Multiple sequence alignment - TraesCS7A01G321600

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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 TraesCS7A01G321600 chr7A 100.000 4062 0 0 498 4559 464575267 464571206 0.000000e+00 7502.0
1 TraesCS7A01G321600 chr7A 100.000 251 0 0 1 251 464575764 464575514 8.930000e-127 464.0
2 TraesCS7A01G321600 chr7B 94.965 3813 102 31 498 4276 418051663 418047907 0.000000e+00 5895.0
3 TraesCS7A01G321600 chr7D 94.446 3799 119 37 498 4272 407074233 407070503 0.000000e+00 5762.0
4 TraesCS7A01G321600 chr6A 88.682 645 55 8 973 1617 504123793 504123167 0.000000e+00 771.0
5 TraesCS7A01G321600 chr6A 89.308 477 44 5 1755 2225 504123176 504122701 3.930000e-165 592.0
6 TraesCS7A01G321600 chr2B 76.279 645 114 26 2497 3111 464466406 464467041 1.590000e-79 307.0
7 TraesCS7A01G321600 chr2A 76.168 642 117 20 2497 3111 530380453 530381085 5.730000e-79 305.0
8 TraesCS7A01G321600 chr2D 76.050 643 116 20 2497 3111 392525787 392526419 2.670000e-77 300.0
9 TraesCS7A01G321600 chr1B 88.800 250 18 6 1 249 53604618 53604378 9.590000e-77 298.0
10 TraesCS7A01G321600 chr1B 82.596 339 28 10 498 818 46514472 46514147 2.090000e-68 270.0
11 TraesCS7A01G321600 chr1B 82.154 325 28 13 498 804 53604329 53604017 7.570000e-63 252.0
12 TraesCS7A01G321600 chr4B 82.424 330 28 9 498 809 475717755 475717438 1.260000e-65 261.0
13 TraesCS7A01G321600 chr4B 73.952 668 116 44 2488 3111 119823533 119822880 2.760000e-52 217.0
14 TraesCS7A01G321600 chr4A 74.478 670 112 40 2488 3111 497441174 497440518 7.630000e-58 235.0
15 TraesCS7A01G321600 chr1D 73.418 711 137 33 2428 3100 53965428 53964732 7.680000e-53 219.0
16 TraesCS7A01G321600 chr4D 73.817 676 112 42 2488 3111 84546348 84545686 1.660000e-49 207.0
17 TraesCS7A01G321600 chr3B 88.333 120 14 0 3299 3418 572078161 572078280 1.320000e-30 145.0
18 TraesCS7A01G321600 chr5D 86.538 104 8 3 3008 3108 502596487 502596587 4.820000e-20 110.0
19 TraesCS7A01G321600 chr5A 83.929 112 18 0 3307 3418 212214940 212215051 1.730000e-19 108.0
20 TraesCS7A01G321600 chr5A 96.774 31 1 0 2491 2521 212214848 212214818 8.000000e-03 52.8
21 TraesCS7A01G321600 chr6D 96.970 33 1 0 2492 2524 205267309 205267277 6.370000e-04 56.5


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 TraesCS7A01G321600 chr7A 464571206 464575764 4558 True 3983.0 7502 100.000 1 4559 2 chr7A.!!$R1 4558
1 TraesCS7A01G321600 chr7B 418047907 418051663 3756 True 5895.0 5895 94.965 498 4276 1 chr7B.!!$R1 3778
2 TraesCS7A01G321600 chr7D 407070503 407074233 3730 True 5762.0 5762 94.446 498 4272 1 chr7D.!!$R1 3774
3 TraesCS7A01G321600 chr6A 504122701 504123793 1092 True 681.5 771 88.995 973 2225 2 chr6A.!!$R1 1252
4 TraesCS7A01G321600 chr2B 464466406 464467041 635 False 307.0 307 76.279 2497 3111 1 chr2B.!!$F1 614
5 TraesCS7A01G321600 chr2A 530380453 530381085 632 False 305.0 305 76.168 2497 3111 1 chr2A.!!$F1 614
6 TraesCS7A01G321600 chr2D 392525787 392526419 632 False 300.0 300 76.050 2497 3111 1 chr2D.!!$F1 614
7 TraesCS7A01G321600 chr1B 53604017 53604618 601 True 275.0 298 85.477 1 804 2 chr1B.!!$R2 803
8 TraesCS7A01G321600 chr4B 119822880 119823533 653 True 217.0 217 73.952 2488 3111 1 chr4B.!!$R1 623
9 TraesCS7A01G321600 chr4A 497440518 497441174 656 True 235.0 235 74.478 2488 3111 1 chr4A.!!$R1 623
10 TraesCS7A01G321600 chr1D 53964732 53965428 696 True 219.0 219 73.418 2428 3100 1 chr1D.!!$R1 672
11 TraesCS7A01G321600 chr4D 84545686 84546348 662 True 207.0 207 73.817 2488 3111 1 chr4D.!!$R1 623

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
860 888 0.028242 CTCGACTCGTTCTCCATCGG 59.972 60.000 0.00 0.00 33.66 4.18 F
863 891 0.248134 GACTCGTTCTCCATCGGTCG 60.248 60.000 0.00 0.00 0.00 4.79 F
971 1003 0.393077 CCGTCCCTCCATCCATACAC 59.607 60.000 0.00 0.00 0.00 2.90 F
1917 1964 2.325082 GGTGTGTGCCGTCATGACC 61.325 63.158 20.03 7.67 0.00 4.02 F
2895 2982 2.434884 CACCGCGACATCAAGCCT 60.435 61.111 8.23 0.00 0.00 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2174 2223 1.372087 CTTCTTCGCATCACCAGCCC 61.372 60.000 0.00 0.0 0.00 5.19 R
2177 2226 2.964740 TCTTCTTCTTCGCATCACCAG 58.035 47.619 0.00 0.0 0.00 4.00 R
2895 2982 0.389817 CGTCGAGCAGGATGTTGGAA 60.390 55.000 0.00 0.0 35.63 3.53 R
2943 3030 2.363018 CTCACGAGGGAGAGGCCA 60.363 66.667 5.01 0.0 38.95 5.36 R
4492 4659 0.104671 CCTTGGTTGGTTGGTTGCTG 59.895 55.000 0.00 0.0 0.00 4.41 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
23 24 4.989797 CCGAGAGATTGATTCCATCTTCAG 59.010 45.833 2.08 0.00 0.00 3.02
28 29 6.935771 AGAGATTGATTCCATCTTCAGTATGC 59.064 38.462 2.08 0.00 34.76 3.14
