Multiple sequence alignment - TraesCS5A01G140400

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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 TraesCS5A01G140400 chr5A 100.000 2642 0 0 1 2642 312505681 312508322 0.000000e+00 4879.0
1 TraesCS5A01G140400 chr5A 89.057 859 61 18 789 1617 317507437 317506582 0.000000e+00 1035.0
2 TraesCS5A01G140400 chr5A 81.716 979 124 38 866 1797 317507332 317506362 0.000000e+00 765.0
3 TraesCS5A01G140400 chr5A 83.230 644 88 16 1898 2531 10844580 10843947 8.200000e-160 573.0
4 TraesCS5A01G140400 chr5A 93.333 165 11 0 632 796 317507829 317507665 7.300000e-61 244.0
5 TraesCS5A01G140400 chr3D 90.566 1007 74 13 627 1617 378023845 378022844 0.000000e+00 1314.0
6 TraesCS5A01G140400 chr3D 95.105 429 20 1 201 628 261309760 261310188 0.000000e+00 675.0
7 TraesCS5A01G140400 chr3D 94.172 429 24 1 201 628 261379000 261379428 0.000000e+00 652.0
8 TraesCS5A01G140400 chr3D 93.035 201 12 2 1 200 261309360 261309559 2.570000e-75 292.0
9 TraesCS5A01G140400 chr3D 93.035 201 13 1 1 200 261378599 261378799 2.570000e-75 292.0
10 TraesCS5A01G140400 chr3D 77.864 515 72 26 1294 1794 378023113 378022627 5.570000e-72 281.0
11 TraesCS5A01G140400 chr3D 86.829 205 20 5 627 829 49483959 49484158 3.420000e-54 222.0
12 TraesCS5A01G140400 chr3D 79.153 307 32 11 1246 1520 63767904 63768210 1.620000e-42 183.0
13 TraesCS5A01G140400 chr3D 87.097 155 20 0 1389 1543 532076429 532076275 2.700000e-40 176.0
14 TraesCS5A01G140400 chr3D 100.000 32 0 0 1766 1797 91386227 91386258 2.840000e-05 60.2
15 TraesCS5A01G140400 chr3A 91.415 629 30 2 1 628 133088662 133089267 0.000000e+00 841.0
16 TraesCS5A01G140400 chr3A 82.620 748 102 16 1799 2529 328930237 328930973 1.030000e-178 636.0
17 TraesCS5A01G140400 chr3A 85.113 309 45 1 1302 1609 742363114 742363422 5.490000e-82 315.0
18 TraesCS5A01G140400 chr3A 86.432 199 20 5 632 828 62264775 62264968 7.410000e-51 211.0
19 TraesCS5A01G140400 chr7A 90.880 625 40 5 5 628 212397263 212397871 0.000000e+00 822.0
20 TraesCS5A01G140400 chr7A 81.952 748 117 12 1799 2533 121934712 121933970 3.740000e-173 617.0
21 TraesCS5A01G140400 chr7A 77.929 367 60 10 1802 2167 707626847 707626501 2.660000e-50 209.0
22 TraesCS5A01G140400 chr4B 89.117 634 63 5 1 628 79447452 79448085 0.000000e+00 784.0
23 TraesCS5A01G140400 chr1A 86.228 639 71 14 1898 2531 572220149 572220775 0.000000e+00 676.0
24 TraesCS5A01G140400 chr5D 82.937 756 102 22 1799 2540 9391154 9390412 0.000000e+00 656.0
25 TraesCS5A01G140400 chr5D 77.057 401 57 12 1244 1609 159293477 159293077 5.770000e-47 198.0
26 TraesCS5A01G140400 chr5D 77.222 180 27 10 1811 1984 543799516 543799345 2.800000e-15 93.5
27 TraesCS5A01G140400 chr7B 81.902 757 97 28 1799 2531 534536621 534537361 1.050000e-168 603.0
28 TraesCS5A01G140400 chr7B 85.246 427 38 6 1192 1617 714611106 714611508 1.460000e-112 416.0
29 TraesCS5A01G140400 chr7D 81.600 750 109 20 1797 2531 592567093 592567828 6.300000e-166 593.0
30 TraesCS5A01G140400 chr7D 87.429 175 20 2 1284 1457 173716641 173716468 1.600000e-47 200.0
31 TraesCS5A01G140400 chr7D 80.478 251 42 7 1243 1489 173716714 173716467 4.490000e-43 185.0
