Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008195.1 Hibiscus syriacus cultivar Beakdansim tig00110814_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: 1119982
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:445460 original size:21 final size:21
Alignment explanation
Indices: 445398--445511 Score: 60
Period size: 21 Copynumber: 5.3 Consensus size: 21
445388 AAATAGTAAG
*
445398 TAAAAAAAACAAATATAAATATA
1 TAAATAAAACAAATA-AAATA-A
* *
445421 TAAA-AAGA-AAA-AGAA-AA
1 TAAATAAAACAAATAAAATAA
445438 TAAATAAAACAAATAAAATAA
1 TAAATAAAACAAATAAAATAA
445459 T-AATAATAACAAAATACGAAAATATA
1 TAAATAA-AAC-AAAT---AAAATA-A
* *
445485 TATATAAAATAAATAAAA-AA
1 TAAATAAAACAAATAAAATAA
445505 GTAAATA
1 -TAAATA
445512 TATATAAATT
Statistics
Matches: 72, Mismatches: 7, Indels: 26
0.69 0.07 0.25
Matches are distributed among these distances:
17 5 0.07
18 4 0.06
19 5 0.07
20 10 0.14
21 15 0.21
22 11 0.15
23 4 0.06
25 10 0.14
26 4 0.06
27 4 0.06
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.20
Consensus pattern (21 bp):
TAAATAAAACAAATAAAATAA
Found at i:446014 original size:12 final size:11
Alignment explanation
Indices: 445986--446026 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
445976 ATACAAAATA
* *
445986 AATAATATAAA
1 AATAATACAAG
445997 AATAATACAAG
1 AATAATACAAG
446008 TAATAATACAAG
1 -AATAATACAAG
446020 AATAATA
1 AATAATA
446027 AAAAGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (11 bp):
AATAATACAAG
Found at i:446075 original size:25 final size:26
Alignment explanation
Indices: 446042--446092 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
446032 AAAGATAAAG
446042 TAAAAAATATA-ATAATAATA-AAATA
1 TAAAAAATATACAT-ATAATATAAATA
446067 TAAAAAATATACATATAATATAAATA
1 TAAAAAATATACATATAATATAAATA
446093 AGTAGAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 17 0.71
26 7 0.29
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (26 bp):
TAAAAAATATACATATAATATAAATA
Found at i:446316 original size:17 final size:18
Alignment explanation
Indices: 446283--446316 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
446273 CTAGGGAAAT
*
446283 CAAAGTTTCTGAAAAAAA
1 CAAAGTTTCTAAAAAAAA
446301 CAAAGTTTC-AAAAAAA
1 CAAAGTTTCTAAAAAAA
446317 CTCCCTCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.59, C:0.12, G:0.09, T:0.21
Consensus pattern (18 bp):
CAAAGTTTCTAAAAAAAA
Found at i:446339 original size:13 final size:13
Alignment explanation
Indices: 446323--446347 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
446313 AAAACTCCCT
446323 CTAAAACATTTGG
1 CTAAAACATTTGG
446336 CTAAAACATTTG
1 CTAAAACATTTG
446348 TCTTGTGGGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (13 bp):
CTAAAACATTTGG
Found at i:446658 original size:37 final size:37
Alignment explanation
Indices: 446560--446661 Score: 141
Period size: 37 Copynumber: 2.8 Consensus size: 37
446550 CTGCTTGTGG
* ** * *
446560 ATCCTATCTTTAGGAGTTTAAATTATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAACTCT
*
446597 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAACTCT
*
446634 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTAAATCCTAG
446662 TAGGACGAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAACTCT
Found at i:448028 original size:106 final size:106
Alignment explanation
Indices: 447395--448951 Score: 2108
Period size: 106 Copynumber: 14.9 Consensus size: 106
447385 GGATTGTTCT
* * ** * * *
447395 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCT-AGAACCGGGAAATTGTTTGTTGAAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA-AATTGGGAAGTTGTTTATTGACA
** * * *
447459 ACCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* ** * *
447501 GAGTCCAATATCCTTCGCTGTAAAGTTGAAATTGAATCTG-AA-T--GAA-AT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * * ** *
447560 TCAGCCG-CCTCTTCATCGTGAAGTTGAGCTTTTGTTGCCTTG
66 CCAGCGGTCC-CTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * *
447602 G-GTTCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
447666 CCAGCGGT-CCTTCGTCGT-AAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
447705 GAGTCCAATATCCTACTCTGTGAAGTTTAAATTGGCTCTGAAATTAGGAA-AT-TAT-TTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
447767 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
447808 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTT-TTT-TTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
447871 CCAGCGGTCCCTTCGACGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
447912 GAGTCCAATATCCTTCGCTGTGAAGTTTAAATTGGCTCTGAAATTGGGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
447977 CCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
448018 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
448083 -CAGC-GTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
448122 GAGTCCAATATCCTTCGTTGTGAAGTTCAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
448187 CCAGCGATCCCTTCATCATGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
448228 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TT-TTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
448291 CCAGTGGTCCCTTCGTTGTGAA-TTGAACTTGCG-TGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
448330 GAGTCCAA-AT-CTTCGCTGTGAAGTTGAAATTGACTCTGAAATT-GGAAGTT-TTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
448391 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
448432 GAGACCAATATCCTTCGTTGTGAATTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * ***
448497 TCGGCGGTCTAATCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * ** *
448538 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTAAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
448603 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
448644 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAGAAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
448709 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
448750 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTTGATCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
448815 CCAGCGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGCCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
448856 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAGTTGTTT-TTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
448920 CCAGCGGTCCCTTCG-CTGTGAAGTTGAACTTG
66 CCAGCGGTCCCTTCGTC-GTGAAGTTGAACTTG
448952 TGTGTCTTGA
Statistics
Matches: 1290, Mismatches: 134, Indels: 55
0.87 0.09 0.04
Matches are distributed among these distances:
99 10 0.01
100 128 0.10
101 33 0.03
102 43 0.03
103 78 0.06
104 306 0.24
105 65 0.05
106 627 0.49
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:448053 original size:210 final size:212
Alignment explanation
Indices: 447395--448951 Score: 2101
Period size: 210 Copynumber: 7.5 Consensus size: 212
447385 GGATTGTTCT
* * ** * * * *
447395 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCT-AGAACCGGGAAATTGTTTGTTGAAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA-AATTGAGAAGTTGTTTATTGACA
** * * * *
447459 ACCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTAA
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGA
** * * * * *
447524 AGTTGAAATTGAATCTG-AA-T--GAA-AT-TTTGTTGACAATCAGCCG-CCTCTTCATCGTGAA
130 AGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCC-CTTCGTCGTGAA
* ** *
447582 GTTGAGCTTTTGTTGCCTTG
194 GTTGAACTTGCGTTGTC-TG
* * * *
447602 G-GTTCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
* * *
447666 CCAGCGGT-CCTTCGTCGT-AAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTACTCTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
* * * *
447729 GTTTAAATTGGCTCTGAAATTAGGAA-AT-TAT-TTGACAACCAGCGGTCCCTTCGTCGTGAAGT
131 GTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
*
447791 TGAACTTGCATTGTCTG
196 TGAACTTGCGTTGTCTG
* *
447808 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTT-TTT-TTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
*
447871 CCAGCGGTCCCTTCGACGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
* * *
447936 GTTTAAATTGGCTCTGAAATTGGGAAGTTATTTATTGACAACCAACGGTCCCTTCGTCGTGAAGT
131 GTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
*
448001 TGAACTTGCGTTGTCTT
196 TGAACTTGCGTTGTCTG
* * *
448018 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
* *
448083 -CAGC-GTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
* * * * * *
448146 GTTCAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGATCCCTTCATCATGAAGT
131 GTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
448211 TGAACTTGCGTTGTCTG
196 TGAACTTGCGTTGTCTG
* *
448228 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TT-TTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
* *
448291 CCAGTGGTCCCTTCGTTGTGAA-TTGAACTTGCG-TGTCTGGAGTCCAA-AT-CTTCGCTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
*
448352 GTTGAAATTGACTCTGAAATT-GGAAGTT-TTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
131 GTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
448415 TGAACTTGCGTTGTCTG
196 TGAACTTGCGTTGTCTG
* * *
448432 GAGACCAATATCCTTCGTTGTGAATTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
* * *** *
448497 TCGGCGGTCTAATCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
* ** *
448562 GTTAAAATTGGCTCTGAAATTAAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
131 GTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
448627 TGAACTTGCGTTGTCTG
196 TGAACTTGCGTTGTCTG
*
448644 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATT-AGAAAGTTGTTTATTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AAGTTGTTTATTGACA
* * * *
448708 ACCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGAAGTCCAATATCCTTCGTTGTGA
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGA
* * * *
448773 AGTTGAAATTTGATCTGAAATTGGGAAATTGTTTATTGACAACCAGCGATCCCTTCGTCGTGAAG
130 AGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
*
448838 TTGAACTTGCGTTGCCTG
195 TTGAACTTGCGTTGTCTG
* *
448856 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAGTTGTTT-TTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
448920 CCAGCGGTCCCTTCG-CTGTGAAGTTGAACTTG
66 CCAGCGGTCCCTTCGTC-GTGAAGTTGAACTTG
448952 TGTGTCTTGA
Statistics
Matches: 1206, Mismatches: 117, Indels: 50
0.88 0.09 0.04
Matches are distributed among these distances:
204 152 0.13
205 34 0.03
206 125 0.10
207 162 0.13
208 45 0.04
209 20 0.02
210 318 0.26
211 51 0.04
212 298 0.25
213 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (212 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
GTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
TGAACTTGCGTTGTCTG
Found at i:450422 original size:14 final size:15
Alignment explanation
Indices: 450405--450474 Score: 74
Period size: 14 Copynumber: 4.7 Consensus size: 15
450395 TTCTTTTTGA
450405 TTTTTGTTCTTTCTT
1 TTTTTGTTCTTTCTT
