Multiple sequence alignment - TraesCS1D01G218800

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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 TraesCS1D01G218800 chr1D 100.000 3346 0 0 1 3346 305770706 305767361 0.000000e+00 6180
1 TraesCS1D01G218800 chr1A 92.447 1827 79 24 797 2606 384776382 384774598 0.000000e+00 2555
2 TraesCS1D01G218800 chr1A 90.640 812 32 12 9 789 384778717 384777919 0.000000e+00 1038
3 TraesCS1D01G218800 chr1A 90.330 424 23 3 2632 3038 384774527 384774105 1.060000e-149 540
4 TraesCS1D01G218800 chr1A 94.141 256 14 1 3092 3346 384774023 384773768 4.050000e-104 388
5 TraesCS1D01G218800 chr1B 93.204 1133 47 11 1495 2606 413205364 413204241 0.000000e+00 1639
6 TraesCS1D01G218800 chr1B 96.950 459 11 2 981 1436 413205833 413205375 0.000000e+00 767
7 TraesCS1D01G218800 chr1B 91.376 487 14 9 368 854 413206652 413206194 2.810000e-180 641
8 TraesCS1D01G218800 chr1B 91.368 475 30 5 2632 3096 413204169 413203696 1.010000e-179 640
9 TraesCS1D01G218800 chr1B 94.086 372 12 3 6 373 413207313 413206948 1.050000e-154 556
10 TraesCS1D01G218800 chr1B 96.835 158 5 0 3189 3346 413203607 413203450 7.120000e-67 265
11 TraesCS1D01G218800 chr6B 85.976 164 21 2 2037 2199 509259632 509259794 1.230000e-39 174
12 TraesCS1D01G218800 chr6D 86.164 159 20 2 2042 2199 315817043 315816886 1.600000e-38 171
13 TraesCS1D01G218800 chr2D 83.140 172 27 2 2042 2212 496637761 496637591 4.470000e-34 156


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 TraesCS1D01G218800 chr1D 305767361 305770706 3345 True 6180.000000 6180 100.000000 1 3346 1 chr1D.!!$R1 3345
1 TraesCS1D01G218800 chr1A 384773768 384778717 4949 True 1130.250000 2555 91.889500 9 3346 4 chr1A.!!$R1 3337
2 TraesCS1D01G218800 chr1B 413203450 413207313 3863 True 751.333333 1639 93.969833 6 3346 6 chr1B.!!$R1 3340

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
960 2820 0.038166 CCAAGACCCCAAGCAAGCTA 59.962 55.0 0.0 0.0 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2626 4749 0.032017 ATAGTTCGCTCCAGAGGGGT 60.032 55.0 11.35 0.86 41.19 4.95 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
103 106 5.819379 TCATTCATGTTCCAGAATACAGAGC 59.181 40.000 0.00 0.00 33.41 4.09
196 203 8.763049 TCACACTGTAAGAATCAATGAACTAG 57.237 34.615 0.00 0.00 37.43 2.57
197 204 8.585018 TCACACTGTAAGAATCAATGAACTAGA 58.415 33.333 0.00 0.00 37.43 2.43
198 205 8.867935 CACACTGTAAGAATCAATGAACTAGAG 58.132 37.037 0.00 0.00 37.43 2.43
465 778 0.785979 CCGCGCACGTAGTTTAACTT 59.214 50.000 8.75 0.00 41.61 2.66
466 779 1.192980 CCGCGCACGTAGTTTAACTTT 59.807 47.619 8.75 0.00 41.61 2.66
467 780 2.408032 CCGCGCACGTAGTTTAACTTTA 59.592 45.455 8.75 0.00 41.61 1.85
468 781 3.121058 CCGCGCACGTAGTTTAACTTTAA 60.121 43.478 8.75 0.00 41.61 1.52
469 782 3.829254 CGCGCACGTAGTTTAACTTTAAC 59.171 43.478 8.75 0.00 41.61 2.01
470 783 4.375305 CGCGCACGTAGTTTAACTTTAACT 60.375 41.667 8.75 0.00 41.61 2.24
556 873 0.528684 GATCTCGGCAGAGTTTCGGG 60.529 60.000 13.75 0.00 44.65 5.14
659 980 0.668096 GTGACACGTACGCCATCCAA 60.668 55.000 16.72 0.00 0.00 3.53
661 982 0.441145 GACACGTACGCCATCCAAAC 59.559 55.000 16.72 0.00 0.00 2.93
789 1110 3.626217 CAGAGCAGCAAGATATCAAAGCA 59.374 43.478 5.32 0.00 0.00 3.91
790 1111 4.095932 CAGAGCAGCAAGATATCAAAGCAA 59.904 41.667 5.32 0.00 0.00 3.91
791 1112 4.703575 AGAGCAGCAAGATATCAAAGCAAA 59.296 37.500 5.32 0.00 0.00 3.68
792 1113 4.995124 AGCAGCAAGATATCAAAGCAAAG 58.005 39.130 5.32 2.15 0.00 2.77
