Multiple sequence alignment - TraesCS7D01G127500

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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 TraesCS7D01G127500 chr7D 100.000 3470 0 0 1 3470 79954305 79957774 0.000000e+00 6408.0
1 TraesCS7D01G127500 chr7A 94.037 1744 71 16 669 2402 82934684 82936404 0.000000e+00 2614.0
2 TraesCS7D01G127500 chr7A 78.342 591 79 27 2563 3141 82936517 82937070 1.540000e-88 337.0
3 TraesCS7D01G127500 chr7B 93.745 1263 57 8 1277 2539 27058579 27059819 0.000000e+00 1875.0
4 TraesCS7D01G127500 chr7B 87.600 1379 95 23 32 1391 27057132 27058453 0.000000e+00 1530.0
5 TraesCS7D01G127500 chr7B 91.687 830 57 4 2643 3470 27059830 27060649 0.000000e+00 1140.0
6 TraesCS7D01G127500 chr5D 93.333 90 6 0 3327 3416 399614612 399614523 2.170000e-27 134.0
7 TraesCS7D01G127500 chr5B 93.333 90 6 0 3327 3416 479726925 479726836 2.170000e-27 134.0
8 TraesCS7D01G127500 chr3D 93.976 83 5 0 3327 3409 183747431 183747513 3.640000e-25 126.0
9 TraesCS7D01G127500 chr3B 91.304 92 8 0 3325 3416 399973210 399973119 3.640000e-25 126.0
10 TraesCS7D01G127500 chr2D 94.048 84 4 1 3327 3409 534928662 534928745 3.640000e-25 126.0
11 TraesCS7D01G127500 chr3A 92.941 85 6 0 3325 3409 405691600 405691516 1.310000e-24 124.0
12 TraesCS7D01G127500 chr4D 91.111 90 8 0 3327 3416 32019542 32019453 4.700000e-24 122.0
13 TraesCS7D01G127500 chr4D 91.111 90 8 0 3327 3416 32019724 32019635 4.700000e-24 122.0
14 TraesCS7D01G127500 chr2A 82.979 94 14 2 758 850 31199064 31199156 2.220000e-12 84.2


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 TraesCS7D01G127500 chr7D 79954305 79957774 3469 False 6408.0 6408 100.000000 1 3470 1 chr7D.!!$F1 3469
1 TraesCS7D01G127500 chr7A 82934684 82937070 2386 False 1475.5 2614 86.189500 669 3141 2 chr7A.!!$F1 2472
2 TraesCS7D01G127500 chr7B 27057132 27060649 3517 False 1515.0 1875 91.010667 32 3470 3 chr7B.!!$F1 3438

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
333 335 0.036010 AAATCAGCGTGGAGAGGGTG 60.036 55.0 0.00 0.0 36.92 4.61 F
402 404 0.548197 TGGGTCAGGATTAACCGGGT 60.548 55.0 6.32 0.0 44.74 5.28 F
2035 2301 1.284657 CGAAGAGCACGATGAGCAAT 58.715 50.0 0.00 0.0 0.00 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1914 2180 1.860641 TATCAGCAACCTTCCCGAGA 58.139 50.0 0.00 0.00 0.00 4.04 R
2377 2643 0.592247 GAAGCAAACTGTGTGCACCG 60.592 55.0 23.88 5.34 44.74 4.94 R
3334 3620 1.160137 GCCTTGCCCTCGCATAATAG 58.840 55.0 0.00 0.00 46.67 1.73 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
17 18 3.059982 GCAAGAAAACCCAGGGCC 58.940 61.111 4.91 0.00 0.00 5.80
18 19 2.931068 GCAAGAAAACCCAGGGCCG 61.931 63.158 4.91 0.00 0.00 6.13
19 20 1.228429 CAAGAAAACCCAGGGCCGA 60.228 57.895 4.91 0.00 0.00 5.54
20 21 0.825840 CAAGAAAACCCAGGGCCGAA 60.826 55.000 4.91 0.00 0.00 4.30
21 22 0.114364 AAGAAAACCCAGGGCCGAAT 59.886 50.000 4.91 0.00 0.00 3.34
22 23 0.114364 AGAAAACCCAGGGCCGAATT 59.886 50.000 4.91 0.00 0.00 2.17
23 24 0.973632 GAAAACCCAGGGCCGAATTT 59.026 50.000 4.91 0.00 0.00 1.82
24 25 1.346395 GAAAACCCAGGGCCGAATTTT 59.654 47.619 4.91 4.25 0.00 1.82
25 26 1.429930 AAACCCAGGGCCGAATTTTT 58.570 45.000 4.91 0.00 0.00 1.94
26 27 2.312424 AACCCAGGGCCGAATTTTTA 57.688 45.000 4.91 0.00 0.00 1.52
27 28 2.543037 ACCCAGGGCCGAATTTTTAT 57.457 45.000 4.91 0.00 0.00 1.40
28 29 3.673543 ACCCAGGGCCGAATTTTTATA 57.326 42.857 4.91 0.00 0.00 0.98
29 30 4.193240 ACCCAGGGCCGAATTTTTATAT 57.807 40.909 4.91 0.00 0.00 0.86
30 31 5.327737 ACCCAGGGCCGAATTTTTATATA 57.672 39.130 4.91 0.00 0.00 0.86
31 32 5.707495 ACCCAGGGCCGAATTTTTATATAA 58.293 37.500 4.91 0.00 0.00 0.98
32 33 6.137559 ACCCAGGGCCGAATTTTTATATAAA 58.862 36.000 4.91 3.71 0.00 1.40
33 34 6.266786 ACCCAGGGCCGAATTTTTATATAAAG 59.733 38.462 4.91 0.00 0.00 1.85
34 35 6.492087 CCCAGGGCCGAATTTTTATATAAAGA 59.508 38.462 7.91 4.61 0.00 2.52
51 52 0.251354 AGAAGATCATGTGTGCGCCT 59.749 50.000 4.18 0.00 0.00 5.52
61 62 2.124060 TGTGCGCCTGCTTGGAAAA 61.124 52.632 4.18 0.00 43.34 2.29
119 120 9.995003 AAAAGTTCCTAAACATAATTTGATGCA 57.005 25.926 0.00 0.00 37.88 3.96
120 121 9.643693 AAAGTTCCTAAACATAATTTGATGCAG 57.356 29.630 0.00 0.00 37.88 4.41
122 123 9.023962 AGTTCCTAAACATAATTTGATGCAGAA 57.976 29.630 0.00 0.00 37.88 3.02
123 124 9.638239 GTTCCTAAACATAATTTGATGCAGAAA 57.362 29.630 0.00 0.00 35.36 2.52
124 125 9.859427 TTCCTAAACATAATTTGATGCAGAAAG 57.141 29.630 0.00 0.00 0.00 2.62
125 126 8.469200 TCCTAAACATAATTTGATGCAGAAAGG 58.531 33.333 0.00 0.00 0.00 3.11
