Multiple sequence alignment - TraesCS3D01G437600

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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 TraesCS3D01G437600 chr3D 100.000 4819 0 0 1 4819 548688147 548683329 0.000000e+00 8900.0
1 TraesCS3D01G437600 chr3D 93.651 63 4 0 685 747 548687399 548687337 1.430000e-15 95.3
2 TraesCS3D01G437600 chr3D 93.651 63 4 0 749 811 548687463 548687401 1.430000e-15 95.3
3 TraesCS3D01G437600 chr3D 91.892 37 3 0 2481 2517 300588495 300588459 9.000000e-03 52.8
4 TraesCS3D01G437600 chr3B 93.275 1829 89 16 2040 3841 727476672 727474851 0.000000e+00 2665.0
5 TraesCS3D01G437600 chr3B 88.223 951 81 11 866 1786 727479298 727478349 0.000000e+00 1107.0
6 TraesCS3D01G437600 chr3B 87.042 764 43 17 3835 4554 727474821 727474070 0.000000e+00 811.0
7 TraesCS3D01G437600 chr3B 90.554 487 36 3 321 798 727481078 727480593 1.890000e-178 636.0
8 TraesCS3D01G437600 chr3B 94.389 303 15 2 1 301 727738296 727737994 9.450000e-127 464.0
9 TraesCS3D01G437600 chr3B 94.141 256 13 1 4566 4819 727474034 727473779 5.850000e-104 388.0
10 TraesCS3D01G437600 chr3B 88.839 224 22 2 4596 4819 732907424 732907644 6.150000e-69 272.0
11 TraesCS3D01G437600 chr3B 97.203 143 4 0 1900 2042 727477071 727476929 4.820000e-60 243.0
12 TraesCS3D01G437600 chr3B 94.845 97 5 0 1782 1878 727477822 727477726 8.350000e-33 152.0
13 TraesCS3D01G437600 chr3A 93.257 875 48 5 1 865 686180903 686180030 0.000000e+00 1279.0
14 TraesCS3D01G437600 chr3A 87.050 888 94 8 888 1755 686179864 686178978 0.000000e+00 983.0
15 TraesCS3D01G437600 chr3A 86.261 444 39 13 4379 4819 686171839 686171415 3.400000e-126 462.0
16 TraesCS3D01G437600 chr3A 84.291 261 33 2 4559 4819 686173435 686173687 1.040000e-61 248.0
17 TraesCS3D01G437600 chr3A 100.000 31 0 0 865 895 686179946 686179916 1.870000e-04 58.4
18 TraesCS3D01G437600 chr1B 77.707 314 58 10 2152 2463 45200453 45200150 1.070000e-41 182.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G437600 chr3D 548683329 548688147 4818 True 3030.200000 8900 95.767333 1 4819 3 chr3D.!!$R2 4818
1 TraesCS3D01G437600 chr3B 727473779 727481078 7299 True 857.428571 2665 92.183286 321 4819 7 chr3B.!!$R2 4498
2 TraesCS3D01G437600 chr3A 686178978 686180903 1925 True 773.466667 1279 93.435667 1 1755 3 chr3A.!!$R2 1754

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
85 86 0.322997 TTACTTTGGATGCACCGGGG 60.323 55.0 6.32 0.84 42.61 5.73 F
1279 2587 0.387202 CGGCGAGAAGATCCATCAGT 59.613 55.0 0.00 0.00 0.00 3.41 F
1875 3742 0.032416 TAAGTCTTCCTAGCCGCCCT 60.032 55.0 0.00 0.00 0.00 5.19 F
1951 4464 0.108662 CCGGCAGATTTCCAAAAGGC 60.109 55.0 0.00 0.00 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1334 2642 0.105778 GATGAAAGAGGAGGAGGGCG 59.894 60.000 0.00 0.00 0.00 6.13 R
2690 5472 0.796312 GTCCACGTGTATGTGCCAAG 59.204 55.000 15.65 0.00 38.55 3.61 R
3475 6276 0.320683 TGTCTGCTCCACACCGAATG 60.321 55.000 0.00 0.00 0.00 2.67 R
3932 6773 1.066002 CCAGAAACTGTGTGCACAAGG 59.934 52.381 23.59 18.87 41.33 3.61 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
24 25 2.440539 TCCTTTGTCTCTTCGAGCAC 57.559 50.000 0.00 0.00 0.00 4.40
31 32 3.089284 TGTCTCTTCGAGCACCTATCAA 58.911 45.455 0.00 0.00 0.00 2.57
84 85 1.540267 TTTACTTTGGATGCACCGGG 58.460 50.000 6.32 0.00 42.61 5.73
85 86 0.322997 TTACTTTGGATGCACCGGGG 60.323 55.000 6.32 0.84 42.61 5.73
93 94 1.910580 GATGCACCGGGGAGGAAGAA 61.911 60.000 8.67 0.00 45.00 2.52
189 190 7.170320 CACTTCCGTAAGCTTACTAACAAAGAA 59.830 37.037 29.00 18.60 36.05 2.52
204 205 9.429359 ACTAACAAAGAATGAGAGTGTATTCAG 57.571 33.333 0.00 0.00 36.11 3.02
234 235 5.862924 TCGAAAAGAAGCTCAACTATTGG 57.137 39.130 0.00 0.00 0.00 3.16
236 237 5.995282 TCGAAAAGAAGCTCAACTATTGGAA 59.005 36.000 0.00 0.00 0.00 3.53
241 242 5.880901 AGAAGCTCAACTATTGGAAGGAAA 58.119 37.500 0.00 0.00 0.00 3.13
243 244 7.633789 AGAAGCTCAACTATTGGAAGGAAATA 58.366 34.615 0.00 0.00 0.00 1.40
275 278 6.851836 TCTTATGGAGGGAATTTAGTCCTCAT 59.148 38.462 15.23 6.00 46.55 2.90
280 283 7.882755 TGGAGGGAATTTAGTCCTCATAAATT 58.117 34.615 15.23 3.93 46.55 1.82
282 285 9.862149 GGAGGGAATTTAGTCCTCATAAATTTA 57.138 33.333 15.23 0.00 46.55 1.40
382 386 8.045176 ACATGTCTAGATTTTTCCTGTAAAGC 57.955 34.615 0.00 0.00 0.00 3.51
392 396 2.695359 TCCTGTAAAGCGGTGAACATC 58.305 47.619 3.13 0.00 0.00 3.06
440 444 2.357154 GGACATTCTGTGTAGGCCCAAT 60.357 50.000 0.00 0.00 42.36 3.16
451 455 1.289160 AGGCCCAATGACTAGCAAGA 58.711 50.000 0.00 0.00 0.00 3.02
473 477 2.166664 ACTAAGGGCAGTGATCTCGAAC 59.833 50.000 0.00 0.00 0.00 3.95
