Multiple sequence alignment - TraesCS4B01G051700

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 TraesCS4B01G051700 chr4B 100.000 3382 0 0 1 3382 40438100 40434719 0.000000e+00 6246
1 TraesCS4B01G051700 chr4B 85.507 2001 216 50 612 2570 40478117 40476149 0.000000e+00 2021
2 TraesCS4B01G051700 chr4B 88.443 1670 148 25 921 2570 40474702 40473058 0.000000e+00 1973
3 TraesCS4B01G051700 chr4B 89.351 1418 118 10 1169 2569 40537803 40536402 0.000000e+00 1751
4 TraesCS4B01G051700 chr4B 87.097 1178 131 10 1401 2570 40609888 40608724 0.000000e+00 1314
5 TraesCS4B01G051700 chr4B 95.679 810 33 2 2575 3382 404512174 404511365 0.000000e+00 1301
6 TraesCS4B01G051700 chr4B 85.826 896 102 16 1656 2537 40480632 40479748 0.000000e+00 928
7 TraesCS4B01G051700 chr4B 92.870 575 22 10 7 572 40234088 40234652 0.000000e+00 817
8 TraesCS4B01G051700 chr4B 89.691 388 37 1 1020 1404 40623860 40623473 3.030000e-135 492
9 TraesCS4B01G051700 chr4B 87.636 275 25 4 2286 2558 40607610 40607343 9.110000e-81 311
10 TraesCS4B01G051700 chr4B 88.742 151 16 1 1020 1169 40548990 40548840 2.070000e-42 183
11 TraesCS4B01G051700 chr4D 87.375 2004 172 33 600 2569 28416173 28414217 0.000000e+00 2224
12 TraesCS4B01G051700 chr4D 88.805 1456 127 12 1020 2450 27554032 27555476 0.000000e+00 1753
13 TraesCS4B01G051700 chr4D 86.732 1530 172 15 1056 2570 27577077 27575564 0.000000e+00 1672
14 TraesCS4B01G051700 chr4D 95.426 809 34 2 2575 3382 396428914 396428108 0.000000e+00 1286
15 TraesCS4B01G051700 chr4D 92.917 593 27 7 1 586 27561677 27561093 0.000000e+00 848
16 TraesCS4B01G051700 chr4A 87.762 1528 155 16 1056 2567 575692796 575694307 0.000000e+00 1757
17 TraesCS4B01G051700 chr4A 92.904 606 30 7 1 599 575735296 575735895 0.000000e+00 869
18 TraesCS4B01G051700 chr4A 87.351 419 37 8 2155 2570 575701020 575701425 1.840000e-127 466
19 TraesCS4B01G051700 chr4A 91.798 317 26 0 1074 1390 575714291 575714607 3.100000e-120 442
20 TraesCS4B01G051700 chr7B 95.981 821 30 3 2565 3382 561071791 561070971 0.000000e+00 1330
21 TraesCS4B01G051700 chr7B 95.802 810 32 2 2575 3382 141816516 141817325 0.000000e+00 1306
22 TraesCS4B01G051700 chr7B 95.080 813 37 3 2571 3382 16508052 16507242 0.000000e+00 1277
23 TraesCS4B01G051700 chr2B 96.411 808 27 1 2575 3382 79649535 79648730 0.000000e+00 1330
24 TraesCS4B01G051700 chr2B 95.303 809 35 3 2575 3382 584709664 584710470 0.000000e+00 1280
25 TraesCS4B01G051700 chr3B 95.438 811 33 1 2576 3382 760292511 760291701 0.000000e+00 1290
26 TraesCS4B01G051700 chr6B 95.314 811 33 4 2575 3382 209230375 209231183 0.000000e+00 1282
27 TraesCS4B01G051700 chr5A 79.650 1086 187 24 1020 2078 576071402 576070324 0.000000e+00 750


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 TraesCS4B01G051700 chr4B 40434719 40438100 3381 True 6246.000000 6246 100.0000 1 3382 1 chr4B.!!$R1 3381
1 TraesCS4B01G051700 chr4B 40536402 40537803 1401 True 1751.000000 1751 89.3510 1169 2569 1 chr4B.!!$R2 1400
2 TraesCS4B01G051700 chr4B 40473058 40480632 7574 True 1640.666667 2021 86.5920 612 2570 3 chr4B.!!$R6 1958
3 TraesCS4B01G051700 chr4B 404511365 404512174 809 True 1301.000000 1301 95.6790 2575 3382 1 chr4B.!!$R5 807
4 TraesCS4B01G051700 chr4B 40234088 40234652 564 False 817.000000 817 92.8700 7 572 1 chr4B.!!$F1 565
5 TraesCS4B01G051700 chr4B 40607343 40609888 2545 True 812.500000 1314 87.3665 1401 2570 2 chr4B.!!$R7 1169
6 TraesCS4B01G051700 chr4D 28414217 28416173 1956 True 2224.000000 2224 87.3750 600 2569 1 chr4D.!!$R3 1969
