Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D05
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: 63323194
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1953226 characters in sequence are not A, C, G, or T
File 67 of 199
Found at i:25292676 original size:19 final size:20
Alignment explanation
Indices: 25292654--25292692 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
25292644 TAATTTGGTC
25292654 ATTTC-CTTTTAATCCCAAA
1 ATTTCTCTTTTAATCCCAAA
*
25292673 ATTTCTGTTTTAATCCCAAA
1 ATTTCTCTTTTAATCCCAAA
25292693 TTAGCCCATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.31, C:0.23, G:0.03, T:0.44
Consensus pattern (20 bp):
ATTTCTCTTTTAATCCCAAA
Found at i:25298435 original size:144 final size:144
Alignment explanation
Indices: 25298053--25298423 Score: 697
Period size: 144 Copynumber: 2.6 Consensus size: 144
25298043 TAAAGACGAA
* * * *
25298053 GGTATAGAACCAGATAACCCGTTTTCTTGCAATTCAAGGCTGCTCAATCCTTTCAGTACCCCAAT
1 GGTATAGAACCAGATAACCTGTTATATTGCAATTCAAGGCTGCTCAATCCTTTCAGTTCCCCAAT
25298118 TCCACGAGGGATTTTCCCTGCAAGATGATTATGAGCCATGTTTATGACAGTGATAGAACGACAAG
66 TCCACGAGGGATTTTCCCTGCAAGATGATTATGAGCCATGTTTATGACAGTGATAGAACGACAAG
25298183 AACTTAACGACTCC
131 AACTTAACGACTCC
25298197 GGTATAGAACCAGATAACCTGTTATATTGCAATTCAAGGCTGCTCAATCCTTTCAGTTCCCCAAT
1 GGTATAGAACCAGATAACCTGTTATATTGCAATTCAAGGCTGCTCAATCCTTTCAGTTCCCCAAT
25298262 TCCACGAGGGATTTTCCCTGCAAGATGATTATGAGCCATGTTTATGACAGTGATAGAACGACAAG
66 TCCACGAGGGATTTTCCCTGCAAGATGATTATGAGCCATGTTTATGACAGTGATAGAACGACAAG
25298327 AACTTAACGACTCC
131 AACTTAACGACTCC
*
25298341 GGTATAGAACCAGATAACCTGTTATATTGCAATTCAAGGCTGCTCAATCTTTTCAGTTCCCCAAT
1 GGTATAGAACCAGATAACCTGTTATATTGCAATTCAAGGCTGCTCAATCCTTTCAGTTCCCCAAT
25298406 TCCACGAGGGATTTTCCC
66 TCCACGAGGGATTTTCCC
25298424 CCAAAACTGA
Statistics
Matches: 222, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
144 222 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.28
Consensus pattern (144 bp):
GGTATAGAACCAGATAACCTGTTATATTGCAATTCAAGGCTGCTCAATCCTTTCAGTTCCCCAAT
TCCACGAGGGATTTTCCCTGCAAGATGATTATGAGCCATGTTTATGACAGTGATAGAACGACAAG
AACTTAACGACTCC
Found at i:25305790 original size:60 final size:60
Alignment explanation
Indices: 25305695--25305814 Score: 186
Period size: 60 Copynumber: 2.0 Consensus size: 60
25305685 TCCGATTCTC
**
25305695 GTCGATTCCGGGATGATCAAGCATAAGGATGATGCAGCCACATCGAATGAGTCTTAGCAT
1 GTCGATTCCGGGATGATCAAGCATAAGGATGATGCAGCCACATCGAACAAGTCTTAGCAT
* * * *
25305755 GTCGATTCTGGGATGATCAAGTATAAGGATTATGCAGCCTCATCGAACAAGTCTTAGCAT
1 GTCGATTCCGGGATGATCAAGCATAAGGATGATGCAGCCACATCGAACAAGTCTTAGCAT
25305815 TTTGGATGTT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (60 bp):
GTCGATTCCGGGATGATCAAGCATAAGGATGATGCAGCCACATCGAACAAGTCTTAGCAT
Found at i:25306638 original size:44 final size:46
Alignment explanation
Indices: 25306551--25306643 Score: 163
Period size: 44 Copynumber: 2.1 Consensus size: 46
25306541 GATTCGCTGT
*
25306551 AATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGG
25306597 AATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGG
25306641 AAT
1 AAT
25306644 AGAGGTGTAA
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 24 0.52
45 3 0.07
46 19 0.41
ACGTcount: A:0.28, C:0.04, G:0.31, T:0.37
Consensus pattern (46 bp):
AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGG
Found at i:25306639 original size:39 final size:44
Alignment explanation
Indices: 25306551--25306656 Score: 141
Period size: 39 Copynumber: 2.5 Consensus size: 44
25306541 GATTCGCTGT
*
25306551 AATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTT--ATGG
25306597 AATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGG-T-T-G
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTATGG
*
25306636 AATGGAATAGAGGTGTAATAG
1 AATGGAATAGAGGCGTAATAG
25306657 CATAAGGAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
39 19 0.33
40 2 0.04
43 1 0.02
44 13 0.23
45 3 0.05
46 19 0.33
ACGTcount: A:0.29, C:0.04, G:0.32, T:0.35
Consensus pattern (44 bp):
AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTATGG
Found at i:25306937 original size:64 final size:63
Alignment explanation
Indices: 25306850--25307018 Score: 173
Period size: 54 Copynumber: 2.8 Consensus size: 63
25306840 TAGTATTAAA
* *
25306850 TATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAAT
1 TATTATTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTCAAAATAAT
* * *
25306913 TATTATTAAATAT-AATTTA--ATAA--A-AATATATAAT--T-T--AATAAAATTCAATATAAT
1 TATTATT--ATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTCAAAATAAT
* *
25306967 TATTCTTATATGAATTTACTAAAATCATATTATATAATACTATAAAA-ATAAT
1 TATTATTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAAT
25307019 ATGTAATCTA
Statistics
Matches: 84, Mismatches: 9, Indels: 27
0.70 0.08 0.22
Matches are distributed among these distances:
52 4 0.05
53 6 0.07
54 21 0.25
55 3 0.04
56 1 0.01
57 2 0.02
58 9 0.11
59 10 0.12
60 2 0.02
61 1 0.01
62 7 0.08
63 8 0.10
64 6 0.07
65 4 0.05
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.42
Consensus pattern (63 bp):
TATTATTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTCAAAATAAT
Found at i:25306954 original size:59 final size:60
Alignment explanation
Indices: 25306774--25306956 Score: 176
Period size: 59 Copynumber: 3.0 Consensus size: 60
25306764 TAAATAATTT
* *
25306774 AATCATATTTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAGA
1 AATCATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATA-A
* * * * * * * ** * * *
25306835 ATTCTTAGTATT-AAAT-ATTCTTATATGAATTTACTAAAATCATAATATATAATACT-ATAA
1 AATCATAAT-TTAAAATAATTATTAT-TAAATATAATTTAATAAAAATATATAAT-TTAATAA
25306895 AAT-ATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAA
1 AATCATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAA
25306954 AAT
1 AAT
25306957 TCAATATAAT
Statistics
Matches: 91, Mismatches: 25, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
58 3 0.03
59 35 0.38
60 17 0.19
61 33 0.36
62 3 0.03
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (60 bp):
AATCATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAA
Found at i:25306957 original size:10 final size:10
Alignment explanation
Indices: 25306895--25306967 Score: 50
Period size: 10 Copynumber: 7.9 Consensus size: 10
25306885 AATACTATAA
25306895 AATATAATTT
1 AATATAATTT
*
25306905 AAAATAA-TT
1 AATATAATTT
*
25306914 -AT-T-ATTA
1 AATATAATTT
25306921 AATATAATTT
1 AATATAATTT
**
25306931 AATA-AAAAT
1 AATATAATTT
25306940 -ATATAATTT
1 AATATAATTT
* *
25306949 AATAAAATTC
1 AATATAATTT
25306959 AATATAATT
1 AATATAATT
25306968 ATTCTTATAT
Statistics
Matches: 46, Mismatches: 11, Indels: 12
0.67 0.16 0.17
Matches are distributed among these distances:
6 1 0.02
7 2 0.04
8 6 0.13
9 9 0.20
10 28 0.61
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (10 bp):
AATATAATTT
Found at i:25307007 original size:117 final size:118
Alignment explanation
Indices: 25306782--25307018 Score: 397
Period size: 120 Copynumber: 2.0 Consensus size: 118
25306772 TTAATCATAT
* * *
25306782 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAGAATTCTTAGTATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTC-TAATATT
25306847 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
65 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAA-ATAA
25306902 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTC-AATA-TA
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTAATATTA
* *
25306965 ATTATTCTTATATGAATTTACTAAAATCATATTATATAATACTATAAAAATAA
66 AATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAATAA
25307018 T
1 T
25307019 ATGTAATCTA
Statistics
Matches: 112, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
116 5 0.04
117 49 0.44
118 3 0.03
120 55 0.49
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (118 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTAATATTA
AATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAATAA
Found at i:25311278 original size:153 final size:155
Alignment explanation
Indices: 25311013--25311291 Score: 409
Period size: 153 Copynumber: 1.8 Consensus size: 155
25311003 GAGCTCAAAT
* * *** * *
25311013 GGATAAAATGCTAAAACTCAGGCTTGGCCTGGCCCGTATTAGTTTTTTATATAATTTTTAAAATA
1 GGATAAAATGCTAAAACCCAAGCTTGGCCCAACCCGCATTAATTTTTTATATAATTTTTAAAATA
*
25311078 TATATAATACATCAAAAATACTAAAAACATTAAAATAAATATTTTCCAACAAATTAAAAATGAGC
66 TATATAATACATCAAAAATACTAAAAACATTAAAACAAATATTTTCCAACAAATTAAAAATGAGC
25311143 CTAAAATTTTGCCCAAGCCCAGCCC
131 CTAAAATTTTGCCCAAGCCCAGCCC
* * **
25311168 GGATAAAATGCTAGAACCCAAGCTTGGCCCAACGCGCATTAATTTTTTATAT-ATTTTT-TTATA
1 GGATAAAATGCTAAAACCCAAGCTTGGCCCAACCCGCATTAATTTTTTATATAATTTTTAAAATA
* * *
25311231 TATATAATATATCAAAAATACTAAAAACATTAAAACAAATGTTTTCCAACAAATTGAAAAT
66 TATATAATACATCAAAAATACTAAAAACATTAAAACAAATATTTTCCAACAAATTAAAAAT
25311292 AAATTAAAAA
Statistics
Matches: 109, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
153 60 0.55
154 6 0.06
155 43 0.39
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.32
Consensus pattern (155 bp):
GGATAAAATGCTAAAACCCAAGCTTGGCCCAACCCGCATTAATTTTTTATATAATTTTTAAAATA
