Multiple sequence alignment - TraesCS3A01G099800

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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 TraesCS3A01G099800 chr3A 100.000 4749 0 0 1 4749 64309156 64304408 0.000000e+00 8770.0
1 TraesCS3A01G099800 chr3A 89.385 358 21 6 2412 2768 64304852 64304511 7.300000e-118 435.0
2 TraesCS3A01G099800 chr3A 89.385 358 21 6 4305 4646 64306745 64306389 7.300000e-118 435.0
3 TraesCS3A01G099800 chr3D 88.852 1785 154 25 2284 4042 51784607 51782842 0.000000e+00 2152.0
4 TraesCS3A01G099800 chr3D 85.358 1325 99 35 456 1740 51786270 51785001 0.000000e+00 1284.0
5 TraesCS3A01G099800 chr3D 91.061 358 15 4 4305 4646 51784471 51784115 7.200000e-128 468.0
6 TraesCS3A01G099800 chr3D 86.822 258 25 4 1948 2201 51784859 51784607 3.620000e-71 279.0
7 TraesCS3A01G099800 chr3D 95.484 155 6 1 4160 4314 545302494 545302341 3.670000e-61 246.0
8 TraesCS3A01G099800 chr3D 83.491 212 15 11 65 264 53101597 53101800 3.780000e-41 180.0
9 TraesCS3A01G099800 chr3D 86.275 102 13 1 460 560 518131308 518131207 5.020000e-20 110.0
10 TraesCS3A01G099800 chr3D 94.737 57 3 0 286 342 51786716 51786660 6.550000e-14 89.8
11 TraesCS3A01G099800 chr3B 85.418 1831 176 28 2284 4042 82838347 82836536 0.000000e+00 1818.0
12 TraesCS3A01G099800 chr3B 84.559 1373 106 52 406 1740 82849780 82848476 0.000000e+00 1264.0
13 TraesCS3A01G099800 chr3B 81.406 1124 110 53 801 1857 82839691 82838600 0.000000e+00 826.0
14 TraesCS3A01G099800 chr3B 83.794 833 100 13 2285 3087 82847994 82847167 0.000000e+00 758.0
15 TraesCS3A01G099800 chr3B 91.961 510 34 6 3088 3590 82847121 82846612 0.000000e+00 708.0
16 TraesCS3A01G099800 chr3B 88.866 476 39 10 834 1300 83444171 83444641 1.480000e-159 573.0
17 TraesCS3A01G099800 chr3B 90.370 405 23 6 3575 3963 82846049 82845645 7.040000e-143 518.0
18 TraesCS3A01G099800 chr3B 85.618 445 46 9 3458 3887 82835303 82834862 7.250000e-123 451.0
19 TraesCS3A01G099800 chr3B 86.236 356 29 9 4309 4646 82838219 82837866 7.510000e-98 368.0
20 TraesCS3A01G099800 chr3B 85.278 360 34 7 4305 4646 82847867 82847509 2.100000e-93 353.0
21 TraesCS3A01G099800 chr3B 86.495 311 21 5 1 291 82851941 82851632 5.930000e-84 322.0
22 TraesCS3A01G099800 chr3B 79.352 494 52 25 1402 1857 83445011 83445492 7.720000e-78 302.0
23 TraesCS3A01G099800 chr3B 85.768 267 24 6 1948 2201 82838612 82838347 2.180000e-68 270.0
24 TraesCS3A01G099800 chr3B 93.168 161 10 1 1965 2124 82848217 82848057 7.950000e-58 235.0
25 TraesCS3A01G099800 chr3B 81.818 209 27 5 59 264 83515014 83515214 1.060000e-36 165.0
26 TraesCS3A01G099800 chr3B 91.379 116 10 0 4305 4420 83445884 83445999 4.920000e-35 159.0
27 TraesCS3A01G099800 chr3B 81.507 146 6 9 166 291 83272974 83273118 3.020000e-17 100.0
28 TraesCS3A01G099800 chr2D 97.260 146 4 0 4160 4305 336814589 336814734 1.020000e-61 248.0
29 TraesCS3A01G099800 chr2D 97.241 145 4 0 4160 4304 129126228 129126372 3.670000e-61 246.0
30 TraesCS3A01G099800 chr7D 96.622 148 5 0 4160 4307 232918545 232918398 3.670000e-61 246.0
31 TraesCS3A01G099800 chr7D 94.839 155 8 0 4160 4314 130631272 130631118 4.750000e-60 243.0
32 TraesCS3A01G099800 chr4D 97.241 145 4 0 4160 4304 87487718 87487862 3.670000e-61 246.0
33 TraesCS3A01G099800 chr4D 96.026 151 5 1 4160 4310 318875465 318875614 1.320000e-60 244.0
34 TraesCS3A01G099800 chr4A 97.241 145 4 0 4160 4304 332848925 332849069 3.670000e-61 246.0
35 TraesCS3A01G099800 chr1A 96.622 148 5 0 4160 4307 139651516 139651369 3.670000e-61 246.0
36 TraesCS3A01G099800 chr5B 90.141 142 12 2 1161 1301 491032940 491033080 2.920000e-42 183.0
37 TraesCS3A01G099800 chr5A 89.209 139 15 0 1163 1301 520093073 520093211 1.760000e-39 174.0
38 TraesCS3A01G099800 chr5A 85.385 130 16 3 443 571 419214398 419214271 1.070000e-26 132.0
39 TraesCS3A01G099800 chr5D 87.333 150 19 0 1152 1301 408999459 408999608 6.320000e-39 172.0
40 TraesCS3A01G099800 chr6D 88.136 118 13 1 460 577 331537984 331537868 6.410000e-29 139.0
41 TraesCS3A01G099800 chr7A 86.842 114 14 1 460 572 640372068 640372181 4.990000e-25 126.0
42 TraesCS3A01G099800 chr7A 84.375 64 9 1 460 522 39113645 39113708 1.430000e-05 62.1
43 TraesCS3A01G099800 chr1B 96.970 33 0 1 2199 2231 653257836 653257805 2.000000e-03 54.7


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 TraesCS3A01G099800 chr3A 64304408 64309156 4748 True 8770.000000 8770 100.000000 1 4749 1 chr3A.!!$R1 4748
1 TraesCS3A01G099800 chr3A 64304511 64306745 2234 True 435.000000 435 89.385000 2412 4646 2 chr3A.!!$R2 2234
2 TraesCS3A01G099800 chr3D 51782842 51786716 3874 True 854.560000 2152 89.366000 286 4646 5 chr3D.!!$R3 4360
3 TraesCS3A01G099800 chr3B 82834862 82839691 4829 True 746.600000 1818 84.889200 801 4646 5 chr3B.!!$R1 3845
4 TraesCS3A01G099800 chr3B 82845645 82851941 6296 True 594.000000 1264 87.946429 1 4646 7 chr3B.!!$R2 4645
5 TraesCS3A01G099800 chr3B 83444171 83445999 1828 False 344.666667 573 86.532333 834 4420 3 chr3B.!!$F3 3586

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
983 2999 0.811616 CCCAACAGCTTAGCTAGGCG 60.812 60.0 20.73 17.35 36.40 5.52 F
1419 3787 0.321387 CTCTCAGCTTTCAGCCTGCA 60.321 55.0 0.00 0.00 43.77 4.41 F
1884 4500 0.033504 ATTCTGGAACACGCACGAGT 59.966 50.0 0.00 0.00 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1865 4481 0.033504 ACTCGTGCGTGTTCCAGAAT 59.966 50.000 0.00 0.0 0.0 2.40 R
