Multiple sequence alignment - TraesCS2A01G543000

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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 TraesCS2A01G543000 chr2A 100.000 4448 0 0 1 4448 753255986 753251539 0.000000e+00 8215.0
1 TraesCS2A01G543000 chr2A 78.512 484 75 18 1 464 753402752 753402278 1.570000e-74 291.0
2 TraesCS2A01G543000 chr2A 84.049 163 13 8 1792 1951 753253883 753253731 1.290000e-30 145.0
3 TraesCS2A01G543000 chr2A 84.049 163 13 8 2104 2256 753254195 753254036 1.290000e-30 145.0
4 TraesCS2A01G543000 chr2A 84.496 129 17 3 2127 2253 515483544 515483417 1.680000e-24 124.0
5 TraesCS2A01G543000 chr2A 82.203 118 10 5 1833 1948 515483525 515483417 1.700000e-14 91.6
6 TraesCS2A01G543000 chr2B 89.210 3698 223 58 816 4389 762506002 762502357 0.000000e+00 4457.0
7 TraesCS2A01G543000 chr2B 91.614 787 41 7 1 767 762506937 762506156 0.000000e+00 1064.0
8 TraesCS2A01G543000 chr2B 79.741 464 71 15 1 444 762915721 762915261 9.290000e-82 315.0
9 TraesCS2A01G543000 chr2B 75.929 619 89 35 28 611 762789765 762789172 3.410000e-66 263.0
10 TraesCS2A01G543000 chr2B 77.062 497 71 24 29 491 762885311 762884824 3.440000e-61 246.0
11 TraesCS2A01G543000 chr2B 84.937 239 25 7 29 256 762793611 762793373 9.620000e-57 231.0
12 TraesCS2A01G543000 chr2B 88.971 136 15 0 2121 2256 762504972 762504837 7.650000e-38 169.0
13 TraesCS2A01G543000 chr2B 85.276 163 11 8 1792 1951 762504684 762504532 5.960000e-34 156.0
14 TraesCS2A01G543000 chr2D 91.762 2707 124 32 824 3453 621550143 621547459 0.000000e+00 3672.0
15 TraesCS2A01G543000 chr2D 87.545 827 56 19 1 794 621551115 621550303 0.000000e+00 913.0
16 TraesCS2A01G543000 chr2D 88.587 368 29 5 3501 3866 621547163 621546807 6.830000e-118 435.0
17 TraesCS2A01G543000 chr2D 94.163 257 15 0 4133 4389 621546014 621545758 4.170000e-105 392.0
18 TraesCS2A01G543000 chr2D 91.600 250 20 1 3886 4134 621546290 621546041 1.180000e-90 344.0
19 TraesCS2A01G543000 chr2D 89.804 255 25 1 1 254 499308785 499309039 4.290000e-85 326.0
20 TraesCS2A01G543000 chr2D 83.626 342 25 12 439 770 499309065 499309385 4.350000e-75 292.0
21 TraesCS2A01G543000 chr2D 83.436 163 14 8 1792 1951 621548847 621548695 6.000000e-29 139.0
22 TraesCS2A01G543000 chr2D 87.500 120 13 2 2132 2250 166797522 166797640 2.160000e-28 137.0
23 TraesCS2A01G543000 chr2D 82.099 162 18 6 2104 2256 621549159 621549000 1.300000e-25 128.0
24 TraesCS2A01G543000 chr2D 83.077 130 10 5 1818 1945 166797521 166797640 1.690000e-19 108.0
25 TraesCS2A01G543000 chr4A 89.412 255 26 1 1 254 153777501 153777247 2.000000e-83 320.0
26 TraesCS2A01G543000 chr1D 84.916 179 22 5 2151 2328 415318184 415318358 4.570000e-40 176.0
27 TraesCS2A01G543000 chr1D 88.060 67 6 2 1837 1902 415318182 415318247 1.330000e-10 78.7
28 TraesCS2A01G543000 chr7D 87.500 104 9 4 2157 2259 63466786 63466686 2.810000e-22 117.0
29 TraesCS2A01G543000 chr7D 95.161 62 3 0 4387 4448 579148808 579148747 1.020000e-16 99.0
30 TraesCS2A01G543000 chr7D 95.000 60 3 0 4388 4447 552141033 552141092 1.320000e-15 95.3
31 TraesCS2A01G543000 chr7D 95.000 60 3 0 4388 4447 552154023 552154082 1.320000e-15 95.3
32 TraesCS2A01G543000 chr6B 95.082 61 3 0 4388 4448 471881981 471882041 3.660000e-16 97.1
