Multiple sequence alignment - TraesCS3B01G249600

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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 TraesCS3B01G249600 chr3B 100.000 4144 0 0 1 4144 397673956 397678099 0.000000e+00 7653.0
1 TraesCS3B01G249600 chr3B 79.767 257 27 11 402 634 18789457 18789202 3.310000e-36 163.0
2 TraesCS3B01G249600 chr1B 92.745 2164 84 31 2006 4144 637911389 637913504 0.000000e+00 3059.0
3 TraesCS3B01G249600 chr1B 100.000 34 0 0 1959 1992 637911356 637911389 3.460000e-06 63.9
4 TraesCS3B01G249600 chr1B 97.059 34 1 0 3155 3188 565340940 565340907 1.610000e-04 58.4
5 TraesCS3B01G249600 chr3D 92.669 1596 70 22 1958 3533 321874647 321873079 0.000000e+00 2255.0
6 TraesCS3B01G249600 chr3D 88.522 1394 64 53 640 1963 321876042 321874675 0.000000e+00 1600.0
7 TraesCS3B01G249600 chr3D 94.384 463 18 4 44 501 321876763 321876304 0.000000e+00 704.0
8 TraesCS3B01G249600 chr3D 84.221 507 52 9 3642 4144 321873039 321872557 6.270000e-128 468.0
9 TraesCS3B01G249600 chr3D 86.395 147 17 3 2884 3030 508465700 508465557 1.540000e-34 158.0
10 TraesCS3B01G249600 chr3D 80.337 178 20 7 2723 2886 508466646 508466470 2.020000e-23 121.0
11 TraesCS3B01G249600 chr3D 84.536 97 5 2 3092 3188 606777910 606777996 2.050000e-13 87.9
12 TraesCS3B01G249600 chr3D 96.875 32 0 1 8 39 321876829 321876799 7.000000e-03 52.8
13 TraesCS3B01G249600 chr3A 90.714 1443 63 26 2136 3531 402133639 402135057 0.000000e+00 1857.0
14 TraesCS3B01G249600 chr3A 88.325 1379 72 41 640 1963 402131414 402132758 0.000000e+00 1572.0
15 TraesCS3B01G249600 chr3A 93.023 430 10 7 44 462 402130869 402131289 9.850000e-171 610.0
16 TraesCS3B01G249600 chr3A 85.069 509 46 12 3642 4144 402135099 402135583 3.720000e-135 492.0
17 TraesCS3B01G249600 chr3A 95.082 183 6 1 1958 2140 402132786 402132965 6.780000e-73 285.0
18 TraesCS3B01G249600 chr3A 97.436 39 0 1 1 39 402130796 402130833 9.620000e-07 65.8
19 TraesCS3B01G249600 chr2D 92.432 1295 44 26 1958 3230 634650714 634649452 0.000000e+00 1799.0
20 TraesCS3B01G249600 chr2D 95.528 1118 23 10 868 1963 634651854 634650742 0.000000e+00 1762.0
21 TraesCS3B01G249600 chr2D 95.336 922 28 5 3224 4144 634648048 634647141 0.000000e+00 1450.0
22 TraesCS3B01G249600 chr1D 95.116 819 27 5 3327 4144 462965301 462966107 0.000000e+00 1279.0
23 TraesCS3B01G249600 chr1D 92.993 842 35 16 2507 3337 462946843 462947671 0.000000e+00 1206.0
24 TraesCS3B01G249600 chr6A 84.100 478 51 14 2593 3053 508249581 508249112 4.920000e-119 438.0
25 TraesCS3B01G249600 chr6A 80.952 147 20 7 402 545 459074051 459074192 4.380000e-20 110.0
26 TraesCS3B01G249600 chr6D 88.550 262 23 6 2545 2802 367749855 367749597 1.120000e-80 311.0
27 TraesCS3B01G249600 chr6D 91.837 98 7 1 404 501 461683274 461683370 7.230000e-28 135.0
28 TraesCS3B01G249600 chr7D 85.321 218 18 7 2971 3188 41306157 41306360 3.250000e-51 213.0
29 TraesCS3B01G249600 chr7D 77.992 259 30 15 401 635 108621984 108621729 2.010000e-28 137.0
30 TraesCS3B01G249600 chr1A 78.210 257 28 12 404 634 293712671 293712417 5.590000e-29 139.0
31 TraesCS3B01G249600 chr1A 77.559 254 34 13 401 635 510905350 510905599 9.350000e-27 132.0
32 TraesCS3B01G249600 chr4A 91.000 100 7 2 402 501 539749850 539749753 2.600000e-27 134.0
