Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 258 of 290
Found at i:88917335 original size:46 final size:46
Alignment explanation
Indices: 88917192--88917328 Score: 124
Period size: 47 Copynumber: 3.0 Consensus size: 46
88917182 CGCATCCCTG
*
88917192 AGTGAACTCAGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATCTC
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATCTC
* * * *
88917240 A-CGAACTCGGACTCAACTCAACGAGTTCGGACAT-TTGCATCCA--TA
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCT-CAACCATCTC
88917285 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
88917329 CTAGTGACAT
Statistics
Matches: 72, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
44 7 0.10
45 3 0.04
46 28 0.39
47 29 0.40
48 1 0.01
49 3 0.04
50 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (46 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCTC
Found at i:88923805 original size:39 final size:39
Alignment explanation
Indices: 88923762--88923839 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
88923752 TAACCATGAA
88923762 ACCTGTTTCATATAAAACTAGACTCAATAAGGAATTTAG
1 ACCTGTTTCATATAAAACTAGACTCAATAAGGAATTTAG
*
88923801 ACCTGTTTCATATAAAACTAGACTTAATAAGGAATTTAG
1 ACCTGTTTCATATAAAACTAGACTCAATAAGGAATTTAG
88923840 GCATATAAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32
Consensus pattern (39 bp):
ACCTGTTTCATATAAAACTAGACTCAATAAGGAATTTAG
Found at i:88927956 original size:28 final size:28
Alignment explanation
Indices: 88927860--88927958 Score: 83
Period size: 28 Copynumber: 3.4 Consensus size: 28
88927850 GTGTTAACTG
* * * *
88927860 GGCCTTAGCCCATATCAATATTAATCTG
1 GGCCGTAGCCCATATCAGTATCAATCTA
* *
88927888 GGCCGTAGCCCGT-TACAGTATCAGAGTATA
1 GGCCGTAGCCCATAT-CAGTATCA-A-TCTA
*
88927918 TTGGCCCTAGCCCATATCAGTATCAATCTA
1 --GGCCGTAGCCCATATCAGTATCAATCTA
88927948 GGCCGTAGCCC
1 GGCCGTAGCCC
88927959 TATTACAAGT
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
27 1 0.02
28 27 0.49
29 1 0.02
30 5 0.09
31 1 0.02
32 19 0.35
33 1 0.02
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.26
Consensus pattern (28 bp):
GGCCGTAGCCCATATCAGTATCAATCTA
Found at i:88927978 original size:60 final size:59
Alignment explanation
Indices: 88927860--88927981 Score: 149
Period size: 60 Copynumber: 2.0 Consensus size: 59
88927850 GTGTTAACTG
* * * *
88927860 GGCCTTAGCCCATATCAATATTAATCTGGGCCGTAGCCCGTTACAGTATCAGAGTATATT
1 GGCCCTAGCCCATATCAATATCAATCTAGGCCGTAGCCCATTACAG-ATCAGAGTATATT
*
88927920 GGCCCTAGCCCATATCAGTATCAATCTAGGCCGTAGCCCTATTACA-AGTC-GAGATATATT
1 GGCCCTAGCCCATATCAATATCAATCTAGGCCGTAGCCC-ATTACAGA-TCAGAG-TATATT
88927980 GG
1 GG
88927982 GCATTGGCCA
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
59 4 0.07
60 45 0.83
61 5 0.09
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (59 bp):
GGCCCTAGCCCATATCAATATCAATCTAGGCCGTAGCCCATTACAGATCAGAGTATATT
Found at i:88937000 original size:20 final size:20
Alignment explanation
Indices: 88936977--88937023 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
88936967 TGCCCACATG
88936977 GGCGTGTCCCAAACCACACA
1 GGCGTGTCCCAAACCACACA
*
88936997 GGCGTGTCCCAAACCACACG
1 GGCGTGTCCCAAACCACACA
88937017 GGCGTGT
1 GGCGTGT
88937024 GACCCCTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.23, C:0.36, G:0.28, T:0.13
Consensus pattern (20 bp):
GGCGTGTCCCAAACCACACA
Found at i:88944557 original size:16 final size:16
Alignment explanation
Indices: 88944536--88944569 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
88944526 TTGTTTGATG
88944536 TAAATGAATCAAAATA
1 TAAATGAATCAAAATA
88944552 TAAATGAATCAAAATA
1 TAAATGAATCAAAATA
88944568 TA
1 TA
88944570 TATGTAAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.26
Consensus pattern (16 bp):
TAAATGAATCAAAATA
Found at i:88948092 original size:23 final size:23
Alignment explanation
Indices: 88948066--88948137 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 23
88948056 GAGCTAAAAC
88948066 GGTAAGCCCCTAAGGACTGAAAT
1 GGTAAGCCCCTAAGGACTGAAAT
* *
88948089 GGTAAGCTCCGAA-GATCTG-AAT
1 GGTAAGCCCCTAAGGA-CTGAAAT
*
88948111 GGTAA-CCTCATAAGAGA-TGAAAT
1 GGTAAGCC-CCTAAG-GACTGAAAT
88948134 GGTA
1 GGTA
88948138 GTTTGCAACA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
21 1 0.03
22 15 0.38
23 21 0.54
24 2 0.05
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (23 bp):
GGTAAGCCCCTAAGGACTGAAAT
Found at i:88948462 original size:17 final size:17
Alignment explanation
Indices: 88948442--88948476 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
88948432 ATCTTGGTCT
88948442 ATATATTATCAAATTCA
1 ATATATTATCAAATTCA
88948459 ATATATTATCAAATTCA
1 ATATATTATCAAATTCA
88948476 A
1 A
88948477 CATACTCAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATATTATCAAATTCA
Found at i:88949331 original size:8 final size:8
Alignment explanation
Indices: 88949318--88949344 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
88949308 CTGTAGGCCT
88949318 TAATAAAA
1 TAATAAAA
88949326 TAATAAAA
1 TAATAAAA
88949334 TAATAAAA
1 TAATAAAA
88949342 TAA
1 TAA
88949345 ATATTTTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (8 bp):
TAATAAAA
Found at i:88950964 original size:15 final size:15
Alignment explanation
Indices: 88950944--88950973 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
88950934 ATGGGCTAGG
*
88950944 TAGAACAGTAAGCAA
1 TAGAACACTAAGCAA
88950959 TAGAACACTAAGCAA
1 TAGAACACTAAGCAA
88950974 GAATGATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.17, G:0.17, T:0.13
Consensus pattern (15 bp):
TAGAACACTAAGCAA
Found at i:88951829 original size:12 final size:12
Alignment explanation
Indices: 88951814--88951857 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
88951804 ACACGGGCTA
88951814 GCACACAGCCTG
1 GCACACAGCCTG
* *
88951826 GCACACAACCTA
1 GCACACAGCCTG
* *
88951838 GCACACGGCATG
1 GCACACAGCCTG
88951850 GCACACAG
1 GCACACAG
88951858 GCGTGTGGGG
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.32, C:0.39, G:0.23, T:0.07
Consensus pattern (12 bp):
GCACACAGCCTG
Found at i:88951831 original size:24 final size:24
Alignment explanation
Indices: 88951811--88951856 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
88951801 GAGACACGGG
*
88951811 CTAGCACACAGCCTGGCACACAAC
1 CTAGCACACAGCATGGCACACAAC
*
88951835 CTAGCACACGGCATGGCACACA
1 CTAGCACACAGCATGGCACACA
88951857 GGCGTGTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.33, C:0.39, G:0.20, T:0.09
Consensus pattern (24 bp):
CTAGCACACAGCATGGCACACAAC
Found at i:88952995 original size:13 final size:13
Alignment explanation
Indices: 88952977--88953010 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
88952967 CAAAATAAAG
88952977 TCATTTCTTAGCT
1 TCATTTCTTAGCT
88952990 TCATTTCTTAGCT
1 TCATTTCTTAGCT
*
88953003 TTATTTCT
1 TCATTTCT
88953011 CACCCAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.15, C:0.21, G:0.06, T:0.59
Consensus pattern (13 bp):
TCATTTCTTAGCT
Found at i:88955833 original size:38 final size:38
Alignment explanation
Indices: 88955791--88955870 Score: 142
Period size: 38 Copynumber: 2.1 Consensus size: 38
88955781 ATAGAAAAAT
* *
88955791 AAGAATAGGGGAGGTGGTAGTTTCGGCTAGAGAGGAAG
1 AAGAATAGGGGAGGTGGCAGTTTCGGCTAGAGAGGAAA
88955829 AAGAATAGGGGAGGTGGCAGTTTCGGCTAGAGAGGAAA
1 AAGAATAGGGGAGGTGGCAGTTTCGGCTAGAGAGGAAA
88955867 AAGA
1 AAGA
88955871 GAGAAAAGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.35, C:0.06, G:0.42, T:0.16
Consensus pattern (38 bp):
AAGAATAGGGGAGGTGGCAGTTTCGGCTAGAGAGGAAA
Found at i:88975656 original size:46 final size:46
Alignment explanation
Indices: 88975589--88975766 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
88975579 TGTAACCCGC
* * *
88975589 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCAGG-TGTTCGCAT
1 CCATAAGAGAACTCGGACTCAACTCAACGAGTTC-GGATGTTCGCAT
* * *
88975635 CCATAAGAGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAG-TT
1 CCATAAGAGAACTCGGACTCAACTCAACGAGTTCGGATG-TTCGCAT
* *** **
88975681 ACATTTCACGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGA-GAACTCGGACTCAACTCAACGAGTTCGGATGTTCGCAT
*
88975728 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATG
1 CCATAAGAGAACTCGGACTCAACTCAACGAGTTCGGATG
88975767 CTCAACCATC
Statistics
Matches: 106, Mismatches: 22, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
45 2 0.02
46 69 0.65
47 35 0.33
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGAGAACTCGGACTCAACTCAACGAGTTCGGATGTTCGCAT
Found at i:88975725 original size:93 final size:93
Alignment explanation
Indices: 88975597--88975767 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
88975587 GCCCATAAGT
* **
88975597 GAACTCGGACTCAACTCAATGAGCTCAGGTGTTCGCATCCATAAGAGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAGGCATTCGCATCCATAAGAGAACTCGGACTCAACTCAA
88975662 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
* *
88975690 GAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCAGG-CATTCGCATCCATAAGAGAACTCGGACTCAACTCA
88975754 ACGAGTTCGGATGC
65 ACGAGTTCGGATGC
88975768 TCAACCATCC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 2 0.03
93 70 0.97
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCAGGCATTCGCATCCATAAGAGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:88983239 original size:46 final size:46
Alignment explanation
Indices: 88983172--88983506 Score: 277
Period size: 46 Copynumber: 7.2 Consensus size: 46
88983162 TGTAACCCGC
* * *
88983172 CCATAAGTGAACTTGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
* * * * *
88983218 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-TTCGCAT
* * * *
88983264 ACATTTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCA--TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
* * * * *
88983311 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-TTCGCAT
* * * *
88983357 ACATTTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCA--TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
* * * * *
88983404 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-TTCGCAT
* * * *
88983450 ACATTTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCA--TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
88983497 CCATAAGTGA
1 CCATAAGTGA
88983507 CATGTCACTT
Statistics
Matches: 218, Mismatches: 56, Indels: 30
0.72 0.18 0.10
Matches are distributed among these distances:
