Multiple sequence alignment - TraesCS3D01G389800

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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 TraesCS3D01G389800 chr3D 100.000 5865 0 0 1 5865 505047229 505053093 0.000000e+00 10831.0
1 TraesCS3D01G389800 chr3D 89.803 814 64 8 5068 5865 92738613 92737803 0.000000e+00 1026.0
2 TraesCS3D01G389800 chr3D 91.064 470 40 2 5068 5536 246610001 246609533 8.290000e-178 634.0
3 TraesCS3D01G389800 chr3D 89.256 484 48 4 5051 5533 417497210 417497690 2.340000e-168 603.0
4 TraesCS3D01G389800 chr3D 89.787 470 45 3 5065 5533 18505832 18506299 3.020000e-167 599.0
5 TraesCS3D01G389800 chr3D 94.444 342 17 2 5525 5865 18506333 18506673 5.210000e-145 525.0
6 TraesCS3D01G389800 chr3D 93.842 341 16 2 5525 5865 417497724 417498059 5.240000e-140 508.0
7 TraesCS3D01G389800 chr3D 87.500 88 6 5 3587 3671 100046113 100046198 4.840000e-16 97.1
8 TraesCS3D01G389800 chr3D 84.615 91 9 5 3587 3674 557294194 557294106 1.050000e-12 86.1
9 TraesCS3D01G389800 chr3A 93.187 2818 90 44 448 3216 643181838 643184602 0.000000e+00 4047.0
10 TraesCS3D01G389800 chr3A 94.947 1880 39 16 3215 5073 643184707 643186551 0.000000e+00 2894.0
11 TraesCS3D01G389800 chr3A 91.341 358 29 2 5509 5865 102128649 102128293 6.830000e-134 488.0
12 TraesCS3D01G389800 chr3A 82.955 88 10 5 3587 3671 734217760 734217845 2.270000e-09 75.0
13 TraesCS3D01G389800 chr3B 93.436 1813 95 12 1837 3630 666783758 666785565 0.000000e+00 2667.0
14 TraesCS3D01G389800 chr3B 95.050 1414 43 13 3673 5077 666785567 666786962 0.000000e+00 2198.0
15 TraesCS3D01G389800 chr3B 87.533 1131 75 35 725 1836 666782631 666783714 0.000000e+00 1247.0
16 TraesCS3D01G389800 chr3B 92.623 732 38 9 1 728 666780360 666781079 0.000000e+00 1038.0
17 TraesCS3D01G389800 chr3B 86.667 90 7 5 3587 3673 127291955 127291868 1.740000e-15 95.3
18 TraesCS3D01G389800 chr7D 90.541 814 60 7 5068 5865 110772719 110771907 0.000000e+00 1061.0
19 TraesCS3D01G389800 chr7D 86.175 434 54 5 3 432 442571235 442570804 1.150000e-126 464.0
20 TraesCS3D01G389800 chr7D 87.500 88 6 5 3587 3671 476515232 476515317 4.840000e-16 97.1
21 TraesCS3D01G389800 chr6D 90.024 822 64 8 5059 5865 35617470 35618288 0.000000e+00 1048.0
22 TraesCS3D01G389800 chr6D 86.406 434 53 5 3 432 242974437 242974868 2.470000e-128 470.0
23 TraesCS3D01G389800 chr1A 89.693 815 69 5 5066 5865 542771298 542770484 0.000000e+00 1026.0
24 TraesCS3D01G389800 chr1A 85.227 88 8 5 3587 3671 138607838 138607923 1.050000e-12 86.1
25 TraesCS3D01G389800 chr5A 86.951 820 87 11 5065 5865 441174906 441174088 0.000000e+00 904.0
26 TraesCS3D01G389800 chr5A 89.552 469 48 1 5068 5536 380265795 380265328 1.410000e-165 593.0
27 TraesCS3D01G389800 chr5A 86.667 435 50 7 3 432 246284960 246284529 5.320000e-130 475.0
28 TraesCS3D01G389800 chr5D 91.033 513 31 2 5368 5865 249101996 249101484 0.000000e+00 678.0
29 TraesCS3D01G389800 chr1D 89.384 471 49 1 5066 5536 453181151 453180682 5.060000e-165 592.0
30 TraesCS3D01G389800 chr1D 95.614 342 11 3 5525 5865 453180651 453180313 4.000000e-151 545.0
31 TraesCS3D01G389800 chr1D 88.158 76 7 2 3587 3661 256999938 256999864 8.100000e-14 89.8
32 TraesCS3D01G389800 chr7A 93.575 358 21 2 5509 5865 628915638 628915282 3.110000e-147 532.0
33 TraesCS3D01G389800 chr7A 86.866 434 51 5 3 432 384319614 384320045 1.140000e-131 481.0
