Multiple sequence alignment - TraesCS1A01G244300

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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 TraesCS1A01G244300 chr1A 100.000 3155 0 0 1 3155 432561254 432558100 0.000000e+00 5827.0
1 TraesCS1A01G244300 chr1D 89.072 2489 151 58 515 2952 335034422 335032004 0.000000e+00 2977.0
2 TraesCS1A01G244300 chr1D 84.317 542 40 20 3 522 335034971 335034453 3.660000e-134 488.0
3 TraesCS1A01G244300 chr1D 88.406 69 5 3 3064 3131 335031893 335031827 2.610000e-11 80.5
4 TraesCS1A01G244300 chr1B 92.179 2084 84 30 491 2539 450454267 450452228 0.000000e+00 2872.0
5 TraesCS1A01G244300 chr1B 86.742 528 39 15 2630 3155 450452075 450451577 2.750000e-155 558.0
6 TraesCS1A01G244300 chr1B 84.926 471 41 11 1 447 450454745 450454281 1.730000e-122 449.0


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 TraesCS1A01G244300 chr1A 432558100 432561254 3154 True 5827.000000 5827 100.000 1 3155 1 chr1A.!!$R1 3154
1 TraesCS1A01G244300 chr1D 335031827 335034971 3144 True 1181.833333 2977 87.265 3 3131 3 chr1D.!!$R1 3128
2 TraesCS1A01G244300 chr1B 450451577 450454745 3168 True 1293.000000 2872 87.949 1 3155 3 chr1B.!!$R1 3154

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
940 1023 0.97504 CACCTCCCACTCCTCTCCTG 60.975 65.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2270 2386 0.535102 AGTCTTGCCCAAAGGACACG 60.535 55.0 0.0 0.0 36.46 4.49 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
20 21 1.495584 GACGCAAGACAAGAACGGCA 61.496 55.000 0.00 0.00 43.62 5.69
51 58 1.880675 GCCAATCTGATCTGCATGGAG 59.119 52.381 20.27 8.12 0.00 3.86
62 69 5.731591 GATCTGCATGGAGATCATCATACA 58.268 41.667 37.87 9.45 45.38 2.29
63 70 5.148651 TCTGCATGGAGATCATCATACAG 57.851 43.478 13.58 16.29 36.56 2.74
64 71 3.671716 TGCATGGAGATCATCATACAGC 58.328 45.455 0.00 0.00 32.92 4.40
167 174 2.262915 CTCTGCACCACCGGAGAC 59.737 66.667 9.46 0.00 40.00 3.36
183 190 3.268330 GGAGACGGAAATGAGGGTAAAC 58.732 50.000 0.00 0.00 0.00 2.01
225 250 4.650972 ACAAGCTTGGGTTTCTATGGTA 57.349 40.909 29.18 0.00 0.00 3.25
245 270 5.242838 TGGTATGTTGAACTGAAATTCACCC 59.757 40.000 0.00 0.00 38.31 4.61
256 281 5.009310 ACTGAAATTCACCCGTTTTAAGACC 59.991 40.000 0.00 0.00 0.00 3.85
257 282 5.134661 TGAAATTCACCCGTTTTAAGACCT 58.865 37.500 0.00 0.00 0.00 3.85
301 328 1.657094 GACCGGTACAGCGTAAACATG 59.343 52.381 7.34 0.00 0.00 3.21
324 355 8.729756 CATGTGAAATGAAACAATACTCTGGTA 58.270 33.333 0.00 0.00 0.00 3.25
325 356 8.094798 TGTGAAATGAAACAATACTCTGGTAC 57.905 34.615 0.00 0.00 0.00 3.34
326 357 7.717436 TGTGAAATGAAACAATACTCTGGTACA 59.283 33.333 0.00 0.00 0.00 2.90
386 417 2.101582 GGCAGGACATAGTAGGAGTGTG 59.898 54.545 0.00 0.00 0.00 3.82
413 444 1.017387 GCCCGAGCAGGTAAAAGATG 58.983 55.000 0.00 0.00 39.53 2.90
430 461 2.766239 TGCACTGCATGATACACCG 58.234 52.632 0.00 0.00 31.71 4.94
444 475 4.327898 TGATACACCGTTTAAATCACGAGC 59.672 41.667 0.00 0.00 40.20 5.03
452 483 5.276395 CCGTTTAAATCACGAGCTATCACTG 60.276 44.000 0.00 0.00 40.20 3.66
454 485 6.470160 GTTTAAATCACGAGCTATCACTGTG 58.530 40.000 0.17 0.17 0.00 3.66
456 487 2.636768 TCACGAGCTATCACTGTGTG 57.363 50.000 7.79 1.25 34.45 3.82
457 488 2.159382 TCACGAGCTATCACTGTGTGA 58.841 47.619 7.79 2.77 46.90 3.58
478 516 2.026905 GCCACCTCAACTTTCAACCCA 61.027 52.381 0.00 0.00 0.00 4.51
479 517 1.681264 CCACCTCAACTTTCAACCCAC 59.319 52.381 0.00 0.00 0.00 4.61
