Multiple sequence alignment - TraesCS1D01G178500

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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 TraesCS1D01G178500 chr1D 100.000 6084 0 0 1 6084 253222708 253216625 0.000000e+00 11236.0
1 TraesCS1D01G178500 chr1D 95.152 165 8 0 499 663 494168465 494168629 1.680000e-65 261.0
2 TraesCS1D01G178500 chr1D 94.578 166 9 0 498 663 229312217 229312052 2.180000e-64 257.0
3 TraesCS1D01G178500 chr1D 84.536 97 12 3 416 510 480634872 480634777 6.490000e-15 93.5
4 TraesCS1D01G178500 chr1B 95.260 2890 91 19 727 3592 359193702 359196569 0.000000e+00 4536.0
5 TraesCS1D01G178500 chr1B 96.409 1782 48 9 3589 5357 359196600 359198378 0.000000e+00 2922.0
6 TraesCS1D01G178500 chr1B 86.617 269 27 6 238 504 359168780 359169041 7.720000e-74 289.0
7 TraesCS1D01G178500 chr1A 94.861 2705 100 18 752 3447 325054570 325051896 0.000000e+00 4189.0
8 TraesCS1D01G178500 chr1A 96.618 1774 46 9 3589 5357 325051559 325049795 0.000000e+00 2931.0
9 TraesCS1D01G178500 chr1A 83.901 764 88 26 1 750 325056634 325055892 0.000000e+00 697.0
10 TraesCS1D01G178500 chr1A 81.835 556 75 21 204 750 325055583 325055045 1.560000e-120 444.0
11 TraesCS1D01G178500 chr1A 98.000 150 3 0 3443 3592 325051739 325051590 1.680000e-65 261.0
12 TraesCS1D01G178500 chr3A 89.542 698 45 12 5379 6075 36946287 36946957 0.000000e+00 859.0
13 TraesCS1D01G178500 chr3A 90.435 575 46 3 5396 5969 37243058 37243624 0.000000e+00 749.0
14 TraesCS1D01G178500 chr5D 90.631 491 21 8 5398 5887 302375962 302376428 4.000000e-176 628.0
15 TraesCS1D01G178500 chr3B 85.472 413 41 12 5397 5802 4300508 4300108 4.390000e-111 412.0
16 TraesCS1D01G178500 chr3B 93.491 169 11 0 498 666 697908142 697907974 1.010000e-62 252.0
17 TraesCS1D01G178500 chr6B 87.749 351 35 2 5452 5802 599764727 599764385 2.640000e-108 403.0
18 TraesCS1D01G178500 chr6B 94.872 39 0 2 299 337 653009195 653009159 6.590000e-05 60.2
19 TraesCS1D01G178500 chr5A 83.478 345 48 4 5397 5740 666324236 666324572 4.580000e-81 313.0
20 TraesCS1D01G178500 chr5A 94.872 39 0 2 299 337 546102111 546102075 6.590000e-05 60.2
21 TraesCS1D01G178500 chr7B 82.730 359 52 7 1403 1760 60070187 60069838 1.650000e-80 311.0
22 TraesCS1D01G178500 chr2D 83.478 345 39 7 5397 5740 82668503 82668176 7.660000e-79 305.0
23 TraesCS1D01G178500 chr2D 95.266 169 8 0 496 664 528480869 528481037 1.010000e-67 268.0
24 TraesCS1D01G178500 chr2D 95.181 166 8 0 499 664 582102115 582101950 4.680000e-66 263.0
25 TraesCS1D01G178500 chr2D 87.719 57 7 0 5746 5802 82668314 82668258 3.940000e-07 67.6
26 TraesCS1D01G178500 chr7D 96.951 164 5 0 495 658 404245326 404245489 6.010000e-70 276.0
27 TraesCS1D01G178500 chr7D 94.872 39 1 1 299 337 17389963 17390000 6.590000e-05 60.2
28 TraesCS1D01G178500 chr7D 94.872 39 1 1 299 337 565531864 565531901 6.590000e-05 60.2
29 TraesCS1D01G178500 chr3D 93.443 183 10 2 497 677 333007849 333007667 2.790000e-68 270.0
30 TraesCS1D01G178500 chr3D 93.714 175 10 1 498 672 90138477 90138304 1.680000e-65 261.0
31 TraesCS1D01G178500 chr3D 91.489 47 2 2 299 344 572217356 572217311 5.090000e-06 63.9
32 TraesCS1D01G178500 chrUn 95.152 165 8 0 499 663 108810833 108810997 1.680000e-65 261.0
