Multiple sequence alignment - TraesCS6A01G305400

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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 TraesCS6A01G305400 chr6A 100.000 4617 0 0 1 4617 538060165 538055549 0.000000e+00 8527
1 TraesCS6A01G305400 chr6A 94.655 711 34 2 3911 4617 549325684 549326394 0.000000e+00 1099
2 TraesCS6A01G305400 chr6A 94.043 705 38 2 3917 4617 579394185 579393481 0.000000e+00 1066
3 TraesCS6A01G305400 chr6A 93.268 713 41 5 3911 4617 583381187 583381898 0.000000e+00 1044
4 TraesCS6A01G305400 chr6B 90.210 3616 235 52 1 3538 585573997 585570423 0.000000e+00 4606
5 TraesCS6A01G305400 chr6B 88.400 250 24 5 3665 3911 585570205 585569958 3.490000e-76 296
6 TraesCS6A01G305400 chr6D 91.143 3026 151 43 585 3538 391943135 391940155 0.000000e+00 3995
7 TraesCS6A01G305400 chr6D 94.332 247 13 1 4 249 391943939 391943693 1.210000e-100 377
8 TraesCS6A01G305400 chr1A 94.538 714 35 2 3908 4617 469372552 469373265 0.000000e+00 1099
9 TraesCS6A01G305400 chr5A 93.944 710 38 3 3912 4617 385311701 385312409 0.000000e+00 1068
10 TraesCS6A01G305400 chr5A 90.295 711 60 6 3913 4615 554291694 554292403 0.000000e+00 922
11 TraesCS6A01G305400 chr3A 91.655 707 55 3 3915 4617 20143115 20142409 0.000000e+00 976
12 TraesCS6A01G305400 chr1D 90.669 718 57 6 3909 4617 286102541 286101825 0.000000e+00 946
13 TraesCS6A01G305400 chr3D 90.682 719 54 11 3909 4617 563988143 563987428 0.000000e+00 944


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 TraesCS6A01G305400 chr6A 538055549 538060165 4616 True 8527 8527 100.0000 1 4617 1 chr6A.!!$R1 4616
1 TraesCS6A01G305400 chr6A 549325684 549326394 710 False 1099 1099 94.6550 3911 4617 1 chr6A.!!$F1 706
2 TraesCS6A01G305400 chr6A 579393481 579394185 704 True 1066 1066 94.0430 3917 4617 1 chr6A.!!$R2 700
3 TraesCS6A01G305400 chr6A 583381187 583381898 711 False 1044 1044 93.2680 3911 4617 1 chr6A.!!$F2 706
4 TraesCS6A01G305400 chr6B 585569958 585573997 4039 True 2451 4606 89.3050 1 3911 2 chr6B.!!$R1 3910
5 TraesCS6A01G305400 chr6D 391940155 391943939 3784 True 2186 3995 92.7375 4 3538 2 chr6D.!!$R1 3534
6 TraesCS6A01G305400 chr1A 469372552 469373265 713 False 1099 1099 94.5380 3908 4617 1 chr1A.!!$F1 709
7 TraesCS6A01G305400 chr5A 385311701 385312409 708 False 1068 1068 93.9440 3912 4617 1 chr5A.!!$F1 705
8 TraesCS6A01G305400 chr5A 554291694 554292403 709 False 922 922 90.2950 3913 4615 1 chr5A.!!$F2 702
9 TraesCS6A01G305400 chr3A 20142409 20143115 706 True 976 976 91.6550 3915 4617 1 chr3A.!!$R1 702
10 TraesCS6A01G305400 chr1D 286101825 286102541 716 True 946 946 90.6690 3909 4617 1 chr1D.!!$R1 708
11 TraesCS6A01G305400 chr3D 563987428 563988143 715 True 944 944 90.6820 3909 4617 1 chr3D.!!$R1 708

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
598 902 0.034477 AAAAGATGTACGGCTGGGGG 60.034 55.0 0.00 0.00 0.00 5.40 F
1337 1698 0.179034 TTGGCCCAATTTTTGCGCTT 60.179 45.0 9.73 0.00 34.93 4.68 F
1900 2267 0.610785 TGATGGGTTCGGGGAAAAGC 60.611 55.0 0.00 0.00 0.00 3.51 F
3583 3974 0.175760 TGCTGTTATGCTCCGGAGTC 59.824 55.0 31.43 23.14 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2540 2922 0.099436 CAATACGCCTTGCAAGAGCC 59.901 55.0 28.05 13.81 41.13 4.70 R
3326 3713 0.729140 GCTTGCGATTCCGTTTGTGG 60.729 55.0 0.00 0.00 38.24 4.17 R
3611 4002 0.037326 TCTGGAACCTGATCACGCAC 60.037 55.0 0.00 0.00 0.00 5.34 R
4406 4969 1.977293 GCGGGCTCCTCCTTCTTCAT 61.977 60.0 0.00 0.00 34.39 2.57 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
55 56 7.877612 ACCCTAAATGTGGAATTTGATGTTTTC 59.122 33.333 0.00 0.00 0.00 2.29
144 145 1.064952 CCGTTGTGAAGGTTGTGTTCC 59.935 52.381 0.00 0.00 0.00 3.62
183 184 2.432874 ACGGTGCTACATACATTGGCTA 59.567 45.455 0.00 0.00 0.00 3.93
227 228 5.910637 TTTTCTCAATGATTTGCAGCAAC 57.089 34.783 7.54 0.00 32.61 4.17
279 571 8.706492 AAATGTTGCATGTATCAGTATTTTGG 57.294 30.769 0.00 0.00 0.00 3.28
282 574 4.276642 TGCATGTATCAGTATTTTGGGCA 58.723 39.130 0.00 0.00 0.00 5.36
283 575 4.097741 TGCATGTATCAGTATTTTGGGCAC 59.902 41.667 0.00 0.00 0.00 5.01
285 577 5.506317 GCATGTATCAGTATTTTGGGCACTC 60.506 44.000 0.00 0.00 0.00 3.51
292 584 4.278170 CAGTATTTTGGGCACTCTGTGAAA 59.722 41.667 1.52 0.00 35.23 2.69
293 585 4.520492 AGTATTTTGGGCACTCTGTGAAAG 59.480 41.667 1.52 0.00 35.23 2.62
301 593 4.320788 GGGCACTCTGTGAAAGAAAATCTG 60.321 45.833 1.52 0.00 35.23 2.90
