Multiple sequence alignment - TraesCS4B01G076400

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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 TraesCS4B01G076400 chr4B 100.000 3620 0 0 1 3620 73100962 73104581 0.000000e+00 6685
1 TraesCS4B01G076400 chr4A 90.489 3091 145 64 588 3620 547928275 547931274 0.000000e+00 3941
2 TraesCS4B01G076400 chr4A 90.909 352 20 8 8 351 547927877 547928224 2.550000e-126 462
3 TraesCS4B01G076400 chr4D 94.787 1995 70 12 644 2632 49501195 49499229 0.000000e+00 3077
4 TraesCS4B01G076400 chr4D 85.338 948 61 26 2684 3620 49499203 49498323 0.000000e+00 909
5 TraesCS4B01G076400 chr4D 88.223 467 32 11 31 487 49501751 49501298 1.480000e-148 536


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 TraesCS4B01G076400 chr4B 73100962 73104581 3619 False 6685.000000 6685 100.000000 1 3620 1 chr4B.!!$F1 3619
1 TraesCS4B01G076400 chr4A 547927877 547931274 3397 False 2201.500000 3941 90.699000 8 3620 2 chr4A.!!$F1 3612
2 TraesCS4B01G076400 chr4D 49498323 49501751 3428 True 1507.333333 3077 89.449333 31 3620 3 chr4D.!!$R1 3589

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
941 999 0.329931 AACACCACCAATATCGCCCA 59.67 50.0 0.0 0.0 0.0 5.36 F
942 1000 0.329931 ACACCACCAATATCGCCCAA 59.67 50.0 0.0 0.0 0.0 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2190 2254 0.308068 CAGCCGTCGACTCGATGTAT 59.692 55.0 14.7 4.84 40.74 2.29 R
2783 2861 0.319297 GCTGCCTTTTCCAAGCACAG 60.319 55.0 0.0 0.00 36.46 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
90 91 3.181490 GGCCAAACTTCTGACTTTTTCGT 60.181 43.478 0.00 0.00 0.00 3.85
119 120 7.944729 AGCCAGACACTTTGATTAACATAAT 57.055 32.000 0.00 0.00 0.00 1.28
121 122 6.974622 GCCAGACACTTTGATTAACATAATGG 59.025 38.462 0.00 0.00 0.00 3.16
122 123 7.483307 CCAGACACTTTGATTAACATAATGGG 58.517 38.462 0.00 0.00 0.00 4.00
168 169 0.606401 CAAGCAGGTACACAGGTGGG 60.606 60.000 4.24 0.00 34.19 4.61
180 181 3.226777 CACAGGTGGGATTGGTGTTTTA 58.773 45.455 0.00 0.00 0.00 1.52
193 194 7.990886 GGATTGGTGTTTTATAGGACTGATGTA 59.009 37.037 0.00 0.00 0.00 2.29
194 195 8.732746 ATTGGTGTTTTATAGGACTGATGTAC 57.267 34.615 0.00 0.00 0.00 2.90
212 213 1.415374 ACACACGCATCGTACAACTC 58.585 50.000 0.00 0.00 38.32 3.01
219 220 2.478894 CGCATCGTACAACTCCACTTTT 59.521 45.455 0.00 0.00 0.00 2.27
276 284 6.835819 TGTATACATGACTGCTATCTACCC 57.164 41.667 0.08 0.00 0.00 3.69
380 389 6.720012 TCTTTTGCAGGAAAAACTTTTGAC 57.280 33.333 1.11 0.00 33.04 3.18
387 396 7.551585 TGCAGGAAAAACTTTTGACTTATTCA 58.448 30.769 0.00 0.00 0.00 2.57
403 412 6.329496 ACTTATTCATAAAACACCAATGCCG 58.671 36.000 0.00 0.00 0.00 5.69
416 425 3.442273 ACCAATGCCGGTACAAATAACAG 59.558 43.478 1.90 0.00 37.57 3.16
419 428 2.702261 TGCCGGTACAAATAACAGTCC 58.298 47.619 1.90 0.00 0.00 3.85
440 449 7.607991 CAGTCCAAGTAACAGAAATTACATCCT 59.392 37.037 0.00 0.00 37.49 3.24
444 453 8.576442 CCAAGTAACAGAAATTACATCCTTGTT 58.424 33.333 0.00 0.00 37.49 2.83
445 454 9.612620 CAAGTAACAGAAATTACATCCTTGTTC 57.387 33.333 0.00 0.00 37.49 3.18
447 456 9.520515 AGTAACAGAAATTACATCCTTGTTCAT 57.479 29.630 0.00 0.00 37.49 2.57
450 459 9.739276 AACAGAAATTACATCCTTGTTCATAGA 57.261 29.630 0.00 0.00 37.28 1.98
451 460 9.167311 ACAGAAATTACATCCTTGTTCATAGAC 57.833 33.333 0.00 0.00 37.28 2.59
455 464 8.873215 AATTACATCCTTGTTCATAGACTACG 57.127 34.615 0.00 0.00 37.28 3.51
458 467 7.400599 ACATCCTTGTTCATAGACTACGTAA 57.599 36.000 0.00 0.00 29.55 3.18
