Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold492
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: 781693
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:159790 original size:79 final size:81
Alignment explanation
Indices: 159634--159792 Score: 232
Period size: 79 Copynumber: 2.0 Consensus size: 81
159624 GATGAAAAGT
* * *
159634 TTAATATTTTGGAGATAAAACCCGGGGTTGGAGTATCTCCTCGGAAATAACAGGGTTGAAGTATC
1 TTAATATTTTGGAAATAAAACCCGGGGTTGGAGTATCCCCTCAGAAATAACAGGGTTGAAGTATC
*
159699 CTCGATTGTGAAAAAA
66 CCCGATTGTGAAAAAA
* * * *
159715 TTAATGTTTTGGAAATAAAA-TCGGGGTTGGAGTATCCCCTTAGAAATAAC-GGGTTGGAGTATC
1 TTAATATTTTGGAAATAAAACCCGGGGTTGGAGTATCCCCTCAGAAATAACAGGGTTGAAGTATC
159778 CCCGATTGTGAAAAA
66 CCCGATTGTGAAAAA
159793 TCAGTGTTCT
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
79 26 0.37
80 26 0.37
81 18 0.26
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (81 bp):
TTAATATTTTGGAAATAAAACCCGGGGTTGGAGTATCCCCTCAGAAATAACAGGGTTGAAGTATC
CCCGATTGTGAAAAAA
Found at i:159819 original size:79 final size:79
Alignment explanation
Indices: 159656--159831 Score: 216
Period size: 79 Copynumber: 2.2 Consensus size: 79
159646 AGATAAAACC
* * * *
159656 CGGGGTTGGAGTATCTCCTCGGAAATAACAGGGTTGAAGTATCCTCGATTGTGAAAAAATTAATG
1 CGGGGTTGGAGTATCCCCTCAGAAATAACAGGGTTGAAGTATCCCCGATTGTGAAAAAATCAATG
159721 TTTTGGAAATAAAAT
66 TTTTGGAAAT-AAAT
* * *
159736 CGGGGTTGGAGTATCCCCTTAGAAATAAC-GGGTTGGAGTATCCCCGATTGTG-AAAAATCAGTG
1 CGGGGTTGGAGTATCCCCTCAGAAATAACAGGGTTGAAGTATCCCCGATTGTGAAAAAATCAATG
159799 TTCTCCTCGGAAAT-AA-
66 TT-T--T-GGAAATAAAT
159815 CGGGGTTGGAGTATCCC
1 CGGGGTTGGAGTATCCC
159832 TAATTGTGAA
Statistics
Matches: 85, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
78 11 0.13
79 39 0.46
80 28 0.33
81 1 0.01
82 6 0.07
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCTCAGAAATAACAGGGTTGAAGTATCCCCGATTGTGAAAAAATCAATG
TTTTGGAAATAAAT
Found at i:159903 original size:131 final size:131
Alignment explanation
Indices: 159669--159926 Score: 378
Period size: 131 Copynumber: 2.0 Consensus size: 131
159659 GGTTGGAGTA
* * *
159669 TCTCCTCGGAAATAACAGGGTTGAAGTATCCTCGATTGTGAAAAAATTAATGTTTTGGAAATAAA
1 TCTCCTCGGAAATAACAGGGTTGAAGTATCCTCAATTGTGAAAAAATCAATGTTTTGAAAATAAA
* * * *
159734 ATCGGGGTTGGAGTATCCCCTTAGAAATAACGGGTTGGAGTATCCCCGATTGTGAAAAATCAGTG
66 ATCAGGGTTAGAGTATCCCCTCAAAAATAACGGGTTGGAGTATCCCCGATTGTGAAAAATCAGTG
159799 T
131 T
* * *
159800 TCTCCTCGGAAATAACGGGGTTGGAGTATCC-CTAATTGTG-AAAAATCAGTGTTTTGAAAATAA
1 TCTCCTCGGAAATAACAGGGTTGAAGTATCCTC-AATTGTGAAAAAATCAATGTTTTGAAAATAA
159863 AA-CTAGGGTTAGAGTATCCCCTCAAAAATAACAGGGTTGGAGTATCCCCGATTGTGAAAAATCA
65 AATC-AGGGTTAGAGTATCCCCTCAAAAATAAC-GGGTTGGAGTATCCCCGATTGTGAAAAATCA
159927 ATATTTTAGA
Statistics
Matches: 114, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
129 1 0.01
130 47 0.41
131 66 0.58
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (131 bp):
TCTCCTCGGAAATAACAGGGTTGAAGTATCCTCAATTGTGAAAAAATCAATGTTTTGAAAATAAA
ATCAGGGTTAGAGTATCCCCTCAAAAATAACGGGTTGGAGTATCCCCGATTGTGAAAAATCAGTG
T
Found at i:159952 original size:79 final size:79
Alignment explanation
Indices: 159809--159962 Score: 204
Period size: 79 Copynumber: 1.9 Consensus size: 79
159799 TTCTCCTCGG
* * * * *
159809 AAATAACGGGGTTGGAGTATCCCTAATTGTGAAAAATCAGTGTTTTGAAAATAAAACTAGGGTTA
1 AAATAACAGGGTTGGAGTATCCCCAATTGTGAAAAATCAATATTTTGAAAATAAAACGAGGGTTA
159874 GAGTATCCCCTCAA
66 GAGTATCCCCTCAA
* *
159888 AAATAACAGGGTTGGAGTATCCCCGATTGTGAAAAATCAATATTTT-AGAAATAAAGTCGA-GGT
1 AAATAACAGGGTTGGAGTATCCCCAATTGTGAAAAATCAATATTTTGA-AAATAAA-ACGAGGGT
*
159951 TAGAGTGTCCCC
64 TAGAGTATCCCC
159963 GATGGTGGGA
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
78 1 0.02
79 62 0.95
80 2 0.03
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.27
Consensus pattern (79 bp):
AAATAACAGGGTTGGAGTATCCCCAATTGTGAAAAATCAATATTTTGAAAATAAAACGAGGGTTA
GAGTATCCCCTCAA
Found at i:159982 original size:130 final size:129
Alignment explanation
Indices: 159710--160011 Score: 333
Period size: 130 Copynumber: 2.3 Consensus size: 129
159700 TCGATTGTGA
* * * * * *
159710 AAAAATTAATGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCCTTAGAAATAACGGGTTGGAGT
1 AAAAATCAGTGTTTTGGAAATAAAATCAGGGTTAGAGTATCCCCTCAAAAATAACGGGTTGGAGT
* * * * * * *
159775 ATCCCCGATTGTGAAAAATCAGTGTTCTCCTCGGAAATAACGGGGTTGGAGTATCCCTAATTGTG
66 ATCCCCGATTGTGAAAAATCAATATTCT-CTCAGAAATAACGAGGTTAGAGTATCCCCAATGGTG
*
159840 AAAAATCAGTGTTTTGAAAATAAAA-CTAGGGTTAGAGTATCCCCTCAAAAATAACAGGGTTGGA
1 AAAAATCAGTGTTTTGGAAATAAAATC-AGGGTTAGAGTATCCCCTCAAAAATAAC-GGGTTGGA
* *
159904 GTATCCCCGATTGTGAAAAATCAATATT-T-T-AGAAATAAAGTCGAGGTTAGAGTGTCCCCGAT
64 GTATCCCCGATTGTGAAAAATCAATATTCTCTCAGAAAT-AA--CGAGGTTAGAGTATCCCCAAT
159966 GGTG
126 GGTG
** ** *
159970 GGAAATGGGTGTTTTGGAAATAAAATCAGGGTTATAGTATCC
1 AAAAATCAGTGTTTTGGAAATAAAATCAGGGTTAGAGTATCC
160012 ACAATTGTGG
Statistics
Matches: 144, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
127 5 0.03
128 3 0.02
129 1 0.01
130 100 0.69
131 35 0.24
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (129 bp):
AAAAATCAGTGTTTTGGAAATAAAATCAGGGTTAGAGTATCCCCTCAAAAATAACGGGTTGGAGT
ATCCCCGATTGTGAAAAATCAATATTCTCTCAGAAATAACGAGGTTAGAGTATCCCCAATGGTG
Found at i:164456 original size:3 final size:3
Alignment explanation
Indices: 164448--164481 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
164438 TCAACCATCA
*
164448 ATG ATG ATG AAG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
164482 AGTTGACTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.32, T:0.29
Consensus pattern (3 bp):
ATG
Found at i:172443 original size:52 final size:51
Alignment explanation
Indices: 172381--173124 Score: 526
Period size: 52 Copynumber: 14.5 Consensus size: 51
172371 TGACTTTATG
** * *
172381 AGGCTTGACCTCCCTATGTAGGTGCCAGCTAATATGGACATAAGGTTCTAT
1 AGGCTTGACCTCCCTATACAGGTGCCAGCTAATGTGGACTTAAGGTTCTAT
* * * * *
172432 AGGACTTGACCTCTCTATATATGTGCCAGCTAATGTGGACTTAAGGTTTTGT
1 AGG-CTTGACCTCCCTATACAGGTGCCAGCTAATGTGGACTTAAGGTTCTAT
* * * ** *
172484 AGCACTTGACCTCTCTATACAAGTGCCAGCTAATGTTAACTTTAA--CTCTAT
1 AG-GCTTGACCTCCCTATACAGGTGCCAGCTAATGTGGAC-TTAAGGTTCTAT
* * * *
172535 AAGGCTTGACCTCCTTATACAAGTGCCAACTAATGTGGACTTAAGGTTTTAT
1 -AGGCTTGACCTCCCTATACAGGTGCCAGCTAATGTGGACTTAAGGTTCTAT
* * * ** ** *
172587 AGGGCTTGACCTCCTTATATAGGTGCTAGCTAATGTCAACTTTGGGTTTTAT
1 A-GGCTTGACCTCCCTATACAGGTGCCAGCTAATGTGGACTTAAGGTTCTAT
* *
172639 AGGGCTTGACCTCCCTATACAAGTGCCATCTAATGTGGACTT--GGATTCTAT
1 A-GGCTTGACCTCCCTATACAGGTGCCAGCTAATGTGGACTTAAGG-TTCTAT
* * *
172690 AGGGCTTAACCTCCCTATACAGGTGCCATCTAATGTGGACTT-AGATTCTAT
1 A-GGCTTGACCTCCCTATACAGGTGCCAGCTAATGTGGACTTAAGGTTCTAT
* * * **
172741 AAGCTTGACCTCCTTATACAAGG-GCCAGTTAATGTGGACTTTGGGTTCTAT
1 AGGCTTGACCTCCCTATAC-AGGTGCCAGCTAATGTGGACTTAAGGTTCTAT
* * * * *
172792 AGGCTTAACCTCCTTATATAAGTGCCAGCTAGTGTGGACTTGAA--TTCTAT
1 AGGCTTGACCTCCCTATACAGGTGCCAGCTAATGTGGACTT-AAGGTTCTAT
* * * * *
172842 AAGGCTTGACCTCCCTACACAGATGCTAGTTAATGTGGACTT-CGAGTTCTAT
1 -AGGCTTGACCTCCCTATACAGGTGCCAGCTAATGTGGACTTAAG-GTTCTAT
** * ** * * * *
172894 AGGGCTTGACCTCCCTATACAAATACCATTTAATATGGACTTCAGATTTTAT
1 A-GGCTTGACCTCCCTATACAGGTGCCAGCTAATGTGGACTTAAGGTTCTAT
* * ** * * *
172946 AAGGTTTGACCTCTCTATACAAATGCCAGCTAGTGTGGACCT-AGATTCTAT
1 -AGGCTTGACCTCCCTATACAGGTGCCAGCTAATGTGGACTTAAGGTTCTAT
* * * * *
172997 AAGGGCTTGACCTCCTTATATAGATGCCAGCTAATGTGCACGTT-GGGTTCTAT
1 -A-GGCTTGACCTCCCTATACAGGTGCCAGCTAATGTGGAC-TTAAGGTTCTAT
** * * * *
173050 AAGGCTTGACCTCTATATATAGGTACAAGCTAGTGTGGACTT--GGATT-TAT
1 -AGGCTTGACCTCCCTATACAGGTGCCAGCTAATGTGGACTTAAGG-TTCTAT
* *
173100 AGGGCTTAACCTGCCTATACAGGTG
1 A-GGCTTGACCTCCCTATACAGGTG
173125 TCAACTAGTG
Statistics
Matches: 561, Mismatches: 108, Indels: 49
0.78 0.15 0.07
Matches are distributed among these distances:
49 1 0.00
50 67 0.12
51 179 0.32
52 298 0.53
53 16 0.03
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (51 bp):
AGGCTTGACCTCCCTATACAGGTGCCAGCTAATGTGGACTTAAGGTTCTAT
Found at i:172543 original size:103 final size:103
Alignment explanation
Indices: 172426--173139 Score: 537
Period size: 103 Copynumber: 7.0 Consensus size: 103
172416 GGACATAAGG
* * * * **
172426 TTCTAT-AGGACTTGACCT-CTCTATATATGTGCCAGCTAATGTGGACTTAAGGTTTTGTAGCAC
1 TTCTATAAGG-CTTGACCTCCT-TATACAAGTGCCAGCTAATGTGGACTTAAGGTTCTATAGGGC
* *
172489 TTGACCT-CTCTATACAAGTGCCAGCTAATGTTAACTTTAA
64 TTAACCTCCT-TATACAAGTGCCAGCTAATGTGAACTTTAA
* * *
172529 CTCTATAAGGCTTGACCTCCTTATACAAGTGCCAACTAATGTGGACTTAAGGTTTTATAGGGCTT
1 TTCTATAAGGCTTGACCTCCTTATACAAGTGCCAGCTAATGTGGACTTAAGGTTCTATAGGGCTT
* * * * * **
172594 GACCTCCTTATATAGGTGCTAGCTAATGTCAACTTTGGG
66 AACCTCCTTATACAAGTGCCAGCTAATGTGAACTTT-AA
* * * *
172633 TTTTATAGGGCTTGACCTCCCTATACAAGTGCCATCTAATGTGGACTT--GGATTCTATAGGGCT
1 TTCTATAAGGCTTGACCTCCTTATACAAGTGCCAGCTAATGTGGACTTAAGG-TTCTATAGGGCT
* * * *
172696 TAACCTCCCTATACAGGTGCCATCTAATGTGGAC-TTAGA
65 TAACCTCCTTATACAAGTGCCAGCTAATGTGAACTTTA-A
* * **
172735 TTCTATAA-GCTTGACCTCCTTATACAAGGGCCAGTTAATGTGGACTTTGGGTTCTATA-GGCTT
1 TTCTATAAGGCTTGACCTCCTTATACAAGTGCCAGCTAATGTGGACTTAAGGTTCTATAGGGCTT
* * * *
172798 AACCTCCTTATATAAGTGCCAGCTAGTGTGGACTTGAA
66 AACCTCCTTATACAAGTGCCAGCTAATGTGAACTTTAA
* * * * *
172836 TTCTATAAGGCTTGACCTCCCTACAC-AGATGCTAGTTAATGTGGACTT-CGAGTTCTATAGGGC
1 TTCTATAAGGCTTGACCTCCTTATACAAG-TGCCAGCTAATGTGGACTTAAG-GTTCTATAGGGC
* * * * ** * * *
172899 TTGACCTCCCTATACAAATACCATTTAATATGGACTTCAGA
64 TTAACCTCCTTATACAAGTGCCAGCTAATGTGAACTTTA-A
* * * * * *
172940 TTTTATAAGGTTTGACCT-CTCTATACAAATGCCAGCTAGTGTGGACCT-AGATTCTATAAGGGC
1 TTCTATAAGGCTTGACCTCCT-TATACAAGTGCCAGCTAATGTGGACTTAAGGTTCTAT-AGGGC
* * * ***
173003 TTGACCTCCTTATA-TAGATGCCAGCTAATGTGCACGTTGGG
64 TTAACCTCCTTATACAAG-TGCCAGCTAATGTGAAC-TTTAA
* * * * *
173044 TTCTATAAGGCTTGACCT-CTATATATAGGTACAAGCTAGTGTGGACTT--GGATT-TATAGGGC
1 TTCTATAAGGCTTGACCTCCT-TATACAAGTGCCAGCTAATGTGGACTTAAGG-TTCTATAGGGC
* * * *
173105 TTAACCTGCC-TATACAGGTGTCAACTAGTGTGAAC
64 TTAACCT-CCTTATACAAGTGCCAGCTAATGTGAAC
173140 CTGGATCTAG
Statistics
Matches: 495, Mismatches: 94, Indels: 45
0.78 0.15 0.07
Matches are distributed among these distances:
101 80 0.16
102 87 0.18
103 167 0.34
104 158 0.32
105 3 0.01
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (103 bp):
TTCTATAAGGCTTGACCTCCTTATACAAGTGCCAGCTAATGTGGACTTAAGGTTCTATAGGGCTT
AACCTCCTTATACAAGTGCCAGCTAATGTGAACTTTAA
Found at i:172647 original size:155 final size:153
Alignment explanation
Indices: 172355--173120 Score: 681
Period size: 155 Copynumber: 5.0 Consensus size: 153
172345 TGAACTAACA
* * * ** * *
172355 CAGCTAATGTGGATTTTGACTT-TATGAGGCTTGACCTCCCTATGTAGGTGCCAGCTAATATGGA
1 CAGCTAATGTGGA-CTTGAATTCTATAAGGCTTGACCTCCCTATACAAGTGCCAGCTAATGTGGA
* * * * *
172419 CATAAGGTTCTATAGGACTTGACCT-CTCTATATATGTGCCAGCTAATGTGGACTTAAGGTTTTG
65 C-TTAGGTTCTATAGGGCTTGACCTCCT-TATATAGGTGCCAGCTAATGTGGACTTTAGGTTTTA
**
172483 TAGCACTTGACCTCTCTATACAAGTGC
128 TAGGGCTTGACCTC-CTATACAAGTGC
