Multiple sequence alignment - TraesCS6D01G035200

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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 TraesCS6D01G035200 chr6D 100.000 3047 0 0 1 3047 14524433 14521387 0.000000e+00 5627.0
1 TraesCS6D01G035200 chr6D 88.541 1597 131 31 1472 3045 14685283 14686850 0.000000e+00 1888.0
2 TraesCS6D01G035200 chr6D 82.864 852 131 13 1213 2058 16139182 16138340 0.000000e+00 750.0
3 TraesCS6D01G035200 chr6D 80.349 229 38 6 995 1221 16139497 16139274 1.880000e-37 167.0
4 TraesCS6D01G035200 chr6D 92.000 50 4 0 1188 1237 16179146 16179195 1.520000e-08 71.3
5 TraesCS6D01G035200 chr6B 92.000 1550 97 10 676 2206 26649481 26651022 0.000000e+00 2150.0
6 TraesCS6D01G035200 chr6B 83.766 770 74 23 2287 3047 26652970 26653697 0.000000e+00 682.0
7 TraesCS6D01G035200 chr6B 85.669 314 35 6 1035 1348 26517447 26517144 3.790000e-84 322.0
8 TraesCS6D01G035200 chr6B 87.671 146 12 4 2153 2293 26651025 26651169 6.760000e-37 165.0
9 TraesCS6D01G035200 chr6B 80.000 230 37 8 995 1221 27896855 27896632 8.740000e-36 161.0
10 TraesCS6D01G035200 chr6B 92.000 50 4 0 1188 1237 27919630 27919679 1.520000e-08 71.3
11 TraesCS6D01G035200 chr6A 86.119 1376 95 29 1292 2647 15707321 15706022 0.000000e+00 1395.0
12 TraesCS6D01G035200 chr6A 93.224 856 49 6 1354 2206 15868255 15869104 0.000000e+00 1251.0
13 TraesCS6D01G035200 chr6A 84.855 898 77 31 2153 3041 15721485 15720638 0.000000e+00 850.0
14 TraesCS6D01G035200 chr6A 82.726 851 133 13 1217 2062 16438699 16437858 0.000000e+00 745.0
15 TraesCS6D01G035200 chr6A 80.774 827 151 8 1218 2040 29365416 29366238 9.210000e-180 640.0
16 TraesCS6D01G035200 chr6A 84.743 544 56 17 16 554 15708768 15708247 1.250000e-143 520.0
17 TraesCS6D01G035200 chr6A 91.530 366 30 1 900 1264 15707683 15707318 1.260000e-138 503.0
18 TraesCS6D01G035200 chr6A 87.755 441 32 5 2607 3047 15869571 15869989 2.110000e-136 496.0
19 TraesCS6D01G035200 chr6A 88.101 395 35 3 1091 1485 15721868 15721486 2.770000e-125 459.0
20 TraesCS6D01G035200 chr6A 93.455 275 18 0 2377 2651 110685592 110685866 2.830000e-110 409.0
21 TraesCS6D01G035200 chr6A 84.234 444 39 14 2166 2604 15869113 15869530 1.320000e-108 403.0
22 TraesCS6D01G035200 chr6A 86.218 312 29 5 607 907 15708232 15707924 2.930000e-85 326.0
23 TraesCS6D01G035200 chr6A 81.140 228 38 4 995 1221 16439028 16438805 8.680000e-41 178.0
24 TraesCS6D01G035200 chr6A 96.386 83 3 0 2901 2983 132844471 132844553 1.470000e-28 137.0
25 TraesCS6D01G035200 chr6A 96.386 83 3 0 2901 2983 165864634 165864716 1.470000e-28 137.0
26 TraesCS6D01G035200 chr6A 95.775 71 2 1 2699 2769 15706026 15705957 2.480000e-21 113.0
27 TraesCS6D01G035200 chr2A 93.651 441 23 2 2377 2813 40142634 40143073 0.000000e+00 654.0
28 TraesCS6D01G035200 chr2A 93.818 275 17 0 2377 2651 46723565 46723291 6.080000e-112 414.0
29 TraesCS6D01G035200 chr2A 94.444 90 3 2 2894 2983 47059230 47059317 1.470000e-28 137.0
30 TraesCS6D01G035200 chr3D 80.998 842 141 15 1218 2051 519881660 519882490 0.000000e+00 651.0
31 TraesCS6D01G035200 chr3B 80.217 829 150 13 1218 2039 684616890 684617711 7.220000e-171 610.0
32 TraesCS6D01G035200 chr7A 93.867 375 22 1 2377 2751 716207200 716207573 5.700000e-157 564.0
33 TraesCS6D01G035200 chr7A 97.590 83 2 0 2901 2983 718304272 718304190 3.170000e-30 143.0
34 TraesCS6D01G035200 chr3A 93.818 275 17 0 2377 2651 698663720 698663994 6.080000e-112 414.0
35 TraesCS6D01G035200 chr1A 93.455 275 18 0 2377 2651 288982076 288982350 2.830000e-110 409.0
36 TraesCS6D01G035200 chr1A 93.455 275 18 0 2377 2651 491793648 491793374 2.830000e-110 409.0
