Multiple sequence alignment - TraesCS1A01G083800

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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 TraesCS1A01G083800 chr1A 100.000 3453 0 0 1 3453 68376317 68372865 0.000000e+00 6377.0
1 TraesCS1A01G083800 chr1A 92.800 625 43 1 1 623 224095867 224095243 0.000000e+00 904.0
2 TraesCS1A01G083800 chr1D 93.586 1824 81 19 626 2439 69181135 69179338 0.000000e+00 2687.0
3 TraesCS1A01G083800 chr1D 92.105 418 15 6 2697 3098 69178796 69178381 1.070000e-159 573.0
4 TraesCS1A01G083800 chr1D 94.828 58 3 0 3396 3453 68438882 68438825 1.320000e-14 91.6
5 TraesCS1A01G083800 chr1D 89.706 68 6 1 3387 3453 465028527 465028460 6.140000e-13 86.1
6 TraesCS1A01G083800 chr1B 92.042 1885 94 25 620 2489 111027142 111025299 0.000000e+00 2599.0
7 TraesCS1A01G083800 chr1B 79.518 249 19 15 2452 2698 111025294 111025076 7.720000e-32 148.0
8 TraesCS1A01G083800 chr5A 92.960 625 42 1 1 623 64788751 64788127 0.000000e+00 909.0
9 TraesCS1A01G083800 chr5A 89.600 625 59 5 1 623 518943920 518943300 0.000000e+00 789.0
10 TraesCS1A01G083800 chr5A 89.600 625 54 6 1 623 311940548 311939933 0.000000e+00 784.0
11 TraesCS1A01G083800 chr4A 91.200 625 50 3 1 623 609567249 609567870 0.000000e+00 845.0
12 TraesCS1A01G083800 chr2A 90.530 623 55 3 1 620 265276391 265277012 0.000000e+00 821.0
13 TraesCS1A01G083800 chr2A 89.760 625 53 4 1 623 568401992 568402607 0.000000e+00 789.0
14 TraesCS1A01G083800 chr2A 94.828 58 3 0 3396 3453 744490967 744491024 1.320000e-14 91.6
15 TraesCS1A01G083800 chr5D 90.240 625 55 4 1 623 24617388 24618008 0.000000e+00 811.0
16 TraesCS1A01G083800 chr7A 91.346 520 40 3 1 518 688157352 688156836 0.000000e+00 706.0
17 TraesCS1A01G083800 chr7A 89.706 68 5 2 3388 3453 221738442 221738509 6.140000e-13 86.1
18 TraesCS1A01G083800 chr7D 91.176 68 5 1 3387 3453 263967509 263967576 1.320000e-14 91.6
19 TraesCS1A01G083800 chr7D 86.567 67 8 1 2555 2621 72447273 72447338 4.780000e-09 73.1
20 TraesCS1A01G083800 chr7B 94.828 58 3 0 3396 3453 68883215 68883272 1.320000e-14 91.6
21 TraesCS1A01G083800 chr5B 92.188 64 4 1 3391 3453 712868982 712868919 4.750000e-14 89.8
22 TraesCS1A01G083800 chr3B 92.188 64 3 2 3391 3453 472908719 472908657 4.750000e-14 89.8
23 TraesCS1A01G083800 chr2B 92.188 64 3 2 3391 3453 704411974 704411912 4.750000e-14 89.8
24 TraesCS1A01G083800 chr3A 87.324 71 8 1 2555 2625 46615647 46615716 2.860000e-11 80.5
25 TraesCS1A01G083800 chr3A 87.879 66 7 1 2558 2623 108919504 108919440 3.700000e-10 76.8
26 TraesCS1A01G083800 chr6B 87.143 70 8 1 2555 2624 499017084 499017152 1.030000e-10 78.7
27 TraesCS1A01G083800 chr6A 87.879 66 7 1 2558 2623 461837050 461836986 3.700000e-10 76.8
28 TraesCS1A01G083800 chr6A 94.444 36 1 1 3134 3169 58033622 58033588 2.000000e-03 54.7


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 TraesCS1A01G083800 chr1A 68372865 68376317 3452 True 6377.0 6377 100.0000 1 3453 1 chr1A.!!$R1 3452
1 TraesCS1A01G083800 chr1A 224095243 224095867 624 True 904.0 904 92.8000 1 623 1 chr1A.!!$R2 622
2 TraesCS1A01G083800 chr1D 69178381 69181135 2754 True 1630.0 2687 92.8455 626 3098 2 chr1D.!!$R3 2472
3 TraesCS1A01G083800 chr1B 111025076 111027142 2066 True 1373.5 2599 85.7800 620 2698 2 chr1B.!!$R1 2078
4 TraesCS1A01G083800 chr5A 64788127 64788751 624 True 909.0 909 92.9600 1 623 1 chr5A.!!$R1 622
5 TraesCS1A01G083800 chr5A 518943300 518943920 620 True 789.0 789 89.6000 1 623 1 chr5A.!!$R3 622
6 TraesCS1A01G083800 chr5A 311939933 311940548 615 True 784.0 784 89.6000 1 623 1 chr5A.!!$R2 622
7 TraesCS1A01G083800 chr4A 609567249 609567870 621 False 845.0 845 91.2000 1 623 1 chr4A.!!$F1 622
8 TraesCS1A01G083800 chr2A 265276391 265277012 621 False 821.0 821 90.5300 1 620 1 chr2A.!!$F1 619
9 TraesCS1A01G083800 chr2A 568401992 568402607 615 False 789.0 789 89.7600 1 623 1 chr2A.!!$F2 622
10 TraesCS1A01G083800 chr5D 24617388 24618008 620 False 811.0 811 90.2400 1 623 1 chr5D.!!$F1 622
11 TraesCS1A01G083800 chr7A 688156836 688157352 516 True 706.0 706 91.3460 1 518 1 chr7A.!!$R1 517

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
146 147 0.391130 GGCGTGGCAATGTAGTCTGA 60.391 55.0 0.0 0.0 0.0 3.27 F
651 656 0.395173 GCGAGAGAGAGAGGGGAAGT 60.395 60.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1895 1910 1.144716 CTTCTCCGCCAGCTGCATA 59.855 57.895 8.66 0.0 41.33 3.14 R
2499 2879 0.242825 GTTCACGTCTGATCCGTCCA 59.757 55.000 0.00 0.0 36.17 4.02 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
57 58 2.161410 ACATATGCGCAATTGACGTGTT 59.839 40.909 24.46 4.16 0.00 3.32
