Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008280.1 Hibiscus syriacus cultivar Beakdansim tig00110940_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: 3557051
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 17
Found at i:292360 original size:19 final size:19
Alignment explanation
Indices: 292336--292374 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
292326 TCGAATGCAT
292336 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
292355 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
292374 T
1 T
292375 GATTTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:292407 original size:64 final size:65
Alignment explanation
Indices: 292271--292500 Score: 213
Period size: 64 Copynumber: 3.5 Consensus size: 65
292261 TTTTCAAAGG
* * * *
292271 CATGCACCGATGCA-TCAATACCATGCATCGATGCA-TCAATGAATAAATTGAAATATCGAATGC
1 CATGCACCGATGCACTC--T-CCATGCATCGATGCACTC-ATGATTTAATTAAAACATCGAATGC
*
292334 ATTC
62 ATTT
292338 CATGCACCGATGCACTCTCCATGCATCGATGCACTC-TGATTTAATTAAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCATGATTTAATTAAAACATCGAATGCATTT
* * ** * * *
292402 GATGCATCGATGCACAATCCATGCATCGATGCAC-CAGGCTATTT--TTCAAACATCGAATGCAC
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCATG--ATTTAATTAAAACATCGAATGCAT
292464 TT
64 TT
* * *
292466 CATGCATCGATGCACTCT-TAGTGCACCGATGCACT
1 CATGCACCGATGCACTCTCCA-TGCATCGATGCACT
292501 AGGAGTCCAA
Statistics
Matches: 139, Mismatches: 17, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
63 2 0.01
64 99 0.71
65 15 0.11
66 7 0.05
67 14 0.10
68 2 0.01
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (65 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCACTCATGATTTAATTAAAACATCGAATGCATTT
Found at i:292480 original size:17 final size:19
Alignment explanation
Indices: 292452--292500 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
292442 ATTTTTCAAA
292452 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
292470 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
292489 CACCGATGCACT
1 CATCGATGCACT
292501 AGGAGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:295028 original size:3 final size:3
Alignment explanation
Indices: 295020--295045 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
295010 AAGGAGAGAC
295020 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
295046 GGTCTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:300549 original size:30 final size:30
Alignment explanation
Indices: 300479--300549 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
300469 CTGCTTAAAA
* *
300479 AGTTTAATTAATTCAGTTTCTCGATTTGAG
1 AGTTTAATTGATTCAATTTCTCGATTTGAG
* * *
300509 -GACTTCATTGATTCAATTTCTTGATTTGAG
1 AG-TTTAATTGATTCAATTTCTCGATTTGAG
300539 AGTTTAATTGA
1 AGTTTAATTGA
300550 GGGTAAAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
29 1 0.03
30 30 0.94
31 1 0.03
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.46
Consensus pattern (30 bp):
AGTTTAATTGATTCAATTTCTCGATTTGAG
Found at i:305387 original size:21 final size:21
Alignment explanation
Indices: 305331--305388 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
305321 ATTCTTACTA
* *
305331 TCGCATTGCGATTTCCCAAAT
1 TCGCGTTGCGATTTTCCAAAT
*
305352 TCGCGTTGCGATTTTCCTAAT
1 TCGCGTTGCGATTTTCCAAAT
305373 TCGCGTTGCGATTTTC
1 TCGCGTTGCGATTTTC
305389 ATAGCGCCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.16, C:0.26, G:0.19, T:0.40
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCAAAT
Found at i:305965 original size:20 final size:20
Alignment explanation
Indices: 305916--305956 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
305906 TTCTAAACTT
* *
305916 AAAATCGAAACATGAAAATG
1 AAAATCGCAACACGAAAATG
305936 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
305956 A
1 A
305957 CTATCGCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.59, C:0.15, G:0.15, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:306011 original size:19 final size:19
Alignment explanation
Indices: 305972--306012 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
305962 GCAATGAGAG
* **
305972 AATCGCAACGCGAAATGAA
1 AATCGCAACGCAAAACCAA
305991 AATCGCAACGCAAAACCAA
1 AATCGCAACGCAAAACCAA
306010 AAT
1 AAT
306013 TGCATTGCGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.24, G:0.15, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCAAAACCAA
Found at i:306082 original size:20 final size:21
Alignment explanation
Indices: 306050--306105 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 21
306040 GATTATCTCA
**
306050 TTGCGATAGTCATTTC-CGCG
1 TTGCGATTTTCATTTCTCGCG
*
306070 TTGCGATTTTCA-TTCTCTCG
1 TTGCGATTTTCATTTCTCGCG
*
306090 TTGTGATTTTCATTTC
1 TTGCGATTTTCATTTC
306106 AACCAAAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 3 0.10
20 24 0.80
21 3 0.10
ACGTcount: A:0.12, C:0.21, G:0.18, T:0.48
Consensus pattern (21 bp):
TTGCGATTTTCATTTCTCGCG
Found at i:307959 original size:188 final size:179
Alignment explanation
Indices: 307563--308022 Score: 637
Period size: 188 Copynumber: 2.5 Consensus size: 179
307553 TAGATTGCTT
* * * *
307563 AGTAAATTTATTCGGTTGCCT-CCAATACTGCTAAAC--TGT-TT-ATTAATACTGTGAAGTTAA
1 AGTAAATTTGTTCGGTTG-CTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTGTGAAGTTAG
*
307623 TATTTGTCTTT-TGTTGTCTTTTGGTTGAAGTAAATTTATTCGGTTGCTGCCTAAAATGTGTATT
65 TATTTGTCTTTGTTTTGTCTTTTGGTTGAAGTAAATTTATTCGGTTGCTGCCTAAAATGTGTATT
*
307687 CTTTAACATTGTGAAGTTAGTATTTGTCTTTATTTTGTCTATTGGTTGAA
130 CTTTAACATTGTGAAGTTAATATTTGTCTTTATTTTGTCTATTGGTTGAA
*
307737 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTGTGAAGTTAGT
* * *
307802 ATTTATCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAAC
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-AAGTAAATTTATTCGGTTGCTG------C--CTAAAA
*
307867 TGTGTATTCTTTAACATTGTGAAGTTAATATTTGTCTTTGTTTTGTCCT-TTGGTTGAA
122 TGTGTATTCTTTAACATTGTGAAGTTAATATTTGTCTTTATTTTGT-CTATTGGTTGAA
* * * *
307925 AGTAAATTTGTTTGTTTGCTGTCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTGTGAAGTTAGT
307990 ATTTGTCTTTGTTTTGTCTTTTGGTTGAAGTAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAAGTAA
308023 TGTAATCCAT
Statistics
Matches: 253, Mismatches: 17, Indels: 19
0.88 0.06 0.07
Matches are distributed among these distances:
173 2 0.01
174 31 0.12
176 3 0.01
177 2 0.01
178 26 0.10
179 15 0.06
180 21 0.08
186 1 0.00
187 6 0.02
188 144 0.57
189 2 0.01
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.48
Consensus pattern (179 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAAGTAAATTTATTCGGTTGCTGCCTAAAATGTGTATTC
TTTAACATTGTGAAGTTAATATTTGTCTTTATTTTGTCTATTGGTTGAA
Found at i:308045 original size:94 final size:94
Alignment explanation
Indices: 307673--308022 Score: 576
Period size: 94 Copynumber: 3.7 Consensus size: 94
307663 CGGTTGCTGC
* * * *
307673 CTAAAATGTGTATTCTTTAACATTGTGAAGTTAGTATTTGTCTTTATTTTGTCTATTGGTTGAAA
1 CTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAA
307738 GTAAATTTGTTCGGTTGCTGCCAATTCTG
66 GTAAATTTGTTCGGTTGCTGCCAATTCTG
*
307767 CTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTTATCTTTGTTTTGTCTTTTGGTTGAAA
1 CTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAA
307832 GTAAATTTGTTCGGTTGCTGCCAATTCTG
66 GTAAATTTGTTCGGTTGCTGCCAATTCTG
* * *
307861 CTAAACTGTGTATTCTTTAACATTGTGAAGTTAATATTTGTCTTTGTTTTGTCCTTTGGTTGAAA
1 CTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAA
* * *
307926 GTAAATTTGTTTGTTTGCTGTCAATTCTG
66 GTAAATTTGTTCGGTTGCTGCCAATTCTG
* *
307955 CTAAACTGTGTATTCTTTAATACTCTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTG-AA
1 CTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAA
308019 GTAA
66 GTAA
308023 TGTAATCCAT
Statistics
Matches: 239, Mismatches: 17, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
93 6 0.03
94 233 0.97
ACGTcount: A:0.22, C:0.11, G:0.19, T:0.48
Consensus pattern (94 bp):
CTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAA
GTAAATTTGTTCGGTTGCTGCCAATTCTG
Found at i:308129 original size:20 final size:19
Alignment explanation
Indices: 308104--308204 Score: 148
Period size: 19 Copynumber: 5.2 Consensus size: 19
308094 TCTTTTGGTT
*
308104 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
308123 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
*
308143 GAAACGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
308162 GGAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
308181 GAAATCAAAAATCGCAACGC
1 GAAAT-GAAAATCGCAACGC
308201 GAAA
1 GAAA
308205 CTATAATCGC
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
19 39 0.53
20 35 0.47
ACGTcount: A:0.49, C:0.21, G:0.22, T:0.09
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:308214 original size:39 final size:38
Alignment explanation
Indices: 308110--308204 Score: 145
Period size: 39 Copynumber: 2.4 Consensus size: 38
308100 GGTTGAAATG
* *
308110 AAAATCGCAACGAGAGAATGAAAATCGCAACGCGAAACG
1 AAAATCGCAACGCGA-AATGAAAATCGCAACGCGAAACA
*
308149 AAAATCGCAACGCGGAATGAAAATCGCAACGCGAAATCA
1 AAAATCGCAACGCGAAATGAAAATCGCAACGCGAAA-CA
308188 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
308205 CTATAATCGC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
38 21 0.41
39 30 0.59
ACGTcount: A:0.48, C:0.22, G:0.21, T:0.08
Consensus pattern (38 bp):
AAAATCGCAACGCGAAATGAAAATCGCAACGCGAAACA
Found at i:308238 original size:19 final size:19
Alignment explanation
Indices: 308211--308370 Score: 142
Period size: 19 Copynumber: 8.8 Consensus size: 19
308201 GAAACTATAA
308211 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
308230 CCGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
308244 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
308263 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