793 1114 3.550678 GCAGCAAGATATCAAAGCAAAGC 59.449 43.478 5.32 7.66 0.00 3.51
816 2671 0.107654 CTCCCACCCACGAATTCCTC 60.108 60.000 0.00 0.00 0.00 3.71
817 2672 1.077716 CCCACCCACGAATTCCTCC 60.078 63.158 0.00 0.00 0.00 4.30
818 2673 1.562672 CCCACCCACGAATTCCTCCT 61.563 60.000 0.00 0.00 0.00 3.69
870 2725 4.029142 TCCCTCCAACCCTTTATATCCA 57.971 45.455 0.00 0.00 0.00 3.41
886 2741 2.854032 CACCACCACCTCCCACCT 60.854 66.667 0.00 0.00 0.00 4.00
891 2746 2.203998 CCACCTCCCACCTCACCT 60.204 66.667 0.00 0.00 0.00 4.00
914 2774 3.506312 CTCGCTCGCGCTCTCTCTC 62.506 68.421 5.56 0.00 39.59 3.20
915 2775 3.572539 CGCTCGCGCTCTCTCTCT 61.573 66.667 5.56 0.00 0.00 3.10
916 2776 2.327940 GCTCGCGCTCTCTCTCTC 59.672 66.667 5.56 0.00 0.00 3.20
917 2777 3.022287 CTCGCGCTCTCTCTCTCC 58.978 66.667 5.56 0.00 0.00 3.71
928 2788 2.243736 TCTCTCTCTCCCTCTCTTTCCC 59.756 54.545 0.00 0.00 0.00 3.97
931 2791 1.064314 TCTCTCCCTCTCTTTCCCTCG 60.064 57.143 0.00 0.00 0.00 4.63
946 2806 2.283894 TCGCCTCCAGCTCCAAGA 60.284 61.111 0.00 0.00 40.39 3.02
947 2807 2.125350 CGCCTCCAGCTCCAAGAC 60.125 66.667 0.00 0.00 40.39 3.01
948 2808 2.270527 GCCTCCAGCTCCAAGACC 59.729 66.667 0.00 0.00 38.99 3.85
949 2809 2.993853 CCTCCAGCTCCAAGACCC 59.006 66.667 0.00 0.00 0.00 4.46
951 2811 1.920325 CTCCAGCTCCAAGACCCCA 60.920 63.158 0.00 0.00 0.00 4.96
953 2813 1.001641 CCAGCTCCAAGACCCCAAG 60.002 63.158 0.00 0.00 0.00 3.61
954 2814 1.676967 CAGCTCCAAGACCCCAAGC 60.677 63.158 0.00 0.00 0.00 4.01
956 2816 1.228552 GCTCCAAGACCCCAAGCAA 60.229 57.895 0.00 0.00 33.21 3.91
957 2817 1.246737 GCTCCAAGACCCCAAGCAAG 61.247 60.000 0.00 0.00 33.21 4.01
958 2818 1.228552 TCCAAGACCCCAAGCAAGC 60.229 57.895 0.00 0.00 0.00 4.01
959 2819 1.228675 CCAAGACCCCAAGCAAGCT 60.229 57.895 0.00 0.00 0.00 3.74
960 2820 0.038166 CCAAGACCCCAAGCAAGCTA 59.962 55.000 0.00 0.00 0.00 3.32
961 2821 1.457346 CAAGACCCCAAGCAAGCTAG 58.543 55.000 0.00 0.00 0.00 3.42
962 2822 1.003580 CAAGACCCCAAGCAAGCTAGA 59.996 52.381 0.00 0.00 0.00 2.43
963 2823 0.908198 AGACCCCAAGCAAGCTAGAG 59.092 55.000 0.00 0.00 0.00 2.43
964 2824 0.746204 GACCCCAAGCAAGCTAGAGC 60.746 60.000 0.00 0.00 42.49 4.09
975 2835 2.424474 GCTAGAGCTAGAGCAGGCA 58.576 57.895 13.22 0.00 45.16 4.75
976 2836 0.749649 GCTAGAGCTAGAGCAGGCAA 59.250 55.000 13.22 0.00 45.16 4.52
977 2837 1.269726 GCTAGAGCTAGAGCAGGCAAG 60.270 57.143 13.22 0.00 45.16 4.01
978 2838 1.340889 CTAGAGCTAGAGCAGGCAAGG 59.659 57.143 4.01 0.00 45.16 3.61
979 2839 0.325110 AGAGCTAGAGCAGGCAAGGA 60.325 55.000 4.01 0.00 45.16 3.36
1138 3227 4.385405 ACGTGGAGGAGCAGCAGC 62.385 66.667 0.00 0.00 42.56 5.25
1143 3232 2.187424 GAGGAGCAGCAGCAGGAG 59.813 66.667 3.17 0.00 45.49 3.69
1149 3238 2.901813 CAGCAGCAGGAGGAGGAG 59.098 66.667 0.00 0.00 0.00 3.69
1440 3532 2.797087 CGACATGTACGTATCCACACCC 60.797 54.545 0.00 0.00 0.00 4.61
1441 3533 2.166870 GACATGTACGTATCCACACCCA 59.833 50.000 0.00 0.00 0.00 4.51
1442 3534 2.769663 ACATGTACGTATCCACACCCAT 59.230 45.455 0.00 0.00 0.00 4.00
1444 3536 2.458620 TGTACGTATCCACACCCATCA 58.541 47.619 0.00 0.00 0.00 3.07
1445 3537 3.035363 TGTACGTATCCACACCCATCAT 58.965 45.455 0.00 0.00 0.00 2.45
1447 3539 1.416401 ACGTATCCACACCCATCATCC 59.584 52.381 0.00 0.00 0.00 3.51
1448 3540 1.416030 CGTATCCACACCCATCATCCA 59.584 52.381 0.00 0.00 0.00 3.41
1449 3541 2.806745 CGTATCCACACCCATCATCCAC 60.807 54.545 0.00 0.00 0.00 4.02
1450 3542 0.552848 ATCCACACCCATCATCCACC 59.447 55.000 0.00 0.00 0.00 4.61
