Multiple sequence alignment - TraesCS4B01G309900

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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 TraesCS4B01G309900 chr4B 100.000 3404 0 0 1 3404 600518772 600515369 0.000000e+00 6287.0
1 TraesCS4B01G309900 chr4B 95.742 2043 69 7 783 2823 600606381 600604355 0.000000e+00 3275.0
2 TraesCS4B01G309900 chr4B 95.018 843 34 6 1647 2486 600599336 600598499 0.000000e+00 1317.0
3 TraesCS4B01G309900 chr4B 92.699 589 42 1 2815 3403 600604116 600603529 0.000000e+00 848.0
4 TraesCS4B01G309900 chr4B 94.737 38 2 0 1072 1109 600606058 600606021 3.670000e-05 60.2
5 TraesCS4B01G309900 chr4A 88.493 2355 161 59 684 2983 683443568 683441269 0.000000e+00 2747.0
6 TraesCS4B01G309900 chr4A 91.667 48 2 2 578 623 574788442 574788395 7.880000e-07 65.8
7 TraesCS4B01G309900 chr4D 93.938 1798 61 14 885 2662 476229826 476228057 0.000000e+00 2673.0
8 TraesCS4B01G309900 chr4D 91.057 246 16 1 648 887 476230102 476229857 9.110000e-86 327.0
9 TraesCS4B01G309900 chr4D 91.480 223 18 1 1 222 485410629 485410851 4.270000e-79 305.0
10 TraesCS4B01G309900 chr4D 85.401 137 20 0 3118 3254 51987135 51986999 3.540000e-30 143.0
11 TraesCS4B01G309900 chr4D 83.942 137 22 0 3118 3254 51922461 51922325 7.660000e-27 132.0
12 TraesCS4B01G309900 chrUn 97.409 579 14 1 1 578 37062281 37062859 0.000000e+00 985.0
13 TraesCS4B01G309900 chrUn 82.530 332 54 3 1105 1436 18084743 18085070 4.300000e-74 289.0
14 TraesCS4B01G309900 chrUn 79.353 402 50 18 6 396 61000746 61000367 5.640000e-63 252.0
15 TraesCS4B01G309900 chrUn 86.364 110 15 0 2295 2404 18133294 18133403 1.660000e-23 121.0
16 TraesCS4B01G309900 chr2B 80.225 1335 207 40 1112 2410 24882780 24884093 0.000000e+00 950.0
17 TraesCS4B01G309900 chr2B 80.304 1315 210 37 1112 2406 24905698 24906983 0.000000e+00 948.0
18 TraesCS4B01G309900 chr2B 80.000 1335 200 51 1116 2410 24889260 24890567 0.000000e+00 924.0
19 TraesCS4B01G309900 chr2B 76.172 256 42 7 3132 3369 798141935 798142189 2.150000e-22 117.0
20 TraesCS4B01G309900 chr2B 92.157 51 4 0 528 578 207848391 207848341 4.710000e-09 73.1
21 TraesCS4B01G309900 chr2B 100.000 36 0 0 530 565 541908630 541908595 2.190000e-07 67.6
22 TraesCS4B01G309900 chr2A 79.623 1325 214 38 1120 2408 15906134 15904830 0.000000e+00 900.0
23 TraesCS4B01G309900 chr2A 80.706 850 132 22 1589 2410 15642268 15643113 1.720000e-177 632.0
24 TraesCS4B01G309900 chr2A 86.719 384 45 5 1116 1499 15641779 15642156 4.060000e-114 422.0
25 TraesCS4B01G309900 chr2A 81.265 411 70 5 1105 1515 14892712 14892309 3.280000e-85 326.0
26 TraesCS4B01G309900 chr3D 89.310 580 52 5 1 577 28867644 28867072 0.000000e+00 719.0
27 TraesCS4B01G309900 chr3D 80.471 297 47 6 3119 3404 350860107 350860403 2.060000e-52 217.0
28 TraesCS4B01G309900 chr3D 82.540 126 22 0 3118 3243 584365239 584365114 9.990000e-21 111.0
29 TraesCS4B01G309900 chr3D 93.333 45 2 1 517 560 17340556 17340600 7.880000e-07 65.8
30 TraesCS4B01G309900 chr2D 86.747 581 64 4 1 577 438016518 438017089 4.790000e-178 634.0