33 TraesCS1D01G178500 chr7A 92.857 98 7 0 5705 5802 448724545 448724642 6.360000e-30 143.0
34 TraesCS1D01G178500 chr2B 93.056 72 5 0 5731 5802 760108627 760108698 8.340000e-19 106.0
35 TraesCS1D01G178500 chr6D 82.051 78 13 1 417 493 431198086 431198009 1.420000e-06 65.8
36 TraesCS1D01G178500 chr5B 95.238 42 0 2 300 341 496602706 496602667 1.420000e-06 65.8
37 TraesCS1D01G178500 chr4A 92.857 42 3 0 452 493 315165845 315165886 1.830000e-05 62.1


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 TraesCS1D01G178500 chr1D 253216625 253222708 6083 True 11236.0 11236 100.0000 1 6084 1 chr1D.!!$R2 6083
1 TraesCS1D01G178500 chr1B 359193702 359198378 4676 False 3729.0 4536 95.8345 727 5357 2 chr1B.!!$F2 4630
2 TraesCS1D01G178500 chr1A 325049795 325056634 6839 True 1704.4 4189 91.0430 1 5357 5 chr1A.!!$R1 5356
3 TraesCS1D01G178500 chr3A 36946287 36946957 670 False 859.0 859 89.5420 5379 6075 1 chr3A.!!$F1 696
4 TraesCS1D01G178500 chr3A 37243058 37243624 566 False 749.0 749 90.4350 5396 5969 1 chr3A.!!$F2 573

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
833 2160 1.074623 CCTCCCCTCTGCTCCATCT 60.075 63.158 0.0 0.0 0.00 2.90 F
936 2264 1.226018 GTTGATCTTTTCGCGCCCG 60.226 57.895 0.0 0.0 0.00 6.13 F
2741 4077 1.471287 GCCCCTGACGTTTGATAAACC 59.529 52.381 0.0 0.0 38.14 3.27 F
3597 5143 3.550842 GCTTGAACCTGATGTTGAACCAC 60.551 47.826 0.0 0.0 37.29 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2020 3350 0.610174 GACAGCTGGGATGTCAGTGA 59.390 55.000 19.93 0.0 45.18 3.41 R
2763 4099 1.202794 TGCAAATCACTGTCAGGCTCA 60.203 47.619 4.53 0.0 0.00 4.26 R
4031 5580 1.179152 TGGCATGTCTCATTTGCAGG 58.821 50.000 0.00 0.0 38.12 4.85 R
5373 6934 0.107459 GAGACCCATCACCCTTCTGC 60.107 60.000 0.00 0.0 0.00 4.26 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 86 2.128771 TCCCTATTGCAAAGCTGACC 57.871 50.000 1.71 0.00 0.00 4.02
122 125 6.489361 GGTCATCTCCATTGAATCAATAGCTT 59.511 38.462 8.29 0.00 32.35 3.74
125 128 4.274214 TCTCCATTGAATCAATAGCTTGCG 59.726 41.667 8.29 0.00 32.35 4.85
127 130 4.274214 TCCATTGAATCAATAGCTTGCGAG 59.726 41.667 8.29 0.00 32.35 5.03
130 133 1.942657 GAATCAATAGCTTGCGAGGCA 59.057 47.619 2.37 0.00 36.47 4.75
147 153 4.778415 AGCAGCCGACGCGTACAG 62.778 66.667 13.97 6.82 41.18 2.74
167 173 6.759497 ACAGTTGCCCATAGAAATTCTTAC 57.241 37.500 0.00 0.00 0.00 2.34
170 176 6.093495 CAGTTGCCCATAGAAATTCTTACGAA 59.907 38.462 0.00 0.00 0.00 3.85
171 177 6.093633 AGTTGCCCATAGAAATTCTTACGAAC 59.906 38.462 0.00 0.00 30.67 3.95
373 1226 7.888424 AGTTTAGTTCTACTCTCTTTCACCTC 58.112 38.462 0.00 0.00 0.00 3.85
374 1227 7.726738 AGTTTAGTTCTACTCTCTTTCACCTCT 59.273 37.037 0.00 0.00 0.00 3.69
377 1230 6.071984 AGTTCTACTCTCTTTCACCTCTTCA 58.928 40.000 0.00 0.00 0.00 3.02
378 1231 6.723977 AGTTCTACTCTCTTTCACCTCTTCAT 59.276 38.462 0.00 0.00 0.00 2.57
382 1235 8.432805 TCTACTCTCTTTCACCTCTTCATTTTT 58.567 33.333 0.00 0.00 0.00 1.94
481 1334 9.685276 ACATATGGAGTAAAATGAGTGAATTCA 57.315 29.630 3.38 3.38 0.00 2.57
512 1365 5.485209 AATCCATATACTCCCTCCGTTTC 57.515 43.478 0.00 0.00 0.00 2.78
513 1366 3.918566 TCCATATACTCCCTCCGTTTCA 58.081 45.455 0.00 0.00 0.00 2.69