450420 TTTTTG-T-TTTCTTT
1 TTTTTGTTCTTTC-TT
450434 TTTTTGCTTCTTTTCTT
1 TTTTTG-TTC-TTTCTT
**
450451 TTTTTGTT-TTTCCC
1 TTTTTGTTCTTTCTT
450465 TTTTTGTTCT
1 TTTTTGTTCT
450475 GATTGAATCT
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
13 4 0.09
14 21 0.45
15 7 0.15
16 3 0.06
17 8 0.17
18 4 0.09
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (15 bp):
TTTTTGTTCTTTCTT
Found at i:450433 original size:17 final size:17
Alignment explanation
Indices: 450411--450460 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
450401 TTGATTTTTG
450411 TTCTTTCTTTTTTTGTT
1 TTCTTTCTTTTTTTGTT
*
450428 TTC--T-TTTTTTTG-C
1 TTCTTTCTTTTTTTGTT
450441 TTCTTTTCTTTTTTTGTT
1 TTC-TTTCTTTTTTTGTT
450459 TT
1 TT
450461 TCCCTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 9
0.70 0.05 0.24
Matches are distributed among these distances:
13 3 0.12
14 8 0.31
15 1 0.04
16 1 0.04
17 11 0.42
18 2 0.08
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.82
Consensus pattern (17 bp):
TTCTTTCTTTTTTTGTT
Found at i:450469 original size:31 final size:30
Alignment explanation
Indices: 450405--450474 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 30
450395 TTCTTTTTGA
**
450405 TTTTTGTTC-TTTCTTTTTTTGTTTTCTTT
1 TTTTTGTTCTTTTCTTTTTTTGTTTTCTCC
450434 TTTTTGCTTCTTTTCTTTTTTTGTTTT-TCCC
1 TTTTTG-TTCTTTTCTTTTTTTGTTTTCT-CC
450465 TTTTTGTTCT
1 TTTTTGTTCT
450475 GATTGAATCT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
29 6 0.17
30 8 0.22
31 22 0.61
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (30 bp):
TTTTTGTTCTTTTCTTTTTTTGTTTTCTCC
Found at i:453900 original size:19 final size:20
Alignment explanation
Indices: 453872--453909 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
453862 TGCAGATGAT
*
453872 GGAAATAAAAT-AAAAGAGA
1 GGAAAAAAAATGAAAAGAGA
453891 GGAAAAAAAATGAAAAGAG
1 GGAAAAAAAATGAAAAGAG
453910 TTAGTAAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (20 bp):
GGAAAAAAAATGAAAAGAGA
Found at i:455482 original size:21 final size:23
Alignment explanation
Indices: 455449--455491 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
455439 AAGTGGCATA
455449 TGAGATTTATCCCGAAGGACCTT
1 TGAGATTTATCCCGAAGGACCTT
*
455472 TGAG-TTT-TCCCGAATGACCT
1 TGAGATTTATCCCGAAGGACCT
455492 ATAAAACCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 3 0.16
23 4 0.21
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (23 bp):
TGAGATTTATCCCGAAGGACCTT
Found at i:456211 original size:63 final size:64
Alignment explanation
Indices: 456056--456233 Score: 205
Period size: 63 Copynumber: 2.8 Consensus size: 64
456046 TCCTTATCAT
* ** *
456056 GTGCATCGATGCACTAACTATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAATGG
1 GTGCATCGATGCACTACCTATGCATCGATACACAAATTGCATTCGATGTTTCCATTTTTAAAGG
* * * * * * * *
456120 GTGCATCAATACAATTCTTGTGTATCGATACACAAATTGCATTCGATGTTTTCA-TTTTAAAGG
1 GTGCATCGATGCACTACCTATGCATCGATACACAAATTGCATTCGATGTTTCCATTTTTAAAGG
* * **
456183 GTGCATCGATGCACTCCCTATGCATCGATGCACTTATTGCATTCGATGTTT
1 GTGCATCGATGCACTACCTATGCATCGATACACAAATTGCATTCGATGTTT
456234 ATTTATTTGA
Statistics
Matches: 92, Mismatches: 22, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
63 49 0.53
64 43 0.47
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (64 bp):
GTGCATCGATGCACTACCTATGCATCGATACACAAATTGCATTCGATGTTTCCATTTTTAAAGG
Found at i:461472 original size:35 final size:35
Alignment explanation
Indices: 461425--461495 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
461415 TCTCTAAGAA
*
461425 AATGAATTGAATGAGATGTTACAAATGAGGAGGAG
1 AATGAATGGAATGAGATGTTACAAATGAGGAGGAG
461460 AATGAATGGAATGAGATGTTACAAATGAGGAGGAG
1 AATGAATGGAATGAGATGTTACAAATGAGGAGGAG
461495 A
1 A
461496 GACTCTCTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.44, C:0.03, G:0.32, T:0.21
Consensus pattern (35 bp):
AATGAATGGAATGAGATGTTACAAATGAGGAGGAG
Found at i:463229 original size:14 final size:14
Alignment explanation
Indices: 463210--463241 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
463200 CACGTTTTAA
463210 AATTCTCTCTCACG
1 AATTCTCTCTCACG
463224 AATTCTCTCTCACG
1 AATTCTCTCTCACG
463238 AATT
1 AATT
463242 TCACAAGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.25, C:0.31, G:0.06, T:0.38
Consensus pattern (14 bp):
AATTCTCTCTCACG
Found at i:468452 original size:12 final size:12
Alignment explanation
Indices: 468437--468496 Score: 68
Period size: 12 Copynumber: 5.0 Consensus size: 12
468427 GATACATTAC
468437 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
468449 CTGATTTCTGAT
1 CTGAATTCTGTT
*
468461 CTGGATTCTGTT
1 CTGAATTCTGTT
*
468473 CTG-ATATCTGAT
1 CTGAAT-TCTGTT
468485 CTGAATTCTGTT
1 CTGAATTCTGTT
468497 TTGATTTTTG
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
11 2 0.05
12 35 0.90
13 2 0.05
ACGTcount: A:0.17, C:0.17, G:0.18, T:0.48
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:468456 original size:48 final size:48
Alignment explanation
Indices: 468400--468503 Score: 131
Period size: 48 Copynumber: 2.2 Consensus size: 48
468390 AAATATTTTA
*
468400 TCTGATTTCTTAAT-TGAATTCTGTTCTGATA-CATTACCTGAATTCTGT
1 TCTGATTTC-TAATCTGAATTCTGTTCTGATATC-TGACCTGAATTCTGT
* * *
468448 TCTGATTTCTGATCTGGATTCTGTTCTGATATCTGATCTGAATTCTGT
1 TCTGATTTCTAATCTGAATTCTGTTCTGATATCTGACCTGAATTCTGT
*
468496 TTTGATTT
1 TCTGATTT
468504 TTGATATCTC
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
47 3 0.06
48 45 0.92
49 1 0.02
ACGTcount: A:0.19, C:0.15, G:0.15, T:0.50
Consensus pattern (48 bp):
TCTGATTTCTAATCTGAATTCTGTTCTGATATCTGACCTGAATTCTGT
Found at i:468508 original size:24 final size:24
Alignment explanation
Indices: 468400--468508 Score: 114
Period size: 24 Copynumber: 4.5 Consensus size: 24
468390 AAATATTTTA
*
468400 TCTGATTTCTTAAT-TGAATTCTGT
1 TCTGATTTC-TGATCTGAATTCTGT
* * *
468424 TCTGA-TACATTACCTGAATTCTGT
1 TCTGATTTC-TGATCTGAATTCTGT
*
468448 TCTGATTTCTGATCTGGATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
468472 TCTGATATCTGATCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
* *
468496 TTTGATTTTTGAT
1 TCTGATTTCTGAT
468509 ATCTCCGTTT
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
23 4 0.06
24 64 0.91
25 2 0.03
ACGTcount: A:0.19, C:0.15, G:0.16, T:0.50
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:497048 original size:65 final size:64
Alignment explanation
Indices: 496977--497160 Score: 196
Period size: 64 Copynumber: 2.9 Consensus size: 64
496967 GAATAAATTG
* *
496977 AACATCGAATGCATTTCATGCACCGATACACATATTATGCATCGATGCACTAAGAG-T-TTTATG
1 AACATCGAATGCATTTCATGCATCGATGCACATATTATGCATCGATGCACTAAG-GCTATTT-TG
497040 AA
64 -A
* *** * **
497042 AACATCGAATGCATTTGATGCATCGATGCATCA-GCCATGTATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTCATGCATCGATGCA-CATATTATGCATCGATGCACTAAGGCTATTTTGA
* *
497106 AACATCGAATGCATTTCATGCATCGATGCAC-TCTTAGTGCACCGATGCACTAAGG
1 AACATCGAATGCATTTCATGCATCGATGCACATATTA-TGCATCGATGCACTAAGG
497161 GTCCAACGGT
Statistics
Matches: 97, Mismatches: 17, Indels: 11
0.78 0.14 0.09
Matches are distributed among these distances:
63 2 0.02
64 45 0.46
65 45 0.46
66 5 0.05
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.29
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACATATTATGCATCGATGCACTAAGGCTATTTTGA
Found at i:497152 original size:64 final size:65
Alignment explanation
Indices: 496977--497159 Score: 191
Period size: 65 Copynumber: 2.8 Consensus size: 65
496967 GAATAAATTG
* * *
496977 AACATCGAATGCATTTCATGCACCGATACACATATTA-TGCATCGATGCACTAAGAGTTTTATGA
1 AACATCGAATGCATTTCATGCATCGATGCAC-TCTTAGTGCATCGATGCACTAAGAGTTTTATGA
497041 A
65 A
* * **
497042 AACATCGAATGCATTTGATGCATCGATGCA-TC--AGCCATGTATCGATGCACTCTG-GCTATTT
1 AACATCGAATGCATTTCATGCATCGATGCACTCTTAG---TGCATCGATGCACTAAGAG-T-TTT
497103 -TG-A
61 ATGAA
*
497106 AACATCGAATGCATTTCATGCATCGATGCACTCTTAGTGCACCGATGCACTAAG
1 AACATCGAATGCATTTCATGCATCGATGCACTCTTAGTGCATCGATGCACTAAG
497160 GGTCCAACGG
Statistics
Matches: 97, Mismatches: 12, Indels: 19
0.76 0.09 0.15
Matches are distributed among these distances:
61 1 0.01
63 1 0.01
64 44 0.45
65 46 0.47
66 3 0.03
67 2 0.02
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACTCTTAGTGCATCGATGCACTAAGAGTTTTATGAA
Found at i:502984 original size:13 final size:13
Alignment explanation
Indices: 502968--502992 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
502958 AAATTGAAAA
502968 TCTAAATTTGATT
1 TCTAAATTTGATT
502981 TCTAAATTTGAT
1 TCTAAATTTGAT
502993 GTTTTTGATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (13 bp):
TCTAAATTTGATT
Found at i:504329 original size:2 final size:2
Alignment explanation
Indices: 504322--504348 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
504312 CAGCTTAAGC
504322 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
504349 CAATTGGCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:504510 original size:21 final size:20
Alignment explanation
Indices: 504443--504512 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
504433 TAAAATGTTT
504443 TAAAGGGGA-AAGTTTAAAG
1 TAAAGGGGAGAAGTTTAAAG
*
504462 TAAAGGGGAGAAATTTAAAG
1 TAAAGGGGAGAAGTTTAAAG
*
504482 TAAAGGGGAGAAGTGTTAAAT
1 TAAAGGGGAGAAGT-TTAAAG
*
504503 TAAGGGGGAG
1 TAAAGGGGAG
504513 TACTTTCAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.20
20 22 0.49
21 14 0.31
ACGTcount: A:0.44, C:0.00, G:0.36, T:0.20
Consensus pattern (20 bp):
TAAAGGGGAGAAGTTTAAAG
Found at i:509023 original size:18 final size:17
Alignment explanation
Indices: 508982--509024 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
508972 TAGTAGGTCA
508982 AACGAAAAAAAAGTGAG
1 AACGAAAAAAAAGTGAG
*
508999 AAAGAAAAAAGAAGATGAG
1 AACGAAAAAA-AAG-TGAG
509018 -ACGAAAA
1 AACGAAAA
509025 GATTGACCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 9 0.41
18 9 0.41
19 4 0.18
ACGTcount: A:0.67, C:0.05, G:0.23, T:0.05
Consensus pattern (17 bp):
AACGAAAAAAAAGTGAG
Found at i:510748 original size:29 final size:29
Alignment explanation
Indices: 510716--510771 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
510706 TTTTCTATCG
*
510716 TTTAGTTGTTTAGTGGTCAGCTATATTCA
1 TTTAGCTGTTTAGTGGTCAGCTATATTCA
* *
510745 TTTAGCTGTTTAGTTGTCAGTTATATT
1 TTTAGCTGTTTAGTGGTCAGCTATATT
510772 TGACACCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.20, C:0.09, G:0.20, T:0.52
Consensus pattern (29 bp):
TTTAGCTGTTTAGTGGTCAGCTATATTCA
Found at i:516748 original size:13 final size:13
Alignment explanation
Indices: 516698--516748 Score: 50
Period size: 13 Copynumber: 4.0 Consensus size: 13
516688 GTGTCATAAA
*
516698 TATGACGCTCATT
1 TATGACGCGCATT
**
516711 TATG-CATGCATT
1 TATGACGCGCATT
* *
516723 TATGACTCACATT
1 TATGACGCGCATT
516736 TATGACGCGCATT
1 TATGACGCGCATT
516749 GAGCGTCATT
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
12 9 0.31
13 20 0.69
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:516840 original size:2 final size:2
Alignment explanation
