Multiple sequence alignment - TraesCS7B01G027300

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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 TraesCS7B01G027300 chr7B 100.000 3197 0 0 1 3197 26035565 26032369 0.000000e+00 5904.0
1 TraesCS7B01G027300 chr7B 94.257 296 17 0 2301 2596 528330253 528329958 1.350000e-123 453.0
2 TraesCS7B01G027300 chr7B 96.528 144 5 0 2156 2299 606149859 606150002 4.120000e-59 239.0
3 TraesCS7B01G027300 chr7D 92.899 1549 93 12 610 2153 78799754 78798218 0.000000e+00 2235.0
4 TraesCS7B01G027300 chr7D 93.786 515 25 4 2684 3197 78795932 78795424 0.000000e+00 767.0
5 TraesCS7B01G027300 chr7D 96.875 96 3 0 2595 2690 78798219 78798124 9.180000e-36 161.0
6 TraesCS7B01G027300 chr1B 93.046 604 39 2 3 605 634500679 634500078 0.000000e+00 880.0
7 TraesCS7B01G027300 chr1B 97.931 145 3 0 2156 2300 511449887 511449743 5.290000e-63 252.0
8 TraesCS7B01G027300 chr1B 94.915 59 1 2 2063 2121 70337201 70337257 1.220000e-14 91.6
9 TraesCS7B01G027300 chr3A 91.941 608 46 2 1 606 692337386 692336780 0.000000e+00 848.0
10 TraesCS7B01G027300 chr3A 94.915 59 2 1 2070 2128 614126433 614126490 1.220000e-14 91.6
11 TraesCS7B01G027300 chr4B 91.928 607 46 2 1 606 52928551 52929155 0.000000e+00 846.0
12 TraesCS7B01G027300 chr4B 99.315 146 1 0 2156 2301 333517324 333517469 6.800000e-67 265.0
13 TraesCS7B01G027300 chr7A 92.066 605 39 6 2595 3197 81916075 81915478 0.000000e+00 843.0
14 TraesCS7B01G027300 chr7A 91.843 613 37 7 2595 3197 81928350 81927741 0.000000e+00 843.0
15 TraesCS7B01G027300 chr7A 91.234 616 50 4 1 613 130300424 130299810 0.000000e+00 835.0
16 TraesCS7B01G027300 chr7A 86.602 724 79 11 1355 2065 81916823 81916105 0.000000e+00 784.0
17 TraesCS7B01G027300 chr7A 85.501 738 84 7 1341 2065 81929107 81928380 0.000000e+00 749.0
18 TraesCS7B01G027300 chr7A 88.657 432 37 4 934 1353 81918058 81917627 1.700000e-142 516.0
19 TraesCS7B01G027300 chr7A 100.000 146 0 0 2156 2301 155307592 155307737 1.460000e-68 270.0
20 TraesCS7B01G027300 chr2A 91.626 609 47 4 1 606 24395360 24395967 0.000000e+00 839.0
21 TraesCS7B01G027300 chr2A 75.970 1315 217 54 823 2055 677545948 677547245 1.280000e-163 586.0
22 TraesCS7B01G027300 chr2A 90.141 71 4 3 2070 2139 755744033 755743965 4.390000e-14 89.8
23 TraesCS7B01G027300 chr3B 91.570 605 50 1 1 605 492229110 492228507 0.000000e+00 833.0
24 TraesCS7B01G027300 chr2D 79.281 1279 190 42 839 2061 533668309 533669568 0.000000e+00 824.0
25 TraesCS7B01G027300 chr2D 77.309 1397 226 47 731 2055 534134913 534136290 0.000000e+00 739.0
26 TraesCS7B01G027300 chr2D 77.498 1311 207 56 816 2061 533658108 533659395 0.000000e+00 706.0
27 TraesCS7B01G027300 chr2D 77.205 1202 189 51 723 1872 533662163 533663331 9.740000e-175 623.0
28 TraesCS7B01G027300 chr2D 76.903 1156 193 46 960 2055 533251687 533252828 3.550000e-164 588.0
29 TraesCS7B01G027300 chr2D 75.433 1327 213 67 822 2055 533165089 533166395 1.010000e-149 540.0
30 TraesCS7B01G027300 chr2D 94.613 297 16 0 2301 2597 489023370 489023666 8.080000e-126 460.0
31 TraesCS7B01G027300 chr2D 82.203 118 17 4 2595 2710 533669602 533669717 7.300000e-17 99.0
32 TraesCS7B01G027300 chr2D 100.000 30 0 0 2726 2755 533659658 533659687 4.460000e-04 56.5
33 TraesCS7B01G027300 chr6A 90.645 620 54 4 1 617 60158986 60159604 0.000000e+00 821.0
34 TraesCS7B01G027300 chr1A 91.133 609 48 4 1 606 361379192 361379797 0.000000e+00 821.0
35 TraesCS7B01G027300 chr1A 94.613 297 16 0 2301 2597 424518910 424518614 8.080000e-126 460.0
36 TraesCS7B01G027300 chr5A 90.600 617 53 4 1 613 126264152 126263537 0.000000e+00 813.0
37 TraesCS7B01G027300 chr5A 96.040 101 4 0 2156 2256 22060798 22060898 7.090000e-37 165.0
38 TraesCS7B01G027300 chr2B 78.521 1285 199 52 839 2061 633584654 633585923 0.000000e+00 773.0
39 TraesCS7B01G027300 chr2B 79.386 1043 169 30 1053 2061 633575446 633576476 0.000000e+00 693.0
40 TraesCS7B01G027300 chr2B 76.141 1052 181 41 1054 2055 632988271 632989302 3.710000e-134 488.0
41 TraesCS7B01G027300 chr2B 94.595 296 16 0 2301 2596 637570489 637570194 2.910000e-125 459.0
42 TraesCS7B01G027300 chr2B 76.335 562 91 22 1523 2061 633254582 633255124 2.450000e-66 263.0
43 TraesCS7B01G027300 chr2B 84.091 132 17 2 816 943 633575142 633575273 1.200000e-24 124.0
44 TraesCS7B01G027300 chr2B 82.540 126 16 4 816 936 633240576 633240700 4.360000e-19 106.0
45 TraesCS7B01G027300 chr2B 96.774 31 1 0 2725 2755 633255358 633255388 6.000000e-03 52.8
46 TraesCS7B01G027300 chrUn 78.303 1037 177 31 1059 2061 26138819 26139841 2.710000e-175 625.0
47 TraesCS7B01G027300 chrUn 94.276 297 17 0 2301 2597 88025765 88026061 3.760000e-124 455.0
48 TraesCS7B01G027300 chrUn 94.276 297 17 0 2301 2597 88028715 88029011 3.760000e-124 455.0
49 TraesCS7B01G027300 chrUn 84.800 125 15 2 816 936 26119867 26119991 4.330000e-24 122.0
50 TraesCS7B01G027300 chr3D 94.595 296 16 0 2301 2596 559081067 559080772 2.910000e-125 459.0
51 TraesCS7B01G027300 chr3D 98.077 52 1 0 2070 2121 153512350 153512401 1.220000e-14 91.6
52 TraesCS7B01G027300 chr5D 94.613 297 13 3 2301 2595 520897097 520896802 1.050000e-124 457.0
53 TraesCS7B01G027300 chr5D 99.310 145 1 0 2156 2300 497958389 497958245 2.450000e-66 263.0
54 TraesCS7B01G027300 chr5D 100.000 52 0 0 2070 2121 162425247 162425298 2.630000e-16 97.1
55 TraesCS7B01G027300 chr4D 94.257 296 17 0 2301 2596 342524476 342524181 1.350000e-123 453.0