33 TraesCS3B01G249600 chr5B 91.667 96 7 1 406 501 599695103 599695009 9.350000e-27 132.0
34 TraesCS3B01G249600 chr6B 90.000 100 9 1 402 501 501774170 501774072 1.210000e-25 128.0


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 TraesCS3B01G249600 chr3B 397673956 397678099 4143 False 7653.000000 7653 100.000000 1 4144 1 chr3B.!!$F1 4143
1 TraesCS3B01G249600 chr1B 637911356 637913504 2148 False 1561.450000 3059 96.372500 1959 4144 2 chr1B.!!$F1 2185
2 TraesCS3B01G249600 chr3D 321872557 321876829 4272 True 1015.960000 2255 91.334200 8 4144 5 chr3D.!!$R1 4136
3 TraesCS3B01G249600 chr3A 402130796 402135583 4787 False 813.633333 1857 91.608167 1 4144 6 chr3A.!!$F1 4143
4 TraesCS3B01G249600 chr2D 634647141 634651854 4713 True 1670.333333 1799 94.432000 868 4144 3 chr2D.!!$R1 3276
5 TraesCS3B01G249600 chr1D 462965301 462966107 806 False 1279.000000 1279 95.116000 3327 4144 1 chr1D.!!$F2 817
6 TraesCS3B01G249600 chr1D 462946843 462947671 828 False 1206.000000 1206 92.993000 2507 3337 1 chr1D.!!$F1 830

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
650 818 0.536460 ATCCACAGTCCCGCGTTTTT 60.536 50.0 4.92 0.00 0.0 1.94 F
1468 1744 0.376152 GTCTGAATGCATGCGACCTG 59.624 55.0 14.09 8.19 0.0 4.00 F
2355 3406 0.188587 TCCGAGCCCTCTGATGGTAT 59.811 55.0 0.89 0.00 0.0 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1499 1790 0.034337 TACGTGCCTTCACACTTCCC 59.966 55.0 0.00 0.00 43.28 3.97 R
2420 3472 0.439985 ATTGCGCGCTATTAGCATCG 59.560 50.0 33.29 16.82 42.58 3.84 R
3973 6548 0.470766 TACACCTGCTCCACGGTTTT 59.529 50.0 0.00 0.00 0.00 2.43 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
35 36 4.133820 GGTGCCAAATGTTTAGCCTTTTT 58.866 39.130 0.00 0.00 0.00 1.94
37 38 4.213270 GTGCCAAATGTTTAGCCTTTTTCC 59.787 41.667 0.00 0.00 0.00 3.13
38 39 4.102367 TGCCAAATGTTTAGCCTTTTTCCT 59.898 37.500 0.00 0.00 0.00 3.36
40 41 5.237815 CCAAATGTTTAGCCTTTTTCCTCC 58.762 41.667 0.00 0.00 0.00 4.30
41 42 5.012046 CCAAATGTTTAGCCTTTTTCCTCCT 59.988 40.000 0.00 0.00 0.00 3.69
42 43 6.464322 CCAAATGTTTAGCCTTTTTCCTCCTT 60.464 38.462 0.00 0.00 0.00 3.36
307 341 1.882623 CTCCACTGCCAAGAAAAGGAC 59.117 52.381 0.00 0.00 0.00 3.85
329 363 5.611374 ACGCATATATTCTGCTGTAACCTT 58.389 37.500 7.96 0.00 37.48 3.50
359 393 3.367395 GGGATTACTATTACGTACGCCCC 60.367 52.174 16.72 6.65 31.53 5.80
360 394 3.255642 GGATTACTATTACGTACGCCCCA 59.744 47.826 16.72 0.00 0.00 4.96
361 395 4.082026 GGATTACTATTACGTACGCCCCAT 60.082 45.833 16.72 4.79 0.00 4.00
362 396 2.806608 ACTATTACGTACGCCCCATG 57.193 50.000 16.72 4.26 0.00 3.66
378 416 3.510719 CCCATGTTTGTATTTTGGAGCG 58.489 45.455 0.00 0.00 0.00 5.03
455 499 6.642733 AGGAACTTTGGAGGATTAGAATCA 57.357 37.500 4.71 0.00 33.33 2.57
501 545 7.829725 TGGTTGTTTGATTCATAGGATTGAAG 58.170 34.615 0.00 0.00 38.90 3.02
502 546 7.669304 TGGTTGTTTGATTCATAGGATTGAAGA 59.331 33.333 0.00 0.00 38.90 2.87
504 548 9.912634 GTTGTTTGATTCATAGGATTGAAGAAA 57.087 29.630 0.00 0.00 38.90 2.52
505 549 9.912634 TTGTTTGATTCATAGGATTGAAGAAAC 57.087 29.630 12.86 12.86 38.90 2.78
535 612 7.141758 TCATACTTCCCAAGATTTCTAGCAT 57.858 36.000 0.00 0.00 0.00 3.79
536 613 7.220030 TCATACTTCCCAAGATTTCTAGCATC 58.780 38.462 0.00 0.00 0.00 3.91
542 619 4.133078 CCAAGATTTCTAGCATCCACTCC 58.867 47.826 0.00 0.00 0.00 3.85
553 630 2.553028 GCATCCACTCCAACCTCTTTGA 60.553 50.000 0.00 0.00 37.39 2.69