32 TraesCS5A01G140400 chr7D 84.884 86 11 2 1713 1797 42182667 42182751 4.690000e-13 86.1
33 TraesCS5A01G140400 chr7D 76.336 131 20 9 1115 1235 195634682 195634553 2.840000e-05 60.2
34 TraesCS5A01G140400 chr4D 83.619 641 89 16 1899 2531 107748096 107748728 2.930000e-164 588.0
35 TraesCS5A01G140400 chr6A 81.392 747 109 22 1799 2531 564676043 564676773 1.360000e-162 582.0
36 TraesCS5A01G140400 chr6A 90.862 383 27 4 1 375 190117248 190116866 8.440000e-140 507.0
37 TraesCS5A01G140400 chr6A 88.265 196 19 2 1613 1805 13082744 13082938 5.690000e-57 231.0
38 TraesCS5A01G140400 chr2A 79.702 739 119 25 1799 2521 757785388 757786111 3.030000e-139 505.0
39 TraesCS5A01G140400 chr2A 90.698 43 4 0 1137 1179 619608711 619608669 1.020000e-04 58.4
40 TraesCS5A01G140400 chr3B 79.442 681 116 20 1806 2472 647227171 647227841 6.660000e-126 460.0
41 TraesCS5A01G140400 chr6D 84.741 367 56 0 1243 1609 291476006 291476372 4.150000e-98 368.0
42 TraesCS5A01G140400 chr6D 97.059 34 1 0 1 34 348703025 348702992 1.020000e-04 58.4
43 TraesCS5A01G140400 chr6D 97.059 34 1 0 1 34 348775574 348775541 1.020000e-04 58.4
44 TraesCS5A01G140400 chr6D 97.059 34 1 0 1 34 370003730 370003697 1.020000e-04 58.4
45 TraesCS5A01G140400 chr2D 81.201 383 55 3 1243 1609 633697588 633697207 2.570000e-75 292.0
46 TraesCS5A01G140400 chr4A 86.503 163 18 2 1305 1463 171916655 171916493 2.700000e-40 176.0
47 TraesCS5A01G140400 chr1D 74.534 483 71 33 1344 1802 453704949 453704495 2.100000e-36 163.0
48 TraesCS5A01G140400 chr1D 97.143 35 1 0 1115 1149 16671518 16671552 2.840000e-05 60.2
49 TraesCS5A01G140400 chr5B 89.286 56 6 0 1128 1183 246151478 246151423 1.310000e-08 71.3
50 TraesCS5A01G140400 chr5B 88.525 61 4 2 1801 1861 393693040 393693097 1.310000e-08 71.3
51 TraesCS5A01G140400 chr6B 91.111 45 4 0 1800 1844 512573247 512573291 7.900000e-06 62.1


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 TraesCS5A01G140400 chr5A 312505681 312508322 2641 False 4879.000000 4879 100.000000 1 2642 1 chr5A.!!$F1 2641
1 TraesCS5A01G140400 chr5A 317506362 317507829 1467 True 681.333333 1035 88.035333 632 1797 3 chr5A.!!$R2 1165
2 TraesCS5A01G140400 chr5A 10843947 10844580 633 True 573.000000 573 83.230000 1898 2531 1 chr5A.!!$R1 633
3 TraesCS5A01G140400 chr3D 378022627 378023845 1218 True 797.500000 1314 84.215000 627 1794 2 chr3D.!!$R2 1167
4 TraesCS5A01G140400 chr3D 261309360 261310188 828 False 483.500000 675 94.070000 1 628 2 chr3D.!!$F4 627
5 TraesCS5A01G140400 chr3D 261378599 261379428 829 False 472.000000 652 93.603500 1 628 2 chr3D.!!$F5 627
6 TraesCS5A01G140400 chr3A 133088662 133089267 605 False 841.000000 841 91.415000 1 628 1 chr3A.!!$F2 627
7 TraesCS5A01G140400 chr3A 328930237 328930973 736 False 636.000000 636 82.620000 1799 2529 1 chr3A.!!$F3 730
8 TraesCS5A01G140400 chr7A 212397263 212397871 608 False 822.000000 822 90.880000 5 628 1 chr7A.!!$F1 623
9 TraesCS5A01G140400 chr7A 121933970 121934712 742 True 617.000000 617 81.952000 1799 2533 1 chr7A.!!$R1 734
10 TraesCS5A01G140400 chr4B 79447452 79448085 633 False 784.000000 784 89.117000 1 628 1 chr4B.!!$F1 627