31 TraesCS4B01G309900 chr2D 89.714 350 29 4 1 346 412279734 412280080 1.120000e-119 440.0
32 TraesCS4B01G309900 chr2D 86.232 276 31 2 305 578 412280007 412280277 3.320000e-75 292.0
33 TraesCS4B01G309900 chr2D 77.852 298 45 12 3118 3395 513034708 513035004 7.560000e-37 165.0
34 TraesCS4B01G309900 chr7A 76.005 821 157 24 1582 2391 66166809 66166018 4.120000e-104 388.0
35 TraesCS4B01G309900 chr7A 80.798 401 57 15 4 392 636699278 636699670 2.570000e-76 296.0
36 TraesCS4B01G309900 chr7A 76.792 293 47 12 3118 3390 37108033 37107742 9.840000e-31 145.0
37 TraesCS4B01G309900 chr7A 91.667 48 2 2 578 623 120468577 120468530 7.880000e-07 65.8
38 TraesCS4B01G309900 chr7B 75.488 820 171 22 1582 2391 3695866 3695067 1.150000e-99 374.0
39 TraesCS4B01G309900 chr7B 80.833 120 23 0 3124 3243 402818999 402819118 1.010000e-15 95.3
40 TraesCS4B01G309900 chr7D 79.926 543 73 20 1 538 167835075 167835586 1.930000e-97 366.0
41 TraesCS4B01G309900 chr7D 75.336 819 162 23 1582 2391 63377830 63377043 1.160000e-94 357.0
42 TraesCS4B01G309900 chr7D 92.823 209 14 1 1 208 155299863 155300071 5.520000e-78 302.0
43 TraesCS4B01G309900 chr7D 76.796 181 32 7 3117 3288 84428034 84428213 3.620000e-15 93.5
44 TraesCS4B01G309900 chr6D 83.523 352 35 10 2 346 409779939 409780274 1.190000e-79 307.0
45 TraesCS4B01G309900 chr6D 80.288 208 30 7 2634 2834 464054972 464054769 2.740000e-31 147.0
46 TraesCS4B01G309900 chr6D 90.000 60 6 0 519 578 54751312 54751371 1.010000e-10 78.7
47 TraesCS4B01G309900 chr1D 79.602 402 48 19 6 396 464275603 464275225 1.210000e-64 257.0
48 TraesCS4B01G309900 chr1D 97.436 39 1 0 527 565 18808422 18808460 2.190000e-07 67.6
49 TraesCS4B01G309900 chr1D 100.000 30 0 0 2546 2575 7806301 7806330 4.750000e-04 56.5
50 TraesCS4B01G309900 chr6B 78.856 402 52 19 6 396 51552703 51552324 1.220000e-59 241.0
51 TraesCS4B01G309900 chr1A 78.856 402 52 19 6 396 515953271 515953650 1.220000e-59 241.0
52 TraesCS4B01G309900 chr1A 88.462 52 6 0 514 565 29154037 29154088 2.840000e-06 63.9
53 TraesCS4B01G309900 chr5D 79.474 190 28 7 3225 3404 400266524 400266712 1.280000e-24 124.0
54 TraesCS4B01G309900 chr5B 95.238 42 2 0 524 565 590549197 590549238 2.190000e-07 67.6
55 TraesCS4B01G309900 chr5A 90.698 43 4 0 2199 2241 514161206 514161248 1.320000e-04 58.4


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 TraesCS4B01G309900 chr4B 600515369 600518772 3403 True 6287.0 6287 100.000000 1 3404 1 chr4B.!!$R1 3403
1 TraesCS4B01G309900 chr4B 600603529 600606381 2852 True 1394.4 3275 94.392667 783 3403 3 chr4B.!!$R3 2620
2 TraesCS4B01G309900 chr4B 600598499 600599336 837 True 1317.0 1317 95.018000 1647 2486 1 chr4B.!!$R2 839
3 TraesCS4B01G309900 chr4A 683441269 683443568 2299 True 2747.0 2747 88.493000 684 2983 1 chr4A.!!$R2 2299
4 TraesCS4B01G309900 chr4D 476228057 476230102 2045 True 1500.0 2673 92.497500 648 2662 2 chr4D.!!$R3 2014
5 TraesCS4B01G309900 chrUn 37062281 37062859 578 False 985.0 985 97.409000 1 578 1 chrUn.!!$F3 577
6 TraesCS4B01G309900 chr2B 24882780 24884093 1313 False 950.0 950 80.225000 1112 2410 1 chr2B.!!$F1 1298