126 127 7.707893 CCTAAACATAATTTGATGCAGAAAGGG 59.292 37.037 0.00 0.00 0.00 3.95
127 128 5.603170 ACATAATTTGATGCAGAAAGGGG 57.397 39.130 0.00 0.00 0.00 4.79
128 129 5.271598 ACATAATTTGATGCAGAAAGGGGA 58.728 37.500 0.00 0.00 0.00 4.81
129 130 5.901276 ACATAATTTGATGCAGAAAGGGGAT 59.099 36.000 0.00 0.00 0.00 3.85
130 131 6.041296 ACATAATTTGATGCAGAAAGGGGATC 59.959 38.462 0.00 0.00 34.14 3.36
131 132 3.454719 TTTGATGCAGAAAGGGGATCA 57.545 42.857 0.00 0.00 40.66 2.92
132 133 2.425143 TGATGCAGAAAGGGGATCAC 57.575 50.000 0.00 0.00 38.04 3.06
133 134 1.918262 TGATGCAGAAAGGGGATCACT 59.082 47.619 0.00 0.00 38.04 3.41
134 135 2.309755 TGATGCAGAAAGGGGATCACTT 59.690 45.455 0.00 0.00 38.04 3.16
135 136 2.205022 TGCAGAAAGGGGATCACTTG 57.795 50.000 0.00 0.00 0.00 3.16
136 137 0.813821 GCAGAAAGGGGATCACTTGC 59.186 55.000 0.00 0.00 0.00 4.01
155 156 1.508088 GCCCGCATGGAAAGACAAG 59.492 57.895 0.00 0.00 37.49 3.16
164 166 3.071874 TGGAAAGACAAGGCGATCAAT 57.928 42.857 0.00 0.00 0.00 2.57
175 177 3.152341 AGGCGATCAATGAAATCCATCC 58.848 45.455 0.00 0.00 33.53 3.51
188 190 4.868172 AATCCATCCATCAAGACAAGGA 57.132 40.909 0.00 0.00 34.12 3.36
191 193 4.335416 TCCATCCATCAAGACAAGGAAAC 58.665 43.478 0.00 0.00 33.17 2.78
251 253 3.873952 GAGGGAAGGTTGAGAAATCGATG 59.126 47.826 0.00 0.00 0.00 3.84
253 255 4.469945 AGGGAAGGTTGAGAAATCGATGTA 59.530 41.667 0.00 0.00 0.00 2.29
262 264 4.393680 TGAGAAATCGATGTAAAAACCCGG 59.606 41.667 0.00 0.00 0.00 5.73
280 282 1.546773 CGGAAGGTGGGGTTCAATTGA 60.547 52.381 3.38 3.38 0.00 2.57
333 335 0.036010 AAATCAGCGTGGAGAGGGTG 60.036 55.000 0.00 0.00 36.92 4.61
334 336 1.903877 AATCAGCGTGGAGAGGGTGG 61.904 60.000 0.00 0.00 36.37 4.61
338 340 3.706373 CGTGGAGAGGGTGGTGGG 61.706 72.222 0.00 0.00 0.00 4.61
341 343 2.450243 GGAGAGGGTGGTGGGAGA 59.550 66.667 0.00 0.00 0.00 3.71
347 349 1.616628 GGGTGGTGGGAGATGAGGT 60.617 63.158 0.00 0.00 0.00 3.85
348 350 1.604378 GGTGGTGGGAGATGAGGTG 59.396 63.158 0.00 0.00 0.00 4.00
370 372 6.152661 GGTGAAATTAAACTGATGGGATGTGA 59.847 38.462 0.00 0.00 0.00 3.58
371 373 7.147846 GGTGAAATTAAACTGATGGGATGTGAT 60.148 37.037 0.00 0.00 0.00 3.06
379 381 4.221262 ACTGATGGGATGTGATTTTTGTGG 59.779 41.667 0.00 0.00 0.00 4.17
387 389 3.303938 TGTGATTTTTGTGGTGATGGGT 58.696 40.909 0.00 0.00 0.00 4.51
389 391 3.320541 GTGATTTTTGTGGTGATGGGTCA 59.679 43.478 0.00 0.00 0.00 4.02
397 399 3.279434 GTGGTGATGGGTCAGGATTAAC 58.721 50.000 0.00 0.00 34.36 2.01
399 401 2.561569 GTGATGGGTCAGGATTAACCG 58.438 52.381 0.00 0.00 44.74 4.44
402 404 0.548197 TGGGTCAGGATTAACCGGGT 60.548 55.000 6.32 0.00 44.74 5.28
404 406 1.839354 GGGTCAGGATTAACCGGGTTA 59.161 52.381 15.52 15.52 44.74 2.85
406 408 2.158856 GGTCAGGATTAACCGGGTTAGG 60.159 54.545 18.36 8.47 44.74 2.69
407 409 2.767960 GTCAGGATTAACCGGGTTAGGA 59.232 50.000 18.36 6.74 44.74 2.94
463 479 8.272889 AGATGCATCCTGATATTGTATTAGCAT 58.727 33.333 23.06 0.00 40.13 3.79
543 559 4.202315 TGTGGTGTATGTACTTGTGAGCTT 60.202 41.667 0.00 0.00 0.00 3.74
636 652 5.389859 TCTGTGGCAAACTTTATGGAATG 57.610 39.130 0.00 0.00 0.00 2.67
640 656 7.014711 TCTGTGGCAAACTTTATGGAATGTTTA 59.985 33.333 0.00 0.00 39.58 2.01
641 657 7.151308 TGTGGCAAACTTTATGGAATGTTTAG 58.849 34.615 0.00 0.00 39.58 1.85
653 669 4.022935 TGGAATGTTTAGAGTGCTTGCAAG 60.023 41.667 22.44 22.44 0.00 4.01
677 693 7.470563 AAGGTTTCATCAAGAAATCACCTTCAC 60.471 37.037 6.62 0.00 45.37 3.18
747 763 4.764679 ACGCATTTTGAAGCACAGATTA 57.235 36.364 0.00 0.00 0.00 1.75
830 846 4.754618 CCAAACATTCCTTAAAGTTTGCCC 59.245 41.667 11.46 0.00 45.65 5.36
835 853 6.418946 ACATTCCTTAAAGTTTGCCCAAAAA 58.581 32.000 0.00 0.00 31.33 1.94
962 982 6.239036 CCGGATTTTATTCATTTCTTCCTCCC 60.239 42.308 0.00 0.00 0.00 4.30
963 983 6.547510 CGGATTTTATTCATTTCTTCCTCCCT 59.452 38.462 0.00 0.00 0.00 4.20
967 987 7.944729 TTTATTCATTTCTTCCTCCCTCTTG 57.055 36.000 0.00 0.00 0.00 3.02
1053 1073 2.606519 TCCTTCCTCCACCCACCG 60.607 66.667 0.00 0.00 0.00 4.94
1095 1115 4.257810 TCCCCCTTCCACCACCGA 62.258 66.667 0.00 0.00 0.00 4.69
1743 2009 4.082523 CATGTCCGCACCGTCCCT 62.083 66.667 0.00 0.00 0.00 4.20
1902 2168 1.376812 GATGGTCGTGGTTGGGGAC 60.377 63.158 0.00 0.00 0.00 4.46
1935 2201 2.365617 TCTCGGGAAGGTTGCTGATATC 59.634 50.000 0.00 0.00 33.29 1.63
2035 2301 1.284657 CGAAGAGCACGATGAGCAAT 58.715 50.000 0.00 0.00 0.00 3.56
2052 2318 8.637196 ATGAGCAATATGATGATGATGAGTTT 57.363 30.769 0.00 0.00 0.00 2.66
2121 2387 3.626930 TGTTACAAGCAGGACCAAAGTT 58.373 40.909 0.00 0.00 0.00 2.66
