Multiple sequence alignment - TraesCS3B01G026600

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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 TraesCS3B01G026600 chr3B 100.000 3399 0 0 1 3399 11560624 11564022 0.000000e+00 6277.0
1 TraesCS3B01G026600 chr3B 80.769 1404 196 34 1045 2407 11511034 11512404 0.000000e+00 1029.0
2 TraesCS3B01G026600 chr3B 79.418 1443 179 50 1045 2440 3205417 3206788 0.000000e+00 911.0
3 TraesCS3B01G026600 chr3B 85.497 593 64 10 109 686 73746408 73745823 1.750000e-167 599.0
4 TraesCS3B01G026600 chr3B 84.424 443 43 13 2743 3160 3210345 3210786 2.440000e-111 412.0
5 TraesCS3B01G026600 chr3D 90.243 2470 141 39 797 3228 9243545 9245952 0.000000e+00 3134.0
6 TraesCS3B01G026600 chr3D 84.263 1417 149 16 1057 2442 9199566 9200939 0.000000e+00 1314.0
7 TraesCS3B01G026600 chr3D 89.209 834 62 13 3 813 9242701 9243529 0.000000e+00 1016.0
8 TraesCS3B01G026600 chr3D 88.644 634 38 7 2530 3133 9200964 9201593 0.000000e+00 741.0
9 TraesCS3B01G026600 chr3D 77.756 1043 180 41 1033 2057 9132093 9131085 8.120000e-166 593.0
10 TraesCS3B01G026600 chr3D 90.345 145 14 0 3250 3394 9245938 9246082 1.240000e-44 191.0
11 TraesCS3B01G026600 chr6D 86.043 609 55 17 109 698 296996090 296995493 8.010000e-176 627.0
12 TraesCS3B01G026600 chr7B 85.857 601 56 13 109 688 275497758 275498350 2.240000e-171 612.0
13 TraesCS3B01G026600 chr7B 93.827 81 5 0 4 84 412798476 412798556 4.610000e-24 122.0
14 TraesCS3B01G026600 chr7B 92.958 71 5 0 16 86 75186576 75186646 1.670000e-18 104.0
15 TraesCS3B01G026600 chr7B 74.742 194 42 6 1037 1228 680692047 680691859 2.810000e-11 80.5
16 TraesCS3B01G026600 chr4A 83.472 599 78 10 109 690 573900328 573899734 3.860000e-149 538.0
17 TraesCS3B01G026600 chr4A 75.021 1185 240 29 1022 2193 656249746 656250887 6.550000e-137 497.0
18 TraesCS3B01G026600 chr4A 73.566 1203 261 38 1067 2260 656480046 656481200 1.140000e-109 407.0
19 TraesCS3B01G026600 chr4A 75.754 895 167 24 1334 2217 655659097 655659952 4.080000e-109 405.0
20 TraesCS3B01G026600 chr4A 78.520 419 85 3 1660 2077 656264772 656265186 1.550000e-68 270.0
21 TraesCS3B01G026600 chr4A 73.381 556 117 17 1385 1922 656556644 656556102 9.690000e-41 178.0
22 TraesCS3B01G026600 chr7A 84.477 554 63 11 109 647 323414695 323414150 3.000000e-145 525.0
23 TraesCS3B01G026600 chr7A 74.065 1230 255 39 1067 2283 47016603 47017781 2.410000e-121 446.0
24 TraesCS3B01G026600 chr7A 73.973 1168 208 54 958 2067 47256465 47255336 5.320000e-103 385.0
25 TraesCS3B01G026600 chr7A 77.436 195 38 4 1037 1228 693406634 693406443 9.970000e-21 111.0
26 TraesCS3B01G026600 chr4D 83.418 591 73 17 109 681 9478837 9478254 3.000000e-145 525.0
27 TraesCS3B01G026600 chr4D 81.667 600 79 16 109 688 99352671 99352083 1.430000e-128 470.0
28 TraesCS3B01G026600 chr2D 82.753 603 72 18 109 687 608787315 608786721 3.030000e-140 508.0
29 TraesCS3B01G026600 chr2D 94.118 68 4 0 20 87 332699999 332700066 1.670000e-18 104.0
30 TraesCS3B01G026600 chr2D 88.095 84 10 0 3 86 148976914 148976997 2.160000e-17 100.0
31 TraesCS3B01G026600 chr2D 88.095 84 10 0 3 86 414661378 414661461 2.160000e-17 100.0
32 TraesCS3B01G026600 chr5D 84.837 521 56 11 109 613 274147344 274146831 1.410000e-138 503.0
33 TraesCS3B01G026600 chr7D 81.940 598 86 10 109 688 489298700 489299293 1.420000e-133 486.0
34 TraesCS3B01G026600 chr7D 74.605 949 192 32 1346 2283 44550961 44551871 4.140000e-99 372.0
35 TraesCS3B01G026600 chr7D 79.167 192 34 4 1037 1225 601843102 601842914 9.900000e-26 128.0
