Multiple sequence alignment - TraesCS2D01G340000

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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 TraesCS2D01G340000 chr2D 100.000 2435 0 0 1 2435 434356470 434354036 0.000000e+00 4497
1 TraesCS2D01G340000 chr2A 88.481 1936 96 49 413 2248 552495324 552497232 0.000000e+00 2222
2 TraesCS2D01G340000 chr2A 95.388 412 14 4 1 411 552494857 552495264 0.000000e+00 651
3 TraesCS2D01G340000 chr2A 93.140 379 21 4 1 378 711105505 711105879 3.540000e-153 551
4 TraesCS2D01G340000 chr2B 86.921 864 46 29 661 1483 513280275 513279438 0.000000e+00 907
5 TraesCS2D01G340000 chr2B 91.240 605 25 13 1 586 513281119 513280524 0.000000e+00 798
6 TraesCS2D01G340000 chr2B 86.525 141 16 1 2103 2243 513279018 513278881 4.190000e-33 152
7 TraesCS2D01G340000 chr2B 81.579 152 13 9 1541 1687 513279445 513279304 7.120000e-21 111
8 TraesCS2D01G340000 chr5A 94.723 379 15 4 1 378 671469179 671469553 3.490000e-163 584
9 TraesCS2D01G340000 chr5A 92.348 379 24 4 1 378 34037566 34037940 3.560000e-148 534
10 TraesCS2D01G340000 chr7A 94.195 379 17 4 1 378 394230986 394231360 7.550000e-160 573
11 TraesCS2D01G340000 chr1A 94.195 379 17 4 1 378 74487963 74488337 7.550000e-160 573
12 TraesCS2D01G340000 chr1A 94.333 300 12 4 80 378 45934581 45934286 2.850000e-124 455
13 TraesCS2D01G340000 chr4A 93.404 379 20 4 1 378 129128922 129128548 7.610000e-155 556


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 TraesCS2D01G340000 chr2D 434354036 434356470 2434 True 4497.0 4497 100.00000 1 2435 1 chr2D.!!$R1 2434
1 TraesCS2D01G340000 chr2A 552494857 552497232 2375 False 1436.5 2222 91.93450 1 2248 2 chr2A.!!$F2 2247
2 TraesCS2D01G340000 chr2B 513278881 513281119 2238 True 492.0 907 86.56625 1 2243 4 chr2B.!!$R1 2242

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
334 346 0.250038 ATCAAGGCACGATCCATCCG 60.250 55.0 0.0 0.0 0.0 4.18 F
1142 1445 0.108281 TGTTGGTCGTCGGTTTGTCA 60.108 50.0 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1275 1578 0.179936 GCAGCCTGATAGCACCTTCT 59.820 55.0 0.0 0.0 34.23 2.85 R
2401 2754 0.320946 CGGGCTTCGACCAAGGTAAA 60.321 55.0 0.0 0.0 42.43 2.01 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
72 76 1.379044 CCACTCAGCCAATCCCCAC 60.379 63.158 0.00 0.00 0.00 4.61
91 95 1.165270 CCACGAACCCATTTCACTCC 58.835 55.000 0.00 0.00 33.24 3.85
210 221 5.539048 ACAATACACGAAGCTACAAAGAGT 58.461 37.500 0.00 0.00 0.00 3.24
211 222 6.684686 ACAATACACGAAGCTACAAAGAGTA 58.315 36.000 0.00 0.00 0.00 2.59
334 346 0.250038 ATCAAGGCACGATCCATCCG 60.250 55.000 0.00 0.00 0.00 4.18
551 621 4.142049 GCAGATGATATCCAGGCTACCTAC 60.142 50.000 0.00 0.00 29.64 3.18
587 665 1.936547 GGCTACTGAAGAATCAAGCCG 59.063 52.381 5.95 0.00 45.11 5.52
590 668 2.191128 ACTGAAGAATCAAGCCGCTT 57.809 45.000 0.00 0.00 34.49 4.68
591 669 1.808945 ACTGAAGAATCAAGCCGCTTG 59.191 47.619 24.60 24.60 42.25 4.01
592 670 1.131883 CTGAAGAATCAAGCCGCTTGG 59.868 52.381 28.54 13.26 41.33 3.61
616 844 2.288152 ACAAAACCCATGCTTAGCAACG 60.288 45.455 12.08 5.46 43.62 4.10
619 847 2.045708 CCCATGCTTAGCAACGCCA 61.046 57.895 12.08 0.00 43.62 5.69
620 848 1.430632 CCATGCTTAGCAACGCCAG 59.569 57.895 12.08 0.00 43.62 4.85
621 849 1.226491 CATGCTTAGCAACGCCAGC 60.226 57.895 12.08 1.68 43.62 4.85
623 851 4.166011 GCTTAGCAACGCCAGCCG 62.166 66.667 0.00 0.00 44.21 5.52
644 872 5.229423 CCGTTCATGAATTCAAAACCACAT 58.771 37.500 21.86 0.98 0.00 3.21
655 891 2.137177 AAACCACATCCCCCACTCCG 62.137 60.000 0.00 0.00 0.00 4.63
657 893 4.489771 CACATCCCCCACTCCGCC 62.490 72.222 0.00 0.00 0.00 6.13
659 895 4.181010 CATCCCCCACTCCGCCAG 62.181 72.222 0.00 0.00 0.00 4.85
796 1055 2.045926 CTCACGGCCCCAGAAAGG 60.046 66.667 0.00 0.00 37.03 3.11
863 1141 2.825836 CATGCGAGGACCAAGGCC 60.826 66.667 0.00 0.00 0.00 5.19
892 1178 3.998672 GGGACAGGACGGACGCAA 61.999 66.667 0.00 0.00 0.00 4.85
982 1276 5.292765 CCTTGACCGGCTATATATATGCAG 58.707 45.833 0.00 7.63 0.00 4.41
986 1282 7.412853 TGACCGGCTATATATATGCAGTAAA 57.587 36.000 0.00 0.50 0.00 2.01
1002 1298 7.458038 TGCAGTAAACATACATACATACACG 57.542 36.000 0.00 0.00 0.00 4.49
1011 1307 2.758423 ACATACATACACGCTCAGGTGA 59.242 45.455 0.00 0.00 40.38 4.02
1014 1310 1.893137 ACATACACGCTCAGGTGAAGA 59.107 47.619 0.00 0.00 40.38 2.87
1017 1313 0.601311 ACACGCTCAGGTGAAGAAGC 60.601 55.000 0.00 0.00 40.38 3.86
1018 1314 0.601046 CACGCTCAGGTGAAGAAGCA 60.601 55.000 0.00 0.00 40.38 3.91
1019 1315 0.320247 ACGCTCAGGTGAAGAAGCAG 60.320 55.000 0.00 0.00 0.00 4.24