522 1375 8.904099 ATACTCCCTCCGTTTCAAAATATAAG 57.096 34.615 0.00 0.00 0.00 1.73
524 1377 6.822170 ACTCCCTCCGTTTCAAAATATAAGTC 59.178 38.462 0.00 0.00 0.00 3.01
528 1381 7.968405 CCCTCCGTTTCAAAATATAAGTCTTTG 59.032 37.037 0.00 0.00 0.00 2.77
547 1400 9.566432 AGTCTTTGTAGAGATTTCAAATGAACT 57.434 29.630 0.00 0.00 33.13 3.01
557 1410 9.855361 GAGATTTCAAATGAACTATCACATACG 57.145 33.333 9.37 0.00 38.69 3.06
559 1412 8.731275 ATTTCAAATGAACTATCACATACGGA 57.269 30.769 0.00 0.00 38.69 4.69
560 1413 8.731275 TTTCAAATGAACTATCACATACGGAT 57.269 30.769 0.00 0.00 38.69 4.18
561 1414 7.713764 TCAAATGAACTATCACATACGGATG 57.286 36.000 5.94 5.94 38.69 3.51
604 1457 9.384764 AGAGTGTAGATTTACTTATTTTGCTCC 57.615 33.333 0.00 0.00 0.00 4.70
605 1458 8.197988 AGTGTAGATTTACTTATTTTGCTCCG 57.802 34.615 0.00 0.00 0.00 4.63
610 1463 8.732746 AGATTTACTTATTTTGCTCCGTATGT 57.267 30.769 0.00 0.00 0.00 2.29
611 1464 9.826574 AGATTTACTTATTTTGCTCCGTATGTA 57.173 29.630 0.00 0.00 0.00 2.29
613 1466 9.609346 ATTTACTTATTTTGCTCCGTATGTAGT 57.391 29.630 0.00 0.00 0.00 2.73
614 1467 9.439500 TTTACTTATTTTGCTCCGTATGTAGTT 57.561 29.630 0.00 0.00 0.00 2.24
617 1470 9.609346 ACTTATTTTGCTCCGTATGTAGTTATT 57.391 29.630 0.00 0.00 0.00 1.40
623 1476 6.399743 TGCTCCGTATGTAGTTATTTGTTGA 58.600 36.000 0.00 0.00 0.00 3.18
627 1480 9.916397 CTCCGTATGTAGTTATTTGTTGAAATC 57.084 33.333 0.00 0.00 33.63 2.17
629 1482 9.916397 CCGTATGTAGTTATTTGTTGAAATCTC 57.084 33.333 0.00 0.00 33.63 2.75
667 1520 2.108970 AGGAACGGAGGAAGTACATCC 58.891 52.381 9.17 9.17 44.89 3.51
682 1535 5.002516 AGTACATCCGTATGTAGTCCTAGC 58.997 45.833 0.46 0.00 45.22 3.42
696 1549 7.103641 TGTAGTCCTAGCGAAATCTCAAAAAT 58.896 34.615 0.00 0.00 0.00 1.82
697 1550 6.428385 AGTCCTAGCGAAATCTCAAAAATG 57.572 37.500 0.00 0.00 0.00 2.32
698 1551 5.940470 AGTCCTAGCGAAATCTCAAAAATGT 59.060 36.000 0.00 0.00 0.00 2.71
699 1552 6.431234 AGTCCTAGCGAAATCTCAAAAATGTT 59.569 34.615 0.00 0.00 0.00 2.71
762 2089 3.332034 ACTTTTCTTGATTACCCGACGG 58.668 45.455 6.99 6.99 0.00 4.79
833 2160 1.074623 CCTCCCCTCTGCTCCATCT 60.075 63.158 0.00 0.00 0.00 2.90
936 2264 1.226018 GTTGATCTTTTCGCGCCCG 60.226 57.895 0.00 0.00 0.00 6.13
1088 2416 3.125316 CAGTACGTTTTCTTGCCCATCTC 59.875 47.826 0.00 0.00 0.00 2.75
1168 2496 3.386486 CGGCTGCTACCAATTATACGAA 58.614 45.455 0.00 0.00 0.00 3.85
1169 2497 3.805422 CGGCTGCTACCAATTATACGAAA 59.195 43.478 0.00 0.00 0.00 3.46
1170 2498 4.271533 CGGCTGCTACCAATTATACGAAAA 59.728 41.667 0.00 0.00 0.00 2.29
1171 2499 5.220700 CGGCTGCTACCAATTATACGAAAAA 60.221 40.000 0.00 0.00 0.00 1.94
1378 2707 4.072088 GTGCGCACGAAGGAACCG 62.072 66.667 26.77 0.00 0.00 4.44
1401 2730 4.092091 GGACGAGCTATTCTGTTCAAGTTG 59.908 45.833 0.00 0.00 0.00 3.16
1404 2733 5.527582 ACGAGCTATTCTGTTCAAGTTGTTT 59.472 36.000 2.11 0.00 0.00 2.83
1411 2740 4.904116 TCTGTTCAAGTTGTTTGCTAACG 58.096 39.130 6.55 0.00 37.06 3.18
1507 2836 2.628178 CAACCTCCTTTTTCTTCCCACC 59.372 50.000 0.00 0.00 0.00 4.61
1580 2909 3.754965 TGCTCATTTCACAGCTAGGTTT 58.245 40.909 0.00 0.00 36.53 3.27
1636 2965 3.039011 TCCTGGAGCCCTTGATACTAAC 58.961 50.000 0.00 0.00 0.00 2.34
1662 2991 7.973388 CACTTCTAAGTAGAGTTCTGAATGGAG 59.027 40.741 0.00 0.00 37.08 3.86