** * * * *
172510 CAGCTAATGTTAACTTTAACTCTATAAGGCTTGACCTCCTTATACAAGTGCCAACTAATGTGGAC
1 CAGCTAATGTGGACTTGAATTCTATAAGGCTTGACCTCCCTATACAAGTGCCAGCTAATGTGGAC
* * ** *
172575 TTAAGGTTTTATAGGGCTTGACCTCCTTATATAGGTGCTAGCTAATGTCAACTTTGGGTTTTATA
66 TT-AGGTTCTATAGGGCTTGACCTCCTTATATAGGTGCCAGCTAATGTGGACTTTAGGTTTTATA
172640 GGGCTTGACCTCCCTATACAAGTGC
130 GGGCTTGACCT-CCTATACAAGTGC
* * * * * *
172665 CATCTAATGTGGACTTGGATTCTATAGGGCTTAACCTCCCTATACAGGTGCCATCTAATGTGGAC
1 CAGCTAATGTGGACTTGAATTCTATAAGGCTTGACCTCCCTATACAAGTGCCAGCTAATGTGGAC
* * * * * *
172730 TTAGATTCTATA-AGCTTGACCTCCTTATACAAGG-GCCAGTTAATGTGGACTTTGGGTTCTATA
66 TTAGGTTCTATAGGGCTTGACCTCCTTATA-TAGGTGCCAGCTAATGTGGACTTTAGGTTTTATA
* *
172793 -GGCTTAACCTCCTTATATAAGTGC
130 GGGCTTGACCTCC-TATACAAGTGC
* * * *
172817 CAGCTAGTGTGGACTTGAATTCTATAAGGCTTGACCTCCCTACAC-AGATGCTAGTTAATGTGGA
1 CAGCTAATGTGGACTTGAATTCTATAAGGCTTGACCTCCCTATACAAG-TGCCAGCTAATGTGGA
* * * ** * ** * * *
172881 CTTCGAGTTCTATAGGGCTTGACCTCCCTATACAAATACCATTTAATATGGACTTCAGATTTTAT
65 CTTAG-GTTCTATAGGGCTTGACCTCCTTATATAGGTGCCAGCTAATGTGGACTTTAGGTTTTAT
* * *
172946 AAGGTTTGACCTCTCTATACAAATGC
129 AGGGCTTGACCTC-CTATACAAGTGC
* * * *
172972 CAGCTAGTGTGGACCT-AGATTCTATAAGGGCTTGACCTCCTTATA-TAGATGCCAGCTAATGTG
1 CAGCTAATGTGGACTTGA-ATTCTATAA-GGCTTGACCTCCCTATACAAG-TGCCAGCTAATGTG
* * * * * * *
173035 CACGTTGGGTTCTATAAGGCTTGACCT-CTATATATAGGTACAAGCTAGTGTGGAC-TT-GGATT
63 GAC-TTAGGTTCTATAGGGCTTGACCTCCT-TATATAGGTGCCAGCTAATGTGGACTTTAGGTTT
*
173097 TATAGGGCTTAACCTGCCTATACA
126 TATAGGGCTTGACCT-CCTATACA
173121 GGTGTCAACT
Statistics
Matches: 495, Mismatches: 98, Indels: 37
0.79 0.16 0.06
Matches are distributed among these distances:
151 3 0.01
152 75 0.15
153 48 0.10
154 76 0.15
155 219 0.44
156 71 0.14
157 3 0.01
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (153 bp):
CAGCTAATGTGGACTTGAATTCTATAAGGCTTGACCTCCCTATACAAGTGCCAGCTAATGTGGAC
TTAGGTTCTATAGGGCTTGACCTCCTTATATAGGTGCCAGCTAATGTGGACTTTAGGTTTTATAG
GGCTTGACCTCCTATACAAGTGC
Found at i:173318 original size:47 final size:47
Alignment explanation
Indices: 173232--173341 Score: 141
Period size: 47 Copynumber: 2.4 Consensus size: 47
173222 TATTTTTTAG
* * * * *
173232 TTTAGGAC-TTTGGAATTAAAAGTCCGTACTTAGAATTCTTTTCAAA
1 TTTAGGACTTTTGGAGTCAAAAATCCATACCTAGAATTCTTTTCAAA
*
173278 TTTAGGACTTTTGGAGTCAAAAATCCATACCTAGAGTTCTTTTCAAA
1 TTTAGGACTTTTGGAGTCAAAAATCCATACCTAGAATTCTTTTCAAA
* *
173325 TTTGGGACTTTTAGAGT
1 TTTAGGACTTTTGGAGT
173342 TAGGATTCCA
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
46 8 0.15
47 47 0.85
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (47 bp):
TTTAGGACTTTTGGAGTCAAAAATCCATACCTAGAATTCTTTTCAAA
Found at i:173713 original size:33 final size:35
Alignment explanation
Indices: 173631--173735 Score: 133
Period size: 33 Copynumber: 3.0 Consensus size: 35
173621 TGATAGAATG
* * ** *
173631 TCCTCAAGAAAGGTTTTGAAAGTTTTTAATGAAACA
1 TCCTCAAAAAAGGCTTT-AAAGTTTTTGTTGAAATA
173667 TCCTCAAAAAAGGCTTTAAAGTTTTTGTTGAAATA
1 TCCTCAAAAAAGGCTTTAAAGTTTTTGTTGAAATA
*
173702 T-C-CAAAAAAGGCTTTGAAGTTTTTGTTGAAATA
1 TCCTCAAAAAAGGCTTTAAAGTTTTTGTTGAAATA
173735 T
1 T
173736 GTTTAAAAGT
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
33 31 0.49
34 1 0.02
35 16 0.25
36 15 0.24
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.36
Consensus pattern (35 bp):
TCCTCAAAAAAGGCTTTAAAGTTTTTGTTGAAATA
Found at i:174157 original size:16 final size:16
Alignment explanation
Indices: 174132--174162 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
174122 GTGAATGAGC
*
174132 ATGTATATAAGTGCAG
1 ATGTAGATAAGTGCAG
174148 ATGTAGATAAGTGCA
1 ATGTAGATAAGTGCA
174163 ATGGCAAGAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.06, G:0.26, T:0.29
Consensus pattern (16 bp):
ATGTAGATAAGTGCAG
Found at i:174881 original size:21 final size:21
Alignment explanation
Indices: 174855--174911 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
174845 AAAAAAATTA
174855 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
174876 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
174897 AATGTATCGATACAT
1 AATGTATCGATACAT
174912 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:174991 original size:19 final size:19
Alignment explanation
Indices: 174967--175034 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
174957 AATTCAACAA
174967 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
174986 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
175001 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
175018 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
175035 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:175006 original size:13 final size:13
Alignment explanation
Indices: 174988--175012 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
174978 ACATAAGTTT
174988 TGTATCGATACAA
1 TGTATCGATACAA
175001 TGTATCGATACA
1 TGTATCGATACA
175013 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:175010 original size:32 final size:32
Alignment explanation
Indices: 174969--175031 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
174959 TTCAACAATT
*
174969 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
175001 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
175032 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:175092 original size:13 final size:13
Alignment explanation
Indices: 175074--175099 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
175064 CATTTTTCTG
175074 TGTATCGATACAT
1 TGTATCGATACAT
175087 TGTATCGATACAT
1 TGTATCGATACAT
175100 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:175096 original size:33 final size:33
Alignment explanation
Indices: 175054--175120 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
175044 GCCAAGGAAA
***
175054 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
175087 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
175120 T
1 T
175121 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:177618 original size:28 final size:27
Alignment explanation
Indices: 177551--177623 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
177541 CTTCACAATC
* *
177551 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
177578 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
177606 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
177624 ACTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:177668 original size:51 final size:51
Alignment explanation
Indices: 177606--177776 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
177596 TTATTTCTGA
* * *
177606 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
177657 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * *
177710 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
177762 GAGGATACTCCAACC
1 GGGGATACTCCAACC
177777 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 36 0.37
52 18 0.19
53 32 0.33
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:177769 original size:105 final size:105
Alignment explanation
Indices: 177437--177776 Score: 273
Period size: 105 Copynumber: 3.2 Consensus size: 105
177427 CTCAATTCTC
* * * * ** *
177437 CACAATCGAGGATATTCCAACTCCGATTTTACTTTCAAAACATTAATTT-T-CTATAATCGGGGA
1 CACAATCGAGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTCTCCTTTAATCGGGGA
*
177500 TACTCCAACTCCGATTTTATTTCCAAAAAAAACACCAATTTCTT
66 TACTCCAACTCCGATTTTATTTCC---AAAAATACCAATTT-TT
* * * ** * * * * * *
177544 CACAATCGGGGACACTCCAACCCC-G-TTAATCATCGGGGATACTCCAA---CCCCGTTATTTCT
1 CACAATCGAGGATACTCCAACCCCGGTTTTATTTTC---AAAACACCAATTTCTCCTTTA-ATC-
* * * * *
177604 GAGGGGATACTCCAACCCCGACTTTATTTTC-AAAATATCGATTTTT
61 --GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT
* * *
177650 CATAATCGGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATCGGGGA
1 CACAATCGAGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTCTCCTTTAATCGGGGA
*
177715 TACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTT
66 TACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT
177755 CACAATCGAGGATACTCCAACC
1 CACAATCGAGGATACTCCAACC
177777 TCGTTATTTC
Statistics
Matches: 174, Mismatches: 44, Indels: 32
0.70 0.18 0.13
Matches are distributed among these distances:
104 25 0.14
105 44 0.25
106 24 0.14
107 36 0.21
108 19 0.11
111 26 0.15
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (105 bp):
CACAATCGAGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTCTCCTTTAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT
Found at i:177795 original size:28 final size:28
Alignment explanation
Indices: 177759--177840 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 28
177749 ATTTTTCACA
*
177759 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
177787 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
177815 --CGAAGGAACACTCCAACCTCGTTATT
1 ATCG--GGGATACTCCAACCTCGTTATT
177841 ATCTCCAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 2 0.04
28 43 0.96
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:181308 original size:20 final size:20
Alignment explanation
Indices: 181285--181357 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
181275 ACAATTCAAA
181285 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
181305 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
181326 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
181346 GTATCGATACAT
1 GTATCGATACAT
181358 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:181329 original size:21 final size:21
Alignment explanation
Indices: 181303--181378 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
181293 ACATGTTGCA
181303 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
181324 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
181344 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
181365 ATGTATCGATACAT
1 ATGTATCGATACAT
181379 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:181336 original size:41 final size:41
Alignment explanation
Indices: 181285--181378 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
181275 ACAATTCAAA
*
181285 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
181326 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
181367 GTATCGATACAT
1 GTATCGATACAT
181379 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:181435 original size:13 final size:13
Alignment explanation
Indices: 181417--181442 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
181407 TACAGCAAGT
181417 ATGTATCGATACA
1 ATGTATCGATACA
181430 ATGTATCGATACA
1 ATGTATCGATACA
181443 CAAAAAATTG
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:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:185525 original size:15 final size:15
Alignment explanation
Indices: 185505--185543 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
185495 TAAAAATGTC
*
185505 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
185520 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
*
185535 CCAAATGAA
1 CAAAATGAA
