Multiple sequence alignment - TraesCS7B01G170200

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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 TraesCS7B01G170200 chr7B 100.000 3430 0 0 1 3430 241759181 241755752 0.000000e+00 6335.0
1 TraesCS7B01G170200 chr7B 93.878 49 2 1 3096 3144 428494106 428494059 4.750000e-09 73.1
2 TraesCS7B01G170200 chr7A 93.010 2203 90 18 745 2909 285170735 285172911 0.000000e+00 3157.0
3 TraesCS7B01G170200 chr7A 93.000 300 17 2 3132 3430 285173537 285173833 5.260000e-118 435.0
4 TraesCS7B01G170200 chr7A 97.006 167 5 0 2930 3096 285173385 285173551 7.250000e-72 281.0
5 TraesCS7B01G170200 chr7A 90.588 85 2 2 1 79 285168404 285168488 1.300000e-19 108.0
6 TraesCS7B01G170200 chr7D 93.666 1421 54 13 745 2148 262285397 262286798 0.000000e+00 2093.0
7 TraesCS7B01G170200 chr7D 93.968 746 31 6 2168 2909 262286964 262287699 0.000000e+00 1116.0
8 TraesCS7B01G170200 chr7D 94.792 288 13 2 3132 3418 262293623 262293909 6.750000e-122 448.0
9 TraesCS7B01G170200 chr7D 97.605 167 4 0 2930 3096 262293471 262293637 1.560000e-73 287.0
10 TraesCS7B01G170200 chr6A 90.161 620 57 4 80 699 609455675 609456290 0.000000e+00 804.0
11 TraesCS7B01G170200 chr6A 97.826 46 1 0 3096 3141 317048327 317048372 2.840000e-11 80.5
12 TraesCS7B01G170200 chr5D 90.492 610 57 1 92 701 196402704 196403312 0.000000e+00 804.0
13 TraesCS7B01G170200 chr5D 83.816 587 89 6 81 665 451887420 451888002 1.390000e-153 553.0
14 TraesCS7B01G170200 chr5D 76.898 619 118 16 1250 1854 424033307 424033914 9.180000e-86 327.0
15 TraesCS7B01G170200 chr5D 72.755 646 130 31 1251 1855 520909996 520910636 3.520000e-40 176.0
16 TraesCS7B01G170200 chr5D 71.987 614 129 29 1278 1856 423973281 423973886 1.280000e-29 141.0
17 TraesCS7B01G170200 chr5D 82.301 113 12 5 1483 1588 429577781 429577892 1.310000e-14 91.6
18 TraesCS7B01G170200 chr2D 83.762 622 89 9 80 699 442158583 442157972 2.290000e-161 579.0
19 TraesCS7B01G170200 chr2D 83.280 622 99 5 81 701 414994520 414993903 4.970000e-158 568.0
20 TraesCS7B01G170200 chr2D 97.778 45 0 1 3096 3140 29184019 29184062 3.670000e-10 76.8
21 TraesCS7B01G170200 chr2D 93.878 49 1 2 3096 3144 445856533 445856487 4.750000e-09 73.1
22 TraesCS7B01G170200 chr3A 84.286 560 76 4 142 701 382945257 382945804 1.400000e-148 536.0
23 TraesCS7B01G170200 chr3A 96.000 50 1 1 3096 3145 28161517 28161565 2.840000e-11 80.5
24 TraesCS7B01G170200 chr3A 94.444 36 1 1 2905 2939 480431014 480430979 2.000000e-03 54.7
25 TraesCS7B01G170200 chr6B 80.960 625 102 14 80 701 505795972 505796582 2.390000e-131 479.0
26 TraesCS7B01G170200 chr6B 97.778 45 1 0 3096 3140 20856284 20856328 1.020000e-10 78.7
27 TraesCS7B01G170200 chr6B 92.308 52 2 2 3096 3147 345206582 345206533 4.750000e-09 73.1
28 TraesCS7B01G170200 chr6B 92.857 42 2 1 39 79 566279831 566279790 3.700000e-05 60.2
29 TraesCS7B01G170200 chr3B 80.750 613 104 12 80 688 795908726 795908124 1.860000e-127 466.0
30 TraesCS7B01G170200 chr3B 100.000 28 0 0 2909 2936 427161852 427161879 6.000000e-03 52.8
31 TraesCS7B01G170200 chr5B 77.199 614 121 13 1250 1855 512212668 512213270 1.180000e-89 340.0
32 TraesCS7B01G170200 chr5B 79.444 180 37 0 1676 1855 656926277 656926456 9.990000e-26 128.0
33 TraesCS7B01G170200 chr5B 79.433 141 23 3 1454 1588 518810330 518810470 1.010000e-15 95.3