7 TraesCS4B01G051700 chr4D 27554032 27555476 1444 False 1753.000000 1753 88.8050 1020 2450 1 chr4D.!!$F1 1430
8 TraesCS4B01G051700 chr4D 27575564 27577077 1513 True 1672.000000 1672 86.7320 1056 2570 1 chr4D.!!$R2 1514
9 TraesCS4B01G051700 chr4D 396428108 396428914 806 True 1286.000000 1286 95.4260 2575 3382 1 chr4D.!!$R4 807
10 TraesCS4B01G051700 chr4D 27561093 27561677 584 True 848.000000 848 92.9170 1 586 1 chr4D.!!$R1 585
11 TraesCS4B01G051700 chr4A 575692796 575694307 1511 False 1757.000000 1757 87.7620 1056 2567 1 chr4A.!!$F1 1511
12 TraesCS4B01G051700 chr4A 575735296 575735895 599 False 869.000000 869 92.9040 1 599 1 chr4A.!!$F4 598
13 TraesCS4B01G051700 chr7B 561070971 561071791 820 True 1330.000000 1330 95.9810 2565 3382 1 chr7B.!!$R2 817
14 TraesCS4B01G051700 chr7B 141816516 141817325 809 False 1306.000000 1306 95.8020 2575 3382 1 chr7B.!!$F1 807
15 TraesCS4B01G051700 chr7B 16507242 16508052 810 True 1277.000000 1277 95.0800 2571 3382 1 chr7B.!!$R1 811
16 TraesCS4B01G051700 chr2B 79648730 79649535 805 True 1330.000000 1330 96.4110 2575 3382 1 chr2B.!!$R1 807
17 TraesCS4B01G051700 chr2B 584709664 584710470 806 False 1280.000000 1280 95.3030 2575 3382 1 chr2B.!!$F1 807
18 TraesCS4B01G051700 chr3B 760291701 760292511 810 True 1290.000000 1290 95.4380 2576 3382 1 chr3B.!!$R1 806
19 TraesCS4B01G051700 chr6B 209230375 209231183 808 False 1282.000000 1282 95.3140 2575 3382 1 chr6B.!!$F1 807
20 TraesCS4B01G051700 chr5A 576070324 576071402 1078 True 750.000000 750 79.6500 1020 2078 1 chr5A.!!$R1 1058

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
570 583 0.035725 AAACTGGGGTAAGCGCCTAC 60.036 55.0 7.67 7.67 46.69 3.18 F
1399 6467 0.031314 CTCCACATGATCCCGTCTCG 59.969 60.0 0.00 0.00 0.00 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2087 8042 0.324738 AGCAGAACTCCGGATCCTGA 60.325 55.0 23.69 8.06 0.0 3.86 R
3126 9668 0.466372 ATCCCTCTGATCGACGCTCA 60.466 55.0 0.96 0.96 0.0 4.26 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
444 457 2.666207 CGGATGGACCCCGTGAAA 59.334 61.111 1.25 0.00 41.91 2.69
515 528 4.697756 CGGCCCGTTCTTGCTGGA 62.698 66.667 0.00 0.00 0.00 3.86
516 529 2.282180 GGCCCGTTCTTGCTGGAA 60.282 61.111 0.00 0.00 0.00 3.53
518 531 2.626780 GCCCGTTCTTGCTGGAACC 61.627 63.158 13.70 0.00 41.58 3.62
521 534 1.597027 CGTTCTTGCTGGAACCCGT 60.597 57.895 13.70 0.00 41.58 5.28
522 535 1.841663 CGTTCTTGCTGGAACCCGTG 61.842 60.000 13.70 0.96 41.58 4.94
523 536 0.534203 GTTCTTGCTGGAACCCGTGA 60.534 55.000 9.98 0.00 39.50 4.35
524 537 0.181587 TTCTTGCTGGAACCCGTGAA 59.818 50.000 0.00 0.00 0.00 3.18
526 539 0.535102 CTTGCTGGAACCCGTGAACT 60.535 55.000 0.00 0.00 0.00 3.01
527 540 0.817634 TTGCTGGAACCCGTGAACTG 60.818 55.000 0.00 0.00 0.00 3.16
529 542 1.450211 CTGGAACCCGTGAACTGGT 59.550 57.895 0.00 0.00 34.81 4.00
531 544 0.393820 TGGAACCCGTGAACTGGTAC 59.606 55.000 0.00 0.00 32.93 3.34
532 545 0.321034 GGAACCCGTGAACTGGTACC 60.321 60.000 4.43 4.43 32.93 3.34
534 547 1.114722 AACCCGTGAACTGGTACCGA 61.115 55.000 7.57 0.00 32.93 4.69
535 548 1.214589 CCCGTGAACTGGTACCGAG 59.785 63.158 7.57 8.50 0.00 4.63
536 549 1.214589 CCGTGAACTGGTACCGAGG 59.785 63.158 7.57 2.58 0.00 4.63
537 550 1.445582 CGTGAACTGGTACCGAGGC 60.446 63.158 7.57 3.98 0.00 4.70
538 551 1.445582 GTGAACTGGTACCGAGGCG 60.446 63.158 7.57 0.00 0.00 5.52
541 554 1.660560 GAACTGGTACCGAGGCGCTA 61.661 60.000 7.64 0.00 0.00 4.26
542 555 1.041447 AACTGGTACCGAGGCGCTAT 61.041 55.000 7.64 0.00 0.00 2.97
543 556 1.286260 CTGGTACCGAGGCGCTATC 59.714 63.158 7.64 5.10 0.00 2.08
544 557 1.452953 CTGGTACCGAGGCGCTATCA 61.453 60.000 7.64 0.00 0.00 2.15