56 TraesCS7B01G027300 chr4D 100.000 54 0 0 2068 2121 177475793 177475740 2.030000e-17 100.0
57 TraesCS7B01G027300 chr5B 100.000 146 0 0 2156 2301 81181826 81181681 1.460000e-68 270.0
58 TraesCS7B01G027300 chr6B 97.279 147 4 0 2156 2302 507622095 507622241 1.900000e-62 250.0
59 TraesCS7B01G027300 chr4A 93.878 147 8 1 2156 2302 621736585 621736730 1.490000e-53 220.0
60 TraesCS7B01G027300 chr1D 100.000 52 0 0 2070 2121 277359782 277359731 2.630000e-16 97.1
61 TraesCS7B01G027300 chr1D 100.000 52 0 0 2070 2121 438324175 438324124 2.630000e-16 97.1


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 TraesCS7B01G027300 chr7B 26032369 26035565 3196 True 5904.000000 5904 100.000000 1 3197 1 chr7B.!!$R1 3196
1 TraesCS7B01G027300 chr7D 78795424 78799754 4330 True 1054.333333 2235 94.520000 610 3197 3 chr7D.!!$R1 2587
2 TraesCS7B01G027300 chr1B 634500078 634500679 601 True 880.000000 880 93.046000 3 605 1 chr1B.!!$R2 602
3 TraesCS7B01G027300 chr3A 692336780 692337386 606 True 848.000000 848 91.941000 1 606 1 chr3A.!!$R1 605
4 TraesCS7B01G027300 chr4B 52928551 52929155 604 False 846.000000 846 91.928000 1 606 1 chr4B.!!$F1 605
5 TraesCS7B01G027300 chr7A 130299810 130300424 614 True 835.000000 835 91.234000 1 613 1 chr7A.!!$R1 612
6 TraesCS7B01G027300 chr7A 81927741 81929107 1366 True 796.000000 843 88.672000 1341 3197 2 chr7A.!!$R3 1856
7 TraesCS7B01G027300 chr7A 81915478 81918058 2580 True 714.333333 843 89.108333 934 3197 3 chr7A.!!$R2 2263
8 TraesCS7B01G027300 chr2A 24395360 24395967 607 False 839.000000 839 91.626000 1 606 1 chr2A.!!$F1 605
9 TraesCS7B01G027300 chr2A 677545948 677547245 1297 False 586.000000 586 75.970000 823 2055 1 chr2A.!!$F2 1232
10 TraesCS7B01G027300 chr3B 492228507 492229110 603 True 833.000000 833 91.570000 1 605 1 chr3B.!!$R1 604
11 TraesCS7B01G027300 chr2D 534134913 534136290 1377 False 739.000000 739 77.309000 731 2055 1 chr2D.!!$F4 1324
12 TraesCS7B01G027300 chr2D 533251687 533252828 1141 False 588.000000 588 76.903000 960 2055 1 chr2D.!!$F3 1095
13 TraesCS7B01G027300 chr2D 533165089 533166395 1306 False 540.000000 540 75.433000 822 2055 1 chr2D.!!$F2 1233
14 TraesCS7B01G027300 chr2D 533658108 533663331 5223 False 461.833333 706 84.901000 723 2755 3 chr2D.!!$F5 2032
15 TraesCS7B01G027300 chr2D 533668309 533669717 1408 False 461.500000 824 80.742000 839 2710 2 chr2D.!!$F6 1871
16 TraesCS7B01G027300 chr6A 60158986 60159604 618 False 821.000000 821 90.645000 1 617 1 chr6A.!!$F1 616
17 TraesCS7B01G027300 chr1A 361379192 361379797 605 False 821.000000 821 91.133000 1 606 1 chr1A.!!$F1 605
18 TraesCS7B01G027300 chr5A 126263537 126264152 615 True 813.000000 813 90.600000 1 613 1 chr5A.!!$R1 612
19 TraesCS7B01G027300 chr2B 633584654 633585923 1269 False 773.000000 773 78.521000 839 2061 1 chr2B.!!$F3 1222
20 TraesCS7B01G027300 chr2B 632988271 632989302 1031 False 488.000000 488 76.141000 1054 2055 1 chr2B.!!$F1 1001
21 TraesCS7B01G027300 chr2B 633575142 633576476 1334 False 408.500000 693 81.738500 816 2061 2 chr2B.!!$F5 1245
22 TraesCS7B01G027300 chrUn 26138819 26139841 1022 False 625.000000 625 78.303000 1059 2061 1 chrUn.!!$F2 1002
23 TraesCS7B01G027300 chrUn 88025765 88029011 3246 False 455.000000 455 94.276000 2301 2597 2 chrUn.!!$F3 296

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
606 619 0.169451 GTGGGCGTTAACATTTCCGG 59.831 55.0 6.39 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2196 3195 0.038166 ATGGACGGGTTGATGTGCTT 59.962 50.0 0.0 0.0 0.0 3.91 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
53 55 0.322456 GCCAGGACAGTTGCCATGTA 60.322 55.000 0.00 0.00 0.00 2.29
77 79 2.777832 AGGAAGAGTTGTCATCTGCC 57.222 50.000 0.00 0.00 42.27 4.85
79 81 2.354259 GGAAGAGTTGTCATCTGCCTG 58.646 52.381 0.00 0.00 39.21 4.85
195 197 2.804697 TCTGCTTACGTGCACACTAA 57.195 45.000 18.64 10.38 38.12 2.24
199 201 3.459145 TGCTTACGTGCACACTAAGAAA 58.541 40.909 25.26 14.68 38.12 2.52
203 205 5.560183 GCTTACGTGCACACTAAGAAATTGT 60.560 40.000 25.26 11.53 30.59 2.71
337 348 1.538876 TTGGGTGTGGGAGAGGAGG 60.539 63.158 0.00 0.00 0.00 4.30
357 368 4.760047 GGCGTGTGGGCGAGATGT 62.760 66.667 0.00 0.00 0.00 3.06
400 411 4.250431 GCGTGCGTGCAAAGTGGT 62.250 61.111 0.00 0.00 34.15 4.16
490 503 0.550914 AGTGAACACCCACACACCAT 59.449 50.000 0.00 0.00 39.42 3.55
510 523 1.079819 CCAGTCCTACGTGGCACTG 60.080 63.158 15.53 15.53 40.47 3.66
532 545 0.743688 AACATGCCAAAGTTCGTGCA 59.256 45.000 0.00 0.00 38.23 4.57
606 619 0.169451 GTGGGCGTTAACATTTCCGG 59.831 55.000 6.39 0.00 0.00 5.14
608 621 0.883153 GGGCGTTAACATTTCCGGTT 59.117 50.000 0.00 0.00 0.00 4.44
637 650 3.252458 AGGCAATGTTACACGGAAGTTTC 59.748 43.478 0.00 0.00 46.40 2.78
638 651 3.561503 GCAATGTTACACGGAAGTTTCC 58.438 45.455 0.63 0.63 46.40 3.13
642 655 5.684550 ATGTTACACGGAAGTTTCCTTTC 57.315 39.130 9.11 0.00 46.40 2.62
643 656 4.773013 TGTTACACGGAAGTTTCCTTTCT 58.227 39.130 9.11 0.00 46.40 2.52
644 657 5.187687 TGTTACACGGAAGTTTCCTTTCTT 58.812 37.500 9.11 0.00 46.40 2.52
645 658 5.648960 TGTTACACGGAAGTTTCCTTTCTTT 59.351 36.000 9.11 0.00 46.40 2.52
646 659 6.151480 TGTTACACGGAAGTTTCCTTTCTTTT 59.849 34.615 9.11 0.00 46.40 2.27
648 661 6.373186 ACACGGAAGTTTCCTTTCTTTTAG 57.627 37.500 9.11 0.00 46.40 1.85
651 664 4.277423 CGGAAGTTTCCTTTCTTTTAGGCA 59.723 41.667 9.11 0.00 45.33 4.75
