Multiple sequence alignment - TraesCS7D01G352400

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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 TraesCS7D01G352400 chr7D 100.000 3427 0 0 1 3427 454073493 454070067 0.000000e+00 6329.0
1 TraesCS7D01G352400 chr7B 91.242 2078 105 33 591 2642 477780933 477778907 0.000000e+00 2758.0
2 TraesCS7D01G352400 chr7B 90.771 791 70 2 2639 3427 477778532 477777743 0.000000e+00 1053.0
3 TraesCS7D01G352400 chr7B 77.681 345 75 2 3083 3425 687549333 687549677 3.470000e-50 209.0
4 TraesCS7D01G352400 chr7B 85.321 109 7 7 239 339 477781235 477781128 1.680000e-18 104.0
5 TraesCS7D01G352400 chr7B 97.778 45 1 0 169 213 477781347 477781303 1.020000e-10 78.7
6 TraesCS7D01G352400 chr7A 92.787 1733 65 14 1152 2866 543783835 543785525 0.000000e+00 2453.0
7 TraesCS7D01G352400 chr7A 89.344 488 25 12 631 1118 543783376 543783836 3.810000e-164 588.0
8 TraesCS7D01G352400 chr7A 85.609 271 12 14 95 340 543782865 543783133 3.390000e-65 259.0
9 TraesCS7D01G352400 chr7A 96.078 51 2 0 47 97 543782797 543782847 2.190000e-12 84.2
10 TraesCS7D01G352400 chr2D 99.278 277 1 1 431 707 616446050 616445775 1.840000e-137 499.0
11 TraesCS7D01G352400 chr2D 77.812 320 67 4 3071 3387 164742997 164743315 9.700000e-46 195.0
12 TraesCS7D01G352400 chr6D 79.121 364 69 7 3071 3427 315366160 315365797 9.500000e-61 244.0
13 TraesCS7D01G352400 chr6D 78.273 359 69 9 3031 3383 9790204 9789849 4.450000e-54 222.0
14 TraesCS7D01G352400 chr5D 78.492 358 69 7 3031 3383 486903842 486904196 9.570000e-56 228.0
15 TraesCS7D01G352400 chr5D 76.519 362 76 8 3071 3427 443002523 443002166 4.510000e-44 189.0
16 TraesCS7D01G352400 chr5B 77.508 329 67 6 3103 3427 293657558 293657233 1.260000e-44 191.0
17 TraesCS7D01G352400 chr2A 76.389 360 76 9 3071 3425 419477047 419476692 5.840000e-43 185.0
18 TraesCS7D01G352400 chr2A 95.652 46 2 0 547 592 751753386 751753341 1.320000e-09 75.0
19 TraesCS7D01G352400 chr3B 95.745 47 2 0 547 593 489366341 489366387 3.670000e-10 76.8
20 TraesCS7D01G352400 chr1A 95.745 47 2 0 547 593 551481952 551481906 3.670000e-10 76.8
21 TraesCS7D01G352400 chr6A 95.652 46 2 0 547 592 473842648 473842693 1.320000e-09 75.0
22 TraesCS7D01G352400 chr6A 95.652 46 1 1 547 591 106697692 106697647 4.740000e-09 73.1
23 TraesCS7D01G352400 chr5A 95.652 46 2 0 547 592 582620786 582620741 1.320000e-09 75.0
24 TraesCS7D01G352400 chrUn 92.157 51 2 2 547 595 81780221 81780171 1.710000e-08 71.3
25 TraesCS7D01G352400 chr1B 97.561 41 1 0 547 587 21276702 21276742 1.710000e-08 71.3


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 TraesCS7D01G352400 chr7D 454070067 454073493 3426 True 6329.000 6329 100.0000 1 3427 1 chr7D.!!$R1 3426
1 TraesCS7D01G352400 chr7B 477777743 477781347 3604 True 998.425 2758 91.2780 169 3427 4 chr7B.!!$R1 3258
2 TraesCS7D01G352400 chr7A 543782797 543785525 2728 False 846.050 2453 90.9545 47 2866 4 chr7A.!!$F1 2819

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
557 646 0.107508 CCAGTGTCAGGCAGGGTATG 60.108 60.0 0.00 0.0 0.00 2.39 F
1137 1277 0.107456 CCAGTCCAGTGCTGTTCAGT 59.893 55.0 1.78 0.0 32.41 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1420 1560 1.740296 CCTGTAGTTGTTCGCGGGG 60.740 63.158 6.13 0.0 0.0 5.73 R
2824 3359 0.382515 CGAACCCAAAACCGAGCAAA 59.617 50.000 0.00 0.0 0.0 3.68 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
17 18 2.563427 CTGCAGCTCTCGTGACGA 59.437 61.111 7.70 7.70 0.00 4.20
18 19 1.799519 CTGCAGCTCTCGTGACGAC 60.800 63.158 2.39 0.00 0.00 4.34
39 40 4.509619 CGACGTACGGGATCGATG 57.490 61.111 21.06 0.00 38.10 3.84
