Multiple sequence alignment - TraesCS4B01G228500

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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 TraesCS4B01G228500 chr4B 100.000 5973 0 0 968 6940 479157011 479151039 0.000000e+00 11031
1 TraesCS4B01G228500 chr4B 100.000 444 0 0 1 444 479157978 479157535 0.000000e+00 821
2 TraesCS4B01G228500 chr4B 79.085 306 58 6 6367 6669 402751910 402752212 9.120000e-49 206
3 TraesCS4B01G228500 chr4A 95.881 4249 109 22 2696 6911 70811551 70807336 0.000000e+00 6817
4 TraesCS4B01G228500 chr4A 95.129 1396 51 7 971 2365 70813178 70811799 0.000000e+00 2185
5 TraesCS4B01G228500 chr4A 97.085 446 10 2 1 444 70813709 70813265 0.000000e+00 749
6 TraesCS4B01G228500 chr4A 95.109 184 9 0 2469 2652 70811798 70811615 2.450000e-74 291
7 TraesCS4B01G228500 chr4D 94.886 4282 122 34 2696 6935 389228890 389224664 0.000000e+00 6604
8 TraesCS4B01G228500 chr4D 93.583 1418 50 6 971 2388 389230558 389229182 0.000000e+00 2076
9 TraesCS4B01G228500 chr4D 97.748 444 7 2 1 444 389231085 389230645 0.000000e+00 761
10 TraesCS4B01G228500 chr4D 94.981 259 11 1 2438 2696 389229182 389228926 8.380000e-109 405
11 TraesCS4B01G228500 chr5D 80.656 305 56 3 6368 6670 219771922 219772225 4.190000e-57 233
12 TraesCS4B01G228500 chr7A 80.328 305 57 3 6368 6670 707151556 707151859 1.950000e-55 228
13 TraesCS4B01G228500 chr7A 76.453 327 62 15 6367 6685 553635370 553635051 5.570000e-36 163
14 TraesCS4B01G228500 chr7D 79.814 322 54 9 6368 6685 614675367 614675053 2.520000e-54 224
15 TraesCS4B01G228500 chr7B 77.676 327 59 14 6367 6685 512870035 512869715 3.310000e-43 187
16 TraesCS4B01G228500 chr7B 95.495 111 3 1 2363 2473 357651484 357651592 7.150000e-40 176
17 TraesCS4B01G228500 chr6B 92.857 126 5 3 2357 2481 507471661 507471539 5.530000e-41 180
18 TraesCS4B01G228500 chr6B 89.474 133 8 5 2357 2486 585524848 585524719 5.570000e-36 163
19 TraesCS4B01G228500 chr6A 92.248 129 6 3 2354 2481 454677960 454678085 5.530000e-41 180
20 TraesCS4B01G228500 chr6D 91.538 130 6 4 2354 2481 317078776 317078902 2.570000e-39 174
21 TraesCS4B01G228500 chr6D 90.226 133 7 5 2357 2486 391925993 391925864 1.200000e-37 169
22 TraesCS4B01G228500 chr3D 93.277 119 5 3 2353 2471 477910550 477910665 9.250000e-39 172
23 TraesCS4B01G228500 chr2A 91.597 119 8 1 2354 2472 205917591 205917707 5.570000e-36 163
24 TraesCS4B01G228500 chr3A 91.597 119 7 3 2353 2471 621328141 621328256 2.000000e-35 161
25 TraesCS4B01G228500 chr5A 75.490 306 68 7 6367 6668 445556176 445556478 7.260000e-30 143


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 TraesCS4B01G228500 chr4B 479151039 479157978 6939 True 5926.0 11031 100.0000 1 6940 2 chr4B.!!$R1 6939
1 TraesCS4B01G228500 chr4A 70807336 70813709 6373 True 2510.5 6817 95.8010 1 6911 4 chr4A.!!$R1 6910
2 TraesCS4B01G228500 chr4D 389224664 389231085 6421 True 2461.5 6604 95.2995 1 6935 4 chr4D.!!$R1 6934

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
137 139 5.639506 TCTTTCACCGATTGTTCTCATCTTC 59.360 40.000 0.00 0.00 0.00 2.87 F
1426 1428 0.034186 TGGAAGCAAGGCATAGTGGG 60.034 55.000 0.00 0.00 0.00 4.61 F
1631 1633 0.105039 GATGTCCCCTCCTTACAGCG 59.895 60.000 0.00 0.00 0.00 5.18 F
2401 2404 0.670546 ACCTGTCGCTCAAACGGATG 60.671 55.000 0.00 0.00 0.00 3.51 F
2402 2405 0.670546 CCTGTCGCTCAAACGGATGT 60.671 55.000 0.00 0.00 0.00 3.06 F
2472 2475 0.755698 TGTGGATCGGAGGGAGTAGC 60.756 60.000 0.00 0.00 0.00 3.58 F
3401 3456 1.305718 AGGAGACCTCTCTGCCACC 60.306 63.158 2.37 0.00 42.48 4.61 F
3440 3495 1.554160 AGGAGAGCAGGTGATCACTTG 59.446 52.381 28.44 28.44 40.83 3.16 F
4212 4277 1.675641 CTGGGTGTTGCCTAGTGCC 60.676 63.158 1.42 0.00 40.58 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1525 1527 0.676782 CAACCCTTTCCCAGCTACCG 60.677 60.000 0.00 0.00 0.00 4.02 R
2456 2459 0.178987 TCAGCTACTCCCTCCGATCC 60.179 60.000 0.00 0.00 0.00 3.36 R
2806 2845 2.040544 GTCCCAAGCATCCACACCG 61.041 63.158 0.00 0.00 0.00 4.94 R
3867 3925 2.618312 GATTTGTGCCCGCATCTGCC 62.618 60.000 0.00 0.00 37.91 4.85 R
4143 4208 4.331717 ACGCACAATGTAAATAGCACTACC 59.668 41.667 0.00 0.00 0.00 3.18 R