652 665 5.048013 CGGAAGTTTCCTTTCTTTTAGGCAT 60.048 40.000 9.11 0.00 45.33 4.40
653 666 6.516693 CGGAAGTTTCCTTTCTTTTAGGCATT 60.517 38.462 9.11 0.00 45.33 3.56
654 667 6.646653 GGAAGTTTCCTTTCTTTTAGGCATTG 59.353 38.462 3.63 0.00 44.11 2.82
655 668 5.541845 AGTTTCCTTTCTTTTAGGCATTGC 58.458 37.500 0.00 0.00 32.59 3.56
656 669 5.305386 AGTTTCCTTTCTTTTAGGCATTGCT 59.695 36.000 8.82 0.00 32.59 3.91
657 670 6.493458 AGTTTCCTTTCTTTTAGGCATTGCTA 59.507 34.615 8.82 0.00 32.59 3.49
658 671 6.515272 TTCCTTTCTTTTAGGCATTGCTAG 57.485 37.500 8.82 0.00 32.59 3.42
660 673 5.648092 TCCTTTCTTTTAGGCATTGCTAGAC 59.352 40.000 8.82 0.00 32.59 2.59
661 674 5.415701 CCTTTCTTTTAGGCATTGCTAGACA 59.584 40.000 8.82 0.00 0.00 3.41
662 675 6.404074 CCTTTCTTTTAGGCATTGCTAGACAG 60.404 42.308 8.82 6.55 0.00 3.51
663 676 4.517285 TCTTTTAGGCATTGCTAGACAGG 58.483 43.478 8.82 0.00 0.00 4.00
664 677 4.225042 TCTTTTAGGCATTGCTAGACAGGA 59.775 41.667 8.82 0.00 0.00 3.86
665 678 3.827008 TTAGGCATTGCTAGACAGGAG 57.173 47.619 8.82 0.00 0.00 3.69
666 679 1.577736 AGGCATTGCTAGACAGGAGT 58.422 50.000 8.82 0.00 0.00 3.85
667 680 1.209019 AGGCATTGCTAGACAGGAGTG 59.791 52.381 8.82 0.00 33.66 3.51
670 683 2.741228 GCATTGCTAGACAGGAGTGGAG 60.741 54.545 0.16 0.00 31.56 3.86
709 722 3.655291 TGGCAGGGGCATAATGTAGAATA 59.345 43.478 0.00 0.00 43.71 1.75
745 758 5.070580 AGGCCTAGTATTTCGTTGCTAATCT 59.929 40.000 1.29 0.00 0.00 2.40
943 969 1.406887 GCGAGCTACTTCCCCATCAAA 60.407 52.381 0.00 0.00 0.00 2.69
946 972 3.947834 CGAGCTACTTCCCCATCAAATTT 59.052 43.478 0.00 0.00 0.00 1.82
947 973 4.035675 CGAGCTACTTCCCCATCAAATTTC 59.964 45.833 0.00 0.00 0.00 2.17
973 1020 7.216494 CCTTCTTCCCTAGATTGATTTCTCTC 58.784 42.308 0.00 0.00 31.54 3.20
1167 1280 3.390521 TCCTGGCGCGACCTCATT 61.391 61.111 10.82 0.00 40.22 2.57
1178 1291 4.096003 CCTCATTGCCGACCCCGT 62.096 66.667 0.00 0.00 0.00 5.28
1191 1304 1.894756 CCCCGTCAACCGCAAGAAA 60.895 57.895 0.00 0.00 43.02 2.52
1388 2323 2.516460 CTGCCTCTGCTCCATGGC 60.516 66.667 6.96 0.00 45.10 4.40
1432 2369 2.183858 GAAAGCGCCGGTTGAACTCC 62.184 60.000 2.29 0.00 0.00 3.85
1449 2386 0.537653 TCCATGCCCATTTCGTCGTA 59.462 50.000 0.00 0.00 0.00 3.43
1455 2392 1.531058 GCCCATTTCGTCGTATGCAAC 60.531 52.381 0.00 0.00 0.00 4.17
1519 2456 0.898789 TCCAGACGAACCTCTCACCC 60.899 60.000 0.00 0.00 0.00 4.61
1588 2526 1.076014 CAGTTTAAGGGGGCCCGTT 59.924 57.895 31.23 31.23 41.95 4.44
1713 2653 4.997395 GCTACAAGTGTCTTCTTTCATGGA 59.003 41.667 0.00 0.00 0.00 3.41
1750 2690 2.750237 GGCTGTGCCCCCTTAACG 60.750 66.667 0.00 0.00 44.06 3.18
1821 2768 1.213799 GACTAACCGTGTCCCGTCC 59.786 63.158 0.00 0.00 33.66 4.79
1823 2770 2.282110 TAACCGTGTCCCGTCCGA 60.282 61.111 0.00 0.00 33.66 4.55
1831 2778 1.743995 GTCCCGTCCGATGGTTTGG 60.744 63.158 5.89 0.00 0.00 3.28
1874 2821 0.250901 CAGGGGTGCTTGCACTACTT 60.251 55.000 22.55 11.44 0.00 2.24
1881 2828 3.482786 GTGCTTGCACTACTTTTCGATG 58.517 45.455 17.36 0.00 0.00 3.84
1888 2835 1.906574 ACTACTTTTCGATGCCCAGGA 59.093 47.619 0.00 0.00 0.00 3.86
1908 2889 6.072230 CCAGGATCAAGAAGAAAAAGGAGAAC 60.072 42.308 0.00 0.00 0.00 3.01
1969 2953 8.146053 TGATAGTAAAGAATGGGTCTTGAAGA 57.854 34.615 0.00 0.00 46.36 2.87
2066 3065 3.030291 ACACCATTTTTCTGGAAGCACA 58.970 40.909 0.00 0.00 39.73 4.57
2068 3067 4.101430 ACACCATTTTTCTGGAAGCACATT 59.899 37.500 0.00 0.00 39.73 2.71
2113 3112 1.522355 CGGGAGCTACATGCACTGG 60.522 63.158 0.00 0.00 45.94 4.00
2117 3116 1.077930 AGCTACATGCACTGGGCTG 60.078 57.895 2.50 1.44 45.94 4.85
2155 3154 4.590400 GCATTGGCATCATACGATACTC 57.410 45.455 0.00 0.00 40.72 2.59
2156 3155 4.248859 GCATTGGCATCATACGATACTCT 58.751 43.478 0.00 0.00 40.72 3.24
2157 3156 4.092529 GCATTGGCATCATACGATACTCTG 59.907 45.833 0.00 0.00 40.72 3.35
2158 3157 3.303881 TGGCATCATACGATACTCTGC 57.696 47.619 0.00 0.00 0.00 4.26
2159 3158 2.893489 TGGCATCATACGATACTCTGCT 59.107 45.455 0.00 0.00 0.00 4.24
2160 3159 4.079253 TGGCATCATACGATACTCTGCTA 58.921 43.478 0.00 0.00 0.00 3.49
2161 3160 4.082733 TGGCATCATACGATACTCTGCTAC 60.083 45.833 0.00 0.00 0.00 3.58
2162 3161 4.082733 GGCATCATACGATACTCTGCTACA 60.083 45.833 0.00 0.00 0.00 2.74
2163 3162 4.854291 GCATCATACGATACTCTGCTACAC 59.146 45.833 0.00 0.00 0.00 2.90
2164 3163 5.562890 GCATCATACGATACTCTGCTACACA 60.563 44.000 0.00 0.00 0.00 3.72
2165 3164 5.419760 TCATACGATACTCTGCTACACAC 57.580 43.478 0.00 0.00 0.00 3.82
2166 3165 4.879545 TCATACGATACTCTGCTACACACA 59.120 41.667 0.00 0.00 0.00 3.72
2167 3166 3.489180 ACGATACTCTGCTACACACAC 57.511 47.619 0.00 0.00 0.00 3.82
2168 3167 2.159558 ACGATACTCTGCTACACACACG 60.160 50.000 0.00 0.00 0.00 4.49
2169 3168 2.095372 CGATACTCTGCTACACACACGA 59.905 50.000 0.00 0.00 0.00 4.35
2170 3169 2.983402 TACTCTGCTACACACACGAC 57.017 50.000 0.00 0.00 0.00 4.34
2171 3170 0.040336 ACTCTGCTACACACACGACG 60.040 55.000 0.00 0.00 0.00 5.12
2172 3171 0.729478 CTCTGCTACACACACGACGG 60.729 60.000 0.00 0.00 0.00 4.79
2173 3172 1.007734 CTGCTACACACACGACGGT 60.008 57.895 0.00 0.00 0.00 4.83
2174 3173 0.596600 CTGCTACACACACGACGGTT 60.597 55.000 0.00 0.00 0.00 4.44
2175 3174 0.872451 TGCTACACACACGACGGTTG 60.872 55.000 0.00 0.00 0.00 3.77
2176 3175 0.872881 GCTACACACACGACGGTTGT 60.873 55.000 0.00 0.00 0.00 3.32
2177 3176 0.850217 CTACACACACGACGGTTGTG 59.150 55.000 23.67 23.67 42.99 3.33
2178 3177 0.528033 TACACACACGACGGTTGTGG 60.528 55.000 27.46 19.52 41.64 4.17
