Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12
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: 24583705
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1509421 characters in sequence are not A, C, G, or T
File 60 of 75
Found at i:19238899 original size:134 final size:136
Alignment explanation
Indices: 19238627--19238906 Score: 402
Period size: 136 Copynumber: 2.1 Consensus size: 136
19238617 GACAGCTGTG
* * * * * * * *
19238627 ATCATAAATCAATGAACTGTTAATAAAGTGTTCATGATCATAAATCAATGAACAGAAGTTGTGAT
1 ATCATAAATCAATGAAATCTTAATAAACTGCTCATCATCATAAATCAATAAACAAAAATTGTGAT
* * *
19238692 AGTAAAATTAACGAGCTTTAAAAAATGACAGTTGTGATCGTAAATCAATGAATTATTTCAAGGGA
66 AGTAAAATTAACGAGCTTTAAAAAATGACAGTTGTGATCGTAAATCAAAGAACTATTTAAAGGGA
19238757 GTTGCA
131 GTTGCA
* *
19238763 ATCATAAATCAATGAAATCTTCATGAACTGCTCATCATCATAAATCAATAAACAAAAATTGTGAT
1 ATCATAAATCAATGAAATCTTAATAAACTGCTCATCATCATAAATCAATAAACAAAAATTGTGAT
* * *
19238828 CGT-AAATTAACGAGCTTT-AAAGATGACAGTTGTGATCGTAAATCAAAGAACTATTTAAATGGA
66 AGTAAAATTAACGAGCTTTAAAAAATGACAGTTGTGATCGTAAATCAAAGAACTATTTAAAGGGA
19238891 GTTGCA
131 GTTGCA
19238897 ATCATAAATC
1 ATCATAAATC
19238907 GACAAACTCT
Statistics
Matches: 128, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
134 56 0.44
135 15 0.12
136 57 0.45
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (136 bp):
ATCATAAATCAATGAAATCTTAATAAACTGCTCATCATCATAAATCAATAAACAAAAATTGTGAT
AGTAAAATTAACGAGCTTTAAAAAATGACAGTTGTGATCGTAAATCAAAGAACTATTTAAAGGGA
GTTGCA
Found at i:19238957 original size:98 final size:98
Alignment explanation
Indices: 19238855--19239069 Score: 250
Period size: 98 Copynumber: 2.2 Consensus size: 98
19238845 TAAAGATGAC
* *
19238855 AGTTGTGATCGTAAATCAAAGAACTATTTAAATGGAGTTGCAATCATAAATCGACAAACTCTTAA
1 AGTTGTGATCATAAATCAAAGAACTATTTAAAAGGAGTTGCAATCATAAATCGACAAACTCTTAA
* * * * *
19238920 TGAAGTGTTCACGGTCGTAAATTAATGAATTGA
66 TGAAATGTTCACGATCATAAATCAATGAACTGA
** * * * ** ** *
19238953 AGTTGTGATCATAAATCAGTGACCTGTTTAAAAGGATTTGTGATTGTAAATCGACGAACTCTTAA
1 AGTTGTGATCATAAATCAAAGAACTATTTAAAAGGAGTTGCAATCATAAATCGACAAACTCTTAA
* *
19239018 TGAAATGTTCATGATCATATATCAATGAACTGA
66 TGAAATGTTCACGATCATAAATCAATGAACTGA
*
19239051 AGTTGTTATCATAAATCAA
1 AGTTGTGATCATAAATCAA
19239070 CGAGCTTTAA
Statistics
Matches: 96, Mismatches: 21, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
98 96 1.00
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.33
Consensus pattern (98 bp):
AGTTGTGATCATAAATCAAAGAACTATTTAAAAGGAGTTGCAATCATAAATCGACAAACTCTTAA
TGAAATGTTCACGATCATAAATCAATGAACTGA
Found at i:19238959 original size:134 final size:135
Alignment explanation
Indices: 19238627--19238968 Score: 411
Period size: 134 Copynumber: 2.5 Consensus size: 135
19238617 GACAGCTGTG
** * * *
19238627 ATCATAAATCAATGAACTGTTAATAAAGTGTTCATGATCATAAATCAATGAACAGAAGTTGTGAT
1 ATCATAAATCAACAAACTCTTAATGAAGTGTTCACGATCATAAATCAATGAACAGAAGTTGTGAT
* * * *
19238692 AGTAAAATTAACGAGCTTTAAAAAATGACAGTTGTGATCGTAAATCAATGAATTATTTCAAGGGA
66 CGT-AAATTAACGAGCTTTAAAAAATGACAGTTGTGATCGTAAATCAAAGAACTATTTAAAGGGA
19238757 GTTGCA
130 GTTGCA
* * * * * * *
19238763 ATCATAAATCAATGAAA-TCTTCATGAACTGCTCATC-ATCATAAATCAATAAACAAAAATTGTG
1 ATCATAAATCAA-CAAACTCTTAATGAAGTGTTCA-CGATCATAAATCAATGAACAGAAGTTGTG
* *
19238826 ATCGTAAATTAACGAGCTTT-AAAGATGACAGTTGTGATCGTAAATCAAAGAACTATTTAAATGG
64 ATCGTAAATTAACGAGCTTTAAAAAATGACAGTTGTGATCGTAAATCAAAGAACTATTTAAAGGG
19238890 AGTTGCA
129 AGTTGCA
* * * * **
19238897 ATCATAAATCGACAAACTCTTAATGAAGTGTTCACGGTCGTAAATTAATGAATTGAAGTTGTGAT
1 ATCATAAATCAACAAACTCTTAATGAAGTGTTCACGATCATAAATCAATGAACAGAAGTTGTGAT
*
19238962 CATAAAT
66 CGTAAAT
19238969 CAGTGACCTG
Statistics
Matches: 171, Mismatches: 31, Indels: 10
0.81 0.15 0.05
Matches are distributed among these distances:
133 4 0.02
134 98 0.57
135 15 0.09
136 52 0.30
137 2 0.01
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (135 bp):
ATCATAAATCAACAAACTCTTAATGAAGTGTTCACGATCATAAATCAATGAACAGAAGTTGTGAT
CGTAAATTAACGAGCTTTAAAAAATGACAGTTGTGATCGTAAATCAAAGAACTATTTAAAGGGAG
TTGCA
Found at i:19239226 original size:133 final size:134
Alignment explanation
Indices: 19239009--19239316 Score: 349
Period size: 133 Copynumber: 2.3 Consensus size: 134
19238999 TAAATCGACG
* * *
19239009 AACTCTTAATGAAATGTTCATGATCATATATCAATGAACTGAAGTTGTTATCATAAATCAACGAG
1 AACTCTTAATGAAATGTTCATGATCATATATCAATAAACTAAAGTTG-TATCATAAATCAACGAA
* *
19239074 CTTTAAAAATGACAGTTGTGATCGTAAATCA-ATGAATTGTTTAAATGGAGTTGCGATCATAAAT
65 CTTTAAAAATGACAGTTGTGATCGTAAATCAGA-GAACTGTTTAAATGAAGTTGCGATCATAAAT
19239138 AAAAAA
129 AAAAAA
* *
19239144 AACTCTTACTGAAGTGTTCATGATCATA-AGTCAATAAA-TCAAAGTTG-ATCATAAATCAACGA
1 AACTCTTAATGAAATGTTCATGATCATATA-TCAATAAACT-AAAGTTGTATCATAAATCAACGA
* * * ** *
19239206 ATTTTAAAAATGGCAGTTGTGATCGTAAATTAGAGAACTGTTTAAATGAAGTTATGATCGT--AT
64 ACTTTAAAAATGACAGTTGTGATCGTAAATCAGAGAACTGTTTAAATGAAGTTGCGATCATAAAT
** **
19239269 ACCGACG
129 A-AAAAA
* * *
19239276 AACTCTTAATGAAATGTTCATGATCGTAAATCAACAAACTA
1 AACTCTTAATGAAATGTTCATGATCATATATCAATAAACTA
19239317 TAAAAATTCC
Statistics
Matches: 146, Mismatches: 21, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
131 3 0.02
132 34 0.23
133 67 0.46
134 3 0.02
135 39 0.27
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.31
Consensus pattern (134 bp):
AACTCTTAATGAAATGTTCATGATCATATATCAATAAACTAAAGTTGTATCATAAATCAACGAAC
TTTAAAAATGACAGTTGTGATCGTAAATCAGAGAACTGTTTAAATGAAGTTGCGATCATAAATAA
AAAA
Found at i:19239380 original size:107 final size:107
Alignment explanation
Indices: 19239189--19239413 Score: 315
Period size: 107 Copynumber: 2.1 Consensus size: 107
19239179 AAATCAAAGT
* * * * * *
19239189 TGATCATAAATCAACGAATTTTAAAAATGGCAGTTGTGATCGTAAATTAGAGAACTGTTTAAATG
1 TGATCGTAAATCAACAAACTATAAAAATGCCAGTTGTGATCGTAAATCAGAGAACTGTTTAAATG
* * *
19239254 AAGTTATGATCGTATACCGACGAACTCTTAATGAAATGTTCA
66 AAGTTATGATCATAAACCGACAAACTCTTAATGAAATGTTCA
* * * *
19239296 TGATCGTAAATCAACAAACTATAAAAATTCCATTTGTGATTGTAAATCAGCGAACTGTTTAAATG
1 TGATCGTAAATCAACAAACTATAAAAATGCCAGTTGTGATCGTAAATCAGAGAACTGTTTAAATG
* *
19239361 GAGTTATGATCATAAACCGACAAACTCTTAATGAAGTGTTCA
66 AAGTTATGATCATAAACCGACAAACTCTTAATGAAATGTTCA
19239403 TGATCGTAAAT
1 TGATCGTAAAT
19239414 TAATGAACTG
Statistics
Matches: 103, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
107 103 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (107 bp):
TGATCGTAAATCAACAAACTATAAAAATGCCAGTTGTGATCGTAAATCAGAGAACTGTTTAAATG
AAGTTATGATCATAAACCGACAAACTCTTAATGAAATGTTCA
Found at i:19245144 original size:29 final size:29
Alignment explanation
Indices: 19245067--19245145 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
19245057 ACAGTCCATC
* * *
19245067 TGGCCTACAAGGCCTGACACATGATCGTG
1 TGGCCCACAAGGCCTGGCACATGACCGTG
* * *
19245096 TGGCTCA-AATGGTCTAGCACATGACCGTG
1 TGGCCCACAA-GGCCTGGCACATGACCGTG
*
19245125 TGGCCCACACGGCCTGGCACA
1 TGGCCCACAAGGCCTGGCACA
19245146 CGTTCATGTG
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
28 2 0.05
29 35 0.92
30 1 0.03
ACGTcount: A:0.23, C:0.30, G:0.28, T:0.19
Consensus pattern (29 bp):
TGGCCCACAAGGCCTGGCACATGACCGTG
Found at i:19250227 original size:13 final size:13
Alignment explanation
Indices: 19250209--19250246 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
19250199 ATGGTAACAA
19250209 GAAATGTTTA-AGT
1 GAAATGTTTATA-T
*
19250222 GAAATGGTTATAT
1 GAAATGTTTATAT
19250235 GAAATGTTTATA
1 GAAATGTTTATA
19250247 AGGATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 21 0.95
14 1 0.05
ACGTcount: A:0.39, C:0.00, G:0.21, T:0.39
Consensus pattern (13 bp):
GAAATGTTTATAT
Found at i:19250228 original size:26 final size:26
Alignment explanation
Indices: 19250185--19250244 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
19250175 AATTATATGT
* **
19250185 AATGTGTAAGTGTTATGGTAACAAGA
1 AATGTTTAAGTGAAATGGTAACAAGA
* * *
19250211 AATGTTTAAGTGAAATGGTTATATGA
1 AATGTTTAAGTGAAATGGTAACAAGA
19250237 AATGTTTA
1 AATGTTTA
19250245 TAAGGATATA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (26 bp):
AATGTTTAAGTGAAATGGTAACAAGA
Found at i:19251033 original size:13 final size:13
Alignment explanation
Indices: 19251015--19251044 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
19251005 TATTGATTAG
19251015 TTGAAATGACATT
1 TTGAAATGACATT
19251028 TTGAAATGACATT
1 TTGAAATGACATT
19251041 TTGA
1 TTGA
19251045 TGTGTGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.40
Consensus pattern (13 bp):
TTGAAATGACATT
Found at i:19256782 original size:81 final size:79
Alignment explanation
Indices: 19256671--19256989 Score: 422
Period size: 81 Copynumber: 4.0 Consensus size: 79
19256661 GGTATAACAG
* *
19256671 TCATTTTACCCTATAGGGGTATTTTAGTCATTTTACCCTATGGGTGTATTTTGGTCATTTTATCC
1 TCATTTTACCCTAT-GGGGTATTTTGGTCATTTTACCCTATGGG-GTATTTTGGTCATTTTACCC
19256736 TATAGGGGTATTTCGA
64 TATAGGGGTATTTCGA
* * * *
19256752 TCATTTTACCCTATGGGGTTATTTTGGTCATTTTACCCTATGGGGTTATTTTAGTTATTTTAACA
1 TCATTTTACCCTATGGGG-TATTTTGGTCATTTTACCCTATGGGG-TATTTTGGTCATTTTACCC
* *
19256817 TATGGGGGTATTTCGG
64 TATAGGGGTATTTCGA
* *
19256833 TCATTTTACCCTATGAGGGTATTTTGGTCATTTTACCCTATGAGGGTATTTCGATCATTTTACCC
1 TCATTTTACCCTATG-GGGTATTTTGGTCATTTTACCCTATG-GGGTATTTTGGTCATTTTACCC
* *
19256898 TGTGGGGGTATTTCGA
64 TATAGGGGTATTTCGA
* * * * *
19256914 TCATTTTACCCTATGAGGTATTTCGGTTATTTTACCCTATGAGGTATTTTGGTTATTTTACCCTA
1 TCATTTTACCCTATGGGGTATTTTGGTCATTTTACCCTATGGGGTATTTTGGTCATTTTACCCTA
*
19256979 TAAGGGTATTT
66 TAGGGGTATTT
19256990 TGGTTATTAT
Statistics
Matches: 209, Mismatches: 25, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
79 28 0.13
80 28 0.13
81 147 0.70
82 6 0.03
ACGTcount: A:0.19, C:0.15, G:0.20, T:0.45
Consensus pattern (79 bp):
TCATTTTACCCTATGGGGTATTTTGGTCATTTTACCCTATGGGGTATTTTGGTCATTTTACCCTA
TAGGGGTATTTCGA
Found at i:19256994 original size:27 final size:27
Alignment explanation
Indices: 19256670--19257002 Score: 382
Period size: 27 Copynumber: 12.4 Consensus size: 27
19256660 GGGTATAACA
* *
19256670 GTCATTTTACCCTATAGGGGTATTTTA
1 GTCATTTTACCCTATGGGGGTATTTTG
*
19256697 GTCATTTTACCCTATGGGTGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
* * *
19256724 GTCATTTTATCCTATAGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTTG
* *
19256751 ATCATTTTACCCTATGGGGTTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
* *
19256778 GTCATTTTACCCTATGGGGTTATTTTA
1 GTCATTTTACCCTATGGGGGTATTTTG
* * * *
19256805 GTTATTTTAACATATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTTG
*
19256832 GTCATTTTACCCTATGAGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
* *
19256859 GTCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTTG
* * *
19256886 ATCATTTTACCCTGTGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTTG
* * *
19256913 ATCATTTTACCCTAT-GAGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTTG
* *
19256939 GTTATTTTACCCTAT-GAGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
* **
19256965 GTTATTTTACCCTATAAGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
* *
19256992 GTTATTATACC
1 GTCATTTTACC
19257003 TATTTTGGGG
Statistics
Matches: 268, Mismatches: 37, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
26 48 0.18
27 220 0.82
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.45
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTTG
Found at i:19259704 original size:17 final size:18
Alignment explanation
Indices: 19259671--19259705 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
19259661 GGTTATCAAA
19259671 TATTTTGTTCATTTTTTT
1 TATTTTGTTCATTTTTTT
*
19259689 TATTTT-TTCCTTTTTTT
1 TATTTTGTTCATTTTTTT
19259706 ACTTTTCCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.09, C:0.09, G:0.03, T:0.80
Consensus pattern (18 bp):
TATTTTGTTCATTTTTTT
Found at i:19266206 original size:7 final size:7
Alignment explanation
Indices: 19266189--19266229 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
19266179 AGCTTCAGTG
19266189 GGGTATTA
1 GGGT-TTA
19266197 GGGTTTA
1 GGGTTTA
19266204 GGGTTTA
1 GGGTTTA
19266211 GGGTTTA
1 GGGTTTA
*
19266218 AGGTTTA
1 GGGTTTA
*
19266225 AGGTT
1 GGGTT
19266230 CAGTGGGGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
7 28 0.88
8 4 0.12
ACGTcount: A:0.20, C:0.00, G:0.39, T:0.41
Consensus pattern (7 bp):
GGGTTTA
Found at i:19272780 original size:18 final size:18
Alignment explanation
Indices: 19272741--19272836 Score: 61
Period size: 18 Copynumber: 5.2 Consensus size: 18
19272731 ATTAGAAAAA
**
19272741 AAAAATAT-AAAAATCAT
1 AAAAATATAAAAAATTGT
19272758 AAAAAATATAAAAAATTGT
1 -AAAAATATAAAAAATTGT
* * * *
19272777 AAAATTTTATAAAATCGT
1 AAAAATATAAAAAATTGT
* *
19272795 AAAAAATTTAAAAAAATATGG
1 -AAAAATAT-AAAAAAT-TGT
*
19272816 AAAAATA-AAAAAATTAT
1 AAAAATATAAAAAATTGT
19272833 AAAA
1 AAAA
19272837 TTTTATAAAG
Statistics
Matches: 61, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
17 5 0.08
18 29 0.48
19 14 0.23
20 12 0.20
21 1 0.02
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (18 bp):
AAAAATATAAAAAATTGT
Found at i:19272836 original size:10 final size:10
Alignment explanation
Indices: 19272739--19272836 Score: 57
Period size: 10 Copynumber: 10.4 Consensus size: 10
19272729 AAATTAGAAA
*
19272739 AAAAAAATAT
1 AAAAAATTAT
*
19272749 -AAAAATCAT
1 AAAAAATTAT
19272758 AAAAAA-TAT
1 AAAAAATTAT
*
19272767 AAAAAATTGT
1 AAAAAATTAT
*
19272777 --AAAATTTT
1 AAAAAATTAT
* **
19272785 ATAAAATCGT
1 AAAAAATTAT
19272795 AAAAAATT-T
1 AAAAAATTAT
*
19272804 AAAAAAATAT
1 AAAAAATTAT
*
19272814 GGAAAAA-TA-
1 -AAAAAATTAT
19272823 AAAAAATTAT
1 AAAAAATTAT
19272833 AAAA
1 AAAA
19272837 TTTTATAAAG
Statistics
Matches: 68, Mismatches: 12, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
8 12 0.18
9 25 0.37
10 26 0.38
11 5 0.07
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:19273075 original size:19 final size:19
Alignment explanation
Indices: 19273053--19273143 Score: 64
Period size: 19 Copynumber: 4.9 Consensus size: 19
19273043 TTTTTTTATG
19273053 ATTTTTATAAAATTTTACA
1 ATTTTTATAAAATTTTACA
* * **
19273072 ATTTTTTTTATTTTTTACA
1 ATTTTTATAAAATTTTACA
* *
19273091 GTTTTTATAAAAATTT-CTA
1 ATTTTTATAAAATTTTAC-A
*
19273110 ATTTTTA-ATCAATTTTA-A
1 ATTTTTATA-AAATTTTACA
*
19273128 ATTTTT-TAAATTTTTA
1 ATTTTTATAAAATTTTA
19273144 TTAAATTTAA
Statistics
Matches: 53, Mismatches: 15, Indels: 10
0.68 0.19 0.13
Matches are distributed among these distances:
17 6 0.11
18 10 0.19
19 37 0.70
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.60
Consensus pattern (19 bp):
ATTTTTATAAAATTTTACA
Found at i:19273139 original size:27 final size:28
Alignment explanation
Indices: 19273109--19273161 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
19273099 AAAAATTTCT
* *
19273109 AATTTTTAATCAATTTTA-AATTTTTTA
1 AATTTTTAATAAATTTAATAATTTTTTA
*
19273136 AATTTTTATTAAATTTAATAATTTTT
1 AATTTTTAATAAATTTAATAATTTTT
19273162 CCAAAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 15 0.68
28 7 0.32
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (28 bp):
AATTTTTAATAAATTTAATAATTTTTTA
Found at i:19273161 original size:20 final size:20
Alignment explanation
Indices: 19273124--19273161 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
19273114 TTAATCAATT
**
19273124 TTAAATTTTTTAAATTTTTA
1 TTAAATTTAATAAATTTTTA
19273144 TTAAATTTAAT-AATTTTT
1 TTAAATTTAATAAATTTTT
19273162 CCAAAATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTAAATTTAATAAATTTTTA
Found at i:19273385 original size:90 final size:88
Alignment explanation
Indices: 19273218--19273418 Score: 210
Period size: 90 Copynumber: 2.2 Consensus size: 88
19273208 TAATAAGAGT
* *
19273218 AGGGGCTTAATTGC-TTTTTTGAAAAAAATTTAAGGATCTTTTTGATGCATTTTGAAAGTTCAAT
1 AGGGGCTTAATTGCTTTTTTTGAAAAAAATTTAAGGATCTTTTTGATGCATTTTAAAAGTTCAAG
*
19273282 TACCCAATTGAGTG-AAAAAAAG
66 TACCAAATTGAGTGAAAAAAAAG
* * * * *
19273304 CAGGGGCTTAATTGCTTTTTTTG-AAGAAGTTTAAGGGGTTTTTTTTTGATGTATTTTAAAAGTT
1 -AGGGGCTTAATTGCTTTTTTTGAAAAAAATTTAA--GG-ATCTTTTTGATGCATTTTAAAAGTT
***
19273368 CAAGTGTTAAATTGAGTGCAAAAAAAAAG
62 CAAGTACCAAATTGAGTG--AAAAAAAAG
*
19273397 AGGGGCTTAATTGTATTTTTTT
1 AGGGGCTTAATTG-CTTTTTTT
19273419 TTAAATTGAG
Statistics
Matches: 94, Mismatches: 12, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
87 23 0.24
88 7 0.07
89 2 0.02
90 34 0.36
92 13 0.14
93 15 0.16
ACGTcount: A:0.32, C:0.07, G:0.21, T:0.40
Consensus pattern (88 bp):
AGGGGCTTAATTGCTTTTTTTGAAAAAAATTTAAGGATCTTTTTGATGCATTTTAAAAGTTCAAG
TACCAAATTGAGTGAAAAAAAAG
Found at i:19276253 original size:28 final size:28
Alignment explanation
Indices: 19276219--19276276 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
19276209 TTACATTCAG
19276219 ATTATTTTTTTTCTTTTAAAATTAAATT
1 ATTATTTTTTTTCTTTTAAAATTAAATT
19276247 ATTATTTTTTTTCTTTTAAAATTAAATT
1 ATTATTTTTTTTCTTTTAAAATTAAATT
19276275 AT
1 AT
19276277 CTTTTAAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (28 bp):
ATTATTTTTTTTCTTTTAAAATTAAATT
Found at i:19281222 original size:361 final size:362
Alignment explanation
Indices: 19280543--19281643 Score: 1573
Period size: 361 Copynumber: 3.0 Consensus size: 362
19280533 GAGTTTAAAT
** *
19280543 AAGCTTTGAAAATGTTTTAGAAATGAAGTGTCCATGGTTAGTGTTGTTTGGACTGGTAGTTGTAG
1 AAGCTTTGAAAATGTTTTAGAAATGAAGTGTCTTTGGTTAGTGTTGTTTGGGCTGGTAGTTGTAG
* * *
19280608 GGTCATCTAGATGGCAAAATTTAACTATCCATATAGAAGGCAAATTGTCTTAAGAGATGTGCTTT
66 GGCCATCTAGATGGCAGAATTTAGCTATCC-------AGG-AAATTGTCTTAAGAGATGTGCTTT
* * *
19280673 TGCCAAAATGTCATATGAGGGGGAGGGGGGATTAGCCACCTAAATTGCATCAGGATTGCTTTAAC
123 TGCCAAAACGTCATTTGAGGGGGAGGGGGGAATAGCCACCTAAATTGCATCAGGATTGCTTTAAC
*
19280738 ATATGTAAAATTGTGTTGATTGCATTTTAATTTATCGAAAGTCCATTTTATGTAATTGTCATATC
188 ATATGTAAAAGTGTGTTGATTGCATTTTAATTTATCGAAAGTCCATTTTATGTAATTGTCATATC
* * * *
19280803 CAAACACGTAGCGGGCGATTTGATATG-GTTTTTAAAATGTCTTTGAGCCTTAGAAAAGGTTGGA
253 CAAACACTTAGAGGGTGATTTGATGTGAG-TTTTAAAATGTCTTTGAGCCTTAGAAAAGGTTGGA
* *
19280867 ATTTGTTTTTCTGATATTTTTATTAAATTATTTTAAAAATGTATTA
317 ATTTGTTTTTATGATATTTTTATTAAATGATTTTAAAAATGTATTA
* *
19280913 AAGCTTTGAAAATGTTTTAAAAATGAAGTGTCTTTGGTTAGTGTTGTTTGGGCTGGTAGTTGCAG
1 AAGCTTTGAAAATGTTTTAGAAATGAAGTGTCTTTGGTTAGTGTTGTTTGGGCTGGTAGTTGTAG
* * *
19280978 GGCCATCTAAATGGTAGAATTTAGCTATCCA-GAAATTGTCTTAAGAGATGTACTTTTGCCAAAA
66 GGCCATCTAGATGGCAGAATTTAGCTATCCAGGAAATTGTCTTAAGAGATGTGCTTTTGCCAAAA
** * * * * *
19281042 CGTCATTTGAACGGGAGGGGGGAATAGTCACGTAAATTGCATCAAGATTGCTTCAACGTATGTAA
131 CGTCATTTGAGGGGGAGGGGGGAATAGCCACCTAAATTGCATCAGGATTGCTTTAACATATGTAA
* *
19281107 AAGTGTGTTAATTGCATTTTAATTTATCGAAAGTCCATTTTATGCAATTGTCATATCCAAACACT
196 AAGTGTGTTGATTGCATTTTAATTTATCGAAAGTCCATTTTATGTAATTGTCATATCCAAACACT
*
19281172 TAGAGGGTGATTTGATGTGAGTTTTAAAATGTCTTTGAGCCTTGGAAAAGGTTGGAATTTGTTTT
261 TAGAGGGTGATTTGATGTGAGTTTTAAAATGTCTTTGAGCCTTAGAAAAGGTTGGAATTTGTTTT
19281237 TATGATATTTTTATTAAATGATTTTAAAAATGTATTA
326 TATGATATTTTTATTAAATGATTTTAAAAATGTATTA
*
19281274 AAGCTTTGAAAATGTTTTAGAAATGAAGTGTCTTTGGTTAGTGTTGTTTGGGTTGGTAGTTGTAG
1 AAGCTTTGAAAATGTTTTAGAAATGAAGTGTCTTTGGTTAGTGTTGTTTGGGCTGGTAGTTGTAG
* * * * *
19281339 GGCCATCTAGATGGCGGAGTTTAGCTATCTAGATGGAGGGCATATTGTCTTCAGAAATGTGCTTT
66 GGCCATCTAGATGGCAGAATTTAGCTATC--CA-GGA----A-ATTGTCTTAAGAGATGTGCTTT
* * * * *
19281404 TACCAAAACGTCATTTG-GGGGGAGGGGGGAATAACCACTTGAATTGCATCAGGATTGTTTTAAC
123 TGCCAAAACGTCATTTGAGGGGGAGGGGGGAATAGCCACCTAAATTGCATCAGGATTGCTTTAAC
* * *
19281468 ATATGTAAAAGTGTGTTGATTGTATTTTAATTTATCGGATGTCCATTTTATGTAATTGTCATATC
188 ATATGTAAAAGTGTGTTGATTGCATTTTAATTTATCGAAAGTCCATTTTATGTAATTGTCATATC
* *
19281533 CAAACACTT--AGGGTGATTTGATGTGATTTTTAAAATGTCTTTGAGCCTTAGAAAATGTTGGAA
253 CAAACACTTAGAGGGTGATTTGATGTGAGTTTTAAAATGTCTTTGAGCCTTAGAAAAGGTTGGAA
* *
19281596 TTTATTTTTATGATATTTTTATTAAATGATTTTAAAACTGTATTA
318 TTTGTTTTTATGATATTTTTATTAAATGATTTTAAAAATGTATTA
19281641 AAG
1 AAG
19281644 TTGTTTAAAT
Statistics
Matches: 658, Mismatches: 63, Indels: 23
0.88 0.08 0.03
Matches are distributed among these distances:
361 328 0.50
362 2 0.00
363 2 0.00
365 2 0.00
367 97 0.15
369 107 0.16
370 120 0.18
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.38
Consensus pattern (362 bp):
AAGCTTTGAAAATGTTTTAGAAATGAAGTGTCTTTGGTTAGTGTTGTTTGGGCTGGTAGTTGTAG
GGCCATCTAGATGGCAGAATTTAGCTATCCAGGAAATTGTCTTAAGAGATGTGCTTTTGCCAAAA
CGTCATTTGAGGGGGAGGGGGGAATAGCCACCTAAATTGCATCAGGATTGCTTTAACATATGTAA
AAGTGTGTTGATTGCATTTTAATTTATCGAAAGTCCATTTTATGTAATTGTCATATCCAAACACT
TAGAGGGTGATTTGATGTGAGTTTTAAAATGTCTTTGAGCCTTAGAAAAGGTTGGAATTTGTTTT
TATGATATTTTTATTAAATGATTTTAAAAATGTATTA
Found at i:19283711 original size:26 final size:26
Alignment explanation
Indices: 19283670--19283720 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
19283660 CACCAATATC
*
19283670 GCAGCAAGGCTACCAGCAACAGTATT
1 GCAGCAAAGCTACCAGCAACAGTATT
* * *
19283696 GCAGCAAAGCTGCCAGTAATAGTAT
1 GCAGCAAAGCTACCAGCAACAGTAT
19283721 ACTTCCTCCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.18
Consensus pattern (26 bp):
GCAGCAAAGCTACCAGCAACAGTATT
Found at i:19283911 original size:27 final size:27
Alignment explanation