34 TraesCS7B01G170200 chr5A 76.835 613 125 11 1250 1855 537626135 537626737 2.550000e-86 329.0
35 TraesCS7B01G170200 chr5A 79.006 181 37 1 1676 1855 649441931 649442111 4.650000e-24 122.0
36 TraesCS7B01G170200 chr5A 78.710 155 27 3 1440 1588 545530950 545531104 7.830000e-17 99.0
37 TraesCS7B01G170200 chr4A 76.615 325 67 8 1278 1596 68126039 68125718 1.640000e-38 171.0
38 TraesCS7B01G170200 chr1A 78.710 155 27 1 1440 1588 20889376 20889222 7.830000e-17 99.0
39 TraesCS7B01G170200 chr1B 78.431 153 27 1 1442 1588 28024807 28024655 1.010000e-15 95.3
40 TraesCS7B01G170200 chr1B 86.567 67 2 7 3096 3161 329933841 329933901 2.210000e-07 67.6
41 TraesCS7B01G170200 chr1B 97.143 35 1 0 2905 2939 31176573 31176539 3.700000e-05 60.2
42 TraesCS7B01G170200 chr3D 94.000 50 1 2 3096 3144 582096312 582096264 1.320000e-09 75.0
43 TraesCS7B01G170200 chr4B 100.000 30 0 0 2907 2936 585637073 585637102 4.780000e-04 56.5


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 TraesCS7B01G170200 chr7B 241755752 241759181 3429 True 6335.00 6335 100.000 1 3430 1 chr7B.!!$R1 3429
1 TraesCS7B01G170200 chr7A 285168404 285173833 5429 False 995.25 3157 93.401 1 3430 4 chr7A.!!$F1 3429
2 TraesCS7B01G170200 chr7D 262285397 262287699 2302 False 1604.50 2093 93.817 745 2909 2 chr7D.!!$F1 2164
3 TraesCS7B01G170200 chr6A 609455675 609456290 615 False 804.00 804 90.161 80 699 1 chr6A.!!$F2 619
4 TraesCS7B01G170200 chr5D 196402704 196403312 608 False 804.00 804 90.492 92 701 1 chr5D.!!$F1 609
5 TraesCS7B01G170200 chr5D 451887420 451888002 582 False 553.00 553 83.816 81 665 1 chr5D.!!$F5 584
6 TraesCS7B01G170200 chr5D 424033307 424033914 607 False 327.00 327 76.898 1250 1854 1 chr5D.!!$F3 604
7 TraesCS7B01G170200 chr2D 442157972 442158583 611 True 579.00 579 83.762 80 699 1 chr2D.!!$R2 619
8 TraesCS7B01G170200 chr2D 414993903 414994520 617 True 568.00 568 83.280 81 701 1 chr2D.!!$R1 620
9 TraesCS7B01G170200 chr3A 382945257 382945804 547 False 536.00 536 84.286 142 701 1 chr3A.!!$F2 559
10 TraesCS7B01G170200 chr6B 505795972 505796582 610 False 479.00 479 80.960 80 701 1 chr6B.!!$F2 621
11 TraesCS7B01G170200 chr3B 795908124 795908726 602 True 466.00 466 80.750 80 688 1 chr3B.!!$R1 608
12 TraesCS7B01G170200 chr5B 512212668 512213270 602 False 340.00 340 77.199 1250 1855 1 chr5B.!!$F1 605
13 TraesCS7B01G170200 chr5A 537626135 537626737 602 False 329.00 329 76.835 1250 1855 1 chr5A.!!$F1 605

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
924 3158 0.036577 CAGTCACCAAGCTCCTCCTG 60.037 60.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2922 5352 0.033109 ATAAGAAAGGTGCTGCCCCC 60.033 55.0 0.0 0.0 38.26 5.4 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
25 26 5.118510 GCACCGAATCAAACCATTAGTTTTG 59.881 40.000 0.00 0.00 46.79 2.44
103 110 2.806608 TTTCGAGAGTACGCCAAAGT 57.193 45.000 0.00 0.00 0.00 2.66
108 115 2.223203 CGAGAGTACGCCAAAGTCGTAT 60.223 50.000 0.00 0.00 43.14 3.06
109 116 3.106672 GAGAGTACGCCAAAGTCGTATG 58.893 50.000 0.00 0.00 43.14 2.39
117 124 5.624292 ACGCCAAAGTCGTATGTTAATTTC 58.376 37.500 0.00 0.00 38.52 2.17
213 221 0.611062 AGCACACCCTACACGCTAGA 60.611 55.000 0.00 0.00 0.00 2.43
278 286 2.359975 CCCGCCAACCTTCACTCC 60.360 66.667 0.00 0.00 0.00 3.85