33 TraesCS2A01G543000 chr6B 93.651 63 4 0 4386 4448 667078339 667078401 1.320000e-15 95.3
34 TraesCS2A01G543000 chr3B 95.082 61 3 0 4388 4448 246441489 246441429 3.660000e-16 97.1
35 TraesCS2A01G543000 chr1B 93.750 64 4 0 4385 4448 140295033 140295096 3.660000e-16 97.1
36 TraesCS2A01G543000 chr7B 93.548 62 4 0 4387 4448 677714395 677714456 4.740000e-15 93.5
37 TraesCS2A01G543000 chr1A 93.548 62 4 0 4387 4448 222038608 222038547 4.740000e-15 93.5


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 TraesCS2A01G543000 chr2A 753251539 753255986 4447 True 2835.000000 8215 89.36600 1 4448 3 chr2A.!!$R3 4447
1 TraesCS2A01G543000 chr2B 762502357 762506937 4580 True 1461.500000 4457 88.76775 1 4389 4 chr2B.!!$R3 4388
2 TraesCS2A01G543000 chr2B 762789172 762793611 4439 True 247.000000 263 80.43300 28 611 2 chr2B.!!$R4 583
3 TraesCS2A01G543000 chr2D 621545758 621551115 5357 True 860.428571 3672 88.45600 1 4389 7 chr2D.!!$R1 4388
4 TraesCS2A01G543000 chr2D 499308785 499309385 600 False 309.000000 326 86.71500 1 770 2 chr2D.!!$F2 769

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
457 504 0.388520 CTGCAAGACCGTCGTCATCA 60.389 55.0 0.0 0.0 41.87 3.07 F
1199 3249 0.400213 TCACAGCCCCATCGAAGTTT 59.600 50.0 0.0 0.0 0.00 2.66 F
2595 5235 0.543277 CCAGTGCTGCCTCTTGGATA 59.457 55.0 0.0 0.0 34.57 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1346 3426 0.325296 ATACAAGCGGGAGGGACTGA 60.325 55.0 0.0 0.0 41.55 3.41 R
2711 5370 1.494824 AGCGTCGTTGACTGGTTAAC 58.505 50.0 0.0 0.0 0.00 2.01 R
4131 7576 0.608035 TCAATCAAACTGCCCGGTCC 60.608 55.0 0.0 0.0 0.00 4.46 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
106 108 7.823745 AAATATATTTCGTGGCTGAATCCTT 57.176 32.000 4.81 0.00 0.00 3.36
122 124 7.048629 TGAATCCTTTTGCAAATGTCTTGTA 57.951 32.000 13.65 0.00 0.00 2.41
265 278 4.458989 TGCGAATTCAAGGTGCTAGAAAAT 59.541 37.500 6.22 0.00 0.00 1.82
301 322 2.270352 ACCGTTGAATTGGAGCTTCA 57.730 45.000 0.00 0.00 0.00 3.02
421 468 5.262009 TGGATATTCGATCGTCTAGGGATT 58.738 41.667 15.94 0.00 0.00 3.01
448 495 0.514691 GAACTGAAGCTGCAAGACCG 59.485 55.000 1.02 0.00 34.07 4.79
457 504 0.388520 CTGCAAGACCGTCGTCATCA 60.389 55.000 0.00 0.00 41.87 3.07
568 625 6.525578 ACGTGACCTGAATCTCAGTTTATA 57.474 37.500 3.15 0.00 42.80 0.98
591 648 1.666888 GCCACACGAATGCTTTGGAAG 60.667 52.381 1.30 0.00 0.00 3.46
592 649 1.879380 CCACACGAATGCTTTGGAAGA 59.121 47.619 1.30 0.00 0.00 2.87
717 811 3.616821 TCTGTTATTCGTTGATGCTTCGG 59.383 43.478 0.00 0.00 0.00 4.30
788 890 9.230122 TGTTCTCTTATTCATGTTATCTTTGCA 57.770 29.630 0.00 0.00 0.00 4.08
794 896 9.162793 CTTATTCATGTTATCTTTGCAATCGTC 57.837 33.333 0.00 0.00 0.00 4.20
813 2495 6.994868 TCGTCAAAATCGGGTAAATTTTTG 57.005 33.333 0.00 0.00 39.33 2.44
814 2496 5.402867 TCGTCAAAATCGGGTAAATTTTTGC 59.597 36.000 0.00 0.00 38.38 3.68
842 2586 4.846779 TTGGCAGTGATTTTTCTACCAC 57.153 40.909 0.00 0.00 28.19 4.16
843 2587 4.098914 TGGCAGTGATTTTTCTACCACT 57.901 40.909 0.00 0.00 40.15 4.00
932 2676 1.139947 GTCCGCTTCCTCTTCTCCG 59.860 63.158 0.00 0.00 0.00 4.63
1196 3246 1.811266 CGTCACAGCCCCATCGAAG 60.811 63.158 0.00 0.00 0.00 3.79
1199 3249 0.400213 TCACAGCCCCATCGAAGTTT 59.600 50.000 0.00 0.00 0.00 2.66
1200 3250 1.202879 TCACAGCCCCATCGAAGTTTT 60.203 47.619 0.00 0.00 0.00 2.43