4999 5065 9.775854 CAGATTAGAGATAACAGATCAACCATT 57.224 33.333 0.00 0.00 0.00 3.16 R
5296 5362 1.270550 CATGTTTCTTCTGCACCCCAC 59.729 52.381 0.00 0.00 0.00 4.61 R
5506 5572 4.074970 CAGCCAAGTCCTACAACAAGAAT 58.925 43.478 0.00 0.00 0.00 2.40 R
6724 6827 0.032912 TGTGGGCCTAGGATACGACA 60.033 55.000 14.75 12.19 46.39 4.35 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
137 139 5.639506 TCTTTCACCGATTGTTCTCATCTTC 59.360 40.000 0.00 0.00 0.00 2.87
1029 1031 2.087501 TGATAGCGAAAAAGGCGACA 57.912 45.000 0.00 0.00 35.00 4.35
1133 1135 0.107897 TCCGGATGCAATGTTACGCT 60.108 50.000 0.00 0.00 0.00 5.07
1210 1212 9.793259 TGTTGGTAGAATTTTGAGAAGATTACT 57.207 29.630 0.00 0.00 0.00 2.24
1260 1262 6.817765 TCAGGTACATGTTCTTGGATTTTC 57.182 37.500 13.39 0.00 0.00 2.29
1311 1313 7.651027 ATTTGGAAGGAGAGGAAAATACATG 57.349 36.000 0.00 0.00 0.00 3.21
1361 1363 5.198602 ACTGCCCTAAAGGATTCTCAATT 57.801 39.130 0.00 0.00 38.24 2.32
1391 1393 7.857456 TGAGAAATAGAATAGGGTAAGCACAA 58.143 34.615 0.00 0.00 0.00 3.33
1401 1403 9.301153 GAATAGGGTAAGCACAATTTATGTTTG 57.699 33.333 0.00 0.00 41.46 2.93
1422 1424 2.883386 GGAATCTGGAAGCAAGGCATAG 59.117 50.000 0.00 0.00 0.00 2.23
1423 1425 3.549794 GAATCTGGAAGCAAGGCATAGT 58.450 45.455 0.00 0.00 0.00 2.12
1426 1428 0.034186 TGGAAGCAAGGCATAGTGGG 60.034 55.000 0.00 0.00 0.00 4.61
1437 1439 5.603170 AGGCATAGTGGGAATCATTTTTG 57.397 39.130 0.00 0.00 0.00 2.44
1484 1486 3.646162 CACATAGCACCACTATCCCCTTA 59.354 47.826 0.00 0.00 39.71 2.69
1525 1527 2.935481 ATTGCTTAAGCTGCTCTTGC 57.065 45.000 26.90 8.14 42.66 4.01
1536 1538 3.019003 GCTCTTGCGGTAGCTGGGA 62.019 63.158 0.00 0.00 45.42 4.37
1602 1604 4.165565 TCCAATGATGATGAGCTCCTTTCT 59.834 41.667 12.15 0.00 0.00 2.52
1631 1633 0.105039 GATGTCCCCTCCTTACAGCG 59.895 60.000 0.00 0.00 0.00 5.18
1706 1708 4.873746 TTGTGGTTGGACAACTTCAAAA 57.126 36.364 14.14 4.50 40.94 2.44
1712 1714 3.374042 TGGACAACTTCAAAACCCAGA 57.626 42.857 0.00 0.00 0.00 3.86
1740 1742 4.600062 AGATTTAGAAACACCCCACCATC 58.400 43.478 0.00 0.00 0.00 3.51
1838 1840 2.098293 CCATGTTTGGCTACGAGGC 58.902 57.895 0.00 0.00 41.77 4.70
1889 1891 2.484264 GGCGAGTAGAAAATGCACAAGT 59.516 45.455 0.00 0.00 0.00 3.16
1892 1894 4.625742 GCGAGTAGAAAATGCACAAGTCTA 59.374 41.667 0.00 0.00 0.00 2.59
2041 2043 1.300971 GCAGATGCTTTGTCCTCGCA 61.301 55.000 0.00 0.00 38.21 5.10
2068 2070 6.535963 TGTCTTACAGATCACATGTCTGAT 57.464 37.500 17.34 8.96 44.57 2.90
2155 2158 5.895636 TTTATGTTGCAATACAGGTCAGG 57.104 39.130 0.59 0.00 0.00 3.86
2179 2182 5.634020 GCATTACTACTATCGCCTTGTTAGG 59.366 44.000 0.00 0.00 45.02 2.69
2282 2285 7.333528 TGGTAATTGAATGAGCCTTAATGAC 57.666 36.000 0.00 0.00 0.00 3.06
2283 2286 6.889177 TGGTAATTGAATGAGCCTTAATGACA 59.111 34.615 0.00 0.00 0.00 3.58
2297 2300 6.145048 GCCTTAATGACATGCAATTAATCTGC 59.855 38.462 11.70 12.76 40.35 4.26
2314 2317 3.476552 TCTGCTGGGTTGTAGTTCAAAG 58.523 45.455 0.00 0.00 37.81 2.77
2315 2318 3.118038 TCTGCTGGGTTGTAGTTCAAAGT 60.118 43.478 0.00 0.00 37.81 2.66
2316 2319 3.626930 TGCTGGGTTGTAGTTCAAAGTT 58.373 40.909 0.00 0.00 37.81 2.66
2317 2320 3.630312 TGCTGGGTTGTAGTTCAAAGTTC 59.370 43.478 0.00 0.00 37.81 3.01
2318 2321 3.630312 GCTGGGTTGTAGTTCAAAGTTCA 59.370 43.478 0.00 0.00 37.81 3.18
2319 2322 4.097286 GCTGGGTTGTAGTTCAAAGTTCAA 59.903 41.667 0.00 0.00 37.81 2.69
2320 2323 5.393678 GCTGGGTTGTAGTTCAAAGTTCAAA 60.394 40.000 0.00 0.00 37.81 2.69
2384 2387 3.442076 ACTCCCTCCGATCCATATTACC 58.558 50.000 0.00 0.00 0.00 2.85
2387 2390 3.173965 CCCTCCGATCCATATTACCTGT 58.826 50.000 0.00 0.00 0.00 4.00
2388 2391 3.195825 CCCTCCGATCCATATTACCTGTC 59.804 52.174 0.00 0.00 0.00 3.51
2389 2392 3.119459 CCTCCGATCCATATTACCTGTCG 60.119 52.174 0.00 0.00 0.00 4.35
2390 2393 2.230508 TCCGATCCATATTACCTGTCGC 59.769 50.000 0.00 0.00 0.00 5.19
2391 2394 2.231478 CCGATCCATATTACCTGTCGCT 59.769 50.000 0.00 0.00 0.00 4.93
2392 2395 3.502920 CGATCCATATTACCTGTCGCTC 58.497 50.000 0.00 0.00 0.00 5.03
2393 2396 3.057526 CGATCCATATTACCTGTCGCTCA 60.058 47.826 0.00 0.00 0.00 4.26
