Multiple sequence alignment - TraesCS1A01G293500

Loading Multiple Alignment...

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 TraesCS1A01G293500 chr1A 100.000 4314 0 0 1 4314 488624316 488620003 0.000000e+00 7967
1 TraesCS1A01G293500 chr1A 96.065 2719 95 4 692 3400 525042600 525039884 0.000000e+00 4418
2 TraesCS1A01G293500 chr1A 98.656 1860 23 2 692 2550 590651066 590652924 0.000000e+00 3295
3 TraesCS1A01G293500 chr1A 97.685 1771 36 3 2544 4314 590671440 590673205 0.000000e+00 3038
4 TraesCS1A01G293500 chr1A 99.630 541 2 0 1 541 590650534 590651074 0.000000e+00 989
5 TraesCS1A01G293500 chr1A 97.782 541 12 0 1 541 525043132 525042592 0.000000e+00 933
6 TraesCS1A01G293500 chr1A 84.321 759 102 10 3559 4314 525031290 525030546 0.000000e+00 726
7 TraesCS1A01G293500 chr1A 88.053 226 27 0 3820 4045 525031087 525030862 7.110000e-68 268
8 TraesCS1A01G293500 chr1A 94.891 137 6 1 4179 4314 590649614 590649478 3.380000e-51 213
9 TraesCS1A01G293500 chr1A 91.912 136 11 0 4179 4314 525043987 525044122 1.580000e-44 191
10 TraesCS1A01G293500 chr7A 97.985 3623 68 3 692 4314 92421938 92425555 0.000000e+00 6281
11 TraesCS1A01G293500 chr7A 98.706 541 7 0 1 541 92421406 92421946 0.000000e+00 961
12 TraesCS1A01G293500 chr7A 100.000 155 0 0 541 695 226759194 226759040 1.960000e-73 287
13 TraesCS1A01G293500 chr7A 99.338 151 1 0 542 692 219852982 219852832 1.530000e-69 274
14 TraesCS1A01G293500 chr7A 92.701 137 9 1 4179 4314 92420486 92420350 3.400000e-46 196
15 TraesCS1A01G293500 chr3A 92.301 3234 184 29 692 3920 732977112 732973939 0.000000e+00 4532
16 TraesCS1A01G293500 chr3A 93.939 825 42 2 3490 4314 26152562 26151746 0.000000e+00 1240
17 TraesCS1A01G293500 chr3A 96.104 539 21 0 3 541 732977642 732977104 0.000000e+00 880
18 TraesCS1A01G293500 chr3A 91.515 165 6 5 3351 3508 26153836 26153673 2.020000e-53 220
19 TraesCS1A01G293500 chr5A 98.310 1716 28 1 1494 3209 41388046 41389760 0.000000e+00 3007
20 TraesCS1A01G293500 chr5A 93.611 1127 55 3 3204 4314 41389959 41391084 0.000000e+00 1666
21 TraesCS1A01G293500 chr5A 93.611 1127 55 3 3204 4314 41392119 41393244 0.000000e+00 1666
22 TraesCS1A01G293500 chr5A 97.229 794 20 1 2416 3209 41391129 41391920 0.000000e+00 1343
23 TraesCS1A01G293500 chr5A 99.074 540 5 0 2 541 41382584 41383123 0.000000e+00 970
24 TraesCS1A01G293500 chr4A 95.508 1781 62 5 692 2471 723795928 723794165 0.000000e+00 2830
25 TraesCS1A01G293500 chr4A 96.111 540 20 1 3 541 723796459 723795920 0.000000e+00 880
26 TraesCS1A01G293500 chr2A 92.503 1894 123 5 692 2581 88741182 88739304 0.000000e+00 2693
27 TraesCS1A01G293500 chr2A 83.448 580 74 16 2803 3370 88732329 88731760 1.780000e-143 520
28 TraesCS1A01G293500 chr2A 93.367 196 12 1 4120 4314 4908360 4908165 5.460000e-74 289
29 TraesCS1A01G293500 chr2A 100.000 152 0 0 542 693 118674024 118674175 9.130000e-72 281
30 TraesCS1A01G293500 chr6B 92.733 1500 87 12 1734 3226 351230068 351228584 0.000000e+00 2146
31 TraesCS1A01G293500 chr6B 97.036 1046 29 2 692 1736 351231417 351230373 0.000000e+00 1759
32 TraesCS1A01G293500 chr6B 84.844 1313 191 6 692 1998 707504305 707502995 0.000000e+00 1315
33 TraesCS1A01G293500 chr6B 96.455 536 18 1 6 541 351231943 351231409 0.000000e+00 883
34 TraesCS1A01G293500 chr6B 81.766 872 119 26 3061 3911 351228806 351227954 0.000000e+00 693
35 TraesCS1A01G293500 chr6B 99.342 152 1 0 542 693 164031989 164032140 4.250000e-70 276
36 TraesCS1A01G293500 chr6B 89.899 198 19 1 3830 4026 351228152 351227955 1.990000e-63 254
37 TraesCS1A01G293500 chr6B 84.211 247 37 2 3724 3969 351228199 351227954 5.580000e-59 239