TATATAATACATCAAAAATACTAAAAACATTAAAACAAATATTTTCCAACAAATTAAAAATGAGC
CTAAAATTTTGCCCAAGCCCAGCCC
Found at i:25311993 original size:31 final size:31
Alignment explanation
Indices: 25311951--25312025 Score: 132
Period size: 31 Copynumber: 2.4 Consensus size: 31
25311941 AAAATTTGTT
25311951 ATTTTAGTCACTCCAGTTAGATAAGTTGTCA
1 ATTTTAGTCACTCCAGTTAGATAAGTTGTCA
* *
25311982 ATTTTAATCACTCCCGTTAGATAAGTTGTCA
1 ATTTTAGTCACTCCAGTTAGATAAGTTGTCA
25312013 ATTTTAGTCACTC
1 ATTTTAGTCACTC
25312026 TACCGTTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (31 bp):
ATTTTAGTCACTCCAGTTAGATAAGTTGTCA
Found at i:25313885 original size:23 final size:23
Alignment explanation
Indices: 25313850--25313897 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
25313840 ATTTTTGAGC
25313850 CTTTTTTAGCAATCA-GCTTTTGTT
1 CTTTTTTAGCAAT-ATGCTTTT-TT
*
25313874 CTTTTTT-TCAATATGCTTTTTT
1 CTTTTTTAGCAATATGCTTTTTT
25313896 CT
1 CT
25313898 AACAAATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 5 0.23
23 10 0.45
24 7 0.32
ACGTcount: A:0.15, C:0.17, G:0.08, T:0.60
Consensus pattern (23 bp):
CTTTTTTAGCAATATGCTTTTTT
Found at i:25316024 original size:6 final size:6
Alignment explanation
Indices: 25316015--25316041 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
25316005 CAGGTACGAC
25316015 GCCAAT GCCAAT GCCAAT GCCAAT GCC
1 GCCAAT GCCAAT GCCAAT GCCAAT GCC
25316042 GACGCCATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.37, G:0.19, T:0.15
Consensus pattern (6 bp):
GCCAAT
Found at i:25317484 original size:21 final size:21
Alignment explanation
Indices: 25317460--25317505 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
25317450 TATTTTTTTA
25317460 TTTTTTTA-TTTTAAAATATT
1 TTTTTTTATTTTTAAAATATT
*
25317480 TTTTTTTATTTTTAAAATAAT
1 TTTTTTTATTTTTAAAATATT
25317501 TTTTT
1 TTTTT
25317506 AGTGTTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTTTTATTTTTAAAATATT
Found at i:25324431 original size:46 final size:46
Alignment explanation
Indices: 25324360--25324448 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
25324350 CCATGGCAAA
* *
25324360 TTGTGAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATACTGAC
1 TTGTGAAAAGTAGGTATGATATTTCAATGAAGAAAACCATACTGAC
* *
25324406 TTGTGAAAAGTAGGTATGATATTTCAGTGAAGGAAACCATACT
1 TTGTGAAAAGTAGGTATGATATTTCAATGAAGAAAACCATACT
25324449 TAGTTATAGC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.29
Consensus pattern (46 bp):
TTGTGAAAAGTAGGTATGATATTTCAATGAAGAAAACCATACTGAC
Found at i:25327051 original size:46 final size:46
Alignment explanation
Indices: 25326979--25327118 Score: 226
Period size: 46 Copynumber: 3.0 Consensus size: 46
25326969 ACAATGCTAT
* * *
25326979 AACTCAGTATGGTTTCCTTCACTGAAATATCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
* *
25327025 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTATTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
*
25327071 AACTTAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
25327117 AA
1 AA
25327119 TTTGTCATGG
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 86 1.00
ACGTcount: A:0.29, C:0.25, G:0.09, T:0.37
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
Found at i:25330497 original size:18 final size:17
Alignment explanation
Indices: 25330464--25330502 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
25330454 TTGTATAAAT
25330464 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
25330482 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
25330499 TGTG
1 TGTG
25330503 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:25330620 original size:8 final size:8
Alignment explanation
Indices: 25330607--25330635 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
25330597 CACTAGAGAC
25330607 CAGTGTTA
1 CAGTGTTA
25330615 CAGTGTTA
1 CAGTGTTA
25330623 CAGTGTTA
1 CAGTGTTA
25330631 CAGTG
1 CAGTG
25330636 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:25330749 original size:23 final size:23
Alignment explanation
Indices: 25330722--25330797 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
25330712 AGTGTTATTG
25330722 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
25330745 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
25330768 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
25330791 ATCAGTG
1 ATCAGTG
25330798 TGGCACTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:25333373 original size:50 final size:50
Alignment explanation
Indices: 25333249--25333497 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
25333239 GATAATAACA
* * ** * *
25333249 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
25333300 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
25333350 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
25333400 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
25333455 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
25333498 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:25333427 original size:100 final size:104
Alignment explanation
Indices: 25333248--25333497 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
25333238 TGATAATAAC
**
25333248 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
25333313 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
25333350 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
25333413 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
25333455 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
25333498 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:25333613 original size:13 final size:13
Alignment explanation
Indices: 25333592--25333623 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
25333582 GCTTGGATCA
*
25333592 TCATCAAATAAAT
1 TCATAAAATAAAT
25333605 TCATAAAATAAAT
1 TCATAAAATAAAT
25333618 TCATAA
1 TCATAA
25333624 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:25333870 original size:30 final size:30
Alignment explanation
Indices: 25333835--25333892 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
25333825 CCTCGACTCT
*
25333835 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
25333865 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
25333893 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:25340958 original size:50 final size:50
Alignment explanation
Indices: 25340834--25341066 Score: 270
Period size: 50 Copynumber: 4.5 Consensus size: 50
25340824 TGATATAACA
* * ** * *
25340834 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
25340885 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
25340935 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
25340985 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
25341040 ATGCCAATGCCATGTCCCAGACATGGT
1 -TGCCAATGCCATGTCCCAGACATGGT
25341067 TACATGGGAT
Statistics
Matches: 156, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.59
51 33 0.21
53 2 0.01
54 1 0.01
55 2 0.01
56 25 0.16
ACGTcount: A:0.21, C:0.30, G:0.24, T:0.25
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:25341012 original size:100 final size:104
Alignment explanation
Indices: 25340833--25341080 Score: 339
Period size: 100 Copynumber: 2.4 Consensus size: 104
25340823 CTGATATAAC
**
25340833 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
25340898 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
25340935 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
25340998 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
25341040 ATGCCAATGCCATGTCCCAGACATGG--TTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
25341081 TTACCCAAAT
Statistics
Matches: 131, Mismatches: 8, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 15 0.11
105 2 0.02
106 24 0.18
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:25341196 original size:13 final size:13
Alignment explanation
Indices: 25341175--25341206 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
25341165 GCTTGGATCA
*
25341175 TCATCAAATAAAT
1 TCATAAAATAAAT
25341188 TCATAAAATAAAT
1 TCATAAAATAAAT
25341201 TCATAA
1 TCATAA
25341207 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:25341452 original size:30 final size:30
Alignment explanation
Indices: 25341417--25341474 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
25341407 CCTCGACTCT
*
25341417 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
25341447 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
25341475 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:25370619 original size:24 final size:24
Alignment explanation
Indices: 25370573--25370619 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
25370563 ATTTATTTAA
* *
25370573 ATGTGTACAATTGAATCAAAATTT
1 ATGTATACAATTGAACCAAAATTT
* *
25370597 ATGTATACATTTGAACCATAATT
1 ATGTATACAATTGAACCAAAATT
25370620 AAAGTTTCAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (24 bp):
ATGTATACAATTGAACCAAAATTT
Found at i:25380352 original size:15 final size:15
Alignment explanation
Indices: 25380318--25380356 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
25380308 ACACAGATCA
*
25380318 AGATGATCATGAGAT
1 AGATGATGATGAGAT
*
25380333 AGATGATGATGAGTT
1 AGATGATGATGAGAT
*
