Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr3
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 26558743
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1281270 characters in sequence are not A, C, G, or T
File 56 of 79
Found at i:18668092 original size:157 final size:158
Alignment explanation
Indices: 18667800--18668174 Score: 716
Period size: 157 Copynumber: 2.4 Consensus size: 158
18667790 ATATAAACTT
*
18667800 TATAAACTTACATAACTATCACATAAACTTATATGTAAACTTACATAATACATAACTTATATGTA
1 TATAAACTTACATAACTATCACATAAACTTATATGTAAACTTACATAATACATAACTTACATGTA
18667865 AACTTACATATAATACATAACTTATAAAAAATTTTTATATAAACTTACATAATACATTACTTACA
66 AACTTACA-ATAATACATAACTTATAAAAAATTTTTATATAAACTTACATAATACATTACTTACA
18667930 TATTAACTTACATAACTTATTAATATTTA
130 TATTAACTTACATAACTTATTAATATTTA
*
18667959 TATAAACTTACATAACTATCACATAAACTTATATGTAAACTTACATAATACATAACTTACATGTT
1 TATAAACTTACATAACTATCACATAAACTTATATGTAAACTTACATAATACATAACTTACATGTA
18668024 AACTTAC-ATAATACATAACTTATAAAAAATTTTTATATAAACTTACATAATACATTACTTACAT
66 AACTTACAATAATACATAACTTATAAAAAATTTTTATATAAACTTACATAATACATTACTTACAT
18668088 ATTAACTTACATAACTTATTAATATTTA
131 ATTAACTTACATAACTTATTAATATTTA
18668116 TATAAACTTACATAACTATCACATAAACTTATATGTAAACTTACATAATACATAACTTA
1 TATAAACTTACATAACTATCACATAAACTTATATGTAAACTTACATAATACATAACTTA
18668175 NNNNNNNNNN
Statistics
Matches: 214, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
157 144 0.67
159 70 0.33
ACGTcount: A:0.46, C:0.15, G:0.01, T:0.38
Consensus pattern (158 bp):
TATAAACTTACATAACTATCACATAAACTTATATGTAAACTTACATAATACATAACTTACATGTA
AACTTACAATAATACATAACTTATAAAAAATTTTTATATAAACTTACATAATACATTACTTACAT
ATTAACTTACATAACTTATTAATATTTA
Found at i:18668168 original size:29 final size:28
Alignment explanation
Indices: 18668057--18668174 Score: 96
Period size: 28 Copynumber: 4.0 Consensus size: 28
18668047 AAAAAATTTT
*
18668057 TATATAAACTTACATAATACATTACTTA
1 TATATAAACTTACATAATACATAACTTA
* * * *
18668085 CATATTAACTTACATAACTTA-TTAA-TATT
1 TATATAAACTTACATAA--TACATAACT-TA
18668114 TATATAAACTTACATAACTATCACATAAACTTA
1 TATATAAACTTACAT-A--AT-ACAT-AACTTA
*
18668147 TATGTAAACTTACATAATACATAACTTA
1 TATATAAACTTACATAATACATAACTTA
18668175 NNNNNNNNNN
Statistics
Matches: 70, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
28 22 0.31
29 20 0.29
30 6 0.09
31 1 0.01
32 3 0.04
33 17 0.24
34 1 0.01
ACGTcount: A:0.46, C:0.15, G:0.01, T:0.38
Consensus pattern (28 bp):
TATATAAACTTACATAATACATAACTTA
Found at i:18674141 original size:43 final size:42
Alignment explanation
Indices: 18674004--18674157 Score: 218
Period size: 42 Copynumber: 3.6 Consensus size: 42
18673994 TTCATGATGA
* * * *
18674004 AAGCGCCACTAAAGAACATTATCTTTAGCGGCATTTTTCTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTTT
* * * *
18674046 AAGCGCCGCTAAATAACATTATCTTTAGCGGCGATTTTTTGT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTTT
*
18674088 AACCGCCGCTAAAGAACATGATCTTTAGCGGCGTCTTTTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGT-TTTTTTTT
18674131 AAGCGCCGCTAAAGAACATGATCTTTA
1 AAGCGCCGCTAAAGAACATGATCTTTA
18674158 ATAGCGTTTT
Statistics
Matches: 99, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
42 66 0.67
43 33 0.33
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (42 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTTT
Found at i:18674169 original size:85 final size:84
Alignment explanation
Indices: 18674007--18674170 Score: 229
Period size: 85 Copynumber: 1.9 Consensus size: 84
18673997 ATGATGAAAG
* * *
18674007 CGCCACTAAAGAACATTATCTTTAGCGGCATTTTTCTTTAAGCGCCGCTAAATAACATTATCTTT
1 CGCCACTAAAGAACATGATCTTTAGCGGCATTTTTCTTTAAGCGCCGCTAAAGAACATGATCTTT
* *
18674072 AGCGGCGATTTTTTGTAAC
66 AACAGCGATTTTTTGTAAC
* * *
18674091 CGCCGCTAAAGAACATGATCTTTAGCGGCGTCTTTTTTTTAAGCGCCGCTAAAGAACATGATCTT
1 CGCCACTAAAGAACATGATCTTTAGCGGCAT-TTTTCTTTAAGCGCCGCTAAAGAACATGATCTT
* *
18674156 TAATAGCGTTTTTTT
65 TAACAGCGATTTTTT
18674171 CTGTAAACGC
Statistics
Matches: 69, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
84 28 0.41
85 41 0.59
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (84 bp):
CGCCACTAAAGAACATGATCTTTAGCGGCATTTTTCTTTAAGCGCCGCTAAAGAACATGATCTTT
AACAGCGATTTTTTGTAAC
Found at i:18674257 original size:21 final size:21
Alignment explanation
Indices: 18674231--18674270 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
18674221 GTTAGTGGCG
*
18674231 CTAAAAAGCGCCGCTAAAAGC
1 CTAAAAAACGCCGCTAAAAGC
18674252 CTAAAAAACGCCGCTAAAA
1 CTAAAAAACGCCGCTAAAA
18674271 ACCTGTTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.28, G:0.15, T:0.10
Consensus pattern (21 bp):
CTAAAAAACGCCGCTAAAAGC
Found at i:18679097 original size:19 final size:18
Alignment explanation
Indices: 18679075--18679115 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
18679065 TTTAATTTCA
*
18679075 TTTTTTTGTTTTTTGTAAT
1 TTTTTTTATTTTTTG-AAT
18679094 TTTTTTTATTTTTTGAAT
1 TTTTTTTATTTTTTGAAT
18679112 TTTT
1 TTTT
18679116 AAAATTATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.12, C:0.00, G:0.07, T:0.80
Consensus pattern (18 bp):
TTTTTTTATTTTTTGAAT
Found at i:18700319 original size:96 final size:97
Alignment explanation
Indices: 18700207--18700381 Score: 237
Period size: 96 Copynumber: 1.8 Consensus size: 97
18700197 AAACACGAAG
* * * * *
18700207 AAGAAGAGCTTGAAAAGGT-GACAGAAAGCCATAAGCTTAAACGAAAGCCACCATCACCGTCATT
1 AAGAAGAGCTTGAAAAGGTAGAAAAAAAG-CATAAACTTAAACGAAAGCAACCATCACCGTCATC
*
18700271 GGAACGCGAA-AAGAAGATCGCTAAACCTGAAA
65 GGAACCCGAATAAGAAGATCGCTAAACCTGAAA
* * * *
18700303 AAGAAGAGCTTGAAAAGGTATAAAAAAAGTATAAACTTAAACGAAAGCAACCATCGCCTTCATCG
1 AAGAAGAGCTTGAAAAGGTAGAAAAAAAGCATAAACTTAAACGAAAGCAACCATCACCGTCATCG
18700368 GAACCCGAATAAGA
66 GAACCCGAATAAGA
18700382 GCTTGAAAGG
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
96 57 0.85
97 10 0.15
ACGTcount: A:0.46, C:0.19, G:0.20, T:0.15
Consensus pattern (97 bp):
AAGAAGAGCTTGAAAAGGTAGAAAAAAAGCATAAACTTAAACGAAAGCAACCATCACCGTCATCG
GAACCCGAATAAGAAGATCGCTAAACCTGAAA
Found at i:18701434 original size:11 final size:11
Alignment explanation
Indices: 18701418--18701442 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
18701408 GATTTGCTGA
18701418 TTTGAGTGATG
1 TTTGAGTGATG
18701429 TTTGAGTGATG
1 TTTGAGTGATG
18701440 TTT
1 TTT
18701443 TGGCTGATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.32, T:0.52
Consensus pattern (11 bp):
TTTGAGTGATG
Found at i:18701530 original size:15 final size:15
Alignment explanation
Indices: 18701510--18701542 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
18701500 AATTAGTGGA
18701510 GTAGTTATATATTAG
1 GTAGTTATATATTAG
18701525 GTAGTTATATATTAG
1 GTAGTTATATATTAG
18701540 GTA
1 GTA
18701543 ACTACTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.45
Consensus pattern (15 bp):
GTAGTTATATATTAG
Found at i:18718497 original size:28 final size:29
Alignment explanation
Indices: 18718466--18718526 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
18718456 TAAAAGACAA
*
18718466 AATCATTATA-TT-GTTTATGTAGTTAAAT
1 AATCATTATACTTCGTCTAT-TAGTTAAAT
*
18718494 AATC-TTGTACTTCGTCTATTAGTTAAAT
1 AATCATTATACTTCGTCTATTAGTTAAAT
18718522 AATCA
1 AATCA
18718527 GTCCATGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
27 4 0.14
28 19 0.68
29 5 0.18
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (29 bp):
AATCATTATACTTCGTCTATTAGTTAAAT
Found at i:18723802 original size:52 final size:51
Alignment explanation
Indices: 18723694--18723866 Score: 185
Period size: 50 Copynumber: 3.4 Consensus size: 51
18723684 ATGATGCTTA
* * * *
18723694 AATGCATGATTTAA-TTAA-GATGCAAAC-TAAATGAACAAATGAG-TTTACTT
1 AATGCATGACTTAATTTAATGATGCAAACTTAACT-AAC--ATGAGAGTTACAT
* *
18723744 AATGCATGACTTAATTTAATGATGCAGACTTAAACTAACATGGGAGTTACAT
1 AATGCATGACTTAATTTAATGATGCAAACTT-AACTAACATGAGAGTTACAT
* *
18723796 AATGCATGTCATAATTT-ATGATGCAAACTTAACTAACATGAGAGTTACAT
1 AATGCATGACTTAATTTAATGATGCAAACTTAACTAACATGAGAGTTACAT
* *
18723846 AATGCATGACTTTATTAAATG
1 AATGCATGACTTAATTTAATG
18723867 CAGAACACAT
Statistics
Matches: 103, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
50 45 0.44
51 23 0.22
52 28 0.27
53 4 0.04
54 3 0.03
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.32
Consensus pattern (51 bp):
AATGCATGACTTAATTTAATGATGCAAACTTAACTAACATGAGAGTTACAT
Found at i:18727771 original size:34 final size:34
Alignment explanation
Indices: 18727700--18727784 Score: 100
Period size: 34 Copynumber: 2.5 Consensus size: 34
18727690 ATGACTCAAA
* *
18727700 AACAAGCTAATAAATTTAGCTTCTTACTCCCACT
1 AACAAGCTAACAAACTTAGCTTCTTACTCCCACT
** *
18727734 AACAAGCTAACAAACTTAGCTT-TCTACTTTCATT
1 AACAAGCTAACAAACTTAGCTTCT-TACTCCCACT
*
18727768 AACAAGTTAACAAACTT
1 AACAAGCTAACAAACTT
18727785 CCTAGAATCA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
33 1 0.02
34 43 0.98
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.32
Consensus pattern (34 bp):
AACAAGCTAACAAACTTAGCTTCTTACTCCCACT
Found at i:18730894 original size:28 final size:28
Alignment explanation
Indices: 18730843--18730912 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
18730833 TTAAATATTT
18730843 TTTTTATATTTTTATTAAAATTTAATGA
1 TTTTTATATTTTTATTAAAATTTAATGA
** *
18730871 TTTTTATAATTTTTA-TAACTTTTATTGA
1 TTTTTAT-ATTTTTATTAAAATTTAATGA
* *
18730899 TTTCTATTTTTTTA
1 TTTTTATATTTTTA
18730913 ATATTTTTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
27 6 0.17
28 23 0.64
29 7 0.19
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (28 bp):
TTTTTATATTTTTATTAAAATTTAATGA
Found at i:18731185 original size:89 final size:90
Alignment explanation
Indices: 18731026--18731252 Score: 303
Period size: 89 Copynumber: 2.5 Consensus size: 90
18731016 TCAAATGAGC
* * * * * * *
18731026 TTTTTGATTTATTTTGACAGTTCAAGTACCCAATTAAGTGTAAAATAAAAGCAGGGGCTTAATTG
1 TTTTTGATGTATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAAAGCAGGGGCTTAACTA
*
18731091 CTTTTTT-GAAAAAGTTTGATGGCA
66 CTTTTTTCGAAAAAGTTTGAGGGCA
* * *
18731115 TTTTTGATGTATTTTAAAAGTTTAAGTACCCAATTGAGTGCAAAAAAAAAGTAGGGGCTTAACTA
1 TTTTTGATGTATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAAAGCAGGGGCTTAACTA
* *
18731180 TTTTTTTCGAAAAAGTTTGAGGGCT
66 CTTTTTTCGAAAAAGTTTGAGGGCA
* * *
18731205 TTTTTGATGTATTTTGAAAGTTCAAATGCCTAATTGAGTGCAAAAAAA
1 TTTTTGATGTATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAA
18731253 GACTTAATTT
Statistics
Matches: 119, Mismatches: 18, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
89 61 0.51
90 58 0.49
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.37
Consensus pattern (90 bp):
TTTTTGATGTATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAAAGCAGGGGCTTAACTA
CTTTTTTCGAAAAAGTTTGAGGGCA
