Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009605.1 Hibiscus syriacus cultivar Beakdansim tig00116989_pilon, whole genome shotgun sequence
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: 9158330
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 35
Found at i:915365 original size:21 final size:21
Alignment explanation
Indices: 915339--915389 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
915329 GTGAAACCTC
915339 TAATGCACACATAATGCCAGA
1 TAATGCACACATAATGCCAGA
* * *
915360 TTATGCACACATAGTGCTAGA
1 TAATGCACACATAATGCCAGA
915381 TAATGCACA
1 TAATGCACA
915390 TAAAGTACAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.24
Consensus pattern (21 bp):
TAATGCACACATAATGCCAGA
Found at i:917816 original size:14 final size:14
Alignment explanation
Indices: 917797--917823 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
917787 ACCATGGTAT
917797 GTTAGAGTCTATTG
1 GTTAGAGTCTATTG
917811 GTTAGAGTCTATT
1 GTTAGAGTCTATT
917824 CTCATTGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.07, G:0.26, T:0.44
Consensus pattern (14 bp):
GTTAGAGTCTATTG
Found at i:919901 original size:30 final size:30
Alignment explanation
Indices: 919867--919936 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
919857 GCGTGTCATA
* *
919867 AATTTATGACAAACAAATGTGTGTTATCTT
1 AATTTATGACAAACAAATGTGTATCATCTT
* *
919897 AATTTATGACACATAAATGTGTATCATCTT
1 AATTTATGACAAACAAATGTGTATCATCTT
919927 AATTTATGAC
1 AATTTATGAC
919937 GGGGGCTTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.40
Consensus pattern (30 bp):
AATTTATGACAAACAAATGTGTATCATCTT
Found at i:919978 original size:13 final size:13
Alignment explanation
Indices: 919962--920023 Score: 79
Period size: 13 Copynumber: 4.8 Consensus size: 13
919952 GCTCAATGAA
919962 CGTCATAAATGCG
1 CGTCATAAATGCG
**
919975 CGTCATAAATGTA
1 CGTCATAAATGCG
*
919988 CGTCATAAATGTG
1 CGTCATAAATGCG
*
920001 TGTCATAAATGCG
1 CGTCATAAATGCG
*
920014 AGTCATAAAT
1 CGTCATAAAT
920024 TTATGACGCA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 43 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (13 bp):
CGTCATAAATGCG
Found at i:919985 original size:26 final size:26
Alignment explanation
Indices: 919956--920011 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
919946 AATGATGCTC
919956 AATGAACGTCATAAATGCGCGTCATA
1 AATGAACGTCATAAATGCGCGTCATA
* * *
919982 AATGTACGTCATAAATGTGTGTCATA
1 AATGAACGTCATAAATGCGCGTCATA
920008 AATG
1 AATG
920012 CGAGTCATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (26 bp):
AATGAACGTCATAAATGCGCGTCATA
Found at i:923331 original size:17 final size:18
Alignment explanation
Indices: 923299--923332 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
923289 TATCCAAAAA
*
923299 ATCCAACATAATGAAATC
1 ATCCAAAATAATGAAATC
923317 ATCCAAAAT-ATGAAAT
1 ATCCAAAATAATGAAAT
923333 TCTTAAAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.18, G:0.06, T:0.24
Consensus pattern (18 bp):
ATCCAAAATAATGAAATC
Found at i:926277 original size:132 final size:133
Alignment explanation
Indices: 926039--926297 Score: 396
Period size: 132 Copynumber: 2.0 Consensus size: 133
926029 GGCATGCAAA
* * * ** *
926039 CTAAAGTTTGAGTCCCTAGGATACCAAAAGTCCTAAACTAGGAGTGTCTCTAAGGTATCTAAAGA
1 CTAAAGTTTGAGTCACTAGGATACCAAAACTCCTAAACTAAGAGCATCTCTAAGGCATCTAAAGA
*
926104 TTCTCTTAATGGCATGTAAATAAGATTCCCTAGGATATGATTGATATCTAGCACACAAGCAACAC
66 TTCTCTTAATGGCATGTAAATAAGATTCCCTAGGACATGATTGATATCTAGCACACAAGCAACAC
926169 ATG
131 ATG
* *
926172 CTAAAGTTTGAGTCACTAGGGTACC-AAACTCCTAAACTAAGAGCATCTTTAAGGCATCTAAAGA
1 CTAAAGTTTGAGTCACTAGGATACCAAAACTCCTAAACTAAGAGCATCTCTAAGGCATCTAAAGA
* *
926236 TTCTCTTAATGGCATGTAAATGAGATT-CCTTGGAACATGATTGATATCTAGCACACAAGCAA
66 TTCTCTTAATGGCATGTAAATAAGATTCCCTAGG-ACATGATTGATATCTAGCACACAAGCAA
926298 ACACTAAACA
Statistics
Matches: 114, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
131 5 0.04
132 86 0.75
133 23 0.20
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.28
Consensus pattern (133 bp):
CTAAAGTTTGAGTCACTAGGATACCAAAACTCCTAAACTAAGAGCATCTCTAAGGCATCTAAAGA
TTCTCTTAATGGCATGTAAATAAGATTCCCTAGGACATGATTGATATCTAGCACACAAGCAACAC
ATG
Found at i:936657 original size:13 final size:13
Alignment explanation
Indices: 936641--936667 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
936631 TAGCAACATG
936641 TACCTCCAACAGT
1 TACCTCCAACAGT
936654 TACCTCCAACAGT
1 TACCTCCAACAGT
936667 T
1 T
936668 CACGACTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.37, G:0.07, T:0.26
Consensus pattern (13 bp):
TACCTCCAACAGT
Found at i:938903 original size:140 final size:140
Alignment explanation
Indices: 938651--938928 Score: 457
Period size: 140 Copynumber: 2.0 Consensus size: 140
938641 CCTGAAACTA
* * * *
938651 TTCTTCATACTTTAAAGGCCTATCGTAGTTCGCGCTCTATTCTTGCTCTGTCCGGACTTGATACA
1 TTCTTCATACATTAAAGGCCTATCCTAGATCGCGCTCCATTCTTGCTCTGTCCGGACTTGATACA
* *
938716 TTGCTGTTGGACTGGCAAGCTAACACATGCAAAGATTGGCTTGAAAAGGTAGCAGCTTCTCGTGA
66 TTGCTGGTGAACTGGCAAGCTAACACATGCAAAGATTGGCTTGAAAAGGTAGCAGCTTCTCGTGA
938781 TCACCTAGGT
131 TCACCTAGGT
* *
938791 TTCTTCATACATTAAAGGCCTATCCTAGATCTCGCTCCATTCTTGCTCTTTCCGGACTTGATACA
1 TTCTTCATACATTAAAGGCCTATCCTAGATCGCGCTCCATTCTTGCTCTGTCCGGACTTGATACA
* * *
938856 TTGCTGGTGAACTGGCAAGCTAACACATGCAAAGATTGGCTTGAAAAGGTAGTATCTTCTCTTGA
66 TTGCTGGTGAACTGGCAAGCTAACACATGCAAAGATTGGCTTGAAAAGGTAGCAGCTTCTCGTGA
938921 TCACCTAG
131 TCACCTAG
938929 ATTTTACTAA
Statistics
Matches: 127, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
140 127 1.00
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.32
Consensus pattern (140 bp):
TTCTTCATACATTAAAGGCCTATCCTAGATCGCGCTCCATTCTTGCTCTGTCCGGACTTGATACA
TTGCTGGTGAACTGGCAAGCTAACACATGCAAAGATTGGCTTGAAAAGGTAGCAGCTTCTCGTGA
TCACCTAGGT
Found at i:944186 original size:43 final size:43
Alignment explanation
Indices: 944053--944424 Score: 327
Period size: 43 Copynumber: 8.6 Consensus size: 43
944043 TCCTTTTCCA
* *
944053 TGTGCAAGGGTAAGCCTTACAGTTTCCCCCAGGTTCATTTGTTG
1 TGTGCAAGGGTAAGCCTTACAGTTT-CCCCAGGTTCCTTTGCTG
* *
944097 TGTGCAAGAGTAAGCCTTACAGTTTCCCCCAGGTTCCTTTGTTG
1 TGTGCAAGGGTAAGCCTTACAGTTT-CCCCAGGTTCCTTTGCTG
* *
944141 TGTGCAAGGGGAAGCCTTATAGTTTCCCCAGGTTCCTTTGCTG
1 TGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTG
* ** * * * **
944184 TGTGAAAACGTAAGCCTTACATTTTTCCAAGGTTCCTTTATTG
1 TGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTG
* *
944227 AGTGCAAGGGTAAGCCTTACAGTTTTCCCCAGGTTCCTTTGTTG
1 TGTGCAAGGGTAAGCCTTACAG-TTTCCCCAGGTTCCTTTGCTG
* * * ** * *
944271 GGTTCAAGGGTAAGACCTTATAGTTT-TACAGGCTCCTTTGCTA
1 TGTGCAAGGGTAAG-CCTTACAGTTTCCCCAGGTTCCTTTGCTG
* * *** * *
944314 TGTGCAAAGGTAAGACCTTATAGTTT-TATAGGCTCCTTTGCTA
1 TGTGCAAGGGTAAG-CCTTACAGTTTCCCCAGGTTCCTTTGCTG
* * * * * * *
944357 TGTGCAAGGGTAAACCTTATAGTTT-CTCAGGCTCTTTTTCTA
1 TGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTG
*
944399 TGTGCAAGGGTAAGACCTTACCGTTT
1 TGTGCAAGGGTAAG-CCTTACAGTTT
944425 TTGCATGCTC
Statistics
Matches: 279, Mismatches: 46, Indels: 7
0.84 0.14 0.02
Matches are distributed among these distances:
42 36 0.13
43 139 0.50
44 97 0.35
45 7 0.03
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (43 bp):
TGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTG
Found at i:944254 original size:87 final size:88
Alignment explanation
Indices: 944054--944267 Score: 299
Period size: 87 Copynumber: 2.5 Consensus size: 88
944044 CCTTTTCCAT
* * * *
944054 GTGCAAGGGTAAGCCTTACAGTTTCCCCCAGGTTCATTTGTTGTGTGCAAGAGTAAGCCTTACAG
1 GTGCAAGGGTAAGCCTTACAGTTTTCCCCAGGTTCCTTTGCTGTGTGCAAAAGTAAGCCTTACAG
* * *
944119 TTTCCCCCAGGTTCCTTTGTTGT
66 TTTCCCCAAGGTTCCTTTATTGA
* *
944142 GTGCAAGGGGAAGCCTTATAG-TTTCCCCAGGTTCCTTTGCTGTGTG-AAAACGTAAGCCTTACA
1 GTGCAAGGGTAAGCCTTACAGTTTTCCCCAGGTTCCTTTGCTGTGTGCAAAA-GTAAGCCTTACA
**
944205 -TTTTTCCAAGGTTCCTTTATTGA
65 GTTTCCCCAAGGTTCCTTTATTGA
944228 GTGCAAGGGTAAGCCTTACAGTTTTCCCCAGGTTCCTTTG
1 GTGCAAGGGTAAGCCTTACAGTTTTCCCCAGGTTCCTTTG
944268 TTGGGTTCAA
Statistics
Matches: 111, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
86 40 0.36
87 52 0.47
88 19 0.17
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (88 bp):
GTGCAAGGGTAAGCCTTACAGTTTTCCCCAGGTTCCTTTGCTGTGTGCAAAAGTAAGCCTTACAG
TTTCCCCAAGGTTCCTTTATTGA
Found at i:944279 original size:130 final size:131
Alignment explanation
Indices: 944062--944339 Score: 362
Period size: 130 Copynumber: 2.1 Consensus size: 131
944052 ATGTGCAAGG
* * *
944062 GTAAGCCTTACAGTTTCCCCCAGGTTCATTTGTTGTGTGCAAGAGTAAGCCTTACAGTTTCCCCC
1 GTAAGCCTTACAGTTTCCCCAAGGTTCATTTATTGAGTGCAAGAGTAAGCCTTACAGTTTCCCCC
* * * *
944127 AGGTTCCTTTGTTGTGTGCAAGGGGAAG-CCTTATAGTTTCCCCAGGTTCCTTTGCTGTGTGAAA
66 AGGTTCCTTTGTTGGGTGCAAGGGGAAGACCTTATAGTTT-CACAGGCTCCTTTGCTATGTGAAA
944191 AC
130 AC
** * * *
944193 GTAAGCCTTACA-TTTTTCCAAGGTTCCTTTATTGAGTGCAAGGGTAAGCCTTACAGTTTTCCCC
1 GTAAGCCTTACAGTTTCCCCAAGGTTCATTTATTGAGTGCAAGAGTAAGCCTTACAGTTTCCCCC
* * * *
944257 AGGTTCCTTTGTTGGGTTCAAGGGTAAGACCTTATAGTTTTACAGGCTCCTTTGCTATGTGCAAA
66 AGGTTCCTTTGTTGGGTGCAAGGGGAAGACCTTATAGTTTCACAGGCTCCTTTGCTATGTGAAAA
*
944322 G
131 C
*
944323 GTAAGACCTTATAGTTT
1 GTAAG-CCTTACAGTTT
944340 TATAGGCTCC
Statistics
Matches: 126, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
130 94 0.75
131 29 0.23
132 3 0.02
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (131 bp):
GTAAGCCTTACAGTTTCCCCAAGGTTCATTTATTGAGTGCAAGAGTAAGCCTTACAGTTTCCCCC
AGGTTCCTTTGTTGGGTGCAAGGGGAAGACCTTATAGTTTCACAGGCTCCTTTGCTATGTGAAAA
C
Found at i:944351 original size:130 final size:129
Alignment explanation
Indices: 944097--944382 Score: 344
Period size: 130 Copynumber: 2.2 Consensus size: 129
944087 TCATTTGTTG
* *
944097 TGTGCAAGAGTAAGCCTTACAGTTTCCCCCAGGTTCCTTTGTTGTGTGCAAGGGGAAGCCTTATA
1 TGTGCAAGGGTAAGCCTTACAGTTTCCCCCAGGTTCCTTTGTTGGGTGCAAGGGGAAGCCTTATA
* * * * * *
944162 GTTTCCCCAGGTTCCTTTGCTGTGTGAAAACGTAAGCCTTACATTTTTCCAAGGTTCCTTTATTG
66 GTTTCCACAGGCTCCTTTGCTATGTGAAAACGTAAGCCTTACAGTTTT-CAAGGCTCCTTTACT-
944227 A
129 A
* * *
944228 -GTGCAAGGGTAAGCCTTACAGTTTTCCCCAGGTTCCTTTGTTGGGTTCAAGGGTAAGACCTTAT
1 TGTGCAAGGGTAAGCCTTACAGTTTCCCCCAGGTTCCTTTGTTGGGTGCAAGGGGAAG-CCTTAT
* * * * *
944292 AGTTT-TACAGGCTCCTTTGCTATGTGCAAAGGTAAGACCTTATAGTTTT-ATAGGCTCCTTTGC
65 AGTTTCCACAGGCTCCTTTGCTATGTGAAAACGTAAG-CCTTACAGTTTTCA-AGGCTCCTTTAC
944355 TA
128 TA
* *
944357 TGTGCAAGGGTAAACCTTATAGTTTC
1 TGTGCAAGGGTAAGCCTTACAGTTTC
944383 TCAGGCTCTT
Statistics
Matches: 132, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
129 2 0.02
130 109 0.83
131 21 0.16
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (129 bp):
TGTGCAAGGGTAAGCCTTACAGTTTCCCCCAGGTTCCTTTGTTGGGTGCAAGGGGAAGCCTTATA
GTTTCCACAGGCTCCTTTGCTATGTGAAAACGTAAGCCTTACAGTTTTCAAGGCTCCTTTACTA
Found at i:944425 original size:85 final size:86
Alignment explanation
Indices: 944228--944448 Score: 243
Period size: 85 Copynumber: 2.6 Consensus size: 86
944218 CCTTTATTGA
* * * * ** *
944228 GTGCAAGGGTAAG-CCTTACAGTTTTCCCCAGGTTCCTTTGTTGGGTTCAAGGGTAAGACCTTAT
1 GTGCAAAGGTAAGACCTTACAGTTTT--TCAGGCTCCTTTGCTATGTGCAAGGGTAAGACCTTAT
944292 AGTTTTACAGGCTCCTTTGCTAT
64 AGTTTTACAGGCTCCTTTGCTAT
*
944315 GTGCAAAGGTAAGACCTTATAGTTTTAT-AGGCTCCTTTGCTATGTGCAAGGGTAA-ACCTTATA
1 GTGCAAAGGTAAGACCTTACAGTTTT-TCAGGCTCCTTTGCTATGTGCAAGGGTAAGACCTTATA
* *
944378 GTTTCT-CAGGCTCTTTTTCTAT
65 GTTT-TACAGGCTCCTTTGCTAT
* * * *
944400 GTGCAAGGGTAAGACCTTACCGTTTTTGCATGCTCCTTTGCTTTGTGCA
1 GTGCAAAGGTAAGACCTTACAGTTTTT-CAGGCTCCTTTGCTATGTGCA
944449 CATTGTAAAT
Statistics
Matches: 114, Mismatches: 16, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
84 1 0.01
85 49 0.43
86 41 0.36
87 12 0.11
88 11 0.10
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (86 bp):
GTGCAAAGGTAAGACCTTACAGTTTTTCAGGCTCCTTTGCTATGTGCAAGGGTAAGACCTTATAG
TTTTACAGGCTCCTTTGCTAT
Found at i:949144 original size:43 final size:43
Alignment explanation
Indices: 949080--949409 Score: 389
Period size: 43 Copynumber: 7.6 Consensus size: 43
949070 TCGCAGGCTT
* *
949080 CTTTGTTGTGTGCAAGGGTAAGCCTTATAGTTTCCCCTGGTTC
1 CTTTGCTGTGTGCAAGGGTAAGCCTTATAGTTTCCCCAGGTTC
* * *
949123 CTTTGCTGTGTGCAAGAGTAAGCCTTACAGTTTCCCCTGGGTTC
1 CTTTGCTGTGTGCAAGGGTAAGCCTTATAGTTTCCCC-AGGTTC
* * *
949167 CTTTGCTGTGTGCAAGGGCAAGCCTTACAGTTTGCCCAGGTTC
1 CTTTGCTGTGTGCAAGGGTAAGCCTTATAGTTTCCCCAGGTTC
* * *
949210 CTTTGCTGTGTGCAAGTGTAAGCCTTATATTTTCCCCAAGTTC
1 CTTTGCTGTGTGCAAGGGTAAGCCTTATAGTTTCCCCAGGTTC
* * *
949253 CTTTGCTATGTGCAAGGGTAATCCTTACAGTTTTCCCCAGGTTC
1 CTTTGCTGTGTGCAAGGGTAAGCCTTATAG-TTTCCCCAGGTTC
*
