Multiple sequence alignment - TraesCS3A01G381200

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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 TraesCS3A01G381200 chr3A 100.000 6486 0 0 1 6486 631586454 631579969 0.000000e+00 11978.0
1 TraesCS3A01G381200 chr3D 94.380 5374 198 48 300 5602 487817703 487812363 0.000000e+00 8155.0
2 TraesCS3A01G381200 chr3D 93.255 341 22 1 5639 5978 487812364 487812024 9.710000e-138 501.0
3 TraesCS3A01G381200 chr3D 89.326 178 17 1 6258 6433 487811831 487811654 8.460000e-54 222.0
4 TraesCS3A01G381200 chr3D 79.104 268 23 19 1 252 487818264 487818014 3.130000e-33 154.0
5 TraesCS3A01G381200 chr3D 97.727 44 1 0 6441 6484 487811570 487811527 6.970000e-10 76.8
6 TraesCS3A01G381200 chr4A 92.755 4003 213 36 2387 6364 618037070 618041020 0.000000e+00 5714.0
7 TraesCS3A01G381200 chr4A 92.409 2740 152 25 3647 6364 621446052 621443347 0.000000e+00 3856.0
8 TraesCS3A01G381200 chr4A 92.979 997 53 8 2387 3382 621448133 621447153 0.000000e+00 1437.0
9 TraesCS3A01G381200 chr4A 90.909 55 3 2 6432 6486 618041185 618041237 9.020000e-09 73.1
10 TraesCS3A01G381200 chr4A 90.909 55 3 2 6432 6486 621443182 621443130 9.020000e-09 73.1
11 TraesCS3A01G381200 chrUn 94.153 2309 110 10 3647 5945 345812521 345814814 0.000000e+00 3493.0
12 TraesCS3A01G381200 chrUn 94.731 1955 83 7 2534 4488 362281758 362279824 0.000000e+00 3022.0
13 TraesCS3A01G381200 chrUn 87.465 359 32 8 6018 6364 472852403 472852046 1.010000e-107 401.0
14 TraesCS3A01G381200 chr3B 95.652 2162 63 11 2579 4738 650805954 650803822 0.000000e+00 3443.0
15 TraesCS3A01G381200 chr3B 91.911 2151 93 33 396 2496 650808077 650805958 0.000000e+00 2933.0
16 TraesCS3A01G381200 chr3B 95.436 1205 48 4 4737 5936 650803718 650802516 0.000000e+00 1914.0
17 TraesCS3A01G381200 chr3B 93.985 133 2 2 280 407 650808223 650808092 5.130000e-46 196.0
18 TraesCS3A01G381200 chr3B 83.333 150 8 8 98 233 650808443 650808297 8.830000e-24 122.0
19 TraesCS3A01G381200 chr7A 85.497 855 110 11 3912 4758 238593132 238592284 0.000000e+00 880.0
20 TraesCS3A01G381200 chr4B 85.514 856 108 14 3912 4758 593368445 593367597 0.000000e+00 880.0
21 TraesCS3A01G381200 chr4B 85.860 587 78 5 4799 5383 593367594 593367011 2.570000e-173 619.0
22 TraesCS3A01G381200 chr7B 85.164 856 111 14 3912 4758 679785734 679784886 0.000000e+00 863.0
23 TraesCS3A01G381200 chr7B 85.520 587 80 5 4799 5383 679784883 679784300 5.560000e-170 608.0
24 TraesCS3A01G381200 chr2D 84.864 588 83 6 4799 5383 522903260 522902676 7.240000e-164 588.0
25 TraesCS3A01G381200 chr2D 80.859 256 29 13 4657 4911 549017854 549018090 3.990000e-42 183.0
26 TraesCS3A01G381200 chr2B 88.793 232 14 6 6242 6467 460323444 460323219 2.300000e-69 274.0
27 TraesCS3A01G381200 chr2B 83.004 253 41 1 4657 4909 109298226 109297976 1.820000e-55 228.0
28 TraesCS3A01G381200 chr1B 82.381 210 34 3 5175 5383 152316573 152316366 5.170000e-41 180.0
29 TraesCS3A01G381200 chr5B 82.667 150 21 3 4932 5077 18274268 18274120 1.900000e-25 128.0
30 TraesCS3A01G381200 chr5B 82.667 150 21 3 4932 5077 18303334 18303186 1.900000e-25 128.0


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 TraesCS3A01G381200 chr3A 631579969 631586454 6485 True 11978.00 11978 100.0000 1 6486 1 chr3A.!!$R1 6485
1 TraesCS3A01G381200 chr3D 487811527 487818264 6737 True 1821.76 8155 90.7584 1 6484 5 chr3D.!!$R1 6483
2 TraesCS3A01G381200 chr4A 618037070 618041237 4167 False 2893.55 5714 91.8320 2387 6486 2 chr4A.!!$F1 4099
3 TraesCS3A01G381200 chr4A 621443130 621448133 5003 True 1788.70 3856 92.0990 2387 6486 3 chr4A.!!$R1 4099
4 TraesCS3A01G381200 chrUn 345812521 345814814 2293 False 3493.00 3493 94.1530 3647 5945 1 chrUn.!!$F1 2298
5 TraesCS3A01G381200 chrUn 362279824 362281758 1934 True 3022.00 3022 94.7310 2534 4488 1 chrUn.!!$R1 1954
6 TraesCS3A01G381200 chr3B 650802516 650808443 5927 True 1721.60 3443 92.0634 98 5936 5 chr3B.!!$R1 5838
7 TraesCS3A01G381200 chr7A 238592284 238593132 848 True 880.00 880 85.4970 3912 4758 1 chr7A.!!$R1 846
8 TraesCS3A01G381200 chr4B 593367011 593368445 1434 True 749.50 880 85.6870 3912 5383 2 chr4B.!!$R1 1471
9 TraesCS3A01G381200 chr7B 679784300 679785734 1434 True 735.50 863 85.3420 3912 5383 2 chr7B.!!$R1 1471
10 TraesCS3A01G381200 chr2D 522902676 522903260 584 True 588.00 588 84.8640 4799 5383 1 chr2D.!!$R1 584

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
