Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007883.1 Hibiscus syriacus cultivar Beakdansim tig00110263_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: 1590433
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 9
Found at i:197019 original size:20 final size:22
Alignment explanation
Indices: 196994--197033 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
196984 TGTTGTATAT
196994 AGCCG-TTGGGGAT-ATTTTGG
1 AGCCGTTTGGGGATGATTTTGG
197014 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
197034 TCTACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 8 0.44
22 5 0.28
ACGTcount: A:0.15, C:0.10, G:0.38, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:197154 original size:20 final size:20
Alignment explanation
Indices: 197125--197198 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
197115 GCAGCCTTCG
*
197125 TGCATGGATGCACAGCAGGA
1 TGCATCGATGCACAGCAGGA
* **
197145 TGCATCGATGCACAACCTTGA
1 TGCATCGATGCAC-AGCAGGA
*
197166 TGCATCGATGCACAGAAGGA
1 TGCATCGATGCACAGCAGGA
197186 TGCATCGATGCAC
1 TGCATCGATGCAC
197199 TAATTGTATT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 28 0.62
21 17 0.38
ACGTcount: A:0.30, C:0.24, G:0.27, T:0.19
Consensus pattern (20 bp):
TGCATCGATGCACAGCAGGA
Found at i:197265 original size:42 final size:41
Alignment explanation
Indices: 197219--197339 Score: 138
Period size: 42 Copynumber: 2.9 Consensus size: 41
197209 CGATGTTTGA
* * *
197219 GTGCATAGATGCACTGTATGGTGCATCGATGCACTAGTGCA-G
1 GTGCATGGATGCACTGTAGGGTGCATAGATGCACT--TGCAGG
* *
197261 GTGCATGGATGCACTGCAGGGATGCATGGATGCA-TTGCAGGG
1 GTGCATGGATGCACTGTAGGG-TGCATAGATGCACTTGCA-GG
197303 GTGCATGGATGCACTGTAGGGGTGCATAGATGCACTT
1 GTGCATGGATGCACTGTA-GGGTGCATAGATGCACTT
197340 TGACACCCTT
Statistics
Matches: 68, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
40 4 0.06
42 48 0.71
43 16 0.24
ACGTcount: A:0.22, C:0.17, G:0.36, T:0.25
Consensus pattern (41 bp):
GTGCATGGATGCACTGTAGGGTGCATAGATGCACTTGCAGG
Found at i:197288 original size:21 final size:20
Alignment explanation
Indices: 197219--197338 Score: 116
Period size: 21 Copynumber: 5.8 Consensus size: 20
197209 CGATGTTTGA
* * *
197219 GTGCATAGATGCACTGTATG
1 GTGCATGGATGCACTGCAGG
*
197239 GTGCATCGATGCACTAGTGCA-G
1 GTGCATGGATGCAC---TGCAGG
197261 GTGCATGGATGCACTGCAGG
1 GTGCATGGATGCACTGCAGG
*
197281 GATGCATGGATGCATTGCAGGG
1 G-TGCATGGATGCACTGCA-GG
*
197303 GTGCATGGATGCACTGTAGGG
1 GTGCATGGATGCACTGCA-GG
*
197324 GTGCATAGATGCACT
1 GTGCATGGATGCACT
197339 TTGACACCCT
Statistics
Matches: 87, Mismatches: 7, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.05
20 15 0.17
21 48 0.55
22 17 0.20
23 3 0.03
ACGTcount: A:0.23, C:0.17, G:0.36, T:0.24
Consensus pattern (20 bp):
GTGCATGGATGCACTGCAGG
Found at i:197439 original size:29 final size:29
Alignment explanation
Indices: 197418--197475 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
197408 AAACTTTGAA
197418 TAAATTCAATT-AAGTACAAAAACATTTTG
1 TAAATTCAATTCAAGTACAAAAACA-TTTG
*
197447 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTACAAAAA-CATTT
197476 TGCCTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 11 0.42
30 13 0.50
31 2 0.08
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTACAAAAACATTTG
Found at i:197470 original size:30 final size:30
Alignment explanation
Indices: 197418--197477 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
197408 AAACTTTGAA
197418 TAAATTCAATTAAGTACAAAAA-CATTTTG
1 TAAATTCAATTAAGTACAAAAACCATTTTG
*
197447 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTACAAAAACCATTTTG
197478 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTACAAAAACCATTTTG
Found at i:200960 original size:23 final size:23
Alignment explanation
Indices: 200923--201033 Score: 104
Period size: 23 Copynumber: 4.8 Consensus size: 23
200913 AAATCAAGCG
200923 AATAAATTAAA-AAATTATTCAAA
1 AATAAA-TAAATAAATTATTCAAA
* **
200946 AATAAATAAATAAATTATTTATT
1 AATAAATAAATAAATTATTCAAA
*
200969 TA-AAATAAA-AAA-TATTCAAAATA
1 AATAAATAAATAAATTATTC--AA-A
**
200992 AATAAATAAATAAATTATTTGAA
1 AATAAATAAATAAATTATTCAAA
201015 AATAAATAAATAAATTATT
1 AATAAATAAATAAATTATT
201034 TTAAAAAAAT
Statistics
Matches: 71, Mismatches: 10, Indels: 14
0.75 0.11 0.15
Matches are distributed among these distances:
20 4 0.06
21 3 0.04
22 12 0.17
23 37 0.52
24 8 0.11
25 3 0.04
26 4 0.06
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.34
Consensus pattern (23 bp):
AATAAATAAATAAATTATTCAAA
Found at i:200989 original size:16 final size:17
Alignment explanation
Indices: 200965--200999 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
200955 ATAAATTATT
*
200965 TATTTAAAATAAA-AAA
1 TATTCAAAATAAATAAA
200981 TATTCAAAATAAATAAA
1 TATTCAAAATAAATAAA
200998 TA
1 TA
201000 AATAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
TATTCAAAATAAATAAA
Found at i:200996 original size:4 final size:4
Alignment explanation
Indices: 200987--201075 Score: 56
Period size: 4 Copynumber: 22.0 Consensus size: 4
200977 AAAATATTCA
* * ** **
200987 AAAT AAAT AAAT AAAT AAAT TATT TGA- AAAT AAAT AAAT AAATT ATTTT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA-T A-AAT
* * *
201036 AAAA AAAT -TAT TAAT AAAT AAAT AAATT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA-T AAAT AAAT AAAT
201076 TATTTATTTA
Statistics
Matches: 65, Mismatches: 15, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
3 3 0.05
4 54 0.83
5 8 0.12
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (4 bp):
AAAT
Found at i:201008 original size:46 final size:44
Alignment explanation
Indices: 200925--201025 Score: 143
Period size: 42 Copynumber: 2.3 Consensus size: 44
200915 ATCAAGCGAA
*
200925 TAAATTAAAAAATTATTCAAAAATAAATAAATAAATTATTTATT
1 TAAAATAAAAAATTATTCAAAAATAAATAAATAAATTATTTATT
* *
200969 TAAAATAAAAAA-TATTC-AAAATAAATAAATAAATAAATTATT
1 TAAAATAAAAAATTATTCAAAAATAAATAAATAAATTATTTATT
201011 TGAAAATAAATAAAT
1 T-AAAATAAA-AAAT
201026 AAATTATTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
42 24 0.47
43 13 0.25
44 14 0.27
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.34
Consensus pattern (44 bp):
TAAAATAAAAAATTATTCAAAAATAAATAAATAAATTATTTATT
Found at i:201020 original size:27 final size:25
Alignment explanation
Indices: 200971--201029 Score: 84
Period size: 27 Copynumber: 2.3 Consensus size: 25
200961 TATTTATTTA
200971 AAATAAA-AAATATTCAAAATAAAT
1 AAATAAATAAATATTCAAAATAAAT
*
200995 AAATAAATAAATTATTTGAAAATAAAT
1 AAATAAATAAA-TA-TTCAAAATAAAT
201022 AAATAAAT
1 AAATAAAT
201030 TATTTTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
24 7 0.23
25 3 0.10
26 2 0.06
27 19 0.61
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (25 bp):
AAATAAATAAATATTCAAAATAAAT
Found at i:201043 original size:69 final size:68
Alignment explanation
Indices: 200923--201081 Score: 180
Period size: 69 Copynumber: 2.3 Consensus size: 68
200913 AAATCAAGCG
* ** *
200923 AATAAATTAAA-AAATTATTCAAAAATAAATAAATAAATTATTTATTTAAAATAAAAAAT-ATTC
1 AATAAA-TAAATAAATTATTTAAAAATAAATAAATAAATTATTTATAAAAAATAAAAAATAAAT-
200986 AAAATA
64 -AAATA
* * **
200992 AATAAATAAATAAATTATTTGAAAATAAATAAATAAATTATTT-TAAAAAAATTATTAATAAATA
1 AATAAATAAATAAATTATTTAAAAATAAATAAATAAATTATTTAT-AAAAAATAAAAAATAAATA
201056 AATA
65 AATA
201060 AATTAAATAAATAAATTATTTA
1 AA-TAAATAAATAAATTATTTA
201082 TTTAAAATAA
Statistics
Matches: 77, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
68 12 0.16
69 63 0.82
70 2 0.03
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (68 bp):
AATAAATAAATAAATTATTTAAAAATAAATAAATAAATTATTTATAAAAAATAAAAAATAAATAA
ATA
Found at i:201100 original size:35 final size:33
Alignment explanation
Indices: 201040--201134 Score: 102
Period size: 34 Copynumber: 2.8 Consensus size: 33
201030 TATTTTAAAA
*
201040 AAATTATTAATAAATAAATAAATTAAATAAATAAATT
1 AAATTATTTA-AAATAAA-AAATTAAA-AAAT-AATT
*
201077 -ATTTATTTAAAATAAAAACATTAAAAAATAATT
1 AAATTATTTAAAATAAAAA-ATTAAAAAATAATT
* *
201110 AAATTATTTGAAATAAAAAAATAAA
1 AAATTATTTAAAATAAAAAATTAAA
201135 TTATTCAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
33 9 0.18
34 22 0.43
35 13 0.25
36 7 0.14
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (33 bp):
AAATTATTTAAAATAAAAAATTAAAAAATAATT
Found at i:201117 original size:34 final size:35
Alignment explanation
Indices: 200986--201135 Score: 125
Period size: 37 Copynumber: 4.3 Consensus size: 35
200976 AAAAATATTC
200986 AAAA-TAAATAAATAAA-TAAATTATTTGAAAATAA
1 AAAATTAAATAAATAAATTAAATTATTT-AAAATAA
** * *
201020 ATAAA-TAAATTATTTTAAA-AAAATTATTAATAAATAA
1 A-AAATTAAA-TA-AATAAATTAAATTATTTA-AAATAA
*
201057 ATAAATTAAATAAATAAATT-ATTTATTTAAAATAA
1 A-AAATTAAATAAATAAATTAAATTATTTAAAATAA
*
201092 AAACATTAAA-AAAT-AATTAAATTATTTGAAATAA
1 AAA-ATTAAATAAATAAATTAAATTATTTAAAATAA
*
201126 AAAAATAAAT
1 AAAATTAAAT
201136 TATTCAAAAT
Statistics
Matches: 95, Mismatches: 12, Indels: 18
0.76 0.10 0.14
Matches are distributed among these distances:
33 9 0.09
34 23 0.24
35 20 0.21
36 14 0.15
37 25 0.26
38 4 0.04
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (35 bp):
AAAATTAAATAAATAAATTAAATTATTTAAAATAA
Found at i:201137 original size:22 final size:22
Alignment explanation
Indices: 201100--201157 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
201090 AAAAACATTA
**
201100 AAAAATAATTAAATTATTTGAAAT
1 AAAAA-AA-TAAATTATTCAAAAT
201124 AAAAAAATAAATTATTCAAAAT
1 AAAAAAATAAATTATTCAAAAT
**
201146 AACCAAATAAAT
1 AAAAAAATAAAT
201158 CACTAATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 23 0.77
23 2 0.07
24 5 0.17
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (22 bp):
AAAAAAATAAATTATTCAAAAT
Found at i:201736 original size:18 final size:18
Alignment explanation
Indices: 201713--201748 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
201703 AAAATAATTG
*
201713 AAATAAATAAATCAAAAT
1 AAATAAATAAATAAAAAT
201731 AAATAAATAAATAAAAAT
1 AAATAAATAAATAAAAAT
201749 TACCTTTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (18 bp):
AAATAAATAAATAAAAAT
Found at i:209877 original size:23 final size:23
Alignment explanation
Indices: 209851--209903 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
209841 AGAATATTTA
*
209851 TGTCTTTATGACATGTTTATCTC
1 TGTCTTTATGACACGTTTATCTC
*
209874 TGTCTTTGTGACACGTTTATCTC
1 TGTCTTTATGACACGTTTATCTC
209897 TGTCTTT
1 TGTCTTT
209904 TTGGCAGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.13, C:0.19, G:0.15, T:0.53
Consensus pattern (23 bp):
TGTCTTTATGACACGTTTATCTC
Found at i:213465 original size:22 final size:23
Alignment explanation
Indices: 213420--213477 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
213410 TCCTTGATAA
* **
213420 AAATATATAATGATTTTTCTTAC
1 AAATATATAATGAATTTTAATAC
213443 AAATATATAAT-AATTTTAATAC
1 AAATATATAATGAATTTTAATAC
*
213465 AAGTATATGAATG
1 AAATATAT-AATG
213478 TTTCAAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 15 0.52
23 14 0.48
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (23 bp):
AAATATATAATGAATTTTAATAC
Found at i:213583 original size:62 final size:63
Alignment explanation
Indices: 213510--213634 Score: 198
Period size: 62 Copynumber: 2.0 Consensus size: 63
213500 ATAAATATAG
* **
213510 GATGAATTTAATACATTTATATGTATTTATCAAATATACAGCATTGTTATTTTTAC-TTGTAT
1 GATGAATTTAATACATTTATATGTATTTATCAAATATACACCAAAGTTATTTTTACTTTGTAT
* *
213572 GATGAATTTAATTCATTTATATGTATTTATCAAATATACACCAAAGTTATTTTTGCTTTGTAT
1 GATGAATTTAATACATTTATATGTATTTATCAAATATACACCAAAGTTATTTTTACTTTGTAT
213635 ATAAGTGTGT
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
62 51 0.89
63 6 0.11
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.48
Consensus pattern (63 bp):
GATGAATTTAATACATTTATATGTATTTATCAAATATACACCAAAGTTATTTTTACTTTGTAT
Found at i:220793 original size:23 final size:23
