Multiple sequence alignment - TraesCS7B01G371000

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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 TraesCS7B01G371000 chr7B 100.000 2288 0 0 1 2288 636982945 636985232 0.000000e+00 4226.0
1 TraesCS7B01G371000 chr7B 85.673 691 67 22 622 1294 634580178 634579502 0.000000e+00 699.0
2 TraesCS7B01G371000 chr7B 85.821 670 54 24 637 1292 636940033 636940675 0.000000e+00 673.0
3 TraesCS7B01G371000 chr7B 85.855 509 56 12 795 1294 634647580 634647079 5.600000e-146 527.0
4 TraesCS7B01G371000 chr7B 88.265 196 15 5 586 776 634647762 634647570 6.360000e-56 228.0
5 TraesCS7B01G371000 chr7D 94.837 1317 41 16 1 1296 575440615 575441925 0.000000e+00 2030.0
6 TraesCS7B01G371000 chr7D 89.690 902 63 21 1406 2288 575441920 575442810 0.000000e+00 1123.0
7 TraesCS7B01G371000 chr7D 80.495 1333 161 68 1 1294 574765133 574763861 0.000000e+00 929.0
8 TraesCS7B01G371000 chr7D 84.371 723 65 27 586 1294 574774558 574773870 0.000000e+00 665.0
9 TraesCS7B01G371000 chr7D 86.022 651 46 20 652 1292 575408057 575408672 0.000000e+00 656.0
10 TraesCS7B01G371000 chr7D 84.131 397 56 5 1659 2052 598178784 598178392 5.970000e-101 377.0
11 TraesCS7B01G371000 chr7A 90.049 824 54 16 1406 2212 665428019 665428831 0.000000e+00 1042.0
12 TraesCS7B01G371000 chr7A 96.815 471 10 2 830 1296 665427555 665428024 0.000000e+00 782.0
13 TraesCS7B01G371000 chr7A 85.251 678 64 21 628 1294 664415345 664414693 0.000000e+00 665.0
14 TraesCS7B01G371000 chr7A 84.421 674 62 26 637 1292 664999447 665000095 6.940000e-175 623.0
15 TraesCS7B01G371000 chr7A 90.698 344 18 10 374 712 665426741 665427075 1.610000e-121 446.0
16 TraesCS7B01G371000 chr7A 84.080 402 49 9 1659 2057 75066133 75066522 7.720000e-100 374.0
17 TraesCS7B01G371000 chr7A 87.349 332 32 7 1 323 665426406 665426736 2.780000e-99 372.0
18 TraesCS7B01G371000 chr7A 85.030 167 20 3 9 175 664418019 664417858 5.060000e-37 165.0
19 TraesCS7B01G371000 chr7A 90.278 72 7 0 652 723 664374387 664374316 6.730000e-16 95.3
20 TraesCS7B01G371000 chr1B 82.482 411 51 12 1655 2053 631962644 631963045 7.830000e-90 340.0
21 TraesCS7B01G371000 chr1B 91.597 119 10 0 1293 1411 448532952 448532834 5.060000e-37 165.0
22 TraesCS7B01G371000 chr1B 90.909 121 11 0 1293 1413 15300330 15300450 1.820000e-36 163.0
23 TraesCS7B01G371000 chr2A 81.728 405 55 11 1659 2057 77237544 77237153 1.020000e-83 320.0
24 TraesCS7B01G371000 chr6A 83.149 362 46 11 1697 2051 94192666 94193019 1.320000e-82 316.0
25 TraesCS7B01G371000 chr3B 82.682 358 54 7 1672 2025 542753925 542753572 6.140000e-81 311.0
26 TraesCS7B01G371000 chr3B 87.879 132 15 1 1286 1417 828461792 828461662 1.090000e-33 154.0
27 TraesCS7B01G371000 chr2D 83.183 333 43 11 1687 2012 76750793 76750467 2.220000e-75 292.0
28 TraesCS7B01G371000 chr4A 79.710 414 60 17 1658 2053 584660593 584661000 6.230000e-71 278.0
29 TraesCS7B01G371000 chr4A 91.525 118 10 0 1293 1410 184570028 184569911 1.820000e-36 163.0
30 TraesCS7B01G371000 chr4A 83.607 122 10 4 1659 1772 644441486 644441367 3.110000e-19 106.0
31 TraesCS7B01G371000 chr3D 94.152 171 9 1 88 257 594534898 594534728 2.250000e-65 259.0
