAGACCAA
66 TTGGTTCAGATATTTTGTGGCGTTTTCCTATAAGCGCCACTAAATGTAACATAGCTTAAGACCAA
950724 ACACTGCGTTTTGTTAAGATACGTTGCGGCGCTTTGGCTCAAGCGCCGCTAAAGCTATTCTTTAA
131 ACACTGCGTTTTGTTAAGATACGTTGCGGCGCTTTGGCTCAAGCGCCGCTAAAGCTATTCTTTAA
* *
950789 CGGCGTTTTCTAGTAAGCGCCACTAATATAAGTATACATCAAAATTAAAACTATGCGTTTTAGTA
196 CGGCG-TTTCTAGTAAGCGCCACTAATATAAGTAT--ATCAAAATTAAAACTACGCGTTTTAGTT
950854 AAGATA
258 AAGATA
950860 -TTTTGCGGCG
1 TTTTTGCGGCG
950870 CTTTCTACGA
Statistics
Matches: 496, Mismatches: 28, Indels: 19
0.91 0.05 0.03
Matches are distributed among these distances:
257 222 0.45
259 17 0.03
260 4 0.01
261 3 0.01
262 3 0.01
263 4 0.01
264 17 0.03
265 10 0.02
266 216 0.44
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32
Consensus pattern (263 bp):
TTTTTGCGGCGTTTTAACGTCAGCGCCACTAATTGAAGTATACATCGAGACCAAAACGGTGCGTT
TTGGTTCAGATATTTTGTGGCGTTTTCCTATAAGCGCCACTAAATGTAACATAGCTTAAGACCAA
ACACTGCGTTTTGTTAAGATACGTTGCGGCGCTTTGGCTCAAGCGCCGCTAAAGCTATTCTTTAA
CGGCGTTTCTAGTAAGCGCCACTAATATAAGTATATCAAAATTAAAACTACGCGTTTTAGTTAAG
ATA
Found at i:951005 original size:116 final size:111
Alignment explanation
Indices: 950835--951082 Score: 257
Period size: 112 Copynumber: 2.2 Consensus size: 111
950825 CATCAAAATT
* * * * ** *
950835 AAAACTATGCGTTTTAGTAAAGATATTTTGCGGCGCTTTCTACGAAACGTCGCTAATACGGTGCT
1 AAAACAATGCGTTTTGGTTAAGATATTTTGCGGCGCTATCTAC-AAACACCGCTAAGAC--T-CT
*
950900 TTAGCGGCGCATATCACAAAGCGCCACTAAATT-TAGGATACGTCAACACCA
62 TTAGCGGCGCATATCA-AAAGCGCCACT-AATTCTAGGATACATCAACACCA
* *
950951 AAAACGATGCGTTTTGGTTAAGATATTTTGTGGCGCATATCGTA-AAACACCGCTAAGACTCTTT
1 AAAACAATGCGTTTTGGTTAAGATATTTTGCGGCGC-TATC-TACAAACACCGCTAAGACTCTTT
* ** * * * *
951015 CGCGGCGTTTTTTAGAAGCGCCACTAATTCTAGGATACATCAACACTA
64 AGCGGCGCATATCAAAAGCGCCACTAATTCTAGGATACATCAACACCA
951063 AAAACAATGCGTTTTGGTTA
1 AAAACAATGCGTTTTGGTTA
951083 GGAGAAATTA
Statistics
Matches: 112, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
111 4 0.04
112 45 0.40
113 13 0.12
114 1 0.01
116 44 0.39
117 3 0.03
118 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.29
Consensus pattern (111 bp):
AAAACAATGCGTTTTGGTTAAGATATTTTGCGGCGCTATCTACAAACACCGCTAAGACTCTTTAG
CGGCGCATATCAAAAGCGCCACTAATTCTAGGATACATCAACACCA
Found at i:951073 original size:112 final size:113
Alignment explanation
Indices: 950918--951168 Score: 301
Period size: 112 Copynumber: 2.2 Consensus size: 113
950908 GCATATCACA
* * * **
950918 AAGCGCCACTAAATT-TAGGATACGTCAACACCAAAAACGATGCGTTTTGGTTA-AGATATTTTG
1 AAGCGCCACT-AATTCTAGGATACATCAACACCAAAAACAATGCGTTTTGGTTAGAGAAATTACG
* * *
950981 TGGCGCATATCGTAAAACACCGCTAAGACTCTTTCGCGGCGT-TTTTTAG
65 TCGCG-ATATCGTAAAACACCGCTAAGACACTTTAGCGGCGTGTTTTTAG
*
951030 AAGCGCCACTAATTCTAGGATACATCAACACTAAAAACAATGCGTTTTGGTTAGGAGAAATTACG
1 AAGCGCCACTAATTCTAGGATACATCAACACCAAAAACAATGCGTTTTGGTTA-GAGAAATTACG
* * * * *
951095 TCGCGTTGTTGTAAAACGCCGCTAAGACACTTTAGCGGCGTGTTTTTTG
65 TCGCGATATCGTAAAACACCGCTAAGACACTTTAGCGGCGTGTTTTTAG
* * *
951144 AAGCACCACTAATTCTTGCATACAT
1 AAGCGCCACTAATTCTAGGATACAT
951169 AAAGACGAAA
Statistics
Matches: 118, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
111 4 0.03
112 45 0.38
113 30 0.25
114 39 0.33
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (113 bp):
AAGCGCCACTAATTCTAGGATACATCAACACCAAAAACAATGCGTTTTGGTTAGAGAAATTACGT
CGCGATATCGTAAAACACCGCTAAGACACTTTAGCGGCGTGTTTTTAG
Found at i:951180 original size:113 final size:113
Alignment explanation
Indices: 950992--951231 Score: 295
Period size: 113 Copynumber: 2.1 Consensus size: 113
950982 GGCGCATATC
* * * * * *
950992 GTAAAACACCGCTAAGACTCTTTCGCGGCGTTTTTTAGAAGCGCCACTAATTCTAGGATACATCA
1 GTAAAACGCCGCTAAGACACTTTAGCGGCGTTTTTTAGAAGCACCACTAATTCTAGCATACATAA
* * * *
951057 ACACTAAAAACAATGCGTTTTGGTTAGGAGAAATTACGTCGCGTTGTT
66 ACACTAAAAACAATGCATTTTGGATAGGAGAAATTACGGCGCGTGGTT
* *
951105 GTAAAACGCCGCTAAGACACTTTAGCGGCGTGTTTTTTGAAGCACCACTAATTCTTGCATACATA
1 GTAAAACGCCGCTAAGACACTTTAGCGGCGT-TTTTTAGAAGCACCACTAATTCTAGCATACATA
* * ** **
951170 AAGAC-GAAAACGTTGCATTTTGGATAGGAGATTTTACGGCGCGTGGTT
65 AACACTAAAAACAATGCATTTTGGATAGGAGAAATTACGGCGCGTGGTT
951218 GT-AAACGCCGCTAA
1 GTAAAACGCCGCTAA
951232 TGATGTTCTT
Statistics
Matches: 108, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
112 12 0.11
113 64 0.59
114 32 0.30
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (113 bp):
GTAAAACGCCGCTAAGACACTTTAGCGGCGTTTTTTAGAAGCACCACTAATTCTAGCATACATAA
ACACTAAAAACAATGCATTTTGGATAGGAGAAATTACGGCGCGTGGTT
Found at i:957302 original size:6 final size:6
Alignment explanation
Indices: 957287--957439 Score: 83
Period size: 6 Copynumber: 24.3 Consensus size: 6
957277 CAGACAAAAC
** *
957287 AATAACA AATAAA AAT-AA AATAAA ACATATAA GTCTGAAA AATAAA ATTAAAA
1 AATAA-A AATAAA AATAAA AATAAA A-ATA-AA -AAT-AAA AATAAA AAT-AAA
* * * * * * *
957340 AATAAC AAGAAA AATATA AATATA AATATA AAGAAA AATAAA ATTAAAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA A--ATAAA
* * * * * *
957390 AATAAC AAGAAA AATAAA AATATA AATAGA AAGAAA AATAAA AACAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
957438 AA
1 AA
957440 CATAAAACTA
Statistics
Matches: 112, Mismatches: 26, Indels: 17
0.72 0.17 0.11
Matches are distributed among these distances:
5 5 0.04
6 82 0.73
7 14 0.12
8 10 0.09
9 1 0.01
ACGTcount: A:0.74, C:0.04, G:0.05, T:0.18
Consensus pattern (6 bp):
AATAAA
Found at i:957411 original size:50 final size:49
