Multiple sequence alignment - TraesCS4B01G017600

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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 TraesCS4B01G017600 chr4B 100.000 4323 0 0 1 4323 13076817 13081139 0.000000e+00 7984.0
1 TraesCS4B01G017600 chr4B 89.668 1113 75 23 2234 3339 13053563 13052484 0.000000e+00 1382.0
2 TraesCS4B01G017600 chr4B 95.006 841 32 7 1227 2065 13054441 13053609 0.000000e+00 1312.0
3 TraesCS4B01G017600 chr4B 88.823 671 55 14 775 1437 13054946 13054288 0.000000e+00 806.0
4 TraesCS4B01G017600 chr4D 91.698 1349 81 19 744 2076 7203572 7204905 0.000000e+00 1842.0
5 TraesCS4B01G017600 chr4D 91.133 1139 53 16 2230 3339 7204948 7206067 0.000000e+00 1500.0
6 TraesCS4B01G017600 chr4D 85.943 1309 100 53 2259 3515 7183559 7182283 0.000000e+00 1321.0
7 TraesCS4B01G017600 chr4D 91.869 701 40 11 744 1438 7185226 7184537 0.000000e+00 963.0
8 TraesCS4B01G017600 chr4D 89.212 723 46 20 1227 1928 7184691 7183980 0.000000e+00 874.0
9 TraesCS4B01G017600 chr4D 87.931 232 17 7 3353 3582 7206127 7206349 3.320000e-66 263.0
10 TraesCS4B01G017600 chr4D 88.660 97 10 1 2115 2210 237030894 237030990 2.730000e-22 117.0
11 TraesCS4B01G017600 chr5A 98.794 746 8 1 1 745 58379729 58378984 0.000000e+00 1327.0
12 TraesCS4B01G017600 chr3B 98.660 746 9 1 4 748 675634238 675633493 0.000000e+00 1321.0
13 TraesCS4B01G017600 chr2B 98.658 745 10 0 1 745 727662778 727662034 0.000000e+00 1321.0
14 TraesCS4B01G017600 chr2B 98.271 752 12 1 1 751 575372192 575371441 0.000000e+00 1315.0
15 TraesCS4B01G017600 chr2B 87.613 662 40 13 3704 4323 106165057 106165718 0.000000e+00 730.0
16 TraesCS4B01G017600 chr1B 98.658 745 10 0 1 745 50334741 50335485 0.000000e+00 1321.0
17 TraesCS4B01G017600 chr1B 98.529 748 10 1 1 747 510838454 510839201 0.000000e+00 1319.0
18 TraesCS4B01G017600 chr1B 97.892 759 12 3 1 758 60592385 60593140 0.000000e+00 1310.0
19 TraesCS4B01G017600 chr1B 89.130 644 45 11 3704 4323 623675591 623676233 0.000000e+00 778.0
20 TraesCS4B01G017600 chr1B 87.385 650 47 9 3709 4323 500626191 500625542 0.000000e+00 713.0
21 TraesCS4B01G017600 chr1A 98.660 746 9 1 1 745 358732202 358732947 0.000000e+00 1321.0
22 TraesCS4B01G017600 chr3A 98.404 752 8 3 1 750 225890222 225890971 0.000000e+00 1319.0
23 TraesCS4B01G017600 chr4A 88.779 1114 73 27 2254 3339 596306163 596305074 0.000000e+00 1317.0
24 TraesCS4B01G017600 chr4A 88.779 1114 73 30 2254 3339 596447163 596448252 0.000000e+00 1317.0
25 TraesCS4B01G017600 chr4A 88.221 815 64 22 1275 2065 596307040 596306234 0.000000e+00 944.0
26 TraesCS4B01G017600 chr4A 88.221 815 64 22 1275 2065 596446286 596447092 0.000000e+00 944.0
27 TraesCS4B01G017600 chr4A 93.034 646 36 6 744 1380 596307529 596306884 0.000000e+00 935.0
28 TraesCS4B01G017600 chr4A 93.907 558 33 1 3766 4323 730521509 730520953 0.000000e+00 841.0
29 TraesCS4B01G017600 chr4A 90.982 621 44 8 771 1380 596445823 596446442 0.000000e+00 826.0
30 TraesCS4B01G017600 chr4A 90.338 621 53 4 3708 4322 446954067 446953448 0.000000e+00 808.0
31 TraesCS4B01G017600 chr4A 89.147 258 10 9 3342 3588 596302856 596302606 5.430000e-79 305.0
32 TraesCS4B01G017600 chrUn 94.265 558 31 1 3766 4323 377802795 377802239 0.000000e+00 852.0
33 TraesCS4B01G017600 chr5B 89.806 618 59 4 3710 4323 355900267 355900884 0.000000e+00 789.0
34 TraesCS4B01G017600 chr5B 89.146 562 48 5 3775 4323 132516918 132516357 0.000000e+00 688.0
35 TraesCS4B01G017600 chr5B 84.444 630 68 14 3709 4323 700432569 700433183 1.040000e-165 593.0
36 TraesCS4B01G017600 chr6D 90.049 613 52 3 3708 4318 409482998 409482393 0.000000e+00 785.0
37 TraesCS4B01G017600 chr6D 92.129 559 37 3 3761 4318 407210247 407209695 0.000000e+00 782.0
38 TraesCS4B01G017600 chr6D 88.776 98 10 1 2115 2211 391736687 391736784 7.590000e-23 119.0
39 TraesCS4B01G017600 chr6D 85.593 118 10 5 2097 2210 240277296 240277182 2.730000e-22 117.0
40 TraesCS4B01G017600 chr7B 91.343 566 45 4 3761 4323 665416020 665415456 0.000000e+00 771.0
41 TraesCS4B01G017600 chr7B 95.161 62 2 1 3711 3771 665416092 665416031 3.560000e-16 97.1
42 TraesCS4B01G017600 chr2A 90.051 583 48 7 3749 4323 776100635 776101215 0.000000e+00 747.0
43 TraesCS4B01G017600 chr7D 89.583 96 10 0 2115 2210 51830940 51831035 5.870000e-24 122.0
44 TraesCS4B01G017600 chr3D 89.583 96 10 0 2115 2210 417604829 417604734 5.870000e-24 122.0
45 TraesCS4B01G017600 chr3D 88.776 98 9 2 2115 2210 505727326 505727229 7.590000e-23 119.0
46 TraesCS4B01G017600 chr3D 88.660 97 9 2 2115 2210 358224790 358224695 2.730000e-22 117.0
47 TraesCS4B01G017600 chr2D 88.660 97 10 1 2115 2210 213448336 213448240 2.730000e-22 117.0
48 TraesCS4B01G017600 chr1D 88.660 97 10 1 2115 2210 34809226 34809322 2.730000e-22 117.0


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 TraesCS4B01G017600 chr4B 13076817 13081139 4322 False 7984.000000 7984 100.000000 1 4323 1 chr4B.!!$F1 4322
