Multiple sequence alignment - TraesCS4D01G004100

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4D01G004100 chr4D 100.000 5640 0 0 1 5640 1820950 1826589 0.000000e+00 10416
1 TraesCS4D01G004100 chr4D 88.308 2985 281 42 2327 5296 1874701 1877632 0.000000e+00 3517
2 TraesCS4D01G004100 chr4D 87.299 2110 201 24 1 2059 1871449 1873542 0.000000e+00 2350
3 TraesCS4D01G004100 chrUn 89.479 4553 388 44 808 5296 47450639 47455164 0.000000e+00 5670
4 TraesCS4D01G004100 chrUn 90.587 3750 312 19 808 4525 47630024 47633764 0.000000e+00 4931
5 TraesCS4D01G004100 chrUn 84.523 2507 313 36 2333 4818 47660277 47662729 0.000000e+00 2410
6 TraesCS4D01G004100 chrUn 85.976 1255 150 10 808 2041 48044673 48045922 0.000000e+00 1319
7 TraesCS4D01G004100 chrUn 85.896 1255 151 10 808 2041 48074944 48076193 0.000000e+00 1314
8 TraesCS4D01G004100 chrUn 84.350 377 37 9 4814 5190 47662758 47663112 3.230000e-92 350
9 TraesCS4D01G004100 chrUn 88.938 226 18 2 257 475 48043345 48043570 7.200000e-69 272
10 TraesCS4D01G004100 chrUn 88.938 226 18 2 257 475 48073616 48073841 7.200000e-69 272
11 TraesCS4D01G004100 chrUn 88.938 226 18 2 257 475 403973322 403973097 7.200000e-69 272
12 TraesCS4D01G004100 chrUn 81.463 205 14 3 624 808 47629794 47629994 4.550000e-31 147
13 TraesCS4D01G004100 chr4B 91.078 3721 293 14 839 4525 3732267 3735982 0.000000e+00 4996
14 TraesCS4D01G004100 chr4B 85.764 2030 187 30 90 2059 3343271 3341284 0.000000e+00 2054
15 TraesCS4D01G004100 chr4B 85.227 1699 233 13 2327 4019 3340185 3338499 0.000000e+00 1731
16 TraesCS4D01G004100 chr4B 85.817 1255 152 10 808 2041 3514407 3513158 0.000000e+00 1308
17 TraesCS4D01G004100 chr4B 85.817 1255 151 11 808 2041 3484433 3483185 0.000000e+00 1306
18 TraesCS4D01G004100 chr4B 86.336 1171 139 7 808 1958 3454319 3453150 0.000000e+00 1256
19 TraesCS4D01G004100 chr4B 87.216 970 117 5 1074 2041 3431599 3430635 0.000000e+00 1098
20 TraesCS4D01G004100 chr4B 84.728 681 73 16 4016 4695 3337652 3337002 0.000000e+00 652
21 TraesCS4D01G004100 chr4B 88.938 226 18 2 257 475 3433270 3433045 7.200000e-69 272
22 TraesCS4D01G004100 chr4B 88.938 226 18 2 257 475 3455639 3455414 7.200000e-69 272
23 TraesCS4D01G004100 chr4B 88.938 226 18 2 257 475 3485753 3485528 7.200000e-69 272
24 TraesCS4D01G004100 chr4B 91.608 143 11 1 334 475 3429079 3428937 4.460000e-46 196
25 TraesCS4D01G004100 chr4A 87.893 2197 241 20 2323 4509 602872948 602875129 0.000000e+00 2560
26 TraesCS4D01G004100 chr4A 84.826 2333 316 26 2323 4647 602609792 602612094 0.000000e+00 2313
27 TraesCS4D01G004100 chr4A 88.400 931 101 5 3536 4461 602722320 602723248 0.000000e+00 1114
28 TraesCS4D01G004100 chr4A 88.141 936 101 3 2783 3716 602726157 602727084 0.000000e+00 1105
29 TraesCS4D01G004100 chr4A 89.583 432 26 6 5009 5439 602613305 602613718 1.080000e-146 531
30 TraesCS4D01G004100 chr4A 86.667 465 45 9 4059 4522 602725315 602725763 3.030000e-137 499
31 TraesCS4D01G004100 chr4A 84.599 461 50 11 4849 5297 602875681 602876132 6.710000e-119 438
32 TraesCS4D01G004100 chr4A 84.641 306 31 9 4559 4850 602875330 602875633 1.990000e-74 291
33 TraesCS4D01G004100 chr4A 92.793 111 7 1 5509 5618 602876171 602876281 5.850000e-35 159
34 TraesCS4D01G004100 chr1B 75.150 2173 492 40 2326 4475 628618556 628616409 0.000000e+00 977
35 TraesCS4D01G004100 chr1A 75.095 2112 487 34 2326 4419 550636077 550633987 0.000000e+00 950
36 TraesCS4D01G004100 chr1D 74.988 2111 491 32 2326 4419 458145198 458143108 0.000000e+00 939
37 TraesCS4D01G004100 chr3B 95.349 129 6 0 5490 5618 323362479 323362351 7.410000e-49 206


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G004100 chr4D 1820950 1826589 5639 False 10416.0 10416 100.000000 1 5640 1 chr4D.!!$F1 5639
1 TraesCS4D01G004100 chr4D 1871449 1877632 6183 False 2933.5 3517 87.803500 1 5296 2 chr4D.!!$F2 5295
2 TraesCS4D01G004100 chrUn 47450639 47455164 4525 False 5670.0 5670 89.479000 808 5296 1 chrUn.!!$F1 4488
3 TraesCS4D01G004100 chrUn 47629794 47633764 3970 False 2539.0 4931 86.025000 624 4525 2 chrUn.!!$F2 3901
4 TraesCS4D01G004100 chrUn 47660277 47663112 2835 False 1380.0 2410 84.436500 2333 5190 2 chrUn.!!$F3 2857
5 TraesCS4D01G004100 chrUn 48043345 48045922 2577 False 795.5 1319 87.457000 257 2041 2 chrUn.!!$F4 1784
6 TraesCS4D01G004100 chrUn 48073616 48076193 2577 False 793.0 1314 87.417000 257 2041 2 chrUn.!!$F5 1784
7 TraesCS4D01G004100 chr4B 3732267 3735982 3715 False 4996.0 4996 91.078000 839 4525 1 chr4B.!!$F1 3686