1201 3251 1.613437 CACAGCCCCATCGAAGTTTTT 59.387 47.619 0.00 0.00 0.00 1.94
1202 3252 1.613437 ACAGCCCCATCGAAGTTTTTG 59.387 47.619 0.00 0.00 0.00 2.44
1209 3259 2.231235 CCATCGAAGTTTTTGGGGGAAG 59.769 50.000 0.00 0.00 0.00 3.46
1213 3263 1.691976 GAAGTTTTTGGGGGAAGGGTG 59.308 52.381 0.00 0.00 0.00 4.61
1219 3269 3.327404 GGGGGAAGGGTGCTTCGA 61.327 66.667 0.00 0.00 34.37 3.71
1226 3276 2.632377 GAAGGGTGCTTCGATTCATCA 58.368 47.619 0.00 0.00 0.00 3.07
1231 3281 5.192927 AGGGTGCTTCGATTCATCAAATTA 58.807 37.500 0.00 0.00 0.00 1.40
1232 3282 5.297776 AGGGTGCTTCGATTCATCAAATTAG 59.702 40.000 0.00 0.00 0.00 1.73
1233 3283 4.972440 GGTGCTTCGATTCATCAAATTAGC 59.028 41.667 0.00 0.00 32.03 3.09
1235 3285 6.204359 GTGCTTCGATTCATCAAATTAGCAT 58.796 36.000 3.63 0.00 38.10 3.79
1236 3286 6.359087 GTGCTTCGATTCATCAAATTAGCATC 59.641 38.462 3.63 0.00 38.10 3.91
1238 3288 6.359087 GCTTCGATTCATCAAATTAGCATCAC 59.641 38.462 0.00 0.00 31.85 3.06
1239 3289 6.304356 TCGATTCATCAAATTAGCATCACC 57.696 37.500 0.00 0.00 0.00 4.02
1240 3290 6.057533 TCGATTCATCAAATTAGCATCACCT 58.942 36.000 0.00 0.00 0.00 4.00
1241 3291 6.017687 TCGATTCATCAAATTAGCATCACCTG 60.018 38.462 0.00 0.00 0.00 4.00
1242 3292 6.017687 CGATTCATCAAATTAGCATCACCTGA 60.018 38.462 0.00 0.00 0.00 3.86
1243 3293 7.308408 CGATTCATCAAATTAGCATCACCTGAT 60.308 37.037 0.00 0.00 34.56 2.90
1244 3294 7.649533 TTCATCAAATTAGCATCACCTGATT 57.350 32.000 0.00 0.00 31.21 2.57
1245 3295 7.268199 TCATCAAATTAGCATCACCTGATTC 57.732 36.000 0.00 0.00 31.21 2.52
1246 3296 7.058525 TCATCAAATTAGCATCACCTGATTCT 58.941 34.615 0.00 0.00 32.92 2.40
1247 3297 6.688637 TCAAATTAGCATCACCTGATTCTG 57.311 37.500 0.00 0.00 30.90 3.02
1248 3298 6.417258 TCAAATTAGCATCACCTGATTCTGA 58.583 36.000 0.00 0.00 30.90 3.27
1249 3299 6.885918 TCAAATTAGCATCACCTGATTCTGAA 59.114 34.615 0.00 0.00 30.90 3.02
1250 3300 6.939132 AATTAGCATCACCTGATTCTGAAG 57.061 37.500 0.00 0.00 30.90 3.02
1331 3411 2.334977 TCCTTTGAGCCCTGTGAGTTA 58.665 47.619 0.00 0.00 0.00 2.24
1349 3429 4.899502 AGTTAACTCATCAACCCACTCAG 58.100 43.478 1.12 0.00 0.00 3.35
1375 3455 1.636340 CGCTTGTATTCGCGGAAGG 59.364 57.895 6.13 0.00 45.17 3.46
1462 3612 0.977395 AGAGCGGTGTTCTTAAGGCT 59.023 50.000 1.85 1.85 0.00 4.58
1534 4165 4.764679 TCCTGACAACATATTTGTGTGC 57.235 40.909 7.66 0.00 35.83 4.57
1590 4221 7.453393 TGGGTGTTGGATATATTCTGAAGATC 58.547 38.462 0.03 1.64 0.00 2.75
1591 4222 7.072328 TGGGTGTTGGATATATTCTGAAGATCA 59.928 37.037 0.03 0.00 0.00 2.92
1693 4324 0.683504 ATCCGAAGACGCTAGGTGGT 60.684 55.000 0.00 0.00 38.29 4.16
1829 4467 4.253685 AGCGCACAATAACTAGATGTTGT 58.746 39.130 11.47 8.96 39.55 3.32
1860 4498 8.655970 GCTTCAATTTATTGGTTGGTATGAAAC 58.344 33.333 2.85 0.00 38.30 2.78
1984 4623 7.103641 CCTTCTCCTTAGTTTAGCACACAATA 58.896 38.462 0.00 0.00 0.00 1.90
2005 4644 7.335422 ACAATAACAAGATGTGAGGAAGCTTAG 59.665 37.037 0.00 0.00 0.00 2.18
2020 4659 7.639378 AGGAAGCTTAGATTTATTGGTTGGTA 58.361 34.615 0.00 0.00 0.00 3.25
2022 4661 8.914011 GGAAGCTTAGATTTATTGGTTGGTATT 58.086 33.333 0.00 0.00 0.00 1.89
2044 4683 9.601971 GTATTAAATTGAACGCTAGTCAACAAA 57.398 29.630 0.00 0.00 0.00 2.83
2081 4720 5.411361 TGATGTTTATGTACAGCCTTGTCAC 59.589 40.000 0.33 0.00 38.76 3.67
2083 4722 6.104146 TGTTTATGTACAGCCTTGTCACTA 57.896 37.500 0.33 0.00 38.76 2.74