557 634 4.605183 TCCACTCCAACCTCTTTGAAAAA 58.395 39.130 0.00 0.00 37.39 1.94
624 776 6.096987 TCCTGTAGGACTAAGATGAACATGAC 59.903 42.308 0.00 0.00 39.78 3.06
630 782 6.070021 AGGACTAAGATGAACATGACATTCCA 60.070 38.462 17.94 3.57 0.00 3.53
635 787 5.512298 AGATGAACATGACATTCCAATCCA 58.488 37.500 0.00 0.00 0.00 3.41
636 788 5.359009 AGATGAACATGACATTCCAATCCAC 59.641 40.000 0.00 0.00 0.00 4.02
637 789 4.405548 TGAACATGACATTCCAATCCACA 58.594 39.130 0.00 0.00 0.00 4.17
650 818 0.536460 ATCCACAGTCCCGCGTTTTT 60.536 50.000 4.92 0.00 0.00 1.94
657 825 3.000727 CAGTCCCGCGTTTTTAGAATCT 58.999 45.455 4.92 0.00 0.00 2.40
658 826 3.000727 AGTCCCGCGTTTTTAGAATCTG 58.999 45.455 4.92 0.00 0.00 2.90
659 827 1.735571 TCCCGCGTTTTTAGAATCTGC 59.264 47.619 4.92 0.00 0.00 4.26
660 828 1.529010 CCCGCGTTTTTAGAATCTGCG 60.529 52.381 4.92 3.82 43.34 5.18
661 829 1.392168 CCGCGTTTTTAGAATCTGCGA 59.608 47.619 11.18 0.00 46.29 5.10
663 831 3.485216 CCGCGTTTTTAGAATCTGCGAAT 60.485 43.478 11.18 0.00 46.29 3.34
664 832 3.474961 CGCGTTTTTAGAATCTGCGAATG 59.525 43.478 4.69 0.00 46.29 2.67
668 836 5.734498 CGTTTTTAGAATCTGCGAATGGAAG 59.266 40.000 0.00 0.00 0.00 3.46
669 837 6.402118 CGTTTTTAGAATCTGCGAATGGAAGA 60.402 38.462 0.00 0.00 0.00 2.87
690 860 1.545582 ACGATTTCATTTGGGTGGCTG 59.454 47.619 0.00 0.00 0.00 4.85
805 976 1.009829 CGAAGGAATTGGAAGGCGAG 58.990 55.000 0.00 0.00 0.00 5.03
1062 1299 2.473664 CTTCTTCCACGGCGACTCGT 62.474 60.000 16.62 0.00 44.91 4.18
1275 1527 2.086094 CATACTCCATGTTGCACTGCA 58.914 47.619 0.00 0.00 36.47 4.41
1278 1530 0.956633 CTCCATGTTGCACTGCACTT 59.043 50.000 2.26 0.00 38.71 3.16
1279 1531 0.669619 TCCATGTTGCACTGCACTTG 59.330 50.000 2.26 7.63 38.71 3.16
1468 1744 0.376152 GTCTGAATGCATGCGACCTG 59.624 55.000 14.09 8.19 0.00 4.00
1499 1790 2.795175 AGTTAGACACACGACACCAG 57.205 50.000 0.00 0.00 0.00 4.00
1561 1853 3.567576 TTTTGTCATATGCCACAACCG 57.432 42.857 8.97 0.00 32.19 4.44
1568 1860 0.606944 TATGCCACAACCGGAACCAC 60.607 55.000 9.46 0.00 0.00 4.16
1717 2017 5.738370 CAAGAGGAACGTGAACTAAAACTG 58.262 41.667 0.00 0.00 0.00 3.16
1927 2237 0.693767 CCTCCTCTTCCCCTGAGCAT 60.694 60.000 0.00 0.00 0.00 3.79
1994 2337 5.337578 AGCTCAGTTATCCTCTTCAGAAC 57.662 43.478 0.00 0.00 0.00 3.01
2002 2345 8.740906 CAGTTATCCTCTTCAGAACAACTAGTA 58.259 37.037 0.00 0.00 0.00 1.82
2003 2346 8.741841 AGTTATCCTCTTCAGAACAACTAGTAC 58.258 37.037 0.00 0.00 0.00 2.73
2004 2347 8.741841 GTTATCCTCTTCAGAACAACTAGTACT 58.258 37.037 0.00 0.00 0.00 2.73
2009 2352 7.169982 CCTCTTCAGAACAACTAGTACTGTTTG 59.830 40.741 12.94 10.80 35.93 2.93
2145 3166 8.328758 TCTCAGCCTAATTAATTACATATGGGG 58.671 37.037 7.80 3.88 0.00 4.96
2182 3209 2.806745 GCTTTGCTTTTCCCCCAGTTTC 60.807 50.000 0.00 0.00 0.00 2.78
2269 3320 2.494073 GTTCGATGTGGAGGAGACTTCT 59.506 50.000 0.00 0.00 44.43 2.85
2355 3406 0.188587 TCCGAGCCCTCTGATGGTAT 59.811 55.000 0.89 0.00 0.00 2.73
2356 3407 0.605589 CCGAGCCCTCTGATGGTATC 59.394 60.000 0.89 0.00 0.00 2.24
2357 3408 1.626686 CGAGCCCTCTGATGGTATCT 58.373 55.000 0.89 0.00 0.00 1.98
2358 3409 1.543802 CGAGCCCTCTGATGGTATCTC 59.456 57.143 0.89 0.00 0.00 2.75
2359 3410 2.603021 GAGCCCTCTGATGGTATCTCA 58.397 52.381 0.89 0.00 0.00 3.27
2360 3411 3.172339 GAGCCCTCTGATGGTATCTCAT 58.828 50.000 0.89 0.00 0.00 2.90