25380348 TGATGATGA
1 AGATGATGA
25380357 AGTATTGGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.36, C:0.03, G:0.31, T:0.31
Consensus pattern (15 bp):
AGATGATGATGAGAT
Found at i:25391922 original size:24 final size:24
Alignment explanation
Indices: 25391873--25391924 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
25391863 ATTTAGCCTT
* *
25391873 ATTTATTTAACAGGGACTAACTTA
1 ATTTATTTAACAGAGACAAACTTA
*
25391897 ATTTATTTAACAGTAGAGAAAC-TA
1 ATTTATTTAACAG-AGACAAACTTA
25391921 ATTT
1 ATTT
25391925 GATCAGGCCC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (24 bp):
ATTTATTTAACAGAGACAAACTTA
Found at i:25393165 original size:4 final size:4
Alignment explanation
Indices: 25393156--25393193 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
25393146 TGAAATTGCT
* *
25393156 TATG TATG TATG TATG TATG TATG TATG CATG CATG TA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TA
25393194 AATTTCTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.26, C:0.05, G:0.24, T:0.45
Consensus pattern (4 bp):
TATG
Found at i:25397752 original size:7 final size:7
Alignment explanation
Indices: 25397728--25397767 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
25397718 AAAGTATTTT
25397728 AAAATTA
1 AAAATTA
*
25397735 AAGATTA
1 AAAATTA
25397742 AAAATTA
1 AAAATTA
*
25397749 AAAAATA
1 AAAATTA
*
25397756 AAAATAA
1 AAAATTA
25397763 AAAAT
1 AAAAT
25397768 ATATTTATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.23
Consensus pattern (7 bp):
AAAATTA
Found at i:25403811 original size:15 final size:15
Alignment explanation
Indices: 25403791--25403823 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
25403781 CTCGAGGAGA
*
25403791 AACAGAGACTTGCTG
1 AACAGAAACTTGCTG
25403806 AACAGAAACTTGCTG
1 AACAGAAACTTGCTG
25403821 AAC
1 AAC
25403824 CTGAAATGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.18
Consensus pattern (15 bp):
AACAGAAACTTGCTG
Found at i:25412786 original size:49 final size:49
Alignment explanation
Indices: 25412723--25412818 Score: 138
Period size: 49 Copynumber: 2.0 Consensus size: 49
25412713 ACATTTCAAG
* * * *
25412723 TTCAAGTAAATTTAGATTTGGATTATTTCGGATTGTGGGTCATTTTATA
1 TTCAAATAAATTTAGATTTGGATTATTTCAGATTATGGATCATTTTATA
* *
25412772 TTCAAATAAATTTAGGTTTGGATTGTTTCAGATTATGGATCATTTTA
1 TTCAAATAAATTTAGATTTGGATTATTTCAGATTATGGATCATTTTA
25412819 GGTTCAAGTC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.28, C:0.06, G:0.19, T:0.47
Consensus pattern (49 bp):
TTCAAATAAATTTAGATTTGGATTATTTCAGATTATGGATCATTTTATA
Found at i:25418856 original size:67 final size:67
Alignment explanation
Indices: 25418738--25418866 Score: 179
Period size: 67 Copynumber: 1.9 Consensus size: 67
25418728 CCATCAGAAA
* * *
25418738 GAAACTATATTGCTTCGTGTAGGAATAGCAATTTAGGAATCGGAGTAATTTGCTTCATTATCAAA
1 GAAACTATATTGCTTCGTGTAGGAATAGCAATTCAGGAATCGGAATAATTTGCTTCACTATCAAA
25418803 CG
66 CG
* * * *
25418805 GAAACTATATTGCTTTGTGTAGGAATAGCAGTTCCA-GAATCTGAATCATTTGCTTCACTATC
1 GAAACTATATTGCTTCGTGTAGGAATAGCAATT-CAGGAATCGGAATAATTTGCTTCACTATC
25418867 TCTCTATATC
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
67 53 0.98
68 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (67 bp):
GAAACTATATTGCTTCGTGTAGGAATAGCAATTCAGGAATCGGAATAATTTGCTTCACTATCAAA
CG
Found at i:25421216 original size:28 final size:28
Alignment explanation
Indices: 25421176--25421232 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
25421166 TGAATATTCA
25421176 AATTTTGAGAAGTAGAGAGTCAGTTATT
1 AATTTTGAGAAGTAGAGAGTCAGTTATT
25421204 AATTTTGAGAAGTAGAGAGTCAGTTATT
1 AATTTTGAGAAGTAGAGAGTCAGTTATT
25421232 A
1 A
25421233 TTTCCTTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.35
Consensus pattern (28 bp):
AATTTTGAGAAGTAGAGAGTCAGTTATT
Found at i:25423304 original size:15 final size:17
Alignment explanation
Indices: 25423261--25423310 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
25423251 ATCATCTCTG
25423261 AATGTTAGATAATATAA
1 AATGTTAGATAATATAA
*
25423278 AAT-TT--ATAATAAAAA
1 AATGTTAGATAAT-ATAA
25423293 AATGTTAGATAATATAA
1 AATGTTAGATAATATAA
25423310 A
1 A
25423311 TAAGTATGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 5 0.19
15 6 0.22
16 4 0.15
17 7 0.26
18 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (17 bp):
AATGTTAGATAATATAA
Found at i:25425045 original size:21 final size:21
Alignment explanation
Indices: 25425019--25425064 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
25425009 TTAATATATT
*
25425019 TTATTTT-ATAAATTTATTTAA
1 TTATTTTAATAAA-TTAATTAA
*
25425040 TTATTTTAATTAATTAATTAA
1 TTATTTTAATAAATTAATTAA
25425061 TTAT
1 TTAT
25425065 ATAATTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTATTTTAATAAATTAATTAA
Found at i:25425047 original size:13 final size:13
Alignment explanation
Indices: 25425008--25425055 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
25424998 TATTTAAGAT
25425008 TTTAATATATTTTA
1 TTTAAT-TATTTTA
* * *
25425022 TTTTATAAATTTA
1 TTTAATTATTTTA
25425035 TTTAATTATTTTA
1 TTTAATTATTTTA
*
25425048 ATTAATTA
1 TTTAATTA
25425056 ATTAATTATA
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
13 22 0.81
14 5 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTAATTATTTTA
Found at i:25425073 original size:21 final size:20
Alignment explanation
Indices: 25425024--25425073 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 20
25425014 ATATTTTATT
*
25425024 TTATA-AATTTATTTAATTA
1 TTATATAATTTAATTAATTA
25425043 TT-T-TAA-TTAATTAATTAA
1 TTATATAATTTAATTAATT-A
25425061 TTATATAATTTAA
1 TTATATAATTTAA
25425074 AAATCTCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
17 9 0.36
18 6 0.24
19 3 0.12
20 3 0.12
21 4 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTATATAATTTAATTAATTA
Found at i:25426620 original size:20 final size:19
Alignment explanation
Indices: 25426579--25426622 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
25426569 AAAAAAAAAA
*
25426579 TAAAAAATATTAACATTAT
1 TAAAAAATATTAAAATTAT
25426598 TAAAAAATATATAAAAGTT-T
1 TAAAAAATAT-TAAAA-TTAT
25426618 TAAAA
1 TAAAA
25426623 TTTTAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 10 0.45
20 10 0.45
21 2 0.09
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (19 bp):
TAAAAAATATTAAAATTAT
Found at i:25426628 original size:28 final size:29
Alignment explanation
Indices: 25426559--25426629 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 29
25426549 TTTTTTAATA
25426559 TTTAAAA-TTTAAAAAAAAAATAAAAAAT
1 TTTAAAATTTTAAAAAAAAAATAAAAAAT
* * * * *
25426587 ATTAACATTATTAAAAAATATAT-AAAAGT
1 TTTAAAATT-TTAAAAAAAAAATAAAAAAT
25426616 TTTAAAATTTTAAA
1 TTTAAAATTTTAAA
25426630 TTTAATTAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
28 10 0.29
29 13 0.38
30 11 0.32
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (29 bp):
TTTAAAATTTTAAAAAAAAAATAAAAAAT
Found at i:25430247 original size:33 final size:33
Alignment explanation
Indices: 25430208--25430381 Score: 228
Period size: 33 Copynumber: 5.3 Consensus size: 33
25430198 CTTTACTTTT
* *
25430208 CTCACCTGCTTTTTTAATGGATTCACC-TTCTCC
1 CTCACCTGCATTTTCAATGGATTCACCTTTC-CC
*
25430241 CTCACCTGGATTTTCAATGGATTCACC-TTCTCC
1 CTCACCTGCATTTTCAATGGATTCACCTTTC-CC
*
25430274 CTCACCTGGATTTTCAATGGATTCACCTTTCCC
1 CTCACCTGCATTTTCAATGGATTCACCTTTCCC
* *
25430307 CTCACCTGC-TTTTACAGTGGATTCACGTTTCCC
1 CTCACCTGCATTTT-CAATGGATTCACCTTTCCC
* *
25430340 CTCGCCTGGATTTTCAATGGATTCACCTTTCCC
1 CTCACCTGCATTTTCAATGGATTCACCTTTCCC
25430373 CTCACCTGC
1 CTCACCTGC
25430382 TGCTACAGGT
Statistics
Matches: 126, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
32 4 0.03
33 115 0.91
34 7 0.06
ACGTcount: A:0.16, C:0.34, G:0.13, T:0.37
Consensus pattern (33 bp):
CTCACCTGCATTTTCAATGGATTCACCTTTCCC
Found at i:25434023 original size:20 final size:20
Alignment explanation
Indices: 25433985--25434023 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
25433975 TTACAAGTTG
*
25433985 TCCTTCAATTCTCTATATTT
1 TCCTTCAATTCGCTATATTT
*
25434005 TCCTTCAATTCGCTTTATT
1 TCCTTCAATTCGCTATATT
25434024 CCAACTGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.26, G:0.03, T:0.54
Consensus pattern (20 bp):
TCCTTCAATTCGCTATATTT
Found at i:25434068 original size:14 final size:14
Alignment explanation
Indices: 25434049--25434078 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
25434039 CCATCTCCTT
*
25434049 TTCGTTTCGTTTCC
1 TTCGTTTCATTTCC
25434063 TTCGTTTCATTTCC
1 TTCGTTTCATTTCC
25434077 TT
1 TT
25434079 TCCATAGCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.03, C:0.27, G:0.10, T:0.60
Consensus pattern (14 bp):
TTCGTTTCATTTCC
Found at i:25439485 original size:43 final size:43
Alignment explanation
Indices: 25439438--25439618 Score: 130
Period size: 43 Copynumber: 4.0 Consensus size: 43
25439428 TAAAGTTAGT
* *
25439438 GGCGTTTTTAAGAAAAGCGCCGCTAAAAGTCATGTTCTTTAGC
1 GGCGTTTTTAAGAAAAGCGCCGCTAAATGTCATGTTCTATAGC
** * * *
25439481 GGCGTCATGTTCGTTGTGGGGAAAGTGCCACTAAATGTCATGTTCTATAGC
1 -G-G-C--GTT--TT-TAAGAAAAGCGCCGCTAAATGTCATGTTCTATAGC
* * * * *
25439532 GGCGTTTGTGAA-AAAAACGTCGCTAAAGGTTATGTTCTATAGC
1 GGCGTTT-TTAAGAAAAGCGCCGCTAAATGTCATGTTCTATAGC
* ** *