34 TraesCS3D01G389800 chr2D 86.636 434 52 5 3 432 217867463 217867032 5.320000e-130 475.0
35 TraesCS3D01G389800 chr2D 86.175 434 54 5 3 432 237146890 237147321 1.150000e-126 464.0
36 TraesCS3D01G389800 chr2D 85.714 98 9 5 3577 3671 621300781 621300876 1.350000e-16 99.0
37 TraesCS3D01G389800 chr6A 86.175 434 54 5 3 432 46160040 46160471 1.150000e-126 464.0
38 TraesCS3D01G389800 chr2A 86.175 434 54 5 3 432 408796477 408796046 1.150000e-126 464.0
39 TraesCS3D01G389800 chr4A 87.500 88 6 5 3587 3671 400405139 400405224 4.840000e-16 97.1
40 TraesCS3D01G389800 chr5B 89.610 77 5 3 3597 3671 568409692 568409767 1.740000e-15 95.3
41 TraesCS3D01G389800 chr5B 88.710 62 4 3 3612 3671 408970908 408970848 8.150000e-09 73.1
42 TraesCS3D01G389800 chr1B 88.732 71 4 4 3604 3671 655251880 655251949 3.770000e-12 84.2
43 TraesCS3D01G389800 chr1B 88.889 63 4 3 3587 3647 655251769 655251830 2.270000e-09 75.0
44 TraesCS3D01G389800 chr1B 93.478 46 1 2 3611 3654 655251832 655251877 3.790000e-07 67.6


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 TraesCS3D01G389800 chr3D 505047229 505053093 5864 False 10831.0 10831 100.0000 1 5865 1 chr3D.!!$F2 5864
1 TraesCS3D01G389800 chr3D 92737803 92738613 810 True 1026.0 1026 89.8030 5068 5865 1 chr3D.!!$R1 797
2 TraesCS3D01G389800 chr3D 18505832 18506673 841 False 562.0 599 92.1155 5065 5865 2 chr3D.!!$F3 800
3 TraesCS3D01G389800 chr3D 417497210 417498059 849 False 555.5 603 91.5490 5051 5865 2 chr3D.!!$F4 814
4 TraesCS3D01G389800 chr3A 643181838 643186551 4713 False 3470.5 4047 94.0670 448 5073 2 chr3A.!!$F2 4625
5 TraesCS3D01G389800 chr3B 666780360 666786962 6602 False 1787.5 2667 92.1605 1 5077 4 chr3B.!!$F1 5076
6 TraesCS3D01G389800 chr7D 110771907 110772719 812 True 1061.0 1061 90.5410 5068 5865 1 chr7D.!!$R1 797
7 TraesCS3D01G389800 chr6D 35617470 35618288 818 False 1048.0 1048 90.0240 5059 5865 1 chr6D.!!$F1 806
8 TraesCS3D01G389800 chr1A 542770484 542771298 814 True 1026.0 1026 89.6930 5066 5865 1 chr1A.!!$R1 799
9 TraesCS3D01G389800 chr5A 441174088 441174906 818 True 904.0 904 86.9510 5065 5865 1 chr5A.!!$R3 800
10 TraesCS3D01G389800 chr5D 249101484 249101996 512 True 678.0 678 91.0330 5368 5865 1 chr5D.!!$R1 497
11 TraesCS3D01G389800 chr1D 453180313 453181151 838 True 568.5 592 92.4990 5066 5865 2 chr1D.!!$R2 799

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
779 2369 0.038892 ACCGTAGACGCGTGAAATGT 60.039 50.000 20.70 5.35 38.18 2.71 F
1415 3039 0.033642 TTGTTGTCGGCGATGGTGTA 59.966 50.000 14.79 0.00 0.00 2.90 F
1567 3193 0.179004 TGGTTGCAGAAATCCCGTGT 60.179 50.000 0.00 0.00 0.00 4.49 F
2376 4063 0.100861 GGGAGAGTGTACTACGCTGC 59.899 60.000 7.01 10.36 44.66 5.25 F
3661 5458 3.008594 ACCACGACCAGAATTATGGAACA 59.991 43.478 25.55 0.00 43.57 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1993 3667 0.662619 CAAACTCAGCGGCTTGACAA 59.337 50.000 0.0 0.0 0.00 3.18 R
2376 4063 5.673514 CCATTTTTGTCCCATTATCAAGGG 58.326 41.667 0.0 0.0 46.90 3.95 R
3424 5221 4.762251 ACAGAAGAGAAATAACAACAGGCC 59.238 41.667 0.0 0.0 0.00 5.19 R
3722 5519 3.838903 GGAGTACCCCCATATTAGAGTGG 59.161 52.174 0.0 0.0 35.22 4.00 R
5202 7027 0.101939 CTAGTTCGGGGGTAGCGTTC 59.898 60.000 0.0 0.0 0.00 3.95 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
21 22 1.007038 GTGTGTCCGAGGCGTTACA 60.007 57.895 0.00 0.00 0.00 2.41