459 468 8.008513 ACATCCTTGTTCATAGACTACGTAAT 57.991 34.615 0.00 0.00 29.55 1.89
483 492 2.586258 ATTACAAGCACTCGAGCGAT 57.414 45.000 13.61 0.00 40.15 4.58
487 496 2.407428 AAGCACTCGAGCGATCCGA 61.407 57.895 13.61 0.00 40.15 4.55
488 497 1.934220 AAGCACTCGAGCGATCCGAA 61.934 55.000 13.61 0.00 40.15 4.30
489 498 1.516386 GCACTCGAGCGATCCGAAA 60.516 57.895 13.61 0.00 35.48 3.46
490 499 1.475441 GCACTCGAGCGATCCGAAAG 61.475 60.000 13.61 0.00 35.48 2.62
492 501 2.277949 TCGAGCGATCCGAAAGCG 60.278 61.111 0.00 0.00 35.78 4.68
494 503 2.849966 CGAGCGATCCGAAAGCGTG 61.850 63.158 0.00 0.00 35.23 5.34
495 504 3.144120 GAGCGATCCGAAAGCGTGC 62.144 63.158 0.00 0.00 35.23 5.34
496 505 4.223964 GCGATCCGAAAGCGTGCC 62.224 66.667 0.00 0.00 35.23 5.01
497 506 3.913573 CGATCCGAAAGCGTGCCG 61.914 66.667 0.00 0.00 35.23 5.69
498 507 3.564027 GATCCGAAAGCGTGCCGG 61.564 66.667 0.00 0.00 44.22 6.13
527 544 6.469782 TCGGGTAAACCTTATTGTAGTAGG 57.530 41.667 0.00 0.00 36.97 3.18
528 545 5.957774 TCGGGTAAACCTTATTGTAGTAGGT 59.042 40.000 0.00 0.00 43.98 3.08
534 551 6.705863 AACCTTATTGTAGTAGGTAGTCGG 57.294 41.667 0.00 0.00 41.33 4.79
535 552 5.136105 ACCTTATTGTAGTAGGTAGTCGGG 58.864 45.833 0.00 0.00 40.42 5.14
541 558 5.057843 TGTAGTAGGTAGTCGGGATGATT 57.942 43.478 0.00 0.00 0.00 2.57
542 559 5.452255 TGTAGTAGGTAGTCGGGATGATTT 58.548 41.667 0.00 0.00 0.00 2.17
543 560 5.895534 TGTAGTAGGTAGTCGGGATGATTTT 59.104 40.000 0.00 0.00 0.00 1.82
544 561 5.952347 AGTAGGTAGTCGGGATGATTTTT 57.048 39.130 0.00 0.00 0.00 1.94
699 749 7.284820 AGAAGTAACCTAAAACTTGCCAAGTA 58.715 34.615 11.10 0.00 41.91 2.24
701 751 4.823790 AACCTAAAACTTGCCAAGTACG 57.176 40.909 11.10 0.00 41.91 3.67
777 829 2.413837 ACGATGAGTTTCCTTTGGACG 58.586 47.619 0.00 0.00 0.00 4.79
851 909 0.537371 CCCGGAAAAAGAGGCTGTGT 60.537 55.000 0.73 0.00 0.00 3.72
869 927 4.129148 GTGGGCCCACCTCCATCC 62.129 72.222 40.65 16.46 40.79 3.51
934 992 1.646912 TCCTCGGAACACCACCAATA 58.353 50.000 0.00 0.00 0.00 1.90
938 996 0.655733 CGGAACACCACCAATATCGC 59.344 55.000 0.00 0.00 0.00 4.58
939 997 1.021968 GGAACACCACCAATATCGCC 58.978 55.000 0.00 0.00 0.00 5.54
940 998 1.021968 GAACACCACCAATATCGCCC 58.978 55.000 0.00 0.00 0.00 6.13
941 999 0.329931 AACACCACCAATATCGCCCA 59.670 50.000 0.00 0.00 0.00 5.36
942 1000 0.329931 ACACCACCAATATCGCCCAA 59.670 50.000 0.00 0.00 0.00 4.12
943 1001 1.024271 CACCACCAATATCGCCCAAG 58.976 55.000 0.00 0.00 0.00 3.61
944 1002 0.623723 ACCACCAATATCGCCCAAGT 59.376 50.000 0.00 0.00 0.00 3.16
945 1003 1.308998 CCACCAATATCGCCCAAGTC 58.691 55.000 0.00 0.00 0.00 3.01
946 1004 1.134098 CCACCAATATCGCCCAAGTCT 60.134 52.381 0.00 0.00 0.00 3.24
947 1005 2.213499 CACCAATATCGCCCAAGTCTC 58.787 52.381 0.00 0.00 0.00 3.36
952 1011 1.112113 TATCGCCCAAGTCTCCACTC 58.888 55.000 0.00 0.00 29.93 3.51
1011 1075 2.615465 CCCAGCCATGAAGGGGACA 61.615 63.158 9.24 0.00 43.57 4.02
1101 1165 2.481289 AGTACTTCAAGCTTGAGGCC 57.519 50.000 31.83 23.68 43.05 5.19
1170 1234 2.158564 CCTCACCATGGCCTACATCATT 60.159 50.000 13.04 0.00 37.84 2.57
1533 1597 3.743899 GCATCATCTTCTTCCTCCTGTCC 60.744 52.174 0.00 0.00 0.00 4.02
1686 1750 4.293648 CCGTCCACGCTGGTCACA 62.294 66.667 4.33 0.00 39.03 3.58
1695 1759 2.734723 CTGGTCACACTCACCGCG 60.735 66.667 0.00 0.00 36.61 6.46
1794 1858 1.296392 CTTCCTCATCACCGCCACA 59.704 57.895 0.00 0.00 0.00 4.17
1839 1903 2.860136 CGCCATGATATACGGCATAGTG 59.140 50.000 9.50 0.00 46.60 2.74
2208 2272 0.308068 CATACATCGAGTCGACGGCT 59.692 55.000 19.16 0.00 39.18 5.52