40 41 1.724929 CGACGTACGGGATCGATGC 60.725 63.158 21.06 8.63 38.10 3.91
41 42 1.371389 GACGTACGGGATCGATGCC 60.371 63.158 24.93 24.93 40.11 4.40
88 89 0.320050 TGTGCAGCTTCCGACACATA 59.680 50.000 0.00 0.00 38.07 2.29
89 90 1.270571 TGTGCAGCTTCCGACACATAA 60.271 47.619 0.00 0.00 38.07 1.90
97 98 1.138036 CCGACACATAACGGCGAGA 59.862 57.895 16.62 0.00 42.55 4.04
98 99 1.138047 CCGACACATAACGGCGAGAC 61.138 60.000 16.62 0.00 42.55 3.36
100 101 0.804933 GACACATAACGGCGAGACCC 60.805 60.000 16.62 0.00 33.26 4.46
106 128 1.597797 TAACGGCGAGACCCAATCGT 61.598 55.000 16.62 0.00 42.13 3.73
122 144 5.149054 CAATCGTTGGAGTGCTATTTCTC 57.851 43.478 0.00 0.00 30.81 2.87
124 146 5.854010 ATCGTTGGAGTGCTATTTCTCTA 57.146 39.130 0.00 0.00 0.00 2.43
125 147 5.854010 TCGTTGGAGTGCTATTTCTCTAT 57.146 39.130 0.00 0.00 0.00 1.98
126 148 6.954487 TCGTTGGAGTGCTATTTCTCTATA 57.046 37.500 0.00 0.00 0.00 1.31
179 206 6.033513 GTGAGCGTTTTAATTAAACTCCATGC 59.966 38.462 17.69 15.57 43.21 4.06
259 328 3.360340 GCGGAAACTGCTGCTGCT 61.360 61.111 17.00 0.00 40.48 4.24
263 332 0.240411 GGAAACTGCTGCTGCTGAAG 59.760 55.000 25.33 12.50 40.66 3.02
264 333 0.240411 GAAACTGCTGCTGCTGAAGG 59.760 55.000 25.33 9.61 40.66 3.46
340 423 2.746904 CGACAAGGTAATCATGCACCAA 59.253 45.455 11.91 0.00 37.28 3.67
343 426 4.088634 ACAAGGTAATCATGCACCAATGT 58.911 39.130 11.91 12.21 37.28 2.71
344 427 4.158394 ACAAGGTAATCATGCACCAATGTC 59.842 41.667 11.91 0.00 34.11 3.06
345 428 4.240881 AGGTAATCATGCACCAATGTCT 57.759 40.909 11.91 0.00 37.28 3.41
346 429 5.372343 AGGTAATCATGCACCAATGTCTA 57.628 39.130 11.91 0.00 37.28 2.59
349 432 5.822519 GGTAATCATGCACCAATGTCTAGAA 59.177 40.000 0.00 0.00 34.77 2.10
350 433 6.318648 GGTAATCATGCACCAATGTCTAGAAA 59.681 38.462 0.00 0.00 34.77 2.52
351 434 6.839124 AATCATGCACCAATGTCTAGAAAA 57.161 33.333 0.00 0.00 0.00 2.29
352 435 6.839124 ATCATGCACCAATGTCTAGAAAAA 57.161 33.333 0.00 0.00 0.00 1.94
372 455 3.866883 AAAAAGGTAATCATGCACCGG 57.133 42.857 0.00 0.00 39.94 5.28
373 456 2.507407 AAAGGTAATCATGCACCGGT 57.493 45.000 0.00 0.00 39.94 5.28
374 457 1.750193 AAGGTAATCATGCACCGGTG 58.250 50.000 30.66 30.66 39.94 4.94
386 469 2.050477 CACCGGTGCACTGATTTTTC 57.950 50.000 27.46 0.98 0.00 2.29
474 563 2.742372 TCGGCAGCGGCTTCTTTC 60.742 61.111 9.17 0.00 40.87 2.62
481 570 0.238553 AGCGGCTTCTTTCTTTTCGC 59.761 50.000 0.00 0.00 41.64 4.70
498 587 2.409870 GCAGGAGACGCCAATTGGG 61.410 63.158 25.73 17.36 40.02 4.12
503 592 1.243902 GAGACGCCAATTGGGTTTGA 58.756 50.000 25.73 0.00 40.77 2.69
516 605 7.416817 CAATTGGGTTTGAAATTTTCTTCACC 58.583 34.615 10.33 11.78 35.07 4.02
525 614 6.003950 TGAAATTTTCTTCACCCTACTCCTG 58.996 40.000 10.33 0.00 30.31 3.86
554 643 2.122413 TCCAGTGTCAGGCAGGGT 60.122 61.111 0.00 0.00 0.00 4.34
557 646 0.107508 CCAGTGTCAGGCAGGGTATG 60.108 60.000 0.00 0.00 0.00 2.39
558 647 0.107508 CAGTGTCAGGCAGGGTATGG 60.108 60.000 0.00 0.00 0.00 2.74
565 654 3.255032 GCAGGGTATGGCAGGGAT 58.745 61.111 0.00 0.00 0.00 3.85
566 655 1.538666 GCAGGGTATGGCAGGGATT 59.461 57.895 0.00 0.00 0.00 3.01
567 656 0.825010 GCAGGGTATGGCAGGGATTG 60.825 60.000 0.00 0.00 0.00 2.67
579 668 3.777465 CAGGGATTGCAAAGTCAGATG 57.223 47.619 1.71 0.00 0.00 2.90
580 669 3.349927 CAGGGATTGCAAAGTCAGATGA 58.650 45.455 1.71 0.00 0.00 2.92
581 670 3.952323 CAGGGATTGCAAAGTCAGATGAT 59.048 43.478 1.71 0.00 0.00 2.45
582 671 4.036498 CAGGGATTGCAAAGTCAGATGATC 59.964 45.833 1.71 0.00 0.00 2.92
583 672 3.317430 GGGATTGCAAAGTCAGATGATCC 59.683 47.826 1.71 1.07 0.00 3.36
584 673 3.949754 GGATTGCAAAGTCAGATGATCCA 59.050 43.478 1.71 0.00 0.00 3.41