1062 1358 1.881903 CGGTTGAGAGGAGCAGAGCA 61.882 60.000 0.00 0.00 0.00 4.26
1067 1365 0.607620 GAGAGGAGCAGAGCACAACT 59.392 55.000 0.00 0.00 0.00 3.16
1068 1366 0.607620 AGAGGAGCAGAGCACAACTC 59.392 55.000 0.00 0.00 46.66 3.01
1116 1419 0.469494 TGTGAGGCTTGTTGCTCTGA 59.531 50.000 0.00 0.00 42.39 3.27
1138 1441 1.600485 GTTGATGTTGGTCGTCGGTTT 59.400 47.619 0.00 0.00 35.01 3.27
1142 1445 0.108281 TGTTGGTCGTCGGTTTGTCA 60.108 50.000 0.00 0.00 0.00 3.58
1174 1477 3.382546 GCGGTAGGAGTTGGTAAGTCATA 59.617 47.826 0.00 0.00 32.34 2.15
1177 1480 5.301045 CGGTAGGAGTTGGTAAGTCATATGA 59.699 44.000 0.00 0.00 30.78 2.15
1178 1481 6.515200 CGGTAGGAGTTGGTAAGTCATATGAG 60.515 46.154 5.42 0.00 30.78 2.90
1179 1482 5.283457 AGGAGTTGGTAAGTCATATGAGC 57.717 43.478 5.42 1.50 32.34 4.26
1180 1483 4.716784 AGGAGTTGGTAAGTCATATGAGCA 59.283 41.667 5.42 0.00 32.34 4.26
1181 1484 5.367937 AGGAGTTGGTAAGTCATATGAGCAT 59.632 40.000 5.42 0.00 32.34 3.79
1185 1488 6.765036 AGTTGGTAAGTCATATGAGCATCTTG 59.235 38.462 5.42 0.00 34.92 3.02
1232 1535 5.401972 TGATGTTTGCGATTTGTTTGATGAC 59.598 36.000 0.00 0.00 0.00 3.06
1257 1560 5.402398 AGTGAGTTCTGAAACTTGTTTTGC 58.598 37.500 0.06 0.00 45.80 3.68
1258 1561 5.183904 AGTGAGTTCTGAAACTTGTTTTGCT 59.816 36.000 0.06 0.00 45.80 3.91
1259 1562 5.863935 GTGAGTTCTGAAACTTGTTTTGCTT 59.136 36.000 0.06 0.00 45.80 3.91
1260 1563 6.366061 GTGAGTTCTGAAACTTGTTTTGCTTT 59.634 34.615 0.06 0.00 45.80 3.51
1261 1564 6.365789 TGAGTTCTGAAACTTGTTTTGCTTTG 59.634 34.615 0.06 0.00 45.80 2.77
1271 1574 3.594134 TGTTTTGCTTTGTTCTTGTGGG 58.406 40.909 0.00 0.00 0.00 4.61
1273 1576 3.971245 TTTGCTTTGTTCTTGTGGGTT 57.029 38.095 0.00 0.00 0.00 4.11
1275 1578 2.451490 TGCTTTGTTCTTGTGGGTTGA 58.549 42.857 0.00 0.00 0.00 3.18
1407 1710 1.164411 CGCCCAAGCACAACTGATTA 58.836 50.000 0.00 0.00 39.83 1.75
1408 1711 1.745087 CGCCCAAGCACAACTGATTAT 59.255 47.619 0.00 0.00 39.83 1.28
1409 1712 2.164219 CGCCCAAGCACAACTGATTATT 59.836 45.455 0.00 0.00 39.83 1.40
1411 1714 3.193267 GCCCAAGCACAACTGATTATTCA 59.807 43.478 0.00 0.00 39.53 2.57
1412 1715 4.676196 GCCCAAGCACAACTGATTATTCAG 60.676 45.833 12.10 12.10 46.11 3.02
1441 1744 3.636764 AGCTAGCTAGAAGAAAGCCTCTC 59.363 47.826 25.15 1.59 41.02 3.20
1442 1745 3.383185 GCTAGCTAGAAGAAAGCCTCTCA 59.617 47.826 25.15 0.00 41.02 3.27
1489 1794 2.349590 CGACCATCTGCTGAAATGTGA 58.650 47.619 0.00 0.00 0.00 3.58
1490 1795 2.094894 CGACCATCTGCTGAAATGTGAC 59.905 50.000 0.00 0.00 0.00 3.67
1506 1811 1.220477 GACAGCAGGGGAAGCTCTC 59.780 63.158 0.00 0.00 41.14 3.20
1520 1825 0.662970 GCTCTCGATTCAGCTAGCGG 60.663 60.000 9.55 9.14 32.48 5.52
1535 1840 1.517475 GCGGTCGAGAAGAAGCTCC 60.517 63.158 0.00 0.00 33.68 4.70
1736 2059 9.444600 TCTTTCAGTTACACTTTTGTAAGAAGT 57.555 29.630 0.00 0.00 46.63 3.01
1789 2117 4.847512 TGGTTATTTCCCCTGTAAGTGAGA 59.152 41.667 0.00 0.00 0.00 3.27
1800 2128 5.337894 CCCTGTAAGTGAGAAGTGATCATGT 60.338 44.000 0.00 0.00 0.00 3.21
1805 2133 8.678199 TGTAAGTGAGAAGTGATCATGTACTAG 58.322 37.037 0.00 0.00 0.00 2.57
1860 2188 3.064545 GTCCACTGAGCAGCATATGTTTC 59.935 47.826 4.29 0.00 0.00 2.78
1865 2193 5.049612 CACTGAGCAGCATATGTTTCCTATG 60.050 44.000 4.29 0.00 0.00 2.23
1873 2201 6.639686 CAGCATATGTTTCCTATGTTGATTGC 59.360 38.462 4.29 0.00 39.03 3.56
1907 2241 2.228582 TCGATTGGTGCAGTTTTCATGG 59.771 45.455 0.00 0.00 0.00 3.66
1926 2266 1.418342 GGCGCGCTTTTCTCACGATA 61.418 55.000 32.29 0.00 0.00 2.92
1937 2277 7.043391 CGCTTTTCTCACGATAGATTACATTCA 60.043 37.037 0.00 0.00 41.38 2.57
1943 2283 6.046593 TCACGATAGATTACATTCACCAACC 58.953 40.000 0.00 0.00 41.38 3.77
1960 2302 0.543174 ACCCTATGGATCGGCTCTCC 60.543 60.000 0.00 0.00 34.81 3.71
2038 2391 3.154689 ATTGGTTCTGCCCCAAAGATGG 61.155 50.000 0.00 0.00 44.70 3.51
2069 2422 4.734402 GCAAATGCTAAAGATCGCCATCAA 60.734 41.667 0.00 0.00 38.21 2.57
2074 2427 2.093306 AAAGATCGCCATCAACGACA 57.907 45.000 0.00 0.00 43.23 4.35
2139 2492 7.567771 CGTGCGGATAGTATTTTGAATCTTCTC 60.568 40.741 0.00 0.00 0.00 2.87
2140 2493 7.224753 GTGCGGATAGTATTTTGAATCTTCTCA 59.775 37.037 0.00 0.00 0.00 3.27
2142 2495 8.064814 GCGGATAGTATTTTGAATCTTCTCAAC 58.935 37.037 0.00 0.00 35.07 3.18
2155 2508 0.621571 TCTCAACAGGGGATCAGGGG 60.622 60.000 0.00 0.00 0.00 4.79
2226 2579 2.510948 CTGCGCTAACAGCCTATCG 58.489 57.895 9.73 0.00 38.18 2.92
2227 2580 0.249073 CTGCGCTAACAGCCTATCGT 60.249 55.000 9.73 0.00 38.18 3.73
2248 2601 4.561606 CGTATACAAGAAGCGGCCATATAC 59.438 45.833 2.24 1.22 0.00 1.47
2249 2602 4.891992 ATACAAGAAGCGGCCATATACT 57.108 40.909 2.24 0.00 0.00 2.12