37 TraesCS6D01G035200 chr1A 96.386 83 3 0 2901 2983 30447448 30447366 1.470000e-28 137.0
38 TraesCS6D01G035200 chr5A 96.386 83 3 0 2901 2983 62542752 62542670 1.470000e-28 137.0


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 TraesCS6D01G035200 chr6D 14521387 14524433 3046 True 5627.000000 5627 100.000000 1 3047 1 chr6D.!!$R1 3046
1 TraesCS6D01G035200 chr6D 14685283 14686850 1567 False 1888.000000 1888 88.541000 1472 3045 1 chr6D.!!$F1 1573
2 TraesCS6D01G035200 chr6D 16138340 16139497 1157 True 458.500000 750 81.606500 995 2058 2 chr6D.!!$R2 1063
3 TraesCS6D01G035200 chr6B 26649481 26653697 4216 False 999.000000 2150 87.812333 676 3047 3 chr6B.!!$F2 2371
4 TraesCS6D01G035200 chr6A 15868255 15869989 1734 False 716.666667 1251 88.404333 1354 3047 3 chr6A.!!$F5 1693
5 TraesCS6D01G035200 chr6A 15720638 15721868 1230 True 654.500000 850 86.478000 1091 3041 2 chr6A.!!$R2 1950
6 TraesCS6D01G035200 chr6A 29365416 29366238 822 False 640.000000 640 80.774000 1218 2040 1 chr6A.!!$F1 822
7 TraesCS6D01G035200 chr6A 15705957 15708768 2811 True 571.400000 1395 88.877000 16 2769 5 chr6A.!!$R1 2753
8 TraesCS6D01G035200 chr6A 16437858 16439028 1170 True 461.500000 745 81.933000 995 2062 2 chr6A.!!$R3 1067
9 TraesCS6D01G035200 chr3D 519881660 519882490 830 False 651.000000 651 80.998000 1218 2051 1 chr3D.!!$F1 833
10 TraesCS6D01G035200 chr3B 684616890 684617711 821 False 610.000000 610 80.217000 1218 2039 1 chr3B.!!$F1 821

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
358 361 0.033306 ACATGTGGCCATATGCACCA 60.033 50.0 34.82 16.53 43.89 4.17 F
853 870 0.391661 CAACCGACAGTGATCCCCAG 60.392 60.0 0.00 0.00 0.00 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1458 1843 0.389948 GTCTGGGCGTGAAGTTCGAT 60.390 55.000 0.0 0.0 0.0 3.59 R
2293 2820 3.008704 ACTTGGTACTGTGGGATGGTAAC 59.991 47.826 0.0 0.0 0.0 2.50 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
48 50 6.984474 GCTTGCTTATCCTGTAAGTATGTGTA 59.016 38.462 0.00 0.00 31.38 2.90
94 96 4.629634 TGTCCAACATAATGCTAGAACGTG 59.370 41.667 0.00 0.00 0.00 4.49
95 97 4.630069 GTCCAACATAATGCTAGAACGTGT 59.370 41.667 0.00 0.00 0.00 4.49
97 99 6.311935 GTCCAACATAATGCTAGAACGTGTAA 59.688 38.462 0.00 0.00 0.00 2.41
98 100 6.874664 TCCAACATAATGCTAGAACGTGTAAA 59.125 34.615 0.00 0.00 0.00 2.01
99 101 7.388224 TCCAACATAATGCTAGAACGTGTAAAA 59.612 33.333 0.00 0.00 0.00 1.52
107 109 5.411361 TGCTAGAACGTGTAAAATGCAATCT 59.589 36.000 0.00 0.00 0.00 2.40
108 110 6.072728 TGCTAGAACGTGTAAAATGCAATCTT 60.073 34.615 0.00 0.00 0.00 2.40
133 135 3.443681 AGAGGTTTAATTTGACATGGCCG 59.556 43.478 0.00 0.00 0.00 6.13
139 141 3.374220 AATTTGACATGGCCGCATATG 57.626 42.857 0.00 0.00 0.00 1.78
141 143 1.596603 TTGACATGGCCGCATATGAG 58.403 50.000 6.97 2.53 0.00 2.90
142 144 0.886043 TGACATGGCCGCATATGAGC 60.886 55.000 6.97 8.26 0.00 4.26
144 146 0.887836 ACATGGCCGCATATGAGCAG 60.888 55.000 16.99 10.16 0.00 4.24
145 147 0.887836 CATGGCCGCATATGAGCAGT 60.888 55.000 16.99 5.10 0.00 4.40
146 148 0.604780 ATGGCCGCATATGAGCAGTC 60.605 55.000 16.99 1.31 0.00 3.51
147 149 1.227645 GGCCGCATATGAGCAGTCA 60.228 57.895 16.99 0.00 37.02 3.41
148 150 0.604780 GGCCGCATATGAGCAGTCAT 60.605 55.000 16.99 0.00 45.82 3.06
149 151 1.233019 GCCGCATATGAGCAGTCATT 58.767 50.000 6.97 0.00 40.84 2.57
150 152 1.605710 GCCGCATATGAGCAGTCATTT 59.394 47.619 6.97 0.00 40.84 2.32
156 158 6.128715 CCGCATATGAGCAGTCATTTAAGTAG 60.129 42.308 6.97 0.00 40.84 2.57
165 167 5.449177 GCAGTCATTTAAGTAGGGCACATTC 60.449 44.000 0.00 0.00 0.00 2.67
206 209 2.741612 CAAATTTTGCTTGGCGTGAGA 58.258 42.857 0.00 0.00 0.00 3.27
208 211 0.883833 ATTTTGCTTGGCGTGAGAGG 59.116 50.000 0.00 0.00 0.00 3.69
