Multiple sequence alignment - TraesCS7D01G093600

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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 TraesCS7D01G093600 chr7D 100.000 5879 0 0 1 5879 56057820 56051942 0.000000e+00 10857
1 TraesCS7D01G093600 chr7D 98.694 3139 34 4 2747 5879 56070891 56067754 0.000000e+00 5563
2 TraesCS7D01G093600 chr7D 98.338 2587 20 5 1 2585 56073458 56070893 0.000000e+00 4518
3 TraesCS7D01G093600 chr7D 80.734 763 85 37 2747 3483 56100422 56099696 6.700000e-149 538
4 TraesCS7D01G093600 chr7A 94.469 2459 113 12 2747 5189 60370790 60368339 0.000000e+00 3766
5 TraesCS7D01G093600 chr7A 94.268 2460 114 15 2747 5189 60402305 60399856 0.000000e+00 3736
6 TraesCS7D01G093600 chr7A 94.230 2461 117 12 2747 5189 59955645 59953192 0.000000e+00 3735
7 TraesCS7D01G093600 chr7A 93.791 2464 123 17 2747 5189 60080890 60078436 0.000000e+00 3675
8 TraesCS7D01G093600 chr7A 93.184 2362 107 27 242 2585 60513845 60511520 0.000000e+00 3421
9 TraesCS7D01G093600 chr7A 93.970 1990 100 10 600 2585 60082865 60080892 0.000000e+00 2992
10 TraesCS7D01G093600 chr7A 93.917 1989 101 10 601 2585 60404279 60402307 0.000000e+00 2985
11 TraesCS7D01G093600 chr7A 93.511 1988 104 11 601 2585 60372757 60370792 0.000000e+00 2933
12 TraesCS7D01G093600 chr7A 92.822 1853 83 15 3915 5751 59934170 59932352 0.000000e+00 2639
13 TraesCS7D01G093600 chr7A 92.661 1853 87 13 3915 5751 60058698 60056879 0.000000e+00 2623
14 TraesCS7D01G093600 chr7A 94.909 1316 43 12 2744 4038 60511523 60510211 0.000000e+00 2037
15 TraesCS7D01G093600 chr7A 94.064 1314 53 11 1290 2594 59805224 59803927 0.000000e+00 1971
16 TraesCS7D01G093600 chr7A 94.687 1167 48 8 2747 3907 60061699 60060541 0.000000e+00 1799
17 TraesCS7D01G093600 chr7A 94.344 1167 52 8 2747 3907 59936905 59935747 0.000000e+00 1777
18 TraesCS7D01G093600 chr7A 93.040 1092 63 8 600 1687 59939390 59938308 0.000000e+00 1583
19 TraesCS7D01G093600 chr7A 92.674 1092 66 9 600 1687 60064182 60063101 0.000000e+00 1561
20 TraesCS7D01G093600 chr7A 93.626 910 42 5 1676 2585 59937800 59936907 0.000000e+00 1345
21 TraesCS7D01G093600 chr7A 93.516 910 43 5 1676 2585 60062594 60061701 0.000000e+00 1339
22 TraesCS7D01G093600 chr7A 93.922 691 29 3 1895 2585 59956324 59955647 0.000000e+00 1031
23 TraesCS7D01G093600 chr7A 95.798 357 11 3 242 594 59939825 59939469 1.840000e-159 573
24 TraesCS7D01G093600 chr7A 93.636 220 14 0 3 222 60514153 60513934 4.390000e-86 329
25 TraesCS7D01G093600 chr7A 93.119 218 15 0 3 220 59816694 59816477 2.640000e-83 320
26 TraesCS7D01G093600 chr7A 90.783 217 20 0 6 222 60386912 60386696 2.070000e-74 291
27 TraesCS7D01G093600 chr7A 87.273 220 13 4 3 222 59940118 59939914 2.740000e-58 237
28 TraesCS7D01G093600 chr7A 87.273 220 13 4 3 222 60064910 60064706 2.740000e-58 237
29 TraesCS7D01G093600 chr4A 92.772 2006 103 20 600 2585 672797508 672795525 0.000000e+00 2863
30 TraesCS7D01G093600 chr4A 92.722 2006 104 20 600 2585 672679278 672677295 0.000000e+00 2857
31 TraesCS7D01G093600 chr4A 92.718 2005 104 17 600 2585 672597922 672595941 0.000000e+00 2856
32 TraesCS7D01G093600 chr4A 92.668 2005 104 16 600 2585 672776244 672774264 0.000000e+00 2848
33 TraesCS7D01G093600 chr4A 91.820 2005 105 22 600 2585 672736204 672734240 0.000000e+00 2739
34 TraesCS7D01G093600 chr4A 92.988 1697 82 5 4190 5879 672633895 672632229 0.000000e+00 2440
35 TraesCS7D01G093600 chr4A 92.929 1697 83 5 4190 5879 672655486 672653820 0.000000e+00 2435
36 TraesCS7D01G093600 chr4A 92.756 1698 82 15 4190 5879 672922766 672921102 0.000000e+00 2416
