Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold1174
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1120009
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 47637 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:401562 original size:56 final size:56
Alignment explanation
Indices: 401446--401590 Score: 269
Period size: 56 Copynumber: 2.6 Consensus size: 56
401436 AGCAATAACA
401446 ATAAGGTCTTCCGTTGGAAACGGAAGACC-T--TAATAAGAAACATTACAATCACT
1 ATAAGGTCTTCCGTTGGAAACGGAAGACCTTAATAATAAGAAACATTACAATCACT
401499 ATAAGGTCTTCCGTTGGAAACGGAAGACCTTAATAATAAGAAACATTACAATCACT
1 ATAAGGTCTTCCGTTGGAAACGGAAGACCTTAATAATAAGAAACATTACAATCACT
401555 ATAAGGTCTTCCGTTGGAAACGGAAGACCTTAATAA
1 ATAAGGTCTTCCGTTGGAAACGGAAGACCTTAATAA
401591 GGATTTATTA
Statistics
Matches: 89, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
53 29 0.33
54 1 0.01
56 59 0.66
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (56 bp):
ATAAGGTCTTCCGTTGGAAACGGAAGACCTTAATAATAAGAAACATTACAATCACT
Found at i:401650 original size:10 final size:10
Alignment explanation
Indices: 401623--401726 Score: 145
Period size: 10 Copynumber: 10.0 Consensus size: 10
401613 ACTTTAATCG
401623 CCATTTGGGT
1 CCATTTGGGT
401633 CGCCATTTGGGT
1 --CCATTTGGGT
401645 CCATTTGGGT
1 CCATTTGGGT
401655 CGCCATTTGGGT
1 --CCATTTGGGT
401667 CCATTTGGGT
1 CCATTTGGGT
*
401677 TCATTTGGGT
1 CCATTTGGGT
401687 CCATTTGGGT
1 CCATTTGGGT
*
401697 TCATTTGGGT
1 CCATTTGGGT
*
401707 TCATTTGGGT
1 CCATTTGGGT
401717 CCATTTGGGT
1 CCATTTGGGT
401727 AAATCGACGC
Statistics
Matches: 86, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
10 66 0.77
12 20 0.23
ACGTcount: A:0.10, C:0.18, G:0.31, T:0.41
Consensus pattern (10 bp):
CCATTTGGGT
Found at i:405735 original size:3 final size:3
Alignment explanation
Indices: 405727--405764 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
405717 ATGATTGAGG
405727 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
405765 GTTTTATAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
TGA
Found at i:408764 original size:13 final size:14
Alignment explanation
Indices: 408737--408769 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
408727 AGGTCAACTC
408737 TCAAGGACAAAAGG
1 TCAAGGACAAAAGG
408751 TCAAGGAC-AAAGG
1 TCAAGGACAAAAGG
408764 TCAAGG
1 TCAAGG
408770 CCATTTGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.45, C:0.15, G:0.30, T:0.09
Consensus pattern (14 bp):
TCAAGGACAAAAGG
Found at i:410728 original size:33 final size:33
Alignment explanation
Indices: 410691--410756 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
410681 GTGACATCTC
*
410691 TTTTCATCATCGGTTTAATGCATAATGTAATAG
1 TTTTCATCATCGGTTAAATGCATAATGTAATAG
*
410724 TTTTCATTATCGGTTAAATGCATAATGTAATAG
1 TTTTCATCATCGGTTAAATGCATAATGTAATAG
410757 GGGGTCTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (33 bp):
TTTTCATCATCGGTTAAATGCATAATGTAATAG
Found at i:422849 original size:48 final size:49
Alignment explanation
Indices: 422779--422991 Score: 169
Period size: 49 Copynumber: 4.4 Consensus size: 49
422769 ATGCATTCGT
* *
422779 TGGTTGAGAATTATGGACATATTTCCTTTC-TCTCATTAATGCACATATGCA
1 TGGTTGAGAATCATGG--ATATTTCCTTTCAT-TCATTAATGCACAGATGCA
*
422830 TGGTTGA-AATCATGGATATTCTCC-TTCATTCATTTAA-GCATAGATGCA
1 TGGTTGAGAATCATGGATATT-TCCTTTCATTCA-TTAATGCACAGATGCA
* * * *
422878 TGGTTGAGAATTATGGCT-TTTCTCTTTCGTTCATTAATG--C--ATG-G
1 TGGTTGAGAATCATGGATATTTC-CTTTCATTCATTAATGCACAGATGCA
* * * *
422922 TTGTTGAGAATTATGGAT-TTTCTCTTTCGTTCATTAATGCATAGATGCA
1 TGGTTGAGAATCATGGATATTTC-CTTTCATTCATTAATGCACAGATGCA
* *
422971 TGGTTGAGAGTTATGGATATT
1 TGGTTGAGAATCATGGATATT
422992 CTTTCTTTCA
Statistics
Matches: 135, Mismatches: 14, Indels: 27
0.77 0.08 0.15
Matches are distributed among these distances:
44 37 0.27
45 3 0.02
47 2 0.01
48 37 0.27
49 40 0.30
50 9 0.07
51 7 0.05
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.42
Consensus pattern (49 bp):
TGGTTGAGAATCATGGATATTTCCTTTCATTCATTAATGCACAGATGCA
Found at i:422934 original size:44 final size:44
Alignment explanation
Indices: 422880--422963 Score: 159
Period size: 44 Copynumber: 1.9 Consensus size: 44
422870 TAGATGCATG
*
422880 GTTGAGAATTATGGCTTTTCTCTTTCGTTCATTAATGCATGGTT
1 GTTGAGAATTATGGATTTTCTCTTTCGTTCATTAATGCATGGTT
422924 GTTGAGAATTATGGATTTTCTCTTTCGTTCATTAATGCAT
1 GTTGAGAATTATGGATTTTCTCTTTCGTTCATTAATGCAT
422964 AGATGCATGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.20, C:0.13, G:0.19, T:0.48
Consensus pattern (44 bp):
GTTGAGAATTATGGATTTTCTCTTTCGTTCATTAATGCATGGTT
Found at i:424419 original size:2 final size:2
Alignment explanation
Indices: 424412--424450 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
424402 AATTTAATTT
424412 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
424451 GGGGCCCTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:438124 original size:9 final size:9
Alignment explanation
Indices: 438110--438171 Score: 56
Period size: 9 Copynumber: 6.8 Consensus size: 9
438100 TTTTTCTCTG
438110 TTGATATTA
1 TTGATATTA
438119 TTGATATTA
1 TTGATATTA
438128 TT-ATTTATTA
1 TTGA--TATTA
438138 TT-ATTATTA
1 TTGA-TATTA
*
438147 TTTATATTA
1 TTGATATTA
*
438156 TTGATACTA
1 TTGATATTA
*
438165 TTTATAT
1 TTGATAT
438172 CACTTATTGA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
8 1 0.02
9 36 0.78
10 9 0.20
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (9 bp):
TTGATATTA
Found at i:438131 original size:12 final size:12
Alignment explanation
Indices: 438114--438166 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
438104 TCTCTGTTGA
438114 TATTATTGATAT
1 TATTATTGATAT
*
438126 TATTATTTATTAT
1 TATTATTGA-TAT
*
438139 TATTATT-ATTT
1 TATTATTGATAT
*
438150 ATATTATTGATAC
1 -TATTATTGATAT
438163 TATT
1 TATT
438167 TATATCACTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
11 2 0.06
12 20 0.59
13 12 0.35
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (12 bp):
TATTATTGATAT
Found at i:438142 original size:16 final size:15
Alignment explanation
Indices: 438123--438171 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 15
438113 ATATTATTGA
438123 TATTATTATTTATTAT
1 TATTATTATTTA-TAT
438139 TATTATTATTTATAT
1 TATTATTATTTATAT
438154 TATTGATACTATTTATAT
1 TATT-AT--TATTTATAT
438172 CACTTATTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.23
16 14 0.47
18 9 0.30
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (15 bp):
TATTATTATTTATAT
Found at i:445288 original size:7 final size:7
Alignment explanation
Indices: 445276--445342 Score: 71
Period size: 7 Copynumber: 9.6 Consensus size: 7
445266 GAGAAGGATC
445276 ATTCGAG
1 ATTCGAG
445283 ATTCGAG
1 ATTCGAG
* *
445290 ATTCAAA
1 ATTCGAG
*
445297 ATACGAG
1 ATTCGAG
*
445304 ATTCGAA
1 ATTCGAG
*
445311 ATACGAG
1 ATTCGAG
*
445318 ATTCAAG
1 ATTCGAG
*
445325 ATTCGAA
1 ATTCGAG
445332 ATTCGAG
1 ATTCGAG
445339 ATTC
1 ATTC
445343 AATATCTAAA
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
7 46 1.00
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (7 bp):
ATTCGAG
Found at i:452059 original size:2 final size:2
Alignment explanation
Indices: 452052--452095 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
452042 TTAATTTGAA
452052 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
452094 AG
1 AG
452096 GGGTGTTGTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:464212 original size:13 final size:13
Alignment explanation
Indices: 464196--464220 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
464186 GTGTACCGGT
464196 ATGTATTCGGTAC
1 ATGTATTCGGTAC
464209 ATGTATTCGGTA
1 ATGTATTCGGTA
464221 ACCATAGTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.40
Consensus pattern (13 bp):
ATGTATTCGGTAC
Found at i:465637 original size:2 final size:2
Alignment explanation
Indices: 465632--465659 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
465622 ATAGAAAAAA
465632 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
465660 ATCATAGGGG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:469172 original size:30 final size:30
Alignment explanation
Indices: 469093--469194 Score: 91
Period size: 30 Copynumber: 3.4 Consensus size: 30
469083 GGGGGGGGGT
* ** *
469093 TGTGGCTAGCATGTAATAATAGGGGGATCC
1 TGTGACTAGCATGTAATGGTAGGAGGATCC
**
469123 TGTTG-CT-GACATGGGATGGTAGGAGGATCC
1 TG-TGACTAG-CATGTAATGGTAGGAGGATCC
**
469153 TGTGACTAGCATGTAATGGTACAAGGATCC
1 TGTGACTAGCATGTAATGGTAGGAGGATCC
*
469183 TGTGACTGGCAT
1 TGTGACTAGCAT
469195 TGGATAGTAG
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
29 3 0.05
30 52 0.90
31 3 0.05
ACGTcount: A:0.25, C:0.15, G:0.33, T:0.27
Consensus pattern (30 bp):
TGTGACTAGCATGTAATGGTAGGAGGATCC
Found at i:469211 original size:30 final size:30
Alignment explanation
Indices: 469112--469211 Score: 87
Period size: 30 Copynumber: 3.3 Consensus size: 30
469102 CATGTAATAA
* * *
469112 TAGGGGGATCCTGTTG-CTGACATGGGATGG
1 TAGGAGGATCCTG-TGACTGGCATTGGATGG
* *
469142 TAGGAGGATCCTGTGACTAGCA-TGTAATGG
1 TAGGAGGATCCTGTGACTGGCATTG-GATGG
** *
469172 TACAAGGATCCTGTGACTGGCATTGGATAG
1 TAGGAGGATCCTGTGACTGGCATTGGATGG
*
469202 TAGGGGGATC
1 TAGGAGGATC
469212 ATGTAGCTGG
Statistics
Matches: 54, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
29 3 0.06
30 49 0.91
31 2 0.04
ACGTcount: A:0.23, C:0.14, G:0.37, T:0.26
Consensus pattern (30 bp):
TAGGAGGATCCTGTGACTGGCATTGGATGG
Found at i:469302 original size:30 final size:30
Alignment explanation
Indices: 469265--470052 Score: 490
Period size: 30 Copynumber: 26.0 Consensus size: 30
469255 TGGCCACTTT
* **
469265 CTGTGGCTGGCATGAGATGGTAGGGAAATC
1 CTGTGGCTGGCATGGGATGGTAGGGGGATC
* * *
469295 CTCTGGCTAGCATTGGATGGTAGGGGGATC
1 CTGTGGCTGGCATGGGATGGTAGGGGGATC
* *
469325 CTGTGGCTGGCATGGAATGGTAGGGGAATC
1 CTGTGGCTGGCATGGGATGGTAGGGGGATC
* * * ** *
469355 TTTTGGCTAGCATGAAATGGAAGGGGGATC
1 CTGTGGCTGGCATGGGATGGTAGGGGGATC
* * *
469385 CTGTGGTTGGCATGGGGTGGTAGGAGGATC
1 CTGTGGCTGGCATGGGATGGTAGGGGGATC
*** * * *
469415 CTGTCATTGGCACT-GGATAGTAGGGAGAGC
1 CTGTGGCTGGCA-TGGGATGGTAGGGGGATC
* *
469445 CTCTGGCTGGCATGGGATGATTA-GGGGATC
1 CTGTGGCTGGCATGGGATG-GTAGGGGGATC
* * ** *
469475 TTTTAACTGGCATGGGATGGTAGGGGGATT
1 CTGTGGCTGGCATGGGATGGTAGGGGGATC
* *
469505 CTCTGGCTGGCATGAGATGGTAGGGGGATC
1 CTGTGGCTGGCATGGGATGGTAGGGGGATC
* *
469535 CTGTGGCTGGAATGGGATGGTAGGAGGATC
1 CTGTGGCTGGCATGGGATGGTAGGGGGATC
* * * * *
469565 ATCTTGTTGGCATGGGATGATAGGGGGATC
1 CTGTGGCTGGCATGGGATGGTAGGGGGATC
* * *
469595 CTGTGACTGGCATGGGATGATTGGGGGATC
1 CTGTGGCTGGCATGGGATGGTAGGGGGATC
* ** *
469625 CTGTGGCTAGCATGTAATAGTAGGGGGATC
1 CTGTGGCTGGCATGGGATGGTAGGGGGATC
* ** *
469655 CTGTTGCTGGCATGGGATGAAAGGGGGGTC
1 CTGTGGCTGGCATGGGATGGTAGGGGGATC
** * *** *
469685 CTGTTACTAGCATCTTATGGTAGGGAGATC
1 CTGTGGCTGGCATGGGATGGTAGGGGGATC
* * * * * * *
469715 TTGTAGCTTGCATGGAATGGCATGGAGATC
1 CTGTGGCTGGCATGGGATGGTAGGGGGATC
* * *
469745 CGGTGGCTAG-ATTGTGATGGTAGGGGGATC
