Multiple sequence alignment - TraesCS6A01G310300

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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 TraesCS6A01G310300 chr6A 100.000 3134 0 0 1 3134 546595236 546598369 0.000000e+00 5788.0
1 TraesCS6A01G310300 chr6D 89.168 2391 122 41 1 2346 400647261 400649559 0.000000e+00 2854.0
2 TraesCS6A01G310300 chr6D 82.679 433 39 16 2632 3053 400649688 400650095 4.970000e-93 351.0
3 TraesCS6A01G310300 chr6D 76.991 113 24 2 2968 3079 445795263 445795374 2.610000e-06 63.9
4 TraesCS6A01G310300 chr6B 89.471 2270 133 52 124 2355 599684666 599686867 0.000000e+00 2771.0
5 TraesCS6A01G310300 chr6B 86.571 350 38 5 2637 2977 599687055 599687404 8.200000e-101 377.0
6 TraesCS6A01G310300 chr6B 89.720 107 10 1 2353 2459 599686946 599687051 5.450000e-28 135.0
7 TraesCS6A01G310300 chr7D 79.594 887 147 20 1136 2017 153773822 153772965 3.460000e-169 604.0
8 TraesCS6A01G310300 chr7D 90.395 177 15 2 2457 2632 29807469 29807294 6.760000e-57 231.0
9 TraesCS6A01G310300 chr7D 90.116 172 15 2 2461 2631 152309564 152309734 4.070000e-54 222.0
10 TraesCS6A01G310300 chr7A 79.392 888 144 20 1136 2017 155646519 155645665 9.680000e-165 590.0
11 TraesCS6A01G310300 chr7B 79.213 890 142 24 1136 2017 115560973 115560119 2.100000e-161 579.0
12 TraesCS6A01G310300 chr7B 88.889 171 15 4 2464 2632 48884103 48883935 1.140000e-49 207.0
13 TraesCS6A01G310300 chr7B 95.455 44 2 0 1826 1869 619072056 619072099 1.560000e-08 71.3
14 TraesCS6A01G310300 chr3A 90.395 177 15 2 2458 2633 573854203 573854028 6.760000e-57 231.0
15 TraesCS6A01G310300 chr3A 89.944 179 16 2 2455 2632 575880764 575880941 2.430000e-56 230.0
16 TraesCS6A01G310300 chr1D 90.286 175 15 2 2461 2634 200883188 200883361 8.740000e-56 228.0
17 TraesCS6A01G310300 chr1A 89.714 175 16 2 2459 2632 574299793 574299620 4.070000e-54 222.0
18 TraesCS6A01G310300 chr4D 90.000 170 14 3 2464 2632 503141514 503141347 1.890000e-52 217.0
19 TraesCS6A01G310300 chr5A 88.304 171 17 3 2464 2632 626366286 626366117 5.300000e-48 202.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G310300 chr6A 546595236 546598369 3133 False 5788.000000 5788 100.000000 1 3134 1 chr6A.!!$F1 3133
1 TraesCS6A01G310300 chr6D 400647261 400650095 2834 False 1602.500000 2854 85.923500 1 3053 2 chr6D.!!$F2 3052
2 TraesCS6A01G310300 chr6B 599684666 599687404 2738 False 1094.333333 2771 88.587333 124 2977 3 chr6B.!!$F1 2853
3 TraesCS6A01G310300 chr7D 153772965 153773822 857 True 604.000000 604 79.594000 1136 2017 1 chr7D.!!$R2 881
4 TraesCS6A01G310300 chr7A 155645665 155646519 854 True 590.000000 590 79.392000 1136 2017 1 chr7A.!!$R1 881
5 TraesCS6A01G310300 chr7B 115560119 115560973 854 True 579.000000 579 79.213000 1136 2017 1 chr7B.!!$R2 881

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
97 98 0.036306 ACTTTCGGCCGAATGAAGGT 59.964 50.0 42.95 30.21 34.6 3.50 F
1029 1082 0.036294 CGGGTTCTCCTTCCCTTGTC 60.036 60.0 0.00 0.00 41.4 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1467 1526 1.606885 CGCCGGGGAAGTAGGTGTAA 61.607 60.0 14.46 0.0 0.0 2.41 R
2420 2580 0.103208 CTGATACGGCACCCAGAGTC 59.897 60.0 0.00 0.0 0.0 3.36 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
34 35 3.591196 TGCTTTGGATATTTGTGTGCC 57.409 42.857 0.00 0.00 0.00 5.01
41 42 1.319614 ATATTTGTGTGCCGCCCACC 61.320 55.000 3.38 0.00 44.01 4.61
69 70 5.831702 AACGACCTTCTAGATACGTCATT 57.168 39.130 0.00 3.34 33.59 2.57
86 87 2.618241 TCATTATCATGGCACTTTCGGC 59.382 45.455 0.00 0.00 0.00 5.54
92 93 2.485122 GGCACTTTCGGCCGAATG 59.515 61.111 37.91 37.91 42.39 2.67
97 98 0.036306 ACTTTCGGCCGAATGAAGGT 59.964 50.000 42.95 30.21 34.60 3.50
98 99 0.447801 CTTTCGGCCGAATGAAGGTG 59.552 55.000 37.32 20.14 33.79 4.00
102 103 1.794222 GGCCGAATGAAGGTGTTCG 59.206 57.895 0.00 0.91 44.89 3.95
109 110 4.653806 GAATGAAGGTGTTCGACTTGAG 57.346 45.455 0.00 0.00 35.17 3.02
111 112 1.070134 TGAAGGTGTTCGACTTGAGGG 59.930 52.381 0.00 0.00 35.17 4.30
112 113 0.396811 AAGGTGTTCGACTTGAGGGG 59.603 55.000 0.00 0.00 0.00 4.79
114 115 1.671379 GTGTTCGACTTGAGGGGCC 60.671 63.158 0.00 0.00 0.00 5.80
115 116 1.841556 TGTTCGACTTGAGGGGCCT 60.842 57.895 0.84 0.00 0.00 5.19
116 117 1.079057 GTTCGACTTGAGGGGCCTC 60.079 63.158 0.84 0.00 43.01 4.70