259 319 0.517316 GAAACACGAGGACATGTGCC 59.483 55.000 14.38 9.76 39.71 5.01 F
861 1291 1.153086 CCACTAGCCATGGTCTGCC 60.153 63.158 14.67 0.00 32.08 4.85 F
1730 2185 0.038744 AGTGGATGAAAGTGCTGGGG 59.961 55.000 0.00 0.00 0.00 4.96 F
1908 2364 0.905357 CCGAGACATCCTGGGTTCTT 59.095 55.000 0.00 0.00 36.17 2.52 F
3081 3537 1.205893 ACCGAGCTGTTCTTCTGATCC 59.794 52.381 0.00 0.00 0.00 3.36 F
4149 5441 1.019278 GTTGGCGACGTGACATCCAT 61.019 55.000 0.00 0.00 33.63 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1449 1898 0.323908 CCAGGGACTTCTCCTCGTCT 60.324 60.000 0.00 0.0 34.60 4.18 R
2038 2494 0.894184 TCTTCCTCGGTGCTTCTCGT 60.894 55.000 0.00 0.0 0.00 4.18 R
3152 3608 0.402861 AACCTGTGGGGAGGAAAGGA 60.403 55.000 0.00 0.0 36.51 3.36 R
3291 3747 5.482006 GGGAATGGAGAAAATGAAAGTTGG 58.518 41.667 0.00 0.0 0.00 3.77 R
4537 5837 0.729116 AAATGCGAGCCAAGATGACG 59.271 50.000 0.00 0.0 0.00 4.35 R
5997 7427 0.038166 GGGGCCTTCACAGAATCACA 59.962 55.000 0.84 0.0 0.00 3.58 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 4.767928 ACCGCCAACAACTCCAATTTATAA 59.232 37.500 0.00 0.00 0.00 0.98
30 31 5.124776 CCGCCAACAACTCCAATTTATAAGA 59.875 40.000 0.00 0.00 0.00 2.10
32 33 7.012894 CCGCCAACAACTCCAATTTATAAGATA 59.987 37.037 0.00 0.00 0.00 1.98
33 34 7.855904 CGCCAACAACTCCAATTTATAAGATAC 59.144 37.037 0.00 0.00 0.00 2.24
52 53 8.539770 AAGATACTAGAGACATGTTGTTGTTG 57.460 34.615 0.00 0.00 0.00 3.33
55 56 8.677148 ATACTAGAGACATGTTGTTGTTGTTT 57.323 30.769 0.00 0.00 0.00 2.83
90 99 7.934855 AAACTAGTAATTACTCTCTCCGTCA 57.065 36.000 21.25 0.36 37.73 4.35
91 100 6.923928 ACTAGTAATTACTCTCTCCGTCAC 57.076 41.667 21.25 0.00 37.73 3.67
92 101 6.413052 ACTAGTAATTACTCTCTCCGTCACA 58.587 40.000 21.25 0.00 37.73 3.58
93 102 7.055378 ACTAGTAATTACTCTCTCCGTCACAT 58.945 38.462 21.25 0.00 37.73 3.21
94 103 6.380095 AGTAATTACTCTCTCCGTCACATC 57.620 41.667 12.50 0.00 0.00 3.06
95 104 5.886474 AGTAATTACTCTCTCCGTCACATCA 59.114 40.000 12.50 0.00 0.00 3.07
96 105 4.640789 ATTACTCTCTCCGTCACATCAC 57.359 45.455 0.00 0.00 0.00 3.06
97 106 1.911057 ACTCTCTCCGTCACATCACA 58.089 50.000 0.00 0.00 0.00 3.58
98 107 1.815613 ACTCTCTCCGTCACATCACAG 59.184 52.381 0.00 0.00 0.00 3.66
99 108 2.087646 CTCTCTCCGTCACATCACAGA 58.912 52.381 0.00 0.00 0.00 3.41
100 109 2.687425 CTCTCTCCGTCACATCACAGAT 59.313 50.000 0.00 0.00 0.00 2.90
101 110 3.092301 TCTCTCCGTCACATCACAGATT 58.908 45.455 0.00 0.00 0.00 2.40
102 111 3.119352 TCTCTCCGTCACATCACAGATTG 60.119 47.826 0.00 0.00 0.00 2.67
103 112 1.662629 CTCCGTCACATCACAGATTGC 59.337 52.381 0.00 0.00 0.00 3.56
104 113 0.729116 CCGTCACATCACAGATTGCC 59.271 55.000 0.00 0.00 0.00 4.52
129 138 5.767277 ACGGTATTCTCTAAAGGGGAAAA 57.233 39.130 0.00 0.00 0.00 2.29
131 140 6.120220 ACGGTATTCTCTAAAGGGGAAAATG 58.880 40.000 0.00 0.00 0.00 2.32
140 149 3.449746 AAGGGGAAAATGGACGATTGA 57.550 42.857 0.00 0.00 0.00 2.57
142 151 3.356290 AGGGGAAAATGGACGATTGAAG 58.644 45.455 0.00 0.00 0.00 3.02
143 152 2.427095 GGGGAAAATGGACGATTGAAGG 59.573 50.000 0.00 0.00 0.00 3.46
181 202 4.940463 AGGGCGAACTAAAAAGGAAAAAC 58.060 39.130 0.00 0.00 0.00 2.43
247 307 3.420839 AGCAAACCTGAAAGAAACACG 57.579 42.857 0.00 0.00 34.07 4.49
259 319 0.517316 GAAACACGAGGACATGTGCC 59.483 55.000 14.38 9.76 39.71 5.01
268 328 2.981560 GACATGTGCCCTGTTGCCG 61.982 63.158 1.15 0.00 0.00 5.69
269 329 2.985282 CATGTGCCCTGTTGCCGT 60.985 61.111 0.00 0.00 0.00 5.68
270 330 2.985282 ATGTGCCCTGTTGCCGTG 60.985 61.111 0.00 0.00 0.00 4.94
275 335 2.045438 CCCTGTTGCCGTGCCATA 60.045 61.111 0.00 0.00 0.00 2.74
276 336 2.406616 CCCTGTTGCCGTGCCATAC 61.407 63.158 0.00 0.00 0.00 2.39
458 813 2.254350 GGCAAAGTTTCGTCCGGC 59.746 61.111 0.00 0.00 0.00 6.13
544 900 3.083997 GATCACCCGAGCCCCACT 61.084 66.667 0.00 0.00 0.00 4.00
599 956 1.429423 GCGCGGGAATGAAAAGGAG 59.571 57.895 8.83 0.00 0.00 3.69
659 1045 4.947147 TGGTGTTGTGCTCCGGCC 62.947 66.667 0.00 0.00 37.74 6.13
660 1046 4.643387 GGTGTTGTGCTCCGGCCT 62.643 66.667 0.00 0.00 37.74 5.19
661 1047 3.050275 GTGTTGTGCTCCGGCCTC 61.050 66.667 0.00 0.00 37.74 4.70
662 1048 4.329545 TGTTGTGCTCCGGCCTCC 62.330 66.667 0.00 0.00 37.74 4.30
663 1049 4.329545 GTTGTGCTCCGGCCTCCA 62.330 66.667 0.00 0.00 37.74 3.86
664 1050 4.020617 TTGTGCTCCGGCCTCCAG 62.021 66.667 0.00 0.00 37.74 3.86
740 1155 3.058501 GGTTACTGTTGCGCTGTTTATGT 60.059 43.478 9.73 1.12 0.00 2.29
861 1291 1.153086 CCACTAGCCATGGTCTGCC 60.153 63.158 14.67 0.00 32.08 4.85
