Multiple sequence alignment - TraesCS5B01G281800

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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 TraesCS5B01G281800 chr5B 100.000 5689 0 0 1 5689 466780664 466786352 0.000000e+00 10506.0
1 TraesCS5B01G281800 chr5B 84.375 416 50 5 1000 1412 466968303 466968706 1.490000e-105 394.0
2 TraesCS5B01G281800 chr5B 84.461 399 46 8 1000 1395 466949656 466950041 4.160000e-101 379.0
3 TraesCS5B01G281800 chr5B 87.500 64 4 2 5627 5689 507933443 507933383 2.840000e-08 71.3
4 TraesCS5B01G281800 chr3B 97.619 1680 34 1 2432 4105 32803521 32805200 0.000000e+00 2876.0
5 TraesCS5B01G281800 chr3B 86.652 1341 133 22 2802 4105 156372150 156370819 0.000000e+00 1443.0
6 TraesCS5B01G281800 chr3B 88.333 60 3 2 5630 5689 578628221 578628276 1.020000e-07 69.4
7 TraesCS5B01G281800 chr7B 95.860 1691 37 6 2429 4105 674199610 674201281 0.000000e+00 2704.0
8 TraesCS5B01G281800 chr1B 95.419 1681 28 11 2431 4105 35278612 35280249 0.000000e+00 2632.0
9 TraesCS5B01G281800 chr1B 88.690 672 41 18 81 726 507473074 507473736 0.000000e+00 787.0
10 TraesCS5B01G281800 chr1B 86.441 413 47 3 1000 1412 507472743 507472340 1.450000e-120 444.0
11 TraesCS5B01G281800 chr5A 97.937 1357 22 1 2755 4105 672512545 672511189 0.000000e+00 2346.0
12 TraesCS5B01G281800 chr5A 86.082 1552 98 61 1 1513 491295249 491296721 0.000000e+00 1561.0
13 TraesCS5B01G281800 chr5A 93.427 928 44 9 1505 2429 491297989 491298902 0.000000e+00 1360.0
14 TraesCS5B01G281800 chr5A 93.190 793 44 10 4896 5685 491299831 491300616 0.000000e+00 1157.0
15 TraesCS5B01G281800 chr5A 92.966 725 24 5 4106 4830 491298894 491299591 0.000000e+00 1031.0
16 TraesCS5B01G281800 chr5A 97.682 302 7 0 2432 2733 672512906 672512605 2.350000e-143 520.0
17 TraesCS5B01G281800 chr5A 83.649 422 60 4 991 1412 491313331 491313743 6.910000e-104 388.0
18 TraesCS5B01G281800 chr5A 96.610 59 1 1 4841 4899 491299647 491299704 4.690000e-16 97.1
19 TraesCS5B01G281800 chr5D 92.412 1542 70 31 1 1513 388103294 388104817 0.000000e+00 2156.0
20 TraesCS5B01G281800 chr5D 92.457 928 47 11 1503 2427 388105678 388106585 0.000000e+00 1304.0
21 TraesCS5B01G281800 chr5D 93.963 762 32 9 4134 4894 388106600 388107348 0.000000e+00 1140.0
22 TraesCS5B01G281800 chr5D 92.600 527 30 9 4896 5421 388107479 388107997 0.000000e+00 749.0
23 TraesCS5B01G281800 chr5D 96.444 225 8 0 5461 5685 388107997 388108221 6.960000e-99 372.0
24 TraesCS5B01G281800 chr5D 83.577 274 41 1 1139 1412 388426200 388426469 2.630000e-63 254.0
25 TraesCS5B01G281800 chr5D 86.486 148 19 1 997 1143 388424096 388424243 1.640000e-35 161.0
26 TraesCS5B01G281800 chr5D 93.478 46 3 0 5579 5624 480977577 480977532 1.020000e-07 69.4
27 TraesCS5B01G281800 chr5D 86.667 60 5 2 5630 5689 453408152 453408096 4.760000e-06 63.9
28 TraesCS5B01G281800 chr6B 98.394 1183 13 1 2929 4105 52226811 52227993 0.000000e+00 2074.0
29 TraesCS5B01G281800 chr6B 98.195 277 5 0 2435 2711 52226233 52226509 8.570000e-133 484.0
30 TraesCS5B01G281800 chr6B 82.099 162 20 5 4571 4730 79881620 79881466 4.630000e-26 130.0
31 TraesCS5B01G281800 chr6B 96.875 32 1 0 5579 5610 157361070 157361101 3.000000e-03 54.7
32 TraesCS5B01G281800 chr6A 98.299 1176 14 1 2938 4107 135003476 135004651 0.000000e+00 2056.0
33 TraesCS5B01G281800 chr6A 98.605 215 3 0 2431 2645 135002877 135003091 1.160000e-101 381.0
34 TraesCS5B01G281800 chr6A 90.000 50 3 1 5642 5689 544479219 544479170 4.760000e-06 63.9
35 TraesCS5B01G281800 chr4A 98.059 1185 15 3 2928 4105 513352771 513353954 0.000000e+00 2054.0
36 TraesCS5B01G281800 chr4A 94.507 1329 44 11 2784 4105 741180575 741179269 0.000000e+00 2023.0