308277 TCTCGTTGCGATTTTCTTT
1 TCGCGTTGCGATTTTCATT
308296 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
308315 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
**
308335 TCGCGTTGCGATAGTCATTTT
1 TCGCGTTGCGATTTTCA--TT
*
308356 TCACGTTGCGATTTT
1 TCGCGTTGCGATTTT
308371 AAGTTCCAGA
Statistics
Matches: 112, Mismatches: 16, Indels: 24
0.74 0.11 0.16
Matches are distributed among these distances:
14 18 0.16
16 6 0.05
17 6 0.05
19 50 0.45
20 18 0.16
21 14 0.12
ACGTcount: A:0.11, C:0.23, G:0.20, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:308254 original size:14 final size:14
Alignment explanation
Indices: 308235--308289 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
308225 TCATTCCGCA
308235 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
308249 TTGCGATTTTCATTTCGCG
1 TTGCGA--TTC---TCTCG
308268 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
308282 TTGCGATT
1 TTGCGATT
308290 TTCTTTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:308256 original size:33 final size:33
Alignment explanation
Indices: 308214--308346 Score: 185
Period size: 33 Copynumber: 3.8 Consensus size: 33
308204 ACTATAATCG
* *
308214 CGTTGCGATTTTCATTCCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
308247 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
308280 CGTTGCGATTTTCTTTTCGCGTTGCGATTTTCATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCG------ATTCTCT
308319 CGTTGCGATTTTCATTTCGCGTTGCGAT
1 CGTTGCGATTTTCATTTCGCGTTGCGAT
308347 AGTCATTTTT
Statistics
Matches: 90, Mismatches: 4, Indels: 12
0.85 0.04 0.11
Matches are distributed among these distances:
33 58 0.64
39 32 0.36
ACGTcount: A:0.10, C:0.24, G:0.20, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:308316 original size:39 final size:37
Alignment explanation
Indices: 308214--308370 Score: 168
Period size: 33 Copynumber: 4.3 Consensus size: 37
308204 ACTATAATCG
* *
308214 CGTTGCGATTTTCATTCCGCATTGCG----ATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCATTCTCT
308247 CGTTGCGATTTTCATTTCGCGTTGCG----ATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCATTCTCT
*
308280 CGTTGCGATTTTCTTTTCGCGTTGCGATTTTCATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGA--TTCATTCTCT
* *
308319 CGTTGCGATTTTCATTTCGCGTTGCGATAGTCATTTTTCA
1 CGTTGCGATTTTCATTTCGCGTTGCGAT--TCA-TTCTCT
308359 CGTTGCGATTTT
1 CGTTGCGATTTT
308371 AAGTTCCAGA
Statistics
Matches: 109, Mismatches: 6, Indels: 11
0.87 0.05 0.09
Matches are distributed among these distances:
33 56 0.51
37 1 0.01
39 36 0.33
40 16 0.15
ACGTcount: A:0.11, C:0.23, G:0.20, T:0.46
Consensus pattern (37 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCATTCTCT
Found at i:308888 original size:21 final size:21
Alignment explanation
Indices: 308829--308889 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
308819 CTCGAGAGTC
308829 CCCTCCCACCGTTCAAGAGGT
1 CCCTCCCACCGTTCAAGAGGT
* ** * *
308850 CACTGTCATCGTTGAAGAGGT
1 CCCTCCCACCGTTCAAGAGGT
*
308871 CCCTCCCACCATTCAAGAG
1 CCCTCCCACCGTTCAAGAG
308890 CCCGATTCAC
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.23, C:0.36, G:0.20, T:0.21
Consensus pattern (21 bp):
CCCTCCCACCGTTCAAGAGGT
Found at i:310404 original size:19 final size:17
Alignment explanation
Indices: 310388--310438 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 17
310378 AAAAATGACT
310388 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
310407 ATCGCAA--CGAGA-GA
1 ATCGCAATGCGAAATGA
310421 ATCGCAATGCGAAATGA
1 ATCGCAATGCGAAATGA
310438 A
1 A
310439 AATCGCAACG
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 8 0.30
16 5 0.19
17 7 0.26
19 7 0.26
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.14
Consensus pattern (17 bp):
ATCGCAATGCGAAATGA
Found at i:310430 original size:33 final size:33
Alignment explanation
Indices: 310388--310481 Score: 145
Period size: 33 Copynumber: 2.8 Consensus size: 33
310378 AAAAATGACT
* *
310388 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
310421 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
310454 ATCGCAACGCGAAACT-AAAATCGCAACG
1 ATCGCAATGCGAAA-TGAAAATCGCAACG
310482 CGAAACTAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 56 0.98
34 1 0.02
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:310444 original size:19 final size:18
Alignment explanation
Indices: 310388--310486 Score: 72
Period size: 19 Copynumber: 5.7 Consensus size: 18
310378 AAAAATGACT
310388 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
310407 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
310421 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
310440 ATCGCAA-CG--A-CAAA
1 ATCGCAAGCGAAATGAAA
310454 ATCGCAACGCGAAACT-AAA
1 ATCGCAA-GCGAAA-TGAAA
310473 ATCGCAACGCGAAA
1 ATCGCAA-GCGAAA
310487 CTAAATTCGC
Statistics
Matches: 66, Mismatches: 3, Indels: 22
0.73 0.03 0.24
Matches are distributed among these distances:
14 20 0.30
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 34 0.52
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.11
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:310503 original size:19 final size:19
Alignment explanation
Indices: 310420--310496 Score: 85
Period size: 19 Copynumber: 4.3 Consensus size: 19
310410 GCAACGAGAG
*
310420 AATCGCAATGCGAAA-TGAA
1 AATCGCAACGCGAAACT-AA
310439 AATCGCAA--CG--AC-AA
1 AATCGCAACGCGAAACTAA
310453 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
310472 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
*
310491 ATTCGC
1 AATCGC
310497 GTTGCGATTT
Statistics
Matches: 51, Mismatches: 1, Indels: 12
0.80 0.02 0.19
Matches are distributed among these distances:
14 10 0.20
15 1 0.02
16 2 0.04
17 2 0.04
18 2 0.04
19 34 0.67
ACGTcount: A:0.45, C:0.25, G:0.17, T:0.13
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:310514 original size:19 final size:19
Alignment explanation
Indices: 310492--310609 Score: 76
Period size: 19 Copynumber: 6.7 Consensus size: 19
310482 CGAAACTAAA
310492 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
310511 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
310526 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
310544 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
310559 -TCTCGTTGCAATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
310577 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
310596 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
310610 AGACATTAAG
Statistics
Matches: 72, Mismatches: 16, Indels: 21
0.66 0.15 0.19
Matches are distributed among these distances:
14 16 0.22
16 6 0.08
17 6 0.08
19 34 0.47
20 10 0.14
ACGTcount: A:0.13, C:0.25, G:0.19, T:0.43
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:310538 original size:33 final size:33
Alignment explanation
Indices: 310496--310589 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
310486 ACTAAATTCG
*
310496 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
310529 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
310562 CGTTGCAATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
310590 AGTCATTTCC
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:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:310608 original size:20 final size:19
Alignment explanation
Indices: 310573--310616 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
310563 GTTGCAATTT
310573 TCATTTCGCATTGCGATAG
1 TCATTTCGCATTGCGATAG
*
310592 TCATTTCCGCGTTGCGATAG
1 TCATTT-CGCATTGCGATAG
*
310612 ACATT
1 TCATT
310617 AAGATGATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.36
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:313161 original size:24 final size:24
Alignment explanation
Indices: 313127--313180 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
313117 CTGAAAAATC
313127 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
313151 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
313175 ATCAAA
1 ATCAAA
313181 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:313194 original size:24 final size:24
Alignment explanation
Indices: 313127--313194 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
313117 CTGAAAAATC
* * *
313127 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
313151 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
313175 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
313195 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:314049 original size:20 final size:20
Alignment explanation
Indices: 314026--314091 Score: 80
Period size: 20 Copynumber: 3.2 Consensus size: 20
314016 AATCTCGTTA
314026 CGATTTACTAAATCGCAATG
1 CGATTTACTAAATCGCAATG
314046 CGA-TTACGTAAATCGCAATG
1 CGATTTAC-TAAATCGCAATG
* **
314066 CGAATTAGGAAAATCGCAATG
1 CGATTTA-CTAAATCGCAATG
314087 CGATT
1 CGATT
314092 ATCACAATAC
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
19 4 0.10
20 18 0.45
21 18 0.45
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (20 bp):
CGATTTACTAAATCGCAATG
Found at i:314079 original size:21 final size:21
Alignment explanation
Indices: 314035--314187 Score: 178
Period size: 21 Copynumber: 7.7 Consensus size: 21
314025 ACGATTTACT
* *
314035 AAATCGCAATGCG-ATTACGT
1 AAATCGCAATGCGAATTAGGA
314055 AAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCGAATTAGGA
314076 AAATCGCAATGCG-ATT----
1 AAATCGCAATGCGAATTAGGA
* *
314092 --ATCACAATACGAATTAGGA
1 AAATCGCAATGCGAATTAGGA
314111 AAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCGAATTAGGA
*
314132 AAATCGTAATGCGAATTAGGA
1 AAATCGCAATGCGAATTAGGA
* * *
314153 AAATCGCAATACGAATTTGGG
1 AAATCGCAATGCGAATTAGGA
314174 AAATCGCAATGCGA
1 AAATCGCAATGCGA
314188 TAGTCAGAAT
Statistics
Matches: 113, Mismatches: 12, Indels: 15
0.81 0.09 0.11