1 CTGTGGCTGGCA-TGGGATGGTAGGGGGATC
** * *
469775 CAATGGCTGGCATGGGATGGTTGGTGGATC
1 CTGTGGCTGGCATGGGATGGTAGGGGGATC
* * * * *
469805 CTGTGACTAGCAAGGAATAGTAGGGGGATC
1 CTGTGGCTGGCATGGGATGGTAGGGGGATC
** * *
469835 CTGTGGCTAACATGGGGTGTTAGGGGGATC
1 CTGTGGCTGGCATGGGATGGTAGGGGGATC
* ** * ** *
469865 CTGTGGCTAGCATGTAATGGCAGAAAGG-TT
1 CTGTGGCTGGCATGGGATGGTAG-GGGGATC
* * *
469895 CTGTGACTGGCATTGGATGGTAAGTATTGTTAGGGGAAC
1 CTGTGGCTGGCATGGGAT-G---GTA--G---GGGGATC
*
469934 CTGTGGCTGGCATGGGAAT-GTA-GGGCAGTC
1 CTGTGGCTGGCATGGG-ATGGTAGGGGGA-TC
* ** *
469964 CTGTGGCTAGCATGTAATGGTAGGGGAATC
1 CTGTGGCTGGCATGGGATGGTAGGGGGATC
* * *
469994 CTGTTGCTTGCATGGGATGGTAGGGGGATT
1 CTGTGGCTGGCATGGGATGGTAGGGGGATC
** *
470024 CTGAAGCTGGCATGGAATGGTAGGGGGAT
1 CTGTGGCTGGCATGGGATGGTAGGGGGAT
470053 TGAATAGAAA
Statistics
Matches: 567, Mismatches: 171, Indels: 40
0.73 0.22 0.05
Matches are distributed among these distances:
29 10 0.02
30 521 0.92
31 11 0.02
34 2 0.00
35 3 0.01
36 1 0.00
38 3 0.01
39 14 0.02
40 2 0.00
ACGTcount: A:0.20, C:0.13, G:0.40, T:0.27
Consensus pattern (30 bp):
CTGTGGCTGGCATGGGATGGTAGGGGGATC
Found at i:470331 original size:30 final size:30
Alignment explanation
Indices: 470146--470334 Score: 155
Period size: 30 Copynumber: 6.3 Consensus size: 30
470136 GTGGCATTAA
*
470146 ATGGTAGGGGGATCCTGTGACTGGCATTGG
1 ATGGTAGGGGGATCCTGTGACTGGCATGGG
* * * * * * * *
470176 ATGGAAGGAGGATCTTTTGGCTAGCATAGA
1 ATGGTAGGGGGATCCTGTGACTGGCATGGG
* * * *
470206 ATGGGAGGGGAATTCTGTGACTGGCATGGC
1 ATGGTAGGGGGATCCTGTGACTGGCATGGG
* * ** *
470236 ATAGTAGGGGGATTCTGTGGTTTGCATGGG
1 ATGGTAGGGGGATCCTGTGACTGGCATGGG
* * * *
470266 GTGGTAGGGGGATCCTCTGGCTGGCAAAGGG
1 ATGGTAGGGGGATCCTGTGACTGGC-ATGGG
*
470297 -TGGTAGGGGGATCCTGTGACTAGCATGGG
1 ATGGTAGGGGGATCCTGTGACTGGCATGGG
470326 ATGGTAGGG
1 ATGGTAGGG
470335 AGCATGTAAT
Statistics
Matches: 121, Mismatches: 36, Indels: 4
0.75 0.22 0.02
Matches are distributed among these distances:
29 4 0.03
30 113 0.93
31 4 0.03
ACGTcount: A:0.20, C:0.12, G:0.43, T:0.25
Consensus pattern (30 bp):
ATGGTAGGGGGATCCTGTGACTGGCATGGG
Found at i:470893 original size:30 final size:30
Alignment explanation
Indices: 470786--471955 Score: 455
Period size: 30 Copynumber: 38.9 Consensus size: 30
470776 CGGTAGGGAA
* * *
470786 ATCCTCTGGCTAGCATTGG-ATGGAAGGGGG
1 ATCCTGTGGCTGGCA-TGGAATGGTAGGGGG
* * *
470816 ATCCTGTTGCATGGTATGGAATGGTAGGGGA
1 ATCCTGTGGC-TGGCATGGAATGGTAGGGGG
* * * * *
470847 ATCTTTTGTCTAGCATGAAATGGTAGGGGG
1 ATCCTGTGGCTGGCATGGAATGGTAGGGGG
* * * *
470877 ATGCTGTGGCTGGCATGGGATGGTAGGAGA
1 ATCCTGTGGCTGGCATGGAATGGTAGGGGG
* *
470907 ATCCTGTGACTGGCATGGGATGGTAGGGGG
1 ATCCTGTGGCTGGCATGGAATGGTAGGGGG
* * ** * **
470937 ATTCTGAGATTGACACTGG-ATACTAGGGGG
1 ATCCTGTGGCTGGCA-TGGAATGGTAGGGGG
* * **
470967 ATCCTCTGGCTGGCATGGGATGGTAAAGGG
1 ATCCTGTGGCTGGCATGGAATGGTAGGGGG
** * * *
470997 ATCCTGTAACTGGTATGGAGTGGTAGGAGG
1 ATCCTGTGGCTGGCATGGAATGGTAGGGGG
* ****** * *
471027 ATTCTGTTAAAATCATGTAATGATAGGGGG
1 ATCCTGTGGCTGGCATGGAATGGTAGGGGG
** ** * *
471057 ATCCTGTGGCTGGCATGGGTTAATAAGGAG
1 ATCCTGTGGCTGGCATGGAATGGTAGGGGG
*** * * ** * *
471087 ATCCTACAGCTTGCGTGGGGTGATAGGATGG
1 ATCCTGTGGCTGGCATGGAATGGTAGG-GGG
*** * *
471118 -TCCTGTGAAAGGCATAGAAAGGTAGGGGG
1 ATCCTGTGGCTGGCATGGAATGGTAGGGGG
* * * * * * *
471147 ATCTTTTGGATAGTATGGAATAGAAGGGGG
1 ATCCTGTGGCTGGCATGGAATGGTAGGGGG
*** *
471177 ATCCTGTCATTGGCACTGG-ATAGTAGGGGG
1 ATCCTGTGGCTGGCA-TGGAATGGTAGGGGG
* *
471207 ATTCTCTGGCTGGCAT-GAGATGGTAGGGGG
1 ATCCTGTGGCTGGCATGGA-ATGGTAGGGGG
471237 ATCCTGTGGCTGGCATTGG-ATGGTA-GGGG
1 ATCCTGTGGCTGGCA-TGGAATGGTAGGGGG
** * * * *
471266 ATCCTGTTACTGGTATGGGATGGCATGGGG
1 ATCCTGTGGCTGGCATGGAATGGTAGGGGG
* *
471296 ATCCTCTGGCTGGCATGGGATGGTAGGGGG
1 ATCCTGTGGCTGGCATGGAATGGTAGGGGG
* * * * *
471326 ATCCTGAT-ACTAGCATGTAATGATAGAGGG
1 ATCCTG-TGGCTGGCATGGAATGGTAGGGGG
* * * *
471356 ATCTTGTGGCTTGCATATG-ATGGAAGGGGG
1 ATCCTGTGGCTGGCAT-GGAATGGTAGGGGG
* * *
471386 AT-CTGGTGGCTGG-ATTGGGATTGTTGGGGG
1 ATCCT-GTGGCTGGCA-TGGAATGGTAGGGGG
* * *
471416 ATCCTGTGACTGGCACGGAATAGTAGGGGG
1 ATCCTGTGGCTGGCATGGAATGGTAGGGGG
** ** *
471446 ATCCTGTGGCTAACATGGGGTAGTAGGGGG
1 ATCCTGTGGCTGGCATGGAATGGTAGGGGG
* *
471476 ATCCTCTGGCTGGCATGGGATGGTAGGGGG
1 ATCCTGTGGCTGGCATGGAATGGTAGGGGG
* * *
471506 ATCCTGTGGCTAGCATGTAATGGTAGGGAG
1 ATCCTGTGGCTGGCATGGAATGGTAGGGGG
* *
471536 ACCCTGGGGATGGCATTGG-ATGGTTAGTATTGGTAGGGGA
1 ATCCT---G-TGGC--TGGCATGG--A--A-TGGTAGGGGG
* * *
471576 ATCCTGTTGCTGGCATGGGATGGTAGAGGG
1 ATCCTGTGGCTGGCATGGAATGGTAGGGGG
* * * ** *
471606 ATCCTGTGACTAGCATGTAATGGTACAGAG
1 ATCCTGTGGCTGGCATGGAATGGTAGGGGG
* *
471636 ATTCTGTGGCTGGCATTGG-ATGATAGGGGG
1 ATCCTGTGGCTGGCA-TGGAATGGTAGGGGG
* *
471666 -TCCTGTGACTGG--T---ATGG-AAGGGG
1 ATCCTGTGGCTGGCATGGAATGGTAGGGGG
* * * *
471689 ATCTTGTGACTGGCCCA-GG-ATAGTAGGGAG
1 ATCCTGTGGCTGG--CATGGAATGGTAGGGGG
* * ** **
471719 ATGCTGTAGCTGGCATGGGGTGGTAAAGGG
1 ATCCTGTGGCTGGCATGGAATGGTAGGGGG
* * *
471749 AACTTCTGGCTGGCAT-GAGATGGTAGGGGG
1 ATCCTGTGGCTGGCATGGA-ATGGTAGGGGG
* * * *
471779 ATCCTGTGACTGGCATTGG-ATTGAATGGGG
1 ATCCTGTGGCTGGCA-TGGAATGGTAGGGGG
* * * * * *
471809 AACTTTTAGCTAGCATGAAATGGTAGGGGG
1 ATCCTGTGGCTGGCATGGAATGGTAGGGGG
* * * *
471839 ATTCTGTGACTGGCATGGCATAGTAGGGGG
1 ATCCTGTGGCTGGCATGGAATGGTAGGGGG
* * **
471869 ATCCTGTGGTTTGCATGGGGTGGTAGGGGG
1 ATCCTGTGGCTGGCATGGAATGGTAGGGGG
* * * *
471899 ATCTTCTGGCTGGTATTGG-GTGGTAGGGGG
1 ATCCTGTGGCTGGCA-TGGAATGGTAGGGGG
** * *
471929 ATCCTGTAACTGGCAAGGGATGGTAGG
1 ATCCTGTGGCTGGCATGGAATGGTAGG
471956 AAGCATGTAC
Statistics
Matches: 815, Mismatches: 275, Indels: 100
0.68 0.23 0.08
Matches are distributed among these distances:
23 5 0.01
24 14 0.02
26 1 0.00
28 6 0.01
29 51 0.06
30 664 0.81
31 37 0.05
32 2 0.00
33 1 0.00
34 7 0.01
35 7 0.01
36 5 0.01
37 2 0.00
39 1 0.00
40 12 0.01
ACGTcount: A:0.21, C:0.12, G:0.40, T:0.27
Consensus pattern (30 bp):
ATCCTGTGGCTGGCATGGAATGGTAGGGGG
Found at i:471650 original size:100 final size:100
Alignment explanation
Indices: 471468--471657 Score: 281
Period size: 100 Copynumber: 1.9 Consensus size: 100
471458 ACATGGGGTA
* * * **
471468 GTAGGGGGATCCTCTGGCTGGCATGGGATGGTAGGGGGATCCTGTGGCTAGCATGTAATGGTAGG
1 GTAGGGGAATCCTCTGGCTGGCATGGGATGGTAGAGGGATCCTGTGACTAGCATGTAATGGTACA
471533 GAGACCCTGGGGATGGCATTGGATGGTTAGTATTG
66 GAGACCCTGGGGATGGCATTGGATGGTTAGTATTG
* *
471568 GTAGGGGAATCCTGTTGCTGGCATGGGATGGTAGAGGGATCCTGTGACTAGCATGTAATGGTACA
1 GTAGGGGAATCCTCTGGCTGGCATGGGATGGTAGAGGGATCCTGTGACTAGCATGTAATGGTACA
** * *
471633 GAGATTCTGTGGCTGGCATTGGATG
66 GAGACCCTGGGGATGGCATTGGATG
471658 ATAGGGGGTC
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
100 79 1.00
ACGTcount: A:0.19, C:0.13, G:0.41, T:0.27
Consensus pattern (100 bp):
GTAGGGGAATCCTCTGGCTGGCATGGGATGGTAGAGGGATCCTGTGACTAGCATGTAATGGTACA
GAGACCCTGGGGATGGCATTGGATGGTTAGTATTG
Found at i:480723 original size:15 final size:16
Alignment explanation
Indices: 480691--480723 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
480681 CATGAAGTAA
*
480691 TTCTCTGTACATTCTT
1 TTCTCAGTACATTCTT
480707 TTCTCAGTACA-TCTT
1 TTCTCAGTACATTCTT
480722 TT
1 TT
480724 ATATCATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.15, C:0.24, G:0.06, T:0.55
Consensus pattern (16 bp):
TTCTCAGTACATTCTT
Found at i:487697 original size:53 final size:53
Alignment explanation
Indices: 487590--487689 Score: 175
Period size: 52 Copynumber: 1.9 Consensus size: 53
487580 GCCGAAATGG
* *
487590 AATCTTGTTAAATTTTTTTTTTTAATTTTCATATGGTTTGTCATTTAATCTTT
1 AATCTTATTAAATTTTTTATTTTAATTTTCATATGGTTTGTCATTTAATCTTT
487643 AATCTTATTAAATTTTTTATTTT-ATTTTCATATGGTTTGTCATTTAA
1 AATCTTATTAAATTTTTTATTTTAATTTTCATATGGTTTGTCATTTAA
487690 ATTTTTAAAC
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 24 0.53
53 21 0.47
ACGTcount: A:0.25, C:0.07, G:0.07, T:0.61
Consensus pattern (53 bp):
AATCTTATTAAATTTTTTATTTTAATTTTCATATGGTTTGTCATTTAATCTTT
Found at i:487950 original size:52 final size:52
Alignment explanation
Indices: 487884--488016 Score: 257
Period size: 52 Copynumber: 2.5 Consensus size: 52
487874 TGTATCNTTT
487884 TTTTAATTTTCATATGGTTTGTCATTTAATCTTTAATCTTATTAAATTTTTTA
1 TTTT-ATTTTCATATGGTTTGTCATTTAATCTTTAATCTTATTAAATTTTTTA
487937 TTTTATTTTCATATGGTTTGTCATTTAATCTTTAATCTTATTAAATTTTTTA
1 TTTTATTTTCATATGGTTTGTCATTTAATCTTTAATCTTATTAAATTTTTTA
487989 TTTTATTTTCATATGGTTTGTCATTTAA
1 TTTTATTTTCATATGGTTTGTCATTTAA
488017 ATTTTTAAAC
Statistics
Matches: 80, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
52 76 0.95
53 4 0.05
ACGTcount: A:0.25, C:0.08, G:0.07, T:0.61
Consensus pattern (52 bp):
TTTTATTTTCATATGGTTTGTCATTTAATCTTTAATCTTATTAAATTTTTTA
Found at i:497120 original size:20 final size:20
Alignment explanation
Indices: 497095--497134 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
497085 TCACAAAGAG
497095 CATAGTAGAAAGTCACCTTT
1 CATAGTAGAAAGTCACCTTT
497115 CATAGTAGAAAGTCACCTTT
1 CATAGTAGAAAGTCACCTTT
497135 GGCTAGTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (20 bp):
CATAGTAGAAAGTCACCTTT
Found at i:502074 original size:2 final size:2
Alignment explanation
Indices: 502067--502166 Score: 146
Period size: 2 Copynumber: 50.0 Consensus size: 2
502057 AATGTTAAAA
** * *
502067 TC TC TC TC TC AA TC TC TC TC TC TC TC TC TG TC TC TC TC TG TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* *
502109 TG TC TG TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
502151 TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC
502167 CTGCTTTTTC
Statistics
Matches: 86, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 86 1.00
ACGTcount: A:0.02, C:0.45, G:0.04, T:0.49
Consensus pattern (2 bp):
TC
Found at i:503762 original size:2 final size:2
Alignment explanation
Indices: 503755--503793 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
503745 AGCTGCTTTG
503755 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
503794 CTAGTACTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:509609 original size:15 final size:15
Alignment explanation
Indices: 509585--509616 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
509575 TTAACAGCCT
*
509585 GAAGAGGAAGAGGAG
1 GAAGAAGAAGAGGAG
509600 GAAGAAGAAGAGGAG
1 GAAGAAGAAGAGGAG
509615 GA
1 GA
509617 TAAGCCTAAG
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:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (15 bp):
GAAGAAGAAGAGGAG
Found at i:511799 original size:165 final size:165
Alignment explanation
Indices: 511580--512014 Score: 457
Period size: 167 Copynumber: 2.6 Consensus size: 165
511570 CATACCACAG
* *** *
511580 GGATCATGATTTGAACAAACTTTAATCTACACTTTAT-AAGGATGCTTCCACACAAGTAACAGCT
1 GGATCATGATTTGAAC-AACTTGAATCTACACTACCTGAA-GATGCTTCCACACAAGTTACAGCT
* * * *
511644 TTTTGCCCAAATGCTTTTTGAGAAGAAGAATTTTTAAGATTTTTC-TCTATATATTCCTATGTAA
64 TTTTGGCCAATTGCTTTTTGAGAAGAAGAATTTTTAAGATTTTTCTTCTATATATCCCTACGTAA
* * * * *
511708 AAATTTAACACCCAATTGTTGCCCTACCCTA-CTCCC-A