7 TraesCS4B01G309900 chr2B 24905698 24906983 1285 False 948.0 948 80.304000 1112 2406 1 chr2B.!!$F3 1294
8 TraesCS4B01G309900 chr2B 24889260 24890567 1307 False 924.0 924 80.000000 1116 2410 1 chr2B.!!$F2 1294
9 TraesCS4B01G309900 chr2A 15904830 15906134 1304 True 900.0 900 79.623000 1120 2408 1 chr2A.!!$R2 1288
10 TraesCS4B01G309900 chr2A 15641779 15643113 1334 False 527.0 632 83.712500 1116 2410 2 chr2A.!!$F1 1294
11 TraesCS4B01G309900 chr3D 28867072 28867644 572 True 719.0 719 89.310000 1 577 1 chr3D.!!$R1 576
12 TraesCS4B01G309900 chr2D 438016518 438017089 571 False 634.0 634 86.747000 1 577 1 chr2D.!!$F1 576
13 TraesCS4B01G309900 chr2D 412279734 412280277 543 False 366.0 440 87.973000 1 578 2 chr2D.!!$F3 577
14 TraesCS4B01G309900 chr7A 66166018 66166809 791 True 388.0 388 76.005000 1582 2391 1 chr7A.!!$R2 809
15 TraesCS4B01G309900 chr7B 3695067 3695866 799 True 374.0 374 75.488000 1582 2391 1 chr7B.!!$R1 809
16 TraesCS4B01G309900 chr7D 167835075 167835586 511 False 366.0 366 79.926000 1 538 1 chr7D.!!$F3 537
17 TraesCS4B01G309900 chr7D 63377043 63377830 787 True 357.0 357 75.336000 1582 2391 1 chr7D.!!$R1 809

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
644 682 0.453390 GCAAGCCGCATTTTCTAGCT 59.547 50.000 0.00 0.0 41.79 3.32 F
700 738 0.657840 GAAGCAGCGATGGCGTTAAT 59.342 50.000 1.46 0.0 46.35 1.40 F
1785 1945 1.000506 GACGACAAGTTCCACTGCCTA 59.999 52.381 0.00 0.0 0.00 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1573 1715 1.154169 GCACGTACCACGATCGACA 60.154 57.895 24.34 0.02 46.05 4.35 R
1834 1994 2.183300 GTCGTGGCAGGCGATGTA 59.817 61.111 3.45 0.00 40.59 2.29 R
3282 3755 0.101399 CTACCATTCGTCTGAGCGCT 59.899 55.000 11.27 11.27 0.00 5.92 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
188 190 3.665675 GAGCATCAACGGCGAGGGT 62.666 63.158 16.62 0.00 36.08 4.34
578 616 3.794270 GCGCAAATCACTCGCCTA 58.206 55.556 0.30 0.00 42.71 3.93
579 617 1.348594 GCGCAAATCACTCGCCTAC 59.651 57.895 0.30 0.00 42.71 3.18
580 618 1.084370 GCGCAAATCACTCGCCTACT 61.084 55.000 0.30 0.00 42.71 2.57
581 619 1.359848 CGCAAATCACTCGCCTACTT 58.640 50.000 0.00 0.00 0.00 2.24
582 620 1.061131 CGCAAATCACTCGCCTACTTG 59.939 52.381 0.00 0.00 0.00 3.16
583 621 2.346803 GCAAATCACTCGCCTACTTGA 58.653 47.619 0.00 0.00 0.00 3.02
584 622 2.742053 GCAAATCACTCGCCTACTTGAA 59.258 45.455 0.00 0.00 0.00 2.69
585 623 3.188460 GCAAATCACTCGCCTACTTGAAA 59.812 43.478 0.00 0.00 0.00 2.69
586 624 4.142600 GCAAATCACTCGCCTACTTGAAAT 60.143 41.667 0.00 0.00 0.00 2.17
587 625 5.327091 CAAATCACTCGCCTACTTGAAATG 58.673 41.667 0.00 0.00 0.00 2.32
588 626 2.346803 TCACTCGCCTACTTGAAATGC 58.653 47.619 0.00 0.00 0.00 3.56
589 627 2.028112 TCACTCGCCTACTTGAAATGCT 60.028 45.455 0.00 0.00 0.00 3.79
590 628 2.744202 CACTCGCCTACTTGAAATGCTT 59.256 45.455 0.00 0.00 0.00 3.91
591 629 3.003480 ACTCGCCTACTTGAAATGCTTC 58.997 45.455 0.00 0.00 0.00 3.86
592 630 1.999735 TCGCCTACTTGAAATGCTTCG 59.000 47.619 0.00 0.00 33.94 3.79
593 631 1.062587 CGCCTACTTGAAATGCTTCGG 59.937 52.381 0.00 0.00 33.94 4.30
