Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008620.1 Hibiscus syriacus cultivar Beakdansim tig00111582_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: 13158977
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 61 of 64
Found at i:12328738 original size:18 final size:18
Alignment explanation
Indices: 12328717--12328753 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
12328707 GTAATTGGAG
12328717 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
12328735 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
12328753 T
1 T
12328754 ATATATTCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:12343086 original size:30 final size:30
Alignment explanation
Indices: 12343052--12343113 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
12343042 CACTTCATAT
12343052 GATCATTTCCATCATTTCACATACCTGGAA
1 GATCATTTCCATCATTTCACATACCTGGAA
12343082 GATCATTTCCATCATTTCACATACCTGGAA
1 GATCATTTCCATCATTTCACATACCTGGAA
12343112 GA
1 GA
12343114 ATTCTCTGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.32
Consensus pattern (30 bp):
GATCATTTCCATCATTTCACATACCTGGAA
Found at i:12343589 original size:64 final size:64
Alignment explanation
Indices: 12343517--12343679 Score: 168
Period size: 64 Copynumber: 2.5 Consensus size: 64
12343507 ATCCCTTGAC
* * *
12343517 GGGTGCATCGATGCACTA-TCTATGCATCGGTACA-TAAATCTCATTCGATGTTTGTATTTTAAG
1 GGGTGCATCGATGCACTACT-TATGCATCGATACACT-AATCGCATTCGATGTTTGTATTTTAAA
12343580 G
64 G
* * * *
12343581 GGGTGCATCGATGCACTACTTGTGCATCGATACACTGATGGCATTCGATGTTTTTATTTTAAAG
1 GGGTGCATCGATGCACTACTTATGCATCGATACACTAATCGCATTCGATGTTTGTATTTTAAAG
* * * * * * *
12343645 GAGTACATCGATACACTTCATGTACATCGATACAC
1 GGGTGCATCGATGCACTACTTATGCATCGATACAC
12343680 ATTGAACAAT
Statistics
Matches: 84, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
64 82 0.98
65 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (64 bp):
GGGTGCATCGATGCACTACTTATGCATCGATACACTAATCGCATTCGATGTTTGTATTTTAAAG
Found at i:12345909 original size:26 final size:26
Alignment explanation
Indices: 12345864--12345913 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
12345854 TATTGGGAGA
* *
12345864 AAGCTAGAATGATTTGGGATGATTTTG
1 AAGCTAGAATGAGTTAGGAT-ATTTTG
12345891 AAGCTA-AATGAGTTAGGATATTT
1 AAGCTAGAATGAGTTAGGATATTT
12345914 ATAGTTGAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 11 0.52
27 6 0.29
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (26 bp):
AAGCTAGAATGAGTTAGGATATTTTG
Found at i:12349281 original size:21 final size:20
Alignment explanation
Indices: 12349195--12349393 Score: 105
Period size: 21 Copynumber: 9.8 Consensus size: 20
12349185 AAATGACCAA
**
12349195 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
12349214 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
12349234 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
12349254 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
12349275 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
12349296 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
12349316 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
* ***
12349337 GAAAATCGCATTACGATTTT
1 CAAAATCGCAACGCGATTTT
* *
12349357 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
12349378 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
12349394 ACACATAAAT
Statistics
Matches: 132, Mismatches: 41, Indels: 13
0.71 0.22 0.07
Matches are distributed among these distances:
19 16 0.12
20 55 0.42
21 61 0.46
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:12349343 original size:20 final size:20
Alignment explanation
Indices: 12349195--12349412 Score: 104
Period size: 20 Copynumber: 10.8 Consensus size: 20
12349185 AAATGACCAA
12349195 CAAAATCGCAACGCGAA-AT
1 CAAAATCGCAACGCGAATAT
* **
12349214 AAAAATCGCAACGCG-ATCCC
1 CAAAATCGCAACGCGAAT-AT
* ** * *
12349234 CAGAATCGCAAATC-AGTTT
1 CAAAATCGCAACGCGAATAT
* *
12349253 CCAAAATCGCAACGCGATTCTT
1 -CAAAATCGCAACGCGAAT-AT
* *
12349275 GAAAATCGCAATGCG-ATAGT
1 CAAAATCGCAACGCGAATA-T
* ** * *
12349295 ACAAATTCGCATTGCGATTTT
1 -CAAAATCGCAACGCGAATAT
12349316 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGAATAT
* *** * *
12349337 GAAAATCGCATTACGATTTT
1 CAAAATCGCAACGCGAATAT
12349357 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGAATAT
* *
12349378 GAAAATCGCAACGCGAACA-
1 CAAAATCGCAACGCGAATAT
12349397 CATAAATCGCAACGCG
1 CA-AAATCGCAACGCG
12349413 TATCCGTAAA
Statistics
Matches: 144, Mismatches: 44, Indels: 21
0.69 0.21 0.10
Matches are distributed among these distances:
18 1 0.01
19 15 0.10
20 68 0.47
21 57 0.40
22 3 0.02
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGAATAT
Found at i:12349355 original size:41 final size:41
Alignment explanation
Indices: 12349276--12349387 Score: 165
Period size: 41 Copynumber: 2.7 Consensus size: 41
12349266 GCGATTCTTG
* *
12349276 AAAATCGCAATGCG-ATA-GTACAAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGAATATG-A-AAA-TCGCATTACGATTTTCC
12349318 AAAATCGCAACGCGAATATGAAAATCGCATTACGATTTTCC
1 AAAATCGCAACGCGAATATGAAAATCGCATTACGATTTTCC
12349359 AAAATCGCAACGCGAATATGAAAATCGCA
1 AAAATCGCAACGCGAATATGAAAATCGCA
12349388 ACGCGAACAC
Statistics
Matches: 66, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
41 45 0.68
42 16 0.24
43 4 0.06
44 1 0.02
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGCGAATATGAAAATCGCATTACGATTTTCC
Found at i:12349422 original size:20 final size:20
Alignment explanation
Indices: 12349360--12349553 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
12349350 CGATTTTCCA
* ** *
12349360 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
12349380 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
12349400 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
12349420 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
12349440 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
12349460 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
12349480 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
12349500 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
12349520 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
12349541 AAATCGCAACGCG
1 AAATCGCAACGCG
12349554 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:12349452 original size:60 final size:60
Alignment explanation
Indices: 12349360--12349553 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
12349350 CGATTTTCCA
* ** * *
12349360 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
12349420 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
12349480 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
12349541 AAATCGCAACGCG
1 AAATCGCAACGCG
12349554 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:12349974 original size:33 final size:33
Alignment explanation
Indices: 12349935--12350005 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
12349925 TTCACTTAGA
* *
12349935 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
12349968 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
12350001 TTTCA
1 TTTCA
12350006 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:12350129 original size:20 final size:21
Alignment explanation
Indices: 12350083--12350161 Score: 92
Period size: 21 Copynumber: 3.8 Consensus size: 21
12350073 TTTGCAGAAG
*
12350083 AGTCGCAACGAGATAAATGAAA
1 AGTCGCAACGAGA-GAATGAAA
*
12350105 A-TCGCAACGAGAGAATG-AC
1 AGTCGCAACGAGAGAATGAAA
*
12350124 TGTCGCAACGAGAGAAATGAAA
1 AGTCGCAACGAGAG-AATGAAA
12350146 AG-CGCAACGAGAGAAT
1 AGTCGCAACGAGAGAAT
12350162 CGCAACGCGA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.02
20 19 0.39
21 26 0.53
22 3 0.06
ACGTcount: A:0.46, C:0.16, G:0.27, T:0.11
Consensus pattern (21 bp):
AGTCGCAACGAGAGAATGAAA
Found at i:12350142 original size:41 final size:41
Alignment explanation
Indices: 12350084--12350161 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
12350074 TTGCAGAAGA
* *
12350084 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAAGCGCAACGAGAGAATGACT
12350125 GTCGCAACGAGAGAAATGAAAAGCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAAGCGCAACGAGAGAAT
12350162 CGCAACGCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.45, C:0.17, G:0.27, T:0.12
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAAGCGCAACGAGAGAATGACT
Found at i:12350177 original size:33 final size:33
Alignment explanation
Indices: 12350137--12350206 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
12350127 CGCAACGAGA
*
12350137 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCACAACGAGAGAATCGCAACGC
*
12350170 GAAATGAAAATCACAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCACAACGAGAGAATCGCAACGC
12350203 GAAA
1 GAAA
12350207 CCAAAATCGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.49, C:0.20, G:0.24, T:0.07
Consensus pattern (33 bp):
GAAATGAAAAGCACAACGAGAGAATCGCAACGC
Found at i:12350213 original size:33 final size:33
Alignment explanation
Indices: 12350150--12350214 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
12350140 ATGAAAAGCG
**
12350150 CAACGAGAGAATCGCAACGCGAAATGAAAATCA
1 CAACGAGAGAATCGCAACGCGAAACCAAAATCA
12350183 CAACGAGAGAATCGCAACGCGAAACCAAAATC
1 CAACGAGAGAATCGCAACGCGAAACCAAAATC
12350215 GTATTGCGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.48, C:0.25, G:0.20, T:0.08
Consensus pattern (33 bp):
CAACGAGAGAATCGCAACGCGAAACCAAAATCA
Found at i:12350240 original size:19 final size:18
Alignment explanation
Indices: 12350218--12350330 Score: 79
Period size: 14 Copynumber: 6.8 Consensus size: 18
12350208 CAAAATCGTA
12350218 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCA-TTCGCG
*
12350237 TTGCGA--TTC--TCTCG
1 TTGCGATTTTCATTCGCG
12350251 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCA-TTCGCG
*
12350270 TTGCGA--TTC--TCTCG
1 TTGCGATTTTCATTCGCG
*
12350284 TTGCGATTGTCATCTCGCG
1 TTGCGATTTTCAT-TCGCG
*
12350303 TTGCGA--TTC--TCTCG
1 TTGCGATTTTCATTCGCG
12350317 TTGCGATTTTCATT
1 TTGCGATTTTCATT
12350331 TCAACCAAAA
Statistics
Matches: 73, Mismatches: 7, Indels: 29
0.67 0.06 0.27
Matches are distributed among these distances:
14 30 0.41
16 8 0.11
17 8 0.11