129 AAATTCAAC-CCCAATGGTGGCCCCACCATATC-CCCGA
* * *
511745 GGATCCTGATTTGAACAACCTTGAATCTACACTACCTGAAGATGCTTTCACACAAGTTACAGTTT
1 GGATCATGATTTGAACAA-CTTGAATCTACACTACCTGAAGATGCTTCCACACAAGTTACAG-CT
* * * *
511810 TTTTGGCCAATTGTTTTTTTAGAGGAAG-ATTTTTAAAGATTTTTCTTCTATATATCCCTACGTG
64 TTTTGGCCAATTGCTTTTTGAGAAGAAGAATTTTT-AAGATTTTTCTTCTATATATCCCTACGTA
* * *
511874 AAAATTCGACCCCGATGGTGGCCCCACCATATCCCCGG
128 AAAATTCAACCCCAATGGTGGCCCCACCATATCCCCGA
* * * *
511912 GGATCATGATCTGAACAGACTTGAATCTGCACGACCTGAAGATGCTTCCACACAAGTTACAACTT
1 GGATCATGATTTGAACA-ACTTGAATCTACACTACCTGAAGATGCTTCCACACAAGTTACAGCTT
* * * *
511977 TTCTGGCCAATTGGTTTTGGAGCAGAAGATTTCTTTAA
65 TT-TGGCCAATTGCTTTTTGAGAAGAAGAATT-TTTAA
512015 AGGATGCCAA
Statistics
Matches: 222, Mismatches: 37, Indels: 19
0.80 0.13 0.07
Matches are distributed among these distances:
164 2 0.01
165 55 0.25
166 59 0.27
167 98 0.44
168 5 0.02
169 3 0.01
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.34
Consensus pattern (165 bp):
GGATCATGATTTGAACAACTTGAATCTACACTACCTGAAGATGCTTCCACACAAGTTACAGCTTT
TTGGCCAATTGCTTTTTGAGAAGAAGAATTTTTAAGATTTTTCTTCTATATATCCCTACGTAAAA
ATTCAACCCCAATGGTGGCCCCACCATATCCCCGA
Found at i:520279 original size:4 final size:4
Alignment explanation
Indices: 520270--520300 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
520260 ATTTTATTTC
*
520270 ATCT ATCT ATTT ATCT ATCT ATCT ATCT ATC
1 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATC
520301 CATCCATCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.52
Consensus pattern (4 bp):
ATCT
Found at i:520287 original size:12 final size:12
Alignment explanation
Indices: 520264--520300 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
520254 AGCAATATTT
520264 TATTTCATCTATC
1 TATTT-ATCTATC
520277 TATTTATCTATC
1 TATTTATCTATC
*
520289 TATCTATCTATC
1 TATTTATCTATC
520301 CATCCATCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 18 0.78
13 5 0.22
ACGTcount: A:0.24, C:0.22, G:0.00, T:0.54
Consensus pattern (12 bp):
TATTTATCTATC
Found at i:520305 original size:4 final size:4
Alignment explanation
Indices: 520298--520330 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
520288 CTATCTATCT
520298 ATCC ATCC ATCC ATCC ATCC ATCC ATCC ATCC A
1 ATCC ATCC ATCC ATCC ATCC ATCC ATCC ATCC A
520331 AATTCATCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.27, C:0.48, G:0.00, T:0.24
Consensus pattern (4 bp):
ATCC
Found at i:521977 original size:2 final size:2
Alignment explanation
Indices: 521970--522008 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
521960 CCTTTTTATA
521970 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
522009 AACTTTTTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:523786 original size:72 final size:72
Alignment explanation
Indices: 523700--523883 Score: 296
Period size: 72 Copynumber: 2.6 Consensus size: 72
523690 TTGTTCGCCT
* * *
523700 AACATTTTTGGACCACATACCTTGGAATAGATAATTAACAATGGTTAATATGTTGCTTAACCAGA
1 AACATTTTTGGACCACATACCTTGGAATAAATAATCAACAATGGCTAATATGTTGCTTAACCAGA
523765 TAAACTG
66 TAAACTG
*
523772 AACATTTTTGGACCACATACCTTGGAATAAATAATCAACAATGGCTAATATGTTGCTTTACCAGA
1 AACATTTTTGGACCACATACCTTGGAATAAATAATCAACAATGGCTAATATGTTGCTTAACCAGA
*
523837 TAAATTG
66 TAAACTG
** *
523844 ATTATTTTTGGACCACATACCTTGGAATAAATAATGAACA
1 AACATTTTTGGACCACATACCTTGGAATAAATAATCAACA
523884 CTGCTTTTAA
Statistics
Matches: 104, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 104 1.00
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (72 bp):
AACATTTTTGGACCACATACCTTGGAATAAATAATCAACAATGGCTAATATGTTGCTTAACCAGA
TAAACTG
Found at i:526861 original size:68 final size:68
Alignment explanation
Indices: 526773--527082 Score: 530
Period size: 68 Copynumber: 4.6 Consensus size: 68
526763 TTAAGAGATT
*
526773 ACAGCAGGGCTTGAACCAACAACCTTTGGGTTACTGGCTAAACACCTAACACACAACATTAAGTG
1 ACAGCAGGGCTTGAACCAACAATCTTTGGGTTACTGGCTAAACACCTAACACACAACATTAAGTG
526838 ACC
66 ACC
*
526841 ACAGCAGGGCTTGAACCAACAATCTTTGGGTTACTGGCTAAACACCTAACACACAACATTAAGTT
1 ACAGCAGGGCTTGAACCAACAATCTTTGGGTTACTGGCTAAACACCTAACACACAACATTAAGTG
*
526906 ATC
66 ACC
* ** * *
526909 ACAGCAGGGCTTGAACCAACAACCTTTCAGTTACTGACTAAACACCTTACACACAACATTAAGTG
1 ACAGCAGGGCTTGAACCAACAATCTTTGGGTTACTGGCTAAACACCTAACACACAACATTAAGTG
526974 ACC
66 ACC
*
526977 ACAGCAGGGCTTGAACCAACAATCTTTGGGTTATTGGCTAAACACCTAACACACAACATTAAGTG
1 ACAGCAGGGCTTGAACCAACAATCTTTGGGTTACTGGCTAAACACCTAACACACAACATTAAGTG
527042 ACC
66 ACC
*
527045 AAAGCAGGGCTTGAACCAACAATCTTTGGGTTACTGGC
1 ACAGCAGGGCTTGAACCAACAATCTTTGGGTTACTGGC
527083 CTAGGAACAC
Statistics
Matches: 224, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 224 1.00
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (68 bp):
ACAGCAGGGCTTGAACCAACAATCTTTGGGTTACTGGCTAAACACCTAACACACAACATTAAGTG
ACC
Found at i:538501 original size:2 final size:2
Alignment explanation
Indices: 538488--538522 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
538478 NNNNNNNNNN
*
538488 AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
538523 CACACACACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:539923 original size:44 final size:45
Alignment explanation
Indices: 539846--539965 Score: 215
Period size: 44 Copynumber: 2.7 Consensus size: 45
539836 CATCTTGGCT
539846 AGCCAAGGGTTTACAATCCACTCTGCTCCTCTACAACATGTTGTA
1 AGCCAAGGGTTTACAATCCACTCTGCTCCTCTACAACATGTTGTA
*
539891 AGCCAAGGGTTTAC-ATCTACTCTGCTCCTCTACAACATGTTGTA
1 AGCCAAGGGTTTACAATCCACTCTGCTCCTCTACAACATGTTGTA
*
539935 AGCCAAGGGTTTACGATCCACTCTGCTCCTC
1 AGCCAAGGGTTTACAATCCACTCTGCTCCTC
539966 ATCACGTTGT
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
44 43 0.60
45 29 0.40
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (45 bp):
AGCCAAGGGTTTACAATCCACTCTGCTCCTCTACAACATGTTGTA
Found at i:550632 original size:10 final size:10
Alignment explanation
Indices: 550617--550664 Score: 60
Period size: 10 Copynumber: 4.8 Consensus size: 10
550607 ATTTTTTTCA
550617 TTTATATATT
1 TTTATATATT
*
550627 TTTATATATG
1 TTTATATATT
*
550637 TATATATATT
1 TTTATATATT
* *
550647 TATATATTTT
1 TTTATATATT
550657 TTTATATA
1 TTTATATA
550665 AAGGACTTTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 32 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (10 bp):
TTTATATATT
Found at i:550640 original size:18 final size:18
Alignment explanation
Indices: 550619--550653 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
550609 TTTTTTCATT
*
550619 TATATATTTTTATATATG
1 TATATATATTTATATATG
550637 TATATATATTTATATAT
1 TATATATATTTATATAT
550654 TTTTTTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (18 bp):
TATATATATTTATATATG
Found at i:557495 original size:2 final size:2
Alignment explanation
Indices: 557490--557545 Score: 94
Period size: 2 Copynumber: 28.0 Consensus size: 2
557480 AAACACACTT
557490 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* *
557532 TG TC TA TC TC TC TC
1 TC TC TC TC TC TC TC
557546 AAAATATGTA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.02, C:0.46, G:0.02, T:0.50
Consensus pattern (2 bp):
TC
Found at i:570083 original size:2 final size:2
Alignment explanation
Indices: 570076--570121 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
570066 TTGAAAACAT
*
570076 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
570117 TA TA T
1 TA TA T
570122 TTGAGTGAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:570859 original size:2 final size:2
Alignment explanation
Indices: 570852--570882 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
570842 TTTCTTTGTG
570852 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
570883 GTTGTTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:577168 original size:11 final size:11
Alignment explanation
Indices: 577152--577180 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
577142 ACGTAGCATC
577152 AGGGGGGGGGG
1 AGGGGGGGGGG
577163 AGGGGGGGGGG
1 AGGGGGGGGGG
577174 -GGGGGGG
1 AGGGGGGG
577181 CCCCCCCCCN
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.07, C:0.00, G:0.93, T:0.00
Consensus pattern (11 bp):
AGGGGGGGGGG
Found at i:586049 original size:2 final size:2
Alignment explanation
Indices: 586042--586082 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
586032 TGATCTCCAC
586042 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
586083 NNNNNNNNNN
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:586641 original size:1 final size:1
Alignment explanation
Indices: 586635--586666 Score: 55
Period size: 1 Copynumber: 32.0 Consensus size: 1
586625 ATGCGAGTTG
*
586635 TTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
586667 GGGGGGGGCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:586650 original size:13 final size:13
Alignment explanation
Indices: 586632--586666 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
586622 ACAATGCGAG
586632 TTGTTTTTTTTTT
1 TTGTTTTTTTTTT
586645 TTGTTTTTTTTTT
1 TTGTTTTTTTTTT
586658 TT-TTTTTTT
1 TTGTTTTTTT
586667 GGGGGGGGCG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 7 0.32
13 15 0.68
ACGTcount: A:0.00, C:0.00, G:0.06, T:0.94
Consensus pattern (13 bp):
TTGTTTTTTTTTT
Found at i:591635 original size:2 final size:2
Alignment explanation
Indices: 591630--591672 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
591620 TCTAATACAT
591630 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
591672 T
1 T
591673 GTAAAATTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:597862 original size:14 final size:14
Alignment explanation
Indices: 597843--597873 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
597833 AATGCGGCGT
597843 TTTATCATAAATAA
1 TTTATCATAAATAA
597857 TTTATCATAAATAA
1 TTTATCATAAATAA
597871 TTT
1 TTT
597874 TCAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (14 bp):
TTTATCATAAATAA
Found at i:598747 original size:37 final size:37
Alignment explanation
Indices: 598654--600073 Score: 2232
Period size: 37 Copynumber: 38.2 Consensus size: 37
598644 CAGGCTAGCG
* *
598654 TCCCTAGCCTAGTGAGTAGTGTTCATCGATTGGGG--
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
* * *
598689 GCCATAGCCTAGTGAGTAGTGTTCACCGATCGGGATC
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
*
598726 TCCCTAGTCTAGTGAGTAGTGTTCACCGATCGGGGTC
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
598763 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
*
598800 TCCTTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
* *
598837 TCCCTAGCCTAGTGAGTAGTGTTCAACGATCGAGGTC
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
* *
598874 TCTCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTT
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
598911 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
*
598948 TCCCTAGCCTAGTGAGTAGTGTTCAACGATCGGGGTC
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
598985 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