149 150 1.393539 CGCAGAAAAATCCACGACGAT 59.606 47.619 0.00 0.00 0.00 3.73
234 235 9.810545 ATCTTAATCAGTCTGTTACTAGAAAGC 57.189 33.333 0.00 0.00 35.76 3.51
263 264 8.490355 CAATAATTCAGTCTTTTTGAAAGTGCC 58.510 33.333 0.87 0.00 38.01 5.01
264 265 5.859205 ATTCAGTCTTTTTGAAAGTGCCT 57.141 34.783 0.87 0.00 38.01 4.75
265 266 4.900635 TCAGTCTTTTTGAAAGTGCCTC 57.099 40.909 0.87 0.00 0.00 4.70
309 310 4.888326 ATAAAGCACCCATCAGCAAAAA 57.112 36.364 0.00 0.00 0.00 1.94
361 364 1.983224 CGTTCCCACTCACCCATCT 59.017 57.895 0.00 0.00 0.00 2.90
362 365 0.108138 CGTTCCCACTCACCCATCTC 60.108 60.000 0.00 0.00 0.00 2.75
363 366 1.280457 GTTCCCACTCACCCATCTCT 58.720 55.000 0.00 0.00 0.00 3.10
364 367 2.467880 GTTCCCACTCACCCATCTCTA 58.532 52.381 0.00 0.00 0.00 2.43
365 368 3.041946 GTTCCCACTCACCCATCTCTAT 58.958 50.000 0.00 0.00 0.00 1.98
366 369 2.964209 TCCCACTCACCCATCTCTATC 58.036 52.381 0.00 0.00 0.00 2.08
367 370 2.520120 TCCCACTCACCCATCTCTATCT 59.480 50.000 0.00 0.00 0.00 1.98
369 372 3.713764 CCCACTCACCCATCTCTATCTTT 59.286 47.826 0.00 0.00 0.00 2.52
370 373 4.202305 CCCACTCACCCATCTCTATCTTTC 60.202 50.000 0.00 0.00 0.00 2.62
371 374 4.406972 CCACTCACCCATCTCTATCTTTCA 59.593 45.833 0.00 0.00 0.00 2.69
372 375 5.104776 CCACTCACCCATCTCTATCTTTCAA 60.105 44.000 0.00 0.00 0.00 2.69
373 376 6.047870 CACTCACCCATCTCTATCTTTCAAG 58.952 44.000 0.00 0.00 0.00 3.02
397 400 2.355363 CCGTCGTCCGCTTTGTGA 60.355 61.111 0.00 0.00 34.38 3.58
410 416 3.456280 GCTTTGTGATCTAGAGCAGGAG 58.544 50.000 11.77 10.42 33.68 3.69
415 421 1.292242 TGATCTAGAGCAGGAGGGGTT 59.708 52.381 6.59 0.00 0.00 4.11
459 465 2.100916 GTGGAACTAGAAGGCATCGCTA 59.899 50.000 0.00 0.00 0.00 4.26
532 538 2.200170 CTGGCCGGTGCAAAGTTAGC 62.200 60.000 2.29 0.00 40.13 3.09
621 627 1.456705 ACCTCAGCCTCGGATCCTC 60.457 63.158 10.75 0.00 0.00 3.71
653 672 3.159472 TGATGGAAGCTGCTTCAATTGT 58.841 40.909 35.27 16.35 41.77 2.71
711 735 2.597510 GCCGTTGCTTCCAACCCT 60.598 61.111 1.43 0.00 46.76 4.34
729 753 1.134580 CCTGAAGCCGTCATCTGTCAT 60.135 52.381 0.00 0.00 35.07 3.06
784 808 2.722094 GAACACAAGGCCACATATCCA 58.278 47.619 5.01 0.00 0.00 3.41
785 809 3.290710 GAACACAAGGCCACATATCCAT 58.709 45.455 5.01 0.00 0.00 3.41
786 810 2.936202 ACACAAGGCCACATATCCATC 58.064 47.619 5.01 0.00 0.00 3.51
793 817 3.021695 GGCCACATATCCATCATCCATG 58.978 50.000 0.00 0.00 0.00 3.66
805 829 0.819582 CATCCATGCTTGACCCAACC 59.180 55.000 0.22 0.00 0.00 3.77
892 928 2.202987 CTCTCGGCCATGCTGACC 60.203 66.667 2.24 0.00 39.19 4.02
929 977 0.733150 CCCAGCCTTAAAGCTTACGC 59.267 55.000 0.00 0.00 42.61 4.42
977 1030 1.066757 TCGTCTGCTCATCTCATCTGC 59.933 52.381 0.00 0.00 0.00 4.26
994 1047 3.579709 TCTGCAGAAAGACTTCATCGAC 58.420 45.455 15.67 0.00 33.64 4.20
1029 1082 0.036294 CGGGTTCTCCTTCCCTTGTC 60.036 60.000 0.00 0.00 41.40 3.18
1344 1397 4.368543 AACGCGACGGGGTTCCTC 62.369 66.667 15.93 0.00 45.07 3.71
2007 2066 2.742372 CCCGACTTCAAGGGCGTG 60.742 66.667 0.00 0.00 41.34 5.34
2143 2214 0.317479 GTCACTGTAGAACGCCTGGT 59.683 55.000 0.00 0.00 0.00 4.00
2144 2215 0.601558 TCACTGTAGAACGCCTGGTC 59.398 55.000 0.00 0.00 0.00 4.02
2145 2216 0.389948 CACTGTAGAACGCCTGGTCC 60.390 60.000 0.00 0.00 0.00 4.46
2146 2217 0.542232 ACTGTAGAACGCCTGGTCCT 60.542 55.000 0.00 0.00 0.00 3.85
2147 2218 0.608640 CTGTAGAACGCCTGGTCCTT 59.391 55.000 0.00 0.00 0.00 3.36
2148 2219 1.002087 CTGTAGAACGCCTGGTCCTTT 59.998 52.381 0.00 0.00 0.00 3.11
2149 2220 1.418637 TGTAGAACGCCTGGTCCTTTT 59.581 47.619 0.00 0.00 0.00 2.27
2150 2221 1.804748 GTAGAACGCCTGGTCCTTTTG 59.195 52.381 0.00 0.00 0.00 2.44
2151 2222 1.172812 AGAACGCCTGGTCCTTTTGC 61.173 55.000 0.00 0.00 0.00 3.68
2152 2223 2.142357 GAACGCCTGGTCCTTTTGCC 62.142 60.000 0.00 0.00 0.00 4.52
2153 2224 3.373565 CGCCTGGTCCTTTTGCCC 61.374 66.667 0.00 0.00 0.00 5.36
2154 2225 3.373565 GCCTGGTCCTTTTGCCCG 61.374 66.667 0.00 0.00 0.00 6.13
2207 2280 3.889227 GCTGTGCCACGATTGCTA 58.111 55.556 0.00 0.00 0.00 3.49
2208 2281 1.717937 GCTGTGCCACGATTGCTAG 59.282 57.895 0.00 0.00 0.00 3.42
2225 2298 3.056107 TGCTAGTTGCTAGTTCGATTGGT 60.056 43.478 0.00 0.00 43.37 3.67
2274 2353 7.833285 TCTGTACATACTACTGCCATTGATA 57.167 36.000 0.00 0.00 0.00 2.15
2351 2430 2.301870 AGTGTCAAATTCCCTAGCGTGA 59.698 45.455 0.00 0.00 0.00 4.35