Found at i:18731898 original size:87 final size:89
Alignment explanation
Indices: 18731767--18731929 Score: 233
Period size: 87 Copynumber: 1.9 Consensus size: 89
18731757 CAACTTTTTC
* * * **
18731767 AAAAAAAGTAATTAAGCCCCTACTCTTTTTTTTTGCACTCAATTGGGTACTTGA-ATTTTCAAAA
1 AAAAAAAGAAATTAAGCCCCAACTCTTTTTTTTGGCACTCAATTGGGTACTTGAGATGCT-AAAA
*
18731831 TGCATCAAAAAGGCCCTCAAACTTT
65 TGCATAAAAAAGGCCCTCAAACTTT
*
18731856 AAAAAAA-AAATTAAGCCCCAAGT-TTTTTTTTGGCACTCAATTGGGTACTTGAGATGCTAAAAT
1 AAAAAAAGAAATTAAGCCCCAACTCTTTTTTTTGGCACTCAATTGGGTACTTGAGATGCTAAAAT
18731919 GCATAAAAAAG
66 GCATAAAAAAG
18731930 ACCTTTCTAC
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
87 43 0.65
88 16 0.24
89 7 0.11
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.31
Consensus pattern (89 bp):
AAAAAAAGAAATTAAGCCCCAACTCTTTTTTTTGGCACTCAATTGGGTACTTGAGATGCTAAAAT
GCATAAAAAAGGCCCTCAAACTTT
Found at i:18732134 original size:10 final size:9
Alignment explanation
Indices: 18732120--18732299 Score: 78
Period size: 10 Copynumber: 18.7 Consensus size: 9
18732110 AAATATAAAA
18732120 ATAAAAATT
1 ATAAAAATT
*
18732129 AATAAAATTT
1 -ATAAAAATT
*
18732139 ATAAGAATT
1 ATAAAAATT
**
18732148 ATCAAATTTT
1 AT-AAAAATT
18732158 AGTAAAAATT
1 A-TAAAAATT
18732168 ATAAAAATT
1 ATAAAAATT
*
18732177 GTAAAAAATT
1 AT-AAAAATT
18732187 ATAAAAAGTGT
1 ATAAAAA-T-T
*
18732198 AAAAAAAATT
1 -ATAAAAATT
18732208 AT-AAAATAT
1 ATAAAAAT-T
*
18732217 ATAGAAA-T
1 ATAAAAATT
18732225 ATATAAAATT
1 ATA-AAAATT
* * *
18732235 TTATAAAGTC
1 ATA-AAAATT
*
18732245 GTAAGAAGATT
1 ATAA-AA-ATT
*
18732256 ATAAAAAAT
1 ATAAAAATT
*
18732265 ATAAAGAAAT
1 ATAAA-AATT
18732275 AT-AAAATT
1 ATAAAAATT
*
18732283 CGTAAAAAATT
1 -AT-AAAAATT
18732294 ATAAAA
1 ATAAAA
18732300 TTTNNNNNNN
Statistics
Matches: 129, Mismatches: 25, Indels: 33
0.69 0.13 0.18
Matches are distributed among these distances:
8 12 0.09
9 45 0.35
10 53 0.41
11 13 0.10
12 6 0.05
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.31
Consensus pattern (9 bp):
ATAAAAATT
Found at i:18732142 original size:19 final size:19
Alignment explanation
Indices: 18732120--18732241 Score: 97
Period size: 19 Copynumber: 6.3 Consensus size: 19
18732110 AAATATAAAA
18732120 ATAAAAATTA-ATAAAATTT
1 ATAAAAATTATA-AAAATTT
* * *
18732139 ATAAGAATTATCAAATTTT
1 ATAAAAATTATAAAAATTT
18732158 AGTAAAAATTATAAAAATTGT
1 A-TAAAAATTATAAAAATT-T
*
18732179 A-AAAAATTATAAAAAGTGTA
1 ATAAAAATTATAAAAA-T-TT
* *
18732199 AAAAAAATTAT-AAAATAT
1 ATAAAAATTATAAAAATTT
* *
18732217 ATAGAAATATATAAAATTTT
1 ATAAAAAT-TATAAAAATTT
18732237 ATAAA
1 ATAAA
18732242 GTCGTAAGAA
Statistics
Matches: 81, Mismatches: 14, Indels: 15
0.74 0.13 0.14
Matches are distributed among these distances:
18 6 0.07
19 34 0.42
20 29 0.36
21 12 0.15
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.34
Consensus pattern (19 bp):
ATAAAAATTATAAAAATTT
Found at i:18732232 original size:29 final size:28
Alignment explanation
Indices: 18732163--18732300 Score: 77
Period size: 29 Copynumber: 4.8 Consensus size: 28
18732153 ATTTTAGTAA
* * *
18732163 AAATTAT-AAAAATTGTAAAAAATTATAA
1 AAATTATAAAAAATTATAAAATA-TATAG
* *
18732191 AAAGTGTAAAAAAAATTATAAAATATATAG
1 AAATTATAAAAA--ATTATAAAATATATAG
** * *
18732221 AAATATATAAAATTTTATAAAGTCGTA-AG
1 AAAT-TATAAAAAATTATAAAAT-ATATAG
*
18732250 AAGATTATAAAAAA-TATAAAGAAATATA-
1 AA-ATTATAAAAAATTATAAA-ATATATAG
*
18732278 AAATTCGTAAAAAATTATAAAAT
1 AAATT-ATAAAAAATTATAAAAT
18732301 TTNNNNNNNN
Statistics
Matches: 82, Mismatches: 18, Indels: 20
0.68 0.15 0.17
Matches are distributed among these distances:
27 3 0.04
28 23 0.28
29 30 0.37
30 11 0.13
31 15 0.18
ACGTcount: A:0.62, C:0.01, G:0.07, T:0.30
Consensus pattern (28 bp):
AAATTATAAAAAATTATAAAATATATAG
Found at i:18732240 original size:50 final size:48
Alignment explanation
Indices: 18732181--18732282 Score: 118
Period size: 48 Copynumber: 2.1 Consensus size: 48
18732171 AAAATTGTAA
* * * *
18732181 AAAATTATAAAAAGT-GTAAAAAAAATTATAAAATATATAGAA-ATATAT
1 AAAATTTTATAAAGTCGT-AAAAAAATTATAAAAAATATA-AAGAAATAT
* *
18732229 AAAATTTTATAAAGTCGTAAGAAGATTATAAAAAATATAAAGAAATAT
1 AAAATTTTATAAAGTCGTAAAAAAATTATAAAAAATATAAAGAAATAT
18732277 AAAATT
1 AAAATT
18732283 CGTAAAAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
47 2 0.04
48 42 0.91
49 2 0.04
ACGTcount: A:0.62, C:0.01, G:0.08, T:0.29
Consensus pattern (48 bp):
AAAATTTTATAAAGTCGTAAAAAAATTATAAAAAATATAAAGAAATAT
Found at i:18733007 original size:28 final size:28
Alignment explanation
Indices: 18732956--18733025 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
18732946 TTAAATATTT
18732956 TTTTTATATTTTTATTAAAATTTAATGA
1 TTTTTATATTTTTATTAAAATTTAATGA
** *
18732984 TTTTTATAATTTTTA-TAACTTTTATTGA
1 TTTTTAT-ATTTTTATTAAAATTTAATGA
* *
18733012 TTTCTATTTTTTTA
1 TTTTTATATTTTTA
18733026 ATATTTTTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
27 6 0.17
28 23 0.64
29 7 0.19
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (28 bp):
TTTTTATATTTTTATTAAAATTTAATGA
Found at i:18733298 original size:89 final size:90
Alignment explanation
Indices: 18733139--18733365 Score: 303
Period size: 89 Copynumber: 2.5 Consensus size: 90
18733129 TCAAATGAGC
* * * * * * *
18733139 TTTTTGATTTATTTTGACAGTTCAAGTACCCAATTAAGTGTAAAATAAAAGCAGGGGCTTAATTG
1 TTTTTGATGTATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAAAGCAGGGGCTTAACTA
*
18733204 CTTTTTT-GAAAAAGTTTGATGGCA
66 CTTTTTTCGAAAAAGTTTGAGGGCA
* * *
18733228 TTTTTGATGTATTTTAAAAGTTTAAGTACCCAATTGAGTGCAAAAAAAAAGTAGGGGCTTAACTA
1 TTTTTGATGTATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAAAGCAGGGGCTTAACTA
* *
18733293 TTTTTTTCGAAAAAGTTTGAGGGCT
66 CTTTTTTCGAAAAAGTTTGAGGGCA
* * *
18733318 TTTTTGATGTATTTTGAAAGTTCAAATGCCTAATTGAGTGCAAAAAAA
1 TTTTTGATGTATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAA
18733366 GACTTAATTT
Statistics
Matches: 119, Mismatches: 18, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
89 61 0.51
90 58 0.49
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.37
Consensus pattern (90 bp):
TTTTTGATGTATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAAAGCAGGGGCTTAACTA
CTTTTTTCGAAAAAGTTTGAGGGCA
Found at i:18734056 original size:10 final size:9
Alignment explanation
Indices: 18734021--18734221 Score: 83
Period size: 10 Copynumber: 21.4 Consensus size: 9
18734011 GACATATAGC
*
18734021 AAAAAATAT
1 AAAAATTAT
18734030 AAAAA-TAT
1 AAAAATTAT
18734038 -AAAA--AT
1 AAAAATTAT
18734044 AAAAATTAAT
1 AAAAATT-AT
*
18734054 AAAATTTAT
1 AAAAATTAT
*
18734063 AAGAATTAT
1 AAAAATTAT
**
18734072 CAAATTTTAGT
1 -AAAAATTA-T
18734083 AAAAATTAT
1 AAAAATTAT
*
18734092 AAAAATTGT
1 AAAAATTAT
18734101 AAAAAATTAT
1 -AAAAATTAT
*
18734111 AAAAAGTGTAAA
1 AAAAA-T-T-AT
18734123 AAAAATTAT
1 AAAAATTAT
18734132 -AAAATATAT
1 AAAAAT-TAT
*
18734141 AGAAA-TAT
1 AAAAATTAT
*
18734149 ATAAAATTTT
1 A-AAAATTAT
* **
18734159 ATAAAGTCGT
1 A-AAAATTAT
18734169 AAGAAGATTAT
1 AA-AA-ATTAT
*
18734180 AAAAAATAT
1 AAAAATTAT
*
18734189 AAAGAAATAT
1 AAA-AATTAT
*
18734199 -AAAATTCGT
1 AAAAATT-AT
18734208 AAAAAATTAT
1 -AAAAATTAT
18734218 AAAA
1 AAAA
18734222 TTTAAATTAA
Statistics
Matches: 147, Mismatches: 25, Indels: 40
0.69 0.12 0.19
Matches are distributed among these distances:
6 2 0.01
7 8 0.05
8 15 0.10
9 50 0.34
10 53 0.36
11 13 0.09
12 6 0.04
ACGTcount: A:0.63, C:0.01, G:0.06, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:18734107 original size:19 final size:20
Alignment explanation
Indices: 18734083--18734135 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 20
18734073 AAATTTTAGT
*
18734083 AAAAATTATAAAAATTGT-A
1 AAAAATTATAAAAAGTGTAA
18734102 AAAAATTATAAAAAGTGTAAA
1 AAAAATTATAAAAAGTGT-AA
18734123 AAAAATTATAAAA
1 AAAAATTATAAAA
18734136 TATATAGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 17 0.55
21 14 0.45
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (20 bp):
AAAAATTATAAAAAGTGTAA
Found at i:18734154 original size:29 final size:28
Alignment explanation
Indices: 18734085--18734222 Score: 77
Period size: 29 Copynumber: 4.8 Consensus size: 28
18734075 ATTTTAGTAA
* * *
18734085 AAATTAT-AAAAATTGTAAAAAATTATAA
1 AAATTATAAAAAATTATAAAATA-TATAG
* *
18734113 AAAGTGTAAAAAAAATTATAAAATATATAG
1 AAATTATAAAAA--ATTATAAAATATATAG
** * *
18734143 AAATATATAAAATTTTATAAAGTCGTA-AG
1 AAAT-TATAAAAAATTATAAAAT-ATATAG
*
18734172 AAGATTATAAAAAA-TATAAAGAAATATA-
1 AA-ATTATAAAAAATTATAAA-ATATATAG
*
18734200 AAATTCGTAAAAAATTATAAAAT
1 AAATT-ATAAAAAATTATAAAAT
18734223 TTAAATTAAT
Statistics
Matches: 82, Mismatches: 18, Indels: 20
0.68 0.15 0.17
Matches are distributed among these distances:
27 3 0.04
28 23 0.28
29 30 0.37
30 11 0.13
31 15 0.18
ACGTcount: A:0.62, C:0.01, G:0.07, T:0.30
Consensus pattern (28 bp):
AAATTATAAAAAATTATAAAATATATAG
Found at i:18734162 original size:50 final size:48
Alignment explanation
Indices: 18734103--18734204 Score: 118
Period size: 48 Copynumber: 2.1 Consensus size: 48
18734093 AAAATTGTAA
* * * *
18734103 AAAATTATAAAAAGT-GTAAAAAAAATTATAAAATATATAGAA-ATATAT
1 AAAATTTTATAAAGTCGT-AAAAAAATTATAAAAAATATA-AAGAAATAT
* *
18734151 AAAATTTTATAAAGTCGTAAGAAGATTATAAAAAATATAAAGAAATAT
1 AAAATTTTATAAAGTCGTAAAAAAATTATAAAAAATATAAAGAAATAT
18734199 AAAATT
1 AAAATT
18734205 CGTAAAAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
47 2 0.04
48 42 0.91
49 2 0.04
ACGTcount: A:0.62, C:0.01, G:0.08, T:0.29
Consensus pattern (48 bp):
AAAATTTTATAAAGTCGTAAAAAAATTATAAAAAATATAAAGAAATAT
Found at i:18734345 original size:28 final size:28
Alignment explanation
Indices: 18734294--18734363 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
18734284 TTAAATATTT
18734294 TTTTTATATTTTTATTAAAATTTAATGA
1 TTTTTATATTTTTATTAAAATTTAATGA
** *
18734322 TTTTTATAATTTTTA-TAACTTTTATTGA
1 TTTTTAT-ATTTTTATTAAAATTTAATGA
* *
18734350 TTTCTATTTTTTTA
1 TTTTTATATTTTTA
18734364 ATATTTTTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
27 6 0.17
28 23 0.64
29 7 0.19
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (28 bp):
TTTTTATATTTTTATTAAAATTTAATGA
Found at i:18734636 original size:89 final size:90
Alignment explanation
Indices: 18734477--18734703 Score: 303
Period size: 89 Copynumber: 2.5 Consensus size: 90
18734467 TCAAATGAGC
* * * * * * *
18734477 TTTTTGATTTATTTTGACAGTTCAAGTACCCAATTAAGTGTAAAATAAAAGCAGGGGCTTAATTG
1 TTTTTGATGTATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAAAGCAGGGGCTTAACTA
*
18734542 CTTTTTT-GAAAAAGTTTGATGGCA
66 CTTTTTTCGAAAAAGTTTGAGGGCA
* * *
18734566 TTTTTGATGTATTTTAAAAGTTTAAGTACCCAATTGAGTGCAAAAAAAAAGTAGGGGCTTAACTA
1 TTTTTGATGTATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAAAGCAGGGGCTTAACTA
* *
18734631 TTTTTTTCGAAAAAGTTTGAGGGCT
66 CTTTTTTCGAAAAAGTTTGAGGGCA