872 1302 1.323271 TGGTCTGCCGATCCTGTCTC 61.323 60.000 0.00 0.00 37.67 3.36
951 1381 1.414866 TTACTGCCACCACCAGCTGA 61.415 55.000 17.39 0.00 33.65 4.26
1308 1754 3.760035 CGCGACTGGTGCTACCCT 61.760 66.667 0.00 0.00 37.50 4.34
1488 1937 1.734477 CTCCGTGGTCAAGCAGTCG 60.734 63.158 0.00 0.00 0.00 4.18
1560 2012 0.871722 CTCGCCGATTCGATCTCTCT 59.128 55.000 7.83 0.00 37.87 3.10
1563 2015 0.242555 GCCGATTCGATCTCTCTCCC 59.757 60.000 7.83 0.00 0.00 4.30
1609 2061 2.417787 GCCATTTAAAGCTCCAGCCTTG 60.418 50.000 0.00 0.00 43.38 3.61
1656 2111 2.176045 GTCCATTTCCCCCGTGAATTT 58.824 47.619 0.00 0.00 0.00 1.82
1694 2149 0.038892 TCGTAACCGTCACAAGCTCC 60.039 55.000 0.00 0.00 35.01 4.70
1703 2158 2.204059 ACAAGCTCCTCCCTGGCT 60.204 61.111 0.00 0.00 37.99 4.75
1730 2185 0.038744 AGTGGATGAAAGTGCTGGGG 59.961 55.000 0.00 0.00 0.00 4.96
1871 2327 2.674033 TGGTGGTGCTGATGCTGC 60.674 61.111 0.00 0.00 40.48 5.25
1908 2364 0.905357 CCGAGACATCCTGGGTTCTT 59.095 55.000 0.00 0.00 36.17 2.52
1968 2424 2.042686 AATTAGCTCCGATGCTTGCA 57.957 45.000 7.38 0.00 43.74 4.08
2038 2494 5.278463 CGAAAGAAAGAAAATTCCAGCAGGA 60.278 40.000 0.00 0.00 43.93 3.86
2074 2530 2.208132 AGAAGTGCCTCTCGAGAAGA 57.792 50.000 17.36 0.00 0.00 2.87
2160 2616 3.195610 TGATCGCCACTGTAGTTCTCATT 59.804 43.478 0.00 0.00 0.00 2.57
2355 2811 2.743752 CGGGCTTGTGTCAGATGCG 61.744 63.158 2.32 0.00 0.00 4.73
2577 3033 3.573110 AGTAGTGCGTTTCTGAAGTAGGT 59.427 43.478 0.00 0.00 0.00 3.08
2819 3275 5.291971 CACTGAGGTTTATTTGCTTGCTTT 58.708 37.500 0.00 0.00 0.00 3.51
2896 3352 1.361793 GCTCTCTTCTGAAGCAGCTG 58.638 55.000 23.32 10.11 33.67 4.24
2995 3451 6.101734 TGGACATAGGAAAGCTAGGATTTGAT 59.898 38.462 0.00 0.00 0.00 2.57
3069 3525 1.819288 TCTGAAGAAGGTACCGAGCTG 59.181 52.381 6.18 0.64 32.39 4.24
3081 3537 1.205893 ACCGAGCTGTTCTTCTGATCC 59.794 52.381 0.00 0.00 0.00 3.36
3095 3551 8.424918 GTTCTTCTGATCCTCCACTATGAATAA 58.575 37.037 0.00 0.00 0.00 1.40
3102 3558 7.348274 TGATCCTCCACTATGAATAAACTCCTT 59.652 37.037 0.00 0.00 0.00 3.36
3129 3585 6.012658 TGGTTTCTTTTCATGCTATGTGTC 57.987 37.500 0.00 0.00 0.00 3.67
3186 3642 2.731217 CAGGTTTCTGTTTCCAAAGCG 58.269 47.619 0.00 0.00 35.57 4.68
3269 3725 5.081032 TCCACCTTTACTATTTTGGGGTTG 58.919 41.667 0.00 0.00 0.00 3.77
3291 3747 7.809806 GGTTGACAGCTCATATAATTATTTGCC 59.190 37.037 2.68 1.69 0.00 4.52
3296 3752 7.506938 ACAGCTCATATAATTATTTGCCCAACT 59.493 33.333 2.68 0.00 0.00 3.16
3588 4044 8.695456 AGAAAAGAAACAAAATCTTTGAGCCTA 58.305 29.630 6.15 0.00 44.22 3.93
3863 5155 9.890352 GATGATGATTATGTTTTAAGAGAAGGC 57.110 33.333 0.00 0.00 0.00 4.35
3869 5161 7.915293 TTATGTTTTAAGAGAAGGCGATGAA 57.085 32.000 0.00 0.00 0.00 2.57
4098 5390 1.257055 TACCTAACGTTCCCACCCCG 61.257 60.000 2.82 0.00 0.00 5.73
4149 5441 1.019278 GTTGGCGACGTGACATCCAT 61.019 55.000 0.00 0.00 33.63 3.41
4467 5765 9.539825 GTATATGCCCTATCATAGAGACAAATG 57.460 37.037 0.00 0.00 32.99 2.32
4537 5837 5.856455 CCGTCAATGTTGTCCAAAATAGTTC 59.144 40.000 0.00 0.00 0.00 3.01
4699 6002 4.563184 GCGACACTTCTTCTAATTCGTGAT 59.437 41.667 0.00 0.00 0.00 3.06
4752 6163 7.670364 TGTAGCATATATAACTGACAGTGCAT 58.330 34.615 9.33 8.39 34.01 3.96
5063 6479 3.394606 AGGAACTTTTTGCTGAGGAGGTA 59.605 43.478 0.00 0.00 27.25 3.08
5117 6533 9.650539 TTGTGCTTTAATATTGCAATAACATGT 57.349 25.926 22.37 3.48 38.50 3.21
5188 6604 9.624373 ATGACTTGAAGCATCTCTATTTAATGT 57.376 29.630 0.00 0.00 0.00 2.71
5234 6654 2.018355 TAACTACCCAGTGACCTGCA 57.982 50.000 0.00 0.00 37.38 4.41
5236 6656 2.247699 ACTACCCAGTGACCTGCATA 57.752 50.000 0.00 0.00 37.38 3.14
5308 6729 4.620803 CGGTCTGCTGAGTTTTACCTGTAT 60.621 45.833 0.00 0.00 0.00 2.29
5320 6741 7.514721 AGTTTTACCTGTATGAACAAGAGGAA 58.485 34.615 0.00 0.00 34.49 3.36
5579 7001 6.528537 ACTAATCCATGCTAGCTGATAGAG 57.471 41.667 17.23 15.82 32.76 2.43
5581 7003 6.723515 ACTAATCCATGCTAGCTGATAGAGAA 59.276 38.462 17.23 0.00 32.76 2.87
5782 7205 3.861840 TGCAGTAGGAATAGCTTGTGAC 58.138 45.455 0.00 0.00 0.00 3.67
5807 7230 5.180304 TCATGTTGTATTTTGTAAGCTCGCA 59.820 36.000 0.00 0.00 0.00 5.10
5824 7247 4.667668 GCTCGCAGCTAATTATTGAATCCG 60.668 45.833 0.00 0.00 38.45 4.18
5878 7306 3.072915 TCAAAGGAAAGAGGACATGCAGA 59.927 43.478 0.00 0.00 0.00 4.26
5901 7329 5.911752 AGTATTCTGTGAATGCTCCTGTAG 58.088 41.667 5.33 0.00 0.00 2.74
5904 7332 3.930336 TCTGTGAATGCTCCTGTAGTTG 58.070 45.455 0.00 0.00 0.00 3.16
