Multiple sequence alignment - TraesCS2A01G284600

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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 TraesCS2A01G284600 chr2A 100.000 2627 0 0 1 2627 478455590 478458216 0.000000e+00 4852.0
1 TraesCS2A01G284600 chr2A 94.488 1651 91 0 1 1651 33472830 33471180 0.000000e+00 2545.0
2 TraesCS2A01G284600 chr2A 94.737 152 7 1 2299 2449 251408295 251408446 4.370000e-58 235.0
3 TraesCS2A01G284600 chr2A 87.000 100 12 1 2525 2624 353449257 353449355 7.690000e-21 111.0
4 TraesCS2A01G284600 chr5D 96.065 1652 64 1 1 1651 375001991 375003642 0.000000e+00 2689.0
5 TraesCS2A01G284600 chr5D 95.039 1653 79 3 1 1651 184453024 184454675 0.000000e+00 2595.0
6 TraesCS2A01G284600 chr5D 94.791 1651 85 1 1 1651 397473181 397471532 0.000000e+00 2571.0
7 TraesCS2A01G284600 chr5D 93.864 1646 96 3 3 1648 397466574 397468214 0.000000e+00 2475.0
8 TraesCS2A01G284600 chr5D 91.908 655 46 7 1651 2300 184455153 184455805 0.000000e+00 909.0
9 TraesCS2A01G284600 chr5D 90.491 652 55 5 1651 2300 375004121 375004767 0.000000e+00 854.0
10 TraesCS2A01G284600 chr5D 95.946 148 5 1 2306 2453 235595443 235595589 3.380000e-59 239.0
11 TraesCS2A01G284600 chr1D 96.002 1651 66 0 1 1651 393952163 393950513 0.000000e+00 2684.0
12 TraesCS2A01G284600 chr1D 91.271 653 44 9 1651 2300 422495843 422496485 0.000000e+00 878.0
13 TraesCS2A01G284600 chr1D 97.203 143 4 0 2306 2448 265139706 265139564 2.610000e-60 243.0
14 TraesCS2A01G284600 chr7A 95.518 1651 70 2 1 1651 692229365 692231011 0.000000e+00 2636.0
15 TraesCS2A01G284600 chr6B 93.164 1653 111 2 1 1651 666360969 666359317 0.000000e+00 2425.0
16 TraesCS2A01G284600 chr6B 84.043 94 12 3 2536 2627 602075605 602075697 1.300000e-13 87.9
17 TraesCS2A01G284600 chr6B 84.444 90 10 4 2541 2627 601887611 601887699 4.660000e-13 86.1
18 TraesCS2A01G284600 chr3A 94.961 1528 76 1 124 1651 720600566 720599040 0.000000e+00 2394.0
19 TraesCS2A01G284600 chr3A 92.958 213 15 0 1 213 31316393 31316181 7.060000e-81 311.0
20 TraesCS2A01G284600 chr3A 95.946 148 5 1 2306 2452 462639809 462639956 3.380000e-59 239.0
21 TraesCS2A01G284600 chr3A 91.503 153 12 1 2298 2450 609178332 609178181 2.650000e-50 209.0
22 TraesCS2A01G284600 chr1A 95.706 652 22 4 1651 2300 205579572 205580219 0.000000e+00 1044.0
23 TraesCS2A01G284600 chr1A 90.789 228 21 0 1424 1651 205578866 205579093 3.280000e-79 305.0
24 TraesCS2A01G284600 chr4A 93.241 651 37 4 1651 2300 444379903 444380547 0.000000e+00 952.0
25 TraesCS2A01G284600 chr4A 91.054 626 51 4 1651 2274 591537498 591536876 0.000000e+00 841.0
26 TraesCS2A01G284600 chr4A 91.054 626 51 4 1651 2274 593074000 593074622 0.000000e+00 841.0
27 TraesCS2A01G284600 chr4A 90.415 626 52 7 1651 2274 592786440 592787059 0.000000e+00 817.0
28 TraesCS2A01G284600 chr4A 97.222 144 4 0 2306 2449 444380518 444380661 7.260000e-61 244.0
29 TraesCS2A01G284600 chr4A 94.231 156 6 3 2299 2452 588445249 588445403 4.370000e-58 235.0
30 TraesCS2A01G284600 chr7D 91.564 652 44 8 1651 2300 39864471 39865113 0.000000e+00 889.0
31 TraesCS2A01G284600 chr7D 94.821 251 11 2 2053 2303 597713091 597712843 8.820000e-105 390.0
32 TraesCS2A01G284600 chr7D 96.622 148 4 1 2306 2452 7974239 7974092 7.260000e-61 244.0
33 TraesCS2A01G284600 chr7D 97.222 144 4 0 2306 2449 596783047 596782904 7.260000e-61 244.0
34 TraesCS2A01G284600 chr7D 92.958 142 10 0 2308 2449 90563841 90563700 9.530000e-50 207.0
35 TraesCS2A01G284600 chr3B 90.337 652 57 4 1651 2300 442047133 442047780 0.000000e+00 850.0
36 TraesCS2A01G284600 chr4B 90.735 626 52 5 1651 2274 20344939 20344318 0.000000e+00 830.0
37 TraesCS2A01G284600 chr4B 80.132 151 29 1 2475 2625 348954365 348954514 7.690000e-21 111.0
38 TraesCS2A01G284600 chr4B 80.986 142 21 4 2476 2615 481015126 481014989 9.940000e-20 108.0
39 TraesCS2A01G284600 chr2B 97.241 145 3 1 2306 2449 402093437 402093581 7.260000e-61 244.0
40 TraesCS2A01G284600 chr6A 93.548 155 6 3 2299 2449 615503215 615503369 7.310000e-56 228.0
41 TraesCS2A01G284600 chr6A 90.789 152 13 1 2299 2449 325081199 325081048 4.430000e-48 202.0
42 TraesCS2A01G284600 chr5A 92.715 151 10 1 2298 2448 379859000 379859149 1.580000e-52 217.0
43 TraesCS2A01G284600 chr7B 90.789 152 12 2 2298 2449 711417442 711417591 4.430000e-48 202.0
44 TraesCS2A01G284600 chr7B 79.310 145 28 2 2471 2615 401563845 401563703 1.660000e-17 100.0
45 TraesCS2A01G284600 chr1B 92.806 139 9 1 2314 2452 23779576 23779439 1.590000e-47 200.0
46 TraesCS2A01G284600 chr5B 81.699 153 25 3 2473 2624 315259921 315259771 9.870000e-25 124.0
47 TraesCS2A01G284600 chr6D 77.922 154 29 5 2473 2625 49129724 49129873 1.000000e-14 91.6
48 TraesCS2A01G284600 chr6D 89.231 65 7 0 2563 2627 372023817 372023753 6.030000e-12 82.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G284600 chr2A 478455590 478458216 2626 False 4852.0 4852 100.0000 1 2627 1 chr2A.!!$F3 2626
1 TraesCS2A01G284600 chr2A 33471180 33472830 1650 True 2545.0 2545 94.4880 1 1651 1 chr2A.!!$R1 1650