Indices: 19283881--19284020 Score: 183
Period size: 27 Copynumber: 5.2 Consensus size: 27
19283871 AGAATAACAG
19283881 TCATTTTACCCTATGGGGGTATTTTGA
1 TCATTTTACCCTATGGGGGTATTTTGA
* ** * *
19283908 TCATTTTACTCTATAAGGGTATTTCGG
1 TCATTTTACCCTATGGGGGTATTTTGA
* *
19283935 TCATTTTATCCTATGGGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTTGA
*
19283962 TCATTTTACCCTGTGGGGGTATTTT-A
1 TCATTTTACCCTATGGGGGTATTTTGA
*
19283988 GTCATTTTACCCTATGGGGGTATTTCGA
1 -TCATTTTACCCTATGGGGGTATTTTGA
19284016 TCATT
1 TCATT
19284021 CATTGACCTC
Statistics
Matches: 96, Mismatches: 15, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
27 95 0.99
28 1 0.01
ACGTcount: A:0.18, C:0.15, G:0.22, T:0.45
Consensus pattern (27 bp):
TCATTTTACCCTATGGGGGTATTTTGA
Found at i:19283948 original size:54 final size:54
Alignment explanation
Indices: 19283878--19284020 Score: 205
Period size: 54 Copynumber: 2.6 Consensus size: 54
19283868 AGGAGAATAA
*
19283878 CAGTCATTTTACCCTATGGGGGTATTTTGATCATTTTACTCTATAAGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTTTGATCATTTTACCCTATAAGGGTATTT
* * * * **
19283932 CGGTCATTTTATCCTATGGGGGTATTTTGGTCATTTTACCCTGTGGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTTTGATCATTTTACCCTATAAGGGTATTT
* *
19283986 TAGTCATTTTACCCTATGGGGGTATTTCGATCATT
1 CAGTCATTTTACCCTATGGGGGTATTTTGATCATT
19284021 CATTGACCTC
Statistics
Matches: 77, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 77 1.00
ACGTcount: A:0.18, C:0.15, G:0.22, T:0.44
Consensus pattern (54 bp):
CAGTCATTTTACCCTATGGGGGTATTTTGATCATTTTACCCTATAAGGGTATTT
Found at i:19285862 original size:37 final size:37
Alignment explanation
Indices: 19285812--19285908 Score: 167
Period size: 37 Copynumber: 2.6 Consensus size: 37
19285802 CTGTTTCAAT
* *
19285812 GTTGCGAGCTTAACTTAGCTAACTCAAATAATTTGAG
1 GTTGCGAGCTTAACTCAGCTAACTCAAATAATTGGAG
19285849 GTTGCGAGCTTAACTCAGCTAACTCAAATAATTGGAG
1 GTTGCGAGCTTAACTCAGCTAACTCAAATAATTGGAG
*
19285886 GTTGCGAGCTTAACTCAACTAAC
1 GTTGCGAGCTTAACTCAGCTAAC
19285909 CTTTAATCAT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (37 bp):
GTTGCGAGCTTAACTCAGCTAACTCAAATAATTGGAG
Found at i:19300962 original size:31 final size:31
Alignment explanation
Indices: 19300924--19300984 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
19300914 AGATAATTTT
* *
19300924 AAAGAGTTTTGTTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTACGATTCAATTACTCTTG
19300955 AAAGAGTTTTATTACGATTCAATTACTCTT
1 AAAGAGTTTTATTACGATTCAATTACTCTT
19300985 CTAATTTGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.43
Consensus pattern (31 bp):
AAAGAGTTTTATTACGATTCAATTACTCTTG
Found at i:19312537 original size:31 final size:31
Alignment explanation
Indices: 19312463--19312537 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
19312453 TTCTTTAAAG
* * *
19312463 GTGTATGATTGAATCAAAATTAAAATTTTAT
1 GTGTATAATTGAACCAAAATCAAAATTTTAT
* * * *
19312494 GTATACATTTGAACCACAATCAAAATTTTAT
1 GTGTATAATTGAACCAAAATCAAAATTTTAT
19312525 GTGTATAATTGAA
1 GTGTATAATTGAA
19312538 TTGAACCAAA
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (31 bp):
GTGTATAATTGAACCAAAATCAAAATTTTAT
Found at i:19318544 original size:17 final size:17
Alignment explanation
Indices: 19318522--19318554 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
19318512 TCTCAGATTT
*
19318522 TGATACTCATATCTTTC
1 TGATACCCATATCTTTC
19318539 TGATACCCATATCTTT
1 TGATACCCATATCTTT
19318555 GACTTTTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.45
Consensus pattern (17 bp):
TGATACCCATATCTTTC
Found at i:19328616 original size:23 final size:23
Alignment explanation
Indices: 19328590--19328633 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
19328580 GCACGCCTCA
*
19328590 ACCTTTTTTTTTCCTTTCTTCCC
1 ACCTTTTTTATTCCTTTCTTCCC
19328613 ACCTTTTTTATTCCTTTCTTC
1 ACCTTTTTTATTCCTTTCTTC
19328634 TTTCTTTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.07, C:0.32, G:0.00, T:0.61
Consensus pattern (23 bp):
ACCTTTTTTATTCCTTTCTTCCC
Found at i:19331104 original size:26 final size:27
Alignment explanation
Indices: 19331024--19331106 Score: 129
Period size: 24 Copynumber: 3.2 Consensus size: 27
19331014 GTTTTGATAG
19331024 TTGTAAATTTGATAAGTTATATCATAT
1 TTGTAAATTTGATAAGTTATATCATAT
*
19331051 TTGTAATTTTGA-AA-TTATAT-ATAT
1 TTGTAAATTTGATAAGTTATATCATAT
19331075 TTGTAAATTTGATAAGTTATATCATA-
1 TTGTAAATTTGATAAGTTATATCATAT
19331101 TTGTAA
1 TTGTAA
19331107 TTATGAAATT
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
24 15 0.29
25 8 0.16
26 14 0.27
27 14 0.27
ACGTcount: A:0.37, C:0.02, G:0.11, T:0.49
Consensus pattern (27 bp):
TTGTAAATTTGATAAGTTATATCATAT
Found at i:19331121 original size:26 final size:24
Alignment explanation
Indices: 19331024--19331122 Score: 85
Period size: 26 Copynumber: 3.8 Consensus size: 24
19331014 GTTTTGATAG
*
19331024 TTGTAAATTTGATAAGTTATATCATA
1 TTGT-AATTTGA-AATTTATATCATA
19331050 TTTGTAATTTTGAAA-TTATAT-ATA
1 -TTGTAA-TTTGAAATTTATATCATA
*
19331074 TTTGTAAATTTGATAAGTTATATCATA
1 -TTGT-AATTTGA-AATTTATATCATA
19331101 TTGTAATTATGAAATTGTATAT
1 TTGTAATT-TGAAATT-TATAT
19331123 ATTTGTTGAA
Statistics
Matches: 64, Mismatches: 1, Indels: 15
0.80 0.01 0.19
Matches are distributed among these distances:
24 13 0.20
25 17 0.27
26 22 0.34
27 12 0.19
ACGTcount: A:0.37, C:0.02, G:0.11, T:0.49
Consensus pattern (24 bp):
TTGTAATTTGAAATTTATATCATA
Found at i:19331126 original size:50 final size:51
Alignment explanation
Indices: 19331024--19331128 Score: 185
Period size: 50 Copynumber: 2.1 Consensus size: 51
19331014 GTTTTGATAG
*
19331024 TTGTAAATTTGATAAGTTATATCATATTTGTAATTTTGAAATTATATATAT
1 TTGTAAATTTGATAAGTTATATCATATTTGTAATTATGAAATTATATATAT
*
19331075 TTGTAAATTTGATAAGTTATATCATA-TTGTAATTATGAAATTGTATATAT
1 TTGTAAATTTGATAAGTTATATCATATTTGTAATTATGAAATTATATATAT
19331125 TTGT
1 TTGT
19331129 TGAAGAAATT
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
50 26 0.50
51 26 0.50
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.50
Consensus pattern (51 bp):
TTGTAAATTTGATAAGTTATATCATATTTGTAATTATGAAATTATATATAT
Found at i:19339389 original size:3 final size:3
Alignment explanation
Indices: 19339381--19339406 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
19339371 CTGTTGTCAT
19339381 CAC CAC CAC CAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CA
19339407 TCATCATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.65, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:19339474 original size:3 final size:3
Alignment explanation
Indices: 19339468--19339498 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
19339458 CCACCACCAC
*
19339468 CAT CAT CAT CAT CAT CAT CAC CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
19339499 GTTGCCGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.39, G:0.00, T:0.29
Consensus pattern (3 bp):
CAT
Found at i:19339538 original size:66 final size:66
Alignment explanation
Indices: 19339343--19339539 Score: 342
Period size: 66 Copynumber: 3.0 Consensus size: 66
19339333 ACATTCTAGA
* * *
19339343 ATCATCATCATCACCATCATCATCGTCT-CTGTTGTCATCACCACCACCACCACCACCACCACCA
1 ATCATCATCATCACCATCATCATCGT-TGCCGATGTCATCACCACCACCACCACCACCACCATCA
19339407 TC
65 TC
19339409 ATCATCATCATCACCATCATCATCGTTGCCGATGTCATCACCACCACCACCACCACCACCATCAT
1 ATCATCATCATCACCATCATCATCGTTGCCGATGTCATCACCACCACCACCACCACCACCATCAT
19339474 C
66 C
*
19339475 ATCATCATCATCACCATCATCATCGTTGCCGATGTCATCACCACCACCACCACCACCATCATCAT
1 ATCATCATCATCACCATCATCATCGTTGCCGATGTCATCACCACCACCACCACCACCACCATCAT
19339540 TTGCTTGTAT
Statistics
Matches: 126, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
65 1 0.01
66 125 0.99
ACGTcount: A:0.28, C:0.44, G:0.06, T:0.22
Consensus pattern (66 bp):
ATCATCATCATCACCATCATCATCGTTGCCGATGTCATCACCACCACCACCACCACCACCATCAT
C
Found at i:19341792 original size:21 final size:21
Alignment explanation
Indices: 19341683--19341792 Score: 96
Period size: 21 Copynumber: 5.2 Consensus size: 21
19341673 TAATAGCATG
* * *
19341683 GGTTTGTACATAGTATAACAT
1 GGTTTGCATATAGTATAACAA
** *
19341704 GGTTCACATATAGTATAATAA
1 GGTTTGCATATAGTATAACAA
*
19341725 GGTTCT-CATATAGTATAATAA
1 GGTT-TGCATATAGTATAACAA
* * *
19341746 GTTTTGCATATAATATAACAT
1 GGTTTGCATATAGTATAACAA
* *
19341767 GGTTTGCATATGGTATAACAG
1 GGTTTGCATATAGTATAACAA
19341788 GGTTT
1 GGTTT
19341793 TTAGAATACA
Statistics
Matches: 72, Mismatches: 15, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
20 1 0.01
21 71 0.99
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (21 bp):
GGTTTGCATATAGTATAACAA
Found at i:19343175 original size:21 final size:21
Alignment explanation
Indices: 19343149--19343188 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
19343139 TGCATTTGAA
* *
19343149 ACAAAAGGGTGTGGTACCTAG
1 ACAAAAAGGTGTGATACCTAG
19343170 ACAAAAAGGTGTGATACCT
1 ACAAAAAGGTGTGATACCT
19343189 CTATGTCTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.15, G:0.28, T:0.20
Consensus pattern (21 bp):
ACAAAAAGGTGTGATACCTAG
Found at i:19357645 original size:5 final size:5
Alignment explanation
Indices: 19357635--19357694 Score: 52
Period size: 5 Copynumber: 11.4 Consensus size: 5
19357625 CATTCATTCT
*
19357635 TTTTA TTTTA TTTTA TTTT- TATTTA TTTGA TTATT- TGTTTA TCATTTA
1 TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA TT-TTA T-TTTA T--TTTA
19357683 TTTTA TTTTA TT
1 TTTTA TTTTA TT
19357695 CCTTTATTCT
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
4 1 0.02
5 36 0.78
6 4 0.09
7 5 0.11
ACGTcount: A:0.20, C:0.02, G:0.03, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:19357661 original size:20 final size:22
Alignment explanation
Indices: 19357636--19357694 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 22
19357626 ATTCATTCTT
19357636 TTTATTTTATTTTATTTT-T-A
1 TTTATTTTATTTTATTTTATCA
*
19357656 TTTATTTGATTATT-TGTTTATCA
1 TTTATTTTATT-TTAT-TTTATCA
19357679 TTTATTTTATTTTATT
1 TTTATTTTATTTTATT
19357695 CCTTTATTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
20 11 0.34
21 5 0.16
22 4 0.12
23 12 0.38
ACGTcount: A:0.20, C:0.02, G:0.03, T:0.75
Consensus pattern (22 bp):
TTTATTTTATTTTATTTTATCA
Found at i:19366746 original size:31 final size:31
Alignment explanation
Indices: 19366711--19366815 Score: 115
Period size: 31 Copynumber: 3.4 Consensus size: 31
19366701 AACATTAAAT
*
19366711 TTAATTTAATATTTATCTTGATAATATTTTC
1 TTAATTTAATATTTATCTTGATAATATTTTA
* * * **
19366742 TTAATTTAATATTAAT-GTGA-GATATTAAA
1 TTAATTTAATATTTATCTTGATAATATTTTA