564 568 2.808543 GTCTCAGGTTGACGCAAGAAAT 59.191 45.455 0.00 0.00 43.62 2.17
569 573 5.516090 TCAGGTTGACGCAAGAAATAAAAC 58.484 37.500 0.00 0.00 43.62 2.43
743 755 2.288825 CCAACGAAGCAGAAGGTAGTCA 60.289 50.000 0.00 0.00 0.00 3.41
761 773 8.709308 AGGTAGTCATGCTAACAAGATAGATTT 58.291 33.333 12.68 0.00 39.83 2.17
800 819 5.529430 TCAATAGTTTCCAACGAAGCAGAAA 59.471 36.000 0.00 0.00 36.23 2.52
801 820 3.971032 AGTTTCCAACGAAGCAGAAAG 57.029 42.857 0.00 0.00 36.23 2.62
836 1992 1.082690 GAGCGGAGAAAAAGCCAGAG 58.917 55.000 0.00 0.00 0.00 3.35
1086 2385 2.033602 AAACCCTACACCTGCCGC 59.966 61.111 0.00 0.00 0.00 6.53
1208 2507 4.704833 GCTGCGGGAGAGGTTGCA 62.705 66.667 0.00 0.00 35.75 4.08
1222 2521 1.532505 GGTTGCAGCGCATACAGAATG 60.533 52.381 11.47 0.00 39.84 2.67
1231 2530 1.473257 GCATACAGAATGGGCTCGACA 60.473 52.381 0.00 0.00 43.62 4.35
1233 2532 0.824109 TACAGAATGGGCTCGACAGG 59.176 55.000 0.00 0.00 43.62 4.00
1253 2552 3.449227 CGTCTACAGCGGCCTCCA 61.449 66.667 0.00 0.00 0.00 3.86
1272 2580 2.655685 GACGGCGGCGAGAAGATC 60.656 66.667 38.93 19.86 0.00 2.75
1279 2587 0.387202 CGGCGAGAAGATCCATCAGT 59.613 55.000 0.00 0.00 0.00 3.41
1294 2602 0.943835 TCAGTTGTGCCGTGACATCG 60.944 55.000 0.00 0.00 0.00 3.84
1295 2603 0.943835 CAGTTGTGCCGTGACATCGA 60.944 55.000 0.00 0.00 0.00 3.59
1334 2642 4.113617 GAAGGTTTTCCAGGCCCC 57.886 61.111 0.00 0.00 43.73 5.80
1349 2657 2.689034 CCCGCCCTCCTCCTCTTT 60.689 66.667 0.00 0.00 0.00 2.52
1351 2659 1.990060 CCGCCCTCCTCCTCTTTCA 60.990 63.158 0.00 0.00 0.00 2.69
1352 2660 1.341156 CCGCCCTCCTCCTCTTTCAT 61.341 60.000 0.00 0.00 0.00 2.57
1355 2663 1.561542 GCCCTCCTCCTCTTTCATCAA 59.438 52.381 0.00 0.00 0.00 2.57
1360 2668 4.655186 CCTCCTCCTCTTTCATCAATCTCT 59.345 45.833 0.00 0.00 0.00 3.10
1376 2684 3.449227 CTGTCGCTCCGCCCACTA 61.449 66.667 0.00 0.00 0.00 2.74
1377 2685 2.758327 TGTCGCTCCGCCCACTAT 60.758 61.111 0.00 0.00 0.00 2.12
1391 2706 1.098050 CACTATGGAGGCAGCAAACC 58.902 55.000 0.00 0.00 0.00 3.27
1421 2745 1.515954 CGGTGAGTGCGATACCCTT 59.484 57.895 0.00 0.00 0.00 3.95
1422 2746 0.806102 CGGTGAGTGCGATACCCTTG 60.806 60.000 0.00 0.00 0.00 3.61
1424 2748 1.090052 GTGAGTGCGATACCCTTGGC 61.090 60.000 0.00 0.00 0.00 4.52
1461 2785 2.808206 GGGTGCGGTGGAGGATAGG 61.808 68.421 0.00 0.00 0.00 2.57
1465 2789 2.731571 GCGGTGGAGGATAGGCACA 61.732 63.158 0.00 0.00 0.00 4.57
1488 2812 4.308526 CTGCACCAGCTTTCGGAT 57.691 55.556 0.00 0.00 42.74 4.18
1498 2822 0.376502 GCTTTCGGATCTTGCTCTGC 59.623 55.000 0.00 0.00 0.00 4.26
1499 2823 0.649475 CTTTCGGATCTTGCTCTGCG 59.351 55.000 0.00 0.00 0.00 5.18
1503 2827 1.227497 GGATCTTGCTCTGCGGGAG 60.227 63.158 0.00 0.00 44.49 4.30
1504 2828 1.680522 GGATCTTGCTCTGCGGGAGA 61.681 60.000 10.17 0.00 44.45 3.71
1505 2829 0.176680 GATCTTGCTCTGCGGGAGAA 59.823 55.000 10.17 0.00 44.45 2.87
1519 2843 1.077089 GGAGAAGTTGCGGCGTCTAC 61.077 60.000 9.37 8.21 0.00 2.59
1522 2846 1.352156 GAAGTTGCGGCGTCTACAGG 61.352 60.000 9.37 0.00 0.00 4.00
1531 2855 3.194719 GTCTACAGGACGGGGTCG 58.805 66.667 0.00 0.00 43.02 4.79
1532 2856 2.044650 TCTACAGGACGGGGTCGG 60.045 66.667 0.00 0.00 41.39 4.79
1533 2857 3.834799 CTACAGGACGGGGTCGGC 61.835 72.222 0.00 0.00 45.30 5.54
1565 2889 4.148825 CCTCCCTGACGGCGGAAG 62.149 72.222 13.24 8.07 0.00 3.46
1596 2920 3.063704 TACATCCGTGCCGTCCGT 61.064 61.111 0.00 0.00 0.00 4.69
1735 3067 1.337118 GCTCCTCCCTCTGATAGTGG 58.663 60.000 0.00 0.00 0.00 4.00
1755 3091 2.170607 GGTGGTTTAGCTAGCTCATCCA 59.829 50.000 23.26 21.38 0.00 3.41
1857 3724 1.145156 CCACCGGCGAATCCATGTA 59.855 57.895 9.30 0.00 34.01 2.29
1862 3729 1.202533 CCGGCGAATCCATGTAAGTCT 60.203 52.381 9.30 0.00 34.01 3.24
1863 3730 2.550978 CGGCGAATCCATGTAAGTCTT 58.449 47.619 0.00 0.00 34.01 3.01
1864 3731 2.540101 CGGCGAATCCATGTAAGTCTTC 59.460 50.000 0.00 0.00 34.01 2.87
1865 3732 2.872858 GGCGAATCCATGTAAGTCTTCC 59.127 50.000 0.00 0.00 34.01 3.46
1866 3733 3.432326 GGCGAATCCATGTAAGTCTTCCT 60.432 47.826 0.00 0.00 34.01 3.36
1867 3734 4.202223 GGCGAATCCATGTAAGTCTTCCTA 60.202 45.833 0.00 0.00 34.01 2.94
1868 3735 4.985409 GCGAATCCATGTAAGTCTTCCTAG 59.015 45.833 0.00 0.00 0.00 3.02
1869 3736 4.985409 CGAATCCATGTAAGTCTTCCTAGC 59.015 45.833 0.00 0.00 0.00 3.42
1870 3737 4.965200 ATCCATGTAAGTCTTCCTAGCC 57.035 45.455 0.00 0.00 0.00 3.93
1871 3738 2.693591 TCCATGTAAGTCTTCCTAGCCG 59.306 50.000 0.00 0.00 0.00 5.52
1872 3739 2.474816 CATGTAAGTCTTCCTAGCCGC 58.525 52.381 0.00 0.00 0.00 6.53
1873 3740 0.822164 TGTAAGTCTTCCTAGCCGCC 59.178 55.000 0.00 0.00 0.00 6.13
1874 3741 0.104487 GTAAGTCTTCCTAGCCGCCC 59.896 60.000 0.00 0.00 0.00 6.13