2 TraesCS2A01G284600 chr5D 397471532 397473181 1649 True 2571.0 2571 94.7910 1 1651 1 chr5D.!!$R1 1650
3 TraesCS2A01G284600 chr5D 397466574 397468214 1640 False 2475.0 2475 93.8640 3 1648 1 chr5D.!!$F2 1645
4 TraesCS2A01G284600 chr5D 375001991 375004767 2776 False 1771.5 2689 93.2780 1 2300 2 chr5D.!!$F4 2299
5 TraesCS2A01G284600 chr5D 184453024 184455805 2781 False 1752.0 2595 93.4735 1 2300 2 chr5D.!!$F3 2299
6 TraesCS2A01G284600 chr1D 393950513 393952163 1650 True 2684.0 2684 96.0020 1 1651 1 chr1D.!!$R2 1650
7 TraesCS2A01G284600 chr1D 422495843 422496485 642 False 878.0 878 91.2710 1651 2300 1 chr1D.!!$F1 649
8 TraesCS2A01G284600 chr7A 692229365 692231011 1646 False 2636.0 2636 95.5180 1 1651 1 chr7A.!!$F1 1650
9 TraesCS2A01G284600 chr6B 666359317 666360969 1652 True 2425.0 2425 93.1640 1 1651 1 chr6B.!!$R1 1650
10 TraesCS2A01G284600 chr3A 720599040 720600566 1526 True 2394.0 2394 94.9610 124 1651 1 chr3A.!!$R3 1527
11 TraesCS2A01G284600 chr1A 205578866 205580219 1353 False 674.5 1044 93.2475 1424 2300 2 chr1A.!!$F1 876
12 TraesCS2A01G284600 chr4A 591536876 591537498 622 True 841.0 841 91.0540 1651 2274 1 chr4A.!!$R1 623
13 TraesCS2A01G284600 chr4A 593074000 593074622 622 False 841.0 841 91.0540 1651 2274 1 chr4A.!!$F3 623
14 TraesCS2A01G284600 chr4A 592786440 592787059 619 False 817.0 817 90.4150 1651 2274 1 chr4A.!!$F2 623
15 TraesCS2A01G284600 chr4A 444379903 444380661 758 False 598.0 952 95.2315 1651 2449 2 chr4A.!!$F4 798
16 TraesCS2A01G284600 chr7D 39864471 39865113 642 False 889.0 889 91.5640 1651 2300 1 chr7D.!!$F1 649
17 TraesCS2A01G284600 chr3B 442047133 442047780 647 False 850.0 850 90.3370 1651 2300 1 chr3B.!!$F1 649
18 TraesCS2A01G284600 chr4B 20344318 20344939 621 True 830.0 830 90.7350 1651 2274 1 chr4B.!!$R1 623

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
794 801 0.394488 TCGGCACCTTCACCAAACAA 60.394 50.0 0.0 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2333 2838 0.249953 TCAAAAGCTGGCGGTCGTAA 60.25 50.0 0.0 0.0 0.0 3.18 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
46 47 9.317827 TGGATGATTATCTCAGATCAGATGTTA 57.682 33.333 5.94 0.00 37.28 2.41
87 88 1.069049 GCTTTTGTCACCAAGCCACAT 59.931 47.619 5.03 0.00 39.70 3.21
102 103 8.220559 ACCAAGCCACATAAATCATCTAGTTAT 58.779 33.333 0.00 0.00 0.00 1.89
135 136 3.845781 ACGCTAGGGTGATGAATGAAT 57.154 42.857 12.26 0.00 0.00 2.57
205 206 1.329171 TTTGTGGTTGCAGCAAGCCT 61.329 50.000 29.78 0.00 44.83 4.58
413 415 5.645929 TCTTGTTGTTTCAGTCAAGTGCTTA 59.354 36.000 0.00 0.00 38.53 3.09
478 481 1.250154 TTCATTTCCTTGCCAGGCCG 61.250 55.000 9.64 0.00 40.58 6.13
580 586 7.502226 AGGTTCTTTGTTCTTATCACATGTTGA 59.498 33.333 0.00 0.00 39.11 3.18
739 746 6.434340 CCTTTCCTTACTCATACAAAAAGCCT 59.566 38.462 0.00 0.00 0.00 4.58
794 801 0.394488 TCGGCACCTTCACCAAACAA 60.394 50.000 0.00 0.00 0.00 2.83
854 863 4.385358 AGCGCCCCTAAATTTAAACATG 57.615 40.909 2.29 0.00 0.00 3.21
891 900 9.357652 CTGAAAACTCATTGTTCTTTTCTGAAA 57.642 29.630 0.00 0.00 38.03 2.69
918 927 3.751175 GCAAACATTGAGCAGTGGTACTA 59.249 43.478 0.00 0.00 0.00 1.82
965 974 1.005630 GCTTCACTCGTGTCTGCCT 60.006 57.895 0.00 0.00 0.00 4.75
1035 1044 3.204827 GCAGCGTGGGCAATCGAT 61.205 61.111 0.00 0.00 43.41 3.59
1101 1111 5.067283 GGAGAACTTTTAGCTTTTCCACACA 59.933 40.000 0.00 0.00 0.00 3.72
1176 1186 5.942236 AGAAATCTTTGATGCTAACTCTGCA 59.058 36.000 0.00 0.00 44.95 4.41
1414 1424 2.978824 GCACAAGGTCGCTCCCTA 59.021 61.111 0.00 0.00 36.75 3.53
1443 1453 3.310774 CCTGTTCATTTATCTGTCCAGCG 59.689 47.826 0.00 0.00 0.00 5.18
1462 1472 2.484770 GCGCAATCCTACATTCCTACCA 60.485 50.000 0.30 0.00 0.00 3.25
1529 1539 6.455647 ACTGTCTGTCAATCGAATCAAACTA 58.544 36.000 0.00 0.00 0.00 2.24
1623 1633 1.599071 TGCTTTTCTCTTGCTCACGTG 59.401 47.619 9.94 9.94 0.00 4.49
1631 1641 3.133946 TGCTCACGTGTAGCACCA 58.866 55.556 27.55 13.46 44.78 4.17
1638 1648 0.963856 ACGTGTAGCACCATCTCCGA 60.964 55.000 0.00 0.00 0.00 4.55
1859 2348 2.544685 TGTGCCCAAACAATTTTGTCG 58.455 42.857 0.00 0.00 41.31 4.35
2087 2592 1.287442 TGGGCTGAATTAATGGGCTCA 59.713 47.619 0.00 0.00 0.00 4.26
2139 2644 6.349363 GGCTGAATCTTATCAACGACCTTTTT 60.349 38.462 0.00 0.00 0.00 1.94
2277 2782 3.399330 GAATTCCACGACCTTCTCACAA 58.601 45.455 0.00 0.00 0.00 3.33
2300 2805 7.913821 ACAAAGAAGGTCGTTAATTTCAGTTTC 59.086 33.333 0.00 0.00 0.00 2.78
2301 2806 6.555812 AGAAGGTCGTTAATTTCAGTTTCC 57.444 37.500 0.00 0.00 0.00 3.13
2302 2807 6.059484 AGAAGGTCGTTAATTTCAGTTTCCA 58.941 36.000 0.00 0.00 0.00 3.53
2303 2808 5.684550 AGGTCGTTAATTTCAGTTTCCAC 57.315 39.130 0.00 0.00 0.00 4.02
2304 2809 4.212636 AGGTCGTTAATTTCAGTTTCCACG 59.787 41.667 0.00 0.00 0.00 4.94
2305 2810 4.024641 GGTCGTTAATTTCAGTTTCCACGT 60.025 41.667 0.00 0.00 0.00 4.49
2306 2811 5.135330 GTCGTTAATTTCAGTTTCCACGTC 58.865 41.667 0.00 0.00 0.00 4.34
2307 2812 5.050567 GTCGTTAATTTCAGTTTCCACGTCT 60.051 40.000 0.00 0.00 0.00 4.18
2308 2813 5.176223 TCGTTAATTTCAGTTTCCACGTCTC 59.824 40.000 0.00 0.00 0.00 3.36
2309 2814 5.050634 CGTTAATTTCAGTTTCCACGTCTCA 60.051 40.000 0.00 0.00 0.00 3.27