37 TraesCS5B01G281800 chr4A 95.434 219 10 0 2542 2760 513352224 513352442 3.260000e-92 350.0
38 TraesCS5B01G281800 chr4A 88.288 222 9 2 2434 2655 741181203 741180999 3.400000e-62 250.0
39 TraesCS5B01G281800 chr2B 90.032 1585 119 17 2431 4000 765029993 765028433 0.000000e+00 2015.0
40 TraesCS5B01G281800 chr2B 86.667 60 5 1 5627 5686 185084591 185084647 4.760000e-06 63.9
41 TraesCS5B01G281800 chr2B 87.719 57 3 2 5630 5686 264555411 264555463 4.760000e-06 63.9
42 TraesCS5B01G281800 chr4B 90.922 1465 115 5 2653 4104 664311552 664310093 0.000000e+00 1953.0
43 TraesCS5B01G281800 chr4B 86.667 60 5 1 5627 5686 179310386 179310442 4.760000e-06 63.9
44 TraesCS5B01G281800 chr4B 97.297 37 1 0 5650 5686 207103980 207104016 4.760000e-06 63.9
45 TraesCS5B01G281800 chr4B 91.489 47 2 2 5642 5686 378533976 378534022 4.760000e-06 63.9
46 TraesCS5B01G281800 chr3D 85.123 773 86 19 2801 3556 9439043 9439803 0.000000e+00 763.0
47 TraesCS5B01G281800 chr1D 84.051 790 94 27 2784 3556 453076014 453076788 0.000000e+00 732.0
48 TraesCS5B01G281800 chr1D 87.059 680 44 18 81 726 378869405 378870074 0.000000e+00 728.0
49 TraesCS5B01G281800 chr1D 85.714 413 48 5 1000 1411 378869074 378868672 5.270000e-115 425.0
50 TraesCS5B01G281800 chr1D 91.463 82 3 1 777 858 378871060 378871137 6.030000e-20 110.0
51 TraesCS5B01G281800 chr1D 97.297 37 1 0 5650 5686 208090301 208090337 4.760000e-06 63.9
52 TraesCS5B01G281800 chr1A 97.628 253 6 0 2424 2676 542367325 542367577 8.750000e-118 435.0
53 TraesCS5B01G281800 chr1A 83.149 451 27 11 81 509 479711308 479711731 3.240000e-97 366.0
54 TraesCS5B01G281800 chr1A 82.132 319 45 5 1000 1315 479710982 479710673 4.370000e-66 263.0
55 TraesCS5B01G281800 chr1A 92.500 40 3 0 5650 5689 122498317 122498278 2.210000e-04 58.4
56 TraesCS5B01G281800 chr1A 89.362 47 3 2 5642 5686 122498313 122498359 2.210000e-04 58.4
57 TraesCS5B01G281800 chr6D 78.862 492 65 21 1002 1491 106953093 106953547 4.310000e-76 296.0
58 TraesCS5B01G281800 chr6D 91.837 49 2 2 5643 5689 295270444 295270396 3.680000e-07 67.6
59 TraesCS5B01G281800 chr6D 94.595 37 2 0 5650 5686 427966158 427966194 2.210000e-04 58.4
60 TraesCS5B01G281800 chr4D 88.333 60 4 1 5630 5689 468691427 468691371 1.020000e-07 69.4
61 TraesCS5B01G281800 chr2A 85.484 62 7 1 5630 5689 402689348 402689287 4.760000e-06 63.9


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 TraesCS5B01G281800 chr5B 466780664 466786352 5688 False 10506.00 10506 100.0000 1 5689 1 chr5B.!!$F1 5688
1 TraesCS5B01G281800 chr3B 32803521 32805200 1679 False 2876.00 2876 97.6190 2432 4105 1 chr3B.!!$F1 1673
2 TraesCS5B01G281800 chr3B 156370819 156372150 1331 True 1443.00 1443 86.6520 2802 4105 1 chr3B.!!$R1 1303
3 TraesCS5B01G281800 chr7B 674199610 674201281 1671 False 2704.00 2704 95.8600 2429 4105 1 chr7B.!!$F1 1676
4 TraesCS5B01G281800 chr1B 35278612 35280249 1637 False 2632.00 2632 95.4190 2431 4105 1 chr1B.!!$F1 1674
5 TraesCS5B01G281800 chr1B 507473074 507473736 662 False 787.00 787 88.6900 81 726 1 chr1B.!!$F2 645
6 TraesCS5B01G281800 chr5A 672511189 672512906 1717 True 1433.00 2346 97.8095 2432 4105 2 chr5A.!!$R1 1673
7 TraesCS5B01G281800 chr5A 491295249 491300616 5367 False 1041.22 1561 92.4550 1 5685 5 chr5A.!!$F2 5684
8 TraesCS5B01G281800 chr5D 388103294 388108221 4927 False 1144.20 2156 93.5752 1 5685 5 chr5D.!!$F1 5684
9 TraesCS5B01G281800 chr5D 388424096 388426469 2373 False 207.50 254 85.0315 997 1412 2 chr5D.!!$F2 415
10 TraesCS5B01G281800 chr6B 52226233 52227993 1760 False 1279.00 2074 98.2945 2435 4105 2 chr6B.!!$F2 1670