78 79 3.705934 TTTGCGGGTCAGGTGCACA 62.706 57.895 20.43 0.00 38.55 4.57
142 143 0.822944 TGCCACATGTGTTGGACTGG 60.823 55.000 23.79 7.68 0.00 4.00
147 148 0.884259 CATGTGTTGGACTGGACGCA 60.884 55.000 0.00 0.00 40.17 5.24
173 175 6.427853 CAGACATGTACCAAGAAGAATGTTCA 59.572 38.462 0.00 0.00 0.00 3.18
188 190 1.375396 TTCATGTGGGCCGACGAAG 60.375 57.895 13.67 5.61 0.00 3.79
207 209 4.556104 CGAAGACGTCAGTTCCTTTGAGTA 60.556 45.833 19.50 0.00 34.56 2.59
208 210 4.506886 AGACGTCAGTTCCTTTGAGTAG 57.493 45.455 19.50 0.00 0.00 2.57
224 226 7.015682 CCTTTGAGTAGGGATGTATGTGATAGT 59.984 40.741 0.00 0.00 0.00 2.12
228 230 6.013379 AGTAGGGATGTATGTGATAGTCTGG 58.987 44.000 0.00 0.00 0.00 3.86
235 237 8.531982 GGATGTATGTGATAGTCTGGCTTAATA 58.468 37.037 0.00 0.00 0.00 0.98
238 240 5.808366 TGTGATAGTCTGGCTTAATAGGG 57.192 43.478 0.00 0.00 0.00 3.53
292 294 1.398390 CCTTTTTCGAGAGCCCATTCG 59.602 52.381 0.00 0.00 38.13 3.34
351 353 4.646492 GCAATTTTAGGATGGGTGACTGAT 59.354 41.667 0.00 0.00 0.00 2.90
362 364 3.390967 TGGGTGACTGATTGAGAAGTTGA 59.609 43.478 0.00 0.00 0.00 3.18
364 366 5.006386 GGGTGACTGATTGAGAAGTTGATT 58.994 41.667 0.00 0.00 0.00 2.57
366 368 5.123027 GGTGACTGATTGAGAAGTTGATTCC 59.877 44.000 0.00 0.00 38.84 3.01
367 369 5.702670 GTGACTGATTGAGAAGTTGATTCCA 59.297 40.000 0.00 0.00 38.84 3.53
368 370 5.936372 TGACTGATTGAGAAGTTGATTCCAG 59.064 40.000 0.00 0.00 38.84 3.86
369 371 6.119240 ACTGATTGAGAAGTTGATTCCAGA 57.881 37.500 0.00 0.00 38.84 3.86
370 372 6.719301 ACTGATTGAGAAGTTGATTCCAGAT 58.281 36.000 0.00 0.00 38.84 2.90
371 373 7.855375 ACTGATTGAGAAGTTGATTCCAGATA 58.145 34.615 0.00 0.00 38.84 1.98
372 374 8.492782 ACTGATTGAGAAGTTGATTCCAGATAT 58.507 33.333 0.00 0.00 38.84 1.63
438 440 2.759535 GTGGGACCAGTCTAGGAGTAAC 59.240 54.545 0.00 0.00 0.00 2.50
444 446 2.159226 CCAGTCTAGGAGTAACGGCAAG 60.159 54.545 0.00 0.00 0.00 4.01
463 465 5.049828 GCAAGTAAGGAAACACATTTTGCT 58.950 37.500 0.00 0.00 36.42 3.91
627 659 8.937634 AGCAGAATTGAAAAATAGCTAAATGG 57.062 30.769 0.00 0.00 0.00 3.16
716 749 1.178276 AGATGCTTCTCGGTCTCGTT 58.822 50.000 0.00 0.00 37.69 3.85
779 2369 0.038892 ACCGTAGACGCGTGAAATGT 60.039 50.000 20.70 5.35 38.18 2.71
787 2394 2.569354 GCGTGAAATGTGCCCCCAA 61.569 57.895 0.00 0.00 0.00 4.12
789 2396 0.173255 CGTGAAATGTGCCCCCAATC 59.827 55.000 0.00 0.00 0.00 2.67
790 2397 1.560505 GTGAAATGTGCCCCCAATCT 58.439 50.000 0.00 0.00 0.00 2.40
791 2398 2.733956 GTGAAATGTGCCCCCAATCTA 58.266 47.619 0.00 0.00 0.00 1.98
792 2399 2.689983 GTGAAATGTGCCCCCAATCTAG 59.310 50.000 0.00 0.00 0.00 2.43
793 2400 2.580322 TGAAATGTGCCCCCAATCTAGA 59.420 45.455 0.00 0.00 0.00 2.43
794 2401 3.011144 TGAAATGTGCCCCCAATCTAGAA 59.989 43.478 0.00 0.00 0.00 2.10
795 2402 3.756082 AATGTGCCCCCAATCTAGAAA 57.244 42.857 0.00 0.00 0.00 2.52
796 2403 2.507407 TGTGCCCCCAATCTAGAAAC 57.493 50.000 0.00 0.00 0.00 2.78
797 2404 1.992557 TGTGCCCCCAATCTAGAAACT 59.007 47.619 0.00 0.00 0.00 2.66
798 2405 2.290896 TGTGCCCCCAATCTAGAAACTG 60.291 50.000 0.00 0.00 0.00 3.16
799 2406 1.340991 TGCCCCCAATCTAGAAACTGC 60.341 52.381 0.00 0.00 0.00 4.40
802 2409 2.239654 CCCCCAATCTAGAAACTGCTCA 59.760 50.000 0.00 0.00 0.00 4.26
805 2412 3.937706 CCCAATCTAGAAACTGCTCACTG 59.062 47.826 0.00 0.00 0.00 3.66
806 2413 3.937706 CCAATCTAGAAACTGCTCACTGG 59.062 47.826 0.00 0.00 0.00 4.00