2250 2603 5.995565 ATACAAGAAGCGGCCATATACTA 57.004 39.130 2.24 0.00 0.00 1.82
2251 2604 4.891992 ACAAGAAGCGGCCATATACTAT 57.108 40.909 2.24 0.00 0.00 2.12
2252 2605 5.228945 ACAAGAAGCGGCCATATACTATT 57.771 39.130 2.24 0.00 0.00 1.73
2253 2606 5.621193 ACAAGAAGCGGCCATATACTATTT 58.379 37.500 2.24 0.00 0.00 1.40
2254 2607 5.470098 ACAAGAAGCGGCCATATACTATTTG 59.530 40.000 2.24 3.20 0.00 2.32
2255 2608 4.579869 AGAAGCGGCCATATACTATTTGG 58.420 43.478 2.24 2.01 34.88 3.28
2256 2609 3.350219 AGCGGCCATATACTATTTGGG 57.650 47.619 2.24 0.00 32.72 4.12
2257 2610 2.910319 AGCGGCCATATACTATTTGGGA 59.090 45.455 2.24 0.00 32.72 4.37
2258 2611 3.007635 GCGGCCATATACTATTTGGGAC 58.992 50.000 2.24 0.00 32.72 4.46
2259 2612 3.558321 GCGGCCATATACTATTTGGGACA 60.558 47.826 2.24 0.00 32.72 4.02
2274 2627 4.537135 TGGGACAATAGTTCAGACACTC 57.463 45.455 0.00 0.00 31.92 3.51
2275 2628 3.901222 TGGGACAATAGTTCAGACACTCA 59.099 43.478 0.00 0.00 31.92 3.41
2276 2629 4.346709 TGGGACAATAGTTCAGACACTCAA 59.653 41.667 0.00 0.00 31.92 3.02
2277 2630 5.163248 TGGGACAATAGTTCAGACACTCAAA 60.163 40.000 0.00 0.00 31.92 2.69
2278 2631 5.940470 GGGACAATAGTTCAGACACTCAAAT 59.060 40.000 0.00 0.00 0.00 2.32
2279 2632 6.431234 GGGACAATAGTTCAGACACTCAAATT 59.569 38.462 0.00 0.00 0.00 1.82
2280 2633 7.606456 GGGACAATAGTTCAGACACTCAAATTA 59.394 37.037 0.00 0.00 0.00 1.40
2281 2634 8.999431 GGACAATAGTTCAGACACTCAAATTAA 58.001 33.333 0.00 0.00 0.00 1.40
2284 2637 9.831737 CAATAGTTCAGACACTCAAATTAAAGG 57.168 33.333 0.00 0.00 0.00 3.11
2285 2638 9.574516 AATAGTTCAGACACTCAAATTAAAGGT 57.425 29.630 0.00 0.00 0.00 3.50
2286 2639 7.497925 AGTTCAGACACTCAAATTAAAGGTC 57.502 36.000 0.00 0.00 0.00 3.85
2287 2640 6.202954 AGTTCAGACACTCAAATTAAAGGTCG 59.797 38.462 0.00 0.00 0.00 4.79
2288 2641 5.607477 TCAGACACTCAAATTAAAGGTCGT 58.393 37.500 0.00 0.00 0.00 4.34
2289 2642 5.694910 TCAGACACTCAAATTAAAGGTCGTC 59.305 40.000 0.00 0.00 0.00 4.20
2290 2643 5.465390 CAGACACTCAAATTAAAGGTCGTCA 59.535 40.000 0.00 0.00 0.00 4.35
2291 2644 6.147821 CAGACACTCAAATTAAAGGTCGTCAT 59.852 38.462 0.00 0.00 0.00 3.06
2292 2645 7.330946 CAGACACTCAAATTAAAGGTCGTCATA 59.669 37.037 0.00 0.00 0.00 2.15
2293 2646 7.545965 AGACACTCAAATTAAAGGTCGTCATAG 59.454 37.037 0.00 0.00 0.00 2.23
2294 2647 7.383687 ACACTCAAATTAAAGGTCGTCATAGA 58.616 34.615 0.00 0.00 0.00 1.98
2295 2648 7.331193 ACACTCAAATTAAAGGTCGTCATAGAC 59.669 37.037 0.00 0.00 40.25 2.59
2306 2659 5.098218 GTCGTCATAGACCTCATCTACAC 57.902 47.826 0.00 0.00 42.90 2.90
2307 2660 4.023878 GTCGTCATAGACCTCATCTACACC 60.024 50.000 0.00 0.00 42.90 4.16
2308 2661 3.253677 CGTCATAGACCTCATCTACACCC 59.746 52.174 0.00 0.00 42.90 4.61
2309 2662 4.475345 GTCATAGACCTCATCTACACCCT 58.525 47.826 0.00 0.00 42.90 4.34
2310 2663 5.632118 GTCATAGACCTCATCTACACCCTA 58.368 45.833 0.00 0.00 42.90 3.53
2311 2664 6.249951 GTCATAGACCTCATCTACACCCTAT 58.750 44.000 0.00 0.00 42.90 2.57
2312 2665 6.376018 GTCATAGACCTCATCTACACCCTATC 59.624 46.154 0.00 0.00 42.90 2.08
2313 2666 4.816048 AGACCTCATCTACACCCTATCA 57.184 45.455 0.00 0.00 35.15 2.15
2314 2667 4.735369 AGACCTCATCTACACCCTATCAG 58.265 47.826 0.00 0.00 35.15 2.90
2315 2668 4.169068 AGACCTCATCTACACCCTATCAGT 59.831 45.833 0.00 0.00 35.15 3.41
2316 2669 5.372959 AGACCTCATCTACACCCTATCAGTA 59.627 44.000 0.00 0.00 35.15 2.74
2317 2670 6.046168 AGACCTCATCTACACCCTATCAGTAT 59.954 42.308 0.00 0.00 35.15 2.12
2318 2671 6.249951 ACCTCATCTACACCCTATCAGTATC 58.750 44.000 0.00 0.00 0.00 2.24
2319 2672 6.183361 ACCTCATCTACACCCTATCAGTATCA 60.183 42.308 0.00 0.00 0.00 2.15
2320 2673 6.151985 CCTCATCTACACCCTATCAGTATCAC 59.848 46.154 0.00 0.00 0.00 3.06
2321 2674 6.853490 TCATCTACACCCTATCAGTATCACT 58.147 40.000 0.00 0.00 0.00 3.41
2322 2675 7.985589 TCATCTACACCCTATCAGTATCACTA 58.014 38.462 0.00 0.00 0.00 2.74
2323 2676 8.615705 TCATCTACACCCTATCAGTATCACTAT 58.384 37.037 0.00 0.00 0.00 2.12
2324 2677 9.907229 CATCTACACCCTATCAGTATCACTATA 57.093 37.037 0.00 0.00 0.00 1.31
2326 2679 9.113797 TCTACACCCTATCAGTATCACTATAGT 57.886 37.037 0.00 0.00 0.00 2.12
2329 2682 8.892530 ACACCCTATCAGTATCACTATAGTACT 58.107 37.037 4.74 2.93 0.00 2.73
2332 2685 9.531942 CCCTATCAGTATCACTATAGTACTACG 57.468 40.741 4.31 2.14 0.00 3.51
2346 2699 9.748708 CTATAGTACTACGTATATCACCTCTCC 57.251 40.741 4.31 0.00 0.00 3.71
2347 2700 6.430962 AGTACTACGTATATCACCTCTCCA 57.569 41.667 0.00 0.00 0.00 3.86
2348 2701 6.835174 AGTACTACGTATATCACCTCTCCAA 58.165 40.000 0.00 0.00 0.00 3.53
2349 2702 7.285566 AGTACTACGTATATCACCTCTCCAAA 58.714 38.462 0.00 0.00 0.00 3.28