Matches are distributed among these distances:
14 9 0.08
15 3 0.03
20 16 0.14
21 85 0.75
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.22
Consensus pattern (21 bp):
AAATCGCAATGCGAATTAGGA
Found at i:316500 original size:24 final size:24
Alignment explanation
Indices: 316456--316502 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
316446 ATAAAGAACC
*
316456 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
316480 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
316503 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:319548 original size:19 final size:20
Alignment explanation
Indices: 319526--319569 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
319516 GAGAAAAGGT
319526 AAAAGTTAA-AATGAAAGAG
1 AAAAGTTAATAATGAAAGAG
* *
319545 AAAAATTAATAATGAAAGAT
1 AAAAGTTAATAATGAAAGAG
319565 AAAAG
1 AAAAG
319570 AAAAAGTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAAGTTAATAATGAAAGAG
Found at i:326461 original size:24 final size:24
Alignment explanation
Indices: 326417--326463 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
326407 ATAAAAAACC
*
326417 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
326441 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
326464 CAACCAACCG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:327720 original size:21 final size:21
Alignment explanation
Indices: 327694--327741 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
327684 TACAAGAAAC
327694 ATTATTATTTCTACCGATTTT
1 ATTATTATTTCTACCGATTTT
* *
327715 ATTATTTTTTCTATCGATTTT
1 ATTATTATTTCTACCGATTTT
327736 ATTATT
1 ATTATT
327742 GTTTGACACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.23, C:0.10, G:0.04, T:0.62
Consensus pattern (21 bp):
ATTATTATTTCTACCGATTTT
Found at i:328470 original size:60 final size:59
Alignment explanation
Indices: 328376--328516 Score: 153
Period size: 60 Copynumber: 2.4 Consensus size: 59
328366 TGACTTGTTT
* *
328376 TAAATTGGT-CTCTAAACTTTTAAATTTTCCAATTTCATTCATAAACTATAAC-TATCATTC
1 TAAATTGGTCCTC-AAACTTTTAAATTTT-CAATTTCATCCACAAACTATAACAT-TCATTC
* * *
328436 TAAATTGGTCCTCAAGCTTTTGAACATTTT-AATTTCATCCCCAAACTATGACATTCATTC
1 TAAATTGGTCCTCAAACTTTT-AA-ATTTTCAATTTCATCCACAAACTATAACATTCATTC
* *
328496 TAAATTAGTCCCCAAACTTTT
1 TAAATTGGTCCTCAAACTTTT
328517 TAAGCATTCC
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
60 58 0.84
61 6 0.09
62 5 0.07
ACGTcount: A:0.33, C:0.21, G:0.06, T:0.40
Consensus pattern (59 bp):
TAAATTGGTCCTCAAACTTTTAAATTTTCAATTTCATCCACAAACTATAACATTCATTC
Found at i:328727 original size:60 final size:60
Alignment explanation
Indices: 328645--328796 Score: 173
Period size: 60 Copynumber: 2.5 Consensus size: 60
328635 TTGAAATATT
* * * * *
328645 TAAATGTTTAGGGACTAGTTTAGAATGAGAGTCATAGTTTAGGTATGAAATTATAATGCCCA
1 TAAA-GTTTAAGGACTAATTTAGAATGAGAGTCATAGTTTAGGGATGAAATTAGAAT-ACCA
* * **
328707 -AAAGTTTAAGGACTAATTTAGAATGGGAGTCATAGTTTAGGGATTAAATTAGAATATTA
1 TAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTTTAGGGATGAAATTAGAATACCA
*
328766 TAAA-TATTAAGGACTAATTTATAATGAGAGT
1 TAAAGT-TTAAGGACTAATTTAGAATGAGAGT
328797 TGTAATTTGA
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
59 2 0.03
60 72 0.94
61 3 0.04
ACGTcount: A:0.39, C:0.05, G:0.21, T:0.34
Consensus pattern (60 bp):
TAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTTTAGGGATGAAATTAGAATACCA
Found at i:330392 original size:18 final size:18
Alignment explanation
Indices: 330369--330408 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
330359 GTCAGCCATG
330369 GAGG-AAAGAGATATAATT
1 GAGGAAAAG-GATATAATT
*
330387 GAGGAAAAGGATATGATT
1 GAGGAAAAGGATATAATT
330405 GAGG
1 GAGG
330409 GTGATACCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.45, C:0.00, G:0.35, T:0.20
Consensus pattern (18 bp):
GAGGAAAAGGATATAATT
Found at i:332147 original size:35 final size:35
Alignment explanation
Indices: 332108--332192 Score: 152
Period size: 35 Copynumber: 2.4 Consensus size: 35
332098 TATGGTAGAC
*
332108 CATGCATGTCAACAATGTATGTTGCAGCATGCACT
1 CATGCATGTCAACAATGTATGTAGCAGCATGCACT
*
332143 CATGCATGTCAACTATGTATGTAGCAGCATGCACT
1 CATGCATGTCAACAATGTATGTAGCAGCATGCACT
332178 CATGCATGTCAACAA
1 CATGCATGTCAACAA
332193 CAGATTTGTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 47 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.27
Consensus pattern (35 bp):
CATGCATGTCAACAATGTATGTAGCAGCATGCACT
Found at i:332874 original size:11 final size:11
Alignment explanation
Indices: 332854--332886 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
332844 ATTATATAAA
332854 AAAAACTATATT
1 AAAAA-TATATT
332866 AAAAATATATT
1 AAAAATATATT
332877 AAAAA-ATATT
1 AAAAATATATT
332887 TATATATCCG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 5 0.24
11 11 0.52
12 5 0.24
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (11 bp):
AAAAATATATT
Found at i:332882 original size:12 final size:12
Alignment explanation
Indices: 332853--332885 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
332843 AATTATATAA
332853 AAAAAACTATATT
1 AAAAAA-TATATT
332866 -AAAAATATATT
1 AAAAAATATATT
332877 AAAAAATAT
1 AAAAAATAT
332886 TTATATATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 6 0.32
12 13 0.68
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (12 bp):
AAAAAATATATT
Found at i:341151 original size:31 final size:31
Alignment explanation
Indices: 341116--341177 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
341106 CATGGCAATT
*
341116 CTTGCATGTTATCTCCTACAGCAAGCTTCTC
1 CTTGCATGTTATCGCCTACAGCAAGCTTCTC
*
341147 CTTGCATGTTATCGCCTACAGCAAGGTTCTC
1 CTTGCATGTTATCGCCTACAGCAAGCTTCTC
341178 TTAAACTAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.16, T:0.34
Consensus pattern (31 bp):
CTTGCATGTTATCGCCTACAGCAAGCTTCTC
Found at i:341444 original size:15 final size:15
Alignment explanation
Indices: 341413--341449 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
341403 ATGATTAAAA
341413 AATAATTTATTACTT
1 AATAATTTATTACTT
*
341428 AATAATTTATTATTT
1 AATAATTTATTACTT
341443 AATAATT
1 AATAATT
341450 CTTTTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (15 bp):
AATAATTTATTACTT
Found at i:352208 original size:60 final size:60
Alignment explanation
Indices: 352131--352270 Score: 185
Period size: 60 Copynumber: 2.3 Consensus size: 60
352121 CTCTCATTTC
352131 AAATTAGTCCCCAAACTTTTAAACATTTCATTTTCATCCTT-AAACTATGA-CTATCATCCT
1 AAATTAGTCCCCAAACTTTTAAACATTTCATTTTCAT-CTTCAAACTATGATCT-TCATCCT
** * * * *
352191 AAATTAGTCCTTAAACTTTTGAACATTTCATTTTCATCTTCAAATTGTGATCTTCATTCT
1 AAATTAGTCCCCAAACTTTTAAACATTTCATTTTCATCTTCAAACTATGATCTTCATCCT
*
352251 AAATTAGTCGCCAAACTTTT
1 AAATTAGTCCCCAAACTTTT
352271 TGAATAATTC
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
59 3 0.04
60 64 0.93
61 2 0.03
ACGTcount: A:0.31, C:0.21, G:0.06, T:0.41
Consensus pattern (60 bp):
AAATTAGTCCCCAAACTTTTAAACATTTCATTTTCATCTTCAAACTATGATCTTCATCCT
Found at i:352296 original size:60 final size:58
Alignment explanation
Indices: 352131--352298 Score: 178
Period size: 60 Copynumber: 2.8 Consensus size: 58
352121 CTCTCATTTC
* *
352131 AAATTAGTCCCCAAACTTTTAAACATTTCATTTTCATCCTTAAACTATGACTATCATCCT
1 AAATTAGT-CCCAAACTTTTGAACATTTCATTTTCATCC-TAAATTATGACTATCATCCT
* * * *
352191 AAATTAGTCCTTAAACTTTTGAACATTTCATTTTCATCTTCAAATTGTGATCT-TCATTCT
1 AAATTAGTCC-CAAACTTTTGAACATTTCATTTTCATCCT-AAATTATGA-CTATCATCCT
* *
352251 AAATTAGTCGCCAAACTTTTTGAATAATTCAATTTT-ATCCTAAATTAT
1 AAATTAGTC-CCAAAC-TTTTGAACATTTC-ATTTTCATCCTAAATTAT
352299 ACATGTATAC
Statistics
Matches: 91, Mismatches: 11, Indels: 12
0.80 0.10 0.11
Matches are distributed among these distances:
59 3 0.03
60 65 0.71
61 18 0.20
62 5 0.05
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.42
Consensus pattern (58 bp):
AAATTAGTCCCAAACTTTTGAACATTTCATTTTCATCCTAAATTATGACTATCATCCT
Found at i:352545 original size:60 final size:60
Alignment explanation
Indices: 352419--352546 Score: 172
Period size: 60 Copynumber: 2.1 Consensus size: 60
352409 CATTTGGATG
* * *
352419 AATTTGGGGATGAAATTGGAAGTTCTAAAAGTTTAAGGACTAATTTAGAATGAAGGTTAT
1 AATTTGAGGATGAAATTAGAAGTTCTAAAAGTTTAAGGACTAATTTAGAATGAAGGTCAT
352479 AATTTGAGGATGAAATTAGAATGTT-TAAAAGTTTAAGGACTAATTT-GAAATG-AGAGTCAT
1 AATTTGAGGATGAAATTAGAA-GTTCTAAAAGTTTAAGGACTAATTTAG-AATGAAG-GTCAT
*
352539 AGTTTGAG
1 AATTTGAG
352547 AACATATGAT
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
59 3 0.05
60 55 0.90
61 3 0.05
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (60 bp):
AATTTGAGGATGAAATTAGAAGTTCTAAAAGTTTAAGGACTAATTTAGAATGAAGGTCAT
Found at i:355534 original size:2 final size:2
Alignment explanation
Indices: 355527--355555 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
355517 ATTAATCTTT
355527 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 T
355556 TTCAATTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:355695 original size:150 final size:150
Alignment explanation
Indices: 355534--355835 Score: 586
Period size: 150 Copynumber: 2.0 Consensus size: 150
355524 TTTTATATAT
355534 ATATATATATATATATATATATTTCAATTAGATCCCTATTTTAAAAATAATACTTTTTACAAATA
1 ATATATATATATATATATATATTTCAATTAGATCCCTATTTTAAAAATAATACTTTTTACAAATA
* *
355599 TATTTATTTCGGGTCGAGTATTATCGGATTTAGATTTTATCTTAAAAAGTCAGATTAGGTTCGGG
66 TATTTATTTCGGGTCGAGTATGATCGGATTTAGATTTTATCTCAAAAAGTCAGATTAGGTTCGGG
355664 TCAAGTGAAATCATCCCTAA
131 TCAAGTGAAATCATCCCTAA
355684 ATATATATATATATATATATATTTCAATTAGATCCCTATTTTAAAAATAATACTTTTTACAAATA
1 ATATATATATATATATATATATTTCAATTAGATCCCTATTTTAAAAATAATACTTTTTACAAATA
355749 TATTTATTTCGGGTCGAGTATGATCGGATTTAGATTTTATCTCAAAAAGTCAGATTAGGTTCGGG
66 TATTTATTTCGGGTCGAGTATGATCGGATTTAGATTTTATCTCAAAAAGTCAGATTAGGTTCGGG
355814 TCAAGTGAAATCATCCCTAA
131 TCAAGTGAAATCATCCCTAA
355834 AT
1 AT