11 TraesCS5B01G281800 chr6A 135002877 135004651 1774 False 1218.50 2056 98.4520 2431 4107 2 chr6A.!!$F1 1676
12 TraesCS5B01G281800 chr4A 513352224 513353954 1730 False 1202.00 2054 96.7465 2542 4105 2 chr4A.!!$F1 1563
13 TraesCS5B01G281800 chr4A 741179269 741181203 1934 True 1136.50 2023 91.3975 2434 4105 2 chr4A.!!$R1 1671
14 TraesCS5B01G281800 chr2B 765028433 765029993 1560 True 2015.00 2015 90.0320 2431 4000 1 chr2B.!!$R1 1569
15 TraesCS5B01G281800 chr4B 664310093 664311552 1459 True 1953.00 1953 90.9220 2653 4104 1 chr4B.!!$R1 1451
16 TraesCS5B01G281800 chr3D 9439043 9439803 760 False 763.00 763 85.1230 2801 3556 1 chr3D.!!$F1 755
17 TraesCS5B01G281800 chr1D 453076014 453076788 774 False 732.00 732 84.0510 2784 3556 1 chr1D.!!$F2 772
18 TraesCS5B01G281800 chr1D 378869405 378871137 1732 False 419.00 728 89.2610 81 858 2 chr1D.!!$F3 777

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
871 911 0.104304 AAAGGCGAACACGTCTGTCT 59.896 50.000 0.00 0.0 41.16 3.41 F
1216 3235 0.392461 TGGATAGTTCAGCGGGTTGC 60.392 55.000 0.00 0.0 46.98 4.17 F
1977 5287 0.248215 GGCATCACGAAATTGCTCGG 60.248 55.000 4.68 0.0 43.22 4.63 F
2120 5430 2.480037 TCTCACGTGCATTTGTGCTTAG 59.520 45.455 11.67 0.0 36.06 2.18 F
2124 5434 3.665409 CACGTGCATTTGTGCTTAGAAAG 59.335 43.478 0.82 0.0 35.49 2.62 F
2348 5659 5.587844 GTCTTTCTGTGCACATGGATATCTT 59.412 40.000 22.00 0.0 0.00 2.40 F
4172 9232 6.774656 AGTATCCAAGCTGATAGGGAATTTTG 59.225 38.462 0.00 0.0 32.25 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1903 5213 0.179100 CAGTGTCAGGCATACCCTCG 60.179 60.000 0.00 0.00 44.09 4.63 R
2172 5482 3.134623 CCTTGTGATCCTACACTGCCATA 59.865 47.826 0.00 0.00 40.87 2.74 R
3164 6863 3.953775 CAGAACCGCACCACCCCT 61.954 66.667 0.00 0.00 0.00 4.79 R
3715 7450 4.019174 CAAGGGAAATATGCAGGACTTGT 58.981 43.478 0.00 0.00 31.89 3.16 R
4172 9232 6.590234 AAGTAAAAATCTGATTGGACACCC 57.410 37.500 3.22 0.00 0.00 4.61 R
4204 9264 3.302434 GCACATTTCGATTGCAAGACATG 59.698 43.478 4.94 9.03 36.22 3.21 R
5259 10494 0.114954 ACATTCCCCACATGCCAGTT 59.885 50.000 0.00 0.00 0.00 3.16 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
155 156 6.425114 CCTGTGACCATCTTTGCAGTATATAC 59.575 42.308 4.60 4.60 0.00 1.47
196 204 2.160417 GCTCAGATCAAACTTTGGACCG 59.840 50.000 1.62 0.00 0.00 4.79
215 223 1.202154 CGTCTCGACAAAGCTACCGAT 60.202 52.381 0.00 0.00 0.00 4.18
298 306 1.918293 ATCCGGGGCAGTGAACTGA 60.918 57.895 14.58 0.00 46.59 3.41
352 360 1.522668 CAACGACTTGCTGAATCCCA 58.477 50.000 0.00 0.00 0.00 4.37
452 481 0.536006 GAGATGCCCCTGATTTCCCG 60.536 60.000 0.00 0.00 0.00 5.14
460 489 2.224548 CCCCTGATTTCCCGATTCCTAC 60.225 54.545 0.00 0.00 0.00 3.18
496 525 1.300233 GACGGCGAATCTGGCTAGG 60.300 63.158 16.62 0.00 0.00 3.02
498 527 1.006805 CGGCGAATCTGGCTAGGAG 60.007 63.158 0.00 0.00 0.00 3.69
531 560 0.179108 CCTCAGAATCGTCGGGGAAC 60.179 60.000 0.00 0.00 0.00 3.62
597 626 2.740055 GCTGGATCGGCGCCTATG 60.740 66.667 26.68 9.50 0.00 2.23
707 740 4.200283 GGACGAGCAGAGGAGGCG 62.200 72.222 0.00 0.00 36.08 5.52
832 872 1.926426 AAGGATGCGAAAGGGGGAGG 61.926 60.000 0.00 0.00 0.00 4.30
868 908 3.720920 CGATAAAAAGGCGAACACGTCTG 60.721 47.826 0.00 0.00 41.16 3.51
869 909 1.375551 AAAAAGGCGAACACGTCTGT 58.624 45.000 0.00 0.00 41.16 3.41
870 910 0.935196 AAAAGGCGAACACGTCTGTC 59.065 50.000 0.00 0.00 41.16 3.51
871 911 0.104304 AAAGGCGAACACGTCTGTCT 59.896 50.000 0.00 0.00 41.16 3.41
922 969 1.523938 GCTATCTTGGCCCACGTCC 60.524 63.158 0.00 0.00 0.00 4.79
1158 1216 2.029844 GTTCAGGTGCGTGCTCTCC 61.030 63.158 0.00 0.00 0.00 3.71
1170 1785 0.685785 TGCTCTCCTCTTGCGGATCT 60.686 55.000 0.00 0.00 31.43 2.75