5907 7335 4.566004 TGTGAATGCTCCTGTAGTTGTAC 58.434 43.478 0.00 0.00 0.00 2.90
5911 7339 5.127194 TGAATGCTCCTGTAGTTGTACCTAG 59.873 44.000 0.00 0.00 0.00 3.02
5920 7348 6.996879 CCTGTAGTTGTACCTAGACATAGCTA 59.003 42.308 0.00 0.00 0.00 3.32
5936 7364 2.154462 AGCTAAACAGCGTGCATCTTT 58.846 42.857 0.00 0.00 40.27 2.52
5940 7368 2.405892 AACAGCGTGCATCTTTGTTC 57.594 45.000 0.00 0.00 0.00 3.18
5959 7389 7.928908 TTGTTCTTTTACTTTTGCTATGCTG 57.071 32.000 0.00 0.00 0.00 4.41
5960 7390 5.920273 TGTTCTTTTACTTTTGCTATGCTGC 59.080 36.000 0.00 0.00 0.00 5.25
5976 7406 1.266718 GCTGCGTTGATGTTCCAAGAA 59.733 47.619 0.00 0.00 0.00 2.52
5977 7407 2.287547 GCTGCGTTGATGTTCCAAGAAA 60.288 45.455 0.00 0.00 0.00 2.52
5978 7408 3.558505 CTGCGTTGATGTTCCAAGAAAG 58.441 45.455 0.00 0.00 0.00 2.62
5980 7410 3.250762 TGCGTTGATGTTCCAAGAAAGAG 59.749 43.478 0.00 0.00 0.00 2.85
5983 7413 4.083802 CGTTGATGTTCCAAGAAAGAGGAC 60.084 45.833 0.00 0.00 32.62 3.85
5985 7415 5.246981 TGATGTTCCAAGAAAGAGGACAT 57.753 39.130 0.00 0.00 32.62 3.06
5986 7416 5.005740 TGATGTTCCAAGAAAGAGGACATG 58.994 41.667 0.00 0.00 32.62 3.21
5987 7417 3.149196 TGTTCCAAGAAAGAGGACATGC 58.851 45.455 0.00 0.00 32.62 4.06
5988 7418 3.149196 GTTCCAAGAAAGAGGACATGCA 58.851 45.455 0.00 0.00 32.62 3.96
5990 7420 2.373169 TCCAAGAAAGAGGACATGCAGT 59.627 45.455 0.00 0.00 0.00 4.40
5991 7421 2.486982 CCAAGAAAGAGGACATGCAGTG 59.513 50.000 0.00 0.00 0.00 3.66
5992 7422 3.144506 CAAGAAAGAGGACATGCAGTGT 58.855 45.455 0.00 0.00 45.83 3.55
5994 7424 4.199432 AGAAAGAGGACATGCAGTGTAG 57.801 45.455 0.00 0.00 42.36 2.74
5995 7425 2.393271 AAGAGGACATGCAGTGTAGC 57.607 50.000 0.00 0.00 42.36 3.58
5997 7427 0.539051 GAGGACATGCAGTGTAGCCT 59.461 55.000 0.00 1.16 42.36 4.58
5999 7429 0.036010 GGACATGCAGTGTAGCCTGT 60.036 55.000 0.00 0.00 44.30 4.00
6000 7430 1.081892 GACATGCAGTGTAGCCTGTG 58.918 55.000 1.73 0.00 42.22 3.66
6001 7431 0.686789 ACATGCAGTGTAGCCTGTGA 59.313 50.000 0.00 0.00 40.95 3.58
6002 7432 1.280133 ACATGCAGTGTAGCCTGTGAT 59.720 47.619 0.00 0.00 40.95 3.06
6003 7433 2.290514 ACATGCAGTGTAGCCTGTGATT 60.291 45.455 0.00 0.00 40.95 2.57
6004 7434 2.099141 TGCAGTGTAGCCTGTGATTC 57.901 50.000 0.00 0.00 34.84 2.52
6005 7435 1.625315 TGCAGTGTAGCCTGTGATTCT 59.375 47.619 0.00 0.00 34.84 2.40
6006 7436 2.005451 GCAGTGTAGCCTGTGATTCTG 58.995 52.381 0.00 0.00 34.84 3.02
6007 7437 2.613977 GCAGTGTAGCCTGTGATTCTGT 60.614 50.000 0.00 0.00 34.84 3.41
6008 7438 2.998670 CAGTGTAGCCTGTGATTCTGTG 59.001 50.000 0.00 0.00 0.00 3.66
6009 7439 2.899900 AGTGTAGCCTGTGATTCTGTGA 59.100 45.455 0.00 0.00 0.00 3.58
6010 7440 3.324846 AGTGTAGCCTGTGATTCTGTGAA 59.675 43.478 0.00 0.00 0.00 3.18
6011 7441 3.681897 GTGTAGCCTGTGATTCTGTGAAG 59.318 47.826 0.00 0.00 0.00 3.02
6012 7442 2.486472 AGCCTGTGATTCTGTGAAGG 57.514 50.000 0.00 0.00 0.00 3.46
6013 7443 0.807496 GCCTGTGATTCTGTGAAGGC 59.193 55.000 0.00 0.00 43.05 4.35
6014 7444 1.457346 CCTGTGATTCTGTGAAGGCC 58.543 55.000 0.00 0.00 0.00 5.19
6015 7445 1.457346 CTGTGATTCTGTGAAGGCCC 58.543 55.000 0.00 0.00 0.00 5.80
6016 7446 0.038166 TGTGATTCTGTGAAGGCCCC 59.962 55.000 0.00 0.00 0.00 5.80
6020 7450 0.038744 ATTCTGTGAAGGCCCCTGTG 59.961 55.000 0.00 0.00 0.00 3.66
6046 7476 5.956642 GCTATCTAACCATAGCTGTACCTC 58.043 45.833 0.00 0.00 45.46 3.85
6051 7481 2.402564 ACCATAGCTGTACCTCTGCAT 58.597 47.619 0.00 0.00 42.26 3.96
6069 7499 4.284378 GCATAGTGCATCTTGGTTCTTC 57.716 45.455 0.00 0.00 44.26 2.87
6081 7511 7.360776 GCATCTTGGTTCTTCTACTTTCTCTTG 60.361 40.741 0.00 0.00 0.00 3.02
6128 7562 2.076863 AGCAACCGTGAAATAGAGCAC 58.923 47.619 0.00 0.00 0.00 4.40
6163 7597 3.766051 AGCATATCATCGGAGCTATGTGA 59.234 43.478 0.00 0.00 33.06 3.58
6185 7619 1.605712 GGTGCTAGCTCGTTGACTGTT 60.606 52.381 17.23 0.00 0.00 3.16
6192 7626 2.159099 AGCTCGTTGACTGTTGAGACAA 60.159 45.455 5.02 0.00 34.85 3.18
6194 7628 3.248602 GCTCGTTGACTGTTGAGACAATT 59.751 43.478 0.00 0.00 36.48 2.32
6218 7652 1.188863 AGGTTTGAATCCTGGCATGC 58.811 50.000 9.90 9.90 33.62 4.06
6221 7694 1.135721 GTTTGAATCCTGGCATGCCTC 59.864 52.381 35.53 24.49 36.94 4.70
6222 7695 0.627451 TTGAATCCTGGCATGCCTCT 59.373 50.000 35.53 16.17 36.94 3.69
6223 7696 0.106868 TGAATCCTGGCATGCCTCTG 60.107 55.000 35.53 24.11 36.94 3.35
6224 7697 1.453762 GAATCCTGGCATGCCTCTGC 61.454 60.000 35.53 16.95 41.53 4.26
6235 7708 2.346766 TGCCTCTGCAAAGTTGAGAA 57.653 45.000 1.66 0.00 46.66 2.87
6236 7709 2.653726 TGCCTCTGCAAAGTTGAGAAA 58.346 42.857 1.66 0.00 46.66 2.52