*
599022 TCCTTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
599059 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
* ** * *
599096 TCCTTTCCCTATAGTGAGTAGTGTTTACCGATCGGGGTG
1 TCCCTAGCC--TAGTGAGTAGTGTTCACCGATCGGGGTC
* *
599135 TCCTTAGCCTAGTGAATAGTGTTCACCGATCGGGGTC
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
* *
599172 TCCTTAGCCGAGTGAGTAGTGTTCACCGATCGGGGGTC
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATC-GGGGTC
599210 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
* * *
599247 TCTCTAGCCTAGTAAGTAGTGTTCACCGATCGGGGTT
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
599284 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
* *
599321 TCCCTAGCCTAGTGGGTAGTGTTCAACGATCGGGGTC
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
599358 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
599395 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
599432 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
* ** * *
599469 TCCTTTCCCTATAGTGAGTAGTGTTTACCGATCGGGGTG
1 TCCCTAGCC--TAGTGAGTAGTGTTCACCGATCGGGGTC
* *
599508 TCCTTAGCCTAGTGAATAGTGTTCACCGATCGGGGTC
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
* *
599545 TCCTTAGCCGAGTGAGTAGTGTTCACCGATCGGGGGTC
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATC-GGGGTC
599583 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
* * *
599620 TCTCTAGCCTAGTAAGTAGTGTTCACCGATCGGGGTT
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
599657 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
* *
599694 TCCCTAGCCTAGTGGGTAGTGTTCAACGATCGGGGTC
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
599731 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
599768 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
599805 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
* ** * *
599842 TCCTTTCCCTATAGTGAGTAGTGTTTACCGATCGGGGTG
1 TCCCTAGCC--TAGTGAGTAGTGTTCACCGATCGGGGTC
* * *
599881 TCCTTAGCCTAGTGAATAGTGTTCACCGATCGGGGTT
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
*
599918 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTG
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
* * *
599955 TCCTTAGCCGAGTGAGTAGTGTTCGCCGATCGGGGTC
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
* * * *
599992 TCCCTAGCCTTGTGAGAAGTGTTCATCGATCGGGGTT
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
*
600029 TCTCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
600066 TCCCTAGC
1 TCCCTAGC
600074 TTCATGGTTT
Statistics
Matches: 1273, Mismatches: 102, Indels: 18
0.91 0.07 0.01
Matches are distributed among these distances:
35 30 0.02
37 1074 0.84
38 70 0.05
39 99 0.08
ACGTcount: A:0.17, C:0.25, G:0.30, T:0.29
Consensus pattern (37 bp):
TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
Found at i:599419 original size:373 final size:372
Alignment explanation
Indices: 598654--600073 Score: 2506
Period size: 373 Copynumber: 3.8 Consensus size: 372
598644 CAGGCTAGCG
* * * *
598654 TCCCTAGCCTAGTGAGTAGTGTTCATCGATTGGGG--GCCATAGCCTAGTGAGTAGTGTTCACCG
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTCTCCCTAGCCTAGTGAGTAGTGTTCACCG
* * ** * * * * *
598717 ATCGGGATCTCC-CT-AGTCTAGTGAGTAGTGTTCACCGATCGGGGTCTCCCTAGCCTAGTGAGT
66 ATCGGGGTCTCCTTTCCCTATAGTGAGTAGTGTTTACCGATCGGGGTGTCCTTAGCCTAGTGAAT
*
598780 AGTGTTCACCGATCGGGGTCTCCTTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTCTCCCTAGC
131 AGTGTTCACCGATCGGGGTCTCCTTAGCCGAGTGAGTAGTGTTCACCGATCGGGGTCTCCCTAGC
* * *
598845 CTAGTGAGTAGTGTTCAACGATCGAGGTCTCTCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGT
196 CTAGTGAGTAGTGTTCACCGATCGGGGTCTCTCTAGCCTAGTAAGTAGTGTTCACCGATCGGGGT
*
598910 TTCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTCTCCCTAGCCTAGTGAGTAGTGTTCAAC
261 TTCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTCTCCCTAGCCTAGTGGGTAGTGTTCAAC
598975 GATCGGGGTCTCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
326 GATCGGGGTCTCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
*
599022 TCCTTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTCTCCCTAGCCTAGTGAGTAGTGTTCACCG
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTCTCCCTAGCCTAGTGAGTAGTGTTCACCG
599087 ATCGGGGTCTCCTTTCCCTATAGTGAGTAGTGTTTACCGATCGGGGTGTCCTTAGCCTAGTGAAT
66 ATCGGGGTCTCCTTTCCCTATAGTGAGTAGTGTTTACCGATCGGGGTGTCCTTAGCCTAGTGAAT
599152 AGTGTTCACCGATCGGGGTCTCCTTAGCCGAGTGAGTAGTGTTCACCGATCGGGGGTCTCCCTAG
131 AGTGTTCACCGATCGGGGTCTCCTTAGCCGAGTGAGTAGTGTTCACCGATC-GGGGTCTCCCTAG
599217 CCTAGTGAGTAGTGTTCACCGATCGGGGTCTCTCTAGCCTAGTAAGTAGTGTTCACCGATCGGGG
195 CCTAGTGAGTAGTGTTCACCGATCGGGGTCTCTCTAGCCTAGTAAGTAGTGTTCACCGATCGGGG
599282 TTTCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTCTCCCTAGCCTAGTGGGTAGTGTTCAA
260 TTTCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTCTCCCTAGCCTAGTGGGTAGTGTTCAA
599347 CGATCGGGGTCTCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
325 CGATCGGGGTCTCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
599395 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTCTCCCTAGCCTAGTGAGTAGTGTTCACCG
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTCTCCCTAGCCTAGTGAGTAGTGTTCACCG
599460 ATCGGGGTCTCCTTTCCCTATAGTGAGTAGTGTTTACCGATCGGGGTGTCCTTAGCCTAGTGAAT
66 ATCGGGGTCTCCTTTCCCTATAGTGAGTAGTGTTTACCGATCGGGGTGTCCTTAGCCTAGTGAAT
599525 AGTGTTCACCGATCGGGGTCTCCTTAGCCGAGTGAGTAGTGTTCACCGATCGGGGGTCTCCCTAG
131 AGTGTTCACCGATCGGGGTCTCCTTAGCCGAGTGAGTAGTGTTCACCGATC-GGGGTCTCCCTAG
599590 CCTAGTGAGTAGTGTTCACCGATCGGGGTCTCTCTAGCCTAGTAAGTAGTGTTCACCGATCGGGG
195 CCTAGTGAGTAGTGTTCACCGATCGGGGTCTCTCTAGCCTAGTAAGTAGTGTTCACCGATCGGGG
599655 TTTCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTCTCCCTAGCCTAGTGGGTAGTGTTCAA
260 TTTCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTCTCCCTAGCCTAGTGGGTAGTGTTCAA
599720 CGATCGGGGTCTCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
325 CGATCGGGGTCTCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
599768 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTCTCCCTAGCCTAGTGAGTAGTGTTCACCG
1 TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTCTCCCTAGCCTAGTGAGTAGTGTTCACCG
599833 ATCGGGGTCTCCTTTCCCTATAGTGAGTAGTGTTTACCGATCGGGGTGTCCTTAGCCTAGTGAAT
66 ATCGGGGTCTCCTTTCCCTATAGTGAGTAGTGTTTACCGATCGGGGTGTCCTTAGCCTAGTGAAT
* * * * *
599898 AGTGTTCACCGATCGGGGTTTCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTGTCCTTAGC
131 AGTGTTCACCGATCGGGGTCTCCTTAGCCGAGTGAGTAGTGTTCACCGATCGGGGTCTCCCTAGC
* * * * * * *
599963 CGAGTGAGTAGTGTTCGCCGATCGGGGTCTCCCTAGCCTTGTGAGAAGTGTTCATCGATCGGGGT
196 CTAGTGAGTAGTGTTCACCGATCGGGGTCTCTCTAGCCTAGTAAGTAGTGTTCACCGATCGGGGT
*
600028 TTCTCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTCTCCCTAGC
261 TTCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTCTCCCTAGC
600074 TTCATGGTTT
Statistics
Matches: 1014, Mismatches: 33, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
368 32 0.03
370 37 0.04
371 1 0.00
372 207 0.20
373 737 0.73
ACGTcount: A:0.17, C:0.25, G:0.30, T:0.29
Consensus pattern (372 bp):
TCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTCTCCCTAGCCTAGTGAGTAGTGTTCACCG
ATCGGGGTCTCCTTTCCCTATAGTGAGTAGTGTTTACCGATCGGGGTGTCCTTAGCCTAGTGAAT
AGTGTTCACCGATCGGGGTCTCCTTAGCCGAGTGAGTAGTGTTCACCGATCGGGGTCTCCCTAGC
CTAGTGAGTAGTGTTCACCGATCGGGGTCTCTCTAGCCTAGTAAGTAGTGTTCACCGATCGGGGT
TTCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTCTCCCTAGCCTAGTGGGTAGTGTTCAAC
GATCGGGGTCTCCCTAGCCTAGTGAGTAGTGTTCACCGATCGGGGTC
Found at i:628399 original size:322 final size:313
Alignment explanation
Indices: 628001--628716 Score: 823
Period size: 322 Copynumber: 2.2 Consensus size: 313
627991 TCATAAGGAG
* * * *
628001 GCATCCTCAGGTAGTGAAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGAGGGGTCA
1 GCATCCTCAGATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCA
* * * *
628066 CAAGAGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATC-TT-CTTC-TCAAAAACTATT
66 CAA-TGGGGGATAAAGTTTTACACAGGAATATATAGAGAAAATCTTTAATTCTTCAAAAACTATT
* * * *
628128 AGGCCAGGAAAGCCCAAATTAAAATGGAAGCATCCTCAGGTAGTGTAGAATTCAAGTTTGTTCAA
130 AGGCCAAGAAAGCCCAAATTAAAATGGAAGCATCCTCAGATAATGTAG-ATTCAAGTTTATTCAA
* *
628193 ATCATGGTCCCCGGGGGTAGGGAGGGGTCACAAGAGGGGGATCAAGTTTTACATAGGAATATATA
194 ATCATGGTCCCCGGGGGTAGGGAGGGGCCACAA-AGGGGG-T-AAATTTT---T----ATATATA
* *
628258 GAG-AAATCTTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAGGAAAGCTCAAATTTGAGTGGG
249 GAGAAAATCTTTAAAAATCTTCTTCTC-AAAACTATTAGGCCAGGAAAGCCCAAATTTGAGTGGA
628322 A
313 A
* * *
628323 GCATTCTCAGATAGTGTACATTCAAGTTTGTTCAAACCATGGTCCCCGGGGGTAGGGTGGGGCCA
1 GCATCCTCAGATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCA
* * *
628388 CAATTGGGGGATAAATTTTTATACAGGAATATATAGAGAAAATCTTTTAAAAAAATTCTTTTAAA
66 CAA-TGGGGGATAAAGTTTTACACAGGAATATATAGAGAAAATC-TTT-----AATTC-TTCAAA
* * **** * * *
628453 AACTATTTGGCCAAGAAAGCTCAAATTGGCGTGTAAGTATCCTCAGATAATGTCGATTCAAGTTT
123 AACTATTAGGCCAAGAAAGCCCAAATTAAAATGGAAGCATCCTCAGATAATGTAGATTCAAGTTT
* * *
628518 ATTCAAATCATGGTCCCTGGGGGTAGGGCGGGGCCACAATGGGGGTAAATTTTTATATATAGAGA
188 ATTCAAATCATGGTCCCCGGGGGTAGGGAGGGGCCACAAAGGGGGTAAATTTTTATATATAGAGA
628583 AAATCTTTAAAAATCTTCTTCTCAAAACTATTAGGCCAGGAAAGCCCAAATTTGAGTGGAA
253 AAATCTTTAAAAATCTTCTTCTCAAAACTATTAGGCCAGGAAAGCCCAAATTTGAGTGGAA
* * * * * * * *
628644 GCATCCCCAGATTGTATAGATTCAAGTTTGTTTAAATAATAGT--CCAGGGGTAGGGTGTGGCCA
1 GCATCCTCAGATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCA
628707 CAATGGGGGA
66 CAATGGGGGA
628717 GGAATATATA
Statistics
Matches: 337, Mismatches: 46, Indels: 26
0.82 0.11 0.06
Matches are distributed among these distances:
318 7 0.02
319 21 0.06
321 80 0.24
322 119 0.35
324 2 0.01
325 1 0.00
328 6 0.02
329 1 0.00
330 8 0.02
331 45 0.13
332 47 0.14
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (313 bp):
GCATCCTCAGATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCA
CAATGGGGGATAAAGTTTTACACAGGAATATATAGAGAAAATCTTTAATTCTTCAAAAACTATTA
GGCCAAGAAAGCCCAAATTAAAATGGAAGCATCCTCAGATAATGTAGATTCAAGTTTATTCAAAT
CATGGTCCCCGGGGGTAGGGAGGGGCCACAAAGGGGGTAAATTTTTATATATAGAGAAAATCTTT
AAAAATCTTCTTCTCAAAACTATTAGGCCAGGAAAGCCCAAATTTGAGTGGAA
Found at i:628420 original size:165 final size:163
Alignment explanation
Indices: 628001--628716 Score: 763
Period size: 166 Copynumber: 4.5 Consensus size: 163
627991 TCATAAGGAG
* * * * *
628001 GCATCCTCAGGTAGTGAAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGAGGGGTCA
1 GCATCCTCAGATAGTGTACATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCA
* * * *
628066 CAAGAGGGGGATCAAGTTTTACATAGGAATATATAGAG---------AAAATCTTCTTCTCAAAA
66 CAA-TGGGGGATAAATTTTTATA-AGGAATATATAGAGAAATCTTTAAAAATCTTCTTCTCAAAA
** *
628122 ACTATTAGGCCAGGAAAGCCCAAATTAAAATGGAA
129 ACTATTAGGCCAGGAAAGCCCAAATTTGAGTGGAA
* * * *
628157 GCATCCTCAGGTAGTGTAGAATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGAGGGGTC
1 GCATCCTCAGATAGTGTA-CATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCC
* * * *
628222 ACAAGAGGGGGATCAAGTTTTACATAGGAATATATAGAGAAATCTTTAAAAATCTTCTTCTCAAA
65 ACAA-TGGGGGATAAATTTTTATA-AGGAATATATAGAGAAATCTTTAAAAATCTTCTTCTCAAA
* *
628287 AACTATTAGGCCAGGAAAGCTCAAATTTGAGTGGGA
128 AACTATTAGGCCAGGAAAGCCCAAATTTGAGTGGAA
* *
628323 GCATTCTCAGATAGTGTACATTCAAGTTTGTTCAAACCATGGTCCCCGGGGGTAGGGTGGGGCCA
1 GCATCCTCAGATAGTGTACATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCA
** *
628388 CAATTGGGGGATAAATTTTTATACAGGAATATATAGAGAAAATCTTTTAAAAAAATTCTT-TTAA
66 CAA-TGGGGGATAAATTTTTATA-AGGAATATATAGAG-AAATC-TTTAAAAATCTTCTTCTCAA
* * * * * *
628452 AAACTATTTGGCCAAGAAAGCTCAAATTGGCGTGTAA
127 AAACTATTAGGCCAGGAAAGCCCAAATTTGAGTGGAA
* * * * *
628489 GTATCCTCAGATAATGT-CGATTCAAGTTTATTCAAATCATGGTCCCTGGGGGTAGGGCGGGGCC
1 GCATCCTCAGATAGTGTAC-ATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCC
*
628553 ACAATGGGGG-TAAATTTTTAT-----ATATAGAGA-AAATCTTTAAAAATCTTCTTCTC-AAAA
65 ACAATGGGGGATAAATTTTTATAAGGAATATATAGAGAAATCTTTAAAAATCTTCTTCTCAAAAA
628610 CTATTAGGCCAGGAAAGCCCAAATTTGAGTGGAA
130 CTATTAGGCCAGGAAAGCCCAAATTTGAGTGGAA
* * * * * * * * *
628644 GCATCCCCAGATTGTATAGATTCAAGTTTGTTTAAATAATAGT--CCAGGGGTAGGGTGTGGCCA
1 GCATCCTCAGATAGTGTACATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCA
628707 CAATGGGGGA
66 CAATGGGGGA
628717 GGAATATATA
Statistics
Matches: 485, Mismatches: 59, Indels: 34
0.84 0.10 0.06
Matches are distributed among these distances:
153 25 0.05
155 77 0.16
156 23 0.05
157 84 0.17
158 8 0.02
164 11 0.02
165 82 0.17
166 162 0.33
167 13 0.03
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (163 bp):
GCATCCTCAGATAGTGTACATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCA
CAATGGGGGATAAATTTTTATAAGGAATATATAGAGAAATCTTTAAAAATCTTCTTCTCAAAAAC
TATTAGGCCAGGAAAGCCCAAATTTGAGTGGAA
Found at i:647972 original size:19 final size:19
Alignment explanation
Indices: 647948--647987 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
647938 GAACAAGTGT
647948 ACTTTTAGAGAGCTGACCC
1 ACTTTTAGAGAGCTGACCC
* *
647967 ACTTTTGGTGAGCTGACCC
1 ACTTTTAGAGAGCTGACCC
647986 AC
1 AC
647988 GACTGATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.28
Consensus pattern (19 bp):
ACTTTTAGAGAGCTGACCC
Found at i:650183 original size:53 final size:53
Alignment explanation
Indices: 650121--650227 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
650111 ATAATAAATA
*
650121 ATACTTGATGATGATGTTGATGCTACTGCTGATAAAATATATAAAATTTTATC
1 ATACTTGATGATGATGTTGATGCAACTGCTGATAAAATATATAAAATTTTATC
650174 ATACTTGATGATGATGTTGATGCAACTGCTGATAAAATATATAAAATTTTATC
1 ATACTTGATGATGATGTTGATGCAACTGCTGATAAAATATATAAAATTTTATC
650227 A
1 A
650228 AGTATTTGAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.38
Consensus pattern (53 bp):
ATACTTGATGATGATGTTGATGCAACTGCTGATAAAATATATAAAATTTTATC
Found at i:651075 original size:2 final size:2
Alignment explanation
Indices: 651068--651102 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
651058 AGATGATATT
651068 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
651103 TTTGTCCTAG
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:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:671050 original size:14 final size:14
Alignment explanation
Indices: 671031--671060 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
671021 CACATTGGTC
671031 GAAAGCAAGAAAAT
1 GAAAGCAAGAAAAT
671045 GAAAGCAAGAAAAT
1 GAAAGCAAGAAAAT
671059 GA
1 GA
671061 CAGTACGGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.63, C:0.07, G:0.23, T:0.07
Consensus pattern (14 bp):
GAAAGCAAGAAAAT
Found at i:679490 original size:2 final size:2
Alignment explanation
Indices: 679483--679522 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
679473 AATACTACCC
679483 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
679523 AAATTAGCCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:698393 original size:15 final size:15
Alignment explanation
Indices: 698373--698403 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
698363 AGTCCCCCTT
698373 TTCTCTCTCTCTTTC
1 TTCTCTCTCTCTTTC
698388 TTCTCTCTCTCTTTC
1 TTCTCTCTCTCTTTC
698403 T
1 T
698404 CTTGTCTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (15 bp):
TTCTCTCTCTCTTTC
Found at i:702282 original size:5 final size:5
Alignment explanation
Indices: 702265--702301 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
702255 AAAAAAAAAA
702265 AAGAG -AGAG -AGAG AAGAG AAGAG AAGAG AAGAG AAGA
1 AAGAG AAGAG AAGAG AAGAG AAGAG AAGAG AAGAG AAGA
702302 AAAAATCTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 8 0.26
5 23 0.74
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (5 bp):
AAGAG
Found at i:712225 original size:2 final size:2
Alignment explanation
Indices: 712218--712252 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
712208 GTATGAACAC
712218 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
712253 ATTAAGAACT
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:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:714235 original size:1 final size:1
Alignment explanation
Indices: 714231--714263 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
714221 GGGGGGGCTG
714231 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
714264 NAAATCAGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:718211 original size:2 final size:2
Alignment explanation
Indices: 718204--718238 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
718194 NNNNNNNNNN
718204 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
718239 ATATTGGTGC
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:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:724508 original size:12 final size:12
Alignment explanation
Indices: 724491--724515 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
724481 TTATATCCAA
724491 TCTGATCCAGAG
1 TCTGATCCAGAG
724503 TCTGATCCAGAG
1 TCTGATCCAGAG
724515 T
1 T
724516 ACTGTTTAAA
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:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (12 bp):
TCTGATCCAGAG
Found at i:729929 original size:1 final size:1
Alignment explanation
Indices: 729923--729955 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
729913 GCACACACAA
729923 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
729956 TCTCTCTCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:729960 original size:2 final size:2
Alignment explanation
Indices: 729955--730001 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
729945 CCCCCCCCCC
729955 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
729997 CT CT C
1 CT CT C
730002 CAACATGATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:738512 original size:2 final size:2
Alignment explanation
Indices: 738505--738533 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
738495 TTGGTCAAGG
738505 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
738534 CAAAACAGAC
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:738774 original size:70 final size:71
Alignment explanation
Indices: 738659--738833 Score: 291
Period size: 72 Copynumber: 2.5 Consensus size: 71
738649 CATCTTCCAT
* *
738659 TCCATGTCAGAACTCCAGACAGGAATCTGGATTTTATGAATCTCTTCAC-TATTCATCACAACTC
1 TCCATGTCAAAACTCCAGACAGGAATCTGGATTTTATGAACCTCTTCACATATTCATCACAACTC
738723 TAA-AGA
66 TAAGA-A
*
738729 TCCATATCAAAACTCCAGACAGGAATCTGGATTTTATGAACCTCTTCACTATATTCATCACAACT
1 TCCATGTCAAAACTCCAGACAGGAATCTGGATTTTATGAACCTCTTCAC-ATATTCATCACAACT
738794 CTAAGAA
65 CTAAGAA
738801 TCCATGTCAAAACTCCAGACAGGAATCTGGATT
1 TCCATGTCAAAACTCCAGACAGGAATCTGGATT
738834 CAGAAATTCT
Statistics
Matches: 98, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
70 46 0.47
72 51 0.52
73 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.29
Consensus pattern (71 bp):
TCCATGTCAAAACTCCAGACAGGAATCTGGATTTTATGAACCTCTTCACATATTCATCACAACTC
TAAGAA
Found at i:741012 original size:2 final size:2
Alignment explanation
Indices: 741007--741038 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
740997 GAGAAAAGGG
741007 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
741039 TTCCTACCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:742697 original size:2 final size:2
Alignment explanation
Indices: 742685--742744 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
742675 TTGTTATTCT
742685 GA GA G- GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
742726 GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA G
742745 TGTGTGTGCA
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 56 0.98
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:749685 original size:16 final size:16
Alignment explanation
Indices: 749664--749697 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
749654 AAAGGTTATA
*
749664 AATTAATTAATTTCTT
1 AATTAATAAATTTCTT
749680 AATTAATAAATTTCTT
1 AATTAATAAATTTCTT
749696 AA
1 AA
749698 AATCAACTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (16 bp):
AATTAATAAATTTCTT
Found at i:770049 original size:2 final size:2
Alignment explanation
Indices: 770042--770100 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
770032 GGGGGTGCTG
770042 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
770084 GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA G
770101 GGGGAAGGAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:773735 original size:2 final size:2
Alignment explanation
Indices: 773730--773818 Score: 178
Period size: 2 Copynumber: 44.5 Consensus size: 2
773720 CCAATTTAAC
773730 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
773772 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
773814 GA GA G
1 GA GA G
773819 TTTTTCTAAG
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 87 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:775386 original size:55 final size:55
Alignment explanation
Indices: 775316--775426 Score: 204
Period size: 55 Copynumber: 2.0 Consensus size: 55
775306 TTTTTTAACC
* *
775316 ACAATAATTTTAATAGTATTATTTATTTATATACTAGTTTACACAACAAAAGGAA
1 ACAATAATTTCAATAGTATTATTCATTTATATACTAGTTTACACAACAAAAGGAA
775371 ACAATAATTTCAATAGTATTATTCATTTATATACTAGTTTACACAACAAAAGGAA
1 ACAATAATTTCAATAGTATTATTCATTTATATACTAGTTTACACAACAAAAGGAA
775426 A
1 A
775427 ATGACACATC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.36
Consensus pattern (55 bp):
ACAATAATTTCAATAGTATTATTCATTTATATACTAGTTTACACAACAAAAGGAA
Found at i:781479 original size:14 final size:14
Alignment explanation
Indices: 781460--781492 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
781450 ATTAACCGCA
781460 AAAAGCAA-TATATC
1 AAAAGCAATTA-ATC
781474 AAAAGCAATTAATC
1 AAAAGCAATTAATC
781488 AAAAG
1 AAAAG
781493 TGATGAAGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 16 0.89
15 2 0.11
ACGTcount: A:0.61, C:0.12, G:0.09, T:0.18
Consensus pattern (14 bp):
AAAAGCAATTAATC
