Multiple sequence alignment - TraesCS6A01G382200

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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 TraesCS6A01G382200 chr6A 100.000 2414 0 0 1 2414 601265672 601263259 0.000000e+00 4458.0
1 TraesCS6A01G382200 chr6A 81.877 1247 160 41 711 1919 602131184 602132402 0.000000e+00 990.0
2 TraesCS6A01G382200 chr6A 82.507 1029 139 29 975 1980 602075607 602076617 0.000000e+00 865.0
3 TraesCS6A01G382200 chr6A 100.000 160 0 0 2597 2756 601263076 601262917 2.080000e-76 296.0
4 TraesCS6A01G382200 chr6A 86.207 116 12 4 2643 2756 558098808 558098695 3.730000e-24 122.0
5 TraesCS6A01G382200 chr6A 98.246 57 1 0 2700 2756 578849127 578849071 1.750000e-17 100.0
6 TraesCS6A01G382200 chr6D 90.633 1580 92 21 592 2149 454996943 454995398 0.000000e+00 2047.0
7 TraesCS6A01G382200 chr6D 81.285 1261 169 44 727 1935 455421595 455422840 0.000000e+00 959.0
8 TraesCS6A01G382200 chr6D 81.240 1226 152 45 710 1890 455424995 455426187 0.000000e+00 918.0
9 TraesCS6A01G382200 chr6D 92.894 577 33 5 1 570 454998182 454997607 0.000000e+00 832.0
10 TraesCS6A01G382200 chr6D 82.595 971 132 23 1040 1996 454962701 454961754 0.000000e+00 822.0
11 TraesCS6A01G382200 chr6B 90.200 1398 101 12 592 1968 692095221 692093839 0.000000e+00 1790.0
12 TraesCS6A01G382200 chr6B 88.326 1165 110 18 815 1963 691944716 691945870 0.000000e+00 1375.0
13 TraesCS6A01G382200 chr6B 84.484 999 113 22 790 1756 692574232 692575220 0.000000e+00 948.0
14 TraesCS6A01G382200 chr6B 87.711 830 47 19 1 805 691943726 691944525 0.000000e+00 917.0
15 TraesCS6A01G382200 chr6B 81.729 1122 146 39 891 1980 692044827 692043733 0.000000e+00 881.0
16 TraesCS6A01G382200 chr6B 93.080 578 30 8 1 570 692096464 692095889 0.000000e+00 837.0
17 TraesCS6A01G382200 chr6B 80.066 1204 166 49 765 1921 692570467 692571643 0.000000e+00 826.0
18 TraesCS6A01G382200 chr6B 87.678 211 21 5 2205 2414 692074865 692074659 9.860000e-60 241.0
19 TraesCS6A01G382200 chr6B 84.167 120 16 3 130 246 692090551 692090432 2.240000e-21 113.0
20 TraesCS6A01G382200 chrUn 88.204 1119 112 10 1300 2414 79450181 79449079 0.000000e+00 1317.0
21 TraesCS6A01G382200 chrUn 87.619 210 22 4 2205 2414 79448869 79448664 9.860000e-60 241.0
22 TraesCS6A01G382200 chrUn 87.179 117 11 4 2642 2756 86729413 86729527 2.230000e-26 130.0
23 TraesCS6A01G382200 chrUn 83.333 120 17 3 130 246 295316484 295316365 1.040000e-19 108.0
24 TraesCS6A01G382200 chrUn 83.333 120 17 3 130 246 295321663 295321544 1.040000e-19 108.0
25 TraesCS6A01G382200 chr2D 80.851 423 64 15 1998 2414 296407046 296407457 1.590000e-82 316.0
26 TraesCS6A01G382200 chr2D 81.793 357 51 10 2060 2414 398721378 398721034 1.250000e-73 287.0
27 TraesCS6A01G382200 chr2D 75.766 359 67 14 2060 2402 27826440 27826086 2.200000e-36 163.0
28 TraesCS6A01G382200 chr2D 96.907 97 3 0 2658 2754 553583553 553583649 2.200000e-36 163.0
29 TraesCS6A01G382200 chr2A 82.740 365 50 13 2057 2414 367684587 367684945 2.060000e-81 313.0