480 518 1.333619 CACCTCAACTTTCAACCCACG 59.666 52.381 0.00 0.00 0.00 4.94
481 519 1.064979 ACCTCAACTTTCAACCCACGT 60.065 47.619 0.00 0.00 0.00 4.49
482 520 2.171027 ACCTCAACTTTCAACCCACGTA 59.829 45.455 0.00 0.00 0.00 3.57
498 536 4.159135 CCCACGTAGTACAGTAGACCAAAT 59.841 45.833 0.38 0.00 41.61 2.32
530 606 7.446769 TGAATGGTACTACACAGAAGCTTTAA 58.553 34.615 0.00 0.00 0.00 1.52
534 610 5.638234 GGTACTACACAGAAGCTTTAACAGG 59.362 44.000 0.00 0.00 0.00 4.00
543 619 6.944862 ACAGAAGCTTTAACAGGATTTCAGAT 59.055 34.615 0.00 0.00 0.00 2.90
552 628 2.098117 CAGGATTTCAGATGAAACGGCC 59.902 50.000 10.04 11.43 45.55 6.13
611 690 2.033492 CCAAACACTGGTCGAAACGTAC 60.033 50.000 0.00 0.00 40.78 3.67
614 693 2.466846 ACACTGGTCGAAACGTACAAG 58.533 47.619 0.00 0.00 0.00 3.16
661 740 1.534595 CAGCTCAGTTTCAGTTCAGCC 59.465 52.381 0.00 0.00 0.00 4.85
685 764 2.256174 CAATCAATCCAGCGTTGCAAG 58.744 47.619 0.00 0.00 0.00 4.01
766 845 2.279186 CGTGACTGACGGTGCACA 60.279 61.111 20.43 0.00 44.85 4.57
767 846 2.585869 CGTGACTGACGGTGCACAC 61.586 63.158 20.43 9.92 44.85 3.82
768 847 1.227263 GTGACTGACGGTGCACACT 60.227 57.895 20.43 1.51 0.00 3.55
769 848 1.227234 TGACTGACGGTGCACACTG 60.227 57.895 20.43 14.63 43.20 3.66
770 849 2.588877 ACTGACGGTGCACACTGC 60.589 61.111 20.43 5.24 45.29 4.40
804 883 3.264947 TCGTCTCAGACACGAGGC 58.735 61.111 5.45 0.00 41.27 4.70
845 924 5.586243 CCCAATCAATCATAAAGTCGTCAGT 59.414 40.000 0.00 0.00 0.00 3.41
873 952 6.910972 CGTAAAAGTTTTCACCTTTCTTCCTC 59.089 38.462 3.60 0.00 31.11 3.71
880 962 3.173965 TCACCTTTCTTCCTCCGATCTT 58.826 45.455 0.00 0.00 0.00 2.40
881 963 3.195825 TCACCTTTCTTCCTCCGATCTTC 59.804 47.826 0.00 0.00 0.00 2.87
882 964 2.502130 ACCTTTCTTCCTCCGATCTTCC 59.498 50.000 0.00 0.00 0.00 3.46
883 965 2.158885 CCTTTCTTCCTCCGATCTTCCC 60.159 54.545 0.00 0.00 0.00 3.97
884 966 2.247699 TTCTTCCTCCGATCTTCCCA 57.752 50.000 0.00 0.00 0.00 4.37
893 975 1.059098 CGATCTTCCCATCCCATCCA 58.941 55.000 0.00 0.00 0.00 3.41
912 994 4.527583 CCTCGCTCTGCTCTGCCC 62.528 72.222 0.00 0.00 0.00 5.36
940 1023 0.975040 CACCTCCCACTCCTCTCCTG 60.975 65.000 0.00 0.00 0.00 3.86
942 1025 2.039624 TCCCACTCCTCTCCTGCC 59.960 66.667 0.00 0.00 0.00 4.85
943 1026 2.040278 CCCACTCCTCTCCTGCCT 59.960 66.667 0.00 0.00 0.00 4.75
946 1029 1.001503 CACTCCTCTCCTGCCTCCT 59.998 63.158 0.00 0.00 0.00 3.69
948 1031 1.457455 CTCCTCTCCTGCCTCCTCC 60.457 68.421 0.00 0.00 0.00 4.30
949 1032 2.445654 CCTCTCCTGCCTCCTCCC 60.446 72.222 0.00 0.00 0.00 4.30
950 1033 2.837291 CTCTCCTGCCTCCTCCCG 60.837 72.222 0.00 0.00 0.00 5.14
973 1062 4.160635 GCCATGAACGAACCCGCG 62.161 66.667 0.00 0.00 39.95 6.46
989 1078 2.505557 CGGCGTAGGACCGTGAAC 60.506 66.667 0.00 0.00 45.70 3.18
990 1079 2.125793 GGCGTAGGACCGTGAACC 60.126 66.667 0.00 0.00 0.00 3.62
1276 1380 3.141488 CCTCCGACTCCACCTCCG 61.141 72.222 0.00 0.00 0.00 4.63
1359 1463 3.073735 CTGCTGCTCCCGGACTCT 61.074 66.667 0.73 0.00 0.00 3.24
1362 1466 4.504916 CTGCTCCCGGACTCTGCG 62.505 72.222 0.73 0.00 0.00 5.18
1425 1529 4.101448 CTCAACCTGCTCCGGGGG 62.101 72.222 1.90 2.58 33.40 5.40
1482 1586 1.153549 CGGCAAGCAGTACCTCTCC 60.154 63.158 0.00 0.00 0.00 3.71
1605 1709 3.686760 GCCAAGAAGGTGAAGCCC 58.313 61.111 0.00 0.00 40.61 5.19
1707 1823 1.333619 TGTTTCAAGAAGCCGTTCAGC 59.666 47.619 0.00 0.00 34.82 4.26
1818 1934 0.317479 ACTCAAACTCGTTCTCCGGG 59.683 55.000 0.00 0.00 44.85 5.73
2073 2189 2.425773 GCGCACTGCAAGAACACG 60.426 61.111 0.30 0.00 45.45 4.49