Alignment explanation
Indices: 957323--957432 Score: 193
Period size: 50 Copynumber: 2.2 Consensus size: 49
957313 ATATAAGTCT
* *
957323 GAAAAATAAAATTAAAAAATAACAAGAAAAATATAAATATAAATATAAA
1 GAAAAATAAAATTAAAAAATAACAAGAAAAATAAAAATATAAATAGAAA
957372 GAAAAATAAAATTAAAAAAATAACAAGAAAAATAAAAATATAAATAGAAA
1 GAAAAATAAAATT-AAAAAATAACAAGAAAAATAAAAATATAAATAGAAA
957422 GAAAAATAAAA
1 GAAAAATAAAA
957433 ACAAAAACAT
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
49 13 0.22
50 45 0.78
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.17
Consensus pattern (49 bp):
GAAAAATAAAATTAAAAAATAACAAGAAAAATAAAAATATAAATAGAAA
Found at i:957438 original size:12 final size:12
Alignment explanation
Indices: 957323--957439 Score: 92
Period size: 12 Copynumber: 9.5 Consensus size: 12
957313 ATATAAGTCT
957323 GAAAAATAAAATTA
1 GAAAAATAAAA--A
*
957337 -AAAAATAACAA
1 GAAAAATAAAAA
*
957348 GAAAAATATAAA
1 GAAAAATAAAAA
* * *
957360 TATAAATATAAA
1 GAAAAATAAAAA
957372 GAAAAATAAAATTA
1 GAAAAATAAAA--A
* *
957386 AAAAAATAACAA
1 GAAAAATAAAAA
957398 GAAAAATAAAAA
1 GAAAAATAAAAA
* * *
957410 TATAAATAGAAA
1 GAAAAATAAAAA
957422 GAAAAATAAAAA
1 GAAAAATAAAAA
*
957434 CAAAAA
1 GAAAAA
957440 CATAAAACTA
Statistics
Matches: 81, Mismatches: 19, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
11 1 0.01
12 61 0.75
13 9 0.11
14 10 0.12
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (12 bp):
GAAAAATAAAAA
Found at i:957921 original size:16 final size:17
Alignment explanation
Indices: 957900--957931 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
957890 ACCTTAGACT
957900 ATTTTTTT-AATTTTTA
1 ATTTTTTTAAATTTTTA
957916 ATTTTTTTAAATTTTT
1 ATTTTTTTAAATTTTT
957932 CTTAAATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (17 bp):
ATTTTTTTAAATTTTTA
Found at i:957936 original size:11 final size:10
Alignment explanation
Indices: 957910--957954 Score: 56
Period size: 11 Copynumber: 4.4 Consensus size: 10
957900 ATTTTTTTAA
957910 TTTTT-AATT
1 TTTTTAAATT
957919 TTTTTAAATT
1 TTTTTAAATT
957929 TTTCTTAAATT
1 TTT-TTAAATT
*
957940 GTTTTTCAATT
1 -TTTTTAAATT
957951 TTTT
1 TTTT
957955 AATTATTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
9 5 0.16
10 11 0.34
11 13 0.41
12 3 0.09
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.71
Consensus pattern (10 bp):
TTTTTAAATT
Found at i:983806 original size:107 final size:107
Alignment explanation
Indices: 983613--983867 Score: 307
Period size: 107 Copynumber: 2.4 Consensus size: 107
983603 ACCCCTAAAT
* * *
983613 GGTAAAATGACTGAAATACCCCCGAAAGGGTAAAATAACCGAAATACCCCTAAAGGGTAAAATAA
1 GGTAAAATGACTGAAATA-CCCC-AAAGGGTAAAATGACTGAAATACCCCTAAAGGATAAAATAA
* * * * *
983678 TTGAAATACCCCTAAATGGTAAAATAACCGAAGTACCTCCAAAG
64 TCGAAATACCCCCAAAGGGTAAAATAACCGAAATACCTCCAAAC
* * * * *
983722 GGTAAAATGACTGTAATACCCTCAAAGGGT-AAATGACTGAAATA-CTCTCAAAGGATAGACTGA
1 GGTAAAATGACTGAAATACCC-CAAAGGGTAAAATGACTGAAATACCCCT-AAAGGATAAAATAA
* *
983785 TCGAAATACCCCCAAAGGGTAAAATGACTGAAATACCTCCAAAC
64 TCGAAATACCCCCAAAGGGTAAAATAACCGAAATACCTCCAAAC
* *
983829 GGTAAAATGACTAAAATACCCCATAGGGTAAAATGACTG
1 GGTAAAATGACTGAAATACCCCAAAGGGTAAAATGACTG
983868 TTATACCCAT
Statistics
Matches: 125, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
106 10 0.08
107 87 0.70
108 10 0.08
109 18 0.14
ACGTcount: A:0.44, C:0.20, G:0.18, T:0.19
Consensus pattern (107 bp):
GGTAAAATGACTGAAATACCCCAAAGGGTAAAATGACTGAAATACCCCTAAAGGATAAAATAATC
GAAATACCCCCAAAGGGTAAAATAACCGAAATACCTCCAAAC
Found at i:983875 original size:26 final size:26
Alignment explanation
Indices: 983602--983867 Score: 266
Period size: 27 Copynumber: 9.9 Consensus size: 26
983592 TAACCCGACT
*
983602 TACCCCTAAATGGTAAAATGACTGAAA
1 TACCCC-AAAGGGTAAAATGACTGAAA
* *
983629 TACCCCCGAAAGGGTAAAATAACCGAAA
1 TA-CCCC-AAAGGGTAAAATGACTGAAA
* *
983657 TACCCCTAAAGGGTAAAATAATTGAAA
1 TACCCC-AAAGGGTAAAATGACTGAAA
* * * *
983684 TACCCCTAAATGGTAAAATAACCGAAG
1 TACCCC-AAAGGGTAAAATGACTGAAA
*
983711 TACCTCCAAAGGGTAAAATGACTGTAA
1 TACC-CCAAAGGGTAAAATGACTGAAA
983738 TACCCTCAAAGGGT-AAATGACTGAAA
1 TACCC-CAAAGGGTAAAATGACTGAAA
* * * *
983764 TACTCTCAAAGGATAGACTGA-TCGAAA
1 TAC-CCCAAAGGGTAAAATGACT-GAAA
983791 TACCCCCAAAGGGTAAAATGACTGAAA
1 TA-CCCCAAAGGGTAAAATGACTGAAA
* *
983818 TACCTCCAAACGGTAAAATGACTAAAA
1 TACC-CCAAAGGGTAAAATGACTGAAA
*
983845 TACCCCATAGGGTAAAATGACTG
1 TACCCCAAAGGGTAAAATGACTG
983868 TTATACCCAT
Statistics
Matches: 200, Mismatches: 30, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
26 41 0.20
27 132 0.66
28 27 0.14
ACGTcount: A:0.44, C:0.20, G:0.17, T:0.19
Consensus pattern (26 bp):
TACCCCAAAGGGTAAAATGACTGAAA
Found at i:990708 original size:19 final size:19
Alignment explanation
Indices: 990670--990723 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
990660 TTCTGTTGCT
* *
990670 GTAAGTGTTTTTGGCTATCG
1 GTAAGTGTTTAT-ACTATCG
990690 GTAAGTGTTTATACTATCG
1 GTAAGTGTTTATACTATCG
990709 GTAAGTGTTTATACT
1 GTAAGTGTTTATACT
990724 TCGCACTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 21 0.66
20 11 0.34
ACGTcount: A:0.22, C:0.09, G:0.24, T:0.44
Consensus pattern (19 bp):
GTAAGTGTTTATACTATCG
Found at i:991198 original size:27 final size:28
Alignment explanation
Indices: 991156--991234 Score: 101
Period size: 27 Copynumber: 2.9 Consensus size: 28
991146 CTTACGCCCG
991156 AAGGGT-AAAATGATCGAAATACCCCCA
1 AAGGGTAAAAATGATCGAAATACCCCCA
* *