30 TraesCS6A01G382200 chr5A 98.214 112 2 0 2643 2754 471469298 471469187 2.170000e-46 196.0
31 TraesCS6A01G382200 chr7A 96.491 114 4 0 2643 2756 502415473 502415586 3.620000e-44 189.0
32 TraesCS6A01G382200 chr7A 80.000 180 31 5 2237 2414 646851740 646851564 8.010000e-26 128.0
33 TraesCS6A01G382200 chr3D 87.898 157 14 5 2260 2414 596979694 596979541 2.180000e-41 180.0
34 TraesCS6A01G382200 chr3A 94.690 113 6 0 2643 2755 12324447 12324335 2.820000e-40 176.0
35 TraesCS6A01G382200 chr3A 92.683 41 3 0 2640 2680 702932300 702932340 2.960000e-05 60.2
36 TraesCS6A01G382200 chr4A 81.183 186 32 3 2229 2413 532599303 532599120 2.210000e-31 147.0
37 TraesCS6A01G382200 chr1B 93.333 45 2 1 2640 2683 385220453 385220409 6.370000e-07 65.8
38 TraesCS6A01G382200 chr4D 97.297 37 1 0 2643 2679 10260848 10260812 2.290000e-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 TraesCS6A01G382200 chr6A 601262917 601265672 2755 True 2377.000000 4458 100.0000 1 2756 2 chr6A.!!$R3 2755
1 TraesCS6A01G382200 chr6A 602131184 602132402 1218 False 990.000000 990 81.8770 711 1919 1 chr6A.!!$F2 1208
2 TraesCS6A01G382200 chr6A 602075607 602076617 1010 False 865.000000 865 82.5070 975 1980 1 chr6A.!!$F1 1005
3 TraesCS6A01G382200 chr6D 454995398 454998182 2784 True 1439.500000 2047 91.7635 1 2149 2 chr6D.!!$R2 2148
4 TraesCS6A01G382200 chr6D 455421595 455426187 4592 False 938.500000 959 81.2625 710 1935 2 chr6D.!!$F1 1225
5 TraesCS6A01G382200 chr6D 454961754 454962701 947 True 822.000000 822 82.5950 1040 1996 1 chr6D.!!$R1 956
6 TraesCS6A01G382200 chr6B 691943726 691945870 2144 False 1146.000000 1375 88.0185 1 1963 2 chr6B.!!$F1 1962
7 TraesCS6A01G382200 chr6B 692090432 692096464 6032 True 913.333333 1790 89.1490 1 1968 3 chr6B.!!$R3 1967
8 TraesCS6A01G382200 chr6B 692570467 692575220 4753 False 887.000000 948 82.2750 765 1921 2 chr6B.!!$F2 1156
9 TraesCS6A01G382200 chr6B 692043733 692044827 1094 True 881.000000 881 81.7290 891 1980 1 chr6B.!!$R1 1089
10 TraesCS6A01G382200 chrUn 79448664 79450181 1517 True 779.000000 1317 87.9115 1300 2414 2 chrUn.!!$R3 1114

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
391 404 0.037326 CTCAGTGCTCGGTTTAGCCA 60.037 55.0 0.0 0.0 42.05 4.75 F
656 1383 0.250124 AATCGTGCGTTGTTCCTGGA 60.250 50.0 0.0 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1353 6136 0.477597 TGTTCACCCCTGGGAAGGAT 60.478 55.0 16.20 0.0 38.96 3.24 R
2166 11537 0.806868 TACGAGCGACCGACAAATCT 59.193 50.0 3.95 0.0 0.00 2.40 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
123 125 1.564348 ACCGGTCCCATTTAGAATGCT 59.436 47.619 0.00 0.00 0.00 3.79
273 282 1.939381 GCAGGATACGTGCAGTGTTGA 60.939 52.381 0.00 0.00 46.39 3.18
329 338 4.970003 GGATTGGTTTGAATAAATCGCTCG 59.030 41.667 0.00 0.00 31.20 5.03
375 388 4.502105 TTTGAATATGGCTAGTGGCTCA 57.498 40.909 0.00 0.00 41.46 4.26
391 404 0.037326 CTCAGTGCTCGGTTTAGCCA 60.037 55.000 0.00 0.00 42.05 4.75