2361 3412 3.582208 GAGCCCTCTGATGGTATCTCATT 59.418 47.826 0.89 0.00 0.00 2.57
2362 3413 3.979347 AGCCCTCTGATGGTATCTCATTT 59.021 43.478 0.89 0.00 0.00 2.32
2363 3414 4.414846 AGCCCTCTGATGGTATCTCATTTT 59.585 41.667 0.89 0.00 0.00 1.82
2364 3415 5.103771 AGCCCTCTGATGGTATCTCATTTTT 60.104 40.000 0.89 0.00 0.00 1.94
2365 3416 5.240403 GCCCTCTGATGGTATCTCATTTTTC 59.760 44.000 0.89 0.00 0.00 2.29
2366 3417 6.599445 CCCTCTGATGGTATCTCATTTTTCT 58.401 40.000 0.00 0.00 0.00 2.52
2367 3418 7.059156 CCCTCTGATGGTATCTCATTTTTCTT 58.941 38.462 0.00 0.00 0.00 2.52
2435 3487 1.693467 TTACCGATGCTAATAGCGCG 58.307 50.000 16.71 16.71 46.26 6.86
2437 3489 2.021584 CCGATGCTAATAGCGCGCA 61.022 57.895 35.10 19.76 46.26 6.09
2512 3564 0.659427 CACTCTGCCGCATGTTATGG 59.341 55.000 0.00 0.00 0.00 2.74
2531 3583 4.387026 TGGTCATGGAAGGTTCTCAAAT 57.613 40.909 0.00 0.00 0.00 2.32
2534 3586 3.445096 GTCATGGAAGGTTCTCAAATGGG 59.555 47.826 0.00 0.00 0.00 4.00
2537 3589 2.225017 TGGAAGGTTCTCAAATGGGGTC 60.225 50.000 0.00 0.00 0.00 4.46
2540 3592 0.322546 GGTTCTCAAATGGGGTCGCT 60.323 55.000 0.00 0.00 0.00 4.93
2561 3616 2.423446 CCTATCACCCTCAGCGCC 59.577 66.667 2.29 0.00 0.00 6.53
2605 3660 1.896694 CCTGCTCCAGGTCTGAGAC 59.103 63.158 3.47 3.47 45.82 3.36
2606 3661 0.614415 CCTGCTCCAGGTCTGAGACT 60.614 60.000 12.92 0.00 45.82 3.24
2617 3673 6.047870 CCAGGTCTGAGACTCTGATATTTTG 58.952 44.000 23.66 8.94 34.88 2.44
2621 3677 6.045955 GTCTGAGACTCTGATATTTTGGACC 58.954 44.000 14.33 0.00 0.00 4.46
2779 3847 4.708177 TGGAAGAGGTAGCATTGCTATTC 58.292 43.478 20.63 18.09 43.30 1.75
2783 3852 6.017523 GGAAGAGGTAGCATTGCTATTCTTTC 60.018 42.308 29.35 26.67 43.30 2.62
2789 3858 3.441572 AGCATTGCTATTCTTTCGCAGTT 59.558 39.130 10.00 0.00 36.99 3.16
2890 3971 1.673168 GGGACGAGGTAGTCACGTAT 58.327 55.000 0.00 0.00 42.62 3.06
2944 4025 3.409570 GAACTCGGGCTTTTCTTACCTT 58.590 45.455 0.00 0.00 0.00 3.50
2992 4073 5.217978 ACAGATGGACATGCACAATTTTT 57.782 34.783 0.00 0.00 0.00 1.94
2997 4078 3.133542 TGGACATGCACAATTTTTCCACA 59.866 39.130 0.00 0.00 0.00 4.17
2999 4080 4.152759 GGACATGCACAATTTTTCCACATG 59.847 41.667 0.00 0.00 39.38 3.21
3000 4081 3.499157 ACATGCACAATTTTTCCACATGC 59.501 39.130 0.00 0.00 37.52 4.06
3001 4082 3.472283 TGCACAATTTTTCCACATGCT 57.528 38.095 0.00 0.00 32.81 3.79
3002 4083 3.391965 TGCACAATTTTTCCACATGCTC 58.608 40.909 0.00 0.00 32.81 4.26
3004 4085 3.676646 GCACAATTTTTCCACATGCTCTC 59.323 43.478 0.00 0.00 0.00 3.20
3005 4086 3.916172 CACAATTTTTCCACATGCTCTCG 59.084 43.478 0.00 0.00 0.00 4.04
3006 4087 3.569701 ACAATTTTTCCACATGCTCTCGT 59.430 39.130 0.00 0.00 0.00 4.18
3007 4088 4.759693 ACAATTTTTCCACATGCTCTCGTA 59.240 37.500 0.00 0.00 0.00 3.43
3008 4089 5.415701 ACAATTTTTCCACATGCTCTCGTAT 59.584 36.000 0.00 0.00 0.00 3.06
3011 4092 7.624360 ATTTTTCCACATGCTCTCGTATTTA 57.376 32.000 0.00 0.00 0.00 1.40
3014 4095 7.624360 TTTCCACATGCTCTCGTATTTATTT 57.376 32.000 0.00 0.00 0.00 1.40
3440 5938 5.808366 ATCAGTCCAGTGTAGACTTTCAA 57.192 39.130 0.00 0.00 41.87 2.69
3554 6052 8.931385 AATTACGGATTCATCAAATTCTTTGG 57.069 30.769 0.19 0.00 40.98 3.28
3555 6053 5.329035 ACGGATTCATCAAATTCTTTGGG 57.671 39.130 0.19 0.00 40.98 4.12
3556 6054 5.016173 ACGGATTCATCAAATTCTTTGGGA 58.984 37.500 0.19 0.00 40.98 4.37
3557 6055 5.480073 ACGGATTCATCAAATTCTTTGGGAA 59.520 36.000 0.19 5.34 40.98 3.97