1 TraesCS4B01G017600 chr4B 13052484 13054946 2462 True 1166.666667 1382 91.165667 775 3339 3 chr4B.!!$R1 2564
2 TraesCS4B01G017600 chr4D 7203572 7206349 2777 False 1201.666667 1842 90.254000 744 3582 3 chr4D.!!$F2 2838
3 TraesCS4B01G017600 chr4D 7182283 7185226 2943 True 1052.666667 1321 89.008000 744 3515 3 chr4D.!!$R1 2771
4 TraesCS4B01G017600 chr5A 58378984 58379729 745 True 1327.000000 1327 98.794000 1 745 1 chr5A.!!$R1 744
5 TraesCS4B01G017600 chr3B 675633493 675634238 745 True 1321.000000 1321 98.660000 4 748 1 chr3B.!!$R1 744
6 TraesCS4B01G017600 chr2B 727662034 727662778 744 True 1321.000000 1321 98.658000 1 745 1 chr2B.!!$R2 744
7 TraesCS4B01G017600 chr2B 575371441 575372192 751 True 1315.000000 1315 98.271000 1 751 1 chr2B.!!$R1 750
8 TraesCS4B01G017600 chr2B 106165057 106165718 661 False 730.000000 730 87.613000 3704 4323 1 chr2B.!!$F1 619
9 TraesCS4B01G017600 chr1B 50334741 50335485 744 False 1321.000000 1321 98.658000 1 745 1 chr1B.!!$F1 744
10 TraesCS4B01G017600 chr1B 510838454 510839201 747 False 1319.000000 1319 98.529000 1 747 1 chr1B.!!$F3 746
11 TraesCS4B01G017600 chr1B 60592385 60593140 755 False 1310.000000 1310 97.892000 1 758 1 chr1B.!!$F2 757
12 TraesCS4B01G017600 chr1B 623675591 623676233 642 False 778.000000 778 89.130000 3704 4323 1 chr1B.!!$F4 619
13 TraesCS4B01G017600 chr1B 500625542 500626191 649 True 713.000000 713 87.385000 3709 4323 1 chr1B.!!$R1 614
14 TraesCS4B01G017600 chr1A 358732202 358732947 745 False 1321.000000 1321 98.660000 1 745 1 chr1A.!!$F1 744
15 TraesCS4B01G017600 chr3A 225890222 225890971 749 False 1319.000000 1319 98.404000 1 750 1 chr3A.!!$F1 749
16 TraesCS4B01G017600 chr4A 596445823 596448252 2429 False 1029.000000 1317 89.327333 771 3339 3 chr4A.!!$F1 2568
17 TraesCS4B01G017600 chr4A 596302606 596307529 4923 True 875.250000 1317 89.795250 744 3588 4 chr4A.!!$R3 2844
18 TraesCS4B01G017600 chr4A 730520953 730521509 556 True 841.000000 841 93.907000 3766 4323 1 chr4A.!!$R2 557
19 TraesCS4B01G017600 chr4A 446953448 446954067 619 True 808.000000 808 90.338000 3708 4322 1 chr4A.!!$R1 614
20 TraesCS4B01G017600 chrUn 377802239 377802795 556 True 852.000000 852 94.265000 3766 4323 1 chrUn.!!$R1 557
21 TraesCS4B01G017600 chr5B 355900267 355900884 617 False 789.000000 789 89.806000 3710 4323 1 chr5B.!!$F1 613
22 TraesCS4B01G017600 chr5B 132516357 132516918 561 True 688.000000 688 89.146000 3775 4323 1 chr5B.!!$R1 548
23 TraesCS4B01G017600 chr5B 700432569 700433183 614 False 593.000000 593 84.444000 3709 4323 1 chr5B.!!$F2 614
24 TraesCS4B01G017600 chr6D 409482393 409482998 605 True 785.000000 785 90.049000 3708 4318 1 chr6D.!!$R3 610
25 TraesCS4B01G017600 chr6D 407209695 407210247 552 True 782.000000 782 92.129000 3761 4318 1 chr6D.!!$R2 557
26 TraesCS4B01G017600 chr7B 665415456 665416092 636 True 434.050000 771 93.252000 3711 4323 2 chr7B.!!$R1 612
27 TraesCS4B01G017600 chr2A 776100635 776101215 580 False 747.000000 747 90.051000 3749 4323 1 chr2A.!!$F1 574

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
968 980 1.078567 GAGCTCCACTTCCCAGCAG 60.079 63.158 0.87 0.00 35.46 4.24 F
1988 2220 0.744874 ACTGACACGTGGATATCCCG 59.255 55.000 21.57 23.13 37.93 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2104 2369 0.179124 CTTGACTGAGCGACCTAGCC 60.179 60.0 0.0 0.0 38.01 3.93 R
3516 6088 0.105039 CCTGGCCACGAGGAAGATAC 59.895 60.0 0.0 0.0 36.89 2.24 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
230 231 2.477245 TGGCTCTAACCTGATTGCCTA 58.523 47.619 0.00 0.00 40.82 3.93
608 609 8.380742 ACCCTTCTAGATTCATTAGAAAGTGA 57.619 34.615 0.00 0.00 36.87 3.41
621 622 9.035890 TCATTAGAAAGTGACTAAGATTGAGGA 57.964 33.333 0.00 0.00 34.13 3.71
946 958 1.634225 CGCGCTACAAATACGGTGG 59.366 57.895 5.56 0.00 0.00 4.61
952 964 2.460918 CTACAAATACGGTGGCTCGAG 58.539 52.381 8.45 8.45 0.00 4.04
968 980 1.078567 GAGCTCCACTTCCCAGCAG 60.079 63.158 0.87 0.00 35.46 4.24
970 984 1.130054 AGCTCCACTTCCCAGCAGAA 61.130 55.000 0.00 0.00 35.46 3.02
1243 1276 4.664267 AGGAGGAGCAGGGCCACA 62.664 66.667 6.18 0.00 0.00 4.17
1709 1873 3.056448 CGATCGATGATAACTAACGTGCG 59.944 47.826 10.26 0.00 0.00 5.34
1710 1874 2.114056 TCGATGATAACTAACGTGCGC 58.886 47.619 0.00 0.00 0.00 6.09
1711 1875 1.849829 CGATGATAACTAACGTGCGCA 59.150 47.619 5.66 5.66 0.00 6.09
1712 1876 2.471370 CGATGATAACTAACGTGCGCAT 59.529 45.455 15.91 0.00 0.00 4.73
1713 1877 3.659108 CGATGATAACTAACGTGCGCATG 60.659 47.826 27.53 27.53 0.00 4.06
1714 1878 1.326245 TGATAACTAACGTGCGCATGC 59.674 47.619 28.93 7.91 43.20 4.06
1919 2087 1.743394 CCGGCAAGTTCCAGGTAATTC 59.257 52.381 0.00 0.00 0.00 2.17
1923 2105 4.556233 GGCAAGTTCCAGGTAATTCAAAC 58.444 43.478 0.00 0.00 0.00 2.93
1988 2220 0.744874 ACTGACACGTGGATATCCCG 59.255 55.000 21.57 23.13 37.93 5.14
2065 2297 1.936203 GCGGCTTTGAAGGTACGTACA 60.936 52.381 26.02 3.72 0.00 2.90
2110 2375 4.415783 AAAAAGGGTGCGGCTAGG 57.584 55.556 0.00 0.00 0.00 3.02