Indices: 516833--516865 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
516823 TTTCGTAAAT
516833 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
516866 TGTAGATTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:523195 original size:14 final size:14
Alignment explanation
Indices: 523172--523204 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
523162 ACTAGTTGCT
523172 AAAGGCTATAGTCA
1 AAAGGCTATAGTCA
*
523186 AAAGGTTATAGTCA
1 AAAGGCTATAGTCA
523200 AAAGG
1 AAAGG
523205 ATGGAATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.45, C:0.09, G:0.24, T:0.21
Consensus pattern (14 bp):
AAAGGCTATAGTCA
Found at i:524232 original size:33 final size:34
Alignment explanation
Indices: 524183--524248 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 34
524173 AAACTAATTT
* * * *
524183 GATGTCATTTCTTACAT-TAATTTGTTAGGTGAA
1 GATGCCATTACTTACATCAAATTAGTTAGGTGAA
524216 GATGCCATTACTTACATCAAATTAGTTAGGTGA
1 GATGCCATTACTTACATCAAATTAGTTAGGTGA
524249 GAGTTAGGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 15 0.54
34 13 0.46
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.39
Consensus pattern (34 bp):
GATGCCATTACTTACATCAAATTAGTTAGGTGAA
Found at i:526621 original size:11 final size:11
Alignment explanation
Indices: 526607--526631 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
526597 GTCTTAGAGG
526607 ATGTTAGCAAC
1 ATGTTAGCAAC
526618 ATGTTAGCAAC
1 ATGTTAGCAAC
526629 ATG
1 ATG
526632 GGGTTAAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (11 bp):
ATGTTAGCAAC
Found at i:528440 original size:20 final size:20
Alignment explanation
Indices: 528378--528448 Score: 64
Period size: 20 Copynumber: 3.9 Consensus size: 20
528368 AAGTTCTAAG
528378 TAAATAAAATAACTAATTCC
1 TAAATAAAATAACTAATTCC
** * *
528398 TAACCAAAA-ATC-CA-T-C
1 TAAATAAAATAACTAATTCC
528414 T-AATAAAATAACTAATTCC
1 TAAATAAAATAACTAATTCC
528433 TAAATAAAATAA-TAAT
1 TAAATAAAATAACTAAT
528449 AAAATAATGA
Statistics
Matches: 38, Mismatches: 8, Indels: 11
0.67 0.14 0.19
Matches are distributed among these distances:
15 5 0.13
16 4 0.11
17 2 0.05
18 2 0.05
19 8 0.21
20 17 0.45
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.28
Consensus pattern (20 bp):
TAAATAAAATAACTAATTCC
Found at i:528452 original size:31 final size:33
Alignment explanation
Indices: 528380--528455 Score: 95
Period size: 35 Copynumber: 2.3 Consensus size: 33
528370 GTTCTAAGTA
*
528380 AATAAAATAACTAATTCCTAACCAAAAATCCATCT
1 AATAAAATAACTAATTCCTAA-CAAAAAT-CATAT
528415 AATAAAATAACTAATTCCTAA-ATAAAAT-A-AT
1 AATAAAATAACTAATTCCTAACA-AAAATCATAT
528446 AATAAAATAA
1 AATAAAATAA
528456 TGAAACTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
31 11 0.28
32 1 0.03
33 1 0.03
34 5 0.13
35 21 0.54
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.26
Consensus pattern (33 bp):
AATAAAATAACTAATTCCTAACAAAAATCATAT
Found at i:530234 original size:182 final size:182
Alignment explanation
Indices: 529916--530364 Score: 729
Period size: 182 Copynumber: 2.5 Consensus size: 182
529906 TACTATCGGC
* * * *
529916 TTTGTAATTTCGAGACCGATTTTATCATATTTTTACATGTTATATTGTTATGGATCGATACATTT
1 TTTGTCATTTTGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTT
* *
529981 TTATAAAGTATCGACACTTTATTGACGCTATAACTTCTTTTCTTTTAAATTCCAAAAGTGTCGAT
66 TTATAAAGTATCAACACTTTATTGACGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGAT
* * * *
530046 ACTTATAATAAAGTATCGACACTTTCAACATATATGGTAGCTCTTTACCGGT
131 ACTTATAATAAAGTATCGACACTATCAACATATACGATAGCGCTTTACCGGT
530098 TTTGTCATTTTGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTT
1 TTTGTCATTTTGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTT
*
530163 TTATAAAGTATCAATACTTTATTGACGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGAT
66 TTATAAAGTATCAACACTTTATTGACGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGAT
* *
530228 ACTTATAATAAAGTATCGACACTATCAACATATCCGATAGCGCTTTACCTGT
131 ACTTATAATAAAGTATCGACACTATCAACATATACGATAGCGCTTTACCGGT
* * *
530280 TTTGTCATTTAT-AAACCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATT
1 TTTGTCATTT-TGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
*
530344 TTTATAAAGTATCGACACTTT
65 TTTATAAAGTATCAACACTTT
530365 CAATATATCT
Statistics
Matches: 248, Mismatches: 18, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
182 247 1.00
183 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (182 bp):
TTTGTCATTTTGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTT
TTATAAAGTATCAACACTTTATTGACGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGAT
ACTTATAATAAAGTATCGACACTATCAACATATACGATAGCGCTTTACCGGT
Found at i:530419 original size:111 final size:112
Alignment explanation
Indices: 530235--530512 Score: 479
Period size: 111 Copynumber: 2.5 Consensus size: 112
530225 GATACTTATA
* * * *
530235 ATAAAGTATCGACACTATCAACATATCCGATAGCGCTTTACCTGTTTTGTCATTTATAAACCGGT
1 ATAAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAAACCGGT
* *
530300 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTATCATTTTTTTACCTGTTATATTGTTATAGATCGATACATTTTT
530347 ATAAAGTATCGACACTTTCAATATATCTGGTAGCG-TTTACCTGTTTTGTCATTTATAAACCGGT
1 ATAAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAAACCGGT
530411 TTTATCATTTTTTTACCTGTTATATTGTTATAGATCGATACATTTTT
66 TTTATCATTTTTTTACCTGTTATATTGTTATAGATCGATACATTTTT
530458 ATAAAGTATCGACACTTTCAATATAT-TCGGTAGCGCTTTACCTGTTTTGTCATTT
1 ATAAAGTATCGACACTTTCAATATATCT-GGTAGCGCTTTACCTGTTTTGTCATTT
530513 TTTACCTGTT
Statistics
Matches: 158, Mismatches: 6, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
110 1 0.01
111 107 0.68
112 50 0.32
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAAACCGGT
TTTATCATTTTTTTACCTGTTATATTGTTATAGATCGATACATTTTT
Found at i:530523 original size:91 final size:91
Alignment explanation
Indices: 530409--530603 Score: 320
Period size: 91 Copynumber: 2.1 Consensus size: 91
530399 TTATAAACCG
*
530409 GTTTTATCATTTTTTTACCTGTTATATTGTTATAGATCGATACATTTTTATAAAGTATCGACACT
1 GTTTTGTCA-TTTTTTACCTGTTATATTGTTATAGATCGATACATTTTTATAAAGTATCGACACT
*
530474 TTCAATATATTC-GGTAGCGCTTTACCT
65 TTCAATATA-TCAGGTAGCGCTTTAACT
* * *
530501 GTTTTGTCATTTTTTACCTGTTATATTGTTATGGATCGATATATTTTTATAAAGTATCTACACTT
1 GTTTTGTCATTTTTTACCTGTTATATTGTTATAGATCGATACATTTTTATAAAGTATCGACACTT
530566 TCAATATATCAGGTAGCGCTTTAACT
66 TCAATATATCAGGTAGCGCTTTAACT
530592 GTTTTGTCATTT
1 GTTTTGTCATTT
530604 ATAGACCAAT
Statistics
Matches: 97, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
90 2 0.02
91 87 0.90
92 8 0.08
ACGTcount: A:0.25, C:0.14, G:0.13, T:0.48
Consensus pattern (91 bp):
GTTTTGTCATTTTTTACCTGTTATATTGTTATAGATCGATACATTTTTATAAAGTATCGACACTT
TCAATATATCAGGTAGCGCTTTAACT
Found at i:530660 original size:202 final size:202
Alignment explanation
Indices: 530298--530674 Score: 578
Period size: 202 Copynumber: 1.9 Consensus size: 202
530288 TTATAAACCG
530298 GTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
1 GTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
* * ** *
530363 TTCAATATATCTGGTAGCGTTTACCTGTTTTGTCATTTATAAACCGGTTTTATCATTTTTTTACC
66 TTCAATATATCAGGTAGCGTTTAACTGTTTTGTCATTTATAAACCAATTTCAT-ATTTTTTTACC
* * *
530428 TGTTATATTGTTATAGATCGATACATTTTTATAAAGTATCGACACTTTCAATATATTCGGTAGCG
130 TGTTATATTATTATAGATCAATACATTTTTATAAAATATCGACACTTTCAATATATTCGGTAGCG
530493 CTTTACCT
195 CTTTACCT
* *
530501 GTTTTGTCA-TTTTTTACCTGTTATATTGTTATGGATCGATATATTTTTATAAAGTATCTACACT
1 GTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
*
530565 TTCAATATATCAGGTAGCGCTTTAACTGTTTTGTCATTTATAGACCAATTGTCAT-TTTTTTTAC
66 TTCAATATATCAGGTAGCG-TTTAACTGTTTTGTCATTTATAAACCAATT-TCATATTTTTTTAC
* * * *
530629 CTGTTATATTATTGTGGATCAATATATTTTTATAAAATATCTACAC
129 CTGTTATATTATTATAGATCAATACATTTTTATAAAATATCGACAC
530675 AAACCGAAAC
Statistics
Matches: 157, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
202 119 0.76
203 35 0.22
204 3 0.02
ACGTcount: A:0.26, C:0.14, G:0.12, T:0.47
Consensus pattern (202 bp):
GTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
TTCAATATATCAGGTAGCGTTTAACTGTTTTGTCATTTATAAACCAATTTCATATTTTTTTACCT
GTTATATTATTATAGATCAATACATTTTTATAAAATATCGACACTTTCAATATATTCGGTAGCGC
TTTACCT
Found at i:530966 original size:20 final size:20
Alignment explanation
Indices: 530943--531100 Score: 136
Period size: 20 Copynumber: 7.8 Consensus size: 20
530933 ATTCGCGTTG
530943 CATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
*
530963 CATTTCACGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
* *
530983 CATTTCGCGTTGCGATAGTTG
1 CATTTCGCGTTGCGAT-TTTC
* ** *
531004 AAAATCGCGTTGCGCTTTTC
1 CATTTCGCGTTGCGATTTTC
* * *
531024 CATTTCGCGTTACGATAGTTG
1 CATTTCGCGTTGCGAT-TTTC
* ** ** **
531045 AAAATCGCAATGTAATTTTC
1 CATTTCGCGTTGCGATTTTC
*
531065 GATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
531085 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
531101 AGTTGACCCG
Statistics
Matches: 101, Mismatches: 35, Indels: 4
0.72 0.25 0.03
Matches are distributed among these distances:
20 77 0.76
21 24 0.24
ACGTcount: A:0.18, C:0.22, G:0.21, T:0.40
Consensus pattern (20 bp):
CATTTCGCGTTGCGATTTTC
Found at i:531013 original size:21 final size:21
Alignment explanation
Indices: 530987--531052 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
530977 ATTTTCCATT
530987 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * ** **
531008 TCGCGTTGCGCT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
*
531028 TCGCGTTACGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
531049 TCGC
1 TCGC
531053 AATGTAATTT
Statistics
Matches: 31, Mismatches: 13, Indels: 2
0.67 0.28 0.04
Matches are distributed among these distances:
20 13 0.42
21 18 0.58
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.33
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:531027 original size:41 final size:41
Alignment explanation
Indices: 530970--531080 Score: 159
Period size: 41 Copynumber: 2.7 Consensus size: 41
530960 TTCCATTTCA
530970 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCG
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCG
* *
531011 CGTTGCGCTTTTCCATTTCGCGTTACGATAGTTGAAAATCG
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCG
** ** *
531052 CAATGTAATTTTCGATTTCGCGTTGCGAT
1 CGTTGCGATTTTCCATTTCGCGTTGCGAT
531081 TTTCCATTTC
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 61 1.00
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCG
Found at i:531641 original size:6 final size:6
Alignment explanation
Indices: 531630--531654 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
531620 TCGTCTCGGA
531630 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
531655 AATACGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:531863 original size:20 final size:20
Alignment explanation
Indices: 531796--531856 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
531786 ATTTTCAACT
* *
531796 ATCGCAACGCAAAATGGAAA