37 TraesCS7D01G093600 chr4A 92.697 1698 84 14 4190 5879 672733001 672731336 0.000000e+00 2412
38 TraesCS7D01G093600 chr4A 92.697 1698 83 15 4190 5879 672773004 672771340 0.000000e+00 2410
39 TraesCS7D01G093600 chr4A 92.638 1698 86 6 4190 5879 672794259 672792593 0.000000e+00 2407
40 TraesCS7D01G093600 chr4A 92.403 1698 86 9 4190 5879 672594675 672593013 0.000000e+00 2381
41 TraesCS7D01G093600 chr4A 92.285 1698 88 9 4190 5879 672676031 672674369 0.000000e+00 2370
42 TraesCS7D01G093600 chr4A 90.879 1228 79 17 600 1808 672658507 672657294 0.000000e+00 1616
43 TraesCS7D01G093600 chr4A 96.100 359 8 4 242 594 672736641 672736283 1.100000e-161 580
44 TraesCS7D01G093600 chr4A 96.100 359 8 4 242 594 672947403 672947045 1.100000e-161 580
45 TraesCS7D01G093600 chr4A 95.822 359 9 4 242 594 672881961 672881603 5.110000e-160 575
46 TraesCS7D01G093600 chr4A 95.543 359 10 4 242 594 672598359 672598001 2.380000e-158 569
47 TraesCS7D01G093600 chr4A 95.543 359 10 4 242 594 672658943 672658585 2.380000e-158 569
48 TraesCS7D01G093600 chr4A 95.543 359 10 4 242 594 672679715 672679357 2.380000e-158 569
49 TraesCS7D01G093600 chr4A 83.025 595 70 20 2910 3483 672920640 672920056 1.460000e-140 510
50 TraesCS7D01G093600 chr4A 94.769 325 13 3 2747 3067 672924016 672923692 2.450000e-138 503
51 TraesCS7D01G093600 chrUn 92.069 933 41 11 3094 4018 372313560 372314467 0.000000e+00 1282
52 TraesCS7D01G093600 chrUn 95.543 359 10 4 242 594 348562322 348562680 2.380000e-158 569
53 TraesCS7D01G093600 chr4D 97.076 171 5 0 2575 2745 509819047 509818877 7.450000e-74 289
54 TraesCS7D01G093600 chr6D 96.512 172 6 0 2574 2745 253749766 253749937 9.640000e-73 285
55 TraesCS7D01G093600 chr5D 96.512 172 5 1 2580 2751 423354214 423354044 3.470000e-72 283
56 TraesCS7D01G093600 chr3D 96.491 171 6 0 2575 2745 402850626 402850796 3.470000e-72 283
57 TraesCS7D01G093600 chr3D 95.954 173 6 1 2577 2748 32278176 32278348 4.490000e-71 279
58 TraesCS7D01G093600 chr3D 96.450 169 6 0 2582 2750 336587999 336588167 4.490000e-71 279
59 TraesCS7D01G093600 chr3D 96.988 166 5 0 2580 2745 346313695 346313530 4.490000e-71 279
60 TraesCS7D01G093600 chr3D 96.988 166 5 0 2580 2745 433194083 433193918 4.490000e-71 279
61 TraesCS7D01G093600 chr2D 97.576 165 4 0 2581 2745 641099197 641099361 3.470000e-72 283


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 TraesCS7D01G093600 chr7D 56051942 56057820 5878 True 10857.000000 10857 100.000000 1 5879 1 chr7D.!!$R1 5878
1 TraesCS7D01G093600 chr7D 56067754 56073458 5704 True 5040.500000 5563 98.516000 1 5879 2 chr7D.!!$R3 5878
2 TraesCS7D01G093600 chr7D 56099696 56100422 726 True 538.000000 538 80.734000 2747 3483 1 chr7D.!!$R2 736
3 TraesCS7D01G093600 chr7A 60399856 60404279 4423 True 3360.500000 3736 94.092500 601 5189 2 chr7A.!!$R9 4588
4 TraesCS7D01G093600 chr7A 60368339 60372757 4418 True 3349.500000 3766 93.990000 601 5189 2 chr7A.!!$R8 4588
5 TraesCS7D01G093600 chr7A 60078436 60082865 4429 True 3333.500000 3675 93.880500 600 5189 2 chr7A.!!$R7 4589
6 TraesCS7D01G093600 chr7A 59953192 59956324 3132 True 2383.000000 3735 94.076000 1895 5189 2 chr7A.!!$R5 3294
7 TraesCS7D01G093600 chr7A 59803927 59805224 1297 True 1971.000000 1971 94.064000 1290 2594 1 chr7A.!!$R1 1304
8 TraesCS7D01G093600 chr7A 60510211 60514153 3942 True 1929.000000 3421 93.909667 3 4038 3 chr7A.!!$R10 4035
9 TraesCS7D01G093600 chr7A 60056879 60064910 8031 True 1511.800000 2623 92.162200 3 5751 5 chr7A.!!$R6 5748