36 TraesCS3B01G026600 chrUn 74.035 1217 255 43 1067 2272 48866847 48865681 1.120000e-119 440.0
37 TraesCS3B01G026600 chrUn 73.295 1378 246 77 958 2277 48987548 48986235 8.840000e-106 394.0
38 TraesCS3B01G026600 chrUn 79.693 261 45 6 454 706 91416754 91416494 7.490000e-42 182.0
39 TraesCS3B01G026600 chr3A 75.238 1050 171 48 1033 2061 11865278 11866259 1.890000e-112 416.0
40 TraesCS3B01G026600 chr1A 81.467 518 73 11 109 618 578783108 578782606 1.470000e-108 403.0
41 TraesCS3B01G026600 chr4B 95.522 67 3 0 12 78 178483705 178483639 1.290000e-19 108.0
42 TraesCS3B01G026600 chr4B 89.286 84 9 0 3 86 188275090 188275173 4.640000e-19 106.0
43 TraesCS3B01G026600 chr5B 92.000 75 6 0 12 86 304412899 304412825 4.640000e-19 106.0


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 TraesCS3B01G026600 chr3B 11560624 11564022 3398 False 6277.0 6277 100.000000 1 3399 1 chr3B.!!$F2 3398
1 TraesCS3B01G026600 chr3B 11511034 11512404 1370 False 1029.0 1029 80.769000 1045 2407 1 chr3B.!!$F1 1362
2 TraesCS3B01G026600 chr3B 3205417 3210786 5369 False 661.5 911 81.921000 1045 3160 2 chr3B.!!$F3 2115
3 TraesCS3B01G026600 chr3B 73745823 73746408 585 True 599.0 599 85.497000 109 686 1 chr3B.!!$R1 577
4 TraesCS3B01G026600 chr3D 9242701 9246082 3381 False 1447.0 3134 89.932333 3 3394 3 chr3D.!!$F2 3391
5 TraesCS3B01G026600 chr3D 9199566 9201593 2027 False 1027.5 1314 86.453500 1057 3133 2 chr3D.!!$F1 2076
6 TraesCS3B01G026600 chr3D 9131085 9132093 1008 True 593.0 593 77.756000 1033 2057 1 chr3D.!!$R1 1024
7 TraesCS3B01G026600 chr6D 296995493 296996090 597 True 627.0 627 86.043000 109 698 1 chr6D.!!$R1 589
8 TraesCS3B01G026600 chr7B 275497758 275498350 592 False 612.0 612 85.857000 109 688 1 chr7B.!!$F2 579
9 TraesCS3B01G026600 chr4A 573899734 573900328 594 True 538.0 538 83.472000 109 690 1 chr4A.!!$R1 581
10 TraesCS3B01G026600 chr4A 656249746 656250887 1141 False 497.0 497 75.021000 1022 2193 1 chr4A.!!$F2 1171
11 TraesCS3B01G026600 chr4A 656480046 656481200 1154 False 407.0 407 73.566000 1067 2260 1 chr4A.!!$F4 1193
12 TraesCS3B01G026600 chr4A 655659097 655659952 855 False 405.0 405 75.754000 1334 2217 1 chr4A.!!$F1 883
13 TraesCS3B01G026600 chr7A 323414150 323414695 545 True 525.0 525 84.477000 109 647 1 chr7A.!!$R2 538
14 TraesCS3B01G026600 chr7A 47016603 47017781 1178 False 446.0 446 74.065000 1067 2283 1 chr7A.!!$F1 1216
15 TraesCS3B01G026600 chr7A 47255336 47256465 1129 True 385.0 385 73.973000 958 2067 1 chr7A.!!$R1 1109
16 TraesCS3B01G026600 chr4D 9478254 9478837 583 True 525.0 525 83.418000 109 681 1 chr4D.!!$R1 572
17 TraesCS3B01G026600 chr4D 99352083 99352671 588 True 470.0 470 81.667000 109 688 1 chr4D.!!$R2 579
18 TraesCS3B01G026600 chr2D 608786721 608787315 594 True 508.0 508 82.753000 109 687 1 chr2D.!!$R1 578
19 TraesCS3B01G026600 chr5D 274146831 274147344 513 True 503.0 503 84.837000 109 613 1 chr5D.!!$R1 504
20 TraesCS3B01G026600 chr7D 489298700 489299293 593 False 486.0 486 81.940000 109 688 1 chr7D.!!$F2 579
21 TraesCS3B01G026600 chr7D 44550961 44551871 910 False 372.0 372 74.605000 1346 2283 1 chr7D.!!$F1 937
22 TraesCS3B01G026600 chrUn 48865681 48866847 1166 True 440.0 440 74.035000 1067 2272 1 chrUn.!!$R1 1205
23 TraesCS3B01G026600 chrUn 48986235 48987548 1313 True 394.0 394 73.295000 958 2277 1 chrUn.!!$R2 1319
24 TraesCS3B01G026600 chr3A 11865278 11866259 981 False 416.0 416 75.238000 1033 2061 1 chr3A.!!$F1 1028
25 TraesCS3B01G026600 chr1A 578782606 578783108 502 True 403.0 403 81.467000 109 618 1 chr1A.!!$R1 509