1753 3083 6.974622 GCTGTATTACCAATTTCATCACCAAG 59.025 38.462 0.00 0.00 0.00 3.61
1903 3233 2.731572 AGCGTACATACCAGTACAGGT 58.268 47.619 14.99 14.99 43.49 4.00
1947 3277 7.216317 GTGAAAACACTTTATACTAATGCGCAG 59.784 37.037 18.32 4.62 0.00 5.18
2017 3347 5.296780 CACAAGTCTGTTCACACAAAGGTAT 59.703 40.000 0.00 0.00 31.64 2.73
2020 3350 7.719633 ACAAGTCTGTTCACACAAAGGTATATT 59.280 33.333 0.00 0.00 28.57 1.28
2070 3400 7.967890 AGGCTGGAAATATTGTTTGAAAAAG 57.032 32.000 0.00 0.00 0.00 2.27
2106 3436 1.878953 TGGAGCTTCCTCGTTTTGAC 58.121 50.000 0.00 0.00 39.06 3.18
2241 3572 5.968676 TGTATTGTACCTCTAGGGCAAAT 57.031 39.130 10.78 5.42 37.58 2.32
2413 3747 4.518211 ACCAAAAGAAGCAGTTCTCTCATG 59.482 41.667 0.00 0.00 42.59 3.07
2638 3974 9.290988 TCTGTGTCTTTTTAGCATTACCATTTA 57.709 29.630 0.00 0.00 0.00 1.40
2685 4021 9.454859 CCAAAAGAGAGGATAATTAAGTTGACT 57.545 33.333 0.00 0.00 0.00 3.41
2721 4057 7.987750 TCCTGTAATCTGCTCTAGTACATAG 57.012 40.000 0.00 0.00 0.00 2.23
2741 4077 1.471287 GCCCCTGACGTTTGATAAACC 59.529 52.381 0.00 0.00 38.14 3.27
2801 4137 6.420913 TTTGCAGAAAAGAGTAGAGGTAGT 57.579 37.500 0.00 0.00 0.00 2.73
3097 4434 6.096001 AGCCAGGAATTACAACAGATGAAATC 59.904 38.462 0.00 0.00 46.04 2.17
3357 4709 8.792633 TGTTTCGTAATTTCCATTCTTGATCTT 58.207 29.630 0.00 0.00 0.00 2.40
3358 4710 9.065871 GTTTCGTAATTTCCATTCTTGATCTTG 57.934 33.333 0.00 0.00 0.00 3.02
3521 5034 3.716431 AGTCATTTGCCATGGAATTCCT 58.284 40.909 24.73 8.22 36.82 3.36
3597 5143 3.550842 GCTTGAACCTGATGTTGAACCAC 60.551 47.826 0.00 0.00 37.29 4.16
3612 5158 7.458397 TGTTGAACCACTGGTTTCTATCTAAT 58.542 34.615 14.88 0.00 46.95 1.73
3944 5492 8.846943 AATTTCACCTTTCTTTGTTTCTTGTT 57.153 26.923 0.00 0.00 0.00 2.83
4018 5567 8.805175 TCTGATTGAAATTCCTGCAAGATTTTA 58.195 29.630 5.41 0.00 34.07 1.52
4026 5575 8.593492 AATTCCTGCAAGATTTTAGAAAACAC 57.407 30.769 0.00 0.00 34.07 3.32
4031 5580 6.454795 TGCAAGATTTTAGAAAACACCATCC 58.545 36.000 0.00 0.00 0.00 3.51
4188 5738 3.938963 GCACCGACTTCATCCTGAAATAA 59.061 43.478 0.00 0.00 35.73 1.40
4525 6075 4.032960 TGAGCCAATGATTAACACAGGT 57.967 40.909 0.00 0.00 0.00 4.00
4615 6165 8.306038 TCTGCTGCATTGTTTTATAATGAAAGT 58.694 29.630 1.31 0.00 37.65 2.66
4736 6290 6.780127 CCCTTTTGGTATGTTGTTTTGTTTG 58.220 36.000 0.00 0.00 38.10 2.93
4807 6366 2.356135 CACGTGGGTATCCTTTCCAAG 58.644 52.381 7.95 0.00 36.39 3.61
4832 6391 1.298157 TGTCGCCTCAAAATCTGCGG 61.298 55.000 2.76 0.00 46.51 5.69
4997 6556 1.213296 ATGCCCTTAGGTGACGGAAT 58.787 50.000 0.00 0.00 34.57 3.01
5023 6582 4.096382 GGAGTTGAAGTTTTGACAGCAAGA 59.904 41.667 0.00 0.00 35.04 3.02
5093 6653 2.188837 TAGCAAGTGATACGAGCACG 57.811 50.000 0.76 0.76 41.04 5.34
5227 6787 4.552767 CGATCATTTGTGCCTATTCGAACC 60.553 45.833 0.00 0.00 0.00 3.62
5357 6918 5.107065 GCCGAGTTATATTGTTACATGAGGC 60.107 44.000 0.00 0.00 0.00 4.70
5358 6919 6.223852 CCGAGTTATATTGTTACATGAGGCT 58.776 40.000 0.00 0.00 0.00 4.58
5359 6920 6.706270 CCGAGTTATATTGTTACATGAGGCTT 59.294 38.462 0.00 0.00 0.00 4.35
5360 6921 7.307396 CCGAGTTATATTGTTACATGAGGCTTG 60.307 40.741 0.00 0.00 0.00 4.01
5361 6922 7.224753 CGAGTTATATTGTTACATGAGGCTTGT 59.775 37.037 0.00 0.00 0.00 3.16