38 TraesCS1A01G293500 chr2B 97.251 1164 31 1 694 1856 748163062 748164225 0.000000e+00 1971
39 TraesCS1A01G293500 chr2B 97.032 539 16 0 3 541 748162530 748163068 0.000000e+00 907
40 TraesCS1A01G293500 chr4B 96.475 539 19 0 3 541 562693716 562693178 0.000000e+00 891
41 TraesCS1A01G293500 chr4B 92.281 583 36 5 2594 3170 562692280 562691701 0.000000e+00 819
42 TraesCS1A01G293500 chr4B 86.921 604 67 5 3082 3676 562691897 562691297 0.000000e+00 667
43 TraesCS1A01G293500 chr4B 90.870 230 20 1 4085 4313 562686702 562686473 1.510000e-79 307
44 TraesCS1A01G293500 chr4B 99.342 152 1 0 540 691 189153187 189153338 4.250000e-70 276
45 TraesCS1A01G293500 chr5D 84.307 822 96 21 2670 3474 228504036 228504841 0.000000e+00 773
46 TraesCS1A01G293500 chr6A 99.351 154 1 0 541 694 600302201 600302048 3.290000e-71 279
47 TraesCS1A01G293500 chr3B 99.346 153 1 0 542 694 100968457 100968305 1.180000e-70 278
48 TraesCS1A01G293500 chr3B 98.693 153 2 0 539 691 817065039 817065191 5.500000e-69 272
49 TraesCS1A01G293500 chr4D 99.333 150 1 0 542 691 498575152 498575301 5.500000e-69 272


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 TraesCS1A01G293500 chr1A 488620003 488624316 4313 True 7967.000000 7967 100.000000 1 4314 1 chr1A.!!$R1 4313
1 TraesCS1A01G293500 chr1A 590671440 590673205 1765 False 3038.000000 3038 97.685000 2544 4314 1 chr1A.!!$F2 1770
2 TraesCS1A01G293500 chr1A 525039884 525043132 3248 True 2675.500000 4418 96.923500 1 3400 2 chr1A.!!$R4 3399
3 TraesCS1A01G293500 chr1A 590650534 590652924 2390 False 2142.000000 3295 99.143000 1 2550 2 chr1A.!!$F3 2549
4 TraesCS1A01G293500 chr1A 525030546 525031290 744 True 497.000000 726 86.187000 3559 4314 2 chr1A.!!$R3 755
5 TraesCS1A01G293500 chr7A 92421406 92425555 4149 False 3621.000000 6281 98.345500 1 4314 2 chr7A.!!$F1 4313
6 TraesCS1A01G293500 chr3A 732973939 732977642 3703 True 2706.000000 4532 94.202500 3 3920 2 chr3A.!!$R2 3917
7 TraesCS1A01G293500 chr3A 26151746 26153836 2090 True 730.000000 1240 92.727000 3351 4314 2 chr3A.!!$R1 963
8 TraesCS1A01G293500 chr5A 41388046 41393244 5198 False 1920.500000 3007 95.690250 1494 4314 4 chr5A.!!$F2 2820
9 TraesCS1A01G293500 chr5A 41382584 41383123 539 False 970.000000 970 99.074000 2 541 1 chr5A.!!$F1 539
10 TraesCS1A01G293500 chr4A 723794165 723796459 2294 True 1855.000000 2830 95.809500 3 2471 2 chr4A.!!$R1 2468
11 TraesCS1A01G293500 chr2A 88739304 88741182 1878 True 2693.000000 2693 92.503000 692 2581 1 chr2A.!!$R3 1889
12 TraesCS1A01G293500 chr2A 88731760 88732329 569 True 520.000000 520 83.448000 2803 3370 1 chr2A.!!$R2 567
13 TraesCS1A01G293500 chr6B 707502995 707504305 1310 True 1315.000000 1315 84.844000 692 1998 1 chr6B.!!$R1 1306
14 TraesCS1A01G293500 chr6B 351227954 351231943 3989 True 995.666667 2146 90.350000 6 4026 6 chr6B.!!$R2 4020
15 TraesCS1A01G293500 chr2B 748162530 748164225 1695 False 1439.000000 1971 97.141500 3 1856 2 chr2B.!!$F1 1853
16 TraesCS1A01G293500 chr4B 562691297 562693716 2419 True 792.333333 891 91.892333 3 3676 3 chr4B.!!$R2 3673
17 TraesCS1A01G293500 chr5D 228504036 228504841 805 False 773.000000 773 84.307000 2670 3474 1 chr5D.!!$F1 804

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
689 691 0.039074 GTCGTCTGTGTAGCAGCACT 60.039 55.000 11.09 0.0 44.66 4.40 F
690 692 0.241213 TCGTCTGTGTAGCAGCACTC 59.759 55.000 11.09 0.0 44.66 3.51 F
2294 2627 1.816074 TGCAGACCCGAACATTAACC 58.184 50.000 0.00 0.0 0.00 2.85 F
2925 3275 5.014858 CCTTTGGTACTACTACTCACAGGA 58.985 45.833 0.00 0.0 30.24 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2356 2689 2.224066 ACTTGACCCTCGAACAGTCTTG 60.224 50.000 9.68 5.89 0.00 3.02 R