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
861 939 0.028505 CGATTTGCAGATCGCCCAAG 59.971 55.0 24.33 0.34 41.9 3.61 F
983 1062 0.454957 CTTCTTGCGCCAAATCCGTG 60.455 55.0 4.18 0.00 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2167 2375 0.320374 TCCTCGTTCACGGCATCTTT 59.680 50.0 0.00 0.00 40.29 2.52 R
2773 6351 0.890542 TCCAACAGACCACAGCATGC 60.891 55.0 10.51 10.51 42.53 4.06 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
52 53 1.714794 ACTGTGAATACTGTGCTCGC 58.285 50.000 0.00 0.00 37.55 5.03
79 80 5.877012 GGGCACACAAGTATATGGATCATAG 59.123 44.000 0.00 0.00 29.42 2.23
80 81 6.467677 GGCACACAAGTATATGGATCATAGT 58.532 40.000 0.00 0.00 29.42 2.12
254 255 7.996758 AACTAATTTGAGGGATAAGAGGAGA 57.003 36.000 0.00 0.00 0.00 3.71
320 322 6.369890 CGGTGAAGAAATGAAGAAGATCTGAA 59.630 38.462 0.00 0.00 0.00 3.02
323 325 6.883217 TGAAGAAATGAAGAAGATCTGAAGGG 59.117 38.462 0.00 0.00 0.00 3.95
342 349 1.052617 GGGGAGTGGAGGAGATAAGC 58.947 60.000 0.00 0.00 0.00 3.09
350 358 0.178958 GAGGAGATAAGCGAGGGGGA 60.179 60.000 0.00 0.00 0.00 4.81
351 359 0.470268 AGGAGATAAGCGAGGGGGAC 60.470 60.000 0.00 0.00 0.00 4.46
353 361 0.822532 GAGATAAGCGAGGGGGACGA 60.823 60.000 0.00 0.00 0.00 4.20
354 362 0.824182 AGATAAGCGAGGGGGACGAG 60.824 60.000 0.00 0.00 0.00 4.18
355 363 0.822532 GATAAGCGAGGGGGACGAGA 60.823 60.000 0.00 0.00 0.00 4.04
356 364 0.824182 ATAAGCGAGGGGGACGAGAG 60.824 60.000 0.00 0.00 0.00 3.20
546 584 4.557695 GCTGACGTGGATTAGTCTCCTATG 60.558 50.000 0.00 0.00 38.16 2.23
568 606 0.673985 CGAAGGTCATGGCGATAGGA 59.326 55.000 0.00 0.00 0.00 2.94
624 662 9.856488 GATAGGAAAAAGGGTTAGATTTCAAAC 57.144 33.333 0.00 0.00 34.31 2.93
667 711 6.648879 TCTGGATAAACTTCAACAAAAGGG 57.351 37.500 0.00 0.00 0.00 3.95
690 734 3.810310 AAACACGAAAATTTGCCCTGA 57.190 38.095 0.00 0.00 0.00 3.86
709 753 3.248171 GCGCCGCTCAACTCTACG 61.248 66.667 0.00 0.00 0.00 3.51
712 756 2.202756 CCGCTCAACTCTACGGGC 60.203 66.667 0.00 0.00 41.95 6.13
718 762 1.080093 CAACTCTACGGGCTTCGCA 60.080 57.895 0.29 0.00 43.89 5.10
729 773 4.113815 CTTCGCATGCCCCCTCCA 62.114 66.667 13.15 0.00 0.00 3.86
740 786 1.952621 CCCCCTCCAAGTCTCAACTA 58.047 55.000 0.00 0.00 33.48 2.24
849 927 4.954092 AAATCCTCTTGTCTCGATTTGC 57.046 40.909 0.00 0.00 34.49 3.68
861 939 0.028505 CGATTTGCAGATCGCCCAAG 59.971 55.000 24.33 0.34 41.90 3.61
871 949 2.424956 AGATCGCCCAAGCAATTCTTTC 59.575 45.455 0.00 0.00 39.83 2.62
951 1030 2.212869 TGTTATCGCCGACGCTAATT 57.787 45.000 0.00 0.00 39.84 1.40
983 1062 0.454957 CTTCTTGCGCCAAATCCGTG 60.455 55.000 4.18 0.00 0.00 4.94
1078 1169 4.631740 TGCTGGACGACCTCCCCA 62.632 66.667 5.33 0.00 38.49 4.96
1330 1427 3.307691 CCATACAGCTTCCAACTTCTCCA 60.308 47.826 0.00 0.00 0.00 3.86
1331 1428 2.262423 ACAGCTTCCAACTTCTCCAC 57.738 50.000 0.00 0.00 0.00 4.02
1377 1478 2.887568 CTCATCCTGTCGCGGCAC 60.888 66.667 10.57 0.00 0.00 5.01
1672 1838 1.902508 CTGACCATCCACCAGTACACT 59.097 52.381 0.00 0.00 0.00 3.55
1816 1982 2.644992 GTGGCGACCTTGCTTTGG 59.355 61.111 0.00 0.00 34.52 3.28
1851 2028 1.131504 GACTGCGTCACTCTAGACCTG 59.868 57.143 0.00 0.00 35.07 4.00
1866 2043 2.359602 CTGTGGGTGCTGCAGGAG 60.360 66.667 17.12 0.00 0.00 3.69
1955 2141 5.617529 CGCTTAATTTGAGTGTGAAGCATGA 60.618 40.000 0.00 0.00 39.36 3.07
1960 2146 1.271001 TGAGTGTGAAGCATGACCCTG 60.271 52.381 0.00 0.00 0.00 4.45
1972 2158 1.377725 GACCCTGTGATGGCTGTGG 60.378 63.158 0.00 0.00 0.00 4.17
2022 2209 2.547826 GGTCCTTACCGTCTATTGCAC 58.452 52.381 0.00 0.00 35.62 4.57
2068 2255 3.960102 AGGAAATGTGGAAAGCAAAGACA 59.040 39.130 0.00 0.00 0.00 3.41