* *
19366771 TGTGATTTAATATTTATCTTGATAGTATTTTA
1 T-TAATTTAATATTTATCTTGATAATATTTTA
19366803 TTAATTTAATATT
1 TTAATTTAATATT
19366816 ATGTGAATAA
Statistics
Matches: 57, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
29 6 0.11
30 16 0.28
31 29 0.51
32 6 0.11
ACGTcount: A:0.35, C:0.03, G:0.08, T:0.54
Consensus pattern (31 bp):
TTAATTTAATATTTATCTTGATAATATTTTA
Found at i:19366782 original size:61 final size:60
Alignment explanation
Indices: 19366704--19366821 Score: 191
Period size: 61 Copynumber: 1.9 Consensus size: 60
19366694 CAAATTTAAC
* *
19366704 ATTAAATTTAATTTAATATTTATCTTGATAATATTTTCTTAATTTAATATTAATGTGAGAT
1 ATTAAATGTAATTTAATATTTATCTTGATAATATTTTATTAATTTAATATT-ATGTGAGAT
* *
19366765 ATTAAATGTGATTTAATATTTATCTTGATAGTATTTTATTAATTTAATATTATGTGA
1 ATTAAATGTAATTTAATATTTATCTTGATAATATTTTATTAATTTAATATTATGTGA
19366822 ATAATTTCAA
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
60 6 0.11
61 47 0.89
ACGTcount: A:0.36, C:0.03, G:0.08, T:0.53
Consensus pattern (60 bp):
ATTAAATGTAATTTAATATTTATCTTGATAATATTTTATTAATTTAATATTATGTGAGAT
Found at i:19369294 original size:274 final size:274
Alignment explanation
Indices: 19368794--19369343 Score: 1010
Period size: 274 Copynumber: 2.0 Consensus size: 274
19368784 TTTTATATGG
* *
19368794 ATTTTACTTATGCAGCCTATACCGTACCGCTAGGCCCAGAGGTCTCCGCACCCCTAGTTACAACC
1 ATTTTACTTATGCAGCCTATACCGTACCGCAAGGCCCAGAGGTCCCCGCACCCCTAGTTACAACC
*
19368859 CTAGTCCAATATTTTGCTTATTATGGATCTAAGATGGACTGTAACCTTTGCCCTCATAGATCCCC
66 CTAGTCCAATATTTTGCTTATTATGGATCTAAGATGGACTGCAACCTTTGCCCTCATAGATCCCC
* *
19368924 TTTCTTGCCTATTGTATTTTATTTTAACATGAATTTGGGTTACACAATTTCTAACATAAACCATA
131 TATCTTGCCTATTGTATTTTATTTTAACAGGAATTTGGGTTACACAATTTCTAACATAAACCATA
* *
19368989 CATTCAACTTAGGAAATTGCATCATAAATCCAAATCAAAAGTATTTCAAAGTCCCAAAATAAGCC
196 CATTAAACTTAGGAAATTGCATCACAAATCCAAATCAAAAGTATTTCAAAGTCCCAAAATAAGCC
*
19369054 AAAACTTTCCAAAT
261 AAAACTTGCCAAAT
*
19369068 ATTTTGCTTATGCAGCCTATACCGTACCGCAAGGCCCAGAGGTCCCCGCACCCCTAGTTACAACC
1 ATTTTACTTATGCAGCCTATACCGTACCGCAAGGCCCAGAGGTCCCCGCACCCCTAGTTACAACC
*
19369133 CTAGTCCAATATTTTGCTTATTATGGATCTACGATGGACTGCAACCTTTGCCCTCATAGATCCCC
66 CTAGTCCAATATTTTGCTTATTATGGATCTAAGATGGACTGCAACCTTTGCCCTCATAGATCCCC
19369198 TATCTTGCCTATTGTATTTTATTTTAACAGGAATTTGGGTTACACAATTTCTAACATAAACCATA
131 TATCTTGCCTATTGTATTTTATTTTAACAGGAATTTGGGTTACACAATTTCTAACATAAACCATA
19369263 CATTAAACTTAGGAAATTGCATCACAAATCCAAATCAAAAGTATTTCAAAGTCCCAAAATAAGCC
196 CATTAAACTTAGGAAATTGCATCACAAATCCAAATCAAAAGTATTTCAAAGTCCCAAAATAAGCC
19369328 AAAACTTGCCAAAT
261 AAAACTTGCCAAAT
19369342 AT
1 AT
19369344 ACTCAACATA
Statistics
Matches: 266, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
274 266 1.00
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.31
Consensus pattern (274 bp):
ATTTTACTTATGCAGCCTATACCGTACCGCAAGGCCCAGAGGTCCCCGCACCCCTAGTTACAACC
CTAGTCCAATATTTTGCTTATTATGGATCTAAGATGGACTGCAACCTTTGCCCTCATAGATCCCC
TATCTTGCCTATTGTATTTTATTTTAACAGGAATTTGGGTTACACAATTTCTAACATAAACCATA
CATTAAACTTAGGAAATTGCATCACAAATCCAAATCAAAAGTATTTCAAAGTCCCAAAATAAGCC
AAAACTTGCCAAAT
Found at i:19371317 original size:17 final size:17
Alignment explanation
Indices: 19371282--19371331 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
19371272 ATACTTCATG
*
19371282 TTAATTTTTTTAAAATT
1 TTAATTTTTTTAAATTT
19371299 TTAATTTTTTTAAATTT
1 TTAATTTTTTTAAATTT
* *
19371316 TTTATAATTTTTAAAT
1 TTAAT-TTTTTTAAAT
19371332 ATTTGATGAC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 20 0.69
18 9 0.31
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTAATTTTTTTAAATTT
Found at i:19372365 original size:19 final size:20
Alignment explanation
Indices: 19372333--19372371 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
19372323 TACTCTTAAA
* *
19372333 AAAGAATTAGAATATAATTT
1 AAAGAATTAAAATAGAATTT
19372353 AAAG-ATTAAAATAGAATTT
1 AAAGAATTAAAATAGAATTT
19372372 TTTTTGTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.33
Consensus pattern (20 bp):
AAAGAATTAAAATAGAATTT
Found at i:19372943 original size:30 final size:30
Alignment explanation
Indices: 19372909--19372971 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
19372899 GCATTTTTCC
*
19372909 TTTCTCATATCA-ACAC-TTTCTTTCTTTCTT
1 TTTCTCAT-TCACACACATGTC-TTCTTTCTT
19372939 TTTCTCATTCACTACACATGTCTTCTTTCTT
1 TTTCTCATTCAC-ACACATGTCTTCTTTCTT
19372970 TT
1 TT
19372972 CCATTTGCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 3 0.10
30 8 0.28
31 15 0.52
32 3 0.10
ACGTcount: A:0.16, C:0.27, G:0.02, T:0.56
Consensus pattern (30 bp):
TTTCTCATTCACACACATGTCTTCTTTCTT
Found at i:19374052 original size:2 final size:2
Alignment explanation
Indices: 19374045--19374074 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
19374035 AATGGAATTC
19374045 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19374075 CATTTAAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19375603 original size:71 final size:72
Alignment explanation
Indices: 19375517--19375661 Score: 283
Period size: 71 Copynumber: 2.0 Consensus size: 72
19375507 CAAGTTAAAA
19375517 AATCATTATTATTAAAATCAAATCAAATTATATTTTTTCATTAATTTATAATTAATTTT-TTTTT
1 AATCATTATTATTAAAATCAAATCAAATTATATTTTTTCATTAATTTATAATTAATTTTATTTTT
19375581 ATGATGT
66 ATGATGT
19375588 AATCATTATTATTAAAATCAAATCAAATTATATTTTTTCATTAATTTATAATTAATTTTATTTTT
1 AATCATTATTATTAAAATCAAATCAAATTATATTTTTTCATTAATTTATAATTAATTTTATTTTT
19375653 ATGATGT
66 ATGATGT
19375660 AA
1 AA
19375662 AAGAAATGTT
Statistics
Matches: 73, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
71 59 0.81
72 14 0.19
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (72 bp):
AATCATTATTATTAAAATCAAATCAAATTATATTTTTTCATTAATTTATAATTAATTTTATTTTT
ATGATGT
Found at i:19379772 original size:14 final size:14
Alignment explanation
Indices: 19379753--19379792 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
19379743 TTGATTGCCA
19379753 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
19379767 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
19379781 GGAAAATGTTTT
1 GTAAAATGTTTT
19379793 ACATTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:19379800 original size:20 final size:20
Alignment explanation
Indices: 19379775--19379814 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
19379765 CCGTAAAATG
*
19379775 ATTTCTGGAAAATGTTTTAC
1 ATTTCTGGAAAATGATTTAC
*
19379795 ATTTCTGTAAAATGATTTAC
1 ATTTCTGGAAAATGATTTAC
19379815 TGGAAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (20 bp):
ATTTCTGGAAAATGATTTAC
Found at i:19379810 original size:34 final size:35
Alignment explanation
Indices: 19379762--19379827 Score: 107
Period size: 34 Copynumber: 1.9 Consensus size: 35
19379752 AGTAAAATGT
*
19379762 TTTCCGTAAAATGATTT-CTGGAAAATGTTTTACA
1 TTTCCGTAAAATGATTTACTGGAAAATATTTTACA
*
19379796 TTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTCCGTAAAATGATTTACTGGAAAATATTTT
19379828 CTGATGTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (35 bp):
TTTCCGTAAAATGATTTACTGGAAAATATTTTACA
Found at i:19380528 original size:47 final size:47
Alignment explanation
Indices: 19380459--19380551 Score: 186
Period size: 47 Copynumber: 2.0 Consensus size: 47
19380449 TGGAGTGAAT
19380459 CCCTTGCGATTAGTGGCTCTCACTGAAACTCCTGATGAAAGCAGAGC
1 CCCTTGCGATTAGTGGCTCTCACTGAAACTCCTGATGAAAGCAGAGC
19380506 CCCTTGCGATTAGTGGCTCTCACTGAAACTCCTGATGAAAGCAGAG
1 CCCTTGCGATTAGTGGCTCTCACTGAAACTCCTGATGAAAGCAGAG
19380552 TTCAGACAAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.26, C:0.27, G:0.24, T:0.24
Consensus pattern (47 bp):
CCCTTGCGATTAGTGGCTCTCACTGAAACTCCTGATGAAAGCAGAGC
Found at i:19387775 original size:20 final size:20
Alignment explanation
Indices: 19387750--19387793 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
19387740 CTAAACTTTT
19387750 AATCCAACACTTTACAATTC
1 AATCCAACACTTTACAATTC
*
19387770 AATCCAACACTTTACAATTG
1 AATCCAACACTTTACAATTC
19387790 AATC
1 AATC
19387794 AAACCCAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.41, C:0.27, G:0.02, T:0.30
Consensus pattern (20 bp):
AATCCAACACTTTACAATTC
Found at i:19387875 original size:17 final size:17
Alignment explanation
Indices: 19387853--19387885 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
19387843 TTTAAATAAA
19387853 TAAATAAATTTCTCAAT
1 TAAATAAATTTCTCAAT
19387870 TAAATAAATTTCTCAA
1 TAAATAAATTTCTCAA
19387886 CCCAATTCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAATAAATTTCTCAAT
Found at i:19389993 original size:21 final size:22
Alignment explanation
Indices: 19389969--19390009 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
19389959 CTATTAATTA
19389969 ATTTATTATTGTT-TTATTACT
1 ATTTATTATTGTTATTATTACT
19389990 ATTTATTATTGTTATTATTA
1 ATTTATTATTGTTATTATTA
19390010 TACTTGATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (22 bp):
ATTTATTATTGTTATTATTACT
Found at i:19395606 original size:21 final size:21
Alignment explanation
Indices: 19395582--19395627 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
19395572 ATTATGTTCA
*
19395582 AAAACGAAAA-GATGAAAAATG
1 AAAACGAAAATGA-AAAAAATG
*
19395603 AAAATGAAAATGAAAAAAATG
1 AAAACGAAAATGAAAAAAATG
19395624 AAAA
1 AAAA
19395628 GTAAAATAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.72, C:0.02, G:0.15, T:0.11
Consensus pattern (21 bp):
AAAACGAAAATGAAAAAAATG
Found at i:19396992 original size:44 final size:44
Alignment explanation
Indices: 19396855--19396993 Score: 113
Period size: 44 Copynumber: 3.2 Consensus size: 44
19396845 AAACGAAACT
* *
19396855 TTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATC
1 TTGCCTTCATCGGTTGCAGTGGAGCTGGTTAAAAATAGCAGATC
* * * * * * * ** * * *
19396899 TTGCCTTCCAGC-ATTAACAGTGAAACAGATCGAAAACA-AAG-CC
1 TTGCCTT-CATCGGTT-GCAGTGGAGCTGGTTAAAAATAGCAGATC
19396942 TTGCCTTCATCGGTTGCAGTGGAGCTGGTTAAAAATAGCAGATC
1 TTGCCTTCATCGGTTGCAGTGGAGCTGGTTAAAAATAGCAGATC
19396986 TTGCCTTC
1 TTGCCTTC
19396994 CTACATTAAC
Statistics
Matches: 64, Mismatches: 26, Indels: 10
0.64 0.26 0.10
Matches are distributed among these distances:
42 17 0.27
43 12 0.19
44 19 0.30
45 16 0.25
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (44 bp):
TTGCCTTCATCGGTTGCAGTGGAGCTGGTTAAAAATAGCAGATC
Found at i:19397441 original size:87 final size:87
Alignment explanation
Indices: 19396855--19397445 Score: 870
Period size: 87 Copynumber: 6.9 Consensus size: 87
19396845 AAACGAAACT
* *
19396855 TTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCAGCATTAACAGT
1 TTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGC
*
19396920 GAAACAGATCGAAAACAAAGCC
66 GAAGCAGATCGAAAACAAAGCC
* * *
19396942 TTGCCTTCATCGGTTGCAGTGGAGCTGGTTAAAAATAGCAGATCTTGCCTTCCTACATTAACAGC
1 TTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGC
19397007 GAAGCAGATCGAAAACAAAGCC
66 GAAGCAGATCGAAAACAAAGCC
*
19397029 TTGCCTCCATCGGTTGCA---GAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTACATTAACAGC
1 TTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGC
*
19397091 AAAGCAGATCGAAAACAAAGCC
66 GAAGCAGATCGAAAACAAAGCC
* * * *
19397113 TTGCCTTCATCGGTT---GTAGAGTTGGTTAAAGATAGCAGATCTTGCCTTCCTGCGTTAACAGC
1 TTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGC
19397175 GAAGCAGATCGAAAACAAAGCC
66 GAAGCAGATCGAAAACAAAGCC
* * *
19397197 TTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGTAGATTTTGCCTTCCTGCGTTAACAGC
1 TTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGC
*
19397262 AAAGCAGATCGAAAACAAAGCC
66 GAAGCAGATCGAAAACAAAGCC
* * * * *
19397284 TTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAACAAATCTTGCCTTCTTGCGTTAACAAC
1 TTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGC
*
19397349 AAAGCAGATCGAAAACAAAGCC
66 GAAGCAGATCGAAAACAAAGCC
* * * * * ** *
19397371 TTGCCTCCATCGGTTGCAGTGAAGCTTGTTAAAGATAACAGATCTTACCCTCCTGCATCGACAGT
1 TTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGC
19397436 GAAGCAGATC
66 GAAGCAGATC
19397446 AAAGATTACA
Statistics
Matches: 460, Mismatches: 38, Indels: 12
0.90 0.07 0.02
Matches are distributed among these distances:
84 154 0.33
87 306 0.67
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (87 bp):
TTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGC
GAAGCAGATCGAAAACAAAGCC
Found at i:19397545 original size:44 final size:44
Alignment explanation
Indices: 19397496--19397704 Score: 142
Period size: 44 Copynumber: 4.8 Consensus size: 44
19397486 GTTGGAAATT
* *
19397496 ACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGTAGACTG-AGAAA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG-AA
** *
19397540 ACAAGTCTTATC-CCCTTGAAGTCACAGTGGGGCAGACTGAAGAA
1 ACAAGTCTTATCTCCC-TGAAGTTGCAGTGGAGCAGACTGAAGAA
* * * * * ***
19397584 GCAAATCTTATCTCCCTGAGGTTGCAGTAGAGCAGATTGAATTCG
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAA-GAA
* * * * *
19397629 ATAA-TCCTATCTCCCTGAAGTTGTAGTGGAGCGGA-TTAA-AA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAA
* * *
19397670 TA-TAGATCTTATCTCTCTGAAGTTGCAGTAGAGCA
1 -ACAAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCA
19397705 TATCGCATCA
Statistics
Matches: 126, Mismatches: 32, Indels: 15
0.73 0.18 0.09
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 30 0.24
44 87 0.69
45 7 0.06
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (44 bp):
ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAA
Found at i:19403278 original size:41 final size:41
Alignment explanation
Indices: 19403229--19403310 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
19403219 ATGCACATAG
19403229 ACAAAAATACTACACTTAGGGCACCAGATCTGACACATTCA
1 ACAAAAATACTACACTTAGGGCACCAGATCTGACACATTCA
19403270 ACAAAAATACTACACTTAGGGCACCAGATCTGACACATTCA
1 ACAAAAATACTACACTTAGGGCACCAGATCTGACACATTCA
19403311 CATATAGTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.41, C:0.27, G:0.12, T:0.20
Consensus pattern (41 bp):
ACAAAAATACTACACTTAGGGCACCAGATCTGACACATTCA
Found at i:19409169 original size:27 final size:26
Alignment explanation
Indices: 19409139--19409197 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 26
19409129 AATTTGGGTT
19409139 ATATTAATGAAA-TATGCCATTTTTTTA
1 ATATTAA-GAAATTA-GCCATTTTTTTA
*
19409166 ATATTTAAGAAATTAGCCCTTTTTTTA
1 ATA-TTAAGAAATTAGCCATTTTTTTA
19409193 ATATT
1 ATATT
19409198 TATTAGTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 2 0.07
27 21 0.72
28 6 0.21
ACGTcount: A:0.36, C:0.08, G:0.07, T:0.49
Consensus pattern (26 bp):
ATATTAAGAAATTAGCCATTTTTTTA
Found at i:19410493 original size:35 final size:35
Alignment explanation
Indices: 19410446--19410537 Score: 105
Period size: 35 Copynumber: 2.6 Consensus size: 35
19410436 ACATGCAATT
* * *
19410446 TTATCTCGGGATTCCCAAGTTCCAGTGTTTAAAAA
1 TTATCTAGGGATTCCCAGGTTCCAGTGTCTAAAAA
** * *
19410481 TTATCCTA-GGATTGTCTGGTTCCAGTGTCTAAAAC
1 TTAT-CTAGGGATTCCCAGGTTCCAGTGTCTAAAAA
19410516 TTATCTAGGGATTCCCAGGTTC
1 TTATCTAGGGATTCCCAGGTTC
19410538 TGACAAGGTC
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
34 3 0.07
35 40 0.89
36 2 0.04
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.36
Consensus pattern (35 bp):
TTATCTAGGGATTCCCAGGTTCCAGTGTCTAAAAA
Found at i:19413069 original size:64 final size:64
Alignment explanation
Indices: 19412962--19413229 Score: 303
Period size: 64 Copynumber: 4.2 Consensus size: 64
19412952 TGCAGGGGTC
* * * *
19412962 ACACAAGCGTGTGTCTAGGCCGTGTAACTCACTGATTATAAAATATGGATCACACAGGCCAAGA
1 ACACGAGCGTGTGTCCAGGCCGTGTAACTCACTGATTACAAAATACGGATCACACAGGCCAAGA
* * * * *
19413026 ACACGGGCGTGTGTCCAGGCTGTGTAACTCACTAATTACAAAATACAGATCACACGGGCCAAGGA
1 ACACGAGCGTGTGTCCAGGCCGTGTAACTCACTGATTACAAAATACGGATCACACAGGCCAA-GA
* ** * *
19413091 TACA-G-GAGTGTGTTTAGGCCATGTAACTCACTGATTAC-AAATACGGATCACACGGGCCAA-A
1 -ACACGAGCGTGTGTCCAGGCCGTGTAACTCACTGATTACAAAATACGGATCACACAGGCCAAGA
** * * *
19413152 GACACGAGCGTGTGTCCAGGTTGTGTAACTCACTGATTACAAAATAAGGATCACACAGGCAAAGG
1 -ACACGAGCGTGTGTCCAGGCCGTGTAACTCACTGATTACAAAATACGGATCACACAGGCCAAGA
19413217 ACAC-AGCGTGTGT
1 ACACGAGCGTGTGT
19413230 TACGCTGTGT
Statistics
Matches: 171, Mismatches: 27, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
61 4 0.02
62 1 0.01
63 57 0.33
64 103 0.60
65 3 0.02
66 3 0.02
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (64 bp):
ACACGAGCGTGTGTCCAGGCCGTGTAACTCACTGATTACAAAATACGGATCACACAGGCCAAGA
Found at i:19413197 original size:127 final size:127
Alignment explanation
Indices: 19412970--19413230 Score: 366
Period size: 127 Copynumber: 2.1 Consensus size: 127
19412960 TCACACAAGC
* * * *
19412970 GTGTGTCTAGGCCGTGTAACTCACTGATTATAAAATATGGATCACACAGGCCAAGAACACGGGCG
1 GTGTGTTTAGGCCATGTAACTCACTGATTATAAAATACGGATCACACAGGCCAAGAACACGAGCG
* * *
19413035 TGTGTCCAGGCTGTGTAACTCACTAATTACAAAATACA-GATCACACGGGCCAAGGATACAGGA
66 TGTGTCCAGGCTGTGTAACTCACTAATTACAAAATA-AGGATCACACAGGCAAAGGACACA-GA
* *
19413098 GTGTGTTTAGGCCATGTAACTCACTGATTA-CAAATACGGATCACACGGGCCAA-AGACACGAGC
1 GTGTGTTTAGGCCATGTAACTCACTGATTATAAAATACGGATCACACAGGCCAAGA-ACACGAGC
* * *
19413161 GTGTGTCCAGGTTGTGTAACTCACTGATTACAAAATAAGGATCACACAGGCAAAGGACACAGC
65 GTGTGTCCAGGCTGTGTAACTCACTAATTACAAAATAAGGATCACACAGGCAAAGGACACAGA
19413224 GTGTGTT
1 GTGTGTT
19413231 ACGCTGTGTA
Statistics
Matches: 119, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
126 10 0.08
127 81 0.68
128 28 0.24
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.22
Consensus pattern (127 bp):
GTGTGTTTAGGCCATGTAACTCACTGATTATAAAATACGGATCACACAGGCCAAGAACACGAGCG
TGTGTCCAGGCTGTGTAACTCACTAATTACAAAATAAGGATCACACAGGCAAAGGACACAGA
Found at i:19414651 original size:23 final size:23
Alignment explanation
Indices: 19414621--19414711 Score: 146
Period size: 23 Copynumber: 4.0 Consensus size: 23
19414611 GTGTTATTAA
*
19414621 TCAGTGGTAGCTTCGGCTACGTT
1 TCAGTGGTAGCTTCGGCTACATT
*
19414644 TCAGTGGTAGCTTCGGCTACATA
1 TCAGTGGTAGCTTCGGCTACATT
*
19414667 ACAGTGGTAGCTTCGGCTACATT
1 TCAGTGGTAGCTTCGGCTACATT
*
19414690 TTAGTGGTAGCTTCGGCTACAT
1 TCAGTGGTAGCTTCGGCTACAT
19414712 AACAGTGTTG
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 62 1.00
ACGTcount: A:0.19, C:0.21, G:0.27, T:0.33
Consensus pattern (23 bp):
TCAGTGGTAGCTTCGGCTACATT
Found at i:19414675 original size:46 final size:46
Alignment explanation
Indices: 19414622--19414718 Score: 176
Period size: 46 Copynumber: 2.1 Consensus size: 46
19414612 TGTTATTAAT
*
19414622 CAGTGGTAGCTTCGGCTACGTTTCAGTGGTAGCTTCGGCTACATAA
1 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGGCTACATAA
*
19414668 CAGTGGTAGCTTCGGCTACATTTTAGTGGTAGCTTCGGCTACATAA
1 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGGCTACATAA
19414714 CAGTG
1 CAGTG
19414719 TTGCACTTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.31
Consensus pattern (46 bp):
CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGGCTACATAA
Found at i:19421749 original size:27 final size:27
Alignment explanation
Indices: 19421719--19421798 Score: 106
Period size: 27 Copynumber: 3.0 Consensus size: 27
19421709 GGAACTGATT
*
19421719 CTTCAGAGTTCGCCATACGTACTATTC
1 CTTCAGAGTTCACCATACGTACTATTC
*
19421746 CTTCAGAGTTCATCATACGTACTATTC
1 CTTCAGAGTTCACCATACGTACTATTC
* * **
19421773 CTTTAGATTTTTCCATACGTACTATT
1 CTTCAGAGTTCACCATACGTACTATT
19421799 TGTTCAAATT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.24, C:0.25, G:0.11, T:0.40
Consensus pattern (27 bp):
CTTCAGAGTTCACCATACGTACTATTC
Found at i:19421809 original size:27 final size:27
Alignment explanation
Indices: 19421731--19421826 Score: 77
Period size: 27 Copynumber: 3.6 Consensus size: 27
19421721 TCAGAGTTCG
* * **
19421731 CCATACGTACTATTCCTTCAGAGTTCAT
1 CCATACGTACTATTTCTTCA-AATTTTT
* * *
19421759 -CATACGTACTATTCCTTTAGATTTTT
1 CCATACGTACTATTTCTTCAAATTTTT
*
19421785 CCATACGTACTATTTGTTCAAATTTTT
1 CCATACGTACTATTTCTTCAAATTTTT
* * *
19421812 TCATACTTACCATTT
1 CCATACGTACTATTT
19421827 TTAGAGTTAG
Statistics
Matches: 55, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
26 3 0.05
27 52 0.95
ACGTcount: A:0.25, C:0.23, G:0.07, T:0.45
Consensus pattern (27 bp):
CCATACGTACTATTTCTTCAAATTTTT
Found at i:19421999 original size:27 final size:28
Alignment explanation
Indices: 19421955--19422022 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 28
19421945 AGGCGCCATG
*
19421955 AAGGCGTTCC-TTTCCATAGATCGTCACA
1 AAGGC-TTCCATTTCCATAGATCGCCACA
* *
19421983 AAGGTTTCCATTT-CATAGATTGCCACA
1 AAGGCTTCCATTTCCATAGATCGCCACA
19422010 AAGGCTTCCATTT
1 AAGGCTTCCATTT
19422023 TATGGTGTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 28 0.80
28 7 0.20
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.32
Consensus pattern (28 bp):
AAGGCTTCCATTTCCATAGATCGCCACA
Found at i:19424729 original size:10 final size:10
Alignment explanation
Indices: 19424714--19424739 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
19424704 TTTAATATTT
19424714 TATTTTTAAA
1 TATTTTTAAA
19424724 TATTTTTAAA
1 TATTTTTAAA
19424734 TATTTT
1 TATTTT
19424740 ATAAGTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TATTTTTAAA
Found at i:19425470 original size:2 final size:2
Alignment explanation