10 TraesCS7D01G093600 chr7A 59932352 59940118 7766 True 1359.000000 2639 92.817167 3 5751 6 chr7A.!!$R4 5748
11 TraesCS7D01G093600 chr4A 672792593 672797508 4915 True 2635.000000 2863 92.705000 600 5879 2 chr4A.!!$R9 5279
12 TraesCS7D01G093600 chr4A 672771340 672776244 4904 True 2629.000000 2848 92.682500 600 5879 2 chr4A.!!$R8 5279
13 TraesCS7D01G093600 chr4A 672632229 672633895 1666 True 2440.000000 2440 92.988000 4190 5879 1 chr4A.!!$R1 1689
14 TraesCS7D01G093600 chr4A 672593013 672598359 5346 True 1935.333333 2856 93.554667 242 5879 3 chr4A.!!$R4 5637
15 TraesCS7D01G093600 chr4A 672674369 672679715 5346 True 1932.000000 2857 93.516667 242 5879 3 chr4A.!!$R6 5637
16 TraesCS7D01G093600 chr4A 672731336 672736641 5305 True 1910.333333 2739 93.539000 242 5879 3 chr4A.!!$R7 5637
17 TraesCS7D01G093600 chr4A 672653820 672658943 5123 True 1540.000000 2435 93.117000 242 5879 3 chr4A.!!$R5 5637
18 TraesCS7D01G093600 chr4A 672920056 672924016 3960 True 1143.000000 2416 90.183333 2747 5879 3 chr4A.!!$R10 3132
19 TraesCS7D01G093600 chrUn 372313560 372314467 907 False 1282.000000 1282 92.069000 3094 4018 1 chrUn.!!$F2 924

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
987 1145 2.106332 CGCCGGCGAACCTAGAAT 59.894 61.111 44.86 0.0 42.83 2.40 F
1288 1446 1.412710 TGATGGATCTAACGCCAGTCC 59.587 52.381 0.00 0.0 37.64 3.85 F
2596 3528 3.117246 TGATGTATACTCCCTCCGTTCCT 60.117 47.826 4.17 0.0 0.00 3.36 F
3332 4318 2.860009 CCTGCAGCCAGTGATATGAAT 58.140 47.619 8.66 0.0 37.38 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2454 3385 1.754234 GGGGCATAGCACACCAAGG 60.754 63.158 0.00 0.00 30.93 3.61 R
2729 3661 2.322339 AAAGTACTCCCTCCGTTCCT 57.678 50.000 0.00 0.00 0.00 3.36 R
3610 4600 1.902765 ATCTGCACACCTCGCCATCA 61.903 55.000 0.00 0.00 0.00 3.07 R
5176 8071 0.388520 GCGTGGTGGAATTCAAAGGC 60.389 55.000 7.93 3.22 0.00 4.35 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
515 591 5.234972 GCATGTTTACATACGGTAAGGTACC 59.765 44.000 2.73 2.73 42.63 3.34
987 1145 2.106332 CGCCGGCGAACCTAGAAT 59.894 61.111 44.86 0.00 42.83 2.40
1288 1446 1.412710 TGATGGATCTAACGCCAGTCC 59.587 52.381 0.00 0.00 37.64 3.85
2225 3156 6.092807 GGCCTAGTGAAGTTCTGTATTGAAAG 59.907 42.308 4.17 0.00 0.00 2.62
2226 3157 6.651225 GCCTAGTGAAGTTCTGTATTGAAAGT 59.349 38.462 4.17 0.00 0.00 2.66
2227 3158 7.173390 GCCTAGTGAAGTTCTGTATTGAAAGTT 59.827 37.037 4.17 0.00 0.00 2.66
2228 3159 9.057089 CCTAGTGAAGTTCTGTATTGAAAGTTT 57.943 33.333 4.17 0.00 0.00 2.66
2229 3160 9.869844 CTAGTGAAGTTCTGTATTGAAAGTTTG 57.130 33.333 4.17 0.00 0.00 2.93
2230 3161 8.506168 AGTGAAGTTCTGTATTGAAAGTTTGA 57.494 30.769 4.17 0.00 0.00 2.69
2231 3162 8.956426 AGTGAAGTTCTGTATTGAAAGTTTGAA 58.044 29.630 4.17 0.00 0.00 2.69
2232 3163 9.567848 GTGAAGTTCTGTATTGAAAGTTTGAAA 57.432 29.630 4.17 0.00 0.00 2.69
2454 3385 7.580523 GTGAAATCAATGCGCGTGATATATATC 59.419 37.037 22.30 14.77 34.60 1.63
2564 3495 5.106157 GGGCTATAGTATTGCAAATGCGAAT 60.106 40.000 16.67 4.29 45.83 3.34
2594 3526 4.501058 GGTTGATGTATACTCCCTCCGTTC 60.501 50.000 4.17 0.00 0.00 3.95
2595 3527 3.228453 TGATGTATACTCCCTCCGTTCC 58.772 50.000 4.17 0.00 0.00 3.62
2596 3528 3.117246 TGATGTATACTCCCTCCGTTCCT 60.117 47.826 4.17 0.00 0.00 3.36
2597 3529 4.105217 TGATGTATACTCCCTCCGTTCCTA 59.895 45.833 4.17 0.00 0.00 2.94
2598 3530 4.524802 TGTATACTCCCTCCGTTCCTAA 57.475 45.455 4.17 0.00 0.00 2.69
2599 3531 4.870636 TGTATACTCCCTCCGTTCCTAAA 58.129 43.478 4.17 0.00 0.00 1.85
2600 3532 5.461327 TGTATACTCCCTCCGTTCCTAAAT 58.539 41.667 4.17 0.00 0.00 1.40
