Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009266.1 Hibiscus syriacus cultivar Beakdansim tig00112921_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: 1543912
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 7
Found at i:214620 original size:11 final size:11
Alignment explanation
Indices: 214602--214635 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
214592 CAACACCATG
214602 CATTGCATTTA
1 CATTGCATTTA
* *
214613 CGTTGCATCTA
1 CATTGCATTTA
214624 CATTGCATTTA
1 CATTGCATTTA
214635 C
1 C
214636 TTTTCACATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.41
Consensus pattern (11 bp):
CATTGCATTTA
Found at i:229872 original size:10 final size:10
Alignment explanation
Indices: 229852--229908 Score: 66
Period size: 10 Copynumber: 6.0 Consensus size: 10
229842 AGGGCACTCG
229852 AAAAAAG-AA
1 AAAAAAGAAA
229861 AAAAAAGAAA
1 AAAAAAGAAA
229871 AAAAAAGAAA
1 AAAAAAGAAA
*
229881 AAGAAAG--A
1 AAAAAAGAAA
*
229889 AAGAAAGAAA
1 AAAAAAGAAA
*
229899 AAGAAAGAAA
1 AAAAAAGAAA
229909 GAAAGAAAAG
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
8 8 0.18
9 7 0.16
10 29 0.66
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:229887 original size:4 final size:4
Alignment explanation
Indices: 229851--229932 Score: 70
Period size: 4 Copynumber: 21.5 Consensus size: 4
229841 TAGGGCACTC
*
229851 GAAA -AAA GAAAA AAAA GAAA -AAA -AAA G-AA -AAA GAAA GAAA GAAA
1 GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
*
229895 G-AA -AAA GAAA GAAA GAAA GAAAA GATA GATAA GAAA GA
1 GAAA GAAA GAAA GAAA GAAA G-AAA GAAA GA-AA GAAA GA
229933 GAATAAGGAA
Statistics
Matches: 65, Mismatches: 4, Indels: 18
0.75 0.05 0.21
Matches are distributed among these distances:
3 17 0.26
4 38 0.58
5 10 0.15
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (4 bp):
GAAA
Found at i:229928 original size:18 final size:18
Alignment explanation
Indices: 229851--229932 Score: 111
Period size: 18 Copynumber: 4.8 Consensus size: 18
229841 TAGGGCACTC
229851 GAAA-AAAGAAA-AAAAA
1 GAAAGAAAGAAAGAAAAA
229867 GAAA-AAA-AAAGAAAAA
1 GAAAGAAAGAAAGAAAAA
229883 GAAAGAAAGAAAGAAAAA
1 GAAAGAAAGAAAGAAAAA
229901 GAAAGAAAGAAAG-AAAA
1 GAAAGAAAGAAAGAAAAA
*
229918 GATAGATAAGAAAGA
1 GAAAGA-AAGAAAGA
229933 GAATAAGGAA
Statistics
Matches: 60, Mismatches: 1, Indels: 7
0.88 0.01 0.10
Matches are distributed among these distances:
15 3 0.05
16 16 0.27
17 12 0.20
18 29 0.48
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (18 bp):
GAAAGAAAGAAAGAAAAA
Found at i:229932 original size:22 final size:22
Alignment explanation
Indices: 229858--229916 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
229848 CTCGAAAAAA
229858 GAAAAA-AAAGAAA-AAA-AAA
1 GAAAAAGAAAGAAAGAAAGAAA
229877 GAAAAAGAAAGAAAGAAAGAAA
1 GAAAAAGAAAGAAAGAAAGAAA
229899 -AAGAAAGAAAGAAAGAAA
1 GAA-AAAGAAAGAAAGAAA
229917 AGATAGATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.17
20 7 0.19
21 5 0.14
22 18 0.50
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (22 bp):
GAAAAAGAAAGAAAGAAAGAAA
Found at i:230542 original size:13 final size:13
Alignment explanation
Indices: 230524--230554 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
230514 ATCCATATCA
230524 AAGATGTTTCTCC
1 AAGATGTTTCTCC
230537 AAGATGTTTCTCC
1 AAGATGTTTCTCC
*
230550 GAGAT
1 AAGAT
230555 TTTTGGATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (13 bp):
AAGATGTTTCTCC
Found at i:232015 original size:42 final size:41
Alignment explanation
Indices: 231960--232051 Score: 112
Period size: 42 Copynumber: 2.2 Consensus size: 41
231950 AGTTGGTAAG
* * * * *
231960 TCCTTTGGATCATCAGTAAGTCTTTCGAGCATGATGTTTAAA
1 TCCTTCGGGTCATCAGTAAGTCTTTCAAGCAAGATG-ATAAA
* *
232002 TCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGATGATAAG
1 TCCTTCGGGTCATCAGTAAGTCTTTCAAGCAAGATGATAAA
232043 TCCTTCGGG
1 TCCTTCGGG
232052 CCTTGCATAA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 12 0.28
42 31 0.72
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.35
Consensus pattern (41 bp):
TCCTTCGGGTCATCAGTAAGTCTTTCAAGCAAGATGATAAA
Found at i:232178 original size:232 final size:232
Alignment explanation
Indices: 231630--232662 Score: 1358
Period size: 233 Copynumber: 4.4 Consensus size: 232
231620 TTATAAGTTA
* * * * *
231630 AAAAATGAGAAAAGTTTCTCATTTAAATCTGAAAATGGAAATTGTTAAAAAGTAAGGAAAGTTTC
1 AAAAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAA-GAAAATTTC
* * * * *
231695 TTACATATTAAACTATTTTCAAAATTGGTAAATCCCTCGGGCCATCAGTAAGTCTTTCGAGCATG
65 TTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATG
* ** *
231760 ATCCTTAAATCCTTCGGGTTGTCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTCCGGG--ATGA
130 ATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCAT--
* * ** * *
231823 CAATAAGACCTTTGGGTTGGATGTTTTCACATGTATGTCG
193 CCATAAGACCTTCGGGCAGGATGTTTTCACATGTCTCTCG
* *
231863 AAAAATGAGAAAGGTTTCTTATTTAAATCTGAAATTTGAAATTTTTGAAAAGTAAGAAAAGTTTC
1 AAAAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAA-TTTC
* * **
231928 TTACCTAGTAAACTATTTCCAAAGTTGGTAAGTCCTTTGGATCATCAGTAAGTCTTTCGAGCATG
65 TTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATG
* * * *
231993 ATGTTTAAATCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGATGATAAGTCCTTCGGGCCTTGC
130 ATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCC
* *
232058 ATAAGACCTTCGGGCAAG-TTTTTTCACATGTCTCTCG
195 ATAAGACCTTCGGGCAGGATGTTTTCACATGTCTCTCG
* *
232095 AAAAATGAGAATGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTTAAAAGTAAGAAAATTTCC
1 AAAAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAATTT-C
* * *
232160 TTACCTAGTAAACTATTTCCAAAGTTGGTAAGTCCCTTGGGGCCATCAGTAAGTCTTTCGAACAT
65 TTACCTAGTAAACTATTTCCAAAATTGGTAAGT-CCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
* * * *
232225 GATGCATAAATCCTTCGGGTCATCTGCAAGTCTTTCGAGCAAGATGATAAGTCCTTTGGGACATC
129 GATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATC
* ** * *
232290 CATAAGACCTTCAGGCAGGATGTTTTCATGTGTCTGTTG
194 CATAAGACCTTCGGGCAGGATGTTTTCACATGTCTCTCG
*
232329 AAAAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTAGAAAAGTAAGAAAAATTTC
1 AAAAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAG-AAAATTTC
* *
232394 TTACCTA-TAAACTATTTCCAAAATTGGTAAGTCCTTCGGGTCATCAGTAAGTCTTTCGAGCAAG
65 TTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATG
* * * * **
232458 ATGCTTAAATCCTTCGGGTCATCTGTAAGTTTTTCGAGCAACATAATAAGTCATTCAAGCCATCC
130 ATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCC
* * *
232523 ATAAGACC-TCCGGCTAGGATGTTTTCACATGCCTCT-T
195 ATAAGACCTTCGGGC-AGGATGTTTTCACATGTCTCTCG
* * * *
232560 TAAAATAGAGAAAAGTTTCTTATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAATGTTT
1 AAAAAT-GAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAA-ATTT
* *
232625 TTTACCTAGTAAACCATTTCCAAAATTGGTAAGTCCTT
64 CTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTT
232663 TATACCATCC
Statistics
Matches: 703, Mismatches: 86, Indels: 22
0.87 0.11 0.03
Matches are distributed among these distances:
231 16 0.02
232 275 0.39
233 329 0.47
234 75 0.11
235 8 0.01
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (232 bp):
AAAAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAATTTCT
TACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGA
TGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCA
TAAGACCTTCGGGCAGGATGTTTTCACATGTCTCTCG
Found at i:233390 original size:134 final size:134
Alignment explanation
Indices: 233013--233379 Score: 502
Period size: 133 Copynumber: 2.7 Consensus size: 134
233003 GCAAATCAAA
* * *
233013 CTTGATTCAATCTTCCCTAAGTGACAGCGGAATGAATCAACGTCCCCATATCTGATTTTCCCTCA
1 CTTGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACATCCCCATATCTGATTTTCCCTCA
* * * * *
233078 AGAAAAAGCAGAACAGATCCCTCTCTTCCAAGATTTGATATTTCCTGAGTAACATTAGAATAAAT
66 AGAAAAAGCGGAACAGATCCCTCTCTTCCAAGATTTGATATTCCCTGAATAACAGTAGAACAAAT
233143 CTGC
131 CTGC
** * * * * *
233147 CTCAATTCAATCTTCCCTGAGTAATATTAGAATGAATCAACATCCCCA-GTCTGATTTTCCCTCA
1 CTTGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACATCCCCATATCTGATTTTCCCTCA
* * * * * *
233211 AGAAAAAGCGGAACAAATCACTCTCTTCCGAGATTTGATATTCCCTTAATAACAGTGGAACAAGT
66 AGAAAAAGCGGAACAGATCCCTCTCTTCCAAGATTTGATATTCCCTGAATAACAGTAGAACAAAT
233276 CTGC
131 CTGC
* *
233280 CTTGATTCAATCTTCCCTGGGTGACAGTGGAATTAATCAACATCCCCATATCTGATTTTCCCTCA
1 CTTGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACATCCCCATATCTGATTTTCCCTCA
* *
233345 AGAAGAAGCGGAACAGATCCCTCTCTTTCAAGATT
66 AGAAAAAGCGGAACAGATCCCTCTCTTCCAAGATT
233380 CAATCTTCCC
Statistics
Matches: 197, Mismatches: 35, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
133 113 0.57
134 84 0.43
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.29
Consensus pattern (134 bp):
CTTGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACATCCCCATATCTGATTTTCCCTCA
AGAAAAAGCGGAACAGATCCCTCTCTTCCAAGATTTGATATTCCCTGAATAACAGTAGAACAAAT
CTGC
Found at i:233445 original size:92 final size:93
Alignment explanation
Indices: 233283--233459 Score: 259
Period size: 92 Copynumber: 1.9 Consensus size: 93
233273 AGTCTGCCTT
** *
233283 GATTCAATCTTCCCTGGGTGACAGTGGAATTAATCAACATCCCCATATCTGATTTTCCCTCAAGA
1 GATTCAATCTTCCCTAAGTGACAGTGGAATGAATCAACATCCCCATATCTGATTTTCCCTCAAGA
233348 AGAAGCGGAACAGATCCCTCTCTTTCAA
66 AGAAGCGGAACAGATCCCTCTCTTTCAA
* * ** *
233376 GATTCAATCTTCCCTAAGTGATAGTGGAATGAGTCAATGT-TCCATATCTGATTTTCCCTCAA-A
1 GATTCAATCTTCCCTAAGTGACAGTGGAATGAATCAACATCCCCATATCTGATTTTCCCTCAAGA
233439 ACGAAGCGGAACAGATCCCTC
66 A-GAAGCGGAACAGATCCCTC
233460 ACTATATTTC
Statistics
Matches: 75, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
91 2 0.03
92 40 0.53
93 33 0.44
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.28
Consensus pattern (93 bp):
GATTCAATCTTCCCTAAGTGACAGTGGAATGAATCAACATCCCCATATCTGATTTTCCCTCAAGA
AGAAGCGGAACAGATCCCTCTCTTTCAA
Found at i:233590 original size:3 final size:3
Alignment explanation
Indices: 233582--233619 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
233572 TTTGTCCCGC
233582 TAT TAT TAT GCTAT T-T TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT --TAT TAT TAT TAT TAT TAT TAT TAT TAT T
233620 TATATTTGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
5 3 0.09
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:236637 original size:12 final size:14
Alignment explanation
Indices: 236620--236652 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
236610 CTATACAATA
236620 TAAAATT-AAA-TT
1 TAAAATTAAAATTT
236632 TAAAATTAAAATTT
1 TAAAATTAAAATTT
236646 TAAAATT
1 TAAAATT
236653 TTAAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 3 0.16
14 9 0.47
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TAAAATTAAAATTT
Found at i:237338 original size:5 final size:5
Alignment explanation
Indices: 237308--237354 Score: 53
Period size: 5 Copynumber: 9.4 Consensus size: 5
237298 TAGTCAGGGT
*
237308 TTTTA TTTT- TATTA TTGTTA -TTTA TTTTA TTTCTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TT-TTA TTTTA TTTTA TTT-TA TTTTA TTTTA TT
237355 ATTTTTGCAG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
4 6 0.17
5 22 0.61
6 8 0.22
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:246653 original size:20 final size:19
Alignment explanation
Indices: 246609--246677 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 19