11 TraesCS5A01G140400 chr1A 572220149 572220775 626 False 676.000000 676 86.228000 1898 2531 1 chr1A.!!$F1 633
12 TraesCS5A01G140400 chr5D 9390412 9391154 742 True 656.000000 656 82.937000 1799 2540 1 chr5D.!!$R1 741
13 TraesCS5A01G140400 chr7B 534536621 534537361 740 False 603.000000 603 81.902000 1799 2531 1 chr7B.!!$F1 732
14 TraesCS5A01G140400 chr7D 592567093 592567828 735 False 593.000000 593 81.600000 1797 2531 1 chr7D.!!$F2 734
15 TraesCS5A01G140400 chr4D 107748096 107748728 632 False 588.000000 588 83.619000 1899 2531 1 chr4D.!!$F1 632
16 TraesCS5A01G140400 chr6A 564676043 564676773 730 False 582.000000 582 81.392000 1799 2531 1 chr6A.!!$F2 732
17 TraesCS5A01G140400 chr2A 757785388 757786111 723 False 505.000000 505 79.702000 1799 2521 1 chr2A.!!$F1 722
18 TraesCS5A01G140400 chr3B 647227171 647227841 670 False 460.000000 460 79.442000 1806 2472 1 chr3B.!!$F1 666

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
310 512 0.179067 TTGCTTTTGTCTCCGTCCGT 60.179 50.0 0.0 0.0 0.0 4.69 F
1039 1531 0.179100 GCTCTGCAACTCTGGCGATA 60.179 55.0 0.0 0.0 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1595 2088 0.459237 GACTGTCGGAGCTGTGATGG 60.459 60.0 0.0 0.0 0.00 3.51 R
2589 3176 0.179116 CGTGCTCCACTCTGATGAGG 60.179 60.0 0.0 0.0 44.29 3.86 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
71 72 2.478031 CGATCCGCGTATAATAGCTGCT 60.478 50.000 7.57 7.57 34.64 4.24
99 101 1.012486 GGTTGACGAGGTAACCAGCG 61.012 60.000 0.00 0.00 44.48 5.18
159 161 1.427368 AGTCAGGTCTCAGAGGTGTCT 59.573 52.381 0.00 0.00 0.00 3.41
219 421 4.864334 CCGAGCCATGGCCCTCAC 62.864 72.222 33.14 17.37 43.17 3.51
310 512 0.179067 TTGCTTTTGTCTCCGTCCGT 60.179 50.000 0.00 0.00 0.00 4.69
450 653 1.005394 GAAGAAACGCCGGTGGAGA 60.005 57.895 21.14 0.00 0.00 3.71
629 833 7.555965 TCCTTCGATCTTCATGTGAATTAAGA 58.444 34.615 0.00 0.00 33.01 2.10
787 991 8.267894 CCCATTCCTTATCTCTTTTCTACAGAA 58.732 37.037 0.00 0.00 0.00 3.02
815 1254 2.650322 GTCTCCATCGTTCCTCTCTCT 58.350 52.381 0.00 0.00 0.00 3.10
1001 1493 0.742281 GCCGCTGCGATGATATCCAT 60.742 55.000 25.45 0.00 38.43 3.41
1017 1509 1.143838 CATGGAGATTGGCCGACGA 59.856 57.895 0.00 0.00 0.00 4.20
1039 1531 0.179100 GCTCTGCAACTCTGGCGATA 60.179 55.000 0.00 0.00 0.00 2.92
1059 1551 0.603707 CTGCCTTGAAGCTGTTCGGA 60.604 55.000 0.00 0.00 35.17 4.55
1089 1581 1.408422 GTGTTGAAATGGAGCAACGC 58.592 50.000 0.00 0.00 45.47 4.84
1112 1604 4.116328 CGCCGGAAGCAGAGACGA 62.116 66.667 5.05 0.00 44.04 4.20
1145 1637 1.741401 CTCGCCGGAGTTGCAATGA 60.741 57.895 5.05 0.00 35.48 2.57
1152 1644 1.536766 CGGAGTTGCAATGAAGCTTCA 59.463 47.619 30.23 30.23 42.14 3.02
1183 1676 1.891919 GTGTTGCGTTGGAGCTCCA 60.892 57.895 32.00 32.00 45.94 3.86
1237 1730 2.510238 GCTGCGTTGGAGCTCGAT 60.510 61.111 7.83 0.00 38.13 3.59
1331 1824 2.125912 GTCGCGACCACTGCATCT 60.126 61.111 28.61 0.00 0.00 2.90
1332 1825 1.738099 GTCGCGACCACTGCATCTT 60.738 57.895 28.61 0.00 0.00 2.40
1342 1835 1.264749 ACTGCATCTTACCTCCGGCA 61.265 55.000 0.00 0.00 0.00 5.69
1345 1838 1.227674 CATCTTACCTCCGGCAGCC 60.228 63.158 0.00 0.00 0.00 4.85
1497 1990 4.555709 TGCAACTCCGGTGGCGTT 62.556 61.111 8.63 2.20 44.96 4.84
1555 2048 0.806868 CGCTGCATCACAACTCCAAT 59.193 50.000 0.00 0.00 0.00 3.16