991183 AAGGGTAAAAAT-ATCGGAATACCCCTA
1 AAGGGTAAAAATGATCGAAATACCCCCA
* *
991210 AAGGGT-AAAATGATTGAAATGCCCC
1 AAGGGTAAAAATGATCGAAATACCCC
991235 ATAGGTAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
26 5 0.11
27 35 0.78
28 5 0.11
ACGTcount: A:0.43, C:0.19, G:0.20, T:0.18
Consensus pattern (28 bp):
AAGGGTAAAAATGATCGAAATACCCCCA
Found at i:991646 original size:28 final size:28
Alignment explanation
Indices: 991584--991647 Score: 92
Period size: 28 Copynumber: 2.3 Consensus size: 28
991574 GTTGCGTTAT
* * * *
991584 CACACTATTATTATATTGGGCTAAGGCC
1 CACACTGTTACTATATCGGGATAAGGCC
991612 CACACTGTTACTATATCGGGATAAGGCC
1 CACACTGTTACTATATCGGGATAAGGCC
991640 CACACTGT
1 CACACTGT
991648 ACTGTTACTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (28 bp):
CACACTGTTACTATATCGGGATAAGGCC
Found at i:1000397 original size:22 final size:22
Alignment explanation
Indices: 1000370--1000412 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1000360 AGTGATATAA
1000370 GGTGGTGCCAAGGTGGTGATAC
1 GGTGGTGCCAAGGTGGTGATAC
** *
1000392 GGTGGTGTTAGGGTGGTGATA
1 GGTGGTGCCAAGGTGGTGATA
1000413 TGTTGGTTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.16, C:0.07, G:0.49, T:0.28
Consensus pattern (22 bp):
GGTGGTGCCAAGGTGGTGATAC
Found at i:1004472 original size:48 final size:47
Alignment explanation
Indices: 1004404--1004495 Score: 121
Period size: 48 Copynumber: 1.9 Consensus size: 47
1004394 AATACACCAT
* *
1004404 TTGTGGATAAGCTACCACATAAATGATGATAACCAACCACATAATACA
1 TTGTGGACAAGCCACCACATAAATGATGATAA-CAACCACATAATACA
* * * *
1004452 TTGTGGACAAGCCACTACATAATTGTTGATAACGACCACATAAT
1 TTGTGGACAAGCCACCACATAAATGATGATAACAACCACATAAT
1004496 CCCAAATAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
47 11 0.29
48 27 0.71
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.25
Consensus pattern (47 bp):
TTGTGGACAAGCCACCACATAAATGATGATAACAACCACATAATACA
Found at i:1006806 original size:17 final size:17
Alignment explanation
Indices: 1006784--1006820 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1006774 CATTAAAACC
*
1006784 CTTCTTGAAATTTCAAA
1 CTTCTTGAAATTTAAAA
*
1006801 CTTCTTGACATTTAAAA
1 CTTCTTGAAATTTAAAA
1006818 CTT
1 CTT
1006821 GTATAAAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.32, C:0.19, G:0.05, T:0.43
Consensus pattern (17 bp):
CTTCTTGAAATTTAAAA
Found at i:1015425 original size:16 final size:16
Alignment explanation
Indices: 1015404--1015436 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1015394 CATTACCAAA
1015404 TCATGAA-TAATAGATT
1 TCATGAACTAATA-ATT
1015420 TCATGAACTAATAATT
1 TCATGAACTAATAATT
1015436 T
1 T
1015437 TAGGAACACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.39
Consensus pattern (16 bp):
TCATGAACTAATAATT
Found at i:1021670 original size:22 final size:21
Alignment explanation
Indices: 1021645--1021689 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1021635 AACACACCAT
*
1021645 TTATGGATAAGCCACCACATAA
1 TTATCGATAA-CCACCACATAA
*
1021667 TTATCGATAACGACCACATAA
1 TTATCGATAACCACCACATAA
1021688 TT
1 TT
1021690 GCAGATAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.40, C:0.22, G:0.11, T:0.27
Consensus pattern (21 bp):
TTATCGATAACCACCACATAA
Found at i:1021696 original size:21 final size:21
Alignment explanation
Indices: 1021658--1021697 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1021648 TGGATAAGCC
*
1021658 ACCACATAATTATCGATAACG
1 ACCACATAATTAGCGATAACG
1021679 ACCACATAATT-GCAGATAA
1 ACCACATAATTAGC-GATAA
1021698 ACTGCCACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.45, C:0.23, G:0.10, T:0.23
Consensus pattern (21 bp):
ACCACATAATTAGCGATAACG
Found at i:1029566 original size:14 final size:14
Alignment explanation
Indices: 1029547--1029574 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1029537 AATGTGTGAA
1029547 ACAAAAAGAGAATT
1 ACAAAAAGAGAATT
1029561 ACAAAAAGAGAATT
1 ACAAAAAGAGAATT
1029575 GGTACAAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.07, G:0.14, T:0.14
Consensus pattern (14 bp):
ACAAAAAGAGAATT
Found at i:1051452 original size:16 final size:16
Alignment explanation
Indices: 1051428--1051471 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 16
1051418 AGTATGATGT
*
1051428 AAATAATAACTACTAG
1 AAATCATAACTACTAG
*
1051444 AAATCATAAATTACTAG
1 AAATCAT-AACTACTAG
1051461 AAATCA-AACTA
1 AAATCATAACTA
1051472 GAAATCATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 4 0.17
16 6 0.25
17 14 0.58
ACGTcount: A:0.57, C:0.14, G:0.05, T:0.25
Consensus pattern (16 bp):
AAATCATAACTACTAG
Found at i:1057238 original size:41 final size:42
Alignment explanation
Indices: 1057181--1057279 Score: 128
Period size: 42 Copynumber: 2.4 Consensus size: 42
1057171 AATGGCCCTG
* * *
1057181 CTCACACGAGCTGTGGGTCGGCATGT-AGCTGCACGATGCTA
1 CTCACACGAGCTGTGGGTCAGAATGTAAGCTACACGATGCTA
* *
1057222 CTCACACGAGCTGTGGGTTAGAATGTAAGCTACACGATGCTG
1 CTCACACGAGCTGTGGGTCAGAATGTAAGCTACACGATGCTA
* *
1057264 TTTACACGAGCTGTGG
1 CTCACACGAGCTGTGG
1057280 AGAATTCACA
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 23 0.46
42 27 0.54
ACGTcount: A:0.22, C:0.23, G:0.30, T:0.24
Consensus pattern (42 bp):
CTCACACGAGCTGTGGGTCAGAATGTAAGCTACACGATGCTA
Found at i:1061091 original size:26 final size:27
Alignment explanation
Indices: 1061062--1061112 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
1061052 GACCGTAATG