1875 3742 0.032416 TAAGTCTTCCTAGCCGCCCT 60.032 55.000 0.00 0.00 0.00 5.19
1898 3765 2.221906 TAGCCGCCCTTCTGTTCGAC 62.222 60.000 0.00 0.00 0.00 4.20
1922 4435 5.120830 CGACTCTGAATTCGAATCCTTTTGT 59.879 40.000 11.83 6.72 37.43 2.83
1926 4439 6.827641 TCTGAATTCGAATCCTTTTGTAACG 58.172 36.000 11.83 0.00 0.00 3.18
1951 4464 0.108662 CCGGCAGATTTCCAAAAGGC 60.109 55.000 0.00 0.00 0.00 4.35
1954 4467 0.737367 GCAGATTTCCAAAAGGCGCC 60.737 55.000 21.89 21.89 0.00 6.53
2056 4828 5.662674 AGTCATACCTCACAAGGAAGTAC 57.337 43.478 0.00 0.00 46.67 2.73
2067 4839 6.246163 TCACAAGGAAGTACATCAGAGTAGA 58.754 40.000 0.00 0.00 0.00 2.59
2079 4851 9.029243 GTACATCAGAGTAGATCAGTTTGAATG 57.971 37.037 0.00 0.00 0.00 2.67
2130 4902 1.480954 TGTTCTGAGATAACTCCCCGC 59.519 52.381 0.00 0.00 41.99 6.13
2172 4944 4.060038 TCTTTCAGGAGTTGACAGTGTC 57.940 45.455 16.68 16.68 35.53 3.67
2200 4972 1.805869 ATCAGCAGCTCTTGTGACAC 58.194 50.000 0.00 0.00 0.00 3.67
2214 4986 3.833442 TGTGACACACGCTTCTATACAG 58.167 45.455 3.56 0.00 37.14 2.74
2244 5016 5.316158 AGCCAGACCTTATTATCAATGCT 57.684 39.130 0.00 0.00 0.00 3.79
2252 5024 6.299141 ACCTTATTATCAATGCTGGTACTGG 58.701 40.000 0.00 0.00 0.00 4.00
2257 5029 3.610040 TCAATGCTGGTACTGGTAGTG 57.390 47.619 0.00 0.00 0.00 2.74
2271 5043 2.976882 TGGTAGTGGCTTCAAGGTAGTT 59.023 45.455 0.00 0.00 0.00 2.24
2300 5072 9.935682 CGACAATATTAAATGTTTGATGCTAGT 57.064 29.630 0.00 0.00 0.00 2.57
2307 5079 5.450376 AATGTTTGATGCTAGTACGAACG 57.550 39.130 0.00 0.00 32.52 3.95
2308 5080 3.904571 TGTTTGATGCTAGTACGAACGT 58.095 40.909 5.03 5.03 32.52 3.99
2316 5088 3.120199 TGCTAGTACGAACGTAACAGTCC 60.120 47.826 8.61 0.00 31.86 3.85
2376 5158 2.985847 GCCAAAGGAGCAGGCGTT 60.986 61.111 0.00 0.00 38.86 4.84
2392 5174 2.612972 GGCGTTGGAGATGTCTTCTTGA 60.613 50.000 0.00 0.00 33.74 3.02
2393 5175 3.067106 GCGTTGGAGATGTCTTCTTGAA 58.933 45.455 0.00 0.00 33.74 2.69
2412 5194 4.133820 TGAAATCAGACGTTGTGTTCCAT 58.866 39.130 0.00 0.00 0.00 3.41
2422 5204 5.547465 ACGTTGTGTTCCATGATAGAAGAA 58.453 37.500 0.00 0.00 0.00 2.52
2430 5212 7.657761 GTGTTCCATGATAGAAGAATACCGATT 59.342 37.037 0.00 0.00 0.00 3.34
2449 5231 7.659186 ACCGATTCCTGTGAGTATTATCTAAC 58.341 38.462 0.00 0.00 0.00 2.34
2525 5307 1.145819 GAGGCCTGGATGTCAGAGC 59.854 63.158 12.00 0.00 46.18 4.09
2538 5320 5.357878 GGATGTCAGAGCCAAATTACATGAA 59.642 40.000 0.00 0.00 0.00 2.57
2539 5321 6.127647 GGATGTCAGAGCCAAATTACATGAAA 60.128 38.462 0.00 0.00 0.00 2.69
2540 5322 6.258230 TGTCAGAGCCAAATTACATGAAAG 57.742 37.500 0.00 0.00 0.00 2.62
2602 5384 5.584442 ACAACCAAATTCAAAACGTAGTCC 58.416 37.500 0.00 0.00 45.00 3.85
2611 5393 6.922247 TTCAAAACGTAGTCCATGTGTTAA 57.078 33.333 0.00 0.00 45.00 2.01
2647 5429 2.717639 ATTCTTGAGTAGCGCCCATT 57.282 45.000 2.29 0.00 0.00 3.16
2667 5449 7.275123 GCCCATTCTTATACAGTAGTATTACGC 59.725 40.741 0.00 0.00 41.15 4.42
2690 5472 6.565999 CGCCGATCCTTGGATTTTCTTAATAC 60.566 42.308 3.43 0.00 0.00 1.89
2693 5475 8.345565 CCGATCCTTGGATTTTCTTAATACTTG 58.654 37.037 3.43 0.00 0.00 3.16
2696 5478 6.951198 TCCTTGGATTTTCTTAATACTTGGCA 59.049 34.615 0.00 0.00 0.00 4.92
2702 5484 8.682710 GGATTTTCTTAATACTTGGCACATACA 58.317 33.333 0.00 0.00 39.30 2.29
2703 5485 9.503427 GATTTTCTTAATACTTGGCACATACAC 57.497 33.333 0.00 0.00 39.30 2.90
2792 5574 3.557185 TGATTGCTTATAGAGTTGCAGCG 59.443 43.478 0.00 0.00 36.75 5.18
2830 5612 7.087007 TCATGCTTATCGTCAGTTAGATCATC 58.913 38.462 0.00 0.00 0.00 2.92
2836 5618 9.319143 CTTATCGTCAGTTAGATCATCCTTTTT 57.681 33.333 0.00 0.00 0.00 1.94
2837 5619 6.968131 TCGTCAGTTAGATCATCCTTTTTG 57.032 37.500 0.00 0.00 0.00 2.44
2839 5621 6.934645 TCGTCAGTTAGATCATCCTTTTTGTT 59.065 34.615 0.00 0.00 0.00 2.83
2840 5622 7.444183 TCGTCAGTTAGATCATCCTTTTTGTTT 59.556 33.333 0.00 0.00 0.00 2.83
2891 5673 6.842163 TCTGTTCTTTGTTCAAACTTGACTC 58.158 36.000 0.00 0.00 36.83 3.36
2937 5719 6.973460 TTTATCTAGGTCTTAGGCCTGTAC 57.027 41.667 16.67 10.51 37.54 2.90
2962 5744 0.322456 TGGAGCCCGGAAGACATTTG 60.322 55.000 0.73 0.00 0.00 2.32
3033 5834 9.173939 CGAACTGCTGGAATAATATCAATTTTC 57.826 33.333 0.00 0.00 0.00 2.29
3038 5839 8.796475 TGCTGGAATAATATCAATTTTCTAGGC 58.204 33.333 0.00 0.00 30.51 3.93
3068 5869 7.493645 GCTTGAAGCCTTAAAGATATTTGCATT 59.506 33.333 5.74 0.00 34.48 3.56
3069 5870 9.374838 CTTGAAGCCTTAAAGATATTTGCATTT 57.625 29.630 0.00 0.00 0.00 2.32
3070 5871 8.931385 TGAAGCCTTAAAGATATTTGCATTTC 57.069 30.769 0.00 0.00 0.00 2.17
3099 5900 8.523658 GCTATTTCCTTTTACTCAGTTCCATTT 58.476 33.333 0.00 0.00 0.00 2.32