2632 2696 2.105328 TGTGACCGTGTCCGTGTG 59.895 61.111 2.23 0.00 0.00 3.82
2633 2697 2.414179 GTGACCGTGTCCGTGTGA 59.586 61.111 2.23 0.00 0.00 3.58
2634 2698 1.660575 GTGACCGTGTCCGTGTGAG 60.661 63.158 2.23 0.00 0.00 3.51
2635 2699 2.049433 GACCGTGTCCGTGTGAGG 60.049 66.667 0.00 0.00 0.00 3.86
2636 2700 2.520020 ACCGTGTCCGTGTGAGGA 60.520 61.111 0.00 0.00 38.11 3.71
2637 2701 2.258591 CCGTGTCCGTGTGAGGAG 59.741 66.667 0.00 0.00 41.68 3.69
2640 2704 1.595993 CGTGTCCGTGTGAGGAGGAT 61.596 60.000 0.00 0.00 41.68 3.24
2641 2705 1.471119 GTGTCCGTGTGAGGAGGATA 58.529 55.000 0.00 0.00 41.68 2.59
2643 2707 2.232941 GTGTCCGTGTGAGGAGGATAAA 59.767 50.000 0.00 0.00 41.68 1.40
2644 2708 2.232941 TGTCCGTGTGAGGAGGATAAAC 59.767 50.000 0.00 0.00 41.68 2.01
2645 2709 2.232941 GTCCGTGTGAGGAGGATAAACA 59.767 50.000 0.00 0.00 41.68 2.83
2647 2711 3.325425 TCCGTGTGAGGAGGATAAACAAA 59.675 43.478 0.00 0.00 34.92 2.83
2648 2712 3.435671 CCGTGTGAGGAGGATAAACAAAC 59.564 47.826 0.00 0.00 0.00 2.93
2650 2714 4.755123 CGTGTGAGGAGGATAAACAAACTT 59.245 41.667 0.00 0.00 0.00 2.66
2651 2715 5.238650 CGTGTGAGGAGGATAAACAAACTTT 59.761 40.000 0.00 0.00 0.00 2.66
2652 2716 6.438763 GTGTGAGGAGGATAAACAAACTTTG 58.561 40.000 0.00 0.00 0.00 2.77
2726 2790 1.923204 GACACAGAGCATCATCGTGAC 59.077 52.381 0.00 0.00 37.82 3.67
2727 2791 1.273327 ACACAGAGCATCATCGTGACA 59.727 47.619 0.00 0.00 37.82 3.58
2728 2792 2.093816 ACACAGAGCATCATCGTGACAT 60.094 45.455 0.00 0.00 37.82 3.06
2749 2827 5.780793 ACATATGGGATTAGGACTACTGGTC 59.219 44.000 7.80 0.00 43.79 4.02
2761 2839 3.489180 CTACTGGTCGTAGGAACTGTG 57.511 52.381 19.53 8.64 41.48 3.66
2764 2842 2.165167 CTGGTCGTAGGAACTGTGGTA 58.835 52.381 1.64 0.00 41.52 3.25
2765 2843 2.163815 CTGGTCGTAGGAACTGTGGTAG 59.836 54.545 1.64 0.00 41.52 3.18
2766 2844 2.165998 GGTCGTAGGAACTGTGGTAGT 58.834 52.381 0.00 0.00 41.52 2.73
2767 2845 3.244875 TGGTCGTAGGAACTGTGGTAGTA 60.245 47.826 1.64 0.00 41.52 1.82
2768 2846 3.376546 GGTCGTAGGAACTGTGGTAGTAG 59.623 52.174 0.00 0.00 41.52 2.57
2769 2847 4.006319 GTCGTAGGAACTGTGGTAGTAGT 58.994 47.826 0.00 0.00 41.52 2.73
2770 2848 4.005650 TCGTAGGAACTGTGGTAGTAGTG 58.994 47.826 0.00 0.00 41.52 2.74
2771 2849 3.128242 CGTAGGAACTGTGGTAGTAGTGG 59.872 52.174 0.00 0.00 41.52 4.00
2772 2850 1.900486 AGGAACTGTGGTAGTAGTGGC 59.100 52.381 0.00 0.00 39.18 5.01
2773 2851 1.900486 GGAACTGTGGTAGTAGTGGCT 59.100 52.381 0.00 0.00 39.18 4.75
2774 2852 2.094130 GGAACTGTGGTAGTAGTGGCTC 60.094 54.545 0.00 0.00 39.18 4.70
2775 2853 2.606751 ACTGTGGTAGTAGTGGCTCT 57.393 50.000 0.00 0.00 38.04 4.09
2776 2854 3.733883 ACTGTGGTAGTAGTGGCTCTA 57.266 47.619 0.00 0.00 38.04 2.43
2777 2855 4.043608 ACTGTGGTAGTAGTGGCTCTAA 57.956 45.455 0.00 0.00 38.04 2.10
2778 2856 4.611367 ACTGTGGTAGTAGTGGCTCTAAT 58.389 43.478 2.01 2.01 38.04 1.73
2779 2857 4.645588 ACTGTGGTAGTAGTGGCTCTAATC 59.354 45.833 0.00 0.00 38.04 1.75
2780 2858 4.868268 TGTGGTAGTAGTGGCTCTAATCT 58.132 43.478 0.00 0.00 0.00 2.40
2781 2859 6.009908 TGTGGTAGTAGTGGCTCTAATCTA 57.990 41.667 0.00 0.00 0.00 1.98
2782 2860 6.611785 TGTGGTAGTAGTGGCTCTAATCTAT 58.388 40.000 0.00 0.00 0.00 1.98
2783 2861 6.715718 TGTGGTAGTAGTGGCTCTAATCTATC 59.284 42.308 0.00 0.00 0.00 2.08
2809 2905 0.951558 TGGAAAAGGCAGCTCGTTTC 59.048 50.000 11.30 11.30 35.44 2.78
2836 2932 1.909700 TGATGTGCAAGGAAAGGACC 58.090 50.000 0.00 0.00 0.00 4.46
2837 2933 0.804989 GATGTGCAAGGAAAGGACCG 59.195 55.000 0.00 0.00 34.73 4.79
