Multiple sequence alignment - TraesCS4D01G221000

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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 TraesCS4D01G221000 chr4D 100.000 5255 0 0 1 5255 378258734 378263988 0.000000e+00 9705.0
1 TraesCS4D01G221000 chr4D 84.190 253 26 10 4907 5153 461108597 461108841 3.160000e-57 233.0
2 TraesCS4D01G221000 chr4A 92.232 1931 109 21 2869 4779 87413667 87411758 0.000000e+00 2697.0
3 TraesCS4D01G221000 chr4A 91.373 881 35 25 695 1550 87415616 87414752 0.000000e+00 1168.0
4 TraesCS4D01G221000 chr4A 93.913 345 17 3 2260 2600 87414008 87413664 7.800000e-143 518.0
5 TraesCS4D01G221000 chr4A 87.755 392 18 8 1894 2261 87414429 87414044 1.050000e-116 431.0
6 TraesCS4D01G221000 chr4A 91.636 275 19 4 1564 1834 87414702 87414428 1.380000e-100 377.0
7 TraesCS4D01G221000 chr4A 84.706 255 24 5 3 254 87417070 87416828 1.890000e-59 241.0
8 TraesCS4D01G221000 chr4A 95.455 66 3 0 2260 2325 173646434 173646369 7.200000e-19 106.0
9 TraesCS4D01G221000 chr4A 96.774 62 1 1 2367 2427 173646383 173646322 9.310000e-18 102.0
10 TraesCS4D01G221000 chr4A 89.474 76 2 2 240 315 87416809 87416740 2.020000e-14 91.6
11 TraesCS4D01G221000 chr4B 94.705 1492 51 11 2260 3731 464158660 464160143 0.000000e+00 2292.0
12 TraesCS4D01G221000 chr4B 93.418 1337 64 12 3715 5034 464160158 464161487 0.000000e+00 1960.0
13 TraesCS4D01G221000 chr4B 89.425 1617 46 39 1 1550 464156105 464157663 0.000000e+00 1923.0
14 TraesCS4D01G221000 chr4B 92.133 572 20 10 1563 2119 464157718 464158279 0.000000e+00 784.0
15 TraesCS4D01G221000 chr4B 91.667 156 13 0 5098 5253 464161485 464161640 3.190000e-52 217.0
16 TraesCS4D01G221000 chr2B 86.122 245 32 2 2612 2855 109981463 109981220 4.040000e-66 263.0
17 TraesCS4D01G221000 chr2B 84.898 245 35 2 2612 2855 109934832 109934589 4.060000e-61 246.0
18 TraesCS4D01G221000 chr2D 86.122 245 31 3 2612 2855 72700521 72700279 1.450000e-65 261.0
19 TraesCS4D01G221000 chr2D 85.306 245 32 3 2612 2855 72440666 72440425 3.140000e-62 250.0
20 TraesCS4D01G221000 chr2D 84.549 233 30 6 4907 5135 626654220 626653990 5.300000e-55 226.0
21 TraesCS4D01G221000 chr2D 82.520 246 37 5 2612 2855 498002932 498003173 1.480000e-50 211.0
22 TraesCS4D01G221000 chr2A 86.179 246 28 5 2612 2855 71348701 71348460 1.450000e-65 261.0
23 TraesCS4D01G221000 chr3A 83.696 276 36 6 2586 2855 523754982 523754710 8.740000e-63 252.0
24 TraesCS4D01G221000 chr3A 85.837 233 26 7 4907 5135 57085078 57085307 1.890000e-59 241.0
25 TraesCS4D01G221000 chr3A 84.549 233 30 6 4907 5135 652272796 652273026 5.300000e-55 226.0
26 TraesCS4D01G221000 chr3B 84.898 245 32 5 4895 5135 44638864 44639107 5.260000e-60 243.0
27 TraesCS4D01G221000 chr6A 87.805 205 23 2 2652 2855 199815526 199815729 6.800000e-59 239.0
28 TraesCS4D01G221000 chr6A 84.337 249 32 7 4891 5134 126792463 126792709 2.450000e-58 237.0
29 TraesCS4D01G221000 chr5A 85.281 231 31 3 4907 5135 581627211 581626982 8.800000e-58 235.0
30 TraesCS4D01G221000 chr5A 98.333 60 1 0 2260 2319 437176259 437176318 7.200000e-19 106.0
31 TraesCS4D01G221000 chr5A 96.774 62 1 1 2367 2427 437176310 437176371 9.310000e-18 102.0
32 TraesCS4D01G221000 chr6B 84.914 232 31 4 4907 5135 366590091 366590321 1.140000e-56 231.0
33 TraesCS4D01G221000 chr3D 82.946 258 41 3 2599 2855 560188335 560188080 4.090000e-56 230.0
34 TraesCS4D01G221000 chr1A 96.774 62 1 1 2367 2427 539293378 539293439 9.310000e-18 102.0
35 TraesCS4D01G221000 chr1A 96.667 60 2 0 2260 2319 539293327 539293386 3.350000e-17 100.0