2367 2527 3.118775 AGCGTGAGAATGGCATACACTAA 60.119 43.478 21.05 6.54 0.00 2.24
2392 2552 0.035739 TAACCTCTGTCCGGCCAAAC 59.964 55.000 2.24 0.00 0.00 2.93
2412 2572 0.593128 GGTAGTTGCTGCTGTTGGTG 59.407 55.000 0.00 0.00 0.00 4.17
2413 2573 1.593196 GTAGTTGCTGCTGTTGGTGA 58.407 50.000 0.00 0.00 0.00 4.02
2417 2577 3.368571 GCTGCTGTTGGTGAGGGC 61.369 66.667 0.00 0.00 0.00 5.19
2420 2580 2.674380 GCTGTTGGTGAGGGCTGG 60.674 66.667 0.00 0.00 0.00 4.85
2421 2581 3.160585 CTGTTGGTGAGGGCTGGA 58.839 61.111 0.00 0.00 0.00 3.86
2459 2619 1.457346 GCTATCAGCAACAGCCACTT 58.543 50.000 0.00 0.00 41.89 3.16
2462 2622 3.679917 GCTATCAGCAACAGCCACTTAGA 60.680 47.826 0.00 0.00 41.89 2.10
2463 2623 3.641434 ATCAGCAACAGCCACTTAGAT 57.359 42.857 0.00 0.00 0.00 1.98
2464 2624 2.703416 TCAGCAACAGCCACTTAGATG 58.297 47.619 0.00 0.00 0.00 2.90
2465 2625 1.741706 CAGCAACAGCCACTTAGATGG 59.258 52.381 0.00 0.00 43.26 3.51
2466 2626 1.352352 AGCAACAGCCACTTAGATGGT 59.648 47.619 0.00 0.00 42.28 3.55
2467 2627 1.470098 GCAACAGCCACTTAGATGGTG 59.530 52.381 0.00 0.00 42.28 4.17
2468 2628 2.783135 CAACAGCCACTTAGATGGTGT 58.217 47.619 5.19 5.19 42.28 4.16
2469 2629 3.149196 CAACAGCCACTTAGATGGTGTT 58.851 45.455 13.93 13.93 41.03 3.32
2470 2630 3.508845 ACAGCCACTTAGATGGTGTTT 57.491 42.857 5.19 0.00 42.28 2.83
2471 2631 3.149196 ACAGCCACTTAGATGGTGTTTG 58.851 45.455 5.19 0.00 42.28 2.93
2472 2632 2.489329 CAGCCACTTAGATGGTGTTTGG 59.511 50.000 0.00 0.00 42.28 3.28
2473 2633 2.108250 AGCCACTTAGATGGTGTTTGGT 59.892 45.455 0.00 0.00 42.28 3.67
2474 2634 2.890945 GCCACTTAGATGGTGTTTGGTT 59.109 45.455 0.00 0.00 42.28 3.67
2475 2635 3.320826 GCCACTTAGATGGTGTTTGGTTT 59.679 43.478 0.00 0.00 42.28 3.27
2476 2636 4.202212 GCCACTTAGATGGTGTTTGGTTTT 60.202 41.667 0.00 0.00 42.28 2.43
2477 2637 5.528870 CCACTTAGATGGTGTTTGGTTTTC 58.471 41.667 0.00 0.00 34.77 2.29
2478 2638 5.508994 CCACTTAGATGGTGTTTGGTTTTCC 60.509 44.000 0.00 0.00 36.31 3.13
2479 2639 7.862622 CCACTTAGATGGTGTTTGGTTTTCCA 61.863 42.308 0.00 0.00 40.63 3.53
2480 2640 9.551883 CCACTTAGATGGTGTTTGGTTTTCCAG 62.552 44.444 0.00 0.00 42.06 3.86
2506 2666 9.452287 GTCTTAGGACTTTTTCTAGTCTCTAGA 57.548 37.037 0.00 2.81 43.26 2.43
2507 2667 9.452287 TCTTAGGACTTTTTCTAGTCTCTAGAC 57.548 37.037 6.06 1.72 43.26 2.59
2537 2697 6.721704 AAAAAGATTCTCAAGAAGGTGCTT 57.278 33.333 0.00 0.00 37.48 3.91
2538 2698 5.956068 AAAGATTCTCAAGAAGGTGCTTC 57.044 39.130 0.00 0.00 40.45 3.86
2552 2712 7.624706 GAAGGTGCTTCTAAAAACTTTTAGC 57.375 36.000 14.49 8.52 45.71 3.09
2553 2713 6.709018 AGGTGCTTCTAAAAACTTTTAGCA 57.291 33.333 14.49 10.57 45.71 3.49
2554 2714 7.107639 AGGTGCTTCTAAAAACTTTTAGCAA 57.892 32.000 14.49 10.01 45.71 3.91
2555 2715 7.552459 AGGTGCTTCTAAAAACTTTTAGCAAA 58.448 30.769 14.49 6.53 45.71 3.68
2556 2716 8.038351 AGGTGCTTCTAAAAACTTTTAGCAAAA 58.962 29.630 14.49 5.99 45.71 2.44
2557 2717 8.661257 GGTGCTTCTAAAAACTTTTAGCAAAAA 58.339 29.630 14.49 5.72 45.71 1.94
2574 2734 1.788229 AAAAGTCCCACCCTGTTTGG 58.212 50.000 0.00 0.00 0.00 3.28
2575 2735 0.634465 AAAGTCCCACCCTGTTTGGT 59.366 50.000 0.00 0.00 39.96 3.67
2576 2736 0.634465 AAGTCCCACCCTGTTTGGTT 59.366 50.000 0.00 0.00 36.12 3.67
2577 2737 0.634465 AGTCCCACCCTGTTTGGTTT 59.366 50.000 0.00 0.00 36.12 3.27
2578 2738 0.750249 GTCCCACCCTGTTTGGTTTG 59.250 55.000 0.00 0.00 36.12 2.93
2579 2739 1.045911 TCCCACCCTGTTTGGTTTGC 61.046 55.000 0.00 0.00 36.12 3.68
2580 2740 1.048160 CCCACCCTGTTTGGTTTGCT 61.048 55.000 0.00 0.00 36.12 3.91
2581 2741 1.698506 CCACCCTGTTTGGTTTGCTA 58.301 50.000 0.00 0.00 36.12 3.49
2582 2742 1.613437 CCACCCTGTTTGGTTTGCTAG 59.387 52.381 0.00 0.00 36.12 3.42
2583 2743 1.613437 CACCCTGTTTGGTTTGCTAGG 59.387 52.381 0.00 0.00 36.12 3.02
2584 2744 1.256812 CCCTGTTTGGTTTGCTAGGG 58.743 55.000 0.00 0.00 38.96 3.53
2585 2745 1.203001 CCCTGTTTGGTTTGCTAGGGA 60.203 52.381 0.00 0.00 46.19 4.20
2586 2746 1.886542 CCTGTTTGGTTTGCTAGGGAC 59.113 52.381 0.00 0.00 0.00 4.46
2587 2747 2.489073 CCTGTTTGGTTTGCTAGGGACT 60.489 50.000 0.00 0.00 46.37 3.85
2588 2748 3.222603 CTGTTTGGTTTGCTAGGGACTT 58.777 45.455 0.00 0.00 41.75 3.01
2589 2749 3.636764 CTGTTTGGTTTGCTAGGGACTTT 59.363 43.478 0.00 0.00 41.75 2.66