401 415 4.385748 GCTCGGTTTAGCCAAGAAATTTTG 59.614 41.667 0.00 0.00 36.45 2.44
407 422 7.382898 GGTTTAGCCAAGAAATTTTGTATCCA 58.617 34.615 0.00 0.00 37.17 3.41
418 433 7.944554 AGAAATTTTGTATCCAGGAAGAGACAA 59.055 33.333 0.00 0.00 44.02 3.18
437 457 5.598830 AGACAAAAGTCTCAAGTGACTCCTA 59.401 40.000 5.38 0.00 45.49 2.94
451 473 3.771479 TGACTCCTATCTGATGCAAGTGT 59.229 43.478 0.00 0.00 0.00 3.55
453 475 5.422012 TGACTCCTATCTGATGCAAGTGTTA 59.578 40.000 0.00 0.00 0.00 2.41
465 487 5.414789 TGCAAGTGTTAGATTACTGGCTA 57.585 39.130 0.00 0.00 42.92 3.93
485 510 2.502142 AGACAGCTTGCCATCAATCA 57.498 45.000 0.00 0.00 0.00 2.57
501 526 6.709397 CCATCAATCAGACAGCTATGTACATT 59.291 38.462 14.77 0.00 40.68 2.71
503 528 7.776933 TCAATCAGACAGCTATGTACATTTC 57.223 36.000 14.77 6.31 40.68 2.17
538 563 4.580580 CCTACCTCTTTTGTTTTGTCAGCT 59.419 41.667 0.00 0.00 0.00 4.24
544 569 0.662619 TTGTTTTGTCAGCTGCTCCG 59.337 50.000 9.47 0.00 0.00 4.63
550 575 1.229428 TGTCAGCTGCTCCGAAAAAG 58.771 50.000 9.47 0.00 0.00 2.27
555 580 0.519077 GCTGCTCCGAAAAAGGACAG 59.481 55.000 0.00 9.59 39.83 3.51
586 611 2.743928 CAGAAGGTCTGGCGGTGC 60.744 66.667 0.00 0.00 40.71 5.01
587 612 3.241530 AGAAGGTCTGGCGGTGCA 61.242 61.111 0.00 0.00 0.00 4.57
590 1317 2.130073 GAAGGTCTGGCGGTGCAAAC 62.130 60.000 0.00 0.00 0.00 2.93
602 1329 3.675775 GCGGTGCAAACCATTATCATGTT 60.676 43.478 0.00 0.00 0.00 2.71
608 1335 7.312154 GTGCAAACCATTATCATGTTCAACTA 58.688 34.615 0.00 0.00 0.00 2.24
656 1383 0.250124 AATCGTGCGTTGTTCCTGGA 60.250 50.000 0.00 0.00 0.00 3.86
657 1384 0.670546 ATCGTGCGTTGTTCCTGGAG 60.671 55.000 0.00 0.00 0.00 3.86
658 1385 2.946762 GTGCGTTGTTCCTGGAGC 59.053 61.111 3.27 3.27 0.00 4.70
659 1386 1.598130 GTGCGTTGTTCCTGGAGCT 60.598 57.895 11.95 0.00 0.00 4.09
701 1428 1.532316 TCCCACGAAACTCGGGTCT 60.532 57.895 0.00 0.00 42.76 3.85
702 1429 1.374252 CCCACGAAACTCGGGTCTG 60.374 63.158 0.00 0.00 42.76 3.51
783 1514 5.070001 GCCTGCATAAACAACTATATCCCA 58.930 41.667 0.00 0.00 0.00 4.37
784 1515 5.048713 GCCTGCATAAACAACTATATCCCAC 60.049 44.000 0.00 0.00 0.00 4.61
803 5310 4.222588 CCCACTTTGATTGGCTCCAAATTA 59.777 41.667 5.34 0.00 39.55 1.40
804 5311 5.279910 CCCACTTTGATTGGCTCCAAATTAA 60.280 40.000 5.34 0.00 39.55 1.40
805 5312 6.408869 CCACTTTGATTGGCTCCAAATTAAT 58.591 36.000 5.34 0.00 39.55 1.40
806 5313 6.880529 CCACTTTGATTGGCTCCAAATTAATT 59.119 34.615 5.34 0.00 39.55 1.40
847 5552 4.547367 CTCCCCATCCGAACCCGC 62.547 72.222 0.00 0.00 0.00 6.13
894 5608 4.703645 GATGGCGATGCTATCTGTAGTA 57.296 45.455 7.76 0.00 42.06 1.82
1019 5749 0.253044 ATGGCGAGGCTTCAGCTTTA 59.747 50.000 11.16 1.84 41.70 1.85
1141 5891 2.827921 TGTGAGTCATCTTGCTGAGCTA 59.172 45.455 5.83 0.00 0.00 3.32
1142 5892 3.450096 TGTGAGTCATCTTGCTGAGCTAT 59.550 43.478 5.83 0.00 0.00 2.97
1143 5893 4.646492 TGTGAGTCATCTTGCTGAGCTATA 59.354 41.667 5.83 0.00 0.00 1.31
1144 5894 5.303845 TGTGAGTCATCTTGCTGAGCTATAT 59.696 40.000 5.83 0.00 0.00 0.86