66 67 5.444877 GCGCAATTGACGTGTTAATGTAGTA 60.445 40.000 10.34 0.00 0.00 1.82
146 147 0.391130 GGCGTGGCAATGTAGTCTGA 60.391 55.000 0.00 0.00 0.00 3.27
160 161 5.546526 TGTAGTCTGATTGCACACACATTA 58.453 37.500 0.00 0.00 0.00 1.90
215 216 2.046796 TCAGTTGGCGCGGCAATA 60.047 55.556 43.73 30.63 0.00 1.90
220 221 0.661020 GTTGGCGCGGCAATATAGTT 59.339 50.000 43.73 0.00 0.00 2.24
283 286 1.592543 CACGCGCATATGCTTAGTTGA 59.407 47.619 24.56 0.00 39.32 3.18
328 331 6.578545 GCACACATATTGATATTTAGTTGGCG 59.421 38.462 0.00 0.00 0.00 5.69
330 333 6.995686 ACACATATTGATATTTAGTTGGCGGA 59.004 34.615 0.00 0.00 0.00 5.54
384 388 5.542779 AGATCTACTTTTGAAGAGCACGTT 58.457 37.500 0.00 0.00 0.00 3.99
407 411 2.747446 CGAGGATTCCAACGGTGAAAAT 59.253 45.455 0.00 0.56 0.00 1.82
410 414 2.560981 GGATTCCAACGGTGAAAATGGT 59.439 45.455 0.00 0.00 34.50 3.55
623 628 2.051941 TCTGTTTTAGACCGGCCGT 58.948 52.632 26.12 12.57 0.00 5.68
643 648 2.028930 GTCCTTTTTGGCGAGAGAGAGA 60.029 50.000 0.00 0.00 35.26 3.10
644 649 2.232452 TCCTTTTTGGCGAGAGAGAGAG 59.768 50.000 0.00 0.00 35.26 3.20
645 650 2.615869 CTTTTTGGCGAGAGAGAGAGG 58.384 52.381 0.00 0.00 0.00 3.69
646 651 0.898320 TTTTGGCGAGAGAGAGAGGG 59.102 55.000 0.00 0.00 0.00 4.30
647 652 0.972983 TTTGGCGAGAGAGAGAGGGG 60.973 60.000 0.00 0.00 0.00 4.79
648 653 1.864263 TTGGCGAGAGAGAGAGGGGA 61.864 60.000 0.00 0.00 0.00 4.81
649 654 1.076632 GGCGAGAGAGAGAGGGGAA 60.077 63.158 0.00 0.00 0.00 3.97
650 655 1.106944 GGCGAGAGAGAGAGGGGAAG 61.107 65.000 0.00 0.00 0.00 3.46
651 656 0.395173 GCGAGAGAGAGAGGGGAAGT 60.395 60.000 0.00 0.00 0.00 3.01
655 660 1.190643 GAGAGAGAGGGGAAGTGTGG 58.809 60.000 0.00 0.00 0.00 4.17
691 696 2.696707 TGTGATTACGGGCTAGGTAAGG 59.303 50.000 0.00 0.00 33.73 2.69
731 736 2.359900 CCTTGTGATTGTGGGCTCTAC 58.640 52.381 0.00 0.00 0.00 2.59
737 742 3.555956 GTGATTGTGGGCTCTACAATACG 59.444 47.826 13.95 0.00 45.82 3.06
781 787 2.119611 TCGGCCAGTCCAGAAGGA 59.880 61.111 2.24 0.00 43.21 3.36
835 841 1.026718 AACATGTAGCAGCTTCGCCC 61.027 55.000 0.00 0.00 0.00 6.13
981 987 1.697982 ACTCCACCTTTATATCGGCCC 59.302 52.381 0.00 0.00 0.00 5.80
984 990 1.423921 CCACCTTTATATCGGCCCCTT 59.576 52.381 0.00 0.00 0.00 3.95
1093 1099 2.892425 CCGAATCAGCTGCGTCCC 60.892 66.667 9.47 0.00 0.00 4.46
1296 1305 2.229792 CAACAAGCTCCAGGTAAAGCA 58.770 47.619 1.61 0.00 41.06 3.91
1343 1354 2.159282 TCGATGGTCTTCCGTTAAGCTC 60.159 50.000 0.00 0.00 34.97 4.09
1511 1526 2.124403 GACGCGGAGGAGACCCTA 60.124 66.667 12.47 0.00 44.53 3.53
1520 1535 2.359967 GGAGACCCTACAGGCGCTT 61.360 63.158 7.64 0.00 40.58 4.68
1699 1714 0.531532 CCCTGCATCACCGAGATCAC 60.532 60.000 0.00 0.00 33.72 3.06
1779 1794 2.965147 TTCGCGGTGAAGCACATGC 61.965 57.895 6.13 0.00 42.49 4.06
2127 2142 2.450107 ACCCCAACGGTAACCCCA 60.450 61.111 0.00 0.00 45.97 4.96
2128 2143 1.853565 ACCCCAACGGTAACCCCAT 60.854 57.895 0.00 0.00 45.97 4.00
2129 2144 1.077285 CCCCAACGGTAACCCCATC 60.077 63.158 0.00 0.00 0.00 3.51
2130 2145 1.686416 CCCAACGGTAACCCCATCA 59.314 57.895 0.00 0.00 0.00 3.07
2145 2160 0.454600 CATCATCACCAGCACCTTGC 59.545 55.000 0.00 0.00 45.46 4.01
2183 2200 4.484236 TGACCATGAAATTCATTGCGTTC 58.516 39.130 5.63 0.00 34.28 3.95
2229 2250 4.559502 GCACCATCGTCAATAGCTAGATCA 60.560 45.833 0.00 0.00 0.00 2.92
2235 2256 5.816682 TCGTCAATAGCTAGATCAGGGATA 58.183 41.667 0.00 0.00 0.00 2.59
2242 2263 5.858876 AGCTAGATCAGGGATAGAGAAGA 57.141 43.478 0.00 0.00 0.00 2.87
2253 2274 4.223659 GGATAGAGAAGATCGCGAAGAAC 58.776 47.826 15.24 5.72 0.00 3.01
2279 2300 1.153249 AAGTGTGTCCGTGGTGTGG 60.153 57.895 0.00 0.00 0.00 4.17
2280 2301 1.906105 AAGTGTGTCCGTGGTGTGGT 61.906 55.000 0.00 0.00 0.00 4.16
2281 2302 2.177580 GTGTGTCCGTGGTGTGGTG 61.178 63.158 0.00 0.00 0.00 4.17
2282 2303 2.188469 GTGTCCGTGGTGTGGTGT 59.812 61.111 0.00 0.00 0.00 4.16
2283 2304 2.177580 GTGTCCGTGGTGTGGTGTG 61.178 63.158 0.00 0.00 0.00 3.82
2288 2309 1.144276 CGTGGTGTGGTGTGTGGTA 59.856 57.895 0.00 0.00 0.00 3.25
2303 2324 1.659098 GTGGTATGTACGAGCAAGTGC 59.341 52.381 0.00 0.00 42.49 4.40
2441 2466 3.056678 TGCAATGCAAGTTGAACTATGGG 60.057 43.478 5.01 0.00 34.76 4.00
2443 2468 2.284754 TGCAAGTTGAACTATGGGCA 57.715 45.000 7.16 4.11 0.00 5.36
2444 2469 2.806434 TGCAAGTTGAACTATGGGCAT 58.194 42.857 7.16 0.00 0.00 4.40
2445 2470 2.492881 TGCAAGTTGAACTATGGGCATG 59.507 45.455 7.16 0.00 0.00 4.06
2494 2874 2.393271 AAGACGGCTCCATCTTCTTG 57.607 50.000 0.00 0.00 28.79 3.02
2495 2875 1.561643 AGACGGCTCCATCTTCTTGA 58.438 50.000 0.00 0.00 0.00 3.02
2496 2876 2.114616 AGACGGCTCCATCTTCTTGAT 58.885 47.619 0.00 0.00 35.40 2.57
2532 2913 0.036765 GTGAACGGGGTGATAGTGCA 60.037 55.000 0.00 0.00 0.00 4.57