8 TraesCS4D01G004100 chr4B 3337002 3343271 6269 True 1479.0 2054 85.239667 90 4695 3 chr4B.!!$R2 4605
9 TraesCS4D01G004100 chr4B 3513158 3514407 1249 True 1308.0 1308 85.817000 808 2041 1 chr4B.!!$R1 1233
10 TraesCS4D01G004100 chr4B 3483185 3485753 2568 True 789.0 1306 87.377500 257 2041 2 chr4B.!!$R5 1784
11 TraesCS4D01G004100 chr4B 3453150 3455639 2489 True 764.0 1256 87.637000 257 1958 2 chr4B.!!$R4 1701
12 TraesCS4D01G004100 chr4B 3428937 3433270 4333 True 522.0 1098 89.254000 257 2041 3 chr4B.!!$R3 1784
13 TraesCS4D01G004100 chr4A 602609792 602613718 3926 False 1422.0 2313 87.204500 2323 5439 2 chr4A.!!$F1 3116
14 TraesCS4D01G004100 chr4A 602722320 602727084 4764 False 906.0 1114 87.736000 2783 4522 3 chr4A.!!$F2 1739
15 TraesCS4D01G004100 chr4A 602872948 602876281 3333 False 862.0 2560 87.481500 2323 5618 4 chr4A.!!$F3 3295
16 TraesCS4D01G004100 chr1B 628616409 628618556 2147 True 977.0 977 75.150000 2326 4475 1 chr1B.!!$R1 2149
17 TraesCS4D01G004100 chr1A 550633987 550636077 2090 True 950.0 950 75.095000 2326 4419 1 chr1A.!!$R1 2093
18 TraesCS4D01G004100 chr1D 458143108 458145198 2090 True 939.0 939 74.988000 2326 4419 1 chr1D.!!$R1 2093

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
135 155 0.249868 TAGCAAGTGAAGCACTGCGT 60.250 50.000 0.22 0.0 44.62 5.24 F
1219 2129 0.321671 ACTGAAGCGTGCCATGTACT 59.678 50.000 0.00 0.0 0.00 2.73 F
1323 2233 1.473677 CTCTTTTGCATGCGGAATCCA 59.526 47.619 14.09 0.0 0.00 3.41 F
2839 9495 1.577736 AGCTAGGGATGAAGCACTGT 58.422 50.000 0.00 0.0 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2069 3003 0.465460 ACACTGTGGTGCCAAACGAT 60.465 50.000 13.09 0.00 46.57 3.73 R
2817 9473 1.683917 AGTGCTTCATCCCTAGCTACG 59.316 52.381 0.00 0.00 38.22 3.51 R
2924 9580 2.359900 ACCTCCACTCAAATTCATCGC 58.640 47.619 0.00 0.00 0.00 4.58 R
4791 13508 0.112995 TTCCCCATATCCCTGCATGC 59.887 55.000 11.82 11.82 0.00 4.06 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 101 1.464997 GCTAGCTTTCTTGTTGGACCG 59.535 52.381 7.70 0.00 0.00 4.79
103 119 1.713937 CGATTATGCCAAGCGCCACA 61.714 55.000 2.29 0.00 36.24 4.17
109 125 2.918345 GCCAAGCGCCACATGAACA 61.918 57.895 2.29 0.00 0.00 3.18
120 136 3.599343 CCACATGAACAACTAGCTAGCA 58.401 45.455 20.91 10.34 0.00 3.49
135 155 0.249868 TAGCAAGTGAAGCACTGCGT 60.250 50.000 0.22 0.00 44.62 5.24
136 156 1.369689 GCAAGTGAAGCACTGCGTG 60.370 57.895 0.22 4.61 44.62 5.34
137 157 1.775039 GCAAGTGAAGCACTGCGTGA 61.775 55.000 11.94 0.00 44.62 4.35
191 212 3.760738 TCAATACAGGTGTTGATTGCCA 58.239 40.909 7.41 0.00 36.10 4.92
198 219 1.255882 GTGTTGATTGCCACATCCCA 58.744 50.000 0.00 0.00 0.00 4.37
236 261 2.111792 TCCCCGATCTGGATCTGGATAA 59.888 50.000 18.35 5.21 42.61 1.75
269 294 0.684479 TACGACTCTGGATGGCTGCT 60.684 55.000 0.00 0.00 0.00 4.24
283 308 4.337264 TGGCTGCTATATATCTCCCTCA 57.663 45.455 0.00 0.00 0.00 3.86
284 309 4.888573 TGGCTGCTATATATCTCCCTCAT 58.111 43.478 0.00 0.00 0.00 2.90
286 311 5.728253 TGGCTGCTATATATCTCCCTCATTT 59.272 40.000 0.00 0.00 0.00 2.32
298 323 1.878088 CCCTCATTTGATCTGCATCGG 59.122 52.381 0.00 0.00 0.00 4.18
413 459 3.390967 TGAAGAGATGGTCTTGGTTGTGA 59.609 43.478 0.00 0.00 46.21 3.58
450 496 5.250235 TGTTGGCGTTTGTTCAAGATAAA 57.750 34.783 0.00 0.00 0.00 1.40
487 533 5.618056 ATCTTGTGTGCACTGTATTCTTG 57.382 39.130 19.41 0.00 0.00 3.02
488 534 4.450976 TCTTGTGTGCACTGTATTCTTGT 58.549 39.130 19.41 0.00 0.00 3.16
550 620 2.280797 GTCTTCAGGTGGTGCGCA 60.281 61.111 5.66 5.66 0.00 6.09
619 1415 2.174349 CAGCTGAAAACGCGAGCC 59.826 61.111 15.93 0.00 32.86 4.70
622 1418 1.441016 GCTGAAAACGCGAGCCAAG 60.441 57.895 15.93 5.77 0.00 3.61
678 1474 7.201956 GGGAGATCTATCTAGTTTTTGCTCTGA 60.202 40.741 0.00 0.00 37.25 3.27
786 1602 3.149196 ACCGTTGATCTTGTGCATTTCT 58.851 40.909 0.00 0.00 0.00 2.52
877 1724 4.108570 TCCCTTGGGATTTCTTGCTAGTA 58.891 43.478 3.91 0.00 0.00 1.82
938 1786 5.291178 TGGATTGTTGATGTGAAAAAGCAG 58.709 37.500 0.00 0.00 0.00 4.24
998 1865 0.472044 TGTGAGCTAACCCTGCAACA 59.528 50.000 0.00 0.00 0.00 3.33
1090 2000 2.612200 GCCATGCTAATCGGCGTAA 58.388 52.632 6.85 0.00 35.79 3.18
1219 2129 0.321671 ACTGAAGCGTGCCATGTACT 59.678 50.000 0.00 0.00 0.00 2.73
1323 2233 1.473677 CTCTTTTGCATGCGGAATCCA 59.526 47.619 14.09 0.00 0.00 3.41
1477 2387 2.862140 GCCACTGACCGGAAAACAAATG 60.862 50.000 9.46 4.39 0.00 2.32
2067 3001 8.985805 CGTACTTCCCAAACTCAATATAATACC 58.014 37.037 0.00 0.00 0.00 2.73
2069 3003 7.878495 ACTTCCCAAACTCAATATAATACCCA 58.122 34.615 0.00 0.00 0.00 4.51
2078 3012 6.430000 ACTCAATATAATACCCATCGTTTGGC 59.570 38.462 2.13 0.00 44.97 4.52