18 1 0.01
19 26 0.36
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (18 bp):
TTGCGATTTTCATTCGCG
Found at i:12350254 original size:14 final size:14
Alignment explanation
Indices: 12350235--12350324 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
12350225 TTTCATTTCG
12350235 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
12350249 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
12350268 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
12350282 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
12350299 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
12350315 CGTTGCGATT
1 CGTTGCGATT
12350325 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:12350260 original size:33 final size:33
Alignment explanation
Indices: 12350218--12350332 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
12350208 CAAAATCGTA
12350218 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
12350251 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
12350284 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
12350317 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
12350333 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:12351198 original size:93 final size:93
Alignment explanation
Indices: 12350893--12351271 Score: 726
Period size: 93 Copynumber: 4.1 Consensus size: 93
12350883 TAGATTGCTT
*
12350893 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
12350958 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
12350986 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACAC--TGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
12351049 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
12351077 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
12351142 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
12351170 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
12351235 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
12351263 AGTAAATTT
1 AGTAAATTT
12351272 ATCCATTCAA
Statistics
Matches: 281, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
91 90 0.32
93 191 0.68
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:12351202 original size:184 final size:185
Alignment explanation
Indices: 12350893--12351273 Score: 728
Period size: 184 Copynumber: 2.1 Consensus size: 185
12350883 TAGATTGCTT
*
12350893 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
12350958 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
12351023 GTGTATTCTTTAACAC-TGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
12351077 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
12351142 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
12351207 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACAC-GTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
12351263 AGTAAATTTAT
1 AGTAAATTTAT
12351274 CCATTCAAGT
Statistics
Matches: 192, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
184 144 0.75
186 48 0.25
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (185 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:12351355 original size:19 final size:19
Alignment explanation
Indices: 12351315--12351443 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
12351305 TAGTTTACTT
* *
12351315 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
12351335 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
12351354 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
12351373 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
12351387 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
12351406 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
12351420 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
12351439 TCGCA
1 TCGCA
12351444 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:12351394 original size:33 final size:32
Alignment explanation
Indices: 12351351--12351443 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
12351341 CGCGAAACCA
**
12351351 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
12351383 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
12351416 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
12351444 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:12351441 original size:52 final size:52
Alignment explanation
Indices: 12351315--12351443 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
12351305 TAGTTTACTT
**
12351315 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
12351367 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
12351420 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
12351444 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:12351461 original size:19 final size:19
Alignment explanation
Indices: 12351439--12351573 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
12351429 GAAACCAAAA
*
12351439 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
12351458 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
12351474 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
12351491 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
12351507 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
12351524 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
12351543 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
12351563 TCGTGTTGCGA
1 TCGCGTTGCGA
12351574 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:12351480 original size:14 final size:14
Alignment explanation
Indices: 12351461--12351517 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
12351451 TTTCATTTCG
12351461 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
12351475 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
12351492 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
12351508 CGTTGCGATT
1 CGTTGCGATT
12351518 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:12351486 original size:33 final size:33
Alignment explanation
Indices: 12351444--12351536 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
12351434 CAAAATCGCA
*
12351444 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
12351477 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
12351510 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
12351537 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:12353514 original size:14 final size:14
Alignment explanation
Indices: 12353495--12353530 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
12353485 ATTGTTTAAT
12353495 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
12353509 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
12353523 TGATTTGT
1 TGATTTGT
12353531 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:12353723 original size:20 final size:19
Alignment explanation
Indices: 12353637--12353735 Score: 138
Period size: 19 Copynumber: 5.5 Consensus size: 19
12353627 AAAATTGACT
12353637 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
12353655 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
12353674 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
12353688 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
12353707 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
12353727 ATCGCAATG
1 ATCGCAATG
12353736 GGAGAATCGC
Statistics
Matches: 72, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 17 0.24
19 22 0.31
20 18 0.25
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:12353765 original size:53 final size:53
Alignment explanation
Indices: 12353637--12353752 Score: 200
Period size: 53 Copynumber: 2.2 Consensus size: 53
12353627 AAAATTGACT
12353637 ATCGCAATGCGAAATG-AAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
* *
12353688 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAATGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
12353741 ATCGCAATGCGA
1 ATCGCAATGCGA
12353753 TTTTAATTTC
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
51 16 0.26
52 12 0.20
53 33 0.54
ACGTcount: A:0.43, C:0.17, G:0.25, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:12353770 original size:19 final size:19
Alignment explanation
Indices: 12353742--12353857 Score: 117
Period size: 19 Copynumber: 6.6 Consensus size: 19
12353732 AATGGGAGAA
* *
12353742 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
12353761 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
12353777 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
12353794 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
12353813 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
12353829 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
12353846 TCCGCATTGCGA
1 T-CGCATTGCGA
12353858 AATGTAATGG
Statistics
Matches: 80, Mismatches: 6, Indels: 21
0.75 0.06 0.20
Matches are distributed among these distances:
14 12 0.15
16 14 0.17
17 11 0.14
18 2 0.03
19 35 0.44
20 6 0.08
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.43
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:12353805 original size:52 final size:52
Alignment explanation
Indices: 12353742--12353857 Score: 205
Period size: 52 Copynumber: 2.2 Consensus size: 52
12353732 AATGGGAGAA
*
12353742 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
12353794 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
12353846 TCCGCATTGCGA
1 T-CGCATTGCGA
12353858 AATGTAATGG
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 51 0.84
53 10 0.16
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.43
Consensus pattern (52 bp):
TCGCATTGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:12353940 original size:19 final size:19
Alignment explanation
Indices: 12353916--12354013 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
12353906 AAAATTGACT
12353916 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
12353935 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
12353954 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
12353968 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
12353987 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
12354007 ATCGCAA
1 ATCGCAA