6237 7710 2.620115 TGCCTCTGCAAAGTTGAGAAAG 59.380 45.455 1.66 0.00 46.66 2.62
6238 7711 2.880890 GCCTCTGCAAAGTTGAGAAAGA 59.119 45.455 1.66 0.00 37.47 2.52
6239 7712 3.316308 GCCTCTGCAAAGTTGAGAAAGAA 59.684 43.478 1.66 0.00 37.47 2.52
6240 7713 4.202050 GCCTCTGCAAAGTTGAGAAAGAAA 60.202 41.667 1.66 0.00 37.47 2.52
6241 7714 5.517904 CCTCTGCAAAGTTGAGAAAGAAAG 58.482 41.667 1.66 0.00 0.00 2.62
6242 7715 5.297776 CCTCTGCAAAGTTGAGAAAGAAAGA 59.702 40.000 1.66 0.00 0.00 2.52
6243 7716 6.124088 TCTGCAAAGTTGAGAAAGAAAGAC 57.876 37.500 0.00 0.00 0.00 3.01
6244 7717 5.647658 TCTGCAAAGTTGAGAAAGAAAGACA 59.352 36.000 0.00 0.00 0.00 3.41
6245 7718 6.150976 TCTGCAAAGTTGAGAAAGAAAGACAA 59.849 34.615 0.00 0.00 0.00 3.18
6246 7719 6.324819 TGCAAAGTTGAGAAAGAAAGACAAG 58.675 36.000 0.00 0.00 0.00 3.16
6247 7720 6.071952 TGCAAAGTTGAGAAAGAAAGACAAGT 60.072 34.615 0.00 0.00 0.00 3.16
6248 7721 6.252228 GCAAAGTTGAGAAAGAAAGACAAGTG 59.748 38.462 0.00 0.00 0.00 3.16
6249 7722 5.491635 AGTTGAGAAAGAAAGACAAGTGC 57.508 39.130 0.00 0.00 0.00 4.40
6250 7723 4.336713 AGTTGAGAAAGAAAGACAAGTGCC 59.663 41.667 0.00 0.00 0.00 5.01
6251 7724 4.156455 TGAGAAAGAAAGACAAGTGCCT 57.844 40.909 0.00 0.00 0.00 4.75
6252 7725 4.130118 TGAGAAAGAAAGACAAGTGCCTC 58.870 43.478 0.00 0.00 0.00 4.70
6253 7726 4.130118 GAGAAAGAAAGACAAGTGCCTCA 58.870 43.478 0.00 0.00 0.00 3.86
6254 7727 4.723309 AGAAAGAAAGACAAGTGCCTCAT 58.277 39.130 0.00 0.00 0.00 2.90
6255 7728 4.518211 AGAAAGAAAGACAAGTGCCTCATG 59.482 41.667 0.00 0.00 0.00 3.07
6256 7729 3.777106 AGAAAGACAAGTGCCTCATGA 57.223 42.857 0.00 0.00 0.00 3.07
6257 7730 4.298103 AGAAAGACAAGTGCCTCATGAT 57.702 40.909 0.00 0.00 0.00 2.45
6263 7736 1.945394 CAAGTGCCTCATGATACCAGC 59.055 52.381 0.00 0.00 0.00 4.85
6346 7825 6.248569 CCAACTGGTAGGAGTATTTGGTAT 57.751 41.667 0.00 0.00 0.00 2.73
6366 7847 1.155155 GGTTGGATGGGTTGGTGGT 59.845 57.895 0.00 0.00 0.00 4.16
6367 7848 1.184970 GGTTGGATGGGTTGGTGGTG 61.185 60.000 0.00 0.00 0.00 4.17
6375 7856 0.179001 GGGTTGGTGGTGCTAACTGT 60.179 55.000 0.00 0.00 38.44 3.55
6377 7858 2.487625 GGGTTGGTGGTGCTAACTGTTA 60.488 50.000 0.00 0.00 38.44 2.41
6383 7864 4.189231 GGTGGTGCTAACTGTTATACCAG 58.811 47.826 24.96 9.16 38.73 4.00
6414 7895 1.680249 GGGACATTCTGAAGAGGGTGC 60.680 57.143 0.00 0.00 0.00 5.01
6435 8031 0.182537 TCCACCACAACTCCCACTTG 59.817 55.000 0.00 0.00 0.00 3.16
6473 8069 3.985019 TTTAGGGCGAACCACAGAATA 57.015 42.857 0.00 0.00 43.89 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 7.671302 ACAACAACAACATGTCTCTAGTATCT 58.329 34.615 0.00 0.00 31.81 1.98
30 31 8.677148 AAACAACAACAACATGTCTCTAGTAT 57.323 30.769 0.00 0.00 31.81 2.12
32 33 7.391148 AAAACAACAACAACATGTCTCTAGT 57.609 32.000 0.00 0.00 31.81 2.57
80 89 2.200373 TCTGTGATGTGACGGAGAGA 57.800 50.000 0.00 0.00 0.00 3.10
81 90 3.185330 CAATCTGTGATGTGACGGAGAG 58.815 50.000 0.00 0.00 34.69 3.20
82 91 2.675032 GCAATCTGTGATGTGACGGAGA 60.675 50.000 0.00 0.00 34.69 3.71
83 92 1.662629 GCAATCTGTGATGTGACGGAG 59.337 52.381 0.00 0.00 34.69 4.63
84 93 1.675714 GGCAATCTGTGATGTGACGGA 60.676 52.381 0.00 0.00 35.68 4.69
86 95 1.441738 TGGCAATCTGTGATGTGACG 58.558 50.000 0.00 0.00 0.00 4.35
88 97 2.226200 CGTTTGGCAATCTGTGATGTGA 59.774 45.455 0.00 0.00 0.00 3.58
89 98 2.587956 CGTTTGGCAATCTGTGATGTG 58.412 47.619 0.00 0.00 0.00 3.21
90 99 1.541147 CCGTTTGGCAATCTGTGATGT 59.459 47.619 0.00 0.00 0.00 3.06
91 100 1.541147 ACCGTTTGGCAATCTGTGATG 59.459 47.619 0.00 0.00 39.70 3.07
92 101 1.909700 ACCGTTTGGCAATCTGTGAT 58.090 45.000 0.00 0.00 39.70 3.06
93 102 2.552599 TACCGTTTGGCAATCTGTGA 57.447 45.000 13.51 0.00 39.70 3.58
94 103 3.440173 AGAATACCGTTTGGCAATCTGTG 59.560 43.478 13.51 2.84 39.70 3.66
95 104 3.686016 AGAATACCGTTTGGCAATCTGT 58.314 40.909 0.00 5.67 39.70 3.41
96 105 3.941483 AGAGAATACCGTTTGGCAATCTG 59.059 43.478 0.00 0.00 39.70 2.90
97 106 4.222124 AGAGAATACCGTTTGGCAATCT 57.778 40.909 0.00 0.00 39.70 2.40
98 107 6.431198 TTTAGAGAATACCGTTTGGCAATC 57.569 37.500 0.00 0.00 39.70 2.67
99 108 5.357032 CCTTTAGAGAATACCGTTTGGCAAT 59.643 40.000 0.00 0.00 39.70 3.56
100 109 4.698304 CCTTTAGAGAATACCGTTTGGCAA 59.302 41.667 0.00 0.00 39.70 4.52
101 110 4.258543 CCTTTAGAGAATACCGTTTGGCA 58.741 43.478 0.00 0.00 39.70 4.92
102 111 3.626217 CCCTTTAGAGAATACCGTTTGGC 59.374 47.826 0.00 0.00 39.70 4.52
103 112 4.080751 TCCCCTTTAGAGAATACCGTTTGG 60.081 45.833 0.00 0.00 42.84 3.28