2085 3019 1.580942 CCATCGTTTGGCACCACAG 59.419 57.895 0.00 0.00 39.09 3.66
2172 3299 5.154222 GCTTCCTTGACTTAAATTTCACCG 58.846 41.667 0.00 0.00 0.00 4.94
2197 3831 4.699637 ACACGAGTTCATCAAGTTGGTAA 58.300 39.130 2.34 0.00 0.00 2.85
2212 3850 9.396022 TCAAGTTGGTAAATGAAGGAAGATATC 57.604 33.333 2.34 0.00 0.00 1.63
2245 4176 7.967771 TTTTCATTTGTATGCATGATGTACG 57.032 32.000 10.16 0.00 29.45 3.67
2250 4181 3.130633 TGTATGCATGATGTACGGCTTC 58.869 45.455 10.16 0.00 0.00 3.86
2252 4183 1.939974 TGCATGATGTACGGCTTCTC 58.060 50.000 0.00 0.00 0.00 2.87
2272 4208 6.740944 TCTCAATTAGTGGATTATTCCGGA 57.259 37.500 0.00 0.00 45.89 5.14
2281 4217 6.113411 AGTGGATTATTCCGGACTTAAGTTG 58.887 40.000 10.02 5.73 45.89 3.16
2282 4218 6.070424 AGTGGATTATTCCGGACTTAAGTTGA 60.070 38.462 10.02 4.57 45.89 3.18
2291 4227 5.815740 TCCGGACTTAAGTTGAGCAATTATC 59.184 40.000 10.02 0.00 0.00 1.75
2293 4229 6.238211 CCGGACTTAAGTTGAGCAATTATCAG 60.238 42.308 10.02 0.00 0.00 2.90
2342 4397 2.826128 TCTACTTGCAGGTACTCACAGG 59.174 50.000 4.29 0.00 34.60 4.00
2386 4441 7.108847 AGTTGATATGCTAGAAGATATTGGCC 58.891 38.462 0.00 0.00 0.00 5.36
2817 9473 4.498323 GTCATTCGCTCATTTGCTCAATTC 59.502 41.667 0.00 0.00 0.00 2.17
2839 9495 1.577736 AGCTAGGGATGAAGCACTGT 58.422 50.000 0.00 0.00 0.00 3.55
2856 9512 5.105554 AGCACTGTTAGTTCATAGTGGAGAG 60.106 44.000 0.00 0.00 40.55 3.20
2859 9515 5.419471 ACTGTTAGTTCATAGTGGAGAGACC 59.581 44.000 0.00 0.00 39.54 3.85
2919 9575 7.456902 AGGTTGTCTATAGAAACCAAAGGAGTA 59.543 37.037 28.99 1.31 44.81 2.59
2924 9580 9.535878 GTCTATAGAAACCAAAGGAGTAGAATG 57.464 37.037 3.40 0.00 0.00 2.67
2943 9599 2.358957 TGCGATGAATTTGAGTGGAGG 58.641 47.619 0.00 0.00 0.00 4.30
2963 9619 7.225734 GTGGAGGTATTTAAGAGAGCAGAAATC 59.774 40.741 0.00 0.00 0.00 2.17
2964 9620 7.126421 TGGAGGTATTTAAGAGAGCAGAAATCT 59.874 37.037 0.00 0.00 0.00 2.40
2980 9636 6.922957 GCAGAAATCTCTTAGGACACTGATAG 59.077 42.308 0.00 0.00 0.00 2.08
2998 9654 6.935208 ACTGATAGTAACTGGAAACCTCAAAC 59.065 38.462 0.00 0.00 0.00 2.93
3004 9660 4.236527 ACTGGAAACCTCAAACTTCAGT 57.763 40.909 0.00 0.00 0.00 3.41
3027 9683 5.476945 GTCTGGTGATTCATTGGTTACCTTT 59.523 40.000 2.07 0.00 0.00 3.11
3030 9686 6.074648 TGGTGATTCATTGGTTACCTTTTCT 58.925 36.000 2.07 0.00 0.00 2.52
3039 9695 5.649782 TGGTTACCTTTTCTAGTCTACGG 57.350 43.478 2.07 0.00 0.00 4.02
3084 9740 0.032403 TTGCTGCACTGGTTGAATGC 59.968 50.000 0.00 0.00 39.88 3.56
3243 9902 1.407979 AGCATTATCAAGCTGCAAGGC 59.592 47.619 1.02 0.00 40.13 4.35
3258 9917 4.194640 TGCAAGGCTTGAGATATCTTGAC 58.805 43.478 30.45 8.60 37.57 3.18
3298 9957 7.124750 GTGTAAGTAGTATTCCTAGGGGTTTCA 59.875 40.741 9.46 0.00 0.00 2.69
3324 9983 5.049129 AGCTCTTACAAATTTGAGTGCACTC 60.049 40.000 35.04 35.04 43.15 3.51
3405 10064 6.306987 TCTTTCCCAGCTCAATAAACTTTCT 58.693 36.000 0.00 0.00 0.00 2.52
3477 10136 4.762251 AGGGTAGATGCAAAGAAACAACTC 59.238 41.667 0.00 0.00 0.00 3.01
3617 10282 3.064958 CAGCCTTGCATAGAACACATCAG 59.935 47.826 0.00 0.00 0.00 2.90
3645 10310 2.550978 AGATATTTTGGTCGTCGGCTG 58.449 47.619 0.00 0.00 0.00 4.85
3678 10343 1.452108 GTCCACAGCTATGGTGCCC 60.452 63.158 11.64 0.00 40.95 5.36
3697 10362 3.015327 CCCCTTGAGAGCTTGAAGATTG 58.985 50.000 0.00 0.00 0.00 2.67
3957 10628 8.494433 ACAGAAGTGAAATCTATGCCCTTATTA 58.506 33.333 0.00 0.00 0.00 0.98
3974 10645 6.294620 CCCTTATTAGAGGACCTTCGTATCAC 60.295 46.154 0.00 0.00 39.25 3.06
3983 10654 3.589988 ACCTTCGTATCACTTCTTGCAG 58.410 45.455 0.00 0.00 0.00 4.41
4040 11561 2.029728 CGATGGCGTTGAAGAAGCTAAG 59.970 50.000 0.00 0.00 0.00 2.18
4165 11686 8.514136 TCCAAAATTACAAAAGCTTACAATCG 57.486 30.769 0.00 0.00 0.00 3.34
4437 11958 4.118410 GGCACATCTTCTACACATCTGAG 58.882 47.826 0.00 0.00 0.00 3.35
4442 11963 5.359576 ACATCTTCTACACATCTGAGTCCTC 59.640 44.000 0.00 0.00 0.00 3.71
4598 12276 7.349598 AGCTGAATATATCTCCCACTGTTTTT 58.650 34.615 0.00 0.00 0.00 1.94
4681 12418 4.660168 GAGGAAGGACCATATGATGCAAT 58.340 43.478 3.65 0.00 42.04 3.56
4683 12420 4.105217 AGGAAGGACCATATGATGCAATGA 59.895 41.667 3.65 0.00 42.04 2.57
4684 12421 5.014858 GGAAGGACCATATGATGCAATGAT 58.985 41.667 3.65 0.00 38.79 2.45
4685 12422 6.012245 AGGAAGGACCATATGATGCAATGATA 60.012 38.462 3.65 0.00 42.04 2.15
4686 12423 6.832384 GGAAGGACCATATGATGCAATGATAT 59.168 38.462 3.65 0.00 33.19 1.63
4687 12424 7.994911 GGAAGGACCATATGATGCAATGATATA 59.005 37.037 3.65 0.00 30.39 0.86
4688 12425 9.570468 GAAGGACCATATGATGCAATGATATAT 57.430 33.333 3.65 0.00 30.39 0.86
4989 13816 5.181245 GTGCAAGCAACTAATGGAGTTTAGA 59.819 40.000 0.00 0.00 46.79 2.10