1061062 CCCCTAGAGGGTAAATGACT-ATTTTT
1 CCCCTAGAGGGTAAATGACTGATTTTT
*
1061088 CCCCTCGAGGGTAAATGACTGATTT
1 CCCCTAGAGGGTAAATGACTGATTT
1061113 GTGCTATGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (27 bp):
CCCCTAGAGGGTAAATGACTGATTTTT
Found at i:1066885 original size:17 final size:17
Alignment explanation
Indices: 1066863--1066897 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1066853 CATAGATATT
1066863 AACTAACACAAAAATAA
1 AACTAACACAAAAATAA
**
1066880 AACTAATGCAAAAATAA
1 AACTAACACAAAAATAA
1066897 A
1 A
1066898 TACATAAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.69, C:0.14, G:0.03, T:0.14
Consensus pattern (17 bp):
AACTAACACAAAAATAA
Found at i:1070735 original size:10 final size:10
Alignment explanation
Indices: 1070722--1070746 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1070712 TGTTCCTCCC
1070722 TTTTCTTCTA
1 TTTTCTTCTA
1070732 TTTTCTTCTA
1 TTTTCTTCTA
1070742 TTTTC
1 TTTTC
1070747 ACCACCCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.20, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTTCTTCTA
Found at i:1075225 original size:27 final size:27
Alignment explanation
Indices: 1075184--1075297 Score: 129
Period size: 27 Copynumber: 4.0 Consensus size: 27
1075174 ATTGAATATA
1075184 AAGGGGTTTGCTAAGTGCTGATTCCCCC
1 AAGGGG-TTGCTAAGTGCTGATTCCCCC
* *
1075212 AAGGGGTTGCTAAGTGTTGATTCCCTGATTC
1 AAGGGGTTGCTAAGTGCTGATTCCC----CC
* *
1075243 ATTGATGGTTGCTAAGTGCTGATTCCCCC
1 A-AG-GGGTTGCTAAGTGCTGATTCCCCC
1075272 AAGGGGTTGCTAAGTGCTGATTCCCC
1 AAGGGGTTGCTAAGTGCTGATTCCCC
1075298 GAATCATTGG
Statistics
Matches: 72, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
27 40 0.56
28 7 0.10
29 2 0.03
31 2 0.03
32 1 0.01
33 20 0.28
ACGTcount: A:0.18, C:0.22, G:0.28, T:0.32
Consensus pattern (27 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCC
Found at i:1075255 original size:33 final size:33
Alignment explanation
Indices: 1075216--1075403 Score: 129
Period size: 33 Copynumber: 5.6 Consensus size: 33
1075206 TCCCCCAAGG
* *
1075216 GGTTGCTAAGTGTTGATTCCCTGATTCATTGAT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGAT
* *
1075249 GGTTGCTAAGTGCTGATTCCCC----CA-AG-G
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGAT
* *
1075276 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGAT
* * *
1075309 GGTTGCTAAATGCTGA-TCCCATCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCC--CG-A--TT-CAT-TG--A-T
* *
1075351 GGTTGCTAAGTGTTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGAT
*
1075384 GGTTGCTAAGTGTTGATTCC
1 GGTTGCTAAGTGCTGATTCC
1075404 ACCGTATTTT
Statistics
Matches: 122, Mismatches: 16, Indels: 34
0.71 0.09 0.20
Matches are distributed among these distances:
27 22 0.18
28 1 0.01
29 2 0.02
31 2 0.02
32 5 0.04
33 55 0.45
34 2 0.02
35 1 0.01
36 2 0.02
37 3 0.02
38 4 0.03
39 2 0.02
40 1 0.01
41 2 0.02
42 14 0.11
43 4 0.03
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.35
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTGAT
Found at i:1075284 original size:60 final size:60
Alignment explanation
Indices: 1075191--1075325 Score: 225
Period size: 60 Copynumber: 2.2 Consensus size: 60
1075181 ATAAAGGGGT
* * *
1075191 TTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGTTGATTCCCTGATTCATTGATGG
1 TTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGATGG
*
1075251 TTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGG
1 TTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGATGG
*
1075311 TTGCTAAATGCTGAT
1 TTGCTAAGTGCTGAT
1075326 CCCATCGTAT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 70 1.00
ACGTcount: A:0.19, C:0.21, G:0.27, T:0.33
Consensus pattern (60 bp):
TTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGATGG
Found at i:1075410 original size:75 final size:77
Alignment explanation
Indices: 1075272--1075473 Score: 309
Period size: 75 Copynumber: 2.6 Consensus size: 77
1075262 TGATTCCCCC
* *
1075272 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAATGCTGATCCCATCGTA-T
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATT
1075336 CTTAAATGTG-A
66 CTTAAATGTGAA
* * * *
1075347 AAGGGGTTGCTAAGTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGTTGATTCCACCGTATT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATT
* *
1075412 TTTGAATGTGAA
66 CTTAAATGTGAA
*
1075424 AAGGGGTTGCTAAGTGCTGATCCCCCGAATCATTGGTGGTTGCTAAGTGC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGC
1075474 GGAATCCACC
Statistics
Matches: 113, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
75 57 0.50
76 9 0.08
77 47 0.42
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (77 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATT
CTTAAATGTGAA
Found at i:1075482 original size:77 final size:75
Alignment explanation
Indices: 1075272--1075484 Score: 302
Period size: 77 Copynumber: 2.8 Consensus size: 75
1075262 TGATTCCCCC
* *
1075272 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAATGCTG-ATCCCATCGTAT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGAAT-CCACCGTAT
1075336 CTTAAATGTGA
65 CTTAAATGTGA
* * * *
1075347 AAGGGGTTGCTAAGTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGTTGATTCCACCGTATT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGAATCCACCGTA-T
* *
1075412 TTTGAATGTGAA
65 CTTAAATGTG-A
* *
1075424 AAGGGGTTGCTAAGTGCTGATCCCCCGAATCATTGGTGGTTGCTAAGTGCGGAATCCACCG
