Multiple sequence alignment - TraesCS6B01G347100

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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 TraesCS6B01G347100 chr6B 100.000 2930 0 0 1 2930 611462496 611459567 0.000000e+00 5411
1 TraesCS6B01G347100 chr6B 97.000 100 2 1 2701 2800 49737657 49737559 1.810000e-37 167
2 TraesCS6B01G347100 chr6D 90.994 2143 95 46 413 2510 407471587 407469498 0.000000e+00 2798
3 TraesCS6B01G347100 chr6D 79.528 508 89 11 1425 1929 407523216 407523711 6.010000e-92 348
4 TraesCS6B01G347100 chr6D 90.335 269 13 6 136 397 407471910 407471648 1.010000e-89 340
5 TraesCS6B01G347100 chr6D 90.058 171 15 2 2633 2801 407469242 407469072 1.370000e-53 220
6 TraesCS6B01G347100 chr6D 84.314 153 4 7 4 139 407472184 407472035 6.590000e-27 132
7 TraesCS6B01G347100 chr6D 90.909 55 5 0 2524 2578 407469444 407469390 1.130000e-09 75
8 TraesCS6B01G347100 chr6A 93.099 1681 66 13 428 2092 553004923 553003277 0.000000e+00 2416
9 TraesCS6B01G347100 chr6A 85.176 425 25 16 2091 2510 553003195 553002804 4.550000e-108 401
10 TraesCS6B01G347100 chr6A 78.740 508 93 10 1425 1929 553055344 553055839 2.820000e-85 326
11 TraesCS6B01G347100 chr6A 80.935 278 28 13 141 405 553005248 553004983 2.300000e-46 196
12 TraesCS6B01G347100 chr7A 79.641 501 86 12 1425 1920 132619506 132619995 2.160000e-91 346
13 TraesCS6B01G347100 chr7A 80.088 226 33 8 1437 1659 216416172 216416388 1.090000e-34 158
14 TraesCS6B01G347100 chr7B 79.518 498 90 8 1437 1931 95045945 95045457 7.770000e-91 344
15 TraesCS6B01G347100 chr7B 78.916 498 93 8 1437 1931 94810448 94809960 7.830000e-86 327
16 TraesCS6B01G347100 chr7B 94.595 74 3 1 2838 2910 21784270 21784343 2.390000e-21 113
17 TraesCS6B01G347100 chr7B 94.595 74 3 1 2839 2911 351906988 351907061 2.390000e-21 113
18 TraesCS6B01G347100 chr7D 78.947 513 90 14 1425 1931 133827706 133828206 1.680000e-87 333
19 TraesCS6B01G347100 chr4A 93.162 117 6 2 2697 2811 679256507 679256623 1.400000e-38 171
20 TraesCS6B01G347100 chr4A 90.476 126 9 3 2705 2828 17385953 17385829 2.340000e-36 163
21 TraesCS6B01G347100 chr3A 96.970 99 2 1 2697 2795 654356221 654356318 6.500000e-37 165
22 TraesCS6B01G347100 chr5B 93.636 110 5 2 2704 2813 347666186 347666079 2.340000e-36 163
23 TraesCS6B01G347100 chr5B 93.333 75 3 2 2838 2910 374104545 374104471 3.090000e-20 110
24 TraesCS6B01G347100 chr4D 93.636 110 5 2 2704 2811 472487441 472487550 2.340000e-36 163
25 TraesCS6B01G347100 chr4D 90.517 116 6 4 2700 2810 449462702 449462817 6.540000e-32 148
26 TraesCS6B01G347100 chr4B 91.453 117 7 3 2698 2811 594844658 594844774 1.090000e-34 158
27 TraesCS6B01G347100 chr4B 93.243 74 4 1 2838 2910 84232808 84232735 1.110000e-19 108
28 TraesCS6B01G347100 chr4B 93.243 74 4 1 2838 2910 293383381 293383454 1.110000e-19 108
29 TraesCS6B01G347100 chr3D 93.421 76 3 2 2837 2910 223480052 223479977 8.580000e-21 111
30 TraesCS6B01G347100 chr3D 93.243 74 4 1 2838 2910 91808629 91808702 1.110000e-19 108
31 TraesCS6B01G347100 chr3D 93.243 74 4 1 2838 2910 553902299 553902226 1.110000e-19 108
32 TraesCS6B01G347100 chr1B 93.243 74 4 1 2838 2910 47094930 47095003 1.110000e-19 108


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 TraesCS6B01G347100 chr6B 611459567 611462496 2929 True 5411.000000 5411 100.000000 1 2930 1 chr6B.!!$R2 2929
1 TraesCS6B01G347100 chr6D 407469072 407472184 3112 True 713.000000 2798 89.322000 4 2801 5 chr6D.!!$R1 2797