210 213 0.884704 TTTGCTTGGCGTGAGAGGAC 60.885 55.000 0.00 0.00 0.00 3.85
211 214 2.038814 TTGCTTGGCGTGAGAGGACA 62.039 55.000 0.00 0.00 0.00 4.02
214 217 0.534412 CTTGGCGTGAGAGGACATCT 59.466 55.000 0.00 0.00 42.61 2.90
215 218 0.976641 TTGGCGTGAGAGGACATCTT 59.023 50.000 0.00 0.00 38.84 2.40
230 233 6.520272 AGGACATCTTCATAGAAGTATGTGC 58.480 40.000 21.39 21.39 37.81 4.57
232 235 6.201806 GGACATCTTCATAGAAGTATGTGCAC 59.798 42.308 22.58 10.75 37.81 4.57
238 241 9.143155 TCTTCATAGAAGTATGTGCACCTTATA 57.857 33.333 15.69 12.17 37.81 0.98
276 279 1.149361 TATTACGCGCGGGCTTTCAG 61.149 55.000 35.22 8.80 36.88 3.02
284 287 1.106285 GCGGGCTTTCAGGAATCAAT 58.894 50.000 0.00 0.00 0.00 2.57
295 298 7.816031 GCTTTCAGGAATCAATCATCAAGAAAA 59.184 33.333 0.00 0.00 0.00 2.29
327 330 5.216622 TCTGTAGGCACCAACTCCTAATAT 58.783 41.667 0.00 0.00 36.76 1.28
334 337 8.967779 AGGCACCAACTCCTAATATAAGTATA 57.032 34.615 0.00 0.00 0.00 1.47
335 338 8.813951 AGGCACCAACTCCTAATATAAGTATAC 58.186 37.037 0.00 0.00 0.00 1.47
346 349 8.869897 CCTAATATAAGTATACGCAACATGTGG 58.130 37.037 0.00 0.00 30.87 4.17
349 352 1.065782 AGTATACGCAACATGTGGCCA 60.066 47.619 19.65 0.00 30.87 5.36
356 359 1.803625 GCAACATGTGGCCATATGCAC 60.804 52.381 34.82 23.08 43.89 4.57
358 361 0.033306 ACATGTGGCCATATGCACCA 60.033 50.000 34.82 16.53 43.89 4.17
378 381 6.035975 GCACCAAACCAAATACATGAATTAGC 59.964 38.462 0.00 0.00 0.00 3.09
383 386 7.961326 AACCAAATACATGAATTAGCTTCCT 57.039 32.000 0.00 0.00 32.49 3.36
386 389 6.239120 CCAAATACATGAATTAGCTTCCTGGG 60.239 42.308 0.00 0.00 34.75 4.45
387 390 5.912149 ATACATGAATTAGCTTCCTGGGA 57.088 39.130 0.00 0.00 34.75 4.37
388 391 3.891049 ACATGAATTAGCTTCCTGGGAC 58.109 45.455 0.00 0.00 34.75 4.46
389 392 3.266772 ACATGAATTAGCTTCCTGGGACA 59.733 43.478 0.00 0.00 34.75 4.02
390 393 3.350219 TGAATTAGCTTCCTGGGACAC 57.650 47.619 0.00 0.00 32.49 3.67
391 394 2.026262 TGAATTAGCTTCCTGGGACACC 60.026 50.000 0.00 0.00 32.49 4.16
392 395 1.668826 ATTAGCTTCCTGGGACACCA 58.331 50.000 0.00 0.00 46.94 4.17
420 425 1.398390 GCAATACTCGGTTTCCAGCAG 59.602 52.381 0.00 0.00 0.00 4.24
424 429 1.122019 ACTCGGTTTCCAGCAGAGGT 61.122 55.000 0.00 0.00 33.58 3.85
437 442 2.079925 GCAGAGGTTTGCTAGGAACTG 58.920 52.381 0.00 2.08 40.89 3.16
440 445 2.972713 AGAGGTTTGCTAGGAACTGTCA 59.027 45.455 0.00 0.00 41.52 3.58
459 464 6.041423 TGTCAGTTATGAAGAGATGCTTGA 57.959 37.500 0.00 0.00 37.14 3.02
468 473 1.988107 AGAGATGCTTGAAGGTTGGGA 59.012 47.619 0.00 0.00 0.00 4.37
530 535 3.694072 CGGGCCTCATTTGTATTTTCTCA 59.306 43.478 0.84 0.00 0.00 3.27
532 537 5.163519 CGGGCCTCATTTGTATTTTCTCAAT 60.164 40.000 0.84 0.00 0.00 2.57
550 555 7.704789 TCTCAATGATTAACATGATGTCTCG 57.295 36.000 0.00 0.00 39.39 4.04
552 557 8.413229 TCTCAATGATTAACATGATGTCTCGTA 58.587 33.333 0.00 0.00 39.39 3.43
553 558 9.201127 CTCAATGATTAACATGATGTCTCGTAT 57.799 33.333 0.00 0.00 39.39 3.06
571 576 6.288941 TCGTATAGAGATCCTAGTCTCCTG 57.711 45.833 6.72 0.00 44.55 3.86
572 577 5.781306 TCGTATAGAGATCCTAGTCTCCTGT 59.219 44.000 6.72 0.00 44.55 4.00
573 578 6.952938 TCGTATAGAGATCCTAGTCTCCTGTA 59.047 42.308 6.72 0.00 44.55 2.74
574 579 7.454066 TCGTATAGAGATCCTAGTCTCCTGTAA 59.546 40.741 6.72 0.00 44.55 2.41
575 580 8.095792 CGTATAGAGATCCTAGTCTCCTGTAAA 58.904 40.741 6.72 0.00 44.55 2.01
576 581 9.969001 GTATAGAGATCCTAGTCTCCTGTAAAT 57.031 37.037 6.72 0.00 44.55 1.40
580 585 8.900802 AGAGATCCTAGTCTCCTGTAAATATCT 58.099 37.037 6.72 0.00 44.55 1.98
581 586 9.528489 GAGATCCTAGTCTCCTGTAAATATCTT 57.472 37.037 0.00 0.00 38.94 2.40
582 587 9.308000 AGATCCTAGTCTCCTGTAAATATCTTG 57.692 37.037 0.00 0.00 0.00 3.02