2925 3275 3.433306 TTGTCGGAACTCCCAAATGAT 57.567 42.857 0.00 0.00 34.14 2.45 R
3234 5947 0.038021 TGGCTGCAGTGGAGCATTTA 59.962 50.000 33.67 16.47 44.68 1.40 R
3728 7594 1.654220 CTTCGTGGCCCTGTTTGTG 59.346 57.895 0.00 0.00 0.00 3.33 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
100 101 8.865090 TGCATTTTTAGATGGGACTAAGAAAAA 58.135 29.630 0.00 0.00 32.85 1.94
536 538 7.410120 AGGTTTCAGAAGATGTCAAGTTTTT 57.590 32.000 0.00 0.00 0.00 1.94
559 561 8.922738 TTTTTATCGAAACTACTTAGCAAACG 57.077 30.769 0.00 0.00 0.00 3.60
560 562 7.872163 TTTATCGAAACTACTTAGCAAACGA 57.128 32.000 0.00 0.00 0.00 3.85
561 563 5.758570 ATCGAAACTACTTAGCAAACGAC 57.241 39.130 0.00 0.00 0.00 4.34
562 564 4.609947 TCGAAACTACTTAGCAAACGACA 58.390 39.130 0.00 0.00 0.00 4.35
563 565 4.442073 TCGAAACTACTTAGCAAACGACAC 59.558 41.667 0.00 0.00 0.00 3.67
564 566 4.207635 CGAAACTACTTAGCAAACGACACA 59.792 41.667 0.00 0.00 0.00 3.72
565 567 5.399604 AAACTACTTAGCAAACGACACAC 57.600 39.130 0.00 0.00 0.00 3.82
567 569 0.580104 ACTTAGCAAACGACACACGC 59.420 50.000 0.00 0.00 46.94 5.34
568 570 0.859232 CTTAGCAAACGACACACGCT 59.141 50.000 0.00 0.00 46.94 5.07
569 571 0.579630 TTAGCAAACGACACACGCTG 59.420 50.000 0.00 0.00 46.94 5.18
570 572 1.218875 TAGCAAACGACACACGCTGG 61.219 55.000 0.00 0.00 46.94 4.85
571 573 2.052237 CAAACGACACACGCTGGC 60.052 61.111 0.00 0.00 46.94 4.85
572 574 3.276846 AAACGACACACGCTGGCC 61.277 61.111 0.00 0.00 46.94 5.36
576 578 2.742372 GACACACGCTGGCCGATT 60.742 61.111 0.00 0.00 41.02 3.34
577 579 2.281484 ACACACGCTGGCCGATTT 60.281 55.556 0.00 0.00 41.02 2.17
578 580 2.176546 CACACGCTGGCCGATTTG 59.823 61.111 0.00 0.00 41.02 2.32
579 581 3.055719 ACACGCTGGCCGATTTGG 61.056 61.111 0.00 0.00 41.02 3.28
580 582 2.745884 CACGCTGGCCGATTTGGA 60.746 61.111 0.00 0.00 42.00 3.53
581 583 2.436646 ACGCTGGCCGATTTGGAG 60.437 61.111 0.00 0.00 42.00 3.86
582 584 2.125147 CGCTGGCCGATTTGGAGA 60.125 61.111 0.00 0.00 42.00 3.71
583 585 2.464459 CGCTGGCCGATTTGGAGAC 61.464 63.158 0.00 0.00 42.00 3.36
584 586 2.464459 GCTGGCCGATTTGGAGACG 61.464 63.158 0.00 0.00 42.00 4.18
585 587 1.218047 CTGGCCGATTTGGAGACGA 59.782 57.895 0.00 0.00 42.00 4.20
586 588 1.079405 TGGCCGATTTGGAGACGAC 60.079 57.895 0.00 0.00 42.00 4.34
587 589 1.079405 GGCCGATTTGGAGACGACA 60.079 57.895 0.00 0.00 42.00 4.35
588 590 1.359459 GGCCGATTTGGAGACGACAC 61.359 60.000 0.00 0.00 42.00 3.67
589 591 0.389948 GCCGATTTGGAGACGACACT 60.390 55.000 0.00 0.00 42.00 3.55
590 592 1.135199 GCCGATTTGGAGACGACACTA 60.135 52.381 0.00 0.00 42.00 2.74
591 593 2.527100 CCGATTTGGAGACGACACTAC 58.473 52.381 0.00 0.00 42.00 2.73
592 594 2.094906 CCGATTTGGAGACGACACTACA 60.095 50.000 0.00 0.00 42.00 2.74
593 595 3.428999 CCGATTTGGAGACGACACTACAT 60.429 47.826 0.00 0.00 42.00 2.29
594 596 3.791887 CGATTTGGAGACGACACTACATC 59.208 47.826 0.00 0.00 30.29 3.06
595 597 3.587797 TTTGGAGACGACACTACATCC 57.412 47.619 0.00 0.00 30.29 3.51
596 598 2.209690 TGGAGACGACACTACATCCA 57.790 50.000 0.00 0.00 34.54 3.41
597 599 2.521126 TGGAGACGACACTACATCCAA 58.479 47.619 0.00 0.00 34.02 3.53
598 600 3.096852 TGGAGACGACACTACATCCAAT 58.903 45.455 0.00 0.00 34.02 3.16
599 601 3.119137 TGGAGACGACACTACATCCAATG 60.119 47.826 0.00 0.00 34.02 2.82
600 602 3.448686 GAGACGACACTACATCCAATGG 58.551 50.000 0.00 0.00 33.60 3.16
601 603 2.832129 AGACGACACTACATCCAATGGT 59.168 45.455 0.00 0.00 33.60 3.55
602 604 3.260884 AGACGACACTACATCCAATGGTT 59.739 43.478 0.00 0.00 33.60 3.67
