Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 135 of 226
Found at i:41984946 original size:40 final size:39
Alignment explanation
Indices: 41984898--41985258 Score: 517
Period size: 40 Copynumber: 9.1 Consensus size: 39
41984888 AGGTCTCGAC
41984898 GATG-ATCCGGGCTAAGTCCGAAGAGCATTCATCGCTAGT
1 GATGTATCCGGGCTAAGTCCGAAGAGCATTCAT-GCTAGT
41984937 GATGTATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAG-TCCGAAGAGCATTCATGCTAGT
41984977 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGT-CCGAAGAGCATTCATGCTAGT
*
41985017 GATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAG-TCCGAAGAGCATTCATGCTAGT
41985057 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGT-CCGAAGAGCATTCATGCTAGT
41985097 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGT-CCGAAGAGCATTCATGCTAGT
*
41985137 GATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAG-TCCGAAGAGCATTCATGCTAGT
* * ** * *
41985177 GATATATCCGTGCTAAACCCCGAAGAGCATTCGTGCTGGT
1 GATGTATCCGGGCT-AAGTCCGAAGAGCATTCATGCTAGT
* * * * *
41985217 GTTATATCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGT
1 GATGTATCCGGGCTAAGT-CCGAAGAGCATTCATGCTAGT
41985257 GA
1 GA
41985259 CGTGTATTCG
Statistics
Matches: 298, Mismatches: 16, Indels: 15
0.91 0.05 0.05
Matches are distributed among these distances:
39 7 0.02
40 271 0.91
41 20 0.07
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
GATGTATCCGGGCTAAGTCCGAAGAGCATTCATGCTAGT
Found at i:41985115 original size:120 final size:120
Alignment explanation
Indices: 41984898--41985258 Score: 582
Period size: 120 Copynumber: 3.0 Consensus size: 120
41984888 AGGTCTCGAC
* *
41984898 GATG-ATCCGGGCTAAG-TCCGAAGAGCATTCATCGCTAGTGATGTATCCGGGCTAAGTTCCGAA
1 GATGTATCCGGGCTAAGTTCCGAAGAGCATTCGT-GCTAGTGATGTATCCGGGCTAAGTCCCGAA
41984961 GAGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
65 GAGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
41985017 GATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
1 GATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
41985082 AGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
66 AGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* * **
41985137 GATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATATCCGTGCTAAACCCCGAAG
1 GATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
* * * * * * *
41985202 AGCATTCGTGCTGGTGTTATATCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGT
66 AGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
41985257 GA
1 GA
41985259 CGTGTATTCG
Statistics
Matches: 227, Mismatches: 13, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
119 4 0.02
120 208 0.92
121 15 0.07
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (120 bp):
GATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
AGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
Found at i:41986673 original size:84 final size:83
Alignment explanation
Indices: 41986512--41986684 Score: 303
Period size: 82 Copynumber: 2.1 Consensus size: 83
41986502 GGCCGGCCAT
*
41986512 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCAAACATGTTGGGGTAGTGCATTATGT
1 GAGCATCGGTGGACAAGATGTTATGGCTAAAAACATGTCAAACATGTTGGGGTAGTGCATTATGT
41986577 AAGGATTAAT-AAATAAA
66 AAGGATTAATAAAATAAA
41986594 GAGCATCGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATCGGTGGACAAGATGTTATGGCTAAAAACATGTC--AAACATGTTGGGGTAGTGCATTAT
41986659 GTAAGGATTAATAAAATAAA
64 GTAAGGATTAATAAAATAAA
*
41986679 GGGCAT
1 GAGCAT
41986685 GGGCAATAAA
Statistics
Matches: 86, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
82 38 0.44
84 36 0.42
85 12 0.14
ACGTcount: A:0.38, C:0.09, G:0.27, T:0.27
Consensus pattern (83 bp):
GAGCATCGGTGGACAAGATGTTATGGCTAAAAACATGTCAAACATGTTGGGGTAGTGCATTATGT
AAGGATTAATAAAATAAA
Found at i:41988717 original size:47 final size:47
Alignment explanation
Indices: 41987948--41988711 Score: 1040
Period size: 47 Copynumber: 16.1 Consensus size: 47
41987938 TATTTGAATA
* * *
41987948 AATGTGAA-AGTGTATATATGTTATAAGGCCTACTGGCCAATGTGAATGG
1 AATGTGAACA-TGTATATATGTGATAAGGCCGAATGGCCAATGTG-AT-G
*** *
41987997 AA-GTGAGTGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATG
1 AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
*
41988043 AATGTGAA-AGTGTATATATATGTGATAAGGCTGAATGGCCAATGTGATG
1 AATGTGAACA-TG--TATATATGTGATAAGGCCGAATGGCCAATGTGATG
41988092 AATGTGAA-AGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACA-TG--TATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
41988141 AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGGATG
1 AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGT-GATG
* *
41988189 AATGTGAACATGCATATATGAGATATAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATATGTGATA-AGGCCGAATGGCCAATGTGATG
* *
41988237 AATGTGAAC-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
41988283 AATGTGAACATTTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * * *
41988330 AATGTGAACATGCATATATGAGATAAAGCCAAATGGCCAATGTGATG
1 AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
*
41988377 AATGTGAA-AGTGTAAATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACA-TGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
41988424 AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
41988471 AATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
41988518 AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
41988565 AATGTGAACATTTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
41988612 AATGTGAACATCGCATATATGAGATAAGGCC-AATGGCCAATGTGATG
1 AATGTGAACAT-GTATATATGTGATAAGGCCGAATGGCCAATGTGATG
41988659 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACA-TGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
*
41988706 GATGTG
1 AATGTG
41988712 GAAGTGATAA
Statistics
Matches: 649, Mismatches: 52, Indels: 30
0.89 0.07 0.04
Matches are distributed among these distances:
46 53 0.08
47 395 0.61
48 89 0.14
49 111 0.17
50 1 0.00
ACGTcount: A:0.33, C:0.10, G:0.29, T:0.27
Consensus pattern (47 bp):
AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
Found at i:41988738 original size:141 final size:141
Alignment explanation
Indices: 41987948--41988711 Score: 1187
Period size: 141 Copynumber: 5.4 Consensus size: 141
41987938 TATTTGAATA
* * * *** *
41987948 AATGTGAAAGTGTATATATGTTATAAGGCCTACTGGCCAATGTGAATGGAA-GTGAGTGTGTATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTG-AT-GAATGTGAACATGTGTA
* * * * *
41988012 TATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAA-AGTGTATATATATGTGATAAGGCTG
64 TGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TG--CATATATGAGATAAGGCCG
41988076 AATGGCCAATGTGATG
126 AATGGCCAATGTGATG
41988092 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTA
1 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTA
41988157 TGTGTGATAAGGCCGAATGGCCAATGTGGATGAATGTGAACATGCATATATGAGATATAGGCCGA
64 TGTGTGATAAGGCCGAATGGCCAATGT-GATGAATGTGAACATGCATATATGAGATA-AGGCCGA
41988222 ATGGCCAATGTGATG
127 ATGGCCAATGTGATG
* * * *
41988237 AATGTG-AACTGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATTTGTATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATG
* *
41988301 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAAGCCAAATGG
66 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGG
41988366 CCAATGTGATG
131 CCAATGTGATG
*
41988377 AATGTGAAAGTGTAAATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATG
41988442 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGG
66 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGG
41988507 CCAATGTGATG
131 CCAATGTGATG
* * *
41988518 AATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATTTGTAT
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTAT
41988582 GTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATCGCATATATGAGATAAGGCC-AAT
65 GTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACAT-GCATATATGAGATAAGGCCGAAT
41988646 GGCCAATGTGATG
129 GGCCAATGTGATG
*
41988659 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTG
41988712 GAAGTGATAA
Statistics
Matches: 578, Mismatches: 32, Indels: 23
0.91 0.05 0.04
Matches are distributed among these distances:
140 27 0.05
141 319 0.55
142 95 0.16
144 30 0.05
145 63 0.11
146 43 0.07
147 1 0.00
ACGTcount: A:0.33, C:0.10, G:0.29, T:0.27
Consensus pattern (141 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATG
TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGG
CCAATGTGATG
Found at i:41991221 original size:38 final size:38
Alignment explanation
Indices: 41991157--41991231 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
41991147 AATCCGAGTT
*
41991157 TAAAGACCCGCTGACTATATGAAGAGATTATGTCCGGG
1 TAAAGACCCGATGACTATATGAAGAGATTATGTCCGGG
* *
41991195 TAAAGACCCGATGGCTATGT-ACAGAGATTATGTCCGG
1 TAAAGACCCGATGACTATATGA-AGAGATTATGTCCGG
41991232 ATTAAAATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.24
Consensus pattern (38 bp):
TAAAGACCCGATGACTATATGAAGAGATTATGTCCGGG
Found at i:41991396 original size:40 final size:40
Alignment explanation
Indices: 41991284--41991635 Score: 559
Period size: 40 Copynumber: 8.9 Consensus size: 40
41991274 AGGTCTCGAC
41991284 GATG-ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
41991323 GATGTATCCGGGCTAAGT--CGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
41991361 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* *
41991401 GATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
41991441 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
41991481 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* *
41991521 GATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* * * * *
41991561 GATATATCCGTGCTAA-ACCCGAAGAGCATTCGTGCTGGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* * * *
41991600 GTTATATCCGGGCTAGGTCCCGAAGAGCAATCATGC
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGC
41991636 CGGTGACGTG
Statistics
Matches: 292, Mismatches: 17, Indels: 7
0.92 0.05 0.02
Matches are distributed among these distances:
38 38 0.13
39 37 0.13
40 217 0.74
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
Found at i:41993021 original size:85 final size:84
Alignment explanation
Indices: 41992878--41993055 Score: 338
Period size: 85 Copynumber: 2.1 Consensus size: 84
41992868 GGCCGGCCAT
41992878 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
41992943 GTAAGGATTAATAAAATAAA
66 GTAA-GATTAATAAAATAAA
41992963 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
41993028 GTAAGATTAATAAAATAAA
66 GTAAGATTAATAAAATAAA
*
41993047 GGGCATGGG
1 GAGCATGGG
41993056 CAATAAAATA
Statistics
Matches: 92, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
84 23 0.25
85 69 0.75
ACGTcount: A:0.38, C:0.08, G:0.28, T:0.26
Consensus pattern (84 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
GTAAGATTAATAAAATAAA
Found at i:41994502 original size:47 final size:48
Alignment explanation
Indices: 41994317--41994722 Score: 553
Period size: 47 Copynumber: 8.6 Consensus size: 48
41994307 TATTTGAATA
* *
41994317 AATGTGAA-AGTGTATATGTGTGATAAGGCCTAATGGCCAATGTGATG
1 AATGTGAACAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
*
41994364 AATGTGAA-AGTGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATG
1 AATGTGAACA--GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
*
41994413 AATGT-AAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