2256 2372 7.959689 TCCATCCATGTGTTAATTTTTGTTG 57.040 32.000 0.00 0.00 0.00 3.33
2295 2411 3.255888 GTCCTTTGGGCAAGACTTTAAGG 59.744 47.826 0.00 0.00 33.80 2.69
2296 2412 2.029020 CCTTTGGGCAAGACTTTAAGGC 60.029 50.000 0.00 0.00 33.80 4.35
2303 2419 3.687698 GGCAAGACTTTAAGGCGATGTTA 59.312 43.478 8.09 0.00 0.00 2.41
2332 2448 2.836372 AGGGTAGTTCGAAGGGGTAAAG 59.164 50.000 0.00 0.00 0.00 1.85
2348 2467 5.163395 GGGGTAAAGTGAGACTCTAATCCTG 60.163 48.000 3.68 0.00 0.00 3.86
2371 2490 0.034337 TTGGACGTCTTTTCTCCCGG 59.966 55.000 16.46 0.00 0.00 5.73
2411 2530 2.276201 CGTCCTCCAAATATTGCGTCA 58.724 47.619 0.00 0.00 0.00 4.35
2413 2532 3.312421 CGTCCTCCAAATATTGCGTCAAT 59.688 43.478 9.46 9.46 37.80 2.57
2476 2596 7.229506 AGTTGCAGGAAATGTTATAAGATAGGC 59.770 37.037 0.00 0.00 0.00 3.93
2480 2600 7.227156 CAGGAAATGTTATAAGATAGGCTGGT 58.773 38.462 0.00 0.00 0.00 4.00
2498 2618 6.719370 AGGCTGGTTGTATTTCAGTGAAAATA 59.281 34.615 21.57 11.72 35.11 1.40
2528 2648 8.794335 AGAGAGTCTTAATTTGGGTATTTCAC 57.206 34.615 0.00 0.00 0.00 3.18
2549 2707 8.728337 TTCACTGAAAATATCATCTTCTGGAG 57.272 34.615 0.00 0.00 37.44 3.86
2550 2708 7.855375 TCACTGAAAATATCATCTTCTGGAGT 58.145 34.615 0.00 0.00 37.44 3.85
2551 2709 8.981659 TCACTGAAAATATCATCTTCTGGAGTA 58.018 33.333 0.00 0.00 37.44 2.59
2553 2711 8.986991 ACTGAAAATATCATCTTCTGGAGTAGT 58.013 33.333 0.00 0.00 37.44 2.73
2556 2714 9.418045 GAAAATATCATCTTCTGGAGTAGTAGC 57.582 37.037 0.00 0.00 0.00 3.58
2557 2715 8.484214 AAATATCATCTTCTGGAGTAGTAGCA 57.516 34.615 0.00 0.00 0.00 3.49
2558 2716 8.663209 AATATCATCTTCTGGAGTAGTAGCAT 57.337 34.615 0.00 0.00 0.00 3.79
2559 2717 6.992664 ATCATCTTCTGGAGTAGTAGCATT 57.007 37.500 0.00 0.00 0.00 3.56
2561 2719 7.898014 TCATCTTCTGGAGTAGTAGCATTTA 57.102 36.000 0.00 0.00 0.00 1.40
2562 2720 8.484214 TCATCTTCTGGAGTAGTAGCATTTAT 57.516 34.615 0.00 0.00 0.00 1.40
2563 2721 9.588096 TCATCTTCTGGAGTAGTAGCATTTATA 57.412 33.333 0.00 0.00 0.00 0.98
2567 2725 9.429359 CTTCTGGAGTAGTAGCATTTATATTGG 57.571 37.037 0.00 0.00 0.00 3.16
2568 2726 7.386851 TCTGGAGTAGTAGCATTTATATTGGC 58.613 38.462 0.00 0.00 0.00 4.52
2569 2727 7.016170 TCTGGAGTAGTAGCATTTATATTGGCA 59.984 37.037 0.00 0.00 0.00 4.92
2570 2728 7.161404 TGGAGTAGTAGCATTTATATTGGCAG 58.839 38.462 0.00 0.00 0.00 4.85
2571 2729 7.162082 GGAGTAGTAGCATTTATATTGGCAGT 58.838 38.462 0.00 0.00 0.00 4.40
2572 2730 7.118390 GGAGTAGTAGCATTTATATTGGCAGTG 59.882 40.741 0.00 0.00 0.00 3.66
2573 2731 7.735917 AGTAGTAGCATTTATATTGGCAGTGA 58.264 34.615 0.00 0.00 0.00 3.41
2574 2732 8.378565 AGTAGTAGCATTTATATTGGCAGTGAT 58.621 33.333 0.00 0.00 0.00 3.06
2575 2733 9.653287 GTAGTAGCATTTATATTGGCAGTGATA 57.347 33.333 0.00 0.00 0.00 2.15
2577 2735 9.745018 AGTAGCATTTATATTGGCAGTGATATT 57.255 29.630 0.00 0.00 0.00 1.28
2585 2743 9.531942 TTATATTGGCAGTGATATTTTTGCTTG 57.468 29.630 0.00 0.00 36.79 4.01
2586 2744 5.465532 TTGGCAGTGATATTTTTGCTTGA 57.534 34.783 0.00 0.00 36.79 3.02
2587 2745 5.465532 TGGCAGTGATATTTTTGCTTGAA 57.534 34.783 0.00 0.00 36.79 2.69
2588 2746 5.851720 TGGCAGTGATATTTTTGCTTGAAA 58.148 33.333 0.00 0.00 36.79 2.69
2589 2747 5.927689 TGGCAGTGATATTTTTGCTTGAAAG 59.072 36.000 0.00 0.00 36.79 2.62
2590 2748 5.349543 GGCAGTGATATTTTTGCTTGAAAGG 59.650 40.000 0.00 0.00 36.79 3.11
2591 2749 6.158598 GCAGTGATATTTTTGCTTGAAAGGA 58.841 36.000 0.00 0.00 33.88 3.36
2592 2750 6.309737 GCAGTGATATTTTTGCTTGAAAGGAG 59.690 38.462 0.00 0.00 33.88 3.69
