Multiple sequence alignment - TraesCS5D01G209500

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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 TraesCS5D01G209500 chr5D 100.000 3173 0 0 1 3173 316251097 316247925 0.000000e+00 5860.0
1 TraesCS5D01G209500 chr5D 84.099 566 76 13 2616 3173 317755076 317755635 4.660000e-148 534.0
2 TraesCS5D01G209500 chr5B 88.678 1528 125 18 85 1606 366013944 366012459 0.000000e+00 1820.0
3 TraesCS5D01G209500 chr5B 93.450 626 34 7 1862 2485 366011980 366011360 0.000000e+00 922.0
4 TraesCS5D01G209500 chr5B 85.897 156 11 7 1708 1852 366012210 366012055 4.240000e-34 156.0
5 TraesCS5D01G209500 chr5B 85.849 106 11 3 476 579 470054396 470054293 3.350000e-20 110.0
6 TraesCS5D01G209500 chr5A 94.218 882 49 2 840 1721 410807237 410806358 0.000000e+00 1345.0
7 TraesCS5D01G209500 chr5A 95.039 645 19 6 1719 2356 410806299 410805661 0.000000e+00 1002.0
8 TraesCS5D01G209500 chr5A 79.006 181 24 11 26 203 576090738 576090569 9.300000e-21 111.0
9 TraesCS5D01G209500 chr5A 79.817 109 13 5 97 203 576091446 576091345 1.580000e-08 71.3
10 TraesCS5D01G209500 chr6D 86.018 565 66 12 2616 3170 162259784 162260345 7.580000e-166 593.0
11 TraesCS5D01G209500 chr6D 76.398 161 32 4 262 416 455637927 455638087 7.290000e-12 82.4
12 TraesCS5D01G209500 chr6D 80.220 91 11 6 677 765 375095066 375095151 9.500000e-06 62.1
13 TraesCS5D01G209500 chr7A 85.613 563 68 12 2616 3169 208802001 208802559 2.120000e-161 579.0
14 TraesCS5D01G209500 chr7A 92.063 63 3 1 2550 2612 205282011 205282071 1.570000e-13 87.9
15 TraesCS5D01G209500 chr7A 92.063 63 3 1 2550 2612 636890369 636890429 1.570000e-13 87.9
16 TraesCS5D01G209500 chr1D 85.842 558 61 15 2627 3173 137070120 137069570 7.630000e-161 577.0
17 TraesCS5D01G209500 chr1D 85.053 562 70 13 2622 3172 15420187 15419629 7.690000e-156 560.0
18 TraesCS5D01G209500 chr1D 79.699 133 21 6 654 782 199332999 199333129 1.210000e-14 91.6
19 TraesCS5D01G209500 chr1D 93.478 46 3 0 285 330 425522541 425522586 5.680000e-08 69.4
20 TraesCS5D01G209500 chr6A 84.683 568 73 12 2616 3173 73386895 73386332 3.580000e-154 555.0
21 TraesCS5D01G209500 chr6A 88.312 77 2 3 2550 2626 589460065 589459996 5.640000e-13 86.1
22 TraesCS5D01G209500 chr6A 89.552 67 2 2 2560 2626 589504399 589504338 2.620000e-11 80.5
23 TraesCS5D01G209500 chr4B 84.164 562 70 13 2623 3173 134989720 134990273 7.800000e-146 527.0
24 TraesCS5D01G209500 chr4B 84.058 69 8 3 172 240 139343625 139343690 2.640000e-06 63.9
25 TraesCS5D01G209500 chr4A 83.986 562 74 15 2616 3171 740573851 740574402 2.800000e-145 525.0
26 TraesCS5D01G209500 chr4A 92.063 63 3 1 2550 2612 299422190 299422130 1.570000e-13 87.9
27 TraesCS5D01G209500 chr7D 83.774 567 77 14 2616 3173 80043423 80043983 1.010000e-144 523.0
28 TraesCS5D01G209500 chr7D 92.727 55 4 0 2550 2604 614074098 614074152 2.620000e-11 80.5
29 TraesCS5D01G209500 chrUn 77.301 326 54 16 84 404 17445002 17444692 1.170000e-39 174.0
30 TraesCS5D01G209500 chrUn 84.762 105 12 4 476 578 403606965 403606863 5.600000e-18 102.0
31 TraesCS5D01G209500 chrUn 84.762 105 12 4 476 578 403608466 403608364 5.600000e-18 102.0
32 TraesCS5D01G209500 chrUn 84.762 105 12 4 476 578 474044188 474044086 5.600000e-18 102.0
33 TraesCS5D01G209500 chr2A 76.490 302 58 9 84 380 661580503 661580210 5.480000e-33 152.0
34 TraesCS5D01G209500 chr2A 81.373 102 16 3 732 831 521377994 521377894 2.620000e-11 80.5
35 TraesCS5D01G209500 chr7B 79.295 227 36 9 84 307 27815206 27815424 7.090000e-32 148.0
36 TraesCS5D01G209500 chr7B 82.105 95 10 7 691 781 191905619 191905710 1.220000e-09 75.0
37 TraesCS5D01G209500 chr3D 85.211 142 19 2 437 576 123284286 123284427 9.170000e-31 145.0
38 TraesCS5D01G209500 chr3D 81.169 154 22 6 431 577 607086282 607086435 2.000000e-22 117.0
39 TraesCS5D01G209500 chr3D 80.189 106 16 4 732 834 611935781 611935884 1.220000e-09 75.0
40 TraesCS5D01G209500 chr3D 85.714 70 8 1 153 222 319831442 319831375 4.390000e-09 73.1
41 TraesCS5D01G209500 chr3B 77.444 266 40 15 136 395 803360034 803360285 1.190000e-29 141.0
42 TraesCS5D01G209500 chr3B 71.897 427 87 25 371 784 130251406 130251812 3.370000e-15 93.5
43 TraesCS5D01G209500 chr3B 100.000 35 0 0 243 277 228711092 228711126 7.350000e-07 65.8
44 TraesCS5D01G209500 chr6B 74.593 307 60 15 538 836 23113209 23113505 5.560000e-23 119.0