* * *
18734656 TTTTTGATGTATTTTGAAAGTTCAAATGCCTAATTGAGTGCAAAAAAA
1 TTTTTGATGTATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAA
18734704 GACTTAATTT
Statistics
Matches: 119, Mismatches: 18, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
89 61 0.51
90 58 0.49
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.37
Consensus pattern (90 bp):
TTTTTGATGTATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAAAGCAGGGGCTTAACTA
CTTTTTTCGAAAAAGTTTGAGGGCA
Found at i:18742762 original size:31 final size:31
Alignment explanation
Indices: 18742726--18742786 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
18742716 CAAAAACACA
* *
18742726 AAAACAAAATCTGGGTCTTCGAGTTTAATTC
1 AAAACAAAAACTGGGTCTTCGAGTTAAATTC
* *
18742757 AAAACAAAAACTGGGTGTTTGAGTTAAATT
1 AAAACAAAAACTGGGTCTTCGAGTTAAATT
18742787 TTTTTTTTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.31
Consensus pattern (31 bp):
AAAACAAAAACTGGGTCTTCGAGTTAAATTC
Found at i:18744708 original size:22 final size:23
Alignment explanation
Indices: 18744661--18744708 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
18744651 ATGATTTGAC
* *
18744661 AAAGAACACAAATTTAAATATTA
1 AAAGAACACAAAATTAAATATAA
18744684 AAAGAGACA-AAAATTAAATA-AA
1 AAAGA-ACACAAAATTAAATATAA
18744706 AAA
1 AAA
18744709 CTAAAATAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 4 0.18
23 15 0.68
24 3 0.14
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (23 bp):
AAAGAACACAAAATTAAATATAA
Found at i:18759100 original size:9 final size:10
Alignment explanation
Indices: 18759025--18759119 Score: 80
Period size: 9 Copynumber: 9.8 Consensus size: 10
18759015 TTGTTGCCGC
18759025 TATTATTATT
1 TATTATTATT
18759035 ATCATTATTATT
1 -T-ATTATTATT
18759047 TA-TATTTATAT
1 TATTA-TTAT-T
18759058 TATTATTA-T
1 TATTATTATT
18759067 TATTATTA-T
1 TATTATTATT
18759076 TATTATTA-T
1 TATTATTATT
*
18759085 CATTATTATT
1 TATTATTATT
18759095 TA-TATT-TCT
1 TATTATTAT-T
18759104 T-TTATTATT
1 TATTATTATT
18759113 TA-TATTA
1 TATTATTA
18759120 GTATTAGAAT
Statistics
Matches: 73, Mismatches: 2, Indels: 20
0.77 0.02 0.21
Matches are distributed among these distances:
8 1 0.01
9 45 0.62
10 8 0.11
11 8 0.11
12 11 0.15
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (10 bp):
TATTATTATT
Found at i:18759112 original size:3 final size:3
Alignment explanation
Indices: 18759025--18759094 Score: 90
Period size: 3 Copynumber: 23.3 Consensus size: 3
18759015 TTGTTGCCGC
*
18759025 TAT TAT TAT TAT CAT TAT TAT T-T ATAT T-T ATAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT -TAT TAT TAT TAT TAT
*
18759070 TAT TAT TAT TAT TAT CAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
18759095 TATATTTCTT
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
2 2 0.03
3 55 0.93
4 2 0.03
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:18762598 original size:19 final size:20
Alignment explanation
Indices: 18762557--18762600 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
18762547 TCTTTTTGCA
**
18762557 TTCATCCATAAGCATTACCT
1 TTCATCCATAAGCATTAAAT
*
18762577 TTCAT-CATATGCATTAAAT
1 TTCATCCATAAGCATTAAAT
18762596 TTCAT
1 TTCAT
18762601 AAAATGTCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.32, C:0.23, G:0.05, T:0.41
Consensus pattern (20 bp):
TTCATCCATAAGCATTAAAT
Found at i:18762741 original size:20 final size:21
Alignment explanation
Indices: 18762701--18762741 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
18762691 ACAAAAGCCA
* *
18762701 TAGATCAAATGTTAGAGAGAT
1 TAGAACAAATGTTAGAAAGAT
18762722 TAGAACAAAT-TTAGAAAGAT
1 TAGAACAAATGTTAGAAAGAT
18762742 ATGTAAGATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.49, C:0.05, G:0.20, T:0.27
Consensus pattern (21 bp):
TAGAACAAATGTTAGAAAGAT
Found at i:18768040 original size:19 final size:20
Alignment explanation
Indices: 18767999--18768042 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
18767989 TCTTTTTGCA
**
18767999 TTCATCCATAAGCATTACCT
1 TTCATCCATAAGCATTAAAT
*
18768019 TTCAT-CATATGCATTAAAT
1 TTCATCCATAAGCATTAAAT
18768038 TTCAT
1 TTCAT
18768043 AAAATGTCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.32, C:0.23, G:0.05, T:0.41
Consensus pattern (20 bp):
TTCATCCATAAGCATTAAAT
Found at i:18768183 original size:20 final size:21
Alignment explanation
Indices: 18768143--18768183 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
18768133 ACAAAAGCCA
* *
18768143 TAGATCAAATGTTAGAGAGAT
1 TAGAACAAATGTTAGAAAGAT
18768164 TAGAACAAAT-TTAGAAAGAT
1 TAGAACAAATGTTAGAAAGAT
18768184 ATGTAAGATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.49, C:0.05, G:0.20, T:0.27
Consensus pattern (21 bp):
TAGAACAAATGTTAGAAAGAT
Found at i:18774473 original size:37 final size:37
Alignment explanation
Indices: 18774432--18774530 Score: 144
Period size: 37 Copynumber: 2.7 Consensus size: 37
18774422 CATATATCGG
* *
18774432 TATGGAATACCAGAAAGGATTATATATCATATGTCAA
1 TATGGAATGCCAGAAAGGATCATATATCATATGTCAA
* **
18774469 TATGGAATGCCAAAAAGGATCATATATCATATGTCGG
1 TATGGAATGCCAGAAAGGATCATATATCATATGTCAA
*
18774506 TATAGAATGCCAGAAAGGATCATAT
1 TATGGAATGCCAGAAAGGATCATAT
18774531 CTAACAATGC
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.27
Consensus pattern (37 bp):
TATGGAATGCCAGAAAGGATCATATATCATATGTCAA
Found at i:18776205 original size:44 final size:44
Alignment explanation
Indices: 18776137--18776420 Score: 248
Period size: 44 Copynumber: 6.3 Consensus size: 44
18776127 CTACCATAGT
* * * * *
18776137 AAATATTATATCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTAA
1 AAATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGCTAC
* * * * *
18776181 AAATCCTATAC-CTCTGAAGTTGCAGTGG-GTCAGATTGAATATACCATAG
1 AAATCTTAT-CTCCCTGAAGTTGCAATGGAG-CAGATT--A-A-AGC-TAC
* * * * *
18776230 GAATCTTATCTTCATAAAGTTGCAATGGAGCAGATGAAAGCTAC
1 AAATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGCTAC
* * * *
18776274 CAATCTTATCTCCCTGAAGTTGTATTGGAGCAAATTAAAGCTAC
1 AAATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGCTAC
* * *
18776318 TAATCTTATCTCCCTGAAGTTGCAATAGAGCATATTAAAGCTAC
1 AAATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGCTAC
* * * *
18776362 AAGTCGTATCTCCCTGAAGTTGTAATGGAGCAAATTAAAGCTAC
1 AAATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGCTAC
*
18776406 CAATCTTATCTCCCT
1 AAATCTTATCTCCCT
18776421 TAAAGCTCCA
Statistics
Matches: 192, Mismatches: 39, Indels: 18
0.77 0.16 0.07
Matches are distributed among these distances:
43 1 0.01
44 155 0.81
45 2 0.01
46 2 0.01
47 2 0.01
48 3 0.02
49 26 0.14
50 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (44 bp):
AAATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGCTAC
Found at i:18776358 original size:88 final size:88
Alignment explanation
Indices: 18776231--18776425 Score: 284
Period size: 88 Copynumber: 2.2 Consensus size: 88
18776221 ATACCATAGG
* * * *
18776231 AATCTTATCTTCATAAAGTTGCAATGGAGCAGATGAAAGCTACCAA-TCTTATCTCCCTGAAGTT
1 AATCTTATCTCCCTAAAGTTGCAATAGAGCAGATGAAAGCTA-CAAGTCGTATCTCCCTGAAGTT
* *
18776295 GTATTGGAGCAAATTAAAGCTACT
65 GTAATGGAGCAAATTAAAGCTACC
* * *
18776319 AATCTTATCTCCCTGAAGTTGCAATAGAGCATATTAAAGCTACAAGTCGTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTAAAGTTGCAATAGAGCAGATGAAAGCTACAAGTCGTATCTCCCTGAAGTTG
18776384 TAATGGAGCAAATTAAAGCTACC
66 TAATGGAGCAAATTAAAGCTACC
18776407 AATCTTATCTCCCTTAAAG
1 AATCTTATCTCCC-TAAAG
18776426 CTCCAAGGAC
Statistics
Matches: 95, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
87 3 0.03
88 88 0.93
89 4 0.04
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (88 bp):
AATCTTATCTCCCTAAAGTTGCAATAGAGCAGATGAAAGCTACAAGTCGTATCTCCCTGAAGTTG
TAATGGAGCAAATTAAAGCTACC
Found at i:18778009 original size:6 final size:6
Alignment explanation
Indices: 18777998--18778082 Score: 107
Period size: 6 Copynumber: 14.2 Consensus size: 6
18777988 TTGTTGCCCC
* * * * *
18777998 TATTAT TATTAT TATTGT TATTGT TATTGT TATTGT TATTGT TATTAT
1 TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT
* *
18778046 TATTAT TATTAT TATTAT TATTAT TCTCAT TATTAT T
1 TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT T
18778083 TATCTTTCTT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 73 1.00
ACGTcount: A:0.26, C:0.02, G:0.06, T:0.66
Consensus pattern (6 bp):
TATTAT
Found at i:18782292 original size:20 final size:20
Alignment explanation
Indices: 18782240--18782292 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
18782230 ATTTTGATGT
*
18782240 GTTAAAATGATTTAAACTTG
1 GTTAAAATCATTTAAACTTG
** * **
18782260 GTTGGAATTATTTGGACTTG
1 GTTAAAATCATTTAAACTTG
18782280 GTTAAAATCATTT
1 GTTAAAATCATTT
18782293 TCACTTTATT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.43
Consensus pattern (20 bp):
GTTAAAATCATTTAAACTTG
Found at i:18794592 original size:152 final size:153
Alignment explanation
Indices: 18794388--18794736 Score: 413
Period size: 152 Copynumber: 2.3 Consensus size: 153
18794378 TATAGATTTG
* * * *
18794388 ATTTTAGTCAACAATGTTAAATGGAACAGTTATGAGAATTTAAGAGTTTGGTTGAAAACCTTTAA
1 ATTTTAATCAACAATGTTAAATGGAGCACTT-TGAGAATTTAAGAGTTTGGTTGAAAACCTTCAA
** * *
18794453 GAA-TTGATTGAGAATCTTAATCAATGATGTTAAATGGATCATTTTTAAGAATTTAGGG-CTT-G
65 -AATTTGATTGAGAATCTTAATCAACAATGTTAAATGGAGCACTTTTAAGAATTTAGGGACTTGG
* *
18794515 -AAAATCTTTTAAGATTTGATTGCAA
129 CAAAATC-TTTAAGATTTAATTGAAA
* * **
18794540 ATTTTAATCAACAATGTTAAATGGAGCACTTTGGAGAATTT-GGGGATTTGGTTGAAAGTCTTCA
1 ATTTTAATCAACAATGTTAAATGGAGCACTTT-GAGAATTTAAGAG-TTTGGTTGAAAACCTTCA
* *
18794604 AAATTTGATTGAGAATCTTAATCAACAATGTTAAATGGAGCACTTTTGAGAATTTAGGGATTTGG
64 AAATTTGATTGAGAATCTTAATCAACAATGTTAAATGGAGCACTTTTAAGAATTTAGGGACTTGG
*
18794669 TCAAAATCTTTCAGATTTAATTGAAA
129 -CAAAATCTTTAAGATTTAATTGAAA
* * *
18794695 ATTTTTATGAACAATGTT-AATGGAGCACTTTTTAGAATTTAA
1 ATTTTAATCAACAATGTTAAATGGAGCAC-TTTGAGAATTTAA
18794737 AATCTTTAAA
Statistics
Matches: 167, Mismatches: 21, Indels: 15
0.82 0.10 0.07
Matches are distributed among these distances:
151 5 0.03
152 102 0.61
153 2 0.01
154 18 0.11
155 34 0.20
156 6 0.04
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.38
Consensus pattern (153 bp):
ATTTTAATCAACAATGTTAAATGGAGCACTTTGAGAATTTAAGAGTTTGGTTGAAAACCTTCAAA
ATTTGATTGAGAATCTTAATCAACAATGTTAAATGGAGCACTTTTAAGAATTTAGGGACTTGGCA
AAATCTTTAAGATTTAATTGAAA
Found at i:18794630 original size:78 final size:76
Alignment explanation
Indices: 18794388--18794735 Score: 316
Period size: 78 Copynumber: 4.6 Consensus size: 76
18794378 TATAGATTTG
* * * * * * *
18794388 ATTTTAGTCAACAATGTTAAATGGAACAGTTATGAGAATTTA-AGAGTTTGGTTGAAAACCTTT-
1 ATTTTAATCAACAATGTTAAATGGAGCACTTTTGAGAATTTAGGGA-TTTGG-TCAAAATCTTTC
*
18794451 AAGAATTGATTGAGA
64 AA-ATTTGATTGA-A