546 559 1.286260 GTACCGAGGCGCTATCAGG 59.714 63.158 7.64 13.53 0.00 3.86
547 560 1.901948 TACCGAGGCGCTATCAGGG 60.902 63.158 7.64 6.46 0.00 4.45
557 570 1.017387 GCTATCAGGGCGAAAACTGG 58.983 55.000 0.00 0.00 35.47 4.00
558 571 1.668419 CTATCAGGGCGAAAACTGGG 58.332 55.000 0.00 0.00 35.47 4.45
559 572 0.254747 TATCAGGGCGAAAACTGGGG 59.745 55.000 0.00 0.00 35.47 4.96
560 573 1.789576 ATCAGGGCGAAAACTGGGGT 61.790 55.000 0.00 0.00 35.47 4.95
561 574 1.128809 TCAGGGCGAAAACTGGGGTA 61.129 55.000 0.00 0.00 35.47 3.69
562 575 0.250989 CAGGGCGAAAACTGGGGTAA 60.251 55.000 0.00 0.00 0.00 2.85
564 577 1.592400 GGGCGAAAACTGGGGTAAGC 61.592 60.000 0.00 0.00 0.00 3.09
566 579 1.500396 CGAAAACTGGGGTAAGCGC 59.500 57.895 0.00 0.00 0.00 5.92
567 580 1.880894 GAAAACTGGGGTAAGCGCC 59.119 57.895 2.29 0.00 46.74 6.53
568 581 0.608308 GAAAACTGGGGTAAGCGCCT 60.608 55.000 2.29 0.00 46.69 5.52
570 583 0.035725 AAACTGGGGTAAGCGCCTAC 60.036 55.000 7.67 7.67 46.69 3.18
571 584 1.196104 AACTGGGGTAAGCGCCTACA 61.196 55.000 17.49 1.95 46.69 2.74
572 585 0.981277 ACTGGGGTAAGCGCCTACAT 60.981 55.000 17.49 0.00 46.69 2.29
573 586 1.045407 CTGGGGTAAGCGCCTACATA 58.955 55.000 17.49 2.85 46.69 2.29
574 587 0.754472 TGGGGTAAGCGCCTACATAC 59.246 55.000 17.49 7.59 46.69 2.39
575 588 0.754472 GGGGTAAGCGCCTACATACA 59.246 55.000 17.49 0.00 43.60 2.29
576 589 1.139455 GGGGTAAGCGCCTACATACAA 59.861 52.381 17.49 0.00 43.60 2.41
578 591 3.007182 GGGGTAAGCGCCTACATACAATA 59.993 47.826 17.49 0.00 43.60 1.90
579 592 3.992427 GGGTAAGCGCCTACATACAATAC 59.008 47.826 17.49 0.00 0.00 1.89
580 593 4.501915 GGGTAAGCGCCTACATACAATACA 60.502 45.833 17.49 0.00 0.00 2.29
581 594 4.446719 GGTAAGCGCCTACATACAATACAC 59.553 45.833 17.49 0.00 0.00 2.90
582 595 3.812156 AGCGCCTACATACAATACACA 57.188 42.857 2.29 0.00 0.00 3.72
583 596 4.131649 AGCGCCTACATACAATACACAA 57.868 40.909 2.29 0.00 0.00 3.33
586 599 4.509970 GCGCCTACATACAATACACAATCA 59.490 41.667 0.00 0.00 0.00 2.57
587 600 5.558273 GCGCCTACATACAATACACAATCAC 60.558 44.000 0.00 0.00 0.00 3.06
589 602 6.036626 CGCCTACATACAATACACAATCACAA 59.963 38.462 0.00 0.00 0.00 3.33
590 603 7.254761 CGCCTACATACAATACACAATCACAAT 60.255 37.037 0.00 0.00 0.00 2.71
591 604 8.070171 GCCTACATACAATACACAATCACAATC 58.930 37.037 0.00 0.00 0.00 2.67
594 607 8.565896 ACATACAATACACAATCACAATCAGT 57.434 30.769 0.00 0.00 0.00 3.41
595 608 8.668353 ACATACAATACACAATCACAATCAGTC 58.332 33.333 0.00 0.00 0.00 3.51
596 609 8.667463 CATACAATACACAATCACAATCAGTCA 58.333 33.333 0.00 0.00 0.00 3.41
598 611 8.114331 ACAATACACAATCACAATCAGTCAAT 57.886 30.769 0.00 0.00 0.00 2.57
676 2581 0.105453 ACCGGGGAGATGAGCTATGT 60.105 55.000 6.32 0.00 0.00 2.29
722 2630 0.610785 TTTTGTCGGGAGGGGATTGC 60.611 55.000 0.00 0.00 0.00 3.56
740 2648 1.081094 GCGTAACAGGTTGCGGTATT 58.919 50.000 20.88 0.00 46.21 1.89
744 2652 3.429272 CGTAACAGGTTGCGGTATTAGGA 60.429 47.826 13.66 0.00 43.27 2.94
745 2653 2.981859 ACAGGTTGCGGTATTAGGAG 57.018 50.000 0.00 0.00 0.00 3.69
746 2654 2.463752 ACAGGTTGCGGTATTAGGAGA 58.536 47.619 0.00 0.00 0.00 3.71
747 2655 2.431057 ACAGGTTGCGGTATTAGGAGAG 59.569 50.000 0.00 0.00 0.00 3.20
748 2656 2.431057 CAGGTTGCGGTATTAGGAGAGT 59.569 50.000 0.00 0.00 0.00 3.24
749 2657 3.105283 AGGTTGCGGTATTAGGAGAGTT 58.895 45.455 0.00 0.00 0.00 3.01
750 2658 3.518303 AGGTTGCGGTATTAGGAGAGTTT 59.482 43.478 0.00 0.00 0.00 2.66
751 2659 4.019591 AGGTTGCGGTATTAGGAGAGTTTT 60.020 41.667 0.00 0.00 0.00 2.43
753 2661 4.811969 TGCGGTATTAGGAGAGTTTTCA 57.188 40.909 0.00 0.00 0.00 2.69
755 2663 4.120589 GCGGTATTAGGAGAGTTTTCAGG 58.879 47.826 0.00 0.00 0.00 3.86