2321 4960 4.223923 CCATACCAAGGATCCCTCATCTAC 59.776 50.000 8.55 0.00 30.89 2.59
2483 5122 3.733337 ACTAGTCTGTGAAAACAGCTGG 58.267 45.455 19.93 0.00 37.63 4.85
2499 5138 4.074970 CAGCTGGAAGACCAAAATGTACT 58.925 43.478 5.57 0.00 46.32 2.73
2508 5148 5.063880 AGACCAAAATGTACTGACCTCAAC 58.936 41.667 0.00 0.00 0.00 3.18
2509 5149 4.787551 ACCAAAATGTACTGACCTCAACA 58.212 39.130 0.00 0.00 0.00 3.33
2512 5152 6.151691 CCAAAATGTACTGACCTCAACATTG 58.848 40.000 6.24 0.00 37.37 2.82
2530 5170 7.384660 TCAACATTGCCAAATGAAATTCACTAC 59.615 33.333 0.00 0.00 45.17 2.73
2595 5235 0.543277 CCAGTGCTGCCTCTTGGATA 59.457 55.000 0.00 0.00 34.57 2.59
2611 5251 8.734386 CCTCTTGGATAAGAAATATGGCAATAC 58.266 37.037 0.00 0.00 42.11 1.89
2666 5314 4.811969 TTACATTTAGGAGGACGAAGCA 57.188 40.909 0.00 0.00 0.00 3.91
2711 5370 9.773328 CTGTTACACCATATCAACTTTTGTATG 57.227 33.333 0.00 0.00 0.00 2.39
2725 5384 6.721321 ACTTTTGTATGTTAACCAGTCAACG 58.279 36.000 2.48 0.00 0.00 4.10
2856 5544 8.565896 AGTGATATGATCTCTGACACTCTATC 57.434 38.462 0.00 0.00 32.84 2.08
2861 5549 7.759489 ATGATCTCTGACACTCTATCCTAAC 57.241 40.000 0.00 0.00 0.00 2.34
2869 5557 6.246163 TGACACTCTATCCTAACAGTCTTGA 58.754 40.000 0.00 0.00 0.00 3.02
2951 5640 6.812656 CAGATTGCAGGCATTTGTTAAACATA 59.187 34.615 0.00 0.00 0.00 2.29
3028 5717 9.160496 AGTAAACTTTGAAGAATGCTAGATGAG 57.840 33.333 0.00 0.00 0.00 2.90
3056 5745 8.616076 CCTTCAATACATGAATAGGAGTTTGAC 58.384 37.037 0.00 0.00 46.62 3.18
3067 5756 9.567776 TGAATAGGAGTTTGACAGTAAATTTGA 57.432 29.630 0.00 0.00 0.00 2.69
3150 5839 3.558931 ATTCTGTGGTCGCATGGAATA 57.441 42.857 0.00 0.00 0.00 1.75
3355 6048 3.636300 GCACATTTATCAGGCATACCCAA 59.364 43.478 0.00 0.00 36.11 4.12
3428 6121 0.765510 AAGGGTCGTCTCAAAGCCTT 59.234 50.000 0.21 0.21 45.95 4.35
3469 6162 3.737172 CTTCAGTTTGGGCCGCCG 61.737 66.667 2.55 0.00 0.00 6.46
3470 6163 4.572571 TTCAGTTTGGGCCGCCGT 62.573 61.111 2.55 0.00 0.00 5.68
3528 6469 3.430374 CCGTACTGAACCTGTATTCCCTG 60.430 52.174 0.00 0.00 0.00 4.45
3556 6500 2.232696 TGATGAACTCGGACGATCCAAA 59.767 45.455 0.00 0.00 35.91 3.28
3574 6518 7.118390 CGATCCAAACTATTCTTGAGACTTTGT 59.882 37.037 0.00 0.00 0.00 2.83
3575 6519 7.730364 TCCAAACTATTCTTGAGACTTTGTC 57.270 36.000 0.00 0.00 0.00 3.18
3576 6520 7.279615 TCCAAACTATTCTTGAGACTTTGTCA 58.720 34.615 0.46 0.00 34.60 3.58
3577 6521 7.939039 TCCAAACTATTCTTGAGACTTTGTCAT 59.061 33.333 0.46 0.00 34.60 3.06
3578 6522 8.019669 CCAAACTATTCTTGAGACTTTGTCATG 58.980 37.037 0.46 0.00 34.60 3.07
3579 6523 6.734104 ACTATTCTTGAGACTTTGTCATGC 57.266 37.500 0.46 0.00 34.60 4.06
3580 6524 6.233434 ACTATTCTTGAGACTTTGTCATGCA 58.767 36.000 0.00 0.00 34.60 3.96
3581 6525 4.818534 TTCTTGAGACTTTGTCATGCAC 57.181 40.909 0.00 0.00 34.60 4.57
3735 6679 2.783828 AGAATCTGCCTATCGACACG 57.216 50.000 0.00 0.00 0.00 4.49
3767 6711 3.865164 GGCTTTCAGTTTCCACACTTTTG 59.135 43.478 0.00 0.00 0.00 2.44
3788 6733 3.379057 TGAGCGTATCTTACATCGGTTGA 59.621 43.478 0.00 0.00 34.32 3.18
3833 6778 6.403878 GGCATGTAGTAGAACTTGTCCTTTA 58.596 40.000 0.00 0.00 0.00 1.85
3869 7305 0.246635 ACTGGGATTCTGAACCGACG 59.753 55.000 0.00 0.00 0.00 5.12
3881 7317 0.388907 AACCGACGTTGGATGTACCG 60.389 55.000 29.00 4.56 42.61 4.02
3891 7335 2.571212 TGGATGTACCGAAATCCATGC 58.429 47.619 8.24 0.00 45.86 4.06