2 TraesCS6B01G347100 chr6A 553002804 553005248 2444 True 1004.333333 2416 86.403333 141 2510 3 chr6A.!!$R1 2369
3 TraesCS6B01G347100 chr7D 133827706 133828206 500 False 333.000000 333 78.947000 1425 1931 1 chr7D.!!$F1 506

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
909 1145 0.109913 CCCTCTATAAAACCCCGGCC 59.89 60.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2265 2629 0.027979 CTTTGCACACGTGACCTGTG 59.972 55.0 25.01 10.84 41.76 3.66 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
34 35 3.854459 CTTTCGCTCGCTTCGGCC 61.854 66.667 0.00 0.00 37.76 6.13
80 81 2.328235 TAGGCACTAGTCGGATCGC 58.672 57.895 0.00 0.00 41.75 4.58
81 82 0.464916 TAGGCACTAGTCGGATCGCA 60.465 55.000 0.00 0.00 41.75 5.10
82 83 1.299468 GGCACTAGTCGGATCGCAG 60.299 63.158 0.00 0.00 0.00 5.18
83 84 1.946650 GCACTAGTCGGATCGCAGC 60.947 63.158 0.00 0.00 0.00 5.25
86 87 1.082431 CTAGTCGGATCGCAGCGAG 60.082 63.158 24.08 9.99 39.91 5.03
87 88 2.450960 CTAGTCGGATCGCAGCGAGG 62.451 65.000 24.08 14.60 39.91 4.63
90 91 2.429907 CGGATCGCAGCGAGGATC 60.430 66.667 24.08 15.58 39.91 3.36
91 92 2.730733 GGATCGCAGCGAGGATCA 59.269 61.111 24.08 0.00 40.61 2.92
93 94 1.372748 GATCGCAGCGAGGATCAGG 60.373 63.158 24.08 0.00 39.91 3.86
149 291 4.099266 ACTGGATCATCTCTAAGTGCTGTC 59.901 45.833 0.00 0.00 0.00 3.51
152 294 4.501229 GGATCATCTCTAAGTGCTGTCAGG 60.501 50.000 1.14 0.00 0.00 3.86
256 405 0.179032 ATTGCACTGTTCCACGGTCA 60.179 50.000 0.00 0.00 35.04 4.02
257 406 0.179032 TTGCACTGTTCCACGGTCAT 60.179 50.000 0.00 0.00 35.04 3.06
268 417 1.676014 CCACGGTCATGTCTTCCTTCC 60.676 57.143 0.00 0.00 0.00 3.46
271 420 2.028020 ACGGTCATGTCTTCCTTCCTTC 60.028 50.000 0.00 0.00 0.00 3.46
272 421 2.234908 CGGTCATGTCTTCCTTCCTTCT 59.765 50.000 0.00 0.00 0.00 2.85
273 422 3.307059 CGGTCATGTCTTCCTTCCTTCTT 60.307 47.826 0.00 0.00 0.00 2.52
274 423 4.657013 GGTCATGTCTTCCTTCCTTCTTT 58.343 43.478 0.00 0.00 0.00 2.52
283 432 1.344438 CCTTCCTTCTTTTGCCAACCC 59.656 52.381 0.00 0.00 0.00 4.11
388 540 1.424638 AGTACTCCCAGTGCACTGTT 58.575 50.000 37.55 23.72 42.27 3.16
389 541 1.070758 AGTACTCCCAGTGCACTGTTG 59.929 52.381 37.55 29.21 42.27 3.33
399 553 1.883021 GCACTGTTGCCATACACCC 59.117 57.895 0.00 0.00 43.66 4.61
405 572 1.145156 TTGCCATACACCCGATCCG 59.855 57.895 0.00 0.00 0.00 4.18
406 573 2.665185 GCCATACACCCGATCCGC 60.665 66.667 0.00 0.00 0.00 5.54
407 574 2.030562 CCATACACCCGATCCGCC 59.969 66.667 0.00 0.00 0.00 6.13
409 576 1.300931 CATACACCCGATCCGCCAG 60.301 63.158 0.00 0.00 0.00 4.85
410 577 3.165160 ATACACCCGATCCGCCAGC 62.165 63.158 0.00 0.00 0.00 4.85
662 876 2.746277 GACAAAGCGACGGGGCAT 60.746 61.111 0.00 0.00 34.64 4.40
682 896 1.623542 AAGGGTAATTCGGCCTCGCT 61.624 55.000 0.00 0.00 36.13 4.93
714 928 3.485431 CGAGCAGGAGCACGCAAG 61.485 66.667 0.00 0.00 46.89 4.01
741 955 2.737376 GTCAGTGACCGTTCGGGC 60.737 66.667 12.54 13.23 40.62 6.13
797 1012 1.754226 ACTTTGGCCGCAGAAAGAAAA 59.246 42.857 17.63 0.24 34.02 2.29
798 1013 2.223805 ACTTTGGCCGCAGAAAGAAAAG 60.224 45.455 17.63 11.43 34.02 2.27
801 1016 2.028130 TGGCCGCAGAAAGAAAAGAAA 58.972 42.857 0.00 0.00 0.00 2.52
802 1017 2.034558 TGGCCGCAGAAAGAAAAGAAAG 59.965 45.455 0.00 0.00 0.00 2.62
855 1086 0.393077 GATGTCCCTCGGTACCATGG 59.607 60.000 11.19 11.19 0.00 3.66
887 1118 1.214062 GGTGCTCCACTGTCTCTCG 59.786 63.158 0.00 0.00 34.40 4.04
909 1145 0.109913 CCCTCTATAAAACCCCGGCC 59.890 60.000 0.00 0.00 0.00 6.13