1558 2051 2.165167 CTGCATCACAACTCCAATGGT 58.835 47.619 0.00 0.00 0.00 3.55
1642 2175 1.672356 GGTGTGCTTGGAGCGTGAT 60.672 57.895 0.00 0.00 46.26 3.06
1682 2215 1.736645 GCCTGTGTTAGCGCGAGAA 60.737 57.895 12.10 0.00 0.00 2.87
1735 2268 2.223947 ACGGCTACGATGTGCATAATCA 60.224 45.455 11.55 0.00 44.60 2.57
1761 2294 0.179468 TACCAAGGCGGCTGATAACC 59.821 55.000 14.21 0.00 39.03 2.85
1778 2311 1.961277 CCCGCAGTTATCATCCGGC 60.961 63.158 0.00 0.00 37.73 6.13
1797 2330 3.493830 TTACGCCTAGCATCGGCCG 62.494 63.158 22.12 22.12 44.73 6.13
1809 2342 1.021968 ATCGGCCGTTTAGAATTGGC 58.978 50.000 27.15 0.00 46.82 4.52
1851 2385 3.160269 CAACAATTTCTCAAGGAGCCCT 58.840 45.455 0.00 0.00 33.87 5.19
1852 2386 4.042809 TCAACAATTTCTCAAGGAGCCCTA 59.957 41.667 0.00 0.00 31.13 3.53
1853 2387 3.956744 ACAATTTCTCAAGGAGCCCTAC 58.043 45.455 0.00 0.00 31.13 3.18
1854 2388 3.282885 CAATTTCTCAAGGAGCCCTACC 58.717 50.000 0.00 0.00 31.13 3.18
1855 2389 2.038863 TTTCTCAAGGAGCCCTACCA 57.961 50.000 0.00 0.00 31.13 3.25
1859 2393 1.839994 CTCAAGGAGCCCTACCATTCA 59.160 52.381 0.00 0.00 31.13 2.57
1995 2545 7.226720 CAGCCGGTCTATAAAAACATATCAACT 59.773 37.037 1.90 0.00 0.00 3.16
2078 2630 1.257743 AGTACATGCAGTCACCGACT 58.742 50.000 0.00 0.00 44.44 4.18
2080 2632 2.037251 AGTACATGCAGTCACCGACTTT 59.963 45.455 0.00 0.00 41.37 2.66
2144 2699 5.803461 CACAGAACCACATCATAAAAGCATG 59.197 40.000 0.00 0.00 0.00 4.06
2242 2798 7.229506 CCATCAGTTTCAGAATTAAGGGGTATC 59.770 40.741 0.00 0.00 0.00 2.24
2533 3120 1.135053 GCGTCCAACCCTTCTAGTCTC 60.135 57.143 0.00 0.00 0.00 3.36
2540 3127 5.480772 TCCAACCCTTCTAGTCTCAACTAAG 59.519 44.000 0.00 0.00 37.53 2.18
2541 3128 5.172205 CAACCCTTCTAGTCTCAACTAAGC 58.828 45.833 0.00 0.00 37.53 3.09
2542 3129 3.770388 ACCCTTCTAGTCTCAACTAAGCC 59.230 47.826 0.00 0.00 37.53 4.35
2543 3130 3.769844 CCCTTCTAGTCTCAACTAAGCCA 59.230 47.826 0.00 0.00 37.53 4.75
2544 3131 4.142049 CCCTTCTAGTCTCAACTAAGCCAG 60.142 50.000 0.00 0.00 37.53 4.85
2545 3132 4.142049 CCTTCTAGTCTCAACTAAGCCAGG 60.142 50.000 0.00 0.00 37.53 4.45
2546 3133 2.761208 TCTAGTCTCAACTAAGCCAGGC 59.239 50.000 1.84 1.84 37.53 4.85
2547 3134 1.352083 AGTCTCAACTAAGCCAGGCA 58.648 50.000 15.80 0.00 32.59 4.75
2548 3135 1.277557 AGTCTCAACTAAGCCAGGCAG 59.722 52.381 15.80 5.61 32.59 4.85
2549 3136 1.276421 GTCTCAACTAAGCCAGGCAGA 59.724 52.381 15.80 2.31 0.00 4.26
2550 3137 1.552337 TCTCAACTAAGCCAGGCAGAG 59.448 52.381 15.80 12.66 0.00 3.35
2551 3138 0.615331 TCAACTAAGCCAGGCAGAGG 59.385 55.000 15.80 3.12 0.00 3.69
2552 3139 0.615331 CAACTAAGCCAGGCAGAGGA 59.385 55.000 15.80 0.00 0.00 3.71
2553 3140 0.615850 AACTAAGCCAGGCAGAGGAC 59.384 55.000 15.80 0.00 0.00 3.85
2554 3141 1.268283 ACTAAGCCAGGCAGAGGACC 61.268 60.000 15.80 0.00 0.00 4.46
2555 3142 1.977293 CTAAGCCAGGCAGAGGACCC 61.977 65.000 15.80 0.00 0.00 4.46
2556 3143 2.477190 TAAGCCAGGCAGAGGACCCT 62.477 60.000 15.80 0.00 0.00 4.34
2557 3144 3.791586 GCCAGGCAGAGGACCCTC 61.792 72.222 6.55 7.98 43.03 4.30
2558 3145 3.465403 CCAGGCAGAGGACCCTCG 61.465 72.222 10.17 6.91 46.90 4.63
2559 3146 4.154347 CAGGCAGAGGACCCTCGC 62.154 72.222 18.07 18.07 46.90 5.03