1 ATCGCAACACGAAATGGAAA
*
531816 ATCGCAACTCGAAATGGAAA
1 ATCGCAACACGAAATGGAAA
531836 ATCGCAACACGAAATGGAAA
1 ATCGCAACACGAAATGGAAA
531856 A
1 A
531857 GCACAACGCG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.49, C:0.20, G:0.20, T:0.11
Consensus pattern (20 bp):
ATCGCAACACGAAATGGAAA
Found at i:531880 original size:40 final size:40
Alignment explanation
Indices: 531779--531891 Score: 120
Period size: 40 Copynumber: 2.8 Consensus size: 40
531769 TAGACTATCG
* * *
531779 CAACGCGATTTTCAACTATCGCAACGCAAAATGGAAAATCG
1 CAACGCGATTTT-AACTATCGCAACGCGAAATGGAAAAGCA
* * ** * *
531820 CAACTCGAAATGGAA-AATCGCAACACGAAATGGAAAAGCA
1 CAACGCG-ATTTTAACTATCGCAACGCGAAATGGAAAAGCA
531860 CAACGCGATTTTAACTATCGCAACGCGAAATG
1 CAACGCGATTTTAACTATCGCAACGCGAAATG
531892 CAACGCAATT
Statistics
Matches: 55, Mismatches: 15, Indels: 5
0.73 0.20 0.07
Matches are distributed among these distances:
39 4 0.07
40 41 0.75
41 8 0.15
42 2 0.04
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.17
Consensus pattern (40 bp):
CAACGCGATTTTAACTATCGCAACGCGAAATGGAAAAGCA
Found at i:533002 original size:16 final size:16
Alignment explanation
Indices: 532977--533011 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
532967 ATTAATTAAA
532977 ATTTTTAAATT-ATAG
1 ATTTTTAAATTGATAG
532992 ATTTCTTAAATTGATAG
1 ATTT-TTAAATTGATAG
533009 ATT
1 ATT
533012 AAATTAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 7 0.39
17 7 0.39
ACGTcount: A:0.37, C:0.03, G:0.09, T:0.51
Consensus pattern (16 bp):
ATTTTTAAATTGATAG
Found at i:535349 original size:10 final size:10
Alignment explanation
Indices: 535350--535398 Score: 62
Period size: 10 Copynumber: 4.5 Consensus size: 10
535340 CGTTTATGTT
535350 TGTTCATTTA
1 TGTTCATTTA
535360 TGTTCGTTCATTTA
1 TGTTC----ATTTA
535374 TGTTCATTTA
1 TGTTCATTTA
535384 TGTTCATTTA
1 TGTTCATTTA
535394 TGTTC
1 TGTTC
535399 GAACAGAGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
10 25 0.71
14 10 0.29
ACGTcount: A:0.16, C:0.12, G:0.12, T:0.59
Consensus pattern (10 bp):
TGTTCATTTA
Found at i:535366 original size:24 final size:25
Alignment explanation
Indices: 535325--535397 Score: 96
Period size: 24 Copynumber: 2.9 Consensus size: 25
535315 GTTTGTGAAC
535325 GTTCGATTATATGTTCGTTTATGTT-T
1 GTTC-ATT-TATGTTCGTTTATGTTAT
*
535351 GTTCATTTATGTTCGTTCAT-TTAT
1 GTTCATTTATGTTCGTTTATGTTAT
*
535375 GTTCATTTATGTTCATTTATGTT
1 GTTCATTTATGTTCGTTTATGTT
535398 CGAACAGAGG
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
23 2 0.05
24 31 0.74
25 5 0.12
26 4 0.10
ACGTcount: A:0.16, C:0.10, G:0.15, T:0.59
Consensus pattern (25 bp):
GTTCATTTATGTTCGTTTATGTTAT
Found at i:535378 original size:14 final size:14
Alignment explanation
Indices: 535337--535378 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
535327 TCGATTATAT
* *
535337 GTTCGTTTATGTTT
1 GTTCATTTATGTTC
535351 GTTCATTTATGTTC
1 GTTCATTTATGTTC
535365 GTTCATTTATGTTC
1 GTTCATTTATGTTC
535379 ATTTATGTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.12, C:0.12, G:0.17, T:0.60
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:535657 original size:22 final size:22
Alignment explanation
Indices: 535627--535704 Score: 86
Period size: 22 Copynumber: 3.5 Consensus size: 22
535617 GAATAAGTTT
*
535627 GTTTTTTGTGTTTGTGTTGTTC
1 GTTTATTGTGTTTGTGTTGTTC
* ** * *
535649 GTTTATTGTGTTCGAATAAGTTT
1 GTTTATTGTGTTTGTGT-TGTTC
535672 GTTT-TTGTGTTTGTGTTGTTC
1 GTTTATTGTGTTTGTGTTGTTC
535693 GTTTATTGTGTT
1 GTTTATTGTGTT
535705 CGTTTATTAT
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
21 7 0.16
22 29 0.67
23 7 0.16
ACGTcount: A:0.08, C:0.04, G:0.26, T:0.63
Consensus pattern (22 bp):
GTTTATTGTGTTTGTGTTGTTC
Found at i:535692 original size:44 final size:45
Alignment explanation
Indices: 535609--535706 Score: 189
Period size: 44 Copynumber: 2.2 Consensus size: 45
535599 CATTCATTTG
535609 TTGTGTTCGAATAAGTTTGTTTTTTGTGTTTGTGTTGTTCGTTTA
1 TTGTGTTCGAATAAGTTTGTTTTTTGTGTTTGTGTTGTTCGTTTA
535654 TTGTGTTCGAATAAGTTTG-TTTTTGTGTTTGTGTTGTTCGTTTA
1 TTGTGTTCGAATAAGTTTGTTTTTTGTGTTTGTGTTGTTCGTTTA
535698 TTGTGTTCG
1 TTGTGTTCG
535707 TTTATTATGT
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 34 0.64
45 19 0.36
ACGTcount: A:0.10, C:0.05, G:0.26, T:0.59
Consensus pattern (45 bp):
TTGTGTTCGAATAAGTTTGTTTTTTGTGTTTGTGTTGTTCGTTTA
Found at i:535734 original size:14 final size:13
Alignment explanation
Indices: 535680--535741 Score: 65
Period size: 13 Copynumber: 4.7 Consensus size: 13
535670 TTGTTTTTGT
*
535680 GTTTGTGTTGTTC
1 GTTTATGTTGTTC
535693 GTTTAT-TGTGTTC
1 GTTTATGT-TGTTC
535706 GTTTAT-TATGTTC
1 GTTTATGT-TGTTC
535719 GTTTATGTTCGTTC
1 GTTTATGTT-GTTC
*
535733 GTTTGTGTT
1 GTTTATGTT
535742 CGCTTACATT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
12 1 0.02
13 29 0.67
14 13 0.30
ACGTcount: A:0.06, C:0.08, G:0.24, T:0.61
Consensus pattern (13 bp):
GTTTATGTTGTTC
Found at i:535855 original size:16 final size:16
Alignment explanation
Indices: 535834--535866 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
535824 AAAAAAATTT
535834 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
535850 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
535866 T
1 T
535867 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:536493 original size:185 final size:183
Alignment explanation
Indices: 536143--536517 Score: 619
Period size: 185 Copynumber: 2.0 Consensus size: 183
536133 TATTAAAATT
*
536143 AAATGTTTTTAATTAAAAAAAAGTTATAATTAACTTAAATAATATATAATTATAAAATAAAAATT
1 AAAT-TTTTTAATTAAAAAAAAGTTACAATTAACTTAAATAATATATAATTATAAAATAAAAATT
536208 TCAGATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGAATCTTAAATTATT
65 TCAGATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGAATCTTAAATTATT
*
536273 AATTGGGTTTTAAATGGTTTGGGCTTAGCCCATATGTTATATATAATATATATA
130 AATTGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTATATATAATATATATA
* *
536327 ATATTTTTTAATTAAAAAAATAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAAT
1 AAATTTTTTAATTAAAAAAA-AG-TTACAATTAACTTAAATAATATATAATTATAAAATAAAAAT
* *
536392 TTTATAT-AATTTTTTAAATTAATTAATATTGATTTAGGTTTAAAAGTTATT-AGATCTTAAATT
64 TTCAGATAAATTTTTT-AATTAATTAATATTGATTTAGGTTTAAAAGTTATTGA-ATCTTAAATT
* *
536455 ATTAATTGGGTTTTAAATGGTTTGGGCTGAGTCCATATGTTATATATAATATATTTA
127 ATTAATTGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTATATATAATATATATA
536512 AAATTT
1 AAATTT
536518 AATTTCGGTT
Statistics
Matches: 178, Mismatches: 9, Indels: 7
0.92 0.05 0.04
Matches are distributed among these distances:
183 16 0.09
184 14 0.08
185 148 0.83
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.45
Consensus pattern (183 bp):
AAATTTTTTAATTAAAAAAAAGTTACAATTAACTTAAATAATATATAATTATAAAATAAAAATTT
CAGATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGAATCTTAAATTATTA
ATTGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTATATATAATATATATA
Found at i:540416 original size:23 final size:21
Alignment explanation
Indices: 540364--540424 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 21
540354 TTTTTTAATT
540364 AAATATAAATAAATTTATAAA
1 AAATATAAATAAATTTATAAA
**
540385 AATAGTATAAATTAAATTTTATTGA
1 AA-A-TATAAA-TAAA-TTTATAAA
*
540410 AAATATAACTAAATT
1 AAATATAAATAAATT
540425 ACAAGGTAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
21 4 0.12
22 5 0.15
23 11 0.33
24 5 0.15
25 8 0.24
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (21 bp):
AAATATAAATAAATTTATAAA
Found at i:540588 original size:24 final size:25
Alignment explanation
Indices: 540560--540611 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
540550 TTTAAAAAAT
540560 TAAAA-TTAATTTTTTATATTTT-TA
1 TAAAATTTAA-TTTTTATATTTTATA
540584 TAAAATTTTAATTTTTATATTTTATA
1 TAAAA-TTTAATTTTTATATTTTATA
540610 TA
1 TA
540612 TTTTTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 5 0.20
25 12 0.48
26 8 0.32
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
TAAAATTTAATTTTTATATTTTATA
Found at i:540599 original size:7 final size:8
Alignment explanation
Indices: 540570--540616 Score: 51
Period size: 8 Copynumber: 5.6 Consensus size: 8
540560 TAAAATTAAT
540570 TTTTTATA
1 TTTTTATA
540578 TTTTTATAAA
1 TTTTTAT--A
*
540588 ATTTTA-A
1 TTTTTATA
540595 TTTTTATA
1 TTTTTATA
540603 TTTTATATA
1 TTTT-TATA
540612 TTTTT
1 TTTTT
540617 TAAAATTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
7 6 0.18
8 13 0.39
9 8 0.24
10 6 0.18
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (8 bp):
TTTTTATA
Found at i:544021 original size:128 final size:128
Alignment explanation
Indices: 543794--544152 Score: 541
Period size: 128 Copynumber: 2.8 Consensus size: 128
543784 CGTCATTGAC
* *
543794 TGAAGGCGCGTTCCCGGGGGCACGCCTTCCATTA--TT-TCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATCATTGCCCTA
**
543856 TTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTA-TTCACA
66 TTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC-AGGGCACA
543919 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATCATTGCCCTA
* * * * * *
543984 TTATGTCACTCATATCCCTCGGGGACATTA-TTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTAGAT-ATATCAGTACCTATTATTTCACAGGGCACA
* *
544047 TGAAGGCGCGTTCCC-AGGGTGCGCCTTCCATTATTTTGTCATAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATCATTGCCCTA
*
544111 TTATGTCACTCATGTCCCTCGGGGGCACTAGATATATCAGTA
66 TTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
544153 AATCAGGTAA
Statistics
Matches: 212, Mismatches: 16, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
125 33 0.16
127 87 0.41
128 92 0.43
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (128 bp):
TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATCATTGCCCTA
TTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACAGGGCACA
Found at i:544590 original size:34 final size:34
Alignment explanation
Indices: 544552--544652 Score: 148
Period size: 34 Copynumber: 3.0 Consensus size: 34
544542 AAATTTAATG
*
544552 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
544586 TTAAATTTCGAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
544620 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
544653 AACATTATCA
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 58 1.00
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:545198 original size:21 final size:20
Alignment explanation
Indices: 545171--545240 Score: 86
Period size: 21 Copynumber: 3.4 Consensus size: 20
545161 GGTATAAAAC
*
545171 CCTGCGGGCTAGGCATGTAA
1 CCTGCGGGCTAGGAATGTAA
*
545191 CCTGGCGGGATAGGAATGTAA
1 CCT-GCGGGCTAGGAATGTAA
*
545212 CCCTGCGGGCTCGGAATGTAA
1 -CCTGCGGGCTAGGAATGTAA
545233 CCCTGCGG
1 -CCTGCGG
545241 AGATGGCATA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
20 3 0.07
21 38 0.86
22 3 0.07
ACGTcount: A:0.20, C:0.26, G:0.36, T:0.19
Consensus pattern (20 bp):
CCTGCGGGCTAGGAATGTAA
Found at i:545272 original size:21 final size:21
Alignment explanation