41994462 AATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGACCAATGTGATG
1 AATGTGAACAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
41994509 AATGTGAACA-TGCATATATGAGATAAGGCTGAATGGCCAATGTGATG
1 AATGTGAACAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
41994556 AATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
41994603 AATGTGAACA-TGCATATATGAGATAAGG-CGAATGGCCAATGTGATG
1 AATGTGAACAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
41994649 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
41994696 GATGTGGA-AGTGTATAAATGTGATAAG
1 AATGTGAACAGTGTATATATGTGATAAG
41994723 TCCCGAAGGG
Statistics
Matches: 325, Mismatches: 26, Indels: 16
0.89 0.07 0.04
Matches are distributed among these distances:
45 1 0.00
46 42 0.13
47 193 0.59
48 2 0.01
49 84 0.26
50 3 0.01
ACGTcount: A:0.34, C:0.09, G:0.29, T:0.28
Consensus pattern (48 bp):
AATGTGAACAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
Found at i:41996900 original size:33 final size:34
Alignment explanation
Indices: 41996857--41996921 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
41996847 TTAAACAAAT
* *
41996857 TAATTACTAACACTTATTTAAGTTGAACTAAAAA
1 TAATTACTAACACGTATTTAAGCTGAACTAAAAA
*
41996891 TAATT-CTAACACGTATTTGAGCTGAACTAAA
1 TAATTACTAACACGTATTTAAGCTGAACTAAA
41996922 TTTAATAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 23 0.82
34 5 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (34 bp):
TAATTACTAACACGTATTTAAGCTGAACTAAAAA
Found at i:42001108 original size:20 final size:18
Alignment explanation
Indices: 42001065--42001109 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
42001055 AAAGGAAGAC
42001065 AGAAAAAGAAATCAAAAA
1 AGAAAAAGAAATCAAAAA
* *
42001083 ATAAAAAGAGAATGAAAAA
1 AGAAAAAGA-AATCAAAAA
42001102 GAGAAAAA
1 -AGAAAAA
42001110 AGGGATTGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 8 0.36
19 8 0.36
20 6 0.27
ACGTcount: A:0.76, C:0.02, G:0.16, T:0.07
Consensus pattern (18 bp):
AGAAAAAGAAATCAAAAA
Found at i:42002768 original size:33 final size:34
Alignment explanation
Indices: 42002725--42002799 Score: 116
Period size: 33 Copynumber: 2.2 Consensus size: 34
42002715 GAGTTAGTTT
* *
42002725 ATTAAATTTAGTTCAGCTTAAATAAGTGTTAG-A
1 ATTAATTTTAGTTCAACTTAAATAAGTGTTAGTA
*
42002758 CTTAATTTTAGTTCAACTTAAATAAGTGTTAGTA
1 ATTAATTTTAGTTCAACTTAAATAAGTGTTAGTA
42002792 ATTAATTT
1 ATTAATTT
42002800 GTTTAAATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 29 0.78
34 8 0.22
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (34 bp):
ATTAATTTTAGTTCAACTTAAATAAGTGTTAGTA
Found at i:42004588 original size:18 final size:17
Alignment explanation
Indices: 42004565--42004603 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
42004555 CTCTTTTTGC
42004565 TCTTTTTCATTCTCTTTT
1 TCTTTTTCATT-TCTTTT
*
42004583 TCTTTTTTGATTTCTTTT
1 TC-TTTTTCATTTCTTTT
42004601 TCT
1 TCT
42004604 GTCTTCCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
17 1 0.05
18 10 0.53
19 8 0.42
ACGTcount: A:0.05, C:0.18, G:0.03, T:0.74
Consensus pattern (17 bp):
TCTTTTTCATTTCTTTT
Found at i:42005959 original size:39 final size:39
Alignment explanation
Indices: 42005901--42005994 Score: 154
Period size: 39 Copynumber: 2.4 Consensus size: 39
42005891 TAGACACTCG
* *
42005901 GATCTGAAACGGAACAGAAAATTAAACTTAGAA-CTAACA
1 GATCTGAAACGAAATAGAAAATTAAACTTAGAATC-AACA
42005940 GATCTGAAACGAAATAGAAAATTAAACTTAGAATCAACA
1 GATCTGAAACGAAATAGAAAATTAAACTTAGAATCAACA
42005979 GATCTGAAACGAAATA
1 GATCTGAAACGAAATA
42005995 CCCAAAACAA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
39 51 0.98
40 1 0.02
ACGTcount: A:0.52, C:0.14, G:0.15, T:0.19
Consensus pattern (39 bp):
GATCTGAAACGAAATAGAAAATTAAACTTAGAATCAACA
Found at i:42010649 original size:36 final size:35
Alignment explanation
Indices: 42010592--42010666 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 35
42010582 GAAAGTGAAA
42010592 AAAAAGAAAAACAAAAAGAGTGCGAGCG-AGAAAATG
1 AAAAAGAAAAACAAAAAGAGTGCGAG-GAAGAAAA-G
* *
42010628 AAAAAGAAAAA-AAAGATGAGTGTGAGGAAGAAAAG
1 AAAAAGAAAAACAAA-AAGAGTGCGAGGAAGAAAAG
42010663 AAAA
1 AAAA
42010667 TTGAAAATGA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
35 9 0.26
36 26 0.74
ACGTcount: A:0.64, C:0.04, G:0.25, T:0.07
Consensus pattern (35 bp):
AAAAAGAAAAACAAAAAGAGTGCGAGGAAGAAAAG
Found at i:42011104 original size:16 final size:15
Alignment explanation
Indices: 42011085--42011114 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
42011075 AGTATCAATT
42011085 TTTGATTGGTGATGAC
1 TTTGATTGG-GATGAC
42011101 TTTGATTGGGATGA
1 TTTGATTGGGATGA
42011115 TGGTTTTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.20, C:0.03, G:0.33, T:0.43
Consensus pattern (15 bp):
TTTGATTGGGATGAC
Found at i:42031065 original size:27 final size:28
Alignment explanation
Indices: 42031035--42031101 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 28
42031025 AACTGAAGGA
42031035 GAAAAAGAAAATG-AA-GAAAAGAAAATT
1 GAAAAAGAAAATGAAATGAAAA-AAAATT
* *
42031062 GAAAAAGAAATTGAAATTGAGAAAAAATT
1 GAAAAAGAAAATGAAA-TGAAAAAAAATT
42031091 GAAAAAGAAAA
1 GAAAAAGAAAA
42031102 AATGTTGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 12 0.35
28 2 0.06
29 16 0.47
30 4 0.12
ACGTcount: A:0.69, C:0.00, G:0.18, T:0.13
Consensus pattern (28 bp):
GAAAAAGAAAATGAAATGAAAAAAAATT
Found at i:42031072 original size:12 final size:12
Alignment explanation
Indices: 42031035--42031077 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
42031025 AACTGAAGGA
*
42031035 GAAAAAGAAAAT
1 GAAAAAGAAATT
42031047 GAAGAAAAGAAAATT
1 G-A-AAAAG-AAATT
42031062 GAAAAAGAAATT
1 GAAAAAGAAATT
42031074 GAAA
1 GAAA
42031078 TTGAGAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 10 0.37
13 6 0.22
14 6 0.22
15 5 0.19
ACGTcount: A:0.70, C:0.00, G:0.19, T:0.12
Consensus pattern (12 bp):
GAAAAAGAAATT
Found at i:42031078 original size:18 final size:17
Alignment explanation
Indices: 42031057--42031094 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
42031047 GAAGAAAAGA
42031057 AAATTGAAAAAGAAATTG
1 AAATTGAAAAA-AAATTG
*
42031075 AAATTGAGAAAAAATTG
1 AAATTGAAAAAAAATTG
42031092 AAA
1 AAA
42031095 AAGAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.63, C:0.00, G:0.16, T:0.21
Consensus pattern (17 bp):
AAATTGAAAAAAAATTG
Found at i:42031103 original size:17 final size:17
Alignment explanation
Indices: 42031062--42031117 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
42031052 AAAGAAAATT
**
42031062 GAAAAAGAAATTGAAATT
1 GAAAAA-AAATTGAAAAA
*
42031080 GAGAAAAAATTGAAAAA
1 GAAAAAAAATTGAAAAA
**
42031097 GAAAAAATGTTGAAAAA
1 GAAAAAAAATTGAAAAA
42031114 GAAA
1 GAAA
42031118 CGAGAGGAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 27 0.84
18 5 0.16
ACGTcount: A:0.66, C:0.00, G:0.18, T:0.16
Consensus pattern (17 bp):
GAAAAAAAATTGAAAAA
Found at i:42043861 original size:304 final size:304
Alignment explanation
Indices: 42043312--42043892 Score: 1054
Period size: 304 Copynumber: 1.9 Consensus size: 304
42043302 CGCTTCTATC
42043312 CTTCATCAAAATTCACCTTAAGCAATATAAGATTCGGGGCAATACTTTTTAGTATTGAAACATTC
1 CTTCATCAAAATTCACCTTAAGCAATATAAGATTCGGGGCAATACTTTTTAGTATTGAAACATTC
42043377 TTGAAGCTTGAGTTCAACTTCCATTCCATTTTATCTATCAATTTATAAATTATTTCTTTATTAAA
66 TTGAAGCTTGAGTTCAACTTCCATTCCATTTTATCTATCAATTTATAAATTATTTCTTTATTAAA
42043442 CCGAACCTATAAAAAACATCAATCCAAGCCATCTTTTGAACCCAAATTGCCTACTTCCGCTTATA
131 CCGAACCTATAAAAAACATCAATCCAAGCCATCTTTTGAACCCAAATTGCCTACTTCCGCTTATA
* * *
42043507 CATCTTCATAACTCAATTTTCATATGACATCAAAACGAAAACTTCTCGTCGAAAATCGGGCAATC
196 CATCTCCATAACTCAATTTTCATACGACATCAAAACAAAAACTTCTCGTCGAAAATCGGGCAATC
42043572 AAGTGAATCGACTCAATATCCCAGGCCGGATCACATCATCTGTT
261 AAGTGAATCGACTCAATATCCCAGGCCGGATCACATCATCTGTT
42043616 CTTCATCAAAATTCACCTTAAGCAATATAAGATTCGGGGCAATACTTTTTAGTATTGAAACATTC
1 CTTCATCAAAATTCACCTTAAGCAATATAAGATTCGGGGCAATACTTTTTAGTATTGAAACATTC
* *
42043681 TTGATGCTTGAGTTCAACTTCCATTCTATTTTATCTATCAATTTATAAATTATTTCTTTATTAAA
66 TTGAAGCTTGAGTTCAACTTCCATTCCATTTTATCTATCAATTTATAAATTATTTCTTTATTAAA
* * **
42043746 CTGAACCTATAAAAAACATCAATCCAAGCCATCTTTTGAACCCAAATTGCTTGTTTCCGCTTATA
131 CCGAACCTATAAAAAACATCAATCCAAGCCATCTTTTGAACCCAAATTGCCTACTTCCGCTTATA
* * *
42043811 CATCTCCATAACTTAATTTTCATACGACATCAAAATAAAAACTTCTCGTCGACAATCGGGCAATC
196 CATCTCCATAACTCAATTTTCATACGACATCAAAACAAAAACTTCTCGTCGAAAATCGGGCAATC
42043876 AAGTGAATCGACTCAAT
261 AAGTGAATCGACTCAAT
42043893 CACCCGGGCC
Statistics
Matches: 265, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
304 265 1.00
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34
Consensus pattern (304 bp):
CTTCATCAAAATTCACCTTAAGCAATATAAGATTCGGGGCAATACTTTTTAGTATTGAAACATTC
TTGAAGCTTGAGTTCAACTTCCATTCCATTTTATCTATCAATTTATAAATTATTTCTTTATTAAA
CCGAACCTATAAAAAACATCAATCCAAGCCATCTTTTGAACCCAAATTGCCTACTTCCGCTTATA
CATCTCCATAACTCAATTTTCATACGACATCAAAACAAAAACTTCTCGTCGAAAATCGGGCAATC
AAGTGAATCGACTCAATATCCCAGGCCGGATCACATCATCTGTT
Found at i:42059381 original size:395 final size:395
Alignment explanation
Indices: 42058651--42059435 Score: 1130
Period size: 395 Copynumber: 2.0 Consensus size: 395
42058641 ATTTGACAAA
* * *
42058651 GTGATACGAGTCACAAAGGCCCAACTCAAGCTCAAGAACGTGATGGGCTCAAATTACCACAGGGC
1 GTGATACGAGTCACAAAGGCCCAACCCAAGCCCAAGAACGTGATGGGCTCAAATTACCACAAGGC
* * * ** *
42058716 CCAATAATGAGGTCAAAGGCTAGGCAAATGCATACGAAACTAAATGGAACCATTCAAGAGTTCAT
66 CCAATAACGAGATCAAAGGCCAGAAAAATGCATACCAAACTAAATGGAACCATTCAAGAGTTCAT
* *
42058781 TAGCAAGGCCTTAGATGTGTATACAAATGAAAAAGAAAATCAAGATTCACTTTCTTGCTTTCAAG
131 TAGCAAGGCCTTAGATGCGTACACAAATGAAAAAGAAAATCAAGATTCACTTTCTTGCTTTCAAG
* *
42058846 AAAATCAAGAAACCGAATCTTGGTCCAATCTTGCTGTTTTGAGCGATTTCAAGAATCAAGAAAAT
196 AAAATCAAGAAACCGAATCTTGGCCCAATCTTGCTGTTTGGAGCGATTTCAAGAATCAAGAAAAT
* ** * *
42058911 CAAGATTTCAAATCTTGGAAATCTTGGCCCAAGAAACTGAATCTTGCAGCTAAGGCGCGTTGGAT
261 CAAGATTTCAAATCTTGGAAATATTGGCCCAAGAAACCAAATCTTGCAGCTAAAGCGCATTGGAT
*
42058976 CTCAGTTACGAGCATCAACGAACCAATTTCAGG-AGAAAACAG-ATCACAAGTCCAAGTTCTTGA
326 CTCAGTTACGAGCATCAACGAACCAATTTC-GGTAGAAAACAGAAT-ACAAGCCCAAGTTCTTGA
42059039 AGACACG
389 AGACACG
* *
42059046 GTGATACGAGTCACAAAGGCCTAACCCAAGCCCAAGAACGTGATGGGCTCAAATTACCACAAGTC
1 GTGATACGAGTCACAAAGGCCCAACCCAAGCCCAAGAACGTGATGGGCTCAAATTACCACAAGGC
* ** * * * * **
42059111 CCAATAACGAGATCAAAGGCCCGAAAAATGTGTTCCAAA-TGAAATGGGACCATTTAGGAGTTTG
66 CCAATAACGAGATCAAAGGCCAGAAAAATGCATACCAAACT-AAATGGAACCATTCAAGAGTTCA
* * *
42059175 TTAGCAAGGCCTTAGATGCGTACATGAAA-GAAAGAGAAAATCAAGATTCACTTTCTTGTTTTCA
130 TTAGCAAGGCCTTAGATGCGTACA-CAAATGAAAAAGAAAATCAAGATTCACTTTCTTGCTTTCA
42059239 AGAAAATCAAGAAACCGAATCTTGGCCCAATCTTGCTGTTTGGAGCGATTTCAAGAATCAAGAAA
194 AGAAAATCAAGAAACCGAATCTTGGCCCAATCTTGCTGTTTGGAGCGATTTCAAGAATCAAGAAA
* * *
42059304 ATCAAGATTTCAAATCTTGGAAATATTTGTCCAGGAAACCAAATCTTGCAG-TCAAAGCGCATTG
259 ATCAAGATTTCAAATCTTGGAAATATTGGCCCAAGAAACCAAATCTTGCAGCT-AAAGCGCATTG
* * **
42059368 GATCTCCGTTACGAGCATCAACGAACCAATTTCGGTAGAAGATGGAATACAAGCCCAAGTTCTTG
323 GATCTCAGTTACGAGCATCAACGAACCAATTTCGGTAGAAAACAGAATACAAGCCCAAGTTCTTG
42059433 AAG
388 AAG
42059436 GCAAGGCCCA
Statistics
Matches: 345, Mismatches: 40, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
394 4 0.01
395 336 0.97
396 5 0.01
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (395 bp):
GTGATACGAGTCACAAAGGCCCAACCCAAGCCCAAGAACGTGATGGGCTCAAATTACCACAAGGC
CCAATAACGAGATCAAAGGCCAGAAAAATGCATACCAAACTAAATGGAACCATTCAAGAGTTCAT