2562 3149 4.459089 GCAGAGGACCCTCGCCAC 62.459 72.222 16.50 4.18 46.90 5.01
2563 3150 3.775654 CAGAGGACCCTCGCCACC 61.776 72.222 10.17 0.00 46.90 4.61
2564 3151 4.316823 AGAGGACCCTCGCCACCA 62.317 66.667 10.17 0.00 46.90 4.17
2565 3152 3.083997 GAGGACCCTCGCCACCAT 61.084 66.667 0.00 0.00 33.06 3.55
2566 3153 3.083997 AGGACCCTCGCCACCATC 61.084 66.667 0.00 0.00 0.00 3.51
2567 3154 3.083997 GGACCCTCGCCACCATCT 61.084 66.667 0.00 0.00 0.00 2.90
2568 3155 2.501610 GACCCTCGCCACCATCTC 59.498 66.667 0.00 0.00 0.00 2.75
2569 3156 3.083997 ACCCTCGCCACCATCTCC 61.084 66.667 0.00 0.00 0.00 3.71
2570 3157 3.083349 CCCTCGCCACCATCTCCA 61.083 66.667 0.00 0.00 0.00 3.86
2571 3158 2.187946 CCTCGCCACCATCTCCAC 59.812 66.667 0.00 0.00 0.00 4.02
2572 3159 2.187946 CTCGCCACCATCTCCACC 59.812 66.667 0.00 0.00 0.00 4.61
2573 3160 2.284625 TCGCCACCATCTCCACCT 60.285 61.111 0.00 0.00 0.00 4.00
2574 3161 2.187946 CGCCACCATCTCCACCTC 59.812 66.667 0.00 0.00 0.00 3.85
2575 3162 2.592308 GCCACCATCTCCACCTCC 59.408 66.667 0.00 0.00 0.00 4.30
2576 3163 1.997874 GCCACCATCTCCACCTCCT 60.998 63.158 0.00 0.00 0.00 3.69
2577 3164 1.910722 CCACCATCTCCACCTCCTG 59.089 63.158 0.00 0.00 0.00 3.86
2578 3165 1.630126 CCACCATCTCCACCTCCTGG 61.630 65.000 0.00 0.00 42.29 4.45
2587 3174 2.284995 ACCTCCTGGTGCTCCTCC 60.285 66.667 6.34 0.00 46.51 4.30
2588 3175 2.040278 CCTCCTGGTGCTCCTCCT 59.960 66.667 6.34 0.00 34.23 3.69
2589 3176 2.063378 CCTCCTGGTGCTCCTCCTC 61.063 68.421 6.34 0.00 34.23 3.71
2590 3177 2.039624 TCCTGGTGCTCCTCCTCC 59.960 66.667 6.34 0.00 34.23 4.30
2591 3178 2.040278 CCTGGTGCTCCTCCTCCT 59.960 66.667 6.34 0.00 34.23 3.69
2592 3179 2.063378 CCTGGTGCTCCTCCTCCTC 61.063 68.421 6.34 0.00 34.23 3.71
2593 3180 1.305633 CTGGTGCTCCTCCTCCTCA 60.306 63.158 6.34 0.00 34.23 3.86
2594 3181 0.690411 CTGGTGCTCCTCCTCCTCAT 60.690 60.000 6.34 0.00 34.23 2.90
2595 3182 0.689080 TGGTGCTCCTCCTCCTCATC 60.689 60.000 6.34 0.00 34.23 2.92
2596 3183 0.689080 GGTGCTCCTCCTCCTCATCA 60.689 60.000 0.00 0.00 0.00 3.07
2597 3184 0.752054 GTGCTCCTCCTCCTCATCAG 59.248 60.000 0.00 0.00 0.00 2.90
2598 3185 0.633378 TGCTCCTCCTCCTCATCAGA 59.367 55.000 0.00 0.00 0.00 3.27
2599 3186 1.331214 GCTCCTCCTCCTCATCAGAG 58.669 60.000 0.00 0.00 41.72 3.35
2600 3187 1.411501 GCTCCTCCTCCTCATCAGAGT 60.412 57.143 0.00 0.00 40.40 3.24
2601 3188 2.309613 CTCCTCCTCCTCATCAGAGTG 58.690 57.143 0.00 0.00 40.40 3.51
2602 3189 1.063341 TCCTCCTCCTCATCAGAGTGG 60.063 57.143 0.00 0.00 40.40 4.00
2603 3190 1.063341 CCTCCTCCTCATCAGAGTGGA 60.063 57.143 0.00 0.00 40.40 4.02
2604 3191 2.309613 CTCCTCCTCATCAGAGTGGAG 58.690 57.143 13.46 13.46 45.49 3.86
2605 3192 0.752054 CCTCCTCATCAGAGTGGAGC 59.248 60.000 9.51 0.00 44.20 4.70
2606 3193 1.482954 CTCCTCATCAGAGTGGAGCA 58.517 55.000 0.00 0.00 40.97 4.26
2607 3194 1.136695 CTCCTCATCAGAGTGGAGCAC 59.863 57.143 0.00 0.00 40.97 4.40
2608 3195 0.179116 CCTCATCAGAGTGGAGCACG 60.179 60.000 0.00 0.00 40.40 5.34
2609 3196 0.179116 CTCATCAGAGTGGAGCACGG 60.179 60.000 0.00 0.00 39.64 4.94
2610 3197 0.900182 TCATCAGAGTGGAGCACGGT 60.900 55.000 0.00 0.00 39.64 4.83
2611 3198 0.738762 CATCAGAGTGGAGCACGGTG 60.739 60.000 3.15 3.15 39.64 4.94