45 TraesCS5D01G209500 chr2B 85.047 107 11 5 733 837 742379700 742379597 1.560000e-18 104.0
46 TraesCS5D01G209500 chr2B 78.261 138 25 5 171 307 49896041 49895908 2.030000e-12 84.2
47 TraesCS5D01G209500 chr2B 79.048 105 19 3 734 836 7779220 7779323 5.680000e-08 69.4
48 TraesCS5D01G209500 chr2B 72.575 299 49 24 543 834 796658061 796658333 2.040000e-07 67.6
49 TraesCS5D01G209500 chr2B 97.222 36 1 0 1673 1708 455475203 455475168 9.500000e-06 62.1
50 TraesCS5D01G209500 chr1A 84.259 108 15 2 472 578 280279893 280279999 1.560000e-18 104.0
51 TraesCS5D01G209500 chr3A 83.654 104 16 1 475 577 41110345 41110448 2.610000e-16 97.1
52 TraesCS5D01G209500 chr3A 81.905 105 18 1 733 836 568245679 568245575 1.570000e-13 87.9
53 TraesCS5D01G209500 chr3A 88.889 63 5 2 134 194 584035637 584035699 3.390000e-10 76.8
54 TraesCS5D01G209500 chr4D 90.476 63 4 1 2550 2612 478272437 478272497 7.290000e-12 82.4


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 TraesCS5D01G209500 chr5D 316247925 316251097 3172 True 5860.0 5860 100.000000 1 3173 1 chr5D.!!$R1 3172
1 TraesCS5D01G209500 chr5D 317755076 317755635 559 False 534.0 534 84.099000 2616 3173 1 chr5D.!!$F1 557
2 TraesCS5D01G209500 chr5B 366011360 366013944 2584 True 966.0 1820 89.341667 85 2485 3 chr5B.!!$R2 2400
3 TraesCS5D01G209500 chr5A 410805661 410807237 1576 True 1173.5 1345 94.628500 840 2356 2 chr5A.!!$R1 1516
4 TraesCS5D01G209500 chr6D 162259784 162260345 561 False 593.0 593 86.018000 2616 3170 1 chr6D.!!$F1 554
5 TraesCS5D01G209500 chr7A 208802001 208802559 558 False 579.0 579 85.613000 2616 3169 1 chr7A.!!$F2 553
6 TraesCS5D01G209500 chr1D 137069570 137070120 550 True 577.0 577 85.842000 2627 3173 1 chr1D.!!$R2 546
7 TraesCS5D01G209500 chr1D 15419629 15420187 558 True 560.0 560 85.053000 2622 3172 1 chr1D.!!$R1 550
8 TraesCS5D01G209500 chr6A 73386332 73386895 563 True 555.0 555 84.683000 2616 3173 1 chr6A.!!$R1 557
9 TraesCS5D01G209500 chr4B 134989720 134990273 553 False 527.0 527 84.164000 2623 3173 1 chr4B.!!$F1 550
10 TraesCS5D01G209500 chr4A 740573851 740574402 551 False 525.0 525 83.986000 2616 3171 1 chr4A.!!$F1 555
11 TraesCS5D01G209500 chr7D 80043423 80043983 560 False 523.0 523 83.774000 2616 3173 1 chr7D.!!$F1 557

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
730 735 0.172803 CGGAGAAAACGTCCCGATCT 59.827 55.0 0.0 0.0 40.53 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2591 2881 0.034198 TCGGCAGTGAACGGATGAAA 59.966 50.0 0.0 0.0 0.0 2.69 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 2.741759 AATCACGAAAAACCCATGCC 57.258 45.000 0.00 0.00 0.00 4.40
29 30 1.923356 ATCACGAAAAACCCATGCCT 58.077 45.000 0.00 0.00 0.00 4.75
30 31 1.243902 TCACGAAAAACCCATGCCTC 58.756 50.000 0.00 0.00 0.00 4.70
31 32 1.202879 TCACGAAAAACCCATGCCTCT 60.203 47.619 0.00 0.00 0.00 3.69
32 33 1.200020 CACGAAAAACCCATGCCTCTC 59.800 52.381 0.00 0.00 0.00 3.20
33 34 0.447801 CGAAAAACCCATGCCTCTCG 59.552 55.000 0.00 0.00 0.00 4.04
34 35 1.534729 GAAAAACCCATGCCTCTCGT 58.465 50.000 0.00 0.00 0.00 4.18
35 36 1.200020 GAAAAACCCATGCCTCTCGTG 59.800 52.381 0.00 0.00 0.00 4.35
40 41 4.528674 CATGCCTCTCGTGGAAGG 57.471 61.111 0.00 0.00 0.00 3.46
41 42 1.900351 CATGCCTCTCGTGGAAGGA 59.100 57.895 0.00 0.00 0.00 3.36
42 43 0.250234 CATGCCTCTCGTGGAAGGAA 59.750 55.000 0.00 0.00 0.00 3.36
43 44 1.134280 CATGCCTCTCGTGGAAGGAAT 60.134 52.381 0.00 0.00 0.00 3.01
44 45 1.860641 TGCCTCTCGTGGAAGGAATA 58.139 50.000 0.00 0.00 0.00 1.75
45 46 2.184533 TGCCTCTCGTGGAAGGAATAA 58.815 47.619 0.00 0.00 0.00 1.40
46 47 2.569853 TGCCTCTCGTGGAAGGAATAAA 59.430 45.455 0.00 0.00 0.00 1.40
47 48 3.199946 TGCCTCTCGTGGAAGGAATAAAT 59.800 43.478 0.00 0.00 0.00 1.40
48 49 3.561725 GCCTCTCGTGGAAGGAATAAATG 59.438 47.826 0.00 0.00 0.00 2.32
49 50 4.130118 CCTCTCGTGGAAGGAATAAATGG 58.870 47.826 0.00 0.00 0.00 3.16
50 51 4.141711 CCTCTCGTGGAAGGAATAAATGGA 60.142 45.833 0.00 0.00 0.00 3.41
51 52 5.428253 CTCTCGTGGAAGGAATAAATGGAA 58.572 41.667 0.00 0.00 0.00 3.53
52 53 5.811190 TCTCGTGGAAGGAATAAATGGAAA 58.189 37.500 0.00 0.00 0.00 3.13
53 54 6.242396 TCTCGTGGAAGGAATAAATGGAAAA 58.758 36.000 0.00 0.00 0.00 2.29
54 55 6.717540 TCTCGTGGAAGGAATAAATGGAAAAA 59.282 34.615 0.00 0.00 0.00 1.94
55 56 7.396055 TCTCGTGGAAGGAATAAATGGAAAAAT 59.604 33.333 0.00 0.00 0.00 1.82
56 57 8.582657 TCGTGGAAGGAATAAATGGAAAAATA 57.417 30.769 0.00 0.00 0.00 1.40