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 TraesCS4D01G221000 chr4D 378258734 378263988 5254 False 9705.000000 9705 100.000000 1 5255 1 chr4D.!!$F1 5254
1 TraesCS4D01G221000 chr4A 87411758 87417070 5312 True 789.085714 2697 90.155571 3 4779 7 chr4A.!!$R1 4776
2 TraesCS4D01G221000 chr4B 464156105 464161640 5535 False 1435.200000 2292 92.269600 1 5253 5 chr4B.!!$F1 5252

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
261 308 0.659123 GTTTTTACACGTGCGGCCAG 60.659 55.000 17.22 0.0 0.00 4.85 F
388 457 1.002134 ACTCCCTCACCGCCAAATG 60.002 57.895 0.00 0.0 0.00 2.32 F
596 666 1.120530 ATAGCTGTAACCACCGAGGG 58.879 55.000 0.00 0.0 43.89 4.30 F
820 1717 1.228276 GATCGGGGGCTCCAATTCC 60.228 63.158 4.16 0.0 34.36 3.01 F
2194 3407 1.448119 TACAGAGGATGCTCGCTCCG 61.448 60.000 8.74 0.0 37.88 4.63 F
2250 3463 0.394488 TCTCAGAGGTGGCCTAGTCG 60.394 60.000 3.32 0.0 31.76 4.18 F
2406 3659 2.159585 TCATTTTTGTAGCACATCCGCG 60.160 45.455 0.00 0.0 36.85 6.46 F
3932 5252 1.081175 GAGCTTTTTGGCAGCCGAC 60.081 57.895 7.03 0.0 38.09 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1573 2545 0.038166 TCCACACAAATCCTGCTCCC 59.962 55.000 0.00 0.00 0.00 4.30 R
2194 3407 1.000717 ACTTGGTGTTAACAATGCGGC 60.001 47.619 10.51 0.00 0.00 6.53 R
2222 3435 1.139853 CCACCTCTGAGAATAGGGCAC 59.860 57.143 6.17 0.00 37.18 5.01 R
2235 3448 1.749638 CGTCGACTAGGCCACCTCT 60.750 63.158 14.70 0.00 34.61 3.69 R
3910 5230 1.202114 CGGCTGCCAAAAAGCTCATAA 59.798 47.619 20.29 0.00 40.64 1.90 R
3927 5247 2.894387 GATGCCAGCAGAGTCGGC 60.894 66.667 7.22 7.22 46.43 5.54 R
3954 5276 3.126858 GCGGCAAAATATTCAGTGTCAGA 59.873 43.478 0.00 0.00 0.00 3.27 R
5188 6517 0.902531 CTTAGGCCTCCTTTCGTCCA 59.097 55.000 9.68 0.00 34.61 4.02 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
54 62 2.501610 CCTCTGGTTAGGCTCCGC 59.498 66.667 0.00 0.00 0.00 5.54
55 63 2.060980 CCTCTGGTTAGGCTCCGCT 61.061 63.158 0.00 0.00 0.00 5.52
88 96 0.824182 CTACCGCCTCCTCCCACTAG 60.824 65.000 0.00 0.00 0.00 2.57
92 100 1.395826 CGCCTCCTCCCACTAGAAGG 61.396 65.000 0.00 0.00 0.00 3.46
114 122 3.225940 ACCTCTTTCCCAGAAAGCTTTG 58.774 45.455 18.30 3.44 0.00 2.77
172 185 3.175710 ACAACCAGCCCCTCCGTT 61.176 61.111 0.00 0.00 0.00 4.44
173 186 2.115266 CAACCAGCCCCTCCGTTT 59.885 61.111 0.00 0.00 0.00 3.60
174 187 1.971695 CAACCAGCCCCTCCGTTTC 60.972 63.158 0.00 0.00 0.00 2.78
175 188 3.205851 AACCAGCCCCTCCGTTTCC 62.206 63.158 0.00 0.00 0.00 3.13
176 189 3.646715 CCAGCCCCTCCGTTTCCA 61.647 66.667 0.00 0.00 0.00 3.53
177 190 2.434331 CAGCCCCTCCGTTTCCAA 59.566 61.111 0.00 0.00 0.00 3.53
260 307 1.355916 GTTTTTACACGTGCGGCCA 59.644 52.632 17.22 0.00 0.00 5.36
261 308 0.659123 GTTTTTACACGTGCGGCCAG 60.659 55.000 17.22 0.00 0.00 4.85
262 309 1.787057 TTTTTACACGTGCGGCCAGG 61.787 55.000 17.22 0.00 0.00 4.45
263 310 2.661840 TTTTACACGTGCGGCCAGGA 62.662 55.000 17.22 0.00 0.00 3.86
264 311 3.583276 TTACACGTGCGGCCAGGAG 62.583 63.158 17.22 0.00 0.00 3.69
318 365 2.930040 CACCACTATTACTCGCACTTGG 59.070 50.000 0.00 0.00 0.00 3.61
338 385 1.243342 TTGCATGCTGGAAACGGGAG 61.243 55.000 20.33 0.00 41.90 4.30
344 391 2.281484 TGGAAACGGGAGCAGTGC 60.281 61.111 7.13 7.13 0.00 4.40
345 392 2.281484 GGAAACGGGAGCAGTGCA 60.281 61.111 19.20 0.00 0.00 4.57
346 393 2.328099 GGAAACGGGAGCAGTGCAG 61.328 63.158 19.20 8.07 0.00 4.41
347 394 1.301716 GAAACGGGAGCAGTGCAGA 60.302 57.895 19.20 0.00 0.00 4.26
348 395 1.294659 GAAACGGGAGCAGTGCAGAG 61.295 60.000 19.20 8.06 0.00 3.35