756 2664 4.120589 CGGTATTAGGAGAGTTTTCAGGC 58.879 47.826 0.00 0.00 0.00 4.85
757 2665 4.141914 CGGTATTAGGAGAGTTTTCAGGCT 60.142 45.833 0.00 0.00 0.00 4.58
758 2666 5.119694 GGTATTAGGAGAGTTTTCAGGCTG 58.880 45.833 8.58 8.58 0.00 4.85
759 2667 2.770164 TAGGAGAGTTTTCAGGCTGC 57.230 50.000 10.34 0.00 0.00 5.25
760 2668 0.321122 AGGAGAGTTTTCAGGCTGCG 60.321 55.000 10.34 0.00 0.00 5.18
761 2669 1.301677 GGAGAGTTTTCAGGCTGCGG 61.302 60.000 10.34 0.00 0.00 5.69
762 2670 0.603975 GAGAGTTTTCAGGCTGCGGT 60.604 55.000 10.34 0.00 0.00 5.68
763 2671 0.685097 AGAGTTTTCAGGCTGCGGTA 59.315 50.000 10.34 0.00 0.00 4.02
764 2672 1.071699 AGAGTTTTCAGGCTGCGGTAA 59.928 47.619 10.34 0.00 0.00 2.85
765 2673 1.197036 GAGTTTTCAGGCTGCGGTAAC 59.803 52.381 10.34 10.57 0.00 2.50
767 2675 1.069227 GTTTTCAGGCTGCGGTAACAG 60.069 52.381 10.34 0.00 40.80 3.16
768 2676 0.394938 TTTCAGGCTGCGGTAACAGA 59.605 50.000 10.34 0.00 40.25 3.41
770 2678 0.613260 TCAGGCTGCGGTAACAGATT 59.387 50.000 10.34 0.00 40.25 2.40
776 2684 2.348666 GCTGCGGTAACAGATTGTGTAG 59.651 50.000 0.00 0.00 39.03 2.74
780 2688 3.242413 GCGGTAACAGATTGTGTAGCATG 60.242 47.826 0.00 0.00 39.03 4.06
794 2727 1.144057 GCATGGTCGGACGAGGATT 59.856 57.895 8.99 0.00 0.00 3.01
814 2747 7.735917 AGGATTGGTCTGACGATTGAAATATA 58.264 34.615 1.07 0.00 0.00 0.86
815 2748 8.210946 AGGATTGGTCTGACGATTGAAATATAA 58.789 33.333 1.07 0.00 0.00 0.98
848 2781 4.013050 GGATTGGAAGAAGAGTTTCCCTG 58.987 47.826 1.88 0.00 42.79 4.45
851 2784 4.618920 TGGAAGAAGAGTTTCCCTGTAC 57.381 45.455 1.88 0.00 42.79 2.90
870 2803 5.472148 TGTACAACGTTCACGAATCCTAAT 58.528 37.500 6.30 0.00 43.02 1.73
909 2842 7.762382 GGTGGATACTCCTTCTGTTAAATTTG 58.238 38.462 0.00 0.00 46.90 2.32
918 2851 9.358872 CTCCTTCTGTTAAATTTGCTTATTTCC 57.641 33.333 0.00 0.00 0.00 3.13
921 2854 9.912634 CTTCTGTTAAATTTGCTTATTTCCTCA 57.087 29.630 0.00 0.57 0.00 3.86
928 2861 7.838771 AATTTGCTTATTTCCTCATCTTTGC 57.161 32.000 0.00 0.00 0.00 3.68
932 2865 4.037327 GCTTATTTCCTCATCTTTGCCCTC 59.963 45.833 0.00 0.00 0.00 4.30
963 2897 0.250553 CCCTTTGGCACCTCAACGTA 60.251 55.000 0.00 0.00 0.00 3.57
1148 6207 3.638160 AGAAGAATTTGCTGTCAGCCAAA 59.362 39.130 21.99 19.85 41.51 3.28
1167 6226 2.938798 AGGCATTCGGGTTCCCCA 60.939 61.111 1.93 0.00 45.83 4.96
1186 6245 2.488355 GGACCTCGATTGCGACGA 59.512 61.111 0.00 0.00 42.51 4.20
1331 6394 2.953466 TGATAACGTCCTTTCCCGAG 57.047 50.000 0.00 0.00 0.00 4.63
1399 6467 0.031314 CTCCACATGATCCCGTCTCG 59.969 60.000 0.00 0.00 0.00 4.04
1544 6626 1.179814 AGCCCGTTCTCTTCGTGTCT 61.180 55.000 0.00 0.00 0.00 3.41
1562 6644 2.745100 CCGTCCTCGTCCGACTCA 60.745 66.667 0.00 0.00 35.01 3.41
1779 6862 0.690762 GGGGTGCAAGAGTTACCTCA 59.309 55.000 0.00 0.00 40.40 3.86
1880 7826 2.383527 CGGCTTCCTTGAGCGTGTC 61.384 63.158 0.00 0.00 43.62 3.67
1881 7827 1.301716 GGCTTCCTTGAGCGTGTCA 60.302 57.895 0.00 0.00 43.62 3.58
1906 7852 0.447801 GTGGATGACCGCATGTTGAC 59.552 55.000 0.00 0.00 45.14 3.18
1923 7872 1.202891 TGACGGTCTGGAGACTCAAGA 60.203 52.381 5.36 5.36 44.20 3.02
1953 7902 5.014858 TGAGTTGGGATTTAGACTACGAGT 58.985 41.667 0.00 0.00 0.00 4.18
2061 8016 1.629861 TGCAGGAAGACCATGTCATCA 59.370 47.619 2.42 0.00 38.94 3.07
2063 8018 3.285484 GCAGGAAGACCATGTCATCAAT 58.715 45.455 2.42 0.00 38.94 2.57
2084 8039 0.973632 TCGCACTGGGTGAGTACATT 59.026 50.000 1.57 0.00 35.23 2.71
2087 8042 3.196901 TCGCACTGGGTGAGTACATTTAT 59.803 43.478 1.57 0.00 35.23 1.40
2093 8048 5.667626 ACTGGGTGAGTACATTTATCAGGAT 59.332 40.000 0.00 0.00 30.86 3.24
2172 8131 4.440112 GCAAGACTTTTAACTGCACACCTT 60.440 41.667 0.00 0.00 0.00 3.50