3899 7343 2.241176 ACCGAAATCCATGCCCTTTCTA 59.759 45.455 9.66 0.00 0.00 2.10
3976 7420 1.202879 TCTTCCCTGTGGATGCGTTTT 60.203 47.619 0.00 0.00 41.40 2.43
4007 7452 0.620556 ATGTTTCTCCCTGCGGATGT 59.379 50.000 0.00 0.00 37.60 3.06
4015 7460 0.523072 CCCTGCGGATGTGTTTCTTG 59.477 55.000 0.00 0.00 0.00 3.02
4017 7462 1.197721 CCTGCGGATGTGTTTCTTGTC 59.802 52.381 0.00 0.00 0.00 3.18
4019 7464 1.144969 GCGGATGTGTTTCTTGTCGA 58.855 50.000 0.00 0.00 0.00 4.20
4042 7487 3.701532 AAATCGTTTGAAGGCGTTGAA 57.298 38.095 0.00 0.00 0.00 2.69
4131 7576 0.108138 CCTTTCCAGAGCTACACGGG 60.108 60.000 0.00 0.00 0.00 5.28
4134 7579 1.255667 TTCCAGAGCTACACGGGGAC 61.256 60.000 0.00 0.00 0.00 4.46
4178 7651 2.163412 GCGCTTACCATGACCATTTCAA 59.837 45.455 0.00 0.00 37.92 2.69
4179 7652 3.181487 GCGCTTACCATGACCATTTCAAT 60.181 43.478 0.00 0.00 37.92 2.57
4183 7656 5.450965 GCTTACCATGACCATTTCAATGAGG 60.451 44.000 0.00 0.00 37.92 3.86
4390 7869 9.830186 ATCCACTCAAGGTATGATATAAGTACT 57.170 33.333 0.00 0.00 37.44 2.73
4391 7870 9.298250 TCCACTCAAGGTATGATATAAGTACTC 57.702 37.037 0.00 0.00 37.44 2.59
4392 7871 8.524487 CCACTCAAGGTATGATATAAGTACTCC 58.476 40.741 0.00 0.00 37.44 3.85
4393 7872 8.524487 CACTCAAGGTATGATATAAGTACTCCC 58.476 40.741 0.00 0.00 37.44 4.30
4394 7873 8.457757 ACTCAAGGTATGATATAAGTACTCCCT 58.542 37.037 0.00 0.00 37.44 4.20
4395 7874 8.880991 TCAAGGTATGATATAAGTACTCCCTC 57.119 38.462 0.00 0.00 31.50 4.30
4396 7875 7.894364 TCAAGGTATGATATAAGTACTCCCTCC 59.106 40.741 0.00 0.00 31.50 4.30
4397 7876 6.424883 AGGTATGATATAAGTACTCCCTCCG 58.575 44.000 0.00 0.00 0.00 4.63
4398 7877 6.011805 AGGTATGATATAAGTACTCCCTCCGT 60.012 42.308 0.00 0.00 0.00 4.69
4399 7878 6.662663 GGTATGATATAAGTACTCCCTCCGTT 59.337 42.308 0.00 0.00 0.00 4.44
4400 7879 6.837471 ATGATATAAGTACTCCCTCCGTTC 57.163 41.667 0.00 0.00 0.00 3.95
4401 7880 5.698104 TGATATAAGTACTCCCTCCGTTCA 58.302 41.667 0.00 0.00 0.00 3.18
4402 7881 5.768662 TGATATAAGTACTCCCTCCGTTCAG 59.231 44.000 0.00 0.00 0.00 3.02
4403 7882 2.599408 AAGTACTCCCTCCGTTCAGA 57.401 50.000 0.00 0.00 0.00 3.27
4404 7883 2.599408 AGTACTCCCTCCGTTCAGAA 57.401 50.000 0.00 0.00 0.00 3.02
4405 7884 3.103080 AGTACTCCCTCCGTTCAGAAT 57.897 47.619 0.00 0.00 0.00 2.40
4406 7885 3.442076 AGTACTCCCTCCGTTCAGAATT 58.558 45.455 0.00 0.00 0.00 2.17
4407 7886 4.607239 AGTACTCCCTCCGTTCAGAATTA 58.393 43.478 0.00 0.00 0.00 1.40
4408 7887 3.889520 ACTCCCTCCGTTCAGAATTAC 57.110 47.619 0.00 0.00 0.00 1.89
4409 7888 3.442076 ACTCCCTCCGTTCAGAATTACT 58.558 45.455 0.00 0.00 0.00 2.24
4410 7889 3.838903 ACTCCCTCCGTTCAGAATTACTT 59.161 43.478 0.00 0.00 0.00 2.24
4411 7890 4.184629 CTCCCTCCGTTCAGAATTACTTG 58.815 47.826 0.00 0.00 0.00 3.16
4412 7891 3.581332 TCCCTCCGTTCAGAATTACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
4413 7892 3.933332 CCCTCCGTTCAGAATTACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
4414 7893 4.562757 CCCTCCGTTCAGAATTACTTGTCA 60.563 45.833 0.00 0.00 0.00 3.58
4415 7894 5.178797 CCTCCGTTCAGAATTACTTGTCAT 58.821 41.667 0.00 0.00 0.00 3.06
4416 7895 6.338146 CCTCCGTTCAGAATTACTTGTCATA 58.662 40.000 0.00 0.00 0.00 2.15
4417 7896 6.816640 CCTCCGTTCAGAATTACTTGTCATAA 59.183 38.462 0.00 0.00 0.00 1.90