2072 2259 3.096489 TGTGGAAAGCAAAGACAATGC 57.904 42.857 0.00 0.00 44.15 3.56
2084 2271 5.905181 GCAAAGACAATGCAAACATTTTGAG 59.095 36.000 15.91 0.00 44.21 3.02
2099 2286 5.351189 ACATTTTGAGTCAGTTTGCAAAACC 59.649 36.000 14.67 2.18 41.33 3.27
2167 2375 2.286713 CCATTGTTTGAGACGCGACAAA 60.287 45.455 15.93 18.49 35.83 2.83
2225 2445 2.598565 TCTATAAGATGCCGTGCTCCT 58.401 47.619 0.00 0.00 0.00 3.69
2336 2586 6.605594 AGAACTGAACTATTAGGACTGAGGAG 59.394 42.308 0.00 0.00 0.00 3.69
2383 2636 8.492673 TTTGGTACTTGTTATGCTATCTTCAG 57.507 34.615 0.00 0.00 0.00 3.02
2450 2703 7.866393 GCTTTAGAACTGTTCTACACTTCTACA 59.134 37.037 25.55 8.77 41.70 2.74
2455 2708 9.614792 AGAACTGTTCTACACTTCTACAATTTT 57.385 29.630 20.85 0.00 38.49 1.82
2487 2740 6.262273 TGTTTACTTTCAGTTCTCCATTGTCC 59.738 38.462 0.00 0.00 0.00 4.02
2504 2757 6.423862 CATTGTCCAAAAGCACAAAATTCTG 58.576 36.000 0.00 0.00 36.14 3.02
2505 2758 3.870419 TGTCCAAAAGCACAAAATTCTGC 59.130 39.130 0.00 0.00 0.00 4.26
2506 2759 4.122046 GTCCAAAAGCACAAAATTCTGCT 58.878 39.130 0.50 0.50 45.92 4.24
2507 2760 5.163468 TGTCCAAAAGCACAAAATTCTGCTA 60.163 36.000 5.84 0.00 43.10 3.49
2508 2761 5.928264 GTCCAAAAGCACAAAATTCTGCTAT 59.072 36.000 5.84 0.00 43.10 2.97
2509 2762 6.089954 GTCCAAAAGCACAAAATTCTGCTATC 59.910 38.462 5.84 0.00 43.10 2.08
2510 2763 5.927689 CCAAAAGCACAAAATTCTGCTATCA 59.072 36.000 5.84 0.00 43.10 2.15
2511 2764 6.592607 CCAAAAGCACAAAATTCTGCTATCAT 59.407 34.615 5.84 0.00 43.10 2.45
2512 2765 7.201496 CCAAAAGCACAAAATTCTGCTATCATC 60.201 37.037 5.84 0.00 43.10 2.92
2513 2766 6.519679 AAGCACAAAATTCTGCTATCATCA 57.480 33.333 5.84 0.00 43.10 3.07
2514 2767 6.710597 AGCACAAAATTCTGCTATCATCAT 57.289 33.333 3.94 0.00 42.07 2.45
2515 2768 7.108841 AGCACAAAATTCTGCTATCATCATT 57.891 32.000 3.94 0.00 42.07 2.57
2516 2769 7.553334 AGCACAAAATTCTGCTATCATCATTT 58.447 30.769 3.94 0.00 42.07 2.32
2517 2770 7.491372 AGCACAAAATTCTGCTATCATCATTTG 59.509 33.333 3.94 0.00 42.07 2.32
2524 2777 3.887110 CTGCTATCATCATTTGGGAAGCA 59.113 43.478 0.00 0.00 35.18 3.91
2532 2785 3.499338 TCATTTGGGAAGCAATCAGTGT 58.501 40.909 0.00 0.00 0.00 3.55
2587 2840 7.718272 TGTTTACTACAGCGACAAGTAATTT 57.282 32.000 0.00 0.00 36.05 1.82
2593 2846 3.250040 ACAGCGACAAGTAATTTGGTCAC 59.750 43.478 0.00 0.00 41.25 3.67
2594 2847 3.498397 CAGCGACAAGTAATTTGGTCACT 59.502 43.478 0.00 0.00 41.25 3.41
2595 2848 4.688879 CAGCGACAAGTAATTTGGTCACTA 59.311 41.667 0.00 0.00 41.25 2.74
2596 2849 4.929808 AGCGACAAGTAATTTGGTCACTAG 59.070 41.667 0.00 0.00 41.25 2.57
2620 2873 3.668447 ACCACTGTCATGTGTCTGATTC 58.332 45.455 0.00 0.00 36.30 2.52
2629 2882 5.809562 GTCATGTGTCTGATTCCTACTTCAG 59.190 44.000 0.00 0.00 40.58 3.02
2701 2955 7.765695 TCACCATTTCAGATAAAAGAGCTTT 57.234 32.000 0.00 0.00 0.00 3.51
2728 2982 6.514048 GCTGCTACATTTATGTCCAGGATTTC 60.514 42.308 17.66 4.99 41.97 2.17
2773 6351 6.483640 GGTTATTGGAGTGCTATCTTAACCAG 59.516 42.308 15.28 0.00 38.02 4.00
2803 6381 0.108585 TCTGTTGGAAGGCTGGTGAC 59.891 55.000 0.00 0.00 0.00 3.67
2804 6382 0.890996 CTGTTGGAAGGCTGGTGACC 60.891 60.000 0.00 0.00 0.00 4.02
2853 6445 4.640201 TGTAATATGGCTGTCTCTTTTGCC 59.360 41.667 0.00 0.00 45.10 4.52
2857 6449 2.387757 TGGCTGTCTCTTTTGCCTTTT 58.612 42.857 0.00 0.00 45.11 2.27
2898 6491 4.648626 TGCTGGCGCTTGGCTCTT 62.649 61.111 7.64 0.00 42.94 2.85
2913 6506 3.181455 TGGCTCTTCTGTTAAGCTGTTCA 60.181 43.478 0.00 0.00 36.29 3.18
2946 6555 7.441890 TTTACTCAAAATCCTATCGTTGCAA 57.558 32.000 0.00 0.00 0.00 4.08