2310 2815 4.813296 AATTTCAGTTTCCACGTCTCAC 57.187 40.909 0.00 0.00 0.00 3.51
2311 2816 2.971660 TTCAGTTTCCACGTCTCACA 57.028 45.000 0.00 0.00 0.00 3.58
2312 2817 2.509052 TCAGTTTCCACGTCTCACAG 57.491 50.000 0.00 0.00 0.00 3.66
2313 2818 2.028876 TCAGTTTCCACGTCTCACAGA 58.971 47.619 0.00 0.00 0.00 3.41
2314 2819 2.034685 TCAGTTTCCACGTCTCACAGAG 59.965 50.000 0.00 0.00 0.00 3.35
2315 2820 2.034685 CAGTTTCCACGTCTCACAGAGA 59.965 50.000 0.00 0.00 36.22 3.10
2316 2821 2.693591 AGTTTCCACGTCTCACAGAGAA 59.306 45.455 0.00 0.00 40.59 2.87
2317 2822 3.053455 GTTTCCACGTCTCACAGAGAAG 58.947 50.000 8.13 8.13 40.59 2.85
2318 2823 1.248486 TCCACGTCTCACAGAGAAGG 58.752 55.000 13.10 9.12 41.22 3.46
2319 2824 0.962489 CCACGTCTCACAGAGAAGGT 59.038 55.000 13.10 5.76 41.22 3.50
2320 2825 1.068194 CCACGTCTCACAGAGAAGGTC 60.068 57.143 13.10 0.00 41.22 3.85
2321 2826 0.875728 ACGTCTCACAGAGAAGGTCG 59.124 55.000 13.10 8.50 41.22 4.79
2322 2827 0.875728 CGTCTCACAGAGAAGGTCGT 59.124 55.000 0.00 0.00 40.59 4.34
2323 2828 1.267261 CGTCTCACAGAGAAGGTCGTT 59.733 52.381 0.00 0.00 40.59 3.85
2324 2829 2.483106 CGTCTCACAGAGAAGGTCGTTA 59.517 50.000 0.00 0.00 40.59 3.18
2325 2830 3.058432 CGTCTCACAGAGAAGGTCGTTAA 60.058 47.826 0.00 0.00 40.59 2.01
2326 2831 4.379603 CGTCTCACAGAGAAGGTCGTTAAT 60.380 45.833 0.00 0.00 40.59 1.40
2327 2832 5.471257 GTCTCACAGAGAAGGTCGTTAATT 58.529 41.667 0.00 0.00 40.59 1.40
2328 2833 5.927115 GTCTCACAGAGAAGGTCGTTAATTT 59.073 40.000 0.00 0.00 40.59 1.82
2329 2834 6.089685 GTCTCACAGAGAAGGTCGTTAATTTC 59.910 42.308 0.00 0.00 40.59 2.17
2330 2835 5.849510 TCACAGAGAAGGTCGTTAATTTCA 58.150 37.500 0.00 0.00 0.00 2.69
2331 2836 5.926542 TCACAGAGAAGGTCGTTAATTTCAG 59.073 40.000 0.00 0.00 0.00 3.02
2332 2837 5.696724 CACAGAGAAGGTCGTTAATTTCAGT 59.303 40.000 0.00 0.00 0.00 3.41
2333 2838 6.202954 CACAGAGAAGGTCGTTAATTTCAGTT 59.797 38.462 0.00 0.00 0.00 3.16
2334 2839 6.766467 ACAGAGAAGGTCGTTAATTTCAGTTT 59.234 34.615 0.00 0.00 0.00 2.66
2365 2870 5.403466 GCCAGCTTTTGACTATCTGTTTTTG 59.597 40.000 0.00 0.00 0.00 2.44
2449 2954 7.023575 GCAAGTTGACATATTTCTTGTAGTGG 58.976 38.462 7.16 0.00 38.09 4.00
2450 2955 7.308589 GCAAGTTGACATATTTCTTGTAGTGGT 60.309 37.037 7.16 0.00 38.09 4.16
2451 2956 9.214957 CAAGTTGACATATTTCTTGTAGTGGTA 57.785 33.333 0.00 0.00 33.27 3.25
2452 2957 8.773404 AGTTGACATATTTCTTGTAGTGGTAC 57.227 34.615 0.00 0.00 0.00 3.34
2453 2958 8.594550 AGTTGACATATTTCTTGTAGTGGTACT 58.405 33.333 0.00 0.00 0.00 2.73
2454 2959 9.216117 GTTGACATATTTCTTGTAGTGGTACTT 57.784 33.333 0.00 0.00 0.00 2.24
2465 2970 9.653287 TCTTGTAGTGGTACTTATTCAATCTTG 57.347 33.333 0.00 0.00 0.00 3.02
2466 2971 7.843490 TGTAGTGGTACTTATTCAATCTTGC 57.157 36.000 0.00 0.00 0.00 4.01
2467 2972 7.620880 TGTAGTGGTACTTATTCAATCTTGCT 58.379 34.615 0.00 0.00 0.00 3.91
2468 2973 8.100791 TGTAGTGGTACTTATTCAATCTTGCTT 58.899 33.333 0.00 0.00 0.00 3.91
2469 2974 7.383102 AGTGGTACTTATTCAATCTTGCTTG 57.617 36.000 0.00 0.00 0.00 4.01
2470 2975 6.942576 AGTGGTACTTATTCAATCTTGCTTGT 59.057 34.615 0.00 0.00 0.00 3.16
2471 2976 7.119846 AGTGGTACTTATTCAATCTTGCTTGTC 59.880 37.037 0.00 0.00 0.00 3.18
2472 2977 7.119846 GTGGTACTTATTCAATCTTGCTTGTCT 59.880 37.037 0.00 0.00 0.00 3.41
2473 2978 7.334421 TGGTACTTATTCAATCTTGCTTGTCTC 59.666 37.037 0.00 0.00 0.00 3.36
2474 2979 6.749923 ACTTATTCAATCTTGCTTGTCTCC 57.250 37.500 0.00 0.00 0.00 3.71
2475 2980 5.649831 ACTTATTCAATCTTGCTTGTCTCCC 59.350 40.000 0.00 0.00 0.00 4.30
2476 2981 3.795688 TTCAATCTTGCTTGTCTCCCT 57.204 42.857 0.00 0.00 0.00 4.20
2477 2982 3.063510 TCAATCTTGCTTGTCTCCCTG 57.936 47.619 0.00 0.00 0.00 4.45
2478 2983 2.373169 TCAATCTTGCTTGTCTCCCTGT 59.627 45.455 0.00 0.00 0.00 4.00
2479 2984 2.486472 ATCTTGCTTGTCTCCCTGTG 57.514 50.000 0.00 0.00 0.00 3.66
2480 2985 1.131638 TCTTGCTTGTCTCCCTGTGT 58.868 50.000 0.00 0.00 0.00 3.72
2481 2986 1.490490 TCTTGCTTGTCTCCCTGTGTT 59.510 47.619 0.00 0.00 0.00 3.32
2482 2987 1.605710 CTTGCTTGTCTCCCTGTGTTG 59.394 52.381 0.00 0.00 0.00 3.33
2483 2988 0.546122 TGCTTGTCTCCCTGTGTTGT 59.454 50.000 0.00 0.00 0.00 3.32
2484 2989 1.064758 TGCTTGTCTCCCTGTGTTGTT 60.065 47.619 0.00 0.00 0.00 2.83
2485 2990 2.024414 GCTTGTCTCCCTGTGTTGTTT 58.976 47.619 0.00 0.00 0.00 2.83
2486 2991 2.427095 GCTTGTCTCCCTGTGTTGTTTT 59.573 45.455 0.00 0.00 0.00 2.43
2487 2992 3.489229 GCTTGTCTCCCTGTGTTGTTTTC 60.489 47.826 0.00 0.00 0.00 2.29
2488 2993 3.358111 TGTCTCCCTGTGTTGTTTTCA 57.642 42.857 0.00 0.00 0.00 2.69
2489 2994 3.897239 TGTCTCCCTGTGTTGTTTTCAT 58.103 40.909 0.00 0.00 0.00 2.57
2490 2995 4.277476 TGTCTCCCTGTGTTGTTTTCATT 58.723 39.130 0.00 0.00 0.00 2.57
2491 2996 4.709397 TGTCTCCCTGTGTTGTTTTCATTT 59.291 37.500 0.00 0.00 0.00 2.32
2492 2997 5.888724 TGTCTCCCTGTGTTGTTTTCATTTA 59.111 36.000 0.00 0.00 0.00 1.40
2493 2998 6.183360 TGTCTCCCTGTGTTGTTTTCATTTAC 60.183 38.462 0.00 0.00 0.00 2.01
2494 2999 5.300792 TCTCCCTGTGTTGTTTTCATTTACC 59.699 40.000 0.00 0.00 0.00 2.85
2495 3000 4.342665 TCCCTGTGTTGTTTTCATTTACCC 59.657 41.667 0.00 0.00 0.00 3.69