32 TraesCS7B01G371000 chr6B 89.231 130 13 1 1283 1411 179700545 179700416 6.540000e-36 161.0
33 TraesCS7B01G371000 chr5D 89.764 127 12 1 1287 1412 420228290 420228164 6.540000e-36 161.0
34 TraesCS7B01G371000 chr4B 89.764 127 12 1 1287 1413 564373932 564374057 6.540000e-36 161.0
35 TraesCS7B01G371000 chr4B 87.313 134 16 1 1290 1422 626735719 626735586 3.940000e-33 152.0
36 TraesCS7B01G371000 chr3A 89.147 129 12 2 1289 1415 619645859 619645987 2.350000e-35 159.0


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 TraesCS7B01G371000 chr7B 636982945 636985232 2287 False 4226.0 4226 100.00000 1 2288 1 chr7B.!!$F2 2287
1 TraesCS7B01G371000 chr7B 634579502 634580178 676 True 699.0 699 85.67300 622 1294 1 chr7B.!!$R1 672
2 TraesCS7B01G371000 chr7B 636940033 636940675 642 False 673.0 673 85.82100 637 1292 1 chr7B.!!$F1 655
3 TraesCS7B01G371000 chr7B 634647079 634647762 683 True 377.5 527 87.06000 586 1294 2 chr7B.!!$R2 708
4 TraesCS7B01G371000 chr7D 575440615 575442810 2195 False 1576.5 2030 92.26350 1 2288 2 chr7D.!!$F2 2287
5 TraesCS7B01G371000 chr7D 574763861 574765133 1272 True 929.0 929 80.49500 1 1294 1 chr7D.!!$R1 1293
6 TraesCS7B01G371000 chr7D 574773870 574774558 688 True 665.0 665 84.37100 586 1294 1 chr7D.!!$R2 708
7 TraesCS7B01G371000 chr7D 575408057 575408672 615 False 656.0 656 86.02200 652 1292 1 chr7D.!!$F1 640
8 TraesCS7B01G371000 chr7A 665426406 665428831 2425 False 660.5 1042 91.22775 1 2212 4 chr7A.!!$F3 2211
9 TraesCS7B01G371000 chr7A 664999447 665000095 648 False 623.0 623 84.42100 637 1292 1 chr7A.!!$F2 655
10 TraesCS7B01G371000 chr7A 664414693 664418019 3326 True 415.0 665 85.14050 9 1294 2 chr7A.!!$R2 1285

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
563 2396 0.532862 AATCTAGCGGCCGGTTCATG 60.533 55.0 37.09 21.79 0.0 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1386 3931 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.0 5.23 0.0 44.66 2.12 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
41 42 5.005094 TGTTAATTAGAACCCCCAAAGTCG 58.995 41.667 0.00 0.00 0.00 4.18
138 144 1.826720 CGGTGGTAGCTAGGTTTGGTA 59.173 52.381 0.00 0.00 0.00 3.25
179 187 5.991606 TGATTAATCCATGACGAACTCATCC 59.008 40.000 12.90 0.00 37.53 3.51
185 193 3.490590 CCATGACGAACTCATCCTCTCAG 60.491 52.174 0.00 0.00 37.53 3.35
191 199 1.774110 ACTCATCCTCTCAGCGTGAT 58.226 50.000 0.00 0.00 0.00 3.06
286 1900 1.917273 TTCCAGTTCTATGCGTACGC 58.083 50.000 32.49 32.49 42.35 4.42
360 1975 8.442632 TGGAGACACATATTTTTCATCATCTC 57.557 34.615 0.00 0.00 33.40 2.75
415 2033 6.834168 AAAACCCAGGTACATGTCTAATTG 57.166 37.500 0.00 0.00 0.00 2.32
563 2396 0.532862 AATCTAGCGGCCGGTTCATG 60.533 55.000 37.09 21.79 0.00 3.07
612 2469 2.579624 TAGCTGGGTAATTGAGGGGA 57.420 50.000 0.00 0.00 0.00 4.81
703 2857 4.985413 ACGATAGCCAACATGTTTGAATG 58.015 39.130 13.55 0.63 42.67 2.67
706 2860 3.472283 AGCCAACATGTTTGAATGCAA 57.528 38.095 13.55 0.00 0.00 4.08
755 2912 2.300723 ACGCCACCACAGAACAGTAATA 59.699 45.455 0.00 0.00 0.00 0.98
776 2973 4.608170 ACTTCCATTCCTCTCTCTCTCT 57.392 45.455 0.00 0.00 0.00 3.10
777 2974 4.536765 ACTTCCATTCCTCTCTCTCTCTC 58.463 47.826 0.00 0.00 0.00 3.20
778 2975 4.230502 ACTTCCATTCCTCTCTCTCTCTCT 59.769 45.833 0.00 0.00 0.00 3.10