282 290 1.065418 CCGCCAACCTTCACTCCTTAT 60.065 52.381 0.00 0.00 0.00 1.73
335 343 0.320374 CCGTCTTCTGCTGGTTGGTA 59.680 55.000 0.00 0.00 0.00 3.25
365 373 2.026014 CTGGCGTTGCGTTGCTTT 59.974 55.556 0.00 0.00 0.00 3.51
366 374 1.160946 TCTGGCGTTGCGTTGCTTTA 61.161 50.000 0.00 0.00 0.00 1.85
401 409 1.018752 CCGCAATGATCACCGTGTCA 61.019 55.000 0.00 2.68 0.00 3.58
408 416 1.271325 TGATCACCGTGTCAAAGCCAT 60.271 47.619 0.00 0.00 0.00 4.40
551 559 2.606717 CGTAGACGCACTGTACAAGA 57.393 50.000 0.00 0.00 0.00 3.02
569 577 1.673920 AGAAATGTGTTCCGCGTTGTT 59.326 42.857 4.92 0.00 0.00 2.83
579 587 0.179215 CCGCGTTGTTCTCATCTTGC 60.179 55.000 4.92 0.00 0.00 4.01
616 624 2.610859 ACGGGGCATCCTGAAGGT 60.611 61.111 0.00 0.00 42.08 3.50
659 667 1.401552 CGTCCAAATCCGATGTTGCAT 59.598 47.619 0.00 0.00 0.00 3.96
667 675 0.244450 CCGATGTTGCATTGCCAACT 59.756 50.000 18.26 9.05 44.12 3.16
694 702 9.321562 ACACGAAGATTTTACACTTTAGAAGAA 57.678 29.630 0.00 0.00 0.00 2.52
701 709 6.607735 TTTACACTTTAGAAGAACCCAACG 57.392 37.500 0.00 0.00 0.00 4.10
702 710 4.411256 ACACTTTAGAAGAACCCAACGA 57.589 40.909 0.00 0.00 0.00 3.85
703 711 4.377897 ACACTTTAGAAGAACCCAACGAG 58.622 43.478 0.00 0.00 0.00 4.18
704 712 4.141779 ACACTTTAGAAGAACCCAACGAGT 60.142 41.667 0.00 0.00 0.00 4.18
705 713 4.814771 CACTTTAGAAGAACCCAACGAGTT 59.185 41.667 0.00 0.00 0.00 3.01
706 714 5.987347 CACTTTAGAAGAACCCAACGAGTTA 59.013 40.000 0.00 0.00 0.00 2.24
707 715 6.649557 CACTTTAGAAGAACCCAACGAGTTAT 59.350 38.462 0.00 0.00 0.00 1.89
708 716 7.172703 CACTTTAGAAGAACCCAACGAGTTATT 59.827 37.037 0.00 0.00 31.68 1.40
709 717 7.172703 ACTTTAGAAGAACCCAACGAGTTATTG 59.827 37.037 0.00 0.00 29.30 1.90
710 718 3.751698 AGAAGAACCCAACGAGTTATTGC 59.248 43.478 0.00 0.00 29.30 3.56
711 719 3.134574 AGAACCCAACGAGTTATTGCA 57.865 42.857 0.00 0.00 0.00 4.08
712 720 2.812011 AGAACCCAACGAGTTATTGCAC 59.188 45.455 0.00 0.00 0.00 4.57
713 721 1.153353 ACCCAACGAGTTATTGCACG 58.847 50.000 0.00 0.00 0.00 5.34
733 741 5.432157 CACGTCTAAGTGACACAATCAAAC 58.568 41.667 8.59 0.00 45.60 2.93
734 742 4.510340 ACGTCTAAGTGACACAATCAAACC 59.490 41.667 8.59 0.00 45.60 3.27
735 743 4.376008 CGTCTAAGTGACACAATCAAACCG 60.376 45.833 8.59 0.00 45.60 4.44
736 744 4.748102 GTCTAAGTGACACAATCAAACCGA 59.252 41.667 8.59 0.00 44.73 4.69
738 746 4.552166 AAGTGACACAATCAAACCGAAG 57.448 40.909 8.59 0.00 39.72 3.79
740 748 2.226330 TGACACAATCAAACCGAAGGG 58.774 47.619 0.00 0.00 44.72 3.95
816 3042 2.443016 CTCCACTCCTCTCCCCCG 60.443 72.222 0.00 0.00 0.00 5.73
829 3063 4.807039 CCCCGTCTACAACCGCCG 62.807 72.222 0.00 0.00 0.00 6.46
833 3067 4.729856 GTCTACAACCGCCGCCGT 62.730 66.667 0.00 0.00 0.00 5.68
834 3068 4.424566 TCTACAACCGCCGCCGTC 62.425 66.667 0.00 0.00 0.00 4.79
835 3069 4.430765 CTACAACCGCCGCCGTCT 62.431 66.667 0.00 0.00 0.00 4.18
847 3081 3.068881 CCGTCTCCACCACACCAT 58.931 61.111 0.00 0.00 0.00 3.55
854 3088 2.349376 CACCACACCATACGGCCA 59.651 61.111 2.24 0.00 34.57 5.36
924 3158 0.036577 CAGTCACCAAGCTCCTCCTG 60.037 60.000 0.00 0.00 0.00 3.86
925 3159 1.197430 AGTCACCAAGCTCCTCCTGG 61.197 60.000 0.00 0.00 0.00 4.45
966 3204 1.438710 CGGCTTCACTTGTTTCGCG 60.439 57.895 0.00 0.00 0.00 5.87
1048 3290 4.570663 CGGCATCGGTCGTCCTCC 62.571 72.222 0.00 0.00 37.35 4.30
1049 3291 3.148279 GGCATCGGTCGTCCTCCT 61.148 66.667 0.00 0.00 0.00 3.69