25439575 GGCGTTTGTGGGAAAAGTGCCGCTAAATGTCATGTTCTATAGC
1 GGCGTTTTTAAGAAAAGCGCCGCTAAATGTCATGTTCTATAGC
25439618 G
1 G
25439619 CCGCAAATTT
Statistics
Matches: 102, Mismatches: 26, Indels: 19
0.69 0.18 0.13
Matches are distributed among these distances:
43 58 0.57
44 2 0.02
45 2 0.02
46 4 0.04
48 4 0.04
49 1 0.01
50 3 0.03
51 28 0.27
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (43 bp):
GGCGTTTTTAAGAAAAGCGCCGCTAAATGTCATGTTCTATAGC
Found at i:25442946 original size:43 final size:43
Alignment explanation
Indices: 25442898--25443259 Score: 366
Period size: 43 Copynumber: 8.3 Consensus size: 43
25442888 TTTTAGAAAT
* * * * *
25442898 AAACGCCGCTAAAGAACAAGACCTTTAGGGGCGCTATTCCGAA
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* *
25442941 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTACCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* * *
25442984 AAACGCCGCTAAAGAGCAAGACCTTTAACGGTGCTTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* * *
25443027 AAATGCCGCTAAAGACCATGACCTTTAGCAGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* *
25443070 AAATGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * * *
25443113 AAACGTCGCTAAAGACTATGACCTTTAGCGGTGATTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * * **
25443156 AAACGCCTCTAACTCTAAAGAACATGACCTTTAGCGGTGCTTTTATCAC
1 AAACG---C---CGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* ** * * * *
25443205 AAACGCCACTAAAGAATAA-ACCTTTACCGGCGCTTATCGCAA
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
25443247 AAACGCCGCTAAA
1 AAACGCCGCTAAA
25443260 AACATAACCT
Statistics
Matches: 268, Mismatches: 45, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
42 29 0.11
43 202 0.75
46 1 0.00
49 36 0.13
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.22
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
Found at i:25443136 original size:129 final size:128
Alignment explanation
Indices: 25442898--25443273 Score: 412
Period size: 129 Copynumber: 2.9 Consensus size: 128
25442888 TTTTAGAAAT
* * * * * *
25442898 AAACGCCGCTAAAGAACAAGACCTTTAGGGGCGCTATTCCGAAAAACGCCGCTAAAGACCATGAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
* * * *
25442963 CTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGAGCAAGACCTTTAACGGTGCTTTTCCCAC
66 CTTTAGCGGCGCTTATCCCACAAACGCCGCTAAAGA-CATGACCTTTAACGGTGATTTTCCCAC
* * * *
25443027 AAATGCCGCTAAAGACCATGACCTTTAGCAGCGCTTTTCCCACAAATGCCGCTAAAGACCAAGAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
* * *
25443092 CTTTAGCGGCGCTTCTCCCACAAACGTCGCTAAAGACTATGACCTTTAGCGGTGATTTTCCCAC
66 CTTTAGCGGCGCTTATCCCACAAACGCCGCTAAAGAC-ATGACCTTTAACGGTGATTTTCCCAC
* * ** * *
25443156 AAACGCCTCTAACTCTAAAGAACATGACCTTTAGCGGTGCTTTTATCACAAACGCCACTAAAGAA
1 AAACG---C---CGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAC
* * * * * *
25443221 TAA-ACCTTTACCGGCGCTTATCGCAAAAACGCCGCTAAAAACATAACCTTTAA
60 CAAGACCTTTAGCGGCGCTTATCCCACAAACGCCGCTAAAGACATGACCTTTAA
25443274 AAAAATATAT
Statistics
Matches: 205, Mismatches: 35, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
128 1 0.00
129 115 0.56
132 1 0.00
133 9 0.04
134 33 0.16
135 46 0.22
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (128 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
CTTTAGCGGCGCTTATCCCACAAACGCCGCTAAAGACATGACCTTTAACGGTGATTTTCCCAC
Found at i:25443193 original size:49 final size:49
Alignment explanation
Indices: 25443121--25443216 Score: 140
Period size: 49 Copynumber: 2.0 Consensus size: 49
25443111 ACAAACGTCG
* *
25443121 CTAAAGACTATGACCTTTAGCGGTGATTTTCCCACAAACGCCTCTAACT
1 CTAAAGACTATGACCTTTAGCGGTGATTTTACCACAAACGCCACTAACT
* *
25443170 CTAAAGAAC-ATGACCTTTAGCGGTGCTTTTATCACAAACGCCACTAA
1 CTAAAG-ACTATGACCTTTAGCGGTGATTTTACCACAAACGCCACTAA
25443217 AGAATAAACC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
49 40 0.95
50 2 0.05
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (49 bp):
CTAAAGACTATGACCTTTAGCGGTGATTTTACCACAAACGCCACTAACT
Found at i:25445715 original size:9 final size:10
Alignment explanation
Indices: 25445696--25445728 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
25445686 ATATTTTAGA
25445696 AAAAAATAAT
1 AAAAAATAAT
25445706 AAAAAA-AAT
1 AAAAAATAAT
25445715 AAAAAATAAT
1 AAAAAATAAT
25445725 AAAA
1 AAAA
25445729 GGTACTTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.41
10 13 0.59
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAATAAT
Found at i:25447414 original size:41 final size:41
Alignment explanation
Indices: 25447368--25447646 Score: 423
Period size: 41 Copynumber: 6.8 Consensus size: 41
25447358 AAAATCAACA
*
25447368 AAAGCCTTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCT
1 AAAGCCCTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCT
* * * *
25447409 AAAGCCCTGAACATTAGCGGCGCTTATTAAAAAACGCCACT
1 AAAGCCCTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCT
* *
25447450 AAATCCCTGAGCATTAGCGGCGCTTATTCAAAAACGCCGCT
1 AAAGCCCTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCT
*
25447491 AAAGCCCTGAGCATTAGCGACGCTTCTTCAAAAACGCCGCT
1 AAAGCCCTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCT
25447532 AAAGCCCTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCT
1 AAAGCCCTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCT
* * *
25447573 AAATCCCTGAGCATTAGCGGCGCTTTTTAAAAAACGCCGCT
1 AAAGCCCTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCT
* * * *
25447614 AAAACCCTAAACATTAGCGGCGCTTTTTCAAAA
1 AAAGCCCTGAGCATTAGCGGCGCTTCTTCAAAA
25447647 TCGCTAATGC
Statistics
Matches: 218, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 218 1.00
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.22
Consensus pattern (41 bp):
AAAGCCCTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCT
Found at i:25447831 original size:40 final size:40
Alignment explanation
Indices: 25447693--25447846 Score: 168
Period size: 40 Copynumber: 3.8 Consensus size: 40
25447683 TGGACTTAGG
* ** *
25447693 TTTTTCGCGGCGCTTTTTGGAAAA-CGCCACTAATGC-TCA
1 TTTTTAGCGGCG-TTTTTTAAAAAGCGCCACTAATGCTTGA
*
25447732 TTTTTAGCGGCGTTTTTTTAAAAAGCGCCACTAATACTTGA
1 TTTTTAGCGGCG-TTTTTTAAAAAGCGCCACTAATGCTTGA
* * *
25447773 TCTTTAGTGGCGTTTTTTAAAAAGCGCCGCTAATGCTTGA
1 TTTTTAGCGGCGTTTTTTAAAAAGCGCCACTAATGCTTGA
* **
25447813 TTTTTAGCGGTGTTTTTTATCCAAGCGCCACTAA
1 TTTTTAGCGGCGTTTTTTA-AAAAGCGCCACTAA
25447847 AAACGCCGCT
Statistics
Matches: 96, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
39 20 0.21
40 53 0.55
41 23 0.24
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTTTAAAAAGCGCCACTAATGCTTGA
Found at i:25447941 original size:43 final size:43
Alignment explanation
Indices: 25447879--25448058 Score: 247
Period size: 43 Copynumber: 4.2 Consensus size: 43
25447869 TGGTGTAGTG
* *
25447879 GTTGGCATCAACTTGTGTTTACGTGTAAGACCACATCTGGGAC
1 GTTGGCATCGACTTGTGTTTACGTGTAAGACCACGTCTGGGAC
*
25447922 GTTGGCATCGACTTATGTTTACGTGTAAGACCACGTCTGGGAC
1 GTTGGCATCGACTTGTGTTTACGTGTAAGACCACGTCTGGGAC
25447965 GTTGGCATCGACTTGTGTTTACGTGTAAGACC-CTGTCTGGGAC
1 GTTGGCATCGACTTGTGTTTACGTGTAAGACCAC-GTCTGGGAC
* *** * *
25448008 AG-TGGCATCGATTTGTAAATACATGTAAGACCACGTCTGGAAC
1 -GTTGGCATCGACTTGTGTTTACGTGTAAGACCACGTCTGGGAC
25448051 GTTGGCAT
1 GTTGGCAT
25448059 TGTACGAACT
Statistics
Matches: 123, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
42 2 0.02
43 119 0.97
44 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (43 bp):
GTTGGCATCGACTTGTGTTTACGTGTAAGACCACGTCTGGGAC
Found at i:25451524 original size:3 final size:3
Alignment explanation
Indices: 25451505--25451558 Score: 51
Period size: 3 Copynumber: 19.0 Consensus size: 3
25451495 AATTTATTTC
* * * *
25451505 ATA AT- ATA ATA ACA ATA ATA TTA ATA ATG ACA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
25451551 ATA A-A ATA
1 ATA ATA ATA
25451559 TCATTTAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
2 6 0.15
3 34 0.85
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:25455490 original size:2 final size:2
Alignment explanation
Indices: 25455485--25455516 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
25455475 AAGGGAAATG
*
25455485 GA GA GA GA GA CA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
25455517 AAAGATGGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:25470635 original size:52 final size:52
Alignment explanation
Indices: 25470578--25470732 Score: 274
Period size: 52 Copynumber: 3.0 Consensus size: 52
25470568 CTAAGAACTT
*
25470578 TGTCTTTCACTTTGTAAAAGTAGATTCCCTTTTATCTGCTCGTTTAACTTTA
1 TGTCTTTCACTTTGTAAAAGTAGATTCCCTCTTATCTGCTCGTTTAACTTTA
*
25470630 TGTCTTTCACTTTGTAAAAGCAGATTCCCTCTTATCTGCTCGTTTAACTTTA
1 TGTCTTTCACTTTGTAAAAGTAGATTCCCTCTTATCTGCTCGTTTAACTTTA
* *
25470682 TGTCTTTCACTTTGTAAAAATAGATTCCCTCTTATCTGCTCGTTTAGCTTT
1 TGTCTTTCACTTTGTAAAAGTAGATTCCCTCTTATCTGCTCGTTTAACTTT
25470733 TATCCCCTAT
Statistics
Matches: 98, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 98 1.00
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.46
Consensus pattern (52 bp):
TGTCTTTCACTTTGTAAAAGTAGATTCCCTCTTATCTGCTCGTTTAACTTTA
Found at i:25471780 original size:52 final size:52
Alignment explanation