Alignment explanation
Indices: 220767--220819 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
220757 AGAATATTTA
*
220767 TGTCTTTATGACATGTTTATCTC
1 TGTCTTTATGACACGTTTATCTC
*
220790 TGTCTTTGTGACACGTTTATCTC
1 TGTCTTTATGACACGTTTATCTC
220813 TGTCTTT
1 TGTCTTT
220820 TTGGCAGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.13, C:0.19, G:0.15, T:0.53
Consensus pattern (23 bp):
TGTCTTTATGACACGTTTATCTC
Found at i:224385 original size:22 final size:23
Alignment explanation
Indices: 224340--224397 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
224330 CCTTGATAAA
* **
224340 AAATATATAATGATTTTTCTTAC
1 AAATATATAATGAATTTTAATAC
224363 AAATATATAAT-AATTTTAATAC
1 AAATATATAATGAATTTTAATAC
*
224385 AAGTATATGAATG
1 AAATATAT-AATG
224398 TTTCAAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 15 0.52
23 14 0.48
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (23 bp):
AAATATATAATGAATTTTAATAC
Found at i:224503 original size:62 final size:63
Alignment explanation
Indices: 224430--224554 Score: 198
Period size: 62 Copynumber: 2.0 Consensus size: 63
224420 ATAAATATAG
* **
224430 GATGAATTTAATACATTTATATGTATTTATCAAATATACAGCATTGTTATTTTTAC-TTGTAT
1 GATGAATTTAATACATTTATATGTATTTATCAAATATACACCAAAGTTATTTTTACTTTGTAT
* *
224492 GATGAATTTAATTCATTTATATGTATTTATCAAATATACACCAAAGTTATTTTTGCTTTGTAT
1 GATGAATTTAATACATTTATATGTATTTATCAAATATACACCAAAGTTATTTTTACTTTGTAT
224555 ATAAGTGTGT
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
62 51 0.89
63 6 0.11
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.48
Consensus pattern (63 bp):
GATGAATTTAATACATTTATATGTATTTATCAAATATACACCAAAGTTATTTTTACTTTGTAT
Found at i:225196 original size:35 final size:35
Alignment explanation
Indices: 225147--225213 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
225137 AACAGTTAAT
* *
225147 TTTAAATAATTATTCTCAACCATGTCTGCACTAAA
1 TTTAAATAACTATTCTCAACCATGTATGCACTAAA
*
225182 TTTAGATAACTATTCTCAACCATGTATGCACT
1 TTTAAATAACTATTCTCAACCATGTATGCACT
225214 TTACATAATG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.34, C:0.21, G:0.07, T:0.37
Consensus pattern (35 bp):
TTTAAATAACTATTCTCAACCATGTATGCACTAAA
Found at i:225358 original size:12 final size:10
Alignment explanation
Indices: 225317--225352 Score: 72
Period size: 10 Copynumber: 3.6 Consensus size: 10
225307 AACATGTATG
225317 AAAAATATAA
1 AAAAATATAA
225327 AAAAATATAA
1 AAAAATATAA
225337 AAAAATATAA
1 AAAAATATAA
225347 AAAAAT
1 AAAAAT
225353 CTATAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (10 bp):
AAAAATATAA
Found at i:230522 original size:20 final size:20
Alignment explanation
Indices: 230497--230748 Score: 205
Period size: 20 Copynumber: 12.5 Consensus size: 20
230487 AATTTTTCAT
* *
230497 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATCTGTA
*
230517 AATCGCAACGCGAA-CATATA
1 AATCGCAACGCGAATC-TGTA
*
230537 AATCGCAACGCGATTCTG-A
1 AATCGCAACGCGAATCTGTA
* * * *
230556 CTATCGCAACGAGTATCCGTAA
1 -AATCGCAACGCGAATCTGT-A
* *
230578 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCTGTA
230598 AATCGCAACGAC-AATAC-GTAA
1 AATCGCAACG-CGAAT-CTGT-A
230619 AATCGCAACGCGTAA-CTGTA
1 AATCGCAACGCG-AATCTGTA
*
230639 AATCGCAACGAGAATAC-GTA
1 AATCGCAACGCGAAT-CTGTA
*
230659 AATCGCAACGCGTATCTGTA
1 AATCGCAACGCGAATCTGTA
*
230679 AATCGCAACGAGAATAC-GTA
1 AATCGCAACGCGAAT-CTGTA
* * *
230699 AATCGCAATGTG-ATTTAGTA
1 AATCGCAACGCGAATCT-GTA
*
230719 AATCGCAATGCGAATCTGTA
1 AATCGCAACGCGAATCTGTA
230739 AATCGCAACG
1 AATCGCAACG
230749 AGATTCTAAC
Statistics
Matches: 190, Mismatches: 24, Indels: 36
0.76 0.10 0.14
Matches are distributed among these distances:
19 6 0.03
20 143 0.75
21 38 0.20
22 3 0.02
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAATCTGTA
Found at i:230601 original size:81 final size:80
Alignment explanation
Indices: 230497--230706 Score: 228
Period size: 81 Copynumber: 2.6 Consensus size: 80
230487 AATTTTTCAT
* * * * *
230497 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATAAATCGCAACGCG-ATTCTG-ACTAT
1 AATCGCAACGCGTATCTGTAAATCGCAACGCGAACATATAAATCGCAACGCGTA-ACTGTA-AAT
* *
230560 CGCAACGAGTATCCGTAA
64 CGCAACGAGAATACGT-A
* * *
230578 AATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTA-AAATCGCAACGCGTAACTGTAAAT
1 AATCGCAACGCGTATCTGTAAATCGCAACG-CGA-ACATATAAATCGCAACGCGTAACTGTAAAT
230642 CGCAACGAGAATACGTA
64 CGCAACGAGAATACGTA
* * **
230659 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAAATCGCAA
1 AATCGCAACGCGTATCTGTAAATCGCAACGCGAACATATAAATCGCAA
230707 TGTGATTTAG
Statistics
Matches: 107, Mismatches: 17, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
79 1 0.01
80 10 0.09
81 56 0.52
82 34 0.32
83 6 0.06
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.18
Consensus pattern (80 bp):
AATCGCAACGCGTATCTGTAAATCGCAACGCGAACATATAAATCGCAACGCGTAACTGTAAATCG
CAACGAGAATACGTA
Found at i:230720 original size:40 final size:40
Alignment explanation
Indices: 230497--230748 Score: 260
Period size: 40 Copynumber: 6.2 Consensus size: 40
230487 AATTTTTCAT
* * * * * **
230497 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATA
1 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTA
* * *
230537 AATCGCAACGCG-ATTCTG-ACTATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGTA-TCTGTA-AATCGCAACGAGAATACGT-A
* *
230578 AATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAA
1 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGT-A
*
230619 AATCGCAACGCGTAACTGTAAATCGCAACGAGAATACGTA
1 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTA
230659 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTA
1 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTA
* * * * *
230699 AATCGCAATGTG-ATTTAGTAAATCGCAATGCGAAT-CTGTA
1 AATCGCAACGCGTATCT-GTAAATCGCAACGAGAATAC-GTA
230739 AATCGCAACG
1 AATCGCAACG
230749 AGATTCTAAC
Statistics
Matches: 182, Mismatches: 23, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
39 6 0.03
40 105 0.58
41 69 0.38
42 2 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (40 bp):
AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTA
Found at i:231867 original size:15 final size:15
Alignment explanation
Indices: 231847--231882 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
231837 AGAAGAAAAG
231847 AAGAAAAAATCCCCA
1 AAGAAAAAATCCCCA
*
231862 AAG-AAAAGTCCCCA
1 AAGAAAAAATCCCCA
231876 AAGAAAA
1 AAGAAAA
231883 TGCCACGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.61, C:0.22, G:0.11, T:0.06
Consensus pattern (15 bp):
AAGAAAAAATCCCCA
Found at i:234247 original size:20 final size:19
Alignment explanation
Indices: 234204--234361 Score: 120
Period size: 19 Copynumber: 8.7 Consensus size: 19
234194 GCAACGAGAG
*
234204 AATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
234223 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAA-ATGAA
* *
234243 TATCGCAACGCGGAAATGAC
1 AATCGCAACGC-GAAATGAA
* * *
234263 TATCACAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
234282 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
* *
234296 AATCACAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
**
234315 AATCGCAA--CG--A-GGG
1 AATCGCAACGCGAAATGAA
*
234329 AATCGCAAAGCGAAATGAA
1 AATCGCAACGCGAAATGAA
234348 AATCGCAACGCGAA
1 AATCGCAACGCGAA
234362 TTTAGTTTCG
Statistics
Matches: 110, Mismatches: 17, Indels: 24
0.73 0.11 0.16
Matches are distributed among these distances:
14 18 0.16
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 49 0.45
20 28 0.25
21 3 0.03
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.13
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:234306 original size:33 final size:33
Alignment explanation
Indices: 234264--234357 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
234254 GGAAATGACT
234264 ATCACAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCACAATGCGAAATGAAAATCGCAACGAGAGA
*
234297 ATCACAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCACAATGCGAAATGAAAATCGCAACGAGAGA
* *
234330 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCACAATGCGAAATGAAAATCGCAACG
234358 CGAATTTAGT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (33 bp):
ATCACAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:234422 original size:33 final size:33
Alignment explanation
Indices: 234367--234446 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
234357 GCGAATTTAG
* *
234367 TTTCGCGTTGCGATTTTATCGTTGCGATTTTCA
1 TTTCGCATTGCGATTCTATCGTTGCGATTTTCA
* *
234400 TTTCGCATTGTGATTCTCTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTCTATCGTTGCGATTTTCA
234433 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
234447 AGACATTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTCTATCGTTGCGATTTTCA
Found at i:234445 original size:19 final size:19
Alignment explanation
Indices: 234388--234446 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
234378 GATTTTATCG
234388 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
234407 TTGTGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
234421 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
234440 TTGCGAT
1 TTGCGAT
234447 AGACATTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
14 5 0.16
16 7 0.23
17 7 0.23
19 12 0.39
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:234572 original size:14 final size:14
Alignment explanation
Indices: 234553--234589 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
234543 CATCAATTAA
234553 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
234567 ACAAATCATCTTTT
1 ACAAATCAACTTTT
234581 ACAAATCAA
1 ACAAATCAA
234590 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:235815 original size:42 final size:42
Alignment explanation
Indices: 235769--235848 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
235759 CGATGACAGT
* * *
235769 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
235811 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
235849 CAGGCGAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:236157 original size:94 final size:94
Alignment explanation
Indices: 236043--236404 Score: 591
Period size: 94 Copynumber: 3.9 Consensus size: 94
236033 TTAAACAGTG
* *
236043 AAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATAAACAGTTTAGCAGAATTGGCAGCAA
1 AAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGTTTAGCAGAATTGGCAGCAA
236108 CCGAACAAATTTACTTTCAACCAAAAGAC
66 CCGAACAAATTTACTTTCAACCAAAAGAC
*
236137 AAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAA
1 AAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGTTTAGCAGAATTGGCAGCAA
236202 CCGAACAAATTTACTTTCAACCAAAAGAC
66 CCGAACAAATTTACTTTCAACCAAAAGAC
* * *
236231 AAAAAAAAGACAAATACTAACTTCACATTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAA
1 AAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGTTTAGCAGAATTGGCAGCAA
* * *
236296 CCGAATAAATTTAC-TTCAAGCAAAAGAA
66 CCGAACAAATTTACTTTCAACCAAAAGAC
* * *
236324 AAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAATTTAGCAGTATTGGTAGCA
1 AAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGTTTAGCAGAATTGGCAGCA
*
236389 ACCGAATAAATTTACT
65 ACCGAACAAATTTACT
236405 AAGCAATCTA
Statistics
Matches: 252, Mismatches: 14, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
93 16 0.06
94 236 0.94
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.22
Consensus pattern (94 bp):
AAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGTTTAGCAGAATTGGCAGCAA
CCGAACAAATTTACTTTCAACCAAAAGAC
Found at i:238132 original size:20 final size:19
Alignment explanation
Indices: 238109--238160 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
238099 TGAAATGAAA
238109 ATCGCAACGAGATAATGACT
1 ATCGCAACGAGA-AATGACT
*
238129 ATCGCAACGCGGAAATGACT
1 ATCGCAACG-AGAAATGACT
*
238149 ATCGCAATGAGA