Indices: 545246--545285 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
545236 TGCGGAGATG
*
545246 GCATATAAACTGGTGGGCTTA
1 GCATATAAACTGGAGGGCTTA
*
545267 GCATATAAAGTGGAGGGCT
1 GCATATAAACTGGAGGGCT
545286 GGGCATGTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.33, T:0.25
Consensus pattern (21 bp):
GCATATAAACTGGAGGGCTTA
Found at i:545291 original size:21 final size:21
Alignment explanation
Indices: 545245--545291 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
545235 CTGCGGAGAT
* *
545245 GGCATATAAACTGGTGGGCTT
1 GGCATATAAACTGGAGGGCTG
* *
545266 AGCATATAAAGTGGAGGGCTG
1 GGCATATAAACTGGAGGGCTG
545287 GGCAT
1 GGCAT
545292 GTACCCCTGC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.13, G:0.36, T:0.23
Consensus pattern (21 bp):
GGCATATAAACTGGAGGGCTG
Found at i:546986 original size:31 final size:30
Alignment explanation
Indices: 546943--547017 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
546933 TTAATAATTC
* * *
546943 TAAATAAATAATAATATAAATATTATTTTAA
1 TAAAAAAATAATAATATAAATA-AATATTAA
* *
546974 TAAAAAAATAAT-ATTTACATAAATATTAA
1 TAAAAAAATAATAATATAAATAAATATTAA
547003 TATAAAAAATAATAA
1 TA-AAAAAATAATAA
547018 CTATTTAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 8 0.22
30 17 0.46
31 12 0.32
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (30 bp):
TAAAAAAATAATAATATAAATAAATATTAA
Found at i:546999 original size:34 final size:34
Alignment explanation
Indices: 546958--547043 Score: 93
Period size: 34 Copynumber: 2.5 Consensus size: 34
546948 AAATAATAAT
* *
546958 ATAAATATTATTTTAATAAAAAAATAA-TATTTAC
1 ATAAATATTAATATAA-AAAAAAATAACTATTTAC
* *
546992 ATAAATATTAATATAAAAAATAATAACTATTTAA
1 ATAAATATTAATATAAAAAAAAATAACTATTTAC
* * *
547026 AAAAATACTAACATAAAA
1 ATAAATATTAATATAAAA
547044 TAAATTTCTT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
33 9 0.20
34 35 0.80
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.34
Consensus pattern (34 bp):
ATAAATATTAATATAAAAAAAAATAACTATTTAC
Found at i:547104 original size:24 final size:25
Alignment explanation
Indices: 547076--547126 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
547066 AAATTTAAAC
547076 TAAAATA-TTGGAGAATTTGAGTTA
1 TAAAATAGTTGGAGAATTTGAGTTA
547100 TAAAATAGTTGGAGAATTTGAGTTA
1 TAAAATAGTTGGAGAATTTGAGTTA
547125 TA
1 TA
547127 TAAGAGAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 7 0.27
25 19 0.73
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (25 bp):
TAAAATAGTTGGAGAATTTGAGTTA
Found at i:547728 original size:16 final size:16
Alignment explanation
Indices: 547707--547754 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
547697 ATTTAGAAGA
*
547707 TAATATTTAATTTGTT
1 TAATATTTAAATTGTT
*
547723 TAATATTTAAATT-TA
1 TAATATTTAAATTGTT
547738 TAATAATTTAAATTGTT
1 TAAT-ATTTAAATTGTT
547755 ATCAAATCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 5 0.19
16 21 0.78
17 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (16 bp):
TAATATTTAAATTGTT
Found at i:548945 original size:31 final size:31
Alignment explanation
Indices: 548907--548965 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
548897 AACTTAAAAG
*
548907 AGTTTTACAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
548938 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
548966 CCATACAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:549016 original size:22 final size:22
Alignment explanation
Indices: 548990--549032 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
548980 TAATAACTTA
548990 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
549012 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
549033 CTAAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:549069 original size:22 final size:22
Alignment explanation
Indices: 549043--549087 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
549033 CTAAAAATTA
549043 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
549065 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
549087 T
1 T
549088 AATAAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:549094 original size:22 final size:22
Alignment explanation
Indices: 549041--549093 Score: 81
Period size: 22 Copynumber: 2.4 Consensus size: 22
549031 TACTAAAAAT
549041 TATT-TAAAATAAATCAATCCA
1 TATTATAAAATAAATCAATCCA
*
549062 TATTTTAAAATAAATCAATCCA
1 TATTATAAAATAAATCAATCCA
549084 TATTAATAAA
1 TATT-ATAAA
549094 TTATTTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 4 0.14
22 21 0.72
23 4 0.14
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (22 bp):
TATTATAAAATAAATCAATCCA
Found at i:549119 original size:54 final size:54
Alignment explanation
Indices: 548980--549833 Score: 1097
Period size: 54 Copynumber: 15.8 Consensus size: 54
548970 ACAACTACAA
*
548980 TAATAACTTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
549034 TAA-AAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
549087 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
549141 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
549195 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
549249 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* *
549303 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATGAATCTATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* * *
549357 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATGAATCGATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
549411 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* * * **
549465 TAATAAATTATTTAAAATAATTCAATCTATACAACTACAATAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATAC
** * ** * ** ** *
549522 TTTTAAAATAAAT-CAATCTATACTAATAAAT-TATTTAAAATAAATCAATCCATGC
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATAC
*
549577 -AACTACA--A--T--AATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* **
549625 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATAC
** * ** * ** ** *
549682 TTTTAAAATAAAT-CAATCCATACTAATAAAT-TATTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATAC
549737 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
549791 TAATAAATTATTTAAAAATAAATCAATCCATATTTTATAATAA
1 TAATAAATTATTT-AAAATAAATCAATCCATATTTTAAAATAA
549834 TTTATTTTAA
Statistics
Matches: 699, Mismatches: 72, Indels: 57
0.84 0.09 0.07
Matches are distributed among these distances:
48 29 0.04
49 4 0.01
50 6 0.01
51 1 0.00
52 1 0.00
53 52 0.07
54 477 0.68
55 47 0.07
56 14 0.02
57 26 0.04
58 42 0.06
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.35
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:549148 original size:22 final size:22
Alignment explanation
Indices: 549099--549147 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
549089 ATAAATTATT
* **
549099 TAAAATAAATCAATCTATATTT
1 TAAAATAAATCAATCCATATAA
549121 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
549144 TAAA
1 TAAA
549148 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:549177 original size:22 final size:22
Alignment explanation
Indices: 549151--549193 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
549141 TAATAAATTA
549151 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
549173 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
549194 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:549202 original size:22 final size:22
Alignment explanation
Indices: 549153--549201 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
549143 ATAAATTATT
**
549153 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
549175 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
549198 TAAA
1 TAAA
549202 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:549256 original size:22 final size:22
Alignment explanation
Indices: 549207--549255 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
549197 ATAAATTATT
**
549207 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
549229 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCCATA-TAA
549252 TAAA
1 TAAA
549256 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:549285 original size:22 final size:22
Alignment explanation
Indices: 549259--549301 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
549249 TAATAAATTA
549259 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
549281 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
549302 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:549310 original size:22 final size:22
Alignment explanation
Indices: 549261--549309 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
549251 ATAAATTATT
**
549261 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
549283 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
549306 TAAA
1 TAAA
549310 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:549373 original size:32 final size:32
Alignment explanation
Indices: 549335--549496 Score: 139
Period size: 32 Copynumber: 5.7 Consensus size: 32
549325 CAATCCATAT
*
549335 TTTAAAATAAATGAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCTATACTAATAAATTA
549367 TTTAAAATAAATC-A---AT-CT-AT--A-T-
1 TTTAAAATAAATCAATCTATACTAATAAATTA
* *
549389 TTTAAAATAAATGAATCGATACTAATAAATTA
1 TTTAAAATAAATCAATCTATACTAATAAATTA
549421 TTTAAAATAAATCAATC----C--AT--A-T-
1 TTTAAAATAAATCAATCTATACTAATAAATTA
*
549443 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCTATACTAATAAATTA
*
549475 TTTAAAATAATTCAATCTATAC
1 TTTAAAATAAATCAATCTATAC
549497 AACTACAATA
Statistics
Matches: 105, Mismatches: 5, Indels: 40
0.70 0.03 0.27
Matches are distributed among these distances:
22 29 0.28
23 3 0.03
24 2 0.02
26 7 0.07
27 4 0.04
28 7 0.07
30 2 0.02
31 3 0.03
32 48 0.46
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.37
Consensus pattern (32 bp):
TTTAAAATAAATCAATCTATACTAATAAATTA
Found at i:549447 original size:22 final size:22
Alignment explanation
Indices: 549421--549463 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
549411 TAATAAATTA
549421 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
549443 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
549464 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:549472 original size:22 final size:22
Alignment explanation
Indices: 549423--549471 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
549413 ATAAATTATT
**
549423 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
549445 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
549468 TAAA
1 TAAA
549472 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:549522 original size:80 final size:80
Alignment explanation
Indices: 549102--549822 Score: 728
Period size: 80 Copynumber: 8.9 Consensus size: 80
549092 AATTATTTAA
*
549102 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
* **
549167 CCAT---ATTTTAA-
66 CCATACAACTAAAAT
** * ** * ** **
549178 AATAAATCAATCCATACTAATAAATTATTTAAAATAAAT-C-AATCCA-TATTTTAAAATAAATC