5000 13832 6.613153 AATGGAGTTTAGACTACTCTGCTT 57.387 37.500 5.56 0.00 41.37 3.91
5088 13922 1.153353 TTCGCGGGTGTCTTTCATTC 58.847 50.000 6.13 0.00 0.00 2.67
5097 13931 3.433615 GGTGTCTTTCATTCGTTCTCTGG 59.566 47.826 0.00 0.00 0.00 3.86
5110 13945 8.717821 CATTCGTTCTCTGGAAAACTATGTTTA 58.282 33.333 0.00 0.00 32.81 2.01
5114 13949 9.543018 CGTTCTCTGGAAAACTATGTTTATTTC 57.457 33.333 0.00 0.00 32.81 2.17
5208 14043 6.772716 TCAGAAAGTGGAGTTTATTCAAGCTT 59.227 34.615 0.00 0.00 0.00 3.74
5298 14133 3.356529 AATGTTGGTGAGATCCTGGTC 57.643 47.619 0.00 0.00 0.00 4.02
5299 14134 0.984230 TGTTGGTGAGATCCTGGTCC 59.016 55.000 0.00 0.00 0.00 4.46
5301 14136 0.984230 TTGGTGAGATCCTGGTCCAC 59.016 55.000 0.00 2.41 0.00 4.02
5302 14137 1.257750 TGGTGAGATCCTGGTCCACG 61.258 60.000 0.00 0.00 0.00 4.94
5304 14139 0.895530 GTGAGATCCTGGTCCACGAA 59.104 55.000 0.00 0.00 0.00 3.85
5307 14142 0.252284 AGATCCTGGTCCACGAAGGT 60.252 55.000 0.00 0.00 39.02 3.50
5310 14145 1.004918 CCTGGTCCACGAAGGTCAC 60.005 63.158 0.00 0.00 39.02 3.67
5311 14146 1.372997 CTGGTCCACGAAGGTCACG 60.373 63.158 0.00 0.00 39.02 4.35
5313 14148 1.372623 GGTCCACGAAGGTCACGAC 60.373 63.158 0.00 0.00 39.02 4.34
5346 14181 5.221422 GCTGACTGGATGTTCTAGCTATCTT 60.221 44.000 0.00 0.00 31.95 2.40
5451 14286 5.160607 TGGGTTACAAGTTATGTCTCTGG 57.839 43.478 0.00 0.00 42.70 3.86
5452 14287 4.841813 TGGGTTACAAGTTATGTCTCTGGA 59.158 41.667 0.00 0.00 42.70 3.86
5453 14288 5.308497 TGGGTTACAAGTTATGTCTCTGGAA 59.692 40.000 0.00 0.00 42.70 3.53
5454 14289 5.642491 GGGTTACAAGTTATGTCTCTGGAAC 59.358 44.000 0.00 0.00 42.70 3.62
5455 14290 6.228258 GGTTACAAGTTATGTCTCTGGAACA 58.772 40.000 0.00 0.00 42.70 3.18
5456 14291 6.147328 GGTTACAAGTTATGTCTCTGGAACAC 59.853 42.308 0.00 0.00 42.70 3.32
5457 14292 5.552870 ACAAGTTATGTCTCTGGAACACT 57.447 39.130 0.00 0.00 37.96 3.55
5458 14293 6.665992 ACAAGTTATGTCTCTGGAACACTA 57.334 37.500 0.00 0.00 37.96 2.74
5459 14294 7.062749 ACAAGTTATGTCTCTGGAACACTAA 57.937 36.000 0.00 0.00 37.96 2.24
5460 14295 7.506114 ACAAGTTATGTCTCTGGAACACTAAA 58.494 34.615 0.00 0.00 37.96 1.85
5461 14296 8.157476 ACAAGTTATGTCTCTGGAACACTAAAT 58.843 33.333 0.00 0.00 37.96 1.40
5462 14297 9.653287 CAAGTTATGTCTCTGGAACACTAAATA 57.347 33.333 0.00 0.00 0.00 1.40
5463 14298 9.654663 AAGTTATGTCTCTGGAACACTAAATAC 57.345 33.333 0.00 0.00 0.00 1.89
5464 14299 9.036980 AGTTATGTCTCTGGAACACTAAATACT 57.963 33.333 0.00 0.00 0.00 2.12
5465 14300 9.088512 GTTATGTCTCTGGAACACTAAATACTG 57.911 37.037 0.00 0.00 0.00 2.74
5466 14301 6.665992 TGTCTCTGGAACACTAAATACTGT 57.334 37.500 0.00 0.00 0.00 3.55
5467 14302 7.062749 TGTCTCTGGAACACTAAATACTGTT 57.937 36.000 0.00 0.00 33.19 3.16
5468 14303 8.185506 TGTCTCTGGAACACTAAATACTGTTA 57.814 34.615 0.00 0.00 30.59 2.41
5469 14304 8.304596 TGTCTCTGGAACACTAAATACTGTTAG 58.695 37.037 0.00 0.00 37.16 2.34
5470 14305 8.521176 GTCTCTGGAACACTAAATACTGTTAGA 58.479 37.037 0.00 0.00 35.45 2.10
5471 14306 9.085645 TCTCTGGAACACTAAATACTGTTAGAA 57.914 33.333 0.00 0.00 35.45 2.10
5472 14307 9.141400 CTCTGGAACACTAAATACTGTTAGAAC 57.859 37.037 0.00 0.00 35.45 3.01
5473 14308 8.644216 TCTGGAACACTAAATACTGTTAGAACA 58.356 33.333 0.00 0.00 35.45 3.18
5474 14309 9.268268 CTGGAACACTAAATACTGTTAGAACAA 57.732 33.333 0.00 0.00 38.66 2.83
5475 14310 9.616156 TGGAACACTAAATACTGTTAGAACAAA 57.384 29.630 0.00 0.00 38.66 2.83
5476 14311 9.874215 GGAACACTAAATACTGTTAGAACAAAC 57.126 33.333 0.00 0.00 38.66 2.93
5477 14312 9.874215 GAACACTAAATACTGTTAGAACAAACC 57.126 33.333 0.00 0.00 38.66 3.27
5478 14313 8.387190 ACACTAAATACTGTTAGAACAAACCC 57.613 34.615 0.00 0.00 38.66 4.11
5479 14314 7.994334 ACACTAAATACTGTTAGAACAAACCCA 59.006 33.333 0.00 0.00 38.66 4.51
5480 14315 8.842280 CACTAAATACTGTTAGAACAAACCCAA 58.158 33.333 0.00 0.00 38.66 4.12
5481 14316 9.582648 ACTAAATACTGTTAGAACAAACCCAAT 57.417 29.630 0.00 0.00 38.66 3.16
5483 14318 6.737254 ATACTGTTAGAACAAACCCAATCG 57.263 37.500 0.00 0.00 38.66 3.34
5484 14319 4.710324 ACTGTTAGAACAAACCCAATCGA 58.290 39.130 0.00 0.00 38.66 3.59
5485 14320 5.127491 ACTGTTAGAACAAACCCAATCGAA 58.873 37.500 0.00 0.00 38.66 3.71
5486 14321 5.591067 ACTGTTAGAACAAACCCAATCGAAA 59.409 36.000 0.00 0.00 38.66 3.46
5487 14322 6.264518 ACTGTTAGAACAAACCCAATCGAAAT 59.735 34.615 0.00 0.00 38.66 2.17
5488 14323 6.442952 TGTTAGAACAAACCCAATCGAAATG 58.557 36.000 0.00 0.00 35.67 2.32
5489 14324 6.039941 TGTTAGAACAAACCCAATCGAAATGT 59.960 34.615 0.00 0.00 35.67 2.71
5490 14325 7.228906 TGTTAGAACAAACCCAATCGAAATGTA 59.771 33.333 0.00 0.00 35.67 2.29