57 58 9.196139 TCGTGGAAGGAATAAATGGAAAAATAT 57.804 29.630 0.00 0.00 0.00 1.28
58 59 9.816354 CGTGGAAGGAATAAATGGAAAAATATT 57.184 29.630 0.00 0.00 0.00 1.28
78 79 1.956297 TTTTTCGTTTCCGAGAGCCA 58.044 45.000 0.00 0.00 45.24 4.75
79 80 1.223187 TTTTCGTTTCCGAGAGCCAC 58.777 50.000 0.00 0.00 45.24 5.01
80 81 0.942410 TTTCGTTTCCGAGAGCCACG 60.942 55.000 0.00 0.00 45.24 4.94
93 94 3.680786 CCACGGACGTGCCTCTCA 61.681 66.667 18.57 0.00 44.16 3.27
94 95 2.430921 CACGGACGTGCCTCTCAC 60.431 66.667 12.16 0.00 39.39 3.51
95 96 2.597805 ACGGACGTGCCTCTCACT 60.598 61.111 0.00 0.00 43.46 3.41
105 106 2.555757 GTGCCTCTCACTGAAGCAAAAT 59.444 45.455 0.81 0.00 42.97 1.82
110 111 3.466836 TCTCACTGAAGCAAAATCGTGT 58.533 40.909 0.00 0.00 0.00 4.49
158 159 6.972901 AGAGAAAACACATCTTTTTCGTTTCC 59.027 34.615 0.00 0.00 44.36 3.13
167 168 2.570442 TTTTCGTTTCCAAGTGGCAC 57.430 45.000 10.29 10.29 34.44 5.01
298 299 0.593128 CAAAACCTTGCCTCTCACGG 59.407 55.000 0.00 0.00 39.79 4.94
314 315 2.619362 CGGAAGCAAAACCGTACCA 58.381 52.632 0.00 0.00 43.53 3.25
401 402 1.586154 CGGGAGCAAAATCGTGCCTT 61.586 55.000 0.00 0.00 46.14 4.35
427 428 3.320826 CGGAAGGGAAAAGGAAAACATGT 59.679 43.478 0.00 0.00 0.00 3.21
429 430 5.680619 GGAAGGGAAAAGGAAAACATGTTT 58.319 37.500 18.13 18.13 0.00 2.83
431 432 6.038161 GGAAGGGAAAAGGAAAACATGTTTTG 59.962 38.462 34.88 0.00 42.26 2.44
433 434 5.879777 AGGGAAAAGGAAAACATGTTTTGTG 59.120 36.000 34.88 0.00 42.26 3.33
435 436 5.448496 GGAAAAGGAAAACATGTTTTGTGCC 60.448 40.000 34.88 28.44 42.26 5.01
436 437 4.486125 AAGGAAAACATGTTTTGTGCCT 57.514 36.364 34.88 29.84 42.26 4.75
437 438 4.058721 AGGAAAACATGTTTTGTGCCTC 57.941 40.909 34.88 21.53 42.26 4.70
440 441 3.354089 AAACATGTTTTGTGCCTCTCG 57.646 42.857 18.13 0.00 38.99 4.04
441 442 1.967319 ACATGTTTTGTGCCTCTCGT 58.033 45.000 0.00 0.00 37.11 4.18
444 445 2.031258 TGTTTTGTGCCTCTCGTGAA 57.969 45.000 0.00 0.00 0.00 3.18
447 448 0.944386 TTTGTGCCTCTCGTGAAAGC 59.056 50.000 2.99 2.99 0.00 3.51
448 449 0.179059 TTGTGCCTCTCGTGAAAGCA 60.179 50.000 7.54 7.54 31.63 3.91
450 451 0.944386 GTGCCTCTCGTGAAAGCAAA 59.056 50.000 11.96 0.00 34.62 3.68
451 452 1.537202 GTGCCTCTCGTGAAAGCAAAT 59.463 47.619 11.96 0.00 34.62 2.32
456 458 3.250744 CTCTCGTGAAAGCAAATCCGTA 58.749 45.455 0.00 0.00 0.00 4.02
466 468 1.066605 GCAAATCCGTACCTCTAGCGA 59.933 52.381 0.00 0.00 0.00 4.93
506 508 0.671796 TCTGTTTTCGAGAGGCACGA 59.328 50.000 0.00 0.00 37.99 4.35
509 511 0.599204 GTTTTCGAGAGGCACGACCA 60.599 55.000 0.00 0.00 43.14 4.02
541 543 2.255252 GCAAAACCATGCGCTCGT 59.745 55.556 9.73 0.00 36.45 4.18
552 554 1.803334 TGCGCTCGTGGAAGTAAAAT 58.197 45.000 9.73 0.00 0.00 1.82
725 730 3.909776 AAAATTCGGAGAAAACGTCCC 57.090 42.857 0.00 0.00 45.90 4.46
728 733 0.604578 TTCGGAGAAAACGTCCCGAT 59.395 50.000 13.77 0.00 43.88 4.18
730 735 0.172803 CGGAGAAAACGTCCCGATCT 59.827 55.000 0.00 0.00 40.53 2.75
740 745 0.736325 GTCCCGATCTTGACACGTGG 60.736 60.000 21.57 1.33 0.00 4.94
776 781 1.335597 CGCCAAGTGACGTACTCTCAA 60.336 52.381 0.00 0.00 39.18 3.02
784 789 0.178941 ACGTACTCTCAACCCACCCT 60.179 55.000 0.00 0.00 0.00 4.34
793 798 1.780309 TCAACCCACCCTGAAGTGATT 59.220 47.619 0.00 0.00 40.34 2.57
799 804 2.488891 CCACCCTGAAGTGATTGTTGGA 60.489 50.000 0.00 0.00 40.34 3.53
805 810 3.565307 TGAAGTGATTGTTGGAAGGCTT 58.435 40.909 0.00 0.00 0.00 4.35
807 812 3.228188 AGTGATTGTTGGAAGGCTTCA 57.772 42.857 27.17 11.78 0.00 3.02
811 816 4.037923 GTGATTGTTGGAAGGCTTCAAAGA 59.962 41.667 27.17 18.89 0.00 2.52
815 820 1.238439 TGGAAGGCTTCAAAGAAGCG 58.762 50.000 27.17 0.00 43.89 4.68
819 824 2.479566 AGGCTTCAAAGAAGCGATCA 57.520 45.000 21.32 0.00 43.89 2.92
822 827 4.517285 AGGCTTCAAAGAAGCGATCATTA 58.483 39.130 21.32 0.00 43.89 1.90
873 878 3.569916 GTGCTCTCACGTGTGAAGA 57.430 52.632 19.74 12.61 39.39 2.87
874 879 1.132588 GTGCTCTCACGTGTGAAGAC 58.867 55.000 19.74 14.86 39.39 3.01
875 880 1.032794 TGCTCTCACGTGTGAAGACT 58.967 50.000 19.74 0.00 39.39 3.24
883 888 1.754745 GTGTGAAGACTCTGGGCCA 59.245 57.895 5.85 5.85 0.00 5.36
886 891 2.125350 GAAGACTCTGGGCCAGCG 60.125 66.667 29.02 25.22 0.00 5.18
1221 1226 3.991051 CGCCTGGTGACGTGGACT 61.991 66.667 0.00 0.00 0.00 3.85
1315 1320 2.384391 GATTTGGATCGCGCCAGCAG 62.384 60.000 0.00 0.00 45.49 4.24
1364 1369 3.968837 ATCCGTGGCCTCCGTACCA 62.969 63.158 3.32 0.00 0.00 3.25