583 588 9.084533 GATCCTAGTCTCCTGTAAATATCTTGT 57.915 37.037 0.00 0.00 0.00 3.16
585 590 9.352191 TCCTAGTCTCCTGTAAATATCTTGTAC 57.648 37.037 0.00 0.00 0.00 2.90
586 591 9.132923 CCTAGTCTCCTGTAAATATCTTGTACA 57.867 37.037 0.00 0.00 0.00 2.90
587 592 9.953697 CTAGTCTCCTGTAAATATCTTGTACAC 57.046 37.037 0.00 0.00 0.00 2.90
588 593 8.362464 AGTCTCCTGTAAATATCTTGTACACA 57.638 34.615 0.00 0.00 0.00 3.72
589 594 8.812972 AGTCTCCTGTAAATATCTTGTACACAA 58.187 33.333 0.00 0.00 0.00 3.33
590 595 9.601217 GTCTCCTGTAAATATCTTGTACACAAT 57.399 33.333 0.00 0.00 35.02 2.71
596 601 9.607988 TGTAAATATCTTGTACACAATACTGGG 57.392 33.333 0.00 0.00 35.02 4.45
597 602 9.826574 GTAAATATCTTGTACACAATACTGGGA 57.173 33.333 0.00 0.00 35.02 4.37
598 603 8.964476 AAATATCTTGTACACAATACTGGGAG 57.036 34.615 0.00 0.00 35.02 4.30
599 604 7.914427 ATATCTTGTACACAATACTGGGAGA 57.086 36.000 0.00 0.00 35.02 3.71
600 605 6.620877 ATCTTGTACACAATACTGGGAGAA 57.379 37.500 0.00 0.00 35.02 2.87
601 606 6.428083 TCTTGTACACAATACTGGGAGAAA 57.572 37.500 0.00 0.00 35.02 2.52
602 607 6.833041 TCTTGTACACAATACTGGGAGAAAA 58.167 36.000 0.00 0.00 35.02 2.29
603 608 7.284074 TCTTGTACACAATACTGGGAGAAAAA 58.716 34.615 0.00 0.00 35.02 1.94
722 727 0.974836 GCGATTTGCCGTTTTTCTCG 59.025 50.000 0.00 0.00 37.76 4.04
750 755 7.547227 ACAGCAATGTTTAAAGTTCTGAGTTT 58.453 30.769 13.46 0.00 33.19 2.66
805 822 0.525668 GCACGGATGTCGAGGTAGTG 60.526 60.000 0.00 0.00 42.43 2.74
833 850 3.056962 ACATCACGCTAGCTATGATCCAG 60.057 47.826 22.02 15.88 30.58 3.86
853 870 0.391661 CAACCGACAGTGATCCCCAG 60.392 60.000 0.00 0.00 0.00 4.45
894 911 6.531948 AGCATCTCGTCAATTAACTACACTTC 59.468 38.462 0.00 0.00 0.00 3.01
902 1165 7.253552 CGTCAATTAACTACACTTCCGACATAC 60.254 40.741 0.00 0.00 0.00 2.39
956 1223 5.918608 TCTTAATTAGGCTCTTAGCTGGTG 58.081 41.667 0.00 0.00 41.99 4.17
958 1225 6.610020 TCTTAATTAGGCTCTTAGCTGGTGTA 59.390 38.462 0.00 0.00 41.99 2.90
1063 1331 1.156803 AGGTACGTCTTCCCACCCA 59.843 57.895 0.00 0.00 0.00 4.51
1476 1861 0.389817 CATCGAACTTCACGCCCAGA 60.390 55.000 0.00 0.00 0.00 3.86
2078 2494 4.579753 TGAGTGACAAACTGCATGATTTCA 59.420 37.500 0.00 0.00 40.07 2.69
2116 2532 3.125316 CAGAGGGCACGAAATAAACAGAC 59.875 47.826 0.00 0.00 0.00 3.51
2124 2540 4.154195 CACGAAATAAACAGACAAGGGGAG 59.846 45.833 0.00 0.00 0.00 4.30
2127 2543 5.350640 CGAAATAAACAGACAAGGGGAGTAC 59.649 44.000 0.00 0.00 0.00 2.73
2172 2589 5.053811 GGGTTCTGTTTATTTGTGTTTGGG 58.946 41.667 0.00 0.00 0.00 4.12
2175 2592 5.176407 TCTGTTTATTTGTGTTTGGGTCG 57.824 39.130 0.00 0.00 0.00 4.79
2176 2593 4.641094 TCTGTTTATTTGTGTTTGGGTCGT 59.359 37.500 0.00 0.00 0.00 4.34
2177 2594 4.922719 TGTTTATTTGTGTTTGGGTCGTC 58.077 39.130 0.00 0.00 0.00 4.20
2178 2595 4.398358 TGTTTATTTGTGTTTGGGTCGTCA 59.602 37.500 0.00 0.00 0.00 4.35
2179 2596 4.822036 TTATTTGTGTTTGGGTCGTCAG 57.178 40.909 0.00 0.00 0.00 3.51
2219 2744 4.165372 TCCTGAGTTTGGAACTTTGTACCT 59.835 41.667 0.00 0.00 43.03 3.08
2231 2756 9.092338 TGGAACTTTGTACCTCTAAATGTACTA 57.908 33.333 0.00 0.00 38.48 1.82
2277 2804 8.262227 AGACTACATCCCGTAAAACAATGAATA 58.738 33.333 0.00 0.00 0.00 1.75
2311 4645 3.994931 AAGTTACCATCCCACAGTACC 57.005 47.619 0.00 0.00 0.00 3.34
2318 4652 3.263425 ACCATCCCACAGTACCAAGTAAG 59.737 47.826 0.00 0.00 0.00 2.34
2358 4694 0.329261 TCCATCCAGGAGCCAAAGTG 59.671 55.000 0.00 0.00 43.07 3.16
2366 4702 3.624777 CAGGAGCCAAAGTGAACCATAT 58.375 45.455 0.00 0.00 0.00 1.78
2375 4711 8.253113 AGCCAAAGTGAACCATATTTTTAGATG 58.747 33.333 0.00 0.00 0.00 2.90
2408 4745 4.290093 ACCCAAGATACATCAGCTACTGA 58.710 43.478 0.00 0.00 44.99 3.41
2415 4752 3.601443 ACATCAGCTACTGAACTGTCC 57.399 47.619 0.74 0.00 44.04 4.02