1 ATCGCAACGAGA
238161 GAATCGCAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.07
20 24 0.86
21 2 0.07
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.17
Consensus pattern (19 bp):
ATCGCAACGAGAAATGACT
Found at i:238240 original size:21 final size:20
Alignment explanation
Indices: 238220--238291 Score: 92
Period size: 20 Copynumber: 3.5 Consensus size: 20
238210 CGATTATCTC
238220 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCAT
** *
238240 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCAT
238261 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
238281 GTTGCGATTTT
1 GTTGCGATTTT
238292 AAGTTTAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
20 30 0.67
21 15 0.33
ACGTcount: A:0.12, C:0.17, G:0.19, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:238878 original size:20 final size:20
Alignment explanation
Indices: 238849--239042 Score: 196
Period size: 20 Copynumber: 9.6 Consensus size: 20
238839 CTTTAAAAAT
238849 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
238869 CGCATTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
238889 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
238910 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
238930 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
*
238950 TGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
238970 CGCTTTGCGATTTTAC--ATA
1 CGCGTTGCGA-TTTACGGATA
* *
238989 TTGTCGTTGCGATTTACGAATA
1 -CG-CGTTGCGATTTACGGATA
239011 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
239032 CTCGTTGCGAT
1 CGCGTTGCGAT
239043 AGTCAGAATC
Statistics
Matches: 141, Mismatches: 24, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
19 3 0.02
20 88 0.62
21 47 0.33
22 3 0.02
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:238997 original size:41 final size:41
Alignment explanation
Indices: 238849--239064 Score: 178
Period size: 41 Copynumber: 5.3 Consensus size: 41
238839 CTTTAAAAAT
* * * *
238849 CGCGTTGCGA-TTTACGGATACGCATTGCGATTTTACGTAT-
1 CGCGTTGCGATTTTACAGATATGCGTTGCGA-TTTACGAATA
* * * * * *
238889 TGTCGTTGCGA-TTTACGGATACGCATTGCGATTTACGTATT
1 CG-CGTTGCGATTTTACAGATATGCGTTGCGATTTACGAATA
* *
238930 CTCGTTGCGA-TTTACAGATATGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTTACAGATATGCGTTGCGATTTACGAATA
* *
238970 CGCTTTGCGATTTTACATAT-TGTCGTTGCGATTTACGAATA
1 CGCGTTGCGATTTTACAGATATG-CGTTGCGATTTACGAATA
* *
239011 CGCGTTGCGATTTTACGGATACT-CGTTGCGATAGT-CAGAAT-
1 CGCGTTGCGATTTTACAGATA-TGCGTTGCGAT-TTAC-GAATA
239052 CGCGTTGCGATTT
1 CGCGTTGCGATTT
239065 ATATGTTCGC
Statistics
Matches: 152, Mismatches: 16, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
40 53 0.35
41 93 0.61
42 5 0.03
43 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (41 bp):
CGCGTTGCGATTTTACAGATATGCGTTGCGATTTACGAATA
Found at i:239058 original size:61 final size:61
Alignment explanation
Indices: 238892--239102 Score: 182
Period size: 61 Copynumber: 3.5 Consensus size: 61
238882 TACGTATTGT
* * * * *
238892 CGTTGCGATTTACGGATACGCATTGCGAT-TTACGTATTC-TCGTTGCGATTTACAGATATG
1 CGTTGCGATTTACGGATACGCGTTGCGATAGTAC-AAATCGTCGTTGCGATTTACAGATACG
* ** * *
238952 CGTTGCGATTTACGGATACGCTTTGCGATTTTACATATTGTCGTTGCGATTTAC-GAATACG
1 CGTTGCGATTTACGGATACGCGTTGCGATAGTACAAATCGTCGTTGCGATTTACAG-ATACG
* * *
239013 CGTTGCGATTTTACGGATACTCGTTGCGATAGT-CAGAATCG-CGTTGCGATTTATATG-TTCG
1 CGTTGCGA-TTTACGGATACGCGTTGCGATAGTACA-AATCGTCGTTGCGATTTACA-GATACG
* ** *
239074 CGTTGCGATTTTCATATTCGCGTTGCGAT
1 CGTTGCGATTTACGGATACGCGTTGCGAT
239103 TCTGGAAAAT
Statistics
Matches: 125, Mismatches: 19, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
60 46 0.37
61 55 0.44
62 23 0.18
63 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (61 bp):
CGTTGCGATTTACGGATACGCGTTGCGATAGTACAAATCGTCGTTGCGATTTACAGATACG
Found at i:239074 original size:20 final size:20
Alignment explanation
Indices: 239051--239103 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
239041 ATAGTCAGAA
*
239051 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
239071 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
239091 TCGCGTTGCGATT
1 TCGCGTTGCGATT
239104 CTGGAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:239090 original size:101 final size:101
Alignment explanation
Indices: 238846--239103 Score: 337
Period size: 101 Copynumber: 2.6 Consensus size: 101
238836 GCGCTTTAAA
* *
238846 AATCGCGTTGCGATTTACGGATACGCATTGCGATTTTACGTATTGTCGTTGCGATTTACGGATAC
1 AATCGCGTTGCGATTTACGGATACGCATTGCGATTTTACATATTGTCGTTGCGATTTACGAATAC
* * *
238911 GCATTGCGATTTACGTATTCTCGTTGCGATTTACAG
66 GCATTGCGATTTACGGATACTCGTTGCGATGTACAG
*
238947 ATAT-GCGTTGCGATTTACGGATACGCTTTGCGATTTTACATATTGTCGTTGCGATTTACGAATA
1 A-ATCGCGTTGCGATTTACGGATACGCATTGCGATTTTACATATTGTCGTTGCGATTTACGAATA
*
239011 CGCGTTGCGATTTTACGGATACTCGTTGCGATAGT-CAG
65 CGCATTGCGA-TTTACGGATACTCGTTGCGAT-GTACAG
** * *
239049 AATCGCGTTGCGATTTATATG-TTCGCGTTGCGATTTT-CATATTCG-CGTTGCGATT
1 AATCGCGTTGCGATTTA-CGGATACGCATTGCGATTTTACATATT-GTCGTTGCGATT
239104 CTGGAAAATC
Statistics
Matches: 140, Mismatches: 11, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
101 85 0.61
102 53 0.38
103 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (101 bp):
AATCGCGTTGCGATTTACGGATACGCATTGCGATTTTACATATTGTCGTTGCGATTTACGAATAC
GCATTGCGATTTACGGATACTCGTTGCGATGTACAG
Found at i:239829 original size:19 final size:19
Alignment explanation
Indices: 239805--239851 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
239795 GCTTTAAGCG
*
239805 ACAATTGCAGCGAAAACGA
1 ACAATTGCAGAGAAAACGA
239824 ACAATTGCAGAGAAAACGA
1 ACAATTGCAGAGAAAACGA
239843 ACAATTGCA
1 ACAATTGCA
239852 TTGACTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.49, C:0.19, G:0.19, T:0.13
Consensus pattern (19 bp):
ACAATTGCAGAGAAAACGA
Found at i:241847 original size:21 final size:21
Alignment explanation
Indices: 241821--241879 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
241811 TAACTGGCCA
*
241821 TTGACCGTTGTTGATTGATCG
1 TTGACCGTCGTTGATTGATCG
* *
241842 TTGACCGTCATTGATCGATCG
1 TTGACCGTCGTTGATTGATCG
*
241863 TTGATCGTCGTTGATTG
1 TTGACCGTCGTTGATTG
241880 GCTGTTGTGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.15, C:0.17, G:0.27, T:0.41
Consensus pattern (21 bp):
TTGACCGTCGTTGATTGATCG
Found at i:241873 original size:10 final size:10
Alignment explanation
Indices: 241839--241877 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
241829 TGTTGATTGA
*
241839 TCGTTGACCG
1 TCGTTGATCG
*
241849 TCATTGATCG
1 TCGTTGATCG
241859 ATCGTTGATCG
1 -TCGTTGATCG
241870 TCGTTGAT
1 TCGTTGAT
241878 TGGCTGTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.38
Consensus pattern (10 bp):
TCGTTGATCG
Found at i:242725 original size:29 final size:29
Alignment explanation
Indices: 242677--242745 Score: 122
Period size: 29 Copynumber: 2.4 Consensus size: 29
242667 AAATTAAATT
242677 AAATGAT-AAAAAATACACTCAAGTTTTG
1 AAATGATAAAAAAATACACTCAAGTTTTG
242705 AAATGATAAAAAAATACACTCAAGTTTTG
1 AAATGATAAAAAAATACACTCAAGTTTTG
242734 AAATGACTAAAA
1 AAATGA-TAAAA
242746 TAACCTCCAG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
28 7 0.18
29 27 0.69
30 5 0.13
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.26
Consensus pattern (29 bp):
AAATGATAAAAAAATACACTCAAGTTTTG
Found at i:243991 original size:18 final size:19
Alignment explanation
Indices: 243956--243992 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
243946 CACGGAATGT
243956 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
243976 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
243993 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:247082 original size:7 final size:7
Alignment explanation
Indices: 246994--247080 Score: 120
Period size: 7 Copynumber: 11.6 Consensus size: 7
246984 CTTTGGACCT
246994 ATAAAAA
1 ATAAAAA
247001 ATAAAAA
1 ATAAAAA
247008 ATAAAAA
1 ATAAAAA
247015 ATAAAAA
1 ATAAAAA
247022 ATAAAAA
1 ATAAAAA
247029 ATAAAAA
1 ATAAAAA
247036 ATAAAAA
1 ATAAAAA
247043 ATAATAAA
1 ATAA-AAA
247051 ATATAATAA
1 ATA-AA-AA
247060 ATAATAAA
1 ATAA-AAA
247068 ATATAATAA
1 ATA-AA-AA
247077 ATAA
1 ATAA
247081 TATAATACTA
Statistics
Matches: 74, Mismatches: 0, Indels: 11
0.87 0.00 0.13
Matches are distributed among these distances:
7 46 0.62
8 15 0.20
9 13 0.18
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (7 bp):
ATAAAAA
Found at i:247087 original size:17 final size:17
Alignment explanation
Indices: 246994--247100 Score: 111
Period size: 17 Copynumber: 6.6 Consensus size: 17
246984 CTTTGGACCT
* *
246994 ATAAAAAATAAAAAATA
1 ATAAATAATAAAATATA
*
247011 AAAAATAA-AAAATA-A
1 ATAAATAATAAAATATA
247026 A-AAATAA-AAAATA-A
1 ATAAATAATAAAATATA
247040 A-AAATAATAAAATATA
1 ATAAATAATAAAATATA
247056 ATAAATAATAAAATATA
1 ATAAATAATAAAATATA
*
247073 ATAAATAATATAATACT-
1 ATAAATAATAAAATA-TA
247090 ATAATATAATA
1 ATAA-ATAATA
247101 TATGTGCAAT
Statistics
Matches: 81, Mismatches: 4, Indels: 9
0.86 0.04 0.10
Matches are distributed among these distances:
14 20 0.25
15 8 0.10
16 7 0.09
17 39 0.48
18 7 0.09
ACGTcount: A:0.75, C:0.01, G:0.00, T:0.24
Consensus pattern (17 bp):
ATAAATAATAAAATATA
Found at i:247236 original size:36 final size:36
Alignment explanation
Indices: 247141--247295 Score: 224
Period size: 37 Copynumber: 4.3 Consensus size: 36
247131 AAATATTTAA
* * *
247141 AAAACTATATAATATATTTTTTTTTCAAAATGTTTTC
1 AAAACTATATATTATA-TATATTTTCAAAATGTTTTC
247178 AAAACCTATATATTATA-A-ATTTTCAAAATGTTTTC
1 AAAA-CTATATATTATATATATTTTCAAAATGTTTTC
247213 AAAACTATATATTATATATATTTTCAAAATGTTTTC
1 AAAACTATATATTATATATATTTTCAAAATGTTTTC
**
247249 AAAAACTATATATTATATATATTTTTGAAATGTTTTC
1 -AAAACTATATATTATATATATTTTCAAAATGTTTTC
247286 AAAACTATAT
1 AAAACTATAT
247296 TATATTAATA
Statistics
Matches: 109, Mismatches: 5, Indels: 9
0.89 0.04 0.07
Matches are distributed among these distances:
34 12 0.11
35 21 0.19
36 27 0.25
37 38 0.35
38 11 0.10
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.46
Consensus pattern (36 bp):
AAAACTATATATTATATATATTTTCAAAATGTTTTC
Found at i:247296 original size:71 final size:70
Alignment explanation
Indices: 247162--247300 Score: 217
Period size: 71 Copynumber: 2.0 Consensus size: 70
247152 ATATATTTTT
*
247162 TTTTCAAAATGTTTTCAAAACCTATATATTATAAATTTTCAAAATGTTTTCAAAACTATATATTA
1 TTTTCAAAATGTTTTCAAAAACTATATATTATAAATTTTCAAAATGTTTTCAAAAC-ATATATTA
247227 TATATA
65 TATATA
**
247233 TTTTCAAAATGTTTTCAAAAACTATATATTATATATATTTTTGAAATGTTTTCAAAAC-TATATT
1 TTTTCAAAATGTTTTCAAAAACTATATATTATA-A-ATTTTCAAAATGTTTTCAAAACATATATT
247297 ATAT
64 ATAT
247301 TAATATATGT
Statistics
Matches: 63, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
71 42 0.67
72 1 0.02
73 20 0.32
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.47
Consensus pattern (70 bp):
TTTTCAAAATGTTTTCAAAAACTATATATTATAAATTTTCAAAATGTTTTCAAAACATATATTAT
ATATA
Found at i:247966 original size:85 final size:85
Alignment explanation
Indices: 247710--248544 Score: 1068
Period size: 85 Copynumber: 10.0 Consensus size: 85
247700 TACCATGTGG
* * * * * * *** * * *
247710 TTGATATGCCCTCGCGTTGAATGAAATCGAACTCGAAAGTCTTCAATAACAGATAACCCTTCTCG
1 TTGATATGCCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCA
247775 CCTTGAGCTATGCTGTAAAT
66 CCTTGAGCTATGCTGTAAAT
* * * *
247795 TTGACAGGCCCTTGAGCTGAATGGAATCAAACTTGAAGGTTTTT-TTGACAGATAGCCCTTCTCA
1 TTGATATGCCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCA
* *
247859 CCTTAAACTATGCTGTAAAT
66 CCTTGAGCTATGCTGTAAAT
*
247879 TTGATATGCCCTTGAGTTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCA
1 TTGATATGCCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCA
*
247944 CCTTGAGTTATGCTGTAAAT
66 CCTTGAGCTATGCTGTAAAT
* * * * * *
247964 TTGATATGCCCTTGAGCTGAATGGAATCGAACTCGAAGGCTTTTGTTGACAAATAACCATTTTCG