779 2976 5.431731 ACTTCCATTCCTCTCTCTCTCTCTA 59.568 44.000 0.00 0.00 0.00 2.43
780 2977 6.103205 ACTTCCATTCCTCTCTCTCTCTCTAT 59.897 42.308 0.00 0.00 0.00 1.98
781 2978 7.294720 ACTTCCATTCCTCTCTCTCTCTCTATA 59.705 40.741 0.00 0.00 0.00 1.31
782 2979 7.016153 TCCATTCCTCTCTCTCTCTCTATAC 57.984 44.000 0.00 0.00 0.00 1.47
783 2980 6.012858 TCCATTCCTCTCTCTCTCTCTATACC 60.013 46.154 0.00 0.00 0.00 2.73
784 2981 5.836024 TTCCTCTCTCTCTCTCTATACCC 57.164 47.826 0.00 0.00 0.00 3.69
785 2982 3.835978 TCCTCTCTCTCTCTCTATACCCG 59.164 52.174 0.00 0.00 0.00 5.28
786 2983 3.596214 CTCTCTCTCTCTCTATACCCGC 58.404 54.545 0.00 0.00 0.00 6.13
787 2984 2.303600 TCTCTCTCTCTCTATACCCGCC 59.696 54.545 0.00 0.00 0.00 6.13
788 2985 2.039216 CTCTCTCTCTCTATACCCGCCA 59.961 54.545 0.00 0.00 0.00 5.69
789 2986 2.156098 CTCTCTCTCTATACCCGCCAC 58.844 57.143 0.00 0.00 0.00 5.01
790 2987 1.493446 TCTCTCTCTATACCCGCCACA 59.507 52.381 0.00 0.00 0.00 4.17
791 2988 2.108425 TCTCTCTCTATACCCGCCACAT 59.892 50.000 0.00 0.00 0.00 3.21
792 2989 3.329814 TCTCTCTCTATACCCGCCACATA 59.670 47.826 0.00 0.00 0.00 2.29
813 3010 4.551215 ATCTCTCTCCCTCTAACCACAT 57.449 45.455 0.00 0.00 0.00 3.21
816 3013 3.366396 TCTCTCCCTCTAACCACATGAC 58.634 50.000 0.00 0.00 0.00 3.06
817 3014 3.011821 TCTCTCCCTCTAACCACATGACT 59.988 47.826 0.00 0.00 0.00 3.41
1212 3757 2.291043 CGGGTACAAGCAGGAGGGT 61.291 63.158 0.00 0.00 0.00 4.34
1259 3804 1.927527 AGTTCAGGCAGGCCCTCAT 60.928 57.895 6.70 0.00 44.09 2.90
1297 3842 9.406113 TCTCCAAGAACTACTAATTAGTACTCC 57.594 37.037 19.30 11.55 40.44 3.85
1298 3843 8.530804 TCCAAGAACTACTAATTAGTACTCCC 57.469 38.462 19.30 10.11 40.44 4.30
1299 3844 8.342270 TCCAAGAACTACTAATTAGTACTCCCT 58.658 37.037 19.30 11.80 40.44 4.20
1300 3845 8.631797 CCAAGAACTACTAATTAGTACTCCCTC 58.368 40.741 19.30 11.76 40.44 4.30
1301 3846 8.631797 CAAGAACTACTAATTAGTACTCCCTCC 58.368 40.741 19.30 6.73 40.44 4.30
1302 3847 7.880623 AGAACTACTAATTAGTACTCCCTCCA 58.119 38.462 19.30 0.69 40.44 3.86
1303 3848 8.512813 AGAACTACTAATTAGTACTCCCTCCAT 58.487 37.037 19.30 2.65 40.44 3.41
1304 3849 8.709272 AACTACTAATTAGTACTCCCTCCATC 57.291 38.462 19.30 0.00 40.44 3.51
1305 3850 7.240167 ACTACTAATTAGTACTCCCTCCATCC 58.760 42.308 19.30 0.00 39.45 3.51
1306 3851 5.078256 ACTAATTAGTACTCCCTCCATCCG 58.922 45.833 16.60 0.00 34.13 4.18
1307 3852 3.897657 ATTAGTACTCCCTCCATCCGA 57.102 47.619 0.00 0.00 0.00 4.55
1308 3853 3.675348 TTAGTACTCCCTCCATCCGAA 57.325 47.619 0.00 0.00 0.00 4.30
1309 3854 2.544844 AGTACTCCCTCCATCCGAAA 57.455 50.000 0.00 0.00 0.00 3.46
1310 3855 2.829023 AGTACTCCCTCCATCCGAAAA 58.171 47.619 0.00 0.00 0.00 2.29
1311 3856 3.385115 AGTACTCCCTCCATCCGAAAAT 58.615 45.455 0.00 0.00 0.00 1.82
1312 3857 4.553678 AGTACTCCCTCCATCCGAAAATA 58.446 43.478 0.00 0.00 0.00 1.40
1313 3858 3.840124 ACTCCCTCCATCCGAAAATAC 57.160 47.619 0.00 0.00 0.00 1.89
1314 3859 3.385115 ACTCCCTCCATCCGAAAATACT 58.615 45.455 0.00 0.00 0.00 2.12
1315 3860 3.780850 ACTCCCTCCATCCGAAAATACTT 59.219 43.478 0.00 0.00 0.00 2.24
1316 3861 4.130118 CTCCCTCCATCCGAAAATACTTG 58.870 47.826 0.00 0.00 0.00 3.16
1317 3862 3.521937 TCCCTCCATCCGAAAATACTTGT 59.478 43.478 0.00 0.00 0.00 3.16