351 398 3.715097 GGGAGCAGTGCAGAGCCT 61.715 66.667 19.20 0.00 0.00 4.58
352 399 2.125188 GGAGCAGTGCAGAGCCTC 60.125 66.667 19.20 4.45 0.00 4.70
388 457 1.002134 ACTCCCTCACCGCCAAATG 60.002 57.895 0.00 0.00 0.00 2.32
441 510 1.384525 CTCACGTGTGGGGTGAAAAA 58.615 50.000 16.51 0.00 43.27 1.94
596 666 1.120530 ATAGCTGTAACCACCGAGGG 58.879 55.000 0.00 0.00 43.89 4.30
624 694 3.068448 GGGGGAGAGAAAAGAGACGATAC 59.932 52.174 0.00 0.00 0.00 2.24
689 759 2.347661 CGACACAGACGAGAAAGCAAAC 60.348 50.000 0.00 0.00 0.00 2.93
738 1606 3.039526 CCTCCCTCCCTCCCTCCT 61.040 72.222 0.00 0.00 0.00 3.69
740 1608 3.036959 TCCCTCCCTCCCTCCTCC 61.037 72.222 0.00 0.00 0.00 4.30
742 1610 3.039526 CCTCCCTCCCTCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
752 1641 3.036959 TCCTCCCTCCTCCCCTCC 61.037 72.222 0.00 0.00 0.00 4.30
753 1642 4.179599 CCTCCCTCCTCCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
754 1643 3.039526 CTCCCTCCTCCCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
755 1644 3.036959 TCCCTCCTCCCCTCCCTC 61.037 72.222 0.00 0.00 0.00 4.30
756 1645 4.548513 CCCTCCTCCCCTCCCTCG 62.549 77.778 0.00 0.00 0.00 4.63
757 1646 3.430497 CCTCCTCCCCTCCCTCGA 61.430 72.222 0.00 0.00 0.00 4.04
814 1711 2.344129 GAATCGATCGGGGGCTCC 59.656 66.667 16.41 0.00 0.00 4.70
815 1712 2.445845 AATCGATCGGGGGCTCCA 60.446 61.111 16.41 0.00 34.36 3.86
816 1713 2.040009 GAATCGATCGGGGGCTCCAA 62.040 60.000 16.41 0.00 34.36 3.53
817 1714 1.418908 AATCGATCGGGGGCTCCAAT 61.419 55.000 16.41 0.00 34.36 3.16
818 1715 1.418908 ATCGATCGGGGGCTCCAATT 61.419 55.000 16.41 0.00 34.36 2.32
819 1716 1.598130 CGATCGGGGGCTCCAATTC 60.598 63.158 4.16 0.00 34.36 2.17
820 1717 1.228276 GATCGGGGGCTCCAATTCC 60.228 63.158 4.16 0.00 34.36 3.01
821 1718 1.994885 GATCGGGGGCTCCAATTCCA 61.995 60.000 4.16 0.00 34.36 3.53
822 1719 2.284515 ATCGGGGGCTCCAATTCCAC 62.285 60.000 4.16 0.00 34.36 4.02
824 1721 2.770130 GGGGCTCCAATTCCACCA 59.230 61.111 0.00 0.00 0.00 4.17
865 1767 4.218478 GCCGGCGTGCGTGTTATC 62.218 66.667 12.58 0.00 0.00 1.75
877 1780 5.616866 CGTGCGTGTTATCTTTCTTGGATTT 60.617 40.000 0.00 0.00 0.00 2.17
1336 2265 2.603473 CCTCCGTCCACTCCCACA 60.603 66.667 0.00 0.00 0.00 4.17
1595 2567 1.815003 GAGCAGGATTTGTGTGGAAGG 59.185 52.381 0.00 0.00 0.00 3.46
1625 2597 4.979197 TGTTTGCATGGATTCGTTTTGTAC 59.021 37.500 0.00 0.00 0.00 2.90
1626 2598 4.837896 TTGCATGGATTCGTTTTGTACA 57.162 36.364 0.00 0.00 0.00 2.90
1657 2629 6.053632 TGATGCTTTGAGGAATTAGTCTCA 57.946 37.500 2.62 2.62 38.14 3.27
1774 2754 6.538742 TGACGATTCCCTCTATTGATCAAAAC 59.461 38.462 13.09 0.00 0.00 2.43
1775 2755 6.414732 ACGATTCCCTCTATTGATCAAAACA 58.585 36.000 13.09 0.00 0.00 2.83
1776 2756 6.540189 ACGATTCCCTCTATTGATCAAAACAG 59.460 38.462 13.09 10.08 0.00 3.16
1777 2757 6.763135 CGATTCCCTCTATTGATCAAAACAGA 59.237 38.462 13.09 13.58 0.00 3.41
1784 2764 8.031277 CCTCTATTGATCAAAACAGAAAAAGGG 58.969 37.037 13.09 8.55 0.00 3.95
1853 2834 4.067896 ACCTGAGAACACTAACATGCTTG 58.932 43.478 0.00 0.00 0.00 4.01
1913 2894 3.099141 ACCCTGGTCCTTGCAAATAATG 58.901 45.455 0.00 0.00 0.00 1.90
2049 3054 5.804639 TGATCTACAGTTGCCATACACTTT 58.195 37.500 0.00 0.00 0.00 2.66
2050 3055 5.643348 TGATCTACAGTTGCCATACACTTTG 59.357 40.000 0.00 0.00 0.00 2.77
2051 3056 5.222079 TCTACAGTTGCCATACACTTTGA 57.778 39.130 0.00 0.00 0.00 2.69
2082 3087 5.251601 TGGCAACTGTTAAACTTTGGTAC 57.748 39.130 0.00 0.00 37.61 3.34
2083 3088 4.951094 TGGCAACTGTTAAACTTTGGTACT 59.049 37.500 0.00 0.00 37.61 2.73