971 1207 2.697751 GAGCATCCTAGGCAAGAAGAGA 59.302 50.000 2.96 0.00 0.00 3.10
974 1210 3.465871 CATCCTAGGCAAGAAGAGAAGC 58.534 50.000 2.96 0.00 0.00 3.86
1224 1466 1.859564 CGACTTCGTCTCGTCGCTG 60.860 63.158 0.00 0.00 45.08 5.18
1352 1600 2.927580 GCTCCCACGTCTTCGACCA 61.928 63.158 0.00 0.00 40.62 4.02
1854 2123 2.778679 GCGAGCTTCAACGCGAAT 59.221 55.556 15.93 0.00 44.91 3.34
1934 2203 1.616628 CCACCTTGGGGTAGGCTCT 60.617 63.158 0.00 0.00 45.41 4.09
1935 2204 0.326238 CCACCTTGGGGTAGGCTCTA 60.326 60.000 0.00 0.00 45.41 2.43
1936 2205 0.831307 CACCTTGGGGTAGGCTCTAC 59.169 60.000 0.00 4.33 45.41 2.59
1978 2254 1.465777 GTTATAGTTGCGGTGGCGTTT 59.534 47.619 0.00 0.00 44.10 3.60
2056 2332 2.223688 CCTGTAGAGGCGTTGAGATGAG 60.224 54.545 0.00 0.00 30.52 2.90
2133 2491 6.068931 CGTTCGGAAACTAACATTGTTACTG 58.931 40.000 5.14 2.03 35.87 2.74
2152 2510 4.603131 ACTGGTATCATTTTGGTGCTCAT 58.397 39.130 0.00 0.00 0.00 2.90
2159 2517 0.831288 TTTTGGTGCTCATGGTGGGG 60.831 55.000 0.00 0.00 0.00 4.96
2160 2518 2.728460 TTTGGTGCTCATGGTGGGGG 62.728 60.000 0.00 0.00 0.00 5.40
2161 2519 3.661648 GGTGCTCATGGTGGGGGT 61.662 66.667 0.00 0.00 0.00 4.95
2162 2520 2.440599 GTGCTCATGGTGGGGGTT 59.559 61.111 0.00 0.00 0.00 4.11
2163 2521 1.688811 GTGCTCATGGTGGGGGTTA 59.311 57.895 0.00 0.00 0.00 2.85
2164 2522 0.394352 GTGCTCATGGTGGGGGTTAG 60.394 60.000 0.00 0.00 0.00 2.34
2165 2523 1.227383 GCTCATGGTGGGGGTTAGG 59.773 63.158 0.00 0.00 0.00 2.69
2166 2524 1.279025 GCTCATGGTGGGGGTTAGGA 61.279 60.000 0.00 0.00 0.00 2.94
2167 2525 1.522900 CTCATGGTGGGGGTTAGGAT 58.477 55.000 0.00 0.00 0.00 3.24
2172 2530 4.295238 TCATGGTGGGGGTTAGGATTTTAA 59.705 41.667 0.00 0.00 0.00 1.52
2190 2548 6.795098 TTTTAAAGCAGAAACTCGAGCATA 57.205 33.333 13.61 0.00 0.00 3.14
2201 2559 5.490139 AACTCGAGCATACATCAAAATGG 57.510 39.130 13.61 0.00 37.19 3.16
2218 2578 6.483307 TCAAAATGGCATGCATAGTAGTACTC 59.517 38.462 21.36 0.00 0.00 2.59
2264 2628 7.268586 GGATATATGTCTTGTTCACTCACAGT 58.731 38.462 0.00 0.00 0.00 3.55
2265 2629 7.436673 GGATATATGTCTTGTTCACTCACAGTC 59.563 40.741 0.00 0.00 0.00 3.51
2266 2630 3.885724 TGTCTTGTTCACTCACAGTCA 57.114 42.857 0.00 0.00 0.00 3.41
2323 2688 5.899547 TGATAACATACAGATGACCTCCAGT 59.100 40.000 0.00 0.00 36.48 4.00
2330 2695 5.505181 ACAGATGACCTCCAGTTAACATT 57.495 39.130 8.61 0.00 0.00 2.71
2417 2785 0.100682 CGAGTATGTCCCCTGTGTCG 59.899 60.000 0.00 0.00 0.00 4.35
2434 2803 2.946762 GTGTGCGAGCAGAAACCC 59.053 61.111 0.00 0.00 0.00 4.11
2437 2806 0.884704 TGTGCGAGCAGAAACCCTTC 60.885 55.000 0.00 0.00 0.00 3.46
2438 2807 0.603975 GTGCGAGCAGAAACCCTTCT 60.604 55.000 0.00 0.00 42.96 2.85
2455 2826 4.216472 CCCTTCTGCTTTACTCTGGAAAAC 59.784 45.833 0.00 0.00 0.00 2.43
2478 2849 0.249868 GGGCTGGCAAGGTCAAAAAC 60.250 55.000 2.88 0.00 0.00 2.43
2493 2865 5.731599 TCAAAAACATGACACCAAAATGC 57.268 34.783 0.00 0.00 0.00 3.56
2510 2882 7.094463 ACCAAAATGCAGAGATTCAGAACTAAG 60.094 37.037 0.00 0.00 0.00 2.18
2511 2883 7.120285 CCAAAATGCAGAGATTCAGAACTAAGA 59.880 37.037 0.00 0.00 0.00 2.10
2512 2884 7.608308 AAATGCAGAGATTCAGAACTAAGAC 57.392 36.000 0.00 0.00 0.00 3.01
2515 2887 6.162079 TGCAGAGATTCAGAACTAAGACAAG 58.838 40.000 0.00 0.00 0.00 3.16
2516 2888 6.015095 TGCAGAGATTCAGAACTAAGACAAGA 60.015 38.462 0.00 0.00 0.00 3.02
2519 2931 6.951198 AGAGATTCAGAACTAAGACAAGAGGA 59.049 38.462 0.00 0.00 0.00 3.71
2522 2934 6.479972 TTCAGAACTAAGACAAGAGGAACA 57.520 37.500 0.00 0.00 0.00 3.18