1 TTGATATGCCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCA
* *
248029 CCTTGAGTTATGTTGTAAAT
66 CCTTGAGCTATGCTGTAAAT
* * ** *
248049 TTGATATGCCCTTGAGCTGAATAGAATCGAACTCGAAGGTTTTTATTGACAGATATACCTTCTCG
1 TTGATATGCCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCA
*
248114 CCTTGAGTTATGCTGTAAAT
66 CCTTGAGCTATGCTGTAAAT
* ** * *
248134 TTGATAT--ACTATGAGCTGAATGGAATTAAACTCGAAGGTTTTTGTTGACATATAACCCTTCTC
1 TTGATATGCCCT-TGAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTC
248197 ACCTTGAGCTATGCTGTAAAT
65 ACCTTGAGCTATGCTGTAAAT
* * *
248218 TTGAAATGCCCTTGAGCTGAATGGAATCGAACTTGAAGGTTTTTGTTGACAGATAGCCCTTCTCG
1 TTGATATGCCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCA
*
248283 TCTTGAGCTATGCTGTAAAT
66 CCTTGAGCTATGCTGTAAAT
* * *
248303 TTGATATGCCTTTGAGCTTAATGGAATCGAACTCGAAGGTTTTCGTTGACAGATAGCCCTTCTCA
1 TTGATATGCCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCA
248368 CCTTGAGCTATGCTGTAAAT
66 CCTTGAGCTATGCTGTAAAT
* * *
248388 TTGATATGCCC--GAGCTGAATAGAATCGAACTTGAAGGTTTTCGTTGACAGAT-GACCCTTCTC
1 TTGATATGCCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAG-CCCTTCTC
*
248450 ACCTTGAGGTATGCTGTAAAT
65 ACCTTGAGCTATGCTGTAAAT
**
248471 TTGATATAG---TT-A----AATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCTTTTCTC
1 TTGATAT-GCCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTC
*
248528 TCCTTGAGCTATGCTGT
65 ACCTTGAGCTATGCTGT
248545 GAACAATTTC
Statistics
Matches: 661, Mismatches: 80, Indels: 25
0.86 0.10 0.03
Matches are distributed among these distances:
78 53 0.08
79 1 0.00
82 2 0.00
83 75 0.11
84 144 0.22
85 384 0.58
86 2 0.00
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (85 bp):
TTGATATGCCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCA
CCTTGAGCTATGCTGTAAAT
Found at i:248159 original size:254 final size:252
Alignment explanation
Indices: 247710--248544 Score: 1058
Period size: 254 Copynumber: 3.3 Consensus size: 252
247700 TACCATGTGG
* * * * * * *** * *
247710 TTGATATGCCCTCGCGTTGAATGAAATCGAACTCGAAAGTCTTCAATAACAGATAACCCTTCTCG
1 TTGATATGCCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAAATAACCCTTCTCG
* * * *
247775 CCTTGAGCTATGCTGTAAATTTGACAGGCCCTTGAGCTGAATGGAATCAAACTTGAAGGTTTTTT
66 CCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTTT
* * * *
247840 TGACAGATAGCCCTTCTCACCTTAAACTATGCTGTAAATTTGATATGCCCTTGAGTTGAATGGAA
131 TGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAATTTGATAT--ACTTGAGCTGAATGGAA
*
247905 TCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCACCTTGAGTTATGCTGTAAAT
194 TCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAAT
* * *
247964 TTGATATGCCCTTGAGCTGAATGGAATCGAACTCGAAGGCTTTTGTTGACAAATAACCATTTTCG
1 TTGATATGCCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAAATAACCCTTCTCG
* * *
248029 CCTTGAGTTATGTTGTAAATTTGATATGCCCTTGAGCTGAATAGAATCGAACTCGAAGGTTTTTA
66 CCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTT-
** * *
248094 TTGACAGATATACCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATACTATGAGCTGAATGGAA
130 TTGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAATTTGATATACT-TGAGCTGAATGGAA
** * *
248159 TTAAACTCGAAGGTTTTTGTTGACATATAACCCTTCTCACCTTGAGCTATGCTGTAAAT
194 TCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAAT
* * * *
248218 TTGAAATGCCCTTGAGCTGAATGGAATCGAACTTGAAGGTTTTTGTTGACAGATAGCCCTTCTCG
1 TTGATATGCCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAAATAACCCTTCTCG
* * * *
248283 TCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTTAATGGAATCGAACTCGAAGGTTTTCG
66 CCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTT-T
* ** *
248348 TTGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAATTTGATATGCCCGAGCTGAATAGAAT
130 TTGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAATTTGATATACTTGAGCTGAATGGAAT
* * *
248413 CGAACTTGAAGGTTTTCGTTGACAGAT-GACCCTTCTCACCTTGAGGTATGCTGTAAAT
195 CGAACTCGAAGGTTTTTGTTGACAGATAG-CCCTTCTCACCTTGAGCTATGCTGTAAAT
* * **
248471 TTGATATAG---TT-A----AATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCTTTTCTC
1 TTGATAT-GCCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAAATAACCCTTCTC
*
248528 TCCTTGAGCTATGCTGT
65 GCCTTGAGCTATGCTGT
248545 GAACAATTTC
Statistics
Matches: 507, Mismatches: 69, Indels: 18
0.85 0.12 0.03
Matches are distributed among these distances:
246 57 0.11
250 1 0.00
251 2 0.00
253 71 0.14
254 335 0.66
255 41 0.08
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (252 bp):
TTGATATGCCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAAATAACCCTTCTCG
CCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTTT
TGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAATTTGATATACTTGAGCTGAATGGAATC
GAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAAT
Found at i:248330 original size:339 final size:336
Alignment explanation
Indices: 247710--248544 Score: 1139
Period size: 339 Copynumber: 2.5 Consensus size: 336
247700 TACCATGTGG
* * * * * *
247710 TTGATATGCCCTCGCGTTGAAT-GAAATCGAACTCGAAAGTCTTCAATAACAGATAACCCTTCTC
1 TTGATATGCCCT-GAGCTGAATAG-AATCGAACTCGAAGGTTTTCATTGACAGATAA-CCTTCTC
* ** *
247774 GCCTTGAGCTATGCTGTAAATTTGACAGGCCCTTGAGCTGAATGGAATCAAACTTGAAGGTTTTT
63 GCCTTGAGCTATGCTGTAAATTTGATA--TACTTGAGCTGAATGGAATCAAACTCGAAGGTTTTT
* * * *
247839 -TTGACAGATAGCCCTTCTCACCTTAAACTATGCTGTAAATTTGATATGCCCTTGAGTTGAATGG
126 GTTGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAATTTGAAATGCCCTTGAGCTGAATGG
*
247903 AATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCACCTTGAGTTATGCTGTAAATTTGA
191 AATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAATTTGA
* *
247968 TATGCCCTTGAGCTGAATGGAATCGAACTCGAAGGCTTTT-GTTGACAAATAACCATTTTCGCCT
256 TATGCCCTTGAGCTGAATGGAATCGAACTCGAAGG-TTTTCGTTGACAAATAACCATTCTCACCT
* *
248032 TGAGTTATGTTGTAAAT
320 TGAGCTATGCTGTAAAT
*
248049 TTGATATGCCCTTGAGCTGAATAGAATCGAACTCGAAGGTTTTTATTGACAGATATACCTTCTCG
1 TTGATATGCCC-TGAGCTGAATAGAATCGAACTCGAAGGTTTTCATTGACAGATA-ACCTTCTCG
* *
248114 CCTTGAGTTATGCTGTAAATTTGATATACTATGAGCTGAATGGAATTAAACTCGAAGGTTTTTGT
64 CCTTGAGCTATGCTGTAAATTTGATATACT-TGAGCTGAATGGAATCAAACTCGAAGGTTTTTGT
* *
248179 TGACATATAACCCTTCTCACCTTGAGCTATGCTGTAAATTTGAAATGCCCTTGAGCTGAATGGAA
128 TGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAATTTGAAATGCCCTTGAGCTGAATGGAA
* **
248244 TCGAACTTGAAGGTTTTTGTTGACAGATAGCCCTTCTCGTCTTGAGCTATGCTGTAAATTTGATA
193 TCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAATTTGATA
* * * * *
248309 TGCCTTTGAGCTTAATGGAATCGAACTCGAAGGTTTTCGTTGACAGATAGCCCTTCTCACCTTGA
258 TGCCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTCGTTGACAAATAACCATTCTCACCTTGA
248374 GCTATGCTGTAAAT
323 GCTATGCTGTAAAT
* * * *
248388 TTGATATGCCC-GAGCTGAATAGAATCGAACTTGAAGGTTTTCGTTGACAGATGACCCTTCTCAC
1 TTGATATGCCCTGAGCTGAATAGAATCGAACTCGAAGGTTTTCATTGACAGAT-AACCTTCTCGC
* * *
248452 CTTGAGGTATGCTGTAAATTTGATATAGTT-A----AATGGAATCGAACTCGAAGGTTTTTGTTG
65 CTTGAGCTATGCTGTAAATTTGATATACTTGAGCTGAATGGAATCAAACTCGAAGGTTTTTGTTG
** *
248512 ACAGATAGCTTTTCTCTCCTTGAGCTATGCTGT
130 ACAGATAGCCCTTCTCACCTTGAGCTATGCTGT
248545 GAACAATTTC
Statistics
Matches: 443, Mismatches: 46, Indels: 22
0.87 0.09 0.04
Matches are distributed among these distances:
331 55 0.12
335 1 0.00
336 1 0.00
337 75 0.17
338 35 0.08
339 273 0.62
340 3 0.01
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (336 bp):
TTGATATGCCCTGAGCTGAATAGAATCGAACTCGAAGGTTTTCATTGACAGATAACCTTCTCGCC
TTGAGCTATGCTGTAAATTTGATATACTTGAGCTGAATGGAATCAAACTCGAAGGTTTTTGTTGA
CAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAATTTGAAATGCCCTTGAGCTGAATGGAATCG
AACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAATTTGATATGC
CCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTCGTTGACAAATAACCATTCTCACCTTGAGCT
ATGCTGTAAAT
Found at i:249929 original size:84 final size:84
Alignment explanation
Indices: 249788--249956 Score: 329
Period size: 84 Copynumber: 2.0 Consensus size: 84
249778 TCTTGAGTGC
*
249788 TCATGTGAAATTAACTATAACAGGTGTTCTTTAACTCCCTTAGTCCATCATTAGCAAAAACTCAT
1 TCATGTGAAATTAACTATAACAGGTGTTCCTTAACTCCCTTAGTCCATCATTAGCAAAAACTCAT
249853 TGTTTAAATAAATTTGGTT
66 TGTTTAAATAAATTTGGTT
249872 TCATGTGAAATTAACTATAACAGGTGTTCCTTAACTCCCTTAGTCCATCATTAGCAAAAACTCAT
1 TCATGTGAAATTAACTATAACAGGTGTTCCTTAACTCCCTTAGTCCATCATTAGCAAAAACTCAT
249937 TGTTTAAATAAATTTGGTT
66 TGTTTAAATAAATTTGGTT
249956 T
1 T
249957 AATTTTCCAT
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (84 bp):
TCATGTGAAATTAACTATAACAGGTGTTCCTTAACTCCCTTAGTCCATCATTAGCAAAAACTCAT
TGTTTAAATAAATTTGGTT
Found at i:253909 original size:14 final size:14
Alignment explanation
Indices: 253886--253918 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
253876 CAAATAAAAG
253886 AAAA-AATATTAAT
1 AAAATAATATTAAT
253899 AAAATAATATTAAT
1 AAAATAATATTAAT
*
253913 ATAATA
1 AAAATA
253919 TAGAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAATAATATTAAT
Found at i:254130 original size:28 final size:27
Alignment explanation
Indices: 254094--254226 Score: 77
Period size: 28 Copynumber: 5.0 Consensus size: 27
254084 ACTATATATT
254094 ATATATATTTTCAAAATATTTTTAAAA
1 ATATATATTTTCAAAATATTTTTAAAA
* *
254121 ACTATATATTAT-ATATATATTTTT---A
1 A-TATATATTTTCA-AAATATTTTTAAAA
* *
254146 A-A-ATGTTTTCAAAAACTATTTATT--AT
1 ATATATATTTTC-AAAA-TATTT-TTAAAA
*
254172 ATATATGTTTTCAAAATATTTTTAAAA
1 ATATATATTTTCAAAATATTTTTAAAA
* *
254199 ACTATATATTAT-ATATATATTTTTAAAA
1 A-TATATATTTTCA-AAATATTTTTAAAA
254227 TGTTTTCAAA
Statistics
Matches: 83, Mismatches: 10, Indels: 25
0.70 0.08 0.21
Matches are distributed among these distances:
22 5 0.06
23 3 0.04
24 6 0.07
25 6 0.07
26 6 0.07
27 10 0.12
28 47 0.57
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.50
Consensus pattern (27 bp):
ATATATATTTTCAAAATATTTTTAAAA
Found at i:254140 original size:39 final size:39
Alignment explanation
Indices: 253924--254373 Score: 441
Period size: 39 Copynumber: 11.9 Consensus size: 39
253914 TAATATAGAA
253924 AAAATCATTTTT-AAAACTATATATCT-TATAT-T-TTTT-
1 AAAAT-ATTTTTCAAAACTATATAT-TATATATATATTTTC
* * *
253960 TAAAT-TGTTTTCAAAACCATATA--ATATGTATATTTTC
1 AAAATAT-TTTTCAAAACTATATATTATATATATATTTTC
253997 AAAAATTATTTTT-AAAAC--TATA-TA-ATATATATTTTC
1 -AAAA-TATTTTTCAAAACTATATATTATATATATATTTTC
* * *
254033 AACAATA-TTTTCAAAACTATATA-T-TATATACATCTTA
1 AA-AATATTTTTCAAAACTATATATTATATATATATTTTC
*
254070 AAAATA-GTTTCAAAACTATATA-T-TATATATATTTTC
1 AAAATATTTTTCAAAACTATATATTATATATATATTTTC
* *
254106 AAAATATTTTTAAAAACTATATATTATATATATATTTTT
1 AAAATATTTTTCAAAACTATATATTATATATATATTTTC
* * *
254145 AAAAT-GTTTTCAAAAACTATTTATTATATATATGTTTTC
1 AAAATATTTTTC-AAAACTATATATTATATATATATTTTC
* *
254184 AAAATATTTTTAAAAACTATATATTATATATATATTTTT
1 AAAATATTTTTCAAAACTATATATTATATATATATTTTC
*
254223 AAAAT-GTTTTCAAAAACTATATA-TATTATATATATGTTTC
1 AAAATATTTTTC-AAAACTATATATTA-TATATATAT-TTTC
*
254263 AAAATA-TTTTCAAAACTATATAATATATATATATTTTC
1 AAAATATTTTTCAAAACTATATATTATATATATATTTTC
254301 AAAA-ATGTTTTCAAAACTATATATTATATAT-T-TTTTC
1 AAAATAT-TTTTCAAAACTATATATTATATATATATTTTC
*
254338 AAAAT-GTTTTCAAAACTATAATATATATATATATAT
1 AAAATATTTTTCAAAACTAT-ATAT-TATATATATAT
254374 ATATATATAT
Statistics
Matches: 352, Mismatches: 30, Indels: 60
0.80 0.07 0.14
Matches are distributed among these distances:
34 9 0.03
35 14 0.04
36 84 0.24
37 45 0.13
38 35 0.10
39 144 0.41
40 21 0.06
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (39 bp):
AAAATATTTTTCAAAACTATATATTATATATATATTTTC
Found at i:254192 original size:78 final size:75
Alignment explanation
Indices: 253931--254373 Score: 505
Period size: 78 Copynumber: 5.9 Consensus size: 75
253921 GAAAAAATCA
* * * * * *
253931 TTTTTAAAACTATATATCT-TATAT-TTTTTTAAATTGTTTTCAAAACCATATA--ATATGTATA
1 TTTTCAAAACTATATAT-TATATATATTTTTCAAAATATTTTCAAAACTATATATTATATATATA
*
253992 TTTTCAAAAATTA