Found at i:785245 original size:3 final size:3
Alignment explanation
Indices: 785239--785273 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
785229 ACAACACAGA
785239 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
785274 ATGAAGAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:785811 original size:21 final size:21
Alignment explanation
Indices: 785786--785978 Score: 230
Period size: 21 Copynumber: 9.3 Consensus size: 21
785776 AAAATTATAG
*
785786 TGAAAATTATAGAATACAAAT
1 TGAAAATTATACAATACAAAT
*
785807 TGAAAATTATAGAATACAAAT
1 TGAAAATTATACAATACAAAT
* *
785828 GGAAAATTATATAATACAAAT
1 TGAAAATTATACAATACAAAT
*
785849 GGAAAATTATACAATACAAA-
1 TGAAAATTATACAATACAAAT
* *
785869 TGAAATTTATAGAATACAAAT
1 TGAAAATTATACAATACAAAT
* *
785890 GGAAAATTATACAATACAAGT
1 TGAAAATTATACAATACAAAT
*
785911 GGAAAATTATACAATACAAA-
1 TGAAAATTATACAATACAAAT
*
785931 TGAAATTTATACAATACAAA-
1 TGAAAATTATACAATACAAAT
* *
785951 TGAATATTTATATAATACAAAT
1 TGAA-AATTATACAATACAAAT
*
785973 AGAAAA
1 TGAAAA
785979 GATCGAATAT
Statistics
Matches: 153, Mismatches: 16, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
20 39 0.25
21 111 0.73
22 3 0.02
ACGTcount: A:0.56, C:0.07, G:0.09, T:0.27
Consensus pattern (21 bp):
TGAAAATTATACAATACAAAT
Found at i:785879 original size:83 final size:82
Alignment explanation
Indices: 785786--785978 Score: 296
Period size: 83 Copynumber: 2.3 Consensus size: 82
785776 AAAATTATAG
* * * *
785786 TGAAAATTATAGAATACAAATTGAAAATTATAGAATACAAATGGAAAATTATATAATACAAATGG
1 TGAAATTTATAGAATACAAATAGAAAATTATACAATACAAATGGAAAATTATACAATACAAAT-G
785851 AAAATTATACAATACAAA
65 AAAATTATACAATACAAA
* *
785869 TGAAATTTATAGAATACAAATGGAAAATTATACAATACAAGTGGAAAATTATACAATACAAATGA
1 TGAAATTTATAGAATACAAATAGAAAATTATACAATACAAATGGAAAATTATACAATACAAATGA
*
785934 AATTTATACAATACAAA
66 AAATTATACAATACAAA
*
785951 TGAATATTTATATAATACAAATAGAAAA
1 TGAA-ATTTATAGAATACAAATAGAAAA
785979 GATCGAATAT
Statistics
Matches: 101, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
82 22 0.22
83 79 0.78
ACGTcount: A:0.56, C:0.07, G:0.09, T:0.27
Consensus pattern (82 bp):
TGAAATTTATAGAATACAAATAGAAAATTATACAATACAAATGGAAAATTATACAATACAAATGA
AAATTATACAATACAAA
Found at i:785888 original size:62 final size:62
Alignment explanation
Indices: 785787--785978 Score: 296
Period size: 62 Copynumber: 3.1 Consensus size: 62
785777 AAATTATAGT
* *
785787 GAAAATTATAGAATACAAATTGAAAATTATAGAATACAAATGGAAAATTATATAATACAAATG
1 GAAAATTATACAATACAAA-TGAAATTTATAGAATACAAATGGAAAATTATATAATACAAATG
* *
785850 GAAAATTATACAATACAAATGAAATTTATAGAATACAAATGGAAAATTATACAATACAAGTG
1 GAAAATTATACAATACAAATGAAATTTATAGAATACAAATGGAAAATTATATAATACAAATG
* * *
785912 GAAAATTATACAATACAAATGAAATTTATACAATACAAAT-GAATATTTATATAATACAAATA
1 GAAAATTATACAATACAAATGAAATTTATAGAATACAAATGGAA-AATTATATAATACAAATG
785974 GAAAA
1 GAAAA
785979 GATCGAATAT
Statistics
Matches: 119, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
61 3 0.03
62 98 0.82
63 18 0.15
ACGTcount: A:0.57, C:0.07, G:0.09, T:0.27
Consensus pattern (62 bp):
GAAAATTATACAATACAAATGAAATTTATAGAATACAAATGGAAAATTATATAATACAAATG
Found at i:796391 original size:158 final size:158
Alignment explanation
Indices: 796098--796417 Score: 622
Period size: 158 Copynumber: 2.0 Consensus size: 158
796088 TTTTAAGAAA
796098 ATTTTACTGCTTTTATATAGGAATAACGTGAATTCTACAACGAACCGTACGCGCATAATTTTCGC
1 ATTTTACTGCTTTTATATAGGAATAACGTGAATTCTACAACGAACCGTACGCGCATAATTTTCGC
796163 GCATGTAACATTTTTTAATGTTACCCGTTGCCAAGTGCGTTGCTAACGCTGAGGGTAATAGTAAA
66 GCATGTAACATTTTTTAATGTTACCCGTTGCCAAGTGCGTTGCTAACGCTGAGGGTAATAGTAAA
796228 TATTATTAACTGCGTCTTAACCAATCAG
131 TATTATTAACTGCGTCTTAACCAATCAG
* *
796256 ATTTNACTGCTTTTATATAGGAATAACGTGAATTCTACAACGAACCGTACGCGCATAATTTTTGC
1 ATTTTACTGCTTTTATATAGGAATAACGTGAATTCTACAACGAACCGTACGCGCATAATTTTCGC
796321 GCATGTAACATTTTTTAATGTTACCCGTTGCCAAGTGCGTTGCTAACGCTGAGGGTAATAGTAAA
66 GCATGTAACATTTTTTAATGTTACCCGTTGCCAAGTGCGTTGCTAACGCTGAGGGTAATAGTAAA
796386 TATTATTAACTGCGTCTTAACCAATCAG
131 TATTATTAACTGCGTCTTAACCAATCAG
796414 ATTT
1 ATTT
796418 CAGTATTTAA
Statistics
Matches: 160, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
158 160 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.34
Consensus pattern (158 bp):
ATTTTACTGCTTTTATATAGGAATAACGTGAATTCTACAACGAACCGTACGCGCATAATTTTCGC
GCATGTAACATTTTTTAATGTTACCCGTTGCCAAGTGCGTTGCTAACGCTGAGGGTAATAGTAAA
TATTATTAACTGCGTCTTAACCAATCAG
Found at i:797843 original size:2 final size:2
Alignment explanation
Indices: 797836--797882 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
797826 ATCGAATATA
797836 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
797878 CT CT C
1 CT CT C
797883 AGTGAAGCAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:801227 original size:4 final size:4
Alignment explanation
Indices: 801218--801298 Score: 162
Period size: 4 Copynumber: 20.2 Consensus size: 4
801208 AATCGGTATT
801218 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
801266 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG A
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG A
801299 GATAAAAAAT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 77 1.00
ACGTcount: A:0.51, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
ATAG
Found at i:813003 original size:2 final size:2
Alignment explanation
Indices: 812998--813044 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
812988 CACTATATAT
812998 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
813040 AG AG A
1 AG AG A
813045 CTTAGTACAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:820710 original size:2 final size:2
Alignment explanation
Indices: 820703--820785 Score: 166
Period size: 2 Copynumber: 41.5 Consensus size: 2
820693 TAACTTATAG
820703 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
820745 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
820786 GCAGGTGGGG
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:822454 original size:4 final size:4
Alignment explanation
Indices: 822430--822470 Score: 55
Period size: 4 Copynumber: 10.2 Consensus size: 4
822420 TGTTGAAAAG
* * *
822430 CTTT CTGT CTTT CTGT CTTT CTTT CTTT CTTT TTTT CTTT C
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT C
822471 ACCTAACAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.00, C:0.24, G:0.05, T:0.71
Consensus pattern (4 bp):
CTTT
Found at i:825374 original size:29 final size:29
Alignment explanation
Indices: 825332--825703 Score: 645
Period size: 29 Copynumber: 12.8 Consensus size: 29
825322 TGCTTTAATT
*
825332 TGCAATGCTTTGCTCATCCTTTAATTCAA
1 TGCAAAGCTTTGCTCATCCTTTAATTCAA
*
825361 TTCAAAGCTTTGCTCATCCTTTAATTCAA
1 TGCAAAGCTTTGCTCATCCTTTAATTCAA
825390 TGCAAAGCTTTGCTCATCCTTTAATTCAA
1 TGCAAAGCTTTGCTCATCCTTTAATTCAA
*
825419 TGCAAAACTTTGCTCATCCTTTAATTCAA
1 TGCAAAGCTTTGCTCATCCTTTAATTCAA
*
825448 TGCAAAACTTTGCTCATCCTTTAATTCAA
1 TGCAAAGCTTTGCTCATCCTTTAATTCAA
*
825477 TGCAAAGTTTTGCTCATCCTTTAATTCAA
1 TGCAAAGCTTTGCTCATCCTTTAATTCAA
*
825506 TGCAAAACTTTGCTCATCCTTTAATTCAA
1 TGCAAAGCTTTGCTCATCCTTTAATTCAA
825535 TGCAAAGCTTTGCTCATCCTTTAATTCAA
1 TGCAAAGCTTTGCTCATCCTTTAATTCAA
*
825564 TGCAAAGCATTGCTCATCCTTTAATTCAA
1 TGCAAAGCTTTGCTCATCCTTTAATTCAA
*
825593 TGCAAAGCTTTTCTCATCCTTTAATTCAA
1 TGCAAAGCTTTGCTCATCCTTTAATTCAA
825622 TGCAAAGCTTTGCTCATCCTTTAATTCAA
1 TGCAAAGCTTTGCTCATCCTTTAATTCAA
* *
825651 TGTAAAGCTTTGCTCATCTTTTAATTCAA
1 TGCAAAGCTTTGCTCATCCTTTAATTCAA
*
825680 TGCAAAACTTTGCTCATCCTTTAA
1 TGCAAAGCTTTGCTCATCCTTTAA
825704 CTATAGATTA
Statistics
Matches: 325, Mismatches: 18, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 325 1.00
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.39
Consensus pattern (29 bp):
TGCAAAGCTTTGCTCATCCTTTAATTCAA
Found at i:829843 original size:2 final size:2
Alignment explanation
Indices: 829836--829916 Score: 144
Period size: 2 Copynumber: 40.5 Consensus size: 2
829826 GTGAAGAATT
*
829836 TC TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
829878 TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
829917 GGTATGTGTG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:834305 original size:6 final size:6
Alignment explanation
Indices: 834285--834328 Score: 56
Period size: 6 Copynumber: 7.3 Consensus size: 6
834275 GATTGGATGA
834285 TTTTTG -TTTTG -TTTTG TTTTTTG TTTTTG TTTTTTG TTTTTG TT
1 TTTTTG TTTTTG TTTTTG -TTTTTG TTTTTG -TTTTTG TTTTTG TT
834329 AAGCTTTGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 10 0.29
6 14 0.40
7 11 0.31
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (6 bp):
TTTTTG
Found at i:834308 original size:7 final size:7
Alignment explanation
Indices: 834296--834325 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
834286 TTTTGTTTTG
834296 TTTTGTT
1 TTTTGTT
834303 TTTTG-T
1 TTTTGTT
834309 TTTTGTT
1 TTTTGTT
834316 TTTTGTT
1 TTTTGTT
834323 TTT
1 TTT
834326 GTTAAGCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (7 bp):
TTTTGTT
Found at i:834314 original size:13 final size:13
Alignment explanation
Indices: 834291--834328 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
834281 ATGATTTTTG
834291 TTTTG-TTTTGTT
1 TTTTGTTTTTGTT
834303 TTTTGTTTTTGTT
1 TTTTGTTTTTGTT
834316 TTTTGTTTTTGTT
1 TTTTGTTTTTGTT
834329 AAGCTTTGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 5 0.20
13 20 0.80
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (13 bp):
TTTTGTTTTTGTT
Found at i:837744 original size:13 final size:13
Alignment explanation
Indices: 837726--837750 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
837716 ACAGGCACTC
837726 TGTTTTTTTTTTT
1 TGTTTTTTTTTTT
837739 TGTTTTTTTTTT
1 TGTTTTTTTTTT
837751 GCATGTTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (13 bp):
TGTTTTTTTTTTT
Found at i:840269 original size:174 final size:170
Alignment explanation
Indices: 839873--840328 Score: 472
Period size: 174 Copynumber: 2.6 Consensus size: 170
839863 CCCTAATTTA
* * * * * * * *
839873 ACGGATAACTCCTCCA-ACAGTTTTCAAGATAAGAAGTTGCTCTTTTGCAAATCAATTGTGCATA
1 ACGGATAACTCCT-TATACAATTTTCAATAGATGAAGTTGTTCTTTCGCAGATCAATTGTGCATA
* *
839937 TATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTATGAAAAAAACACCAGCTGT
65 TATCAGAGGTGTGCACATAGCTAGGATTTTGATTTCTG-------A--AAAAAAACACCAGCTGT
* * *
840002 TGAACTTGGTCATTTTTGGCAAAATATTGCATATAGGGTACCCCTAGTGT
121 TGAACATCGACATTTTTGGCAAAATATTGCATATAGGGTACCCCTAGTGT
* * * * **
840052 ATGGATAACTTCTTATACAATTTTCAATATATGAAGTTGTTCTTTTGCAGATCAATTGTGTGTAT
1 ACGGATAACTCCTTATACAATTTTCAATAGATGAAGTTGTTCTTTCGCAGATCAATTGTGCATAT
* *
840117 ATTAGAGGTGCATGTGCACATAGCTAGGGTTTTGATTTCTGAAAAAAAATC-CCAGCTGTTGAAC
66 ATCAGA-G-G--TGTGCACATAGCTAGGATTTTGATTTCTGAAAAAAAA-CACCAGCTGTTGAAC
* *
840181 ATCGACACTTTTTGGCAAAATATTGCATATAGGGTACCCTTTTATTGT
126 ATCGACA-TTTTTGGCAAAATATTGCATATAGGGTACCC--CTAGTGT
* *
840229 ACGGATAACTCCTTCTACAGTTTTC-A-AGAT-AAGTTGTTCTTTCGCAGATCAATTGTGCATAT