* ** * * * * *
18794466 ATCTTAATCAATGATGTTAAATGGATCATTTTTAAGAATTTAGGG-CTT-G--AAAATCTTTTAA
1 ATTTTAATCAACAATGTTAAATGGAGCACTTTTGAGAATTTAGGGATTTGGTCAAAATCTTTCAA
18794527 GATTTGATTGCAA
66 -ATTTGATTG-AA
* * * *
18794540 ATTTTAATCAACAATGTTAAATGGAGCACTTTGGAGAATTTGGGGATTTGGTTGAAAGTC-TTCA
1 ATTTTAATCAACAATGTTAAATGGAGCACTTTTGAGAATTTAGGGATTTGG-TCAAAATCTTTC-
18794604 AAATTTGATTGAGA
64 AAATTTGATTGA-A
* *
18794618 ATCTTAATCAACAATGTTAAATGGAGCACTTTTGAGAATTTAGGGATTTGGTCAAAATCTTTCAG
1 ATTTTAATCAACAATGTTAAATGGAGCACTTTTGAGAATTTAGGGATTTGGTCAAAATCTTTCAA
*
18794683 ATTTAATTGAAA
66 ATTTGATTG-AA
* * *
18794695 ATTTTTATGAACAATGTT-AATGGAGCACTTTTTAGAATTTA
1 ATTTTAATCAACAATGTTAAATGGAGCACTTTTGAGAATTTA
18794736 AAATCTTTAA
Statistics
Matches: 224, Mismatches: 34, Indels: 26
0.79 0.12 0.09
Matches are distributed among these distances:
73 8 0.04
74 49 0.22
75 3 0.01
76 24 0.11
77 34 0.15
78 98 0.44
79 8 0.04
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.38
Consensus pattern (76 bp):
ATTTTAATCAACAATGTTAAATGGAGCACTTTTGAGAATTTAGGGATTTGGTCAAAATCTTTCAA
ATTTGATTGAA
Found at i:18799215 original size:240 final size:240
Alignment explanation
Indices: 18798792--18799270 Score: 931
Period size: 240 Copynumber: 2.0 Consensus size: 240
18798782 ATACACTTAA
18798792 CAAACCAACTAGCCTATACATACCACATAACCAAAATTTCCAACCTTTTAAGTACCGAAACCATA
1 CAAACCAACTAGCCTATACATACCACATAACCAAAATTTCCAACCTTTTAAGTACCGAAACCATA
*
18798857 ACTGGATAGTTTGAAGGGATCTCCGATGATTTCCAACCCGAGCGAGCCTTCGGAACACCATAAAC
66 ACTGGATAGTTTGAAGGGATCTCCGACGATTTCCAACCCGAGCGAGCCTTCGGAACACCATAAAC
18798922 ATAGAAAAATAAAACAAAGTAAGCTATAAAGCTTAGTAAGTTGATATGTAAATAATAAGCAATCT
131 ATAGAAAAATAAAACAAAGTAAGCTATAAAGCTTAGTAAGTTGATATGTAAATAATAAGCAATCT
18798987 GTTAACCTGCTTTTACCAATCCTCACAACATGTTCTCAAGATAAC
196 GTTAACCTGCTTTTACCAATCCTCACAACATGTTCTCAAGATAAC
18799032 CAAACCAACTAGCCTATACATACCACATAACCAAAATTTCCAACCTTTTAAGTACCGAAACCATA
1 CAAACCAACTAGCCTATACATACCACATAACCAAAATTTCCAACCTTTTAAGTACCGAAACCATA
* *
18799097 ACTGGATAGTTTGATGGGATCTCCGACGATTTCCAACCCGAGCGAGCCTTCGGAACACTATAAAC
66 ACTGGATAGTTTGAAGGGATCTCCGACGATTTCCAACCCGAGCGAGCCTTCGGAACACCATAAAC
18799162 ATAGAAAAATAAAACAAAGTAAGCTATAAAGCTTAGTAAGTTGATATGTAAATAATAAGCAATCT
131 ATAGAAAAATAAAACAAAGTAAGCTATAAAGCTTAGTAAGTTGATATGTAAATAATAAGCAATCT
18799227 GTTAACCTGCTTTTACCAATCCTCACAACATGTTCTCAAGATAA
196 GTTAACCTGCTTTTACCAATCCTCACAACATGTTCTCAAGATAA
18799271 TACAATAAAA
Statistics
Matches: 236, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
240 236 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.25
Consensus pattern (240 bp):
CAAACCAACTAGCCTATACATACCACATAACCAAAATTTCCAACCTTTTAAGTACCGAAACCATA
ACTGGATAGTTTGAAGGGATCTCCGACGATTTCCAACCCGAGCGAGCCTTCGGAACACCATAAAC
ATAGAAAAATAAAACAAAGTAAGCTATAAAGCTTAGTAAGTTGATATGTAAATAATAAGCAATCT
GTTAACCTGCTTTTACCAATCCTCACAACATGTTCTCAAGATAAC
Found at i:18800436 original size:43 final size:43
Alignment explanation
Indices: 18800373--18800534 Score: 132
Period size: 43 Copynumber: 3.8 Consensus size: 43
18800363 TACCGTAACA
* * *** * *
18800373 ATGCC-ATATCCCAGATATGGTCTTACATGTAATCTCGTATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACAAAATCACATATCG
*
18800415 ATGCCAATAG-CCCAGCCATGGTCTTACACAAAATCACATATCG
1 ATGCCAAT-GTCCCAGACATGGTCTTACACAAAATCACATATCG
* * * * *
18800458 ATGCCAATGTCCTAGACATGGTCTTACACGAAGTCTCATATCA
1 ATGCCAATGTCCCAGACATGGTCTTACACAAAATCACATATCG
* * * * *
18800501 ATTCC-ATATCCCATATATGGTCTTACACATAATC
1 ATGCCAATGTCCCAGACATGGTCTTACACAAAATC
18800535 TCGGTAACCC
Statistics
Matches: 95, Mismatches: 22, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
42 28 0.29
43 67 0.71
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.29
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACAAAATCACATATCG
Found at i:18811790 original size:30 final size:30
Alignment explanation
Indices: 18811754--18811819 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
18811744 ATGTTAGCGG
* *
18811754 GTGACTGTTTTGTTATTTTCTTAAAGTTTA
1 GTGACTGTTTTGTTATTTTCTCAAAGTTGA
18811784 GTGACTGTTTTGTTATTTTCTCAAAGTTGA
1 GTGACTGTTTTGTTATTTTCTCAAAGTTGA
18811814 GTGACT
1 GTGACT
18811820 CTTGGTGTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.20, C:0.09, G:0.20, T:0.52
Consensus pattern (30 bp):
GTGACTGTTTTGTTATTTTCTCAAAGTTGA
Found at i:18815947 original size:29 final size:29
Alignment explanation
Indices: 18815905--18815991 Score: 147
Period size: 29 Copynumber: 3.0 Consensus size: 29
18815895 CTCAGAGCCC
18815905 CCCATGTGCAATGCTATAAGTTATTTAGA
1 CCCATGTGCAATGCTATAAGTTATTTAGA
**
18815934 CCCATGTGTGATGCTATAAGTTATTTAGA
1 CCCATGTGCAATGCTATAAGTTATTTAGA
*
18815963 CTCATGTGCAATGCTATAAGTTATTTAGA
1 CCCATGTGCAATGCTATAAGTTATTTAGA
18815992 AAGTGCTTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (29 bp):
CCCATGTGCAATGCTATAAGTTATTTAGA
Found at i:18818953 original size:15 final size:15
Alignment explanation
Indices: 18818907--18818955 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
18818897 AAGGCTATTT
* *
18818907 TTGATAAATTAAATA
1 TTGAAAAATTAAATG
*
18818922 TT-AAAAATGTAAGTG
1 TTGAAAAAT-TAAATG
18818937 TTGAAAAATTAAATG
1 TTGAAAAATTAAATG
18818952 TTGA
1 TTGA
18818956 TTTTAAGTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 5 0.18
15 17 0.61
16 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (15 bp):
TTGAAAAATTAAATG
Found at i:18819065 original size:5 final size:5
Alignment explanation
Indices: 18819055--18819079 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
18819045 AATGAATTAG
18819055 AATAA AATAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA
18819080 CTGAATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:18820497 original size:21 final size:21
Alignment explanation
Indices: 18820484--18820533 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
18820474 GTGTCCCCTC
18820484 CACATGGGCATGTGTGTCCTT
1 CACATGGGCATGTGTGTCCTT
18820505 CACATGGGCATGTGTGTCCTT
1 CACATGGGCATGTGTGTCCTT
18820526 CACATGGG
1 CACATGGG
18820534 TGTGTTGACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.16, C:0.24, G:0.30, T:0.30
Consensus pattern (21 bp):
CACATGGGCATGTGTGTCCTT
Found at i:18820502 original size:23 final size:23
Alignment explanation
Indices: 18820472--18820523 Score: 81
Period size: 21 Copynumber: 2.3 Consensus size: 23
18820462 TCACACGAGC
18820472 GTGTGTCCCCTCCACATGGGCAT
1 GTGTGTCCCCTCCACATGGGCAT
*
18820495 GTGTGT--CCTTCACATGGGCAT
1 GTGTGTCCCCTCCACATGGGCAT
18820516 GTGTGTCC
1 GTGTGTCC
18820524 TTCACATGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 20 0.77
23 6 0.23
ACGTcount: A:0.12, C:0.29, G:0.29, T:0.31
Consensus pattern (23 bp):
GTGTGTCCCCTCCACATGGGCAT
Found at i:18822010 original size:9 final size:9
Alignment explanation
Indices: 18821992--18822036 Score: 63
Period size: 9 Copynumber: 5.0 Consensus size: 9
18821982 ATAATTAATT
*
18821992 AATTTTAAA
1 AATTTAAAA
18822001 AATTTAAAA
1 AATTTAAAA
18822010 AATTTAAAA
1 AATTTAAAA
* *
18822019 ACTATAAAA
1 AATTTAAAA
18822028 AATTTAAAA
1 AATTTAAAA
18822037 TTATAAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (9 bp):
AATTTAAAA
Found at i:18822015 original size:17 final size:17
Alignment explanation
Indices: 18821995--18822055 Score: 72
Period size: 18 Copynumber: 3.5 Consensus size: 17
18821985 ATTAATTAAT
18821995 TTTAAAAATTTAAAAAA
1 TTTAAAAATTTAAAAAA
*
18822012 TTTAAAAACTATAAAAAA
1 TTTAAAAA-TTTAAAAAA
18822030 TTT-AAAA-TTATAAAAA
1 TTTAAAAATTTA-AAAAA
18822046 TTATAAAAAT
1 TT-TAAAAAT
18822056 ATTTTCTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
15 2 0.05
16 7 0.19
17 13 0.35
18 15 0.41
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (17 bp):
TTTAAAAATTTAAAAAA
Found at i:18822026 original size:26 final size:25
Alignment explanation
Indices: 18821997--18822055 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 25
18821987 TAATTAATTT
18821997 TAAAAATTTAAAAAATT-TAAAAACTA
1 TAAAAATTT--AAAATTATAAAAACTA
*
18822023 TAAAAAATTTAAAATTATAAAAATTA
1 T-AAAAATTTAAAATTATAAAAACTA
18822049 TAAAAAT
1 TAAAAAT
18822056 ATTTTCTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 12 0.40
26 10 0.33
27 8 0.27
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (25 bp):
TAAAAATTTAAAATTATAAAAACTA
Found at i:18822045 original size:9 final size:8
Alignment explanation
Indices: 18821995--18822055 Score: 61
Period size: 9 Copynumber: 7.1 Consensus size: 8
18821985 ATTAATTAAT
18821995 TTTAAAAA
1 TTTAAAAA
18822003 TTTAAAAAA
1 TTT-AAAAA
18822012 TTTAAAAA
1 TTTAAAAA
*
18822020 CTATAAAAAA
1 -T-TTAAAAA
18822030 TTT-AAAA
1 TTTAAAAA
18822037 TTATAAAAA
1 TT-TAAAAA
18822046 TTATAAAAA
1 TT-TAAAAA
18822055 T
1 T
18822056 ATTTTCTAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
7 6 0.13
8 10 0.22
9 24 0.52
10 6 0.13
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (8 bp):
TTTAAAAA
Found at i:18824128 original size:2 final size:2
Alignment explanation
Indices: 18824123--18824155 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
18824113 CTCTTTTTCT
18824123 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18824156 CATTTCTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18827131 original size:3 final size:3
Alignment explanation
Indices: 18827123--18827161 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
18827113 TCTAGAGCAG
18827123 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
18827162 CATTTTTGGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:18829018 original size:7 final size:8
Alignment explanation
Indices: 18829002--18829026 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
18828992 GTCTCTTTTC
18829002 TTTTATTT
1 TTTTATTT
18829010 TTTTATTT
1 TTTTATTT
18829018 TTTTATTT
1 TTTTATTT
18829026 T
1 T
18829027 ATAACACATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTATTT
Found at i:18831251 original size:29 final size:29
Alignment explanation
Indices: 18831213--18831276 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
18831203 TGTGTGTCGC
* * *
18831213 CACACAGTCGTGTGGTAGGCCGTGTATGG
1 CACACGGTCGTGTAGTAGGCCGTGTAAGG
*
18831242 CACACGGTCGTGTAGTAGGTCGTGTAAGG
1 CACACGGTCGTGTAGTAGGCCGTGTAAGG
18831271 CACACG
1 CACACG
18831277 ACAGTGTGGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.20, C:0.22, G:0.36, T:0.22
Consensus pattern (29 bp):
CACACGGTCGTGTAGTAGGCCGTGTAAGG
Found at i:18831788 original size:18 final size:19
Alignment explanation
Indices: 18831765--18831813 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
18831755 GTTGTAAAGT
*
18831765 TTTATTTTTATTTATTTA-
1 TTTATTTTTATTTACTTAG
18831783 TTTATTTATT-TTTACTTAG
1 TTTATTT-TTATTTACTTAG
18831802 TTTAATTTTTAT
1 TTT-ATTTTTAT
18831814 GTAAATATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 14 0.54