586 675 2.349590 TGCAAAGTCAGATGATCCACG 58.650 47.619 0.00 0.00 0.00 4.94
587 676 1.063174 GCAAAGTCAGATGATCCACGC 59.937 52.381 0.00 0.00 0.00 5.34
588 677 1.667724 CAAAGTCAGATGATCCACGCC 59.332 52.381 0.00 0.00 0.00 5.68
589 678 0.179000 AAGTCAGATGATCCACGCCC 59.821 55.000 0.00 0.00 0.00 6.13
602 691 4.148825 CGCCCCTCCACTTCTCCG 62.149 72.222 0.00 0.00 0.00 4.63
619 708 1.684983 TCCGGTGGTATCGAGATTTCC 59.315 52.381 0.00 0.00 0.00 3.13
622 711 3.123804 CGGTGGTATCGAGATTTCCTTG 58.876 50.000 0.00 0.00 0.00 3.61
624 713 4.372656 GGTGGTATCGAGATTTCCTTGAG 58.627 47.826 0.00 0.00 38.63 3.02
626 715 5.395324 GGTGGTATCGAGATTTCCTTGAGAA 60.395 44.000 0.00 0.00 38.63 2.87
627 716 5.520649 GTGGTATCGAGATTTCCTTGAGAAC 59.479 44.000 0.00 0.00 38.63 3.01
628 717 4.740695 GGTATCGAGATTTCCTTGAGAACG 59.259 45.833 0.00 0.00 38.63 3.95
629 718 3.232213 TCGAGATTTCCTTGAGAACGG 57.768 47.619 0.00 0.00 32.95 4.44
680 769 5.300752 CCAGATACGAGATTGCAACCTTAT 58.699 41.667 0.00 0.00 0.00 1.73
681 770 5.760253 CCAGATACGAGATTGCAACCTTATT 59.240 40.000 0.00 0.00 0.00 1.40
682 771 6.929049 CCAGATACGAGATTGCAACCTTATTA 59.071 38.462 0.00 0.00 0.00 0.98
684 773 6.929606 AGATACGAGATTGCAACCTTATTACC 59.070 38.462 0.00 0.00 0.00 2.85
709 798 2.371910 AAGAACTTGAGCTAGGCGTC 57.628 50.000 0.00 0.00 0.00 5.19
710 799 1.551452 AGAACTTGAGCTAGGCGTCT 58.449 50.000 0.00 0.00 0.00 4.18
711 800 1.474879 AGAACTTGAGCTAGGCGTCTC 59.525 52.381 0.00 0.00 0.00 3.36
712 801 0.171455 AACTTGAGCTAGGCGTCTCG 59.829 55.000 0.00 0.00 32.20 4.04
713 802 0.961358 ACTTGAGCTAGGCGTCTCGT 60.961 55.000 0.00 0.00 32.20 4.18
714 803 0.248296 CTTGAGCTAGGCGTCTCGTC 60.248 60.000 0.00 0.00 32.20 4.20
724 813 1.058404 GCGTCTCGTCTGGTACAAAC 58.942 55.000 0.00 0.00 38.70 2.93
961 1057 6.318900 CACCCCCACTTAATTCAGAAATCTAC 59.681 42.308 0.00 0.00 0.00 2.59
964 1060 5.527582 CCCACTTAATTCAGAAATCTACCGG 59.472 44.000 0.00 0.00 0.00 5.28
985 1081 0.891373 TCCTCTGTTTCCTCTGCTCG 59.109 55.000 0.00 0.00 0.00 5.03
1044 1155 2.356313 ACTCGCCGCACACAAGAG 60.356 61.111 0.00 0.00 35.28 2.85
1087 1201 3.551454 GCAGAACAAATCAAGCAAGCTCA 60.551 43.478 0.00 0.00 33.18 4.26
1088 1202 4.613944 CAGAACAAATCAAGCAAGCTCAA 58.386 39.130 0.00 0.00 0.00 3.02
1089 1203 4.680110 CAGAACAAATCAAGCAAGCTCAAG 59.320 41.667 0.00 0.00 0.00 3.02
1118 1258 4.212214 ACTCGTTTCTTGCTCAGTTCATTC 59.788 41.667 0.00 0.00 0.00 2.67
1119 1259 3.498397 TCGTTTCTTGCTCAGTTCATTCC 59.502 43.478 0.00 0.00 0.00 3.01
1120 1260 3.250762 CGTTTCTTGCTCAGTTCATTCCA 59.749 43.478 0.00 0.00 0.00 3.53
1121 1261 4.612259 CGTTTCTTGCTCAGTTCATTCCAG 60.612 45.833 0.00 0.00 0.00 3.86
1122 1262 3.777106 TCTTGCTCAGTTCATTCCAGT 57.223 42.857 0.00 0.00 0.00 4.00
1123 1263 3.668447 TCTTGCTCAGTTCATTCCAGTC 58.332 45.455 0.00 0.00 0.00 3.51
1124 1264 2.479566 TGCTCAGTTCATTCCAGTCC 57.520 50.000 0.00 0.00 0.00 3.85
1125 1265 1.699083 TGCTCAGTTCATTCCAGTCCA 59.301 47.619 0.00 0.00 0.00 4.02
1126 1266 2.289882 TGCTCAGTTCATTCCAGTCCAG 60.290 50.000 0.00 0.00 0.00 3.86
1127 1267 2.289945 GCTCAGTTCATTCCAGTCCAGT 60.290 50.000 0.00 0.00 0.00 4.00
1128 1268 3.332919 CTCAGTTCATTCCAGTCCAGTG 58.667 50.000 0.00 0.00 0.00 3.66
1129 1269 1.808945 CAGTTCATTCCAGTCCAGTGC 59.191 52.381 0.00 0.00 0.00 4.40
1130 1270 1.701847 AGTTCATTCCAGTCCAGTGCT 59.298 47.619 0.00 0.00 0.00 4.40
1131 1271 1.808945 GTTCATTCCAGTCCAGTGCTG 59.191 52.381 0.00 0.00 0.00 4.41
1132 1272 1.059098 TCATTCCAGTCCAGTGCTGT 58.941 50.000 0.00 0.00 32.41 4.40
1133 1273 1.421268 TCATTCCAGTCCAGTGCTGTT 59.579 47.619 0.00 0.00 32.41 3.16