2601 3533 6.613699 TGTATACTCCCTCCGTTCCTAAATA 58.386 40.000 4.17 0.00 0.00 1.40
2602 3534 6.491403 TGTATACTCCCTCCGTTCCTAAATAC 59.509 42.308 4.17 0.00 0.00 1.89
2603 3535 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
2604 3536 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
2605 3537 4.161754 ACTCCCTCCGTTCCTAAATACTTG 59.838 45.833 0.00 0.00 0.00 3.16
2606 3538 4.098894 TCCCTCCGTTCCTAAATACTTGT 58.901 43.478 0.00 0.00 0.00 3.16
2607 3539 5.271598 TCCCTCCGTTCCTAAATACTTGTA 58.728 41.667 0.00 0.00 0.00 2.41
2608 3540 5.901276 TCCCTCCGTTCCTAAATACTTGTAT 59.099 40.000 0.00 0.00 0.00 2.29
2609 3541 6.384886 TCCCTCCGTTCCTAAATACTTGTATT 59.615 38.462 0.60 0.60 0.00 1.89
2610 3542 7.052248 CCCTCCGTTCCTAAATACTTGTATTT 58.948 38.462 18.75 18.75 34.41 1.40
2611 3543 7.555195 CCCTCCGTTCCTAAATACTTGTATTTT 59.445 37.037 19.61 8.09 32.49 1.82
2612 3544 8.953313 CCTCCGTTCCTAAATACTTGTATTTTT 58.047 33.333 19.61 4.83 32.49 1.94
2616 3548 9.712359 CGTTCCTAAATACTTGTATTTTTAGGC 57.288 33.333 19.61 10.85 45.31 3.93
2627 3559 9.995003 ACTTGTATTTTTAGGCATTTCAAATGA 57.005 25.926 14.65 0.00 0.00 2.57
2629 3561 9.995003 TTGTATTTTTAGGCATTTCAAATGACT 57.005 25.926 22.35 22.35 41.04 3.41
2634 3566 9.638239 TTTTTAGGCATTTCAAATGACTATCAC 57.362 29.630 23.80 0.32 39.21 3.06
2635 3567 7.936496 TTAGGCATTTCAAATGACTATCACA 57.064 32.000 23.80 8.54 39.21 3.58
2636 3568 8.523915 TTAGGCATTTCAAATGACTATCACAT 57.476 30.769 23.80 1.95 39.21 3.21
2637 3569 9.625747 TTAGGCATTTCAAATGACTATCACATA 57.374 29.630 23.80 7.51 39.21 2.29
2638 3570 7.934457 AGGCATTTCAAATGACTATCACATAC 58.066 34.615 17.52 0.00 35.20 2.39
2639 3571 6.852853 GGCATTTCAAATGACTATCACATACG 59.147 38.462 14.65 0.00 0.00 3.06
2640 3572 6.852853 GCATTTCAAATGACTATCACATACGG 59.147 38.462 14.65 0.00 0.00 4.02
2641 3573 7.254761 GCATTTCAAATGACTATCACATACGGA 60.255 37.037 14.65 0.00 0.00 4.69
2642 3574 8.777413 CATTTCAAATGACTATCACATACGGAT 58.223 33.333 3.82 0.00 0.00 4.18
2643 3575 7.713764 TTCAAATGACTATCACATACGGATG 57.286 36.000 5.94 5.94 39.16 3.51
2645 3577 7.947282 TCAAATGACTATCACATACGGATGTA 58.053 34.615 14.23 2.61 44.82 2.29
2646 3578 8.585018 TCAAATGACTATCACATACGGATGTAT 58.415 33.333 14.23 10.02 44.82 2.29
2687 3619 7.036220 AGTGTAGATTCACTCATTTTACTCCG 58.964 38.462 0.00 0.00 44.07 4.63
2688 3620 6.812160 GTGTAGATTCACTCATTTTACTCCGT 59.188 38.462 0.00 0.00 35.68 4.69
2689 3621 7.972277 GTGTAGATTCACTCATTTTACTCCGTA 59.028 37.037 0.00 0.00 35.68 4.02
2690 3622 8.692710 TGTAGATTCACTCATTTTACTCCGTAT 58.307 33.333 0.00 0.00 0.00 3.06
2691 3623 8.969267 GTAGATTCACTCATTTTACTCCGTATG 58.031 37.037 0.00 0.00 0.00 2.39
2692 3624 7.556844 AGATTCACTCATTTTACTCCGTATGT 58.443 34.615 0.00 0.00 0.00 2.29
2693 3625 8.692710 AGATTCACTCATTTTACTCCGTATGTA 58.307 33.333 0.00 0.00 0.00 2.29
2694 3626 8.873215 ATTCACTCATTTTACTCCGTATGTAG 57.127 34.615 0.00 0.00 0.00 2.74
2695 3627 7.400599 TCACTCATTTTACTCCGTATGTAGT 57.599 36.000 0.00 0.00 0.00 2.73
2696 3628 7.478322 TCACTCATTTTACTCCGTATGTAGTC 58.522 38.462 0.00 0.00 0.00 2.59
2697 3629 6.696148 CACTCATTTTACTCCGTATGTAGTCC 59.304 42.308 0.00 0.00 0.00 3.85
2698 3630 6.606395 ACTCATTTTACTCCGTATGTAGTCCT 59.394 38.462 0.00 0.00 0.00 3.85
2699 3631 7.123847 ACTCATTTTACTCCGTATGTAGTCCTT 59.876 37.037 0.00 0.00 0.00 3.36
2700 3632 7.844009 TCATTTTACTCCGTATGTAGTCCTTT 58.156 34.615 0.00 0.00 0.00 3.11
2701 3633 7.762615 TCATTTTACTCCGTATGTAGTCCTTTG 59.237 37.037 0.00 0.00 0.00 2.77
2702 3634 6.594788 TTTACTCCGTATGTAGTCCTTTGT 57.405 37.500 0.00 0.00 0.00 2.83