2496 3001 4.343814 CCCTGTGTTGTTTTCATTTACCCT 59.656 41.667 0.00 0.00 0.00 4.34
2497 3002 5.288804 CCTGTGTTGTTTTCATTTACCCTG 58.711 41.667 0.00 0.00 0.00 4.45
2498 3003 5.163457 CCTGTGTTGTTTTCATTTACCCTGT 60.163 40.000 0.00 0.00 0.00 4.00
2499 3004 5.897050 TGTGTTGTTTTCATTTACCCTGTC 58.103 37.500 0.00 0.00 0.00 3.51
2500 3005 5.419155 TGTGTTGTTTTCATTTACCCTGTCA 59.581 36.000 0.00 0.00 0.00 3.58
2501 3006 6.097554 TGTGTTGTTTTCATTTACCCTGTCAT 59.902 34.615 0.00 0.00 0.00 3.06
2502 3007 7.285629 TGTGTTGTTTTCATTTACCCTGTCATA 59.714 33.333 0.00 0.00 0.00 2.15
2503 3008 7.807907 GTGTTGTTTTCATTTACCCTGTCATAG 59.192 37.037 0.00 0.00 0.00 2.23
2504 3009 7.504238 TGTTGTTTTCATTTACCCTGTCATAGT 59.496 33.333 0.00 0.00 0.00 2.12
2505 3010 8.357402 GTTGTTTTCATTTACCCTGTCATAGTT 58.643 33.333 0.00 0.00 0.00 2.24
2506 3011 8.106247 TGTTTTCATTTACCCTGTCATAGTTC 57.894 34.615 0.00 0.00 0.00 3.01
2507 3012 7.942341 TGTTTTCATTTACCCTGTCATAGTTCT 59.058 33.333 0.00 0.00 0.00 3.01
2508 3013 8.793592 GTTTTCATTTACCCTGTCATAGTTCTT 58.206 33.333 0.00 0.00 0.00 2.52
2509 3014 8.934023 TTTCATTTACCCTGTCATAGTTCTTT 57.066 30.769 0.00 0.00 0.00 2.52
2510 3015 8.561738 TTCATTTACCCTGTCATAGTTCTTTC 57.438 34.615 0.00 0.00 0.00 2.62
2511 3016 7.918076 TCATTTACCCTGTCATAGTTCTTTCT 58.082 34.615 0.00 0.00 0.00 2.52
2512 3017 8.041323 TCATTTACCCTGTCATAGTTCTTTCTC 58.959 37.037 0.00 0.00 0.00 2.87
2513 3018 4.457834 ACCCTGTCATAGTTCTTTCTCG 57.542 45.455 0.00 0.00 0.00 4.04
2514 3019 3.833070 ACCCTGTCATAGTTCTTTCTCGT 59.167 43.478 0.00 0.00 0.00 4.18
2515 3020 4.177026 CCCTGTCATAGTTCTTTCTCGTG 58.823 47.826 0.00 0.00 0.00 4.35
2516 3021 4.177026 CCTGTCATAGTTCTTTCTCGTGG 58.823 47.826 0.00 0.00 0.00 4.94
2517 3022 4.322049 CCTGTCATAGTTCTTTCTCGTGGT 60.322 45.833 0.00 0.00 0.00 4.16
2518 3023 5.209818 TGTCATAGTTCTTTCTCGTGGTT 57.790 39.130 0.00 0.00 0.00 3.67
2519 3024 6.335471 TGTCATAGTTCTTTCTCGTGGTTA 57.665 37.500 0.00 0.00 0.00 2.85
2520 3025 6.931838 TGTCATAGTTCTTTCTCGTGGTTAT 58.068 36.000 0.00 0.00 0.00 1.89
2521 3026 6.811665 TGTCATAGTTCTTTCTCGTGGTTATG 59.188 38.462 0.00 0.00 0.00 1.90
2522 3027 6.812160 GTCATAGTTCTTTCTCGTGGTTATGT 59.188 38.462 0.00 0.00 0.00 2.29
2523 3028 7.972277 GTCATAGTTCTTTCTCGTGGTTATGTA 59.028 37.037 0.00 0.00 0.00 2.29
2524 3029 8.692710 TCATAGTTCTTTCTCGTGGTTATGTAT 58.307 33.333 0.00 0.00 0.00 2.29
2525 3030 8.969267 CATAGTTCTTTCTCGTGGTTATGTATC 58.031 37.037 0.00 0.00 0.00 2.24
2526 3031 6.034591 AGTTCTTTCTCGTGGTTATGTATCG 58.965 40.000 0.00 0.00 0.00 2.92
2527 3032 5.571784 TCTTTCTCGTGGTTATGTATCGT 57.428 39.130 0.00 0.00 0.00 3.73
2528 3033 6.682423 TCTTTCTCGTGGTTATGTATCGTA 57.318 37.500 0.00 0.00 0.00 3.43
2529 3034 6.722301 TCTTTCTCGTGGTTATGTATCGTAG 58.278 40.000 0.00 0.00 0.00 3.51
2530 3035 6.539826 TCTTTCTCGTGGTTATGTATCGTAGA 59.460 38.462 0.00 0.00 45.75 2.59
2531 3036 6.872628 TTCTCGTGGTTATGTATCGTAGAT 57.127 37.500 0.00 0.00 45.12 1.98
2532 3037 6.477669 TCTCGTGGTTATGTATCGTAGATC 57.522 41.667 0.00 0.00 45.12 2.75
2533 3038 6.228995 TCTCGTGGTTATGTATCGTAGATCT 58.771 40.000 0.00 0.00 45.12 2.75
2534 3039 6.709397 TCTCGTGGTTATGTATCGTAGATCTT 59.291 38.462 0.00 0.00 45.12 2.40
2535 3040 7.874528 TCTCGTGGTTATGTATCGTAGATCTTA 59.125 37.037 0.00 0.00 45.12 2.10
2536 3041 8.557592 TCGTGGTTATGTATCGTAGATCTTAT 57.442 34.615 0.00 0.00 45.12 1.73
2537 3042 8.663025 TCGTGGTTATGTATCGTAGATCTTATC 58.337 37.037 0.00 0.00 45.12 1.75
2538 3043 7.909121 CGTGGTTATGTATCGTAGATCTTATCC 59.091 40.741 0.00 0.00 45.12 2.59
2539 3044 8.958506 GTGGTTATGTATCGTAGATCTTATCCT 58.041 37.037 0.00 0.00 45.12 3.24
2540 3045 9.529823 TGGTTATGTATCGTAGATCTTATCCTT 57.470 33.333 0.00 0.00 45.12 3.36
2546 3051 9.745880 TGTATCGTAGATCTTATCCTTTGTTTC 57.254 33.333 0.00 0.00 45.12 2.78
2547 3052 9.968870 GTATCGTAGATCTTATCCTTTGTTTCT 57.031 33.333 0.00 0.00 45.12 2.52
2549 3054 8.294954 TCGTAGATCTTATCCTTTGTTTCTCT 57.705 34.615 0.00 0.00 0.00 3.10
2550 3055 8.407064 TCGTAGATCTTATCCTTTGTTTCTCTC 58.593 37.037 0.00 0.00 0.00 3.20
2551 3056 8.191446 CGTAGATCTTATCCTTTGTTTCTCTCA 58.809 37.037 0.00 0.00 0.00 3.27
2553 3058 8.961294 AGATCTTATCCTTTGTTTCTCTCATG 57.039 34.615 0.00 0.00 0.00 3.07
2554 3059 8.547173 AGATCTTATCCTTTGTTTCTCTCATGT 58.453 33.333 0.00 0.00 0.00 3.21
2555 3060 9.171877 GATCTTATCCTTTGTTTCTCTCATGTT 57.828 33.333 0.00 0.00 0.00 2.71
2556 3061 8.327941 TCTTATCCTTTGTTTCTCTCATGTTG 57.672 34.615 0.00 0.00 0.00 3.33
2557 3062 4.836125 TCCTTTGTTTCTCTCATGTTGC 57.164 40.909 0.00 0.00 0.00 4.17
2558 3063 4.464008 TCCTTTGTTTCTCTCATGTTGCT 58.536 39.130 0.00 0.00 0.00 3.91
2559 3064 4.276678 TCCTTTGTTTCTCTCATGTTGCTG 59.723 41.667 0.00 0.00 0.00 4.41
2560 3065 3.631145 TTGTTTCTCTCATGTTGCTGC 57.369 42.857 0.00 0.00 0.00 5.25
2561 3066 2.574450 TGTTTCTCTCATGTTGCTGCA 58.426 42.857 0.00 0.00 0.00 4.41
2562 3067 3.151554 TGTTTCTCTCATGTTGCTGCAT 58.848 40.909 1.84 0.00 0.00 3.96
2563 3068 3.189910 TGTTTCTCTCATGTTGCTGCATC 59.810 43.478 1.84 2.97 0.00 3.91