594 632 2.084546 GCCTACTTGAAATGCTTCGGT 58.915 47.619 0.00 0.00 33.94 4.69
595 633 2.159517 GCCTACTTGAAATGCTTCGGTG 60.160 50.000 0.00 0.00 33.94 4.94
596 634 2.420022 CCTACTTGAAATGCTTCGGTGG 59.580 50.000 0.00 0.00 33.94 4.61
597 635 1.981256 ACTTGAAATGCTTCGGTGGT 58.019 45.000 0.00 0.00 33.94 4.16
598 636 2.306847 ACTTGAAATGCTTCGGTGGTT 58.693 42.857 0.00 0.00 33.94 3.67
599 637 2.034558 ACTTGAAATGCTTCGGTGGTTG 59.965 45.455 0.00 0.00 33.94 3.77
600 638 1.686355 TGAAATGCTTCGGTGGTTGT 58.314 45.000 0.00 0.00 33.94 3.32
601 639 2.852449 TGAAATGCTTCGGTGGTTGTA 58.148 42.857 0.00 0.00 33.94 2.41
602 640 3.417101 TGAAATGCTTCGGTGGTTGTAT 58.583 40.909 0.00 0.00 33.94 2.29
603 641 4.580868 TGAAATGCTTCGGTGGTTGTATA 58.419 39.130 0.00 0.00 33.94 1.47
604 642 5.004448 TGAAATGCTTCGGTGGTTGTATAA 58.996 37.500 0.00 0.00 33.94 0.98
605 643 5.473846 TGAAATGCTTCGGTGGTTGTATAAA 59.526 36.000 0.00 0.00 33.94 1.40
606 644 6.151985 TGAAATGCTTCGGTGGTTGTATAAAT 59.848 34.615 0.00 0.00 33.94 1.40
607 645 7.337184 TGAAATGCTTCGGTGGTTGTATAAATA 59.663 33.333 0.00 0.00 33.94 1.40
608 646 6.861065 ATGCTTCGGTGGTTGTATAAATAG 57.139 37.500 0.00 0.00 0.00 1.73
609 647 5.979993 TGCTTCGGTGGTTGTATAAATAGA 58.020 37.500 0.00 0.00 0.00 1.98
610 648 6.588204 TGCTTCGGTGGTTGTATAAATAGAT 58.412 36.000 0.00 0.00 0.00 1.98
611 649 7.051623 TGCTTCGGTGGTTGTATAAATAGATT 58.948 34.615 0.00 0.00 0.00 2.40
612 650 7.011950 TGCTTCGGTGGTTGTATAAATAGATTG 59.988 37.037 0.00 0.00 0.00 2.67
613 651 7.225931 GCTTCGGTGGTTGTATAAATAGATTGA 59.774 37.037 0.00 0.00 0.00 2.57
614 652 9.104965 CTTCGGTGGTTGTATAAATAGATTGAA 57.895 33.333 0.00 0.00 0.00 2.69
615 653 8.428186 TCGGTGGTTGTATAAATAGATTGAAC 57.572 34.615 0.00 0.00 0.00 3.18
616 654 8.041919 TCGGTGGTTGTATAAATAGATTGAACA 58.958 33.333 0.00 0.00 0.00 3.18
617 655 8.670135 CGGTGGTTGTATAAATAGATTGAACAA 58.330 33.333 0.00 0.00 0.00 2.83
630 668 6.973229 AGATTGAACAAAAATATGGCAAGC 57.027 33.333 0.00 0.00 0.00 4.01
631 669 5.876460 AGATTGAACAAAAATATGGCAAGCC 59.124 36.000 3.61 3.61 30.50 4.35
632 670 3.583806 TGAACAAAAATATGGCAAGCCG 58.416 40.909 6.60 0.00 39.42 5.52
633 671 2.008752 ACAAAAATATGGCAAGCCGC 57.991 45.000 6.60 0.00 39.42 6.53
634 672 1.274728 ACAAAAATATGGCAAGCCGCA 59.725 42.857 6.60 0.00 45.17 5.69
635 673 2.093553 ACAAAAATATGGCAAGCCGCAT 60.094 40.909 6.60 0.00 45.17 4.73
636 674 2.937799 CAAAAATATGGCAAGCCGCATT 59.062 40.909 6.60 5.47 45.17 3.56
637 675 2.985957 AAATATGGCAAGCCGCATTT 57.014 40.000 13.72 13.72 45.17 2.32
638 676 2.985957 AATATGGCAAGCCGCATTTT 57.014 40.000 6.60 0.00 45.17 1.82
639 677 2.514205 ATATGGCAAGCCGCATTTTC 57.486 45.000 6.60 0.00 45.17 2.29
640 678 1.473258 TATGGCAAGCCGCATTTTCT 58.527 45.000 6.60 0.00 45.17 2.52
641 679 1.473258 ATGGCAAGCCGCATTTTCTA 58.527 45.000 6.60 0.00 45.17 2.10
642 680 0.810648 TGGCAAGCCGCATTTTCTAG 59.189 50.000 6.60 0.00 45.17 2.43
643 681 0.526310 GGCAAGCCGCATTTTCTAGC 60.526 55.000 0.00 0.00 45.17 3.42
644 682 0.453390 GCAAGCCGCATTTTCTAGCT 59.547 50.000 0.00 0.00 41.79 3.32