2084 3089 5.419471 TGGCAACTGTTAAACTTTGGTACTT 59.581 36.000 0.00 0.00 37.61 2.24
2095 3100 3.692593 ACTTTGGTACTTGTTGTGTGTCC 59.307 43.478 0.00 0.00 0.00 4.02
2123 3336 4.100035 TCTGGAGGCAGAACACTACATATG 59.900 45.833 0.00 0.00 0.00 1.78
2164 3377 7.590689 GTCAAACCATTGTAATTTTTGCATTGG 59.409 33.333 13.92 13.92 45.90 3.16
2194 3407 1.448119 TACAGAGGATGCTCGCTCCG 61.448 60.000 8.74 0.00 37.88 4.63
2195 3408 3.910490 AGAGGATGCTCGCTCCGC 61.910 66.667 8.74 4.05 37.88 5.54
2235 3448 5.815581 AGTGTTATTTGTGCCCTATTCTCA 58.184 37.500 0.00 0.00 0.00 3.27
2250 3463 0.394488 TCTCAGAGGTGGCCTAGTCG 60.394 60.000 3.32 0.00 31.76 4.18
2254 3467 2.754658 AGGTGGCCTAGTCGACGG 60.755 66.667 10.46 7.56 28.47 4.79
2361 3611 3.532102 ACTGTTAAGGTCTTCATCCCCT 58.468 45.455 0.00 0.00 0.00 4.79
2404 3657 5.233957 TCATCATTTTTGTAGCACATCCG 57.766 39.130 0.00 0.00 0.00 4.18
2406 3659 2.159585 TCATTTTTGTAGCACATCCGCG 60.160 45.455 0.00 0.00 36.85 6.46
2426 3679 3.487544 GCGCTTGGTTGAATAATCTGTCC 60.488 47.826 0.00 0.00 0.00 4.02
2429 3682 4.156008 GCTTGGTTGAATAATCTGTCCGTT 59.844 41.667 0.00 0.00 0.00 4.44
2437 3691 7.591421 TGAATAATCTGTCCGTTACCAGATA 57.409 36.000 2.85 0.00 45.32 1.98
2462 3716 7.633193 TTTGTACCAAGCAAGTCTTTCTTTA 57.367 32.000 0.00 0.00 33.63 1.85
2525 3779 8.891720 CACCAAAAAGAATTCTTGGAATTTCAA 58.108 29.630 25.02 0.00 41.88 2.69
2604 3858 9.927668 TTTTCTCAAAGATAATTTTAAGGCCTG 57.072 29.630 5.69 0.00 0.00 4.85
2634 3888 8.816894 TGCTTTGTAGGAATTCTATAGGATAGG 58.183 37.037 5.23 0.00 0.00 2.57
2635 3889 7.766738 GCTTTGTAGGAATTCTATAGGATAGGC 59.233 40.741 5.23 0.00 0.00 3.93
2648 3902 9.469097 TCTATAGGATAGGCTATCTGAAGAAAC 57.531 37.037 28.46 13.05 35.52 2.78
2650 3904 8.677870 ATAGGATAGGCTATCTGAAGAAACAT 57.322 34.615 28.46 5.64 35.52 2.71
2651 3905 7.385894 AGGATAGGCTATCTGAAGAAACATT 57.614 36.000 28.46 0.00 35.52 2.71
2679 3933 9.094578 TCTATAGATCCCTTTGATTTGTAGGAG 57.905 37.037 0.00 0.00 33.02 3.69
2681 3935 5.995446 AGATCCCTTTGATTTGTAGGAGTC 58.005 41.667 0.00 0.00 32.41 3.36
2684 3938 4.469945 TCCCTTTGATTTGTAGGAGTCGAT 59.530 41.667 0.00 0.00 0.00 3.59
2761 4015 5.543507 ACATTAGCTCAGACCTATTGGAG 57.456 43.478 0.00 0.00 37.04 3.86
2841 4095 5.624159 TGTCATCTCATTTCCTGTGACTTT 58.376 37.500 0.00 0.00 37.46 2.66
2866 4135 5.474876 CCTATTCCTATGAACCAAAGGATGC 59.525 44.000 0.00 0.00 39.14 3.91
3100 4374 7.512992 AGCATTACAGCTTCCTTAATACAGAT 58.487 34.615 0.00 0.00 43.70 2.90
3319 4596 3.008485 GGGACAGGAATTGACTTCTCAGT 59.992 47.826 0.00 0.00 35.17 3.41
3386 4663 3.141398 TCCACTTGCAGTTAAAGCTGAG 58.859 45.455 0.00 1.82 38.70 3.35
3449 4726 4.023291 AGAAGCCAAAAACTCCAAACTCA 58.977 39.130 0.00 0.00 0.00 3.41
3754 5060 9.736023 GTTAATTAAGCTATAATGCTGCAGTTT 57.264 29.630 16.64 12.00 43.24 2.66
3794 5100 9.918630 AAAAACATGATTTCCAGAGATTTACTG 57.081 29.630 0.00 0.00 35.43 2.74
3825 5136 9.623000 ATTCCACTTGTACTATATTGTTTACCC 57.377 33.333 0.00 0.00 0.00 3.69
3840 5151 6.870971 TGTTTACCCAGTGTGATCTTAAAC 57.129 37.500 0.00 0.00 0.00 2.01
3883 5203 9.220767 ACTGATCCAGAAAAAGTCTACAATAAC 57.779 33.333 0.45 0.00 33.56 1.89
3887 5207 8.833231 TCCAGAAAAAGTCTACAATAACTCAG 57.167 34.615 0.00 0.00 33.56 3.35
3888 5208 7.878127 TCCAGAAAAAGTCTACAATAACTCAGG 59.122 37.037 0.00 0.00 33.56 3.86
3889 5209 7.878127 CCAGAAAAAGTCTACAATAACTCAGGA 59.122 37.037 0.00 0.00 33.56 3.86
3894 5214 9.574516 AAAAGTCTACAATAACTCAGGAATTGT 57.425 29.630 10.67 10.67 44.01 2.71
3919 5239 9.289782 GTTATCCATTTCCAGTATTATGAGCTT 57.710 33.333 0.00 0.00 0.00 3.74