35 36 2.812591 CCATCTTCAGTATGCCATCTGC 59.187 50.000 0.00 0.00 41.77 4.26
79 80 6.554334 TGCCTTTGTAACTAGAACATGTTC 57.446 37.500 27.69 27.69 39.78 3.18
83 84 6.934645 CCTTTGTAACTAGAACATGTTCAGGA 59.065 38.462 33.92 20.27 41.84 3.86
98 99 7.121168 ACATGTTCAGGATTAATACAACCACTG 59.879 37.037 0.00 0.00 0.00 3.66
117 118 5.064707 CCACTGATTATTAGAAACCACACCG 59.935 44.000 0.00 0.00 0.00 4.94
134 135 4.853007 ACACCGAGTGATAACCTACTAGT 58.147 43.478 10.46 0.00 36.96 2.57
518 519 2.643551 TGCACTAATTTGCCTCCTAGC 58.356 47.619 0.00 0.00 42.25 3.42
552 557 3.328505 GGCAATCATTGTGGTTTTGGAG 58.671 45.455 0.00 0.00 0.00 3.86
607 617 1.228367 CCAGGCAGCAAAGTGAGGT 60.228 57.895 0.00 0.00 0.00 3.85
608 618 1.239968 CCAGGCAGCAAAGTGAGGTC 61.240 60.000 0.00 0.00 0.00 3.85
630 640 6.315393 GGTCGGAGAAATTAATTCACAAGCTA 59.685 38.462 0.10 0.00 39.69 3.32
810 838 1.758906 AACCCAACCCAACCCAACG 60.759 57.895 0.00 0.00 0.00 4.10
811 839 2.196229 CCCAACCCAACCCAACGA 59.804 61.111 0.00 0.00 0.00 3.85
812 840 1.901464 CCCAACCCAACCCAACGAG 60.901 63.158 0.00 0.00 0.00 4.18
813 841 2.561037 CCAACCCAACCCAACGAGC 61.561 63.158 0.00 0.00 0.00 5.03
814 842 1.826054 CAACCCAACCCAACGAGCA 60.826 57.895 0.00 0.00 0.00 4.26
815 843 1.076632 AACCCAACCCAACGAGCAA 60.077 52.632 0.00 0.00 0.00 3.91
820 848 0.378962 CAACCCAACGAGCAACGAAA 59.621 50.000 10.05 0.00 45.77 3.46
821 849 0.379316 AACCCAACGAGCAACGAAAC 59.621 50.000 10.05 0.00 45.77 2.78
822 850 1.281656 CCCAACGAGCAACGAAACC 59.718 57.895 10.05 0.00 45.77 3.27
823 851 1.281656 CCAACGAGCAACGAAACCC 59.718 57.895 10.05 0.00 45.77 4.11
824 852 1.440938 CCAACGAGCAACGAAACCCA 61.441 55.000 10.05 0.00 45.77 4.51
825 853 0.378962 CAACGAGCAACGAAACCCAA 59.621 50.000 10.05 0.00 45.77 4.12
826 854 0.379316 AACGAGCAACGAAACCCAAC 59.621 50.000 10.05 0.00 45.77 3.77
827 855 1.083015 CGAGCAACGAAACCCAACG 60.083 57.895 0.00 0.00 45.77 4.10
860 888 0.028242 CTCGACTCGTTCTCCATCGG 59.972 60.000 0.00 0.00 33.66 4.18
863 891 0.248134 GACTCGTTCTCCATCGGTCG 60.248 60.000 0.00 0.00 0.00 4.79
934 966 0.740868 TCAAATCCAAGCGAGCCGAG 60.741 55.000 0.00 0.00 0.00 4.63
951 983 4.035102 GCCAAACCGGAGCTCCCT 62.035 66.667 27.20 9.59 36.56 4.20
952 984 2.269241 CCAAACCGGAGCTCCCTC 59.731 66.667 27.20 2.48 36.56 4.30
971 1003 0.393077 CCGTCCCTCCATCCATACAC 59.607 60.000 0.00 0.00 0.00 2.90
1354 1401 2.894257 ATGCGCTGGTGGTCCTTCA 61.894 57.895 9.73 0.00 34.23 3.02
1917 1964 2.325082 GGTGTGTGCCGTCATGACC 61.325 63.158 20.03 7.67 0.00 4.02
2895 2982 2.434884 CACCGCGACATCAAGCCT 60.435 61.111 8.23 0.00 0.00 4.58
2943 3030 1.301479 GGCGAAGGTGTCCGACTTT 60.301 57.895 0.00 0.00 0.00 2.66
3510 3642 1.446272 CGAGTTCAGCTTCGGGTCC 60.446 63.158 0.00 0.00 0.00 4.46
3568 3700 8.960591 CCTACTCAACCATGTAAAGATTTGATT 58.039 33.333 0.00 0.00 0.00 2.57
3700 3833 6.509656 TCATAATTTTGCAAGAGATGGATGC 58.490 36.000 12.18 0.00 0.00 3.91
3746 3885 3.562973 TGGCGGTTAATTTAACGTTGTGA 59.437 39.130 11.99 0.00 39.54 3.58
3778 3917 5.182760 AGAAGATGAAATGAAACCACAGAGC 59.817 40.000 0.00 0.00 0.00 4.09
3791 3935 5.683876 ACCACAGAGCATGTAGATTTAGT 57.316 39.130 0.00 0.00 41.41 2.24
3792 3936 6.054860 ACCACAGAGCATGTAGATTTAGTT 57.945 37.500 0.00 0.00 41.41 2.24
3831 3979 2.555325 GGGTTTGTACTTGGTAGGTTGC 59.445 50.000 0.00 0.00 0.00 4.17
3928 4088 6.936900 GGTACATGGATGCAACTATAAGTCAT 59.063 38.462 0.00 0.00 0.00 3.06
3929 4089 8.094548 GGTACATGGATGCAACTATAAGTCATA 58.905 37.037 0.00 0.00 0.00 2.15
3930 4090 7.969536 ACATGGATGCAACTATAAGTCATAC 57.030 36.000 0.00 0.00 0.00 2.39
3963 4123 5.869344 TGATTTGATTCTCTACCGTCTTGTG 59.131 40.000 0.00 0.00 0.00 3.33
3966 4126 2.724977 TTCTCTACCGTCTTGTGCTG 57.275 50.000 0.00 0.00 0.00 4.41
3982 4144 6.593770 TCTTGTGCTGGTAGTACAATAATGTG 59.406 38.462 11.81 1.90 46.75 3.21
3984 4146 3.868661 TGCTGGTAGTACAATAATGTGCG 59.131 43.478 2.06 0.00 45.63 5.34
3995 4157 4.622313 ACAATAATGTGCGTTGCTGATTTG 59.378 37.500 0.00 0.00 38.69 2.32
4034 4196 4.295870 TCTCTGCAAGTAGTTGTTGTACG 58.704 43.478 11.85 0.00 35.92 3.67
4067 4229 7.930865 TGAACGTCCACATGAATATGAATATGA 59.069 33.333 0.00 0.00 37.73 2.15
4135 4297 3.034721 TCTTGTGGCTTACGTCGAAAT 57.965 42.857 0.00 0.00 0.00 2.17
4210 4373 6.430308 TGAACAACTGTTACAAGTGGTACAAA 59.570 34.615 0.00 0.00 38.29 2.83
4211 4374 7.121463 TGAACAACTGTTACAAGTGGTACAAAT 59.879 33.333 0.00 0.00 38.29 2.32
4212 4375 8.508883 AACAACTGTTACAAGTGGTACAAATA 57.491 30.769 0.00 0.00 36.78 1.40
4213 4376 8.508883 ACAACTGTTACAAGTGGTACAAATAA 57.491 30.769 0.00 0.00 44.16 1.40
4255 4422 3.616821 GCTCACCAAACAAACAAGGAAAC 59.383 43.478 0.00 0.00 0.00 2.78
4296 4463 7.541916 AATAGACCCATAGGAGTTACTAAGC 57.458 40.000 0.00 0.00 36.73 3.09