316 608 3.542712 AATCTGACGACAATGTTGCAC 57.457 42.857 0.00 0.00 0.00 4.57
317 609 0.858583 TCTGACGACAATGTTGCACG 59.141 50.000 0.00 9.94 37.32 5.34
321 613 2.068716 CGACAATGTTGCACGCACG 61.069 57.895 0.00 0.00 0.00 5.34
323 615 2.111932 GACAATGTTGCACGCACGGA 62.112 55.000 0.00 0.00 0.00 4.69
325 617 0.387112 CAATGTTGCACGCACGGAAT 60.387 50.000 0.00 0.00 0.00 3.01
330 624 2.286563 TGTTGCACGCACGGAATATATG 59.713 45.455 0.00 0.00 0.00 1.78
336 630 6.103330 TGCACGCACGGAATATATGTTATAT 58.897 36.000 0.00 0.00 0.00 0.86
341 635 7.979537 ACGCACGGAATATATGTTATATCACAT 59.020 33.333 7.63 7.63 40.61 3.21
343 637 8.551205 GCACGGAATATATGTTATATCACATGG 58.449 37.037 11.95 0.00 37.93 3.66
356 650 9.912634 GTTATATCACATGGGATTTTATTGTGG 57.087 33.333 17.29 0.00 38.52 4.17
384 678 5.751680 CATAATCAATGTTTAGGCGGTCTG 58.248 41.667 0.00 0.00 0.00 3.51
385 679 3.627395 ATCAATGTTTAGGCGGTCTGA 57.373 42.857 0.00 0.00 0.00 3.27
386 680 2.695359 TCAATGTTTAGGCGGTCTGAC 58.305 47.619 0.00 0.00 0.00 3.51
387 681 2.301870 TCAATGTTTAGGCGGTCTGACT 59.698 45.455 7.85 0.00 40.99 3.41
388 682 3.512329 TCAATGTTTAGGCGGTCTGACTA 59.488 43.478 7.85 0.00 37.04 2.59
392 686 0.396695 TTAGGCGGTCTGACTAGGGG 60.397 60.000 7.85 0.00 40.05 4.79
393 687 1.284111 TAGGCGGTCTGACTAGGGGA 61.284 60.000 7.85 0.00 37.04 4.81
439 735 3.380142 CACGGGCCATAAAATACATTGC 58.620 45.455 4.39 0.00 0.00 3.56
446 742 4.990426 GCCATAAAATACATTGCCATGGAC 59.010 41.667 18.40 7.64 34.64 4.02
457 753 1.549620 TGCCATGGACGAAATTTGCAT 59.450 42.857 18.40 0.00 0.00 3.96
481 779 8.690884 CATACACAAAACATTTGGGATATACCA 58.309 33.333 1.12 1.12 41.20 3.25
483 781 6.495181 ACACAAAACATTTGGGATATACCACA 59.505 34.615 6.02 0.00 41.03 4.17
505 803 2.020131 CAGGCGTGATGAGCAATCC 58.980 57.895 0.00 0.00 34.00 3.01
519 817 3.334691 AGCAATCCTCAAATCGTTCGAA 58.665 40.909 0.00 0.00 0.00 3.71
524 822 6.745450 GCAATCCTCAAATCGTTCGAATTAAA 59.255 34.615 0.00 0.00 0.00 1.52
525 823 7.272515 GCAATCCTCAAATCGTTCGAATTAAAA 59.727 33.333 0.00 0.00 0.00 1.52
526 824 9.123709 CAATCCTCAAATCGTTCGAATTAAAAA 57.876 29.630 0.00 0.00 0.00 1.94
527 825 9.855021 AATCCTCAAATCGTTCGAATTAAAAAT 57.145 25.926 0.00 0.00 0.00 1.82
528 826 8.667987 TCCTCAAATCGTTCGAATTAAAAATG 57.332 30.769 0.00 0.00 0.00 2.32
570 874 2.070262 AAAAGAAGGCATTTGCTCGC 57.930 45.000 2.12 0.00 41.70 5.03
598 902 0.034477 AAAAGATGTACGGCTGGGGG 60.034 55.000 0.00 0.00 0.00 5.40
600 904 3.792736 GATGTACGGCTGGGGGCA 61.793 66.667 0.00 0.00 44.01 5.36
603 907 4.468689 GTACGGCTGGGGGCAGTC 62.469 72.222 0.00 0.00 45.63 3.51
604 908 4.715130 TACGGCTGGGGGCAGTCT 62.715 66.667 0.00 0.00 45.63 3.24
655 960 2.574399 GCACGACCCTCTCCAGAC 59.426 66.667 0.00 0.00 0.00 3.51
763 1084 0.251787 GACCAAAATGCCCCTGACCT 60.252 55.000 0.00 0.00 0.00 3.85
811 1132 2.679716 CAGGCTGGGAAGGAAGGG 59.320 66.667 6.61 0.00 0.00 3.95
812 1133 2.615288 AGGCTGGGAAGGAAGGGG 60.615 66.667 0.00 0.00 0.00 4.79
830 1151 4.133796 GGCATGCCGGGTCAAAGC 62.134 66.667 23.48 2.45 0.00 3.51
855 1176 1.062525 GGCAGCGCGGTAATTTCAG 59.937 57.895 11.92 0.00 0.00 3.02
856 1177 1.583709 GCAGCGCGGTAATTTCAGC 60.584 57.895 11.92 4.33 0.00 4.26
859 1180 2.403378 GCGCGGTAATTTCAGCCCA 61.403 57.895 8.83 0.00 0.00 5.36
860 1181 1.721487 CGCGGTAATTTCAGCCCAG 59.279 57.895 0.00 0.00 0.00 4.45
861 1182 0.742990 CGCGGTAATTTCAGCCCAGA 60.743 55.000 0.00 0.00 0.00 3.86
862 1183 1.680338 GCGGTAATTTCAGCCCAGAT 58.320 50.000 0.00 0.00 0.00 2.90
864 1185 2.223572 GCGGTAATTTCAGCCCAGATTG 60.224 50.000 0.00 0.00 0.00 2.67
865 1186 2.223572 CGGTAATTTCAGCCCAGATTGC 60.224 50.000 0.00 0.00 0.00 3.56
866 1187 2.223572 GGTAATTTCAGCCCAGATTGCG 60.224 50.000 0.00 0.00 0.00 4.85
867 1188 1.549203 AATTTCAGCCCAGATTGCGT 58.451 45.000 0.00 0.00 0.00 5.24
869 1190 0.960364 TTTCAGCCCAGATTGCGTCC 60.960 55.000 0.00 0.00 0.00 4.79
870 1191 1.841302 TTCAGCCCAGATTGCGTCCT 61.841 55.000 0.00 0.00 0.00 3.85
871 1192 2.110967 CAGCCCAGATTGCGTCCTG 61.111 63.158 0.00 0.00 0.00 3.86
872 1193 3.512516 GCCCAGATTGCGTCCTGC 61.513 66.667 0.00 0.00 46.70 4.85
953 1296 3.195698 GATTCCACCACTCGCCGC 61.196 66.667 0.00 0.00 0.00 6.53
997 1356 2.335011 CCGTAGCCGATCGCATCA 59.665 61.111 10.32 0.00 41.38 3.07
1148 1507 4.077188 GACGGTGAGCTTGCGTGC 62.077 66.667 0.00 0.00 0.00 5.34
1157 1516 2.327343 GCTTGCGTGCCAGTGATCA 61.327 57.895 0.00 0.00 0.00 2.92