2423 4760 3.306780 GCTACTGAACTGTCCTGCCTAAA 60.307 47.826 0.00 0.00 0.00 1.85
2425 4762 3.744660 ACTGAACTGTCCTGCCTAAAAG 58.255 45.455 0.00 0.00 0.00 2.27
2438 4775 5.385509 TGCCTAAAAGAAACAGTTATGCC 57.614 39.130 0.00 0.00 0.00 4.40
2439 4776 4.830046 TGCCTAAAAGAAACAGTTATGCCA 59.170 37.500 0.00 0.00 0.00 4.92
2442 4779 3.942130 AAAGAAACAGTTATGCCAGCC 57.058 42.857 0.00 0.00 0.00 4.85
2448 4786 5.366768 AGAAACAGTTATGCCAGCCTATAGA 59.633 40.000 0.00 0.00 0.00 1.98
2461 4799 9.806448 TGCCAGCCTATAGAATATAAATTTGAA 57.194 29.630 0.00 0.00 0.00 2.69
2527 4871 2.016318 CACAACTCACCTCAAGTGCAA 58.984 47.619 0.00 0.00 46.81 4.08
2528 4872 2.032550 CACAACTCACCTCAAGTGCAAG 59.967 50.000 0.00 0.00 46.81 4.01
2529 4873 1.605710 CAACTCACCTCAAGTGCAAGG 59.394 52.381 0.37 0.37 46.81 3.61
2580 4925 4.271776 AGTGCAGTAAAAGACCGTTTGTAC 59.728 41.667 0.00 0.00 0.00 2.90
2617 5002 8.948631 TCAGAGTTGAACATTAGAATCCATAC 57.051 34.615 0.00 0.00 0.00 2.39
2632 5017 8.006298 AGAATCCATACTATGCTCTACTATGC 57.994 38.462 0.00 0.00 0.00 3.14
2806 5194 3.895656 TCCAAGGTTATCTATCTCCACGG 59.104 47.826 0.00 0.00 0.00 4.94
2807 5195 3.641906 CCAAGGTTATCTATCTCCACGGT 59.358 47.826 0.00 0.00 0.00 4.83
2860 5253 4.081198 ACTCTGCTCTTCAAAGATACTGGG 60.081 45.833 0.00 0.00 33.93 4.45
2898 5291 7.495606 CAGTACATTGGTAAAGCAGTCATCATA 59.504 37.037 0.00 0.00 0.00 2.15
2899 5292 8.213679 AGTACATTGGTAAAGCAGTCATCATAT 58.786 33.333 0.00 0.00 0.00 1.78
2900 5293 7.502120 ACATTGGTAAAGCAGTCATCATATC 57.498 36.000 0.00 0.00 0.00 1.63
2901 5294 7.056006 ACATTGGTAAAGCAGTCATCATATCA 58.944 34.615 0.00 0.00 0.00 2.15
2902 5295 7.722728 ACATTGGTAAAGCAGTCATCATATCAT 59.277 33.333 0.00 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.178932 AGGTGGGTCACTAGTGCAGA 60.179 55.000 18.45 0.00 34.40 4.26
1 2 0.036952 CAGGTGGGTCACTAGTGCAG 60.037 60.000 18.45 0.00 34.40 4.41
2 3 0.471022 TCAGGTGGGTCACTAGTGCA 60.471 55.000 18.45 7.76 34.40 4.57
3 4 0.905357 ATCAGGTGGGTCACTAGTGC 59.095 55.000 18.45 12.70 34.40 4.40
4 5 1.406069 GCATCAGGTGGGTCACTAGTG 60.406 57.143 17.17 17.17 34.40 2.74
5 6 0.905357 GCATCAGGTGGGTCACTAGT 59.095 55.000 0.00 0.00 34.40 2.57
6 7 1.198713 AGCATCAGGTGGGTCACTAG 58.801 55.000 0.00 0.00 34.40 2.57
7 8 1.278985 CAAGCATCAGGTGGGTCACTA 59.721 52.381 0.00 0.00 34.40 2.74
8 9 0.037303 CAAGCATCAGGTGGGTCACT 59.963 55.000 0.00 0.00 34.40 3.41
9 10 1.589716 GCAAGCATCAGGTGGGTCAC 61.590 60.000 0.00 0.00 0.00 3.67
10 11 1.303561 GCAAGCATCAGGTGGGTCA 60.304 57.895 0.00 0.00 0.00 4.02
11 12 0.610232 AAGCAAGCATCAGGTGGGTC 60.610 55.000 0.00 0.00 0.00 4.46
12 13 0.698238 TAAGCAAGCATCAGGTGGGT 59.302 50.000 0.00 0.00 0.00 4.51
13 14 1.952296 GATAAGCAAGCATCAGGTGGG 59.048 52.381 0.00 0.00 0.00 4.61
14 15 1.952296 GGATAAGCAAGCATCAGGTGG 59.048 52.381 0.00 0.00 0.00 4.61
48 50 8.823220 ACATTACAGGATTAGCCAGTTAAAAT 57.177 30.769 0.00 0.00 37.58 1.82
107 109 5.782047 CCATGTCAAATTAAACCTCTGCAA 58.218 37.500 0.00 0.00 0.00 4.08
108 110 4.321899 GCCATGTCAAATTAAACCTCTGCA 60.322 41.667 0.00 0.00 0.00 4.41
116 118 3.883830 ATGCGGCCATGTCAAATTAAA 57.116 38.095 2.24 0.00 0.00 1.52
117 119 4.582240 TCATATGCGGCCATGTCAAATTAA 59.418 37.500 2.24 0.00 32.85 1.40
118 120 4.140536 TCATATGCGGCCATGTCAAATTA 58.859 39.130 2.24 0.00 32.85 1.40
119 121 2.957680 TCATATGCGGCCATGTCAAATT 59.042 40.909 2.24 0.00 32.85 1.82
133 135 6.148480 CCCTACTTAAATGACTGCTCATATGC 59.852 42.308 0.00 0.00 35.96 3.14
139 141 3.623510 GTGCCCTACTTAAATGACTGCTC 59.376 47.826 0.00 0.00 0.00 4.26
141 143 3.343617 TGTGCCCTACTTAAATGACTGC 58.656 45.455 0.00 0.00 0.00 4.40
142 144 5.647658 TGAATGTGCCCTACTTAAATGACTG 59.352 40.000 0.00 0.00 0.00 3.51