2590 2750 4.027437 TGTTTGGTTTGCTAGGGACTTTT 58.973 39.130 0.00 0.00 41.75 2.27
2591 2751 4.468153 TGTTTGGTTTGCTAGGGACTTTTT 59.532 37.500 0.00 0.00 41.75 1.94
2628 2788 4.983671 AAAAGTCTCTGGAACCAAACAC 57.016 40.909 0.00 0.00 0.00 3.32
2629 2789 2.640316 AGTCTCTGGAACCAAACACC 57.360 50.000 0.00 0.00 0.00 4.16
2630 2790 1.143073 AGTCTCTGGAACCAAACACCC 59.857 52.381 0.00 0.00 0.00 4.61
2631 2791 0.476771 TCTCTGGAACCAAACACCCC 59.523 55.000 0.00 0.00 0.00 4.95
2632 2792 0.478507 CTCTGGAACCAAACACCCCT 59.521 55.000 0.00 0.00 0.00 4.79
2633 2793 0.476771 TCTGGAACCAAACACCCCTC 59.523 55.000 0.00 0.00 0.00 4.30
2634 2794 0.889186 CTGGAACCAAACACCCCTCG 60.889 60.000 0.00 0.00 0.00 4.63
2635 2795 1.602605 GGAACCAAACACCCCTCGG 60.603 63.158 0.00 0.00 0.00 4.63
2658 2818 4.778415 CGACGGGCGTCTGTCCTG 62.778 72.222 22.72 6.45 44.37 3.86
2660 2820 3.916392 GACGGGCGTCTGTCCTGTG 62.916 68.421 18.41 0.00 42.93 3.66
2683 2843 4.434520 CGGGAGAGAGAATTTTGAGGTAC 58.565 47.826 0.00 0.00 0.00 3.34
2691 2851 0.034477 ATTTTGAGGTACTGCCGGGG 60.034 55.000 2.18 0.00 41.55 5.73
2692 2852 2.132089 TTTTGAGGTACTGCCGGGGG 62.132 60.000 2.18 0.00 41.55 5.40
2766 2930 4.116961 TGCACGCATTAGTATAACCTCAC 58.883 43.478 0.00 0.00 0.00 3.51
2777 2941 5.721232 AGTATAACCTCACGACTTCCTTTG 58.279 41.667 0.00 0.00 0.00 2.77
2798 2962 3.320541 TGGCAATTCCAAAGTACAGTTGG 59.679 43.478 17.99 17.99 45.89 3.77
2819 2983 2.104967 CGTCCACCAGAATACCTACCA 58.895 52.381 0.00 0.00 0.00 3.25
2829 2997 1.492764 ATACCTACCAACCCAGACCG 58.507 55.000 0.00 0.00 0.00 4.79
2835 3003 1.302511 CCAACCCAGACCGGACAAG 60.303 63.158 9.46 0.00 36.56 3.16
2839 3007 1.746615 CCCAGACCGGACAAGCATG 60.747 63.158 9.46 0.00 36.56 4.06
2842 3010 0.798776 CAGACCGGACAAGCATGAAC 59.201 55.000 9.46 0.00 0.00 3.18
2865 3038 5.998363 ACGAGAAAAATAGGAAAAGTCTGCT 59.002 36.000 0.00 0.00 0.00 4.24
2870 3043 4.495690 AATAGGAAAAGTCTGCTCTCCC 57.504 45.455 0.00 0.00 0.00 4.30
2877 3050 2.486472 AGTCTGCTCTCCCAATGTTG 57.514 50.000 0.00 0.00 0.00 3.33
2888 3061 2.134789 CCAATGTTGGCTTCCTAGCT 57.865 50.000 0.00 0.00 46.90 3.32
2891 3064 3.367703 CCAATGTTGGCTTCCTAGCTTTG 60.368 47.826 0.00 0.00 46.90 2.77
2926 3099 0.179124 CGTGTTGGTTTGGTTGGGTG 60.179 55.000 0.00 0.00 0.00 4.61
2939 3112 0.178992 TTGGGTGGTTGAGCAAGGAG 60.179 55.000 0.00 0.00 0.00 3.69
2958 3131 6.683974 AGGAGTGCACAATGAATATAACAC 57.316 37.500 21.04 0.00 0.00 3.32
2981 3156 8.390354 ACACGAAAATATATGTCACAGTGAATG 58.610 33.333 4.32 0.00 0.00 2.67
2995 3170 6.073058 TCACAGTGAATGTAGTGAAGCAAATC 60.073 38.462 0.00 0.00 41.41 2.17
2998 3173 5.413833 AGTGAATGTAGTGAAGCAAATCTGG 59.586 40.000 0.00 0.00 0.00 3.86
3015 3190 7.282224 GCAAATCTGGTGTTATAGATGTTGGTA 59.718 37.037 0.00 0.00 34.09 3.25
3053 3229 8.514594 TGACTTTATCAAGCTTGATTAGGTTTG 58.485 33.333 39.03 24.74 45.13 2.93
3054 3230 8.635765 ACTTTATCAAGCTTGATTAGGTTTGA 57.364 30.769 39.03 20.74 45.13 2.69
3055 3231 8.734386 ACTTTATCAAGCTTGATTAGGTTTGAG 58.266 33.333 39.03 26.08 45.13 3.02
3056 3232 8.635765 TTTATCAAGCTTGATTAGGTTTGAGT 57.364 30.769 39.03 18.99 45.13 3.41
3057 3233 8.635765 TTATCAAGCTTGATTAGGTTTGAGTT 57.364 30.769 39.03 18.81 45.13 3.01
3058 3234 9.733556 TTATCAAGCTTGATTAGGTTTGAGTTA 57.266 29.630 39.03 18.77 45.13 2.24
3059 3235 7.672983 TCAAGCTTGATTAGGTTTGAGTTAG 57.327 36.000 25.16 0.00 42.49 2.34
3060 3236 6.655003 TCAAGCTTGATTAGGTTTGAGTTAGG 59.345 38.462 25.16 0.00 42.49 2.69
3061 3237 6.374417 AGCTTGATTAGGTTTGAGTTAGGA 57.626 37.500 0.00 0.00 0.00 2.94
3062 3238 6.174049 AGCTTGATTAGGTTTGAGTTAGGAC 58.826 40.000 0.00 0.00 0.00 3.85
3063 3239 5.938125 GCTTGATTAGGTTTGAGTTAGGACA 59.062 40.000 0.00 0.00 0.00 4.02
3064 3240 6.430000 GCTTGATTAGGTTTGAGTTAGGACAA 59.570 38.462 0.00 0.00 0.00 3.18
3065 3241 7.121315 GCTTGATTAGGTTTGAGTTAGGACAAT 59.879 37.037 0.00 0.00 0.00 2.71
3066 3242 9.667107 CTTGATTAGGTTTGAGTTAGGACAATA 57.333 33.333 0.00 0.00 0.00 1.90
3073 3249 9.668497 AGGTTTGAGTTAGGACAATATTAGAAC 57.332 33.333 0.00 0.00 0.00 3.01
3074 3250 9.668497 GGTTTGAGTTAGGACAATATTAGAACT 57.332 33.333 0.00 0.00 0.00 3.01
3084 3260 7.550906 AGGACAATATTAGAACTTCAAGTCTGC 59.449 37.037 0.00 0.00 0.00 4.26
3085 3261 7.334421 GGACAATATTAGAACTTCAAGTCTGCA 59.666 37.037 0.00 0.00 0.00 4.41
3086 3262 8.621532 ACAATATTAGAACTTCAAGTCTGCAA 57.378 30.769 0.00 0.00 0.00 4.08