4297 4464 4.224762 AGACCCATAGGAGTTACTAAGCC 58.775 47.826 0.00 0.00 36.73 4.35
4298 4465 3.315596 ACCCATAGGAGTTACTAAGCCC 58.684 50.000 0.00 0.00 36.73 5.19
4299 4466 3.051264 ACCCATAGGAGTTACTAAGCCCT 60.051 47.826 0.00 0.00 36.73 5.19
4300 4467 3.579151 CCCATAGGAGTTACTAAGCCCTC 59.421 52.174 0.00 0.00 33.47 4.30
4301 4468 3.579151 CCATAGGAGTTACTAAGCCCTCC 59.421 52.174 0.00 0.00 43.14 4.30
4304 4471 3.035055 GGAGTTACTAAGCCCTCCTCT 57.965 52.381 0.00 0.00 40.30 3.69
4305 4472 4.181799 GGAGTTACTAAGCCCTCCTCTA 57.818 50.000 0.00 0.00 40.30 2.43
4306 4473 3.890756 GGAGTTACTAAGCCCTCCTCTAC 59.109 52.174 0.00 0.00 40.30 2.59
4307 4474 3.890756 GAGTTACTAAGCCCTCCTCTACC 59.109 52.174 0.00 0.00 0.00 3.18
4308 4475 2.964464 GTTACTAAGCCCTCCTCTACCC 59.036 54.545 0.00 0.00 0.00 3.69
4309 4476 1.016415 ACTAAGCCCTCCTCTACCCA 58.984 55.000 0.00 0.00 0.00 4.51
4310 4477 1.343176 ACTAAGCCCTCCTCTACCCAC 60.343 57.143 0.00 0.00 0.00 4.61
4311 4478 1.016415 TAAGCCCTCCTCTACCCACT 58.984 55.000 0.00 0.00 0.00 4.00
4312 4479 0.618968 AAGCCCTCCTCTACCCACTG 60.619 60.000 0.00 0.00 0.00 3.66
4313 4480 2.066999 GCCCTCCTCTACCCACTGG 61.067 68.421 0.00 0.00 37.80 4.00
4326 4493 4.015872 ACCCACTGGTGTATGTAAACTG 57.984 45.455 0.00 0.00 45.58 3.16
4327 4494 3.393278 ACCCACTGGTGTATGTAAACTGT 59.607 43.478 0.00 0.00 45.58 3.55
4328 4495 4.000988 CCCACTGGTGTATGTAAACTGTC 58.999 47.826 0.00 0.00 0.00 3.51
4329 4496 4.504165 CCCACTGGTGTATGTAAACTGTCA 60.504 45.833 0.00 0.00 0.00 3.58
4330 4497 5.060506 CCACTGGTGTATGTAAACTGTCAA 58.939 41.667 0.00 0.00 0.00 3.18
4331 4498 5.529430 CCACTGGTGTATGTAAACTGTCAAA 59.471 40.000 0.00 0.00 0.00 2.69
4332 4499 6.293407 CCACTGGTGTATGTAAACTGTCAAAG 60.293 42.308 0.00 0.00 0.00 2.77
4333 4500 6.481976 CACTGGTGTATGTAAACTGTCAAAGA 59.518 38.462 0.00 0.00 0.00 2.52
4334 4501 7.173218 CACTGGTGTATGTAAACTGTCAAAGAT 59.827 37.037 0.00 0.00 0.00 2.40
4335 4502 8.372459 ACTGGTGTATGTAAACTGTCAAAGATA 58.628 33.333 0.00 0.00 0.00 1.98
4336 4503 9.383519 CTGGTGTATGTAAACTGTCAAAGATAT 57.616 33.333 0.00 0.00 0.00 1.63
4337 4504 9.378551 TGGTGTATGTAAACTGTCAAAGATATC 57.621 33.333 0.00 0.00 0.00 1.63
4338 4505 8.540492 GGTGTATGTAAACTGTCAAAGATATCG 58.460 37.037 0.00 0.00 0.00 2.92
4339 4506 9.297586 GTGTATGTAAACTGTCAAAGATATCGA 57.702 33.333 0.00 0.00 0.00 3.59
4340 4507 9.297586 TGTATGTAAACTGTCAAAGATATCGAC 57.702 33.333 0.00 0.00 0.00 4.20
4341 4508 9.297586 GTATGTAAACTGTCAAAGATATCGACA 57.702 33.333 10.36 10.36 37.33 4.35
4342 4509 7.576750 TGTAAACTGTCAAAGATATCGACAC 57.423 36.000 7.58 0.53 34.83 3.67
4343 4510 7.149307 TGTAAACTGTCAAAGATATCGACACA 58.851 34.615 7.58 4.43 34.83 3.72
4344 4511 7.817478 TGTAAACTGTCAAAGATATCGACACAT 59.183 33.333 7.58 0.00 34.83 3.21
4345 4512 9.297586 GTAAACTGTCAAAGATATCGACACATA 57.702 33.333 7.58 1.24 34.83 2.29
4346 4513 7.757097 AACTGTCAAAGATATCGACACATAC 57.243 36.000 7.58 0.00 34.83 2.39
4347 4514 6.863275 ACTGTCAAAGATATCGACACATACA 58.137 36.000 7.58 2.80 34.83 2.29
4348 4515 7.492524 ACTGTCAAAGATATCGACACATACAT 58.507 34.615 7.58 0.00 34.83 2.29
4349 4516 8.630037 ACTGTCAAAGATATCGACACATACATA 58.370 33.333 7.58 0.00 34.83 2.29
4350 4517 8.797266 TGTCAAAGATATCGACACATACATAC 57.203 34.615 7.58 0.00 34.83 2.39
4351 4518 8.410141 TGTCAAAGATATCGACACATACATACA 58.590 33.333 7.58 0.00 34.83 2.29
4352 4519 9.411801 GTCAAAGATATCGACACATACATACAT 57.588 33.333 0.00 0.00 0.00 2.29
4362 4529 9.498176 TCGACACATACATACATACATACTACT 57.502 33.333 0.00 0.00 0.00 2.57
4363 4530 9.756461 CGACACATACATACATACATACTACTC 57.244 37.037 0.00 0.00 0.00 2.59
4365 4532 8.727910 ACACATACATACATACATACTACTCCG 58.272 37.037 0.00 0.00 0.00 4.63
4366 4533 8.727910 CACATACATACATACATACTACTCCGT 58.272 37.037 0.00 0.00 0.00 4.69
4367 4534 8.944029 ACATACATACATACATACTACTCCGTC 58.056 37.037 0.00 0.00 0.00 4.79
4368 4535 6.477669 ACATACATACATACTACTCCGTCG 57.522 41.667 0.00 0.00 0.00 5.12
4369 4536 3.892918 ACATACATACTACTCCGTCGC 57.107 47.619 0.00 0.00 0.00 5.19
4370 4537 3.208594 ACATACATACTACTCCGTCGCA 58.791 45.455 0.00 0.00 0.00 5.10
4371 4538 3.819337 ACATACATACTACTCCGTCGCAT 59.181 43.478 0.00 0.00 0.00 4.73
4372 4539 4.999311 ACATACATACTACTCCGTCGCATA 59.001 41.667 0.00 0.00 0.00 3.14
4373 4540 5.471116 ACATACATACTACTCCGTCGCATAA 59.529 40.000 0.00 0.00 0.00 1.90
4374 4541 6.150641 ACATACATACTACTCCGTCGCATAAT 59.849 38.462 0.00 0.00 0.00 1.28
4375 4542 4.795268 ACATACTACTCCGTCGCATAATG 58.205 43.478 0.00 0.00 0.00 1.90
4376 4543 4.277672 ACATACTACTCCGTCGCATAATGT 59.722 41.667 0.00 0.00 0.00 2.71
4377 4544 5.471116 ACATACTACTCCGTCGCATAATGTA 59.529 40.000 0.00 0.00 0.00 2.29