2264 8240 1.043022 CTTCCAGCCAAGCCAACTTT 58.957 50.000 0.00 0.00 32.29 2.66
2266 8242 0.752054 TCCAGCCAAGCCAACTTTTG 59.248 50.000 0.00 0.00 32.29 2.44
2267 8243 0.752054 CCAGCCAAGCCAACTTTTGA 59.248 50.000 0.00 0.00 32.29 2.69
2284 8260 4.846779 TTTGAAAGCCATGTCCTGTTAC 57.153 40.909 0.00 0.00 0.00 2.50
2285 8261 3.788227 TGAAAGCCATGTCCTGTTACT 57.212 42.857 0.00 0.00 0.00 2.24
2286 8262 4.901197 TGAAAGCCATGTCCTGTTACTA 57.099 40.909 0.00 0.00 0.00 1.82
2330 8847 2.288948 TGCTCCCAAATTGTTCATGCAC 60.289 45.455 0.00 0.00 0.00 4.57
2383 8907 8.743085 ACATAATCAACAATGCATCTAGTTCT 57.257 30.769 0.00 0.00 0.00 3.01
2411 8940 7.637631 AAGTTTTAAATGGTTTGTTTGGCAT 57.362 28.000 0.00 0.00 0.00 4.40
2415 8944 2.837532 ATGGTTTGTTTGGCATGGAC 57.162 45.000 0.00 0.00 0.00 4.02
2416 8945 1.489481 TGGTTTGTTTGGCATGGACA 58.511 45.000 0.00 0.00 0.00 4.02
2455 8984 6.166984 TCAGACCAAGTATCAGGAATCATC 57.833 41.667 0.00 0.00 0.00 2.92
2463 8992 6.690194 AGTATCAGGAATCATCAAGTTTGC 57.310 37.500 0.00 0.00 0.00 3.68
2504 9034 6.153000 TGCCTTTTTCTGTTAACAAGGTGTTA 59.847 34.615 19.62 0.00 41.45 2.41
2573 9103 8.609176 GTGAGAAATTGTTGTGTTTGACTACTA 58.391 33.333 0.00 0.00 32.14 1.82
2956 9498 4.903054 TGACAGTAAGAGAGTCGAGGTAA 58.097 43.478 0.00 0.00 35.09 2.85
2963 9505 4.159244 AGAGAGTCGAGGTAATAGCAGT 57.841 45.455 0.00 0.00 0.00 4.40
3008 9550 1.825474 CCGTAACCAGATCACCTCAGT 59.175 52.381 0.00 0.00 0.00 3.41
3062 9604 2.148768 TGTACTCGAGCGAGAAACTGA 58.851 47.619 24.81 6.52 44.53 3.41
3063 9605 2.095869 TGTACTCGAGCGAGAAACTGAC 60.096 50.000 24.81 12.59 44.53 3.51
3126 9668 5.615289 AGAAAGACACAATAAGCAGACAGT 58.385 37.500 0.00 0.00 0.00 3.55
3174 9716 2.034878 CAGGTAGCATCAGAGTAGGCA 58.965 52.381 0.00 0.00 0.00 4.75
3277 9819 4.586306 TGACTATAGTGGACAGAGGTGA 57.414 45.455 10.90 0.00 0.00 4.02
3333 9875 1.517257 GGAGATGTCAGGACGCGTG 60.517 63.158 20.70 1.51 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 78 1.890510 GCGTGTCGGGGACAAAAGT 60.891 57.895 0.00 0.00 44.49 2.66
74 79 1.566018 GAGCGTGTCGGGGACAAAAG 61.566 60.000 0.00 0.00 44.49 2.27
75 80 1.595929 GAGCGTGTCGGGGACAAAA 60.596 57.895 0.00 0.00 44.49 2.44
76 81 2.029964 GAGCGTGTCGGGGACAAA 59.970 61.111 0.00 0.00 44.49 2.83
100 111 1.070445 GCAGGAGGGTCGGATCATG 59.930 63.158 0.00 0.00 0.00 3.07
101 112 2.143419 GGCAGGAGGGTCGGATCAT 61.143 63.158 0.00 0.00 0.00 2.45
154 167 1.134877 CAGGATCTGACACATCACGCT 60.135 52.381 0.00 0.00 32.44 5.07
162 175 1.222936 CAGCCCCAGGATCTGACAC 59.777 63.158 2.63 0.00 32.44 3.67
506 519 0.534203 GTTCACGGGTTCCAGCAAGA 60.534 55.000 0.00 0.00 0.00 3.02
507 520 0.535102 AGTTCACGGGTTCCAGCAAG 60.535 55.000 0.00 0.00 0.00 4.01
510 523 1.966451 CCAGTTCACGGGTTCCAGC 60.966 63.158 0.00 0.00 0.00 4.85
513 526 0.321034 GGTACCAGTTCACGGGTTCC 60.321 60.000 7.15 8.01 41.69 3.62
514 527 0.668401 CGGTACCAGTTCACGGGTTC 60.668 60.000 13.54 2.40 41.69 3.62
515 528 1.114722 TCGGTACCAGTTCACGGGTT 61.115 55.000 13.54 0.00 41.69 4.11
516 529 1.530013 CTCGGTACCAGTTCACGGGT 61.530 60.000 13.54 6.98 46.09 5.28
518 531 1.214589 CCTCGGTACCAGTTCACGG 59.785 63.158 13.54 0.00 0.00 4.94
521 534 2.967397 CGCCTCGGTACCAGTTCA 59.033 61.111 13.54 0.00 0.00 3.18
522 535 1.660560 TAGCGCCTCGGTACCAGTTC 61.661 60.000 13.54 0.00 38.83 3.01
523 536 1.041447 ATAGCGCCTCGGTACCAGTT 61.041 55.000 13.54 0.00 42.41 3.16
524 537 1.453762 GATAGCGCCTCGGTACCAGT 61.454 60.000 13.54 0.00 42.41 4.00
526 539 1.452953 CTGATAGCGCCTCGGTACCA 61.453 60.000 13.54 0.00 42.41 3.25
527 540 1.286260 CTGATAGCGCCTCGGTACC 59.714 63.158 2.29 0.16 42.41 3.34