2612 3199 1.188219 ATCAGAGTGGAGCACGGTGT 61.188 55.000 10.24 0.00 39.64 4.16
2613 3200 1.665916 CAGAGTGGAGCACGGTGTG 60.666 63.158 10.24 0.00 39.64 3.82
2614 3201 2.357517 GAGTGGAGCACGGTGTGG 60.358 66.667 10.24 0.00 39.64 4.17
2620 3207 3.821995 AGCACGGTGTGGTCAAAC 58.178 55.556 10.24 0.00 40.38 2.93
2621 3208 1.078072 AGCACGGTGTGGTCAAACA 60.078 52.632 10.24 0.00 40.38 2.83
2622 3209 0.678366 AGCACGGTGTGGTCAAACAA 60.678 50.000 10.24 0.00 40.38 2.83
2623 3210 0.383949 GCACGGTGTGGTCAAACAAT 59.616 50.000 10.24 0.00 33.64 2.71
2624 3211 1.863624 GCACGGTGTGGTCAAACAATG 60.864 52.381 10.24 0.00 33.64 2.82
2625 3212 0.383949 ACGGTGTGGTCAAACAATGC 59.616 50.000 0.00 0.00 0.00 3.56
2626 3213 0.383590 CGGTGTGGTCAAACAATGCA 59.616 50.000 0.00 0.00 0.00 3.96
2627 3214 1.000385 CGGTGTGGTCAAACAATGCAT 60.000 47.619 0.00 0.00 0.00 3.96
2628 3215 2.676076 GGTGTGGTCAAACAATGCATC 58.324 47.619 0.00 0.00 0.00 3.91
2629 3216 2.297033 GGTGTGGTCAAACAATGCATCT 59.703 45.455 0.00 0.00 0.00 2.90
2630 3217 3.311106 GTGTGGTCAAACAATGCATCTG 58.689 45.455 0.00 3.44 0.00 2.90
2631 3218 2.957680 TGTGGTCAAACAATGCATCTGT 59.042 40.909 0.00 4.13 0.00 3.41
2632 3219 3.243468 TGTGGTCAAACAATGCATCTGTG 60.243 43.478 13.05 5.48 0.00 3.66
2633 3220 2.957680 TGGTCAAACAATGCATCTGTGT 59.042 40.909 13.05 6.07 0.00 3.72
2634 3221 4.023279 GTGGTCAAACAATGCATCTGTGTA 60.023 41.667 13.05 2.83 0.00 2.90
2635 3222 4.216042 TGGTCAAACAATGCATCTGTGTAG 59.784 41.667 13.05 5.91 0.00 2.74
2636 3223 4.216257 GGTCAAACAATGCATCTGTGTAGT 59.784 41.667 13.05 0.00 0.00 2.73
2637 3224 5.411361 GGTCAAACAATGCATCTGTGTAGTA 59.589 40.000 13.05 0.00 0.00 1.82
2638 3225 6.402550 GGTCAAACAATGCATCTGTGTAGTAG 60.403 42.308 13.05 1.75 0.00 2.57
2639 3226 6.147821 GTCAAACAATGCATCTGTGTAGTAGT 59.852 38.462 13.05 0.00 0.00 2.73
2640 3227 6.368791 TCAAACAATGCATCTGTGTAGTAGTC 59.631 38.462 13.05 0.00 0.00 2.59
2641 3228 4.759782 ACAATGCATCTGTGTAGTAGTCC 58.240 43.478 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 101 2.030363 CCTATCTGACGAGGAGCATGTC 60.030 54.545 1.94 0.00 34.46 3.06
629 833 3.503891 CCGGTTGAAACGAACACTTTTT 58.496 40.909 3.25 0.00 0.00 1.94
726 930 1.424638 CACCGGAGATAAGGATGGGT 58.575 55.000 9.46 0.00 0.00 4.51
787 991 0.903454 AACGATGGAGACGAAGGGGT 60.903 55.000 0.00 0.00 34.70 4.95
908 1400 2.360475 GGTGTCCCCTCTTGCAGC 60.360 66.667 0.00 0.00 0.00 5.25
996 1488 0.109342 GTCGGCCAATCTCCATGGAT 59.891 55.000 16.63 0.00 40.56 3.41
1001 1493 2.721167 CCTCGTCGGCCAATCTCCA 61.721 63.158 2.24 0.00 0.00 3.86
1017 1509 3.076092 CCAGAGTTGCAGAGCCCT 58.924 61.111 0.00 0.00 0.00 5.19
1039 1531 0.886490 CCGAACAGCTTCAAGGCAGT 60.886 55.000 0.00 0.00 33.48 4.40
1069 1561 1.001378 GCGTTGCTCCATTTCAACACT 60.001 47.619 6.03 0.00 41.80 3.55
1076 1568 3.061848 CCCCGCGTTGCTCCATTT 61.062 61.111 4.92 0.00 0.00 2.32
1112 1604 2.358003 GAGGCTTCACTGCAGCGT 60.358 61.111 15.27 0.89 38.24 5.07
1145 1637 4.295119 ACGCGTCCGGTGAAGCTT 62.295 61.111 5.58 0.00 42.88 3.74
1172 1664 2.403132 AGCACCTGTGGAGCTCCAAC 62.403 60.000 36.66 27.77 45.99 3.77
1183 1676 2.267006 CTCCATCGCAGCACCTGT 59.733 61.111 0.00 0.00 33.43 4.00
1237 1730 2.357881 CAGCAAGAGCAGCACCGA 60.358 61.111 0.00 0.00 45.49 4.69