2322 4977 1.680338 AAGCACAACACTGAGGGTTC 58.320 50.000 0.00 0.0 0.0 3.62 R
4651 8609 1.463056 CGTGTCACATTTGCATACGGT 59.537 47.619 3.42 0.0 0.0 4.83 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
28 29 2.424379 GGATGGTTTGTAATCCCCTCCC 60.424 54.545 0.00 0.00 37.04 4.30
31 32 3.543661 TGGTTTGTAATCCCCTCCCTAA 58.456 45.455 0.00 0.00 0.00 2.69
32 33 4.123745 TGGTTTGTAATCCCCTCCCTAAT 58.876 43.478 0.00 0.00 0.00 1.73
35 36 5.516044 GTTTGTAATCCCCTCCCTAATTGT 58.484 41.667 0.00 0.00 0.00 2.71
40 41 2.815158 TCCCCTCCCTAATTGTTTTGC 58.185 47.619 0.00 0.00 0.00 3.68
52 53 8.306761 CCCTAATTGTTTTGCTTGACTTTCTAT 58.693 33.333 0.00 0.00 0.00 1.98
64 65 8.956426 TGCTTGACTTTCTATTATTGTTAAGGG 58.044 33.333 0.00 0.00 0.00 3.95
81 82 3.560636 AGGGTTTTATGGATGTCTCGG 57.439 47.619 0.00 0.00 0.00 4.63
85 86 3.531538 GTTTTATGGATGTCTCGGCTGA 58.468 45.455 0.00 0.00 0.00 4.26
102 103 4.935808 CGGCTGAGTTTTGACCTTACTTAT 59.064 41.667 0.00 0.00 0.00 1.73
131 132 4.532314 ACTAGTGTAGTAGTTGTTGGGC 57.468 45.455 0.00 0.00 37.23 5.36
151 152 2.483876 CCACTTGTATATGTGGCTCGG 58.516 52.381 10.91 0.00 42.84 4.63
189 190 3.693578 TGTGCAAAGTGTCAATCTTGTCA 59.306 39.130 0.00 0.00 0.00 3.58
209 221 8.552083 TTGTCAATATGAAGATCCGATTATGG 57.448 34.615 0.00 0.00 0.00 2.74
220 232 1.536766 CCGATTATGGCATTCACGCAT 59.463 47.619 4.78 0.00 0.00 4.73
245 265 7.312899 TCATATATACATACTGGTCACTTGCG 58.687 38.462 0.00 0.00 0.00 4.85
256 276 1.330521 GTCACTTGCGAGCAACTTCAA 59.669 47.619 6.39 0.00 0.00 2.69
266 286 2.893489 GAGCAACTTCAAAATGGGTCCT 59.107 45.455 0.00 0.00 0.00 3.85
290 600 7.121168 CCTTATACCTTCTTCAATTCTTGCACA 59.879 37.037 0.00 0.00 0.00 4.57
295 605 5.221106 CCTTCTTCAATTCTTGCACACAGAA 60.221 40.000 1.93 1.93 0.00 3.02
308 618 3.635331 CACACAGAAGCTTGGTGAATTG 58.365 45.455 26.26 14.87 36.42 2.32
342 652 6.098124 CCCCAAAATTCCTATGTGCTATCAAA 59.902 38.462 0.00 0.00 0.00 2.69
343 653 7.364585 CCCCAAAATTCCTATGTGCTATCAAAA 60.365 37.037 0.00 0.00 0.00 2.44
344 654 7.492344 CCCAAAATTCCTATGTGCTATCAAAAC 59.508 37.037 0.00 0.00 0.00 2.43
345 655 8.034215 CCAAAATTCCTATGTGCTATCAAAACA 58.966 33.333 0.00 0.00 0.00 2.83
346 656 9.590451 CAAAATTCCTATGTGCTATCAAAACAT 57.410 29.630 0.00 0.00 38.13 2.71
390 732 6.476378 AGTTAACAGAAATACCTGATGCACT 58.524 36.000 8.61 0.00 37.59 4.40
404 746 7.739825 ACCTGATGCACTTTCATATATACAGT 58.260 34.615 0.00 0.00 0.00 3.55
492 2491 5.733676 TGTGTGCATCTTAGCTATTCTGAA 58.266 37.500 0.00 0.00 34.99 3.02
502 2501 4.277515 AGCTATTCTGAAGCAAGTGTCA 57.722 40.909 4.33 0.00 42.62 3.58
526 2525 5.585047 ACTCTTTATGTTTTGTATCCGCTCC 59.415 40.000 0.00 0.00 0.00 4.70
538 2537 1.953559 TCCGCTCCATGCTACATTTC 58.046 50.000 0.00 0.00 40.11 2.17
604 2606 2.959707 AGAGCCGGTATAGGACAAAGAG 59.040 50.000 1.90 0.00 0.00 2.85
605 2607 1.413077 AGCCGGTATAGGACAAAGAGC 59.587 52.381 1.90 0.00 0.00 4.09
606 2608 1.413077 GCCGGTATAGGACAAAGAGCT 59.587 52.381 1.90 0.00 0.00 4.09
607 2609 2.803492 GCCGGTATAGGACAAAGAGCTG 60.803 54.545 1.90 0.00 0.00 4.24
622 2624 1.601759 GCTGGCTCACTTGCTCCAA 60.602 57.895 0.00 0.00 0.00 3.53
623 2625 1.174712 GCTGGCTCACTTGCTCCAAA 61.175 55.000 0.00 0.00 0.00 3.28
652 2655 5.389098 CCTTGTGTTAATTAACGGTGTCTCG 60.389 44.000 20.51 6.22 39.00 4.04
683 2690 5.044558 TGTGATGCGTGCGACTATTAATTA 58.955 37.500 0.00 0.00 0.00 1.40
696 2703 9.724839 GCGACTATTAATTAAAACCAGCAAATA 57.275 29.630 1.21 0.00 0.00 1.40
706 2713 9.749340 ATTAAAACCAGCAAATAACCTACTACT 57.251 29.630 0.00 0.00 0.00 2.57
731 2738 4.085357 ACTAACACAGCTTTCATGGTGA 57.915 40.909 6.62 0.00 38.63 4.02
735 2742 4.510038 ACACAGCTTTCATGGTGATTTC 57.490 40.909 6.62 0.00 38.63 2.17
748 2755 3.646162 TGGTGATTTCGGGCTACTATCAT 59.354 43.478 0.00 0.00 0.00 2.45
749 2756 4.836175 TGGTGATTTCGGGCTACTATCATA 59.164 41.667 0.00 0.00 0.00 2.15
750 2757 5.047306 TGGTGATTTCGGGCTACTATCATAG 60.047 44.000 0.00 0.00 0.00 2.23
830 2842 8.420222 AGTCAGATCTGTTTCTCCATTATACTG 58.580 37.037 21.92 0.00 0.00 2.74
832 2844 9.421399 TCAGATCTGTTTCTCCATTATACTGTA 57.579 33.333 21.92 0.00 0.00 2.74
864 2876 7.199541 TGAATTGAAGAGAAAGAGAAAGCAG 57.800 36.000 0.00 0.00 0.00 4.24
879 2891 1.132500 AGCAGGGCCATCTACCTAAC 58.868 55.000 6.18 0.00 34.71 2.34
890 2902 3.818961 TCTACCTAACGACAACGACAG 57.181 47.619 0.00 0.00 42.66 3.51
905 2920 7.360101 CGACAACGACAGATTCCTTCTTTTAAT 60.360 37.037 0.00 0.00 42.66 1.40
906 2921 8.842358 ACAACGACAGATTCCTTCTTTTAATA 57.158 30.769 0.00 0.00 29.93 0.98
907 2922 9.280174 ACAACGACAGATTCCTTCTTTTAATAA 57.720 29.630 0.00 0.00 29.93 1.40
937 2953 9.099454 GACTAATGATCCTTTAACTACAACTGG 57.901 37.037 0.00 0.00 0.00 4.00
942 2958 1.467342 CTTTAACTACAACTGGGCCGC 59.533 52.381 0.00 0.00 0.00 6.53
983 2999 0.811616 CCCAACAGCTTAGCTAGGCG 60.812 60.000 20.73 17.35 36.40 5.52
1006 3024 2.545731 GCGAGGAGGAGAGAATGAAAC 58.454 52.381 0.00 0.00 0.00 2.78
1010 3028 5.510520 GCGAGGAGGAGAGAATGAAACATAT 60.511 44.000 0.00 0.00 0.00 1.78
1036 3066 2.674380 GCTTGGCACTGGGAGTGG 60.674 66.667 5.90 0.00 46.01 4.00
1125 3170 1.358830 ATCTCCCTGGCTTCCATGGG 61.359 60.000 13.02 11.70 39.34 4.00
1146 3191 1.494960 CTCTTCCCTTCTCCCTGGAG 58.505 60.000 6.88 6.88 43.21 3.86
1170 3215 1.406887 GGGTATGTGCAAGTGGACGAT 60.407 52.381 0.00 0.00 39.39 3.73
1221 3266 3.151022 CAGTCGGAGAGGAGCCCC 61.151 72.222 0.00 0.00 36.95 5.80