2839 2935 2.282180 TGCAAGGAAAGGACCGGC 60.282 61.111 0.00 0.00 36.30 6.13
2840 2936 3.431725 GCAAGGAAAGGACCGGCG 61.432 66.667 0.00 0.00 34.73 6.46
2841 2937 2.345991 CAAGGAAAGGACCGGCGA 59.654 61.111 9.30 0.00 34.73 5.54
2842 2938 1.078426 CAAGGAAAGGACCGGCGAT 60.078 57.895 9.30 0.00 34.73 4.58
2843 2939 1.078426 AAGGAAAGGACCGGCGATG 60.078 57.895 9.30 0.00 34.73 3.84
2844 2940 1.838073 AAGGAAAGGACCGGCGATGT 61.838 55.000 9.30 0.00 34.73 3.06
2894 2990 5.565592 AATGCTCACATTGATTTCGCTAA 57.434 34.783 0.00 0.00 44.90 3.09
2918 3014 8.950403 AACTAGCACGTTTATTTTCTGATTTC 57.050 30.769 0.00 0.00 0.00 2.17
2919 3015 8.324163 ACTAGCACGTTTATTTTCTGATTTCT 57.676 30.769 0.00 0.00 0.00 2.52
2920 3016 8.230486 ACTAGCACGTTTATTTTCTGATTTCTG 58.770 33.333 0.00 0.00 0.00 3.02
2985 3081 6.951971 AGAGGTCAAAGCTATCATTACTTGT 58.048 36.000 0.00 0.00 0.00 3.16
2998 3094 9.561270 CTATCATTACTTGTAGGACGTATGATG 57.439 37.037 11.49 1.78 0.00 3.07
3038 3136 4.141959 TGAGATTGGTATGCGATGAACTCA 60.142 41.667 0.00 0.00 0.00 3.41
3043 3141 2.476619 GGTATGCGATGAACTCAATCGG 59.523 50.000 7.80 0.00 38.17 4.18
3096 3216 2.428530 AGCAGCACGTCATGATCTCTTA 59.571 45.455 0.00 0.00 0.00 2.10
3140 3269 6.228258 AGTCAAGCGTGAAAGTATAAAAGGA 58.772 36.000 3.20 0.00 34.87 3.36
3141 3270 6.708949 AGTCAAGCGTGAAAGTATAAAAGGAA 59.291 34.615 3.20 0.00 34.87 3.36
3142 3271 7.015877 GTCAAGCGTGAAAGTATAAAAGGAAG 58.984 38.462 3.20 0.00 34.87 3.46
3143 3272 6.148811 TCAAGCGTGAAAGTATAAAAGGAAGG 59.851 38.462 0.00 0.00 0.00 3.46
3144 3273 5.801380 AGCGTGAAAGTATAAAAGGAAGGA 58.199 37.500 0.00 0.00 0.00 3.36
3155 3284 7.890655 AGTATAAAAGGAAGGATTTCAGTGCTT 59.109 33.333 0.00 0.00 34.90 3.91
3229 3363 0.529773 ATGGGCACGTACGCTGTATG 60.530 55.000 16.72 6.83 0.00 2.39
3284 3418 1.737355 AACGAACGGAGTGGGAACGA 61.737 55.000 0.00 0.00 45.00 3.85
3289 3423 1.215647 CGGAGTGGGAACGAAGGAG 59.784 63.158 0.00 0.00 0.00 3.69
3293 3427 0.832135 AGTGGGAACGAAGGAGCTCA 60.832 55.000 17.19 0.00 0.00 4.26
3294 3428 0.390472 GTGGGAACGAAGGAGCTCAG 60.390 60.000 17.19 6.13 0.00 3.35
3295 3429 1.448717 GGGAACGAAGGAGCTCAGC 60.449 63.158 17.19 2.76 0.00 4.26
3296 3430 1.594310 GGAACGAAGGAGCTCAGCT 59.406 57.895 17.19 0.00 43.88 4.24
3378 3512 0.757188 TTTTGCGTGTGGATTGGGGT 60.757 50.000 0.00 0.00 0.00 4.95
3379 3513 1.459455 TTTGCGTGTGGATTGGGGTG 61.459 55.000 0.00 0.00 0.00 4.61
3385 3519 0.110295 TGTGGATTGGGGTGTGTCTG 59.890 55.000 0.00 0.00 0.00 3.51
3388 3522 1.710244 TGGATTGGGGTGTGTCTGAAT 59.290 47.619 0.00 0.00 0.00 2.57
3397 3531 2.341257 GTGTGTCTGAATGCTGACGAT 58.659 47.619 6.26 0.00 43.52 3.73
3405 3539 0.178767 AATGCTGACGATGGCTGCTA 59.821 50.000 0.00 0.00 0.00 3.49
3412 3546 0.107654 ACGATGGCTGCTACTTTCCC 60.108 55.000 0.00 0.00 0.00 3.97
3418 3552 2.041620 TGGCTGCTACTTTCCCTCAAAT 59.958 45.455 0.00 0.00 0.00 2.32
3419 3553 3.092301 GGCTGCTACTTTCCCTCAAATT 58.908 45.455 0.00 0.00 0.00 1.82
3420 3554 3.119352 GGCTGCTACTTTCCCTCAAATTG 60.119 47.826 0.00 0.00 0.00 2.32
3423 3557 5.105595 GCTGCTACTTTCCCTCAAATTGATT 60.106 40.000 0.00 0.00 0.00 2.57
3443 3577 1.134220 TGATTCCCTGCCACGTAATCC 60.134 52.381 0.00 0.00 0.00 3.01
3461 3595 6.094464 CGTAATCCTTTTTCCTCCGGTAAAAT 59.906 38.462 0.00 0.00 32.99 1.82
3466 3600 5.163550 CCTTTTTCCTCCGGTAAAATCATCC 60.164 44.000 0.00 0.00 32.99 3.51
3484 3618 2.100631 CGCATCTGGACGTGGTTCC 61.101 63.158 0.00 0.00 36.03 3.62
3517 3651 0.249031 GCCTATTGCCGGAAATGTGC 60.249 55.000 18.71 15.55 0.00 4.57