185544 ATTGATGTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.51, C:0.15, G:0.21, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:187618 original size:20 final size:21
Alignment explanation
Indices: 187549--187626 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 21
187539 AATGTCCAAA
*
187549 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
187569 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
187594 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
187614 TTGTATCGATACA
1 ATGTATCGATACA
187627 CTGTATCGAT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
20 30 0.64
24 3 0.06
25 14 0.30
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:187633 original size:13 final size:13
Alignment explanation
Indices: 187615--187639 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
187605 CATTTTTCTT
187615 TGTATCGATACAC
1 TGTATCGATACAC
187628 TGTATCGATACA
1 TGTATCGATACA
187640 GGGTGATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:190112 original size:20 final size:20
Alignment explanation
Indices: 190089--190161 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
190079 ACAATTCAAA
190089 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
190109 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
190130 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
190150 GTATCGATACAT
1 GTATCGATACAT
190162 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:190133 original size:21 final size:21
Alignment explanation
Indices: 190107--190182 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
190097 ACATGTTGCA
190107 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
190128 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
190148 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
190169 ATGTATCGATACAT
1 ATGTATCGATACAT
190183 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:190140 original size:41 final size:41
Alignment explanation
Indices: 190089--190182 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
190079 ACAATTCAAA
*
190089 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
190130 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
190171 GTATCGATACAT
1 GTATCGATACAT
190183 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:190239 original size:13 final size:13
Alignment explanation
Indices: 190221--190246 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
190211 TACAGCAAGT
190221 ATGTATCGATACA
1 ATGTATCGATACA
190234 ATGTATCGATACA
1 ATGTATCGATACA
190247 CAAAAAATTG
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:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:200257 original size:15 final size:15
Alignment explanation
Indices: 200237--200303 Score: 73
Period size: 15 Copynumber: 4.4 Consensus size: 15
200227 TCTCTTCAAA
200237 AAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAG
200252 AAAAAAAAAAAACAA-
1 AAAAAAAAAAAA-AAG
*
200267 AAAAAACAAAACAAAG
1 AAAAAA-AAAAAAAAG
* * *
200283 AAAAAGAGAGAAAAG
1 AAAAAAAAAAAAAAG
200298 AAAAAA
1 AAAAAA
200304 CCTACTTAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
15 31 0.72
16 12 0.28
ACGTcount: A:0.87, C:0.04, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAAG
Found at i:200303 original size:1 final size:1
Alignment explanation
Indices: 200234--200287 Score: 63
Period size: 1 Copynumber: 54.0 Consensus size: 1
200224 CCTTCTCTTC
* * * * *
200234 AAAAAAAAAAAAAAAAAGAAAAAAAAAAAACAAAAAAAACAAAACAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
200288 GAGAGAAAAG
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.91, C:0.06, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Found at i:201353 original size:55 final size:55
Alignment explanation
Indices: 201269--203046 Score: 2779
Period size: 55 Copynumber: 32.3 Consensus size: 55
201259 TCCGCTTTTT
* * *
201269 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
201324 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
*
201379 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
* * *
201434 AGTCCTCAACGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
* * *
201489 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
* * *
201544 AGTCCTCAAAGAGCAGGACATCTTTCAAAGCCCACACAAGTTGGTGGCATTGTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
* * *
201599 AGTCCTCAAAGAGCAAGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
* * *
201654 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
201709 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
* * *
201764 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACCCAAGTTGGTGGCATTTTCT
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
201819 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
*
201874 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
*
201929 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
* *
201984 AGTCCTCAAAGAGCAGGACACCTCTAAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
*
202039 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
*
202094 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
* * *
202149 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACCCAAGTTGGTGGCATTTTCT
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
* *
202204 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
202259 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
* * *
202314 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACCCAAGTTGGTGGCATTTTCT
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
202369 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
*
202424 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
*
202479 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
* *
202534 AGTCCTCAAAGAGCAGGACACCTCTAAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
*
202589 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
*
202644 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
* * *
202699 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACCCAAGTTGGTGGCATTTTCT
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
* *
202754 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
* * *
202809 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
* * * *
202864 AGTCCCCAAAGAACAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
* * * *
202919 ATTCCCCAAAGAGCAGGACA-CTTTTCAAAGCCCACACAAGTGGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACACCTTTT-AAAGCCCACACAAGTTGGTGGCA-TTTTCC
* * ** *
202974 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACATGAGTTGGTGGCACTTTT-T
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
* *
203029 ACTCCTCAATGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
203047 TACAATTTAT
Statistics
Matches: 1623, Mismatches: 90, Indels: 20
0.94 0.05 0.01
Matches are distributed among these distances:
54 15 0.01
55 1593 0.98
56 15 0.01
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
Found at i:201540 original size:29 final size:29
Alignment explanation
Indices: 201452--201540 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 29
201442 ACGAGCAGGA
201452 CACCTCTTAAAGCCCACACAAGTTGGTGG
1 CACCTCTTAAAGCCCACACAAGTTGGTGG
* * **
201481 CACCT-TT-CAGTCCC-CA-AAG-AGCAGG
1 CACCTCTTAAAG-CCCACACAAGTTGGTGG
201506 ACACCTCTTAAAGCCCACACAAGTTGGTGG
1 -CACCTCTTAAAGCCCACACAAGTTGGTGG
201536 CACCT
1 CACCT
201541 TTCAGTCCTC
Statistics
Matches: 45, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
25 3 0.07
26 8 0.18
27 9 0.20
28 9 0.20
29 13 0.29
30 3 0.07
ACGTcount: A:0.28, C:0.34, G:0.19, T:0.19
Consensus pattern (29 bp):
CACCTCTTAAAGCCCACACAAGTTGGTGG
Found at i:201731 original size:26 final size:26
Alignment explanation
Indices: 201646--201733 Score: 70
Period size: 26 Copynumber: 3.3 Consensus size: 26
201636 AAGTTGGTGG
*
201646 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * * **
201672 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
*
201701 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
201727 CACCTTT
1 CACCTTT
201734 TAAAGCCCAC
Statistics
Matches: 45, Mismatches: 12, Indels: 10
0.67 0.18 0.15
Matches are distributed among these distances:
25 3 0.07
26 15 0.33
27 8 0.18
28 8 0.18
29 8 0.18
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.18, T:0.20
Consensus pattern (26 bp):
CACCTTTCAGTCCACAAAGAGCAGGA
Found at i:201954 original size:27 final size:27
Alignment explanation
Indices: 201869--202006 Score: 68
Period size: 27 Copynumber: 5.0 Consensus size: 27
201859 TTGGTGGCAT
201869 TTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTCCAGTCCTCAAAGAGCAGGACACC
* * * * ** *
201896 TTTCAAAGCCCACACAAGTTGGTGG-CA-T
1 TTTC-CAGTCCTCA-AAG-AGCAGGACACC
201924 TTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTCCAGTCCTCAAAGAGCAGGACACC
* * * * ** *
201951 TTTCAAAGCCCACACAAGTTGGTGG-CA-T
1 TTTC-CAGTCCTCA-AAG-AGCAGGACACC
201979 TTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTCCAGTCCTCAAAGAGCAGGACACC
202006 T
1 T
202007 CTAAAAGCCC
Statistics
Matches: 73, Mismatches: 28, Indels: 20
0.60 0.23 0.17
Matches are distributed among these distances:
25 6 0.08
26 10 0.14
27 21 0.29
28 20 0.27
29 10 0.14
30 6 0.08
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.22
Consensus pattern (27 bp):
TTTCCAGTCCTCAAAGAGCAGGACACC
Found at i:202504 original size:27 final size:27
Alignment explanation
Indices: 202419--202556 Score: 68
Period size: 27 Copynumber: 5.0 Consensus size: 27
202409 TTGGTGGCAT
202419 TTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTCCAGTCCTCAAAGAGCAGGACACC
* * * * ** *
202446 TTTCAAAGCCCACACAAGTTGGTGG-CA-T
1 TTTC-CAGTCCTCA-AAG-AGCAGGACACC
202474 TTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTCCAGTCCTCAAAGAGCAGGACACC
* * * * ** *
202501 TTTCAAAGCCCACACAAGTTGGTGG-CA-T
1 TTTC-CAGTCCTCA-AAG-AGCAGGACACC
202529 TTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTCCAGTCCTCAAAGAGCAGGACACC
202556 T
1 T
202557 CTAAAAGCCC
Statistics
Matches: 73, Mismatches: 28, Indels: 20
0.60 0.23 0.17
Matches are distributed among these distances:
25 6 0.08
26 10 0.14
27 21 0.29
28 20 0.27
29 10 0.14
30 6 0.08
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.22
Consensus pattern (27 bp):
TTTCCAGTCCTCAAAGAGCAGGACACC
Found at i:202915 original size:29 final size:29
Alignment explanation
Indices: 202772--202915 Score: 101
Period size: 29 Copynumber: 5.2 Consensus size: 29
202762 AAGAGCAGGA
202772 CACCTCTTAAAGCCCACACAAGTTGGTGG
1 CACCTCTTAAAGCCCACACAAGTTGGTGG
* * **
202801 CACCT-TT-CAGTCCC-CA-AAG-AGCAGG
1 CACCTCTTAAAG-CCCACACAAGTTGGTGG
202826 ACACCTCTTAAAGCCCACACAAGTTGGTGG
1 -CACCTCTTAAAGCCCACACAAGTTGGTGG
* *** *
202856 CACCT-TT-CAGTCCC-CA-AAGAACAG-GA
1 CACCTCTTAAAG-CCCACACAAG-TTGGTGG
202882 CACCTCTTAAAGCCCACACAAGTTGGTGG
1 CACCTCTTAAAGCCCACACAAGTTGGTGG
202911 CACCT
1 CACCT
202916 TTCATTCCCC
Statistics
Matches: 83, Mismatches: 18, Indels: 28
0.64 0.14 0.22