603 605 3.334691 ACGACACTACATCCAATGGTTG 58.665 45.455 8.70 8.70 33.60 3.77
604 606 3.244422 ACGACACTACATCCAATGGTTGT 60.244 43.478 18.68 18.68 38.85 3.32
605 607 3.125146 CGACACTACATCCAATGGTTGTG 59.875 47.826 22.43 15.35 36.45 3.33
606 608 2.819608 ACACTACATCCAATGGTTGTGC 59.180 45.455 22.43 0.00 36.45 4.57
607 609 3.084039 CACTACATCCAATGGTTGTGCT 58.916 45.455 22.43 7.39 36.45 4.40
608 610 4.260985 CACTACATCCAATGGTTGTGCTA 58.739 43.478 22.43 5.46 36.45 3.49
609 611 4.094887 CACTACATCCAATGGTTGTGCTAC 59.905 45.833 22.43 0.00 36.45 3.58
610 612 3.153369 ACATCCAATGGTTGTGCTACA 57.847 42.857 14.61 0.00 34.73 2.74
611 613 3.084039 ACATCCAATGGTTGTGCTACAG 58.916 45.455 14.61 0.00 34.73 2.74
612 614 2.949177 TCCAATGGTTGTGCTACAGT 57.051 45.000 0.00 0.00 0.00 3.55
613 615 3.222173 TCCAATGGTTGTGCTACAGTT 57.778 42.857 0.00 0.00 0.00 3.16
614 616 3.561143 TCCAATGGTTGTGCTACAGTTT 58.439 40.909 0.00 0.00 0.00 2.66
615 617 4.720046 TCCAATGGTTGTGCTACAGTTTA 58.280 39.130 0.00 0.00 0.00 2.01
616 618 5.321102 TCCAATGGTTGTGCTACAGTTTAT 58.679 37.500 0.00 0.00 0.00 1.40
617 619 5.414454 TCCAATGGTTGTGCTACAGTTTATC 59.586 40.000 0.00 0.00 0.00 1.75
618 620 5.393027 CCAATGGTTGTGCTACAGTTTATCC 60.393 44.000 0.00 0.00 0.00 2.59
619 621 4.634012 TGGTTGTGCTACAGTTTATCCT 57.366 40.909 0.00 0.00 0.00 3.24
620 622 4.575885 TGGTTGTGCTACAGTTTATCCTC 58.424 43.478 0.00 0.00 0.00 3.71
621 623 4.286032 TGGTTGTGCTACAGTTTATCCTCT 59.714 41.667 0.00 0.00 0.00 3.69
622 624 4.631813 GGTTGTGCTACAGTTTATCCTCTG 59.368 45.833 0.00 0.00 37.65 3.35
623 625 3.861840 TGTGCTACAGTTTATCCTCTGC 58.138 45.455 0.00 0.00 35.37 4.26
624 626 3.260632 TGTGCTACAGTTTATCCTCTGCA 59.739 43.478 0.00 0.00 35.37 4.41
625 627 4.080919 TGTGCTACAGTTTATCCTCTGCAT 60.081 41.667 0.00 0.00 35.37 3.96
626 628 4.272018 GTGCTACAGTTTATCCTCTGCATG 59.728 45.833 0.00 0.00 35.37 4.06
627 629 3.812053 GCTACAGTTTATCCTCTGCATGG 59.188 47.826 0.00 0.00 35.37 3.66
628 630 4.443457 GCTACAGTTTATCCTCTGCATGGA 60.443 45.833 10.46 10.46 38.06 3.41
629 631 4.785346 ACAGTTTATCCTCTGCATGGAT 57.215 40.909 20.53 20.53 45.37 3.41
630 632 4.458397 ACAGTTTATCCTCTGCATGGATG 58.542 43.478 23.67 14.55 43.48 3.51
631 633 3.819337 CAGTTTATCCTCTGCATGGATGG 59.181 47.826 23.67 7.65 43.48 3.51
632 634 3.461085 AGTTTATCCTCTGCATGGATGGT 59.539 43.478 23.67 8.14 43.48 3.55
633 635 4.079558 AGTTTATCCTCTGCATGGATGGTT 60.080 41.667 23.67 7.86 43.48 3.67
634 636 4.524802 TTATCCTCTGCATGGATGGTTT 57.475 40.909 23.67 7.57 43.48 3.27
635 637 2.133281 TCCTCTGCATGGATGGTTTG 57.867 50.000 4.66 0.00 0.00 2.93
636 638 1.634973 TCCTCTGCATGGATGGTTTGA 59.365 47.619 4.66 0.00 0.00 2.69
637 639 2.242965 TCCTCTGCATGGATGGTTTGAT 59.757 45.455 4.66 0.00 0.00 2.57
638 640 3.028850 CCTCTGCATGGATGGTTTGATT 58.971 45.455 0.00 0.00 0.00 2.57
639 641 3.181479 CCTCTGCATGGATGGTTTGATTG 60.181 47.826 0.00 0.00 0.00 2.67
640 642 3.697542 CTCTGCATGGATGGTTTGATTGA 59.302 43.478 0.00 0.00 0.00 2.57
641 643 3.444742 TCTGCATGGATGGTTTGATTGAC 59.555 43.478 0.00 0.00 0.00 3.18
642 644 3.163467 TGCATGGATGGTTTGATTGACA 58.837 40.909 0.00 0.00 0.00 3.58
643 645 3.193903 TGCATGGATGGTTTGATTGACAG 59.806 43.478 0.00 0.00 0.00 3.51
644 646 3.194116 GCATGGATGGTTTGATTGACAGT 59.806 43.478 0.00 0.00 0.00 3.55
645 647 4.740268 CATGGATGGTTTGATTGACAGTG 58.260 43.478 0.00 0.00 0.00 3.66
646 648 3.831323 TGGATGGTTTGATTGACAGTGT 58.169 40.909 0.00 0.00 0.00 3.55
647 649 3.820467 TGGATGGTTTGATTGACAGTGTC 59.180 43.478 16.68 16.68 0.00 3.67
648 650 3.120199 GGATGGTTTGATTGACAGTGTCG 60.120 47.826 18.17 0.00 34.95 4.35
649 651 2.912771 TGGTTTGATTGACAGTGTCGT 58.087 42.857 18.17 9.57 34.95 4.34