2394 2397 4.558697 CGATCCATATTACCTGTCGCTCAA 60.559 45.833 0.00 0.00 0.00 3.02
2395 2398 4.746535 TCCATATTACCTGTCGCTCAAA 57.253 40.909 0.00 0.00 0.00 2.69
2396 2399 4.439057 TCCATATTACCTGTCGCTCAAAC 58.561 43.478 0.00 0.00 0.00 2.93
2397 2400 3.245284 CCATATTACCTGTCGCTCAAACG 59.755 47.826 0.00 0.00 0.00 3.60
2398 2401 1.722011 ATTACCTGTCGCTCAAACGG 58.278 50.000 0.00 0.00 0.00 4.44
2399 2402 0.675083 TTACCTGTCGCTCAAACGGA 59.325 50.000 0.00 0.00 0.00 4.69
2400 2403 0.892755 TACCTGTCGCTCAAACGGAT 59.107 50.000 0.00 0.00 0.00 4.18
2401 2404 0.670546 ACCTGTCGCTCAAACGGATG 60.671 55.000 0.00 0.00 0.00 3.51
2402 2405 0.670546 CCTGTCGCTCAAACGGATGT 60.671 55.000 0.00 0.00 0.00 3.06
2403 2406 1.403647 CCTGTCGCTCAAACGGATGTA 60.404 52.381 0.00 0.00 0.00 2.29
2404 2407 2.540515 CTGTCGCTCAAACGGATGTAT 58.459 47.619 0.00 0.00 0.00 2.29
2405 2408 2.535984 CTGTCGCTCAAACGGATGTATC 59.464 50.000 0.00 0.00 0.00 2.24
2406 2409 2.165641 TGTCGCTCAAACGGATGTATCT 59.834 45.455 0.00 0.00 0.00 1.98
2407 2410 3.379057 TGTCGCTCAAACGGATGTATCTA 59.621 43.478 0.00 0.00 0.00 1.98
2408 2411 3.975670 GTCGCTCAAACGGATGTATCTAG 59.024 47.826 0.00 0.00 0.00 2.43
2409 2412 2.726760 CGCTCAAACGGATGTATCTAGC 59.273 50.000 0.00 0.00 0.00 3.42
2410 2413 3.717707 GCTCAAACGGATGTATCTAGCA 58.282 45.455 0.00 0.00 0.00 3.49
2411 2414 3.491267 GCTCAAACGGATGTATCTAGCAC 59.509 47.826 0.00 0.00 0.00 4.40
2412 2415 4.737946 GCTCAAACGGATGTATCTAGCACT 60.738 45.833 0.00 0.00 0.00 4.40
2413 2416 4.682787 TCAAACGGATGTATCTAGCACTG 58.317 43.478 0.00 0.00 0.00 3.66
2414 2417 4.401202 TCAAACGGATGTATCTAGCACTGA 59.599 41.667 0.00 0.00 0.00 3.41
2415 2418 5.105513 TCAAACGGATGTATCTAGCACTGAA 60.106 40.000 0.00 0.00 0.00 3.02
2416 2419 5.339008 AACGGATGTATCTAGCACTGAAA 57.661 39.130 0.00 0.00 0.00 2.69
2417 2420 5.537300 ACGGATGTATCTAGCACTGAAAT 57.463 39.130 0.00 0.00 0.00 2.17
2418 2421 6.650427 ACGGATGTATCTAGCACTGAAATA 57.350 37.500 0.00 0.00 0.00 1.40
2419 2422 6.448006 ACGGATGTATCTAGCACTGAAATAC 58.552 40.000 0.00 0.00 0.00 1.89
2420 2423 5.569441 CGGATGTATCTAGCACTGAAATACG 59.431 44.000 0.00 0.00 0.00 3.06
2421 2424 6.448006 GGATGTATCTAGCACTGAAATACGT 58.552 40.000 0.00 0.00 0.00 3.57
2422 2425 6.583050 GGATGTATCTAGCACTGAAATACGTC 59.417 42.308 0.00 8.28 37.78 4.34
2423 2426 6.694877 TGTATCTAGCACTGAAATACGTCT 57.305 37.500 0.00 0.00 0.00 4.18
2424 2427 7.797038 TGTATCTAGCACTGAAATACGTCTA 57.203 36.000 0.00 0.00 0.00 2.59
2425 2428 7.862648 TGTATCTAGCACTGAAATACGTCTAG 58.137 38.462 0.00 0.00 0.00 2.43
2426 2429 7.713942 TGTATCTAGCACTGAAATACGTCTAGA 59.286 37.037 0.00 0.00 36.50 2.43
2427 2430 7.753309 ATCTAGCACTGAAATACGTCTAGAT 57.247 36.000 10.29 10.29 37.49 1.98
2428 2431 8.850007 ATCTAGCACTGAAATACGTCTAGATA 57.150 34.615 13.10 0.00 39.33 1.98
2429 2432 8.085720 TCTAGCACTGAAATACGTCTAGATAC 57.914 38.462 0.00 0.00 29.74 2.24
2430 2433 6.694877 AGCACTGAAATACGTCTAGATACA 57.305 37.500 0.00 0.00 0.00 2.29
2431 2434 7.278461 AGCACTGAAATACGTCTAGATACAT 57.722 36.000 0.00 0.00 0.00 2.29
2432 2435 7.364200 AGCACTGAAATACGTCTAGATACATC 58.636 38.462 0.00 0.00 0.00 3.06
2433 2436 7.013369 AGCACTGAAATACGTCTAGATACATCA 59.987 37.037 0.00 0.00 0.00 3.07
2434 2437 7.648112 GCACTGAAATACGTCTAGATACATCAA 59.352 37.037 0.00 0.00 0.00 2.57
2435 2438 9.684448 CACTGAAATACGTCTAGATACATCAAT 57.316 33.333 0.00 0.00 0.00 2.57
2455 2458 7.609760 TCAATTTGAGCGACAAGTAATATGT 57.390 32.000 0.00 0.00 39.77 2.29
2456 2459 7.463544 TCAATTTGAGCGACAAGTAATATGTG 58.536 34.615 0.00 0.00 39.77 3.21
2472 2475 0.755698 TGTGGATCGGAGGGAGTAGC 60.756 60.000 0.00 0.00 0.00 3.58
2489 2492 7.451566 AGGGAGTAGCTGATTTTACAATGTTTT 59.548 33.333 0.00 0.00 0.00 2.43
2565 2568 7.112122 AGTCATTCTAACCTACAAATCATGCA 58.888 34.615 0.00 0.00 0.00 3.96
2659 2662 9.702726 CTTTATAGATCAATTGTGTAAACACCG 57.297 33.333 10.58 0.00 45.88 4.94
2671 2674 7.908827 TGTGTAAACACCGTGTCATATTTAT 57.091 32.000 4.23 0.00 45.88 1.40
2746 2785 9.770503 CTGTTCTGACTAATCAATCAAAATGAG 57.229 33.333 0.00 0.00 33.30 2.90
2788 2827 1.352017 TCTCTTCCTCCTGCATTGCAA 59.648 47.619 13.18 0.00 38.41 4.08
2796 2835 5.421277 TCCTCCTGCATTGCAAAATTAATG 58.579 37.500 13.18 0.00 38.41 1.90