2175 2441 5.586243 CGAAGAGGACATTGTTGATGGTATT 59.414 40.000 0.00 0.00 40.21 1.89
2185 2451 4.678256 TGTTGATGGTATTTTGGGGCTTA 58.322 39.130 0.00 0.00 0.00 3.09
2235 2501 1.352404 CGACGACGAGGATGAGGAC 59.648 63.158 0.00 0.00 42.66 3.85
2242 2508 2.361438 GACGAGGATGAGGACGGTTATT 59.639 50.000 0.00 0.00 0.00 1.40
2256 2522 7.110155 AGGACGGTTATTTGTGAGATTTACAT 58.890 34.615 0.00 0.00 0.00 2.29
2280 2546 4.441913 GGATTGGCAGGTAACAATTGGATG 60.442 45.833 10.83 2.21 37.43 3.51
2284 2550 3.119495 GGCAGGTAACAATTGGATGTGTC 60.119 47.826 10.83 0.00 41.41 3.67
2288 2554 3.505680 GGTAACAATTGGATGTGTCTGCA 59.494 43.478 10.83 0.00 32.81 4.41
2296 2562 7.557358 ACAATTGGATGTGTCTGCATATTTCTA 59.443 33.333 10.83 0.00 30.82 2.10
2307 2573 7.970061 TGTCTGCATATTTCTATTGCTTTCAAC 59.030 33.333 0.00 0.00 34.60 3.18
2308 2574 8.186821 GTCTGCATATTTCTATTGCTTTCAACT 58.813 33.333 0.00 0.00 34.60 3.16
2320 2586 6.698008 TTGCTTTCAACTGATATACCATGG 57.302 37.500 11.19 11.19 0.00 3.66
2322 2588 4.580167 GCTTTCAACTGATATACCATGGCA 59.420 41.667 13.04 0.00 0.00 4.92
2323 2589 5.278169 GCTTTCAACTGATATACCATGGCAG 60.278 44.000 13.04 13.06 0.00 4.85
2324 2590 5.372343 TTCAACTGATATACCATGGCAGT 57.628 39.130 13.04 13.76 41.19 4.40
2327 2593 3.480470 ACTGATATACCATGGCAGTTGC 58.520 45.455 13.04 0.00 36.49 4.17
2357 2623 5.222089 GGCCCTCTAGATAACTACTGTAGGA 60.222 48.000 18.38 6.93 0.00 2.94
2377 2643 9.982651 TGTAGGATTAGTAACAAGATATTGAGC 57.017 33.333 7.16 0.00 0.00 4.26
2379 2645 7.155328 AGGATTAGTAACAAGATATTGAGCGG 58.845 38.462 7.16 0.00 0.00 5.52
2385 2651 2.009051 CAAGATATTGAGCGGTGCACA 58.991 47.619 20.43 0.00 0.00 4.57
2402 2668 2.221169 CACACAGTTTGCTTCAGCCTA 58.779 47.619 0.00 0.00 41.18 3.93
2406 2672 4.256920 CACAGTTTGCTTCAGCCTATAGT 58.743 43.478 0.00 0.00 41.18 2.12
2424 2690 1.814394 AGTTACGCCTGTACGATGTGA 59.186 47.619 0.00 0.00 36.70 3.58
2425 2691 2.426024 AGTTACGCCTGTACGATGTGAT 59.574 45.455 0.00 0.00 36.70 3.06
2426 2692 2.485266 TACGCCTGTACGATGTGATG 57.515 50.000 0.00 0.00 36.70 3.07
2427 2693 0.530744 ACGCCTGTACGATGTGATGT 59.469 50.000 0.00 0.00 36.70 3.06
2428 2694 0.923403 CGCCTGTACGATGTGATGTG 59.077 55.000 0.00 0.00 34.06 3.21
2429 2695 1.290203 GCCTGTACGATGTGATGTGG 58.710 55.000 0.00 0.00 0.00 4.17
2436 2702 3.126001 ACGATGTGATGTGGTCTTTGT 57.874 42.857 0.00 0.00 0.00 2.83
2437 2703 2.807967 ACGATGTGATGTGGTCTTTGTG 59.192 45.455 0.00 0.00 0.00 3.33
2438 2704 2.413239 CGATGTGATGTGGTCTTTGTGC 60.413 50.000 0.00 0.00 0.00 4.57
2445 2711 4.766373 TGATGTGGTCTTTGTGCATATGTT 59.234 37.500 4.29 0.00 0.00 2.71
2481 2757 7.601705 ATTCCTTTCCATTTTTCAGACTCAA 57.398 32.000 0.00 0.00 0.00 3.02
2482 2758 7.416964 TTCCTTTCCATTTTTCAGACTCAAA 57.583 32.000 0.00 0.00 0.00 2.69
2483 2759 6.805713 TCCTTTCCATTTTTCAGACTCAAAC 58.194 36.000 0.00 0.00 0.00 2.93
2485 2761 6.698766 CCTTTCCATTTTTCAGACTCAAACTG 59.301 38.462 0.00 0.00 36.80 3.16
2498 2774 3.555956 ACTCAAACTGTCTGCGTTGTTAG 59.444 43.478 0.00 0.00 0.00 2.34
2499 2775 2.869801 TCAAACTGTCTGCGTTGTTAGG 59.130 45.455 0.00 0.00 0.00 2.69
2511 2787 5.968254 TGCGTTGTTAGGATACAGTGATTA 58.032 37.500 0.00 0.00 41.41 1.75
2512 2788 6.578944 TGCGTTGTTAGGATACAGTGATTAT 58.421 36.000 0.00 0.00 41.41 1.28
2513 2789 6.478673 TGCGTTGTTAGGATACAGTGATTATG 59.521 38.462 0.00 0.00 41.41 1.90
2514 2790 6.564125 GCGTTGTTAGGATACAGTGATTATGC 60.564 42.308 0.00 0.00 41.41 3.14
2515 2791 6.701841 CGTTGTTAGGATACAGTGATTATGCT 59.298 38.462 0.00 0.00 41.41 3.79
2516 2792 7.306807 CGTTGTTAGGATACAGTGATTATGCTG 60.307 40.741 0.00 0.00 41.41 4.41
2517 2793 6.524734 TGTTAGGATACAGTGATTATGCTGG 58.475 40.000 0.00 0.00 37.07 4.85
2518 2794 6.099701 TGTTAGGATACAGTGATTATGCTGGT 59.900 38.462 0.00 0.00 37.07 4.00
2519 2795 5.636903 AGGATACAGTGATTATGCTGGTT 57.363 39.130 0.00 0.00 37.07 3.67
2520 2796 5.615289 AGGATACAGTGATTATGCTGGTTC 58.385 41.667 0.00 0.00 37.07 3.62
2521 2797 5.130975 AGGATACAGTGATTATGCTGGTTCA 59.869 40.000 0.00 0.00 37.07 3.18
2522 2798 6.000219 GGATACAGTGATTATGCTGGTTCAT 59.000 40.000 0.00 0.00 37.07 2.57
2523 2799 6.488006 GGATACAGTGATTATGCTGGTTCATT 59.512 38.462 0.00 0.00 37.07 2.57
2524 2800 7.661437 GGATACAGTGATTATGCTGGTTCATTA 59.339 37.037 0.00 0.00 37.07 1.90
2525 2801 6.683974 ACAGTGATTATGCTGGTTCATTAC 57.316 37.500 0.00 0.00 37.07 1.89
2526 2802 6.179756 ACAGTGATTATGCTGGTTCATTACA 58.820 36.000 0.00 0.00 37.07 2.41
2527 2803 6.658816 ACAGTGATTATGCTGGTTCATTACAA 59.341 34.615 0.00 0.00 37.07 2.41