1192 5975 1.113788 TTTTGTGCTGGCTCTTGCTT 58.886 45.000 0.00 0.00 39.59 3.91
1197 5980 0.606401 TGCTGGCTCTTGCTTACACC 60.606 55.000 0.00 0.00 39.59 4.16
1285 6068 0.736672 GGCGGACGACTTCTTCTTCC 60.737 60.000 0.00 0.00 38.97 3.46
1287 6070 0.889306 CGGACGACTTCTTCTTCCCT 59.111 55.000 0.00 0.00 39.13 4.20
1305 6088 3.388841 GGTCTCAAGAAGGCCGGA 58.611 61.111 5.05 0.00 40.77 5.14
1338 6121 2.659244 GCGGGTTCGAACGTCACA 60.659 61.111 21.34 0.00 39.00 3.58
1532 6315 2.094182 TCTTCACTAAGACCATCACCGC 60.094 50.000 0.00 0.00 36.80 5.68
1533 6316 1.262417 TCACTAAGACCATCACCGCA 58.738 50.000 0.00 0.00 0.00 5.69
1780 6564 3.294493 GCCTCCGCAGTTGGCAAA 61.294 61.111 0.00 0.00 45.46 3.68
1788 6572 1.203052 CGCAGTTGGCAAATCTCCATT 59.797 47.619 0.00 0.00 45.17 3.16
1790 6576 2.494870 GCAGTTGGCAAATCTCCATTCT 59.505 45.455 0.00 0.00 43.97 2.40
1823 6621 0.944386 ACCGTGTGTTCATTGCTGAC 59.056 50.000 0.00 0.00 0.00 3.51
1834 6640 7.148255 TGTGTTCATTGCTGACTAAATGATACC 60.148 37.037 0.00 0.00 41.23 2.73
1893 10103 7.369607 TGTGTATGTTCCATTTGATTGTCTTG 58.630 34.615 0.00 0.00 0.00 3.02
1963 10178 9.436957 TTTTAGTGACATGTCCTCTATTTCTTC 57.563 33.333 22.85 0.00 0.00 2.87
2003 11374 4.165180 TGATCCATTCCTTGACCGGAAATA 59.835 41.667 9.46 0.00 45.53 1.40
2044 11415 2.125512 GGACGCACCTGCCTAGTG 60.126 66.667 0.00 0.00 37.91 2.74
2068 11439 0.179073 CAGTCACCCTATTGCCTCGG 60.179 60.000 0.00 0.00 0.00 4.63
2108 11479 1.812571 CCCGCATGAGGGCATAATTAC 59.187 52.381 22.54 0.00 45.72 1.89
2166 11537 4.130857 TGGTCGCATGTTCTGAAACTTAA 58.869 39.130 0.00 0.00 36.30 1.85
2172 11543 7.059945 GTCGCATGTTCTGAAACTTAAGATTTG 59.940 37.037 10.09 1.68 36.30 2.32
2181 11615 3.314541 ACTTAAGATTTGTCGGTCGCT 57.685 42.857 10.09 0.00 0.00 4.93
2196 11630 2.129607 GTCGCTCGTACCAAGTTTCAA 58.870 47.619 0.00 0.00 0.00 2.69
2202 11636 5.574055 CGCTCGTACCAAGTTTCAATAGTTA 59.426 40.000 0.00 0.00 0.00 2.24
2220 12087 8.696175 CAATAGTTAAAACATTTTTGTCGGTCC 58.304 33.333 0.00 0.00 0.00 4.46
2246 12113 6.015519 TGGGATCTGAAATTCACGATTTTGTT 60.016 34.615 8.54 0.00 38.06 2.83
2255 12122 0.820074 ACGATTTTGTTGGTCGCCCA 60.820 50.000 0.00 0.00 38.85 5.36
2258 12125 2.357637 CGATTTTGTTGGTCGCCCATAT 59.642 45.455 0.00 0.00 41.49 1.78
2347 12214 2.673775 TTGAAAGCCCTCATCACCAA 57.326 45.000 0.00 0.00 0.00 3.67
2358 12225 3.550030 CCTCATCACCAAAAACACGAACC 60.550 47.826 0.00 0.00 0.00 3.62
2375 12242 6.928492 ACACGAACCTGCAAATGAAATTTAAT 59.072 30.769 0.00 0.00 46.64 1.40
2623 12494 7.396540 ACAAATTAAAATCCTCTCGCATTCT 57.603 32.000 0.00 0.00 0.00 2.40
2644 12515 9.472995 CATTCTTTGACGTGTATGTTACATTAC 57.527 33.333 2.23 2.97 41.34 1.89
2646 12517 8.456904 TCTTTGACGTGTATGTTACATTACTC 57.543 34.615 2.23 4.65 41.34 2.59
2647 12518 7.543172 TCTTTGACGTGTATGTTACATTACTCC 59.457 37.037 2.23 0.02 41.34 3.85
2648 12519 5.653507 TGACGTGTATGTTACATTACTCCC 58.346 41.667 2.23 0.00 41.34 4.30
2649 12520 5.014808 ACGTGTATGTTACATTACTCCCC 57.985 43.478 2.23 0.00 41.34 4.81