Matches are distributed among these distances:
25 3 0.04
26 17 0.20
27 19 0.23
28 19 0.23
29 22 0.27
30 3 0.04
ACGTcount: A:0.29, C:0.33, G:0.19, T:0.19
Consensus pattern (29 bp):
CACCTCTTAAAGCCCACACAAGTTGGTGG
Found at i:203648 original size:1 final size:1
Alignment explanation
Indices: 203642--203683 Score: 66
Period size: 1 Copynumber: 42.0 Consensus size: 1
203632 AAAGTGTTTG
**
203642 AAAAAAAAAAAAAAAAAAAAAATTAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
203684 TTAAATGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.95, C:0.00, G:0.00, T:0.05
Consensus pattern (1 bp):
A
Found at i:203671 original size:20 final size:20
Alignment explanation
Indices: 203646--203688 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
203636 TGTTTGAAAA
203646 AAAAAAAAAAAAAAAAAATT
1 AAAAAAAAAAAAAAAAAATT
203666 AAAAAAAAAAAAAAAAAATT
1 AAAAAAAAAAAAAAAAAATT
203686 AAA
1 AAA
203689 TGTATCGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (20 bp):
AAAAAAAAAAAAAAAAAATT
Found at i:203713 original size:21 final size:21
Alignment explanation
Indices: 203687--203743 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
203677 AAAAAAATTA
203687 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
203708 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
203729 AATGTATCGATACAT
1 AATGTATCGATACAT
203744 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:203827 original size:19 final size:18
Alignment explanation
Indices: 203799--203866 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
203789 AATTCAACAA
203799 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
*
203817 TTTTATATCGATAC--AA-
1 -TTTGTATCGATACATAAG
203833 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
203849 TATTGTATCGATACATAA
1 T-TTGTATCGATACATAA
203867 TTAGCTACTG
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
13 10 0.24
15 2 0.05
17 2 0.05
19 27 0.66
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:203838 original size:32 final size:32
Alignment explanation
Indices: 203801--203863 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
203791 TTCAACAATT
*
203801 TGTATCGATACATAAGTTTTATATCGATACAA
1 TGTATCGATACATAAGTATTATATCGATACAA
*
203833 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTATATCGATACA
203864 TAATTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTATATCGATACAA
Found at i:203924 original size:13 final size:13
Alignment explanation
Indices: 203906--203931 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
203896 CATTTTTCTG
203906 TGTATCGATACAT
1 TGTATCGATACAT
203919 TGTATCGATACAT
1 TGTATCGATACAT
203932 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:203928 original size:33 final size:33
Alignment explanation
Indices: 203886--203952 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
203876 GCCAAGGAAA
***
203886 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
203919 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
203952 T
1 T
203953 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:206473 original size:28 final size:27
Alignment explanation
Indices: 206406--206478 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
206396 CTTCACAATC
* *
206406 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
206433 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
206461 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
206479 ACTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:206523 original size:51 final size:51
Alignment explanation
Indices: 206461--206631 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
206451 TTATTTCTGA
* * *
206461 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
206512 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * *
206565 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
206617 GAGGATACTCCAACC
1 GGGGATACTCCAACC
206632 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 36 0.37
52 18 0.19
53 32 0.33
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:206650 original size:28 final size:28
Alignment explanation
Indices: 206614--206695 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 28
206604 ATTTTTCACA
*
206614 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
206642 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
206670 -T-GAAGGAACACTCCAACCTCGTTATT
1 ATCG--GGGATACTCCAACCTCGTTATT
206696 ATCTCCAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 1 0.02
27 1 0.02
28 43 0.96
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.28
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:211310 original size:33 final size:34
Alignment explanation
Indices: 211244--211314 Score: 90
Period size: 33 Copynumber: 2.1 Consensus size: 34
211234 AGGAAAGATC
* * *
211244 AAAGAAAGAGAGAAAAAGGGAGAAGCAAGGAAGAA
1 AAAGAAAGAAAGAAAAA-GAAGAAGCAAAGAAGAA
*
211279 AAAGAAAGAAAGAAAAA-AAGAAGGAAAGAAGAA
1 AAAGAAAGAAAGAAAAAGAAGAAGCAAAGAAGAA
211312 AAA
1 AAA
211315 AACAAGGGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 16 0.50
35 16 0.50
ACGTcount: A:0.70, C:0.01, G:0.28, T:0.00
Consensus pattern (34 bp):
AAAGAAAGAAAGAAAAAGAAGAAGCAAAGAAGAA
Found at i:211312 original size:19 final size:20
Alignment explanation
Indices: 211282--211321 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
211272 GGAAGAAAAA
*
211282 GAAAGAAAGAAAAAAAGAAG
1 GAAAGAAAGAAAAAAACAAG
211302 GAAAG-AAGAAAAAAACAAG
1 GAAAGAAAGAAAAAAACAAG
211321 G
1 G
211322 GGAGAAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.72, C:0.03, G:0.25, T:0.00
Consensus pattern (20 bp):
GAAAGAAAGAAAAAAACAAG
Found at i:212972 original size:15 final size:15
Alignment explanation
Indices: 212952--212981 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
212942 ACACAATATT
212952 TGGTACATTTTTATG
1 TGGTACATTTTTATG
212967 TGGTACATTTTTATG
1 TGGTACATTTTTATG
212982 CATATCTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.20, T:0.53
Consensus pattern (15 bp):
TGGTACATTTTTATG
Found at i:218009 original size:20 final size:20
Alignment explanation
Indices: 217984--218057 Score: 94
Period size: 20 Copynumber: 3.7 Consensus size: 20
217974 TACTCAGATA
217984 TATCGATACATTTTTCAATG
1 TATCGATACATTTTTCAATG
* * * * *
218004 TATCGATACCTGTATGAAAG
1 TATCGATACATTTTTCAATG
*
218024 TATCAATACATTTTTCAATG
1 TATCGATACATTTTTCAATG
218044 TATCGATACATTTT
1 TATCGATACATTTT
218058 ATTTTTTTAC
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (20 bp):
TATCGATACATTTTTCAATG
Found at i:218009 original size:50 final size:50
Alignment explanation
Indices: 217951--218104 Score: 125
Period size: 50 Copynumber: 3.3 Consensus size: 50
217941 TGAATAGTAC
217951 ATGTATCGATACATTCTGTTTTTTACTCAGATATATCGATACATTTTTCA
1 ATGTATCGATACATTCTGTTTTTTACTCAGATATATCGATACATTTTTCA
* *
218001 ATGTATCGATAC---CTG-----TA-T--GAAAGTATCAATACATTTTTCA
1 ATGTATCGATACATTCTGTTTTTTACTCAGATA-TATCGATACATTTTTCA
* * * * *
218041 ATGTATCGATACATTTTATTTTTTTACCCAAATGTATCGATACA-TTTTCA
1 ATGTATCGATACATTCT-GTTTTTTACTCAGATATATCGATACATTTTTCA
* *
218091 ATGCATTGATACAT
1 ATGTATCGATACAT
218105 CTAGTTAATT
Statistics
Matches: 80, Mismatches: 11, Indels: 26
0.68 0.09 0.22
Matches are distributed among these distances:
39 3 0.04
40 28 0.35
41 1 0.01
42 2 0.03
43 1 0.01
47 3 0.04
49 2 0.03
50 30 0.38
51 9 0.11
52 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.43
Consensus pattern (50 bp):
ATGTATCGATACATTCTGTTTTTTACTCAGATATATCGATACATTTTTCA
Found at i:219497 original size:13 final size:13
Alignment explanation
Indices: 219479--219503 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
219469 TGAATATGTG
219479 CCAAAATATCTTT
1 CCAAAATATCTTT
219492 CCAAAATATCTT
1 CCAAAATATCTT
219504 ATTTGCCCTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (13 bp):
CCAAAATATCTTT
Found at i:221514 original size:81 final size:81
Alignment explanation
Indices: 221359--221618 Score: 353
Period size: 81 Copynumber: 3.2 Consensus size: 81
221349 AAGTGGTAAT
* * * * * **
221359 TCATGCATGAAATTAAAACAAATGCTAAT-AAATAGCTACTGAAAAATAAGAAAGTTACA-ATTA
1 TCATGCATGAAATTAAAACAAAAGCAAATGAAATAGCTGCTGAAAAATAAGAAAGTAACAGCTGC
221422 TCGAAAAAGGATATAAA
66 T-GAAAAAGGATATAAA
* * *
221439 TCATGCACGAAATTAAAACAAAAGCAAATGAAACAGCTGCTGAAAAATAAGAAAGTAATAGCTGC
1 TCATGCATGAAATTAAAACAAAAGCAAATGAAATAGCTGCTGAAAAATAAGAAAGTAACAGCTGC
*
221504 TGAAAGAGGATATAAA
66 TGAAAAAGGATATAAA
* *
221520 TCATGCATAAAATTAAAACAAAAGAAAATGAAATAGCTGCTGAAAAATAAGAAAGTAACAGCTGC
1 TCATGCATGAAATTAAAACAAAAGCAAATGAAATAGCTGCTGAAAAATAAGAAAGTAACAGCTGC
* * *
221585 TGAAAAAGAATACAAT
66 TGAAAAAGGATATAAA
221601 TCATGCATGAAATTAAAA
1 TCATGCATGAAATTAAAA
221619 GTTGATGATC
Statistics
Matches: 157, Mismatches: 21, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
80 26 0.17
81 129 0.82
82 2 0.01
ACGTcount: A:0.53, C:0.11, G:0.15, T:0.20
Consensus pattern (81 bp):
TCATGCATGAAATTAAAACAAAAGCAAATGAAATAGCTGCTGAAAAATAAGAAAGTAACAGCTGC
TGAAAAAGGATATAAA
Found at i:221710 original size:31 final size:30
Alignment explanation
Indices: 221653--221710 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
221643 ATTAATTTGC
** *
221653 AAAAAGAAAGAAAGAAACGGCTACAATAAG
1 AAAAAGAAAGAAAGAAAAAGCAACAATAAG
221683 AAAAAGAAATGAAAGAAAAAGCAACAAT
1 AAAAAGAAA-GAAAGAAAAAGCAACAAT
221711 TGTTGAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 9 0.38
31 15 0.62
ACGTcount: A:0.67, C:0.09, G:0.17, T:0.07
Consensus pattern (30 bp):
AAAAAGAAAGAAAGAAAAAGCAACAATAAG
Found at i:222003 original size:12 final size:12
Alignment explanation
Indices: 221988--222062 Score: 78
Period size: 12 Copynumber: 6.2 Consensus size: 12
221978 ACCATACCAG
*
221988 CAACAATAGCAA
1 CAACAACAGCAA
*
222000 CAACAACGGCAA
1 CAACAACAGCAA
*
222012 CAACACCAGCAA
1 CAACAACAGCAA
* *
222024 CAACAATAACAA
1 CAACAACAGCAA
*
222036 TAACAACAGCAA
1 CAACAACAGCAA
*
222048 CAAACATCAGCAA
1 C-AACAACAGCAA
222061 CA
1 CA
222063 GTAATGGTAG
Statistics
Matches: 50, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
12 39 0.78
13 11 0.22
ACGTcount: A:0.56, C:0.31, G:0.08, T:0.05
Consensus pattern (12 bp):
CAACAACAGCAA
Found at i:223571 original size:13 final size:13
Alignment explanation
Indices: 223553--223577 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
223543 CATAAAGTGT
223553 TGTATCGATACAA
1 TGTATCGATACAA
223566 TGTATCGATACA
1 TGTATCGATACA
223578 TAAGTGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:223588 original size:32 final size:33
Alignment explanation
Indices: 223533--223596 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 33
223523 TTCAATGATT
223533 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
223566 TGTATCGATACAT-AAGTGTTGTATCGATACA
1 TGTATCGATACATAAAGTGTTGTATCGATACA
223597 TAAGTTTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 18 0.58
33 13 0.42
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.34
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:223590 original size:19 final size:19
Alignment explanation