2528 2804 6.968904 CAGTGATTATGCTGGTTCATTACAAC 59.031 38.462 0.00 0.00 0.00 3.32
2529 2805 6.658816 AGTGATTATGCTGGTTCATTACAACA 59.341 34.615 0.00 0.00 0.00 3.33
2530 2806 7.340232 AGTGATTATGCTGGTTCATTACAACAT 59.660 33.333 0.00 0.00 0.00 2.71
2531 2807 7.645340 GTGATTATGCTGGTTCATTACAACATC 59.355 37.037 0.00 0.00 0.00 3.06
2532 2808 4.989279 ATGCTGGTTCATTACAACATCC 57.011 40.909 0.00 0.00 0.00 3.51
2533 2809 4.032960 TGCTGGTTCATTACAACATCCT 57.967 40.909 0.00 0.00 0.00 3.24
2534 2810 4.406456 TGCTGGTTCATTACAACATCCTT 58.594 39.130 0.00 0.00 0.00 3.36
2535 2811 4.458989 TGCTGGTTCATTACAACATCCTTC 59.541 41.667 0.00 0.00 0.00 3.46
2536 2812 4.702131 GCTGGTTCATTACAACATCCTTCT 59.298 41.667 0.00 0.00 0.00 2.85
2537 2813 5.392380 GCTGGTTCATTACAACATCCTTCTG 60.392 44.000 0.00 0.00 0.00 3.02
2538 2814 5.875224 TGGTTCATTACAACATCCTTCTGA 58.125 37.500 0.00 0.00 0.00 3.27
2539 2815 6.484288 TGGTTCATTACAACATCCTTCTGAT 58.516 36.000 0.00 0.00 0.00 2.90
2550 2826 5.578005 CATCCTTCTGATGCAAAATGTCT 57.422 39.130 0.00 0.00 44.16 3.41
2551 2827 5.340803 CATCCTTCTGATGCAAAATGTCTG 58.659 41.667 0.00 0.00 44.16 3.51
2552 2828 3.192001 TCCTTCTGATGCAAAATGTCTGC 59.808 43.478 0.00 0.00 40.35 4.26
2553 2829 2.905959 TCTGATGCAAAATGTCTGCG 57.094 45.000 0.00 0.00 42.97 5.18
2554 2830 2.153645 TCTGATGCAAAATGTCTGCGT 58.846 42.857 0.00 0.00 42.97 5.24
2555 2831 2.553602 TCTGATGCAAAATGTCTGCGTT 59.446 40.909 0.00 0.00 42.97 4.84
2556 2832 3.004629 TCTGATGCAAAATGTCTGCGTTT 59.995 39.130 0.00 0.00 42.97 3.60
2557 2833 3.051327 TGATGCAAAATGTCTGCGTTTG 58.949 40.909 0.00 0.00 42.97 2.93
2558 2834 2.575694 TGCAAAATGTCTGCGTTTGT 57.424 40.000 0.00 0.00 42.97 2.83
2559 2835 2.886081 TGCAAAATGTCTGCGTTTGTT 58.114 38.095 0.00 0.00 42.97 2.83
2560 2836 4.033990 TGCAAAATGTCTGCGTTTGTTA 57.966 36.364 0.00 0.00 42.97 2.41
2561 2837 4.041049 TGCAAAATGTCTGCGTTTGTTAG 58.959 39.130 0.00 0.00 42.97 2.34
2565 2841 7.018826 GCAAAATGTCTGCGTTTGTTAGTATA 58.981 34.615 0.00 0.00 34.37 1.47
2568 2844 6.642683 ATGTCTGCGTTTGTTAGTATACAC 57.357 37.500 5.50 0.00 0.00 2.90
2576 2852 7.008538 TGCGTTTGTTAGTATACACTGATTACG 59.991 37.037 5.50 7.61 36.14 3.18
2586 2862 3.674997 ACACTGATTACGCTGGTTCATT 58.325 40.909 0.00 0.00 0.00 2.57
2621 2897 7.194112 TCTGAATGTTAGGACCAACATATGA 57.806 36.000 10.38 13.73 46.00 2.15
2630 2906 3.877508 GGACCAACATATGACCAAGTAGC 59.122 47.826 10.38 0.00 0.00 3.58
2633 2909 5.918608 ACCAACATATGACCAAGTAGCTAG 58.081 41.667 10.38 0.00 0.00 3.42
2644 2920 4.100189 ACCAAGTAGCTAGGTCATTAGCAG 59.900 45.833 0.00 0.00 46.69 4.24
2646 2922 3.300388 AGTAGCTAGGTCATTAGCAGCA 58.700 45.455 0.00 0.00 46.69 4.41
2657 2933 1.737838 TTAGCAGCAATTCAGTCCCG 58.262 50.000 0.00 0.00 0.00 5.14
2666 2942 0.674895 ATTCAGTCCCGCTGCTCAAC 60.675 55.000 0.00 0.00 44.66 3.18
2722 2998 2.642139 CTAGGCAGCATGTTTTGTGG 57.358 50.000 0.00 0.00 39.31 4.17
2727 3003 1.530419 AGCATGTTTTGTGGGGCGA 60.530 52.632 0.00 0.00 0.00 5.54
2734 3010 1.065709 GTTTTGTGGGGCGATAGGAGA 60.066 52.381 0.00 0.00 0.00 3.71
2787 3064 3.347216 ACAAGACAATACCACTGGCATC 58.653 45.455 0.00 0.00 0.00 3.91
2810 3087 5.471116 TCTGTCCTTGAGTTCATGTCATTTG 59.529 40.000 0.00 0.00 0.00 2.32
2820 3097 7.095102 TGAGTTCATGTCATTTGTACATCACAG 60.095 37.037 0.00 0.00 38.72 3.66
2824 3101 7.610865 TCATGTCATTTGTACATCACAGTCTA 58.389 34.615 0.00 0.00 38.72 2.59
2825 3102 8.093927 TCATGTCATTTGTACATCACAGTCTAA 58.906 33.333 0.00 0.00 38.72 2.10
2835 3112 3.917329 TCACAGTCTAACTCCTGAACG 57.083 47.619 0.00 0.00 32.93 3.95
2846 3123 0.032952 TCCTGAACGAACTTCACCCG 59.967 55.000 0.00 0.00 33.65 5.28
2872 3149 2.430465 TGATTGCTTTCCTCAGTGCTC 58.570 47.619 0.00 0.00 0.00 4.26
2880 3157 1.742140 CCTCAGTGCTCTGCTGCAG 60.742 63.158 23.31 23.31 44.20 4.41
2919 3196 5.814764 ATCAGTATCTGTCGTTTACTCGT 57.185 39.130 0.00 0.00 32.61 4.18
2920 3197 5.618056 TCAGTATCTGTCGTTTACTCGTT 57.382 39.130 0.00 0.00 32.61 3.85
2921 3198 6.005583 TCAGTATCTGTCGTTTACTCGTTT 57.994 37.500 0.00 0.00 32.61 3.60
2922 3199 6.441274 TCAGTATCTGTCGTTTACTCGTTTT 58.559 36.000 0.00 0.00 32.61 2.43
2965 3242 7.010460 CCACTTCAATTTTTCCTGTTTTGTCTC 59.990 37.037 0.00 0.00 0.00 3.36
2969 3246 6.750039 TCAATTTTTCCTGTTTTGTCTCGAAC 59.250 34.615 0.00 0.00 0.00 3.95
2973 3250 3.724374 TCCTGTTTTGTCTCGAACGATT 58.276 40.909 0.00 0.00 0.00 3.34
3010 3287 3.726557 AAAGAGAGCATCATCACCCAA 57.273 42.857 0.00 0.00 37.82 4.12
3027 3304 2.362077 CCCAAACCTTCTTCAGTTGGTG 59.638 50.000 0.00 0.00 32.53 4.17
3039 3316 3.476552 TCAGTTGGTGTCCATTTGTCTC 58.523 45.455 0.00 0.00 31.53 3.36