1475 1480 2.101415 CGGAGGATTCATGTCTGTGCTA 59.899 50.000 0.00 0.00 0.00 3.49
1589 1594 3.592059 GATTGCCAGTGGTACGTCTAAA 58.408 45.455 11.74 0.00 0.00 1.85
1926 2208 0.916809 AGCAAAGGGTAATAGGGCGT 59.083 50.000 0.00 0.00 0.00 5.68
1940 2222 1.951602 AGGGCGTTTAACACAGTTTCC 59.048 47.619 0.00 0.00 0.00 3.13
1941 2223 1.951602 GGGCGTTTAACACAGTTTCCT 59.048 47.619 0.00 0.00 0.00 3.36
1947 2229 4.320202 CGTTTAACACAGTTTCCTCCATGG 60.320 45.833 4.97 4.97 37.10 3.66
1988 2271 7.397892 TTTAGATGGTGTTTGAACTGAAACA 57.602 32.000 0.00 0.00 42.26 2.83
1998 2281 6.071952 TGTTTGAACTGAAACAAGAGCTCTTT 60.072 34.615 26.44 12.68 41.70 2.52
2301 2591 8.001881 TCTAGCTAGCTATGTGAATAATAGGC 57.998 38.462 24.36 0.00 0.00 3.93
2361 2651 3.627395 AAAGTTCGTCCTGGCATATGA 57.373 42.857 6.97 0.00 0.00 2.15
2377 2667 9.206870 CTGGCATATGATTTTGTTGTTAGTTTT 57.793 29.630 6.97 0.00 0.00 2.43
2378 2668 9.202273 TGGCATATGATTTTGTTGTTAGTTTTC 57.798 29.630 6.97 0.00 0.00 2.29
2379 2669 9.202273 GGCATATGATTTTGTTGTTAGTTTTCA 57.798 29.630 6.97 0.00 0.00 2.69
2384 2674 8.909708 TGATTTTGTTGTTAGTTTTCAGTCTG 57.090 30.769 0.00 0.00 0.00 3.51
2408 2698 4.018506 TGACCCAAATCTTGCTTCATAGGA 60.019 41.667 0.00 0.00 0.00 2.94
2413 2703 4.348863 AATCTTGCTTCATAGGATCGCT 57.651 40.909 1.76 0.00 0.00 4.93
2415 2705 4.937201 TCTTGCTTCATAGGATCGCTTA 57.063 40.909 1.76 0.00 0.00 3.09
2416 2706 5.474578 TCTTGCTTCATAGGATCGCTTAT 57.525 39.130 1.76 0.00 0.00 1.73
2417 2707 5.858381 TCTTGCTTCATAGGATCGCTTATT 58.142 37.500 1.76 0.00 0.00 1.40
2425 2715 6.997655 TCATAGGATCGCTTATTCTGAATGT 58.002 36.000 13.01 0.00 0.00 2.71
2430 2720 6.926272 AGGATCGCTTATTCTGAATGTAGAAC 59.074 38.462 13.01 6.09 39.33 3.01
2464 2754 5.542635 TCCACTAAGGCGGAGTATATTCAAT 59.457 40.000 0.00 0.00 37.29 2.57
2465 2755 5.869888 CCACTAAGGCGGAGTATATTCAATC 59.130 44.000 0.00 0.00 0.00 2.67
2466 2756 5.869888 CACTAAGGCGGAGTATATTCAATCC 59.130 44.000 0.00 0.00 0.00 3.01
2485 2775 3.371965 TCCGAGCTCTTTTATGGTACCT 58.628 45.455 14.36 1.08 0.00 3.08
2486 2776 3.132289 TCCGAGCTCTTTTATGGTACCTG 59.868 47.826 14.36 0.00 0.00 4.00
2487 2777 3.458189 CGAGCTCTTTTATGGTACCTGG 58.542 50.000 14.36 0.00 0.00 4.45
2488 2778 3.741388 CGAGCTCTTTTATGGTACCTGGG 60.741 52.174 14.36 0.00 0.00 4.45
2489 2779 2.509964 AGCTCTTTTATGGTACCTGGGG 59.490 50.000 14.36 0.00 0.00 4.96
2490 2780 2.422945 GCTCTTTTATGGTACCTGGGGG 60.423 54.545 14.36 0.00 38.88 5.40
2504 2794 3.884318 GGGGGTTGCATTGGTTGT 58.116 55.556 0.00 0.00 0.00 3.32
2505 2795 1.370810 GGGGGTTGCATTGGTTGTG 59.629 57.895 0.00 0.00 0.00 3.33
2506 2796 1.301637 GGGGTTGCATTGGTTGTGC 60.302 57.895 0.00 0.00 42.81 4.57
2511 2801 3.590127 TGCATTGGTTGTGCATGTG 57.410 47.368 0.00 0.00 46.76 3.21
2512 2802 0.751452 TGCATTGGTTGTGCATGTGT 59.249 45.000 0.00 0.00 46.76 3.72
2513 2803 1.959282 TGCATTGGTTGTGCATGTGTA 59.041 42.857 0.00 0.00 46.76 2.90
2514 2804 2.363359 TGCATTGGTTGTGCATGTGTAA 59.637 40.909 0.00 0.00 46.76 2.41
2515 2805 3.006644 TGCATTGGTTGTGCATGTGTAAT 59.993 39.130 0.00 0.00 46.76 1.89
2516 2806 4.219288 TGCATTGGTTGTGCATGTGTAATA 59.781 37.500 0.00 0.00 46.76 0.98
2517 2807 5.105432 TGCATTGGTTGTGCATGTGTAATAT 60.105 36.000 0.00 0.00 46.76 1.28
2518 2808 5.232626 GCATTGGTTGTGCATGTGTAATATG 59.767 40.000 0.00 0.00 42.08 1.78
2519 2809 5.973899 TTGGTTGTGCATGTGTAATATGT 57.026 34.783 0.00 0.00 37.79 2.29
2520 2810 5.559427 TGGTTGTGCATGTGTAATATGTC 57.441 39.130 0.00 0.00 37.79 3.06
2521 2811 5.006386 TGGTTGTGCATGTGTAATATGTCA 58.994 37.500 0.00 0.00 37.79 3.58
2522 2812 5.106357 TGGTTGTGCATGTGTAATATGTCAC 60.106 40.000 0.00 0.00 40.23 3.67
2523 2813 5.331902 GTTGTGCATGTGTAATATGTCACC 58.668 41.667 0.00 0.00 39.63 4.02
2524 2814 4.583871 TGTGCATGTGTAATATGTCACCA 58.416 39.130 0.00 0.00 39.63 4.17
2525 2815 5.006386 TGTGCATGTGTAATATGTCACCAA 58.994 37.500 0.00 0.00 39.63 3.67
2526 2816 5.474876 TGTGCATGTGTAATATGTCACCAAA 59.525 36.000 0.00 0.00 39.63 3.28
2527 2817 6.015940 TGTGCATGTGTAATATGTCACCAAAA 60.016 34.615 0.00 0.00 39.63 2.44
2528 2818 6.527722 GTGCATGTGTAATATGTCACCAAAAG 59.472 38.462 0.00 0.00 37.79 2.27
2529 2819 6.208402 TGCATGTGTAATATGTCACCAAAAGT 59.792 34.615 0.00 0.00 37.79 2.66
2530 2820 7.391833 TGCATGTGTAATATGTCACCAAAAGTA 59.608 33.333 0.00 0.00 37.79 2.24
2531 2821 8.405531 GCATGTGTAATATGTCACCAAAAGTAT 58.594 33.333 0.00 0.00 37.79 2.12
2545 2835 9.595823 TCACCAAAAGTATACTACAGATTAAGC 57.404 33.333 5.65 0.00 0.00 3.09