2564 3069 3.345508 TTCTCTCATGTTGCTGCATCT 57.654 42.857 1.84 0.00 0.00 2.90
2565 3070 2.629051 TCTCTCATGTTGCTGCATCTG 58.371 47.619 1.84 1.64 0.00 2.90
2566 3071 2.027469 TCTCTCATGTTGCTGCATCTGT 60.027 45.455 1.84 0.00 0.00 3.41
2567 3072 2.747989 CTCTCATGTTGCTGCATCTGTT 59.252 45.455 1.84 0.00 0.00 3.16
2568 3073 3.937079 CTCTCATGTTGCTGCATCTGTTA 59.063 43.478 1.84 0.00 0.00 2.41
2569 3074 3.937079 TCTCATGTTGCTGCATCTGTTAG 59.063 43.478 1.84 0.00 0.00 2.34
2570 3075 2.421073 TCATGTTGCTGCATCTGTTAGC 59.579 45.455 1.84 0.00 37.93 3.09
2571 3076 1.894881 TGTTGCTGCATCTGTTAGCA 58.105 45.000 1.84 0.00 44.92 3.49
2572 3077 2.439409 TGTTGCTGCATCTGTTAGCAT 58.561 42.857 1.84 0.00 45.76 3.79
2573 3078 3.608796 TGTTGCTGCATCTGTTAGCATA 58.391 40.909 1.84 3.54 45.76 3.14
2574 3079 4.201657 TGTTGCTGCATCTGTTAGCATAT 58.798 39.130 1.84 0.00 45.76 1.78
2575 3080 4.641541 TGTTGCTGCATCTGTTAGCATATT 59.358 37.500 1.84 0.00 45.76 1.28
2576 3081 4.823790 TGCTGCATCTGTTAGCATATTG 57.176 40.909 0.00 0.00 42.05 1.90
2577 3082 3.004002 TGCTGCATCTGTTAGCATATTGC 59.996 43.478 0.00 0.00 42.05 3.56
2593 3098 7.520119 GCATATTGCATTACCATCATCATTG 57.480 36.000 0.00 0.00 44.26 2.82
2594 3099 7.094631 GCATATTGCATTACCATCATCATTGT 58.905 34.615 0.00 0.00 44.26 2.71
2595 3100 7.274904 GCATATTGCATTACCATCATCATTGTC 59.725 37.037 0.00 0.00 44.26 3.18
2596 3101 6.718522 ATTGCATTACCATCATCATTGTCA 57.281 33.333 0.00 0.00 0.00 3.58
2597 3102 6.527057 TTGCATTACCATCATCATTGTCAA 57.473 33.333 0.00 0.00 0.00 3.18
2598 3103 6.527057 TGCATTACCATCATCATTGTCAAA 57.473 33.333 0.00 0.00 0.00 2.69
2599 3104 6.331845 TGCATTACCATCATCATTGTCAAAC 58.668 36.000 0.00 0.00 0.00 2.93
2600 3105 5.750067 GCATTACCATCATCATTGTCAAACC 59.250 40.000 0.00 0.00 0.00 3.27
2601 3106 6.406177 GCATTACCATCATCATTGTCAAACCT 60.406 38.462 0.00 0.00 0.00 3.50
2602 3107 6.513806 TTACCATCATCATTGTCAAACCTG 57.486 37.500 0.00 0.00 0.00 4.00
2603 3108 4.410099 ACCATCATCATTGTCAAACCTGT 58.590 39.130 0.00 0.00 0.00 4.00
2604 3109 4.219070 ACCATCATCATTGTCAAACCTGTG 59.781 41.667 0.00 0.00 0.00 3.66
2605 3110 4.460034 CCATCATCATTGTCAAACCTGTGA 59.540 41.667 0.00 0.00 0.00 3.58
2606 3111 5.126545 CCATCATCATTGTCAAACCTGTGAT 59.873 40.000 0.00 0.00 0.00 3.06
2607 3112 6.319405 CCATCATCATTGTCAAACCTGTGATA 59.681 38.462 0.00 0.00 0.00 2.15
2608 3113 7.013942 CCATCATCATTGTCAAACCTGTGATAT 59.986 37.037 0.00 0.00 0.00 1.63
2609 3114 7.558161 TCATCATTGTCAAACCTGTGATATC 57.442 36.000 0.00 0.00 0.00 1.63
2610 3115 7.341030 TCATCATTGTCAAACCTGTGATATCT 58.659 34.615 3.98 0.00 0.00 1.98
2611 3116 7.830697 TCATCATTGTCAAACCTGTGATATCTT 59.169 33.333 3.98 0.00 0.00 2.40
2612 3117 9.112725 CATCATTGTCAAACCTGTGATATCTTA 57.887 33.333 3.98 0.00 0.00 2.10
2613 3118 9.857656 ATCATTGTCAAACCTGTGATATCTTAT 57.142 29.630 3.98 0.00 0.00 1.73
2614 3119 9.112725 TCATTGTCAAACCTGTGATATCTTATG 57.887 33.333 3.98 0.00 0.00 1.90
2615 3120 7.864108 TTGTCAAACCTGTGATATCTTATGG 57.136 36.000 3.98 4.03 0.00 2.74
2616 3121 6.957631 TGTCAAACCTGTGATATCTTATGGT 58.042 36.000 3.98 4.62 0.00 3.55
2617 3122 6.823182 TGTCAAACCTGTGATATCTTATGGTG 59.177 38.462 3.98 0.00 0.00 4.17
2618 3123 6.260936 GTCAAACCTGTGATATCTTATGGTGG 59.739 42.308 3.98 4.50 0.00 4.61
2619 3124 5.975988 AACCTGTGATATCTTATGGTGGT 57.024 39.130 3.98 0.67 0.00 4.16
2620 3125 7.126573 TCAAACCTGTGATATCTTATGGTGGTA 59.873 37.037 3.98 0.00 0.00 3.25
2621 3126 6.420913 ACCTGTGATATCTTATGGTGGTAC 57.579 41.667 3.98 0.00 0.00 3.34
2622 3127 5.307196 ACCTGTGATATCTTATGGTGGTACC 59.693 44.000 4.43 4.43 39.22 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
135 136 7.578571 GCCCATGTTCCTATTATTGTTTGTTCA 60.579 37.037 0.00 0.00 0.00 3.18
205 206 4.728102 CGTCGGGCGTACAAGGCA 62.728 66.667 0.00 0.00 38.57 4.75
413 415 9.736414 AAAATGCATATGAGACAGCTATCTATT 57.264 29.630 6.97 0.00 0.00 1.73
478 481 5.163754 CCACCGAGAACAACATCCTTTATTC 60.164 44.000 0.00 0.00 0.00 1.75
580 586 7.198390 GCATATGCACAACAAATAGAATCTGT 58.802 34.615 22.84 0.00 41.59 3.41
739 746 7.115805 CGTCTGTATTTACAAGAACAACAGCTA 59.884 37.037 0.00 0.00 35.50 3.32
854 863 7.931275 ACAATGAGTTTTCAGTAAAGAGGAAC 58.069 34.615 0.00 0.00 36.61 3.62
891 900 4.221262 ACCACTGCTCAATGTTTGCAATAT 59.779 37.500 0.00 0.00 36.22 1.28
987 996 2.746277 GCCATCGGGTGAACGCTT 60.746 61.111 0.00 0.00 36.17 4.68
1030 1039 3.119602 ACGTATATAGCGCAACCATCGAT 60.120 43.478 11.47 0.00 0.00 3.59
1034 1043 3.575630 CTCACGTATATAGCGCAACCAT 58.424 45.455 11.47 0.00 0.00 3.55
1035 1044 2.287970 CCTCACGTATATAGCGCAACCA 60.288 50.000 11.47 0.00 0.00 3.67
1176 1186 4.158394 GGTTTGTCACTGCCATAATCACAT 59.842 41.667 0.00 0.00 0.00 3.21
1414 1424 4.785376 ACAGATAAATGAACAGGAGGGAGT 59.215 41.667 0.00 0.00 0.00 3.85
1443 1453 4.423625 AGTGGTAGGAATGTAGGATTGC 57.576 45.455 0.00 0.00 0.00 3.56
1462 1472 4.377021 TCGATTTCAACAGCAACAGTAGT 58.623 39.130 0.00 0.00 0.00 2.73
1529 1539 3.760684 GCAAACTCATTCATTCTCTGGGT 59.239 43.478 0.00 0.00 0.00 4.51
1573 1583 7.167468 ACTGCGTCAATTTCAAAATAGAACAAC 59.833 33.333 0.00 0.00 0.00 3.32
1599 1609 3.403038 GTGAGCAAGAGAAAAGCACCTA 58.597 45.455 0.00 0.00 0.00 3.08