TAGCAAGGCCTTAGATGCGTACACAAATGAAAAAGAAAATCAAGATTCACTTTCTTGCTTTCAAG
AAAATCAAGAAACCGAATCTTGGCCCAATCTTGCTGTTTGGAGCGATTTCAAGAATCAAGAAAAT
CAAGATTTCAAATCTTGGAAATATTGGCCCAAGAAACCAAATCTTGCAGCTAAAGCGCATTGGAT
CTCAGTTACGAGCATCAACGAACCAATTTCGGTAGAAAACAGAATACAAGCCCAAGTTCTTGAAG
ACACG
Found at i:42065756 original size:17 final size:17
Alignment explanation
Indices: 42065724--42065757 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
42065714 ATGAAAATCA
42065724 GGCCAATTTGTCAAAGT
1 GGCCAATTTGTCAAAGT
42065741 GGCCTAATTTGT-AAAGT
1 GGCC-AATTTGTCAAAGT
42065758 TTTATTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (17 bp):
GGCCAATTTGTCAAAGT
Found at i:42068850 original size:38 final size:38
Alignment explanation
Indices: 42068808--42068885 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
42068798 TTGAATCAGA
*
42068808 GATAGGATAATTGGGTGGCAAGATCAATTAAAAATTGT
1 GATAGGATAATTGGGCGGCAAGATCAATTAAAAATTGT
42068846 GATAGGATAATTGGGCGGCAAGATCAATTAAAAATTGT
1 GATAGGATAATTGGGCGGCAAGATCAATTAAAAATTGT
42068884 GA
1 GA
42068886 ATAGAAAACG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.40, C:0.06, G:0.27, T:0.27
Consensus pattern (38 bp):
GATAGGATAATTGGGCGGCAAGATCAATTAAAAATTGT
Found at i:42075470 original size:27 final size:27
Alignment explanation
Indices: 42075439--42075616 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
42075429 TAAATTGTAC
*
42075439 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
42075466 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
42075492 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAATTGACTATGT
* *
42075520 GGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
42075547 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* * * *
42075575 GGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
42075602 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
42075617 GACTTAATAT
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 104 0.81
28 24 0.19
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:42075500 original size:54 final size:55
Alignment explanation
Indices: 42075439--42075616 Score: 236
Period size: 54 Copynumber: 3.3 Consensus size: 55
42075429 TAAATTGTAC
* **
42075439 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT
1 AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
* * * *
42075494 -GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTGACTATG-T
1 AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
* *
42075547 AGCACTAAGTGTGCGAGTTTGATTATGTGGCACTAAGTGTGCGAGTTGATTAT-AT
1 AGCACTAAGTGTGCGA-TTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
*
42075602 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
42075617 GACTTAATAT
Statistics
Matches: 107, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
53 1 0.01
54 60 0.56
55 46 0.43
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (55 bp):
AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
Found at i:42083734 original size:27 final size:27
Alignment explanation
Indices: 42083703--42083880 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
42083693 TAAATTGTAC
*
42083703 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
42083730 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
42083756 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAATTGACTATGT
* *
42083784 GGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
42083811 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* * * *
42083839 GGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
42083866 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
42083881 GACTTAATAT
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 104 0.81
28 24 0.19
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:42083764 original size:54 final size:55
Alignment explanation
Indices: 42083703--42083880 Score: 236
Period size: 54 Copynumber: 3.3 Consensus size: 55
42083693 TAAATTGTAC
* **
42083703 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT
1 AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
* * * *
42083758 -GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTGACTATG-T
1 AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
* *
42083811 AGCACTAAGTGTGCGAGTTTGATTATGTGGCACTAAGTGTGCGAGTTGATTAT-AT
1 AGCACTAAGTGTGCGA-TTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
*
42083866 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
42083881 GACTTAATAT
Statistics
Matches: 107, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
53 1 0.01
54 60 0.56
55 46 0.43
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (55 bp):
AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
Found at i:42086008 original size:11 final size:11
Alignment explanation
Indices: 42085992--42086016 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
42085982 CTCAAAACAG
42085992 CAAAATTGGAC
1 CAAAATTGGAC
42086003 CAAAATTGGAC
1 CAAAATTGGAC
42086014 CAA
1 CAA
42086017 GATTTGTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.20, G:0.16, T:0.16
Consensus pattern (11 bp):
CAAAATTGGAC
Found at i:42091566 original size:15 final size:16
Alignment explanation
Indices: 42091546--42091577 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
42091536 GGAAATTGAA
42091546 AAAGAAAAAGAA-ATG
1 AAAGAAAAAGAAGATG
42091561 AAAGAAAAAGAAGATG
1 AAAGAAAAAGAAGATG
42091577 A
1 A
42091578 GATTGAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAGAAGATG
Found at i:42091643 original size:21 final size:21
Alignment explanation
Indices: 42091604--42091643 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
42091594 GAAAGTATGT
* *
42091604 AAGAAACGAGTGTAATTGAAA
1 AAGAAACAAGAGTAATTGAAA
*
42091625 AAGAAACAAGAGTAGTTGA
1 AAGAAACAAGAGTAATTGA
42091644 GTTTTCTATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.05, G:0.25, T:0.17
Consensus pattern (21 bp):
AAGAAACAAGAGTAATTGAAA
Found at i:42096383 original size:37 final size:37
Alignment explanation
Indices: 42096329--42096480 Score: 155
Period size: 37 Copynumber: 3.9 Consensus size: 37
42096319 TATGATCACT
*
42096329 TATCAC-TTGTC-CCTGATCAGATAAGTGTAGCCACC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
* * * *
42096364 TATCAGTTTGTTTCTTGATCAGATAAATGTAGCCACT
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
42096401 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCAC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGC-----C-A-C-C
*
42096446 TTATCACTTTGTCTCTTGATCAGATAAGTATAGCC
1 -TATCACTTTGTCTCTTGATCAGATAAGTGTAGCC
42096481 GAAGCTATCA
Statistics
Matches: 96, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
35 5 0.05
36 4 0.04
37 51 0.53
41 1 0.01
42 1 0.01
43 1 0.01
44 1 0.01
46 32 0.33
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (37 bp):
TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
Found at i:42096464 original size:46 final size:46
Alignment explanation
Indices: 42096397--42096612 Score: 272
Period size: 46 Copynumber: 4.6 Consensus size: 46
42096387 TAAATGTAGC
* * *
42096397 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTAT
* *
42096443 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTAT
*
42096489 CACTTATCACTTT-TCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTAT
* * * *
42096534 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTATAGCCAAAGCTAT
*
42096586 CACTTATCACTTTATCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
42096613 AGTACTCAAA
Statistics
Matches: 152, Mismatches: 11, Indels: 14
0.86 0.06 0.08
Matches are distributed among these distances:
45 40 0.26
46 71 0.47
47 1 0.01
50 1 0.01
51 2 0.01
52 37 0.24
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTAT
Found at i:42096558 original size:52 final size:51
Alignment explanation
Indices: 42096486--42096598 Score: 154
Period size: 52 Copynumber: 2.2 Consensus size: 51
42096476 TAGCCGAAGC
* * **
42096486 TATCACTTATCACTTTTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTT-TCACTTGTCACTTGATCAGATAAGTATAGCCAAAGCTACCACT
* *
42096538 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTT-CACTTGTCACTTGATCAGATAAGTATAGCCAAAGCTACCACT
42096590 TATCACTTT
1 TATCACTTT
42096599 ATCACTTGAT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
51 1 0.02
52 53 0.98
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (51 bp):
TATCACTTTCACTTGTCACTTGATCAGATAAGTATAGCCAAAGCTACCACT
Found at i:42102310 original size:20 final size:20
Alignment explanation
Indices: 42102287--42102330 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
42102277 AGCTCCAACC
*
42102287 AGCTCATTTGAGATCAATTT
1 AGCTCATTCGAGATCAATTT
* *
42102307 AGCTTATTCGAGCTCAATTT
1 AGCTCATTCGAGATCAATTT
42102327 AGCT
1 AGCT
42102331 TTCCATCAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (20 bp):
AGCTCATTCGAGATCAATTT
Found at i:42106919 original size:20 final size:20
Alignment explanation
Indices: 42106896--42106939 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
42106886 AGCTCTAACC
*
42106896 AGCTCATTTGAGCTCAATTT
1 AGCTCATTCGAGCTCAATTT
42106916 AGCTCATTCGAGCTCAATTT
1 AGCTCATTCGAGCTCAATTT
42106936 AGCT
1 AGCT
42106940 TTCCATCAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (20 bp):
AGCTCATTCGAGCTCAATTT
Found at i:42107117 original size:5 final size:5
Alignment explanation
Indices: 42107107--42107137 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
42107097 TTGTTATGTG
42107107 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA T
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA T
42107138 ATGTCTTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTTAA
Found at i:42116536 original size:33 final size:34
Alignment explanation
Indices: 42116485--42116559 Score: 116
Period size: 33 Copynumber: 2.2 Consensus size: 34
42116475 AGATTTAAAC
*
42116485 AAATTAATTACTAACACTTATTTAAGGTGAACTA
1 AAATTAATTACTAACACTTATTTAAGCTGAACTA
*
42116519 AAATTAATT-CTAACACTTATTTGAGCTGAACTA
1 AAATTAATTACTAACACTTATTTAAGCTGAACTA
*
42116552 AATTTAAT
1 AAATTAAT
42116560 AAACTAACTC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
33 29 0.76
34 9 0.24
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.37
Consensus pattern (34 bp):
AAATTAATTACTAACACTTATTTAAGCTGAACTA
Found at i:42118341 original size:20 final size:20
Alignment explanation
Indices: 42118305--42118361 Score: 64
Period size: 18 Copynumber: 2.9 Consensus size: 20
42118295 TCAATCTCAA
*
42118305 TCTCTTTTTACTCTTTTTCAT
1 TCTCTTTTT-CTGTTTTTCAT
*
42118326 TCTCTTTTTCTG-TTTTGAT
1 TCTCTTTTTCTGTTTTTCAT
*
42118345 T-TCTTTTTCTGTCTTTC
1 TCTCTTTTTCTGTTTTTC
42118362 TTTCATTACA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
18 10 0.32
19 10 0.32
20 2 0.06
21 9 0.29
ACGTcount: A:0.05, C:0.21, G:0.05, T:0.68
Consensus pattern (20 bp):
TCTCTTTTTCTGTTTTTCAT
Found at i:42122483 original size:30 final size:30
Alignment explanation
Indices: 42122449--42122506 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
42122439 TTCGAGCTTG
*
42122449 GGGACAAAGA-TGTAATTATGCAAAAGTTTA
1 GGGACAAA-ATTGTAATTATCCAAAAGTTTA
*
42122479 GGGACAAAATTGTAATTTTCCAAAAGTT
1 GGGACAAAATTGTAATTATCCAAAAGTT
42122507 GAGTCGAAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 24 0.96
ACGTcount: A:0.41, C:0.09, G:0.21, T:0.29
Consensus pattern (30 bp):
GGGACAAAATTGTAATTATCCAAAAGTTTA