1320 1813 0.537188 CGGAGGTAAGATGCAGTGGT 59.463 55.000 0.00 0.00 0.00 4.16
1520 2013 3.028130 CGGGCATCGACGCTACTA 58.972 61.111 2.49 0.00 42.43 1.82
1555 2048 1.438651 GAGCTGTAATGCAACGACCA 58.561 50.000 0.00 0.00 34.99 4.02
1558 2051 0.739462 CCGGAGCTGTAATGCAACGA 60.739 55.000 0.00 0.00 36.80 3.85
1595 2088 0.459237 GACTGTCGGAGCTGTGATGG 60.459 60.000 0.00 0.00 0.00 3.51
1642 2175 4.488136 CCCATGCAGCGCCCACTA 62.488 66.667 2.29 0.00 0.00 2.74
1682 2215 1.978580 ACTTCCCGTCAACATCTTCCT 59.021 47.619 0.00 0.00 0.00 3.36
1735 2268 1.153429 GCCGCCTTGGTAATCGTCT 60.153 57.895 0.00 0.00 41.21 4.18
1778 2311 3.938112 GCCGATGCTAGGCGTAAG 58.062 61.111 2.21 0.00 45.58 2.34
1809 2342 4.013728 TGACCCGGTTAAAATTGGATGAG 58.986 43.478 0.00 0.00 0.00 2.90
1935 2484 4.473477 TTGAAAAATTGTTGACCCGGTT 57.527 36.364 0.00 0.00 0.00 4.44
1995 2545 3.311110 GGAGGGAGTGTGCGTGGA 61.311 66.667 0.00 0.00 0.00 4.02
2485 3072 1.879430 CGTCGTTGGTGTCGTTGGT 60.879 57.895 0.00 0.00 0.00 3.67
2491 3078 2.042520 TTTGCTGCGTCGTTGGTGTC 62.043 55.000 0.00 0.00 0.00 3.67
2533 3120 0.615331 TCCTCTGCCTGGCTTAGTTG 59.385 55.000 21.03 7.38 0.00 3.16
2540 3127 3.791586 GAGGGTCCTCTGCCTGGC 61.792 72.222 12.87 12.87 39.80 4.85
2541 3128 3.465403 CGAGGGTCCTCTGCCTGG 61.465 72.222 14.34 0.00 40.69 4.45
2542 3129 4.154347 GCGAGGGTCCTCTGCCTG 62.154 72.222 14.34 0.77 40.69 4.85
2545 3132 4.459089 GTGGCGAGGGTCCTCTGC 62.459 72.222 18.54 18.54 40.69 4.26
2546 3133 3.775654 GGTGGCGAGGGTCCTCTG 61.776 72.222 14.34 9.28 40.69 3.35
2547 3134 3.625632 ATGGTGGCGAGGGTCCTCT 62.626 63.158 14.34 0.00 40.69 3.69
2548 3135 3.083997 ATGGTGGCGAGGGTCCTC 61.084 66.667 6.94 6.94 39.55 3.71
2549 3136 3.083997 GATGGTGGCGAGGGTCCT 61.084 66.667 0.00 0.00 0.00 3.85
2550 3137 3.083997 AGATGGTGGCGAGGGTCC 61.084 66.667 0.00 0.00 0.00 4.46
2551 3138 2.501610 GAGATGGTGGCGAGGGTC 59.498 66.667 0.00 0.00 0.00 4.46
2552 3139 3.083997 GGAGATGGTGGCGAGGGT 61.084 66.667 0.00 0.00 0.00 4.34
2553 3140 3.083349 TGGAGATGGTGGCGAGGG 61.083 66.667 0.00 0.00 0.00 4.30
2554 3141 2.187946 GTGGAGATGGTGGCGAGG 59.812 66.667 0.00 0.00 0.00 4.63
2555 3142 2.187946 GGTGGAGATGGTGGCGAG 59.812 66.667 0.00 0.00 0.00 5.03
2556 3143 2.284625 AGGTGGAGATGGTGGCGA 60.285 61.111 0.00 0.00 0.00 5.54
2557 3144 2.187946 GAGGTGGAGATGGTGGCG 59.812 66.667 0.00 0.00 0.00 5.69
2558 3145 1.997874 AGGAGGTGGAGATGGTGGC 60.998 63.158 0.00 0.00 0.00 5.01
2559 3146 1.910722 CAGGAGGTGGAGATGGTGG 59.089 63.158 0.00 0.00 0.00 4.61
2571 3158 2.040278 AGGAGGAGCACCAGGAGG 59.960 66.667 2.07 0.00 42.21 4.30
2572 3159 2.063378 GGAGGAGGAGCACCAGGAG 61.063 68.421 2.07 0.00 38.94 3.69
2573 3160 2.039624 GGAGGAGGAGCACCAGGA 59.960 66.667 2.07 0.00 38.94 3.86
2574 3161 2.040278 AGGAGGAGGAGCACCAGG 59.960 66.667 2.07 0.00 38.94 4.45
2575 3162 0.690411 ATGAGGAGGAGGAGCACCAG 60.690 60.000 2.07 0.00 38.94 4.00
2576 3163 0.689080 GATGAGGAGGAGGAGCACCA 60.689 60.000 2.07 0.00 38.94 4.17
2577 3164 0.689080 TGATGAGGAGGAGGAGCACC 60.689 60.000 0.00 0.00 0.00 5.01
2578 3165 0.752054 CTGATGAGGAGGAGGAGCAC 59.248 60.000 0.00 0.00 0.00 4.40
2579 3166 0.633378 TCTGATGAGGAGGAGGAGCA 59.367 55.000 0.00 0.00 0.00 4.26
