Multiple sequence alignment - TraesCS5B01G317200

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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 TraesCS5B01G317200 chr5B 100.000 3714 0 0 1 3714 500531231 500527518 0.000000e+00 6859
1 TraesCS5B01G317200 chr5D 93.033 3574 145 46 1 3544 414811805 414808306 0.000000e+00 5125
2 TraesCS5B01G317200 chr5A 93.980 2691 115 22 866 3544 527491687 527489032 0.000000e+00 4028
3 TraesCS5B01G317200 chr5A 88.713 567 27 19 1 555 527492472 527491931 0.000000e+00 658
4 TraesCS5B01G317200 chr7A 78.598 813 140 22 1207 2000 280071602 280070805 1.190000e-139 507
5 TraesCS5B01G317200 chr7A 99.422 173 1 0 3542 3714 703343203 703343031 7.740000e-82 315
6 TraesCS5B01G317200 chr7A 75.719 626 128 15 2076 2679 280070689 280070066 3.630000e-75 292
7 TraesCS5B01G317200 chr7D 78.288 806 139 23 1212 1993 258238048 258237255 1.550000e-133 486
8 TraesCS5B01G317200 chr7D 76.874 627 119 15 2076 2679 258237155 258236532 7.690000e-87 331
9 TraesCS5B01G317200 chr7B 78.315 807 137 24 1212 1993 237509468 237508675 1.550000e-133 486
10 TraesCS5B01G317200 chr7B 97.790 181 2 2 3536 3714 748166698 748166878 1.000000e-80 311
11 TraesCS5B01G317200 chr7B 97.765 179 4 0 3536 3714 731032672 731032494 3.600000e-80 309
12 TraesCS5B01G317200 chrUn 100.000 172 0 0 3543 3714 2356221 2356050 5.990000e-83 318
13 TraesCS5B01G317200 chr6B 99.422 173 1 0 3542 3714 293134235 293134063 7.740000e-82 315
14 TraesCS5B01G317200 chr6A 98.864 176 1 1 3537 3712 4689427 4689253 2.780000e-81 313
15 TraesCS5B01G317200 chr1B 98.305 177 3 0 3538 3714 31162446 31162622 1.000000e-80 311
16 TraesCS5B01G317200 chr1B 97.238 181 5 0 3534 3714 24671639 24671819 1.300000e-79 307
17 TraesCS5B01G317200 chr3A 97.253 182 3 1 3535 3714 28777676 28777495 1.300000e-79 307


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 TraesCS5B01G317200 chr5B 500527518 500531231 3713 True 6859.0 6859 100.0000 1 3714 1 chr5B.!!$R1 3713
1 TraesCS5B01G317200 chr5D 414808306 414811805 3499 True 5125.0 5125 93.0330 1 3544 1 chr5D.!!$R1 3543
2 TraesCS5B01G317200 chr5A 527489032 527492472 3440 True 2343.0 4028 91.3465 1 3544 2 chr5A.!!$R1 3543
3 TraesCS5B01G317200 chr7A 280070066 280071602 1536 True 399.5 507 77.1585 1207 2679 2 chr7A.!!$R2 1472
4 TraesCS5B01G317200 chr7D 258236532 258238048 1516 True 408.5 486 77.5810 1212 2679 2 chr7D.!!$R1 1467
5 TraesCS5B01G317200 chr7B 237508675 237509468 793 True 486.0 486 78.3150 1212 1993 1 chr7B.!!$R1 781

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
602 622 0.109319 GCCAGGCCAACACAAATACG 60.109 55.0 5.01 0.0 0.00 3.06 F
1390 1437 0.178975 CGTGGCTAGGGAGATCCTCT 60.179 60.0 0.00 0.0 44.06 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1844 1903 1.371267 CCGACGAAGCTGTTCACGA 60.371 57.895 0.00 0.0 35.49 4.35 R
2960 3092 0.250640 ACAGGGCAGTTGCAGAAGAG 60.251 55.000 6.43 0.0 44.36 2.85 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
29 30 0.983378 AGGGCAGGTTAATCGCCTCT 60.983 55.000 17.25 11.65 45.50 3.69
154 160 1.200716 CATGTATGGCCCAATCGATGC 59.799 52.381 0.00 0.00 0.00 3.91
175 181 1.342819 AGCTATACTGGCTGTAGCTGC 59.657 52.381 17.66 15.58 46.78 5.25
176 182 1.342819 GCTATACTGGCTGTAGCTGCT 59.657 52.381 7.57 7.57 41.70 4.24
177 183 2.558795 GCTATACTGGCTGTAGCTGCTA 59.441 50.000 5.02 5.02 41.70 3.49
178 184 3.194542 GCTATACTGGCTGTAGCTGCTAT 59.805 47.826 13.20 0.00 41.70 2.97