2539 2920 0.034059 GGGTGATAGTGCATCCGGAG 59.966 60.000 11.34 3.17 32.09 4.63
2569 2950 3.264450 TCTGAATCTTTTCTCCACCTCCC 59.736 47.826 0.00 0.00 32.78 4.30
2572 2953 2.415983 TCTTTTCTCCACCTCCCAGA 57.584 50.000 0.00 0.00 0.00 3.86
2598 2997 0.973632 TCCCTCTACAGAAAGCGCAA 59.026 50.000 11.47 0.00 0.00 4.85
2599 2998 1.066858 TCCCTCTACAGAAAGCGCAAG 60.067 52.381 11.47 0.00 43.44 4.01
2610 3009 4.024893 CAGAAAGCGCAAGTAGAAAGTGAA 60.025 41.667 11.47 0.00 41.68 3.18
2611 3010 4.212214 AGAAAGCGCAAGTAGAAAGTGAAG 59.788 41.667 11.47 0.00 41.68 3.02
2612 3011 3.386768 AGCGCAAGTAGAAAGTGAAGA 57.613 42.857 11.47 0.00 41.68 2.87
2613 3012 3.321497 AGCGCAAGTAGAAAGTGAAGAG 58.679 45.455 11.47 0.00 41.68 2.85
2614 3013 2.159774 GCGCAAGTAGAAAGTGAAGAGC 60.160 50.000 0.30 0.00 41.68 4.09
2615 3014 2.091277 CGCAAGTAGAAAGTGAAGAGCG 59.909 50.000 0.00 0.00 35.42 5.03
2616 3015 2.159774 GCAAGTAGAAAGTGAAGAGCGC 60.160 50.000 0.00 0.00 0.00 5.92
2617 3016 2.371910 AGTAGAAAGTGAAGAGCGCC 57.628 50.000 2.29 0.00 0.00 6.53
2618 3017 1.896465 AGTAGAAAGTGAAGAGCGCCT 59.104 47.619 2.29 0.00 0.00 5.52
2619 3018 2.300437 AGTAGAAAGTGAAGAGCGCCTT 59.700 45.455 2.29 7.40 37.93 4.35
2620 3019 3.510360 AGTAGAAAGTGAAGAGCGCCTTA 59.490 43.478 2.29 0.00 34.68 2.69
2621 3020 3.402628 AGAAAGTGAAGAGCGCCTTAA 57.597 42.857 2.29 0.00 34.68 1.85
2622 3021 3.740115 AGAAAGTGAAGAGCGCCTTAAA 58.260 40.909 2.29 0.00 34.68 1.52
2641 3047 2.462456 ATCGAAGACATGTGTGCAGT 57.538 45.000 1.15 0.00 42.51 4.40
2645 3051 4.314961 TCGAAGACATGTGTGCAGTTAAT 58.685 39.130 1.15 0.00 0.00 1.40
2652 3058 7.940850 AGACATGTGTGCAGTTAATTAACTTT 58.059 30.769 24.99 6.24 43.57 2.66
2730 3136 4.383770 CCTTCTATACGGGGCTTCAAAGAA 60.384 45.833 0.00 0.00 0.00 2.52
2733 3139 4.939439 TCTATACGGGGCTTCAAAGAAAAC 59.061 41.667 0.00 0.00 0.00 2.43
2751 3157 7.519032 AGAAAACCTTAATTTGGATGAACGA 57.481 32.000 0.00 0.00 0.00 3.85
2842 3250 1.993370 CACCTCGACACGGATTCTTTC 59.007 52.381 0.00 0.00 0.00 2.62
2853 3261 5.008316 ACACGGATTCTTTCTTTTAGCGTTT 59.992 36.000 0.00 0.00 0.00 3.60
2858 3266 8.385111 CGGATTCTTTCTTTTAGCGTTTACATA 58.615 33.333 0.00 0.00 0.00 2.29
3003 3425 4.594123 TTGATTGTGTAGAACTCGGTCA 57.406 40.909 0.00 0.00 0.00 4.02
3012 3434 3.045601 AGAACTCGGTCAGGTTCATTG 57.954 47.619 8.24 0.00 42.76 2.82
3022 3444 4.984785 GGTCAGGTTCATTGAAAAGCTTTC 59.015 41.667 13.10 6.91 32.40 2.62
3032 3454 8.721019 TCATTGAAAAGCTTTCTCAACATTTT 57.279 26.923 25.45 14.62 32.19 1.82
3046 3468 8.402798 TCTCAACATTTTTAAAGCACCATCTA 57.597 30.769 0.00 0.00 0.00 1.98
3047 3469 8.514594 TCTCAACATTTTTAAAGCACCATCTAG 58.485 33.333 0.00 0.00 0.00 2.43
3147 3569 9.914834 ATAAACTAAGATTAGTACAAATGCCCA 57.085 29.630 5.71 0.00 42.86 5.36
3148 3570 8.823220 AAACTAAGATTAGTACAAATGCCCAT 57.177 30.769 5.71 0.00 42.86 4.00
3149 3571 7.807977 ACTAAGATTAGTACAAATGCCCATG 57.192 36.000 3.42 0.00 41.92 3.66
3150 3572 7.346471 ACTAAGATTAGTACAAATGCCCATGT 58.654 34.615 3.42 0.00 41.92 3.21
3151 3573 6.455360 AAGATTAGTACAAATGCCCATGTG 57.545 37.500 0.00 0.00 32.30 3.21
3152 3574 5.509498 AGATTAGTACAAATGCCCATGTGT 58.491 37.500 8.94 8.94 41.79 3.72
3153 3575 5.951747 AGATTAGTACAAATGCCCATGTGTT 59.048 36.000 9.20 0.00 39.76 3.32
3154 3576 3.940209 AGTACAAATGCCCATGTGTTG 57.060 42.857 9.20 0.38 39.76 3.33
3155 3577 2.029110 AGTACAAATGCCCATGTGTTGC 60.029 45.455 9.20 4.19 39.76 4.17
3156 3578 0.757512 ACAAATGCCCATGTGTTGCA 59.242 45.000 0.00 0.00 35.84 4.08
3157 3579 1.140452 ACAAATGCCCATGTGTTGCAA 59.860 42.857 0.00 0.00 35.84 4.08
3158 3580 1.532007 CAAATGCCCATGTGTTGCAAC 59.468 47.619 22.83 22.83 38.69 4.17
3159 3581 0.319727 AATGCCCATGTGTTGCAACG 60.320 50.000 23.79 9.92 38.69 4.10
3160 3582 2.049248 GCCCATGTGTTGCAACGG 60.049 61.111 23.79 18.58 0.00 4.44
3161 3583 2.560119 GCCCATGTGTTGCAACGGA 61.560 57.895 23.79 13.42 0.00 4.69
3162 3584 2.037053 CCCATGTGTTGCAACGGAA 58.963 52.632 23.79 12.52 0.00 4.30
3163 3585 0.039256 CCCATGTGTTGCAACGGAAG 60.039 55.000 23.79 13.74 0.00 3.46
3164 3586 0.950836 CCATGTGTTGCAACGGAAGA 59.049 50.000 23.79 6.40 0.00 2.87
3165 3587 1.334960 CCATGTGTTGCAACGGAAGAC 60.335 52.381 23.79 16.16 0.00 3.01
3166 3588 1.333308 CATGTGTTGCAACGGAAGACA 59.667 47.619 23.79 20.89 31.83 3.41
3167 3589 1.454201 TGTGTTGCAACGGAAGACAA 58.546 45.000 23.79 1.33 0.00 3.18
3168 3590 1.813178 TGTGTTGCAACGGAAGACAAA 59.187 42.857 23.79 0.57 0.00 2.83
3169 3591 2.229062 TGTGTTGCAACGGAAGACAAAA 59.771 40.909 23.79 0.00 0.00 2.44
3170 3592 2.596862 GTGTTGCAACGGAAGACAAAAC 59.403 45.455 23.79 9.09 0.00 2.43
3171 3593 2.490115 TGTTGCAACGGAAGACAAAACT 59.510 40.909 23.79 0.00 0.00 2.66
3172 3594 2.842208 TGCAACGGAAGACAAAACTG 57.158 45.000 0.00 0.00 0.00 3.16