3049 3326 4.759693 TGTCCATTTGTCTCGCAAGTAAAT 59.240 37.500 0.00 0.00 38.47 1.40
3085 3362 6.608808 ACTTAACCCCTCGCTAATCTACTAAA 59.391 38.462 0.00 0.00 0.00 1.85
3143 3429 3.003480 GTCACCTCCATAAGCAACACTC 58.997 50.000 0.00 0.00 0.00 3.51
3146 3432 2.237392 ACCTCCATAAGCAACACTCTCC 59.763 50.000 0.00 0.00 0.00 3.71
3175 3461 6.833416 CACCATATTCATAAAAACCCTCCTCA 59.167 38.462 0.00 0.00 0.00 3.86
3196 3482 5.646606 TCAATGTTCATCATGTCAGCATTG 58.353 37.500 16.90 16.90 41.46 2.82
3202 3488 3.128068 TCATCATGTCAGCATTGTTCAGC 59.872 43.478 0.00 0.00 31.99 4.26
3212 3498 3.192212 AGCATTGTTCAGCCTCTAAAAGC 59.808 43.478 0.00 0.00 0.00 3.51
3221 3507 3.957497 CAGCCTCTAAAAGCCTCTCTCTA 59.043 47.826 0.00 0.00 0.00 2.43
3227 3513 6.603997 CCTCTAAAAGCCTCTCTCTACAGTTA 59.396 42.308 0.00 0.00 0.00 2.24
3255 3541 2.283298 ACCAATGTCATCTGCTAAGCG 58.717 47.619 0.00 0.00 0.00 4.68
3260 3546 3.089573 TGTCATCTGCTAAGCGATCTG 57.910 47.619 0.00 0.00 0.00 2.90
3278 3564 2.487762 TCTGCTACTTTTCCGCAATTGG 59.512 45.455 7.72 0.00 32.66 3.16
3300 3586 5.172205 GGTCTCCTTGATTTCTGTGACTAC 58.828 45.833 0.00 0.00 0.00 2.73
3334 3620 5.163814 CCAATACTCTGTAGCTTTGCAGAAC 60.164 44.000 13.70 0.00 40.68 3.01
3348 3634 1.801178 GCAGAACTATTATGCGAGGGC 59.199 52.381 0.00 0.00 40.52 5.19
3390 3676 2.282462 CCAGACCCCACCTTGTGC 60.282 66.667 0.00 0.00 31.34 4.57
3423 3709 0.615331 ACTGGATGCACCACAGGTAG 59.385 55.000 15.81 4.50 44.64 3.18
3437 3723 4.576463 CCACAGGTAGTATCTGCATTTTCC 59.424 45.833 10.48 0.00 35.78 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.931068 CGGCCCTGGGTTTTCTTGC 61.931 63.158 15.56 0.00 0.00 4.01
1 2 0.825840 TTCGGCCCTGGGTTTTCTTG 60.826 55.000 15.56 0.00 0.00 3.02
2 3 0.114364 ATTCGGCCCTGGGTTTTCTT 59.886 50.000 15.56 0.00 0.00 2.52
3 4 0.114364 AATTCGGCCCTGGGTTTTCT 59.886 50.000 15.56 0.00 0.00 2.52
4 5 0.973632 AAATTCGGCCCTGGGTTTTC 59.026 50.000 15.56 0.00 0.00 2.29
5 6 1.429930 AAAATTCGGCCCTGGGTTTT 58.570 45.000 15.56 9.71 0.00 2.43
6 7 1.429930 AAAAATTCGGCCCTGGGTTT 58.570 45.000 15.56 3.39 0.00 3.27
7 8 2.312424 TAAAAATTCGGCCCTGGGTT 57.688 45.000 15.56 0.11 0.00 4.11
8 9 2.543037 ATAAAAATTCGGCCCTGGGT 57.457 45.000 15.56 0.00 0.00 4.51
9 10 6.492087 TCTTTATATAAAAATTCGGCCCTGGG 59.508 38.462 8.86 8.86 0.00 4.45
10 11 7.519032 TCTTTATATAAAAATTCGGCCCTGG 57.481 36.000 9.15 0.00 0.00 4.45
11 12 8.846211 TCTTCTTTATATAAAAATTCGGCCCTG 58.154 33.333 9.15 0.00 0.00 4.45
12 13 8.990163 TCTTCTTTATATAAAAATTCGGCCCT 57.010 30.769 9.15 0.00 0.00 5.19
13 14 9.841880 GATCTTCTTTATATAAAAATTCGGCCC 57.158 33.333 9.15 0.00 0.00 5.80
23 24 8.282592 GCGCACACATGATCTTCTTTATATAAA 58.717 33.333 0.30 7.66 0.00 1.40
24 25 7.095229 GGCGCACACATGATCTTCTTTATATAA 60.095 37.037 10.83 0.00 0.00 0.98
25 26 6.368791 GGCGCACACATGATCTTCTTTATATA 59.631 38.462 10.83 0.00 0.00 0.86
26 27 5.180117 GGCGCACACATGATCTTCTTTATAT 59.820 40.000 10.83 0.00 0.00 0.86
27 28 4.511454 GGCGCACACATGATCTTCTTTATA 59.489 41.667 10.83 0.00 0.00 0.98
28 29 3.313526 GGCGCACACATGATCTTCTTTAT 59.686 43.478 10.83 0.00 0.00 1.40
29 30 2.677836 GGCGCACACATGATCTTCTTTA 59.322 45.455 10.83 0.00 0.00 1.85
30 31 1.470098 GGCGCACACATGATCTTCTTT 59.530 47.619 10.83 0.00 0.00 2.52
31 32 1.089920 GGCGCACACATGATCTTCTT 58.910 50.000 10.83 0.00 0.00 2.52
32 33 0.251354 AGGCGCACACATGATCTTCT 59.749 50.000 10.83 0.00 0.00 2.85
33 34 0.376152 CAGGCGCACACATGATCTTC 59.624 55.000 10.83 0.00 0.00 2.87
34 35 1.651240 GCAGGCGCACACATGATCTT 61.651 55.000 10.83 0.00 38.36 2.40
61 62 4.355549 TGGATTTCTTTGATCCCATTGCT 58.644 39.130 1.03 0.00 41.97 3.91
106 107 5.857471 TCCCCTTTCTGCATCAAATTATG 57.143 39.130 0.00 0.00 0.00 1.90
117 118 0.813821 GCAAGTGATCCCCTTTCTGC 59.186 55.000 0.00 0.00 0.00 4.26
119 120 0.678048 GCGCAAGTGATCCCCTTTCT 60.678 55.000 0.30 0.00 41.68 2.52
120 121 1.657751 GGCGCAAGTGATCCCCTTTC 61.658 60.000 10.83 0.00 41.68 2.62
122 123 2.044946 GGCGCAAGTGATCCCCTT 60.045 61.111 10.83 0.00 41.68 3.95
123 124 4.115199 GGGCGCAAGTGATCCCCT 62.115 66.667 10.83 0.00 41.68 4.79
135 136 4.179579 GTCTTTCCATGCGGGCGC 62.180 66.667 0.00 0.00 42.35 6.53
136 137 2.257286 CTTGTCTTTCCATGCGGGCG 62.257 60.000 0.00 0.00 36.21 6.13
145 146 3.009723 TCATTGATCGCCTTGTCTTTCC 58.990 45.455 0.00 0.00 0.00 3.13
146 147 4.685169 TTCATTGATCGCCTTGTCTTTC 57.315 40.909 0.00 0.00 0.00 2.62
155 156 2.886523 TGGATGGATTTCATTGATCGCC 59.113 45.455 0.00 0.00 35.97 5.54
164 166 4.951715 CCTTGTCTTGATGGATGGATTTCA 59.048 41.667 0.00 0.00 0.00 2.69