1319 3645 7.311364 TCGGTAACTATTTGCTTAACCATTC 57.689 36.000 0.00 0.00 0.00 2.67
1338 3667 6.610020 ACCATTCTCCATTTTCATCATCATGT 59.390 34.615 0.00 0.00 0.00 3.21
1346 3675 7.611079 TCCATTTTCATCATCATGTTGTGACTA 59.389 33.333 3.76 0.27 40.28 2.59
1382 3750 0.667993 TACTTGTTGGTTGCTGCTGC 59.332 50.000 8.89 8.89 40.20 5.25
1383 3751 1.039233 ACTTGTTGGTTGCTGCTGCT 61.039 50.000 17.00 0.00 40.48 4.24
1384 3752 0.596600 CTTGTTGGTTGCTGCTGCTG 60.597 55.000 17.00 0.77 40.48 4.41
1385 3753 2.355481 GTTGGTTGCTGCTGCTGC 60.355 61.111 22.51 22.51 40.48 5.25
1386 3754 2.520020 TTGGTTGCTGCTGCTGCT 60.520 55.556 27.67 0.00 40.48 4.24
1387 3755 2.852180 TTGGTTGCTGCTGCTGCTG 61.852 57.895 27.67 16.73 40.48 4.41
1418 3786 1.025647 CCTCTCAGCTTTCAGCCTGC 61.026 60.000 0.00 0.00 43.77 4.85
1419 3787 0.321387 CTCTCAGCTTTCAGCCTGCA 60.321 55.000 0.00 0.00 43.77 4.41
1420 3788 0.321387 TCTCAGCTTTCAGCCTGCAG 60.321 55.000 6.78 6.78 43.77 4.41
1425 3793 1.004511 AGCTTTCAGCCTGCAGATTCT 59.995 47.619 17.39 6.28 43.77 2.40
1439 3807 1.553704 AGATTCTTACACCGGTGGTCC 59.446 52.381 36.47 17.93 31.02 4.46
1487 3855 5.808366 TCTTGGACCAAGGCTAGTATATG 57.192 43.478 29.76 5.02 41.33 1.78
1512 3931 0.529378 CTTCTGCCAGCCACCAATTC 59.471 55.000 0.00 0.00 0.00 2.17
1542 3990 8.244494 TGTAAGCATAATCGCATCTTCTAATC 57.756 34.615 0.00 0.00 0.00 1.75
1556 4008 5.423015 TCTTCTAATCATGCTTCTGTCCAC 58.577 41.667 0.00 0.00 0.00 4.02
1563 4015 0.836606 TGCTTCTGTCCACTCACCAA 59.163 50.000 0.00 0.00 0.00 3.67
1564 4016 1.211703 TGCTTCTGTCCACTCACCAAA 59.788 47.619 0.00 0.00 0.00 3.28
1654 4106 0.669625 GTACAAGTCCTGCGACACCC 60.670 60.000 0.00 0.00 41.87 4.61
1720 4174 8.982685 GTCCAGTCACATACAGTATTTATCATG 58.017 37.037 0.00 0.00 0.00 3.07
1721 4175 8.704668 TCCAGTCACATACAGTATTTATCATGT 58.295 33.333 0.00 0.00 0.00 3.21
1722 4176 9.330063 CCAGTCACATACAGTATTTATCATGTT 57.670 33.333 0.00 0.00 0.00 2.71
1740 4194 7.107639 TCATGTTCCGTCTTATCACTCATAA 57.892 36.000 0.00 0.00 0.00 1.90
1741 4195 7.726216 TCATGTTCCGTCTTATCACTCATAAT 58.274 34.615 0.00 0.00 0.00 1.28
1742 4196 8.204160 TCATGTTCCGTCTTATCACTCATAATT 58.796 33.333 0.00 0.00 0.00 1.40
1743 4197 9.476202 CATGTTCCGTCTTATCACTCATAATTA 57.524 33.333 0.00 0.00 0.00 1.40
1744 4198 9.698309 ATGTTCCGTCTTATCACTCATAATTAG 57.302 33.333 0.00 0.00 0.00 1.73
1745 4199 8.141909 TGTTCCGTCTTATCACTCATAATTAGG 58.858 37.037 0.00 0.00 0.00 2.69
1747 4201 8.246430 TCCGTCTTATCACTCATAATTAGGTT 57.754 34.615 0.00 0.00 0.00 3.50
1750 4234 9.314321 CGTCTTATCACTCATAATTAGGTTTGT 57.686 33.333 0.00 0.00 0.00 2.83
1806 4415 3.664107 TCTGAAACTTCCCATCTTCACG 58.336 45.455 0.00 0.00 0.00 4.35
1807 4416 2.744202 CTGAAACTTCCCATCTTCACGG 59.256 50.000 0.00 0.00 0.00 4.94
1814 4423 1.211949 TCCCATCTTCACGGATTTCCC 59.788 52.381 0.00 0.00 0.00 3.97
1816 4425 2.423373 CCCATCTTCACGGATTTCCCAT 60.423 50.000 0.00 0.00 34.14 4.00
1836 4445 5.356751 CCCATTACTTTTACATGCTGTGCTA 59.643 40.000 0.00 0.00 0.00 3.49
1859 4475 9.734620 GCTACATGCACATAATATTTTGAAGAA 57.265 29.630 12.19 0.79 42.31 2.52
1881 4497 2.399396 AAAATTCTGGAACACGCACG 57.601 45.000 0.00 0.00 0.00 5.34
1882 4498 1.588674 AAATTCTGGAACACGCACGA 58.411 45.000 0.00 0.00 0.00 4.35
1883 4499 1.148310 AATTCTGGAACACGCACGAG 58.852 50.000 0.00 0.00 0.00 4.18
1884 4500 0.033504 ATTCTGGAACACGCACGAGT 59.966 50.000 0.00 0.00 0.00 4.18
1885 4501 0.874175 TTCTGGAACACGCACGAGTG 60.874 55.000 0.00 0.00 46.83 3.51
1897 4513 2.194800 CACGAGTGTGCGTATCATCT 57.805 50.000 0.00 0.00 43.59 2.90
1898 4514 3.334272 CACGAGTGTGCGTATCATCTA 57.666 47.619 0.00 0.00 43.59 1.98
1899 4515 3.890128 CACGAGTGTGCGTATCATCTAT 58.110 45.455 0.00 0.00 43.59 1.98
1900 4516 4.290969 CACGAGTGTGCGTATCATCTATT 58.709 43.478 0.00 0.00 43.59 1.73
1901 4517 5.449304 CACGAGTGTGCGTATCATCTATTA 58.551 41.667 0.00 0.00 43.59 0.98
1902 4518 5.912955 CACGAGTGTGCGTATCATCTATTAA 59.087 40.000 0.00 0.00 43.59 1.40
1903 4519 6.416750 CACGAGTGTGCGTATCATCTATTAAA 59.583 38.462 0.00 0.00 43.59 1.52
1904 4520 6.976349 ACGAGTGTGCGTATCATCTATTAAAA 59.024 34.615 0.00 0.00 43.61 1.52
1905 4521 7.490079 ACGAGTGTGCGTATCATCTATTAAAAA 59.510 33.333 0.00 0.00 43.61 1.94
1926 4542 5.825593 AAAAGGGAAAGGGGAGAAAAATC 57.174 39.130 0.00 0.00 0.00 2.17
1927 4543 3.474798 AGGGAAAGGGGAGAAAAATCC 57.525 47.619 0.00 0.00 38.76 3.01
1936 4552 3.458044 GGAGAAAAATCCCCTCCAGTT 57.542 47.619 0.00 0.00 44.42 3.16
1937 4553 4.586306 GGAGAAAAATCCCCTCCAGTTA 57.414 45.455 0.00 0.00 44.42 2.24
1938 4554 4.527944 GGAGAAAAATCCCCTCCAGTTAG 58.472 47.826 0.00 0.00 44.42 2.34
1939 4555 3.948473 GAGAAAAATCCCCTCCAGTTAGC 59.052 47.826 0.00 0.00 0.00 3.09
1940 4556 3.333680 AGAAAAATCCCCTCCAGTTAGCA 59.666 43.478 0.00 0.00 0.00 3.49
1941 4557 3.372440 AAAATCCCCTCCAGTTAGCAG 57.628 47.619 0.00 0.00 0.00 4.24
1942 4558 1.972588 AATCCCCTCCAGTTAGCAGT 58.027 50.000 0.00 0.00 0.00 4.40
1943 4559 2.868964 ATCCCCTCCAGTTAGCAGTA 57.131 50.000 0.00 0.00 0.00 2.74
1944 4560 2.634639 TCCCCTCCAGTTAGCAGTAA 57.365 50.000 0.00 0.00 0.00 2.24
1945 4561 3.130734 TCCCCTCCAGTTAGCAGTAAT 57.869 47.619 0.00 0.00 0.00 1.89
1946 4562 3.460825 TCCCCTCCAGTTAGCAGTAATT 58.539 45.455 0.00 0.00 0.00 1.40
1947 4563 4.627015 TCCCCTCCAGTTAGCAGTAATTA 58.373 43.478 0.00 0.00 0.00 1.40
1948 4564 4.407945 TCCCCTCCAGTTAGCAGTAATTAC 59.592 45.833 7.57 7.57 0.00 1.89
1949 4565 4.163458 CCCCTCCAGTTAGCAGTAATTACA 59.837 45.833 17.65 0.00 0.00 2.41