12354014 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:12354045 original size:53 final size:53
Alignment explanation
Indices: 12353916--12354032 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
12353906 AAAATTGACT
12353916 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
12353968 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
12354021 ATCGCAATGCGA
1 ATCGCAATGCGA
12354033 TTTTCATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.45
53 35 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:12356367 original size:12 final size:12
Alignment explanation
Indices: 12356350--12356374 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12356340 TCTTCGGGGA
12356350 CTTTTTCTTCTT
1 CTTTTTCTTCTT
12356362 CTTTTTCTTCTT
1 CTTTTTCTTCTT
12356374 C
1 C
12356375 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:12356583 original size:24 final size:24
Alignment explanation
Indices: 12356549--12356595 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
12356539 CTGAAACATC
12356549 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
12356573 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
12356596 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:12356895 original size:20 final size:20
Alignment explanation
Indices: 12356870--12357125 Score: 235
Period size: 20 Copynumber: 12.8 Consensus size: 20
12356860 CGGTTAACAA
*
12356870 ATTCTCGTTGTGATTTACAG
1 ATTCTCGTTGCGATTTACAG
*
12356890 ATTCTCGTTGCGATTTACGG
1 ATTCTCGTTGCGATTTACAG
*
12356910 ATTATCGTTGCGATTTACAG
1 ATTCTCGTTGCGATTTACAG
*
12356930 ATTCTCGTTGCGATTTACGG
1 ATTCTCGTTGCGATTTACAG
* *
12356950 ATTATCGTTGCGATTTATAG
1 ATTCTCGTTGCGATTTACAG
*
12356970 ATTCTCGTTGCGATTTACGG
1 ATTCTCGTTGCGATTTACAG
* *
12356990 ATTATCGTTGCGATTTACGG
1 ATTCTCGTTGCGATTTACAG
* * * *
12357010 ATACGCGTTGCGATATACGG
1 ATTCTCGTTGCGATTTACAG
* * * *
12357030 ATACGCATTGCGATTTACGG
1 ATTCTCGTTGCGATTTACAG
* * * *
12357050 ATACGCGTTGCGATATACGG
1 ATTCTCGTTGCGATTTACAG
* * *
12357070 ATACACGTTGCGATTTA-TG
1 ATTCTCGTTGCGATTTACAG
* * * *
12357089 TGTTCGCGTTGCGATTTTCAT
1 -ATTCTCGTTGCGATTTACAG
*
12357110 ATTCGCGTTGCGATTT
1 ATTCTCGTTGCGATTT
12357126 TGGAAAATCG
Statistics
Matches: 203, Mismatches: 31, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
19 1 0.00
20 202 1.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (20 bp):
ATTCTCGTTGCGATTTACAG
Found at i:12356929 original size:40 final size:40
Alignment explanation
Indices: 12356874--12357086 Score: 279
Period size: 40 Copynumber: 5.3 Consensus size: 40
12356864 TAACAAATTC
*
12356874 TCGTTGTGATTTACAGATTCTCGTTGCGATTTACGGATTA
1 TCGTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTA
12356914 TCGTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTA
1 TCGTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTA
*
12356954 TCGTTGCGATTTATAGATTCTCGTTGCGATTTACGGATTA
1 TCGTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTA
* * * *
12356994 TCGTTGCGATTTACGGATACGCGTTGCGATATACGGA-TA
1 TCGTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTA
* * * *
12357033 -CGCATTGCGATTTACGGATACGCGTTGCGATATACGGA-TA
1 TCG--TTGCGATTTACAGATTCTCGTTGCGATTTACGGATTA
*
12357073 CACGTTGCGATTTA
1 -TCGTTGCGATTTA
12357087 TGTGTTCGCG
Statistics
Matches: 162, Mismatches: 7, Indels: 8
0.92 0.04 0.05
Matches are distributed among these distances:
38 2 0.01
39 2 0.01
40 156 0.96
42 2 0.01
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (40 bp):
TCGTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTA
Found at i:12356945 original size:60 final size:60
Alignment explanation
Indices: 12356870--12357125 Score: 259
Period size: 60 Copynumber: 4.3 Consensus size: 60
12356860 CGGTTAACAA
* * *
12356870 ATTCTCGTTGTGATTTACAGATTCTCGTTGCGATTTACGGATTATCGTTGCGATTTACAG
1 ATTCTCGTTGCGATTTACGGATACTCGTTGCGATTTACGGATTATCGTTGCGATTTACAG
** * *
12356930 ATTCTCGTTGCGATTTACGGATTA-TCGTTGCGATTTATAGATTCTCGTTGCGATTTACGG
1 ATTCTCGTTGCGATTTACGGA-TACTCGTTGCGATTTACGGATTATCGTTGCGATTTACAG
* * * *
12356990 ATTATCGTTGCGATTTACGGATACGCGTTGCGATATACGGA-TA-CGCATTGCGATTTACGG
1 ATTCTCGTTGCGATTTACGGATACTCGTTGCGATTTACGGATTATCG--TTGCGATTTACAG
* * * * * ** * *
12357050 ATACGCGTTGCGATATACGGATACACGTTGCGATTTATGTG-TTCGCGTTGCGATTTTCAT
1 ATTCTCGTTGCGATTTACGGATACTCGTTGCGATTTACG-GATTATCGTTGCGATTTACAG
*
12357110 ATTCGCGTTGCGATTT
1 ATTCTCGTTGCGATTT
12357126 TGGAAAATCG
Statistics
Matches: 163, Mismatches: 26, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
58 2 0.01
59 3 0.02
60 153 0.94
61 3 0.02
62 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (60 bp):
ATTCTCGTTGCGATTTACGGATACTCGTTGCGATTTACGGATTATCGTTGCGATTTACAG
Found at i:12357142 original size:21 final size:21
Alignment explanation
Indices: 12357112--12357194 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
12357102 ATTTTCATAT
*
12357112 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
12357133 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
12357154 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
12357175 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
12357195 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:12357185 original size:42 final size:43
Alignment explanation
Indices: 12357092--12357190 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
12357082 ATTTATGTGT
* *
12357092 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
12357133 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
12357175 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
12357191 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:12358355 original size:37 final size:36
Alignment explanation
Indices: 12358268--12358392 Score: 103
Period size: 35 Copynumber: 3.4 Consensus size: 36
12358258 ATTATTTATA
* *
12358268 TAAATAATATGTATACTATAT-TTATTTCAAAAACCATTT
1 TAAA-AATATATATACTATATGTT-TTT-AAAAA-TATTT
*
12358307 TAAAAA-CTATATACTATATGTTTTTAAAAATATTT
1 TAAAAATATATATACTATATGTTTTTAAAAATATTT
* * *
12358342 TAAAAAT-TATATATTATATGTTTTCAAGAATGTATTTT
1 TAAAAATATATATACTATATGTTTTTAA-AA-ATA-TTT
*
12358380 TAAAACTATATAT
1 TAAAAATATATAT
12358393 GTTTTACAAA
Statistics
Matches: 73, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
35 28 0.38
36 7 0.10
37 16 0.22
38 13 0.18
39 9 0.12
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (36 bp):
TAAAAATATATATACTATATGTTTTTAAAAATATTT
Found at i:12358508 original size:37 final size:36
Alignment explanation
Indices: 12358279--12358582 Score: 200
Period size: 39 Copynumber: 8.3 Consensus size: 36
12358269 AAATAATATG
* **
12358279 TATACTATATTTA-TTTCAAAAACCA-TTTTAAAAAC
1 TATA-TATATATATTTTCAAAAATGATTTTTAAAAAC
* * *
12358314 TATATACTATATGTTTTTAAAAAT-A-TTTTAAAAAT
1 TATATA-TATATATTTTCAAAAATGATTTTTAAAAAC
* *
12358349 TATATATTATATGTTTTCAAGAATGTATTTTT-AAAAC
1 TATATA-TATATATTTTCAAAAATG-ATTTTTAAAAAC
* * **
12358386 --TATATATGT-TTTACAAAACCGATTTTTAAAAAC
1 TATATATATATATTTTCAAAAATGATTTTTAAAAAC
* *
12358419 TATATATTATATATGTTTTCAAAAGTG-TGTTTTCAAAAC
1 TATATA-TATATA--TTTTCAAAAATGAT-TTTTAAAAAC
*
12358458 CATATTATATATATTTTCAAAAATCGATTTTTAAAAAAC
1 TATA-TATATATATTTTCAAAAAT-GATTTTT-AAAAAC
* *
12358497 TATATATTATATTATTTTCAAAAACCG-TTTTCTAAAAAT
1 TATATA-TATA-TATTTTCAAAAA-TGATTTT-TAAAAAC
* *
12358536 TATATATTATATGTTTTTAAAAAAT-ATTTTTAAAAAC
1 TATATA-TATAT-ATTTTCAAAAATGATTTTTAAAAAC
12358573 TATAT-TATAT
1 TATATATATAT
12358583 TATTATATAT
Statistics
Matches: 217, Mismatches: 29, Indels: 46
0.74 0.10 0.16
Matches are distributed among these distances:
32 6 0.03
33 13 0.06
34 6 0.03
35 52 0.24
36 12 0.06
37 26 0.12
38 17 0.08
39 69 0.32
40 16 0.07
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.45
Consensus pattern (36 bp):
TATATATATATATTTTCAAAAATGATTTTTAAAAAC
Found at i:12359805 original size:71 final size:71
Alignment explanation
Indices: 12359689--12359829 Score: 282
Period size: 71 Copynumber: 2.0 Consensus size: 71
12359679 CAATAGTAGG
12359689 TACCATTTATCTACTTTACCCTTAAAAATAACTCATAAATTTGGATAAGCCAAGTTATTAAAATA
1 TACCATTTATCTACTTTACCCTTAAAAATAACTCATAAATTTGGATAAGCCAAGTTATTAAAATA
12359754 ACGTTA
66 ACGTTA
12359760 TACCATTTATCTACTTTACCCTTAAAAATAACTCATAAATTTGGATAAGCCAAGTTATTAAAATA
1 TACCATTTATCTACTTTACCCTTAAAAATAACTCATAAATTTGGATAAGCCAAGTTATTAAAATA
12359825 ACGTT
66 ACGTT
12359830 TTCTTTTTGG
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 70 1.00
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.35
Consensus pattern (71 bp):
TACCATTTATCTACTTTACCCTTAAAAATAACTCATAAATTTGGATAAGCCAAGTTATTAAAATA
ACGTTA
Found at i:12363375 original size:19 final size:19
Alignment explanation
Indices: 12363329--12363371 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
12363319 ATTATAAAAC
12363329 AATT-AATCAGATTAATTT
1 AATTAAATCAGATTAATTT
**
12363347 AATTTGATCAG-TTAATTT
1 AATTAAATCAGATTAATTT
12363365 AATTAAA
1 AATTAAA
12363372 ATCAAATTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (19 bp):
AATTAAATCAGATTAATTT
Found at i:12368731 original size:14 final size:14
Alignment explanation
Indices: 12368712--12368741 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
12368702 TAATATTTTT
12368712 TATTTTTTAAAAAA
1 TATTTTTTAAAAAA
12368726 TATTTTTTAAAAAA
1 TATTTTTTAAAAAA
12368740 TA
1 TA
12368742 ATAATAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATTTTTTAAAAAA
Found at i:12379527 original size:20 final size:21
Alignment explanation
Indices: 12379502--12379553 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
12379492 TTTTCCCAAT
*
12379502 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
12379522 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
12379543 TCGCAATGCGA
1 TCGCAATGCGA
12379554 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:12379567 original size:20 final size:20
Alignment explanation
Indices: 12379542--12379656 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
12379532 AATTGGGAAA
*
12379542 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
12379562 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
12379583 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
12379603 TTCGCAACGCGATACTAACT
1 ATCGCAACGCGATACTGACT
* *