1090 3332 1.001597 GTATCGATCCACCCGACAGTC 60.002 57.143 0.00 0.00 38.97 3.51
1097 3339 1.219124 CACCCGACAGTCCATCCAG 59.781 63.158 0.00 0.00 0.00 3.86
1121 3363 2.159627 GTGCTTGTGGAAGTGGTATTCG 59.840 50.000 0.00 0.00 0.00 3.34
1151 3393 2.125147 CCTGATTTGGAGGCGCGA 60.125 61.111 12.10 0.00 0.00 5.87
1176 3418 1.654220 GCTGCGAGCTTGGTTTTCA 59.346 52.632 2.37 0.00 38.45 2.69
1241 3485 3.065306 CACAGGGCCGGTAGTGAA 58.935 61.111 9.55 0.00 33.99 3.18
1380 3624 1.813859 CTCAATCTACGGGCCGACA 59.186 57.895 35.78 18.76 0.00 4.35
1635 3888 3.000819 CCCGACACTGGGTGCCTA 61.001 66.667 0.00 0.00 44.76 3.93
1638 3891 1.671742 CGACACTGGGTGCCTAGTT 59.328 57.895 4.42 0.00 36.98 2.24
1743 3996 4.978863 TACTGCTGCAACGGCGCA 62.979 61.111 10.83 0.00 45.35 6.09
1800 4053 1.669115 GCAGCTCTTCAAGTCGGCA 60.669 57.895 0.00 0.00 0.00 5.69
1806 4059 1.675310 CTTCAAGTCGGCATGCCCA 60.675 57.895 30.79 16.91 0.00 5.36
1863 4116 0.466189 CCTTCACCTGCAACCACACT 60.466 55.000 0.00 0.00 0.00 3.55
1922 4178 6.183360 CCTTACAGGTACCTTCCTCTGAATAC 60.183 46.154 13.15 0.00 35.37 1.89
1923 4179 4.031611 ACAGGTACCTTCCTCTGAATACC 58.968 47.826 13.15 0.00 36.78 2.73
1940 4196 6.283694 TGAATACCTTCTGATGCTATGACAC 58.716 40.000 0.00 0.00 32.29 3.67
2014 4278 6.095860 TCAACAATGATATTTTCTCTGGGCTG 59.904 38.462 0.00 0.00 0.00 4.85
2071 4342 3.244249 ACGGGGAAAGAAGAGAAAGTGAG 60.244 47.826 0.00 0.00 0.00 3.51
2158 4429 1.593166 CCATCCCCATCCCCACCTTT 61.593 60.000 0.00 0.00 0.00 3.11
2160 4431 1.645402 ATCCCCATCCCCACCTTTCG 61.645 60.000 0.00 0.00 0.00 3.46
2161 4432 2.440247 CCCATCCCCACCTTTCGC 60.440 66.667 0.00 0.00 0.00 4.70
2162 4433 2.440247 CCATCCCCACCTTTCGCC 60.440 66.667 0.00 0.00 0.00 5.54
2164 4435 1.000896 CATCCCCACCTTTCGCCTT 60.001 57.895 0.00 0.00 0.00 4.35
2165 4436 0.611896 CATCCCCACCTTTCGCCTTT 60.612 55.000 0.00 0.00 0.00 3.11
2361 4788 2.034221 GAGGTTTCCAAGCCGCCT 59.966 61.111 0.00 0.00 34.07 5.52
2434 4861 3.071479 GTTTCAGCTTGTTATGACCGGA 58.929 45.455 9.46 0.00 0.00 5.14
2435 4862 2.672961 TCAGCTTGTTATGACCGGAG 57.327 50.000 9.46 0.00 0.00 4.63
2447 4874 4.821589 CCGGAGAAGGCAGGCGAC 62.822 72.222 0.00 0.00 0.00 5.19
2463 4890 2.032620 GCGACTCTTCATCCCTAGGAA 58.967 52.381 11.48 0.00 34.34 3.36
2468 4895 5.011533 CGACTCTTCATCCCTAGGAATGATT 59.988 44.000 12.01 0.00 34.34 2.57
2470 4897 6.836242 ACTCTTCATCCCTAGGAATGATTTC 58.164 40.000 12.01 0.00 34.34 2.17
2504 4934 4.844349 TTAGGATCAAAAGAGGACCAGG 57.156 45.455 0.00 0.00 0.00 4.45
2581 5011 0.317160 AGAACATGACGCGTCCTCAA 59.683 50.000 34.34 17.91 0.00 3.02
2777 5207 7.816995 GGAAGGCTGTAAGATCTGAATATACTG 59.183 40.741 0.00 0.12 34.07 2.74
2897 5327 8.756864 GTTCGCATAGGAAAACATAAACAAAAA 58.243 29.630 0.00 0.00 0.00 1.94
2919 5349 7.710676 AAAATGTAACATTAGGGCATGTACA 57.289 32.000 0.00 0.00 36.30 2.90
2920 5350 7.710676 AAATGTAACATTAGGGCATGTACAA 57.289 32.000 0.00 0.00 36.30 2.41
2921 5351 6.693315 ATGTAACATTAGGGCATGTACAAC 57.307 37.500 0.00 0.00 36.30 3.32
2922 5352 4.632251 TGTAACATTAGGGCATGTACAACG 59.368 41.667 0.00 0.00 36.30 4.10
2923 5353 2.639065 ACATTAGGGCATGTACAACGG 58.361 47.619 0.00 0.00 35.51 4.44
2924 5354 1.946768 CATTAGGGCATGTACAACGGG 59.053 52.381 0.00 0.00 0.00 5.28
2926 5356 1.628238 TAGGGCATGTACAACGGGGG 61.628 60.000 0.00 0.00 0.00 5.40