949297 CTTTGTTGTGTGCAAGGGTAAGACCTTATAGTTT-CCCAGGTTC
1 CTTTGCTGTGTGCAAGGGTAAG-CCTTATAGTTTCCCCAGGTTC
* ** *
949340 CTTTTCCAT-TGAAAGGGTAAGACCTTATAGTTT-CCCA-GTCTC
1 CTTTGCTGTGTGCAAGGGTAAG-CCTTATAGTTTCCCCAGGT-TC
* *
949382 TTTTGCTATGTGCAAGGGTAAGACCTTA
1 CTTTGCTGTGTGCAAGGGTAAG-CCTTA
949410 CCATTTTTGC
Statistics
Matches: 249, Mismatches: 33, Indels: 10
0.85 0.11 0.03
Matches are distributed among these distances:
41 2 0.01
42 35 0.14
43 132 0.53
44 73 0.29
45 7 0.03
ACGTcount: A:0.18, C:0.22, G:0.23, T:0.36
Consensus pattern (43 bp):
CTTTGCTGTGTGCAAGGGTAAGCCTTATAGTTTCCCCAGGTTC
Found at i:949231 original size:87 final size:87
Alignment explanation
Indices: 949088--949410 Score: 388
Period size: 87 Copynumber: 3.7 Consensus size: 87
949078 TTCTTTGTTG
* * *
949088 TGTGCAAGGGTAAGCCTTATAGTTTCCCCTGGTTCCTTTGCTGTGTGCAAGAGTAAG-CCTTACA
1 TGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGACCTTACA
* *
949152 GTTTCCCCTGGGTTCCTTTGCTG
66 GTTTCCCC-AGGTTCCTTTGCTA
* * * *
949175 TGTGCAAGGGCAAGCCTTACAGTTTGCCCAGGTTCCTTTGCTGTGTGCAAGTGTAAG-CCTTATA
1 TGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGACCTTACA
* *
949239 TTTTCCCCAAGTTCCTTTGCTA
66 GTTTCCCCAGGTTCCTTTGCTA
* * *
949261 TGTGCAAGGGTAATCCTTACAGTTTTCCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGACCTTAT
1 TGTGCAAGGGTAAGCCTTACAG-TTTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGACCTTAC
* *
949326 AGTTT-CCCAGGTTCCTTTTCCA
65 AGTTTCCCCAGGTTCCTTTGCTA
* * * *
949348 T-TGAAAGGGTAAGACCTTATAGTTT-CCCA-GTCTCTTTTGCTATGTGCAAGGGTAAGACCTTA
1 TGTGCAAGGGTAAG-CCTTACAGTTTCCCCAGGT-TCCTTTGCTGTGTGCAAGGGTAAGACCTTA
949410 C
64 C
949411 CATTTTTGCA
Statistics
Matches: 206, Mismatches: 26, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
84 2 0.01
85 31 0.15
86 44 0.21
87 119 0.58
88 10 0.05
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (87 bp):
TGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGACCTTACA
GTTTCCCCAGGTTCCTTTGCTA
Found at i:949313 original size:130 final size:129
Alignment explanation
Indices: 949080--949410 Score: 427
Period size: 130 Copynumber: 2.5 Consensus size: 129
949070 TCGCAGGCTT
* * * *
949080 CTTTGTTGTGTGCAAGGGTAAGCCTTATAGTTTCCCCTGGTTCCTTTGCTGTGTGCAAGAGTAAG
1 CTTTGCTGTGTGCAAGGGTAAGCCTTATAGTTTCCCC-AGTTCCTTTGCTATGTGCAAGGGTAAG
*
949145 CCTTACAGTTTCCCCTGGGTTCCTTTGCTGTGTGCAAGGGCAAG-CCTTACAGTTTGCCCAGGTT
65 CCTTACAGTTTCCCCTAGGTTCCTTTGCTGTGTGCAAGGGCAAGACCTTACAGTTT-CCCAGGTT
949209 C
129 C
* * *
949210 CTTTGCTGTGTGCAAGTGTAAGCCTTATATTTTCCCCAAGTTCCTTTGCTATGTGCAAGGGTAAT
1 CTTTGCTGTGTGCAAGGGTAAGCCTTATAGTTTCCCC-AGTTCCTTTGCTATGTGCAAGGGTAAG
* * *
949275 CCTTACAGTTTTCCCC-AGGTTCCTTTGTTGTGTGCAAGGGTAAGACCTTATAGTTTCCCAGGTT
65 CCTTACAG-TTTCCCCTAGGTTCCTTTGCTGTGTGCAAGGGCAAGACCTTACAGTTTCCCAGGTT
949339 C
129 C
* ** * *
949340 CTTTTCCAT-TGAAAGGGTAAGACCTTATAGTTT-CCCAGTCTCTTTTGCTATGTGCAAGGGTAA
1 CTTTGCTGTGTGCAAGGGTAAG-CCTTATAGTTTCCCCAGT-TCCTTTGCTATGTGCAAGGGTAA
949403 GACCTTAC
64 G-CCTTAC
949411 CATTTTTGCA
Statistics
Matches: 176, Mismatches: 20, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
128 3 0.02
129 35 0.20
130 121 0.69
131 17 0.10
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (129 bp):
CTTTGCTGTGTGCAAGGGTAAGCCTTATAGTTTCCCCAGTTCCTTTGCTATGTGCAAGGGTAAGC
CTTACAGTTTCCCCTAGGTTCCTTTGCTGTGTGCAAGGGCAAGACCTTACAGTTTCCCAGGTTC
Found at i:957490 original size:31 final size:32
Alignment explanation
Indices: 957450--957509 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
957440 GGGCATATGA
*
957450 CATACTATATATAGT-TTTAAAAATATAAGTT
1 CATACTATATATAATATTTAAAAATATAAGTT
*
957481 CATATTATATATAATATTTAAAAATATAA
1 CATACTATATATAATATTTAAAAATATAA
957510 CATATAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 13 0.50
32 13 0.50
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (32 bp):
CATACTATATATAATATTTAAAAATATAAGTT
Found at i:957514 original size:22 final size:23
Alignment explanation
Indices: 957489--957541 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 23
957479 TTCATATTAT
957489 ATATAATATTTAAAAATAT-AAC
1 ATATAATATTTAAAAATATAAAC
* ** *
957511 ATATAGT-TTTGTAAATATAAAT
1 ATATAATATTTAAAAATATAAAC
957533 ATATAATAT
1 ATATAATAT
957542 ATATAGTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
21 9 0.38
22 14 0.58
23 1 0.04
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (23 bp):
ATATAATATTTAAAAATATAAAC
Found at i:957531 original size:29 final size:31
Alignment explanation
Indices: 957499--957558 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
957489 ATATAATATT
*
957499 TAAAAATAT-A-ACATATAGTTTTGTAAATA
1 TAAAAATATAATACATATAGTTTTGAAAATA
* *
957528 TAAATATATAATATATATAGTTTTGAAAATA
1 TAAAAATATAATACATATAGTTTTGAAAATA
957559 ATATGCATAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 8 0.31
30 1 0.04
31 17 0.65
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.40
Consensus pattern (31 bp):
TAAAAATATAATACATATAGTTTTGAAAATA
Found at i:957560 original size:21 final size:21
Alignment explanation
Indices: 957535--957578 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
957525 ATATAAATAT
*
957535 ATAATATATATAGTTTTGAAA
1 ATAATATACATAGTTTTGAAA
*
957556 ATAATATGCATAGTTTTGAAA
1 ATAATATACATAGTTTTGAAA
957577 AT
1 AT
957579 TGTAGATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.41
Consensus pattern (21 bp):
ATAATATACATAGTTTTGAAA
Found at i:957701 original size:31 final size:29
Alignment explanation
Indices: 957599--957731 Score: 139
Period size: 28 Copynumber: 4.6 Consensus size: 29
957589 CTGTATAGTT
*
957599 AAAATAATATAT-TATATAGATAGTTTTG
1 AAAATAATATATATATATATATAGTTTTG
* *
957627 AAAATAATATATATGTATATA-A-TTTTA
1 AAAATAATATATATATATATATAGTTTTG
**
957654 AAAATAATATGCATATAT-TATAGTTTTG
1 AAAATAATATATATATATATATAGTTTTG
**
957682 AAAATAATATATTATATATATTATAACTTTG
1 AAAATAATATA-TATATATA-TATAGTTTTG
*
957713 AAAATAACATATATCATAT
1 AAAATAATATATAT-ATAT
957732 GTACATTATA
Statistics
Matches: 86, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
26 2 0.02
27 20 0.23
28 27 0.31
29 12 0.14
30 3 0.03
31 22 0.26
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.42
Consensus pattern (29 bp):
AAAATAATATATATATATATATAGTTTTG
Found at i:957718 original size:28 final size:26
Alignment explanation
Indices: 957623--957726 Score: 61
Period size: 31 Copynumber: 3.7 Consensus size: 26
957613 TATAGATAGT
*
957623 TTTGAAAATA-ATATATATGTATATAA
1 TTTGAAAATATATATATATAT-TATAA
* *
957649 TTTTAAAA-ATAATATGCATATATTATAGT
1 TTTGAAAATAT-ATAT--ATATATTATA-A
957678 TTTGAAAATAATATATTATATATATTATAA
1 TTTG--AA-AATATA-TATATATATTATAA
*
957708 CTTTGAAAATA-ACATATAT
1 -TTTGAAAATATATATATAT
957727 CATATGTACA
Statistics
Matches: 61, Mismatches: 6, Indels: 22
0.69 0.07 0.25
Matches are distributed among these distances:
25 1 0.02
26 13 0.21
27 5 0.08
28 8 0.13
29 10 0.16
31 16 0.26
32 3 0.05
33 5 0.08
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (26 bp):
TTTGAAAATATATATATATATTATAA
Found at i:957845 original size:5 final size:5
Alignment explanation
Indices: 957835--957902 Score: 54
Period size: 5 Copynumber: 14.0 Consensus size: 5
957825 TATGTATATT
*
957835 TTTTA TTTTA TTTTAA TTTTA TTTTA TTTT- TATGTA -TTTA -TTTA TTTT-
1 TTTTA TTTTA TTTT-A TTTTA TTTTA TTTTA T-TTTA TTTTA TTTTA TTTTA
* * *
957883 TATTA TTTAA TTTAA TTTTA
1 TTTTA TTTTA TTTTA TTTTA
957903 GGTTCATTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
4 11 0.21
5 36 0.69
6 5 0.10
ACGTcount: A:0.25, C:0.00, G:0.01, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:957848 original size:11 final size:11
Alignment explanation
Indices: 957834--957886 Score: 56
Period size: 11 Copynumber: 4.7 Consensus size: 11
957824 ATATGTATAT
957834 TTTTTATTTTA
1 TTTTTATTTTA
*
957845 TTTTAATTTTA
1 TTTTTATTTTA
957856 -TTTTATTTTTA
1 TTTTTA-TTTTA
957867 TGTATTTA-TTTA
1 T-T-TTTATTTTA
957879 TTTTTATT
1 TTTTTATT
957887 ATTTAATTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
10 8 0.23
11 17 0.49
12 5 0.14
13 1 0.03
14 4 0.11
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:957880 original size:18 final size:17
Alignment explanation
Indices: 957831--957902 Score: 67
Period size: 18 Copynumber: 4.1 Consensus size: 17
957821 TATATATGTA
*
957831 TATTTTTTATTT-TATTT
1 TATTATTTATTTAT-TTT
*
957848 TAAT-TTTATTTTATTTT
1 TATTATTTA-TTTATTTT
957865 TATGTATTTATTTATTTT
1 TAT-TATTTATTTATTTT
*
957883 TATTATTTAATTTAATTT
1 TATTATTT-ATTTATTTT
957901 TA
1 TA
957903 GGTTCATTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
16 4 0.09
17 16 0.34
18 23 0.49
19 4 0.09
ACGTcount: A:0.25, C:0.00, G:0.01, T:0.74
Consensus pattern (17 bp):
TATTATTTATTTATTTT
Found at i:957893 original size:42 final size:40
Alignment explanation
Indices: 957825--957902 Score: 104
Period size: 42 Copynumber: 1.9 Consensus size: 40
957815 GTGTATTATA
* *
957825 TATGTATATTTTTTATTTTATTTTAATTTTATTTTATTTT
1 TATGTATATTATTTATTTTATTTTAATTTAATTTTATTTT
957865 TATGTAT-TTATTTATTTTTATTATTTAATTTAATTTTA
1 TATGTATATTATTTA-TTTTA-T-TTTAATTTAATTTTA
957903 GGTTCATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 6 0.18
40 12 0.36
41 1 0.03
42 14 0.42
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (40 bp):
TATGTATATTATTTATTTTATTTTAATTTAATTTTATTTT
Found at i:966041 original size:12 final size:12
Alignment explanation
Indices: 966026--966051 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
966016 TGATCAGGAA
966026 GTTGAGCTCGTT
1 GTTGAGCTCGTT
966038 GTTGAGCTCGTT
1 GTTGAGCTCGTT
966050 GT
1 GT
966052 GTAGGTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.35, T:0.42
Consensus pattern (12 bp):
GTTGAGCTCGTT
Found at i:967047 original size:2 final size:2
Alignment explanation
Indices: 967040--967079 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
967030 CTTATTCAAT
967040 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
967080 TATATATATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:969444 original size:29 final size:31
Alignment explanation
Indices: 969374--969447 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 31
969364 GAAAATTACC
* * *
969374 ACTTTGGTCCCTAAACTTTTCTAAACTTTAT
1 ACTTTGATCACTAAACTTTTCTAAAATTTAT
*
969405 ACTTTGGTCACTAAAC-TTTC-AAAATTTAT
1 ACTTTGATCACTAAACTTTTCTAAAATTTAT
969434 GA-TTTGATCACTAA
1 -ACTTTGATCACTAA
969448 CCAAAATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 19 0.49
30 5 0.13
31 15 0.38
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.42
Consensus pattern (31 bp):
ACTTTGATCACTAAACTTTTCTAAAATTTAT
Found at i:979816 original size:59 final size:58
Alignment explanation
Indices: 979689--979903 Score: 202
Period size: 59 Copynumber: 3.6 Consensus size: 58
979679 CTTCCCCTTT
* * * **
979689 CATTTTAGCACACGAAGTGCCCTAT-TCGAAAATTCATACCATTAGTATGATTTTGTTAC
1 CATTTTAGCACA-TAAATGCCCTATCT-GAAAATCCATACCATTAGTATGATTTCCTTAC
*
979748 CATTTTAGCACATGAAATGCCCTATATGAAAATCCATACCATTAGTATGATTTCCTTATC
1 CATTTTAGCACAT-AAATGCCCTATCTGAAAATCCATACCATTAGTATGATTTCCTTA-C
* * * * * * * * *
979808 C-TTGTAGCACCCTTAGTGCTCTATCTGGAAACCCATA-CACTCAGTATGATTCCCTTAC
1 CATTTTAGCA-CATAAATGCCCTATCTGAAAATCCATACCA-TTAGTATGATTTCCTTAC
*
979866 CATTTTAGCACATAATATGCCCTATCTGGAAATCCATA
1 CATTTTAGCACATAA-ATGCCCTATCTGAAAATCCATA
979904 TTTTCAATAT
Statistics
Matches: 128, Mismatches: 21, Indels: 14
0.79 0.13 0.09
Matches are distributed among these distances:
58 7 0.05
59 116 0.91
60 5 0.04
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.33
Consensus pattern (58 bp):
CATTTTAGCACATAAATGCCCTATCTGAAAATCCATACCATTAGTATGATTTCCTTAC
Found at i:979858 original size:118 final size:117
Alignment explanation
Indices: 979732--979994 Score: 314
Period size: 118 Copynumber: 2.2 Consensus size: 117
979722 TCATACCATT
** *
979732 AGTATGATTTTGTTACCATTTTAGCACATGAA-ATGCCCTATATGAAAATCCATACCATT-AGTA
1 AGTATGATTTCCTTACCATTTTAGCACAT-AATATGCCCTATATGAAAATCCATA-CATTCAATA
* * * * * * *
979795 TGATTTCCTTATCCTTGTAGCACCCTTAGTGCTCTATCTGGAAACCCATACACTC
64 TCATTTCCTTATCATT-TAGCACACTCAGCGCTCCATATGGAAACCCATACACTC
* * * **
979850 AGTATGATTCCCTTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCATATTTTCAATATC
1 AGTATGATTTCCTTACCATTTTAGCACATAATATGCCCTATATGAAAATCCATACATTCAATATC
* * *
979915 ATTTCCTTATCATTTAGTACACTCAGCGCTCCATATGGAAATCTATACACTC
66 ATTTCCTTATCATTTAGCACACTCAGCGCTCCATATGGAAACCCATACACTC
*
979967 AGTATGATTTCCTTATCATTTTAGCACA
1 AGTATGATTTCCTTACCATTTTAGCACA
979995 CAAAGTGTCA
Statistics
Matches: 123, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
117 60 0.49
118 63 0.51
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (117 bp):