12379623 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
12379643 TTCGCAACGCGATA
1 ATCGCAACGCGATA
12379657 ATACATAATC
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 63 0.79
21 13 0.16
22 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:12379644 original size:40 final size:41
Alignment explanation
Indices: 12379539--12379676 Score: 152
Period size: 41 Copynumber: 3.4 Consensus size: 41
12379529 GCGAATTGGG
* * *
12379539 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* * *
12379580 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATACTA-
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
*** *
12379620 ACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* * *
12379661 ATAATCGTAATGCGAT
1 AAAATCGCAACGCGAT
12379677 TTTCAAAGCG
Statistics
Matches: 78, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
40 33 0.42
41 45 0.58
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.25
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:12379873 original size:22 final size:22
Alignment explanation
Indices: 12379845--12379888 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
12379835 ATTCTCTCAC
*
12379845 CCATCTCCGACGAAATCTGTCT
1 CCATCTCCGACGAAATCCGTCT
*
12379867 CCATCTCCGGCGAAATCCGTCT
1 CCATCTCCGACGAAATCCGTCT
12379889 ATCTCCATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.39, G:0.16, T:0.25
Consensus pattern (22 bp):
CCATCTCCGACGAAATCCGTCT
Found at i:12381497 original size:18 final size:18
Alignment explanation
Indices: 12381471--12381515 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
12381461 CTCCACTTCG
*
12381471 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
12381489 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
12381507 GAGCCATCA
1 GAGCCATCA
12381516 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:12382015 original size:20 final size:20
Alignment explanation
Indices: 12381990--12382032 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
12381980 ATAGTTACTT
12381990 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
12382010 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
12382030 TCG
1 TCG
12382033 TAATGCAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.26, G:0.23, T:0.16
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:12382083 original size:18 final size:18
Alignment explanation
Indices: 12382060--12382122 Score: 73
Period size: 18 Copynumber: 3.8 Consensus size: 18
12382050 CGCAACGACA
12382060 AAATCGCAATGCGAAATG
1 AAATCGCAATGCGAAATG
*
12382078 AAATCGCAA--CG--A-C
1 AAATCGCAATGCGAAATG
*
12382091 AAATCGCAACGCGAAATG
1 AAATCGCAATGCGAAATG
12382109 AAATCGCAATGCGA
1 AAATCGCAATGCGA
12382123 TTTGTGTTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
13 9 0.24
14 1 0.03
15 2 0.05
16 2 0.05
17 1 0.03
18 22 0.59
ACGTcount: A:0.44, C:0.22, G:0.21, T:0.13
Consensus pattern (18 bp):
AAATCGCAATGCGAAATG
Found at i:12382098 original size:31 final size:32
Alignment explanation
Indices: 12382029--12382117 Score: 135
Period size: 31 Copynumber: 2.8 Consensus size: 32
12382019 GGAAATGGCT
* *
12382029 ATCGTAATGCAAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
12382062 ATCGCAATGCGAAATGAAATCGCAACGAC-AA
1 ATCGCAATGCGAAATGAAATCGCAACGACAAA
*
12382093 ATCGCAACGCGAAATGAAATCGCAA
1 ATCGCAATGCGAAATGAAATCGCAA
12382118 TGCGATTTGT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
31 26 0.49
32 13 0.25
33 14 0.26
ACGTcount: A:0.47, C:0.21, G:0.18, T:0.13
Consensus pattern (32 bp):
ATCGCAATGCGAAATGAAATCGCAACGACAAA
Found at i:12382107 original size:13 final size:14
Alignment explanation
Indices: 12382046--12382107 Score: 56
Period size: 13 Copynumber: 4.3 Consensus size: 14
12382036 TGCAAAATGA
*
12382046 AAATCGCAACGACA
1 AAATCGCAACGACG
*
12382060 AAATCGCAATGCGAAATG
1 AAATCGCAA--CG--ACG
12382078 AAATCGCAACGAC-
1 AAATCGCAACGACG
12382091 AAATCGCAACG-CG
1 AAATCGCAACGACG
12382104 AAAT
1 AAAT
12382108 GAAATCGCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
12 1 0.03
13 15 0.38
14 10 0.25
16 4 0.10
18 10 0.25
ACGTcount: A:0.47, C:0.24, G:0.18, T:0.11
Consensus pattern (14 bp):
AAATCGCAACGACG
Found at i:12382153 original size:14 final size:14
Alignment explanation
Indices: 12382134--12382191 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
12382124 TTGTGTTTCG
12382134 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
12382148 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
*
12382164 CGCGTTACGATTTTGT
1 --CGTTGCGATTTTGT
12382180 CGTTGCGATTTT
1 CGTTGCGATTTT
12382192 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.61
16 4 0.11
18 10 0.28
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:12382168 original size:32 final size:33
Alignment explanation
Indices: 12382129--12382207 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
12382119 GCGATTTGTG
12382129 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
12382161 TTTCGCGTTACGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
12382194 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
12382208 ATCCATTTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
32 26 0.60
33 17 0.40
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:12382219 original size:20 final size:20
Alignment explanation
Indices: 12382194--12382255 Score: 88
Period size: 20 Copynumber: 3.1 Consensus size: 20
12382184 GCGATTTTCA
*
12382194 TTTCGCATTGCGATATCCAT
1 TTTCGCATTGCGATAGCCAT
*
12382214 TTTCGCGTTGCGATAGCCAT
1 TTTCGCATTGCGATAGCCAT
* *
12382234 TTTTGCATTGCGATAGTCAT
1 TTTCGCATTGCGATAGCCAT
12382254 TT
1 TT
12382256 CGCGCTACGA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.18, C:0.21, G:0.19, T:0.42
Consensus pattern (20 bp):
TTTCGCATTGCGATAGCCAT
Found at i:12384127 original size:14 final size:14
Alignment explanation
Indices: 12384108--12384143 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
12384098 ATTGTTTAAT
12384108 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
12384122 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
12384136 TGATTTGT
1 TGATTTGT
12384144 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:12384266 original size:32 final size:33
Alignment explanation
Indices: 12384230--12384306 Score: 111
Period size: 32 Copynumber: 2.4 Consensus size: 33
12384220 CAAAACAACT
* ***
12384230 ATCGCAACGCGAAATGGCTATCGCAACGAG-AA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
12384262 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
12384295 ATCGCAATGCGA
1 ATCGCAATGCGA
12384307 TTTTCATTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 26 0.65
33 14 0.35
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:12384267 original size:13 final size:14
Alignment explanation
Indices: 12384249--12384301 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
12384239 CGAAATGGCT
12384249 ATCGCAACGAG-AA
1 ATCGCAACGAGAAA
12384262 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
12384281 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
12384295 ATCGCAA
1 ATCGCAA
12384302 TGCGATTTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
13 7 0.21
14 11 0.32
15 3 0.09
17 3 0.09
18 1 0.03
19 9 0.26
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:12384282 original size:19 final size:17
Alignment explanation
Indices: 12384260--12384306 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 17
12384250 TCGCAACGAG
12384260 AAATCGCAATGCGAAATGA
1 AAATCGCAATGCG-AA-GA
12384279 AAATCGCAA--CG-AGA
1 AAATCGCAATGCGAAGA
12384293 AAATCGCAATGCGA
1 AAATCGCAATGCGA
12384307 TTTTCATTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
14 11 0.44
15 1 0.04
16 2 0.08
17 2 0.08
19 9 0.36
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (17 bp):
AAATCGCAATGCGAAGA
Found at i:12384350 original size:20 final size:20
Alignment explanation
Indices: 12384325--12384382 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
12384315 TCGCATTGCG
*
12384325 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
12384345 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
12384365 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
12384383 TCAAATGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:12388194 original size:33 final size:33
Alignment explanation
Indices: 12388152--12388278 Score: 184
Period size: 33 Copynumber: 3.8 Consensus size: 33
12388142 GGAAATTACT
12388152 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
12388185 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
12388217 TTTCGCAATGCGAAATGAAAATCGTAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
12388251 ATCACAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
12388279 CGAATTTAAT
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
32 1 0.01
33 80 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:12388259 original size:66 final size:66
Alignment explanation
Indices: 12388153--12388285 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
12388143 GAAATTACTA
* *
12388153 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGCAACGCGAAT
12388218 T
66 T
* *
12388219 TCGCAATGCGAAATGAAAATCGTAACGAGGGAATCACAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGCAACGCGAAT
12388284 T
66 T
12388285 T
1 T
12388286 AATTTCGCGT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:12388310 original size:14 final size:14
Alignment explanation
Indices: 12388293--12388363 Score: 88
Period size: 14 Copynumber: 4.7 Consensus size: 14
12388283 TTTAATTTCG
12388293 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
12388307 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
12388326 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
12388340 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
12388354 CGTTGCGATT
1 CGTTGCGATT
12388364 TTCATTTCGC
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
14 34 0.68
16 3 0.06
17 3 0.06
19 10 0.20
ACGTcount: A:0.08, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:12388329 original size:33 final size:33
Alignment explanation
Indices: 12388278--12388349 Score: 126
Period size: 33 Copynumber: 2.2 Consensus size: 33