246599 TTCAAGAAAA
*
246609 GTAAAACCTCCAGGTCATTT
1 GTAAAACCTCCATGT-ATTT
*
246629 CTAAAACCTCCATGTAGTTT
1 GTAAAACCTCCATGTA-TTT
* * *
246649 GTAAAGCATCCGTGTAATTT
1 GTAAAACCTCCATGT-ATTT
246669 GTAAAACCT
1 GTAAAACCT
246678 TTAGGTAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 1 0.03
20 37 0.95
21 1 0.03
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (19 bp):
GTAAAACCTCCATGTATTT
Found at i:246806 original size:37 final size:37
Alignment explanation
Indices: 246755--247173 Score: 424
Period size: 37 Copynumber: 11.6 Consensus size: 37
246745 CATTCATAGG
* *
246755 ACCTTCACAAAAGAGTAGTAAAGTAATGCCAATTTCA
1 ACCTTCACAGAAGAGTAGTGAAGTAATGCCAATTTCA
* * * * *
246792 ACCTTCACGGAAGAGTAGTAAAGTGAT-TCAA-TCCA
1 ACCTTCACAGAAGAGTAGTGAAGTAATGCCAATTTCA
* *
246827 ACCTTCACAAAAGAGTAGTGAAGTTAAT--CATTTTTCA
1 ACCTTCACAGAAGAGTAGTGAAG-TAATGCCA-ATTTCA
* * * *
246864 ACTTTCACGGAAGAGTAGTGATGTTAAT-CAAATTTCA
1 ACCTTCACAGAAGAGTAGTGAAG-TAATGCCAATTTCA
*
246901 ACCTTCACAAAAGAGTAGTGAAGTAATGCCAATTTCA
1 ACCTTCACAGAAGAGTAGTGAAGTAATGCCAATTTCA
*
246938 ACCTTCACAAAAGAGTAGTGAAGTAATGCCAATTTCA
1 ACCTTCACAGAAGAGTAGTGAAGTAATGCCAATTTCA
* * *
246975 ACCTTCACAGAAGAGCAATGAAGCAATGCCAATTTCA
1 ACCTTCACAGAAGAGTAGTGAAGTAATGCCAATTTCA
* *
247012 ACCTTCATAGAAGAGTAGTGAAGTAATGCAAATTTCA
1 ACCTTCACAGAAGAGTAGTGAAGTAATGCCAATTTCA
*
247049 ACCTTCACAGAAGAGTACTGAAGTCAAT---AATTCTCA
1 ACCTTCACAGAAGAGTAGTGAAGT-AATGCCAATT-TCA
*
247085 ACCTTCACGGAAGAGTAGTGAAG---T---AA-TTCA
1 ACCTTCACAGAAGAGTAGTGAAGTAATGCCAATTTCA
*
247115 ACCTTCACAGAAGAGTAGTGAAGTAAAT--C-ATTCTTA
1 ACCTTCACAGAAGAGTAGTGAAGT-AATGCCAATT-TCA
* *
247151 GCCTTCACGGAAGAGTAGTGAAG
1 ACCTTCACAGAAGAGTAGTGAAG
247174 CAAGATCCGA
Statistics
Matches: 329, Mismatches: 39, Indels: 29
0.83 0.10 0.07
Matches are distributed among these distances:
30 25 0.08
31 1 0.00
32 3 0.01
34 2 0.01
35 30 0.09
36 57 0.17
37 207 0.63
38 4 0.01
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (37 bp):
ACCTTCACAGAAGAGTAGTGAAGTAATGCCAATTTCA
Found at i:247117 original size:30 final size:30
Alignment explanation
Indices: 247045--247140 Score: 120
Period size: 30 Copynumber: 3.0 Consensus size: 30
247035 TAATGCAAAT
*
247045 TTCAACCTTCACAGAAGAGTACTGAAGTCAATAA
1 TTCAACCTTCACAGAAGAGTAGTGAAG----TAA
*
247079 TTCTCAACCTTCACGGAAGAGTAGTGAAGTAA
1 -T-TCAACCTTCACAGAAGAGTAGTGAAGTAA
247111 TTCAACCTTCACAGAAGAGTAGTGAAGTAA
1 TTCAACCTTCACAGAAGAGTAGTGAAGTAA
247141 ATCATTCTTA
Statistics
Matches: 57, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
30 28 0.49
31 1 0.02
32 3 0.05
35 1 0.02
36 24 0.42
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.24
Consensus pattern (30 bp):
TTCAACCTTCACAGAAGAGTAGTGAAGTAA
Found at i:247156 original size:66 final size:66
Alignment explanation
Indices: 247045--247173 Score: 213
Period size: 66 Copynumber: 2.0 Consensus size: 66
247035 TAATGCAAAT
*
247045 TTCAACCTTCACAGAAGAGTACTGAAGTCAATAATTCTCAACCTTCACGGAAGAGTAGTGAAGTA
1 TTCAACCTTCACAGAAGAGTACTGAAGTAAATAATTCTCAACCTTCACGGAAGAGTAGTGAAGTA
247110 A
66 A
* * * *
247111 TTCAACCTTCACAGAAGAGTAGTGAAGTAAATCATTCTTAGCCTTCACGGAAGAGTAGTGAAG
1 TTCAACCTTCACAGAAGAGTACTGAAGTAAATAATTCTCAACCTTCACGGAAGAGTAGTGAAG
247174 CAAGATCCGA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (66 bp):
TTCAACCTTCACAGAAGAGTACTGAAGTAAATAATTCTCAACCTTCACGGAAGAGTAGTGAAGTA
A
Found at i:247368 original size:5 final size:5
Alignment explanation
Indices: 247351--247397 Score: 60
Period size: 5 Copynumber: 9.2 Consensus size: 5
247341 GTGACGTTTC
*
247351 TATTA TA-TA TATTA TATTA TTATTA TATAA TATTA TATTA TTATTA T
1 TATTA TATTA TATTA TATTA -TATTA TATTA TATTA TATTA -TATTA T
247398 TAAATTATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
4 4 0.11
5 23 0.62
6 10 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:247373 original size:3 final size:3
Alignment explanation
Indices: 247351--247399 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
247341 GTGACGTTTC
*
247351 TAT TA- TAT ATAT TA- TAT TAT TAT TAT ATAA TAT TA- TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT
247395 TAT TA
1 TAT TA
247400 AATTATTTAC
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
2 6 0.15
3 28 0.72
4 5 0.13
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:247385 original size:21 final size:21
Alignment explanation
Indices: 247351--247405 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
247341 GTGACGTTTC
247351 TATTATAT-ATATTATATTAT
1 TATTATATAATATTATATTAT
247371 TATTATATAATATTATATTAT
1 TATTATATAATATTATATTAT
247392 TATTAT-TAA-ATTAT
1 TATTATATAATATTAT
247406 TTACAAGATC
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
19 5 0.15
20 11 0.32
21 18 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TATTATATAATATTATATTAT
Found at i:253343 original size:3 final size:3
Alignment explanation
Indices: 253335--253373 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
253325 AATTAAAAAT
253335 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
253374 TTTTCAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:254106 original size:100 final size:100
Alignment explanation
Indices: 253992--254201 Score: 393
Period size: 100 Copynumber: 2.1 Consensus size: 100
253982 CATCATCATC
* *
253992 ATTTTTAAAAAGAAATACTAGTTATAAAACTTTTATAAAATTATTCATATTTTAAATTACTTACC
1 ATTTTGAAAGAGAAATACTAGTTATAAAACTTTTATAAAATTATTCATATTTTAAATTACTTACC
254057 CTCAAAGTTTTCCTATATTAAACTATATATATAGG
66 CTCAAAGTTTTCCTATATTAAACTATATATATAGG
254092 ATTTTGAAAGAGAAATACTAGTTATAAAACTTTTATAAAATTATTCATATTTTAAATTACTTACC
1 ATTTTGAAAGAGAAATACTAGTTATAAAACTTTTATAAAATTATTCATATTTTAAATTACTTACC
*
254157 CTCAAAGTTTTCCTATATTAGACTATATATATAGG
66 CTCAAAGTTTTCCTATATTAAACTATATATATAGG
254192 ATTTTGAAAG
1 ATTTTGAAAG
254202 GGTAAAAAAT
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
100 107 1.00
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.41
Consensus pattern (100 bp):
ATTTTGAAAGAGAAATACTAGTTATAAAACTTTTATAAAATTATTCATATTTTAAATTACTTACC
CTCAAAGTTTTCCTATATTAAACTATATATATAGG
Found at i:278255 original size:35 final size:34
Alignment explanation
Indices: 278170--278256 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
278160 ATTTGGTATT
*
278170 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
278204 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
278242 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
278257 ACTGAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:278867 original size:18 final size:18
Alignment explanation
Indices: 278840--278877 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
278830 GTAATGGAAA
* *
278840 GGTTGTGGCATCATATAT
1 GGTTGCGGCATCATAAAT
278858 GGTTGCGGCATCATAAAT
1 GGTTGCGGCATCATAAAT
278876 GG
1 GG
278878 CTGTGGTGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.13, G:0.32, T:0.32
Consensus pattern (18 bp):
GGTTGCGGCATCATAAAT
Found at i:289120 original size:23 final size:23
Alignment explanation
Indices: 289048--289178 Score: 126
Period size: 23 Copynumber: 5.7 Consensus size: 23
289038 AGTCGAGGGT
* * *
289048 TCTACATGGTCCTTCAGGATA-A
1 TCTACGTGGTCCTTCGGGACATA
*
289070 TTCTACGTGATCCTTCGGGACA-A
1 -TCTACGTGGTCCTTCGGGACATA
*
289093 TTCTACGTAGTCCTTCGGGACATA
1 -TCTACGTGGTCCTTCGGGACATA
* *
289117 TCTATGTGGTCCTTTGGGACATA
1 TCTACGTGGTCCTTCGGGACATA
* *
289140 TCTACGTGGT-CTTCGGGATATT
1 TCTACGTGGTCCTTCGGGACATA
289162 TCTACGTGG-CACTTCGG
1 TCTACGTGGTC-CTTCGG
289179 TGCTTATTCT
Statistics
Matches: 92, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
22 18 0.20
23 73 0.79
24 1 0.01
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.34
Consensus pattern (23 bp):
TCTACGTGGTCCTTCGGGACATA
Found at i:289954 original size:13 final size:13
Alignment explanation
Indices: 289905--289957 Score: 65
Period size: 13 Copynumber: 4.1 Consensus size: 13
289895 GATAATTATA
289905 AAATTAGATATTTT
1 AAATTA-ATATTTT
*
289919 ATATTAATACTTTT
1 AAATTAATA-TTTT
289933 AAA--AATATTTT
1 AAATTAATATTTT
289944 AAATTAATATTTT
1 AAATTAATATTTT
289957 A
1 A
289958 TTTATTTATG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
11 7 0.21
12 4 0.12
13 12 0.35
14 11 0.32
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (13 bp):
AAATTAATATTTT
Found at i:290335 original size:7 final size:7
Alignment explanation
Indices: 290323--290349 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
290313 TAGAGATTAA
290323 GGTTTAG
1 GGTTTAG
290330 GGTTTAG
1 GGTTTAG
290337 GGTTTAG
1 GGTTTAG
290344 GGTTTA
1 GGTTTA
290350 TAGGTTATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.41, T:0.44
Consensus pattern (7 bp):
GGTTTAG
Found at i:291058 original size:20 final size:19
Alignment explanation
Indices: 291033--291073 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
291023 AAAAGAATCA
291033 AAATGAAAAACGAACAAAAG
1 AAATGAAAAACGAA-AAAAG
* *
291053 AAATGAAGAATGAAAAAAG
1 AAATGAAAAACGAAAAAAG
291072 AA
1 AA
291074 TAAAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.71, C:0.05, G:0.17, T:0.07
Consensus pattern (19 bp):
AAATGAAAAACGAAAAAAG
Found at i:291089 original size:28 final size:27
Alignment explanation
Indices: 291034--291091 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
291024 AAAGAATCAA
* * *
291034 AATGAAAAACGAACAAAAGAAATGAAG
1 AATGAAAAAAGAACAAAAAAAAAGAAG
*
291061 AATGAAAAAAGAATAAAAAAAAAGAAAG
1 AATGAAAAAAGAACAAAAAAAAAG-AAG
291089 AAT
1 AAT
291092 AAAGGAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.72, C:0.03, G:0.16, T:0.09
Consensus pattern (27 bp):
AATGAAAAAAGAACAAAAAAAAAGAAG
Found at i:291183 original size:2 final size:2
Alignment explanation
Indices: 291176--291201 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
291166 TAAATAATAC
291176 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
291202 GATGACATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:302603 original size:28 final size:28
Alignment explanation
Indices: 302545--302621 Score: 84
Period size: 28 Copynumber: 2.8 Consensus size: 28
302535 ATTTTTTGTG
* * *
302545 ACTATTTTATCATTTCGGTTTTCTTACC
1 ACTATTTTATCATTTCGATTTACTCACC
* *
302573 ACTATTTTATCATTTTGATTTACTCATC
1 ACTATTTTATCATTTCGATTTACTCACC
* *
302601 ACTCTTTTATC-TTTGGATTTA
1 ACTATTTTATCATTTCGATTTA
302622 ATATTTTTGT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
27 9 0.21
28 33 0.79
ACGTcount: A:0.21, C:0.18, G:0.06, T:0.55
Consensus pattern (28 bp):
ACTATTTTATCATTTCGATTTACTCACC
Found at i:302861 original size:21 final size:20
Alignment explanation
Indices: 302806--302861 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
302796 GTCAAATAAT
302806 AAATAAGTATTAGATAAATTA
1 AAATAAGTATTA-ATAAATTA
* * *
302827 AAACACGTCTTTAATAAATTA
1 AAATAAGT-ATTAATAAATTA
302848 AAATAAGTAATTAA
1 AAATAAGT-ATTAA
302862 ACCTTTCTTA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.32
Consensus pattern (20 bp):
AAATAAGTATTAATAAATTA
Found at i:302938 original size:13 final size:14
Alignment explanation
Indices: 302911--302940 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
302901 TTTATTATTT
302911 AAAATAATTCAAAA
1 AAAATAATTCAAAA
*
302925 AAAATATTTCAAAA
1 AAAATAATTCAAAA
302939 AA
1 AA
302941 TAATTTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAATAATTCAAAA
Found at i:305693 original size:18 final size:20
Alignment explanation
Indices: 305658--305694 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