3087 3263 9.236006 ACAATATTAGAACTTCAAGTCTGCAAT 57.764 29.630 0.00 0.00 0.00 3.56
3091 3267 8.854614 ATTAGAACTTCAAGTCTGCAATTACT 57.145 30.769 0.00 0.00 0.00 2.24
3092 3268 8.677148 TTAGAACTTCAAGTCTGCAATTACTT 57.323 30.769 0.00 3.56 36.38 2.24
3093 3269 7.573968 AGAACTTCAAGTCTGCAATTACTTT 57.426 32.000 6.13 0.00 33.72 2.66
3094 3270 7.420800 AGAACTTCAAGTCTGCAATTACTTTG 58.579 34.615 6.13 3.88 33.72 2.77
3095 3271 6.076981 ACTTCAAGTCTGCAATTACTTTGG 57.923 37.500 6.13 3.56 33.72 3.28
3096 3272 5.827797 ACTTCAAGTCTGCAATTACTTTGGA 59.172 36.000 6.13 0.92 33.72 3.53
3097 3273 6.321181 ACTTCAAGTCTGCAATTACTTTGGAA 59.679 34.615 6.13 7.17 35.02 3.53
3098 3274 6.899393 TCAAGTCTGCAATTACTTTGGAAT 57.101 33.333 6.13 0.00 35.02 3.01
3099 3275 6.680810 TCAAGTCTGCAATTACTTTGGAATG 58.319 36.000 6.13 0.00 35.02 2.67
3100 3276 5.649782 AGTCTGCAATTACTTTGGAATGG 57.350 39.130 0.00 0.00 35.02 3.16
3101 3277 5.324409 AGTCTGCAATTACTTTGGAATGGA 58.676 37.500 0.00 0.00 35.02 3.41
3102 3278 5.416952 AGTCTGCAATTACTTTGGAATGGAG 59.583 40.000 0.00 0.00 35.02 3.86
3103 3279 4.706476 TCTGCAATTACTTTGGAATGGAGG 59.294 41.667 0.00 0.00 35.02 4.30
3104 3280 3.768757 TGCAATTACTTTGGAATGGAGGG 59.231 43.478 0.00 0.00 35.75 4.30
3105 3281 4.023291 GCAATTACTTTGGAATGGAGGGA 58.977 43.478 0.00 0.00 35.75 4.20
3106 3282 4.098501 GCAATTACTTTGGAATGGAGGGAG 59.901 45.833 0.00 0.00 35.75 4.30
3107 3283 5.264395 CAATTACTTTGGAATGGAGGGAGT 58.736 41.667 0.00 0.00 0.00 3.85
3108 3284 6.423182 CAATTACTTTGGAATGGAGGGAGTA 58.577 40.000 0.00 0.00 0.00 2.59
3109 3285 5.693769 TTACTTTGGAATGGAGGGAGTAG 57.306 43.478 0.00 0.00 0.00 2.57
3110 3286 2.239907 ACTTTGGAATGGAGGGAGTAGC 59.760 50.000 0.00 0.00 0.00 3.58
3111 3287 1.213296 TTGGAATGGAGGGAGTAGCC 58.787 55.000 0.00 0.00 0.00 3.93
3123 3299 2.760374 GGAGTAGCCCTGAATGATTCG 58.240 52.381 0.18 0.00 0.00 3.34
3124 3300 2.103263 GGAGTAGCCCTGAATGATTCGT 59.897 50.000 0.18 0.00 0.00 3.85
3125 3301 3.321111 GGAGTAGCCCTGAATGATTCGTA 59.679 47.826 0.18 0.00 0.00 3.43
3126 3302 4.021016 GGAGTAGCCCTGAATGATTCGTAT 60.021 45.833 0.18 0.00 0.00 3.06
3127 3303 5.140747 AGTAGCCCTGAATGATTCGTATC 57.859 43.478 0.18 0.00 0.00 2.24
3128 3304 4.588951 AGTAGCCCTGAATGATTCGTATCA 59.411 41.667 7.21 7.21 44.52 2.15
3129 3305 4.422073 AGCCCTGAATGATTCGTATCAA 57.578 40.909 8.88 0.00 43.67 2.57
3130 3306 4.978099 AGCCCTGAATGATTCGTATCAAT 58.022 39.130 8.88 0.09 43.67 2.57
3131 3307 5.380043 AGCCCTGAATGATTCGTATCAATT 58.620 37.500 8.88 4.49 43.67 2.32
3132 3308 6.533730 AGCCCTGAATGATTCGTATCAATTA 58.466 36.000 8.88 0.00 43.67 1.40
3133 3309 6.998074 AGCCCTGAATGATTCGTATCAATTAA 59.002 34.615 8.88 0.00 43.67 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.866910 GGCACACAAATATCCAAAGCATG 59.133 43.478 0.00 0.00 0.00 4.06
48 49 6.709397 TGATAATGACGTATCTAGAAGGTCGT 59.291 38.462 16.07 14.35 35.12 4.34
62 63 3.309682 CGAAAGTGCCATGATAATGACGT 59.690 43.478 0.00 0.00 0.00 4.34
63 64 3.303329 CCGAAAGTGCCATGATAATGACG 60.303 47.826 0.00 0.00 0.00 4.35
69 70 0.813610 CGGCCGAAAGTGCCATGATA 60.814 55.000 24.07 0.00 44.48 2.15
86 87 2.080286 AGTCGAACACCTTCATTCGG 57.920 50.000 6.54 0.00 46.01 4.30
92 93 1.608283 CCCCTCAAGTCGAACACCTTC 60.608 57.143 0.00 0.00 0.00 3.46
97 98 1.827399 GAGGCCCCTCAAGTCGAACA 61.827 60.000 9.42 0.00 42.31 3.18
98 99 1.079057 GAGGCCCCTCAAGTCGAAC 60.079 63.158 9.42 0.00 42.31 3.95
119 120 1.770294 TTTTTCTGCGTGAACCCCTT 58.230 45.000 0.00 0.00 33.88 3.95
120 121 1.886542 GATTTTTCTGCGTGAACCCCT 59.113 47.619 0.00 0.00 33.88 4.79
121 122 1.067846 GGATTTTTCTGCGTGAACCCC 60.068 52.381 0.00 0.00 33.88 4.95
122 123 1.611491 TGGATTTTTCTGCGTGAACCC 59.389 47.619 0.00 0.00 33.88 4.11
156 157 2.194271 GGTTCTGTCGTAGCAGCATAC 58.806 52.381 0.00 0.00 36.49 2.39
159 160 0.608130 ATGGTTCTGTCGTAGCAGCA 59.392 50.000 0.00 0.00 34.68 4.41
160 161 1.661112 GAATGGTTCTGTCGTAGCAGC 59.339 52.381 0.00 0.00 36.49 5.25
161 162 2.093973 AGGAATGGTTCTGTCGTAGCAG 60.094 50.000 0.00 0.00 37.81 4.24
162 163 1.899814 AGGAATGGTTCTGTCGTAGCA 59.100 47.619 0.00 0.00 0.00 3.49
163 164 2.674796 AGGAATGGTTCTGTCGTAGC 57.325 50.000 0.00 0.00 0.00 3.58
234 235 9.252962 ACTTTCAAAAAGACTGAATTATTGCAG 57.747 29.630 6.44 0.00 38.10 4.41