5491 14326 6.009115 AGAACAAACCCAATCGAAATGTAC 57.991 37.500 0.00 0.00 0.00 2.90
5492 14327 5.768164 AGAACAAACCCAATCGAAATGTACT 59.232 36.000 0.00 0.00 0.00 2.73
5493 14328 6.938030 AGAACAAACCCAATCGAAATGTACTA 59.062 34.615 0.00 0.00 0.00 1.82
5494 14329 7.446013 AGAACAAACCCAATCGAAATGTACTAA 59.554 33.333 0.00 0.00 0.00 2.24
5495 14330 7.696992 ACAAACCCAATCGAAATGTACTAAT 57.303 32.000 0.00 0.00 0.00 1.73
5496 14331 7.535139 ACAAACCCAATCGAAATGTACTAATG 58.465 34.615 0.00 0.00 0.00 1.90
5497 14332 5.751243 ACCCAATCGAAATGTACTAATGC 57.249 39.130 0.00 0.00 0.00 3.56
5498 14333 5.437060 ACCCAATCGAAATGTACTAATGCT 58.563 37.500 0.00 0.00 0.00 3.79
5499 14334 5.527582 ACCCAATCGAAATGTACTAATGCTC 59.472 40.000 0.00 0.00 0.00 4.26
5500 14335 5.760253 CCCAATCGAAATGTACTAATGCTCT 59.240 40.000 0.00 0.00 0.00 4.09
5501 14336 6.293081 CCCAATCGAAATGTACTAATGCTCTG 60.293 42.308 0.00 0.00 0.00 3.35
5502 14337 5.914085 ATCGAAATGTACTAATGCTCTGC 57.086 39.130 0.00 0.00 0.00 4.26
5503 14338 4.754322 TCGAAATGTACTAATGCTCTGCA 58.246 39.130 0.00 0.00 44.86 4.41
5504 14339 4.566759 TCGAAATGTACTAATGCTCTGCAC 59.433 41.667 0.00 0.00 43.04 4.57
5505 14340 4.260375 CGAAATGTACTAATGCTCTGCACC 60.260 45.833 0.00 0.00 43.04 5.01
5506 14341 4.494091 AATGTACTAATGCTCTGCACCT 57.506 40.909 0.00 0.00 43.04 4.00
5507 14342 3.251479 TGTACTAATGCTCTGCACCTG 57.749 47.619 0.00 0.00 43.04 4.00
5518 14353 0.607217 CTGCACCTGTGAGCCAATCA 60.607 55.000 0.51 0.00 34.79 2.57
5536 14371 6.857964 GCCAATCAAACGGATGTATATCAAAG 59.142 38.462 1.63 0.00 36.02 2.77
5543 14378 4.588951 ACGGATGTATATCAAAGAGAGGCA 59.411 41.667 1.63 0.00 34.90 4.75
5565 14400 5.636543 GCATCATATTATTTTGCCTTGCTCC 59.363 40.000 0.00 0.00 0.00 4.70
5570 14405 4.724074 TTATTTTGCCTTGCTCCATCTG 57.276 40.909 0.00 0.00 0.00 2.90
5581 14416 1.134159 GCTCCATCTGAATGTCTGCCT 60.134 52.381 0.00 0.00 0.00 4.75
5582 14417 2.103771 GCTCCATCTGAATGTCTGCCTA 59.896 50.000 0.00 0.00 0.00 3.93
5583 14418 3.244491 GCTCCATCTGAATGTCTGCCTAT 60.244 47.826 0.00 0.00 0.00 2.57
5584 14419 4.020751 GCTCCATCTGAATGTCTGCCTATA 60.021 45.833 0.00 0.00 0.00 1.31
5618 14454 0.392998 CTGTATCCACACCACCTGCC 60.393 60.000 0.00 0.00 0.00 4.85
5619 14455 1.130678 TGTATCCACACCACCTGCCA 61.131 55.000 0.00 0.00 0.00 4.92
5620 14456 0.392998 GTATCCACACCACCTGCCAG 60.393 60.000 0.00 0.00 0.00 4.85
5621 14457 2.196997 TATCCACACCACCTGCCAGC 62.197 60.000 0.00 0.00 0.00 4.85
5623 14459 4.584518 CACACCACCTGCCAGCCA 62.585 66.667 0.00 0.00 0.00 4.75
5624 14460 3.819652 ACACCACCTGCCAGCCAA 61.820 61.111 0.00 0.00 0.00 4.52
5625 14461 3.297620 CACCACCTGCCAGCCAAC 61.298 66.667 0.00 0.00 0.00 3.77
5626 14462 4.603535 ACCACCTGCCAGCCAACC 62.604 66.667 0.00 0.00 0.00 3.77
5627 14463 4.601794 CCACCTGCCAGCCAACCA 62.602 66.667 0.00 0.00 0.00 3.67
5628 14464 2.521465 CACCTGCCAGCCAACCAA 60.521 61.111 0.00 0.00 0.00 3.67
5629 14465 2.132996 CACCTGCCAGCCAACCAAA 61.133 57.895 0.00 0.00 0.00 3.28
5630 14466 2.133641 ACCTGCCAGCCAACCAAAC 61.134 57.895 0.00 0.00 0.00 2.93
5631 14467 2.336088 CTGCCAGCCAACCAAACG 59.664 61.111 0.00 0.00 0.00 3.60
5632 14468 2.441164 TGCCAGCCAACCAAACGT 60.441 55.556 0.00 0.00 0.00 3.99
5633 14469 2.027460 GCCAGCCAACCAAACGTG 59.973 61.111 0.00 0.00 0.00 4.49
5634 14470 2.485795 GCCAGCCAACCAAACGTGA 61.486 57.895 0.00 0.00 0.00 4.35
5635 14471 2.010582 GCCAGCCAACCAAACGTGAA 62.011 55.000 0.00 0.00 0.00 3.18
5636 14472 0.248866 CCAGCCAACCAAACGTGAAC 60.249 55.000 0.00 0.00 0.00 3.18
5637 14473 0.453793 CAGCCAACCAAACGTGAACA 59.546 50.000 0.00 0.00 0.00 3.18
5638 14474 0.738389 AGCCAACCAAACGTGAACAG 59.262 50.000 0.00 0.00 0.00 3.16
5639 14475 0.454196 GCCAACCAAACGTGAACAGT 59.546 50.000 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 9.672673 AGCTATCTCACATACATGTTTTAAGTT 57.327 29.630 2.30 0.00 39.39 2.66
52 53 6.968263 AGAAAGCTAGCTATCTCACATACA 57.032 37.500 19.70 0.00 0.00 2.29
56 57 5.667539 ACAAGAAAGCTAGCTATCTCACA 57.332 39.130 19.70 0.00 0.00 3.58
57 58 5.293079 CCAACAAGAAAGCTAGCTATCTCAC 59.707 44.000 19.70 6.19 0.00 3.51
58 59 5.187772 TCCAACAAGAAAGCTAGCTATCTCA 59.812 40.000 19.70 0.00 0.00 3.27
59 60 5.522097 GTCCAACAAGAAAGCTAGCTATCTC 59.478 44.000 19.70 14.74 0.00 2.75
61 62 4.572795 GGTCCAACAAGAAAGCTAGCTATC 59.427 45.833 19.70 0.00 0.00 2.08
62 63 4.518249 GGTCCAACAAGAAAGCTAGCTAT 58.482 43.478 19.70 4.27 0.00 2.97
68 84 2.568623 ATCGGTCCAACAAGAAAGCT 57.431 45.000 0.00 0.00 0.00 3.74
103 119 5.152623 TCACTTGCTAGCTAGTTGTTCAT 57.847 39.130 26.17 3.46 30.18 2.57