12388268 AAATCGCAAC
*
12388278 GCGAATTTAATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTAATTTCGCGTTGCGATTCTCTCGTT
*
12388311 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTAATTTCGCGTTGCGATTCTCTCGTT
12388344 GCGATT
1 GCGATT
12388350 CTCTCGTTGC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.43
Consensus pattern (33 bp):
GCGATTTTAATTTCGCGTTGCGATTCTCTCGTT
Found at i:12388506 original size:14 final size:14
Alignment explanation
Indices: 12388487--12388523 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
12388477 CATCAATTAA
12388487 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
12388501 ACAAATCACCTTTT
1 ACAAATCAACTTTT
12388515 ACAAATCAA
1 ACAAATCAA
12388524 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:12389809 original size:21 final size:21
Alignment explanation
Indices: 12389743--12389809 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
12389733 ATGAATCGGG
*
12389743 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
12389763 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
12389785 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
12389806 CTCT
1 CTCT
12389810 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:12390490 original size:61 final size:62
Alignment explanation
Indices: 12390421--12390549 Score: 233
Period size: 61 Copynumber: 2.1 Consensus size: 62
12390411 TAAAGTAGAC
*
12390421 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACTGATCTCCTCACGCAAGGC-TG
1 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATG
12390482 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCA-TG
12390545 ACCTC
1 ACCTC
12390550 ATCACGTAAC
Statistics
Matches: 65, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
61 58 0.89
63 7 0.11
ACGTcount: A:0.23, C:0.37, G:0.19, T:0.21
Consensus pattern (62 bp):
ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATG
Found at i:12392010 original size:20 final size:20
Alignment explanation
Indices: 12391981--12392041 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
12391971 TTTTGGTTGA
12391981 AATGAAAATCGCAACGAGAT
1 AATGAAAATCGCAACGAGAT
* *
12392001 AATGAGAATCGCAACGCG--
1 AATGAAAATCGCAACGAGAT
**
12392019 AATGACTATCGCAACGAGAT
1 AATGAAAATCGCAACGAGAT
12392039 AAT
1 AAT
12392042 CGCAACGCGA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
18 15 0.44
20 19 0.56
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.16
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAT
Found at i:12392065 original size:32 final size:32
Alignment explanation
Indices: 12392007--12392067 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
12391997 AGATAATGAG
**
12392007 AATCGCAACGCGAATGACTATCGCAACGAGAT
1 AATCGCAACGCGAATGAAAATCGCAACGAGAT
12392039 AATCGCAACGCGAAATGAAAAT-GCAACGA
1 AATCGCAACGCG-AATGAAAATCGCAACGA
12392068 AGCGCGTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
32 19 0.73
33 7 0.27
ACGTcount: A:0.43, C:0.23, G:0.21, T:0.13
Consensus pattern (32 bp):
AATCGCAACGCGAATGAAAATCGCAACGAGAT
Found at i:12392703 original size:20 final size:20
Alignment explanation
Indices: 12392659--12392707 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
12392649 TATGTAAATC
* *
12392659 GCGTTGCGAAAGTTAGAATC
1 GCGTTGCGAAAGTCAGAATA
*
12392679 GCGTTGCGAAAGTCAGTATA
1 GCGTTGCGAAAGTCAGAATA
*
12392699 TCGTTGCGA
1 GCGTTGCGA
12392708 TTTTGTATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.27
Consensus pattern (20 bp):
GCGTTGCGAAAGTCAGAATA
Found at i:12392737 original size:16 final size:16
Alignment explanation
Indices: 12392716--12392748 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
12392706 GATTTTGTAT
12392716 TATCGCATTGCGATAG
1 TATCGCATTGCGATAG
12392732 TATCGCATTGCGATAG
1 TATCGCATTGCGATAG
12392748 T
1 T
12392749 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (16 bp):
TATCGCATTGCGATAG
Found at i:12393813 original size:13 final size:13
Alignment explanation
Indices: 12393795--12393822 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
12393785 CTGCTTCTCA
12393795 ATATATATTATAT
1 ATATATATTATAT
12393808 ATATATATTATAT
1 ATATATATTATAT
12393821 AT
1 AT
12393823 GCCACACATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATATATATTATAT
Found at i:12394098 original size:55 final size:54
Alignment explanation
Indices: 12394015--12394124 Score: 211
Period size: 55 Copynumber: 2.0 Consensus size: 54
12394005 CCTGTCAAGC
12394015 ACTGCACCTGAAATCCAATAAACTGCGTCTTACTTTTGTGGAAATTATTTTCTA
1 ACTGCACCTGAAATCCAATAAACTGCGTCTTACTTTTGTGGAAATTATTTTCTA
12394069 ACTGCACCATGAAATCCAATAAACTGCGTCTTACTTTTGTGGAAATTATTTTCTA
1 ACTGCACC-TGAAATCCAATAAACTGCGTCTTACTTTTGTGGAAATTATTTTCTA
12394124 A
1 A
12394125 TTGATGCTTT
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
54 8 0.15
55 47 0.85
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (54 bp):
ACTGCACCTGAAATCCAATAAACTGCGTCTTACTTTTGTGGAAATTATTTTCTA
Found at i:12395377 original size:6 final size:6
Alignment explanation
Indices: 12395366--12395392 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
12395356 GTCGTTTGTT
12395366 GGTGCA GGTGCA GGTGCA GGTGCA GGT
1 GGTGCA GGTGCA GGTGCA GGTGCA GGT
12395393 ACATGTGCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.15, G:0.52, T:0.19
Consensus pattern (6 bp):
GGTGCA
Found at i:12395400 original size:18 final size:18
Alignment explanation
Indices: 12395366--12395400 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12395356 GTCGTTTGTT
*
12395366 GGTGCAGGTGCAGGTGCA
1 GGTGCAGGTACAGGTGCA
*
12395384 GGTGCAGGTACATGTGC
1 GGTGCAGGTACAGGTGC
12395401 TCCACCATCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.17, G:0.46, T:0.20
Consensus pattern (18 bp):
GGTGCAGGTACAGGTGCA
Found at i:12395836 original size:30 final size:30
Alignment explanation
Indices: 12395800--12395863 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
12395790 TTATGATTTA
12395800 AATGTTGCCAATAATAGTCTGGATCTGAAG
1 AATGTTGCCAATAATAGTCTGGATCTGAAG
12395830 AATGTTGCCAATAATAGTCTGGATCTGAAG
1 AATGTTGCCAATAATAGTCTGGATCTGAAG
12395860 AATG
1 AATG
12395864 CAGCCACTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.30
Consensus pattern (30 bp):
AATGTTGCCAATAATAGTCTGGATCTGAAG
Found at i:12405366 original size:60 final size:60
Alignment explanation
Indices: 12405298--12405440 Score: 157
Period size: 60 Copynumber: 2.4 Consensus size: 60
12405288 CTTTAAAATG
* * *
12405298 TTTCAATTTCATCCCTAAACTATCA-CTATCATTCTAAATTAGTC-CTTAAAATTTTG-AGCA
1 TTTCAATTTCATCCC-AAACTATCACCT-TCATTCCAAATTAGTCTC-CAAAATTTTGAAACA
** *
12405358 TTTCAATTTCATCCCCAAACTAAGACCTTCATTCCAAATTAGTCTCCAAACTTTTGAAACA
1 TTTCAATTTCAT-CCCAAACTATCACCTTCATTCCAAATTAGTCTCCAAAATTTTGAAACA
* *
12405419 TTCCAATTTTATCCCAAACTAT
1 TTTCAATTTCATCCCAAACTAT
12405441 ATGTATATAC
Statistics
Matches: 70, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
60 51 0.73
61 19 0.27
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.37
Consensus pattern (60 bp):
TTTCAATTTCATCCCAAACTATCACCTTCATTCCAAATTAGTCTCCAAAATTTTGAAACA
Found at i:12409556 original size:27 final size:28
Alignment explanation
Indices: 12409518--12409571 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
12409508 TAGAAACCAT
12409518 ATCTTCATTACA-TTAAAGCCACAGAAC
1 ATCTTCATTACATTTAAAGCCACAGAAC
12409545 ATCTTCATTACATTTAAAGCCACAGAA
1 ATCTTCATTACATTTAAAGCCACAGAA
12409572 GAGAAAAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 12 0.46
28 14 0.54
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.28
Consensus pattern (28 bp):
ATCTTCATTACATTTAAAGCCACAGAAC
Found at i:12417728 original size:40 final size:38
Alignment explanation
Indices: 12417638--12417730 Score: 109
Period size: 38 Copynumber: 2.4 Consensus size: 38
12417628 TGTTGTTGTC
*
12417638 AACCGAAAATATTATGAATAATGTAATATTTTAAGTTT
1 AACCGAAAATATTATGAATAATGTAAAATTTTAAGTTT
*
12417676 AATCGAAAATATTATGAATAA-GATAAAATTTATATTA-TTT
1 AACCGAAAATATTATGAATAATG-TAAAATTT-TA--AGTTT
*
12417716 AACCTAAAATATTAT
1 AACCGAAAATATTAT
12417731 ATTTTAAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
37 1 0.02
38 27 0.57
39 2 0.04
40 16 0.34
41 1 0.02
ACGTcount: A:0.48, C:0.05, G:0.08, T:0.39
Consensus pattern (38 bp):
AACCGAAAATATTATGAATAATGTAAAATTTTAAGTTT
Found at i:12418938 original size:22 final size:24
Alignment explanation
Indices: 12418884--12418946 Score: 87
Period size: 22 Copynumber: 2.7 Consensus size: 24
12418874 ACATATAGCT
12418884 TAATATTA-TTATTATTCATTGTA
1 TAATATTATTTATTATTCATTGTA
12418907 TAAATATTATTTATTATTCA-T-TA
1 T-AATATTATTTATTATTCATTGTA
*
12418930 TAATTTTATTTATTATT
1 TAATATTATTTATTATT
12418947 ACAAATTAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
22 15 0.41
23 4 0.11
24 8 0.22
25 10 0.27
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (24 bp):
TAATATTATTTATTATTCATTGTA
Found at i:12422233 original size:17 final size:17
Alignment explanation
Indices: 12422213--12422277 Score: 71
Period size: 17 Copynumber: 3.9 Consensus size: 17
12422203 ATACAATATT
12422213 GTAAAAGATATAGTACA
1 GTAAAAGATATAGTACA
* *
12422230 GTAAATGATACAGTACA
1 GTAAAAGATATAGTACA
* *
12422247 ATAAAA-AAATAGTACAA
1 GTAAAAGATATAGTAC-A
12422264 G-AAAAGATATAGTA
1 GTAAAAGATATAGTA
12422278 TGAAAAAAGG
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
16 11 0.29
17 27 0.71
ACGTcount: A:0.57, C:0.06, G:0.15, T:0.22
Consensus pattern (17 bp):
GTAAAAGATATAGTACA
Found at i:12425052 original size:84 final size:84
Alignment explanation
Indices: 12424984--12425848 Score: 840
Period size: 84 Copynumber: 10.4 Consensus size: 84
12424974 CTGAATGTAA
* * * *
12424984 TCGAACTCGGAGGTCTTCGGTTGGCAGATAACCCTTCTCGACTTAAACTATACTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
*
12425049 GCCTTGGAGCTGAGCTTAG
66 GCCTTGGAGCTGAGCGTAG
* * * * * * * *
12425068 TCGAACTCAAAGGTCTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATAATGT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
*** *
12425132 GCCCTCAAAGTTGAGCGTAG
66 G-CCTTGGAGCTGAGCGTAG
** * * * *
12425152 TTAAACTCGAGGGTC--T--TTGGCAGATAGCTCTTCTCGTCTTAAGCTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
12425213 GCCTTGGAGCTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* * * * * * * *