19 7 0.27
20 5 0.19
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTATTTTTATTTACTTAG
Found at i:18831793 original size:22 final size:22
Alignment explanation
Indices: 18831764--18831813 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
18831754 AGTTGTAAAG
* *
18831764 TTTTATTTTTATTTA-TTTATT
1 TTTTATTTTTACTTAGTTTAAT
18831785 TATTTATTTTTACTTAGTTTAAT
1 T-TTTATTTTTACTTAGTTTAAT
18831808 TTTTAT
1 TTTTAT
18831814 GTAAATATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 18 0.72
23 6 0.24
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTATTTTTACTTAGTTTAAT
Found at i:18838222 original size:14 final size:15
Alignment explanation
Indices: 18838203--18838243 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
18838193 AAGTTTTATT
18838203 TTTATTTTTATTTA-
1 TTTATTTTTATTTAG
*
18838217 TTTATTTTTACTTAG
1 TTTATTTTTATTTAG
18838232 TTTAATTTTTAT
1 TTT-ATTTTTAT
18838244 GTAAATATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 13 0.57
15 3 0.13
16 7 0.30
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (15 bp):
TTTATTTTTATTTAG
Found at i:18839403 original size:5 final size:5
Alignment explanation
Indices: 18839389--18839491 Score: 91
Period size: 5 Copynumber: 20.4 Consensus size: 5
18839379 ATGGGGGTAG
* * * * * *
18839389 GATAT GATTT GATTT GATAT GATAT GATAA GCTAT GATTT GATTT GATAT
1 GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT
* * * *
18839439 GATAT GATAT GATAG GATAG GATAG GATCT G-TAT GAAATAT GATAT GATAT
1 GATAT GATAT GATAT GATAT GATAT GATAT GATAT G--ATAT GATAT GATAT
18839490 GA
1 GA
18839492 AATATTAAGA
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
4 3 0.04
5 76 0.92
7 4 0.05
ACGTcount: A:0.36, C:0.02, G:0.23, T:0.39
Consensus pattern (5 bp):
GATAT
Found at i:18839427 original size:30 final size:30
Alignment explanation
Indices: 18839391--18839447 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
18839381 GGGGGTAGGA
18839391 TATGATTTGATTTGATATGATATGATAAGC
1 TATGATTTGATTTGATATGATATGATAAGC
18839421 TATGATTTGATTTGATATGATATGATA
1 TATGATTTGATTTGATATGATATGATA
18839448 TGATAGGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.46
Consensus pattern (30 bp):
TATGATTTGATTTGATATGATATGATAAGC
Found at i:18841729 original size:25 final size:25
Alignment explanation
Indices: 18841701--18841751 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
18841691 AAATGTCAAG
*
18841701 TTTAG-TACCAAATTAAACCAAAAAA
1 TTTAGATACCAAATTAAA-AAAAAAA
*
18841726 TTTAGATACTAAATTAAAAAAAAAA
1 TTTAGATACCAAATTAAAAAAAAAA
18841751 T
1 T
18841752 CAAATTTAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.59, C:0.10, G:0.04, T:0.27
Consensus pattern (25 bp):
TTTAGATACCAAATTAAAAAAAAAA
Found at i:18845675 original size:21 final size:21
Alignment explanation
Indices: 18845633--18845675 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
18845623 TTTGATTGAC
* * *
18845633 AAAATATAATATTATTTTAAA
1 AAAATATAATATCACTTAAAA
*
18845654 AAAATATCATATCACTTAAAA
1 AAAATATAATATCACTTAAAA
18845675 A
1 A
18845676 CATATTTTTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAATATAATATCACTTAAAA
Found at i:18856088 original size:94 final size:94
Alignment explanation
Indices: 18855927--18856114 Score: 358
Period size: 94 Copynumber: 2.0 Consensus size: 94
18855917 CGGCTAAATC
18855927 TGGTTTGGTACTGGGAGGACAGAGGAGAAATCTTAGTAAGCCAAGTTCTGGAGTATTAGCAAGAG
1 TGGTTTGGTACTGGGAGGACAGAGGAGAAATCTTAGTAAGCCAAGTTCTGGAGTATTAGCAAGAG
18855992 CTTATGTGATGAAAGCTAAGAGGGATGTT
66 CTTATGTGATGAAAGCTAAGAGGGATGTT
*
18856021 TGGTTTGGTACTGGGAGGACAGATGAGAAATCTTAGTAAGCCAAGTTCTGGAGTATTAGCAAGAG
1 TGGTTTGGTACTGGGAGGACAGAGGAGAAATCTTAGTAAGCCAAGTTCTGGAGTATTAGCAAGAG
*
18856086 CTTATGTGGTGAAAGCTAAGAGGGATGTT
66 CTTATGTGATGAAAGCTAAGAGGGATGTT
18856115 GATCTACCTG
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 92 1.00
ACGTcount: A:0.30, C:0.10, G:0.33, T:0.27
Consensus pattern (94 bp):
TGGTTTGGTACTGGGAGGACAGAGGAGAAATCTTAGTAAGCCAAGTTCTGGAGTATTAGCAAGAG
CTTATGTGATGAAAGCTAAGAGGGATGTT
Found at i:18858146 original size:72 final size:72
Alignment explanation
Indices: 18858029--18858173 Score: 281
Period size: 72 Copynumber: 2.0 Consensus size: 72
18858019 CTTCTTTTAG
*
18858029 GCGAAGATCTTAAGGGTAACAATCCCCCAACGCATTAGGTCTATCAATTTGTTGTATCGTGCGAA
1 GCGAAGATCTTAAGGGTAACAATCCCCCAACGCATTAGGTCTATCAATTTGCTGTATCGTGCGAA
18858094 GGTATGT
66 GGTATGT
18858101 GCGAAGATCTTAAGGGTAACAATCCCCCAACGCATTAGGTCTATCAATTTGCTGTATCGTGCGAA
1 GCGAAGATCTTAAGGGTAACAATCCCCCAACGCATTAGGTCTATCAATTTGCTGTATCGTGCGAA
18858166 GGTATGT
66 GGTATGT
18858173 G
1 G
18858174 TTGATTTTTG
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (72 bp):
GCGAAGATCTTAAGGGTAACAATCCCCCAACGCATTAGGTCTATCAATTTGCTGTATCGTGCGAA
GGTATGT
Found at i:18858587 original size:54 final size:54
Alignment explanation
Indices: 18858498--18858605 Score: 146
Period size: 54 Copynumber: 2.0 Consensus size: 54
18858488 AGAGACTTTC
* *
18858498 ATTTTGGGTCACACGGGCGTGTGCTTTAACGTGTGCTAGACCGTGTAACTCTCT
1 ATTTTGGGTCACACGGGCGTGTGCTTCAACGTGTGCTAAACCGTGTAACTCTCT
* * * *
18858552 ATTTTGGGTCACACGGGGGTGTGC-TCAGCCTTGTGCTAAACCGTGTAATTCTCT
1 ATTTTGGGTCACACGGGCGTGTGCTTCA-ACGTGTGCTAAACCGTGTAACTCTCT
18858606 GAGTTGCCCC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
53 2 0.04
54 45 0.96
ACGTcount: A:0.17, C:0.22, G:0.28, T:0.33
Consensus pattern (54 bp):
ATTTTGGGTCACACGGGCGTGTGCTTCAACGTGTGCTAAACCGTGTAACTCTCT
Found at i:18870687 original size:9 final size:9
Alignment explanation
Indices: 18870673--18870705 Score: 66
Period size: 9 Copynumber: 3.7 Consensus size: 9
18870663 CGCATAGCCT
18870673 ATACATGCC
1 ATACATGCC
18870682 ATACATGCC
1 ATACATGCC
18870691 ATACATGCC
1 ATACATGCC
18870700 ATACAT
1 ATACAT
18870706 TCAAACATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.36, C:0.30, G:0.09, T:0.24
Consensus pattern (9 bp):
ATACATGCC
Found at i:18876170 original size:15 final size:14
Alignment explanation
Indices: 18876150--18876200 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 14
18876140 TAAACTAGTG
*
18876150 TAATAACAATATCAA
1 TAATAACATTAT-AA
*
18876165 TAATAATATTAGTAA
1 TAATAACATTA-TAA
18876180 TAATAACATTGATAA
1 TAATAACATT-ATAA
18876195 TAATAA
1 TAATAA
18876201 TAAATTAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
15 29 0.94
16 2 0.06
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (14 bp):
TAATAACATTATAA
Found at i:18876198 original size:18 final size:18
Alignment explanation
Indices: 18876172--18876216 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
18876162 CAATAATAAT
* *
18876172 ATTAGTAATAATAACATTG
1 ATTAATAATAATAA-ATTA
18876191 A-TAATAATAATAAATTA
1 ATTAATAATAATAAATTA
18876208 ATTAATAAT
1 ATTAATAAT
18876217 CTAATTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 4 0.17
18 18 0.78
19 1 0.04
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (18 bp):
ATTAATAATAATAAATTA
Found at i:18877461 original size:17 final size:17
Alignment explanation
Indices: 18877441--18877482 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
18877431 TGGACTGTTA
* *
18877441 TTTTATTTGGTTTTTAT
1 TTTTATTTGGATTTGAT
*
18877458 TTTTATTTTGATTTGAT
1 TTTTATTTGGATTTGAT
18877475 TTTTATTT
1 TTTTATTT
18877483 ATTATGGGCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.10, T:0.76
Consensus pattern (17 bp):
TTTTATTTGGATTTGAT
Found at i:18883870 original size:14 final size:16
Alignment explanation
Indices: 18883836--18883872 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
18883826 TTTATAATAT
*
18883836 AAATTCAATGATTATA
1 AAATTTAATGATTATA
18883852 AAATTTAAT-ATTA-A
1 AAATTTAATGATTATA
18883866 AAATTTA
1 AAATTTA
18883873 GTACTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 8 0.40
15 4 0.20
16 8 0.40
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (16 bp):
AAATTTAATGATTATA
Found at i:18887306 original size:72 final size:71
Alignment explanation
Indices: 18887229--18887371 Score: 277
Period size: 71 Copynumber: 2.0 Consensus size: 71
18887219 GAAAAACGTT
18887229 AAAATTTATATTAATTTATTTTTTATTTTTTCATAAGCAAGAAATATAAAAGAAAATTATATAAT
1 AAAATTTATA-TAATTTATTTTTTATTTTTTCATAAGCAAGAAATATAAAAGAAAATTATATAAT
18887294 TACTTTA
65 TACTTTA
18887301 AAAATTTATATAATTTATTTTTTATTTTTTCATAAGCAAGAAATATAAAAGAAAATTATATAATT
1 AAAATTTATATAATTTATTTTTTATTTTTTCATAAGCAAGAAATATAAAAGAAAATTATATAATT
18887366 ACTTTA
66 ACTTTA
18887372 TTTTTAAATA
Statistics
Matches: 71, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
71 61 0.86
72 10 0.14
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.45
Consensus pattern (71 bp):
AAAATTTATATAATTTATTTTTTATTTTTTCATAAGCAAGAAATATAAAAGAAAATTATATAATT
ACTTTA
Found at i:18894290 original size:32 final size:33
Alignment explanation
Indices: 18894254--18894322 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 33
18894244 TTTTCATATG
* ** * *
18894254 TTTTTACGTTTTTGTTTTCTTTTTCTT-TTTTC
1 TTTTTACCTTTTTCCTTTCTTCTTATTGTTTTC
*
18894286 TTTTTCCCTTTTTCCTTTCTTCTTATTGTTTTC
1 TTTTTACCTTTTTCCTTTCTTCTTATTGTTTTC
18894319 TTTT
1 TTTT
18894323 CTCCTTTATT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
32 21 0.70
33 9 0.30
ACGTcount: A:0.03, C:0.17, G:0.04, T:0.75
Consensus pattern (33 bp):
TTTTTACCTTTTTCCTTTCTTCTTATTGTTTTC
Found at i:18894956 original size:63 final size:63
Alignment explanation
Indices: 18894855--18895014 Score: 187
Period size: 63 Copynumber: 2.5 Consensus size: 63
18894845 ACGACCGTAT
* * * * *
18894855 GCCATGTAACTCACTGTTTAGAATTTATAGTCACACGGGCTAAAGACACGGACATGTGTCCAG
1 GCCATGTAACTCACTGTTTTGAATTTAGAGTCAAACGGGCCAAAGACACGGACATGTGTCCAA
* * * * * *
18894918 GCCATGTAATTCATTGTTTTGAATTTAGGGTCAAACGGGCCAGAGACACGGGCTTGTGTCCAA
1 GCCATGTAACTCACTGTTTTGAATTTAGAGTCAAACGGGCCAAAGACACGGACATGTGTCCAA
*
18894981 GCCGTGTAACTCACTGTTTTGGGAATTT-GAGTCA
1 GCCATGTAACTCACTGTTTT--GAATTTAGAGTCA
18895015 TACTGCCGTG
Statistics
Matches: 80, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
63 69 0.86
64 5 0.06
65 6 0.08
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (63 bp):
GCCATGTAACTCACTGTTTTGAATTTAGAGTCAAACGGGCCAAAGACACGGACATGTGTCCAA
Found at i:18895656 original size:18 final size:18
Alignment explanation
Indices: 18895633--18895693 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 18
18895623 GACTCTACAT
*
18895633 TTGTATCTGAATTTGTAA
1 TTGTATCTGAATATGTAA
*
18895651 TTGTATCTG-ATATGT-T
1 TTGTATCTGAATATGTAA
* *
18895667 TTGTATCTAAATCTGTAA
1 TTGTATCTGAATATGTAA
*
18895685 GTGTATCTG
1 TTGTATCTG
18895694 GTATGTTCTG
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
16 8 0.24
17 10 0.29
18 16 0.47
ACGTcount: A:0.25, C:0.08, G:0.18, T:0.49
Consensus pattern (18 bp):
TTGTATCTGAATATGTAA