109 125 3.007398 AGTGCTTCACTTGCTAGCTAGTT 59.993 43.478 26.17 9.89 42.59 2.24
135 155 8.402472 AGAAAAACGTGTGATGAGTATTTTTCA 58.598 29.630 16.96 0.00 42.69 2.69
136 156 8.782533 AGAAAAACGTGTGATGAGTATTTTTC 57.217 30.769 9.98 9.98 41.51 2.29
137 157 9.581099 AAAGAAAAACGTGTGATGAGTATTTTT 57.419 25.926 0.00 0.00 32.15 1.94
236 261 5.350633 CAGAGTCGTACTACTGTAGCTAGT 58.649 45.833 14.55 0.47 34.71 2.57
269 294 8.613922 TGCAGATCAAATGAGGGAGATATATA 57.386 34.615 0.00 0.00 0.00 0.86
298 323 0.805322 CGTGATGAGGAGTGAGCAGC 60.805 60.000 0.00 0.00 0.00 5.25
413 459 3.058501 CGCCAACAATTCTAACGGAAAGT 60.059 43.478 0.00 0.00 37.49 2.66
450 496 6.650390 GCACACAAGATAAAACCAATGGATTT 59.350 34.615 6.16 9.80 32.59 2.17
487 533 0.100503 AAAACTGTGGCTTCGCACAC 59.899 50.000 0.00 0.00 38.08 3.82
488 534 0.380378 GAAAACTGTGGCTTCGCACA 59.620 50.000 0.00 0.00 0.00 4.57
550 620 7.956328 TGAGTCCTCTGTATTACATGTTAGT 57.044 36.000 2.30 0.00 0.00 2.24
619 1415 0.678048 GGGAAGTAGGTGCAGGCTTG 60.678 60.000 0.00 0.00 0.00 4.01
622 1418 1.078143 CTGGGAAGTAGGTGCAGGC 60.078 63.158 0.00 0.00 0.00 4.85
786 1602 6.459066 TGAACAAACACCAAGAATTCAAACA 58.541 32.000 8.44 0.00 0.00 2.83
877 1724 8.954834 AGGATAATCAGATTCAGTCACTAGAT 57.045 34.615 0.00 0.00 0.00 1.98
998 1865 1.874299 ATCCAGAACCCCCGCCATTT 61.874 55.000 0.00 0.00 0.00 2.32
1029 1896 1.155889 CAAGCATGCTGGTCACGTAA 58.844 50.000 23.48 0.00 0.00 3.18
1090 2000 1.584724 AGGTCTTTGATCCCATCGGT 58.415 50.000 0.00 0.00 0.00 4.69
1219 2129 1.374125 CGACGATGTCAGTGGCCAA 60.374 57.895 7.24 0.00 32.09 4.52
1323 2233 3.296709 GATGTCGTGGGCGTGGAGT 62.297 63.158 0.00 0.00 39.49 3.85
1477 2387 2.456119 CGGACCGCTCAATCAGTGC 61.456 63.158 0.00 0.00 0.00 4.40
2041 2951 8.985805 GGTATTATATTGAGTTTGGGAAGTACG 58.014 37.037 0.00 0.00 0.00 3.67
2069 3003 0.465460 ACACTGTGGTGCCAAACGAT 60.465 50.000 13.09 0.00 46.57 3.73
2144 3150 9.860898 GTGAAATTTAAGTCAAGGAAGCATTAT 57.139 29.630 0.00 0.00 0.00 1.28
2158 3285 5.754890 ACTCGTGTTACGGTGAAATTTAAGT 59.245 36.000 1.24 0.00 42.81 2.24
2172 3299 4.510340 ACCAACTTGATGAACTCGTGTTAC 59.490 41.667 2.32 0.00 36.39 2.50
2245 4176 6.073003 CGGAATAATCCACTAATTGAGAAGCC 60.073 42.308 0.00 0.00 46.97 4.35
2250 4181 6.525629 AGTCCGGAATAATCCACTAATTGAG 58.474 40.000 5.23 0.00 46.97 3.02
2252 4183 8.671384 TTAAGTCCGGAATAATCCACTAATTG 57.329 34.615 5.23 0.00 46.97 2.32
2272 4208 6.721318 TCCCTGATAATTGCTCAACTTAAGT 58.279 36.000 1.12 1.12 0.00 2.24
2303 4239 7.625185 GCAAGTAGAAACTAATTGAGAAGCTGG 60.625 40.741 18.52 0.00 33.75 4.85
2310 4246 7.819900 AGTACCTGCAAGTAGAAACTAATTGAG 59.180 37.037 18.52 13.25 33.75 3.02
2342 4397 5.765182 TCAACTTCTGGTTCATTTTCCTCTC 59.235 40.000 0.00 0.00 35.74 3.20
2386 4441 6.861572 CCATCACATTTTGCTATAATCTGCAG 59.138 38.462 7.63 7.63 40.46 4.41
2502 4560 6.128172 CCTTTGACATTTGAGATACTGACCAC 60.128 42.308 0.00 0.00 0.00 4.16
2779 4837 3.488553 CGAATGACATCATGCATGTTGCT 60.489 43.478 29.28 19.57 46.53 3.91
2817 9473 1.683917 AGTGCTTCATCCCTAGCTACG 59.316 52.381 0.00 0.00 38.22 3.51
2878 9534 6.378710 AGACAACCTAAGAAAACTTTGAGC 57.621 37.500 0.00 0.00 0.00 4.26
2919 9575 4.264253 TCCACTCAAATTCATCGCATTCT 58.736 39.130 0.00 0.00 0.00 2.40
2924 9580 2.359900 ACCTCCACTCAAATTCATCGC 58.640 47.619 0.00 0.00 0.00 4.58
2963 9619 6.829298 TCCAGTTACTATCAGTGTCCTAAGAG 59.171 42.308 0.00 0.00 0.00 2.85
2964 9620 6.728411 TCCAGTTACTATCAGTGTCCTAAGA 58.272 40.000 0.00 0.00 0.00 2.10
2980 9636 5.589050 ACTGAAGTTTGAGGTTTCCAGTTAC 59.411 40.000 0.00 0.00 0.00 2.50
2998 9654 4.330250 ACCAATGAATCACCAGACTGAAG 58.670 43.478 3.32 0.00 0.00 3.02
3004 9660 4.927267 AGGTAACCAATGAATCACCAGA 57.073 40.909 0.00 0.00 37.17 3.86
3084 9740 3.814842 TCAAGTGCTTGAGTTGGTACATG 59.185 43.478 10.26 0.00 43.90 3.21
3243 9902 7.171167 GTGTCATCCATGTCAAGATATCTCAAG 59.829 40.741 5.51 0.00 0.00 3.02
3258 9917 3.325870 ACTTACACGTGTGTCATCCATG 58.674 45.455 30.83 13.18 43.74 3.66
3298 9957 5.049129 GTGCACTCAAATTTGTAAGAGCTCT 60.049 40.000 21.37 11.45 0.00 4.09
3324 9983 3.947834 CAGTATAGGCTGGAAACCCAAAG 59.052 47.826 0.00 0.00 32.40 2.77
3433 10092 2.031674 GCCTTTGCAGCCAACAAGGT 62.032 55.000 12.91 0.00 37.27 3.50
3477 10136 4.261741 CCACATTTCAAACCAAGAGAGGTG 60.262 45.833 0.00 0.00 42.25 4.00
3617 10282 6.355638 CGACGACCAAAATATCTTTCTATGC 58.644 40.000 0.00 0.00 0.00 3.14
3678 10343 4.332268 GCTACAATCTTCAAGCTCTCAAGG 59.668 45.833 0.00 0.00 32.18 3.61
3697 10362 1.448013 GCAGGTGTTCGAGGGCTAC 60.448 63.158 0.00 0.00 0.00 3.58
3896 10567 2.130193 CCTCCCATTCCTCCATTGAGA 58.870 52.381 0.00 0.00 41.42 3.27