808 2415 1.970640 TCTAGAAACTGCTCACTGGCA 59.029 47.619 0.00 0.00 40.15 4.92
809 2416 2.568956 TCTAGAAACTGCTCACTGGCAT 59.431 45.455 0.00 0.00 41.63 4.40
810 2417 1.531423 AGAAACTGCTCACTGGCATG 58.469 50.000 0.00 0.00 41.63 4.06
811 2418 1.202855 AGAAACTGCTCACTGGCATGT 60.203 47.619 0.00 0.00 41.63 3.21
812 2419 2.038952 AGAAACTGCTCACTGGCATGTA 59.961 45.455 0.00 0.00 41.63 2.29
813 2420 1.813513 AACTGCTCACTGGCATGTAC 58.186 50.000 0.00 0.00 41.63 2.90
814 2421 0.979665 ACTGCTCACTGGCATGTACT 59.020 50.000 0.00 0.00 41.63 2.73
815 2422 2.179427 ACTGCTCACTGGCATGTACTA 58.821 47.619 0.00 0.00 41.63 1.82
816 2423 2.167281 ACTGCTCACTGGCATGTACTAG 59.833 50.000 0.00 0.00 41.63 2.57
817 2424 1.134699 TGCTCACTGGCATGTACTAGC 60.135 52.381 0.00 0.00 37.29 3.42
818 2425 1.134699 GCTCACTGGCATGTACTAGCA 60.135 52.381 11.28 0.00 0.00 3.49
819 2426 2.484417 GCTCACTGGCATGTACTAGCAT 60.484 50.000 11.28 0.00 0.00 3.79
820 2427 3.388308 CTCACTGGCATGTACTAGCATC 58.612 50.000 11.28 0.00 0.00 3.91
821 2428 2.103094 TCACTGGCATGTACTAGCATCC 59.897 50.000 11.28 0.00 0.00 3.51
822 2429 2.103771 CACTGGCATGTACTAGCATCCT 59.896 50.000 11.28 0.00 0.00 3.24
823 2430 2.366916 ACTGGCATGTACTAGCATCCTC 59.633 50.000 11.28 0.00 0.00 3.71
824 2431 1.694150 TGGCATGTACTAGCATCCTCC 59.306 52.381 11.28 0.00 0.00 4.30
825 2432 1.002544 GGCATGTACTAGCATCCTCCC 59.997 57.143 11.28 0.00 0.00 4.30
826 2433 1.337260 GCATGTACTAGCATCCTCCCG 60.337 57.143 5.42 0.00 0.00 5.14
827 2434 0.969894 ATGTACTAGCATCCTCCCGC 59.030 55.000 0.00 0.00 0.00 6.13
828 2435 0.106167 TGTACTAGCATCCTCCCGCT 60.106 55.000 0.00 0.00 42.34 5.52
854 2461 0.108662 CACTAGCAGCGACACATCCA 60.109 55.000 0.00 0.00 0.00 3.41
893 2509 2.479837 CAGCTCGAAGGTAAACACACA 58.520 47.619 0.00 0.00 0.00 3.72
895 2511 2.159014 AGCTCGAAGGTAAACACACACA 60.159 45.455 0.00 0.00 0.00 3.72
947 2568 4.019771 ACAGTTCAAAAAGGCAAGGGAAAA 60.020 37.500 0.00 0.00 0.00 2.29
1028 2649 1.216941 GACGACGAAGCCGACCAAAA 61.217 55.000 0.00 0.00 39.50 2.44
1117 2738 4.452733 GCCTCCCACTCCGTTCGG 62.453 72.222 4.74 4.74 0.00 4.30
1248 2872 4.264638 GCTCTCTCTCTCCGCGGC 62.265 72.222 23.51 0.00 0.00 6.53
1271 2895 4.728110 GGGGTTAGGCGCGGGTTT 62.728 66.667 8.83 0.00 0.00 3.27
1357 2981 4.292178 CCTGGATCTCGGCGCTCC 62.292 72.222 7.64 6.51 0.00 4.70
1375 2999 4.082523 TAGTCGGCCAGCCACTGC 62.083 66.667 18.26 3.30 35.37 4.40
1382 3006 2.433446 CCAGCCACTGCCTGTCTT 59.567 61.111 0.00 0.00 38.69 3.01
1383 3007 1.970114 CCAGCCACTGCCTGTCTTG 60.970 63.158 0.00 0.00 38.69 3.02
1384 3008 1.228063 CAGCCACTGCCTGTCTTGT 60.228 57.895 0.00 0.00 38.69 3.16
1386 3010 0.106519 AGCCACTGCCTGTCTTGTTT 60.107 50.000 0.00 0.00 38.69 2.83
1387 3011 0.746659 GCCACTGCCTGTCTTGTTTT 59.253 50.000 0.00 0.00 0.00 2.43
1388 3012 1.136891 GCCACTGCCTGTCTTGTTTTT 59.863 47.619 0.00 0.00 0.00 1.94
1406 3030 3.414549 TTTTCTCAAGTTGTTGTCGGC 57.585 42.857 2.11 0.00 34.98 5.54
1407 3031 0.934496 TTCTCAAGTTGTTGTCGGCG 59.066 50.000 0.00 0.00 34.98 6.46
1408 3032 0.103390 TCTCAAGTTGTTGTCGGCGA 59.897 50.000 4.99 4.99 34.98 5.54
1415 3039 0.033642 TTGTTGTCGGCGATGGTGTA 59.966 50.000 14.79 0.00 0.00 2.90
1428 3052 1.712056 TGGTGTAGGCTGTGTGTAGT 58.288 50.000 0.00 0.00 0.00 2.73
1433 3057 0.895530 TAGGCTGTGTGTAGTGAGGC 59.104 55.000 0.00 0.00 0.00 4.70
1437 3061 2.809601 GTGTGTAGTGAGGCCGCG 60.810 66.667 0.00 0.00 0.00 6.46