2964 6573 1.814394 CAAGCTTGCAGCATCTAACCA 59.186 47.619 14.65 0.00 45.56 3.67
2983 6592 8.593679 TCTAACCAAAATGAGTGATGTCTTCTA 58.406 33.333 0.00 0.00 0.00 2.10
3079 6688 6.932356 ATGCTATCTTGAACACCATGTTAG 57.068 37.500 0.00 0.00 41.28 2.34
3102 6711 7.239166 AGTGTTATGAAGAATCAATGTAGCG 57.761 36.000 0.00 0.00 39.49 4.26
3174 6784 3.631144 CATTGCTGAAAAGCACGAAAGA 58.369 40.909 0.00 0.00 45.32 2.52
3188 6798 4.527564 CACGAAAGACATGGTTTCAGTTC 58.472 43.478 17.93 6.12 34.16 3.01
3189 6799 3.247648 ACGAAAGACATGGTTTCAGTTCG 59.752 43.478 17.93 15.86 38.10 3.95
3190 6800 3.493129 CGAAAGACATGGTTTCAGTTCGA 59.507 43.478 17.93 0.00 36.01 3.71
3201 6811 7.441890 TGGTTTCAGTTCGAAATGCTAATTA 57.558 32.000 20.19 0.00 45.21 1.40
3219 6829 4.612264 ATTATGCATCATTTGGGAAGCC 57.388 40.909 0.19 0.00 30.82 4.35
3228 6838 0.538057 TTTGGGAAGCCAGCTGTGAG 60.538 55.000 13.81 0.00 0.00 3.51
3230 6840 1.073897 GGGAAGCCAGCTGTGAGTT 59.926 57.895 13.81 0.00 0.00 3.01
3231 6841 0.538287 GGGAAGCCAGCTGTGAGTTT 60.538 55.000 13.81 1.32 0.00 2.66
3232 6842 1.322442 GGAAGCCAGCTGTGAGTTTT 58.678 50.000 13.81 0.00 0.00 2.43
3257 6867 2.292828 TTTTTGAGGGAGGAAGCCAG 57.707 50.000 0.00 0.00 0.00 4.85
3258 6868 0.251341 TTTTGAGGGAGGAAGCCAGC 60.251 55.000 0.00 0.00 0.00 4.85
3259 6869 1.136329 TTTGAGGGAGGAAGCCAGCT 61.136 55.000 0.00 0.00 0.00 4.24
3260 6870 1.845627 TTGAGGGAGGAAGCCAGCTG 61.846 60.000 6.78 6.78 0.00 4.24
3261 6871 2.204059 AGGGAGGAAGCCAGCTGT 60.204 61.111 13.81 0.00 0.00 4.40
3262 6872 2.045536 GGGAGGAAGCCAGCTGTG 60.046 66.667 13.81 5.37 0.00 3.66
3263 6873 2.596851 GGGAGGAAGCCAGCTGTGA 61.597 63.158 13.81 0.00 0.00 3.58
3264 6874 1.078567 GGAGGAAGCCAGCTGTGAG 60.079 63.158 13.81 0.00 0.00 3.51
3265 6875 1.676384 GAGGAAGCCAGCTGTGAGT 59.324 57.895 13.81 0.00 0.00 3.41
3266 6876 0.036022 GAGGAAGCCAGCTGTGAGTT 59.964 55.000 13.81 0.00 0.00 3.01
3267 6877 0.250640 AGGAAGCCAGCTGTGAGTTG 60.251 55.000 13.81 0.00 0.00 3.16
3269 6879 0.536006 GAAGCCAGCTGTGAGTTGGT 60.536 55.000 13.81 0.00 46.79 3.67
3270 6880 0.820891 AAGCCAGCTGTGAGTTGGTG 60.821 55.000 13.81 0.00 46.79 4.17
3271 6881 2.912624 GCCAGCTGTGAGTTGGTGC 61.913 63.158 13.81 1.18 46.79 5.01
3272 6882 1.228063 CCAGCTGTGAGTTGGTGCT 60.228 57.895 13.81 0.00 41.12 4.40
3273 6883 1.233285 CCAGCTGTGAGTTGGTGCTC 61.233 60.000 13.81 0.00 41.12 4.26
3274 6884 0.533531 CAGCTGTGAGTTGGTGCTCA 60.534 55.000 5.25 0.00 42.56 4.26
3275 6885 0.250209 AGCTGTGAGTTGGTGCTCAG 60.250 55.000 0.00 0.00 45.03 3.35
3276 6886 1.849976 GCTGTGAGTTGGTGCTCAGC 61.850 60.000 0.00 0.00 45.03 4.26
3277 6887 0.533531 CTGTGAGTTGGTGCTCAGCA 60.534 55.000 0.00 0.00 45.03 4.41
3278 6888 0.107263 TGTGAGTTGGTGCTCAGCAA 60.107 50.000 0.00 10.07 45.03 3.91
3282 6892 3.368822 TTGGTGCTCAGCAATGCC 58.631 55.556 0.00 0.00 43.00 4.40
3283 6893 1.228644 TTGGTGCTCAGCAATGCCT 60.229 52.632 0.00 0.00 43.00 4.75
3284 6894 0.828762 TTGGTGCTCAGCAATGCCTT 60.829 50.000 0.00 0.00 43.00 4.35
3299 6909 3.500448 TGCCTTGTGTCTGATTGGTAA 57.500 42.857 0.00 0.00 0.00 2.85
3305 6915 6.173339 CCTTGTGTCTGATTGGTAATACAGT 58.827 40.000 0.00 0.00 0.00 3.55
3362 6972 4.104102 TCTTGGGTGTCAGATTACCACTTT 59.896 41.667 8.59 0.00 38.74 2.66
3382 6992 9.559958 CCACTTTAATACAGCTATTGTTGAAAG 57.440 33.333 0.00 0.75 41.29 2.62
3394 7004 6.293955 GCTATTGTTGAAAGAGTTGGCAAGTA 60.294 38.462 7.71 0.00 0.00 2.24
3395 7005 5.906113 TTGTTGAAAGAGTTGGCAAGTAA 57.094 34.783 7.71 0.00 0.00 2.24
3396 7006 5.906113 TGTTGAAAGAGTTGGCAAGTAAA 57.094 34.783 7.71 0.00 0.00 2.01
3397 7007 6.274157 TGTTGAAAGAGTTGGCAAGTAAAA 57.726 33.333 7.71 0.00 0.00 1.52