Found at i:42123036 original size:97 final size:100
Alignment explanation
Indices: 42122842--42123122 Score: 292
Period size: 97 Copynumber: 2.9 Consensus size: 100
42122832 TAAATAATGG
* * * * *
42122842 TCACGTGTGTAGTACTAAGTGAAGGTTACTATGTGTACCGAGAAGCTTTGAG-CATGTGTATAGT
1 TCACGTGTGTAGTACTAAGTGAAGGCTACTATGTGTACTGAAAAGCTTTG-GTCACGTGTGTAGT
* * * * *
42122906 ACTGTGTGAATGCTACTACGTCTATCGGTAAAC-T-A
65 ACTATGTGAAGGCTACTACGT-GAGCCGTAAACTTGA
* * * * *
42122941 -C-GGTGTGTAGTACTAAGTGAAGGCTACAATGGGTACTGAAAAGCTTTGGTCACATATGTAGTA
1 TCACGTGTGTAGTACTAAGTGAAGGCTACTATGTGTACTGAAAAGCTTTGGTCACGTGTGTAGTA
42123004 CTATGTGAAGGCTACTACGTGAGCCGTAAAACTTGA
66 CTATGTGAAGGCTACTACGTGAGCCGT-AAACTTGA
* * * *
42123040 TCACGT-TGTAGTACTATGTGAAGGCTACTACGTGAACTGTAAAA-C--TGATCACGTGTGTAGT
1 TCACGTGTGTAGTACTAAGTGAAGGCTACTATGTGTACTG-AAAAGCTTTGGTCACGTGTGTAGT
42123101 ACTATGTGAAGGCTACTACGTG
65 ACTATGTGAAGGCTACTACGTG
42123123 TACCGAATGA
Statistics
Matches: 151, Mismatches: 24, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
96 5 0.03
97 72 0.48
98 37 0.25
99 1 0.01
100 30 0.20
101 6 0.04
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (100 bp):
TCACGTGTGTAGTACTAAGTGAAGGCTACTATGTGTACTGAAAAGCTTTGGTCACGTGTGTAGTA
CTATGTGAAGGCTACTACGTGAGCCGTAAACTTGA
Found at i:42123057 original size:49 final size:49
Alignment explanation
Indices: 42122997--42123127 Score: 219
Period size: 49 Copynumber: 2.7 Consensus size: 49
42122987 TGGTCACATA
*
42122997 TGTAGTACTATGTGAAGGCTACTACGTGAGCCGTAAAACTTGATCACGT-
1 TGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAAC-TGATCACGTG
*
42123046 TGTAGTACTATGTGAAGGCTACTACGTGAACTGTAAAACTGATCACGTG
1 TGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTGATCACGTG
*
42123095 TGTAGTACTATGTGAAGGCTACTACGTGTACCG
1 TGTAGTACTATGTGAAGGCTACTACGTGAACCG
42123128 AATGATAAAA
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
48 9 0.12
49 68 0.88
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (49 bp):
TGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTGATCACGTG
Found at i:42130455 original size:51 final size:51
Alignment explanation
Indices: 42130345--42130683 Score: 234
Period size: 51 Copynumber: 6.7 Consensus size: 51
42130335 TGTCGATGAA
* * * * * *
42130345 CACGTGTGTAGTACTGTGTGGAGGCTACTACGTGTATCAATAAA-TAATG-GT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGAGAAACT--TGAGT
* * *
42130396 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGAGAAGCTTTGAG-
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGAGAAAC-TTGAGT
* * * * * **
42130447 CACGTGTGTAGTACTGTGTGAATGCTACTACGTCTATCG-GTAAACTACAGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGAG-AAACTTGAGT
* * * * *
42130498 TACATGTGTAGTACTAAGTGAAGGCTACAATGGGTACCGA-AAAGCTTTG-GT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGAGAAA-C-TTGAGT
*
42130549 CACGTATGTAGTACTATGTGAAGGCTACTATGTG-AGCCGTA-AAACTTGA-T
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTA-CCG-AGAAACTTGAGT
* * ** * * *
42130599 CACGTGTGTAGTACTATGTGAAGACTACAACATG-AACTATAAAAC-TGA-T
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGA-GAAACTTGAGT
* *
42130648 CACGTGTGTAGTACTATGTGAAGGTTACTACGTGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTA
42130684 TCGAATGATA
Statistics
Matches: 226, Mismatches: 48, Indels: 29
0.75 0.16 0.10
Matches are distributed among these distances:
48 1 0.00
49 35 0.15
50 47 0.21
51 136 0.60
52 6 0.03
53 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (51 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGAGAAACTTGAGT
Found at i:42130521 original size:102 final size:101
Alignment explanation
Indices: 42130345--42130578 Score: 319
Period size: 102 Copynumber: 2.3 Consensus size: 101
42130335 TGTCGATGAA
* *
42130345 CACGTGTGTAGTACTGTGTGGAGGCTACTACGTGTATCAATAAATAATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTCTATCAATAAATAA-GGTCACATGTGTAGTAC
* * *
42130410 TAAGTGAAGGCTACTATGTGTACCGAGAAGCTTTGAG-
65 TAAGTGAAGGCTACAATGGGTACCGAAAAGCTTTG-GT
* ** *
42130447 CACGTGTGTAGTACTGTGTGAATGCTACTACGTCTATCGGTAAACTACA-GTTACATGTGTAGTA
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTCTATCAATAAA-TA-AGGTCACATGTGTAGTA
42130511 CTAAGTGAAGGCTACAATGGGTACCGAAAAGCTTTGGT
64 CTAAGTGAAGGCTACAATGGGTACCGAAAAGCTTTGGT
* *
42130549 CACGTATGTAGTACTATGTGAAGGCTACTA
1 CACGTGTGTAGTACTGTGTGAAGGCTACTA
42130579 TGTGAGCCGT
Statistics
Matches: 117, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
101 1 0.01
102 113 0.97
103 2 0.02
104 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (101 bp):
CACGTGTGTAGTACTGTGTGAAGGCTACTACGTCTATCAATAAATAAGGTCACATGTGTAGTACT
AAGTGAAGGCTACAATGGGTACCGAAAAGCTTTGGT
Found at i:42130594 original size:102 final size:101
Alignment explanation
Indices: 42130395--42130628 Score: 283
Period size: 102 Copynumber: 2.3 Consensus size: 101
42130385 TAAATAATGG
* * * *
42130395 TCACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGAGAAGCTTTGAGCACGTGTGTAGTA
1 TCACATGTGTAGTACTAAGTGAAGGCTACAATGGGTACCGAAAAGCTTTGAGCACGTATGTAGTA
* * * * *
42130460 CTGTGTGAATGCTACTACGTCTATCGGTAAACTACA
66 CTATGTGAAGGCTACTACGTCGAGCCGTAAACTACA
*
42130496 GTTACATGTGTAGTACTAAGTGAAGGCTACAATGGGTACCGAAAAGCTTTG-GTCACGTATGTAG
1 -TCACATGTGTAGTACTAAGTGAAGGCTACAATGGGTACCGAAAAGCTTTGAG-CACGTATGTAG
* **
42130560 TACTATGTGAAGGCTACTATGT-GAGCCGTAAAACTTGA
64 TACTATGTGAAGGCTACTACGTCGAGCCGT-AAACTACA
* * *
42130598 TCACGTGTGTAGTACTATGTGAAGACTACAA
1 TCACATGTGTAGTACTAAGTGAAGGCTACAA
42130629 CATGAACTAT
Statistics
Matches: 113, Mismatches: 17, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
101 32 0.28
102 81 0.72
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (101 bp):
TCACATGTGTAGTACTAAGTGAAGGCTACAATGGGTACCGAAAAGCTTTGAGCACGTATGTAGTA
CTATGTGAAGGCTACTACGTCGAGCCGTAAACTACA
Found at i:42130667 original size:49 final size:50
Alignment explanation
Indices: 42130548--42130670 Score: 167
Period size: 50 Copynumber: 2.5 Consensus size: 50
42130538 AAAGCTTTGG
* * * ** * *
42130548 TCACGTATGTAGTACTATGTGAAGGCTACTATGTGAGCCGTAAAACTTGA
1 TCACGTGTGTAGTACTATGTGAAGACTACAACATGAACCATAAAACTTGA
*
42130598 TCACGTGTGTAGTACTATGTGAAGACTACAACATGAACTATAAAAC-TGA
1 TCACGTGTGTAGTACTATGTGAAGACTACAACATGAACCATAAAACTTGA
42130647 TCACGTGTGTAGTACTATGTGAAG
1 TCACGTGTGTAGTACTATGTGAAG
42130671 GTTACTACGT
Statistics
Matches: 65, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
49 27 0.42
50 38 0.58
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGAAGACTACAACATGAACCATAAAACTTGA
Found at i:42139809 original size:33 final size:34
Alignment explanation
Indices: 42139756--42139843 Score: 103
Period size: 33 Copynumber: 2.6 Consensus size: 34
42139746 CTGGAATAAA
* *
42139756 TTAAATAA--GTTAGTTTATTAAATTTAGTTCA-G
1 TTAAATAAGTGTTAG-TAATTAAATTTAGTTCACC
*
42139788 TTGAAATAAGTGTTAG-AATTAATTTTAGTTCACC
1 TT-AAATAAGTGTTAGTAATTAAATTTAGTTCACC
42139822 TTAAATAAGTGTTAGTAATTAA
1 TTAAATAAGTGTTAGTAATTAA
42139844 TTTGTTTAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
32 2 0.04
33 33 0.69
34 8 0.17
35 5 0.10
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.43
Consensus pattern (34 bp):
TTAAATAAGTGTTAGTAATTAAATTTAGTTCACC
Found at i:42141702 original size:12 final size:12
Alignment explanation
Indices: 42141679--42141720 Score: 54
Period size: 10 Copynumber: 3.7 Consensus size: 12
42141669 CGTGAGTGAG
42141679 AAAAGAATATTGA
1 AAAAGAA-ATTGA
42141692 AAAAGAAATTG-
1 AAAAGAAATTGA
42141703 AAAA-AAA-TGA
1 AAAAGAAATTGA
42141713 AAAAGAAA
1 AAAAGAAA
42141721 AAGATGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 2 0.07
10 7 0.26
11 7 0.26
12 4 0.15
13 7 0.26
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (12 bp):
AAAAGAAATTGA
Found at i:42141815 original size:34 final size:33
Alignment explanation
Indices: 42141753--42141824 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
42141743 AACAAAAGAA
*
42141753 AGTG-AAAAGCAAAAAGAGCCTGACAAGAAATCG
1 AGTGAAAAAGCAAAAAGAGCCTGAAAAGAAA-CG
* *
42141786 ATTGAAAAAG-AAAGAGAGCCTGTAAAAGAAACG
1 AGTGAAAAAGCAAAAAGAGCCTG-AAAAGAAACG
42141819 AGTGAA
1 AGTGAA
42141825 GAGAGTAATC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
33 21 0.64
34 12 0.36
ACGTcount: A:0.53, C:0.11, G:0.25, T:0.11
Consensus pattern (33 bp):
AGTGAAAAAGCAAAAAGAGCCTGAAAAGAAACG
Found at i:42151574 original size:25 final size:24
Alignment explanation
Indices: 42151546--42151596 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
42151536 TTAAAACTAC
42151546 TTCTAA-AGAAAAACTCAAGAGAGAA
1 TTCTAAGAG-AAAACTCAA-AGAGAA
*
42151571 TTCTAGGAGAAAACTCAAAGAGAA
1 TTCTAAGAGAAAACTCAAAGAGAA
42151595 TT
1 TT
42151597 TTTTTCACTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 8 0.33
25 14 0.58
26 2 0.08
ACGTcount: A:0.51, C:0.12, G:0.18, T:0.20
Consensus pattern (24 bp):
TTCTAAGAGAAAACTCAAAGAGAA
Found at i:42152472 original size:33 final size:34
Alignment explanation
Indices: 42152421--42152495 Score: 107
Period size: 33 Copynumber: 2.2 Consensus size: 34
42152411 AGATTTAAAC
*
42152421 AAATTAATTACTAACACTTATTTAAGTTGAACAA
1 AAATTAATTACTAACACTTATTTAAGCTGAACAA
* *
42152455 AAATTAATT-CTAACACTTATTTGAGCTGAACTA
1 AAATTAATTACTAACACTTATTTAAGCTGAACAA
*
42152488 AATTTAAT
1 AAATTAAT
42152496 AAACTAACTC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 28 0.76
34 9 0.24
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (34 bp):
AAATTAATTACTAACACTTATTTAAGCTGAACAA
Found at i:42154274 original size:18 final size:17
Alignment explanation
Indices: 42154251--42154289 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
42154241 CTCTTTTTGC
42154251 TCTTTTTCATTCTCTTTT
1 TCTTTTTCATT-TCTTTT
*
42154269 TCTTTTTTGATTTCTTTT
1 TC-TTTTTCATTTCTTTT
42154287 TCT
1 TCT
42154290 GTCTTCCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
17 1 0.05
18 10 0.53
19 8 0.42
ACGTcount: A:0.05, C:0.18, G:0.03, T:0.74
Consensus pattern (17 bp):
TCTTTTTCATTTCTTTT
Found at i:42158520 original size:47 final size:47
Alignment explanation
Indices: 42158468--42158965 Score: 852
Period size: 47 Copynumber: 10.6 Consensus size: 47
42158458 GATAATTGTG
* *
42158468 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
42158515 ATGTGAAAGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
42158562 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
42158609 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
42158656 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
42158703 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
42158750 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * *
42158797 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGTCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
42158844 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
42158893 ATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
42158940 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
42158966 TCCCGAAGGG
Statistics
Matches: 432, Mismatches: 17, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
47 388 0.90
49 44 0.10
ACGTcount: A:0.34, C:0.08, G:0.29, T:0.30
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:42158700 original size:22 final size:22
Alignment explanation
Indices: 42158672--42158747 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
42158662 AAGTGTATAT
42158672 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCCGAATGGCCA
* * ***