3558 6056 5.807011 CGGATTCATCAAATTCTTTGGGAAC 59.193 40.000 8.64 5.34 40.98 3.62
3559 6057 6.572119 CGGATTCATCAAATTCTTTGGGAACA 60.572 38.462 8.64 0.00 40.98 3.18
3560 6058 7.333323 GGATTCATCAAATTCTTTGGGAACAT 58.667 34.615 8.64 0.00 42.32 2.71
3615 6144 3.665173 GAGCAAATCTCAAACTAGGCG 57.335 47.619 0.00 0.00 41.51 5.52
3616 6145 3.262420 GAGCAAATCTCAAACTAGGCGA 58.738 45.455 0.00 0.00 41.51 5.54
3617 6146 3.265791 AGCAAATCTCAAACTAGGCGAG 58.734 45.455 0.00 0.00 0.00 5.03
3618 6147 2.223135 GCAAATCTCAAACTAGGCGAGC 60.223 50.000 0.00 0.00 0.00 5.03
3619 6148 3.265791 CAAATCTCAAACTAGGCGAGCT 58.734 45.455 0.00 0.00 0.00 4.09
3620 6149 2.593346 ATCTCAAACTAGGCGAGCTG 57.407 50.000 0.00 0.00 0.00 4.24
3621 6150 1.257743 TCTCAAACTAGGCGAGCTGT 58.742 50.000 0.00 0.00 0.00 4.40
3622 6151 2.443416 TCTCAAACTAGGCGAGCTGTA 58.557 47.619 0.00 0.00 0.00 2.74
3623 6152 3.024547 TCTCAAACTAGGCGAGCTGTAT 58.975 45.455 0.00 0.00 0.00 2.29
3624 6153 3.119291 CTCAAACTAGGCGAGCTGTATG 58.881 50.000 0.00 0.00 0.00 2.39
3625 6154 2.496070 TCAAACTAGGCGAGCTGTATGT 59.504 45.455 0.00 0.00 0.00 2.29
3626 6155 3.697542 TCAAACTAGGCGAGCTGTATGTA 59.302 43.478 0.00 0.00 0.00 2.29
3627 6156 4.341235 TCAAACTAGGCGAGCTGTATGTAT 59.659 41.667 0.00 0.00 0.00 2.29
3628 6157 4.506886 AACTAGGCGAGCTGTATGTATC 57.493 45.455 0.00 0.00 0.00 2.24
3629 6158 3.487372 ACTAGGCGAGCTGTATGTATCA 58.513 45.455 0.00 0.00 0.00 2.15
3630 6159 3.504134 ACTAGGCGAGCTGTATGTATCAG 59.496 47.826 0.00 0.00 36.18 2.90
3847 6414 3.005155 GCTTGGGGATCAATATTGTGCTC 59.995 47.826 14.97 8.52 34.45 4.26
3856 6423 6.094603 GGATCAATATTGTGCTCAAAGTCTGT 59.905 38.462 14.97 0.00 37.11 3.41
3909 6482 3.254166 ACTGCACAAAGGAACACATGATC 59.746 43.478 0.00 0.00 0.00 2.92
3951 6526 1.214367 ACCGTAAACTGTCACTTGCG 58.786 50.000 0.00 0.00 0.00 4.85
3973 6548 5.460419 GCGTGTTGTTCCAATGAAATAAACA 59.540 36.000 0.00 0.00 32.52 2.83
4027 6603 5.455056 AGAAGACTATCACGACAAACTGT 57.545 39.130 0.00 0.00 0.00 3.55
4028 6604 5.844004 AGAAGACTATCACGACAAACTGTT 58.156 37.500 0.00 0.00 0.00 3.16
4029 6605 5.921408 AGAAGACTATCACGACAAACTGTTC 59.079 40.000 0.00 0.00 0.00 3.18
4079 6655 0.812014 TTTGTCGCGGCAAAGTCTGA 60.812 50.000 32.98 12.17 33.91 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 3.904339 ACTCTCAGTGCTAAAAAGGAGGA 59.096 43.478 0.00 0.00 0.00 3.71
59 90 5.968387 AACTAAAGGCGATTAATGTCTCG 57.032 39.130 0.00 0.00 37.92 4.04
329 363 3.576982 CGTAATAGTAATCCCTCTGGCCA 59.423 47.826 4.71 4.71 0.00 5.36
359 393 4.173036 ACCGCTCCAAAATACAAACATG 57.827 40.909 0.00 0.00 0.00 3.21
360 394 5.250200 TCTACCGCTCCAAAATACAAACAT 58.750 37.500 0.00 0.00 0.00 2.71
361 395 4.643463 TCTACCGCTCCAAAATACAAACA 58.357 39.130 0.00 0.00 0.00 2.83
362 396 5.616488 TTCTACCGCTCCAAAATACAAAC 57.384 39.130 0.00 0.00 0.00 2.93
378 416 4.338400 ACTTCCTGTTGCAGTTTTTCTACC 59.662 41.667 0.00 0.00 0.00 3.18
428 466 6.500589 TCTAATCCTCCAAAGTTCCTATGG 57.499 41.667 0.00 0.00 35.49 2.74
469 513 9.083422 TCCTATGAATCAAACAACCAACATAAA 57.917 29.630 0.00 0.00 0.00 1.40
470 514 8.642935 TCCTATGAATCAAACAACCAACATAA 57.357 30.769 0.00 0.00 0.00 1.90
507 551 8.739972 GCTAGAAATCTTGGGAAGTATGAAAAA 58.260 33.333 0.00 0.00 0.00 1.94
508 552 7.888021 TGCTAGAAATCTTGGGAAGTATGAAAA 59.112 33.333 0.00 0.00 0.00 2.29