3398 7008 6.872920 TGTTGAAAGAGTTGGCAAGTAAAAT 58.127 32.000 7.71 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.875948 TGTTCTGTACACAAAGTGCATATT 57.124 33.333 0.00 0.00 42.11 1.28
1 2 6.875948 TTGTTCTGTACACAAAGTGCATAT 57.124 33.333 0.00 0.00 42.11 1.78
52 53 3.884895 TCCATATACTTGTGTGCCCAAG 58.115 45.455 6.38 6.38 45.83 3.61
79 80 5.414454 TGTGTGGACATTTATAAGCCAAGAC 59.586 40.000 0.00 0.00 0.00 3.01
80 81 5.565509 TGTGTGGACATTTATAAGCCAAGA 58.434 37.500 0.00 0.00 0.00 3.02
93 94 7.394016 TCTATTGTGTTCTATTGTGTGGACAT 58.606 34.615 0.00 0.00 30.13 3.06
238 239 7.846823 AGAAAAGTAATCTCCTCTTATCCCTCA 59.153 37.037 0.00 0.00 0.00 3.86
254 255 2.745821 GCCCCGAAACGAGAAAAGTAAT 59.254 45.455 0.00 0.00 0.00 1.89
294 296 5.641209 CAGATCTTCTTCATTTCTTCACCGT 59.359 40.000 0.00 0.00 0.00 4.83
323 325 1.052617 GCTTATCTCCTCCACTCCCC 58.947 60.000 0.00 0.00 0.00 4.81
339 346 2.756283 CTCTCGTCCCCCTCGCTT 60.756 66.667 0.00 0.00 0.00 4.68
342 349 0.680280 TCTTTCTCTCGTCCCCCTCG 60.680 60.000 0.00 0.00 0.00 4.63
350 358 3.492337 ACAGAGGAGTTCTTTCTCTCGT 58.508 45.455 0.00 0.00 35.89 4.18
351 359 4.481463 GAACAGAGGAGTTCTTTCTCTCG 58.519 47.826 0.00 0.00 43.46 4.04
388 401 2.287194 CACCCCCTTCTCCCCCAT 60.287 66.667 0.00 0.00 0.00 4.00
546 584 2.377628 TATCGCCATGACCTTCGGCC 62.378 60.000 0.00 0.00 43.17 6.13
568 606 3.195825 GGCTCAGCGGTAGGATTACATAT 59.804 47.826 0.00 0.00 0.00 1.78
690 734 3.068691 TAGAGTTGAGCGGCGCCT 61.069 61.111 30.40 18.75 0.00 5.52
695 739 2.202756 GCCCGTAGAGTTGAGCGG 60.203 66.667 0.00 0.00 43.40 5.52
712 756 3.643595 TTGGAGGGGGCATGCGAAG 62.644 63.158 12.44 0.00 0.00 3.79
718 762 0.846427 TTGAGACTTGGAGGGGGCAT 60.846 55.000 0.00 0.00 0.00 4.40
729 773 5.717178 TGGTAGCTCTTGATAGTTGAGACTT 59.283 40.000 0.00 0.00 37.33 3.01
849 927 1.386533 AGAATTGCTTGGGCGATCTG 58.613 50.000 0.00 0.00 41.36 2.90
871 949 1.272781 GACGACGGATTGAGAGCAAG 58.727 55.000 0.00 0.00 37.45 4.01
956 1035 0.606130 TGGCGCAAGAAGATGAAGCA 60.606 50.000 10.83 0.00 43.02 3.91
1166 1257 1.483004 TGAACTTGTCGGTGGAAGTGA 59.517 47.619 0.00 0.00 32.66 3.41
1307 1404 2.680339 GAGAAGTTGGAAGCTGTATGGC 59.320 50.000 0.00 0.00 0.00 4.40
1330 1427 4.770874 GGCGGCGTGGTGTATGGT 62.771 66.667 9.37 0.00 0.00 3.55
1331 1428 4.467084 AGGCGGCGTGGTGTATGG 62.467 66.667 9.37 0.00 0.00 2.74
1377 1478 2.935201 GTTGCAGATGTAGAAGCTGGAG 59.065 50.000 0.00 0.00 31.67 3.86
1672 1838 2.267642 GTGCAGGCCACCACGATA 59.732 61.111 5.01 0.00 38.55 2.92
1770 1936 3.751175 CGAACAATAACACCATGTCACCT 59.249 43.478 0.00 0.00 0.00 4.00
1851 2028 0.745845 CATACTCCTGCAGCACCCAC 60.746 60.000 8.66 0.00 0.00 4.61
1866 2043 0.597637 CCCACGTCTCGGCATCATAC 60.598 60.000 0.00 0.00 0.00 2.39
1955 2141 2.129555 GACCACAGCCATCACAGGGT 62.130 60.000 0.00 0.00 40.74 4.34
1960 2146 0.813184 CCATTGACCACAGCCATCAC 59.187 55.000 0.00 0.00 0.00 3.06
1972 2158 1.237285 AACAGCTCACGGCCATTGAC 61.237 55.000 2.24 0.03 43.05 3.18
2022 2209 1.250328 ACACACCATCAATGCCACAG 58.750 50.000 0.00 0.00 0.00 3.66
2068 2255 7.007313 CAAACTGACTCAAAATGTTTGCATT 57.993 32.000 8.07 0.00 46.38 3.56
2072 2259 6.406093 TTGCAAACTGACTCAAAATGTTTG 57.594 33.333 13.51 13.51 45.69 2.93
2084 2271 4.091365 GTGTCAAAGGTTTTGCAAACTGAC 59.909 41.667 12.39 17.64 26.79 3.51
2099 2286 2.926200 CGATGCCTAGTGAGTGTCAAAG 59.074 50.000 0.00 0.00 0.00 2.77
2167 2375 0.320374 TCCTCGTTCACGGCATCTTT 59.680 50.000 0.00 0.00 40.29 2.52
2225 2445 9.381038 AGCAAGGAGTCCAAAGTATTATAGATA 57.619 33.333 12.86 0.00 0.00 1.98