2179 3178 1.519676 CACACACGACGGTTGTGGA 60.520 57.895 27.46 0.00 41.64 4.02
2180 3179 1.519898 ACACACGACGGTTGTGGAC 60.520 57.895 27.46 0.00 41.64 4.02
2181 3180 2.278989 ACACGACGGTTGTGGACG 60.279 61.111 27.46 8.12 41.64 4.79
2182 3181 2.026445 CACGACGGTTGTGGACGA 59.974 61.111 18.86 0.00 33.69 4.20
2183 3182 1.372499 CACGACGGTTGTGGACGAT 60.372 57.895 18.86 0.00 33.69 3.73
2184 3183 1.080974 ACGACGGTTGTGGACGATC 60.081 57.895 0.00 0.00 0.00 3.69
2185 3184 1.211969 CGACGGTTGTGGACGATCT 59.788 57.895 0.00 0.00 0.00 2.75
2186 3185 0.797249 CGACGGTTGTGGACGATCTC 60.797 60.000 0.00 0.00 0.00 2.75
2187 3186 0.458025 GACGGTTGTGGACGATCTCC 60.458 60.000 0.00 4.71 39.97 3.71
2188 3187 1.516386 CGGTTGTGGACGATCTCCG 60.516 63.158 0.00 0.00 43.03 4.63
2193 3192 2.748647 TGGACGATCTCCGCACGA 60.749 61.111 0.00 0.00 43.03 4.35
2194 3193 2.119029 TGGACGATCTCCGCACGAT 61.119 57.895 0.00 0.00 43.03 3.73
2195 3194 1.658717 GGACGATCTCCGCACGATG 60.659 63.158 0.00 0.00 43.32 3.84
2196 3195 1.355563 GACGATCTCCGCACGATGA 59.644 57.895 0.00 0.00 43.32 2.92
2197 3196 0.248498 GACGATCTCCGCACGATGAA 60.248 55.000 0.00 0.00 43.32 2.57
2198 3197 0.248661 ACGATCTCCGCACGATGAAG 60.249 55.000 0.00 0.00 43.32 3.02
2199 3198 1.543941 CGATCTCCGCACGATGAAGC 61.544 60.000 0.00 0.00 0.00 3.86
2200 3199 0.528466 GATCTCCGCACGATGAAGCA 60.528 55.000 0.00 0.00 0.00 3.91
2201 3200 0.807667 ATCTCCGCACGATGAAGCAC 60.808 55.000 0.00 0.00 0.00 4.40
2202 3201 1.737735 CTCCGCACGATGAAGCACA 60.738 57.895 0.00 0.00 0.00 4.57
2203 3202 1.079197 TCCGCACGATGAAGCACAT 60.079 52.632 0.00 0.00 42.47 3.21
2211 3210 3.650647 ATGAAGCACATCAACCCGT 57.349 47.368 0.00 0.00 33.46 5.28
2212 3211 1.453155 ATGAAGCACATCAACCCGTC 58.547 50.000 0.00 0.00 33.46 4.79
2213 3212 0.605319 TGAAGCACATCAACCCGTCC 60.605 55.000 0.00 0.00 0.00 4.79
2214 3213 0.605319 GAAGCACATCAACCCGTCCA 60.605 55.000 0.00 0.00 0.00 4.02
2215 3214 0.038166 AAGCACATCAACCCGTCCAT 59.962 50.000 0.00 0.00 0.00 3.41
2216 3215 0.677731 AGCACATCAACCCGTCCATG 60.678 55.000 0.00 0.00 0.00 3.66
2217 3216 1.802636 CACATCAACCCGTCCATGC 59.197 57.895 0.00 0.00 0.00 4.06
2218 3217 1.745115 ACATCAACCCGTCCATGCG 60.745 57.895 0.00 0.00 0.00 4.73
2219 3218 1.745115 CATCAACCCGTCCATGCGT 60.745 57.895 0.00 0.00 0.00 5.24
2220 3219 1.449601 ATCAACCCGTCCATGCGTC 60.450 57.895 0.00 0.00 0.00 5.19
2221 3220 3.487202 CAACCCGTCCATGCGTCG 61.487 66.667 0.00 0.00 0.00 5.12
2222 3221 3.687102 AACCCGTCCATGCGTCGA 61.687 61.111 0.00 0.00 0.00 4.20
2223 3222 3.014085 AACCCGTCCATGCGTCGAT 62.014 57.895 0.00 0.00 0.00 3.59
2224 3223 2.202878 CCCGTCCATGCGTCGATT 60.203 61.111 0.00 0.00 0.00 3.34
2225 3224 2.237751 CCCGTCCATGCGTCGATTC 61.238 63.158 0.00 0.00 0.00 2.52
2226 3225 1.518352 CCGTCCATGCGTCGATTCA 60.518 57.895 0.00 0.00 0.00 2.57
2227 3226 1.081556 CCGTCCATGCGTCGATTCAA 61.082 55.000 0.00 0.00 0.00 2.69
2228 3227 0.718904 CGTCCATGCGTCGATTCAAA 59.281 50.000 0.00 0.00 0.00 2.69
2229 3228 1.267038 CGTCCATGCGTCGATTCAAAG 60.267 52.381 0.00 0.00 0.00 2.77
2230 3229 1.732259 GTCCATGCGTCGATTCAAAGT 59.268 47.619 0.00 0.00 0.00 2.66
2231 3230 1.731709 TCCATGCGTCGATTCAAAGTG 59.268 47.619 0.00 0.00 0.00 3.16
2232 3231 1.731709 CCATGCGTCGATTCAAAGTGA 59.268 47.619 0.00 0.00 0.00 3.41
2233 3232 2.159430 CCATGCGTCGATTCAAAGTGAA 59.841 45.455 0.00 0.00 41.09 3.18
2234 3233 2.941891 TGCGTCGATTCAAAGTGAAC 57.058 45.000 0.00 0.00 39.45 3.18
2235 3234 1.529438 TGCGTCGATTCAAAGTGAACC 59.471 47.619 0.00 0.00 39.45 3.62
2236 3235 1.798813 GCGTCGATTCAAAGTGAACCT 59.201 47.619 0.00 0.00 39.45 3.50
2237 3236 2.991190 GCGTCGATTCAAAGTGAACCTA 59.009 45.455 0.00 0.00 39.45 3.08
2238 3237 3.181533 GCGTCGATTCAAAGTGAACCTAC 60.182 47.826 0.00 0.00 39.45 3.18
2239 3238 3.985279 CGTCGATTCAAAGTGAACCTACA 59.015 43.478 0.00 0.00 39.45 2.74
2240 3239 4.143389 CGTCGATTCAAAGTGAACCTACAC 60.143 45.833 0.00 0.00 39.45 2.90
2241 3240 4.151867 GTCGATTCAAAGTGAACCTACACC 59.848 45.833 0.00 0.00 39.45 4.16
2242 3241 3.122948 CGATTCAAAGTGAACCTACACCG 59.877 47.826 0.00 0.00 39.45 4.94
2243 3242 3.547054 TTCAAAGTGAACCTACACCGT 57.453 42.857 0.00 0.00 41.12 4.83
2244 3243 3.547054 TCAAAGTGAACCTACACCGTT 57.453 42.857 0.00 0.00 41.12 4.44
2245 3244 4.669206 TCAAAGTGAACCTACACCGTTA 57.331 40.909 0.00 0.00 41.12 3.18
2246 3245 5.021033 TCAAAGTGAACCTACACCGTTAA 57.979 39.130 0.00 0.00 41.12 2.01
2247 3246 5.426504 TCAAAGTGAACCTACACCGTTAAA 58.573 37.500 0.00 0.00 41.12 1.52
2248 3247 6.056884 TCAAAGTGAACCTACACCGTTAAAT 58.943 36.000 0.00 0.00 41.12 1.40
2249 3248 7.215789 TCAAAGTGAACCTACACCGTTAAATA 58.784 34.615 0.00 0.00 41.12 1.40
2250 3249 7.171337 TCAAAGTGAACCTACACCGTTAAATAC 59.829 37.037 0.00 0.00 41.12 1.89
2251 3250 6.350629 AGTGAACCTACACCGTTAAATACT 57.649 37.500 0.00 0.00 41.12 2.12
2252 3251 6.393171 AGTGAACCTACACCGTTAAATACTC 58.607 40.000 0.00 0.00 41.12 2.59
2253 3252 5.578336 GTGAACCTACACCGTTAAATACTCC 59.422 44.000 0.00 0.00 35.07 3.85
2254 3253 5.245751 TGAACCTACACCGTTAAATACTCCA 59.754 40.000 0.00 0.00 0.00 3.86
2255 3254 5.945144 ACCTACACCGTTAAATACTCCAT 57.055 39.130 0.00 0.00 0.00 3.41
2256 3255 5.910614 ACCTACACCGTTAAATACTCCATC 58.089 41.667 0.00 0.00 0.00 3.51
2257 3256 4.980434 CCTACACCGTTAAATACTCCATCG 59.020 45.833 0.00 0.00 0.00 3.84
2258 3257 4.460948 ACACCGTTAAATACTCCATCGT 57.539 40.909 0.00 0.00 0.00 3.73
2259 3258 4.178540 ACACCGTTAAATACTCCATCGTG 58.821 43.478 0.00 0.00 0.00 4.35