104 113 5.093849 TCCCCTTTAGAGAATACCGTTTG 57.906 43.478 0.00 0.00 0.00 2.93
129 138 7.611855 AGAGTTATTTTTCCTTCAATCGTCCAT 59.388 33.333 0.00 0.00 0.00 3.41
131 140 7.379098 AGAGTTATTTTTCCTTCAATCGTCC 57.621 36.000 0.00 0.00 0.00 4.79
140 149 6.717997 TCGCCCTAAAAGAGTTATTTTTCCTT 59.282 34.615 0.00 0.00 34.35 3.36
142 151 6.505044 TCGCCCTAAAAGAGTTATTTTTCC 57.495 37.500 0.00 0.00 34.35 3.13
143 152 7.591165 AGTTCGCCCTAAAAGAGTTATTTTTC 58.409 34.615 0.00 0.00 34.35 2.29
181 202 2.023673 TCCAAGGAGCACACAAGTTTG 58.976 47.619 0.00 0.00 0.00 2.93
259 319 3.187058 GTATGGCACGGCAACAGG 58.813 61.111 0.00 0.00 0.00 4.00
268 328 3.264897 CAGCGGCTCGTATGGCAC 61.265 66.667 0.00 0.00 0.00 5.01
271 331 0.599991 TATTGCAGCGGCTCGTATGG 60.600 55.000 10.92 0.00 41.91 2.74
272 332 1.217001 TTATTGCAGCGGCTCGTATG 58.783 50.000 10.92 0.00 41.91 2.39
273 333 1.597663 GTTTATTGCAGCGGCTCGTAT 59.402 47.619 10.92 1.38 41.91 3.06
274 334 1.003851 GTTTATTGCAGCGGCTCGTA 58.996 50.000 10.92 0.00 41.91 3.43
275 335 0.953471 TGTTTATTGCAGCGGCTCGT 60.953 50.000 10.92 0.00 41.91 4.18
276 336 0.167908 TTGTTTATTGCAGCGGCTCG 59.832 50.000 10.92 0.00 41.91 5.03
277 337 1.985684 GTTTGTTTATTGCAGCGGCTC 59.014 47.619 10.92 0.00 41.91 4.70
278 338 1.665735 CGTTTGTTTATTGCAGCGGCT 60.666 47.619 10.92 0.00 41.91 5.52
421 774 1.817740 CGGCCCATGTTATTGTAGGGG 60.818 57.143 0.00 0.00 39.96 4.79
422 775 1.604604 CGGCCCATGTTATTGTAGGG 58.395 55.000 0.00 0.00 42.55 3.53
526 881 4.176752 GTGGGGCTCGGGTGATCC 62.177 72.222 0.00 0.00 0.00 3.36
587 944 6.232581 TCTGATCTCTCCTCCTTTTCATTC 57.767 41.667 0.00 0.00 0.00 2.67
599 956 1.035923 TGCCGTGATCTGATCTCTCC 58.964 55.000 17.82 8.72 0.00 3.71
628 985 0.949105 ACACCAACAGCGACGGATTC 60.949 55.000 0.00 0.00 0.00 2.52
629 986 0.534203 AACACCAACAGCGACGGATT 60.534 50.000 0.00 0.00 0.00 3.01
659 1045 3.437795 CCGCAAAGGCAGCTGGAG 61.438 66.667 17.12 0.00 41.24 3.86
720 1135 4.822036 AACATAAACAGCGCAACAGTAA 57.178 36.364 11.47 0.00 0.00 2.24
740 1155 2.975536 CTCGGCGGAGGTGGTAAA 59.024 61.111 13.25 0.00 36.61 2.01
794 1209 1.145803 GGTTAGTTGACCGTGACTGC 58.854 55.000 0.00 0.00 0.00 4.40
850 1280 1.227764 CAGGATCGGCAGACCATGG 60.228 63.158 11.19 11.19 34.57 3.66
861 1291 2.725008 GAGGCCGAGACAGGATCG 59.275 66.667 0.00 0.00 39.86 3.69
875 1305 1.616865 TGATTAGTTATCCCGGCGAGG 59.383 52.381 9.30 8.47 40.63 4.63
876 1306 2.673833 GTGATTAGTTATCCCGGCGAG 58.326 52.381 9.30 0.00 31.87 5.03
918 1348 1.209128 CAGTAATAAGCCACTCCGCG 58.791 55.000 0.00 0.00 0.00 6.46
1449 1898 0.323908 CCAGGGACTTCTCCTCGTCT 60.324 60.000 0.00 0.00 34.60 4.18
1560 2012 2.500590 ACTAGTAGGAGGCAGTAGGGA 58.499 52.381 1.45 0.00 0.00 4.20
1563 2015 4.462133 TGCTTACTAGTAGGAGGCAGTAG 58.538 47.826 14.92 2.53 0.00 2.57
1656 2111 1.541147 GACCAGCAACTGCAAGCAATA 59.459 47.619 4.22 0.00 45.16 1.90
1694 2149 1.378250 CTGCCAGAAAGCCAGGGAG 60.378 63.158 0.00 0.00 34.52 4.30
1703 2158 2.886523 CACTTTCATCCACTGCCAGAAA 59.113 45.455 0.00 0.00 0.00 2.52
1730 2185 6.224584 GTGAAATAGATAGGTAACCTGGAGC 58.775 44.000 0.00 0.00 34.61 4.70
1871 2327 0.951040 GGCAGTTTCCTCACTGTCCG 60.951 60.000 2.95 0.00 42.63 4.79
1890 2346 1.406069 CCAAGAACCCAGGATGTCTCG 60.406 57.143 0.00 0.00 0.00 4.04
1968 2424 1.073284 AGGAACAACGGTATTGCCAGT 59.927 47.619 0.00 0.00 36.97 4.00
1983 2439 6.004408 TGGTCAGCGTATTTAAAAAGGAAC 57.996 37.500 0.00 0.00 0.00 3.62
2038 2494 0.894184 TCTTCCTCGGTGCTTCTCGT 60.894 55.000 0.00 0.00 0.00 4.18
2074 2530 4.460382 CACATCAACCTTGTAAGCAATCCT 59.540 41.667 0.00 0.00 33.65 3.24
2125 2581 1.078214 CGATCAGGAGGGCAAGCAA 60.078 57.895 0.00 0.00 0.00 3.91
2226 2682 2.886523 TGAATCTGCCACAAAAGTCCAG 59.113 45.455 0.00 0.00 0.00 3.86
2355 2811 5.233988 CAAGAATCCACCTTCTCCGATATC 58.766 45.833 0.00 0.00 34.40 1.63
2819 3275 9.166173 CAGTTGATTCAGTCTTTATCAATACCA 57.834 33.333 8.77 0.00 39.61 3.25
2905 3361 3.995705 CACCACCACCAATGCTTTTATTG 59.004 43.478 0.00 0.00 37.70 1.90
2995 3451 9.559732 CTACATATTACAGATGTTCCCATGAAA 57.440 33.333 0.00 0.00 38.47 2.69
3069 3525 5.860941 TCATAGTGGAGGATCAGAAGAAC 57.139 43.478 0.00 0.00 36.25 3.01
3081 3537 6.889198 TCCAAGGAGTTTATTCATAGTGGAG 58.111 40.000 0.00 0.00 0.00 3.86
3095 3551 5.208121 TGAAAAGAAACCATCCAAGGAGTT 58.792 37.500 0.00 0.00 0.00 3.01
3102 3558 5.716228 ACATAGCATGAAAAGAAACCATCCA 59.284 36.000 0.00 0.00 0.00 3.41
3129 3585 9.784531 AGGACATTTCAGGTAGATATTTACATG 57.215 33.333 10.85 10.85 36.84 3.21