1609 1619 0.958822 TGCTACACGTGAGCAAGAGA 59.041 50.000 28.48 13.45 46.71 3.10
1623 1633 1.589196 GCGTCGGAGATGGTGCTAC 60.589 63.158 0.00 0.00 45.11 3.58
1638 1648 2.882876 CTACTAGCACCACCGCGT 59.117 61.111 4.92 0.00 36.85 6.01
1673 2162 7.861629 TCTCAGGAATACATTTCCTTACACAT 58.138 34.615 4.15 0.00 46.21 3.21
1984 2479 9.906660 CTCGGCCTTTTTGCAATATATTTATTA 57.093 29.630 0.00 0.00 0.00 0.98
2087 2592 3.769844 CCGATTAGGTGTCTATATGGGCT 59.230 47.826 0.00 0.00 34.51 5.19
2189 2694 2.362369 GCTAGCTGTCTGCCCAGGA 61.362 63.158 7.70 0.00 44.23 3.86
2277 2782 6.544564 TGGAAACTGAAATTAACGACCTTCTT 59.455 34.615 0.00 0.00 0.00 2.52
2300 2805 0.962489 ACCTTCTCTGTGAGACGTGG 59.038 55.000 0.00 3.55 38.51 4.94
2301 2806 1.400371 CGACCTTCTCTGTGAGACGTG 60.400 57.143 0.00 0.00 38.51 4.49
2302 2807 0.875728 CGACCTTCTCTGTGAGACGT 59.124 55.000 0.00 0.00 38.51 4.34
2303 2808 0.875728 ACGACCTTCTCTGTGAGACG 59.124 55.000 0.00 1.05 38.51 4.18
2304 2809 4.500603 TTAACGACCTTCTCTGTGAGAC 57.499 45.455 0.00 0.00 38.51 3.36
2305 2810 5.723672 AATTAACGACCTTCTCTGTGAGA 57.276 39.130 0.00 0.00 36.86 3.27
2306 2811 5.926542 TGAAATTAACGACCTTCTCTGTGAG 59.073 40.000 0.00 0.00 0.00 3.51
2307 2812 5.849510 TGAAATTAACGACCTTCTCTGTGA 58.150 37.500 0.00 0.00 0.00 3.58
2308 2813 5.696724 ACTGAAATTAACGACCTTCTCTGTG 59.303 40.000 0.00 0.00 0.00 3.66
2309 2814 5.855045 ACTGAAATTAACGACCTTCTCTGT 58.145 37.500 0.00 0.00 0.00 3.41
2310 2815 6.787085 AACTGAAATTAACGACCTTCTCTG 57.213 37.500 0.00 0.00 0.00 3.35
2311 2816 7.115947 CGTAAACTGAAATTAACGACCTTCTCT 59.884 37.037 0.00 0.00 0.00 3.10
2312 2817 7.115378 TCGTAAACTGAAATTAACGACCTTCTC 59.885 37.037 0.00 0.00 0.00 2.87
2313 2818 6.925165 TCGTAAACTGAAATTAACGACCTTCT 59.075 34.615 0.00 0.00 0.00 2.85
2314 2819 7.005958 GTCGTAAACTGAAATTAACGACCTTC 58.994 38.462 13.22 0.00 41.61 3.46
2315 2820 6.881017 GTCGTAAACTGAAATTAACGACCTT 58.119 36.000 13.22 0.00 41.61 3.50
2316 2821 6.457851 GTCGTAAACTGAAATTAACGACCT 57.542 37.500 13.22 0.00 41.61 3.85
2318 2823 5.300393 CGGTCGTAAACTGAAATTAACGAC 58.700 41.667 15.27 15.27 45.11 4.34
2319 2824 4.143347 GCGGTCGTAAACTGAAATTAACGA 60.143 41.667 0.00 0.00 36.22 3.85
2320 2825 4.076985 GCGGTCGTAAACTGAAATTAACG 58.923 43.478 0.00 0.00 36.22 3.18
2321 2826 4.083908 TGGCGGTCGTAAACTGAAATTAAC 60.084 41.667 0.00 0.00 36.22 2.01
2322 2827 4.063689 TGGCGGTCGTAAACTGAAATTAA 58.936 39.130 0.00 0.00 36.22 1.40
2323 2828 3.661944 TGGCGGTCGTAAACTGAAATTA 58.338 40.909 0.00 0.00 36.22 1.40
2324 2829 2.482721 CTGGCGGTCGTAAACTGAAATT 59.517 45.455 0.00 0.00 36.22 1.82
2325 2830 2.073816 CTGGCGGTCGTAAACTGAAAT 58.926 47.619 0.00 0.00 36.22 2.17
2326 2831 1.504359 CTGGCGGTCGTAAACTGAAA 58.496 50.000 0.00 0.00 36.22 2.69
2327 2832 0.947180 GCTGGCGGTCGTAAACTGAA 60.947 55.000 0.00 0.00 36.22 3.02
2328 2833 1.373748 GCTGGCGGTCGTAAACTGA 60.374 57.895 0.00 0.00 36.22 3.41
2329 2834 0.949105 AAGCTGGCGGTCGTAAACTG 60.949 55.000 0.00 0.00 37.31 3.16
2330 2835 0.250166 AAAGCTGGCGGTCGTAAACT 60.250 50.000 0.00 0.00 0.00 2.66
2331 2836 0.589708 AAAAGCTGGCGGTCGTAAAC 59.410 50.000 0.00 0.00 0.00 2.01
2332 2837 0.589223 CAAAAGCTGGCGGTCGTAAA 59.411 50.000 0.00 0.00 0.00 2.01
2333 2838 0.249953 TCAAAAGCTGGCGGTCGTAA 60.250 50.000 0.00 0.00 0.00 3.18
2334 2839 0.947180 GTCAAAAGCTGGCGGTCGTA 60.947 55.000 0.00 0.00 0.00 3.43
2376 2881 6.877236 AGGTCATTGTTTTTCATTTGTGACT 58.123 32.000 0.00 0.00 36.06 3.41
2378 2883 7.821359 TGAAAGGTCATTGTTTTTCATTTGTGA 59.179 29.630 8.06 0.00 35.34 3.58
2380 2885 7.823799 ACTGAAAGGTCATTGTTTTTCATTTGT 59.176 29.630 10.82 6.04 38.45 2.83
2449 2954 7.201652 GGGAGACAAGCAAGATTGAATAAGTAC 60.202 40.741 4.93 0.00 34.20 2.73
2450 2955 6.823689 GGGAGACAAGCAAGATTGAATAAGTA 59.176 38.462 4.93 0.00 34.20 2.24
2451 2956 5.649831 GGGAGACAAGCAAGATTGAATAAGT 59.350 40.000 4.93 0.00 34.20 2.24
2452 2957 5.884792 AGGGAGACAAGCAAGATTGAATAAG 59.115 40.000 4.93 0.00 34.20 1.73
2453 2958 5.649395 CAGGGAGACAAGCAAGATTGAATAA 59.351 40.000 4.93 0.00 34.20 1.40
2454 2959 5.188434 CAGGGAGACAAGCAAGATTGAATA 58.812 41.667 4.93 0.00 34.20 1.75
2455 2960 4.015084 CAGGGAGACAAGCAAGATTGAAT 58.985 43.478 4.93 0.00 34.20 2.57
2456 2961 3.181440 ACAGGGAGACAAGCAAGATTGAA 60.181 43.478 4.93 0.00 34.20 2.69
2457 2962 2.373169 ACAGGGAGACAAGCAAGATTGA 59.627 45.455 4.93 0.00 34.20 2.57
2458 2963 2.486982 CACAGGGAGACAAGCAAGATTG 59.513 50.000 0.00 0.00 36.22 2.67
2459 2964 2.107204 ACACAGGGAGACAAGCAAGATT 59.893 45.455 0.00 0.00 0.00 2.40
2460 2965 1.701847 ACACAGGGAGACAAGCAAGAT 59.298 47.619 0.00 0.00 0.00 2.40
2461 2966 1.131638 ACACAGGGAGACAAGCAAGA 58.868 50.000 0.00 0.00 0.00 3.02
2462 2967 1.605710 CAACACAGGGAGACAAGCAAG 59.394 52.381 0.00 0.00 0.00 4.01
2463 2968 1.064758 ACAACACAGGGAGACAAGCAA 60.065 47.619 0.00 0.00 0.00 3.91
2464 2969 0.546122 ACAACACAGGGAGACAAGCA 59.454 50.000 0.00 0.00 0.00 3.91
2465 2970 1.680338 AACAACACAGGGAGACAAGC 58.320 50.000 0.00 0.00 0.00 4.01
2466 2971 3.694072 TGAAAACAACACAGGGAGACAAG 59.306 43.478 0.00 0.00 0.00 3.16