2650 12521 4.141869 ACGTGTATGTTACATTACTCCCCC 60.142 45.833 2.23 0.00 41.34 5.40
2670 12994 1.755395 GTCCGGGTTTATTGGGCCC 60.755 63.158 17.59 17.59 39.03 5.80
2673 12997 3.610976 GGGTTTATTGGGCCCGTG 58.389 61.111 19.37 0.00 32.16 4.94
2676 13000 1.663379 GGTTTATTGGGCCCGTGAGC 61.663 60.000 19.37 7.18 0.00 4.26
2677 13001 0.963355 GTTTATTGGGCCCGTGAGCA 60.963 55.000 19.37 0.00 0.00 4.26
2678 13002 0.251386 TTTATTGGGCCCGTGAGCAA 60.251 50.000 19.37 4.57 0.00 3.91
2679 13003 0.251386 TTATTGGGCCCGTGAGCAAA 60.251 50.000 19.37 3.69 0.00 3.68
2680 13004 0.679640 TATTGGGCCCGTGAGCAAAG 60.680 55.000 19.37 0.00 0.00 2.77
2681 13005 4.659172 TGGGCCCGTGAGCAAAGG 62.659 66.667 19.37 0.00 0.00 3.11
2682 13006 4.344865 GGGCCCGTGAGCAAAGGA 62.345 66.667 5.69 0.00 0.00 3.36
2683 13007 2.747855 GGCCCGTGAGCAAAGGAG 60.748 66.667 0.00 0.00 0.00 3.69
2685 13009 1.743252 GCCCGTGAGCAAAGGAGAG 60.743 63.158 0.00 0.00 0.00 3.20
2686 13010 1.078848 CCCGTGAGCAAAGGAGAGG 60.079 63.158 0.00 0.00 0.00 3.69
2687 13011 1.743252 CCGTGAGCAAAGGAGAGGC 60.743 63.158 0.00 0.00 0.00 4.70
2688 13012 2.097038 CGTGAGCAAAGGAGAGGCG 61.097 63.158 0.00 0.00 0.00 5.52
2691 13015 1.188219 TGAGCAAAGGAGAGGCGTCT 61.188 55.000 9.04 9.04 34.86 4.18
2702 13026 2.570442 GAGGCGTCTCTTCCTGTTAG 57.430 55.000 10.47 0.00 37.07 2.34
2703 13027 1.135333 GAGGCGTCTCTTCCTGTTAGG 59.865 57.143 10.47 0.00 37.07 2.69
2704 13028 0.460459 GGCGTCTCTTCCTGTTAGGC 60.460 60.000 0.00 0.00 34.61 3.93
2705 13029 0.460459 GCGTCTCTTCCTGTTAGGCC 60.460 60.000 0.00 0.00 34.61 5.19
2706 13030 0.175989 CGTCTCTTCCTGTTAGGCCC 59.824 60.000 0.00 0.00 34.61 5.80
2708 13032 1.909986 GTCTCTTCCTGTTAGGCCCTT 59.090 52.381 0.00 0.00 34.61 3.95
2709 13033 2.093394 GTCTCTTCCTGTTAGGCCCTTC 60.093 54.545 0.00 0.00 34.61 3.46
2710 13034 0.902531 TCTTCCTGTTAGGCCCTTCG 59.097 55.000 0.00 0.00 34.61 3.79
2711 13035 0.107654 CTTCCTGTTAGGCCCTTCGG 60.108 60.000 0.00 0.00 34.61 4.30
2712 13036 0.838987 TTCCTGTTAGGCCCTTCGGT 60.839 55.000 0.00 0.00 34.61 4.69
2713 13037 1.221021 CCTGTTAGGCCCTTCGGTC 59.779 63.158 0.00 0.00 0.00 4.79
2714 13038 1.221021 CTGTTAGGCCCTTCGGTCC 59.779 63.158 0.00 0.00 32.27 4.46
2716 13040 2.037687 TTAGGCCCTTCGGTCCGA 59.962 61.111 10.71 10.71 32.27 4.55
2717 13041 2.353610 TTAGGCCCTTCGGTCCGAC 61.354 63.158 15.07 1.77 34.89 4.79
2720 13044 2.493501 GCCCTTCGGTCCGACTAC 59.506 66.667 15.07 0.00 34.89 2.73
2721 13045 3.073742 GCCCTTCGGTCCGACTACC 62.074 68.421 15.07 0.00 34.89 3.18
2723 13047 1.252904 CCCTTCGGTCCGACTACCAA 61.253 60.000 15.07 0.00 39.71 3.67
2724 13048 0.172803 CCTTCGGTCCGACTACCAAG 59.827 60.000 15.07 7.47 39.71 3.61
2725 13049 0.172803 CTTCGGTCCGACTACCAAGG 59.827 60.000 15.07 0.00 39.71 3.61
2728 13052 0.604578 CGGTCCGACTACCAAGGAAA 59.395 55.000 4.91 0.00 39.71 3.13
2732 13056 4.621274 CGGTCCGACTACCAAGGAAAATTA 60.621 45.833 4.91 0.00 39.71 1.40
2734 13058 5.884232 GGTCCGACTACCAAGGAAAATTAAT 59.116 40.000 0.00 0.00 39.50 1.40