1172 1787 1.110442 CTCTCCTCTTGCGGATCTGT 58.890 55.000 2.89 0.00 31.43 3.41
1173 1788 1.480137 CTCTCCTCTTGCGGATCTGTT 59.520 52.381 2.89 0.00 31.43 3.16
1174 1789 1.902508 TCTCCTCTTGCGGATCTGTTT 59.097 47.619 2.89 0.00 31.43 2.83
1178 1793 2.621338 CTCTTGCGGATCTGTTTGCTA 58.379 47.619 2.89 0.00 0.00 3.49
1179 1794 2.346803 TCTTGCGGATCTGTTTGCTAC 58.653 47.619 2.89 0.00 0.00 3.58
1180 1795 2.028112 TCTTGCGGATCTGTTTGCTACT 60.028 45.455 2.89 0.00 0.00 2.57
1185 3191 2.349886 CGGATCTGTTTGCTACTTCTGC 59.650 50.000 0.00 0.00 0.00 4.26
1192 3211 0.397941 TTGCTACTTCTGCTGGTGCT 59.602 50.000 0.00 0.00 40.48 4.40
1196 3215 2.093973 GCTACTTCTGCTGGTGCTCTTA 60.094 50.000 0.00 0.00 40.48 2.10
1214 3233 3.709653 TCTTATGGATAGTTCAGCGGGTT 59.290 43.478 0.00 0.00 0.00 4.11
1215 3234 2.332063 ATGGATAGTTCAGCGGGTTG 57.668 50.000 0.00 0.00 0.00 3.77
1216 3235 0.392461 TGGATAGTTCAGCGGGTTGC 60.392 55.000 0.00 0.00 46.98 4.17
1463 3487 2.728007 GTTGGGGCTTCTTATCAAGCT 58.272 47.619 5.24 0.00 46.89 3.74
1476 3500 1.441515 CAAGCTGTGTGCATGACGC 60.442 57.895 0.00 0.00 42.37 5.19
1492 3516 5.391950 GCATGACGCCTTTCATCTAAGAAAA 60.392 40.000 0.00 0.00 37.09 2.29
1493 3517 6.678900 GCATGACGCCTTTCATCTAAGAAAAT 60.679 38.462 0.00 0.00 37.09 1.82
1494 3518 6.182039 TGACGCCTTTCATCTAAGAAAATG 57.818 37.500 0.00 0.00 37.09 2.32
1495 3519 4.986622 ACGCCTTTCATCTAAGAAAATGC 58.013 39.130 0.00 0.00 37.09 3.56
1496 3520 4.458989 ACGCCTTTCATCTAAGAAAATGCA 59.541 37.500 0.00 0.00 37.09 3.96
1497 3521 5.032863 CGCCTTTCATCTAAGAAAATGCAG 58.967 41.667 0.00 0.00 37.09 4.41
1498 3522 5.163723 CGCCTTTCATCTAAGAAAATGCAGA 60.164 40.000 0.00 0.00 37.09 4.26
1499 3523 6.264088 GCCTTTCATCTAAGAAAATGCAGAG 58.736 40.000 0.00 0.00 37.09 3.35
1500 3524 6.264088 CCTTTCATCTAAGAAAATGCAGAGC 58.736 40.000 0.00 0.00 37.09 4.09
1501 3525 5.475273 TTCATCTAAGAAAATGCAGAGCG 57.525 39.130 0.00 0.00 0.00 5.03
1545 4853 7.043590 GCTTGAATCAATATGATTGTGCTTGTC 60.044 37.037 10.12 0.00 46.20 3.18
1548 4857 9.176460 TGAATCAATATGATTGTGCTTGTCTAA 57.824 29.630 10.12 0.00 46.20 2.10
1551 4860 6.318648 TCAATATGATTGTGCTTGTCTAACCC 59.681 38.462 0.00 0.00 0.00 4.11
1554 4863 2.719531 TTGTGCTTGTCTAACCCACA 57.280 45.000 0.00 0.00 34.90 4.17
1577 4887 7.496920 CACAGTGTGGACTAATAACATGATCAT 59.503 37.037 15.86 1.18 0.00 2.45
1589 4899 5.947228 AACATGATCATCACTCAAACGTT 57.053 34.783 4.86 0.00 0.00 3.99
1590 4900 5.536554 ACATGATCATCACTCAAACGTTC 57.463 39.130 4.86 0.00 0.00 3.95
1591 4901 4.996758 ACATGATCATCACTCAAACGTTCA 59.003 37.500 4.86 0.00 0.00 3.18
1592 4902 5.121298 ACATGATCATCACTCAAACGTTCAG 59.879 40.000 4.86 3.24 0.00 3.02
1593 4903 4.881920 TGATCATCACTCAAACGTTCAGA 58.118 39.130 12.85 8.37 0.00 3.27
1594 4904 4.925646 TGATCATCACTCAAACGTTCAGAG 59.074 41.667 22.08 22.08 35.56 3.35
1595 4905 4.584327 TCATCACTCAAACGTTCAGAGA 57.416 40.909 27.47 18.62 33.69 3.10
1596 4906 4.550422 TCATCACTCAAACGTTCAGAGAG 58.450 43.478 27.47 21.94 33.69 3.20
1600 4910 4.112634 CACTCAAACGTTCAGAGAGTCAA 58.887 43.478 27.47 0.00 37.45 3.18
1621 4931 1.414550 TGGATGAATTGCATGGCATGG 59.585 47.619 27.48 10.64 38.76 3.66
1632 4942 2.293955 GCATGGCATGGCTTTTGTTTTT 59.706 40.909 27.48 0.00 0.00 1.94
1638 4948 7.992754 TGGCATGGCTTTTGTTTTTAAATAT 57.007 28.000 21.08 0.00 0.00 1.28
1641 4951 9.340695 GGCATGGCTTTTGTTTTTAAATATTTC 57.659 29.630 12.86 0.00 0.00 2.17
1731 5041 2.315925 TTTCTCGATGATGAGGGTGC 57.684 50.000 0.00 0.00 36.61 5.01
1801 5111 1.000396 GTGCTCCTGGGATGCCTTT 60.000 57.895 4.35 0.00 0.00 3.11
1840 5150 5.818136 TGAAGTTGCTTGGCTACATTATC 57.182 39.130 6.83 1.49 36.81 1.75