355836 TCGGGTCAAG
Statistics
Matches: 150, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
150 150 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (150 bp):
ATATATATATATATATATATATTTCAATTAGATCCCTATTTTAAAAATAATACTTTTTACAAATA
TATTTATTTCGGGTCGAGTATGATCGGATTTAGATTTTATCTCAAAAAGTCAGATTAGGTTCGGG
TCAAGTGAAATCATCCCTAA
Found at i:355838 original size:27 final size:27
Alignment explanation
Indices: 355808--355868 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
355798 TCAGATTAGG
355808 TTCGGGTCAAGTGAAATCATCCCTAAA
1 TTCGGGTCAAGTGAAATCATCCCTAAA
* *
355835 TTCGGGTCAAGTGAAATTATCTCTAAA
1 TTCGGGTCAAGTGAAATCATCCCTAAA
*
355862 CTCGGGT
1 TTCGGGT
355869 AATGCATGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (27 bp):
TTCGGGTCAAGTGAAATCATCCCTAAA
Found at i:356381 original size:21 final size:19
Alignment explanation
Indices: 356355--356407 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 19
356345 CATATTCACA
356355 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTT--CG
*
356376 TTGCGATTTATTCCAAGTTCG
1 TTGCGA--TAGTCCAAGTTCG
356397 TTGCGATAGTC
1 TTGCGATAGTC
356408 TAAAATCGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 4 0.14
21 14 0.50
23 10 0.36
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.36
Consensus pattern (19 bp):
TTGCGATAGTCCAAGTTCG
Found at i:356862 original size:21 final size:21
Alignment explanation
Indices: 356788--356877 Score: 85
Period size: 21 Copynumber: 4.2 Consensus size: 21
356778 ACCAGTCGTT
*
356788 GCGATTTTGGACTATCGCAA-
1 GCGAATTTGGACTATCGCAAC
*
356808 -CGAATTTGGAATAAATCGCAAC
1 GCGAATTTGGACT--ATCGCAAC
* *
356830 TATCGCATTTGGACTATCGCAAC
1 --GCGAATTTGGACTATCGCAAC
*
356853 GCGAATTTGGACTATCGCAAT
1 GCGAATTTGGACTATCGCAAC
356874 GCGA
1 GCGA
356878 TTTACATATT
Statistics
Matches: 57, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
19 10 0.18
21 29 0.51
23 8 0.14
25 10 0.18
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (21 bp):
GCGAATTTGGACTATCGCAAC
Found at i:356937 original size:21 final size:21
Alignment explanation
Indices: 356886--357053 Score: 186
Period size: 21 Copynumber: 8.2 Consensus size: 21
356876 GATTTACATA
*
356886 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
* *
356907 -T--AAATGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
356925 TTCGCGTTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
356946 TTCGCGTTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* * *
356967 TCCGCATTGCGATAGT-CGAC
1 TTCGCATTGCGATAGTCCAAG
* *
356987 TATCGCATTGCGAT-TTACATA-
1 T-TCGCATTGCGATAGTCCA-AG
357008 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
357029 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
357050 TTCG
1 TTCG
357054 TGTTACGAAT
Statistics
Matches: 124, Mismatches: 15, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
18 14 0.11
19 1 0.01
20 18 0.15
21 90 0.73
22 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:362708 original size:41 final size:42
Alignment explanation
Indices: 362658--362744 Score: 122
Period size: 41 Copynumber: 2.1 Consensus size: 42
362648 TCGCAACGCA
* * * *
362658 ATAGTCGAAGTTTGTGTTGCGATTCATT-CTAATTCGTTGCG
1 ATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTTGCG
*
362699 ATAGGCGAAGTTCGCGTTGCGATTCCTTCCAAATTCGTTGCG
1 ATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTTGCG
362741 ATAG
1 ATAG
362745 TCCAAATATT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 24 0.60
42 16 0.40
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (42 bp):
ATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTTGCG
Found at i:362832 original size:6 final size:6
Alignment explanation
Indices: 362821--362848 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
362811 AGACACGTAT
362821 GACCAC GACCAC GACCAC GACCAC GACC
1 GACCAC GACCAC GACCAC GACCAC GACC
362849 CGAGACGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.50, G:0.18, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:363654 original size:21 final size:21
Alignment explanation
Indices: 363628--363785 Score: 71
Period size: 21 Copynumber: 7.5 Consensus size: 21
363618 TTGGACTATA
*
363628 GCAACGAATTTGGAATGAATC
1 GCAACGAACTTGGAATGAATC
* **
363649 GCAACGCGAACTTCGCCT--ATC
1 GCAA--CGAACTTGGAATGAATC
363670 GCAACGAA-TTGGAATGAATC
1 GCAACGAACTTGGAATGAATC
* **
363690 GCAACGCGAACTTCGCCTG--TC
1 GCAA--CGAACTTGGAATGAATC
*
363711 GCAACTAA-TTGGAATGAATC
1 GCAACGAACTTGGAATGAATC
* **
363731 GCAACGCGAACTTCG--TCTATC
1 GCAA--CGAACTTGGAATGAATC
* *
363752 GCAACGAATTTGGAATAAATC
1 GCAACGAACTTGGAATGAATC
363773 GCAAAGCGAACTT
1 GC-AA-CGAACTT
363786 CGACTATCGC
Statistics
Matches: 98, Mismatches: 23, Indels: 30
0.65 0.15 0.20
Matches are distributed among these distances:
18 9 0.09
19 14 0.14
20 13 0.13
21 31 0.32
22 9 0.09
23 22 0.22
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.22
Consensus pattern (21 bp):
GCAACGAACTTGGAATGAATC
Found at i:363687 original size:41 final size:42
Alignment explanation
Indices: 363623--363795 Score: 269
Period size: 41 Copynumber: 4.2 Consensus size: 42
363613 AATATTTGGA
*
363623 CTATAGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
363665 CTATCGCAACGAA-TTGGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
* * *
363706 CTGTCGCAACTAA-TTGGAATGAATCGCAACGCGAACTTCGT
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
* * *
363747 CTATCGCAACGAATTTGGAATAAATCGCAAAGCGAACTTCGA
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
363789 CTATCGC
1 CTATCGC
363796 GTTGCGAATC
Statistics
Matches: 121, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
41 77 0.64
42 44 0.36
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (42 bp):
CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
Found at i:363794 original size:21 final size:21
Alignment explanation
Indices: 363728--363795 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
363718 ATTGGAATGA
* *
363728 ATCGCAACGCGAACTTCGTCT
1 ATCGCAAAGCGAACTTCGACT
* * *
363749 ATCGC-AA-CGAATTTGGAAT
1 ATCGCAAAGCGAACTTCGACT
363768 AAATCGCAAAGCGAACTTCGACT
1 --ATCGCAAAGCGAACTTCGACT
363791 ATCGC
1 ATCGC
363796 GTTGCGAATC
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
19 8 0.23
20 1 0.03
21 15 0.43
22 2 0.06
23 9 0.26
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.22
Consensus pattern (21 bp):
ATCGCAAAGCGAACTTCGACT
Found at i:369703 original size:21 final size:24
Alignment explanation
Indices: 369679--369727 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 24
369669 CGTTTTTTGA
369679 TTTTAAT-AC-TTAATTTTA-TTT
1 TTTTAATCACATTAATTTTAGTTT
369700 TTTTAATCACATTAATTTTAGTTT
1 TTTTAATCACATTAATTTTAGTTT
369724 TTTT
1 TTTT
369728 TTGTTTAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 7 0.28
22 2 0.08
23 9 0.36
24 7 0.28
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (24 bp):
TTTTAATCACATTAATTTTAGTTT
Found at i:382612 original size:60 final size:59
Alignment explanation
Indices: 382535--382685 Score: 162
Period size: 60 Copynumber: 2.5 Consensus size: 59
382525 CCCTCATTTC
* * *
382535 AAATTAGTCCCTTAACTTTTAAACATTTCAATTTCATCCTTAAACGATGACTATT-ATTCT
1 AAATTAGTCCC-AAACTTTTAAACATTTCAATTTCATCCCTAAACGATGA-TATTCATCCT
* ***
382595 AAATTAGTCCTCAAACTTTTAAACATTTCATTTTCATCCCTAAGTTATGATATTCATCCT
1 AAATTAGTCC-CAAACTTTTAAACATTTCAATTTCATCCCTAAACGATGATATTCATCCT
*
382655 AAATT-GATCCCCAAACTTTTTAAATATTTCA
1 AAATTAG-T-CCCAAAC-TTTTAAACATTTCA
382686 TTTTTATACT
Statistics
Matches: 78, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
59 5 0.06
60 57 0.73
61 16 0.21
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.41
Consensus pattern (59 bp):
AAATTAGTCCCAAACTTTTAAACATTTCAATTTCATCCCTAAACGATGATATTCATCCT
Found at i:382883 original size:60 final size:59
Alignment explanation
Indices: 382819--383006 Score: 207
Period size: 60 Copynumber: 3.1 Consensus size: 59
382809 TTTGGATGAA
* * * *
382819 TTTGGGGATGAAATTGAAAGATTTAAAAGTTTAGGGACCAATTTATAATGAGATTTATAG
1 TTTGGGGATGAAATTGAAAGATTTAAAAGTTTAAGGACTAATTTA-AATGAGAGTCATAG
* * *
382879 TTTGGGGATAAAATTTAAATG-TTCAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAG
1 TTTGGGGATGAAATTGAAA-GATTTAAAAGTTTAAGGACTAATTTA-AATGAGAGTCATAG
** * * * *
382939 TTTAAGGATGGAATTGAAATATTTAAAATTTTAAGGACTAATTTGAAATGAGAGTCATGG
1 TTTGGGGATGAAATTGAAAGATTTAAAAGTTTAAGGACTAATTT-AAATGAGAGTCATAG
*
382999 TTTAGGGA
1 TTTGGGGA
383007 CATGATGAAA
Statistics
Matches: 107, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
60 105 0.98
61 2 0.02
ACGTcount: A:0.39, C:0.04, G:0.23, T:0.35
Consensus pattern (59 bp):
TTTGGGGATGAAATTGAAAGATTTAAAAGTTTAAGGACTAATTTAAATGAGAGTCATAG
Found at i:396185 original size:21 final size:22
Alignment explanation
Indices: 396159--396200 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
396149 GGTGAAAAAA
396159 CCGGATC-AATTTTTATCCGAT
1 CCGGATCGAATTTTTATCCGAT
*
396180 CCGGATCGATTTTTTATCCGA
1 CCGGATCGAATTTTTATCCGA
396201 CTTTATGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (22 bp):
CCGGATCGAATTTTTATCCGAT
Found at i:398208 original size:14 final size:14
Alignment explanation
Indices: 398189--398221 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
398179 CGCTGGGCAT
398189 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
398203 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
398217 ACGAG
1 CCGAG
398222 CTATGCGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.39, G:0.30, T:0.06
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:398239 original size:23 final size:23
Alignment explanation
Indices: 398204--398255 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
398194 GCCATCCGAC
* *
398204 CGAGGCCATCCGAACGAGCTATG
1 CGAGGGCAGCCGAACGAGCTATG
*
398227 CGAGGGCAGCCGAGCGAGCTATG
1 CGAGGGCAGCCGAACGAGCTATG