2546 2836 9.601217 CACCAAAAGTATACTACAGATTAAGCT 57.399 33.333 5.65 0.00 0.00 3.74
2558 2848 8.430431 ACTACAGATTAAGCTTTTCTATACCCC 58.570 37.037 3.20 0.00 0.00 4.95
2559 2849 7.453141 ACAGATTAAGCTTTTCTATACCCCT 57.547 36.000 3.20 0.00 0.00 4.79
2560 2850 8.562949 ACAGATTAAGCTTTTCTATACCCCTA 57.437 34.615 3.20 0.00 0.00 3.53
2561 2851 8.430431 ACAGATTAAGCTTTTCTATACCCCTAC 58.570 37.037 3.20 0.00 0.00 3.18
2562 2852 8.652290 CAGATTAAGCTTTTCTATACCCCTACT 58.348 37.037 3.20 0.00 0.00 2.57
2563 2853 9.893975 AGATTAAGCTTTTCTATACCCCTACTA 57.106 33.333 3.20 0.00 0.00 1.82
2570 2860 9.217278 GCTTTTCTATACCCCTACTAATAAAGC 57.783 37.037 0.00 0.00 36.82 3.51
2575 2865 9.443365 TCTATACCCCTACTAATAAAGCAAAGT 57.557 33.333 0.00 0.00 0.00 2.66
2576 2866 9.490379 CTATACCCCTACTAATAAAGCAAAGTG 57.510 37.037 0.00 0.00 0.00 3.16
2577 2867 6.135819 ACCCCTACTAATAAAGCAAAGTGT 57.864 37.500 0.00 0.00 0.00 3.55
2578 2868 5.944007 ACCCCTACTAATAAAGCAAAGTGTG 59.056 40.000 0.00 0.00 0.00 3.82
2579 2869 5.944007 CCCCTACTAATAAAGCAAAGTGTGT 59.056 40.000 0.00 0.00 0.00 3.72
2580 2870 6.433093 CCCCTACTAATAAAGCAAAGTGTGTT 59.567 38.462 0.00 0.00 0.00 3.32
2581 2871 7.039993 CCCCTACTAATAAAGCAAAGTGTGTTT 60.040 37.037 0.00 0.00 30.92 2.83
2582 2872 8.021396 CCCTACTAATAAAGCAAAGTGTGTTTC 58.979 37.037 0.00 0.00 29.15 2.78
2583 2873 8.021396 CCTACTAATAAAGCAAAGTGTGTTTCC 58.979 37.037 0.00 0.00 29.15 3.13
2584 2874 6.745116 ACTAATAAAGCAAAGTGTGTTTCCC 58.255 36.000 0.00 0.00 29.15 3.97
2585 2875 2.979814 AAAGCAAAGTGTGTTTCCCC 57.020 45.000 0.00 0.00 29.15 4.81
2586 2876 1.859302 AAGCAAAGTGTGTTTCCCCA 58.141 45.000 0.00 0.00 0.00 4.96
2587 2877 1.859302 AGCAAAGTGTGTTTCCCCAA 58.141 45.000 0.00 0.00 0.00 4.12
2588 2878 2.397597 AGCAAAGTGTGTTTCCCCAAT 58.602 42.857 0.00 0.00 0.00 3.16
2589 2879 2.771372 AGCAAAGTGTGTTTCCCCAATT 59.229 40.909 0.00 0.00 0.00 2.32
2590 2880 3.199727 AGCAAAGTGTGTTTCCCCAATTT 59.800 39.130 0.00 0.00 29.82 1.82
2591 2881 3.944650 GCAAAGTGTGTTTCCCCAATTTT 59.055 39.130 0.00 0.00 27.47 1.82
2592 2882 4.397730 GCAAAGTGTGTTTCCCCAATTTTT 59.602 37.500 0.00 0.00 27.47 1.94
2609 2899 0.871722 TTTTCATCCGTTCACTGCCG 59.128 50.000 0.00 0.00 0.00 5.69
2610 2900 0.034198 TTTCATCCGTTCACTGCCGA 59.966 50.000 0.00 0.00 0.00 5.54
2611 2901 0.034198 TTCATCCGTTCACTGCCGAA 59.966 50.000 0.00 0.00 0.00 4.30
2612 2902 0.249120 TCATCCGTTCACTGCCGAAT 59.751 50.000 0.00 0.00 0.00 3.34
2613 2903 1.086696 CATCCGTTCACTGCCGAATT 58.913 50.000 0.00 0.00 0.00 2.17
2614 2904 1.468520 CATCCGTTCACTGCCGAATTT 59.531 47.619 0.00 0.00 0.00 1.82
2620 2910 4.142687 CCGTTCACTGCCGAATTTAAAGAT 60.143 41.667 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.812609 GGCATGGGTTTTTCGTGATTTTT 59.187 39.130 0.00 0.00 0.00 1.94
7 8 3.070878 AGGCATGGGTTTTTCGTGATTTT 59.929 39.130 0.00 0.00 0.00 1.82
8 9 2.632512 AGGCATGGGTTTTTCGTGATTT 59.367 40.909 0.00 0.00 0.00 2.17
9 10 2.231235 GAGGCATGGGTTTTTCGTGATT 59.769 45.455 0.00 0.00 0.00 2.57
10 11 1.818674 GAGGCATGGGTTTTTCGTGAT 59.181 47.619 0.00 0.00 0.00 3.06
11 12 1.202879 AGAGGCATGGGTTTTTCGTGA 60.203 47.619 0.00 0.00 0.00 4.35
12 13 1.200020 GAGAGGCATGGGTTTTTCGTG 59.800 52.381 0.00 0.00 0.00 4.35
13 14 1.534729 GAGAGGCATGGGTTTTTCGT 58.465 50.000 0.00 0.00 0.00 3.85
14 15 0.447801 CGAGAGGCATGGGTTTTTCG 59.552 55.000 0.00 0.00 0.00 3.46
15 16 1.200020 CACGAGAGGCATGGGTTTTTC 59.800 52.381 0.00 0.00 0.00 2.29
16 17 1.247567 CACGAGAGGCATGGGTTTTT 58.752 50.000 0.00 0.00 0.00 1.94
17 18 0.609131 CCACGAGAGGCATGGGTTTT 60.609 55.000 0.00 0.00 0.00 2.43
18 19 1.002134 CCACGAGAGGCATGGGTTT 60.002 57.895 0.00 0.00 0.00 3.27
19 20 1.488705 TTCCACGAGAGGCATGGGTT 61.489 55.000 0.00 0.00 34.03 4.11
20 21 1.903877 CTTCCACGAGAGGCATGGGT 61.904 60.000 0.00 0.00 34.03 4.51
21 22 1.153289 CTTCCACGAGAGGCATGGG 60.153 63.158 0.00 0.00 34.03 4.00
22 23 1.153289 CCTTCCACGAGAGGCATGG 60.153 63.158 0.00 0.00 34.58 3.66
23 24 0.250234 TTCCTTCCACGAGAGGCATG 59.750 55.000 0.00 0.00 0.00 4.06
24 25 1.207791 ATTCCTTCCACGAGAGGCAT 58.792 50.000 0.00 0.00 0.00 4.40
25 26 1.860641 TATTCCTTCCACGAGAGGCA 58.139 50.000 0.00 0.00 0.00 4.75
26 27 2.981859 TTATTCCTTCCACGAGAGGC 57.018 50.000 0.00 0.00 0.00 4.70
27 28 4.130118 CCATTTATTCCTTCCACGAGAGG 58.870 47.826 0.00 0.00 0.00 3.69
28 29 5.023533 TCCATTTATTCCTTCCACGAGAG 57.976 43.478 0.00 0.00 0.00 3.20