1442 3066 2.441348 TAGTGAGGCCGCGGATGA 60.441 61.111 33.48 7.78 0.00 2.92
1444 3068 4.148825 GTGAGGCCGCGGATGACT 62.149 66.667 33.48 20.50 0.00 3.41
1445 3069 2.441348 TGAGGCCGCGGATGACTA 60.441 61.111 33.48 6.20 0.00 2.59
1453 3077 0.999406 CGCGGATGACTAGTTTGGTG 59.001 55.000 0.00 0.00 0.00 4.17
1454 3078 1.403647 CGCGGATGACTAGTTTGGTGA 60.404 52.381 0.00 0.00 0.00 4.02
1463 3087 7.756722 GGATGACTAGTTTGGTGATGAAATTTG 59.243 37.037 0.00 0.00 0.00 2.32
1464 3088 6.446318 TGACTAGTTTGGTGATGAAATTTGC 58.554 36.000 0.00 0.00 0.00 3.68
1506 3132 5.562113 CGAGGTGATTTTTGTAGTTTGGGAC 60.562 44.000 0.00 0.00 0.00 4.46
1508 3134 4.276431 GGTGATTTTTGTAGTTTGGGACGA 59.724 41.667 0.00 0.00 0.00 4.20
1565 3191 1.923356 AATGGTTGCAGAAATCCCGT 58.077 45.000 0.00 0.00 0.00 5.28
1567 3193 0.179004 TGGTTGCAGAAATCCCGTGT 60.179 50.000 0.00 0.00 0.00 4.49
1652 3280 7.764443 AGTCTAGCTGATTTACGCTTTTAATCA 59.236 33.333 0.00 0.00 37.68 2.57
1696 3324 8.966868 TCTAGGTTGTTTCAGATTTTGTTTCTT 58.033 29.630 0.00 0.00 0.00 2.52
1774 3403 7.911205 TGACATAAACCACTTAAACGAACAAAG 59.089 33.333 0.00 0.00 0.00 2.77
1846 3518 5.620206 TGTTGTTCTAGAAGGCTTCATTGA 58.380 37.500 27.70 18.49 0.00 2.57
1861 3534 5.766670 GCTTCATTGATTAGGGATGACATCA 59.233 40.000 17.08 0.00 30.10 3.07
1993 3667 2.977456 TGGCGTCGCTGCATTTGT 60.977 55.556 18.11 0.00 36.28 2.83
2141 3822 8.911918 TCATGCCACTTAAACTTAAAACTCTA 57.088 30.769 0.00 0.00 0.00 2.43
2376 4063 0.100861 GGGAGAGTGTACTACGCTGC 59.899 60.000 7.01 10.36 44.66 5.25
3424 5221 3.507786 TGTGTCGTTGTAGAATCCATCG 58.492 45.455 0.00 0.00 0.00 3.84
3661 5458 3.008594 ACCACGACCAGAATTATGGAACA 59.991 43.478 25.55 0.00 43.57 3.18
3714 5511 6.461640 GCCAGAAACTTGTAAACTCTACCTA 58.538 40.000 0.00 0.00 0.00 3.08
3722 5519 7.600960 ACTTGTAAACTCTACCTAGCAGTAAC 58.399 38.462 0.00 0.00 0.00 2.50
3795 5592 8.429493 TGCAATTGTCTACAGAATTCTGATAG 57.571 34.615 36.15 29.15 46.59 2.08
3971 5770 3.459965 CTCGAGGGCAGCAGAGCT 61.460 66.667 3.91 0.00 40.77 4.09
4518 6317 7.223971 CGCATGTTTAAGGTGCTAAGAGTTATA 59.776 37.037 0.00 0.00 36.74 0.98
4527 6326 6.757010 AGGTGCTAAGAGTTATATTTGTGTCG 59.243 38.462 0.00 0.00 0.00 4.35
4530 6329 7.274904 GTGCTAAGAGTTATATTTGTGTCGTCA 59.725 37.037 0.00 0.00 0.00 4.35
4602 6401 2.144730 CTTGCCTCATGCTGCTATCTC 58.855 52.381 0.00 0.00 42.00 2.75
4832 6638 2.726832 ACTTCCTGTCGTGCTACTTC 57.273 50.000 0.00 0.00 0.00 3.01
4976 6797 4.639310 TCCTTCACTAAGATCGTGTAGTCC 59.361 45.833 4.39 0.00 34.37 3.85
5016 6837 7.425577 ACTACGGTATTTTCAACTGGTTTAC 57.574 36.000 0.00 0.00 0.00 2.01
5061 6886 3.936453 CGGTTAGCCTATTGCAGTTTACA 59.064 43.478 0.00 0.00 44.83 2.41
5063 6888 5.277345 CGGTTAGCCTATTGCAGTTTACATC 60.277 44.000 0.00 0.00 44.83 3.06
5096 6921 4.864334 GCAGACCCCGCATCCAGG 62.864 72.222 0.00 0.00 0.00 4.45
5152 6977 1.613836 GCCCATTATTCTGGCCAGAG 58.386 55.000 33.16 21.74 39.30 3.35
5176 7001 2.360350 CTGCATTGGTGTCCGGCT 60.360 61.111 0.00 0.00 0.00 5.52
5199 7024 3.733684 CGTAAATATTTTTGCCGCAGCCT 60.734 43.478 5.91 0.00 38.69 4.58
5219 7044 2.976356 GAACGCTACCCCCGAACT 59.024 61.111 0.00 0.00 0.00 3.01
5358 7183 1.517832 CATGGACGACTCTGGGGAC 59.482 63.158 0.00 0.00 0.00 4.46
5393 7219 2.716244 CCGCGCTAGATCTGACGT 59.284 61.111 17.22 0.00 0.00 4.34
5804 7705 2.173020 CATCGCAGGCGCACACATA 61.173 57.895 10.83 0.00 38.40 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 1.207329 GGTCGGCTCTGATACCAACTT 59.793 52.381 0.00 0.00 32.04 2.66