1875 5185 2.173356 TCCCCTGGACAATGAAGCATAG 59.827 50.000 0.00 0.00 0.00 2.23
1903 5213 3.140325 TGTGAAACCACTGATTCCCTC 57.860 47.619 0.00 0.00 35.63 4.30
1907 5217 0.905357 AACCACTGATTCCCTCGAGG 59.095 55.000 25.36 25.36 0.00 4.63
1930 5240 0.760567 TGCCTGACACTGACCAGAGT 60.761 55.000 3.76 1.69 34.98 3.24
1943 5253 3.582647 TGACCAGAGTTTCAATAGAGCCA 59.417 43.478 0.00 0.00 0.00 4.75
1945 5255 5.184892 ACCAGAGTTTCAATAGAGCCAAT 57.815 39.130 0.00 0.00 0.00 3.16
1957 5267 1.304381 AGCCAATGGTGTCCGCAAT 60.304 52.632 0.00 0.00 0.00 3.56
1972 5282 1.584761 CGCAATGGCATCACGAAATTG 59.415 47.619 14.76 2.91 41.24 2.32
1976 5286 0.447406 TGGCATCACGAAATTGCTCG 59.553 50.000 0.00 0.00 44.50 5.03
1977 5287 0.248215 GGCATCACGAAATTGCTCGG 60.248 55.000 4.68 0.00 43.22 4.63
2120 5430 2.480037 TCTCACGTGCATTTGTGCTTAG 59.520 45.455 11.67 0.00 36.06 2.18
2124 5434 3.665409 CACGTGCATTTGTGCTTAGAAAG 59.335 43.478 0.82 0.00 35.49 2.62
2153 5463 8.454106 GTGCATTTTCATCTTACAGTAGTTCAT 58.546 33.333 0.00 0.00 0.00 2.57
2154 5464 8.668353 TGCATTTTCATCTTACAGTAGTTCATC 58.332 33.333 0.00 0.00 0.00 2.92
2155 5465 8.887717 GCATTTTCATCTTACAGTAGTTCATCT 58.112 33.333 0.00 0.00 0.00 2.90
2348 5659 5.587844 GTCTTTCTGTGCACATGGATATCTT 59.412 40.000 22.00 0.00 0.00 2.40
4172 9232 6.774656 AGTATCCAAGCTGATAGGGAATTTTG 59.225 38.462 0.00 0.00 32.25 2.44
4204 9264 7.970614 CCAATCAGATTTTTACTTAGTTGAGCC 59.029 37.037 0.00 0.00 0.00 4.70
4246 9306 5.242171 TGTGCAGTCAATCATGATTTCTTGT 59.758 36.000 18.41 0.00 38.01 3.16
4247 9307 6.430616 TGTGCAGTCAATCATGATTTCTTGTA 59.569 34.615 18.41 12.44 38.01 2.41
4248 9308 6.744537 GTGCAGTCAATCATGATTTCTTGTAC 59.255 38.462 18.41 18.75 38.01 2.90
4315 9375 4.036380 AGGTTCTCATTTTCGTGACAAACC 59.964 41.667 0.00 0.00 38.21 3.27
4394 9454 1.269517 GCCACAAATTTGCAGAACCGA 60.270 47.619 18.12 0.00 0.00 4.69
4489 9549 2.230992 GCAGTTTGTGGTTGGATGCATA 59.769 45.455 0.00 0.00 32.58 3.14
4490 9550 3.119029 GCAGTTTGTGGTTGGATGCATAT 60.119 43.478 0.00 0.00 32.58 1.78
4497 9557 5.255687 TGTGGTTGGATGCATATATGATCC 58.744 41.667 23.67 23.67 36.19 3.36
4519 9579 8.843308 ATCCCTTGAATGATATTTCTTTCCAA 57.157 30.769 8.60 0.00 35.95 3.53
4750 9810 7.907214 TCTGAACTTCTTATCTTGTAAAGGC 57.093 36.000 0.00 0.00 46.24 4.35
4753 9813 8.044060 TGAACTTCTTATCTTGTAAAGGCATG 57.956 34.615 0.00 0.00 46.24 4.06
4804 9864 1.009829 GCCATGAACGACAGCCTAAG 58.990 55.000 0.00 0.00 0.00 2.18
4830 9890 4.589908 ACCCCATGAATCAGTTAGTTCAC 58.410 43.478 0.00 0.00 37.19 3.18
4833 9893 5.491070 CCCATGAATCAGTTAGTTCACAGA 58.509 41.667 0.00 0.00 37.19 3.41
4894 9998 4.130857 TCAATGGACAACAAGCGTTTCTA 58.869 39.130 0.00 0.00 31.13 2.10
4908 10142 7.642586 ACAAGCGTTTCTATTGTTTACTGTTTC 59.357 33.333 0.00 0.00 33.49 2.78
4923 10157 8.564574 GTTTACTGTTTCCAACTGATGATGTTA 58.435 33.333 1.02 0.00 34.78 2.41
4927 10161 8.299570 ACTGTTTCCAACTGATGATGTTATTTC 58.700 33.333 1.02 0.00 34.78 2.17
4966 10200 4.325030 ACCTTTGGGTTTTCTGACTTCAGA 60.325 41.667 4.76 4.76 46.44 3.27
5130 10365 1.214062 CCACTGAGGAGAGCGTCAC 59.786 63.158 0.00 0.00 41.22 3.67
5179 10414 0.629058 AATCACCGTTTGGCCCCTAT 59.371 50.000 0.00 0.00 39.70 2.57
5180 10415 0.629058 ATCACCGTTTGGCCCCTATT 59.371 50.000 0.00 0.00 39.70 1.73
5181 10416 0.406361 TCACCGTTTGGCCCCTATTT 59.594 50.000 0.00 0.00 39.70 1.40
5186 10421 2.159114 CCGTTTGGCCCCTATTTGAATG 60.159 50.000 0.00 0.00 0.00 2.67
5196 10431 3.510719 CCTATTTGAATGGTTGTTGCGG 58.489 45.455 0.00 0.00 0.00 5.69
5200 10435 1.614996 TGAATGGTTGTTGCGGTGAT 58.385 45.000 0.00 0.00 0.00 3.06
5233 10468 0.099968 CGGCAATGAAGGTGATGCTG 59.900 55.000 0.00 0.00 38.79 4.41