217 224 0.763986 TCGCTGGATGGATGGATGGA 60.764 55.000 0.00 0.00 0.00 3.41
218 225 0.327259 CGCTGGATGGATGGATGGAT 59.673 55.000 0.00 0.00 0.00 3.41
219 226 1.835494 GCTGGATGGATGGATGGATG 58.165 55.000 0.00 0.00 0.00 3.51
220 227 1.616187 GCTGGATGGATGGATGGATGG 60.616 57.143 0.00 0.00 0.00 3.51
221 228 1.990327 CTGGATGGATGGATGGATGGA 59.010 52.381 0.00 0.00 0.00 3.41
222 229 2.581246 CTGGATGGATGGATGGATGGAT 59.419 50.000 0.00 0.00 0.00 3.41
223 230 2.310647 TGGATGGATGGATGGATGGATG 59.689 50.000 0.00 0.00 0.00 3.51
224 231 2.357881 GGATGGATGGATGGATGGATGG 60.358 54.545 0.00 0.00 0.00 3.51
225 232 2.136974 TGGATGGATGGATGGATGGA 57.863 50.000 0.00 0.00 0.00 3.41
226 233 2.651190 TGGATGGATGGATGGATGGAT 58.349 47.619 0.00 0.00 0.00 3.41
227 234 2.310647 TGGATGGATGGATGGATGGATG 59.689 50.000 0.00 0.00 0.00 3.51
228 235 2.357881 GGATGGATGGATGGATGGATGG 60.358 54.545 0.00 0.00 0.00 3.51
381 394 1.665916 CATGGGCGATGGAGCTACG 60.666 63.158 0.98 0.00 37.29 3.51
430 443 2.433145 CTCACGCGCCTCATGTGT 60.433 61.111 5.73 0.00 35.20 3.72
431 444 1.153842 CTCACGCGCCTCATGTGTA 60.154 57.895 5.73 0.00 35.20 2.90
444 457 4.021894 CCTCATGTGTATGCCTACTCCTAC 60.022 50.000 0.74 0.00 34.21 3.18
445 458 4.804597 TCATGTGTATGCCTACTCCTACT 58.195 43.478 0.74 0.00 34.21 2.57
446 459 5.948842 TCATGTGTATGCCTACTCCTACTA 58.051 41.667 0.74 0.00 34.21 1.82
554 574 4.814294 GCTCCACCGCCGATCGTT 62.814 66.667 15.09 0.00 36.19 3.85
556 576 3.642778 CTCCACCGCCGATCGTTGT 62.643 63.158 15.09 4.98 36.19 3.32
560 580 3.192922 CCGCCGATCGTTGTTCCC 61.193 66.667 15.09 0.00 36.19 3.97
561 581 3.192922 CGCCGATCGTTGTTCCCC 61.193 66.667 15.09 0.00 0.00 4.81
562 582 2.822701 GCCGATCGTTGTTCCCCC 60.823 66.667 15.09 0.00 0.00 5.40
592 612 3.604667 CTTTGCGTGCCAGGCCAA 61.605 61.111 9.64 2.89 0.00 4.52
593 613 3.846602 CTTTGCGTGCCAGGCCAAC 62.847 63.158 9.64 0.00 0.00 3.77
597 617 3.215568 CGTGCCAGGCCAACACAA 61.216 61.111 19.06 0.00 33.89 3.33
598 618 2.780094 CGTGCCAGGCCAACACAAA 61.780 57.895 19.06 0.00 33.89 2.83
599 619 1.747774 GTGCCAGGCCAACACAAAT 59.252 52.632 9.64 0.00 34.43 2.32
600 620 0.965439 GTGCCAGGCCAACACAAATA 59.035 50.000 9.64 0.00 34.43 1.40
601 621 0.965439 TGCCAGGCCAACACAAATAC 59.035 50.000 9.64 0.00 0.00 1.89
602 622 0.109319 GCCAGGCCAACACAAATACG 60.109 55.000 5.01 0.00 0.00 3.06
603 623 0.525761 CCAGGCCAACACAAATACGG 59.474 55.000 5.01 0.00 0.00 4.02
604 624 1.529226 CAGGCCAACACAAATACGGA 58.471 50.000 5.01 0.00 0.00 4.69
605 625 1.883275 CAGGCCAACACAAATACGGAA 59.117 47.619 5.01 0.00 0.00 4.30
606 626 1.883926 AGGCCAACACAAATACGGAAC 59.116 47.619 5.01 0.00 0.00 3.62
607 627 1.883926 GGCCAACACAAATACGGAACT 59.116 47.619 0.00 0.00 0.00 3.01
608 628 2.095415 GGCCAACACAAATACGGAACTC 60.095 50.000 0.00 0.00 0.00 3.01
609 629 2.550606 GCCAACACAAATACGGAACTCA 59.449 45.455 0.00 0.00 0.00 3.41
636 656 9.270640 CACAAATATCGTACTACTACTCCTACT 57.729 37.037 0.00 0.00 0.00 2.57
639 659 9.632807 AAATATCGTACTACTACTCCTACTACG 57.367 37.037 0.00 0.00 0.00 3.51
653 676 4.228097 TACGTCCGTCGCGCTAGC 62.228 66.667 5.56 4.06 44.19 3.42
656 679 4.493747 GTCCGTCGCGCTAGCCTT 62.494 66.667 9.66 0.00 41.18 4.35
657 680 4.492160 TCCGTCGCGCTAGCCTTG 62.492 66.667 9.66 0.00 41.18 3.61
659 682 4.796231 CGTCGCGCTAGCCTTGGT 62.796 66.667 9.66 0.00 41.18 3.67
678 701 2.311854 CCTTGGATGCCCCTCCACT 61.312 63.158 0.00 0.00 44.97 4.00
720 743 2.198406 CATCATCAATTTGGCCAAGCG 58.802 47.619 19.48 11.18 0.00 4.68