2735 13059 6.376299 GGTCCGACTACCAAGGAAAATTAATT 59.624 38.462 0.00 0.00 39.50 1.40
2736 13060 7.248437 GTCCGACTACCAAGGAAAATTAATTG 58.752 38.462 0.39 0.00 35.60 2.32
2737 13061 6.376018 TCCGACTACCAAGGAAAATTAATTGG 59.624 38.462 0.39 1.56 46.20 3.16
2738 13062 6.376018 CCGACTACCAAGGAAAATTAATTGGA 59.624 38.462 9.65 0.00 44.04 3.53
2739 13063 7.094118 CCGACTACCAAGGAAAATTAATTGGAA 60.094 37.037 9.65 0.00 44.04 3.53
2740 13064 8.301002 CGACTACCAAGGAAAATTAATTGGAAA 58.699 33.333 9.65 0.00 44.04 3.13
2741 13065 9.639601 GACTACCAAGGAAAATTAATTGGAAAG 57.360 33.333 9.65 8.52 44.04 2.62
2742 13066 9.374711 ACTACCAAGGAAAATTAATTGGAAAGA 57.625 29.630 9.65 0.00 44.04 2.52
2743 13067 9.860898 CTACCAAGGAAAATTAATTGGAAAGAG 57.139 33.333 9.65 0.00 44.04 2.85
2744 13068 8.262601 ACCAAGGAAAATTAATTGGAAAGAGT 57.737 30.769 9.65 0.00 44.04 3.24
2748 13072 7.910584 AGGAAAATTAATTGGAAAGAGTGCAT 58.089 30.769 0.39 0.00 0.00 3.96
2750 13074 6.973229 AAATTAATTGGAAAGAGTGCATGC 57.027 33.333 11.82 11.82 0.00 4.06
2751 13075 5.664294 ATTAATTGGAAAGAGTGCATGCA 57.336 34.783 18.46 18.46 0.00 3.96
2752 13076 5.664294 TTAATTGGAAAGAGTGCATGCAT 57.336 34.783 25.64 12.95 0.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
123 125 2.058001 ATCTGATCCCGTCACGGCA 61.058 57.895 12.05 0.00 46.86 5.69
255 264 2.233676 TCATCAACACTGCACGTATCCT 59.766 45.455 0.00 0.00 0.00 3.24
273 282 0.823769 TGCTCGGCCGTCTCTATCAT 60.824 55.000 27.15 0.00 0.00 2.45
375 388 3.233355 CTTGGCTAAACCGAGCACT 57.767 52.632 0.00 0.00 43.30 4.40
427 442 4.029520 ACTTGCATCAGATAGGAGTCACT 58.970 43.478 0.00 0.00 0.00 3.41
437 457 6.765036 CCAGTAATCTAACACTTGCATCAGAT 59.235 38.462 0.00 0.00 0.00 2.90
465 487 2.753452 CTGATTGATGGCAAGCTGTCTT 59.247 45.455 0.00 0.00 40.90 3.01
485 510 6.127703 ACGTACAGAAATGTACATAGCTGTCT 60.128 38.462 30.88 19.24 43.39 3.41
538 563 1.140052 TGTCTGTCCTTTTTCGGAGCA 59.860 47.619 0.00 0.00 32.70 4.26
544 569 4.983671 ACCAAGTTGTCTGTCCTTTTTC 57.016 40.909 1.45 0.00 0.00 2.29
550 575 3.139077 CTGGTAACCAAGTTGTCTGTCC 58.861 50.000 1.45 0.00 30.80 4.02
555 580 3.816994 ACCTTCTGGTAACCAAGTTGTC 58.183 45.455 1.45 0.00 46.43 3.18
585 610 8.028938 AGTTAGTTGAACATGATAATGGTTTGC 58.971 33.333 0.00 0.00 40.86 3.68
586 611 9.559958 GAGTTAGTTGAACATGATAATGGTTTG 57.440 33.333 0.00 0.00 40.86 2.93
587 612 8.450964 CGAGTTAGTTGAACATGATAATGGTTT 58.549 33.333 0.00 0.00 40.86 3.27
590 1317 7.770801 TCGAGTTAGTTGAACATGATAATGG 57.229 36.000 0.00 0.00 40.86 3.16
602 1329 3.118884 GGGTGGCTTATCGAGTTAGTTGA 60.119 47.826 0.00 0.00 0.00 3.18
608 1335 0.175073 GACGGGTGGCTTATCGAGTT 59.825 55.000 0.00 0.00 0.00 3.01
645 1372 2.017138 GAGCTAGCTCCAGGAACAAC 57.983 55.000 30.89 5.24 37.11 3.32
670 1397 2.031516 GTGGGACTCTCGTCGTCGA 61.032 63.158 4.42 4.42 44.12 4.20
680 1407 1.080025 CCCGAGTTTCGTGGGACTC 60.080 63.158 0.00 0.00 46.41 3.36
783 1514 9.435688 GTTAATTAATTTGGAGCCAATCAAAGT 57.564 29.630 5.91 0.56 36.49 2.66
784 1515 8.594687 CGTTAATTAATTTGGAGCCAATCAAAG 58.405 33.333 5.91 0.00 36.49 2.77