2350 2703 6.636562 ACTACGTATATCACCTCTCCAAAG 57.363 41.667 0.00 0.00 0.00 2.77
2351 2704 4.323553 ACGTATATCACCTCTCCAAAGC 57.676 45.455 0.00 0.00 0.00 3.51
2352 2705 3.961408 ACGTATATCACCTCTCCAAAGCT 59.039 43.478 0.00 0.00 0.00 3.74
2353 2706 4.038162 ACGTATATCACCTCTCCAAAGCTC 59.962 45.833 0.00 0.00 0.00 4.09
2354 2707 4.038042 CGTATATCACCTCTCCAAAGCTCA 59.962 45.833 0.00 0.00 0.00 4.26
2355 2708 4.686191 ATATCACCTCTCCAAAGCTCAG 57.314 45.455 0.00 0.00 0.00 3.35
2356 2709 0.322975 TCACCTCTCCAAAGCTCAGC 59.677 55.000 0.00 0.00 0.00 4.26
2357 2710 0.324285 CACCTCTCCAAAGCTCAGCT 59.676 55.000 0.00 0.00 42.56 4.24
2358 2711 0.612744 ACCTCTCCAAAGCTCAGCTC 59.387 55.000 0.00 0.00 38.25 4.09
2359 2712 0.612229 CCTCTCCAAAGCTCAGCTCA 59.388 55.000 0.00 0.00 38.25 4.26
2360 2713 1.002888 CCTCTCCAAAGCTCAGCTCAA 59.997 52.381 0.00 0.00 38.25 3.02
2361 2714 2.075338 CTCTCCAAAGCTCAGCTCAAC 58.925 52.381 0.00 0.00 38.25 3.18
2362 2715 1.417517 TCTCCAAAGCTCAGCTCAACA 59.582 47.619 0.00 0.00 38.25 3.33
2363 2716 2.158769 TCTCCAAAGCTCAGCTCAACAA 60.159 45.455 0.00 0.00 38.25 2.83
2364 2717 1.949525 TCCAAAGCTCAGCTCAACAAC 59.050 47.619 0.00 0.00 38.25 3.32
2365 2718 1.677576 CCAAAGCTCAGCTCAACAACA 59.322 47.619 0.00 0.00 38.25 3.33
2366 2719 2.099592 CCAAAGCTCAGCTCAACAACAA 59.900 45.455 0.00 0.00 38.25 2.83
2367 2720 3.111098 CAAAGCTCAGCTCAACAACAAC 58.889 45.455 0.00 0.00 38.25 3.32
2368 2721 2.338577 AGCTCAGCTCAACAACAACT 57.661 45.000 0.00 0.00 30.62 3.16
2369 2722 2.648059 AGCTCAGCTCAACAACAACTT 58.352 42.857 0.00 0.00 30.62 2.66
2370 2723 3.019564 AGCTCAGCTCAACAACAACTTT 58.980 40.909 0.00 0.00 30.62 2.66
2371 2724 3.445096 AGCTCAGCTCAACAACAACTTTT 59.555 39.130 0.00 0.00 30.62 2.27
2372 2725 3.549070 GCTCAGCTCAACAACAACTTTTG 59.451 43.478 0.00 0.00 0.00 2.44
2373 2726 7.065256 AGCTCAGCTCAACAACAACTTTTGT 62.065 40.000 0.00 0.00 39.41 2.83
2374 2727 9.818526 AAGCTCAGCTCAACAACAACTTTTGTT 62.819 37.037 0.00 0.00 46.43 2.83
2386 2739 4.799419 AACTTTTGTTGCATTGCATGAC 57.201 36.364 12.95 9.29 41.77 3.06
2387 2740 4.062677 ACTTTTGTTGCATTGCATGACT 57.937 36.364 12.95 0.00 38.76 3.41
2388 2741 5.199024 ACTTTTGTTGCATTGCATGACTA 57.801 34.783 12.95 2.86 38.76 2.59
2389 2742 5.599732 ACTTTTGTTGCATTGCATGACTAA 58.400 33.333 12.95 8.96 38.76 2.24
2390 2743 6.225318 ACTTTTGTTGCATTGCATGACTAAT 58.775 32.000 12.95 0.00 38.76 1.73
2391 2744 6.707161 ACTTTTGTTGCATTGCATGACTAATT 59.293 30.769 12.95 0.47 38.76 1.40
2392 2745 7.227116 ACTTTTGTTGCATTGCATGACTAATTT 59.773 29.630 12.95 0.16 38.76 1.82
2393 2746 7.493743 TTTGTTGCATTGCATGACTAATTTT 57.506 28.000 12.95 0.00 38.76 1.82
2394 2747 8.599055 TTTGTTGCATTGCATGACTAATTTTA 57.401 26.923 12.95 0.00 38.76 1.52
2395 2748 7.815398 TGTTGCATTGCATGACTAATTTTAG 57.185 32.000 12.95 0.00 38.76 1.85
2396 2749 6.310956 TGTTGCATTGCATGACTAATTTTAGC 59.689 34.615 12.95 0.00 38.76 3.09
2397 2750 5.350633 TGCATTGCATGACTAATTTTAGCC 58.649 37.500 7.38 0.00 31.53 3.93
2398 2751 5.127519 TGCATTGCATGACTAATTTTAGCCT 59.872 36.000 7.38 0.00 31.53 4.58
2399 2752 6.044682 GCATTGCATGACTAATTTTAGCCTT 58.955 36.000 3.15 0.00 34.09 4.35
2400 2753 6.019318 GCATTGCATGACTAATTTTAGCCTTG 60.019 38.462 3.15 0.00 34.09 3.61
2401 2754 6.588719 TTGCATGACTAATTTTAGCCTTGT 57.411 33.333 0.00 0.00 34.09 3.16
2402 2755 6.588719 TGCATGACTAATTTTAGCCTTGTT 57.411 33.333 0.00 0.00 34.09 2.83
2403 2756 6.991938 TGCATGACTAATTTTAGCCTTGTTT 58.008 32.000 0.00 0.00 34.09 2.83
2404 2757 8.116651 TGCATGACTAATTTTAGCCTTGTTTA 57.883 30.769 0.00 0.00 34.09 2.01
2405 2758 8.026607 TGCATGACTAATTTTAGCCTTGTTTAC 58.973 33.333 0.00 0.00 34.09 2.01
2406 2759 7.488150 GCATGACTAATTTTAGCCTTGTTTACC 59.512 37.037 0.00 0.00 34.09 2.85
2407 2760 8.739972 CATGACTAATTTTAGCCTTGTTTACCT 58.260 33.333 0.00 0.00 34.09 3.08
2408 2761 8.700439 TGACTAATTTTAGCCTTGTTTACCTT 57.300 30.769 0.00 0.00 34.09 3.50
2409 2762 8.573035 TGACTAATTTTAGCCTTGTTTACCTTG 58.427 33.333 0.00 0.00 34.09 3.61
2410 2763 7.892609 ACTAATTTTAGCCTTGTTTACCTTGG 58.107 34.615 0.00 0.00 34.09 3.61
2411 2764 6.740944 AATTTTAGCCTTGTTTACCTTGGT 57.259 33.333 0.00 0.00 0.00 3.67
2412 2765 5.777850 TTTTAGCCTTGTTTACCTTGGTC 57.222 39.130 0.00 0.00 0.00 4.02
2413 2766 1.892209 AGCCTTGTTTACCTTGGTCG 58.108 50.000 0.00 0.00 0.00 4.79
2414 2767 1.418637 AGCCTTGTTTACCTTGGTCGA 59.581 47.619 0.00 0.00 0.00 4.20
2415 2768 2.158726 AGCCTTGTTTACCTTGGTCGAA 60.159 45.455 0.00 0.00 0.00 3.71
2416 2769 2.225727 GCCTTGTTTACCTTGGTCGAAG 59.774 50.000 0.00 0.00 0.00 3.79
2417 2770 2.225727 CCTTGTTTACCTTGGTCGAAGC 59.774 50.000 0.00 0.00 0.00 3.86