650 652 2.869801 TGGTTTGATTGACAGTGTCGTC 59.130 45.455 18.17 17.59 34.95 4.20
651 653 2.223377 GGTTTGATTGACAGTGTCGTCC 59.777 50.000 18.17 9.70 34.95 4.79
652 654 2.163818 TTGATTGACAGTGTCGTCCC 57.836 50.000 18.17 8.05 34.95 4.46
653 655 1.044611 TGATTGACAGTGTCGTCCCA 58.955 50.000 18.17 10.37 34.95 4.37
654 656 1.414550 TGATTGACAGTGTCGTCCCAA 59.585 47.619 18.17 7.71 34.95 4.12
655 657 2.158885 TGATTGACAGTGTCGTCCCAAA 60.159 45.455 18.17 6.37 34.95 3.28
656 658 2.404923 TTGACAGTGTCGTCCCAAAA 57.595 45.000 18.17 2.49 34.95 2.44
657 659 2.631160 TGACAGTGTCGTCCCAAAAT 57.369 45.000 18.17 0.00 34.95 1.82
658 660 2.489971 TGACAGTGTCGTCCCAAAATC 58.510 47.619 18.17 0.00 34.95 2.17
659 661 1.459592 GACAGTGTCGTCCCAAAATCG 59.540 52.381 7.68 0.00 0.00 3.34
660 662 0.796312 CAGTGTCGTCCCAAAATCGG 59.204 55.000 0.00 0.00 0.00 4.18
661 663 0.953960 AGTGTCGTCCCAAAATCGGC 60.954 55.000 0.00 0.00 0.00 5.54
662 664 0.953960 GTGTCGTCCCAAAATCGGCT 60.954 55.000 0.00 0.00 0.00 5.52
663 665 0.609151 TGTCGTCCCAAAATCGGCTA 59.391 50.000 0.00 0.00 0.00 3.93
664 666 1.208535 TGTCGTCCCAAAATCGGCTAT 59.791 47.619 0.00 0.00 0.00 2.97
665 667 1.597663 GTCGTCCCAAAATCGGCTATG 59.402 52.381 0.00 0.00 0.00 2.23
666 668 0.307760 CGTCCCAAAATCGGCTATGC 59.692 55.000 0.00 0.00 0.00 3.14
667 669 1.388547 GTCCCAAAATCGGCTATGCA 58.611 50.000 0.00 0.00 0.00 3.96
668 670 1.334869 GTCCCAAAATCGGCTATGCAG 59.665 52.381 0.00 0.00 0.00 4.41
677 679 3.303605 GCTATGCAGCGTCGTCTG 58.696 61.111 10.96 10.96 38.22 3.51
678 680 1.517257 GCTATGCAGCGTCGTCTGT 60.517 57.895 15.01 3.10 38.22 3.41
679 681 1.746727 GCTATGCAGCGTCGTCTGTG 61.747 60.000 15.01 1.44 38.22 3.66
680 682 0.456824 CTATGCAGCGTCGTCTGTGT 60.457 55.000 15.01 8.75 36.49 3.72
681 683 0.806241 TATGCAGCGTCGTCTGTGTA 59.194 50.000 15.01 8.04 36.49 2.90
682 684 0.456824 ATGCAGCGTCGTCTGTGTAG 60.457 55.000 15.01 0.00 36.49 2.74
683 685 2.437343 GCAGCGTCGTCTGTGTAGC 61.437 63.158 15.01 1.16 36.49 3.58
684 686 1.081442 CAGCGTCGTCTGTGTAGCA 60.081 57.895 8.07 0.00 0.00 3.49
685 687 1.067743 CAGCGTCGTCTGTGTAGCAG 61.068 60.000 8.07 0.00 46.34 4.24
686 688 2.437343 GCGTCGTCTGTGTAGCAGC 61.437 63.158 0.00 0.00 44.66 5.25
687 689 1.081442 CGTCGTCTGTGTAGCAGCA 60.081 57.895 0.00 0.00 44.66 4.41
688 690 1.337817 CGTCGTCTGTGTAGCAGCAC 61.338 60.000 0.00 4.04 44.66 4.40
689 691 0.039074 GTCGTCTGTGTAGCAGCACT 60.039 55.000 11.09 0.00 44.66 4.40
690 692 0.241213 TCGTCTGTGTAGCAGCACTC 59.759 55.000 11.09 0.00 44.66 3.51
910 914 5.296283 GCTGCACTTCTCTATGATGAAACAT 59.704 40.000 0.00 0.00 0.00 2.71
1253 1272 6.498303 AGGTTATTTGAGAAAAGGGAGCATTT 59.502 34.615 0.00 0.00 0.00 2.32
1396 1416 3.650139 AGCATTTCGAACGTCTAGTTGT 58.350 40.909 0.00 0.00 44.35 3.32
2115 2446 7.956420 AACAATATCACGACTACAAGTTCAA 57.044 32.000 0.00 0.00 0.00 2.69
2294 2627 1.816074 TGCAGACCCGAACATTAACC 58.184 50.000 0.00 0.00 0.00 2.85
2356 2689 6.865411 TCCAACAGGTAACAAGGTTAAAAAC 58.135 36.000 0.00 0.00 41.41 2.43
2925 3275 5.014858 CCTTTGGTACTACTACTCACAGGA 58.985 45.833 0.00 0.00 30.24 3.86
3234 5947 4.508551 TGATGATAAGACACCCAGCATT 57.491 40.909 0.00 0.00 0.00 3.56
3405 6127 1.140312 ATGGGGAGTCCGTGCATATT 58.860 50.000 2.26 0.00 38.76 1.28
3591 7455 4.062991 GACCTCACACGGACAAAAATAGT 58.937 43.478 0.00 0.00 0.00 2.12
3597 7461 7.094975 CCTCACACGGACAAAAATAGTATTTGA 60.095 37.037 8.88 0.00 39.56 2.69
3825 7750 1.228245 GGCTGCAACCTCAGGAACA 60.228 57.895 0.00 0.00 34.74 3.18
4039 8023 4.552365 CCGCCATGGGACGAGCAT 62.552 66.667 15.13 0.00 0.00 3.79
4177 8211 1.600916 GCGGCTGGTCTTTTCCTGT 60.601 57.895 0.00 0.00 0.00 4.00