4378 4545 6.150641 ACATACTACTCCGTCGCATAATGTAT 59.849 38.462 0.00 0.00 0.00 2.29
4379 4546 7.335171 ACATACTACTCCGTCGCATAATGTATA 59.665 37.037 0.00 0.00 0.00 1.47
4380 4547 5.936054 ACTACTCCGTCGCATAATGTATAC 58.064 41.667 0.00 0.00 0.00 1.47
4381 4548 5.704515 ACTACTCCGTCGCATAATGTATACT 59.295 40.000 4.17 0.00 0.00 2.12
4382 4549 6.875726 ACTACTCCGTCGCATAATGTATACTA 59.124 38.462 4.17 0.00 0.00 1.82
4383 4550 6.179504 ACTCCGTCGCATAATGTATACTAG 57.820 41.667 4.17 0.00 0.00 2.57
4384 4551 5.704515 ACTCCGTCGCATAATGTATACTAGT 59.295 40.000 0.00 0.00 0.00 2.57
4385 4552 5.934921 TCCGTCGCATAATGTATACTAGTG 58.065 41.667 5.39 0.00 0.00 2.74
4386 4553 5.471116 TCCGTCGCATAATGTATACTAGTGT 59.529 40.000 5.39 0.39 0.00 3.55
4387 4554 5.793952 CCGTCGCATAATGTATACTAGTGTC 59.206 44.000 5.39 0.00 0.00 3.67
4388 4555 6.368213 CGTCGCATAATGTATACTAGTGTCA 58.632 40.000 5.39 2.36 0.00 3.58
4389 4556 6.854381 CGTCGCATAATGTATACTAGTGTCAA 59.146 38.462 5.39 0.00 0.00 3.18
4390 4557 7.377662 CGTCGCATAATGTATACTAGTGTCAAA 59.622 37.037 5.39 0.00 0.00 2.69
4391 4558 9.027129 GTCGCATAATGTATACTAGTGTCAAAA 57.973 33.333 5.39 0.00 0.00 2.44
4392 4559 9.589111 TCGCATAATGTATACTAGTGTCAAAAA 57.411 29.630 5.39 0.00 0.00 1.94
4418 4585 8.581253 AAAGTCTTACATTATGAAAAGGAGGG 57.419 34.615 0.00 0.00 0.00 4.30
4419 4586 6.663734 AGTCTTACATTATGAAAAGGAGGGG 58.336 40.000 0.00 0.00 0.00 4.79
4420 4587 6.447084 AGTCTTACATTATGAAAAGGAGGGGA 59.553 38.462 0.00 0.00 0.00 4.81
4421 4588 7.129504 AGTCTTACATTATGAAAAGGAGGGGAT 59.870 37.037 0.00 0.00 0.00 3.85
4422 4589 8.437575 GTCTTACATTATGAAAAGGAGGGGATA 58.562 37.037 0.00 0.00 0.00 2.59
4423 4590 8.660435 TCTTACATTATGAAAAGGAGGGGATAG 58.340 37.037 0.00 0.00 0.00 2.08
4424 4591 6.848562 ACATTATGAAAAGGAGGGGATAGT 57.151 37.500 0.00 0.00 0.00 2.12
4425 4592 7.947782 ACATTATGAAAAGGAGGGGATAGTA 57.052 36.000 0.00 0.00 0.00 1.82
4426 4593 8.525729 ACATTATGAAAAGGAGGGGATAGTAT 57.474 34.615 0.00 0.00 0.00 2.12
4427 4594 8.960064 ACATTATGAAAAGGAGGGGATAGTATT 58.040 33.333 0.00 0.00 0.00 1.89
4428 4595 9.813826 CATTATGAAAAGGAGGGGATAGTATTT 57.186 33.333 0.00 0.00 0.00 1.40
4430 4597 9.640952 TTATGAAAAGGAGGGGATAGTATTTTG 57.359 33.333 0.00 0.00 0.00 2.44
4431 4598 7.278724 TGAAAAGGAGGGGATAGTATTTTGA 57.721 36.000 0.00 0.00 0.00 2.69
4432 4599 7.882755 TGAAAAGGAGGGGATAGTATTTTGAT 58.117 34.615 0.00 0.00 0.00 2.57
4433 4600 8.343787 TGAAAAGGAGGGGATAGTATTTTGATT 58.656 33.333 0.00 0.00 0.00 2.57
4434 4601 9.201989 GAAAAGGAGGGGATAGTATTTTGATTT 57.798 33.333 0.00 0.00 0.00 2.17
4453 4620 9.781834 TTTGATTTATAGTTGTAATTTGAGCGG 57.218 29.630 0.00 0.00 0.00 5.52
4454 4621 8.500753 TGATTTATAGTTGTAATTTGAGCGGT 57.499 30.769 0.00 0.00 0.00 5.68
4455 4622 9.602568 TGATTTATAGTTGTAATTTGAGCGGTA 57.397 29.630 0.00 0.00 0.00 4.02
4460 4627 6.811253 AGTTGTAATTTGAGCGGTAAATCA 57.189 33.333 0.00 0.00 0.00 2.57
4461 4628 7.391148 AGTTGTAATTTGAGCGGTAAATCAT 57.609 32.000 0.00 0.00 0.00 2.45
4462 4629 7.472543 AGTTGTAATTTGAGCGGTAAATCATC 58.527 34.615 0.00 0.00 0.00 2.92
4463 4630 6.371809 TGTAATTTGAGCGGTAAATCATCC 57.628 37.500 0.00 0.00 0.00 3.51
4467 4634 4.594123 TTGAGCGGTAAATCATCCGATA 57.406 40.909 7.79 0.00 45.75 2.92
4468 4635 3.909430 TGAGCGGTAAATCATCCGATAC 58.091 45.455 7.79 0.00 45.75 2.24
4469 4636 2.915463 GAGCGGTAAATCATCCGATACG 59.085 50.000 7.79 0.00 45.75 3.06
4470 4637 3.611057 GAGCGGTAAATCATCCGATACGT 60.611 47.826 7.79 0.00 45.75 3.57
4471 4638 4.378770 GAGCGGTAAATCATCCGATACGTA 60.379 45.833 7.79 0.00 45.75 3.57
4472 4639 6.174633 GAGCGGTAAATCATCCGATACGTAG 61.175 48.000 7.79 0.00 45.75 3.51
4474 4641 5.633830 GGTAAATCATCCGATACGTAGGA 57.366 43.478 6.06 6.06 41.30 2.94
4482 4649 5.977489 ATCCGATACGTAGGATGATTTCA 57.023 39.130 13.94 0.00 44.88 2.69
4483 4650 5.977489 TCCGATACGTAGGATGATTTCAT 57.023 39.130 0.08 0.00 39.70 2.57
4484 4651 6.340962 TCCGATACGTAGGATGATTTCATT 57.659 37.500 0.08 0.00 36.57 2.57
4485 4652 6.387465 TCCGATACGTAGGATGATTTCATTC 58.613 40.000 0.08 0.00 36.57 2.67
4486 4653 6.015772 TCCGATACGTAGGATGATTTCATTCA 60.016 38.462 0.08 0.00 36.57 2.57
4487 4654 6.813649 CCGATACGTAGGATGATTTCATTCAT 59.186 38.462 0.08 0.00 39.04 2.57
4495 4662 4.585955 ATGATTTCATTCATCAGGCAGC 57.414 40.909 0.00 0.00 34.12 5.25
4496 4663 3.358118 TGATTTCATTCATCAGGCAGCA 58.642 40.909 0.00 0.00 0.00 4.41
4497 4664 3.764972 TGATTTCATTCATCAGGCAGCAA 59.235 39.130 0.00 0.00 0.00 3.91
4498 4665 3.581024 TTTCATTCATCAGGCAGCAAC 57.419 42.857 0.00 0.00 0.00 4.17
4499 4666 1.466856 TCATTCATCAGGCAGCAACC 58.533 50.000 0.00 0.00 0.00 3.77
4500 4667 1.179152 CATTCATCAGGCAGCAACCA 58.821 50.000 0.00 0.00 0.00 3.67
4501 4668 1.546923 CATTCATCAGGCAGCAACCAA 59.453 47.619 0.00 0.00 0.00 3.67