29 30 5.429681 TTCCATTTATTCCTTCCACGAGA 57.570 39.130 0.00 0.00 0.00 4.04
30 31 6.509418 TTTTCCATTTATTCCTTCCACGAG 57.491 37.500 0.00 0.00 0.00 4.18
31 32 6.902771 TTTTTCCATTTATTCCTTCCACGA 57.097 33.333 0.00 0.00 0.00 4.35
32 33 9.816354 AATATTTTTCCATTTATTCCTTCCACG 57.184 29.630 0.00 0.00 0.00 4.94
76 77 3.680786 TGAGAGGCACGTCCGTGG 61.681 66.667 20.09 3.84 45.49 4.94
87 88 3.070018 ACGATTTTGCTTCAGTGAGAGG 58.930 45.455 0.00 0.00 0.00 3.69
88 89 3.496130 ACACGATTTTGCTTCAGTGAGAG 59.504 43.478 0.00 0.00 34.16 3.20
89 90 3.466836 ACACGATTTTGCTTCAGTGAGA 58.533 40.909 0.00 0.00 34.16 3.27
90 91 3.496130 AGACACGATTTTGCTTCAGTGAG 59.504 43.478 0.00 0.00 34.16 3.51
91 92 3.466836 AGACACGATTTTGCTTCAGTGA 58.533 40.909 0.00 0.00 34.16 3.41
92 93 3.496130 AGAGACACGATTTTGCTTCAGTG 59.504 43.478 0.00 0.00 35.89 3.66
93 94 3.733337 AGAGACACGATTTTGCTTCAGT 58.267 40.909 0.00 0.00 0.00 3.41
94 95 3.742882 TGAGAGACACGATTTTGCTTCAG 59.257 43.478 0.00 0.00 0.00 3.02
95 96 3.494626 GTGAGAGACACGATTTTGCTTCA 59.505 43.478 0.00 0.00 39.78 3.02
132 133 7.488150 GGAAACGAAAAAGATGTGTTTTCTCTT 59.512 33.333 7.74 2.09 41.01 2.85
136 137 6.879188 TGGAAACGAAAAAGATGTGTTTTC 57.121 33.333 0.00 0.00 40.19 2.29
139 140 5.804979 CACTTGGAAACGAAAAAGATGTGTT 59.195 36.000 0.00 0.00 0.00 3.32
140 141 5.339990 CACTTGGAAACGAAAAAGATGTGT 58.660 37.500 0.00 0.00 0.00 3.72
141 142 4.739716 CCACTTGGAAACGAAAAAGATGTG 59.260 41.667 0.00 0.00 37.39 3.21
142 143 4.736464 GCCACTTGGAAACGAAAAAGATGT 60.736 41.667 0.00 0.00 37.39 3.06
143 144 3.735746 GCCACTTGGAAACGAAAAAGATG 59.264 43.478 0.00 0.00 37.39 2.90
144 145 3.383185 TGCCACTTGGAAACGAAAAAGAT 59.617 39.130 0.00 0.00 37.39 2.40
145 146 2.755655 TGCCACTTGGAAACGAAAAAGA 59.244 40.909 0.00 0.00 37.39 2.52
146 147 2.857748 GTGCCACTTGGAAACGAAAAAG 59.142 45.455 0.00 0.00 37.39 2.27
153 154 2.335011 GCCGTGCCACTTGGAAAC 59.665 61.111 0.00 0.00 37.39 2.78
171 172 2.278013 GCTTCCGCGAGAGGTACG 60.278 66.667 8.23 0.00 0.00 3.67
193 194 6.405278 TTTTTCCTTCTTTTAGAGGCAAGG 57.595 37.500 0.00 0.00 35.81 3.61
244 245 0.465097 CGGCCATGGCTCTCAGAAAT 60.465 55.000 34.70 0.00 41.60 2.17
274 275 3.440522 GTGAGAGGCAAGGTTTTGTATCC 59.559 47.826 0.00 0.00 36.65 2.59
278 279 1.308998 CGTGAGAGGCAAGGTTTTGT 58.691 50.000 0.00 0.00 36.65 2.83
298 299 2.032290 GTGAGTGGTACGGTTTTGCTTC 60.032 50.000 0.00 0.00 0.00 3.86
401 402 3.300239 TTTCCTTTTCCCTTCCGTGAA 57.700 42.857 0.00 0.00 0.00 3.18
406 407 4.955811 ACATGTTTTCCTTTTCCCTTCC 57.044 40.909 0.00 0.00 0.00 3.46
407 408 6.597672 ACAAAACATGTTTTCCTTTTCCCTTC 59.402 34.615 29.21 0.00 40.06 3.46
417 418 4.051237 GAGAGGCACAAAACATGTTTTCC 58.949 43.478 29.21 25.88 41.46 3.13
427 428 1.333619 GCTTTCACGAGAGGCACAAAA 59.666 47.619 0.00 0.00 0.00 2.44
429 430 0.179059 TGCTTTCACGAGAGGCACAA 60.179 50.000 8.05 0.00 32.29 3.33
431 432 0.944386 TTTGCTTTCACGAGAGGCAC 59.056 50.000 10.78 0.00 35.28 5.01
433 434 1.131315 GGATTTGCTTTCACGAGAGGC 59.869 52.381 0.00 0.00 0.00 4.70
435 436 2.069273 ACGGATTTGCTTTCACGAGAG 58.931 47.619 0.00 0.00 0.00 3.20
436 437 2.163818 ACGGATTTGCTTTCACGAGA 57.836 45.000 0.00 0.00 0.00 4.04
437 438 2.093783 GGTACGGATTTGCTTTCACGAG 59.906 50.000 0.00 0.00 0.00 4.18
440 441 3.335579 AGAGGTACGGATTTGCTTTCAC 58.664 45.455 0.00 0.00 0.00 3.18
441 442 3.695830 AGAGGTACGGATTTGCTTTCA 57.304 42.857 0.00 0.00 0.00 2.69
444 445 2.481449 CGCTAGAGGTACGGATTTGCTT 60.481 50.000 0.00 0.00 0.00 3.91
447 448 3.431922 TTCGCTAGAGGTACGGATTTG 57.568 47.619 0.00 0.00 0.00 2.32
448 449 3.737355 GCTTTCGCTAGAGGTACGGATTT 60.737 47.826 0.00 0.00 0.00 2.17
450 451 1.337387 GCTTTCGCTAGAGGTACGGAT 59.663 52.381 0.00 0.00 0.00 4.18
451 452 0.737219 GCTTTCGCTAGAGGTACGGA 59.263 55.000 0.00 0.00 0.00 4.69
488 490 0.784778 GTCGTGCCTCTCGAAAACAG 59.215 55.000 0.00 0.00 39.01 3.16
490 492 0.599204 TGGTCGTGCCTCTCGAAAAC 60.599 55.000 0.00 0.00 39.01 2.43
491 493 0.320374 ATGGTCGTGCCTCTCGAAAA 59.680 50.000 0.00 0.00 39.01 2.29
493 495 1.215382 CATGGTCGTGCCTCTCGAA 59.785 57.895 0.00 0.00 39.01 3.71
494 496 2.885113 CATGGTCGTGCCTCTCGA 59.115 61.111 0.00 0.00 38.35 4.04
495 497 2.887568 GCATGGTCGTGCCTCTCG 60.888 66.667 3.93 0.00 39.18 4.04
530 532 0.739462 TTACTTCCACGAGCGCATGG 60.739 55.000 11.47 14.81 37.32 3.66
536 538 2.474032 GCACGATTTTACTTCCACGAGC 60.474 50.000 0.00 0.00 0.00 5.03