305648 AAACCATAAT
*
305658 TTTTTTATAAACATGTCTAA
1 TTTTTTATAAACAGGTCTAA
305678 TTTTTTA-AAA-AGGTCTA
1 TTTTTTATAAACAGGTCTA
305695 TATTAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 6 0.38
19 3 0.19
20 7 0.44
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.49
Consensus pattern (20 bp):
TTTTTTATAAACAGGTCTAA
Found at i:306585 original size:20 final size:20
Alignment explanation
Indices: 306539--306592 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
306529 TACCGATCCA
*
306539 AACAATATCGATATCAATATG
1 AACAATATCAATA-CAATATG
* *
306560 -AGAATATCAATACTATATG
1 AACAATATCAATACAATATG
306579 AACAATATCAATAC
1 AACAATATCAATAC
306593 GTCAAGACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.50, C:0.15, G:0.07, T:0.28
Consensus pattern (20 bp):
AACAATATCAATACAATATG
Found at i:307794 original size:31 final size:32
Alignment explanation
Indices: 307730--307804 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 32
307720 GATATATCAC
*
307730 ATATCATGTCACATAAGGTGATGATGTGTTAT
1 ATATCATGTCACATAAGGTGATGATGCGTTAT
*
307762 AT-TCATGTCAC-TATAGGTGATTATAGCG-TAT
1 ATATCATGTCACATA-AGGTGATGAT-GCGTTAT
*
307793 ATATCACGTCAC
1 ATATCATGTCAC
307805 CCAAGATGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
30 2 0.05
31 23 0.62
32 12 0.32
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.36
Consensus pattern (32 bp):
ATATCATGTCACATAAGGTGATGATGCGTTAT
Found at i:312687 original size:23 final size:23
Alignment explanation
Indices: 312647--312691 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
312637 TTATACGCGG
* *
312647 TCTTTCGGGACAATTCTATGTGA
1 TCTTTCGAGACAAATCTATGTGA
*
312670 TCTTTCGAGATAAATCTATGTG
1 TCTTTCGAGACAAATCTATGTG
312692 GCACTTCGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (23 bp):
TCTTTCGAGACAAATCTATGTGA
Found at i:312719 original size:24 final size:24
Alignment explanation
Indices: 312692--312762 Score: 133
Period size: 24 Copynumber: 3.0 Consensus size: 24
312682 AATCTATGTG
312692 GCACTTCGGTGCATATTCTACGTT
1 GCACTTCGGTGCATATTCTACGTT
312716 GCACTTCGGTGCATATTCTACGTT
1 GCACTTCGGTGCATATTCTACGTT
*
312740 GCACTTCGGTGCAAATTCTACGT
1 GCACTTCGGTGCATATTCTACGT
312763 GGTAGTTTCG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.35
Consensus pattern (24 bp):
GCACTTCGGTGCATATTCTACGTT
Found at i:315674 original size:23 final size:24
Alignment explanation
Indices: 315640--315688 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
315630 CGGGACATAC
*
315640 AGTGGTCCTTCGAGAC-ATTTCAT
1 AGTGGTCCTTCGAGACAAATTCAT
* *
315663 AGTGGTCTTTCGGGACAAATTCAT
1 AGTGGTCCTTCGAGACAAATTCAT
315687 AG
1 AG
315689 CCCTTAGTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (24 bp):
AGTGGTCCTTCGAGACAAATTCAT
Found at i:319781 original size:23 final size:22
Alignment explanation
Indices: 319730--319795 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 22
319720 AGGGTTCATA
*
319730 GGTCATTCGGGACA-T-ACAGT
1 GGTCATTCGGGACATTCATAGT
*
319750 GGTCCTTCGGGACATTTCATAGT
1 GGTCATTCGGGACA-TTCATAGT
319773 GGTCATTCGGGACAAATTCATAG
1 GGTCATTCGGGAC--ATTCATAG
319796 CCCCTAGTGG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
20 13 0.34
22 1 0.03
23 16 0.42
24 7 0.18
25 1 0.03
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (22 bp):
GGTCATTCGGGACATTCATAGT
Found at i:335830 original size:21 final size:21
Alignment explanation
Indices: 335783--335830 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
335773 ATAAGTGTAT
* *
335783 CGAAGTATCACATATATGTTC
1 CGAAGGATCACATATATGTCC
* *
335804 CAAAGGATTACATATATGTCC
1 CGAAGGATCACATATATGTCC
335825 CGAAGG
1 CGAAGG
335831 GCCACATAGA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (21 bp):
CGAAGGATCACATATATGTCC
Found at i:340584 original size:17 final size:17
Alignment explanation
Indices: 340562--340595 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
340552 TCCATAAATC
*
340562 CAAAATCCAACAATCCA
1 CAAAATCAAACAATCCA
*
340579 CAAAATCAAACATTCCA
1 CAAAATCAAACAATCCA
340596 AAATATTCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.32, G:0.00, T:0.15
Consensus pattern (17 bp):
CAAAATCAAACAATCCA
Found at i:342623 original size:20 final size:20
Alignment explanation
Indices: 342594--342631 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
342584 CCCCTTCAAA
*
342594 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
342614 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
342632 TGCACCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.26, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:349921 original size:13 final size:13
Alignment explanation
Indices: 349903--349929 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
349893 TTCTCTATGA
349903 AGAAAGCCACGTG
1 AGAAAGCCACGTG
349916 AGAAAGCCACGTG
1 AGAAAGCCACGTG
349929 A
1 A
349930 AACTTGGGTA
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:0.41, C:0.22, G:0.30, T:0.07
Consensus pattern (13 bp):
AGAAAGCCACGTG
Found at i:360049 original size:51 final size:52
Alignment explanation
Indices: 359921--360079 Score: 216
Period size: 52 Copynumber: 3.0 Consensus size: 52
359911 GTTGGCAATA
* *
359921 TAGTGTGATCATGATATTATATGCAATATTTTATCTAT-GCTTGATGCCTCAC
1 TAGTTTGATCATTATATTATATGCAATATTTTATCT-TCGCTTGATGCCTCAC
359973 TAGTTTGATCATTATATTATATGCAATATTTTATCTTCGCTTGATGCCTCA-
1 TAGTTTGATCATTATATTATATGCAATATTTTATCTTCGCTTGATGCCTCAC
* * *
360024 TAGTTTGATCATTTTTTTATATGCAATACTTTTATCTTC-CTGTTGATGCCTTAC
1 TAGTTTGATCATTATATTATATGCAATA-TTTTATCTTCGC--TTGATGCCTCAC
360078 TA
1 TA
360080 ATCCTCATAT
Statistics
Matches: 97, Mismatches: 5, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
51 28 0.29
52 57 0.59
53 10 0.10
54 2 0.02
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.47
Consensus pattern (52 bp):
TAGTTTGATCATTATATTATATGCAATATTTTATCTTCGCTTGATGCCTCAC
Found at i:360161 original size:82 final size:82
Alignment explanation
Indices: 360024--360180 Score: 260
Period size: 82 Copynumber: 1.9 Consensus size: 82
360014 TGATGCCTCA
** * *
360024 TAGTTTGATCATTTTTTTATATGCAATACTTTTATCTTCCTGTTGATGCCTTACTAATCCTCATA
1 TAGTTTGATCATGATATTATATGCAATACTTTTATCTTCCGGTTGATGCCTTACTAATCCTCATA
*
360089 TGCCATCTTTGCCTTAC
66 CGCCATCTTTGCCTTAC
*
360106 TAGTTTGATCATGATATTATATGCAGTACTTTTATCTTCCGGTTGATGCCTTACTAATCCTCATA
1 TAGTTTGATCATGATATTATATGCAATACTTTTATCTTCCGGTTGATGCCTTACTAATCCTCATA
360171 CGCCATCTTT
66 CGCCATCTTT
360181 CTGTAAAATC
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
82 69 1.00
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.45
Consensus pattern (82 bp):
TAGTTTGATCATGATATTATATGCAATACTTTTATCTTCCGGTTGATGCCTTACTAATCCTCATA
CGCCATCTTTGCCTTAC
Found at i:361785 original size:3 final size:3
Alignment explanation
Indices: 361779--361805 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
361769 AAGTATTTTT
361779 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
361806 GTTCTATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:362083 original size:20 final size:20
Alignment explanation
Indices: 362058--362118 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
362048 ACAGTTTCCA
362058 AATTCGCAACGCGATTTTAT
1 AATTCGCAACGCGATTTTAT
**
362078 TTTTCGCAACGCGAATTTCTA-
1 AATTCGCAACGCG-ATTT-TAT
*
362099 AATTCACAACGCGATTTTAT
1 AATTCGCAACGCGATTTTAT
362119 CTGATAAACT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
19 2 0.06
20 15 0.45
21 14 0.42
22 2 0.06
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (20 bp):
AATTCGCAACGCGATTTTAT
Found at i:369653 original size:55 final size:55
Alignment explanation
Indices: 369587--369692 Score: 176
Period size: 55 Copynumber: 1.9 Consensus size: 55
369577 GCGTTCATAT
*
369587 GATTCATGAAGAAGAACATTCGATGAATGAAGAAATTTGAACCTGACTGAAGAGC
1 GATTCATGAAGAAGAACATTCGATGAATGAAGAAATTTGAAACTGACTGAAGAGC
* * *
369642 GATTCATGAAGAAGGATATTCGATGAATGAAGAAATTTGAAACTGATTGAA
1 GATTCATGAAGAAGAACATTCGATGAATGAAGAAATTTGAAACTGACTGAA
369693 TACCGATCCA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 47 1.00
ACGTcount: A:0.42, C:0.09, G:0.24, T:0.25
Consensus pattern (55 bp):
GATTCATGAAGAAGAACATTCGATGAATGAAGAAATTTGAAACTGACTGAAGAGC
Found at i:369709 original size:55 final size:55
Alignment explanation
Indices: 369595--369709 Score: 149
Period size: 55 Copynumber: 2.1 Consensus size: 55
369585 ATGATTCATG
* * * **
369595 AAGAAGAACATTCGATGAATGAAGAAATTTGAACCTGACTGAAGAGCGATTCATG
1 AAGAAGAACATTCGATGAATGAAGAAATTTGAAACTGACTGAAGACCGATCCACA
* * * *
369650 AAGAAGGATATTCGATGAATGAAGAAATTTGAAACTGATTGAATACCGATCCACA
1 AAGAAGAACATTCGATGAATGAAGAAATTTGAAACTGACTGAAGACCGATCCACA
369705 AAGAA
1 AAGAA
369710 AGACATCCTA
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.22
Consensus pattern (55 bp):
AAGAAGAACATTCGATGAATGAAGAAATTTGAAACTGACTGAAGACCGATCCACA
Found at i:373427 original size:125 final size:125
Alignment explanation
Indices: 373205--373431 Score: 321
Period size: 125 Copynumber: 1.8 Consensus size: 125
373195 TGCCCACATT
* * ** ** *
373205 GGGGCATGAATAAACCCACATCATGTTGAGATGACAAGATTTGGACCAATTAGTCATGAAGAATG
1 GGGGCACGAATAAACCCACATCATATTGAGATGACAAGATTCAGACCAAGAAGGCATGAAGAATG
*
373270 AGCCTTACAAATTGAGGTGATGGGGTATTTTGAAGGCACGTACCAGTATGAGATAATGTC
66 AGCCTTACAAATTGAGGTGATGGGGCATTTTGAAGGCACGTACCAGTATGAGATAATGTC
* *
373330 GGGGCACGACTAAACCCACATCATATTGAGATGATAAGATTCAGACCAAGAAGGCATTGAA-AAT
1 GGGGCACGAATAAACCCACATCATATTGAGATGACAAGATTCAGACCAAGAAGGCA-TGAAGAAT
* * *
373394 GAGCCTTATAATTTGAGGTGTTGGGGCATTTTGAAGGC
65 GAGCCTTACAAATTGAGGTGATGGGGCATTTTGAAGGC
373432 TCTTACCTGA
Statistics
Matches: 88, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
125 84 0.95
126 4 0.05
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.25
Consensus pattern (125 bp):
GGGGCACGAATAAACCCACATCATATTGAGATGACAAGATTCAGACCAAGAAGGCATGAAGAATG
AGCCTTACAAATTGAGGTGATGGGGCATTTTGAAGGCACGTACCAGTATGAGATAATGTC
Found at i:374688 original size:37 final size:37
Alignment explanation
Indices: 374638--374751 Score: 176
Period size: 37 Copynumber: 3.1 Consensus size: 37
374628 AAAGTCAAGT
*
374638 CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTGAGC
1 CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTAAGC
*
374675 CTTCACCAAAGAGTAGTGAAGCAAA-CCATCTTAAGC
1 CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTAAGC
* * *
374711 CTTCACCGAAGAGTAGTGAAGCATATCCTTTTTAAGC
1 CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTAAGC
374748 CTTC
1 CTTC
374752 TCGGAAGAGT
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
36 32 0.46
37 38 0.54
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (37 bp):
CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTAAGC
Found at i:374723 original size:36 final size:36
Alignment explanation
Indices: 374638--374777 Score: 156
Period size: 37 Copynumber: 3.8 Consensus size: 36
374628 AAAGTCAAGT
* *
374638 CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTGAGC
1 CTTCACCAAAGAGTAGTGAAGCAAA-CCATCTTAAGC
374675 CTTCACCAAAGAGTAGTGAAGCAAACCATCTTAAGC
1 CTTCACCAAAGAGTAGTGAAGCAAACCATCTTAAGC
* * * *
374711 CTTCACCGAAGAGTAGTGAAGCATATCCTTTTTAAGC
1 CTTCACCAAAGAGTAGTGAAGCA-AACCATCTTAAGC
* ** *
374748 CTTCTCGGAAGAGT-GTTGGAGCAAACCATC
1 CTTCACCAAAGAGTAG-TGAAGCAAACCATC
374778 AGACAATCAG
Statistics
Matches: 89, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
36 36 0.40
37 53 0.60