1233 1592 2.461110 CGCCAAGAAATCGTCCGGG 61.461 63.158 0.00 0.00 0.00 5.73
1241 1600 1.332889 AAATCGTCCGGGGGAGGTAC 61.333 60.000 0.00 0.00 38.56 3.34
1244 1605 2.792947 CGTCCGGGGGAGGTACATG 61.793 68.421 0.00 0.00 33.46 3.21
1256 1617 1.061812 AGGTACATGCATCCTCCTCCT 60.062 52.381 0.00 0.00 0.00 3.69
1260 1621 4.141482 GGTACATGCATCCTCCTCCTTTTA 60.141 45.833 0.00 0.00 0.00 1.52
1268 1629 3.394645 TCCTCCTCCTTTTATCCCCTTC 58.605 50.000 0.00 0.00 0.00 3.46
1269 1630 2.443632 CCTCCTCCTTTTATCCCCTTCC 59.556 54.545 0.00 0.00 0.00 3.46
1273 1634 2.238898 CTCCTTTTATCCCCTTCCGTGT 59.761 50.000 0.00 0.00 0.00 4.49
1319 1680 2.030805 GCTGAAAGTTTGACGCCATCTT 60.031 45.455 0.00 0.00 35.30 2.40
1336 1697 0.603439 CTTGGCCCAATTTTTGCGCT 60.603 50.000 9.73 0.00 34.93 5.92
1337 1698 0.179034 TTGGCCCAATTTTTGCGCTT 60.179 45.000 9.73 0.00 34.93 4.68
1362 1727 1.414181 CTCTCTGTGTGTGTTGGGAGT 59.586 52.381 0.00 0.00 0.00 3.85
1372 1737 3.013921 TGTGTTGGGAGTTGTTGAGTTC 58.986 45.455 0.00 0.00 0.00 3.01
1416 1781 6.934645 GGATGTCAAATCGATTGGGATTACTA 59.065 38.462 12.25 0.00 39.62 1.82
1436 1801 3.123392 AGAGAGTAGGAAAGGGGAAGG 57.877 52.381 0.00 0.00 0.00 3.46
1439 1804 2.120312 GAGTAGGAAAGGGGAAGGGAG 58.880 57.143 0.00 0.00 0.00 4.30
1448 1813 0.910338 GGGGAAGGGAGAAGGTGTAC 59.090 60.000 0.00 0.00 0.00 2.90
1459 1824 6.781014 AGGGAGAAGGTGTACGATATGATTTA 59.219 38.462 0.00 0.00 0.00 1.40
1483 1848 6.963322 ACCCTTATGAGAGAGCAGTAAAAAT 58.037 36.000 0.00 0.00 0.00 1.82
1531 1897 3.254060 ACGAGATTCAGTGGAATTGACG 58.746 45.455 0.00 0.00 43.69 4.35
1613 1979 4.112634 TGCCCTCTTGTTGAAGGTATTT 57.887 40.909 0.00 0.00 0.00 1.40
1658 2024 6.152661 TGAGAAAACACAAAACAGAACCAGAT 59.847 34.615 0.00 0.00 0.00 2.90
1900 2267 0.610785 TGATGGGTTCGGGGAAAAGC 60.611 55.000 0.00 0.00 0.00 3.51
1906 2273 1.598685 TTCGGGGAAAAGCACGGTC 60.599 57.895 0.00 0.00 0.00 4.79
1909 2276 3.733960 GGGAAAAGCACGGTCGGC 61.734 66.667 0.00 0.00 0.00 5.54
1945 2312 7.657354 GCTGAAGTTTTGGGTTATTCATTCTTT 59.343 33.333 0.00 0.00 30.13 2.52
1966 2333 4.695217 TGACAGGTTTGTGTTTTCTCAC 57.305 40.909 0.00 0.00 37.76 3.51
1986 2353 5.348986 TCACGAATCTACCAATAGCAGTTC 58.651 41.667 0.00 0.00 0.00 3.01
2014 2381 5.640189 AGGAAAGTCAATCTTGATGCTTG 57.360 39.130 0.00 0.00 39.73 4.01
2441 2823 6.633500 TTTCTCCTTGTGGAATAGTTTGTG 57.367 37.500 0.00 0.00 42.66 3.33
2467 2849 6.201806 CCTTCTCTTTTGCTGATAGATAACGG 59.798 42.308 0.00 0.00 0.00 4.44
2481 2863 5.407407 AGATAACGGTGTGATCTCTTGTT 57.593 39.130 0.00 0.36 28.09 2.83
2482 2864 5.171476 AGATAACGGTGTGATCTCTTGTTG 58.829 41.667 0.00 0.00 28.09 3.33
2483 2865 2.910688 ACGGTGTGATCTCTTGTTGT 57.089 45.000 0.00 0.00 0.00 3.32
2540 2922 0.967380 GGTTGGATGTGCCCTTGGAG 60.967 60.000 0.00 0.00 34.97 3.86
2654 3036 4.744137 TGATCTTTCAATTTTTGCCGTGTG 59.256 37.500 0.00 0.00 0.00 3.82
2760 3143 8.120465 TGTTTCGAAACAGAGAACTTCAATAAC 58.880 33.333 33.86 8.13 43.45 1.89
2790 3173 7.439356 CCATATACACAAGTTGTATCACAGGAG 59.561 40.741 8.49 0.00 46.84 3.69
2885 3271 7.444703 ACTGAATTCCTTCTATCTTTAGGCT 57.555 36.000 2.27 0.00 32.29 4.58
2888 3274 8.738645 TGAATTCCTTCTATCTTTAGGCTTTC 57.261 34.615 2.27 0.00 32.29 2.62
2982 3368 9.090103 TCGAAGGTATGATCTCCATAATAAACT 57.910 33.333 0.00 0.00 39.29 2.66
3073 3459 1.235281 GCACGGGACTTCCAAGGAAC 61.235 60.000 0.00 0.00 37.91 3.62
3110 3496 1.070108 CCATTTGCAGAGATCGCATCG 60.070 52.381 0.00 0.00 39.58 3.84
3161 3547 2.138320 ACGCCGATTGATATTGCTCTG 58.862 47.619 0.00 0.00 0.00 3.35
3172 3558 9.160496 GATTGATATTGCTCTGGAGGTATTAAG 57.840 37.037 0.00 0.00 0.00 1.85
3175 3561 8.713971 TGATATTGCTCTGGAGGTATTAAGAAA 58.286 33.333 0.00 0.00 0.00 2.52
3176 3562 8.910351 ATATTGCTCTGGAGGTATTAAGAAAC 57.090 34.615 0.00 0.00 0.00 2.78
3195 3581 1.276989 ACGAAACCCTTTCTATCGCCA 59.723 47.619 0.00 0.00 37.52 5.69
3200 3586 5.365619 GAAACCCTTTCTATCGCCATCTAA 58.634 41.667 0.00 0.00 36.73 2.10
3216 3602 0.808755 CTAATCGTTTGGGTGCCACC 59.191 55.000 4.93 4.93 37.60 4.61
3226 3613 2.186155 GGTGCCACCCGTATTTTCC 58.814 57.895 1.17 0.00 30.04 3.13
3236 3623 5.361285 CCACCCGTATTTTCCATTTCCATTA 59.639 40.000 0.00 0.00 0.00 1.90
3261 3648 2.708051 AGTGCCTGAACATGACATCTG 58.292 47.619 0.00 0.00 0.00 2.90
3449 3836 1.026584 TCGTTGTGTCGACAAGGAGA 58.973 50.000 21.95 14.64 46.80 3.71
3509 3900 5.185454 TGGCGGAATAATGGAGCTAATATG 58.815 41.667 0.00 0.00 0.00 1.78