1134 1274 1.808945 CATTCCAGTCCAGTGCTGTTC 59.191 52.381 0.00 0.00 32.41 3.18
1135 1275 0.836606 TTCCAGTCCAGTGCTGTTCA 59.163 50.000 0.00 0.00 32.41 3.18
1136 1276 0.394192 TCCAGTCCAGTGCTGTTCAG 59.606 55.000 0.00 0.00 32.41 3.02
1137 1277 0.107456 CCAGTCCAGTGCTGTTCAGT 59.893 55.000 1.78 0.00 32.41 3.41
1138 1278 1.344438 CCAGTCCAGTGCTGTTCAGTA 59.656 52.381 1.78 0.00 32.41 2.74
1139 1279 2.224281 CCAGTCCAGTGCTGTTCAGTAA 60.224 50.000 1.78 0.00 32.41 2.24
1140 1280 3.557898 CCAGTCCAGTGCTGTTCAGTAAT 60.558 47.826 1.78 0.00 32.41 1.89
1141 1281 3.434641 CAGTCCAGTGCTGTTCAGTAATG 59.565 47.826 10.38 10.38 0.00 1.90
1142 1282 3.324846 AGTCCAGTGCTGTTCAGTAATGA 59.675 43.478 16.87 0.00 0.00 2.57
1143 1283 3.681897 GTCCAGTGCTGTTCAGTAATGAG 59.318 47.826 16.87 9.15 0.00 2.90
1144 1284 2.417933 CCAGTGCTGTTCAGTAATGAGC 59.582 50.000 16.87 0.00 0.00 4.26
1145 1285 3.069289 CAGTGCTGTTCAGTAATGAGCA 58.931 45.455 9.38 9.38 37.33 4.26
1146 1286 3.124806 CAGTGCTGTTCAGTAATGAGCAG 59.875 47.826 26.51 26.51 45.77 4.24
1150 1290 2.079158 TGTTCAGTAATGAGCAGCTGC 58.921 47.619 31.53 31.53 42.49 5.25
1457 1597 3.628646 ATGGTTCTGCTGGACCCGC 62.629 63.158 17.83 0.04 28.00 6.13
2367 2521 6.799926 ATGTGTGCATATAACGCATCAATA 57.200 33.333 9.77 0.10 43.45 1.90
2377 2531 1.276844 GCATCAATACGCGTCTGCC 59.723 57.895 18.63 3.06 38.08 4.85
2471 2626 4.154737 TCCAGAAAGATCGTTGCAATGAAG 59.845 41.667 24.39 6.64 0.00 3.02
2493 2648 4.514441 AGAAAGCTCAATGATAAGATGCCG 59.486 41.667 0.00 0.00 0.00 5.69
2620 2775 1.271543 TGTTCAGCTGGGACATTGAGG 60.272 52.381 15.13 0.00 38.20 3.86
2649 3181 4.725556 TCTAGAACATGTCGTTGCAAAC 57.274 40.909 0.00 0.00 45.31 2.93
2689 3224 2.141517 CTGTGCTGGACAAGACAAGAG 58.858 52.381 3.02 0.00 32.80 2.85
2824 3359 0.252421 TCTCACTCCAGATGTGGCCT 60.252 55.000 3.32 0.00 44.60 5.19
2856 3391 4.122515 GTTCGTGCTCGCGCTGAC 62.123 66.667 5.56 0.00 36.97 3.51
2867 3402 2.432628 CGCTGACCCGTGACTTCC 60.433 66.667 0.00 0.00 0.00 3.46
2919 3454 1.516386 CGTTCATGCCGCGTACTCT 60.516 57.895 4.92 0.00 0.00 3.24
2929 3464 2.664698 GCCGCGTACTCTTTTTCTTTGG 60.665 50.000 4.92 0.00 0.00 3.28
3046 3583 0.530744 CCTACGGCTACAAGCACTGA 59.469 55.000 0.78 0.00 44.75 3.41
3049 3586 1.226746 ACGGCTACAAGCACTGAAAC 58.773 50.000 0.78 0.00 44.75 2.78
3057 3594 2.111756 CAAGCACTGAAACGAGCAAAC 58.888 47.619 0.00 0.00 0.00 2.93
3061 3598 1.326245 CACTGAAACGAGCAAACGACA 59.674 47.619 5.12 2.59 37.03 4.35
3075 3612 3.961480 AACGACATGTCTTCCTCATCA 57.039 42.857 22.95 0.00 0.00 3.07
3085 3622 2.313041 TCTTCCTCATCACCCTCTCTCA 59.687 50.000 0.00 0.00 0.00 3.27
3088 3625 1.612950 CCTCATCACCCTCTCTCATCG 59.387 57.143 0.00 0.00 0.00 3.84
3089 3626 1.612950 CTCATCACCCTCTCTCATCGG 59.387 57.143 0.00 0.00 0.00 4.18
3094 3631 2.560119 CCCTCTCTCATCGGAGCCG 61.560 68.421 1.74 1.74 41.13 5.52
3107 3644 0.611714 GGAGCCGACCAGACCTTTTA 59.388 55.000 0.00 0.00 0.00 1.52
3113 3650 4.713321 AGCCGACCAGACCTTTTATAGTAA 59.287 41.667 0.00 0.00 0.00 2.24
3116 3653 5.814188 CCGACCAGACCTTTTATAGTAAACC 59.186 44.000 0.00 0.00 0.00 3.27
3125 3662 8.021955 ACCTTTTATAGTAAACCGTCGAAAAG 57.978 34.615 0.00 0.00 34.14 2.27
3139 3676 4.141680 GTCGAAAAGTTGTCGTGCTAATG 58.858 43.478 14.92 0.00 39.52 1.90
3147 3684 2.710377 TGTCGTGCTAATGCTCCAAAT 58.290 42.857 0.00 0.00 40.48 2.32
3155 3692 1.927487 AATGCTCCAAATGACCAGCA 58.073 45.000 0.00 0.00 45.65 4.41
3175 3712 4.943705 AGCACACCAGAATAACAACCATAG 59.056 41.667 0.00 0.00 0.00 2.23
3178 3715 5.063438 CACACCAGAATAACAACCATAGTCG 59.937 44.000 0.00 0.00 0.00 4.18
3194 3731 5.335269 CCATAGTCGATGAAGAGAAGCGTAT 60.335 44.000 0.00 0.00 37.82 3.06