Found at i:18895684 original size:34 final size:34
Alignment explanation
Indices: 18895632--18895707 Score: 107
Period size: 34 Copynumber: 2.2 Consensus size: 34
18895622 GGACTCTACA
* * *
18895632 TTTGTATCTGAATTTGTAATTGTATCTGATATGT
1 TTTGTATCTAAATCTGTAAGTGTATCTGATATGT
*
18895666 TTTGTATCTAAATCTGTAAGTGTATCTGGTATGT
1 TTTGTATCTAAATCTGTAAGTGTATCTGATATGT
*
18895700 TCTGTATC
1 TTTGTATC
18895708 CATTTCTAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.22, C:0.09, G:0.18, T:0.50
Consensus pattern (34 bp):
TTTGTATCTAAATCTGTAAGTGTATCTGATATGT
Found at i:18905994 original size:4 final size:4
Alignment explanation
Indices: 18905985--18906080 Score: 178
Period size: 4 Copynumber: 24.5 Consensus size: 4
18905975 TATCTAAACA
18905985 ATGT ATGT ATG- -TGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
18906031 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
18906079 AT
1 AT
18906081 TTGTTTGTTT
Statistics
Matches: 90, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.02
4 88 0.98
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:18906155 original size:23 final size:23
Alignment explanation
Indices: 18906110--18906172 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
18906100 TTATTAACAT
***
18906110 TGTTCGTGAACATGTTTGTTTAA
1 TGTTCGTGAACATGTTCAATTAA
18906133 TGTTCGTGAACATGTTCAATTAA
1 TGTTCGTGAACATGTTCAATTAA
**
18906156 -GTTAAATGAACATGTTC
1 TGTT-CGTGAACATGTTC
18906173 GTAAACATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
22 3 0.09
23 31 0.91
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.41
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCAATTAA
Found at i:18906202 original size:14 final size:14
Alignment explanation
Indices: 18906183--18906214 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
18906173 GTAAACATTA
18906183 AACAAATGAACATG
1 AACAAATGAACATG
18906197 AACAAATGAACATG
1 AACAAATGAACATG
18906211 AACA
1 AACA
18906215 CACATAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.59, C:0.16, G:0.12, T:0.12
Consensus pattern (14 bp):
AACAAATGAACATG
Found at i:18908056 original size:125 final size:125
Alignment explanation
Indices: 18907834--18908086 Score: 461
Period size: 125 Copynumber: 2.0 Consensus size: 125
18907824 CATAAAGTGA
* *
18907834 ATTTGCGATTCCTTGTTTCCCACTTAAACTATAAACAGTTGAGTTACCATTTAATTCAAGACAAT
1 ATTTGCGATTCCTGGTTTCCCACTTAAACTATAAACAGTTGAGTTACCAGTTAATTCAAGACAAT
18907899 AATATCAATGTTTTATTGGTGAAGGTGTCACCCCTCCCCACCCCCATTTTATTATTAATT
66 AATATCAATGTTTTATTGGTGAAGGTGTCACCCCTCCCCACCCCCATTTTATTATTAATT
18907959 ATTTGCGATTCCTGGTTTCCCACTTAAACTATAAACAGTTGAGTTACCAGTTAATTCAAGACAAT
1 ATTTGCGATTCCTGGTTTCCCACTTAAACTATAAACAGTTGAGTTACCAGTTAATTCAAGACAAT
* **
18908024 AATATCAATGTTTTATTGGTGAAGGTGTCACCCCTTCCCACCCCTGTTTTATTATTAATT
66 AATATCAATGTTTTATTGGTGAAGGTGTCACCCCTCCCCACCCCCATTTTATTATTAATT
18908084 ATT
1 ATT
18908087 ATTATATTTT
Statistics
Matches: 123, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
125 123 1.00
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.38
Consensus pattern (125 bp):
ATTTGCGATTCCTGGTTTCCCACTTAAACTATAAACAGTTGAGTTACCAGTTAATTCAAGACAAT
AATATCAATGTTTTATTGGTGAAGGTGTCACCCCTCCCCACCCCCATTTTATTATTAATT
Found at i:18910006 original size:16 final size:17
Alignment explanation
Indices: 18909985--18910017 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
18909975 AAAATCAACC
18909985 AAAAAAGAAAA-GAAAA
1 AAAAAAGAAAAGGAAAA
18910001 AAAAAAGAAAAGGAAAA
1 AAAAAAGAAAAGGAAAA
18910018 CAAATCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAAGGAAAA
Found at i:18911880 original size:9 final size:9
Alignment explanation
Indices: 18911866--18911902 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
18911856 TATAGTTTGA
18911866 TATTCGAAT
1 TATTCGAAT
18911875 TATTCGAAT
1 TATTCGAAT
*
18911884 TATTCGAGT
1 TATTCGAAT
18911893 TATTCGAAT
1 TATTCGAAT
18911902 T
1 T
18911903 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:18912575 original size:17 final size:15
Alignment explanation
Indices: 18912518--18912577 Score: 50
Period size: 14 Copynumber: 3.9 Consensus size: 15
18912508 TATCGAGATA
* *
18912518 ATTTTTCAAAAAATC
1 ATTTTTAAAAAAATT
18912533 A-TTTTAAAAAAATT
1 ATTTTTAAAAAAATT
**
18912547 ATTTGAACAAAAAATTT
1 ATTTTTA-AAAAAA-TT
*
18912564 ATTTTTTAAAAAAT
1 ATTTTTAAAAAAAT
18912578 ATATAAAATT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
14 12 0.34
15 5 0.14
16 12 0.34
17 6 0.17
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (15 bp):
ATTTTTAAAAAAATT
Found at i:18913818 original size:8 final size:7
Alignment explanation
Indices: 18913790--18913817 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
18913780 TTGTAAATTA
18913790 AATTTTT
1 AATTTTT
18913797 AATTTTT
1 AATTTTT
18913804 AATTTTT
1 AATTTTT
18913811 AATTTTT
1 AATTTTT
18913818 TTCTTAGCCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
AATTTTT
Found at i:18925921 original size:9 final size:9
Alignment explanation
Indices: 18925904--18925949 Score: 74
Period size: 9 Copynumber: 5.1 Consensus size: 9
18925894 TAAGTTTTCG
18925904 AATTCGAAT
1 AATTCGAAT
*
18925913 AACTCGAAT
1 AATTCGAAT
18925922 AATTCGAAT
1 AATTCGAAT
*
18925931 AATTCAAAT
1 AATTCGAAT
18925940 AATTCGAAT
1 AATTCGAAT
18925949 A
1 A
18925950 TCAAACTNNN
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.48, C:0.13, G:0.09, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:18926903 original size:2 final size:2
Alignment explanation
Indices: 18926891--18926939 Score: 59
Period size: 2 Copynumber: 26.0 Consensus size: 2
18926881 TTCTCCCACA
*
18926891 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT -T AT AG AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
18926930 AT GT AT AT AT
1 AT AT AT AT AT
18926940 TTTTTTAAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
1 3 0.08
2 37 0.93
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18927773 original size:5 final size:5
Alignment explanation
Indices: 18927763--18927788 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
18927753 AAAATCACTT
18927763 AATAA AATAA AATAA AATAA AATAA A
1 AATAA AATAA AATAA AATAA AATAA A
18927789 CTTTTTCGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:18928097 original size:9 final size:9
Alignment explanation
Indices: 18928083--18928113 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
18928073 GTTAAACGAA
18928083 TCGAGTTAT
1 TCGAGTTAT
*
18928092 TCGAGTTAA
1 TCGAGTTAT
18928101 TCGAGTTAT
1 TCGAGTTAT
18928110 TCGA
1 TCGA
18928114 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:18932992 original size:18 final size:18
Alignment explanation
Indices: 18932943--18932992 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
18932933 TAAGAAAACA
*
18932943 TTTTGAAATTGAATAATG
1 TTTTGAAAATGAATAATG
* *
18932961 ATTTGTAAATGAATAATG
1 TTTTGAAAATGAATAATG
*
18932979 TTTTGAAAACGAAT
1 TTTTGAAAATGAAT
18932993 GATGCGATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.42, C:0.02, G:0.16, T:0.40
Consensus pattern (18 bp):
TTTTGAAAATGAATAATG
Found at i:18933365 original size:25 final size:25
Alignment explanation
Indices: 18933319--18933367 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
18933309 CTGTCTTTGA
** *
18933319 TAGTATATCCTGAAACTGCTATAGG
1 TAGTATATAATGAAACTACTATAGG
*
18933344 TAGTATATAATGAGACTACTATAG
1 TAGTATATAATGAAACTACTATAG
18933368 ATAGACAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (25 bp):
TAGTATATAATGAAACTACTATAGG
Found at i:18939517 original size:22 final size:22
Alignment explanation
Indices: 18939486--18939529 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
18939476 TTTGAAATAA
18939486 GTTAGATTCATAGTGAGCCAAC
1 GTTAGATTCATAGTGAGCCAAC
*
18939508 GTTAGTTTCATAGTGAGCCAAC
1 GTTAGATTCATAGTGAGCCAAC
18939530 ACATAATAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (22 bp):
GTTAGATTCATAGTGAGCCAAC
Found at i:18945028 original size:21 final size:21
Alignment explanation
Indices: 18944989--18945028 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
18944979 GGCCATGTAG
*
18944989 AAAACATAAATTTAAAAATGA
1 AAAACATAAATATAAAAATGA
* *
18945010 AAAATATAAATATATAAAT
1 AAAACATAAATATAAAAAT
18945029 TGTTTGTCAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.28
Consensus pattern (21 bp):
AAAACATAAATATAAAAATGA
Found at i:18950805 original size:49 final size:49
Alignment explanation
Indices: 18950733--18950830 Score: 162
Period size: 49 Copynumber: 2.0 Consensus size: 49
18950723 CTCCCAGAAG
18950733 ATAAAGACATAAATGTGACTGACTGGA-TCGACAATACATCAGATTGGAC
1 ATAAAGACATAAATGTGACTGACTGGACT-GACAATACATCAGATTGGAC
**
18950782 ATAAAGACATAAATGTGACTGACTGGACTGACAATACATTGGATTGGAC
1 ATAAAGACATAAATGTGACTGACTGGACTGACAATACATCAGATTGGAC
18950831 TCATGTAGAA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
49 45 0.98
50 1 0.02
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.23
Consensus pattern (49 bp):
ATAAAGACATAAATGTGACTGACTGGACTGACAATACATCAGATTGGAC
Found at i:18951971 original size:13 final size:13
Alignment explanation
Indices: 18951953--18951978 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18951943 TTGAATTATC
18951953 ATCATAATACATA
1 ATCATAATACATA
18951966 ATCATAATACATA
1 ATCATAATACATA
18951979 TGAGAGGAAG
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:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (13 bp):
ATCATAATACATA
Found at i:18953236 original size:17 final size:17
Alignment explanation
Indices: 18953214--18953252 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
18953204 ATCATTTGGA
18953214 CCACACAGGCATGTGGG
1 CCACACAGGCATGTGGG
* *
18953231 CCACACGGGCGTGTGGG
1 CCACACAGGCATGTGGG
*
18953248 TCACA
1 CCACA
18953253 TTGGCTGGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.21, C:0.31, G:0.36, T:0.13
Consensus pattern (17 bp):
CCACACAGGCATGTGGG
Found at i:18959542 original size:31 final size:31
Alignment explanation
Indices: 18959467--18959534 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
18959457 TTACAAAATG
* **
18959467 GTCATTGAACTATTTGAAAGTTTTCATTGAA
1 GTCACTGAACTATTCAAAAGTTTTCATTGAA
* *
18959498 GTCACTGAACTATTCAAAAGTTTTTATTTAA
1 GTCACTGAACTATTCAAAAGTTTTCATTGAA
18959529 GTCACT
1 GTCACT
18959535 AGGCTATTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.41
Consensus pattern (31 bp):
GTCACTGAACTATTCAAAAGTTTTCATTGAA
Found at i:18960270 original size:392 final size:393
Alignment explanation
Indices: 18959529--18960306 Score: 1515
Period size: 393 Copynumber: 2.0 Consensus size: 393
18959519 TTTTATTTAA
18959529 GTCACTAGGCTATTAATTTTTTTTCTTAAAAACCTGGGTAGCAAGATCTAAGAGATGACTCAACA
1 GTCACTAGGCTATTAATTTTTTTTCTTAAAAACCTGGGTAGCAAGATCTAAGAGATGACTCAACA