1950 4566 5.338871 CCCCTCCAGTTAGCAGTAATTACAA 60.339 44.000 17.65 0.43 0.00 2.41
1951 4567 6.357367 CCCTCCAGTTAGCAGTAATTACAAT 58.643 40.000 17.65 5.57 0.00 2.71
1952 4568 7.419750 CCCCTCCAGTTAGCAGTAATTACAATA 60.420 40.741 17.65 4.66 0.00 1.90
1953 4569 8.157476 CCCTCCAGTTAGCAGTAATTACAATAT 58.843 37.037 17.65 3.58 0.00 1.28
1954 4570 9.561069 CCTCCAGTTAGCAGTAATTACAATATT 57.439 33.333 17.65 1.69 0.00 1.28
2029 4663 2.371179 CCATCTGCAGTGGTATGAGGAT 59.629 50.000 20.76 0.51 31.96 3.24
2125 4759 5.390387 ACCTTTCAAATTGCTAAGGGTACA 58.610 37.500 21.89 0.00 41.14 2.90
2145 4782 8.459635 GGGTACATAGAAATTTCCTTCTTGTTC 58.540 37.037 14.61 8.85 36.95 3.18
2164 4810 8.617809 TCTTGTTCCTTATTACAAATATTCCGC 58.382 33.333 0.00 0.00 34.17 5.54
2167 4813 7.771361 TGTTCCTTATTACAAATATTCCGCTCA 59.229 33.333 0.00 0.00 0.00 4.26
2173 4819 7.907214 ATTACAAATATTCCGCTCATCCTAC 57.093 36.000 0.00 0.00 0.00 3.18
2200 4846 8.538409 AAATTGAGAACTTTGGCATGAAATAC 57.462 30.769 0.00 0.00 0.00 1.89
2201 4847 6.899393 TTGAGAACTTTGGCATGAAATACT 57.101 33.333 0.00 0.00 0.00 2.12
2202 4848 6.500684 TGAGAACTTTGGCATGAAATACTC 57.499 37.500 0.00 0.00 0.00 2.59
2203 4849 5.415701 TGAGAACTTTGGCATGAAATACTCC 59.584 40.000 0.00 0.00 0.00 3.85
2204 4850 4.706962 AGAACTTTGGCATGAAATACTCCC 59.293 41.667 0.00 0.00 0.00 4.30
2205 4851 4.322057 ACTTTGGCATGAAATACTCCCT 57.678 40.909 0.00 0.00 0.00 4.20
2206 4852 4.273318 ACTTTGGCATGAAATACTCCCTC 58.727 43.478 0.00 0.00 0.00 4.30
2207 4853 4.018050 ACTTTGGCATGAAATACTCCCTCT 60.018 41.667 0.00 0.00 0.00 3.69
2208 4854 3.565764 TGGCATGAAATACTCCCTCTG 57.434 47.619 0.00 0.00 0.00 3.35
2209 4855 2.846206 TGGCATGAAATACTCCCTCTGT 59.154 45.455 0.00 0.00 0.00 3.41
2210 4856 4.037222 TGGCATGAAATACTCCCTCTGTA 58.963 43.478 0.00 0.00 0.00 2.74
2211 4857 4.660303 TGGCATGAAATACTCCCTCTGTAT 59.340 41.667 0.00 0.00 32.60 2.29
2212 4858 5.221722 TGGCATGAAATACTCCCTCTGTATC 60.222 44.000 0.00 0.00 31.08 2.24
2213 4859 5.221722 GGCATGAAATACTCCCTCTGTATCA 60.222 44.000 0.00 0.00 31.08 2.15
2214 4860 6.291377 GCATGAAATACTCCCTCTGTATCAA 58.709 40.000 0.00 0.00 31.08 2.57
2215 4861 6.767902 GCATGAAATACTCCCTCTGTATCAAA 59.232 38.462 0.00 0.00 31.08 2.69
2216 4862 7.283127 GCATGAAATACTCCCTCTGTATCAAAA 59.717 37.037 0.00 0.00 31.08 2.44
2217 4863 9.347240 CATGAAATACTCCCTCTGTATCAAAAT 57.653 33.333 0.00 0.00 31.08 1.82
2218 4864 8.737168 TGAAATACTCCCTCTGTATCAAAATG 57.263 34.615 0.00 0.00 31.08 2.32
2219 4865 8.328758 TGAAATACTCCCTCTGTATCAAAATGT 58.671 33.333 0.00 0.00 31.08 2.71
2220 4866 9.832445 GAAATACTCCCTCTGTATCAAAATGTA 57.168 33.333 0.00 0.00 31.08 2.29
2222 4868 9.838339 AATACTCCCTCTGTATCAAAATGTAAG 57.162 33.333 0.00 0.00 31.08 2.34
2223 4869 6.653989 ACTCCCTCTGTATCAAAATGTAAGG 58.346 40.000 0.00 0.00 0.00 2.69
2224 4870 5.437060 TCCCTCTGTATCAAAATGTAAGGC 58.563 41.667 0.00 0.00 0.00 4.35
2225 4871 4.273480 CCCTCTGTATCAAAATGTAAGGCG 59.727 45.833 0.00 0.00 0.00 5.52
2226 4872 4.876107 CCTCTGTATCAAAATGTAAGGCGT 59.124 41.667 0.00 0.00 0.00 5.68
2227 4873 5.354234 CCTCTGTATCAAAATGTAAGGCGTT 59.646 40.000 0.00 0.00 0.00 4.84
2228 4874 6.128007 CCTCTGTATCAAAATGTAAGGCGTTT 60.128 38.462 0.00 0.00 37.88 3.60
2229 4875 7.209471 TCTGTATCAAAATGTAAGGCGTTTT 57.791 32.000 0.00 0.00 44.53 2.43
2230 4876 7.653647 TCTGTATCAAAATGTAAGGCGTTTTT 58.346 30.769 0.00 0.00 42.53 1.94
2231 4877 7.593273 TCTGTATCAAAATGTAAGGCGTTTTTG 59.407 33.333 0.00 2.46 42.53 2.44
2232 4878 7.426410 TGTATCAAAATGTAAGGCGTTTTTGA 58.574 30.769 15.26 15.26 42.53 2.69
2233 4879 7.593273 TGTATCAAAATGTAAGGCGTTTTTGAG 59.407 33.333 17.00 3.50 42.53 3.02
2234 4880 5.897050 TCAAAATGTAAGGCGTTTTTGAGT 58.103 33.333 10.94 0.00 42.53 3.41
2235 4881 5.974751 TCAAAATGTAAGGCGTTTTTGAGTC 59.025 36.000 10.94 0.00 42.53 3.36
2236 4882 5.767816 AAATGTAAGGCGTTTTTGAGTCT 57.232 34.783 0.00 0.00 32.77 3.24
2237 4883 5.358298 AATGTAAGGCGTTTTTGAGTCTC 57.642 39.130 0.00 0.00 0.00 3.36
2238 4884 3.799366 TGTAAGGCGTTTTTGAGTCTCA 58.201 40.909 0.00 0.00 0.00 3.27
2239 4885 4.193090 TGTAAGGCGTTTTTGAGTCTCAA 58.807 39.130 11.36 11.36 34.03 3.02
2240 4886 4.819630 TGTAAGGCGTTTTTGAGTCTCAAT 59.180 37.500 15.95 1.57 36.11 2.57
2241 4887 4.489679 AAGGCGTTTTTGAGTCTCAATC 57.510 40.909 15.95 8.92 36.11 2.67
2242 4888 3.744660 AGGCGTTTTTGAGTCTCAATCT 58.255 40.909 15.95 5.08 36.11 2.40
2243 4889 4.894784 AGGCGTTTTTGAGTCTCAATCTA 58.105 39.130 15.95 0.00 36.11 1.98
2244 4890 5.305585 AGGCGTTTTTGAGTCTCAATCTAA 58.694 37.500 15.95 5.20 36.11 2.10
2245 4891 5.763204 AGGCGTTTTTGAGTCTCAATCTAAA 59.237 36.000 15.95 10.76 36.11 1.85
2246 4892 5.851703 GGCGTTTTTGAGTCTCAATCTAAAC 59.148 40.000 21.33 21.33 36.11 2.01
2247 4893 5.851703 GCGTTTTTGAGTCTCAATCTAAACC 59.148 40.000 23.37 16.79 36.11 3.27
2248 4894 6.371389 CGTTTTTGAGTCTCAATCTAAACCC 58.629 40.000 23.37 10.10 36.11 4.11
2249 4895 6.017440 CGTTTTTGAGTCTCAATCTAAACCCA 60.017 38.462 23.37 5.24 36.11 4.51
2250 4896 7.468084 CGTTTTTGAGTCTCAATCTAAACCCAA 60.468 37.037 23.37 9.73 36.11 4.12
2251 4897 7.889873 TTTTGAGTCTCAATCTAAACCCAAA 57.110 32.000 15.95 1.02 36.11 3.28
2252 4898 7.889873 TTTGAGTCTCAATCTAAACCCAAAA 57.110 32.000 15.95 0.00 36.11 2.44
2253 4899 7.889873 TTGAGTCTCAATCTAAACCCAAAAA 57.110 32.000 11.36 0.00 30.26 1.94
2273 4919 6.687081 AAAAACGTCTTCCAGTTTGATACA 57.313 33.333 0.00 0.00 40.07 2.29