3121 5922 0.178068 TAAATGAGCTCGCACCTCCC 59.822 55.000 9.64 0.00 0.00 4.30
3122 5923 2.543067 AAATGAGCTCGCACCTCCCC 62.543 60.000 9.64 0.00 0.00 4.81
3236 6037 7.939784 AAGGATATGGAGGTTTGTTTACTTC 57.060 36.000 0.00 0.00 0.00 3.01
3243 6044 6.891388 TGGAGGTTTGTTTACTTCTACTCAA 58.109 36.000 0.00 0.00 0.00 3.02
3318 6119 4.230455 CCTAGACTCATCTCCTGGGATTT 58.770 47.826 0.00 0.00 36.29 2.17
3353 6154 4.207955 TCATGTACTGTAGCCTGTAGGAG 58.792 47.826 1.17 0.00 37.39 3.69
3355 6156 4.849813 TGTACTGTAGCCTGTAGGAGTA 57.150 45.455 1.17 0.00 37.39 2.59
3360 6161 5.024118 ACTGTAGCCTGTAGGAGTAATTGT 58.976 41.667 1.17 0.00 37.39 2.71
3394 6195 2.763249 AGAAAAGCAGTTGTTCGCTG 57.237 45.000 0.00 0.00 38.82 5.18
3420 6221 4.611366 GCATTTTAGTTCCTTTGTTCGTCG 59.389 41.667 0.00 0.00 0.00 5.12
3433 6234 2.225019 TGTTCGTCGGTACTTGACTCTC 59.775 50.000 14.09 6.94 34.17 3.20
3438 6239 3.434641 CGTCGGTACTTGACTCTCAGTTA 59.565 47.826 14.09 0.00 34.17 2.24
3449 6250 8.091449 ACTTGACTCTCAGTTAAATAGACCAAG 58.909 37.037 0.00 0.00 34.40 3.61
3467 6268 4.335594 ACCAAGAGTAAGACTTGTTTGTGC 59.664 41.667 0.00 0.00 41.88 4.57
3492 6298 1.375908 GCATTCGGTGTGGAGCAGA 60.376 57.895 0.00 0.00 0.00 4.26
3527 6333 3.071747 TGTGTACCCACTACTTCATTGCA 59.928 43.478 0.00 0.00 42.34 4.08
3528 6334 4.261801 GTGTACCCACTACTTCATTGCAT 58.738 43.478 0.00 0.00 38.61 3.96
3529 6335 4.700213 GTGTACCCACTACTTCATTGCATT 59.300 41.667 0.00 0.00 38.61 3.56
3533 6339 5.540911 ACCCACTACTTCATTGCATTTTTG 58.459 37.500 0.00 0.00 0.00 2.44
3549 6355 7.859598 TGCATTTTTGTTTTTACATGCTAAGG 58.140 30.769 0.00 0.00 35.12 2.69
3789 6595 0.168128 GGCCGAAGTGGTCAATTTCG 59.832 55.000 0.00 0.00 44.04 3.46
3792 6598 2.413837 CCGAAGTGGTCAATTTCGTCT 58.586 47.619 4.39 0.00 41.39 4.18
3805 6611 1.317613 TTCGTCTGTGGCAAATGCTT 58.682 45.000 5.25 0.00 41.70 3.91
3830 6636 9.745018 TTATCTGATCTTTGATCTCCTTTTTGT 57.255 29.630 8.71 0.00 0.00 2.83
3886 6727 7.814587 GCACTACTCTGCATATGTTATATGTCA 59.185 37.037 4.29 7.70 37.11 3.58
3932 6773 4.507710 TCCATGTGACTCTTACTGCATTC 58.492 43.478 0.00 0.00 0.00 2.67
3933 6774 3.624861 CCATGTGACTCTTACTGCATTCC 59.375 47.826 0.00 0.00 0.00 3.01
3939 6780 3.077359 ACTCTTACTGCATTCCTTGTGC 58.923 45.455 0.00 0.00 42.81 4.57
3945 6786 0.669619 TGCATTCCTTGTGCACACAG 59.330 50.000 21.56 18.73 46.76 3.66
3961 6802 3.002656 CACACAGTTTCTGGCAAGTACAG 59.997 47.826 0.00 0.00 35.51 2.74
4009 6850 1.448540 ATGCCAAACTCCTCTCGCG 60.449 57.895 0.00 0.00 0.00 5.87
4046 6887 4.867599 GGTCGGGTCGATGCCGTC 62.868 72.222 0.00 0.00 38.42 4.79
4107 6948 1.006102 AGACGTGGAAGGCTGAACG 60.006 57.895 13.34 13.34 41.64 3.95
4113 6954 1.079057 GGAAGGCTGAACGGAGGAC 60.079 63.158 0.00 0.00 0.00 3.85
4137 6978 1.539496 GGCGCAAGTTGGGATACGATA 60.539 52.381 22.92 0.00 41.68 2.92
4152 6993 6.936279 GGATACGATATCCCTCAAAATCAGA 58.064 40.000 11.03 0.00 32.09 3.27
4153 6994 6.814146 GGATACGATATCCCTCAAAATCAGAC 59.186 42.308 11.03 0.00 32.09 3.51
4154 6995 4.621991 ACGATATCCCTCAAAATCAGACG 58.378 43.478 0.00 0.00 0.00 4.18
4155 6996 3.430218 CGATATCCCTCAAAATCAGACGC 59.570 47.826 0.00 0.00 0.00 5.19
4156 6997 2.787473 ATCCCTCAAAATCAGACGCA 57.213 45.000 0.00 0.00 0.00 5.24
4157 6998 2.099141 TCCCTCAAAATCAGACGCAG 57.901 50.000 0.00 0.00 0.00 5.18
4158 6999 1.623311 TCCCTCAAAATCAGACGCAGA 59.377 47.619 0.00 0.00 0.00 4.26
4159 7000 1.734465 CCCTCAAAATCAGACGCAGAC 59.266 52.381 0.00 0.00 0.00 3.51
4208 7049 2.255406 TGCAAAAATGTATGCACCCCT 58.745 42.857 0.00 0.00 46.87 4.79
4219 7060 1.301293 GCACCCCTTTCTCCTCCAG 59.699 63.158 0.00 0.00 0.00 3.86
4223 7064 1.492133 CCCCTTTCTCCTCCAGTGCA 61.492 60.000 0.00 0.00 0.00 4.57
4224 7065 0.035630 CCCTTTCTCCTCCAGTGCAG 60.036 60.000 0.00 0.00 0.00 4.41
4228 7086 1.130054 TTCTCCTCCAGTGCAGCCTT 61.130 55.000 0.00 0.00 0.00 4.35
4265 7123 4.997395 CCAGTGTAGCATACTGAACTTGTT 59.003 41.667 14.27 0.00 46.52 2.83
4268 7126 5.928839 AGTGTAGCATACTGAACTTGTTGAG 59.071 40.000 0.00 0.00 43.54 3.02
4322 7180 8.764558 TGTACCACTGAAGTTTGTACCATATAT 58.235 33.333 13.50 0.00 34.94 0.86
4327 7185 9.988350 CACTGAAGTTTGTACCATATATTTCAC 57.012 33.333 0.00 0.00 0.00 3.18
4328 7186 9.733556 ACTGAAGTTTGTACCATATATTTCACA 57.266 29.630 0.00 0.00 0.00 3.58
4371 7254 3.259876 ACAAAGCTACATGTCGGTCCTTA 59.740 43.478 0.00 0.00 0.00 2.69
4380 7263 1.183549 GTCGGTCCTTAGAGCTCCAA 58.816 55.000 10.93 1.36 38.41 3.53
4440 7323 6.090129 ACAATATCGAAAATCAAAACCACCG 58.910 36.000 0.00 0.00 0.00 4.94
4457 7340 4.673403 GACTGCACATGTCGGTCA 57.327 55.556 22.09 8.59 39.13 4.02
4467 7350 0.815095 ATGTCGGTCAGCATACACGA 59.185 50.000 0.00 0.00 0.00 4.35