56 57 1.875963 CACCTGACCCGCAAACATC 59.124 57.895 0.00 0.00 0.00 3.06
113 114 1.154169 CATGTGGCATGTCGTGTGC 60.154 57.895 0.00 1.76 41.78 4.57
120 121 0.961019 GTCCAACACATGTGGCATGT 59.039 50.000 28.64 8.75 34.19 3.21
128 129 0.884259 TGCGTCCAGTCCAACACATG 60.884 55.000 0.00 0.00 0.00 3.21
142 143 1.726791 CTTGGTACATGTCTGTGCGTC 59.273 52.381 0.00 0.00 38.72 5.19
147 148 5.869579 ACATTCTTCTTGGTACATGTCTGT 58.130 37.500 0.00 0.00 39.30 3.41
173 175 2.264794 GTCTTCGTCGGCCCACAT 59.735 61.111 0.16 0.00 0.00 3.21
188 190 3.576648 CCTACTCAAAGGAACTGACGTC 58.423 50.000 9.11 9.11 40.86 4.34
207 209 3.580458 GCCAGACTATCACATACATCCCT 59.420 47.826 0.00 0.00 0.00 4.20
208 210 3.580458 AGCCAGACTATCACATACATCCC 59.420 47.826 0.00 0.00 0.00 3.85
224 226 6.565974 AGTCTATCATCCCTATTAAGCCAGA 58.434 40.000 0.00 0.00 0.00 3.86
228 230 8.582657 TGAGTAGTCTATCATCCCTATTAAGC 57.417 38.462 0.00 0.00 0.00 3.09
235 237 8.964533 ATTGTTATGAGTAGTCTATCATCCCT 57.035 34.615 0.00 0.00 37.36 4.20
264 266 4.941873 GGGCTCTCGAAAAAGGAGAAATTA 59.058 41.667 3.01 0.00 39.86 1.40
292 294 7.535997 ACACACTTAACTTTGAAGTTCTTTCC 58.464 34.615 12.05 0.00 45.65 3.13
313 315 1.890876 ATTGCTCCACGCTAAACACA 58.109 45.000 0.00 0.00 40.11 3.72
319 321 3.620427 TCCTAAAATTGCTCCACGCTA 57.380 42.857 0.00 0.00 40.11 4.26
351 353 6.317140 GTGCATATCTGGAATCAACTTCTCAA 59.683 38.462 0.00 0.00 34.08 3.02
362 364 3.244009 CCTCACTCGTGCATATCTGGAAT 60.244 47.826 0.00 0.00 0.00 3.01
364 366 1.683385 CCTCACTCGTGCATATCTGGA 59.317 52.381 0.00 0.00 0.00 3.86
366 368 2.099756 TGTCCTCACTCGTGCATATCTG 59.900 50.000 0.00 0.00 0.00 2.90
367 369 2.379005 TGTCCTCACTCGTGCATATCT 58.621 47.619 0.00 0.00 0.00 1.98
368 370 2.871182 TGTCCTCACTCGTGCATATC 57.129 50.000 0.00 0.00 0.00 1.63
369 371 3.610040 TTTGTCCTCACTCGTGCATAT 57.390 42.857 0.00 0.00 0.00 1.78
370 372 3.610040 ATTTGTCCTCACTCGTGCATA 57.390 42.857 0.00 0.00 0.00 3.14
371 373 2.479566 ATTTGTCCTCACTCGTGCAT 57.520 45.000 0.00 0.00 0.00 3.96
372 374 1.872952 CAATTTGTCCTCACTCGTGCA 59.127 47.619 0.00 0.00 0.00 4.57
438 440 3.915437 AATGTGTTTCCTTACTTGCCG 57.085 42.857 0.00 0.00 0.00 5.69
444 446 6.503524 TGAGAAGCAAAATGTGTTTCCTTAC 58.496 36.000 0.00 0.00 45.82 2.34
716 749 0.401356 TTGCAGGTTCAGAGATGCCA 59.599 50.000 0.00 0.00 37.89 4.92
779 2369 1.340991 GCAGTTTCTAGATTGGGGGCA 60.341 52.381 0.00 0.00 0.00 5.36
787 2394 2.568956 TGCCAGTGAGCAGTTTCTAGAT 59.431 45.455 0.00 0.00 38.00 1.98
789 2396 2.462456 TGCCAGTGAGCAGTTTCTAG 57.538 50.000 2.57 0.00 38.00 2.43
798 2405 1.134699 TGCTAGTACATGCCAGTGAGC 60.135 52.381 7.48 0.00 0.00 4.26
799 2406 2.967599 TGCTAGTACATGCCAGTGAG 57.032 50.000 7.48 0.00 0.00 3.51
802 2409 2.366916 GAGGATGCTAGTACATGCCAGT 59.633 50.000 7.48 0.00 39.02 4.00
805 2412 1.002544 GGGAGGATGCTAGTACATGCC 59.997 57.143 7.48 0.00 39.02 4.40
806 2413 1.337260 CGGGAGGATGCTAGTACATGC 60.337 57.143 0.00 0.00 38.55 4.06
808 2415 0.969894 GCGGGAGGATGCTAGTACAT 59.030 55.000 0.00 0.00 0.00 2.29
809 2416 0.106167 AGCGGGAGGATGCTAGTACA 60.106 55.000 0.00 0.00 40.28 2.90
810 2417 0.315568 CAGCGGGAGGATGCTAGTAC 59.684 60.000 0.00 0.00 40.03 2.73
811 2418 0.827925 CCAGCGGGAGGATGCTAGTA 60.828 60.000 0.00 0.00 40.03 1.82
812 2419 2.136878 CCAGCGGGAGGATGCTAGT 61.137 63.158 0.00 0.00 40.03 2.57