144 146 5.648092 ACTGAATGTGCCCTACTTAAATGAC 59.352 40.000 0.00 0.00 0.00 3.06
145 147 5.815581 ACTGAATGTGCCCTACTTAAATGA 58.184 37.500 0.00 0.00 0.00 2.57
146 148 7.047891 TCTACTGAATGTGCCCTACTTAAATG 58.952 38.462 0.00 0.00 0.00 2.32
147 149 7.195374 TCTACTGAATGTGCCCTACTTAAAT 57.805 36.000 0.00 0.00 0.00 1.40
148 150 6.614694 TCTACTGAATGTGCCCTACTTAAA 57.385 37.500 0.00 0.00 0.00 1.52
149 151 6.212791 ACTTCTACTGAATGTGCCCTACTTAA 59.787 38.462 0.00 0.00 0.00 1.85
150 152 5.720041 ACTTCTACTGAATGTGCCCTACTTA 59.280 40.000 0.00 0.00 0.00 2.24
156 158 1.740025 GCACTTCTACTGAATGTGCCC 59.260 52.381 15.51 0.00 43.35 5.36
165 167 4.012319 GCATGTTCATGCACTTCTACTG 57.988 45.455 26.29 0.00 46.25 2.74
188 191 1.270550 CCTCTCACGCCAAGCAAAATT 59.729 47.619 0.00 0.00 0.00 1.82
199 202 2.593346 ATGAAGATGTCCTCTCACGC 57.407 50.000 0.00 0.00 31.03 5.34
201 204 6.463995 ACTTCTATGAAGATGTCCTCTCAC 57.536 41.667 13.42 0.00 35.76 3.51
206 209 6.098838 TGCACATACTTCTATGAAGATGTCCT 59.901 38.462 13.42 0.00 39.89 3.85
208 211 6.201806 GGTGCACATACTTCTATGAAGATGTC 59.798 42.308 20.43 11.48 39.89 3.06
210 213 6.286758 AGGTGCACATACTTCTATGAAGATG 58.713 40.000 20.43 13.24 34.77 2.90
211 214 6.491714 AGGTGCACATACTTCTATGAAGAT 57.508 37.500 20.43 1.64 34.77 2.40
215 218 9.542462 GTTTATAAGGTGCACATACTTCTATGA 57.458 33.333 20.43 0.00 34.77 2.15
256 259 0.531090 TGAAAGCCCGCGCGTAATAT 60.531 50.000 29.95 11.88 41.18 1.28
257 260 1.149361 CTGAAAGCCCGCGCGTAATA 61.149 55.000 29.95 7.07 41.18 0.98
295 298 6.010219 AGTTGGTGCCTACAGATTTGTTTAT 58.990 36.000 0.00 0.00 38.76 1.40
300 303 2.749621 GGAGTTGGTGCCTACAGATTTG 59.250 50.000 5.68 0.00 0.00 2.32
306 309 6.614087 ACTTATATTAGGAGTTGGTGCCTACA 59.386 38.462 5.68 0.00 36.53 2.74
327 330 3.199677 GGCCACATGTTGCGTATACTTA 58.800 45.455 15.06 0.00 0.00 2.24
334 337 0.740149 CATATGGCCACATGTTGCGT 59.260 50.000 16.25 9.25 37.97 5.24
335 338 0.595567 GCATATGGCCACATGTTGCG 60.596 55.000 24.51 0.00 37.61 4.85
346 349 2.758736 TTTGGTTTGGTGCATATGGC 57.241 45.000 4.56 0.00 45.13 4.40
349 352 6.788598 TCATGTATTTGGTTTGGTGCATAT 57.211 33.333 0.00 0.00 0.00 1.78
356 359 7.492344 GGAAGCTAATTCATGTATTTGGTTTGG 59.508 37.037 18.99 0.00 39.91 3.28
358 361 8.253113 CAGGAAGCTAATTCATGTATTTGGTTT 58.747 33.333 18.99 10.47 43.19 3.27
378 381 0.478507 AGGTTTGGTGTCCCAGGAAG 59.521 55.000 0.00 0.00 43.15 3.46
383 386 1.150536 GCTCAGGTTTGGTGTCCCA 59.849 57.895 0.00 0.00 39.65 4.37
386 389 3.412386 AGTATTGCTCAGGTTTGGTGTC 58.588 45.455 0.00 0.00 0.00 3.67
387 390 3.412386 GAGTATTGCTCAGGTTTGGTGT 58.588 45.455 0.00 0.00 43.58 4.16
388 391 2.416547 CGAGTATTGCTCAGGTTTGGTG 59.583 50.000 2.63 0.00 44.33 4.17
389 392 2.615493 CCGAGTATTGCTCAGGTTTGGT 60.615 50.000 2.63 0.00 44.33 3.67
390 393 2.009774 CCGAGTATTGCTCAGGTTTGG 58.990 52.381 2.63 0.00 44.33 3.28
391 394 2.699954 ACCGAGTATTGCTCAGGTTTG 58.300 47.619 10.71 0.00 43.42 2.93
394 397 2.354805 GGAAACCGAGTATTGCTCAGGT 60.355 50.000 10.71 10.71 45.80 4.00
396 399 2.932614 CTGGAAACCGAGTATTGCTCAG 59.067 50.000 2.63 0.00 44.33 3.35
397 400 2.935238 GCTGGAAACCGAGTATTGCTCA 60.935 50.000 2.63 0.00 44.33 4.26
398 401 1.666189 GCTGGAAACCGAGTATTGCTC 59.334 52.381 0.00 0.00 40.77 4.26
399 402 1.003118 TGCTGGAAACCGAGTATTGCT 59.997 47.619 0.00 0.00 0.00 3.91
400 403 1.398390 CTGCTGGAAACCGAGTATTGC 59.602 52.381 0.00 0.00 0.00 3.56
420 425 3.244249 ACTGACAGTTCCTAGCAAACCTC 60.244 47.826 1.07 0.88 0.00 3.85
424 429 6.109156 TCATAACTGACAGTTCCTAGCAAA 57.891 37.500 23.79 4.92 39.51 3.68
431 436 5.293079 GCATCTCTTCATAACTGACAGTTCC 59.707 44.000 23.79 0.00 39.51 3.62
435 440 6.104665 TCAAGCATCTCTTCATAACTGACAG 58.895 40.000 0.00 0.00 31.27 3.51