723 746 2.298446 TCATCAATTTGGCCAAGCGAAA 59.702 40.909 19.48 3.35 40.15 3.46
724 747 2.147436 TCAATTTGGCCAAGCGAAAC 57.853 45.000 19.48 0.00 38.86 2.78
763 806 3.945434 GCACTGATGATGCGCCGG 61.945 66.667 4.18 0.00 32.45 6.13
765 808 2.202932 ACTGATGATGCGCCGGAC 60.203 61.111 5.05 0.00 0.00 4.79
788 832 5.302568 ACCATCATCATCAACGCCATTAATT 59.697 36.000 0.00 0.00 0.00 1.40
793 837 9.985730 ATCATCATCAACGCCATTAATTAAATT 57.014 25.926 1.21 0.00 0.00 1.82
817 864 1.376812 GAACCGATCGCCCTGGTTT 60.377 57.895 10.32 0.00 45.63 3.27
820 867 2.183300 CGATCGCCCTGGTTTCGA 59.817 61.111 0.26 5.62 36.63 3.71
826 873 2.513897 CCCTGGTTTCGATCCGCC 60.514 66.667 0.00 0.00 0.00 6.13
827 874 2.513897 CCTGGTTTCGATCCGCCC 60.514 66.667 0.00 0.00 0.00 6.13
831 878 2.585247 GTTTCGATCCGCCCTCCG 60.585 66.667 0.00 0.00 0.00 4.63
850 897 4.880426 TCCCCCGATGGAGCTCCC 62.880 72.222 29.95 14.48 35.39 4.30
852 899 4.888325 CCCCGATGGAGCTCCCCT 62.888 72.222 29.95 17.32 35.39 4.79
960 1007 2.524148 GCACCACCCCAAAAGCCT 60.524 61.111 0.00 0.00 0.00 4.58
1008 1055 0.811616 GCGAAGAATCCATGGCGACT 60.812 55.000 6.96 2.62 0.00 4.18
1356 1403 3.188786 GAGACGCGCATGGTGGTC 61.189 66.667 5.73 5.38 0.00 4.02
1390 1437 0.178975 CGTGGCTAGGGAGATCCTCT 60.179 60.000 0.00 0.00 44.06 3.69
1844 1903 4.444081 CTCCCGTCTCGTCCCCCT 62.444 72.222 0.00 0.00 0.00 4.79
2488 2617 2.359169 GCTCTCCGTCATGGGGTCA 61.359 63.158 0.00 0.00 40.23 4.02
2986 3119 2.939103 CTGCAACTGCCCTGTAAGATAC 59.061 50.000 0.00 0.00 41.18 2.24
3120 3260 1.559219 TGACACAGTGGATGGGGTATG 59.441 52.381 5.31 0.00 36.22 2.39
3122 3262 2.439507 GACACAGTGGATGGGGTATGAT 59.560 50.000 5.31 0.00 36.22 2.45
3123 3263 2.439507 ACACAGTGGATGGGGTATGATC 59.560 50.000 5.31 0.00 36.22 2.92
3135 3275 3.541632 GGGTATGATCACGTCCAAACAT 58.458 45.455 0.00 0.00 0.00 2.71
3136 3276 3.312421 GGGTATGATCACGTCCAAACATG 59.688 47.826 0.00 0.00 0.00 3.21
3154 3295 7.064490 CCAAACATGGCTGGTAAATATCAAAAC 59.936 37.037 7.08 0.00 0.00 2.43
3183 3328 2.496871 CCAACCAAGCAAGCATATCCAA 59.503 45.455 0.00 0.00 0.00 3.53
3210 3355 4.799678 ACAGTGACAGTAGATTCTTGTCG 58.200 43.478 11.86 3.49 32.68 4.35
3223 3368 0.733909 CTTGTCGCGTGATCAGCTGA 60.734 55.000 20.79 20.79 0.00 4.26
3230 3375 1.792993 GCGTGATCAGCTGAAATGCAC 60.793 52.381 28.75 25.40 34.99 4.57
3252 3397 4.638421 ACCGCTAAGTTATTGCAAATGCTA 59.362 37.500 1.71 0.00 42.66 3.49
3255 3400 6.697019 CCGCTAAGTTATTGCAAATGCTAAAT 59.303 34.615 1.71 0.00 42.66 1.40
3274 3420 7.649705 TGCTAAATATTTGCGTGTTTTCTGAAA 59.350 29.630 11.05 0.00 0.00 2.69
3296 3442 2.052468 TGTGAGGATGGCATGAGCTAT 58.948 47.619 3.81 0.00 45.42 2.97
3303 3449 2.336945 TGGCATGAGCTATCAACAGG 57.663 50.000 0.00 0.00 39.39 4.00
3304 3450 1.134007 TGGCATGAGCTATCAACAGGG 60.134 52.381 0.00 0.00 39.39 4.45
3305 3451 1.133976 GGCATGAGCTATCAACAGGGT 60.134 52.381 0.00 0.00 39.39 4.34
3306 3452 2.648059 GCATGAGCTATCAACAGGGTT 58.352 47.619 0.00 0.00 39.39 4.11
3307 3453 3.433598 GGCATGAGCTATCAACAGGGTTA 60.434 47.826 0.00 0.00 39.39 2.85
3308 3454 3.561725 GCATGAGCTATCAACAGGGTTAC 59.438 47.826 0.00 0.00 39.39 2.50
3474 3620 0.179108 GCTACGCTACAACCTCTGGG 60.179 60.000 0.00 0.00 38.88 4.45
3475 3621 0.460311 CTACGCTACAACCTCTGGGG 59.540 60.000 0.00 0.00 41.89 4.96
3478 3624 2.301738 GCTACAACCTCTGGGGGCT 61.302 63.158 0.00 0.00 40.03 5.19
3500 3646 1.523758 AAGATTGCTCCGTGGTGAAC 58.476 50.000 0.00 0.00 0.00 3.18
3546 3692 1.851658 GTGCAACAACATCCAACCAC 58.148 50.000 0.00 0.00 36.32 4.16