Indices: 25471723--25471823 Score: 166
Period size: 52 Copynumber: 1.9 Consensus size: 52
25471713 ATAAGGGATA
25471723 AAAGCTAAACAAACAAATAAGAGGGAATCTACTTTTACAAAGTGAAAGACAT
1 AAAGCTAAACAAACAAATAAGAGGGAATCTACTTTTACAAAGTGAAAGACAT
* * * *
25471775 AAAGCTAAACGAGCAGATAAGAGGGAATCTGCTTTTACAAAGTGAAAGA
1 AAAGCTAAACAAACAAATAAGAGGGAATCTACTTTTACAAAGTGAAAGA
25471824 TAAATATTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.49, C:0.13, G:0.20, T:0.19
Consensus pattern (52 bp):
AAAGCTAAACAAACAAATAAGAGGGAATCTACTTTTACAAAGTGAAAGACAT
Found at i:25471993 original size:16 final size:16
Alignment explanation
Indices: 25471969--25472004 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
25471959 CTGTTCATGA
*
25471969 ATGTCTTTCCAAAGAG
1 ATGTATTTCCAAAGAG
25471985 ATGTATTTCCAAAGAG
1 ATGTATTTCCAAAGAG
25472001 ATGT
1 ATGT
25472005 GTCTTCATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Consensus pattern (16 bp):
ATGTATTTCCAAAGAG
Found at i:25478286 original size:18 final size:18
Alignment explanation
Indices: 25478263--25478299 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
25478253 AATATTGTGT
* *
25478263 TTTAGTTTTGTTTGTGCA
1 TTTAGTGTTGTTTATGCA
25478281 TTTAGTGTTGTTTATGCA
1 TTTAGTGTTGTTTATGCA
25478299 T
1 T
25478300 GTTTTGCTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.05, G:0.22, T:0.59
Consensus pattern (18 bp):
TTTAGTGTTGTTTATGCA
Found at i:25478976 original size:22 final size:20
Alignment explanation
Indices: 25478951--25478990 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
25478941 GTGGCTAATA
25478951 TTTGATAACTTAGAATAATTTC
1 TTTGATAA-TTAG-ATAATTTC
*
25478973 TTTGTTAATTAGATAATT
1 TTTGATAATTAGATAATT
25478991 AGTCGATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 4 0.24
22 7 0.41
ACGTcount: A:0.35, C:0.05, G:0.10, T:0.50
Consensus pattern (20 bp):
TTTGATAATTAGATAATTTC
Found at i:25480011 original size:89 final size:89
Alignment explanation
Indices: 25479908--25480135 Score: 255
Period size: 89 Copynumber: 2.6 Consensus size: 89
25479898 TTAATGGTGC
*** ** * **
25479908 AAAAA-ACTCTCAAACTTTTTCAAAAGGAGCAATTAAGCTCTTGTTTTTTTTTCCACTCATTTGA
1 AAAAAGACTCTCAAACTTTAAAAAAAAAAGCAATTAAGCCCTTACTTTTTTTTCCACTCATTTGA
*
25479972 ATACTTAAACTTTCAAAATGCTTAA
66 ATACTTAAACTTTCAAAATGCAT-A
* * * *
25479997 AAAAAGCCT-TCAAACCTTAAAAAAAAAAGCAATTAAGCCCTTACTTTTTTTTGCACTCATTTGG
1 AAAAAGACTCTCAAACTTTAAAAAAAAAAGCAATTAAGCCCTTACTTTTTTTTCCACTCATTTGA
* *
25480061 GTACTTGAACTTTCAAAATGCATA
66 ATACTTAAACTTTCAAAATGCATA
*
25480085 AAAAAGACTCTCAAACTTTAAAAAAAAAAAAGAAATTAAGTCCCTT-CTTTT
1 AAAAAGACTCTCAAACTTT--AAAAAAAAAAGCAATTAAG-CCCTTACTTTT
25480136 ATTAAAAATT
Statistics
Matches: 116, Mismatches: 18, Indels: 8
0.82 0.13 0.06
Matches are distributed among these distances:
88 9 0.08
89 77 0.66
90 2 0.02
91 23 0.20
92 5 0.04
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.33
Consensus pattern (89 bp):
AAAAAGACTCTCAAACTTTAAAAAAAAAAGCAATTAAGCCCTTACTTTTTTTTCCACTCATTTGA
ATACTTAAACTTTCAAAATGCATA
Found at i:25480239 original size:20 final size:18
Alignment explanation
Indices: 25480214--25480299 Score: 66
Period size: 20 Copynumber: 4.6 Consensus size: 18
25480204 AAAATAATTC
*
25480214 AAATATTAAAATATTAGAAA
1 AAATATAAAAATA-TA-AAA
25480234 AAATATAAAAATATAAAA
1 AAATATAAAAATATAAAA
*
25480252 AAATCGTAAAAA-ATTATAAA
1 AAAT-ATAAAAATA-TA-AAA
* * *
25480272 ATATATAGATATATAAAA
1 AAATATAAAAATATAAAA
*
25480290 AATTATAAAA
1 AAATATAAAA
25480300 TTTTATAAAG
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
18 17 0.33
19 16 0.31
20 19 0.37
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.28
Consensus pattern (18 bp):
AAATATAAAAATATAAAA
Found at i:25480296 original size:10 final size:9
Alignment explanation
Indices: 25480231--25480299 Score: 52
Period size: 10 Copynumber: 7.4 Consensus size: 9
25480221 AAAATATTAG
25480231 AAAAAATAT
1 AAAAAATAT
25480240 -AAAAATAT
1 AAAAAATAT
*
25480248 AAAAAAATCGT
1 -AAAAAAT-AT
25480259 AAAAAAT-T
1 AAAAAATAT
*
25480267 ATAAAATAT
1 AAAAAATAT
* *
25480276 ATAGATATAT
1 A-AAAAATAT
25480286 AAAAAATTAT
1 AAAAAA-TAT
25480296 AAAA
1 AAAA
25480300 TTTTATAAAG
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
8 15 0.32
9 5 0.11
10 26 0.55
11 1 0.02
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.26
Consensus pattern (9 bp):
AAAAAATAT
Found at i:25480573 original size:35 final size:35
Alignment explanation
Indices: 25480507--25480575 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
25480497 GGTCATTAAT
* **
25480507 TTTTTTATGATTTTTATAAAATTTTAAAATTTTTA
1 TTTTTTACGATTTTTATAAAAAATTAAAATTTTTA
*
25480542 TTTTTTACGATTTTTATAAAAAATTATAATTTTT
1 TTTTTTACGATTTTTATAAAAAATTAAAATTTTT
25480576 CGTAAATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (35 bp):
TTTTTTACGATTTTTATAAAAAATTAAAATTTTTA
Found at i:25480636 original size:46 final size:46
Alignment explanation
Indices: 25480533--25480641 Score: 118
Period size: 46 Copynumber: 2.4 Consensus size: 46
25480523 TAAAATTTTA
*
25480533 AAATTT-TTATTTTTTACGATTTTTATAAAAAATTATAATTTTTCGT
1 AAATTTATTATTTTTTAC-ATTTTTATAAAAAATTATAAATTTTCGT
* *
25480579 AAATTTA-TATTTTTTA-ATTTTTATTAAAATTTAATAAATTTTC-T
1 AAATTTATTATTTTTTACATTTTTATAAAAAATT-ATAAATTTTCGT
*
25480623 AGCATTTATTATTTATTTA
1 A-AATTTATTATTT-TTTA
25480642 TATATATTTC
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
44 16 0.30
45 14 0.26
46 20 0.37
47 4 0.07
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.58
Consensus pattern (46 bp):
AAATTTATTATTTTTTACATTTTTATAAAAAATTATAAATTTTCGT
Found at i:25481265 original size:19 final size:19
Alignment explanation
Indices: 25481238--25481289 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
25481228 ATATTTTACC
* *
25481238 ATTACTAAAAAATTTTATAA
1 ATTA-TAAAAAATTTAAAAA
25481258 ATTATAAAAAGA-TTAAAAA
1 ATTATAAAAA-ATTTAAAAA
*
25481277 AATATAAAAAATT
1 ATTATAAAAAATT
25481290 ATTTTAGAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 1 0.04
19 21 0.78
20 5 0.19
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (19 bp):
ATTATAAAAAATTTAAAAA
Found at i:25488295 original size:14 final size:15
Alignment explanation
Indices: 25488276--25488317 Score: 59
Period size: 14 Copynumber: 2.8 Consensus size: 15
25488266 TCATTAATTG
25488276 ATATATTTTTATA-A
1 ATATATTTTTATATA
25488290 ATATATTTTTAATATA
1 ATATATTTTT-ATATA
*
25488306 AAATATTTTTAT
1 ATATATTTTTAT
25488318 TCACTTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 10 0.40
15 5 0.20
16 10 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATATATTTTTATATA
Found at i:25488307 original size:17 final size:16
Alignment explanation
Indices: 25488278--25488316 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
25488268 ATTAATTGAT
*
25488278 ATATTTTT-ATA-AAT
1 ATATTTTTAATATAAA
25488292 ATATTTTTAATATAAA
1 ATATTTTTAATATAAA
25488308 ATATTTTTA
1 ATATTTTTA
25488317 TTCACTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.36
15 3 0.14
16 11 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATATTTTTAATATAAA
Found at i:25489167 original size:20 final size:20
Alignment explanation
Indices: 25489122--25489167 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
25489112 ATTTAAAAAT
* * *
25489122 ATAATTTTTATAATTTTCTA
1 ATAATTATTATAATATTATA
*
25489142 AAAATTATTATAATATTATA
1 ATAATTATTATAATATTATA
25489162 ATAATT
1 ATAATT
25489168 TCTAATCATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
ATAATTATTATAATATTATA
Found at i:25494653 original size:19 final size:21
Alignment explanation
Indices: 25494615--25494653 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
25494605 GTTTAAATTT
25494615 TATTTTCTTTACAATTTAATC
1 TATTTTCTTTACAATTTAATC
*
25494636 TATTTT-TTT-CATTTTAAT
1 TATTTTCTTTACAATTTAAT
25494654 ATCGCACATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (21 bp):
TATTTTCTTTACAATTTAATC
Found at i:25498601 original size:92 final size:92
Alignment explanation
Indices: 25498447--25498627 Score: 276
Period size: 92 Copynumber: 2.0 Consensus size: 92
25498437 TCAATGCATC
* *
25498447 AATAAAATAAGGGGAAGGTTTTCTAAAATTTTATATAAATATAAGTATCTTAAATACAATGATCT
1 AATAAAATAAGGGGAAAGTTTTCTAAAATTTTATATAAACATAAGTATCTTAAATACAATGATCT
25498512 TGTAAAAAAAAT-AGAATTTAAATGTATA
66 TGT-AAAAAAATGA-AATTTAAATGTATA
* *
25498540 AATAAAATAAGGGGAAAGTTTTCTAAAA-TTTATATAAACGTAAGTATCTTAAATACGATGATCT
1 AATAAAATAAGGGGAAAGTTTTCTAAAATTTTATATAAACATAAGTATCTTAAATACAATGATCT
* *
25498604 TGTGATAAAATGAAATTTAAATGT
66 TGTAAAAAAATGAAATTTAAATGT
25498628 CAAATATGTC
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
91 17 0.21
92 37 0.46
93 27 0.33
ACGTcount: A:0.48, C:0.05, G:0.13, T:0.34
Consensus pattern (92 bp):
AATAAAATAAGGGGAAAGTTTTCTAAAATTTTATATAAACATAAGTATCTTAAATACAATGATCT
TGTAAAAAAATGAAATTTAAATGTATA
Found at i:25498709 original size:105 final size:106
Alignment explanation
Indices: 25498536--25498732 Score: 270
Period size: 105 Copynumber: 1.9 Consensus size: 106
25498526 AATTTAAATG
* ** * * * **
25498536 TATAAATAAAATAAGGGGAAAGTTTTCTAAAATTTATATAAACGTAAGTATCTTAAATACGATGA
1 TATAAATAAAATAAAGGGAAAGTTTTAAAAAAATTATATAAACATAAATATCTTAAATACGAAAA
*
25498601 TCTTGTGATAAAATGAAATTTAAATGTCAAATATGTCGATA