12425232 TCAAACTCGAAGGTCTTTTAG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATG
1 TCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATG
* * *
12425296 TGCCCTTGAAGCTGAGTGTAA
65 TG-CCTTGGAGCTGAGCGTAG
* * * * *
12425317 TCGAACTTGAGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGC
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
12425378 GCCTTGGAGCTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* * * * * * *
12425397 TCGAACTTGAAGGTCTTTGGGTGGCATATAACCCTTCTTGACTTAAGTTATGCTGCAAATTATAT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
*
12425462 GCCTTGGAGCTGAACGTAG
66 GCCTTGGAGCTGAGCGTAG
* * * * * * * *
12425481 TCGAACTCGAAGGTATTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
* *
12425546 GCATTGGAGCTGAGCATAG
66 GCCTTGGAGCTGAGCGTAG
* ** * * *
12425565 TTGAACTCGAAGGTCTTTTATTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATAT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
* *
12425630 ACCTTGGAGCTGAACGTAG
66 GCCTTGGAGCTGAGCGTAG
* * * * * * * *
12425649 TCGAACTCGAATGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
*** * * *
12425714 GCCCTCAAAGTTGAGTGTAA
66 G-CCTTGGAGCTGAGCGTAG
** * *
12425734 TCGAACTCGGGGGAC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
12425795 GCCTTGGAGCTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
*
12425814 TCGAACTCGAAGGTCTTTGGTTGGCAAATAACCCT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCT
12425849 ACTTGTCTTG
Statistics
Matches: 623, Mismatches: 140, Indels: 36
0.78 0.18 0.05
Matches are distributed among these distances:
80 80 0.13
81 115 0.18
82 4 0.01
83 38 0.06
84 337 0.54
85 49 0.08
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (84 bp):
TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
GCCTTGGAGCTGAGCGTAG
Found at i:12425331 original size:165 final size:165
Alignment explanation
Indices: 12424971--12425833 Score: 853
Period size: 165 Copynumber: 5.2 Consensus size: 165
12424961 GTTTGCCTCT
* * * *
12424971 GAGCTGAATGTAATCGAACTCG-GAGGTCTTCGGTTGGCAGATAACCCTTCTCGACTTAAACTAT
1 GAGCTGAACGTAGTCGAACTCGAG-GGTC-T--GTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
* * * *
12425035 ACTGCAAATGATGTGCCTTGGAGCTGAGCTTAGTCGAACTCAAAGGTC-TTTGGTGACAGATAAC
62 GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTAGTGACAGATAAC
* * * * **
12425099 CCTTCTAGCCTTGAGTTATGCTGTAAATAATGTGCCCTCA
127 CCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTTG
* * * ** * *
12425139 AAGTTGAGCGTAGTTAAACTCGAGGGTCT-TTGGCAGATAGCTCTTCTCGTCTTAAGCTATGCTG
1 GAGCTGAACGTAGTCGAACTCGAGGGTCTGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTG
*
12425203 CAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTAGTGACAGATAACCCTT
66 CAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTAGTGACAGATAACCCTT
* * *
12425268 CTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTTG
131 CTAGACTTAAGTTATGCTGCAAATGATGTG-CCTTG
* ** * * *
12425304 AAGCTGAGTGTAATCGAACTTGAGGGTCT-TTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTG
1 GAGCTGAACGTAGTCGAACTCGAGGGTCTGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTG
* * ** * *
12425368 CAAATGATGCGCCTTGGAGCTGAGCGTAGTCGAACTTGAAGGTCTTTGGGTGGCATATAACCCTT
66 CAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTAGTGACAGATAACCCTT
* * *
12425433 CTTGACTTAAGTTATGCTGCAAATTATATGCCTTG
131 CTAGACTTAAGTTATGCTGCAAATGATGTGCCTTG
* * * * * *
12425468 GAGCTGAACGTAGTCGAACTCGAAGGTATTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATG
1 GAGCTGAACGTAGTCGAACTCG-AGG--GTCTGTTGGCAGATAGCCCTTCTCGACTTAAGCTATG
* * * * * *
12425533 TTGCAAATGATGTGCATTGGAGCTGAGCATAGTTGAACTCGAAGGTCTTTTATTGGCAGATAACC
63 CTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTAGTGACAGATAACC
* * * *
12425598 CTTCTCGATTTAAGTTATGCTGCAAATGATATACCTTG
128 CTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTG
** * * * *
12425636 GAGCTGAACGTAGTCGAACTCGAATGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATG
1 GAGCTGAACGTAGTCGAACTCGAGGGTC---TGTTGGCAGATAGCCCTTCTCGACTTAAGCTATG
* *** * * * ** * *
12425701 TTGCAAATGATGTGCCCTCAAAGTTGAGTGTAATCGAACTCGGGGGAC-TTT-G-G-CAGATAGC
63 CTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTAGTGACAGATAAC
* *
12425762 CCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTG
127 CCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTG
* *
12425801 GAGCTGAGCGTAGTCGAACTCGAAGGTCT-TTGG
1 GAGCTGAACGTAGTCGAACTCGAGGGTCTGTTGG
12425834 TTGGCAAATA
Statistics
Matches: 594, Mismatches: 91, Indels: 27
0.83 0.13 0.04
Matches are distributed among these distances:
161 4 0.01
162 1 0.00
164 93 0.16
165 261 0.44
166 1 0.00
167 4 0.01
168 208 0.35
169 22 0.04
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (165 bp):
GAGCTGAACGTAGTCGAACTCGAGGGTCTGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTG
CAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTAGTGACAGATAACCCTT
CTAGACTTAAGTTATGCTGCAAATGATGTGCCTTG
Found at i:12425754 original size:417 final size:413
Alignment explanation
Indices: 12424984--12425853 Score: 1143
Period size: 417 Copynumber: 2.1 Consensus size: 413
12424974 CTGAATGTAA
* * * * *
12424984 TCGAACTCGGAGGTCTTCGGTTGGCAGATAACCCTTCTCGACTTAAACTATACTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTTGGCAAATAACCCTTCTTGACTTAAACTATACTGCAAATGATAT
* * *
12425049 GCCTTGGAGCTGAGCTTAGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAG
66 GCCTTGGAGCTGAACGTAGTCGAACTCAAAGGTCTTTGGTGACAAATAACCCTTCTAGCCTTGAG
* * * * * * *
12425114 TTATGCTGTAAATAATGTGCCCTCAAAGTTGAGCGTAGTTAAACTCGAGGGTCTTTGGCAGATAG
131 CTATGCTGCAAATAATGTGCCATCAAAGCTGAGCATAGTTAAACTCGAAGGTCTTTGGCAGATAA
* * * *
12425179 CTCTTCTCGTCTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAG
196 CCCTTCTCGTCTTAAGCTATGCTGCAAATGATATACCTTGGAGCTGAACGTAGTCAAACTCGAAG
* * * **
12425244 GTCTTTTAGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTTGAAGCT
261 GTCTTTTAGTGACAAATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCCTCAAAGCT
* * *
12425309 GAGTGTAATCGAACTTGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATG
326 GAGTGTAATCGAACTCGAGGGACTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATG
12425374 ATGCGCCTTGGAGCTGAGCGTAG
391 ATGCGCCTTGGAGCTGAGCGTAG
* * * ** * *
12425397 TCGAACTTGAAGGTCTTTGGGTGGCATATAACCCTTCTTGACTTAAGTTATGCTGCAAATTATAT
1 TCGAACTCGAAGGTCTTTGGTTGGCAAATAACCCTTCTTGACTTAAACTATACTGCAAATGATAT
* * * * * *
12425462 GCCTTGGAGCTGAACGTAGTCGAACTCGAAGGTATTTTGTTGGCAAATAGCCCTTCTTGCCTTGA
66 GCCTTGGAGCTGAACGTAGTCGAACTCAAAGGT-CTTTGGTGACAAATAACCCTTCTAGCCTTGA
* * *** *
12425527 GCTATGTTGCAAATGATGTG-CATTGGAGCTGAGCATAGTTGAACTCGAAGGTCTTTTATTGGCA
130 GCTATGCTGCAAATAATGTGCCATCAAAGCTGAGCATAGTTAAACTCGAAGGTC---T-TTGGCA
* *
12425591 GATAACCCTTCTCGAT-TTAAGTTATGCTGCAAATGATATACCTTGGAGCTGAACGTAGTCGAAC
191 GATAACCCTTCTCG-TCTTAAGCTATGCTGCAAATGATATACCTTGGAGCTGAACGTAGTCAAAC
* * * * *
12425655 TCGAATGTCTTTT-GTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCCT
255 TCGAAGGTCTTTTAG-TGACAAATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCCT
* *
12425719 CAAAGTTGAGTGTAATCGAACTCGGGGGACTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCT
319 CAAAGCTGAGTGTAATCGAACTCGAGGGACTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCT
*
12425784 GCAAATGATGTGCCTTGGAGCTGAGCGTAG
384 GCAAATGATGCGCCTTGGAGCTGAGCGTAG
*
12425814 TCGAACTCGAAGGTCTTTGGTTGGCAAATAACCCTACTTG
1 TCGAACTCGAAGGTCTTTGGTTGGCAAATAACCCTTCTTG
12425854 TCTTGAGCTA
Statistics
Matches: 391, Mismatches: 59, Indels: 10
0.85 0.13 0.02
Matches are distributed among these distances:
413 109 0.28
414 41 0.10
416 2 0.01
417 238 0.61
418 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (413 bp):
TCGAACTCGAAGGTCTTTGGTTGGCAAATAACCCTTCTTGACTTAAACTATACTGCAAATGATAT
GCCTTGGAGCTGAACGTAGTCGAACTCAAAGGTCTTTGGTGACAAATAACCCTTCTAGCCTTGAG
CTATGCTGCAAATAATGTGCCATCAAAGCTGAGCATAGTTAAACTCGAAGGTCTTTGGCAGATAA
CCCTTCTCGTCTTAAGCTATGCTGCAAATGATATACCTTGGAGCTGAACGTAGTCAAACTCGAAG
GTCTTTTAGTGACAAATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCCTCAAAGCT
GAGTGTAATCGAACTCGAGGGACTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATG
ATGCGCCTTGGAGCTGAGCGTAG
Found at i:12429321 original size:7 final size:7
Alignment explanation
Indices: 12429309--12429337 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
12429299 AAATGTCTAA
12429309 ATGCATG
1 ATGCATG
12429316 ATGCATG
1 ATGCATG
12429323 ATGCATG
1 ATGCATG
12429330 ATGCATG
1 ATGCATG
12429337 A
1 A
12429338 AATGTCTGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (7 bp):
ATGCATG
Found at i:12431161 original size:18 final size:18
Alignment explanation
Indices: 12431116--12431162 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
12431106 AAACGAATAT
*
12431116 TAAATAAATCAAAAGGAAA
1 TAAATAAAT-AAAAAGAAA
*
12431135 -AAATAAAATAAAAATAAA
1 TAAAT-AAATAAAAAGAAA
12431153 TAAATAAATA
1 TAAATAAATA
12431163 CTAGATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.19
Consensus pattern (18 bp):
TAAATAAATAAAAAGAAA
Found at i:12433678 original size:39 final size:38
Alignment explanation
Indices: 12433619--12433696 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 38
12433609 AGGTACAAAT
*
12433619 AGTATACTTTAGGAGGCAATGACGCATTTTAAGTCATAA
1 AGTATACTTTAGGAGACAATGACGCA-TTTAAGTCATAA
*
12433658 AGTATACTTTAGGAGACAATGATGCATTTAAGTCATAA
1 AGTATACTTTAGGAGACAATGACGCATTTAAGTCATAA
12433696 A
1 A
12433697 AAATGATAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
38 13 0.35
39 24 0.65
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (38 bp):
AGTATACTTTAGGAGACAATGACGCATTTAAGTCATAA
Found at i:12433767 original size:15 final size:16
Alignment explanation
Indices: 12433745--12433782 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
12433735 AGTAATAAAA
12433745 ATAAATTTT-AATGATT
1 ATAAATTTTCAAT-ATT
12433761 A-AAATTTTCAATATT
1 ATAAATTTTCAATATT
12433776 ATAAATT
1 ATAAATT
12433783 AGTAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAATTTTCAATATT
Found at i:12438603 original size:49 final size:49
Alignment explanation
Indices: 12438544--12438641 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