541 543 3.596214 GAGAGGCACGATTTTACTTCCA 58.404 45.455 0.00 0.00 0.00 3.53
672 676 3.859411 TTTTTCTGCACGTGTTTTCCT 57.141 38.095 18.38 0.00 0.00 3.36
673 677 6.576551 TTTATTTTTCTGCACGTGTTTTCC 57.423 33.333 18.38 0.00 0.00 3.13
725 730 2.444624 CCGCCACGTGTCAAGATCG 61.445 63.158 15.65 5.90 0.00 3.69
746 751 2.358003 ACTTGGCGTGCTCTCAGC 60.358 61.111 0.00 0.00 42.82 4.26
747 752 1.005748 TCACTTGGCGTGCTCTCAG 60.006 57.895 0.00 0.00 43.46 3.35
759 764 2.035449 TGGGTTGAGAGTACGTCACTTG 59.965 50.000 0.00 0.00 37.72 3.16
765 770 0.178941 AGGGTGGGTTGAGAGTACGT 60.179 55.000 0.00 0.00 0.00 3.57
776 781 1.149101 ACAATCACTTCAGGGTGGGT 58.851 50.000 0.00 0.00 37.75 4.51
784 789 3.228188 AGCCTTCCAACAATCACTTCA 57.772 42.857 0.00 0.00 0.00 3.02
793 798 2.362077 GCTTCTTTGAAGCCTTCCAACA 59.638 45.455 18.34 0.00 37.30 3.33
799 804 2.783135 TGATCGCTTCTTTGAAGCCTT 58.217 42.857 21.72 12.20 40.02 4.35
805 810 7.413000 GCAACTAGTTAATGATCGCTTCTTTGA 60.413 37.037 8.04 0.00 0.00 2.69
807 812 6.595716 AGCAACTAGTTAATGATCGCTTCTTT 59.404 34.615 8.04 0.00 0.00 2.52
811 816 5.665459 AGAGCAACTAGTTAATGATCGCTT 58.335 37.500 8.04 0.40 34.82 4.68
870 875 4.400961 GCGCTGGCCCAGAGTCTT 62.401 66.667 16.85 0.00 33.92 3.01
873 878 2.196997 TATTTGCGCTGGCCCAGAGT 62.197 55.000 16.85 0.00 38.85 3.24
874 879 1.442526 CTATTTGCGCTGGCCCAGAG 61.443 60.000 16.85 13.50 38.85 3.35
875 880 1.451927 CTATTTGCGCTGGCCCAGA 60.452 57.895 16.85 0.00 38.85 3.86
886 891 3.748048 TGTTGTCTGAGCTCACTATTTGC 59.252 43.478 13.74 0.89 0.00 3.68
888 893 4.993584 CAGTGTTGTCTGAGCTCACTATTT 59.006 41.667 13.74 0.00 37.27 1.40
986 991 1.284982 GACCATCGATCATTCGGGCG 61.285 60.000 0.00 0.00 45.53 6.13
1213 1218 3.066814 GCCGTCCCTAGTCCACGT 61.067 66.667 5.07 0.00 0.00 4.49
1315 1320 3.941483 CGGGGGATCAATGATGTTATAGC 59.059 47.826 0.00 0.00 0.00 2.97
1364 1369 0.485099 AGACCAGGAGGACAGTCAGT 59.515 55.000 2.17 0.00 38.69 3.41
1500 1505 2.048127 GACTGACACTGCCCCGAC 60.048 66.667 0.00 0.00 0.00 4.79
1589 1594 5.825507 GTTTCAAGCAAGAGTGATGAAACT 58.174 37.500 17.67 0.00 46.48 2.66
1926 2208 3.572255 GCCATGGAGGAAACTGTGTTAAA 59.428 43.478 18.40 0.00 44.43 1.52
1940 2222 4.569180 AATCCGCGGGCCATGGAG 62.569 66.667 27.83 6.95 34.75 3.86
1941 2223 3.653664 AAAATCCGCGGGCCATGGA 62.654 57.895 27.83 15.39 35.96 3.41
1947 2229 1.790755 AAAAAGAAAAATCCGCGGGC 58.209 45.000 27.83 8.07 0.00 6.13
1988 2271 8.572855 AAGCAAAATATGTCTAAAGAGCTCTT 57.427 30.769 23.49 23.49 37.91 2.85
2301 2591 3.248602 ACGCTGTTGTAAAGAAAGAGCAG 59.751 43.478 6.19 0.00 42.42 4.24
2361 2651 8.519526 TCACAGACTGAAAACTAACAACAAAAT 58.480 29.630 10.08 0.00 0.00 1.82
2377 2667 3.743521 CAAGATTTGGGTCACAGACTGA 58.256 45.455 10.08 0.00 32.47 3.41
2378 2668 2.227388 GCAAGATTTGGGTCACAGACTG 59.773 50.000 0.00 0.00 32.47 3.51
2379 2669 2.107204 AGCAAGATTTGGGTCACAGACT 59.893 45.455 0.00 0.00 32.47 3.24
2380 2670 2.508526 AGCAAGATTTGGGTCACAGAC 58.491 47.619 0.00 0.00 0.00 3.51
2381 2671 2.957402 AGCAAGATTTGGGTCACAGA 57.043 45.000 0.00 0.00 0.00 3.41
2382 2672 2.886523 TGAAGCAAGATTTGGGTCACAG 59.113 45.455 0.00 0.00 0.00 3.66
2383 2673 2.942804 TGAAGCAAGATTTGGGTCACA 58.057 42.857 0.00 0.00 0.00 3.58
2384 2674 4.096984 CCTATGAAGCAAGATTTGGGTCAC 59.903 45.833 0.00 0.00 0.00 3.67
2408 2698 6.821388 AGGTTCTACATTCAGAATAAGCGAT 58.179 36.000 0.00 0.00 36.93 4.58
2416 2706 9.449719 GGAAGAAATAAGGTTCTACATTCAGAA 57.550 33.333 0.00 0.00 36.84 3.02
2417 2707 8.602424 TGGAAGAAATAAGGTTCTACATTCAGA 58.398 33.333 0.00 0.00 36.84 3.27
2425 2715 7.336396 GCCTTAGTGGAAGAAATAAGGTTCTA 58.664 38.462 10.96 0.00 44.06 2.10
2464 2754 3.132289 CAGGTACCATAAAAGAGCTCGGA 59.868 47.826 15.94 0.00 0.00 4.55
2465 2755 3.458189 CAGGTACCATAAAAGAGCTCGG 58.542 50.000 15.94 4.72 0.00 4.63
2466 2756 3.458189 CCAGGTACCATAAAAGAGCTCG 58.542 50.000 15.94 0.00 0.00 5.03
2487 2777 1.370810 CACAACCAATGCAACCCCC 59.629 57.895 0.00 0.00 0.00 5.40
2488 2778 1.301637 GCACAACCAATGCAACCCC 60.302 57.895 0.00 0.00 42.88 4.95
2489 2779 4.359475 GCACAACCAATGCAACCC 57.641 55.556 0.00 0.00 42.88 4.11
2494 2784 2.721274 TACACATGCACAACCAATGC 57.279 45.000 0.00 0.00 43.68 3.56
2495 2785 6.331845 ACATATTACACATGCACAACCAATG 58.668 36.000 0.00 0.00 0.00 2.82
2496 2786 6.152492 TGACATATTACACATGCACAACCAAT 59.848 34.615 0.00 0.00 0.00 3.16
2497 2787 5.474876 TGACATATTACACATGCACAACCAA 59.525 36.000 0.00 0.00 0.00 3.67