66 TCTTGTGACAAAATGAAATTTAAATGTCAAATATGTCGATA
* *
25498642 TATAAATAAAATAAAGGG-AATTTTTAAAAAAATTATATAAATATAAATATCTTAAATACGAAAA
1 TATAAATAAAATAAAGGGAAAGTTTTAAAAAAATTATATAAACATAAATATCTTAAATACGAAAA
* *
25498706 TCTTGTTACAAAATGAGATTTAAATGT
66 TCTTGTGACAAAATGAAATTTAAATGT
25498733 GCATTGTTTT
Statistics
Matches: 78, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
105 61 0.78
106 17 0.22
ACGTcount: A:0.49, C:0.06, G:0.12, T:0.34
Consensus pattern (106 bp):
TATAAATAAAATAAAGGGAAAGTTTTAAAAAAATTATATAAACATAAATATCTTAAATACGAAAA
TCTTGTGACAAAATGAAATTTAAATGTCAAATATGTCGATA
Found at i:25511406 original size:40 final size:40
Alignment explanation
Indices: 25511362--25511440 Score: 158
Period size: 40 Copynumber: 2.0 Consensus size: 40
25511352 TTTTGCCCAA
25511362 CACTCCCCTCATTCTTGTTTATTTTTCCAATTTTTTTTTT
1 CACTCCCCTCATTCTTGTTTATTTTTCCAATTTTTTTTTT
25511402 CACTCCCCTCATTCTTGTTTATTTTTCCAATTTTTTTTT
1 CACTCCCCTCATTCTTGTTTATTTTTCCAATTTTTTTTT
25511441 AAATTATCTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.13, C:0.25, G:0.03, T:0.59
Consensus pattern (40 bp):
CACTCCCCTCATTCTTGTTTATTTTTCCAATTTTTTTTTT
Found at i:25518631 original size:43 final size:44
Alignment explanation
Indices: 25518566--25518652 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 44
25518556 CATGTTATAA
*
25518566 TCATATACGATGCCAATGTCCCAGACATGGTCTTACACGAAATC
1 TCATATACGATGCCAATGTCCCAAACATGGTCTTACACGAAATC
25518610 TCATAT-CGATGCCAATGTCCCAAACATGGTCTTACACGAAATC
1 TCATATACGATGCCAATGTCCCAAACATGGTCTTACACGAAATC
25518653 ATACCTCGGA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
43 36 0.86
44 6 0.14
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (44 bp):
TCATATACGATGCCAATGTCCCAAACATGGTCTTACACGAAATC
Found at i:25530333 original size:21 final size:21
Alignment explanation
Indices: 25530289--25530343 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
25530279 TTTGATACAT
* **
25530289 TTTTATAATTTTTTTATTCTAA
1 TTTT-TAATATTTTTATTAAAA
25530311 TTTTTAATATTTTTATTAAAA
1 TTTTTAATATTTTTATTAAAA
25530332 --TTTAATATTTTT
1 TTTTTAATATTTTT
25530344 TATTTTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 12 0.40
21 14 0.47
22 4 0.13
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTTAATATTTTTATTAAAA
Found at i:25535411 original size:45 final size:45
Alignment explanation
Indices: 25535341--25535441 Score: 159
Period size: 45 Copynumber: 2.2 Consensus size: 45
25535331 GTAACGGTAG
25535341 CAGTAACAGTAACAGTATTCAACACACAAAGTACT-GAATCTGTAA
1 CAGTAACAGTAACAGTATTCAACACACAAAGT-CTCGAATCTGTAA
* * *
25535386 TAGTAACAGTAACAGTATTCGACACACAAAGTGTCGAATCTGTAA
1 CAGTAACAGTAACAGTATTCAACACACAAAGTCTCGAATCTGTAA
25535431 CAGTAACAGTA
1 CAGTAACAGTA
25535442 GTTGGCATAT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
44 1 0.02
45 50 0.98
ACGTcount: A:0.43, C:0.19, G:0.16, T:0.23
Consensus pattern (45 bp):
CAGTAACAGTAACAGTATTCAACACACAAAGTCTCGAATCTGTAA
Found at i:25536694 original size:30 final size:29
Alignment explanation
Indices: 25536660--25536716 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
25536650 TTATCAAATA
25536660 AATAAA-ATCTTTTAATATAATAATTTAATT
1 AATAAATATCTTTTAAT-TAA-AATTTAATT
* *
25536690 AATAAATTTCTTTTACTTAAAATTTAA
1 AATAAATATCTTTTAATTAAAATTTAA
25536717 GAAAATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.29
30 9 0.38
31 8 0.33
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (29 bp):
AATAAATATCTTTTAATTAAAATTTAATT
Found at i:25536840 original size:17 final size:16
Alignment explanation
Indices: 25536809--25536852 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
25536799 GATTTATTTA
25536809 ATAATATAATATCATT
1 ATAATATAATATCATT
*
25536825 ATAATTTAATTATCATT
1 ATAATATAA-TATCATT
*
25536842 AATTATATAAT
1 -ATAATATAAT
25536853 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 8 0.35
17 8 0.35
18 7 0.30
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (16 bp):
ATAATATAATATCATT
Found at i:25540714 original size:2 final size:2
Alignment explanation
Indices: 25540707--25540749 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
25540697 ATGAAAGCTG
25540707 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25540749 A
1 A
25540750 AGGTGGAATC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25542795 original size:2 final size:2
Alignment explanation
Indices: 25542788--25542817 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
25542778 CAGAATCACA
25542788 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25542818 TTGGTGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25544820 original size:18 final size:19
Alignment explanation
Indices: 25544777--25544820 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
25544767 TACGTTTATT
*
25544777 TTATTTAAATTAAGATTTA
1 TTATTTAAATTAAGATGTA
* *
25544796 TTTTTTAAATTTA-ATGTA
1 TTATTTAAATTAAGATGTA
25544814 TTATTTA
1 TTATTTA
25544821 TTTTATTATT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
TTATTTAAATTAAGATGTA
Found at i:25546449 original size:25 final size:25
Alignment explanation
Indices: 25546421--25546561 Score: 98
Period size: 25 Copynumber: 5.8 Consensus size: 25
25546411 CAGCTCTTAT
*
25546421 GAGCATCCCAATATATGGCTCTCTG
1 GAGCTTCCCAATATATGGCTCTCTG
* * *
25546446 GAGCTTCCCGATATA--GCTCGCTT
1 GAGCTTCCCAATATATGGCTCTCTG
* * *
25546469 GAACTTCCCGATATATGGCTATCTG
1 GAGCTTCCCAATATATGGCTCTCTG
*
25546494 GAGCTTCCTAAT-TAATGGCTCT-TCG
1 GAGCTTCCCAATAT-ATGGCTCTCT-G
* * *
25546519 GAGCTACCCATTAT-TGGCTCGCAT-
1 GAGCTTCCCAATATATGGCTCTC-TG
*
25546543 GAGCTTCCCGAT-TATGGCT
1 GAGCTTCCCAATATATGGCT
25546562 TTTATGAGCT
Statistics
Matches: 89, Mismatches: 19, Indels: 17
0.71 0.15 0.14
Matches are distributed among these distances:
23 21 0.24
24 22 0.25
25 44 0.49
26 2 0.02
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.31
Consensus pattern (25 bp):
GAGCTTCCCAATATATGGCTCTCTG
Found at i:25546464 original size:23 final size:23
Alignment explanation
Indices: 25546433--25546501 Score: 75
Period size: 23 Copynumber: 2.9 Consensus size: 23
25546423 GCATCCCAAT
*
25546433 ATATGGCTCTCTGGAGCTTCCCG
1 ATATAGCTCTCTGGAGCTTCCCG
* * *
25546456 ATATAGCTCGCTTGAACTTCCCG
1 ATATAGCTCTCTGGAGCTTCCCG
*
25546479 ATATATGGCTATCTGGAGCTTCC
1 ATATA--GCTCTCTGGAGCTTCC
25546502 TAATTAATGG
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
23 24 0.67
25 12 0.33
ACGTcount: A:0.19, C:0.28, G:0.22, T:0.32
Consensus pattern (23 bp):
ATATAGCTCTCTGGAGCTTCCCG
Found at i:25546546 original size:24 final size:24
Alignment explanation
Indices: 25546519--25546580 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
25546509 TGGCTCTTCG
*
25546519 GAGCTACCCATTATTGGCTCGCAT
1 GAGCTTCCCATTATTGGCTCGCAT
***
25546543 GAGCTTCCCGATTA-TGGCTTTTAT
1 GAGCTTCCC-ATTATTGGCTCGCAT
25546567 GAGCTTCCCATTAT
1 GAGCTTCCCATTAT
25546581 ACAACCCAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 4 0.12
24 24 0.75
25 4 0.12
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.35
Consensus pattern (24 bp):
GAGCTTCCCATTATTGGCTCGCAT
Found at i:25551671 original size:14 final size:14
Alignment explanation
Indices: 25551654--25551680 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
25551644 ATTTAATTCT
25551654 TGAAAATTAAAATG
1 TGAAAATTAAAATG
25551668 TGAAAATTAAAAT
1 TGAAAATTAAAAT
25551681 ATTTGTGGTT
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:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (14 bp):
TGAAAATTAAAATG
Found at i:25553064 original size:26 final size:26
Alignment explanation
Indices: 25553020--25553072 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
25553010 TTATACAAAC
*
25553020 AATACTTTAAGTTAGTT-AATTGAAAT
1 AATACTTTAAGTAAGTTAAATT-AAAT
* *
25553046 AATATTTTAAGTAATTTAAATTAAAT
1 AATACTTTAAGTAAGTTAAATTAAAT
25553072 A
1 A
25553073 TATAAGTCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (26 bp):
AATACTTTAAGTAAGTTAAATTAAAT
Found at i:25553152 original size:24 final size:24
Alignment explanation
Indices: 25553085--25553158 Score: 73
Period size: 24 Copynumber: 3.1 Consensus size: 24
25553075 TAAGTCATAT
25553085 ATTAGATATTA-ATAATATAATAACA
1 ATTA-ATATTACA-AATATAATAACA
* **
25553110 ATTACTATTAC-TTTGATAATAACA
1 ATTAATATTACAAAT-ATAATAACA
25553134 ATTAATATTACAAATATAAT-ACA
1 ATTAATATTACAAATATAATAACA
25553157 AT
1 AT
25553159 ATAGTGTATC
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
23 6 0.15
24 29 0.73
25 5 0.12
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (24 bp):
ATTAATATTACAAATATAATAACA
Found at i:25555912 original size:21 final size:21
Alignment explanation
Indices: 25555888--25555938 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
25555878 GGTCTAAACA
25555888 CCCATGTGAAGGCCACACACG
1 CCCATGTGAAGGCCACACACG
* **
25555909 CCCATGTGGAGGGGACACACG
1 CCCATGTGAAGGCCACACACG
*
25555930 CCCGTGTGA
1 CCCATGTGA
25555939 GTAACCCGTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.33, G:0.31, T:0.12
Consensus pattern (21 bp):
CCCATGTGAAGGCCACACACG
Found at i:25556023 original size:21 final size:21
Alignment explanation
Indices: 25555990--25556029 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
25555980 TGCAGAGTAG