AGTATGATTTCCTTACCATTTTAGCACATAATATGCCCTATATGAAAATCCATACATTCAATATC
ATTTCCTTATCATTTAGCACACTCAGCGCTCCATATGGAAACCCATACACTC
Found at i:979923 original size:59 final size:59
Alignment explanation
Indices: 979718--979994 Score: 203
Period size: 59 Copynumber: 4.7 Consensus size: 59
979708 CCCTATTCGA
* ** * *
979718 AAATTCATACCATT-AGTATGATTTTGTTACCATTTTAGCACATGAA-ATGCCCTATATGA
1 AAATCCATA-CATTCAGTATGATTTCCTTACCATTTTAGCACAT-AATATGCCCTATCTGG
* * *
979777 AAATCCATACCATT-AGTATGATTTCCTTATCC-TTGTAGCACCCT--TAGTGCTCTATCTGG
1 AAATCCATA-CATTCAGTATGATTTCCTTA-CCATTTTAGCA-CATAATA-TGCCCTATCTGG
* * *
979836 AAACCCATACACTCAGTATGATTCCCTTACCATTTTAGCACATAATATGCCCTATCTGG
1 AAATCCATACATTCAGTATGATTTCCTTACCATTTTAGCACATAATATGCCCTATCTGG
** * * * * * ** *
979895 AAATCCATATTTTCAATATCATTTCCTTATCA-TTTAGTACACTCA-GCGCTCC-ATATGG
1 AAATCCATACATTCAGTATGATTTCCTTACCATTTTAGCACA-TAATATGC-CCTATCTGG
* * *
979953 AAATCTATACACTCAGTATGATTTCCTTATCATTTTAGCACA
1 AAATCCATACATTCAGTATGATTTCCTTACCATTTTAGCACA
979995 CAAAGTGTCA
Statistics
Matches: 173, Mismatches: 34, Indels: 22
0.76 0.15 0.10
Matches are distributed among these distances:
58 49 0.28
59 118 0.68
60 6 0.03
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.36
Consensus pattern (59 bp):
AAATCCATACATTCAGTATGATTTCCTTACCATTTTAGCACATAATATGCCCTATCTGG
Found at i:979977 original size:58 final size:58
Alignment explanation
Indices: 979634--980001 Score: 198
Period size: 59 Copynumber: 6.3 Consensus size: 58
979624 CCTTTTATTA
* * * * * * *
979634 TTAGCACTCTCAGTGCTCTATCTGGAAGAT-CATACACTTAGTACGCTTCCCCTT-TCATT
1 TTAGCACACTAAGTGCTCCATCTGGAA-ATCCATACACTCAGTATGATT-TCCTTATCA-T
* * * * ** *
979693 TTAGCACACGAAGTGC-CCTAT-TCGAAAATTCATAC-CATTAGTATGATTTTGTTACCATT
1 TTAGCACACTAAGTGCTCC-ATCT-GGAAATCCATACAC-TCAGTATGATTTCCTTATCA-T
* * * * *
979752 TTAGCACA-TGAAATGC-CCTATATGAAAATCCATAC-CATTAGTATGATTTCCTTATCCT
1 TTAGCACACT-AAGTGCTCC-ATCTGGAAATCCATACAC-TCAGTATGATTTCCTTATCAT
* * * * * *
979810 TGTAGCACCCTTAGTGCTCTATCTGGAAACCCATACACTCAGTATGATTCCCTTACCATT
1 T-TAGCACACTAAGTGCTCCATCTGGAAATCCATACACTCAGTATGATTTCCTTATCA-T
* *** * *
979870 TTAGCACA-TAATATGC-CCTATCTGGAAATCCATATTTTCAATATCATTTCCTTATCAT
1 TTAGCACACTAA-GTGCTCC-ATCTGGAAATCCATACACTCAGTATGATTTCCTTATCAT
* * * * *
979928 TTAGTACACTCAGCGCTCCATATGGAAATCTATACACTCAGTATGATTTCCTTATCATT
1 TTAGCACACTAAGTGCTCCATCTGGAAATCCATACACTCAGTATGATTTCCTTATCA-T
*
979987 TTAGCACACAAAGTG
1 TTAGCACACTAAGTG
980002 TCATTCGGTA
Statistics
Matches: 236, Mismatches: 56, Indels: 34
0.72 0.17 0.10
Matches are distributed among these distances:
58 53 0.22
59 177 0.75
60 6 0.03
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (58 bp):
TTAGCACACTAAGTGCTCCATCTGGAAATCCATACACTCAGTATGATTTCCTTATCAT
Found at i:981586 original size:18 final size:18
Alignment explanation
Indices: 981562--981599 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
981552 ATCAAAAGGG
*
981562 AAAAAAAAAGCTAAAAAAT
1 AAAAAAAAA-CCAAAAAAT
981581 AAAAAAAAACCAAAAAAT
1 AAAAAAAAACCAAAAAAT
981599 A
1 A
981600 GTAAATGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.82, C:0.08, G:0.03, T:0.08
Consensus pattern (18 bp):
AAAAAAAAACCAAAAAAT
Found at i:983166 original size:12 final size:12
Alignment explanation
Indices: 983145--983175 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
983135 AATAGGTTGG
*
983145 GAAAATAAAAAA
1 GAAAAAAAAAAA
983157 GAAAAAAAAAAA
1 GAAAAAAAAAAA
983169 GAAAAAA
1 GAAAAAA
983176 GAGGCAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (12 bp):
GAAAAAAAAAAA
Found at i:983818 original size:26 final size:26
Alignment explanation
Indices: 983789--983843 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
983779 GCTTCTACCA
983789 CAACAACAATAGGCATTCAAACAACC
1 CAACAACAATAGGCATTCAAACAACC
*
983815 CAACAACAATAGGCATTCGAACAACC
1 CAACAACAATAGGCATTCAAACAACC
983841 CAA
1 CAA
983844 AGGTAAGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.49, C:0.31, G:0.09, T:0.11
Consensus pattern (26 bp):
CAACAACAATAGGCATTCAAACAACC
Found at i:988546 original size:107 final size:107
Alignment explanation
Indices: 988357--988577 Score: 406
Period size: 107 Copynumber: 2.1 Consensus size: 107
988347 CCCAGTGATT
988357 GATTTTGAGATGCCTATATGTCAAAGGGAAATCAAGAATTATGATAATGAGGAGGAATCTGACTT
1 GATTTTGAGATGCCTATATGTCAAAGGGAAATCAAGAATTATGATAATGAGGAGGAATCTGACTT
** *
988422 ATCTTCTGAAATGCTAAAAATGGTTGAAGGAGAAGATAAGTA
66 ATCTTCAAAAATACTAAAAATGGTTGAAGGAGAAGATAAGTA
*
988464 GATTTTGAGATGCCTATATGTCAAAGGGAAATCAATAATTATGATAATGAGGAGGAATCTGACTT
1 GATTTTGAGATGCCTATATGTCAAAGGGAAATCAAGAATTATGATAATGAGGAGGAATCTGACTT
988529 ATCTTCAAAAATACTAAAAATGGTTGAAGGAGAAGATAAGTA
66 ATCTTCAAAAATACTAAAAATGGTTGAAGGAGAAGATAAGTA
988571 GATTTTG
1 GATTTTG
988578 CCTCATGAAG
Statistics
Matches: 110, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
107 110 1.00
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.29
Consensus pattern (107 bp):
GATTTTGAGATGCCTATATGTCAAAGGGAAATCAAGAATTATGATAATGAGGAGGAATCTGACTT
ATCTTCAAAAATACTAAAAATGGTTGAAGGAGAAGATAAGTA
Found at i:993269 original size:27 final size:27
Alignment explanation
Indices: 993193--993342 Score: 105
Period size: 27 Copynumber: 5.4 Consensus size: 27
993183 TTTGTGTGTA
* * *
993193 TATATATATATATATAATTTTTAAA-AA
1 TATAT-TATATATATAGTTTTGAAATAG
993220 TAATAATTATTATATATAG--TTGAAATAG
1 T-AT-ATTA-TATATATAGTTTTGAAATAG
993248 TATATTATATATATAGTTTTG-AA-AG
1 TATATTATATATATAGTTTTGAAATAG
* *
993273 TAATATGTACATATTATAGTTTTAAAATAG
1 T-ATAT-TATATA-TATAGTTTTGAAATAG
*
993303 TATATATTACATATATAGTTTTGAAAGTA-
1 --TATATTATATATATAGTTTTGAAA-TAG
*
993332 AATATTATATA
1 TATATTATATA
993343 GATTTGAAAA
Statistics
Matches: 101, Mismatches: 8, Indels: 28
0.74 0.06 0.20
Matches are distributed among these distances:
25 12 0.12
26 10 0.10
27 25 0.25
28 15 0.15
29 24 0.24
30 10 0.10
31 4 0.04
32 1 0.01
ACGTcount: A:0.45, C:0.01, G:0.08, T:0.45
Consensus pattern (27 bp):
TATATTATATATATAGTTTTGAAATAG
Found at i:993340 original size:23 final size:23
Alignment explanation
Indices: 993314--993361 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
993304 ATATATTACA
* *
993314 TATATAGTTTTGAAAGTAAATAT
1 TATATAGATTTGAAAATAAATAT
993337 TATATAGATTTGAAAATAAATAT
1 TATATAGATTTGAAAATAAATAT
993360 TA
1 TA
993362 GTGCATTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (23 bp):
TATATAGATTTGAAAATAAATAT
Found at i:993380 original size:4 final size:4
Alignment explanation
Indices: 993371--993421 Score: 102
Period size: 4 Copynumber: 12.8 Consensus size: 4
993361 AGTGCATTAT
993371 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
993419 ATA
1 ATA
993422 TATTACTCTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:993440 original size:5 final size:5
Alignment explanation
Indices: 993430--993456 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
993420 TATATTACTC
993430 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
993457 ATTTAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:993460 original size:18 final size:18
Alignment explanation
Indices: 993437--993472 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
993427 CTCTTTTATT
* *
993437 TTATTTTATTTTATTTTA
1 TTATTTAATTTAATTTTA
993455 TTATTTAATTTAATTTTA
1 TTATTTAATTTAATTTTA
993473 GGTTCATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TTATTTAATTTAATTTTA
Found at i:999153 original size:52 final size:52
Alignment explanation
Indices: 999096--999208 Score: 208
Period size: 52 Copynumber: 2.2 Consensus size: 52
999086 CTTGGAGAAA
* *
999096 ACTTGTTCTCCCTTTAGATGATAAAACAAATCATTAATCCTGGGAATATGAT
1 ACTTGTTCTCCCTTTAGATGATAAAACAAATCATCAATCCTCGGAATATGAT
999148 ACTTGTTCTCCCTTTAGATGATAAAACAAATCATCAATCCTCGGAATATGAT
1 ACTTGTTCTCCCTTTAGATGATAAAACAAATCATCAATCCTCGGAATATGAT
999200 ACTTGTTCT
1 ACTTGTTCT
999209 TGATAGTCAC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 59 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.35
Consensus pattern (52 bp):
ACTTGTTCTCCCTTTAGATGATAAAACAAATCATCAATCCTCGGAATATGAT
Found at i:1000297 original size:81 final size:81
Alignment explanation
Indices: 1000162--1000507 Score: 487
Period size: 81 Copynumber: 4.3 Consensus size: 81
1000152 TTTTAGATCA
* ** * * * *
1000162 AAATGCACTGTTAAACATTTATTC-TTTCCTCTAAAGGCATTTAACCTTTCATCTAACTTGCATT
1 AAATGCACAGTTAGGCATTTAATCTTTTACTC-AAAGGCATTTAACCTTTCATCTAACTAGCATG
* *
1000226 ATTTGCATCTTTCTGCC
65 ATTGGCACCTTTCTGCC
* * *
1000243 AAATGCACAGTTAGGCATTTAATCTTTTGCCCAAAGGCATTTAACCTTTCATCTAACTAGCATGG
1 AAATGCACAGTTAGGCATTTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTAGCATGA
* *
1000308 TTGACACCTTTCTACC
66 TTGGCACCTTTCTGCC
* * * *
1000324 AAATGCACAGTTAGACATTTAATCTATTACTCAAAGGCATTTAACCTTTCATCAAACTACCATGA
1 AAATGCACAGTTAGGCATTTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTAGCATGA
1000389 TTGGCACCTTTCTGCC
66 TTGGCACCTTTCTGCC
* * *
1000405 AAATGCACAGTTAGGCATTTAATCTTATACTCAAAGGCATTTAACCTTTCATCGAAGTAGCATGA
1 AAATGCACAGTTAGGCATTTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTAGCATGA
1000470 TTGGCACCTTTCTGCC
66 TTGGCACCTTTCTGCC
1000486 AAATGCACAGTTAGGCATTTAA
1 AAATGCACAGTTAGGCATTTAA
1000508 CATTTCATCT
Statistics
Matches: 236, Mismatches: 28, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
81 231 0.98
82 5 0.02
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (81 bp):
AAATGCACAGTTAGGCATTTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTAGCATGA
TTGGCACCTTTCTGCC
Found at i:1000531 original size:59 final size:58
Alignment explanation
Indices: 1000439--1000565 Score: 191
Period size: 59 Copynumber: 2.2 Consensus size: 58
1000429 TTATACTCAA
* * **
1000439 AGGCATTTAACCTTTCATCGAAGTAGCATGATTGGCACCTTTCTGCCAAATGCACAGTT
1 AGGCATTTAACATTTCATCGAACTAGCATGATTGGCACCTTTCTG-CAAATGCACAACT
* *
1000498 AGGCATTTAACATTTCATCTAACTAGTATGATTGGCACCTTTCTGCAAATGCACAACT
1 AGGCATTTAACATTTCATCGAACTAGCATGATTGGCACCTTTCTGCAAATGCACAACT
1000556 AGGCATTTAA
1 AGGCATTTAA
1000566 TCTTTTACTC
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
58 21 0.34
59 41 0.66
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (58 bp):
AGGCATTTAACATTTCATCGAACTAGCATGATTGGCACCTTTCTGCAAATGCACAACT
Found at i:1000593 original size:220 final size:221
Alignment explanation
Indices: 1000277--1000734 Score: 749
Period size: 220 Copynumber: 2.1 Consensus size: 221
1000267 TTTTGCCCAA
* * **
1000277 AGGCATTTAACCTTTCATCTAACTAGCATGGTTGACACCTTTCTACCAAATGCACAGTTAGACAT
1 AGGCATTTAACATTTCATCTAACTAGCATGATTGACACCTTTCTACCAAATGCACAACTAGACAT
1000342 TTAATCTATTACTCAAAGGCATTTAACCTTTCATCAAACTACCATGATTGGCACCTTTCTGCCAA
66 TTAATCTATTACTCAAAGGCATTTAACCTTTCATCAAACTACCATGATTGGCACCTTTCTGCCAA
*
1000407 ATGCACAGTTAGGCATTTAATCTTATACTCAAAGGCATTTAACCTTTCATCGAAGTAGCATGATT
131 ATGCACAGTTAGGCATTTAATCTTATACTCAAAGGCATTTAACCTTTCATCGAACTAGCATGATT
1000472 GGCACCTTTCTGCCAAATGC-ACAGTT
196 GGCACCTTTCTGCCAAATGCAAC-GTT
* * * *
1000498 AGGCATTTAACATTTCATCTAACTAGTATGATTGGCACCTTTCT-GCAAATGCACAACTAGGCAT
1 AGGCATTTAACATTTCATCTAACTAGCATGATTGACACCTTTCTACCAAATGCACAACTAGACAT
* * * *
1000562 TTAATCTTTTACTCAAAGGCATTTAACCTTTCATCGAAGTAGCATGATTGGCACCTTTCTGCCAA
66 TTAATCTATTACTCAAAGGCATTTAACCTTTCATCAAACTACCATGATTGGCACCTTTCTGCCAA
* *
1000627 ATGCACAGTTAGGCATTTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTAGCATGATT
131 ATGCACAGTTAGGCATTTAATCTTATACTCAAAGGCATTTAACCTTTCATCGAACTAGCATGATT
1000692 GGCACCTTTCTGCCAAATGCAACGTT
196 GGCACCTTTCTGCCAAATGCAACGTT
*
1000718 AGGCATTTAATATTTCA
1 AGGCATTTAACATTTCA
1000735 CTCAAAGGCA
Statistics
Matches: 220, Mismatches: 16, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
220 178 0.81
221 42 0.19
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (221 bp):
AGGCATTTAACATTTCATCTAACTAGCATGATTGACACCTTTCTACCAAATGCACAACTAGACAT
TTAATCTATTACTCAAAGGCATTTAACCTTTCATCAAACTACCATGATTGGCACCTTTCTGCCAA
ATGCACAGTTAGGCATTTAATCTTATACTCAAAGGCATTTAACCTTTCATCGAACTAGCATGATT
GGCACCTTTCTGCCAAATGCAACGTT
Found at i:1000609 original size:139 final size:140
Alignment explanation
Indices: 1000358--1000646 Score: 508
Period size: 139 Copynumber: 2.1 Consensus size: 140
1000348 TATTACTCAA
* **
1000358 AGGCATTTAACCTTTCATCAAACTACCATGATTGGCACCTTTCTGCCAAATGCACAGTTAGGCAT
1 AGGCATTTAACATTTCATCAAACTACCATGATTGGCACCTTTCTGCCAAATGCACAACTAGGCAT
1000423 TTAATCTTATACTCAAAGGCATTTAACCTTTCATCGAAGTAGCATGATTGGCACCTTTCTGCCAA
66 TTAATCTTATACTCAAAGGCATTTAACCTTTCATCGAAGTAGCATGATTGGCACCTTTCTGCCAA
1000488 ATGCACAGTT
131 ATGCACAGTT
* **
1000498 AGGCATTTAACATTTCATCTAACTAGTATGATTGGCACCTTTCTG-CAAATGCACAACTAGGCAT