510 554 6.957631 TGCTAGAAATCTTGGGAAGTATGAA 58.042 36.000 0.00 0.00 0.00 2.57
511 555 6.560003 TGCTAGAAATCTTGGGAAGTATGA 57.440 37.500 0.00 0.00 0.00 2.15
512 556 6.429385 GGATGCTAGAAATCTTGGGAAGTATG 59.571 42.308 0.00 0.00 0.00 2.39
514 558 5.428457 TGGATGCTAGAAATCTTGGGAAGTA 59.572 40.000 0.00 0.00 0.00 2.24
515 559 4.228210 TGGATGCTAGAAATCTTGGGAAGT 59.772 41.667 0.00 0.00 0.00 3.01
516 560 4.578105 GTGGATGCTAGAAATCTTGGGAAG 59.422 45.833 0.00 0.00 0.00 3.46
519 563 4.133078 GAGTGGATGCTAGAAATCTTGGG 58.867 47.826 0.00 0.00 0.00 4.12
522 566 5.189180 GTTGGAGTGGATGCTAGAAATCTT 58.811 41.667 0.00 0.00 0.00 2.40
524 568 3.879892 GGTTGGAGTGGATGCTAGAAATC 59.120 47.826 0.00 0.00 0.00 2.17
525 569 3.525199 AGGTTGGAGTGGATGCTAGAAAT 59.475 43.478 0.00 0.00 0.00 2.17
526 570 2.912956 AGGTTGGAGTGGATGCTAGAAA 59.087 45.455 0.00 0.00 0.00 2.52
535 612 3.943671 TTTCAAAGAGGTTGGAGTGGA 57.056 42.857 0.00 0.00 37.85 4.02
557 634 6.638873 TGCATCATACGAAAAACAAACGATTT 59.361 30.769 0.00 0.00 0.00 2.17
562 639 7.332003 TGATTGCATCATACGAAAAACAAAC 57.668 32.000 0.00 0.00 33.59 2.93
566 643 7.332003 TGTTTGATTGCATCATACGAAAAAC 57.668 32.000 0.00 0.00 41.99 2.43
573 650 8.464770 TTTTAAGCTGTTTGATTGCATCATAC 57.535 30.769 10.50 10.50 40.30 2.39
609 761 7.283807 TGGATTGGAATGTCATGTTCATCTTAG 59.716 37.037 0.00 0.00 0.00 2.18
612 764 5.359009 GTGGATTGGAATGTCATGTTCATCT 59.641 40.000 0.00 0.00 0.00 2.90
619 771 3.379372 GGACTGTGGATTGGAATGTCATG 59.621 47.826 0.00 0.00 0.00 3.07
624 776 1.382522 CGGGACTGTGGATTGGAATG 58.617 55.000 0.00 0.00 0.00 2.67
630 782 0.536460 AAAACGCGGGACTGTGGATT 60.536 50.000 12.47 0.00 0.00 3.01
635 787 2.243602 TTCTAAAAACGCGGGACTGT 57.756 45.000 12.47 0.00 0.00 3.55
636 788 3.000727 AGATTCTAAAAACGCGGGACTG 58.999 45.455 12.47 0.00 0.00 3.51
637 789 3.000727 CAGATTCTAAAAACGCGGGACT 58.999 45.455 12.47 0.00 0.00 3.85
650 818 4.112634 CGTTCTTCCATTCGCAGATTCTA 58.887 43.478 0.00 0.00 35.04 2.10
657 825 3.070748 TGAAATCGTTCTTCCATTCGCA 58.929 40.909 0.00 0.00 34.60 5.10
658 826 3.740044 TGAAATCGTTCTTCCATTCGC 57.260 42.857 0.00 0.00 34.60 4.70
659 827 5.512788 CCAAATGAAATCGTTCTTCCATTCG 59.487 40.000 0.00 0.00 34.60 3.34
660 828 5.807011 CCCAAATGAAATCGTTCTTCCATTC 59.193 40.000 0.00 0.00 34.60 2.67
661 829 5.245977 ACCCAAATGAAATCGTTCTTCCATT 59.754 36.000 0.00 0.00 34.60 3.16
663 831 4.022416 CACCCAAATGAAATCGTTCTTCCA 60.022 41.667 0.00 0.00 34.60 3.53
664 832 4.485163 CACCCAAATGAAATCGTTCTTCC 58.515 43.478 0.00 0.00 34.60 3.46
668 836 2.231235 AGCCACCCAAATGAAATCGTTC 59.769 45.455 0.00 0.00 0.00 3.95
669 837 2.029110 CAGCCACCCAAATGAAATCGTT 60.029 45.455 0.00 0.00 0.00 3.85
787 957 1.383523 CCTCGCCTTCCAATTCCTTC 58.616 55.000 0.00 0.00 0.00 3.46
790 961 2.121538 GCCCTCGCCTTCCAATTCC 61.122 63.158 0.00 0.00 0.00 3.01
1062 1299 4.320870 GGTCGGTCCATCTTACTGAAAAA 58.679 43.478 0.00 0.00 34.13 1.94
1092 1329 3.495193 CTGCAAACCATCAACAAGATCG 58.505 45.455 0.00 0.00 33.72 3.69
1093 1330 3.841643 CCTGCAAACCATCAACAAGATC 58.158 45.455 0.00 0.00 33.72 2.75
1094 1331 2.028748 GCCTGCAAACCATCAACAAGAT 60.029 45.455 0.00 0.00 37.48 2.40
1095 1332 1.340889 GCCTGCAAACCATCAACAAGA 59.659 47.619 0.00 0.00 0.00 3.02
1275 1527 7.494298 AGACAAAAACAAACAAAACAGACAAGT 59.506 29.630 0.00 0.00 0.00 3.16