2806 2845 9.693157 GCATTGCAAAATTAATGACAATAACTC 57.307 29.630 1.71 0.00 36.61 3.01
2856 2895 7.915397 GGGTGCTTATTGTTTGTATATTGACAG 59.085 37.037 0.00 0.00 0.00 3.51
2857 2896 8.673711 GGTGCTTATTGTTTGTATATTGACAGA 58.326 33.333 0.00 0.00 0.00 3.41
2937 2991 7.492020 TCATTTGATCCTGTGTTGTTTCTTTTG 59.508 33.333 0.00 0.00 0.00 2.44
2942 2996 9.126151 TGATCCTGTGTTGTTTCTTTTGTATTA 57.874 29.630 0.00 0.00 0.00 0.98
3151 3206 9.807649 GTTTCTCATGCAACATATCCTATTTTT 57.192 29.630 0.00 0.00 0.00 1.94
3215 3270 4.470304 AGAAAGTGTTCACTAGGGGATACC 59.530 45.833 5.87 0.00 46.83 2.73
3354 3409 4.805219 GTTTATGAAACGGGTTGCAGAAT 58.195 39.130 0.76 0.00 30.28 2.40
3401 3456 1.305718 AGGAGACCTCTCTGCCACC 60.306 63.158 2.37 0.00 42.48 4.61
3440 3495 1.554160 AGGAGAGCAGGTGATCACTTG 59.446 52.381 28.44 28.44 40.83 3.16
3492 3550 5.536538 AGCCTCACTCATCTTTGATCGTATA 59.463 40.000 0.00 0.00 0.00 1.47
3505 3563 8.551205 TCTTTGATCGTATAAAATCTGCATGTC 58.449 33.333 0.00 0.00 0.00 3.06
3875 3933 9.918630 ATATTTTTATTCTGTATTGGCAGATGC 57.081 29.630 0.00 0.00 43.99 3.91
4092 4157 8.265055 TGGTTAATTGTTAGTCTTAGATCCCTG 58.735 37.037 0.00 0.00 0.00 4.45
4098 4163 6.728411 TGTTAGTCTTAGATCCCTGTAGTCA 58.272 40.000 0.00 0.00 0.00 3.41
4143 4208 8.129161 TGAAACATGAAGCACAAATAACTTTG 57.871 30.769 0.00 0.00 45.92 2.77
4169 4234 6.677781 AGTGCTATTTACATTGTGCGTAAT 57.322 33.333 0.00 0.00 0.00 1.89
4212 4277 1.675641 CTGGGTGTTGCCTAGTGCC 60.676 63.158 1.42 0.00 40.58 5.01
5296 5362 3.098377 TCAAACATCCCATTCCACCATG 58.902 45.455 0.00 0.00 0.00 3.66
5506 5572 4.448395 CCTGTTCGACACCGTTAATTTACA 59.552 41.667 0.00 0.00 37.05 2.41
5725 5791 1.139058 ACCAAACTAGCTATGCCGAGG 59.861 52.381 0.00 0.00 0.00 4.63
5813 5879 3.669536 GCCAATAAGATCCCTAGCTGAC 58.330 50.000 0.00 0.00 0.00 3.51
6182 6248 3.487563 AGCGCTTGGTTACAATAAAGC 57.512 42.857 2.64 0.00 41.26 3.51
6183 6249 2.163613 AGCGCTTGGTTACAATAAAGCC 59.836 45.455 2.64 0.00 41.56 4.35
6234 6300 4.620982 CTTGGGTCAATTGGAGTTTGTTC 58.379 43.478 5.42 0.00 0.00 3.18
6365 6431 7.552050 AAATCAATGTGTTTATTTGAGGGGA 57.448 32.000 0.00 0.00 0.00 4.81
6392 6459 6.679327 GGTGGTACCTCAGAATAACATTTC 57.321 41.667 14.36 0.00 34.73 2.17
6474 6541 0.109132 CAAAGCCGGTTGGATGAAGC 60.109 55.000 1.90 0.00 37.49 3.86
6503 6570 2.044135 GCTTTTGGCGTTCTCTTTTCG 58.956 47.619 0.00 0.00 0.00 3.46
6568 6636 3.363970 GCGATTCGACTCACAATGTTGTT 60.364 43.478 10.88 0.00 39.91 2.83
6570 6638 5.613795 GCGATTCGACTCACAATGTTGTTTA 60.614 40.000 10.88 0.00 39.91 2.01
6572 6640 6.346598 CGATTCGACTCACAATGTTGTTTAGT 60.347 38.462 0.00 9.29 39.91 2.24
6573 6641 5.651172 TCGACTCACAATGTTGTTTAGTG 57.349 39.130 12.76 0.00 39.91 2.74
6574 6642 5.113383 TCGACTCACAATGTTGTTTAGTGT 58.887 37.500 12.76 3.39 39.91 3.55
6575 6643 5.583061 TCGACTCACAATGTTGTTTAGTGTT 59.417 36.000 12.76 0.00 39.91 3.32
6576 6644 5.676744 CGACTCACAATGTTGTTTAGTGTTG 59.323 40.000 12.76 3.83 39.91 3.33
6577 6645 6.456315 CGACTCACAATGTTGTTTAGTGTTGA 60.456 38.462 12.76 0.00 39.91 3.18
6578 6646 6.785191 ACTCACAATGTTGTTTAGTGTTGAG 58.215 36.000 8.90 6.89 39.91 3.02
6579 6647 6.374333 ACTCACAATGTTGTTTAGTGTTGAGT 59.626 34.615 8.90 7.37 39.91 3.41
6580 6648 6.550843 TCACAATGTTGTTTAGTGTTGAGTG 58.449 36.000 0.00 0.00 39.91 3.51
6581 6649 6.150307 TCACAATGTTGTTTAGTGTTGAGTGT 59.850 34.615 0.00 0.00 39.91 3.55
6582 6650 6.806249 CACAATGTTGTTTAGTGTTGAGTGTT 59.194 34.615 0.00 0.00 39.91 3.32
6583 6651 7.965655 CACAATGTTGTTTAGTGTTGAGTGTTA 59.034 33.333 0.00 0.00 39.91 2.41
6584 6652 8.181573 ACAATGTTGTTTAGTGTTGAGTGTTAG 58.818 33.333 0.00 0.00 38.47 2.34
6585 6653 7.859325 ATGTTGTTTAGTGTTGAGTGTTAGT 57.141 32.000 0.00 0.00 0.00 2.24
6586 6654 7.298507 TGTTGTTTAGTGTTGAGTGTTAGTC 57.701 36.000 0.00 0.00 0.00 2.59
6587 6655 6.035220 TGTTGTTTAGTGTTGAGTGTTAGTCG 59.965 38.462 0.00 0.00 0.00 4.18
6588 6656 5.893687 TGTTTAGTGTTGAGTGTTAGTCGA 58.106 37.500 0.00 0.00 0.00 4.20
6589 6657 5.745294 TGTTTAGTGTTGAGTGTTAGTCGAC 59.255 40.000 7.70 7.70 33.47 4.20
6590 6658 5.762825 TTAGTGTTGAGTGTTAGTCGACT 57.237 39.130 23.66 23.66 33.90 4.18