3534 3925 3.374042 TCCTTGTGGGTTGAAAGAACA 57.626 42.857 0.00 0.00 36.25 3.18
3538 3929 3.080300 TGTGGGTTGAAAGAACACTGT 57.920 42.857 0.00 0.00 33.44 3.55
3540 3931 2.357952 GTGGGTTGAAAGAACACTGTCC 59.642 50.000 0.00 0.00 0.00 4.02
3542 3933 2.618709 GGGTTGAAAGAACACTGTCCTG 59.381 50.000 0.00 0.00 0.00 3.86
3543 3934 2.618709 GGTTGAAAGAACACTGTCCTGG 59.381 50.000 0.00 0.00 0.00 4.45
3544 3935 3.279434 GTTGAAAGAACACTGTCCTGGT 58.721 45.455 0.00 0.00 0.00 4.00
3546 3937 2.771943 TGAAAGAACACTGTCCTGGTCT 59.228 45.455 0.00 0.00 40.11 3.85
3547 3938 2.918712 AAGAACACTGTCCTGGTCTG 57.081 50.000 0.00 0.00 37.21 3.51
3548 3939 1.051812 AGAACACTGTCCTGGTCTGG 58.948 55.000 0.00 0.00 36.81 3.86
3549 3940 0.759346 GAACACTGTCCTGGTCTGGT 59.241 55.000 0.00 0.00 0.00 4.00
3550 3941 1.141053 GAACACTGTCCTGGTCTGGTT 59.859 52.381 0.00 0.00 0.00 3.67
3551 3942 1.213296 ACACTGTCCTGGTCTGGTTT 58.787 50.000 0.00 0.00 0.00 3.27
3574 3965 4.424061 TTGTTGTGAGATGCTGTTATGC 57.576 40.909 0.00 0.00 0.00 3.14
3575 3966 3.678289 TGTTGTGAGATGCTGTTATGCT 58.322 40.909 0.00 0.00 0.00 3.79
3576 3967 3.686241 TGTTGTGAGATGCTGTTATGCTC 59.314 43.478 0.00 0.00 0.00 4.26
3577 3968 2.910199 TGTGAGATGCTGTTATGCTCC 58.090 47.619 0.00 0.00 0.00 4.70
3578 3969 1.863454 GTGAGATGCTGTTATGCTCCG 59.137 52.381 0.00 0.00 0.00 4.63
3579 3970 1.202568 TGAGATGCTGTTATGCTCCGG 60.203 52.381 0.00 0.00 0.00 5.14
3580 3971 1.069204 GAGATGCTGTTATGCTCCGGA 59.931 52.381 2.93 2.93 0.00 5.14
3581 3972 1.069823 AGATGCTGTTATGCTCCGGAG 59.930 52.381 27.83 27.83 0.00 4.63
3582 3973 0.833287 ATGCTGTTATGCTCCGGAGT 59.167 50.000 31.43 16.28 0.00 3.85
3583 3974 0.175760 TGCTGTTATGCTCCGGAGTC 59.824 55.000 31.43 23.14 0.00 3.36
3584 3975 0.530870 GCTGTTATGCTCCGGAGTCC 60.531 60.000 31.43 17.08 0.00 3.85
3595 3986 2.494677 CGGAGTCCGGTGAAGATCT 58.505 57.895 24.39 0.00 44.15 2.75
3596 3987 0.382515 CGGAGTCCGGTGAAGATCTC 59.617 60.000 24.39 0.00 44.15 2.75
3597 3988 1.475403 GGAGTCCGGTGAAGATCTCA 58.525 55.000 0.00 0.00 0.00 3.27
3598 3989 1.825474 GGAGTCCGGTGAAGATCTCAA 59.175 52.381 0.00 0.00 35.22 3.02
3599 3990 2.417515 GGAGTCCGGTGAAGATCTCAAC 60.418 54.545 0.00 0.00 38.52 3.18
3600 3991 2.231478 GAGTCCGGTGAAGATCTCAACA 59.769 50.000 0.00 0.00 42.46 3.33
3601 3992 2.632996 AGTCCGGTGAAGATCTCAACAA 59.367 45.455 0.00 0.00 42.46 2.83
3602 3993 3.071023 AGTCCGGTGAAGATCTCAACAAA 59.929 43.478 0.00 0.00 42.46 2.83
3603 3994 4.003648 GTCCGGTGAAGATCTCAACAAAT 58.996 43.478 0.00 0.00 42.46 2.32
3604 3995 4.002982 TCCGGTGAAGATCTCAACAAATG 58.997 43.478 0.00 0.00 42.46 2.32
3605 3996 3.426695 CCGGTGAAGATCTCAACAAATGC 60.427 47.826 0.00 0.00 42.46 3.56
3606 3997 3.189080 CGGTGAAGATCTCAACAAATGCA 59.811 43.478 0.00 0.00 42.46 3.96
3607 3998 4.670992 CGGTGAAGATCTCAACAAATGCAG 60.671 45.833 0.00 0.00 42.46 4.41
3608 3999 4.456911 GGTGAAGATCTCAACAAATGCAGA 59.543 41.667 0.00 0.00 41.87 4.26
3609 4000 5.048504 GGTGAAGATCTCAACAAATGCAGAA 60.049 40.000 0.00 0.00 41.87 3.02
3610 4001 6.349944 GGTGAAGATCTCAACAAATGCAGAAT 60.350 38.462 0.00 0.00 41.87 2.40
3611 4002 6.527023 GTGAAGATCTCAACAAATGCAGAATG 59.473 38.462 0.00 0.00 35.22 2.67
3612 4003 6.208007 TGAAGATCTCAACAAATGCAGAATGT 59.792 34.615 0.00 0.00 39.31 2.71
3613 4004 5.950883 AGATCTCAACAAATGCAGAATGTG 58.049 37.500 0.00 0.00 39.31 3.21
3622 4013 3.891786 GCAGAATGTGCGTGATCAG 57.108 52.632 0.00 0.00 43.99 2.90
3623 4014 0.376152 GCAGAATGTGCGTGATCAGG 59.624 55.000 11.07 11.07 43.99 3.86
3624 4015 1.730501 CAGAATGTGCGTGATCAGGT 58.269 50.000 16.27 0.00 0.00 4.00
3625 4016 2.079158 CAGAATGTGCGTGATCAGGTT 58.921 47.619 16.27 3.25 0.00 3.50
3626 4017 2.094894 CAGAATGTGCGTGATCAGGTTC 59.905 50.000 16.27 11.61 0.00 3.62
3627 4018 1.398390 GAATGTGCGTGATCAGGTTCC 59.602 52.381 16.27 5.87 0.00 3.62
3628 4019 0.324614 ATGTGCGTGATCAGGTTCCA 59.675 50.000 16.27 10.72 0.00 3.53
3647 4038 6.657541 GGTTCCAGAAAACAATATGTCACCTA 59.342 38.462 0.00 0.00 0.00 3.08
3655 4050 5.179452 ACAATATGTCACCTACCTTTGCT 57.821 39.130 0.00 0.00 0.00 3.91
3663 4058 1.075536 ACCTACCTTTGCTTCCTTGGG 59.924 52.381 0.00 0.00 0.00 4.12
3669 4064 2.038659 CTTTGCTTCCTTGGGTTGGAA 58.961 47.619 0.00 0.00 40.85 3.53
3673 4068 1.270305 GCTTCCTTGGGTTGGAAAAGC 60.270 52.381 0.00 0.00 42.29 3.51
3674 4069 1.344438 CTTCCTTGGGTTGGAAAAGCC 59.656 52.381 0.00 0.00 42.29 4.35