1 AATAAATCAATCCATA-TTTTAAAATAAAT-CAATCCATACTAATAAATTA-TTTAAAATAAATC
*
549240 AATCTATACTAA-TAAATTATTT
63 AATCCATAC-AACTAAA--A--T
549262 AAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
1 --AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
***
549327 ATCCATA-TTTTAAAAT
64 ATCCATACAACTAAAAT
* * *
549343 AAATGAATCTATACTAATAAATTATTTAAAATAAATC-A---AT-CT-AT--A-T-TTTAAAATA
1 -AATAAATCAAT-C-CAT--A-T-TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATA
* *
549398 AATGAATCGATACTAA-TAAATTATTT
59 AATCAATCCATAC-AACTAAA--A--T
*
549424 AAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAATTCA
1 --AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
* *
549489 ATCTATACAACTACAAT
64 ATCCATACAACTAAAAT
*
549506 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
* *
549571 CCATGCAACTACAAT
66 CCATACAACTAAAAT
549586 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
*
549651 CCATACAACTACAAT
66 CCATACAACTAAAAT
549666 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
*
549731 TCATACTAA-TAAATTATTT
66 CCATAC-AACTAAA--A--T
549750 AAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAAATAAATC
1 --AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTT-AAAATAAATC
549815 AATCCATA
63 AATCCATA
549823 TTTTATAATA
Statistics
Matches: 545, Mismatches: 50, Indels: 89
0.80 0.07 0.13
Matches are distributed among these distances:
75 2 0.00
76 70 0.13
77 16 0.03
78 7 0.01
79 3 0.01
80 244 0.45
81 11 0.02
82 18 0.03
83 1 0.00
84 9 0.02
85 18 0.03
86 127 0.23
87 19 0.03
ACGTcount: A:0.52, C:0.13, G:0.01, T:0.35
Consensus pattern (80 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATACAACTAAAAT
Found at i:549632 original size:22 final size:22
Alignment explanation
Indices: 549559--549632 Score: 62
Period size: 22 Copynumber: 3.2 Consensus size: 22
549549 AAATTATTTA
549559 AAATAAATCAATCCATGCAACTACA-
1 AAATAAATCAATCCAT---ACTA-AT
**
549584 ATAATAAATCAATCCATA-TTTT
1 A-AATAAATCAATCCATACTAAT
549606 AAAATAAATCAATCCATACTAAT
1 -AAATAAATCAATCCATACTAAT
549629 AAAT
1 AAAT
549633 TATTTAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
22 21 0.51
23 4 0.10
25 1 0.02
26 15 0.37
ACGTcount: A:0.53, C:0.18, G:0.01, T:0.28
Consensus pattern (22 bp):
AAATAAATCAATCCATACTAAT
Found at i:549642 original size:32 final size:32
Alignment explanation
Indices: 549603--549822 Score: 215
Period size: 32 Copynumber: 7.7 Consensus size: 32
549593 CAATCCATAT
549603 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
549635 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
549665 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
549683 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
549715 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
549747 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
549769 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
549801 TTTAAAAATAAATCAATCCATA
1 TTT-AAAATAAATCAATCCATA
549823 TTTTATAATA
Statistics
Matches: 159, Mismatches: 2, Indels: 53
0.74 0.01 0.25
Matches are distributed among these distances:
20 1 0.01
22 30 0.19
23 3 0.02
24 3 0.02
25 1 0.01
26 18 0.11
28 4 0.03
30 2 0.01
31 4 0.03
32 75 0.47
33 18 0.11
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.34
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:549712 original size:22 final size:23
Alignment explanation
Indices: 549637--549711 Score: 82
Period size: 22 Copynumber: 3.2 Consensus size: 23
549627 ATAAATTATT
549637 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
**
549659 CTACAATAATAAATCAATCCATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
549685 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
549708 TAAA
1 TAAA
549712 TTATTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 16 0.37
23 8 0.19
25 3 0.07
26 16 0.37
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:549725 original size:14 final size:14
Alignment explanation
Indices: 549706--549758 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
549696 AATCCATACT
549706 AATAAATTATTTAA
1 AATAAATTATTTAA
* *
549720 AATAAATCAATTCATACT
1 AATAAAT-TATT--TA-A
549738 AATAAATTATTTAA
1 AATAAATTATTTAA
549752 AATAAAT
1 AATAAAT
549759 CAATCCATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 14 0.45
15 5 0.16
17 5 0.16
18 7 0.23
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.38
Consensus pattern (14 bp):
AATAAATTATTTAA
Found at i:549773 original size:22 final size:22
Alignment explanation
Indices: 549747--549789 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
549737 TAATAAATTA
549747 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
549769 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
549790 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:549798 original size:22 final size:22
Alignment explanation
Indices: 549749--549797 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
549739 ATAAATTATT
**
549749 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
549771 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
549794 TAAA
1 TAAA
549798 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:549841 original size:15 final size:15
Alignment explanation
Indices: 549821--549940 Score: 204
Period size: 15 Copynumber: 8.0 Consensus size: 15
549811 AATCAATCCA
*
549821 TATTTTATAATAATT
1 TATTTTATAATAAAT
*
549836 TATTTTAAAATAAAT
1 TATTTTATAATAAAT
549851 TATTTTATAATAAAT
1 TATTTTATAATAAAT
549866 TATTTTATAATAAAT
1 TATTTTATAATAAAT
549881 TATTTTATAATAAAT
1 TATTTTATAATAAAT
549896 TATTTTATAATAAAT
1 TATTTTATAATAAAT
*
549911 TATTTTAAAATAAAT
1 TATTTTATAATAAAT
*
549926 TATTTTAAAATAAAT
1 TATTTTATAATAAAT
549941 AACCTTATTA
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 101 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTTATAATAAAT
Found at i:549846 original size:37 final size:33
Alignment explanation
Indices: 549766--549940 Score: 125
Period size: 30 Copynumber: 5.5 Consensus size: 33
549756 AATCAATCCA
*
549766 TATTTTAAAATAAATCAATCCATACTAATAAAT
1 TATTTTAAAATAAATCAATCCATAATAATAAAT
* *
549799 TATTTAAAAATAAATCAATCCATATTTTATAATAATT
1 TATTTTAAAATAAATCAATCCATA----ATAATAAAT
* * *
549836 TATTTTAAAATAAAT-TAT--TTTATAATAAAT
1 TATTTTAAAATAAATCAATCCATAATAATAAAT
* * * *
549866 TATTTTATAATAAAT-TAT--TTTATAATAAAT
1 TATTTTAAAATAAATCAATCCATAATAATAAAT
* * **
549896 TATTTTATAATAAAT-TAT-TTTAA-AATAAAT
1 TATTTTAAAATAAATCAATCCATAATAATAAAT
549926 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
549941 AACCTTATTA
Statistics
Matches: 126, Mismatches: 11, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
30 76 0.60
31 3 0.02
33 23 0.18
34 1 0.01
36 2 0.02
37 21 0.17
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (33 bp):
TATTTTAAAATAAATCAATCCATAATAATAAAT
Found at i:551612 original size:8 final size:8
Alignment explanation
Indices: 551599--551628 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
551589 CAAACTCCAA
551599 TTATTATT
1 TTATTATT
551607 TTATTATAT
1 TTATTAT-T
551616 TTATTATT
1 TTATTATT
551624 TTATT
1 TTATT
551629 CTACTTTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (8 bp):
TTATTATT
Found at i:555891 original size:156 final size:156
Alignment explanation
Indices: 555660--555972 Score: 626
Period size: 156 Copynumber: 2.0 Consensus size: 156
555650 TTTCTTGAAG
555660 AAAATATAGTTGTGGCGCAAAACATAACTCCATGGTTTGCGGACATGGCCAATTATTTGGCCACA
1 AAAATATAGTTGTGGCGCAAAACATAACTCCATGGTTTGCGGACATGGCCAATTATTTGGCCACA
555725 TGTAAGTTACAATTAGATTTACCGAGAGCTGAAATCAATCAAATTAAATGAGAATCCCGATACTA
66 TGTAAGTTACAATTAGATTTACCGAGAGCTGAAATCAATCAAATTAAATGAGAATCCCGATACTA
555790 TATTTGGGATGATCCTTATTTATGGA
131 TATTTGGGATGATCCTTATTTATGGA
555816 AAAATATAGTTGTGGCGCAAAACATAACTCCATGGTTTGCGGACATGGCCAATTATTTGGCCACA
1 AAAATATAGTTGTGGCGCAAAACATAACTCCATGGTTTGCGGACATGGCCAATTATTTGGCCACA
555881 TGTAAGTTACAATTAGATTTACCGAGAGCTGAAATCAATCAAATTAAATGAGAATCCCGATACTA
66 TGTAAGTTACAATTAGATTTACCGAGAGCTGAAATCAATCAAATTAAATGAGAATCCCGATACTA
555946 TATTTGGGATGATCCTTATTTATGGA
131 TATTTGGGATGATCCTTATTTATGGA
555972 A
1 A
555973 GCACTGCTCG
Statistics
Matches: 157, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
156 157 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (156 bp):
AAAATATAGTTGTGGCGCAAAACATAACTCCATGGTTTGCGGACATGGCCAATTATTTGGCCACA
TGTAAGTTACAATTAGATTTACCGAGAGCTGAAATCAATCAAATTAAATGAGAATCCCGATACTA
TATTTGGGATGATCCTTATTTATGGA
Found at i:560835 original size:23 final size:23
Alignment explanation
Indices: 560790--560835 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
560780 GAGTCGAGGG
* *
560790 TTCTACGCGGTCCTTTGATACAT
1 TTCTACGCGGTCCTTCGAGACAT
560813 TTCTACGCGGTCCTTCGAGACAT
1 TTCTACGCGGTCCTTCGAGACAT
560836 CTATGTGGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.17, C:0.28, G:0.20, T:0.35
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCGAGACAT
Found at i:567835 original size:46 final size:44
Alignment explanation
Indices: 567783--567873 Score: 119
Period size: 44 Copynumber: 2.0 Consensus size: 44
567773 GAGTCGAGAG
* *
567783 TTCTACGCGGTCCTTTGGGATAATTCTACGTGGTCCTTTGGAACAT
1 TTCTACGCCGTCCTTTGGGA-AA-TCTACGTGGTCCTTCGGAACAT
* * *
567829 TTCTACGCCGTCCTTTGGGACATCTATGTGGTCCTTCGGTACAT
1 TTCTACGCCGTCCTTTGGGAAATCTACGTGGTCCTTCGGAACAT
567873 T
1 T
567874 CTATGTGGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 20 0.50
45 1 0.03
46 19 0.47
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.37
Consensus pattern (44 bp):
TTCTACGCCGTCCTTTGGGAAATCTACGTGGTCCTTCGGAACAT
Found at i:567851 original size:23 final size:23
Alignment explanation
Indices: 567783--567851 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
567773 GAGTCGAGAG
* *
567783 TTCTACGCGGTCCTTTGGGATAA
1 TTCTACGCGGTCCTTTGGGACAT
* *
567806 TTCTACGTGGTCCTTTGGAACAT
1 TTCTACGCGGTCCTTTGGGACAT
*
567829 TTCTACGCCGTCCTTTGGGACAT
1 TTCTACGCGGTCCTTTGGGACAT
567852 CTATGTGGTC
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (23 bp):
TTCTACGCGGTCCTTTGGGACAT
Found at i:567879 original size:22 final size:22
Alignment explanation
Indices: 567783--567882 Score: 87
Period size: 23 Copynumber: 4.5 Consensus size: 22
567773 GAGTCGAGAG
*
567783 TTCTACGCGGTCCTTTGGGATA-A
1 TTCTACGTGGTCCTTT-GGA-ACA
567806 TTCTACGTGGTCCTTTGGAACA
1 TTCTACGTGGTCCTTTGGAACA
** *
567828 TTTCTACGCCGTCCTTTGGGACA
1 -TTCTACGTGGTCCTTTGGAACA
* * *
567851 -TCTATGTGGTCCTTCGGTACA
1 TTCTACGTGGTCCTTTGGAACA
*
567872 TTCTATGTGGT
1 TTCTACGTGGT
567883 ATTTCGGTGC
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
21 17 0.26
22 14 0.22
23 34 0.52
ACGTcount: A:0.15, C:0.23, G:0.24, T:0.38
Consensus pattern (22 bp):
TTCTACGTGGTCCTTTGGAACA
Found at i:567888 original size:22 final size:22
Alignment explanation
Indices: 567851--567895 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
567841 CTTTGGGACA
*
567851 TCTATGTGGTCCTTCGGTACAT
1 TCTATGTGGTACTTCGGTACAT
* *
567873 TCTATGTGGTATTTCGGTGCAT