1451 3543 0.549902 TCCACACCCATCATCCACCT 60.550 55.000 0.00 0.00 0.00 4.00
1452 3544 1.212375 CCACACCCATCATCCACCTA 58.788 55.000 0.00 0.00 0.00 3.08
1453 3545 1.776667 CCACACCCATCATCCACCTAT 59.223 52.381 0.00 0.00 0.00 2.57
1454 3546 2.224621 CCACACCCATCATCCACCTATC 60.225 54.545 0.00 0.00 0.00 2.08
1455 3547 2.057922 ACACCCATCATCCACCTATCC 58.942 52.381 0.00 0.00 0.00 2.59
1456 3548 2.057140 CACCCATCATCCACCTATCCA 58.943 52.381 0.00 0.00 0.00 3.41
1457 3549 2.057922 ACCCATCATCCACCTATCCAC 58.942 52.381 0.00 0.00 0.00 4.02
1458 3550 1.352352 CCCATCATCCACCTATCCACC 59.648 57.143 0.00 0.00 0.00 4.61
1459 3551 1.352352 CCATCATCCACCTATCCACCC 59.648 57.143 0.00 0.00 0.00 4.61
1460 3552 2.057140 CATCATCCACCTATCCACCCA 58.943 52.381 0.00 0.00 0.00 4.51
1461 3553 1.507140 TCATCCACCTATCCACCCAC 58.493 55.000 0.00 0.00 0.00 4.61
1462 3554 1.009552 TCATCCACCTATCCACCCACT 59.990 52.381 0.00 0.00 0.00 4.00
1463 3555 1.846439 CATCCACCTATCCACCCACTT 59.154 52.381 0.00 0.00 0.00 3.16
1464 3556 1.580059 TCCACCTATCCACCCACTTC 58.420 55.000 0.00 0.00 0.00 3.01
1465 3557 0.178068 CCACCTATCCACCCACTTCG 59.822 60.000 0.00 0.00 0.00 3.79
1466 3558 0.902531 CACCTATCCACCCACTTCGT 59.097 55.000 0.00 0.00 0.00 3.85
1467 3559 1.278127 CACCTATCCACCCACTTCGTT 59.722 52.381 0.00 0.00 0.00 3.85
1468 3560 1.982958 ACCTATCCACCCACTTCGTTT 59.017 47.619 0.00 0.00 0.00 3.60
1469 3561 3.055675 CACCTATCCACCCACTTCGTTTA 60.056 47.826 0.00 0.00 0.00 2.01
1470 3562 3.197116 ACCTATCCACCCACTTCGTTTAG 59.803 47.826 0.00 0.00 0.00 1.85
1471 3563 3.197116 CCTATCCACCCACTTCGTTTAGT 59.803 47.826 0.00 0.00 0.00 2.24
1477 3569 3.930848 CACCCACTTCGTTTAGTATCCAC 59.069 47.826 0.00 0.00 0.00 4.02
1493 3585 0.974010 CCACCCCAGCTCATGCAAAT 60.974 55.000 0.00 0.00 42.74 2.32
1503 3595 6.294286 CCCAGCTCATGCAAATTCAAAATTTT 60.294 34.615 0.00 0.00 42.74 1.82
1553 3645 3.003689 CGAATTACACCATCTGCATTCCC 59.996 47.826 0.00 0.00 0.00 3.97
1560 3652 1.818060 CCATCTGCATTCCCGTTTCAA 59.182 47.619 0.00 0.00 0.00 2.69
1570 3662 2.048601 TCCCGTTTCAACCAGTAGGAA 58.951 47.619 0.00 0.00 38.69 3.36
1592 3684 6.148480 GGAATAAAGCGATCTACTACTACCGA 59.852 42.308 0.00 0.00 0.00 4.69
1618 3710 3.270877 ACTGAACCATAATTGAGGTCGC 58.729 45.455 4.36 1.95 37.07 5.19
1656 3748 8.677300 TGATCATTTAACTGAGGCAGATTTAAC 58.323 33.333 0.82 0.00 35.18 2.01
2039 4137 5.092105 TGACGAATGTTTGTTTGTTGTGAG 58.908 37.500 0.00 0.00 0.00 3.51
2203 4301 2.887568 GCAGACCGAGATGGCGTG 60.888 66.667 0.00 0.00 43.94 5.34
2385 4502 2.916269 TCTCTCTCTCTCTCTTGTCCCA 59.084 50.000 0.00 0.00 0.00 4.37
2416 4533 5.760253 TCAACTGTCATGGTCTCTTCTTTTC 59.240 40.000 0.00 0.00 0.00 2.29
2492 4609 2.491693 GGATTTCGCCATTGTTGGAAGA 59.508 45.455 0.00 0.00 46.92 2.87
2493 4610 3.428045 GGATTTCGCCATTGTTGGAAGAG 60.428 47.826 0.00 0.00 46.92 2.85
2494 4611 2.559698 TTCGCCATTGTTGGAAGAGA 57.440 45.000 0.00 0.00 46.92 3.10
2495 4612 2.559698 TCGCCATTGTTGGAAGAGAA 57.440 45.000 0.00 0.00 46.92 2.87
2497 4614 1.470098 CGCCATTGTTGGAAGAGAAGG 59.530 52.381 0.00 0.00 46.92 3.46
2498 4615 2.795329 GCCATTGTTGGAAGAGAAGGA 58.205 47.619 0.00 0.00 46.92 3.36
2499 4616 3.359950 GCCATTGTTGGAAGAGAAGGAT 58.640 45.455 0.00 0.00 46.92 3.24
2500 4617 3.379688 GCCATTGTTGGAAGAGAAGGATC 59.620 47.826 0.00 0.00 46.92 3.36
2501 4618 4.592942 CCATTGTTGGAAGAGAAGGATCA 58.407 43.478 0.00 0.00 46.92 2.92
2502 4619 4.639310 CCATTGTTGGAAGAGAAGGATCAG 59.361 45.833 0.00 0.00 46.92 2.90
2503 4620 4.982241 TTGTTGGAAGAGAAGGATCAGT 57.018 40.909 0.00 0.00 0.00 3.41