Indices: 223532--223615 Score: 108
Period size: 19 Copynumber: 4.7 Consensus size: 19
223522 TTTCAATGAT
223532 TTGTATCGATACATAAAGTG
1 TTGTATCGATACAT-AAGTG
223552 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
223566 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
*
223584 TTGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTG
223603 TTGTATCGATACA
1 TTGTATCGATACA
223616 ATGTAAACTA
Statistics
Matches: 57, Mismatches: 1, Indels: 13
0.80 0.01 0.18
Matches are distributed among these distances:
13 11 0.19
15 2 0.04
17 2 0.04
19 30 0.53
20 12 0.21
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:223676 original size:13 final size:13
Alignment explanation
Indices: 223658--223682 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
223648 ATTACCCAAA
223658 TGTATCGATACAT
1 TGTATCGATACAT
223671 TGTATCGATACA
1 TGTATCGATACA
223683 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:223735 original size:52 final size:52
Alignment explanation
Indices: 223691--223819 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
223681 CACTGATCTT
*
223691 TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
223743 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
223795 TGTATTGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
223820 TCATATTTCG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:232166 original size:32 final size:32
Alignment explanation
Indices: 232058--232241 Score: 191
Period size: 31 Copynumber: 5.8 Consensus size: 32
232048 TTCAAATACC
* *
232058 TTCTT-AAAGTCCACGACTCAGTGGCAATCTC
1 TTCTTCAAAGTCCACGACTCAGTGGCATTCTT
* *
232089 TTC-TCAAAGCCCACGACTCAGTAGCATT-TT
1 TTCTTCAAAGTCCACGACTCAGTGGCATTCTT
* *
232119 GTC-TCAAAGTTCACGACTCAGTGGCATTCTT
1 TTCTTCAAAGTCCACGACTCAGTGGCATTCTT
232150 TTCTTCAAAGTCCACGACTCAGTGGCA-TCTT
1 TTCTTCAAAGTCCACGACTCAGTGGCATTCTT
* * *
232181 TTCTTCAAAATCCATGACTCCGTGGCACCTT-TT
1 TTCTTCAAAGTCCACGACTCAGTGGCA--TTCTT
* * *
232214 TCTTTTCAAAGTCCACAACTCCGTGGCA
1 T-TCTTCAAAGTCCACGACTCAGTGGCA
232242 CCCTTTTAAG
Statistics
Matches: 129, Mismatches: 17, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
30 26 0.20
31 55 0.43
32 22 0.17
33 3 0.02
34 23 0.18
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.32
Consensus pattern (32 bp):
TTCTTCAAAGTCCACGACTCAGTGGCATTCTT
Found at i:232235 original size:34 final size:32
Alignment explanation
Indices: 232148--232755 Score: 415
Period size: 34 Copynumber: 19.1 Consensus size: 32
232138 AGTGGCATTC
** * * *
232148 TTTTCTTCAAAGTCCACGACTCAGTGGCATC-
1 TTTTCTTTTAAGTCCACAACTCCGTGGCACCT
** * **
232179 TTTTCTTCAAAATCCATGACTCCGTGGCACCT
1 TTTTCTTTTAAGTCCACAACTCCGTGGCACCT
232211 TTTTCTTTTCAAAGTCCACAACTCCGTGGCACC-
1 TTTTCTTTT--AAGTCCACAACTCCGTGGCACCT
*
232244 ----CTTTTAAG-CCAACAACTCTGTGGCATCCT
1 TTTTCTTTTAAGTCC-ACAACTCCGTGGCA-CCT
* *
232273 TTTTCCTTCTAAGTCCACAACTCCGTGGTACC-
1 TTTT-CTTTTAAGTCCACAACTCCGTGGCACCT
*
232305 ----CTTTTAAGCCCACAACTCCGTGGCACTCT
1 TTTTCTTTTAAGTCCACAACTCCGTGGCAC-CT
* * *
232334 TTTTCCTTCTAAGACCATAACTCCGTGGCACC-
1 TTTT-CTTTTAAGTCCACAACTCCGTGGCACCT
* *
232366 ----CGTTTAAGCCCACAACTCCGTGGCACTCT
1 TTTTCTTTTAAGTCCACAACTCCGTGGCAC-CT
* * *
232395 TTTCCCTTTTAAGTCCACGACTTCGTGGCACCCTT
1 TTT-TCTTTTAAGTCCACAACTCCGTGGCA-CC-T
*
232430 TTTTCCTTTAAAGTCCACAACTCCGTGGCACCT
1 TTTT-CTTTTAAGTCCACAACTCCGTGGCACCT
* * *
232463 TGTTCCTTTTAAGTCCACAACTCTGTGGCATCT
1 T-TTTCTTTTAAGTCCACAACTCCGTGGCACCT
*
232496 TTTTCCTTTTAAAGTCCACAACTTCGTGGCACCT
1 TTTT-CTTTT-AAGTCCACAACTCCGTGGCACCT
* * *
232530 TTTCCTTTTAAGTCCACAACTTCATGGCACC-
1 TTTTCTTTTAAGTCCACAACTCCGTGGCACCT
*
232561 ----CTTTTAAGCCCACAACTCCGTGGCACTCT
1 TTTTCTTTTAAGTCCACAACTCCGTGGCAC-CT
* *
232590 TTTTCCTTCTAAGTCCACAACTTCGTGGCACCT
1 TTTT-CTTTTAAGTCCACAACTCCGTGGCACCT
* *
232623 TTTTCTTTTTAAAGCCCACAACTCTGTGGCACTCT
1 TTTTC-TTTT-AAGTCCACAACTCCGTGGCAC-CT
** * * * *
232658 TTTTCCTTCCAAGTCTACAACTCTGTAGTACC-
1 TTTT-CTTTTAAGTCCACAACTCCGTGGCACCT
*
232690 ----CTTTTAAAGCCCACAACTCCGTGGCACTCT
1 TTTTCTTTT-AAGTCCACAACTCCGTGGCAC-CT
*
232720 TTTTCCCTTTTAAGTCCACAACTCCGTGGCATCT
1 TTTT--CTTTTAAGTCCACAACTCCGTGGCACCT
232754 TT
1 TT
232756 CCTCTCCAAA
Statistics
Matches: 459, Mismatches: 66, Indels: 101
0.73 0.11 0.16
Matches are distributed among these distances:
26 2 0.00
27 87 0.19
28 21 0.05
29 6 0.01
31 27 0.06
32 31 0.07
33 51 0.11
34 172 0.37
35 56 0.12
36 6 0.01
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.34
Consensus pattern (32 bp):
TTTTCTTTTAAGTCCACAACTCCGTGGCACCT
Found at i:232259 original size:27 final size:26
Alignment explanation
Indices: 232226--232397 Score: 110
Period size: 27 Copynumber: 5.9 Consensus size: 26
232216 TTTTCAAAGT
232226 CCACAACTCCGTGGCACCCTTTTAAG
1 CCACAACTCCGTGGCACCCTTTTAAG
* *
232252 CCAACAACTCTGTGGCATCCTTTTTCCTTCTAAG
1 CC-ACAACTCCGTGGCA--C-----CCTTTTAAG
*
232286 TCCACAACTCCGTGGTACCCTTTTAAG
1 -CCACAACTCCGTGGCACCCTTTTAAG
*
232313 CCCACAACTCCGTGGCACTCTTTTTCCTTCTAAG
1 -CCACAACTCCGTGGCA--C-----CCTTTTAAG
* *
232347 ACCATAACTCCGTGGCACCCGTTTAAG
1 -CCACAACTCCGTGGCACCCTTTTAAG
*
232374 CCCACAACTCCGTGGCACTCTTTT
1 -CCACAACTCCGTGGCACCCTTTT
232398 CCCTTTTAAG
Statistics
Matches: 114, Mismatches: 16, Indels: 31
0.71 0.10 0.19
Matches are distributed among these distances:
26 2 0.02
27 63 0.55
29 2 0.02
32 2 0.02
34 43 0.38
35 2 0.02
ACGTcount: A:0.21, C:0.36, G:0.14, T:0.29
Consensus pattern (26 bp):
CCACAACTCCGTGGCACCCTTTTAAG
Found at i:232294 original size:61 final size:62
Alignment explanation
Indices: 232197--232750 Score: 586
Period size: 61 Copynumber: 8.7 Consensus size: 62
232187 AAAATCCATG
* * *
232197 ACTCCGTGGCAC-CTTTTTCTTTTCAAAGTCCACAACTCCGTGGCACCCTTTT-AAGCCAACA
1 ACTCCGTGGCACTCTTTTTC-CTTCTAAGTCCACAACTCCGTGGCACCCTTTTAAAGCCCACA
* *
232258 ACTCTGTGGCA-TCCTTTTTCCTTCTAAGTCCACAACTCCGTGGTACCCTTTT-AAGCCCACA
1 ACTCCGTGGCACT-CTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCCTTTTAAAGCCCACA
* * *
232319 ACTCCGTGGCACTCTTTTTCCTTCTAAGACCATAACTCCGTGGCACCCGTTT-AAGCCCACA
1 ACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCCTTTTAAAGCCCACA
* * * * *
232380 ACTCCGTGGCACTCTTTTCCCTTTTAAGTCCACGACTTCGTGGCACCCTTTTTTCCTTTAAAGTC
1 ACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCC-----T--TTTAAAGCC
232445 CACA
59 CACA
* * * *
232449 ACTCCGTGGCAC-CTTGTTCCTTTTAAGTCCACAACTCTGTGGCATCTTTTTCCTTTTAAAGTCC
1 ACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCA-C-----CCTTTTAAAGCCC
232513 ACA
60 ACA
* * * *
232516 ACTTCGTGGCAC-C-TTTTCCTTTTAAGTCCACAACTTCATGGCACCCTTTT-AAGCCCACA
1 ACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCCTTTTAAAGCCCACA
*
232575 ACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTTCGTGGCACCTTTTTCTTTTTAAAGCCC
1 ACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACC-----C-TTTTAAAGCCC
232640 ACA
60 ACA
* * * * * *
232643 ACTCTGTGGCACTCTTTTTCCTTCCAAGTCTACAACTCTGTAGTACCCTTTTAAAGCCCACA
1 ACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCCTTTTAAAGCCCACA
*
232705 ACTCCGTGGCACTCTTTTTCCCTTTTAAGTCCACAACTCCGTGGCA
1 ACTCCGTGGCACTCTTTTT-CCTTCTAAGTCCACAACTCCGTGGCA
232751 TCTTTCCTCT
Statistics
Matches: 420, Mismatches: 46, Indels: 52
0.81 0.09 0.10
Matches are distributed among these distances:
59 19 0.05
60 7 0.02
61 173 0.41
62 40 0.10
63 21 0.05
65 1 0.00
66 27 0.06
67 29 0.07
68 79 0.19
69 22 0.05
74 2 0.00
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.33
Consensus pattern (62 bp):
ACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCCTTTTAAAGCCCACA
Found at i:232573 original size:27 final size:27
Alignment explanation
Indices: 232533--232592 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
232523 GGCACCTTTT
* *
232533 CCTTTTAAGTCCACAACTTCATGGCAC
1 CCTTTTAAGCCCACAACTCCATGGCAC
*
232560 CCTTTTAAGCCCACAACTCCGTGGCAC
1 CCTTTTAAGCCCACAACTCCATGGCAC
*
232587 TCTTTT
1 CCTTTT
232593 TCCTTCTAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.22, C:0.35, G:0.12, T:0.32
Consensus pattern (27 bp):
CCTTTTAAGCCCACAACTCCATGGCAC
Found at i:232743 original size:35 final size:35
Alignment explanation
Indices: 232688--232755 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 35
232678 CTCTGTAGTA
232688 CCCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
1 CCCTTTTAAAGCCCACAACTCCGTGGCA-TCTTTTT
*
232724 CCCTTTT-AAGTCCACAACTCCGTGGCATCTTT
1 CCCTTTTAAAGCCCACAACTCCGTGGCATCTTT
232756 CCTCTCCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 5 0.16
35 19 0.61
36 7 0.23
ACGTcount: A:0.19, C:0.35, G:0.12, T:0.34
Consensus pattern (35 bp):
CCCTTTTAAAGCCCACAACTCCGTGGCATCTTTTT
Found at i:232805 original size:32 final size:31
Alignment explanation
Indices: 232764--232897 Score: 171
Period size: 32 Copynumber: 4.2 Consensus size: 31
232754 TTCCTCTCCA
232764 AAGCCCACACAAGTCGGTGGCAACCCTTTTCC
1 AAGCCCACACAAGTCGGTGGCAACCC-TTTCC
*
232796 AAGCCCACACAAGTCGATGGCAACCCTTTCC
1 AAGCCCACACAAGTCGGTGGCAACCCTTTCC
* * * *
232827 AAAGCCCACATAAGTCAGTGGCAACCACTCTCTA
1 -AAGCCCACACAAGTCGGTGGCAACC-CTTTC-C
*
232861 AAGCCCACACAAGTCGGTGGCAACCC-TTCT
1 AAGCCCACACAAGTCGGTGGCAACCCTTTCC
232891 AAGCCCA
1 AAGCCCA
232898 ATATCGCTGG
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
30 7 0.08
31 7 0.08
32 48 0.54
33 27 0.30
ACGTcount: A:0.30, C:0.37, G:0.17, T:0.16
Consensus pattern (31 bp):
AAGCCCACACAAGTCGGTGGCAACCCTTTCC
Found at i:232833 original size:64 final size:65
Alignment explanation
Indices: 232760--232888 Score: 190
Period size: 65 Copynumber: 2.0 Consensus size: 65
232750 ATCTTTCCTC
* * *
232760 TCCAAAGCCCACACAAGTCGGTGGCAACC-CT-TTTCCAAGCCCACACAAGTCGATGGCAACCCT
1 TCCAAAGCCCACACAAGTCAGTGGCAACCACTCTCT-AAAGCCCACACAAGTCGATGGCAACCCT
232823 T
65 T
* *
232824 TCCAAAGCCCACATAAGTCAGTGGCAACCACTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTT
1 TCCAAAGCCCACACAAGTCAGTGGCAACCACTCTCTAAAGCCCACACAAGTCGATGGCAACCCTT
232889 CTAAGCCCAA
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
64 27 0.47
65 29 0.50
66 2 0.03
ACGTcount: A:0.29, C:0.36, G:0.17, T:0.17
Consensus pattern (65 bp):
TCCAAAGCCCACACAAGTCAGTGGCAACCACTCTCTAAAGCCCACACAAGTCGATGGCAACCCTT
Found at i:233001 original size:43 final size:43
Alignment explanation
Indices: 232936--233298 Score: 316
Period size: 43 Copynumber: 8.0 Consensus size: 43
232926 GCACCTTTAT
* *
232936 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCAA
* *
232979 CTTCAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA-----A
* *
233027 TCTTTAAGTCCAAT-GCAGCTGGCCTTGAATCAGCACATTGGCAC
1 -CTTTAAGTCCAATATC-GCTGGCCTTGAATCAGCACATTGGCAA
* * * *
233071 CTTCAACTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA-----A
* *
233119 TCTTTAAGTCCAAT-GCAGCTGGCCTTGAATCAGCACATTGGCAC
1 -CTTTAAGTCCAATATC-GCTGGCCTTGAATCAGCACATTGGCAA
** * *
233163 CTCCAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATT---G-----G-CAA
* * * *
233215 CTTTAAATCCAATGTCGCTGGCCTTGAATCAGCACATTAGCAC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCAA
*