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGAATCCACCG
1075485 ATAACGGATA
Statistics
Matches: 121, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
75 55 0.45
76 10 0.08
77 56 0.46
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGAATCCACCGTATC
TTAAATGTGA
Found at i:1081860 original size:13 final size:13
Alignment explanation
Indices: 1081842--1081867 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1081832 GTTCGTAAGG
1081842 GATGTGAGGCATT
1 GATGTGAGGCATT
1081855 GATGTGAGGCATT
1 GATGTGAGGCATT
1081868 CTTGGCCTAT
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:0.23, C:0.08, G:0.38, T:0.31
Consensus pattern (13 bp):
GATGTGAGGCATT
Found at i:1089865 original size:70 final size:69
Alignment explanation
Indices: 1089753--1089897 Score: 245
Period size: 70 Copynumber: 2.1 Consensus size: 69
1089743 TATTATCTTC
1089753 AAGTAAGTTTTTTTATTTAAAAAACTTTATGAGCTAGATAATCAAAATAGAGACCCCAAATACGG
1 AAGTAAGTTTTTTTATTTAAAAAACTTTATGAGCTAGATAATCAAAATAGAGACCCCAAATACGG
1089818 AAGA
66 AAGA
* * * *
1089822 AAGTAAGTTTTTTTTATTTAAAAAACTTTGTGAGCTAGATAATCAAAATAGATACCCTAAATATG
1 AAGTAAG-TTTTTTTATTTAAAAAACTTTATGAGCTAGATAATCAAAATAGAGACCCCAAATACG
1089887 GAAGA
65 GAAGA
1089892 AAGTAA
1 AAGTAA
1089898 ATCAACACAC
Statistics
Matches: 71, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
69 7 0.10
70 64 0.90
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (69 bp):
AAGTAAGTTTTTTTATTTAAAAAACTTTATGAGCTAGATAATCAAAATAGAGACCCCAAATACGG
AAGA
Found at i:1093731 original size:20 final size:20
Alignment explanation
Indices: 1093689--1093731 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1093679 CTAACGAAAG
** *
1093689 ATATACTATAAATATTAATA
1 ATATACTATAAATAGAAAAA
1093709 ATATACTATAAATAGAAAAA
1 ATATACTATAAATAGAAAAA
1093729 ATA
1 ATA
1093732 AATGCAAACG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (20 bp):
ATATACTATAAATAGAAAAA
Found at i:1108876 original size:10 final size:10
Alignment explanation
Indices: 1108856--1108891 Score: 51
Period size: 9 Copynumber: 3.9 Consensus size: 10
1108846 AAGTCACCGA
1108856 TTCTC-TTTT
1 TTCTCTTTTT
1108865 TTCTCTTTTT
1 TTCTCTTTTT
1108875 TTCT-TTTTT
1 TTCTCTTTTT
1108884 TT-TCTTTT
1 TTCTCTTTT
1108892 CAAGAGTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 1 0.04
9 16 0.64
10 8 0.32
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (10 bp):
TTCTCTTTTT
Found at i:1124614 original size:14 final size:12
Alignment explanation
Indices: 1124585--1124622 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
1124575 CACATTTGAC
1124585 AATAAAAAATAA
1 AATAAAAAATAA
1124597 AATAAAAGAATGAA
1 AATAAAA-AAT-AA
1124611 AAT-AAAAATAA
1 AATAAAAAATAA
1124622 A
1 A
1124623 TTTCCTATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 3 0.12
12 10 0.42
13 6 0.25
14 5 0.21
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (12 bp):
AATAAAAAATAA
Found at i:1131616 original size:12 final size:12
Alignment explanation
Indices: 1131599--1131623 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1131589 GCCAAAGACG
1131599 AAAGAAAGGAAA
1 AAAGAAAGGAAA
1131611 AAAGAAAGGAAA
1 AAAGAAAGGAAA
1131623 A
1 A
1131624 TCAGCAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AAAGAAAGGAAA
Found at i:1136130 original size:16 final size:16
Alignment explanation
Indices: 1136106--1136149 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 16
1136096 AGTATGATGT
*
1136106 AAATAATAACTACTAG
1 AAATCATAACTACTAG
*
1136122 AAATCATAAATTACTAG
1 AAATCAT-AACTACTAG
1136139 AAATCA-AACTA
1 AAATCATAACTA
1136150 GAAATCATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 4 0.17
16 6 0.25
17 14 0.58
ACGTcount: A:0.57, C:0.14, G:0.05, T:0.25
Consensus pattern (16 bp):
AAATCATAACTACTAG
Found at i:1137918 original size:28 final size:28
Alignment explanation
Indices: 1137886--1137941 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
1137876 TTCTGACTAG
1137886 TAGGAGTAATATTAGAGGTGAAAAAATT
1 TAGGAGTAATATTAGAGGTGAAAAAATT
*
1137914 TAGGAGTAATATTAGAGGTGCAAAAATT
1 TAGGAGTAATATTAGAGGTGAAAAAATT
1137942 AGTTTTTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.45, C:0.02, G:0.25, T:0.29
Consensus pattern (28 bp):
TAGGAGTAATATTAGAGGTGAAAAAATT
Found at i:1141282 original size:21 final size:22
Alignment explanation
Indices: 1141256--1141296 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1141246 CAAGTCTATC
1141256 AAATAAACATA-AAATTCAAAG
1 AAATAAACATACAAATTCAAAG
* *
1141277 AAATAAGCATACTAATTCAA
1 AAATAAACATACAAATTCAA
1141297 CCATTTAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.61, C:0.12, G:0.05, T:0.22
Consensus pattern (22 bp):
AAATAAACATACAAATTCAAAG
Found at i:1141970 original size:42 final size:41
Alignment explanation
Indices: 1141873--1141974 Score: 132
Period size: 42 Copynumber: 2.5 Consensus size: 41
1141863 TGAAATGGCC
* * *
1141873 CTGCTCACACAAGCTGTGGGTCGGCATGTAGCTACACGATG
1 CTGCTCACACGAGCTGTGGGTCAGAATGTAGCTACACGATG
* * *
1141914 CTACTCACAGGAGCTGTGGGTTAGAATGTAAGCTACACGATG
1 CTGCTCACACGAGCTGTGGGTCAGAATGT-AGCTACACGATG
*
1141956 CTGCTTACACGAGCTGTGG
1 CTGCTCACACGAGCTGTGG
1141975 AGAATTCACA
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
41 23 0.45
42 28 0.55
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.24
Consensus pattern (41 bp):
CTGCTCACACGAGCTGTGGGTCAGAATGTAGCTACACGATG
Found at i:1145849 original size:26 final size:27