803 5310 3.243068 GCAAGCATCCGATTCCGTTAATT 60.243 43.478 0.00 0.00 0.00 1.40
804 5311 2.290641 GCAAGCATCCGATTCCGTTAAT 59.709 45.455 0.00 0.00 0.00 1.40
805 5312 1.668751 GCAAGCATCCGATTCCGTTAA 59.331 47.619 0.00 0.00 0.00 2.01
806 5313 1.295792 GCAAGCATCCGATTCCGTTA 58.704 50.000 0.00 0.00 0.00 3.18
847 5552 2.040544 CAAACAGGGTAGGCTGCGG 61.041 63.158 0.00 0.00 0.00 5.69
888 5602 5.486063 AGGGTGATTTGTGTATGGTACTACA 59.514 40.000 0.00 0.00 0.00 2.74
889 5603 5.815740 CAGGGTGATTTGTGTATGGTACTAC 59.184 44.000 0.00 0.00 0.00 2.73
894 5608 2.446435 GCAGGGTGATTTGTGTATGGT 58.554 47.619 0.00 0.00 0.00 3.55
1141 5891 9.574458 CTGACGAATTAAGATGAACGGATATAT 57.426 33.333 0.00 0.00 0.00 0.86
1142 5892 7.541091 GCTGACGAATTAAGATGAACGGATATA 59.459 37.037 0.00 0.00 0.00 0.86
1143 5893 6.366332 GCTGACGAATTAAGATGAACGGATAT 59.634 38.462 0.00 0.00 0.00 1.63
1144 5894 5.690409 GCTGACGAATTAAGATGAACGGATA 59.310 40.000 0.00 0.00 0.00 2.59
1162 5912 0.304705 AGCACAAAACGAAGCTGACG 59.695 50.000 11.16 11.16 35.72 4.35
1192 5975 1.867166 TTTGACGAATGCACGGTGTA 58.133 45.000 10.24 5.57 37.61 2.90
1197 5980 2.011932 TTCGTTTTGACGAATGCACG 57.988 45.000 9.98 0.00 45.60 5.34
1285 6068 1.078848 CGGCCTTCTTGAGACCAGG 60.079 63.158 0.00 0.00 0.00 4.45
1287 6070 1.125093 TTCCGGCCTTCTTGAGACCA 61.125 55.000 0.00 0.00 0.00 4.02
1305 6088 1.813192 CGCAGGGTTGTTGGTGTTT 59.187 52.632 0.00 0.00 0.00 2.83
1353 6136 0.477597 TGTTCACCCCTGGGAAGGAT 60.478 55.000 16.20 0.00 38.96 3.24
1780 6564 7.283354 GGTTATTCTTCCGAAAAGAATGGAGAT 59.717 37.037 24.34 9.78 44.22 2.75
1823 6621 3.496130 CAGCTCGCTTGGGTATCATTTAG 59.504 47.826 0.00 0.00 0.00 1.85
1834 6640 1.781555 CACGTTACAGCTCGCTTGG 59.218 57.895 0.00 0.00 0.00 3.61
2028 11399 2.125512 CCACTAGGCAGGTGCGTC 60.126 66.667 0.00 0.00 43.26 5.19
2044 11415 1.819632 CAATAGGGTGACTGGCGCC 60.820 63.158 22.73 22.73 46.77 6.53
2050 11421 1.338136 CCCGAGGCAATAGGGTGACT 61.338 60.000 0.00 0.00 40.60 3.41
2068 11439 2.464459 CCAGCGACTTTGCGGATCC 61.464 63.158 0.00 0.00 40.67 3.36
2144 11515 2.254546 AGTTTCAGAACATGCGACCA 57.745 45.000 0.00 0.00 38.26 4.02
2166 11537 0.806868 TACGAGCGACCGACAAATCT 59.193 50.000 3.95 0.00 0.00 2.40
2172 11543 1.513586 CTTGGTACGAGCGACCGAC 60.514 63.158 3.95 0.00 40.09 4.79
2181 11615 9.107177 TGTTTTAACTATTGAAACTTGGTACGA 57.893 29.630 9.48 0.00 39.18 3.43
2196 11630 8.079809 CAGGACCGACAAAAATGTTTTAACTAT 58.920 33.333 0.00 0.00 0.00 2.12
2202 11636 3.181470 CCCAGGACCGACAAAAATGTTTT 60.181 43.478 0.00 0.00 0.00 2.43
2220 12087 5.824904 AAATCGTGAATTTCAGATCCCAG 57.175 39.130 0.00 0.00 31.78 4.45
2337 12204 3.315191 AGGTTCGTGTTTTTGGTGATGAG 59.685 43.478 0.00 0.00 0.00 2.90
2347 12214 3.791973 TCATTTGCAGGTTCGTGTTTT 57.208 38.095 0.00 0.00 0.00 2.43
2596 12467 6.119144 TGCGAGAGGATTTTAATTTGTAGC 57.881 37.500 0.00 0.00 0.00 3.58
2611 12482 1.391485 CACGTCAAAGAATGCGAGAGG 59.609 52.381 0.00 0.00 34.24 3.69