12438534 ATGGAGAGGC
12438544 GTACCACAAATAAAATCAGAAATATATAAGATAAACTACATCAAGTTAA
1 GTACCACAAATAAAATCAGAAATATATAAGATAAACTACATCAAGTTAA
*
12438593 GTACCGCAAATAAAATCAGAAATATATAAGATAAACTACATCAAGTTAA
1 GTACCACAAATAAAATCAGAAATATATAAGATAAACTACATCAAGTTAA
12438642 CTTAGATCCA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.54, C:0.14, G:0.09, T:0.22
Consensus pattern (49 bp):
GTACCACAAATAAAATCAGAAATATATAAGATAAACTACATCAAGTTAA
Found at i:12438890 original size:17 final size:18
Alignment explanation
Indices: 12438868--12438907 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 18
12438858 AGGTTCATTT
*
12438868 TATTTTTTATATAAT-TG
1 TATTTTTTATAAAATCTG
12438885 TA--TTTTATAAAATCTG
1 TATTTTTTATAAAATCTG
12438901 TATTTTT
1 TATTTTT
12438908 ATTAGTACGT
Statistics
Matches: 19, Mismatches: 1, Indels: 5
0.76 0.04 0.20
Matches are distributed among these distances:
15 10 0.53
16 4 0.21
17 2 0.11
18 3 0.16
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (18 bp):
TATTTTTTATAAAATCTG
Found at i:12438892 original size:15 final size:16
Alignment explanation
Indices: 12438872--12438906 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
12438862 TCATTTTATT
*
12438872 TTTTATATAAT-TGTA
1 TTTTATAAAATCTGTA
12438887 TTTTATAAAATCTGTA
1 TTTTATAAAATCTGTA
12438903 TTTT
1 TTTT
12438907 TATTAGTACG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.60
Consensus pattern (16 bp):
TTTTATAAAATCTGTA
Found at i:12441498 original size:27 final size:26
Alignment explanation
Indices: 12441451--12441501 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
12441441 TAGTATTAAT
*
12441451 TATTTTTATTTTATTATATTATATTA
1 TATTTTTATTTTAATATATTATATTA
12441477 TATTTTTAATTTTTAATA-ATTATAT
1 TATTTTT-A-TTTTAATATATTATAT
12441502 CTTTATGAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 7 0.32
27 8 0.36
28 7 0.32
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (26 bp):
TATTTTTATTTTAATATATTATATTA
Found at i:12448686 original size:24 final size:24
Alignment explanation
Indices: 12448652--12448708 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
12448642 AGCCTATTTT
*
12448652 TCTTGGCTCTGTTCTGTTTGAATG
1 TCTTGGTTCTGTTCTGTTTGAATG
12448676 TCTTGGTTCTGTTCTGTTTGAATG
1 TCTTGGTTCTGTTCTGTTTGAATG
12448700 TCTTGGTTC
1 TCTTGGTTC
12448709 ATGCTTTTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.07, C:0.16, G:0.25, T:0.53
Consensus pattern (24 bp):
TCTTGGTTCTGTTCTGTTTGAATG
Found at i:12457078 original size:15 final size:15
Alignment explanation
Indices: 12457058--12457095 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
12457048 GTTTACTTCA
*
12457058 GAATGATTAAGCGCT
1 GAATGATTAAACGCT
*
12457073 GAATGATTAAATGCT
1 GAATGATTAAACGCT
12457088 GAATGATT
1 GAATGATT
12457096 CAGAGGCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.37, C:0.08, G:0.24, T:0.32
Consensus pattern (15 bp):
GAATGATTAAACGCT
Found at i:12461336 original size:15 final size:15
Alignment explanation
Indices: 12461316--12461375 Score: 102
Period size: 15 Copynumber: 4.0 Consensus size: 15
12461306 CGTAGGACTC
12461316 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
12461331 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
12461346 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
* *
12461361 CTACGTCTCGAAGGA
1 CTACATCCCGAAGGA
12461376 TTATTATACC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 43 1.00
ACGTcount: A:0.32, C:0.32, G:0.22, T:0.15
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:12461557 original size:12 final size:12
Alignment explanation
Indices: 12461523--12461557 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
12461513 TATCATGTTC
**
12461523 TCATATCACAGG
1 TCATATCACATA
12461535 TCATATCACATA
1 TCATATCACATA
12461547 TCATATCACAT
1 TCATATCACAT
12461558 GAACATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (12 bp):
TCATATCACATA
Found at i:12461954 original size:64 final size:64
Alignment explanation
Indices: 12461866--12462086 Score: 223
Period size: 64 Copynumber: 3.5 Consensus size: 64
12461856 TAATGAAGGT
* * * **
12461866 ATGCATCGATTCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTATT-ATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAAAGGTATTCGATGT-TTCATTATTAATGGG
* ** **
12461930 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGTATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAAAGGTATTCGATGTTTCATTATTAATGGG
* ** * * **
12461994 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTTTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAAAGGTATTCGATG-TTTCATTATTAATGGG
**
12462057 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
12462087 ACACCTTCAA
Statistics
Matches: 135, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
63 4 0.03
64 125 0.93
65 6 0.04
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAAAGGTATTCGATGTTTCATTATTAATGGG
Found at i:12468237 original size:15 final size:15
Alignment explanation
Indices: 12468217--12468249 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
12468207 CGTAGGACTC
12468217 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
12468232 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
12468247 CTA
1 CTA
12468250 TTATACCCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.18, T:0.15
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:12468428 original size:12 final size:12
Alignment explanation
Indices: 12468392--12468428 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
12468382 TATATCATGT
12468392 TATCATATCACA
1 TATCATATCACA
**
12468404 GGTCATATCACA
1 TATCATATCACA
12468416 TATCATATCACA
1 TATCATATCACA
12468428 T
1 T
12468429 GAACATATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.38, C:0.24, G:0.05, T:0.32
Consensus pattern (12 bp):
TATCATATCACA
Found at i:12468841 original size:64 final size:62
Alignment explanation
Indices: 12468733--12468852 Score: 168
Period size: 64 Copynumber: 1.9 Consensus size: 62
12468723 TAATGAAGGT
* *
12468733 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTATTATTATTGTTGGG
1 ATGCATCGATGCACTACTGATGCATCGATGCATAAAAGGCATTCGATGT-TT-TTATTGTTGGG
* * **
12468797 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTTTTATT
1 ATGCATCGATGCACTACTGATGCATCGATGCATAAAAGGCATTCGATGTTTTTATT
12468853 TTAAAGAGTG
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
62 5 0.10
63 2 0.04
64 43 0.86
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.37
Consensus pattern (62 bp):
ATGCATCGATGCACTACTGATGCATCGATGCATAAAAGGCATTCGATGTTTTTATTGTTGGG
Found at i:12471918 original size:38 final size:39
Alignment explanation
Indices: 12471867--12471957 Score: 130
Period size: 38 Copynumber: 2.4 Consensus size: 39
12471857 AATTAAAAAT
12471867 GTAAACTAAACAAATGATCACTAATGTT-AAAAAAAAGG
1 GTAAACTAAACAAATGATCACTAATGTTCAAAAAAAAGG
* * * *
12471905 GTAAACTATACAAATGATCATTAATGTTCAACAAAAGGG
1 GTAAACTAAACAAATGATCACTAATGTTCAAAAAAAAGG
*
12471944 GTAAACTACACAAA
1 GTAAACTAAACAAA
12471958 AATAAGTTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
38 26 0.55
39 21 0.45
ACGTcount: A:0.52, C:0.13, G:0.13, T:0.22
Consensus pattern (39 bp):
GTAAACTAAACAAATGATCACTAATGTTCAAAAAAAAGG
Found at i:12477744 original size:42 final size:42
Alignment explanation
Indices: 12477688--12477768 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
12477678 ACTTAAGTAA
*
12477688 TAATTTGAAATTTTTTAAAACAATTTCATATATATTTTAAACT
1 TAATTTGAAATTTTTAAAAACAATTTCATATAT-TTTTAAACT
* * *
12477731 TAATTT-AATTTTTTAAAAATAATTTCATGTATTTTTAA
1 TAATTTGAAATTTTTAAAAACAATTTCATATATTTTTAA
12477769 TAAAAATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 6 0.18
42 22 0.65
43 6 0.18
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (42 bp):
TAATTTGAAATTTTTAAAAACAATTTCATATATTTTTAAACT
Found at i:12477993 original size:2 final size:2
Alignment explanation
Indices: 12477986--12478026 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
12477976 TAATTTGATA
12477986 AT AT AT AT A- AT AT AT AT AT AT -T AT AT AT -T AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12478025 AT
1 AT
12478027 TATTGTTAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.08
2 33 0.92
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:12477997 original size:9 final size:9
Alignment explanation
Indices: 12477983--12478026 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
12477973 ATTTAATTTG
12477983 ATAATATAT
1 ATAATATAT
12477992 ATAATATAT
1 ATAATATAT
12478001 AT-ATATTAT
1 ATAATA-TAT
*
12478010 ATATTATAT
1 ATAATATAT
12478019 AT-ATATAT
1 ATAATATAT
12478027 TATTGTTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
8 8 0.26
9 21 0.68
10 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
ATAATATAT
Found at i:12478002 original size:11 final size:11
Alignment explanation
Indices: 12477986--12478025 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
12477976 TAATTTGATA
12477986 ATATATATAAT
1 ATATATATAAT
12477997 ATATATAT-AT
1 ATATATATAAT
*
12478007 -TATATATTAT
1 ATATATATAAT
12478017 ATATATATA
1 ATATATATA
12478026 TTATTGTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
9 7 0.27
10 4 0.15
11 15 0.58
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
ATATATATAAT
Found at i:12478012 original size:20 final size:20
Alignment explanation
Indices: 12477987--12478029 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
12477977 AATTTGATAA
12477987 TATATATAATATATATATAT
1 TATATATAATATATATATAT
*
12478007 TATATATTATATATATATAT
1 TATATATAATATATATATAT
12478027 TAT
1 TAT
12478030 TGTTAACTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TATATATAATATATATATAT
Found at i:12478254 original size:2 final size:2
Alignment explanation
Indices: 12478242--12478277 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
12478232 ATTGATTTAA
*
12478242 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12478278 AAAAATTAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12481136 original size:165 final size:165
Alignment explanation
Indices: 12480818--12481626 Score: 1248
Period size: 165 Copynumber: 4.9 Consensus size: 165
12480808 CGGTTGGTAT
* *