2532 2944 2.369860 ACAAGAGGAACAGACTGCATCA 59.630 45.455 1.25 0.00 0.00 3.07
2535 2947 2.836372 AGAGGAACAGACTGCATCATCA 59.164 45.455 19.48 0.00 0.00 3.07
2536 2948 2.935201 GAGGAACAGACTGCATCATCAC 59.065 50.000 14.94 0.00 0.00 3.06
2542 2954 1.841919 AGACTGCATCATCACCATGGA 59.158 47.619 21.47 0.00 0.00 3.41
2546 2958 3.200605 ACTGCATCATCACCATGGAACTA 59.799 43.478 21.47 0.16 0.00 2.24
2578 2990 6.468000 GCATGGTTAGCGTTGAAATAAACTAC 59.532 38.462 0.00 0.00 0.00 2.73
2580 2992 7.733402 TGGTTAGCGTTGAAATAAACTACTT 57.267 32.000 0.00 0.00 0.00 2.24
2581 2993 8.830201 TGGTTAGCGTTGAAATAAACTACTTA 57.170 30.769 0.00 0.00 0.00 2.24
2582 2994 8.928733 TGGTTAGCGTTGAAATAAACTACTTAG 58.071 33.333 0.00 0.00 0.00 2.18
2583 2995 8.929746 GGTTAGCGTTGAAATAAACTACTTAGT 58.070 33.333 0.00 0.00 38.39 2.24
2593 3005 2.427232 ACTACTTAGTTTCGCGTGCA 57.573 45.000 5.77 0.00 31.13 4.57
2594 3006 2.325761 ACTACTTAGTTTCGCGTGCAG 58.674 47.619 5.77 0.00 31.13 4.41
2595 3007 1.654105 CTACTTAGTTTCGCGTGCAGG 59.346 52.381 5.77 1.01 0.00 4.85
2596 3008 0.032952 ACTTAGTTTCGCGTGCAGGA 59.967 50.000 11.29 0.00 0.00 3.86
2599 3011 1.289109 TAGTTTCGCGTGCAGGAAGC 61.289 55.000 11.29 5.76 45.96 3.86
2600 3012 3.353836 TTTCGCGTGCAGGAAGCC 61.354 61.111 11.29 0.00 44.83 4.35
2620 3108 1.673033 CGGGCGATGAGAAAAGTCTGT 60.673 52.381 0.00 0.00 32.80 3.41
2623 3111 2.417719 GCGATGAGAAAAGTCTGTGGT 58.582 47.619 0.00 0.00 32.80 4.16
2640 3128 2.294233 GTGGTGTCACAGTGAAATGCAT 59.706 45.455 4.32 0.00 43.13 3.96
2641 3129 2.293955 TGGTGTCACAGTGAAATGCATG 59.706 45.455 4.32 0.00 0.00 4.06
2642 3130 2.352030 GGTGTCACAGTGAAATGCATGG 60.352 50.000 4.32 0.00 0.00 3.66
2644 3132 3.004629 GTGTCACAGTGAAATGCATGGAA 59.995 43.478 4.32 0.00 0.00 3.53
2645 3133 3.004629 TGTCACAGTGAAATGCATGGAAC 59.995 43.478 4.32 0.00 0.00 3.62
2652 3157 2.159352 TGAAATGCATGGAACGCTGATG 60.159 45.455 0.00 0.00 0.00 3.07
2653 3158 1.466856 AATGCATGGAACGCTGATGT 58.533 45.000 0.00 0.00 0.00 3.06
2669 3174 4.676196 GCTGATGTGAAATTGAGGCGATTT 60.676 41.667 0.00 0.00 30.94 2.17
2679 3184 8.087750 TGAAATTGAGGCGATTTCAAAGTTAAT 58.912 29.630 16.48 0.00 45.56 1.40
2684 3189 8.909708 TGAGGCGATTTCAAAGTTAATTAATG 57.090 30.769 0.31 0.00 0.00 1.90
2685 3190 8.735315 TGAGGCGATTTCAAAGTTAATTAATGA 58.265 29.630 0.31 0.00 0.00 2.57
2748 3254 0.745128 AGAGCGGAGGACTGTAGTCG 60.745 60.000 5.99 0.00 45.65 4.18
2769 3275 5.234543 GTCGTTGCAGATAAATCCTTAGGTC 59.765 44.000 0.00 0.00 0.00 3.85
2865 3371 7.995463 TTTTGAAACGGAGGTAAAAGATTTG 57.005 32.000 0.00 0.00 0.00 2.32
2866 3372 5.116069 TGAAACGGAGGTAAAAGATTTGC 57.884 39.130 0.00 0.00 0.00 3.68
2867 3373 4.022676 TGAAACGGAGGTAAAAGATTTGCC 60.023 41.667 2.19 2.19 0.00 4.52
2868 3374 3.434940 ACGGAGGTAAAAGATTTGCCT 57.565 42.857 11.53 11.53 0.00 4.75
2869 3375 3.344515 ACGGAGGTAAAAGATTTGCCTC 58.655 45.455 23.58 23.58 39.95 4.70
2870 3376 3.244770 ACGGAGGTAAAAGATTTGCCTCA 60.245 43.478 28.89 0.00 41.22 3.86
2871 3377 3.947834 CGGAGGTAAAAGATTTGCCTCAT 59.052 43.478 28.89 6.21 41.22 2.90
2872 3378 4.035675 CGGAGGTAAAAGATTTGCCTCATC 59.964 45.833 28.89 17.77 41.22 2.92
2873 3379 4.339530 GGAGGTAAAAGATTTGCCTCATCC 59.660 45.833 28.89 16.65 41.22 3.51
2874 3380 4.934356 AGGTAAAAGATTTGCCTCATCCA 58.066 39.130 6.65 0.00 0.00 3.41
2875 3381 5.522641 AGGTAAAAGATTTGCCTCATCCAT 58.477 37.500 6.65 0.00 0.00 3.41
2876 3382 5.960202 AGGTAAAAGATTTGCCTCATCCATT 59.040 36.000 6.65 0.00 0.00 3.16