233258 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGC
233299 GCCTTTGTCA
Statistics
Matches: 259, Mismatches: 36, Indels: 50
0.75 0.10 0.14
Matches are distributed among these distances:
43 144 0.56
44 3 0.01
46 1 0.00
48 3 0.01
49 72 0.28
51 1 0.00
52 35 0.14
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.29
Consensus pattern (43 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCAA
Found at i:233052 original size:92 final size:92
Alignment explanation
Indices: 232885--233356 Score: 705
Period size: 92 Copynumber: 5.0 Consensus size: 92
232875 CGGTGGCAAC
* *
232885 CCTTCTAAGCCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTTATCTTTAAGTCCAATG
1 CCTTC-AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATG
*
232950 TAGCTGGCCTTGAATCAGCACATTGGCA
65 CAGCTGGCCTTGAATCAGCACATTGGCA
*
232978 ACTTCAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGC
1 CCTTCAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGC
233043 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* *
233070 CCTTCAACTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGC
1 CCTTCAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGC
233135 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* * *
233162 CCTCCAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAATCCAA
1 CCTTCAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TT-T-ATCTTTAAGTCCAA
*
233227 TGTC-GCTGGCCTTGAATCAGCACATTAGCA
63 TG-CAGCTGGCCTTGAATCAGCACATTGGCA
* *
233257 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTTAAGTCCA
1 CCTTCAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TT-T-ATC-TTTAAGTCCA
* * *
233322 ATGTC-GTTGGCCTTGAATCAGCATATTGGCG
62 ATG-CAGCTGGCCTTGAATCAGCACATTGGCA
233353 CCTT
1 CCTT
233357 TGTCATTTTT
Statistics
Matches: 354, Mismatches: 20, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
92 214 0.60
93 6 0.02
94 1 0.00
95 92 0.26
96 41 0.12
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (92 bp):
CCTTCAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGC
AGCTGGCCTTGAATCAGCACATTGGCA
Found at i:233073 original size:21 final size:20
Alignment explanation
Indices: 233049--233116 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 20
233039 ATGCAGCTGG
233049 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCA-ATTGGCA
* *
233070 CCTTCAACTC--CAATATCGCTA
1 CCTTGAA-TCAGCAAT-TGGC-A
233091 GCCTTGAATCAGCATATTGGCA
1 -CCTTGAATCAGCA-ATTGGCA
233113 CCTT
1 CCTT
233117 TATCTTTAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 14
0.67 0.07 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.14
21 13 0.36
22 9 0.25
23 5 0.14
24 2 0.06
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.28
Consensus pattern (20 bp):
CCTTGAATCAGCAATTGGCA
Found at i:233339 original size:53 final size:54
Alignment explanation
Indices: 233259--233412 Score: 229
Period size: 53 Copynumber: 2.8 Consensus size: 54
233249 CATTAGCACC
*
233259 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCA-TCT
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATTCT
* *
233312 TTTAAGTCCAATGTCGTTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATTTTTT
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCA--TTCT
* * *
233368 TTTAAGTCCAATGTCACTGGCCTTGAATCAGCACATTGGCACCTT
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCGCCTT
233413 CATCTTTAAC
Statistics
Matches: 91, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
53 48 0.53
56 43 0.47
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (54 bp):
TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATTCT
Found at i:234286 original size:13 final size:13
Alignment explanation
Indices: 234268--234292 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
234258 CATAAAGTGT
234268 TGTATCGATACAA
1 TGTATCGATACAA
234281 TGTATCGATACA
1 TGTATCGATACA
234293 TAAGTGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:234309 original size:19 final size:19
Alignment explanation
Indices: 234247--234349 Score: 128
Period size: 19 Copynumber: 5.7 Consensus size: 19
234237 TTTCAACGAT
234247 TTGTATCGATACATAAAGTG
1 TTGTATCGATACAT-AAGTG
234267 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
234281 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
* *
234299 TTGTATTGATACATAAATG
1 TTGTATCGATACATAAGTG
*
234318 TTGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTG
234337 TTGTATCGATACA
1 TTGTATCGATACA
234350 ATGTAAGCTA
Statistics
Matches: 72, Mismatches: 5, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
13 11 0.15
15 2 0.03
17 2 0.03
19 45 0.62
20 12 0.17
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:234410 original size:13 final size:13
Alignment explanation
Indices: 234392--234416 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
234382 ATTACCCAAA
234392 TGTATCGATACAT
1 TGTATCGATACAT
234405 TGTATCGATACA
1 TGTATCGATACA
234417 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:240777 original size:21 final size:21
Alignment explanation
Indices: 240744--240788 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
240734 TTGCAAGTTG
*
240744 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
240766 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
240786 AAA
1 AAA
240789 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:242612 original size:15 final size:15
Alignment explanation
Indices: 242592--242622 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
242582 TAAAAATGTC
*
242592 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
242607 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
242622 C
1 C
242623 CAAACAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:244719 original size:13 final size:13
Alignment explanation
Indices: 244701--244739 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
244691 ATATTTTTCT
244701 TTGTATCGATACA
1 TTGTATCGATACA
244714 TTGTATCGATACA
1 TTGTATCGATACA
*
244727 CTGTATCGATACA
1 TTGTATCGATACA
244740 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:244885 original size:21 final size:21
Alignment explanation
Indices: 244861--244907 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
244851 AAATCTTTTG
244861 CAAAAT-ACTT-GTTTTTCACTT
1 CAAAATAACTTCGTTTTTCA--T
244882 C-AAATAACTTCGTTTTTCAT
1 CAAAATAACTTCGTTTTTCAT
244902 CAAAAT
1 CAAAAT
244908 CAGCATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (21 bp):
CAAAATAACTTCGTTTTTCAT
Found at i:244904 original size:20 final size:19
Alignment explanation
Indices: 244863--244905 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
244853 ATCTTTTGCA
244863 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
244883 AAATAACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
244903 AAA
1 AAA
244906 ATCAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:247296 original size:13 final size:13
Alignment explanation
Indices: 247278--247303 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
247268 TACAGCAAGT
247278 ATGTATCGATACA
1 ATGTATCGATACA
247291 ATGTATCGATACA
1 ATGTATCGATACA
247304 CAAAAAATTG
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:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:249505 original size:14 final size:15
Alignment explanation
Indices: 249480--249510 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
249470 AATGTGGTTT
249480 ATTTTTCTTTTTTGC
1 ATTTTTCTTTTTTGC
249495 ATTTTTC-TTTTTGC
1 ATTTTTCTTTTTTGC
249509 AT
1 AT
249511 GCTTACACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.10, C:0.13, G:0.06, T:0.71
Consensus pattern (15 bp):
ATTTTTCTTTTTTGC
Found at i:252112 original size:19 final size:20
Alignment explanation
Indices: 252088--252139 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
252078 GTAGCCAAAC
**
252088 TTGTATCGATACAC-AAAGT
1 TTGTATCGATACACAAAAAA
252107 TTGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
252127 TTGTATCGATACA
1 TTGTATCGATACA
252140 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.31
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:256213 original size:15 final size:15
Alignment explanation
Indices: 256195--256224 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
256185 CCAAATTGAG
256195 GAAGCTCAAAATGAA
1 GAAGCTCAAAATGAA
*
256210 GAAGCTCCAAATGAA
1 GAAGCTCAAAATGAA
256225 ATCGATGAAC
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:0.50, C:0.17, G:0.20, T:0.13
Consensus pattern (15 bp):
GAAGCTCAAAATGAA
Found at i:256220 original size:16 final size:16
Alignment explanation
Indices: 256184--256224 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
256174 GATAAAAATG
* *
256184 TCCAAATTGAGGAAGC
1 TCCAAAATGAAGAAGC
256200 T-CAAAATGAAGAAGC
1 TCCAAAATGAAGAAGC
256215 TCC-AAATGAA
1 TCCAAAATGAA
256225 ATCGATGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 20 0.91
16 2 0.09
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (16 bp):
TCCAAAATGAAGAAGC
Found at i:258257 original size:20 final size:20
Alignment explanation
Indices: 258232--258311 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
258222 AATGTCCAAA
258232 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATGTTTCT
* *
258252 ATGTATCGATACATATGGAAATTCA
1 ATGTATCGATAC--AT-G--TTTCT
*
258277 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATGTTTCT
*
258297 TTGTATCGATACATG
1 ATGTATCGATACATG
258312 GTATCGATAC
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
20 28 0.58
22 2 0.04
23 3 0.06
25 15 0.31
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATGTTTCT
Found at i:258317 original size:13 final size:13
Alignment explanation
Indices: 258298--258335 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
258288 CATTTTTCTT
258298 TGTATCGATACA-
1 TGTATCGATACAC
258310 TGGTATCGATACAC
1 T-GTATCGATACAC
258324 TGTATCGATACA
1 TGTATCGATACA
258336 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 1 0.04
13 22 0.92
14 1 0.04
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:258496 original size:20 final size:20
Alignment explanation
Indices: 258453--258498 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
258443 AAATCTTTTG
258453 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
258474 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
258494 CAAAA
1 CAAAA
258499 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:260921 original size:13 final size:13
Alignment explanation
Indices: 260903--260928 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
260893 TACACAAAGT
260903 ATGTATCGATACA
1 ATGTATCGATACA
260916 ATGTATCGATACA
1 ATGTATCGATACA
260929 CAAAAAATTG
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:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:260926 original size:32 final size:33
Alignment explanation
Indices: 260885--260948 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
260875 TAGCCAAACT
**
260885 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