3525 3659 2.398554 CGGAAATGTGCGGTCTGGG 61.399 63.158 0.00 0.00 34.49 4.45
3526 3660 2.700773 GGAAATGTGCGGTCTGGGC 61.701 63.158 0.00 0.00 0.00 5.36
3527 3661 2.676471 AAATGTGCGGTCTGGGCC 60.676 61.111 0.00 0.00 0.00 5.80
3528 3662 3.210012 AAATGTGCGGTCTGGGCCT 62.210 57.895 4.53 0.00 0.00 5.19
3573 3708 1.917872 AGCTTCGACTTGTCCTCTCT 58.082 50.000 0.00 0.00 0.00 3.10
3574 3709 1.816224 AGCTTCGACTTGTCCTCTCTC 59.184 52.381 0.00 0.00 0.00 3.20
3589 3724 4.225492 TCCTCTCTCGTATTATCGGATCCT 59.775 45.833 10.75 0.00 0.00 3.24
3601 3740 1.974957 TCGGATCCTCAAGGTTCAACA 59.025 47.619 10.75 0.00 35.99 3.33
3608 3747 5.772825 TCCTCAAGGTTCAACAAAATCTG 57.227 39.130 0.00 0.00 36.34 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.568349 ACAATCTCAAATTATAGAGGTGCTGA 58.432 34.615 0.00 0.00 32.76 4.26
1 2 7.798596 ACAATCTCAAATTATAGAGGTGCTG 57.201 36.000 0.00 0.00 32.76 4.41
3 4 7.283127 TCCAACAATCTCAAATTATAGAGGTGC 59.717 37.037 0.00 0.00 32.76 5.01
4 5 8.737168 TCCAACAATCTCAAATTATAGAGGTG 57.263 34.615 0.00 0.00 32.76 4.00
5 6 9.927081 ATTCCAACAATCTCAAATTATAGAGGT 57.073 29.630 0.00 0.00 32.76 3.85
19 20 9.760077 CTTTACGGTAGTATATTCCAACAATCT 57.240 33.333 0.00 0.00 32.12 2.40
20 21 9.538508 ACTTTACGGTAGTATATTCCAACAATC 57.461 33.333 0.00 0.00 32.12 2.67
90 91 0.843309 TCAAAGTGTCTGGCTTCCCA 59.157 50.000 0.00 0.00 39.32 4.37
119 120 4.826616 TGGATACTAATGATCCACTCCCA 58.173 43.478 0.13 0.00 46.40 4.37
121 122 6.042093 TGAACTGGATACTAATGATCCACTCC 59.958 42.308 0.13 0.00 46.40 3.85
122 123 7.055667 TGAACTGGATACTAATGATCCACTC 57.944 40.000 0.13 2.19 46.40 3.51
168 169 7.865706 ACATCAGTCCTATAAAACACCAATC 57.134 36.000 0.00 0.00 0.00 2.67
180 181 2.758423 TGCGTGTGTACATCAGTCCTAT 59.242 45.455 0.00 0.00 0.00 2.57
193 194 1.415374 GAGTTGTACGATGCGTGTGT 58.585 50.000 2.33 0.00 41.39 3.72
194 195 0.713883 GGAGTTGTACGATGCGTGTG 59.286 55.000 2.33 0.00 41.39 3.82
212 213 4.621034 CCGTTTTATAAGCTGCAAAAGTGG 59.379 41.667 1.02 1.71 0.00 4.00
219 220 4.082517 TGCATTTCCGTTTTATAAGCTGCA 60.083 37.500 1.02 0.00 33.89 4.41
307 315 9.618890 AACAACTAGTATCTCAATATGTTGCAT 57.381 29.630 0.00 0.00 37.59 3.96
362 371 7.551585 TGAATAAGTCAAAAGTTTTTCCTGCA 58.448 30.769 0.00 0.00 31.51 4.41
380 389 5.748152 CCGGCATTGGTGTTTTATGAATAAG 59.252 40.000 0.00 0.00 0.00 1.73
387 396 3.422796 TGTACCGGCATTGGTGTTTTAT 58.577 40.909 0.00 0.00 43.68 1.40
390 399 1.693627 TTGTACCGGCATTGGTGTTT 58.306 45.000 0.00 0.00 43.68 2.83
395 404 3.442273 ACTGTTATTTGTACCGGCATTGG 59.558 43.478 0.00 0.00 0.00 3.16
397 406 3.692593 GGACTGTTATTTGTACCGGCATT 59.307 43.478 0.00 0.00 0.00 3.56
403 412 7.658575 TCTGTTACTTGGACTGTTATTTGTACC 59.341 37.037 0.00 0.00 0.00 3.34
416 425 7.923414 AGGATGTAATTTCTGTTACTTGGAC 57.077 36.000 0.00 0.00 35.94 4.02
419 428 9.612620 GAACAAGGATGTAATTTCTGTTACTTG 57.387 33.333 0.00 0.00 39.40 3.16
448 457 8.866956 GTGCTTGTAATTGTTATTACGTAGTCT 58.133 33.333 0.00 0.00 45.96 3.24
449 458 8.866956 AGTGCTTGTAATTGTTATTACGTAGTC 58.133 33.333 0.00 0.00 45.96 2.59
450 459 8.767478 AGTGCTTGTAATTGTTATTACGTAGT 57.233 30.769 0.00 0.00 45.96 2.73
451 460 8.048436 CGAGTGCTTGTAATTGTTATTACGTAG 58.952 37.037 0.00 0.00 45.96 3.51
455 464 6.900299 GCTCGAGTGCTTGTAATTGTTATTAC 59.100 38.462 15.13 0.00 44.16 1.89
458 467 4.032900 CGCTCGAGTGCTTGTAATTGTTAT 59.967 41.667 13.91 0.00 0.00 1.89
459 468 3.366724 CGCTCGAGTGCTTGTAATTGTTA 59.633 43.478 13.91 0.00 0.00 2.41