1 AGGCATTTAACATTTCATCAAACTACCATGATTGGCACCTTTCTGCCAAATGCACAACTAGGCAT
*
1000562 TTAATCTTTTACTCAAAGGCATTTAACCTTTCATCGAAGTAGCATGATTGGCACCTTTCTGCCAA
66 TTAATCTTATACTCAAAGGCATTTAACCTTTCATCGAAGTAGCATGATTGGCACCTTTCTGCCAA
1000627 ATGCACAGTT
131 ATGCACAGTT
1000637 AGGCATTTAA
1 AGGCATTTAA
1000647 TCTTTTACTC
Statistics
Matches: 142, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
139 101 0.71
140 41 0.29
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (140 bp):
AGGCATTTAACATTTCATCAAACTACCATGATTGGCACCTTTCTGCCAAATGCACAACTAGGCAT
TTAATCTTATACTCAAAGGCATTTAACCTTTCATCGAAGTAGCATGATTGGCACCTTTCTGCCAA
ATGCACAGTT
Found at i:1000791 original size:301 final size:302
Alignment explanation
Indices: 1000196--1000808 Score: 971
Period size: 301 Copynumber: 2.0 Consensus size: 302
1000186 TTTCCTCTAA
* * * * * **
1000196 AGGCATTTAACCTTTCATCTAACTTGCATTATTTGCATCTTTCTGCCAAATGCACAGTTAGGCAT
1 AGGCATTTAACATTTCATCTAACTAGCATGATTGGCACCTTTCTGCCAAATGCACAACTAGGCAT
* * *
1000261 TTAATCTTTTGCCCAAAGGCATTTAACCTTTCATCTAACTAGCATGGTTGACACCTTTCTACCAA
66 TTAATCTTTTACCCAAAGGCATTTAACCTTTCATCGAACTAGCATGATTGACACCTTTCTACCAA
1000326 ATGCACAGTTAGACATTTAATCTATTACTCAAAGGCATTTAACCTTTCATCAAACTACCATGATT
131 ATGCACAGTTAGACATTTAATCTATTACTCAAAGGCATTTAACCTTTCATCAAACTACCATGATT
*
1000391 GGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAATCTTATACTCAAAGGCATTTAACCTTTCA
196 GGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAATATTATACTCAAAGGCATTTAACCTTTCA
* * *
1000456 TCGAAGTAGCATGATTGGCACCTTTCTGCCAAATGCACAGTT
261 TCGAACTAGCATGATTGGCACATTTCTACCAAATGCACAGTT
*
1000498 AGGCATTTAACATTTCATCTAACTAGTATGATTGGCACCTTTCTG-CAAATGCACAACTAGGCAT
1 AGGCATTTAACATTTCATCTAACTAGCATGATTGGCACCTTTCTGCCAAATGCACAACTAGGCAT
* * * *
1000562 TTAATCTTTTACTCAAAGGCATTTAACCTTTCATCGAAGTAGCATGATTGGCACCTTTCTGCCAA
66 TTAATCTTTTACCCAAAGGCATTTAACCTTTCATCGAACTAGCATGATTGACACCTTTCTACCAA
* * * *
1000627 ATGCACAGTTAGGCATTTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTAGCATGATT
131 ATGCACAGTTAGACATTTAATCTATTACTCAAAGGCATTTAACCTTTCATCAAACTACCATGATT
1000692 GGCACCTTTCTGCCAAATGCA-ACGTTAGGCATTTAATATT-TCACTCAAAGGCATTTAACCTTT
196 GGCACCTTTCTGCCAAATGCACA-GTTAGGCATTTAATATTAT-ACTCAAAGGCATTTAACCTTT
*
1000755 CATCTAACTAGCATGATTGGCACATTTCTACCAAATGCACAGTT
259 CATCGAACTAGCATGATTGGCACATTTCTACCAAATGCACAGTT
1000799 AGGCATTTAA
1 AGGCATTTAA
1000809 TCTTTTATTT
Statistics
Matches: 285, Mismatches: 24, Indels: 5
0.91 0.08 0.02
Matches are distributed among these distances:
300 2 0.01
301 244 0.86
302 39 0.14
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.34
Consensus pattern (302 bp):
AGGCATTTAACATTTCATCTAACTAGCATGATTGGCACCTTTCTGCCAAATGCACAACTAGGCAT
TTAATCTTTTACCCAAAGGCATTTAACCTTTCATCGAACTAGCATGATTGACACCTTTCTACCAA
ATGCACAGTTAGACATTTAATCTATTACTCAAAGGCATTTAACCTTTCATCAAACTACCATGATT
GGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAATATTATACTCAAAGGCATTTAACCTTTCA
TCGAACTAGCATGATTGGCACATTTCTACCAAATGCACAGTT
Found at i:1000828 original size:81 final size:81
Alignment explanation
Indices: 1000498--1000815 Score: 523
Period size: 81 Copynumber: 3.9 Consensus size: 81
1000488 ATGCACAGTT
* * **
1000498 AGGCATTTAACATTTCATCTAACTAGTATGATTGGCACCTTTCTG-CAAATGCACAACTAGGCAT
1 AGGCATTTAACCTTTCATCTAACTAGCATGATTGGCACCTTTCTGCCAAATGCACAGTTAGGCAT
1000562 TTAATCTTTTACTCAA
66 TTAATCTTTTACTCAA
* *
1000578 AGGCATTTAACCTTTCATCGAAGTAGCATGATTGGCACCTTTCTGCCAAATGCACAGTTAGGCAT
1 AGGCATTTAACCTTTCATCTAACTAGCATGATTGGCACCTTTCTGCCAAATGCACAGTTAGGCAT
1000643 TTAATCTTTTACTCAA
66 TTAATCTTTTACTCAA
1000659 AGGCATTTAACCTTTCATCTAACTAGCATGATTGGCACCTTTCTGCCAAATGCA-ACGTTAGGCA
1 AGGCATTTAACCTTTCATCTAACTAGCATGATTGGCACCTTTCTGCCAAATGCACA-GTTAGGCA
* *
1000723 TTTAATATTTCACTCAA
65 TTTAATCTTTTACTCAA
* *
1000740 AGGCATTTAACCTTTCATCTAACTAGCATGATTGGCACATTTCTACCAAATGCACAGTTAGGCAT
1 AGGCATTTAACCTTTCATCTAACTAGCATGATTGGCACCTTTCTGCCAAATGCACAGTTAGGCAT
1000805 TTAATCTTTTA
66 TTAATCTTTTA
1000816 TTTTAAAACA
Statistics
Matches: 221, Mismatches: 14, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
80 42 0.19
81 178 0.81
82 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (81 bp):
AGGCATTTAACCTTTCATCTAACTAGCATGATTGGCACCTTTCTGCCAAATGCACAGTTAGGCAT
TTAATCTTTTACTCAA
Found at i:1007967 original size:323 final size:324
Alignment explanation
Indices: 1007407--1008044 Score: 931
Period size: 323 Copynumber: 2.0 Consensus size: 324
1007397 TCTTTCCTCT
** * *
1007407 AAAGGCATTTAACCTTTCATCTAACTTGTACTATTAGCACCTTTATTCCAAATGCACAGTTAGAC
1 AAAGGCATTTAACCTTTCATCTAACAAGCACTATTAGCACCTTTATGCCAAATGCACAGTTAGAC
* *
1007472 ATTTAATCTTTTACCCAAAGGCATTTAACCTTTCATCTAACTAGCATGATTGGCACCTTTCTACC
66 ATTTAATATTTTACCCAAAGGCATTTAACATTTCATCTAACTAGCATGATTGGCACCTTTCTACC
* *
1007537 AAATGCACAGCTAGACATTTAATCTTTTACTGCAAGGCTTTTAACCTTTCATCTAAATAGCATGA
131 AAATGCACAGCTAGACATTTAAACTTTTACTGCAAGGCATTTAACCTTTCATCTAAATAGCATGA
** * * *
1007602 TTGGTACCTTTCATCCAAATGCACAGTTAGGCATTTAATCTTTTACTCAAAGGCATTTAACCTTT
196 TTGACACCTTTCATCCAAATGCACAGTTAAGCATTCAATCTTTCACTCAAAGGCATTTAACCTTT
*
1007667 CATCTAACTAGCATGATTGGCA-AGTTCTACCAAATGCACAATTAGGTATTTAATATTTTACTC
261 CATCTAACTAGCATGATTGGCATAGTTCTACCAAATGCACAATTAGGGATTTAATATTTTACTC
* * * *
1007730 AAAGGCATTTAACCTTTCATCTAACAAGCA-TAATTGGCATCTTTCTGCCAAATGCACAGTTAGG
1 AAAGGCATTTAACCTTTCATCTAACAAGCACT-ATTAGCACCTTTATGCCAAATGCACAGTTAGA
* *
1007794 CATTTAATATTTTACTCAAAGGCATTTAACATTTCATCTAACTAGCATGATTGGCACCTTTCTGC
65 CATTTAATATTTTACCCAAAGGCATTTAACATTTCATCTAACTAGCATGATTGGCACCTTTCTAC
* * * *
1007859 CAAATGCACAGTTAGGCATTTAAACTTTTACT-CAAAGGCATTTAACCTTTCGTCTAACTAGCAT
130 CAAATGCACAGCTAGACATTTAAACTTTTACTGC-AAGGCATTTAACCTTTCATCTAAATAGCAT
* * * * * *
1007923 GATTGACACCTTTCCTTCAAATGCACAGTTAAGTATTCAATCTTTCATTCAAAGGTATTTAATCT
194 GATTGACACCTTTCATCCAAATGCACAGTTAAGCATTCAATCTTTCACTCAAAGGCATTTAACCT
* ** *
1007988 TTCATCTAACTAGCATGATTGGCATATTTCTGTCAAATGCACAGTTAGGGATTTAAT
259 TTCATCTAACTAGCATGATTGGCATAGTTCTACCAAATGCACAATTAGGGATTTAAT
1008045 CTTTCAGTTT
Statistics
Matches: 278, Mismatches: 34, Indels: 5
0.88 0.11 0.02
Matches are distributed among these distances:
322 2 0.01
323 249 0.90
324 27 0.10
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.35
Consensus pattern (324 bp):
AAAGGCATTTAACCTTTCATCTAACAAGCACTATTAGCACCTTTATGCCAAATGCACAGTTAGAC
ATTTAATATTTTACCCAAAGGCATTTAACATTTCATCTAACTAGCATGATTGGCACCTTTCTACC
AAATGCACAGCTAGACATTTAAACTTTTACTGCAAGGCATTTAACCTTTCATCTAAATAGCATGA
TTGACACCTTTCATCCAAATGCACAGTTAAGCATTCAATCTTTCACTCAAAGGCATTTAACCTTT
CATCTAACTAGCATGATTGGCATAGTTCTACCAAATGCACAATTAGGGATTTAATATTTTACTC
Found at i:1008050 original size:81 final size:81
Alignment explanation
Indices: 1007390--1008048 Score: 862
Period size: 81 Copynumber: 8.1 Consensus size: 81
1007380 CATTGTTAAA
* * * * * *
1007390 CATTTATTC-TTTCCTCTAAAGGCATTTAACCTTTCATCTAACTTGTACT-ATTAGCACCTTTAT
1 CATTTAATCTTTTACTC-AAAGGCATTTAACCTTTCATCTAACTAGCA-TGATTGGCACCTTTCT
* *
1007453 TCCAAATGCACAGTTAGA
64 GCCAAATGCACAGTTAGG
* *
1007471 CATTTAATCTTTTACCCAAAGGCATTTAACCTTTCATCTAACTAGCATGATTGGCACCTTTCTAC
1 CATTTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTAGCATGATTGGCACCTTTCTGC
* *
1007536 CAAATGCACAGCTAGA
66 CAAATGCACAGTTAGG
* * *
1007552 CATTTAATCTTTTACTGC-AAGGCTTTTAACCTTTCATCTAAATAGCATGATTGGTACCTTTCAT
1 CATTTAATCTTTTACT-CAAAGGCATTTAACCTTTCATCTAACTAGCATGATTGGCACCTTTC-T
1007616 -CCAAATGCACAGTTAGG
64 GCCAAATGCACAGTTAGG
** *
1007633 CATTTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTAGCATGATTGGCA-AGTTCTAC
1 CATTTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTAGCATGATTGGCACCTTTCTGC
*
1007697 CAAATGCACAATTAGG
66 CAAATGCACAGTTAGG
* * * * *
1007713 TATTTAATATTTTACTCAAAGGCATTTAACCTTTCATCTAACAAGCATAATTGGCATCTTTCTGC
1 CATTTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTAGCATGATTGGCACCTTTCTGC
1007778 CAAATGCACAGTTAGG
66 CAAATGCACAGTTAGG
* *
1007794 CATTTAATATTTTACTCAAAGGCATTTAACATTTCATCTAACTAGCATGATTGGCACCTTTCTGC
1 CATTTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTAGCATGATTGGCACCTTTCTGC
1007859 CAAATGCACAGTTAGG
66 CAAATGCACAGTTAGG
* * *
1007875 CATTTAAACTTTTACTCAAAGGCATTTAACCTTTCGTCTAACTAGCATGATTGACACCTTTCCT-
1 CATTTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTAGCATGATTGGCACCTTT-CTG
* *
1007939 TCAAATGCACAGTTAAG
65 CCAAATGCACAGTTAGG
* * * * * * ** *
1007956 TATTCAATCTTTCATTCAAAGGTATTTAATCTTTCATCTAACTAGCATGATTGGCATATTTCTGT
1 CATTTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTAGCATGATTGGCACCTTTCTGC
1008021 CAAATGCACAGTTAGG
66 CAAATGCACAGTTAGG
*
1008037 GATTTAATCTTT
1 CATTTAATCTTT
1008049 CAGTTTAAAA
Statistics
Matches: 514, Mismatches: 55, Indels: 18
0.88 0.09 0.03
Matches are distributed among these distances:
79 1 0.00
80 75 0.15
81 429 0.83
82 9 0.02
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.36
Consensus pattern (81 bp):
CATTTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTAGCATGATTGGCACCTTTCTGC
CAAATGCACAGTTAGG
Found at i:1013841 original size:29 final size:29
Alignment explanation
Indices: 1013774--1013838 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
1013764 ATATTTGTAG
*
1013774 AAGTTTAGGGGTTAAAAAGGTAATTTCAAA
1 AAGTTTA-GGGATAAAAAGGTAATTTCAAA
*
1013804 ATGTTTAGGGATAAAAAGTGTAATTT-ATAA
1 AAGTTTAGGGATAAAAAG-GTAATTTCA-AA
1013834 AAGTT
1 AAGTT
1013839 AGGTGTTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 11 0.37
30 19 0.63
ACGTcount: A:0.43, C:0.02, G:0.22, T:0.34
Consensus pattern (29 bp):
AAGTTTAGGGATAAAAAGGTAATTTCAAA
Found at i:1015013 original size:19 final size:19
Alignment explanation
Indices: 1014971--1015015 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
1014961 ACTATGCTGA
*
1014971 AAATTAATGTTAGAATGTTG
1 AAATTGATGTTAG-ATGTTG
1014991 AAATTGATGTTAG-TGTGTG
1 AAATTGATGTTAGATGT-TG
1015010 AAATTG
1 AAATTG
1015016 GCCATTTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 3 0.13
19 8 0.35
20 12 0.52
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (19 bp):
AAATTGATGTTAGATGTTG
Found at i:1016308 original size:26 final size:26
Alignment explanation
Indices: 1016279--1016332 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
1016269 GTTTTGGTAT
1016279 AATGGCACCTTCGAGTGCAATAGATA
1 AATGGCACCTTCGAGTGCAATAGATA
* *
1016305 AATGGCACCTTCGAGTGCGATTGATA
1 AATGGCACCTTCGAGTGCAATAGATA
1016331 AA
1 AA
1016333 CAACATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (26 bp):
AATGGCACCTTCGAGTGCAATAGATA
Found at i:1025343 original size:18 final size:18
Alignment explanation
Indices: 1025317--1025356 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
1025307 TTCATTTTTC
1025317 TCATATATTTACAAATTG
1 TCATATATTTACAAATTG
*
1025335 TCATCTATTTACAAATTG
1 TCATATATTTACAAATTG
1025353 TCAT
1 TCAT
1025357 GGTACATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.45
Consensus pattern (18 bp):
TCATATATTTACAAATTG
Found at i:1045427 original size:20 final size:21
Alignment explanation
Indices: 1045402--1045452 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1045392 ATAAAGACAT
1045402 TATCGATACTC-GA-GGTCCAA
1 TATCGATACTCTGATGGT-CAA
* *
1045422 TATCGATACCCTGATGGTCAG
1 TATCGATACTCTGATGGTCAA
1045443 TATCGATACT
1 TATCGATACT
1045453 GAGACATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 10 0.38
21 13 0.50
22 3 0.12
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (21 bp):
TATCGATACTCTGATGGTCAA
Found at i:1045547 original size:85 final size:84
Alignment explanation
Indices: 1045442--1045599 Score: 192
Period size: 86 Copynumber: 1.9 Consensus size: 84
1045432 CTGATGGTCA
* ** ** * *
1045442 GTATCGATACTGAGACA-TTTTTGAAAACATCAAAGCTGAGTTTGGTATCGATACCCAGGGTAGA
1 GTATCGATACTAAGACATTTTTTGAAAACATCAAAGCAAAAATTGGTATCGATAACCA-AGT-GA
1045506 GTATCGATACTCCCCATATGG
64 GTATCGATACTCCCCATATGG
** * *
1045527 GTATCGATACTAAGGTATTTTTTTAAAACATCGAAGCAAAAATTGGTATCGATAACCAAGTGAGT
1 GTATCGATACTAAGACATTTTTTGAAAACATCAAAGCAAAAATTGGTATCGATAACCAAGTGAGT
1045592 ATCGATAC
66 ATCGATAC
1045600 CCATGGGTAC
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
84 12 0.20
85 16 0.26
86 33 0.54
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.29
Consensus pattern (84 bp):
GTATCGATACTAAGACATTTTTTGAAAACATCAAAGCAAAAATTGGTATCGATAACCAAGTGAGT
ATCGATACTCCCCATATGG
Found at i:1054702 original size:21 final size:21
Alignment explanation
Indices: 1054659--1054702 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1054649 CGATGAACTG
* * **
1054659 TGGCTTTGTAATAGATCTGCT
1 TGGCTTTGTAACAGAGCACCT
1054680 TGGCTTTGTAACAGAGCACCT
1 TGGCTTTGTAACAGAGCACCT
1054701 TG
1 TG