18959594 CTCGGTACAGTAGATCAGTACCCATCAACGAGTAGAAGAACATATCTTAGATCCAAGTCGATCTA
66 CTCGGTACAGTAGATCAGTACCCATCAACGAGTAGAAGAACATATCTTAGATCCAAGTCGATCTA
18959659 ACAGTTAGTGTTAGAGATTAGAGAAGAAAATGGTTTGGGTTGTGGTTCATAGATTCGTAACGTTC
131 ACAGTTAGTGTTAGAGATTAGAGAAGAAAATGGTTTGGGTTGTGGTTCATAGATTCGTAACGTTC
18959724 AAAGTTGTTTTATGAAAAAAAAAATTGGGCTGTAGAAGAGAAAGGGAAAGAGAGCTTTCGATTGG
196 AAAGTTGTTTTATGAAAAAAAAAATTGGGCTGTAGAAGAGAAAGGGAAAGAGAGCTTTCGATTGG
18959789 TGCAAGCAGTGCGAACAAAGAAGCCGTACAATAACGATTTTAACAACTCAGTGACTTAAATGAAA
261 TGCAAGCAGTGCGAACAAAGAAGCCGTACAATAACGATTTTAACAACTCAGTGACTTAAATGAAA
18959854 ACTTTTGAATAGTTCAATGACCATTTTGTAACTTTTTGAAGATGAGTGACCATAATATAAATTTT
326 ACTTTTGAATAGTTCAATGACCATTTTGTAACTTTTTGAAGATGAGTGACCATAATATAAATTTT
18959919 ATG
391 ATG
18959922 GTCACTAGGCTATTAATTTTTTTTCTTAAAAACCTGGGTAGCAAGATCTAAGAGATGACTCAACA
1 GTCACTAGGCTATTAATTTTTTTTCTTAAAAACCTGGGTAGCAAGATCTAAGAGATGACTCAACA
18959987 CTCGGTACAGTAGATCAGTACCCATCAACGAGTAGAAGAACATATCTTAGATCCAAGTCGATCTA
66 CTCGGTACAGTAGATCAGTACCCATCAACGAGTAGAAGAACATATCTTAGATCCAAGTCGATCTA
18960052 ACAGTTAGTTGTTAGAGA-TAGAGAAGAAAATGGTTTGGGTTGTGGTTCATAGATTCGTAACGTT
131 ACAGTTAG-TGTTAGAGATTAGAGAAGAAAATGGTTTGGGTTGTGGTTCATAGATTCGTAACGTT
*
18960116 CAAAGTTGTTTTATG-AAAAAAAAATTGGGCTGTAGGAGAGAAAGGGAAAGAGAGCTTTCGATTG
195 CAAAGTTGTTTTATGAAAAAAAAAATTGGGCTGTAGAAGAGAAAGGGAAAGAGAGCTTTCGATTG
18960180 GTGCAAGCAGTGCGAACAAAGAAGCCGTACAATAACGATTTTAACAACTCAGTGACTTAAATGAA
260 GTGCAAGCAGTGCGAACAAAGAAGCCGTACAATAACGATTTTAACAACTCAGTGACTTAAATGAA
*
18960245 AACTTTTGAATAGTTCAATGACCATTTTGTAACTTTTTGAAGTTGAGTGACCATAATATAAA
325 AACTTTTGAATAGTTCAATGACCATTTTGTAACTTTTTGAAGATGAGTGACCATAATATAAA
18960307 CTTATTAATA
Statistics
Matches: 382, Mismatches: 2, Indels: 3
0.99 0.01 0.01
Matches are distributed among these distances:
392 174 0.46
393 199 0.52
394 9 0.02
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (393 bp):
GTCACTAGGCTATTAATTTTTTTTCTTAAAAACCTGGGTAGCAAGATCTAAGAGATGACTCAACA
CTCGGTACAGTAGATCAGTACCCATCAACGAGTAGAAGAACATATCTTAGATCCAAGTCGATCTA
ACAGTTAGTGTTAGAGATTAGAGAAGAAAATGGTTTGGGTTGTGGTTCATAGATTCGTAACGTTC
AAAGTTGTTTTATGAAAAAAAAAATTGGGCTGTAGAAGAGAAAGGGAAAGAGAGCTTTCGATTGG
TGCAAGCAGTGCGAACAAAGAAGCCGTACAATAACGATTTTAACAACTCAGTGACTTAAATGAAA
ACTTTTGAATAGTTCAATGACCATTTTGTAACTTTTTGAAGATGAGTGACCATAATATAAATTTT
ATG
Found at i:18975942 original size:30 final size:29
Alignment explanation
Indices: 18975906--18975974 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 29
18975896 TGATTGACCC
* *
18975906 ATCCCTTTTCGTAATTCGATAACCGAAGTT
1 ATCCCTTTTCGTAATTCGACAACC-AAATT
* * *
18975936 ATCCCTTTTTGTAGTTCGACAGCCAAATT
1 ATCCCTTTTCGTAATTCGACAACCAAATT
18975965 ATCCCTTTTC
1 ATCCCTTTTC
18975975 ATTGTTTGAC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 13 0.39
30 20 0.61
ACGTcount: A:0.23, C:0.26, G:0.12, T:0.39
Consensus pattern (29 bp):
ATCCCTTTTCGTAATTCGACAACCAAATT
Found at i:18976088 original size:30 final size:30
Alignment explanation
Indices: 18975992--18976074 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
18975982 GACGGTCATC
* *
18975992 ACCATCCCTTTTCATAATTTGATAGCCAAA
1 ACCATCCCTTTTCATAGTTCGATAGCCAAA
* *
18976022 GCTATCCCTTTTCATAGTTCGATAGCCAAA
1 ACCATCCCTTTTCATAGTTCGATAGCCAAA
18976052 ACCATCCCTTTTCATAGTTCGAT
1 ACCATCCCTTTTCATAGTTCGAT
18976075 GATCGTCACC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.35
Consensus pattern (30 bp):
ACCATCCCTTTTCATAGTTCGATAGCCAAA
Found at i:18976091 original size:89 final size:89
Alignment explanation
Indices: 18975904--18976123 Score: 271
Period size: 89 Copynumber: 2.5 Consensus size: 89
18975894 GATGATTGAC
* * * ** **
18975904 CCATCCCTTTTCGTAATTCGATAACCGAAGTTATCCCTTTTTGTAGTTCGACAGCCAAATTATCC
1 CCATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATAGTTCGACAGCCAAACCATCC
* * *
18975969 CTTTTCATTGTTTGACGGTCATCA
66 CTTTTCATAGTTCGACGATCATCA
* * *
18975993 CCATCCCTTTTCATAATTTGATAGCCAAAGCTATCCCTTTTCATAGTTCGATAGCCAAAACCATC
1 CCATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATAGTTCGACAGCC-AAACCATC
* *
18976058 CCTTTTCATAGTTCGATGATCGTCA
65 CCTTTTCATAGTTCGACGATCATCA
* *
18976083 CCATCCTTTTTCATAA-TCGATAGTCGAAGCTATCCCTTTTC
1 CCATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTC
18976124 GATTTGTCAA
Statistics
Matches: 111, Mismatches: 19, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
89 70 0.63
90 41 0.37
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.37
Consensus pattern (89 bp):
CCATCCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATAGTTCGACAGCCAAACCATCC
CTTTTCATAGTTCGACGATCATCA
Found at i:18976943 original size:16 final size:15
Alignment explanation
Indices: 18976917--18976946 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
18976907 TATCTTATTT
18976917 TAATTACTTAATTAC
1 TAATTACTTAATTAC
18976932 TAATTCACTTAATTA
1 TAATT-ACTTAATTA
18976947 ACCTTGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (15 bp):
TAATTACTTAATTAC
Found at i:18979690 original size:25 final size:24
Alignment explanation
Indices: 18979656--18979710 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
18979646 GAGCTATAAA
* *
18979656 CGGTAAGCTCATACGAGCTGAGTAT
1 CGGTAAGCTCATAAGAGCTG-GAAT
*
18979681 CGGTAAGCTCATAAGAGTTGGAAT
1 CGGTAAGCTCATAAGAGCTGGAAT
18979705 CGGTAA
1 CGGTAA
18979711 CCCTAATGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 9 0.33
25 18 0.67
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (24 bp):
CGGTAAGCTCATAAGAGCTGGAAT
Found at i:18984329 original size:18 final size:19
Alignment explanation
Indices: 18984306--18984347 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
18984296 TTTATCTAAG
* *
18984306 TTTTATAA-TATTAATTTT
1 TTTTATAATTATAAATGTT
18984324 TTTTATAATTATAAATGTT
1 TTTTATAATTATAAATGTT
18984343 TTTTA
1 TTTTA
18984348 GAGTTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTTATAATTATAAATGTT
Found at i:18985551 original size:13 final size:14
Alignment explanation
Indices: 18985533--18985569 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
18985523 AATGGCATAT
18985533 AAATAATATAAAC-
1 AAATAATATAAACG
18985546 AAATAA-ATAAACG
1 AAATAATATAAACG
18985559 AAATGAATATA
1 AAAT-AATATA
18985570 TAAAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 10 0.48
14 2 0.10
15 3 0.14
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.22
Consensus pattern (14 bp):
AAATAATATAAACG
Found at i:18993984 original size:14 final size:14
Alignment explanation
Indices: 18993961--18993993 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
18993951 CAAAAGAAAC
18993961 TATAGAGGCCCAAA
1 TATAGAGGCCCAAA
*
18993975 TATAGTGGCCCAAA
1 TATAGAGGCCCAAA
18993989 -ATAGA
1 TATAGA
18993994 TTCAAGAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.42, C:0.18, G:0.21, T:0.18
Consensus pattern (14 bp):
TATAGAGGCCCAAA
Found at i:18995088 original size:17 final size:18
Alignment explanation
Indices: 18995066--18995102 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
18995056 TAAAAGCATG
18995066 TTAATAATT-TGAAATTT
1 TTAATAATTATGAAATTT
18995083 TTAATAATTAATGAAATTT
1 TTAATAATT-ATGAAATTT
18995102 T
1 T
18995103 ATAACTCGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.50
19 9 0.50
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (18 bp):
TTAATAATTATGAAATTT
Found at i:19001532 original size:44 final size:44
Alignment explanation
Indices: 19001482--19001828 Score: 405
Period size: 44 Copynumber: 8.1 Consensus size: 44
19001472 TAAAGCCAGT
* * *
19001482 AATCCTATCTTCCTAGTCAGCAGTGGAATGGGTTGAAGATTGTG
1 AATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTG
* *
19001526 AGTCCTATCTCGCTGGTCAGCAGTGGAATAGGTTGAAGATTGT-
1 AATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTG
19001569 AAGTCCTATCTCCCTGGTCAGCAGTGG-A-A---T--AG---GTG
1 AA-TCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTG
* *
19001604 AATCCTATCTCCCTAGTCAGCAGTGGAATAGGTTGACGATTGTG
1 AATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTG
* * * * ****
19001648 AATCCTATCACCCCGGTCAGCAGTGGAATAGGCTGAAAATAAACA
1 AATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGAT-TGTG
*
19001693 AATCCTATCTCCCTAGTCAGCAGTGGAATAGGTTGAA-ATT-TG
1 AATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTG
*
19001735 TAAGTCCTATCTTCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTG
1 -AA-TCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTG
*
19001781 AATCCTATCTCCCTGGTTAGCAGTGGAATAGGTTGAAGATTGTG
1 AATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTG
19001825 AATC
1 AATC
19001829 TTACTTCCCC
Statistics
Matches: 256, Mismatches: 30, Indels: 34
0.80 0.09 0.11
Matches are distributed among these distances:
34 25 0.10
35 3 0.01
36 1 0.00
37 2 0.01
39 2 0.01
41 1 0.00
42 1 0.00
43 4 0.02
44 177 0.69
45 38 0.15
46 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.29
Consensus pattern (44 bp):
AATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTG
Found at i:19001615 original size:34 final size:34
Alignment explanation
Indices: 19001572--19001636 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
19001562 AGATTGTAAG
*
19001572 TCCTATCTCCCTGGTCAGCAGTGGAATAGGTGAA
1 TCCTATCTCCCTAGTCAGCAGTGGAATAGGTGAA
19001606 TCCTATCTCCCTAGTCAGCAGTGGAATAGGT
1 TCCTATCTCCCTAGTCAGCAGTGGAATAGGT
19001637 TGACGATTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.28
Consensus pattern (34 bp):
TCCTATCTCCCTAGTCAGCAGTGGAATAGGTGAA
Found at i:19001849 original size:89 final size:88
Alignment explanation
Indices: 19001596--19001855 Score: 294
Period size: 89 Copynumber: 2.9 Consensus size: 88
19001586 TCAGCAGTGG
* * *
19001596 AATAGGTGAATCCTATCTCCCTAGTCAGCAGTGGAATAGGTTGACGATTGTGAATCCTA-TCACC
1 AATAAGTGAATCCTATCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCCTACT-TCC
19001660 CCGGTCAGCAGTGGAATAGGCTGAA
65 CC-GTCAGCAGTGGAATAGGCTGAA
***
19001685 AATAAACAAATCCTATCTCCCTAGTCAGCAGTGGAATAGGTTGAA-ATT-TGTAAGTCCTATCTT
1 AATAAGTGAATCCTATCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGTG-AA-TCCTA-CTT
** *
19001748 CCTGGTCAGCAGTGGAATAGGTTGAA
63 CCCCGTCAGCAGTGGAATAGGCTGAA
* * * * *
19001774 GAT-TGTGAATCCTATCTCCCTGGTTAGCAGTGGAATAGGTTGAAGATTGTGAATCTTACTTCCC
1 AATAAGTGAATCCTATCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCCTACTTCCC
*
19001838 CGACATTGCAGTGGAATA
66 CGTCA--GCAGTGGAATA
19001856 AATTGAAGGT
Statistics
Matches: 143, Mismatches: 20, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
87 10 0.07
88 44 0.31
89 84 0.59
90 4 0.03
91 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.28
Consensus pattern (88 bp):
AATAAGTGAATCCTATCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCCTACTTCCC
CGTCAGCAGTGGAATAGGCTGAA
Found at i:19002378 original size:169 final size:169