2274 4920 6.877611 AAAACGTCTTCCAGTTTGATACAT 57.122 33.333 0.00 0.00 40.07 2.29
2275 4921 7.972832 AAAACGTCTTCCAGTTTGATACATA 57.027 32.000 0.00 0.00 40.07 2.29
2276 4922 7.596749 AAACGTCTTCCAGTTTGATACATAG 57.403 36.000 0.00 0.00 38.90 2.23
2277 4923 5.661458 ACGTCTTCCAGTTTGATACATAGG 58.339 41.667 0.00 0.00 0.00 2.57
2278 4924 5.050490 CGTCTTCCAGTTTGATACATAGGG 58.950 45.833 0.00 0.00 0.00 3.53
2279 4925 5.163447 CGTCTTCCAGTTTGATACATAGGGA 60.163 44.000 0.00 0.00 0.00 4.20
2280 4926 6.284459 GTCTTCCAGTTTGATACATAGGGAG 58.716 44.000 0.00 0.00 0.00 4.30
2281 4927 5.964477 TCTTCCAGTTTGATACATAGGGAGT 59.036 40.000 0.00 0.00 0.00 3.85
2282 4928 5.614324 TCCAGTTTGATACATAGGGAGTG 57.386 43.478 0.00 0.00 0.00 3.51
2322 4977 9.831737 CTCAAATAATCCTTGACTTTAGTGTTG 57.168 33.333 0.00 0.00 0.00 3.33
2386 5041 7.039722 TCTTTTCCAGGTATAGAAATGGGTT 57.960 36.000 0.00 0.00 32.33 4.11
4646 8604 7.151999 ACCGAAACATACAATGCAAGAATTA 57.848 32.000 0.00 0.00 0.00 1.40
4647 8605 7.771183 ACCGAAACATACAATGCAAGAATTAT 58.229 30.769 0.00 0.00 0.00 1.28
4648 8606 7.701924 ACCGAAACATACAATGCAAGAATTATG 59.298 33.333 0.00 0.00 0.00 1.90
4649 8607 7.914871 CCGAAACATACAATGCAAGAATTATGA 59.085 33.333 0.00 0.00 0.00 2.15
4650 8608 8.736742 CGAAACATACAATGCAAGAATTATGAC 58.263 33.333 0.00 0.00 0.00 3.06
4651 8609 9.571810 GAAACATACAATGCAAGAATTATGACA 57.428 29.630 0.00 0.00 0.00 3.58
4652 8610 8.915871 AACATACAATGCAAGAATTATGACAC 57.084 30.769 0.00 0.00 0.00 3.67
4653 8611 7.483307 ACATACAATGCAAGAATTATGACACC 58.517 34.615 0.00 0.00 0.00 4.16
4654 8612 4.985413 ACAATGCAAGAATTATGACACCG 58.015 39.130 0.00 0.00 0.00 4.94
4655 8613 4.458989 ACAATGCAAGAATTATGACACCGT 59.541 37.500 0.00 0.00 0.00 4.83
4656 8614 5.645929 ACAATGCAAGAATTATGACACCGTA 59.354 36.000 0.00 0.00 0.00 4.02
4657 8615 6.318648 ACAATGCAAGAATTATGACACCGTAT 59.681 34.615 0.00 0.00 0.00 3.06
4658 8616 5.733226 TGCAAGAATTATGACACCGTATG 57.267 39.130 0.00 0.00 0.00 2.39
4659 8617 4.035091 TGCAAGAATTATGACACCGTATGC 59.965 41.667 0.00 0.00 0.00 3.14
4660 8618 4.035091 GCAAGAATTATGACACCGTATGCA 59.965 41.667 0.00 0.00 0.00 3.96
4661 8619 5.448496 GCAAGAATTATGACACCGTATGCAA 60.448 40.000 0.00 0.00 0.00 4.08
4662 8620 6.550843 CAAGAATTATGACACCGTATGCAAA 58.449 36.000 0.00 0.00 0.00 3.68
4663 8621 6.942532 AGAATTATGACACCGTATGCAAAT 57.057 33.333 0.00 0.00 0.00 2.32
4664 8622 6.728200 AGAATTATGACACCGTATGCAAATG 58.272 36.000 0.00 0.00 0.00 2.32
4665 8623 6.318648 AGAATTATGACACCGTATGCAAATGT 59.681 34.615 0.00 0.00 0.00 2.71
4666 8624 3.763097 ATGACACCGTATGCAAATGTG 57.237 42.857 0.00 0.00 0.00 3.21
4667 8625 2.772287 TGACACCGTATGCAAATGTGA 58.228 42.857 13.71 0.00 0.00 3.58
4668 8626 2.482336 TGACACCGTATGCAAATGTGAC 59.518 45.455 13.71 9.27 0.00 3.67
4669 8627 2.482336 GACACCGTATGCAAATGTGACA 59.518 45.455 13.71 0.00 0.00 3.58
4670 8628 2.225491 ACACCGTATGCAAATGTGACAC 59.775 45.455 13.71 0.00 0.00 3.67
4671 8629 1.463056 ACCGTATGCAAATGTGACACG 59.537 47.619 0.22 0.00 0.00 4.49
4672 8630 1.463056 CCGTATGCAAATGTGACACGT 59.537 47.619 0.22 0.00 0.00 4.49
4673 8631 2.473868 CCGTATGCAAATGTGACACGTC 60.474 50.000 0.00 0.00 0.00 4.34
4674 8632 2.473868 CGTATGCAAATGTGACACGTCC 60.474 50.000 0.00 0.00 0.00 4.79
4675 8633 0.516877 ATGCAAATGTGACACGTCCG 59.483 50.000 0.00 0.00 0.00 4.79
4676 8634 1.206578 GCAAATGTGACACGTCCGG 59.793 57.895 0.00 0.00 0.00 5.14
4677 8635 1.206578 CAAATGTGACACGTCCGGC 59.793 57.895 0.00 0.00 0.00 6.13
4678 8636 1.964373 AAATGTGACACGTCCGGCC 60.964 57.895 0.00 0.00 0.00 6.13
4679 8637 2.668185 AAATGTGACACGTCCGGCCA 62.668 55.000 2.24 0.00 0.00 5.36
4680 8638 3.589654 ATGTGACACGTCCGGCCAG 62.590 63.158 2.24 0.00 0.00 4.85
4681 8639 4.295119 GTGACACGTCCGGCCAGT 62.295 66.667 2.24 0.00 0.00 4.00
4682 8640 3.542676 TGACACGTCCGGCCAGTT 61.543 61.111 2.24 0.00 0.00 3.16
4683 8641 2.201708 TGACACGTCCGGCCAGTTA 61.202 57.895 2.24 0.00 0.00 2.24
4684 8642 1.217244 GACACGTCCGGCCAGTTAT 59.783 57.895 2.24 0.00 0.00 1.89
4685 8643 0.804933 GACACGTCCGGCCAGTTATC 60.805 60.000 2.24 0.00 0.00 1.75
4686 8644 1.216977 CACGTCCGGCCAGTTATCA 59.783 57.895 2.24 0.00 0.00 2.15
4687 8645 0.390603 CACGTCCGGCCAGTTATCAA 60.391 55.000 2.24 0.00 0.00 2.57
4688 8646 0.390735 ACGTCCGGCCAGTTATCAAC 60.391 55.000 2.24 0.00 0.00 3.18
4689 8647 0.108329 CGTCCGGCCAGTTATCAACT 60.108 55.000 2.24 0.00 44.06 3.16
4690 8648 1.674817 CGTCCGGCCAGTTATCAACTT 60.675 52.381 2.24 0.00 40.46 2.66
4691 8649 2.417651 CGTCCGGCCAGTTATCAACTTA 60.418 50.000 2.24 0.00 40.46 2.24
4692 8650 3.602483 GTCCGGCCAGTTATCAACTTAA 58.398 45.455 2.24 0.00 40.46 1.85
4693 8651 4.004982 GTCCGGCCAGTTATCAACTTAAA 58.995 43.478 2.24 0.00 40.46 1.52
4694 8652 4.456566 GTCCGGCCAGTTATCAACTTAAAA 59.543 41.667 2.24 0.00 40.46 1.52
4695 8653 5.048573 GTCCGGCCAGTTATCAACTTAAAAA 60.049 40.000 2.24 0.00 40.46 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.514160 AGGGAGGGGATTACAAACCATC 59.486 50.000 0.00 0.00 34.52 3.51
52 53 9.762381 AGACATCCATAAAACCCTTAACAATAA 57.238 29.630 0.00 0.00 0.00 1.40
64 65 3.531538 TCAGCCGAGACATCCATAAAAC 58.468 45.455 0.00 0.00 0.00 2.43
66 67 2.766263 ACTCAGCCGAGACATCCATAAA 59.234 45.455 3.36 0.00 42.34 1.40
72 73 2.413453 GTCAAAACTCAGCCGAGACATC 59.587 50.000 3.36 0.00 42.34 3.06
81 82 8.947115 ACATAATAAGTAAGGTCAAAACTCAGC 58.053 33.333 0.00 0.00 0.00 4.26
151 152 4.703645 TGCACAGTGTAGAGATCACTAC 57.296 45.455 19.84 19.84 43.14 2.73