1318 3863 3.877508 CCCTCCATCCGAAAATACTTGTC 59.122 47.826 0.00 0.00 0.00 3.18
1319 3864 4.513442 CCTCCATCCGAAAATACTTGTCA 58.487 43.478 0.00 0.00 0.00 3.58
1320 3865 4.941263 CCTCCATCCGAAAATACTTGTCAA 59.059 41.667 0.00 0.00 0.00 3.18
1321 3866 5.414454 CCTCCATCCGAAAATACTTGTCAAA 59.586 40.000 0.00 0.00 0.00 2.69
1322 3867 6.403636 CCTCCATCCGAAAATACTTGTCAAAG 60.404 42.308 0.00 0.00 39.49 2.77
1323 3868 5.414454 TCCATCCGAAAATACTTGTCAAAGG 59.586 40.000 0.00 0.00 37.76 3.11
1324 3869 5.414454 CCATCCGAAAATACTTGTCAAAGGA 59.586 40.000 0.00 0.00 37.76 3.36
1325 3870 6.072175 CCATCCGAAAATACTTGTCAAAGGAA 60.072 38.462 0.00 0.00 37.76 3.36
1326 3871 7.362920 CCATCCGAAAATACTTGTCAAAGGAAT 60.363 37.037 0.00 0.00 37.76 3.01
1327 3872 6.908825 TCCGAAAATACTTGTCAAAGGAATG 58.091 36.000 0.00 0.00 37.76 2.67
1328 3873 6.072175 TCCGAAAATACTTGTCAAAGGAATGG 60.072 38.462 0.00 0.00 37.76 3.16
1329 3874 6.072175 CCGAAAATACTTGTCAAAGGAATGGA 60.072 38.462 0.00 0.00 37.76 3.41
1330 3875 7.362920 CCGAAAATACTTGTCAAAGGAATGGAT 60.363 37.037 0.00 0.00 37.76 3.41
1331 3876 8.673711 CGAAAATACTTGTCAAAGGAATGGATA 58.326 33.333 0.00 0.00 37.76 2.59
1335 3880 9.574516 AATACTTGTCAAAGGAATGGATATACC 57.425 33.333 0.00 0.00 37.76 2.73
1336 3881 7.213178 ACTTGTCAAAGGAATGGATATACCT 57.787 36.000 0.00 0.00 37.76 3.08
1337 3882 8.331931 ACTTGTCAAAGGAATGGATATACCTA 57.668 34.615 0.00 0.00 37.76 3.08
1338 3883 8.778059 ACTTGTCAAAGGAATGGATATACCTAA 58.222 33.333 0.00 0.00 37.76 2.69
1339 3884 9.627123 CTTGTCAAAGGAATGGATATACCTAAA 57.373 33.333 0.00 0.00 39.86 1.85
1341 3886 9.573166 TGTCAAAGGAATGGATATACCTAAATG 57.427 33.333 0.00 0.00 39.86 2.32
1342 3887 9.574516 GTCAAAGGAATGGATATACCTAAATGT 57.425 33.333 0.00 0.00 39.86 2.71
1395 3940 5.997732 CATTTCTGCAACAAGTATTTCCG 57.002 39.130 0.00 0.00 0.00 4.30
1396 3941 4.497473 TTTCTGCAACAAGTATTTCCGG 57.503 40.909 0.00 0.00 0.00 5.14
1397 3942 3.410631 TCTGCAACAAGTATTTCCGGA 57.589 42.857 0.00 0.00 0.00 5.14
1398 3943 3.071479 TCTGCAACAAGTATTTCCGGAC 58.929 45.455 1.83 0.00 0.00 4.79
1399 3944 1.801771 TGCAACAAGTATTTCCGGACG 59.198 47.619 1.83 0.00 0.00 4.79
1400 3945 1.129811 GCAACAAGTATTTCCGGACGG 59.870 52.381 1.83 3.96 0.00 4.79
1401 3946 2.690786 CAACAAGTATTTCCGGACGGA 58.309 47.619 1.83 9.76 43.52 4.69
1402 3947 2.667473 ACAAGTATTTCCGGACGGAG 57.333 50.000 13.64 3.15 46.06 4.63
1403 3948 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
1404 3949 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
1405 3950 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
1406 3951 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
1407 3952 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
1408 3953 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
1409 3954 0.967380 TTTCCGGACGGAGGGAGTAC 60.967 60.000 13.64 0.00 46.06 2.73
1410 3955 1.856539 TTCCGGACGGAGGGAGTACT 61.857 60.000 13.64 0.00 46.06 2.73
1454 3999 1.670967 CGGTGGACTTCTTCGGGTAAC 60.671 57.143 0.00 0.00 0.00 2.50
1459 4004 4.219288 GTGGACTTCTTCGGGTAACTAAGA 59.781 45.833 0.00 0.00 36.97 2.10
1483 4028 2.229792 GATTCCTTGGTGCTGTTGACA 58.770 47.619 0.00 0.00 0.00 3.58
1525 4071 5.230097 CACGTTTCTTCTCTTTTGCCTTTTC 59.770 40.000 0.00 0.00 0.00 2.29