Alignment explanation
Indices: 19001897--19002617 Score: 1079
Period size: 169 Copynumber: 4.3 Consensus size: 169
19001887 CTGACGTTAT
* * * *
19001897 AGCGGAGCAGATTAAAGCTGAAGGCAACGAATCTTATCTCCCGGGCGTTAAGACTTGAAATAGCT
1 AGCGGAGCAGATTAAAGCTGAAGGCAGCGAATCTTATCTCCCTGGTGTTAAGACTTGAAAAAGCT
* * *
19001962 GAAGTGGAGCGGATTAAAGCTGTGGGCAGCGAGTCCTATCTCTTTGGAATTATAGTGGAACAGAT
66 GAAGTGGAGCGGATTAAAGCTGTGGGCAGCAAATCCTATCTCTTTGGCATTATAGTGGAACAGAT
19002027 TAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCGTTGC
131 TAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCGTTGC
*
19002066 AGCGGAGCAGATTAAAGCTGAAGGCAGCGAATCTTATCT-CCTCGGTGTTAAGACTGGAAAAAAG
1 AGCGGAGCAGATTAAAGCTGAAGGCAGCGAATCTTATCTCCCT-GGTGTTAAGACTTG-AAAAAG
* * *
19002130 CTGAAGTGGAGCGGATTAAAGCTGTGGGCAAG-GAATCCAATCTCTTTGGCATTATAGTGTAACA
64 CTGAAGTGGAGCGGATTAAAGCTGTGGGC-AGCAAATCCTATCTCTTTGGCATTATAGTGGAACA
* * *
19002194 GATTAAAGTTAAAGGTAGCCAATCTTGTTTCCCTAGCATTGC
128 GATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCGTTGC
* * *
19002236 AGCAGAGCAAATTAAAGCTGAGGGCAGCGAATCTTATCTCCCTGGCT-TTAAGACTTGAAAAAGC
1 AGCGGAGCAGATTAAAGCTGAAGGCAGCGAATCTTATCTCCCTGG-TGTTAAGACTTGAAAAAGC
*
19002300 TGAAGTGGAGCGGATTAAAGTTGTGGGCAGCAAATCCTATCTCTTTGGCATTATAGTGGAACAGA
65 TGAAGTGGAGCGGATTAAAGCTGTGGGCAGCAAATCCTATCTCTTTGGCATTATAGTGGAACAGA
* *
19002365 TTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGTGTTGT
130 TTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCGTTGC
* * *
19002405 AGCGGAGCAGATTAAAGCTGAGGGCAGCGAATTTTATCTCCCTGGTGTTAAGACTTGAAATAGCT
1 AGCGGAGCAGATTAAAGCTGAAGGCAGCGAATCTTATCTCCCTGGTGTTAAGACTTGAAAAAGCT
* * *
19002470 GAGGTGGAGCGGATTAAAGCTGTGGGTAGCAAATCCTATCTCTTTGGCATTATAGTGGAATAGAT
66 GAAGTGGAGCGGATTAAAGCTGTGGGCAGCAAATCCTATCTCTTTGGCATTATAGTGGAACAGAT
* * * * * *
19002535 TAAGGCTAAAGGTAGCAAATCTGGTTTCCCTGGTGTTGT
131 TAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCGTTGC
* *
19002574 AGCGGGGCAGATTAAAGCTGAAGGCAGCGAATCTCATCTCCCTG
1 AGCGGAGCAGATTAAAGCTGAAGGCAGCGAATCTTATCTCCCTG
19002618 ACGATAAAAT
Statistics
Matches: 504, Mismatches: 41, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
168 5 0.01
169 345 0.68
170 148 0.29
171 6 0.01
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.26
Consensus pattern (169 bp):
AGCGGAGCAGATTAAAGCTGAAGGCAGCGAATCTTATCTCCCTGGTGTTAAGACTTGAAAAAGCT
GAAGTGGAGCGGATTAAAGCTGTGGGCAGCAAATCCTATCTCTTTGGCATTATAGTGGAACAGAT
TAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCGTTGC
Found at i:19007039 original size:14 final size:15
Alignment explanation
Indices: 19007001--19007041 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
19006991 AGGAACAACA
19007001 GAAACAAAAAAGGAG
1 GAAACAAAAAAGGAG
19007016 GAAACAAAAAAGGAG
1 GAAACAAAAAAGGAG
* *
19007031 AAAATAAAAAA
1 GAAACAAAAAA
19007042 CAAAAAAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.73, C:0.05, G:0.20, T:0.02
Consensus pattern (15 bp):
GAAACAAAAAAGGAG
Found at i:19011180 original size:33 final size:33
Alignment explanation
Indices: 19011137--19011207 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
19011127 CCTCCACCGG
*
19011137 GGTAATGTCTTTCTCATTAGTTTATGGAATGGA
1 GGTAACGTCTTTCTCATTAGTTTATGGAATGGA
*
19011170 GGTAACGTCTTTCTCATTGGTTTATGGAATGGA
1 GGTAACGTCTTTCTCATTAGTTTATGGAATGGA
19011203 GGTAA
1 GGTAA
19011208 TCTTGCCCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.24, C:0.10, G:0.27, T:0.39
Consensus pattern (33 bp):
GGTAACGTCTTTCTCATTAGTTTATGGAATGGA
Found at i:19012669 original size:144 final size:144
Alignment explanation
Indices: 19012473--19012774 Score: 419
Period size: 144 Copynumber: 2.1 Consensus size: 144
19012463 AAATCATTTG
* * * * ** * *
19012473 TCCCTAAAGTTACAGTGGGTTGGATTGAAGTTACCATAGCGAATCTTATCTCCATGAAGTTACAG
1 TCCCTAAAGTTGCAATGGGTCGGATTAAAACTACCATAGCAAATCTTATCTCCATAAAGTTACAG
* *
19012538 TGGAGTAAGATAAAGCTACAAGTCCTATACCCCTGAAGTTATAGTAGGTC-GAATCGAAACTACA
66 TGGAGCAAGATAAAGCTACAAGTCCTATACCCCTGAAGTTACAGTAGGTCAGAAT-GAAACTACA
*
19012602 ACGGCAAATCTTGTC
130 ACGGCAAATCTTATC
* *
19012617 TCCCTAAAGTTGCAATGGGTCGGATTAAAACTA-CAGTAGCAAATCTTATCTCCCTAAAGTTGCA
1 TCCCTAAAGTTGCAATGGGTCGGATTAAAACTACCA-TAGCAAATCTTATCTCCATAAAGTTACA
* * *
19012681 GTGGAGCAAGATAAAGCTACAAGTCCTATACCCCTGAAGTTGCAGTGGGTCAGACTGAAACTACA
65 GTGGAGCAAGATAAAGCTACAAGTCCTATACCCCTGAAGTTACAGTAGGTCAGAATGAAACTACA
*
19012746 ACGGCGAATCTTATC
130 ACGGCAAATCTTATC
19012761 TCCCTAAAGTTGCA
1 TCCCTAAAGTTGCA
19012775 GTAGAGCAAA
Statistics
Matches: 139, Mismatches: 17, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
143 2 0.01
144 134 0.96
145 3 0.02
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (144 bp):
TCCCTAAAGTTGCAATGGGTCGGATTAAAACTACCATAGCAAATCTTATCTCCATAAAGTTACAG
TGGAGCAAGATAAAGCTACAAGTCCTATACCCCTGAAGTTACAGTAGGTCAGAATGAAACTACAA
CGGCAAATCTTATC
Found at i:19012701 original size:50 final size:49
Alignment explanation
Indices: 19012605--19012868 Score: 150
Period size: 50 Copynumber: 5.5 Consensus size: 49
19012595 AACTACAACG
* * * *
19012605 GCAAATCTTGTCTCCCTAAAGTTGCAATGGGTCGGATTAAAACTACAGTA
1 GCAAATCTTATCTCCCTAAAGTTGCAGTGGGTCAGATTAAAGCTACA-TA
19012655 GCAAATCTTATCTCCCTAAAGTTGCAGTGGAG-CAAGA-TAAAGCTACA-A
1 GCAAATCTTATCTCCCTAAAGTTGCAGTGG-GTC-AGATTAAAGCTACATA
* * *
19012703 G----TCCTATAC-CCCTGAAGTTGCAGTGGGTCAGACTGAAA-CTACA-A
1 GCAAATCTTAT-CTCCCTAAAGTTGCAGTGGGTCAGA-TTAAAGCTACATA
* * * *
19012747 CGGCGAATCTTATCTCCCTAAAGTTGCAGTAGAG-CAAAATAAAG---C-TA
1 --GCAAATCTTATCTCCCTAAAGTTGCAGT-GGGTCAGATTAAAGCTACATA
* * * *
19012794 -CAAATCCTA-CACCCTTGAAGTTGTAGTGGGTCAGATTGAAA-CTACAGTA
1 GCAAATCTTATCTCCC-TAAAGTTGCAGTGGGTCAGATT-AAAGCTACA-TA
* *
19012843 GCGAATCTTATCTCCTTAAAGTTGCA
1 GCAAATCTTATCTCCCTAAAGTTGCA
19012869 ATGGAGCAAG
Statistics
Matches: 161, Mismatches: 27, Indels: 52
0.67 0.11 0.22
Matches are distributed among these distances:
43 10 0.06
44 49 0.30
45 7 0.04
46 1 0.01
47 3 0.02
48 2 0.01
49 6 0.04
50 75 0.47
51 8 0.05
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.26
Consensus pattern (49 bp):
GCAAATCTTATCTCCCTAAAGTTGCAGTGGGTCAGATTAAAGCTACATA
Found at i:19013037 original size:282 final size:282
Alignment explanation
Indices: 19012658--19013165 Score: 748
Period size: 282 Copynumber: 1.8 Consensus size: 282
19012648 TACAGTAGCA
* *
19012658 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAAGATAAAGCTACAAGTCCTATACCCCTGAAGTTG
1 AATCTTATCTCCATAAAGTTGCAGTGGAGCAAGATAAAGCTACAAATCCTATACCCCTGAAGTTG
*
19012723 CAGTGGGTCAGACTGAAACTACAACGGCGAATCTTATCTCCCTAAAGTTGCAGTAGAGCAAAATA
66 CAGTGGGTCAGACTGAAACTACAACAGCGAATCTTATCTCCCTAAAGTTGCAGTAGAGCAAAATA
* * * * * * ** * *
19012788 AAGCTACAAATCCTACACCCTTGAAGTTGTAGTGGGTCAGATTGAAACTACAGTAGCGAATCTTA
131 AAGCTACAAATCCTACACCCCTAAAGATGCAATGGGTCAGAATGAAACTACAACAACAAATCTTA
19012853 TCTCCTTAAAGTTGCAATGGAGCAAGATGAAGCTACAAATCCGATACCCTTGAAGTTGTAGTGGA
196 TCTCCTTAAAGTTGCAATGGAGCAAGATGAAGCTACAAATCCGATACCCTTGAAGTTGTAGTGGA
19012918 TAGGATTGAAACTACGATGGCG
261 TAGGATTGAAACTACGATGGCG
* * * *
19012940 AATCTTATCTCCATGAAGTTGCAGTGGAGTAAGATAAAGCTACAAATCTTATACCCTTGAAGTTG
1 AATCTTATCTCCATAAAGTTGCAGTGGAGCAAGATAAAGCTACAAATCCTATACCCCTGAAGTTG
* * * * * *
19013005 CAGTGTGTC-GAATTGAAACTACAATAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGAT
66 CAGTGGGTCAG-ACTGAAACTACAACAGCGAATCTTATCTCCCTAAAGTTGCAGTAGAGCAAAAT
* * **
19013069 GAAGCTACAAATCCTATACCCCTAAAGATGCAATGGGTTGGAATGAAACTACAACAACAAATCTT
130 AAAGCTACAAATCCTACACCCCTAAAGATGCAATGGGTCAGAATGAAACTACAACAACAAATCTT
*
19013134 ATCTCTTTAAAGTTGCAATGGAGCAAGATGAA
195 ATCTCCTTAAAGTTGCAATGGAGCAAGATGAA
19013166 ACTGTGACAC
Statistics
Matches: 197, Mismatches: 28, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
281 1 0.01
282 196 0.99
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (282 bp):
AATCTTATCTCCATAAAGTTGCAGTGGAGCAAGATAAAGCTACAAATCCTATACCCCTGAAGTTG
CAGTGGGTCAGACTGAAACTACAACAGCGAATCTTATCTCCCTAAAGTTGCAGTAGAGCAAAATA
AAGCTACAAATCCTACACCCCTAAAGATGCAATGGGTCAGAATGAAACTACAACAACAAATCTTA
TCTCCTTAAAGTTGCAATGGAGCAAGATGAAGCTACAAATCCGATACCCTTGAAGTTGTAGTGGA
TAGGATTGAAACTACGATGGCG
Found at i:19013165 original size:94 final size:94
Alignment explanation
Indices: 19012618--19013162 Score: 667
Period size: 94 Copynumber: 5.8 Consensus size: 94
19012608 AATCTTGTCT
* * * * *
19012618 CCCTAAAGTTGCAATGGGTCGGATTAAAACTACAGTAGCAAATCTTATCTCCCTAAAGTTGCAGT
1 CCCTGAAGTTGCAGTGGGTCGGATTGAAACTACAATAGCGAATCTTATCTCCCTAAAGTTGCAGT
*
19012683 GGAGCAAGATAAAGCTACAAGTCCTATAC
66 GGAGCAAGATAAAGCTACAAATCCTATAC
* * **
19012712 CCCTGAAGTTGCAGTGGGTCAGACTGAAACTACAACGGCGAATCTTATCTCCCTAAAGTTGCAGT
1 CCCTGAAGTTGCAGTGGGTCGGATTGAAACTACAATAGCGAATCTTATCTCCCTAAAGTTGCAGT
* * *
19012777 AGAGCAAAATAAAGCTACAAATCCTACAC
66 GGAGCAAGATAAAGCTACAAATCCTATAC
* * * * * *
19012806 CCTTGAAGTTGTAGTGGGTCAGATTGAAACTACAGTAGCGAATCTTATCTCCTTAAAGTTGCAAT
1 CCCTGAAGTTGCAGTGGGTCGGATTGAAACTACAATAGCGAATCTTATCTCCCTAAAGTTGCAGT
* *
19012871 GGAGCAAGATGAAGCTACAAATCCGATAC
66 GGAGCAAGATAAAGCTACAAATCCTATAC
* * * * * * * *
19012900 CCTTGAAGTTGTAGTGGATAGGATTGAAACTACGATGGCGAATCTTATCTCCATGAAGTTGCAGT
1 CCCTGAAGTTGCAGTGGGTCGGATTGAAACTACAATAGCGAATCTTATCTCCCTAAAGTTGCAGT
* *
19012965 GGAGTAAGATAAAGCTACAAATCTTATAC
66 GGAGCAAGATAAAGCTACAAATCCTATAC
* * * *
19012994 CCTTGAAGTTGCAGTGTGTCGAATTGAAACTACAATAGCGAATCTTATCTCCCTGAAGTTGCAGT
1 CCCTGAAGTTGCAGTGGGTCGGATTGAAACTACAATAGCGAATCTTATCTCCCTAAAGTTGCAGT
*
19013059 GGAGCAAGATGAAGCTACAAATCCTATAC
66 GGAGCAAGATAAAGCTACAAATCCTATAC
* * * * * * * * ** *
19013088 CCCTAAAGATGCAATGGGTTGGAATGAAACTACAACAACAAATCTTATCTCTTTAAAGTTGCAAT
1 CCCTGAAGTTGCAGTGGGTCGGATTGAAACTACAATAGCGAATCTTATCTCCCTAAAGTTGCAGT
19013153 GGAGCAAGAT
66 GGAGCAAGAT
19013163 GAAACTGTGA
Statistics
Matches: 386, Mismatches: 65, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
94 386 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (94 bp):
CCCTGAAGTTGCAGTGGGTCGGATTGAAACTACAATAGCGAATCTTATCTCCCTAAAGTTGCAGT
GGAGCAAGATAAAGCTACAAATCCTATAC
Found at i:19013403 original size:3 final size:3
Alignment explanation
Indices: 19013389--19013417 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
19013379 TCGTCCGGCC
19013389 TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
19013418 AAGTCCATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:19013481 original size:18 final size:18
Alignment explanation
Indices: 19013460--19013498 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
19013450 AATACAAAAA
19013460 AAAAAAAACTAAAAGCCC
1 AAAAAAAACTAAAAGCCC
** *
19013478 AAAAAACCCTTAAAGCCC
1 AAAAAAAACTAAAAGCCC
19013496 AAA
1 AAA
19013499 GACCACTTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.26, G:0.05, T:0.08
Consensus pattern (18 bp):
AAAAAAAACTAAAAGCCC
Done.