4418 7897 7.333423 CCTCCGTTCAGAATTACTTGTCATAAA 59.667 37.037 0.00 0.00 0.00 1.40
4419 7898 8.610248 TCCGTTCAGAATTACTTGTCATAAAA 57.390 30.769 0.00 0.00 0.00 1.52
4420 7899 9.058174 TCCGTTCAGAATTACTTGTCATAAAAA 57.942 29.630 0.00 0.00 0.00 1.94
4421 7900 9.840427 CCGTTCAGAATTACTTGTCATAAAAAT 57.160 29.630 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 97 3.667360 ACATTTGCAAAAGGATTCAGCC 58.333 40.909 17.19 0.00 0.00 4.85
106 108 8.579006 AGAATTCAGATACAAGACATTTGCAAA 58.421 29.630 15.44 15.44 0.00 3.68
239 252 0.250901 AGCACCTTGAATTCGCAGGT 60.251 50.000 19.11 19.11 0.00 4.00
265 278 5.186215 TCAACGGTTATGACTTCAGGTATGA 59.814 40.000 0.00 0.00 0.00 2.15
301 322 9.785982 AGAAAAATAGTCAGAGAAGCTAAAACT 57.214 29.630 0.00 0.00 0.00 2.66
421 468 2.158769 TGCAGCTTCAGTTCCTTGAGAA 60.159 45.455 0.00 0.00 0.00 2.87
448 495 1.891178 TCGACAACGATGATGACGAC 58.109 50.000 0.00 0.00 43.81 4.34
568 625 1.337074 CCAAAGCATTCGTGTGGCAAT 60.337 47.619 0.00 0.00 0.00 3.56
591 648 5.649782 AACAACTTCCATTGGATCATGTC 57.350 39.130 6.15 0.00 33.63 3.06
592 649 6.423776 AAAACAACTTCCATTGGATCATGT 57.576 33.333 6.15 8.81 33.63 3.21
645 702 9.555727 AAAAAGAGCAAGTCAACTGTAATAGTA 57.444 29.630 0.00 0.00 39.18 1.82
649 706 6.038271 ACGAAAAAGAGCAAGTCAACTGTAAT 59.962 34.615 0.00 0.00 0.00 1.89
717 811 4.743151 TGTCAGATTCACGTGACAGTTAAC 59.257 41.667 19.90 12.69 46.35 2.01
788 890 7.359681 GCAAAAATTTACCCGATTTTGACGATT 60.360 33.333 12.49 0.00 42.48 3.34
794 896 7.170658 TCAGAAGCAAAAATTTACCCGATTTTG 59.829 33.333 5.67 5.67 42.66 2.44
813 2495 3.863142 AAATCACTGCCAATCAGAAGC 57.137 42.857 0.00 0.00 45.72 3.86
814 2496 6.022163 AGAAAAATCACTGCCAATCAGAAG 57.978 37.500 0.00 0.00 45.72 2.85
842 2586 1.898459 CTGTGCGCTTGTGCTGAGAG 61.898 60.000 9.73 0.00 36.97 3.20
843 2587 1.957695 CTGTGCGCTTGTGCTGAGA 60.958 57.895 9.73 0.00 36.97 3.27
1179 3209 0.321653 AACTTCGATGGGGCTGTGAC 60.322 55.000 3.12 0.00 0.00 3.67
1188 3238 1.917872 TCCCCCAAAAACTTCGATGG 58.082 50.000 3.12 0.00 0.00 3.51
1196 3246 0.762842 AGCACCCTTCCCCCAAAAAC 60.763 55.000 0.00 0.00 0.00 2.43
1199 3249 1.155155 GAAGCACCCTTCCCCCAAA 59.845 57.895 0.00 0.00 41.30 3.28
1200 3250 2.851045 GAAGCACCCTTCCCCCAA 59.149 61.111 0.00 0.00 41.30 4.12
1201 3251 3.646715 CGAAGCACCCTTCCCCCA 61.647 66.667 0.00 0.00 43.66 4.96
1202 3252 2.211468 AATCGAAGCACCCTTCCCCC 62.211 60.000 0.00 0.00 43.66 5.40
1209 3259 4.376340 AATTTGATGAATCGAAGCACCC 57.624 40.909 0.00 0.00 33.92 4.61
1213 3263 6.359087 GTGATGCTAATTTGATGAATCGAAGC 59.641 38.462 0.00 0.00 33.92 3.86
1219 3269 7.834881 ATCAGGTGATGCTAATTTGATGAAT 57.165 32.000 0.00 0.00 32.68 2.57
1226 3276 7.114754 TCTTCAGAATCAGGTGATGCTAATTT 58.885 34.615 0.00 0.00 38.37 1.82
1231 3281 4.163649 TGATCTTCAGAATCAGGTGATGCT 59.836 41.667 0.00 0.00 41.08 3.79
1232 3282 4.272991 GTGATCTTCAGAATCAGGTGATGC 59.727 45.833 0.00 0.00 34.49 3.91
1233 3283 5.672503 AGTGATCTTCAGAATCAGGTGATG 58.327 41.667 0.00 0.00 34.49 3.07
1235 3285 5.012458 ACAAGTGATCTTCAGAATCAGGTGA 59.988 40.000 0.00 0.00 0.00 4.02
1236 3286 5.243981 ACAAGTGATCTTCAGAATCAGGTG 58.756 41.667 0.00 0.00 0.00 4.00
1238 3288 5.704515 ACAACAAGTGATCTTCAGAATCAGG 59.295 40.000 0.00 0.00 0.00 3.86
1239 3289 6.798315 ACAACAAGTGATCTTCAGAATCAG 57.202 37.500 0.00 0.00 0.00 2.90