3547 3693 1.408702 GTGCAACAACATCCAACCACT 59.591 47.619 0.00 0.00 36.32 4.00
3548 3694 1.408340 TGCAACAACATCCAACCACTG 59.592 47.619 0.00 0.00 0.00 3.66
3549 3695 5.889511 GTGCAACAACATCCAACCACTGG 62.890 52.174 0.00 0.00 41.62 4.00
3550 3696 2.031120 CAACAACATCCAACCACTGGT 58.969 47.619 0.00 0.00 46.51 4.00
3551 3697 1.691196 ACAACATCCAACCACTGGTG 58.309 50.000 0.00 0.00 46.51 4.17
3562 3708 2.049435 CACTGGTGGAAAAAGGGCC 58.951 57.895 0.00 0.00 0.00 5.80
3563 3709 0.469892 CACTGGTGGAAAAAGGGCCT 60.470 55.000 0.00 0.00 0.00 5.19
3564 3710 0.264657 ACTGGTGGAAAAAGGGCCTT 59.735 50.000 14.48 14.48 0.00 4.35
3565 3711 1.343985 ACTGGTGGAAAAAGGGCCTTT 60.344 47.619 25.68 25.68 34.94 3.11
3566 3712 1.070601 CTGGTGGAAAAAGGGCCTTTG 59.929 52.381 31.06 12.80 33.64 2.77
3567 3713 0.396435 GGTGGAAAAAGGGCCTTTGG 59.604 55.000 31.06 0.00 33.64 3.28
3568 3714 1.128200 GTGGAAAAAGGGCCTTTGGT 58.872 50.000 31.06 21.81 33.64 3.67
3569 3715 1.070134 GTGGAAAAAGGGCCTTTGGTC 59.930 52.381 31.06 27.31 33.64 4.02
3570 3716 0.317160 GGAAAAAGGGCCTTTGGTCG 59.683 55.000 31.06 0.00 33.64 4.79
3571 3717 0.319555 GAAAAAGGGCCTTTGGTCGC 60.320 55.000 31.06 14.98 33.64 5.19
3572 3718 2.082629 AAAAAGGGCCTTTGGTCGCG 62.083 55.000 31.06 0.00 33.64 5.87
3576 3722 3.733960 GGCCTTTGGTCGCGGTTC 61.734 66.667 6.13 0.00 0.00 3.62
3577 3723 4.084888 GCCTTTGGTCGCGGTTCG 62.085 66.667 6.13 0.00 40.15 3.95
3588 3734 2.953821 CGGTTCGCAACTGCCATT 59.046 55.556 0.00 0.00 37.91 3.16
3589 3735 2.167161 CGGTTCGCAACTGCCATTA 58.833 52.632 0.00 0.00 37.91 1.90
3590 3736 0.096976 CGGTTCGCAACTGCCATTAG 59.903 55.000 0.00 0.00 37.91 1.73
3591 3737 1.165270 GGTTCGCAACTGCCATTAGT 58.835 50.000 0.00 0.00 37.91 2.24
3592 3738 1.130561 GGTTCGCAACTGCCATTAGTC 59.869 52.381 0.00 0.00 37.91 2.59
3593 3739 1.075542 TTCGCAACTGCCATTAGTCG 58.924 50.000 0.00 0.00 37.91 4.18
3594 3740 1.060937 CGCAACTGCCATTAGTCGC 59.939 57.895 0.00 0.00 37.91 5.19
3595 3741 1.060937 GCAACTGCCATTAGTCGCG 59.939 57.895 0.00 0.00 34.31 5.87
3596 3742 1.715585 CAACTGCCATTAGTCGCGG 59.284 57.895 6.13 0.00 37.39 6.46
3597 3743 1.019278 CAACTGCCATTAGTCGCGGT 61.019 55.000 6.13 0.00 46.47 5.68
3598 3744 1.295423 ACTGCCATTAGTCGCGGTT 59.705 52.632 6.13 0.00 41.86 4.44
3599 3745 1.019278 ACTGCCATTAGTCGCGGTTG 61.019 55.000 6.13 0.00 41.86 3.77
3600 3746 2.309764 CTGCCATTAGTCGCGGTTGC 62.310 60.000 6.13 0.28 37.91 4.17
3629 3775 4.781959 CGACCGGGCGCGACTAAA 62.782 66.667 21.25 0.00 0.00 1.85
3630 3776 2.884207 GACCGGGCGCGACTAAAG 60.884 66.667 26.13 9.07 0.00 1.85
3631 3777 4.446413 ACCGGGCGCGACTAAAGG 62.446 66.667 26.13 13.40 0.00 3.11
3652 3798 2.666812 CCCCCTTTAGTCGCGGTT 59.333 61.111 6.13 0.00 0.00 4.44
3653 3799 1.743995 CCCCCTTTAGTCGCGGTTG 60.744 63.158 6.13 0.00 0.00 3.77
3654 3800 2.396157 CCCCTTTAGTCGCGGTTGC 61.396 63.158 6.13 0.00 37.91 4.17
3655 3801 1.375523 CCCTTTAGTCGCGGTTGCT 60.376 57.895 6.13 2.31 39.65 3.91
3656 3802 0.953960 CCCTTTAGTCGCGGTTGCTT 60.954 55.000 6.13 0.00 39.65 3.91
3657 3803 1.673626 CCCTTTAGTCGCGGTTGCTTA 60.674 52.381 6.13 0.00 39.65 3.09
3658 3804 2.070783 CCTTTAGTCGCGGTTGCTTAA 58.929 47.619 6.13 0.00 39.65 1.85
3659 3805 2.093783 CCTTTAGTCGCGGTTGCTTAAG 59.906 50.000 6.13 9.06 39.65 1.85
3660 3806 2.728690 TTAGTCGCGGTTGCTTAAGA 57.271 45.000 6.13 0.00 39.65 2.10
3661 3807 2.728690 TAGTCGCGGTTGCTTAAGAA 57.271 45.000 6.13 0.00 39.65 2.52
3662 3808 1.145803 AGTCGCGGTTGCTTAAGAAC 58.854 50.000 6.13 7.82 39.65 3.01