4196 8246 6.751157 TCCTGTGTTTAATTAAGAGACACGA 58.249 36.000 19.40 12.52 42.53 4.35
4307 8357 1.375853 CGGATGGGAGCATTTTCGCA 61.376 55.000 0.00 0.00 43.05 5.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
536 538 7.381948 TGTCGTTTGCTAAGTAGTTTCGATAAA 59.618 33.333 0.00 0.00 0.00 1.40
537 539 6.862608 TGTCGTTTGCTAAGTAGTTTCGATAA 59.137 34.615 0.00 0.00 0.00 1.75
538 540 6.306356 GTGTCGTTTGCTAAGTAGTTTCGATA 59.694 38.462 0.00 0.00 0.00 2.92
539 541 5.118203 GTGTCGTTTGCTAAGTAGTTTCGAT 59.882 40.000 0.00 0.00 0.00 3.59
540 542 4.442073 GTGTCGTTTGCTAAGTAGTTTCGA 59.558 41.667 0.00 0.00 0.00 3.71
541 543 4.207635 TGTGTCGTTTGCTAAGTAGTTTCG 59.792 41.667 0.00 0.00 0.00 3.46
542 544 5.429615 GTGTGTCGTTTGCTAAGTAGTTTC 58.570 41.667 0.00 0.00 0.00 2.78
543 545 4.026310 CGTGTGTCGTTTGCTAAGTAGTTT 60.026 41.667 0.00 0.00 34.52 2.66
544 546 3.488310 CGTGTGTCGTTTGCTAAGTAGTT 59.512 43.478 0.00 0.00 34.52 2.24
545 547 3.047796 CGTGTGTCGTTTGCTAAGTAGT 58.952 45.455 0.00 0.00 34.52 2.73
546 548 2.160013 GCGTGTGTCGTTTGCTAAGTAG 60.160 50.000 0.00 0.00 42.13 2.57
547 549 1.788308 GCGTGTGTCGTTTGCTAAGTA 59.212 47.619 0.00 0.00 42.13 2.24
548 550 0.580104 GCGTGTGTCGTTTGCTAAGT 59.420 50.000 0.00 0.00 42.13 2.24
549 551 0.859232 AGCGTGTGTCGTTTGCTAAG 59.141 50.000 0.00 0.00 42.13 2.18
550 552 0.579630 CAGCGTGTGTCGTTTGCTAA 59.420 50.000 0.00 0.00 42.13 3.09
551 553 1.218875 CCAGCGTGTGTCGTTTGCTA 61.219 55.000 0.00 0.00 42.13 3.49
552 554 2.534019 CCAGCGTGTGTCGTTTGCT 61.534 57.895 0.00 0.00 42.13 3.91
553 555 2.052237 CCAGCGTGTGTCGTTTGC 60.052 61.111 0.00 0.00 42.13 3.68
554 556 2.052237 GCCAGCGTGTGTCGTTTG 60.052 61.111 0.00 0.00 42.13 2.93
555 557 3.276846 GGCCAGCGTGTGTCGTTT 61.277 61.111 0.00 0.00 42.13 3.60
559 561 2.325082 AAATCGGCCAGCGTGTGTC 61.325 57.895 2.24 0.00 0.00 3.67
560 562 2.281484 AAATCGGCCAGCGTGTGT 60.281 55.556 2.24 0.00 0.00 3.72
561 563 2.176546 CAAATCGGCCAGCGTGTG 59.823 61.111 2.24 0.00 0.00 3.82
562 564 3.055719 CCAAATCGGCCAGCGTGT 61.056 61.111 2.24 0.00 0.00 4.49
563 565 2.745884 TCCAAATCGGCCAGCGTG 60.746 61.111 2.24 0.00 33.14 5.34
564 566 2.436646 CTCCAAATCGGCCAGCGT 60.437 61.111 2.24 0.00 33.14 5.07
565 567 2.125147 TCTCCAAATCGGCCAGCG 60.125 61.111 2.24 0.00 33.14 5.18
566 568 2.464459 CGTCTCCAAATCGGCCAGC 61.464 63.158 2.24 0.00 33.14 4.85
567 569 1.084370 GTCGTCTCCAAATCGGCCAG 61.084 60.000 2.24 0.00 33.14 4.85
568 570 1.079405 GTCGTCTCCAAATCGGCCA 60.079 57.895 2.24 0.00 33.14 5.36
569 571 1.079405 TGTCGTCTCCAAATCGGCC 60.079 57.895 0.00 0.00 33.14 6.13
570 572 0.389948 AGTGTCGTCTCCAAATCGGC 60.390 55.000 0.00 0.00 33.14 5.54
571 573 2.094906 TGTAGTGTCGTCTCCAAATCGG 60.095 50.000 0.00 0.00 0.00 4.18
572 574 3.211803 TGTAGTGTCGTCTCCAAATCG 57.788 47.619 0.00 0.00 0.00 3.34
573 575 4.113354 GGATGTAGTGTCGTCTCCAAATC 58.887 47.826 0.00 0.00 0.00 2.17
574 576 3.513912 TGGATGTAGTGTCGTCTCCAAAT 59.486 43.478 0.00 0.00 30.15 2.32
575 577 2.894765 TGGATGTAGTGTCGTCTCCAAA 59.105 45.455 0.00 0.00 30.15 3.28
576 578 2.521126 TGGATGTAGTGTCGTCTCCAA 58.479 47.619 0.00 0.00 30.15 3.53
577 579 2.209690 TGGATGTAGTGTCGTCTCCA 57.790 50.000 0.00 0.00 0.00 3.86
578 580 3.448686 CATTGGATGTAGTGTCGTCTCC 58.551 50.000 0.00 0.00 0.00 3.71
579 581 3.119101 ACCATTGGATGTAGTGTCGTCTC 60.119 47.826 10.37 0.00 0.00 3.36
580 582 2.832129 ACCATTGGATGTAGTGTCGTCT 59.168 45.455 10.37 0.00 0.00 4.18
581 583 3.247006 ACCATTGGATGTAGTGTCGTC 57.753 47.619 10.37 0.00 0.00 4.20
582 584 3.244422 ACAACCATTGGATGTAGTGTCGT 60.244 43.478 16.24 0.00 36.95 4.34
583 585 3.125146 CACAACCATTGGATGTAGTGTCG 59.875 47.826 17.19 1.97 36.57 4.35