4502 4669 0.961019 TTCATCAGGCAGCAACCAAC 59.039 50.000 0.00 0.00 0.00 3.77
4503 4670 0.895100 TCATCAGGCAGCAACCAACC 60.895 55.000 0.00 0.00 0.00 3.77
4504 4671 1.153524 ATCAGGCAGCAACCAACCA 59.846 52.632 0.00 0.00 0.00 3.67
4505 4672 0.469705 ATCAGGCAGCAACCAACCAA 60.470 50.000 0.00 0.00 0.00 3.67
4506 4673 1.067916 CAGGCAGCAACCAACCAAC 59.932 57.895 0.00 0.00 0.00 3.77
4507 4674 2.133641 AGGCAGCAACCAACCAACC 61.134 57.895 0.00 0.00 0.00 3.77
4508 4675 2.430610 GGCAGCAACCAACCAACCA 61.431 57.895 0.00 0.00 0.00 3.67
4509 4676 1.519719 GCAGCAACCAACCAACCAA 59.480 52.632 0.00 0.00 0.00 3.67
4510 4677 0.530431 GCAGCAACCAACCAACCAAG 60.530 55.000 0.00 0.00 0.00 3.61
4511 4678 0.104671 CAGCAACCAACCAACCAAGG 59.895 55.000 0.00 0.00 0.00 3.61
4512 4679 0.325203 AGCAACCAACCAACCAAGGT 60.325 50.000 0.00 0.00 45.91 3.50
4525 4692 6.822442 ACCAACCAAGGTTAATTAAAACTGG 58.178 36.000 3.82 14.69 39.34 4.00
4526 4693 5.699001 CCAACCAAGGTTAATTAAAACTGGC 59.301 40.000 15.62 0.00 34.48 4.85
4527 4694 6.284459 CAACCAAGGTTAATTAAAACTGGCA 58.716 36.000 15.62 0.00 34.48 4.92
4528 4695 6.680148 ACCAAGGTTAATTAAAACTGGCAT 57.320 33.333 15.62 1.63 34.48 4.40
4529 4696 6.697395 ACCAAGGTTAATTAAAACTGGCATC 58.303 36.000 15.62 0.00 34.48 3.91
4530 4697 6.496911 ACCAAGGTTAATTAAAACTGGCATCT 59.503 34.615 15.62 0.87 34.48 2.90
4531 4698 7.016170 ACCAAGGTTAATTAAAACTGGCATCTT 59.984 33.333 15.62 0.00 34.48 2.40
4532 4699 8.527810 CCAAGGTTAATTAAAACTGGCATCTTA 58.472 33.333 0.00 0.00 34.48 2.10
4537 4704 9.678941 GTTAATTAAAACTGGCATCTTATAGGC 57.321 33.333 0.00 0.00 0.00 3.93
4538 4705 7.896383 AATTAAAACTGGCATCTTATAGGCA 57.104 32.000 0.00 0.00 36.32 4.75
4539 4706 7.896383 ATTAAAACTGGCATCTTATAGGCAA 57.104 32.000 0.00 0.00 39.95 4.52
4540 4707 5.582689 AAAACTGGCATCTTATAGGCAAC 57.417 39.130 0.00 0.00 39.95 4.17
4541 4708 3.931907 ACTGGCATCTTATAGGCAACA 57.068 42.857 0.00 0.00 39.95 3.33
4542 4709 3.813443 ACTGGCATCTTATAGGCAACAG 58.187 45.455 0.00 0.00 39.95 3.16
4543 4710 3.200825 ACTGGCATCTTATAGGCAACAGT 59.799 43.478 0.00 0.00 39.95 3.55
4544 4711 3.808728 TGGCATCTTATAGGCAACAGTC 58.191 45.455 0.00 0.00 36.32 3.51
4545 4712 2.802816 GGCATCTTATAGGCAACAGTCG 59.197 50.000 0.00 0.00 36.32 4.18
4546 4713 3.492656 GGCATCTTATAGGCAACAGTCGA 60.493 47.826 0.00 0.00 36.32 4.20
4547 4714 3.491267 GCATCTTATAGGCAACAGTCGAC 59.509 47.826 7.70 7.70 41.41 4.20
4548 4715 4.737946 GCATCTTATAGGCAACAGTCGACT 60.738 45.833 13.58 13.58 41.41 4.18
4549 4716 5.507482 GCATCTTATAGGCAACAGTCGACTA 60.507 44.000 19.57 0.19 41.41 2.59
4550 4717 5.752892 TCTTATAGGCAACAGTCGACTAG 57.247 43.478 19.57 14.87 41.41 2.57
4551 4718 4.579340 TCTTATAGGCAACAGTCGACTAGG 59.421 45.833 19.57 9.71 41.41 3.02
4552 4719 0.815734 TAGGCAACAGTCGACTAGGC 59.184 55.000 19.57 21.45 41.41 3.93
4553 4720 1.185618 AGGCAACAGTCGACTAGGCA 61.186 55.000 27.85 0.00 41.41 4.75
4554 4721 0.320421 GGCAACAGTCGACTAGGCAA 60.320 55.000 26.39 0.00 0.00 4.52
4555 4722 1.676014 GGCAACAGTCGACTAGGCAAT 60.676 52.381 26.39 7.55 0.00 3.56
4556 4723 2.418197 GGCAACAGTCGACTAGGCAATA 60.418 50.000 26.39 0.00 0.00 1.90
4557 4724 3.458189 GCAACAGTCGACTAGGCAATAT 58.542 45.455 19.57 0.00 0.00 1.28
4558 4725 3.246226 GCAACAGTCGACTAGGCAATATG 59.754 47.826 19.57 5.91 0.00 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 6.913170 ACATGTTCTAGTTACAAAGGCATTG 58.087 36.000 0.12 0.12 44.95 2.82
60 61 8.918202 AATCCTGAACATGTTCTAGTTACAAA 57.082 30.769 32.57 13.23 40.14 2.83
98 99 6.103997 TCACTCGGTGTGGTTTCTAATAATC 58.896 40.000 10.01 0.00 46.20 1.75
110 111 2.758979 AGTAGGTTATCACTCGGTGTGG 59.241 50.000 10.01 0.00 46.20 4.17
167 168 8.455598 TGCTTTCCGCATTTATACTTAAAAAC 57.544 30.769 0.00 0.00 45.47 2.43
184 185 2.154462 ACCATTCTCTTGTGCTTTCCG 58.846 47.619 0.00 0.00 0.00 4.30
214 215 3.625313 GCAGAGAAGCCTTTACCATTCTC 59.375 47.826 5.81 5.81 45.15 2.87
220 221 2.481289 ACAGCAGAGAAGCCTTTACC 57.519 50.000 0.00 0.00 34.23 2.85
224 225 3.169099 TCTCTAACAGCAGAGAAGCCTT 58.831 45.455 0.40 0.00 46.29 4.35
225 226 2.813907 TCTCTAACAGCAGAGAAGCCT 58.186 47.619 0.40 0.00 46.29 4.58
578 588 1.903294 CTGCCTGGCTTCTCAGCTA 59.097 57.895 21.03 0.00 46.44 3.32
579 589 2.669849 CTGCCTGGCTTCTCAGCT 59.330 61.111 21.03 0.00 46.44 4.24
607 617 7.414098 GCTTAGCTTGTGAATTAATTTCTCCGA 60.414 37.037 1.43 0.00 35.23 4.55
608 618 6.688813 GCTTAGCTTGTGAATTAATTTCTCCG 59.311 38.462 1.43 0.00 35.23 4.63
630 640 5.459762 CGTTGAAATTCAAGTGTCAATGCTT 59.540 36.000 8.88 0.00 37.00 3.91
810 838 1.370051 GCGTTGGGTTTCGTTGCTC 60.370 57.895 0.00 0.00 0.00 4.26
811 839 2.719354 GCGTTGGGTTTCGTTGCT 59.281 55.556 0.00 0.00 0.00 3.91