Indices: 19425463--19425489 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19425453 TCCTCCCTGT
19425463 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 T
19425490 CCGTGAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19429916 original size:21 final size:21
Alignment explanation
Indices: 19429892--19429933 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
19429882 TTCTTAGTTA
19429892 AATTACTTAGTTAATTTTTAG
1 AATTACTTAGTTAATTTTTAG
19429913 AATTACTTAGTTAATTTTTAG
1 AATTACTTAGTTAATTTTTAG
19429934 TTTTTAAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.52
Consensus pattern (21 bp):
AATTACTTAGTTAATTTTTAG
Found at i:19436209 original size:22 final size:24
Alignment explanation
Indices: 19436184--19436227 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
19436174 AATTTGTTCA
19436184 ACTTTAACTT-TTAT-TCAAAAAC
1 ACTTTAACTTGTTATATCAAAAAC
*
19436206 ACTTTAATTTGTTATATCAAAA
1 ACTTTAACTTGTTATATCAAAA
19436228 CATATTATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.43
Consensus pattern (24 bp):
ACTTTAACTTGTTATATCAAAAAC
Found at i:19438840 original size:20 final size:20
Alignment explanation
Indices: 19438811--19438848 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
19438801 GAACCAGATG
*
19438811 AAATGGTAGATAAAACTACA
1 AAATGATAGATAAAACTACA
*
19438831 AAATGATAGATCAAACTA
1 AAATGATAGATAAAACTA
19438849 TACGCCAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.11, G:0.13, T:0.21
Consensus pattern (20 bp):
AAATGATAGATAAAACTACA
Found at i:19442663 original size:19 final size:20
Alignment explanation
Indices: 19442633--19442675 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
19442623 GCTATAGGTA
19442633 TAATATCTGTTCCGACCAGG
1 TAATATCTGTTCCGACCAGG
* *
19442653 TAATA-CTGTTCTGACTAGG
1 TAATATCTGTTCCGACCAGG
19442672 TAAT
1 TAAT
19442676 TCGAAGATGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (20 bp):
TAATATCTGTTCCGACCAGG
Found at i:19443923 original size:22 final size:22
Alignment explanation
Indices: 19443881--19443924 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
19443871 CCCATGTTTC
*
19443881 TTTTAATTTATTTAATTTTGAA
1 TTTTAATTTATTTAATGTTGAA
*
19443903 TTTTAGTTTAATTTAA-GTTGAA
1 TTTTAATTT-ATTTAATGTTGAA
19443925 AATAAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (22 bp):
TTTTAATTTATTTAATGTTGAA
Found at i:19444645 original size:15 final size:15
Alignment explanation
Indices: 19444625--19444665 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
19444615 CAAAACCCAT
19444625 AACACCAACCTTCAA
1 AACACCAACCTTCAA
*
19444640 AACACCAAAC--CAA
1 AACACCAACCTTCAA
*
19444653 AACACCCACCTTC
1 AACACCAACCTTC
19444666 CTCCATAAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
13 11 0.52
15 10 0.48
ACGTcount: A:0.46, C:0.44, G:0.00, T:0.10
Consensus pattern (15 bp):
AACACCAACCTTCAA
Found at i:19446801 original size:40 final size:40
Alignment explanation
Indices: 19446757--19446842 Score: 154
Period size: 40 Copynumber: 2.1 Consensus size: 40
19446747 TGCTACTTCA
*
19446757 AAAAGTCATATTTAAGGTTTGATCAGATTTTTGACTTTGT
1 AAAAGTCATATTTAAGGTTTGATCAGATTTTTGACTTCGT
*
19446797 AAAAGACATATTTAAGGTTTGATCAGATTTTTGACTTCGT
1 AAAAGTCATATTTAAGGTTTGATCAGATTTTTGACTTCGT
19446837 AAAAGT
1 AAAAGT
19446843 TTTATTTAGA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.41
Consensus pattern (40 bp):
AAAAGTCATATTTAAGGTTTGATCAGATTTTTGACTTCGT
Found at i:19451827 original size:124 final size:125
Alignment explanation
Indices: 19451602--19451850 Score: 482
Period size: 124 Copynumber: 2.0 Consensus size: 125
19451592 AGGTAAATTT
19451602 AGTAATAGTTTAATGGCATTGGATATAGTTTATCCTTAAATTAAAAAATCAATTATATTTTAAAA
1 AGTAATAGTTTAATGGCATTGGATATAGTTTATCCTTAAATTAAAAAATCAATTATATTTTAAAA
*
19451667 ATAATAAAATACTGAAATTTATATTTATTATTTAATTATTATATGTCAA-TAATAACTAG
66 ATAATAAAATACTGAAATTTATATTTATTATATAATTATTATATGTCAAGTAATAACTAG
19451726 AGTAATAGTTTAATGGCATTGGATATAGTTTATCCTTAAATTAAAAAATCAATTATATTTTAAAA
1 AGTAATAGTTTAATGGCATTGGATATAGTTTATCCTTAAATTAAAAAATCAATTATATTTTAAAA
19451791 ATAATAAAATACTGAAATTTATATTTATTATATAATTATTATATGTCAAGTAATAACTAG
66 ATAATAAAATACTGAAATTTATATTTATTATATAATTATTATATGTCAAGTAATAACTAG
19451851 TTATTTTAAA
Statistics
Matches: 123, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
124 113 0.92
125 10 0.08
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (125 bp):
AGTAATAGTTTAATGGCATTGGATATAGTTTATCCTTAAATTAAAAAATCAATTATATTTTAAAA
ATAATAAAATACTGAAATTTATATTTATTATATAATTATTATATGTCAAGTAATAACTAG
Found at i:19453534 original size:12 final size:12
Alignment explanation
Indices: 19453504--19453536 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
19453494 TATATATTTT
19453504 AAAATT-ATATA
1 AAAATTAATATA
19453515 AAAA-TAATATA
1 AAAATTAATATA
19453526 AAAATTAATAT
1 AAAATTAATAT
19453537 GGGCGGGCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:19462760 original size:18 final size:19
Alignment explanation
Indices: 19462718--19462768 Score: 77
Period size: 18 Copynumber: 2.7 Consensus size: 19
19462708 ATTTCATTTC
*
19462718 TCATTTCATCATTTCATATT
1 TCATTTC-TCATCTCATATT
19462738 TCATTTCTCATCTCATA-T
1 TCATTTCTCATCTCATATT
19462756 TCATTTCTCATCT
1 TCATTTCTCATCT
19462769 TTGCCATCTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 14 0.47
19 9 0.30
20 7 0.23
ACGTcount: A:0.22, C:0.25, G:0.00, T:0.53
Consensus pattern (19 bp):
TCATTTCTCATCTCATATT
Found at i:19467467 original size:11 final size:11
Alignment explanation
Indices: 19467453--19467478 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
19467443 ATTTATCAGC
19467453 TATTATTATTT
1 TATTATTATTT
19467464 TATTATTATTT
1 TATTATTATTT
19467475 TATT
1 TATT
19467479 CCAAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TATTATTATTT
Found at i:19471978 original size:22 final size:22
Alignment explanation
Indices: 19471953--19471994 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
19471943 TATTTTCTTC
19471953 CTTA-TTATTCTATTTTAATTAT
1 CTTAGTTATT-TATTTTAATTAT
19471975 CTTAGTTATTTATTTTAATT
1 CTTAGTTATTTATTTTAATT
19471995 GTTTTATCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.64
Consensus pattern (22 bp):
CTTAGTTATTTATTTTAATTAT
Found at i:19473836 original size:5 final size:5
Alignment explanation
Indices: 19473826--19473850 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
19473816 CGAAAATTGA
19473826 TTAAT TTAAT TTAAT TTAAT TTAAT
1 TTAAT TTAAT TTAAT TTAAT TTAAT
19473851 AAATAATGTC
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTAAT
Found at i:19510278 original size:34 final size:34
Alignment explanation
Indices: 19510233--19510346 Score: 94
Period size: 34 Copynumber: 3.4 Consensus size: 34
19510223 TAGTTGAGTT
19510233 ATGGCAACATATGAAGTCCGTTAGGACAATAAAC
1 ATGGCAACATATGAAGTCCGTTAGGACAATAAAC
* * **
19510267 ATGGCATCATAT-AA-T--G-TAAGACCATAGCTGGAC
1 ATGGCAACATATGAAGTCCGTTAGGA-CA-A--TAAAC
*
19510300 TATGGCAACATATGAAGTCCGTCAGGACAATAAAC
1 -ATGGCAACATATGAAGTCCGTTAGGACAATAAAC
*
19510335 ATGGCATCATAT
1 ATGGCAACATAT
19510347 TATGTAAGAC
Statistics
Matches: 60, Mismatches: 10, Indels: 20
0.67 0.11 0.22
Matches are distributed among these distances:
29 4 0.07
30 3 0.05
31 1 0.02
32 1 0.02
33 5 0.08
34 33 0.55
35 5 0.08
36 1 0.02
37 1 0.02
38 3 0.05
39 3 0.05
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (34 bp):
ATGGCAACATATGAAGTCCGTTAGGACAATAAAC
Found at i:19510327 original size:68 final size:68
Alignment explanation
Indices: 19510211--19510665 Score: 502
Period size: 68 Copynumber: 6.7 Consensus size: 68
19510201 AGTCTATAAG
* * * * ** *
19510211 AGTGTAAGACTATAGTTGAGTTATGGCAACATATGAAGTCCGTTAGGACAATAAACATGGCATCA
1 AGTGTAAGACCATAGCTGGGCTATGGCAACATATGAAGTCCGCCAGGACAATAAACATGACATCA
19510276 TAT
66 TAT
* * * *
19510279 AATGTAAGACCATAGCTGGACTATGGCAACATATGAAGTCCGTCAGGACAATAAACATGGCATCA
1 AGTGTAAGACCATAGCTGGGCTATGGCAACATATGAAGTCCGCCAGGACAATAAACATGACATCA
19510344 TATT
66 TA-T
* * * * *
19510348 A-TGTAAGACCATAGTTGGGCTATGGCAACATATGAAATTCGCCAGGATAATAAACATGACACCA
1 AGTGTAAGACCATAGCTGGGCTATGGCAACATATGAAGTCCGCCAGGACAATAAACATGACATCA
19510412 TAT
66 TAT
* * * * **
19510415 AGTGTAAGACCATAGCTGGGCTATGGCAATATATGAAGTCCGCCAGGACCATTAATATGGTATCA
1 AGTGTAAGACCATAGCTGGGCTATGGCAACATATGAAGTCCGCCAGGACAATAAACATGACATCA
19510480 TAT
66 TAT
* * * * * * *
19510483 AGTGTAAGACTATAGTTGGGTTAT-GCTAGCATATGAAGTCCACCAAGATAATAAACATGACATC
1 AGTGTAAGACCATAGCTGGGCTATGGC-AACATATGAAGTCCGCCAGGACAATAAACATGACATC
*
19510547 AAAT
65 ATAT
* * *
19510551 AGTGTAAGACCATAGCTGGGCTATGGAAACATCTGAAGTCCGCTAGGACAATAAACATGACATCA
1 AGTGTAAGACCATAGCTGGGCTATGGCAACATATGAAGTCCGCCAGGACAATAAACATGACATCA
*
19510616 TGT
66 TAT
* * * * * **
19510619 AGT-TAAGATCATAGTTAGGCTATTGCAATATATGAAGTTTGCCAGGA
1 AGTGTAAGACCATAGCTGGGCTATGGCAACATATGAAGTCCGCCAGGA
19510666 TGGTAAACAT
Statistics
Matches: 321, Mismatches: 62, Indels: 9
0.82 0.16 0.02
Matches are distributed among these distances:
67 38 0.12
68 280 0.87
69 3 0.01
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (68 bp):
AGTGTAAGACCATAGCTGGGCTATGGCAACATATGAAGTCCGCCAGGACAATAAACATGACATCA
TAT
Found at i:19515529 original size:14 final size:14
Alignment explanation
Indices: 19515510--19515549 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
19515500 TTGATTGCCA
19515510 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
19515524 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
19515538 GTAAAATGTTTT
1 GTAAAATGTTTT
19515550 ACTTTTCTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:19515556 original size:34 final size:35
Alignment explanation
Indices: 19515518--19515584 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
19515508 CAGTAAAATG
* *
19515518 TTTTCCGTAAAATGATTT-CTGTAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
19515552 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
19515585 CTAGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:19515558 original size:20 final size:20
Alignment explanation
Indices: 19515533--19515572 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
19515523 CGTAAAATGA
*
19515533 TTTCTGTAAAATGTTTTACT
1 TTTCTGTAAAATGATTTACT
19515553 TTTCTGTAAAATGATTTACT
1 TTTCTGTAAAATGATTTACT
19515573 GGAAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.53
Consensus pattern (20 bp):
TTTCTGTAAAATGATTTACT
Found at i:19518010 original size:12 final size:12
Alignment explanation
Indices: 19517993--19518020 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
19517983 CTAAAATAAG
19517993 ATAAAATAACAT
1 ATAAAATAACAT