584 586 3.119849 GCACAACCATTGGATGTAGTGTC 60.120 47.826 17.19 2.98 36.57 3.67
585 587 2.819608 GCACAACCATTGGATGTAGTGT 59.180 45.455 17.19 5.05 36.57 3.55
586 588 3.084039 AGCACAACCATTGGATGTAGTG 58.916 45.455 17.19 13.45 36.57 2.74
587 589 3.439857 AGCACAACCATTGGATGTAGT 57.560 42.857 17.19 6.01 36.57 2.73
588 590 4.260985 TGTAGCACAACCATTGGATGTAG 58.739 43.478 17.19 12.76 36.57 2.74
589 591 4.260985 CTGTAGCACAACCATTGGATGTA 58.739 43.478 17.19 0.98 36.57 2.29
590 592 3.084039 CTGTAGCACAACCATTGGATGT 58.916 45.455 12.47 12.47 39.28 3.06
591 593 3.084039 ACTGTAGCACAACCATTGGATG 58.916 45.455 10.37 10.80 34.12 3.51
592 594 3.439857 ACTGTAGCACAACCATTGGAT 57.560 42.857 10.37 0.00 34.12 3.41
593 595 2.949177 ACTGTAGCACAACCATTGGA 57.051 45.000 10.37 0.00 34.12 3.53
594 596 5.393027 GGATAAACTGTAGCACAACCATTGG 60.393 44.000 0.00 0.00 34.12 3.16
595 597 5.415701 AGGATAAACTGTAGCACAACCATTG 59.584 40.000 0.00 0.00 0.00 2.82
596 598 5.570320 AGGATAAACTGTAGCACAACCATT 58.430 37.500 0.00 0.00 0.00 3.16
597 599 5.045578 AGAGGATAAACTGTAGCACAACCAT 60.046 40.000 0.00 0.00 0.00 3.55
598 600 4.286032 AGAGGATAAACTGTAGCACAACCA 59.714 41.667 0.00 0.00 0.00 3.67
599 601 4.631813 CAGAGGATAAACTGTAGCACAACC 59.368 45.833 0.00 0.00 0.00 3.77
600 602 4.093556 GCAGAGGATAAACTGTAGCACAAC 59.906 45.833 0.00 0.00 36.62 3.32
601 603 4.253685 GCAGAGGATAAACTGTAGCACAA 58.746 43.478 0.00 0.00 36.62 3.33
602 604 3.260632 TGCAGAGGATAAACTGTAGCACA 59.739 43.478 0.00 0.00 36.62 4.57
603 605 3.861840 TGCAGAGGATAAACTGTAGCAC 58.138 45.455 0.00 0.00 36.62 4.40
604 606 4.445453 CATGCAGAGGATAAACTGTAGCA 58.555 43.478 0.00 0.00 36.62 3.49
605 607 3.812053 CCATGCAGAGGATAAACTGTAGC 59.188 47.826 1.80 0.00 36.62 3.58
606 608 5.282055 TCCATGCAGAGGATAAACTGTAG 57.718 43.478 6.58 0.00 36.62 2.74
607 609 5.455183 CCATCCATGCAGAGGATAAACTGTA 60.455 44.000 19.72 0.00 43.90 2.74
608 610 4.458397 CATCCATGCAGAGGATAAACTGT 58.542 43.478 19.72 0.00 43.90 3.55
609 611 3.819337 CCATCCATGCAGAGGATAAACTG 59.181 47.826 19.72 10.96 43.90 3.16
610 612 3.461085 ACCATCCATGCAGAGGATAAACT 59.539 43.478 19.72 0.07 43.90 2.66
611 613 3.825328 ACCATCCATGCAGAGGATAAAC 58.175 45.455 19.72 0.00 43.90 2.01
612 614 4.524802 AACCATCCATGCAGAGGATAAA 57.475 40.909 19.72 0.00 43.90 1.40
613 615 4.079844 TCAAACCATCCATGCAGAGGATAA 60.080 41.667 19.72 0.00 43.90 1.75
614 616 3.459227 TCAAACCATCCATGCAGAGGATA 59.541 43.478 19.72 4.45 43.90 2.59
615 617 2.242965 TCAAACCATCCATGCAGAGGAT 59.757 45.455 15.72 15.72 46.61 3.24
616 618 1.634973 TCAAACCATCCATGCAGAGGA 59.365 47.619 12.56 12.56 39.97 3.71
617 619 2.133281 TCAAACCATCCATGCAGAGG 57.867 50.000 1.59 1.59 0.00 3.69
618 620 3.697542 TCAATCAAACCATCCATGCAGAG 59.302 43.478 0.00 0.00 0.00 3.35
619 621 3.444742 GTCAATCAAACCATCCATGCAGA 59.555 43.478 0.00 0.00 0.00 4.26
620 622 3.193903 TGTCAATCAAACCATCCATGCAG 59.806 43.478 0.00 0.00 0.00 4.41
621 623 3.163467 TGTCAATCAAACCATCCATGCA 58.837 40.909 0.00 0.00 0.00 3.96
622 624 3.194116 ACTGTCAATCAAACCATCCATGC 59.806 43.478 0.00 0.00 0.00 4.06
623 625 4.219070 ACACTGTCAATCAAACCATCCATG 59.781 41.667 0.00 0.00 0.00 3.66
624 626 4.410099 ACACTGTCAATCAAACCATCCAT 58.590 39.130 0.00 0.00 0.00 3.41
625 627 3.820467 GACACTGTCAATCAAACCATCCA 59.180 43.478 4.17 0.00 32.09 3.41
626 628 3.120199 CGACACTGTCAATCAAACCATCC 60.120 47.826 9.84 0.00 32.09 3.51
627 629 3.498397 ACGACACTGTCAATCAAACCATC 59.502 43.478 9.84 0.00 32.09 3.51
628 630 3.476552 ACGACACTGTCAATCAAACCAT 58.523 40.909 9.84 0.00 32.09 3.55
629 631 2.869801 GACGACACTGTCAATCAAACCA 59.130 45.455 9.84 0.00 38.75 3.67