2580 3167 1.331214 CTCTGATGAGGAGGAGGAGC 58.669 60.000 0.00 0.00 36.70 4.70
2581 3168 2.309613 CACTCTGATGAGGAGGAGGAG 58.690 57.143 0.00 0.00 44.29 3.69
2582 3169 1.063341 CCACTCTGATGAGGAGGAGGA 60.063 57.143 0.00 0.00 44.29 3.71
2583 3170 1.063341 TCCACTCTGATGAGGAGGAGG 60.063 57.143 0.00 0.00 44.29 4.30
2584 3171 2.450867 TCCACTCTGATGAGGAGGAG 57.549 55.000 0.00 0.00 44.29 3.69
2585 3172 1.687682 GCTCCACTCTGATGAGGAGGA 60.688 57.143 16.81 6.83 44.29 3.71
2586 3173 0.752054 GCTCCACTCTGATGAGGAGG 59.248 60.000 16.81 3.24 44.29 4.30
2587 3174 1.136695 GTGCTCCACTCTGATGAGGAG 59.863 57.143 12.98 12.98 44.29 3.69
2588 3175 1.189752 GTGCTCCACTCTGATGAGGA 58.810 55.000 0.00 0.00 44.29 3.71
2589 3176 0.179116 CGTGCTCCACTCTGATGAGG 60.179 60.000 0.00 0.00 44.29 3.86
2590 3177 0.179116 CCGTGCTCCACTCTGATGAG 60.179 60.000 0.00 0.00 45.43 2.90
2591 3178 0.900182 ACCGTGCTCCACTCTGATGA 60.900 55.000 0.00 0.00 31.34 2.92
2592 3179 0.738762 CACCGTGCTCCACTCTGATG 60.739 60.000 0.00 0.00 31.34 3.07
2593 3180 1.188219 ACACCGTGCTCCACTCTGAT 61.188 55.000 0.00 0.00 31.34 2.90
2594 3181 1.832608 ACACCGTGCTCCACTCTGA 60.833 57.895 0.00 0.00 31.34 3.27
2595 3182 1.665916 CACACCGTGCTCCACTCTG 60.666 63.158 0.00 0.00 31.34 3.35
2596 3183 2.737180 CACACCGTGCTCCACTCT 59.263 61.111 0.00 0.00 31.34 3.24
2597 3184 2.357517 CCACACCGTGCTCCACTC 60.358 66.667 0.00 0.00 31.34 3.51
2598 3185 3.161450 ACCACACCGTGCTCCACT 61.161 61.111 0.00 0.00 31.34 4.00
2599 3186 2.665185 GACCACACCGTGCTCCAC 60.665 66.667 0.00 0.00 31.34 4.02
2600 3187 2.258748 TTTGACCACACCGTGCTCCA 62.259 55.000 0.00 0.00 31.34 3.86
2601 3188 1.525077 TTTGACCACACCGTGCTCC 60.525 57.895 0.00 0.00 31.34 4.70
2602 3189 1.092921 TGTTTGACCACACCGTGCTC 61.093 55.000 0.00 0.00 31.34 4.26
2603 3190 0.678366 TTGTTTGACCACACCGTGCT 60.678 50.000 0.00 0.00 31.34 4.40
2604 3191 0.383949 ATTGTTTGACCACACCGTGC 59.616 50.000 0.00 0.00 31.34 5.34
2605 3192 1.863624 GCATTGTTTGACCACACCGTG 60.864 52.381 0.00 0.00 0.00 4.94
2606 3193 0.383949 GCATTGTTTGACCACACCGT 59.616 50.000 0.00 0.00 0.00 4.83
2607 3194 0.383590 TGCATTGTTTGACCACACCG 59.616 50.000 0.00 0.00 0.00 4.94
2608 3195 2.297033 AGATGCATTGTTTGACCACACC 59.703 45.455 0.00 0.00 0.00 4.16
2609 3196 3.243501 ACAGATGCATTGTTTGACCACAC 60.244 43.478 0.00 0.00 0.00 3.82
2610 3197 2.957680 ACAGATGCATTGTTTGACCACA 59.042 40.909 0.00 0.00 0.00 4.17
2611 3198 3.243501 ACACAGATGCATTGTTTGACCAC 60.244 43.478 0.00 0.00 0.00 4.16
2612 3199 2.957680 ACACAGATGCATTGTTTGACCA 59.042 40.909 0.00 0.00 0.00 4.02
2613 3200 3.648339 ACACAGATGCATTGTTTGACC 57.352 42.857 0.00 0.00 0.00 4.02
2614 3201 5.362556 ACTACACAGATGCATTGTTTGAC 57.637 39.130 7.76 0.00 0.00 3.18
2615 3202 6.230472 ACTACTACACAGATGCATTGTTTGA 58.770 36.000 7.76 0.00 0.00 2.69
2616 3203 6.402550 GGACTACTACACAGATGCATTGTTTG 60.403 42.308 7.76 4.27 0.00 2.93
2617 3204 5.643777 GGACTACTACACAGATGCATTGTTT 59.356 40.000 7.76 6.81 0.00 2.83
2618 3205 5.178797 GGACTACTACACAGATGCATTGTT 58.821 41.667 7.76 5.38 0.00 2.83
2619 3206 4.759782 GGACTACTACACAGATGCATTGT 58.240 43.478 0.00 3.96 0.00 2.71


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

AutoCloner maintained by Alex Coulton.