2593 2751 6.810182 CAGTGATATTTTTGCTTGAAAGGAGG 59.190 38.462 0.00 0.00 0.00 4.30
2594 2752 6.071165 AGTGATATTTTTGCTTGAAAGGAGGG 60.071 38.462 0.00 0.00 0.00 4.30
2604 2762 1.892474 TGAAAGGAGGGAAATTTGCCG 59.108 47.619 21.45 0.00 44.30 5.69
2650 2866 4.082787 AGTTAAATTTGTGATGGAGGTGCG 60.083 41.667 0.00 0.00 0.00 5.34
2715 2931 5.901276 TCCTTTGTTAACTAGACCGGGATAT 59.099 40.000 6.32 0.00 0.00 1.63
2716 2932 7.068702 TCCTTTGTTAACTAGACCGGGATATA 58.931 38.462 6.32 0.00 0.00 0.86
2729 2945 3.514309 CCGGGATATACTACCCTTCCAAG 59.486 52.174 0.00 0.00 43.57 3.61
2811 3027 7.850492 GTCAAATTTTGTTTTGTAATGCTGTCC 59.150 33.333 8.89 0.00 37.73 4.02
2881 3100 9.599866 CTGTACTTGAGATTTGGTGTATGATTA 57.400 33.333 0.00 0.00 0.00 1.75
2882 3101 9.599866 TGTACTTGAGATTTGGTGTATGATTAG 57.400 33.333 0.00 0.00 0.00 1.73
2883 3102 9.601217 GTACTTGAGATTTGGTGTATGATTAGT 57.399 33.333 0.00 0.00 0.00 2.24
2887 3106 9.599866 TTGAGATTTGGTGTATGATTAGTAGTG 57.400 33.333 0.00 0.00 0.00 2.74
2895 3114 6.816640 GGTGTATGATTAGTAGTGTTGCTTCA 59.183 38.462 0.00 0.00 0.00 3.02
2902 3121 7.913297 TGATTAGTAGTGTTGCTTCACAAAAAC 59.087 33.333 12.64 6.59 40.82 2.43
2912 3131 4.989797 TGCTTCACAAAAACATTGCTATGG 59.010 37.500 12.77 0.00 36.01 2.74
2913 3132 4.990426 GCTTCACAAAAACATTGCTATGGT 59.010 37.500 12.77 2.58 36.01 3.55
2914 3133 5.119125 GCTTCACAAAAACATTGCTATGGTC 59.881 40.000 12.77 0.00 36.01 4.02
2945 3164 4.082026 CCCCTCTTTCCATGTGTTCATTTC 60.082 45.833 0.00 0.00 31.15 2.17
2948 3167 6.154445 CCTCTTTCCATGTGTTCATTTCTTG 58.846 40.000 0.00 0.00 31.15 3.02
2950 3169 7.040478 CCTCTTTCCATGTGTTCATTTCTTGTA 60.040 37.037 0.00 0.00 31.15 2.41
2951 3170 8.231692 TCTTTCCATGTGTTCATTTCTTGTAA 57.768 30.769 0.00 0.00 31.15 2.41
2954 3173 9.829507 TTTCCATGTGTTCATTTCTTGTAAATT 57.170 25.926 0.00 0.00 31.15 1.82
2956 3175 9.829507 TCCATGTGTTCATTTCTTGTAAATTTT 57.170 25.926 0.00 0.00 31.15 1.82
2958 3177 9.782028 CATGTGTTCATTTCTTGTAAATTTTCG 57.218 29.630 0.00 0.00 31.15 3.46
2960 3179 7.489435 TGTGTTCATTTCTTGTAAATTTTCGCA 59.511 29.630 0.00 0.00 0.00 5.10
2961 3180 8.487176 GTGTTCATTTCTTGTAAATTTTCGCAT 58.513 29.630 0.00 0.00 0.00 4.73
2962 3181 8.698854 TGTTCATTTCTTGTAAATTTTCGCATC 58.301 29.630 0.00 0.00 0.00 3.91
2963 3182 8.698854 GTTCATTTCTTGTAAATTTTCGCATCA 58.301 29.630 0.00 0.00 0.00 3.07
2984 3203 8.020819 GCATCATTGCTTACAAAGTTGTACTAA 58.979 33.333 3.38 1.17 45.77 2.24
2988 3207 9.807386 CATTGCTTACAAAGTTGTACTAACTAC 57.193 33.333 3.38 0.00 42.84 2.73
2999 3218 7.270047 AGTTGTACTAACTACAAGCTGACAAA 58.730 34.615 8.39 0.00 44.46 2.83
3001 3220 6.812998 TGTACTAACTACAAGCTGACAAAGT 58.187 36.000 0.00 0.00 31.99 2.66
3002 3221 6.700081 TGTACTAACTACAAGCTGACAAAGTG 59.300 38.462 0.00 0.00 31.99 3.16
3003 3222 5.914033 ACTAACTACAAGCTGACAAAGTGA 58.086 37.500 0.00 0.00 0.00 3.41
3004 3223 5.753921 ACTAACTACAAGCTGACAAAGTGAC 59.246 40.000 0.00 0.00 0.00 3.67
3007 3226 5.126067 ACTACAAGCTGACAAAGTGACAAT 58.874 37.500 0.00 0.00 0.00 2.71
3008 3227 4.297299 ACAAGCTGACAAAGTGACAATG 57.703 40.909 0.00 0.00 0.00 2.82
3009 3228 3.067180 ACAAGCTGACAAAGTGACAATGG 59.933 43.478 0.00 0.00 0.00 3.16
3051 3275 3.871485 AGCACTTTCCATCAGCTCTAAG 58.129 45.455 0.00 0.00 0.00 2.18
3053 3277 2.941720 CACTTTCCATCAGCTCTAAGGC 59.058 50.000 0.00 0.00 0.00 4.35
3054 3278 2.092699 ACTTTCCATCAGCTCTAAGGCC 60.093 50.000 0.00 0.00 0.00 5.19
3055 3279 0.465705 TTCCATCAGCTCTAAGGCCG 59.534 55.000 0.00 0.00 0.00 6.13