2260 3259 3.000925 CACCGTTAAATACTCCATCGTGC 59.999 47.826 0.00 0.00 0.00 5.34
2261 3260 2.217847 CCGTTAAATACTCCATCGTGCG 59.782 50.000 0.00 0.00 0.00 5.34
2262 3261 2.347292 CGTTAAATACTCCATCGTGCGC 60.347 50.000 0.00 0.00 0.00 6.09
2263 3262 2.588027 TAAATACTCCATCGTGCGCA 57.412 45.000 5.66 5.66 0.00 6.09
2264 3263 1.290203 AAATACTCCATCGTGCGCAG 58.710 50.000 12.22 5.26 0.00 5.18
2265 3264 0.175760 AATACTCCATCGTGCGCAGT 59.824 50.000 12.22 5.77 0.00 4.40
2266 3265 0.175760 ATACTCCATCGTGCGCAGTT 59.824 50.000 12.22 0.00 0.00 3.16
2267 3266 0.457853 TACTCCATCGTGCGCAGTTC 60.458 55.000 12.22 0.00 0.00 3.01
2268 3267 2.792290 CTCCATCGTGCGCAGTTCG 61.792 63.158 12.22 12.20 42.12 3.95
2269 3268 3.112075 CCATCGTGCGCAGTTCGT 61.112 61.111 12.22 0.00 41.07 3.85
2270 3269 2.667318 CCATCGTGCGCAGTTCGTT 61.667 57.895 12.22 3.04 41.07 3.85
2271 3270 1.225475 CATCGTGCGCAGTTCGTTC 60.225 57.895 12.22 0.00 41.07 3.95
2272 3271 2.716828 ATCGTGCGCAGTTCGTTCG 61.717 57.895 12.22 9.53 41.07 3.95
2273 3272 4.409588 CGTGCGCAGTTCGTTCGG 62.410 66.667 12.22 0.00 41.07 4.30
2274 3273 4.719616 GTGCGCAGTTCGTTCGGC 62.720 66.667 12.22 0.00 41.07 5.54
2275 3274 4.961511 TGCGCAGTTCGTTCGGCT 62.962 61.111 5.66 0.00 41.07 5.52
2276 3275 2.807895 GCGCAGTTCGTTCGGCTA 60.808 61.111 0.30 0.00 41.07 3.93
2277 3276 2.165301 GCGCAGTTCGTTCGGCTAT 61.165 57.895 0.30 0.00 41.07 2.97
2278 3277 1.693083 GCGCAGTTCGTTCGGCTATT 61.693 55.000 0.30 0.00 41.07 1.73
2279 3278 0.025001 CGCAGTTCGTTCGGCTATTG 59.975 55.000 0.00 0.00 0.00 1.90
2280 3279 1.076332 GCAGTTCGTTCGGCTATTGT 58.924 50.000 0.00 0.00 0.00 2.71
2281 3280 1.060698 GCAGTTCGTTCGGCTATTGTC 59.939 52.381 0.00 0.00 0.00 3.18
2282 3281 1.320555 CAGTTCGTTCGGCTATTGTCG 59.679 52.381 0.00 0.00 43.50 4.35
2283 3282 1.068055 AGTTCGTTCGGCTATTGTCGT 60.068 47.619 0.29 0.00 42.59 4.34
2284 3283 1.319669 GTTCGTTCGGCTATTGTCGTC 59.680 52.381 0.29 0.00 42.59 4.20
2285 3284 0.179156 TCGTTCGGCTATTGTCGTCC 60.179 55.000 0.29 0.00 42.59 4.79
2286 3285 0.457166 CGTTCGGCTATTGTCGTCCA 60.457 55.000 0.29 0.00 42.59 4.02
2287 3286 0.997196 GTTCGGCTATTGTCGTCCAC 59.003 55.000 0.29 0.00 42.59 4.02
2288 3287 0.604073 TTCGGCTATTGTCGTCCACA 59.396 50.000 0.29 0.00 42.59 4.17
2289 3288 0.108992 TCGGCTATTGTCGTCCACAC 60.109 55.000 0.29 0.00 42.59 3.82
2290 3289 0.389296 CGGCTATTGTCGTCCACACA 60.389 55.000 0.00 0.00 36.42 3.72
2291 3290 1.359848 GGCTATTGTCGTCCACACAG 58.640 55.000 0.00 0.00 33.41 3.66
2292 3291 0.721718 GCTATTGTCGTCCACACAGC 59.278 55.000 0.00 0.00 36.58 4.40
2293 3292 1.939381 GCTATTGTCGTCCACACAGCA 60.939 52.381 0.00 0.00 40.71 4.41
2294 3293 1.995484 CTATTGTCGTCCACACAGCAG 59.005 52.381 0.00 0.00 33.41 4.24
2295 3294 0.106708 ATTGTCGTCCACACAGCAGT 59.893 50.000 0.00 0.00 33.41 4.40
2296 3295 0.107897 TTGTCGTCCACACAGCAGTT 60.108 50.000 0.00 0.00 33.41 3.16
2297 3296 0.107897 TGTCGTCCACACAGCAGTTT 60.108 50.000 0.00 0.00 0.00 2.66
2298 3297 0.582005 GTCGTCCACACAGCAGTTTC 59.418 55.000 0.00 0.00 0.00 2.78
2299 3298 0.874175 TCGTCCACACAGCAGTTTCG 60.874 55.000 0.00 0.00 0.00 3.46
2338 3337 6.593382 GGCCACTATGAAAAATACATTTTGCA 59.407 34.615 9.91 9.91 46.26 4.08
2362 3361 6.461110 TCTATACAAGGCCACTAACAGTAC 57.539 41.667 5.01 0.00 0.00 2.73
2476 3475 1.927487 TTCCTTCCTTGCATGCATGT 58.073 45.000 26.79 0.00 0.00 3.21
2480 3479 1.890625 TTCCTTGCATGCATGTGGGC 61.891 55.000 26.79 13.77 0.00 5.36
2490 3489 1.952990 TGCATGTGGGCGTATTAATGG 59.047 47.619 0.00 0.00 36.28 3.16
2501 3500 4.883006 GGCGTATTAATGGTCCCAGTTAAA 59.117 41.667 0.00 0.00 0.00 1.52
2870 7048 4.279671 ACGAATTGGTTTCATGTGGCTAAA 59.720 37.500 0.00 0.00 33.66 1.85
2871 7049 5.047377 ACGAATTGGTTTCATGTGGCTAAAT 60.047 36.000 0.00 0.00 33.66 1.40
2872 7050 5.868801 CGAATTGGTTTCATGTGGCTAAATT 59.131 36.000 0.00 0.00 33.66 1.82
2876 7054 8.721019 ATTGGTTTCATGTGGCTAAATTATTG 57.279 30.769 0.00 0.00 0.00 1.90
2911 7089 7.770433 TCTGGTTTTCTTGTCCATGATACTATG 59.230 37.037 0.00 0.00 0.00 2.23
3046 7388 1.089920 GATTTCGGTGATGCAGTGCT 58.910 50.000 17.60 1.28 0.00 4.40
3107 7456 6.819284 TCAGTTTTCTGCATTTGAAATCCTT 58.181 32.000 0.96 0.00 46.59 3.36
3123 7472 5.665916 AATCCTTTGTTTATTCTGCCTGG 57.334 39.130 0.00 0.00 0.00 4.45
3129 7478 3.340034 TGTTTATTCTGCCTGGTAACCG 58.660 45.455 0.00 0.00 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.693797 CTTGTGAGCACATGACAACC 57.306 50.000 0.00 0.00 41.52 3.77
36 37 4.582701 TTTTTACATGGCAACTGTCCTG 57.417 40.909 0.00 0.00 37.61 3.86
77 79 3.788766 GCCCTAACGTGCACGCAG 61.789 66.667 37.35 31.03 44.43 5.18
79 81 3.788766 CTGCCCTAACGTGCACGC 61.789 66.667 37.35 20.98 44.43 5.34
195 197 2.224426 TGCAGGGTACACGACAATTTCT 60.224 45.455 0.00 0.00 0.00 2.52
199 201 2.264005 TTTGCAGGGTACACGACAAT 57.736 45.000 6.67 0.00 0.00 2.71
203 205 1.301423 GTGTTTTGCAGGGTACACGA 58.699 50.000 0.00 0.00 32.56 4.35
357 368 1.533625 GCTAGTGTGTGGGCATTTGA 58.466 50.000 0.00 0.00 0.00 2.69
400 411 1.965930 GATGCAGTTCGCCCACACA 60.966 57.895 0.00 0.00 41.33 3.72
437 450 2.968156 CGTTTCACCACGCGGGAA 60.968 61.111 11.66 5.18 41.15 3.97
443 456 4.007940 CACGGCCGTTTCACCACG 62.008 66.667 32.11 11.33 40.02 4.94
510 523 2.218530 GCACGAACTTTGGCATGTTTTC 59.781 45.455 7.62 0.00 0.00 2.29
532 545 0.458669 ATCCGCGTCCTTTCGTATGT 59.541 50.000 4.92 0.00 0.00 2.29
608 621 7.175293 ACTTCCGTGTAACATTGCCTATAAAAA 59.825 33.333 0.00 0.00 35.74 1.94
637 650 5.415701 TGTCTAGCAATGCCTAAAAGAAAGG 59.584 40.000 0.00 0.00 37.17 3.11