19518005 ATAAAATAACAT
1 ATAAAATAACAT
19518017 ATAA
1 ATAA
19518021 CATAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (12 bp):
ATAAAATAACAT
Found at i:19519825 original size:7 final size:7
Alignment explanation
Indices: 19519815--19519844 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
19519805 TTCTTTTCGA
19519815 TTTTTAT
1 TTTTTAT
19519822 TTTTTAT
1 TTTTTAT
19519829 TTTTATAT
1 TTTT-TAT
19519837 TTTTTAT
1 TTTTTAT
19519844 T
1 T
19519845 AATTTGATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTTAT
Found at i:19519841 original size:15 final size:14
Alignment explanation
Indices: 19519815--19519844 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
19519805 TTCTTTTCGA
19519815 TTTTTATTTTTTAT
1 TTTTTATTTTTTAT
19519829 TTTTATATTTTTTAT
1 TTTT-TATTTTTTAT
19519844 T
1 T
19519845 AATTTGATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTATTTTTTAT
Found at i:19520328 original size:8 final size:8
Alignment explanation
Indices: 19520315--19520350 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
19520305 AAATTAATTC
19520315 AAAAAAAT
1 AAAAAAAT
19520323 AAAAAAAT
1 AAAAAAAT
19520331 AAAGAAAAT
1 AAA-AAAAT
*
19520340 TAAAAAAT
1 AAAAAAAT
19520348 AAA
1 AAA
19520351 TTGGTTTTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 18 0.72
9 7 0.28
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (8 bp):
AAAAAAAT
Found at i:19520344 original size:17 final size:17
Alignment explanation
Indices: 19520318--19520350 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
19520308 TTAATTCAAA
19520318 AAAATAAAAAAATAAAG
1 AAAATAAAAAAATAAAG
*
19520335 AAAATTAAAAAATAAA
1 AAAATAAAAAAATAAA
19520351 TTGGTTTTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (17 bp):
AAAATAAAAAAATAAAG
Found at i:19520450 original size:18 final size:18
Alignment explanation
Indices: 19520429--19520464 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
19520419 ATTAGTTCTA
19520429 AAAAAGAGAAAAAAAATT
1 AAAAAGAGAAAAAAAATT
*
19520447 AAAAAGATAAAAAAAATT
1 AAAAAGAGAAAAAAAATT
19520465 TCCCTTTTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (18 bp):
AAAAAGAGAAAAAAAATT
Found at i:19523781 original size:30 final size:30
Alignment explanation
Indices: 19523741--19523810 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
19523731 TAGACTTTTT
19523741 AAAT-ATAAAATTGTACA-TTAATCTCTTAA
1 AAATGATAAAATTGTA-ATTTAATCTCTTAA
* * *
19523770 ATATGATAAAATTTTAATTTAATCTTTTAA
1 AAATGATAAAATTGTAATTTAATCTCTTAA
*
19523800 AAATTATAAAA
1 AAATGATAAAA
19523811 ATATTAACTA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 4 0.12
30 30 0.88
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (30 bp):
AAATGATAAAATTGTAATTTAATCTCTTAA
Found at i:19525746 original size:19 final size:20
Alignment explanation
Indices: 19525722--19525771 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
19525712 ACATAAAAAA
19525722 AATAAAATGTAATATAA-AT-
1 AATAAAAT-TAATATAACATG
19525741 AATAAAATTAATATAACATG
1 AATAAAATTAATATAACATG
19525761 AAT-AAATTAAT
1 AATAAAATTAAT
19525772 TTCAATAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.28
19 18 0.62
20 3 0.10
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (20 bp):
AATAAAATTAATATAACATG
Found at i:19529289 original size:196 final size:194
Alignment explanation
Indices: 19528878--19529498 Score: 753
Period size: 196 Copynumber: 3.2 Consensus size: 194
19528868 ATGACAAGAA
19528878 AAAAGTTGAGGTACCAAATTATGTCAAAAATTAAAGTATAAAGATTAAATTTCAAAATTGAGCAT
1 AAAAGTTGAGGTACCAAATTATGTCAAAAATTAAAGTATAAAGATTAAATTTCAAAATTGAGCAT
* *
19528943 ATCATAGGCACCAAATTTG-AATTTGACCAATGTTATATGTAATCTTAAAAAAGAAGTAAAAGGT
66 ATCATAGG-ACCAAATTTGAAATTTGACCATTG-T-TATGTAATCTCAAAAAAGAAGTAAAA-GT
* * * *
19529007 CGTGTATTTGGACACGTGTACATCAACATTTTAATCAAAACGAAGCATTTAG-GATGACTATGAC
127 CGTGTATTTGGACA-GTGTACGTCAACATTTTAATCAGAATGAAGTATTTAGTG-TGACTATGAC
*
19529071 ATTAT
190 ATAAT
* *
19529076 AAAAGTTGAGGTACCAAAATATGTCAAAAATTAAAGTATACAGATTAAATTTCAAAATTGAGCAT
1 AAAAGTTGAGGTACCAAATTATGTCAAAAATTAAAGTATAAAGATTAAATTTCAAAATTGAGCAT
* *
19529141 ATCATAGGACCAAATTTGAAATTTGACTATTGTTATGTAATCTCAAAAAAGAAGTAAAATGTCAT
66 ATCATAGGACCAAATTTGAAATTTGACCATTGTTATGTAATCTCAAAAAAGAAGTAAAA-GTCGT
* *
19529206 GTATTTGGACATGTGTATGTCAACATTTTAA-CTAGAATGAAGTATTTAGTGTGACTATGACGTA
130 GTATTTGGACA-GTGTACGTCAACATTTTAATC-AGAATGAAGTATTTAGTGTGACTATGACATA
19529270 AT
193 AT
* ** * * * *
19529272 AAAAGTTGAGGTACCAAATTATATCAAAACGTAAAGTATAGAGATTAAGTTTCATATTTGAGCAT
1 AAAAGTTGAGGTACCAAATTATGTCAAAAATTAAAGTATAAAGATTAAATTTCAAAATTGAGCAT
* * * * *
19529337 AAT-ATACGAACCAACA-TTAAAATTTGACCATTATTATATAATCTC---AAAGAAGTAAAAGTT
66 -ATCATA-GGACCAA-ATTTGAAATTTGACCATTGTTATGTAATCTCAAAAAAGAAGTAAAAGTC
* * *
19529397 GTATATTTGGGTACA-TGTACGTCAACATTTTAATCAGAATGAAATATTTAGAT-T-AGCAATGA
128 GTGTATTT-GG-ACAGTGTACGTCAACATTTTAATCAGAATGAAGTATTTAG-TGTGA-CTATGA
*
19529459 CATTAT
189 CATAAT
19529465 AAAAGTTGAGGTACCAAATTATGTC-AAAATTAAA
1 AAAAGTTGAGGTACCAAATTATGTCAAAAATTAAA
19529499 TCCAAAACTT
Statistics
Matches: 373, Mismatches: 39, Indels: 28
0.85 0.09 0.06
Matches are distributed among these distances:
192 8 0.02
193 74 0.20
194 16 0.04
195 4 0.01
196 143 0.38
197 45 0.12
198 83 0.22
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.32
Consensus pattern (194 bp):
AAAAGTTGAGGTACCAAATTATGTCAAAAATTAAAGTATAAAGATTAAATTTCAAAATTGAGCAT
ATCATAGGACCAAATTTGAAATTTGACCATTGTTATGTAATCTCAAAAAAGAAGTAAAAGTCGTG
TATTTGGACAGTGTACGTCAACATTTTAATCAGAATGAAGTATTTAGTGTGACTATGACATAAT
Found at i:19531938 original size:18 final size:18
Alignment explanation
Indices: 19531915--19531951 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
19531905 AAAAATTGTT
19531915 GAGAGTACCATCAAATGA
1 GAGAGTACCATCAAATGA
*
19531933 GAGAGTGCCATCAAATGA
1 GAGAGTACCATCAAATGA
19531951 G
1 G
19531952 GATACTGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.16, G:0.27, T:0.16
Consensus pattern (18 bp):
GAGAGTACCATCAAATGA
Found at i:19542213 original size:41 final size:42
Alignment explanation
Indices: 19542134--19542232 Score: 146
Period size: 41 Copynumber: 2.4 Consensus size: 42
19542124 TGCAGTTTCT
* *
19542134 CCACAGCTCGTATGAGCAACATCGTGTAGCTAACATCCTGAC
1 CCACAGCTCGTGTGAGCAACATCGTATAGCTAACATCCTGAC
* * *
19542176 CCATAGCTCGTGTGAGCAGCAT-GTATAGCTAACATCCTGAT
1 CCACAGCTCGTGTGAGCAACATCGTATAGCTAACATCCTGAC
19542217 CCACAGCTCGTGTGAG
1 CCACAGCTCGTGTGAG
19542233 AAGACCTATT
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 32 0.63
42 19 0.37
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.23
Consensus pattern (42 bp):
CCACAGCTCGTGTGAGCAACATCGTATAGCTAACATCCTGAC
Found at i:19544780 original size:19 final size:20
Alignment explanation
Indices: 19544758--19544803 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
19544748 TTAATTTAAG
*
19544758 TAATTTAGTTTAATT-ACCT
1 TAATTTAGCTTAATTAACCT
* *
19544777 TAATTTCGCTTAATTAACTT
1 TAATTTAGCTTAATTAACCT
19544797 TAATTTA
1 TAATTTA
19544804 TTTTTTAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.33, C:0.11, G:0.04, T:0.52
Consensus pattern (20 bp):
TAATTTAGCTTAATTAACCT
Found at i:19552508 original size:45 final size:45
Alignment explanation
Indices: 19552433--19552604 Score: 204
Period size: 45 Copynumber: 3.8 Consensus size: 45
19552423 TACACGATGG
* * * * * *
19552433 ATCAACACATAGC-ACCACCCTTATAGTCAATGATACTCAGTGGA
1 ATCAACACACAACAACCACCTTTATAATCAATGATACCCGGTGGA
* * * * *
19552477 ATCAGCACATAGCAACCACCTTCATAATCAAT-AGCACCCGGTGGA
1 ATCAACACACAACAACCACCTTTATAATCAATGA-TACCCGGTGGA
19552522 ATCAACACACAACAACCACCTTTATAATCAATGATACCCGGTGGA
1 ATCAACACACAACAACCACCTTTATAATCAATGATACCCGGTGGA
* *
19552567 ATCAGCACACAACAACCACCTTTATAATCAATGGTACC
1 ATCAACACACAACAACCACCTTTATAATCAATGATACC
19552605 TGGTACACAT
Statistics
Matches: 111, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
44 13 0.12
45 97 0.87
46 1 0.01
ACGTcount: A:0.38, C:0.30, G:0.12, T:0.20
Consensus pattern (45 bp):
ATCAACACACAACAACCACCTTTATAATCAATGATACCCGGTGGA
Found at i:19560252 original size:19 final size:19
Alignment explanation
Indices: 19560228--19560275 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
19560218 AAAAAATATA
19560228 TATATTTTTCATAATTTTC
1 TATATTTTTCATAATTTTC
** *
19560247 TATATTTTTTGTAATTTTT
1 TATATTTTTCATAATTTTC
19560266 TATCATTTTT
1 TAT-ATTTTT
19560276 ATATTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 19 0.76
20 6 0.24
ACGTcount: A:0.23, C:0.06, G:0.02, T:0.69
Consensus pattern (19 bp):
TATATTTTTCATAATTTTC
Found at i:19560255 original size:10 final size:10
Alignment explanation
Indices: 19560228--19560299 Score: 53
Period size: 10 Copynumber: 7.4 Consensus size: 10
19560218 AAAAAATATA
19560228 TATATTTTTC
1 TATATTTTTC
*
19560238 -ATAATTTTC
1 TATATTTTTC
19560247 TATATTTTT-
1 TATATTTTTC
*
19560256 TGTAATTTTT-
1 TAT-ATTTTTC
*
19560266 TATCATTTTTA
1 TAT-ATTTTTC
*
19560277 TAT-TTTTTT
1 TATATTTTTC
*
19560286 TATAATTTTC
1 TATATTTTTC
19560296 TATA
1 TATA
19560300 GTTTCTTTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
9 18 0.36
10 29 0.58
11 3 0.06
ACGTcount: A:0.25, C:0.06, G:0.01, T:0.68
Consensus pattern (10 bp):
TATATTTTTC
Found at i:19560275 original size:11 final size:10
Alignment explanation
Indices: 19560226--19560314 Score: 51
Period size: 10 Copynumber: 8.8 Consensus size: 10
19560216 TTAAAAAATA
19560226 TATATATTTTT
1 TATAT-TTTTT
* * *
19560237 CATAATTTTC
1 TATATTTTTT
19560247 TATATTTTTT
1 TATATTTTTT
19560257 GTA-A-TTTTT
1 -TATATTTTTT
*
19560266 TATCATTTTTA
1 TAT-ATTTTTT
19560277 TAT-TTTTTT
1 TATATTTTTT
* *
19560286 TATAATTTTC
1 TATATTTTTT
19560296 TATAGTTTCTTT
1 TATA-TTT-TTT
19560308 TA-ATTTT
1 TATATTTT
19560315 CTATAATTAT
Statistics
Matches: 59, Mismatches: 12, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
8 2 0.03
9 14 0.24
10 24 0.41
11 15 0.25
12 4 0.07
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.69
Consensus pattern (10 bp):
TATATTTTTT
Found at i:19560284 original size:20 final size:22
Alignment explanation
Indices: 19560261--19560319 Score: 72
Period size: 20 Copynumber: 2.9 Consensus size: 22
19560251 TTTTTTGTAA
*
19560261 TTTTTTATCATTTT-TATA-TT
1 TTTTTTATAATTTTCTATAGTT
19560281 TTTTTTATAATTTTCTATAG-T
1 TTTTTTATAATTTTCTATAGTT
*
19560302 TTCTTT-TAATTTTCTATA
1 TTTTTTATAATTTTCTATA
19560320 ATTATTTGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 25 0.71
21 10 0.29
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTTTTATAATTTTCTATAGTT
Found at i:19560453 original size:27 final size:27