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (36 bp):
CTTCACCAAAGAGTAGTGAAGCAAACCATCTTAAGC
Found at i:374760 original size:73 final size:73
Alignment explanation
Indices: 374638--374777 Score: 192
Period size: 73 Copynumber: 1.9 Consensus size: 73
374628 AAAGTCAAGT
*
374638 CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTGAGCCTTCACCAAAGAGTAG-TGAAGCAAACC
1 CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTAAGCCTTCACCAAAGAGT-GTTGAAGCAAACC
374702 ATCTTAAGC
65 ATCTTAAGC
* * * * ** *
374711 CTTCACCGAAGAGTAGTGAAGCATATCCTTTTTAAGCCTTCTCGGAAGAGTGTTGGAGCAAACCA
1 CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTAAGCCTTCACCAAAGAGTGTTGAAGCAAACCA
374776 TC
66 TC
374778 AGACAATCAG
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
72 1 0.02
73 57 0.98
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (73 bp):
CTTCACCAAAGAGTAGTGAAGCAAATCCATTTTAAGCCTTCACCAAAGAGTGTTGAAGCAAACCA
TCTTAAGC
Found at i:375201 original size:54 final size:54
Alignment explanation
Indices: 375137--375462 Score: 564
Period size: 54 Copynumber: 6.1 Consensus size: 54
375127 ATAGTAAAGT
375137 AGAAG-AGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
*
375190 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGAGAGCGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
* ** *
375244 AGAAGAAGATGTTCGAGTTCCATACTTCCTAGAGAAAGAGGGAGAAAACTCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
* *
375298 AGAACAAGATGTTCGAGTTCCGTACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
375352 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
* *
375406 AGAAGAAGATGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAATCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
375460 AGA
1 AGA
375463 GAATGTTGAG
Statistics
Matches: 256, Mismatches: 16, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
53 5 0.02
54 251 0.98
ACGTcount: A:0.36, C:0.19, G:0.27, T:0.17
Consensus pattern (54 bp):
AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
Found at i:375534 original size:55 final size:55
Alignment explanation
Indices: 375466--375774 Score: 382
Period size: 55 Copynumber: 5.7 Consensus size: 55
375456 CGTAAGAGAA
375466 TGTT-GAGTCTTATACTTTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGAT
1 TGTTCGAGTCTTATACTTTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGAT
* *
375520 TGTTCGAGTCTTATAATCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGAT
1 TGTTCGAGTCTTATACTTTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGAT
*
375575 TGTTCGAGTCTTATACTTTCTGAAGAAATAGGGAGCA-ACCACGATTGTTGAAGAT
1 TGTTCGAGTCTTATACTTTCTGAAGGAATAGGGAGCAGA-CACGATTGTTGAAGAT
* * *
375630 TG-TCTGAGT-TTATACTCTCTGAAAGAATAGGGACCA-ACACGATTGTTGAAGAT
1 TGTTC-GAGTCTTATACTTTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGAT
* * * * * *
375683 TATTCGAGT-TCTATACTTCCTGAAAGAAAGAGGGAGC-GAACCCG-TTTTATGAAGAT
1 TGTTCGAGTCT-TATACTTTCTG-AAGGAATAGGGAGCAG-ACACGATTGT-TGAAGAT
* *
375739 TGTTCGAGTCTTATACTTCCTGAAGGAGTAGGGAGC
1 TGTTCGAGTCTTATACTTTCTGAAGGAATAGGGAGC
375775 GGGCTCGTTA
Statistics
Matches: 223, Mismatches: 22, Indels: 19
0.84 0.08 0.07
Matches are distributed among these distances:
53 22 0.10
54 42 0.19
55 128 0.57
56 30 0.13
57 1 0.00
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (55 bp):
TGTTCGAGTCTTATACTTTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGAT
Found at i:375738 original size:164 final size:165
Alignment explanation
Indices: 375469--375774 Score: 417
Period size: 164 Copynumber: 1.9 Consensus size: 165
375459 AAGAGAATGT
* * * *
375469 TGAGTCTTATACTTTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTAT
1 TGAGTCTTATACTCTCTGAAAGAATAGGGACCAGACACGATTGTTGAAGATTATTCGAGTCTTAT
* * *
375534 AATCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTTTCTGAA
66 AATCTCTGAAGAAAGAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTTCCTGAA
375599 GAAATAGGGAGCAACCACGATTGTTGAAGATTGTC
131 GAAATAGGGAGCAACCACGATTGTTGAAGATTGTC
375634 TGAGT-TTATACTCTCTGAAAGAATAGGGACCA-ACACGATTGTTGAAGATTATTCGAGT-TCTA
1 TGAGTCTTATACTCTCTGAAAGAATAGGGACCAGACACGATTGTTGAAGATTATTCGAGTCT-TA
* * *
375696 TACT-TCCTGAAAGAAAGAGGGAGC-GAACCCG-TTTTATGAAGATTGTTCGAGTCTTATACTTC
65 TAATCT-CTG-AAGAAAGAGGGAGCAG-ACACGATTGT-TGAAGATTGTTCGAGTCTTATACTTC
* *
375758 CTGAAGGAGTAGGGAGC
126 CTGAAGAAATAGGGAGC
375775 GGGCTCGTTA
Statistics
Matches: 124, Mismatches: 12, Indels: 11
0.84 0.08 0.07
Matches are distributed among these distances:
162 2 0.02
163 37 0.30
164 80 0.65
165 5 0.04
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.30
Consensus pattern (165 bp):
TGAGTCTTATACTCTCTGAAAGAATAGGGACCAGACACGATTGTTGAAGATTATTCGAGTCTTAT
AATCTCTGAAGAAAGAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTTCCTGAA
GAAATAGGGAGCAACCACGATTGTTGAAGATTGTC
Found at i:381257 original size:7 final size:7
Alignment explanation
Indices: 381245--381271 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
381235 GGCCATGCAC
381245 GCTGCCT
1 GCTGCCT
381252 GCTGCCT
1 GCTGCCT
381259 GCTGCCT
1 GCTGCCT
381266 GCTGCC
1 GCTGCC
381272 AACGTGGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.44, G:0.30, T:0.26
Consensus pattern (7 bp):
GCTGCCT
Found at i:383509 original size:24 final size:24
Alignment explanation
Indices: 383477--383577 Score: 166
Period size: 24 Copynumber: 4.2 Consensus size: 24
383467 TTCACACGGT
*
383477 AGTCCCCCATCATACGGAGGTGGG
1 AGTCCACCATCATACGGAGGTGGG
*
383501 AGTCCCCCATCATACGGAGGTGGG
1 AGTCCACCATCATACGGAGGTGGG
383525 AGTCCACCATCATACGGAGGTGGG
1 AGTCCACCATCATACGGAGGTGGG
* *
383549 AGTCCACCATCATACGGTGGTGGA
1 AGTCCACCATCATACGGAGGTGGG
383573 AGTCC
1 AGTCC
383578 GCCAACTCCC
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 74 1.00
ACGTcount: A:0.23, C:0.28, G:0.32, T:0.18
Consensus pattern (24 bp):
AGTCCACCATCATACGGAGGTGGG
Found at i:386045 original size:15 final size:15
Alignment explanation
Indices: 386025--386062 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
386015 TAACATAATA
386025 TAAGGTACATGAGTT
1 TAAGGTACATGAGTT
* *
386040 TAAGGTGCGTGAGTT
1 TAAGGTACATGAGTT
386055 TAAGGTAC
1 TAAGGTAC
386063 GCACTAGGCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.29, C:0.08, G:0.32, T:0.32
Consensus pattern (15 bp):
TAAGGTACATGAGTT
Found at i:386384 original size:17 final size:18
Alignment explanation
Indices: 386347--386397 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 18
386337 TGATCATTGT
*
386347 AATCATATGATATA-TGTA
1 AATCATATGATA-ACTGAA
386365 AAT-ATATGATAACTGAA
1 AATCATATGATAACTGAA
*
386382 AATCATCTGATAACTG
1 AATCATATGATAACTG
386398 TAAACATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 1 0.03
17 14 0.48
18 14 0.48
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (18 bp):
AATCATATGATAACTGAA
Found at i:387535 original size:2 final size:2
Alignment explanation
Indices: 387528--387555 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
387518 TTAAATTCCA
387528 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
387556 CCTTTATCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:388354 original size:32 final size:32
Alignment explanation
Indices: 388317--388383 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
388307 TATTCTCATC
388317 ATCAAAACATCAAATTTAATCCAAATCCAATA
1 ATCAAAACATCAAATTTAATCCAAATCCAATA
*
388349 ATCAAAACATCAAATTTAATTCAAATCCAATA
1 ATCAAAACATCAAATTTAATCCAAATCCAATA
388381 ATC
1 ATC
388384 TTTTAAAACC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.27
Consensus pattern (32 bp):
ATCAAAACATCAAATTTAATCCAAATCCAATA
Found at i:388861 original size:15 final size:14
Alignment explanation
Indices: 388833--388870 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
388823 GACTTGATAT
388833 TTACAA-ATTTCCA
1 TTACAATATTTCCA
388846 TTACAATATCTTCCA
1 TTACAATAT-TTCCA
*
388861 TTAAAATATT
1 TTACAATATT
388871 ATTTAGTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 6 0.27
14 3 0.14
15 13 0.59
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.42
Consensus pattern (14 bp):
TTACAATATTTCCA
Found at i:393280 original size:17 final size:17
Alignment explanation
Indices: 393230--393281 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
393220 AAAACATCTG
* *
393230 ATTTATAAATATCTGAT
1 ATTTGTAAATATATGAT
*
393247 AATTGT-AATCATATGAT
1 ATTTGTAAAT-ATATGAT
*
393264 ATTTGTAAATATTTGAT
1 ATTTGTAAATATATGAT
393281 A
1 A
393282 ACTGAAAATC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
16 3 0.11
17 22 0.79
18 3 0.11
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.46
Consensus pattern (17 bp):
ATTTGTAAATATATGAT
Found at i:393307 original size:35 final size:34
Alignment explanation
Indices: 393208--393299 Score: 100
Period size: 34 Copynumber: 2.7 Consensus size: 34
393198 TTAATATGTG
*
393208 TTTGATAACTGTAAAA-CATCTGAT-TTATAAATA
1 TTTGATAACTG-AAAATCATCTGATATTGTAAATA
* * * *
393241 TCTGATAATTG-TAATCATATGATATTTGTAAATA
1 TTTGATAACTGAAAATCATCTGATA-TTGTAAATA
393275 TTTGATAACTGAAAATCATCTGATA
1 TTTGATAACTGAAAATCATCTGATA
393300 ACTGTAAACA
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
31 2 0.04
32 7 0.15
33 9 0.20
34 17 0.37
35 11 0.24
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (34 bp):
TTTGATAACTGAAAATCATCTGATATTGTAAATA
Found at i:394625 original size:3 final size:3
Alignment explanation
Indices: 394617--394645 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
394607 AATTTTAATT
394617 TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
394646 ATTAATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:394636 original size:14 final size:14
Alignment explanation
Indices: 394617--394643 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
394607 AATTTTAATT
394617 TTATTATTATTATA
1 TTATTATTATTATA
394631 TTATTATTATTAT
1 TTATTATTATTAT
394644 TAATTAATAT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATTATTATTATA
Found at i:402136 original size:16 final size:16
Alignment explanation
Indices: 402115--402148 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
402105 CCCCTCGCAG
*
402115 ATCAACATATACATAC
1 ATCAACACATACATAC
402131 ATCAACACATACATAC
1 ATCAACACATACATAC
402147 AT
1 AT
402149 GATACATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (16 bp):
ATCAACACATACATAC
Found at i:402478 original size:36 final size:35
Alignment explanation
Indices: 402438--402549 Score: 111
Period size: 36 Copynumber: 3.2 Consensus size: 35
402428 TTTTAGGGTG
*
402438 TTTTTCTTGAAACAAAATTTTGTCTCTCTTGAGACA
1 TTTTTCTTAAAACAAAA-TTTGTCTCTCTTGAGACA
* * *
402474 TTTTT-ATAAAAGAAAATTTGTCTCAT-TTAAGACAA
1 TTTTTCTTAAAACAAAATTTGTCTC-TCTTGAGAC-A
* * * *
402509 TTTCTCTTAAAACAAACTTCGTCTCGCTTGAGACA
1 TTTTTCTTAAAACAAAATTTGTCTCTCTTGAGACA
402544 TTTTTC
1 TTTTTC
402550 CTTTGATATA
Statistics
Matches: 60, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
34 14 0.23
35 20 0.33
36 26 0.43
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (35 bp):
TTTTTCTTAAAACAAAATTTGTCTCTCTTGAGACA
Found at i:403002 original size:30 final size:27
Alignment explanation
Indices: 402918--403004 Score: 84
Period size: 30 Copynumber: 3.0 Consensus size: 27
402908 CTCTTGAGAC
402918 TGTTTCTCTTGAAACAAATCTTTGAGTT
1 TGTTTCTCTTGAAA-AAATCTTTGAGTT
* * *
402946 TGTTCCTTTTGAAAAAAAAATATTTGAGTT
1 TGTTTCTCTTG---AAAAAATCTTTGAGTT
402976 TGTTTCTCTTGACAAAATCATCTTTGAGT