2111 2376 1.458927 AAAAAGGGTGCGGCTAGGT 59.541 52.632 0.00 0.00 0.00 3.08
2113 2378 2.798148 AAAAGGGTGCGGCTAGGTCG 62.798 60.000 0.00 0.00 0.00 4.79
2120 2385 2.409651 CGGCTAGGTCGCTCAGTC 59.590 66.667 0.00 0.00 0.00 3.51
2121 2386 2.407428 CGGCTAGGTCGCTCAGTCA 61.407 63.158 0.00 0.00 0.00 3.41
2122 2387 1.890894 GGCTAGGTCGCTCAGTCAA 59.109 57.895 0.00 0.00 0.00 3.18
2123 2388 0.179124 GGCTAGGTCGCTCAGTCAAG 60.179 60.000 0.00 0.00 0.00 3.02
2124 2389 0.528470 GCTAGGTCGCTCAGTCAAGT 59.472 55.000 0.00 0.00 0.00 3.16
2125 2390 1.734047 GCTAGGTCGCTCAGTCAAGTG 60.734 57.143 0.00 0.00 0.00 3.16
2126 2391 1.813178 CTAGGTCGCTCAGTCAAGTGA 59.187 52.381 0.00 0.00 33.52 3.41
2127 2392 1.261480 AGGTCGCTCAGTCAAGTGAT 58.739 50.000 0.00 0.00 38.03 3.06
2128 2393 2.447443 AGGTCGCTCAGTCAAGTGATA 58.553 47.619 0.00 0.00 38.03 2.15
2130 2395 3.449018 AGGTCGCTCAGTCAAGTGATATT 59.551 43.478 0.00 0.00 38.03 1.28
2131 2396 3.553511 GGTCGCTCAGTCAAGTGATATTG 59.446 47.826 0.00 0.00 38.03 1.90
2132 2397 3.000724 GTCGCTCAGTCAAGTGATATTGC 59.999 47.826 0.00 0.00 38.03 3.56
2133 2398 2.931969 CGCTCAGTCAAGTGATATTGCA 59.068 45.455 0.00 0.00 0.00 4.08
2134 2399 3.558829 CGCTCAGTCAAGTGATATTGCAT 59.441 43.478 0.00 0.00 0.00 3.96
2137 2402 6.563567 CGCTCAGTCAAGTGATATTGCATAAG 60.564 42.308 0.00 0.00 0.00 1.73
2138 2403 6.481313 GCTCAGTCAAGTGATATTGCATAAGA 59.519 38.462 0.00 0.00 0.00 2.10
2139 2404 7.011763 GCTCAGTCAAGTGATATTGCATAAGAA 59.988 37.037 0.00 0.00 0.00 2.52
2140 2405 8.429493 TCAGTCAAGTGATATTGCATAAGAAG 57.571 34.615 0.00 0.00 0.00 2.85
2142 2407 8.886719 CAGTCAAGTGATATTGCATAAGAAGAA 58.113 33.333 0.00 0.00 0.00 2.52
2143 2408 9.453572 AGTCAAGTGATATTGCATAAGAAGAAA 57.546 29.630 0.00 0.00 0.00 2.52
2192 2478 7.407393 TTGTATGAATCTCCATGCAAAATCA 57.593 32.000 0.00 0.00 42.97 2.57
2195 2481 7.977293 TGTATGAATCTCCATGCAAAATCAAAG 59.023 33.333 0.00 0.00 36.47 2.77
2197 2483 5.481122 TGAATCTCCATGCAAAATCAAAGGA 59.519 36.000 0.00 0.00 0.00 3.36
2198 2484 4.789012 TCTCCATGCAAAATCAAAGGAC 57.211 40.909 0.00 0.00 0.00 3.85
2199 2485 4.410099 TCTCCATGCAAAATCAAAGGACT 58.590 39.130 0.00 0.00 0.00 3.85
2200 2486 5.569355 TCTCCATGCAAAATCAAAGGACTA 58.431 37.500 0.00 0.00 0.00 2.59
2201 2487 6.189859 TCTCCATGCAAAATCAAAGGACTAT 58.810 36.000 0.00 0.00 0.00 2.12
2204 2490 6.039717 TCCATGCAAAATCAAAGGACTATAGC 59.960 38.462 0.00 0.00 0.00 2.97
2205 2491 6.183360 CCATGCAAAATCAAAGGACTATAGCA 60.183 38.462 0.00 0.00 0.00 3.49
2206 2492 7.431249 CATGCAAAATCAAAGGACTATAGCAT 58.569 34.615 0.00 0.00 38.23 3.79
2207 2493 7.031226 TGCAAAATCAAAGGACTATAGCATC 57.969 36.000 0.00 0.00 0.00 3.91
2208 2494 6.138761 GCAAAATCAAAGGACTATAGCATCG 58.861 40.000 0.00 0.00 0.00 3.84
2209 2495 6.017934 GCAAAATCAAAGGACTATAGCATCGA 60.018 38.462 0.00 0.00 0.00 3.59
2211 2497 7.721286 AAATCAAAGGACTATAGCATCGAAG 57.279 36.000 0.00 0.00 0.00 3.79
2212 2498 6.656632 ATCAAAGGACTATAGCATCGAAGA 57.343 37.500 0.00 0.00 45.75 2.87
2213 2499 5.833082 TCAAAGGACTATAGCATCGAAGAC 58.167 41.667 0.00 0.00 42.51 3.01
2214 2500 5.594725 TCAAAGGACTATAGCATCGAAGACT 59.405 40.000 0.00 0.00 42.51 3.24
2215 2501 6.096987 TCAAAGGACTATAGCATCGAAGACTT 59.903 38.462 0.00 0.00 42.51 3.01
2217 2503 6.811253 AGGACTATAGCATCGAAGACTTAG 57.189 41.667 0.00 0.00 42.51 2.18
2219 2505 5.048643 GGACTATAGCATCGAAGACTTAGCA 60.049 44.000 0.00 0.00 42.51 3.49
2221 2507 6.806751 ACTATAGCATCGAAGACTTAGCAAA 58.193 36.000 0.00 0.00 42.51 3.68
2222 2508 7.265673 ACTATAGCATCGAAGACTTAGCAAAA 58.734 34.615 0.00 0.00 42.51 2.44
2224 2510 4.319177 AGCATCGAAGACTTAGCAAAACT 58.681 39.130 0.00 0.00 42.51 2.66
2225 2511 4.153117 AGCATCGAAGACTTAGCAAAACTG 59.847 41.667 0.00 0.00 42.51 3.16
2227 2513 5.334105 GCATCGAAGACTTAGCAAAACTGAA 60.334 40.000 0.00 0.00 42.51 3.02
2228 2514 6.658831 CATCGAAGACTTAGCAAAACTGAAA 58.341 36.000 0.00 0.00 42.51 2.69
2229 2515 6.671614 TCGAAGACTTAGCAAAACTGAAAA 57.328 33.333 0.00 0.00 0.00 2.29
2230 2516 7.079182 TCGAAGACTTAGCAAAACTGAAAAA 57.921 32.000 0.00 0.00 0.00 1.94
2256 2542 5.729974 AAAGAAAAACTCGGTACTCACAC 57.270 39.130 0.00 0.00 0.00 3.82
2716 3030 3.475774 GCGCCGTACCTGAACACG 61.476 66.667 0.00 0.00 37.89 4.49
2782 3096 3.365291 GATCGTGTGCCCGCACCTA 62.365 63.158 16.77 3.16 45.63 3.08
2899 3228 3.519930 GGCTCCGAGTCCGAGTCC 61.520 72.222 9.76 7.87 38.22 3.85
2900 3229 3.878519 GCTCCGAGTCCGAGTCCG 61.879 72.222 9.76 0.00 38.22 4.79
2901 3230 2.125229 CTCCGAGTCCGAGTCCGA 60.125 66.667 0.74 0.00 38.22 4.55
2902 3231 2.125229 TCCGAGTCCGAGTCCGAG 60.125 66.667 0.00 0.00 38.22 4.63
2903 3232 2.436292 CCGAGTCCGAGTCCGAGT 60.436 66.667 0.00 0.00 38.22 4.18
2904 3233 2.462782 CCGAGTCCGAGTCCGAGTC 61.463 68.421 6.32 6.32 38.22 3.36
2905 3234 2.462782 CGAGTCCGAGTCCGAGTCC 61.463 68.421 9.78 0.00 38.22 3.85
3184 3513 3.723348 GTGTTCCGCGCCAAGGAC 61.723 66.667 0.00 0.00 37.53 3.85
3247 3585 2.183811 CACGAGCAGGAGCAGGAG 59.816 66.667 0.00 0.00 45.49 3.69