3173 3595 2.360844 TGCAACGGAAGACAAAACTGA 58.639 42.857 0.00 0.00 0.00 3.41
3174 3596 2.096819 TGCAACGGAAGACAAAACTGAC 59.903 45.455 0.00 0.00 0.00 3.51
3175 3597 2.096819 GCAACGGAAGACAAAACTGACA 59.903 45.455 0.00 0.00 0.00 3.58
3176 3598 3.243068 GCAACGGAAGACAAAACTGACAT 60.243 43.478 0.00 0.00 0.00 3.06
3177 3599 4.282068 CAACGGAAGACAAAACTGACATG 58.718 43.478 0.00 0.00 0.00 3.21
3178 3600 3.804036 ACGGAAGACAAAACTGACATGA 58.196 40.909 0.00 0.00 0.00 3.07
3179 3601 3.560068 ACGGAAGACAAAACTGACATGAC 59.440 43.478 0.00 0.00 0.00 3.06
3180 3602 3.559655 CGGAAGACAAAACTGACATGACA 59.440 43.478 0.00 0.00 0.00 3.58
3181 3603 4.214119 CGGAAGACAAAACTGACATGACAT 59.786 41.667 0.00 0.00 0.00 3.06
3182 3604 5.455392 GGAAGACAAAACTGACATGACATG 58.545 41.667 14.02 14.02 0.00 3.21
3183 3605 5.239306 GGAAGACAAAACTGACATGACATGA 59.761 40.000 22.19 0.00 0.00 3.07
3184 3606 6.238731 GGAAGACAAAACTGACATGACATGAA 60.239 38.462 22.19 8.67 0.00 2.57
3185 3607 6.064846 AGACAAAACTGACATGACATGAAC 57.935 37.500 22.19 14.62 0.00 3.18
3186 3608 5.824624 AGACAAAACTGACATGACATGAACT 59.175 36.000 22.19 0.00 0.00 3.01
3187 3609 6.017605 AGACAAAACTGACATGACATGAACTC 60.018 38.462 22.19 9.71 0.00 3.01
3188 3610 4.997905 AAACTGACATGACATGAACTCG 57.002 40.909 22.19 11.91 0.00 4.18
3189 3611 2.341257 ACTGACATGACATGAACTCGC 58.659 47.619 22.19 4.73 0.00 5.03
3190 3612 1.662629 CTGACATGACATGAACTCGCC 59.337 52.381 22.19 3.02 0.00 5.54
3191 3613 1.276138 TGACATGACATGAACTCGCCT 59.724 47.619 22.19 0.00 0.00 5.52
3192 3614 2.495669 TGACATGACATGAACTCGCCTA 59.504 45.455 22.19 0.00 0.00 3.93
3193 3615 3.119291 GACATGACATGAACTCGCCTAG 58.881 50.000 22.19 0.00 0.00 3.02
3194 3616 2.159043 ACATGACATGAACTCGCCTAGG 60.159 50.000 22.19 3.67 0.00 3.02
3195 3617 1.557099 TGACATGAACTCGCCTAGGT 58.443 50.000 11.31 0.00 0.00 3.08
3196 3618 1.204704 TGACATGAACTCGCCTAGGTG 59.795 52.381 16.70 16.70 0.00 4.00
3197 3619 1.476891 GACATGAACTCGCCTAGGTGA 59.523 52.381 23.46 23.46 0.00 4.02
3198 3620 1.899814 ACATGAACTCGCCTAGGTGAA 59.100 47.619 24.81 11.44 33.98 3.18
3199 3621 2.501723 ACATGAACTCGCCTAGGTGAAT 59.498 45.455 24.81 13.81 33.98 2.57
3200 3622 3.704566 ACATGAACTCGCCTAGGTGAATA 59.295 43.478 24.81 12.13 33.98 1.75
3201 3623 3.795623 TGAACTCGCCTAGGTGAATAC 57.204 47.619 24.81 17.66 33.98 1.89
3202 3624 3.093814 TGAACTCGCCTAGGTGAATACA 58.906 45.455 24.81 19.69 33.98 2.29
3203 3625 3.119245 TGAACTCGCCTAGGTGAATACAC 60.119 47.826 24.81 14.62 45.27 2.90
3234 3656 9.985730 TGATGATTTCATTATTTCTTTATGGCC 57.014 29.630 0.00 0.00 36.57 5.36
3240 3662 7.042797 TCATTATTTCTTTATGGCCTTCAGC 57.957 36.000 3.32 0.00 42.60 4.26
3254 3676 5.175090 GCCTTCAGCCATACAATCTTTAC 57.825 43.478 0.00 0.00 34.35 2.01
3255 3677 4.640201 GCCTTCAGCCATACAATCTTTACA 59.360 41.667 0.00 0.00 34.35 2.41
3256 3678 5.125417 GCCTTCAGCCATACAATCTTTACAA 59.875 40.000 0.00 0.00 34.35 2.41
3257 3679 6.350110 GCCTTCAGCCATACAATCTTTACAAA 60.350 38.462 0.00 0.00 34.35 2.83
3258 3680 7.601856 CCTTCAGCCATACAATCTTTACAAAA 58.398 34.615 0.00 0.00 0.00 2.44
3259 3681 7.542130 CCTTCAGCCATACAATCTTTACAAAAC 59.458 37.037 0.00 0.00 0.00 2.43
3260 3682 6.919721 TCAGCCATACAATCTTTACAAAACC 58.080 36.000 0.00 0.00 0.00 3.27
3261 3683 5.799936 CAGCCATACAATCTTTACAAAACCG 59.200 40.000 0.00 0.00 0.00 4.44
3262 3684 4.561213 GCCATACAATCTTTACAAAACCGC 59.439 41.667 0.00 0.00 0.00 5.68
3263 3685 5.621329 GCCATACAATCTTTACAAAACCGCT 60.621 40.000 0.00 0.00 0.00 5.52
3264 3686 6.403855 GCCATACAATCTTTACAAAACCGCTA 60.404 38.462 0.00 0.00 0.00 4.26
3265 3687 6.964934 CCATACAATCTTTACAAAACCGCTAC 59.035 38.462 0.00 0.00 0.00 3.58
3266 3688 7.361371 CCATACAATCTTTACAAAACCGCTACA 60.361 37.037 0.00 0.00 0.00 2.74
3267 3689 6.380095 ACAATCTTTACAAAACCGCTACAA 57.620 33.333 0.00 0.00 0.00 2.41
3268 3690 6.797454 ACAATCTTTACAAAACCGCTACAAA 58.203 32.000 0.00 0.00 0.00 2.83
3269 3691 7.259161 ACAATCTTTACAAAACCGCTACAAAA 58.741 30.769 0.00 0.00 0.00 2.44
3270 3692 7.923878 ACAATCTTTACAAAACCGCTACAAAAT 59.076 29.630 0.00 0.00 0.00 1.82
3271 3693 9.400638 CAATCTTTACAAAACCGCTACAAAATA 57.599 29.630 0.00 0.00 0.00 1.40
3273 3695 8.958175 TCTTTACAAAACCGCTACAAAATATG 57.042 30.769 0.00 0.00 0.00 1.78
3274 3696 8.569641 TCTTTACAAAACCGCTACAAAATATGT 58.430 29.630 0.00 0.00 46.36 2.29
3275 3697 8.508800 TTTACAAAACCGCTACAAAATATGTG 57.491 30.769 0.00 0.00 43.77 3.21
3276 3698 4.920927 ACAAAACCGCTACAAAATATGTGC 59.079 37.500 0.00 0.00 43.77 4.57
3277 3699 4.775058 AAACCGCTACAAAATATGTGCA 57.225 36.364 0.00 0.00 43.77 4.57
3278 3700 4.981806 AACCGCTACAAAATATGTGCAT 57.018 36.364 0.00 0.00 43.77 3.96