494 503 4.534141 TTACCCGATTCCGCCGGC 62.534 66.667 19.07 19.07 45.24 6.13
495 504 2.175621 GTTTACCCGATTCCGCCGG 61.176 63.158 0.00 0.00 46.10 6.13
496 505 2.175621 GGTTTACCCGATTCCGCCG 61.176 63.158 0.00 0.00 0.00 6.46
497 506 0.393402 AAGGTTTACCCGATTCCGCC 60.393 55.000 0.00 0.00 38.74 6.13
498 507 2.314323 TAAGGTTTACCCGATTCCGC 57.686 50.000 0.00 0.00 38.74 5.54
500 509 6.351711 ACTACAATAAGGTTTACCCGATTCC 58.648 40.000 0.00 0.00 38.74 3.01
501 510 7.654923 CCTACTACAATAAGGTTTACCCGATTC 59.345 40.741 0.00 0.00 38.74 2.52
504 521 5.957774 ACCTACTACAATAAGGTTTACCCGA 59.042 40.000 0.00 0.00 40.82 5.14
506 523 8.311395 ACTACCTACTACAATAAGGTTTACCC 57.689 38.462 0.00 0.00 40.82 3.69
509 526 7.285401 CCCGACTACCTACTACAATAAGGTTTA 59.715 40.741 0.00 0.00 40.82 2.01
510 527 6.097412 CCCGACTACCTACTACAATAAGGTTT 59.903 42.308 0.00 0.00 40.82 3.27
618 666 9.815306 TTAGAGAGATTGTAGTGCCTCTTATAT 57.185 33.333 0.00 0.00 36.25 0.86
621 669 7.956328 TTTAGAGAGATTGTAGTGCCTCTTA 57.044 36.000 0.00 0.00 36.25 2.10
652 702 7.342318 TCTAACGTATTGTTTCTTAGTGCAC 57.658 36.000 9.40 9.40 42.09 4.57
837 895 1.402787 CCCACACACAGCCTCTTTTT 58.597 50.000 0.00 0.00 0.00 1.94
866 924 5.453903 CGAAAACATGAGTAGGGAGATGGAT 60.454 44.000 0.00 0.00 0.00 3.41
869 927 4.759782 ACGAAAACATGAGTAGGGAGATG 58.240 43.478 0.00 0.00 0.00 2.90
934 992 1.617947 GGAGTGGAGACTTGGGCGAT 61.618 60.000 0.00 0.00 30.16 4.58
938 996 1.952621 TTAGGGAGTGGAGACTTGGG 58.047 55.000 0.00 0.00 30.16 4.12
939 997 2.436173 GGATTAGGGAGTGGAGACTTGG 59.564 54.545 0.00 0.00 30.16 3.61
940 998 3.379452 AGGATTAGGGAGTGGAGACTTG 58.621 50.000 0.00 0.00 30.16 3.16
941 999 3.786213 AGGATTAGGGAGTGGAGACTT 57.214 47.619 0.00 0.00 30.16 3.01
942 1000 4.810345 CTTAGGATTAGGGAGTGGAGACT 58.190 47.826 0.00 0.00 33.98 3.24
943 1001 3.322541 GCTTAGGATTAGGGAGTGGAGAC 59.677 52.174 0.00 0.00 0.00 3.36
944 1002 3.052109 TGCTTAGGATTAGGGAGTGGAGA 60.052 47.826 0.00 0.00 0.00 3.71
945 1003 3.309296 TGCTTAGGATTAGGGAGTGGAG 58.691 50.000 0.00 0.00 0.00 3.86
946 1004 3.414759 TGCTTAGGATTAGGGAGTGGA 57.585 47.619 0.00 0.00 0.00 4.02
947 1005 3.711704 TCTTGCTTAGGATTAGGGAGTGG 59.288 47.826 0.00 0.00 0.00 4.00
952 1011 5.745227 TGTTTCTCTTGCTTAGGATTAGGG 58.255 41.667 0.00 0.00 0.00 3.53
1101 1165 1.743252 GGTGAAGGAGCTCTTGCGG 60.743 63.158 14.64 0.00 45.42 5.69
1170 1234 4.690719 ATGGCGGCGTTGACGGAA 62.691 61.111 9.37 0.00 40.23 4.30
1239 1303 3.047877 GGAACGGCCGTGGAGTTG 61.048 66.667 34.95 0.00 0.00 3.16
1695 1759 2.671963 GGGTCGGTTTGGGAGCAC 60.672 66.667 0.00 0.00 33.71 4.40
1914 1978 4.658901 ACCACCTTCTTGAAGTAGGAGAAA 59.341 41.667 22.46 0.00 35.03 2.52
2004 2068 2.753043 GTGAGCATGGCCACCCAG 60.753 66.667 8.16 0.00 46.24 4.45
2172 2236 2.972505 GTGGTCACCGTGGTGCTG 60.973 66.667 14.25 0.00 45.04 4.41
2190 2254 0.308068 CAGCCGTCGACTCGATGTAT 59.692 55.000 14.70 4.84 40.74 2.29
2644 2708 4.142469 ACGAGGAGGAAACAACAAAGTTTG 60.142 41.667 14.13 14.13 41.48 2.93
2645 2709 4.014406 ACGAGGAGGAAACAACAAAGTTT 58.986 39.130 0.00 0.00 43.90 2.66
2647 2711 2.943033 CACGAGGAGGAAACAACAAAGT 59.057 45.455 0.00 0.00 0.00 2.66
2648 2712 2.943033 ACACGAGGAGGAAACAACAAAG 59.057 45.455 0.00 0.00 0.00 2.77
2650 2714 2.169769 AGACACGAGGAGGAAACAACAA 59.830 45.455 0.00 0.00 0.00 2.83
2651 2715 1.760613 AGACACGAGGAGGAAACAACA 59.239 47.619 0.00 0.00 0.00 3.33
2652 2716 2.036089 AGAGACACGAGGAGGAAACAAC 59.964 50.000 0.00 0.00 0.00 3.32
2726 2790 5.105716 CGACCAGTAGTCCTAATCCCATATG 60.106 48.000 0.00 0.00 43.08 1.78