3343 3681 4.783621 TGCATGGCCGCTGGAGAC 62.784 66.667 0.00 0.00 0.00 3.36
3345 3683 2.270205 CATGGCCGCTGGAGACTT 59.730 61.111 0.00 0.00 0.00 3.01
3351 5911 2.320587 CCGCTGGAGACTTGTGTGC 61.321 63.158 0.00 0.00 0.00 4.57
3354 5914 0.533755 GCTGGAGACTTGTGTGCTGT 60.534 55.000 0.00 0.00 0.00 4.40
3445 6012 2.172851 TGTAAGTTGCCAACCTACCG 57.827 50.000 12.55 0.00 29.22 4.02
3496 6068 1.810959 TAAATACAAGGGCGTTGCGT 58.189 45.000 19.00 5.90 40.15 5.24
3516 6088 5.635280 TGCGTCTCTTTTTCAGTATCTTCAG 59.365 40.000 0.00 0.00 0.00 3.02
3520 6092 9.015577 CGTCTCTTTTTCAGTATCTTCAGTATC 57.984 37.037 0.00 0.00 0.00 2.24
3534 6106 1.115467 AGTATCTTCCTCGTGGCCAG 58.885 55.000 5.11 0.00 0.00 4.85
3554 6126 5.103000 CCAGGAAAGAGATAACGTGTACTG 58.897 45.833 0.00 0.00 0.00 2.74
3564 6136 6.973843 AGATAACGTGTACTGTTAGTCACAA 58.026 36.000 13.92 0.00 35.45 3.33
3588 6160 6.963049 AACAATTAGTCCAGTTTAGCTACG 57.037 37.500 0.00 0.00 0.00 3.51
3589 6161 5.416947 ACAATTAGTCCAGTTTAGCTACGG 58.583 41.667 0.00 0.00 0.00 4.02
3590 6162 5.186409 ACAATTAGTCCAGTTTAGCTACGGA 59.814 40.000 0.00 0.00 0.00 4.69
3591 6163 4.978083 TTAGTCCAGTTTAGCTACGGAG 57.022 45.455 0.00 0.00 0.00 4.63
3592 6164 3.083122 AGTCCAGTTTAGCTACGGAGA 57.917 47.619 0.00 0.00 0.00 3.71
3593 6165 3.428532 AGTCCAGTTTAGCTACGGAGAA 58.571 45.455 0.00 0.00 0.00 2.87
3594 6166 4.024670 AGTCCAGTTTAGCTACGGAGAAT 58.975 43.478 0.00 0.00 0.00 2.40
3595 6167 4.466726 AGTCCAGTTTAGCTACGGAGAATT 59.533 41.667 0.00 0.00 0.00 2.17
3596 6168 5.046520 AGTCCAGTTTAGCTACGGAGAATTT 60.047 40.000 0.00 0.00 0.00 1.82
3597 6169 5.063564 GTCCAGTTTAGCTACGGAGAATTTG 59.936 44.000 0.00 0.00 0.00 2.32
3598 6170 4.332819 CCAGTTTAGCTACGGAGAATTTGG 59.667 45.833 0.00 0.00 0.00 3.28
3599 6171 5.175859 CAGTTTAGCTACGGAGAATTTGGA 58.824 41.667 0.00 0.00 0.00 3.53
3600 6172 5.817816 CAGTTTAGCTACGGAGAATTTGGAT 59.182 40.000 0.00 0.00 0.00 3.41
3601 6173 6.018669 CAGTTTAGCTACGGAGAATTTGGATC 60.019 42.308 0.00 0.00 0.00 3.36
3602 6174 3.099267 AGCTACGGAGAATTTGGATCG 57.901 47.619 0.00 0.00 0.00 3.69
3603 6175 2.693591 AGCTACGGAGAATTTGGATCGA 59.306 45.455 0.00 0.00 0.00 3.59
3604 6176 3.322254 AGCTACGGAGAATTTGGATCGAT 59.678 43.478 0.00 0.00 0.00 3.59
3605 6177 4.058817 GCTACGGAGAATTTGGATCGATT 58.941 43.478 0.00 0.00 0.00 3.34
3606 6178 4.511826 GCTACGGAGAATTTGGATCGATTT 59.488 41.667 0.00 0.00 0.00 2.17
3607 6179 5.007724 GCTACGGAGAATTTGGATCGATTTT 59.992 40.000 0.00 0.00 0.00 1.82
3608 6180 6.202188 GCTACGGAGAATTTGGATCGATTTTA 59.798 38.462 0.00 0.00 0.00 1.52
3609 6181 6.995511 ACGGAGAATTTGGATCGATTTTAA 57.004 33.333 0.00 0.00 0.00 1.52
3610 6182 7.385778 ACGGAGAATTTGGATCGATTTTAAA 57.614 32.000 0.00 2.35 0.00 1.52
3611 6183 7.996385 ACGGAGAATTTGGATCGATTTTAAAT 58.004 30.769 0.00 4.66 0.00 1.40
3612 6184 7.915397 ACGGAGAATTTGGATCGATTTTAAATG 59.085 33.333 0.00 0.00 0.00 2.32
3613 6185 7.096477 CGGAGAATTTGGATCGATTTTAAATGC 60.096 37.037 0.00 6.15 0.00 3.56
3614 6186 7.706179 GGAGAATTTGGATCGATTTTAAATGCA 59.294 33.333 16.64 0.00 0.00 3.96
3615 6187 8.638685 AGAATTTGGATCGATTTTAAATGCAG 57.361 30.769 16.64 0.00 0.00 4.41
3616 6188 7.707893 AGAATTTGGATCGATTTTAAATGCAGG 59.292 33.333 16.64 0.00 0.00 4.85
3617 6189 6.522625 TTTGGATCGATTTTAAATGCAGGA 57.477 33.333 0.00 0.00 0.00 3.86
3618 6190 6.522625 TTGGATCGATTTTAAATGCAGGAA 57.477 33.333 0.00 0.00 0.00 3.36
3619 6191 6.135290 TGGATCGATTTTAAATGCAGGAAG 57.865 37.500 0.00 0.00 0.00 3.46
3620 6192 5.067674 TGGATCGATTTTAAATGCAGGAAGG 59.932 40.000 0.00 0.00 0.00 3.46
3621 6193 5.299279 GGATCGATTTTAAATGCAGGAAGGA 59.701 40.000 0.00 0.00 0.00 3.36
3622 6194 5.818136 TCGATTTTAAATGCAGGAAGGAG 57.182 39.130 0.00 0.00 0.00 3.69
3623 6195 5.496556 TCGATTTTAAATGCAGGAAGGAGA 58.503 37.500 0.00 0.00 0.00 3.71
3624 6196 5.943416 TCGATTTTAAATGCAGGAAGGAGAA 59.057 36.000 0.00 0.00 0.00 2.87
3625 6197 6.094048 TCGATTTTAAATGCAGGAAGGAGAAG 59.906 38.462 0.00 0.00 0.00 2.85
3626 6198 5.982890 TTTTAAATGCAGGAAGGAGAAGG 57.017 39.130 0.00 0.00 0.00 3.46
3627 6199 4.927267 TTAAATGCAGGAAGGAGAAGGA 57.073 40.909 0.00 0.00 0.00 3.36
3628 6200 3.814504 AAATGCAGGAAGGAGAAGGAA 57.185 42.857 0.00 0.00 0.00 3.36
3629 6201 4.328118 AAATGCAGGAAGGAGAAGGAAT 57.672 40.909 0.00 0.00 0.00 3.01
3630 6202 4.328118 AATGCAGGAAGGAGAAGGAATT 57.672 40.909 0.00 0.00 0.00 2.17
3631 6203 5.456921 AATGCAGGAAGGAGAAGGAATTA 57.543 39.130 0.00 0.00 0.00 1.40
3632 6204 4.222124 TGCAGGAAGGAGAAGGAATTAC 57.778 45.455 0.00 0.00 0.00 1.89
3633 6205 3.846588 TGCAGGAAGGAGAAGGAATTACT 59.153 43.478 0.00 0.00 0.00 2.24
3634 6206 4.080863 TGCAGGAAGGAGAAGGAATTACTC 60.081 45.833 0.00 0.00 0.00 2.59
3635 6207 4.163268 GCAGGAAGGAGAAGGAATTACTCT 59.837 45.833 0.00 0.00 0.00 3.24
3636 6208 5.338789 GCAGGAAGGAGAAGGAATTACTCTT 60.339 44.000 0.00 0.00 0.00 2.85
3637 6209 6.345298 CAGGAAGGAGAAGGAATTACTCTTC 58.655 44.000 7.90 7.90 39.55 2.87
3638 6210 5.427157 AGGAAGGAGAAGGAATTACTCTTCC 59.573 44.000 20.90 20.90 44.29 3.46