1054703 ATTCTTTATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.36
Consensus pattern (21 bp):
TGGCTTTGTAACAGAGCACCT
Found at i:1061942 original size:15 final size:15
Alignment explanation
Indices: 1061922--1061951 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1061912 AATTACCATT
*
1061922 TTCCATTGAAATATC
1 TTCCATTAAAATATC
1061937 TTCCATTAAAATATC
1 TTCCATTAAAATATC
1061952 ACATAGTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.20, G:0.03, T:0.40
Consensus pattern (15 bp):
TTCCATTAAAATATC
Found at i:1072004 original size:16 final size:15
Alignment explanation
Indices: 1071983--1072013 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1071973 GGGCAAATTA
1071983 AATTCAGGTTAATTTT
1 AATTCAGGTT-ATTTT
1071999 AATTCAGGTTATTTT
1 AATTCAGGTTATTTT
1072014 CAGTTTGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.29, C:0.06, G:0.13, T:0.52
Consensus pattern (15 bp):
AATTCAGGTTATTTT
Found at i:1072043 original size:16 final size:16
Alignment explanation
Indices: 1072016--1072056 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
1072006 GTTATTTTCA
1072016 GTTTGA-TTACTTTAT
1 GTTTGAGTTACTTTAT
1072031 GTTTGAGTTACTTTAT
1 GTTTGAGTTACTTTAT
1072047 GTTTGAGTTA
1 GTTTGAGTTA
1072057 ATTTTGGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 6 0.24
16 19 0.76
ACGTcount: A:0.20, C:0.05, G:0.20, T:0.56
Consensus pattern (16 bp):
GTTTGAGTTACTTTAT
Found at i:1072066 original size:16 final size:16
Alignment explanation
Indices: 1072016--1072072 Score: 66
Period size: 16 Copynumber: 3.7 Consensus size: 16
1072006 GTTATTTTCA
*
1072016 GTTTGA-TTACTTTAT
1 GTTTGAGTTAATTTAT
*
1072031 GTTTGAGTTACTTTAT
1 GTTTGAGTTAATTTAT
1072047 GTTTGAGTTAATTT-T
1 GTTTGAGTTAATTTAT
1072062 GGTTT-AGTTAA
1 -GTTTGAGTTAA
1072073 ATTCTAGTCA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
15 13 0.33
16 26 0.67
ACGTcount: A:0.21, C:0.04, G:0.19, T:0.56
Consensus pattern (16 bp):
GTTTGAGTTAATTTAT
Found at i:1086688 original size:30 final size:29
Alignment explanation
Indices: 1086570--1086764 Score: 131
Period size: 30 Copynumber: 6.5 Consensus size: 29
1086560 GACGAAGATA
* * * *
1086570 TAATCTCACGCAGATGTCAAAACGGTGAAC
1 TAATCCCATGCAGATGTCAGAACGG-GAAT
* * * *
1086600 TAATCCCATGTATATGCCAGAACGGGGAAC
1 TAATCCCATGCAGATGTCAGAAC-GGGAAT
* * * *
1086630 TAATCTCATACATG-GGTCAAAACGGGGAAT
1 TAATCCCATGCA-GATGTCAGAAC-GGGAAT
* *
1086660 TAATCCTATGCAGATGTTAGAACAGGGAAT
1 TAATCCCATGCAGATGTCAGAAC-GGGAAT
* * *
1086690 TAATCCCATGTAGATGCCAGGACGAGGAAT
1 TAATCCCATGCAGATGTCAGAACG-GGAAT
** *
1086720 TAATCCCATAAAGATGTCAGAATGGGGAAT
1 TAATCCCATGCAGATGTCAGAA-CGGGAAT
*
1086750 TAATCTCATGCAGAT
1 TAATCCCATGCAGAT
1086765 ATAATAAATG
Statistics
Matches: 126, Mismatches: 34, Indels: 10
0.74 0.20 0.06
Matches are distributed among these distances:
29 2 0.02
30 121 0.96
31 3 0.02
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (29 bp):
TAATCCCATGCAGATGTCAGAACGGGAAT
Found at i:1086724 original size:90 final size:90
Alignment explanation
Indices: 1086570--1086764 Score: 225
Period size: 90 Copynumber: 2.2 Consensus size: 90
1086560 GACGAAGATA
* * * * * *
1086570 TAATCTCACGCAGATGTCAAAAC-GGTGAACTAATCCCATGTATATGCCAGAACGGGGAACTAAT
1 TAATCTCATGCAGATGTTAGAACAGG-GAATTAATCCCATGTAGATGCCAGAACGAGGAACTAAT
* *
1086634 CTCATACATG-GGTCAAAACGGGGAAT
65 CCCATA-AAGAGGTCAAAACGGGGAAT
* *
1086660 TAATC-CTATGCAGATGTTAGAACAGGGAATTAATCCCATGTAGATGCCAGGACGAGGAATTAAT
1 TAATCTC-ATGCAGATGTTAGAACAGGGAATTAATCCCATGTAGATGCCAGAACGAGGAACTAAT
* * *
1086724 CCCATAAAGATGTCAGAATGGGGAAT
65 CCCATAAAGAGGTCAAAACGGGGAAT
1086750 TAATCTCATGCAGAT
1 TAATCTCATGCAGAT
1086765 ATAATAAATG
Statistics
Matches: 88, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
89 3 0.03
90 82 0.93
91 3 0.03
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (90 bp):
TAATCTCATGCAGATGTTAGAACAGGGAATTAATCCCATGTAGATGCCAGAACGAGGAACTAATC
CCATAAAGAGGTCAAAACGGGGAAT
Found at i:1087358 original size:13 final size:13
Alignment explanation
Indices: 1087340--1087373 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1087330 GGTTTTGAAA
*
1087340 AAAGTCAACGGTC
1 AAAGTCAACAGTC
*
1087353 AAAGTCAATAGTC
1 AAAGTCAACAGTC
1087366 AAAGTCAA
1 AAAGTCAA
1087374 ATTCAACGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.18
Consensus pattern (13 bp):
AAAGTCAACAGTC
Found at i:1089851 original size:24 final size:25
Alignment explanation
Indices: 1089818--1089869 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
1089808 GGTTTTTCAA
1089818 AAATCATTTTT-CATACCTTTTTTTT
1 AAATCATTTTTACA-ACCTTTTTTTT
**
1089843 AAATC-TTTTTACAATTTTTTTTTT
1 AAATCATTTTTACAACCTTTTTTTT
1089867 AAA
1 AAA
1089870 AAAAAATCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.60
Consensus pattern (25 bp):
AAATCATTTTTACAACCTTTTTTTT
Found at i:1090513 original size:30 final size:29
Alignment explanation
Indices: 1090479--1090692 Score: 178
Period size: 30 Copynumber: 7.1 Consensus size: 29
1090469 GACGGATATA
* *
1090479 TAATCTCATGCTGATGTCAGAACAGGGAAC
1 TAATCTCATGCT-ATGTCAGAACGGGGAAT
* * *
1090509 TAATCCCATGCATATGTCAAAACGGGGAAC
1 TAATCTCATGC-TATGTCAGAACGGGGAAT
* * * * * *
1090539 TAATCCCATGCAGAGGTTAAAACAGGGAAT
1 TAATCTCATGC-TATGTCAGAACGGGGAAT
1090569 TAATCTCATGCATATGTCAGAA-GGGAGAAT
1 TAATCTCATGC-TATGTCAGAACGGG-GAAT
* * ** *
1090599 TAAACCCATGAAAATGTTAGAACGGGGAAT
1 TAATCTCATG-CTATGTCAGAACGGGGAAT
* *
1090629 TAATCTCATACAGATGTCAGAACGGGGAAT
1 TAATCTCATGC-TATGTCAGAACGGGGAAT
*
1090659 TAATCTCATGCATATGTCAGAATGGGGAAT
1 TAATCTCATGC-TATGTCAGAACGGGGAAT
1090689 TAAT
1 TAAT
1090693 AACGATGTCA
Statistics
Matches: 151, Mismatches: 28, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
29 2 0.01
30 145 0.96
31 4 0.03
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.24
Consensus pattern (29 bp):
TAATCTCATGCTATGTCAGAACGGGGAAT
Found at i:1090607 original size:90 final size:90
Alignment explanation
Indices: 1090479--1090691 Score: 259
Period size: 90 Copynumber: 2.4 Consensus size: 90
1090469 GACGGATATA
* * * * *
1090479 TAATCTCATGC-TGATGTCAGAACAGGGAACTAATCCCATGCATATGTCAAAACGGGGAACTAAT
1 TAATCTCATGCAT-ATGTCAGAACGGGGAATTAAACCCATGAAAATGTCAAAACGGGGAACTAAT
* *
1090543 CCCATGCAGAGGTTAAAACAGGGAAT
65 CCCATACAGAGGTCAAAACAGGGAAT
* * *
1090569 TAATCTCATGCATATGTCAGAA-GGGAGAATTAAACCCATGAAAATGTTAGAACGGGGAATTAAT
1 TAATCTCATGCATATGTCAGAACGGG-GAATTAAACCCATGAAAATGTCAAAACGGGGAACTAAT
* * * *
1090633 CTCATACAGATGTCAGAACGGGGAAT
65 CCCATACAGAGGTCAAAACAGGGAAT
*
1090659 TAATCTCATGCATATGTCAGAATGGGGAATTAA
1 TAATCTCATGCATATGTCAGAACGGGGAATTAA
1090692 TAACGATGTC
Statistics
Matches: 106, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
89 2 0.02
90 100 0.94
91 4 0.04
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (90 bp):
TAATCTCATGCATATGTCAGAACGGGGAATTAAACCCATGAAAATGTCAAAACGGGGAACTAATC
CCATACAGAGGTCAAAACAGGGAAT
Found at i:1090686 original size:60 final size:60
Alignment explanation
Indices: 1090479--1090692 Score: 225
Period size: 60 Copynumber: 3.6 Consensus size: 60
1090469 GACGGATATA
* * * * *
1090479 TAATCTCATGC-TGATGTCAGAACAGGGAACTAATCCCATGCATATGTCAAAACGGGGAAC
1 TAATCCCATGCAT-ATGTCAGAACAGGGAATTAATCTCATGCATATGTCAGAACGGGGAAT
* * * *
1090539 TAATCCCATGCAGAGGTTAAAACAGGGAATTAATCTCATGCATATGTCAGAA-GGGAGAAT
1 TAATCCCATGCATATGTCAGAACAGGGAATTAATCTCATGCATATGTCAGAACGGG-GAAT
* * * * * * *
1090599 TAAACCCATGAAAATGTTAGAACGGGGAATTAATCTCATACAGATGTCAGAACGGGGAAT
1 TAATCCCATGCATATGTCAGAACAGGGAATTAATCTCATGCATATGTCAGAACGGGGAAT
* **
1090659 TAATCTCATGCATATGTCAGAATGGGGAATTAAT
1 TAATCCCATGCATATGTCAGAACAGGGAATTAAT
1090693 AACGATGTCA
Statistics
Matches: 128, Mismatches: 23, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
59 3 0.02
60 122 0.95
61 3 0.02
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.24
Consensus pattern (60 bp):
TAATCCCATGCATATGTCAGAACAGGGAATTAATCTCATGCATATGTCAGAACGGGGAAT
Found at i:1090736 original size:2 final size:2
Alignment explanation
Indices: 1090729--1090768 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1090719 GATATGTCGC
1090729 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1090769 GATCACAAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1090951 original size:117 final size:118
Alignment explanation
Indices: 1090743--1090981 Score: 403
Period size: 117 Copynumber: 2.0 Consensus size: 118
1090733 ATATATATAT
*
1090743 ATATATATATATATATATATATATATGATCACAAACATGTTTACAGACAGCAACATATAACATAA
1 ATATATATATATATATATATATATATGATCACAAACATGTTTACAGACAACAACATATAACATAA
*
1090808 CACGTTAAATATATCGAACAAGTCAAGGGGACACACCTATAAGAGAAAAATGC
66 CACATTAAATATATCGAACAAGTCAAGGGGACACACCTATAAGAGAAAAATGC
*
1090861 ATATATATATATATATATATA-ATCA-GATCACAAACATGTTTACAGATAACAACATATAACATA
1 ATATATATATATATATATATATAT-ATGATCACAAACATGTTTACAGACAACAACATATAACATA
*
1090924 ACACATTAAATATATCGAAC-AGATCAAGGGGACATACCTATAAGAGAAAAATGC
65 ACACATTAAATATATCGAACAAG-TCAAGGGGACACACCTATAAGAGAAAAATGC
1090978 ATAT
1 ATAT
1090982 CATCCAAGCC
Statistics
Matches: 115, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
116 2 0.02
117 91 0.79
118 22 0.19
ACGTcount: A:0.49, C:0.15, G:0.11, T:0.26
Consensus pattern (118 bp):
ATATATATATATATATATATATATATGATCACAAACATGTTTACAGACAACAACATATAACATAA
CACATTAAATATATCGAACAAGTCAAGGGGACACACCTATAAGAGAAAAATGC
Found at i:1092475 original size:16 final size:16
Alignment explanation
Indices: 1092454--1092491 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
1092444 GATGTCACAT
1092454 CACTTTTAAAACTTTC
1 CACTTTTAAAACTTTC
1092470 CACTTTTAAAACTTTC
1 CACTTTTAAAACTTTC
1092486 CACTTT
1 CACTTT
1092492 GAAGAAAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.45
Consensus pattern (16 bp):
CACTTTTAAAACTTTC
Found at i:1092971 original size:54 final size:54
Alignment explanation
Indices: 1092889--1093411 Score: 651
Period size: 54 Copynumber: 9.7 Consensus size: 54
1092879 TTTTCAAATC
* * * * * *
1092889 ATTAT-AAGTTCTTTGGGGTGCACACTTAGTGTCAATACAGTAGTTTATAAACTT
1 ATTATGAA-TTCTGTGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTT
* *
1092943 ATTATAAATTATGTGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTT
1 ATTATGAATTCTGTGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTT
*
1092997 ATTATGAATT-TCGTGGGTTGCACACTTAGTGTCGATATGGTCGTTCATAAACTT
1 ATTATGAATTCT-GTGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTT
* * *
1093051 ATTAGGAATTCTGTGAGTTACACACTTAGTG-CTGATACGGTCGTTCATAAACTT
1 ATTATGAATTCTGTGGGTTGCACACTTAGTGTC-GATACGGTCGTTCATAAACTT
** * * *
1093105 ATTATGAATTTCT-TGGGTTGCACACTTAGTGTCGATACAATCATTTATAAAATT
1 ATTATGAA-TTCTGTGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTT
* * * *
1093159 ATTATGAATTTTATGGGTTGCACACTTAGTGTCGATACGGTGGTTAATAAACTT
1 ATTATGAATTCTGTGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTT
* * *
1093213 ATTATGAATTCTATGGGTTGCACACTTAGTATCAATACGGTCGTTCATAAACTT
1 ATTATGAATTCTGTGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTT
** * * *
1093267 ATTATGAATTCCATGGGTTGCACATTTAGTGCCGATACAGTCGTTCATAAACTT
1 ATTATGAATTCTGTGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTT
* ** *
1093321 ATTATGAATTCTGTGGGATATACACTTAGT-ACTGATACGGTCGTTCATAAACTT
1 ATTATGAATTCTGTGGGTTGCACACTTAGTGTC-GATACGGTCGTTCATAAACTT
* *
1093375 AATATGAATTCCGTGGGTTGCACACTTAGTGTCGATA
1 ATTATGAATTCTGTGGGTTGCACACTTAGTGTCGATA
1093412 GTACACATGG
Statistics
Matches: 407, Mismatches: 53, Indels: 18
0.85 0.11 0.04
Matches are distributed among these distances:
53 6 0.01
54 392 0.96
55 9 0.02
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (54 bp):
ATTATGAATTCTGTGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTT
Found at i:1099887 original size:54 final size:54
Alignment explanation
Indices: 1099795--1100209 Score: 525
Period size: 54 Copynumber: 7.7 Consensus size: 54
1099785 TTTTCAAATC
* * * *
1099795 ATTAT-AAGTTCTTTGGGGTGCACACGTAGTGCCGATACGATCGTTCATAAACTT
1 ATTATGAA-TTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTT
* * * * *
1099849 ATTATGAATTCTGTGGGTTGTACTCTTAGTGCCAATACGGTCGCTCATAAAATT
1 ATTATGAATTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTT
* ** *
1099903 ATTATGAATTATGTGGGTTGCACACTTAGTGCCGATATTGTTGTTCATAAACTT
1 ATTATGAATTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTT
** **
1099957 ATTATGAATT-TCGTGGGTTGCACACTTAGTGTTGATACAATCGTTCATAAACTT
1 ATTATGAATTCT-GTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTT
* *
1100011 ATTATGAATTAC-GTGGGTTGCACACTTAGTACCGATACGGTCGTTCATAAACCT
1 ATTATGAATT-CTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTT
* *