3927 5247 5.357878 TCCAGTATTATGAGCTTTTTGGCAG 59.642 40.000 0.00 0.00 34.17 4.85
3932 5252 1.081175 GAGCTTTTTGGCAGCCGAC 60.081 57.895 7.03 0.00 38.09 4.79
3953 5275 3.383185 ACTCTGCTGGCATCTCTAGTAAC 59.617 47.826 0.00 0.00 0.00 2.50
3954 5276 3.636300 CTCTGCTGGCATCTCTAGTAACT 59.364 47.826 0.00 0.00 0.00 2.24
4204 5526 6.901887 CAGCGTAAAAACACTATATGCTTCTG 59.098 38.462 0.00 0.00 39.28 3.02
4616 5939 5.124297 TGTTTGTGGCTGATGAGTTATGATG 59.876 40.000 0.00 0.00 0.00 3.07
4653 5979 7.387673 TGTGCGAATGGAGTATATTTTATCTGG 59.612 37.037 0.00 0.00 0.00 3.86
4793 6121 4.466828 GTGTCAAGTTCGATTTGTGATGG 58.533 43.478 9.24 0.00 0.00 3.51
4800 6128 4.695455 AGTTCGATTTGTGATGGATCGTTT 59.305 37.500 5.10 0.00 42.29 3.60
4832 6160 5.468409 TGTGAAAGCTCATTTGATCGTTACA 59.532 36.000 0.00 0.00 33.05 2.41
4847 6175 8.378172 TGATCGTTACATTGTCTCTTCTTTTT 57.622 30.769 0.00 0.00 0.00 1.94
4851 6179 6.513393 CGTTACATTGTCTCTTCTTTTTGGCT 60.513 38.462 0.00 0.00 0.00 4.75
4919 6248 1.760192 AGGCAGCTTTGCTTCATAGG 58.240 50.000 0.00 0.00 36.40 2.57
4927 6256 6.238842 GCAGCTTTGCTTCATAGGATATGAAA 60.239 38.462 12.04 0.00 36.40 2.69
4929 6258 7.861372 CAGCTTTGCTTCATAGGATATGAAAAG 59.139 37.037 12.04 12.76 36.40 2.27
4965 6294 9.690913 AGAAAAATCATAGGAAATGAGATGACA 57.309 29.630 0.00 0.00 31.41 3.58
4985 6314 8.604640 ATGACATGCATCTCAACTCTTATAAG 57.395 34.615 8.81 6.11 28.85 1.73
4986 6315 7.785033 TGACATGCATCTCAACTCTTATAAGA 58.215 34.615 14.42 14.42 0.00 2.10
5010 6339 8.162085 AGAAAATAGATGTCCTGTGATGCATAT 58.838 33.333 0.00 0.00 0.00 1.78
5046 6375 9.558396 TTTTTCATTGAATCTAGGCAATGTTTT 57.442 25.926 21.92 0.00 46.97 2.43
5047 6376 9.558396 TTTTCATTGAATCTAGGCAATGTTTTT 57.442 25.926 21.92 0.00 46.97 1.94
5072 6401 9.664332 TTTTTCTTTGAAAATGTGAAGGATTGA 57.336 25.926 6.35 0.00 0.00 2.57
5073 6402 9.835389 TTTTCTTTGAAAATGTGAAGGATTGAT 57.165 25.926 1.85 0.00 0.00 2.57
5074 6403 9.835389 TTTCTTTGAAAATGTGAAGGATTGATT 57.165 25.926 0.00 0.00 0.00 2.57
5075 6404 9.480053 TTCTTTGAAAATGTGAAGGATTGATTC 57.520 29.630 0.00 0.00 0.00 2.52
5076 6405 8.863086 TCTTTGAAAATGTGAAGGATTGATTCT 58.137 29.630 0.00 0.00 0.00 2.40
5077 6406 9.485206 CTTTGAAAATGTGAAGGATTGATTCTT 57.515 29.630 0.00 0.00 0.00 2.52
5109 6438 7.232737 ACATACGAATAGACATCCATTCCTACA 59.767 37.037 0.00 0.00 0.00 2.74
5118 6447 5.640147 ACATCCATTCCTACAAACCAAAGA 58.360 37.500 0.00 0.00 0.00 2.52
5122 6451 6.552008 TCCATTCCTACAAACCAAAGAGATT 58.448 36.000 0.00 0.00 0.00 2.40
5202 6531 2.981859 TCTTATGGACGAAAGGAGGC 57.018 50.000 0.00 0.00 0.00 4.70
5216 6545 2.462723 AGGAGGCCTAAGAAGTGAGAC 58.537 52.381 4.42 0.00 28.47 3.36
5225 6554 4.800993 CCTAAGAAGTGAGACGCATTGTAG 59.199 45.833 0.00 0.00 0.00 2.74
5242 6571 7.475015 GCATTGTAGCTCAAATTCTATGAACA 58.525 34.615 0.00 0.00 39.62 3.18
5253 6582 8.820933 TCAAATTCTATGAACAGCGATAGAAAG 58.179 33.333 0.00 0.00 41.97 2.62
5254 6583 8.820933 CAAATTCTATGAACAGCGATAGAAAGA 58.179 33.333 0.00 0.00 41.97 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 60 1.132643 GTAGTGGTAGTGGTCAGAGCG 59.867 57.143 0.00 0.00 0.00 5.03
53 61 1.477295 GGTAGTGGTAGTGGTCAGAGC 59.523 57.143 0.00 0.00 0.00 4.09
54 62 1.743958 CGGTAGTGGTAGTGGTCAGAG 59.256 57.143 0.00 0.00 0.00 3.35
55 63 1.830279 CGGTAGTGGTAGTGGTCAGA 58.170 55.000 0.00 0.00 0.00 3.27
88 96 3.680490 CTTTCTGGGAAAGAGGTCCTTC 58.320 50.000 12.94 0.00 37.85 3.46
92 100 2.869101 AGCTTTCTGGGAAAGAGGTC 57.131 50.000 19.99 5.95 35.91 3.85
114 122 8.745590 TCTTATATTCCTTGCCCTTTTGTTAAC 58.254 33.333 0.00 0.00 0.00 2.01