1 TCTATGTGGTACTTCGGTACAT
567895 T
1 T
567896 TTATACGAGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.13, C:0.18, G:0.24, T:0.44
Consensus pattern (22 bp):
TCTATGTGGTACTTCGGTACAT
Found at i:569759 original size:23 final size:23
Alignment explanation
Indices: 569733--569788 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
569723 TATTTGGGAC
569733 TAAATTAAAAAACTCAAAA-AAAT
1 TAAATTAAAAAACT-AAAATAAAT
* ** *
569756 TAAATTTATTAACTAAAATATAT
1 TAAATTAAAAAACTAAAATAAAT
569779 TAAATTAAAA
1 TAAATTAAAA
569789 TTAAAATACC
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (23 bp):
TAAATTAAAAAACTAAAATAAAT
Found at i:570776 original size:21 final size:23
Alignment explanation
Indices: 570738--570781 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
570728 TTTCTATTTT
*
570738 TTTTGTCTTTTTTGTTTTTGATA
1 TTTTGTCTTTTCTGTTTTTGATA
570761 TTTT-TCTTTTCT-TTTTTGATA
1 TTTTGTCTTTTCTGTTTTTGATA
570782 ATAATAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 7 0.35
23 4 0.20
ACGTcount: A:0.09, C:0.07, G:0.09, T:0.75
Consensus pattern (23 bp):
TTTTGTCTTTTCTGTTTTTGATA
Found at i:571167 original size:55 final size:55
Alignment explanation
Indices: 571108--571636 Score: 589
Period size: 55 Copynumber: 9.6 Consensus size: 55
571098 AGACGAGTAT
*
571108 GCTCCACTATTCTTTCAGGGAGATA-AGACTCGAGA-AATCTT-TGGAAAACGGGTTC
1 GCTCC-CTATTCTTTCAGGGAGATATAGACTCGA-ACAATCTTCT-GAAAATGGGTTC
* * * *
571163 GCTCCCTATTATTTC-GGGAAATATATAACTCGAACAATCTTCTGAAAACGGGTTC
1 GCTCCCTATTCTTTCAGGGAGATATA-GACTCGAACAATCTTCTGAAAATGGGTTC
* *
571218 GCTCCCTATTCTTTCAAGGAGTATATA-ACTTGAACAATCTTCTGAAAATGGGTTC
1 GCTCCCTATTCTTTCAGGGAG-ATATAGACTCGAACAATCTTCTGAAAATGGGTTC
* * * * *
571273 GCTCCCTATTCTCTCAGGGAG-TATAAAACTCGAACAATCTTTTGAAAACGGGTTT
1 GCTCCCTATTCTTTCAGGGAGATAT-AGACTCGAACAATCTTCTGAAAATGGGTTC
* * *
571328 GTTCCCTATTCTTTCAAGGAG-TATAGAACTCGAACAATCTTCTGAAAATGAGTTC
1 GCTCCCTATTCTTTCAGGGAGATATAG-ACTCGAACAATCTTCTGAAAATGGGTTC
** * * *
571383 GCTCCCTATTCTTTTTGAGAG-TATAAAACTCGAA-AAGTCTTCTGAAAATTGGTTC
1 GCTCCCTATTCTTTCAGGGAGATAT-AGACTCGAACAA-TCTTCTGAAAATGGGTTC
* * *
571438 GCTCCCTATTCTCTCAGGGAG-TATAGGACTCGAACAATCTTATGAAAACGGGTTC
1 GCTCCCTATTCTTTCAGGGAGATATA-GACTCGAACAATCTTCTGAAAATGGGTTC
* *
571493 GCTGCCTATTCTTTTAGGGAG-TATAGAACTCGAACAATCTTCTGAAAATGGGTTC
1 GCTCCCTATTCTTTCAGGGAGATATAG-ACTCGAACAATCTTCTGAAAATGGGTTC
* * *
571548 GATCCCTATTCTTTCAGGGAG-TATAGAACTCGAACAATCTTCTAAAAATAGGTTC
1 GCTCCCTATTCTTTCAGGGAGATATAG-ACTCGAACAATCTTCTGAAAATGGGTTC
*
571603 GCTCCCTATTCTTTTAGGGAG-TATAGAACTCGAA
1 GCTCCCTATTCTTTCAGGGAGATATAG-ACTCGAA
571637 TAAGGGAGTA
Statistics
Matches: 410, Mismatches: 50, Indels: 28
0.84 0.10 0.06
Matches are distributed among these distances:
53 10 0.02
54 17 0.04
55 371 0.90
56 7 0.02
57 5 0.01
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (55 bp):
GCTCCCTATTCTTTCAGGGAGATATAGACTCGAACAATCTTCTGAAAATGGGTTC
Found at i:571280 original size:110 final size:109
Alignment explanation
Indices: 571108--571636 Score: 663
Period size: 110 Copynumber: 4.8 Consensus size: 109
571098 AGACGAGTAT
*
571108 GCTCCACTATTCTTTCAGGGAG-ATA-AGACTCGAGA-AATCTT-TGGAAAACGGGTTCGCTCCC
1 GCTCC-CTATTCTTTCAGGGAGTATAGA-ACTCGA-ACAATCTTCT-GAAAATGGGTTCGCTCCC
* * *
571169 TATTATTTCGGGAAATATATAACTCGAACAATCTTCTGAAAACGGGTTC
62 TATTCTTTCGGG-AGTATAAAACTCGAACAATCTTCTGAAAACGGGTTC
* * *
571218 GCTCCCTATTCTTTCAAGGAGTATATAACTTGAACAATCTTCTGAAAATGGGTTCGCTCCCTATT
1 GCTCCCTATTCTTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAAATGGGTTCGCTCCCTATT
* * *
571283 CTCTCAGGGAGTATAAAACTCGAACAATCTTTTGAAAACGGGTTT
66 CTTTC-GGGAGTATAAAACTCGAACAATCTTCTGAAAACGGGTTC
* * *
571328 GTTCCCTATTCTTTCAAGGAGTATAGAACTCGAACAATCTTCTGAAAATGAGTTCGCTCCCTATT
1 GCTCCCTATTCTTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAAATGGGTTCGCTCCCTATT
* * **
571393 CTTTTTGAGAGTATAAAACTCGAA-AAGTCTTCTGAAAATTGGTTC
66 C-TTTCGGGAGTATAAAACTCGAACAA-TCTTCTGAAAACGGGTTC
* * * * *
571438 GCTCCCTATTCTCTCAGGGAGTATAGGACTCGAACAATCTTATGAAAACGGGTTCGCTGCCTATT
1 GCTCCCTATTCTTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAAATGGGTTCGCTCCCTATT
* * *
571503 CTTTTAGGGAGTATAGAACTCGAACAATCTTCTGAAAATGGGTTC
66 C-TTTCGGGAGTATAAAACTCGAACAATCTTCTGAAAACGGGTTC
* * *
571548 GATCCCTATTCTTTCAGGGAGTATAGAACTCGAACAATCTTCTAAAAATAGGTTCGCTCCCTATT
1 GCTCCCTATTCTTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAAATGGGTTCGCTCCCTATT
* *
571613 CTTTTAGGGAGTATAGAACTCGAA
66 C-TTTCGGGAGTATAAAACTCGAA
571637 TAAGGGAGTA
Statistics
Matches: 371, Mismatches: 40, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
109 18 0.05
110 344 0.93
111 9 0.02
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (109 bp):
GCTCCCTATTCTTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAAATGGGTTCGCTCCCTATT
CTTTCGGGAGTATAAAACTCGAACAATCTTCTGAAAACGGGTTC
Found at i:571360 original size:165 final size:165
Alignment explanation
Indices: 571108--571636 Score: 717
Period size: 165 Copynumber: 3.2 Consensus size: 165
571098 AGACGAGTAT
* * *
571108 GCTCCACTATTCTTTCAGGGAG-ATAAGACTCGAGA-AATCTTTGGAAAACGGGTTCGCTCCCTA
1 GCTCC-CTATTCTCTCAGGGAGTATAAAACTCGA-ACAATCTTTTGAAAACGGGTTCGCTCCCTA
* * * *
571171 TTATTTC-GGGAAATATATAACTCGAACAATCTTCTGAAAACGGGTTCGCTCCCTATTCTTTCAA
64 TTCTTTCAGGG-AGTATAGAACTCGAACAATCTTCTGAAAATGGGTTCGCTCCCTATTCTTTCAA
* * *
571235 GGAGTATATAACTTGAACAATCTTCTGAAAATGGGTTC
128 GGAGTATAAAACTCGAACAATCTTCTGAAAATAGGTTC
* *
571273 GCTCCCTATTCTCTCAGGGAGTATAAAACTCGAACAATCTTTTGAAAACGGGTTTGTTCCCTATT
1 GCTCCCTATTCTCTCAGGGAGTATAAAACTCGAACAATCTTTTGAAAACGGGTTCGCTCCCTATT
* * **
571338 CTTTCAAGGAGTATAGAACTCGAACAATCTTCTGAAAATGAGTTCGCTCCCTATTCTTT-TTGAG
66 CTTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAAATGGGTTCGCTCCCTATTCTTTCAAG-G
*
571402 AGTATAAAACTCGAA-AAGTCTTCTGAAAATTGGTTC
130 AGTATAAAACTCGAACAA-TCTTCTGAAAATAGGTTC
** * *
571438 GCTCCCTATTCTCTCAGGGAGTATAGGACTCGAACAATCTTATGAAAACGGGTTCGCTGCCTATT
1 GCTCCCTATTCTCTCAGGGAGTATAAAACTCGAACAATCTTTTGAAAACGGGTTCGCTCCCTATT
* * *
571503 CTTTTAGGGAGTATAGAACTCGAACAATCTTCTGAAAATGGGTTCGATCCCTATTCTTTCAGGGA
66 CTTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAAATGGGTTCGCTCCCTATTCTTTCAAGGA
* *
571568 GTATAGAACTCGAACAATCTTCTAAAAATAGGTTC
131 GTATAAAACTCGAACAATCTTCTGAAAATAGGTTC
* * *
571603 GCTCCCTATTCTTTTAGGGAGTATAGAACTCGAA
1 GCTCCCTATTCTCTCAGGGAGTATAAAACTCGAA
571637 TAAGGGAGTA
Statistics
Matches: 323, Mismatches: 34, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
164 19 0.06
165 299 0.93
166 5 0.02
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (165 bp):
GCTCCCTATTCTCTCAGGGAGTATAAAACTCGAACAATCTTTTGAAAACGGGTTCGCTCCCTATT
CTTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAAATGGGTTCGCTCCCTATTCTTTCAAGGA
GTATAAAACTCGAACAATCTTCTGAAAATAGGTTC
Found at i:571644 original size:21 final size:21
Alignment explanation
Indices: 571618--571657 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
571608 CTATTCTTTT
571618 AGGGAGTATAGAACTCGAATA
1 AGGGAGTATAGAACTCGAATA
571639 AGGGAGTATAGAACTCGAA
1 AGGGAGTATAGAACTCGAA
571658 CAATCTTCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.42, C:0.10, G:0.30, T:0.17
Consensus pattern (21 bp):
AGGGAGTATAGAACTCGAATA
Found at i:571689 original size:76 final size:76
Alignment explanation
Indices: 571563--571712 Score: 264
Period size: 76 Copynumber: 2.0 Consensus size: 76
571553 CTATTCTTTC
* *
571563 AGGGAGTATAGAACTCGAACAATCTTCTAAAAATAGGTTCGCTCCCTATTCTTTTAGGGAGTATA
1 AGGGAGTATAGAACTCGAACAATCTTCTAAAAATAGGTTCACTCCCTATTCTTTCAGGGAGTATA
571628 GAACTCGAATA
66 GAACTCGAATA
* *
571639 AGGGAGTATAGAACTCGAACAATCTTCTGAAAATGGGTTCACTCCCTATTCTTTCAGGGAGTATA
1 AGGGAGTATAGAACTCGAACAATCTTCTAAAAATAGGTTCACTCCCTATTCTTTCAGGGAGTATA
571704 GAACTCGAA
66 GAACTCGAA
571713 CAATCTTCGG
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 70 1.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (76 bp):
AGGGAGTATAGAACTCGAACAATCTTCTAAAAATAGGTTCACTCCCTATTCTTTCAGGGAGTATA
GAACTCGAATA
Found at i:571726 original size:55 final size:54
Alignment explanation
Indices: 571639--571813 Score: 217
Period size: 55 Copynumber: 3.2 Consensus size: 54
571629 AACTCGAATA
* *
571639 AGGGAGTATAGAACTCGAACAATCTTCTGAAAATGGGT-TCACTCCCTATTCTTTC
1 AGGGAGTATAGAACTCGAACAATCTTC-GAAAATGAGTCT-GCTCCCTATTCTTTC
* * *
571694 AGGGAGTATAGAACTCGAACAATCTTCGGAAAACGAGTCTGCTCCTTCTTCTTTC
1 AGGGAGTATAGAACTCGAACAATCTTC-GAAAATGAGTCTGCTCCCTATTCTTTC
* * * *
571749 AGGGAATATAGAACTTGAACAATCTTCAACAAATGTGTCTGCTCCCTATTCTTTC
1 AGGGAGTATAGAACTCGAACAATCTTCGA-AAATGAGTCTGCTCCCTATTCTTTC
*
571804 AAGGAGTATA
1 AGGGAGTATA
571814 AGACTCAAAC
Statistics
Matches: 103, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
54 1 0.01
55 101 0.98
56 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.30
Consensus pattern (54 bp):
AGGGAGTATAGAACTCGAACAATCTTCGAAAATGAGTCTGCTCCCTATTCTTTC
Found at i:571746 original size:131 final size:131
Alignment explanation
Indices: 571508--571763 Score: 401
Period size: 131 Copynumber: 2.0 Consensus size: 131
571498 CTATTCTTTT
571508 AGGGAGTATAGAACTCGAACAATCTTCTGAAAATGGGTTCGATCCCTATTCTTTCAGGGAGTATA
1 AGGGAGTATAGAACTCGAACAATCTTCTGAAAATGGGTTCGATCCCTATTCTTTCAGGGAGTATA
* * * *
571573 GAACTCGAACAATCTTCTAAAAATAGGTTCGCTCCCTATTCTTTTAGGGAGTATAGAACTCGAAT
66 GAACTCGAACAATCTTCGAAAAAGAGGTTCGCTCCCTATTCTTTCAGGGAATATAGAACTCGAAT
571638 A
131 A
571639 AGGGAGTATAGAACTCGAACAATCTTCTGAAAATGGGTTC-ACTCCCTATTCTTTCAGGGAGTAT
1 AGGGAGTATAGAACTCGAACAATCTTCTGAAAATGGGTTCGA-TCCCTATTCTTTCAGGGAGTAT
* * *
571703 AGAACTCGAACAATCTTCGGAAAACGA-G-TCTGCTCCTTCTTCTTTCAGGGAATATAGAACT
65 AGAACTCGAACAATCTTC-GAAAAAGAGGTTC-GCTCCCTATTCTTTCAGGGAATATAGAACT
571764 TGAACAATCT
Statistics
Matches: 115, Mismatches: 7, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
130 3 0.03
131 107 0.93
132 5 0.04
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (131 bp):
AGGGAGTATAGAACTCGAACAATCTTCTGAAAATGGGTTCGATCCCTATTCTTTCAGGGAGTATA
GAACTCGAACAATCTTCGAAAAAGAGGTTCGCTCCCTATTCTTTCAGGGAATATAGAACTCGAAT
A
Found at i:571771 original size:186 final size:186
Alignment explanation
Indices: 571453--571813 Score: 514
Period size: 186 Copynumber: 1.9 Consensus size: 186
571443 CTATTCTCTC
* * * *
571453 AGGGAGTATAGGACTCGAACAATCTTATGAAAACGGGTTCGCTGCCTATTCTTTTAGGGAGTATA
1 AGGGAGTATAGAACTCGAACAATCTTATGAAAACGGGTTCACTCCCTATTCTTTCAGGGAGTATA
* * * *
571518 GAACTCGAACAATCTTCTGAAAATGGGTTCGATCCCTATTCTTTCAGGGAGTATAGAACTCGAAC
66 GAACTCGAACAATCTTCGGAAAACGAGTTCGATCCCTATTCTTTCAGGGAATATAGAACTCGAAC
* *
571583 AATCTTCTAA-AAATAG-GT-TCGCTCCCTATTCTTTTAGGGAGTATAGAACTCGAATA
131 AATCTTC-AACAAAT-GTGTCT-GCTCCCTATTCTTTCAAGGAGTATAGAACTCGAATA
* *
571639 AGGGAGTATAGAACTCGAACAATCTTCTGAAAATGGGTTCACTCCCTATTCTTTCAGGGAGTATA
1 AGGGAGTATAGAACTCGAACAATCTTATGAAAACGGGTTCACTCCCTATTCTTTCAGGGAGTATA
* * * *
571704 GAACTCGAACAATCTTCGGAAAACGAG-TCTGCTCCTTCTTCTTTCAGGGAATATAGAACTTGAA
66 GAACTCGAACAATCTTCGGAAAACGAGTTC-GATCCCTATTCTTTCAGGGAATATAGAACTCGAA