3653 6225 2.992476 TTCCGGAGAGAAGGAAGGG 58.008 57.895 3.34 0.00 41.19 3.95
3654 6226 1.265454 TTCCGGAGAGAAGGAAGGGC 61.265 60.000 3.34 0.00 41.19 5.19
3655 6227 1.687493 CCGGAGAGAAGGAAGGGCT 60.687 63.158 0.00 0.00 0.00 5.19
3656 6228 1.681486 CCGGAGAGAAGGAAGGGCTC 61.681 65.000 0.00 0.00 0.00 4.70
3657 6229 0.972983 CGGAGAGAAGGAAGGGCTCA 60.973 60.000 0.00 0.00 0.00 4.26
3658 6230 1.506025 GGAGAGAAGGAAGGGCTCAT 58.494 55.000 0.00 0.00 0.00 2.90
3659 6231 1.416030 GGAGAGAAGGAAGGGCTCATC 59.584 57.143 0.00 0.00 0.00 2.92
3660 6232 1.068434 GAGAGAAGGAAGGGCTCATCG 59.932 57.143 0.00 0.00 0.00 3.84
3661 6233 0.827368 GAGAAGGAAGGGCTCATCGT 59.173 55.000 0.00 0.00 0.00 3.73
3662 6234 0.827368 AGAAGGAAGGGCTCATCGTC 59.173 55.000 0.00 0.00 0.00 4.20
3663 6235 0.537188 GAAGGAAGGGCTCATCGTCA 59.463 55.000 0.00 0.00 0.00 4.35
3664 6236 1.139853 GAAGGAAGGGCTCATCGTCAT 59.860 52.381 0.00 0.00 0.00 3.06
3665 6237 0.755686 AGGAAGGGCTCATCGTCATC 59.244 55.000 0.00 0.00 0.00 2.92
3666 6238 0.465705 GGAAGGGCTCATCGTCATCA 59.534 55.000 0.00 0.00 0.00 3.07
3667 6239 1.576356 GAAGGGCTCATCGTCATCAC 58.424 55.000 0.00 0.00 0.00 3.06
3668 6240 0.179000 AAGGGCTCATCGTCATCACC 59.821 55.000 0.00 0.00 0.00 4.02
3669 6241 1.227674 GGGCTCATCGTCATCACCC 60.228 63.158 0.00 0.00 0.00 4.61
3670 6242 1.227674 GGCTCATCGTCATCACCCC 60.228 63.158 0.00 0.00 0.00 4.95
3671 6243 1.522092 GCTCATCGTCATCACCCCA 59.478 57.895 0.00 0.00 0.00 4.96
3672 6244 0.107456 GCTCATCGTCATCACCCCAT 59.893 55.000 0.00 0.00 0.00 4.00
3673 6245 1.475751 GCTCATCGTCATCACCCCATT 60.476 52.381 0.00 0.00 0.00 3.16
3674 6246 2.224281 GCTCATCGTCATCACCCCATTA 60.224 50.000 0.00 0.00 0.00 1.90
3675 6247 3.393800 CTCATCGTCATCACCCCATTAC 58.606 50.000 0.00 0.00 0.00 1.89
3676 6248 2.104111 TCATCGTCATCACCCCATTACC 59.896 50.000 0.00 0.00 0.00 2.85
3677 6249 0.834612 TCGTCATCACCCCATTACCC 59.165 55.000 0.00 0.00 0.00 3.69
3678 6250 0.544223 CGTCATCACCCCATTACCCA 59.456 55.000 0.00 0.00 0.00 4.51
3679 6251 1.142870 CGTCATCACCCCATTACCCAT 59.857 52.381 0.00 0.00 0.00 4.00
3680 6252 2.810400 CGTCATCACCCCATTACCCATC 60.810 54.545 0.00 0.00 0.00 3.51
3681 6253 2.443255 GTCATCACCCCATTACCCATCT 59.557 50.000 0.00 0.00 0.00 2.90
3682 6254 3.117512 GTCATCACCCCATTACCCATCTT 60.118 47.826 0.00 0.00 0.00 2.40
3683 6255 4.104102 GTCATCACCCCATTACCCATCTTA 59.896 45.833 0.00 0.00 0.00 2.10
3684 6256 4.350816 TCATCACCCCATTACCCATCTTAG 59.649 45.833 0.00 0.00 0.00 2.18
3685 6257 4.015617 TCACCCCATTACCCATCTTAGA 57.984 45.455 0.00 0.00 0.00 2.10
3686 6258 4.577096 TCACCCCATTACCCATCTTAGAT 58.423 43.478 0.00 0.00 0.00 1.98
3687 6259 4.597507 TCACCCCATTACCCATCTTAGATC 59.402 45.833 0.00 0.00 0.00 2.75
3688 6260 4.350816 CACCCCATTACCCATCTTAGATCA 59.649 45.833 0.00 0.00 0.00 2.92
3689 6261 5.014544 CACCCCATTACCCATCTTAGATCAT 59.985 44.000 0.00 0.00 0.00 2.45
3690 6262 5.251700 ACCCCATTACCCATCTTAGATCATC 59.748 44.000 0.00 0.00 0.00 2.92
3691 6263 5.490357 CCCCATTACCCATCTTAGATCATCT 59.510 44.000 0.00 0.00 0.00 2.90
3692 6264 6.352565 CCCCATTACCCATCTTAGATCATCTC 60.353 46.154 0.00 0.00 0.00 2.75
3693 6265 6.352565 CCCATTACCCATCTTAGATCATCTCC 60.353 46.154 0.00 0.00 0.00 3.71
3694 6266 6.214208 CCATTACCCATCTTAGATCATCTCCA 59.786 42.308 0.00 0.00 0.00 3.86
3695 6267 7.256799 CCATTACCCATCTTAGATCATCTCCAA 60.257 40.741 0.00 0.00 0.00 3.53
3696 6268 7.690454 TTACCCATCTTAGATCATCTCCAAA 57.310 36.000 0.00 0.00 0.00 3.28
3697 6269 6.581388 ACCCATCTTAGATCATCTCCAAAA 57.419 37.500 0.00 0.00 0.00 2.44
3698 6270 6.599445 ACCCATCTTAGATCATCTCCAAAAG 58.401 40.000 0.00 0.00 0.00 2.27
3699 6271 6.002704 CCCATCTTAGATCATCTCCAAAAGG 58.997 44.000 0.00 0.00 0.00 3.11
3700 6272 5.472820 CCATCTTAGATCATCTCCAAAAGGC 59.527 44.000 0.00 0.00 0.00 4.35
3701 6273 4.697514 TCTTAGATCATCTCCAAAAGGCG 58.302 43.478 0.00 0.00 0.00 5.52
3702 6274 1.673168 AGATCATCTCCAAAAGGCGC 58.327 50.000 0.00 0.00 0.00 6.53
3705 6277 1.019278 TCATCTCCAAAAGGCGCGTC 61.019 55.000 0.21 0.21 0.00 5.19
3716 6288 2.033194 GGCGCGTCAGGTTTTAGCT 61.033 57.895 5.47 0.00 0.00 3.32
4085 6749 4.974438 TTGGACAGGCCCCGGTCT 62.974 66.667 15.44 0.00 40.20 3.85
4230 6894 2.755876 AGGACGAGCGAGCCATGA 60.756 61.111 0.00 0.00 0.00 3.07
4268 6932 4.175489 CCGGAGCACGTCGTCGAT 62.175 66.667 9.47 0.00 42.24 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.134280 GGTGACTGCAGATACTGGCAT 60.134 52.381 23.35 0.00 39.65 4.40
230 231 1.004440 GCCTGTTTCCGAGCACTCT 60.004 57.895 0.00 0.00 0.00 3.24
608 609 6.023603 TCTAACACCCTTCCTCAATCTTAGT 58.976 40.000 0.00 0.00 0.00 2.24
621 622 7.606456 CACATGTAAATACAGTCTAACACCCTT 59.394 37.037 0.00 0.00 39.92 3.95
769 775 2.580867 CGTGCTCCTGCTCTACGC 60.581 66.667 0.00 0.00 40.48 4.42
772 778 2.679996 TGGCGTGCTCCTGCTCTA 60.680 61.111 0.00 0.00 40.48 2.43
773 779 4.385405 GTGGCGTGCTCCTGCTCT 62.385 66.667 0.00 0.00 40.48 4.09
886 898 4.814294 GTGCGGCTACGTGGAGGG 62.814 72.222 1.81 0.00 43.45 4.30
946 958 2.185608 GGGAAGTGGAGCTCGAGC 59.814 66.667 30.01 30.01 42.49 5.03