189 190 7.830697 TGAATGCCATAATCGGATCTTCATATT 59.169 33.333 0.00 0.00 0.00 1.28
209 221 8.271487 CAGTATGTATATATGATGCGTGAATGC 58.729 37.037 0.00 0.00 0.00 3.56
220 232 7.175990 TCGCAAGTGACCAGTATGTATATATGA 59.824 37.037 0.00 0.00 39.48 2.15
245 265 2.893489 AGGACCCATTTTGAAGTTGCTC 59.107 45.455 0.00 0.00 0.00 4.26
256 276 6.652205 TGAAGAAGGTATAAGGACCCATTT 57.348 37.500 0.00 0.00 40.74 2.32
290 600 4.460263 TGTACAATTCACCAAGCTTCTGT 58.540 39.130 0.00 0.00 0.00 3.41
295 605 2.162681 GCCTGTACAATTCACCAAGCT 58.837 47.619 0.00 0.00 0.00 3.74
367 709 6.743575 AGTGCATCAGGTATTTCTGTTAAC 57.256 37.500 0.00 0.00 36.25 2.01
426 2184 6.256539 ACTGTACAAATTCATCGTATCTGCAG 59.743 38.462 7.63 7.63 0.00 4.41
492 2491 6.095440 ACAAAACATAAAGAGTGACACTTGCT 59.905 34.615 10.01 0.00 0.00 3.91
502 2501 5.585047 GGAGCGGATACAAAACATAAAGAGT 59.415 40.000 0.00 0.00 0.00 3.24
538 2537 7.850982 CCGACAAAGGATGATTTTATTAACTCG 59.149 37.037 0.00 0.00 0.00 4.18
604 2606 1.174712 TTTGGAGCAAGTGAGCCAGC 61.175 55.000 0.00 0.00 34.23 4.85
605 2607 0.595095 GTTTGGAGCAAGTGAGCCAG 59.405 55.000 0.00 0.00 34.23 4.85
606 2608 0.823356 GGTTTGGAGCAAGTGAGCCA 60.823 55.000 0.00 0.00 34.23 4.75
607 2609 0.538287 AGGTTTGGAGCAAGTGAGCC 60.538 55.000 0.00 0.00 34.23 4.70
622 2624 4.763279 CCGTTAATTAACACAAGGGAGGTT 59.237 41.667 24.27 0.00 35.99 3.50
623 2625 4.202493 ACCGTTAATTAACACAAGGGAGGT 60.202 41.667 24.27 17.72 35.99 3.85
652 2655 2.738521 ACGCATCACACGAGCCAC 60.739 61.111 0.00 0.00 0.00 5.01
683 2690 8.380867 AGTAGTAGTAGGTTATTTGCTGGTTTT 58.619 33.333 0.00 0.00 0.00 2.43
696 2703 7.401246 AGCTGTGTTAGTAGTAGTAGTAGGTT 58.599 38.462 0.00 0.00 0.00 3.50
699 2706 8.944029 TGAAAGCTGTGTTAGTAGTAGTAGTAG 58.056 37.037 0.00 0.00 0.00 2.57
700 2707 8.853077 TGAAAGCTGTGTTAGTAGTAGTAGTA 57.147 34.615 0.00 0.00 0.00 1.82
701 2708 7.756395 TGAAAGCTGTGTTAGTAGTAGTAGT 57.244 36.000 0.00 0.00 0.00 2.73
702 2709 7.702772 CCATGAAAGCTGTGTTAGTAGTAGTAG 59.297 40.741 0.00 0.00 0.00 2.57
703 2710 7.177921 ACCATGAAAGCTGTGTTAGTAGTAGTA 59.822 37.037 0.00 0.00 0.00 1.82
704 2711 6.014499 ACCATGAAAGCTGTGTTAGTAGTAGT 60.014 38.462 0.00 0.00 0.00 2.73
705 2712 6.311445 CACCATGAAAGCTGTGTTAGTAGTAG 59.689 42.308 0.00 0.00 0.00 2.57
706 2713 6.014925 TCACCATGAAAGCTGTGTTAGTAGTA 60.015 38.462 0.00 0.00 0.00 1.82
707 2714 4.997395 CACCATGAAAGCTGTGTTAGTAGT 59.003 41.667 0.00 0.00 0.00 2.73
731 2738 7.956328 TGATACTATGATAGTAGCCCGAAAT 57.044 36.000 21.16 3.22 44.72 2.17
735 2742 7.810282 GCAATATGATACTATGATAGTAGCCCG 59.190 40.741 21.16 9.09 44.72 6.13
748 2755 3.576550 TGGCTGGACGCAATATGATACTA 59.423 43.478 0.00 0.00 41.67 1.82
749 2756 2.368548 TGGCTGGACGCAATATGATACT 59.631 45.455 0.00 0.00 41.67 2.12
750 2757 2.766313 TGGCTGGACGCAATATGATAC 58.234 47.619 0.00 0.00 41.67 2.24
788 2795 1.695242 TGACTCAACGCCCCTAGAAAA 59.305 47.619 0.00 0.00 0.00 2.29
791 2798 0.039180 TCTGACTCAACGCCCCTAGA 59.961 55.000 0.00 0.00 0.00 2.43
837 2849 8.636213 TGCTTTCTCTTTCTCTTCAATTCAATT 58.364 29.630 0.00 0.00 0.00 2.32
838 2850 8.174733 TGCTTTCTCTTTCTCTTCAATTCAAT 57.825 30.769 0.00 0.00 0.00 2.57
852 2864 1.357079 AGATGGCCCTGCTTTCTCTTT 59.643 47.619 0.00 0.00 0.00 2.52
864 2876 1.117150 TGTCGTTAGGTAGATGGCCC 58.883 55.000 0.00 0.00 0.00 5.80
879 2891 2.947852 AGAAGGAATCTGTCGTTGTCG 58.052 47.619 0.00 0.00 36.88 4.35
942 2958 1.421485 GAGCAGGACGCATCAAACG 59.579 57.895 0.00 0.00 46.13 3.60
983 2999 0.673437 CATTCTCTCCTCCTCGCCTC 59.327 60.000 0.00 0.00 0.00 4.70
1036 3066 1.416030 GATGAGGAGGAGGAGAAAGCC 59.584 57.143 0.00 0.00 0.00 4.35
1074 3113 4.080863 ACAGTGGTCTTGTTCTTCTCACTT 60.081 41.667 0.00 0.00 32.51 3.16
1125 3170 1.631071 CCAGGGAGAAGGGAAGAGGC 61.631 65.000 0.00 0.00 0.00 4.70
1128 3173 1.093408 TCTCCAGGGAGAAGGGAAGA 58.907 55.000 15.51 0.00 46.89 2.87
1146 3191 1.003118 TCCACTTGCACATACCCTGTC 59.997 52.381 0.00 0.00 35.29 3.51
1319 3645 6.750501 GTCACAACATGATGATGAAAATGGAG 59.249 38.462 10.29 0.00 40.28 3.86
1346 3675 9.651913 CCAACAAGTAAAATGGTTAAGCATATT 57.348 29.630 19.84 13.11 0.00 1.28
1387 3755 2.125188 GAGAGGACCTGCAGCAGC 60.125 66.667 17.81 4.06 42.57 5.25
1388 3756 1.218585 CTGAGAGGACCTGCAGCAG 59.781 63.158 16.23 16.23 0.00 4.24
1389 3757 3.385469 CTGAGAGGACCTGCAGCA 58.615 61.111 8.66 0.00 0.00 4.41
1390 3758 2.125188 GCTGAGAGGACCTGCAGC 60.125 66.667 23.06 23.06 45.64 5.25
1391 3759 0.324285 AAAGCTGAGAGGACCTGCAG 59.676 55.000 6.78 6.78 0.00 4.41
1418 3786 2.618053 GACCACCGGTGTAAGAATCTG 58.382 52.381 31.80 16.02 35.25 2.90
1419 3787 1.553704 GGACCACCGGTGTAAGAATCT 59.446 52.381 31.80 1.91 35.25 2.40
1420 3788 2.019948 GGACCACCGGTGTAAGAATC 57.980 55.000 31.80 17.92 35.25 2.52
1487 3855 0.957888 GTGGCTGGCAGAAGAGGAAC 60.958 60.000 20.86 0.00 0.00 3.62
1512 3931 6.418585 AGATGCGATTATGCTTACATGATG 57.581 37.500 0.00 0.00 37.04 3.07
1542 3990 1.271001 TGGTGAGTGGACAGAAGCATG 60.271 52.381 0.00 0.00 0.00 4.06
1563 4015 6.458210 CAGAAAGATTACATTGGCAACCTTT 58.542 36.000 0.00 5.77 0.00 3.11
1564 4016 5.047092 CCAGAAAGATTACATTGGCAACCTT 60.047 40.000 0.00 0.00 0.00 3.50
1654 4106 2.223688 TGACAATTTGGTCAACGGCTTG 60.224 45.455 0.78 0.00 44.34 4.01
1720 4174 8.142551 ACCTAATTATGAGTGATAAGACGGAAC 58.857 37.037 0.00 0.00 29.78 3.62
1721 4175 8.246430 ACCTAATTATGAGTGATAAGACGGAA 57.754 34.615 0.00 0.00 29.78 4.30
1722 4176 7.834881 ACCTAATTATGAGTGATAAGACGGA 57.165 36.000 0.00 0.00 29.78 4.69