Alignment explanation
Indices: 1145820--1145870 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
1145810 GACCGTAATG
1145820 CCCCTAAAGGGTAAATGACT-ATTTTT
1 CCCCTAAAGGGTAAATGACTGATTTTT
**
1145846 CCCCTCGAGGGTAAATGACTGATTT
1 CCCCTAAAGGGTAAATGACTGATTT
1145871 GTGCTATGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (27 bp):
CCCCTAAAGGGTAAATGACTGATTTTT
Found at i:1175896 original size:70 final size:69
Alignment explanation
Indices: 1175784--1175928 Score: 254
Period size: 70 Copynumber: 2.1 Consensus size: 69
1175774 TATTATCTTC
1175784 AAGTAAGTTTTTTTATTTAAAAAACTTTATGAGCCAAATAATCAAAATAGAGACCCCAAATACGG
1 AAGTAAGTTTTTTTATTTAAAAAACTTTATGAGCCAAATAATCAAAATAGAGACCCCAAATACGG
1175849 AAGA
66 AAGA
* * *
1175853 AAGTAAGTTTTTTTTATTTAAAAAACTTTGTGAGCCAGATAATCAAAATAGAGACCCTAAATACG
1 AAGTAAG-TTTTTTTATTTAAAAAACTTTATGAGCCAAATAATCAAAATAGAGACCCCAAATACG
1175918 GAAGA
65 GAAGA
1175923 AAGTAA
1 AAGTAA
1175929 ATCAACACAC
Statistics
Matches: 72, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
69 7 0.10
70 65 0.90
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.28
Consensus pattern (69 bp):
AAGTAAGTTTTTTTATTTAAAAAACTTTATGAGCCAAATAATCAAAATAGAGACCCCAAATACGG
AAGA
Found at i:1193838 original size:16 final size:16
Alignment explanation
Indices: 1193817--1193848 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1193807 GTTATCTTGC
*
1193817 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
1193833 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
1193849 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:1196974 original size:50 final size:50
Alignment explanation
Indices: 1196920--1197026 Score: 151
Period size: 50 Copynumber: 2.1 Consensus size: 50
1196910 GCATGAGAGT
* *
1196920 TCTCATATCAGTGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACC
1 TCTCATATCAGTACCAATGCCATGTCCCAGACATGGTCTTACGGGGGACC
* * * * *
1196970 TCTCATCTCGGTACCAATGCCATGTCCCAGATATGGTCTTATGTGGGACC
1 TCTCATATCAGTACCAATGCCATGTCCCAGACATGGTCTTACGGGGGACC
1197020 TCTCATA
1 TCTCATA
1197027 ACCTCAATAA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.21, C:0.30, G:0.21, T:0.28
Consensus pattern (50 bp):
TCTCATATCAGTACCAATGCCATGTCCCAGACATGGTCTTACGGGGGACC
Found at i:1197045 original size:56 final size:52
Alignment explanation
Indices: 1196931--1197052 Score: 140
Period size: 50 Copynumber: 2.3 Consensus size: 52
1196921 CTCATATCAG
* **
1196931 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCAATA
* * *
1196983 --CCAATGCCATGTCCCAGATATGGTCTTATGTGGGACCTCTCATAACCTCAATAA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCAT---CTCAAT-A
1197037 TGCCAATGCCATGTCC
1 TGCCAATGCCATGTCC
1197053 TATTTTTGTT
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
50 39 0.67
53 4 0.07
54 1 0.02
56 14 0.24
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.26
Consensus pattern (52 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCAATA
Found at i:1203632 original size:50 final size:50
Alignment explanation
Indices: 1203562--1203700 Score: 163
Period size: 50 Copynumber: 2.8 Consensus size: 50
1203552 TACTACAAAT
* * * ** * * *
1203562 TCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATTGGTGCCCA-
1 TCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATATCGGTACCAAC
* *
1203611 TGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTACCAAC
1 T-CCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATATCGGTACCAAC
*
1203662 TCCATGTCCTAGACATGGTCTTACGTGGGACCTCTCATA
1 TCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATA
1203701 ACCTCAATAA
Statistics
Matches: 75, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
49 1 0.01
50 73 0.97
51 1 0.01
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.29
Consensus pattern (50 bp):
TCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATATCGGTACCAAC
Found at i:1216031 original size:41 final size:41
Alignment explanation
Indices: 1215958--1216066 Score: 130
Period size: 41 Copynumber: 2.7 Consensus size: 41
1215948 CCAAATGTGT
* * * * **
1215958 AAACAGGGGAACGTAAGTGCTATTT-GGAGTACCGTAGTAC
1 AAACAAGGGCACGTATGTGCAATTTAGGAGTACCAAAGTAC
* *
1215998 AAATAAGGGCACGTATGTGCAATTTAGGGGTACCAAAGTAC
1 AAACAAGGGCACGTATGTGCAATTTAGGAGTACCAAAGTAC
*
1216039 AAACAAGGGCATGTATGTGCAATTTAGG
1 AAACAAGGGCACGTATGTGCAATTTAGG
1216067 TATAATTAAC
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
40 20 0.34
41 38 0.66
ACGTcount: A:0.35, C:0.14, G:0.28, T:0.23
Consensus pattern (41 bp):
AAACAAGGGCACGTATGTGCAATTTAGGAGTACCAAAGTAC
Found at i:1224515 original size:29 final size:29
Alignment explanation
Indices: 1224474--1224545 Score: 72
Period size: 29 Copynumber: 2.5 Consensus size: 29
1224464 ACTCACCTGT
* * *
1224474 CACACAGTTGTGTGTCACACACGATCGGG
1 CACACACTCGTGTGTCACACACGACCGGG
** *
1224503 CACACACTCGTGTGTTGCACACGGCCGGG
1 CACACACTCGTGTGTCACACACGACCGGG
* *
1224532 CACACGCCCGTGTG
1 CACACACTCGTGTG
1224546 GCGTCGATAG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.19, C:0.33, G:0.29, T:0.18
Consensus pattern (29 bp):
CACACACTCGTGTGTCACACACGACCGGG
Found at i:1225074 original size:5 final size:5
Alignment explanation
Indices: 1225064--1225109 Score: 62
Period size: 5 Copynumber: 9.6 Consensus size: 5
1225054 AGAAGAGGGA
1225064 AAAAG AAAAG AAAAG AAAAG AAAAG -AAAG AAAA- AGAAAG -AAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG A-AAAG AAAAG AAA