3663 3809 0.165295 GTCGCGGTTGCTTAAGAACC 59.835 55.000 19.09 19.09 39.71 3.62
3667 3813 2.535588 GGTTGCTTAAGAACCGCGA 58.464 52.632 8.23 0.00 33.85 5.87
3668 3814 0.165295 GGTTGCTTAAGAACCGCGAC 59.835 55.000 8.23 0.93 37.34 5.19
3669 3815 1.145803 GTTGCTTAAGAACCGCGACT 58.854 50.000 8.23 0.30 35.64 4.18
3670 3816 2.331194 GTTGCTTAAGAACCGCGACTA 58.669 47.619 8.23 0.00 35.64 2.59
3671 3817 2.728690 TGCTTAAGAACCGCGACTAA 57.271 45.000 8.23 0.00 0.00 2.24
3672 3818 3.029320 TGCTTAAGAACCGCGACTAAA 57.971 42.857 8.23 0.00 0.00 1.85
3673 3819 2.991190 TGCTTAAGAACCGCGACTAAAG 59.009 45.455 8.23 4.60 0.00 1.85
3674 3820 2.347755 GCTTAAGAACCGCGACTAAAGG 59.652 50.000 8.23 0.00 0.00 3.11
3675 3821 2.000429 TAAGAACCGCGACTAAAGGC 58.000 50.000 8.23 0.00 0.00 4.35
3676 3822 0.672711 AAGAACCGCGACTAAAGGCC 60.673 55.000 8.23 0.00 0.00 5.19
3677 3823 2.046604 AACCGCGACTAAAGGCCC 60.047 61.111 8.23 0.00 0.00 5.80
3678 3824 3.945304 AACCGCGACTAAAGGCCCG 62.945 63.158 8.23 0.00 0.00 6.13
3679 3825 4.446413 CCGCGACTAAAGGCCCGT 62.446 66.667 8.23 0.00 0.00 5.28
3680 3826 2.884207 CGCGACTAAAGGCCCGTC 60.884 66.667 0.00 0.02 0.00 4.79
3681 3827 2.510918 GCGACTAAAGGCCCGTCC 60.511 66.667 0.00 0.00 0.00 4.79
3682 3828 2.975536 CGACTAAAGGCCCGTCCA 59.024 61.111 0.00 0.00 37.29 4.02
3683 3829 1.447314 CGACTAAAGGCCCGTCCAC 60.447 63.158 0.00 0.00 37.29 4.02
3684 3830 1.447314 GACTAAAGGCCCGTCCACG 60.447 63.158 0.00 0.00 37.29 4.94
3685 3831 2.163601 GACTAAAGGCCCGTCCACGT 62.164 60.000 0.00 0.00 37.29 4.49
3686 3832 1.740296 CTAAAGGCCCGTCCACGTG 60.740 63.158 9.08 9.08 37.29 4.49
3687 3833 3.242897 TAAAGGCCCGTCCACGTGG 62.243 63.158 29.26 29.26 37.29 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 3.657448 ATTCGTCCGCGTGCATGGA 62.657 57.895 8.27 4.56 39.49 3.41
68 70 1.815421 GTATGTGGAGCACCGCTGG 60.815 63.158 14.99 0.00 45.89 4.85
78 80 1.327460 GTACGCTACGTCGTATGTGGA 59.673 52.381 11.95 7.97 45.16 4.02
174 180 1.609555 ACTGCAGCTACTCCGTATAGC 59.390 52.381 15.27 2.47 44.56 2.97
175 181 3.315470 TGAACTGCAGCTACTCCGTATAG 59.685 47.826 15.27 0.00 0.00 1.31
176 182 3.284617 TGAACTGCAGCTACTCCGTATA 58.715 45.455 15.27 0.00 0.00 1.47
177 183 2.100197 TGAACTGCAGCTACTCCGTAT 58.900 47.619 15.27 0.00 0.00 3.06
178 184 1.541379 TGAACTGCAGCTACTCCGTA 58.459 50.000 15.27 0.00 0.00 4.02
217 224 1.216175 CTCACCAACCCATCCATCCAT 59.784 52.381 0.00 0.00 0.00 3.41
218 225 0.625316 CTCACCAACCCATCCATCCA 59.375 55.000 0.00 0.00 0.00 3.41
219 226 0.753111 GCTCACCAACCCATCCATCC 60.753 60.000 0.00 0.00 0.00 3.51
220 227 0.034186 TGCTCACCAACCCATCCATC 60.034 55.000 0.00 0.00 0.00 3.51
221 228 0.409092 TTGCTCACCAACCCATCCAT 59.591 50.000 0.00 0.00 0.00 3.41
222 229 0.539438 GTTGCTCACCAACCCATCCA 60.539 55.000 0.00 0.00 46.44 3.41
223 230 2.267045 GTTGCTCACCAACCCATCC 58.733 57.895 0.00 0.00 46.44 3.51
381 394 2.067013 GTTCGGTTCAGTTCAGTAGCC 58.933 52.381 0.00 0.00 0.00 3.93
421 434 2.968574 AGGAGTAGGCATACACATGAGG 59.031 50.000 11.63 0.00 33.67 3.86
430 443 4.536888 AGCTAGCTAGTAGGAGTAGGCATA 59.463 45.833 17.69 0.00 0.00 3.14
431 444 3.332485 AGCTAGCTAGTAGGAGTAGGCAT 59.668 47.826 17.69 0.00 0.00 4.40
444 457 4.350441 GCCGGCCGAGCTAGCTAG 62.350 72.222 30.73 18.12 0.00 3.42
575 595 3.604667 TTGGCCTGGCACGCAAAG 61.605 61.111 22.05 0.00 0.00 2.77
592 612 3.799366 TGTGTGAGTTCCGTATTTGTGT 58.201 40.909 0.00 0.00 0.00 3.72
593 613 4.804608 TTGTGTGAGTTCCGTATTTGTG 57.195 40.909 0.00 0.00 0.00 3.33