2927 5357 3.138128 GGCATGTACAACGGGGGC 61.138 66.667 0.00 0.00 0.00 5.80
2928 5358 2.360600 GCATGTACAACGGGGGCA 60.361 61.111 0.00 0.00 0.00 5.36
2929 5359 2.406616 GCATGTACAACGGGGGCAG 61.407 63.158 0.00 0.00 0.00 4.85
2930 5360 2.045340 ATGTACAACGGGGGCAGC 60.045 61.111 0.00 0.00 0.00 5.25
2931 5361 2.901281 ATGTACAACGGGGGCAGCA 61.901 57.895 0.00 0.00 0.00 4.41
2932 5362 3.053896 GTACAACGGGGGCAGCAC 61.054 66.667 0.00 0.00 0.00 4.40
2937 5820 4.660938 ACGGGGGCAGCACCTTTC 62.661 66.667 15.19 0.00 39.10 2.62
2940 5823 1.382629 GGGGGCAGCACCTTTCTTA 59.617 57.895 15.19 0.00 39.10 2.10
2946 5829 3.367395 GGGCAGCACCTTTCTTATTTCAC 60.367 47.826 0.00 0.00 39.10 3.18
3096 5979 5.828328 GCTTAATTAAATACACAGAGGGCCT 59.172 40.000 5.25 5.25 0.00 5.19
3097 5980 6.321435 GCTTAATTAAATACACAGAGGGCCTT 59.679 38.462 7.89 0.00 0.00 4.35
3098 5981 7.147897 GCTTAATTAAATACACAGAGGGCCTTT 60.148 37.037 7.89 0.00 0.00 3.11
3099 5982 9.403583 CTTAATTAAATACACAGAGGGCCTTTA 57.596 33.333 7.89 0.00 0.00 1.85
3100 5983 9.930158 TTAATTAAATACACAGAGGGCCTTTAT 57.070 29.630 7.89 0.00 0.00 1.40
3109 5992 7.168905 ACACAGAGGGCCTTTATATATAAAGC 58.831 38.462 28.73 24.07 44.85 3.51
3110 5993 6.313905 CACAGAGGGCCTTTATATATAAAGCG 59.686 42.308 28.73 23.60 44.85 4.68
3111 5994 5.817816 CAGAGGGCCTTTATATATAAAGCGG 59.182 44.000 28.73 21.72 44.85 5.52
3112 5995 5.104485 AGAGGGCCTTTATATATAAAGCGGG 60.104 44.000 28.73 21.19 44.85 6.13
3113 5996 4.079958 AGGGCCTTTATATATAAAGCGGGG 60.080 45.833 28.73 20.93 44.85 5.73
3114 5997 3.630769 GGCCTTTATATATAAAGCGGGGC 59.369 47.826 28.73 26.57 44.85 5.80
3115 5998 3.311596 GCCTTTATATATAAAGCGGGGCG 59.688 47.826 28.73 19.18 44.85 6.13
3116 5999 4.761975 CCTTTATATATAAAGCGGGGCGA 58.238 43.478 28.73 4.28 44.85 5.54
3117 6000 5.180271 CCTTTATATATAAAGCGGGGCGAA 58.820 41.667 28.73 3.68 44.85 4.70
3118 6001 5.644636 CCTTTATATATAAAGCGGGGCGAAA 59.355 40.000 28.73 4.75 44.85 3.46
3119 6002 6.183360 CCTTTATATATAAAGCGGGGCGAAAG 60.183 42.308 28.73 14.22 44.85 2.62
3136 6019 5.285798 CGAAAGCCTTTTTCGGTAATACA 57.714 39.130 12.72 0.00 45.17 2.29
3137 6020 5.321516 CGAAAGCCTTTTTCGGTAATACAG 58.678 41.667 12.72 0.00 45.17 2.74
3138 6021 5.121142 CGAAAGCCTTTTTCGGTAATACAGA 59.879 40.000 12.72 0.00 45.17 3.41
3139 6022 6.496338 AAAGCCTTTTTCGGTAATACAGAG 57.504 37.500 0.00 0.00 0.00 3.35
3140 6023 5.416271 AGCCTTTTTCGGTAATACAGAGA 57.584 39.130 0.00 0.00 0.00 3.10
3141 6024 5.420409 AGCCTTTTTCGGTAATACAGAGAG 58.580 41.667 0.00 0.00 0.00 3.20
3142 6025 4.571176 GCCTTTTTCGGTAATACAGAGAGG 59.429 45.833 11.96 11.96 0.00 3.69
3143 6026 5.116882 CCTTTTTCGGTAATACAGAGAGGG 58.883 45.833 9.84 3.71 0.00 4.30
3144 6027 5.338137 CCTTTTTCGGTAATACAGAGAGGGT 60.338 44.000 9.84 0.00 0.00 4.34
3145 6028 4.996788 TTTCGGTAATACAGAGAGGGTC 57.003 45.455 0.00 0.00 0.00 4.46
3146 6029 3.657398 TCGGTAATACAGAGAGGGTCA 57.343 47.619 0.00 0.00 0.00 4.02
3185 6068 3.653344 GGGTGAAACTTCCATCTTTTGC 58.347 45.455 0.00 0.00 36.74 3.68
3203 6086 4.325028 TTGCATTGCAACATCAAACTCT 57.675 36.364 19.77 0.00 43.99 3.24
3215 6098 8.454106 GCAACATCAAACTCTCACATATAACTT 58.546 33.333 0.00 0.00 0.00 2.66
3241 6125 4.814147 TGTGTGCACAAATTTCTGTCAAA 58.186 34.783 23.59 0.00 38.56 2.69
3289 6173 2.472816 CAACAGTTCAAACATGCCCAC 58.527 47.619 0.00 0.00 0.00 4.61