3279 3701 4.981806 ACCGCTACAAAATATGTGCATT 57.018 36.364 0.00 0.00 43.77 3.56
3280 3702 6.443934 AACCGCTACAAAATATGTGCATTA 57.556 33.333 0.00 0.00 43.77 1.90
3281 3703 6.633500 ACCGCTACAAAATATGTGCATTAT 57.367 33.333 0.00 0.00 43.77 1.28
3282 3704 7.038154 ACCGCTACAAAATATGTGCATTATT 57.962 32.000 0.00 0.00 43.77 1.40
3283 3705 7.138736 ACCGCTACAAAATATGTGCATTATTC 58.861 34.615 0.00 0.00 43.77 1.75
3284 3706 7.138081 CCGCTACAAAATATGTGCATTATTCA 58.862 34.615 0.00 0.00 43.77 2.57
3285 3707 7.809331 CCGCTACAAAATATGTGCATTATTCAT 59.191 33.333 0.00 0.00 43.77 2.57
3286 3708 9.184062 CGCTACAAAATATGTGCATTATTCATT 57.816 29.630 0.00 0.00 43.77 2.57
3296 3718 8.967664 ATGTGCATTATTCATTTTATGGCTTT 57.032 26.923 0.00 0.00 0.00 3.51
3297 3719 8.789825 TGTGCATTATTCATTTTATGGCTTTT 57.210 26.923 0.00 0.00 0.00 2.27
3298 3720 8.881743 TGTGCATTATTCATTTTATGGCTTTTC 58.118 29.630 0.00 0.00 0.00 2.29
3299 3721 9.101655 GTGCATTATTCATTTTATGGCTTTTCT 57.898 29.630 0.00 0.00 0.00 2.52
3332 3754 8.983702 TTTCTATAACCAGTGTTTTAGGTGTT 57.016 30.769 0.00 0.00 36.93 3.32
3337 3759 8.927675 ATAACCAGTGTTTTAGGTGTTATTCA 57.072 30.769 0.00 0.00 35.42 2.57
3338 3760 7.833285 AACCAGTGTTTTAGGTGTTATTCAT 57.167 32.000 0.00 0.00 35.42 2.57
3339 3761 7.448748 ACCAGTGTTTTAGGTGTTATTCATC 57.551 36.000 0.00 0.00 33.57 2.92
3340 3762 7.231467 ACCAGTGTTTTAGGTGTTATTCATCT 58.769 34.615 0.00 0.00 40.95 2.90
3341 3763 8.380099 ACCAGTGTTTTAGGTGTTATTCATCTA 58.620 33.333 0.00 0.00 38.58 1.98
3342 3764 9.396022 CCAGTGTTTTAGGTGTTATTCATCTAT 57.604 33.333 0.00 0.00 39.21 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 5.806654 AGTGTCCTGCCAATTAAAACATT 57.193 34.783 0.00 0.00 0.00 2.71
12 13 1.073763 TGCAACTAGTGTCCTGCCAAT 59.926 47.619 13.36 0.00 31.01 3.16
146 147 7.384660 CCAACTAAACATTAATGTGTGTGCAAT 59.615 33.333 21.46 0.59 41.61 3.56
155 156 6.010219 AGTCCTGCCAACTAAACATTAATGT 58.990 36.000 15.47 15.47 44.20 2.71
160 161 5.418840 CCAATAGTCCTGCCAACTAAACATT 59.581 40.000 0.00 0.00 33.19 2.71
238 241 5.888161 CCAATAGTCCTTCTGCCAACTAAAT 59.112 40.000 0.00 0.00 0.00 1.40
283 286 2.881074 CAACTAGAGTACATGCAGCGT 58.119 47.619 0.00 0.00 0.00 5.07
328 331 4.293415 TGTTTCGACGAACTAGTCTTTCC 58.707 43.478 10.38 0.00 38.90 3.13
330 333 4.922103 GGATGTTTCGACGAACTAGTCTTT 59.078 41.667 10.38 0.00 38.90 2.52
384 388 1.375396 CACCGTTGGAATCCTCGCA 60.375 57.895 0.00 0.00 0.00 5.10
407 411 2.739913 CGCACTTCGGAATTAAGAACCA 59.260 45.455 0.00 0.00 33.78 3.67
410 414 4.755411 AGATCGCACTTCGGAATTAAGAA 58.245 39.130 0.00 0.00 39.05 2.52
478 482 6.432607 AGCAAACATGTGAACAGATATGAG 57.567 37.500 0.00 0.00 0.00 2.90
623 628 2.232452 CTCTCTCTCTCGCCAAAAAGGA 59.768 50.000 0.00 0.00 41.22 3.36
643 648 3.580319 GCCCACCACACTTCCCCT 61.580 66.667 0.00 0.00 0.00 4.79
644 649 3.580319 AGCCCACCACACTTCCCC 61.580 66.667 0.00 0.00 0.00 4.81
645 650 2.282462 CAGCCCACCACACTTCCC 60.282 66.667 0.00 0.00 0.00 3.97
646 651 2.282462 CCAGCCCACCACACTTCC 60.282 66.667 0.00 0.00 0.00 3.46
647 652 1.898574 CACCAGCCCACCACACTTC 60.899 63.158 0.00 0.00 0.00 3.01
648 653 2.195683 CACCAGCCCACCACACTT 59.804 61.111 0.00 0.00 0.00 3.16
649 654 3.889692 CCACCAGCCCACCACACT 61.890 66.667 0.00 0.00 0.00 3.55
668 673 2.685850 ACCTAGCCCGTAATCACAAC 57.314 50.000 0.00 0.00 0.00 3.32
731 736 3.098555 GCCGACAAGCCCGTATTG 58.901 61.111 0.00 0.00 0.00 1.90
769 775 2.775911 TTGCTGATCCTTCTGGACTG 57.224 50.000 0.00 0.00 46.51 3.51
770 776 2.092538 CCATTGCTGATCCTTCTGGACT 60.093 50.000 0.00 0.00 46.51 3.85
772 778 1.409241 GCCATTGCTGATCCTTCTGGA 60.409 52.381 0.00 0.00 39.78 3.86
781 787 0.105593 AGTCGATCGCCATTGCTGAT 59.894 50.000 11.09 0.00 34.81 2.90
785 791 0.447801 AAACAGTCGATCGCCATTGC 59.552 50.000 11.09 0.00 0.00 3.56
851 857 1.025647 ACCGAGTGTACTCCGAGCTC 61.026 60.000 2.73 2.73 39.79 4.09
902 908 4.427661 AGTCTCGCAGCTGTCGCC 62.428 66.667 20.86 13.07 36.60 5.54
904 910 1.069924 CAAGAGTCTCGCAGCTGTCG 61.070 60.000 16.64 18.63 0.00 4.35
961 967 1.697982 GGGCCGATATAAAGGTGGAGT 59.302 52.381 0.00 0.00 0.00 3.85
1135 1141 4.643387 GTGGGCGGTGCTCTTGGT 62.643 66.667 0.00 0.00 0.00 3.67
1343 1354 3.858812 CACAACATGCATATCAAAACCGG 59.141 43.478 0.00 0.00 0.00 5.28
1699 1714 4.154347 GCTCCAGGTCCTGCTCGG 62.154 72.222 13.99 0.00 0.00 4.63
1895 1910 1.144716 CTTCTCCGCCAGCTGCATA 59.855 57.895 8.66 0.00 41.33 3.14
2127 2142 2.877975 GCAAGGTGCTGGTGATGAT 58.122 52.632 0.00 0.00 40.96 2.45
2128 2143 4.402851 GCAAGGTGCTGGTGATGA 57.597 55.556 0.00 0.00 40.96 2.92
2145 2160 6.346896 TCATGGTCAAGATGAGAAGAATCAG 58.653 40.000 0.00 0.00 31.44 2.90
2155 2170 6.334989 GCAATGAATTTCATGGTCAAGATGA 58.665 36.000 12.50 0.00 37.15 2.92