645 683 1.670811 GCAAGCCGCATTTTCTAGCTA 59.329 47.619 0.00 0.00 41.79 3.32
646 684 2.286654 GCAAGCCGCATTTTCTAGCTAG 60.287 50.000 15.01 15.01 41.79 3.42
660 698 4.082845 TCTAGCTAGTGGAGATACATGGC 58.917 47.826 20.10 0.00 0.00 4.40
700 738 0.657840 GAAGCAGCGATGGCGTTAAT 59.342 50.000 1.46 0.00 46.35 1.40
759 811 2.124736 GGCATCTAGGCGTTGGCA 60.125 61.111 0.00 0.00 42.47 4.92
776 828 2.031516 CACAACCAGCGAGCTCCAG 61.032 63.158 8.47 0.00 0.00 3.86
777 829 3.123620 CAACCAGCGAGCTCCAGC 61.124 66.667 8.47 6.83 42.49 4.85
1077 1185 3.717294 AAGCCCGATCACGCCCTT 61.717 61.111 0.00 0.00 38.29 3.95
1162 1270 2.669569 GCCTGAACAAGCGCCTCA 60.670 61.111 2.29 0.86 0.00 3.86
1785 1945 1.000506 GACGACAAGTTCCACTGCCTA 59.999 52.381 0.00 0.00 0.00 3.93
1951 2129 1.152419 TGTGTCTTCCTCCCCGACA 60.152 57.895 0.00 0.00 35.49 4.35
2355 2550 0.035343 TCGTCATCGAGGAGGTGTCT 60.035 55.000 18.00 0.00 41.35 3.41
2570 2793 6.486253 TGTTTTAGTTGCATTGCACAAAAA 57.514 29.167 11.66 14.22 38.71 1.94
2593 2816 3.006967 ACAAAGGTTCATACGACTCTGCT 59.993 43.478 0.00 0.00 0.00 4.24
2619 2842 6.630131 TCATTGGAACTAGATGATACCCCTA 58.370 40.000 0.00 0.00 0.00 3.53
2620 2843 7.256399 TCATTGGAACTAGATGATACCCCTAT 58.744 38.462 0.00 0.00 0.00 2.57
2639 2864 5.178061 CCTATGTGTTGCAGTGAGAACATA 58.822 41.667 10.36 8.72 34.69 2.29
2741 2966 6.554419 ACACATGATTTGTTGTATTGGATCG 58.446 36.000 0.00 0.00 36.00 3.69
2748 2973 8.180920 TGATTTGTTGTATTGGATCGTTATGTG 58.819 33.333 0.00 0.00 0.00 3.21
2813 3038 7.562135 TGAGAGAAGTAAAAGTAGTGGTGTTT 58.438 34.615 0.00 0.00 0.00 2.83
2839 3311 1.246649 TGGGATGTGTGCATGTTGAC 58.753 50.000 0.00 0.00 35.07 3.18
2841 3313 1.200716 GGGATGTGTGCATGTTGACAG 59.799 52.381 0.00 0.00 35.07 3.51
2879 3352 3.513515 GGGGTGAAACAATTCATAGGCAA 59.486 43.478 0.00 0.00 46.67 4.52
2896 3369 2.095213 GGCAACATTTTCATGCATGCAG 59.905 45.455 26.69 17.32 43.53 4.41
2936 3409 2.040813 AGTGAAGTTGATGAGGTGGCAT 59.959 45.455 0.00 0.00 0.00 4.40
2992 3465 9.654663 GGCGATCAACTAAGTATATAGGATTTT 57.345 33.333 0.00 0.00 0.00 1.82
3026 3499 4.096682 AGCTGCATTGCACAAAACAAATTT 59.903 33.333 7.38 0.00 33.79 1.82
3129 3602 7.937394 AGATATTGTTAAACCTTTCCCCTATCG 59.063 37.037 0.00 0.00 0.00 2.92
3132 3605 2.420058 AAACCTTTCCCCTATCGCAG 57.580 50.000 0.00 0.00 0.00 5.18
3158 3631 3.325806 GGGAGAGCCTTCTTCCCC 58.674 66.667 0.00 0.00 42.61 4.81
3161 3634 0.326143 GGAGAGCCTTCTTCCCCTCT 60.326 60.000 0.00 0.00 37.38 3.69
3169 3642 2.632512 CCTTCTTCCCCTCTATCTCAGC 59.367 54.545 0.00 0.00 0.00 4.26
3177 3650 1.588674 CTCTATCTCAGCCGACGAGT 58.411 55.000 0.00 0.00 0.00 4.18
3248 3721 2.253610 AGGGTATTCCTTGTGTGTCGA 58.746 47.619 0.00 0.00 45.47 4.20
3282 3755 1.269448 GATTTTGGTTCTCGCAAGGCA 59.731 47.619 0.00 0.00 38.47 4.75
3284 3757 1.795170 TTTGGTTCTCGCAAGGCAGC 61.795 55.000 0.00 0.00 38.47 5.25
3294 3767 3.684990 AAGGCAGCGCTCAGACGA 61.685 61.111 7.13 0.00 34.06 4.20
3300 3773 0.179137 CAGCGCTCAGACGAATGGTA 60.179 55.000 7.13 0.00 34.06 3.25
3316 3789 2.901249 TGGTAGCACTTATTCGCTTCC 58.099 47.619 0.00 0.00 43.76 3.46
3319 3792 0.535335 AGCACTTATTCGCTTCCGGA 59.465 50.000 0.00 0.00 33.81 5.14