2616 4739 0.467384 AGCACACTGTTCTCTGCTGT 59.533 50.000 0.00 0.00 38.56 4.40
2618 4741 1.262683 GCACACTGTTCTCTGCTGTTC 59.737 52.381 0.00 0.00 0.00 3.18
2620 4743 2.799412 CACACTGTTCTCTGCTGTTCTC 59.201 50.000 0.00 0.00 0.00 2.87
2622 4745 1.346068 ACTGTTCTCTGCTGTTCTCCC 59.654 52.381 0.00 0.00 0.00 4.30
2623 4746 0.687354 TGTTCTCTGCTGTTCTCCCC 59.313 55.000 0.00 0.00 0.00 4.81
2624 4747 0.035915 GTTCTCTGCTGTTCTCCCCC 60.036 60.000 0.00 0.00 0.00 5.40
2679 4848 8.406297 GGAAAAGGTGATTTACTATGATTGGAC 58.594 37.037 0.00 0.00 0.00 4.02
2803 4991 2.093181 ACTGTATATGCAGCGTTGGGAA 60.093 45.455 19.44 0.00 39.96 3.97
2895 5083 1.266160 TAATTCCCCTCGGCGTTCCA 61.266 55.000 6.85 0.00 0.00 3.53
2940 5135 1.076549 GCAGGGTGGTGGAAATGGA 59.923 57.895 0.00 0.00 0.00 3.41
2941 5136 0.967380 GCAGGGTGGTGGAAATGGAG 60.967 60.000 0.00 0.00 0.00 3.86
2945 5140 0.676782 GGTGGTGGAAATGGAGGTCG 60.677 60.000 0.00 0.00 0.00 4.79
2976 5172 0.396435 ATTGTGTCTGAGGCAACGGA 59.604 50.000 0.00 0.00 46.39 4.69
3008 5204 5.011431 TGTCAGTGACAGATTCAGTCAGATT 59.989 40.000 22.06 0.00 45.77 2.40
3013 5209 6.873076 AGTGACAGATTCAGTCAGATTTTCTC 59.127 38.462 11.69 0.00 45.77 2.87
3016 5212 5.636965 ACAGATTCAGTCAGATTTTCTCACG 59.363 40.000 0.00 0.00 0.00 4.35
3038 5234 5.406780 ACGAGAAACAGCTTAGTCAGAAATG 59.593 40.000 0.00 0.00 0.00 2.32
3131 5371 2.678336 GTTACCATACACAGCTTCTGCC 59.322 50.000 0.00 0.00 40.80 4.85
3141 5381 2.099756 ACAGCTTCTGCCAAAAGAACAC 59.900 45.455 0.00 0.00 40.80 3.32
3142 5382 1.683385 AGCTTCTGCCAAAAGAACACC 59.317 47.619 0.00 0.00 40.80 4.16
3143 5383 1.600413 GCTTCTGCCAAAAGAACACCG 60.600 52.381 0.00 0.00 32.75 4.94
3144 5384 1.946768 CTTCTGCCAAAAGAACACCGA 59.053 47.619 0.00 0.00 32.75 4.69
3145 5385 1.305201 TCTGCCAAAAGAACACCGAC 58.695 50.000 0.00 0.00 0.00 4.79
3146 5386 1.021202 CTGCCAAAAGAACACCGACA 58.979 50.000 0.00 0.00 0.00 4.35
3147 5387 1.403679 CTGCCAAAAGAACACCGACAA 59.596 47.619 0.00 0.00 0.00 3.18
3148 5388 1.403679 TGCCAAAAGAACACCGACAAG 59.596 47.619 0.00 0.00 0.00 3.16
3149 5389 1.404035 GCCAAAAGAACACCGACAAGT 59.596 47.619 0.00 0.00 0.00 3.16
3150 5390 2.159296 GCCAAAAGAACACCGACAAGTT 60.159 45.455 0.00 0.00 0.00 2.66
3151 5391 3.065648 GCCAAAAGAACACCGACAAGTTA 59.934 43.478 0.00 0.00 0.00 2.24
3152 5392 4.594136 CCAAAAGAACACCGACAAGTTAC 58.406 43.478 0.00 0.00 0.00 2.50
3153 5393 4.334481 CCAAAAGAACACCGACAAGTTACT 59.666 41.667 0.00 0.00 0.00 2.24
3154 5394 5.263185 CAAAAGAACACCGACAAGTTACTG 58.737 41.667 0.00 0.00 0.00 2.74
3155 5395 2.480845 AGAACACCGACAAGTTACTGC 58.519 47.619 0.00 0.00 0.00 4.40
3156 5396 2.159014 AGAACACCGACAAGTTACTGCA 60.159 45.455 0.00 0.00 0.00 4.41
3157 5397 1.865865 ACACCGACAAGTTACTGCAG 58.134 50.000 13.48 13.48 0.00 4.41
3158 5398 1.138266 ACACCGACAAGTTACTGCAGT 59.862 47.619 25.12 25.12 0.00 4.40
3159 5399 1.792949 CACCGACAAGTTACTGCAGTC 59.207 52.381 25.56 10.38 0.00 3.51
3161 5401 1.767289 CGACAAGTTACTGCAGTCGT 58.233 50.000 25.56 13.65 44.87 4.34
3162 5402 2.124903 CGACAAGTTACTGCAGTCGTT 58.875 47.619 25.56 12.43 44.87 3.85
3163 5403 2.153247 CGACAAGTTACTGCAGTCGTTC 59.847 50.000 25.56 12.06 44.87 3.95
3164 5404 2.475487 GACAAGTTACTGCAGTCGTTCC 59.525 50.000 25.56 7.80 0.00 3.62
3165 5405 2.159014 ACAAGTTACTGCAGTCGTTCCA 60.159 45.455 25.56 0.52 0.00 3.53
3166 5406 3.067106 CAAGTTACTGCAGTCGTTCCAT 58.933 45.455 25.56 0.00 0.00 3.41
3167 5407 2.688507 AGTTACTGCAGTCGTTCCATG 58.311 47.619 25.56 0.00 0.00 3.66
3168 5408 2.037251 AGTTACTGCAGTCGTTCCATGT 59.963 45.455 25.56 0.00 0.00 3.21