2183 2200 0.249155 CTGCAACCCAGCAACACAAG 60.249 55.000 0.00 0.00 45.13 3.16
2207 2228 5.126396 TGATCTAGCTATTGACGATGGTG 57.874 43.478 0.00 0.00 0.00 4.17
2229 2250 2.570415 TCGCGATCTTCTCTATCCCT 57.430 50.000 3.71 0.00 0.00 4.20
2235 2256 3.191581 TCTTGTTCTTCGCGATCTTCTCT 59.808 43.478 10.88 0.00 0.00 3.10
2242 2263 2.724977 TCACTCTTGTTCTTCGCGAT 57.275 45.000 10.88 0.00 0.00 4.58
2253 2274 1.860950 CACGGACACACTTCACTCTTG 59.139 52.381 0.00 0.00 0.00 3.02
2279 2300 2.357327 TGCTCGTACATACCACACAC 57.643 50.000 0.00 0.00 0.00 3.82
2280 2301 2.297880 ACTTGCTCGTACATACCACACA 59.702 45.455 0.00 0.00 0.00 3.72
2281 2302 2.666508 CACTTGCTCGTACATACCACAC 59.333 50.000 0.00 0.00 0.00 3.82
2282 2303 2.929161 GCACTTGCTCGTACATACCACA 60.929 50.000 0.00 0.00 38.21 4.17
2283 2304 1.659098 GCACTTGCTCGTACATACCAC 59.341 52.381 0.00 0.00 38.21 4.16
2288 2309 2.100631 GCCGCACTTGCTCGTACAT 61.101 57.895 0.00 0.00 39.32 2.29
2303 2324 3.703939 CTCGAGACTCGACACGCCG 62.704 68.421 23.27 9.15 44.82 6.46
2464 2748 0.947244 AGCCGTCTTTGACAAAGCAG 59.053 50.000 20.95 16.22 38.39 4.24
2494 2874 0.249073 CGTCTGATCCGTCCACCATC 60.249 60.000 0.00 0.00 0.00 3.51
2495 2875 0.970937 ACGTCTGATCCGTCCACCAT 60.971 55.000 0.00 0.00 31.97 3.55
2496 2876 1.605451 ACGTCTGATCCGTCCACCA 60.605 57.895 0.00 0.00 31.97 4.17
2497 2877 1.153823 CACGTCTGATCCGTCCACC 60.154 63.158 0.00 0.00 36.17 4.61
2499 2879 0.242825 GTTCACGTCTGATCCGTCCA 59.757 55.000 0.00 0.00 36.17 4.02
2500 2880 0.797249 CGTTCACGTCTGATCCGTCC 60.797 60.000 0.00 0.00 36.17 4.79
2501 2881 0.797249 CCGTTCACGTCTGATCCGTC 60.797 60.000 0.00 0.00 36.17 4.79
2502 2882 1.211969 CCGTTCACGTCTGATCCGT 59.788 57.895 0.00 0.00 39.52 4.69
2503 2883 1.516386 CCCGTTCACGTCTGATCCG 60.516 63.158 0.00 0.00 37.74 4.18
2532 2913 0.399091 TCAGATTCCAGCCTCCGGAT 60.399 55.000 3.57 0.00 30.99 4.18
2539 2920 4.337836 GGAGAAAAGATTCAGATTCCAGCC 59.662 45.833 0.00 0.00 38.06 4.85
2541 2922 5.356470 GGTGGAGAAAAGATTCAGATTCCAG 59.644 44.000 0.00 0.00 37.05 3.86
2569 2950 3.360867 TCTGTAGAGGGAGCTTCTTCTG 58.639 50.000 16.76 0.30 0.00 3.02
2572 2953 3.055458 GCTTTCTGTAGAGGGAGCTTCTT 60.055 47.826 7.75 0.00 0.00 2.52
2598 2997 1.896465 AGGCGCTCTTCACTTTCTACT 59.104 47.619 7.64 0.00 0.00 2.57
2599 2998 2.371910 AGGCGCTCTTCACTTTCTAC 57.628 50.000 7.64 0.00 0.00 2.59
2610 3009 2.094182 TGTCTTCGATTTAAGGCGCTCT 60.094 45.455 7.64 0.00 33.68 4.09
2611 3010 2.268298 TGTCTTCGATTTAAGGCGCTC 58.732 47.619 7.64 0.00 33.68 5.03
2612 3011 2.380084 TGTCTTCGATTTAAGGCGCT 57.620 45.000 7.64 0.00 33.68 5.92
2613 3012 2.351726 ACATGTCTTCGATTTAAGGCGC 59.648 45.455 0.00 0.00 33.68 6.53
2614 3013 3.370978 ACACATGTCTTCGATTTAAGGCG 59.629 43.478 0.00 0.00 33.68 5.52
2615 3014 4.651994 CACACATGTCTTCGATTTAAGGC 58.348 43.478 0.00 0.00 0.00 4.35
2616 3015 4.154015 TGCACACATGTCTTCGATTTAAGG 59.846 41.667 0.00 0.00 0.00 2.69
2617 3016 5.106948 ACTGCACACATGTCTTCGATTTAAG 60.107 40.000 0.00 0.00 0.00 1.85
2618 3017 4.754618 ACTGCACACATGTCTTCGATTTAA 59.245 37.500 0.00 0.00 0.00 1.52
2619 3018 4.314961 ACTGCACACATGTCTTCGATTTA 58.685 39.130 0.00 0.00 0.00 1.40
2620 3019 3.141398 ACTGCACACATGTCTTCGATTT 58.859 40.909 0.00 0.00 0.00 2.17
2621 3020 2.771089 ACTGCACACATGTCTTCGATT 58.229 42.857 0.00 0.00 0.00 3.34
2622 3021 2.462456 ACTGCACACATGTCTTCGAT 57.538 45.000 0.00 0.00 0.00 3.59
2645 3051 7.968405 GTGACTTCTGCTTCAAAAGAAAGTTAA 59.032 33.333 0.00 0.00 32.23 2.01
2652 3058 4.094887 GTGTGTGACTTCTGCTTCAAAAGA 59.905 41.667 0.00 0.00 0.00 2.52
2668 3074 2.501316 CAGGGGTATCAGATGTGTGTGA 59.499 50.000 0.00 0.00 31.56 3.58
2716 3122 1.328279 AGGTTTTCTTTGAAGCCCCG 58.672 50.000 0.00 0.00 30.94 5.73
2730 3136 7.651704 CACTTTCGTTCATCCAAATTAAGGTTT 59.348 33.333 0.00 0.00 0.00 3.27
2733 3139 6.908825 TCACTTTCGTTCATCCAAATTAAGG 58.091 36.000 0.00 0.00 0.00 2.69
2759 3165 9.283768 TCACTTGATATTTAATGTGTCAACACT 57.716 29.630 13.94 0.00 46.55 3.55
2805 3213 1.021390 GTGATGGTCAGGGCGTTCTG 61.021 60.000 1.54 1.54 36.17 3.02
3003 3425 6.127366 TGTTGAGAAAGCTTTTCAATGAACCT 60.127 34.615 25.58 12.94 33.82 3.50
3012 3434 9.425893 GCTTTAAAAATGTTGAGAAAGCTTTTC 57.574 29.630 14.05 12.73 43.34 2.29
3022 3444 8.514594 TCTAGATGGTGCTTTAAAAATGTTGAG 58.485 33.333 0.00 0.00 0.00 3.02
3032 3454 4.345257 CCTAGGCTCTAGATGGTGCTTTAA 59.655 45.833 0.00 0.00 0.00 1.52
3046 3468 7.866870 AGATCAAAGATAAAAACCTAGGCTCT 58.133 34.615 9.30 0.00 0.00 4.09
3047 3469 9.047371 GTAGATCAAAGATAAAAACCTAGGCTC 57.953 37.037 9.30 0.00 0.00 4.70
3121 3543 9.914834 TGGGCATTTGTACTAATCTTAGTTTAT 57.085 29.630 7.84 0.00 40.96 1.40
3122 3544 9.914834 ATGGGCATTTGTACTAATCTTAGTTTA 57.085 29.630 7.84 0.00 40.96 2.01