6591 6659 6.866010 TTAGTGTTGAGTGTTAGTCGACTA 57.134 37.500 21.25 21.25 33.90 2.59
6592 6660 5.762825 AGTGTTGAGTGTTAGTCGACTAA 57.237 39.130 29.57 29.57 33.90 2.24
6593 6661 6.140303 AGTGTTGAGTGTTAGTCGACTAAA 57.860 37.500 33.50 22.23 39.84 1.85
6594 6662 6.567050 AGTGTTGAGTGTTAGTCGACTAAAA 58.433 36.000 33.50 27.83 39.84 1.52
6604 6695 8.540492 GTGTTAGTCGACTAAAATGTGATATGG 58.460 37.037 33.50 0.00 39.84 2.74
6670 6761 1.988107 TGGCCACAGAAGAAAGGATCT 59.012 47.619 0.00 0.00 41.32 2.75
6672 6763 1.742268 GCCACAGAAGAAAGGATCTGC 59.258 52.381 2.86 0.00 45.50 4.26
6675 6766 2.746362 CACAGAAGAAAGGATCTGCCAC 59.254 50.000 2.86 0.00 45.50 5.01
6714 6817 7.001674 TGAGGTAGCACCAATTTAAAGAGAAA 58.998 34.615 7.86 0.00 41.95 2.52
6734 6837 9.838339 AGAGAAATTTATTCAATGTCGTATCCT 57.162 29.630 0.00 0.00 34.53 3.24
6738 6841 7.907214 ATTTATTCAATGTCGTATCCTAGGC 57.093 36.000 2.96 0.00 0.00 3.93
6739 6842 3.746045 TTCAATGTCGTATCCTAGGCC 57.254 47.619 2.96 0.00 0.00 5.19
6740 6843 1.968493 TCAATGTCGTATCCTAGGCCC 59.032 52.381 2.96 0.00 0.00 5.80
6741 6844 1.691976 CAATGTCGTATCCTAGGCCCA 59.308 52.381 2.96 0.00 0.00 5.36
6742 6845 1.339097 ATGTCGTATCCTAGGCCCAC 58.661 55.000 2.96 0.39 0.00 4.61
6743 6846 0.032912 TGTCGTATCCTAGGCCCACA 60.033 55.000 2.96 0.00 0.00 4.17
6744 6847 1.339097 GTCGTATCCTAGGCCCACAT 58.661 55.000 2.96 0.00 0.00 3.21
6745 6848 1.272769 GTCGTATCCTAGGCCCACATC 59.727 57.143 2.96 0.00 0.00 3.06
6746 6849 0.608640 CGTATCCTAGGCCCACATCC 59.391 60.000 2.96 0.00 0.00 3.51
6747 6850 1.729586 GTATCCTAGGCCCACATCCA 58.270 55.000 2.96 0.00 0.00 3.41
6748 6851 2.269940 GTATCCTAGGCCCACATCCAT 58.730 52.381 2.96 0.00 0.00 3.41
6749 6852 1.366319 ATCCTAGGCCCACATCCATC 58.634 55.000 2.96 0.00 0.00 3.51
6750 6853 1.121407 TCCTAGGCCCACATCCATCG 61.121 60.000 2.96 0.00 0.00 3.84
6751 6854 1.302033 CTAGGCCCACATCCATCGC 60.302 63.158 0.00 0.00 0.00 4.58
6752 6855 2.043604 CTAGGCCCACATCCATCGCA 62.044 60.000 0.00 0.00 0.00 5.10
6753 6856 2.324014 TAGGCCCACATCCATCGCAC 62.324 60.000 0.00 0.00 0.00 5.34
6754 6857 3.211963 GCCCACATCCATCGCACC 61.212 66.667 0.00 0.00 0.00 5.01
6755 6858 2.271821 CCCACATCCATCGCACCA 59.728 61.111 0.00 0.00 0.00 4.17
6756 6859 1.378382 CCCACATCCATCGCACCAA 60.378 57.895 0.00 0.00 0.00 3.67
6757 6860 0.752743 CCCACATCCATCGCACCAAT 60.753 55.000 0.00 0.00 0.00 3.16
6777 6880 6.988622 CAATTTGGTTTGGACATATGCAAT 57.011 33.333 1.58 0.00 35.89 3.56
6790 6893 6.080648 ACATATGCAATACAAGCCTTCATG 57.919 37.500 1.58 0.00 0.00 3.07
6807 6910 2.359848 TCATGTGCTTCAATGCATAGCC 59.640 45.455 15.60 8.78 45.23 3.93
6808 6911 1.105457 TGTGCTTCAATGCATAGCCC 58.895 50.000 15.60 6.49 45.23 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 0.535780 ACCTACGACGTCAGTGTGGA 60.536 55.000 24.82 6.73 0.00 4.02
26 27 1.268896 ACAACCTACGACGTCAGTGTG 60.269 52.381 17.16 11.59 0.00 3.82
27 28 1.027357 ACAACCTACGACGTCAGTGT 58.973 50.000 17.16 8.09 0.00 3.55
28 29 2.129823 AACAACCTACGACGTCAGTG 57.870 50.000 17.16 1.48 0.00 3.66
29 30 2.466846 CAAACAACCTACGACGTCAGT 58.533 47.619 17.16 16.08 0.00 3.41
30 31 1.790623 CCAAACAACCTACGACGTCAG 59.209 52.381 17.16 10.90 0.00 3.51
137 139 6.158520 AGGAATTGGGGAAAATTAAGGAATGG 59.841 38.462 0.00 0.00 29.89 3.16
364 366 0.235665 CATTCGCGGCGCAAATATCT 59.764 50.000 32.61 0.68 0.00 1.98
969 971 3.960571 AGATCAGGAAAATCCACCACAG 58.039 45.455 0.00 0.00 39.61 3.66
974 976 4.622740 CGCAAAAAGATCAGGAAAATCCAC 59.377 41.667 0.00 0.00 39.61 4.02
1029 1031 3.133464 CATGCGGCCCATTGTCGT 61.133 61.111 0.00 0.00 29.71 4.34
1133 1135 6.096141 TCAACTAAAGCAGTTTGGAAATCACA 59.904 34.615 0.00 0.00 45.54 3.58
1210 1212 3.128349 GTTTTTGCTCTGGACACGTAGA 58.872 45.455 0.00 0.00 0.00 2.59
1311 1313 3.489785 CACAGTTTGACTTACGGTCTCAC 59.510 47.826 0.00 0.00 44.74 3.51
1379 1381 5.777732 TCCAAACATAAATTGTGCTTACCCT 59.222 36.000 0.00 0.00 38.99 4.34
1391 1393 6.855763 TGCTTCCAGATTCCAAACATAAAT 57.144 33.333 0.00 0.00 0.00 1.40
1401 1403 1.772836 ATGCCTTGCTTCCAGATTCC 58.227 50.000 0.00 0.00 0.00 3.01
1437 1439 5.849510 ACAAATAACAAAGGCCTTGGTAAC 58.150 37.500 26.18 0.00 40.61 2.50