2877 3383 7.125391 AGGTAAAAGATTTGCCTCATCCATTA 58.875 34.615 6.65 0.00 0.00 1.90
2878 3384 7.619302 AGGTAAAAGATTTGCCTCATCCATTAA 59.381 33.333 6.65 0.00 0.00 1.40
2879 3385 8.257306 GGTAAAAGATTTGCCTCATCCATTAAA 58.743 33.333 3.12 0.00 0.00 1.52
2880 3386 9.822185 GTAAAAGATTTGCCTCATCCATTAAAT 57.178 29.630 0.00 0.00 0.00 1.40
2884 3390 9.425248 AAGATTTGCCTCATCCATTAAATAAGA 57.575 29.630 0.00 0.00 0.00 2.10
2885 3391 9.075678 AGATTTGCCTCATCCATTAAATAAGAG 57.924 33.333 0.00 0.00 0.00 2.85
2886 3392 9.071276 GATTTGCCTCATCCATTAAATAAGAGA 57.929 33.333 0.00 0.00 0.00 3.10
2887 3393 8.821686 TTTGCCTCATCCATTAAATAAGAGAA 57.178 30.769 0.00 0.00 0.00 2.87
2888 3394 8.455903 TTGCCTCATCCATTAAATAAGAGAAG 57.544 34.615 0.00 0.00 0.00 2.85
2889 3395 7.805163 TGCCTCATCCATTAAATAAGAGAAGA 58.195 34.615 0.00 0.00 0.00 2.87
2890 3396 8.274322 TGCCTCATCCATTAAATAAGAGAAGAA 58.726 33.333 0.00 0.00 0.00 2.52
2891 3397 9.294614 GCCTCATCCATTAAATAAGAGAAGAAT 57.705 33.333 0.00 0.00 0.00 2.40
2924 3430 5.755330 GTTTTACATACAAAACGGCATGG 57.245 39.130 0.00 0.00 38.30 3.66
2925 3431 5.224135 GTTTTACATACAAAACGGCATGGT 58.776 37.500 0.00 0.00 38.30 3.55
2926 3432 6.380190 GTTTTACATACAAAACGGCATGGTA 58.620 36.000 0.00 0.00 38.30 3.25
2927 3433 6.570672 TTTACATACAAAACGGCATGGTAA 57.429 33.333 0.00 0.00 0.00 2.85
2928 3434 6.761099 TTACATACAAAACGGCATGGTAAT 57.239 33.333 0.00 0.00 0.00 1.89
2929 3435 7.860918 TTACATACAAAACGGCATGGTAATA 57.139 32.000 0.00 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.034221 GTTCAGGACCCACAGCCC 59.966 66.667 0.00 0.00 0.00 5.19
1 2 0.178990 AAAGTTCAGGACCCACAGCC 60.179 55.000 0.00 0.00 0.00 4.85
15 16 2.668280 GCCGAAGCGAGCGAAAGTT 61.668 57.895 0.00 0.00 0.00 2.66
34 35 1.153168 CCCATCTTGGTAGGGCACG 60.153 63.158 0.00 0.00 35.17 5.34
69 70 2.543802 CCTCGCTGCGATCCGACTA 61.544 63.158 26.15 0.00 34.61 2.59
73 74 2.429907 GATCCTCGCTGCGATCCG 60.430 66.667 26.15 13.83 34.61 4.18
76 77 1.829970 TCCTGATCCTCGCTGCGAT 60.830 57.895 26.15 11.14 34.61 4.58
78 79 2.279120 GTCCTGATCCTCGCTGCG 60.279 66.667 17.25 17.25 0.00 5.18
79 80 1.227205 CAGTCCTGATCCTCGCTGC 60.227 63.158 0.00 0.00 0.00 5.25
80 81 1.440893 CCAGTCCTGATCCTCGCTG 59.559 63.158 0.00 0.00 0.00 5.18
81 82 1.760086 CCCAGTCCTGATCCTCGCT 60.760 63.158 0.00 0.00 0.00 4.93
82 83 2.801631 CCCCAGTCCTGATCCTCGC 61.802 68.421 0.00 0.00 0.00 5.03
83 84 2.801631 GCCCCAGTCCTGATCCTCG 61.802 68.421 0.00 0.00 0.00 4.63
86 87 3.866582 CCGCCCCAGTCCTGATCC 61.867 72.222 0.00 0.00 0.00 3.36
87 88 4.554036 GCCGCCCCAGTCCTGATC 62.554 72.222 0.00 0.00 0.00 2.92
91 92 4.733725 TAAGGCCGCCCCAGTCCT 62.734 66.667 5.55 0.00 35.39 3.85
93 94 2.437895 GTTAAGGCCGCCCCAGTC 60.438 66.667 5.55 0.00 35.39 3.51
149 291 4.478371 TGCGATCTGGCAGGCCTG 62.478 66.667 29.34 29.34 38.17 4.85
196 338 1.363145 CGAAAATGGGTAGCGCGGAA 61.363 55.000 8.83 0.00 0.00 4.30
256 405 3.829026 GGCAAAAGAAGGAAGGAAGACAT 59.171 43.478 0.00 0.00 0.00 3.06
257 406 3.222603 GGCAAAAGAAGGAAGGAAGACA 58.777 45.455 0.00 0.00 0.00 3.41
268 417 0.750249 AACGGGGTTGGCAAAAGAAG 59.250 50.000 0.00 0.00 0.00 2.85
271 420 1.365999 GGAACGGGGTTGGCAAAAG 59.634 57.895 0.00 0.00 0.00 2.27
272 421 1.381327 TGGAACGGGGTTGGCAAAA 60.381 52.632 0.00 0.00 0.00 2.44
273 422 2.128507 GTGGAACGGGGTTGGCAAA 61.129 57.895 0.00 0.00 0.00 3.68
274 423 2.519780 GTGGAACGGGGTTGGCAA 60.520 61.111 0.00 0.00 0.00 4.52