172 185 2.114411 GCGGGGTTGGAGTTGGAA 59.886 61.111 0.00 0.00 0.00 3.53
173 186 2.285889 TTTGCGGGGTTGGAGTTGGA 62.286 55.000 0.00 0.00 0.00 3.53
174 187 1.395826 TTTTGCGGGGTTGGAGTTGG 61.396 55.000 0.00 0.00 0.00 3.77
175 188 0.461961 TTTTTGCGGGGTTGGAGTTG 59.538 50.000 0.00 0.00 0.00 3.16
176 189 0.462375 GTTTTTGCGGGGTTGGAGTT 59.538 50.000 0.00 0.00 0.00 3.01
177 190 0.684805 TGTTTTTGCGGGGTTGGAGT 60.685 50.000 0.00 0.00 0.00 3.85
260 307 0.896226 GCACGGTAAACTCCTCTCCT 59.104 55.000 0.00 0.00 0.00 3.69
261 308 0.458025 CGCACGGTAAACTCCTCTCC 60.458 60.000 0.00 0.00 0.00 3.71
262 309 0.458025 CCGCACGGTAAACTCCTCTC 60.458 60.000 0.00 0.00 0.00 3.20
263 310 1.590147 CCGCACGGTAAACTCCTCT 59.410 57.895 0.00 0.00 0.00 3.69
264 311 2.098831 GCCGCACGGTAAACTCCTC 61.099 63.158 11.27 0.00 37.65 3.71
318 365 1.080569 CCCGTTTCCAGCATGCAAC 60.081 57.895 21.98 14.12 31.97 4.17
338 385 2.745492 GGTGAGGCTCTGCACTGC 60.745 66.667 16.72 0.00 35.43 4.40
344 391 2.555199 CCTATTTTCGGTGAGGCTCTG 58.445 52.381 16.72 5.87 0.00 3.35
345 392 2.990066 CCTATTTTCGGTGAGGCTCT 57.010 50.000 16.72 0.00 0.00 4.09
350 397 2.614057 GTGATGGCCTATTTTCGGTGAG 59.386 50.000 3.32 0.00 0.00 3.51
351 398 2.238646 AGTGATGGCCTATTTTCGGTGA 59.761 45.455 3.32 0.00 0.00 4.02
352 399 2.614057 GAGTGATGGCCTATTTTCGGTG 59.386 50.000 3.32 0.00 0.00 4.94
456 525 3.459063 CTCCCTCGAACCCCGTCC 61.459 72.222 0.00 0.00 39.75 4.79
606 676 5.106078 ACACCAGTATCGTCTCTTTTCTCTC 60.106 44.000 0.00 0.00 0.00 3.20
608 678 4.859798 CACACCAGTATCGTCTCTTTTCTC 59.140 45.833 0.00 0.00 0.00 2.87
689 759 3.716006 CGCGCTCACCCACACTTG 61.716 66.667 5.56 0.00 0.00 3.16
719 1587 4.179599 GAGGGAGGGAGGGAGGGG 62.180 77.778 0.00 0.00 0.00 4.79
720 1588 4.179599 GGAGGGAGGGAGGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
721 1589 3.039526 AGGAGGGAGGGAGGGAGG 61.040 72.222 0.00 0.00 0.00 4.30
722 1590 2.612251 GAGGAGGGAGGGAGGGAG 59.388 72.222 0.00 0.00 0.00 4.30
723 1591 3.036959 GGAGGAGGGAGGGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
724 1592 4.179599 GGGAGGAGGGAGGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
725 1593 3.039526 AGGGAGGAGGGAGGGAGG 61.040 72.222 0.00 0.00 0.00 4.30
738 1606 3.036959 GAGGGAGGGGAGGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
740 1608 3.430497 TCGAGGGAGGGGAGGAGG 61.430 72.222 0.00 0.00 0.00 4.30
742 1610 3.752167 GGTCGAGGGAGGGGAGGA 61.752 72.222 0.00 0.00 0.00 3.71
814 1711 2.527547 GAAGCGGCGTGGTGGAATTG 62.528 60.000 9.37 0.00 0.00 2.32
815 1712 2.282180 AAGCGGCGTGGTGGAATT 60.282 55.556 9.37 0.00 0.00 2.17
816 1713 2.746277 GAAGCGGCGTGGTGGAAT 60.746 61.111 9.37 0.00 0.00 3.01
817 1714 3.469863 AAGAAGCGGCGTGGTGGAA 62.470 57.895 9.37 0.00 0.00 3.53
818 1715 3.876589 GAAGAAGCGGCGTGGTGGA 62.877 63.158 9.37 0.00 0.00 4.02
819 1716 3.423154 GAAGAAGCGGCGTGGTGG 61.423 66.667 9.37 0.00 0.00 4.61
820 1717 3.423154 GGAAGAAGCGGCGTGGTG 61.423 66.667 9.37 0.00 0.00 4.17
822 1719 4.735132 TCGGAAGAAGCGGCGTGG 62.735 66.667 9.37 0.00 37.03 4.94
863 1765 7.716560 CAGAAAACCCAAAAATCCAAGAAAGAT 59.283 33.333 0.00 0.00 0.00 2.40
865 1767 6.260714 CCAGAAAACCCAAAAATCCAAGAAAG 59.739 38.462 0.00 0.00 0.00 2.62
877 1780 0.259356 ACGTCCCCAGAAAACCCAAA 59.741 50.000 0.00 0.00 0.00 3.28
1308 2237 4.698625 ACGGAGGGCGGGAACTCT 62.699 66.667 0.00 0.00 34.22 3.24
1573 2545 0.038166 TCCACACAAATCCTGCTCCC 59.962 55.000 0.00 0.00 0.00 4.30
1595 2567 3.670055 CGAATCCATGCAAACAAGAACAC 59.330 43.478 0.00 0.00 0.00 3.32
1625 2597 2.222886 CCTCAAAGCATCAACGTCGATG 60.223 50.000 12.21 12.21 44.69 3.84