812 840 2.724358 CGCGTTGGGTTTCGTTGC 60.724 61.111 0.00 0.00 0.00 4.17
813 841 2.051703 CCGCGTTGGGTTTCGTTG 60.052 61.111 4.92 0.00 0.00 4.10
814 842 2.203042 TCCGCGTTGGGTTTCGTT 60.203 55.556 4.92 0.00 38.76 3.85
815 843 2.968697 GTCCGCGTTGGGTTTCGT 60.969 61.111 4.92 0.00 38.76 3.85
860 888 0.899720 TTGTAGGTGGGTGGATCGAC 59.100 55.000 0.00 0.00 0.00 4.20
863 891 0.255033 GGGTTGTAGGTGGGTGGATC 59.745 60.000 0.00 0.00 0.00 3.36
934 966 3.978571 GAGGGAGCTCCGGTTTGGC 62.979 68.421 26.36 10.66 41.52 4.52
942 974 4.467107 AGGGACGGAGGGAGCTCC 62.467 72.222 25.59 25.59 40.04 4.70
951 983 0.263468 TGTATGGATGGAGGGACGGA 59.737 55.000 0.00 0.00 0.00 4.69
952 984 0.393077 GTGTATGGATGGAGGGACGG 59.607 60.000 0.00 0.00 0.00 4.79
953 985 0.393077 GGTGTATGGATGGAGGGACG 59.607 60.000 0.00 0.00 0.00 4.79
954 986 0.765510 GGGTGTATGGATGGAGGGAC 59.234 60.000 0.00 0.00 0.00 4.46
955 987 0.345146 TGGGTGTATGGATGGAGGGA 59.655 55.000 0.00 0.00 0.00 4.20
956 988 1.074405 CATGGGTGTATGGATGGAGGG 59.926 57.143 0.00 0.00 0.00 4.30
957 989 1.776667 ACATGGGTGTATGGATGGAGG 59.223 52.381 0.00 0.00 36.63 4.30
971 1003 1.381872 AGGGAGGAGACGACATGGG 60.382 63.158 0.00 0.00 0.00 4.00
1354 1401 4.467107 GGCCTCCTCCTCCTCGGT 62.467 72.222 0.00 0.00 0.00 4.69
1797 1844 1.883084 GTTCCCGGCGAGTATGCAG 60.883 63.158 9.30 0.00 36.28 4.41
2174 2223 1.372087 CTTCTTCGCATCACCAGCCC 61.372 60.000 0.00 0.00 0.00 5.19
2177 2226 2.964740 TCTTCTTCTTCGCATCACCAG 58.035 47.619 0.00 0.00 0.00 4.00
2895 2982 0.389817 CGTCGAGCAGGATGTTGGAA 60.390 55.000 0.00 0.00 35.63 3.53
2943 3030 2.363018 CTCACGAGGGAGAGGCCA 60.363 66.667 5.01 0.00 38.95 5.36
3201 3333 3.109619 GTCGAGGATCTTGTCGATGTTC 58.890 50.000 15.20 3.30 46.22 3.18
3324 3456 2.436646 GCCACCACCTCCGACATG 60.437 66.667 0.00 0.00 0.00 3.21
3372 3504 4.736896 GACCGGACCACGCACTCC 62.737 72.222 9.46 0.00 42.52 3.85
3540 3672 8.328758 TCAAATCTTTACATGGTTGAGTAGGAT 58.671 33.333 0.00 0.00 0.00 3.24
3592 3724 3.314693 TCACCCTTCCTACACAGAAACT 58.685 45.455 0.00 0.00 0.00 2.66
3595 3727 4.993705 AATTCACCCTTCCTACACAGAA 57.006 40.909 0.00 0.00 0.00 3.02
3649 3781 8.682936 AACTTGTTCTGATTTCTCACTGTATT 57.317 30.769 0.00 0.00 0.00 1.89
3650 3782 8.153550 AGAACTTGTTCTGATTTCTCACTGTAT 58.846 33.333 14.36 0.00 0.00 2.29
3746 3885 6.183360 GGTTTCATTTCATCTTCTCGACGAAT 60.183 38.462 0.00 0.00 0.00 3.34
3791 3935 7.124448 ACAAACCCACCACTACTAAAATTTCAA 59.876 33.333 0.00 0.00 0.00 2.69
3792 3936 6.608002 ACAAACCCACCACTACTAAAATTTCA 59.392 34.615 0.00 0.00 0.00 2.69
3929 4089 8.643324 GGTAGAGAATCAAATCATGGTAGTAGT 58.357 37.037 0.00 0.00 37.82 2.73
3930 4090 7.810282 CGGTAGAGAATCAAATCATGGTAGTAG 59.190 40.741 0.00 0.00 37.82 2.57
3963 4123 3.869246 ACGCACATTATTGTACTACCAGC 59.131 43.478 0.00 0.00 33.76 4.85
3966 4126 4.331717 AGCAACGCACATTATTGTACTACC 59.668 41.667 0.00 0.00 33.76 3.18
3982 4144 4.582459 GAGAGATAACAAATCAGCAACGC 58.418 43.478 0.00 0.00 0.00 4.84
3984 4146 5.786401 ACGAGAGATAACAAATCAGCAAC 57.214 39.130 0.00 0.00 0.00 4.17
3995 4157 5.807520 TGCAGAGAATGAAACGAGAGATAAC 59.192 40.000 0.00 0.00 0.00 1.89
4034 4196 2.869801 TCATGTGGACGTTCAAGTGTTC 59.130 45.455 0.00 0.00 0.00 3.18
4110 4272 3.001533 TCGACGTAAGCCACAAGAAAAAC 59.998 43.478 0.00 0.00 45.62 2.43
4135 4297 7.488322 CAACTGTCCTTGAAATGGTCTTTAAA 58.512 34.615 0.00 0.00 31.98 1.52
4210 4373 6.069963 AGCTACCAGAGACTTCACCAAATTAT 60.070 38.462 0.00 0.00 0.00 1.28
4211 4374 5.248477 AGCTACCAGAGACTTCACCAAATTA 59.752 40.000 0.00 0.00 0.00 1.40
4212 4375 4.042187 AGCTACCAGAGACTTCACCAAATT 59.958 41.667 0.00 0.00 0.00 1.82
4213 4376 3.584848 AGCTACCAGAGACTTCACCAAAT 59.415 43.478 0.00 0.00 0.00 2.32
4276 4443 3.324268 GGGCTTAGTAACTCCTATGGGTC 59.676 52.174 0.00 0.00 0.00 4.46
4277 4444 3.051264 AGGGCTTAGTAACTCCTATGGGT 60.051 47.826 0.00 0.00 0.00 4.51
4278 4445 3.579151 GAGGGCTTAGTAACTCCTATGGG 59.421 52.174 0.00 0.00 0.00 4.00
4279 4446 3.579151 GGAGGGCTTAGTAACTCCTATGG 59.421 52.174 9.70 0.00 44.74 2.74
4280 4447 4.875561 GGAGGGCTTAGTAACTCCTATG 57.124 50.000 9.70 0.00 44.74 2.23
4285 4452 3.890756 GGTAGAGGAGGGCTTAGTAACTC 59.109 52.174 0.00 0.00 0.00 3.01
4286 4453 3.373987 GGGTAGAGGAGGGCTTAGTAACT 60.374 52.174 0.00 0.00 0.00 2.24
4287 4454 2.964464 GGGTAGAGGAGGGCTTAGTAAC 59.036 54.545 0.00 0.00 0.00 2.50
4288 4455 2.588720 TGGGTAGAGGAGGGCTTAGTAA 59.411 50.000 0.00 0.00 0.00 2.24
4289 4456 2.091444 GTGGGTAGAGGAGGGCTTAGTA 60.091 54.545 0.00 0.00 0.00 1.82
4290 4457 1.016415 TGGGTAGAGGAGGGCTTAGT 58.984 55.000 0.00 0.00 0.00 2.24
4291 4458 1.062810 AGTGGGTAGAGGAGGGCTTAG 60.063 57.143 0.00 0.00 0.00 2.18
4292 4459 1.016415 AGTGGGTAGAGGAGGGCTTA 58.984 55.000 0.00 0.00 0.00 3.09