398250 CGAGGG
1 CGAGGG
398256 AATCCGAGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.23, C:0.27, G:0.40, T:0.10
Consensus pattern (23 bp):
CGAGGGCAGCCGAACGAGCTATG
Found at i:398262 original size:23 final size:23
Alignment explanation
Indices: 398211--398263 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
398201 GACCGAGGCC
* *
398211 ATCCGAACGAGCTATGCGAGGGC
1 ATCCGAGCGAGCTATGCGAGGGA
*
398234 AGCCGAGCGAGCTATGCGAGGGA
1 ATCCGAGCGAGCTATGCGAGGGA
398257 ATCCGAG
1 ATCCGAG
398264 GGCAGCCGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.26, C:0.25, G:0.38, T:0.11
Consensus pattern (23 bp):
ATCCGAGCGAGCTATGCGAGGGA
Found at i:398264 original size:33 final size:33
Alignment explanation
Indices: 398227--398293 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
398217 ACGAGCTATG
398227 CGAGGGCAGCCGAGCGAGCTATGCGAGGGAATC
1 CGAGGGCAGCCGAGCGAGCTATGCGAGGGAATC
* *
398260 CGAGGGCAGCCGAGCGATCTATGCGAGGGCATC
1 CGAGGGCAGCCGAGCGAGCTATGCGAGGGAATC
398293 C
1 C
398294 CGAGCGAGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.22, C:0.27, G:0.40, T:0.10
Consensus pattern (33 bp):
CGAGGGCAGCCGAGCGAGCTATGCGAGGGAATC
Found at i:398355 original size:29 final size:29
Alignment explanation
Indices: 398309--398364 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
398299 GAGCAAGGGT
**
398309 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAAAGCATGGCGACCTACA
398338 AGGTCGCCCGGAAAGCATGGCGACCTA
1 AGGTCGCCCGGAAAGCATGGCGACCTA
398365 TGTGTTGGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.23, C:0.30, G:0.34, T:0.12
Consensus pattern (29 bp):
AGGTCGCCCGGAAAGCATGGCGACCTACA
Found at i:399282 original size:111 final size:109
Alignment explanation
Indices: 399156--399359 Score: 302
Period size: 109 Copynumber: 1.8 Consensus size: 109
399146 GCAGTGCCCT
** * *
399156 CAAAAAAGTATATATATAGTGGCGTTTTTCTAATAAACGTCACTATAGATGGATCTATTGCGATG
1 CAAAAAAGTATATATATAGT-G-GTTTTTCTAATAAACACCACTATAGATGGACCTATTGCGACG
399221 TTTTTTTC-AAAAAACGCCACTATTATTGCATAAGCCCAAAAAATCC
64 -TTTTTTCAAAAAAACGCCACTATTATTGCATAAGCCCAAAAAATCC
* * *
399267 CAAAAAAGTATATATATGGTGGTTTTTTTAATAAACACCACTATATATGGACCTATTGCGACGTT
1 CAAAAAAGTATATATATAGTGGTTTTTCTAATAAACACCACTATAGATGGACCTATTGCGACGTT
399332 TTTTCAAAAAAAACGCCACTATTATTGC
66 TTTTC-AAAAAAACGCCACTATTATTGC
399360 CCCAAAATCG
Statistics
Matches: 84, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
108 7 0.08
109 36 0.43
110 22 0.26
111 19 0.23
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (109 bp):
CAAAAAAGTATATATATAGTGGTTTTTCTAATAAACACCACTATAGATGGACCTATTGCGACGTT
TTTTCAAAAAAACGCCACTATTATTGCATAAGCCCAAAAAATCC
Found at i:399905 original size:24 final size:23
Alignment explanation
Indices: 399876--399946 Score: 79
Period size: 24 Copynumber: 3.0 Consensus size: 23
399866 AATTTATTCG
*
399876 TTTATGCTCGTTCATTTATGTTCA
1 TTTATG-TCGTTCGTTTATGTTCA
* **
399900 TTTATGTTCGTTTGTTTATGTTTG
1 TTTATG-TCGTTCGTTTATGTTCA
399924 TTTATGTCCGTTCGTTTATGTTC
1 TTTATGT-CGTTCGTTTATGTTC
399947 TCCAAACCCC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
23 1 0.03
24 38 0.97
ACGTcount: A:0.11, C:0.13, G:0.17, T:0.59
Consensus pattern (23 bp):
TTTATGTCGTTCGTTTATGTTCA
Found at i:404162 original size:21 final size:21
Alignment explanation
Indices: 404116--404155 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
404106 TCTATAAATT
*
404116 CCTAA-ACATAAATCCTTAAA
1 CCTAATACATAAATCCCTAAA
404136 CCTAATACATAAATCCCTAA
1 CCTAATACATAAATCCCTAA
404156 CCATAATCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (21 bp):
CCTAATACATAAATCCCTAAA
Found at i:404790 original size:17 final size:18
Alignment explanation
Indices: 404749--404795 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
404739 TGTTTCTGAG
*
404749 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGTCAA
404767 GGAATTGGAATCTGTCAA
1 GGAATTGGAATCTGTCAA
404785 -GAATTGGAATC
1 GGAATTGGAATC
404796 CAATTCCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 11 0.39
18 17 0.61
ACGTcount: A:0.34, C:0.09, G:0.30, T:0.28
Consensus pattern (18 bp):
GGAATTGGAATCTGTCAA
Found at i:405596 original size:258 final size:254
Alignment explanation
Indices: 405153--405758 Score: 831
Period size: 258 Copynumber: 2.4 Consensus size: 254
405143 CCGAGACCCG
*
405153 ACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATGTGAATTAGAAACTCG----ACCC
1 ACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAAC-CGACCCACCC
* * * *
405214 GAAATAATAATAAAATTATTTTTATTCAATAAAAATAGTGACTTAATTGGGAAAAAATATATAGA
65 GAAATAATAAAAAAATTATTTTTATTCAATAAAAACAATGACTTAATTGGAAAAAAATATATAGA
* *
405279 GAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATTTTTTTTTGGGTCGG
130 GAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTTGGGTCGG
* * * *
405344 GTCGGATATTTTTCACCCTAAACCCG-AACCCGACCCGAATATCACAGTTTAAAAAATCGAC-CT
195 GT--G---TTTTTCACCCTAAACCCGAAACCCAACCCGAATATCACACTTAAAAAAACCGACTC-
405407 A
254 A
* *
405408 ACCCGACCAAAATAAAGTTTCACCTGACCCAACCCGAATATATGAATTAGAAATCCGACCCAACC
1 ACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAA-CCGACCC-ACC
*
405473 CGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAATGACTTAATT-GAAAAAAAT-TATAT
64 CGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAATGACTTAATTGGAAAAAAATATATAG
*
405536 ATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTTGGGTCG
129 AGAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTTGGGTCG
*
405601 GGTGTTTTTCACCCTAAACCCGAACTCAACCCAACCCGAATATCACACTTAAAAAAACCGACTCG
194 GGTGTTTTTCACCCTAAACCCG-A---AACCCAACCCGAATATCACACTTAAAAAAACCGACTCA
* *
405666 ACCCGACCAAAAAAAAGTTTCACCCGACCTGACCCGAATATATGAATTAGAAACCCGACCCGACC
1 ACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAA-CCGACCC-ACC
405731 CG--A-AATAAAAAAA-TATTTTTATTCAATA
64 CGAAATAATAAAAAAATTATTTTTATTCAATA
405759 TATAAATAAG
Statistics
Matches: 317, Mismatches: 22, Indels: 25
0.87 0.06 0.07
Matches are distributed among these distances:
253 18 0.06
254 15 0.05
255 62 0.20
256 3 0.01
258 161 0.51
259 9 0.03
260 49 0.15
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.27
Consensus pattern (254 bp):
ACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCGACCCACCCG
AAATAATAAAAAAATTATTTTTATTCAATAAAAACAATGACTTAATTGGAAAAAAATATATAGAG
AGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTTGGGTCGGG
TGTTTTTCACCCTAAACCCGAAACCCAACCCGAATATCACACTTAAAAAAACCGACTCA
Found at i:409053 original size:158 final size:160
Alignment explanation
Indices: 408831--409150 Score: 617
Period size: 158 Copynumber: 2.0 Consensus size: 160
408821 AGCAAATCCA
408831 GTCAAGATGAGAAGAACCGCGAAAATAGTTCTCTGATAGACAATCTACCATTGACAAGACTCCAC
1 GTCAAGATGAGAAGAACCGCGAAAATAGTTCTCTGATAGACAATCTACCATTGACAAGACTCCAC
408896 GATGATAAGCTTAGTGAATGGGAGGCAAGAAGATACGGCTAAATGGCTGCCCGACTTCTACGTGA
66 GATGATAAGCTTAGTGAATGGGAGGCAAGAAGATACGGCTAAATGGCTGCCCGACTTCTACGTGA
408961 CGTAAAGATAACTT-AAAGTTCCA-GTATT
131 CGTAAAGATAACTTAAAAGTTCCAGGTATT
408989 GTCAAGATGAGAAGAACCGCGAAAATAGTTCTCTGATAGACAATCTACCATTGACAAGACTCCAC
1 GTCAAGATGAGAAGAACCGCGAAAATAGTTCTCTGATAGACAATCTACCATTGACAAGACTCCAC
*
409054 GATGATAAGCTTAGTGAATGGGAGGCAAGAAGATACGGCTCAATGGCTGCCCGACTTCTACGTGA
66 GATGATAAGCTTAGTGAATGGGAGGCAAGAAGATACGGCTAAATGGCTGCCCGACTTCTACGTGA
409119 CGTAAAGATAACTTAAAAGTTCCAGGTATT
131 CGTAAAGATAACTTAAAAGTTCCAGGTATT
409149 GT
1 GT
409151 TGTGGGCTAA
Statistics
Matches: 159, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
158 143 0.90
159 9 0.06
160 7 0.04
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (160 bp):
GTCAAGATGAGAAGAACCGCGAAAATAGTTCTCTGATAGACAATCTACCATTGACAAGACTCCAC
GATGATAAGCTTAGTGAATGGGAGGCAAGAAGATACGGCTAAATGGCTGCCCGACTTCTACGTGA
CGTAAAGATAACTTAAAAGTTCCAGGTATT
Found at i:416079 original size:21 final size:21
Alignment explanation
Indices: 416049--416101 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
416039 AACGCGATCC
416049 CCAG-AATCGCAAATCAGTTT
1 CCAGAAATCGCAAATCAGTTT
416069 CCAGAAATCGCAAATCAGTTT
1 CCAGAAATCGCAAATCAGTTT
416090 CCA-AAATCGCAA
1 CCAGAAATCGCAA
416102 CGCGATTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 13 0.41
21 19 0.59
ACGTcount: A:0.40, C:0.26, G:0.13, T:0.21
Consensus pattern (21 bp):
CCAGAAATCGCAAATCAGTTT
Found at i:416118 original size:21 final size:20
Alignment explanation
Indices: 416092--416189 Score: 70
Period size: 21 Copynumber: 4.8 Consensus size: 20
416082 ATCAGTTTCC
416092 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* * * *
416113 AAAATCGCGATGCGATAGTAG
1 AAAATCGCAACGCGAT-TTTG
* ** *
416134 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTT-G
* * *
416155 ATAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTG
416175 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
416190 ACACATAAAT
Statistics
Matches: 57, Mismatches: 18, Indels: 5
0.71 0.22 0.06
Matches are distributed among these distances:
20 15 0.26
21 42 0.74
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:416251 original size:20 final size:20
Alignment explanation
Indices: 416157--416348 Score: 226
Period size: 20 Copynumber: 9.6 Consensus size: 20
416147 GATTTTCCAT
* ** *
416157 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
416177 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
416197 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
416217 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
416237 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
416257 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
416277 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
416297 AATCGCAACG-ATATACATAA
1 AATCGCAACGCGTATCCGT-A
416317 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
416337 AATCGCAACGCG
1 AATCGCAACGCG
416349 ATATTTAAAG
Statistics