45 6 0.03
46 107 0.49
47 99 0.45
48 6 0.03
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
Found at i:88983289 original size:47 final size:47
Alignment explanation
Indices: 88983226--88983484 Score: 286
Period size: 47 Copynumber: 5.6 Consensus size: 47
88983216 ATCCATAAGT
88983226 GAACTCGGACTCAACTCAACGAGTTCAGATGCCTAGTTACATTTCAC
1 GAACTCGGACTCAACTCAACGAGTTCAGATGCCTAGTTACATTTCAC
* * * * *
88983273 GAACTCGGACTCAACTCAACGAGTTC-G--GAC-A-TTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCAGATGCCTAGTT-ACAT--TTCA-C
88983319 GAACTCGGACTCAACTCAACGAGTTCAGATGCCTAGTTACATTTCAC
1 GAACTCGGACTCAACTCAACGAGTTCAGATGCCTAGTTACATTTCAC
* * * * *
88983366 GAACTCGGACTCAACTCAACGAGTTC-G--GAC-A-TTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCAGATGCCTAGTT-ACAT--TTCA-C
88983412 GAACTCGGACTCAACTCAACGAGTTCAGATGCCTAGTTACATTTCAC
1 GAACTCGGACTCAACTCAACGAGTTCAGATGCCTAGTTACATTTCAC
88983459 GAACTCGGACTCAACTCAACGAGTTC
1 GAACTCGGACTCAACTCAACGAGTTC
88983485 GGACATTCGC
Statistics
Matches: 174, Mismatches: 20, Indels: 36
0.76 0.09 0.16
Matches are distributed among these distances:
42 4 0.02
43 8 0.05
44 4 0.02
45 4 0.02
46 54 0.31
47 80 0.46
48 4 0.02
49 4 0.02
50 8 0.05
51 4 0.02
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (47 bp):
GAACTCGGACTCAACTCAACGAGTTCAGATGCCTAGTTACATTTCAC
Found at i:88983308 original size:93 final size:93
Alignment explanation
Indices: 88983180--88983506 Score: 618
Period size: 93 Copynumber: 3.5 Consensus size: 93
88983170 GCCCATAAGT
* * * *
88983180 GAACTTGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
88983245 CGAGTTCAGATGCCTAGTTACATTTCAC
66 CGAGTTCAGATGCCTAGTTACATTTCAC
88983273 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
88983338 CGAGTTCAGATGCCTAGTTACATTTCAC
66 CGAGTTCAGATGCCTAGTTACATTTCAC
88983366 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
88983431 CGAGTTCAGATGCCTAGTTACATTTCAC
66 CGAGTTCAGATGCCTAGTTACATTTCAC
88983459 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGA
88983507 CATGTCACTT
Statistics
Matches: 230, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 230 1.00
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCAGATGCCTAGTTACATTTCAC
Found at i:88985194 original size:25 final size:25
Alignment explanation
Indices: 88985160--88985214 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
88985150 GGCCTTAAAT
88985160 GGTTAGTTTTGTAATTTGATAATAA
1 GGTTAGTTTTGTAATTTGATAATAA
*
88985185 GGTTAGTTTTGTAATTTGTTAATAA
1 GGTTAGTTTTGTAATTTGATAATAA
88985210 GGTTA
1 GGTTA
88985215 ATTAAAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.29, C:0.00, G:0.22, T:0.49
Consensus pattern (25 bp):
GGTTAGTTTTGTAATTTGATAATAA
Found at i:88987758 original size:24 final size:24
Alignment explanation
Indices: 88987722--88987798 Score: 61
Period size: 24 Copynumber: 3.3 Consensus size: 24
88987712 GGTTGTGTCG
88987722 TTTA-TTTCTGTAAGTGTTTATACA
1 TTTATTTTC-GTAAGTGTTTATACA
** * *
88987746 TTTATTTTCGTAAG-GAGTCT-CG
1 TTTATTTTCGTAAGTGTTTATACA
* * *
88987768 TTTATTTTCGTAGGTTTTTATATA
1 TTTATTTTCGTAAGTGTTTATACA
88987792 TTTATTT
1 TTTATTT
88987799 ATTTGCGTTT
Statistics
Matches: 39, Mismatches: 11, Indels: 6
0.70 0.20 0.11
Matches are distributed among these distances:
22 14 0.36
23 5 0.13
24 16 0.41
25 4 0.10
ACGTcount: A:0.21, C:0.08, G:0.14, T:0.57
Consensus pattern (24 bp):
TTTATTTTCGTAAGTGTTTATACA
Found at i:88992988 original size:19 final size:19
Alignment explanation
Indices: 88992952--88992990 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
88992942 TTTTCATCAT
* *
88992952 AGTAAAATAAAATAATAAA
1 AGTAAAACAAAACAATAAA
*
88992971 AGTAAAACAAAACCATAAA
1 AGTAAAACAAAACAATAAA
88992990 A
1 A
88992991 ATAGTTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.72, C:0.08, G:0.05, T:0.15
Consensus pattern (19 bp):
AGTAAAACAAAACAATAAA
Found at i:88993502 original size:28 final size:29
Alignment explanation
Indices: 88993429--88993516 Score: 94
Period size: 28 Copynumber: 3.1 Consensus size: 29
88993419 AGCATGGCTG
* * * *
88993429 CCAGATACAGA-AA-ATGTGACAGAGTCA
1 CCAGATACAGATAATTTGTGGCATAGCCA
*
88993456 CCAGATACAGATATTTTGTGGCAGT-GCCA
1 CCAGATACAGATAATTTGTGGCA-TAGCCA
88993485 CCAGA-ACAGATAATTTGTGGCATAGCCA
1 CCAGATACAGATAATTTGTGGCATAGCCA
88993513 CCAG
1 CCAG
88993517 GACGCTTCCT
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
27 12 0.24
28 25 0.49
29 14 0.27
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (29 bp):
CCAGATACAGATAATTTGTGGCATAGCCA
Found at i:89000828 original size:19 final size:19
Alignment explanation
Indices: 89000792--89000830 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
89000782 TTTTCATCAT
* *
89000792 AGTAAAATAAAATAATAAA
1 AGTAAAACAAAACAATAAA
*
89000811 AGTAAAACAAAACCATAAA
1 AGTAAAACAAAACAATAAA
89000830 A
1 A
89000831 ATAATTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.72, C:0.08, G:0.05, T:0.15
Consensus pattern (19 bp):
AGTAAAACAAAACAATAAA
Found at i:89001342 original size:28 final size:28
Alignment explanation
Indices: 89001294--89001359 Score: 89
Period size: 28 Copynumber: 2.3 Consensus size: 28
89001284 GTGACAGAGT
* *
89001294 CACCAGATACAGATATTTTGTGGCAGT-GC
1 CACCAGA-ACAGATAATTTGTGGCA-TAAC
89001323 CACCAGAACAGATAATTTGTGGCATAAC
1 CACCAGAACAGATAATTTGTGGCATAAC
89001351 CACCAGAAC
1 CACCAGAAC
89001360 GCTTCCTCCA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 1 0.03
28 26 0.76
29 7 0.21
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (28 bp):
CACCAGAACAGATAATTTGTGGCATAAC
Found at i:89001509 original size:28 final size:28
Alignment explanation
Indices: 89001466--89001526 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
89001456 TAACCCTAGC
*
89001466 GGTATAAAGGTCATTTAGCATACATAGG
1 GGTATAAAGGTAATTTAGCATACATAGG
* *
89001494 GGTATAATGGTAATTTTGCATACATAGG
1 GGTATAAAGGTAATTTAGCATACATAGG
89001522 GGTAT
1 GGTAT
89001527 TCTAGTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.33, C:0.08, G:0.26, T:0.33
Consensus pattern (28 bp):
GGTATAAAGGTAATTTAGCATACATAGG
Found at i:89004716 original size:42 final size:42
Alignment explanation
Indices: 89004564--89004727 Score: 160
Period size: 42 Copynumber: 3.9 Consensus size: 42
89004554 AATCATTCCA
* *
89004564 ATGCCATATCCCAGATATGGTCTTACA-TAGGATCTCATATCG
1 ATGCCATATCCCAGATATGGTCTTACACGA-AATCTCATATCG
* * * *
89004606 ATGCCAATAGCTCA-ACTATGGTCTTACACG-ATTCTCATATCA
1 ATGCC-ATATCCCAGA-TATGGTCTTACACGAAATCTCATATCG
* * *
89004648 ATTCCATGT-CCAGACATGGTCTTACACGAAATCTCATAAT-G
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCAT-ATCG
89004689 ATGCCATATCCCAGATATGGTCTTACACGTAAA-CTCATA
1 ATGCCATATCCCAGATATGGTCTTACACG-AAATCTCATA
89004728 ACCCTAATGT
Statistics
Matches: 98, Mismatches: 16, Indels: 17
0.75 0.12 0.13
Matches are distributed among these distances:
40 15 0.15
41 18 0.18
42 44 0.45
43 21 0.21
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
Found at i:89012268 original size:42 final size:40
Alignment explanation
Indices: 89012105--89012269 Score: 159
Period size: 42 Copynumber: 3.9 Consensus size: 40
89012095 AATCATTCCA
* * * *
89012105 ATGCCATATCCTAGATATGGTCTTACATGGGATCTCATATCG
1 ATGCCATATCCCA-ATATGGTCTTACA-CGAAACTCATATCG
* ** *
89012147 ATGCCAATAGCCCAACTATGGTCTTACACGATTCTCATATCA
1 ATGCC-ATATCCCAA-TATGGTCTTACACGAAACTCATATCG
* *
89012189 ATGCCATGTCCCAGATATGGTCTTACACGAAATCTCATAGCG
1 ATGCCATATCCCA-ATATGGTCTTACACGAAA-CTCATATCG
*
89012231 ATGTCATATCCCGAATATGGTCTTACACGTAAACTCATA
1 ATGCCATATCCC-AATATGGTCTTACACG-AAACTCATA
89012270 ACCCTAATGT
Statistics
Matches: 103, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
41 21 0.20
42 60 0.58
43 22 0.21
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.30
Consensus pattern (40 bp):
ATGCCATATCCCAATATGGTCTTACACGAAACTCATATCG
Found at i:89012268 original size:84 final size:84
Alignment explanation
Indices: 89012103--89012269 Score: 212
Period size: 84 Copynumber: 2.0 Consensus size: 84
89012093 AGAATCATTC
* * ** *
89012103 CAATGCCATATCCTAGATATGGTCTTACATGGGATCTCATATCGATGCCAATAGCCCAACTATGG
1 CAATGCCATATCCCAGATATGGTCTTACACGAAATCTCATAGCGATGCCAATAGCCCAACTATGG
**
89012168 TCTTACACGATTCTCATAT
66 TCTTACACGAAACTCATAT
* * *
89012187 CAATGCCATGTCCCAGATATGGTCTTACACGAAATCTCATAGCGATGTC-ATATCCCGAA-TATG
1 CAATGCCATATCCCAGATATGGTCTTACACGAAATCTCATAGCGATGCCAATAGCCC-AACTATG
89012250 GTCTTACACGTAAACTCATA
65 GTCTTACACG-AAACTCATA
89012270 ACCCTAATGT
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
83 20 0.28
84 51 0.72
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (84 bp):
CAATGCCATATCCCAGATATGGTCTTACACGAAATCTCATAGCGATGCCAATAGCCCAACTATGG
TCTTACACGAAACTCATAT
Found at i:89014106 original size:30 final size:30
Alignment explanation
Indices: 89014071--89014134 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
89014061 TATAGAGGAC
*
89014071 TTGGTCATTTTGTTATGTTTCATAATTGAT
1 TTGGTCATTTTGTCATGTTTCATAATTGAT
89014101 TTGGTCATTTTGTCATGTTTCATAATTGAT
1 TTGGTCATTTTGTCATGTTTCATAATTGAT
89014131 TTGG
1 TTGG
89014135 CCAAATGTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.19, C:0.08, G:0.19, T:0.55
Consensus pattern (30 bp):
TTGGTCATTTTGTCATGTTTCATAATTGAT
Found at i:89016082 original size:49 final size:49
Alignment explanation
Indices: 89015916--89016140 Score: 297
Period size: 49 Copynumber: 4.5 Consensus size: 49
89015906 TGAGGTCGCA
* * * * * *
89015916 TGTGTAGTACTAAGTGCAGGCTACAATGCGTACCCGAAAACTGTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-T-TGGTCACG
* **
89015967 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT-GGTCACG
89016017 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACG
* * *
89016066 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACG
* *
89016115 TGTGCAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
89016141 TGCGTATCAG
Statistics
Matches: 156, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
49 78 0.50
50 46 0.29
51 32 0.21
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.28
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACG
Found at i:89016094 original size:99 final size:100
Alignment explanation
Indices: 89015909--89016151 Score: 310
Period size: 99 Copynumber: 2.4 Consensus size: 100
89015899 TCTATTGTGA
* * * *
89015909 GGTCGCATGTGTAGTACTAAGTGCAGGCTACAATGCGTACCCGAAAACTGTGATCACGTGTGTAG