260917 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
260949 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:266590 original size:129 final size:129
Alignment explanation
Indices: 266347--266601 Score: 384
Period size: 129 Copynumber: 2.0 Consensus size: 129
266337 TACGAGGTCG
*
266347 CTATGAACAATTGAATTTCATTAAAGAAAAGAGGTTGAAAGTGATCTAACATGGACAGATGTATC
1 CTATGAACAATTGAATTTCATTAAAGAAAAGAGGTTGAAAGTGATCCAACATGGACAGATGTATC
* * * *
266412 AAAAAAGAATATTGAGGGCCCATGATAAGAAAATTCGTCCAAGACAGTTTCATGAAGGAGATCA
66 AAAAAAGAATATTGAGGGCACATGATAAAAAAATCCATCCAAGACAGTTTCATGAAGGAGATCA
* * *
266476 CTATGAACAATTGAATTTCATTGAAGAAAAGAGGTTGAAAGTGATCCGACATGGGCAGATGTATC
1 CTATGAACAATTGAATTTCATTAAAGAAAAGAGGTTGAAAGTGATCCAACATGGACAGATGTATC
* * *** *
266541 AAAAGAGAATATTGAGGGCATATGATAAAAAAATCCATTTGAGATAGTTTCATGAAGGAGA
66 AAAAAAGAATATTGAGGGCACATGATAAAAAAATCCATCCAAGACAGTTTCATGAAGGAGA
266602 ATTGGTATTG
Statistics
Matches: 112, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
129 112 1.00
ACGTcount: A:0.42, C:0.11, G:0.22, T:0.25
Consensus pattern (129 bp):
CTATGAACAATTGAATTTCATTAAAGAAAAGAGGTTGAAAGTGATCCAACATGGACAGATGTATC
AAAAAAGAATATTGAGGGCACATGATAAAAAAATCCATCCAAGACAGTTTCATGAAGGAGATCA
Found at i:266806 original size:12 final size:13
Alignment explanation
Indices: 266783--266819 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
266773 GTACTTTGCT
266783 TAAA-AAAGTAAA
1 TAAATAAAGTAAA
266795 TAAATAAA-TAAA
1 TAAATAAAGTAAA
*
266807 TAATTAAAGTAAA
1 TAAATAAAGTAAA
266820 AAAAGTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 15 0.68
13 7 0.32
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.24
Consensus pattern (13 bp):
TAAATAAAGTAAA
Found at i:267736 original size:77 final size:78
Alignment explanation
Indices: 267541--267743 Score: 291
Period size: 78 Copynumber: 2.6 Consensus size: 78
267531 GCGGCCCATT
* * * * *
267541 CATTTCCTAGTCATATCCTTTTCCCTCAATTTCTAGATGATATTGATGCATCCTAGAGCCTAATA
1 CATTTCCCAATCATATCCTTTTCCCTCAATTGCCAGATGATATTGATGAATCCTAGAGCCTAATA
*
267606 GGTGCAGACCATA
66 GGTGCAGACCACA
* * *
267619 CATTTTCCAATCATATCATTTTCCCTCAATTGCCAAATGATATTGATGAATCCTAGAGCCTAAT-
1 CATTTCCCAATCATATCCTTTTCCCTCAATTGCCAGATGATATTGATGAATCCTAGAGCCTAATA
267683 GGTGCAGACCACA
66 GGTGCAGACCACA
* * *
267696 CATTTCCCAATCATATCCTTTTCCTTCAACTGCGAGATGATATTGATG
1 CATTTCCCAATCATATCCTTTTCCCTCAATTGCCAGATGATATTGATG
267744 CATGAAAGAG
Statistics
Matches: 110, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
77 54 0.49
78 56 0.51
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (78 bp):
CATTTCCCAATCATATCCTTTTCCCTCAATTGCCAGATGATATTGATGAATCCTAGAGCCTAATA
GGTGCAGACCACA
Found at i:267754 original size:77 final size:78
Alignment explanation
Indices: 267541--267760 Score: 298
Period size: 77 Copynumber: 2.8 Consensus size: 78
267531 GCGGCCCATT
* * * *
267541 CATTTCCTAGTCATATCCTTTTCCCTCAATTTCTAGATGATATTGATGCATCCTAGAGCCTAATA
1 CATTTCCCAATCATATCCTTTTCCCTCAATTGCCAGATGATATTGATGCATCCTAGAGCCTAATA
*
267606 GGTGCAGACCATA
66 GGTGCAGACCACA
* * * *
267619 CATTTTCCAATCATATCATTTTCCCTCAATTGCCAAATGATATTGATGAATCCTAGAGCCTAAT-
1 CATTTCCCAATCATATCCTTTTCCCTCAATTGCCAGATGATATTGATGCATCCTAGAGCCTAATA
267683 GGTGCAGACCACA
66 GGTGCAGACCACA
* * * ***
267696 CATTTCCCAATCATATCCTTTTCCTTCAACTGCGAGATGATATTGATGCATGAAAGAGCCTAATA
1 CATTTCCCAATCATATCCTTTTCCCTCAATTGCCAGATGATATTGATGCATCCTAGAGCCTAATA
267761 CCTTGGGGCA
Statistics
Matches: 122, Mismatches: 19, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
77 66 0.54
78 56 0.46
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.33
Consensus pattern (78 bp):
CATTTCCCAATCATATCCTTTTCCCTCAATTGCCAGATGATATTGATGCATCCTAGAGCCTAATA
GGTGCAGACCACA
Found at i:268527 original size:42 final size:42
Alignment explanation
Indices: 268463--270627 Score: 1000
Period size: 42 Copynumber: 51.5 Consensus size: 42
268453 AAACTTTCTT
* *
268463 TTCTTTACCCTTTGTTTGCCCATCAGCTTTGACCTGGGAGAC
1 TTCTTTACCCTTTGTCTGCCCGTCAGCTTTGACCTGGGAGAC
* * *
268505 TTCTTTACCCTTTGTCTACCCATCAGCTTTGACCCGGGAGAC
1 TTCTTTACCCTTTGTCTGCCCGTCAGCTTTGACCTGGGAGAC
* * * * *
268547 TTCTTTTCCCTTTATCTGCCCATCAACTTTGA-CTCAGGAGAC
1 TTCTTTACCCTTTGTCTGCCCGTCAGCTTTGACCT-GGGAGAC
* * * *
268589 TT-TTTTCCCTTTATCTGCCCATCAGCTTTGACCTAGGAGAC
1 TTCTTTACCCTTTGTCTGCCCGTCAGCTTTGACCTGGGAGAC
* *
268630 TT-TTTTCCCTTTGTCTGCCCGTCGGCTTTGACCT-GGAGAC
1 TTCTTTACCCTTTGTCTGCCCGTCAGCTTTGACCTGGGAGAC
* * ** * **
268670 TTCTTTACCATTTGTTTGCCTATTAGCTTTGA-CTCGAAAGAC
1 TTCTTTACCCTTTGTCTGCCCGTCAGCTTTGACCT-GGGAGAC
* * * * * *
268712 TTTTTTACCCTTTTTTCTTCCCATCAGCTTTGACTTAGGAGAC
1 TTCTTTACCC-TTTGTCTGCCCGTCAGCTTTGACCTGGGAGAC
* * ** * * *
268755 TTTTTTACCCCTTGTCTATCTGTCGGCTTTGACCTGGAAGAC
1 TTCTTTACCCTTTGTCTGCCCGTCAGCTTTGACCTGGGAGAC
* * * *
268797 TTTTTTA-CCTTTGTTTGCCCATCTA-CTTT-AACTCGGGAGAC
1 TTCTTTACCCTTTGTCTGCCCGTC-AGCTTTGACCT-GGGAGAC
* * * * *
268838 TTCTTTTCCCTTTGTATGCCCGTTAGCTTTGA-CTCGAGAAAC
1 TTCTTTACCCTTTGTCTGCCCGTCAGCTTTGACCT-GGGAGAC
* * * * **
268880 TTATTTTCCCTTTGTTTGCCCGTCAACTTTGACCTAAGAGACC
1 TTCTTTACCCTTTGTCTGCCCGTCAGCTTTGACCTGGGAGA-C
* * * * *
268923 TT-TTTACTCTTTATTTG-CCGTCAACTTTGACCCGGGAGAC
1 TTCTTTACCCTTTGTCTGCCCGTCAGCTTTGACCTGGGAGAC
* * ** *
268963 TTCTTTACCATTTGTCTACTTGTCAGCTTTGA-CTCAGGAGA-
1 TTCTTTACCCTTTGTCTGCCCGTCAGCTTTGACCT-GGGAGAC
* * * *
269004 --CTTTACCCTTTGTTTGCCCATCAGCTTTAACCTAGGAGAC
1 TTCTTTACCCTTTGTCTGCCCGTCAGCTTTGACCTGGGAGAC
** * * ** * * *
269044 TTCTACACCTTTTGTCTACCAATCGGCTATGA-CTCGGGAGAT
1 TTCTTTACCCTTTGTCTGCCCGTCAGCTTTGACCT-GGGAGAC
* * *
269086 TTCTTCACTCTTT-TCTGCCCGTCAGCTTTGACTTGGGAGAC
1 TTCTTTACCCTTTGTCTGCCCGTCAGCTTTGACCTGGGAGAC
** * * * * *
269127 TTCTTTACTTTTTATCTACCCCTC-GACTTTGATCTGGGAGAA
1 TTCTTTACCCTTTGTCTGCCCGTCAG-CTTTGACCTGGGAGAC
* * * ** *
269169 TTCTTTATCCTTTGTTTGCCAGTTGGCTTTGACCCGGGAGAC
1 TTCTTTACCCTTTGTCTGCCCGTCAGCTTTGACCTGGGAGAC
* * ** * *** *
269211 TTTTTTA-CCTTTTTCTGCTTGTCAACTTTGACCAAAGAAAC
1 TTCTTTACCCTTTGTCTGCCCGTCAGCTTTGACCTGGGAGAC
* * * * * * * * *
269252 TTATTTACCTTTTGTCAGCCCTTCGGCTATAACCCGAGAGAC
1 TTCTTTACCCTTTGTCTGCCCGTCAGCTTTGACCTGGGAGAC
* * *
269294 TTCTTTATCCC-TTGTCTACCCATC-GACTTTGA-CTCGGGAAAC
1 TTCTTTA-CCCTTTGTCTGCCCGTCAG-CTTTGACCT-GGGAGAC
* * * ***
269336 TT-TTTTCCCTTTTGTTTGCCCGTTAGCTTTGACCCAAGAGAC
1 TTCTTTACCC-TTTGTCTGCCCGTCAGCTTTGACCTGGGAGAC
** * *
269378 TTCTCCACCCTTTGTCTGCCCGTCAACTTTGACCTGAGAGAC
1 TTCTTTACCCTTTGTCTGCCCGTCAGCTTTGACCTGGGAGAC
* * * ** * *
269420 TTCATTACCCTTTCTCTACTTGTCAGCTTTAACCTAGGAGAC
1 TTCTTTACCCTTTGTCTGCCCGTCAGCTTTGACCTGGGAGAC
* ** * * * ***
269462 TTTTTTACCCTTTGGT-TGCTAGCCAGTTTTGAAGC-AAAAGAC
1 TTCTTTACCCTTT-GTCTGCCCGTCAGCTTTG-ACCTGGGAGAC
* * *
269504 TT-TTTGACCCTTTGT-TCGCCCATC-GACTTTGACCCGAGAGACC
1 TTCTTT-ACCCTTTGTCT-GCCCGTCAG-CTTTGACCTGGGAGA-C
* * * **
269547 TTTTTACCCCTTGTCACCCTTTGTCTGCTCGTGAACTTTGATCC-AAGAGAC
1 ---TT----CTT-T-ACCCTTTGTCTGCCCGTCAGCTTTGA-CCTGGGAGAC
* * ** * *
269598 TTTTTTACCCTTTGTCTACTTGTCAGCTTTAACTTGGGAGAC
1 TTCTTTACCCTTTGTCTGCCCGTCAGCTTTGACCTGGGAGAC
* * * * ***
269640 TTCTTTACCCTTTGTTTGCCCATTAACTTTGA-CTCAAAAGAC
1 TTCTTTACCCTTTGTCTGCCCGTCAGCTTTGACCT-GGGAGAC
* * * ***
269682 TTCTTTACCCTTTGTCAGCCCATC-GATTTTGACCTAAAAGAC
1 TTCTTTACCCTTTGTCTGCCCGTCAG-CTTTGACCTGGGAGAC
* * * * * *
269724 TT-TTTCACCCCTTGTTTTCCTGTCAACTTTGACCCGGGAGAC
1 TTCTTT-ACCCTTTGTCTGCCCGTCAGCTTTGACCTGGGAGAC
* * * *
269766 TTCTATACCTTTTGTCTACCCATC-GACTTT-ACCTCGGGAGAC
1 TTCTTTACCCTTTGTCTGCCCGTCAG-CTTTGACCT-GGGAGAC
* * * *
269808 TT-TTTCACCTTTTGTCTACCCATCAGCTTTGACCTGGGAGAA
1 TTCTTT-ACCCTTTGTCTGCCCGTCAGCTTTGACCTGGGAGAC
* * * * ** * * *
269850 TTATTTTCCCTTTGTTTGCCTGTCTTCTTTG-GCTCGAGAGGC
1 TTCTTTACCCTTTGTCTGCCCGTCAGCTTTGACCT-GGGAGAC
* * * *
269892 TTCTTCACCCTTTATCTGCTCGTCAGCTTT-AACTCGGGAGAC
1 TTCTTTACCCTTTGTCTGCCCGTCAGCTTTGACCT-GGGAGAC
* * * * * *
269934 TTCTTTACCCCTTGTCTACCCGTTAGCTTTAACTTGGGAAAC
1 TTCTTTACCCTTTGTCTGCCCGTCAGCTTTGACCTGGGAGAC
* ** * * * *
269976 TTATTTTTCTTTTGTCTGCCCGTCAGCTTT-AACTCAGAAGAC
1 TTCTTTACCCTTTGTCTGCCCGTCAGCTTTGACCT-GGGAGAC
* ** **
270018 TTCTTTACCCTTTGCCTGCCTATTGGCTTTGA-CTCGGGAGAC
1 TTCTTTACCCTTTGTCTGCCCGTCAGCTTTGACCT-GGGAGAC
* * * * ** *
270060 TT-TTTCACCTTTTTTTTGCCCATTGGCTTTGACCCGGGAGAC
1 TTCTTT-ACCCTTTGTCTGCCCGTCAGCTTTGACCTGGGAGAC
* * * * *
270102 TTCTTTACCCTTTGTCTACCCATTAACTTTGACCTAGGAGAC
1 TTCTTTACCCTTTGTCTGCCCGTCAGCTTTGACCTGGGAGAC
* * * * * * **
270144 TTTTTTACCCTTTGTATGCCCATCGGCTTGGACCCGAAAGAC
1 TTCTTTACCCTTTGTCTGCCCGTCAGCTTTGACCTGGGAGAC
* * * *
270186 TTCTTTACCCTTTGTTTGCCTGTC-GACTTAGATCT-GGAGA-
1 TTCTTTACCCTTTGTCTGCCCGTCAG-CTTTGACCTGGGAGAC
* * * * *
270226 TTACTTTACCCTTTATCTGCTCAT-TGACTTTGACTTGGGAGAC
1 TT-CTTTACCCTTTGTCTGCCCGTCAG-CTTTGACCTGGGAGAC
* * * **
270269 ATT-TTTACCCTTTGTCTGCCCGTCGGCTTGGACCCGAAAGAC
1 -TTCTTTACCCTTTGTCTGCCCGTCAGCTTTGACCTGGGAGAC
* * * *
270311 TTCTTTACCCTTTGTTTGCCTGTC-GACTTAGATCT-GGAGA-
1 TTCTTTACCCTTTGTCTGCCCGTCAG-CTTTGACCTGGGAGAC
* * * * *
270351 TTACTTTACCCTTTATCTGCTCAT-TGACTTTGACTTGGGAGAC
1 TT-CTTTACCCTTTGTCTGCCCGTCAG-CTTTGACCTGGGAGAC
* *
270394 ATT-TTTACCCTTTGTCTGCCCGTCGGCTTTGACTTGGGAGAC
1 -TTCTTTACCCTTTGTCTGCCCGTCAGCTTTGACCTGGGAGAC
* ** * *
270436 TT-TTTCACCCTTTGT-TCGCCTGTTGGCTTT-AACTCGGGAGAG
1 TTCTTT-ACCCTTTGTCT-GCCCGTCAGCTTTGACCT-GGGAGAC
* * * * *
270478 TTCTTTACCTTTTATCTGCCTGTCAACTTTGACTTGGGAGACTTGAC
1 TTCTTTACCCTTTGTCTGCCCGTCAGCTTTGACCT-GG-GA---GAC
* * * *
270525 TTCTTTACCCATTATCTGCCCATCGGCTTTGACCTGGGAGAC
1 TTCTTTACCCTTTGTCTGCCCGTCAGCTTTGACCTGGGAGAC
* *
270567 TTCTTTACCCTTTGTCTGCCCGTC-GATTTTGACTTGGGAGAC
1 TTCTTTACCCTTTGTCTGCCCGTCAG-CTTTGACCTGGGAGAC
270609 TTCTTTACCCTTTGTCTGC
1 TTCTTTACCCTTTGTCTGC
270628 TTTGACCCAA
Statistics
Matches: 1603, Mismatches: 419, Indels: 202
0.72 0.19 0.09
Matches are distributed among these distances:
39 29 0.02
40 25 0.02
41 305 0.19
42 1086 0.68
43 80 0.05
44 9 0.01
45 2 0.00
46 4 0.00
47 30 0.02
48 2 0.00
51 3 0.00
52 25 0.02
53 3 0.00
ACGTcount: A:0.17, C:0.27, G:0.17, T:0.39
Consensus pattern (42 bp):
TTCTTTACCCTTTGTCTGCCCGTCAGCTTTGACCTGGGAGAC
Found at i:269682 original size:178 final size:176
Alignment explanation
Indices: 269383--269738 Score: 443
Period size: 178 Copynumber: 2.0 Consensus size: 176
269373 GAGACTTCTC
*
269383 CACCCTTTGTCTGCCCGTCAACTTTGACCTGAGAGACTTCATTACCCTTTCTCTACTTGTCAGCT
1 CACCCTTTGTCTGCCCGTCAACTTTGACCTAAGAGACTTCATTACCCTTTCTCTACTTGTCAGCT
*
269448 TTAACCTAGGAGACTTTTTTACCCTTTGGTTGCTAGCCAGTTTTGAAGCAAAAGACTT-TTTGAC
66 TTAACCTAGGAGACTTCTTTACCCTTTGGTTGC-A-CCAGTTTTGAAGCAAAAGACTTCTTT-AC
* *
269512 CCTTTGTTC-GCCCATCGACTTTGACCCGAGAGACCTTTTT-ACCCCTTGT
128 CCTTTG-TCAGCCCATCGACTTTGACCCAAAAGA-CTTTTTCACCCCTTGT
* * ** *
269561 CACCCTTTGTCTGCTCGTGAACTTTGATCC-AAGAGACTTTTTTACCCTTTGTCTACTTGTCAGC
1 CACCCTTTGTCTGCCCGTCAACTTTGA-CCTAAGAGACTTCATTACCCTTTCTCTACTTGTCAGC
* * * * **
269625 TTTAACTTGGGAGACTTCTTTACCCTTTGTTTGC-CCATTAACTTTGACTCAAAAGACTTCTTTA
65 TTTAACCTAGGAGACTTCTTTACCCTTTGGTTGCACCAGT---TTTGAAGCAAAAGACTTCTTTA
* *
269689 CCCTTTGTCAGCCCATCGATTTTGACCTAAAAGACTTTTTCACCCCTTGT