437 442 6.036953 CCTTCAAGCATCTCTTCATAACTGAC 59.963 42.308 0.00 0.00 31.27 3.51
440 445 6.059787 ACCTTCAAGCATCTCTTCATAACT 57.940 37.500 0.00 0.00 31.27 2.24
497 502 1.668151 GAGGCCCGTCCGATTATGC 60.668 63.158 0.00 0.00 40.77 3.14
498 503 0.321671 ATGAGGCCCGTCCGATTATG 59.678 55.000 0.00 0.00 40.77 1.90
505 510 2.052782 AATACAAATGAGGCCCGTCC 57.947 50.000 0.00 0.00 0.00 4.79
506 511 3.694566 AGAAAATACAAATGAGGCCCGTC 59.305 43.478 0.00 0.00 0.00 4.79
532 537 9.284968 TCTCTATACGAGACATCATGTTAATCA 57.715 33.333 0.00 0.00 43.72 2.57
544 549 8.186941 AGGAGACTAGGATCTCTATACGAGACA 61.187 44.444 9.53 0.00 45.86 3.41
546 551 6.153851 CAGGAGACTAGGATCTCTATACGAGA 59.846 46.154 9.53 4.91 46.73 4.04
547 552 6.070995 ACAGGAGACTAGGATCTCTATACGAG 60.071 46.154 9.53 0.00 44.01 4.18
548 553 5.781306 ACAGGAGACTAGGATCTCTATACGA 59.219 44.000 9.53 0.00 44.01 3.43
549 554 6.045072 ACAGGAGACTAGGATCTCTATACG 57.955 45.833 9.53 0.00 44.01 3.06
550 555 9.969001 ATTTACAGGAGACTAGGATCTCTATAC 57.031 37.037 9.53 0.00 44.01 1.47
554 559 8.900802 AGATATTTACAGGAGACTAGGATCTCT 58.099 37.037 9.53 0.00 44.01 3.10
556 561 9.308000 CAAGATATTTACAGGAGACTAGGATCT 57.692 37.037 0.00 0.00 40.21 2.75
557 562 9.084533 ACAAGATATTTACAGGAGACTAGGATC 57.915 37.037 0.00 0.00 40.21 3.36
559 564 9.352191 GTACAAGATATTTACAGGAGACTAGGA 57.648 37.037 0.00 0.00 40.21 2.94
560 565 9.132923 TGTACAAGATATTTACAGGAGACTAGG 57.867 37.037 0.00 0.00 40.21 3.02
561 566 9.953697 GTGTACAAGATATTTACAGGAGACTAG 57.046 37.037 0.00 0.00 40.21 2.57
564 569 8.997621 TTGTGTACAAGATATTTACAGGAGAC 57.002 34.615 0.00 0.00 0.00 3.36
570 575 9.607988 CCCAGTATTGTGTACAAGATATTTACA 57.392 33.333 0.00 0.00 39.47 2.41
571 576 9.826574 TCCCAGTATTGTGTACAAGATATTTAC 57.173 33.333 0.00 0.81 39.47 2.01
573 578 8.768397 TCTCCCAGTATTGTGTACAAGATATTT 58.232 33.333 0.00 0.00 39.47 1.40
574 579 8.319057 TCTCCCAGTATTGTGTACAAGATATT 57.681 34.615 0.00 0.00 39.47 1.28
575 580 7.914427 TCTCCCAGTATTGTGTACAAGATAT 57.086 36.000 0.00 0.00 39.47 1.63
576 581 7.727578 TTCTCCCAGTATTGTGTACAAGATA 57.272 36.000 0.00 0.00 39.47 1.98
577 582 6.620877 TTCTCCCAGTATTGTGTACAAGAT 57.379 37.500 0.00 0.00 39.47 2.40
578 583 6.428083 TTTCTCCCAGTATTGTGTACAAGA 57.572 37.500 0.00 0.00 39.47 3.02
579 584 7.504924 TTTTTCTCCCAGTATTGTGTACAAG 57.495 36.000 0.00 0.00 39.47 3.16
612 617 3.750639 TTTTGTTTCGCAAACTCTCGT 57.249 38.095 11.34 0.00 45.70 4.18
634 639 3.576982 TGTCGGTACAGTGGATTTCTTCT 59.423 43.478 0.00 0.00 0.00 2.85
635 640 3.921677 TGTCGGTACAGTGGATTTCTTC 58.078 45.455 0.00 0.00 0.00 2.87
646 651 0.528924 TCGGTCCATTGTCGGTACAG 59.471 55.000 0.00 0.00 36.83 2.74
722 727 8.129211 ACTCAGAACTTTAAACATTGCTGTAAC 58.871 33.333 0.00 0.00 33.36 2.50
762 768 6.153067 CACTCGTCTAGAAGTTGACAAGAAT 58.847 40.000 5.55 0.00 33.18 2.40
765 771 3.670991 GCACTCGTCTAGAAGTTGACAAG 59.329 47.826 5.55 0.00 33.18 3.16
768 785 2.981140 GTGCACTCGTCTAGAAGTTGAC 59.019 50.000 10.32 0.00 0.00 3.18
805 822 1.021390 AGCTAGCGTGATGTGCAACC 61.021 55.000 9.55 0.00 34.36 3.77
833 850 1.745489 GGGGATCACTGTCGGTTGC 60.745 63.158 0.00 0.00 0.00 4.17
853 870 3.117171 CTCTGTGCCTGCGAGTGC 61.117 66.667 0.00 0.00 43.20 4.40
879 896 7.544566 AGTGTATGTCGGAAGTGTAGTTAATTG 59.455 37.037 0.00 0.00 0.00 2.32
902 1165 4.696877 TGATTAGCAAAGGACATGTGAGTG 59.303 41.667 1.15 0.00 0.00 3.51
958 1225 1.198713 CAGTAGCCAGTGGAGTGGAT 58.801 55.000 15.20 0.21 40.44 3.41
1063 1331 4.974721 CAGGGTGGGGCGCTTGTT 62.975 66.667 7.64 0.00 38.41 2.83
1075 1343 3.063084 GTCGTCGGAGAGCAGGGT 61.063 66.667 0.00 0.00 36.95 4.34
1458 1843 0.389948 GTCTGGGCGTGAAGTTCGAT 60.390 55.000 0.00 0.00 0.00 3.59