813 2420 2.739784 CCAGCGGGAGGATGCTAG 59.260 66.667 0.00 0.00 40.03 3.42
823 2430 3.470888 CTAGTGGGTCCCAGCGGG 61.471 72.222 12.21 7.24 46.11 6.13
824 2431 4.162690 GCTAGTGGGTCCCAGCGG 62.163 72.222 12.21 5.19 32.34 5.52
825 2432 3.376935 CTGCTAGTGGGTCCCAGCG 62.377 68.421 12.21 3.61 32.34 5.18
826 2433 2.586792 CTGCTAGTGGGTCCCAGC 59.413 66.667 12.21 12.51 32.34 4.85
827 2434 2.586792 GCTGCTAGTGGGTCCCAG 59.413 66.667 12.21 0.10 32.34 4.45
828 2435 3.390521 CGCTGCTAGTGGGTCCCA 61.391 66.667 6.47 6.47 0.00 4.37
921 2540 4.712337 TCCCTTGCCTTTTTGAACTGTTAA 59.288 37.500 0.00 0.00 0.00 2.01
925 2546 3.817709 TTCCCTTGCCTTTTTGAACTG 57.182 42.857 0.00 0.00 0.00 3.16
1028 2649 4.367023 TCGGCGGCGTTGCTTACT 62.367 61.111 31.06 0.00 34.52 2.24
1117 2738 2.766229 GGAGGAGGAGGGGACAGC 60.766 72.222 0.00 0.00 0.00 4.40
1248 2872 4.832608 GCGCCTAACCCCGGTCAG 62.833 72.222 0.00 0.00 0.00 3.51
1271 2895 0.893270 CAAATCGCTTCCCCACCACA 60.893 55.000 0.00 0.00 0.00 4.17
1357 2981 2.185350 CAGTGGCTGGCCGACTAG 59.815 66.667 13.34 0.00 39.42 2.57
1386 3010 2.223157 CGCCGACAACAACTTGAGAAAA 60.223 45.455 0.00 0.00 0.00 2.29
1387 3011 1.329292 CGCCGACAACAACTTGAGAAA 59.671 47.619 0.00 0.00 0.00 2.52
1388 3012 0.934496 CGCCGACAACAACTTGAGAA 59.066 50.000 0.00 0.00 0.00 2.87
1389 3013 0.103390 TCGCCGACAACAACTTGAGA 59.897 50.000 0.00 0.00 0.00 3.27
1390 3014 1.136252 CATCGCCGACAACAACTTGAG 60.136 52.381 0.00 0.00 0.00 3.02
1391 3015 0.865111 CATCGCCGACAACAACTTGA 59.135 50.000 0.00 0.00 0.00 3.02
1392 3016 0.110238 CCATCGCCGACAACAACTTG 60.110 55.000 0.00 0.00 0.00 3.16
1393 3017 0.534203 ACCATCGCCGACAACAACTT 60.534 50.000 0.00 0.00 0.00 2.66
1394 3018 1.070786 ACCATCGCCGACAACAACT 59.929 52.632 0.00 0.00 0.00 3.16
1395 3019 1.206578 CACCATCGCCGACAACAAC 59.793 57.895 0.00 0.00 0.00 3.32
1396 3020 0.033642 TACACCATCGCCGACAACAA 59.966 50.000 0.00 0.00 0.00 2.83
1397 3021 0.389296 CTACACCATCGCCGACAACA 60.389 55.000 0.00 0.00 0.00 3.33
1398 3022 1.082117 CCTACACCATCGCCGACAAC 61.082 60.000 0.00 0.00 0.00 3.32
1399 3023 1.216977 CCTACACCATCGCCGACAA 59.783 57.895 0.00 0.00 0.00 3.18
1400 3024 2.889617 CCTACACCATCGCCGACA 59.110 61.111 0.00 0.00 0.00 4.35
1401 3025 2.585247 GCCTACACCATCGCCGAC 60.585 66.667 0.00 0.00 0.00 4.79
1402 3026 2.758327 AGCCTACACCATCGCCGA 60.758 61.111 0.00 0.00 0.00 5.54
1403 3027 2.586079 CAGCCTACACCATCGCCG 60.586 66.667 0.00 0.00 0.00 6.46
1404 3028 1.815421 CACAGCCTACACCATCGCC 60.815 63.158 0.00 0.00 0.00 5.54
1405 3029 1.079127 ACACAGCCTACACCATCGC 60.079 57.895 0.00 0.00 0.00 4.58
1406 3030 0.037326 ACACACAGCCTACACCATCG 60.037 55.000 0.00 0.00 0.00 3.84
1407 3031 2.233922 ACTACACACAGCCTACACCATC 59.766 50.000 0.00 0.00 0.00 3.51
1408 3032 2.028112 CACTACACACAGCCTACACCAT 60.028 50.000 0.00 0.00 0.00 3.55
1415 3039 1.674057 GCCTCACTACACACAGCCT 59.326 57.895 0.00 0.00 0.00 4.58
1428 3052 2.441348 TAGTCATCCGCGGCCTCA 60.441 61.111 23.51 2.57 0.00 3.86
1433 3057 0.108329 ACCAAACTAGTCATCCGCGG 60.108 55.000 22.12 22.12 0.00 6.46
1437 3061 7.396540 AATTTCATCACCAAACTAGTCATCC 57.603 36.000 0.00 0.00 0.00 3.51
1442 3066 6.040842 ACTGCAAATTTCATCACCAAACTAGT 59.959 34.615 0.00 0.00 0.00 2.57
1444 3068 6.183360 ACACTGCAAATTTCATCACCAAACTA 60.183 34.615 0.00 0.00 0.00 2.24
1445 3069 5.051816 CACTGCAAATTTCATCACCAAACT 58.948 37.500 0.00 0.00 0.00 2.66
1453 3077 5.291971 ACTCCAAACACTGCAAATTTCATC 58.708 37.500 0.00 0.00 0.00 2.92