3169 5409 2.806244 GTTACTGCAGTCGTTCCATGTT 59.194 45.455 25.56 0.00 0.00 2.71
3170 5410 1.967319 ACTGCAGTCGTTCCATGTTT 58.033 45.000 15.25 0.00 0.00 2.83
3171 5411 3.120321 ACTGCAGTCGTTCCATGTTTA 57.880 42.857 15.25 0.00 0.00 2.01
3172 5412 3.674997 ACTGCAGTCGTTCCATGTTTAT 58.325 40.909 15.25 0.00 0.00 1.40
3173 5413 3.684788 ACTGCAGTCGTTCCATGTTTATC 59.315 43.478 15.25 0.00 0.00 1.75
3174 5414 3.935203 CTGCAGTCGTTCCATGTTTATCT 59.065 43.478 5.25 0.00 0.00 1.98
3175 5415 3.932710 TGCAGTCGTTCCATGTTTATCTC 59.067 43.478 0.00 0.00 0.00 2.75
3176 5416 3.000322 GCAGTCGTTCCATGTTTATCTCG 60.000 47.826 0.00 0.00 0.00 4.04
3177 5417 4.421058 CAGTCGTTCCATGTTTATCTCGA 58.579 43.478 0.00 0.00 0.00 4.04
3178 5418 5.043903 CAGTCGTTCCATGTTTATCTCGAT 58.956 41.667 0.00 0.00 0.00 3.59
3179 5419 5.174035 CAGTCGTTCCATGTTTATCTCGATC 59.826 44.000 0.00 0.00 0.00 3.69
3180 5420 5.067936 AGTCGTTCCATGTTTATCTCGATCT 59.932 40.000 0.00 0.00 0.00 2.75
3181 5421 6.262496 AGTCGTTCCATGTTTATCTCGATCTA 59.738 38.462 0.00 0.00 0.00 1.98
3182 5422 6.916387 GTCGTTCCATGTTTATCTCGATCTAA 59.084 38.462 0.00 0.00 0.00 2.10
3183 5423 7.434307 GTCGTTCCATGTTTATCTCGATCTAAA 59.566 37.037 0.00 0.00 0.00 1.85
3184 5424 7.977293 TCGTTCCATGTTTATCTCGATCTAAAA 59.023 33.333 0.00 0.00 0.00 1.52
3185 5425 8.765219 CGTTCCATGTTTATCTCGATCTAAAAT 58.235 33.333 0.00 0.00 0.00 1.82
3221 5508 5.810074 ACAAGTAAAAGTCCAATGCACAAAC 59.190 36.000 0.00 0.00 0.00 2.93
3295 5582 5.212532 AGGAGGAGAAGATTTGATGATCG 57.787 43.478 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.849911 ACGAGTAGCACGTAGTACAGTA 58.150 45.455 0.38 0.00 41.61 2.74
1 2 2.693069 ACGAGTAGCACGTAGTACAGT 58.307 47.619 0.38 5.83 41.61 3.55
2 3 3.862267 AGTACGAGTAGCACGTAGTACAG 59.138 47.826 0.00 5.34 44.39 2.74
3 4 3.849911 AGTACGAGTAGCACGTAGTACA 58.150 45.455 0.00 0.00 44.39 2.90
4 5 3.061535 CGAGTACGAGTAGCACGTAGTAC 60.062 52.174 0.00 7.90 45.58 2.73
152 159 8.251026 CAGTGTGAAATTGAGATGGTAGTAGTA 58.749 37.037 0.00 0.00 0.00 1.82
196 203 4.142315 TGCCTGACACGGTAAATACTACTC 60.142 45.833 0.00 0.00 0.00 2.59
197 204 3.765511 TGCCTGACACGGTAAATACTACT 59.234 43.478 0.00 0.00 0.00 2.57
198 205 3.861689 GTGCCTGACACGGTAAATACTAC 59.138 47.826 0.00 0.00 40.07 2.73
348 360 0.613260 TCCACTGAGAAATCACCGGG 59.387 55.000 6.32 0.00 0.00 5.73
465 778 4.405756 AGGAAGAGGTCTCCAGAGTTAA 57.594 45.455 0.00 0.00 0.00 2.01
466 779 4.090090 CAAGGAAGAGGTCTCCAGAGTTA 58.910 47.826 0.00 0.00 0.00 2.24
467 780 2.903135 CAAGGAAGAGGTCTCCAGAGTT 59.097 50.000 0.00 0.00 0.00 3.01
468 781 2.110899 TCAAGGAAGAGGTCTCCAGAGT 59.889 50.000 0.00 0.00 0.00 3.24
469 782 2.495669 GTCAAGGAAGAGGTCTCCAGAG 59.504 54.545 0.00 0.00 0.00 3.35
470 783 2.530701 GTCAAGGAAGAGGTCTCCAGA 58.469 52.381 0.00 0.00 0.00 3.86
816 2671 0.182299 GCCAAAGGAGAGGATGGAGG 59.818 60.000 0.00 0.00 34.82 4.30
817 2672 0.179062 CGCCAAAGGAGAGGATGGAG 60.179 60.000 0.00 0.00 34.82 3.86
818 2673 0.909610 ACGCCAAAGGAGAGGATGGA 60.910 55.000 0.00 0.00 34.82 3.41
870 2725 2.529389 GAGGTGGGAGGTGGTGGT 60.529 66.667 0.00 0.00 0.00 4.16
912 2772 1.398692 CGAGGGAAAGAGAGGGAGAG 58.601 60.000 0.00 0.00 0.00 3.20
914 2774 1.681486 GGCGAGGGAAAGAGAGGGAG 61.681 65.000 0.00 0.00 0.00 4.30
915 2775 1.686110 GGCGAGGGAAAGAGAGGGA 60.686 63.158 0.00 0.00 0.00 4.20
916 2776 1.681486 GAGGCGAGGGAAAGAGAGGG 61.681 65.000 0.00 0.00 0.00 4.30
917 2777 1.681486 GGAGGCGAGGGAAAGAGAGG 61.681 65.000 0.00 0.00 0.00 3.69