388 540 2.818841 CGGATCGGGTGTATGGCA 59.181 61.111 0.00 0.00 0.00 4.92
389 541 2.665185 GCGGATCGGGTGTATGGC 60.665 66.667 2.13 0.00 0.00 4.40
391 543 1.300931 CTGGCGGATCGGGTGTATG 60.301 63.158 2.13 0.00 0.00 2.39
392 544 3.138625 CTGGCGGATCGGGTGTAT 58.861 61.111 2.13 0.00 0.00 2.29
399 553 1.861542 TTTTTGGTGCTGGCGGATCG 61.862 55.000 0.00 0.00 0.00 3.69
498 711 2.666190 AAAGCTGCTTCGCTCGCA 60.666 55.556 16.28 0.00 39.86 5.10
662 876 0.105408 GCGAGGCCGAATTACCCTTA 59.895 55.000 0.00 0.00 38.22 2.69
714 928 0.952984 GGTCACTGACAGCTGGCTTC 60.953 60.000 22.80 8.59 33.68 3.86
771 986 1.808411 TCTGCGGCCAAAGTAAAGAG 58.192 50.000 2.24 0.00 0.00 2.85
887 1118 1.071857 CCGGGGTTTTATAGAGGGAGC 59.928 57.143 0.00 0.00 0.00 4.70
909 1145 1.460305 ATGGACTGGAGGGGATCGG 60.460 63.158 0.00 0.00 0.00 4.18
946 1182 2.191400 TCTTGCCTAGGATGCTCTGTT 58.809 47.619 14.75 0.00 0.00 3.16
971 1207 2.847234 TCAGGTGGTGGGTCGCTT 60.847 61.111 0.00 0.00 0.00 4.68
974 1210 2.973899 CTCTCAGGTGGTGGGTCG 59.026 66.667 0.00 0.00 0.00 4.79
1269 1517 2.954753 CTGCGCCGTCTTGAACCAC 61.955 63.158 4.18 0.00 0.00 4.16
1352 1600 2.279408 GGCCGAGGGAGTAGGACT 59.721 66.667 0.00 0.00 0.00 3.85
1470 1718 2.789917 CAGCGGCTCATGCAGAAC 59.210 61.111 0.00 0.00 41.91 3.01
1909 2178 3.260100 CCCCAAGGTGGAGCAGGT 61.260 66.667 0.00 0.00 40.96 4.00
1978 2254 0.541392 ACACTCTCCACACAGCAACA 59.459 50.000 0.00 0.00 0.00 3.33
2105 2463 4.753107 ACAATGTTAGTTTCCGAACGATGT 59.247 37.500 0.00 0.00 40.75 3.06
2109 2467 6.068931 CAGTAACAATGTTAGTTTCCGAACG 58.931 40.000 10.52 0.00 40.75 3.95
2133 2491 3.701040 ACCATGAGCACCAAAATGATACC 59.299 43.478 0.00 0.00 0.00 2.73
2152 2510 4.679331 CTTTAAAATCCTAACCCCCACCA 58.321 43.478 0.00 0.00 0.00 4.17
2159 2517 7.021790 CGAGTTTCTGCTTTAAAATCCTAACC 58.978 38.462 0.00 0.00 29.47 2.85
2160 2518 7.803724 TCGAGTTTCTGCTTTAAAATCCTAAC 58.196 34.615 0.00 0.00 29.47 2.34
2161 2519 7.360946 GCTCGAGTTTCTGCTTTAAAATCCTAA 60.361 37.037 15.13 0.00 29.47 2.69
2162 2520 6.092259 GCTCGAGTTTCTGCTTTAAAATCCTA 59.908 38.462 15.13 0.00 29.47 2.94
2163 2521 5.106515 GCTCGAGTTTCTGCTTTAAAATCCT 60.107 40.000 15.13 0.00 29.47 3.24
2164 2522 5.089411 GCTCGAGTTTCTGCTTTAAAATCC 58.911 41.667 15.13 0.00 29.47 3.01
2165 2523 5.689819 TGCTCGAGTTTCTGCTTTAAAATC 58.310 37.500 15.13 0.00 0.00 2.17
2166 2524 5.689383 TGCTCGAGTTTCTGCTTTAAAAT 57.311 34.783 15.13 0.00 0.00 1.82
2167 2525 5.689383 ATGCTCGAGTTTCTGCTTTAAAA 57.311 34.783 15.13 0.00 0.00 1.52
2172 2530 3.319137 TGTATGCTCGAGTTTCTGCTT 57.681 42.857 15.13 0.00 0.00 3.91
2190 2548 5.595542 ACTACTATGCATGCCATTTTGATGT 59.404 36.000 16.68 3.91 35.34 3.06
2201 2559 7.962964 TTTAATGGAGTACTACTATGCATGC 57.037 36.000 11.82 11.82 0.00 4.06
2218 2578 9.799106 ATATCCCTTCACTCAGTATTTTAATGG 57.201 33.333 0.00 0.00 0.00 3.16
2230 2590 7.125659 TGAACAAGACATATATCCCTTCACTCA 59.874 37.037 0.00 0.00 0.00 3.41
2234 2594 7.125659 TGAGTGAACAAGACATATATCCCTTCA 59.874 37.037 0.00 0.00 0.00 3.02
2264 2628 0.391793 TTTGCACACGTGACCTGTGA 60.392 50.000 25.01 0.43 41.43 3.58
2265 2629 0.027979 CTTTGCACACGTGACCTGTG 59.972 55.000 25.01 10.84 41.76 3.66
2266 2630 1.714899 GCTTTGCACACGTGACCTGT 61.715 55.000 25.01 0.00 0.00 4.00
2357 2725 6.238484 CCGGAGCCATCTCTTTTACTTTATTG 60.238 42.308 0.00 0.00 39.31 1.90
2417 2785 1.166531 AAGGGTTTCTGCTCGCACAC 61.167 55.000 0.00 0.00 0.00 3.82
2434 2803 6.566197 ATGTTTTCCAGAGTAAAGCAGAAG 57.434 37.500 0.00 0.00 31.84 2.85