3320 3793 0.651031 GCACTTATTCGCTTCCGGAC 59.349 55.000 1.83 0.00 34.56 4.79
3322 3795 2.194271 CACTTATTCGCTTCCGGACTC 58.806 52.381 1.83 0.00 34.56 3.36
3372 3845 2.329539 GATTGGATGGAGCTCCGGCA 62.330 60.000 27.43 11.20 41.70 5.69
3383 3856 3.181474 GGAGCTCCGGCATATATTCCTAC 60.181 52.174 19.06 0.00 41.70 3.18
3384 3857 2.766828 AGCTCCGGCATATATTCCTACC 59.233 50.000 0.00 0.00 41.70 3.18
3385 3858 2.500098 GCTCCGGCATATATTCCTACCA 59.500 50.000 0.00 0.00 38.54 3.25
3390 3863 3.430929 CGGCATATATTCCTACCAGCTCC 60.431 52.174 0.00 0.00 0.00 4.70
3393 3866 0.603569 ATATTCCTACCAGCTCCGCG 59.396 55.000 0.00 0.00 0.00 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
188 190 2.992689 TTGTAGCTCCGCCACCGA 60.993 61.111 0.00 0.00 36.29 4.69
566 604 3.375299 GCATTTCAAGTAGGCGAGTGATT 59.625 43.478 0.00 0.00 0.00 2.57
578 616 1.981256 ACCACCGAAGCATTTCAAGT 58.019 45.000 0.00 0.00 32.67 3.16
579 617 2.034558 ACAACCACCGAAGCATTTCAAG 59.965 45.455 0.00 0.00 32.67 3.02
580 618 2.028130 ACAACCACCGAAGCATTTCAA 58.972 42.857 0.00 0.00 32.67 2.69
581 619 1.686355 ACAACCACCGAAGCATTTCA 58.314 45.000 0.00 0.00 32.67 2.69
582 620 5.554822 TTATACAACCACCGAAGCATTTC 57.445 39.130 0.00 0.00 0.00 2.17
583 621 5.968528 TTTATACAACCACCGAAGCATTT 57.031 34.783 0.00 0.00 0.00 2.32
584 622 7.051623 TCTATTTATACAACCACCGAAGCATT 58.948 34.615 0.00 0.00 0.00 3.56
585 623 6.588204 TCTATTTATACAACCACCGAAGCAT 58.412 36.000 0.00 0.00 0.00 3.79
586 624 5.979993 TCTATTTATACAACCACCGAAGCA 58.020 37.500 0.00 0.00 0.00 3.91
587 625 7.225931 TCAATCTATTTATACAACCACCGAAGC 59.774 37.037 0.00 0.00 0.00 3.86
588 626 8.657074 TCAATCTATTTATACAACCACCGAAG 57.343 34.615 0.00 0.00 0.00 3.79
589 627 8.885722 GTTCAATCTATTTATACAACCACCGAA 58.114 33.333 0.00 0.00 0.00 4.30
590 628 8.041919 TGTTCAATCTATTTATACAACCACCGA 58.958 33.333 0.00 0.00 0.00 4.69
591 629 8.203937 TGTTCAATCTATTTATACAACCACCG 57.796 34.615 0.00 0.00 0.00 4.94
604 642 9.101655 GCTTGCCATATTTTTGTTCAATCTATT 57.898 29.630 0.00 0.00 0.00 1.73
605 643 7.712205 GGCTTGCCATATTTTTGTTCAATCTAT 59.288 33.333 6.79 0.00 0.00 1.98
606 644 7.041107 GGCTTGCCATATTTTTGTTCAATCTA 58.959 34.615 6.79 0.00 0.00 1.98
607 645 5.876460 GGCTTGCCATATTTTTGTTCAATCT 59.124 36.000 6.79 0.00 0.00 2.40
608 646 5.220453 CGGCTTGCCATATTTTTGTTCAATC 60.220 40.000 12.45 0.00 0.00 2.67
609 647 4.630940 CGGCTTGCCATATTTTTGTTCAAT 59.369 37.500 12.45 0.00 0.00 2.57
610 648 3.993081 CGGCTTGCCATATTTTTGTTCAA 59.007 39.130 12.45 0.00 0.00 2.69
611 649 3.583806 CGGCTTGCCATATTTTTGTTCA 58.416 40.909 12.45 0.00 0.00 3.18
612 650 2.348362 GCGGCTTGCCATATTTTTGTTC 59.652 45.455 12.45 0.00 37.76 3.18
613 651 2.289320 TGCGGCTTGCCATATTTTTGTT 60.289 40.909 12.45 0.00 45.60 2.83
614 652 1.274728 TGCGGCTTGCCATATTTTTGT 59.725 42.857 12.45 0.00 45.60 2.83
615 653 2.007360 TGCGGCTTGCCATATTTTTG 57.993 45.000 12.45 0.00 45.60 2.44
616 654 2.985957 ATGCGGCTTGCCATATTTTT 57.014 40.000 12.45 0.00 45.60 1.94
617 655 2.985957 AATGCGGCTTGCCATATTTT 57.014 40.000 12.45 0.00 45.60 1.82