4468 7351 0.815095 TGTCGGTCAGCATACACGAT 59.185 50.000 0.00 0.00 35.90 3.73
4504 7388 7.862512 TTATTGTTGGGGTAATAAACTACGG 57.137 36.000 0.00 0.00 0.00 4.02
4510 7394 6.655078 TGGGGTAATAAACTACGGACTATC 57.345 41.667 0.00 0.00 0.00 2.08
4511 7395 5.241506 TGGGGTAATAAACTACGGACTATCG 59.758 44.000 0.00 0.00 0.00 2.92
4514 7398 4.924305 AATAAACTACGGACTATCGGCA 57.076 40.909 0.00 0.00 0.00 5.69
4517 7401 1.022735 ACTACGGACTATCGGCACTG 58.977 55.000 0.00 0.00 0.00 3.66
4530 7414 3.390135 TCGGCACTGTGAACTTAAGAAG 58.610 45.455 12.86 1.43 0.00 2.85
4550 7435 2.699954 GACAATGGTCGAAGGATGTGT 58.300 47.619 0.00 0.00 33.68 3.72
4554 7439 0.756294 TGGTCGAAGGATGTGTGTGT 59.244 50.000 0.00 0.00 0.00 3.72
4556 7441 1.540363 GGTCGAAGGATGTGTGTGTGT 60.540 52.381 0.00 0.00 0.00 3.72
4558 7443 1.138069 TCGAAGGATGTGTGTGTGTGT 59.862 47.619 0.00 0.00 0.00 3.72
4562 7447 1.065491 AGGATGTGTGTGTGTGTGTGT 60.065 47.619 0.00 0.00 0.00 3.72
4573 7484 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
4575 7486 1.265635 GTGTGTGTGTGTGTGTGTGTT 59.734 47.619 0.00 0.00 0.00 3.32
4576 7487 1.950216 TGTGTGTGTGTGTGTGTGTTT 59.050 42.857 0.00 0.00 0.00 2.83
4585 7496 1.226831 GTGTGTGTTTGGCGTTGGG 60.227 57.895 0.00 0.00 0.00 4.12
4599 7510 1.739371 CGTTGGGTCTAGCTACTTGGC 60.739 57.143 0.00 0.00 0.00 4.52
4654 7565 1.558167 TATTTCCCGCAGTGGCCTCA 61.558 55.000 3.32 0.00 36.38 3.86
4713 7624 2.496470 ACTTAGGACGATGGTTGGTCTC 59.504 50.000 0.00 0.00 31.78 3.36
4759 7670 2.108952 ACCAATCCTGGAGCCCATATTC 59.891 50.000 1.52 0.00 46.92 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 9.801873 TCCAAAGTAAAAGAATTCACTTTTCAG 57.198 29.630 15.35 9.77 45.12 3.02
76 77 2.528127 TTCTTCCTCCCCGGTGCA 60.528 61.111 0.00 0.00 0.00 4.57
84 85 7.829706 AGTTGTTTATAATGGTCTTCTTCCTCC 59.170 37.037 0.00 0.00 0.00 4.30
85 86 8.794335 AGTTGTTTATAATGGTCTTCTTCCTC 57.206 34.615 0.00 0.00 0.00 3.71
124 125 3.151554 ACCGGAATGGAAGTTTACCAAC 58.848 45.455 9.46 0.00 42.00 3.77
189 190 3.764434 ACACGTCCTGAATACACTCTCAT 59.236 43.478 0.00 0.00 0.00 2.90
204 205 1.865340 AGCTTCTTTTCGAACACGTCC 59.135 47.619 0.00 0.00 0.00 4.79
234 235 8.989980 CCTCCATAAGACGTAAATATTTCCTTC 58.010 37.037 3.39 0.00 0.00 3.46
236 237 7.291651 TCCCTCCATAAGACGTAAATATTTCCT 59.708 37.037 3.39 0.00 0.00 3.36
243 244 8.491958 ACTAAATTCCCTCCATAAGACGTAAAT 58.508 33.333 0.00 0.00 0.00 1.40
280 283 6.818281 ACATTGGTAGGCTAGTAACCATAA 57.182 37.500 7.66 0.00 42.65 1.90
282 285 5.190925 TGAACATTGGTAGGCTAGTAACCAT 59.809 40.000 7.66 0.00 42.65 3.55
374 378 3.664276 CGTTGATGTTCACCGCTTTACAG 60.664 47.826 0.00 0.00 0.00 2.74
377 381 2.485903 ACGTTGATGTTCACCGCTTTA 58.514 42.857 0.00 0.00 35.63 1.85
382 386 2.411031 GCACTTACGTTGATGTTCACCG 60.411 50.000 0.00 0.00 38.29 4.94
392 396 1.463528 GCTAAAGCGGCACTTACGTTG 60.464 52.381 1.45 0.00 37.75 4.10
440 444 2.903784 TGCCCTTAGTTCTTGCTAGTCA 59.096 45.455 0.00 0.00 0.00 3.41
451 455 2.457598 TCGAGATCACTGCCCTTAGTT 58.542 47.619 0.00 0.00 0.00 2.24
473 477 2.558359 CCCCCAAGCACTTGTTCTTAAG 59.442 50.000 9.41 0.00 38.85 1.85
719 731 2.341846 ACCTTCTGCTTCGTTGGAAA 57.658 45.000 0.00 0.00 0.00 3.13
743 755 7.222872 CCTCCTGAAATCTATCTTGTTAGCAT 58.777 38.462 0.00 0.00 0.00 3.79
779 791 5.063880 ACTTTCTGCTTCGTTGGAAACTAT 58.936 37.500 0.00 0.00 46.99 2.12
783 795 4.448210 ACTACTTTCTGCTTCGTTGGAAA 58.552 39.130 0.00 0.00 0.00 3.13
800 819 1.135257 GCTCAGTGATGCACGACTACT 60.135 52.381 8.99 0.00 39.64 2.57
801 820 1.272781 GCTCAGTGATGCACGACTAC 58.727 55.000 8.99 0.00 39.64 2.73
836 1992 3.689649 AGCGACAGTTCATATTTTGTCCC 59.310 43.478 0.00 0.00 37.29 4.46
1156 2455 2.251371 GGCAAAGCGAACGTCACC 59.749 61.111 0.00 0.00 0.00 4.02
1160 2459 1.828331 GAACTCGGCAAAGCGAACGT 61.828 55.000 0.00 0.00 0.00 3.99
1208 2507 1.528824 AGCCCATTCTGTATGCGCT 59.471 52.632 9.73 1.19 42.22 5.92
1225 2524 1.994507 CTGTAGACGCCCCTGTCGAG 61.995 65.000 0.00 0.00 43.70 4.04
1263 2562 2.606725 GCACAACTGATGGATCTTCTCG 59.393 50.000 0.00 0.00 0.00 4.04
1272 2580 0.884259 TGTCACGGCACAACTGATGG 60.884 55.000 0.00 0.00 0.00 3.51
1279 2587 1.666553 GGTCGATGTCACGGCACAA 60.667 57.895 0.00 0.00 39.76 3.33
1334 2642 0.105778 GATGAAAGAGGAGGAGGGCG 59.894 60.000 0.00 0.00 0.00 6.13
1342 2650 4.679106 GCGACAGAGATTGATGAAAGAGGA 60.679 45.833 0.00 0.00 0.00 3.71
1344 2652 4.431809 AGCGACAGAGATTGATGAAAGAG 58.568 43.478 0.00 0.00 0.00 2.85
1346 2654 3.555139 GGAGCGACAGAGATTGATGAAAG 59.445 47.826 0.00 0.00 0.00 2.62
1349 2657 1.066152 CGGAGCGACAGAGATTGATGA 59.934 52.381 0.00 0.00 0.00 2.92
1351 2659 3.955291 CGGAGCGACAGAGATTGAT 57.045 52.632 0.00 0.00 0.00 2.57