3056 3280 1.596477 CCATCAGCTCTAAGGCCGC 60.596 63.158 0.00 0.00 0.00 6.53
3059 3283 4.899239 CAGCTCTAAGGCCGCCCG 62.899 72.222 5.55 0.00 35.76 6.13
3117 3341 1.940613 CATTAGGCCGTTGTAGCTTCC 59.059 52.381 0.00 0.00 0.00 3.46
3127 3351 0.325296 TGTAGCTTCCCGTGGGAGAT 60.325 55.000 7.85 4.28 46.06 2.75
3133 3357 3.087065 CCCGTGGGAGATGGGTTT 58.913 61.111 0.00 0.00 45.31 3.27
3134 3358 1.382629 CCCGTGGGAGATGGGTTTT 59.617 57.895 0.00 0.00 45.31 2.43
3138 3362 0.890683 GTGGGAGATGGGTTTTGCTG 59.109 55.000 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.127533 GATTGGCTCGCCGTTGCT 61.128 61.111 3.14 0.00 39.42 3.91
51 58 1.016130 CCGGCCGCTGTATGATGATC 61.016 60.000 22.85 0.00 0.00 2.92
100 107 0.539438 TGTTGCATGTCCCCTTGACC 60.539 55.000 0.00 0.00 43.78 4.02
167 174 2.093869 TCTCGGTTTACCCTCATTTCCG 60.094 50.000 0.00 0.00 38.16 4.30
225 250 3.888930 ACGGGTGAATTTCAGTTCAACAT 59.111 39.130 0.00 0.00 45.45 2.71
245 270 7.412672 GGCAGTCACTTATAAGGTCTTAAAACG 60.413 40.741 16.73 1.48 0.00 3.60
256 281 5.007385 ACGGTTAGGCAGTCACTTATAAG 57.993 43.478 11.05 11.05 0.00 1.73
257 282 5.410355 AACGGTTAGGCAGTCACTTATAA 57.590 39.130 0.00 0.00 0.00 0.98
301 328 8.094798 TGTACCAGAGTATTGTTTCATTTCAC 57.905 34.615 0.00 0.00 0.00 3.18
324 355 0.032952 TTCTTACGCTGTTCGCCTGT 59.967 50.000 0.00 0.00 43.23 4.00
325 356 1.359848 ATTCTTACGCTGTTCGCCTG 58.640 50.000 0.00 0.00 43.23 4.85
326 357 2.094390 TGTATTCTTACGCTGTTCGCCT 60.094 45.455 0.00 0.00 43.23 5.52
327 358 2.264813 TGTATTCTTACGCTGTTCGCC 58.735 47.619 0.00 0.00 43.23 5.54
328 359 3.367025 AGTTGTATTCTTACGCTGTTCGC 59.633 43.478 0.00 0.00 43.23 4.70
329 360 5.511088 AAGTTGTATTCTTACGCTGTTCG 57.489 39.130 0.00 0.00 45.38 3.95
330 361 9.821662 ATTTAAAGTTGTATTCTTACGCTGTTC 57.178 29.630 0.00 0.00 0.00 3.18
341 372 8.188799 GCCCTACAGGAATTTAAAGTTGTATTC 58.811 37.037 0.00 0.00 38.24 1.75
342 373 7.672239 TGCCCTACAGGAATTTAAAGTTGTATT 59.328 33.333 0.00 0.00 38.24 1.89
395 426 1.017387 GCATCTTTTACCTGCTCGGG 58.983 55.000 0.00 0.00 36.97 5.14
398 429 2.159462 GCAGTGCATCTTTTACCTGCTC 60.159 50.000 11.09 0.00 36.84 4.26
413 444 1.086696 AACGGTGTATCATGCAGTGC 58.913 50.000 8.58 8.58 0.00 4.40
430 461 6.090898 ACACAGTGATAGCTCGTGATTTAAAC 59.909 38.462 7.81 0.00 0.00 2.01
454 485 1.967319 TGAAAGTTGAGGTGGCTCAC 58.033 50.000 0.00 0.00 32.47 3.51
456 487 1.609072 GGTTGAAAGTTGAGGTGGCTC 59.391 52.381 0.00 0.00 0.00 4.70
457 488 1.692411 GGTTGAAAGTTGAGGTGGCT 58.308 50.000 0.00 0.00 0.00 4.75
468 506 3.986277 ACTGTACTACGTGGGTTGAAAG 58.014 45.455 3.26 0.00 0.00 2.62
478 516 8.742777 TGATTAATTTGGTCTACTGTACTACGT 58.257 33.333 0.00 0.00 0.00 3.57
479 517 9.745880 ATGATTAATTTGGTCTACTGTACTACG 57.254 33.333 0.00 0.00 0.00 3.51
498 536 9.599866 CTTCTGTGTAGTACCATTCATGATTAA 57.400 33.333 0.00 0.00 0.00 1.40
507 545 7.221450 TGTTAAAGCTTCTGTGTAGTACCATT 58.779 34.615 0.00 0.00 0.00 3.16
530 606 2.749621 GCCGTTTCATCTGAAATCCTGT 59.250 45.455 8.48 0.00 44.69 4.00
534 610 2.091541 TGGGCCGTTTCATCTGAAATC 58.908 47.619 8.48 2.92 44.69 2.17
543 619 0.470766 ACTGTAACTGGGCCGTTTCA 59.529 50.000 16.61 15.96 0.00 2.69
552 628 5.152623 TCTCAAATCCTCACTGTAACTGG 57.847 43.478 0.00 0.00 0.00 4.00
611 690 3.565482 TGAAACTCTGGCAGTAAAGCTTG 59.435 43.478 15.27 0.00 32.30 4.01
614 693 2.095516 GCTGAAACTCTGGCAGTAAAGC 60.096 50.000 15.27 11.98 32.30 3.51
661 740 0.729116 AACGCTGGATTGATTGCTCG 59.271 50.000 0.00 0.00 0.00 5.03