Matches: 145, Mismatches: 23, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
19 6 0.04
20 132 0.91
21 7 0.05
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:416765 original size:33 final size:33
Alignment explanation
Indices: 416726--416796 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
416716 TTCACTTAGA
*
416726 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
416759 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
416792 TTTCA
1 TTTCA
416797 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:416936 original size:14 final size:14
Alignment explanation
Indices: 416917--416971 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
416907 AGAATGACTG
416917 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
416931 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
416950 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
416964 TCGCAACG
1 TCGCAACG
416972 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:417023 original size:14 final size:14
Alignment explanation
Indices: 417004--417093 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
416994 TTTCATTTCG
417004 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
417018 CGTTGCGACAGTCATTTCG
1 CGTTGCG--A-T--TCTCT
417037 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
417051 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
417068 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
417084 CGTTGCGATT
1 CGTTGCGATT
417094 TCATTTCAAC
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 28 0.45
15 1 0.02
16 7 0.11
17 7 0.11
18 1 0.02
19 18 0.29
ACGTcount: A:0.10, C:0.27, G:0.24, T:0.39
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:417073 original size:19 final size:18
Alignment explanation
Indices: 416982--417097 Score: 76
Period size: 19 Copynumber: 6.9 Consensus size: 18
416972 CGAAACCAAA
* *
416982 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATC
417001 TCGCGTTGCGA-TTC-TC
1 TCGCGTTGCGATTTCATC
** *
417017 T--CGTTGCGACAGTCATT
1 TCGCGTTGCGA-TTTCATC
417034 TCGCGTTGCGA-TTC-TC
1 TCGCGTTGCGATTTCATC
417050 T--CGTTGCGATTGTCATC
1 TCGCGTTGCGATT-TCATC
417067 TCGCGTTGCGA-TTC-TC
1 TCGCGTTGCGATTTCATC
417083 T--CGTTGCGATTTCAT
1 TCGCGTTGCGATTTCAT
417098 TTCAACCAAA
Statistics
Matches: 79, Mismatches: 6, Indels: 27
0.71 0.05 0.24
Matches are distributed among these distances:
14 24 0.30
15 4 0.05
16 12 0.15
17 12 0.15
18 1 0.01
19 26 0.33
ACGTcount: A:0.11, C:0.26, G:0.22, T:0.41
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATC
Found at i:417092 original size:33 final size:33
Alignment explanation
Indices: 416987--417100 Score: 185
Period size: 33 Copynumber: 3.5 Consensus size: 33
416977 CCAAATCGCA
*
416987 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
**
417020 TTGCGACAGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
*
417053 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
417086 TTGCGATT-TCATTTC
1 TTGCGATTGTCATTTC
417101 AACCAAAAGA
Statistics
Matches: 74, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
32 6 0.08
33 68 0.92
ACGTcount: A:0.11, C:0.25, G:0.22, T:0.42
Consensus pattern (33 bp):
TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
Found at i:419140 original size:92 final size:93
Alignment explanation
Indices: 418731--419283 Score: 1006
Period size: 92 Copynumber: 6.1 Consensus size: 93
418721 TAGATTGCTT
*
418731 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACT-TGTATT-TTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
418794 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
418822 AGTAAATTTGTTCGG-TGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AA-A-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
418883 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
418911 AGTAAATTTGTTCGGTTG-TGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
418974 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
419001 AGT-AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
419065 -TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
419092 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
419157 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
419185 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCT-AACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
419249 TTTGTCTTTGTTTTGTC-TTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
419276 AGTAAATT
1 AGTAAATT
419284 CCATTCAAGT
Statistics
Matches: 451, Mismatches: 1, Indels: 20
0.96 0.00 0.04
Matches are distributed among these distances:
89 97 0.22
90 98 0.22
91 75 0.17
92 122 0.27
93 59 0.13
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:419362 original size:19 final size:19
Alignment explanation
Indices: 419322--419412 Score: 93
Period size: 19 Copynumber: 5.0 Consensus size: 19
419312 TAGTTTACTT
* *
419322 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
419342 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
419361 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
419380 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
419394 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
419413 GCAACGACAA
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
14 9 0.15
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 31 0.53
20 13 0.22
ACGTcount: A:0.47, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:419401 original size:33 final size:30
Alignment explanation
Indices: 419358--419439 Score: 98
Period size: 33 Copynumber: 2.7 Consensus size: 30
419348 CGCGAAACCA
**
419358 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAA--GCAACGAC
419390 AGAATCGCAACGCGAAACCAAAAGCAACGAC
1 A-AATCGCAACGCGAAACCAAAAGCAACGAC
419421 AAATCG---CGCGAAACCAAAA
1 AAATCGCAACGCGAAACCAAAA
419440 TCGCATTGCG
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
27 13 0.28
30 5 0.11
31 9 0.19
32 1 0.02
33 19 0.40
ACGTcount: A:0.49, C:0.27, G:0.18, T:0.06
Consensus pattern (30 bp):
AAATCGCAACGCGAAACCAAAAGCAACGAC
Found at i:419432 original size:27 final size:29
Alignment explanation
Indices: 419382--419439 Score: 84
Period size: 27 Copynumber: 2.0 Consensus size: 29
419372 AATGAAAATC
419382 GCAACGACAGAATCGCAACGCGAAACCAAAA
1 GCAACGACAGAATCG--ACGCGAAACCAAAA
419413 GCAACGACA-AATCG-CGCGAAACCAAAA
1 GCAACGACAGAATCGACGCGAAACCAAAA
419440 TCGCATTGCG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 13 0.48
30 5 0.19
31 9 0.33
ACGTcount: A:0.48, C:0.29, G:0.19, T:0.03
Consensus pattern (29 bp):
GCAACGACAGAATCGACGCGAAACCAAAA
Found at i:419481 original size:32 final size:32
Alignment explanation
Indices: 419445--419535 Score: 146
Period size: 32 Copynumber: 2.8 Consensus size: 32
419435 CAAAATCGCA
*
419445 TTGCGATTTTCATTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTCGCGTTGCGATTCTGTCG
*
419477 TTGCGATTTTCATTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTCGCGTTGCGATTCTGTCG
*
419509 TTGCGATTTTAATTTCGCGTTGCGATT
1 TTGCGATTTTCA-TTCGCGTTGCGATT
419536 TTGGTTTCGC
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
32 41 0.76
33 13 0.24
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (32 bp):
TTGCGATTTTCATTCGCGTTGCGATTCTGTCG
Found at i:419487 original size:12 final size:14
Alignment explanation
Indices: 419461--419516 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
419451 TTTTCATTCG
419461 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
*
419475 CGTTGCGATTTTCATT
1 CGTTGCGA--TTCTTT
*
419491 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
419507 CGTTGCGATT
1 CGTTGCGATT
419517 TTAATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
14 16 0.46
16 13 0.37
18 6 0.17
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.45
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:419564 original size:20 final size:20
Alignment explanation
Indices: 419507--419572 Score: 100
Period size: 19 Copynumber: 3.4 Consensus size: 20
419497 GCGATTCTGT
419507 CGTTGCGATTTTAA-TTTCG
1 CGTTGCGATTTTAAGTTTCG
*
419526 CGTTGCGATTTT-GGTTTCG
1 CGTTGCGATTTTAAGTTTCG
419545 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTAAGTTTCG
*
419565 TGTTGCGA
1 CGTTGCGA
419573 AAGTAAACTA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 29 0.69
20 13 0.31
ACGTcount: A:0.12, C:0.15, G:0.27, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTTTAAGTTTCG
Found at i:420035 original size:42 final size:42
Alignment explanation
Indices: 419959--420038 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
419949 GACTCGCCTG
* * *
419959 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCCA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCCA
* * *
420001 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
420039 ACTGTCATCA
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:0.21, C:0.40, G:0.17, T:0.21
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCCA
Found at i:421463 original size:14 final size:14
Alignment explanation
Indices: 421444--421479 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
421434 ATTGTTTAAT
421444 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
421458 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
421472 TGATTTGT
1 TGATTTGT
421480 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:421602 original size:19 final size:19
Alignment explanation
Indices: 421586--421687 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
421576 AAAAATGACT
421586 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
421605 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
421624 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
421638 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
421657 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