3304 6188 5.303078 ACATGCCCACACAGTAAAACAATTA 59.697 36.000 0.00 0.00 0.00 1.40
3369 6253 3.113191 TGAAATGGGGGTGCAACATAT 57.887 42.857 3.06 0.00 39.98 1.78
3407 6291 5.910637 AACGACGCAACAAACTAGAATAA 57.089 34.783 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 6.910536 CATCTAGATGTGTCCTAAACAACC 57.089 41.667 22.42 0.00 40.31 3.77
117 124 5.188434 TGACCCATGCTCTTCTTTTCTATG 58.812 41.667 0.00 0.00 0.00 2.23
124 131 5.324409 TGTAAATTGACCCATGCTCTTCTT 58.676 37.500 0.00 0.00 0.00 2.52
213 221 5.238583 GTTTTGTGAGAGTGTAGGCATAGT 58.761 41.667 0.00 0.00 0.00 2.12
335 343 1.079819 CGCCAGAGTGTTCCATCGT 60.080 57.895 0.00 0.00 0.00 3.73
379 387 3.940640 CGGTGATCATTGCGGCCG 61.941 66.667 24.05 24.05 0.00 6.13
408 416 2.091885 ACTTCAGGAAGGGTTTCAAGCA 60.092 45.455 13.19 0.00 42.53 3.91
551 559 1.673920 AGAACAACGCGGAACACATTT 59.326 42.857 12.47 0.00 0.00 2.32
569 577 0.671472 CACGTGCCTGCAAGATGAGA 60.671 55.000 11.95 0.00 34.07 3.27
579 587 1.067846 TCTACTTGCTACACGTGCCTG 60.068 52.381 17.22 7.07 0.00 4.85
616 624 1.348696 TGACAGAAGAGCAAGGCATGA 59.651 47.619 0.00 0.00 0.00 3.07
659 667 5.527951 TGTAAAATCTTCGTGTAGTTGGCAA 59.472 36.000 0.00 0.00 0.00 4.52
667 675 9.970395 TCTTCTAAAGTGTAAAATCTTCGTGTA 57.030 29.630 0.00 0.00 0.00 2.90
694 702 1.153353 CGTGCAATAACTCGTTGGGT 58.847 50.000 0.00 0.00 0.00 4.51
701 709 5.437383 GTCACTTAGACGTGCAATAACTC 57.563 43.478 0.00 0.00 37.53 3.01
816 3042 4.729856 ACGGCGGCGGTTGTAGAC 62.730 66.667 35.05 0.00 0.00 2.59
829 3063 1.895020 TATGGTGTGGTGGAGACGGC 61.895 60.000 0.00 0.00 0.00 5.68
830 3064 0.108329 GTATGGTGTGGTGGAGACGG 60.108 60.000 0.00 0.00 0.00 4.79
831 3065 0.457853 CGTATGGTGTGGTGGAGACG 60.458 60.000 0.00 0.00 0.00 4.18
832 3066 0.108329 CCGTATGGTGTGGTGGAGAC 60.108 60.000 0.00 0.00 0.00 3.36
833 3067 1.895020 GCCGTATGGTGTGGTGGAGA 61.895 60.000 2.17 0.00 37.67 3.71
834 3068 1.449601 GCCGTATGGTGTGGTGGAG 60.450 63.158 2.17 0.00 37.67 3.86
835 3069 2.666207 GCCGTATGGTGTGGTGGA 59.334 61.111 2.17 0.00 37.67 4.02
847 3081 1.681076 GGAGGAAAAGGTGGCCGTA 59.319 57.895 0.00 0.00 0.00 4.02
854 3088 1.079336 GCTACGCGGAGGAAAAGGT 60.079 57.895 22.20 0.00 0.00 3.50
924 3158 1.576421 CGCTGTTGCTTTCCTGTCC 59.424 57.895 0.00 0.00 36.97 4.02
925 3159 1.081840 GCGCTGTTGCTTTCCTGTC 60.082 57.895 0.00 0.00 36.97 3.51
958 3196 0.438445 CTCGAATTGAGCGCGAAACA 59.562 50.000 12.10 2.75 38.03 2.83
1039 3278 0.812549 GTGAGAAGGAGGAGGACGAC 59.187 60.000 0.00 0.00 0.00 4.34
1047 3289 2.260822 TGGAAGAAGGTGAGAAGGAGG 58.739 52.381 0.00 0.00 0.00 4.30
1048 3290 3.307339 CCTTGGAAGAAGGTGAGAAGGAG 60.307 52.174 0.00 0.00 31.85 3.69
1049 3291 2.639839 CCTTGGAAGAAGGTGAGAAGGA 59.360 50.000 0.00 0.00 31.85 3.36
1090 3332 1.278985 TCCACAAGCACTACTGGATGG 59.721 52.381 0.00 0.00 0.00 3.51
1097 3339 2.256117 ACCACTTCCACAAGCACTAC 57.744 50.000 0.00 0.00 32.09 2.73
1176 3418 2.549754 CGAACACTCAGCTCACCAAATT 59.450 45.455 0.00 0.00 0.00 1.82
1626 3879 0.472925 TGAGGTCAACTAGGCACCCA 60.473 55.000 0.00 0.00 0.00 4.51
1638 3891 2.049156 CAGCGCTCGTTGAGGTCA 60.049 61.111 7.13 0.00 0.00 4.02
1725 3978 3.499737 GCGCCGTTGCAGCAGTAT 61.500 61.111 0.00 0.00 37.11 2.12
1743 3996 0.901580 ACGTGTCAGGGTTCCCGTAT 60.902 55.000 1.91 0.00 0.00 3.06
1800 4053 0.995024 AGCTGTAGGACTTTGGGCAT 59.005 50.000 0.00 0.00 0.00 4.40