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGAAAACTGTGATCACGTGTGTAG
* **
89015974 TACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
66 TACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * *
89016009 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-T-TGGTCACGTGTGTA
1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGAAAACTGTGATCACGTGTGTA
*
89016072 GTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
65 GTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * * *
89016108 GGTCGCATGTGCAGTACTATGTGCAGGCTACTATGCGTATCAGA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGA
89016152 TAGCTTTGGC
Statistics
Matches: 123, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
98 37 0.30
99 45 0.37
100 1 0.01
101 40 0.33
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.28
Consensus pattern (100 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGAAAACTGTGATCACGTGTGTAG
TACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:89021231 original size:30 final size:30
Alignment explanation
Indices: 89021195--89021255 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
89021185 ACTGACTGAC
*
89021195 TAAGGATTTGACGGAAAATTCTCGAAAGAA
1 TAAGGATTTGACGAAAAATTCTCGAAAGAA
89021225 TAAGGATTTGACGAAAAATTCTCGAAAGAA
1 TAAGGATTTGACGAAAAATTCTCGAAAGAA
89021255 T
1 T
89021256 GACCATCCCC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.25
Consensus pattern (30 bp):
TAAGGATTTGACGAAAAATTCTCGAAAGAA
Found at i:89031260 original size:47 final size:47
Alignment explanation
Indices: 89031207--89031892 Score: 1086
Period size: 47 Copynumber: 14.5 Consensus size: 47
89031197 ATTCAGCCAA
*
89031207 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGCGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
89031254 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
* *
89031301 GAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
* *
89031348 GAAAGTGTATGTATGTAATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
*
89031395 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGCGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
89031442 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
*
89031489 GAAAGTGTATGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGT
1 GAAA--G--TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
*
89031540 GAAAGTGTATGTATATATG-TAAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAGTGTA--TATATGTGAT-AAGGCCTAATGGCCGATGTGATGAATGT
*
89031589 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGCGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
*
89031636 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGCGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
* *
89031683 GAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
* *
89031730 GAAAGTGTATATATGTAATAAGGCCTAATGGCCGATGCGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
89031777 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
* * * * * * * *
89031824 GAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTAATGGATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
* *
89031871 GAAAGTGCATAAATGTGATAAG
1 GAAAGTGTATATATGTGATAAG
89031893 TCCCGAAAGG
Statistics
Matches: 594, Mismatches: 37, Indels: 16
0.92 0.06 0.02
Matches are distributed among these distances:
47 502 0.85
48 2 0.00
49 45 0.08
51 45 0.08
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
Found at i:89032067 original size:37 final size:37
Alignment explanation
Indices: 89032011--89032089 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
89032001 CCGAGCTCTA
* ** *
89032011 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGAAGATTATGTCCGGGT
*
89032048 AAGACCCGATAACTTCGTGTGAAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGAAGATTATGTCCGGGT
89032085 AAGAC
1 AAGAC
89032090 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGAAGATTATGTCCGGGT
Found at i:89036201 original size:20 final size:19
Alignment explanation
Indices: 89036139--89036210 Score: 51
Period size: 20 Copynumber: 3.6 Consensus size: 19
89036129 TATCAGGATA
89036139 CACCAAAGTG-ATAAACAAGG
1 CACCAAAGTGCAT-AAC-AGG
**
89036159 CATGAAAGTGCAT-ACAGAAG
1 CACCAAAGTGCATAACAG--G
89036179 CACCAAAGTGCATAACTAGG
1 CACCAAAGTGCATAAC-AGG
89036199 CA-CAAATGTGCA
1 CACCAAA-GTGCA
89036211 GTTAGGGCAT
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
18 2 0.05
19 6 0.14
20 28 0.67
21 4 0.10
22 2 0.05
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.14
Consensus pattern (19 bp):
CACCAAAGTGCATAACAGG
Found at i:89036294 original size:40 final size:40
Alignment explanation
Indices: 89036223--89036360 Score: 127
Period size: 40 Copynumber: 3.5 Consensus size: 40
89036213 TAGGGCATCA
* * * * *
89036223 TAATGCAAACAAGAGCATGAATAT-GCTATCAAGAGTACTG
1 TAATGCTAACAGGAGCACGAATGTGGC-ATCAAGAGCACTG
* * * *
89036263 TAATGCTAATAGGAGCAC-AGATGTGGGATCAAAAGCACTA
1 TAATGCTAACAGGAGCACGA-ATGTGGCATCAAGAGCACTG
* * * *
89036303 TAGTGCTAACAAGAGCACGAATGTGTCATCAAGAGCATTG
1 TAATGCTAACAGGAGCACGAATGTGGCATCAAGAGCACTG
89036343 TAATGCTAACAGGAGCAC
1 TAATGCTAACAGGAGCAC
89036361 CTTAGTGCTA
Statistics
Matches: 76, Mismatches: 19, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
39 1 0.01
40 73 0.96
41 2 0.03
ACGTcount: A:0.39, C:0.17, G:0.23, T:0.21
Consensus pattern (40 bp):
TAATGCTAACAGGAGCACGAATGTGGCATCAAGAGCACTG
Found at i:89046631 original size:55 final size:55
Alignment explanation
Indices: 89046569--89046862 Score: 192
Period size: 55 Copynumber: 5.4 Consensus size: 55
89046559 CCTGGTCTAC
89046569 TAATGGCCGGCACCAAGTACGAAAAAAAATTCAAAATTTTTTTGTGCTGGCCTTG
1 TAATGGCCGGCACCAAGTACGAAAAAAAATTCAAAATTTTTTTGTGCTGGCCTTG
* ** ** * * **** * * * **
89046624 TAATGGCCGGCACC-AG-ACTACTAGTATTTAAAAAAAAATTGGTCCTGGTCTAC
1 TAATGGCCGGCACCAAGTACGAAAAAAAATTCAAAATTTTTTTGTGCTGGCCTTG
** * * *
89046677 TAATGGCTAGCACCAAGTACAAAAAAAAATTCAAATTTTTTTTGTGTTGGCCTTG
1 TAATGGCCGGCACCAAGTACGAAAAAAAATTCAAAATTTTTTTGTGCTGGCCTTG
* * * * *
89046732 TAATGGCCGGCACCAGAGTACCAATATTTAAAAA---AGAAA---TTTGGTCCTGGTCTTC
1 TAATGGCCGGCACCA-AGTACGAA-A---AAAAATTCA-AAATTTTTTTGTGCTGGCCTTG
* *
89046787 TAATGGCCGGCACCAAGCAAGAAAAAAAATTC-AAATTTTTTTAGTGCTGGCCTTG
1 TAATGGCCGGCACCAAGTACGAAAAAAAATTCAAAATTTTTTT-GTGCTGGCCTTG
*
89046842 TAATGGCCGACACCAGAGTAC
1 TAATGGCCGGCACCA-AGTAC
89046863 TAGTATTTAA
Statistics
Matches: 168, Mismatches: 55, Indels: 31
0.66 0.22 0.12
Matches are distributed among these distances:
50 5 0.03
51 3 0.02
53 34 0.20
54 12 0.07
55 95 0.57
56 10 0.06
57 2 0.01
58 2 0.01
60 5 0.03
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (55 bp):
TAATGGCCGGCACCAAGTACGAAAAAAAATTCAAAATTTTTTTGTGCTGGCCTTG
Found at i:89046812 original size:110 final size:108
Alignment explanation
Indices: 89046498--89046909 Score: 551
Period size: 108 Copynumber: 3.7 Consensus size: 108
89046488 AAAAAAATTG
* *
89046498 GTGCTGGCCTTGTAATGGCCTGCACCAG-GCTACCAGTATTTAAAAAATATATTTTTTTGGTCCT
1 GTGCTGGCCTTGTAATGGCCGGCACCAGAG-TACCAGTATTTAAAAAA-A-A----ATTGGTCCT
* *
89046562 GGTCTACTAATGGCCGGCACCAAGTACGAAAAAAAATTCAAAATTTTTTT
59 GGTCTACTAATGGCCGGCACCAAGTAAGAAAAAAAATTCAAATTTTTTTT
* *
89046612 GTGCTGGCCTTGTAATGGCCGGCACCAGACTACTAGTATTTAAAAAAAAATTGGTCCTGGTCTAC
1 GTGCTGGCCTTGTAATGGCCGGCACCAGAGTACCAGTATTTAAAAAAAAATTGGTCCTGGTCTAC
**
89046677 TAATGGCTAGCACCAAGTACA-AAAAAAAATTCAAATTTTTTTT
66 TAATGGCCGGCACCAAGTA-AGAAAAAAAATTCAAATTTTTTTT
* *
89046720 GTGTTGGCCTTGTAATGGCCGGCACCAGAGTACCAATATTTAAAAAAGAAATTTGGTCCTGGTCT
1 GTGCTGGCCTTGTAATGGCCGGCACCAGAGTACCAGTATTTAAAAAA-AAA-TTGGTCCTGGTCT
* * *
89046785 TCTAATGGCCGGCACCAAGCAAGAAAAAAAATTCAAATTTTTTTA
64 ACTAATGGCCGGCACCAAGTAAGAAAAAAAATTCAAATTTTTTTT
* * * *
89046830 GTGCTGGCCTTGTAATGGCCGACACCAGAGTACTAGTATTTAAAAAAAAATTGGTCTTGG-CTTT
1 GTGCTGGCCTTGTAATGGCCGGCACCAGAGTACCAGTATTTAAAAAAAAATTGGTCCTGGTC-TA
89046894 CTAATGGCCGGCACCA
65 CTAATGGCCGGCACCA
89046910 GGGACTTTTT
Statistics
Matches: 270, Mismatches: 22, Indels: 18
0.87 0.07 0.06
Matches are distributed among these distances:
107 1 0.00
108 123 0.46
109 7 0.03
110 94 0.35
112 1 0.00
113 1 0.00
114 43 0.16
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30
Consensus pattern (108 bp):
GTGCTGGCCTTGTAATGGCCGGCACCAGAGTACCAGTATTTAAAAAAAAATTGGTCCTGGTCTAC
TAATGGCCGGCACCAAGTAAGAAAAAAAATTCAAATTTTTTTT
Found at i:89048938 original size:14 final size:14
Alignment explanation
Indices: 89048919--89048945 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
89048909 AATTAAATAA
89048919 AATATAAAATTTTG
1 AATATAAAATTTTG
89048933 AATATAAAATTTT
1 AATATAAAATTTT
89048946 ATAAATTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (14 bp):
AATATAAAATTTTG
Found at i:89048977 original size:18 final size:18
Alignment explanation
Indices: 89048954--89049020 Score: 82
Period size: 18 Copynumber: 3.8 Consensus size: 18
89048944 TTATAAATTT
*
89048954 AAATGAAAATAAATACTA
1 AAATGAAAATAAATAATA
* *
89048972 AAATGAAAATAAATATTT
1 AAATGAAAATAAATAATA
*
89048990 AAATGAAAATAAAAAATA
1 AAATGAAAATAAATAATA
*
89049008 ATATGAAAA-AAAT
1 AAATGAAAATAAAT
89049021 TTATATTAGG
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
17 3 0.07
18 39 0.93
ACGTcount: A:0.69, C:0.01, G:0.06, T:0.24
Consensus pattern (18 bp):
AAATGAAAATAAATAATA
Found at i:89048992 original size:36 final size:35
Alignment explanation
Indices: 89048950--89049020 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 35
89048940 AATTTTATAA
* *
89048950 ATTTAAATGAAAATAAATACTAAAATGAAAATAAAT
1 ATTTAAATGAAAATAAAAAATAAAATGAAAA-AAAT
*
89048986 ATTTAAATGAAAATAAAAAATAATATGAAAAAAAT
1 ATTTAAATGAAAATAAAAAATAAAATGAAAAAAAT
89049021 TTATATTAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 4 0.12
36 28 0.88
ACGTcount: A:0.66, C:0.01, G:0.06, T:0.27
Consensus pattern (35 bp):
ATTTAAATGAAAATAAAAAATAAAATGAAAAAAAT
Found at i:89049156 original size:5 final size:6
Alignment explanation
Indices: 89049141--89049196 Score: 87
Period size: 6 Copynumber: 9.5 Consensus size: 6
89049131 AAATGAAATG
*
89049141 AAATTG AAATT- AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
*
89049188 AAATGA AAA
1 AAATTA AAA
89049197 AAAAAGTTGA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
5 5 0.10
6 43 0.90
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (6 bp):
AAATTA
Found at i:89049233 original size:11 final size:11