952 964 0.034670 ATTCTGCTGGGAAGTGGAGC 60.035 55.000 0.00 0.00 0.00 4.70
968 980 2.670414 GCTAGCTCTGTGTGTGTGATTC 59.330 50.000 7.70 0.00 0.00 2.52
970 984 1.898472 AGCTAGCTCTGTGTGTGTGAT 59.102 47.619 12.68 0.00 0.00 3.06
1200 1233 4.099170 CTTCCGTGCTGCTGCTGC 62.099 66.667 22.51 22.51 40.48 5.25
1744 1912 0.098200 TCTCGATCACCGTTAGCACG 59.902 55.000 0.00 0.00 46.71 5.34
1750 1918 1.445582 GCCGTTCTCGATCACCGTT 60.446 57.895 0.00 0.00 39.71 4.44
1825 1993 0.966875 TGTTGGCCAGGTGCATGATC 60.967 55.000 5.11 0.00 43.89 2.92
1919 2087 1.640428 TTCGAGCGGCATCTAGTTTG 58.360 50.000 1.45 0.00 0.00 2.93
1923 2105 2.728839 GAGAAATTCGAGCGGCATCTAG 59.271 50.000 1.45 0.00 0.00 2.43
1947 2166 1.017177 GTCAGTGCGCCGTTATCCAA 61.017 55.000 4.18 0.00 0.00 3.53
1957 2176 1.300156 TGTCAGTCAGTCAGTGCGC 60.300 57.895 0.00 0.00 0.00 6.09
1988 2220 1.398390 CTTGGCCGAGAAATACTGCAC 59.602 52.381 15.76 0.00 0.00 4.57
2065 2297 8.019656 TGAGTAAAGAAAGAGAAGTTGGTACT 57.980 34.615 0.00 0.00 35.68 2.73
2104 2369 0.179124 CTTGACTGAGCGACCTAGCC 60.179 60.000 0.00 0.00 38.01 3.93
2106 2371 1.813178 TCACTTGACTGAGCGACCTAG 59.187 52.381 0.00 0.00 0.00 3.02
2107 2372 1.905637 TCACTTGACTGAGCGACCTA 58.094 50.000 0.00 0.00 0.00 3.08
2108 2373 1.261480 ATCACTTGACTGAGCGACCT 58.739 50.000 0.00 0.00 0.00 3.85
2109 2374 2.941453 TATCACTTGACTGAGCGACC 57.059 50.000 0.00 0.00 0.00 4.79
2110 2375 3.000724 GCAATATCACTTGACTGAGCGAC 59.999 47.826 0.00 0.00 0.00 5.19
2111 2376 3.190079 GCAATATCACTTGACTGAGCGA 58.810 45.455 0.00 0.00 0.00 4.93
2113 2378 6.481313 TCTTATGCAATATCACTTGACTGAGC 59.519 38.462 0.00 0.00 0.00 4.26
2114 2379 8.429493 TTCTTATGCAATATCACTTGACTGAG 57.571 34.615 0.00 0.00 0.00 3.35
2116 2381 8.429493 TCTTCTTATGCAATATCACTTGACTG 57.571 34.615 0.00 0.00 0.00 3.51
2117 2382 9.453572 TTTCTTCTTATGCAATATCACTTGACT 57.546 29.630 0.00 0.00 0.00 3.41
2160 2425 9.970395 TGCATGGAGATTCATACAAAAATATTC 57.030 29.630 0.00 0.00 0.00 1.75
2164 2429 9.675464 ATTTTGCATGGAGATTCATACAAAAAT 57.325 25.926 13.63 5.87 45.52 1.82
2165 2430 9.153721 GATTTTGCATGGAGATTCATACAAAAA 57.846 29.630 13.63 4.23 45.52 1.94
2167 2432 7.838884 TGATTTTGCATGGAGATTCATACAAA 58.161 30.769 0.00 0.00 38.12 2.83
2171 2457 7.342541 TCCTTTGATTTTGCATGGAGATTCATA 59.657 33.333 3.72 0.00 0.00 2.15
2172 2458 6.155565 TCCTTTGATTTTGCATGGAGATTCAT 59.844 34.615 3.72 0.00 0.00 2.57
2174 2460 5.809051 GTCCTTTGATTTTGCATGGAGATTC 59.191 40.000 0.00 0.00 0.00 2.52
2181 2467 6.798482 TGCTATAGTCCTTTGATTTTGCATG 58.202 36.000 0.84 0.00 0.00 4.06
2184 2470 6.017934 TCGATGCTATAGTCCTTTGATTTTGC 60.018 38.462 0.84 0.00 0.00 3.68
2189 2475 6.266558 AGTCTTCGATGCTATAGTCCTTTGAT 59.733 38.462 0.84 0.00 0.00 2.57
2190 2476 5.594725 AGTCTTCGATGCTATAGTCCTTTGA 59.405 40.000 0.84 0.00 0.00 2.69
2191 2477 5.837437 AGTCTTCGATGCTATAGTCCTTTG 58.163 41.667 0.84 0.00 0.00 2.77
2192 2478 6.472686 AAGTCTTCGATGCTATAGTCCTTT 57.527 37.500 0.84 0.00 0.00 3.11
2195 2481 5.048643 TGCTAAGTCTTCGATGCTATAGTCC 60.049 44.000 0.84 0.00 0.00 3.85
2197 2483 6.392625 TTGCTAAGTCTTCGATGCTATAGT 57.607 37.500 0.84 0.00 0.00 2.12
2198 2484 7.436673 AGTTTTGCTAAGTCTTCGATGCTATAG 59.563 37.037 0.00 0.00 0.00 1.31
2199 2485 7.222805 CAGTTTTGCTAAGTCTTCGATGCTATA 59.777 37.037 0.00 0.00 0.00 1.31
2200 2486 6.036517 CAGTTTTGCTAAGTCTTCGATGCTAT 59.963 38.462 0.00 0.00 0.00 2.97
2201 2487 5.348724 CAGTTTTGCTAAGTCTTCGATGCTA 59.651 40.000 0.00 0.00 0.00 3.49
2204 2490 5.845985 TCAGTTTTGCTAAGTCTTCGATG 57.154 39.130 0.00 0.00 0.00 3.84
2205 2491 6.861065 TTTCAGTTTTGCTAAGTCTTCGAT 57.139 33.333 0.00 0.00 0.00 3.59
2206 2492 6.671614 TTTTCAGTTTTGCTAAGTCTTCGA 57.328 33.333 0.00 0.00 0.00 3.71
2227 2513 8.517056 TGAGTACCGAGTTTTTCTTTTCTTTTT 58.483 29.630 0.00 0.00 0.00 1.94
2228 2514 7.966753 GTGAGTACCGAGTTTTTCTTTTCTTTT 59.033 33.333 0.00 0.00 0.00 2.27
2229 2515 7.120138 TGTGAGTACCGAGTTTTTCTTTTCTTT 59.880 33.333 0.00 0.00 0.00 2.52
2230 2516 6.596497 TGTGAGTACCGAGTTTTTCTTTTCTT 59.404 34.615 0.00 0.00 0.00 2.52
2231 2517 6.036844 GTGTGAGTACCGAGTTTTTCTTTTCT 59.963 38.462 0.00 0.00 0.00 2.52
2232 2518 6.190264 GTGTGAGTACCGAGTTTTTCTTTTC 58.810 40.000 0.00 0.00 0.00 2.29
2233 2519 5.065602 GGTGTGAGTACCGAGTTTTTCTTTT 59.934 40.000 0.00 0.00 0.00 2.27
2234 2520 4.573607 GGTGTGAGTACCGAGTTTTTCTTT 59.426 41.667 0.00 0.00 0.00 2.52
2235 2521 4.124970 GGTGTGAGTACCGAGTTTTTCTT 58.875 43.478 0.00 0.00 0.00 2.52
2237 2523 2.804527 GGGTGTGAGTACCGAGTTTTTC 59.195 50.000 0.00 0.00 41.79 2.29
2607 2896 2.795175 TCTCGGAGCCTAATTAAGCG 57.205 50.000 0.00 0.00 0.00 4.68
2716 3030 1.204312 GGCGAACTTGAACGACTGC 59.796 57.895 0.00 0.00 34.48 4.40
2729 3043 4.287781 TTCCAGCACGACGGCGAA 62.288 61.111 22.49 0.00 41.64 4.70
2804 3118 3.782244 CTTGCCGTGCTCGTGCTC 61.782 66.667 17.89 6.24 40.48 4.26
2899 3228 2.438614 TGCTCCTCCTCGGACTCG 60.439 66.667 0.00 0.00 36.69 4.18
2900 3229 2.124693 CCTGCTCCTCCTCGGACTC 61.125 68.421 0.00 0.00 36.69 3.36