2727 2791 5.017490 CGACCAGTAGTCCTAATCCCATAT 58.983 45.833 0.00 0.00 43.08 1.78
2728 2792 4.141088 ACGACCAGTAGTCCTAATCCCATA 60.141 45.833 0.00 0.00 43.08 2.74
2749 2827 3.128242 CCACTACTACCACAGTTCCTACG 59.872 52.174 0.00 0.00 38.80 3.51
2761 2839 6.943718 ACAGATAGATTAGAGCCACTACTACC 59.056 42.308 0.00 0.00 0.00 3.18
2764 2842 5.242838 GCACAGATAGATTAGAGCCACTACT 59.757 44.000 0.00 0.00 0.00 2.57
2765 2843 5.242838 AGCACAGATAGATTAGAGCCACTAC 59.757 44.000 0.00 0.00 0.00 2.73
2766 2844 5.389520 AGCACAGATAGATTAGAGCCACTA 58.610 41.667 0.00 0.00 0.00 2.74
2767 2845 4.222336 AGCACAGATAGATTAGAGCCACT 58.778 43.478 0.00 0.00 0.00 4.00
2768 2846 4.599047 AGCACAGATAGATTAGAGCCAC 57.401 45.455 0.00 0.00 0.00 5.01
2769 2847 4.202295 CCAAGCACAGATAGATTAGAGCCA 60.202 45.833 0.00 0.00 0.00 4.75
2770 2848 4.039730 TCCAAGCACAGATAGATTAGAGCC 59.960 45.833 0.00 0.00 0.00 4.70
2771 2849 5.207110 TCCAAGCACAGATAGATTAGAGC 57.793 43.478 0.00 0.00 0.00 4.09
2772 2850 7.226325 CCTTTTCCAAGCACAGATAGATTAGAG 59.774 40.741 0.00 0.00 0.00 2.43
2773 2851 7.050377 CCTTTTCCAAGCACAGATAGATTAGA 58.950 38.462 0.00 0.00 0.00 2.10
2774 2852 6.238593 GCCTTTTCCAAGCACAGATAGATTAG 60.239 42.308 0.00 0.00 0.00 1.73
2775 2853 5.590259 GCCTTTTCCAAGCACAGATAGATTA 59.410 40.000 0.00 0.00 0.00 1.75
2776 2854 4.400567 GCCTTTTCCAAGCACAGATAGATT 59.599 41.667 0.00 0.00 0.00 2.40
2777 2855 3.950395 GCCTTTTCCAAGCACAGATAGAT 59.050 43.478 0.00 0.00 0.00 1.98
2778 2856 3.244875 TGCCTTTTCCAAGCACAGATAGA 60.245 43.478 0.00 0.00 0.00 1.98
2779 2857 3.084039 TGCCTTTTCCAAGCACAGATAG 58.916 45.455 0.00 0.00 0.00 2.08
2780 2858 3.084039 CTGCCTTTTCCAAGCACAGATA 58.916 45.455 0.00 0.00 35.88 1.98
2781 2859 1.891150 CTGCCTTTTCCAAGCACAGAT 59.109 47.619 0.00 0.00 35.88 2.90
2782 2860 1.321474 CTGCCTTTTCCAAGCACAGA 58.679 50.000 0.00 0.00 35.88 3.41
2783 2861 0.319297 GCTGCCTTTTCCAAGCACAG 60.319 55.000 0.00 0.00 36.46 3.66
2830 2926 0.536460 ACAAAACATCGCCGGTCCTT 60.536 50.000 1.90 0.00 0.00 3.36
2831 2927 1.072505 ACAAAACATCGCCGGTCCT 59.927 52.632 1.90 0.00 0.00 3.85
2832 2928 1.209127 CACAAAACATCGCCGGTCC 59.791 57.895 1.90 0.00 0.00 4.46
2834 2930 0.869730 GTACACAAAACATCGCCGGT 59.130 50.000 1.90 0.00 0.00 5.28
2835 2931 1.153353 AGTACACAAAACATCGCCGG 58.847 50.000 0.00 0.00 0.00 6.13
2836 2932 2.961522 AAGTACACAAAACATCGCCG 57.038 45.000 0.00 0.00 0.00 6.46
2837 2933 3.972502 GTCAAAGTACACAAAACATCGCC 59.027 43.478 0.00 0.00 0.00 5.54
2839 2935 4.208355 CCGTCAAAGTACACAAAACATCG 58.792 43.478 0.00 0.00 0.00 3.84
2840 2936 3.972502 GCCGTCAAAGTACACAAAACATC 59.027 43.478 0.00 0.00 0.00 3.06
2841 2937 3.243267 GGCCGTCAAAGTACACAAAACAT 60.243 43.478 0.00 0.00 0.00 2.71
2842 2938 2.097791 GGCCGTCAAAGTACACAAAACA 59.902 45.455 0.00 0.00 0.00 2.83
2843 2939 2.097791 TGGCCGTCAAAGTACACAAAAC 59.902 45.455 0.00 0.00 0.00 2.43
2844 2940 2.366533 TGGCCGTCAAAGTACACAAAA 58.633 42.857 0.00 0.00 0.00 2.44
2894 2990 8.230486 CAGAAATCAGAAAATAAACGTGCTAGT 58.770 33.333 0.00 0.00 0.00 2.57
2916 3012 9.739276 AGTACAATTTACTCAAATCCATCAGAA 57.261 29.630 0.00 0.00 33.09 3.02
2917 3013 9.166173 CAGTACAATTTACTCAAATCCATCAGA 57.834 33.333 0.00 0.00 33.09 3.27
2918 3014 8.400947 CCAGTACAATTTACTCAAATCCATCAG 58.599 37.037 0.00 0.00 33.09 2.90
2919 3015 7.148086 GCCAGTACAATTTACTCAAATCCATCA 60.148 37.037 0.00 0.00 33.09 3.07
2920 3016 7.148086 TGCCAGTACAATTTACTCAAATCCATC 60.148 37.037 0.00 0.00 33.09 3.51