5254 10489 5.634020 GCTGTAACTTCAGTTCGACAACTAT 59.366 40.000 0.00 0.00 41.24 2.12
5255 10490 6.805271 GCTGTAACTTCAGTTCGACAACTATA 59.195 38.462 0.00 0.00 41.24 1.31
5256 10491 7.488471 GCTGTAACTTCAGTTCGACAACTATAT 59.512 37.037 0.00 0.00 41.24 0.86
5257 10492 9.355215 CTGTAACTTCAGTTCGACAACTATATT 57.645 33.333 0.00 0.00 41.24 1.28
5258 10493 9.701098 TGTAACTTCAGTTCGACAACTATATTT 57.299 29.630 0.00 0.00 41.24 1.40
5270 10505 7.011016 TCGACAACTATATTTAACTGGCATGTG 59.989 37.037 0.00 0.00 0.00 3.21
5275 10511 2.685106 TTTAACTGGCATGTGGGGAA 57.315 45.000 0.00 0.00 0.00 3.97
5363 10600 1.552226 CGCCGCAGATAAGTCGTTTA 58.448 50.000 0.00 0.00 0.00 2.01
5366 10603 2.281762 GCCGCAGATAAGTCGTTTAGTG 59.718 50.000 0.00 0.00 0.00 2.74
5591 10829 5.455872 TCTTATGAAATACTCCCTCCGTCT 58.544 41.667 0.00 0.00 0.00 4.18
5637 10875 7.438160 TGACACTACACTACAACATTTTCTGAG 59.562 37.037 0.00 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
155 156 5.467735 TGAGCATCGATGTCCTTGATTTATG 59.532 40.000 25.47 0.00 38.61 1.90
196 204 2.159421 TCATCGGTAGCTTTGTCGAGAC 60.159 50.000 0.00 0.00 35.07 3.36
215 223 4.125703 GTTGGATTTTGCATTGTTGGTCA 58.874 39.130 0.00 0.00 0.00 4.02
283 291 1.515521 GGTTTCAGTTCACTGCCCCG 61.516 60.000 1.74 0.00 43.46 5.73
298 306 4.553938 CGATTTTGTTACTGCTCGTGGTTT 60.554 41.667 0.00 0.00 0.00 3.27
333 341 1.197721 GTGGGATTCAGCAAGTCGTTG 59.802 52.381 0.00 0.00 36.67 4.10
352 360 3.717294 GTGATGGTCCCCGGCTGT 61.717 66.667 0.00 0.00 0.00 4.40
433 462 0.536006 CGGGAAATCAGGGGCATCTC 60.536 60.000 0.00 0.00 0.00 2.75
596 625 2.721803 TTTCCGCTGGATTTGCCCCA 62.722 55.000 0.00 0.00 34.97 4.96
597 626 1.329913 ATTTCCGCTGGATTTGCCCC 61.330 55.000 0.00 0.00 34.97 5.80
858 898 1.336980 GGGGAAGAGACAGACGTGTTC 60.337 57.143 0.00 0.00 36.88 3.18
859 899 0.680061 GGGGAAGAGACAGACGTGTT 59.320 55.000 0.00 0.00 36.88 3.32
1128 1186 1.613925 CACCTGAACTGGACTCTCGAA 59.386 52.381 4.82 0.00 0.00 3.71
1158 1216 1.446907 AGCAAACAGATCCGCAAGAG 58.553 50.000 0.00 0.00 43.02 2.85
1170 1785 2.221169 CACCAGCAGAAGTAGCAAACA 58.779 47.619 0.00 0.00 0.00 2.83
1172 1787 1.202806 AGCACCAGCAGAAGTAGCAAA 60.203 47.619 0.00 0.00 45.49 3.68
1173 1788 0.397941 AGCACCAGCAGAAGTAGCAA 59.602 50.000 0.00 0.00 45.49 3.91
1174 1789 0.036952 GAGCACCAGCAGAAGTAGCA 60.037 55.000 0.00 0.00 45.49 3.49
1178 1793 2.355513 CCATAAGAGCACCAGCAGAAGT 60.356 50.000 0.00 0.00 45.49 3.01
1179 1794 2.093288 TCCATAAGAGCACCAGCAGAAG 60.093 50.000 0.00 0.00 45.49 2.85
1180 1795 1.908619 TCCATAAGAGCACCAGCAGAA 59.091 47.619 0.00 0.00 45.49 3.02
1185 3191 5.282055 TGAACTATCCATAAGAGCACCAG 57.718 43.478 0.00 0.00 0.00 4.00
1192 3211 3.305720 ACCCGCTGAACTATCCATAAGA 58.694 45.455 0.00 0.00 0.00 2.10
1196 3215 1.747206 GCAACCCGCTGAACTATCCAT 60.747 52.381 0.00 0.00 37.77 3.41
1217 3236 1.271379 CTGCTCCACAACACATGCAAT 59.729 47.619 0.00 0.00 0.00 3.56
1222 3241 1.609208 GTTCCTGCTCCACAACACAT 58.391 50.000 0.00 0.00 0.00 3.21
1224 3247 0.814010 ACGTTCCTGCTCCACAACAC 60.814 55.000 0.00 0.00 0.00 3.32
1342 3365 2.950309 TCCTCGACATTGTAGTAGAGCC 59.050 50.000 0.00 0.00 39.15 4.70
1476 3500 6.264088 GCTCTGCATTTTCTTAGATGAAAGG 58.736 40.000 0.00 0.00 37.27 3.11
1492 3516 2.236223 CTCCAGGACACGCTCTGCAT 62.236 60.000 0.00 0.00 0.00 3.96
1493 3517 2.917227 TCCAGGACACGCTCTGCA 60.917 61.111 0.00 0.00 0.00 4.41
1494 3518 2.125753 CTCCAGGACACGCTCTGC 60.126 66.667 0.00 0.00 0.00 4.26
1495 3519 1.214062 GACTCCAGGACACGCTCTG 59.786 63.158 0.00 0.00 0.00 3.35
1496 3520 1.979693 GGACTCCAGGACACGCTCT 60.980 63.158 0.00 0.00 0.00 4.09
1497 3521 1.939769 GAGGACTCCAGGACACGCTC 61.940 65.000 0.00 0.00 0.00 5.03