3693 4248 1.273211 CCAGGATCATTGGGGTTGGTT 60.273 52.381 7.44 0.00 31.87 3.67
3694 4249 2.539302 CAGGATCATTGGGGTTGGTTT 58.461 47.619 0.00 0.00 0.00 3.27
3695 4250 2.905736 CAGGATCATTGGGGTTGGTTTT 59.094 45.455 0.00 0.00 0.00 2.43
3698 4253 3.582647 GGATCATTGGGGTTGGTTTTTCT 59.417 43.478 0.00 0.00 0.00 2.52
3708 4263 0.181587 TGGTTTTTCTCCGGTCAGCA 59.818 50.000 0.00 0.00 0.00 4.41
3721 4276 0.036765 GTCAGCATCACGGGTTGGTA 60.037 55.000 0.00 0.00 0.00 3.25
3743 4298 1.090052 GCCAATTCTTCCTCCGACCG 61.090 60.000 0.00 0.00 0.00 4.79
3790 4345 4.437239 GGAAGCATCATCGTCCATATAGG 58.563 47.826 0.00 0.00 35.18 2.57
3791 4346 4.160439 GGAAGCATCATCGTCCATATAGGA 59.840 45.833 0.00 0.00 46.75 2.94
3799 4355 3.543112 TCCATATAGGACCGCACCA 57.457 52.632 0.00 0.00 43.07 4.17
3852 4409 0.323302 TTCACCGTGCCTGATTGCTA 59.677 50.000 0.00 0.00 0.00 3.49
3868 4425 5.072193 TGATTGCTAAATAGATCTGGAGGCA 59.928 40.000 5.18 6.79 0.00 4.75
3903 4460 2.352960 GCCAAATGTCTCGTCCTGAATC 59.647 50.000 0.00 0.00 0.00 2.52
3947 4504 2.122813 CCCTATCCTGTCCGGCCT 60.123 66.667 0.00 0.00 0.00 5.19
4024 4581 5.425630 GACCTATCCTATCCGTTTTGTGTT 58.574 41.667 0.00 0.00 0.00 3.32
4185 4744 3.338250 GGCCCCACCTGTCATCCA 61.338 66.667 0.00 0.00 34.51 3.41
4188 4747 2.001803 CCCCACCTGTCATCCACAT 58.998 57.895 0.00 0.00 33.23 3.21
4195 4754 2.237143 ACCTGTCATCCACATGTCGAAT 59.763 45.455 0.00 0.00 33.23 3.34
4337 4899 3.845259 GCCGCCCACCTCGTCATA 61.845 66.667 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 5.010516 TCAAATTCCACATTTAGGGTGTGTG 59.989 40.000 5.65 0.00 44.15 3.82
46 47 8.549548 CAAAACTTGCAACATATGAAAACATCA 58.450 29.630 10.38 0.00 43.67 3.07
59 60 8.709386 ACAAAATACATACAAAACTTGCAACA 57.291 26.923 0.00 0.00 0.00 3.33
118 119 2.021457 CAACCTTCACAACGGAGGTTT 58.979 47.619 1.86 0.00 40.47 3.27
144 145 1.847999 CGTGAAACAACTTTGCAGCAG 59.152 47.619 0.00 0.00 35.74 4.24
279 571 4.516698 TCAGATTTTCTTTCACAGAGTGCC 59.483 41.667 0.00 0.00 32.98 5.01
282 574 5.463724 GTCGTCAGATTTTCTTTCACAGAGT 59.536 40.000 0.00 0.00 31.12 3.24
283 575 5.463392 TGTCGTCAGATTTTCTTTCACAGAG 59.537 40.000 0.00 0.00 31.12 3.35
285 577 5.657470 TGTCGTCAGATTTTCTTTCACAG 57.343 39.130 0.00 0.00 0.00 3.66
292 584 4.275689 TGCAACATTGTCGTCAGATTTTCT 59.724 37.500 0.00 0.00 0.00 2.52
293 585 4.379793 GTGCAACATTGTCGTCAGATTTTC 59.620 41.667 0.00 0.00 36.32 2.29
301 593 0.991770 GTGCGTGCAACATTGTCGTC 60.992 55.000 0.00 6.25 35.74 4.20
316 608 7.749539 TGTGATATAACATATATTCCGTGCG 57.250 36.000 0.00 0.00 0.00 5.34
317 609 8.551205 CCATGTGATATAACATATATTCCGTGC 58.449 37.037 5.32 0.00 38.75 5.34
330 624 9.912634 CCACAATAAAATCCCATGTGATATAAC 57.087 33.333 5.82 0.00 43.01 1.89
336 630 3.450457 GCCCACAATAAAATCCCATGTGA 59.550 43.478 5.82 0.00 43.01 3.58
341 635 3.242867 TGTTGCCCACAATAAAATCCCA 58.757 40.909 0.00 0.00 38.27 4.37
343 637 7.271511 TGATTATGTTGCCCACAATAAAATCC 58.728 34.615 0.00 0.00 39.50 3.01
376 670 1.457831 ATCCCCTAGTCAGACCGCC 60.458 63.158 0.00 0.00 0.00 6.13
392 686 3.515286 TCGGACACGCGGAGGATC 61.515 66.667 12.47 0.00 40.69 3.36
393 687 3.823330 GTCGGACACGCGGAGGAT 61.823 66.667 12.47 0.00 40.69 3.24
402 698 1.805945 GTGCTCGGATGTCGGACAC 60.806 63.158 13.92 7.50 39.77 3.67
426 722 6.707440 TTCGTCCATGGCAATGTATTTTAT 57.293 33.333 6.96 0.00 31.27 1.40
439 735 4.104776 GTGTATGCAAATTTCGTCCATGG 58.895 43.478 4.97 4.97 0.00 3.66
446 742 7.320797 CCAAATGTTTTGTGTATGCAAATTTCG 59.679 33.333 0.00 0.00 38.05 3.46
457 753 7.670140 TGTGGTATATCCCAAATGTTTTGTGTA 59.330 33.333 0.00 0.00 35.92 2.90
505 803 9.112789 TGTCATTTTTAATTCGAACGATTTGAG 57.887 29.630 0.00 0.00 0.00 3.02
524 822 8.837099 TGTTTGGGATATCCTAAATGTCATTT 57.163 30.769 29.42 14.98 45.97 2.32
525 823 8.837099 TTGTTTGGGATATCCTAAATGTCATT 57.163 30.769 29.42 0.00 45.97 2.57
526 824 8.837099 TTTGTTTGGGATATCCTAAATGTCAT 57.163 30.769 29.42 0.00 45.97 3.06
527 825 8.657387 TTTTGTTTGGGATATCCTAAATGTCA 57.343 30.769 29.42 21.60 45.97 3.58
555 854 1.138247 CCTGCGAGCAAATGCCTTC 59.862 57.895 0.94 0.00 43.38 3.46
570 874 1.061131 CGTACATCTTTTCGCAGCCTG 59.939 52.381 0.00 0.00 0.00 4.85
598 902 1.135632 GTAGAGGTGACGACAGACTGC 60.136 57.143 1.25 0.00 0.00 4.40
600 904 1.001746 TCGTAGAGGTGACGACAGACT 59.998 52.381 0.00 0.00 43.99 3.24
602 906 3.921257 TCGTAGAGGTGACGACAGA 57.079 52.632 0.00 0.00 43.99 3.41
644 949 4.135153 CGCGGTGTCTGGAGAGGG 62.135 72.222 0.00 0.00 0.00 4.30