594 614 7.412563 CGATATTTGTGTGAGTTCCGTATTTGT 60.413 37.037 0.00 0.00 0.00 2.83
595 615 6.899771 CGATATTTGTGTGAGTTCCGTATTTG 59.100 38.462 0.00 0.00 0.00 2.32
596 616 6.592607 ACGATATTTGTGTGAGTTCCGTATTT 59.407 34.615 0.00 0.00 0.00 1.40
597 617 6.103997 ACGATATTTGTGTGAGTTCCGTATT 58.896 36.000 0.00 0.00 0.00 1.89
598 618 5.657474 ACGATATTTGTGTGAGTTCCGTAT 58.343 37.500 0.00 0.00 0.00 3.06
599 619 5.063180 ACGATATTTGTGTGAGTTCCGTA 57.937 39.130 0.00 0.00 0.00 4.02
600 620 3.921677 ACGATATTTGTGTGAGTTCCGT 58.078 40.909 0.00 0.00 0.00 4.69
601 621 5.100259 AGTACGATATTTGTGTGAGTTCCG 58.900 41.667 0.00 0.00 0.00 4.30
602 622 7.256286 AGTAGTACGATATTTGTGTGAGTTCC 58.744 38.462 0.00 0.00 0.00 3.62
603 623 9.219497 GTAGTAGTACGATATTTGTGTGAGTTC 57.781 37.037 0.00 0.00 0.00 3.01
604 624 8.954350 AGTAGTAGTACGATATTTGTGTGAGTT 58.046 33.333 2.04 0.00 33.97 3.01
605 625 8.503458 AGTAGTAGTACGATATTTGTGTGAGT 57.497 34.615 2.04 0.00 33.97 3.41
606 626 8.068977 GGAGTAGTAGTACGATATTTGTGTGAG 58.931 40.741 2.04 0.00 33.97 3.51
607 627 7.772292 AGGAGTAGTAGTACGATATTTGTGTGA 59.228 37.037 2.04 0.00 33.97 3.58
608 628 7.928103 AGGAGTAGTAGTACGATATTTGTGTG 58.072 38.462 2.04 0.00 33.97 3.82
609 629 9.050601 GTAGGAGTAGTAGTACGATATTTGTGT 57.949 37.037 2.04 0.00 33.97 3.72
636 656 4.228097 GCTAGCGCGACGGACGTA 62.228 66.667 12.10 0.00 44.60 3.57
639 659 4.493747 AAGGCTAGCGCGACGGAC 62.494 66.667 12.10 0.00 36.88 4.79
653 676 1.380380 GGGCATCCAAGGACCAAGG 60.380 63.158 0.00 0.00 0.00 3.61
654 677 1.380380 GGGGCATCCAAGGACCAAG 60.380 63.158 0.00 0.00 35.00 3.61
655 678 1.856873 AGGGGCATCCAAGGACCAA 60.857 57.895 0.00 0.00 38.24 3.67
656 679 2.204291 AGGGGCATCCAAGGACCA 60.204 61.111 0.00 0.00 38.24 4.02
657 680 2.597903 GAGGGGCATCCAAGGACC 59.402 66.667 0.00 0.00 38.24 4.46
658 681 2.308722 TGGAGGGGCATCCAAGGAC 61.309 63.158 8.12 0.00 46.45 3.85
659 682 2.127065 TGGAGGGGCATCCAAGGA 59.873 61.111 8.12 0.00 46.45 3.36
678 701 0.173255 GGTAACTGCGGGCGTTAGTA 59.827 55.000 0.00 0.00 0.00 1.82
700 723 2.159212 TCGCTTGGCCAAATTGATGATG 60.159 45.455 20.91 5.38 0.00 3.07
720 743 1.081840 GAAGCAGTGCAGGCGTTTC 60.082 57.895 19.20 7.33 36.08 2.78
723 746 2.358003 GAGAAGCAGTGCAGGCGT 60.358 61.111 19.20 1.67 36.08 5.68
724 747 2.047465 AGAGAAGCAGTGCAGGCG 60.047 61.111 19.20 0.00 36.08 5.52
727 750 0.458197 CCGAGAGAGAAGCAGTGCAG 60.458 60.000 19.20 0.00 0.00 4.41
728 751 1.588597 CCGAGAGAGAAGCAGTGCA 59.411 57.895 19.20 0.00 0.00 4.57
729 752 1.809209 GCCGAGAGAGAAGCAGTGC 60.809 63.158 7.13 7.13 0.00 4.40
730 753 0.735632 GTGCCGAGAGAGAAGCAGTG 60.736 60.000 0.00 0.00 35.56 3.66
763 806 1.667236 TGGCGTTGATGATGATGGTC 58.333 50.000 0.00 0.00 0.00 4.02
765 808 4.834357 TTAATGGCGTTGATGATGATGG 57.166 40.909 1.27 0.00 0.00 3.51
788 832 4.201970 GGGCGATCGGTTCAATTCAATTTA 60.202 41.667 18.30 0.00 0.00 1.40
793 837 0.251916 AGGGCGATCGGTTCAATTCA 59.748 50.000 18.30 0.00 0.00 2.57
802 846 2.644555 ATCGAAACCAGGGCGATCGG 62.645 60.000 18.30 1.63 40.35 4.18
837 884 3.237741 GGAGGGGAGCTCCATCGG 61.238 72.222 33.29 0.00 46.66 4.18
960 1007 1.746220 CTTTGGTTCGGGTGTTGTTGA 59.254 47.619 0.00 0.00 0.00 3.18
1035 1082 1.214589 GGCGAGCGAAAGGTACAGA 59.785 57.895 0.00 0.00 45.11 3.41
1441 1488 3.053291 GATGGCGCGGTGGAACAA 61.053 61.111 8.83 0.00 44.16 2.83
1560 1607 1.810853 CATCTGGTGCGCGATCACA 60.811 57.895 12.10 1.03 38.66 3.58
1844 1903 1.371267 CCGACGAAGCTGTTCACGA 60.371 57.895 0.00 0.00 35.49 4.35