1575 4121 2.958355 AGGTTGCCATATGTATTGTGCC 59.042 45.455 1.24 0.00 0.00 5.01
1581 4127 4.582656 TGCCATATGTATTGTGCCCTTTAC 59.417 41.667 1.24 0.00 0.00 2.01
1624 4170 9.153303 TACGGATAGACCTCCTGTCATATACGT 62.153 44.444 17.63 17.63 45.70 3.57
1625 4171 9.153303 ACGGATAGACCTCCTGTCATATACGTA 62.153 44.444 14.58 0.00 44.12 3.57
1693 4239 2.282110 CCCACGGACATTGCACCA 60.282 61.111 0.00 0.00 0.00 4.17
1798 4344 7.334421 TGTTTTAGGTGCTTGCAAAATTTTGTA 59.666 29.630 27.13 22.18 40.24 2.41
1811 4357 9.228949 TGCAAAATTTTGTAGCCAAATGATATT 57.771 25.926 27.13 0.00 40.14 1.28
1822 4368 4.320057 GCCAAATGATATTCGAGGAGCTTG 60.320 45.833 0.00 0.00 0.00 4.01
1871 4418 2.358322 AAATCTGAAACGTGGGTGGT 57.642 45.000 0.00 0.00 0.00 4.16
1925 4473 4.335082 TCATTCGTTGTTATTTGGCGAG 57.665 40.909 0.00 0.00 33.09 5.03
1977 4525 5.953183 CTCATAAGCAATGCCACAAAGTTA 58.047 37.500 0.00 0.00 35.38 2.24
1983 4531 3.922240 GCAATGCCACAAAGTTACTGATG 59.078 43.478 0.00 0.00 0.00 3.07
1988 4536 5.347342 TGCCACAAAGTTACTGATGTTTTG 58.653 37.500 1.95 0.00 35.47 2.44
1995 4555 9.651913 ACAAAGTTACTGATGTTTTGTCAATTT 57.348 25.926 0.00 0.00 37.39 1.82
2021 4581 8.918961 TTTTATTTTACTATTCATTGCGTGGG 57.081 30.769 0.00 0.00 0.00 4.61
2022 4582 7.633193 TTATTTTACTATTCATTGCGTGGGT 57.367 32.000 0.00 0.00 0.00 4.51
2023 4583 4.955925 TTTACTATTCATTGCGTGGGTG 57.044 40.909 0.00 0.00 0.00 4.61
2024 4584 1.094785 ACTATTCATTGCGTGGGTGC 58.905 50.000 0.00 0.00 0.00 5.01
2025 4585 1.093972 CTATTCATTGCGTGGGTGCA 58.906 50.000 0.00 0.00 44.61 4.57
2026 4586 0.808125 TATTCATTGCGTGGGTGCAC 59.192 50.000 8.80 8.80 46.25 4.57
2027 4587 1.876497 ATTCATTGCGTGGGTGCACC 61.876 55.000 28.57 28.57 46.25 5.01
2056 4631 2.233922 GGTGCAGCCACTACTTTCTCTA 59.766 50.000 4.03 0.00 41.75 2.43
2062 4637 4.024670 AGCCACTACTTTCTCTATTCGGT 58.975 43.478 0.00 0.00 0.00 4.69
2080 4655 6.460664 TTCGGTATATATGCACATGTTTCG 57.539 37.500 0.00 0.00 0.00 3.46
2147 4727 4.318332 TGAGAGTGGCATGTTTACTTCTG 58.682 43.478 0.00 0.00 0.00 3.02
2170 4751 5.711976 TGATGATGCAGAGGTCGAGATATAA 59.288 40.000 0.00 0.00 0.00 0.98
2174 4755 2.094442 GCAGAGGTCGAGATATAAGCCC 60.094 54.545 0.00 0.00 0.00 5.19
2183 4764 4.899457 TCGAGATATAAGCCCCTCTTTTCA 59.101 41.667 0.00 0.00 36.25 2.69
2224 4805 9.677567 TGTTTATTTCCATCGAAAGAAAAAGAG 57.322 29.630 14.80 0.00 45.69 2.85
2225 4806 9.678941 GTTTATTTCCATCGAAAGAAAAAGAGT 57.321 29.630 14.80 3.97 45.69 3.24
2253 4838 2.170012 AGCCTCCGGACCTTACAATA 57.830 50.000 0.00 0.00 0.00 1.90
2256 4841 2.744166 GCCTCCGGACCTTACAATAACC 60.744 54.545 0.00 0.00 0.00 2.85
2257 4842 2.770232 CCTCCGGACCTTACAATAACCT 59.230 50.000 0.00 0.00 0.00 3.50
2258 4843 3.199289 CCTCCGGACCTTACAATAACCTT 59.801 47.826 0.00 0.00 0.00 3.50
2259 4844 4.189231 CTCCGGACCTTACAATAACCTTG 58.811 47.826 0.00 0.00 0.00 3.61
2260 4845 3.839490 TCCGGACCTTACAATAACCTTGA 59.161 43.478 0.00 0.00 0.00 3.02
2261 4846 4.472108 TCCGGACCTTACAATAACCTTGAT 59.528 41.667 0.00 0.00 0.00 2.57
2262 4847 5.662208 TCCGGACCTTACAATAACCTTGATA 59.338 40.000 0.00 0.00 0.00 2.15
2263 4848 5.989777 CCGGACCTTACAATAACCTTGATAG 59.010 44.000 0.00 0.00 0.00 2.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 4.286291 TCTTCTTTTTCTAGGTGGGAGGTC 59.714 45.833 0.00 0.00 0.00 3.85