42158694 ATGTGATGAATG-TGAAAGTGTATA
1 ATGTGAT-AAGGCCG-AA-TGGCCA
42158718 TATGTGATAAGGCCGAATGGCCA
1 -ATGTGATAAGGCCGAATGGCCA
42158741 ATGTGAT
1 ATGTGAT
42158748 GAATGTGAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 15 0.38
23 8 0.21
24 8 0.21
25 8 0.21
ACGTcount: A:0.33, C:0.11, G:0.30, T:0.26
Consensus pattern (22 bp):
ATGTGATAAGGCCGAATGGCCA
Found at i:42166552 original size:15 final size:16
Alignment explanation
Indices: 42166534--42166566 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
42166524 AAACTCCAGC
42166534 AGGTAAAAGAAAG-AA
1 AGGTAAAAGAAAGTAA
*
42166549 AGGTGAAAGAAAGTAA
1 AGGTAAAAGAAAGTAA
42166565 AG
1 AG
42166567 AAACACCCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.61, C:0.00, G:0.30, T:0.09
Consensus pattern (16 bp):
AGGTAAAAGAAAGTAA
Found at i:42169423 original size:23 final size:23
Alignment explanation
Indices: 42169374--42169426 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
42169364 AAACCTGTAT
42169374 TTAAAATGTTCAGCTAAAGACACA
1 TTAAAATGTTCAGCT-AAGACACA
* *
42169398 TTAAAATGTTGTAGCT-AGACATA
1 TTAAAATGTT-CAGCTAAGACACA
42169421 TTAAAA
1 TTAAAA
42169427 AAACAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 12 0.46
24 10 0.38
25 4 0.15
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.30
Consensus pattern (23 bp):
TTAAAATGTTCAGCTAAGACACA
Found at i:42172241 original size:15 final size:15
Alignment explanation
Indices: 42172223--42172254 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
42172213 TTCTCCATTT
42172223 TCTTTTTCTCTCATC
1 TCTTTTTCTCTCATC
*
42172238 TCTTTTTTTCTCATC
1 TCTTTTTCTCTCATC
42172253 TC
1 TC
42172255 GAGTTCGTTT
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:0.06, C:0.31, G:0.00, T:0.62
Consensus pattern (15 bp):
TCTTTTTCTCTCATC
Found at i:42174965 original size:49 final size:49
Alignment explanation
Indices: 42174905--42175228 Score: 246
Period size: 49 Copynumber: 6.4 Consensus size: 49
42174895 GCCATGTCCT
42174905 AGACATGGTCTTACATGGGATGTTTCTTGTACTGCCAATGTCATATCCC
1 AGACATGGTCTTACATGGGATGTTTCTTGTACTGCCAATGTCATATCCC
* * * * *
42174954 AGATATAGTCTTACATGGGA-GTTCTCATATCG-GC-GCCCATGTCATGTCCC
1 AGACATGGTCTTACATGGGATGTT-TC-T-T-GTACTGCCAATGTCATATCCC
** ** * * * * * *
42175004 AGACATGGTCTTACGGGGGACCTCTCATCT-CGGTGCCAATGCCATGTCCT
1 AGACATGGTCTTACATGGGATGTTTCTTGTAC--TGCCAATGTCATATCCC
* *
42175054 AGACATGGTCTTACATGGGAACTCTCATGATCTCAATG-A-TGCCAATGTCATGTCCC
1 AGACATGGTCTTACATGGG-A-TGT--T--TCT---TGTACTGCCAATGTCATATCCC
* *
42175110 AAACATGGTCTTACATGGGATGTTTCTTATACTGCCAATGTCATATCCC
1 AGACATGGTCTTACATGGGATGTTTCTTGTACTGCCAATGTCATATCCC
** * *
42175159 AGGTATGGTCTTACATGAGATATTTCTTGTACTGCCAATGTCATATCCC
1 AGACATGGTCTTACATGGGATGTTTCTTGTACTGCCAATGTCATATCCC
* *
42175208 ATATATGGTCTTACATGGGAT
1 AGACATGGTCTTACATGGGAT
42175229 TTCTCATATC
Statistics
Matches: 217, Mismatches: 37, Indels: 42
0.73 0.12 0.14
Matches are distributed among these distances:
47 2 0.01
48 5 0.02
49 97 0.45
50 66 0.30
51 4 0.02
52 4 0.02
54 2 0.01
55 1 0.00
56 35 0.16
59 1 0.00
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (49 bp):
AGACATGGTCTTACATGGGATGTTTCTTGTACTGCCAATGTCATATCCC
Found at i:42175005 original size:50 final size:50
Alignment explanation
Indices: 42174938--42175332 Score: 233
Period size: 50 Copynumber: 7.8 Consensus size: 50
42174928 TTCTTGTACT
* * * **
42174938 GCCAATGTCATATCCCAGATATAGTCTTACATGGGAGTTCTCATATCGGC
1 GCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGC
* ** * *
42174988 GCCCATGTCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGT
1 GCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGC
* * * **
42175038 GCCAATGCCATGTCCTAGACATGGTCTTACATGGGAACTCTCATGATCTCAATGAT
1 GCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GGC
* ** * * *
42175094 GCCAATGTCATGTCCCAAACATGGTCTTACATGGGATGTTTCTTATAC--T
1 GCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGGC
* ** * ** * *
42175143 GCCAATGTCATATCCCAGGTATGGTCTTACATGAGATATTTC-T-T-GTAC
1 GCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCG-GC
* * * ** **
42175191 TGCCAATGTCATATCCCATATATGGTCTTACATGGGATTTCTCATATCGAT
1 -GCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGC
* * * ** * *
42175242 GCCCATGCCATGTCCCGGACATGGTCTTACGGGGGACCTCTCATCTCGGT
1 GCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGC
*** * * *
42175292 GCCAACACCATGTCACATACATGGTCTTACATGGGATCTCT
1 GCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTCT
42175333 TTACCCAAAT
Statistics
Matches: 272, Mismatches: 59, Indels: 28
0.76 0.16 0.08
Matches are distributed among these distances:
47 1 0.00
48 1 0.00
49 74 0.27
50 149 0.55
51 2 0.01
52 1 0.00
53 3 0.01
54 1 0.00
55 1 0.00
56 39 0.14
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (50 bp):
GCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGC
Found at i:42182202 original size:9 final size:9
Alignment explanation
Indices: 42182188--42182216 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
42182178 TATCGTCTTA
42182188 AAATAAAAG
1 AAATAAAAG
42182197 AAATAAAAG
1 AAATAAAAG
42182206 AAATAAAAG
1 AAATAAAAG
42182215 AA
1 AA
42182217 GCAAGCATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.10
Consensus pattern (9 bp):
AAATAAAAG
Found at i:42182681 original size:50 final size:50
Alignment explanation
Indices: 42182605--42182744 Score: 172
Period size: 50 Copynumber: 2.8 Consensus size: 50
42182595 TCTTGTACTA
* * * * *
42182605 CCAATGTCATATCCCAGATATAGTCTTACATGGGAATTCTCATATCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGAACTCTCATATCGGTG
* ** * *
42182655 CCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGAACTCTCATATCGGTG
* *
42182705 CCAATGCCATGTCCAAGACATGGTCTTACATGGGATCTCT
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGAACTCT
42182745 TTACCCAAAT
Statistics
Matches: 75, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 75 1.00
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (50 bp):
CCAATGCCATGTCCCAGACATGGTCTTACATGGGAACTCTCATATCGGTG
Found at i:42186061 original size:14 final size:14
Alignment explanation
Indices: 42186042--42186069 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
42186032 AGTAAAAGTA
42186042 TCCAATGAATTAGC
1 TCCAATGAATTAGC
42186056 TCCAATGAATTAGC
1 TCCAATGAATTAGC
42186070 ATCGATTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (14 bp):
TCCAATGAATTAGC
Found at i:42191427 original size:45 final size:45
Alignment explanation
Indices: 42191328--42191436 Score: 123
Period size: 45 Copynumber: 2.4 Consensus size: 45
42191318 ATTATAATCT
* *
42191328 ATTAAAACCTAAGAT-TGAATTTATAAGAAAATTAAAATCTAAACC
1 ATTAAAACCTAAAATCT-AATTTATAAGAAAATTAAAATCTAAACA
* * * *
42191373 ACTATAACCTAAAATCTAATTTATAAGAAAGTTAAAAT-TTAACAA
1 ATTAAAACCTAAAATCTAATTTATAAGAAAATTAAAATCTAAAC-A
*
42191418 ATTAGAACCTAAAATCTAA
1 ATTAAAACCTAAAATCTAA
42191437 AAAGAACAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
44 4 0.07
45 49 0.91
46 1 0.02
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.29
Consensus pattern (45 bp):
ATTAAAACCTAAAATCTAATTTATAAGAAAATTAAAATCTAAACA
Found at i:42192882 original size:18 final size:18
Alignment explanation
Indices: 42192859--42192896 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
42192849 CCTTTCATGG
*
42192859 TTTTCACTTTCTTTCTTT
1 TTTTCACTTTCCTTCTTT
*
42192877 TTTTCATTTTCCTTCTTT
1 TTTTCACTTTCCTTCTTT
42192895 TT
1 TT
42192897 CTCTTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTCACTTTCCTTCTTT
Found at i:42198839 original size:15 final size:15
Alignment explanation
Indices: 42198821--42198851 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
42198811 GTTCACAAAC
42198821 ATATAATTCAATTTA
1 ATATAATTCAATTTA
42198836 ATATAATTCAATTTA
1 ATATAATTCAATTTA
42198851 A
1 A
42198852 AACATATAAA
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:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (15 bp):
ATATAATTCAATTTA
Found at i:42207379 original size:20 final size:20
Alignment explanation
Indices: 42207356--42207407 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
42207346 TTTTTACTCT
42207356 TTTTTGTCATTTTTCCTTTC
1 TTTTTGTCATTTTTCCTTTC
* * *
42207376 TTTTTCTCATTTTTCTTTTT
1 TTTTTGTCATTTTTCCTTTC
42207396 TTTTTG-CATTTT
1 TTTTTGTCATTTT
42207408 CATTCTTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.06, C:0.15, G:0.04, T:0.75
Consensus pattern (20 bp):
TTTTTGTCATTTTTCCTTTC
Found at i:42207405 original size:19 final size:21
Alignment explanation
Indices: 42207355--42207407 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 21
42207345 TTTTTTACTC
42207355 TTTTTTGTCATTTTTCCTTTCT
1 TTTTTTG-CATTTTTCCTTTCT
*
42207377 TTTTCT-CATTTTT-CTTT-T
1 TTTTTTGCATTTTTCCTTTCT
42207395 TTTTTTGCATTTT
1 TTTTTTGCATTTT
42207408 CATTCTTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 6 0.21
19 10 0.36
20 7 0.25
22 5 0.18
ACGTcount: A:0.06, C:0.15, G:0.04, T:0.75
Consensus pattern (21 bp):
TTTTTTGCATTTTTCCTTTCT
Found at i:42207416 original size:19 final size:18
Alignment explanation
Indices: 42207356--42207416 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 18
42207346 TTTTTACTCT
*
42207356 TTTTTGTCATTTTTCCTTTC
1 TTTTTCTCATTTTT-C-TTC
*
42207376 TTTTTCTCATTTTTCTTT
1 TTTTTCTCATTTTTCTTC
*
42207394 TTTTTTTGCA-TTTTCATTC
1 TTTTTCT-CATTTTTC-TTC
42207413 TTTT
1 TTTT
42207417 CTTTTTCTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 13 0.37
19 9 0.26
20 13 0.37
ACGTcount: A:0.07, C:0.16, G:0.03, T:0.74
Consensus pattern (18 bp):
TTTTTCTCATTTTTCTTC
Found at i:42218406 original size:25 final size:25
Alignment explanation
Indices: 42218353--42218406 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
42218343 ATTTTATTTT
* *
42218353 AATTATCTAATTTTTCAATTTATTG
1 AATTATCTAATTTTTCAATTAATTA
42218378 AATTAT-TAATATTTT-ATATTAATTA
1 AATTATCTAAT-TTTTCA-ATTAATTA
42218403 AATT
1 AATT
42218407 TTTGAGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.56
Consensus pattern (25 bp):
AATTATCTAATTTTTCAATTAATTA
Found at i:42221677 original size:60 final size:60
Alignment explanation
Indices: 42221584--42221698 Score: 230
Period size: 60 Copynumber: 1.9 Consensus size: 60
42221574 CCAAGAGCTG
42221584 ACCTAGGGAATTTTACAATATTAATCAAGTTAGGGACCATACATATTGATAAATTCAAAA
1 ACCTAGGGAATTTTACAATATTAATCAAGTTAGGGACCATACATATTGATAAATTCAAAA
42221644 ACCTAGGGAATTTTACAATATTAATCAAGTTAGGGACCATACATATTGATAAATT
1 ACCTAGGGAATTTTACAATATTAATCAAGTTAGGGACCATACATATTGATAAATT
42221699 TTTGAGTGAC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (60 bp):
ACCTAGGGAATTTTACAATATTAATCAAGTTAGGGACCATACATATTGATAAATTCAAAA
Found at i:42228912 original size:21 final size:21
Alignment explanation
Indices: 42228887--42228936 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
42228877 GTTGTTGAGA
42228887 AGGAAGTTGCTGCTGTAGAAG
1 AGGAAGTTGCTGCTGTAGAAG
*
42228908 AGGAAGTTGCTGTTGTAGAAG
1 AGGAAGTTGCTGCTGTAGAAG
42228929 AGGAAGTT
1 AGGAAGTT
42228937 ATTGCTGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.30, C:0.06, G:0.38, T:0.26
Consensus pattern (21 bp):
AGGAAGTTGCTGCTGTAGAAG
Found at i:42233802 original size:40 final size:40
Alignment explanation
Indices: 42233709--42233809 Score: 125
Period size: 40 Copynumber: 2.6 Consensus size: 40
42233699 AAAATCCTTG
* *
42233709 TTATAATTATTGTAATTATAA--TTTACGATCAAATATTA
1 TTATAATTATTGTAATTATAATTTTTACGATAAAACATTA
* * * *