1 ACGGATAACTCCTTATACAATTTTCAATAGATGAAGTTGTTCTTTCGCAGATCAATTGTGCATAT
* *
840291 ATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGA
66 ATCAGAGGTGTGCACATAGCTAGGATTTTGATTTCTGA
840329 TAATATATGA
Statistics
Matches: 237, Mismatches: 31, Indels: 27
0.80 0.11 0.09
Matches are distributed among these distances:
170 27 0.11
172 1 0.00
173 1 0.00
174 58 0.24
175 35 0.15
176 2 0.01
177 26 0.11
178 1 0.00
179 58 0.24
180 1 0.00
181 1 0.00
183 26 0.11
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.36
Consensus pattern (170 bp):
ACGGATAACTCCTTATACAATTTTCAATAGATGAAGTTGTTCTTTCGCAGATCAATTGTGCATAT
ATCAGAGGTGTGCACATAGCTAGGATTTTGATTTCTGAAAAAAAACACCAGCTGTTGAACATCGA
CATTTTTGGCAAAATATTGCATATAGGGTACCCCTAGTGT
Found at i:840387 original size:179 final size:176
Alignment explanation
Indices: 839873--840399 Score: 622
Period size: 179 Copynumber: 3.0 Consensus size: 176
839863 CCCTAATTTA
* * * *
839873 ACGGATAACTCCTCCAACAGTTTTCAAGATAAGAAGTTGCTCTTTTGCAAATCAATTGTGCATAT
1 ACGGATAACTCCTTCTACAGTTTTCAAGAT-A-AAGTTGTTCTTTTGCAGATCAATTGTGCATAT
*
839938 ATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTATGAAAAAAACACCAGCTGTT
64 ATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAA-TTATGAAAAAAATACCAGCTGTT
*
840003 GAACTTGGTCATTTTTGGCAAAATATTGCATATAGGGTACCCCTAGTGT
128 GAACTTAGTCATTTTTGGCAAAATATTGCATATAGGGTACCCCTAGTGT
* * * * * **
840052 ATGGATAACTTCTTATACAATTTTCAATATATGAAGTTGTTCTTTTGCAGATCAATTGTGTGTAT
1 ACGGATAACTCCTTCTACAGTTTTCAAGATA--AAGTTGTTCTTTTGCAGATCAATTGTGCATAT
* * * * *
840117 ATTAGAGGTGCATGTGCACATAGCTAGGGTTTTGATTTCTG------A--AAAAAAATCCCAGCT
64 ATCAGA-G-G--TGTGCATATTGCTAGGATTTTGATTTCTGATAATTATGAAAAAAATACCAGCT
* * * * *
840174 GTTGAACATCGACACTTTTTGGCAAAATATTGCATATAGGGTACCCTTTTATTGT
125 GTTGAACTTAGTCA-TTTTTGGCAAAATATTGCATATAGGGTACCC--CTAGTGT
*
840229 ACGGATAACTCCTTCTACAGTTTTCAAGAT-AAGTTGTTCTTTCGCAGATCAATTGTGCATATAT
1 ACGGATAACTCCTTCTACAGTTTTCAAGATAAAGTTGTTCTTTTGCAGATCAATTGTGCATATAT
840293 CAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATATATGAAAAAAATACCAGCTGTTGA
66 CAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAAT-TATGAAAAAAATACCAGCTGTTGA
* * *
840358 ACTTAGTTATTTCTGGCAAAAATATTGCATATAGAGTACCCC
130 ACTTAGTCATTTTTGGC-AAAATATTGCATATAGGGTACCCC
840400 ATTTCTGTAG
Statistics
Matches: 288, Mismatches: 42, Indels: 38
0.78 0.11 0.10
Matches are distributed among these distances:
170 26 0.09
172 1 0.00
173 1 0.00
174 58 0.20
175 31 0.11
176 1 0.00
177 31 0.11
178 8 0.03
179 103 0.36
180 1 0.00
181 1 0.00
183 26 0.09
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (176 bp):
ACGGATAACTCCTTCTACAGTTTTCAAGATAAAGTTGTTCTTTTGCAGATCAATTGTGCATATAT
CAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTATGAAAAAAATACCAGCTGTTGAA
CTTAGTCATTTTTGGCAAAATATTGCATATAGGGTACCCCTAGTGT
Found at i:840856 original size:132 final size:132
Alignment explanation
Indices: 840619--840884 Score: 523
Period size: 132 Copynumber: 2.0 Consensus size: 132
840609 GAATTTTGGT
840619 TACTTATCCAGCAACTCATGCTGGACTCACAAACGGTCACTGTTAATCATTCAAGTTTCCATTAG
1 TACTTATCCAGCAACTCATGCTGGACTCACAAACGGTCACTGTTAATCATTCAAGTTTCCATTAG
*
840684 CACCACAGTTTGTAATGCAGGTCTTTGGATAATTGTAATACAGTACTTGTAGTGATGTGTTCAGG
66 CACCACAGTTTGTAATGCAGATCTTTGGATAATTGTAATACAGTACTTGTAGTGATGTGTTCAGG
840749 AC
131 AC
840751 TACTTATCCAGCAACTCATGCTGGACTCACAAACGGTCACTGTTAATCATTCAAGTTTCCATTAG
1 TACTTATCCAGCAACTCATGCTGGACTCACAAACGGTCACTGTTAATCATTCAAGTTTCCATTAG
840816 CACCACAGTTTGTAATGCAGATCTTTGGATAATTGTAATACAGTACTTGTAGTGATGTGTTCAGG
66 CACCACAGTTTGTAATGCAGATCTTTGGATAATTGTAATACAGTACTTGTAGTGATGTGTTCAGG
840881 AC
131 AC
840883 TA
1 TA
840885 AAATAATTGT
Statistics
Matches: 133, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
132 133 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (132 bp):
TACTTATCCAGCAACTCATGCTGGACTCACAAACGGTCACTGTTAATCATTCAAGTTTCCATTAG
CACCACAGTTTGTAATGCAGATCTTTGGATAATTGTAATACAGTACTTGTAGTGATGTGTTCAGG
AC
Found at i:842545 original size:177 final size:177
Alignment explanation
Indices: 842339--842888 Score: 951
Period size: 177 Copynumber: 3.1 Consensus size: 177
842329 TTCAGATGCT
*
842339 AGGAGGTTAAGGTTGTGTTGGACCAGGTTAAAGTTTTTGTTGCAGGTGCCCTTTGATAGCAATAT
1 AGGAGGTTAAGGTT-T-TTGGAGCAGGTTAAAGTTTTTGTTGCAGGTGCCCTTTGATAGCAATAT
842404 CTAAGTTACTGCTGGTCCGTACTTCACCAAACTTGCATGGATGGTGTGTCTTATGATACTGATGC
64 CTAAGTTACTGCTGGTCCGTACTTCACCAAACTTGCATGGATGGTGTGTCTTATGATACTGATGC
842469 ACCAGACAGGCTTGAGTGCTGAATCTGAGCTATAGGTTTCGGATGCTGG
129 ACCAGACAGGCTTGAGTGCTGAATCTGAGCTATAGGTTTCGGATGCTGG
842518 AGGAGGTTAAGGTTTTTGGAGCAGGTTAAAGTTTTTGTTGCAGGTGCCCTTTGATAGCAATATCT
1 AGGAGGTTAAGGTTTTTGGAGCAGGTTAAAGTTTTTGTTGCAGGTGCCCTTTGATAGCAATATCT
842583 AAGTTACTGCTGGTCCGTACTTCACCAAACTTGCATGGATGGTGTGTCTTATGATACTGATGCAC
66 AAGTTACTGCTGGTCCGTACTTCACCAAACTTGCATGGATGGTGTGTCTTATGATACTGATGCAC
* * * * *
842648 CAGGCAGGCTTGGGTGCTGAATCTGAGCTATAGGTTACAGATGCTGA
131 CAGACAGGCTTGAGTGCTGAATCTGAGCTATAGGTTTCGGATGCTGG
* * *
842695 AGGAGGTTAAGGTTTTTAGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCTGAT-G-ATGATAT
1 AGGAGGTTAAGGTTTTTGGAGCAGGTTAAAGTTTTTGTTGCAGGTGCCCTTTGATAGCA--ATAT
* *
842758 CTTAGTTACTGCAGGTCCGTACTTCACCAAACTTGCATGGATGGTGTGTCTTATGATACTGATGC
64 CTAAGTTACTGCTGGTCCGTACTTCACCAAACTTGCATGGATGGTGTGTCTTATGATACTGATGC
842823 ACCAGACAGGCTTGAGTGCTGAATCTGAGCTATAGGTTTCGGATGCTGG
129 ACCAGACAGGCTTGAGTGCTGAATCTGAGCTATAGGTTTCGGATGCTGG
842872 AGGAGGTTAAGGTTTTT
1 AGGAGGTTAAGGTTTTT
842889 NNNNNNNNNN
Statistics
Matches: 353, Mismatches: 16, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
175 1 0.00
176 1 0.00
177 336 0.95
178 1 0.00
179 14 0.04
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.33
Consensus pattern (177 bp):
AGGAGGTTAAGGTTTTTGGAGCAGGTTAAAGTTTTTGTTGCAGGTGCCCTTTGATAGCAATATCT
AAGTTACTGCTGGTCCGTACTTCACCAAACTTGCATGGATGGTGTGTCTTATGATACTGATGCAC
CAGACAGGCTTGAGTGCTGAATCTGAGCTATAGGTTTCGGATGCTGG
Found at i:842562 original size:19 final size:19
Alignment explanation
Indices: 842515--842554 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
842505 TTTCGGATGC
* *
842515 TGGAGGAGGTTAAGGTTTT
1 TGGAGCAGGTTAAAGTTTT
842534 TGGAGCAGGTTAAAGTTTT
1 TGGAGCAGGTTAAAGTTTT
842553 TG
1 TG
842555 TTGCAGGTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.03, G:0.38, T:0.38
Consensus pattern (19 bp):
TGGAGCAGGTTAAAGTTTT
Found at i:843617 original size:15 final size:15
Alignment explanation
Indices: 843597--843632 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
843587 ATACAATATT
*
843597 ATATTGTATCATACG
1 ATATTGTATAATACG
*
843612 ATATTGTATAATATG
1 ATATTGTATAATACG
843627 ATATTG
1 ATATTG
843633 GATTCTGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.44
Consensus pattern (15 bp):
ATATTGTATAATACG
Found at i:843727 original size:15 final size:15
Alignment explanation
Indices: 843709--843812 Score: 50
Period size: 15 Copynumber: 6.4 Consensus size: 15
843699 CGTATCATAC
843709 GATATTGTATAATAT
1 GATATTGTATAATAT
843724 GATATTGGTTTATATGATAT
1 GATATT-G--TATA--ATAT
*
843744 -ATTATTGTATCATAT
1 GA-TATTGTATAATAT
*
843759 GATACAATATGTAT-GTAT
1 GAT---AT-TGTATAATAT
*
843777 GATATTGTATTATAT
1 GATATTGTATAATAT
* *
843792 AATATTGTATTATAT
1 GATATTGTATAATAT
*
843807 AATATT
1 GATATT
843813 TTACTTTATC
Statistics
Matches: 73, Mismatches: 4, Indels: 24
0.72 0.04 0.24
Matches are distributed among these distances:
14 5 0.07
15 36 0.49
16 2 0.03
17 3 0.04
18 12 0.16
19 7 0.10
20 8 0.11
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (15 bp):
GATATTGTATAATAT
Found at i:843754 original size:50 final size:49
Alignment explanation
Indices: 843598--843762 Score: 161
Period size: 50 Copynumber: 3.3 Consensus size: 49
843588 TACAATATTA
* * * *
843598 TATTGTATCATACGATATTGTATAATATGATATTGGATTCTGTAATTTAC
1 TATTGTATCATACGATATTGTATAATATGATATTGG-TTATATAATATAT
* * * * * * * * *
843648 AATTATATCACACGAAACTGTATTATATCATATT-GTAATATTATATAT
1 TATTGTATCATACGATATTGTATAATATGATATTGGTTATATAATATAT
* *
843696 TATCGTATCATACGATATTGTATAATATGATATTGGTTTATATGATATAT
1 TATTGTATCATACGATATTGTATAATATGATATTGG-TTATATAATATAT
*
843746 TATTGTATCATATGATA
1 TATTGTATCATACGATA
843763 CAATATGTAT
Statistics
Matches: 88, Mismatches: 25, Indels: 4
0.75 0.21 0.03
Matches are distributed among these distances:
48 33 0.38
49 2 0.02
50 53 0.60
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.45
Consensus pattern (49 bp):
TATTGTATCATACGATATTGTATAATATGATATTGGTTATATAATATAT
Found at i:848342 original size:6 final size:6
Alignment explanation
Indices: 848328--848359 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
848318 TGCTATACCC
*
848328 TCGGCG TCGGTG TCGGCG TCGGCG TCGGCG TC
1 TCGGCG TCGGCG TCGGCG TCGGCG TCGGCG TC
848360 CGGACCTGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.31, G:0.47, T:0.22
Consensus pattern (6 bp):
TCGGCG
Found at i:848689 original size:177 final size:177
Alignment explanation
Indices: 848497--849198 Score: 1224
Period size: 177 Copynumber: 4.0 Consensus size: 177
848487 GACTCCTAAA
* * * * * *
848497 TTTCAGATGCTGGAGGAGGTAAAGGTTGTTGGACCAGGTTAAAGTTTTTGTTGCTGGTGCCCTTT
1 TTTCGGATGCTGGAGGAGGTTAAGGTTTTTGGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTTT
* * * *
848562 GATAGCAATATCTAAGTTACTGCAGGTCCATACTTCACCAAACTTGCATGGATGGTGTGTCTTAT
66 GATAGTAATATCTAAGTTACTGCTGGTCCGTACTTCACCAAACTTGCAAGGATGGTGTGTCTTAT
*
848627 GATACTGATGCACCAAACAGGCTTGAGTGCTGAATCTGAGCTATAGG
131 GATACTGATGCACCAGACAGGCTTGAGTGCTGAATCTGAGCTATAGG
848674 TTTCGGATGCTGGAGGAGGTTAAGGTTTTTGGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTTT
1 TTTCGGATGCTGGAGGAGGTTAAGGTTTTTGGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTTT
*
848739 GATAGTAATATCTAAGTTACTGCTGGTCCGTACTTCACCAAACTTTCAAGGATGGTGTGTCTTAT
66 GATAGTAATATCTAAGTTACTGCTGGTCCGTACTTCACCAAACTTGCAAGGATGGTGTGTCTTAT
*
848804 GATACTGATGCACCAGACAGGCTTGAGTGCTGAATCTGAGCAATAGG
131 GATACTGATGCACCAGACAGGCTTGAGTGCTGAATCTGAGCTATAGG
848851 TTTCGGATGCTGGAGGAGGTTAAGGTTTTTGGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTTT
1 TTTCGGATGCTGGAGGAGGTTAAGGTTTTTGGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTTT
848916 GATAGTAATATCTAAGTTACTGCTGGTCCGTACTTCACCAAACTTGCAAGGATGGTGTGTCTTAT
66 GATAGTAATATCTAAGTTACTGCTGGTCCGTACTTCACCAAACTTGCAAGGATGGTGTGTCTTAT
* *
848981 GATACTGATGCACCAGGCAGGCTTGGGTGCTGAATCTGAGCTATAGG
131 GATACTGATGCACCAGACAGGCTTGAGTGCTGAATCTGAGCTATAGG
*
849028 TTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTTT
1 TTTCGGATGCTGGAGGAGGTTAAGGTTTTTGGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTTT
* * *
849093 GATAGTAATATCTAAGTTACTGCTGGTCCGTACTTCACCAGACTTCCATGGATGGTGTGTCTTAT
66 GATAGTAATATCTAAGTTACTGCTGGTCCGTACTTCACCAAACTTGCAAGGATGGTGTGTCTTAT
*
849158 GATACTGATGCACCAGACAGGCTTGAATGCTGAATCTGAGC
131 GATACTGATGCACCAGACAGGCTTGAGTGCTGAATCTGAGC
849199 CATACGTTAA
Statistics
Matches: 501, Mismatches: 24, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
177 501 1.00