765 844 4.701765 AGAAAGATGCCTACTATGCAGTG 58.298 43.478 0.00 0.00 42.92 3.66
766 845 4.500545 CGAGAAAGATGCCTACTATGCAGT 60.501 45.833 0.00 0.00 42.92 4.40
767 846 3.986572 CGAGAAAGATGCCTACTATGCAG 59.013 47.826 0.00 0.00 42.92 4.41
768 847 3.384789 ACGAGAAAGATGCCTACTATGCA 59.615 43.478 0.00 0.00 43.97 3.96
769 848 3.983741 ACGAGAAAGATGCCTACTATGC 58.016 45.455 0.00 0.00 0.00 3.14
770 849 5.009110 TGAGACGAGAAAGATGCCTACTATG 59.991 44.000 0.00 0.00 0.00 2.23
771 850 5.133941 TGAGACGAGAAAGATGCCTACTAT 58.866 41.667 0.00 0.00 0.00 2.12
772 851 4.524053 TGAGACGAGAAAGATGCCTACTA 58.476 43.478 0.00 0.00 0.00 1.82
773 852 3.357203 TGAGACGAGAAAGATGCCTACT 58.643 45.455 0.00 0.00 0.00 2.57
774 853 3.378742 TCTGAGACGAGAAAGATGCCTAC 59.621 47.826 0.00 0.00 0.00 3.18
823 902 7.514280 CGAGACTGACGACTTTATGATTGATTG 60.514 40.741 0.00 0.00 0.00 2.67
824 903 6.473778 CGAGACTGACGACTTTATGATTGATT 59.526 38.462 0.00 0.00 0.00 2.57
825 904 5.974158 CGAGACTGACGACTTTATGATTGAT 59.026 40.000 0.00 0.00 0.00 2.57
826 905 5.106277 ACGAGACTGACGACTTTATGATTGA 60.106 40.000 0.00 0.00 34.70 2.57
845 924 7.201670 GGAAGAAAGGTGAAAACTTTTACGAGA 60.202 37.037 0.00 0.00 38.21 4.04
873 952 0.326264 GGATGGGATGGGAAGATCGG 59.674 60.000 0.00 0.00 0.00 4.18
880 962 1.344953 CGAGGTTGGATGGGATGGGA 61.345 60.000 0.00 0.00 0.00 4.37
881 963 1.149174 CGAGGTTGGATGGGATGGG 59.851 63.158 0.00 0.00 0.00 4.00
882 964 1.526917 GCGAGGTTGGATGGGATGG 60.527 63.158 0.00 0.00 0.00 3.51
883 965 0.533755 GAGCGAGGTTGGATGGGATG 60.534 60.000 0.00 0.00 0.00 3.51
884 966 0.692419 AGAGCGAGGTTGGATGGGAT 60.692 55.000 0.00 0.00 0.00 3.85
893 975 2.264166 GCAGAGCAGAGCGAGGTT 59.736 61.111 0.00 0.00 0.00 3.50
954 1037 3.496131 CGGGTTCGTTCATGGCGG 61.496 66.667 9.90 0.00 0.00 6.13
973 1062 2.125793 GGTTCACGGTCCTACGCC 60.126 66.667 0.00 0.00 37.37 5.68
982 1071 0.887387 ATGGTTGGTTCGGTTCACGG 60.887 55.000 0.00 0.00 44.45 4.94
983 1072 0.237235 CATGGTTGGTTCGGTTCACG 59.763 55.000 0.00 0.00 46.11 4.35
985 1074 0.538516 CCCATGGTTGGTTCGGTTCA 60.539 55.000 11.73 0.00 41.91 3.18
986 1075 1.873270 GCCCATGGTTGGTTCGGTTC 61.873 60.000 11.73 0.00 41.91 3.62
987 1076 1.906333 GCCCATGGTTGGTTCGGTT 60.906 57.895 11.73 0.00 41.91 4.44
988 1077 2.282887 GCCCATGGTTGGTTCGGT 60.283 61.111 11.73 0.00 41.91 4.69
989 1078 3.068064 GGCCCATGGTTGGTTCGG 61.068 66.667 11.73 0.00 41.91 4.30
990 1079 3.439540 CGGCCCATGGTTGGTTCG 61.440 66.667 11.73 1.38 41.91 3.95
1161 1265 1.028868 GCAGCTGGCCCTTGTAGAAG 61.029 60.000 17.12 0.00 36.11 2.85
1276 1380 4.475135 GCGGGAGGAGTTGGAGGC 62.475 72.222 0.00 0.00 0.00 4.70
1344 1448 4.828925 GCAGAGTCCGGGAGCAGC 62.829 72.222 0.00 0.00 0.00 5.25
1605 1709 0.173708 GGGACAGCTTCTCGTACAGG 59.826 60.000 0.00 0.00 0.00 4.00
1684 1800 2.354510 TGAACGGCTTCTTGAAACACTG 59.645 45.455 0.00 0.00 0.00 3.66
1685 1801 2.614057 CTGAACGGCTTCTTGAAACACT 59.386 45.455 0.00 0.00 0.00 3.55
1686 1802 2.854805 GCTGAACGGCTTCTTGAAACAC 60.855 50.000 0.00 0.00 0.00 3.32
1707 1823 1.846541 GCTTCTTCCGGATCGAGAAG 58.153 55.000 28.74 28.74 45.72 2.85
2178 2294 1.516386 ACGAATCCTAGTGCGTGCG 60.516 57.895 0.00 0.00 35.44 5.34
2256 2372 5.874895 AAGGACACGAAGCTAATTAAACC 57.125 39.130 0.00 0.00 0.00 3.27
2270 2386 0.535102 AGTCTTGCCCAAAGGACACG 60.535 55.000 0.00 0.00 36.46 4.49
2295 2411 7.096312 CGAACTACCCTTATTTACTAACATCGC 60.096 40.741 0.00 0.00 0.00 4.58
2296 2412 8.131100 TCGAACTACCCTTATTTACTAACATCG 58.869 37.037 0.00 0.00 0.00 3.84