1 TGTTTCTCTTGA-AAAA--ATCTTTGAGT
403005 CTATTTCTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
27 1 0.02
28 13 0.28
30 30 0.64
31 3 0.06
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.45
Consensus pattern (27 bp):
TGTTTCTCTTGAAAAAATCTTTGAGTT
Found at i:403362 original size:28 final size:28
Alignment explanation
Indices: 403308--403365 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
403298 CTTTTGAAAC
* *
403308 ACAAATCTTTGAGTCTTTTTATTTTGAA
1 ACAAATCTTTGAGTCTGTTTATCTTGAA
*
403336 ACAAATCTTTGAGT-TGGTTTCTCTTGAA
1 ACAAATCTTTGAGTCT-GTTTATCTTGAA
403364 AC
1 AC
403366 CATAATCCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.45
Consensus pattern (28 bp):
ACAAATCTTTGAGTCTGTTTATCTTGAA
Found at i:403856 original size:3 final size:3
Alignment explanation
Indices: 403848--403898 Score: 88
Period size: 3 Copynumber: 17.7 Consensus size: 3
403838 TAATTTTAAT
403848 TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA -TA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
403894 TTA TT
1 TTA TT
403899 TAATATATTA
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 4 0.09
3 42 0.91
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:405754 original size:21 final size:23
Alignment explanation
Indices: 405730--405771 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
405720 CATTTCACTG
405730 ATATTT-TGTTTATT-TATTTTT
1 ATATTTATGTTTATTATATTTTT
*
405751 ATATTTATTTTTATTATATTT
1 ATATTTATGTTTATTATATTT
405772 GAATATTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 7 0.39
23 5 0.28
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (23 bp):
ATATTTATGTTTATTATATTTTT
Found at i:405757 original size:12 final size:12
Alignment explanation
Indices: 405740--405764 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
405730 ATATTTTGTT
405740 TATTTATTTTTA
1 TATTTATTTTTA
405752 TATTTATTTTTA
1 TATTTATTTTTA
405764 T
1 T
405765 TATATTTGAA
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TATTTATTTTTA
Found at i:405769 original size:15 final size:16
Alignment explanation
Indices: 405738--405771 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
405728 TGATATTTTG
*
405738 TTTATTTATTTTTATA
1 TTTATTTATTATTATA
405754 TTTATTT-TTATTATA
1 TTTATTTATTATTATA
405769 TTT
1 TTT
405772 GAATATTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTATTTATTATTATA
Found at i:405777 original size:23 final size:21
Alignment explanation
Indices: 405730--405778 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 21
405720 CATTTCACTG
**
405730 ATATTTTGTTTATTTATTTTT
1 ATATTTTGTTTATTTATTTGA
*
405751 ATATTTATTTTTATTATATTTGA
1 ATATTT-TGTTTATT-TATTTGA
405774 ATATT
1 ATATT
405779 GATTATCCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 6 0.26
22 7 0.30
23 10 0.43
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (21 bp):
ATATTTTGTTTATTTATTTGA
Found at i:412082 original size:26 final size:26
Alignment explanation
Indices: 412053--412108 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
412043 TTCAGATCTA
* *
412053 GAATAGGATCAACCATAGATGCCTCT
1 GAATAGGACCAACCATAGATGCCTAT
* *
412079 GAATTGGACCAACCGTAGATGCCTAT
1 GAATAGGACCAACCATAGATGCCTAT
412105 GAAT
1 GAAT
412109 CAAAGGCATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.23
Consensus pattern (26 bp):
GAATAGGACCAACCATAGATGCCTAT
Found at i:413163 original size:20 final size:20
Alignment explanation
Indices: 413135--413185 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
413125 ATGCAAGCAA
* *
413135 TATCAATACCAAAAGG-GGAG
1 TATCGATACCAAAAGGAAG-G
* *
413155 TATCGATACTATAAGGAAGG
1 TATCGATACCAAAAGGAAGG
413175 TATCGATACCA
1 TATCGATACCA
413186 TTGTTTACAG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.22
Consensus pattern (20 bp):
TATCGATACCAAAAGGAAGG
Found at i:413259 original size:22 final size:21
Alignment explanation
Indices: 413222--413278 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
413212 TGATACCATA
413222 ATAGAGTATC-ATTACCATGGT
1 ATAGAGTATCGA-TACCATGGT
413243 ATAGTAGTATCGATACCATGGT
1 ATAG-AGTATCGATACCATGGT
*
413265 A-AGGGTATCGATAC
1 ATAGAGTATCGATAC
413279 TATTGAGCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
20 10 0.30
21 6 0.18
22 16 0.48
23 1 0.03
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (21 bp):
ATAGAGTATCGATACCATGGT
Found at i:413969 original size:81 final size:81
Alignment explanation
Indices: 413832--414871 Score: 1480
Period size: 81 Copynumber: 12.9 Consensus size: 81
413822 TGAATAATTA
* ** *
413832 TTTGAATAAAAGATTAATAACCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAAGTATGCCAGTTAGA
413897 TGAAAGGTTAAATACC
66 TGAAAGGTTAAATACC
*
413913 TTTGAATAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAAGTATGCCAGTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAAGTATGCCAGTTAGA
413978 TGAAAGGTTAAATACC
66 TGAAAGGTTAAATACC
* * *
413994 TTTGAGTAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGGTATCAAGTATGCTAGTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAAGTATGCCAGTTAGA
414059 TGAAAGGTTAAATACC
66 TGAAAGGTTAAATACC
* * * * *
414075 TTTGAGTAAAAGATTAATAGCCTAGTTGTACATTTGACAGAAAGGTGTCAAATATGCCGGTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAAGTATGCCAGTTAGA
414140 TGAAAGGTTAAATACC
66 TGAAAGGTTAAATACC
* * * * *
414156 TTTGAGTAAAATATTAAT-GCCTAGCTTTGCATTTGACCGAAAGGTTTCAAGTATGCCAATTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAAGTATGCCAGTTAGA
*
414220 TGAAATGTTAAATACC
66 TGAAAGGTTAAATACC
* *
414236 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGT-TAGTTATGCCAATTAG
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAAG-TATGCCAGTTAG
*
414300 ATGAAAGGTTAAATACT
65 ATGAAAGGTTAAATACC
* * * * * *
414317 TTTGAGTAAAAGATTAGTGGCCTAGCTGTGCATGTGATAGAAATGTGTCAATTATGCCAGTAAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAAGTATGCCAGTTAGA
414382 TGAAAGGTTAAATACC
66 TGAAAGGTTAAATACC
* * *
414398 TTTGAGTAAAAGATTAATGGCCTAGCTGTG-ATTTTGAAAAAAATGTGTCAAGTATGCCAGTTAG
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCA-TTTGACAGAAAGGTGTCAAGTATGCCAGTTAG
414462 ATGAAAGGTTAAATACC
65 ATGAAAGGTTAAATACC
* * *
414479 TTTGAGTAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGGTATCAAGTATGCCAATTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAAGTATGCCAGTTAGA
414544 TGAAAGGTTAAATACC
66 TGAAAGGTTAAATACC
* * *
414560 TTTGAGTAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGGTGTCAAATATGCCGGTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAAGTATGCCAGTTAGA
414625 TGAAAGGTTAAATACC
66 TGAAAGGTTAAATACC
* * *
414641 TTTGAGTAAAAGATTAAT-GCCTAGCTGTGCATTTGACCGAAAGGTGTCAAGTATGTCAATTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAAGTATGCCAGTTAGA
* *
414705 TGAAAGGATAAATACA
66 TGAAAGGTTAAATACC
* * * * *
414721 TTTGAGTAAAAGATTAATGGCCTAGCTATTCATTTGACAGAAAGGTGT-TAGTTATTCCAATTAG
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAAG-TATGCCAGTTAG
**
414785 ATGAAAGGTTAAATATG
65 ATGAAAGGTTAAATACC
* * * * ** * * * *
414802 TTTGAGTAAAAGATTAGTGGCCTAGATGCGAAAGTGATAGAAAGATGTCAATTATG-CAGTAAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAAGTATGCCAGTTAGA
414866 TGAAAG
66 TGAAAG
414872 AAGATTATTG
Statistics
Matches: 865, Mismatches: 86, Indels: 17
0.89 0.09 0.02
Matches are distributed among these distances:
80 160 0.18
81 702 0.81
82 3 0.00
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (81 bp):
TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAAGTATGCCAGTTAGA
TGAAAGGTTAAATACC
Found at i:414665 original size:404 final size:404
Alignment explanation
Indices: 413832--414826 Score: 1512
Period size: 404 Copynumber: 2.5 Consensus size: 404
413822 TGAATAATTA
* * *
413832 TTTGAATAAAAGATTAATAACCTAGCTGTGCATTTGACAGAAAGGTGTCAA-TTATGCCAGTTAG
1 TTTGAGTAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGGTGT-AAGTTATGCCAATTAG
* *
413896 ATGAAAGGTTAAATACCTTTGAATAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGT
65 ATGAAAGGTTAAATACATTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGT
* *
413961 CAAGTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGCTGTGCA
130 CAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCA
* * *
414026 TTTGACAGAAAGGTATCAAGTATGCTAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTA
195 TTTGAAAAAAAGGTATCAAGTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTA
* * **
414091 ATAGCCTAGTTGTACATTTGACAGAAAGGTGTCAAATATGCCGGTTAGATGAAAGGTTAAATACC
260 ATAGCCTAGCTGTACATTTGACAGAAAGGTATCAAATATGCCAATTAGATGAAAGGTTAAATACC
* * * * *
414156 TTTGAGTAAAATATTAATGCCTAGCTTTGCATTTGACCGAAAGGTTTCAAGTATGCCAATTAGAT
325 TTTGAGTAAAAGATTAATGCCTAGCTGTGCATTTGACAGAAAGGTGTCAAATATGCCAATTAGAT
*
414221 GAAATGTTAAATACC
390 GAAAGGTTAAATACC
* *
414236 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTTAGTTATGCCAATTAGA
1 TTTGAGTAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGGTGTAAGTTATGCCAATTAGA
* * * * *
414301 TGAAAGGTTAAATACTTTTGAGTAAAAGATTAGTGGCCTAGCTGTGCATGTGATAGAAATGTGTC
66 TGAAAGGTTAAATACATTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTC
*
414366 AATTATGCCAGTAAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTG-AT
131 AATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCA-
* *
414430 TTTGAAAAAAATGTGTCAAGTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTA
195 TTTGAAAAAAAGGTATCAAGTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTA
* *
414495 ATAGCCTAGCTGTGCATTTGACAGAAAGGTATCAAGTATGCCAATTAGATGAAAGGTTAAATACC
260 ATAGCCTAGCTGTACATTTGACAGAAAGGTATCAAATATGCCAATTAGATGAAAGGTTAAATACC
**
414560 TTTGAGTAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGGTGTCAAATATGCCGGTTAGA
325 TTTGAGTAAAAGATTAAT-GCCTAGCTGTGCATTTGACAGAAAGGTGTCAAATATGCCAATTAGA
414625 TGAAAGGTTAAATACC
389 TGAAAGGTTAAATACC
* *
414641 TTTGAGTAAAAGATTAAT-GCCTAGCTGTGCATTTGACCGAAAGGTGTCAAG-TATGTCAATTAG
1 TTTGAGTAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGGTGT-AAGTTATGCCAATTAG
* * *
414704 ATGAAAGGATAAATACATTTGAGTAAAAGATTAATGGCCTAGCTATTCATTTGACAGAAAGGTGT
65 ATGAAAGGTTAAATACATTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGT
* * * * ** *
414769 TAGTTATTCCAATTAGATGAAAGGTTAAATATGTTTGAGTAAAAGATTAGTGGCCTAG
130 CAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCTAG
414827 ATGCGAAAGT
Statistics
Matches: 535, Mismatches: 52, Indels: 8
0.90 0.09 0.01
Matches are distributed among these distances:
403 2 0.00
404 458 0.86
405 75 0.14
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.30
Consensus pattern (404 bp):
TTTGAGTAAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGGTGTAAGTTATGCCAATTAGA
TGAAAGGTTAAATACATTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTC
AATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCAT
TTGAAAAAAAGGTATCAAGTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAA
TAGCCTAGCTGTACATTTGACAGAAAGGTATCAAATATGCCAATTAGATGAAAGGTTAAATACCT
TTGAGTAAAAGATTAATGCCTAGCTGTGCATTTGACAGAAAGGTGTCAAATATGCCAATTAGATG
AAAGGTTAAATACC
Found at i:414747 original size:485 final size:484
Alignment explanation
Indices: 413832--414871 Score: 1753
Period size: 485 Copynumber: 2.1 Consensus size: 484
413822 TGAATAATTA
* * ** * * *
413832 TTTGAATAAAAGATTAATAACCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA
1 TTTGAGTAAAAGATTAGTGGCCTAGCTGTGCATGTGATAGAAA-GTGTCAATTATGCCAGTAAGA
* *
413897 TGAAAGGTTAAATACCTTTGAATAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTC
65 TGAAAGGTTAAATACCTTTGAATAAAAGATTAATGGCCTAGCTGTGCATTTGAAAAAAAGGTGTC
413962 AAGTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGCTGTGCAT
130 AAGTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGCTGTGCAT
* *
414027 TTGACAGAAAGGTATCAAGTATGCTAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAA
195 TTGACAGAAAGGTATCAAGTATGCCAATTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAA
*
414092 TAGCCTAGTTGTACATTTGACAGAAAGGTGTCAAATATGCCGGTTAGATGAAAGGTTAAATACCT
260 TAGCCTAGCTGTACATTTGACAGAAAGGTGTCAAATATGCCGGTTAGATGAAAGGTTAAATACCT
* * *
414157 TTGAGTAAAATATTAATGCCTAGCTTTGCATTTGACCGAAAGGTTTCAAGTATGCCAATTAGATG
325 TTGAGTAAAAGATTAATGCCTAGCTGTGCATTTGACCGAAAGGTGTCAAGTATGCCAATTAGATG
* * * *
414222 AAATGTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTTAG
390 AAAGGATAAATACATTTGAGTAAAAGATTAATGGCCTAGCTATGCATTTGACAGAAAGGTGTTAG
414287 TTATGCCAATTAGATGAAAGGTTAAATACT-
455 TTATGCCAATTAGATGAAAGGTTAAATA-TG
414317 TTTGAGTAAAAGATTAGTGGCCTAGCTGTGCATGTGATAGAAATGTGTCAATTATGCCAGTAAGA
1 TTTGAGTAAAAGATTAGTGGCCTAGCTGTGCATGTGATAGAAA-GTGTCAATTATGCCAGTAAGA
* *
414382 TGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTG-ATTTTGAAAAAAATGTGT
65 TGAAAGGTTAAATACCTTTGAATAAAAGATTAATGGCCTAGCTGTGCA-TTTGAAAAAAAGGTGT
414446 CAAGTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGCTGTGCA
129 CAAGTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGCTGTGCA
414511 TTTGACAGAAAGGTATCAAGTATGCCAATTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTA
194 TTTGACAGAAAGGTATCAAGTATGCCAATTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTA
*
414576 ATAGCCTAGCTGTGCATTTGACAGAAAGGTGTCAAATATGCCGGTTAGATGAAAGGTTAAATACC
259 ATAGCCTAGCTGTACATTTGACAGAAAGGTGTCAAATATGCCGGTTAGATGAAAGGTTAAATACC
*
414641 TTTGAGTAAAAGATTAATGCCTAGCTGTGCATTTGACCGAAAGGTGTCAAGTATGTCAATTAGAT
324 TTTGAGTAAAAGATTAATGCCTAGCTGTGCATTTGACCGAAAGGTGTCAAGTATGCCAATTAGAT
*
414706 GAAAGGATAAATACATTTGAGTAAAAGATTAATGGCCTAGCTATTCATTTGACAGAAAGGTGTTA
389 GAAAGGATAAATACATTTGAGTAAAAGATTAATGGCCTAGCTATGCATTTGACAGAAAGGTGTTA
*
414771 GTTATTCCAATTAGATGAAAGGTTAAATATG
454 GTTATGCCAATTAGATGAAAGGTTAAATATG
* * * *
414802 TTTGAGTAAAAGATTAGTGGCCTAGATGCGAAAGTGATAGAAAGATGTCAATTATG-CAGTAAGA
1 TTTGAGTAAAAGATTAGTGGCCTAGCTGTGCATGTGATAGAAAG-TGTCAATTATGCCAGTAAGA
414866 TGAAAG
65 TGAAAG
414872 AAGATTATTG
Statistics
Matches: 522, Mismatches: 30, Indels: 7
0.93 0.05 0.01
Matches are distributed among these distances:
484 17 0.03
485 505 0.97
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (484 bp):
TTTGAGTAAAAGATTAGTGGCCTAGCTGTGCATGTGATAGAAAGTGTCAATTATGCCAGTAAGAT
GAAAGGTTAAATACCTTTGAATAAAAGATTAATGGCCTAGCTGTGCATTTGAAAAAAAGGTGTCA
AGTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGCTGTGCATT
TGACAGAAAGGTATCAAGTATGCCAATTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAAT
AGCCTAGCTGTACATTTGACAGAAAGGTGTCAAATATGCCGGTTAGATGAAAGGTTAAATACCTT
TGAGTAAAAGATTAATGCCTAGCTGTGCATTTGACCGAAAGGTGTCAAGTATGCCAATTAGATGA
AAGGATAAATACATTTGAGTAAAAGATTAATGGCCTAGCTATGCATTTGACAGAAAGGTGTTAGT
TATGCCAATTAGATGAAAGGTTAAATATG
Found at i:416002 original size:20 final size:20
Alignment explanation
Indices: 415957--416005 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 20
415947 CAATGAACAT
415957 TATCGATATTGATTGAAGTAG
1 TATCGATATTGATTGAAG-AG
415978 TATCGATATTGATGTGAAG-G
1 TATCGATATTGAT-TGAAGAG
415998 TATCGATA
1 TATCGATA
416006 CCAAGAGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.33
21 13 0.48
22 5 0.19
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.37
Consensus pattern (20 bp):
TATCGATATTGATTGAAGAG
Found at i:421020 original size:20 final size:20
Alignment explanation
Indices: 420975--421046 Score: 69
Period size: 20 Copynumber: 3.5 Consensus size: 20
420965 CGATGAACAT
*
420975 TATCGATATTGAT-TGAAGTAG
1 TATCGATACTGATGTGAAG--G
420996 TATCGATACTGATGTGAAGG
1 TATCGATACTGATGTGAAGG
421016 TATCGATACCATGA-GT-AAGG
1 TATCGATA-C-TGATGTGAAGG
*
421036 TATCGACACTG
1 TATCGATACTG
421047 TAATTGAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
18 2 0.04
19 1 0.02
20 20 0.43
21 15 0.33
22 8 0.17
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (20 bp):
TATCGATACTGATGTGAAGG
Found at i:421612 original size:2 final size:2
Alignment explanation
Indices: 421605--421632 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
421595 GGTAAATACA
421605 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
421633 TATGAATATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:421942 original size:81 final size:80
Alignment explanation
Indices: 421724--422467 Score: 1001
Period size: 81 Copynumber: 9.2 Consensus size: 80
421714 CTAGCTTTGC
* * * * **
421724 AAAAGATTAATAGCCTAGTTGTACATTTGACAGAAAGGTGTCAAATATGCCGGTTAGATGAAAGG
1 AAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGT-AAGTATGCCAATTAGATGAAAGG
421789 TTAAATACCTTTGAGT
65 TTAAATACCTTTGAGT
* * * * *
421805 AAAATATTAAT-GCCTAGCTTTGCATTTGACCGAAAGGTTTCAAGTATGCCAATTAGATGAAATG
1 AAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGT-AAGTATGCCAATTAGATGAAAGG
421869 TTAAATACCTTTGAGT
65 TTAAATACCTTTGAGT
*
421885 AAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTTAGTTATGCCAATTAGATGAAAGG
1 AAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTAAG-TATGCCAATTAGATGAAAGG
*
421950 TTAAATACTTTTGAGT
65 TTAAATACCTTTGAGT
* * * * * * *
421966 AAAAGATTAGTGGCCTAGCTGTGCATGTGATAGAAATGTGTCAATTATGCCAGTAAGATGAAAGG
1 AAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGT-AAGTATGCCAATTAGATGAAAGG
422031 TTAAATACCTTTGAGT
65 TTAAATACCTTTGAGT
* * * *
422047 AAAAGATTAATGGCCTAGCTGTG-ATTTTGAAAAAAATGTGTCAAGTATGCCAGTTAGATGAAAG
1 AAAAGATTAATGGCCTAGCTGTGCA-TTTGACAGAAAGGTGT-AAGTATGCCAATTAGATGAAAG
422111 GTTAAATACCTTTGAGT
64 GTTAAATACCTTTGAGT
* *
422128 AAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGGTATCAAGTATGCCAATTAGATGAAAGG
1 AAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGT-AAGTATGCCAATTAGATGAAAGG
422193 TTAAATACCTTTGAGT
65 TTAAATACCTTTGAGT
* * **
422209 AAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGGTGTCAAATATGCCGGTTAGATGAAAGG
1 AAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGT-AAGTATGCCAATTAGATGAAAGG
422274 TTAAATACCTTTGAGT
65 TTAAATACCTTTGAGT
* *
422290 AAAAGATTAAT-GCCTAGCTGTGCATTTGACCGAAAGGTGTCAAGTATGTCAATTAGATGAAAGG
1 AAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGT-AAGTATGCCAATTAGATGAAAGG
* *
422354 ATAAATACATTTGAGT
65 TTAAATACCTTTGAGT
* * * *
422370 -AAAGATTAATGGCCTAGCTATTCATTTGACAGAAAGGTGTTAGTTATTCCAATTAGATGAAAGG
1 AAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTAAG-TATGCCAATTAGATGAAAGG
**
422434 TTAAATATGTTTGAGT
65 TTAAATACCTTTGAGT
*
422450 AAAAGATTAGTGGCCTAG
1 AAAAGATTAATGGCCTAG
422468 ATGCGAAAGT
Statistics
Matches: 596, Mismatches: 59, Indels: 16
0.89 0.09 0.02
Matches are distributed among these distances:
79 12 0.02
80 192 0.32
81 390 0.65
82 2 0.00
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (80 bp):
AAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTAAGTATGCCAATTAGATGAAAGGT
TAAATACCTTTGAGT
Found at i:422151 original size:243 final size:242
Alignment explanation
Indices: 421724--422512 Score: 1138
Period size: 243 Copynumber: 3.3 Consensus size: 242
421714 CTAGCTTTGC
* * * * *
421724 AAAAGATTAATAGCCTAGTTGTACATTTGACAGAAAGGTGTCAAATATGCCGGTTAGATGAAAGG
1 AAAAGATTAATAGCCTAGCTGTGCATGTGACAGAAAGGTGTCAAATATGCCAGTAAGATGAAAGG
* * *
421789 TTAAATACCTTTGAGTAAAATATTAATGCCTAGCTTTGCATTTGACCGAAAGGTTTCAAGTATGC
66 TTAAATACCTTTGAGTAAAAGATTAATGCCTAGCTGTGCATTTGACCGAAAGGTGTCAAGTATGC
*
421854 CAATTAGATGAAATGTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGA
131 CAATTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGA
421919 AAGGTGTTAGTTATGCCAATTAGATGAAAGGTTAAATACTTTTGAGT
196 AAGGTGTTAGTTATGCCAATTAGATGAAAGGTTAAATACTTTTGAGT
* * * * *
421966 AAAAGATTAGTGGCCTAGCTGTGCATGTGATAGAAATGTGTCAATTATGCCAGTAAGATGAAAGG
1 AAAAGATTAATAGCCTAGCTGTGCATGTGACAGAAAGGTGTCAAATATGCCAGTAAGATGAAAGG
*** *
422031 TTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTG-ATTTTGAAAAAAATGTGTCAAGTAT
66 TTAAATACCTTTGAGTAAAAGATTAAT-GCCTAGCTGTGCA-TTTGACCGAAAGGTGTCAAGTAT
* *
422095 GCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGCTGTGCATTTGACA
129 GCCAATTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACA
* * *
422160 GAAAGGTATCAAG-TATGCCAATTAGATGAAAGGTTAAATACCTTTGAGT
194 GAAAGGTGT-TAGTTATGCCAATTAGATGAAAGGTTAAATACTTTTGAGT
* * *
422209 AAAAGATTAATAGCCTAGCTGTGCATTTGACAGAAAGGTGTCAAATATGCCGGTTAGATGAAAGG
1 AAAAGATTAATAGCCTAGCTGTGCATGTGACAGAAAGGTGTCAAATATGCCAGTAAGATGAAAGG
*
422274 TTAAATACCTTTGAGTAAAAGATTAATGCCTAGCTGTGCATTTGACCGAAAGGTGTCAAGTATGT
66 TTAAATACCTTTGAGTAAAAGATTAATGCCTAGCTGTGCATTTGACCGAAAGGTGTCAAGTATGC
* * * *
422339 CAATTAGATGAAAGGATAAATACATTTGAGT-AAAGATTAATGGCCTAGCTATTCATTTGACAGA
131 CAATTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGA
*
422403 AAGGTGTTAGTTATTCCAATTAGATGAAAGGTTAAATA-TGTTTGAGT
196 AAGGTGTTAGTTATGCCAATTAGATGAAAGGTTAAATACT-TTTGAGT
* * * * * * * * *
422450 AAAAGATTAGTGGCCTAGATGCGAAAGTGATAGAAAGATGTCAATTATG-CAGTAAGATGAAAG
1 AAAAGATTAATAGCCTAGCTGTGCATGTGACAGAAAGGTGTCAAATATGCCAGTAAGATGAAAG
422513 AAGATTATTG
Statistics
Matches: 483, Mismatches: 58, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
240 14 0.03
241 108 0.22
242 141 0.29
243 218 0.45
244 2 0.00
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (242 bp):
AAAAGATTAATAGCCTAGCTGTGCATGTGACAGAAAGGTGTCAAATATGCCAGTAAGATGAAAGG
TTAAATACCTTTGAGTAAAAGATTAATGCCTAGCTGTGCATTTGACCGAAAGGTGTCAAGTATGC
CAATTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGA
AAGGTGTTAGTTATGCCAATTAGATGAAAGGTTAAATACTTTTGAGT
Found at i:423641 original size:20 final size:20
Alignment explanation
Indices: 423596--423644 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 20
423586 CAATGAACAT
423596 TATCGATATTGATTGAAGTAG
1 TATCGATATTGATTGAAG-AG
423617 TATCGATATTGATGTGAAG-G
1 TATCGATATTGAT-TGAAGAG
423637 TATCGATA
1 TATCGATA
423645 CCAAGAGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.33
21 13 0.48
22 5 0.19
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.37
Consensus pattern (20 bp):
TATCGATATTGATTGAAGAG
Found at i:428658 original size:20 final size:20
Alignment explanation
Indices: 428613--428684 Score: 69
Period size: 20 Copynumber: 3.5 Consensus size: 20
428603 CGATGAACAT
*
428613 TATCGATATTGAT-TGAAGTAG
1 TATCGATACTGATGTGAAG--G
428634 TATCGATACTGATGTGAAGG
1 TATCGATACTGATGTGAAGG
428654 TATCGATACCATGA-GT-AAGG
1 TATCGATA-C-TGATGTGAAGG
*
428674 TATCGACACTG
1 TATCGATACTG
428685 TAATTGAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
18 2 0.04
19 1 0.02
20 20 0.43
21 15 0.33
22 8 0.17
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (20 bp):
TATCGATACTGATGTGAAGG
Found at i:429253 original size:2 final size:2
Alignment explanation
Indices: 429246--429271 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
429236 GGGAAATACA
429246 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
429272 TATGAATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:429587 original size:24 final size:23
Alignment explanation
Indices: 429522--429597 Score: 71
Period size: 24 Copynumber: 3.2 Consensus size: 23
429512 CCTTCAGGAT
*
429522 AATTCTACGTGGTTCTTCGGGACA
1 AATTCTACGTGG-CCTTCGGGACA
* **
429546 AATTCTATGTTATCCTTCGGGACA