2703 3635 6.594788 TTACTCCGTATGTAGTCCTTTGTT 57.405 37.500 0.00 0.00 0.00 2.83
2704 3636 4.817517 ACTCCGTATGTAGTCCTTTGTTG 58.182 43.478 0.00 0.00 0.00 3.33
2705 3637 4.525487 ACTCCGTATGTAGTCCTTTGTTGA 59.475 41.667 0.00 0.00 0.00 3.18
2706 3638 5.011329 ACTCCGTATGTAGTCCTTTGTTGAA 59.989 40.000 0.00 0.00 0.00 2.69
2707 3639 5.856156 TCCGTATGTAGTCCTTTGTTGAAA 58.144 37.500 0.00 0.00 0.00 2.69
2708 3640 6.469410 TCCGTATGTAGTCCTTTGTTGAAAT 58.531 36.000 0.00 0.00 0.00 2.17
2709 3641 6.370442 TCCGTATGTAGTCCTTTGTTGAAATG 59.630 38.462 0.00 0.00 0.00 2.32
2710 3642 6.021596 CGTATGTAGTCCTTTGTTGAAATGC 58.978 40.000 0.00 0.00 0.00 3.56
2711 3643 6.128282 CGTATGTAGTCCTTTGTTGAAATGCT 60.128 38.462 0.00 0.00 0.00 3.79
2712 3644 6.655078 ATGTAGTCCTTTGTTGAAATGCTT 57.345 33.333 0.00 0.00 0.00 3.91
2713 3645 7.759489 ATGTAGTCCTTTGTTGAAATGCTTA 57.241 32.000 0.00 0.00 0.00 3.09
2714 3646 7.202016 TGTAGTCCTTTGTTGAAATGCTTAG 57.798 36.000 0.00 0.00 0.00 2.18
2715 3647 6.995686 TGTAGTCCTTTGTTGAAATGCTTAGA 59.004 34.615 0.00 0.00 0.00 2.10
2716 3648 6.959639 AGTCCTTTGTTGAAATGCTTAGAA 57.040 33.333 0.00 0.00 0.00 2.10
2717 3649 7.346751 AGTCCTTTGTTGAAATGCTTAGAAA 57.653 32.000 0.00 0.00 0.00 2.52
2718 3650 7.428826 AGTCCTTTGTTGAAATGCTTAGAAAG 58.571 34.615 0.00 0.00 0.00 2.62
2719 3651 7.285401 AGTCCTTTGTTGAAATGCTTAGAAAGA 59.715 33.333 0.00 0.00 0.00 2.52
2720 3652 7.379797 GTCCTTTGTTGAAATGCTTAGAAAGAC 59.620 37.037 0.00 0.00 0.00 3.01
2721 3653 7.068103 TCCTTTGTTGAAATGCTTAGAAAGACA 59.932 33.333 0.00 0.00 0.00 3.41
2722 3654 7.706179 CCTTTGTTGAAATGCTTAGAAAGACAA 59.294 33.333 0.00 0.00 0.00 3.18
2723 3655 8.633075 TTTGTTGAAATGCTTAGAAAGACAAG 57.367 30.769 0.00 0.00 0.00 3.16
2724 3656 7.333528 TGTTGAAATGCTTAGAAAGACAAGT 57.666 32.000 0.00 0.00 0.00 3.16
2725 3657 8.445275 TGTTGAAATGCTTAGAAAGACAAGTA 57.555 30.769 0.00 0.00 0.00 2.24
2726 3658 9.066892 TGTTGAAATGCTTAGAAAGACAAGTAT 57.933 29.630 0.00 0.00 0.00 2.12
2727 3659 9.899226 GTTGAAATGCTTAGAAAGACAAGTATT 57.101 29.630 0.00 0.00 38.29 1.89
2732 3664 9.959721 AATGCTTAGAAAGACAAGTATTTAGGA 57.040 29.630 0.00 0.00 34.65 2.94
2733 3665 9.959721 ATGCTTAGAAAGACAAGTATTTAGGAA 57.040 29.630 0.00 0.00 0.00 3.36
2734 3666 9.216117 TGCTTAGAAAGACAAGTATTTAGGAAC 57.784 33.333 0.00 0.00 0.00 3.62
2735 3667 8.381387 GCTTAGAAAGACAAGTATTTAGGAACG 58.619 37.037 0.00 0.00 0.00 3.95
2736 3668 8.767478 TTAGAAAGACAAGTATTTAGGAACGG 57.233 34.615 0.00 0.00 0.00 4.44
2737 3669 7.001099 AGAAAGACAAGTATTTAGGAACGGA 57.999 36.000 0.00 0.00 0.00 4.69
2738 3670 7.097834 AGAAAGACAAGTATTTAGGAACGGAG 58.902 38.462 0.00 0.00 0.00 4.63
2739 3671 5.340439 AGACAAGTATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
2740 3672 4.161754 AGACAAGTATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
2741 3673 4.098894 ACAAGTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
2742 3674 4.161754 ACAAGTATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
2743 3675 3.991683 AGTATTTAGGAACGGAGGGAGT 58.008 45.455 0.00 0.00 0.00 3.85
2744 3676 5.134725 AGTATTTAGGAACGGAGGGAGTA 57.865 43.478 0.00 0.00 0.00 2.59
2745 3677 4.892345 AGTATTTAGGAACGGAGGGAGTAC 59.108 45.833 0.00 0.00 0.00 2.73
2843 3780 4.864247 CCACAAAACCTTCAACTGTTTCTG 59.136 41.667 0.00 0.00 33.76 3.02
3332 4318 2.860009 CCTGCAGCCAGTGATATGAAT 58.140 47.619 8.66 0.00 37.38 2.57
3700 4690 3.809077 CCAATGTGCTTGTACGGGTACG 61.809 54.545 4.67 0.00 38.85 3.67
3715 4705 3.340953 TACGCGGACGGTAGTTGGC 62.341 63.158 12.47 0.00 46.04 4.52
5175 8070 3.849951 CCGCCGCCACACTCCTAT 61.850 66.667 0.00 0.00 0.00 2.57