571768 CAATCTTCAACAAATGTGTCTGCTCCCTATTCTTTCAAGGAGTATA
130 CAATCTTCAACAAATGTGTCTGCTCCCTATTCTTTCAAGGAGTATA
571814 AGACTCAAAC
Statistics
Matches: 155, Mismatches: 16, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
185 5 0.03
186 149 0.96
187 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (186 bp):
AGGGAGTATAGAACTCGAACAATCTTATGAAAACGGGTTCACTCCCTATTCTTTCAGGGAGTATA
GAACTCGAACAATCTTCGGAAAACGAGTTCGATCCCTATTCTTTCAGGGAATATAGAACTCGAAC
AATCTTCAACAAATGTGTCTGCTCCCTATTCTTTCAAGGAGTATAGAACTCGAATA
Found at i:574918 original size:252 final size:250
Alignment explanation
Indices: 574466--574933 Score: 695
Period size: 252 Copynumber: 1.9 Consensus size: 250
574456 TGAATTCAAA
* * * *
574466 TTTATTGTATATATATTATAATCGCCTTTATCGGACTAGTTGAAGGGTTCATATCATCATAGAGT
1 TTTATTGTATATATATTATAATCCCCTTTATCGGACTAGCTGAAGGGTTCATATCATCACAAAGT
* *
574531 CTTCGACCTGACAATTGCAGTGGAGCAAACACCAAACTGCCAAGTATCCGAGCAATGTCATGGTT
66 CTTCGACCTGACAATTACAGTGGAACAAACACCAAACTGCCAAGTATCCGAGCAATGTCATGGTT
* * * *
574596 TGAATACAATCTATTCATAAAGCCAGGGCTTTTGAGTGTCCTTTATAACCAATTGCTTTAGTGGA
131 TAAATACAATATATTCATAAAGCCAGGGCTTTTGAGTGTCCTCTATAACCAATTGCTTTAGTGAA
* *
574661 ATAGCTTAGTTTTATCGTATACATATATAATTATATTCTGGGTATATGGATTAGC
196 ATAGCTCAGCTTTATCGTATACATATATAATTATATTCTGGGTATATGGATTAGC
* *
574716 TTTATTGTATATATATATTATAATCCCCTTTATC-GAGCTAGCTGAATGGTTCATCTCATCACAA
1 TTTATTG--TATATATATTATAATCCCCTTTATCGGA-CTAGCTGAAGGGTTCATATCATCACAA
* * * *
574780 AGTCTTCGACCTGACAATTACAGTGGAACAAACATCGAACTGCCAAGTATCCGAGCATTTTCATG
63 AGTCTTCGACCTGACAATTACAGTGGAACAAACACCAAACTGCCAAGTATCCGAGCAATGTCATG
* * * *
574845 GTTTAAATACAATATATTTATAAAGCCAGGGCTTTTGAGTTTCCTCTATAGCCAATTGCTTTATT
128 GTTTAAATACAATATATTCATAAAGCCAGGGCTTTTGAGTGTCCTCTATAACCAATTGCTTTAGT
*
574910 GAAATAGCTCAGCTTTATTGTATA
193 GAAATAGCTCAGCTTTATCGTATA
574934 TAATTACATT
Statistics
Matches: 192, Mismatches: 23, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
250 7 0.04
251 2 0.01
252 183 0.95
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (250 bp):
TTTATTGTATATATATTATAATCCCCTTTATCGGACTAGCTGAAGGGTTCATATCATCACAAAGT
CTTCGACCTGACAATTACAGTGGAACAAACACCAAACTGCCAAGTATCCGAGCAATGTCATGGTT
TAAATACAATATATTCATAAAGCCAGGGCTTTTGAGTGTCCTCTATAACCAATTGCTTTAGTGAA
ATAGCTCAGCTTTATCGTATACATATATAATTATATTCTGGGTATATGGATTAGC
Found at i:583154 original size:14 final size:15
Alignment explanation
Indices: 583121--583149 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
583111 AACAAGGTAA
583121 AATTT-GTAATTTTT
1 AATTTAGTAATTTTT
583135 AATTTAGTAATTTTT
1 AATTTAGTAATTTTT
583150 GTTTATTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (15 bp):
AATTTAGTAATTTTT
Found at i:585123 original size:21 final size:21
Alignment explanation
Indices: 585072--585124 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
585062 ATTATGACTA
585072 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
585093 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
585114 TCGCAATGCGA
1 TCGCAATGCGA
585125 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:585139 original size:20 final size:21
Alignment explanation
Indices: 585114--585165 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
585104 TTTTCCCAAT
*
585114 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
585134 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
585155 TCGCAATGCGA
1 TCGCAATGCGA
585166 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:585219 original size:20 final size:20
Alignment explanation
Indices: 585194--585267 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
585184 AATTCTCCTA
*
585194 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACAT
* *
585214 ATTCGCGTTGCGATTTTCAT
1 ATTCGCATTGCGATTTACAT
*
585234 AATTCGCATTGCGATTTACTT
1 -ATTCGCATTGCGATTTACAT
585255 ATTCGCATTGCGA
1 ATTCGCATTGCGA
585268 ATTGGGAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
20 30 0.64
21 17 0.36
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACAT
Found at i:585282 original size:41 final size:41
Alignment explanation
Indices: 585196--585282 Score: 104
Period size: 41 Copynumber: 2.1 Consensus size: 41
585186 TTCTCCTAAT
* ** *
585196 TCGCATTGCGATTTACGTATTCGCGTTGCGATTTTCATAAT
1 TCGCATTGCGATTTACGTATTCGCATTGCGATTGGCATAAA
* *
585237 TCGCATTGCGATTTACTTATTCGCATTGCGAATTGGGA-AAA
1 TCGCATTGCGATTTACGTATTCGCATTGCG-ATTGGCATAAA
585278 TCGCA
1 TCGCA
585283 ACGCGAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 35 0.90
42 4 0.10
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.37
Consensus pattern (41 bp):
TCGCATTGCGATTTACGTATTCGCATTGCGATTGGCATAAA
Found at i:585288 original size:21 final size:20
Alignment explanation
Indices: 585264--585331 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
585254 TATTCGCATT
585264 GCGAATTGGGAAAATCGCAAC
1 GCGAATT-GGAAAATCGCAAC
*
585285 GCGAAATTGGAAAATCGCAAT
1 GCG-AATTGGAAAATCGCAAC
** * *
585306 GCGAATACGTAAATCGCAAT
1 GCGAATTGGAAAATCGCAAC
585326 GCGAAT
1 GCGAAT
585332 CTTACTATCG
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
20 20 0.48
21 18 0.43
22 4 0.10
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
GCGAATTGGAAAATCGCAAC
Found at i:585321 original size:20 final size:20
Alignment explanation
Indices: 585296--585371 Score: 118
Period size: 20 Copynumber: 3.8 Consensus size: 20
585286 CGAAATTGGA
585296 AAATCGCAATGCGAATACGT
1 AAATCGCAATGCGAATACGT
*
585316 AAATCGCAATGCGAAT-CTT
1 AAATCGCAATGCGAATACGT
*
585335 ACTATCGCAATGCGAATACGT
1 A-AATCGCAATGCGAATACGT
585356 AAATCGCAATGCGAAT
1 AAATCGCAATGCGAAT
585372 CTTACTATTG
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
19 3 0.06
20 44 0.88
21 3 0.06
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.22
Consensus pattern (20 bp):
AAATCGCAATGCGAATACGT
Found at i:585351 original size:40 final size:40
Alignment explanation
Indices: 585298--585389 Score: 175
Period size: 40 Copynumber: 2.3 Consensus size: 40
585288 AAATTGGAAA
585298 ATCGCAATGCGAATACGTAAATCGCAATGCGAATCTTACT
1 ATCGCAATGCGAATACGTAAATCGCAATGCGAATCTTACT
585338 ATCGCAATGCGAATACGTAAATCGCAATGCGAATCTTACT
1 ATCGCAATGCGAATACGTAAATCGCAATGCGAATCTTACT
*
585378 ATTGCAATGCGA
1 ATCGCAATGCGA
585390 TTTACATAGC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (40 bp):
ATCGCAATGCGAATACGTAAATCGCAATGCGAATCTTACT
Found at i:585384 original size:20 final size:20
Alignment explanation
Indices: 585298--585389 Score: 107
Period size: 20 Copynumber: 4.6 Consensus size: 20
585288 AAATTGGAAA
* *
585298 ATCGCAATGCGAATACGTA-A
1 ATCGCAATGCGAAT-CTTACT
585318 ATCGCAATGCGAATCTTACT
1 ATCGCAATGCGAATCTTACT
* *
585338 ATCGCAATGCGAATACGTA-A
1 ATCGCAATGCGAAT-CTTACT
585358 ATCGCAATGCGAATCTTACT
1 ATCGCAATGCGAATCTTACT
*
585378 ATTGCAATGCGA
1 ATCGCAATGCGA
585390 TTTACATAGC
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
19 6 0.10
20 53 0.85
21 3 0.05
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGAATCTTACT
Found at i:585655 original size:27 final size:27
Alignment explanation
Indices: 585599--585658 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
585589 ATCGCCGGCG
* *
585599 AAATCCCTCACAACCATTCACAGTCAA
1 AAATCCCTCACAACCATTCAAAATCAA
* *
585626 AAATCCCTCACAATCATTCAGAAATGAA
1 AAATCCCTCACAACCATTCA-AAATCAA
585654 AAATC
1 AAATC
585659 AACCTCCGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 19 0.68
28 9 0.32
ACGTcount: A:0.45, C:0.30, G:0.05, T:0.20
Consensus pattern (27 bp):
AAATCCCTCACAACCATTCAAAATCAA
Found at i:585946 original size:19 final size:19
Alignment explanation
Indices: 585908--585974 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
585898 TTCGAGAATG
585908 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
585928 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
585947 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
585966 AAAATCGCA
1 AAAATCGCA
585975 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 30 0.73
20 11 0.27
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:585992 original size:19 final size:19
Alignment explanation
Indices: 585970--586148 Score: 127
Period size: 19 Copynumber: 10.1 Consensus size: 19
585960 GAAACCAAAA
*
585970 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
585989 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
586003 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
586022 TCGCGTTGCAATTTTCATT
1 TCGCGTTGCGATTTTCATT
586041 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
586055 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
586074 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
586088 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
586107 TCCGCATTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
586127 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
586147 TC
1 TC
586149 AACCAAAAGA
Statistics
Matches: 125, Mismatches: 18, Indels: 34
0.71 0.10 0.19
Matches are distributed among these distances:
14 30 0.24
16 7 0.06
17 8 0.06
19 50 0.40
20 29 0.23
21 1 0.01
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:586058 original size:52 final size:52
Alignment explanation
Indices: 585970--586082 Score: 190
Period size: 52 Copynumber: 2.2 Consensus size: 52
585960 GAAACCAAAA
* * **
585970 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCGTTGCAATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
586022 TCGCGTTGCAATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
1 TCGCGTTGCAATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
586074 TCGCGTTGC
1 TCGCGTTGC
586083 GATTCTCTCG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 57 1.00
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (52 bp):
TCGCGTTGCAATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
Found at i:586062 original size:33 final size:33
Alignment explanation
Indices: 586036--586123 Score: 158
Period size: 33 Copynumber: 2.6 Consensus size: 33
586026 GTTGCAATTT
586036 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
586069 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
*
586102 TCATTTCCGCATTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
586124 ATTATCTCGT
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 39 0.74
34 14 0.26
ACGTcount: A:0.12, C:0.26, G:0.22, T:0.40
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
Found at i:586063 original size:14 final size:14
Alignment explanation
Indices: 586044--586099 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
586034 TTTCATTTCG
586044 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
586058 CGTTGCGATAGTCATTTCG
1 CGTTGCGAT--TC---TCT
586077 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
586091 CGTTGCGAT
1 CGTTGCGAT
586100 AGTCATTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 20 0.57
16 2 0.06
17 2 0.06
19 11 0.31
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Done.