2901 3230 2.043450 CCTGCTCCTCCTCGGACT 60.043 66.667 0.00 0.00 36.69 3.85
2902 3231 2.043852 TCCTGCTCCTCCTCGGAC 60.044 66.667 0.00 0.00 36.69 4.79
2903 3232 2.043852 GTCCTGCTCCTCCTCGGA 60.044 66.667 0.00 0.00 40.30 4.55
2904 3233 3.151022 GGTCCTGCTCCTCCTCGG 61.151 72.222 0.00 0.00 0.00 4.63
2905 3234 2.363018 TGGTCCTGCTCCTCCTCG 60.363 66.667 0.00 0.00 0.00 4.63
3184 3513 3.672295 GAAGCCCTCGTCCTGCTGG 62.672 68.421 2.58 2.58 35.08 4.85
3232 3567 4.869440 CGCTCCTGCTCCTGCTCG 62.869 72.222 0.00 0.00 40.48 5.03
3339 3677 1.656652 ACACACAGCACACAAGTCTC 58.343 50.000 0.00 0.00 0.00 3.36
3340 3678 2.168521 AGTACACACAGCACACAAGTCT 59.831 45.455 0.00 0.00 0.00 3.24
3343 3681 2.030823 CACAGTACACACAGCACACAAG 59.969 50.000 0.00 0.00 0.00 3.16
3345 3683 1.066502 ACACAGTACACACAGCACACA 60.067 47.619 0.00 0.00 0.00 3.72
3351 5911 3.728076 ACCACTACACAGTACACACAG 57.272 47.619 0.00 0.00 32.21 3.66
3354 5914 2.689471 ACGAACCACTACACAGTACACA 59.311 45.455 0.00 0.00 32.21 3.72
3445 6012 2.292267 CATGGACATGCCTTGGTAGTC 58.708 52.381 11.70 0.00 37.98 2.59
3516 6088 0.105039 CCTGGCCACGAGGAAGATAC 59.895 60.000 0.00 0.00 36.89 2.24
3520 6092 3.068881 TTCCTGGCCACGAGGAAG 58.931 61.111 18.57 0.00 43.39 3.46
3534 6106 7.311408 ACTAACAGTACACGTTATCTCTTTCC 58.689 38.462 7.98 0.00 0.00 3.13
3554 6126 7.927048 ACTGGACTAATTGTTTTGTGACTAAC 58.073 34.615 0.00 0.00 0.00 2.34
3564 6136 6.370718 CCGTAGCTAAACTGGACTAATTGTTT 59.629 38.462 0.00 0.00 36.69 2.83
3588 6160 7.706179 TGCATTTAAAATCGATCCAAATTCTCC 59.294 33.333 0.00 0.00 0.00 3.71
3589 6161 8.633075 TGCATTTAAAATCGATCCAAATTCTC 57.367 30.769 0.00 0.00 0.00 2.87
3590 6162 7.707893 CCTGCATTTAAAATCGATCCAAATTCT 59.292 33.333 0.00 0.00 0.00 2.40
3591 6163 7.706179 TCCTGCATTTAAAATCGATCCAAATTC 59.294 33.333 0.00 0.79 0.00 2.17
3592 6164 7.555087 TCCTGCATTTAAAATCGATCCAAATT 58.445 30.769 0.00 0.00 0.00 1.82
3593 6165 7.111247 TCCTGCATTTAAAATCGATCCAAAT 57.889 32.000 0.00 2.35 0.00 2.32
3594 6166 6.522625 TCCTGCATTTAAAATCGATCCAAA 57.477 33.333 0.00 0.00 0.00 3.28
3595 6167 6.405731 CCTTCCTGCATTTAAAATCGATCCAA 60.406 38.462 0.00 0.00 0.00 3.53
3596 6168 5.067674 CCTTCCTGCATTTAAAATCGATCCA 59.932 40.000 0.00 0.00 0.00 3.41
3597 6169 5.299279 TCCTTCCTGCATTTAAAATCGATCC 59.701 40.000 0.00 0.00 0.00 3.36
3598 6170 6.260936 TCTCCTTCCTGCATTTAAAATCGATC 59.739 38.462 0.00 0.00 0.00 3.69
3599 6171 6.122277 TCTCCTTCCTGCATTTAAAATCGAT 58.878 36.000 0.00 0.00 0.00 3.59
3600 6172 5.496556 TCTCCTTCCTGCATTTAAAATCGA 58.503 37.500 0.00 0.00 0.00 3.59
3601 6173 5.818136 TCTCCTTCCTGCATTTAAAATCG 57.182 39.130 0.00 0.00 0.00 3.34
3602 6174 6.378280 TCCTTCTCCTTCCTGCATTTAAAATC 59.622 38.462 0.00 0.00 0.00 2.17
3603 6175 6.256053 TCCTTCTCCTTCCTGCATTTAAAAT 58.744 36.000 0.00 0.00 0.00 1.82
3604 6176 5.640147 TCCTTCTCCTTCCTGCATTTAAAA 58.360 37.500 0.00 0.00 0.00 1.52
3605 6177 5.255397 TCCTTCTCCTTCCTGCATTTAAA 57.745 39.130 0.00 0.00 0.00 1.52
3606 6178 4.927267 TCCTTCTCCTTCCTGCATTTAA 57.073 40.909 0.00 0.00 0.00 1.52
3607 6179 4.927267 TTCCTTCTCCTTCCTGCATTTA 57.073 40.909 0.00 0.00 0.00 1.40
3608 6180 3.814504 TTCCTTCTCCTTCCTGCATTT 57.185 42.857 0.00 0.00 0.00 2.32
3609 6181 4.328118 AATTCCTTCTCCTTCCTGCATT 57.672 40.909 0.00 0.00 0.00 3.56
3610 6182 4.476479 AGTAATTCCTTCTCCTTCCTGCAT 59.524 41.667 0.00 0.00 0.00 3.96
3611 6183 3.846588 AGTAATTCCTTCTCCTTCCTGCA 59.153 43.478 0.00 0.00 0.00 4.41
3612 6184 4.163268 AGAGTAATTCCTTCTCCTTCCTGC 59.837 45.833 0.00 0.00 0.00 4.85
3613 6185 5.948742 AGAGTAATTCCTTCTCCTTCCTG 57.051 43.478 0.00 0.00 0.00 3.86
3614 6186 5.427157 GGAAGAGTAATTCCTTCTCCTTCCT 59.573 44.000 0.00 0.00 44.57 3.36
3615 6187 5.676552 GGAAGAGTAATTCCTTCTCCTTCC 58.323 45.833 0.00 0.00 44.57 3.46
3616 6188 5.353111 CGGAAGAGTAATTCCTTCTCCTTC 58.647 45.833 12.13 0.00 45.60 3.46
3617 6189 4.162509 CCGGAAGAGTAATTCCTTCTCCTT 59.837 45.833 0.00 0.00 45.60 3.36
3618 6190 3.707102 CCGGAAGAGTAATTCCTTCTCCT 59.293 47.826 0.00 0.00 45.60 3.69
3619 6191 3.705072 TCCGGAAGAGTAATTCCTTCTCC 59.295 47.826 0.00 3.41 45.60 3.71
3620 6192 4.645588 TCTCCGGAAGAGTAATTCCTTCTC 59.354 45.833 5.23 4.37 45.60 2.87
3621 6193 4.611367 TCTCCGGAAGAGTAATTCCTTCT 58.389 43.478 5.23 0.00 45.60 2.85
3622 6194 4.939271 CTCTCCGGAAGAGTAATTCCTTC 58.061 47.826 17.79 0.00 45.60 3.46
3635 6207 1.265454 GCCCTTCCTTCTCTCCGGAA 61.265 60.000 5.23 0.00 37.69 4.30
3636 6208 1.686110 GCCCTTCCTTCTCTCCGGA 60.686 63.158 2.93 2.93 0.00 5.14
3637 6209 1.681486 GAGCCCTTCCTTCTCTCCGG 61.681 65.000 0.00 0.00 0.00 5.14
3638 6210 0.972983 TGAGCCCTTCCTTCTCTCCG 60.973 60.000 0.00 0.00 0.00 4.63
3639 6211 1.416030 GATGAGCCCTTCCTTCTCTCC 59.584 57.143 0.00 0.00 0.00 3.71
3640 6212 1.068434 CGATGAGCCCTTCCTTCTCTC 59.932 57.143 0.00 0.00 0.00 3.20
3641 6213 1.118838 CGATGAGCCCTTCCTTCTCT 58.881 55.000 0.00 0.00 0.00 3.10
3642 6214 0.827368 ACGATGAGCCCTTCCTTCTC 59.173 55.000 0.00 0.00 0.00 2.87
3643 6215 0.827368 GACGATGAGCCCTTCCTTCT 59.173 55.000 0.00 0.00 0.00 2.85