1376 2684 3.064324 GCGGTTTGCTGCCTCCAT 61.064 61.111 0.00 0.00 41.02 3.41
1377 2685 4.577677 TGCGGTTTGCTGCCTCCA 62.578 61.111 0.00 0.00 46.11 3.86
1401 2716 2.420568 GGGTATCGCACTCACCGGA 61.421 63.158 9.46 0.00 32.84 5.14
1402 2717 1.956629 AAGGGTATCGCACTCACCGG 61.957 60.000 0.00 0.00 32.84 5.28
1445 2769 2.109181 GCCTATCCTCCACCGCAC 59.891 66.667 0.00 0.00 0.00 5.34
1454 2778 4.899239 GCGCGCTGTGCCTATCCT 62.899 66.667 26.67 0.00 42.08 3.24
1475 2799 0.326264 AGCAAGATCCGAAAGCTGGT 59.674 50.000 0.00 0.00 33.67 4.00
1488 2812 1.188219 ACTTCTCCCGCAGAGCAAGA 61.188 55.000 14.36 0.00 42.90 3.02
1499 2823 2.221906 TAGACGCCGCAACTTCTCCC 62.222 60.000 0.00 0.00 0.00 4.30
1503 2827 1.352156 CCTGTAGACGCCGCAACTTC 61.352 60.000 0.00 0.00 0.00 3.01
1504 2828 1.374252 CCTGTAGACGCCGCAACTT 60.374 57.895 0.00 0.00 0.00 2.66
1505 2829 2.261671 CCTGTAGACGCCGCAACT 59.738 61.111 0.00 0.00 0.00 3.16
1515 2839 2.044650 CCGACCCCGTCCTGTAGA 60.045 66.667 0.00 0.00 0.00 2.59
1554 2878 0.896940 AGTACTTCCTTCCGCCGTCA 60.897 55.000 0.00 0.00 0.00 4.35
1735 3067 3.118592 ACTGGATGAGCTAGCTAAACCAC 60.119 47.826 23.95 9.21 0.00 4.16
1755 3091 3.712016 AAAGGCCAAAACCAAACAACT 57.288 38.095 5.01 0.00 0.00 3.16
1841 3708 0.539986 ACTTACATGGATTCGCCGGT 59.460 50.000 1.90 0.00 40.66 5.28
1844 3711 2.872858 GGAAGACTTACATGGATTCGCC 59.127 50.000 0.00 0.00 37.10 5.54
1857 3724 0.910088 AAGGGCGGCTAGGAAGACTT 60.910 55.000 9.56 0.00 0.00 3.01
1862 3729 0.759436 CTAGGAAGGGCGGCTAGGAA 60.759 60.000 9.56 0.00 0.00 3.36
1863 3730 1.152525 CTAGGAAGGGCGGCTAGGA 60.153 63.158 9.56 0.00 0.00 2.94
1864 3731 2.873525 GCTAGGAAGGGCGGCTAGG 61.874 68.421 9.56 0.00 0.00 3.02
1865 3732 2.737830 GCTAGGAAGGGCGGCTAG 59.262 66.667 9.56 3.18 0.00 3.42
1866 3733 2.842936 GGCTAGGAAGGGCGGCTA 60.843 66.667 9.56 0.00 0.00 3.93
1872 3739 3.090532 AAGGGCGGCTAGGAAGGG 61.091 66.667 9.56 0.00 0.00 3.95
1873 3740 2.066999 AGAAGGGCGGCTAGGAAGG 61.067 63.158 9.56 0.00 0.00 3.46
1874 3741 1.144936 CAGAAGGGCGGCTAGGAAG 59.855 63.158 9.56 0.00 0.00 3.46
1875 3742 1.198759 AACAGAAGGGCGGCTAGGAA 61.199 55.000 9.56 0.00 0.00 3.36
1898 3765 5.120830 ACAAAAGGATTCGAATTCAGAGTCG 59.879 40.000 18.62 4.46 44.11 4.18
1926 4439 4.179579 GAAATCTGCCGGGTGCGC 62.180 66.667 2.18 0.00 45.60 6.09
1954 4467 0.250038 CACAGTATCTCGCCCATGGG 60.250 60.000 27.87 27.87 38.57 4.00
2042 4555 5.398603 ACTCTGATGTACTTCCTTGTGAG 57.601 43.478 6.32 8.14 0.00 3.51
2043 4556 6.246163 TCTACTCTGATGTACTTCCTTGTGA 58.754 40.000 6.32 0.00 0.00 3.58
2045 4558 6.892456 TGATCTACTCTGATGTACTTCCTTGT 59.108 38.462 6.32 5.05 0.00 3.16
2056 4828 6.018098 GCCATTCAAACTGATCTACTCTGATG 60.018 42.308 0.00 0.00 0.00 3.07
2067 4839 5.482878 AGAGAAATTGGCCATTCAAACTGAT 59.517 36.000 18.95 0.00 0.00 2.90
2079 4851 1.888512 TGTGCTTCAGAGAAATTGGCC 59.111 47.619 0.00 0.00 0.00 5.36
2172 4944 3.377346 AGAGCTGCTGATAATGTACCG 57.623 47.619 7.01 0.00 0.00 4.02
2200 4972 5.220303 GCTTCAAGAACTGTATAGAAGCGTG 60.220 44.000 16.01 0.00 45.42 5.34
2214 4986 6.823689 TGATAATAAGGTCTGGCTTCAAGAAC 59.176 38.462 0.00 0.00 0.00 3.01
2244 5016 2.018355 TGAAGCCACTACCAGTACCA 57.982 50.000 0.00 0.00 0.00 3.25
2252 5024 4.151867 CGAAAACTACCTTGAAGCCACTAC 59.848 45.833 0.00 0.00 0.00 2.73
2257 5029 3.135994 TGTCGAAAACTACCTTGAAGCC 58.864 45.455 0.00 0.00 0.00 4.35
2271 5043 9.853555 AGCATCAAACATTTAATATTGTCGAAA 57.146 25.926 0.00 0.00 0.00 3.46
2299 5071 1.971962 CACGGACTGTTACGTTCGTAC 59.028 52.381 11.74 2.23 46.70 3.67
2300 5072 1.601903 ACACGGACTGTTACGTTCGTA 59.398 47.619 11.74 0.78 46.70 3.43
2302 5074 1.971962 GTACACGGACTGTTACGTTCG 59.028 52.381 8.43 6.51 42.04 3.95
2303 5075 2.287547 TGGTACACGGACTGTTACGTTC 60.288 50.000 8.43 0.00 42.04 3.95
2304 5076 1.680735 TGGTACACGGACTGTTACGTT 59.319 47.619 8.43 4.63 42.04 3.99
2305 5077 1.267806 CTGGTACACGGACTGTTACGT 59.732 52.381 5.79 5.79 45.25 3.57
2306 5078 1.536766 TCTGGTACACGGACTGTTACG 59.463 52.381 0.00 4.63 33.91 3.18
2307 5079 2.555757 ACTCTGGTACACGGACTGTTAC 59.444 50.000 0.00 0.00 33.91 2.50
2308 5080 2.867624 ACTCTGGTACACGGACTGTTA 58.132 47.619 0.00 0.00 33.91 2.41
2316 5088 5.230942 AGATCAGAAAAACTCTGGTACACG 58.769 41.667 0.00 0.00 46.10 4.49
2344 5126 4.216687 TCCTTTGGCCTAAAACACAATACG 59.783 41.667 3.32 0.00 0.00 3.06
2374 5156 6.652481 TCTGATTTCAAGAAGACATCTCCAAC 59.348 38.462 0.00 0.00 37.42 3.77
2376 5158 6.169094 GTCTGATTTCAAGAAGACATCTCCA 58.831 40.000 0.00 0.00 37.42 3.86
2412 5194 6.549736 TCACAGGAATCGGTATTCTTCTATCA 59.450 38.462 0.00 0.00 41.18 2.15