2960 3092 0.250640 ACAGGGCAGTTGCAGAAGAG 60.251 55.000 6.43 0.00 44.36 2.85
2961 3093 1.055849 TACAGGGCAGTTGCAGAAGA 58.944 50.000 6.43 0.00 44.36 2.87
2962 3094 1.808945 CTTACAGGGCAGTTGCAGAAG 59.191 52.381 6.43 0.00 44.36 2.85
3020 3155 8.928270 ATAGAGACATTTGTTTCTTAGTACCG 57.072 34.615 8.80 0.00 39.73 4.02
3067 3202 7.175119 CAGGTACTACTAGTAGCATTATGCTCA 59.825 40.741 26.54 9.19 46.10 4.26
3113 3253 2.285977 GTTTGGACGTGATCATACCCC 58.714 52.381 0.00 0.00 0.00 4.95
3120 3260 1.131126 CAGCCATGTTTGGACGTGATC 59.869 52.381 0.00 0.00 46.92 2.92
3122 3262 0.888736 CCAGCCATGTTTGGACGTGA 60.889 55.000 0.00 0.00 46.92 4.35
3123 3263 1.172180 ACCAGCCATGTTTGGACGTG 61.172 55.000 17.03 0.00 46.92 4.49
3135 3275 6.849085 ACATGTTTTGATATTTACCAGCCA 57.151 33.333 0.00 0.00 0.00 4.75
3136 3276 7.700656 GTGTACATGTTTTGATATTTACCAGCC 59.299 37.037 2.30 0.00 0.00 4.85
3154 3295 2.607771 GCTTGCTTGGTTGGTGTACATG 60.608 50.000 0.00 0.00 0.00 3.21
3183 3328 6.717540 ACAAGAATCTACTGTCACTGTAGACT 59.282 38.462 22.78 14.84 43.75 3.24
3210 3355 0.448990 TGCATTTCAGCTGATCACGC 59.551 50.000 19.04 17.54 34.99 5.34
3223 3368 3.192422 TGCAATAACTTAGCGGTGCATTT 59.808 39.130 0.00 0.00 37.09 2.32
3230 3375 4.032703 AGCATTTGCAATAACTTAGCGG 57.967 40.909 0.00 0.00 45.16 5.52
3252 3397 8.825745 ACAATTTCAGAAAACACGCAAATATTT 58.174 25.926 0.00 0.00 0.00 1.40
3255 3400 6.975197 TCACAATTTCAGAAAACACGCAAATA 59.025 30.769 0.00 0.00 0.00 1.40
3274 3420 1.214673 AGCTCATGCCATCCTCACAAT 59.785 47.619 0.00 0.00 40.80 2.71
3320 3466 2.183555 GCTTTGGCCATGCTCAGC 59.816 61.111 20.04 12.99 0.00 4.26
3468 3614 1.760192 CAATCTTTGAGCCCCCAGAG 58.240 55.000 0.00 0.00 0.00 3.35
3474 3620 0.678048 ACGGAGCAATCTTTGAGCCC 60.678 55.000 0.00 0.00 0.00 5.19
3475 3621 0.449388 CACGGAGCAATCTTTGAGCC 59.551 55.000 0.00 0.00 0.00 4.70
3478 3624 1.071542 TCACCACGGAGCAATCTTTGA 59.928 47.619 0.00 0.00 0.00 2.69
3520 3666 4.241590 TGGATGTTGTTGCACAAAGATC 57.758 40.909 8.47 8.47 40.15 2.75
3544 3690 0.469892 AGGCCCTTTTTCCACCAGTG 60.470 55.000 0.00 0.00 0.00 3.66
3545 3691 0.264657 AAGGCCCTTTTTCCACCAGT 59.735 50.000 0.00 0.00 0.00 4.00
3546 3692 1.070601 CAAAGGCCCTTTTTCCACCAG 59.929 52.381 5.84 0.00 30.60 4.00
3547 3693 1.127343 CAAAGGCCCTTTTTCCACCA 58.873 50.000 5.84 0.00 30.60 4.17
3548 3694 0.396435 CCAAAGGCCCTTTTTCCACC 59.604 55.000 5.84 0.00 30.60 4.61
3549 3695 1.070134 GACCAAAGGCCCTTTTTCCAC 59.930 52.381 5.84 0.00 30.60 4.02
3550 3696 1.419381 GACCAAAGGCCCTTTTTCCA 58.581 50.000 5.84 0.00 30.60 3.53
3551 3697 0.317160 CGACCAAAGGCCCTTTTTCC 59.683 55.000 5.84 0.00 30.60 3.13
3552 3698 0.319555 GCGACCAAAGGCCCTTTTTC 60.320 55.000 5.84 5.31 30.60 2.29
3553 3699 1.745890 GCGACCAAAGGCCCTTTTT 59.254 52.632 5.84 0.00 30.60 1.94
3554 3700 2.561037 CGCGACCAAAGGCCCTTTT 61.561 57.895 5.84 0.00 30.60 2.27
3555 3701 2.983592 CGCGACCAAAGGCCCTTT 60.984 61.111 1.93 1.93 33.58 3.11
3559 3705 3.733960 GAACCGCGACCAAAGGCC 61.734 66.667 8.23 0.00 0.00 5.19
3560 3706 4.084888 CGAACCGCGACCAAAGGC 62.085 66.667 8.23 0.00 44.57 4.35
3561 3707 4.084888 GCGAACCGCGACCAAAGG 62.085 66.667 8.23 0.00 44.55 3.11
3571 3717 0.096976 CTAATGGCAGTTGCGAACCG 59.903 55.000 0.00 0.00 43.26 4.44
3572 3718 1.130561 GACTAATGGCAGTTGCGAACC 59.869 52.381 0.00 0.00 43.26 3.62
3573 3719 1.201921 CGACTAATGGCAGTTGCGAAC 60.202 52.381 0.00 0.00 43.26 3.95
3574 3720 1.075542 CGACTAATGGCAGTTGCGAA 58.924 50.000 0.00 0.00 43.26 4.70