188 190 9.034544 GCAAAAATCTTAACAGATCACAAGTTT 57.965 29.630 0.00 0.00 39.00 2.66
191 193 8.578308 TTGCAAAAATCTTAACAGATCACAAG 57.422 30.769 0.00 0.00 39.00 3.16
194 196 8.579682 AACTTGCAAAAATCTTAACAGATCAC 57.420 30.769 0.00 0.00 39.00 3.06
221 223 5.640158 TCTCAACCTTCCCTCTAAACAAA 57.360 39.130 0.00 0.00 0.00 2.83
229 231 3.611766 TCGATTTCTCAACCTTCCCTC 57.388 47.619 0.00 0.00 0.00 4.30
262 264 4.681074 TTTTCAATTGAACCCCACCTTC 57.319 40.909 20.35 0.00 33.13 3.46
286 288 8.125978 TCTCCTCTGCACATTTCAATTAATTT 57.874 30.769 0.00 0.00 0.00 1.82
289 291 7.523293 TTTCTCCTCTGCACATTTCAATTAA 57.477 32.000 0.00 0.00 0.00 1.40
290 292 7.523293 TTTTCTCCTCTGCACATTTCAATTA 57.477 32.000 0.00 0.00 0.00 1.40
292 294 6.409524 TTTTTCTCCTCTGCACATTTCAAT 57.590 33.333 0.00 0.00 0.00 2.57
293 295 5.850557 TTTTTCTCCTCTGCACATTTCAA 57.149 34.783 0.00 0.00 0.00 2.69
324 326 1.003573 ATCTCCCACCACCCTCTCC 59.996 63.158 0.00 0.00 0.00 3.71
328 330 1.307343 CCTCATCTCCCACCACCCT 60.307 63.158 0.00 0.00 0.00 4.34
333 335 3.372440 AATTTCACCTCATCTCCCACC 57.628 47.619 0.00 0.00 0.00 4.61
334 336 5.946377 AGTTTAATTTCACCTCATCTCCCAC 59.054 40.000 0.00 0.00 0.00 4.61
338 340 7.201767 CCCATCAGTTTAATTTCACCTCATCTC 60.202 40.741 0.00 0.00 0.00 2.75
341 343 6.493166 TCCCATCAGTTTAATTTCACCTCAT 58.507 36.000 0.00 0.00 0.00 2.90
347 349 7.959658 ATCACATCCCATCAGTTTAATTTCA 57.040 32.000 0.00 0.00 0.00 2.69
348 350 9.657419 AAAATCACATCCCATCAGTTTAATTTC 57.343 29.630 0.00 0.00 0.00 2.17
370 372 2.899256 CCTGACCCATCACCACAAAAAT 59.101 45.455 0.00 0.00 0.00 1.82
371 373 2.091610 TCCTGACCCATCACCACAAAAA 60.092 45.455 0.00 0.00 0.00 1.94
379 381 2.561569 CGGTTAATCCTGACCCATCAC 58.438 52.381 0.00 0.00 32.14 3.06
387 389 3.119009 TCCTAACCCGGTTAATCCTGA 57.881 47.619 11.24 1.41 0.00 3.86
389 391 2.977580 GGATCCTAACCCGGTTAATCCT 59.022 50.000 23.26 7.19 34.81 3.24
436 452 8.761689 TGCTAATACAATATCAGGATGCATCTA 58.238 33.333 25.28 10.92 34.76 1.98
438 454 7.854557 TGCTAATACAATATCAGGATGCATC 57.145 36.000 18.81 18.81 34.76 3.91
515 531 7.065803 GCTCACAAGTACATACACCACATTATT 59.934 37.037 0.00 0.00 0.00 1.40
519 535 4.020218 AGCTCACAAGTACATACACCACAT 60.020 41.667 0.00 0.00 0.00 3.21
520 536 3.323691 AGCTCACAAGTACATACACCACA 59.676 43.478 0.00 0.00 0.00 4.17
615 631 5.138125 ACATTCCATAAAGTTTGCCACAG 57.862 39.130 0.00 0.00 0.00 3.66
636 652 3.990318 AACCTTGCAAGCACTCTAAAC 57.010 42.857 21.43 0.00 0.00 2.01
640 656 2.057137 TGAAACCTTGCAAGCACTCT 57.943 45.000 21.43 2.81 0.00 3.24
641 657 2.294233 TGATGAAACCTTGCAAGCACTC 59.706 45.455 21.43 15.27 0.00 3.51
653 669 6.152379 GTGAAGGTGATTTCTTGATGAAACC 58.848 40.000 0.00 0.00 46.08 3.27
677 693 5.567534 CGATTTTATTGTTCCACAACTTCCG 59.432 40.000 0.00 0.00 41.40 4.30
724 740 4.764679 ATCTGTGCTTCAAAATGCGTTA 57.235 36.364 0.00 0.00 0.00 3.18
757 773 1.411977 CATTGGTGAAAGTGGTGGCAA 59.588 47.619 0.00 0.00 0.00 4.52
758 774 1.039068 CATTGGTGAAAGTGGTGGCA 58.961 50.000 0.00 0.00 0.00 4.92
860 878 8.922058 ATGCTCATGATGAAAACAGTAAAATC 57.078 30.769 0.00 0.00 0.00 2.17
861 879 9.715121 AAATGCTCATGATGAAAACAGTAAAAT 57.285 25.926 0.00 0.00 0.00 1.82
1914 2180 1.860641 TATCAGCAACCTTCCCGAGA 58.139 50.000 0.00 0.00 0.00 4.04
1935 2201 2.360852 CTGTCCCAAGGCAGCCAG 60.361 66.667 15.80 5.46 0.00 4.85
2052 2318 7.547697 TTCATTCGTATCCCAATCCACTATA 57.452 36.000 0.00 0.00 0.00 1.31
2121 2387 5.126222 TGCAGACATTGTTGTAGAACCAAAA 59.874 36.000 0.00 0.00 35.79 2.44
2175 2441 3.202151 CCTCCTTATGTCTAAGCCCCAAA 59.798 47.826 0.00 0.00 34.21 3.28
2185 2451 3.972638 AGCATGTCATCCTCCTTATGTCT 59.027 43.478 0.00 0.00 0.00 3.41
2235 2501 7.315247 TCCATGTAAATCTCACAAATAACCG 57.685 36.000 0.00 0.00 0.00 4.44
2242 2508 5.015515 TGCCAATCCATGTAAATCTCACAA 58.984 37.500 0.00 0.00 0.00 3.33
2256 2522 2.830923 CCAATTGTTACCTGCCAATCCA 59.169 45.455 4.43 0.00 31.15 3.41
2280 2546 7.475015 TGAAAGCAATAGAAATATGCAGACAC 58.525 34.615 0.00 0.00 42.45 3.67
2284 2550 8.186163 TCAGTTGAAAGCAATAGAAATATGCAG 58.814 33.333 0.00 0.00 42.45 4.41
2296 2562 6.239120 GCCATGGTATATCAGTTGAAAGCAAT 60.239 38.462 14.67 0.00 36.22 3.56
2327 2593 3.041946 AGTTATCTAGAGGGCCAACTGG 58.958 50.000 6.18 7.05 38.53 4.00
2328 2594 4.896482 AGTAGTTATCTAGAGGGCCAACTG 59.104 45.833 6.18 0.58 0.00 3.16
2329 2595 4.896482 CAGTAGTTATCTAGAGGGCCAACT 59.104 45.833 6.18 7.38 0.00 3.16
2330 2596 4.650131 ACAGTAGTTATCTAGAGGGCCAAC 59.350 45.833 6.18 0.00 0.00 3.77
2331 2597 4.880164 ACAGTAGTTATCTAGAGGGCCAA 58.120 43.478 6.18 0.00 0.00 4.52