638 651 6.404074 CCTGTCTAGCAATGCCTAAAAGAAAG 60.404 42.308 0.00 2.39 0.00 2.62
642 655 4.517285 TCCTGTCTAGCAATGCCTAAAAG 58.483 43.478 0.00 0.00 0.00 2.27
643 656 4.019321 ACTCCTGTCTAGCAATGCCTAAAA 60.019 41.667 0.00 0.00 0.00 1.52
644 657 3.519510 ACTCCTGTCTAGCAATGCCTAAA 59.480 43.478 0.00 0.00 0.00 1.85
645 658 3.107601 ACTCCTGTCTAGCAATGCCTAA 58.892 45.455 0.00 0.00 0.00 2.69
646 659 2.432146 CACTCCTGTCTAGCAATGCCTA 59.568 50.000 0.00 0.00 0.00 3.93
648 661 1.661341 CACTCCTGTCTAGCAATGCC 58.339 55.000 0.00 0.00 0.00 4.40
651 664 2.114616 CCTCCACTCCTGTCTAGCAAT 58.885 52.381 0.00 0.00 0.00 3.56
652 665 1.561643 CCTCCACTCCTGTCTAGCAA 58.438 55.000 0.00 0.00 0.00 3.91
653 666 0.324738 CCCTCCACTCCTGTCTAGCA 60.325 60.000 0.00 0.00 0.00 3.49
654 667 1.045911 CCCCTCCACTCCTGTCTAGC 61.046 65.000 0.00 0.00 0.00 3.42
655 668 0.397816 CCCCCTCCACTCCTGTCTAG 60.398 65.000 0.00 0.00 0.00 2.43
656 669 1.704082 CCCCCTCCACTCCTGTCTA 59.296 63.158 0.00 0.00 0.00 2.59
657 670 2.452114 CCCCCTCCACTCCTGTCT 59.548 66.667 0.00 0.00 0.00 3.41
658 671 3.403558 GCCCCCTCCACTCCTGTC 61.404 72.222 0.00 0.00 0.00 3.51
660 673 3.406200 CAGCCCCCTCCACTCCTG 61.406 72.222 0.00 0.00 0.00 3.86
661 674 3.615811 TCAGCCCCCTCCACTCCT 61.616 66.667 0.00 0.00 0.00 3.69
662 675 3.403558 GTCAGCCCCCTCCACTCC 61.404 72.222 0.00 0.00 0.00 3.85
663 676 3.775654 CGTCAGCCCCCTCCACTC 61.776 72.222 0.00 0.00 0.00 3.51
664 677 4.640690 ACGTCAGCCCCCTCCACT 62.641 66.667 0.00 0.00 0.00 4.00
665 678 4.394712 CACGTCAGCCCCCTCCAC 62.395 72.222 0.00 0.00 0.00 4.02
690 703 4.253685 CCGTATTCTACATTATGCCCCTG 58.746 47.826 0.00 0.00 0.00 4.45
695 708 3.684788 CAGGCCCGTATTCTACATTATGC 59.315 47.826 0.00 0.00 0.00 3.14
696 709 5.147330 TCAGGCCCGTATTCTACATTATG 57.853 43.478 0.00 0.00 0.00 1.90
726 739 8.814235 GCAACTAAGATTAGCAACGAAATACTA 58.186 33.333 0.00 0.00 34.09 1.82
745 758 0.250945 TGATGTTGGGCCGCAACTAA 60.251 50.000 26.99 15.14 33.97 2.24
943 969 6.855375 ATCAATCTAGGGAAGAAGGGAAAT 57.145 37.500 0.00 0.00 37.89 2.17
946 972 5.973124 AGAAATCAATCTAGGGAAGAAGGGA 59.027 40.000 0.00 0.00 37.89 4.20
947 973 6.101005 AGAGAAATCAATCTAGGGAAGAAGGG 59.899 42.308 0.00 0.00 37.89 3.95
973 1020 1.266989 GCTTGAAAGAACAAGGGGTCG 59.733 52.381 0.00 0.00 44.87 4.79
1006 1076 7.185565 TCTTTCTTCTTCCTAGAGATCTTCCA 58.814 38.462 0.00 0.00 0.00 3.53
1178 1291 1.452145 GGGCAGTTTCTTGCGGTTGA 61.452 55.000 0.00 0.00 45.00 3.18
1252 1373 3.660865 AGTCTGCGAACCGAAAGTAATT 58.339 40.909 0.00 0.00 0.00 1.40
1292 1413 4.077184 GGGACATGTCGACCGGCA 62.077 66.667 19.33 0.00 0.00 5.69
1388 2323 1.407437 CCGTTGATGGAGAAGAAGGGG 60.407 57.143 0.00 0.00 0.00 4.79
1416 2352 3.254024 ATGGAGTTCAACCGGCGCT 62.254 57.895 7.64 0.00 0.00 5.92
1432 2369 1.334059 GCATACGACGAAATGGGCATG 60.334 52.381 0.00 0.00 0.00 4.06
1500 2437 0.898789 GGGTGAGAGGTTCGTCTGGA 60.899 60.000 0.00 0.00 0.00 3.86
1519 2456 0.667993 TCAAAAGCCAAACGAGCCAG 59.332 50.000 0.00 0.00 0.00 4.85
1668 2606 4.448732 GCGCCACATTTCAGAAGAATTTTT 59.551 37.500 0.00 0.00 32.89 1.94
1677 2616 2.076100 CTTGTAGCGCCACATTTCAGA 58.924 47.619 10.04 0.00 0.00 3.27
1681 2620 1.535462 GACACTTGTAGCGCCACATTT 59.465 47.619 10.04 0.00 0.00 2.32
1683 2622 0.321671 AGACACTTGTAGCGCCACAT 59.678 50.000 10.04 0.00 0.00 3.21
1713 2653 0.754472 AACCAAGCAAGTGCAGCATT 59.246 45.000 0.00 0.00 45.16 3.56
1750 2690 2.298300 CAGCACAAAATCGTCGTTCAC 58.702 47.619 0.00 0.00 0.00 3.18
1821 2768 1.468520 CTACCACAAGCCAAACCATCG 59.531 52.381 0.00 0.00 0.00 3.84
1823 2770 2.969821 TCTACCACAAGCCAAACCAT 57.030 45.000 0.00 0.00 0.00 3.55
1831 2778 6.072175 TGTGATAAACCAATTCTACCACAAGC 60.072 38.462 0.00 0.00 0.00 4.01
1874 2821 1.559219 TCTTGATCCTGGGCATCGAAA 59.441 47.619 0.00 0.00 0.00 3.46
1881 2828 3.194329 CCTTTTTCTTCTTGATCCTGGGC 59.806 47.826 0.00 0.00 0.00 5.36
1888 2835 6.129179 TGGTGTTCTCCTTTTTCTTCTTGAT 58.871 36.000 0.00 0.00 0.00 2.57
1908 2889 2.625737 CAGACTGATGCTACCTTGGTG 58.374 52.381 0.00 0.00 0.00 4.17
1969 2953 6.432607 CAACTCATCATTGCTGACACTATT 57.567 37.500 0.00 0.00 33.22 1.73
2095 3094 1.522355 CCAGTGCATGTAGCTCCCG 60.522 63.158 0.00 0.00 45.94 5.14
2113 3112 2.475466 CGACATCACATGGGCAGCC 61.475 63.158 1.26 1.26 33.60 4.85
2117 3116 1.096967 TGCATCGACATCACATGGGC 61.097 55.000 0.00 0.00 33.60 5.36
2151 3150 1.196127 CGTCGTGTGTGTAGCAGAGTA 59.804 52.381 0.00 0.00 0.00 2.59
2152 3151 0.040336 CGTCGTGTGTGTAGCAGAGT 60.040 55.000 0.00 0.00 0.00 3.24
2153 3152 0.729478 CCGTCGTGTGTGTAGCAGAG 60.729 60.000 0.00 0.00 0.00 3.35
2154 3153 1.284715 CCGTCGTGTGTGTAGCAGA 59.715 57.895 0.00 0.00 0.00 4.26
2155 3154 0.596600 AACCGTCGTGTGTGTAGCAG 60.597 55.000 0.00 0.00 0.00 4.24
2156 3155 0.872451 CAACCGTCGTGTGTGTAGCA 60.872 55.000 0.00 0.00 0.00 3.49
2157 3156 0.872881 ACAACCGTCGTGTGTGTAGC 60.873 55.000 0.00 0.00 0.00 3.58
2158 3157 0.850217 CACAACCGTCGTGTGTGTAG 59.150 55.000 14.31 0.00 41.22 2.74
2159 3158 0.528033 CCACAACCGTCGTGTGTGTA 60.528 55.000 18.69 0.00 44.00 2.90
2160 3159 1.812093 CCACAACCGTCGTGTGTGT 60.812 57.895 18.69 9.00 44.00 3.72
2161 3160 1.519676 TCCACAACCGTCGTGTGTG 60.520 57.895 15.18 15.18 44.00 3.82
2162 3161 1.519898 GTCCACAACCGTCGTGTGT 60.520 57.895 13.13 4.16 44.00 3.72
2163 3162 2.582265 CGTCCACAACCGTCGTGTG 61.582 63.158 8.59 8.59 44.90 3.82
2164 3163 2.079020 ATCGTCCACAACCGTCGTGT 62.079 55.000 0.00 0.00 32.26 4.49