1 AATTCTACG-TGGCCTTCGGGACA
* *
429570 TATTCTACGTGGCACTTCGGTACA
1 AATTCTACGTGGC-CTTCGGGACA
429594 AATT
1 AATT
429598 ATGTGAGCAG
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
23 2 0.05
24 37 0.93
25 1 0.03
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.36
Consensus pattern (23 bp):
AATTCTACGTGGCCTTCGGGACA
Found at i:439211 original size:20 final size:21
Alignment explanation
Indices: 439166--439215 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
439156 CAATGAACAT
*
439166 TATCGATATTGATTGAAGTAG
1 TATCGATACTGATTGAAGTAG
439187 TATCGATACTGATGTGAA-T-G
1 TATCGATACTGAT-TGAAGTAG
439207 TATCGATAC
1 TATCGATAC
439216 CAAGAGTAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 10 0.37
21 13 0.48
22 4 0.15
ACGTcount: A:0.32, C:0.10, G:0.22, T:0.36
Consensus pattern (21 bp):
TATCGATACTGATTGAAGTAG
Found at i:441827 original size:31 final size:31
Alignment explanation
Indices: 441790--441863 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
441780 AAGAGTCAAG
* *
441790 GGTTACCTATGTCTTTCAAGACATATGGACA
1 GGTTACCTATGTCCTTCAAGACATATCGACA
* ** *
441821 GTTTACCTATGTCCTTCGGGATATATCGACA
1 GGTTACCTATGTCCTTCAAGACATATCGACA
441852 GGTTACCTATGT
1 GGTTACCTATGT
441864 TATTCGGAAC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.35
Consensus pattern (31 bp):
GGTTACCTATGTCCTTCAAGACATATCGACA
Found at i:441870 original size:31 final size:30
Alignment explanation
Indices: 441790--441877 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 30
441780 AAGAGTCAAG
** *
441790 GGTTACCTATGTCTTTCAAGACATATGGACA
1 GGTTACCTATGT-TTTCGGGACATATCGACA
* * *
441821 GTTTACCTATGTCCTTCGGGATATATCGACA
1 GGTTACCTATGT-TTTCGGGACATATCGACA
*
441852 GGTTACCTATGTTATTCGGAACATAT
1 GGTTACCTATGTT-TTCGGGACATAT
441878 GGATAGGTCC
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (30 bp):
GGTTACCTATGTTTTCGGGACATATCGACA
Found at i:442242 original size:8 final size:8
Alignment explanation
Indices: 442229--442864 Score: 833
Period size: 8 Copynumber: 80.8 Consensus size: 8
442219 GTGTGTGTGT
442229 ATGTATGC
1 ATGTATGC
442237 ATGTATGC
1 ATGTATGC
442245 ATGTATGC
1 ATGTATGC
442253 ATGTATGC
1 ATGTATGC
442261 ATGTATGC
1 ATGTATGC
442269 ATGTATGC
1 ATGTATGC
442277 ATGTATGC
1 ATGTATGC
442285 ATGTATGC
1 ATGTATGC
442293 ATGTATGC
1 ATGTATGC
*
442301 ATGTATGT
1 ATGTATGC
*
442309 ATGTATGT
1 ATGTATGC
442317 ATGTATG-
1 ATGTATGC
*
442324 -TATAT--
1 ATGTATGC
*
442329 ATGTATGT
1 ATGTATGC
442337 ATGTATGC
1 ATGTATGC
442345 ATGTATGC
1 ATGTATGC
442353 ATGTATGC
1 ATGTATGC
442361 ATGTATGC
1 ATGTATGC
442369 ATGTATGC
1 ATGTATGC
442377 ATGTATGC
1 ATGTATGC
442385 ATGTATGC
1 ATGTATGC
*
442393 ATGCATGC
1 ATGTATGC
*
442401 ATGCATGC
1 ATGTATGC
442409 ATGTATGC
1 ATGTATGC
* *
442417 ATGCATGT
1 ATGTATGC
*
442425 ATGCAT--
1 ATGTATGC
*
442431 ATGTATGT
1 ATGTATGC
*
442439 ATGTATGT
1 ATGTATGC
442447 ATGTATGC
1 ATGTATGC
442455 ATGTATGC
1 ATGTATGC
442463 ATGTATGC
1 ATGTATGC
*
442471 A--TATGT
1 ATGTATGC
*
442477 ATGTATGT
1 ATGTATGC
*
442485 ATGTATGT
1 ATGTATGC
442493 ATGTATGC
1 ATGTATGC
442501 A--TATGC
1 ATGTATGC
*
442507 ATATATGC
1 ATGTATGC
442515 ATGTATGC
1 ATGTATGC
442523 ATGTATGC
1 ATGTATGC
*
442531 ATGTATGT
1 ATGTATGC
*
442539 ATGTATGT
1 ATGTATGC
*
442547 ATGTATGT
1 ATGTATGC
*
442555 ATGTATGT
1 ATGTATGC
*
442563 ATGTATGT
1 ATGTATGC
*
442571 ATGTATGT
1 ATGTATGC
*
442579 ATGTATGT
1 ATGTATGC
*
442587 ATGTATGT
1 ATGTATGC
*
442595 ATGTATGT
1 ATGTATGC
*
442603 ATGTATGT
1 ATGTATGC
*
442611 ATGTATGT
1 ATGTATGC
*
442619 ATGTATGT
1 ATGTATGC
*
442627 ATGTATGT
1 ATGTATGC
*
442635 ATGTATGT
1 ATGTATGC
442643 ATGTATGC
1 ATGTATGC
*
442651 ATGCATGC
1 ATGTATGC
442659 ATGTATGC
1 ATGTATGC
*
442667 ATGCATGC
1 ATGTATGC
*
442675 ATGTATGT
1 ATGTATGC
442683 ATGTATGC
1 ATGTATGC
*
442691 ATGCATGC
1 ATGTATGC
* *
442699 TTGCATGC
1 ATGTATGC
442707 ATGTATGC
1 ATGTATGC
*
442715 ATGCATGC
1 ATGTATGC
* *
442723 ATGCATGT
1 ATGTATGC
442731 ATGTATGC
1 ATGTATGC
442739 ATGTATGC
1 ATGTATGC
442747 ATGTATGC
1 ATGTATGC
442755 ATGTATGC
1 ATGTATGC
*
442763 ATGCATGC
1 ATGTATGC
442771 ATGTATGC
1 ATGTATGC
*
442779 ATGCATGC
1 ATGTATGC
442787 ATGTATGC
1 ATGTATGC
*
442795 ATGCATGC
1 ATGTATGC
442803 ATGTATGC
1 ATGTATGC
442811 ATGTATGC
1 ATGTATGC
442819 ATGTATGC
1 ATGTATGC
442827 ATGTATGC
1 ATGTATGC
442835 ATGTATGC
1 ATGTATGC
442843 ATGTATGC
1 ATGTATGC
442851 ATGTATGC
1 ATGTATGC
442859 ATGTAT
1 ATGTAT
442865 TTTTTATATG
Statistics
Matches: 584, Mismatches: 35, Indels: 18
0.92 0.05 0.03
Matches are distributed among these distances:
6 24 0.04
8 560 0.96
ACGTcount: A:0.25, C:0.10, G:0.24, T:0.40
Consensus pattern (8 bp):
ATGTATGC
Found at i:445640 original size:8 final size:8
Alignment explanation
Indices: 445627--446086 Score: 581
Period size: 8 Copynumber: 58.8 Consensus size: 8
445617 TACTTTTCAT
445627 ATACATGC
1 ATACATGC
445635 ATACATGC
1 ATACATGC
445643 ATACATGC
1 ATACATGC
445651 ATACATGC
1 ATACATGC
*
445659 ATGCATGC
1 ATACATGC
445667 ATACATGC
1 ATACATGC
445675 ATACATGC
1 ATACATGC
445683 ATACATGC
1 ATACATGC
*
445691 ATGCATGC
1 ATACATGC
445699 ATACATGC
1 ATACATGC
*
445707 ATACATAC
1 ATACATGC
**
445715 ATACATAT
1 ATACATGC
445723 ATACATGC
1 ATACATGC
*
445731 ATACATAC
1 ATACATGC
*
445739 ATACATAC
1 ATACATGC
*
445747 ATACATAC
1 ATACATGC
*
445755 ATACATAC
1 ATACATGC
445763 ATACATGC
1 ATACATGC
445771 AT--A--C
1 ATACATGC
445775 ATACATGC
1 ATACATGC
445783 ATACATGC
1 ATACATGC
445791 ATACATGC
1 ATACATGC
*
445799 ATATATGC
1 ATACATGC
445807 AT--ATGC
1 ATACATGC
*
445813 ATACATAC
1 ATACATGC
*
445821 ATACATAC
1 ATACATGC
*
445829 ATATATATGC
1 --ATACATGC
445839 ATACATGC
1 ATACATGC
445847 ATACATGC
1 ATACATGC
*
445855 ATACATAC
1 ATACATGC
*
445863 ATACATAC
1 ATACATGC
445871 ATACATATGC
1 ATAC--ATGC
445881 ATACATGC
1 ATACATGC
445889 ATACATGC
1 ATACATGC
445897 ATACATGC
1 ATACATGC
* *
445905 ATGCATAC
1 ATACATGC
*
445913 ATGCATGC
1 ATACATGC
445921 ATACATGC
1 ATACATGC
445929 ATACATGC
1 ATACATGC
445937 ATACATG-
1 ATACATGC
445944 ---CATGC
1 ATACATGC
445949 ATACATGC
1 ATACATGC
445957 ATACATGC
1 ATACATGC
445965 ATACATGC
1 ATACATGC
445973 ATACATGC
1 ATACATGC
*
445981 ATACATAC
1 ATACATGC
445989 ATACATAG-
1 ATACAT-GC
*
445997 ATACATAC
1 ATACATGC
*
446005 ATACATAC
1 ATACATGC
446013 ATACATG-
1 ATACATGC
446020 ---CATGC
1 ATACATGC
446025 ATACATGC
1 ATACATGC
446033 ATACATGC
1 ATACATGC
446041 ATACATGC
1 ATACATGC
446049 ATACATGC
1 ATACATGC
446057 ATACATGC
1 ATACATGC
446065 ATACATGC
1 ATACATGC
446073 ATACATGC
1 ATACATGC
446081 ATACAT
1 ATACAT
446087 ACACACACAC
Statistics
Matches: 407, Mismatches: 25, Indels: 40
0.86 0.05 0.08
Matches are distributed among these distances:
4 11 0.03
6 8 0.02
8 375 0.92
10 13 0.03
ACGTcount: A:0.40, C:0.24, G:0.10, T:0.26
Consensus pattern (8 bp):
ATACATGC
Found at i:446486 original size:31 final size:31
Alignment explanation
Indices: 446429--446524 Score: 95
Period size: 31 Copynumber: 3.1 Consensus size: 31
446419 GTCCCAAAGG
* *
446429 ACCTATCCATATGTTCCGAATA-ACATAGGTA
1 ACCTATCCATATATCCCGAA-AGACATAGGTA
* * *
446460 ACCTGTCGATATATCCCGAAGGACATAGGTA
1 ACCTATCCATATATCCCGAAAGACATAGGTA
* * **
446491 AACTATCCATATGTCTTGAAAGACATAGGTA
1 ACCTATCCATATATCCCGAAAGACATAGGTA
446522 ACC
1 ACC
446525 CTCGACTCTT
Statistics
Matches: 51, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (31 bp):
ACCTATCCATATATCCCGAAAGACATAGGTA
Found at i:449125 original size:20 final size:21
Alignment explanation
Indices: 449102--449151 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
449092 CTTACTCTTG
449102 GTATCGATAC-A-TTCACATCA
1 GTATCGATACTACTTCA-ATCA
449122 GTATCGATACTACTTCAATCA
1 GTATCGATACTACTTCAATCA
*
449143 ATATCGATA
1 GTATCGATA
449152 ATGTTCATCG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 10 0.37
21 13 0.48
22 4 0.15
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.32
Consensus pattern (21 bp):
GTATCGATACTACTTCAATCA
Found at i:457370 original size:28 final size:26
Alignment explanation
Indices: 457339--457394 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 26
457329 AAACGAGTTT
457339 ACAAAAGATTCAATAAATGAGCTTATAA
1 ACAAAA-A-TCAATAAATGAGCTTATAA
* *
457367 AC--AAATCGATAAATGAGCTTATAC
1 ACAAAAATCAATAAATGAGCTTATAA
457391 ACAA
1 ACAA
457395 CTCAATAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
24 19 0.79
25 1 0.04
26 2 0.08
28 2 0.08
ACGTcount: A:0.52, C:0.14, G:0.11, T:0.23
Consensus pattern (26 bp):
ACAAAAATCAATAAATGAGCTTATAA
Found at i:457378 original size:24 final size:24
Alignment explanation
Indices: 457348--457403 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
457338 TACAAAAGAT
457348 TCAATAAATGAGCTTATAAACAAA
1 TCAATAAATGAGCTTATAAACAAA
* * *
457372 TCGATAAATGAGCTTATACACAAC
1 TCAATAAATGAGCTTATAAACAAA
457396 TCAATAAA
1 TCAATAAA
457404 CAAGCATGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.50, C:0.16, G:0.09, T:0.25
Consensus pattern (24 bp):
TCAATAAATGAGCTTATAAACAAA
Found at i:457664 original size:17 final size:16
Alignment explanation
Indices: 457621--457666 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
457611 ATGTGTTGTT
* *
457621 AAAAGAGATGTTACAA
1 AAAAAAGATATTACAA
457637 AAAAAAGATATTACAA
1 AAAAAAGATATTACAA
457653 AAAAAAGTATATTA
1 AAAAAAG-ATATTA
457667 TGAGAAGAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 21 0.78
17 6 0.22
ACGTcount: A:0.63, C:0.04, G:0.11, T:0.22
Consensus pattern (16 bp):
AAAAAAGATATTACAA
Found at i:463980 original size:21 final size:21
Alignment explanation
Indices: 463954--464003 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
463944 GTACGTTGAT
* *
463954 GACATGCTCGTTGTAGGCTCA
1 GACATGCACGTTGCAGGCTCA
463975 GACATGCACGTTGCAGGCTCA
1 GACATGCACGTTGCAGGCTCA
463996 GACATGCA
1 GACATGCA
464004 AGAGATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.24, C:0.26, G:0.28, T:0.22
Consensus pattern (21 bp):
GACATGCACGTTGCAGGCTCA
Found at i:465071 original size:21 final size:20
Alignment explanation
Indices: 465047--465110 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
465037 AACTTTGAAA
465047 AAATGATTTTCAAAGTTTGGT
1 AAATG-TTTTCAAAGTTTGGT
*
465068 AAATG-TTTC----TTT-GA
1 AAATGTTTTCAAAGTTTGGT
465082 AAATGGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
465103 AAATGTTT
1 AAATGTTT
465111 CTTTGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 4 0.12
16 4 0.12
19 4 0.12
20 7 0.21
21 10 0.29
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (20 bp):
AAATGTTTTCAAAGTTTGGT
Found at i:465085 original size:35 final size:36
Alignment explanation
Indices: 465039--465160 Score: 176
Period size: 35 Copynumber: 3.4 Consensus size: 36
465029 TGGTAACCAA
465039 CTTTGAAAAAATGATTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGATTTTCAAAGTTTGGTAAATGTTT
*
465076 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
* *
465111 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GATTTTCAAAGTTTGGTAAATGTTT
*
465148 -GTTGAAAAATGAT
1 CTTTGAAAAATGAT
465161 AATGGGATAA
Statistics
Matches: 78, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
35 36 0.46
36 14 0.18
37 28 0.36
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
Found at i:468626 original size:21 final size:21
Alignment explanation
Indices: 468600--468649 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
468590 GTACGTTGAT
* *
468600 GACATGCTCGTTGTAGGCTCA
1 GACATGCACGTTGCAGGCTCA