1525 1527 0.676782 CAACCCTTTCCCAGCTACCG 60.677 60.000 0.00 0.00 0.00 4.02
1536 1538 1.778383 TCCCTCCCTGCAACCCTTT 60.778 57.895 0.00 0.00 0.00 3.11
1602 1604 2.268920 GGGACATCGGCTGCAAGA 59.731 61.111 0.50 0.09 34.07 3.02
1631 1633 1.681486 GCAGGCTAGGAGGGTGAGTC 61.681 65.000 0.00 0.00 0.00 3.36
1679 1681 4.186856 AGTTGTCCAACCACAAAACTTG 57.813 40.909 6.55 0.00 42.06 3.16
1706 1708 5.014123 TGTTTCTAAATCTCATGGTCTGGGT 59.986 40.000 0.00 0.00 0.00 4.51
1712 1714 4.044065 TGGGGTGTTTCTAAATCTCATGGT 59.956 41.667 0.00 0.00 0.00 3.55
1838 1840 2.064762 GCTAAGATACTGAGGCATGCG 58.935 52.381 12.44 0.00 0.00 4.73
1889 1891 3.276857 AGGTGTAGCGTCTTCGATTAGA 58.723 45.455 0.00 0.00 39.71 2.10
1892 1894 3.276857 TCTAGGTGTAGCGTCTTCGATT 58.723 45.455 0.00 0.00 39.71 3.34
1940 1942 3.932580 TAGGACAGCGTGCGCCTTG 62.933 63.158 13.21 8.48 43.17 3.61
1941 1943 3.649277 CTAGGACAGCGTGCGCCTT 62.649 63.158 13.21 0.00 43.17 4.35
1942 1944 4.135153 CTAGGACAGCGTGCGCCT 62.135 66.667 13.21 8.49 43.17 5.52
1954 1956 1.461897 GTTTAACGCGCTTTGCTAGGA 59.538 47.619 5.73 0.00 43.27 2.94
1967 1969 1.540267 TGGGAATGGCCAGTTTAACG 58.460 50.000 13.05 0.00 38.95 3.18
2006 2008 5.945784 AGCATCTGCCAACATAGAAAACTAA 59.054 36.000 0.00 0.00 43.38 2.24
2010 2012 5.010922 ACAAAGCATCTGCCAACATAGAAAA 59.989 36.000 0.00 0.00 43.38 2.29
2094 2096 6.998673 GGCTAATGGGAAGTACAACATATTCT 59.001 38.462 0.00 0.00 0.00 2.40
2101 2103 4.216411 TGAGGCTAATGGGAAGTACAAC 57.784 45.455 0.00 0.00 0.00 3.32
2155 2158 5.634020 CCTAACAAGGCGATAGTAGTAATGC 59.366 44.000 0.00 0.00 39.35 3.56
2179 2182 0.098376 CCAGAAGCTTCTTCATGCGC 59.902 55.000 26.44 0.00 34.74 6.09
2282 2285 4.116961 CAACCCAGCAGATTAATTGCATG 58.883 43.478 18.49 14.32 43.92 4.06
2283 2286 3.770933 ACAACCCAGCAGATTAATTGCAT 59.229 39.130 18.49 6.90 43.92 3.96
2297 2300 5.828299 TTGAACTTTGAACTACAACCCAG 57.172 39.130 0.00 0.00 38.29 4.45
2384 2387 1.990799 TACATCCGTTTGAGCGACAG 58.009 50.000 0.00 0.00 0.00 3.51
2387 2390 3.550233 GCTAGATACATCCGTTTGAGCGA 60.550 47.826 0.00 0.00 0.00 4.93
2388 2391 2.726760 GCTAGATACATCCGTTTGAGCG 59.273 50.000 0.00 0.00 0.00 5.03
2389 2392 3.491267 GTGCTAGATACATCCGTTTGAGC 59.509 47.826 0.00 0.00 0.00 4.26
2390 2393 4.742167 CAGTGCTAGATACATCCGTTTGAG 59.258 45.833 0.00 0.00 0.00 3.02
2391 2394 4.401202 TCAGTGCTAGATACATCCGTTTGA 59.599 41.667 0.00 0.00 0.00 2.69
2392 2395 4.682787 TCAGTGCTAGATACATCCGTTTG 58.317 43.478 0.00 0.00 0.00 2.93
2393 2396 5.339008 TTCAGTGCTAGATACATCCGTTT 57.661 39.130 0.00 0.00 0.00 3.60
2394 2397 5.339008 TTTCAGTGCTAGATACATCCGTT 57.661 39.130 0.00 0.00 0.00 4.44
2395 2398 5.537300 ATTTCAGTGCTAGATACATCCGT 57.463 39.130 0.00 0.00 0.00 4.69
2396 2399 5.569441 CGTATTTCAGTGCTAGATACATCCG 59.431 44.000 0.00 0.00 0.00 4.18
2397 2400 6.448006 ACGTATTTCAGTGCTAGATACATCC 58.552 40.000 0.00 0.00 0.00 3.51
2398 2401 7.364200 AGACGTATTTCAGTGCTAGATACATC 58.636 38.462 0.00 0.00 0.00 3.06
2399 2402 7.278461 AGACGTATTTCAGTGCTAGATACAT 57.722 36.000 0.00 0.00 0.00 2.29
2400 2403 6.694877 AGACGTATTTCAGTGCTAGATACA 57.305 37.500 0.00 0.00 0.00 2.29
2401 2404 8.085720 TCTAGACGTATTTCAGTGCTAGATAC 57.914 38.462 0.00 0.00 30.90 2.24
2402 2405 8.850007 ATCTAGACGTATTTCAGTGCTAGATA 57.150 34.615 13.10 0.00 40.48 1.98
2403 2406 7.753309 ATCTAGACGTATTTCAGTGCTAGAT 57.247 36.000 10.29 10.29 38.62 1.98
2404 2407 7.713942 TGTATCTAGACGTATTTCAGTGCTAGA 59.286 37.037 0.00 7.14 37.74 2.43
2405 2408 7.862648 TGTATCTAGACGTATTTCAGTGCTAG 58.137 38.462 0.00 0.00 0.00 3.42
2406 2409 7.797038 TGTATCTAGACGTATTTCAGTGCTA 57.203 36.000 0.00 0.00 0.00 3.49
2407 2410 6.694877 TGTATCTAGACGTATTTCAGTGCT 57.305 37.500 0.00 0.00 0.00 4.40
2408 2411 7.139392 TGATGTATCTAGACGTATTTCAGTGC 58.861 38.462 0.00 0.00 0.00 4.40
2409 2412 9.684448 ATTGATGTATCTAGACGTATTTCAGTG 57.316 33.333 0.00 0.00 0.00 3.66
2415 2418 9.197694 GCTCAAATTGATGTATCTAGACGTATT 57.802 33.333 0.00 0.00 0.00 1.89
2416 2419 7.539022 CGCTCAAATTGATGTATCTAGACGTAT 59.461 37.037 0.00 0.00 0.00 3.06
2417 2420 6.856426 CGCTCAAATTGATGTATCTAGACGTA 59.144 38.462 0.00 0.00 0.00 3.57