Alignment explanation
Indices: 89049217--89049247 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
89049207 AAAGACCCTT
89049217 CCTATGTCAGG
1 CCTATGTCAGG
*
89049228 CCTATGTTAGG
1 CCTATGTCAGG
89049239 CCTATGTCA
1 CCTATGTCA
89049248 CTAAAACTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.19, C:0.26, G:0.23, T:0.32
Consensus pattern (11 bp):
CCTATGTCAGG
Found at i:89049349 original size:54 final size:54
Alignment explanation
Indices: 89049282--89049389 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
89049272 CCAATGGCCG
89049282 ACCTTAACCCACCTTTTTTTTTCATTTCATATTTTTTTTCCAATTTTGCCCTTA
1 ACCTTAACCCACCTTTTTTTTTCATTTCATATTTTTTTTCCAATTTTGCCCTTA
89049336 ACCTTAACCCACCTTTTTTTTTCATTTCATATTTTTTTTCCAATTTTGCCCTTA
1 ACCTTAACCCACCTTTTTTTTTCATTTCATATTTTTTTTCCAATTTTGCCCTTA
89049390 CTTTAGCCAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.19, C:0.26, G:0.02, T:0.54
Consensus pattern (54 bp):
ACCTTAACCCACCTTTTTTTTTCATTTCATATTTTTTTTCCAATTTTGCCCTTA
Found at i:89055642 original size:109 final size:107
Alignment explanation
Indices: 89055390--89055698 Score: 383
Period size: 107 Copynumber: 2.9 Consensus size: 107
89055380 ATAAAAAAAA
* *
89055390 TTAAATATTGGTACTCTAGTGCC-AGCCATTACAAGGCCAGCACAAAAAAAAAATTGAA-TTTTT
1 TTAAATATTGGTACTCTGGTGCCGA-CCATTACAAGGCCAGCAC-CAAAAAAAATTGAATTTTTT
** * *
89055453 TCGTACTTGGTGCCACCCATTACAAGGCCAAGACCAATTTTTTT
64 TCGTACTTGGTGCCGGCCATTAGAAGACCAAGACCAATTTTTTT
* * * *
89055497 TTAAATATTGGTAGT-TCGGTGCTGGCCATTACAAGGCCAGCACCAAAAAAATTTGAATTTTTTT
1 TTAAATATTGGTACTCT-GGTGCCGACCATTACAAGGCCAGCACCAAAAAAAATTGAATTTTTTT
* * *
89055561 CATACTTGGTGTCGGCCATTAGAAGACCAGGACCAAAATTTTTTT
65 CGTACTTGGTGCCGGCCATTAGAAGACCAAGACC--AATTTTTTT
* * *
89055606 TTAAATACTGGTACTCTGGTGCCGACCATTATAAGGCCAGCACCAAAAAAAATTGAATTTTTTTT
1 TTAAATATTGGTACTCTGGTGCCGACCATTACAAGGCCAGCACCAAAAAAAATTGAATTTTTTTC
* *
89055671 GTAC-TGTTGCCGGCCATTAGAAGGCCAA
66 GTACTTGGTGCCGGCCATTAGAAGACCAA
89055699 AACAAACAAA
Statistics
Matches: 171, Mismatches: 25, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
106 13 0.08
107 69 0.40
108 20 0.12
109 68 0.40
110 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Consensus pattern (107 bp):
TTAAATATTGGTACTCTGGTGCCGACCATTACAAGGCCAGCACCAAAAAAAATTGAATTTTTTTC
GTACTTGGTGCCGGCCATTAGAAGACCAAGACCAATTTTTTT
Found at i:89060547 original size:3 final size:3
Alignment explanation
Indices: 89060503--89060528 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
89060493 GATGGGCAAC
89060503 TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TC
89060529 TGATTTCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:89062351 original size:22 final size:23
Alignment explanation
Indices: 89062312--89062364 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
89062302 CAGGTCATTG
*
89062312 GAGCTTACGTATTTAGCTCGAA-A
1 GAGCTTACGTATTCAGCTC-AATA
*
89062335 GAGCTTA-TTATTCAGCTCAATA
1 GAGCTTACGTATTCAGCTCAATA
89062357 GAGCTTAC
1 GAGCTTAC
89062365 TGTTTATCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 2 0.08
22 17 0.65
23 7 0.27
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (23 bp):
GAGCTTACGTATTCAGCTCAATA
Found at i:89062364 original size:45 final size:46
Alignment explanation
Indices: 89062256--89062366 Score: 113
Period size: 46 Copynumber: 2.4 Consensus size: 46
89062246 GAACTCACCC
89062256 CAGCTC-ATATGAGCTTACTGATTCAGCTCGTAAAAGCCTACTATTT
1 CAGCTCAATA-GAGCTTACTGATTCAGCTCGTAAAAGCCTACTATTT
* * * * * *
89062302 CAGGTCATTGGAGCTTAC-GTATTTAGCTCG-AAAGAGCTTATTA-TT
1 CAGCTCAATAGAGCTTACTG-ATTCAGCTCGTAAA-AGCCTACTATTT
89062347 CAGCTCAATAGAGCTTACTG
1 CAGCTCAATAGAGCTTACTG
89062367 TTTATCAACT
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
45 21 0.40
46 30 0.58
47 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (46 bp):
CAGCTCAATAGAGCTTACTGATTCAGCTCGTAAAAGCCTACTATTT
Found at i:89070376 original size:35 final size:36
Alignment explanation
Indices: 89070337--89070454 Score: 111
Period size: 35 Copynumber: 3.3 Consensus size: 36
89070327 TAATATTTCA
89070337 ATCCAA-AATATCAAAACACCATCCTTTTAGCATTT
1 ATCCAAGAATATCAAAACACCATCCTTTTAGCATTT
* * ** **
89070372 ATCCAATAATACCGAATGC-CC--CCTTTCTAATATTT
1 ATCCAAGAATATC-AAAACACCATCCTTT-TAGCATTT
89070407 CAATCCAA-AATATCAAAACACCATCCTTTTAGCATTT
1 --ATCCAAGAATATCAAAACACCATCCTTTTAGCATTT
89070444 ATCCAAGAATA
1 ATCCAAGAATA
89070455 CCGTATGCAC
Statistics
Matches: 64, Mismatches: 10, Indels: 17
0.70 0.11 0.19
Matches are distributed among these distances:
34 5 0.08
35 21 0.33
36 18 0.28
37 15 0.23
38 5 0.08
ACGTcount: A:0.39, C:0.26, G:0.04, T:0.31
Consensus pattern (36 bp):
ATCCAAGAATATCAAAACACCATCCTTTTAGCATTT
Found at i:89070436 original size:72 final size:72
Alignment explanation
Indices: 89070319--89070462 Score: 270
Period size: 72 Copynumber: 2.0 Consensus size: 72
89070309 CTCATATTTT
*
89070319 CCCCTTTCTAATATTTCAATCCAAAATATCAAAACACCATCCTTTTAGCATTTATCCAATAATAC
1 CCCCTTTCTAATATTTCAATCCAAAATATCAAAACACCATCCTTTTAGCATTTATCCAAGAATAC
89070384 CGAATGC
66 CGAATGC
89070391 CCCCTTTCTAATATTTCAATCCAAAATATCAAAACACCATCCTTTTAGCATTTATCCAAGAATAC
1 CCCCTTTCTAATATTTCAATCCAAAATATCAAAACACCATCCTTTTAGCATTTATCCAAGAATAC
*
89070456 CGTATGC
66 CGAATGC
89070463 ACAATTTGTC
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.32
Consensus pattern (72 bp):
CCCCTTTCTAATATTTCAATCCAAAATATCAAAACACCATCCTTTTAGCATTTATCCAAGAATAC
CGAATGC
Found at i:89072246 original size:54 final size:54
Alignment explanation
Indices: 89072182--89072288 Score: 205
Period size: 54 Copynumber: 2.0 Consensus size: 54
89072172 TCTATCCGAC
89072182 ACGATAGAAATAGGTACCCCGTGTAATCTCACAATCTGAGAAACATACAATTCG
1 ACGATAGAAATAGGTACCCCGTGTAATCTCACAATCTGAGAAACATACAATTCG
*
89072236 ACGATAGAAATAGGTACCCCGTGTAATCTCACAATCTGAGAAACGTACAATTC
1 ACGATAGAAATAGGTACCCCGTGTAATCTCACAATCTGAGAAACATACAATTC
89072289 AGCTAGTTTA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.22
Consensus pattern (54 bp):
ACGATAGAAATAGGTACCCCGTGTAATCTCACAATCTGAGAAACATACAATTCG
Found at i:89077748 original size:28 final size:28
Alignment explanation
Indices: 89077685--89077807 Score: 149
Period size: 28 Copynumber: 4.4 Consensus size: 28
89077675 ATATTAAGTC
* *
89077685 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATACAATCAAACT
* *
89077712 TGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATACAATCAAACT
*
89077740 CGCACACTTAGTGCTACACAATCAAACT
1 CGCACACTTAGTGCTATACAATCAAACT
* * * *
89077768 TGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATACAA-TCAAACT
89077797 CGCACACTTAG
1 CGCACACTTAG
89077808 CGCCAATCTC
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
27 21 0.25
28 47 0.57
29 15 0.18
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATACAATCAAACT
Found at i:89077913 original size:101 final size:101
Alignment explanation
Indices: 89077769--89077969 Score: 402
Period size: 101 Copynumber: 2.0 Consensus size: 101
89077759 AATCAAACTT
89077769 GCACACTTAGTGCTGTACAATTTAAACCCGCACACTTAGCGCCAATCTCATGATCATAAATGTTT
1 GCACACTTAGTGCTGTACAATTTAAACCCGCACACTTAGCGCCAATCTCATGATCATAAATGTTT
89077834 ATACCCGCACACTTAGTGCCGAGATCAACAACTCAC
66 ATACCCGCACACTTAGTGCCGAGATCAACAACTCAC
89077870 GCACACTTAGTGCTGTACAATTTAAACCCGCACACTTAGCGCCAATCTCATGATCATAAATGTTT
1 GCACACTTAGTGCTGTACAATTTAAACCCGCACACTTAGCGCCAATCTCATGATCATAAATGTTT
89077935 ATACCCGCACACTTAGTGCCGAGATCAACAACTCA
66 ATACCCGCACACTTAGTGCCGAGATCAACAACTCA
89077970 ATACATCTCA
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 100 1.00
ACGTcount: A:0.32, C:0.29, G:0.14, T:0.25
Consensus pattern (101 bp):
GCACACTTAGTGCTGTACAATTTAAACCCGCACACTTAGCGCCAATCTCATGATCATAAATGTTT
ATACCCGCACACTTAGTGCCGAGATCAACAACTCAC
Found at i:89078235 original size:61 final size:61
Alignment explanation
Indices: 89078140--89078261 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
89078130 TAATTCCAAG
89078140 TCGGCTACTCGATGACCTTCGATTTCCCCTTGTTGGACGCCTCTCCTTTAGGTTCTTGAGC
1 TCGGCTACTCGATGACCTTCGATTTCCCCTTGTTGGACGCCTCTCCTTTAGGTTCTTGAGC
89078201 TCGGCTACTCGATGACCTTCGATTTCCCCTTGTTGGACGCCTCTCCTTTAGGTTCTTGAGC
1 TCGGCTACTCGATGACCTTCGATTTCCCCTTGTTGGACGCCTCTCCTTTAGGTTCTTGAGC
89078262 ATAAATAAAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.11, C:0.31, G:0.21, T:0.36
Consensus pattern (61 bp):
TCGGCTACTCGATGACCTTCGATTTCCCCTTGTTGGACGCCTCTCCTTTAGGTTCTTGAGC
Found at i:89089209 original size:9 final size:9
Alignment explanation
Indices: 89089197--89089221 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
89089187 AAAATGTATT
89089197 TTATTTTTA
1 TTATTTTTA
89089206 TTATTTTTA
1 TTATTTTTA
89089215 TTATTTT
1 TTATTTT
89089222 AATGTCTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTATTTTTA
Found at i:89090631 original size:48 final size:46
Alignment explanation
Indices: 89090511--89090631 Score: 136
Period size: 46 Copynumber: 2.6 Consensus size: 46
89090501 TGATATGTGT
* * *
89090511 GCTAATGTAAGACATGTCTGGGACATGCATCGGCCACATTATTAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACAATATTAAA
* * *
89090557 GCCAGTGTAAGATATGTCTGGGACATGCATCGGCCTCGAGATA-TACAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-A-ATATTA-AA
* *
89090605 GCTAGTGTAAGACCTATCTGGGACATG
1 GCTAGTGTAAGACATGTCTGGGACATG
89090632 GCGTTAGCTT
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
46 33 0.53
47 3 0.05
48 26 0.42
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACAATATTAAA
Found at i:89095902 original size:29 final size:29
Alignment explanation
Indices: 89095839--89095906 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
89095829 TAGTCAACCG
*
89095839 CGCACACTTGGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
89095868 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
89095897 CGCACACTTA
1 CGCACACTTA
89095907 CCTTTTTCCG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 3 0.09
29 30 0.91
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:89096030 original size:175 final size:174
Alignment explanation
Indices: 89095728--89096056 Score: 595
Period size: 175 Copynumber: 1.9 Consensus size: 174
89095718 AACTCAAGGT
* *
89095728 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
* *
89095793 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAGTCAACCGCGCACACTTGGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