2165 3164 1.342082 GATCGTCCACAACCGTCGTG 61.342 60.000 0.00 0.00 0.00 4.35
2166 3165 1.080974 GATCGTCCACAACCGTCGT 60.081 57.895 0.00 0.00 0.00 4.34
2167 3166 0.797249 GAGATCGTCCACAACCGTCG 60.797 60.000 0.00 0.00 0.00 5.12
2168 3167 0.458025 GGAGATCGTCCACAACCGTC 60.458 60.000 6.39 0.00 46.10 4.79
2169 3168 1.590147 GGAGATCGTCCACAACCGT 59.410 57.895 6.39 0.00 46.10 4.83
2170 3169 4.496670 GGAGATCGTCCACAACCG 57.503 61.111 6.39 0.00 46.10 4.44
2177 3176 1.658717 CATCGTGCGGAGATCGTCC 60.659 63.158 2.13 2.13 42.85 4.79
2178 3177 0.248498 TTCATCGTGCGGAGATCGTC 60.248 55.000 0.00 0.00 41.72 4.20
2179 3178 0.248661 CTTCATCGTGCGGAGATCGT 60.249 55.000 0.00 0.00 41.72 3.73
2180 3179 1.543941 GCTTCATCGTGCGGAGATCG 61.544 60.000 0.00 0.00 42.76 3.69
2181 3180 0.528466 TGCTTCATCGTGCGGAGATC 60.528 55.000 0.00 0.00 0.00 2.75
2182 3181 0.807667 GTGCTTCATCGTGCGGAGAT 60.808 55.000 0.00 0.00 0.00 2.75
2183 3182 1.446099 GTGCTTCATCGTGCGGAGA 60.446 57.895 0.00 0.00 0.00 3.71
2184 3183 1.086067 ATGTGCTTCATCGTGCGGAG 61.086 55.000 0.00 0.00 29.76 4.63
2185 3184 1.079197 ATGTGCTTCATCGTGCGGA 60.079 52.632 0.00 0.00 29.76 5.54
2186 3185 1.349627 GATGTGCTTCATCGTGCGG 59.650 57.895 6.68 0.00 42.57 5.69
2187 3186 4.961622 GATGTGCTTCATCGTGCG 57.038 55.556 6.68 0.00 42.57 5.34
2193 3192 1.453155 GACGGGTTGATGTGCTTCAT 58.547 50.000 0.00 0.00 39.77 2.57
2194 3193 0.605319 GGACGGGTTGATGTGCTTCA 60.605 55.000 0.00 0.00 0.00 3.02
2195 3194 0.605319 TGGACGGGTTGATGTGCTTC 60.605 55.000 0.00 0.00 0.00 3.86
2196 3195 0.038166 ATGGACGGGTTGATGTGCTT 59.962 50.000 0.00 0.00 0.00 3.91
2197 3196 0.677731 CATGGACGGGTTGATGTGCT 60.678 55.000 0.00 0.00 0.00 4.40
2198 3197 1.802636 CATGGACGGGTTGATGTGC 59.197 57.895 0.00 0.00 0.00 4.57
2199 3198 1.802636 GCATGGACGGGTTGATGTG 59.197 57.895 0.00 0.00 0.00 3.21
2200 3199 1.745115 CGCATGGACGGGTTGATGT 60.745 57.895 0.00 0.00 0.00 3.06
2201 3200 1.705337 GACGCATGGACGGGTTGATG 61.705 60.000 0.00 0.00 37.37 3.07
2202 3201 1.449601 GACGCATGGACGGGTTGAT 60.450 57.895 0.00 0.00 37.37 2.57
2203 3202 2.047655 GACGCATGGACGGGTTGA 60.048 61.111 0.00 0.00 37.37 3.18
2204 3203 3.487202 CGACGCATGGACGGGTTG 61.487 66.667 0.00 0.00 37.37 3.77
2205 3204 2.515996 AATCGACGCATGGACGGGTT 62.516 55.000 0.00 0.00 37.37 4.11
2206 3205 2.901051 GAATCGACGCATGGACGGGT 62.901 60.000 0.00 0.00 37.37 5.28
2207 3206 2.202878 AATCGACGCATGGACGGG 60.203 61.111 0.00 0.00 37.37 5.28
2208 3207 1.081556 TTGAATCGACGCATGGACGG 61.082 55.000 0.00 0.00 37.37 4.79
2209 3208 0.718904 TTTGAATCGACGCATGGACG 59.281 50.000 0.00 0.00 39.50 4.79
2210 3209 1.732259 ACTTTGAATCGACGCATGGAC 59.268 47.619 0.00 0.00 0.00 4.02
2211 3210 1.731709 CACTTTGAATCGACGCATGGA 59.268 47.619 0.00 0.00 0.00 3.41
2212 3211 1.731709 TCACTTTGAATCGACGCATGG 59.268 47.619 0.00 0.00 0.00 3.66
2213 3212 3.155998 GTTCACTTTGAATCGACGCATG 58.844 45.455 0.00 0.00 38.79 4.06
2214 3213 2.159627 GGTTCACTTTGAATCGACGCAT 59.840 45.455 0.00 0.00 38.79 4.73
2215 3214 1.529438 GGTTCACTTTGAATCGACGCA 59.471 47.619 0.00 0.00 38.79 5.24
2216 3215 1.798813 AGGTTCACTTTGAATCGACGC 59.201 47.619 0.00 0.00 42.12 5.19
2217 3216 3.985279 TGTAGGTTCACTTTGAATCGACG 59.015 43.478 7.60 0.00 43.20 5.12
2218 3217 4.151867 GGTGTAGGTTCACTTTGAATCGAC 59.848 45.833 5.70 5.70 42.12 4.20
2219 3218 4.312443 GGTGTAGGTTCACTTTGAATCGA 58.688 43.478 0.00 0.00 42.12 3.59
2220 3219 3.122948 CGGTGTAGGTTCACTTTGAATCG 59.877 47.826 0.00 0.00 42.12 3.34
2221 3220 4.062991 ACGGTGTAGGTTCACTTTGAATC 58.937 43.478 0.00 0.00 38.79 2.52
2222 3221 4.081322 ACGGTGTAGGTTCACTTTGAAT 57.919 40.909 0.00 0.00 38.79 2.57
2223 3222 3.547054 ACGGTGTAGGTTCACTTTGAA 57.453 42.857 0.00 0.00 38.28 2.69
2224 3223 3.547054 AACGGTGTAGGTTCACTTTGA 57.453 42.857 0.00 0.00 38.28 2.69
2225 3224 5.738118 TTTAACGGTGTAGGTTCACTTTG 57.262 39.130 0.00 0.00 38.28 2.77
2226 3225 7.219322 AGTATTTAACGGTGTAGGTTCACTTT 58.781 34.615 0.00 0.00 38.28 2.66
2227 3226 6.762333 AGTATTTAACGGTGTAGGTTCACTT 58.238 36.000 0.00 0.00 38.28 3.16
2228 3227 6.350629 AGTATTTAACGGTGTAGGTTCACT 57.649 37.500 0.00 0.00 38.28 3.41
2229 3228 5.578336 GGAGTATTTAACGGTGTAGGTTCAC 59.422 44.000 0.00 0.00 37.57 3.18
2230 3229 5.245751 TGGAGTATTTAACGGTGTAGGTTCA 59.754 40.000 0.00 0.00 0.00 3.18
2231 3230 5.723295 TGGAGTATTTAACGGTGTAGGTTC 58.277 41.667 0.00 0.00 0.00 3.62
2232 3231 5.743636 TGGAGTATTTAACGGTGTAGGTT 57.256 39.130 0.00 0.00 0.00 3.50
2233 3232 5.450965 CGATGGAGTATTTAACGGTGTAGGT 60.451 44.000 0.00 0.00 0.00 3.08
2234 3233 4.980434 CGATGGAGTATTTAACGGTGTAGG 59.020 45.833 0.00 0.00 0.00 3.18
2235 3234 5.457799 CACGATGGAGTATTTAACGGTGTAG 59.542 44.000 0.00 0.00 0.00 2.74
2236 3235 5.342433 CACGATGGAGTATTTAACGGTGTA 58.658 41.667 0.00 0.00 0.00 2.90
2237 3236 4.178540 CACGATGGAGTATTTAACGGTGT 58.821 43.478 0.00 0.00 0.00 4.16
2238 3237 3.000925 GCACGATGGAGTATTTAACGGTG 59.999 47.826 0.00 0.00 0.00 4.94
2239 3238 3.192466 GCACGATGGAGTATTTAACGGT 58.808 45.455 0.00 0.00 0.00 4.83
2240 3239 2.217847 CGCACGATGGAGTATTTAACGG 59.782 50.000 0.00 0.00 0.00 4.44
2241 3240 2.347292 GCGCACGATGGAGTATTTAACG 60.347 50.000 0.30 0.00 0.00 3.18
2242 3241 2.605818 TGCGCACGATGGAGTATTTAAC 59.394 45.455 5.66 0.00 0.00 2.01
2243 3242 2.863740 CTGCGCACGATGGAGTATTTAA 59.136 45.455 5.66 0.00 0.00 1.52
2244 3243 2.159156 ACTGCGCACGATGGAGTATTTA 60.159 45.455 5.66 0.00 36.15 1.40