1225110 GAAGGAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
4 9 0.24
5 28 0.76
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:1225082 original size:15 final size:14
Alignment explanation
Indices: 1225064--1225109 Score: 67
Period size: 14 Copynumber: 3.2 Consensus size: 14
1225054 AGAAGAGGGA
1225064 AAAAGAAAAGAAAAG
1 AAAAGAAAAG-AAAG
1225079 AAAAGAAAAGAAAG
1 AAAAGAAAAGAAAG
1225093 AAAA-AGAAAGAAAG
1 AAAAGA-AAAGAAAG
1225107 AAA
1 AAA
1225110 GAAGGAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
13 1 0.03
14 19 0.63
15 10 0.33
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAGAAAG
Found at i:1231576 original size:32 final size:32
Alignment explanation
Indices: 1231526--1231604 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 32
1231516 CCACATGCCT
* * *
1231526 GTGTAGGCCAACACGCCCAAATTGGCCTTGCTC
1 GTGT-GGCCCACACGCCCAAATTGACCTAGCTC
* *
1231559 GTGTGGCCCACATGCCCAACTTGACCTAGCTC
1 GTGTGGCCCACACGCCCAAATTGACCTAGCTC
*
1231591 GTGTAGCCCACACG
1 GTGTGGCCCACACG
1231605 ACCACAAACT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
32 35 0.90
33 4 0.10
ACGTcount: A:0.20, C:0.35, G:0.24, T:0.20
Consensus pattern (32 bp):
GTGTGGCCCACACGCCCAAATTGACCTAGCTC
Found at i:1231993 original size:20 final size:20
Alignment explanation
Indices: 1231970--1232009 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1231960 GGAGAAGAGG
1231970 GAAAAAGAAAAGAA-AAAAAA
1 GAAAAAG-AAAGAAGAAAAAA
1231990 GAAAAAGAAAGAAGAAAAAA
1 GAAAAAGAAAGAAGAAAAAA
1232010 ATTTAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (20 bp):
GAAAAAGAAAGAAGAAAAAA
Found at i:1232010 original size:15 final size:15
Alignment explanation
Indices: 1231971--1231999 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1231961 GAGAAGAGGG
1231971 AAAAAG-AAAAGAAA
1 AAAAAGAAAAAGAAA
1231985 AAAAAGAAAAAGAAA
1 AAAAAGAAAAAGAAA
1232000 GAAGAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAGAAA
Found at i:1237703 original size:50 final size:50
Alignment explanation
Indices: 1237642--1237748 Score: 135
Period size: 50 Copynumber: 2.1 Consensus size: 50
1237632 ACATAGGAGT
* * * *
1237642 TCTCATATCGGTGCCCATGCTATGTCCCAGAC-CTGGTCTTACGGGGGACC
1 TCTCATATCGGTGCCAACGCCATGTCCCAGACAC-GGTCTTACAGGGGACC
* * *
1237692 TCTCATCTCGGTGCCAACGCCATGTCCCATACACGGTCTTACATGGGACC
1 TCTCATATCGGTGCCAACGCCATGTCCCAGACACGGTCTTACAGGGGACC
1237742 TCTCATA
1 TCTCATA
1237749 ATCTCAATGA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
50 47 0.98
51 1 0.02
ACGTcount: A:0.19, C:0.34, G:0.21, T:0.26
Consensus pattern (50 bp):
TCTCATATCGGTGCCAACGCCATGTCCCAGACACGGTCTTACAGGGGACC
Found at i:1242122 original size:28 final size:28
Alignment explanation
Indices: 1242086--1242160 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 28
1242076 TAGATTGTTT
*
1242086 TGGCAGACTTCCACATTTAAGATCATAC
1 TGGCGGACTTCCACATTTAAGATCATAC
** * *
1242114 TGGCGGACTTCCATGTTTAAGATCGTCC
1 TGGCGGACTTCCACATTTAAGATCATAC
** *
1242142 TAACGAACTTCCACATTTA
1 TGGCGGACTTCCACATTTA
1242161 TGGTAATGCC
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (28 bp):
TGGCGGACTTCCACATTTAAGATCATAC
Found at i:1243655 original size:29 final size:31
Alignment explanation
Indices: 1243595--1243659 Score: 84
Period size: 29 Copynumber: 2.2 Consensus size: 31
1243585 GGCATTTCCC
1243595 ATTAAATATGATTAATGATTAAATTAGTTTA
1 ATTAAATATGATTAATGATTAAATTAGTTTA
1243626 ATTAAATCATGATT-ATG-TT-AATTA-TGTTA
1 ATTAAAT-ATGATTAATGATTAAATTAGT-TTA
1243655 ATTAA
1 ATTAA
1243660 GTTAAATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
28 1 0.03
29 13 0.41
30 2 0.06
31 10 0.31
32 6 0.19
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (31 bp):
ATTAAATATGATTAATGATTAAATTAGTTTA
Found at i:1246748 original size:72 final size:72
Alignment explanation
Indices: 1246662--1246827 Score: 316
Period size: 72 Copynumber: 2.3 Consensus size: 72
1246652 GATACCTAGG
1246662 TTAAGTATTGATACCGTATTTAGCTTTGGTGTTTTGAAAATCAAGTTAAAATACTCAAGTATCGA
1 TTAAGTATTGATACCGTATTTAGCTTTGGTGTTTTGAAAATCAAGTTAAAATACTCAAGTATCGA
1246727 AACCAAT
66 AACCAAT
1246734 TTAAGTATTGATACCGTATTTAGCTTTGGTGTTTTGAAAATCAAGTTAAAATACTCAAGTATCGA
1 TTAAGTATTGATACCGTATTTAGCTTTGGTGTTTTGAAAATCAAGTTAAAATACTCAAGTATCGA
1246799 AACCAAT
66 AACCAAT
*
1246806 TTAAGTATTAATACCGT-TTTAG
1 TTAAGTATTGATACCGTATTTAG
1246828 AATTTTTCAA
Statistics
Matches: 93, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
71 5 0.05
72 88 0.95
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (72 bp):
TTAAGTATTGATACCGTATTTAGCTTTGGTGTTTTGAAAATCAAGTTAAAATACTCAAGTATCGA
AACCAAT
Found at i:1249001 original size:44 final size:44
Alignment explanation
Indices: 1248938--1249026 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
1248928 TTTTTAGAAA
1248938 CATTAGTTTAACTCTCAATCCAGCCAAAATAGAACCATCACGTT
1 CATTAGTTTAACTCTCAATCCAGCCAAAATAGAACCATCACGTT
1248982 CATTAGTTTAACTCTCAATCCAGCCAAAATAGAACCATCACGTT
1 CATTAGTTTAACTCTCAATCCAGCCAAAATAGAACCATCACGTT
1249026 C
1 C
1249027 CAAAGTTAGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.36, C:0.28, G:0.09, T:0.27
Consensus pattern (44 bp):
CATTAGTTTAACTCTCAATCCAGCCAAAATAGAACCATCACGTT
Found at i:1251213 original size:10 final size:10
Alignment explanation
Indices: 1251198--1251226 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
1251188 ATTGTGTGTT
1251198 TGAATAGAAA
1 TGAATAGAAA
1251208 TGAATAG-AA