5362 6923 8.807948 AGTTATATTGTTACATGAGGCTTGTT 57.192 30.769 0.00 0.00 0.00 2.83
5363 6924 8.677300 AGTTATATTGTTACATGAGGCTTGTTG 58.323 33.333 0.00 0.00 0.00 3.33
5364 6925 8.458843 GTTATATTGTTACATGAGGCTTGTTGT 58.541 33.333 0.00 0.59 0.00 3.32
5365 6926 4.829064 TTGTTACATGAGGCTTGTTGTC 57.171 40.909 0.00 0.00 0.00 3.18
5366 6927 4.085357 TGTTACATGAGGCTTGTTGTCT 57.915 40.909 0.00 0.00 0.00 3.41
5367 6928 4.460263 TGTTACATGAGGCTTGTTGTCTT 58.540 39.130 0.00 0.00 0.00 3.01
5368 6929 4.275689 TGTTACATGAGGCTTGTTGTCTTG 59.724 41.667 0.00 0.00 0.00 3.02
5369 6930 2.936202 ACATGAGGCTTGTTGTCTTGT 58.064 42.857 0.00 0.00 0.00 3.16
5370 6931 3.290710 ACATGAGGCTTGTTGTCTTGTT 58.709 40.909 0.00 0.00 0.00 2.83
5371 6932 3.316308 ACATGAGGCTTGTTGTCTTGTTC 59.684 43.478 0.00 0.00 0.00 3.18
5372 6933 2.997980 TGAGGCTTGTTGTCTTGTTCA 58.002 42.857 0.00 0.00 0.00 3.18
5373 6934 2.945008 TGAGGCTTGTTGTCTTGTTCAG 59.055 45.455 0.00 0.00 0.00 3.02
5374 6935 1.678101 AGGCTTGTTGTCTTGTTCAGC 59.322 47.619 0.00 0.00 0.00 4.26
5375 6936 1.405105 GGCTTGTTGTCTTGTTCAGCA 59.595 47.619 0.00 0.00 0.00 4.41
5376 6937 2.542411 GGCTTGTTGTCTTGTTCAGCAG 60.542 50.000 0.00 0.00 0.00 4.24
5377 6938 2.355756 GCTTGTTGTCTTGTTCAGCAGA 59.644 45.455 0.00 0.00 0.00 4.26
5378 6939 3.181497 GCTTGTTGTCTTGTTCAGCAGAA 60.181 43.478 0.00 0.00 0.00 3.02
5379 6940 4.595116 CTTGTTGTCTTGTTCAGCAGAAG 58.405 43.478 0.00 0.00 33.63 2.85
5380 6941 2.945008 TGTTGTCTTGTTCAGCAGAAGG 59.055 45.455 0.00 0.00 33.63 3.46
5381 6942 2.260844 TGTCTTGTTCAGCAGAAGGG 57.739 50.000 0.00 0.00 33.63 3.95
5382 6943 1.490490 TGTCTTGTTCAGCAGAAGGGT 59.510 47.619 0.00 0.00 33.63 4.34
5383 6944 1.876156 GTCTTGTTCAGCAGAAGGGTG 59.124 52.381 0.00 0.00 46.38 4.61
5476 7038 4.559063 CATCCCCTGCTCCTGCCG 62.559 72.222 0.00 0.00 38.71 5.69
5493 7055 1.433879 CGTGACCGGATCTGAGACC 59.566 63.158 9.46 0.00 0.00 3.85
5500 7062 1.028905 CGGATCTGAGACCCTGAGAC 58.971 60.000 0.00 0.00 0.00 3.36
5523 7085 3.062466 CCGCGTCCTCTCTCCACA 61.062 66.667 4.92 0.00 0.00 4.17
5534 7096 1.151810 TCTCCACAGCCCCTCCTTT 60.152 57.895 0.00 0.00 0.00 3.11
5643 7205 1.600076 CAGCCACTCAGCTTGCTGT 60.600 57.895 20.20 1.48 44.69 4.40
5836 7398 1.602323 GGCCATTTCGACACCACCA 60.602 57.895 0.00 0.00 0.00 4.17
6005 7567 2.647297 GCTTGGTGCTGCAACCTC 59.353 61.111 16.16 0.00 41.16 3.85
6028 7590 4.435970 TCGAGCTCGGGCCCTGTA 62.436 66.667 33.98 11.09 40.29 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 4.948608 TGTCGTAGAACTTTTGCAACAA 57.051 36.364 0.00 0.00 39.69 2.83
12 13 5.743026 TTCATGTCGTAGAACTTTTGCAA 57.257 34.783 0.00 0.00 39.69 4.08
84 86 0.596083 GATGACCGTCAGATCCAGCG 60.596 60.000 7.41 0.00 0.00 5.18
88 90 1.403814 TGGAGATGACCGTCAGATCC 58.596 55.000 20.61 20.61 36.20 3.36
92 94 2.967599 TCAATGGAGATGACCGTCAG 57.032 50.000 7.41 0.00 0.00 3.51
130 133 4.778415 CTGTACGCGTCGGCTGCT 62.778 66.667 18.63 0.00 36.88 4.24
138 144 0.459585 CTATGGGCAACTGTACGCGT 60.460 55.000 19.17 19.17 0.00 6.01
145 151 5.810525 CGTAAGAATTTCTATGGGCAACTG 58.189 41.667 0.00 0.00 43.02 3.16
184 190 8.786826 TGTCCCTGTAAAATAGAGTACAAATG 57.213 34.615 0.00 0.00 30.11 2.32
206 212 2.424956 GGCCTGAGTGGATGAAAATGTC 59.575 50.000 0.00 0.00 38.35 3.06