618 656 2.985957 AAATGCGGCTTGCCATATTT 57.014 40.000 12.45 13.19 45.60 1.40
619 657 2.431782 AGAAAATGCGGCTTGCCATATT 59.568 40.909 12.45 8.24 45.60 1.28
620 658 2.034124 AGAAAATGCGGCTTGCCATAT 58.966 42.857 12.45 2.39 45.60 1.78
621 659 1.473258 AGAAAATGCGGCTTGCCATA 58.527 45.000 12.45 0.00 45.60 2.74
622 660 1.406539 CTAGAAAATGCGGCTTGCCAT 59.593 47.619 12.45 0.00 45.60 4.40
623 661 0.810648 CTAGAAAATGCGGCTTGCCA 59.189 50.000 12.45 0.00 45.60 4.92
624 662 0.526310 GCTAGAAAATGCGGCTTGCC 60.526 55.000 0.00 0.75 45.60 4.52
625 663 0.453390 AGCTAGAAAATGCGGCTTGC 59.547 50.000 0.00 0.00 46.70 4.01
626 664 2.939103 ACTAGCTAGAAAATGCGGCTTG 59.061 45.455 27.45 0.00 34.88 4.01
627 665 2.939103 CACTAGCTAGAAAATGCGGCTT 59.061 45.455 27.45 0.00 34.88 4.35
628 666 2.555199 CACTAGCTAGAAAATGCGGCT 58.445 47.619 27.45 0.00 37.08 5.52
629 667 1.599542 CCACTAGCTAGAAAATGCGGC 59.400 52.381 27.45 0.00 0.00 6.53
630 668 3.126831 CTCCACTAGCTAGAAAATGCGG 58.873 50.000 27.45 13.87 0.00 5.69
631 669 4.046938 TCTCCACTAGCTAGAAAATGCG 57.953 45.455 27.45 8.95 0.00 4.73
632 670 6.516718 TGTATCTCCACTAGCTAGAAAATGC 58.483 40.000 27.45 14.85 0.00 3.56
633 671 7.601886 CCATGTATCTCCACTAGCTAGAAAATG 59.398 40.741 27.45 14.21 0.00 2.32
634 672 7.675062 CCATGTATCTCCACTAGCTAGAAAAT 58.325 38.462 27.45 13.94 0.00 1.82
635 673 6.463049 GCCATGTATCTCCACTAGCTAGAAAA 60.463 42.308 27.45 10.16 0.00 2.29
636 674 5.011125 GCCATGTATCTCCACTAGCTAGAAA 59.989 44.000 27.45 10.50 0.00 2.52
637 675 4.524714 GCCATGTATCTCCACTAGCTAGAA 59.475 45.833 27.45 10.84 0.00 2.10
638 676 4.082845 GCCATGTATCTCCACTAGCTAGA 58.917 47.826 27.45 6.69 0.00 2.43
639 677 3.119673 CGCCATGTATCTCCACTAGCTAG 60.120 52.174 19.44 19.44 0.00 3.42
640 678 2.820197 CGCCATGTATCTCCACTAGCTA 59.180 50.000 0.00 0.00 0.00 3.32
641 679 1.615883 CGCCATGTATCTCCACTAGCT 59.384 52.381 0.00 0.00 0.00 3.32
642 680 1.613925 TCGCCATGTATCTCCACTAGC 59.386 52.381 0.00 0.00 0.00 3.42
643 681 3.858877 GCTTCGCCATGTATCTCCACTAG 60.859 52.174 0.00 0.00 0.00 2.57
644 682 2.035961 GCTTCGCCATGTATCTCCACTA 59.964 50.000 0.00 0.00 0.00 2.74
645 683 1.202580 GCTTCGCCATGTATCTCCACT 60.203 52.381 0.00 0.00 0.00 4.00
646 684 1.221414 GCTTCGCCATGTATCTCCAC 58.779 55.000 0.00 0.00 0.00 4.02
660 698 6.504799 GCTTCAACGCTTATAAAATTGCTTCG 60.505 38.462 0.00 0.00 0.00 3.79
667 705 4.094294 TCGCTGCTTCAACGCTTATAAAAT 59.906 37.500 0.00 0.00 0.00 1.82
700 738 3.342377 TGTGGAATGCGAGGAACAATA 57.658 42.857 0.00 0.00 0.00 1.90
759 811 2.345244 CTGGAGCTCGCTGGTTGT 59.655 61.111 7.83 0.00 0.00 3.32
776 828 0.464554 GGGTATGGAAGACCTGCAGC 60.465 60.000 8.66 0.00 37.13 5.25
777 829 0.179073 CGGGTATGGAAGACCTGCAG 60.179 60.000 6.78 6.78 36.55 4.41
855 911 2.609002 CGCATAGACAACAGCAGCATTA 59.391 45.455 0.00 0.00 0.00 1.90
1060 1168 3.717294 AAGGGCGTGATCGGGCTT 61.717 61.111 9.49 0.20 37.56 4.35
1140 1248 2.048222 CGCTTGTTCAGGCCGAGA 60.048 61.111 0.00 0.00 0.00 4.04
1293 1401 2.066999 GGCGAGGAAGTCCAGGGAT 61.067 63.158 0.00 0.00 38.89 3.85
1573 1715 1.154169 GCACGTACCACGATCGACA 60.154 57.895 24.34 0.02 46.05 4.35