1863 4116 4.523083 GGCAGAAGGTAATGGTGTAATCA 58.477 43.478 0.00 0.00 0.00 2.57
1922 4178 4.036852 TCGTAGTGTCATAGCATCAGAAGG 59.963 45.833 0.00 0.00 0.00 3.46
1923 4179 5.175090 TCGTAGTGTCATAGCATCAGAAG 57.825 43.478 0.00 0.00 0.00 2.85
1940 4196 9.737427 AACACTATGATTTCAACTAGATCGTAG 57.263 33.333 12.70 12.70 41.69 3.51
1987 4251 6.501781 CCCAGAGAAAATATCATTGTTGAGC 58.498 40.000 0.00 0.00 34.73 4.26
2071 4342 2.489722 CCTTGCTCCAAGCCTAACTTTC 59.510 50.000 0.00 0.00 41.51 2.62
2158 4429 1.904287 AGGCATTGTAACAAAGGCGA 58.096 45.000 0.00 0.00 37.71 5.54
2160 4431 3.988819 TCAAAGGCATTGTAACAAAGGC 58.011 40.909 2.06 0.00 40.11 4.35
2161 4432 5.010012 AGACTCAAAGGCATTGTAACAAAGG 59.990 40.000 2.06 0.00 40.11 3.11
2162 4433 6.016777 AGAGACTCAAAGGCATTGTAACAAAG 60.017 38.462 5.02 0.00 40.11 2.77
2164 4435 5.376625 AGAGACTCAAAGGCATTGTAACAA 58.623 37.500 5.02 0.00 40.11 2.83
2165 4436 4.973168 AGAGACTCAAAGGCATTGTAACA 58.027 39.130 5.02 0.00 40.11 2.41
2361 4788 1.068753 CCGCCACAACAATTGCCAA 59.931 52.632 5.05 0.00 0.00 4.52
2371 4798 3.276091 CAAGCACGACCGCCACAA 61.276 61.111 0.00 0.00 0.00 3.33
2434 4861 1.188219 TGAAGAGTCGCCTGCCTTCT 61.188 55.000 0.00 0.00 36.78 2.85
2435 4862 0.107945 ATGAAGAGTCGCCTGCCTTC 60.108 55.000 0.00 0.00 36.48 3.46
2500 4930 1.118838 CTCTTCCTCTAGTGCCCTGG 58.881 60.000 0.00 0.00 0.00 4.45
2504 4934 1.133407 CACGTCTCTTCCTCTAGTGCC 59.867 57.143 0.00 0.00 0.00 5.01
2581 5011 6.062095 ACTAGAACAACTACAATTGCCAACT 58.938 36.000 5.05 0.00 32.47 3.16
2691 5121 1.281287 AGTGCTGCACTGATCAGGATT 59.719 47.619 32.54 6.26 43.63 3.01
2897 5327 6.183360 CGTTGTACATGCCCTAATGTTACATT 60.183 38.462 15.22 15.22 41.09 2.71
2909 5339 2.439519 CCCCCGTTGTACATGCCC 60.440 66.667 0.00 0.00 0.00 5.36
2911 5341 2.360600 TGCCCCCGTTGTACATGC 60.361 61.111 0.00 0.00 0.00 4.06
2912 5342 2.406616 GCTGCCCCCGTTGTACATG 61.407 63.158 0.00 0.00 0.00 3.21
2913 5343 2.045340 GCTGCCCCCGTTGTACAT 60.045 61.111 0.00 0.00 0.00 2.29
2914 5344 3.561241 TGCTGCCCCCGTTGTACA 61.561 61.111 0.00 0.00 0.00 2.90
2916 5346 4.338710 GGTGCTGCCCCCGTTGTA 62.339 66.667 0.00 0.00 0.00 2.41
2919 5349 4.218686 AAAGGTGCTGCCCCCGTT 62.219 61.111 0.00 0.00 38.26 4.44
2920 5350 4.660938 GAAAGGTGCTGCCCCCGT 62.661 66.667 0.00 0.00 38.26 5.28
2921 5351 2.478335 TAAGAAAGGTGCTGCCCCCG 62.478 60.000 0.00 0.00 38.26 5.73
2922 5352 0.033109 ATAAGAAAGGTGCTGCCCCC 60.033 55.000 0.00 0.00 38.26 5.40
2923 5353 1.852633 AATAAGAAAGGTGCTGCCCC 58.147 50.000 0.00 0.00 38.26 5.80
2924 5354 2.825532 TGAAATAAGAAAGGTGCTGCCC 59.174 45.455 0.00 0.00 38.26 5.36
2926 5356 3.670627 CGGTGAAATAAGAAAGGTGCTGC 60.671 47.826 0.00 0.00 0.00 5.25
2927 5357 3.119849 CCGGTGAAATAAGAAAGGTGCTG 60.120 47.826 0.00 0.00 0.00 4.41
2928 5358 3.081804 CCGGTGAAATAAGAAAGGTGCT 58.918 45.455 0.00 0.00 0.00 4.40
2929 5359 2.415491 GCCGGTGAAATAAGAAAGGTGC 60.415 50.000 1.90 0.00 0.00 5.01
2930 5360 3.081804 AGCCGGTGAAATAAGAAAGGTG 58.918 45.455 1.90 0.00 0.00 4.00
2931 5361 3.434940 AGCCGGTGAAATAAGAAAGGT 57.565 42.857 1.90 0.00 0.00 3.50
2932 5362 5.733373 GCATTAGCCGGTGAAATAAGAAAGG 60.733 44.000 1.90 0.00 33.58 3.11
2937 5820 3.003689 CCAGCATTAGCCGGTGAAATAAG 59.996 47.826 1.90 0.00 43.56 1.73
2940 5823 1.392589 CCAGCATTAGCCGGTGAAAT 58.607 50.000 1.90 0.00 43.56 2.17
2946 5829 0.031178 GATTTGCCAGCATTAGCCGG 59.969 55.000 0.00 0.00 43.56 6.13