3575 3721 1.358725 GCGACTAATGGCAGTTGCGA 61.359 55.000 14.22 0.00 44.02 5.10
3576 3722 1.060937 GCGACTAATGGCAGTTGCG 59.939 57.895 0.00 0.70 44.02 4.85
3578 3724 1.019278 ACCGCGACTAATGGCAGTTG 61.019 55.000 8.23 0.00 33.66 3.16
3579 3725 0.321298 AACCGCGACTAATGGCAGTT 60.321 50.000 8.23 0.00 0.00 3.16
3580 3726 1.019278 CAACCGCGACTAATGGCAGT 61.019 55.000 8.23 0.00 0.00 4.40
3581 3727 1.715585 CAACCGCGACTAATGGCAG 59.284 57.895 8.23 0.00 0.00 4.85
3582 3728 2.395360 GCAACCGCGACTAATGGCA 61.395 57.895 8.23 0.00 0.00 4.92
3583 3729 2.403586 GCAACCGCGACTAATGGC 59.596 61.111 8.23 0.00 0.00 4.40
3612 3758 4.781959 TTTAGTCGCGCCCGGTCG 62.782 66.667 0.00 0.00 34.56 4.79
3613 3759 2.884207 CTTTAGTCGCGCCCGGTC 60.884 66.667 0.00 0.00 34.56 4.79
3614 3760 4.446413 CCTTTAGTCGCGCCCGGT 62.446 66.667 0.00 0.00 34.56 5.28
3635 3781 1.743995 CAACCGCGACTAAAGGGGG 60.744 63.158 8.23 0.00 44.84 5.40
3636 3782 2.396157 GCAACCGCGACTAAAGGGG 61.396 63.158 8.23 0.00 45.85 4.79
3637 3783 0.953960 AAGCAACCGCGACTAAAGGG 60.954 55.000 8.23 0.00 45.49 3.95
3638 3784 1.717194 TAAGCAACCGCGACTAAAGG 58.283 50.000 8.23 0.00 45.49 3.11
3639 3785 2.991190 TCTTAAGCAACCGCGACTAAAG 59.009 45.455 8.23 1.88 45.49 1.85
3640 3786 3.029320 TCTTAAGCAACCGCGACTAAA 57.971 42.857 8.23 0.00 45.49 1.85
3641 3787 2.728690 TCTTAAGCAACCGCGACTAA 57.271 45.000 8.23 0.00 45.49 2.24
3642 3788 2.331194 GTTCTTAAGCAACCGCGACTA 58.669 47.619 8.23 0.00 45.49 2.59
3643 3789 1.145803 GTTCTTAAGCAACCGCGACT 58.854 50.000 8.23 0.00 45.49 4.18
3644 3790 0.165295 GGTTCTTAAGCAACCGCGAC 59.835 55.000 8.23 0.00 45.49 5.19
3645 3791 2.535588 GGTTCTTAAGCAACCGCGA 58.464 52.632 8.23 0.00 45.49 5.87
3649 3795 0.165295 GTCGCGGTTCTTAAGCAACC 59.835 55.000 19.09 19.09 40.12 3.77
3650 3796 1.145803 AGTCGCGGTTCTTAAGCAAC 58.854 50.000 6.13 3.71 0.00 4.17
3651 3797 2.728690 TAGTCGCGGTTCTTAAGCAA 57.271 45.000 6.13 0.00 0.00 3.91
3652 3798 2.728690 TTAGTCGCGGTTCTTAAGCA 57.271 45.000 6.13 0.00 0.00 3.91
3653 3799 2.347755 CCTTTAGTCGCGGTTCTTAAGC 59.652 50.000 6.13 0.00 0.00 3.09
3654 3800 2.347755 GCCTTTAGTCGCGGTTCTTAAG 59.652 50.000 6.13 11.57 0.00 1.85
3655 3801 2.340337 GCCTTTAGTCGCGGTTCTTAA 58.660 47.619 6.13 2.46 0.00 1.85
3656 3802 1.404583 GGCCTTTAGTCGCGGTTCTTA 60.405 52.381 6.13 0.00 0.00 2.10
3657 3803 0.672711 GGCCTTTAGTCGCGGTTCTT 60.673 55.000 6.13 0.00 0.00 2.52
3658 3804 1.079336 GGCCTTTAGTCGCGGTTCT 60.079 57.895 6.13 5.42 0.00 3.01
3659 3805 2.104859 GGGCCTTTAGTCGCGGTTC 61.105 63.158 6.13 0.00 0.00 3.62
3660 3806 2.046604 GGGCCTTTAGTCGCGGTT 60.047 61.111 6.13 0.00 0.00 4.44
3661 3807 4.446413 CGGGCCTTTAGTCGCGGT 62.446 66.667 6.13 0.00 35.43 5.68
3662 3808 4.446413 ACGGGCCTTTAGTCGCGG 62.446 66.667 6.13 0.00 41.92 6.46
3663 3809 2.884207 GACGGGCCTTTAGTCGCG 60.884 66.667 0.84 0.00 43.02 5.87
3664 3810 2.510918 GGACGGGCCTTTAGTCGC 60.511 66.667 0.84 0.00 35.87 5.19
3665 3811 1.447314 GTGGACGGGCCTTTAGTCG 60.447 63.158 0.84 0.00 37.63 4.18
3666 3812 1.447314 CGTGGACGGGCCTTTAGTC 60.447 63.158 0.84 7.66 37.63 2.59
3667 3813 2.212110 ACGTGGACGGGCCTTTAGT 61.212 57.895 0.84 0.00 44.95 2.24
3668 3814 1.740296 CACGTGGACGGGCCTTTAG 60.740 63.158 7.95 0.00 44.95 1.85
3669 3815 2.344500 CACGTGGACGGGCCTTTA 59.656 61.111 7.95 0.00 44.95 1.85
3670 3816 4.636435 CCACGTGGACGGGCCTTT 62.636 66.667 31.31 0.00 42.34 3.11


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

AutoCloner maintained by Alex Coulton.