2402 2655 7.174107 AGCATATAAGCTCCATTGTTTTGTT 57.826 32.000 0.00 0.00 42.18 2.83
2403 2656 6.780457 AGCATATAAGCTCCATTGTTTTGT 57.220 33.333 0.00 0.00 42.18 2.83
2404 2657 9.241317 CTAAAGCATATAAGCTCCATTGTTTTG 57.759 33.333 2.41 0.00 45.89 2.44
2405 2658 9.189156 TCTAAAGCATATAAGCTCCATTGTTTT 57.811 29.630 2.41 0.00 45.89 2.43
2406 2659 8.752005 TCTAAAGCATATAAGCTCCATTGTTT 57.248 30.769 2.41 0.00 45.89 2.83
2450 2703 7.290110 CTGAAAGTAAACAGGGGAGAAAATT 57.710 36.000 0.00 0.00 0.00 1.82
2504 2757 4.924305 TTGCTTCCCAAATGATGATAGC 57.076 40.909 0.00 0.00 0.00 2.97
2505 2758 6.264744 ACTGATTGCTTCCCAAATGATGATAG 59.735 38.462 0.00 0.00 36.92 2.08
2506 2759 6.040054 CACTGATTGCTTCCCAAATGATGATA 59.960 38.462 0.00 0.00 36.92 2.15
2507 2760 4.960469 ACTGATTGCTTCCCAAATGATGAT 59.040 37.500 0.00 0.00 36.92 2.45
2508 2761 4.158949 CACTGATTGCTTCCCAAATGATGA 59.841 41.667 0.00 0.00 36.92 2.92
2509 2762 4.081862 ACACTGATTGCTTCCCAAATGATG 60.082 41.667 0.00 0.00 36.92 3.07
2510 2763 4.091549 ACACTGATTGCTTCCCAAATGAT 58.908 39.130 0.00 0.00 36.92 2.45
2511 2764 3.499338 ACACTGATTGCTTCCCAAATGA 58.501 40.909 0.00 0.00 36.92 2.57
2512 2765 3.947910 ACACTGATTGCTTCCCAAATG 57.052 42.857 0.00 0.00 36.92 2.32
2513 2766 4.961438 AAACACTGATTGCTTCCCAAAT 57.039 36.364 0.00 0.00 36.92 2.32
2514 2767 4.440880 CAAAACACTGATTGCTTCCCAAA 58.559 39.130 0.00 0.00 36.92 3.28
2515 2768 3.181467 CCAAAACACTGATTGCTTCCCAA 60.181 43.478 0.00 0.00 37.94 4.12
2516 2769 2.364970 CCAAAACACTGATTGCTTCCCA 59.635 45.455 0.00 0.00 0.00 4.37
2517 2770 2.365293 ACCAAAACACTGATTGCTTCCC 59.635 45.455 0.00 0.00 0.00 3.97
2524 2777 2.035066 GCTGAGCACCAAAACACTGATT 59.965 45.455 0.00 0.00 0.00 2.57
2532 2785 1.961793 AACTACGCTGAGCACCAAAA 58.038 45.000 4.88 0.00 0.00 2.44
2587 2840 2.168496 GACAGTGGTAGCTAGTGACCA 58.832 52.381 12.38 12.38 43.55 4.02
2593 2846 3.445450 AGACACATGACAGTGGTAGCTAG 59.555 47.826 0.00 0.00 43.72 3.42
2594 2847 3.193479 CAGACACATGACAGTGGTAGCTA 59.807 47.826 0.00 0.00 43.72 3.32
2595 2848 2.028658 CAGACACATGACAGTGGTAGCT 60.029 50.000 0.00 0.00 43.72 3.32
2596 2849 2.029020 TCAGACACATGACAGTGGTAGC 60.029 50.000 0.00 0.00 43.72 3.58
2620 2873 6.631016 TCAACAATAGCTGTACTGAAGTAGG 58.369 40.000 3.61 0.00 37.23 3.18
2629 2882 8.073768 TGCTAACTTTTTCAACAATAGCTGTAC 58.926 33.333 0.00 0.00 37.23 2.90
2701 2955 3.544684 CTGGACATAAATGTAGCAGCCA 58.455 45.455 0.00 0.00 41.95 4.75
2773 6351 0.890542 TCCAACAGACCACAGCATGC 60.891 55.000 10.51 10.51 42.53 4.06
2803 6381 3.058016 CCAATGGCAGCATAAATAGACGG 60.058 47.826 0.00 0.00 0.00 4.79
2804 6382 4.151258 CCAATGGCAGCATAAATAGACG 57.849 45.455 0.00 0.00 0.00 4.18
2857 6449 5.593502 AGTAAACCGATAAACCCACACAAAA 59.406 36.000 0.00 0.00 0.00 2.44
2860 6452 4.066490 CAGTAAACCGATAAACCCACACA 58.934 43.478 0.00 0.00 0.00 3.72
2861 6453 3.120095 GCAGTAAACCGATAAACCCACAC 60.120 47.826 0.00 0.00 0.00 3.82
2898 6491 5.368145 ACTGACAATGAACAGCTTAACAGA 58.632 37.500 0.00 0.00 37.61 3.41
3042 6651 8.599055 TCAAGATAGCATAACAAGAAGCATAG 57.401 34.615 0.00 0.00 0.00 2.23
3079 6688 7.005062 ACGCTACATTGATTCTTCATAACAC 57.995 36.000 0.00 0.00 0.00 3.32
3098 6707 5.515797 ACAGTTCTGAAGCATATACGCTA 57.484 39.130 6.83 0.00 42.89 4.26
3102 6711 7.038659 ACAGAGAACAGTTCTGAAGCATATAC 58.961 38.462 21.00 2.10 43.75 1.47
3201 6811 1.760613 CTGGCTTCCCAAATGATGCAT 59.239 47.619 0.00 0.00 41.58 3.96
3239 6849 0.251341 GCTGGCTTCCTCCCTCAAAA 60.251 55.000 0.00 0.00 0.00 2.44
3240 6850 1.136329 AGCTGGCTTCCTCCCTCAAA 61.136 55.000 0.00 0.00 0.00 2.69
3241 6851 1.539869 AGCTGGCTTCCTCCCTCAA 60.540 57.895 0.00 0.00 0.00 3.02