1240 3290 7.572523 AAACAACAAGTGATCTTCAGAATCA 57.427 32.000 0.00 0.00 0.00 2.57
1241 3291 8.749499 CAAAAACAACAAGTGATCTTCAGAATC 58.251 33.333 0.00 0.00 0.00 2.52
1242 3292 7.223387 GCAAAAACAACAAGTGATCTTCAGAAT 59.777 33.333 0.00 0.00 0.00 2.40
1243 3293 6.531240 GCAAAAACAACAAGTGATCTTCAGAA 59.469 34.615 0.00 0.00 0.00 3.02
1244 3294 6.035843 GCAAAAACAACAAGTGATCTTCAGA 58.964 36.000 0.00 0.00 0.00 3.27
1245 3295 5.806502 TGCAAAAACAACAAGTGATCTTCAG 59.193 36.000 0.00 0.00 0.00 3.02
1246 3296 5.718146 TGCAAAAACAACAAGTGATCTTCA 58.282 33.333 0.00 0.00 0.00 3.02
1247 3297 6.035843 TCTGCAAAAACAACAAGTGATCTTC 58.964 36.000 0.00 0.00 0.00 2.87
1248 3298 5.964758 TCTGCAAAAACAACAAGTGATCTT 58.035 33.333 0.00 0.00 0.00 2.40
1249 3299 5.581126 TCTGCAAAAACAACAAGTGATCT 57.419 34.783 0.00 0.00 0.00 2.75
1250 3300 5.176223 CCATCTGCAAAAACAACAAGTGATC 59.824 40.000 0.00 0.00 0.00 2.92
1287 3337 3.615110 GCTCGTGGATATCGAACCATGAT 60.615 47.826 22.47 0.00 46.60 2.45
1331 3411 2.039084 GGACTGAGTGGGTTGATGAGTT 59.961 50.000 0.00 0.00 0.00 3.01
1338 3418 1.679898 GGAGGGACTGAGTGGGTTG 59.320 63.158 0.00 0.00 41.55 3.77
1339 3419 1.539124 GGGAGGGACTGAGTGGGTT 60.539 63.158 0.00 0.00 41.55 4.11
1340 3420 2.122954 GGGAGGGACTGAGTGGGT 59.877 66.667 0.00 0.00 41.55 4.51
1341 3421 3.077556 CGGGAGGGACTGAGTGGG 61.078 72.222 0.00 0.00 41.55 4.61
1342 3422 3.775654 GCGGGAGGGACTGAGTGG 61.776 72.222 0.00 0.00 41.55 4.00
1346 3426 0.325296 ATACAAGCGGGAGGGACTGA 60.325 55.000 0.00 0.00 41.55 3.41
1349 3429 0.529992 CGAATACAAGCGGGAGGGAC 60.530 60.000 0.00 0.00 0.00 4.46
1373 3453 4.660521 TGGTACAGTTGCCTCCCT 57.339 55.556 0.00 0.00 0.00 4.20
1391 3475 7.066766 ACAGATTTGAGCCAGATCAATTTCTAC 59.933 37.037 0.00 0.00 38.90 2.59
1398 3482 8.985315 ATATTTACAGATTTGAGCCAGATCAA 57.015 30.769 0.00 0.00 37.41 2.57
1462 3612 1.965930 GGCGTGCACATTCTCCACA 60.966 57.895 18.64 0.00 0.00 4.17
1534 4165 0.613853 TACCTCCCTGACTGAACCCG 60.614 60.000 0.00 0.00 0.00 5.28
1600 4231 5.065859 CCAATACTTATCAATTCACGGCACA 59.934 40.000 0.00 0.00 0.00 4.57
1693 4324 2.203139 CCACTGAACACGGCACCA 60.203 61.111 0.00 0.00 0.00 4.17
1829 4467 7.296628 ACCAACCAATAAATTGAAGCTTACA 57.703 32.000 0.00 0.00 40.14 2.41
1860 4498 1.528586 CTCTTGTTGACCAGCGTTCAG 59.471 52.381 0.00 0.00 0.00 3.02
1984 4623 5.489792 TCTAAGCTTCCTCACATCTTGTT 57.510 39.130 0.00 0.00 0.00 2.83
2020 4659 9.180678 CTTTTGTTGACTAGCGTTCAATTTAAT 57.819 29.630 0.00 0.00 0.00 1.40
2022 4661 7.921787 TCTTTTGTTGACTAGCGTTCAATTTA 58.078 30.769 0.00 0.00 0.00 1.40
2044 4683 6.248433 ACATAAACATCACCAACCTCATCTT 58.752 36.000 0.00 0.00 0.00 2.40
2119 4758 2.216046 ACATCTTGTGACTGTGTGCTG 58.784 47.619 0.00 0.00 0.00 4.41
2305 4944 6.149616 AGAAATCTGTAGATGAGGGATCCTT 58.850 40.000 12.58 3.01 34.49 3.36
2349 4988 2.960384 TCGTTCTGTTCCAGGTGTAGAA 59.040 45.455 0.00 0.00 31.51 2.10
2365 5004 8.583765 GGAATTATTGCAAAAACTACATCGTTC 58.416 33.333 1.71 0.00 0.00 3.95
2422 5061 6.357367 AGGTGCCAAAACTATACTTCCATAG 58.643 40.000 0.00 0.00 35.09 2.23
2483 5122 5.305585 TGAGGTCAGTACATTTTGGTCTTC 58.694 41.667 0.00 0.00 0.00 2.87
2499 5138 3.229293 TCATTTGGCAATGTTGAGGTCA 58.771 40.909 0.00 0.00 40.78 4.02
2508 5148 7.837202 ATGTAGTGAATTTCATTTGGCAATG 57.163 32.000 0.00 2.01 41.25 2.82
2509 5149 8.723311 CAAATGTAGTGAATTTCATTTGGCAAT 58.277 29.630 16.60 0.00 45.96 3.56