74 76 5.067674 ACATGCTTGTATGTTTGTGTTCTGT 59.932 36.000 2.92 0.00 38.05 3.41
166 174 1.474478 GCTGAGAGGATGAGTTCGTCA 59.526 52.381 3.94 0.00 40.87 4.35
179 187 2.571212 AGTCCTCTATCACGCTGAGAG 58.429 52.381 4.04 4.04 37.08 3.20
185 193 7.822658 AGATTAAGAATAGTCCTCTATCACGC 58.177 38.462 0.00 0.00 36.02 5.34
286 1900 4.161333 CCGCATGCAGAGTTTCTTTTAAG 58.839 43.478 19.57 0.00 0.00 1.85
313 1927 5.775195 CCATCCTCTGACATGTAGGTGTATA 59.225 44.000 11.99 0.00 31.16 1.47
415 2033 4.883585 TCATGTATGTTCCTTCATTGAGCC 59.116 41.667 0.00 0.00 0.00 4.70
703 2857 0.541764 TTGGGGTCAACCTCCATTGC 60.542 55.000 9.36 0.00 40.03 3.56
755 2912 4.230502 AGAGAGAGAGAGAGGAATGGAAGT 59.769 45.833 0.00 0.00 0.00 3.01
776 2973 4.018324 AGAGAGATATGTGGCGGGTATAGA 60.018 45.833 0.00 0.00 0.00 1.98
777 2974 4.274147 AGAGAGATATGTGGCGGGTATAG 58.726 47.826 0.00 0.00 0.00 1.31
778 2975 4.270834 GAGAGAGATATGTGGCGGGTATA 58.729 47.826 0.00 0.00 0.00 1.47
779 2976 3.093057 GAGAGAGATATGTGGCGGGTAT 58.907 50.000 0.00 0.00 0.00 2.73
780 2977 2.515854 GAGAGAGATATGTGGCGGGTA 58.484 52.381 0.00 0.00 0.00 3.69
781 2978 1.333177 GAGAGAGATATGTGGCGGGT 58.667 55.000 0.00 0.00 0.00 5.28
782 2979 0.605589 GGAGAGAGATATGTGGCGGG 59.394 60.000 0.00 0.00 0.00 6.13
783 2980 0.605589 GGGAGAGAGATATGTGGCGG 59.394 60.000 0.00 0.00 0.00 6.13
784 2981 1.543802 GAGGGAGAGAGATATGTGGCG 59.456 57.143 0.00 0.00 0.00 5.69
785 2982 2.888212 AGAGGGAGAGAGATATGTGGC 58.112 52.381 0.00 0.00 0.00 5.01
786 2983 4.770010 GGTTAGAGGGAGAGAGATATGTGG 59.230 50.000 0.00 0.00 0.00 4.17
787 2984 5.242838 GTGGTTAGAGGGAGAGAGATATGTG 59.757 48.000 0.00 0.00 0.00 3.21
788 2985 5.103473 TGTGGTTAGAGGGAGAGAGATATGT 60.103 44.000 0.00 0.00 0.00 2.29
789 2986 5.389520 TGTGGTTAGAGGGAGAGAGATATG 58.610 45.833 0.00 0.00 0.00 1.78
790 2987 5.671463 TGTGGTTAGAGGGAGAGAGATAT 57.329 43.478 0.00 0.00 0.00 1.63
791 2988 5.134509 TCATGTGGTTAGAGGGAGAGAGATA 59.865 44.000 0.00 0.00 0.00 1.98
792 2989 4.078922 TCATGTGGTTAGAGGGAGAGAGAT 60.079 45.833 0.00 0.00 0.00 2.75
813 3010 5.658190 TGATTGGATCATGAGTACTCAGTCA 59.342 40.000 28.29 18.11 43.61 3.41
816 3013 5.757320 GGTTGATTGGATCATGAGTACTCAG 59.243 44.000 28.29 19.96 43.61 3.35
817 3014 5.189539 TGGTTGATTGGATCATGAGTACTCA 59.810 40.000 27.07 27.07 44.59 3.41
1212 3757 2.520982 CAGGGGACGCGGAGGATA 60.521 66.667 12.47 0.00 0.00 2.59
1296 3841 3.877508 GACAAGTATTTTCGGATGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
1297 3842 4.513442 TGACAAGTATTTTCGGATGGAGG 58.487 43.478 0.00 0.00 0.00 4.30
1298 3843 6.403636 CCTTTGACAAGTATTTTCGGATGGAG 60.404 42.308 0.00 0.00 0.00 3.86
1299 3844 5.414454 CCTTTGACAAGTATTTTCGGATGGA 59.586 40.000 0.00 0.00 0.00 3.41
1300 3845 5.414454 TCCTTTGACAAGTATTTTCGGATGG 59.586 40.000 0.00 0.00 0.00 3.51
1301 3846 6.494893 TCCTTTGACAAGTATTTTCGGATG 57.505 37.500 0.00 0.00 0.00 3.51
1302 3847 7.362920 CCATTCCTTTGACAAGTATTTTCGGAT 60.363 37.037 0.00 0.00 0.00 4.18
1303 3848 6.072175 CCATTCCTTTGACAAGTATTTTCGGA 60.072 38.462 0.00 0.00 0.00 4.55
1304 3849 6.072175 TCCATTCCTTTGACAAGTATTTTCGG 60.072 38.462 0.00 0.00 0.00 4.30
1305 3850 6.908825 TCCATTCCTTTGACAAGTATTTTCG 58.091 36.000 0.00 0.00 0.00 3.46