2418 2771 1.886886 TGTTTACCTTGGTCGAAGCC 58.113 50.000 0.00 0.00 0.00 4.35
2419 2772 1.162698 GTTTACCTTGGTCGAAGCCC 58.837 55.000 0.00 0.00 0.00 5.19
2420 2773 0.320946 TTTACCTTGGTCGAAGCCCG 60.321 55.000 0.00 0.00 40.25 6.13
2421 2774 2.175035 TTACCTTGGTCGAAGCCCGG 62.175 60.000 0.00 0.00 39.14 5.73
2423 2776 4.394712 CTTGGTCGAAGCCCGGCT 62.395 66.667 5.94 5.94 43.55 5.52
2424 2777 4.388499 TTGGTCGAAGCCCGGCTC 62.388 66.667 13.72 5.61 43.55 4.70
2426 2779 4.388499 GGTCGAAGCCCGGCTCAA 62.388 66.667 13.72 0.00 43.55 3.02
2427 2780 3.119096 GTCGAAGCCCGGCTCAAC 61.119 66.667 13.72 7.68 38.25 3.18
2428 2781 3.621805 TCGAAGCCCGGCTCAACA 61.622 61.111 13.72 0.00 38.25 3.33
2429 2782 2.668212 CGAAGCCCGGCTCAACAA 60.668 61.111 13.72 0.00 38.25 2.83
2430 2783 2.954611 GAAGCCCGGCTCAACAAC 59.045 61.111 13.72 0.00 38.25 3.32
2431 2784 1.600916 GAAGCCCGGCTCAACAACT 60.601 57.895 13.72 0.00 38.25 3.16
2432 2785 0.321298 GAAGCCCGGCTCAACAACTA 60.321 55.000 13.72 0.00 38.25 2.24
2433 2786 0.605589 AAGCCCGGCTCAACAACTAC 60.606 55.000 13.72 0.00 38.25 2.73
2434 2787 2.388232 GCCCGGCTCAACAACTACG 61.388 63.158 0.71 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 53 2.912956 GGGGATTGGCTGAGTGGATATA 59.087 50.000 0.00 0.00 0.00 0.86
72 76 1.165270 GGAGTGAAATGGGTTCGTGG 58.835 55.000 0.00 0.00 39.30 4.94
91 95 2.562298 TGCCCTCATACTTTGCAAAAGG 59.438 45.455 16.72 16.72 0.00 3.11
122 126 3.369471 GGTAGAGTTGTTGCTGCCTATGA 60.369 47.826 0.00 0.00 34.52 2.15
210 221 2.029020 CGCATCATTGGGTAGCTAGCTA 60.029 50.000 20.67 20.67 0.00 3.32
211 222 1.270518 CGCATCATTGGGTAGCTAGCT 60.271 52.381 23.12 23.12 0.00 3.32
212 223 1.151668 CGCATCATTGGGTAGCTAGC 58.848 55.000 14.67 14.67 0.00 3.42
213 224 1.800805 CCGCATCATTGGGTAGCTAG 58.199 55.000 0.00 0.00 34.12 3.42
324 336 1.037493 TGGTTAGGACGGATGGATCG 58.963 55.000 0.00 0.00 0.00 3.69
334 346 5.091261 AGATTGACAGTGATGGTTAGGAC 57.909 43.478 0.00 0.00 0.00 3.85
586 664 2.134346 CATGGGTTTTGTTTCCAAGCG 58.866 47.619 0.00 0.00 33.90 4.68
587 665 1.872952 GCATGGGTTTTGTTTCCAAGC 59.127 47.619 0.00 0.00 37.95 4.01
590 668 3.244044 GCTAAGCATGGGTTTTGTTTCCA 60.244 43.478 0.00 0.00 34.79 3.53
591 669 3.244044 TGCTAAGCATGGGTTTTGTTTCC 60.244 43.478 0.00 0.00 31.71 3.13
592 670 3.988819 TGCTAAGCATGGGTTTTGTTTC 58.011 40.909 0.00 0.00 31.71 2.78
616 844 0.810648 TGAATTCATGAACGGCTGGC 59.189 50.000 11.07 0.00 0.00 4.85
619 847 3.320541 TGGTTTTGAATTCATGAACGGCT 59.679 39.130 11.07 0.00 0.00 5.52
620 848 3.428534 GTGGTTTTGAATTCATGAACGGC 59.571 43.478 11.07 14.64 0.00 5.68
621 849 4.615949 TGTGGTTTTGAATTCATGAACGG 58.384 39.130 11.07 0.00 0.00 4.44
623 851 5.639082 GGGATGTGGTTTTGAATTCATGAAC 59.361 40.000 11.07 19.36 0.00 3.18
625 853 4.222588 GGGGATGTGGTTTTGAATTCATGA 59.777 41.667 9.40 0.00 0.00 3.07
626 854 4.506758 GGGGATGTGGTTTTGAATTCATG 58.493 43.478 9.40 0.00 0.00 3.07
627 855 3.519107 GGGGGATGTGGTTTTGAATTCAT 59.481 43.478 9.40 0.00 0.00 2.57
629 857 2.903135 TGGGGGATGTGGTTTTGAATTC 59.097 45.455 0.00 0.00 0.00 2.17
630 858 2.637382 GTGGGGGATGTGGTTTTGAATT 59.363 45.455 0.00 0.00 0.00 2.17
644 872 4.000620 TACTGGCGGAGTGGGGGA 62.001 66.667 0.00 0.00 35.96 4.81
655 891 6.362820 GCGATTAACTAGTGATTAGTACTGGC 59.637 42.308 5.39 0.00 41.80 4.85
657 893 6.577800 CCGCGATTAACTAGTGATTAGTACTG 59.422 42.308 8.23 0.00 41.80 2.74
659 895 5.341727 GCCGCGATTAACTAGTGATTAGTAC 59.658 44.000 8.23 0.00 41.80 2.73
796 1055 3.093172 CCTCCCCTCCCTGCCTTC 61.093 72.222 0.00 0.00 0.00 3.46
863 1141 1.997874 CTGTCCCCCTCCCTCCTTG 60.998 68.421 0.00 0.00 0.00 3.61
892 1178 9.998106 ATTTACACGGCTCTGAATTATAATACT 57.002 29.630 0.00 0.00 0.00 2.12
899 1185 5.128827 AGGAGATTTACACGGCTCTGAATTA 59.871 40.000 0.00 0.00 0.00 1.40
982 1276 7.096189 CCTGAGCGTGTATGTATGTATGTTTAC 60.096 40.741 0.00 0.00 0.00 2.01
986 1282 4.341235 ACCTGAGCGTGTATGTATGTATGT 59.659 41.667 0.00 0.00 0.00 2.29
1002 1298 0.036022 ACCTGCTTCTTCACCTGAGC 59.964 55.000 0.00 0.00 0.00 4.26
1011 1307 3.009473 TCAATCCAGCTAACCTGCTTCTT 59.991 43.478 0.00 0.00 41.98 2.52
1014 1310 2.356535 CCTCAATCCAGCTAACCTGCTT 60.357 50.000 0.00 0.00 41.98 3.91
1017 1313 2.237143 TCACCTCAATCCAGCTAACCTG 59.763 50.000 0.00 0.00 41.41 4.00
1018 1314 2.503356 CTCACCTCAATCCAGCTAACCT 59.497 50.000 0.00 0.00 0.00 3.50
1019 1315 2.501723 TCTCACCTCAATCCAGCTAACC 59.498 50.000 0.00 0.00 0.00 2.85
1062 1358 1.609061 CCTCATGCCGTCTTGAGTTGT 60.609 52.381 8.32 0.00 40.76 3.32
1067 1365 1.899814 AGTAACCTCATGCCGTCTTGA 59.100 47.619 0.00 0.00 0.00 3.02