529 542 1.901948 CCCTGATAGCGCCTCGGTA 60.902 63.158 2.29 0.61 43.69 4.02
531 544 4.671569 GCCCTGATAGCGCCTCGG 62.672 72.222 2.29 6.60 0.00 4.63
538 551 1.017387 CCAGTTTTCGCCCTGATAGC 58.983 55.000 0.00 0.00 0.00 2.97
541 554 1.000896 CCCCAGTTTTCGCCCTGAT 60.001 57.895 0.00 0.00 0.00 2.90
542 555 1.128809 TACCCCAGTTTTCGCCCTGA 61.129 55.000 0.00 0.00 0.00 3.86
543 556 0.250989 TTACCCCAGTTTTCGCCCTG 60.251 55.000 0.00 0.00 0.00 4.45
544 557 0.037734 CTTACCCCAGTTTTCGCCCT 59.962 55.000 0.00 0.00 0.00 5.19
546 559 1.880894 GCTTACCCCAGTTTTCGCC 59.119 57.895 0.00 0.00 0.00 5.54
547 560 1.500396 CGCTTACCCCAGTTTTCGC 59.500 57.895 0.00 0.00 0.00 4.70
548 561 1.500396 GCGCTTACCCCAGTTTTCG 59.500 57.895 0.00 0.00 0.00 3.46
549 562 0.608308 AGGCGCTTACCCCAGTTTTC 60.608 55.000 7.64 0.00 0.00 2.29
550 563 0.694196 TAGGCGCTTACCCCAGTTTT 59.306 50.000 7.64 0.00 0.00 2.43
551 564 0.035725 GTAGGCGCTTACCCCAGTTT 60.036 55.000 18.21 0.00 0.00 2.66
552 565 1.196104 TGTAGGCGCTTACCCCAGTT 61.196 55.000 24.77 0.00 0.00 3.16
553 566 0.981277 ATGTAGGCGCTTACCCCAGT 60.981 55.000 24.77 5.24 0.00 4.00
554 567 1.045407 TATGTAGGCGCTTACCCCAG 58.955 55.000 24.77 0.00 0.00 4.45
555 568 0.754472 GTATGTAGGCGCTTACCCCA 59.246 55.000 24.77 8.86 0.00 4.96
556 569 0.754472 TGTATGTAGGCGCTTACCCC 59.246 55.000 24.77 13.67 0.00 4.95
557 570 2.607631 TTGTATGTAGGCGCTTACCC 57.392 50.000 24.77 13.99 0.00 3.69
558 571 4.446719 GTGTATTGTATGTAGGCGCTTACC 59.553 45.833 24.77 11.61 0.00 2.85
559 572 5.045215 TGTGTATTGTATGTAGGCGCTTAC 58.955 41.667 21.65 21.65 0.00 2.34
560 573 5.265350 TGTGTATTGTATGTAGGCGCTTA 57.735 39.130 7.64 0.00 0.00 3.09
561 574 4.131649 TGTGTATTGTATGTAGGCGCTT 57.868 40.909 7.64 0.52 0.00 4.68
562 575 3.812156 TGTGTATTGTATGTAGGCGCT 57.188 42.857 7.64 0.00 0.00 5.92
564 577 5.522097 TGTGATTGTGTATTGTATGTAGGCG 59.478 40.000 0.00 0.00 0.00 5.52
566 579 9.108284 TGATTGTGATTGTGTATTGTATGTAGG 57.892 33.333 0.00 0.00 0.00 3.18
568 581 9.665719 ACTGATTGTGATTGTGTATTGTATGTA 57.334 29.630 0.00 0.00 0.00 2.29
570 583 8.667463 TGACTGATTGTGATTGTGTATTGTATG 58.333 33.333 0.00 0.00 0.00 2.39
571 584 8.791327 TGACTGATTGTGATTGTGTATTGTAT 57.209 30.769 0.00 0.00 0.00 2.29
572 585 8.614469 TTGACTGATTGTGATTGTGTATTGTA 57.386 30.769 0.00 0.00 0.00 2.41
573 586 7.509141 TTGACTGATTGTGATTGTGTATTGT 57.491 32.000 0.00 0.00 0.00 2.71
574 587 7.427318 CGATTGACTGATTGTGATTGTGTATTG 59.573 37.037 0.00 0.00 0.00 1.90
575 588 7.334171 TCGATTGACTGATTGTGATTGTGTATT 59.666 33.333 0.00 0.00 0.00 1.89
576 589 6.818142 TCGATTGACTGATTGTGATTGTGTAT 59.182 34.615 0.00 0.00 0.00 2.29
578 591 4.996758 TCGATTGACTGATTGTGATTGTGT 59.003 37.500 0.00 0.00 0.00 3.72
579 592 5.319139 GTCGATTGACTGATTGTGATTGTG 58.681 41.667 5.79 0.00 42.08 3.33
580 593 4.091945 CGTCGATTGACTGATTGTGATTGT 59.908 41.667 11.37 0.00 43.21 2.71
581 594 4.493057 CCGTCGATTGACTGATTGTGATTG 60.493 45.833 11.37 0.00 43.21 2.67
582 595 3.618594 CCGTCGATTGACTGATTGTGATT 59.381 43.478 11.37 0.00 43.21 2.57
583 596 3.190079 CCGTCGATTGACTGATTGTGAT 58.810 45.455 11.37 0.00 43.21 3.06
586 599 1.359848 GCCGTCGATTGACTGATTGT 58.640 50.000 11.37 0.00 43.21 2.71
587 600 0.298707 CGCCGTCGATTGACTGATTG 59.701 55.000 11.37 0.00 43.21 2.67
589 602 1.807226 TCGCCGTCGATTGACTGAT 59.193 52.632 11.37 0.00 43.21 2.90
590 603 3.270000 TCGCCGTCGATTGACTGA 58.730 55.556 11.37 3.85 43.21 3.41
598 611 3.744719 CTCCAAGGTCGCCGTCGA 61.745 66.667 0.00 0.00 43.28 4.20
676 2581 6.156519 CAGTAATTATCCCGATCGTTCATGA 58.843 40.000 15.09 0.00 0.00 3.07
712 2620 0.252197 ACCTGTTACGCAATCCCCTC 59.748 55.000 0.00 0.00 0.00 4.30