763 1084 1.135139 GCTCTCTTCGGCTGTGTCATA 59.865 52.381 0.00 0.00 0.00 2.15
812 1133 3.451894 CTTTGACCCGGCATGCCC 61.452 66.667 30.79 17.06 0.00 5.36
855 1176 3.512516 GCAGGACGCAATCTGGGC 61.513 66.667 0.00 0.00 41.79 5.36
856 1177 3.197790 CGCAGGACGCAATCTGGG 61.198 66.667 0.00 0.00 42.60 4.45
1134 1493 3.730761 CTGGCACGCAAGCTCACC 61.731 66.667 0.00 0.00 45.62 4.02
1148 1507 1.604378 GACCCCACCTGATCACTGG 59.396 63.158 7.48 7.48 40.30 4.00
1241 1600 4.077822 GGATAAAAGGAGGAGGATGCATG 58.922 47.826 2.46 0.00 0.00 4.06
1244 1605 2.224892 GGGGATAAAAGGAGGAGGATGC 60.225 54.545 0.00 0.00 0.00 3.91
1256 1617 2.164338 GCAACACGGAAGGGGATAAAA 58.836 47.619 0.00 0.00 40.46 1.52
1260 1621 0.609131 CAAGCAACACGGAAGGGGAT 60.609 55.000 0.00 0.00 40.46 3.85
1268 1629 5.220154 CGTACTAATCTAACAAGCAACACGG 60.220 44.000 0.00 0.00 0.00 4.94
1269 1630 5.570206 TCGTACTAATCTAACAAGCAACACG 59.430 40.000 0.00 0.00 0.00 4.49
1273 1634 7.413657 GCCAAATCGTACTAATCTAACAAGCAA 60.414 37.037 0.00 0.00 0.00 3.91
1337 1698 3.694072 CCCAACACACACAGAGAGAAAAA 59.306 43.478 0.00 0.00 0.00 1.94
1342 1703 1.414181 ACTCCCAACACACACAGAGAG 59.586 52.381 0.00 0.00 0.00 3.20
1346 1707 1.750193 ACAACTCCCAACACACACAG 58.250 50.000 0.00 0.00 0.00 3.66
1362 1727 1.071699 CCTTCCTCCCGAACTCAACAA 59.928 52.381 0.00 0.00 0.00 2.83
1372 1737 1.408822 CCCATTCTTTCCTTCCTCCCG 60.409 57.143 0.00 0.00 0.00 5.14
1416 1781 2.293251 CCCTTCCCCTTTCCTACTCTCT 60.293 54.545 0.00 0.00 0.00 3.10
1436 1801 6.867293 GGTAAATCATATCGTACACCTTCTCC 59.133 42.308 0.00 0.00 0.00 3.71
1439 1804 6.756221 AGGGTAAATCATATCGTACACCTTC 58.244 40.000 0.00 0.00 0.00 3.46
1448 1813 7.704472 GCTCTCTCATAAGGGTAAATCATATCG 59.296 40.741 0.00 0.00 0.00 2.92
1459 1824 6.374417 TTTTTACTGCTCTCTCATAAGGGT 57.626 37.500 0.00 0.00 0.00 4.34
1483 1848 3.621268 GCATAGATCACACGCCAAGTTTA 59.379 43.478 0.00 0.00 0.00 2.01
1487 1852 0.578683 CGCATAGATCACACGCCAAG 59.421 55.000 0.00 0.00 0.00 3.61
1488 1853 0.108377 ACGCATAGATCACACGCCAA 60.108 50.000 0.00 0.00 0.00 4.52
1531 1897 4.215613 AGGCACAAGATTAACGGAGAAAAC 59.784 41.667 0.00 0.00 0.00 2.43
1634 2000 5.949735 TCTGGTTCTGTTTTGTGTTTTCTC 58.050 37.500 0.00 0.00 0.00 2.87
1642 2008 4.320494 GCATCGAATCTGGTTCTGTTTTGT 60.320 41.667 0.00 0.00 34.56 2.83
1658 2024 1.370810 TGCACACTCCAGCATCGAA 59.629 52.632 0.00 0.00 35.51 3.71
1801 2168 9.480053 AACTTGGTCATTTCATTTTCAGTATTG 57.520 29.630 0.00 0.00 0.00 1.90
1810 2177 8.408043 TCATCAGTAACTTGGTCATTTCATTT 57.592 30.769 0.00 0.00 0.00 2.32
1811 2178 8.408043 TTCATCAGTAACTTGGTCATTTCATT 57.592 30.769 0.00 0.00 0.00 2.57
1812 2179 8.408043 TTTCATCAGTAACTTGGTCATTTCAT 57.592 30.769 0.00 0.00 0.00 2.57
1813 2180 7.502226 ACTTTCATCAGTAACTTGGTCATTTCA 59.498 33.333 0.00 0.00 0.00 2.69
1814 2181 7.875971 ACTTTCATCAGTAACTTGGTCATTTC 58.124 34.615 0.00 0.00 0.00 2.17
1849 2216 9.212641 GCACATATGTATTCACTTATCAGTCAT 57.787 33.333 8.32 0.00 0.00 3.06
1870 2237 2.381911 GAACCCATCATTCCTGCACAT 58.618 47.619 0.00 0.00 0.00 3.21
1900 2267 1.361668 CCAAGATCTTGCCGACCGTG 61.362 60.000 27.01 9.41 39.16 4.94
1906 2273 0.731417 CTTCAGCCAAGATCTTGCCG 59.269 55.000 27.01 16.71 39.16 5.69
1909 2276 4.553323 CCAAAACTTCAGCCAAGATCTTG 58.447 43.478 25.75 25.75 40.13 3.02
1945 2312 3.126171 CGTGAGAAAACACAAACCTGTCA 59.874 43.478 0.00 0.00 40.34 3.58
1966 2333 3.182572 GCGAACTGCTATTGGTAGATTCG 59.817 47.826 13.53 13.53 40.28 3.34
1986 2353 4.858935 TCAAGATTGACTTTCCTTTTGCG 58.141 39.130 0.00 0.00 36.61 4.85
2014 2381 6.758886 GCCATTAGTATCTATGCATCAGTACC 59.241 42.308 0.19 0.00 0.00 3.34
2441 2823 6.292596 CGTTATCTATCAGCAAAAGAGAAGGC 60.293 42.308 0.00 0.00 0.00 4.35
2467 2849 7.981789 TCCTGATAATACAACAAGAGATCACAC 59.018 37.037 0.00 0.00 0.00 3.82
2507 2889 4.289672 ACATCCAACCAAACAGATAGTCCT 59.710 41.667 0.00 0.00 0.00 3.85
2510 2892 3.758554 GCACATCCAACCAAACAGATAGT 59.241 43.478 0.00 0.00 0.00 2.12
2540 2922 0.099436 CAATACGCCTTGCAAGAGCC 59.901 55.000 28.05 13.81 41.13 4.70
2828 3214 4.085357 ACCAACACTAACAGAGAATGCA 57.915 40.909 0.00 0.00 0.00 3.96
2885 3271 0.859232 GCGTGCTGAGTTTCGAGAAA 59.141 50.000 0.00 0.00 0.00 2.52
2888 3274 1.669158 CGAGCGTGCTGAGTTTCGAG 61.669 60.000 0.00 0.00 0.00 4.04
2924 3310 3.040795 GACATCAGCATTTGCATAAGCG 58.959 45.455 5.20 0.00 46.23 4.68
2982 3368 1.527380 GGGTTTGCACAAGACCGGA 60.527 57.895 9.46 0.00 34.22 5.14