1 TGAATAGAAA
1251217 TGAATAGAAA
1 TGAATAGAAA
1251227 ATGAGAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.59, C:0.00, G:0.21, T:0.21
Consensus pattern (10 bp):
TGAATAGAAA
Found at i:1254915 original size:28 final size:28
Alignment explanation
Indices: 1254844--1254981 Score: 97
Period size: 27 Copynumber: 5.1 Consensus size: 28
1254834 AAATTAGTTA
* * * *
1254844 TTTACCCTCCA-AGGGCATTACGATCAT
1 TTTACCCTTCAGAGGGTATTTCGGTCAT
*
1254871 TTTA-CCTTACAG-GGGTACTTCGGTCAT
1 TTTACCCTT-CAGAGGGTATTTCGGTCAT
* *
1254898 TTTACCCTTCAGAGGGTATTTTGGTCAA
1 TTTACCCTTCAGAGGGTATTTCGGTCAT
* * *
1254926 TATACCCATCA-AGGGTATTTCAGTCAT
1 TTTACCCTTCAGAGGGTATTTCGGTCAT
** * **
1254953 TTTTTCCATCA-AGGGTATTTTAGTCAT
1 TTTACCCTTCAGAGGGTATTTCGGTCAT
1254980 TT
1 TT
1254982 AACAACCTTT
Statistics
Matches: 90, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
26 3 0.03
27 62 0.69
28 25 0.28
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.38
Consensus pattern (28 bp):
TTTACCCTTCAGAGGGTATTTCGGTCAT
Found at i:1285744 original size:20 final size:20
Alignment explanation
Indices: 1285715--1285758 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1285705 ATATTATATT
* * *
1285715 AAAAGGGTGTTTTATGTTTA
1 AAAAGAGTGTTTTAGGGTTA
1285735 AAAAGAGTGTTTTAGGGTTA
1 AAAAGAGTGTTTTAGGGTTA
1285755 AAAA
1 AAAA
1285759 TTGGGTATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.25, T:0.36
Consensus pattern (20 bp):
AAAAGAGTGTTTTAGGGTTA
Found at i:1296146 original size:18 final size:19
Alignment explanation
Indices: 1296123--1296158 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1296113 TCCCTTAATG
1296123 ATTAGATTCTCAA-AATCC
1 ATTAGATTCTCAATAATCC
*
1296141 ATTAGATTGTCAATAATC
1 ATTAGATTCTCAATAATC
1296159 GTAGCAGCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (19 bp):
ATTAGATTCTCAATAATCC
Found at i:1301751 original size:17 final size:16
Alignment explanation
Indices: 1301712--1301761 Score: 64
Period size: 18 Copynumber: 2.9 Consensus size: 16
1301702 TCTTATTCCT
*
1301712 TCATTCAACATTCCTCAA
1 TCATTCATCATT-CTC-A
1301730 TCATTCATTCATTCTCA
1 TCATTCA-TCATTCTCA
1301747 TCATTCATCATTCTC
1 TCATTCATCATTCTC
1301762 TGTTTTCTCC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 8 0.27
17 8 0.27
18 10 0.33
19 4 0.13
ACGTcount: A:0.26, C:0.32, G:0.00, T:0.42
Consensus pattern (16 bp):
TCATTCATCATTCTCA
Found at i:1316734 original size:18 final size:17
Alignment explanation
Indices: 1316707--1316740 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
1316697 AGAAATAATA
1316707 AAATAAAATAATGAAAG
1 AAATAAAATAATGAAAG
1316724 AAATAAAAATAATGAAA
1 AAAT-AAAATAATGAAA
1316741 TCGAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.18
Consensus pattern (17 bp):
AAATAAAATAATGAAAG
Found at i:1326949 original size:20 final size:20
Alignment explanation
Indices: 1326924--1326988 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
1326914 TACGAGATTT
*
1326924 ACACTTCGGTTTCCCTGTTC
1 ACACTTCGGTGTCCCTGTTC
* * *
1326944 ACACTTCAGTGCCCCTATAT-
1 ACACTTCGGTGTCCCTGT-TC
*
1326964 ACACTTCGGTGTCCTTGTTC
1 ACACTTCGGTGTCCCTGTTC
1326984 ACACT
1 ACACT
1326989 ACGATGCCCT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
19 1 0.03
20 33 0.94
21 1 0.03
ACGTcount: A:0.17, C:0.34, G:0.14, T:0.35
Consensus pattern (20 bp):
ACACTTCGGTGTCCCTGTTC
Found at i:1328424 original size:12 final size:13
Alignment explanation
Indices: 1328407--1328435 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1328397 ATTTACACAA
1328407 CCTAGCACAT-GG
1 CCTAGCACATAGG
1328419 CCTAGCACATAGG
1 CCTAGCACATAGG
1328432 CCTA
1 CCTA
1328436 TGTGGTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.28, C:0.34, G:0.21, T:0.17
Consensus pattern (13 bp):
CCTAGCACATAGG
Found at i:1328527 original size:12 final size:12
Alignment explanation
Indices: 1328510--1328536 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1328500 TCAGAGAGTT
1328510 ACACGGGTGAGG
1 ACACGGGTGAGG
1328522 ACACGGGTGAGG
1 ACACGGGTGAGG
1328534 ACA
1 ACA
1328537 GAAGCTAGGA
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:0.30, C:0.19, G:0.44, T:0.07
Consensus pattern (12 bp):
ACACGGGTGAGG
Found at i:1328669 original size:121 final size:121
Alignment explanation
Indices: 1328441--1328721 Score: 393
Period size: 121 Copynumber: 2.3 Consensus size: 121
1328431 GCCTATGTGG
** * *
1328441 TTATTTCGAGAGTTACACGACCTAGCGCACGGGCGTGTGGTTTGGCCGTGTGACCAAACTCAGAG
1 TTATTTCGATTGTTACACGGCCTGGCGCACGGGCGTGTGGTTTGGCCGTGTGACCAAACTCAGAG
* * *
1328506 AGTTACACGGGTGAGGACACGGGTGAGGACAGAAGCTAGGACATGAACATCTGTCC
66 AGTTACACGGGTGAGGACACGGATGAAGACACAAGCTAGGACATGAACATCTGTCC
*
1328562 TTATTTCGATTGTTACACGGCCTGGCGTACGGGCGTGTGGTTTGGCCGTGTGACCAAACTCAGAG
1 TTATTTCGATTGTTACACGGCCTGGCGCACGGGCGTGTGGTTTGGCCGTGTGACCAAACTCAGAG
* * * * * *
1328627 AGTTACATGGGTGAGGACTCGGATGAAGACACAAGTTGGGACATGAACGTGTGTCC
66 AGTTACACGGGTGAGGACACGGATGAAGACACAAGCTAGGACATGAACATCTGTCC
* * *
1328683 TTACTTCAATTGTTACACGGCCTGAG-ACACGGGCGTGTG
1 TTATTTCGATTGTTACACGGCCTG-GCGCACGGGCGTGTG
1328722 TCTCAACTGT
Statistics
Matches: 141, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
121 140 0.99
122 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.24
Consensus pattern (121 bp):
TTATTTCGATTGTTACACGGCCTGGCGCACGGGCGTGTGGTTTGGCCGTGTGACCAAACTCAGAG
AGTTACACGGGTGAGGACACGGATGAAGACACAAGCTAGGACATGAACATCTGTCC
Done.