65 TTTT-AAAAA-TG
* *
254005 TTTTTAAAACTATATA--ATATATA-TTTTCAACAATATTTTCAAAACTATATA-T-TATATACA
1 TTTTCAAAACTATATATTATATATATTTTTCAA-AATATTTTCAAAACTATATATTATATATATA
*
254065 TCTTAAAAATAG
65 TTTTAAAAAT-G
*
254077 -TTTCAAAACTATATATTATATATA-TTTTCAAAATATTTTTAAAAACTATATATTATATATATA
1 TTTTCAAAACTATATATTATATATATTTTTCAAAATA-TTTTCAAAACTATATATTATATATATA
*
254140 TTTTTAAAATG
65 TTTTAAAAATG
* *
254151 TTTTCAAAAACTATTTATTATATATATGTTTTCAAAATATTTTTAAAAACTATATATTATATATA
1 TTTTC-AAAACTATATATTATATATAT-TTTTCAAAATA-TTTTCAAAACTATATATTATATATA
*
254216 TATTTTTAAAATG
63 TATTTTAAAAATG
* *
254229 TTTTCAAAAACTATATATATTATATATATGTTTCAAAATATTTTCAAAACTATATAATATATATA
1 TTTTC-AAAAC--TATATATTATATATATTTTTCAAAATATTTTCAAAACTATATATTATATATA
254294 TATTTTCAAAAATG
63 TATTTT-AAAAATG
*
254308 TTTTCAAAACTATATATTATATAT-TTTTTCAAAATGTTTTCAAAACTATAATATATATATATAT
1 TTTTCAAAACTATATATTATATATATTTTTCAAAATATTTTCAAAACTAT-ATAT-TATATATAT
254372 AT
64 AT
254374 ATATATATAT
Statistics
Matches: 328, Mismatches: 22, Indels: 35
0.85 0.06 0.09
Matches are distributed among these distances:
71 15 0.05
72 20 0.06
73 55 0.17
74 18 0.05
75 42 0.13
76 36 0.11
77 11 0.03
78 95 0.29
79 21 0.06
80 15 0.05
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.47
Consensus pattern (75 bp):
TTTTCAAAACTATATATTATATATATTTTTCAAAATATTTTCAAAACTATATATTATATATATAT
TTTAAAAATG
Found at i:254365 original size:2 final size:2
Alignment explanation
Indices: 254354--254387 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
254344 TTTTCAAAAC
254354 TA TA -A 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 TA T
254388 TTGAATACCG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:255398 original size:25 final size:25
Alignment explanation
Indices: 255362--255418 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
255352 AGGTTATATA
*
255362 TTGTTTTTATATTAGAGTCTGAAAT
1 TTGTTTTAATATTAGAGTCTGAAAT
255387 TTGTTTTAATATTAGAGTCTGAAAT
1 TTGTTTTAATATTAGAGTCTGAAAT
255412 TTGTTTT
1 TTGTTTT
255419 TATACTGTGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.26, C:0.04, G:0.16, T:0.54
Consensus pattern (25 bp):
TTGTTTTAATATTAGAGTCTGAAAT
Found at i:259968 original size:14 final size:14
Alignment explanation
Indices: 259949--259982 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
259939 AAATATAATT
259949 TATTTTACAAAAAA
1 TATTTTACAAAAAA
* *
259963 TATTTTTCGAAAAA
1 TATTTTACAAAAAA
259977 TATTTT
1 TATTTT
259983 TATTAAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (14 bp):
TATTTTACAAAAAA
Found at i:260220 original size:90 final size:89
Alignment explanation
Indices: 260010--260276 Score: 307
Period size: 85 Copynumber: 3.0 Consensus size: 89
260000 CTTTAGATTC
* ** *
260010 ATTAGTCATTATTTGCGTGGAGTATTATGATGTGACATCTTGATTTTTTATATAATTATTTATAT
1 ATTAATCATTATTT-CAAGGAGTATTATGATGTGACATCATGATTTTTTATATAATTATTTATAT
260075 TTAAA--TTT--T-TAATAATTCGA
65 TTAAATTTTTAATCTAATAATTCGA
* * * *
260095 ATTAACCATTATATGTGAA-GAGTATTATGACGTGACATCAT-ATTTTTTTATATAATTTTTTAT
1 ATTAATCATTAT-T-TCAAGGAGTATTATGATGTGACATCATGA-TTTTTTATATAATTATTTAT
260158 ATTTAAATTTTTAATCTAATAATTTC-A
63 ATTTAAATTTTTAATCTAATAA-TTCGA
*
260185 ATTAATCATTATTTACAAGGAGTATTATGATGTGACATCATGACTTTTTCATATAATTATTTATA
1 ATTAATCATTATTT-CAAGGAGTATTATGATGTGACATCATGA-TTTTTTATATAATTATTTATA
* * *
260250 TTTAATTTTTTAATCGAGTAATTCGA
64 TTTAAATTTTTAATCTAATAATTCGA
260276 A
1 A
260277 ATACACATTG
Statistics
Matches: 152, Mismatches: 17, Indels: 20
0.80 0.09 0.11
Matches are distributed among these distances:
84 1 0.01
85 56 0.37
86 1 0.01
87 4 0.03
88 1 0.01
89 4 0.03
90 42 0.28
91 43 0.28
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.48
Consensus pattern (89 bp):
ATTAATCATTATTTCAAGGAGTATTATGATGTGACATCATGATTTTTTATATAATTATTTATATT
TAAATTTTTAATCTAATAATTCGA
Found at i:262787 original size:38 final size:37
Alignment explanation
Indices: 262713--262788 Score: 91
Period size: 39 Copynumber: 2.0 Consensus size: 37
262703 GTTATAAAAT
* *
262713 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
262750 ATTTATATAATTTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-A-TTTTCTTTAAAAAATTGAAAATCATAAA
262788 A
1 A
262789 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
37 8 0.24
38 7 0.21
39 18 0.55
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:264045 original size:29 final size:29
Alignment explanation
Indices: 263990--264059 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
263980 GTGGAGTTAG
* *
263990 AAAATTTATTTTAGGTATCAAATTTTTTT
1 AAAAATTATTTTAGGTATCAAATTTTTAT
* *
264019 AAAAATTATTTTGAGGTGTTAAA-TTTTAT
1 AAAAATTATTTT-AGGTATCAAATTTTTAT
*
264048 AAAGATTATTTT
1 AAAAATTATTTT
264060 TCAGAAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 27 0.77
30 8 0.23
ACGTcount: A:0.37, C:0.01, G:0.10, T:0.51
Consensus pattern (29 bp):
AAAAATTATTTTAGGTATCAAATTTTTAT
Found at i:264124 original size:31 final size:31
Alignment explanation
Indices: 264089--264148 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
264079 TAGAGTATAT
*
264089 TACTCTCAAGTGCCCATTAATCGTACGCTTA
1 TACTCTCAAGTGCCCATTAATCATACGCTTA
*
264120 TACTCTCAAGTGCCGATTAATCATACGCT
1 TACTCTCAAGTGCCCATTAATCATACGCT
264149 CGGATAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.27, C:0.28, G:0.13, T:0.32
Consensus pattern (31 bp):
TACTCTCAAGTGCCCATTAATCATACGCTTA
Found at i:267938 original size:24 final size:24
Alignment explanation
Indices: 267902--267952 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
267892 TAAAAAAAAG
267902 AAAAAAGAGAAAAAATATATA-ATA
1 AAAAAAGA-AAAAAATATATACATA
* *
267926 AAAAAATAAAAAAATGTATACATA
1 AAAAAAGAAAAAAATATATACATA
267950 AAA
1 AAA
267953 GTAAATCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.18
Consensus pattern (24 bp):
AAAAAAGAAAAAAATATATACATA
Found at i:268107 original size:18 final size:18
Alignment explanation
Indices: 268078--268124 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
268068 AAATCATAGC
* *
268078 AAAATAACAAAAAAATGA
1 AAAATAAAAAAAAAATAA
* *
268096 AATATAAAAAAAGAATAA
1 AAAATAAAAAAAAAATAA
268114 AAAATAAAAAA
1 AAAATAAAAAA
268125 TATTAGATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.81, C:0.02, G:0.04, T:0.13
Consensus pattern (18 bp):
AAAATAAAAAAAAAATAA
Found at i:272317 original size:23 final size:21
Alignment explanation
Indices: 272266--272329 Score: 67
Period size: 23 Copynumber: 3.0 Consensus size: 21
272256 ATTCCCCTGT
272266 GGGGGGGAATCGGTTCCTCTTCA
1 GGGGGGGAATCGGTTCC-C-TCA
**
272289 AAGGGGGAATCGGTTCCCTCA
1 GGGGGGGAATCGGTTCCCTCA
*
272310 TGGGGGGG-ATCGATTCCCTC
1 -GGGGGGGAATCGGTTCCCTC
272330 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 14 0.40
22 6 0.17
23 15 0.43
ACGTcount: A:0.16, C:0.23, G:0.38, T:0.23
Consensus pattern (21 bp):
GGGGGGGAATCGGTTCCCTCA
Found at i:272321 original size:21 final size:21
Alignment explanation
Indices: 272265--272329 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
272255 GATTCCCCTG
272265 TGGGGGGGAATCGGTTCCTCTTCA
1 TGGGGGGG-ATCGGTTCC-C-TCA
** *
272289 AAGGGGGAATCGGTTCCCTCA
1 TGGGGGGGATCGGTTCCCTCA
*
272310 TGGGGGGGATCGATTCCCTC
1 TGGGGGGGATCGGTTCCCTC
272330 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
21 19 0.56
22 1 0.03
23 9 0.26
24 5 0.15
ACGTcount: A:0.15, C:0.23, G:0.37, T:0.25
Consensus pattern (21 bp):
TGGGGGGGATCGGTTCCCTCA
Found at i:278251 original size:21 final size:21
Alignment explanation
Indices: 278222--278262 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
278212 TGTTTCTGGC
*
278222 TATTTTGGGGTCGATCTCGGA
1 TATTCTGGGGTCGATCTCGGA
*
278243 TATTCTGGGGTCGTTCTCGG
1 TATTCTGGGGTCGATCTCGG
278263 TTATCTCGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.10, C:0.17, G:0.34, T:0.39
Consensus pattern (21 bp):
TATTCTGGGGTCGATCTCGGA
Found at i:278723 original size:14 final size:13
Alignment explanation
Indices: 278679--278722 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
278669 TATTATATAG
278679 TTTTCAAAAATGA
1 TTTTCAAAAATGA
* *
278692 TTTTAAAAAATAA
1 TTTTCAAAAATGA
*
278705 GTTTTCCAAAATGA
1 -TTTTCAAAAATGA
278719 TTTT
1 TTTT
278723 TTAAAACTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 15 0.60
14 10 0.40
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (13 bp):
TTTTCAAAAATGA
Found at i:278810 original size:39 final size:37
Alignment explanation
Indices: 278767--278889 Score: 101
Period size: 35 Copynumber: 3.3 Consensus size: 37
278757 GTTTTTAAAA
*
278767 ACTATATATTATATTTTCAAAATGATTTCAAAACTATAT
1 ACTATATATTA-ATTTTCAAAATG-TTTAAAAACTATAT
*
278806 AC--TATA-TAATTTTCAAAATGTTTTAAAACTTATAT
1 ACTATATATTAATTTTCAAAATGTTTAAAAAC-TATAT
* * * *
278841 ATTGTATA-TAAGATTTCAAAAATGTTTTAAAAACTACAT
1 ACTATATATTAA-TTTTC-AAAATG-TTTAAAAACTATAT
*
278880 AATATATATT
1 ACTATATATT
278890 TCAAAAAATA
Statistics
Matches: 70, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
34 8 0.11
35 18 0.26
36 2 0.03
37 11 0.16
38 4 0.06
39 18 0.26
40 9 0.13
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (37 bp):
ACTATATATTAATTTTCAAAATGTTTAAAAACTATAT
Found at i:278897 original size:35 final size:34
Alignment explanation
Indices: 278720--278933 Score: 139
Period size: 39 Copynumber: 5.9 Consensus size: 34
278710 CCAAAATGAT
* *
278720 TTTTTAAAACTATATATTATATAAATTTTCAAAAAATG
1 TTTTAAAAACTATATA--ATATATA-TTTC-AAAAATG
*
278758 TTTTTAAAAACTATATATTATAT-TTTC-AAAATG
1 -TTTTAAAAACTATATAATATATATTTCAAAAATG
* * *
278791 ATTTCAAAACTATATACTATATAATTTTC-AAAATG
1 TTTTAAAAACTATATAATATAT-A-TTTCAAAAATG
*
278826 TTTT-AAAACTTATATATTGTATATAAGATTTCAAAAATG
1 TTTTAAAAAC-TATATA----ATAT-ATATTTCAAAAATG
* *
278865 TTTTAAAAACTACATAATATATATTTCAAAAAATATT
1 TTTTAAAAACTATATAATATATATTTC--AAAA-ATG
* * *
278902 TTTTGAAAACTATATACTATATTTTTTCAAAA
1 TTTTAAAAACTATATAATATA-TATTTCAAAA
278934 CTTTTTCAAA
Statistics
Matches: 144, Mismatches: 16, Indels: 33
0.75 0.08 0.17
Matches are distributed among these distances:
32 19 0.13
33 6 0.04
34 11 0.08
35 27 0.19
36 8 0.06
37 24 0.17
38 9 0.06
39 34 0.24
40 6 0.04
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.44
Consensus pattern (34 bp):
TTTTAAAAACTATATAATATATATTTCAAAAATG
Found at i:278939 original size:35 final size:35
Alignment explanation
Indices: 278718--278957 Score: 172
Period size: 37 Copynumber: 6.7 Consensus size: 35
278708 TTCCAAAATG
*
278718 ATTTTTT-AAAACTATATATTATATAAATTTTCAAAAA
1 ATTTTTTAAAAACTATATACTATAT--ATTTTC-AAAA
278755 ATGTTTTTAAAAACTATATA-T-TATATTTTC-AAA
1 AT-TTTTTAAAAACTATATACTATATATTTTCAAAA
** *
278788 ATGATTTCAAAACTATATACTATATAATTTTC-AAA
1 ATTTTTTAAAAACTATATACTATAT-ATTTTCAAAA
* * *
278823 ATGTTTT-AAAACTTATATATTGTATATAAGATTTCAAAA
1 ATTTTTTAAAAAC-TATATA--CTATAT-A-TTTTCAAAA
* * *
278862 ATGTTTTAAAAACTACATAATATATA-TTTCAAAAAA
1 ATTTTTTAAAAACTATATACTATATATTTTC--AAAA
* *
278898 TATTTTTTGAAAACTATATACTATATTTTTTCAAAA
1 -ATTTTTTAAAAACTATATACTATATATTTTCAAAA
* * *
278934 CTTTTTCAAAAAAT-TATACTATAT
1 ATTTTTTAAAAACTATATACTATAT
278958 TACTATAATA
Statistics
Matches: 171, Mismatches: 17, Indels: 33
0.77 0.08 0.15
Matches are distributed among these distances:
32 14 0.08
33 6 0.04
34 22 0.13
35 37 0.22
36 9 0.05
37 38 0.22
38 14 0.08
39 26 0.15
40 5 0.03
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (35 bp):
ATTTTTTAAAAACTATATACTATATATTTTCAAAA
Found at i:279696 original size:84 final size:83
Alignment explanation
Indices: 279579--280715 Score: 1022
Period size: 84 Copynumber: 13.7 Consensus size: 83
279569 ATGAAATCAG
* * * * * *
279579 ACTCGGAGGTCTTCGGTTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCT
1 ACTCGAAGGTCTTTGG-TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCT
* *
279644 TGGAGCTGAACGTAGGCGA
65 TGGAGCTGAGCGTAGTCGA
* * * * *
279663 ACTCGAAGGTCTTTTGGTCACAAATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCC
1 ACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CC
* * *
279728 TCGAAGCTGAGCGTAGTTGA
64 TTGGAGCTGAGCGTAGTCGA
* * * *
279748 ACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGGCTTGAGTTATGCTGTAAATGATATGCCTT
1 ACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTT
*
279813 GGAGCTGAGCGTAATCGA
66 GGAGCTGAGCGTAGTCGA
* * * * * * *
279831 ACTTGAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTACTGCAAATGATATGCCT
1 ACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCT
279896 TGGAGCTGAGCGTAGTCGA
65 TGGAGCTGAGCGTAGTCGA
* * * * *
279915 ACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATATGCCCT
1 ACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCT
* * * * *
279980 CGAAGCTGAGTGCAATCGA
65 TGGAGCTGAGCGTAGTCGA
** * * *
279999 ACTCGGGGGTCTTT-G-G-CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
1 ACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTT
*
280061 GGAGCTGAGCGAAGTCGA
66 GGAGCTGAGCGTAGTCGA
* * * * *
280079 ACTCGAAGGTCTTTTAGTGACAGACAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCC
1 ACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CC
* * * *
280144 TCGAAGCTGAGTGTAATCGA
64 TTGGAGCTGAGCGTAGTCGA
** * * * * *
280164 ACTCGGGGGTCTTT-G-G-CAGATAGCTCTTCTCGACTTAA-TCTATGCTGCAAATGACGTGTCT
1 ACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGACTTAAGT-TATGCTGCAAATGATGTGCCT
* * *
280225 TAGAGCTGAGCGAAGTCAA
65 TGGAGCTGAGCGTAGTCGA
* * * * * * *
280244 ACTCGAAGGTCTTTTGGTGACAGACAACCTTTCTAGCCTTGAGTTATGTTGTAAATGATGTTCCC
1 ACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATG-TGCC
* * ** * *
280309 TCGAAGCTGAGTATAATCAA
64 TTGGAGCTGAGCGTAGTCGA
** * * ** * *
280329 ACTCGGGGGGTCTTT--AG-CAGATAACCCTTCTCGACTTAACCTATGCTACAAATGATGTGCTT
1 ACTC-GAAGGTCTTTGGTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCT
* *
280391 TGGAGCTGAACGTAGTTGA
65 TGGAGCTGAGCGTAGTCGA
* * * * * * *
280410 AGTCAAAGGTCTTTGGTTGGCAAATAACCCTTCTCGAGTTAAGTTATGCTGCAAATGATATGCCT
1 ACTCGAAGGTCTTTGG-TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCT
280475 TGGAGCTGAGCGTAGTCGA
65 TGGAGCTGAGCGTAGTCGA
* * * * *
280494 ACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATAATGTGCCC
1 ACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CC
* * * * *
280559 TCGAAGCTGAGTGTAATTGA
64 TTGGAGCTGAGCGTAGTCGA
** * * * **
280579 ACTCGGGGGTCTTT-G-G-CAGATAGCCCTTCTCGACTTAAGCTATGCCACAAATGATGTGCCTT
1 ACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTT
* *
280641 TGAGCTGAGCGTAGTCAA
66 GGAGCTGAGCGTAGTCGA
* *
280659 ACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATG
1 ACTCGAAGGTCTTTGG-TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATG
280716 TTGTCTTTAA
Statistics
Matches: 830, Mismatches: 196, Indels: 54
0.77 0.18 0.05
Matches are distributed among these distances:
80 84 0.10
81 122 0.15
82 35 0.04
83 77 0.09
84 395 0.48
85 112 0.13
86 5 0.01
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (83 bp):
ACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTT
GGAGCTGAGCGTAGTCGA
Found at i:280169 original size:165 final size:164
Alignment explanation
Indices: 279686--280715 Score: 1001
Period size: 165 Copynumber: 6.2 Consensus size: 164
279676 TTGGTCACAA
* * * * * * * *
279686 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAGTTGAACT
1 ATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACT
* * *
279751 CGAAGGTCTTTGGTGACAGATAACCCTTCTAGGCTTGAGTTATGCTGTAAATGATATG-CCTTGG
65 CGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGA
* * **
279815 AGCTGAGCGTAATCGAACTTGAAGGTCTTTTGTTGGCAG
130 AGCTGAGTGTAATCGAACTCGGGGGTC---T-TTGGCAG
* * * * * *
279854 ACAACCCTTCTAGACTTAAGTTGTACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
*
279919 GAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATATGCCCTCGAA
66 GAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAA
*
279984 GCTGAGTGCAATCGAACTCGGGGGTCTTTGGCAG
131 GCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAG
* *
280018 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGAAGTCGAACTC
1 ATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* * *
280083 GAAGGTCTTTTAGTGACAGACAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGA
66 GAAGGTC-TTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGA
280148 AGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAG
130 AGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAG
* * * * * * * *
280183 ATAGCTCTTCTCGACTTAATCTATGCTGCAAATGACGTGTCTTAGAGCTGAGCGAAGTCAAACTC
1 ATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* * * * *
280248 GAAGGTCTTTTGGTGACAGACAACCTTTCTAGCCTTGAGTTATGTTGTAAATGATGTTCCCTCGA
66 GAAGGTC-TTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGA
* * *
280313 AGCTGAGTATAATCAAACTCGGGGGGTCTTTAGCAG
130 AGCTGAGTGTAATCGAACTC-GGGGGTCTTTGGCAG
* * * * * *
280349 ATAACCCTTCTCGACTTAACCTATGCTACAAATGATGTGCTTTGGAGCTGAACGTAGTTGAAGTC
1 ATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* * * * ** * * * *
280414 AAAGGTCTTTGGTTGGCAAATAACCCTTCTCGAGTTAAGTTATGCTGCAAATGATATG-CCTTGG
66 GAAGGTCTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGA
* * **
280478 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAG
130 AGCTGAGTGTAATCGAACTCGGGGGTC-TTT-G-G-CAG
* * * * * * * * * * * *
280517 ATAACCCTTCTAGCCTTGAGTTATGTTGTAAATAATGTGCCCTCGAAGCTGAGTGTAATTGAACT
1 ATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACT
** * * * * * *** * * *
280582 CGGGGGTCTTT-G-G-CAGATAGCCCTTCTCGACTTAAGCTATGCCACAAATGATGTGCCTTTG-
65 CGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGA
* * * **
280643 AGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGCAG
130 AGCTGAGTGTAATCGAACTCGGGGGTC--T--TTGGCAG
*
280682 ATAACCCTTCTCGACTTAAGTTATGCTGCAAATG
1 ATAACCCTTCTCGACTTAAGCTATGCTGCAAATG
280716 TTGTCTTTAA
Statistics
Matches: 735, Mismatches: 114, Indels: 29
0.84 0.13 0.03
Matches are distributed among these distances:
164 76 0.10
165 346 0.47
166 113 0.15
167 80 0.11
168 94 0.13
169 26 0.04
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (164 bp):
ATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
GAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAA
GCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAG
Found at i:280460 original size:250 final size:249
Alignment explanation
Indices: 279598--280715 Score: 857
Period size: 249 Copynumber: 4.5 Consensus size: 249
279588 TCTTCGGTTG
* * ** * * *
279598 GCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAACGTAGGCGA
1 GCAGATAACCCTTCTCGACTTAACCTATGCCACAAATGATGTGCCTTTGAGCTGAACGTAGTCAA
* ** * * * * **
279663 ACTCGAAGGTCTTTTGG-TCACAAATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCC
66 ACTCAAAGGTC-TTTGGTTGGCAAATAACCCTTCTCGACTTAAGTTATGCTGCAAATGACATGCC
* * * ** * *
279727 CTCGAAGCTGAGCGTAGTTGAACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTAGGCTTGAGT
130 TTAG-AGCTGAGCGAAGTCAAACTCGAAGGTCTTTTGGTGACAGACAACCCTTCTAGCCTTGAGT
* * * * * ** * * ** *
279791 TATGCTGTAAATGATATG-CCTTGGAGCTGAGCGTAATCGAACTTGAAGGTCTTTTGTTG
194 TATGTTGTAAATAATGTGCCCTCGAAGCTGAGTATAATCAAACTCGGGGGTC---T-TTA
* * ** * * ** * * * *
279850 GCAGACAACCCTTCTAGACTTAAGTTGTACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGA
1 GCAGATAACCCTTCTCGACTTAACCTATGCCACAAATGATGTGCCTTTGAGCTGAACGTAGTCAA
* * * * * * * * * *
279915 ACTCGAAGGTCTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATATGCCC
66 ACTCAAAGGTCTTTGGTTGGCAAATAACCCTTCTCGACTTAAGTTATGCTGCAAATGACATGCCT
* * * ** * * * * * *
279979 TCGAAGCTGAGTGCAA-TCGAACTCGGGGGTC-TTT-G-G-CAGATAGCCCTTCTCGACTTAAGC
131 TAG-AGCTGAGCG-AAGTCAAACTCGAAGGTCTTTTGGTGACAGACAACCCTTCTAGCCTTGAGT
* * * * * * * * **
280039 TATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGA-AGTCGAACTCGAAGGTCTTTTA
194 TATGTTGTAAATAATGTGCCCTCGAAGCTGAG-TATAATCAAACTCGGGGGTC-TTTA
* * * * ** *** * * ** *
280095 GTGACAGACAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 --G-CAGATAACCCTTCTCGACTTAACCTATGCCACAAATGATGTGCCTTTG-AGCTGAACGTAG
* *** * * * *
280160 TCGAACTCGGGGGTC--T--TTGGCAGATAGCTCTTCTCGACTTAA-TCTATGCTGCAAATGACG
62 TCAAACTCAAAGGTCTTTGGTTGGCAAATAACCCTTCTCGACTTAAGT-TATGCTGCAAATGACA
* *
280220 TGTCTTAGAGCTGAGCGAAGTCAAACTCGAAGGTCTTTTGGTGACAGACAACCTTTCTAGCCTTG
126 TGCCTTAGAGCTGAGCGAAGTCAAACTCGAAGGTCTTTTGGTGACAGACAACCCTTCTAGCCTTG
* *
280285 AGTTATGTTGTAAATGATGTTCCCTCGAAGCTGAGTATAATCAAACTCGGGGGGTCTTTA
191 AGTTATGTTGTAAATAATGTGCCCTCGAAGCTGAGTATAATCAAACTC-GGGGGTCTTTA
* **
280345 GCAGATAACCCTTCTCGACTTAACCTATGCTACAAATGATGTG-CTTTGGAGCTGAACGTAGTTG
1 GCAGATAACCCTTCTCGACTTAACCTATGCCACAAATGATGTGCCTTT-GAGCTGAACGTAGTCA
* * *
280409 AAGTCAAAGGTCTTTGGTTGGCAAATAACCCTTCTCGAGTTAAGTTATGCTGCAAATGATATGCC
65 AACTCAAAGGTCTTTGGTTGGCAAATAACCCTTCTCGACTTAAGTTATGCTGCAAATGACATGCC
* * * *
280474 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTT
130 TTAGAGCTGAGCGAAGTCAAACTCGAAGGTCTTTTGGTGACAGACAACCCTTCTAGCCTTGAGTT
* ** *
280539 ATGTTGTAAATAATGTGCCCTCGAAGCTGAGTGTAATTGAACTCGGGGGTCTTTG
195 ATGTTGTAAATAATGTGCCCTCGAAGCTGAGTATAATCAAACTCGGGGGTCTTTA
* * *
280594 GCAGATAGCCCTTCTCGACTTAAGCTATGCCACAAATGATGTGCCTTTGAGCTGAGCGTAGTCAA
1 GCAGATAACCCTTCTCGACTTAACCTATGCCACAAATGATGTGCCTTTGAGCTGAACGTAGTCAA
* *
280659 ACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATG
66 ACTCAAAGGTCTTTGGTTGGCAAATAACCCTTCTCGACTTAAGTTATGCTGCAAATG
280716 TTGTCTTTAA
Statistics
Matches: 723, Mismatches: 120, Indels: 49
0.81 0.13 0.05
Matches are distributed among these distances:
244 2 0.00
245 23 0.03
246 62 0.09
247 38 0.05
248 106 0.15
249 174 0.24
250 166 0.23
251 82 0.11
252 70 0.10
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (249 bp):
GCAGATAACCCTTCTCGACTTAACCTATGCCACAAATGATGTGCCTTTGAGCTGAACGTAGTCAA
ACTCAAAGGTCTTTGGTTGGCAAATAACCCTTCTCGACTTAAGTTATGCTGCAAATGACATGCCT
TAGAGCTGAGCGAAGTCAAACTCGAAGGTCTTTTGGTGACAGACAACCCTTCTAGCCTTGAGTTA
TGTTGTAAATAATGTGCCCTCGAAGCTGAGTATAATCAAACTCGGGGGTCTTTA
Found at i:280516 original size:415 final size:416
Alignment explanation
Indices: 279585--280715 Score: 1364
Period size: 415 Copynumber: 2.7 Consensus size: 416
279575 TCAGACTCGG
* *
279585 AGGTCTTCGGTTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGC
1 AGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGC
* * * *
279650 TGAACGTAGGCGAACTCGAAGGTCTTTTGGTCACAAATAACCCTTCTAGCCTTGAGTTATGCTGT
66 TGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGT
* * ** *
279715 AAATGATGTGCCCTCGAAGCTGAGCGTAGTTGAACTCGAAGGTCTTTGGTGACAGATAACCCTTC
131 AAATGATGTGCCCTCGAAGCTGAGTGTAATTGAACTCGGGGGTCTTT-G-G-CAGATAGCCCTTC
* * * * * * * *
279780 TAGGCTTGAGT-TATGCTGTAAATGATATGCCTTGGAGCTGAGCGTAA-TCGAACTTGAAGGTCT
193 TCGACTT-AATCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCG-AAGTCAAACTCGAAGGTCT
* * * * * * *
279843 TTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTACTGCAAATGATATGCCTTGGAGCTGAGCG
256 TTTGGTGACAGACAACCCTTCTAGACTTAAGTTATACTGCAAATGATATCCCTCGAAGCTGAGCA
* * * * * ** * **
279908 TAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGAT
321 TAATCAAACTCGAAGGTCTTT-GAGACAGATAACCCTTCTAGACTTAACCTATGCTACAAATGAT
** **
279973 ATGCCCTCGAAGCTGAGTGCAATCGAACTCGG
385 ATGCCCTCGAAGCTGAACGCAATCGAACTCAA
* *
280005 GGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGC
1 AGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGC
* * *
280066 TGAGCGAAGTCGAACTCGAAGGTCTTTTAGTGACAGACAACCCTTCTAGCCTTGAGTTATGCTGT
66 TGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGT
* *
280131 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCTCTTCTCG
131 AAATGATGTGCCCTCGAAGCTGAGTGTAATTGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
* *
280196 ACTTAATCTATGCTGCAAATGACGTGTCTTAGAGCTGAGCGAAGTCAAACTCGAAGGTCTTTTGG
196 ACTTAATCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCGAAGTCAAACTCGAAGGTCTTTTGG