5176 8071 2.586079 CGCCGCCACACTCCTATG 60.586 66.667 0.00 0.00 0.00 2.23
5177 8072 2.897350 GCCGCCACACTCCTATGC 60.897 66.667 0.00 0.00 0.00 3.14
5178 8073 2.203070 CCGCCACACTCCTATGCC 60.203 66.667 0.00 0.00 0.00 4.40
5179 8074 2.735772 CCGCCACACTCCTATGCCT 61.736 63.158 0.00 0.00 0.00 4.75
5180 8075 1.221840 CGCCACACTCCTATGCCTT 59.778 57.895 0.00 0.00 0.00 4.35
5181 8076 0.392998 CGCCACACTCCTATGCCTTT 60.393 55.000 0.00 0.00 0.00 3.11
5182 8077 1.098050 GCCACACTCCTATGCCTTTG 58.902 55.000 0.00 0.00 0.00 2.77
5183 8078 1.340017 GCCACACTCCTATGCCTTTGA 60.340 52.381 0.00 0.00 0.00 2.69
5184 8079 2.879756 GCCACACTCCTATGCCTTTGAA 60.880 50.000 0.00 0.00 0.00 2.69
5185 8080 3.624777 CCACACTCCTATGCCTTTGAAT 58.375 45.455 0.00 0.00 0.00 2.57
5186 8081 4.019174 CCACACTCCTATGCCTTTGAATT 58.981 43.478 0.00 0.00 0.00 2.17
5187 8082 4.096984 CCACACTCCTATGCCTTTGAATTC 59.903 45.833 0.00 0.00 0.00 2.17
5188 8083 4.096984 CACACTCCTATGCCTTTGAATTCC 59.903 45.833 2.27 0.00 0.00 3.01
5189 8084 4.263905 ACACTCCTATGCCTTTGAATTCCA 60.264 41.667 2.27 0.00 0.00 3.53
5190 8085 4.096984 CACTCCTATGCCTTTGAATTCCAC 59.903 45.833 2.27 0.00 0.00 4.02
5191 8086 3.631250 TCCTATGCCTTTGAATTCCACC 58.369 45.455 2.27 0.00 0.00 4.61
5192 8087 3.011144 TCCTATGCCTTTGAATTCCACCA 59.989 43.478 2.27 0.00 0.00 4.17
5193 8088 3.131046 CCTATGCCTTTGAATTCCACCAC 59.869 47.826 2.27 0.00 0.00 4.16
5194 8089 0.958091 TGCCTTTGAATTCCACCACG 59.042 50.000 2.27 0.00 0.00 4.94
5195 8090 0.388520 GCCTTTGAATTCCACCACGC 60.389 55.000 2.27 0.00 0.00 5.34
5196 8091 1.247567 CCTTTGAATTCCACCACGCT 58.752 50.000 2.27 0.00 0.00 5.07
5197 8092 1.200020 CCTTTGAATTCCACCACGCTC 59.800 52.381 2.27 0.00 0.00 5.03
5198 8093 2.154462 CTTTGAATTCCACCACGCTCT 58.846 47.619 2.27 0.00 0.00 4.09
5199 8094 3.334691 CTTTGAATTCCACCACGCTCTA 58.665 45.455 2.27 0.00 0.00 2.43
5429 8329 5.048991 GCTGAACCGACAAAGATTTTTCCTA 60.049 40.000 0.00 0.00 0.00 2.94
5505 8405 5.109210 CAGAAGTATGCCAACGAGTAATCA 58.891 41.667 0.00 0.00 0.00 2.57
5731 8634 3.244561 TGTCCCAGACTTCTTTGATCCAC 60.245 47.826 0.00 0.00 33.15 4.02
5775 8678 1.368641 CGGCGGACATGAAATCTCAA 58.631 50.000 0.00 0.00 34.49 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
985 1143 3.748083 CGTCCATGGGATGAGATTCATT 58.252 45.455 13.02 0.00 40.94 2.57
987 1145 1.202687 GCGTCCATGGGATGAGATTCA 60.203 52.381 13.02 0.00 40.94 2.57
1024 1182 3.339093 GGGAGTGGGGTTGGAGGG 61.339 72.222 0.00 0.00 0.00 4.30
1288 1446 3.256281 GGCAACAAGGAGGAGAAGG 57.744 57.895 0.00 0.00 0.00 3.46
2225 3156 5.920840 GCCTAAATTCCTCTGTGTTTCAAAC 59.079 40.000 0.00 0.00 0.00 2.93
2226 3157 5.833131 AGCCTAAATTCCTCTGTGTTTCAAA 59.167 36.000 0.00 0.00 0.00 2.69
2227 3158 5.241506 CAGCCTAAATTCCTCTGTGTTTCAA 59.758 40.000 0.00 0.00 0.00 2.69
2228 3159 4.761739 CAGCCTAAATTCCTCTGTGTTTCA 59.238 41.667 0.00 0.00 0.00 2.69
2229 3160 4.156739 CCAGCCTAAATTCCTCTGTGTTTC 59.843 45.833 0.00 0.00 0.00 2.78
2230 3161 4.082125 CCAGCCTAAATTCCTCTGTGTTT 58.918 43.478 0.00 0.00 0.00 2.83
2231 3162 3.074538 ACCAGCCTAAATTCCTCTGTGTT 59.925 43.478 0.00 0.00 0.00 3.32
2232 3163 2.644798 ACCAGCCTAAATTCCTCTGTGT 59.355 45.455 0.00 0.00 0.00 3.72
2454 3385 1.754234 GGGGCATAGCACACCAAGG 60.754 63.158 0.00 0.00 30.93 3.61
2564 3495 7.027874 AGGGAGTATACATCAACCAAAGAAA 57.972 36.000 5.50 0.00 0.00 2.52
2601 3533 9.995003 TCATTTGAAATGCCTAAAAATACAAGT 57.005 25.926 12.86 0.00 0.00 3.16
2603 3535 9.995003 AGTCATTTGAAATGCCTAAAAATACAA 57.005 25.926 12.86 0.00 0.00 2.41
2608 3540 9.638239 GTGATAGTCATTTGAAATGCCTAAAAA 57.362 29.630 11.99 0.11 0.00 1.94