2418 2421 5.687730 CGCTCAAATTGATGTATCTAGACGT 59.312 40.000 0.00 0.00 0.00 4.34
2419 2422 5.915196 TCGCTCAAATTGATGTATCTAGACG 59.085 40.000 0.00 0.00 0.00 4.18
2420 2423 6.697455 TGTCGCTCAAATTGATGTATCTAGAC 59.303 38.462 0.00 0.00 0.00 2.59
2421 2424 6.805713 TGTCGCTCAAATTGATGTATCTAGA 58.194 36.000 0.00 0.00 0.00 2.43
2422 2425 7.223582 ACTTGTCGCTCAAATTGATGTATCTAG 59.776 37.037 0.00 0.00 35.48 2.43
2423 2426 7.041721 ACTTGTCGCTCAAATTGATGTATCTA 58.958 34.615 0.00 0.00 35.48 1.98
2424 2427 5.877012 ACTTGTCGCTCAAATTGATGTATCT 59.123 36.000 0.00 0.00 35.48 1.98
2425 2428 6.111768 ACTTGTCGCTCAAATTGATGTATC 57.888 37.500 0.00 0.00 35.48 2.24
2426 2429 7.609760 TTACTTGTCGCTCAAATTGATGTAT 57.390 32.000 0.00 0.00 35.48 2.29
2427 2430 7.609760 ATTACTTGTCGCTCAAATTGATGTA 57.390 32.000 0.00 0.00 35.48 2.29
2428 2431 5.940192 TTACTTGTCGCTCAAATTGATGT 57.060 34.783 0.00 0.00 35.48 3.06
2429 2432 8.124823 ACATATTACTTGTCGCTCAAATTGATG 58.875 33.333 0.00 0.00 35.48 3.07
2430 2433 8.124823 CACATATTACTTGTCGCTCAAATTGAT 58.875 33.333 0.00 0.00 35.48 2.57
2431 2434 7.413988 CCACATATTACTTGTCGCTCAAATTGA 60.414 37.037 0.00 0.00 35.48 2.57
2432 2435 6.688385 CCACATATTACTTGTCGCTCAAATTG 59.312 38.462 0.00 0.00 35.48 2.32
2433 2436 6.597672 TCCACATATTACTTGTCGCTCAAATT 59.402 34.615 0.00 0.00 35.48 1.82
2434 2437 6.112734 TCCACATATTACTTGTCGCTCAAAT 58.887 36.000 0.00 0.00 35.48 2.32
2435 2438 5.483811 TCCACATATTACTTGTCGCTCAAA 58.516 37.500 0.00 0.00 35.48 2.69
2436 2439 5.079689 TCCACATATTACTTGTCGCTCAA 57.920 39.130 0.00 0.00 34.61 3.02
2455 2458 0.468214 CAGCTACTCCCTCCGATCCA 60.468 60.000 0.00 0.00 0.00 3.41
2456 2459 0.178987 TCAGCTACTCCCTCCGATCC 60.179 60.000 0.00 0.00 0.00 3.36
2626 2629 7.293073 ACACAATTGATCTATAAAGGCCTCAT 58.707 34.615 13.59 5.24 0.00 2.90
2671 2674 8.807948 TCATTTTGGGGAAAACAACAAAATAA 57.192 26.923 12.19 0.00 46.09 1.40
2788 2827 7.392113 TCCACACCGAGTTATTGTCATTAATTT 59.608 33.333 0.00 0.00 0.00 1.82
2796 2835 2.351726 GCATCCACACCGAGTTATTGTC 59.648 50.000 0.00 0.00 0.00 3.18
2806 2845 2.040544 GTCCCAAGCATCCACACCG 61.041 63.158 0.00 0.00 0.00 4.94
3215 3270 4.202202 ACTGGAGATGAAGAAGATAAGCGG 60.202 45.833 0.00 0.00 0.00 5.52
3440 3495 9.499479 AGGATACATCATATCAAAACAGATGAC 57.501 33.333 7.62 0.22 38.62 3.06
3492 3550 3.755378 GACTGGTCAGACATGCAGATTTT 59.245 43.478 11.15 0.00 0.00 1.82
3695 3753 3.208747 AGTTCTGGGTCGTCATTTTGT 57.791 42.857 0.00 0.00 0.00 2.83
3867 3925 2.618312 GATTTGTGCCCGCATCTGCC 62.618 60.000 0.00 0.00 37.91 4.85
3875 3933 4.898829 TCTTTCATATGATTTGTGCCCG 57.101 40.909 6.17 0.00 0.00 6.13
4073 4131 7.179966 TGACTACAGGGATCTAAGACTAACAA 58.820 38.462 0.00 0.00 0.00 2.83
4143 4208 4.331717 ACGCACAATGTAAATAGCACTACC 59.668 41.667 0.00 0.00 0.00 3.18
4999 5065 9.775854 CAGATTAGAGATAACAGATCAACCATT 57.224 33.333 0.00 0.00 0.00 3.16
5296 5362 1.270550 CATGTTTCTTCTGCACCCCAC 59.729 52.381 0.00 0.00 0.00 4.61
5506 5572 4.074970 CAGCCAAGTCCTACAACAAGAAT 58.925 43.478 0.00 0.00 0.00 2.40
5813 5879 4.396478 TGACTGTCTCCTAAGATGAACTCG 59.604 45.833 9.51 0.00 33.08 4.18
6182 6248 2.639839 ACAATATCCGGATGAAGAGGGG 59.360 50.000 27.55 9.67 0.00 4.79
6183 6249 3.324846 TCACAATATCCGGATGAAGAGGG 59.675 47.826 27.55 12.88 0.00 4.30
6320 6386 6.561737 TTTATGAAATTTGCAGGTACGTCA 57.438 33.333 0.00 0.00 0.00 4.35
6384 6450 7.815840 TTGACTCCAAATGTCAGAAATGTTA 57.184 32.000 0.00 0.00 43.98 2.41
6392 6459 7.874940 TCTAAAACATTGACTCCAAATGTCAG 58.125 34.615 2.53 2.14 43.98 3.51
6396 6463 7.829725 TCCATCTAAAACATTGACTCCAAATG 58.170 34.615 0.00 0.00 35.67 2.32
6403 6470 6.484288 TCACCATCCATCTAAAACATTGACT 58.516 36.000 0.00 0.00 0.00 3.41
6474 6541 2.202479 GCCAAAAGCTTAGCGCCG 60.202 61.111 2.29 0.00 40.39 6.46
6484 6551 2.044135 GCGAAAAGAGAACGCCAAAAG 58.956 47.619 0.00 0.00 45.35 2.27
6568 6636 5.762825 AGTCGACTAACACTCAACACTAA 57.237 39.130 18.46 0.00 0.00 2.24
6570 6638 5.762825 TTAGTCGACTAACACTCAACACT 57.237 39.130 29.57 1.81 33.83 3.55
6572 6640 6.982141 ACATTTTAGTCGACTAACACTCAACA 59.018 34.615 32.29 15.94 38.09 3.33
6573 6641 7.168637 TCACATTTTAGTCGACTAACACTCAAC 59.831 37.037 32.29 0.00 38.09 3.18