3050 3436 1.369625 CTTGGAAGTCCCGTGCATAC 58.630 55.000 0.00 0.00 37.93 2.39
3073 3459 6.073167 TGCAAATGGTAAATGCAGATTTGTTG 60.073 34.615 0.00 0.00 44.52 3.33
3110 3496 2.109126 GTCGTCATGGCCCAGCTTC 61.109 63.158 0.00 0.00 0.00 3.86
3143 3529 2.740981 CTCCAGAGCAATATCAATCGGC 59.259 50.000 0.00 0.00 0.00 5.54
3161 3547 5.494724 AGGGTTTCGTTTCTTAATACCTCC 58.505 41.667 0.00 0.00 0.00 4.30
3172 3558 3.181513 GGCGATAGAAAGGGTTTCGTTTC 60.182 47.826 0.00 0.00 44.29 2.78
3175 3561 1.276989 TGGCGATAGAAAGGGTTTCGT 59.723 47.619 0.00 0.00 44.29 3.85
3176 3562 2.018542 TGGCGATAGAAAGGGTTTCG 57.981 50.000 0.00 0.00 44.29 3.46
3191 3577 1.330521 CACCCAAACGATTAGATGGCG 59.669 52.381 0.00 0.00 0.00 5.69
3195 3581 2.365582 GTGGCACCCAAACGATTAGAT 58.634 47.619 6.29 0.00 34.18 1.98
3216 3602 6.857956 TGTGTAATGGAAATGGAAAATACGG 58.142 36.000 0.00 0.00 0.00 4.02
3218 3604 9.139174 CACTTGTGTAATGGAAATGGAAAATAC 57.861 33.333 0.00 0.00 0.00 1.89
3219 3605 7.816995 GCACTTGTGTAATGGAAATGGAAAATA 59.183 33.333 2.61 0.00 0.00 1.40
3226 3613 4.218200 TCAGGCACTTGTGTAATGGAAATG 59.782 41.667 2.61 0.00 34.60 2.32
3236 3623 1.949525 GTCATGTTCAGGCACTTGTGT 59.050 47.619 2.61 0.00 34.60 3.72
3261 3648 3.474034 GCGACTGCAGAGCGACAC 61.474 66.667 28.37 13.28 42.15 3.67
3326 3713 0.729140 GCTTGCGATTCCGTTTGTGG 60.729 55.000 0.00 0.00 38.24 4.17
3449 3836 4.936685 AGAAAAGGGATACTCCAGCTTT 57.063 40.909 0.00 0.00 38.64 3.51
3463 3850 7.095649 GCCATTTTACAGCTTACAAAGAAAAGG 60.096 37.037 0.00 0.00 0.00 3.11
3509 3900 4.398319 TCTTTCAACCCACAAGGATCTTC 58.602 43.478 0.00 0.00 39.89 2.87
3550 3941 5.691305 GCATAACAGCATCTCACAACAAAAA 59.309 36.000 0.00 0.00 0.00 1.94
3551 3942 5.009911 AGCATAACAGCATCTCACAACAAAA 59.990 36.000 0.00 0.00 36.85 2.44
3554 3945 3.678289 AGCATAACAGCATCTCACAACA 58.322 40.909 0.00 0.00 36.85 3.33
3555 3946 3.064545 GGAGCATAACAGCATCTCACAAC 59.935 47.826 0.00 0.00 36.85 3.32
3557 3948 2.739609 CGGAGCATAACAGCATCTCACA 60.740 50.000 0.00 0.00 36.85 3.58
3558 3949 1.863454 CGGAGCATAACAGCATCTCAC 59.137 52.381 0.00 0.00 36.85 3.51
3559 3950 1.202568 CCGGAGCATAACAGCATCTCA 60.203 52.381 0.00 0.00 36.85 3.27
3560 3951 1.069204 TCCGGAGCATAACAGCATCTC 59.931 52.381 0.00 0.00 36.85 2.75
3561 3952 1.069823 CTCCGGAGCATAACAGCATCT 59.930 52.381 20.67 0.00 36.85 2.90
3562 3953 1.202580 ACTCCGGAGCATAACAGCATC 60.203 52.381 31.56 0.00 36.85 3.91
3563 3954 0.833287 ACTCCGGAGCATAACAGCAT 59.167 50.000 31.56 4.57 36.85 3.79
3564 3955 0.175760 GACTCCGGAGCATAACAGCA 59.824 55.000 31.56 0.00 36.85 4.41
3565 3956 0.530870 GGACTCCGGAGCATAACAGC 60.531 60.000 31.56 10.02 0.00 4.40
3566 3957 0.249073 CGGACTCCGGAGCATAACAG 60.249 60.000 31.56 13.78 44.15 3.16
3567 3958 1.813859 CGGACTCCGGAGCATAACA 59.186 57.895 31.56 0.00 44.15 2.41
3568 3959 4.732106 CGGACTCCGGAGCATAAC 57.268 61.111 31.56 16.35 44.15 1.89
3578 3969 1.475403 TGAGATCTTCACCGGACTCC 58.525 55.000 9.46 0.00 0.00 3.85
3579 3970 2.231478 TGTTGAGATCTTCACCGGACTC 59.769 50.000 9.46 5.70 34.94 3.36
3580 3971 2.248248 TGTTGAGATCTTCACCGGACT 58.752 47.619 9.46 0.00 34.94 3.85
3581 3972 2.743636 TGTTGAGATCTTCACCGGAC 57.256 50.000 9.46 0.00 34.94 4.79
3582 3973 3.762407 TTTGTTGAGATCTTCACCGGA 57.238 42.857 9.46 0.00 34.94 5.14
3583 3974 3.426695 GCATTTGTTGAGATCTTCACCGG 60.427 47.826 0.00 0.00 34.94 5.28
3584 3975 3.189080 TGCATTTGTTGAGATCTTCACCG 59.811 43.478 0.00 0.00 34.94 4.94
3585 3976 4.456911 TCTGCATTTGTTGAGATCTTCACC 59.543 41.667 0.00 0.00 34.94 4.02
3586 3977 5.618056 TCTGCATTTGTTGAGATCTTCAC 57.382 39.130 0.00 0.00 34.94 3.18
3587 3978 6.208007 ACATTCTGCATTTGTTGAGATCTTCA 59.792 34.615 0.00 0.00 0.00 3.02
3588 3979 6.527023 CACATTCTGCATTTGTTGAGATCTTC 59.473 38.462 0.00 0.00 0.00 2.87
3589 3980 6.387465 CACATTCTGCATTTGTTGAGATCTT 58.613 36.000 0.00 0.00 0.00 2.40
3590 3981 5.621555 GCACATTCTGCATTTGTTGAGATCT 60.622 40.000 0.00 0.00 46.29 2.75
3591 3982 4.561606 GCACATTCTGCATTTGTTGAGATC 59.438 41.667 0.00 0.00 46.29 2.75
3592 3983 4.491676 GCACATTCTGCATTTGTTGAGAT 58.508 39.130 0.00 0.00 46.29 2.75
3593 3984 3.904571 GCACATTCTGCATTTGTTGAGA 58.095 40.909 0.00 0.00 46.29 3.27
3604 3995 0.376152 CCTGATCACGCACATTCTGC 59.624 55.000 0.00 0.00 43.21 4.26
3605 3996 1.730501 ACCTGATCACGCACATTCTG 58.269 50.000 0.00 0.00 0.00 3.02
3606 3997 2.350522 GAACCTGATCACGCACATTCT 58.649 47.619 0.00 0.00 0.00 2.40