2303 2419 5.129980 CCCCTTCGAACTACCCTTATTTACT 59.870 44.000 0.00 0.00 0.00 2.24
2332 2448 4.187694 CAAAGGCAGGATTAGAGTCTCAC 58.812 47.826 0.00 0.00 0.00 3.51
2348 2467 1.535896 GGAGAAAAGACGTCCAAAGGC 59.464 52.381 13.01 0.00 0.00 4.35
2371 2490 2.253603 GCCGATGCAAATTTCACACTC 58.746 47.619 0.00 0.00 37.47 3.51
2411 2530 5.430007 TGGGTTTGACGTATTCGGATTATT 58.570 37.500 0.00 0.00 41.85 1.40
2413 2532 4.468765 TGGGTTTGACGTATTCGGATTA 57.531 40.909 0.00 0.00 41.85 1.75
2549 2707 7.962964 TCACTGCCAATATAAATGCTACTAC 57.037 36.000 0.00 0.00 0.00 2.73
2551 2709 9.745018 AATATCACTGCCAATATAAATGCTACT 57.255 29.630 0.00 0.00 0.00 2.57
2559 2717 9.531942 CAAGCAAAAATATCACTGCCAATATAA 57.468 29.630 0.00 0.00 35.33 0.98
2561 2719 7.784037 TCAAGCAAAAATATCACTGCCAATAT 58.216 30.769 0.00 0.00 35.33 1.28
2562 2720 7.167924 TCAAGCAAAAATATCACTGCCAATA 57.832 32.000 0.00 0.00 35.33 1.90
2563 2721 6.040209 TCAAGCAAAAATATCACTGCCAAT 57.960 33.333 0.00 0.00 35.33 3.16
2564 2722 5.465532 TCAAGCAAAAATATCACTGCCAA 57.534 34.783 0.00 0.00 35.33 4.52
2565 2723 5.465532 TTCAAGCAAAAATATCACTGCCA 57.534 34.783 0.00 0.00 35.33 4.92
2566 2724 5.349543 CCTTTCAAGCAAAAATATCACTGCC 59.650 40.000 0.00 0.00 35.33 4.85
2567 2725 6.158598 TCCTTTCAAGCAAAAATATCACTGC 58.841 36.000 0.00 0.00 34.96 4.40
2568 2726 6.810182 CCTCCTTTCAAGCAAAAATATCACTG 59.190 38.462 0.00 0.00 0.00 3.66
2569 2727 6.071165 CCCTCCTTTCAAGCAAAAATATCACT 60.071 38.462 0.00 0.00 0.00 3.41
2570 2728 6.071391 TCCCTCCTTTCAAGCAAAAATATCAC 60.071 38.462 0.00 0.00 0.00 3.06
2571 2729 6.015918 TCCCTCCTTTCAAGCAAAAATATCA 58.984 36.000 0.00 0.00 0.00 2.15
2572 2730 6.530019 TCCCTCCTTTCAAGCAAAAATATC 57.470 37.500 0.00 0.00 0.00 1.63
2573 2731 6.933514 TTCCCTCCTTTCAAGCAAAAATAT 57.066 33.333 0.00 0.00 0.00 1.28
2574 2732 6.739331 TTTCCCTCCTTTCAAGCAAAAATA 57.261 33.333 0.00 0.00 0.00 1.40
2575 2733 5.628797 TTTCCCTCCTTTCAAGCAAAAAT 57.371 34.783 0.00 0.00 0.00 1.82
2576 2734 5.628797 ATTTCCCTCCTTTCAAGCAAAAA 57.371 34.783 0.00 0.00 0.00 1.94
2577 2735 5.628797 AATTTCCCTCCTTTCAAGCAAAA 57.371 34.783 0.00 0.00 0.00 2.44
2578 2736 5.367302 CAAATTTCCCTCCTTTCAAGCAAA 58.633 37.500 0.00 0.00 0.00 3.68
2579 2737 4.743348 GCAAATTTCCCTCCTTTCAAGCAA 60.743 41.667 0.00 0.00 0.00 3.91
2580 2738 3.244181 GCAAATTTCCCTCCTTTCAAGCA 60.244 43.478 0.00 0.00 0.00 3.91
2581 2739 3.329386 GCAAATTTCCCTCCTTTCAAGC 58.671 45.455 0.00 0.00 0.00 4.01
2582 2740 3.614870 CGGCAAATTTCCCTCCTTTCAAG 60.615 47.826 0.00 0.00 0.00 3.02
2583 2741 2.298729 CGGCAAATTTCCCTCCTTTCAA 59.701 45.455 0.00 0.00 0.00 2.69
2584 2742 1.892474 CGGCAAATTTCCCTCCTTTCA 59.108 47.619 0.00 0.00 0.00 2.69
2585 2743 2.167662 TCGGCAAATTTCCCTCCTTTC 58.832 47.619 0.00 0.00 0.00 2.62
2586 2744 2.302587 TCGGCAAATTTCCCTCCTTT 57.697 45.000 0.00 0.00 0.00 3.11
2587 2745 2.302587 TTCGGCAAATTTCCCTCCTT 57.697 45.000 0.00 0.00 0.00 3.36
2588 2746 2.102578 CATTCGGCAAATTTCCCTCCT 58.897 47.619 0.00 0.00 0.00 3.69
2589 2747 2.099405 TCATTCGGCAAATTTCCCTCC 58.901 47.619 0.00 0.00 0.00 4.30
2590 2748 3.866883 TTCATTCGGCAAATTTCCCTC 57.133 42.857 0.00 0.00 0.00 4.30
2591 2749 4.383010 GGATTTCATTCGGCAAATTTCCCT 60.383 41.667 0.00 0.00 0.00 4.20
2592 2750 3.871006 GGATTTCATTCGGCAAATTTCCC 59.129 43.478 0.00 0.00 0.00 3.97
2593 2751 4.502962 TGGATTTCATTCGGCAAATTTCC 58.497 39.130 0.00 0.00 0.00 3.13
2594 2752 7.202526 TCTATGGATTTCATTCGGCAAATTTC 58.797 34.615 0.00 0.00 37.30 2.17