89095858 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
89095902 ACTTACCTTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTAT
1 ACTTACC-TTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTAT
89095967 AGAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATG
65 AGAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATG
* *
89096032 TACTTTAAACTCGCACACTTAGTGC
130 CACTTTAAACTCACACACTTAGTGC
89096057 TGTACAATTT
Statistics
Matches: 148, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
174 7 0.05
175 141 0.95
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:89096048 original size:29 final size:30
Alignment explanation
Indices: 89096009--89096087 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
89095999 CTTAATAATC
89096009 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
89096039 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
89096068 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
89096088 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:89102904 original size:15 final size:15
Alignment explanation
Indices: 89102884--89102913 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
89102874 TGTGTTAGAA
89102884 CACATTCGAGTGGCT
1 CACATTCGAGTGGCT
*
89102899 CACATTCTAGTGGCT
1 CACATTCGAGTGGCT
89102914 ATAGCAGTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.30
Consensus pattern (15 bp):
CACATTCGAGTGGCT
Found at i:89108680 original size:153 final size:153
Alignment explanation
Indices: 89108477--89108929 Score: 685
Period size: 153 Copynumber: 3.0 Consensus size: 153
89108467 ACTATCCGAG
* * * **
89108477 TTTGTTTTTGAGTTTAATTTGAGATTTCTTAATACTAATTAAAAATTTAAAAATACTATTAAGCT
1 TTTGTTTTTGAGTTTAAATTGAGACTTCTTAATACTAATTAAAAAATTAAAAATGTTATTAAGCT
* * * *
89108542 TGTGAATTACTTAAATCTAGTATTCA-ATTACTCAAATCCAATCACCGTGATAACTACAATAATT
66 TGTGAAATACTTAAATCTAGTATT-AGAATACTCAAATCCAGTCACCGTGATAACTAGAATAATT
* *
89108606 TGTGAGAATACGTATTTCGTATAA
130 TCTGAGAATATGTATTTCGTATAA
*
89108630 TTTGTTTTTGAGTTTAAATTGAAACTTCTTAATACTAATTAAAAAATTAAAAATGTTATTAAGCT
1 TTTGTTTTTGAGTTTAAATTGAGACTTCTTAATACTAATTAAAAAATTAAAAATGTTATTAAGCT
* * * *
89108695 TGTGAAATACTTAAATCTAGTATTAGAATACTCAAATCTAGTAACAGTGATAATTAGAATAATTT
66 TGTGAAATACTTAAATCTAGTATTAGAATACTCAAATCCAGTCACCGTGATAACTAGAATAATTT
* *
89108760 CTGAGAATATGTATTTTGTATAG
131 CTGAGAATATGTATTTCGTATAA
* *
89108783 TTTGTTATTGAGTTTAAATTGAGACTTCTTAATACTAATTAAAAACTTAAAAATGTTATTAAGCT
1 TTTGTTTTTGAGTTTAAATTGAGACTTCTTAATACTAATTAAAAAATTAAAAATGTTATTAAGCT
* *
89108848 TGTGAAATAATTAAATCTAGCATTAGAATA-TCAAATCCAGTCACCGTGATAACTAGAATAATTT
66 TGTGAAATACTTAAATCTAGTATTAGAATACTCAAATCCAGTCACCGTGATAACTAGAATAATTT
89108912 CTGAGAATATGTATTTCG
131 CTGAGAATATGTATTTCG
89108930 CTTAAGAAAG
Statistics
Matches: 271, Mismatches: 28, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
152 48 0.18
153 223 0.82
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.40
Consensus pattern (153 bp):
TTTGTTTTTGAGTTTAAATTGAGACTTCTTAATACTAATTAAAAAATTAAAAATGTTATTAAGCT
TGTGAAATACTTAAATCTAGTATTAGAATACTCAAATCCAGTCACCGTGATAACTAGAATAATTT
CTGAGAATATGTATTTCGTATAA
Found at i:89111456 original size:27 final size:28
Alignment explanation
Indices: 89111372--89111469 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
89111362 CATGAGATTG
* * * *
89111372 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
89111401 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
89111429 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
89111456 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
89111470 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:89111480 original size:27 final size:27
Alignment explanation
Indices: 89111400--89111482 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
89111390 TAAATTGTAC
* *
89111400 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
89111428 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
89111455 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
89111482 A
1 A
89111483 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:89111483 original size:29 final size:27
Alignment explanation
Indices: 89111372--89111483 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
89111362 CATGAGATTG
** * *
89111372 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
89111401 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
89111429 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
89111456 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
89111484 TTTTGAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:89121777 original size:44 final size:44
Alignment explanation
Indices: 89121727--89121814 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
89121717 GTTGCACAAG
89121727 GGAAAGAGGACTATGTGTGCAGATTGAAGAAGAGCTTGTATGGT
1 GGAAAGAGGACTATGTGTGCAGATTGAAGAAGAGCTTGTATGGT
89121771 GGAAAGAGGACTATGTGTGCAGATTGAAGAAGAGCTTGTATGGT
1 GGAAAGAGGACTATGTGTGCAGATTGAAGAAGAGCTTGTATGGT
89121815 TTGAAGCAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.32, C:0.07, G:0.36, T:0.25
Consensus pattern (44 bp):
GGAAAGAGGACTATGTGTGCAGATTGAAGAAGAGCTTGTATGGT
Found at i:89121818 original size:21 final size:20
Alignment explanation
Indices: 89121750--89121820 Score: 54
Period size: 21 Copynumber: 3.3 Consensus size: 20
89121740 TGTGTGCAGA
89121750 TTGAAGAAGAGCTTGTATGG
1 TTGAAGAAGAGCTTGTATGG
* * *
89121770 TGGAAAGAGGA-CTATGTGTGCAG
1 TTG-AAGAAGAGCT-TGTATG--G
89121793 ATTGAAGAAGAGCTTGTATGG
1 -TTGAAGAAGAGCTTGTATGG
89121814 TTTGAAG
1 -TTGAAG
89121821 CAAGCTCCAA
Statistics
Matches: 38, Mismatches: 7, Indels: 11
0.68 0.12 0.20
Matches are distributed among these distances:
20 4 0.11
21 18 0.47
23 12 0.32
24 4 0.11
ACGTcount: A:0.31, C:0.06, G:0.35, T:0.28
Consensus pattern (20 bp):
TTGAAGAAGAGCTTGTATGG
Found at i:89127868 original size:26 final size:26
Alignment explanation
Indices: 89127833--89127887 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
89127823 TAATTCATGG
* *
89127833 TGGTGCTTGATATCGAGTGGTATCTA
1 TGGTGCTTGATATCAAGTGGCATCTA
*
89127859 TGGTGTTTGATATCAAGTGGCATCTA
1 TGGTGCTTGATATCAAGTGGCATCTA
89127885 TGG
1 TGG
89127888 GATATGTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.20, C:0.11, G:0.31, T:0.38
Consensus pattern (26 bp):
TGGTGCTTGATATCAAGTGGCATCTA
Found at i:89128087 original size:2 final size:2
Alignment explanation
Indices: 89128074--89128104 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
89128064 CAATACTGAA
*
89128074 AC AC AC AT AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
89128105 TATATATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.45, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:89131435 original size:14 final size:14
Alignment explanation
Indices: 89131416--89131448 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
89131406 AAGCAAATAA
89131416 TTAAAATATTTATT
1 TTAAAATATTTATT
89131430 TTAAAATATTTATT
1 TTAAAATATTTATT
89131444 TTAAA
1 TTAAA
89131449 CATGCTAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTAAAATATTTATT
Found at i:89133923 original size:20 final size:20
Alignment explanation
Indices: 89133898--89133939 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
89133888 TTGATCTCAA
89133898 AAATGATAAAAAATTTATTT
1 AAATGATAAAAAATTTATTT
*
89133918 AAATGATAAAAATTTTATTT
1 AAATGATAAAAAATTTATTT
89133938 AA
1 AA
89133940 TTATTTAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (20 bp):
AAATGATAAAAAATTTATTT
Found at i:89137295 original size:36 final size:36
Alignment explanation
Indices: 89137248--89137320 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
89137238 TTAAGATATC
89137248 CATTTTGGTATACGGTCTTTTGCCTTCACCGCTCTT
1 CATTTTGGTATACGGTCTTTTGCCTTCACCGCTCTT
89137284 CATTTTGGTATACGGTCTTTTGCCTTCACCGCTCTT
1 CATTTTGGTATACGGTCTTTTGCCTTCACCGCTCTT
89137320 C
1 C
89137321 CAGTCTCACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.11, C:0.29, G:0.16, T:0.44
Consensus pattern (36 bp):
CATTTTGGTATACGGTCTTTTGCCTTCACCGCTCTT
Found at i:89140817 original size:33 final size:33
Alignment explanation
Indices: 89140778--89140844 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
89140768 ATATTTTAAA
*
89140778 AGGATAGTTTAAACAAATATTTTTAATTATATC
1 AGGATAGTTTAAACAAATATTTTTAATTACATC
*
89140811 AGGATAGTTTAAACAATTATTTTTAATTACATC
1 AGGATAGTTTAAACAAATATTTTTAATTACATC
89140844 A
1 A
89140845 AAATATTCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (33 bp):
AGGATAGTTTAAACAAATATTTTTAATTACATC
Found at i:89153172 original size:47 final size:49
Alignment explanation
Indices: 89153071--89153173 Score: 131
Period size: 46 Copynumber: 2.1 Consensus size: 49
89153061 TTGCACATTG
* *
89153071 TCACATATCACACACCGAAGCCATAGCCCAGCTATGGTCTTACACGGAAA
1 TCACATAT-ACACACCGAAGCCATAGCCCAGATATAGTCTTACACGGAAA
* * *
89153121 -CACATAT-CACACTGATGCCATA-TCCAGATATAGTCTTACACGGAAA
1 TCACATATACACACCGAAGCCATAGCCCAGATATAGTCTTACACGGAAA
89153167 TCACATA
1 TCACATA
89153174 ATCATATTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
46 21 0.45
47 19 0.40
49 7 0.15
ACGTcount: A:0.36, C:0.29, G:0.14, T:0.21
Consensus pattern (49 bp):
TCACATATACACACCGAAGCCATAGCCCAGATATAGTCTTACACGGAAA
Found at i:89157401 original size:18 final size:19
Alignment explanation
Indices: 89157375--89157411 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
89157365 TTTTAACCTT
*
89157375 TTAATATAAA-AATAAAAG
1 TTAAAATAAATAATAAAAG
89157393 TTAAAATAAATAATAAAAG
1 TTAAAATAAATAATAAAAG
89157412 AAAAACTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (19 bp):
TTAAAATAAATAATAAAAG
Found at i:89158065 original size:40 final size:40
Alignment explanation
Indices: 89158010--89158091 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
89158000 AAACCGAACC
89158010 AGGTGGGTAACGAGAAACCTAAAAATCAGTAAACTACGAA
1 AGGTGGGTAACGAGAAACCTAAAAATCAGTAAACTACGAA
*
89158050 AGGTGGGTAACGAGAAACCTGAAAATCAGTAAACTACGAA
1 AGGTGGGTAACGAGAAACCTAAAAATCAGTAAACTACGAA
89158090 AG
1 AG
89158092 CTGAAATTGA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.46, C:0.15, G:0.24, T:0.15
Consensus pattern (40 bp):
AGGTGGGTAACGAGAAACCTAAAAATCAGTAAACTACGAA
Found at i:89165692 original size:3 final size:3
Alignment explanation
Indices: 89165684--89165732 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
89165674 AGTCATTCTG