713 2621 0.696501 AACCTGTTACGCAATCCCCT 59.303 50.000 0.00 0.00 0.00 4.79
717 2625 0.179200 CCGCAACCTGTTACGCAATC 60.179 55.000 0.00 0.00 0.00 2.67
722 2630 2.861935 CCTAATACCGCAACCTGTTACG 59.138 50.000 0.00 0.00 0.00 3.18
740 2648 1.066858 CGCAGCCTGAAAACTCTCCTA 60.067 52.381 0.00 0.00 0.00 2.94
744 2652 0.685097 TACCGCAGCCTGAAAACTCT 59.315 50.000 0.00 0.00 0.00 3.24
745 2653 1.197036 GTTACCGCAGCCTGAAAACTC 59.803 52.381 0.00 0.00 0.00 3.01
746 2654 1.235724 GTTACCGCAGCCTGAAAACT 58.764 50.000 0.00 0.00 0.00 2.66
747 2655 0.948678 TGTTACCGCAGCCTGAAAAC 59.051 50.000 0.00 0.00 0.00 2.43
748 2656 1.202710 TCTGTTACCGCAGCCTGAAAA 60.203 47.619 0.00 0.00 36.49 2.29
749 2657 0.394938 TCTGTTACCGCAGCCTGAAA 59.605 50.000 0.00 0.00 36.49 2.69
750 2658 0.613260 ATCTGTTACCGCAGCCTGAA 59.387 50.000 0.00 0.00 36.49 3.02
751 2659 0.613260 AATCTGTTACCGCAGCCTGA 59.387 50.000 0.00 0.00 36.49 3.86
753 2661 0.324943 ACAATCTGTTACCGCAGCCT 59.675 50.000 0.00 0.00 36.49 4.58
755 2663 1.156736 ACACAATCTGTTACCGCAGC 58.843 50.000 0.00 0.00 36.49 5.25
756 2664 2.348666 GCTACACAATCTGTTACCGCAG 59.651 50.000 0.00 0.00 37.81 5.18
757 2665 2.289133 TGCTACACAATCTGTTACCGCA 60.289 45.455 0.00 0.00 33.91 5.69
758 2666 2.343101 TGCTACACAATCTGTTACCGC 58.657 47.619 0.00 0.00 33.91 5.68
759 2667 3.309682 CCATGCTACACAATCTGTTACCG 59.690 47.826 0.00 0.00 33.91 4.02
760 2668 4.261801 ACCATGCTACACAATCTGTTACC 58.738 43.478 0.00 0.00 33.91 2.85
761 2669 4.032900 CGACCATGCTACACAATCTGTTAC 59.967 45.833 0.00 0.00 33.91 2.50
762 2670 4.180817 CGACCATGCTACACAATCTGTTA 58.819 43.478 0.00 0.00 33.91 2.41
763 2671 3.002791 CGACCATGCTACACAATCTGTT 58.997 45.455 0.00 0.00 33.91 3.16
764 2672 2.621338 CGACCATGCTACACAATCTGT 58.379 47.619 0.00 0.00 36.82 3.41
765 2673 1.935873 CCGACCATGCTACACAATCTG 59.064 52.381 0.00 0.00 0.00 2.90
767 2675 1.933853 GTCCGACCATGCTACACAATC 59.066 52.381 0.00 0.00 0.00 2.67
768 2676 1.739035 CGTCCGACCATGCTACACAAT 60.739 52.381 0.00 0.00 0.00 2.71
770 2678 1.214325 CGTCCGACCATGCTACACA 59.786 57.895 0.00 0.00 0.00 3.72
776 2684 1.144057 AATCCTCGTCCGACCATGC 59.856 57.895 0.00 0.00 0.00 4.06
780 2688 1.141234 GACCAATCCTCGTCCGACC 59.859 63.158 0.00 0.00 0.00 4.79
794 2727 8.956533 TGATTTATATTTCAATCGTCAGACCA 57.043 30.769 0.00 0.00 32.83 4.02
814 2747 3.056107 TCTTCCAATCCGACGTCTGATTT 60.056 43.478 26.54 13.32 29.24 2.17
815 2748 2.496070 TCTTCCAATCCGACGTCTGATT 59.504 45.455 24.30 24.30 31.36 2.57
848 2781 7.689953 ATATTAGGATTCGTGAACGTTGTAC 57.310 36.000 5.00 3.67 40.80 2.90
851 2784 7.646526 TGTCTATATTAGGATTCGTGAACGTTG 59.353 37.037 5.00 0.00 40.80 4.10
870 2803 6.375830 AGTATCCACCGATCTCTGTCTATA 57.624 41.667 0.00 0.00 0.00 1.31
904 2837 6.820152 GGCAAAGATGAGGAAATAAGCAAATT 59.180 34.615 0.00 0.00 0.00 1.82
909 2842 3.956848 AGGGCAAAGATGAGGAAATAAGC 59.043 43.478 0.00 0.00 0.00 3.09
918 2851 2.817423 GCGCGAGGGCAAAGATGAG 61.817 63.158 12.10 0.00 39.92 2.90
944 2877 0.250553 TACGTTGAGGTGCCAAAGGG 60.251 55.000 0.00 0.00 31.37 3.95
948 2882 2.552599 TGAATACGTTGAGGTGCCAA 57.447 45.000 0.00 0.00 0.00 4.52
960 2894 2.600731 GCGGAGAGGATGATGAATACG 58.399 52.381 0.00 0.00 0.00 3.06
963 2897 0.319728 CGGCGGAGAGGATGATGAAT 59.680 55.000 0.00 0.00 0.00 2.57
1011 2959 3.364889 TTCGTCGGCTGATAGTATTGG 57.635 47.619 0.00 0.00 0.00 3.16
1043 2991 2.202892 GGCGAGGGTGGAATCGTC 60.203 66.667 0.00 0.00 40.97 4.20
1044 2992 2.240162 GAAGGCGAGGGTGGAATCGT 62.240 60.000 0.00 0.00 40.97 3.73
1045 2993 1.521681 GAAGGCGAGGGTGGAATCG 60.522 63.158 0.00 0.00 41.79 3.34
1048 2999 3.327404 GGGAAGGCGAGGGTGGAA 61.327 66.667 0.00 0.00 0.00 3.53