2498 2788 5.006386 TGACATATTACACATGCACAACCA 58.994 37.500 0.00 0.00 0.00 3.67
2499 2789 5.331902 GTGACATATTACACATGCACAACC 58.668 41.667 0.00 0.00 37.05 3.77
2500 2790 5.106357 TGGTGACATATTACACATGCACAAC 60.106 40.000 0.00 0.00 38.57 3.32
2501 2791 5.006386 TGGTGACATATTACACATGCACAA 58.994 37.500 0.00 0.00 38.57 3.33
2502 2792 4.583871 TGGTGACATATTACACATGCACA 58.416 39.130 0.00 0.00 38.57 4.57
2503 2793 5.559427 TTGGTGACATATTACACATGCAC 57.441 39.130 0.00 0.00 42.32 4.57
2504 2794 6.208402 ACTTTTGGTGACATATTACACATGCA 59.792 34.615 10.06 0.00 42.32 3.96
2505 2795 6.620678 ACTTTTGGTGACATATTACACATGC 58.379 36.000 10.06 0.00 42.32 4.06
2519 2809 9.595823 GCTTAATCTGTAGTATACTTTTGGTGA 57.404 33.333 11.40 2.49 43.54 4.02
2520 2810 9.601217 AGCTTAATCTGTAGTATACTTTTGGTG 57.399 33.333 11.40 0.00 43.54 4.17
2532 2822 8.430431 GGGGTATAGAAAAGCTTAATCTGTAGT 58.570 37.037 19.71 9.26 0.00 2.73
2533 2823 8.652290 AGGGGTATAGAAAAGCTTAATCTGTAG 58.348 37.037 19.71 0.00 0.00 2.74
2534 2824 8.562949 AGGGGTATAGAAAAGCTTAATCTGTA 57.437 34.615 19.71 15.74 0.00 2.74
2535 2825 7.453141 AGGGGTATAGAAAAGCTTAATCTGT 57.547 36.000 19.71 16.54 0.00 3.41
2536 2826 8.652290 AGTAGGGGTATAGAAAAGCTTAATCTG 58.348 37.037 19.71 0.00 0.00 2.90
2537 2827 8.800515 AGTAGGGGTATAGAAAAGCTTAATCT 57.199 34.615 16.33 16.33 0.00 2.40
2544 2834 9.217278 GCTTTATTAGTAGGGGTATAGAAAAGC 57.783 37.037 0.00 0.00 37.73 3.51
2549 2839 9.443365 ACTTTGCTTTATTAGTAGGGGTATAGA 57.557 33.333 0.00 0.00 0.00 1.98
2550 2840 9.490379 CACTTTGCTTTATTAGTAGGGGTATAG 57.510 37.037 0.00 0.00 0.00 1.31
2551 2841 8.995577 ACACTTTGCTTTATTAGTAGGGGTATA 58.004 33.333 0.00 0.00 0.00 1.47
2552 2842 7.773690 CACACTTTGCTTTATTAGTAGGGGTAT 59.226 37.037 0.00 0.00 0.00 2.73
2553 2843 7.107542 CACACTTTGCTTTATTAGTAGGGGTA 58.892 38.462 0.00 0.00 0.00 3.69
2554 2844 5.944007 CACACTTTGCTTTATTAGTAGGGGT 59.056 40.000 0.00 0.00 0.00 4.95
2555 2845 5.944007 ACACACTTTGCTTTATTAGTAGGGG 59.056 40.000 0.00 0.00 0.00 4.79
2556 2846 7.448748 AACACACTTTGCTTTATTAGTAGGG 57.551 36.000 0.00 0.00 0.00 3.53
2557 2847 8.021396 GGAAACACACTTTGCTTTATTAGTAGG 58.979 37.037 0.00 0.00 0.00 3.18
2558 2848 8.021396 GGGAAACACACTTTGCTTTATTAGTAG 58.979 37.037 0.00 0.00 0.00 2.57
2559 2849 7.040271 GGGGAAACACACTTTGCTTTATTAGTA 60.040 37.037 0.00 0.00 0.00 1.82
2560 2850 6.239204 GGGGAAACACACTTTGCTTTATTAGT 60.239 38.462 0.00 0.00 0.00 2.24
2561 2851 6.156519 GGGGAAACACACTTTGCTTTATTAG 58.843 40.000 0.00 0.00 0.00 1.73
2562 2852 5.598830 TGGGGAAACACACTTTGCTTTATTA 59.401 36.000 0.00 0.00 40.38 0.98
2563 2853 4.407296 TGGGGAAACACACTTTGCTTTATT 59.593 37.500 0.00 0.00 40.38 1.40
2564 2854 3.964031 TGGGGAAACACACTTTGCTTTAT 59.036 39.130 0.00 0.00 40.38 1.40
2565 2855 3.366396 TGGGGAAACACACTTTGCTTTA 58.634 40.909 0.00 0.00 40.38 1.85
2566 2856 2.183679 TGGGGAAACACACTTTGCTTT 58.816 42.857 0.00 0.00 40.38 3.51
2567 2857 1.859302 TGGGGAAACACACTTTGCTT 58.141 45.000 0.00 0.00 40.38 3.91
2568 2858 3.605946 TGGGGAAACACACTTTGCT 57.394 47.368 0.00 0.00 40.38 3.91
2589 2879 1.265635 CGGCAGTGAACGGATGAAAAA 59.734 47.619 0.00 0.00 0.00 1.94
2590 2880 0.871722 CGGCAGTGAACGGATGAAAA 59.128 50.000 0.00 0.00 0.00 2.29
2591 2881 0.034198 TCGGCAGTGAACGGATGAAA 59.966 50.000 0.00 0.00 0.00 2.69
2592 2882 0.034198 TTCGGCAGTGAACGGATGAA 59.966 50.000 0.00 0.00 0.00 2.57
2593 2883 0.249120 ATTCGGCAGTGAACGGATGA 59.751 50.000 0.00 0.00 0.00 2.92
2594 2884 1.086696 AATTCGGCAGTGAACGGATG 58.913 50.000 0.00 0.00 0.00 3.51
2595 2885 1.821216 AAATTCGGCAGTGAACGGAT 58.179 45.000 0.00 0.00 0.00 4.18
2596 2886 2.459060 TAAATTCGGCAGTGAACGGA 57.541 45.000 0.00 0.00 0.00 4.69
2597 2887 3.187637 TCTTTAAATTCGGCAGTGAACGG 59.812 43.478 0.00 0.00 0.00 4.44
2598 2888 4.398549 TCTTTAAATTCGGCAGTGAACG 57.601 40.909 0.00 0.00 0.00 3.95
2599 2889 7.637709 AAAATCTTTAAATTCGGCAGTGAAC 57.362 32.000 0.00 0.00 0.00 3.18
2660 2950 2.243478 TGGGCAGAAATATAAGTGGGCA 59.757 45.455 0.00 0.00 0.00 5.36
2671 2961 0.896940 CCAGCTGTGTGGGCAGAAAT 60.897 55.000 13.81 0.00 38.70 2.17
2727 3018 1.336440 TGGTTGTCCTGTGCGAAAATG 59.664 47.619 0.00 0.00 34.23 2.32
2729 3020 1.464734 TTGGTTGTCCTGTGCGAAAA 58.535 45.000 0.00 0.00 34.23 2.29
3130 3445 8.311109 GGGGACATGTGTTGAAAATTTATAAGT 58.689 33.333 1.15 0.00 0.00 2.24
3136 3451 3.386402 ACGGGGACATGTGTTGAAAATTT 59.614 39.130 1.15 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.