3242 6852 2.123632 AGCTGGCTTCCTCCCTCA 59.876 61.111 0.00 0.00 0.00 3.86
3243 6853 2.297129 ACAGCTGGCTTCCTCCCTC 61.297 63.158 19.93 0.00 0.00 4.30
3244 6854 2.204059 ACAGCTGGCTTCCTCCCT 60.204 61.111 19.93 0.00 0.00 4.20
3245 6855 2.045536 CACAGCTGGCTTCCTCCC 60.046 66.667 19.93 0.00 0.00 4.30
3246 6856 1.078567 CTCACAGCTGGCTTCCTCC 60.079 63.158 19.93 0.00 0.00 4.30
3247 6857 0.036022 AACTCACAGCTGGCTTCCTC 59.964 55.000 19.93 0.00 0.00 3.71
3249 6859 1.239968 CCAACTCACAGCTGGCTTCC 61.240 60.000 19.93 0.00 0.00 3.46
3250 6860 0.536006 ACCAACTCACAGCTGGCTTC 60.536 55.000 19.93 0.00 34.87 3.86
3251 6861 0.820891 CACCAACTCACAGCTGGCTT 60.821 55.000 19.93 0.00 34.87 4.35
3252 6862 1.228063 CACCAACTCACAGCTGGCT 60.228 57.895 19.93 0.00 34.87 4.75
3253 6863 2.912624 GCACCAACTCACAGCTGGC 61.913 63.158 19.93 4.24 34.87 4.85
3254 6864 1.228063 AGCACCAACTCACAGCTGG 60.228 57.895 19.93 7.28 37.48 4.85
3255 6865 0.533531 TGAGCACCAACTCACAGCTG 60.534 55.000 13.48 13.48 41.72 4.24
3256 6866 0.250209 CTGAGCACCAACTCACAGCT 60.250 55.000 0.00 0.00 41.72 4.24
3257 6867 1.849976 GCTGAGCACCAACTCACAGC 61.850 60.000 0.00 0.00 41.72 4.40
3258 6868 0.533531 TGCTGAGCACCAACTCACAG 60.534 55.000 1.40 0.00 41.72 3.66
3259 6869 0.107263 TTGCTGAGCACCAACTCACA 60.107 50.000 6.64 0.00 41.72 3.58
3260 6870 1.068748 CATTGCTGAGCACCAACTCAC 60.069 52.381 6.64 0.00 41.72 3.51
3261 6871 1.241165 CATTGCTGAGCACCAACTCA 58.759 50.000 6.64 0.00 44.32 3.41
3262 6872 0.109412 GCATTGCTGAGCACCAACTC 60.109 55.000 6.64 0.00 38.71 3.01
3263 6873 1.530013 GGCATTGCTGAGCACCAACT 61.530 55.000 6.64 0.00 38.71 3.16
3264 6874 1.080298 GGCATTGCTGAGCACCAAC 60.080 57.895 6.64 0.00 38.71 3.77
3265 6875 0.828762 AAGGCATTGCTGAGCACCAA 60.829 50.000 6.64 0.00 38.71 3.67
3266 6876 1.228644 AAGGCATTGCTGAGCACCA 60.229 52.632 6.64 0.00 38.71 4.17
3267 6877 1.214589 CAAGGCATTGCTGAGCACC 59.785 57.895 6.64 5.38 38.71 5.01
3268 6878 0.388134 CACAAGGCATTGCTGAGCAC 60.388 55.000 6.64 0.00 38.71 4.40
3269 6879 0.824595 ACACAAGGCATTGCTGAGCA 60.825 50.000 11.69 1.40 40.27 4.26
3270 6880 0.109412 GACACAAGGCATTGCTGAGC 60.109 55.000 11.69 0.00 40.27 4.26
3271 6881 1.199327 CAGACACAAGGCATTGCTGAG 59.801 52.381 11.69 1.51 40.27 3.35
3272 6882 1.202794 TCAGACACAAGGCATTGCTGA 60.203 47.619 11.69 12.81 40.27 4.26
3273 6883 1.241165 TCAGACACAAGGCATTGCTG 58.759 50.000 11.69 10.64 40.27 4.41
3274 6884 2.211250 ATCAGACACAAGGCATTGCT 57.789 45.000 11.69 0.00 40.27 3.91
3275 6885 2.602878 CAATCAGACACAAGGCATTGC 58.397 47.619 11.69 0.00 40.27 3.56
3276 6886 2.559668 ACCAATCAGACACAAGGCATTG 59.440 45.455 10.01 10.01 42.46 2.82
3277 6887 2.880443 ACCAATCAGACACAAGGCATT 58.120 42.857 0.00 0.00 0.00 3.56
3278 6888 2.592102 ACCAATCAGACACAAGGCAT 57.408 45.000 0.00 0.00 0.00 4.40
3279 6889 3.500448 TTACCAATCAGACACAAGGCA 57.500 42.857 0.00 0.00 0.00 4.75
3280 6890 4.941263 TGTATTACCAATCAGACACAAGGC 59.059 41.667 0.00 0.00 0.00 4.35
3281 6891 6.092670 CACTGTATTACCAATCAGACACAAGG 59.907 42.308 0.00 0.00 0.00 3.61
3282 6892 6.873605 TCACTGTATTACCAATCAGACACAAG 59.126 38.462 0.00 0.00 0.00 3.16
3283 6893 6.649141 GTCACTGTATTACCAATCAGACACAA 59.351 38.462 0.00 0.00 0.00 3.33
3284 6894 6.163476 GTCACTGTATTACCAATCAGACACA 58.837 40.000 0.00 0.00 0.00 3.72
3305 6915 9.337396 AGTAATGAAATAACTTGTCAGTTGTCA 57.663 29.630 0.00 0.50 43.54 3.58
3362 6972 8.946085 CCAACTCTTTCAACAATAGCTGTATTA 58.054 33.333 0.00 0.00 37.23 0.98


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

AutoCloner maintained by Alex Coulton.