4293 4460 0.618968 CAGTGGGTAGAGGAGGGCTT 60.619 60.000 0.00 0.00 0.00 4.35
4294 4461 1.002274 CAGTGGGTAGAGGAGGGCT 59.998 63.158 0.00 0.00 0.00 5.19
4295 4462 2.066999 CCAGTGGGTAGAGGAGGGC 61.067 68.421 0.00 0.00 0.00 5.19
4296 4463 4.382852 CCAGTGGGTAGAGGAGGG 57.617 66.667 0.00 0.00 0.00 4.30
4306 4473 4.000988 GACAGTTTACATACACCAGTGGG 58.999 47.826 15.21 5.06 41.29 4.61
4307 4474 4.637276 TGACAGTTTACATACACCAGTGG 58.363 43.478 7.91 7.91 34.19 4.00
4308 4475 6.481976 TCTTTGACAGTTTACATACACCAGTG 59.518 38.462 0.00 0.00 0.00 3.66
4309 4476 6.588204 TCTTTGACAGTTTACATACACCAGT 58.412 36.000 0.00 0.00 0.00 4.00
4310 4477 7.672983 ATCTTTGACAGTTTACATACACCAG 57.327 36.000 0.00 0.00 0.00 4.00
4311 4478 9.378551 GATATCTTTGACAGTTTACATACACCA 57.621 33.333 0.00 0.00 0.00 4.17
4312 4479 8.540492 CGATATCTTTGACAGTTTACATACACC 58.460 37.037 0.34 0.00 0.00 4.16
4313 4480 9.297586 TCGATATCTTTGACAGTTTACATACAC 57.702 33.333 0.34 0.00 0.00 2.90
4314 4481 9.297586 GTCGATATCTTTGACAGTTTACATACA 57.702 33.333 0.34 0.00 38.46 2.29
4315 4482 9.297586 TGTCGATATCTTTGACAGTTTACATAC 57.702 33.333 7.58 0.00 42.69 2.39
4325 4492 8.410141 TGTATGTATGTGTCGATATCTTTGACA 58.590 33.333 7.58 7.58 44.86 3.58
4326 4493 8.797266 TGTATGTATGTGTCGATATCTTTGAC 57.203 34.615 0.34 1.98 38.98 3.18
4336 4503 9.498176 AGTAGTATGTATGTATGTATGTGTCGA 57.502 33.333 0.00 0.00 0.00 4.20
4337 4504 9.756461 GAGTAGTATGTATGTATGTATGTGTCG 57.244 37.037 0.00 0.00 0.00 4.35
4339 4506 8.727910 CGGAGTAGTATGTATGTATGTATGTGT 58.272 37.037 0.00 0.00 0.00 3.72
4340 4507 8.727910 ACGGAGTAGTATGTATGTATGTATGTG 58.272 37.037 0.00 0.00 41.94 3.21
4341 4508 8.859236 ACGGAGTAGTATGTATGTATGTATGT 57.141 34.615 0.00 0.00 41.94 2.29
4361 4528 6.022208 CACTAGTATACATTATGCGACGGAG 58.978 44.000 5.50 0.00 0.00 4.63
4362 4529 5.471116 ACACTAGTATACATTATGCGACGGA 59.529 40.000 5.50 0.00 0.00 4.69
4363 4530 5.696822 ACACTAGTATACATTATGCGACGG 58.303 41.667 5.50 0.00 0.00 4.79
4364 4531 6.368213 TGACACTAGTATACATTATGCGACG 58.632 40.000 5.50 0.00 0.00 5.12
4365 4532 8.570096 TTTGACACTAGTATACATTATGCGAC 57.430 34.615 5.50 0.00 0.00 5.19
4366 4533 9.589111 TTTTTGACACTAGTATACATTATGCGA 57.411 29.630 5.50 0.00 0.00 5.10
4392 4559 9.025041 CCCTCCTTTTCATAATGTAAGACTTTT 57.975 33.333 0.00 0.00 0.00 2.27
4393 4560 7.615757 CCCCTCCTTTTCATAATGTAAGACTTT 59.384 37.037 0.00 0.00 0.00 2.66
4394 4561 7.036863 TCCCCTCCTTTTCATAATGTAAGACTT 60.037 37.037 0.00 0.00 0.00 3.01
4395 4562 6.447084 TCCCCTCCTTTTCATAATGTAAGACT 59.553 38.462 0.00 0.00 0.00 3.24
4396 4563 6.659824 TCCCCTCCTTTTCATAATGTAAGAC 58.340 40.000 0.00 0.00 0.00 3.01
4397 4564 6.901615 TCCCCTCCTTTTCATAATGTAAGA 57.098 37.500 0.00 0.00 0.00 2.10
4398 4565 8.440771 ACTATCCCCTCCTTTTCATAATGTAAG 58.559 37.037 0.00 0.00 0.00 2.34
4399 4566 8.344939 ACTATCCCCTCCTTTTCATAATGTAA 57.655 34.615 0.00 0.00 0.00 2.41
4400 4567 7.947782 ACTATCCCCTCCTTTTCATAATGTA 57.052 36.000 0.00 0.00 0.00 2.29
4401 4568 6.848562 ACTATCCCCTCCTTTTCATAATGT 57.151 37.500 0.00 0.00 0.00 2.71
4402 4569 9.813826 AAATACTATCCCCTCCTTTTCATAATG 57.186 33.333 0.00 0.00 0.00 1.90
4404 4571 9.640952 CAAAATACTATCCCCTCCTTTTCATAA 57.359 33.333 0.00 0.00 0.00 1.90
4405 4572 9.009675 TCAAAATACTATCCCCTCCTTTTCATA 57.990 33.333 0.00 0.00 0.00 2.15
4406 4573 7.882755 TCAAAATACTATCCCCTCCTTTTCAT 58.117 34.615 0.00 0.00 0.00 2.57
4407 4574 7.278724 TCAAAATACTATCCCCTCCTTTTCA 57.721 36.000 0.00 0.00 0.00 2.69
4408 4575 8.768501 AATCAAAATACTATCCCCTCCTTTTC 57.231 34.615 0.00 0.00 0.00 2.29
4427 4594 9.781834 CCGCTCAAATTACAACTATAAATCAAA 57.218 29.630 0.00 0.00 0.00 2.69
4428 4595 8.952278 ACCGCTCAAATTACAACTATAAATCAA 58.048 29.630 0.00 0.00 0.00 2.57
4429 4596 8.500753 ACCGCTCAAATTACAACTATAAATCA 57.499 30.769 0.00 0.00 0.00 2.57
4434 4601 9.602568 TGATTTACCGCTCAAATTACAACTATA 57.397 29.630 0.00 0.00 0.00 1.31
4435 4602 8.500753 TGATTTACCGCTCAAATTACAACTAT 57.499 30.769 0.00 0.00 0.00 2.12
4436 4603 7.908827 TGATTTACCGCTCAAATTACAACTA 57.091 32.000 0.00 0.00 0.00 2.24
4437 4604 6.811253 TGATTTACCGCTCAAATTACAACT 57.189 33.333 0.00 0.00 0.00 3.16
4438 4605 6.691388 GGATGATTTACCGCTCAAATTACAAC 59.309 38.462 0.00 0.00 0.00 3.32
4439 4606 6.457663 CGGATGATTTACCGCTCAAATTACAA 60.458 38.462 0.00 0.00 42.55 2.41
4440 4607 5.007234 CGGATGATTTACCGCTCAAATTACA 59.993 40.000 0.00 0.00 42.55 2.41
4441 4608 5.440685 CGGATGATTTACCGCTCAAATTAC 58.559 41.667 0.00 0.00 42.55 1.89
4442 4609 5.666969 CGGATGATTTACCGCTCAAATTA 57.333 39.130 0.00 0.00 42.55 1.40
4443 4610 4.552166 CGGATGATTTACCGCTCAAATT 57.448 40.909 0.00 0.00 42.55 1.82
4452 4619 5.633830 TCCTACGTATCGGATGATTTACC 57.366 43.478 0.00 0.00 35.99 2.85