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (177 bp):
TTTCGGATGCTGGAGGAGGTTAAGGTTTTTGGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTTT
GATAGTAATATCTAAGTTACTGCTGGTCCGTACTTCACCAAACTTGCAAGGATGGTGTGTCTTAT
GATACTGATGCACCAGACAGGCTTGAGTGCTGAATCTGAGCTATAGG
Found at i:848706 original size:19 final size:19
Alignment explanation
Indices: 848684--848723 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
848674 TTTCGGATGC
* *
848684 TGGAGGAGGTTAAGGTTTT
1 TGGAGCAGGTTAAAGTTTT
*
848703 TGGAGCTGGTTAAAGTTTT
1 TGGAGCAGGTTAAAGTTTT
848722 TG
1 TG
848724 TTGCAGGTGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.20, C:0.03, G:0.38, T:0.40
Consensus pattern (19 bp):
TGGAGCAGGTTAAAGTTTT
Found at i:848883 original size:19 final size:19
Alignment explanation
Indices: 848861--848900 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
848851 TTTCGGATGC
* *
848861 TGGAGGAGGTTAAGGTTTT
1 TGGAGCAGGTTAAAGTTTT
*
848880 TGGAGCTGGTTAAAGTTTT
1 TGGAGCAGGTTAAAGTTTT
848899 TG
1 TG
848901 TTGCAGGTGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.20, C:0.03, G:0.38, T:0.40
Consensus pattern (19 bp):
TGGAGCAGGTTAAAGTTTT
Found at i:849335 original size:158 final size:158
Alignment explanation
Indices: 849046--849360 Score: 445
Period size: 158 Copynumber: 2.0 Consensus size: 158
849036 GCTGGAGGAG
*** *
849046 GTTAAGGTTTTTAGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTTTGATAGTAATATCTAAGTT
1 GTTAAGGTTTTTAGAGCTGGTTAAAGTTTTTGAAACAGGTGCCCTCTGATAGTAATATCTAAGTT
* ** *
849111 ACTGCTGGTCCGTACTTCACCAGACTTCCATGGATGGTGTGTCTTATGATACTGATGCACCAGAC
66 ACTACTGGTCCGTACTTCACCAGACTTCCATGGATGGTGCATCTAATGATACTGATGCACCAGAC
849176 AGGCTTGAATGCTGAATCTGAGCCATAC
131 AGGCTTGAATGCTGAATCTGAGCCATAC
* * *
849204 GTTAAGGTTTTTAGAGCTGGTTATAGTTTTTGAAACAGGTGCCCTCTGAT-GATTATATCTTAGT
1 GTTAAGGTTTTTAGAGCTGGTTAAAGTTTTTGAAACAGGTGCCCTCTGATAG-TAATATCTAAGT
* * * *
849268 TATTACTTGTCC-TAACTTCACCAGACTTCCTTGGATGGTGCATCTAATGATACTGATGCACCTG
65 TACTACTGGTCCGT-ACTTCACCAGACTTCCATGGATGGTGCATCTAATGATACTGATGCACCAG
* *
849332 ACAGGTTTGAATGCTGAGTCTGAGCCATA
129 ACAGGCTTGAATGCTGAATCTGAGCCATA
849361 GGTTTCAGAT
Statistics
Matches: 138, Mismatches: 17, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
157 2 0.01
158 136 0.99
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (158 bp):
GTTAAGGTTTTTAGAGCTGGTTAAAGTTTTTGAAACAGGTGCCCTCTGATAGTAATATCTAAGTT
ACTACTGGTCCGTACTTCACCAGACTTCCATGGATGGTGCATCTAATGATACTGATGCACCAGAC
AGGCTTGAATGCTGAATCTGAGCCATAC
Found at i:850157 original size:28 final size:28
Alignment explanation
Indices: 850125--850178 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
850115 TACATTTTTT
850125 TGATATT-TTATGT-TATGATATTGTATCA
1 TGATATTGTTATGTATA-G-TATTGTATCA
850153 TGATATTGTTATGTATAGTATTGTAT
1 TGATATTGTTATGTATAGTATTGTAT
850179 ATTATGATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 15 0.62
29 7 0.29
30 2 0.08
ACGTcount: A:0.28, C:0.02, G:0.17, T:0.54
Consensus pattern (28 bp):
TGATATTGTTATGTATAGTATTGTATCA
Found at i:850194 original size:15 final size:15
Alignment explanation
Indices: 850125--850198 Score: 66
Period size: 15 Copynumber: 5.1 Consensus size: 15
850115 TACATTTTTT
* *
850125 TGATATTTTATGTTA
1 TGATATTGTATATTA
*
850140 TGATATTG--TATCA
1 TGATATTGTATATTA
850153 TGATATTGT-TATGTA
1 TGATATTGTATAT-TA
850168 T-AGTATTGTATATTA
1 TGA-TATTGTATATTA
*
850183 TGATATTATATATTA
1 TGATATTGTATATTA
850198 T
1 T
850199 TGTATTATTA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
13 11 0.22
14 4 0.08
15 30 0.61
16 4 0.08
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.54
Consensus pattern (15 bp):
TGATATTGTATATTA
Found at i:851296 original size:16 final size:15
Alignment explanation
Indices: 851266--851311 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
851256 ATTTAATATG
851266 ATAAAGGTG-GTCTC
1 ATAAAGGTGAGTCTC
851280 ATAAAGGTGAAGTCTC
1 ATAAAGGTG-AGTCTC
*
851296 ATAACGGTGATGTCTC
1 ATAAAGGTGA-GTCTC
851312 GTCTCGGTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 9 0.32
15 1 0.04
16 18 0.64
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.28
Consensus pattern (15 bp):
ATAAAGGTGAGTCTC
Found at i:862208 original size:2 final size:2
Alignment explanation
Indices: 862201--862232 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
862191 CAAGTTTAGA
*
862201 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
862233 NTATGAATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:866197 original size:2 final size:2
Alignment explanation
Indices: 866190--866217 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
866180 CTATTAAAGC
866190 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
866218 NNNNNNNNNN
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:869099 original size:17 final size:17
Alignment explanation
Indices: 869077--869118 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
869067 TTTTTTATTC
869077 ATTTTAATGGGGAGTTG
1 ATTTTAATGGGGAGTTG
* *
869094 ATTTTAGTTGGGAGTTG
1 ATTTTAATGGGGAGTTG
*
869111 TTTTTAAT
1 ATTTTAAT
869119 CAACTCTCCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (17 bp):
ATTTTAATGGGGAGTTG
Found at i:884912 original size:12 final size:12
Alignment explanation
Indices: 884895--884921 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
884885 CAACAAAGTG
884895 TAGATTCAGAAA
1 TAGATTCAGAAA
884907 TAGATTCAGAAA
1 TAGATTCAGAAA
884919 TAG
1 TAG
884922 CGCCTTTCAA
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:0.48, C:0.07, G:0.19, T:0.26
Consensus pattern (12 bp):
TAGATTCAGAAA
Found at i:887537 original size:32 final size:33
Alignment explanation
Indices: 887494--887566 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 33
887484 ATTGACCCGG
887494 GTTGAAAATTGACCC-GGGGGTCATTTTTCAAC
1 GTTGAAAATTGACCCGGGGGGTCATTTTTCAAC
*
887526 GTTGAATATTGACCCGGGGGGTCATTTTTCAAC
1 GTTGAAAATTGACCCGGGGGGTCATTTTTCAAC
887559 GTTGAAAA
1 GTTGAAAA
887567 CTGAGACCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 14 0.37
33 24 0.63
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (33 bp):
GTTGAAAATTGACCCGGGGGGTCATTTTTCAAC
Found at i:895248 original size:2 final size:2
Alignment explanation
Indices: 895243--895278 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
895233 CACACATAAA
895243 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
895279 TTTGACAGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:897834 original size:10 final size:9
Alignment explanation
Indices: 897808--897849 Score: 57
Period size: 9 Copynumber: 4.4 Consensus size: 9
897798 GTCAGGTTTT
*
897808 TTTTTTATA
1 TTTTATATA
897817 TTTTATATA
1 TTTTATATA
897826 TTTTCATATA
1 TTTT-ATATA
897836 TATTTATATA
1 T-TTTATATA
897846 TTTT
1 TTTT
897850 TAATTTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 15 0.50
10 12 0.40
11 3 0.10
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTTATATA
Found at i:897851 original size:10 final size:10
Alignment explanation
Indices: 897807--897851 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
897797 TGTCAGGTTT
*
897807 TTTTTTTATA
1 TTTTTATATA
897817 -TTTTATATA
1 TTTTTATATA
*
897826 TTTTCATATA
1 TTTTTATATA
*
897836 TATTTATATA
1 TTTTTATATA
897846 TTTTTA
1 TTTTTA
897852 ATTTAAAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
9 8 0.28
10 21 0.72
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTTATATA
Found at i:898219 original size:40 final size:40
Alignment explanation
Indices: 898171--898602 Score: 695
Period size: 40 Copynumber: 10.8 Consensus size: 40
898161 CATTCAGTTC
*
898171 CTTAAATTCATTACAAAACACATA-CTTAAAAAAACTCACT
1 CTTAAATTCATTACAAAACACATACCTT-AATAAACTCACT
* * *
898211 CTTTAATTCATTACAAATCACATACCATAATAAACTCACT
1 CTTAAATTCATTACAAAACACATACCTTAATAAACTCACT
* *
898251 CTTTAATTCATTACAAAAACACATACCTTAATAAACCCACT
1 CTTAAATTCATTAC-AAAACACATACCTTAATAAACTCACT
898292 CTTAAATTCATTACAAAACACATACCTTAATAAACTCACT
1 CTTAAATTCATTACAAAACACATACCTTAATAAACTCACT
* *
898332 TTTAAATTCATTACAAAAACACATACCTTAATAAACCCACT
1 CTTAAATTCATTAC-AAAACACATACCTTAATAAACTCACT
*
898373 CTTAAATTCATTACAAAACACATACCTTAGTAAACTCACT
1 CTTAAATTCATTACAAAACACATACCTTAATAAACTCACT
* *
898413 CTTAAATTCATTACAAAACATATACCTTAGTAAACTCACT
1 CTTAAATTCATTACAAAACACATACCTTAATAAACTCACT
*
898453 CTTAAATTCATTACAAAACACATACCTTAGTAAACTCACT
1 CTTAAATTCATTACAAAACACATACCTTAATAAACTCACT
*
898493 CTTAAATTCATTACAAAACACATACCTTAATAAACTCAGT
1 CTTAAATTCATTACAAAACACATACCTTAATAAACTCACT
*
898533 CTTAAATTCATTACAAAACACATACCTTAATAAATTCACT
1 CTTAAATTCATTACAAAACACATACCTTAATAAACTCACT
*
898573 TTTAAATTCATTACAAAACACATACCTTAA
1 CTTAAATTCATTACAAAACACATACCTTAA
898603 AGTGACGTGA
Statistics
Matches: 368, Mismatches: 21, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
40 292 0.79
41 76 0.21
ACGTcount: A:0.45, C:0.24, G:0.01, T:0.31
Consensus pattern (40 bp):
CTTAAATTCATTACAAAACACATACCTTAATAAACTCACT
Found at i:903506 original size:2 final size:2
Alignment explanation
Indices: 903499--903564 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
903489 CACATTCAAT
903499 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
903541 TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC
903565 CATACCGGCT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:906532 original size:2 final size:2
Alignment explanation
Indices: 906525--906569 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
906515 CATCTGTTTT
906525 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
906567 AG A
1 AG A
906570 TGGTTACTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:910478 original size:2 final size:2
Alignment explanation
Indices: 910471--910520 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
910461 TTACAAATCC
910471 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C- CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
910512 CT CT CT CT C
1 CT CT CT CT C
910521 ACACACACAC
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:912074 original size:12 final size:12
Alignment explanation
Indices: 912057--912081 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
912047 GTACAATGTT
912057 GACTAATATCAA
1 GACTAATATCAA
912069 GACTAATATCAA
1 GACTAATATCAA
912081 G
1 G
912082 GTTCTTCGTC
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:0.48, C:0.16, G:0.12, T:0.24
Consensus pattern (12 bp):
GACTAATATCAA
Found at i:912860 original size:8 final size:8
Alignment explanation
Indices: 912844--912891 Score: 55
Period size: 8 Copynumber: 6.1 Consensus size: 8
912834 ACTCCGCCAG
912844 TTTTT-TT
1 TTTTTGTT
912851 TTTTTGTT
1 TTTTTGTT
912859 TTTTTG-T
1 TTTTTGTT
912866 TTTTTGTT
1 TTTTTGTT
*
912874 TGGTTTGTT
1 T-TTTTGTT
*
912883 TGTTTGTT
1 TTTTTGTT
912891 T
1 T
912892 GTTCAAAACC
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
7 12 0.32
8 18 0.49
9 7 0.19
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (8 bp):
TTTTTGTT
Done.