3898 10569 2.130193 CTCCTCCCATTCCTCCATTGA 58.870 52.381 0.00 0.00 0.00 2.57
3899 10570 1.849039 ACTCCTCCCATTCCTCCATTG 59.151 52.381 0.00 0.00 0.00 2.82
3957 10628 3.970842 AGAAGTGATACGAAGGTCCTCT 58.029 45.455 0.00 0.00 0.00 3.69
3983 10654 1.327690 TGGAGGCATACGACCCAGTC 61.328 60.000 0.00 0.00 0.00 3.51
4040 11561 5.914743 TGGAGACATTGGACGTTCCATATTC 60.915 44.000 7.43 5.01 40.63 1.75
4165 11686 1.936547 CTCGAGCTTTGGGCAATACTC 59.063 52.381 0.00 0.00 44.79 2.59
4170 11691 1.308069 GCATCTCGAGCTTTGGGCAA 61.308 55.000 7.81 0.00 44.79 4.52
4207 11728 1.711060 CTCAGCTCGAGTCTCCGGAC 61.711 65.000 15.13 0.00 42.41 4.79
4422 11943 4.019858 TGGAGGACTCAGATGTGTAGAAG 58.980 47.826 1.32 0.00 0.00 2.85
4442 11963 7.337480 TGATGAATATTTGTCTCCATGTTGG 57.663 36.000 0.00 0.00 39.43 3.77
4598 12276 0.597568 CGATCCTGGCAAGCAAAACA 59.402 50.000 0.00 0.00 0.00 2.83
4708 12445 9.880157 ACTCAAAACTAGTAGAAGTTGTAACAA 57.120 29.630 3.59 0.00 39.62 2.83
4783 13500 4.020573 CCATATCCCTGCATGCATTTGATT 60.021 41.667 22.97 10.72 0.00 2.57
4791 13508 0.112995 TTCCCCATATCCCTGCATGC 59.887 55.000 11.82 11.82 0.00 4.06
4900 13698 1.599916 GCTAGATAGTCCGCCACGAAC 60.600 57.143 0.00 0.00 0.00 3.95
4904 13702 0.315568 CCAGCTAGATAGTCCGCCAC 59.684 60.000 0.00 0.00 0.00 5.01
4953 13764 3.988379 TGCTTGCACTAAACAAAGGAG 57.012 42.857 0.00 0.00 0.00 3.69
4962 13773 4.651778 ACTCCATTAGTTGCTTGCACTAA 58.348 39.130 14.76 14.76 40.26 2.24
4989 13816 3.323403 AGAACAGAGCAAAGCAGAGTAGT 59.677 43.478 0.00 0.00 0.00 2.73
5000 13832 3.136763 CTGCTTTCAGAGAACAGAGCAA 58.863 45.455 6.20 0.00 42.95 3.91
5070 13904 1.011968 CGAATGAAAGACACCCGCGA 61.012 55.000 8.23 0.00 0.00 5.87
5083 13917 6.464222 ACATAGTTTTCCAGAGAACGAATGA 58.536 36.000 17.97 0.00 32.84 2.57
5088 13922 9.543018 GAAATAAACATAGTTTTCCAGAGAACG 57.457 33.333 0.03 0.00 0.00 3.95
5110 13945 8.546083 AGACTATTGACTGGTCTATCAGAAAT 57.454 34.615 0.00 0.18 43.28 2.17
5114 13949 7.870826 CAGTAGACTATTGACTGGTCTATCAG 58.129 42.308 0.00 0.00 46.03 2.90
5159 13994 4.971830 CAGTCATTTGTGTTGTTGCAGTAG 59.028 41.667 0.00 0.00 0.00 2.57
5208 14043 1.003118 AGTTACAAATCAGCAGCCGGA 59.997 47.619 5.05 0.00 0.00 5.14
5220 14055 9.952030 TGAATTCCTATGACATACAGTTACAAA 57.048 29.630 2.27 0.00 0.00 2.83
5298 14133 1.071019 CATCGTCGTGACCTTCGTGG 61.071 60.000 0.00 0.00 42.93 4.94
5299 14134 0.109919 TCATCGTCGTGACCTTCGTG 60.110 55.000 0.00 0.00 0.00 4.35
5301 14136 2.638329 GTCATCGTCGTGACCTTCG 58.362 57.895 13.60 0.00 42.04 3.79
5307 14142 1.212751 CAGCAGGTCATCGTCGTGA 59.787 57.895 0.00 0.00 0.00 4.35
5310 14145 0.799917 CAGTCAGCAGGTCATCGTCG 60.800 60.000 0.00 0.00 0.00 5.12
5311 14146 0.459237 CCAGTCAGCAGGTCATCGTC 60.459 60.000 0.00 0.00 0.00 4.20
5313 14148 0.463204 ATCCAGTCAGCAGGTCATCG 59.537 55.000 0.00 0.00 0.00 3.84
5383 14218 1.627834 AGACAGAGCCCCAGAAGAAAG 59.372 52.381 0.00 0.00 0.00 2.62
5439 14274 9.088512 CAGTATTTAGTGTTCCAGAGACATAAC 57.911 37.037 0.00 0.00 0.00 1.89
5440 14275 8.812972 ACAGTATTTAGTGTTCCAGAGACATAA 58.187 33.333 0.00 0.00 36.50 1.90
5441 14276 8.362464 ACAGTATTTAGTGTTCCAGAGACATA 57.638 34.615 0.00 0.00 36.50 2.29
5442 14277 7.246171 ACAGTATTTAGTGTTCCAGAGACAT 57.754 36.000 0.00 0.00 36.50 3.06
5443 14278 6.665992 ACAGTATTTAGTGTTCCAGAGACA 57.334 37.500 0.00 0.00 36.50 3.41
5444 14279 8.521176 TCTAACAGTATTTAGTGTTCCAGAGAC 58.479 37.037 12.78 0.00 44.20 3.36
5445 14280 8.645814 TCTAACAGTATTTAGTGTTCCAGAGA 57.354 34.615 12.78 8.53 44.20 3.10
5446 14281 9.141400 GTTCTAACAGTATTTAGTGTTCCAGAG 57.859 37.037 12.78 6.73 44.20 3.35
5447 14282 8.644216 TGTTCTAACAGTATTTAGTGTTCCAGA 58.356 33.333 12.78 9.38 44.20 3.86
5448 14283 8.827177 TGTTCTAACAGTATTTAGTGTTCCAG 57.173 34.615 12.78 7.58 44.20 3.86
5449 14284 9.616156 TTTGTTCTAACAGTATTTAGTGTTCCA 57.384 29.630 12.78 5.42 44.20 3.53
5450 14285 9.874215 GTTTGTTCTAACAGTATTTAGTGTTCC 57.126 33.333 12.78 3.44 44.20 3.62
5451 14286 9.874215 GGTTTGTTCTAACAGTATTTAGTGTTC 57.126 33.333 12.78 2.21 44.20 3.18
5453 14288 7.994334 TGGGTTTGTTCTAACAGTATTTAGTGT 59.006 33.333 0.00 0.00 41.37 3.55
5454 14289 8.385898 TGGGTTTGTTCTAACAGTATTTAGTG 57.614 34.615 0.00 0.00 40.50 2.74
5455 14290 8.983702 TTGGGTTTGTTCTAACAGTATTTAGT 57.016 30.769 0.00 0.00 40.50 2.24
5457 14292 8.723311 CGATTGGGTTTGTTCTAACAGTATTTA 58.277 33.333 0.00 0.00 40.50 1.40
5458 14293 7.446013 TCGATTGGGTTTGTTCTAACAGTATTT 59.554 33.333 0.00 0.00 40.50 1.40
5459 14294 6.938030 TCGATTGGGTTTGTTCTAACAGTATT 59.062 34.615 0.00 0.00 40.50 1.89
5460 14295 6.469410 TCGATTGGGTTTGTTCTAACAGTAT 58.531 36.000 0.00 0.00 40.50 2.12