89165684 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
89165732 T
1 T
89165733 NNNNNNNNNN
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:89167597 original size:19 final size:20
Alignment explanation
Indices: 89167553--89167597 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
89167543 AACGTCTCTT
*
89167553 TATGCA-TTCATTTCATGCA
1 TATGCATTTCATTACATGCA
89167572 T-TCGCATTTCATTACAT-CA
1 TAT-GCATTTCATTACATGCA
89167591 TATGCAT
1 TATGCAT
89167598 CAAAGATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
18 1 0.05
19 11 0.50
20 10 0.45
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.42
Consensus pattern (20 bp):
TATGCATTTCATTACATGCA
Found at i:89171356 original size:46 final size:45
Alignment explanation
Indices: 89171306--89171436 Score: 128
Period size: 43 Copynumber: 2.9 Consensus size: 45
89171296 ATCAAAGATA
89171306 ACAGATCTCGCCTTCCCATGCTGGTGGCGAAGCAGATCGAAGGA-AT
1 ACAGATCTCGCCTTCCCATGCTGGTGGCGAAGCAGATCGAA--ATAT
* * * * *
89171352 ACAGATCTTGTCTT--CATGTACTGG-CGTGAAGTAGATC-AAATAT
1 ACAGATCTCGCCTTCCCATG--CTGGTGGCGAAGCAGATCGAAATAT
* *
89171395 ACAGATCTCGCATTCCCATACTGGTGGCGAAGCAGATCGAAA
1 ACAGATCTCGCCTTCCCATGCTGGTGGCGAAGCAGATCGAAA
89171437 GAAAGTAGAT
Statistics
Matches: 66, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
42 1 0.02
43 17 0.26
44 16 0.24
45 16 0.24
46 16 0.24
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (45 bp):
ACAGATCTCGCCTTCCCATGCTGGTGGCGAAGCAGATCGAAATAT
Found at i:89171366 original size:90 final size:90
Alignment explanation
Indices: 89171261--89171661 Score: 512
Period size: 89 Copynumber: 4.5 Consensus size: 90
89171251 GTTGAAAAGC
* * *
89171261 AGCAGATATTGTCTTCATGTACTGGCGTAAAGTAGATCAAAGATAACAGATCTCGCCTTCCCATG
1 AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTCGCCTTCCCATA
*
89171326 CTGGTGGCGAAGCAGATCGAAGGAA
66 CTGGTGGCGAAGCAGATCGAAAGAA
* *
89171351 TA-CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAATAT-ACAGATCTCGCATTCCCAT
1 -AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTCGCCTTCCCAT
89171414 ACTGGTGGCGAAGCAGATCGAAAGAA
65 ACTGGTGGCGAAGCAGATCGAAAGAA
* * * * *
89171440 AGTAGATATTGTCTTCATGTA-TCAGCGTGAAGTAGATCAAAG-TCAACAGATCTTGTCTTCCCA
1 AGCAGATCTTGTCTTCATGTACT-GGCGTGAAGTAGATCAAAGAT-AACAGATCTCGCCTTCCCA
89171503 TACTGGTGGCGAAGCAGATC-AAAGAA
64 TACTGGTGGCGAAGCAGATCGAAAGAA
* * * *
89171529 AGTAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGA-AACAGATCTTGTCTCCCCATA
1 AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTCGCCTTCCCATA
* * * * *
89171593 CTGGTGGTGGAGTAGGTTG-AAGAA
66 CTGGTGGCGAAGCAGATCGAAAGAA
* *
89171617 AACAGATCGTGTCTTCATGTACTGGCGTGAAAG-AGATCAAAGATA
1 AGCAGATCTTGTCTTCATGTACTGGCGTG-AAGTAGATCAAAGATA
89171662 GTAGGTCCTG
Statistics
Matches: 277, Mismatches: 24, Indels: 20
0.86 0.07 0.06
Matches are distributed among these distances:
88 77 0.28
89 124 0.45
90 75 0.27
91 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.26
Consensus pattern (90 bp):
AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTCGCCTTCCCATA
CTGGTGGCGAAGCAGATCGAAAGAA
Found at i:89171640 original size:45 final size:43
Alignment explanation
Indices: 89171263--89171659 Score: 264
Period size: 45 Copynumber: 9.0 Consensus size: 43
89171253 TGAAAAGCAG
* *
89171263 CAGATATTGTCTTCATGTACTGGCGTAAAGTAGATCAAAGATAA
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGA-AA
* * * * * *
89171307 CAGATCTCGCCTTCCCATG--CTGGTGGCGAAGCAGATCGAAGGAATA
1 CAGATCTTGTCTT--CATGTACTGG-CGTGAAGTAGATC-AAAGAA-A
* *
89171353 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAATATA
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAA
* *** * * *
89171396 CAGATCTCG-CATTCCCATACTGGTGGCGAAGCAGATCGAAAGAAA
1 CAGATCTTGTC-TTCATGTACTGG-CGTGAAGTAGATC-AAAGAAA
* * * *
89171441 GTAGATATTGTCTTCATGTA-TCAGCGTGAAGTAGATCAAAGTCAA
1 -CAGATCTTGTCTTCATGTACT-GGCGTGAAGTAGATCAAAG-AAA
*** * * *
89171486 CAGATCTTGTCTTCCCATACTGGTGGCGAAGCAGATCAAAGAAA
1 CAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGAAA
*
89171530 GTAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAA
1 -CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAA
* *** * * * **
89171574 CAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGGTTGAAGAAAA
1 CAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAG-AAA
*
89171619 CAGATCGTGTCTTCATGTACTGGCGTGAAAG-AGATCAAAGA
1 CAGATCTTGTCTTCATGTACTGGCGTG-AAGTAGATCAAAGA
89171660 TAGTAGGTCC
Statistics
Matches: 260, Mismatches: 73, Indels: 41
0.70 0.20 0.11
Matches are distributed among these distances:
42 1 0.00
43 37 0.14
44 90 0.35
45 95 0.37
46 36 0.14
47 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.26
Consensus pattern (43 bp):
CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAA
Found at i:89171950 original size:264 final size:264
Alignment explanation
Indices: 89171609--89172176 Score: 1010
Period size: 264 Copynumber: 2.1 Consensus size: 264
89171599 GTGGAGTAGG
* * *
89171609 TTGAAGAAAACAGATCGTGTCTTCATGTACTGGCGTGAAAGAGATCAAAGATAGTAGGTCCTGTC
1 TTGAA-AAAGCAGATCCTGTCTTCATGTACTGGCGTGAAGGAGATCAAAGATAGTAGGTCCTGTC
* * * *
89171674 TTCCTATATTGGTAGCGAAGTGGATCGAATATACATATTTTATCTTCCCATACCGGCGGCGAAGT
65 TTCCTATATTGGTAGCGAAGTGGATCAAAAATACATATTTTATCTTCCCATACCGACAGCGAAGT
89171739 AGATTGAAGATTACAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTT
130 AGATTGAAGATTACAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTT
*
89171804 ACCTCCCTGAAGTTGCAGTGGAGTATATTGAAGCCAGTAATTCTACCTCCCCGGTCGGCAGTGGA
195 ACCTCCCTGAAGTTGCAGTGGAGTATATTGAAGCCAGCAATTCTACCTCCCCGGTCGGCAGTGGA
89171869 ATCGA
260 ATCGA
* *
89171874 TTGAAAAAGCAGATCCCGTCTTCATGTACTGGTGTGAAGGAGATCAAAGATAGTAGGTCCTGTCT
1 TTGAAAAAGCAGATCCTGTCTTCATGTACTGGCGTGAAGGAGATCAAAGATAGTAGGTCCTGTCT
*
89171939 TCCTGTATTGGTAGCGAAGTGGATCAAAAATACATATTTTATCTTCCCATACCGACAGCGAAGTA
66 TCCTATATTGGTAGCGAAGTGGATCAAAAATACATATTTTATCTTCCCATACCGACAGCGAAGTA
89172004 GATTGAAGATTACAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTA
131 GATTGAAGATTACAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTA
89172069 CCTCCCTGAAGTTGCAGTGGAGTATATTGAAGCCAGCAATTCTACCTCCCCGGTCGGCAGTGGAA
196 CCTCCCTGAAGTTGCAGTGGAGTATATTGAAGCCAGCAATTCTACCTCCCCGGTCGGCAGTGGAA
89172134 TCGA
261 TCGA
* *
89172138 TTGAAAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAG
1 TTGAAAAAGCAGATCCTGTCTTCATGTACTGGCGTGAAG
89172177 TATATCGAAG
Statistics
Matches: 288, Mismatches: 15, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
264 283 0.98
265 5 0.02
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (264 bp):
TTGAAAAAGCAGATCCTGTCTTCATGTACTGGCGTGAAGGAGATCAAAGATAGTAGGTCCTGTCT
TCCTATATTGGTAGCGAAGTGGATCAAAAATACATATTTTATCTTCCCATACCGACAGCGAAGTA
GATTGAAGATTACAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTA
CCTCCCTGAAGTTGCAGTGGAGTATATTGAAGCCAGCAATTCTACCTCCCCGGTCGGCAGTGGAA
TCGA
Found at i:89173713 original size:3 final size:3
Alignment explanation
Indices: 89173705--89173759 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
89173695 AGTCATTCTG
89173705 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
89173753 TTA TTA T
1 TTA TTA T
89173760 CAACATGTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:89173909 original size:14 final size:13
Alignment explanation
Indices: 89173893--89173918 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
89173883 TTGTATAGTT
89173893 TTTTTTTTGTTTC
1 TTTTTTTTGTTTC
89173906 TTTTTTTTGTTTC
1 TTTTTTTTGTTTC
89173919 ATATGTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.85
Consensus pattern (13 bp):
TTTTTTTTGTTTC
Found at i:89178568 original size:22 final size:22
Alignment explanation
Indices: 89178543--89178585 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
89178533 CGCCACTTGC
*
89178543 TCTGCCATCGTCGGACCTAACT
1 TCTGCCATCGCCGGACCTAACT
* *
89178565 TCTGTCATCGCCGTACCTAAC
1 TCTGCCATCGCCGGACCTAAC
89178586 CCCTTCCCAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.19, C:0.37, G:0.16, T:0.28
Consensus pattern (22 bp):
TCTGCCATCGCCGGACCTAACT
Found at i:89179368 original size:18 final size:20
Alignment explanation
Indices: 89179345--89179389 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
89179335 GCATACGTTT
89179345 TTTTATAA-T-ATATACATA
1 TTTTATAATTCATATACATA
*
89179363 TTTTATAATTCATATATATA
1 TTTTATAATTCATATACATA
89179383 TTTTATA
1 TTTTATA
89179390 TTTTATAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 8 0.33
19 1 0.04
20 15 0.62
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTTATAATTCATATACATA
Found at i:89179396 original size:18 final size:18
Alignment explanation
Indices: 89179345--89179396 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 18
89179335 GCATACGTTT
*
89179345 TTTTATAATATATACATA
1 TTTTATATTATATACATA
*
89179363 TTTTATAATTCATATATATA
1 TTTTAT-ATT-ATATACATA
*
89179383 TTTTATATTTTATA
1 TTTTATATTATATA
89179397 ATTTCTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 10 0.34
19 5 0.17
20 14 0.48
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTATATTATATACATA
Found at i:89179549 original size:28 final size:27
Alignment explanation
Indices: 89179475--89179549 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 27
89179465 TATACATACT
89179475 TATATATTTTTCATAATTTTTATGTACA
1 TATATATTTTTCAT-ATTTTTATGTACA
* * * * *
89179503 TATATA-TATGCATACTTTTATATTCAA
1 TATATATTTTTCATATTTTTATGTAC-A
89179530 TAATATATTTTTCATATTTT
1 T-ATATATTTTTCATATTTT
89179550 CATAAATTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
26 9 0.25
27 7 0.19
28 11 0.31
29 9 0.25
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.56
Consensus pattern (27 bp):
TATATATTTTTCATATTTTTATGTACA
Found at i:89183561 original size:19 final size:17
Alignment explanation
Indices: 89183512--89183562 Score: 50
Period size: 19 Copynumber: 2.9 Consensus size: 17
89183502 AATGAAGATG
89183512 ATGAAAAA-TAAAAGAA
1 ATGAAAAAGTAAAAGAA
* *
89183528 AAGAAAAAGAAAAAAGAGA
1 ATGAAAAAG-TAAAAGA-A
89183547 ATGAAAAAGTCAAAAG
1 ATGAAAAAGT-AAAAG
89183563 GAGAGGCCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
16 7 0.26
18 6 0.22
19 14 0.52
ACGTcount: A:0.73, C:0.02, G:0.18, T:0.08
Consensus pattern (17 bp):
ATGAAAAAGTAAAAGAA
Found at i:89184888 original size:50 final size:50
Alignment explanation
Indices: 89184807--89185143 Score: 239
Period size: 50 Copynumber: 6.7 Consensus size: 50