263 264 3.181509 GCATGACATGAGCAACTCTTGAG 60.182 47.826 19.76 0.00 37.70 3.02
264 265 2.745821 GCATGACATGAGCAACTCTTGA 59.254 45.455 19.76 0.00 37.70 3.02
265 266 2.747989 AGCATGACATGAGCAACTCTTG 59.252 45.455 19.76 8.47 40.17 3.02
361 364 5.404366 CGACGGTTGAAACTTGAAAGATAGA 59.596 40.000 0.00 0.00 0.00 1.98
362 365 5.176958 ACGACGGTTGAAACTTGAAAGATAG 59.823 40.000 1.53 0.00 0.00 2.08
363 366 5.051816 ACGACGGTTGAAACTTGAAAGATA 58.948 37.500 1.53 0.00 0.00 1.98
364 367 3.875134 ACGACGGTTGAAACTTGAAAGAT 59.125 39.130 1.53 0.00 0.00 2.40
365 368 3.264104 ACGACGGTTGAAACTTGAAAGA 58.736 40.909 1.53 0.00 0.00 2.52
366 369 3.545426 GGACGACGGTTGAAACTTGAAAG 60.545 47.826 1.53 0.00 0.00 2.62
367 370 2.352342 GGACGACGGTTGAAACTTGAAA 59.648 45.455 1.53 0.00 0.00 2.69
369 372 1.574134 GGACGACGGTTGAAACTTGA 58.426 50.000 1.53 0.00 0.00 3.02
370 373 0.231279 CGGACGACGGTTGAAACTTG 59.769 55.000 1.53 0.00 39.42 3.16
371 374 1.493134 GCGGACGACGGTTGAAACTT 61.493 55.000 1.53 0.00 44.51 2.66
372 375 1.952635 GCGGACGACGGTTGAAACT 60.953 57.895 1.53 0.00 44.51 2.66
373 376 2.547798 GCGGACGACGGTTGAAAC 59.452 61.111 1.53 0.00 44.51 2.78
397 400 1.694048 CCAACCCCTCCTGCTCTAGAT 60.694 57.143 0.00 0.00 0.00 1.98
415 421 1.051556 TAGGTGTGTGCAGGTGACCA 61.052 55.000 3.63 0.00 0.00 4.02
438 444 1.134670 AGCGATGCCTTCTAGTTCCAC 60.135 52.381 0.00 0.00 0.00 4.02
459 465 2.370349 ACTCGTCAATCAGAGATCGGT 58.630 47.619 0.00 0.00 37.87 4.69
621 627 2.149578 GCTTCCATCAGATTGATCCCG 58.850 52.381 0.00 0.00 34.28 5.14
653 672 2.231529 GAGCCTTGACTAGCTATCCGA 58.768 52.381 0.00 0.00 40.11 4.55
711 735 1.276138 ACATGACAGATGACGGCTTCA 59.724 47.619 6.95 0.00 39.11 3.02
738 762 2.280524 TTGCTGTCAACCGGTCGG 60.281 61.111 8.04 7.97 42.03 4.79
784 808 2.381911 GTTGGGTCAAGCATGGATGAT 58.618 47.619 0.00 0.00 0.00 2.45
785 809 1.616725 GGTTGGGTCAAGCATGGATGA 60.617 52.381 0.00 0.00 40.92 2.92
786 810 0.819582 GGTTGGGTCAAGCATGGATG 59.180 55.000 0.00 0.00 40.92 3.51
793 817 1.119684 AAGGTTTGGTTGGGTCAAGC 58.880 50.000 3.24 3.24 41.51 4.01
805 829 3.370672 GTGTGTGCTTTTCCAAAGGTTTG 59.629 43.478 0.00 0.00 37.90 2.93
977 1030 4.738124 TGCTAGTCGATGAAGTCTTTCTG 58.262 43.478 0.00 0.00 34.31 3.02
994 1047 1.592669 CCGACTCGCCCATTGCTAG 60.593 63.158 0.00 0.00 38.67 3.42
1006 1059 1.898885 GGGAAGGAGAACCCGACTC 59.101 63.158 0.00 0.00 40.87 3.36
1201 1254 2.187946 CAGGTAGCCCTTGAGCCG 59.812 66.667 0.00 0.00 39.89 5.52
1351 1404 2.268920 CATCTGGGACACGGTGGG 59.731 66.667 13.48 0.00 0.00 4.61
1452 1511 3.943691 TAAAGGTGCCGGCCGTGT 61.944 61.111 26.77 14.31 0.00 4.49
1467 1526 1.606885 CGCCGGGGAAGTAGGTGTAA 61.607 60.000 14.46 0.00 0.00 2.41
1993 2052 3.423154 CGCCACGCCCTTGAAGTC 61.423 66.667 0.00 0.00 0.00 3.01
2120 2179 1.000163 AGGCGTTCTACAGTGACAGTG 60.000 52.381 8.80 8.80 0.00 3.66
2172 2243 2.626780 CCTGCAGAGACGGACGTGA 61.627 63.158 17.39 0.00 0.00 4.35
2204 2277 3.522553 ACCAATCGAACTAGCAACTAGC 58.477 45.455 1.54 0.00 46.19 3.42
2205 2278 4.744570 TGACCAATCGAACTAGCAACTAG 58.255 43.478 0.00 0.08 39.72 2.57
2206 2279 4.794278 TGACCAATCGAACTAGCAACTA 57.206 40.909 0.00 0.00 0.00 2.24
2207 2280 3.678056 TGACCAATCGAACTAGCAACT 57.322 42.857 0.00 0.00 0.00 3.16
2208 2281 4.391830 TCAATGACCAATCGAACTAGCAAC 59.608 41.667 0.00 0.00 0.00 4.17
2339 2418 0.178068 GCCATTCTCACGCTAGGGAA 59.822 55.000 14.59 0.00 0.00 3.97
2351 2430 8.466798 GGTTACAAAATTAGTGTATGCCATTCT 58.533 33.333 13.05 0.00 31.72 2.40
2367 2527 2.433436 GCCGGACAGAGGTTACAAAAT 58.567 47.619 5.05 0.00 0.00 1.82
2392 2552 0.884704 ACCAACAGCAGCAACTACCG 60.885 55.000 0.00 0.00 0.00 4.02
2412 2572 2.284995 ACCCAGAGTCCAGCCCTC 60.285 66.667 0.00 0.00 0.00 4.30
2413 2573 2.608988 CACCCAGAGTCCAGCCCT 60.609 66.667 0.00 0.00 0.00 5.19
2417 2577 1.330655 ATACGGCACCCAGAGTCCAG 61.331 60.000 0.00 0.00 0.00 3.86
2420 2580 0.103208 CTGATACGGCACCCAGAGTC 59.897 60.000 0.00 0.00 0.00 3.36
2421 2581 1.330655 CCTGATACGGCACCCAGAGT 61.331 60.000 0.00 0.00 0.00 3.24
2455 2615 5.068460 TGGAAAACCAAACACCATCTAAGTG 59.932 40.000 0.00 0.00 41.15 3.16
2459 2619 4.798882 ACTGGAAAACCAAACACCATCTA 58.201 39.130 0.00 0.00 0.00 1.98
2462 2622 3.642141 AGACTGGAAAACCAAACACCAT 58.358 40.909 0.00 0.00 0.00 3.55
2463 2623 3.094484 AGACTGGAAAACCAAACACCA 57.906 42.857 0.00 0.00 0.00 4.17