3123 3545 8.686334 CATGGGCATTTGTACTAATCTTAGTTT 58.314 33.333 7.84 0.00 40.96 2.66
3124 3546 7.834181 ACATGGGCATTTGTACTAATCTTAGTT 59.166 33.333 7.84 0.00 40.96 2.24
3125 3547 7.283127 CACATGGGCATTTGTACTAATCTTAGT 59.717 37.037 7.68 7.68 45.39 2.24
3126 3548 7.283127 ACACATGGGCATTTGTACTAATCTTAG 59.717 37.037 0.00 0.00 30.66 2.18
3127 3549 7.116075 ACACATGGGCATTTGTACTAATCTTA 58.884 34.615 0.00 0.00 30.66 2.10
3128 3550 5.951747 ACACATGGGCATTTGTACTAATCTT 59.048 36.000 0.00 0.00 30.66 2.40
3129 3551 5.509498 ACACATGGGCATTTGTACTAATCT 58.491 37.500 0.00 0.00 30.66 2.40
3130 3552 5.835113 ACACATGGGCATTTGTACTAATC 57.165 39.130 0.00 0.00 30.66 1.75
3131 3553 5.624281 GCAACACATGGGCATTTGTACTAAT 60.624 40.000 0.00 0.00 31.15 1.73
3132 3554 4.321601 GCAACACATGGGCATTTGTACTAA 60.322 41.667 0.00 0.00 31.15 2.24
3133 3555 3.192422 GCAACACATGGGCATTTGTACTA 59.808 43.478 0.00 0.00 31.15 1.82
3134 3556 2.029110 GCAACACATGGGCATTTGTACT 60.029 45.455 0.00 0.00 31.15 2.73
3135 3557 2.288702 TGCAACACATGGGCATTTGTAC 60.289 45.455 0.00 0.00 31.15 2.90
3136 3558 1.966354 TGCAACACATGGGCATTTGTA 59.034 42.857 0.00 0.00 31.15 2.41
3137 3559 0.757512 TGCAACACATGGGCATTTGT 59.242 45.000 0.00 0.00 33.54 2.83
3138 3560 1.532007 GTTGCAACACATGGGCATTTG 59.468 47.619 24.52 0.00 37.39 2.32
3139 3561 1.873069 CGTTGCAACACATGGGCATTT 60.873 47.619 28.01 0.00 37.39 2.32
3140 3562 0.319727 CGTTGCAACACATGGGCATT 60.320 50.000 28.01 0.00 37.39 3.56
3141 3563 1.289694 CGTTGCAACACATGGGCAT 59.710 52.632 28.01 0.00 37.39 4.40
3142 3564 2.726909 CGTTGCAACACATGGGCA 59.273 55.556 28.01 0.00 35.41 5.36
3143 3565 2.049248 CCGTTGCAACACATGGGC 60.049 61.111 28.01 0.00 0.00 5.36
3144 3566 0.039256 CTTCCGTTGCAACACATGGG 60.039 55.000 28.01 19.95 0.00 4.00
3145 3567 0.950836 TCTTCCGTTGCAACACATGG 59.049 50.000 28.01 20.30 0.00 3.66
3146 3568 1.333308 TGTCTTCCGTTGCAACACATG 59.667 47.619 28.01 15.31 0.00 3.21
3147 3569 1.674359 TGTCTTCCGTTGCAACACAT 58.326 45.000 28.01 0.00 0.00 3.21
3148 3570 1.454201 TTGTCTTCCGTTGCAACACA 58.546 45.000 28.01 20.52 0.00 3.72
3149 3571 2.553079 TTTGTCTTCCGTTGCAACAC 57.447 45.000 28.01 18.28 0.00 3.32
3150 3572 2.490115 AGTTTTGTCTTCCGTTGCAACA 59.510 40.909 28.01 7.99 0.00 3.33
3151 3573 2.851824 CAGTTTTGTCTTCCGTTGCAAC 59.148 45.455 19.89 19.89 0.00 4.17
3152 3574 2.750166 TCAGTTTTGTCTTCCGTTGCAA 59.250 40.909 0.00 0.00 0.00 4.08
3153 3575 2.096819 GTCAGTTTTGTCTTCCGTTGCA 59.903 45.455 0.00 0.00 0.00 4.08
3154 3576 2.096819 TGTCAGTTTTGTCTTCCGTTGC 59.903 45.455 0.00 0.00 0.00 4.17
3155 3577 4.035091 TCATGTCAGTTTTGTCTTCCGTTG 59.965 41.667 0.00 0.00 0.00 4.10
3156 3578 4.035208 GTCATGTCAGTTTTGTCTTCCGTT 59.965 41.667 0.00 0.00 0.00 4.44
3157 3579 3.560068 GTCATGTCAGTTTTGTCTTCCGT 59.440 43.478 0.00 0.00 0.00 4.69
3158 3580 3.559655 TGTCATGTCAGTTTTGTCTTCCG 59.440 43.478 0.00 0.00 0.00 4.30
3159 3581 5.239306 TCATGTCATGTCAGTTTTGTCTTCC 59.761 40.000 12.54 0.00 0.00 3.46
3160 3582 6.304356 TCATGTCATGTCAGTTTTGTCTTC 57.696 37.500 12.54 0.00 0.00 2.87
3161 3583 6.319658 AGTTCATGTCATGTCAGTTTTGTCTT 59.680 34.615 12.54 0.00 0.00 3.01
3162 3584 5.824624 AGTTCATGTCATGTCAGTTTTGTCT 59.175 36.000 12.54 0.00 0.00 3.41
3163 3585 6.064846 AGTTCATGTCATGTCAGTTTTGTC 57.935 37.500 12.54 0.00 0.00 3.18
3164 3586 5.277490 CGAGTTCATGTCATGTCAGTTTTGT 60.277 40.000 12.54 0.00 0.00 2.83
3165 3587 5.142265 CGAGTTCATGTCATGTCAGTTTTG 58.858 41.667 12.54 0.00 0.00 2.44
3166 3588 4.319766 GCGAGTTCATGTCATGTCAGTTTT 60.320 41.667 12.54 0.00 0.00 2.43
3167 3589 3.187227 GCGAGTTCATGTCATGTCAGTTT 59.813 43.478 12.54 0.00 0.00 2.66
3168 3590 2.738846 GCGAGTTCATGTCATGTCAGTT 59.261 45.455 12.54 0.00 0.00 3.16
3169 3591 2.341257 GCGAGTTCATGTCATGTCAGT 58.659 47.619 12.54 4.10 0.00 3.41
3170 3592 1.662629 GGCGAGTTCATGTCATGTCAG 59.337 52.381 12.54 7.11 0.00 3.51
3171 3593 1.276138 AGGCGAGTTCATGTCATGTCA 59.724 47.619 12.54 0.00 0.00 3.58
3172 3594 2.015736 AGGCGAGTTCATGTCATGTC 57.984 50.000 12.54 7.51 0.00 3.06
3173 3595 2.159043 CCTAGGCGAGTTCATGTCATGT 60.159 50.000 12.54 0.00 0.00 3.21
3174 3596 2.159043 ACCTAGGCGAGTTCATGTCATG 60.159 50.000 9.30 6.47 0.00 3.07
3175 3597 2.111384 ACCTAGGCGAGTTCATGTCAT 58.889 47.619 9.30 0.00 0.00 3.06
3176 3598 1.204704 CACCTAGGCGAGTTCATGTCA 59.795 52.381 9.30 0.00 0.00 3.58
3177 3599 1.476891 TCACCTAGGCGAGTTCATGTC 59.523 52.381 9.30 0.00 0.00 3.06
3178 3600 1.557099 TCACCTAGGCGAGTTCATGT 58.443 50.000 9.30 0.00 0.00 3.21
3179 3601 2.672961 TTCACCTAGGCGAGTTCATG 57.327 50.000 9.30 0.00 0.00 3.07
3180 3602 3.704566 TGTATTCACCTAGGCGAGTTCAT 59.295 43.478 9.30 0.00 0.00 2.57