1498 3522 1.979693 GAGGACTCCAGGACACGCT 60.980 63.158 0.00 0.00 0.00 5.07
1499 3523 1.608717 ATGAGGACTCCAGGACACGC 61.609 60.000 0.00 0.00 0.00 5.34
1500 3524 0.174389 CATGAGGACTCCAGGACACG 59.826 60.000 0.00 0.00 0.00 4.49
1501 3525 0.107945 GCATGAGGACTCCAGGACAC 60.108 60.000 0.00 0.00 0.00 3.67
1551 4860 6.818142 TGATCATGTTATTAGTCCACACTGTG 59.182 38.462 6.19 6.19 33.62 3.66
1554 4863 7.712639 GTGATGATCATGTTATTAGTCCACACT 59.287 37.037 14.30 0.00 36.55 3.55
1567 4876 5.469760 TGAACGTTTGAGTGATGATCATGTT 59.530 36.000 14.30 7.42 0.00 2.71
1571 4880 4.881920 TCTGAACGTTTGAGTGATGATCA 58.118 39.130 0.46 0.00 0.00 2.92
1572 4881 5.164233 TCTCTGAACGTTTGAGTGATGATC 58.836 41.667 22.64 1.39 0.00 2.92
1577 4887 3.380320 TGACTCTCTGAACGTTTGAGTGA 59.620 43.478 26.13 18.99 38.00 3.41
1589 4899 4.880120 GCAATTCATCCATTGACTCTCTGA 59.120 41.667 0.00 0.00 36.39 3.27
1590 4900 4.638865 TGCAATTCATCCATTGACTCTCTG 59.361 41.667 0.00 0.00 36.39 3.35
1591 4901 4.851843 TGCAATTCATCCATTGACTCTCT 58.148 39.130 0.00 0.00 36.39 3.10
1592 4902 5.507482 CCATGCAATTCATCCATTGACTCTC 60.507 44.000 0.00 0.00 36.39 3.20
1593 4903 4.341235 CCATGCAATTCATCCATTGACTCT 59.659 41.667 0.00 0.00 36.39 3.24
1594 4904 4.617959 CCATGCAATTCATCCATTGACTC 58.382 43.478 0.00 0.00 36.39 3.36
1595 4905 3.181469 GCCATGCAATTCATCCATTGACT 60.181 43.478 0.00 0.00 36.39 3.41
1596 4906 3.128349 GCCATGCAATTCATCCATTGAC 58.872 45.455 0.00 0.00 36.39 3.18
1600 4910 2.038426 CCATGCCATGCAATTCATCCAT 59.962 45.455 0.00 0.00 43.62 3.41
1632 4942 7.526608 CCTCAACTTGCAAGTCGAAATATTTA 58.473 34.615 31.20 5.07 38.57 1.40
1638 4948 1.333619 GCCTCAACTTGCAAGTCGAAA 59.666 47.619 31.20 15.83 38.57 3.46
1641 4951 1.205064 CGCCTCAACTTGCAAGTCG 59.795 57.895 31.20 24.48 38.57 4.18
1673 4983 3.640967 TCTGCCAAAAACCTGCATAGTTT 59.359 39.130 8.73 8.73 39.07 2.66
1731 5041 8.715998 CATAGATTTCTTCCATTCCTATTGTCG 58.284 37.037 0.00 0.00 0.00 4.35
1801 5111 4.523083 ACTTCAAGTGTTTGTAAGCCTGA 58.477 39.130 0.00 0.00 35.73 3.86
1875 5185 1.880027 CAGTGGTTTCACAAGTAGGGC 59.120 52.381 0.00 0.00 45.91 5.19
1903 5213 0.179100 CAGTGTCAGGCATACCCTCG 60.179 60.000 0.00 0.00 44.09 4.63
1907 5217 0.613260 TGGTCAGTGTCAGGCATACC 59.387 55.000 0.00 0.00 0.00 2.73
1930 5240 4.016444 GGACACCATTGGCTCTATTGAAA 58.984 43.478 1.54 0.00 0.00 2.69
1943 5253 0.971959 ATGCCATTGCGGACACCATT 60.972 50.000 0.00 0.00 41.78 3.16
1945 5255 2.035469 ATGCCATTGCGGACACCA 59.965 55.556 0.00 0.00 41.78 4.17
1957 5267 0.447406 CGAGCAATTTCGTGATGCCA 59.553 50.000 0.00 0.00 40.93 4.92
1972 5282 2.826428 TCTATGTGCATTTCTCCGAGC 58.174 47.619 0.00 0.00 0.00 5.03
1976 5286 3.825328 ACCCATCTATGTGCATTTCTCC 58.175 45.455 0.00 0.00 0.00 3.71
1977 5287 5.822519 TGTAACCCATCTATGTGCATTTCTC 59.177 40.000 0.00 0.00 0.00 2.87
2031 5341 5.716703 CCAGGGGATGACTTTCTAAATTTGT 59.283 40.000 0.00 0.00 0.00 2.83
2120 5430 6.151691 TGTAAGATGAAAATGCACTGCTTTC 58.848 36.000 1.98 5.78 0.00 2.62
2124 5434 5.051891 ACTGTAAGATGAAAATGCACTGC 57.948 39.130 0.00 0.00 37.43 4.40
2125 5435 7.369803 ACTACTGTAAGATGAAAATGCACTG 57.630 36.000 0.00 0.00 37.43 3.66
2153 5463 8.759481 TGCCATATTAAACAAACCATATGAGA 57.241 30.769 3.65 0.00 0.00 3.27
2154 5464 8.632679 ACTGCCATATTAAACAAACCATATGAG 58.367 33.333 3.65 0.00 0.00 2.90
2155 5465 8.412456 CACTGCCATATTAAACAAACCATATGA 58.588 33.333 3.65 0.00 0.00 2.15
2156 5466 8.196771 ACACTGCCATATTAAACAAACCATATG 58.803 33.333 0.00 0.00 0.00 1.78
2157 5467 8.305046 ACACTGCCATATTAAACAAACCATAT 57.695 30.769 0.00 0.00 0.00 1.78
2158 5468 7.710676 ACACTGCCATATTAAACAAACCATA 57.289 32.000 0.00 0.00 0.00 2.74
2159 5469 6.603940 ACACTGCCATATTAAACAAACCAT 57.396 33.333 0.00 0.00 0.00 3.55