1068 1366 2.386661 AGTAACCTCATGCCGTCTTG 57.613 50.000 0.00 0.00 0.00 3.02
1069 1367 3.097614 ACTAGTAACCTCATGCCGTCTT 58.902 45.455 0.00 0.00 0.00 3.01
1073 1376 2.550978 CCAACTAGTAACCTCATGCCG 58.449 52.381 0.00 0.00 0.00 5.69
1116 1419 1.270625 ACCGACGACCAACATCAACAT 60.271 47.619 0.00 0.00 0.00 2.71
1138 1441 2.425592 CCGCCTGGTGAACTGACA 59.574 61.111 9.25 0.00 0.00 3.58
1178 1481 3.128938 AGAATCAAGCAAGAGCAAGATGC 59.871 43.478 0.00 0.00 45.49 3.91
1179 1482 4.395231 TCAGAATCAAGCAAGAGCAAGATG 59.605 41.667 0.00 0.00 45.49 2.90
1180 1483 4.586884 TCAGAATCAAGCAAGAGCAAGAT 58.413 39.130 0.00 0.00 45.49 2.40
1181 1484 4.011966 TCAGAATCAAGCAAGAGCAAGA 57.988 40.909 0.00 0.00 45.49 3.02
1185 1488 3.501445 ACACTTCAGAATCAAGCAAGAGC 59.499 43.478 0.00 0.00 42.56 4.09
1188 1491 5.428496 TCAACACTTCAGAATCAAGCAAG 57.572 39.130 0.00 0.00 0.00 4.01
1194 1497 5.522456 GCAAACATCAACACTTCAGAATCA 58.478 37.500 0.00 0.00 0.00 2.57
1232 1535 5.470845 AAACAAGTTTCAGAACTCACTCG 57.529 39.130 0.00 0.00 45.18 4.18
1257 1560 4.202050 CCTTCTCAACCCACAAGAACAAAG 60.202 45.833 0.00 0.00 0.00 2.77
1258 1561 3.699038 CCTTCTCAACCCACAAGAACAAA 59.301 43.478 0.00 0.00 0.00 2.83
1259 1562 3.287222 CCTTCTCAACCCACAAGAACAA 58.713 45.455 0.00 0.00 0.00 2.83
1260 1563 2.241176 ACCTTCTCAACCCACAAGAACA 59.759 45.455 0.00 0.00 0.00 3.18
1261 1564 2.618709 CACCTTCTCAACCCACAAGAAC 59.381 50.000 0.00 0.00 0.00 3.01
1271 1574 2.093235 AGCCTGATAGCACCTTCTCAAC 60.093 50.000 0.00 0.00 34.23 3.18
1273 1576 1.483827 CAGCCTGATAGCACCTTCTCA 59.516 52.381 0.00 0.00 34.23 3.27
1275 1578 0.179936 GCAGCCTGATAGCACCTTCT 59.820 55.000 0.00 0.00 34.23 2.85
1414 1717 9.543474 AGAGGCTTTCTTCTAGCTAGCTAGCTA 62.543 44.444 39.71 39.71 45.34 3.32
1441 1744 3.160047 AGCCAGAGCCCGGAGATG 61.160 66.667 0.73 0.00 41.25 2.90
1442 1745 2.841988 GAGCCAGAGCCCGGAGAT 60.842 66.667 0.73 0.00 41.25 2.75
1489 1794 2.654079 CGAGAGCTTCCCCTGCTGT 61.654 63.158 0.00 0.00 41.30 4.40
1490 1795 1.684386 ATCGAGAGCTTCCCCTGCTG 61.684 60.000 0.00 0.00 41.30 4.41
1506 1811 0.658829 CTCGACCGCTAGCTGAATCG 60.659 60.000 13.57 15.13 0.00 3.34
1520 1825 0.459411 GCTGGGAGCTTCTTCTCGAC 60.459 60.000 0.00 0.00 38.45 4.20
1535 1840 3.964031 AGAAGGTGGATTAGTAGAGCTGG 59.036 47.826 0.00 0.00 0.00 4.85
1542 1847 8.660295 TGAAGAAGTAAGAAGGTGGATTAGTA 57.340 34.615 0.00 0.00 0.00 1.82
1543 1848 7.235812 ACTGAAGAAGTAAGAAGGTGGATTAGT 59.764 37.037 0.00 0.00 37.36 2.24
1736 2059 6.231951 TCACCAAACGAATCCACATAACTAA 58.768 36.000 0.00 0.00 0.00 2.24
1741 2069 4.647611 ACTTCACCAAACGAATCCACATA 58.352 39.130 0.00 0.00 0.00 2.29
1789 2117 8.972127 AGATGTTACACTAGTACATGATCACTT 58.028 33.333 13.29 0.00 0.00 3.16
1800 2128 9.946165 CATTACGATTGAGATGTTACACTAGTA 57.054 33.333 0.00 0.00 0.00 1.82
1805 2133 7.399523 GTTCCATTACGATTGAGATGTTACAC 58.600 38.462 0.00 0.00 0.00 2.90
1860 2188 4.217118 GGCCATAGAAGCAATCAACATAGG 59.783 45.833 0.00 0.00 0.00 2.57
1865 2193 2.017049 ACGGCCATAGAAGCAATCAAC 58.983 47.619 2.24 0.00 0.00 3.18
1873 2201 1.867233 CCAATCGAACGGCCATAGAAG 59.133 52.381 2.24 0.00 0.00 2.85
1907 2241 3.411351 TCGTGAGAAAAGCGCGCC 61.411 61.111 30.33 12.88 38.97 6.53
1926 2266 5.431731 TCCATAGGGTTGGTGAATGTAATCT 59.568 40.000 0.00 0.00 38.01 2.40
1937 2277 0.694444 AGCCGATCCATAGGGTTGGT 60.694 55.000 4.55 0.00 38.01 3.67
1967 2316 9.732853 GCATTTGCCTACATGTCATCTTCTGAC 62.733 44.444 0.00 0.00 43.96 3.51
2069 2422 1.891919 ACCGCAATGCAACTGTCGT 60.892 52.632 5.91 0.00 0.00 4.34
2074 2427 1.466856 ATCATCACCGCAATGCAACT 58.533 45.000 5.91 0.00 0.00 3.16
2139 2492 1.304282 CACCCCTGATCCCCTGTTG 59.696 63.158 0.00 0.00 0.00 3.33
2140 2493 1.151587 ACACCCCTGATCCCCTGTT 60.152 57.895 0.00 0.00 0.00 3.16
2142 2495 2.735772 CGACACCCCTGATCCCCTG 61.736 68.421 0.00 0.00 0.00 4.45
2155 2508 1.003116 GAATGCCATCTGATGCGACAC 60.003 52.381 12.17 0.30 0.00 3.67
2211 2564 4.414999 TGTATACGATAGGCTGTTAGCG 57.585 45.455 0.00 0.00 43.62 4.26
2226 2579 5.721232 AGTATATGGCCGCTTCTTGTATAC 58.279 41.667 0.00 0.00 0.00 1.47
2227 2580 5.995565 AGTATATGGCCGCTTCTTGTATA 57.004 39.130 0.00 0.00 0.00 1.47
2248 2601 7.106239 AGTGTCTGAACTATTGTCCCAAATAG 58.894 38.462 3.07 3.07 43.10 1.73
2249 2602 7.016153 AGTGTCTGAACTATTGTCCCAAATA 57.984 36.000 0.00 0.00 0.00 1.40
2250 2603 5.880901 AGTGTCTGAACTATTGTCCCAAAT 58.119 37.500 0.00 0.00 0.00 2.32
2251 2604 5.163248 TGAGTGTCTGAACTATTGTCCCAAA 60.163 40.000 0.00 0.00 0.00 3.28
2252 2605 4.346709 TGAGTGTCTGAACTATTGTCCCAA 59.653 41.667 0.00 0.00 0.00 4.12
2253 2606 3.901222 TGAGTGTCTGAACTATTGTCCCA 59.099 43.478 0.00 0.00 0.00 4.37