2437 2806 5.355350 CCCTATGTTTTCCAGAGTAAAGCAG 59.645 44.000 0.00 0.00 31.84 4.24
2438 2807 5.253330 CCCTATGTTTTCCAGAGTAAAGCA 58.747 41.667 0.00 0.00 32.68 3.91
2439 2808 4.096532 GCCCTATGTTTTCCAGAGTAAAGC 59.903 45.833 0.00 0.00 30.10 3.51
2440 2809 5.355350 CAGCCCTATGTTTTCCAGAGTAAAG 59.645 44.000 0.00 0.00 30.10 1.85
2455 2826 0.034186 TTGACCTTGCCAGCCCTATG 60.034 55.000 0.00 0.00 0.00 2.23
2478 2849 4.713824 ATCTCTGCATTTTGGTGTCATG 57.286 40.909 0.00 0.00 0.00 3.07
2493 2865 7.035004 CCTCTTGTCTTAGTTCTGAATCTCTG 58.965 42.308 0.00 0.00 0.00 3.35
2510 2882 2.533266 TGCAGTCTGTTCCTCTTGTC 57.467 50.000 0.93 0.00 0.00 3.18
2511 2883 2.369860 TGATGCAGTCTGTTCCTCTTGT 59.630 45.455 0.93 0.00 0.00 3.16
2512 2884 3.049708 TGATGCAGTCTGTTCCTCTTG 57.950 47.619 0.93 0.00 0.00 3.02
2515 2887 2.935201 GTGATGATGCAGTCTGTTCCTC 59.065 50.000 0.93 3.16 0.00 3.71
2516 2888 2.355513 GGTGATGATGCAGTCTGTTCCT 60.356 50.000 0.93 0.00 0.00 3.36
2519 2931 2.865119 TGGTGATGATGCAGTCTGTT 57.135 45.000 0.93 0.00 0.00 3.16
2522 2934 1.841919 TCCATGGTGATGATGCAGTCT 59.158 47.619 12.58 0.00 0.00 3.24
2535 2947 0.328258 GCACCACCTAGTTCCATGGT 59.672 55.000 12.58 0.00 46.53 3.55
2536 2948 0.327924 TGCACCACCTAGTTCCATGG 59.672 55.000 4.97 4.97 38.26 3.66
2542 2954 2.618045 GCTAACCATGCACCACCTAGTT 60.618 50.000 0.00 0.00 0.00 2.24
2546 2958 1.377202 CGCTAACCATGCACCACCT 60.377 57.895 0.00 0.00 0.00 4.00
2578 2990 1.126846 CTTCCTGCACGCGAAACTAAG 59.873 52.381 15.93 5.29 0.00 2.18
2580 2992 1.289109 GCTTCCTGCACGCGAAACTA 61.289 55.000 15.93 0.00 42.31 2.24
2581 2993 2.607892 GCTTCCTGCACGCGAAACT 61.608 57.895 15.93 0.00 42.31 2.66
2582 2994 2.127232 GCTTCCTGCACGCGAAAC 60.127 61.111 15.93 1.18 42.31 2.78
2583 2995 3.353836 GGCTTCCTGCACGCGAAA 61.354 61.111 15.93 0.00 45.15 3.46
2593 3005 3.854669 CTCATCGCCCGGCTTCCT 61.855 66.667 8.05 0.00 0.00 3.36
2594 3006 2.869503 TTTCTCATCGCCCGGCTTCC 62.870 60.000 8.05 0.00 0.00 3.46
2595 3007 1.024579 TTTTCTCATCGCCCGGCTTC 61.025 55.000 8.05 0.00 0.00 3.86
2596 3008 1.002624 TTTTCTCATCGCCCGGCTT 60.003 52.632 8.05 0.00 0.00 4.35
2599 3011 0.108138 AGACTTTTCTCATCGCCCGG 60.108 55.000 0.00 0.00 0.00 5.73
2600 3012 1.002366 CAGACTTTTCTCATCGCCCG 58.998 55.000 0.00 0.00 0.00 6.13
2601 3013 1.734465 CACAGACTTTTCTCATCGCCC 59.266 52.381 0.00 0.00 0.00 6.13
2602 3014 1.734465 CCACAGACTTTTCTCATCGCC 59.266 52.381 0.00 0.00 0.00 5.54
2620 3108 2.049888 TGCATTTCACTGTGACACCA 57.950 45.000 10.56 2.74 0.00 4.17
2623 3111 2.861274 TCCATGCATTTCACTGTGACA 58.139 42.857 10.56 4.27 0.00 3.58
2630 3118 1.199789 TCAGCGTTCCATGCATTTCAC 59.800 47.619 0.00 0.00 31.07 3.18
2640 3128 3.145286 TCAATTTCACATCAGCGTTCCA 58.855 40.909 0.00 0.00 0.00 3.53
2641 3129 3.426695 CCTCAATTTCACATCAGCGTTCC 60.427 47.826 0.00 0.00 0.00 3.62
2642 3130 3.751621 CCTCAATTTCACATCAGCGTTC 58.248 45.455 0.00 0.00 0.00 3.95
2644 3132 1.470098 GCCTCAATTTCACATCAGCGT 59.530 47.619 0.00 0.00 0.00 5.07
2645 3133 1.530441 CGCCTCAATTTCACATCAGCG 60.530 52.381 0.00 0.00 34.70 5.18
2653 3158 5.452078 ACTTTGAAATCGCCTCAATTTCA 57.548 34.783 7.08 7.08 46.21 2.69
2683 3188 9.462174 GTTTGTGTTTCAATCATCTGTAAATCA 57.538 29.630 0.00 0.00 35.84 2.57
2684 3189 8.915654 GGTTTGTGTTTCAATCATCTGTAAATC 58.084 33.333 0.00 0.00 35.84 2.17
2685 3190 7.594758 CGGTTTGTGTTTCAATCATCTGTAAAT 59.405 33.333 0.00 0.00 35.84 1.40
2695 3201 3.982576 AGGTCGGTTTGTGTTTCAATC 57.017 42.857 0.00 0.00 35.84 2.67