454 1307 9.941664 GAATTCACTCATTTTACTCCATATGTG 57.058 33.333 0.00 0.00 0.00 3.21
460 1313 9.383519 GAGTATGAATTCACTCATTTTACTCCA 57.616 33.333 21.79 0.00 40.74 3.86
461 1314 9.606631 AGAGTATGAATTCACTCATTTTACTCC 57.393 33.333 25.43 15.29 42.99 3.85
481 1334 9.495382 GGAGGGAGTATATGGATTTTAGAGTAT 57.505 37.037 0.00 0.00 0.00 2.12
493 1346 4.682778 TTGAAACGGAGGGAGTATATGG 57.317 45.455 0.00 0.00 0.00 2.74
494 1347 8.848474 ATATTTTGAAACGGAGGGAGTATATG 57.152 34.615 0.00 0.00 0.00 1.78
521 1374 9.566432 AGTTCATTTGAAATCTCTACAAAGACT 57.434 29.630 0.00 0.00 37.04 3.24
537 1390 7.272244 ACATCCGTATGTGATAGTTCATTTGA 58.728 34.615 0.00 0.00 44.79 2.69
545 1398 9.901172 TGTCTATATACATCCGTATGTGATAGT 57.099 33.333 17.08 3.55 45.99 2.12
578 1431 9.384764 GGAGCAAAATAAGTAAATCTACACTCT 57.615 33.333 0.00 0.00 0.00 3.24
579 1432 8.328864 CGGAGCAAAATAAGTAAATCTACACTC 58.671 37.037 0.00 0.00 0.00 3.51
580 1433 7.822822 ACGGAGCAAAATAAGTAAATCTACACT 59.177 33.333 0.00 0.00 0.00 3.55
581 1434 7.971455 ACGGAGCAAAATAAGTAAATCTACAC 58.029 34.615 0.00 0.00 0.00 2.90
582 1435 9.826574 ATACGGAGCAAAATAAGTAAATCTACA 57.173 29.630 0.00 0.00 0.00 2.74
584 1437 9.826574 ACATACGGAGCAAAATAAGTAAATCTA 57.173 29.630 0.00 0.00 0.00 1.98
591 1444 9.609346 AATAACTACATACGGAGCAAAATAAGT 57.391 29.630 0.00 0.00 0.00 2.24
595 1448 8.276252 ACAAATAACTACATACGGAGCAAAAT 57.724 30.769 0.00 0.00 0.00 1.82
597 1450 7.388224 TCAACAAATAACTACATACGGAGCAAA 59.612 33.333 0.00 0.00 0.00 3.68
598 1451 6.874664 TCAACAAATAACTACATACGGAGCAA 59.125 34.615 0.00 0.00 0.00 3.91
599 1452 6.399743 TCAACAAATAACTACATACGGAGCA 58.600 36.000 0.00 0.00 0.00 4.26
600 1453 6.897259 TCAACAAATAACTACATACGGAGC 57.103 37.500 0.00 0.00 0.00 4.70
603 1456 9.916397 GAGATTTCAACAAATAACTACATACGG 57.084 33.333 0.00 0.00 31.94 4.02
639 1492 8.174733 TGTACTTCCTCCGTTCCTAAATATAG 57.825 38.462 0.00 0.00 0.00 1.31
648 1501 1.202382 CGGATGTACTTCCTCCGTTCC 60.202 57.143 21.78 0.00 45.03 3.62
653 1506 4.826183 ACTACATACGGATGTACTTCCTCC 59.174 45.833 16.71 9.45 44.77 4.30
658 1511 5.472820 GCTAGGACTACATACGGATGTACTT 59.527 44.000 16.71 6.62 44.77 2.24
660 1513 4.142945 CGCTAGGACTACATACGGATGTAC 60.143 50.000 16.71 8.04 44.77 2.90
667 1520 5.049612 TGAGATTTCGCTAGGACTACATACG 60.050 44.000 0.00 0.00 0.00 3.06
833 2160 1.571457 CCTAGGGAGGGAGAGTCAGAA 59.429 57.143 0.00 0.00 39.48 3.02
936 2264 1.468914 GAGGGGTGAAATGAAAGCGAC 59.531 52.381 0.00 0.00 0.00 5.19
1168 2496 2.496899 ATCTGTCGGGTGCTGATTTT 57.503 45.000 0.00 0.00 0.00 1.82
1169 2497 2.496899 AATCTGTCGGGTGCTGATTT 57.503 45.000 0.00 0.00 32.95 2.17
1170 2498 3.627395 TTAATCTGTCGGGTGCTGATT 57.373 42.857 0.00 0.00 37.90 2.57
1171 2499 3.270877 GTTTAATCTGTCGGGTGCTGAT 58.729 45.455 0.00 0.00 0.00 2.90
1249 2578 6.034683 CGACATAACTTCCCTATTTATAGCGC 59.965 42.308 0.00 0.00 0.00 5.92
1378 2707 3.851098 ACTTGAACAGAATAGCTCGTCC 58.149 45.455 0.00 0.00 0.00 4.79
1401 2730 6.308675 TGAAAATATCGAACCGTTAGCAAAC 58.691 36.000 0.00 0.00 0.00 2.93
1404 2733 5.412640 TCTGAAAATATCGAACCGTTAGCA 58.587 37.500 0.00 0.00 0.00 3.49
1411 2740 3.253432 GGGGCATCTGAAAATATCGAACC 59.747 47.826 0.00 0.00 0.00 3.62
1442 2771 2.747855 CGGGGGAGCTTCAGTTGC 60.748 66.667 0.00 0.00 0.00 4.17