931 2791 2.270527 GGTCTTGGAGCTGGAGGC 59.729 66.667 0.00 0.00 42.19 4.70
943 2803 1.280421 CTCTAGCTTGCTTGGGGTCTT 59.720 52.381 0.00 0.00 0.00 3.01
946 2806 1.301293 GCTCTAGCTTGCTTGGGGT 59.699 57.895 0.00 0.00 38.21 4.95
947 2807 4.232310 GCTCTAGCTTGCTTGGGG 57.768 61.111 0.00 0.00 38.21 4.96
957 2817 0.749649 TTGCCTGCTCTAGCTCTAGC 59.250 55.000 12.21 12.21 42.66 3.42
958 2818 1.340889 CCTTGCCTGCTCTAGCTCTAG 59.659 57.143 3.26 0.00 42.66 2.43
959 2819 1.063642 TCCTTGCCTGCTCTAGCTCTA 60.064 52.381 3.26 0.00 42.66 2.43
960 2820 0.325110 TCCTTGCCTGCTCTAGCTCT 60.325 55.000 3.26 0.00 42.66 4.09
961 2821 0.104671 CTCCTTGCCTGCTCTAGCTC 59.895 60.000 3.26 0.00 42.66 4.09
962 2822 0.325110 TCTCCTTGCCTGCTCTAGCT 60.325 55.000 3.26 0.00 42.66 3.32
963 2823 0.104671 CTCTCCTTGCCTGCTCTAGC 59.895 60.000 0.00 0.00 42.50 3.42
964 2824 0.104671 GCTCTCCTTGCCTGCTCTAG 59.895 60.000 0.00 0.00 0.00 2.43
965 2825 1.670949 CGCTCTCCTTGCCTGCTCTA 61.671 60.000 0.00 0.00 0.00 2.43
966 2826 2.988800 GCTCTCCTTGCCTGCTCT 59.011 61.111 0.00 0.00 0.00 4.09
967 2827 2.308968 ATCGCTCTCCTTGCCTGCTC 62.309 60.000 0.00 0.00 0.00 4.26
968 2828 2.308968 GATCGCTCTCCTTGCCTGCT 62.309 60.000 0.00 0.00 0.00 4.24
969 2829 1.886777 GATCGCTCTCCTTGCCTGC 60.887 63.158 0.00 0.00 0.00 4.85
970 2830 1.591059 CGATCGCTCTCCTTGCCTG 60.591 63.158 0.26 0.00 0.00 4.85
971 2831 2.790791 CCGATCGCTCTCCTTGCCT 61.791 63.158 10.32 0.00 0.00 4.75
972 2832 2.279784 CCGATCGCTCTCCTTGCC 60.280 66.667 10.32 0.00 0.00 4.52
973 2833 1.590259 GACCGATCGCTCTCCTTGC 60.590 63.158 10.32 0.00 0.00 4.01
974 2834 1.298713 CGACCGATCGCTCTCCTTG 60.299 63.158 10.32 0.00 42.43 3.61
975 2835 3.111939 CGACCGATCGCTCTCCTT 58.888 61.111 10.32 0.00 42.43 3.36
1138 3227 1.062581 TCCTTGATCCTCCTCCTCCTG 60.063 57.143 0.00 0.00 0.00 3.86
1143 3232 2.698274 GTCTTCTCCTTGATCCTCCTCC 59.302 54.545 0.00 0.00 0.00 4.30
1149 3238 0.537188 TGCCGTCTTCTCCTTGATCC 59.463 55.000 0.00 0.00 0.00 3.36
1440 3532 2.057140 TGGGTGGATAGGTGGATGATG 58.943 52.381 0.00 0.00 0.00 3.07
1441 3533 2.057922 GTGGGTGGATAGGTGGATGAT 58.942 52.381 0.00 0.00 0.00 2.45
1442 3534 1.009552 AGTGGGTGGATAGGTGGATGA 59.990 52.381 0.00 0.00 0.00 2.92
1444 3536 2.127708 GAAGTGGGTGGATAGGTGGAT 58.872 52.381 0.00 0.00 0.00 3.41
1445 3537 1.580059 GAAGTGGGTGGATAGGTGGA 58.420 55.000 0.00 0.00 0.00 4.02
1447 3539 0.902531 ACGAAGTGGGTGGATAGGTG 59.097 55.000 0.00 0.00 42.51 4.00
1448 3540 1.652947 AACGAAGTGGGTGGATAGGT 58.347 50.000 0.00 0.00 45.00 3.08
1449 3541 2.781681 AAACGAAGTGGGTGGATAGG 57.218 50.000 0.00 0.00 45.00 2.57
1450 3542 4.467198 ACTAAACGAAGTGGGTGGATAG 57.533 45.455 0.00 0.00 45.00 2.08
1451 3543 5.069516 GGATACTAAACGAAGTGGGTGGATA 59.930 44.000 0.00 0.00 45.00 2.59
1452 3544 4.141779 GGATACTAAACGAAGTGGGTGGAT 60.142 45.833 0.00 0.00 45.00 3.41
1453 3545 3.196254 GGATACTAAACGAAGTGGGTGGA 59.804 47.826 0.00 0.00 45.00 4.02
1454 3546 3.055675 TGGATACTAAACGAAGTGGGTGG 60.056 47.826 0.00 0.00 38.45 4.61
1455 3547 3.930848 GTGGATACTAAACGAAGTGGGTG 59.069 47.826 0.00 0.00 38.45 4.61
1456 3548 3.055602 GGTGGATACTAAACGAAGTGGGT 60.056 47.826 0.00 0.00 38.45 4.51
1457 3549 3.528532 GGTGGATACTAAACGAAGTGGG 58.471 50.000 0.00 0.00 38.45 4.61
1458 3550 3.528532 GGGTGGATACTAAACGAAGTGG 58.471 50.000 0.00 0.00 38.45 4.00
1459 3551 3.055675 TGGGGTGGATACTAAACGAAGTG 60.056 47.826 0.00 0.00 38.45 3.16
1460 3552 3.175594 TGGGGTGGATACTAAACGAAGT 58.824 45.455 0.00 0.00 40.48 3.01
1461 3553 3.793559 CTGGGGTGGATACTAAACGAAG 58.206 50.000 0.00 0.00 37.61 3.79