3091 5974 4.204799 CCCCGCTTTATATATAAAGGCCC 58.795 47.826 32.05 20.88 45.78 5.80
3096 5979 5.122711 GCTTTCGCCCCGCTTTATATATAAA 59.877 40.000 15.47 15.47 0.00 1.40
3097 5980 4.632688 GCTTTCGCCCCGCTTTATATATAA 59.367 41.667 0.81 0.81 0.00 0.98
3098 5981 4.186159 GCTTTCGCCCCGCTTTATATATA 58.814 43.478 0.00 0.00 0.00 0.86
3099 5982 3.007635 GCTTTCGCCCCGCTTTATATAT 58.992 45.455 0.00 0.00 0.00 0.86
3100 5983 2.419667 GCTTTCGCCCCGCTTTATATA 58.580 47.619 0.00 0.00 0.00 0.86
3101 5984 1.235724 GCTTTCGCCCCGCTTTATAT 58.764 50.000 0.00 0.00 0.00 0.86
3102 5985 2.697819 GCTTTCGCCCCGCTTTATA 58.302 52.632 0.00 0.00 0.00 0.98
3103 5986 3.509659 GCTTTCGCCCCGCTTTAT 58.490 55.556 0.00 0.00 0.00 1.40
3113 5996 2.691984 TTACCGAAAAAGGCTTTCGC 57.308 45.000 13.76 7.41 46.89 4.70
3115 5998 6.370718 TCTCTGTATTACCGAAAAAGGCTTTC 59.629 38.462 13.76 0.41 33.69 2.62
3116 5999 6.235664 TCTCTGTATTACCGAAAAAGGCTTT 58.764 36.000 6.68 6.68 33.69 3.51
3117 6000 5.801380 TCTCTGTATTACCGAAAAAGGCTT 58.199 37.500 0.00 0.00 33.69 4.35
3118 6001 5.416271 TCTCTGTATTACCGAAAAAGGCT 57.584 39.130 0.00 0.00 33.69 4.58
3119 6002 4.571176 CCTCTCTGTATTACCGAAAAAGGC 59.429 45.833 0.00 0.00 33.69 4.35
3120 6003 5.116882 CCCTCTCTGTATTACCGAAAAAGG 58.883 45.833 0.00 0.00 37.30 3.11
3121 6004 5.731591 ACCCTCTCTGTATTACCGAAAAAG 58.268 41.667 0.00 0.00 0.00 2.27
3122 6005 5.246656 TGACCCTCTCTGTATTACCGAAAAA 59.753 40.000 0.00 0.00 0.00 1.94
3123 6006 4.773674 TGACCCTCTCTGTATTACCGAAAA 59.226 41.667 0.00 0.00 0.00 2.29
3124 6007 4.346730 TGACCCTCTCTGTATTACCGAAA 58.653 43.478 0.00 0.00 0.00 3.46
3125 6008 3.972133 TGACCCTCTCTGTATTACCGAA 58.028 45.455 0.00 0.00 0.00 4.30
3126 6009 3.657398 TGACCCTCTCTGTATTACCGA 57.343 47.619 0.00 0.00 0.00 4.69
3127 6010 4.621991 CATTGACCCTCTCTGTATTACCG 58.378 47.826 0.00 0.00 0.00 4.02
3128 6011 4.101741 AGCATTGACCCTCTCTGTATTACC 59.898 45.833 0.00 0.00 0.00 2.85
3129 6012 5.283457 AGCATTGACCCTCTCTGTATTAC 57.717 43.478 0.00 0.00 0.00 1.89
3130 6013 6.042093 CCTTAGCATTGACCCTCTCTGTATTA 59.958 42.308 0.00 0.00 0.00 0.98
3131 6014 5.163258 CCTTAGCATTGACCCTCTCTGTATT 60.163 44.000 0.00 0.00 0.00 1.89
3132 6015 4.346418 CCTTAGCATTGACCCTCTCTGTAT 59.654 45.833 0.00 0.00 0.00 2.29
3133 6016 3.706594 CCTTAGCATTGACCCTCTCTGTA 59.293 47.826 0.00 0.00 0.00 2.74
3134 6017 2.503356 CCTTAGCATTGACCCTCTCTGT 59.497 50.000 0.00 0.00 0.00 3.41
3135 6018 2.744494 GCCTTAGCATTGACCCTCTCTG 60.744 54.545 0.00 0.00 39.53 3.35
3136 6019 1.488393 GCCTTAGCATTGACCCTCTCT 59.512 52.381 0.00 0.00 39.53 3.10
3137 6020 1.210478 TGCCTTAGCATTGACCCTCTC 59.790 52.381 0.00 0.00 46.52 3.20
3138 6021 1.289160 TGCCTTAGCATTGACCCTCT 58.711 50.000 0.00 0.00 46.52 3.69
3139 6022 3.882131 TGCCTTAGCATTGACCCTC 57.118 52.632 0.00 0.00 46.52 4.30
3185 6068 4.862350 TGTGAGAGTTTGATGTTGCAATG 58.138 39.130 0.59 0.00 0.00 2.82
3269 6153 2.159128 TGTGGGCATGTTTGAACTGTTG 60.159 45.455 0.00 0.00 0.00 3.33
3270 6154 2.106566 TGTGGGCATGTTTGAACTGTT 58.893 42.857 0.00 0.00 0.00 3.16
3271 6155 1.408702 GTGTGGGCATGTTTGAACTGT 59.591 47.619 0.00 0.00 0.00 3.55
3289 6173 5.219633 GTGTGCCCTAATTGTTTTACTGTG 58.780 41.667 0.00 0.00 0.00 3.66
3304 6188 5.700402 AATAGAGATTTAGTGTGTGCCCT 57.300 39.130 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.