1476 1861 1.360194 CCGCAGAGTACTCGACGAGT 61.360 60.000 31.23 31.23 45.54 4.18
2043 2458 4.926140 TTGTCACTCATCATCGAGCTAT 57.074 40.909 0.00 0.00 36.42 2.97
2116 2532 5.912892 ACAACAAAATTTGTACTCCCCTTG 58.087 37.500 12.11 6.58 44.59 3.61
2124 2540 7.006537 CACACACACAACAACAAAATTTGTAC 58.993 34.615 12.11 0.00 44.59 2.90
2127 2543 5.380651 CCACACACACAACAACAAAATTTG 58.619 37.500 3.89 3.89 0.00 2.32
2172 2589 5.299782 AGGTTCTAAGATCCATACTGACGAC 59.700 44.000 0.00 0.00 0.00 4.34
2175 2592 5.836358 AGGAGGTTCTAAGATCCATACTGAC 59.164 44.000 0.00 0.00 34.08 3.51
2176 2593 5.835819 CAGGAGGTTCTAAGATCCATACTGA 59.164 44.000 0.00 0.00 34.08 3.41
2177 2594 5.835819 TCAGGAGGTTCTAAGATCCATACTG 59.164 44.000 0.00 0.00 34.08 2.74
2178 2595 6.031964 TCAGGAGGTTCTAAGATCCATACT 57.968 41.667 0.00 0.00 34.08 2.12
2179 2596 5.836358 ACTCAGGAGGTTCTAAGATCCATAC 59.164 44.000 0.83 0.00 34.08 2.39
2250 2775 6.103997 TCATTGTTTTACGGGATGTAGTCTC 58.896 40.000 0.00 0.00 33.75 3.36
2293 2820 3.008704 ACTTGGTACTGTGGGATGGTAAC 59.991 47.826 0.00 0.00 0.00 2.50
2311 4645 7.849804 ACTGGTAATATCAGTTGCTTACTTG 57.150 36.000 0.00 0.00 42.17 3.16
2318 4652 7.801716 TGGAATTACTGGTAATATCAGTTGC 57.198 36.000 11.81 0.13 42.17 4.17
2349 4685 7.775053 TCTAAAAATATGGTTCACTTTGGCT 57.225 32.000 0.00 0.00 0.00 4.75
2392 4729 5.068460 AGGACAGTTCAGTAGCTGATGTATC 59.932 44.000 0.00 3.15 40.39 2.24
2408 4745 4.532834 TGTTTCTTTTAGGCAGGACAGTT 58.467 39.130 0.00 0.00 0.00 3.16
2415 4752 5.048083 TGGCATAACTGTTTCTTTTAGGCAG 60.048 40.000 0.00 0.00 34.88 4.85
2423 4760 3.160679 AGGCTGGCATAACTGTTTCTT 57.839 42.857 3.38 0.00 0.00 2.52
2425 4762 5.611374 TCTATAGGCTGGCATAACTGTTTC 58.389 41.667 3.38 0.00 0.00 2.78
2461 4799 6.601613 TGGACATTCTTCTTGTAAACACAAGT 59.398 34.615 15.12 0.00 45.26 3.16
2462 4800 7.026631 TGGACATTCTTCTTGTAAACACAAG 57.973 36.000 10.56 10.56 46.11 3.16
2471 4810 5.011329 ACATTGCAATGGACATTCTTCTTGT 59.989 36.000 35.85 14.33 40.70 3.16
2472 4811 5.475719 ACATTGCAATGGACATTCTTCTTG 58.524 37.500 35.85 13.72 40.70 3.02
2480 4819 4.771577 TCAGGTTTACATTGCAATGGACAT 59.228 37.500 35.85 26.20 40.70 3.06
2528 4872 7.285858 ACTGAAGAAGTAGGTGTCTGATATACC 59.714 40.741 0.00 0.00 37.36 2.73
2529 4873 8.228035 ACTGAAGAAGTAGGTGTCTGATATAC 57.772 38.462 0.00 0.00 37.36 1.47
2580 4925 7.026631 TGTTCAACTCTGATTAAACAGGTTG 57.973 36.000 24.74 24.74 42.76 3.77
2611 4993 6.721668 ACAAGCATAGTAGAGCATAGTATGGA 59.278 38.462 18.29 0.00 33.57 3.41
2613 4995 9.914131 TTTACAAGCATAGTAGAGCATAGTATG 57.086 33.333 14.84 14.84 35.18 2.39
2617 5002 7.661968 TCCTTTACAAGCATAGTAGAGCATAG 58.338 38.462 0.87 0.00 0.00 2.23
2632 5017 5.875359 GGAGGTCATAGTGTTCCTTTACAAG 59.125 44.000 0.00 0.00 0.00 3.16
2690 5076 8.815141 TGAATTTTAATTGGTGATGTCAGTTG 57.185 30.769 0.00 0.00 0.00 3.16
2691 5077 8.859090 TCTGAATTTTAATTGGTGATGTCAGTT 58.141 29.630 0.00 0.00 0.00 3.16
2860 5253 3.191371 CCAATGTACTGAAAGGTTGGAGC 59.809 47.826 0.00 0.00 38.04 4.70
2898 5291 9.678260 GGAAGATTTAGAAGGCATATGTATGAT 57.322 33.333 4.29 0.00 35.75 2.45
2899 5292 8.659527 TGGAAGATTTAGAAGGCATATGTATGA 58.340 33.333 4.29 0.00 35.75 2.15
2900 5293 8.853077 TGGAAGATTTAGAAGGCATATGTATG 57.147 34.615 4.29 0.00 36.78 2.39
2901 5294 9.458727 CATGGAAGATTTAGAAGGCATATGTAT 57.541 33.333 4.29 0.00 0.00 2.29
2902 5295 7.391554 GCATGGAAGATTTAGAAGGCATATGTA 59.608 37.037 4.29 0.00 0.00 2.29
2988 5381 8.066612 TCAGAAAAACCTTCATGAAGTTTTCT 57.933 30.769 34.32 34.32 44.97 2.52
2989 5382 8.702163 TTCAGAAAAACCTTCATGAAGTTTTC 57.298 30.769 32.40 32.40 40.23 2.29


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

AutoCloner maintained by Alex Coulton.