2422 5204 9.529823 TTAGATAATACTCACAGGAATCGGTAT 57.470 33.333 0.00 0.00 0.00 2.73
2449 5231 9.239002 GCTAGTACAACACATAGACTAGAAATG 57.761 37.037 10.72 0.00 41.32 2.32
2525 5307 9.410556 CTCCAAACTAACTTTCATGTAATTTGG 57.589 33.333 15.59 15.59 43.12 3.28
2538 5320 3.502211 CGGTCATTGCTCCAAACTAACTT 59.498 43.478 0.00 0.00 0.00 2.66
2539 5321 3.074412 CGGTCATTGCTCCAAACTAACT 58.926 45.455 0.00 0.00 0.00 2.24
2540 5322 2.414161 GCGGTCATTGCTCCAAACTAAC 60.414 50.000 0.00 0.00 0.00 2.34
2602 5384 2.162208 AGACATTGCCGCTTAACACATG 59.838 45.455 0.00 0.00 0.00 3.21
2611 5393 4.342862 AGAATACATAGACATTGCCGCT 57.657 40.909 0.00 0.00 0.00 5.52
2647 5429 7.065085 GGATCGGCGTAATACTACTGTATAAGA 59.935 40.741 6.85 0.00 38.33 2.10
2667 5449 8.345565 CAAGTATTAAGAAAATCCAAGGATCGG 58.654 37.037 1.37 0.00 33.08 4.18
2690 5472 0.796312 GTCCACGTGTATGTGCCAAG 59.204 55.000 15.65 0.00 38.55 3.61
2693 5475 1.006832 GATGTCCACGTGTATGTGCC 58.993 55.000 15.65 0.00 38.55 5.01
2696 5478 3.064207 GTGTTGATGTCCACGTGTATGT 58.936 45.455 15.65 0.00 0.00 2.29
2702 5484 3.799366 TGTTAAGTGTTGATGTCCACGT 58.201 40.909 0.00 0.00 36.69 4.49
2703 5485 5.356882 AATGTTAAGTGTTGATGTCCACG 57.643 39.130 0.00 0.00 36.69 4.94
2771 5553 3.557595 ACGCTGCAACTCTATAAGCAATC 59.442 43.478 0.00 0.00 36.44 2.67
2773 5555 2.672874 CACGCTGCAACTCTATAAGCAA 59.327 45.455 0.00 0.00 36.44 3.91
2792 5574 3.814049 GCATGAGCGAGTAATGCAC 57.186 52.632 0.00 0.00 44.83 4.57
2806 5588 6.309980 GGATGATCTAACTGACGATAAGCATG 59.690 42.308 0.00 0.00 0.00 4.06
2807 5589 6.210385 AGGATGATCTAACTGACGATAAGCAT 59.790 38.462 0.00 0.00 0.00 3.79
2937 5719 1.819632 CTTCCGGGCTCCATTTCCG 60.820 63.158 0.00 0.00 43.05 4.30
2962 5744 5.009610 TGGCTTACCTTCAAATTGAGTTCAC 59.990 40.000 0.00 0.00 36.63 3.18
3004 5805 1.299541 ATTATTCCAGCAGTTCGGCG 58.700 50.000 0.00 0.00 39.27 6.46
3038 5839 6.690194 ATATCTTTAAGGCTTCAAGCACAG 57.310 37.500 12.53 0.00 44.75 3.66
3068 5869 8.635765 AACTGAGTAAAAGGAAATAGCATGAA 57.364 30.769 0.00 0.00 0.00 2.57
3069 5870 7.336931 GGAACTGAGTAAAAGGAAATAGCATGA 59.663 37.037 0.00 0.00 0.00 3.07
3070 5871 7.121168 TGGAACTGAGTAAAAGGAAATAGCATG 59.879 37.037 0.00 0.00 0.00 4.06
3088 5889 6.348458 CGAGCTCATTTAACAAATGGAACTGA 60.348 38.462 15.40 0.00 46.40 3.41
3099 5900 2.346803 GAGGTGCGAGCTCATTTAACA 58.653 47.619 15.40 0.00 42.03 2.41
3112 5913 1.672356 CTGAAACAGGGGAGGTGCG 60.672 63.158 0.00 0.00 0.00 5.34
3122 5923 1.986882 AGCTTCCCAACCTGAAACAG 58.013 50.000 0.00 0.00 0.00 3.16
3236 6037 9.529325 TCACCGTAAATAGAATGATTTGAGTAG 57.471 33.333 0.00 0.00 31.51 2.57
3243 6044 7.624360 TGCTTTCACCGTAAATAGAATGATT 57.376 32.000 0.00 0.00 0.00 2.57
3273 6074 4.274459 GGTCACAGATCTCCATTTGCATAC 59.726 45.833 0.00 0.00 0.00 2.39
3318 6119 7.710907 GCTACAGTACATGATGTATTCTTCCAA 59.289 37.037 8.72 0.00 35.05 3.53
3353 6154 7.553881 TCTAAAAGCAGCTATCCACAATTAC 57.446 36.000 0.00 0.00 0.00 1.89
3355 6156 7.466746 TTTCTAAAAGCAGCTATCCACAATT 57.533 32.000 0.00 0.00 0.00 2.32
3383 6184 1.032014 AAATGCACCAGCGAACAACT 58.968 45.000 0.00 0.00 46.23 3.16
3391 6192 3.942130 AAGGAACTAAAATGCACCAGC 57.058 42.857 0.00 0.00 38.49 4.85
3394 6195 4.679654 CGAACAAAGGAACTAAAATGCACC 59.320 41.667 0.00 0.00 38.49 5.01
3420 6221 7.975058 GGTCTATTTAACTGAGAGTCAAGTACC 59.025 40.741 0.00 0.00 0.00 3.34
3433 6234 9.930693 AAGTCTTACTCTTGGTCTATTTAACTG 57.069 33.333 0.00 0.00 0.00 3.16
3438 6239 9.057089 CAAACAAGTCTTACTCTTGGTCTATTT 57.943 33.333 9.82 0.05 41.22 1.40
3449 6250 4.875544 TGTGCACAAACAAGTCTTACTC 57.124 40.909 19.28 0.00 0.00 2.59
3467 6268 1.269174 TCCACACCGAATGCAAATGTG 59.731 47.619 10.50 10.50 40.28 3.21
3475 6276 0.320683 TGTCTGCTCCACACCGAATG 60.321 55.000 0.00 0.00 0.00 2.67
3492 6298 2.104281 GGGTACACAGGAACAGAGTTGT 59.896 50.000 0.00 0.00 39.87 3.32
3566 6372 9.141400 CTTGAGGTCTACAAAATACAAGACTAC 57.859 37.037 0.00 0.00 38.69 2.73
3614 6420 2.197875 ACCGCCGCTCCCTAGTAT 59.802 61.111 0.00 0.00 0.00 2.12
3716 6522 6.317391 CAGTCAAGTTTTGAAGAAACTCCTCT 59.683 38.462 4.80 2.14 42.15 3.69
3789 6595 3.691118 TCAGATAAGCATTTGCCACAGAC 59.309 43.478 0.00 0.00 43.38 3.51
3792 6598 4.529897 AGATCAGATAAGCATTTGCCACA 58.470 39.130 0.00 0.00 43.38 4.17
3805 6611 9.745018 AACAAAAAGGAGATCAAAGATCAGATA 57.255 29.630 9.43 0.00 0.00 1.98
3830 6636 1.616725 GGGTCACATGGATCTTGCCAA 60.617 52.381 0.00 0.00 42.16 4.52
3886 6727 5.224888 TCTCGTAAACACGTTTAAGCAGAT 58.775 37.500 9.78 0.00 36.86 2.90
3932 6773 1.066002 CCAGAAACTGTGTGCACAAGG 59.934 52.381 23.59 18.87 41.33 3.61
3933 6774 1.534595 GCCAGAAACTGTGTGCACAAG 60.535 52.381 23.59 21.60 41.33 3.16