1834 1994 2.183300 GTCGTGGCAGGCGATGTA 59.817 61.111 3.45 0.00 40.59 2.29
2124 2306 4.840005 GCCTTCCCCGGCTCGAAG 62.840 72.222 14.16 14.16 46.63 3.79
2170 2355 2.281761 CAGCGCCAACTTCCCTGT 60.282 61.111 2.29 0.00 0.00 4.00
2355 2550 2.345991 GCGAACAGGGTAGCACCA 59.654 61.111 7.49 0.00 41.02 4.17
2410 2605 5.988310 TCAATCATGAATGCAGTTTCCTT 57.012 34.783 5.85 0.00 30.99 3.36
2570 2793 3.746492 GCAGAGTCGTATGAACCTTTGTT 59.254 43.478 0.00 0.00 37.42 2.83
2571 2794 3.006967 AGCAGAGTCGTATGAACCTTTGT 59.993 43.478 0.00 0.00 0.00 2.83
2577 2800 5.446473 CCAATGAAAGCAGAGTCGTATGAAC 60.446 44.000 0.00 0.00 0.00 3.18
2593 2816 6.389869 AGGGGTATCATCTAGTTCCAATGAAA 59.610 38.462 0.00 0.00 33.44 2.69
2619 2842 3.433274 CGTATGTTCTCACTGCAACACAT 59.567 43.478 0.00 0.00 35.37 3.21
2620 2843 2.799978 CGTATGTTCTCACTGCAACACA 59.200 45.455 0.00 0.00 35.37 3.72
2639 2864 7.775053 ATAATATATTGCAACCAATTCCCGT 57.225 32.000 0.00 0.00 41.68 5.28
2786 3011 7.562135 ACACCACTACTTTTACTTCTCTCAAA 58.438 34.615 0.00 0.00 0.00 2.69
2813 3038 6.379417 TCAACATGCACACATCCCATTTTATA 59.621 34.615 0.00 0.00 32.87 0.98
2858 3330 4.021544 TGTTGCCTATGAATTGTTTCACCC 60.022 41.667 0.00 0.00 44.36 4.61
2866 3338 6.314152 TGCATGAAAATGTTGCCTATGAATTG 59.686 34.615 0.00 0.00 35.51 2.32
2879 3352 6.869695 TCTTAATCTGCATGCATGAAAATGT 58.130 32.000 30.64 11.96 0.00 2.71
2945 3418 8.958119 TCGCCACTACTTCAATCTATTTTAAT 57.042 30.769 0.00 0.00 0.00 1.40
2992 3465 5.009510 TGTGCAATGCAGCTAAAAACTAGAA 59.990 36.000 8.73 0.00 40.08 2.10
2993 3466 4.518590 TGTGCAATGCAGCTAAAAACTAGA 59.481 37.500 8.73 0.00 40.08 2.43
3005 3478 5.858159 CAAATTTGTTTTGTGCAATGCAG 57.142 34.783 8.73 0.00 40.08 4.41
3106 3579 5.824097 GCGATAGGGGAAAGGTTTAACAATA 59.176 40.000 0.00 0.00 0.00 1.90
3129 3602 1.730451 GCTCTCCCTAGTCGTCCTGC 61.730 65.000 0.00 0.00 0.00 4.85
3132 3605 0.396001 AAGGCTCTCCCTAGTCGTCC 60.396 60.000 0.00 0.00 45.62 4.79
3158 3631 1.529438 GACTCGTCGGCTGAGATAGAG 59.471 57.143 14.22 5.63 36.93 2.43
3161 3634 1.158484 CGGACTCGTCGGCTGAGATA 61.158 60.000 14.22 0.00 36.93 1.98
3177 3650 3.467226 GGGAGGCGAATCCACGGA 61.467 66.667 8.41 0.00 41.52 4.69
3248 3721 8.625467 AGAACCAAAATCCTACCTATCTAAGT 57.375 34.615 0.00 0.00 0.00 2.24
3282 3755 0.101399 CTACCATTCGTCTGAGCGCT 59.899 55.000 11.27 11.27 0.00 5.92
3284 3757 0.179137 TGCTACCATTCGTCTGAGCG 60.179 55.000 0.00 0.00 32.53 5.03
3294 3767 3.877508 GGAAGCGAATAAGTGCTACCATT 59.122 43.478 0.00 0.00 41.46 3.16
3300 3773 0.535335 TCCGGAAGCGAATAAGTGCT 59.465 50.000 0.00 0.00 44.97 4.40
3319 3792 2.101582 CGAATTTGAGGAGGATCGGAGT 59.898 50.000 0.00 0.00 34.37 3.85
3320 3793 2.101582 ACGAATTTGAGGAGGATCGGAG 59.898 50.000 0.00 0.00 34.37 4.63
3322 3795 2.604046 ACGAATTTGAGGAGGATCGG 57.396 50.000 0.00 0.00 34.37 4.18
3352 3825 1.072159 CCGGAGCTCCATCCAATCC 59.928 63.158 31.67 2.97 39.53 3.01
3353 3826 1.599240 GCCGGAGCTCCATCCAATC 60.599 63.158 31.67 8.58 39.53 2.67
3357 3830 1.195115 TATATGCCGGAGCTCCATCC 58.805 55.000 31.67 18.70 40.80 3.51


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

AutoCloner maintained by Alex Coulton.