2245 3244 1.290203 CTGCGCACGATGGAGTATTT 58.710 50.000 5.66 0.00 0.00 1.40
2246 3245 0.175760 ACTGCGCACGATGGAGTATT 59.824 50.000 5.66 0.00 36.15 1.89
2247 3246 0.175760 AACTGCGCACGATGGAGTAT 59.824 50.000 5.66 0.00 36.98 2.12
2248 3247 0.457853 GAACTGCGCACGATGGAGTA 60.458 55.000 5.66 0.00 36.98 2.59
2249 3248 1.738099 GAACTGCGCACGATGGAGT 60.738 57.895 5.66 0.00 39.92 3.85
2250 3249 2.792290 CGAACTGCGCACGATGGAG 61.792 63.158 5.66 0.00 0.00 3.86
2251 3250 2.809174 CGAACTGCGCACGATGGA 60.809 61.111 5.66 0.00 0.00 3.41
2252 3251 2.548587 GAACGAACTGCGCACGATGG 62.549 60.000 23.36 8.92 46.04 3.51
2253 3252 1.225475 GAACGAACTGCGCACGATG 60.225 57.895 23.36 9.31 46.04 3.84
2254 3253 2.716828 CGAACGAACTGCGCACGAT 61.717 57.895 23.36 13.13 46.04 3.73
2255 3254 3.391631 CGAACGAACTGCGCACGA 61.392 61.111 23.36 0.00 46.04 4.35
2256 3255 4.409588 CCGAACGAACTGCGCACG 62.410 66.667 16.21 16.21 46.04 5.34
2257 3256 4.719616 GCCGAACGAACTGCGCAC 62.720 66.667 5.66 0.00 46.04 5.34
2258 3257 2.829043 ATAGCCGAACGAACTGCGCA 62.829 55.000 10.98 10.98 46.04 6.09
2259 3258 1.693083 AATAGCCGAACGAACTGCGC 61.693 55.000 0.00 0.00 46.04 6.09
2261 3260 1.060698 GACAATAGCCGAACGAACTGC 59.939 52.381 0.00 0.00 0.00 4.40
2262 3261 1.320555 CGACAATAGCCGAACGAACTG 59.679 52.381 0.00 0.00 0.00 3.16
2263 3262 1.068055 ACGACAATAGCCGAACGAACT 60.068 47.619 0.00 0.00 0.00 3.01
2264 3263 1.319669 GACGACAATAGCCGAACGAAC 59.680 52.381 0.00 0.00 0.00 3.95
2265 3264 1.621107 GACGACAATAGCCGAACGAA 58.379 50.000 0.00 0.00 0.00 3.85
2266 3265 0.179156 GGACGACAATAGCCGAACGA 60.179 55.000 0.00 0.00 0.00 3.85
2267 3266 0.457166 TGGACGACAATAGCCGAACG 60.457 55.000 0.00 0.00 0.00 3.95
2268 3267 0.997196 GTGGACGACAATAGCCGAAC 59.003 55.000 0.00 0.00 0.00 3.95
2269 3268 0.604073 TGTGGACGACAATAGCCGAA 59.396 50.000 0.00 0.00 0.00 4.30
2270 3269 0.108992 GTGTGGACGACAATAGCCGA 60.109 55.000 0.00 0.00 35.91 5.54
2271 3270 0.389296 TGTGTGGACGACAATAGCCG 60.389 55.000 0.00 0.00 35.91 5.52
2272 3271 1.359848 CTGTGTGGACGACAATAGCC 58.640 55.000 0.00 0.00 35.91 3.93
2273 3272 0.721718 GCTGTGTGGACGACAATAGC 59.278 55.000 10.75 10.75 38.88 2.97
2274 3273 1.995484 CTGCTGTGTGGACGACAATAG 59.005 52.381 0.00 0.00 35.91 1.73
2275 3274 1.343142 ACTGCTGTGTGGACGACAATA 59.657 47.619 0.00 0.00 35.91 1.90
2276 3275 0.106708 ACTGCTGTGTGGACGACAAT 59.893 50.000 0.00 0.00 35.91 2.71
2277 3276 0.107897 AACTGCTGTGTGGACGACAA 60.108 50.000 0.00 0.00 35.91 3.18
2278 3277 0.107897 AAACTGCTGTGTGGACGACA 60.108 50.000 0.00 0.00 0.00 4.35
2279 3278 0.582005 GAAACTGCTGTGTGGACGAC 59.418 55.000 0.00 0.00 0.00 4.34
2280 3279 0.874175 CGAAACTGCTGTGTGGACGA 60.874 55.000 0.00 0.00 0.00 4.20
2281 3280 1.151777 ACGAAACTGCTGTGTGGACG 61.152 55.000 2.91 5.20 0.00 4.79
2282 3281 1.003866 GAACGAAACTGCTGTGTGGAC 60.004 52.381 2.91 0.00 0.00 4.02
2283 3282 1.295792 GAACGAAACTGCTGTGTGGA 58.704 50.000 2.91 0.00 0.00 4.02
2284 3283 0.307760 GGAACGAAACTGCTGTGTGG 59.692 55.000 0.00 0.00 0.00 4.17
2285 3284 0.307760 GGGAACGAAACTGCTGTGTG 59.692 55.000 0.00 0.00 0.00 3.82
2286 3285 0.180406 AGGGAACGAAACTGCTGTGT 59.820 50.000 0.00 0.00 0.00 3.72
2287 3286 1.308998 AAGGGAACGAAACTGCTGTG 58.691 50.000 0.00 0.00 0.00 3.66
2288 3287 2.922740 TAAGGGAACGAAACTGCTGT 57.077 45.000 0.00 0.00 0.00 4.40
2289 3288 4.250464 TGTATAAGGGAACGAAACTGCTG 58.750 43.478 0.00 0.00 0.00 4.41
2290 3289 4.546829 TGTATAAGGGAACGAAACTGCT 57.453 40.909 0.00 0.00 0.00 4.24
2291 3290 5.217895 CTTGTATAAGGGAACGAAACTGC 57.782 43.478 0.00 0.00 0.00 4.40
2314 3313 7.593875 TGCAAAATGTATTTTTCATAGTGGC 57.406 32.000 0.04 0.36 37.86 5.01
2338 3337 6.041751 GGTACTGTTAGTGGCCTTGTATAGAT 59.958 42.308 3.32 0.00 0.00 1.98
2362 3361 5.009854 ACATCATTAAATTTTGCCTCGGG 57.990 39.130 0.00 0.00 0.00 5.14
2398 3397 7.656948 ACATGCATGCAAGTATTAAACAAGTTT 59.343 29.630 25.90 0.00 36.63 2.66
2438 3437 6.814954 AGGAATGAGAAGGAAGTAGCATAA 57.185 37.500 0.00 0.00 0.00 1.90
2440 3439 5.397334 GGAAGGAATGAGAAGGAAGTAGCAT 60.397 44.000 0.00 0.00 0.00 3.79
2476 3475 1.142060 CTGGGACCATTAATACGCCCA 59.858 52.381 16.27 16.27 42.95 5.36
2504 3503 4.578871 ACTTTGCAAGCCAACTTTTCTTT 58.421 34.783 0.00 0.00 32.29 2.52
2515 3514 3.503748 ACTCAATGACTACTTTGCAAGCC 59.496 43.478 0.00 0.00 33.20 4.35
2516 3515 4.756084 ACTCAATGACTACTTTGCAAGC 57.244 40.909 0.00 0.00 33.20 4.01
2520 3519 7.203255 AGGTAAAACTCAATGACTACTTTGC 57.797 36.000 0.00 0.00 33.20 3.68
2841 7019 3.507233 ACATGAAACCAATTCGTCTGCAT 59.493 39.130 0.00 0.00 41.18 3.96
2854 7032 8.034804 AGAACAATAATTTAGCCACATGAAACC 58.965 33.333 0.00 0.00 0.00 3.27
2870 7048 8.697507 AGAAAACCAGACTTCAGAACAATAAT 57.302 30.769 0.00 0.00 0.00 1.28
2871 7049 8.405531 CAAGAAAACCAGACTTCAGAACAATAA 58.594 33.333 0.00 0.00 0.00 1.40
2872 7050 7.556275 ACAAGAAAACCAGACTTCAGAACAATA 59.444 33.333 0.00 0.00 0.00 1.90
2876 7054 5.220873 GGACAAGAAAACCAGACTTCAGAAC 60.221 44.000 0.00 0.00 0.00 3.01
2911 7089 6.601332 TGGGATTTAGGACACATAATCCTTC 58.399 40.000 11.28 0.00 44.64 3.46
2974 7314 8.824781 CATTACAATAGTCTGATTGGAACTCTG 58.175 37.037 0.00 0.00 41.39 3.35
3046 7388 7.900782 AAAGCAGATAAAAACTCGCTAAGTA 57.099 32.000 0.00 0.00 37.17 2.24
3107 7456 3.754323 CGGTTACCAGGCAGAATAAACAA 59.246 43.478 1.13 0.00 0.00 2.83
3123 7472 4.615223 GCAATTTTTCAGTCCCTCGGTTAC 60.615 45.833 0.00 0.00 0.00 2.50
3129 7478 4.789012 TGATGCAATTTTTCAGTCCCTC 57.211 40.909 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.