1309 3854 9.574516 GGTATATCCATTCCTTTGACAAGTATT 57.425 33.333 0.00 0.00 35.97 1.89
1310 3855 8.949421 AGGTATATCCATTCCTTTGACAAGTAT 58.051 33.333 0.00 0.00 39.02 2.12
1311 3856 8.331931 AGGTATATCCATTCCTTTGACAAGTA 57.668 34.615 0.00 0.00 39.02 2.24
1312 3857 7.213178 AGGTATATCCATTCCTTTGACAAGT 57.787 36.000 0.00 0.00 39.02 3.16
1313 3858 9.627123 TTTAGGTATATCCATTCCTTTGACAAG 57.373 33.333 0.00 0.00 39.02 3.16
1315 3860 9.573166 CATTTAGGTATATCCATTCCTTTGACA 57.427 33.333 0.00 0.00 39.02 3.58
1316 3861 9.574516 ACATTTAGGTATATCCATTCCTTTGAC 57.425 33.333 0.00 0.00 39.02 3.18
1355 3900 8.749499 GCAGAAATGCATAAAAGTGAATGTATC 58.251 33.333 0.00 0.00 29.57 2.24
1356 3901 8.252417 TGCAGAAATGCATAAAAGTGAATGTAT 58.748 29.630 0.00 0.00 40.23 2.29
1357 3902 7.600960 TGCAGAAATGCATAAAAGTGAATGTA 58.399 30.769 0.00 0.00 40.23 2.29
1358 3903 6.457355 TGCAGAAATGCATAAAAGTGAATGT 58.543 32.000 0.00 0.00 40.23 2.71
1359 3904 6.954616 TGCAGAAATGCATAAAAGTGAATG 57.045 33.333 0.00 0.00 40.23 2.67
1360 3905 6.930164 TGTTGCAGAAATGCATAAAAGTGAAT 59.070 30.769 0.00 0.00 44.94 2.57
1361 3906 6.279123 TGTTGCAGAAATGCATAAAAGTGAA 58.721 32.000 0.00 0.00 44.94 3.18
1362 3907 5.840715 TGTTGCAGAAATGCATAAAAGTGA 58.159 33.333 0.00 0.00 44.94 3.41
1363 3908 6.201425 ACTTGTTGCAGAAATGCATAAAAGTG 59.799 34.615 17.52 0.00 44.94 3.16
1364 3909 6.282930 ACTTGTTGCAGAAATGCATAAAAGT 58.717 32.000 0.00 14.67 44.94 2.66
1365 3910 6.774354 ACTTGTTGCAGAAATGCATAAAAG 57.226 33.333 0.00 10.15 44.94 2.27
1366 3911 8.830201 AATACTTGTTGCAGAAATGCATAAAA 57.170 26.923 0.00 0.00 44.94 1.52
1367 3912 8.830201 AAATACTTGTTGCAGAAATGCATAAA 57.170 26.923 0.00 1.50 44.94 1.40
1368 3913 7.545265 GGAAATACTTGTTGCAGAAATGCATAA 59.455 33.333 0.00 2.60 44.94 1.90
1369 3914 7.035004 GGAAATACTTGTTGCAGAAATGCATA 58.965 34.615 0.00 0.00 44.94 3.14
1370 3915 5.870978 GGAAATACTTGTTGCAGAAATGCAT 59.129 36.000 3.44 0.00 44.94 3.96
1371 3916 5.229423 GGAAATACTTGTTGCAGAAATGCA 58.771 37.500 0.00 0.00 43.81 3.96
1372 3917 4.324402 CGGAAATACTTGTTGCAGAAATGC 59.676 41.667 0.00 0.00 0.00 3.56
1373 3918 4.858692 CCGGAAATACTTGTTGCAGAAATG 59.141 41.667 0.00 0.00 0.00 2.32
1374 3919 4.764823 TCCGGAAATACTTGTTGCAGAAAT 59.235 37.500 0.00 0.00 0.00 2.17
1375 3920 4.023536 GTCCGGAAATACTTGTTGCAGAAA 60.024 41.667 5.23 0.00 0.00 2.52
1376 3921 3.500680 GTCCGGAAATACTTGTTGCAGAA 59.499 43.478 5.23 0.00 0.00 3.02
1377 3922 3.071479 GTCCGGAAATACTTGTTGCAGA 58.929 45.455 5.23 0.00 0.00 4.26
1378 3923 2.159707 CGTCCGGAAATACTTGTTGCAG 60.160 50.000 5.23 0.00 0.00 4.41
1379 3924 1.801771 CGTCCGGAAATACTTGTTGCA 59.198 47.619 5.23 0.00 0.00 4.08
1380 3925 1.129811 CCGTCCGGAAATACTTGTTGC 59.870 52.381 5.23 0.00 37.50 4.17
1381 3926 2.671396 CTCCGTCCGGAAATACTTGTTG 59.329 50.000 5.23 0.00 44.66 3.33
1382 3927 2.354403 CCTCCGTCCGGAAATACTTGTT 60.354 50.000 5.23 0.00 44.66 2.83
1383 3928 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
1384 3929 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
1385 3930 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
1386 3931 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
1387 3932 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
1388 3933 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