1462 3554 2.093341 GCTGGGGTGGATACTAAACGAA 60.093 50.000 0.00 0.00 37.61 3.85
1463 3555 1.483415 GCTGGGGTGGATACTAAACGA 59.517 52.381 0.00 0.00 37.61 3.85
1464 3556 1.485066 AGCTGGGGTGGATACTAAACG 59.515 52.381 0.00 0.00 37.61 3.60
1465 3557 2.504175 TGAGCTGGGGTGGATACTAAAC 59.496 50.000 0.00 0.00 37.61 2.01
1466 3558 2.840511 TGAGCTGGGGTGGATACTAAA 58.159 47.619 0.00 0.00 37.61 1.85
1467 3559 2.561209 TGAGCTGGGGTGGATACTAA 57.439 50.000 0.00 0.00 37.61 2.24
1468 3560 2.329267 CATGAGCTGGGGTGGATACTA 58.671 52.381 0.00 0.00 37.61 1.82
1469 3561 1.135094 CATGAGCTGGGGTGGATACT 58.865 55.000 0.00 0.00 37.61 2.12
1470 3562 0.536006 GCATGAGCTGGGGTGGATAC 60.536 60.000 0.00 0.00 37.91 2.24
1471 3563 0.987613 TGCATGAGCTGGGGTGGATA 60.988 55.000 0.00 0.00 42.74 2.59
1477 3569 1.187974 TGAATTTGCATGAGCTGGGG 58.812 50.000 0.00 0.00 42.74 4.96
1503 3595 5.422331 TCTGTTTGTTGTTAATTTGGGACCA 59.578 36.000 0.00 0.00 0.00 4.02
1553 3645 5.628134 GCTTTATTCCTACTGGTTGAAACG 58.372 41.667 0.00 0.00 34.23 3.60
1560 3652 5.834204 AGTAGATCGCTTTATTCCTACTGGT 59.166 40.000 0.00 0.00 36.46 4.00
1570 3662 7.684937 ATTCGGTAGTAGTAGATCGCTTTAT 57.315 36.000 0.00 0.00 0.00 1.40
1592 3684 7.415206 GCGACCTCAATTATGGTTCAGTTTATT 60.415 37.037 3.47 0.00 36.59 1.40
1618 3710 6.910972 CAGTTAAATGATCATGCTGCACTAAG 59.089 38.462 9.46 0.00 0.00 2.18
1656 3748 4.678840 GCCCAATTGGACTGCAGATTTAAG 60.679 45.833 26.60 4.70 37.39 1.85
2014 4110 6.096036 TCACAACAAACAAACATTCGTCAAT 58.904 32.000 0.00 0.00 0.00 2.57
2039 4137 1.725931 GCGTTGTTGTAGCATCTGCAC 60.726 52.381 4.79 1.91 45.16 4.57
2222 4320 2.024871 GAGACGGCGTCGATGGAG 59.975 66.667 31.59 0.00 37.67 3.86
2385 4502 0.603707 CCATGACAGTTGACACCGCT 60.604 55.000 0.00 0.00 0.00 5.52
2416 4533 4.825634 ACGGTAAAGGGAAAAGAAAAGGAG 59.174 41.667 0.00 0.00 0.00 3.69
2492 4609 7.278875 GTTCTTCCATTCATACTGATCCTTCT 58.721 38.462 0.00 0.00 0.00 2.85
2493 4610 6.201806 CGTTCTTCCATTCATACTGATCCTTC 59.798 42.308 0.00 0.00 0.00 3.46
2494 4611 6.051717 CGTTCTTCCATTCATACTGATCCTT 58.948 40.000 0.00 0.00 0.00 3.36
2495 4612 5.453903 CCGTTCTTCCATTCATACTGATCCT 60.454 44.000 0.00 0.00 0.00 3.24
2497 4614 5.601662 TCCGTTCTTCCATTCATACTGATC 58.398 41.667 0.00 0.00 0.00 2.92
2498 4615 5.614324 TCCGTTCTTCCATTCATACTGAT 57.386 39.130 0.00 0.00 0.00 2.90
2499 4616 5.601662 GATCCGTTCTTCCATTCATACTGA 58.398 41.667 0.00 0.00 0.00 3.41
2500 4617 4.445718 CGATCCGTTCTTCCATTCATACTG 59.554 45.833 0.00 0.00 0.00 2.74
2501 4618 4.501571 CCGATCCGTTCTTCCATTCATACT 60.502 45.833 0.00 0.00 0.00 2.12
2502 4619 3.741344 CCGATCCGTTCTTCCATTCATAC 59.259 47.826 0.00 0.00 0.00 2.39
2503 4620 3.639561 TCCGATCCGTTCTTCCATTCATA 59.360 43.478 0.00 0.00 0.00 2.15
2606 4729 2.377136 GGGGGAGAACAGCAGAGAA 58.623 57.895 0.00 0.00 0.00 2.87
2607 4730 4.136978 GGGGGAGAACAGCAGAGA 57.863 61.111 0.00 0.00 0.00 3.10
2624 4747 3.003173 TTCGCTCCAGAGGGGTGG 61.003 66.667 11.35 0.00 41.19 4.61
2626 4749 0.032017 ATAGTTCGCTCCAGAGGGGT 60.032 55.000 11.35 0.86 41.19 4.95
2627 4750 1.069358 GAATAGTTCGCTCCAGAGGGG 59.931 57.143 11.35 0.00 41.19 4.79
2679 4848 0.664466 CACGATGTCCGATCCATCCG 60.664 60.000 0.00 0.00 41.76 4.18
2778 4947 4.083855 CCCAACGCTGCATATACAGTTATG 60.084 45.833 4.86 1.99 39.96 1.90
2803 4991 1.710816 TTCCGGTGAGGCCAATTTTT 58.289 45.000 5.01 0.00 40.77 1.94
2895 5083 0.106708 TTCAGAGCTCCTGCACGTTT 59.893 50.000 10.93 0.00 42.62 3.60
2926 5121 0.676782 CGACCTCCATTTCCACCACC 60.677 60.000 0.00 0.00 0.00 4.61