3199 3736 3.664486 CGATGAAGAGAAGCGTATAACGG 59.336 47.826 1.25 0.00 42.82 4.44
3202 3739 4.669318 TGAAGAGAAGCGTATAACGGAAG 58.331 43.478 1.25 0.00 42.82 3.46
3207 3744 4.618965 AGAAGCGTATAACGGAAGGATTC 58.381 43.478 1.25 0.00 46.67 2.52
3234 3771 2.440539 AGACACATGAACGGAGACAC 57.559 50.000 0.00 0.00 0.00 3.67
3235 3772 1.060713 GACACATGAACGGAGACACG 58.939 55.000 0.00 0.00 40.31 4.49
3244 3781 1.154908 CGGAGACACGCGAAAAACG 60.155 57.895 15.93 6.27 45.66 3.60
3274 3811 2.767505 AGATCCACCGAAGACAAACAC 58.232 47.619 0.00 0.00 0.00 3.32
3281 3818 0.595567 CGAAGACAAACACCGACCGA 60.596 55.000 0.00 0.00 0.00 4.69
3286 3823 0.395312 ACAAACACCGACCGAATCCT 59.605 50.000 0.00 0.00 0.00 3.24
3288 3825 0.953960 AAACACCGACCGAATCCTGC 60.954 55.000 0.00 0.00 0.00 4.85
3295 3832 0.671251 GACCGAATCCTGCGAGATCT 59.329 55.000 0.00 0.00 0.00 2.75
3297 3834 0.943359 CCGAATCCTGCGAGATCTGC 60.943 60.000 0.00 5.01 0.00 4.26
3299 3836 0.943359 GAATCCTGCGAGATCTGCCG 60.943 60.000 0.00 0.00 0.00 5.69
3329 3866 1.681793 CTCCATACACCTTCCGACGAT 59.318 52.381 0.00 0.00 0.00 3.73
3361 3898 2.105128 CGAGACAAGGGCTAGGCG 59.895 66.667 10.58 0.00 0.00 5.52
3383 3920 6.406961 GGCGGGGAGAATTTTATTTCATCTTT 60.407 38.462 0.00 0.00 0.00 2.52
3396 3933 8.937634 TTATTTCATCTTTAAGGAGTCGTACC 57.062 34.615 0.00 0.00 0.00 3.34
3410 3947 2.178235 GTACCCGCCTCGCATTTCC 61.178 63.158 0.00 0.00 0.00 3.13
3411 3948 3.726595 TACCCGCCTCGCATTTCCG 62.727 63.158 0.00 0.00 0.00 4.30
3417 3954 3.403277 CTCGCATTTCCGAGCAGG 58.597 61.111 0.00 0.00 46.69 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.799519 GTCGTCACGAGAGCTGCAG 60.800 63.158 10.11 10.11 36.23 4.41
1 2 2.255554 GTCGTCACGAGAGCTGCA 59.744 61.111 0.00 0.00 36.23 4.41
22 23 1.724929 GCATCGATCCCGTACGTCG 60.725 63.158 17.61 17.61 37.05 5.12
23 24 1.371389 GGCATCGATCCCGTACGTC 60.371 63.158 15.21 4.35 37.05 4.34
24 25 2.726274 GGCATCGATCCCGTACGT 59.274 61.111 15.21 0.00 37.05 3.57
25 26 2.428569 CGGCATCGATCCCGTACG 60.429 66.667 19.87 8.69 39.67 3.67
26 27 2.049433 CCGGCATCGATCCCGTAC 60.049 66.667 25.39 0.00 42.87 3.67
27 28 3.986006 GCCGGCATCGATCCCGTA 61.986 66.667 25.39 0.00 42.87 4.02
88 89 2.125673 CGATTGGGTCTCGCCGTT 60.126 61.111 0.00 0.00 38.44 4.44
89 90 2.939261 AACGATTGGGTCTCGCCGT 61.939 57.895 0.00 0.00 39.71 5.68
100 101 4.872691 AGAGAAATAGCACTCCAACGATTG 59.127 41.667 0.00 0.00 34.13 2.67
106 128 7.093068 TGGTGTTATAGAGAAATAGCACTCCAA 60.093 37.037 9.64 0.00 41.01 3.53
113 135 5.470437 GGCCTTGGTGTTATAGAGAAATAGC 59.530 44.000 0.00 0.00 0.00 2.97
121 143 1.406341 GCGTGGCCTTGGTGTTATAGA 60.406 52.381 3.32 0.00 0.00 1.98
122 144 1.014352 GCGTGGCCTTGGTGTTATAG 58.986 55.000 3.32 0.00 0.00 1.31
124 146 2.038269 CGCGTGGCCTTGGTGTTAT 61.038 57.895 3.32 0.00 0.00 1.89
125 147 2.666862 CGCGTGGCCTTGGTGTTA 60.667 61.111 3.32 0.00 0.00 2.41
126 148 4.868116 ACGCGTGGCCTTGGTGTT 62.868 61.111 12.93 0.00 0.00 3.32
179 206 1.179174 TGCGGTCCGGATGAGATAGG 61.179 60.000 14.38 0.00 0.00 2.57
259 328 2.039084 GTCAGCCTTCTTCTTCCCTTCA 59.961 50.000 0.00 0.00 0.00 3.02
263 332 1.404851 CGAGTCAGCCTTCTTCTTCCC 60.405 57.143 0.00 0.00 0.00 3.97
264 333 1.404851 CCGAGTCAGCCTTCTTCTTCC 60.405 57.143 0.00 0.00 0.00 3.46
305 388 1.529152 TTGTCGGCTTCGTCCTGCTA 61.529 55.000 0.00 0.00 35.06 3.49
352 435 3.056891 CACCGGTGCATGATTACCTTTTT 60.057 43.478 24.02 0.00 34.77 1.94
353 436 2.491693 CACCGGTGCATGATTACCTTTT 59.508 45.455 24.02 0.00 34.77 2.27
354 437 2.091541 CACCGGTGCATGATTACCTTT 58.908 47.619 24.02 0.00 34.77 3.11
355 438 1.750193 CACCGGTGCATGATTACCTT 58.250 50.000 24.02 0.00 34.77 3.50