1507 2836 1.652124 ACGCTATCGCAGTACAAAACG 59.348 47.619 0.00 0.00 39.84 3.60
1577 2906 7.712639 TCATATCAGCTGACTATCAAGGAAAAC 59.287 37.037 20.97 0.00 0.00 2.43
1580 2909 6.983906 TCATATCAGCTGACTATCAAGGAA 57.016 37.500 20.97 0.00 0.00 3.36
1636 2965 7.831753 TCCATTCAGAACTCTACTTAGAAGTG 58.168 38.462 5.15 0.00 40.07 3.16
1662 2991 7.617041 ATCTAACAGGAGCAATTCTTACAAC 57.383 36.000 0.00 0.00 0.00 3.32
1753 3083 3.010420 GACTGAACCAAGGCCATACTTC 58.990 50.000 5.01 0.53 0.00 3.01
1903 3233 5.745312 TTCACTCAGAGGCAGAATTCTAA 57.255 39.130 7.86 0.00 0.00 2.10
1947 3277 1.134699 TCCTGCGAACTGTGGATGATC 60.135 52.381 0.00 0.00 0.00 2.92
2017 3347 2.840038 ACAGCTGGGATGTCAGTGAATA 59.160 45.455 19.93 0.00 37.12 1.75
2020 3350 0.610174 GACAGCTGGGATGTCAGTGA 59.390 55.000 19.93 0.00 45.18 3.41
2143 3474 3.855154 GCATCGGCATAAACACAACAACA 60.855 43.478 0.00 0.00 40.72 3.33
2289 3621 6.204359 CAGGCATGCTCAATAAACTGTAATC 58.796 40.000 18.92 0.00 0.00 1.75
2375 3709 7.575155 GCTTCTTTTGGTTTACCCAGACTAATC 60.575 40.741 0.00 0.00 46.31 1.75
2413 3747 8.337532 GCTCCAAATGCAATAAAATCCAATTAC 58.662 33.333 0.00 0.00 0.00 1.89
2683 4019 8.893727 GCAGATTACAGGATAACAAAATACAGT 58.106 33.333 0.00 0.00 0.00 3.55
2685 4021 9.109393 GAGCAGATTACAGGATAACAAAATACA 57.891 33.333 0.00 0.00 0.00 2.29
2721 4057 1.471287 GGTTTATCAAACGTCAGGGGC 59.529 52.381 0.00 0.00 42.29 5.80
2763 4099 1.202794 TGCAAATCACTGTCAGGCTCA 60.203 47.619 4.53 0.00 0.00 4.26
2801 4137 3.689347 ACTTGCATATCAGTGGAAAGCA 58.311 40.909 0.00 0.00 0.00 3.91
2843 4179 6.705302 TCCAGCAGAATAACATCAGATATCC 58.295 40.000 0.00 0.00 0.00 2.59
2860 4196 2.110901 AGCAGAAACAGATCCAGCAG 57.889 50.000 0.00 0.00 0.00 4.24
2981 4317 2.158682 ACAGTCAGTACAATGCCACCAA 60.159 45.455 0.00 0.00 0.00 3.67
3097 4434 5.240403 TGTCTCCTCATGAATCACTCTATCG 59.760 44.000 0.00 0.00 0.00 2.92
3521 5034 1.891933 TATCAAGGGACCTGGCATCA 58.108 50.000 0.00 0.00 0.00 3.07
3612 5158 9.787532 CATCTTCAAGTTTTCTGTTAGAAACAA 57.212 29.630 3.65 0.00 43.25 2.83
3736 5284 7.093945 GGTTATATGTCCAGTCAAACACCAAAT 60.094 37.037 0.00 0.00 0.00 2.32
3737 5285 6.207810 GGTTATATGTCCAGTCAAACACCAAA 59.792 38.462 0.00 0.00 0.00 3.28
4018 5567 2.380064 TTGCAGGGATGGTGTTTTCT 57.620 45.000 0.00 0.00 0.00 2.52
4026 5575 2.133281 TGTCTCATTTGCAGGGATGG 57.867 50.000 6.87 0.49 0.00 3.51
4031 5580 1.179152 TGGCATGTCTCATTTGCAGG 58.821 50.000 0.00 0.00 38.12 4.85
4176 5726 8.734386 ACAAAAGAGCTAAGTTATTTCAGGATG 58.266 33.333 0.00 0.00 37.54 3.51
4188 5738 7.122204 ACACAAAAGGTAACAAAAGAGCTAAGT 59.878 33.333 0.00 0.00 41.41 2.24
4454 6004 3.306472 ACCAACAGCCTTGTTTCCTAA 57.694 42.857 0.00 0.00 45.01 2.69
4525 6075 2.680841 GTTTGCCACTGTCACACACTTA 59.319 45.455 0.00 0.00 0.00 2.24
4555 6105 2.032634 GCATCGAGGCGTTCAACCA 61.033 57.895 6.20 0.00 0.00 3.67
4615 6165 5.700373 GCCAAAGTCCTGCAAAATATGAAAA 59.300 36.000 0.00 0.00 0.00 2.29
4736 6290 5.909477 TGAGCAAATTGGATCAATTCATCC 58.091 37.500 0.50 0.50 42.32 3.51
4997 6556 3.202906 CTGTCAAAACTTCAACTCCGGA 58.797 45.455 2.93 2.93 0.00 5.14
5023 6582 2.284625 TCCGGTGATGAGGGCAGT 60.285 61.111 0.00 0.00 0.00 4.40
5093 6653 5.984926 TCAATGGCAAGTTGATCAAAAAGAC 59.015 36.000 10.35 5.47 31.07 3.01