2254 2607 4.537135 TGAGTGTCTGAACTATTGTCCC 57.463 45.455 0.00 0.00 0.00 4.46
2255 2608 7.440523 AATTTGAGTGTCTGAACTATTGTCC 57.559 36.000 0.00 0.00 0.00 4.02
2258 2611 9.831737 CCTTTAATTTGAGTGTCTGAACTATTG 57.168 33.333 0.00 0.00 0.00 1.90
2259 2612 9.574516 ACCTTTAATTTGAGTGTCTGAACTATT 57.425 29.630 0.00 0.00 0.00 1.73
2260 2613 9.220767 GACCTTTAATTTGAGTGTCTGAACTAT 57.779 33.333 0.00 0.00 0.00 2.12
2261 2614 7.384115 CGACCTTTAATTTGAGTGTCTGAACTA 59.616 37.037 0.00 0.00 0.00 2.24
2262 2615 6.202954 CGACCTTTAATTTGAGTGTCTGAACT 59.797 38.462 0.00 0.00 0.00 3.01
2263 2616 6.018180 ACGACCTTTAATTTGAGTGTCTGAAC 60.018 38.462 0.00 0.00 0.00 3.18
2264 2617 6.053005 ACGACCTTTAATTTGAGTGTCTGAA 58.947 36.000 0.00 0.00 0.00 3.02
2265 2618 5.607477 ACGACCTTTAATTTGAGTGTCTGA 58.393 37.500 0.00 0.00 0.00 3.27
2266 2619 5.465390 TGACGACCTTTAATTTGAGTGTCTG 59.535 40.000 0.00 0.00 0.00 3.51
2267 2620 5.607477 TGACGACCTTTAATTTGAGTGTCT 58.393 37.500 0.00 0.00 0.00 3.41
2268 2621 5.917541 TGACGACCTTTAATTTGAGTGTC 57.082 39.130 0.00 0.00 0.00 3.67
2269 2622 7.331193 GTCTATGACGACCTTTAATTTGAGTGT 59.669 37.037 0.00 0.00 0.00 3.55
2270 2623 7.676393 GTCTATGACGACCTTTAATTTGAGTG 58.324 38.462 0.00 0.00 0.00 3.51
2271 2624 7.829378 GTCTATGACGACCTTTAATTTGAGT 57.171 36.000 0.00 0.00 0.00 3.41
2284 2637 4.023878 GGTGTAGATGAGGTCTATGACGAC 60.024 50.000 0.00 0.00 41.33 4.34
2285 2638 4.135306 GGTGTAGATGAGGTCTATGACGA 58.865 47.826 0.00 0.00 41.33 4.20
2286 2639 3.253677 GGGTGTAGATGAGGTCTATGACG 59.746 52.174 0.00 0.00 41.33 4.35
2287 2640 4.475345 AGGGTGTAGATGAGGTCTATGAC 58.525 47.826 0.00 0.00 41.33 3.06
2288 2641 4.816048 AGGGTGTAGATGAGGTCTATGA 57.184 45.455 0.00 0.00 41.33 2.15
2289 2642 6.249192 TGATAGGGTGTAGATGAGGTCTATG 58.751 44.000 0.00 0.00 41.33 2.23
2290 2643 6.046168 ACTGATAGGGTGTAGATGAGGTCTAT 59.954 42.308 0.00 0.00 41.33 1.98
2291 2644 5.372959 ACTGATAGGGTGTAGATGAGGTCTA 59.627 44.000 0.00 0.00 38.42 2.59
2292 2645 4.169068 ACTGATAGGGTGTAGATGAGGTCT 59.831 45.833 0.00 0.00 41.11 3.85
2293 2646 4.475345 ACTGATAGGGTGTAGATGAGGTC 58.525 47.826 0.00 0.00 0.00 3.85
2294 2647 4.544564 ACTGATAGGGTGTAGATGAGGT 57.455 45.455 0.00 0.00 0.00 3.85
2295 2648 6.151985 GTGATACTGATAGGGTGTAGATGAGG 59.848 46.154 0.00 0.00 0.00 3.86
2296 2649 6.945435 AGTGATACTGATAGGGTGTAGATGAG 59.055 42.308 0.00 0.00 0.00 2.90
2297 2650 6.853490 AGTGATACTGATAGGGTGTAGATGA 58.147 40.000 0.00 0.00 0.00 2.92
2298 2651 8.815565 ATAGTGATACTGATAGGGTGTAGATG 57.184 38.462 0.00 0.00 0.00 2.90
2300 2653 9.113797 ACTATAGTGATACTGATAGGGTGTAGA 57.886 37.037 4.10 0.00 0.00 2.59
2303 2656 8.892530 AGTACTATAGTGATACTGATAGGGTGT 58.107 37.037 15.90 0.00 0.00 4.16
2306 2659 9.531942 CGTAGTACTATAGTGATACTGATAGGG 57.468 40.741 15.90 1.15 31.65 3.53
2328 2681 5.241949 AGCTTTGGAGAGGTGATATACGTAG 59.758 44.000 0.08 0.00 0.00 3.51
2329 2682 5.138276 AGCTTTGGAGAGGTGATATACGTA 58.862 41.667 0.00 0.00 0.00 3.57
2330 2683 3.961408 AGCTTTGGAGAGGTGATATACGT 59.039 43.478 0.00 0.00 0.00 3.57
2331 2684 4.038042 TGAGCTTTGGAGAGGTGATATACG 59.962 45.833 0.00 0.00 0.00 3.06
2332 2685 5.537188 CTGAGCTTTGGAGAGGTGATATAC 58.463 45.833 0.00 0.00 0.00 1.47
2333 2686 4.039730 GCTGAGCTTTGGAGAGGTGATATA 59.960 45.833 0.00 0.00 0.00 0.86
2334 2687 3.181456 GCTGAGCTTTGGAGAGGTGATAT 60.181 47.826 0.00 0.00 0.00 1.63
2335 2688 2.169352 GCTGAGCTTTGGAGAGGTGATA 59.831 50.000 0.00 0.00 0.00 2.15
2336 2689 1.065564 GCTGAGCTTTGGAGAGGTGAT 60.066 52.381 0.00 0.00 0.00 3.06
2337 2690 0.322975 GCTGAGCTTTGGAGAGGTGA 59.677 55.000 0.00 0.00 0.00 4.02
2338 2691 0.324285 AGCTGAGCTTTGGAGAGGTG 59.676 55.000 0.00 0.00 33.89 4.00
2339 2692 0.612744 GAGCTGAGCTTTGGAGAGGT 59.387 55.000 9.00 0.00 39.88 3.85
2340 2693 0.612229 TGAGCTGAGCTTTGGAGAGG 59.388 55.000 9.00 0.00 39.88 3.69
2341 2694 2.075338 GTTGAGCTGAGCTTTGGAGAG 58.925 52.381 9.00 0.00 39.88 3.20
2342 2695 1.417517 TGTTGAGCTGAGCTTTGGAGA 59.582 47.619 9.00 0.00 39.88 3.71
2343 2696 1.888215 TGTTGAGCTGAGCTTTGGAG 58.112 50.000 9.00 0.00 39.88 3.86
2344 2697 1.949525 GTTGTTGAGCTGAGCTTTGGA 59.050 47.619 9.00 0.00 39.88 3.53
2345 2698 1.677576 TGTTGTTGAGCTGAGCTTTGG 59.322 47.619 9.00 0.00 39.88 3.28
2346 2699 3.111098 GTTGTTGTTGAGCTGAGCTTTG 58.889 45.455 9.00 0.00 39.88 2.77
2347 2700 3.019564 AGTTGTTGTTGAGCTGAGCTTT 58.980 40.909 9.00 0.00 39.88 3.51
2348 2701 2.648059 AGTTGTTGTTGAGCTGAGCTT 58.352 42.857 9.00 0.00 39.88 3.74
2349 2702 2.338577 AGTTGTTGTTGAGCTGAGCT 57.661 45.000 6.69 6.69 43.88 4.09