89184797 GTAGTGGAGT
* * * * * * *
89184807 AGATTGAAGCTACAACGGTGAATGTTGCTTCCGTGACTTTGCAATTAAAA
1 AGATTGAAGCCACAACAGCGAATCTTACTTCCCTGACGTTGCAATTAAAA
* * * * ** *
89184857 AGATTGAAGCCATAACAGCAAATCTTACTTCCCTGACGATGCAGTGGAAC
1 AGATTGAAGCCACAACAGCGAATCTTACTTCCCTGACGTTGCAATTAAAA
* * * * * * **
89184907 AGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGATATTGCAATTAAAA
1 AGATTGAAGCCACAACAGCGAATCTTACTTCCCTGACGTTGCAATTAAAA
* * * ** *
89184957 ACATTGAAGCCACAAC-GACGAATCTTACTTCCCTGACGATGCAGTGGAAC
1 AGATTGAAGCCACAACAG-CGAATCTTACTTCCCTGACGTTGCAATTAAAA
* * * * * * *
89185007 AGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGCAATTAAAA
1 AGATTGAAGCCACAACAGCGAATCTTACTTCCCTGACGTTGCAATTAAAA
* * * * *
89185057 AGATTGAAGCCACAATAGCGAATCTTACTTCTCTGGCGGTGCAA-TAGAAT
1 AGATTGAAGCCACAACAGCGAATCTTACTTCCCTGACGTTGCAATTA-AAA
* **
89185107 AGATTGAAGCTACAAC-GACGAATCTTGTTTCCCTGAC
1 AGATTGAAGCCACAACAG-CGAATCTTACTTCCCTGAC
89185144 ATTGTAGTTA
Statistics
Matches: 211, Mismatches: 72, Indels: 8
0.73 0.25 0.03
Matches are distributed among these distances:
49 4 0.02
50 206 0.98
51 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (50 bp):
AGATTGAAGCCACAACAGCGAATCTTACTTCCCTGACGTTGCAATTAAAA
Found at i:89185165 original size:100 final size:99
Alignment explanation
Indices: 89184807--89185147 Score: 466
Period size: 100 Copynumber: 3.4 Consensus size: 99
89184797 GTAGTGGAGT
* * ** * *
89184807 AGATTGAAGCTACAACGGTGAATGTTGCTTCCGTGACTTTGCAATTAAAAAGATTGAAGCCATAA
1 AGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAA
*
89184872 CAGCAAATCTTACTTCCCTGACGATGCAGTGGAAC
66 -AGCGAATCTTACTTCCCTGACGATGCAGTGGAAC
* *
89184907 AGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGATATTGCAATTAAAAACATTGAAGCCACAA
1 AGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAA
*
89184972 CGACGAATCTTACTTCCCTGACGATGCAGTGGAAC
66 AG-CGAATCTTACTTCCCTGACGATGCAGTGGAAC
89185007 AGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAA
1 AGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAA
* * * * * *
89185072 TAGCGAATCTTACTTCTCTGGCGGTGCAATAGAAT
66 -AGCGAATCTTACTTCCCTGACGATGCAGTGGAAC
* ** * *
89185107 AGATTGAAGCTACAACGACGAATCTTGTTTCCCTGACATTG
1 AGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGACATTG
89185148 TAGTTAATCA
Statistics
Matches: 215, Mismatches: 24, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
99 1 0.00
100 213 0.99
101 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (99 bp):
AGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGCAATTAAAAAGATTGAAGCCACAA
AGCGAATCTTACTTCCCTGACGATGCAGTGGAAC
Found at i:89185365 original size:44 final size:43
Alignment explanation
Indices: 89185306--89185427 Score: 131
Period size: 44 Copynumber: 2.8 Consensus size: 43
89185296 AATCGCATCT
*
89185306 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAA-ATC
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATT-AA-AAGATC
* * * *
89185350 AATCCTATCTTCCTGAAGTTACAGTGAAGCAGATTAAAATGATG
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAA-GATC
* *
89185394 GATCTTATC-TCTCTGAAGTTGCAGTAGAGCAGAT
1 AATCTTATCTTC-CTGAAGTTGCAGTGGAGCAGAT
89185428 CGCATCAGAC
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
42 2 0.03
43 4 0.06
44 59 0.91
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (43 bp):
AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAAGATC
Found at i:89185706 original size:44 final size:43
Alignment explanation
Indices: 89185588--89185708 Score: 127
Period size: 45 Copynumber: 2.7 Consensus size: 43
89185578 ATCACACCAT
* *
89185588 AACAAGTCTTATCTCCCTAAAGTTGCAGTGAAGCAGACTGAAG
1 AACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG
** * *
89185631 ATATCAAACCTTATCTCCCTGAAGCTGCAGTGGAGCA-AGTTGAAG
1 A-A-CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CTGAAG
* *
89185676 CAACAAGTCTTATCTCCCTGACGTTACAGTGGA
1 -AACAAGTCTTATCTCCCTGAAGTTGCAGTGGA
89185709 ATAGACTAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 7
0.78 0.14 0.09
Matches are distributed among these distances:
43 1 0.02
44 27 0.43
45 34 0.54
46 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (43 bp):
AACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG
Found at i:89185752 original size:16 final size:16
Alignment explanation
Indices: 89185731--89185762 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
89185721 TAGGAATCTC
*
89185731 GCCCCCTAAGGTTACA
1 GCCCCCTAAAGTTACA
89185747 GCCCCCTAAAGTTACA
1 GCCCCCTAAAGTTACA
89185763 ACAGAGTGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.38, G:0.16, T:0.19
Consensus pattern (16 bp):
GCCCCCTAAAGTTACA
Found at i:89186181 original size:22 final size:22
Alignment explanation
Indices: 89186156--89186198 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
89186146 CGCCACTTGC
89186156 TCTGCCATCGCCGCACCTAACT
1 TCTGCCATCGCCGCACCTAACT
* *
89186178 TCTGTCATCGTCGCACCTAAC
1 TCTGCCATCGCCGCACCTAAC
89186199 CCCTGCCTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.19, C:0.42, G:0.14, T:0.26
Consensus pattern (22 bp):
TCTGCCATCGCCGCACCTAACT
Found at i:89187285 original size:18 final size:20
Alignment explanation
Indices: 89187264--89187308 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
89187254 TGCATACGTT
89187264 TTTTATAA-T-ATATACATA
1 TTTTATAATTCATATACATA
*
89187282 TTTTATAATTCATATATATA
1 TTTTATAATTCATATACATA
89187302 TTTTATA
1 TTTTATA
89187309 TTTTATAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 8 0.33
19 1 0.04
20 15 0.62
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTTATAATTCATATACATA
Found at i:89187315 original size:18 final size:18
Alignment explanation
Indices: 89187264--89187315 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 18
89187254 TGCATACGTT
*
89187264 TTTTATAATATATACATA
1 TTTTATATTATATACATA
*
89187282 TTTTATAATTCATATATATA
1 TTTTAT-ATT-ATATACATA
*
89187302 TTTTATATTTTATA
1 TTTTATATTATATA
89187316 ATTTCTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 10 0.34
19 5 0.17
20 14 0.48
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTATATTATATACATA
Found at i:89192097 original size:123 final size:123
Alignment explanation
Indices: 89191878--89192127 Score: 500
Period size: 123 Copynumber: 2.0 Consensus size: 123
89191868 TGAAATCTAA
89191878 AAAGGATAATCAATTGTTCAAGTCATGTAAAGCAATCGAGTCCCAATACGTTAGGGTACGATTTC
1 AAAGGATAATCAATTGTTCAAGTCATGTAAAGCAATCGAGTCCCAATACGTTAGGGTACGATTTC
89191943 TCAAAATCCCTGAACTTTGAATATCGCTTTTATTTCATGCGAAAATATTCTTTTTGAG
66 TCAAAATCCCTGAACTTTGAATATCGCTTTTATTTCATGCGAAAATATTCTTTTTGAG
89192001 AAAGGATAATCAATTGTTCAAGTCATGTAAAGCAATCGAGTCCCAATACGTTAGGGTACGATTTC
1 AAAGGATAATCAATTGTTCAAGTCATGTAAAGCAATCGAGTCCCAATACGTTAGGGTACGATTTC
89192066 TCAAAATCCCTGAACTTTGAATATCGCTTTTATTTCATGCGAAAATATTCTTTTTGAG
66 TCAAAATCCCTGAACTTTGAATATCGCTTTTATTTCATGCGAAAATATTCTTTTTGAG
89192124 AAAG
1 AAAG
89192128 CAATATGCCA
Statistics
Matches: 127, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
123 127 1.00
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (123 bp):
AAAGGATAATCAATTGTTCAAGTCATGTAAAGCAATCGAGTCCCAATACGTTAGGGTACGATTTC
TCAAAATCCCTGAACTTTGAATATCGCTTTTATTTCATGCGAAAATATTCTTTTTGAG
Found at i:89199230 original size:28 final size:28
Alignment explanation
Indices: 89199198--89199269 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
89199188 TTTAATAAGT
*
89199198 TCGCACACTTAGTGCTTAATAATCAAAC
1 TCGCACACTTAGTGCTTAACAATCAAAC
* *
89199226 TCGCACACTTAGTGCTTCACAATTAAAC
1 TCGCACACTTAGTGCTTAACAATCAAAC
*
89199254 TCGTACACTTAGTGCT
1 TCGCACACTTAGTGCT
89199270 AATTTTTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31
Consensus pattern (28 bp):
TCGCACACTTAGTGCTTAACAATCAAAC
Found at i:89207690 original size:56 final size:56
Alignment explanation
Indices: 89207599--89207721 Score: 176
Period size: 55 Copynumber: 2.2 Consensus size: 56
89207589 GAGATTGGCG
* * *
89207599 CTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAG-TTGATTATATAGCA
* *
89207656 CTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCGAGTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAGTTGATTATATAGCA
*
89207711 CTGAGTGTGCG
1 CTAAGTGTGCG
89207722 GACTTAATAT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
55 23 0.38
56 22 0.37
57 15 0.25
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.33
Consensus pattern (56 bp):
CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAGTTGATTATATAGCA
Found at i:89207708 original size:27 final size:28
Alignment explanation
Indices: 89207599--89207721 Score: 176
Period size: 28 Copynumber: 4.4 Consensus size: 28
89207589 GAGATTGGCG
* * * *
89207599 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
89207628 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
89207656 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
89207684 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
89207711 CTGAGTGTGCG
1 CTAAGTGTGCG
89207722 GACTTAATAT
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 24 0.28
28 48 0.55
29 15 0.17
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.33
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:89207732 original size:27 final size:27
Alignment explanation
Indices: 89207624--89207734 Score: 116
Period size: 28 Copynumber: 4.0 Consensus size: 27
89207614 TAAATTGTAC
* * *
89207624 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
89207652 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
89207680 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
89207707 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
89207734 A
1 A
89207735 CTTTTGAATC
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
27 30 0.39
28 47 0.61
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:89210051 original size:28 final size:28
Alignment explanation
Indices: 89210019--89210090 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
89210009 TTTAATAAGT
*
89210019 TCGCACACTTAGTGCTTAATAATCAAAC
1 TCGCACACTTAGTGCTTAACAATCAAAC
* *
89210047 TCGCACACTTAGTGCTTCACAATTAAAC
1 TCGCACACTTAGTGCTTAACAATCAAAC
*
89210075 TCGTACACTTAGTGCT
1 TCGCACACTTAGTGCT
89210091 AATTTTTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31
Consensus pattern (28 bp):
TCGCACACTTAGTGCTTAACAATCAAAC
Found at i:89215374 original size:9 final size:9