2609 3541 8.801299 TGTGATAGTCATTTGAAATGCCTAAAA 58.199 29.630 11.99 2.26 0.00 1.52
2610 3542 8.347004 TGTGATAGTCATTTGAAATGCCTAAA 57.653 30.769 11.99 2.57 0.00 1.85
2611 3543 7.936496 TGTGATAGTCATTTGAAATGCCTAA 57.064 32.000 11.99 0.00 0.00 2.69
2612 3544 9.056005 GTATGTGATAGTCATTTGAAATGCCTA 57.944 33.333 10.59 10.59 0.00 3.93
2613 3545 7.254898 CGTATGTGATAGTCATTTGAAATGCCT 60.255 37.037 12.86 9.73 0.00 4.75
2614 3546 6.852853 CGTATGTGATAGTCATTTGAAATGCC 59.147 38.462 12.86 1.61 0.00 4.40
2615 3547 6.852853 CCGTATGTGATAGTCATTTGAAATGC 59.147 38.462 12.86 8.33 0.00 3.56
2616 3548 8.141835 TCCGTATGTGATAGTCATTTGAAATG 57.858 34.615 11.54 11.54 0.00 2.32
2617 3549 8.777413 CATCCGTATGTGATAGTCATTTGAAAT 58.223 33.333 0.00 0.00 0.00 2.17
2618 3550 7.768582 ACATCCGTATGTGATAGTCATTTGAAA 59.231 33.333 0.00 0.00 44.79 2.69
2619 3551 7.272244 ACATCCGTATGTGATAGTCATTTGAA 58.728 34.615 0.00 0.00 44.79 2.69
2620 3552 6.816136 ACATCCGTATGTGATAGTCATTTGA 58.184 36.000 0.00 0.00 44.79 2.69
2621 3553 8.650714 CATACATCCGTATGTGATAGTCATTTG 58.349 37.037 3.56 0.00 46.70 2.32
2622 3554 8.763049 CATACATCCGTATGTGATAGTCATTT 57.237 34.615 3.56 0.00 46.70 2.32
2663 3595 6.812160 ACGGAGTAAAATGAGTGAATCTACAC 59.188 38.462 0.00 0.00 41.94 2.90
2664 3596 6.931838 ACGGAGTAAAATGAGTGAATCTACA 58.068 36.000 0.00 0.00 41.94 2.74
2683 3615 5.068234 TCAACAAAGGACTACATACGGAG 57.932 43.478 0.00 0.00 0.00 4.63
2684 3616 5.471556 TTCAACAAAGGACTACATACGGA 57.528 39.130 0.00 0.00 0.00 4.69
2685 3617 6.542852 CATTTCAACAAAGGACTACATACGG 58.457 40.000 0.00 0.00 0.00 4.02
2686 3618 6.021596 GCATTTCAACAAAGGACTACATACG 58.978 40.000 0.00 0.00 0.00 3.06
2687 3619 7.145932 AGCATTTCAACAAAGGACTACATAC 57.854 36.000 0.00 0.00 0.00 2.39
2688 3620 7.759489 AAGCATTTCAACAAAGGACTACATA 57.241 32.000 0.00 0.00 0.00 2.29
2689 3621 6.655078 AAGCATTTCAACAAAGGACTACAT 57.345 33.333 0.00 0.00 0.00 2.29
2690 3622 6.995686 TCTAAGCATTTCAACAAAGGACTACA 59.004 34.615 0.00 0.00 0.00 2.74
2691 3623 7.435068 TCTAAGCATTTCAACAAAGGACTAC 57.565 36.000 0.00 0.00 0.00 2.73
2692 3624 8.458573 TTTCTAAGCATTTCAACAAAGGACTA 57.541 30.769 0.00 0.00 0.00 2.59
2693 3625 6.959639 TTCTAAGCATTTCAACAAAGGACT 57.040 33.333 0.00 0.00 0.00 3.85
2694 3626 7.379797 GTCTTTCTAAGCATTTCAACAAAGGAC 59.620 37.037 0.00 0.00 0.00 3.85
2695 3627 7.068103 TGTCTTTCTAAGCATTTCAACAAAGGA 59.932 33.333 0.00 0.00 0.00 3.36
2696 3628 7.202526 TGTCTTTCTAAGCATTTCAACAAAGG 58.797 34.615 0.00 0.00 0.00 3.11
2697 3629 8.633075 TTGTCTTTCTAAGCATTTCAACAAAG 57.367 30.769 0.00 0.00 0.00 2.77
2698 3630 8.250332 ACTTGTCTTTCTAAGCATTTCAACAAA 58.750 29.630 0.00 0.00 0.00 2.83
2699 3631 7.771183 ACTTGTCTTTCTAAGCATTTCAACAA 58.229 30.769 0.00 0.00 0.00 2.83
2700 3632 7.333528 ACTTGTCTTTCTAAGCATTTCAACA 57.666 32.000 0.00 0.00 0.00 3.33
2701 3633 9.899226 AATACTTGTCTTTCTAAGCATTTCAAC 57.101 29.630 0.00 0.00 0.00 3.18
2706 3638 9.959721 TCCTAAATACTTGTCTTTCTAAGCATT 57.040 29.630 0.00 0.00 0.00 3.56
2707 3639 9.959721 TTCCTAAATACTTGTCTTTCTAAGCAT 57.040 29.630 0.00 0.00 0.00 3.79
2708 3640 9.216117 GTTCCTAAATACTTGTCTTTCTAAGCA 57.784 33.333 0.00 0.00 0.00 3.91
2709 3641 8.381387 CGTTCCTAAATACTTGTCTTTCTAAGC 58.619 37.037 0.00 0.00 0.00 3.09
2710 3642 8.870879 CCGTTCCTAAATACTTGTCTTTCTAAG 58.129 37.037 0.00 0.00 0.00 2.18
2711 3643 8.587608 TCCGTTCCTAAATACTTGTCTTTCTAA 58.412 33.333 0.00 0.00 0.00 2.10
2712 3644 8.125978 TCCGTTCCTAAATACTTGTCTTTCTA 57.874 34.615 0.00 0.00 0.00 2.10
2713 3645 7.001099 TCCGTTCCTAAATACTTGTCTTTCT 57.999 36.000 0.00 0.00 0.00 2.52