421677 ATCGCAATGCG
1 ATCGCAATGCG
421688 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:421736 original size:33 final size:33
Alignment explanation
Indices: 421694--421908 Score: 205
Period size: 33 Copynumber: 6.5 Consensus size: 33
421684 TGCGTTTATA
421694 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
*
421727 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
*
421763 -TTTCG--TTGCGATTTTCATTTCGCATTGCGA-TTTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
** *
421797 ATTTCGCATTGCGA-T-T-TAATTGCGATTTTA
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
* *
421827 ATTTCGCATTGCGATTCTGTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
*
421860 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
421893 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
421909 TTCATTTCGC
Statistics
Matches: 161, Mismatches: 8, Indels: 26
0.83 0.04 0.13
Matches are distributed among these distances:
29 6 0.04
30 17 0.11
31 2 0.01
32 2 0.01
33 98 0.61
34 4 0.02
35 12 0.07
36 8 0.05
37 6 0.04
38 6 0.04
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
Found at i:421740 original size:19 final size:19
Alignment explanation
Indices: 421716--421994 Score: 257
Period size: 19 Copynumber: 16.4 Consensus size: 19
421706 GATTATCTCG
421716 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
421735 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
421754 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
421768 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
421787 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
421805 TTGCGA-TTT-A------A
1 TTGCGATTTTCATTTCGCA
*
421816 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
421835 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
421849 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
421868 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
421882 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
421901 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
421920 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
421934 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
421954 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
421968 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
421987 TTGCGATT
1 TTGCGATT
421995 GTATTTTCCG
Statistics
Matches: 217, Mismatches: 9, Indels: 68
0.74 0.03 0.23
Matches are distributed among these distances:
11 7 0.03
12 3 0.01
13 1 0.00
14 35 0.16
16 31 0.14
17 28 0.13
18 24 0.11
19 76 0.35
20 12 0.06
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:421756 original size:52 final size:50
Alignment explanation
Indices: 421694--421994 Score: 287
Period size: 52 Copynumber: 5.9 Consensus size: 50
421684 TGCGTTTATA
*
421694 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATT-T-TCATTGCGATTTTCATTTCGCATTGCGATTTTC
*
421746 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGA-TTTC
1 ATTTCGCATTGCGA-T-TTTCATTGCGATTTTCATTTCGCATTGCGATTTTC
* *
421797 ATTTCGCATTGCGA-TTTAATTGCGATTTTAATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGATTTTCATTGCGATTTTCATTTCGCATTGCGATTTTC
* * * * *
421844 -TGTCG--TTGCGATTTTCATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCATTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
* * * *
421893 ATTTCGCATTGCGATTTTCATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCATTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
* *
421945 ATTTCCGCATTGCGATTTTCATGTTGGGATTTTCATTTCGCGTTGCGATT
1 ATTT-CGCATTGCGATTTTCA--TTGCGATTTTCATTTCGCATTGCGATT
421995 GTATTTTCCG
Statistics
Matches: 219, Mismatches: 15, Indels: 29
0.83 0.06 0.11
Matches are distributed among these distances:
44 6 0.03
45 10 0.05
46 8 0.04
47 12 0.05
48 27 0.12
49 3 0.01
50 4 0.02
51 18 0.08
52 90 0.41
53 30 0.14
54 5 0.02
55 6 0.03
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.46
Consensus pattern (50 bp):
ATTTCGCATTGCGATTTTCATTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:421901 original size:114 final size:118
Alignment explanation
Indices: 421735--421994 Score: 397
Period size: 114 Copynumber: 2.2 Consensus size: 118
421725 TCATTTCGCA
*
421735 TTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGA-TTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
421799 TTCGCATTGCGA-T-T-TAATTGCGATTTTAATTT-CGCATTGCGATTCTGTC-G
66 TTCGCATTGCGATTCTCTAATTGCGATTTTAATTTCCGCATTGCGATT-T-TCAG
421849 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
** *
421914 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATG
66 TTCGCATTGCGATTCTCTAATTGCGATTTTAATTTCCGCATTGCGATTTTCA-G
* *
421968 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
421995 GTATTTTCCG
Statistics
Matches: 133, Mismatches: 6, Indels: 9
0.90 0.04 0.06
Matches are distributed among these distances:
114 57 0.43
115 18 0.14
116 1 0.01
117 3 0.02
118 16 0.12
119 38 0.29
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (118 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
TTCGCATTGCGATTCTCTAATTGCGATTTTAATTTCCGCATTGCGATTTTCAG
Found at i:421959 original size:34 final size:33
Alignment explanation
Indices: 421901--421994 Score: 136
Period size: 34 Copynumber: 2.8 Consensus size: 33
421891 TCATTTCGCA
421901 TTGCGATTTTCATTTCGCATTGCGATTCTC-TCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCAT-G
*
421934 TTGCGATTTTCATTTCCGCATTGCGATTTTCATG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCATG
* *
421968 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
421995 GTATTTTCCG
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
33 26 0.46
34 29 0.52
35 1 0.02
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCATG
Found at i:424276 original size:12 final size:12
Alignment explanation
Indices: 424259--424283 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
424249 TCTTCGGGGA
424259 CTTTTTCTTCTT
1 CTTTTTCTTCTT
424271 CTTTTTCTTCTT
1 CTTTTTCTTCTT
424283 C
1 C
424284 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:424403 original size:20 final size:20
Alignment explanation
Indices: 424375--424739 Score: 415
Period size: 20 Copynumber: 18.4 Consensus size: 20
424365 AAATTTCAGT
* * * *
424375 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
424395 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
424415 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
424435 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
424455 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
424475 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
424495 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
424515 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
424535 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
424555 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
424575 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
424595 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
424615 GTTGCGATAT-CGGATACGC
1 GTTGCGATTTACGGATACGC
* *
424634 ATT---ATTTTAC-CATACGC
1 GTTGCGA-TTTACGGATACGC
*
424651 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
424671 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
424691 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
424711 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
424731 GTTGCGATT
1 GTTGCGATT
424740 ATGGAAAATC
Statistics
Matches: 301, Mismatches: 30, Indels: 28
0.84 0.08 0.08
Matches are distributed among these distances:
16 1 0.00
17 10 0.03
18 1 0.00
19 21 0.07
20 263 0.87
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:425327 original size:2 final size:2
Alignment explanation
Indices: 425320--425370 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
425310 TCATCAAATT
425320 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
425362 TA TA TA TA T
1 TA TA TA TA T
425371 TACAAAATTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:427624 original size:35 final size:35
Alignment explanation
Indices: 427578--427653 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
427568 AAAACAGTCC
* *
427578 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
427613 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
427648 TCAATT
1 TCAATT
427654 AAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:428217 original size:130 final size:126
Alignment explanation
Indices: 428039--428300 Score: 407
Period size: 130 Copynumber: 2.0 Consensus size: 126
428029 CATTCAGTCT
* * **
428039 TAATTATTTATATAATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTA
1 TAATTATTTATATAATCAATTTGGTCCTAAATTAAATAAAATTAAATAAATTAATCATTTAACCA
* *
428104 GGATCTGACATGTGTTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACC
66 GGATCTGACATGTGTTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACC
428165 TAATTATTTATATATGCTATCAATTTGGTCCTAAATTAAATAAAATTAAATAAATTAATCATTTA
1 TAATTATTTATATA----ATCAATTTGGTCCTAAATTAAATAAAATTAAATAAATTAATCATTTA
* * *
428230 ACCAGGATCTGACATGTGTTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACC
62 ACCAGGATCTGACATGTGTTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACC
428295 TAATTA
1 TAATTA
428301 GAAGAAAATT
Statistics
Matches: 123, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
126 14 0.11
130 109 0.89
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (126 bp):
TAATTATTTATATAATCAATTTGGTCCTAAATTAAATAAAATTAAATAAATTAATCATTTAACCA
GGATCTGACATGTGTTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACC
Found at i:428789 original size:16 final size:18
Alignment explanation
Indices: 428768--428801 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
428758 ATTTCTTATT
428768 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