Alignment explanation
Indices: 19560387--19560460 Score: 80
Period size: 27 Copynumber: 2.7 Consensus size: 27
19560377 AGTTTTTCTG
* *
19560387 ATTTTTTATTAATTTTTAT-ATTTATA
1 ATTTTCTATTAATTTTTATAATGTATA
*
19560413 ATTTTCTAAATAATTTTTATAATGGTAT-
1 ATTTTCT-ATTAATTTTTATAAT-GTATA
*
19560441 GTTTTCTATTAATTTTTATA
1 ATTTTCTATTAATTTTTATA
19560461 TATTTTTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
26 6 0.15
27 23 0.57
28 8 0.20
29 3 0.08
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.62
Consensus pattern (27 bp):
ATTTTCTATTAATTTTTATAATGTATA
Found at i:19561992 original size:22 final size:21
Alignment explanation
Indices: 19561948--19562000 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
19561938 TATTTATAAA
*
19561948 TTTTTTAT-AATTTTGTATGT
1 TTTTTTATAAATTTTGTATAT
*
19561968 TTTTTTATAGAATTTTGTGTAT
1 TTTTTTATA-AATTTTGTATAT
*
19561990 TTTTATATAAA
1 TTTTTTATAAA
19562001 AAAAGCTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 8 0.29
21 2 0.07
22 18 0.64
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.64
Consensus pattern (21 bp):
TTTTTTATAAATTTTGTATAT
Found at i:19574455 original size:27 final size:26
Alignment explanation
Indices: 19574425--19574478 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
19574415 CTCTTTCGAG
*
19574425 TTAATAAATTCTCTTTGAGCTTTCTTT
1 TTAAGAAATTCTC-TTGAGCTTTCTTT
* * *
19574452 TTAAGAATTTTTCTTGAGTTTTCTTT
1 TTAAGAAATTCTCTTGAGCTTTCTTT
19574478 T
1 T
19574479 AGAATAGTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.20, C:0.11, G:0.09, T:0.59
Consensus pattern (26 bp):
TTAAGAAATTCTCTTGAGCTTTCTTT
Found at i:19575412 original size:10 final size:10
Alignment explanation
Indices: 19575394--19575429 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
19575384 ATAAGAAGTC
19575394 TAAAGAATATA
1 TAAA-AATATA
19575405 TAAAAATATA
1 TAAAAATATA
19575415 TAAAAATATA
1 TAAAAATATA
19575425 -AAAAA
1 TAAAAA
19575430 CCCCAAACTC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 5 0.20
10 16 0.64
11 4 0.16
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (10 bp):
TAAAAATATA
Found at i:19577534 original size:20 final size:20
Alignment explanation
Indices: 19577480--19577535 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
19577470 TGAAAAAATC
** *
19577480 AAAGTATCGATACCCTTAGT
1 AAAGTATCGATACTTTTAAT
* * *
19577500 TAAGTATTGACACTTTTAAT
1 AAAGTATCGATACTTTTAAT
19577520 AAAGTATCGATACTTT
1 AAAGTATCGATACTTT
19577536 ATCAGGGTAT
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (20 bp):
AAAGTATCGATACTTTTAAT
Found at i:19578417 original size:28 final size:28
Alignment explanation
Indices: 19578369--19578442 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 28
19578359 ATACAGAGGG
* *
19578369 CACCGAAGTGGATTAACAGAATAGAACAA
1 CACCGAAGT-GCTTATCAGAATAGAACAA
*
19578398 CACC-AATGTGCTTATCAGAATAGAGCAA
1 CACCGAA-GTGCTTATCAGAATAGAACAA
19578426 CACCGAAGTGCTTATCA
1 CACCGAAGTGCTTATCA
19578443 AAACAGAGAG
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
28 32 0.80
29 8 0.20
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.19
Consensus pattern (28 bp):
CACCGAAGTGCTTATCAGAATAGAACAA
Found at i:19578450 original size:28 final size:28
Alignment explanation
Indices: 19578395--19578450 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
19578385 CAGAATAGAA
* *
19578395 CAACACCAATGTGCTTATCAGAATAGAG
1 CAACACCAATGTGCTTATCAAAACAGAG
19578423 CAACACCGAA-GTGCTTATCAAAACAGAG
1 CAACACC-AATGTGCTTATCAAAACAGAG
19578451 AGCTCATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 23 0.92
29 2 0.08
ACGTcount: A:0.41, C:0.23, G:0.18, T:0.18
Consensus pattern (28 bp):
CAACACCAATGTGCTTATCAAAACAGAG
Found at i:19584930 original size:25 final size:25
Alignment explanation
Indices: 19584902--19584951 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
19584892 CTTTTACAAC
* *
19584902 ATTAGAAAACATACCCCATTTAGAG
1 ATTAGAAAACATAACACATTTAGAG
**
19584927 ATTAGAACTCATAACACATTTAGAG
1 ATTAGAAAACATAACACATTTAGAG
19584952 GATTTTGTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.26
Consensus pattern (25 bp):
ATTAGAAAACATAACACATTTAGAG
Found at i:19586872 original size:175 final size:177
Alignment explanation
Indices: 19586581--19586932 Score: 690
Period size: 175 Copynumber: 2.0 Consensus size: 177
19586571 TGGAAGTCTT
19586581 CTAGTTTCTAAGCATAGATAGGCTTGTGGTGGGCTTTGGCAAAGATGGCGTTGTAGAAATATGAG
1 CTAGTTTCTAAGCATAGATAGGCTTGTGGTGGGCTTTGGCAAAGATGGCGTTGTAGAAATATGAG
19586646 TCAAGGTGGAGATTTGTTAAGAATGACTCCTATTTTCAGTCAAATTTGAGAAATAATCTTCTAGT
66 TCAAGGTGGAGATTTGTTAAGAATGACTCCTATTTTCAGTCAAATTTGAGAAATAATCTTCTAGT
19586711 TAAACTCTATTTATTTGTTTCAATCAAACACTGA-T-GTTTAGATTA
131 TAAACTCTATTTATTTGTTTCAATCAAACACTGATTAGTTTAGATTA
19586756 CTAGTTTCTAAGCATAGATAGGCTTGTGGTGGGCTTTGGCAAAGATGGCGTTGTAGAAATATGAG
1 CTAGTTTCTAAGCATAGATAGGCTTGTGGTGGGCTTTGGCAAAGATGGCGTTGTAGAAATATGAG
19586821 TCAAGGTGGAGATTTGTTAAGAATGACTCCTATTTTCAGTCAAATTTGAGAAATAATCTTCTAGT
66 TCAAGGTGGAGATTTGTTAAGAATGACTCCTATTTTCAGTCAAATTTGAGAAATAATCTTCTAGT
19586886 TAAACTCTATTTATTTGTTTCAATCAAACACTGATTAGTTTAGATTA
131 TAAACTCTATTTATTTGTTTCAATCAAACACTGATTAGTTTAGATTA
19586933 TTTTAGTATT
Statistics
Matches: 175, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
175 164 0.94
176 1 0.01
177 10 0.06
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (177 bp):
CTAGTTTCTAAGCATAGATAGGCTTGTGGTGGGCTTTGGCAAAGATGGCGTTGTAGAAATATGAG
TCAAGGTGGAGATTTGTTAAGAATGACTCCTATTTTCAGTCAAATTTGAGAAATAATCTTCTAGT
TAAACTCTATTTATTTGTTTCAATCAAACACTGATTAGTTTAGATTA
Found at i:19589743 original size:15 final size:17
Alignment explanation
Indices: 19589718--19589749 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
19589708 AGTAACAATA
19589718 ATTAGTACAGTA-ACAG
1 ATTAGTACAGTATACAG
19589734 ATTA-TACAGTATACAG
1 ATTAGTACAGTATACAG
19589750 GTCCTACTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (17 bp):
ATTAGTACAGTATACAG
Found at i:19590217 original size:323 final size:323
Alignment explanation
Indices: 19589629--19590280 Score: 1012
Period size: 323 Copynumber: 2.0 Consensus size: 323
19589619 GCCCTTTTCA
*
19589629 GTATCAGTGACAATAACAGTTTGGGCTTTAGCCCATCTAAGCGCAAAAGCAATCATGTTTTTGAG
1 GTATCAGTGACAATAACAGTTTGGGCTTTAGCCCATCTAAGCGCAAAAGCAATCATGTGTTTGAG
* * *
19589694 CCTTGGCCCATTACAGTAACAATAATTAGTACAGTAACAGATTATACAGTATACAGGTCCTACTC
66 CCTTAGCCCATTACAGTAACAATAATTAGTACAGTAACAGATCATACAGTATACAGCTCCTACTC
* *
19589759 AACCAGCCTCTACACTCCATTTGGGCATATAATCAACCCACTCATCCCTACACTCCAAAGTAGTA
131 AACCAACCTCTACACTCCATTTGGGCATATAATCAACCCACCCATCCCTACACTCCAAAGTAGTA
* *
19589824 CCAAATGAGGCACTAGACAGTAGTTGTAGCTGAACTACCAGTAAGTTAGGCTCGAGGACTTTCAG
196 CCAAATGAAGCACTAGACAGTAGTTGCAGCTGAACTACCAGTAAGTTAGGCTCGAGGACTTTCAG
*
19589889 TACACTTCCTCCAATCAATATCAATCCCCAACCCAATGCAATGTATCATACAGTCATGTCATG
261 TACACTTCCTCCAATCAATATCAATCCCCAACCCAATGCAATGCATCATACAGTCATGTCATG
* * *
19589952 GTATCAGTGACAATAACAGTTTGGGCTTTAGCCCATCTAAGTGCAGAAGCAATCATGTGTTTGGG
1 GTATCAGTGACAATAACAGTTTGGGCTTTAGCCCATCTAAGCGCAAAAGCAATCATGTGTTTGAG
* * *
19590017 CCTTAGCCCATTACAGTAACAATAATTAGTACAGT-CCTA-CTCA-ACCAGCCTCTACA-CTCC-
66 CCTTAGCCCATTACAGTAACAATAATTAGTACAGTAAC-AGATCATA-CAG--TATACAGCTCCT
**
19590077 ATCTTCGTCCAACCT-TACACTCCATGTTGGG-ATATAATCAACCCACCCATCCCTACACTCCAA
127 A-C-TCAACCAACCTCTACACTCCAT-TTGGGCATATAATCAACCCACCCATCCCTACACTCCAA
* * *
19590140 AGTAGTACCAAATGAAGCACTAGACAGTAGTTGCAGTTGAATTGCCAGTAAGTTAGGCTCGAGGA
189 AGTAGTACCAAATGAAGCACTAGACAGTAGTTGCAGCTGAACTACCAGTAAGTTAGGCTCGAGGA
19590205 CTTTCAGTACACTTCCTCCAATCAATATCAATCCCCAACCCAATGCAATGCATCATACAGTCATG
254 CTTTCAGTACACTTCCTCCAATCAATATCAATCCCCAACCCAATGCAATGCATCATACAGTCATG
19590270 TCATG
319 TCATG
19590275 GTATCA
1 GTATCA
19590281 TGTATAAATG
Statistics
Matches: 302, Mismatches: 20, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
321 1 0.00
322 7 0.02
323 276 0.91
324 18 0.06
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.26
Consensus pattern (323 bp):
GTATCAGTGACAATAACAGTTTGGGCTTTAGCCCATCTAAGCGCAAAAGCAATCATGTGTTTGAG
CCTTAGCCCATTACAGTAACAATAATTAGTACAGTAACAGATCATACAGTATACAGCTCCTACTC
AACCAACCTCTACACTCCATTTGGGCATATAATCAACCCACCCATCCCTACACTCCAAAGTAGTA
CCAAATGAAGCACTAGACAGTAGTTGCAGCTGAACTACCAGTAAGTTAGGCTCGAGGACTTTCAG
TACACTTCCTCCAATCAATATCAATCCCCAACCCAATGCAATGCATCATACAGTCATGTCATG
Found at i:19596862 original size:17 final size:17
Alignment explanation
Indices: 19596842--19596876 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
19596832 AGTTCTCGAA
19596842 AAAATATCGAAA-AAATT
1 AAAATATC-AAAGAAATT
19596859 AAAATATCAAAGAAATT
1 AAAATATCAAAGAAATT
19596876 A
1 A
19596877 TAGCATGGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.18
17 14 0.82
ACGTcount: A:0.66, C:0.06, G:0.06, T:0.23
Consensus pattern (17 bp):
AAAATATCAAAGAAATT
Found at i:19597050 original size:18 final size:18
Alignment explanation
Indices: 19597027--19597062 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
19597017 TTAAATACCC
19597027 AGTCTTTCCTTGCCAGAG
1 AGTCTTTCCTTGCCAGAG
19597045 AGTCTTTCCTTGCCAGAG
1 AGTCTTTCCTTGCCAGAG
19597063 CTTATCCTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.28, G:0.22, T:0.33
Consensus pattern (18 bp):
AGTCTTTCCTTGCCAGAG
Found at i:19601195 original size:24 final size:24
Alignment explanation
Indices: 19601168--19601242 Score: 77
Period size: 23 Copynumber: 3.2 Consensus size: 24
19601158 TAGGTTGACT
19601168 ATGTGAGATATTATGGGTGGAAGC
1 ATGTGAGATATTATGGGTGGAAGC
* * *
19601192 ATGTG-GATA-GAGTAGGTTG-A-C
1 ATGTGAGATATTA-TGGGTGGAAGC
19601213 TATGTGAGATATTATGGGTGGAAGC
1 -ATGTGAGATATTATGGGTGGAAGC
19601238 ATGTG
1 ATGTG
19601243 GGGTGGATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
21 1 0.03
22 7 0.18
23 18 0.46
24 12 0.31
25 1 0.03
ACGTcount: A:0.28, C:0.04, G:0.37, T:0.31
Consensus pattern (24 bp):
ATGTGAGATATTATGGGTGGAAGC
Found at i:19601213 original size:46 final size:46
Alignment explanation
Indices: 19601146--19601243 Score: 196
Period size: 46 Copynumber: 2.1 Consensus size: 46
19601136 GACATAGGTG
19601146 ATGTGGATAGAGTAGGTTGACTATGTGAGATATTATGGGTGGAAGC
1 ATGTGGATAGAGTAGGTTGACTATGTGAGATATTATGGGTGGAAGC
19601192 ATGTGGATAGAGTAGGTTGACTATGTGAGATATTATGGGTGGAAGC
1 ATGTGGATAGAGTAGGTTGACTATGTGAGATATTATGGGTGGAAGC
19601238 ATGTGG
1 ATGTGG
19601244 GGTGGATATT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 52 1.00
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (46 bp):
ATGTGGATAGAGTAGGTTGACTATGTGAGATATTATGGGTGGAAGC
Done.