42233747 CTATAATTATTGTAATTTTAATTTTTTCGGTAAAACATTA
1 TTATAATTATTGTAATTATAATTTTTACGATAAAACATTA
*
42233787 TTATAATTATGGTAATTATAATT
1 TTATAATTATTGTAATTATAATT
42233810 ATTATATTCG
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
38 19 0.37
40 33 0.63
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.50
Consensus pattern (40 bp):
TTATAATTATTGTAATTATAATTTTTACGATAAAACATTA
Found at i:42237894 original size:37 final size:38
Alignment explanation
Indices: 42237836--42237913 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 38
42237826 TTACGAAGTC
* * *
42237836 TTACCTGGACATAATCTCCACACGAAGTTATCGGGT-T
1 TTACCCGGACAAAATCTCCACACGAAGTCATCGGGTCT
*
42237873 TTACCCGGACAAAAT-TCCCACACGTAGTCATCGGGTCT
1 TTACCCGGACAAAATCT-CCACACGAAGTCATCGGGTCT
42237911 TTA
1 TTA
42237914 GAGCTCGGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
36 1 0.03
37 30 0.86
38 4 0.11
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (38 bp):
TTACCCGGACAAAATCTCCACACGAAGTCATCGGGTCT
Found at i:42238108 original size:47 final size:47
Alignment explanation
Indices: 42238030--42238389 Score: 585
Period size: 47 Copynumber: 7.6 Consensus size: 47
42238020 CCCTTCGGGA
* * * * * *
42238030 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
42238077 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
42238124 CTTATCACATATATACACTCTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
42238171 CTTATCACATATATACGCTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42238218 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
42238265 CTTATCACATATATACACTCTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42238312 CTTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC----ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42238363 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
42238390 TATTCAAATA
Statistics
Matches: 293, Mismatches: 16, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
47 247 0.84
51 46 0.16
ACGTcount: A:0.29, C:0.31, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:42241986 original size:40 final size:40
Alignment explanation
Indices: 42241942--42242096 Score: 152
Period size: 40 Copynumber: 3.9 Consensus size: 40
42241932 GAATACACGT
* * *
42241942 CACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
** * *
42241982 CACCAGCACGAATGCTCTTCGGGGTTTAGCACGGATATAT
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
* * * **
42242022 CACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATATGGT
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATAT-AA
* *
42242063 CACTTAGCAC-AAAGC-CTTCGGGACTTAGCCCGGA
1 CAC-CAGCACGAATGCTCTTCGGGACTTAGCCCGGA
42242097 CATCATTCAA
Statistics
Matches: 96, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
40 82 0.85
41 8 0.08
42 6 0.06
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (40 bp):
CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
Found at i:42242443 original size:29 final size:29
Alignment explanation
Indices: 42242404--42242482 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
42242394 CTTAATAATC
*
42242404 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
42242434 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
42242463 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
42242483 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:42244436 original size:37 final size:37
Alignment explanation
Indices: 42244386--42244464 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
42244376 TTATTACGAA
* *
42244386 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
42244423 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
42244460 GTCTT
1 GTCTT
42244465 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:42254765 original size:20 final size:20
Alignment explanation
Indices: 42254737--42254813 Score: 109
Period size: 20 Copynumber: 3.9 Consensus size: 20
42254727 AAGACTATAA
*
42254737 ACCACTCCATTTACTTACTT
1 ACCATTCCATTTACTTACTT
42254757 ACCATTCCATTTACTTACTT
1 ACCATTCCATTTACTTACTT
* *
42254777 TCCATTTCATTTACTTACTT
1 ACCATTCCATTTACTTACTT
* *
42254797 TCTATTCCATTTACTTA
1 ACCATTCCATTTACTTA
42254814 GCATAAGCTT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.23, C:0.29, G:0.00, T:0.48
Consensus pattern (20 bp):
ACCATTCCATTTACTTACTT
Found at i:42254779 original size:15 final size:16
Alignment explanation
Indices: 42254751--42254783 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
42254741 CTCCATTTAC
42254751 TTACTTACCATTCCAT
1 TTACTTACCATTCCAT
*
42254767 TTACTTA-CTTTCCAT
1 TTACTTACCATTCCAT
42254782 TT
1 TT
42254784 CATTTACTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.21, C:0.27, G:0.00, T:0.52
Consensus pattern (16 bp):
TTACTTACCATTCCAT
Found at i:42261905 original size:65 final size:65
Alignment explanation
Indices: 42261828--42261962 Score: 207
Period size: 65 Copynumber: 2.1 Consensus size: 65
42261818 GGCCTATGGC
* * *
42261828 AGTTGATGGGAATAGTTTAACTTATGCGACTAACTAGAGTGTATAGCATCTATAAGGCCCGTGAT
1 AGTTGATGGGAATAGTGTAACTTAAGCGACTAACTAGAGCGTATAGCATCTATAAGGCCCGTGAT
* * * *
42261893 AGTTTATGGGAATAGTGTAACTTAAGCGACTAACTAGCGCGTATTGCATGTATAAGGCCCGTGAT
1 AGTTGATGGGAATAGTGTAACTTAAGCGACTAACTAGAGCGTATAGCATCTATAAGGCCCGTGAT
42261958 AGTTG
1 AGTTG
42261963 GCTAGGGCCA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (65 bp):
AGTTGATGGGAATAGTGTAACTTAAGCGACTAACTAGAGCGTATAGCATCTATAAGGCCCGTGAT
Found at i:42262603 original size:13 final size:13
Alignment explanation
Indices: 42262584--42262647 Score: 83
Period size: 13 Copynumber: 4.9 Consensus size: 13
42262574 TAAACCAAAT
42262584 TTTTCAAAAGTAC
1 TTTTCAAAAGTAC
* *
42262597 TTCTCAAAAGCAC
1 TTTTCAAAAGTAC
* * *
42262610 TTTTCCACAGCAC
1 TTTTCAAAAGTAC
42262623 TTTTCAAAAGTAC
1 TTTTCAAAAGTAC
42262636 TTTTCAAAAGTA
1 TTTTCAAAAGTA
42262648 ATGAAGAACT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 43 1.00
ACGTcount: A:0.36, C:0.22, G:0.08, T:0.34
Consensus pattern (13 bp):
TTTTCAAAAGTAC
Found at i:42264867 original size:45 final size:45
Alignment explanation
Indices: 42264769--42264867 Score: 128
Period size: 45 Copynumber: 2.2 Consensus size: 45
42264759 ATCGATAACG
* *
42264769 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGTTGAATCT
1 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTATCGAATCT
* * * *
42264814 GTAGCAGTAACGGTAACAGTATTCGACACACAAATTATCGAAT-T
1 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTATCGAATCT
42264858 AGTAACAGTA
1 -GTAACAGTA
42264868 GTCAGCACAT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
44 1 0.02
45 45 0.98
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.24
Consensus pattern (45 bp):
GTAACAGTAACAGTAACAGTATTCAACACACAAAGTATCGAATCT
Found at i:42266435 original size:24 final size:23
Alignment explanation
Indices: 42266400--42266459 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 23
42266390 TGTTATGTCT
42266400 TAATTAATTAATTAAT-TAATTCCA
1 TAATTAA-TAATTAATATAATT-CA
*
42266424 TAATATAATAATTAATATAATTTA
1 TAAT-TAATAATTAATATAATTCA
42266448 TAATTTAATAAT
1 TAA-TTAATAAT
42266460 AGATAAAACC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
24 23 0.72
25 9 0.28
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (23 bp):
TAATTAATAATTAATATAATTCA
Found at i:42267945 original size:14 final size:14
Alignment explanation
Indices: 42267926--42267962 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
42267916 GTAGTTTCTT
*
42267926 AAAAAAAATTTGAA
1 AAAAAAAATTTCAA
42267940 AAAAAAAA-TTCAA
1 AAAAAAAATTTCAA
42267953 AAAAAAAATT
1 AAAAAAAATT
42267963 GGTTTCCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.19
Consensus pattern (14 bp):
AAAAAAAATTTCAA
Found at i:42268022 original size:15 final size:15
Alignment explanation
Indices: 42267999--42268040 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
42267989 GATATCAAGT
42267999 TGAAAAAAAAATTTCG
1 TGAAAAAAAAA-TTCG
42268015 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTCG
42268030 TGAAAAAAAAA
1 TGAAAAAAAAA
42268041 GAAGAAGCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 15 0.58
16 11 0.42
ACGTcount: A:0.64, C:0.05, G:0.12, T:0.19
Consensus pattern (15 bp):
TGAAAAAAAAATTCG
Found at i:42271713 original size:70 final size:70
Alignment explanation
Indices: 42271555--42271693 Score: 253
Period size: 70 Copynumber: 2.0 Consensus size: 70
42271545 GAGTTATTTG
* *
42271555 GTTCAAA-AATAAGAAAAGACATCAGTTTTTATGGCACATTAAGTGGATGTTTTTGACCATTCGG
1 GTTCAAAGAATAAGAAAATACATCAGTTTTTATGGCACATTAAGTAGATGTTTTTGACCATTCGG
42271619 TTACC
66 TTACC
42271624 GTTCAAAGAATAAGAAAATACATCAGTTTTTATGGCACATTAAGTAGATGTTTTTGACCATTCGG
1 GTTCAAAGAATAAGAAAATACATCAGTTTTTATGGCACATTAAGTAGATGTTTTTGACCATTCGG
42271689 TTACC
66 TTACC
42271694 TTGTTTTAGC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
69 7 0.10
70 60 0.90
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (70 bp):
GTTCAAAGAATAAGAAAATACATCAGTTTTTATGGCACATTAAGTAGATGTTTTTGACCATTCGG
TTACC
Found at i:42276075 original size:17 final size:17
Alignment explanation
Indices: 42276049--42276098 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
42276039 TTCAGTAACT
*
42276049 ATTTCACATTCATTTCA
1 ATTTCCCATTCATTTCA
42276066 ATTTCCCATTCATTTCA
1 ATTTCCCATTCATTTCA
*
42276083 ATTTACCATTCCATTT
1 ATTTCCCATT-CATTT
42276099 TAATAATTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 25 0.83
18 5 0.17
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (17 bp):
ATTTCCCATTCATTTCA
Found at i:42278184 original size:24 final size:24
Alignment explanation
Indices: 42278157--42278208 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
42278147 ATGTCTTAAT
42278157 TAATTAAT-TAATTTCATAATATAA
1 TAATTAATATAATTT-ATAATATAA
*
42278181 TAATTAATATAATTTATAATTTAA
1 TAATTAATATAATTTATAATATAA
42278205 TAAT
1 TAAT
42278209 AGATAAAACC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 20 0.77
25 6 0.23
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
TAATTAATATAATTTATAATATAA
Found at i:42294882 original size:12 final size:12
Alignment explanation
Indices: 42294845--42294895 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
42294835 TATCATAGTT
42294845 CTTACTT-CTT-
1 CTTACTTGCTTA
* *
42294855 CTTTACTTACTCA
1 C-TTACTTGCTTA
*
42294868 CTTACTTGTTTA
1 CTTACTTGCTTA
42294880 CTTACTTGCTTA
1 CTTACTTGCTTA
42294892 CTTA
1 CTTA
42294896 AATAACTTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
10 1 0.03
11 6 0.18
12 25 0.76
13 1 0.03
ACGTcount: A:0.18, C:0.25, G:0.04, T:0.53
Consensus pattern (12 bp):
CTTACTTGCTTA
Found at i:42295225 original size:50 final size:50
Alignment explanation
Indices: 42295097--42295338 Score: 209
Period size: 50 Copynumber: 4.7 Consensus size: 50
42295087 GATAATAACA
* ** * * *
42295097 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCTTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* * * **
42295146 TGCCAATGCCATATCCTAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* ** *
42295196 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * * *
42295246 TGCCAACGCCATGTCCCAAACATGGTATTACATGGGACCTCTCATACTATCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC--A-TATC---GG
* * *
42295302 TGCCAATGCCATGTTCTAAACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
42295339 TCTCATCACC
Statistics
Matches: 155, Mismatches: 30, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