1454 3078 5.280654 ACTCCAAACACTGCAAATTTCAT 57.719 34.783 0.00 0.00 0.00 2.57
1463 3087 2.225491 TCGCATAAACTCCAAACACTGC 59.775 45.455 0.00 0.00 0.00 4.40
1464 3088 3.120199 CCTCGCATAAACTCCAAACACTG 60.120 47.826 0.00 0.00 0.00 3.66
1506 3132 1.656095 GCCGTCTGACAGAAATTCTCG 59.344 52.381 6.76 5.35 0.00 4.04
1508 3134 1.714794 CGCCGTCTGACAGAAATTCT 58.285 50.000 6.76 0.00 0.00 2.40
1565 3191 8.576442 ACATATCACATCGATCATACTACAACA 58.424 33.333 0.00 0.00 35.39 3.33
1606 3232 3.525199 ACTTTGCTCTATCTGGGACCAAT 59.475 43.478 0.00 0.00 0.00 3.16
1652 3280 5.723887 ACCTAGAACCAGAAATCATCTCACT 59.276 40.000 0.00 0.00 35.73 3.41
1696 3324 3.825585 TGACAGCAAAGCATTTCCATGTA 59.174 39.130 0.00 0.00 35.03 2.29
1701 3329 2.523015 CGATGACAGCAAAGCATTTCC 58.477 47.619 0.00 0.00 35.03 3.13
1774 3403 8.784043 TCAGAAGGAGCATAAGTTTTAAAGTTC 58.216 33.333 0.59 0.00 0.00 3.01
1787 3416 5.538813 ACCATATACGTTCAGAAGGAGCATA 59.461 40.000 9.87 4.91 0.00 3.14
1846 3518 3.972638 AGAGCACTGATGTCATCCCTAAT 59.027 43.478 10.36 0.00 0.00 1.73
1993 3667 0.662619 CAAACTCAGCGGCTTGACAA 59.337 50.000 0.00 0.00 0.00 3.18
2376 4063 5.673514 CCATTTTTGTCCCATTATCAAGGG 58.326 41.667 0.00 0.00 46.90 3.95
3424 5221 4.762251 ACAGAAGAGAAATAACAACAGGCC 59.238 41.667 0.00 0.00 0.00 5.19
3595 5392 7.876068 TGAAACCACGACAAGAATTATAGAACT 59.124 33.333 0.00 0.00 0.00 3.01
3600 5397 7.658167 TGAACTGAAACCACGACAAGAATTATA 59.342 33.333 0.00 0.00 0.00 0.98
3645 5442 4.111577 TCCCTCTGTTCCATAATTCTGGT 58.888 43.478 9.50 0.00 37.57 4.00
3661 5458 7.750947 AACAGTAATGGTTAATACTCCCTCT 57.249 36.000 0.00 0.00 30.09 3.69
3714 5511 4.348168 CCCCATATTAGAGTGGTTACTGCT 59.652 45.833 0.00 0.00 37.25 4.24
3722 5519 3.838903 GGAGTACCCCCATATTAGAGTGG 59.161 52.174 0.00 0.00 35.22 4.00
3971 5770 4.013728 GTGAGCATTACCCATGTAACCAA 58.986 43.478 0.00 0.00 39.66 3.67
4518 6317 0.249699 TCCTGCGTGACGACACAAAT 60.250 50.000 17.71 0.00 46.20 2.32
4527 6326 2.674796 AAAGAGGTATCCTGCGTGAC 57.325 50.000 0.00 0.00 31.76 3.67
4530 6329 3.767673 TCAGTTAAAGAGGTATCCTGCGT 59.232 43.478 0.00 0.00 31.76 5.24
4602 6401 5.801350 TCATCATCAGCTTTCGGTAAAAG 57.199 39.130 0.00 0.00 46.05 2.27
4832 6638 2.872732 TCGTCCCTATAGTTAGGCCAG 58.127 52.381 5.01 0.00 43.34 4.85
4976 6797 1.657094 GTAGTTGTTCCCACGTATGCG 59.343 52.381 0.19 0.19 44.93 4.73
5061 6886 3.948473 TCTGCTAGAGTTGCTCTAACGAT 59.052 43.478 7.22 0.00 41.74 3.73
5063 6888 3.430931 GTCTGCTAGAGTTGCTCTAACG 58.569 50.000 7.22 0.00 41.74 3.18
5165 6990 1.184431 TATTTACGAGCCGGACACCA 58.816 50.000 5.05 0.00 0.00 4.17
5176 7001 3.430931 GCTGCGGCAAAAATATTTACGA 58.569 40.909 14.08 4.12 38.54 3.43
5202 7027 0.101939 CTAGTTCGGGGGTAGCGTTC 59.898 60.000 0.00 0.00 0.00 3.95
5219 7044 1.537348 CGCAAGCCCGCAGTTATACTA 60.537 52.381 0.00 0.00 0.00 1.82
5255 7080 0.106519 CTGCAGGGGGATAGGGTTTG 60.107 60.000 5.57 0.00 0.00 2.93
5382 7208 2.323447 CGCGCGACGTCAGATCTA 59.677 61.111 28.94 0.00 36.87 1.98
5450 7277 2.278206 GCTCGCAGCGATCGAAGA 60.278 61.111 19.91 10.39 45.75 2.87
5461 7289 2.878429 GAAGTCCTCGAGCTCGCA 59.122 61.111 30.97 18.15 39.60 5.10
5759 7660 1.107945 GCCCGTCTAGAAGAAGAGCT 58.892 55.000 7.30 0.00 0.00 4.09
5804 7705 2.654079 CGCAGGTCAGCCTCCTTCT 61.654 63.158 0.00 0.00 44.97 2.85


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

AutoCloner maintained by Alex Coulton.