3607 3998 1.398390 GGAACCTGATCACGCACATTC 59.602 52.381 0.00 0.00 0.00 2.67
3608 3999 1.271325 TGGAACCTGATCACGCACATT 60.271 47.619 0.00 0.00 0.00 2.71
3609 4000 0.324614 TGGAACCTGATCACGCACAT 59.675 50.000 0.00 0.00 0.00 3.21
3610 4001 0.320683 CTGGAACCTGATCACGCACA 60.321 55.000 0.00 0.00 0.00 4.57
3611 4002 0.037326 TCTGGAACCTGATCACGCAC 60.037 55.000 0.00 0.00 0.00 5.34
3612 4003 0.684535 TTCTGGAACCTGATCACGCA 59.315 50.000 0.00 0.00 0.00 5.24
3613 4004 1.808411 TTTCTGGAACCTGATCACGC 58.192 50.000 0.00 0.00 0.00 5.34
3614 4005 3.138304 TGTTTTCTGGAACCTGATCACG 58.862 45.455 0.00 0.00 0.00 4.35
3615 4006 5.712152 ATTGTTTTCTGGAACCTGATCAC 57.288 39.130 0.00 3.11 0.00 3.06
3616 4007 6.947733 ACATATTGTTTTCTGGAACCTGATCA 59.052 34.615 0.00 0.00 0.00 2.92
3617 4008 7.121168 TGACATATTGTTTTCTGGAACCTGATC 59.879 37.037 1.56 0.00 0.00 2.92
3618 4009 6.947733 TGACATATTGTTTTCTGGAACCTGAT 59.052 34.615 1.56 0.00 0.00 2.90
3619 4010 6.206634 GTGACATATTGTTTTCTGGAACCTGA 59.793 38.462 0.00 0.00 0.00 3.86
3620 4011 6.381801 GTGACATATTGTTTTCTGGAACCTG 58.618 40.000 0.00 0.00 0.00 4.00
3621 4012 5.476945 GGTGACATATTGTTTTCTGGAACCT 59.523 40.000 0.00 0.00 0.00 3.50
3622 4013 5.476945 AGGTGACATATTGTTTTCTGGAACC 59.523 40.000 0.00 0.00 0.00 3.62
3623 4014 6.575162 AGGTGACATATTGTTTTCTGGAAC 57.425 37.500 0.00 0.00 0.00 3.62
3624 4015 6.657541 GGTAGGTGACATATTGTTTTCTGGAA 59.342 38.462 0.00 0.00 0.00 3.53
3625 4016 6.012858 AGGTAGGTGACATATTGTTTTCTGGA 60.013 38.462 0.00 0.00 0.00 3.86
3626 4017 6.180472 AGGTAGGTGACATATTGTTTTCTGG 58.820 40.000 0.00 0.00 0.00 3.86
3627 4018 7.687941 AAGGTAGGTGACATATTGTTTTCTG 57.312 36.000 0.00 0.00 0.00 3.02
3628 4019 7.309194 GCAAAGGTAGGTGACATATTGTTTTCT 60.309 37.037 0.00 0.00 0.00 2.52
3647 4038 1.413118 CAACCCAAGGAAGCAAAGGT 58.587 50.000 0.00 0.00 0.00 3.50
3655 4050 1.343478 TGGCTTTTCCAACCCAAGGAA 60.343 47.619 0.00 0.00 43.21 3.36
3663 4058 3.368739 CCAATGATCCTGGCTTTTCCAAC 60.369 47.826 0.00 0.00 46.01 3.77
3669 4064 0.712380 ACCCCAATGATCCTGGCTTT 59.288 50.000 5.57 0.00 32.10 3.51
3673 4068 0.336048 ACCAACCCCAATGATCCTGG 59.664 55.000 4.29 4.29 0.00 4.45
3674 4069 2.236489 AACCAACCCCAATGATCCTG 57.764 50.000 0.00 0.00 0.00 3.86
3675 4070 3.274281 AAAACCAACCCCAATGATCCT 57.726 42.857 0.00 0.00 0.00 3.24
3676 4071 3.582647 AGAAAAACCAACCCCAATGATCC 59.417 43.478 0.00 0.00 0.00 3.36
3678 4073 3.582647 GGAGAAAAACCAACCCCAATGAT 59.417 43.478 0.00 0.00 0.00 2.45
3683 4238 0.468400 CCGGAGAAAAACCAACCCCA 60.468 55.000 0.00 0.00 0.00 4.96
3693 4248 1.808411 GTGATGCTGACCGGAGAAAA 58.192 50.000 9.46 0.00 0.00 2.29
3694 4249 0.389817 CGTGATGCTGACCGGAGAAA 60.390 55.000 9.46 0.00 0.00 2.52
3695 4250 1.215382 CGTGATGCTGACCGGAGAA 59.785 57.895 9.46 0.00 0.00 2.87
3698 4253 3.770040 CCCGTGATGCTGACCGGA 61.770 66.667 9.46 0.00 43.01 5.14
3708 4263 1.376295 GGCGTTACCAACCCGTGAT 60.376 57.895 0.00 0.00 38.86 3.06
3721 4276 0.323629 TCGGAGGAAGAATTGGCGTT 59.676 50.000 0.00 0.00 0.00 4.84
3768 4323 4.160439 TCCTATATGGACGATGATGCTTCC 59.840 45.833 0.00 0.00 40.56 3.46
3769 4324 5.330455 TCCTATATGGACGATGATGCTTC 57.670 43.478 0.00 0.00 40.56 3.86
3795 4350 1.903877 CTAGACAGGCCCCAGTGGTG 61.904 65.000 8.74 1.86 36.04 4.17
3799 4355 2.041265 CCCTAGACAGGCCCCAGT 59.959 66.667 0.00 0.00 41.08 4.00
3810 4366 1.751927 GTCTCCGTTCGCCCCTAGA 60.752 63.158 0.00 0.00 0.00 2.43
3836 4392 2.128771 ATTTAGCAATCAGGCACGGT 57.871 45.000 0.00 0.00 35.83 4.83
3852 4409 2.492025 TGGGTGCCTCCAGATCTATTT 58.508 47.619 0.00 0.00 38.11 1.40
3868 4425 2.419011 TTTGGCCACTGCGTATGGGT 62.419 55.000 3.88 0.00 37.73 4.51
3903 4460 1.815003 GATGGAGTTGGCCTGAAACAG 59.185 52.381 3.32 0.00 0.00 3.16
3947 4504 1.592064 GTTTTACCCCAAACGGACGA 58.408 50.000 0.00 0.00 0.00 4.20
4060 4617 2.895372 GTCCGCCGCGATCCAAAT 60.895 61.111 15.93 0.00 0.00 2.32
4195 4754 2.624838 ACTTAAAGAAGGACGTCGACCA 59.375 45.455 15.97 0.00 36.95 4.02
4201 4760 3.806157 GCTTCCCACTTAAAGAAGGACGT 60.806 47.826 0.00 0.00 37.95 4.34
4333 4895 0.539986 GCCGTTCCAGAACCCTATGA 59.460 55.000 4.99 0.00 38.03 2.15
4337 4899 1.073199 CTTGCCGTTCCAGAACCCT 59.927 57.895 4.99 0.00 38.03 4.34
4406 4969 1.977293 GCGGGCTCCTCCTTCTTCAT 61.977 60.000 0.00 0.00 34.39 2.57
4461 5025 2.166346 TTGATGGTGAAGGGGGCCA 61.166 57.895 4.39 0.00 36.64 5.36


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

AutoCloner maintained by Alex Coulton.