1626 2598 2.002586 CCTCAAAGCATCAACGTCGAT 58.997 47.619 0.00 0.00 0.00 3.59
1657 2629 3.039743 AGCATCACCATCATCAGAGACT 58.960 45.455 0.00 0.00 0.00 3.24
1774 2754 9.996554 ATGGTTTTTACTAATTCCCTTTTTCTG 57.003 29.630 0.00 0.00 0.00 3.02
1838 2819 4.451096 CGTCCTTACAAGCATGTTAGTGTT 59.549 41.667 0.00 0.00 41.05 3.32
1853 2834 2.685897 AGATGACTGAGCTCGTCCTTAC 59.314 50.000 25.43 17.16 0.00 2.34
1913 2894 3.181492 GGCTTTCTGGCTATTGAAGAAGC 60.181 47.826 0.00 0.00 38.32 3.86
2049 3054 1.355381 ACAGTTGCCAAGGGATCATCA 59.645 47.619 0.00 0.00 0.00 3.07
2050 3055 2.134789 ACAGTTGCCAAGGGATCATC 57.865 50.000 0.00 0.00 0.00 2.92
2051 3056 2.610438 AACAGTTGCCAAGGGATCAT 57.390 45.000 0.00 0.00 0.00 2.45
2082 3087 2.794910 CAGAGTACGGACACACAACAAG 59.205 50.000 0.00 0.00 0.00 3.16
2083 3088 2.482316 CCAGAGTACGGACACACAACAA 60.482 50.000 0.00 0.00 0.00 2.83
2084 3089 1.067974 CCAGAGTACGGACACACAACA 59.932 52.381 0.00 0.00 0.00 3.33
2123 3336 2.034221 GACCAGGCAGGAACCCAC 59.966 66.667 1.67 0.00 41.22 4.61
2164 3377 3.929610 GCATCCTCTGTAAGTCTCACAAC 59.070 47.826 0.00 0.00 33.76 3.32
2194 3407 1.000717 ACTTGGTGTTAACAATGCGGC 60.001 47.619 10.51 0.00 0.00 6.53
2195 3408 2.034053 ACACTTGGTGTTAACAATGCGG 59.966 45.455 10.51 2.92 45.08 5.69
2219 3432 2.912956 ACCTCTGAGAATAGGGCACAAA 59.087 45.455 6.17 0.00 37.18 2.83
2222 3435 1.139853 CCACCTCTGAGAATAGGGCAC 59.860 57.143 6.17 0.00 37.18 5.01
2235 3448 1.749638 CGTCGACTAGGCCACCTCT 60.750 63.158 14.70 0.00 34.61 3.69
2250 3463 4.096682 ACTGAGCAGAAAGTATCTACCGTC 59.903 45.833 4.21 0.00 36.32 4.79
2254 3467 8.030106 AGTAACAACTGAGCAGAAAGTATCTAC 58.970 37.037 4.21 0.99 36.32 2.59
2404 3657 3.487544 GGACAGATTATTCAACCAAGCGC 60.488 47.826 0.00 0.00 0.00 5.92
2406 3659 3.689649 ACGGACAGATTATTCAACCAAGC 59.310 43.478 0.00 0.00 0.00 4.01
2437 3691 6.715347 AAGAAAGACTTGCTTGGTACAAAT 57.285 33.333 7.70 0.00 39.88 2.32
2525 3779 4.159135 ACGGTATCGACAACTTGGTAGAAT 59.841 41.667 0.34 0.00 40.11 2.40
2604 3858 7.499232 TCCTATAGAATTCCTACAAAGCAAAGC 59.501 37.037 0.00 0.00 0.00 3.51
2761 4015 9.396022 TCACTTGGTTCATAGGATAAGAATTTC 57.604 33.333 0.00 0.00 30.42 2.17
2841 4095 6.691491 GCATCCTTTGGTTCATAGGAATAGGA 60.691 42.308 10.27 12.46 42.85 2.94
2866 4135 6.292168 CGATTTCGCAACCTATTACACTTAGG 60.292 42.308 0.00 0.00 41.74 2.69
3319 4596 4.081142 TCAACAACTCAGAGTCCTCAAACA 60.081 41.667 2.72 0.00 0.00 2.83
3778 5084 8.160765 TGGAATAACACAGTAAATCTCTGGAAA 58.839 33.333 0.00 0.00 37.25 3.13
3802 5108 8.044908 ACTGGGTAAACAATATAGTACAAGTGG 58.955 37.037 0.00 0.00 0.00 4.00
3873 5184 9.832445 GGATAACAATTCCTGAGTTATTGTAGA 57.168 33.333 9.03 3.32 40.54 2.59
3874 5185 9.613428 TGGATAACAATTCCTGAGTTATTGTAG 57.387 33.333 9.03 0.00 40.54 2.74
3894 5214 9.866655 AAAGCTCATAATACTGGAAATGGATAA 57.133 29.630 0.00 0.00 0.00 1.75
3896 5216 8.773033 AAAAGCTCATAATACTGGAAATGGAT 57.227 30.769 0.00 0.00 0.00 3.41
3909 5229 2.159198 CGGCTGCCAAAAAGCTCATAAT 60.159 45.455 20.29 0.00 40.64 1.28
3910 5230 1.202114 CGGCTGCCAAAAAGCTCATAA 59.798 47.619 20.29 0.00 40.64 1.90
3919 5239 4.063529 CAGAGTCGGCTGCCAAAA 57.936 55.556 20.29 0.00 0.00 2.44
3927 5247 2.894387 GATGCCAGCAGAGTCGGC 60.894 66.667 7.22 7.22 46.43 5.54
3932 5252 3.636300 AGTTACTAGAGATGCCAGCAGAG 59.364 47.826 0.00 0.00 0.00 3.35
3939 5261 4.642885 AGTGTCAGAGTTACTAGAGATGCC 59.357 45.833 0.00 0.00 0.00 4.40
3953 5275 4.728882 GCGGCAAAATATTCAGTGTCAGAG 60.729 45.833 0.00 0.00 0.00 3.35
3954 5276 3.126858 GCGGCAAAATATTCAGTGTCAGA 59.873 43.478 0.00 0.00 0.00 3.27