2595 5235 7.283127 CACAGTAGGTGTATTGCCATATTTCTT 59.717 37.037 0.00 0.00 42.75 2.52
2666 5314 1.780919 AGTCCTAAGGTGGGCAAAGTT 59.219 47.619 0.00 0.00 33.35 2.66
2711 5370 1.494824 AGCGTCGTTGACTGGTTAAC 58.505 50.000 0.00 0.00 0.00 2.01
2791 5450 6.238508 GTTTACATACGAAAGGAACATCACG 58.761 40.000 0.00 0.00 0.00 4.35
2856 5544 7.962964 TGATTTTACTGTCAAGACTGTTAGG 57.037 36.000 16.14 0.00 42.30 2.69
2951 5640 4.951715 TCAATCAGGCTAATTGCATCAAGT 59.048 37.500 5.44 0.00 45.15 3.16
3150 5839 7.201767 GCTTCAAATAATACCACTTGATCAGCT 60.202 37.037 0.00 0.00 32.59 4.24
3355 6048 0.315568 GCGATCGAGTGGCCTAGATT 59.684 55.000 21.57 0.00 33.74 2.40
3428 6121 5.334569 GGACGTTAACTTTGCTTATCTTGCA 60.335 40.000 3.71 0.00 38.80 4.08
3469 6162 0.743345 GCTATGGTGGGGAACGTGAC 60.743 60.000 0.00 0.00 0.00 3.67
3470 6163 1.195442 TGCTATGGTGGGGAACGTGA 61.195 55.000 0.00 0.00 0.00 4.35
3476 6169 1.272425 CCAGTTTTGCTATGGTGGGGA 60.272 52.381 0.00 0.00 0.00 4.81
3483 6176 4.357142 CTGCATTAGCCAGTTTTGCTATG 58.643 43.478 0.00 0.00 40.75 2.23
3528 6469 5.117355 TCGTCCGAGTTCATCAATATACC 57.883 43.478 0.00 0.00 0.00 2.73
3556 6500 6.148480 GTGCATGACAAAGTCTCAAGAATAGT 59.852 38.462 0.00 0.00 33.15 2.12
3735 6679 1.620822 ACTGAAAGCCACAATGGACC 58.379 50.000 0.00 0.00 39.92 4.46
3767 6711 3.961182 TCAACCGATGTAAGATACGCTC 58.039 45.455 0.00 0.00 0.00 5.03
3788 6733 4.242475 CCGTGCATACACCGTATGATATT 58.758 43.478 16.36 0.00 44.40 1.28
3833 6778 7.691993 ATCCCAGTGGTATCTTACTAACAAT 57.308 36.000 8.74 0.00 0.00 2.71
3881 7317 4.526970 TGACTAGAAAGGGCATGGATTTC 58.473 43.478 0.00 0.00 33.97 2.17
3888 7332 4.666512 ACACAAATGACTAGAAAGGGCAT 58.333 39.130 0.00 0.00 0.00 4.40
3976 7420 3.319689 GGGAGAAACATTTTGTCCGGAAA 59.680 43.478 5.23 0.00 0.00 3.13
4019 7464 3.112580 CAACGCCTTCAAACGATTTTGT 58.887 40.909 0.00 0.00 42.51 2.83
4042 7487 5.263599 TGATGCAAACCAGAACCATAATCT 58.736 37.500 0.00 0.00 0.00 2.40
4095 7540 2.908688 AGGAACACAAAATGGCCAAC 57.091 45.000 10.96 0.00 31.16 3.77
4131 7576 0.608035 TCAATCAAACTGCCCGGTCC 60.608 55.000 0.00 0.00 0.00 4.46
4134 7579 2.609350 CAAATCAATCAAACTGCCCGG 58.391 47.619 0.00 0.00 0.00 5.73
4135 7580 1.994779 GCAAATCAATCAAACTGCCCG 59.005 47.619 0.00 0.00 0.00 6.13
4136 7581 2.349590 GGCAAATCAATCAAACTGCCC 58.650 47.619 0.00 0.00 42.86 5.36
4178 7651 3.815809 TCAAAACTTCGTTGGTCCTCAT 58.184 40.909 0.00 0.00 0.00 2.90
4179 7652 3.269538 TCAAAACTTCGTTGGTCCTCA 57.730 42.857 0.00 0.00 0.00 3.86
4183 7656 3.314080 TGGTGATCAAAACTTCGTTGGTC 59.686 43.478 0.00 0.00 36.76 4.02
4373 7852 6.011805 ACGGAGGGAGTACTTATATCATACCT 60.012 42.308 0.00 0.00 0.00 3.08
4389 7868 4.184629 CAAGTAATTCTGAACGGAGGGAG 58.815 47.826 0.00 0.00 0.00 4.30
4390 7869 3.581332 ACAAGTAATTCTGAACGGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
4391 7870 3.933332 GACAAGTAATTCTGAACGGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
4392 7871 4.566004 TGACAAGTAATTCTGAACGGAGG 58.434 43.478 0.00 0.00 0.00 4.30
4393 7872 7.827819 TTATGACAAGTAATTCTGAACGGAG 57.172 36.000 0.00 0.00 0.00 4.63
4394 7873 8.610248 TTTTATGACAAGTAATTCTGAACGGA 57.390 30.769 0.00 0.00 0.00 4.69
4395 7874 9.840427 ATTTTTATGACAAGTAATTCTGAACGG 57.160 29.630 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.