1278 1530 7.254590 CCAAGACAAAAACAAACAAAACAGACA 60.255 33.333 0.00 0.00 0.00 3.41
1279 1531 7.068955 CCAAGACAAAAACAAACAAAACAGAC 58.931 34.615 0.00 0.00 0.00 3.51
1499 1790 0.034337 TACGTGCCTTCACACTTCCC 59.966 55.000 0.00 0.00 43.28 3.97
1561 1853 5.585047 GGAATAATCAGTGTGTAGTGGTTCC 59.415 44.000 0.00 0.00 32.86 3.62
1568 1860 6.758886 GTGAGGAAGGAATAATCAGTGTGTAG 59.241 42.308 0.00 0.00 0.00 2.74
2004 2347 4.877251 ACGAGGCTGTTAAACTTACAAACA 59.123 37.500 0.00 0.00 0.00 2.83
2009 2352 2.803956 TGCACGAGGCTGTTAAACTTAC 59.196 45.455 0.00 0.00 45.15 2.34
2145 3166 1.318158 AAGCTGCAGCCAAGCCATAC 61.318 55.000 34.39 3.66 43.38 2.39
2182 3209 3.706594 TCTGTCCCAGAAACAGCCTATAG 59.293 47.826 0.00 0.00 43.09 1.31
2399 3451 8.936864 GCATCGGTAATTCTTACTATATTTGCT 58.063 33.333 0.00 0.00 36.39 3.91
2407 3459 7.966753 CGCTATTAGCATCGGTAATTCTTACTA 59.033 37.037 15.64 0.00 42.58 1.82
2409 3461 6.453922 GCGCTATTAGCATCGGTAATTCTTAC 60.454 42.308 15.64 0.00 42.58 2.34
2412 3464 3.927142 GCGCTATTAGCATCGGTAATTCT 59.073 43.478 15.64 0.00 42.58 2.40
2413 3465 3.241678 CGCGCTATTAGCATCGGTAATTC 60.242 47.826 15.64 0.00 42.58 2.17
2415 3467 2.259618 CGCGCTATTAGCATCGGTAAT 58.740 47.619 15.64 4.12 42.58 1.89
2416 3468 1.693467 CGCGCTATTAGCATCGGTAA 58.307 50.000 15.64 0.00 42.58 2.85
2420 3472 0.439985 ATTGCGCGCTATTAGCATCG 59.560 50.000 33.29 16.82 42.58 3.84
2421 3473 1.728971 AGATTGCGCGCTATTAGCATC 59.271 47.619 33.29 17.39 42.58 3.91
2435 3487 1.093159 CAAGCCTCACTGGAGATTGC 58.907 55.000 0.00 0.00 44.26 3.56
2437 3489 0.622665 CCCAAGCCTCACTGGAGATT 59.377 55.000 0.00 0.00 44.26 2.40
2480 3532 4.687215 GAGTGGAGCGCAGTGGCA 62.687 66.667 11.47 0.00 41.24 4.92
2512 3564 3.445096 CCCATTTGAGAACCTTCCATGAC 59.555 47.826 0.00 0.00 0.00 3.06
2537 3589 1.341531 CTGAGGGTGATAGGGTAAGCG 59.658 57.143 0.00 0.00 0.00 4.68
2540 3592 1.410004 CGCTGAGGGTGATAGGGTAA 58.590 55.000 0.00 0.00 0.00 2.85
2549 3604 1.452651 AATGATGGCGCTGAGGGTG 60.453 57.895 7.64 0.00 0.00 4.61
2561 3616 1.033746 AGCCGCTCAACCCAATGATG 61.034 55.000 0.00 0.00 0.00 3.07
2603 3658 7.040409 ACTGTTTTGGTCCAAAATATCAGAGTC 60.040 37.037 32.54 19.69 43.66 3.36
2605 3660 7.040478 TGACTGTTTTGGTCCAAAATATCAGAG 60.040 37.037 32.54 21.92 43.66 3.35
2606 3661 6.775142 TGACTGTTTTGGTCCAAAATATCAGA 59.225 34.615 32.54 19.45 43.66 3.27
2617 3673 6.325919 TCAATAACATGACTGTTTTGGTCC 57.674 37.500 0.00 0.00 43.05 4.46
2653 3719 9.864034 AAACAATATTCGAATATGAGCTTAACG 57.136 29.630 27.01 11.95 32.17 3.18
2779 3847 1.532437 TCAGCACATGAACTGCGAAAG 59.468 47.619 0.00 0.00 39.79 2.62
2789 3858 7.333323 TCAGAAGAGATTAATTCAGCACATGA 58.667 34.615 0.00 0.00 35.62 3.07
2890 3971 2.110967 CGACCTCTCGCCGTTCCTA 61.111 63.158 0.00 0.00 31.91 2.94
2944 4025 4.400120 ACCCGTTGTAGGCTTTGAAATTA 58.600 39.130 0.00 0.00 0.00 1.40
2992 4073 7.552687 AGAAAAATAAATACGAGAGCATGTGGA 59.447 33.333 0.00 0.00 0.00 4.02
3230 5724 9.297037 TCGTGATCTCTTCATATGATTAACCTA 57.703 33.333 6.17 0.00 36.54 3.08
3231 5725 8.085296 GTCGTGATCTCTTCATATGATTAACCT 58.915 37.037 6.17 0.00 36.54 3.50
3312 5806 7.123247 TGGGGTACAACTCTTACTAGTACAATC 59.877 40.741 0.91 0.00 37.40 2.67
3313 5807 6.955851 TGGGGTACAACTCTTACTAGTACAAT 59.044 38.462 0.91 0.00 37.40 2.71
3440 5938 6.818142 TGTTTTGATGATGATATGACGTGACT 59.182 34.615 0.00 0.00 0.00 3.41