468621 GACATGCACGTTGCAGGCTCA
1 GACATGCACGTTGCAGGCTCA
468642 GACATGCA
1 GACATGCA
468650 AGAGATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.24, C:0.26, G:0.28, T:0.22
Consensus pattern (21 bp):
GACATGCACGTTGCAGGCTCA
Found at i:469717 original size:21 final size:20
Alignment explanation
Indices: 469693--469756 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
469683 AACTTTGAAA
469693 AAATGATTTTCAAAGTTTGGT
1 AAATG-TTTTCAAAGTTTGGT
*
469714 AAATG-TTTC----TTT-GA
1 AAATGTTTTCAAAGTTTGGT
469728 AAATGGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
469749 AAATGTTT
1 AAATGTTT
469757 CTTTGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 4 0.12
16 4 0.12
19 4 0.12
20 7 0.21
21 10 0.29
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (20 bp):
AAATGTTTTCAAAGTTTGGT
Found at i:469731 original size:35 final size:36
Alignment explanation
Indices: 469685--469806 Score: 176
Period size: 35 Copynumber: 3.4 Consensus size: 36
469675 TGGTAACCAA
469685 CTTTGAAAAAATGATTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGATTTTCAAAGTTTGGTAAATGTTT
*
469722 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
* *
469757 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GATTTTCAAAGTTTGGTAAATGTTT
*
469794 -GTTGAAAAATGAT
1 CTTTGAAAAATGAT
469807 AATGGGATAA
Statistics
Matches: 78, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
35 36 0.46
36 14 0.18
37 28 0.36
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
Found at i:476855 original size:15 final size:15
Alignment explanation
Indices: 476835--476863 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
476825 GATCCGGATG
476835 TTCCGGGTACCCGAT
1 TTCCGGGTACCCGAT
476850 TTCCGGGTACCCGA
1 TTCCGGGTACCCGA
476864 AAATCCGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.34, G:0.28, T:0.24
Consensus pattern (15 bp):
TTCCGGGTACCCGAT
Found at i:482852 original size:32 final size:31
Alignment explanation
Indices: 482816--482892 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
482806 TGGGGCCATG
*
482816 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** * **
482848 GGGCCTACCCGATAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
482879 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
482893 GTCACATTAG
Statistics
Matches: 35, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
31 23 0.66
32 12 0.34
ACGTcount: A:0.27, C:0.31, G:0.26, T:0.16
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:493546 original size:17 final size:19
Alignment explanation
Indices: 493513--493547 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
493503 TCAACATCTC
493513 GATTGCCCTCTTCAAACTA
1 GATTGCCCTCTTCAAACTA
493532 GATT-CCCTC-TCAAACT
1 GATTGCCCTCTTCAAACT
493548 GAACAAAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 5 0.31
19 4 0.25
ACGTcount: A:0.26, C:0.34, G:0.09, T:0.31
Consensus pattern (19 bp):
GATTGCCCTCTTCAAACTA
Found at i:493741 original size:14 final size:14
Alignment explanation
Indices: 493724--493750 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
493714 TTCCCTTTTA
493724 ACTTTTCTCTCTCT
1 ACTTTTCTCTCTCT
493738 ACTTTTCTCTCTC
1 ACTTTTCTCTCTC
493751 CCATTTTTCC
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:0.07, C:0.37, G:0.00, T:0.56
Consensus pattern (14 bp):
ACTTTTCTCTCTCT
Found at i:496446 original size:56 final size:56
Alignment explanation
Indices: 496273--496492 Score: 291
Period size: 56 Copynumber: 3.9 Consensus size: 56
496263 ATTTTTAGCT
* * * *
496273 AAATCTATGACTGGTATCTCTCTATTTACAGCAGTATCAAATAGCTGTGAAAAGAGG
1 AAAT-TATGGCTGGTATCTCTCTATTTACAGCAGTATAAAATAGCTATGGAAAGAGG
* * *
496330 AAATTATGGCTGGTAGCTCTCTATTTACAGAAGTAT-AAATAGCTATGGAAAGACG
1 AAATTATGGCTGGTATCTCTCTATTTACAGCAGTATAAAATAGCTATGGAAAGAGG
* *
496385 AAATTATGGCTGGTATCTCTTTCA-TTCCAGCAGTATAAAATAGCTATGGAAAGAGG
1 AAATTATGGCTGGTATCTCTCT-ATTTACAGCAGTATAAAATAGCTATGGAAAGAGG
* * * *
496441 AAATTATGGCTAGCATCTTTCTATTTACAGCAGTATAAAATAGTTATGGAAA
1 AAATTATGGCTGGTATCTCTCTATTTACAGCAGTATAAAATAGCTATGGAAA
496493 AAACTATATA
Statistics
Matches: 143, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
55 47 0.33
56 92 0.64
57 4 0.03
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.31
Consensus pattern (56 bp):
AAATTATGGCTGGTATCTCTCTATTTACAGCAGTATAAAATAGCTATGGAAAGAGG
Found at i:496477 original size:111 final size:113
Alignment explanation
Indices: 496273--496492 Score: 302
Period size: 111 Copynumber: 2.0 Consensus size: 113
496263 ATTTTTAGCT
* *
496273 AAATCTATGACTGGTATCTCTCTATTTACAGCAGTATCAAATAGCTGTGAAAAGAGGAAATTATG
1 AAATCTATGACTGGTATCTCTCTATTTACAGCAGTATAAAATAGCTATGAAAAGAGGAAATTATG
* *
496338 GCTGGTAGCTCTCTATTTACAGAAGTAT-AAATAGCTATGGAAAGACG
66 GCTAGCAGCTCTCTATTTACAGAAGTATAAAATAGCTATGGAAAGACG
* * * *
496385 AAAT-TATGGCTGGTATCTCTTTCA-TTCCAGCAGTATAAAATAGCTATGGAAAGAGGAAATTAT
1 AAATCTATGACTGGTATCTCTCT-ATTTACAGCAGTATAAAATAGCTATGAAAAGAGGAAATTAT
* * * *
496448 GGCTAGCATCTTTCTATTTACAGCAGTATAAAATAGTTATGGAAA
65 GGCTAGCAGCTCTCTATTTACAGAAGTATAAAATAGCTATGGAAA
496493 AAACTATATA
Statistics
Matches: 94, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
111 75 0.80
112 19 0.20
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.31
Consensus pattern (113 bp):
AAATCTATGACTGGTATCTCTCTATTTACAGCAGTATAAAATAGCTATGAAAAGAGGAAATTATG
GCTAGCAGCTCTCTATTTACAGAAGTATAAAATAGCTATGGAAAGACG
Found at i:507729 original size:18 final size:18
Alignment explanation
Indices: 507706--507756 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
507696 AAAGGATAAT
507706 GATGGTCCTGGGGGTAAA
1 GATGGTCCTGGGGGTAAA
507724 GATGGTCCTGGGGGTAAA
1 GATGGTCCTGGGGGTAAA
*
507742 GATGGTCCAGGGGGT
1 GATGGTCCTGGGGGT
507757 TCGAAGGGGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.20, C:0.12, G:0.47, T:0.22
Consensus pattern (18 bp):
GATGGTCCTGGGGGTAAA
Found at i:514670 original size:19 final size:20
Alignment explanation
Indices: 514620--514673 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
514610 TCAGAGTCTT
* *
514620 CTGTTTTATTAAAGTGTTTA
1 CTGTTCTATTAAAGTATTTA
*
514640 TTGTTCTATTAAAGTATTTA
1 CTGTTCTATTAAAGTATTTA
*
514660 CT-TTCTTTTAAAGT
1 CTGTTCTATTAAAGT
514674 CTTCAAGACT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 11 0.38
20 18 0.62
ACGTcount: A:0.26, C:0.07, G:0.11, T:0.56
Consensus pattern (20 bp):
CTGTTCTATTAAAGTATTTA
Found at i:524617 original size:383 final size:383
Alignment explanation
Indices: 523910--524679 Score: 1495
Period size: 383 Copynumber: 2.0 Consensus size: 383
523900 TTGATATTCC
*
523910 CTTATGTATTGAGAGAACTCGTTTGAGCTATATTCTTCTCTGTTGTCTGTGCGCAAGCAATATAT
1 CTTATGTATTGAGAGAACTCGTTTGAGCTATATTCTTCTCCGTTGTCTGTGCGCAAGCAATATAT
*
523975 CTTCTTTTCCACTTCTCATTCAGTTAACTCTTTGAACTCTTTAAACTTTGAGAATGTGTCAGATT
66 CTTCTTTCCCACTTCTCATTCAGTTAACTCTTTGAACTCTTTAAACTTTGAGAATGTGTCAGATT
* *
524040 TTTCTTTCATAAAGAAAACCCACATATACCTGGAGAAGTCATCAATGAATGTTACCATGTACCGC
131 TTTCTTTCATAAAGAAAACCCACATATACCTGGAGAAGTCATCAATGAATGTTACCATATACCAC
524105 ATACTGCTAATTGCTTAACCGGTTCGAACACATTAGAGTGAACTAACTCTAACGGTTCTTTTACT
196 ATACTGCTAATTGCTTAACCGGTTCGAACACATTAGAGTGAACTAACTCTAACGGTTCTTTTACT
524170 TTAAACTTTGACTCGTCATATGGTAATTGGTGTGCTTTACCATACTGGAATCCCGCAGAGATCAT
261 TTAAACTTTGACTCGTCATATGGTAATTGGTGTGCTTTACCATACTGGAATCCCGCAGAGATCAT
524235 GTATGTTCTCACGTCTAGTTGAGGAAGCCCCTTAAGCATCGACTTCTTCACCATCACA
326 GTATGTTCTCACGTCTAGTTGAGGAAGCCCCTTAAGCATCGACTTCTTCACCATCACA
524293 CTTATGTATTGAGAGAACTCGTTTGAGCTATATTCTTCTCCGTTGTCTGTGCGCAAGCAATATAT
1 CTTATGTATTGAGAGAACTCGTTTGAGCTATATTCTTCTCCGTTGTCTGTGCGCAAGCAATATAT
524358 CTTCTTTCCCACTTCTCATTCAGTTAACTCTTTGAACTCTTTAAACTTTGAGAATGTGTCAGATT
66 CTTCTTTCCCACTTCTCATTCAGTTAACTCTTTGAACTCTTTAAACTTTGAGAATGTGTCAGATT
524423 TTTCTTTCATAAAGAAAACCCACATATACCTGGAGAAGTCATCAATGAATGTTACCATATACCAC
131 TTTCTTTCATAAAGAAAACCCACATATACCTGGAGAAGTCATCAATGAATGTTACCATATACCAC
*
524488 ATACTGCTAATTGCTTAACCGGTTCGAACACATTAGAGTGAACTAACTCTAACGGTTCTTTTGCT
196 ATACTGCTAATTGCTTAACCGGTTCGAACACATTAGAGTGAACTAACTCTAACGGTTCTTTTACT
524553 TTAAACTTTGACTCGTCATATGGTAATTGGTGTGCTTTACCATACTGGAATCCCGCAGAGATCAT
261 TTAAACTTTGACTCGTCATATGGTAATTGGTGTGCTTTACCATACTGGAATCCCGCAGAGATCAT
524618 GTATGTTCTCACGTCTAGTTGAGGAAGCCCCTTAAGCATCGACTTCTTCACCATCACA
326 GTATGTTCTCACGTCTAGTTGAGGAAGCCCCTTAAGCATCGACTTCTTCACCATCACA
524676 CTTA
1 CTTA
524680 GCTTGGAATA
Statistics
Matches: 382, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
383 382 1.00
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (383 bp):
CTTATGTATTGAGAGAACTCGTTTGAGCTATATTCTTCTCCGTTGTCTGTGCGCAAGCAATATAT
CTTCTTTCCCACTTCTCATTCAGTTAACTCTTTGAACTCTTTAAACTTTGAGAATGTGTCAGATT
TTTCTTTCATAAAGAAAACCCACATATACCTGGAGAAGTCATCAATGAATGTTACCATATACCAC
ATACTGCTAATTGCTTAACCGGTTCGAACACATTAGAGTGAACTAACTCTAACGGTTCTTTTACT
TTAAACTTTGACTCGTCATATGGTAATTGGTGTGCTTTACCATACTGGAATCCCGCAGAGATCAT
GTATGTTCTCACGTCTAGTTGAGGAAGCCCCTTAAGCATCGACTTCTTCACCATCACA
Found at i:526632 original size:90 final size:89
Alignment explanation
Indices: 526515--526691 Score: 309
Period size: 90 Copynumber: 2.0 Consensus size: 89
526505 TAATCCCGAA
* * *
526515 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCTTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAATCC-TAATATGAT
526580 TAGGGTAACTTGGATATAAAAGGAT
65 TAGGGTAACTTGGATATAAAAGGAT
526605 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAATCCTAATATGATT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAATCCTAATATGATT
*
526670 AGGGTAACTTGGCTATAAAAGG
66 AGGGTAACTTGGATATAAAAGG
526692 GTGTGTTAGG
Statistics
Matches: 83, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 31 0.37
90 52 0.63
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.38
Consensus pattern (89 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAATCCTAATATGATT
AGGGTAACTTGGATATAAAAGGAT
Found at i:529461 original size:2 final size:2
Alignment explanation
Indices: 529449--529495 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
529439 AAATGATTTC
*
529449 AT AT AT TT 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 AT
529491 AT AT A
1 AT AT A
529496 GAGAGAGAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:531317 original size:81 final size:81
Alignment explanation
Indices: 531194--531480 Score: 391
Period size: 81 Copynumber: 3.6 Consensus size: 81
531184 GAAAAGTGAT
* * *
531194 AATTATGCCA-TTAGATGAAAGGTTAAATACCATTGAGTAAAAGATTAATGGCCTAGTTGTGCAT
1 AATTATGTCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCAT
*
531258 TTGACAGAAAGATGAT-
66 TTGACAGAAAGGTG-TC
*
531274 AATTATGTCAGCTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCAT
1 AATTATGTCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCAT
*
531339 TTGACAGAATGGTGTC
66 TTGACAGAAAGGTGTC
* * * **
531355 AATTAT-TCCAATTAGATGCAAGGTTAAATACATTTGAGTAAAAGATTAATGGCCTAGCTGTTAA
1 AATTATGT-CAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCA
531419 TTTGACAGAAAGGTGTC
65 TTTGACAGAAAGGTGTC
* * ** *
531436 AATTATGTCAGTGAGATGAAATGTTAAATGTCTTTGGGTAAAAGA
1 AATTATGTCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGA
531481 CAAAATGCTT
Statistics
Matches: 182, Mismatches: 21, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
80 11 0.06
81 170 0.93
82 1 0.01
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (81 bp):
AATTATGTCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCAT
TTGACAGAAAGGTGTC
Done.