2464 2624 4.037565 CCTAAGACTGGAAAACCAAACACC 59.962 45.833 0.00 0.00 0.00 4.16
2465 2625 4.885325 TCCTAAGACTGGAAAACCAAACAC 59.115 41.667 0.00 0.00 0.00 3.32
2466 2626 4.885325 GTCCTAAGACTGGAAAACCAAACA 59.115 41.667 0.00 0.00 40.10 2.83
2467 2627 5.434352 GTCCTAAGACTGGAAAACCAAAC 57.566 43.478 0.00 0.00 40.10 2.93
2480 2640 9.452287 TCTAGAGACTAGAAAAAGTCCTAAGAC 57.548 37.037 0.00 0.00 45.86 3.01
2481 2641 9.452287 GTCTAGAGACTAGAAAAAGTCCTAAGA 57.548 37.037 9.60 0.00 45.86 2.10
2514 2674 6.721704 AAGCACCTTCTTGAGAATCTTTTT 57.278 33.333 0.00 0.00 34.92 1.94
2515 2675 6.324561 GAAGCACCTTCTTGAGAATCTTTT 57.675 37.500 0.00 0.00 37.49 2.27
2516 2676 5.956068 GAAGCACCTTCTTGAGAATCTTT 57.044 39.130 0.00 0.00 37.49 2.52
2554 2714 2.115427 CCAAACAGGGTGGGACTTTTT 58.885 47.619 0.00 0.00 32.03 1.94
2555 2715 1.007842 ACCAAACAGGGTGGGACTTTT 59.992 47.619 0.00 0.00 43.89 2.27
2556 2716 0.634465 ACCAAACAGGGTGGGACTTT 59.366 50.000 0.00 0.00 43.89 2.66
2557 2717 0.634465 AACCAAACAGGGTGGGACTT 59.366 50.000 0.00 0.00 41.32 3.01
2558 2718 0.634465 AAACCAAACAGGGTGGGACT 59.366 50.000 0.00 0.00 41.32 3.85
2559 2719 0.750249 CAAACCAAACAGGGTGGGAC 59.250 55.000 0.00 0.00 41.32 4.46
2560 2720 1.045911 GCAAACCAAACAGGGTGGGA 61.046 55.000 0.00 0.00 41.32 4.37
2561 2721 1.048160 AGCAAACCAAACAGGGTGGG 61.048 55.000 0.00 0.00 41.32 4.61
2562 2722 1.613437 CTAGCAAACCAAACAGGGTGG 59.387 52.381 0.00 0.00 41.32 4.61
2563 2723 1.613437 CCTAGCAAACCAAACAGGGTG 59.387 52.381 0.00 0.00 41.32 4.61
2564 2724 1.480498 CCCTAGCAAACCAAACAGGGT 60.480 52.381 0.00 0.00 45.04 4.34
2565 2725 1.203001 TCCCTAGCAAACCAAACAGGG 60.203 52.381 0.00 0.00 43.52 4.45
2566 2726 1.886542 GTCCCTAGCAAACCAAACAGG 59.113 52.381 0.00 0.00 45.67 4.00
2567 2727 2.863809 AGTCCCTAGCAAACCAAACAG 58.136 47.619 0.00 0.00 0.00 3.16
2568 2728 3.306472 AAGTCCCTAGCAAACCAAACA 57.694 42.857 0.00 0.00 0.00 2.83
2569 2729 4.665833 AAAAGTCCCTAGCAAACCAAAC 57.334 40.909 0.00 0.00 0.00 2.93
2606 2766 4.159693 GGTGTTTGGTTCCAGAGACTTTTT 59.840 41.667 8.93 0.00 0.00 1.94
2607 2767 3.699538 GGTGTTTGGTTCCAGAGACTTTT 59.300 43.478 8.93 0.00 0.00 2.27
2608 2768 3.288092 GGTGTTTGGTTCCAGAGACTTT 58.712 45.455 8.93 0.00 0.00 2.66
2609 2769 2.422945 GGGTGTTTGGTTCCAGAGACTT 60.423 50.000 8.93 0.00 0.00 3.01
2610 2770 1.143073 GGGTGTTTGGTTCCAGAGACT 59.857 52.381 8.93 0.00 0.00 3.24
2611 2771 1.605753 GGGTGTTTGGTTCCAGAGAC 58.394 55.000 1.90 1.90 0.00 3.36
2612 2772 0.476771 GGGGTGTTTGGTTCCAGAGA 59.523 55.000 0.00 0.00 0.00 3.10
2613 2773 0.478507 AGGGGTGTTTGGTTCCAGAG 59.521 55.000 0.00 0.00 0.00 3.35
2614 2774 0.476771 GAGGGGTGTTTGGTTCCAGA 59.523 55.000 0.00 0.00 0.00 3.86
2615 2775 0.889186 CGAGGGGTGTTTGGTTCCAG 60.889 60.000 0.00 0.00 0.00 3.86
2616 2776 1.149627 CGAGGGGTGTTTGGTTCCA 59.850 57.895 0.00 0.00 0.00 3.53
2617 2777 1.602605 CCGAGGGGTGTTTGGTTCC 60.603 63.158 0.00 0.00 0.00 3.62
2618 2778 1.602605 CCCGAGGGGTGTTTGGTTC 60.603 63.158 0.00 0.00 38.25 3.62
2619 2779 1.432023 ATCCCGAGGGGTGTTTGGTT 61.432 55.000 8.53 0.00 44.74 3.67
2620 2780 1.848886 GATCCCGAGGGGTGTTTGGT 61.849 60.000 8.53 0.00 44.74 3.67
2621 2781 1.077716 GATCCCGAGGGGTGTTTGG 60.078 63.158 8.53 0.00 44.74 3.28
2622 2782 1.077716 GGATCCCGAGGGGTGTTTG 60.078 63.158 8.53 0.00 44.74 2.93
2623 2783 2.306384 GGGATCCCGAGGGGTGTTT 61.306 63.158 17.02 0.00 44.74 2.83
2624 2784 2.691252 GGGATCCCGAGGGGTGTT 60.691 66.667 17.02 0.00 44.74 3.32
2643 2803 3.991051 CACAGGACAGACGCCCGT 61.991 66.667 0.00 0.00 0.00 5.28
2658 2818 2.675348 CTCAAAATTCTCTCTCCCGCAC 59.325 50.000 0.00 0.00 0.00 5.34
2660 2820 2.284190 CCTCAAAATTCTCTCTCCCGC 58.716 52.381 0.00 0.00 0.00 6.13
2683 2843 1.609208 CATAGAATTTCCCCCGGCAG 58.391 55.000 0.00 0.00 0.00 4.85
2684 2844 0.467290 GCATAGAATTTCCCCCGGCA 60.467 55.000 0.00 0.00 0.00 5.69
2766 2930 1.885887 TGGAATTGCCAAAGGAAGTCG 59.114 47.619 0.00 0.00 45.87 4.18
2777 2941 3.860754 GCCAACTGTACTTTGGAATTGCC 60.861 47.826 23.53 7.28 45.69 4.52
2798 2962 1.202498 GGTAGGTATTCTGGTGGACGC 60.202 57.143 0.00 0.00 0.00 5.19
2819 2983 1.779061 ATGCTTGTCCGGTCTGGGTT 61.779 55.000 0.00 0.00 38.76 4.11
2829 2997 3.896648 TTTTCTCGTTCATGCTTGTCC 57.103 42.857 0.00 0.00 0.00 4.02
2835 3003 7.084486 ACTTTTCCTATTTTTCTCGTTCATGC 58.916 34.615 0.00 0.00 0.00 4.06