3543 6041 7.361116 GCCACAAATATGTTCCCAAAGAATTTG 60.361 37.037 0.00 0.00 46.54 2.32
3544 6042 6.654582 GCCACAAATATGTTCCCAAAGAATTT 59.345 34.615 0.00 0.00 36.65 1.82
3545 6043 6.013466 AGCCACAAATATGTTCCCAAAGAATT 60.013 34.615 0.00 0.00 37.82 2.17
3546 6044 5.484998 AGCCACAAATATGTTCCCAAAGAAT 59.515 36.000 0.00 0.00 37.82 2.40
3547 6045 4.837860 AGCCACAAATATGTTCCCAAAGAA 59.162 37.500 0.00 0.00 37.82 2.52
3548 6046 4.415596 AGCCACAAATATGTTCCCAAAGA 58.584 39.130 0.00 0.00 37.82 2.52
3549 6047 4.806640 AGCCACAAATATGTTCCCAAAG 57.193 40.909 0.00 0.00 37.82 2.77
3550 6048 6.865834 AATAGCCACAAATATGTTCCCAAA 57.134 33.333 0.00 0.00 37.82 3.28
3551 6049 6.351711 CCAAATAGCCACAAATATGTTCCCAA 60.352 38.462 0.00 0.00 37.82 4.12
3552 6050 5.128499 CCAAATAGCCACAAATATGTTCCCA 59.872 40.000 0.00 0.00 37.82 4.37
3553 6051 5.362430 TCCAAATAGCCACAAATATGTTCCC 59.638 40.000 0.00 0.00 37.82 3.97
3554 6052 6.463995 TCCAAATAGCCACAAATATGTTCC 57.536 37.500 0.00 0.00 37.82 3.62
3555 6053 7.771183 TCTTCCAAATAGCCACAAATATGTTC 58.229 34.615 0.00 0.00 37.82 3.18
3556 6054 7.716799 TCTTCCAAATAGCCACAAATATGTT 57.283 32.000 0.00 0.00 37.82 2.71
3557 6055 7.902920 ATCTTCCAAATAGCCACAAATATGT 57.097 32.000 0.00 0.00 41.61 2.29
3604 6133 2.496070 ACATACAGCTCGCCTAGTTTGA 59.504 45.455 0.00 0.00 0.00 2.69
3605 6134 2.893637 ACATACAGCTCGCCTAGTTTG 58.106 47.619 0.00 0.00 0.00 2.93
3606 6135 4.341235 TGATACATACAGCTCGCCTAGTTT 59.659 41.667 0.00 0.00 0.00 2.66
3607 6136 3.889538 TGATACATACAGCTCGCCTAGTT 59.110 43.478 0.00 0.00 0.00 2.24
3608 6137 3.487372 TGATACATACAGCTCGCCTAGT 58.513 45.455 0.00 0.00 0.00 2.57
3609 6138 4.090138 CTGATACATACAGCTCGCCTAG 57.910 50.000 0.00 0.00 0.00 3.02
3618 6147 8.734386 TGAGTATAGTGATGCTGATACATACAG 58.266 37.037 0.00 0.00 38.27 2.74
3619 6148 8.635765 TGAGTATAGTGATGCTGATACATACA 57.364 34.615 0.00 0.00 0.00 2.29
3620 6149 9.566530 CTTGAGTATAGTGATGCTGATACATAC 57.433 37.037 0.00 0.00 0.00 2.39
3621 6150 9.301897 ACTTGAGTATAGTGATGCTGATACATA 57.698 33.333 0.00 0.00 0.00 2.29
3622 6151 8.087136 CACTTGAGTATAGTGATGCTGATACAT 58.913 37.037 0.00 0.00 44.52 2.29
3623 6152 7.428826 CACTTGAGTATAGTGATGCTGATACA 58.571 38.462 0.00 0.00 44.52 2.29
3624 6153 6.865726 CCACTTGAGTATAGTGATGCTGATAC 59.134 42.308 4.66 0.00 44.52 2.24
3625 6154 6.777580 TCCACTTGAGTATAGTGATGCTGATA 59.222 38.462 4.66 0.00 44.52 2.15
3626 6155 5.600069 TCCACTTGAGTATAGTGATGCTGAT 59.400 40.000 4.66 0.00 44.52 2.90
3627 6156 4.956075 TCCACTTGAGTATAGTGATGCTGA 59.044 41.667 4.66 0.00 44.52 4.26
3628 6157 5.268118 TCCACTTGAGTATAGTGATGCTG 57.732 43.478 4.66 0.00 44.52 4.41
3629 6158 5.528043 CTCCACTTGAGTATAGTGATGCT 57.472 43.478 4.66 0.00 44.52 3.79
3847 6414 6.259608 GGACATCATCTTCCATACAGACTTTG 59.740 42.308 0.00 0.00 0.00 2.77
3856 6423 3.829026 CCTCGAGGACATCATCTTCCATA 59.171 47.826 28.21 0.00 37.39 2.74
3909 6482 7.307396 CGGTAAATAGGATGTGTTAGCATTCTG 60.307 40.741 0.00 0.00 35.59 3.02
3973 6548 0.470766 TACACCTGCTCCACGGTTTT 59.529 50.000 0.00 0.00 0.00 2.43
4027 6603 5.687780 ACGTCCCCTTTCTTAAAAGAAGAA 58.312 37.500 5.38 0.00 45.01 2.52
4028 6604 5.300411 ACGTCCCCTTTCTTAAAAGAAGA 57.700 39.130 5.38 0.00 45.01 2.87
4029 6605 5.529800 TGAACGTCCCCTTTCTTAAAAGAAG 59.470 40.000 5.38 1.50 45.01 2.85


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

AutoCloner maintained by Alex Coulton.