* * * ** * * *
280261 TGACAGACAACCTTTCTAGCCTTGAGTTATGTTGTAAATGATGTTCCCTCGAAGCTGAGTATAAT
261 TGACAGACAACCCTTCTAGACTTAAGTTATACTGCAAATGAT-ATCCCTCGAAGCTGAGCATAAT
** * *
280326 CAAACTCGGGGGGTCTTT-AG-CAGATAACCCTTCTCGACTTAACCTATGCTACAAATGATGTG-
325 CAAACTC-GAAGGTCTTTGAGACAGATAACCCTTCTAGACTTAACCTATGCTACAAATGATATGC
* * * * * * *
280388 CTTTGGAGCTGAACGTAGTTGAAGTCAA
389 CCTCGAAGCTGAACGCAATCGAACTCAA
* * * *
280416 AGGTCTTTGGTTGGCAAATAACCCTTCTCGAGTTAAGTTATGCTGCAAATGATATGCCTTGGAGC
1 AGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGC
*
280481 TGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGTTGT
66 TGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGT
*
280546 AAATAATGTGCCCTCGAAGCTGAGTGTAATTGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
131 AAATGATGTGCCCTCGAAGCTGAGTGTAATTGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
* ** * *
280611 ACTTAAGCTATGCCACAAATGATGTGCCTTTGAGCTGAGCGTAGTCAAACTCGAAGGTC-TTTGG
196 ACTTAATCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCGAAGTCAAACTCGAAGGTCTTTTGG
* * * *
280675 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATG
261 -TGACAGACAACCCTTCTAGACTTAAGTTATACTGCAAATG
280716 TTGTCTTTAA
Statistics
Matches: 606, Mismatches: 96, Indels: 23
0.84 0.13 0.03
Matches are distributed among these distances:
411 21 0.03
412 37 0.06
413 98 0.16
414 27 0.04
415 266 0.44
416 153 0.25
420 4 0.01
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (416 bp):
AGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGC
TGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGT
AAATGATGTGCCCTCGAAGCTGAGTGTAATTGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
ACTTAATCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCGAAGTCAAACTCGAAGGTCTTTTGG
TGACAGACAACCCTTCTAGACTTAAGTTATACTGCAAATGATATCCCTCGAAGCTGAGCATAATC
AAACTCGAAGGTCTTTGAGACAGATAACCCTTCTAGACTTAACCTATGCTACAAATGATATGCCC
TCGAAGCTGAACGCAATCGAACTCAA
Found at i:285963 original size:12 final size:10
Alignment explanation
Indices: 285922--285972 Score: 52
Period size: 10 Copynumber: 5.0 Consensus size: 10
285912 AATGTTAAAT
*
285922 GAATTAAAAA
1 GAATAAAAAA
285932 GAATAAAAAA
1 GAATAAAAAA
285942 GAGA-AAAAAA
1 GA-ATAAAAAA
285952 GATATAATAAAA
1 GA-ATAA-AAAA
285964 -AATAAAAAA
1 GAATAAAAAA
285973 ATGTATACAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
9 4 0.11
10 24 0.67
11 4 0.11
12 4 0.11
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.14
Consensus pattern (10 bp):
GAATAAAAAA
Found at i:285971 original size:23 final size:23
Alignment explanation
Indices: 285933--285986 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
285923 AATTAAAAAG
285933 AATAAAAAAGAGAAAAAAAGATAT
1 AATAAAAAAGAGAAAAAAAG-TAT
* *
285957 AATAAAAAATA-AAAAAATGTAT
1 AATAAAAAAGAGAAAAAAAGTAT
285979 ACATAAAA
1 A-ATAAAA
285987 GTAAATCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 4 0.15
23 13 0.48
24 10 0.37
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.17
Consensus pattern (23 bp):
AATAAAAAAGAGAAAAAAAGTAT
Found at i:285991 original size:22 final size:22
Alignment explanation
Indices: 285927--285986 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
285917 TAAATGAATT
* *
285927 AAAAAGA-ATAA-AAAAGAGAA
1 AAAAAGATATAATAAAAAATAA
285947 AAAAAGATATAATAAAAAATAA
1 AAAAAGATATAATAAAAAATAA
285969 AAAAATG-TATACATAAAA
1 AAAAA-GATATA-ATAAAA
285987 GTAAATCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 7 0.21
21 4 0.12
22 16 0.47
23 7 0.21
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (22 bp):
AAAAAGATATAATAAAAAATAA
Found at i:286608 original size:20 final size:21
Alignment explanation
Indices: 286583--286634 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
286573 TTTTCCCAAT
*
286583 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
286603 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
286624 TCGCAATGCGA
1 TCGCAATGCGA
286635 TATTGACTAT
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:286648 original size:20 final size:20
Alignment explanation
Indices: 286623--286732 Score: 105
Period size: 20 Copynumber: 5.5 Consensus size: 20
286613 AATTTGGAAA
* *
286623 ATCGCAATGCGATATTGACT
1 ATCGCAACGCGATACTGACT
* * *
286643 ATCGCAACACGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
286664 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
286684 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
286704 TTCGCAATGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
286724 TTCGCAACG
1 ATCGCAACG
286733 AGATTCTGAA
Statistics
Matches: 76, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 58 0.76
21 14 0.18
22 2 0.03
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:286665 original size:41 final size:41
Alignment explanation
Indices: 286620--286697 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
286610 GCGAATTTGG
* *
286620 AAAATCGCAATGCGATATTGACTATCGCAACACGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACACGATAATAC
* *
286661 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATA
1 AAAATCGCAACGCGATACTGACTATCGCAACACGATA
286698 CTGACTTTCG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACACGATAATAC
Found at i:286741 original size:20 final size:20
Alignment explanation
Indices: 286665--286732 Score: 118
Period size: 20 Copynumber: 3.4 Consensus size: 20
286655 TAATACAAAA
286665 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
286685 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
* *
286705 TCGCAATGCGATTCTGACTT
1 TCGCAACGCGATACTGACTT
286725 TCGCAACG
1 TCGCAACG
286733 AGATTCTGAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:286749 original size:40 final size:40
Alignment explanation
Indices: 286619--286751 Score: 135
Period size: 40 Copynumber: 3.3 Consensus size: 40
286609 TGCGAATTTG
* *
286619 GAAAATCGCAATGCGATAT-TGACTATCGCAAC-ACGATAAT
1 GAAAATCGCAATGCGAT-TCTGACTTTCGCAACGA-GATACT
* * * *
286659 ACAAAATCGCAACGCGATACTGACTTTCGCAACGCGATACT
1 -GAAAATCGCAATGCGATTCTGACTTTCGCAACGAGATACT
*** *
286700 GACTTTCGCAATGCGATTCTGACTTTCGCAACGAGATTCT
1 GAAAATCGCAATGCGATTCTGACTTTCGCAACGAGATACT
286740 GAAAATCGCAAT
1 GAAAATCGCAAT
286752 CATCTTCAAA
Statistics
Matches: 73, Mismatches: 17, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
40 41 0.56
41 32 0.44
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (40 bp):
GAAAATCGCAATGCGATTCTGACTTTCGCAACGAGATACT
Found at i:286970 original size:20 final size:20
Alignment explanation
Indices: 286948--287045 Score: 169
Period size: 20 Copynumber: 4.9 Consensus size: 20
286938 ATTCATTTGA
*
286948 CTATCGCAACGCGAAAATGA
1 CTATCGCAACGCGAAAATGG
286968 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
286988 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
287008 CCATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
287028 CTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
287046 CGCAATGCGA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 74 1.00
ACGTcount: A:0.38, C:0.26, G:0.22, T:0.14
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:288751 original size:41 final size:42
Alignment explanation
Indices: 288697--288788 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
288687 CCTCTTCAAC
* *
288697 GATGACAGTGGCCTCTTGAACG-GTGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
* *
288738 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
288780 GATGACAGG
1 GATGACAGG
288789 TGAGTCGGGC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 20 0.44
42 25 0.56
ACGTcount: A:0.21, C:0.15, G:0.42, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:288753 original size:21 final size:21
Alignment explanation
Indices: 288724--288784 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
288714 GAACGGTGGG
*
288724 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* **
288745 GGGGCCTCTTGAACGATTG-GA
1 GGGGACTCTTGAGGGA-TGAGA
288766 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
288785 CAGGTGAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.13, G:0.43, T:0.23
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:289201 original size:20 final size:20
Alignment explanation
Indices: 289151--289205 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
289141 AAACTTACTT
* *
289151 TCGCAACGTGAAAATGGCTA
1 TCGCAACGCGGAAATGGCTA
289171 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGGCTA
* *
289191 TCGTAATGCGGAAAT
1 TCGCAACGCGGAAAT
289206 TGCGATTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.20, G:0.27, T:0.20
Consensus pattern (20 bp):
TCGCAACGCGGAAATGGCTA
Found at i:289228 original size:19 final size:19
Alignment explanation
Indices: 289204--289259 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
289194 TAATGCGGAA
289204 ATTGCGATTTTCATTTCGC
1 ATTGCGATTTTCATTTCGC
*
289223 ATTGCGA-TTT--TGTCG-
1 ATTGCGATTTTCATTTCGC
289238 -TTGCGATTTTCATTTCGC
1 ATTGCGATTTTCATTTCGC
289256 ATTG
1 ATTG
289260 TGATAGCCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 6 0.20
15 3 0.10
16 4 0.13
17 4 0.13
18 3 0.10
19 10 0.33
ACGTcount: A:0.14, C:0.18, G:0.20, T:0.48
Consensus pattern (19 bp):
ATTGCGATTTTCATTTCGC
Found at i:289284 original size:20 final size:19
Alignment explanation
Indices: 289248--289291 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
289238 TTGCGATTTT
**
289248 CATTTCGCATTGTGATAGC
1 CATTTCGCATTACGATAGC
*
289267 CATTTCCGCATTACGATAGT
1 CATTT-CGCATTACGATAGC
289287 CATTT
1 CATTT
289292 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.39
Consensus pattern (19 bp):
CATTTCGCATTACGATAGC
Found at i:289870 original size:18 final size:18
Alignment explanation
Indices: 289843--289888 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
289833 GGTCGATCAA
289843 GTGATGGCTCTGGGTGAG
1 GTGATGGCTCTGGGTGAG
*
289861 GTGATAGCTCTGGGTGAG
1 GTGATGGCTCTGGGTGAG
289879 GTGATGGCTC
1 GTGATGGCTC
289889 CCGAAGTGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.13, C:0.13, G:0.46, T:0.28
Consensus pattern (18 bp):
GTGATGGCTCTGGGTGAG
Found at i:291233 original size:20 final size:20
Alignment explanation
Indices: 291208--291245 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
291198 AATAGTTTCT
291208 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
*
291228 GAAAATGACAATCGCAAC
1 GAAAATGAAAATCGCAAC
291246 GTGAATTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.21, G:0.16, T:0.11
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:291547 original size:20 final size:21
Alignment explanation
Indices: 291522--291570 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
291512 TCTGAGAGAT
291522 AGAGAT-AGACGGATTTCGCC
1 AGAGATGAGACGGATTTCGCC
* *
291542 AGAGATGGGGACGGATTTCGTC
1 AGAGAT-GAGACGGATTTCGCC
*
291564 GGAGATG
1 AGAGATG
291571 GGTGAGAGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 6 0.25
21 1 0.04
22 17 0.71
ACGTcount: A:0.27, C:0.14, G:0.39, T:0.20
Consensus pattern (21 bp):
AGAGATGAGACGGATTTCGCC
Found at i:291556 original size:22 final size:22
Alignment explanation
Indices: 291529--291572 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
291519 GATAGAGATA
291529 GACGGATTTCGCCAGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
* *
291551 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
291573 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCAGAGATGGG
Found at i:291812 original size:20 final size:19
Alignment explanation
Indices: 291739--291812 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
291729 CGCTTTTAAA
*
291739 ATCGCATTGCGATTATGTATT
1 ATCGCATTGCGA-TA-GTAGT
* *
291760 ATCTCATTGCGAAAGTAAGT
1 ATCGCATTGCGATAGT-AGT
*
291780 ATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATAGT-AGT