2467 2972 3.691575 TGAAAACAACACAGGGAGACAA 58.308 40.909 0.00 0.00 0.00 3.18
2468 2973 3.358111 TGAAAACAACACAGGGAGACA 57.642 42.857 0.00 0.00 0.00 3.41
2469 2974 4.918810 AATGAAAACAACACAGGGAGAC 57.081 40.909 0.00 0.00 0.00 3.36
2470 2975 5.300792 GGTAAATGAAAACAACACAGGGAGA 59.699 40.000 0.00 0.00 0.00 3.71
2471 2976 5.508994 GGGTAAATGAAAACAACACAGGGAG 60.509 44.000 0.00 0.00 0.00 4.30
2472 2977 4.342665 GGGTAAATGAAAACAACACAGGGA 59.657 41.667 0.00 0.00 0.00 4.20
2473 2978 4.343814 AGGGTAAATGAAAACAACACAGGG 59.656 41.667 0.00 0.00 0.00 4.45
2474 2979 5.163457 ACAGGGTAAATGAAAACAACACAGG 60.163 40.000 0.00 0.00 0.00 4.00
2475 2980 5.901552 ACAGGGTAAATGAAAACAACACAG 58.098 37.500 0.00 0.00 0.00 3.66
2476 2981 5.419155 TGACAGGGTAAATGAAAACAACACA 59.581 36.000 0.00 0.00 0.00 3.72
2477 2982 5.897050 TGACAGGGTAAATGAAAACAACAC 58.103 37.500 0.00 0.00 0.00 3.32
2478 2983 6.723298 ATGACAGGGTAAATGAAAACAACA 57.277 33.333 0.00 0.00 0.00 3.33
2479 2984 7.882179 ACTATGACAGGGTAAATGAAAACAAC 58.118 34.615 0.00 0.00 0.00 3.32
2480 2985 8.472007 AACTATGACAGGGTAAATGAAAACAA 57.528 30.769 0.00 0.00 0.00 2.83
2481 2986 7.942341 AGAACTATGACAGGGTAAATGAAAACA 59.058 33.333 0.00 0.00 0.00 2.83
2482 2987 8.336801 AGAACTATGACAGGGTAAATGAAAAC 57.663 34.615 0.00 0.00 0.00 2.43
2483 2988 8.934023 AAGAACTATGACAGGGTAAATGAAAA 57.066 30.769 0.00 0.00 0.00 2.29
2484 2989 8.934023 AAAGAACTATGACAGGGTAAATGAAA 57.066 30.769 0.00 0.00 0.00 2.69
2485 2990 8.383175 AGAAAGAACTATGACAGGGTAAATGAA 58.617 33.333 0.00 0.00 0.00 2.57
2486 2991 7.918076 AGAAAGAACTATGACAGGGTAAATGA 58.082 34.615 0.00 0.00 0.00 2.57
2487 2992 7.010552 CGAGAAAGAACTATGACAGGGTAAATG 59.989 40.741 0.00 0.00 0.00 2.32
2488 2993 7.042335 CGAGAAAGAACTATGACAGGGTAAAT 58.958 38.462 0.00 0.00 0.00 1.40
2489 2994 6.014840 ACGAGAAAGAACTATGACAGGGTAAA 60.015 38.462 0.00 0.00 0.00 2.01
2490 2995 5.479375 ACGAGAAAGAACTATGACAGGGTAA 59.521 40.000 0.00 0.00 0.00 2.85
2491 2996 5.014858 ACGAGAAAGAACTATGACAGGGTA 58.985 41.667 0.00 0.00 0.00 3.69
2492 2997 3.833070 ACGAGAAAGAACTATGACAGGGT 59.167 43.478 0.00 0.00 0.00 4.34
2493 2998 4.177026 CACGAGAAAGAACTATGACAGGG 58.823 47.826 0.00 0.00 0.00 4.45
2494 2999 4.177026 CCACGAGAAAGAACTATGACAGG 58.823 47.826 0.00 0.00 0.00 4.00
2495 3000 4.810790 ACCACGAGAAAGAACTATGACAG 58.189 43.478 0.00 0.00 0.00 3.51
2496 3001 4.866508 ACCACGAGAAAGAACTATGACA 57.133 40.909 0.00 0.00 0.00 3.58
2497 3002 6.812160 ACATAACCACGAGAAAGAACTATGAC 59.188 38.462 0.00 0.00 0.00 3.06
2498 3003 6.931838 ACATAACCACGAGAAAGAACTATGA 58.068 36.000 0.00 0.00 0.00 2.15
2499 3004 8.873215 ATACATAACCACGAGAAAGAACTATG 57.127 34.615 0.00 0.00 0.00 2.23
2500 3005 7.861372 CGATACATAACCACGAGAAAGAACTAT 59.139 37.037 0.00 0.00 0.00 2.12
2501 3006 7.148188 ACGATACATAACCACGAGAAAGAACTA 60.148 37.037 0.00 0.00 0.00 2.24
2502 3007 6.034591 CGATACATAACCACGAGAAAGAACT 58.965 40.000 0.00 0.00 0.00 3.01
2503 3008 5.803967 ACGATACATAACCACGAGAAAGAAC 59.196 40.000 0.00 0.00 0.00 3.01
2504 3009 5.957798 ACGATACATAACCACGAGAAAGAA 58.042 37.500 0.00 0.00 0.00 2.52
2505 3010 5.571784 ACGATACATAACCACGAGAAAGA 57.428 39.130 0.00 0.00 0.00 2.52
2506 3011 6.722301 TCTACGATACATAACCACGAGAAAG 58.278 40.000 0.00 0.00 0.00 2.62
2507 3012 6.682423 TCTACGATACATAACCACGAGAAA 57.318 37.500 0.00 0.00 0.00 2.52
2508 3013 6.709397 AGATCTACGATACATAACCACGAGAA 59.291 38.462 0.00 0.00 0.00 2.87
2509 3014 6.228995 AGATCTACGATACATAACCACGAGA 58.771 40.000 0.00 0.00 0.00 4.04
2510 3015 6.483385 AGATCTACGATACATAACCACGAG 57.517 41.667 0.00 0.00 0.00 4.18
2511 3016 6.872628 AAGATCTACGATACATAACCACGA 57.127 37.500 0.00 0.00 0.00 4.35
2512 3017 7.909121 GGATAAGATCTACGATACATAACCACG 59.091 40.741 0.00 0.00 0.00 4.94
2513 3018 8.958506 AGGATAAGATCTACGATACATAACCAC 58.041 37.037 0.00 0.00 0.00 4.16
2514 3019 9.529823 AAGGATAAGATCTACGATACATAACCA 57.470 33.333 0.00 0.00 0.00 3.67
2520 3025 9.745880 GAAACAAAGGATAAGATCTACGATACA 57.254 33.333 0.00 0.00 0.00 2.29
2521 3026 9.968870 AGAAACAAAGGATAAGATCTACGATAC 57.031 33.333 0.00 0.00 0.00 2.24
2523 3028 8.919145 AGAGAAACAAAGGATAAGATCTACGAT 58.081 33.333 0.00 0.00 0.00 3.73
2524 3029 8.294954 AGAGAAACAAAGGATAAGATCTACGA 57.705 34.615 0.00 0.00 0.00 3.43
2525 3030 8.191446 TGAGAGAAACAAAGGATAAGATCTACG 58.809 37.037 0.00 0.00 0.00 3.51
2528 3033 8.547173 ACATGAGAGAAACAAAGGATAAGATCT 58.453 33.333 0.00 0.00 0.00 2.75
2529 3034 8.729805 ACATGAGAGAAACAAAGGATAAGATC 57.270 34.615 0.00 0.00 0.00 2.75
2530 3035 8.954350 CAACATGAGAGAAACAAAGGATAAGAT 58.046 33.333 0.00 0.00 0.00 2.40
2531 3036 7.094634 GCAACATGAGAGAAACAAAGGATAAGA 60.095 37.037 0.00 0.00 0.00 2.10
2532 3037 7.025963 GCAACATGAGAGAAACAAAGGATAAG 58.974 38.462 0.00 0.00 0.00 1.73
2533 3038 6.716628 AGCAACATGAGAGAAACAAAGGATAA 59.283 34.615 0.00 0.00 0.00 1.75
2534 3039 6.149973 CAGCAACATGAGAGAAACAAAGGATA 59.850 38.462 0.00 0.00 0.00 2.59
2535 3040 5.048224 CAGCAACATGAGAGAAACAAAGGAT 60.048 40.000 0.00 0.00 0.00 3.24
2536 3041 4.276678 CAGCAACATGAGAGAAACAAAGGA 59.723 41.667 0.00 0.00 0.00 3.36