3152 3608 0.402861 AACCTGTGGGGAGGAAAGGA 60.403 55.000 0.00 0.00 36.51 3.36
3269 3725 7.452880 TGGGCAAATAATTATATGAGCTGTC 57.547 36.000 0.00 0.00 0.00 3.51
3291 3747 5.482006 GGGAATGGAGAAAATGAAAGTTGG 58.518 41.667 0.00 0.00 0.00 3.77
3863 5155 7.439356 TCTTCTGCTATAACAAGGATTTCATCG 59.561 37.037 0.00 0.00 0.00 3.84
3869 5161 8.435187 TCATCATCTTCTGCTATAACAAGGATT 58.565 33.333 0.00 0.00 0.00 3.01
4098 5390 9.875691 AACAAAATTTTCTCTGGATATTTAGGC 57.124 29.630 0.00 0.00 0.00 3.93
4211 5509 4.400251 ACAGCACCAACATTCATATCCAAG 59.600 41.667 0.00 0.00 0.00 3.61
4467 5765 8.961294 TTGAATAGAAACGTTCAGAGTACTAC 57.039 34.615 0.00 0.00 35.91 2.73
4510 5810 3.701532 TTTGGACAACATTGACGGTTC 57.298 42.857 0.00 0.00 0.00 3.62
4537 5837 0.729116 AAATGCGAGCCAAGATGACG 59.271 50.000 0.00 0.00 0.00 4.35
4678 5981 6.952935 ACATCACGAATTAGAAGAAGTGTC 57.047 37.500 0.00 0.00 0.00 3.67
4699 6002 1.024271 GCTTGTTGCTCACCTGAACA 58.976 50.000 0.00 0.00 38.95 3.18
5090 6506 9.904647 CATGTTATTGCAATATTAAAGCACAAC 57.095 29.630 19.51 12.52 38.11 3.32
5213 6629 2.910319 TGCAGGTCACTGGGTAGTTAAT 59.090 45.455 0.00 0.00 45.04 1.40
5234 6654 5.148502 AGGATTACCACGGTCAGATCTTAT 58.851 41.667 0.00 0.00 38.94 1.73
5236 6656 3.375699 AGGATTACCACGGTCAGATCTT 58.624 45.455 0.00 0.00 38.94 2.40
5320 6741 5.653769 CACCATTATGTCCAGGAAACTCAAT 59.346 40.000 0.00 0.00 40.21 2.57
5357 6778 1.747956 CCGATCACAATCTCGTCTCG 58.252 55.000 0.00 0.00 33.11 4.04
5389 6810 1.452110 TGATTGCCTCATCGGTGTTG 58.548 50.000 0.00 0.00 34.25 3.33
5579 7001 1.459450 TGCTTTGCCCGGTTATCTTC 58.541 50.000 0.00 0.00 0.00 2.87
5581 7003 3.149196 CATATGCTTTGCCCGGTTATCT 58.851 45.455 0.00 0.00 0.00 1.98
5782 7205 5.734498 GCGAGCTTACAAAATACAACATGAG 59.266 40.000 0.00 0.00 0.00 2.90
5807 7230 7.826252 AGCATATCACGGATTCAATAATTAGCT 59.174 33.333 0.00 0.00 0.00 3.32
5878 7306 4.833478 ACAGGAGCATTCACAGAATACT 57.167 40.909 0.00 0.00 0.00 2.12
5887 7315 3.838317 AGGTACAACTACAGGAGCATTCA 59.162 43.478 0.00 0.00 0.00 2.57
5891 7319 4.015084 GTCTAGGTACAACTACAGGAGCA 58.985 47.826 0.00 0.00 0.00 4.26
5901 7329 6.476053 GCTGTTTAGCTATGTCTAGGTACAAC 59.524 42.308 0.00 0.00 46.57 3.32
5920 7348 2.358898 AGAACAAAGATGCACGCTGTTT 59.641 40.909 0.00 0.00 31.73 2.83
5936 7364 5.920273 GCAGCATAGCAAAAGTAAAAGAACA 59.080 36.000 0.00 0.00 0.00 3.18
5940 7368 4.475944 ACGCAGCATAGCAAAAGTAAAAG 58.524 39.130 0.00 0.00 0.00 2.27
5959 7389 3.365364 CCTCTTTCTTGGAACATCAACGC 60.365 47.826 0.00 0.00 39.30 4.84
5960 7390 4.065088 TCCTCTTTCTTGGAACATCAACG 58.935 43.478 0.00 0.00 39.30 4.10
5976 7406 1.065854 GGCTACACTGCATGTCCTCTT 60.066 52.381 5.25 0.00 42.09 2.85
5977 7407 0.539051 GGCTACACTGCATGTCCTCT 59.461 55.000 5.25 0.00 42.09 3.69
5978 7408 0.539051 AGGCTACACTGCATGTCCTC 59.461 55.000 5.25 0.00 42.09 3.71
5980 7410 2.772739 CAGGCTACACTGCATGTCC 58.227 57.895 5.25 3.04 42.09 4.02
5985 7415 1.625315 AGAATCACAGGCTACACTGCA 59.375 47.619 0.00 0.00 42.21 4.41
5986 7416 2.005451 CAGAATCACAGGCTACACTGC 58.995 52.381 0.00 0.00 42.21 4.40
5987 7417 2.998670 CACAGAATCACAGGCTACACTG 59.001 50.000 0.00 0.00 44.03 3.66
5988 7418 2.899900 TCACAGAATCACAGGCTACACT 59.100 45.455 0.00 0.00 0.00 3.55
5990 7420 3.306989 CCTTCACAGAATCACAGGCTACA 60.307 47.826 0.00 0.00 0.00 2.74
5991 7421 3.265791 CCTTCACAGAATCACAGGCTAC 58.734 50.000 0.00 0.00 0.00 3.58
5992 7422 2.355108 GCCTTCACAGAATCACAGGCTA 60.355 50.000 0.58 0.00 43.06 3.93
5994 7424 0.807496 GCCTTCACAGAATCACAGGC 59.193 55.000 0.00 0.00 40.13 4.85
5995 7425 1.457346 GGCCTTCACAGAATCACAGG 58.543 55.000 0.00 0.00 0.00 4.00
5997 7427 0.038166 GGGGCCTTCACAGAATCACA 59.962 55.000 0.84 0.00 0.00 3.58
5999 7429 0.329261 CAGGGGCCTTCACAGAATCA 59.671 55.000 0.84 0.00 0.00 2.57
6000 7430 0.329596 ACAGGGGCCTTCACAGAATC 59.670 55.000 0.84 0.00 0.00 2.52
6001 7431 0.038744 CACAGGGGCCTTCACAGAAT 59.961 55.000 0.84 0.00 0.00 2.40
6002 7432 1.059584 TCACAGGGGCCTTCACAGAA 61.060 55.000 0.84 0.00 0.00 3.02
6003 7433 0.842030 ATCACAGGGGCCTTCACAGA 60.842 55.000 0.84 0.00 0.00 3.41
6004 7434 0.679002 CATCACAGGGGCCTTCACAG 60.679 60.000 0.84 0.00 0.00 3.66
6005 7435 1.379916 CATCACAGGGGCCTTCACA 59.620 57.895 0.84 0.00 0.00 3.58
6006 7436 2.048603 GCATCACAGGGGCCTTCAC 61.049 63.158 0.84 0.00 0.00 3.18
6007 7437 0.913934 TAGCATCACAGGGGCCTTCA 60.914 55.000 0.84 0.00 0.00 3.02
6008 7438 0.475906 ATAGCATCACAGGGGCCTTC 59.524 55.000 0.84 0.00 0.00 3.46