1100065 ATTACGAATT-TCGTGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTT
1 ATTATGAATTCT-GTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTT
* * *
1100119 ATTATGAATTCCGTGGGTTGCACACTTAGTGTCAATACGGTCGTTCATAAACTT
1 ATTATGAATTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTT
*
1100173 ATTATGAATTAC-GTGGGTTGCACACTTAGTGTCGATA
1 ATTATGAATT-CTGTGGGTTGCACACTTAGTGCCGATA
1100210 GTACACATAT
Statistics
Matches: 315, Mismatches: 38, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
53 1 0.00
54 311 0.99
55 3 0.01
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (54 bp):
ATTATGAATTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTT
Found at i:1099985 original size:108 final size:108
Alignment explanation
Indices: 1099808--1100209 Score: 581
Period size: 108 Copynumber: 3.7 Consensus size: 108
1099798 ATAAGTTCTT
* * * *
1099808 TGGGGTGCACACGTAGTGCCGATACGATCGTTCATAAACTTATTATGAA-TTCTGTGGGTTGTAC
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTTC-GTGGGTTGCAC
* * * * * *
1099872 TCTTAGTGCCAATACGGTCGCTCATAAAATTATTATGAATTATG
65 ACTTAGTGTCGATACGGTCGTTCATAAACTTATTATGAATTACG
** *
1099916 TGGGTTGCACACTTAGTGCCGATATTGTTGTTCATAAACTTATTATGAATTTCGTGGGTTGCACA
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTTCGTGGGTTGCACA
* **
1099981 CTTAGTGTTGATACAATCGTTCATAAACTTATTATGAATTACG
66 CTTAGTGTCGATACGGTCGTTCATAAACTTATTATGAATTACG
* * *
1100024 TGGGTTGCACACTTAGTACCGATACGGTCGTTCATAAACCTATTACGAATTTCGTGGGTTGCACA
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTTCGTGGGTTGCACA
*
1100089 CTTAGTGTCGATACGGTCGTTCATAAACTTATTATGAATTCCG
66 CTTAGTGTCGATACGGTCGTTCATAAACTTATTATGAATTACG
* * *
1100132 TGGGTTGCACACTTAGTGTCAATACGGTCGTTCATAAACTTATTATGAATTACGTGGGTTGCACA
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTTCGTGGGTTGCACA
1100197 CTTAGTGTCGATA
66 CTTAGTGTCGATA
1100210 GTACACATAT
Statistics
Matches: 261, Mismatches: 32, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
108 258 0.99
109 3 0.01
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.35
Consensus pattern (108 bp):
TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTTCGTGGGTTGCACA
CTTAGTGTCGATACGGTCGTTCATAAACTTATTATGAATTACG
Found at i:1100083 original size:162 final size:162
Alignment explanation
Indices: 1099808--1100202 Score: 578
Period size: 162 Copynumber: 2.4 Consensus size: 162
1099798 ATAAGTTCTT
* * * *
1099808 TGGGGTGCACACGTAGTGCCGATACGATCGTTCATAAACTTATTATGAATT-CTGTGGGTTGTAC
1 TGGGTTGCACACTTAGTGTCGATACGATCGTTCATAAACTTATTATGAATTAC-GTGGGTTGCAC
* * * *
1099872 TCTTAGTGCCAATACGGTCGCTCATAAAATTATTATGAATTATGTGGGTTGCACACTTAGTGCCG
65 ACTTAGTACCAATACGGTCGCTCATAAAACTATTACGAATTATGTGGGTTGCACACTTAGTGCCG
** * *
1099937 ATATTGTTGTTCATAAACTTATTATGAATTTCG
130 ATACGGTCGTTCATAAACTTATTATGAATTCCG
* *
1099970 TGGGTTGCACACTTAGTGTTGATACAATCGTTCATAAACTTATTATGAATTACGTGGGTTGCACA
1 TGGGTTGCACACTTAGTGTCGATACGATCGTTCATAAACTTATTATGAATTACGTGGGTTGCACA
* * * *
1100035 CTTAGTACCGATACGGTCGTTCATAAACCTATTACGAATT-TCGTGGGTTGCACACTTAGTGTCG
66 CTTAGTACCAATACGGTCGCTCATAAAACTATTACGAATTAT-GTGGGTTGCACACTTAGTGCCG
1100099 ATACGGTCGTTCATAAACTTATTATGAATTCCG
130 ATACGGTCGTTCATAAACTTATTATGAATTCCG
* *
1100132 TGGGTTGCACACTTAGTGTCAATACGGTCGTTCATAAACTTATTATGAATTACGTGGGTTGCACA
1 TGGGTTGCACACTTAGTGTCGATACGATCGTTCATAAACTTATTATGAATTACGTGGGTTGCACA
1100197 CTTAGT
66 CTTAGT
1100203 GTCGATAGTA
Statistics
Matches: 209, Mismatches: 22, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
161 1 0.00
162 207 0.99
163 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.35
Consensus pattern (162 bp):
TGGGTTGCACACTTAGTGTCGATACGATCGTTCATAAACTTATTATGAATTACGTGGGTTGCACA
CTTAGTACCAATACGGTCGCTCATAAAACTATTACGAATTATGTGGGTTGCACACTTAGTGCCGA
TACGGTCGTTCATAAACTTATTATGAATTCCG
Found at i:1100145 original size:27 final size:27
Alignment explanation
Indices: 1100115--1100200 Score: 68
Period size: 27 Copynumber: 3.2 Consensus size: 27
1100105 TCGTTCATAA
1100115 ACTTATTATGAATTCCGTGGGTTGCAC
1 ACTTATTATGAATTCCGTGGGTTGCAC
* * * * * * *
1100142 ACTTAGTGTCAATACGGT-CGTT-CATAA
1 ACTTATTATGAATTCCGTGGGTTGC--AC
*
1100169 ACTTATTATGAATTACGTGGGTTGCAC
1 ACTTATTATGAATTCCGTGGGTTGCAC
1100196 ACTTA
1 ACTTA
1100201 GTGTCGATAG
Statistics
Matches: 40, Mismatches: 15, Indels: 8
0.63 0.24 0.13
Matches are distributed among these distances:
25 1 0.03
26 3 0.08
27 32 0.80
28 3 0.08
29 1 0.03
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (27 bp):
ACTTATTATGAATTCCGTGGGTTGCAC
Found at i:1100650 original size:20 final size:19
Alignment explanation
Indices: 1100625--1100711 Score: 79
Period size: 18 Copynumber: 4.6 Consensus size: 19
1100615 GGAATCCATG
1100625 GTATCGATACTTTCCTATCA
1 GTATCGATAC-TTCCTATCA
* * *
1100645 GTATCGATACCTAC-AGCA
1 GTATCGATACTTCCTATCA
*
1100663 GTATCGATACCTTCCTATTA
1 GTATCGATA-CTTCCTATCA
* * *
1100683 GTATCGATACCTAC-AACA
1 GTATCGATACTTCCTATCA
1100701 GTATCGATACT
1 GTATCGATACT
1100712 AATTGCATCA
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
18 24 0.45
19 8 0.15
20 21 0.40
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (19 bp):
GTATCGATACTTCCTATCA
Found at i:1100666 original size:18 final size:18
Alignment explanation
Indices: 1100643--1100710 Score: 82
Period size: 18 Copynumber: 3.7 Consensus size: 18
1100633 ACTTTCCTAT
*
1100643 CAGTATCGATACCTACAG
1 CAGTATCGATACCTACAA
* *
1100661 CAGTATCGATACCTTCCTAT
1 CAGTATCGATACC-TAC-AA
*
1100681 TAGTATCGATACCTACAA
1 CAGTATCGATACCTACAA
1100699 CAGTATCGATAC
1 CAGTATCGATAC
1100711 TAATTGCATC
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
18 25 0.60
19 4 0.10
20 13 0.31
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.28
Consensus pattern (18 bp):
CAGTATCGATACCTACAA
Found at i:1100678 original size:38 final size:38
Alignment explanation
Indices: 1100625--1100710 Score: 145
Period size: 38 Copynumber: 2.3 Consensus size: 38
1100615 GGAATCCATG
* *
1100625 GTATCGATACTTTCCTATCAGTATCGATACCTACAGCA
1 GTATCGATACCTTCCTATCAGTATCGATACCTACAACA
*
1100663 GTATCGATACCTTCCTATTAGTATCGATACCTACAACA
1 GTATCGATACCTTCCTATCAGTATCGATACCTACAACA
1100701 GTATCGATAC
1 GTATCGATAC
1100711 TAATTGCATC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 45 1.00
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (38 bp):
GTATCGATACCTTCCTATCAGTATCGATACCTACAACA
Found at i:1106032 original size:14 final size:15
Alignment explanation
Indices: 1106013--1106047 Score: 54
Period size: 14 Copynumber: 2.3 Consensus size: 15
1106003 AAAGTTATTT
1106013 TAAAATTTTA-AAAA
1 TAAAATTTTATAAAA
1106027 TAAAATTTTATTAAAA
1 TAAAATTTTA-TAAAA
1106043 TAAAA
1 TAAAA
1106048 ATAAATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.53
16 9 0.47
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAAATTTTATAAAA
Found at i:1111646 original size:29 final size:29
Alignment explanation
Indices: 1111562--1111646 Score: 77
Period size: 29 Copynumber: 2.9 Consensus size: 29
1111552 ATATATAACT
* *
1111562 TTTTACAA-TTATATTTTGGTC-CTTAAAC
1 TTTTAAAATTTATATTTTGGTCAC-CAAAC
* *
1111590 TTCTGTAAAGTTTATACTTTT-GTTACCAAAC
1 TT-T-TAAAATTTATA-TTTTGGTCACCAAAC
1111621 TTTTAAAATTTATATTTTGGTCACCA
1 TTTTAAAATTTATATTTTGGTCACCA
1111647 GTTAAAATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
28 6 0.13
29 17 0.38
30 4 0.09
31 13 0.29
32 5 0.11
ACGTcount: A:0.29, C:0.14, G:0.08, T:0.48
Consensus pattern (29 bp):
TTTTAAAATTTATATTTTGGTCACCAAAC
Found at i:1121597 original size:20 final size:21
Alignment explanation
Indices: 1121558--1121598 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1121548 CACTTCATCT
*
1121558 CATTAAGCTAACCTTTGAGCTC
1 CATTAAGCT-ACCCTTGAGCTC
1121580 CATTAAGCT-CCCTTGAGCT
1 CATTAAGCTACCCTTGAGCT
1121599 AAGTGAGCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
22 9 0.50
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.32
Consensus pattern (21 bp):
CATTAAGCTACCCTTGAGCTC
Found at i:1124849 original size:82 final size:83
Alignment explanation
Indices: 1124742--1125005 Score: 365
Period size: 82 Copynumber: 3.2 Consensus size: 83
1124732 AGCGGCCGAT
* * * * * *
1124742 ATAGGGTT-ATCTATAGTGACATTTTTTCAACAAACGCCACAACAAAGTGGTACTTTAGTGGTGT
1 ATAGGGTTCATCTATAGTGGCATTTTTTCAACAAACGCCGCAACAGAGTAGTACTTTAGCGGCGT
* * * *
1124806 TTTAATACGAATGTCGTA
66 TTTTATACAAATGCCGCA
* *
1124824 ATA-GGTTCATCTATAGTGGCATTTTTTTAACAAACGACGCAACAGAGTAGTACTTTAGCGGCGT
1 ATAGGGTTCATCTATAGTGGCATTTTTTCAACAAACGCCGCAACAGAGTAGTACTTTAGCGGCGT
1124888 TTTTATACAAATGCCGCA
66 TTTTATACAAATGCCGCA
* *
1124906 ATAGGGTTCA-CTATAGTGGTGA-TTTTTCAACAAACGCCGCAACAGAGTATTACTTTAGCGGCG
1 ATAGGGTTCATCTATAGTGG-CATTTTTTCAACAAACGCCGCAACAGAGTAGTACTTTAGCGGCG
1124969 TTTTTATACAAATGCCGCA
65 TTTTTATACAAATGCCGCA
1124988 ATAGGGTTCATCTATAGT
1 ATAGGGTTCATCTATAGT
1125006 TGCGTTCTTT
Statistics
Matches: 162, Mismatches: 16, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
81 4 0.02
82 144 0.89
83 14 0.09
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (83 bp):
ATAGGGTTCATCTATAGTGGCATTTTTTCAACAAACGCCGCAACAGAGTAGTACTTTAGCGGCGT
TTTTATACAAATGCCGCA
Found at i:1125011 original size:41 final size:40
Alignment explanation
Indices: 1124797--1125011 Score: 148
Period size: 41 Copynumber: 5.2 Consensus size: 40
1124787 AGTGGTACTT
* * * * *
1124797 TAGTGGTGTTTTAATACGAATGTCGTAATA-GGTTCATCTA
1 TAGTGGCGTTTTTATACAAATGCCGCAATAGGGTTCA-CTA
* * * * * * *
1124837 TAGTGGCATTTTTTTAACAAACGACGCAACAGAGTAGT-ACTT
1 TAGTGGCGTTTTTAT-ACAAATGCCGCAATAGGGT--TCACTA
*
1124879 TAGCGGCGTTTTTATACAAATGCCGCAATAGGGTTCACTA
1 TAGTGGCGTTTTTATACAAATGCCGCAATAGGGTTCACTA
* * * * * *
1124919 TAGTGGTGATTTTTCA-ACAAACGCCGCAACAGAGTATTACTT
1 TAGTGGCG-TTTTT-ATACAAATGCCGCAATAGGGT-TCACTA
*
1124961 TAGCGGCGTTTTTATACAAATGCCGCAATAGGGTTCATCTA
1 TAGTGGCGTTTTTATACAAATGCCGCAATAGGGTTCA-CTA
*
1125002 TAGTTGCGTT
1 TAGTGGCGTT
1125012 CTTTCCCCAA
Statistics
Matches: 130, Mismatches: 35, Indels: 19
0.71 0.19 0.10
Matches are distributed among these distances:
39 1 0.01
40 23 0.18
41 77 0.59
42 27 0.21
43 1 0.01
44 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.33
Consensus pattern (40 bp):
TAGTGGCGTTTTTATACAAATGCCGCAATAGGGTTCACTA
Found at i:1125440 original size:19 final size:20
Alignment explanation
Indices: 1125404--1125442 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1125394 CATCAAGTAG
*
1125404 TTTTTATTTACGCCTGTTTTT
1 TTTTTATTTA-GCATGTTTTT
1125425 TTTTTATTT-GCATGTTTT
1 TTTTTATTTAGCATGTTTT
1125443 GATTTGGCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
21 9 0.53
ACGTcount: A:0.10, C:0.10, G:0.10, T:0.69
Consensus pattern (20 bp):
TTTTTATTTAGCATGTTTTT
Found at i:1126920 original size:34 final size:34
Alignment explanation
Indices: 1126875--1126941 Score: 93
Period size: 34 Copynumber: 1.9 Consensus size: 34
1126865 AATAGGAATT
1126875 ACAACTTCTCTC-GATATAACAAGGAGAAAACAATA
1 ACAACTTCTCTCTGATA-AA-AAGGAGAAAACAATA
1126910 ACAA-TTCTCTCTTGATAAAAAGGAGAAAACAA
1 ACAACTTCTCTC-TGATAAAAAGGAGAAAACAA
1126942 CTCTCAAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
34 20 0.67
35 6 0.20
36 4 0.13
ACGTcount: A:0.49, C:0.18, G:0.12, T:0.21
Consensus pattern (34 bp):
ACAACTTCTCTCTGATAAAAAGGAGAAAACAATA
Found at i:1131867 original size:42 final size:42
Alignment explanation
Indices: 1131821--1132052 Score: 207
Period size: 43 Copynumber: 5.5 Consensus size: 42
1131811 ATTAAAAACA
*
1131821 CCACTAAAAACAAGAGTATTAGCAGTGTTTGTAGCAAAAATG
1 CCACTAAAAACAAGAGAATTAGCAGTGTTTGTAGCAAAAATG
* * * *
1131863 CCACTAAAGACAAGAGAATTAGCAGCGTTTGTGGTAAAAAAT-
1 CCACTAAAAACAAGAGAATTAGCAGTGTTTGTAG-CAAAAATG
* * * * * * * *
1131905 TCACTAAATACAAAAGAATTAGCCGTGCTTGTGGGAAAAAAAG
1 CCACTAAAAACAAGAGAATTAGCAGTGTTTGT-AGCAAAAATG
**
1131948 CCACTAAAGAA-AAGAGAATTAGCAGAATTTGTAGCAAGAAATG
1 CCACTAAA-AACAAGAGAATTAGCAGTGTTTGTAGCAA-AAATG
* * * * * *
1131991 ACACTAAAGACAATATAATTAGCGGTGTTTGTGGCAAAAAATG
1 CCACTAAAAACAAGAGAATTAGCAGTGTTTGTAGC-AAAAATG
*
1132034 CCACTAAATACAAGAGAAT
1 CCACTAAAAACAAGAGAAT
1132053 AAGCGACGTT
Statistics
Matches: 149, Mismatches: 34, Indels: 13
0.76 0.17 0.07
Matches are distributed among these distances:
42 66 0.44
43 80 0.54
44 3 0.02
ACGTcount: A:0.45, C:0.14, G:0.20, T:0.22
Consensus pattern (42 bp):
CCACTAAAAACAAGAGAATTAGCAGTGTTTGTAGCAAAAATG
Found at i:1131945 original size:43 final size:42
Alignment explanation
Indices: 1131821--1132083 Score: 152
Period size: 43 Copynumber: 6.2 Consensus size: 42
1131811 ATTAAAAACA
* * * * * * * *
1131821 CCACTAAAAACAAGAGTATTAGCAGTGTTTGTAGCAAAAATG
1 CCACTAAAGACAAAAGAATTAGCAGCGCTTGTGGAAAAAAAG