1052 3006 2.529389 AACAGGGAAGGCGAGGGT 60.529 61.111 0.00 0.00 0.00 4.34
1103 6156 4.388499 TCGGCTGTTTCCTCGCCC 62.388 66.667 0.00 0.00 40.70 6.13
1109 6162 1.305201 TCTTGTTGTCGGCTGTTTCC 58.695 50.000 0.00 0.00 0.00 3.13
1167 6226 2.181021 GTCGCAATCGAGGTCCGT 59.819 61.111 0.00 0.00 46.46 4.69
1232 6291 2.265739 GTCAGGCGGCACAGATCA 59.734 61.111 13.08 0.00 0.00 2.92
1331 6394 0.390735 AGATGTCGCGGTGGTAAACC 60.391 55.000 6.13 0.00 46.60 3.27
1457 6532 0.610174 AGCACATGTCATCGTCCTGT 59.390 50.000 0.00 0.00 0.00 4.00
1459 6534 1.202302 CGTAGCACATGTCATCGTCCT 60.202 52.381 0.00 0.00 0.00 3.85
1544 6626 2.435586 GAGTCGGACGAGGACGGA 60.436 66.667 1.89 0.00 44.46 4.69
1562 6644 0.543749 GCTTGGCTATCTCCCACTGT 59.456 55.000 0.00 0.00 30.65 3.55
1779 6862 2.692557 CTGGTATGTAGTCTCTGCAGCT 59.307 50.000 9.47 2.89 28.38 4.24
1880 7826 1.452110 TGCGGTCATCCACAAGATTG 58.548 50.000 0.00 0.00 30.59 2.67
1881 7827 2.019249 CATGCGGTCATCCACAAGATT 58.981 47.619 0.00 0.00 30.59 2.40
1902 7848 1.613925 CTTGAGTCTCCAGACCGTCAA 59.386 52.381 2.96 7.07 45.85 3.18
1906 7852 2.558795 TCTTTCTTGAGTCTCCAGACCG 59.441 50.000 3.14 0.00 45.85 4.79
2061 8016 2.224426 TGTACTCACCCAGTGCGAAATT 60.224 45.455 0.00 0.00 40.53 1.82
2063 8018 0.753867 TGTACTCACCCAGTGCGAAA 59.246 50.000 0.00 0.00 40.53 3.46
2084 8039 2.365617 GCAGAACTCCGGATCCTGATAA 59.634 50.000 23.69 0.00 0.00 1.75
2087 8042 0.324738 AGCAGAACTCCGGATCCTGA 60.325 55.000 23.69 8.06 0.00 3.86
2093 8048 0.984230 ATGGAAAGCAGAACTCCGGA 59.016 50.000 2.93 2.93 31.37 5.14
2172 8131 1.587043 CTGGCGTCCGTGAGAGAGAA 61.587 60.000 0.00 0.00 0.00 2.87
2264 8240 4.098914 AGTAACAGGACATGGCTTTCAA 57.901 40.909 0.00 0.00 0.00 2.69
2266 8242 4.833390 ACTAGTAACAGGACATGGCTTTC 58.167 43.478 0.00 0.00 0.00 2.62
2267 8243 4.910458 ACTAGTAACAGGACATGGCTTT 57.090 40.909 0.00 0.00 0.00 3.51
2284 8260 7.912250 CAGCAAGCAATAAAATCACCTAACTAG 59.088 37.037 0.00 0.00 0.00 2.57
2285 8261 7.628366 GCAGCAAGCAATAAAATCACCTAACTA 60.628 37.037 0.00 0.00 44.79 2.24
2286 8262 6.624423 CAGCAAGCAATAAAATCACCTAACT 58.376 36.000 0.00 0.00 0.00 2.24
2359 8883 9.661187 GAAGAACTAGATGCATTGTTGATTATG 57.339 33.333 15.15 0.00 0.00 1.90
2383 8907 8.884726 GCCAAACAAACCATTTAAAACTTAGAA 58.115 29.630 0.00 0.00 0.00 2.10
2411 8940 1.284491 TGCTTCCATATTGCCTGTCCA 59.716 47.619 0.00 0.00 0.00 4.02
2415 8944 3.252701 GTCTGATGCTTCCATATTGCCTG 59.747 47.826 0.00 0.00 0.00 4.85
2416 8945 3.484407 GTCTGATGCTTCCATATTGCCT 58.516 45.455 0.00 0.00 0.00 4.75
2484 9013 7.066525 CCAGAGTAACACCTTGTTAACAGAAAA 59.933 37.037 8.56 0.00 43.57 2.29
2504 9034 1.280421 GGGATTGACTTGAGCCAGAGT 59.720 52.381 0.00 0.00 0.00 3.24
2573 9103 8.903820 GGAAATACTAGTTGCTGTTTATCCAAT 58.096 33.333 0.00 0.00 0.00 3.16
2944 9486 3.628487 GTGACTGCTATTACCTCGACTCT 59.372 47.826 0.00 0.00 0.00 3.24
2956 9498 4.263462 TGAGGATTTTGGTGTGACTGCTAT 60.263 41.667 0.00 0.00 0.00 2.97
2963 9505 4.825085 GGTTACTTGAGGATTTTGGTGTGA 59.175 41.667 0.00 0.00 0.00 3.58
3008 9550 2.106074 GCCATGGCGATGTTGACGA 61.106 57.895 23.48 0.00 0.00 4.20
3062 9604 3.869065 TGGAAGACAAAGAAACAGACGT 58.131 40.909 0.00 0.00 0.00 4.34
3063 9605 3.248602 CCTGGAAGACAAAGAAACAGACG 59.751 47.826 0.00 0.00 34.07 4.18
3126 9668 0.466372 ATCCCTCTGATCGACGCTCA 60.466 55.000 0.96 0.96 0.00 4.26
3254 9796 6.262056 TCACCTCTGTCCACTATAGTCATA 57.738 41.667 1.26 0.00 0.00 2.15
3277 9819 2.092429 TGAGTCAGTTTGTTTCAGCCCT 60.092 45.455 0.00 0.00 0.00 5.19
3333 9875 3.616379 GCAGTCTTGTCTATCTTGCTGTC 59.384 47.826 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.