6009 7439 0.475906 GATAGCATCACAGGGGCCTT 59.524 55.000 0.84 0.00 0.00 4.35
6010 7440 0.401105 AGATAGCATCACAGGGGCCT 60.401 55.000 0.84 0.00 0.00 5.19
6011 7441 1.352083 TAGATAGCATCACAGGGGCC 58.648 55.000 0.00 0.00 0.00 5.80
6012 7442 2.551071 GGTTAGATAGCATCACAGGGGC 60.551 54.545 0.00 0.00 0.00 5.80
6013 7443 2.705658 TGGTTAGATAGCATCACAGGGG 59.294 50.000 0.00 0.00 0.00 4.79
6014 7444 4.630644 ATGGTTAGATAGCATCACAGGG 57.369 45.455 0.00 0.00 40.92 4.45
6015 7445 5.174395 GCTATGGTTAGATAGCATCACAGG 58.826 45.833 7.50 0.00 46.91 4.00
6051 7481 6.360370 AAGTAGAAGAACCAAGATGCACTA 57.640 37.500 0.00 0.00 0.00 2.74
6114 7548 1.135083 ACGGAGGTGCTCTATTTCACG 60.135 52.381 0.00 0.00 34.20 4.35
6163 7597 0.898320 AGTCAACGAGCTAGCACCAT 59.102 50.000 18.83 0.00 0.00 3.55
6185 7619 7.944554 AGGATTCAAACCTTCTTAATTGTCTCA 59.055 33.333 0.00 0.00 33.55 3.27
6192 7626 5.332743 TGCCAGGATTCAAACCTTCTTAAT 58.667 37.500 0.00 0.00 35.35 1.40
6194 7628 4.380843 TGCCAGGATTCAAACCTTCTTA 57.619 40.909 0.00 0.00 35.35 2.10
6218 7652 5.297776 TCTTTCTTTCTCAACTTTGCAGAGG 59.702 40.000 9.34 0.00 0.00 3.69
6221 7694 5.883661 TGTCTTTCTTTCTCAACTTTGCAG 58.116 37.500 0.00 0.00 0.00 4.41
6222 7695 5.895636 TGTCTTTCTTTCTCAACTTTGCA 57.104 34.783 0.00 0.00 0.00 4.08
6223 7696 6.252228 CACTTGTCTTTCTTTCTCAACTTTGC 59.748 38.462 0.00 0.00 0.00 3.68
6224 7697 6.252228 GCACTTGTCTTTCTTTCTCAACTTTG 59.748 38.462 0.00 0.00 0.00 2.77
6225 7698 6.325596 GCACTTGTCTTTCTTTCTCAACTTT 58.674 36.000 0.00 0.00 0.00 2.66
6226 7699 5.163612 GGCACTTGTCTTTCTTTCTCAACTT 60.164 40.000 0.00 0.00 0.00 2.66
6227 7700 4.336713 GGCACTTGTCTTTCTTTCTCAACT 59.663 41.667 0.00 0.00 0.00 3.16
6228 7701 4.336713 AGGCACTTGTCTTTCTTTCTCAAC 59.663 41.667 0.00 0.00 27.25 3.18
6229 7702 4.526970 AGGCACTTGTCTTTCTTTCTCAA 58.473 39.130 0.00 0.00 27.25 3.02
6230 7703 4.130118 GAGGCACTTGTCTTTCTTTCTCA 58.870 43.478 0.00 0.00 41.55 3.27
6231 7704 4.130118 TGAGGCACTTGTCTTTCTTTCTC 58.870 43.478 0.00 0.00 41.55 2.87
6232 7705 4.156455 TGAGGCACTTGTCTTTCTTTCT 57.844 40.909 0.00 0.00 41.55 2.52
6233 7706 4.516698 TCATGAGGCACTTGTCTTTCTTTC 59.483 41.667 0.00 0.00 41.55 2.62
6234 7707 4.464008 TCATGAGGCACTTGTCTTTCTTT 58.536 39.130 0.00 0.00 41.55 2.52
6235 7708 4.090761 TCATGAGGCACTTGTCTTTCTT 57.909 40.909 0.00 0.00 41.55 2.52
6236 7709 3.777106 TCATGAGGCACTTGTCTTTCT 57.223 42.857 0.00 0.00 41.55 2.52
6237 7710 4.333926 GGTATCATGAGGCACTTGTCTTTC 59.666 45.833 0.09 0.00 41.55 2.62
6238 7711 4.263462 TGGTATCATGAGGCACTTGTCTTT 60.263 41.667 0.09 0.00 41.55 2.52
6239 7712 3.264193 TGGTATCATGAGGCACTTGTCTT 59.736 43.478 0.09 0.00 41.55 3.01
6240 7713 2.840038 TGGTATCATGAGGCACTTGTCT 59.160 45.455 0.09 0.00 41.55 3.41
6241 7714 3.201290 CTGGTATCATGAGGCACTTGTC 58.799 50.000 0.09 0.00 41.55 3.18
6242 7715 2.681976 GCTGGTATCATGAGGCACTTGT 60.682 50.000 0.09 0.00 41.55 3.16
6243 7716 1.945394 GCTGGTATCATGAGGCACTTG 59.055 52.381 0.09 0.00 41.55 3.16
6244 7717 1.842562 AGCTGGTATCATGAGGCACTT 59.157 47.619 0.09 0.00 41.55 3.16
6246 7719 2.338577 AAGCTGGTATCATGAGGCAC 57.661 50.000 0.09 0.00 0.00 5.01
6247 7720 2.369860 CCTAAGCTGGTATCATGAGGCA 59.630 50.000 0.09 0.00 0.00 4.75
6248 7721 2.634940 TCCTAAGCTGGTATCATGAGGC 59.365 50.000 0.09 0.71 0.00 4.70
6249 7722 3.306641 GCTCCTAAGCTGGTATCATGAGG 60.307 52.174 0.09 0.00 45.55 3.86
6250 7723 3.924144 GCTCCTAAGCTGGTATCATGAG 58.076 50.000 0.09 0.00 45.55 2.90
6271 7744 0.898320 AGCACCACCTACAGCTACAG 59.102 55.000 0.00 0.00 35.19 2.74
6307 7783 2.821366 GGTGCAGCCATCTCCACG 60.821 66.667 4.03 0.00 37.17 4.94
6336 7815 3.818773 CCCATCCAACCGATACCAAATAC 59.181 47.826 0.00 0.00 0.00 1.89
6346 7825 1.074072 CACCAACCCATCCAACCGA 59.926 57.895 0.00 0.00 0.00 4.69
6366 7847 6.406624 GGCTACTTCTGGTATAACAGTTAGCA 60.407 42.308 29.33 16.55 40.30 3.49
6367 7848 5.984323 GGCTACTTCTGGTATAACAGTTAGC 59.016 44.000 25.10 25.10 39.23 3.09
6375 7856 3.051650 TCCCTGGGCTACTTCTGGTATAA 60.052 47.826 8.22 0.00 0.00 0.98
6377 7858 1.294068 TCCCTGGGCTACTTCTGGTAT 59.706 52.381 8.22 0.00 0.00 2.73
6383 7864 1.840635 AGAATGTCCCTGGGCTACTTC 59.159 52.381 8.22 8.27 0.00 3.01
6414 7895 0.401738 AGTGGGAGTTGTGGTGGATG 59.598 55.000 0.00 0.00 0.00 3.51
6422 7903 1.488812 TGTGCTACAAGTGGGAGTTGT 59.511 47.619 0.00 0.00 43.55 3.32
6423 7904 2.254546 TGTGCTACAAGTGGGAGTTG 57.745 50.000 0.00 0.00 34.77 3.16


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

AutoCloner maintained by Alex Coulton.