Alignment explanation
Indices: 89215360--89215417 Score: 52
Period size: 9 Copynumber: 6.6 Consensus size: 9
89215350 GCAACCCAAT
89215360 TTTTATTTA
1 TTTTATTTA
89215369 TTTTATTT-
1 TTTTATTTA
89215377 TATTTACTTTA
1 T-TTTA-TTTA
89215388 -TTTA-TTA
1 TTTTATTTA
*
89215395 CTTTATTTTA
1 TTTTA-TTTA
89215405 TTTTA-TTA
1 TTTTATTTA
89215413 TTTTA
1 TTTTA
89215418 CAACTTATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
7 3 0.07
8 13 0.31
9 16 0.38
10 10 0.24
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTTATTTA
Found at i:89215375 original size:5 final size:5
Alignment explanation
Indices: 89215360--89215411 Score: 54
Period size: 5 Copynumber: 10.4 Consensus size: 5
89215350 GCAACCCAAT
* *
89215360 TTTTA -TTTA TTTTA TTTTA -TTTA CTTTA TTTATTA CTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TT-TTA TTTTA TTTTA TTTTA
89215410 TT
1 TT
89215412 ATTTTACAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
4 8 0.20
5 27 0.68
6 2 0.05
7 3 0.08
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:89217469 original size:15 final size:15
Alignment explanation
Indices: 89217444--89217478 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
89217434 GACTCTATTT
*
89217444 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
89217458 TAATTAATATTAAGA
1 TAATTAATATTAAGA
89217473 TAATTA
1 TAATTA
89217479 TTAACGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:89220330 original size:35 final size:35
Alignment explanation
Indices: 89220291--89220360 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
89220281 TAGATGGTAT
89220291 ATAACACTTGGTTATTCTCATTAAGTTTGTAAATA
1 ATAACACTTGGTTATTCTCATTAAGTTTGTAAATA
89220326 ATAACACTTGGTTATTCTCATTAAGTTTGTAAATA
1 ATAACACTTGGTTATTCTCATTAAGTTTGTAAATA
89220361 CATCTATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (35 bp):
ATAACACTTGGTTATTCTCATTAAGTTTGTAAATA
Found at i:89221278 original size:33 final size:33
Alignment explanation
Indices: 89221236--89221304 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
89221226 TTAACATGTG
*
89221236 TTTCAATTGTACTAAATTGTAACAAATTAATAA
1 TTTCAATTGTACTAAATTGTAACAAACTAATAA
*
89221269 TTTCAATTGTACTAAATTGTAATAAACTAATAA
1 TTTCAATTGTACTAAATTGTAACAAACTAATAA
89221302 TTT
1 TTT
89221305 TACTATCATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.42
Consensus pattern (33 bp):
TTTCAATTGTACTAAATTGTAACAAACTAATAA
Found at i:89222291 original size:42 final size:44
Alignment explanation
Indices: 89222219--89222324 Score: 137
Period size: 42 Copynumber: 2.5 Consensus size: 44
89222209 CATCATGAAC
*
89222219 ATGGTTTCTTCCACGTTGCATTGTCTTGTCA-AGTCATTGATTTA
1 ATGGTTGCTTCCACGTTGCATTGTCTTGTCACA-TCATTGATTTA
*
89222263 ATGGTTGCTTCCAC-TT-CATTGTCTTGTCACATTATTGATTTA
1 ATGGTTGCTTCCACGTTGCATTGTCTTGTCACATCATTGATTTA
* * *
89222305 ATGTTTGTTTCCACATTGCA
1 ATGGTTGCTTCCACGTTGCA
89222325 ATCTCTTTTG
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
42 35 0.64
43 5 0.09
44 15 0.27
ACGTcount: A:0.19, C:0.19, G:0.16, T:0.46
Consensus pattern (44 bp):
ATGGTTGCTTCCACGTTGCATTGTCTTGTCACATCATTGATTTA
Found at i:89228571 original size:20 final size:18
Alignment explanation
Indices: 89228521--89228573 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
89228511 GTTCTTCATA
89228521 AAAATTTAAAAAATTATT
1 AAAATTTAAAAAATTATT
* *
89228539 AAAA-TTATTAAAATTTTGAT
1 AAAATTTA-AAAAATTAT--T
89228559 AAAATTTAAAAAATT
1 AAAATTTAAAAAATT
89228574 CAATAATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 3 0.11
18 11 0.39
20 11 0.39
21 3 0.11
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
AAAATTTAAAAAATTATT
Found at i:89235200 original size:18 final size:18
Alignment explanation
Indices: 89235177--89235269 Score: 123
Period size: 18 Copynumber: 5.2 Consensus size: 18
89235167 CCCAACTACT
*
89235177 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
89235195 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
* *
89235213 GTATATGTGAATAGTATC
1 GTATACGTGAATAGTACC
**
89235231 GTATACGTGAATAGTGTC
1 GTATACGTGAATAGTACC
*
89235249 GTATATGTGAATAGTACC
1 GTATACGTGAATAGTACC
89235267 GTA
1 GTA
89235270 AACGGTCGTA
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 65 1.00
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:89235234 original size:36 final size:36
Alignment explanation
Indices: 89235177--89235269 Score: 150
Period size: 36 Copynumber: 2.6 Consensus size: 36
89235167 CCCAACTACT
* *
89235177 GTATACGTGAACAGTACCGTATACGTGAATAGTGCC
1 GTATATGTGAATAGTACCGTATACGTGAATAGTGCC
* *
89235213 GTATATGTGAATAGTATCGTATACGTGAATAGTGTC
1 GTATATGTGAATAGTACCGTATACGTGAATAGTGCC
89235249 GTATATGTGAATAGTACCGTA
1 GTATATGTGAATAGTACCGTA
89235270 AACGGTCGTA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (36 bp):
GTATATGTGAATAGTACCGTATACGTGAATAGTGCC
Found at i:89238785 original size:19 final size:19
Alignment explanation
Indices: 89238752--89238804 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
89238742 CACCAATTTC
*
89238752 TTTTAAAAA-ATAAAAATA
1 TTTTAAAAATAAAAAAATA
*
89238770 TTTTAAAAATAAAAAAGTA
1 TTTTAAAAATAAAAAAATA
89238789 TTTTAAAAATAAAAAA
1 TTTTAAAAATAAAAAA
89238805 TAAAAAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 9 0.28
19 23 0.72
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (19 bp):
TTTTAAAAATAAAAAAATA
Found at i:89238803 original size:7 final size:7
Alignment explanation
Indices: 89238793--89238817 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
89238783 AAAGTATTTT
89238793 AAAAATA
1 AAAAATA
89238800 AAAAATA
1 AAAAATA
89238807 AAAAATA
1 AAAAATA
89238814 AAAA
1 AAAA
89238818 TATATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:89246355 original size:19 final size:20
Alignment explanation
Indices: 89246314--89246355 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
89246304 GTTTCTATGT
* *
89246314 CATTGTGATATTTATTATTG
1 CATTGTGATATTTAATATAG
*
89246334 CATTGT-ATATTTAATGTAG
1 CATTGTGATATTTAATATAG
89246353 CAT
1 CAT
89246356 CACATCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (20 bp):
CATTGTGATATTTAATATAG
Found at i:89246394 original size:64 final size:65
Alignment explanation
Indices: 89246314--89246441 Score: 240
Period size: 65 Copynumber: 2.0 Consensus size: 65
89246304 GTTTCTATGT
*
89246314 CATTGTGATATTTATTATTGCA-TTGTATATTTAATGTAGCATCACATCATTTTTTACTCGATTC
1 CATTGTGATAATTATTATTGCATTTGTATATTTAATGTAGCATCACATCATTTTTTACTCGATTC
89246378 CATTGTGATAATTATTATTGCATTTGTATATTTAATGTAGCATCACATCATTTTTTACTCGATT
1 CATTGTGATAATTATTATTGCATTTGTATATTTAATGTAGCATCACATCATTTTTTACTCGATT
89246442 TCAAACTTCT
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
64 21 0.34
65 41 0.66
ACGTcount: A:0.27, C:0.13, G:0.11, T:0.48
Consensus pattern (65 bp):
CATTGTGATAATTATTATTGCATTTGTATATTTAATGTAGCATCACATCATTTTTTACTCGATTC
Found at i:89246730 original size:79 final size:79
Alignment explanation
Indices: 89246599--89246756 Score: 316
Period size: 79 Copynumber: 2.0 Consensus size: 79
89246589 CAACACGTTG
89246599 TGTCCTAACGTATTGGATGTGACGCATTGATTTTTCGAAATAAATACTTTTTAAAAAAATAATAA
1 TGTCCTAACGTATTGGATGTGACGCATTGATTTTTCGAAATAAATACTTTTTAAAAAAATAATAA
89246664 AGGAAATATTCCGA
66 AGGAAATATTCCGA
89246678 TGTCCTAACGTATTGGATGTGACGCATTGATTTTTCGAAATAAATACTTTTTAAAAAAATAATAA
1 TGTCCTAACGTATTGGATGTGACGCATTGATTTTTCGAAATAAATACTTTTTAAAAAAATAATAA
89246743 AGGAAATATTCCGA
66 AGGAAATATTCCGA
89246757 GTTTGGGATT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.34
Consensus pattern (79 bp):
TGTCCTAACGTATTGGATGTGACGCATTGATTTTTCGAAATAAATACTTTTTAAAAAAATAATAA
AGGAAATATTCCGA
Found at i:89250077 original size:24 final size:24
Alignment explanation
Indices: 89250050--89250095 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
89250040 AGAACAATCC
* *
89250050 CAAAAGGAAATGCAGGAGCAGCTT
1 CAAAAGCAAATGAAGGAGCAGCTT
*
89250074 CAAAAGCAAATGAATGAGCAGC
1 CAAAAGCAAATGAAGGAGCAGC
89250096 AAAATATGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (24 bp):
CAAAAGCAAATGAAGGAGCAGCTT
Found at i:89257967 original size:44 final size:45
Alignment explanation
Indices: 89257917--89258038 Score: 171
Period size: 45 Copynumber: 2.7 Consensus size: 45
89257907 TAACAGATCG
89257917 AGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACT-AA-GTAGGCA
1 AGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTGAAGGT-GGCA
*
89257961 AGTCTTATC-CACCTGAAGTTGCAGT-GAGGCAGACTGAAGGTGGCA
1 AGTCTTATCTC-CCTGAAGTTACAGTGGA-GCAGACTGAAGGTGGCA
*
89258006 AATCTTATCTCCCTGAAGTTACAGTGGAGCAGA
1 AGTCTTATCTCCCTGAAGTTACAGTGGAGCAGA
89258039 TTAAAGCTGG
Statistics
Matches: 69, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
43 3 0.04
44 29 0.42
45 32 0.46
46 5 0.07
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (45 bp):
AGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTGAAGGTGGCA
Found at i:89258070 original size:89 final size:88
Alignment explanation
Indices: 89257919--89258250 Score: 286
Period size: 89 Copynumber: 3.8 Consensus size: 88
89257909 ACAGATCGAG
* * *
89257919 TCTTATCTCCCTGAAGTTACAGTGGAGCAGACT-AAGTAGGCAAGTCTTATCCAC-CTGAAGTTG
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGT-GGTAA-TCCTATCC-CGCTGAAGTTG
*
89257982 CAGTGAGGCAGACTGAAGGTGGCAAA
63 CAGTGAGGCAGACTGAAGATGGCAAA
**
89258008 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCTGGTAATCCTATTTCGCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAG-TGGTAATCCTATCCCGCTGAAGTTGCA
* * * **** *
89258073 GTGA-GCGGA-TTAAAACCTTAGA
65 GTGAGGCAGACTGAAGATGGCAAA
* * ** * * * * * *
89258095 TCTTATCTCTCTGAAGTTGCA-AAGAACAGATCACA-T-CTAGTCTTATCCTC-CTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGTGGTAATCCTATCC-CGCTGAAGTTGCA
89258156 GTGAGGCAGACTGAAGATGGCAAA
65 GTGAGGCAGACTGAAGATGGCAAA
* ** * *
89258180 TCTTATCTCCTTGAAGTTGTAGTGGAGCAGATTAAAGCCGGTAATCCTATCCCGCTGAAGTTGTA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAG-TGGTAATCCTATCCCGCTGAAGTTGCA
89258245 GT-AGGC
65 GTGAGGC
89258251 GGATTAAAAC
Statistics
Matches: 185, Mismatches: 47, Indels: 23
0.73 0.18 0.09
Matches are distributed among these distances:
83 22 0.12
84 6 0.03
85 24 0.13
86 18 0.10
87 24 0.13
88 10 0.05
89 73 0.39
90 7 0.04
91 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (88 bp):
TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGTGGTAATCCTATCCCGCTGAAGTTGCAG
TGAGGCAGACTGAAGATGGCAAA
Done.