48 1 0.01
49 38 0.25
50 78 0.50
52 1 0.01
53 3 0.02
56 34 0.22
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:42297956 original size:40 final size:39
Alignment explanation
Indices: 42297912--42298246 Score: 325
Period size: 40 Copynumber: 8.4 Consensus size: 39
42297902 ATAAGAGCAT
*
42297912 GTATGTGCAATTCAGGGTGCCAAAG-ACCAAACAGGGGCAC
1 GTATGTGC-ATTCAGGGTACCAAAGTA-CAAACAGGGGCAC
* * *
42297952 GTATGTGCATTTAAGGGTACTAAAGTACAAATAGGGGCAC
1 GTATGTGCA-TTCAGGGTACCAAAGTACAAACAGGGGCAC
* * *
42297992 GTATGTGCATTCAGGGGCACCGAAA-TACAATCAGTGGCAC
1 GTATGTGCATTCA-GGGTACC-AAAGTACAAACAGGGGCAC
* *
42298032 GTATGTGCATTCAGGGGTACCGAAGTACAAACAAGGGCAC
1 GTATGTGCATTCA-GGGTACCAAAGTACAAACAGGGGCAC
* **
42298072 GTATGTGTATTCAGGGGTACTGAAGTACAAACAGGGGCAC
1 GTATGTGCATTCA-GGGTACCAAAGTACAAACAGGGGCAC
**
42298112 GTAT-TGCATTCAGGGGTACTGAAGTACAAACAGGGGCAC
1 GTATGTGCATTCA-GGGTACCAAAGTACAAACAGGGGCAC
*** * * *
42298151 GTATGTGCATTCAGGGGTATTGAAGTACTAATAGGGGCAT
1 GTATGTGCATTCA-GGGTACCAAAGTACAAACAGGGGCAC
* ** * *
42298191 GTATGTGCATTCAAGAGTACTGAAGTACAAATAGGGGCAT
1 GTATGTGCATTC-AGGGTACCAAAGTACAAACAGGGGCAC
*
42298231 GTACGTGCATTCAGGG
1 GTATGTGCATTCAGGG
42298247 ACATATCTTT
Statistics
Matches: 260, Mismatches: 28, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
39 47 0.18
40 208 0.80
41 5 0.02
ACGTcount: A:0.31, C:0.17, G:0.30, T:0.22
Consensus pattern (39 bp):
GTATGTGCATTCAGGGTACCAAAGTACAAACAGGGGCAC
Found at i:42298009 original size:20 final size:20
Alignment explanation
Indices: 42297984--42298167 Score: 99
Period size: 20 Copynumber: 9.2 Consensus size: 20
42297974 AAGTACAAAT
42297984 AGGGGCACGTATGTGCATTC
1 AGGGGCACGTATGTGCATTC
** * *
42298004 AGGGGCACCG-AAATACAATC
1 AGGGGCA-CGTATGTGCATTC
*
42298024 AGTGGCACGTATGTGCATTC
1 AGGGGCACGTATGTGCATTC
* * * **
42298044 AGGGGTACCG-AAGTACAAAC
1 AGGGGCA-CGTATGTGCATTC
* *
42298064 AAGGGCACGTATGTGTATTC
1 AGGGGCACGTATGTGCATTC
* * * **
42298084 AGGGGTAC-TGAAGTACAAAC
1 AGGGGCACGT-ATGTGCATTC
42298104 AGGGGCACGTAT-TGCATTC
1 AGGGGCACGTATGTGCATTC
* * * **
42298123 AGGGGTAC-TGAAGTACAAAC
1 AGGGGCACGT-ATGTGCATTC
42298143 AGGGGCACGTATGTGCATTC
1 AGGGGCACGTATGTGCATTC
42298163 AGGGG
1 AGGGG
42298168 TATTGAAGTA
Statistics
Matches: 111, Mismatches: 44, Indels: 18
0.64 0.25 0.10
Matches are distributed among these distances:
18 1 0.01
19 17 0.15
20 87 0.78
21 6 0.05
ACGTcount: A:0.29, C:0.18, G:0.32, T:0.20
Consensus pattern (20 bp):
AGGGGCACGTATGTGCATTC
Found at i:42298032 original size:80 final size:80
Alignment explanation
Indices: 42297943--42298246 Score: 414
Period size: 80 Copynumber: 3.8 Consensus size: 80
42297933 AAAGACCAAA
* * *
42297943 CAGGGGCACGTATGTGCATTTAAGGGTACTAAAGTACAAATAGGGGCACGTATGTGCATTCAGGG
1 CAGGGGCACGTATGTGCATTCAAGGGTACTGAAGTACAAACAGGGGCACGTATGTGCATTCAGGG
* * *
42298008 GCACCGAAATACAAT
66 GTACTGAAGTACAAT
* * * * *
42298023 CAGTGGCACGTATGTGCATTCAGGGGTACCGAAGTACAAACAAGGGCACGTATGTGTATTCAGGG
1 CAGGGGCACGTATGTGCATTCAAGGGTACTGAAGTACAAACAGGGGCACGTATGTGCATTCAGGG
*
42298088 GTACTGAAGTACAAA
66 GTACTGAAGTACAAT
*
42298103 CAGGGGCACGTAT-TGCATTCAGGGGTACTGAAGTACAAACAGGGGCACGTATGTGCATTCAGGG
1 CAGGGGCACGTATGTGCATTCAAGGGTACTGAAGTACAAACAGGGGCACGTATGTGCATTCAGGG
*
42298167 GTATTGAAGTACTAAT
66 GTACTGAAGTAC-AAT
* * * * *
42298183 -AGGGGCATGTATGTGCATTCAAGAGTACTGAAGTACAAATAGGGGCATGTACGTGCATTCAGGG
1 CAGGGGCACGTATGTGCATTCAAGGGTACTGAAGTACAAACAGGGGCACGTATGTGCATTCAGGG
42298247 ACATATCTTT
Statistics
Matches: 198, Mismatches: 24, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
79 70 0.35
80 128 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.22
Consensus pattern (80 bp):
CAGGGGCACGTATGTGCATTCAAGGGTACTGAAGTACAAACAGGGGCACGTATGTGCATTCAGGG
GTACTGAAGTACAAT
Found at i:42298177 original size:119 final size:119
Alignment explanation
Indices: 42297912--42298246 Score: 431
Period size: 119 Copynumber: 2.8 Consensus size: 119
42297902 ATAAGAGCAT
* * * *
42297912 GTATGTGCAATTCA-GGGTGCCAAAG-ACCAAACAGGGGCACGTATGTGCATTTAAGGGTACTAA
1 GTATGTGC-ATTCAGGGGTACCGAAGTA-CAAACAGGGGCACGTATGTGCATTCAAGGGTACTGA
* *
42297975 AGTACAAATAGGGGCACGTATGTGCATTCAGGGGCACCGAAATACAATCAGTGGCAC
64 AGTACAAATAGGGGCACGTAT-TGCATTCAGGGGCACCGAAATACAAACAGGGGCAC
* * *
42298032 GTATGTGCATTCAGGGGTACCGAAGTACAAACAAGGGCACGTATGTGTATTCAGGGGTACTGAAG
1 GTATGTGCATTCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGCATTCAAGGGTACTGAAG
* * * *
42298097 TACAAACAGGGGCACGTATTGCATTCAGGGGTACTGAAGTACAAACAGGGGCAC
66 TACAAATAGGGGCACGTATTGCATTCAGGGGCACCGAAATACAAACAGGGGCAC
** * * * *
42298151 GTATGTGCATTCAGGGGTATTGAAGTACTAATAGGGGCATGTATGTGCATTCAAGAGTACTGAAG
1 GTATGTGCATTCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGCATTCAAGGGTACTGAAG
* *
42298216 TACAAATAGGGGCATGTACGTGCATTCAGGG
66 TACAAATAGGGGCACGTA-TTGCATTCAGGG
42298247 ACATATCTTT
Statistics
Matches: 187, Mismatches: 25, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
119 107 0.57
120 79 0.42
121 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.30, T:0.22
Consensus pattern (119 bp):
GTATGTGCATTCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGCATTCAAGGGTACTGAAG
TACAAATAGGGGCACGTATTGCATTCAGGGGCACCGAAATACAAACAGGGGCAC
Found at i:42304089 original size:19 final size:20
Alignment explanation
Indices: 42304044--42304089 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
42304034 CATCATGTTC
*
42304044 ATATTTTTAGCATAATTTAA
1 ATATTTTTAGAATAATTTAA
* *
42304064 TTA-TTTTATAAT-ATTTAA
1 ATATTTTTAGAATAATTTAA
42304082 ATATTTTT
1 ATATTTTT
42304090 CGACAAGAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
18 8 0.38
19 11 0.52
20 2 0.10
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (20 bp):
ATATTTTTAGAATAATTTAA
Found at i:42308023 original size:30 final size:30
Alignment explanation
Indices: 42307989--42308051 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
42307979 TTTGATAGGA
42307989 TATTCATTGCAATTTGCATCAACAATCACT
1 TATTCATTGCAATTTGCATCAACAATCACT
* *
42308019 TATTCATTGCAATTTGCATCGACCATCACT
1 TATTCATTGCAATTTGCATCAACAATCACT
42308049 TAT
1 TAT
42308052 CCTATTATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.30, C:0.24, G:0.08, T:0.38
Consensus pattern (30 bp):
TATTCATTGCAATTTGCATCAACAATCACT
Found at i:42315316 original size:3 final size:3
Alignment explanation
Indices: 42315310--42315339 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
42315300 GTTGTTGTTG
42315310 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
42315340 CTCAGTTCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:42319630 original size:27 final size:28
Alignment explanation
Indices: 42319588--42319657 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
42319578 ATTTTTAATG
42319588 CATG-TTTTAATATGTCATAG-CTAGTA
1 CATGTTTTTAATATGTCATAGTCTAGTA
* * *
42319614 CATGTTTTTAATTTGTCTTAGTCTATTA
1 CATGTTTTTAATATGTCATAGTCTAGTA
42319642 CATGTTTTTAATATGT
1 CATGTTTTTAATATGT
42319658 TCATGTTTCA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
26 4 0.11
27 14 0.37
28 20 0.53
ACGTcount: A:0.26, C:0.10, G:0.13, T:0.51
Consensus pattern (28 bp):
CATGTTTTTAATATGTCATAGTCTAGTA
Found at i:42320462 original size:16 final size:17
Alignment explanation
Indices: 42320431--42320463 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
42320421 AATAAATAAA
42320431 TTAACTAAATTAATTTT
1 TTAACTAAATTAATTTT
*
42320448 TTAATTAAA-TAATTTT
1 TTAACTAAATTAATTTT
42320464 CTCGATCCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
TTAACTAAATTAATTTT
Found at i:42325849 original size:33 final size:32
Alignment explanation
Indices: 42325807--42325915 Score: 156
Period size: 33 Copynumber: 3.5 Consensus size: 32
42325797 TTTGGTGGAT
42325807 TCAGCACTTAGCAACCACCAGTGATTCGGGGAA
1 TCAGCACTTAGCAACCACC-GTGATTCGGGGAA
42325840 TCAGCACTTAGCAACCACCGCTGATTCGGGGAA
1 TCAGCACTTAGCAACCACCG-TGATTCGGGGAA
*
42325873 TCAGCACTTAGCAACC-CC----TTGGGGGAA
1 TCAGCACTTAGCAACCACCGTGATTCGGGGAA
42325900 TCAGCACTTAGCAACC
1 TCAGCACTTAGCAACC
42325916 CCCTTTTATA
Statistics
Matches: 74, Mismatches: 1, Indels: 8
0.89 0.01 0.10
Matches are distributed among these distances:
27 24 0.32
32 3 0.04
33 47 0.64
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.18
Consensus pattern (32 bp):
TCAGCACTTAGCAACCACCGTGATTCGGGGAA
Found at i:42325896 original size:26 final size:27
Alignment explanation
Indices: 42325834--42325917 Score: 105
Period size: 27 Copynumber: 2.9 Consensus size: 27
42325824 CCAGTGATTC
*
42325834 GGGGAATCAGCACTTAGCAACCACCGCTGATTC
1 GGGGAATCAGCACTTAGCAA-C-CC-C---TTG
42325867 GGGGAATCAGCACTTAGCAACCCCTTG
1 GGGGAATCAGCACTTAGCAACCCCTTG
42325894 GGGGAATCAGCACTTAGCAACCCC
1 GGGGAATCAGCACTTAGCAACCCC
42325918 CTTTTATACT
Statistics
Matches: 50, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
27 26 0.52
30 1 0.02
31 2 0.04
32 1 0.02
33 20 0.40
ACGTcount: A:0.27, C:0.31, G:0.25, T:0.17
Consensus pattern (27 bp):
GGGGAATCAGCACTTAGCAACCCCTTG
Found at i:42331019 original size:39 final size:40
Alignment explanation
Indices: 42330974--42331198 Score: 233
Period size: 40 Copynumber: 5.7 Consensus size: 40
42330964 GCTCCTCGTT
* * * *
42330974 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
42331014 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
42331053 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
42331093 CAAAGGCCTTCGGGGCTTAACCCGGAACTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
42331133 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
42331174 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
42331199 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 22, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
39 38 0.24
40 105 0.67
41 14 0.09
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:42331207 original size:41 final size:41
Alignment explanation
Indices: 42331130--42331207 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
42331120 CTTGTATCTC
* * *
42331130 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
42331171 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
42331208 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:42332055 original size:18 final size:18
Alignment explanation
Indices: 42332032--42332069 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
42332022 CCATCACATA
42332032 GCAAGATTTAGACCATGG
1 GCAAGATTTAGACCATGG
42332050 GCAAGATTTAGACCATGG
1 GCAAGATTTAGACCATGG
42332068 GC
1 GC
42332070 TAGGTAGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (18 bp):
GCAAGATTTAGACCATGG
Found at i:42338987 original size:39 final size:40
Alignment explanation
Indices: 42338942--42339166 Score: 233
Period size: 40 Copynumber: 5.7 Consensus size: 40
42338932 GCTCCTCGTT
* * * *
42338942 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
42338982 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
42339021 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
42339061 CAAAGGCCTTCGGGGCTTAACCCGGAACTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
42339101 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
42339142 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
42339167 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 22, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
39 38 0.24
40 105 0.67
41 14 0.09
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:42339175 original size:41 final size:41