2160 5470 6.151985 CCTACACTGCCATATTAAACAAACCA 59.848 38.462 0.00 0.00 0.00 3.67
2172 5482 3.134623 CCTTGTGATCCTACACTGCCATA 59.865 47.826 0.00 0.00 40.87 2.74
3164 6863 3.953775 CAGAACCGCACCACCCCT 61.954 66.667 0.00 0.00 0.00 4.79
3715 7450 4.019174 CAAGGGAAATATGCAGGACTTGT 58.981 43.478 0.00 0.00 31.89 3.16
4172 9232 6.590234 AAGTAAAAATCTGATTGGACACCC 57.410 37.500 3.22 0.00 0.00 4.61
4204 9264 3.302434 GCACATTTCGATTGCAAGACATG 59.698 43.478 4.94 9.03 36.22 3.21
4351 9411 3.395639 TCACGTGTTTCATTACCCACTC 58.604 45.455 16.51 0.00 0.00 3.51
4446 9506 8.927411 ACTGCTAAGCCCAAATTCATATATTTT 58.073 29.630 0.00 0.00 0.00 1.82
4447 9507 8.482852 ACTGCTAAGCCCAAATTCATATATTT 57.517 30.769 0.00 0.00 0.00 1.40
4519 9579 8.806146 ACCAAATTGAATAAACAAGAGCTATGT 58.194 29.630 0.00 0.00 33.22 2.29
4750 9810 5.840243 TCCTAATGCAAATTGAGGTCATG 57.160 39.130 0.00 0.00 0.00 3.07
4753 9813 5.841957 ACATCCTAATGCAAATTGAGGTC 57.158 39.130 0.00 0.00 36.26 3.85
4762 9822 5.991606 GCACTGAGTATACATCCTAATGCAA 59.008 40.000 5.50 0.00 36.26 4.08
4804 9864 4.589908 ACTAACTGATTCATGGGGTTGTC 58.410 43.478 0.00 0.00 0.00 3.18
4830 9890 3.985925 GCTGAAAAAGACAAGCCATTCTG 59.014 43.478 0.00 0.00 0.00 3.02
4833 9893 3.801293 GCTGCTGAAAAAGACAAGCCATT 60.801 43.478 0.00 0.00 0.00 3.16
4908 10142 4.336433 AGCCGAAATAACATCATCAGTTGG 59.664 41.667 0.00 0.00 0.00 3.77
4923 10157 0.527565 GATGTTGCACCAGCCGAAAT 59.472 50.000 0.00 0.00 41.13 2.17
4927 10161 2.562912 GTGATGTTGCACCAGCCG 59.437 61.111 0.00 0.00 41.13 5.52
4966 10200 9.224267 CCTGTGGAAAATATCGATGAATTATCT 57.776 33.333 8.54 0.00 33.44 1.98
4973 10207 4.408921 AGTCCCTGTGGAAAATATCGATGA 59.591 41.667 8.54 0.00 44.07 2.92
4975 10209 5.012148 CCTAGTCCCTGTGGAAAATATCGAT 59.988 44.000 2.16 2.16 44.07 3.59
4989 10224 3.951663 CCAAAAAGGTACCTAGTCCCTG 58.048 50.000 16.67 7.06 0.00 4.45
5130 10365 3.002656 ACATCAACTCTTGTGCAACGAAG 59.997 43.478 0.00 0.00 42.39 3.79
5179 10414 1.751351 TCACCGCAACAACCATTCAAA 59.249 42.857 0.00 0.00 0.00 2.69
5180 10415 1.393603 TCACCGCAACAACCATTCAA 58.606 45.000 0.00 0.00 0.00 2.69
5181 10416 1.614996 ATCACCGCAACAACCATTCA 58.385 45.000 0.00 0.00 0.00 2.57
5186 10421 2.131972 GGAAAAATCACCGCAACAACC 58.868 47.619 0.00 0.00 0.00 3.77
5196 10431 3.004944 TGCCGGTAAACTGGAAAAATCAC 59.995 43.478 12.29 0.00 45.36 3.06
5200 10435 3.637229 TCATTGCCGGTAAACTGGAAAAA 59.363 39.130 9.67 3.33 43.03 1.94
5254 10489 4.323569 TTCCCCACATGCCAGTTAAATA 57.676 40.909 0.00 0.00 0.00 1.40
5255 10490 2.917713 TCCCCACATGCCAGTTAAAT 57.082 45.000 0.00 0.00 0.00 1.40
5256 10491 2.685106 TTCCCCACATGCCAGTTAAA 57.315 45.000 0.00 0.00 0.00 1.52
5257 10492 2.225242 ACATTCCCCACATGCCAGTTAA 60.225 45.455 0.00 0.00 0.00 2.01
5258 10493 1.357420 ACATTCCCCACATGCCAGTTA 59.643 47.619 0.00 0.00 0.00 2.24
5259 10494 0.114954 ACATTCCCCACATGCCAGTT 59.885 50.000 0.00 0.00 0.00 3.16
5260 10495 0.114954 AACATTCCCCACATGCCAGT 59.885 50.000 0.00 0.00 0.00 4.00
5261 10496 0.819582 GAACATTCCCCACATGCCAG 59.180 55.000 0.00 0.00 0.00 4.85
5270 10505 4.409247 AGTGTGGATACTAGAACATTCCCC 59.591 45.833 0.00 0.00 37.61 4.81
5275 10511 6.012858 TCCCAAAAGTGTGGATACTAGAACAT 60.013 38.462 0.00 0.00 41.65 2.71
5363 10600 2.267006 CATGACGCCTGAGCCACT 59.733 61.111 0.00 0.00 34.57 4.00
5366 10603 2.202987 CTCCATGACGCCTGAGCC 60.203 66.667 0.00 0.00 34.57 4.70
5591 10829 4.864806 GTCAGAAAGCGTCTTACATCATGA 59.135 41.667 0.00 0.00 32.70 3.07
5606 10844 7.715265 AATGTTGTAGTGTAGTGTCAGAAAG 57.285 36.000 0.00 0.00 0.00 2.62
5655 10893 7.136289 TGTCCCATAATGTAAGACGTTTTTC 57.864 36.000 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.