2940 5135 2.037772 ACAATTTCAGTCAGAGCGACCT 59.962 45.455 0.00 0.00 46.69 3.85
2941 5136 2.158449 CACAATTTCAGTCAGAGCGACC 59.842 50.000 0.00 0.00 46.69 4.79
2945 5140 4.060900 TCAGACACAATTTCAGTCAGAGC 58.939 43.478 0.00 0.00 34.80 4.09
3013 5209 3.902150 TCTGACTAAGCTGTTTCTCGTG 58.098 45.455 0.00 0.00 0.00 4.35
3016 5212 6.425114 TGACATTTCTGACTAAGCTGTTTCTC 59.575 38.462 0.00 0.00 0.00 2.87
3038 5234 7.065085 GCATGGATTATATCATGTACCAGTGAC 59.935 40.741 0.00 0.00 41.83 3.67
3131 5371 5.263185 CAGTAACTTGTCGGTGTTCTTTTG 58.737 41.667 0.00 0.00 0.00 2.44
3141 5381 1.060713 CGACTGCAGTAACTTGTCGG 58.939 55.000 21.73 0.00 44.29 4.79
3143 5383 2.475487 GGAACGACTGCAGTAACTTGTC 59.525 50.000 21.73 11.10 0.00 3.18
3144 5384 2.159014 TGGAACGACTGCAGTAACTTGT 60.159 45.455 21.73 10.62 0.00 3.16
3145 5385 2.479837 TGGAACGACTGCAGTAACTTG 58.520 47.619 21.73 9.96 0.00 3.16
3146 5386 2.902705 TGGAACGACTGCAGTAACTT 57.097 45.000 21.73 11.05 0.00 2.66
3147 5387 2.037251 ACATGGAACGACTGCAGTAACT 59.963 45.455 21.73 6.54 0.00 2.24
3148 5388 2.413837 ACATGGAACGACTGCAGTAAC 58.586 47.619 21.73 7.49 0.00 2.50
3149 5389 2.831685 ACATGGAACGACTGCAGTAA 57.168 45.000 21.73 1.74 0.00 2.24
3150 5390 2.831685 AACATGGAACGACTGCAGTA 57.168 45.000 21.73 2.67 0.00 2.74
3151 5391 1.967319 AAACATGGAACGACTGCAGT 58.033 45.000 21.88 21.88 0.00 4.40
3152 5392 3.935203 AGATAAACATGGAACGACTGCAG 59.065 43.478 13.48 13.48 0.00 4.41
3153 5393 3.932710 GAGATAAACATGGAACGACTGCA 59.067 43.478 0.00 0.00 0.00 4.41
3154 5394 3.000322 CGAGATAAACATGGAACGACTGC 60.000 47.826 0.00 0.00 0.00 4.40
3155 5395 4.421058 TCGAGATAAACATGGAACGACTG 58.579 43.478 0.00 0.00 0.00 3.51
3156 5396 4.713824 TCGAGATAAACATGGAACGACT 57.286 40.909 0.00 0.00 0.00 4.18
3157 5397 5.282510 AGATCGAGATAAACATGGAACGAC 58.717 41.667 0.00 0.00 0.00 4.34
3158 5398 5.515797 AGATCGAGATAAACATGGAACGA 57.484 39.130 0.00 0.00 0.00 3.85
3159 5399 7.694388 TTTAGATCGAGATAAACATGGAACG 57.306 36.000 0.00 0.00 0.00 3.95
3162 5402 9.698309 GAGATTTTAGATCGAGATAAACATGGA 57.302 33.333 0.00 0.00 0.00 3.41
3163 5403 8.930760 GGAGATTTTAGATCGAGATAAACATGG 58.069 37.037 0.00 0.00 0.00 3.66
3164 5404 9.481340 TGGAGATTTTAGATCGAGATAAACATG 57.519 33.333 4.76 0.00 0.00 3.21
3165 5405 9.482627 GTGGAGATTTTAGATCGAGATAAACAT 57.517 33.333 4.76 3.42 0.00 2.71
3166 5406 8.474831 TGTGGAGATTTTAGATCGAGATAAACA 58.525 33.333 4.76 0.00 0.00 2.83
3167 5407 8.873215 TGTGGAGATTTTAGATCGAGATAAAC 57.127 34.615 4.76 0.00 0.00 2.01
3168 5408 9.534565 CTTGTGGAGATTTTAGATCGAGATAAA 57.465 33.333 0.00 0.00 0.00 1.40
3169 5409 8.914011 TCTTGTGGAGATTTTAGATCGAGATAA 58.086 33.333 0.00 0.00 0.00 1.75
3170 5410 8.465273 TCTTGTGGAGATTTTAGATCGAGATA 57.535 34.615 0.00 0.00 0.00 1.98
3171 5411 7.286546 TCTCTTGTGGAGATTTTAGATCGAGAT 59.713 37.037 0.00 0.00 45.20 2.75
3172 5412 6.603599 TCTCTTGTGGAGATTTTAGATCGAGA 59.396 38.462 0.00 0.00 45.20 4.04
3173 5413 6.800543 TCTCTTGTGGAGATTTTAGATCGAG 58.199 40.000 0.00 0.00 45.20 4.04
3174 5414 6.775594 TCTCTTGTGGAGATTTTAGATCGA 57.224 37.500 0.00 0.00 45.20 3.59
3186 5426 5.467063 GGACTTTTACTTGTCTCTTGTGGAG 59.533 44.000 0.00 0.00 43.12 3.86
3187 5427 5.104693 TGGACTTTTACTTGTCTCTTGTGGA 60.105 40.000 0.00 0.00 34.01 4.02
3221 5508 3.887621 TTTCCTTGTAGGGTCTCATCG 57.112 47.619 0.00 0.00 35.59 3.84
3295 5582 0.645868 GCGATGCGTCTACTGTTTCC 59.354 55.000 4.05 0.00 0.00 3.13


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

AutoCloner maintained by Alex Coulton.