1389 3934 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
1390 3935 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
1391 3936 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
1392 3937 0.982852 TAGTACTCCCTCCGTCCGGA 60.983 60.000 0.00 0.00 42.90 5.14
1393 3938 0.107017 TTAGTACTCCCTCCGTCCGG 60.107 60.000 0.00 0.00 0.00 5.14
1394 3939 1.978454 ATTAGTACTCCCTCCGTCCG 58.022 55.000 0.00 0.00 0.00 4.79
1395 3940 6.267242 AGAATTAATTAGTACTCCCTCCGTCC 59.733 42.308 0.00 0.00 0.00 4.79
1396 3941 7.231115 AGAGAATTAATTAGTACTCCCTCCGTC 59.769 40.741 0.00 0.00 0.00 4.79
1397 3942 7.068061 AGAGAATTAATTAGTACTCCCTCCGT 58.932 38.462 0.00 0.00 0.00 4.69
1398 3943 7.527568 AGAGAATTAATTAGTACTCCCTCCG 57.472 40.000 0.00 0.00 0.00 4.63
1399 3944 9.590828 ACTAGAGAATTAATTAGTACTCCCTCC 57.409 37.037 0.00 0.00 0.00 4.30
1454 3999 2.352960 GCACCAAGGAATCGCTTCTTAG 59.647 50.000 0.00 0.00 0.00 2.18
1459 4004 0.250901 ACAGCACCAAGGAATCGCTT 60.251 50.000 0.00 0.00 0.00 4.68
1483 4028 2.296471 CGTGGTGTAGGAGAGTCAACTT 59.704 50.000 0.00 0.00 0.00 2.66
1525 4071 4.520111 TGTCATTGACCAACCAGAGAAATG 59.480 41.667 14.05 0.00 0.00 2.32
1643 4189 4.109766 CCACGCTCGTACAGAATAATCAA 58.890 43.478 0.00 0.00 0.00 2.57
1653 4199 1.372499 GAACAGCCACGCTCGTACA 60.372 57.895 0.00 0.00 36.40 2.90
1693 4239 1.079405 CAATCGTGGGTGTAGCGGT 60.079 57.895 0.00 0.00 0.00 5.68
1798 4344 3.072184 AGCTCCTCGAATATCATTTGGCT 59.928 43.478 0.00 0.00 0.00 4.75
1811 4357 1.968493 ACTTTGTACCAAGCTCCTCGA 59.032 47.619 6.61 0.00 0.00 4.04
1822 4368 6.554334 TGAGCACAATCTTTACTTTGTACC 57.446 37.500 0.00 0.00 34.42 3.34
1871 4418 7.509141 TGAAATGAAATACAACTCTTGCTCA 57.491 32.000 0.00 0.00 0.00 4.26
1995 4555 9.360093 CCCACGCAATGAATAGTAAAATAAAAA 57.640 29.630 0.00 0.00 0.00 1.94
1999 4559 6.459024 GCACCCACGCAATGAATAGTAAAATA 60.459 38.462 0.00 0.00 0.00 1.40
2008 4568 1.586028 GTGCACCCACGCAATGAAT 59.414 52.632 5.22 0.00 45.14 2.57
2017 4577 2.411290 CACGTTTGGTGCACCCAC 59.589 61.111 32.62 25.88 45.19 4.61
2018 4578 2.830827 CCACGTTTGGTGCACCCA 60.831 61.111 32.62 20.45 45.62 4.51
2019 4579 3.601685 CCCACGTTTGGTGCACCC 61.602 66.667 32.62 16.62 45.62 4.61
2020 4580 2.831284 ACCCACGTTTGGTGCACC 60.831 61.111 29.67 29.67 45.62 5.01
2021 4581 2.411290 CACCCACGTTTGGTGCAC 59.589 61.111 18.29 8.80 46.13 4.57
2025 4585 3.216292 GCTGCACCCACGTTTGGT 61.216 61.111 0.59 0.59 42.10 3.67
2026 4586 3.977244 GGCTGCACCCACGTTTGG 61.977 66.667 0.50 0.00 43.50 3.28
2027 4587 3.215568 TGGCTGCACCCACGTTTG 61.216 61.111 0.50 0.00 37.83 2.93
2028 4588 3.216292 GTGGCTGCACCCACGTTT 61.216 61.111 15.29 0.00 45.13 3.60
2056 4631 6.649141 ACGAAACATGTGCATATATACCGAAT 59.351 34.615 0.00 0.00 0.00 3.34
2118 4695 7.341805 AGTAAACATGCCACTCTCATTCTTAT 58.658 34.615 0.00 0.00 0.00 1.73
2119 4696 6.711277 AGTAAACATGCCACTCTCATTCTTA 58.289 36.000 0.00 0.00 0.00 2.10
2147 4727 4.717233 ATATCTCGACCTCTGCATCATC 57.283 45.455 0.00 0.00 0.00 2.92
2160 4740 4.899457 TGAAAAGAGGGGCTTATATCTCGA 59.101 41.667 0.00 0.00 35.24 4.04
2170 4751 3.966665 TGTGAAAAATGAAAAGAGGGGCT 59.033 39.130 0.00 0.00 0.00 5.19
2240 4825 6.812998 TCTATCAAGGTTATTGTAAGGTCCG 58.187 40.000 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.