291800 ATCGCATTGCGAT
1 ATCGCATTGCGAT
291813 TTTCCAAATT
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
19 2 0.05
20 31 0.70
21 11 0.25
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.34
Consensus pattern (19 bp):
ATCGCATTGCGATAGTAGT
Found at i:291887 original size:20 final size:21
Alignment explanation
Indices: 291801--291894 Score: 145
Period size: 21 Copynumber: 4.5 Consensus size: 21
291791 ATAGTCAGTA
291801 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
291822 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
*
291843 TCGTATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* **
291864 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCAAAT
291884 TCGCATTGCGA
1 TCGCATTGCGA
291895 ATTGGGAAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
20 17 0.25
21 51 0.75
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:291936 original size:21 final size:22
Alignment explanation
Indices: 291884--291936 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
291874 ATTTACTTAT
291884 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
291905 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
291926 TCGCATTGCGA
1 TCGCATTGCGA
291937 TAGTCATAAT
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:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:294776 original size:23 final size:23
Alignment explanation
Indices: 294750--294794 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
294740 GACATTATAT
*
294750 GGCACTACGGTGCATTTCTACGC
1 GGCACTACGGTGCATTTATACGC
*
294773 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCATTTATACG
294795 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.29
Consensus pattern (23 bp):
GGCACTACGGTGCATTTATACGC
Found at i:296362 original size:10 final size:10
Alignment explanation
Indices: 296343--296375 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
296333 AAATTAGACT
296343 AATAAAATGA
1 AATAAAATGA
*
296353 AATGAAATGA
1 AATAAAATGA
296363 AATAAAAT-A
1 AATAAAATGA
296372 AATA
1 AATA
296376 TTAATAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 5 0.24
10 16 0.76
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (10 bp):
AATAAAATGA
Found at i:296384 original size:38 final size:38
Alignment explanation
Indices: 296305--296392 Score: 101
Period size: 39 Copynumber: 2.3 Consensus size: 38
296295 CCTTGACAAA
* *
296305 AATAAAATAAATGAAACTAAATTAAATTAAATTAGACT
1 AATAAAATAAATGAAACTAAATAAAATAAAATTAGACT
296343 AATAAAATGAAATGAAA-TGAAATAAAATAAATATTA-A-T
1 AATAAAAT-AAATGAAACT-AAATAAAATAAA-ATTAGACT
*
296381 AATAATATAAAT
1 AATAAAATAAAT
296393 TATATAATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
37 4 0.09
38 17 0.39
39 19 0.43
40 4 0.09
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (38 bp):
AATAAAATAAATGAAACTAAATAAAATAAAATTAGACT
Found at i:296540 original size:39 final size:40
Alignment explanation
Indices: 296497--296579 Score: 123
Period size: 40 Copynumber: 2.1 Consensus size: 40
296487 GATTTTAAAA
* * * *
296497 ATATAAGTTTTC-CAAAATGTTTTTTTAAAACTTTATATT
1 ATATAAATTTTCAAAAAATGTTTTTTAAAAACTATATATT
296536 ATATAAATTTTCAAAAAATGTTTTTTAAAAACTATATATT
1 ATATAAATTTTCAAAAAATGTTTTTTAAAAACTATATATT
296576 ATAT
1 ATAT
296580 TGTCAAAATG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
39 11 0.28
40 28 0.72
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (40 bp):
ATATAAATTTTCAAAAAATGTTTTTTAAAAACTATATATT
Found at i:296600 original size:32 final size:32
Alignment explanation
Indices: 296563--296642 Score: 99
Period size: 35 Copynumber: 2.4 Consensus size: 32
296553 ATGTTTTTTA
296563 AAAACTATATATTAT-ATTGTCAAAATGATTTC
1 AAAACTATATATTATAATTGTCAAAATG-TTTC
* *
296595 AAAACTATATACTATATAATTTTCAAAATGTTTT
1 AAAACTATATA-T-TATAATTGTCAAAATGTTTC
296629 AAAACTTATATATT
1 AAAAC-TATATATT
296643 GTATATAAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
32 11 0.26
33 2 0.05
34 12 0.29
35 17 0.40
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (32 bp):
AAAACTATATATTATAATTGTCAAAATGTTTC
Found at i:296639 original size:35 final size:34
Alignment explanation
Indices: 296497--296641 Score: 127
Period size: 34 Copynumber: 4.1 Consensus size: 34
296487 GATTTTAAAA
*
296497 ATATAAGTTTTCCAAAATGTTTTTTTAAAACTTTATATT
1 ATATAA-TTTT-CAAAATG--TTTTTAAAACTATATA-T
296536 ATATAAATTTTCAAAAAATGTTTTTTAAAAACTATATAT
1 ATAT-AATTTTC--AAAATG-TTTTT-AAAACTATATAT
* * *
296575 -TAT-ATTGTCAAAATGATTTCAAAACTATATACT
1 ATATAATTTTCAAAATGTTTTTAAAACTATATA-T
296608 ATATAATTTTCAAAATG-TTTTAAAACT-TATAT
1 ATATAATTTTCAAAATGTTTTTAAAACTATATAT
296640 AT
1 AT
296642 TGTATATAAG
Statistics
Matches: 93, Mismatches: 6, Indels: 21
0.77 0.05 0.17
Matches are distributed among these distances:
32 14 0.15
33 8 0.09
34 18 0.19
35 11 0.12
36 5 0.05
38 4 0.04
39 15 0.16
40 18 0.19
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.46
Consensus pattern (34 bp):
ATATAATTTTCAAAATGTTTTTAAAACTATATAT
Found at i:298875 original size:32 final size:31
Alignment explanation
Indices: 298839--298915 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
298829 CGGGGCCGTG
*
298839 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
298871 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
298902 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
298916 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:298898 original size:63 final size:63
Alignment explanation
Indices: 298792--298915 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
298782 CCCTAAGGGA
* * ** *
298792 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
298855 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
298916 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:299823 original size:5 final size:5
Alignment explanation
Indices: 299813--299865 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
299803 AACGGTCAAC
* *
299813 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG
299862 GGTC
1 GGTC
299866 AGACCGGTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 32 0.80
7 8 0.20
ACGTcount: A:0.08, C:0.23, G:0.51, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:299828 original size:17 final size:17
Alignment explanation
Indices: 299806--299866 Score: 77
Period size: 17 Copynumber: 3.3 Consensus size: 17
299796 AACGGTCAAC
299806 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
299823 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAA----C-GGTCGGGTCG
299845 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
299862 GGTCA
1 GGTCA
299867 GACCGGTCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
17 21 0.54
18 1 0.03
21 1 0.03
22 16 0.41
ACGTcount: A:0.11, C:0.23, G:0.48, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:299833 original size:7 final size:7
Alignment explanation
Indices: 299786--299816 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
299776 GTCAAAGAAA
299786 GTCAACG
1 GTCAACG
299793 GTCAACG
1 GTCAACG
299800 GTCAACG
1 GTCAACG
299807 GTCAACG
1 GTCAACG
299814 GTC
1 GTC
299817 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:299841 original size:22 final size:22
Alignment explanation
Indices: 299799--299865 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
299789 AACGGTCAAC
*
299799 GGTCAACGGTCAACGGTCGGGTCG
1 GGTCAACGGTC--GGGTCGGGTCG
299823 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
299845 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
299866 AGACCGGTCA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
22 31 0.74
24 11 0.26
ACGTcount: A:0.12, C:0.24, G:0.46, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:299880 original size:9 final size:9
Alignment explanation
Indices: 299862--299960 Score: 81
Period size: 9 Copynumber: 10.3 Consensus size: 9
299852 GGTCGGGTCG
*
299862 GGTCAGACC
1 GGTCAAACC
299871 GGTCAAACC
1 GGTCAAACC
* *
299880 GATTCAGACC
1 G-GTCAAACC
299890 GGTCAAACC
1 GGTCAAACC
*
299899 GGTTCGAACC
1 GG-TCAAACC
*
299909 GGTTGAAACC
1 GG-TCAAACC
299919 GGTCAAACC
1 GGTCAAACC
299928 GGTCAGAACC
1 GGTCA-AACC
* *
299938 GGTTGAAAACT
1 GG-T-CAAACC
299949 GGTCAAACC
1 GGTCAAACC
299958 GGT
1 GGT
299961 TTCCAGCAGC
Statistics
Matches: 72, Mismatches: 13, Indels: 10
0.76 0.14 0.11
Matches are distributed among these distances:
9 35 0.49
10 30 0.42
11 6 0.08
12 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:299919 original size:29 final size:31
Alignment explanation
Indices: 299887--299961 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
299877 ACCGATTCAG
299887 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
299916 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
299946 ACTGGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
299962 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 15 0.36
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:299939 original size:19 final size:19
Alignment explanation
Indices: 299862--299960 Score: 80
Period size: 19 Copynumber: 5.2 Consensus size: 19
299852 GGTCGGGTCG
299862 GGTCAG-ACCGGTCAAACC
1 GGTCAGAACCGGTCAAACC
*
299880 GATTCAG-ACCGGTCAAACC
1 G-GTCAGAACCGGTCAAACC
*
299899 GGTTC-GAACCGGTTGAAACC
1 GG-TCAGAACCGG-TCAAACC
299919 GGTCA-AACCGGTCAGAACC
1 GGTCAGAACCGGTCA-AACC
* * *
299938 GGTTGAAAACTGGTCAAACC
1 GG-TCAGAACCGGTCAAACC
299958 GGT
1 GGT
299961 TTCCAGCAGC
Statistics
Matches: 67, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
18 4 0.06
19 39 0.58
20 16 0.24
21 8 0.12
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.16
Consensus pattern (19 bp):
GGTCAGAACCGGTCAAACC
Found at i:299959 original size:20 final size:21
Alignment explanation
Indices: 299923--299961 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
299913 GAAACCGGTC
299923 AAACCGGTCAGAACCGGTTGA
1 AAACCGGTCAGAACCGGTTGA
*
299944 AAACTGGTCA-AACCGGTT
1 AAACCGGTCAGAACCGGTT
299962 TCCAGCAGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (21 bp):
AAACCGGTCAGAACCGGTTGA
Found at i:306220 original size:32 final size:31
Alignment explanation
Indices: 306182--306258 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
306172 CGGGTTCGTG
*
306182 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
306214 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
306245 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
306259 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:307140 original size:7 final size:7
Alignment explanation
Indices: 307128--307158 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
307118 GTCAAAGAAA
307128 GTCAACG
1 GTCAACG
307135 GTCAACG
1 GTCAACG
307142 GTCAACG
1 GTCAACG
307149 GTCAACG
1 GTCAACG
307156 GTC
1 GTC
307159 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:307165 original size:5 final size:5
Alignment explanation
Indices: 307155--307212 Score: 53
Period size: 5 Copynumber: 10.8 Consensus size: 5
307145 AACGGTCAAC
* * *
307155 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GTTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
307204 GGTCG GGTC
1 GGTCG GGTC
307213 AGACCGGTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
5 36 0.84
7 7 0.16
ACGTcount: A:0.07, C:0.22, G:0.50, T:0.21
Consensus pattern (5 bp):
GGTCG
Found at i:307176 original size:22 final size:22
Alignment explanation
Indices: 307148--307212 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
307138 AACGGTCAAC
307148 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
307170 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
307192 GTTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
307213 AGACCGGTCA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.09, C:0.23, G:0.48, T:0.20
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Done.