2537 3042 4.543692 CAGCAACATGAGAGAAACAAAGG 58.456 43.478 0.00 0.00 0.00 3.11
2538 3043 3.979495 GCAGCAACATGAGAGAAACAAAG 59.021 43.478 0.00 0.00 0.00 2.77
2539 3044 3.380954 TGCAGCAACATGAGAGAAACAAA 59.619 39.130 0.00 0.00 0.00 2.83
2540 3045 2.950975 TGCAGCAACATGAGAGAAACAA 59.049 40.909 0.00 0.00 0.00 2.83
2541 3046 2.574450 TGCAGCAACATGAGAGAAACA 58.426 42.857 0.00 0.00 0.00 2.83
2542 3047 3.439476 AGATGCAGCAACATGAGAGAAAC 59.561 43.478 4.07 0.00 0.00 2.78
2543 3048 3.439129 CAGATGCAGCAACATGAGAGAAA 59.561 43.478 4.07 0.00 0.00 2.52
2544 3049 3.007635 CAGATGCAGCAACATGAGAGAA 58.992 45.455 4.07 0.00 0.00 2.87
2545 3050 2.027469 ACAGATGCAGCAACATGAGAGA 60.027 45.455 4.07 0.00 0.00 3.10
2546 3051 2.357075 ACAGATGCAGCAACATGAGAG 58.643 47.619 4.07 0.00 0.00 3.20
2547 3052 2.484742 ACAGATGCAGCAACATGAGA 57.515 45.000 4.07 0.00 0.00 3.27
2548 3053 3.487042 GCTAACAGATGCAGCAACATGAG 60.487 47.826 4.07 0.00 35.35 2.90
2549 3054 2.421073 GCTAACAGATGCAGCAACATGA 59.579 45.455 4.07 0.00 35.35 3.07
2550 3055 2.162809 TGCTAACAGATGCAGCAACATG 59.837 45.455 4.07 0.81 42.09 3.21
2551 3056 2.439409 TGCTAACAGATGCAGCAACAT 58.561 42.857 4.07 0.00 42.09 2.71
2552 3057 1.894881 TGCTAACAGATGCAGCAACA 58.105 45.000 4.07 0.00 42.09 3.33
2556 3061 3.004002 TGCAATATGCTAACAGATGCAGC 59.996 43.478 0.00 0.00 45.31 5.25
2557 3062 4.823790 TGCAATATGCTAACAGATGCAG 57.176 40.909 3.78 0.00 45.31 4.41
2558 3063 5.777850 AATGCAATATGCTAACAGATGCA 57.222 34.783 3.78 0.00 45.31 3.96
2559 3064 6.088824 GGTAATGCAATATGCTAACAGATGC 58.911 40.000 3.78 0.00 45.31 3.91
2560 3065 7.205737 TGGTAATGCAATATGCTAACAGATG 57.794 36.000 3.78 0.00 45.31 2.90
2561 3066 7.666804 TGATGGTAATGCAATATGCTAACAGAT 59.333 33.333 3.78 0.00 45.31 2.90
2562 3067 6.997476 TGATGGTAATGCAATATGCTAACAGA 59.003 34.615 3.78 0.00 45.31 3.41
2563 3068 7.205737 TGATGGTAATGCAATATGCTAACAG 57.794 36.000 3.78 0.00 45.31 3.16
2564 3069 7.447853 TGATGATGGTAATGCAATATGCTAACA 59.552 33.333 3.78 0.00 45.31 2.41
2565 3070 7.819644 TGATGATGGTAATGCAATATGCTAAC 58.180 34.615 3.78 0.00 45.31 2.34
2566 3071 7.999450 TGATGATGGTAATGCAATATGCTAA 57.001 32.000 3.78 0.00 45.31 3.09
2567 3072 8.463607 CAATGATGATGGTAATGCAATATGCTA 58.536 33.333 3.78 0.00 45.31 3.49
2568 3073 7.039293 ACAATGATGATGGTAATGCAATATGCT 60.039 33.333 3.78 0.00 45.31 3.79
2569 3074 7.094631 ACAATGATGATGGTAATGCAATATGC 58.905 34.615 0.00 0.00 45.29 3.14
2570 3075 8.301002 TGACAATGATGATGGTAATGCAATATG 58.699 33.333 0.00 0.00 0.00 1.78
2571 3076 8.411991 TGACAATGATGATGGTAATGCAATAT 57.588 30.769 0.00 0.00 0.00 1.28
2572 3077 7.820578 TGACAATGATGATGGTAATGCAATA 57.179 32.000 0.00 0.00 0.00 1.90
2573 3078 6.718522 TGACAATGATGATGGTAATGCAAT 57.281 33.333 0.00 0.00 0.00 3.56
2574 3079 6.527057 TTGACAATGATGATGGTAATGCAA 57.473 33.333 0.00 0.00 0.00 4.08
2575 3080 6.331845 GTTTGACAATGATGATGGTAATGCA 58.668 36.000 0.00 0.00 0.00 3.96
2576 3081 5.750067 GGTTTGACAATGATGATGGTAATGC 59.250 40.000 0.00 0.00 0.00 3.56
2577 3082 6.976349 CAGGTTTGACAATGATGATGGTAATG 59.024 38.462 0.00 0.00 0.00 1.90
2578 3083 6.664816 ACAGGTTTGACAATGATGATGGTAAT 59.335 34.615 0.00 0.00 0.00 1.89
2579 3084 6.009589 ACAGGTTTGACAATGATGATGGTAA 58.990 36.000 0.00 0.00 0.00 2.85
2580 3085 5.415389 CACAGGTTTGACAATGATGATGGTA 59.585 40.000 0.00 0.00 0.00 3.25
2581 3086 4.219070 CACAGGTTTGACAATGATGATGGT 59.781 41.667 0.00 0.00 0.00 3.55
2582 3087 4.460034 TCACAGGTTTGACAATGATGATGG 59.540 41.667 0.00 0.00 0.00 3.51
2583 3088 5.632244 TCACAGGTTTGACAATGATGATG 57.368 39.130 0.00 0.00 0.00 3.07
2584 3089 7.997223 AGATATCACAGGTTTGACAATGATGAT 59.003 33.333 5.32 9.41 0.00 2.45
2585 3090 7.341030 AGATATCACAGGTTTGACAATGATGA 58.659 34.615 5.32 4.27 0.00 2.92
2586 3091 7.563888 AGATATCACAGGTTTGACAATGATG 57.436 36.000 5.32 3.01 0.00 3.07
2587 3092 9.857656 ATAAGATATCACAGGTTTGACAATGAT 57.142 29.630 5.32 6.49 0.00 2.45
2588 3093 9.112725 CATAAGATATCACAGGTTTGACAATGA 57.887 33.333 5.32 0.00 0.00 2.57
2589 3094 8.347771 CCATAAGATATCACAGGTTTGACAATG 58.652 37.037 5.32 0.00 0.00 2.82
2590 3095 8.055181 ACCATAAGATATCACAGGTTTGACAAT 58.945 33.333 5.32 0.00 0.00 2.71
2591 3096 7.336679 CACCATAAGATATCACAGGTTTGACAA 59.663 37.037 5.32 0.00 0.00 3.18
2592 3097 6.823182 CACCATAAGATATCACAGGTTTGACA 59.177 38.462 5.32 0.00 0.00 3.58
2593 3098 6.260936 CCACCATAAGATATCACAGGTTTGAC 59.739 42.308 5.32 0.00 0.00 3.18
2594 3099 6.069673 ACCACCATAAGATATCACAGGTTTGA 60.070 38.462 5.32 0.00 0.00 2.69
2595 3100 6.122277 ACCACCATAAGATATCACAGGTTTG 58.878 40.000 5.32 4.10 0.00 2.93
2596 3101 6.327386 ACCACCATAAGATATCACAGGTTT 57.673 37.500 5.32 0.00 0.00 3.27
2597 3102 5.975988 ACCACCATAAGATATCACAGGTT 57.024 39.130 5.32 0.00 0.00 3.50
2598 3103 5.307196 GGTACCACCATAAGATATCACAGGT 59.693 44.000 7.15 4.56 38.42 4.00
2599 3104 5.306937 TGGTACCACCATAAGATATCACAGG 59.693 44.000 11.60 3.93 44.79 4.00
2600 3105 6.419484 TGGTACCACCATAAGATATCACAG 57.581 41.667 11.60 0.00 44.79 3.66


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

AutoCloner maintained by Alex Coulton.