356 439 3.476740 CACCGGTGCATGATTACCT 57.523 52.632 24.02 0.00 34.77 3.08
367 450 1.336440 TGAAAAATCAGTGCACCGGTG 59.664 47.619 30.66 30.66 0.00 4.94
368 451 1.608590 CTGAAAAATCAGTGCACCGGT 59.391 47.619 14.63 0.00 33.32 5.28
369 452 1.068333 CCTGAAAAATCAGTGCACCGG 60.068 52.381 14.63 6.49 36.06 5.28
370 453 1.666888 GCCTGAAAAATCAGTGCACCG 60.667 52.381 14.63 2.63 36.06 4.94
371 454 1.337167 GGCCTGAAAAATCAGTGCACC 60.337 52.381 14.63 0.00 36.40 5.01
372 455 1.340889 TGGCCTGAAAAATCAGTGCAC 59.659 47.619 9.40 9.40 36.40 4.57
373 456 1.702182 TGGCCTGAAAAATCAGTGCA 58.298 45.000 3.32 0.00 36.40 4.57
374 457 2.407090 GTTGGCCTGAAAAATCAGTGC 58.593 47.619 3.32 7.63 36.06 4.40
375 458 2.034558 ACGTTGGCCTGAAAAATCAGTG 59.965 45.455 3.32 0.00 36.06 3.66
376 459 2.034558 CACGTTGGCCTGAAAAATCAGT 59.965 45.455 3.32 0.00 36.06 3.41
377 460 2.607771 CCACGTTGGCCTGAAAAATCAG 60.608 50.000 3.32 0.00 37.48 2.90
378 461 1.339610 CCACGTTGGCCTGAAAAATCA 59.660 47.619 3.32 0.00 0.00 2.57
379 462 1.336795 CCCACGTTGGCCTGAAAAATC 60.337 52.381 3.32 0.00 35.79 2.17
380 463 0.678950 CCCACGTTGGCCTGAAAAAT 59.321 50.000 3.32 0.00 35.79 1.82
436 520 1.068885 GCTCGTCTACGGATGGATCTG 60.069 57.143 2.24 0.00 40.29 2.90
471 555 0.865769 GCGTCTCCTGCGAAAAGAAA 59.134 50.000 0.00 0.00 0.00 2.52
472 556 0.949105 GGCGTCTCCTGCGAAAAGAA 60.949 55.000 0.00 0.00 0.00 2.52
474 563 1.227999 TTGGCGTCTCCTGCGAAAAG 61.228 55.000 0.00 0.00 35.26 2.27
481 570 0.609131 AACCCAATTGGCGTCTCCTG 60.609 55.000 19.75 5.28 37.83 3.86
498 587 7.014326 AGGAGTAGGGTGAAGAAAATTTCAAAC 59.986 37.037 8.55 3.16 38.69 2.93
503 592 6.200878 TCAGGAGTAGGGTGAAGAAAATTT 57.799 37.500 0.00 0.00 0.00 1.82
516 605 4.187694 GAGTGCTGATTTTCAGGAGTAGG 58.812 47.826 6.38 0.00 46.42 3.18
548 637 0.825010 CAATCCCTGCCATACCCTGC 60.825 60.000 0.00 0.00 0.00 4.85
550 639 1.538666 GCAATCCCTGCCATACCCT 59.461 57.895 0.00 0.00 46.13 4.34
560 649 3.726557 TCATCTGACTTTGCAATCCCT 57.273 42.857 0.00 0.00 0.00 4.20
561 650 3.317430 GGATCATCTGACTTTGCAATCCC 59.683 47.826 0.00 0.00 0.00 3.85
562 651 3.949754 TGGATCATCTGACTTTGCAATCC 59.050 43.478 0.00 0.19 33.56 3.01
564 653 3.376234 CGTGGATCATCTGACTTTGCAAT 59.624 43.478 0.00 0.00 0.00 3.56
565 654 2.743664 CGTGGATCATCTGACTTTGCAA 59.256 45.455 0.00 0.00 0.00 4.08
566 655 2.349590 CGTGGATCATCTGACTTTGCA 58.650 47.619 0.00 0.00 0.00 4.08
567 656 1.063174 GCGTGGATCATCTGACTTTGC 59.937 52.381 0.00 0.00 0.00 3.68
570 659 0.179000 GGGCGTGGATCATCTGACTT 59.821 55.000 0.00 0.00 0.00 3.01
571 660 1.690219 GGGGCGTGGATCATCTGACT 61.690 60.000 0.00 0.00 0.00 3.41
573 662 1.383109 AGGGGCGTGGATCATCTGA 60.383 57.895 0.00 0.00 0.00 3.27
574 663 1.070445 GAGGGGCGTGGATCATCTG 59.930 63.158 0.00 0.00 0.00 2.90
575 664 2.143419 GGAGGGGCGTGGATCATCT 61.143 63.158 0.00 0.00 0.00 2.90
577 666 2.366837 TGGAGGGGCGTGGATCAT 60.367 61.111 0.00 0.00 0.00 2.45
579 668 2.595009 GAAGTGGAGGGGCGTGGATC 62.595 65.000 0.00 0.00 0.00 3.36
580 669 2.610859 AAGTGGAGGGGCGTGGAT 60.611 61.111 0.00 0.00 0.00 3.41
581 670 3.319198 GAAGTGGAGGGGCGTGGA 61.319 66.667 0.00 0.00 0.00 4.02
582 671 3.316573 GAGAAGTGGAGGGGCGTGG 62.317 68.421 0.00 0.00 0.00 4.94
583 672 2.266055 GAGAAGTGGAGGGGCGTG 59.734 66.667 0.00 0.00 0.00 5.34
584 673 3.003763 GGAGAAGTGGAGGGGCGT 61.004 66.667 0.00 0.00 0.00 5.68
586 675 3.787001 CCGGAGAAGTGGAGGGGC 61.787 72.222 0.00 0.00 0.00 5.80
587 676 2.284699 ACCGGAGAAGTGGAGGGG 60.285 66.667 9.46 0.00 0.00 4.79
588 677 2.982130 CACCGGAGAAGTGGAGGG 59.018 66.667 9.46 0.00 0.00 4.30
602 691 4.099573 TCTCAAGGAAATCTCGATACCACC 59.900 45.833 0.00 0.00 0.00 4.61