3644 6216 0.537188 TGACGATGAGCCCTTCCTTC 59.463 55.000 0.00 0.00 0.00 3.46
3645 6217 1.139853 GATGACGATGAGCCCTTCCTT 59.860 52.381 0.00 0.00 0.00 3.36
3646 6218 0.755686 GATGACGATGAGCCCTTCCT 59.244 55.000 0.00 0.00 0.00 3.36
3647 6219 0.465705 TGATGACGATGAGCCCTTCC 59.534 55.000 0.00 0.00 0.00 3.46
3648 6220 1.576356 GTGATGACGATGAGCCCTTC 58.424 55.000 0.00 0.00 0.00 3.46
3649 6221 0.179000 GGTGATGACGATGAGCCCTT 59.821 55.000 0.00 0.00 0.00 3.95
3650 6222 1.690219 GGGTGATGACGATGAGCCCT 61.690 60.000 0.00 0.00 27.67 5.19
3651 6223 1.227674 GGGTGATGACGATGAGCCC 60.228 63.158 0.00 0.00 27.67 5.19
3652 6224 1.227674 GGGGTGATGACGATGAGCC 60.228 63.158 0.00 0.00 32.91 4.70
3653 6225 0.107456 ATGGGGTGATGACGATGAGC 59.893 55.000 0.00 0.00 0.00 4.26
3654 6226 2.627515 AATGGGGTGATGACGATGAG 57.372 50.000 0.00 0.00 0.00 2.90
3655 6227 2.104111 GGTAATGGGGTGATGACGATGA 59.896 50.000 0.00 0.00 0.00 2.92
3656 6228 2.494059 GGTAATGGGGTGATGACGATG 58.506 52.381 0.00 0.00 0.00 3.84
3657 6229 1.420138 GGGTAATGGGGTGATGACGAT 59.580 52.381 0.00 0.00 0.00 3.73
3658 6230 0.834612 GGGTAATGGGGTGATGACGA 59.165 55.000 0.00 0.00 0.00 4.20
3659 6231 0.544223 TGGGTAATGGGGTGATGACG 59.456 55.000 0.00 0.00 0.00 4.35
3660 6232 2.443255 AGATGGGTAATGGGGTGATGAC 59.557 50.000 0.00 0.00 0.00 3.06
3661 6233 2.787956 AGATGGGTAATGGGGTGATGA 58.212 47.619 0.00 0.00 0.00 2.92
3662 6234 3.600448 AAGATGGGTAATGGGGTGATG 57.400 47.619 0.00 0.00 0.00 3.07
3663 6235 4.577096 TCTAAGATGGGTAATGGGGTGAT 58.423 43.478 0.00 0.00 0.00 3.06
3664 6236 4.015617 TCTAAGATGGGTAATGGGGTGA 57.984 45.455 0.00 0.00 0.00 4.02
3665 6237 4.350816 TGATCTAAGATGGGTAATGGGGTG 59.649 45.833 0.00 0.00 0.00 4.61
3666 6238 4.577096 TGATCTAAGATGGGTAATGGGGT 58.423 43.478 0.00 0.00 0.00 4.95
3667 6239 5.490357 AGATGATCTAAGATGGGTAATGGGG 59.510 44.000 0.00 0.00 0.00 4.96
3668 6240 6.352565 GGAGATGATCTAAGATGGGTAATGGG 60.353 46.154 0.00 0.00 0.00 4.00
3669 6241 6.214208 TGGAGATGATCTAAGATGGGTAATGG 59.786 42.308 0.00 0.00 0.00 3.16
3670 6242 7.250032 TGGAGATGATCTAAGATGGGTAATG 57.750 40.000 0.00 0.00 0.00 1.90
3671 6243 7.878621 TTGGAGATGATCTAAGATGGGTAAT 57.121 36.000 0.00 0.00 0.00 1.89
3672 6244 7.690454 TTTGGAGATGATCTAAGATGGGTAA 57.310 36.000 0.00 0.00 29.12 2.85
3673 6245 7.202130 CCTTTTGGAGATGATCTAAGATGGGTA 60.202 40.741 0.00 0.00 44.07 3.69
3674 6246 6.410157 CCTTTTGGAGATGATCTAAGATGGGT 60.410 42.308 0.00 0.00 44.07 4.51
3675 6247 6.002704 CCTTTTGGAGATGATCTAAGATGGG 58.997 44.000 0.00 0.00 44.07 4.00
3676 6248 5.472820 GCCTTTTGGAGATGATCTAAGATGG 59.527 44.000 0.00 0.00 44.07 3.51
3677 6249 5.178996 CGCCTTTTGGAGATGATCTAAGATG 59.821 44.000 0.00 0.00 42.35 2.90
3678 6250 5.303971 CGCCTTTTGGAGATGATCTAAGAT 58.696 41.667 0.00 0.00 42.35 2.40
3679 6251 4.697514 CGCCTTTTGGAGATGATCTAAGA 58.302 43.478 0.00 0.00 42.35 2.10
3680 6252 3.249559 GCGCCTTTTGGAGATGATCTAAG 59.750 47.826 0.00 0.00 42.35 2.18
3681 6253 3.206150 GCGCCTTTTGGAGATGATCTAA 58.794 45.455 0.00 0.00 42.35 2.10
3682 6254 2.803133 CGCGCCTTTTGGAGATGATCTA 60.803 50.000 0.00 0.00 42.35 1.98
3683 6255 1.673168 GCGCCTTTTGGAGATGATCT 58.327 50.000 0.00 0.00 42.35 2.75
3684 6256 0.305922 CGCGCCTTTTGGAGATGATC 59.694 55.000 0.00 0.00 42.35 2.92
3685 6257 0.392998 ACGCGCCTTTTGGAGATGAT 60.393 50.000 5.73 0.00 42.35 2.45
3686 6258 1.003839 ACGCGCCTTTTGGAGATGA 60.004 52.632 5.73 0.00 42.35 2.92
3687 6259 1.298157 TGACGCGCCTTTTGGAGATG 61.298 55.000 5.73 0.00 42.35 2.90
3688 6260 1.003839 TGACGCGCCTTTTGGAGAT 60.004 52.632 5.73 0.00 42.35 2.75
3689 6261 1.667830 CTGACGCGCCTTTTGGAGA 60.668 57.895 5.73 0.00 42.35 3.71
3690 6262 2.680913 CCTGACGCGCCTTTTGGAG 61.681 63.158 5.73 0.00 44.07 3.86
3691 6263 2.668212 CCTGACGCGCCTTTTGGA 60.668 61.111 5.73 0.00 44.07 3.53
3692 6264 2.070654 AAACCTGACGCGCCTTTTGG 62.071 55.000 5.73 2.56 44.18 3.28
3693 6265 0.248866 AAAACCTGACGCGCCTTTTG 60.249 50.000 5.73 0.00 0.00 2.44
3694 6266 1.265905 CTAAAACCTGACGCGCCTTTT 59.734 47.619 5.73 0.53 0.00 2.27
3695 6267 0.872388 CTAAAACCTGACGCGCCTTT 59.128 50.000 5.73 0.00 0.00 3.11
3696 6268 1.574702 GCTAAAACCTGACGCGCCTT 61.575 55.000 5.73 0.00 0.00 4.35
3697 6269 2.033194 GCTAAAACCTGACGCGCCT 61.033 57.895 5.73 0.00 0.00 5.52
3698 6270 1.967597 GAGCTAAAACCTGACGCGCC 61.968 60.000 5.73 0.00 0.00 6.53
3699 6271 1.289109 TGAGCTAAAACCTGACGCGC 61.289 55.000 5.73 0.00 0.00 6.86
3700 6272 0.438830 GTGAGCTAAAACCTGACGCG 59.561 55.000 3.53 3.53 0.00 6.01
3701 6273 0.438830 CGTGAGCTAAAACCTGACGC 59.561 55.000 0.00 0.00 33.60 5.19
3818 6453 1.136690 CGAGCGCGGCAATTTATAGA 58.863 50.000 8.83 0.00 0.00 1.98
4085 6749 1.553248 ACGTCCCGGAAATTCATCTGA 59.447 47.619 0.73 0.00 0.00 3.27
4209 6873 3.453679 GGCTCGCTCGTCCTCCTT 61.454 66.667 0.00 0.00 0.00 3.36
4257 6921 1.912983 CATGCTCATCGACGACGTG 59.087 57.895 4.58 5.47 40.69 4.49


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

AutoCloner maintained by Alex Coulton.