5227 6787 8.328146 CAACACCACATTCAACTATATAACTCG 58.672 37.037 0.00 0.00 0.00 4.18
5357 6918 4.497006 CCTTCTGCTGAACAAGACAACAAG 60.497 45.833 1.33 0.00 0.00 3.16
5358 6919 3.378112 CCTTCTGCTGAACAAGACAACAA 59.622 43.478 1.33 0.00 0.00 2.83
5359 6920 2.945008 CCTTCTGCTGAACAAGACAACA 59.055 45.455 1.33 0.00 0.00 3.33
5360 6921 2.291741 CCCTTCTGCTGAACAAGACAAC 59.708 50.000 1.33 0.00 0.00 3.32
5361 6922 2.092429 ACCCTTCTGCTGAACAAGACAA 60.092 45.455 1.33 0.00 0.00 3.18
5362 6923 1.490490 ACCCTTCTGCTGAACAAGACA 59.510 47.619 1.33 0.00 0.00 3.41
5363 6924 1.876156 CACCCTTCTGCTGAACAAGAC 59.124 52.381 1.33 0.00 0.00 3.01
5364 6925 1.768275 TCACCCTTCTGCTGAACAAGA 59.232 47.619 1.33 0.00 0.00 3.02
5365 6926 2.260844 TCACCCTTCTGCTGAACAAG 57.739 50.000 1.33 0.00 0.00 3.16
5366 6927 2.507484 CATCACCCTTCTGCTGAACAA 58.493 47.619 1.33 0.00 0.00 2.83
5367 6928 1.271543 CCATCACCCTTCTGCTGAACA 60.272 52.381 1.33 0.00 0.00 3.18
5368 6929 1.457346 CCATCACCCTTCTGCTGAAC 58.543 55.000 1.33 0.00 0.00 3.18
5369 6930 0.329261 CCCATCACCCTTCTGCTGAA 59.671 55.000 5.85 5.85 0.00 3.02
5370 6931 0.842030 ACCCATCACCCTTCTGCTGA 60.842 55.000 0.00 0.00 0.00 4.26
5371 6932 0.393537 GACCCATCACCCTTCTGCTG 60.394 60.000 0.00 0.00 0.00 4.41
5372 6933 0.548682 AGACCCATCACCCTTCTGCT 60.549 55.000 0.00 0.00 0.00 4.24
5373 6934 0.107459 GAGACCCATCACCCTTCTGC 60.107 60.000 0.00 0.00 0.00 4.26
5374 6935 0.176680 CGAGACCCATCACCCTTCTG 59.823 60.000 0.00 0.00 0.00 3.02
5375 6936 1.617947 GCGAGACCCATCACCCTTCT 61.618 60.000 0.00 0.00 0.00 2.85
5376 6937 1.153349 GCGAGACCCATCACCCTTC 60.153 63.158 0.00 0.00 0.00 3.46
5377 6938 2.990479 GCGAGACCCATCACCCTT 59.010 61.111 0.00 0.00 0.00 3.95
5378 6939 3.461773 CGCGAGACCCATCACCCT 61.462 66.667 0.00 0.00 0.00 4.34
5379 6940 3.718210 GACGCGAGACCCATCACCC 62.718 68.421 15.93 0.00 0.00 4.61
5380 6941 2.202756 GACGCGAGACCCATCACC 60.203 66.667 15.93 0.00 0.00 4.02
5381 6942 1.226717 GAGACGCGAGACCCATCAC 60.227 63.158 15.93 0.00 0.00 3.06
5382 6943 2.761195 CGAGACGCGAGACCCATCA 61.761 63.158 15.93 0.00 44.57 3.07
5383 6944 2.024871 CGAGACGCGAGACCCATC 59.975 66.667 15.93 0.00 44.57 3.51
5476 7038 0.684805 AGGGTCTCAGATCCGGTCAC 60.685 60.000 0.00 0.00 38.00 3.67
5486 7048 1.687493 GGGGGTCTCAGGGTCTCAG 60.687 68.421 0.00 0.00 0.00 3.35
5487 7049 2.450243 GGGGGTCTCAGGGTCTCA 59.550 66.667 0.00 0.00 0.00 3.27
5488 7050 1.990614 GTGGGGGTCTCAGGGTCTC 60.991 68.421 0.00 0.00 0.00 3.36
5489 7051 2.122954 GTGGGGGTCTCAGGGTCT 59.877 66.667 0.00 0.00 0.00 3.85
5490 7052 3.009714 GGTGGGGGTCTCAGGGTC 61.010 72.222 0.00 0.00 0.00 4.46
5523 7085 2.304831 GGAGCTCAAAGGAGGGGCT 61.305 63.158 17.19 0.00 41.67 5.19
5626 7188 1.600076 CACAGCAAGCTGAGTGGCT 60.600 57.895 27.17 1.90 46.30 4.75
5817 7379 2.686816 GGTGGTGTCGAAATGGCCG 61.687 63.158 0.00 0.00 0.00 6.13
5823 7385 2.280524 CCGCTGGTGGTGTCGAAA 60.281 61.111 0.00 0.00 0.00 3.46
5998 7560 2.811317 CTCGACGCTGGAGGTTGC 60.811 66.667 0.00 0.00 0.00 4.17
6024 7586 2.093306 TGCCAAATCCGACTGTACAG 57.907 50.000 21.44 21.44 0.00 2.74
6028 7590 1.202758 TCTGTTGCCAAATCCGACTGT 60.203 47.619 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.