4460 4627 5.977489 TGAAATCATCCTACGTATCGGAT 57.023 39.130 9.91 9.91 40.59 4.18
4461 4628 5.977489 ATGAAATCATCCTACGTATCGGA 57.023 39.130 6.06 6.06 28.78 4.55
4462 4629 6.156519 TGAATGAAATCATCCTACGTATCGG 58.843 40.000 0.00 0.00 35.10 4.18
4463 4630 7.818493 ATGAATGAAATCATCCTACGTATCG 57.182 36.000 0.00 0.00 35.07 2.92
4474 4641 3.958147 TGCTGCCTGATGAATGAAATCAT 59.042 39.130 0.00 0.00 42.62 2.45
4475 4642 3.358118 TGCTGCCTGATGAATGAAATCA 58.642 40.909 0.00 0.00 33.13 2.57
4476 4643 4.110482 GTTGCTGCCTGATGAATGAAATC 58.890 43.478 0.00 0.00 0.00 2.17
4477 4644 3.118884 GGTTGCTGCCTGATGAATGAAAT 60.119 43.478 0.00 0.00 0.00 2.17
4478 4645 2.231964 GGTTGCTGCCTGATGAATGAAA 59.768 45.455 0.00 0.00 0.00 2.69
4479 4646 1.820519 GGTTGCTGCCTGATGAATGAA 59.179 47.619 0.00 0.00 0.00 2.57
4480 4647 1.272037 TGGTTGCTGCCTGATGAATGA 60.272 47.619 0.00 0.00 0.00 2.57
4481 4648 1.179152 TGGTTGCTGCCTGATGAATG 58.821 50.000 0.00 0.00 0.00 2.67
4482 4649 1.547372 GTTGGTTGCTGCCTGATGAAT 59.453 47.619 0.00 0.00 0.00 2.57
4483 4650 0.961019 GTTGGTTGCTGCCTGATGAA 59.039 50.000 0.00 0.00 0.00 2.57
4484 4651 0.895100 GGTTGGTTGCTGCCTGATGA 60.895 55.000 0.00 0.00 0.00 2.92
4485 4652 1.180456 TGGTTGGTTGCTGCCTGATG 61.180 55.000 0.00 0.00 0.00 3.07
4486 4653 0.469705 TTGGTTGGTTGCTGCCTGAT 60.470 50.000 0.00 0.00 0.00 2.90
4487 4654 1.076412 TTGGTTGGTTGCTGCCTGA 60.076 52.632 0.00 0.00 0.00 3.86
4488 4655 1.067916 GTTGGTTGGTTGCTGCCTG 59.932 57.895 0.00 0.00 0.00 4.85
4489 4656 2.133641 GGTTGGTTGGTTGCTGCCT 61.134 57.895 0.00 0.00 0.00 4.75
4490 4657 1.965754 TTGGTTGGTTGGTTGCTGCC 61.966 55.000 0.00 0.00 0.00 4.85
4491 4658 0.530431 CTTGGTTGGTTGGTTGCTGC 60.530 55.000 0.00 0.00 0.00 5.25
4492 4659 0.104671 CCTTGGTTGGTTGGTTGCTG 59.895 55.000 0.00 0.00 0.00 4.41
4493 4660 0.325203 ACCTTGGTTGGTTGGTTGCT 60.325 50.000 0.00 0.00 36.89 3.91
4494 4661 2.207580 ACCTTGGTTGGTTGGTTGC 58.792 52.632 0.00 0.00 36.89 4.17
4501 4668 6.686885 GCCAGTTTTAATTAACCTTGGTTGGT 60.687 38.462 14.67 1.11 43.11 3.67
4502 4669 5.699001 GCCAGTTTTAATTAACCTTGGTTGG 59.301 40.000 14.67 5.55 30.21 3.77
4503 4670 6.284459 TGCCAGTTTTAATTAACCTTGGTTG 58.716 36.000 14.67 0.00 30.21 3.77
4504 4671 6.487299 TGCCAGTTTTAATTAACCTTGGTT 57.513 33.333 10.11 10.11 30.21 3.67
4505 4672 6.496911 AGATGCCAGTTTTAATTAACCTTGGT 59.503 34.615 16.46 0.00 30.21 3.67
4506 4673 6.935167 AGATGCCAGTTTTAATTAACCTTGG 58.065 36.000 13.13 13.13 0.00 3.61
4511 4678 9.678941 GCCTATAAGATGCCAGTTTTAATTAAC 57.321 33.333 0.00 0.00 0.00 2.01
4512 4679 9.415008 TGCCTATAAGATGCCAGTTTTAATTAA 57.585 29.630 0.00 0.00 0.00 1.40
4513 4680 8.988546 TGCCTATAAGATGCCAGTTTTAATTA 57.011 30.769 0.00 0.00 0.00 1.40
4514 4681 7.896383 TGCCTATAAGATGCCAGTTTTAATT 57.104 32.000 0.00 0.00 0.00 1.40
4515 4682 7.341769 TGTTGCCTATAAGATGCCAGTTTTAAT 59.658 33.333 0.00 0.00 0.00 1.40
4516 4683 6.661377 TGTTGCCTATAAGATGCCAGTTTTAA 59.339 34.615 0.00 0.00 0.00 1.52
4517 4684 6.184068 TGTTGCCTATAAGATGCCAGTTTTA 58.816 36.000 0.00 0.00 0.00 1.52
4518 4685 5.016173 TGTTGCCTATAAGATGCCAGTTTT 58.984 37.500 0.00 0.00 0.00 2.43
4519 4686 4.599041 TGTTGCCTATAAGATGCCAGTTT 58.401 39.130 0.00 0.00 0.00 2.66
4520 4687 4.202441 CTGTTGCCTATAAGATGCCAGTT 58.798 43.478 0.00 0.00 0.00 3.16
4521 4688 3.200825 ACTGTTGCCTATAAGATGCCAGT 59.799 43.478 0.00 0.00 0.00 4.00
4522 4689 3.812053 GACTGTTGCCTATAAGATGCCAG 59.188 47.826 0.00 0.00 0.00 4.85
4523 4690 3.741075 CGACTGTTGCCTATAAGATGCCA 60.741 47.826 0.00 0.00 0.00 4.92
4524 4691 2.802816 CGACTGTTGCCTATAAGATGCC 59.197 50.000 0.00 0.00 0.00 4.40
4525 4692 3.491267 GTCGACTGTTGCCTATAAGATGC 59.509 47.826 8.70 0.00 0.00 3.91
4526 4693 4.938080 AGTCGACTGTTGCCTATAAGATG 58.062 43.478 19.30 0.00 0.00 2.90
4527 4694 5.241949 CCTAGTCGACTGTTGCCTATAAGAT 59.758 44.000 28.12 0.00 0.00 2.40
4528 4695 4.579340 CCTAGTCGACTGTTGCCTATAAGA 59.421 45.833 28.12 1.85 0.00 2.10
4529 4696 4.793353 GCCTAGTCGACTGTTGCCTATAAG 60.793 50.000 28.12 12.49 0.00 1.73
4530 4697 3.067742 GCCTAGTCGACTGTTGCCTATAA 59.932 47.826 28.12 2.62 0.00 0.98
4531 4698 2.621998 GCCTAGTCGACTGTTGCCTATA 59.378 50.000 28.12 3.41 0.00 1.31
4532 4699 1.409427 GCCTAGTCGACTGTTGCCTAT 59.591 52.381 28.12 0.45 0.00 2.57
4533 4700 0.815734 GCCTAGTCGACTGTTGCCTA 59.184 55.000 28.12 4.99 0.00 3.93
4534 4701 1.185618 TGCCTAGTCGACTGTTGCCT 61.186 55.000 28.12 2.06 0.00 4.75
4535 4702 0.320421 TTGCCTAGTCGACTGTTGCC 60.320 55.000 28.12 11.64 0.00 4.52
4536 4703 1.726853 ATTGCCTAGTCGACTGTTGC 58.273 50.000 28.12 24.28 0.00 4.17


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

AutoCloner maintained by Alex Coulton.