619 708 1.335324 CCAAGCAAAGCCGTTCTCAAG 60.335 52.381 0.00 0.00 0.00 3.02
622 711 0.889186 TCCCAAGCAAAGCCGTTCTC 60.889 55.000 0.00 0.00 0.00 2.87
624 713 0.039165 CTTCCCAAGCAAAGCCGTTC 60.039 55.000 0.00 0.00 0.00 3.95
626 715 1.150536 TCTTCCCAAGCAAAGCCGT 59.849 52.632 0.00 0.00 0.00 5.68
627 716 1.581447 GTCTTCCCAAGCAAAGCCG 59.419 57.895 0.00 0.00 0.00 5.52
628 717 1.581447 CGTCTTCCCAAGCAAAGCC 59.419 57.895 0.00 0.00 0.00 4.35
629 718 1.081175 GCGTCTTCCCAAGCAAAGC 60.081 57.895 0.00 0.00 0.00 3.51
694 783 0.961358 ACGAGACGCCTAGCTCAAGT 60.961 55.000 0.00 0.00 0.00 3.16
698 787 1.353804 CAGACGAGACGCCTAGCTC 59.646 63.158 0.00 0.00 0.00 4.09
699 788 2.115911 CCAGACGAGACGCCTAGCT 61.116 63.158 0.00 0.00 0.00 3.32
709 798 3.927142 GGATCTTGTTTGTACCAGACGAG 59.073 47.826 0.00 0.00 33.06 4.18
710 799 3.322541 TGGATCTTGTTTGTACCAGACGA 59.677 43.478 0.00 0.00 29.74 4.20
711 800 3.659786 TGGATCTTGTTTGTACCAGACG 58.340 45.455 0.00 0.00 29.74 4.18
712 801 4.003648 CCTGGATCTTGTTTGTACCAGAC 58.996 47.826 0.00 0.00 45.02 3.51
713 802 3.907474 TCCTGGATCTTGTTTGTACCAGA 59.093 43.478 0.00 0.00 45.02 3.86
714 803 4.256920 CTCCTGGATCTTGTTTGTACCAG 58.743 47.826 0.00 0.00 42.82 4.00
854 945 2.236146 TCTTCCAGATCTTTTAGCGGCA 59.764 45.455 1.45 0.00 0.00 5.69
961 1057 0.977395 AGAGGAAACAGAGGAACCGG 59.023 55.000 0.00 0.00 0.00 5.28
964 1060 2.694213 GAGCAGAGGAAACAGAGGAAC 58.306 52.381 0.00 0.00 0.00 3.62
1087 1201 2.139118 GCAAGAAACGAGTGAGAGCTT 58.861 47.619 0.00 0.00 0.00 3.74
1088 1202 1.342819 AGCAAGAAACGAGTGAGAGCT 59.657 47.619 0.00 0.00 0.00 4.09
1089 1203 1.724082 GAGCAAGAAACGAGTGAGAGC 59.276 52.381 0.00 0.00 0.00 4.09
1118 1258 0.107456 ACTGAACAGCACTGGACTGG 59.893 55.000 2.21 0.00 39.55 4.00
1119 1259 2.820059 TACTGAACAGCACTGGACTG 57.180 50.000 2.21 2.87 41.08 3.51
1120 1260 3.324846 TCATTACTGAACAGCACTGGACT 59.675 43.478 2.21 0.00 34.19 3.85
1121 1261 3.664107 TCATTACTGAACAGCACTGGAC 58.336 45.455 2.21 0.00 34.19 4.02
1122 1262 3.866066 GCTCATTACTGAACAGCACTGGA 60.866 47.826 2.21 0.00 34.19 3.86
1123 1263 2.417933 GCTCATTACTGAACAGCACTGG 59.582 50.000 2.21 0.00 34.19 4.00
1124 1264 3.069289 TGCTCATTACTGAACAGCACTG 58.931 45.455 1.46 0.00 28.41 3.66
1125 1265 3.332919 CTGCTCATTACTGAACAGCACT 58.667 45.455 1.10 0.00 38.41 4.40
1126 1266 3.736530 CTGCTCATTACTGAACAGCAC 57.263 47.619 1.10 0.00 38.41 4.40
1129 1269 2.095532 GCAGCTGCTCATTACTGAACAG 59.904 50.000 31.33 8.67 44.77 3.16
1130 1270 2.079158 GCAGCTGCTCATTACTGAACA 58.921 47.619 31.33 0.00 38.21 3.18
1131 1271 2.821307 GCAGCTGCTCATTACTGAAC 57.179 50.000 31.33 0.00 38.21 3.18
1144 1284 4.748679 GACGCCGCAAAGCAGCTG 62.749 66.667 10.11 10.11 28.67 4.24
1146 1286 4.748679 CTGACGCCGCAAAGCAGC 62.749 66.667 0.00 0.00 0.00 5.25
1147 1287 4.748679 GCTGACGCCGCAAAGCAG 62.749 66.667 1.90 0.00 35.69 4.24
1150 1290 3.490759 ATCGCTGACGCCGCAAAG 61.491 61.111 0.00 0.00 39.84 2.77
1151 1291 3.787676 CATCGCTGACGCCGCAAA 61.788 61.111 0.00 0.00 39.84 3.68
1152 1292 4.733371 TCATCGCTGACGCCGCAA 62.733 61.111 0.00 0.00 39.84 4.85
1174 1314 1.299648 CGGCAACCCTGGAATCAGA 59.700 57.895 0.00 0.00 43.49 3.27
1333 1473 3.610619 CTGGACCATGGCGAGCACA 62.611 63.158 13.04 1.05 0.00 4.57
1420 1560 1.740296 CCTGTAGTTGTTCGCGGGG 60.740 63.158 6.13 0.00 0.00 5.73
2254 2400 3.958147 CTGCACGTGCCCGGAGAAT 62.958 63.158 35.72 0.00 41.18 2.40
2471 2626 4.320057 CCGGCATCTTATCATTGAGCTTTC 60.320 45.833 0.00 0.00 0.00 2.62
2493 2648 4.441087 GCAGACAAAATCGAAAACAGAACC 59.559 41.667 0.00 0.00 0.00 3.62
2620 2775 3.130693 ACGACATGTTCTAGAAGGCCTAC 59.869 47.826 5.16 0.00 0.00 3.18