3181 3603 3.093814 TGTATTCACCTAGGCGAGTTCA 58.906 45.455 9.30 2.92 0.00 3.18
3182 3604 3.119245 TGTGTATTCACCTAGGCGAGTTC 60.119 47.826 9.30 0.00 43.26 3.01
3183 3605 2.829720 TGTGTATTCACCTAGGCGAGTT 59.170 45.455 9.30 0.00 43.26 3.01
3184 3606 2.453521 TGTGTATTCACCTAGGCGAGT 58.546 47.619 9.30 4.09 43.26 4.18
3185 3607 3.735237 ATGTGTATTCACCTAGGCGAG 57.265 47.619 9.30 0.00 43.26 5.03
3186 3608 4.037565 CACTATGTGTATTCACCTAGGCGA 59.962 45.833 9.30 0.69 42.73 5.54
3187 3609 4.037565 TCACTATGTGTATTCACCTAGGCG 59.962 45.833 9.30 0.00 42.73 5.52
3188 3610 5.531122 TCACTATGTGTATTCACCTAGGC 57.469 43.478 9.30 0.00 42.73 3.93
3189 3611 7.290110 TCATCACTATGTGTATTCACCTAGG 57.710 40.000 7.41 7.41 42.73 3.02
3190 3612 9.770097 AAATCATCACTATGTGTATTCACCTAG 57.230 33.333 11.48 11.48 43.46 3.02
3191 3613 9.764363 GAAATCATCACTATGTGTATTCACCTA 57.236 33.333 0.00 0.00 43.26 3.08
3192 3614 8.267183 TGAAATCATCACTATGTGTATTCACCT 58.733 33.333 0.00 0.00 37.14 4.00
3193 3615 8.437360 TGAAATCATCACTATGTGTATTCACC 57.563 34.615 0.00 0.00 37.14 4.02
3208 3630 9.985730 GGCCATAAAGAAATAATGAAATCATCA 57.014 29.630 0.00 0.00 43.67 3.07
3214 3636 7.981225 GCTGAAGGCCATAAAGAAATAATGAAA 59.019 33.333 5.01 0.00 34.27 2.69
3215 3637 7.491682 GCTGAAGGCCATAAAGAAATAATGAA 58.508 34.615 5.01 0.00 34.27 2.57
3216 3638 7.042797 GCTGAAGGCCATAAAGAAATAATGA 57.957 36.000 5.01 0.00 34.27 2.57
3232 3654 4.640201 TGTAAAGATTGTATGGCTGAAGGC 59.360 41.667 0.00 0.00 41.50 4.35
3233 3655 6.757897 TTGTAAAGATTGTATGGCTGAAGG 57.242 37.500 0.00 0.00 0.00 3.46
3234 3656 7.542130 GGTTTTGTAAAGATTGTATGGCTGAAG 59.458 37.037 0.00 0.00 0.00 3.02
3235 3657 7.375053 GGTTTTGTAAAGATTGTATGGCTGAA 58.625 34.615 0.00 0.00 0.00 3.02
3236 3658 6.348950 CGGTTTTGTAAAGATTGTATGGCTGA 60.349 38.462 0.00 0.00 0.00 4.26
3237 3659 5.799936 CGGTTTTGTAAAGATTGTATGGCTG 59.200 40.000 0.00 0.00 0.00 4.85
3238 3660 5.621329 GCGGTTTTGTAAAGATTGTATGGCT 60.621 40.000 0.00 0.00 0.00 4.75
3239 3661 4.561213 GCGGTTTTGTAAAGATTGTATGGC 59.439 41.667 0.00 0.00 0.00 4.40
3240 3662 5.949735 AGCGGTTTTGTAAAGATTGTATGG 58.050 37.500 0.00 0.00 0.00 2.74
3241 3663 7.523219 TGTAGCGGTTTTGTAAAGATTGTATG 58.477 34.615 0.00 0.00 0.00 2.39
3242 3664 7.675962 TGTAGCGGTTTTGTAAAGATTGTAT 57.324 32.000 0.00 0.00 0.00 2.29
3243 3665 7.493743 TTGTAGCGGTTTTGTAAAGATTGTA 57.506 32.000 0.00 0.00 0.00 2.41
3244 3666 6.380095 TTGTAGCGGTTTTGTAAAGATTGT 57.620 33.333 0.00 0.00 0.00 2.71
3245 3667 7.687005 TTTTGTAGCGGTTTTGTAAAGATTG 57.313 32.000 0.00 0.00 0.00 2.67
3247 3669 9.567848 CATATTTTGTAGCGGTTTTGTAAAGAT 57.432 29.630 0.00 0.00 0.00 2.40
3248 3670 8.569641 ACATATTTTGTAGCGGTTTTGTAAAGA 58.430 29.630 0.00 0.00 36.57 2.52
3249 3671 8.635124 CACATATTTTGTAGCGGTTTTGTAAAG 58.365 33.333 0.00 0.00 36.57 1.85
3250 3672 7.115095 GCACATATTTTGTAGCGGTTTTGTAAA 59.885 33.333 0.00 0.00 36.57 2.01
3251 3673 6.583050 GCACATATTTTGTAGCGGTTTTGTAA 59.417 34.615 0.00 0.00 36.57 2.41
3252 3674 6.087522 GCACATATTTTGTAGCGGTTTTGTA 58.912 36.000 0.00 0.00 36.57 2.41
3253 3675 4.920927 GCACATATTTTGTAGCGGTTTTGT 59.079 37.500 0.00 0.00 36.57 2.83
3254 3676 4.920340 TGCACATATTTTGTAGCGGTTTTG 59.080 37.500 0.00 0.00 36.57 2.44
3255 3677 5.127693 TGCACATATTTTGTAGCGGTTTT 57.872 34.783 0.00 0.00 36.57 2.43
3256 3678 4.775058 TGCACATATTTTGTAGCGGTTT 57.225 36.364 0.00 0.00 36.57 3.27
3257 3679 4.981806 ATGCACATATTTTGTAGCGGTT 57.018 36.364 0.00 0.00 36.57 4.44
3258 3680 4.981806 AATGCACATATTTTGTAGCGGT 57.018 36.364 0.00 0.00 36.57 5.68
3259 3681 7.138081 TGAATAATGCACATATTTTGTAGCGG 58.862 34.615 7.74 0.00 36.57 5.52
3260 3682 8.732413 ATGAATAATGCACATATTTTGTAGCG 57.268 30.769 7.74 0.00 36.57 4.26
3271 3693 8.967664 AAAGCCATAAAATGAATAATGCACAT 57.032 26.923 0.00 0.00 0.00 3.21
3272 3694 8.789825 AAAAGCCATAAAATGAATAATGCACA 57.210 26.923 0.00 0.00 0.00 4.57
3273 3695 9.101655 AGAAAAGCCATAAAATGAATAATGCAC 57.898 29.630 0.00 0.00 0.00 4.57
3306 3728 9.582648 AACACCTAAAACACTGGTTATAGAAAT 57.417 29.630 0.00 0.00 35.82 2.17
3307 3729 8.983702 AACACCTAAAACACTGGTTATAGAAA 57.016 30.769 0.00 0.00 35.82 2.52
3312 3734 8.927675 TGAATAACACCTAAAACACTGGTTAT 57.072 30.769 0.00 0.00 35.82 1.89
3313 3735 8.927675 ATGAATAACACCTAAAACACTGGTTA 57.072 30.769 0.00 0.00 35.82 2.85
3314 3736 7.724061 AGATGAATAACACCTAAAACACTGGTT 59.276 33.333 0.00 0.00 39.43 3.67
3315 3737 7.231467 AGATGAATAACACCTAAAACACTGGT 58.769 34.615 0.00 0.00 33.87 4.00
3316 3738 7.687941 AGATGAATAACACCTAAAACACTGG 57.312 36.000 0.00 0.00 0.00 4.00
3419 3841 9.653287 CATACATCCGTATGTTATAGTCCAATT 57.347 33.333 0.00 0.00 46.70 2.32


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

AutoCloner maintained by Alex Coulton.