4616 5939 2.414559 CCATTCGCACACAAGTGGAATC 60.415 50.000 5.08 0.00 45.98 2.52
4793 6121 7.009174 TGAGCTTTCACAAAAAGAAAAACGATC 59.991 33.333 1.85 0.00 34.84 3.69
4800 6128 8.721019 ATCAAATGAGCTTTCACAAAAAGAAA 57.279 26.923 1.85 0.00 34.16 2.52
4886 6215 6.127730 GCAAAGCTGCCTTATAGTTTTCCTAA 60.128 38.462 0.00 0.00 43.26 2.69
4905 6234 7.710896 ACTTTTCATATCCTATGAAGCAAAGC 58.289 34.615 14.14 0.00 38.98 3.51
4945 6274 6.540083 TGCATGTCATCTCATTTCCTATGAT 58.460 36.000 0.00 0.00 31.49 2.45
4985 6314 6.630444 ATGCATCACAGGACATCTATTTTC 57.370 37.500 0.00 0.00 0.00 2.29
4986 6315 7.940688 TCATATGCATCACAGGACATCTATTTT 59.059 33.333 0.19 0.00 0.00 1.82
4997 6326 9.976511 AAAAATTCTTATCATATGCATCACAGG 57.023 29.630 0.19 0.00 0.00 4.00
5046 6375 9.664332 TCAATCCTTCACATTTTCAAAGAAAAA 57.336 25.926 8.75 0.00 32.99 1.94
5047 6376 9.835389 ATCAATCCTTCACATTTTCAAAGAAAA 57.165 25.926 7.30 7.30 0.00 2.29
5048 6377 9.835389 AATCAATCCTTCACATTTTCAAAGAAA 57.165 25.926 0.00 0.00 0.00 2.52
5049 6378 9.480053 GAATCAATCCTTCACATTTTCAAAGAA 57.520 29.630 0.00 0.00 0.00 2.52
5050 6379 8.863086 AGAATCAATCCTTCACATTTTCAAAGA 58.137 29.630 0.00 0.00 0.00 2.52
5051 6380 9.485206 AAGAATCAATCCTTCACATTTTCAAAG 57.515 29.630 0.00 0.00 0.00 2.77
5078 6407 9.862371 GAATGGATGTCTATTCGTATGTAGAAT 57.138 33.333 3.79 0.00 40.88 2.40
5079 6408 8.304596 GGAATGGATGTCTATTCGTATGTAGAA 58.695 37.037 11.40 0.00 42.52 2.10
5080 6409 7.670140 AGGAATGGATGTCTATTCGTATGTAGA 59.330 37.037 11.08 0.00 42.52 2.59
5081 6410 7.831753 AGGAATGGATGTCTATTCGTATGTAG 58.168 38.462 11.08 0.00 42.52 2.74
5082 6411 7.776618 AGGAATGGATGTCTATTCGTATGTA 57.223 36.000 11.08 0.00 42.52 2.29
5083 6412 6.672266 AGGAATGGATGTCTATTCGTATGT 57.328 37.500 11.08 0.00 42.52 2.29
5084 6413 7.602753 TGTAGGAATGGATGTCTATTCGTATG 58.397 38.462 18.12 0.00 42.11 2.39
5085 6414 7.776618 TGTAGGAATGGATGTCTATTCGTAT 57.223 36.000 18.12 8.84 42.11 3.06
5086 6415 7.591421 TTGTAGGAATGGATGTCTATTCGTA 57.409 36.000 13.82 13.82 42.52 3.43
5087 6416 6.479972 TTGTAGGAATGGATGTCTATTCGT 57.520 37.500 15.33 15.33 42.52 3.85
5088 6417 6.202954 GGTTTGTAGGAATGGATGTCTATTCG 59.797 42.308 11.40 0.00 42.52 3.34
5089 6418 7.054124 TGGTTTGTAGGAATGGATGTCTATTC 58.946 38.462 9.77 9.77 41.37 1.75
5090 6419 6.969043 TGGTTTGTAGGAATGGATGTCTATT 58.031 36.000 0.00 0.00 0.00 1.73
5091 6420 6.575244 TGGTTTGTAGGAATGGATGTCTAT 57.425 37.500 0.00 0.00 0.00 1.98
5092 6421 6.381498 TTGGTTTGTAGGAATGGATGTCTA 57.619 37.500 0.00 0.00 0.00 2.59
5093 6422 4.927267 TGGTTTGTAGGAATGGATGTCT 57.073 40.909 0.00 0.00 0.00 3.41
5094 6423 5.710099 TCTTTGGTTTGTAGGAATGGATGTC 59.290 40.000 0.00 0.00 0.00 3.06
5095 6424 5.640147 TCTTTGGTTTGTAGGAATGGATGT 58.360 37.500 0.00 0.00 0.00 3.06
5096 6425 5.945784 TCTCTTTGGTTTGTAGGAATGGATG 59.054 40.000 0.00 0.00 0.00 3.51
5100 6429 7.452880 TGAATCTCTTTGGTTTGTAGGAATG 57.547 36.000 0.00 0.00 0.00 2.67
5135 6464 9.241919 TCACATGACATATGAATTTTGTAGGTT 57.758 29.630 10.38 0.00 0.00 3.50
5136 6465 8.806429 TCACATGACATATGAATTTTGTAGGT 57.194 30.769 10.38 0.00 0.00 3.08
5185 6514 1.580059 AGGCCTCCTTTCGTCCATAA 58.420 50.000 0.00 0.00 0.00 1.90
5188 6517 0.902531 CTTAGGCCTCCTTTCGTCCA 59.097 55.000 9.68 0.00 34.61 4.02
5202 6531 3.589988 ACAATGCGTCTCACTTCTTAGG 58.410 45.455 0.00 0.00 0.00 2.69
5216 6545 6.291067 TCATAGAATTTGAGCTACAATGCG 57.709 37.500 0.00 0.00 38.36 4.73
5225 6554 4.864916 TCGCTGTTCATAGAATTTGAGC 57.135 40.909 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.