2649 3181 3.121030 CAAAGCAGACCGCCTCCG 61.121 66.667 0.00 0.00 44.04 4.63
2689 3224 3.809905 ACACTTCACTCTCCAAAAGGAC 58.190 45.455 0.00 0.00 0.00 3.85
2824 3359 0.382515 CGAACCCAAAACCGAGCAAA 59.617 50.000 0.00 0.00 0.00 3.68
2856 3391 3.277211 TTCTCGCGGAAGTCACGGG 62.277 63.158 6.13 0.00 44.34 5.28
2867 3402 3.361053 GGTCGTATATGATTGTTCTCGCG 59.639 47.826 0.00 0.00 0.00 5.87
2910 3445 4.461992 TTCCAAAGAAAAAGAGTACGCG 57.538 40.909 3.53 3.53 0.00 6.01
3002 3539 7.197017 GCGGTCTACCAACATAGATATAGATG 58.803 42.308 0.00 0.00 33.78 2.90
3033 3570 1.136224 GCTCGTTTCAGTGCTTGTAGC 60.136 52.381 0.00 0.00 42.82 3.58
3046 3583 2.210116 AGACATGTCGTTTGCTCGTTT 58.790 42.857 19.85 0.00 34.09 3.60
3049 3586 1.126846 GGAAGACATGTCGTTTGCTCG 59.873 52.381 19.85 0.00 34.09 5.03
3057 3594 2.544685 GGTGATGAGGAAGACATGTCG 58.455 52.381 19.85 0.00 34.09 4.35
3061 3598 3.037549 GAGAGGGTGATGAGGAAGACAT 58.962 50.000 0.00 0.00 0.00 3.06
3075 3612 1.456705 GGCTCCGATGAGAGAGGGT 60.457 63.158 0.00 0.00 41.42 4.34
3088 3625 0.611714 TAAAAGGTCTGGTCGGCTCC 59.388 55.000 0.00 0.00 0.00 4.70
3089 3626 2.693267 ATAAAAGGTCTGGTCGGCTC 57.307 50.000 0.00 0.00 0.00 4.70
3094 3631 6.401394 ACGGTTTACTATAAAAGGTCTGGTC 58.599 40.000 0.00 0.00 0.00 4.02
3095 3632 6.364568 ACGGTTTACTATAAAAGGTCTGGT 57.635 37.500 0.00 0.00 0.00 4.00
3096 3633 5.517770 CGACGGTTTACTATAAAAGGTCTGG 59.482 44.000 0.00 0.00 0.00 3.86
3099 3636 7.581011 TTTCGACGGTTTACTATAAAAGGTC 57.419 36.000 0.00 0.00 0.00 3.85
3101 3638 8.021955 ACTTTTCGACGGTTTACTATAAAAGG 57.978 34.615 13.62 0.46 37.13 3.11
3107 3644 5.117592 CGACAACTTTTCGACGGTTTACTAT 59.882 40.000 0.00 0.00 38.85 2.12
3113 3650 1.325338 CACGACAACTTTTCGACGGTT 59.675 47.619 4.37 0.00 39.83 4.44
3116 3653 0.575390 AGCACGACAACTTTTCGACG 59.425 50.000 4.37 0.00 39.83 5.12
3125 3662 1.438651 TGGAGCATTAGCACGACAAC 58.561 50.000 0.00 0.00 45.49 3.32
3139 3676 0.242017 GTGTGCTGGTCATTTGGAGC 59.758 55.000 0.00 0.00 44.35 4.70
3147 3684 2.105649 TGTTATTCTGGTGTGCTGGTCA 59.894 45.455 0.00 0.00 0.00 4.02
3155 3692 5.046878 TCGACTATGGTTGTTATTCTGGTGT 60.047 40.000 0.00 0.00 0.00 4.16
3175 3712 4.376279 CGTTATACGCTTCTCTTCATCGAC 59.624 45.833 0.00 0.00 33.65 4.20
3178 3715 4.856664 TCCGTTATACGCTTCTCTTCATC 58.143 43.478 0.00 0.00 40.91 2.92
3194 3731 6.103997 GTCTACATGTTGAATCCTTCCGTTA 58.896 40.000 11.64 0.00 0.00 3.18
3199 3736 6.992063 ATGTGTCTACATGTTGAATCCTTC 57.008 37.500 11.64 0.00 45.54 3.46
3227 3764 1.203313 CCGTTTTTCGCGTGTCTCC 59.797 57.895 5.77 0.00 38.35 3.71
3234 3771 0.515564 ACTTGGATCCGTTTTTCGCG 59.484 50.000 7.39 0.00 38.35 5.87
3235 3772 2.997986 TCTACTTGGATCCGTTTTTCGC 59.002 45.455 7.39 0.00 38.35 4.70
3263 3800 1.574134 TTCGGTCGGTGTTTGTCTTC 58.426 50.000 0.00 0.00 0.00 2.87
3274 3811 2.076622 ATCTCGCAGGATTCGGTCGG 62.077 60.000 0.00 0.00 0.00 4.79
3281 3818 1.068753 CGGCAGATCTCGCAGGATT 59.931 57.895 15.83 0.00 0.00 3.01
3286 3823 2.440247 TCTCCGGCAGATCTCGCA 60.440 61.111 15.83 0.00 0.00 5.10
3288 3825 1.064946 GTGTCTCCGGCAGATCTCG 59.935 63.158 0.00 0.00 32.08 4.04
3295 3832 3.311110 GGAGGTGTGTCTCCGGCA 61.311 66.667 0.00 0.00 43.19 5.69
3316 3853 0.738975 TCTAGCATCGTCGGAAGGTG 59.261 55.000 0.00 0.00 0.00 4.00
3344 3881 2.105128 CGCCTAGCCCTTGTCTCG 59.895 66.667 0.00 0.00 0.00 4.04
3395 3932 4.830765 TCGGAAATGCGAGGCGGG 62.831 66.667 0.00 0.00 0.00 6.13
3396 3933 3.264897 CTCGGAAATGCGAGGCGG 61.265 66.667 15.44 0.00 0.00 6.13
3405 3942 1.880027 GTTTGTGTCCTGCTCGGAAAT 59.120 47.619 0.00 0.00 45.32 2.17


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

AutoCloner maintained by Alex Coulton.