25555990 ACACGACCATGTGAAAATCTC
1 ACACGACCATGTGAAAATCTC
* *
25556011 ACACGCCCGTGTGAAAATC
1 ACACGACCATGTGAAAATC
25556030 GACAAAATCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.30, G:0.17, T:0.17
Consensus pattern (21 bp):
ACACGACCATGTGAAAATCTC
Found at i:25569814 original size:30 final size:30
Alignment explanation
Indices: 25569763--25569853 Score: 112
Period size: 30 Copynumber: 3.0 Consensus size: 30
25569753 GATTCCATAG
* *
25569763 GTCCCTGTATGTTTCATAAATTTAATATTTA
1 GTCCCTGTAT-TTTTATAAATTTAAAATTTA
25569794 GTCCCTGTATTTTTATAAATTTAAAATTTA
1 GTCCCTGTATTTTTATAAATTTAAAATTTA
* * *
25569824 GTCTCTTTATTTTTA-AAATTTTTAAATTTA
1 GTCCCTGTATTTTTATAAA-TTTAAAATTTA
25569854 AGTTTAATAG
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
29 3 0.06
30 41 0.76
31 10 0.19
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.53
Consensus pattern (30 bp):
GTCCCTGTATTTTTATAAATTTAAAATTTA
Found at i:25570109 original size:20 final size:20
Alignment explanation
Indices: 25570084--25570123 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
25570074 CGTAAAATGA
*
25570084 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
25570104 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
25570124 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:25570113 original size:34 final size:35
Alignment explanation
Indices: 25570069--25570135 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
25570059 CAGTAAAATA
*
25570069 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
25570103 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
25570136 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:25570139 original size:14 final size:15
Alignment explanation
Indices: 25570063--25570139 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
25570053 GATTGCCAGT
* *
25570063 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
25570077 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
25570091 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
25570111 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
25570126 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
25570140 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:25572559 original size:34 final size:35
Alignment explanation
Indices: 25572501--25572567 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
25572491 CAAACATCAG
25572501 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
*
25572536 AAAATATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAA
25572568 TATTTTACTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 17 0.55
35 14 0.45
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:25575085 original size:13 final size:13
Alignment explanation
Indices: 25575063--25575096 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
25575053 CATCTATTGG
*
25575063 AATATAATATTTA
1 AATATTATATTTA
*
25575076 ATTATTATATTTA
1 AATATTATATTTA
25575089 AATATTAT
1 AATATTAT
25575097 TTATATATTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
AATATTATATTTA
Found at i:25575105 original size:24 final size:24
Alignment explanation
Indices: 25575070--25575115 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
25575060 TGGAATATAA
*
25575070 TATTTAATTATTATATTTAAATAT
1 TATTTAATTATTATAATTAAATAT
*
25575094 TATTT-ATATATTCTAATTAAAT
1 TATTTAAT-TATTATAATTAAAT
25575116 TTAATAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 2 0.11
24 17 0.89
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
TATTTAATTATTATAATTAAATAT
Found at i:25575367 original size:13 final size:13
Alignment explanation
Indices: 25575346--25575396 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
25575336 ACACTCAAAT
25575346 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
* *
25575359 TTCTCAAAAGTAC
1 TTTTCAAAAGCAC
*
25575372 TTTTCCATAA-CAC
1 TTTT-CAAAAGCAC
25575385 TTTTCAAAAGCA
1 TTTTCAAAAGCA
25575397 ATGAAGAACT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
12 4 0.13
13 22 0.73
14 4 0.13
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.33
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:25579071 original size:10 final size:10
Alignment explanation
Indices: 25579056--25579111 Score: 57
Period size: 9 Copynumber: 5.8 Consensus size: 10
25579046 GTTGAACTTA
25579056 TTTTTAATAT
1 TTTTTAATAT
25579066 TTTTTAA-AT
1 TTTTTAATAT
25579075 TTTTTAA-AT
1 TTTTTAATAT
25579084 TTTTT-ATGA-
1 TTTTTAAT-AT
25579093 TTTTTAATGAT
1 TTTTTAAT-AT
*
25579104 TTATTAAT
1 TTTTTAAT
25579112 TGAATCGTCC
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
8 1 0.02
9 21 0.51
10 12 0.29
11 7 0.17
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (10 bp):
TTTTTAATAT
Found at i:25579263 original size:13 final size:13
Alignment explanation
Indices: 25579247--25579272 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25579237 AAATTTCTAA
25579247 ATATTTTATAATT
1 ATATTTTATAATT
25579260 ATATTTTATAATT
1 ATATTTTATAATT
25579273 TTTTTAGAAT
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATATTTTATAATT
Found at i:25586661 original size:203 final size:211
Alignment explanation
Indices: 25586403--25586873 Score: 550
Period size: 203 Copynumber: 2.2 Consensus size: 211
25586393 AACTCTCTAG
* * *
25586403 TGACAATGTATCAAATATTATTCTTATCTTTTATTGTTTTTAAAAAATAAAATAAATTGA-GTCA
1 TGACAATATATCAAATATTATTCTTATATTTTATTATTTTTAAAAAATAAAATAAATTGAGGTCA
* ** * * **
25586467 ATCATCTCAAAG-TTGAAAAATATAAACTCAATCATAGCCTAAAATAGTTTGGGTCTCTTTTTT-
66 ATCAGCTCAAAGCTAAAAAAATATAAACTCAATCACAACAAAAAATAGTTTGGGTCTCTTTTTTA
*
25586530 AAAA-A-ATA-TT-TATTTTACCATA-CCTTATAGGATC-TTTGCCAACCCCTAACTTTACTTAT
131 AAAATATATATTTATATTTTACCATATCC-TAGAGGA-CATTTGCCAACCCCTAACTTTACTTAT
25586589 A-AAGTCTAAA-AATTCAC
194 AGAA-TCTAAATAATTCAC
* * *
25586606 TGACAATATATTAAATATTATTCTTATATTTTATTATATTTAAACAATAAAATAAATTGAGGTCA
1 TGACAATATATCAAATATTATTCTTATATTTTATTATTTTTAAAAAATAAAATAAATTGAGGTCA
* * * *
25586671 ATTAGCTCAAAGCTAAAAAAATATAAATTCAATCACAATAAAAAATAGTTTGGTTCTCTTTTTTA
66 ATCAGCTCAAAGCTAAAAAAATATAAACTCAATCACAACAAAAAATAGTTTGGGTCTCTTTTTTA
* * * *
25586736 AAAATATATATTTTTAAAATATTTTACTATATCCTAGAGTACATTTGTCAACCCCTAATTTTACT
131 AAAATATATA--TTT---ATATTTTACCATATCCTAGAGGACATTTGCCAACCCCTAACTTTACT
*
25586801 TATAGAATCTAAATATTTCAC
191 TATAGAATCTAAATAATTCAC
* * *
25586822 TGAGAATATATCAATTATTATTCCTATATTTTATTATTTTTAATAAAATAAA
1 TGACAATATATCAAATATTATTCTTATATTTTATTATTTTTAA-AAAATAAA
25586874 TTCAACTCAA
Statistics
Matches: 222, Mismatches: 29, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
203 54 0.24
204 14 0.06
205 42 0.19
206 4 0.02
207 1 0.00
208 3 0.01
211 2 0.01
214 1 0.00
215 46 0.21
216 48 0.22
217 7 0.03
ACGTcount: A:0.41, C:0.13, G:0.07, T:0.40
Consensus pattern (211 bp):
TGACAATATATCAAATATTATTCTTATATTTTATTATTTTTAAAAAATAAAATAAATTGAGGTCA
ATCAGCTCAAAGCTAAAAAAATATAAACTCAATCACAACAAAAAATAGTTTGGGTCTCTTTTTTA
AAAATATATATTTATATTTTACCATATCCTAGAGGACATTTGCCAACCCCTAACTTTACTTATAG
AATCTAAATAATTCAC
Found at i:25589097 original size:11 final size:11
Alignment explanation
Indices: 25589081--25589145 Score: 64
Period size: 11 Copynumber: 6.0 Consensus size: 11
25589071 AATTAATCAC
25589081 ATTAATATTAA
1 ATTAATATTAA
25589092 ATTAATA--AA
1 ATTAATATTAA
* *
25589101 A-TATTATCAA
1 ATTAATATTAA
*
25589111 GATAAATATTAA
1 -ATTAATATTAA
25589123 ATTAATATTAA
1 ATTAATATTAA
25589134 TATTAATATTAA
1 -ATTAATATTAA
25589146 TTGTTTCTTG
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
8 4 0.09
9 3 0.07
10 2 0.05
11 18 0.41
12 17 0.39
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (11 bp):
ATTAATATTAA
Found at i:25589134 original size:6 final size:6
Alignment explanation
Indices: 25589115--25589146 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
25589105 TATCAAGATA
25589115 AATATT AA-ATT AATATT AATATT AATATT AAT
1 AATATT AATATT AATATT AATATT AATATT AAT
25589147 TGTTTCTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
AATATT
Found at i:25589141 original size:23 final size:22
Alignment explanation
Indices: 25589081--25589145 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 22
25589071 AATTAATCAC
25589081 ATTAATATTAAATTAATA--AA
1 ATTAATATTAAATTAATATTAA
* * *
25589101 A-TATTATCAAGATAAATATTAA
1 ATTAATATTAA-ATTAATATTAA
25589123 ATTAATATTAATATTAATATTAA
1 ATTAATATTAA-ATTAATATTAA
25589146 TTGTTTCTTG
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
19 7 0.21
20 7 0.21
22 3 0.09
23 17 0.50
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (22 bp):
ATTAATATTAAATTAATATTAA
Found at i:25589618 original size:52 final size:50
Alignment explanation
Indices: 25589543--25589649 Score: 151
Period size: 52 Copynumber: 2.1 Consensus size: 50
25589533 AAAAGCTAAA
* * * *
25589543 TAAATAAAAATGAGATTCTATTAGATTAATTATCTTTTTGAAGTTAAAAATC
1 TAAATAAAAATAAAATTCAATTAGATTAATTA--TTTTTGAACTTAAAAATC
*
25589595 TAAATAAAAATAAAATTCAATTAGATTAATTATTTTTGAACTTATAAATC
1 TAAATAAAAATAAAATTCAATTAGATTAATTATTTTTGAACTTAAAAATC
25589645 TAAAT
1 TAAAT
25589650 TTGACTCAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
50 21 0.42
52 29 0.58
ACGTcount: A:0.48, C:0.06, G:0.07, T:0.40