2612 12483 2.061773 ACACGTCAAAGAATGCGAGAG 58.938 47.619 0.00 0.00 34.24 3.20
2617 12488 5.922546 TGTAACATACACGTCAAAGAATGC 58.077 37.500 0.00 0.00 32.89 3.56
2623 12494 6.591062 GGGAGTAATGTAACATACACGTCAAA 59.409 38.462 0.00 0.00 42.23 2.69
2650 12521 2.116533 GCCCAATAAACCCGGACGG 61.117 63.158 0.73 3.25 37.81 4.79
2651 12522 2.116533 GGCCCAATAAACCCGGACG 61.117 63.158 0.73 0.00 0.00 4.79
2652 12523 1.755395 GGGCCCAATAAACCCGGAC 60.755 63.158 19.95 0.00 32.92 4.79
2653 12524 2.684735 GGGCCCAATAAACCCGGA 59.315 61.111 19.95 0.00 32.92 5.14
2656 12527 1.000646 TCACGGGCCCAATAAACCC 60.001 57.895 24.92 0.00 40.51 4.11
2664 12988 4.659172 CCTTTGCTCACGGGCCCA 62.659 66.667 24.92 0.00 0.00 5.36
2670 12994 2.097038 CGCCTCTCCTTTGCTCACG 61.097 63.158 0.00 0.00 0.00 4.35
2671 12995 1.004440 ACGCCTCTCCTTTGCTCAC 60.004 57.895 0.00 0.00 0.00 3.51
2672 12996 1.188219 AGACGCCTCTCCTTTGCTCA 61.188 55.000 0.00 0.00 0.00 4.26
2673 12997 0.459411 GAGACGCCTCTCCTTTGCTC 60.459 60.000 1.56 0.00 37.56 4.26
2683 13007 1.135333 CCTAACAGGAAGAGACGCCTC 59.865 57.143 0.00 0.00 37.67 4.70
2685 13009 0.460459 GCCTAACAGGAAGAGACGCC 60.460 60.000 0.00 0.00 37.67 5.68
2686 13010 0.460459 GGCCTAACAGGAAGAGACGC 60.460 60.000 0.00 0.00 37.67 5.19
2687 13011 0.175989 GGGCCTAACAGGAAGAGACG 59.824 60.000 0.84 0.00 37.67 4.18
2688 13012 1.574263 AGGGCCTAACAGGAAGAGAC 58.426 55.000 2.82 0.00 37.67 3.36
2691 13015 0.902531 CGAAGGGCCTAACAGGAAGA 59.097 55.000 6.41 0.00 37.67 2.87
2692 13016 3.460648 CGAAGGGCCTAACAGGAAG 57.539 57.895 6.41 0.00 37.67 3.46
2706 13030 0.172803 CCTTGGTAGTCGGACCGAAG 59.827 60.000 20.26 11.12 42.99 3.79
2708 13032 0.251297 TTCCTTGGTAGTCGGACCGA 60.251 55.000 13.88 13.88 42.99 4.69
2709 13033 0.604578 TTTCCTTGGTAGTCGGACCG 59.395 55.000 7.84 7.84 42.99 4.79
2710 13034 2.845363 TTTTCCTTGGTAGTCGGACC 57.155 50.000 4.14 0.00 40.21 4.46
2711 13035 6.997239 ATTAATTTTCCTTGGTAGTCGGAC 57.003 37.500 0.00 0.00 0.00 4.79
2712 13036 6.376018 CCAATTAATTTTCCTTGGTAGTCGGA 59.624 38.462 0.00 0.00 34.69 4.55
2713 13037 6.376018 TCCAATTAATTTTCCTTGGTAGTCGG 59.624 38.462 0.00 0.00 39.33 4.79
2714 13038 7.385778 TCCAATTAATTTTCCTTGGTAGTCG 57.614 36.000 0.00 0.00 39.33 4.18
2716 13040 9.374711 TCTTTCCAATTAATTTTCCTTGGTAGT 57.625 29.630 0.00 0.00 39.33 2.73
2717 13041 9.860898 CTCTTTCCAATTAATTTTCCTTGGTAG 57.139 33.333 0.00 1.09 39.33 3.18
2720 13044 7.118245 GCACTCTTTCCAATTAATTTTCCTTGG 59.882 37.037 0.00 0.00 39.60 3.61
2721 13045 7.656948 TGCACTCTTTCCAATTAATTTTCCTTG 59.343 33.333 0.00 0.00 0.00 3.61
2723 13047 7.301868 TGCACTCTTTCCAATTAATTTTCCT 57.698 32.000 0.00 0.00 0.00 3.36
2724 13048 7.413328 GCATGCACTCTTTCCAATTAATTTTCC 60.413 37.037 14.21 0.00 0.00 3.13
2725 13049 7.118101 TGCATGCACTCTTTCCAATTAATTTTC 59.882 33.333 18.46 0.00 0.00 2.29
2728 13052 6.040209 TGCATGCACTCTTTCCAATTAATT 57.960 33.333 18.46 0.00 0.00 1.40
2732 13056 3.857052 CATGCATGCACTCTTTCCAATT 58.143 40.909 25.37 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.