630 632 2.223377 GGACGACACTGTCAATCAAACC 59.777 50.000 9.84 0.00 40.72 3.27
631 633 2.223377 GGGACGACACTGTCAATCAAAC 59.777 50.000 9.84 0.00 40.72 2.93
632 634 2.158885 TGGGACGACACTGTCAATCAAA 60.159 45.455 9.84 0.00 40.72 2.69
633 635 1.414550 TGGGACGACACTGTCAATCAA 59.585 47.619 9.84 0.00 40.72 2.57
634 636 1.044611 TGGGACGACACTGTCAATCA 58.955 50.000 9.84 0.00 40.72 2.57
635 637 2.163818 TTGGGACGACACTGTCAATC 57.836 50.000 9.84 6.03 40.72 2.67
636 638 2.631160 TTTGGGACGACACTGTCAAT 57.369 45.000 9.84 0.00 40.72 2.57
637 639 2.404923 TTTTGGGACGACACTGTCAA 57.595 45.000 9.84 0.00 40.72 3.18
638 640 2.489971 GATTTTGGGACGACACTGTCA 58.510 47.619 9.84 0.00 40.72 3.58
639 641 1.459592 CGATTTTGGGACGACACTGTC 59.540 52.381 0.00 0.00 38.17 3.51
640 642 1.508632 CGATTTTGGGACGACACTGT 58.491 50.000 0.00 0.00 0.00 3.55
641 643 0.796312 CCGATTTTGGGACGACACTG 59.204 55.000 0.00 0.00 0.00 3.66
642 644 0.953960 GCCGATTTTGGGACGACACT 60.954 55.000 0.00 0.00 0.00 3.55
643 645 0.953960 AGCCGATTTTGGGACGACAC 60.954 55.000 0.00 0.00 0.00 3.67
644 646 0.609151 TAGCCGATTTTGGGACGACA 59.391 50.000 0.00 0.00 0.00 4.35
645 647 1.597663 CATAGCCGATTTTGGGACGAC 59.402 52.381 0.00 0.00 0.00 4.34
646 648 1.948104 CATAGCCGATTTTGGGACGA 58.052 50.000 0.00 0.00 0.00 4.20
647 649 0.307760 GCATAGCCGATTTTGGGACG 59.692 55.000 0.00 0.00 0.00 4.79
648 650 1.334869 CTGCATAGCCGATTTTGGGAC 59.665 52.381 0.00 0.00 0.00 4.46
649 651 1.679139 CTGCATAGCCGATTTTGGGA 58.321 50.000 0.00 0.00 0.00 4.37
650 652 0.031178 GCTGCATAGCCGATTTTGGG 59.969 55.000 0.00 0.00 44.33 4.12
651 653 3.557207 GCTGCATAGCCGATTTTGG 57.443 52.632 0.00 0.00 44.33 3.28
660 662 1.517257 ACAGACGACGCTGCATAGC 60.517 57.895 15.95 0.00 46.62 2.97
661 663 0.456824 ACACAGACGACGCTGCATAG 60.457 55.000 15.95 8.64 39.51 2.23
662 664 0.806241 TACACAGACGACGCTGCATA 59.194 50.000 15.95 8.34 39.51 3.14
663 665 0.456824 CTACACAGACGACGCTGCAT 60.457 55.000 15.95 9.09 39.51 3.96
664 666 1.081442 CTACACAGACGACGCTGCA 60.081 57.895 15.95 0.00 39.51 4.41
665 667 2.437343 GCTACACAGACGACGCTGC 61.437 63.158 15.95 0.00 39.51 5.25
666 668 1.081442 TGCTACACAGACGACGCTG 60.081 57.895 14.87 14.87 41.63 5.18
667 669 3.351450 TGCTACACAGACGACGCT 58.649 55.556 0.00 0.00 0.00 5.07
910 914 4.470334 AAAGCCAAGCAAAACTTTCTGA 57.530 36.364 0.00 0.00 36.04 3.27
1994 2324 6.147328 GTGAACAAACAGAGTTACCTGTATCC 59.853 42.308 6.86 0.00 45.82 2.59
2115 2446 4.112634 TGGTAGGCCTCTCATTTTGTTT 57.887 40.909 9.68 0.00 35.27 2.83
2294 2627 5.728351 TTTTGTTCTGAACTTGTAGACGG 57.272 39.130 20.18 0.00 0.00 4.79
2356 2689 2.224066 ACTTGACCCTCGAACAGTCTTG 60.224 50.000 9.68 5.89 0.00 3.02
2925 3275 3.433306 TTGTCGGAACTCCCAAATGAT 57.567 42.857 0.00 0.00 34.14 2.45
3234 5947 0.038021 TGGCTGCAGTGGAGCATTTA 59.962 50.000 33.67 16.47 44.68 1.40
3272 5985 6.376864 TGTTGGAAGAAGACTTGATTTTGACA 59.623 34.615 0.00 0.00 36.39 3.58
3405 6127 8.817100 CACTTAATTAAGTAGTGCATTCGATCA 58.183 33.333 26.38 0.00 44.19 2.92
3519 7383 2.427095 ACAAGAACTGTGCTTTTGGTCC 59.573 45.455 0.00 0.00 36.69 4.46
3557 7421 0.459237 GTGAGGTCGGTGAGATGCAG 60.459 60.000 0.00 0.00 0.00 4.41
3597 7461 5.940470 ACCGCTGTTCTTCTAATTTCTGAAT 59.060 36.000 0.00 0.00 0.00 2.57
3728 7594 1.654220 CTTCGTGGCCCTGTTTGTG 59.346 57.895 0.00 0.00 0.00 3.33
3834 7759 2.763881 GCTTCGCTCGTTGTCGAC 59.236 61.111 9.11 9.11 41.35 4.20
4026 8010 1.890979 GCTCCATGCTCGTCCCATG 60.891 63.158 0.00 5.96 39.74 3.66
4039 8023 4.344865 GCGGGAGGGTTTGCTCCA 62.345 66.667 0.00 0.00 41.34 3.86
4177 8211 5.630680 GTCGGTCGTGTCTCTTAATTAAACA 59.369 40.000 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.