* * * *
1131863 CCACTAAAGACAAGAGAATTAGCAGCGTTTGTGGTAAAAAAT
1 CCACTAAAGACAAAAGAATTAGCAGCGCTTGTGGAAAAAAAG
* * * *
1131905 TCACTAAATACAAAAGAATTAGCCGTGCTTGTGGGAAAAAAAG
1 CCACTAAAGACAAAAGAATTAGCAGCGCTTGT-GGAAAAAAAG
*** * * *
1131948 CCACTAAAGA-AAAGAGAATTAGCAGAATTTGTAGCAAGAAATG
1 CCACTAAAGACAAA-AGAATTAGCAGCGCTTGT-GGAAAAAAAG
* * * * * * *
1131991 ACACTAAAGACAATATAATTAGCGGTGTTTGTGGCAAAAAATG
1 CCACTAAAGACAAAAGAATTAGCAGCGCTTGTGG-AAAAAAAG
* * * * *
1132034 CCACTAAATACAAGAGAATAAGC-GACGTTTGTGGAAAGAAACG
1 CCACTAAAGACAAAAGAATTAGCAG-CGCTTGTGGAAA-AAAAG
1132077 CCACTAA
1 CCACTAA
1132084 TTACAGAGTA
Statistics
Matches: 175, Mismatches: 40, Indels: 11
0.77 0.18 0.05
Matches are distributed among these distances:
42 69 0.39
43 104 0.59
44 2 0.01
ACGTcount: A:0.44, C:0.14, G:0.21, T:0.21
Consensus pattern (42 bp):
CCACTAAAGACAAAAGAATTAGCAGCGCTTGTGGAAAAAAAG
Found at i:1132065 original size:86 final size:86
Alignment explanation
Indices: 1131822--1132083 Score: 273
Period size: 86 Copynumber: 3.1 Consensus size: 86
1131812 TTAAAAACAC
* * * *
1131822 CACTAAAAACAAGAGTATTAGCAGTGTTTGTAGC-AAAAATGCCACTAAAGACAAGAGAATTAGC
1 CACTAAAGACAAAAGAATTAGCAGTGTTTGTGGCAAAAAATGCCACTAAAGACAAGAGAATTAGC
*
1131886 -AGCGTTTGTGGTAAA-AAAT-T
66 GA-CGTTTGTGG-AAAGAAATGA
* * * * * *
1131906 CACTAAATACAAAAGAATTAGCCGTGCTTGTGGGAAAAAAAGCCACTAAAGAAAAGAGAATTAGC
1 CACTAAAGACAAAAGAATTAGCAGTGTTTGTGGCAAAAAATGCCACTAAAGACAAGAGAATTAGC
* * *
1131971 AGA-ATTTGTAGCAAGAAATGA
66 -GACGTTTGTGGAAAGAAATGA
* * * * *
1131992 CACTAAAGACAATATAATTAGCGGTGTTTGTGGCAAAAAATGCCACTAAATACAAGAGAATAAGC
1 CACTAAAGACAAAAGAATTAGCAGTGTTTGTGGCAAAAAATGCCACTAAAGACAAGAGAATTAGC
* *
1132057 GACGTTTGTGGAAAGAAACGC
66 GACGTTTGTGGAAAGAAATGA
1132078 CACTAA
1 CACTAA
1132084 TTACAGAGTA
Statistics
Matches: 144, Mismatches: 28, Indels: 10
0.79 0.15 0.05
Matches are distributed among these distances:
84 29 0.20
85 40 0.28
86 74 0.51
87 1 0.01
ACGTcount: A:0.44, C:0.14, G:0.21, T:0.21
Consensus pattern (86 bp):
CACTAAAGACAAAAGAATTAGCAGTGTTTGTGGCAAAAAATGCCACTAAAGACAAGAGAATTAGC
GACGTTTGTGGAAAGAAATGA
Found at i:1141566 original size:22 final size:22
Alignment explanation
Indices: 1141543--1141590 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
1141533 CTTGGAGAAG
*
1141543 AAAGATAAAAGAGGAAAGAGAGA
1 AAAGA-AAAAAAGGAAAGAGAGA
*
1141566 AAAGAAAAAAAGGAAAGAGAAA
1 AAAGAAAAAAAGGAAAGAGAGA
1141588 AAA
1 AAA
1141591 TATAGAGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (22 bp):
AAAGAAAAAAAGGAAAGAGAGA
Found at i:1155478 original size:45 final size:44
Alignment explanation
Indices: 1155409--1155512 Score: 181
Period size: 45 Copynumber: 2.3 Consensus size: 44
1155399 TTATAAAAAC
*
1155409 ATTTCAGAGAAAAGTAACAATTTTACTAAACAAACACAAATTAT
1 ATTTTAGAGAAAAGTAACAATTTTACTAAACAAACACAAATTAT
*
1155453 ATTTTTAGAGAAAAGTAACAATTTTACTAAACACACACAAATTAT
1 A-TTTTAGAGAAAAGTAACAATTTTACTAAACAAACACAAATTAT
1155498 ATTTTAGAGAAAAGT
1 ATTTTAGAGAAAAGT
1155513 TACATATTGT
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
44 15 0.26
45 42 0.74
ACGTcount: A:0.50, C:0.12, G:0.09, T:0.30
Consensus pattern (44 bp):
ATTTTAGAGAAAAGTAACAATTTTACTAAACAAACACAAATTAT
Found at i:1158383 original size:41 final size:40
Alignment explanation
Indices: 1158337--1158414 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
1158327 CTCTAAGTGT
*
1158337 AAAAAAATATTAATATTAAAAATATAAGTAACTTAGGCTGC
1 AAAAAAATATTAATATT-AAAATATAAGTAACTCAGGCTGC
1158378 AAAAAAATATTAATATTAAAATATAAGTAACTCAGGC
1 AAAAAAATATTAATATTAAAATATAAGTAACTCAGGC
1158415 ATGATGTAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 19 0.53
41 17 0.47
ACGTcount: A:0.55, C:0.08, G:0.09, T:0.28
Consensus pattern (40 bp):
AAAAAAATATTAATATTAAAATATAAGTAACTCAGGCTGC
Found at i:1164642 original size:13 final size:13
Alignment explanation
Indices: 1164624--1164655 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1164614 TGTGACTCGT
1164624 AACCGATTACCCA
1 AACCGATTACCCA
*
1164637 AACCGATTACCCG
1 AACCGATTACCCA
1164650 AACCGA
1 AACCGA
1164656 GACCCGATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.38, C:0.38, G:0.12, T:0.12
Consensus pattern (13 bp):
AACCGATTACCCA
Found at i:1164846 original size:16 final size:16
Alignment explanation
Indices: 1164825--1164855 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1164815 CCTAAACCAA
1164825 AAATCAACCCGAACAG
1 AAATCAACCCGAACAG
*
1164841 AAATCAATCCGAACA
1 AAATCAACCCGAACA
1164856 AAAAATAACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.29, G:0.10, T:0.10
Consensus pattern (16 bp):
AAATCAACCCGAACAG
Found at i:1165869 original size:18 final size:18
Alignment explanation
Indices: 1165846--1165886 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1165836 ACCGGTCACA
*
1165846 ACCCGACCCGACCCGTTG
1 ACCCGACCCAACCCGTTG
*
1165864 ACCCGACCCAACTCGTTG
1 ACCCGACCCAACCCGTTG
1165882 ACCCG
1 ACCCG
1165887 TTGACCATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.20, C:0.49, G:0.20, T:0.12
Consensus pattern (18 bp):
ACCCGACCCAACCCGTTG
Found at i:1167236 original size:18 final size:18
Alignment explanation
Indices: 1167210--1167245 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1167200 TCGAAAGGAC
*
1167210 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1167228 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
1167246 CGGATGGCAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1168423 original size:12 final size:12
Alignment explanation
Indices: 1168408--1168477 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
1168398 GATACATTAC
1168408 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
1168420 CTGATTTCTGAT
1 CTGAATTCTGTT
*
1168432 CTGGATTCTGTT
1 CTGAATTCTGTT
*
1168444 CTG-ATATCTGAT
1 CTGAAT-TCTGTT
1168456 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
1168468 TTGATTTCTG
1 CTGAATTCTG
1168478 ATATCTCCGT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
11 2 0.04
12 43 0.91
13 2 0.04
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.50
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:1168439 original size:24 final size:24
Alignment explanation
Indices: 1168408--1168479 Score: 117
Period size: 24 Copynumber: 3.0 Consensus size: 24
1168398 GATACATTAC
1168408 CTGAATTCTGTTCTGATTTCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
* *
1168432 CTGGATTCTGTTCTGATATCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
*
1168456 CTGAATTCTGTTTTGATTTCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
1168480 ATCTCCGTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.17, C:0.15, G:0.18, T:0.50
Consensus pattern (24 bp):
CTGAATTCTGTTCTGATTTCTGAT
Found at i:1168446 original size:48 final size:49
Alignment explanation
Indices: 1168372--1168479 Score: 134
Period size: 48 Copynumber: 2.3 Consensus size: 49
1168362 AAATATTTTA
* *
1168372 TCTGATTTC-GA-CTTGAATTCTTTTCTGATA-CATTACCTGAATTCTGT
1 TCTGATTTCTGATCTTGAATTCTGTTCTGATATC-TGACCTGAATTCTGT
* *
1168419 TCTGATTTCTGATC-TGGATTCTGTTCTGATATCTGATCTGAATTCTGT
1 TCTGATTTCTGATCTTGAATTCTGTTCTGATATCTGACCTGAATTCTGT
*
1168467 TTTGATTTCTGAT
1 TCTGATTTCTGAT
1168480 ATCTCCGTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
47 9 0.17
48 42 0.79
49 2 0.04
ACGTcount: A:0.19, C:0.17, G:0.16, T:0.49
Consensus pattern (49 bp):
TCTGATTTCTGATCTTGAATTCTGTTCTGATATCTGACCTGAATTCTGT
Found at i:1170574 original size:13 final size:13
Alignment explanation
Indices: 1170555--1170609 Score: 53
Period size: 13 Copynumber: 4.5 Consensus size: 13
1170545 AACCCGACCC
1170555 GACCCGACCCGTT
1 GACCCGACCCGTT
* * *
1170568 TACCCGATCTGTT
1 GACCCGACCCGTT
1170581 GACCCGACCC---
1 GACCCGACCCGTT
*
1170591 AACCCGACCCGTT
1 GACCCGACCCGTT
1170604 GACCCG
1 GACCCG
1170610 TTGATCGTTG
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
10 9 0.29
13 22 0.71
ACGTcount: A:0.18, C:0.45, G:0.20, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1170609 original size:8 final size:8
Alignment explanation
Indices: 1170596--1170630 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
1170586 GACCCAACCC
1170596 GACCCGTT
1 GACCCGTT
1170604 GACCCGTT
1 GACCCGTT
*
1170612 GA-TCGTT
1 GACCCGTT
1170619 GACCCGTT
1 GACCCGTT
1170627 GACC
1 GACC
1170631 GTTTACCGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 6 0.25
8 18 0.75
ACGTcount: A:0.14, C:0.34, G:0.26, T:0.26
Consensus pattern (8 bp):
GACCCGTT
Found at i:1170618 original size:15 final size:15
Alignment explanation
Indices: 1170599--1170647 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
1170589 CCAACCCGAC
1170599 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
*
1170614 TCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
*
1170629 CCGTTTACCGTCGTTGA
1 CCGTTGACC--CGTTGA
1170646 CC
1 CC
1170648 AAAACTTTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 21 0.72
17 8 0.28
ACGTcount: A:0.12, C:0.33, G:0.24, T:0.31
Consensus pattern (15 bp):
CCGTTGACCCGTTGA
Found at i:1171963 original size:18 final size:18
Alignment explanation
Indices: 1171937--1171977 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1171927 TCGAAAGGAC
* *
1171937 TGAAGTAAATGATAAGAT
1 TGAATTAAATAATAAGAT
1171955 TGAATTAAATAATAAGAT
1 TGAATTAAATAATAAGAT
*
1171973 CGAAT
1 TGAAT
1171978 GACAGGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.51, C:0.02, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAATTAAATAATAAGAT
Found at i:1173158 original size:12 final size:12
Alignment explanation
Indices: 1173138--1173207 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
1173128 GATACATTAC
*
1173138 CTGAATTCTGTT
1 CTGATTTCTGTT
*
1173150 CTGATTTCTGAT
1 CTGATTTCTGTT
1173162 CTAGA-TTCTGTT
1 CT-GATTTCTGTT
* * *
1173174 ATGATATCTGAT
1 CTGATTTCTGTT
*
1173186 CTGAATTCTGTT
1 CTGATTTCTGTT
*
1173198 TTGATTTCTG
1 CTGATTTCTG
1173208 ATATCTCCGT
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
11 2 0.05
12 40 0.91
13 2 0.05
ACGTcount: A:0.19, C:0.14, G:0.17, T:0.50
Consensus pattern (12 bp):
CTGATTTCTGTT
Found at i:1173169 original size:24 final size:24
Alignment explanation
Indices: 1173115--1173209 Score: 104
Period size: 24 Copynumber: 4.0 Consensus size: 24
1173105 ATTTTCGACT
* * *
1173115 TGAATTCTGTTATGA-TACATTACC
1 TGAATTCTGTTATGATTTC-TGATC
*
1173139 TGAATTCTGTTCTGATTTCTGATC
1 TGAATTCTGTTATGATTTCTGATC
*
1173163 T-AGATTCTGTTATGATATCTGATC
1 TGA-ATTCTGTTATGATTTCTGATC
*
1173187 TGAATTCTGTTTTGATTTCTGAT
1 TGAATTCTGTTATGATTTCTGAT
1173210 ATCTCCGTTT
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
23 1 0.02
24 56 0.93
25 3 0.05
ACGTcount: A:0.22, C:0.14, G:0.16, T:0.48
Consensus pattern (24 bp):
TGAATTCTGTTATGATTTCTGATC
Found at i:1173172 original size:48 final size:48
Alignment explanation
Indices: 1173118--1173209 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
1173108 TTCGACTTGA
*
1173118 ATTCTGTTATGATA-CATTACCTGAATTCTGTTCTGATTTCTGATCTAG
1 ATTCTGTTATGATATC-TGACCTGAATTCTGTTCTGATTTCTGATCTAG
* *
1173166 ATTCTGTTATGATATCTGATCTGAATTCTGTTTTGATTTCTGAT
1 ATTCTGTTATGATATCTGACCTGAATTCTGTTCTGATTTCTGAT
1173210 ATCTCCGTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
48 39 0.98
49 1 0.03
ACGTcount: A:0.22, C:0.14, G:0.15, T:0.49
Consensus pattern (48 bp):
ATTCTGTTATGATATCTGACCTGAATTCTGTTCTGATTTCTGATCTAG
Found at i:1174068 original size:46 final size:46
Alignment explanation
Indices: 1174018--1174137 Score: 132
Period size: 46 Copynumber: 2.6 Consensus size: 46
1174008 CTAACTTGAA
* *
1174018 AATCTAAAGGTTAATCTGAACCAAAACCAACCCGAATTGACCCGAT
1 AATCTAAAGGTTAATCCGAACCAAAACCAACCCAAATTGACCCGAT
* * * * *
1174064 AATCTAAAGGTTGATCCGAACCGAAACCAACTCAAATTGACCTGAA
1 AATCTAAAGGTTAATCCGAACCAAAACCAACCCAAATTGACCCGAT
* * * *
1174110 AATATAAAGCTTGACCCGAACCGAAAAC
1 AATCTAAAGGTTAATCCGAACC-AAAAC
1174138 GACCGATTCA
Statistics
Matches: 62, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
46 58 0.94
47 4 0.06
ACGTcount: A:0.42, C:0.25, G:0.14, T:0.18
Consensus pattern (46 bp):
AATCTAAAGGTTAATCCGAACCAAAACCAACCCAAATTGACCCGAT
Found at i:1177132 original size:103 final size:103
Alignment explanation
Indices: 1176951--1177152 Score: 386
Period size: 103 Copynumber: 2.0 Consensus size: 103
1176941 CCTTTCCTCC
1176951 TCTTGTAATTTTCATTTCTTTGACATTGCACAGTGGAGCCTGCAATTTACAAGTTCATTTTCTGC
1 TCTTGTAATTTTCATTTCTTTGACATTGCACAGTGGAGCCTGCAATTTACAAGTTCATTTTCTGC
1177016 TAATGATGATATCTTTCAACATATAATTATAAAGAGTA
66 TAATGATGATATCTTTCAACATATAATTATAAAGAGTA
*
1177054 TCTTGTAATTTTCATTTCTTTGACATTGCACAGTGGAGCCTGCGATTTACAAGTTCATTTTCTGC