6574 6642 7.204604 TCACATTTTAGTCGACTAACACTCAA 58.795 34.615 32.29 24.15 38.09 3.02
6575 6643 6.741109 TCACATTTTAGTCGACTAACACTCA 58.259 36.000 32.29 17.93 38.09 3.41
6576 6644 7.813852 ATCACATTTTAGTCGACTAACACTC 57.186 36.000 32.29 0.00 38.09 3.51
6577 6645 9.302345 CATATCACATTTTAGTCGACTAACACT 57.698 33.333 32.29 18.97 38.09 3.55
6578 6646 8.540492 CCATATCACATTTTAGTCGACTAACAC 58.460 37.037 32.29 0.00 38.09 3.32
6579 6647 8.255206 ACCATATCACATTTTAGTCGACTAACA 58.745 33.333 32.29 27.35 38.09 2.41
6580 6648 8.644318 ACCATATCACATTTTAGTCGACTAAC 57.356 34.615 32.29 0.09 38.09 2.34
6581 6649 8.471609 TGACCATATCACATTTTAGTCGACTAA 58.528 33.333 29.57 29.57 32.69 2.24
6582 6650 8.002984 TGACCATATCACATTTTAGTCGACTA 57.997 34.615 21.25 21.25 29.99 2.59
6583 6651 6.873997 TGACCATATCACATTTTAGTCGACT 58.126 36.000 23.66 23.66 29.99 4.18
6584 6652 7.064134 TGTTGACCATATCACATTTTAGTCGAC 59.936 37.037 7.70 7.70 36.92 4.20
6585 6653 7.100409 TGTTGACCATATCACATTTTAGTCGA 58.900 34.615 0.00 0.00 36.92 4.20
6586 6654 7.064609 ACTGTTGACCATATCACATTTTAGTCG 59.935 37.037 0.00 0.00 36.92 4.18
6587 6655 8.268850 ACTGTTGACCATATCACATTTTAGTC 57.731 34.615 0.00 0.00 36.92 2.59
6588 6656 8.635765 AACTGTTGACCATATCACATTTTAGT 57.364 30.769 0.00 0.00 36.92 2.24
6590 6658 9.173021 CCTAACTGTTGACCATATCACATTTTA 57.827 33.333 2.69 0.00 36.92 1.52
6591 6659 7.669722 ACCTAACTGTTGACCATATCACATTTT 59.330 33.333 2.69 0.00 36.92 1.82
6592 6660 7.121168 CACCTAACTGTTGACCATATCACATTT 59.879 37.037 2.69 0.00 36.92 2.32
6593 6661 6.599244 CACCTAACTGTTGACCATATCACATT 59.401 38.462 2.69 0.00 36.92 2.71
6594 6662 6.115446 CACCTAACTGTTGACCATATCACAT 58.885 40.000 2.69 0.00 36.92 3.21
6658 6749 1.066143 TCCGTGGCAGATCCTTTCTTC 60.066 52.381 0.00 0.00 35.26 2.87
6670 6761 0.396435 AACTCTCACATTCCGTGGCA 59.604 50.000 0.00 0.00 46.36 4.92
6672 6763 2.341257 CTCAACTCTCACATTCCGTGG 58.659 52.381 0.00 0.00 46.36 4.94
6675 6766 2.751166 ACCTCAACTCTCACATTCCG 57.249 50.000 0.00 0.00 0.00 4.30
6714 6817 6.879458 GGCCTAGGATACGACATTGAATAAAT 59.121 38.462 14.75 0.00 46.39 1.40
6720 6823 1.968493 GGGCCTAGGATACGACATTGA 59.032 52.381 14.75 0.00 46.39 2.57
6724 6827 0.032912 TGTGGGCCTAGGATACGACA 60.033 55.000 14.75 12.19 46.39 4.35
6725 6828 1.272769 GATGTGGGCCTAGGATACGAC 59.727 57.143 14.75 9.65 46.39 4.34
6730 6833 1.366319 GATGGATGTGGGCCTAGGAT 58.634 55.000 14.75 0.00 0.00 3.24
6732 6835 1.372683 CGATGGATGTGGGCCTAGG 59.627 63.158 3.67 3.67 0.00 3.02
6733 6836 1.302033 GCGATGGATGTGGGCCTAG 60.302 63.158 4.53 0.00 0.00 3.02
6734 6837 2.069430 TGCGATGGATGTGGGCCTA 61.069 57.895 4.53 0.00 0.00 3.93
6735 6838 3.410628 TGCGATGGATGTGGGCCT 61.411 61.111 4.53 0.00 0.00 5.19
6736 6839 3.211963 GTGCGATGGATGTGGGCC 61.212 66.667 0.00 0.00 0.00 5.80
6737 6840 3.211963 GGTGCGATGGATGTGGGC 61.212 66.667 0.00 0.00 0.00 5.36
6738 6841 0.752743 ATTGGTGCGATGGATGTGGG 60.753 55.000 0.00 0.00 0.00 4.61
6739 6842 1.105457 AATTGGTGCGATGGATGTGG 58.895 50.000 0.00 0.00 0.00 4.17
6740 6843 2.532235 CAAATTGGTGCGATGGATGTG 58.468 47.619 0.00 0.00 0.00 3.21
6741 6844 1.477700 CCAAATTGGTGCGATGGATGT 59.522 47.619 3.34 0.00 32.82 3.06
6742 6845 2.212869 CCAAATTGGTGCGATGGATG 57.787 50.000 3.34 0.00 32.82 3.51
6754 6857 6.988622 ATTGCATATGTCCAAACCAAATTG 57.011 33.333 4.29 0.00 0.00 2.32
6755 6858 7.619050 TGTATTGCATATGTCCAAACCAAATT 58.381 30.769 4.29 0.00 0.00 1.82
6756 6859 7.180322 TGTATTGCATATGTCCAAACCAAAT 57.820 32.000 4.29 0.00 0.00 2.32
6757 6860 6.596309 TGTATTGCATATGTCCAAACCAAA 57.404 33.333 4.29 0.00 0.00 3.28
6808 6911 9.611627 TGACATTATCAACACGCTTTAACCGTG 62.612 40.741 20.24 20.24 45.79 4.94
6837 6941 1.246056 CGTAGTTGACCCCGACCTCA 61.246 60.000 0.00 0.00 0.00 3.86
6863 6967 2.532465 GAAGGGGCCTGGGTTACGAC 62.532 65.000 0.84 0.00 0.00 4.34
6872 6976 3.456277 ACAAACTATCTAGAAGGGGCCTG 59.544 47.826 0.84 0.00 0.00 4.85
6878 6983 4.878397 CCAAGCCACAAACTATCTAGAAGG 59.122 45.833 0.00 0.00 0.00 3.46
6912 7017 2.603075 AAAACAGCTTATGGCCTCCA 57.397 45.000 3.32 0.00 43.05 3.86


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

AutoCloner maintained by Alex Coulton.