2332 2598 4.537945 ACAGTAGTTATCTAGAGGGCCA 57.462 45.455 6.18 0.00 0.00 5.36
2333 2599 5.011586 CCTACAGTAGTTATCTAGAGGGCC 58.988 50.000 6.84 0.00 0.00 5.80
2334 2600 5.878627 TCCTACAGTAGTTATCTAGAGGGC 58.121 45.833 6.84 0.00 0.00 5.19
2335 2601 9.675464 CTAATCCTACAGTAGTTATCTAGAGGG 57.325 40.741 6.84 0.00 0.00 4.30
2357 2623 6.202954 GCACCGCTCAATATCTTGTTACTAAT 59.797 38.462 0.00 0.00 33.87 1.73
2377 2643 0.592247 GAAGCAAACTGTGTGCACCG 60.592 55.000 23.88 5.34 44.74 4.94
2379 2645 1.831343 CTGAAGCAAACTGTGTGCAC 58.169 50.000 23.88 16.95 44.74 4.57
2385 2651 4.559862 ACTATAGGCTGAAGCAAACTGT 57.440 40.909 4.43 0.00 44.36 3.55
2402 2668 3.628942 TCACATCGTACAGGCGTAACTAT 59.371 43.478 0.00 0.00 0.00 2.12
2406 2672 2.164827 ACATCACATCGTACAGGCGTAA 59.835 45.455 0.00 0.00 0.00 3.18
2424 2690 5.243507 TCAAACATATGCACAAAGACCACAT 59.756 36.000 1.58 0.00 0.00 3.21
2425 2691 4.582240 TCAAACATATGCACAAAGACCACA 59.418 37.500 1.58 0.00 0.00 4.17
2426 2692 5.119931 TCAAACATATGCACAAAGACCAC 57.880 39.130 1.58 0.00 0.00 4.16
2427 2693 5.981088 ATCAAACATATGCACAAAGACCA 57.019 34.783 1.58 0.00 0.00 4.02
2428 2694 7.312154 TGTTATCAAACATATGCACAAAGACC 58.688 34.615 1.58 0.00 40.69 3.85
2429 2695 8.741101 TTGTTATCAAACATATGCACAAAGAC 57.259 30.769 1.58 0.00 44.85 3.01
2465 2741 6.382869 AGACAGTTTGAGTCTGAAAAATGG 57.617 37.500 6.77 0.00 44.23 3.16
2481 2757 2.902705 TCCTAACAACGCAGACAGTT 57.097 45.000 0.00 0.00 0.00 3.16
2482 2758 3.257375 TGTATCCTAACAACGCAGACAGT 59.743 43.478 0.00 0.00 0.00 3.55
2483 2759 3.845178 TGTATCCTAACAACGCAGACAG 58.155 45.455 0.00 0.00 0.00 3.51
2485 2761 3.612860 CACTGTATCCTAACAACGCAGAC 59.387 47.826 0.00 0.00 0.00 3.51
2498 2774 5.368145 TGAACCAGCATAATCACTGTATCC 58.632 41.667 0.00 0.00 31.76 2.59
2499 2775 7.502120 AATGAACCAGCATAATCACTGTATC 57.498 36.000 0.00 0.00 31.76 2.24
2511 2787 4.603131 AGGATGTTGTAATGAACCAGCAT 58.397 39.130 0.00 0.00 35.57 3.79
2512 2788 4.032960 AGGATGTTGTAATGAACCAGCA 57.967 40.909 0.00 0.00 0.00 4.41
2513 2789 4.702131 AGAAGGATGTTGTAATGAACCAGC 59.298 41.667 0.00 0.00 0.00 4.85
2514 2790 5.939883 TCAGAAGGATGTTGTAATGAACCAG 59.060 40.000 0.00 0.00 0.00 4.00
2515 2791 5.875224 TCAGAAGGATGTTGTAATGAACCA 58.125 37.500 0.00 0.00 0.00 3.67
2516 2792 6.789262 CATCAGAAGGATGTTGTAATGAACC 58.211 40.000 0.00 0.00 46.81 3.62
2529 2805 4.142227 GCAGACATTTTGCATCAGAAGGAT 60.142 41.667 0.00 0.00 41.17 3.24
2530 2806 3.192001 GCAGACATTTTGCATCAGAAGGA 59.808 43.478 0.00 0.00 41.17 3.36
2531 2807 3.508762 GCAGACATTTTGCATCAGAAGG 58.491 45.455 0.00 0.00 41.17 3.46
2532 2808 3.168963 CGCAGACATTTTGCATCAGAAG 58.831 45.455 0.00 0.00 41.59 2.85
2533 2809 2.553602 ACGCAGACATTTTGCATCAGAA 59.446 40.909 0.00 0.00 41.59 3.02
2534 2810 2.153645 ACGCAGACATTTTGCATCAGA 58.846 42.857 0.00 0.00 41.59 3.27
2535 2811 2.624316 ACGCAGACATTTTGCATCAG 57.376 45.000 0.00 0.00 41.59 2.90
2536 2812 3.051327 CAAACGCAGACATTTTGCATCA 58.949 40.909 0.00 0.00 41.59 3.07
2537 2813 3.052036 ACAAACGCAGACATTTTGCATC 58.948 40.909 0.00 0.00 41.59 3.91
2538 2814 3.096489 ACAAACGCAGACATTTTGCAT 57.904 38.095 0.00 0.00 41.59 3.96
2539 2815 2.575694 ACAAACGCAGACATTTTGCA 57.424 40.000 0.00 0.00 41.59 4.08
2540 2816 4.041723 ACTAACAAACGCAGACATTTTGC 58.958 39.130 0.00 0.00 34.22 3.68
2541 2817 8.012809 TGTATACTAACAAACGCAGACATTTTG 58.987 33.333 4.17 0.00 36.49 2.44
2542 2818 8.013378 GTGTATACTAACAAACGCAGACATTTT 58.987 33.333 4.17 0.00 0.00 1.82
2543 2819 7.386848 AGTGTATACTAACAAACGCAGACATTT 59.613 33.333 4.17 0.00 34.74 2.32
2544 2820 6.872020 AGTGTATACTAACAAACGCAGACATT 59.128 34.615 4.17 0.00 34.74 2.71
2545 2821 6.310467 CAGTGTATACTAACAAACGCAGACAT 59.690 38.462 4.17 0.00 34.74 3.06
2546 2822 5.631929 CAGTGTATACTAACAAACGCAGACA 59.368 40.000 4.17 0.00 34.74 3.41
2547 2823 5.860182 TCAGTGTATACTAACAAACGCAGAC 59.140 40.000 4.17 0.00 34.74 3.51
2548 2824 6.016213 TCAGTGTATACTAACAAACGCAGA 57.984 37.500 4.17 0.00 34.74 4.26
2549 2825 6.887376 ATCAGTGTATACTAACAAACGCAG 57.113 37.500 4.17 0.00 34.74 5.18
2550 2826 7.008538 CGTAATCAGTGTATACTAACAAACGCA 59.991 37.037 4.17 0.00 34.74 5.24
2551 2827 7.325180 CGTAATCAGTGTATACTAACAAACGC 58.675 38.462 4.17 0.00 34.74 4.84
2552 2828 7.219535 AGCGTAATCAGTGTATACTAACAAACG 59.780 37.037 4.17 7.41 34.74 3.60
2553 2829 8.318876 CAGCGTAATCAGTGTATACTAACAAAC 58.681 37.037 4.17 0.00 34.74 2.93
2554 2830 7.490079 CCAGCGTAATCAGTGTATACTAACAAA 59.510 37.037 4.17 0.00 34.74 2.83