2714 3646 6.313164 CCTCCGTTCCTAAATACTTGTCTTTC 59.687 42.308 0.00 0.00 0.00 2.62
2715 3647 6.171213 CCTCCGTTCCTAAATACTTGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
2716 3648 5.338137 CCCTCCGTTCCTAAATACTTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
2717 3649 4.161754 CCCTCCGTTCCTAAATACTTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
2718 3650 4.161001 TCCCTCCGTTCCTAAATACTTGTC 59.839 45.833 0.00 0.00 0.00 3.18
2719 3651 4.098894 TCCCTCCGTTCCTAAATACTTGT 58.901 43.478 0.00 0.00 0.00 3.16
2720 3652 4.161754 ACTCCCTCCGTTCCTAAATACTTG 59.838 45.833 0.00 0.00 0.00 3.16
2721 3653 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
2722 3654 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
2723 3655 4.892345 AGTACTCCCTCCGTTCCTAAATAC 59.108 45.833 0.00 0.00 0.00 1.89
2724 3656 5.134725 AGTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
2725 3657 3.991683 AGTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
2726 3658 3.463048 AGTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
2727 3659 3.463048 AAGTACTCCCTCCGTTCCTAA 57.537 47.619 0.00 0.00 0.00 2.69
2728 3660 3.463048 AAAGTACTCCCTCCGTTCCTA 57.537 47.619 0.00 0.00 0.00 2.94
2729 3661 2.322339 AAAGTACTCCCTCCGTTCCT 57.678 50.000 0.00 0.00 0.00 3.36
2730 3662 3.413846 AAAAAGTACTCCCTCCGTTCC 57.586 47.619 0.00 0.00 0.00 3.62
2843 3780 6.887626 ATCGAGTCCTAGAAAAGATAGTCC 57.112 41.667 0.00 0.00 0.00 3.85
3078 4033 7.229707 TCTGTATTTCCCGACAATTTTCTTTCA 59.770 33.333 0.00 0.00 0.00 2.69
3079 4034 7.537649 GTCTGTATTTCCCGACAATTTTCTTTC 59.462 37.037 0.00 0.00 0.00 2.62
3332 4318 1.913951 ATGGCTTGGTGATGGCGAGA 61.914 55.000 0.00 0.00 0.00 4.04
3520 4510 6.520272 TCCAAACCATCGATTTGACAAAAAT 58.480 32.000 10.77 0.00 39.01 1.82
3610 4600 1.902765 ATCTGCACACCTCGCCATCA 61.903 55.000 0.00 0.00 0.00 3.07
3700 4690 2.813908 CTGCCAACTACCGTCCGC 60.814 66.667 0.00 0.00 0.00 5.54
3715 4705 3.114616 CTCCGGCAGCGTCAACTG 61.115 66.667 0.00 0.00 40.80 3.16
5175 8070 0.958091 CGTGGTGGAATTCAAAGGCA 59.042 50.000 7.93 0.00 0.00 4.75
5176 8071 0.388520 GCGTGGTGGAATTCAAAGGC 60.389 55.000 7.93 3.22 0.00 4.35
5177 8072 1.200020 GAGCGTGGTGGAATTCAAAGG 59.800 52.381 7.93 0.00 0.00 3.11
5178 8073 2.154462 AGAGCGTGGTGGAATTCAAAG 58.846 47.619 7.93 0.00 0.00 2.77
5179 8074 2.270352 AGAGCGTGGTGGAATTCAAA 57.730 45.000 7.93 0.00 0.00 2.69
5180 8075 3.270027 CATAGAGCGTGGTGGAATTCAA 58.730 45.455 7.93 0.00 0.00 2.69
5181 8076 2.905075 CATAGAGCGTGGTGGAATTCA 58.095 47.619 7.93 0.00 0.00 2.57
5182 8077 1.599542 GCATAGAGCGTGGTGGAATTC 59.400 52.381 0.00 0.00 0.00 2.17
5183 8078 1.668419 GCATAGAGCGTGGTGGAATT 58.332 50.000 0.00 0.00 0.00 2.17
5184 8079 3.386543 GCATAGAGCGTGGTGGAAT 57.613 52.632 0.00 0.00 0.00 3.01
5185 8080 4.932789 GCATAGAGCGTGGTGGAA 57.067 55.556 0.00 0.00 0.00 3.53
5194 8089 3.137533 GTGGAATTCAGAGGCATAGAGC 58.862 50.000 7.93 0.00 44.65 4.09
5195 8090 3.135348 TGGTGGAATTCAGAGGCATAGAG 59.865 47.826 7.93 0.00 0.00 2.43
5196 8091 3.114606 TGGTGGAATTCAGAGGCATAGA 58.885 45.455 7.93 0.00 0.00 1.98
5197 8092 3.209410 GTGGTGGAATTCAGAGGCATAG 58.791 50.000 7.93 0.00 0.00 2.23
5198 8093 2.419990 CGTGGTGGAATTCAGAGGCATA 60.420 50.000 7.93 0.00 0.00 3.14
5199 8094 1.679944 CGTGGTGGAATTCAGAGGCAT 60.680 52.381 7.93 0.00 0.00 4.40
5505 8405 0.984230 TCTCCGCTCTTTGTTGGGAT 59.016 50.000 0.00 0.00 0.00 3.85
5828 8731 5.909621 TTCAATACAGAACTACGCTACCT 57.090 39.130 0.00 0.00 0.00 3.08


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

AutoCloner maintained by Alex Coulton.