2985 3081 1.133294 TGGAGGCCATCATACGTCCTA 60.133 52.381 5.01 0.00 40.65 2.94
2998 3094 3.222603 TCTCAAAGTTCTTTTGGAGGCC 58.777 45.455 0.00 0.00 45.05 5.19
3038 3136 4.683832 GATACTACTGTTGACTGCCGATT 58.316 43.478 0.00 0.00 0.00 3.34
3043 3141 3.777465 TCCGATACTACTGTTGACTGC 57.223 47.619 0.00 0.00 0.00 4.40
3096 3216 6.240894 TGACTTGAGCAGAAAATAACCTCAT 58.759 36.000 0.00 0.00 33.10 2.90
3111 3231 1.599542 ACTTTCACGCTTGACTTGAGC 59.400 47.619 0.00 0.00 36.79 4.26
3140 3269 1.537202 GACGCAAGCACTGAAATCCTT 59.463 47.619 0.00 0.00 45.62 3.36
3141 3270 1.160137 GACGCAAGCACTGAAATCCT 58.840 50.000 0.00 0.00 45.62 3.24
3142 3271 0.179215 CGACGCAAGCACTGAAATCC 60.179 55.000 0.00 0.00 45.62 3.01
3143 3272 0.790866 GCGACGCAAGCACTGAAATC 60.791 55.000 16.42 0.00 45.62 2.17
3144 3273 1.207593 GCGACGCAAGCACTGAAAT 59.792 52.632 16.42 0.00 45.62 2.17
3229 3363 2.655474 CGAACACGCTGACAGTAACTAC 59.345 50.000 3.99 0.00 0.00 2.73
3294 3428 0.037512 TGAACTGAGCTGAGCTGAGC 60.038 55.000 20.79 18.32 43.39 4.26
3295 3429 1.404449 CCTGAACTGAGCTGAGCTGAG 60.404 57.143 19.35 19.35 45.01 3.35
3296 3430 0.607112 CCTGAACTGAGCTGAGCTGA 59.393 55.000 13.71 0.99 39.88 4.26
3297 3431 0.607112 TCCTGAACTGAGCTGAGCTG 59.393 55.000 13.71 0.00 39.88 4.24
3298 3432 0.896923 CTCCTGAACTGAGCTGAGCT 59.103 55.000 6.69 6.69 43.88 4.09
3299 3433 0.894141 TCTCCTGAACTGAGCTGAGC 59.106 55.000 0.00 0.00 0.00 4.26
3300 3434 4.737352 GCTTATCTCCTGAACTGAGCTGAG 60.737 50.000 0.00 0.00 0.00 3.35
3301 3435 3.131933 GCTTATCTCCTGAACTGAGCTGA 59.868 47.826 0.00 0.00 0.00 4.26
3302 3436 3.456280 GCTTATCTCCTGAACTGAGCTG 58.544 50.000 0.00 0.00 0.00 4.24
3310 3444 2.237143 CACCTGTGGCTTATCTCCTGAA 59.763 50.000 0.00 0.00 0.00 3.02
3378 3512 2.340337 CATCGTCAGCATTCAGACACA 58.660 47.619 0.00 0.00 34.48 3.72
3379 3513 1.662629 CCATCGTCAGCATTCAGACAC 59.337 52.381 0.00 0.00 34.48 3.67
3385 3519 1.094073 AGCAGCCATCGTCAGCATTC 61.094 55.000 0.00 0.00 0.00 2.67
3388 3522 1.153568 GTAGCAGCCATCGTCAGCA 60.154 57.895 0.00 0.00 0.00 4.41
3397 3531 1.064003 TTGAGGGAAAGTAGCAGCCA 58.936 50.000 0.00 0.00 0.00 4.75
3418 3552 1.271871 ACGTGGCAGGGAATCAATCAA 60.272 47.619 12.33 0.00 0.00 2.57
3419 3553 0.327924 ACGTGGCAGGGAATCAATCA 59.672 50.000 12.33 0.00 0.00 2.57
3420 3554 2.325583 TACGTGGCAGGGAATCAATC 57.674 50.000 12.33 0.00 0.00 2.67
3423 3557 1.134220 GGATTACGTGGCAGGGAATCA 60.134 52.381 33.88 6.15 0.00 2.57
3461 3595 1.141665 CACGTCCAGATGCGGATGA 59.858 57.895 0.00 0.00 43.72 2.92
3466 3600 2.100631 GGAACCACGTCCAGATGCG 61.101 63.158 0.00 0.00 37.65 4.73
3484 3618 0.186873 ATAGGCCCCATCCAGCTTTG 59.813 55.000 0.00 0.00 0.00 2.77
3525 3659 1.587547 GAATCATTGACTCCCGAGGC 58.412 55.000 0.00 0.00 36.85 4.70
3526 3660 1.539065 CGGAATCATTGACTCCCGAGG 60.539 57.143 8.50 0.00 39.31 4.63
3527 3661 1.409064 TCGGAATCATTGACTCCCGAG 59.591 52.381 16.87 2.59 40.69 4.63
3528 3662 1.409064 CTCGGAATCATTGACTCCCGA 59.591 52.381 18.63 18.63 42.92 5.14
3530 3664 3.543680 TTCTCGGAATCATTGACTCCC 57.456 47.619 8.50 0.42 0.00 4.30
3532 3666 7.319646 AGCTATATTCTCGGAATCATTGACTC 58.680 38.462 2.88 0.00 0.00 3.36
3573 3708 4.404640 ACCTTGAGGATCCGATAATACGA 58.595 43.478 5.98 0.00 38.94 3.43
3574 3709 4.785511 ACCTTGAGGATCCGATAATACG 57.214 45.455 5.98 0.00 38.94 3.06
3589 3724 7.035004 CAGTTTCAGATTTTGTTGAACCTTGA 58.965 34.615 0.00 0.00 33.36 3.02


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

AutoCloner maintained by Alex Coulton.