2699 3205 2.876550 AGCTAAGGTCGGTTTGTGTTTC 59.123 45.455 0.00 0.00 0.00 2.78
2700 3206 2.876550 GAGCTAAGGTCGGTTTGTGTTT 59.123 45.455 0.00 0.00 0.00 2.83
2701 3207 2.158871 TGAGCTAAGGTCGGTTTGTGTT 60.159 45.455 0.00 0.00 32.15 3.32
2748 3254 4.024809 GCGACCTAAGGATTTATCTGCAAC 60.025 45.833 0.00 0.00 0.00 4.17
2769 3275 3.564027 GCCGGATTCGAACCAGCG 61.564 66.667 5.05 0.00 39.00 5.18
2840 3346 7.010645 GCAAATCTTTTACCTCCGTTTCAAAAA 59.989 33.333 0.00 0.00 0.00 1.94
2841 3347 6.477360 GCAAATCTTTTACCTCCGTTTCAAAA 59.523 34.615 0.00 0.00 0.00 2.44
2842 3348 5.980715 GCAAATCTTTTACCTCCGTTTCAAA 59.019 36.000 0.00 0.00 0.00 2.69
2843 3349 5.508320 GGCAAATCTTTTACCTCCGTTTCAA 60.508 40.000 0.00 0.00 0.00 2.69
2844 3350 4.022676 GGCAAATCTTTTACCTCCGTTTCA 60.023 41.667 0.00 0.00 0.00 2.69
2845 3351 4.217767 AGGCAAATCTTTTACCTCCGTTTC 59.782 41.667 0.00 0.00 0.00 2.78
2846 3352 4.149598 AGGCAAATCTTTTACCTCCGTTT 58.850 39.130 0.00 0.00 0.00 3.60
2847 3353 3.756963 GAGGCAAATCTTTTACCTCCGTT 59.243 43.478 7.70 0.00 40.91 4.44
2848 3354 3.244770 TGAGGCAAATCTTTTACCTCCGT 60.245 43.478 13.97 0.00 45.22 4.69
2849 3355 3.343617 TGAGGCAAATCTTTTACCTCCG 58.656 45.455 13.97 0.00 45.22 4.63
2850 3356 4.339530 GGATGAGGCAAATCTTTTACCTCC 59.660 45.833 13.97 3.19 45.22 4.30
2851 3357 4.949856 TGGATGAGGCAAATCTTTTACCTC 59.050 41.667 10.92 10.92 45.87 3.85
2852 3358 4.934356 TGGATGAGGCAAATCTTTTACCT 58.066 39.130 0.00 0.00 0.00 3.08
2853 3359 5.859205 ATGGATGAGGCAAATCTTTTACC 57.141 39.130 0.00 0.00 0.00 2.85
2854 3360 9.822185 ATTTAATGGATGAGGCAAATCTTTTAC 57.178 29.630 0.00 0.00 0.00 2.01
2858 3364 9.425248 TCTTATTTAATGGATGAGGCAAATCTT 57.575 29.630 0.00 0.00 0.00 2.40
2859 3365 9.075678 CTCTTATTTAATGGATGAGGCAAATCT 57.924 33.333 0.00 0.00 0.00 2.40
2860 3366 9.071276 TCTCTTATTTAATGGATGAGGCAAATC 57.929 33.333 0.00 0.00 0.00 2.17
2861 3367 9.425248 TTCTCTTATTTAATGGATGAGGCAAAT 57.575 29.630 0.00 0.00 0.00 2.32
2862 3368 8.821686 TTCTCTTATTTAATGGATGAGGCAAA 57.178 30.769 0.00 0.00 0.00 3.68
2863 3369 8.274322 TCTTCTCTTATTTAATGGATGAGGCAA 58.726 33.333 0.00 0.00 0.00 4.52
2864 3370 7.805163 TCTTCTCTTATTTAATGGATGAGGCA 58.195 34.615 0.00 0.00 0.00 4.75
2865 3371 8.682936 TTCTTCTCTTATTTAATGGATGAGGC 57.317 34.615 0.00 0.00 0.00 4.70
2892 3398 9.458374 CGTTTTGTATGTAAAACTCCAAATTCT 57.542 29.630 13.82 0.00 44.39 2.40
2893 3399 8.696175 CCGTTTTGTATGTAAAACTCCAAATTC 58.304 33.333 13.82 0.00 44.39 2.17
2894 3400 7.170151 GCCGTTTTGTATGTAAAACTCCAAATT 59.830 33.333 13.82 0.00 44.39 1.82
2895 3401 6.643360 GCCGTTTTGTATGTAAAACTCCAAAT 59.357 34.615 13.82 0.00 44.39 2.32
2896 3402 5.978322 GCCGTTTTGTATGTAAAACTCCAAA 59.022 36.000 13.82 0.00 44.39 3.28
2897 3403 5.067413 TGCCGTTTTGTATGTAAAACTCCAA 59.933 36.000 13.82 0.00 44.39 3.53
2898 3404 4.579340 TGCCGTTTTGTATGTAAAACTCCA 59.421 37.500 13.82 9.44 44.39 3.86
2899 3405 5.110940 TGCCGTTTTGTATGTAAAACTCC 57.889 39.130 13.82 7.76 44.39 3.85
2900 3406 5.571357 CCATGCCGTTTTGTATGTAAAACTC 59.429 40.000 13.82 8.47 44.39 3.01
2901 3407 5.010213 ACCATGCCGTTTTGTATGTAAAACT 59.990 36.000 13.82 0.00 44.39 2.66
2902 3408 5.224135 ACCATGCCGTTTTGTATGTAAAAC 58.776 37.500 0.00 0.00 43.59 2.43
2903 3409 5.455056 ACCATGCCGTTTTGTATGTAAAA 57.545 34.783 0.00 0.00 0.00 1.52
2904 3410 6.570672 TTACCATGCCGTTTTGTATGTAAA 57.429 33.333 0.00 0.00 0.00 2.01
2905 3411 6.761099 ATTACCATGCCGTTTTGTATGTAA 57.239 33.333 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.