1 TCTTGTAATTTTCATTTCTTTGACATTGCACAGTGGAGCCTGCAATTTACAAGTTCATTTTCTGC
*
1177119 TAATGATGTTATCTTTCAACATATAATTATAAAG
66 TAATGATGATATCTTTCAACATATAATTATAAAG
1177153 CGTAGCATGC
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 97 1.00
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.42
Consensus pattern (103 bp):
TCTTGTAATTTTCATTTCTTTGACATTGCACAGTGGAGCCTGCAATTTACAAGTTCATTTTCTGC
TAATGATGATATCTTTCAACATATAATTATAAAGAGTA
Found at i:1181844 original size:32 final size:31
Alignment explanation
Indices: 1181808--1181888 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
1181798 AACTTTTTTT
*
1181808 ATATTTTTAATTTTGTAAA-AATATTTATATAA
1 ATATTTTTAATTTTGTAAAGAA-A-ATATATAA
* * *
1181840 ATATTGTGAATTTTTTAAAGAAAATATATAA
1 ATATTTTTAATTTTGTAAAGAAAATATATAA
1181871 ATATTTTATAA-TTTGTAA
1 ATATTTT-TAATTTTGTAA
1181889 TATTATACAA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
31 19 0.47
32 19 0.47
33 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.49
Consensus pattern (31 bp):
ATATTTTTAATTTTGTAAAGAAAATATATAA
Found at i:1182273 original size:78 final size:78
Alignment explanation
Indices: 1182144--1182295 Score: 277
Period size: 78 Copynumber: 1.9 Consensus size: 78
1182134 GCGATTAACA
* *
1182144 AGGACCCATGAATTTTAGCATTCTAAATATAGTCCAAGAAAGATTTTAAAAGCTATCTTTGAGCC
1 AGGACCCATGAATTTTAGCATTCTAAACATAGTCCAAGAAAGATTATAAAAGCTATCTTTGAGCC
1182209 TCTTTCTTATTCG
66 TCTTTCTTATTCG
*
1182222 AGGACCCATGAATTTTAGCTTTCTAAACATAGTCCAAGAAAGATTATAAAAGCTATCTTTGAGCC
1 AGGACCCATGAATTTTAGCATTCTAAACATAGTCCAAGAAAGATTATAAAAGCTATCTTTGAGCC
1182287 TCTTTCTTA
66 TCTTTCTTA
1182296 CTCCGACTTG
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 71 1.00
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (78 bp):
AGGACCCATGAATTTTAGCATTCTAAACATAGTCCAAGAAAGATTATAAAAGCTATCTTTGAGCC
TCTTTCTTATTCG
Found at i:1182873 original size:187 final size:187
Alignment explanation
Indices: 1182552--1183223 Score: 744
Period size: 187 Copynumber: 3.6 Consensus size: 187
1182542 ACATAACAAG
* * ** * * *
1182552 TTGTACATAAAATGTTATTAGAGTTT-AGCTGATGAGACCTTAGATATTCATACGGTAACAAAAT
1 TTGTACCTAAAATATTACCAGAGTTTAAGCTGATGTGACCTTAGACATTCCTACGGTAACAAAAT
* * * * *
1182616 AAGTTAAAAGCTAAAAATGTTATGAATATCTATAAGAAATTTAGTTGTGTCTAAGAATGTTATTG
66 AAGTTAAAAGCTAAAAATGTTATGAATATCTATAAGAAATCTGGTTGTGCCCAAGAATGTTATCG
* *
1182681 TTCACTAAGAAAGTAGGTTGCAATTTGGAATGTTAATTTTCTTTGTAATAAAATCGA
131 TTCACTAAGAAAGTAGGTTGCGATATGGAATGTTAATTTTCTTTGTAATAAAATCGA
** * * * * *
1182738 TTGCGCCTAAAATGTTACCAGAGTTTAAGCTGATGGGGCCTTATACATTCCTATGGTAACAAAAT
1 TTGTACCTAAAATATTACCAGAGTTTAAGCTGATGTGACCTTAGACATTCCTACGGTAACAAAAT
1182803 AAGTTAAAAGCTAAAAATGTTATGAATATCTATAAGAAATCTGGTTGTGCCCAAGAATGTTATCG
66 AAGTTAAAAGCTAAAAATGTTATGAATATCTATAAGAAATCTGGTTGTGCCCAAGAATGTTATCG
* *
1182868 TTCACTAATAAAGTAGGTTGCGATATGGAATGTTATTTTTCTTTGTAATAAAATC-A
131 TTCACTAAGAAAGTAGGTTGCGATATGGAATGTTAATTTTCTTTGTAATAAAATCGA
* * * * * *
1182924 GTTGTATCTAAAATATTACCAAAGTTTAAGCTGATATGACCTTAGACAAT-CTCATGATAACAAA
1 -TTGTACCTAAAATATTACCAGAGTTTAAGCTGATGTGACCTTAGACATTCCT-ACGGTAACAAA
* * * * ** * ** *
1182988 ATAAATTAAAATCTAAAAATGTTTTAAATATCTATAAGAAATAAGATTGCCCCCAAGAATATTAT
64 ATAAGTTAAAAGCTAAAAATGTTATGAATATCTATAAGAAATCTGGTTGTGCCCAAGAATGTTAT
* * ** * * *
1183053 CAG-TCGCTAAGAAAGTATGTTGCGATATGGAATGTTAATATTT-TGAGTAATAAATTTGG
129 C-GTTCACTAAGAAAGTAGGTTGCGATATGGAATGTTAAT-TTTCTTTGTAATAAAATCGA
* * * * * * *
1183112 TTGTACCTAAAATATTACTAGATTTTAAGTTGATGTGACCTTAGATATAACC-ACAGTAACTAAA
1 TTGTACCTAAAATATTACCAGAGTTTAAGCTGATGTGACCTTAGACAT-TCCTACGGTAACAAAA
* * * *
1183176 TATGTTAAAAGCTAAAAATGTTATGAATATATATGATAAATCTGGTTG
65 TAAGTTAAAAGCTAAAAATGTTATGAATATCTATAAGAAATCTGGTTG
1183224 CGTCAAGAAT
Statistics
Matches: 404, Mismatches: 74, Indels: 15
0.82 0.15 0.03
Matches are distributed among these distances:
186 24 0.06
187 375 0.93
188 4 0.01
189 1 0.00
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.35
Consensus pattern (187 bp):
TTGTACCTAAAATATTACCAGAGTTTAAGCTGATGTGACCTTAGACATTCCTACGGTAACAAAAT
AAGTTAAAAGCTAAAAATGTTATGAATATCTATAAGAAATCTGGTTGTGCCCAAGAATGTTATCG
TTCACTAAGAAAGTAGGTTGCGATATGGAATGTTAATTTTCTTTGTAATAAAATCGA
Found at i:1183607 original size:147 final size:146
Alignment explanation
Indices: 1183336--1183682 Score: 382
Period size: 147 Copynumber: 2.4 Consensus size: 146
1183326 ATTTGATGAT
* * * * * *
1183336 CGATACTTTTAAATATTG-AAAATTTGAAGATAAGATCGAAATTTAAAATAT-AGATATTAATCT
1 CGATACTTTTAAATATTGAAAAAGTTGATGATAAGATCGATAGTTAAAATATCAGAAATTAATCG
1183399 ATGATGATCAATACTTTTAAATACTGAAAAAGTTGAAGATGAGACCGAAAGTTAAAATATCGATA
66 ATGATGATCAATACTTTTAAATACTGAAAAAGTTGAAGATGAGACCGAAAGTTAAAATATCGATA
* **
1183464 CT-TATACGGTGATAAA
131 -TGCATACACTGATAAA
* *
1183480 CGATACTTTTAAATAGTGAAAAAGTCGATGATAAGATCGATAGTTAAAATATCA-AAACTT-ATG
1 CGATACTTTTAAATATTGAAAAAGTTGATGATAAGATCGATAGTTAAAATATCAGAAA-TTAAT-
* * * ** *
1183543 CGCTGATGATCGATACTTTTAAATATTGAAAAAAGTTGATA-ATGAGATTGACAGTTAAAATATC
64 CGATGATGATCAATACTTTTAAATACTG-AAAAAGTTGA-AGATGAGACCGAAAGTTAAAATATC
* * *
1183607 GATATGCATGCACTGATGAT
127 GATATGCATACACTGATAAA
* *
1183627 CGATACTTTTATATATTGAAAAAGTTGATGAAGATATGATCGATAGTTAAAATATC
1 CGATACTTTTAAATATTGAAAAAGTTGAT---GATAAGATCGATAGTTAAAATATC
1183683 GATGCATATA
Statistics
Matches: 169, Mismatches: 24, Indels: 14
0.82 0.12 0.07
Matches are distributed among these distances:
144 17 0.10
145 32 0.19
146 28 0.17
147 68 0.40
148 1 0.01
150 23 0.14
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.32
Consensus pattern (146 bp):
CGATACTTTTAAATATTGAAAAAGTTGATGATAAGATCGATAGTTAAAATATCAGAAATTAATCG
ATGATGATCAATACTTTTAAATACTGAAAAAGTTGAAGATGAGACCGAAAGTTAAAATATCGATA
TGCATACACTGATAAA
Found at i:1183623 original size:74 final size:74
Alignment explanation
Indices: 1183329--1183685 Score: 372
Period size: 73 Copynumber: 4.9 Consensus size: 74
1183319 ACTTAATATT
* * *
1183329 TGATGATCGATACTTTTAAATATTG-AAAATTTGA-AGATAAGATCGAAATTTAAAATATAGATA
1 TGATGATCGATACTTTTAAATATTGAAAAAGTTGATAGATAAGATCGAAAGTTAAAATATCGATA
1183392 -TTAAT-CTA-
66 CTT-ATGC-AC
* * * *
1183400 TGATGATCAATACTTTTAAATACTGAAAAAGTTGA-AGATGAGACCGAAAGTTAAAATATCGATA
1 TGATGATCGATACTTTTAAATATTGAAAAAGTTGATAGATAAGATCGAAAGTTAAAATATCGATA
* **
1183464 CTTATACGG
66 CTTATGCAC
* * * * * * *
1183473 TGATAAACGATACTTTTAAATAGTGAAAAAGTCGAT-GATAAGATCGATAGTTAAAATATCAAAA
1 TGATGATCGATACTTTTAAATATTGAAAAAGTTGATAGATAAGATCGAAAGTTAAAATATCGATA
*
1183537 CTTATGCGC
66 CTTATGCAC
* * *
1183546 TGATGATCGATACTTTTAAATATTGAAAAAAGTTGATA-ATGAGATTGACAGTTAAAATATCGAT
1 TGATGATCGATACTTTTAAATATTG-AAAAAGTTGATAGATAAGATCGAAAGTTAAAATATCGAT
*
1183610 A-TGCATGCAC
65 ACT-TATGCAC
* * *
1183620 TGATGATCGATACTTTTATATATTGAAAAAGTTGATGAAGATATGATCGATAGTTAAAATATCGA
1 TGATGATCGATACTTTTAAATATTGAAAAAGTTGAT--AGATAAGATCGAAAGTTAAAATATCGA
1183685 T
64 T
1183686 GCATATATTA
Statistics
Matches: 239, Mismatches: 36, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
71 23 0.10
72 35 0.15
73 97 0.41
74 61 0.26
75 1 0.00
76 22 0.09
ACGTcount: A:0.42, C:0.09, G:0.17, T:0.32
Consensus pattern (74 bp):
TGATGATCGATACTTTTAAATATTGAAAAAGTTGATAGATAAGATCGAAAGTTAAAATATCGATA
CTTATGCAC
Found at i:1185248 original size:52 final size:52
Alignment explanation
Indices: 1185165--1185478 Score: 414
Period size: 52 Copynumber: 5.9 Consensus size: 52
1185155 TTAACATTTA
*
1185165 ATCTAACTTGCATTATTGACACCTTTCTGCCAAATGCATAGTTAGGCCTTTC
1 ATCTAACTTGCATTATTGACACCTTTCTGCCAAATGCACAGTTAGGCCTTTC
* * *
1185217 ATCTAACTTGCATTATTGACACCTTTTTGCCAAATGCACAATTAGGCATTTC
1 ATCTAACTTGCATTATTGACACCTTTCTGCCAAATGCACAGTTAGGCCTTTC
* * *
1185269 ATCTAACTTGCATTATTGGCACCCTTCTGCCAAATGCACAGTTAGACCTTTC
1 ATCTAACTTGCATTATTGACACCTTTCTGCCAAATGCACAGTTAGGCCTTTC
*
1185321 ATCTAACTTGCATTATTGACACCTTTCTGCCAAATGCACATTTAGGCCTTTC
1 ATCTAACTTGCATTATTGACACCTTTCTGCCAAATGCACAGTTAGGCCTTTC
* * *
1185373 ATCTAACTTGCATTATTGACACCTTTATGCCAATATGCATAGTTAGGCATTTAACTAATC
1 ATCTAACTTGCATTATTGACACCTTTCTGCCAA-ATGCACAGTTAGGC------CT-TTC
* *
1185433 ATCTAACTTGCATTATT-AGCACATTTATGCCAATATGCACAGTTAG
1 ATCTAACTTGCATTATTGA-CACCTTTCTGCCAA-ATGCACAGTTAG
1185479 ACATTTAACT
Statistics
Matches: 233, Mismatches: 20, Indels: 10
0.89 0.08 0.04
Matches are distributed among these distances:
52 174 0.75
53 12 0.05
59 3 0.01
60 44 0.19
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (52 bp):
ATCTAACTTGCATTATTGACACCTTTCTGCCAAATGCACAGTTAGGCCTTTC
Found at i:1185254 original size:26 final size:26
Alignment explanation
Indices: 1185173--1185412 Score: 70
Period size: 26 Copynumber: 9.2 Consensus size: 26
1185163 TAATCTAACT
*
1185173 TGCATTATTGACACCTTTCTGCCAAA
1 TGCATTATTGACACCTTTATGCCAAA
** * *
1185199 TGCA-TAGTT-AGGCCTTTCAT-CTAACT
1 TGCATTA-TTGACACCTTT-ATGCCAA-A
*
1185225 TGCATTATTGACACCTTTTTGCCAAA
1 TGCATTATTGACACCTTTATGCCAAA
** * * *
1185251 TGCACAATTAGGCA--TTTCAT-CTAACT
1 TGCATTATT-GACACCTTT-ATGCCAA-A
* * *
1185277 TGCATTATTGGCACCCTTCTGCCAAA
1 TGCATTATTGACACCTTTATGCCAAA
* * * *
1185303 TGCA-CAGTT-AGACCTTTCAT-CTAACT
1 TGCATTA-TTGACACCTTT-ATGCCAA-A
*
1185329 TGCATTATTGACACCTTTCTGCCAAA
1 TGCATTATTGACACCTTTATGCCAAA
* * ** * *
1185355 TGCA-CATTTAGGCCTTTCAT-CTAACT
1 TGCATTATTGACACCTTT-ATGCCAA-A
1185381 TGCATTATTGACACCTTTATGCCAATA
1 TGCATTATTGACACCTTTATGCCAA-A
1185408 TGCAT
1 TGCAT
1185413 AGTTAGGCAT
Statistics
Matches: 144, Mismatches: 48, Indels: 43
0.61 0.20 0.18
Matches are distributed among these distances:
25 42 0.29
26 55 0.38
27 47 0.33
ACGTcount: A:0.26, C:0.25, G:0.12, T:0.36
Consensus pattern (26 bp):
TGCATTATTGACACCTTTATGCCAAA
Found at i:1185393 original size:156 final size:160
Alignment explanation
Indices: 1185101--1185481 Score: 518
Period size: 156 Copynumber: 2.3 Consensus size: 160
1185091 AATACACTGT
* *
1185101 TTTTCATCTAACTTGCATTAGTAGCACCTTTCTGCCAAATGCACATTTAGACATTTAACATTTAA
1 TTTTCATCTAACTTGCATTATTAGCACCTTTCTGCCAAATGCACAGTTAGAC-----ACATTTAA
*
1185166 TCTAACTTGCATTATTGACACCTTTCTGCCAAATGCATAGTTAGGCCTTTCATCTAACTTGCATT
61 TCTAACTTGCATTATTGACACCTTTCTGCCAAATGCACAGTTAGGCCTTTCATCTAACTTGCATT
*
1185231 ATTGACACCTTTTTGCCAA-ATGCACAATTAGGCA
126 ATTGACACCTTTATGCCAATATGCACAATTAGGCA
* * *
1185265 -TTTCATCTAACTTGCATTATTGGCACCCTTCTGCCAAATGCACAGTTAGAC-C-TTTCATCTAA
1 TTTTCATCTAACTTGCATTATTAGCACCTTTCTGCCAAATGCACAGTTAGACACATTTAATCTAA
*
1185327 CTTGCATTATTGACACCTTTCTGCCAAATGCACATTTAGGCCTTTCATCTAACTTGCATTATTGA
66 CTTGCATTATTGACACCTTTCTGCCAAATGCACAGTTAGGCCTTTCATCTAACTTGCATTATTGA
* *
1185392 CACCTTTATGCCAATATGCATAGTTAGGCA
131 CACCTTTATGCCAATATGCACAATTAGGCA
* *
1185422 TTTAACTAATCATCTAACTTGCATTATTAGCACATTTATGCCAATATGCACAGTTAGACA
1 -TT---T--TCATCTAACTTGCATTATTAGCACCTTTCTGCCAA-ATGCACAGTTAGACA
1185482 TTTAACTTTT
Statistics
Matches: 193, Mismatches: 14, Indels: 18
0.86 0.06 0.08
Matches are distributed among these distances:
156 85 0.44
157 14 0.07
159 1 0.01
162 1 0.01
163 47 0.24
164 31 0.16
165 14 0.07
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.36
Consensus pattern (160 bp):
TTTTCATCTAACTTGCATTATTAGCACCTTTCTGCCAAATGCACAGTTAGACACATTTAATCTAA
CTTGCATTATTGACACCTTTCTGCCAAATGCACAGTTAGGCCTTTCATCTAACTTGCATTATTGA
CACCTTTATGCCAATATGCACAATTAGGCA
Found at i:1185411 original size:27 final size:27
Alignment explanation
Indices: 1185329--1185412 Score: 68
Period size: 27 Copynumber: 3.2 Consensus size: 27
1185319 TCATCTAACT
*
1185329 TGCATTATTGACACCTTTCTGCCAA-A
1 TGCATTATTGACACCTTTATGCCAATA
* * ** *
1185355 TGCA-CATTTAGGCCTTTCAT-CTAACT-
1 TGCATTATTGACACCTTT-ATGCCAA-TA
1185381 TGCATTATTGACACCTTTATGCCAATA
1 TGCATTATTGACACCTTTATGCCAATA
1185408 TGCAT
1 TGCAT
1185413 AGTTAGGCAT
Statistics
Matches: 41, Mismatches: 11, Indels: 11
0.65 0.17 0.17
Matches are distributed among these distances:
25 12 0.29
26 12 0.29
27 17 0.41
ACGTcount: A:0.26, C:0.25, G:0.12, T:0.37
Consensus pattern (27 bp):
TGCATTATTGACACCTTTATGCCAATA
Found at i:1185460 original size:60 final size:60
Alignment explanation
Indices: 1185371--1185488 Score: 193
Period size: 60 Copynumber: 2.0 Consensus size: 60
1185361 TTTAGGCCTT
* * *
1185371 TCATCTAACTTGCATTATTGACACCTTTATGCCAATATGCATAGTTAGGCATTTAACTAA
1 TCATCTAACTTGCATTATTGACACATTTATGCCAATATGCACAGTTAGACATTTAACTAA
1185431 TCATCTAACTTGCATTATT-AGCACATTTATGCCAATATGCACAGTTAGACATTTAACT
1 TCATCTAACTTGCATTATTGA-CACATTTATGCCAATATGCACAGTTAGACATTTAACT
1185489 TTTCTTCATT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
59 1 0.02
60 53 0.98
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.36
Consensus pattern (60 bp):
TCATCTAACTTGCATTATTGACACATTTATGCCAATATGCACAGTTAGACATTTAACTAA
Done.