1774 4383 3.498777 GGAAGTTTCAGAAGTAGTGGTGC 59.501 47.826 0.00 0.00 0.00 5.01
1806 4415 6.980397 CAGCATGTAAAAGTAATGGGAAATCC 59.020 38.462 0.00 0.00 0.00 3.01
1807 4416 7.992180 CAGCATGTAAAAGTAATGGGAAATC 57.008 36.000 0.00 0.00 0.00 2.17
1861 4477 2.356382 TCGTGCGTGTTCCAGAATTTTT 59.644 40.909 0.00 0.00 0.00 1.94
1862 4478 1.944024 TCGTGCGTGTTCCAGAATTTT 59.056 42.857 0.00 0.00 0.00 1.82
1863 4479 1.531149 CTCGTGCGTGTTCCAGAATTT 59.469 47.619 0.00 0.00 0.00 1.82
1864 4480 1.148310 CTCGTGCGTGTTCCAGAATT 58.852 50.000 0.00 0.00 0.00 2.17
1865 4481 0.033504 ACTCGTGCGTGTTCCAGAAT 59.966 50.000 0.00 0.00 0.00 2.40
1866 4482 0.874175 CACTCGTGCGTGTTCCAGAA 60.874 55.000 0.00 0.00 0.00 3.02
1867 4483 1.299850 CACTCGTGCGTGTTCCAGA 60.300 57.895 0.00 0.00 0.00 3.86
1868 4484 1.591594 ACACTCGTGCGTGTTCCAG 60.592 57.895 0.00 0.00 45.27 3.86
1869 4485 1.880796 CACACTCGTGCGTGTTCCA 60.881 57.895 5.43 0.00 45.27 3.53
1870 4486 2.928361 CACACTCGTGCGTGTTCC 59.072 61.111 5.43 0.00 45.27 3.62
1878 4494 2.194800 AGATGATACGCACACTCGTG 57.805 50.000 0.00 0.00 46.56 4.35
1879 4495 4.569761 AATAGATGATACGCACACTCGT 57.430 40.909 0.00 0.00 45.49 4.18
1880 4496 6.986424 TTTAATAGATGATACGCACACTCG 57.014 37.500 0.00 0.00 0.00 4.18
1903 4519 5.073144 GGATTTTTCTCCCCTTTCCCTTTTT 59.927 40.000 0.00 0.00 0.00 1.94
1904 4520 4.597507 GGATTTTTCTCCCCTTTCCCTTTT 59.402 41.667 0.00 0.00 0.00 2.27
1905 4521 4.168101 GGATTTTTCTCCCCTTTCCCTTT 58.832 43.478 0.00 0.00 0.00 3.11
1906 4522 3.791320 GGATTTTTCTCCCCTTTCCCTT 58.209 45.455 0.00 0.00 0.00 3.95
1907 4523 3.474798 GGATTTTTCTCCCCTTTCCCT 57.525 47.619 0.00 0.00 0.00 4.20
1916 4532 3.458044 AACTGGAGGGGATTTTTCTCC 57.542 47.619 0.00 0.00 45.36 3.71
1917 4533 3.948473 GCTAACTGGAGGGGATTTTTCTC 59.052 47.826 0.00 0.00 0.00 2.87
1918 4534 3.333680 TGCTAACTGGAGGGGATTTTTCT 59.666 43.478 0.00 0.00 0.00 2.52
1919 4535 3.696548 CTGCTAACTGGAGGGGATTTTTC 59.303 47.826 0.00 0.00 0.00 2.29
1920 4536 3.076032 ACTGCTAACTGGAGGGGATTTTT 59.924 43.478 0.00 0.00 38.54 1.94
1921 4537 2.649816 ACTGCTAACTGGAGGGGATTTT 59.350 45.455 0.00 0.00 38.54 1.82
1922 4538 2.279173 ACTGCTAACTGGAGGGGATTT 58.721 47.619 0.00 0.00 38.54 2.17
1923 4539 1.972588 ACTGCTAACTGGAGGGGATT 58.027 50.000 0.00 0.00 38.54 3.01
1924 4540 2.868964 TACTGCTAACTGGAGGGGAT 57.131 50.000 0.00 0.00 38.54 3.85
1925 4541 2.634639 TTACTGCTAACTGGAGGGGA 57.365 50.000 0.00 0.00 38.54 4.81
1926 4542 3.933861 AATTACTGCTAACTGGAGGGG 57.066 47.619 0.00 0.00 38.54 4.79
1927 4543 5.353394 TGTAATTACTGCTAACTGGAGGG 57.647 43.478 16.33 0.00 38.54 4.30
1928 4544 9.561069 AATATTGTAATTACTGCTAACTGGAGG 57.439 33.333 16.33 0.00 38.54 4.30
1994 4628 7.446319 CCACTGCAGATGGAGAAAATAATGATA 59.554 37.037 23.35 0.00 39.87 2.15
2145 4782 7.607991 AGGATGAGCGGAATATTTGTAATAAGG 59.392 37.037 0.00 0.00 0.00 2.69
2161 4807 4.191544 TCTCAATTTTGTAGGATGAGCGG 58.808 43.478 0.00 0.00 37.89 5.52
2163 4809 6.749923 AGTTCTCAATTTTGTAGGATGAGC 57.250 37.500 0.00 0.00 37.89 4.26
2164 4810 8.025445 CCAAAGTTCTCAATTTTGTAGGATGAG 58.975 37.037 0.00 0.00 36.65 2.90
2167 4813 6.267471 TGCCAAAGTTCTCAATTTTGTAGGAT 59.733 34.615 4.23 0.00 36.65 3.24
2173 4819 6.847956 TTCATGCCAAAGTTCTCAATTTTG 57.152 33.333 0.00 0.00 37.70 2.44
2200 4846 5.529060 GCCTTACATTTTGATACAGAGGGAG 59.471 44.000 0.00 0.00 0.00 4.30
2201 4847 5.437060 GCCTTACATTTTGATACAGAGGGA 58.563 41.667 0.00 0.00 0.00 4.20
2202 4848 4.273480 CGCCTTACATTTTGATACAGAGGG 59.727 45.833 0.00 0.00 0.00 4.30
2203 4849 4.876107 ACGCCTTACATTTTGATACAGAGG 59.124 41.667 0.00 0.00 0.00 3.69
2204 4850 6.422776 AACGCCTTACATTTTGATACAGAG 57.577 37.500 0.00 0.00 0.00 3.35
2205 4851 6.811253 AAACGCCTTACATTTTGATACAGA 57.189 33.333 0.00 0.00 0.00 3.41
2206 4852 7.593273 TCAAAAACGCCTTACATTTTGATACAG 59.407 33.333 8.07 0.00 43.18 2.74
2207 4853 7.426410 TCAAAAACGCCTTACATTTTGATACA 58.574 30.769 8.07 0.00 43.18 2.29
2208 4854 7.593644 ACTCAAAAACGCCTTACATTTTGATAC 59.406 33.333 11.53 0.00 45.43 2.24
2209 4855 7.653647 ACTCAAAAACGCCTTACATTTTGATA 58.346 30.769 11.53 0.00 45.43 2.15
2210 4856 6.512297 ACTCAAAAACGCCTTACATTTTGAT 58.488 32.000 11.53 2.61 45.43 2.57
2211 4857 5.897050 ACTCAAAAACGCCTTACATTTTGA 58.103 33.333 10.86 10.86 44.80 2.69
2212 4858 5.977129 AGACTCAAAAACGCCTTACATTTTG 59.023 36.000 0.00 0.00 41.69 2.44
2213 4859 6.144078 AGACTCAAAAACGCCTTACATTTT 57.856 33.333 0.00 0.00 0.00 1.82
2214 4860 5.298276 TGAGACTCAAAAACGCCTTACATTT 59.702 36.000 1.64 0.00 0.00 2.32
2215 4861 4.819630 TGAGACTCAAAAACGCCTTACATT 59.180 37.500 1.64 0.00 0.00 2.71
2216 4862 4.385825 TGAGACTCAAAAACGCCTTACAT 58.614 39.130 1.64 0.00 0.00 2.29
2217 4863 3.799366 TGAGACTCAAAAACGCCTTACA 58.201 40.909 1.64 0.00 0.00 2.41
2218 4864 4.806342 TTGAGACTCAAAAACGCCTTAC 57.194 40.909 15.58 0.00 32.71 2.34
2219 4865 5.305585 AGATTGAGACTCAAAAACGCCTTA 58.694 37.500 21.29 0.00 40.12 2.69
2220 4866 4.137543 AGATTGAGACTCAAAAACGCCTT 58.862 39.130 21.29 2.74 40.12 4.35
2221 4867 3.744660 AGATTGAGACTCAAAAACGCCT 58.255 40.909 21.29 3.49 40.12 5.52
2222 4868 5.607119 TTAGATTGAGACTCAAAAACGCC 57.393 39.130 21.29 7.29 40.12 5.68
2223 4869 5.851703 GGTTTAGATTGAGACTCAAAAACGC 59.148 40.000 24.29 17.97 40.12 4.84
2224 4870 6.017440 TGGGTTTAGATTGAGACTCAAAAACG 60.017 38.462 24.29 0.00 40.12 3.60
2225 4871 7.272037 TGGGTTTAGATTGAGACTCAAAAAC 57.728 36.000 23.76 23.76 40.12 2.43