2623 2781 7.605449 CACCTCCATCACAAATTTAACTTCAT 58.395 34.615 0.00 0.00 0.00 2.57
2624 2782 6.516527 GCACCTCCATCACAAATTTAACTTCA 60.517 38.462 0.00 0.00 0.00 3.02
2650 2866 2.555757 GGAGCATGAGGTATTTGCATCC 59.444 50.000 0.00 0.00 38.84 3.51
2715 2931 5.917545 ACCTTTTTCTTGGAAGGGTAGTA 57.082 39.130 7.03 0.00 45.35 1.82
2716 2932 4.808767 ACCTTTTTCTTGGAAGGGTAGT 57.191 40.909 7.03 0.00 45.35 2.73
2729 2945 6.455647 CAAAATCCCACTCCTAACCTTTTTC 58.544 40.000 0.00 0.00 0.00 2.29
2811 3027 3.997021 AGCTGAATAAACACTTGTCTCGG 59.003 43.478 0.00 0.00 0.00 4.63
2881 3100 5.637006 TGTTTTTGTGAAGCAACACTACT 57.363 34.783 12.91 0.00 40.87 2.57
2882 3101 6.695245 CAATGTTTTTGTGAAGCAACACTAC 58.305 36.000 12.91 7.63 40.87 2.73
2883 3102 5.290643 GCAATGTTTTTGTGAAGCAACACTA 59.709 36.000 12.91 4.56 40.87 2.74
2887 3106 4.863152 AGCAATGTTTTTGTGAAGCAAC 57.137 36.364 0.00 0.00 36.72 4.17
2895 3114 6.581712 ACAAAGACCATAGCAATGTTTTTGT 58.418 32.000 9.78 9.78 35.92 2.83
2902 3121 3.131046 GGGGAACAAAGACCATAGCAATG 59.869 47.826 0.00 0.00 0.00 2.82
2912 3131 2.158519 TGGAAAGAGGGGGAACAAAGAC 60.159 50.000 0.00 0.00 0.00 3.01
2913 3132 2.140224 TGGAAAGAGGGGGAACAAAGA 58.860 47.619 0.00 0.00 0.00 2.52
2914 3133 2.675658 TGGAAAGAGGGGGAACAAAG 57.324 50.000 0.00 0.00 0.00 2.77
2958 3177 6.381801 AGTACAACTTTGTAAGCAATGATGC 58.618 36.000 3.38 0.00 46.34 3.91
2960 3179 9.284968 AGTTAGTACAACTTTGTAAGCAATGAT 57.715 29.630 3.38 0.00 44.46 2.45
2961 3180 8.671384 AGTTAGTACAACTTTGTAAGCAATGA 57.329 30.769 3.38 0.00 44.46 2.57
2962 3181 9.807386 GTAGTTAGTACAACTTTGTAAGCAATG 57.193 33.333 13.48 0.00 44.46 2.82
2963 3182 9.550406 TGTAGTTAGTACAACTTTGTAAGCAAT 57.450 29.630 13.48 0.00 44.46 3.56
2970 3189 7.224167 GTCAGCTTGTAGTTAGTACAACTTTGT 59.776 37.037 8.41 0.00 45.07 2.83
2971 3190 7.223971 TGTCAGCTTGTAGTTAGTACAACTTTG 59.776 37.037 8.41 7.56 45.07 2.77
2978 3197 6.921857 TCACTTTGTCAGCTTGTAGTTAGTAC 59.078 38.462 0.00 0.00 0.00 2.73
2984 3203 4.137116 TGTCACTTTGTCAGCTTGTAGT 57.863 40.909 0.00 0.00 0.00 2.73
2988 3207 3.551454 CCCATTGTCACTTTGTCAGCTTG 60.551 47.826 0.00 0.00 0.00 4.01
2999 3218 0.114954 ACCAATGGCCCATTGTCACT 59.885 50.000 29.61 10.61 46.69 3.41
3001 3220 2.612285 TTACCAATGGCCCATTGTCA 57.388 45.000 29.61 16.97 46.69 3.58
3002 3221 3.030291 TCATTACCAATGGCCCATTGTC 58.970 45.455 29.61 0.00 46.69 3.18
3003 3222 3.113191 TCATTACCAATGGCCCATTGT 57.887 42.857 29.61 21.00 46.69 2.71
3007 3226 3.395054 TGATTCATTACCAATGGCCCA 57.605 42.857 0.00 0.00 39.38 5.36
3008 3227 5.567423 GCTTATGATTCATTACCAATGGCCC 60.567 44.000 4.14 0.00 39.38 5.80
3009 3228 5.010922 TGCTTATGATTCATTACCAATGGCC 59.989 40.000 4.14 0.00 39.38 5.36
3016 3235 7.333528 TGGAAAGTGCTTATGATTCATTACC 57.666 36.000 4.14 0.00 0.00 2.85
3022 3241 5.298777 AGCTGATGGAAAGTGCTTATGATTC 59.701 40.000 0.00 0.00 0.00 2.52
3051 3275 3.583086 GCTTCATTACGGGCGGCC 61.583 66.667 20.04 20.04 0.00 6.13
3053 3277 1.024579 AGTTGCTTCATTACGGGCGG 61.025 55.000 0.00 0.00 0.00 6.13
3054 3278 1.593006 CTAGTTGCTTCATTACGGGCG 59.407 52.381 0.00 0.00 0.00 6.13
3055 3279 2.629051 ACTAGTTGCTTCATTACGGGC 58.371 47.619 0.00 0.00 0.00 6.13
3056 3280 8.428186 TTTAATACTAGTTGCTTCATTACGGG 57.572 34.615 0.00 0.00 0.00 5.28
3083 3307 2.356741 GCCTAATGTAGGGTTGCCAAGA 60.357 50.000 3.56 0.00 46.32 3.02
3117 3341 1.595093 GCAAAACCCATCTCCCACGG 61.595 60.000 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.