Consensus pattern (50 bp):
TAAATAAAAATAAAATTCAATTAGATTAATTATTTTTGAACTTAAAAATC
Found at i:25590572 original size:12 final size:12
Alignment explanation
Indices: 25590555--25590579 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25590545 GTAAAACACT
25590555 TAAATAATATTA
1 TAAATAATATTA
25590567 TAAATAATATTA
1 TAAATAATATTA
25590579 T
1 T
25590580 GTTGGAGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAATAATATTA
Found at i:25596116 original size:18 final size:19
Alignment explanation
Indices: 25596095--25596131 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
25596085 AGAAAAAAAT
25596095 AAATATG-CATATATATAA
1 AAATATGACATATATATAA
25596113 AAATATGTACATATATATA
1 AAATATG-ACATATATATA
25596132 TGTAGGTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.35
Consensus pattern (19 bp):
AAATATGACATATATATAA
Found at i:25597829 original size:25 final size:28
Alignment explanation
Indices: 25597784--25597838 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
25597774 TTAAGAACAC
*
25597784 ATATATATTATATAAAGAAAT-ATGTAT
1 ATATATACTATATAAAGAAATCATGTAT
25597811 ATATATACTATAT-AA-AAATGCATGTAT
1 ATATATACTATATAAAGAAAT-CATGTAT
25597838 A
1 A
25597839 AGTTTAGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 4 0.16
26 2 0.08
27 19 0.76
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.38
Consensus pattern (28 bp):
ATATATACTATATAAAGAAATCATGTAT
Found at i:25598527 original size:18 final size:19
Alignment explanation
Indices: 25598500--25598538 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
25598490 TTGTTTTAGG
* *
25598500 TAAAATAAAATGAAA-AAA
1 TAAAAGAAAATAAAAGAAA
25598518 TAAAAGAAAATAAAAGAAA
1 TAAAAGAAAATAAAAGAAA
25598537 TA
1 TA
25598539 TATAAACAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (19 bp):
TAAAAGAAAATAAAAGAAA
Found at i:25601738 original size:19 final size:19
Alignment explanation
Indices: 25601714--25601752 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
25601704 TTATTAAAAT
25601714 ATTATAACAAATT-TAGAAA
1 ATTATAA-AAATTATAGAAA
25601733 ATTATAAAAATTATAGAAA
1 ATTATAAAAATTATAGAAA
25601752 A
1 A
25601753 ATATGTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (19 bp):
ATTATAAAAATTATAGAAA
Found at i:25601912 original size:75 final size:74
Alignment explanation
Indices: 25601789--25601931 Score: 164
Period size: 75 Copynumber: 1.9 Consensus size: 74
25601779 AATATTAAGT
* *** *
25601789 ATTATAAAATAGTATTAATGTATTGTGAAAAAAATGAAAAATCATAG-AAATTATATAAATTACA
1 ATTATAAAATAGTATTAATATATTACAAAAAAAATGAAAAAT-ATAGAAAATTATAAAAATTA-A
25601853 AAAATAGCAAA
64 AAAATAGCAAA
* * *
25601864 ATTATAAAATATTTTTAATATATTACAAAAAAAACTGAAAGAAT-TAGAAAATTTTAAAAATTAA
1 ATTATAAAATAGTATTAATATATTACAAAAAAAA-TGAAA-AATATAGAAAATTATAAAAATTAA
25601928 AAAA
64 AAAA
25601932 CTAAAAATTA
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
75 36 0.63
76 18 0.32
77 3 0.05
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.31
Consensus pattern (74 bp):
ATTATAAAATAGTATTAATATATTACAAAAAAAATGAAAAATATAGAAAATTATAAAAATTAAAA
AATAGCAAA
Found at i:25603192 original size:46 final size:46
Alignment explanation
Indices: 25603125--25603218 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
25603115 TCAAAACAAA
25603125 ATAACATTTTTCGGAACAATAATTAATTAAGATAACTAACTTTAAT
1 ATAACATTTTTCGGAACAATAATTAATTAAGATAACTAACTTTAAT
25603171 ATAACATTTTTCGGAACAATAATTAATTAAGATAACTAACTTTAAT
1 ATAACATTTTTCGGAACAATAATTAATTAAGATAACTAACTTTAAT
25603217 AT
1 AT
25603219 TAATTAAGTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.37
Consensus pattern (46 bp):
ATAACATTTTTCGGAACAATAATTAATTAAGATAACTAACTTTAAT
Found at i:25603539 original size:21 final size:22
Alignment explanation
Indices: 25603508--25603548 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
25603498 GTAGTAATTC
*
25603508 TTATGATTTTTATAATTTTTTT
1 TTATGATTTTTATAAATTTTTT
25603530 TTATG-TTTTTATAAATTTT
1 TTATGATTTTTATAAATTTT
25603549 GAAGTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (22 bp):
TTATGATTTTTATAAATTTTTT
Found at i:25603560 original size:28 final size:27
Alignment explanation
Indices: 25603528--25603601 Score: 73
Period size: 25 Copynumber: 2.8 Consensus size: 27
25603518 TATAATTTTT
*
25603528 TTTTATGTTT-TTATAAATTTTGAAGTAA
1 TTTTATATTTGTTAT-AATTTTGAA-TAA
*
25603556 TTTTATATTTGTTATAATTTTTAATAA
1 TTTTATATTTGTTATAATTTTGAATAA
* *
25603583 --TTATTTTTATTATAATTTT
1 TTTTATATTTGTTATAATTTT
25603602 AGCCAACTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
25 17 0.41
27 3 0.07
28 17 0.41
29 4 0.10
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (27 bp):
TTTTATATTTGTTATAATTTTGAATAA
Found at i:25611771 original size:41 final size:41
Alignment explanation
Indices: 25611720--25611902 Score: 174
Period size: 41 Copynumber: 4.5 Consensus size: 41
25611710 TTTAAACAGA
* ** *
25611720 TTCACTGGCACTTCA-CCTGATAGGCTTATAGTTTAATTCCG
1 TTCACCGGCACTT-AGCCTGATAGGCTTATAGCCTAATTCAG
* * *
25611761 TTCACCGGCACTTAGCCTGTTAGGCCTATAGCCTGATTCAG
1 TTCACCGGCACTTAGCCTGATAGGCTTATAGCCTAATTCAG
* * * * *
25611802 TTCACCAGCACTTAGCCTGCTAGGCTTGTAGCCTGATTCAA
1 TTCACCGGCACTTAGCCTGATAGGCTTATAGCCTAATTCAG
* * * *
25611843 CTCACCGGCACTTAGCCTGCT-GGACGTATAGTCC-AATTCAA
1 TTCACCGGCACTTAGCCTGATAGG-CTTATAG-CCTAATTCAG
25611884 TTCACCGGCACTTAGCCTG
1 TTCACCGGCACTTAGCCTG
25611903 CTAGACGTAT
Statistics
Matches: 121, Mismatches: 18, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
40 3 0.02
41 116 0.96
42 2 0.02
ACGTcount: A:0.21, C:0.30, G:0.20, T:0.30
Consensus pattern (41 bp):
TTCACCGGCACTTAGCCTGATAGGCTTATAGCCTAATTCAG
Found at i:25611903 original size:41 final size:41
Alignment explanation
Indices: 25611761--25611919 Score: 196
Period size: 41 Copynumber: 3.9 Consensus size: 41
25611751 TTTAATTCCG
* * *
25611761 TTCACCGGCACTTAGCCTGTTAGGCCTATAGCCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCGTATAGCCTGATTCAA
* * *
25611802 TTCACCAGCACTTAGCCTGCTAGGCTTGTAGCCTGATTCAA
1 TTCACCGGCACTTAGCCTGCTAGGCGTATAGCCTGATTCAA
* *
25611843 CTCACCGGCACTTAGCCTGCT-GGACGTATAGTCC-AATTCAA
1 TTCACCGGCACTTAGCCTGCTAGG-CGTATAG-CCTGATTCAA
* *
25611884 TTCACCGGCACTTAGCCTGCTAGACGTATAGTCTGA
1 TTCACCGGCACTTAGCCTGCTAGGCGTATAGCCTGA
25611920 ATAATTTCAC
Statistics
Matches: 100, Mismatches: 14, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
40 3 0.03
41 94 0.94
42 3 0.03
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.28
Consensus pattern (41 bp):
TTCACCGGCACTTAGCCTGCTAGGCGTATAGCCTGATTCAA
Found at i:25614380 original size:18 final size:18
Alignment explanation
Indices: 25614344--25614382 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
25614334 TTATTATTGT
**
25614344 TAAAATTTTCTATTAAAA
1 TAAAATTTTAAATTAAAA
*
25614362 TAAAATTTTAAATTTAAA
1 TAAAATTTTAAATTAAAA
25614380 TAA
1 TAA
25614383 TTTATTATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAAATTTTAAATTAAAA
Found at i:25615726 original size:22 final size:24
Alignment explanation
Indices: 25615695--25615746 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
25615685 TTATAGAGTT
* *
25615695 AAAAATACTAGAT-ATATC-TATA
1 AAAAAAACTAGATAAAATCATATA
25615717 AAAAAAACTAGATAAAATCATATA
1 AAAAAAACTAGATAAAATCATATA
25615741 AAAAAA
1 AAAAAA
25615747 TTTGTATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 12 0.46
23 4 0.15
24 10 0.38
ACGTcount: A:0.65, C:0.08, G:0.04, T:0.23
Consensus pattern (24 bp):
AAAAAAACTAGATAAAATCATATA
Found at i:25615864 original size:15 final size:16
Alignment explanation
Indices: 25615842--25615883 Score: 68
Period size: 15 Copynumber: 2.7 Consensus size: 16
25615832 GTTTATATAT
25615842 ATAAAAAAAATTTCAA
1 ATAAAAAAAATTTCAA
*
25615858 A-AAAAAAAATTTTAA
1 ATAAAAAAAATTTCAA
25615873 ATAAAAAAAAT
1 ATAAAAAAAAT
25615884 CAAAAAATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (16 bp):
ATAAAAAAAATTTCAA
Found at i:25615929 original size:29 final size:28
Alignment explanation
Indices: 25615891--25616009 Score: 125
Period size: 29 Copynumber: 4.1 Consensus size: 28
25615881 AATCAAAAAA
25615891 TACATTTTGACCTCTAAACTTTTTGAAAT
1 TACATTTTGACC-CTAAACTTTTTGAAAT
* *
25615920 TATATTTTGACCCATAAACCTTTTGAAAT
1 TACATTTTGACCC-TAAACTTTTTGAAAT
*
25615949 TACATTTTGACCC-ATAACATTTTTTAAAT
1 TACATTTTGACCCTA-AAC-TTTTTGAAAT
*
25615978 TACATTTTTACCCCTAAA-TTTTCTCGAAAT
1 TACATTTTGA-CCCTAAACTTTT-T-GAAAT
25616008 TA
1 TA
25616010 TGTTTCGGCC
Statistics
Matches: 76, Mismatches: 7, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
27 1 0.01
28 8 0.11
29 55 0.72
30 11 0.14
31 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.05, T:0.44
Consensus pattern (28 bp):
TACATTTTGACCCTAAACTTTTTGAAAT
Found at i:25616279 original size:10 final size:10
Alignment explanation
Indices: 25616260--25616309 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
25616250 TTTTTCGAAG
*
25616260 GAAAAAAGAA
1 GAAAAGAGAA
25616270 GAAAAGAGAA
1 GAAAAGAGAA
25616280 GAAAAGAGAA
1 GAAAAGAGAA
* *
25616290 -AGAGGAGAA
1 GAAAAGAGAA
25616299 GAAAAGA-AA
1 GAAAAGAGAA
25616308 GA
1 GA
25616310 GTACCGGCGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 11 0.32
10 23 0.68
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
GAAAAGAGAA
Done.