12480818 ATAGCCCTTCTCGACTTAAGTTATACTACAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* * * * *
12480883 GAAGGTCTTTGG-TGACAGATAACCCTTCTAGTA-TTGAGTTATGTTGTAAATGATGTGCCCTCG
66 AAAGGTCTTTGGTTGGCAGATAACCCTTCTCG-ACTTAAGTTATGTTGCAAATGATGTGCCCTCG
* *
12480946 AAGCTGAGTGTAATCTAACTCGAGGGTATTTGGCAG
130 AAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAG
*
12480982 ATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTACCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* * *
12481047 AAAGTTCTTTGGTTGGCAGATAACCCTTCTCAACTTAAGTTATGTTGCAAATGATATGCCCTCGA
66 AAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGTTGCAAATGATGTGCCCTCGA
12481112 AGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAG
131 AGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAG
* * *
12481147 ATAACCCTTCTCAACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGAGTAGTCGAAACT
1 ATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCG-AACT
* *
12481212 CAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTCAAATAATGTGCCCTC
65 CAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGTTG-CAAATGATGTGCCCTC
* *
12481277 AAAGCTGAGTGTAATCGAACTCGATGGTCTTTGGCAG
129 GAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAG
* *
12481314 ATAACCCTTCTCGACTTAAGCTATACTACAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
*
12481379 AAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGATGCAAATGATGTGCCCTCGA
66 AAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGTTGCAAATGATGTGCCCTCGA
*
12481444 AGCTGAGTATAATCGAACTCGAGGGTCTTTGGCAG
131 AGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAG
*
12481479 ATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCGAACTC
1 ATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* * * * * * * *
12481544 GAAGGTCTTT-GTTGGCAAATAGCCCTTCTCGCCTTGAGTTATGTTGCAAATAATGTG-CCTTGG
66 AAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGTTGCAAATGATGTGCCCTCGA
* *
12481607 AGCTGAGCGTAGTCGAACTC
131 AGCTGAGTGTAATCGAACTC
12481627 AAAGGTTTTT
Statistics
Matches: 594, Mismatches: 47, Indels: 9
0.91 0.07 0.01
Matches are distributed among these distances:
163 21 0.04
164 114 0.19
165 253 0.43
166 100 0.17
167 106 0.18
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.30
Consensus pattern (165 bp):
ATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
AAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGTTGCAAATGATGTGCCCTCGA
AGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAG
Found at i:12481314 original size:332 final size:331
Alignment explanation
Indices: 12480822--12481655 Score: 1266
Period size: 332 Copynumber: 2.5 Consensus size: 331
12480812 TGGTATATAG
* * *
12480822 CCCTTCTCGACTTAAGTTATACTACAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
1 CCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGAGTAGTCGAACTCGAAG
* * * *
12480887 GTCTTTGG-TGACAGATAACCCTTCTAGTA-TTGAGTTATGTTGT-AAATGATGTGCCCTCGAAG
66 GTCTTTGGTTGGCAGATAACCCTTCTCG-ACTTGAGTTATGTTGTCAAATAATGTGCCCTCAAAG
* * *
12480949 CTGAGTGTAATCTAACTCGAGGGTATTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAA
130 CTGAGTGTAATCGAACTCGAGGGTATTTGGCAGATAACCCTTCTCGACTTAAGCTATACTACAAA
*
12481014 TGATGTACCTTGGAGCTGAGCGTAGTCGAACTCAAAGTTCTTTGGTTGGCAGATAACCCTTCTCA
195 TGATGTACCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCA
* *
12481079 ACTTAAGTTATGTTGCAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGG
260 ACTTAAGTTATGATGCAAATGATATGCCCTCGAAGCTGAGTATAATCGAACTCGAGGGTCTTTGG
12481144 CAGATAA
325 CAGATAA
* *
12481151 CCCTTCTCAACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGAGTAGTCGAAACTCAAA
1 CCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGAGTAGTCG-AACTCGAA
* *
12481216 GGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTCAAATAATGTGCCCTCAAAG
65 GGTCTTTGGTTGGCAGATAACCCTTCTCGACTTGAGTTATGTTGTCAAATAATGTGCCCTCAAAG
* *
12481281 CTGAGTGTAATCGAACTCGATGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATACTACAAA
130 CTGAGTGTAATCGAACTCGAGGGTATTTGGCAGATAACCCTTCTCGACTTAAGCTATACTACAAA
* *
12481346 TGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCG
195 TGATGTACCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCA
*
12481411 ACTTAAGTTATGATGCAAATGATGTGCCCTCGAAGCTGAGTATAATCGAACTCGAGGGTCTTTGG
260 ACTTAAGTTATGATGCAAATGATATGCCCTCGAAGCTGAGTATAATCGAACTCGAGGGTCTTTGG
*
12481476 CAGATAG
325 CAGATAA
*
12481483 CCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCGAACTCGAAG
1 CCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGAGTAGTCGAACTCGAAG
* * * ***
12481548 GTCTTT-GTTGGCAAATAGCCCTTCTCGCCTTGAGTTATGTTG-CAAATAATGTG-CCTTGGAGC
66 GTCTTTGGTTGGCAGATAACCCTTCTCGACTTGAGTTATGTTGTCAAATAATGTGCCCTCAAAGC
* * * * *
12481610 TGAGCGTAGTCGAACTCAAAGGTTTTTGTTGGCAGATAACCCTTCT
131 TGAGTGTAATCGAACTC-GAGG-GTAT-TTGGCAGATAACCCTTCT
12481656 AGCCTTGAGT
Statistics
Matches: 458, Mismatches: 40, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
328 21 0.05
329 65 0.14
330 50 0.11
331 61 0.13
332 261 0.57
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.30
Consensus pattern (331 bp):
CCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGAGTAGTCGAACTCGAAG
GTCTTTGGTTGGCAGATAACCCTTCTCGACTTGAGTTATGTTGTCAAATAATGTGCCCTCAAAGC
TGAGTGTAATCGAACTCGAGGGTATTTGGCAGATAACCCTTCTCGACTTAAGCTATACTACAAAT
GATGTACCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCAA
CTTAAGTTATGATGCAAATGATATGCCCTCGAAGCTGAGTATAATCGAACTCGAGGGTCTTTGGC
AGATAA
Found at i:12488451 original size:3 final size:3
Alignment explanation
Indices: 12488434--12488484 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
12488424 CCCATTTTTT
*
12488434 TTA TTT TTA TT- TTA TTA TTA TTA TTA -TA TTA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12488479 TTA TTA
1 TTA TTA
12488485 ATAAATACTT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 6 0.14
3 37 0.86
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:12488451 original size:14 final size:14
Alignment explanation
Indices: 12488429--12488483 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 14
12488419 GTTTGCCCAT
*
12488429 TTTTTTTATTTTTA
1 TTTTATTATTTTTA
*
12488443 TTTTATTATTATTA
1 TTTTATTATTTTTA
*
12488457 TTATATTATTATATTA
1 TTTTATTATT-T-TTA
12488473 TTATTATTATT
1 TT-TTATTATT
12488484 AATAAATACT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
14 21 0.64
16 5 0.15
17 7 0.21
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTTATTATTTTTA
Found at i:12488466 original size:22 final size:22
Alignment explanation
Indices: 12488440--12488482 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
12488430 TTTTTTATTT
*
12488440 TTATTTTATTATTATTATTATA
1 TTATTATATTATTATTATTATA
12488462 TTATTATATTATTATTATTAT
1 TTATTATATTATTATTATTAT
12488483 TAATAAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
TTATTATATTATTATTATTATA
Found at i:12488468 original size:25 final size:25
Alignment explanation
Indices: 12488435--12488484 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
12488425 CCATTTTTTT
* *
12488435 TATTTTTATTTTATTATTATTATTA
1 TATTATTATATTATTATTATTATTA
12488460 TATTATTATATTATTATTATTATTA
1 TATTATTATATTATTATTATTATTA
12488485 ATAAATACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (25 bp):
TATTATTATATTATTATTATTATTA
Found at i:12488498 original size:25 final size:25
Alignment explanation
Indices: 12488441--12488499 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
12488431 TTTTTATTTT
* *
12488441 TATTTTATTATTATTATTATATTAT
1 TATTTTATTATTATTATTATATAAA
*
12488466 TATATTATTATTATTATTA-ATAAA
1 TATTTTATTATTATTATTATATAAA
12488490 TACTTTTATT
1 TA-TTTTATT
12488500 TATTTTCAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 5 0.17
25 24 0.83
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.63
Consensus pattern (25 bp):
TATTTTATTATTATTATTATATAAA
Found at i:12489594 original size:30 final size:31
Alignment explanation
Indices: 12489507--12489594 Score: 74
Period size: 30 Copynumber: 2.8 Consensus size: 31
12489497 AATCTTTACG
*
12489507 ATTTAGTCACTGCAATTAATTTCAATATGTTTTA
1 ATTTAGTCATTGCAATTAATTT---TATGTTTTA
* **
12489541 ATTTGGT-ATT-CTAATTTTGTTTTAT-TTTTA
1 ATTTAGTCATTGC-AA-TTAATTTTATGTTTTA
12489571 ATTTAGTCATTGCAATTAATTTTA
1 ATTTAGTCATTGCAATTAATTTTA
12489595 ATATGTTTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
30 18 0.42
31 8 0.19
32 2 0.05
33 4 0.09
34 11 0.26
ACGTcount: A:0.28, C:0.08, G:0.09, T:0.55
Consensus pattern (31 bp):
ATTTAGTCATTGCAATTAATTTTATGTTTTA
Found at i:12499641 original size:13 final size:13
Alignment explanation
Indices: 12499623--12499647 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12499613 ATATAGTTAG
12499623 AATTTTAATATAA
1 AATTTTAATATAA
12499636 AATTTTAATATA
1 AATTTTAATATA
12499648 TTAATACTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AATTTTAATATAA
Found at i:12500323 original size:22 final size:23
Alignment explanation
Indices: 12500267--12500324 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
12500257 ATATGTCACA
*
12500267 ATTATATATATTTTTTTAAATTAT
1 ATTAT-TATATTTTTTTAAATAAT
* *
12500291 ACT-TTAAATTTTTTTAAA-AAT
1 ATTATTATATTTTTTTAAATAAT
12500312 ATTATTATATTTT
1 ATTATTATATTTT
12500325 AAAAACCCTA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
21 4 0.14
22 21 0.75
23 1 0.04
24 2 0.07
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (23 bp):
ATTATTATATTTTTTTAAATAAT
Found at i:12506222 original size:18 final size:19
Alignment explanation
Indices: 12506187--12506228 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
12506177 CTCCTCTTCT
*
12506187 CCACCGACCATCGTACC-A
1 CCACCGACCATCGCACCAA
* *
12506205 CCACCGGCCGTCGCACCAA
1 CCACCGACCATCGCACCAA
12506224 CCACC
1 CCACC
12506229 ACCCACTGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.24, C:0.55, G:0.14, T:0.07
Consensus pattern (19 bp):
CCACCGACCATCGCACCAA
Found at i:12510706 original size:2 final size:2
Alignment explanation
Indices: 12510699--12510723 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12510689 ACTTTAGACC
12510699 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
12510724 TTAAACATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.