2839 3007 6.797513 GCAGACTTTTCCTATTTTTCTCGTTC 59.202 38.462 0.00 0.00 0.00 3.95
2842 3010 6.370166 AGAGCAGACTTTTCCTATTTTTCTCG 59.630 38.462 0.00 0.00 0.00 4.04
2887 3060 2.222289 CGTGAGCGTTCGATACACAAAG 60.222 50.000 0.00 0.00 0.00 2.77
2888 3061 1.717113 CGTGAGCGTTCGATACACAAA 59.283 47.619 0.00 0.00 0.00 2.83
2939 3112 7.789341 TTTTCGTGTTATATTCATTGTGCAC 57.211 32.000 10.75 10.75 0.00 4.57
2981 3156 6.743575 ATAACACCAGATTTGCTTCACTAC 57.256 37.500 0.00 0.00 0.00 2.73
3027 3203 8.514594 CAAACCTAATCAAGCTTGATAAAGTCA 58.485 33.333 35.78 18.38 46.60 3.41
3036 3212 6.655003 TCCTAACTCAAACCTAATCAAGCTTG 59.345 38.462 20.81 20.81 0.00 4.01
3039 3215 5.938125 TGTCCTAACTCAAACCTAATCAAGC 59.062 40.000 0.00 0.00 0.00 4.01
3048 3224 9.668497 AGTTCTAATATTGTCCTAACTCAAACC 57.332 33.333 0.00 0.00 0.00 3.27
3058 3234 7.550906 GCAGACTTGAAGTTCTAATATTGTCCT 59.449 37.037 0.00 0.00 0.00 3.85
3059 3235 7.334421 TGCAGACTTGAAGTTCTAATATTGTCC 59.666 37.037 0.00 0.00 0.00 4.02
3060 3236 8.256611 TGCAGACTTGAAGTTCTAATATTGTC 57.743 34.615 0.00 0.60 0.00 3.18
3061 3237 8.621532 TTGCAGACTTGAAGTTCTAATATTGT 57.378 30.769 0.00 0.00 0.00 2.71
3065 3241 9.944376 AGTAATTGCAGACTTGAAGTTCTAATA 57.056 29.630 0.00 0.00 0.00 0.98
3066 3242 8.854614 AGTAATTGCAGACTTGAAGTTCTAAT 57.145 30.769 0.00 0.00 0.00 1.73
3067 3243 8.677148 AAGTAATTGCAGACTTGAAGTTCTAA 57.323 30.769 0.00 0.00 34.61 2.10
3068 3244 8.559536 CAAAGTAATTGCAGACTTGAAGTTCTA 58.440 33.333 0.00 0.00 36.05 2.10
3069 3245 7.420800 CAAAGTAATTGCAGACTTGAAGTTCT 58.579 34.615 0.00 0.00 36.05 3.01
3070 3246 6.638468 CCAAAGTAATTGCAGACTTGAAGTTC 59.362 38.462 0.00 0.00 36.05 3.01
3071 3247 6.321181 TCCAAAGTAATTGCAGACTTGAAGTT 59.679 34.615 0.00 0.00 36.05 2.66
3072 3248 5.827797 TCCAAAGTAATTGCAGACTTGAAGT 59.172 36.000 0.00 0.00 36.05 3.01
3073 3249 6.317789 TCCAAAGTAATTGCAGACTTGAAG 57.682 37.500 10.43 0.00 36.05 3.02
3074 3250 6.707440 TTCCAAAGTAATTGCAGACTTGAA 57.293 33.333 10.43 8.38 36.05 2.69
3075 3251 6.294675 CCATTCCAAAGTAATTGCAGACTTGA 60.295 38.462 10.43 3.84 36.05 3.02
3076 3252 5.865552 CCATTCCAAAGTAATTGCAGACTTG 59.134 40.000 10.43 6.26 36.05 3.16
3077 3253 5.774690 TCCATTCCAAAGTAATTGCAGACTT 59.225 36.000 5.23 5.23 37.73 3.01
3078 3254 5.324409 TCCATTCCAAAGTAATTGCAGACT 58.676 37.500 0.00 0.00 37.73 3.24
3079 3255 5.393461 CCTCCATTCCAAAGTAATTGCAGAC 60.393 44.000 0.00 0.00 37.73 3.51
3080 3256 4.706476 CCTCCATTCCAAAGTAATTGCAGA 59.294 41.667 0.00 0.00 37.73 4.26
3081 3257 4.142093 CCCTCCATTCCAAAGTAATTGCAG 60.142 45.833 0.00 0.00 37.73 4.41
3082 3258 3.768757 CCCTCCATTCCAAAGTAATTGCA 59.231 43.478 0.00 0.00 37.73 4.08
3083 3259 4.023291 TCCCTCCATTCCAAAGTAATTGC 58.977 43.478 0.00 0.00 37.73 3.56
3084 3260 5.264395 ACTCCCTCCATTCCAAAGTAATTG 58.736 41.667 0.00 0.00 38.84 2.32
3085 3261 5.536497 ACTCCCTCCATTCCAAAGTAATT 57.464 39.130 0.00 0.00 0.00 1.40
3086 3262 5.398012 GCTACTCCCTCCATTCCAAAGTAAT 60.398 44.000 0.00 0.00 0.00 1.89
3087 3263 4.080526 GCTACTCCCTCCATTCCAAAGTAA 60.081 45.833 0.00 0.00 0.00 2.24
3088 3264 3.454812 GCTACTCCCTCCATTCCAAAGTA 59.545 47.826 0.00 0.00 0.00 2.24
3089 3265 2.239907 GCTACTCCCTCCATTCCAAAGT 59.760 50.000 0.00 0.00 0.00 2.66
3090 3266 2.422093 GGCTACTCCCTCCATTCCAAAG 60.422 54.545 0.00 0.00 0.00 2.77
3091 3267 1.564348 GGCTACTCCCTCCATTCCAAA 59.436 52.381 0.00 0.00 0.00 3.28
3092 3268 1.213296 GGCTACTCCCTCCATTCCAA 58.787 55.000 0.00 0.00 0.00 3.53
3093 3269 2.930935 GGCTACTCCCTCCATTCCA 58.069 57.895 0.00 0.00 0.00 3.53
3102 3278 8.730426 GATACGAATCATTCAGGGCTACTCCC 62.730 50.000 0.00 0.00 42.61 4.30
3103 3279 2.103263 ACGAATCATTCAGGGCTACTCC 59.897 50.000 0.00 0.00 0.00 3.85
3104 3280 3.460857 ACGAATCATTCAGGGCTACTC 57.539 47.619 0.00 0.00 0.00 2.59
3105 3281 4.588951 TGATACGAATCATTCAGGGCTACT 59.411 41.667 0.00 0.00 37.20 2.57
3106 3282 4.883083 TGATACGAATCATTCAGGGCTAC 58.117 43.478 0.00 0.00 37.20 3.58
3107 3283 5.545063 TTGATACGAATCATTCAGGGCTA 57.455 39.130 0.00 0.00 41.73 3.93
3108 3284 4.422073 TTGATACGAATCATTCAGGGCT 57.578 40.909 0.00 0.00 41.73 5.19
3109 3285 5.695851 AATTGATACGAATCATTCAGGGC 57.304 39.130 0.00 0.00 41.73 5.19


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

AutoCloner maintained by Alex Coulton.