3939 6780 2.942376 TGTACTTGCCAGAAACTGTGTG 59.058 45.455 0.00 0.00 0.00 3.82
3945 6786 1.537202 CTGCCTGTACTTGCCAGAAAC 59.463 52.381 0.00 0.00 31.38 2.78
3972 6813 0.325933 TGGGAGATTGTGCTGAGGTG 59.674 55.000 0.00 0.00 0.00 4.00
3978 6819 0.040058 TTGGCATGGGAGATTGTGCT 59.960 50.000 0.00 0.00 37.70 4.40
4083 6924 1.374758 GCCTTCCACGTCTGGTCTG 60.375 63.158 0.00 0.00 38.90 3.51
4084 6925 1.534235 AGCCTTCCACGTCTGGTCT 60.534 57.895 0.00 0.00 38.90 3.85
4107 6948 2.743928 CTTGCGCCACTGTCCTCC 60.744 66.667 4.18 0.00 0.00 4.30
4113 6954 0.676466 TATCCCAACTTGCGCCACTG 60.676 55.000 4.18 0.00 0.00 3.66
4137 6978 2.237143 TCTGCGTCTGATTTTGAGGGAT 59.763 45.455 0.00 0.00 0.00 3.85
4147 6988 1.445066 CTGCGTGTCTGCGTCTGAT 60.445 57.895 0.00 0.00 37.81 2.90
4148 6989 2.050077 CTGCGTGTCTGCGTCTGA 60.050 61.111 0.00 0.00 37.81 3.27
4149 6990 2.355126 ACTGCGTGTCTGCGTCTG 60.355 61.111 0.00 0.00 37.81 3.51
4150 6991 2.355126 CACTGCGTGTCTGCGTCT 60.355 61.111 1.24 0.00 37.81 4.18
4151 6992 2.354656 TCACTGCGTGTCTGCGTC 60.355 61.111 8.22 0.00 37.81 5.19
4152 6993 2.658593 GTCACTGCGTGTCTGCGT 60.659 61.111 8.22 0.00 37.81 5.24
4153 6994 2.355126 AGTCACTGCGTGTCTGCG 60.355 61.111 8.22 0.00 37.81 5.18
4154 6995 0.241213 TAGAGTCACTGCGTGTCTGC 59.759 55.000 11.51 5.71 32.72 4.26
4155 6996 2.706555 TTAGAGTCACTGCGTGTCTG 57.293 50.000 11.51 0.00 32.72 3.51
4156 6997 2.820197 TGATTAGAGTCACTGCGTGTCT 59.180 45.455 7.79 7.79 34.96 3.41
4157 6998 3.217599 TGATTAGAGTCACTGCGTGTC 57.782 47.619 8.22 3.86 34.79 3.67
4158 6999 3.660501 TTGATTAGAGTCACTGCGTGT 57.339 42.857 8.22 0.00 34.79 4.49
4159 7000 3.740832 TGTTTGATTAGAGTCACTGCGTG 59.259 43.478 0.00 2.79 34.45 5.34
4204 7045 1.301293 GCACTGGAGGAGAAAGGGG 59.699 63.158 0.00 0.00 0.00 4.79
4208 7049 1.130054 AGGCTGCACTGGAGGAGAAA 61.130 55.000 0.50 0.00 0.00 2.52
4223 7064 0.034670 GATCCTTCAGTGGCAAGGCT 60.035 55.000 5.85 0.00 40.43 4.58
4224 7065 1.034292 GGATCCTTCAGTGGCAAGGC 61.034 60.000 3.84 0.00 40.43 4.35
4228 7086 2.777536 ACTGGATCCTTCAGTGGCA 58.222 52.632 14.23 0.00 43.07 4.92
4265 7123 9.793259 AGTTTCTCTTATGTGAAATAAACCTCA 57.207 29.630 8.53 0.00 37.78 3.86
4289 7147 6.769512 ACAAACTTCAGTGGTACATGATAGT 58.230 36.000 0.00 0.83 44.52 2.12
4371 7254 4.100373 AGGAACAGAGTAATTGGAGCTCT 58.900 43.478 14.64 0.00 39.89 4.09
4380 7263 5.355350 GCACTGCAATAAGGAACAGAGTAAT 59.645 40.000 0.00 0.00 34.25 1.89
4413 7296 7.383843 GGTGGTTTTGATTTTCGATATTGTTGT 59.616 33.333 0.00 0.00 0.00 3.32
4415 7298 6.584563 CGGTGGTTTTGATTTTCGATATTGTT 59.415 34.615 0.00 0.00 0.00 2.83
4427 7310 1.336755 GTGCAGTCGGTGGTTTTGATT 59.663 47.619 0.00 0.00 0.00 2.57
4428 7311 0.951558 GTGCAGTCGGTGGTTTTGAT 59.048 50.000 0.00 0.00 0.00 2.57
4440 7323 1.630244 GCTGACCGACATGTGCAGTC 61.630 60.000 1.15 7.81 0.00 3.51
4454 7337 6.771076 TGATTGTTAAATCGTGTATGCTGAC 58.229 36.000 0.00 0.00 44.47 3.51
4504 7388 2.656560 AGTTCACAGTGCCGATAGTC 57.343 50.000 0.00 0.00 0.00 2.59
4510 7394 3.184581 GTCTTCTTAAGTTCACAGTGCCG 59.815 47.826 1.63 0.00 0.00 5.69
4511 7395 4.127171 TGTCTTCTTAAGTTCACAGTGCC 58.873 43.478 1.63 0.00 0.00 5.01
4514 7398 6.357367 ACCATTGTCTTCTTAAGTTCACAGT 58.643 36.000 1.63 0.00 0.00 3.55
4517 7401 5.694910 TCGACCATTGTCTTCTTAAGTTCAC 59.305 40.000 1.63 0.00 39.47 3.18
4530 7414 2.416547 CACACATCCTTCGACCATTGTC 59.583 50.000 0.00 0.00 38.18 3.18
4550 7435 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
4554 7439 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
4556 7441 1.598882 AACACACACACACACACACA 58.401 45.000 0.00 0.00 0.00 3.72
4558 7443 1.268079 CCAAACACACACACACACACA 59.732 47.619 0.00 0.00 0.00 3.72
4562 7447 1.237954 ACGCCAAACACACACACACA 61.238 50.000 0.00 0.00 0.00 3.72
4573 7484 0.605589 AGCTAGACCCAACGCCAAAC 60.606 55.000 0.00 0.00 0.00 2.93
4575 7486 0.248289 GTAGCTAGACCCAACGCCAA 59.752 55.000 0.00 0.00 0.00 4.52
4576 7487 0.613853 AGTAGCTAGACCCAACGCCA 60.614 55.000 0.00 0.00 0.00 5.69
4585 7496 2.464865 CATCACGCCAAGTAGCTAGAC 58.535 52.381 0.00 0.00 0.00 2.59
4599 7510 3.940852 TGAAATGTTCAGGATCCATCACG 59.059 43.478 15.82 0.00 34.08 4.35
4636 7547 2.044946 GAGGCCACTGCGGGAAAT 60.045 61.111 5.01 0.00 38.85 2.17
4639 7550 2.364973 TATGAGGCCACTGCGGGA 60.365 61.111 5.01 0.00 38.85 5.14
4672 7583 1.049289 ATAGGGACTTCACGGGGAGC 61.049 60.000 0.00 0.00 41.75 4.70
4673 7584 1.962100 GTATAGGGACTTCACGGGGAG 59.038 57.143 0.00 0.00 41.75 4.30
4713 7624 1.097547 GCCGGTGATGGTGAATGGAG 61.098 60.000 1.90 0.00 0.00 3.86
4759 7670 2.709475 GCAACGCTTATCAGGCCG 59.291 61.111 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.