127 CCCTTTGTCAGCCCATCGACTTTGACCCAAAAGACTTTTTCACCCCTTGT
269739 TTTCCTGTCA
Statistics
Matches: 154, Mismatches: 17, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
175 4 0.03
177 8 0.05
178 137 0.89
179 5 0.03
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.38
Consensus pattern (176 bp):
CACCCTTTGTCTGCCCGTCAACTTTGACCTAAGAGACTTCATTACCCTTTCTCTACTTGTCAGCT
TTAACCTAGGAGACTTCTTTACCCTTTGGTTGCACCAGTTTTGAAGCAAAAGACTTCTTTACCCT
TTGTCAGCCCATCGACTTTGACCCAAAAGACTTTTTCACCCCTTGT
Found at i:270643 original size:76 final size:76
Alignment explanation
Indices: 270562--270704 Score: 182
Period size: 76 Copynumber: 1.9 Consensus size: 76
270552 TTTGACCTGG
* * * * *
270562 GAGACTTCTTT-ACC-CTTTGTCTGCCCGTCGATTTTGACTTGGGAGACTTCTTTACCCTTTGTC
1 GAGACTT-TTTCACCTC-TTGTCTACCCGTCGACTTTGACTTAGGAGACTTCTTTACCCCTTATC
270625 TGCTTTGACCCAA
64 TGCTTTGACCCAA
** *
270638 GAGACTTTTTCACCTCTTGTCTACTTGTCGGCTTTGACTTAGGAGACTTCTTTACCCCTTATCTG
1 GAGACTTTTTCACCTCTTGTCTACCCGTCGACTTTGACTTAGGAGACTTCTTTACCCCTTATCTG
270703 CT
66 CT
270705 GGTCAACTTA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
75 3 0.05
76 53 0.93
77 1 0.02
ACGTcount: A:0.15, C:0.27, G:0.17, T:0.41
Consensus pattern (76 bp):
GAGACTTTTTCACCTCTTGTCTACCCGTCGACTTTGACTTAGGAGACTTCTTTACCCCTTATCTG
CTTTGACCCAA
Found at i:270684 original size:42 final size:42
Alignment explanation
Indices: 270620--270727 Score: 101
Period size: 42 Copynumber: 2.6 Consensus size: 42
270610 TCTTTACCCT
* ** * * *
270620 TTGTCTGCTTTGACCCAAGAGACTT-TTTCACCTCTTGTCTAC
1 TTGTCAGCTTTGACTTAGGAGACTTCTTT-ACCCCTTATCTAC
* *
270662 TTGTCGGCTTTGACTTAGGAGACTTCTTTACCCCTTATCTGC
1 TTGTCAGCTTTGACTTAGGAGACTTCTTTACCCCTTATCTAC
* * *
270704 TGGTCAACTTAGACTTAGGAGACT
1 TTGTCAGCTTTGACTTAGGAGACT
270728 CATTTTTTTT
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
42 51 0.94
43 3 0.06
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.38
Consensus pattern (42 bp):
TTGTCAGCTTTGACTTAGGAGACTTCTTTACCCCTTATCTAC
Found at i:271341 original size:31 final size:31
Alignment explanation
Indices: 271305--271363 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
271295 AGAATTAAAA
271305 AATTAAAAAATTTAATT-AATTA-ATTATTCTT
1 AATT-AAAAA-TTAATTAAATTATATTATTCTT
271336 AATTAAAAATTAATTAAATTATATTATT
1 AATTAAAAATTAATTAAATTATATTATT
271364 TCATTTTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 6 0.23
30 10 0.38
31 10 0.38
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (31 bp):
AATTAAAAATTAATTAAATTATATTATTCTT
Found at i:273310 original size:20 final size:20
Alignment explanation
Indices: 273282--273333 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
273272 ATATTTCAAA
*
273282 GTATCGATACATAGGTATTT
1 GTATCGATACATACGTATTT
*
273302 GTATGGATACATACGTATTT
1 GTATCGATACATACGTATTT
*
273322 GTATCAATACAT
1 GTATCGATACAT
273334 TATGGTTGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (20 bp):
GTATCGATACATACGTATTT
Found at i:279819 original size:21 final size:22
Alignment explanation
Indices: 279795--279844 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
279785 ATCAAATCTT
* *
279795 CTTCAAATTTCTT-ATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
279816 CTTCAAAATACTTCATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
279838 --TCAAAAT
1 CTTCAAAAT
279845 CATCAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 7 0.27
21 11 0.42
22 8 0.31
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (22 bp):
CTTCAAAATACTTCATTTTTCA
Found at i:281925 original size:20 final size:19
Alignment explanation
Indices: 281882--281931 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
281872 ACATTATGCT
**
281882 TTGTATCGATACAAGTTCA
1 TTGTATCGATACAAGGACA
*
281901 TTGTATCGATACATGGACAA
1 TTGTATCGATACAAGGAC-A
281921 TTGTATCGATA
1 TTGTATCGATA
281932 TATGAAACTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACAAGGACA
Found at i:281989 original size:20 final size:19
Alignment explanation
Indices: 281964--282038 Score: 71
Period size: 20 Copynumber: 3.7 Consensus size: 19
281954 CTACCACTGT
281964 TTGTATCGATACATGGCACA
1 TTGTATCGATACATGG-ACA
*
281984 TTGTATCGATACATTGTATCA
1 TTGTATCGATACA-TGGA-CA
* *
282005 ATGTATCAATACATGATGA-A
1 TTGTATCGATACATG--GACA
282025 TTGTATCGATACAT
1 TTGTATCGATACAT
282039 TACTTCAAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
20 29 0.64
21 15 0.33
22 1 0.02
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATGGACA
Found at i:294361 original size:52 final size:52
Alignment explanation
Indices: 294283--294411 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
294273 CAAAATATGA
* *
294283 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
*
294335 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
294387 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
294412 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
Found at i:294424 original size:52 final size:51
Alignment explanation
Indices: 294283--294431 Score: 219
Period size: 52 Copynumber: 2.9 Consensus size: 51
294273 CAAAATATGA
*
294283 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
* *
294335 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
*
294387 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
294432 ATGTATCGAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 87 0.98
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGC
Found at i:294438 original size:13 final size:13
Alignment explanation
Indices: 294420--294444 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
294410 CAAAGATCAG
294420 TGTATCGATACAA
1 TGTATCGATACAA
294433 TGTATCGATACA
1 TGTATCGATACA
294445 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:294522 original size:33 final size:33
Alignment explanation
Indices: 294485--294551 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
294475 AGTAGCTTAA
294485 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
294518 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
294551 A
1 A
294552 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:294525 original size:13 final size:13
Alignment explanation
Indices: 294507--294531 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
294497 CAAAAAAATA
294507 TGTATCGATACAT
1 TGTATCGATACAT
294520 TGTATCGATACA
1 TGTATCGATACA
294532 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:297131 original size:51 final size:52
Alignment explanation
Indices: 297074--297196 Score: 169
Period size: 51 Copynumber: 2.4 Consensus size: 52
297064 CAATTCTCCG
* * *
297074 CAATCGGGGATATTCCAACTCCAATTTTATTTTC-AAAACACTAA-TTTTCTA
1 CAATCGGGGATACTCCAACTCCAATTTTATTTCCAAAAACACCAATTTTTC-A
* *
297125 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTTTCA
1 CAATCGGGGATACTCCAACTCCAATTTTATTTCC-AAAAACACCAATTTTTCA
297178 CAATCGGGGATACTCCAAC
1 CAATCGGGGATACTCCAAC
297197 CCCATTAATC
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
51 30 0.48
53 28 0.44
54 5 0.08
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.32
Consensus pattern (52 bp):
CAATCGGGGATACTCCAACTCCAATTTTATTTCCAAAAACACCAATTTTTCA
Found at i:297188 original size:53 final size:51
Alignment explanation
Indices: 297074--297196 Score: 167
Period size: 53 Copynumber: 2.4 Consensus size: 51
297064 CAATTCTCCG
* * *
297074 CAATCGGGGATATTCCAACTCCAATTTTATTTTCAAAACACTAATTTTCTA
1 CAATCGGGGATACTCCAACTCCAATTTTATTTCCAAAACACCAATTTTCTA
* *
297125 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTT-TCA
1 CAATCGGGGATACTCCAACTCCAATTTTATTTCC--AAAACACCAATTTTCT-A
297178 CAATCGGGGATACTCCAAC
1 CAATCGGGGATACTCCAAC
297197 CCCATTAATC
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
51 30 0.48
52 1 0.02
53 32 0.51
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.32
Consensus pattern (51 bp):
CAATCGGGGATACTCCAACTCCAATTTTATTTCCAAAACACCAATTTTCTA
Found at i:297210 original size:27 final size:27
Alignment explanation
Indices: 297180--297254 Score: 96
Period size: 27 Copynumber: 2.7 Consensus size: 27
297170 ATTTTTCACA
297180 ATCGGGGATACTCCAACCCCATTAATC
1 ATCGGGGATACTCCAACCCCATTAATC
* * *
297207 ATCGGGGATACTCCAACCCCGTTATTT
1 ATCGGGGATACTCCAACCCCATTAATC
* *
297234 TTGAGGGGATACTCCAACCCC
1 AT-CGGGGATACTCCAACCCC
297255 TGCTTTATTC
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 25 0.60
28 17 0.40
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCATTAATC
Found at i:297359 original size:79 final size:79
Alignment explanation
Indices: 297207--297381 Score: 201
Period size: 79 Copynumber: 2.2 Consensus size: 79
297197 CCCATTAATC
* * * * *
297207 ATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCTGCTTTATTCTTAAAAT
1 ATCGAGGATACTCCAACCCCGTTATTTCTGAAGGGATACTCCAACCCCTGCTTTATTCTCAAAAC
**
297272 ATGGATTTCTCATA
66 ATCAATTTCTCATA
* * * *
297286 ATTGAGGATACTCCAACCCCGTTATTTCTGAAGGGATACTCCAATCTC-GGTTTCATT-TCCAAA
1 ATCGAGGATACTCCAACCCCGTTATTTCTGAAGGGATACTCCAACCCCTGCTTT-ATTCT-CAAA
*
297349 ACATCAATTTCTCTTA
64 ACATCAATTTCTCATA
*
297365 ATCGGGGATACTCCAAC
1 ATCGAGGATACTCCAAC
297382 TCCGATTTTA
Statistics
Matches: 80, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
78 5 0.06
79 75 0.94
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (79 bp):
ATCGAGGATACTCCAACCCCGTTATTTCTGAAGGGATACTCCAACCCCTGCTTTATTCTCAAAAC
ATCAATTTCTCATA
Found at i:297379 original size:51 final size:51
Alignment explanation
Indices: 297318--297476 Score: 196
Period size: 51 Copynumber: 3.1 Consensus size: 51
297308 TATTTCTGAA
* * * *
297318 GGGATACTCCAA-TCTCGGTTTCATTTCCAAAACATCAATTTCTCTTAATCG
1 GGGATACTCCAACTC-CGATTTTATTTCCAAAACACCAATTTCTCATAATCG
* * *
297369 GGGATACTCCAACTCCGATTTTATTTCTAAAACACCCATTTTTCATAATCG
1 GGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTCTCATAATCG
* * *
297420 GGGATACTCCAACTCCGATTTTATTTCCAAAGCACCGACTTT-TCACAATCG
1 GGGATACTCCAACTCCGATTTTATTTCCAAAACACC-AATTTCTCATAATCG
297471 GGGATA
1 GGGATA
297477 TAGACACCTC
Statistics
Matches: 94, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
51 89 0.95
52 5 0.05
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (51 bp):
GGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTCTCATAATCG
Found at i:297784 original size:34 final size:35
Alignment explanation
Indices: 297746--297812 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
297736 CCTTACAACA
297746 CTATC-TTTC-AAGGCTAAAATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAAATAG-AACCTCTCTCT
*
297780 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAAATAGAACCTCTC
297813 AATCACTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.41
37 12 0.41
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAAATAGAACCTCTCTCT
Found at i:298288 original size:13 final size:13
Alignment explanation
Indices: 298270--298295 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
298260 CAATTTTTGG
298270 TGTATCGATACAT
1 TGTATCGATACAT
298283 TGTATCGATACAT
1 TGTATCGATACAT
298296 ACTTGGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Done.