2350 2703 3.427161 AAAGTTGTTGTTGAGCTGAGC 57.573 42.857 0.00 0.00 0.00 4.26
2351 2704 4.737054 ACAAAAGTTGTTGTTGAGCTGAG 58.263 39.130 0.00 0.00 42.22 3.35
2352 2705 4.782019 ACAAAAGTTGTTGTTGAGCTGA 57.218 36.364 0.00 0.00 42.22 4.26
2362 2715 4.911053 CATGCAATGCAACAAAAGTTGTT 58.089 34.783 13.45 0.54 44.92 2.83
2363 2716 4.034279 GTCATGCAATGCAACAAAAGTTGT 59.966 37.500 13.45 0.00 46.21 3.32
2364 2717 4.271533 AGTCATGCAATGCAACAAAAGTTG 59.728 37.500 13.45 3.17 46.21 3.16
2365 2718 4.444536 AGTCATGCAATGCAACAAAAGTT 58.555 34.783 13.45 0.00 46.21 2.66
2366 2719 4.062677 AGTCATGCAATGCAACAAAAGT 57.937 36.364 13.45 0.00 46.21 2.66
2367 2720 6.715344 ATTAGTCATGCAATGCAACAAAAG 57.285 33.333 13.45 0.00 46.21 2.27
2368 2721 7.493743 AAATTAGTCATGCAATGCAACAAAA 57.506 28.000 13.45 6.20 46.21 2.44
2369 2722 7.493743 AAAATTAGTCATGCAATGCAACAAA 57.506 28.000 13.45 3.22 46.21 2.83
2370 2723 7.148606 GCTAAAATTAGTCATGCAATGCAACAA 60.149 33.333 13.45 4.90 46.21 2.83
2371 2724 6.310956 GCTAAAATTAGTCATGCAATGCAACA 59.689 34.615 13.45 0.00 46.21 3.33
2372 2725 6.237915 GGCTAAAATTAGTCATGCAATGCAAC 60.238 38.462 13.45 7.01 46.21 4.17
2373 2726 5.811613 GGCTAAAATTAGTCATGCAATGCAA 59.188 36.000 13.45 0.00 46.21 4.08
2374 2727 5.127519 AGGCTAAAATTAGTCATGCAATGCA 59.872 36.000 11.44 11.44 46.21 3.96
2375 2728 5.594926 AGGCTAAAATTAGTCATGCAATGC 58.405 37.500 7.47 0.00 46.21 3.56
2377 2730 7.174107 ACAAGGCTAAAATTAGTCATGCAAT 57.826 32.000 9.26 0.00 37.53 3.56
2378 2731 6.588719 ACAAGGCTAAAATTAGTCATGCAA 57.411 33.333 9.26 0.00 37.53 4.08
2379 2732 6.588719 AACAAGGCTAAAATTAGTCATGCA 57.411 33.333 9.26 0.00 37.53 3.96
2380 2733 7.488150 GGTAAACAAGGCTAAAATTAGTCATGC 59.512 37.037 9.26 0.00 37.53 4.06
2381 2734 8.739972 AGGTAAACAAGGCTAAAATTAGTCATG 58.260 33.333 7.47 7.80 39.29 3.07
2382 2735 8.879427 AGGTAAACAAGGCTAAAATTAGTCAT 57.121 30.769 7.47 0.00 37.83 3.06
2383 2736 8.573035 CAAGGTAAACAAGGCTAAAATTAGTCA 58.427 33.333 7.47 0.00 37.83 3.41
2384 2737 8.027189 CCAAGGTAAACAAGGCTAAAATTAGTC 58.973 37.037 0.00 0.00 35.65 2.59
2385 2738 7.507956 ACCAAGGTAAACAAGGCTAAAATTAGT 59.492 33.333 0.00 0.00 33.32 2.24
2386 2739 7.892609 ACCAAGGTAAACAAGGCTAAAATTAG 58.107 34.615 0.00 0.00 0.00 1.73
2387 2740 7.308710 CGACCAAGGTAAACAAGGCTAAAATTA 60.309 37.037 0.00 0.00 0.00 1.40
2388 2741 6.516028 CGACCAAGGTAAACAAGGCTAAAATT 60.516 38.462 0.00 0.00 0.00 1.82
2389 2742 5.048294 CGACCAAGGTAAACAAGGCTAAAAT 60.048 40.000 0.00 0.00 0.00 1.82
2390 2743 4.276431 CGACCAAGGTAAACAAGGCTAAAA 59.724 41.667 0.00 0.00 0.00 1.52
2391 2744 3.816523 CGACCAAGGTAAACAAGGCTAAA 59.183 43.478 0.00 0.00 0.00 1.85
2392 2745 3.071312 TCGACCAAGGTAAACAAGGCTAA 59.929 43.478 0.00 0.00 0.00 3.09
2393 2746 2.633967 TCGACCAAGGTAAACAAGGCTA 59.366 45.455 0.00 0.00 0.00 3.93
2394 2747 1.418637 TCGACCAAGGTAAACAAGGCT 59.581 47.619 0.00 0.00 0.00 4.58
2395 2748 1.886886 TCGACCAAGGTAAACAAGGC 58.113 50.000 0.00 0.00 0.00 4.35
2396 2749 2.225727 GCTTCGACCAAGGTAAACAAGG 59.774 50.000 0.00 0.00 31.94 3.61
2397 2750 2.225727 GGCTTCGACCAAGGTAAACAAG 59.774 50.000 0.00 0.00 31.94 3.16
2398 2751 2.223745 GGCTTCGACCAAGGTAAACAA 58.776 47.619 0.00 0.00 31.94 2.83
2399 2752 1.543871 GGGCTTCGACCAAGGTAAACA 60.544 52.381 0.00 0.00 31.94 2.83
2400 2753 1.162698 GGGCTTCGACCAAGGTAAAC 58.837 55.000 0.00 0.00 31.94 2.01
2401 2754 0.320946 CGGGCTTCGACCAAGGTAAA 60.321 55.000 0.00 0.00 42.43 2.01
2402 2755 1.294138 CGGGCTTCGACCAAGGTAA 59.706 57.895 0.00 0.00 42.43 2.85
2403 2756 2.652095 CCGGGCTTCGACCAAGGTA 61.652 63.158 0.00 0.00 42.43 3.08
2404 2757 4.016706 CCGGGCTTCGACCAAGGT 62.017 66.667 0.00 0.00 42.43 3.50
2406 2759 4.394712 AGCCGGGCTTCGACCAAG 62.395 66.667 17.69 0.00 42.43 3.61
2407 2760 4.388499 GAGCCGGGCTTCGACCAA 62.388 66.667 24.71 0.00 39.88 3.67
2409 2762 4.388499 TTGAGCCGGGCTTCGACC 62.388 66.667 24.71 10.47 39.88 4.79
2410 2763 3.119096 GTTGAGCCGGGCTTCGAC 61.119 66.667 24.71 20.12 39.88 4.20
2411 2764 3.171828 TTGTTGAGCCGGGCTTCGA 62.172 57.895 24.71 13.07 39.88 3.71
2412 2765 2.668212 TTGTTGAGCCGGGCTTCG 60.668 61.111 24.71 0.00 39.88 3.79
2413 2766 0.321298 TAGTTGTTGAGCCGGGCTTC 60.321 55.000 24.71 16.27 39.88 3.86
2414 2767 0.605589 GTAGTTGTTGAGCCGGGCTT 60.606 55.000 24.71 7.74 39.88 4.35
2415 2768 1.003718 GTAGTTGTTGAGCCGGGCT 60.004 57.895 24.13 24.13 43.88 5.19
2416 2769 2.388232 CGTAGTTGTTGAGCCGGGC 61.388 63.158 12.11 12.11 0.00 6.13
2417 2770 3.870606 CGTAGTTGTTGAGCCGGG 58.129 61.111 2.18 0.00 0.00 5.73


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

AutoCloner maintained by Alex Coulton.