5461 14296 5.856156 TCGATTGGGTTTGTTCTAACAGTA 58.144 37.500 0.00 0.00 40.50 2.74
5462 14297 4.710324 TCGATTGGGTTTGTTCTAACAGT 58.290 39.130 0.00 0.00 40.50 3.55
5463 14298 5.682943 TTCGATTGGGTTTGTTCTAACAG 57.317 39.130 0.00 0.00 40.50 3.16
5464 14299 6.039941 ACATTTCGATTGGGTTTGTTCTAACA 59.960 34.615 0.00 0.00 37.08 2.41
5465 14300 6.443792 ACATTTCGATTGGGTTTGTTCTAAC 58.556 36.000 0.00 0.00 0.00 2.34
5466 14301 6.642707 ACATTTCGATTGGGTTTGTTCTAA 57.357 33.333 0.00 0.00 0.00 2.10
5467 14302 6.938030 AGTACATTTCGATTGGGTTTGTTCTA 59.062 34.615 0.00 0.00 0.00 2.10
5468 14303 5.768164 AGTACATTTCGATTGGGTTTGTTCT 59.232 36.000 0.00 0.00 0.00 3.01
5469 14304 6.009115 AGTACATTTCGATTGGGTTTGTTC 57.991 37.500 0.00 0.00 0.00 3.18
5470 14305 7.513371 TTAGTACATTTCGATTGGGTTTGTT 57.487 32.000 0.00 0.00 0.00 2.83
5471 14306 7.535139 CATTAGTACATTTCGATTGGGTTTGT 58.465 34.615 0.00 0.00 0.00 2.83
5472 14307 6.472163 GCATTAGTACATTTCGATTGGGTTTG 59.528 38.462 0.00 0.00 0.00 2.93
5473 14308 6.377146 AGCATTAGTACATTTCGATTGGGTTT 59.623 34.615 0.00 0.00 0.00 3.27
5474 14309 5.885912 AGCATTAGTACATTTCGATTGGGTT 59.114 36.000 0.00 0.00 0.00 4.11
5475 14310 5.437060 AGCATTAGTACATTTCGATTGGGT 58.563 37.500 0.00 0.00 0.00 4.51
5476 14311 5.760253 AGAGCATTAGTACATTTCGATTGGG 59.240 40.000 0.00 0.00 0.00 4.12
5477 14312 6.653183 CAGAGCATTAGTACATTTCGATTGG 58.347 40.000 0.00 0.00 0.00 3.16
5478 14313 6.132056 GCAGAGCATTAGTACATTTCGATTG 58.868 40.000 0.00 0.00 0.00 2.67
5479 14314 5.817296 TGCAGAGCATTAGTACATTTCGATT 59.183 36.000 0.00 0.00 31.71 3.34
5480 14315 5.235186 GTGCAGAGCATTAGTACATTTCGAT 59.765 40.000 0.00 0.00 41.91 3.59
5481 14316 4.566759 GTGCAGAGCATTAGTACATTTCGA 59.433 41.667 0.00 0.00 41.91 3.71
5482 14317 4.260375 GGTGCAGAGCATTAGTACATTTCG 60.260 45.833 0.00 0.00 41.91 3.46
5483 14318 4.878397 AGGTGCAGAGCATTAGTACATTTC 59.122 41.667 0.00 0.00 41.91 2.17
5484 14319 4.637534 CAGGTGCAGAGCATTAGTACATTT 59.362 41.667 0.00 0.00 41.91 2.32
5485 14320 4.194640 CAGGTGCAGAGCATTAGTACATT 58.805 43.478 0.00 0.00 41.91 2.71
5486 14321 3.198635 ACAGGTGCAGAGCATTAGTACAT 59.801 43.478 0.00 0.00 41.91 2.29
5487 14322 2.567169 ACAGGTGCAGAGCATTAGTACA 59.433 45.455 0.00 0.00 41.91 2.90
5488 14323 2.932614 CACAGGTGCAGAGCATTAGTAC 59.067 50.000 0.00 0.00 41.91 2.73
5489 14324 2.831526 TCACAGGTGCAGAGCATTAGTA 59.168 45.455 0.00 0.00 41.91 1.82
5490 14325 1.625315 TCACAGGTGCAGAGCATTAGT 59.375 47.619 0.00 0.00 41.91 2.24
5491 14326 2.277969 CTCACAGGTGCAGAGCATTAG 58.722 52.381 0.00 0.00 41.91 1.73
5492 14327 2.391616 CTCACAGGTGCAGAGCATTA 57.608 50.000 0.00 0.00 41.91 1.90
5493 14328 3.244764 CTCACAGGTGCAGAGCATT 57.755 52.632 0.00 0.00 41.91 3.56
5497 14332 0.322277 ATTGGCTCACAGGTGCAGAG 60.322 55.000 0.00 0.00 35.26 3.35
5498 14333 0.321919 GATTGGCTCACAGGTGCAGA 60.322 55.000 0.00 0.00 35.26 4.26
5499 14334 0.607217 TGATTGGCTCACAGGTGCAG 60.607 55.000 0.00 0.00 35.26 4.41
5500 14335 0.178995 TTGATTGGCTCACAGGTGCA 60.179 50.000 0.00 0.00 35.26 4.57
5501 14336 0.961019 TTTGATTGGCTCACAGGTGC 59.039 50.000 0.00 0.00 32.17 5.01
5502 14337 1.069022 CGTTTGATTGGCTCACAGGTG 60.069 52.381 0.00 0.00 32.17 4.00
5503 14338 1.238439 CGTTTGATTGGCTCACAGGT 58.762 50.000 0.00 0.00 32.17 4.00
5504 14339 0.523072 CCGTTTGATTGGCTCACAGG 59.477 55.000 0.00 0.00 32.17 4.00
5505 14340 1.522668 TCCGTTTGATTGGCTCACAG 58.477 50.000 0.00 0.00 32.17 3.66
5506 14341 1.811965 CATCCGTTTGATTGGCTCACA 59.188 47.619 0.00 0.00 32.17 3.58
5507 14342 1.812571 ACATCCGTTTGATTGGCTCAC 59.187 47.619 0.00 0.00 32.17 3.51
5518 14353 5.992217 GCCTCTCTTTGATATACATCCGTTT 59.008 40.000 0.00 0.00 0.00 3.60
5543 14378 6.982160 TGGAGCAAGGCAAAATAATATGAT 57.018 33.333 0.00 0.00 0.00 2.45
5565 14400 8.080417 CCATTTTTATAGGCAGACATTCAGATG 58.920 37.037 0.00 0.00 39.25 2.90
5570 14405 6.039717 TGCTCCATTTTTATAGGCAGACATTC 59.960 38.462 0.00 0.00 0.00 2.67
5581 14416 8.710239 TGGATACAGTAGTGCTCCATTTTTATA 58.290 33.333 15.27 0.00 46.17 0.98
5582 14417 7.573710 TGGATACAGTAGTGCTCCATTTTTAT 58.426 34.615 15.27 0.00 46.17 1.40
5583 14418 6.953101 TGGATACAGTAGTGCTCCATTTTTA 58.047 36.000 15.27 0.00 46.17 1.52
5584 14419 5.815581 TGGATACAGTAGTGCTCCATTTTT 58.184 37.500 15.27 0.00 46.17 1.94
5618 14454 0.453793 TGTTCACGTTTGGTTGGCTG 59.546 50.000 0.00 0.00 0.00 4.85
5619 14455 0.738389 CTGTTCACGTTTGGTTGGCT 59.262 50.000 0.00 0.00 0.00 4.75
5620 14456 0.454196 ACTGTTCACGTTTGGTTGGC 59.546 50.000 0.00 0.00 0.00 4.52


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.