2555 2831 6.976349 CCAGCGTAATCAGTGTATACTAACAA 59.024 38.462 4.17 0.00 34.74 2.83
2556 2832 6.095860 ACCAGCGTAATCAGTGTATACTAACA 59.904 38.462 4.17 0.00 34.74 2.41
2557 2833 6.501781 ACCAGCGTAATCAGTGTATACTAAC 58.498 40.000 4.17 0.00 34.74 2.34
2558 2834 6.704289 ACCAGCGTAATCAGTGTATACTAA 57.296 37.500 4.17 0.00 34.74 2.24
2559 2835 6.319405 TGAACCAGCGTAATCAGTGTATACTA 59.681 38.462 4.17 0.00 34.74 1.82
2560 2836 5.126545 TGAACCAGCGTAATCAGTGTATACT 59.873 40.000 4.17 0.00 37.75 2.12
2561 2837 5.345702 TGAACCAGCGTAATCAGTGTATAC 58.654 41.667 0.00 0.00 0.00 1.47
2565 2841 2.831685 TGAACCAGCGTAATCAGTGT 57.168 45.000 0.00 0.00 0.00 3.55
2568 2844 5.121611 TGTTGTAATGAACCAGCGTAATCAG 59.878 40.000 0.00 0.00 0.00 2.90
2576 2852 4.702131 AGAAGGATGTTGTAATGAACCAGC 59.298 41.667 0.00 0.00 0.00 4.85
2586 2862 7.103641 GTCCTAACATTCAGAAGGATGTTGTA 58.896 38.462 11.41 0.00 40.17 2.41
2621 2897 4.030913 TGCTAATGACCTAGCTACTTGGT 58.969 43.478 2.90 2.90 43.96 3.67
2630 2906 5.121811 ACTGAATTGCTGCTAATGACCTAG 58.878 41.667 0.00 0.00 0.00 3.02
2633 2909 3.065925 GGACTGAATTGCTGCTAATGACC 59.934 47.826 0.00 0.00 0.00 4.02
2641 2917 2.042831 AGCGGGACTGAATTGCTGC 61.043 57.895 0.00 0.00 39.42 5.25
2657 2933 1.081840 GTTGGCGAAGTTGAGCAGC 60.082 57.895 0.00 0.00 34.54 5.25
2666 2942 0.307760 GTGTCACCAAGTTGGCGAAG 59.692 55.000 22.25 9.59 42.67 3.79
2713 2989 0.693622 TCCTATCGCCCCACAAAACA 59.306 50.000 0.00 0.00 0.00 2.83
2722 2998 1.883926 GAGACTTCTCTCCTATCGCCC 59.116 57.143 0.00 0.00 37.56 6.13
2734 3010 3.474798 TCATGTGGTAGGGAGACTTCT 57.525 47.619 0.00 0.00 0.00 2.85
2787 3064 5.240183 ACAAATGACATGAACTCAAGGACAG 59.760 40.000 0.00 0.00 0.00 3.51
2810 3087 5.899120 TCAGGAGTTAGACTGTGATGTAC 57.101 43.478 0.00 0.00 36.17 2.90
2820 3097 4.680567 GTGAAGTTCGTTCAGGAGTTAGAC 59.319 45.833 0.00 0.00 46.18 2.59
2824 3101 2.484947 GGGTGAAGTTCGTTCAGGAGTT 60.485 50.000 0.00 0.00 46.18 3.01
2825 3102 1.070289 GGGTGAAGTTCGTTCAGGAGT 59.930 52.381 0.00 0.00 46.18 3.85
2880 3157 8.798402 AGATACTGATATTACTGACTAGTTGCC 58.202 37.037 0.00 0.00 38.36 4.52
2897 3174 5.814764 ACGAGTAAACGACAGATACTGAT 57.185 39.130 5.76 0.00 34.67 2.90
2920 3197 2.495270 TGGCAACAGCTGAAGTGAAAAA 59.505 40.909 23.35 0.00 46.17 1.94
2921 3198 2.098614 TGGCAACAGCTGAAGTGAAAA 58.901 42.857 23.35 2.15 46.17 2.29
2922 3199 1.761449 TGGCAACAGCTGAAGTGAAA 58.239 45.000 23.35 4.50 46.17 2.69
2965 3242 5.734855 AAAGGTGGATGAATAATCGTTCG 57.265 39.130 0.00 0.00 35.99 3.95
2973 3250 8.713971 TGCTCTCTTTATAAAGGTGGATGAATA 58.286 33.333 22.11 1.47 36.67 1.75
3010 3287 2.241176 TGGACACCAACTGAAGAAGGTT 59.759 45.455 0.00 0.00 30.44 3.50
3027 3304 4.742438 TTTACTTGCGAGACAAATGGAC 57.258 40.909 8.31 0.00 37.96 4.02
3039 3316 7.823149 AAGTTACAGGTACTATTTACTTGCG 57.177 36.000 0.00 0.00 36.02 4.85
3049 3326 4.949856 CGAGGGGTTAAGTTACAGGTACTA 59.050 45.833 0.00 0.00 36.02 1.82
3085 3362 5.934043 GCAAAAAGGACCTTGCTATTTCAAT 59.066 36.000 7.72 0.00 43.68 2.57
3094 3371 2.549064 ATTGGCAAAAAGGACCTTGC 57.451 45.000 7.72 7.87 45.79 4.01
3112 3398 5.688807 CTTATGGAGGTGACAAGATGGAAT 58.311 41.667 0.00 0.00 0.00 3.01
3143 3429 7.193595 GGTTTTTATGAATATGGTGAACGGAG 58.806 38.462 0.00 0.00 0.00 4.63
3146 3432 7.095695 AGGGTTTTTATGAATATGGTGAACG 57.904 36.000 0.00 0.00 0.00 3.95
3175 3461 5.654603 ACAATGCTGACATGATGAACATT 57.345 34.783 0.00 0.69 37.07 2.71
3202 3488 4.953579 ACTGTAGAGAGAGGCTTTTAGAGG 59.046 45.833 0.00 0.00 0.00 3.69
3212 3498 6.183360 GGTTCCAGAATAACTGTAGAGAGAGG 60.183 46.154 0.00 0.00 44.40 3.69
3221 3507 5.630121 TGACATTGGTTCCAGAATAACTGT 58.370 37.500 0.00 0.00 44.40 3.55
3227 3513 3.698040 GCAGATGACATTGGTTCCAGAAT 59.302 43.478 0.00 0.00 0.00 2.40
3232 3518 3.065925 GCTTAGCAGATGACATTGGTTCC 59.934 47.826 0.00 0.00 0.00 3.62
3255 3541 4.346129 CAATTGCGGAAAAGTAGCAGATC 58.654 43.478 0.00 0.00 42.19 2.75
3260 3546 2.488153 AGACCAATTGCGGAAAAGTAGC 59.512 45.455 0.00 0.00 0.00 3.58
3278 3564 6.031751 AGTAGTCACAGAAATCAAGGAGAC 57.968 41.667 0.00 0.00 0.00 3.36
3300 3586 8.839310 AGCTACAGAGTATTGGCAATATAAAG 57.161 34.615 21.82 14.70 0.00 1.85
3334 3620 1.160137 GCCTTGCCCTCGCATAATAG 58.840 55.000 0.00 0.00 46.67 1.73
3348 3634 4.227864 AGGGAATTTCTAGACAGCCTTG 57.772 45.455 0.00 0.00 0.00 3.61
3423 3709 4.271291 GTCCTCTTCGGAAAATGCAGATAC 59.729 45.833 0.00 0.00 45.32 2.24
3437 3723 3.032017 ACATCAACAGTGTCCTCTTCG 57.968 47.619 0.00 0.00 0.00 3.79
3448 3734 3.091545 AGCCCCAACATAACATCAACAG 58.908 45.455 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.