428784 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
428802 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:428883 original size:22 final size:21
Alignment explanation
Indices: 428858--428917 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
428848 AATATACATT
* *
428858 TATATAAATATATTTTTATTCA
1 TATATAAA-ATATTTTGATTAA
*
428880 TATATTGAAATATTTTGATTAA
1 TATA-TAAAATATTTTGATTAA
*
428902 AATATAAACATATTTT
1 TATATAAA-ATATTTT
428918 AAATACTAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
21 3 0.10
22 25 0.81
23 3 0.10
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.50
Consensus pattern (21 bp):
TATATAAAATATTTTGATTAA
Found at i:431483 original size:25 final size:23
Alignment explanation
Indices: 431429--431483 Score: 56
Period size: 25 Copynumber: 2.3 Consensus size: 23
431419 AAGATGAACT
* *
431429 TATAAAATTTTAGAATGAAAATT
1 TATAAAATTTTAGAAGGAAAATA
* *
431452 TACAAAATTTTAGAGAAGGAAGATA
1 TATAAAATTTT--AGAAGGAAAATA
431477 TATAAAA
1 TATAAAA
431484 ATACTTCAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
23 10 0.40
25 15 0.60
ACGTcount: A:0.55, C:0.02, G:0.13, T:0.31
Consensus pattern (23 bp):
TATAAAATTTTAGAAGGAAAATA
Found at i:432663 original size:35 final size:35
Alignment explanation
Indices: 432594--432665 Score: 108
Period size: 35 Copynumber: 2.1 Consensus size: 35
432584 CGTTAAAAAT
* * **
432594 ATATTAATATACTAAATTAAAAGCATGGTTCATAA
1 ATATTAATAAACTAAATTAAAAGCAAGGCCCATAA
432629 ATATTAATAAACTAAATTAAAAGCAAGGCCCATAA
1 ATATTAATAAACTAAATTAAAAGCAAGGCCCATAA
432664 AT
1 AT
432666 TTATTTCTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.29
Consensus pattern (35 bp):
ATATTAATAAACTAAATTAAAAGCAAGGCCCATAA
Found at i:447052 original size:6 final size:6
Alignment explanation
Indices: 447041--447069 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
447031 TGGTTTCAGT
447041 TCCAGC TCCAGC TCCAGC TCCAGC TCCAG
1 TCCAGC TCCAGC TCCAGC TCCAGC TCCAG
447070 TTTCACTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.48, G:0.17, T:0.17
Consensus pattern (6 bp):
TCCAGC
Found at i:460444 original size:18 final size:17
Alignment explanation
Indices: 460418--460462 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
460408 TTTATGAGGG
*
460418 AATTAGAATCTGTGAAGA
1 AATTGGAATCTGT-AAGA
* *
460436 AATTGGAATCTGTCAGG
1 AATTGGAATCTGTAAGA
460453 AATTGGAATC
1 AATTGGAATC
460463 CAATTCCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.29
Consensus pattern (17 bp):
AATTGGAATCTGTAAGA
Found at i:460458 original size:17 final size:18
Alignment explanation
Indices: 460416--460462 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
460406 TGTTTATGAG
*
460416 GGAATTAGAATCTGTGAA
1 GGAATTGGAATCTGTGAA
* *
460434 GAAATTGGAATCTGT-CA
1 GGAATTGGAATCTGTGAA
460451 GGAATTGGAATC
1 GGAATTGGAATC
460463 CAATTCCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.36, C:0.09, G:0.28, T:0.28
Consensus pattern (18 bp):
GGAATTGGAATCTGTGAA
Found at i:461780 original size:18 final size:17
Alignment explanation
Indices: 461750--461783 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
461740 AATTATATAT
*
461750 ATTTTTTATGAATTTAA
1 ATTTTTTAAGAATTTAA
461767 ATTTTTTAAAGAATTTA
1 ATTTTTT-AAGAATTTA
461784 TATAAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (17 bp):
ATTTTTTAAGAATTTAA
Found at i:461966 original size:18 final size:18
Alignment explanation
Indices: 461943--461989 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
461933 ACATTCTCAA
*
461943 TAATCTTATTCTCGCCGG
1 TAATCTTATTCCCGCCGG
461961 TAATCTTATTCCCGCCGG
1 TAATCTTATTCCCGCCGG
461979 TAATCTTATTC
1 TAATCTTATTC
461990 ACGTTGATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.19, C:0.28, G:0.13, T:0.40
Consensus pattern (18 bp):
TAATCTTATTCCCGCCGG
Found at i:462000 original size:18 final size:18
Alignment explanation
Indices: 461942--462005 Score: 74
Period size: 18 Copynumber: 3.6 Consensus size: 18
461932 AACATTCTCA
*
461942 ATAATCTTATTCTCGCCG
1 ATAATCTTATTCACGCCG
* *
461960 GTAATCTTATTCCCGCCG
1 ATAATCTTATTCACGCCG
* **
461978 GTAATCTTATTCACGTTG
1 ATAATCTTATTCACGCCG
461996 ATAATCTTAT
1 ATAATCTTAT
462006 ATTCCGTGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.41
Consensus pattern (18 bp):
ATAATCTTATTCACGCCG
Found at i:474232 original size:2 final size:2
Alignment explanation
Indices: 474225--474262 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
474215 CACAATGAGT
*
474225 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
474263 AATTCAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:475914 original size:38 final size:38
Alignment explanation
Indices: 475831--475914 Score: 105
Period size: 38 Copynumber: 2.2 Consensus size: 38
475821 AGAGCTTATA
* *
475831 AACGAGTCAATAAACGACAATGTTCATGAACATAAATG
1 AACGAGTCAATAAACAACAATGTTCATGAACATAAACG
* * * *
475869 ACCGAGTCAATAAATAACATTGTTCGTGAACATAAACG
1 AACGAGTCAATAAACAACAATGTTCATGAACATAAACG
*
475907 AATGAGTC
1 AACGAGTC
475915 CATACTATGT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.23
Consensus pattern (38 bp):
AACGAGTCAATAAACAACAATGTTCATGAACATAAACG
Found at i:485529 original size:16 final size:16
Alignment explanation
Indices: 485508--485542 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
485498 ATTAAAGACT
*
485508 AAAAATAAAATATTTA
1 AAAAATAAAATATATA
*
485524 AAAAATAAATTATATA
1 AAAAATAAAATATATA
485540 AAA
1 AAA
485543 TTAAAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAATAAAATATATA
Found at i:485896 original size:15 final size:15
Alignment explanation
Indices: 485873--485902 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
485863 TTGAAATTTA
485873 TTTTATTTTATTAAT
1 TTTTATTTTATTAAT
*
485888 TTTTGTTTTATTAAT
1 TTTTATTTTATTAAT
485903 CCTATTAATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (15 bp):
TTTTATTTTATTAAT
Found at i:494766 original size:17 final size:17
Alignment explanation
Indices: 494744--494790 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 17
494734 ATAATGACCA
* *
494744 CTACAATCACTCTCCAG
1 CTACAAACACCCTCCAG
494761 CTACAAACACCCTCCAG
1 CTACAAACACCCTCCAG
494778 CTACAAACACCCT
1 CTACAAACACCCT
494791 ATTCAGCAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.34, C:0.45, G:0.04, T:0.17
Consensus pattern (17 bp):
CTACAAACACCCTCCAG
Found at i:499180 original size:11 final size:11
Alignment explanation
Indices: 499164--499188 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
499154 ATTAATTTTA
499164 AAAAAAATATT
1 AAAAAAATATT
499175 AAAAAAATATT
1 AAAAAAATATT
499186 AAA
1 AAA
499189 TTCTAATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAAAAAATATT
Found at i:500033 original size:16 final size:16
Alignment explanation
Indices: 500012--500045 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
500002 CTTTTTCTTC
500012 GATTTGTGGTAATTTT
1 GATTTGTGGTAATTTT
500028 GATTTGTGGTAATTTT
1 GATTTGTGGTAATTTT
500044 GA
1 GA
500046 GTACGAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.53
Consensus pattern (16 bp):
GATTTGTGGTAATTTT
Found at i:500210 original size:33 final size:33
Alignment explanation
Indices: 500168--500231 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
500158 TTTTATTAAT
*
500168 TAATTTCCGATATAATCCAATATTAACATTTCC
1 TAATTTCCGATAGAATCCAATATTAACATTTCC
*
500201 TAATTTCCGATAGAATCTAATATTAACATTT
1 TAATTTCCGATAGAATCCAATATTAACATTT
500232 TCAGTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.38, C:0.17, G:0.05, T:0.41
Consensus pattern (33 bp):
TAATTTCCGATAGAATCCAATATTAACATTTCC
Found at i:509322 original size:3 final size:3
Alignment explanation
Indices: 509309--509342 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
509299 CTTTAATAAA
509309 ATT ATTT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT
509343 GTAAATTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:512357 original size:77 final size:75
Alignment explanation
Indices: 512270--512445 Score: 205
Period size: 75 Copynumber: 2.3 Consensus size: 75
512260 ACTATAATGG
*** * *
512270 CGAA-ATAAATTCATTAATAATATATTTTAAAA-TAAGGTATAGTAGTTTTTCTGAAACTATAAT
1 CGAATATAAATTCATTAATAATATATTTTAAAATTAAGGTATA--A-CAATCCCGAAACTATAAT
*
512333 A-TCATATTTTATT
63 ACT-ATATTTTAAT
* * *
512346 CGAATATAAATTCATGACTAATATATTTTAAAATTAAGGTATAACAATCCCGGAACTATAATACT
1 CGAATATAAATTCATTAATAATATATTTTAAAATTAAGGTATAACAATCCCGAAACTATAATACT
512411 ATATTTTAAT
66 ATATTTTAAT
*
512421 CAAATATAAATTCATTAATAATATA
1 CGAATATAAATTCATTAATAATATA
512446 ACATTATCCT
Statistics
Matches: 85, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
75 44 0.52
76 6 0.07
77 26 0.31
78 9 0.11
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.39
Consensus pattern (75 bp):
CGAATATAAATTCATTAATAATATATTTTAAAATTAAGGTATAACAATCCCGAAACTATAATACT
ATATTTTAAT
Found at i:517165 original size:15 final size:15
Alignment explanation
Indices: 517145--517175 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
517135 GTTAATCATC
517145 TATGTAGAGTTACCA
1 TATGTAGAGTTACCA
517160 TATGTAGAGTTACCA
1 TATGTAGAGTTACCA
517175 T
1 T
517176 GTATGGTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (15 bp):
TATGTAGAGTTACCA
Found at i:519164 original size:35 final size:33
Alignment explanation
Indices: 519125--519210 Score: 104
Period size: 32 Copynumber: 2.6 Consensus size: 33
519115 AAAAAAAAAA
*
519125 TCGGGGTCGGGTTAGGTTTTTTTTAAGTGTGATAT
1 TCGGGGTCGGGTTAGG--GTTTTTAAGTGTGATAT
* *
519160 TCGGGTTCGGG-TCGGGTTTTTAAGTGTGATAT
1 TCGGGGTCGGGTTAGGGTTTTTAAGTGTGATAT
*
519192 TC-GGGTCGGGTTTGGGTTT
1 TCGGGGTCGGGTTAGGGTTT
519211 ATGGTGAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
31 7 0.16
32 25 0.56
34 3 0.07
35 10 0.22
ACGTcount: A:0.10, C:0.08, G:0.38, T:0.43
Consensus pattern (33 bp):
TCGGGGTCGGGTTAGGGTTTTTAAGTGTGATAT
Done.