2226 4872 7.889873 TTGGGTTTAGATTGAGACTCAAAAA 57.110 32.000 21.29 14.25 40.12 1.94
2227 4873 7.889873 TTTGGGTTTAGATTGAGACTCAAAA 57.110 32.000 21.29 9.11 40.12 2.44
2228 4874 7.889873 TTTTGGGTTTAGATTGAGACTCAAA 57.110 32.000 21.29 2.97 40.12 2.69
2229 4875 7.889873 TTTTTGGGTTTAGATTGAGACTCAA 57.110 32.000 19.85 19.85 41.09 3.02
2250 4896 6.687081 TGTATCAAACTGGAAGACGTTTTT 57.313 33.333 0.00 0.00 37.43 1.94
2251 4897 6.877611 ATGTATCAAACTGGAAGACGTTTT 57.122 33.333 0.00 0.00 37.43 2.43
2252 4898 6.594159 CCTATGTATCAAACTGGAAGACGTTT 59.406 38.462 0.00 0.00 37.43 3.60
2253 4899 6.106673 CCTATGTATCAAACTGGAAGACGTT 58.893 40.000 0.00 0.00 37.43 3.99
2254 4900 5.395324 CCCTATGTATCAAACTGGAAGACGT 60.395 44.000 0.00 0.00 37.43 4.34
2255 4901 5.050490 CCCTATGTATCAAACTGGAAGACG 58.950 45.833 0.00 0.00 37.43 4.18
2256 4902 6.127026 ACTCCCTATGTATCAAACTGGAAGAC 60.127 42.308 0.00 0.00 37.43 3.01
2257 4903 5.964477 ACTCCCTATGTATCAAACTGGAAGA 59.036 40.000 0.00 0.00 37.43 2.87
2258 4904 6.051717 CACTCCCTATGTATCAAACTGGAAG 58.948 44.000 0.00 0.00 42.29 3.46
2259 4905 5.629133 GCACTCCCTATGTATCAAACTGGAA 60.629 44.000 0.00 0.00 0.00 3.53
2260 4906 4.141711 GCACTCCCTATGTATCAAACTGGA 60.142 45.833 0.00 0.00 0.00 3.86
2261 4907 4.130118 GCACTCCCTATGTATCAAACTGG 58.870 47.826 0.00 0.00 0.00 4.00
2262 4908 4.769688 TGCACTCCCTATGTATCAAACTG 58.230 43.478 0.00 0.00 0.00 3.16
2263 4909 5.186198 GTTGCACTCCCTATGTATCAAACT 58.814 41.667 0.00 0.00 0.00 2.66
2264 4910 4.941263 TGTTGCACTCCCTATGTATCAAAC 59.059 41.667 0.00 0.00 0.00 2.93
2265 4911 5.172687 TGTTGCACTCCCTATGTATCAAA 57.827 39.130 0.00 0.00 0.00 2.69
2266 4912 4.835284 TGTTGCACTCCCTATGTATCAA 57.165 40.909 0.00 0.00 0.00 2.57
2267 4913 6.498303 AGATATGTTGCACTCCCTATGTATCA 59.502 38.462 0.00 0.00 0.00 2.15
2268 4914 6.940739 AGATATGTTGCACTCCCTATGTATC 58.059 40.000 0.00 0.00 0.00 2.24
2269 4915 6.728164 AGAGATATGTTGCACTCCCTATGTAT 59.272 38.462 0.00 0.00 0.00 2.29
2270 4916 6.077993 AGAGATATGTTGCACTCCCTATGTA 58.922 40.000 0.00 0.00 0.00 2.29
2271 4917 4.904251 AGAGATATGTTGCACTCCCTATGT 59.096 41.667 0.00 0.00 0.00 2.29
2272 4918 5.480642 AGAGATATGTTGCACTCCCTATG 57.519 43.478 0.00 0.00 0.00 2.23
2273 4919 6.318913 AGTAGAGATATGTTGCACTCCCTAT 58.681 40.000 0.00 0.00 0.00 2.57
2274 4920 5.706447 AGTAGAGATATGTTGCACTCCCTA 58.294 41.667 0.00 0.00 0.00 3.53
2275 4921 4.551671 AGTAGAGATATGTTGCACTCCCT 58.448 43.478 0.00 0.00 0.00 4.20
2276 4922 4.342378 TGAGTAGAGATATGTTGCACTCCC 59.658 45.833 0.00 0.00 31.96 4.30
2277 4923 5.521906 TGAGTAGAGATATGTTGCACTCC 57.478 43.478 0.00 0.00 31.96 3.85
2278 4924 9.534565 TTATTTGAGTAGAGATATGTTGCACTC 57.465 33.333 0.00 0.00 33.26 3.51
2281 4927 9.494271 GGATTATTTGAGTAGAGATATGTTGCA 57.506 33.333 0.00 0.00 0.00 4.08
2282 4928 9.717942 AGGATTATTTGAGTAGAGATATGTTGC 57.282 33.333 0.00 0.00 0.00 4.17
2305 4952 4.165372 AGGGTTCAACACTAAAGTCAAGGA 59.835 41.667 0.00 0.00 23.74 3.36
2322 4977 1.680338 AAGCACAACACTGAGGGTTC 58.320 50.000 0.00 0.00 0.00 3.62
2386 5041 6.173339 CCTTCAGATTAAGAAGTGGCTTGTA 58.827 40.000 0.00 0.00 40.62 2.41
4646 8604 3.126858 GTCACATTTGCATACGGTGTCAT 59.873 43.478 9.51 0.00 0.00 3.06
4647 8605 2.482336 GTCACATTTGCATACGGTGTCA 59.518 45.455 9.51 0.00 0.00 3.58
4648 8606 2.482336 TGTCACATTTGCATACGGTGTC 59.518 45.455 9.51 6.10 0.00 3.67
4649 8607 2.225491 GTGTCACATTTGCATACGGTGT 59.775 45.455 0.00 0.00 0.00 4.16
4650 8608 2.724533 CGTGTCACATTTGCATACGGTG 60.725 50.000 3.42 0.00 0.00 4.94
4651 8609 1.463056 CGTGTCACATTTGCATACGGT 59.537 47.619 3.42 0.00 0.00 4.83
4652 8610 1.463056 ACGTGTCACATTTGCATACGG 59.537 47.619 3.42 0.00 0.00 4.02
4653 8611 2.473868 GGACGTGTCACATTTGCATACG 60.474 50.000 3.42 0.00 0.00 3.06
4654 8612 2.473868 CGGACGTGTCACATTTGCATAC 60.474 50.000 3.42 0.00 0.00 2.39
4655 8613 1.729517 CGGACGTGTCACATTTGCATA 59.270 47.619 3.42 0.00 0.00 3.14
4656 8614 0.516877 CGGACGTGTCACATTTGCAT 59.483 50.000 3.42 0.00 0.00 3.96
4657 8615 1.502990 CCGGACGTGTCACATTTGCA 61.503 55.000 0.00 0.00 0.00 4.08
4658 8616 1.206578 CCGGACGTGTCACATTTGC 59.793 57.895 0.00 0.00 0.00 3.68
4659 8617 1.206578 GCCGGACGTGTCACATTTG 59.793 57.895 5.05 0.00 0.00 2.32
4660 8618 1.964373 GGCCGGACGTGTCACATTT 60.964 57.895 5.05 0.00 0.00 2.32
4661 8619 2.358247 GGCCGGACGTGTCACATT 60.358 61.111 5.05 0.00 0.00 2.71
4662 8620 3.589654 CTGGCCGGACGTGTCACAT 62.590 63.158 5.28 0.00 0.00 3.21
4663 8621 4.293648 CTGGCCGGACGTGTCACA 62.294 66.667 5.28 0.00 0.00 3.58
4664 8622 2.424705 TAACTGGCCGGACGTGTCAC 62.425 60.000 21.41 0.00 0.00 3.67
4665 8623 1.537814 ATAACTGGCCGGACGTGTCA 61.538 55.000 21.41 0.00 0.00 3.58
4666 8624 0.804933 GATAACTGGCCGGACGTGTC 60.805 60.000 21.41 7.10 0.00 3.67
4667 8625 1.217244 GATAACTGGCCGGACGTGT 59.783 57.895 21.41 1.63 0.00 4.49
4668 8626 0.390603 TTGATAACTGGCCGGACGTG 60.391 55.000 21.41 0.77 0.00 4.49
4669 8627 0.390735 GTTGATAACTGGCCGGACGT 60.391 55.000 21.41 1.09 0.00 4.34
4670 8628 0.108329 AGTTGATAACTGGCCGGACG 60.108 55.000 21.41 0.24 41.01 4.79
4671 8629 2.109425 AAGTTGATAACTGGCCGGAC 57.891 50.000 21.41 0.56 41.91 4.79
4672 8630 3.985019 TTAAGTTGATAACTGGCCGGA 57.015 42.857 21.41 0.00 41.91 5.14
4673 8631 5.379732 TTTTTAAGTTGATAACTGGCCGG 57.620 39.130 11.02 11.02 41.91 6.13


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

AutoCloner maintained by Alex Coulton.