Alignment explanation
Indices: 42339098--42339175 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
42339088 CTTGTATCTC
* * *
42339098 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
42339139 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
42339176 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:42342947 original size:17 final size:17
Alignment explanation
Indices: 42342925--42342968 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
42342915 GATTAAGATC
42342925 GAGTGGAAAATCGAGGA
1 GAGTGGAAAATCGAGGA
*
42342942 GAGTGGAAAATTGAGGA
1 GAGTGGAAAATCGAGGA
42342959 GAGTGGAAAA
1 GAGTGGAAAA
42342969 GTACCAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.43, C:0.02, G:0.41, T:0.14
Consensus pattern (17 bp):
GAGTGGAAAATCGAGGA
Found at i:42344998 original size:14 final size:15
Alignment explanation
Indices: 42344973--42345002 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
42344963 ATTGGTTGAA
42344973 TGGAACTTGGTCATT
1 TGGAACTTGGTCATT
42344988 TGGAA-TTGGTCATT
1 TGGAACTTGGTCATT
42345002 T
1 T
42345003 TATGCCTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.20, C:0.10, G:0.27, T:0.43
Consensus pattern (15 bp):
TGGAACTTGGTCATT
Found at i:42354221 original size:23 final size:21
Alignment explanation
Indices: 42354185--42354228 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
42354175 TTTTAGGTCT
42354185 TTAGGAATTTATTTATTTAGTAA
1 TTAGGAATTTATTT-TTT-GTAA
42354208 TTAGG-ATTTAATTTTTTGTAA
1 TTAGGAATTT-ATTTTTTGTAA
42354229 AATAAAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 4 0.20
22 7 0.35
23 9 0.45
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.55
Consensus pattern (21 bp):
TTAGGAATTTATTTTTTGTAA
Found at i:42355114 original size:73 final size:72
Alignment explanation
Indices: 42354969--42355135 Score: 199
Period size: 73 Copynumber: 2.3 Consensus size: 72
42354959 AAAATAAGCA
* * * *
42354969 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAGACCTAAGCCCAACGACGTCGTTTCCCAAGCTTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAACATAAGCCCAACGACGCCGTTTCCCAAGCTTT
**
42355034 TGGGGAT
66 CAGGGAT
* * ****
42355041 TTAGCGGCGTTTCTGAGAAAGCGCCACAAAAAAACATAAGCCCAACGATGCCGTTTTGTGAGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCAC-AAAAAACATAAGCCCAACGACGCCGTTTCCCAAGCTT
42355106 TCAGGGAT
65 TCAGGGAT
* *
42355114 TTAGCGGCATTTTTAAGAAAGC
1 TTAGCGGCGTTTTTGAGAAAGC
42355136 ACCGCTAATG
Statistics
Matches: 79, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
72 25 0.32
73 54 0.68
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (72 bp):
TTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAACATAAGCCCAACGACGCCGTTTCCCAAGCTTT
CAGGGAT
Found at i:42355177 original size:114 final size:114
Alignment explanation
Indices: 42355040--42355376 Score: 514
Period size: 114 Copynumber: 3.0 Consensus size: 114
42355030 CTTTTGGGGA
* * *
42355040 TTTAGCGGCGTTTCTGAGAAAGCGCCACAAAAAAACATAAGCCCAACGATGCCGTTTTGTGAGCT
1 TTTAGCGGCGTTTCTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGCT
* *
42355105 TTCAGGGATTTAGCGGCATTTTTAAGAAAGCACCGCTAATGCTCAGGGC
66 TTCAGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
* **
42355154 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACATCGTTTTGTGAGCT
1 TTTAGCGGCGTTTCTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGCT
* *
42355219 TTCGGGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGC
66 TTCAGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
* ** *
42355268 ATTAGCGGCGCTTTCCCAGAAA-CGCCGCAAAAAAACCTAAGCCCAACGACGCTGTTTTGTGAGC
1 TTTAGCGGCG-TTTCTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGC
* *
42355332 TTTTAGGGACTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTC
65 TTTCAGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTC
42355377 CCAAAAGCGC
Statistics
Matches: 201, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
114 193 0.96
115 8 0.04
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.25
Consensus pattern (114 bp):
TTTAGCGGCGTTTCTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGCT
TTCAGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
Found at i:42355462 original size:94 final size:94
Alignment explanation
Indices: 42355281--42355462 Score: 269
Period size: 95 Copynumber: 1.9 Consensus size: 94
42355271 AGCGGCGCTT
* * * *
42355281 TCCCAGAAACGCCGCAAAAAAACCTAAGCCCAACGACGCTGTTTTGTGAGCTTTTAGGGACTTAG
1 TCCCAGAAACGCCGCAAAAAAACCTAAGCCCAACGACACCGTTTTCTGAGCTTTCAGGGACTTAG
42355346 CGGCGTTTTTAAGAAAGCGCCGCTAATGC
66 CGGCGTTTTTAAGAAAGCGCCGCTAATGC
* *
42355375 TCCCA-AAAGCGCCGCAAAAAAAACCTAAGCCCAACGACACCGTTTTCTGAGCTTTCGGGGATTT
1 TCCCAGAAA-CGCCGC-AAAAAAACCTAAGCCCAACGACACCGTTTTCTGAGCTTTCAGGGACTT
*
42355439 AGCGG-GTTTTTAAGAAAGTGCCGC
64 AGCGGCGTTTTTAAGAAAGCGCCGC
42355463 AAAAAATTAT
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
93 3 0.04
94 29 0.37
95 47 0.59
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.22
Consensus pattern (94 bp):
TCCCAGAAACGCCGCAAAAAAACCTAAGCCCAACGACACCGTTTTCTGAGCTTTCAGGGACTTAG
CGGCGTTTTTAAGAAAGCGCCGCTAATGC
Found at i:42355849 original size:14 final size:14
Alignment explanation
Indices: 42355830--42355863 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
42355820 AAGTATGGGT
42355830 TTAGGGATTATGGA
1 TTAGGGATTATGGA
42355844 TTAGGGATTATGGA
1 TTAGGGATTATGGA
42355858 TTAGGG
1 TTAGGG
42355864 GTTGAGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.38, T:0.35
Consensus pattern (14 bp):
TTAGGGATTATGGA
Found at i:42355908 original size:22 final size:23
Alignment explanation
Indices: 42355876--42355927 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
42355866 TGAGATTTAA
*
42355876 GGTTTAGGGGTTAGA-GGGTTAG
1 GGTTTAAGGGTTAGACGGGTTAG
*
42355898 GGTTTAAGGGTTAGACGTGTTAG
1 GGTTTAAGGGTTAGACGGGTTAG
*
42355921 GGGTTAA
1 GGTTTAA
42355928 AAGTTAGGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 14 0.54
23 12 0.46
ACGTcount: A:0.21, C:0.02, G:0.44, T:0.33
Consensus pattern (23 bp):
GGTTTAAGGGTTAGACGGGTTAG
Found at i:42355933 original size:23 final size:22
Alignment explanation
Indices: 42355885--42355934 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
42355875 AGGTTTAGGG
* **
42355885 GTTAGAGGGTTAGGGTTTAAGG
1 GTTAGAGGGTTAGGGGTTAAAA
*
42355907 GTTAGACGTGTTAGGGGTTAAAA
1 GTTAGA-GGGTTAGGGGTTAAAA
42355930 GTTAG
1 GTTAG
42355935 GGATTTAGGG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.26, C:0.02, G:0.40, T:0.32
Consensus pattern (22 bp):
GTTAGAGGGTTAGGGGTTAAAA
Found at i:42356193 original size:14 final size:13
Alignment explanation
Indices: 42356180--42356214 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
42356170 TAAGGTTTAG
42356180 GAGTTAGGGGTTA
1 GAGTTAGGGGTTA
42356193 GATGTTAGGGGTTAA
1 GA-GTTAGGGGTT-A
42356208 GAGTTAG
1 GAGTTAG
42356215 AGATTTAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 2 0.10
14 15 0.75
15 3 0.15
ACGTcount: A:0.26, C:0.00, G:0.43, T:0.31
Consensus pattern (13 bp):
GAGTTAGGGGTTA
Found at i:42356206 original size:21 final size:21
Alignment explanation
Indices: 42356176--42356215 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
42356166 GATTTAAGGT
* *
42356176 TTAGGAGTTAGGGGTTAGATG
1 TTAGGAGTTAAGAGTTAGATG
*
42356197 TTAGGGGTTAAGAGTTAGA
1 TTAGGAGTTAAGAGTTAGA
42356216 GATTTAAGGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.40, T:0.33
Consensus pattern (21 bp):
TTAGGAGTTAAGAGTTAGATG
Found at i:42356372 original size:296 final size:296
Alignment explanation
Indices: 42355711--42356373 Score: 804
Period size: 298 Copynumber: 2.2 Consensus size: 296
42355701 ATTATTTAAA
* * * * * * *
42355711 ATAATTGTAAAAGAGATAATAATAAATTTGTTTAGGGTTTTTG-GTTTAGGGTATATGATTTATT
1 ATAATTGTAAAAGAGATAATAATAAATTTATTGA-AGATTATGAGTATA-GGTATAT-AATTATT
* * * * * *
42355775 TAAAATTTAAGGCCGGTTTAGGAGTTCATATTTTAAGGTTTAGGGAAGTATGGGTTTAGGGATTA
63 TAAGATTTAAGGCCGGTTTAAGAGTTCATATTTTAAGGTTTAAGGAAGTACGGATTTAGGAATTA
* * *
42355840 TGGATTAGGGATTATGGATTAGGGGTTGAGATTTAAGGTTTAGGGGTTAGAGGGTTAGGGTTTAA
128 TGAATTAGGGATTATGGATTAAGGGTTGAGATTTAAGGTTTAGGAGTTAGAGGGTTAGGGTTTAA
* * * * * * *
42355905 GGGTTAGACGTGTTAGGGGTTAAAAGTTAGGGATTTAGGGGTCGAGTTAGGGTTTTGGGTTTAGA
193 GGGTTAGACGAGTTAGAGATTAAAAGTTAGAGATTCAGGGGTCGAGTTAAGGTTTTGAGTTTAGA
42355970 TTAATTATTTTTTAATTTATATTTTAAATATGTTCTTAT
258 TTAATTATTTTTTAATTTATATTTTAAATATGTTCTTAT
* * * * * * *
42356009 ATAATTGTAAAAGAGATAATAATAAATTTGTTTAAGGTTTTTAGTTTAGGGTATATGATTAATTT
1 ATAATTGTAAAAGAGATAATAATAAATTTATTGAAGATTATGAGTATA-GGTATATAATT-ATTT
42356074 AAGATTTAAGGCCGGTTTAAGAGTTCATATTTTAAGGTTTAAGG-AGTACGGATTTAGGAATTAT
64 AAGATTTAAGGCCGGTTTAAGAGTTCATATTTTAAGGTTTAAGGAAGTACGGATTTAGGAATTAT
* * *
42356138 GAATTAGGGATTATGGTTTAAGGGTTGAGATTTAAGGTTTAGGAGTTAG-GGGTTA-GATGTTAG
129 GAATTAGGGATTATGGATTAAGGGTTGAGATTTAAGGTTTAGGAGTTAGAGGGTTAGGGT-TTAA
* * *
42356201 GGGTTA-A-GAGTTAGAGATTTAAGGTTTCGAGATTCAGGGGTCGAGTTAAGGTTTTGAGTTTAG
193 GGGTTAGACGAGTTAGAGATTAAAAG-TTAGAGATTCAGGGGTCGAGTTAAGGTTTTGAGTTTAG
42356264 ATTAATTATTTTTTTAATTTATATTTTAAATATGTTCTTAT
257 ATTAATTA-TTTTTTAATTTATATTTTAAATATGTTCTTAT
* *
42356305 ATAATTGTAAAATAGATAATAATAAATCAAATATATTGAA-ATTATGAGTATA-GTTTA-AATTA
1 ATAATTGTAAAAGAGATAATAATAAAT----T-TATTGAAGATTATGAGTATAGGTATATAATTA
42356367 TTTAAGA
61 TTTAAGA
42356374 GATATATAAT
Statistics
Matches: 319, Mismatches: 36, Indels: 22
0.85 0.10 0.06
Matches are distributed among these distances:
294 12 0.04
295 44 0.14
296 81 0.25
297 72 0.23
298 96 0.30
300 9 0.03
301 5 0.02
ACGTcount: A:0.32, C:0.02, G:0.25, T:0.41
Consensus pattern (296 bp):
ATAATTGTAAAAGAGATAATAATAAATTTATTGAAGATTATGAGTATAGGTATATAATTATTTAA
GATTTAAGGCCGGTTTAAGAGTTCATATTTTAAGGTTTAAGGAAGTACGGATTTAGGAATTATGA
ATTAGGGATTATGGATTAAGGGTTGAGATTTAAGGTTTAGGAGTTAGAGGGTTAGGGTTTAAGGG
TTAGACGAGTTAGAGATTAAAAGTTAGAGATTCAGGGGTCGAGTTAAGGTTTTGAGTTTAGATTA
ATTATTTTTTAATTTATATTTTAAATATGTTCTTAT
Found at i:42357038 original size:88 final size:89
Alignment explanation
Indices: 42356888--42357051 Score: 276
Period size: 88 Copynumber: 1.9 Consensus size: 89
42356878 CGCCGCAAAA
* * *
42356888 AATAAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGCATTGCAAAACGGCATCATTTTGT
1 AATAAATCAATTTATAAAAAAACAAAATAAAAAATTTTTAGAATAGCAAAACGGCATCATTTTGT
*
42356953 TGAAAATGAAATAGCGGCGTTTTT
66 TCAAAATGAAATAGCGGCGTTTTT
*
42356977 AATAAATCAATTTAT-AAAAAACAAAATAAAAAATTTTTAGAATAGCAAAACGGCGTCATTTTGT
1 AATAAATCAATTTATAAAAAAACAAAATAAAAAATTTTTAGAATAGCAAAACGGCATCATTTTGT
42357041 TCAAAATGAAA
66 TCAAAATGAAA
42357052 AAAATTTTGC
Statistics
Matches: 70, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
88 55 0.79
89 15 0.21
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.30
Consensus pattern (89 bp):
AATAAATCAATTTATAAAAAAACAAAATAAAAAATTTTTAGAATAGCAAAACGGCATCATTTTGT
TCAAAATGAAATAGCGGCGTTTTT
Found at i:42357169 original size:22 final size:24
Alignment explanation
Indices: 42357132--42357184 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
42357122 AAAACGCCGC
*
42357132 AAAAAATAAATCAATTTATAA-AT
1 AAAAAATAAATAAATTTATAACAT
*
42357155 AAAAAATAAA-AAATTTTTAACAT
1 AAAAAATAAATAAATTTATAACAT
42357178 AACAAAA
1 AA-AAAA
42357185 CGGCATCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 8 0.31
23 14 0.54
24 4 0.15
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (24 bp):
AAAAAATAAATAAATTTATAACAT
Done.