Multiple sequence alignment - TraesCS6D01G289600

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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 TraesCS6D01G289600 chr6D 100.000 6166 0 0 1 6166 400551173 400545008 0.000000e+00 11387.0
1 TraesCS6D01G289600 chr6A 93.153 5272 210 61 638 5856 546552155 546546982 0.000000e+00 7596.0
2 TraesCS6D01G289600 chr6A 92.405 316 24 0 5851 6166 546504408 546504093 9.430000e-123 451.0
3 TraesCS6D01G289600 chr6A 86.571 417 34 12 246 651 546553539 546553134 2.040000e-119 440.0
4 TraesCS6D01G289600 chr6A 86.071 280 35 3 87 365 546553813 546553537 1.300000e-76 298.0
5 TraesCS6D01G289600 chr6B 95.224 3706 125 24 1573 5247 599445621 599441937 0.000000e+00 5816.0
6 TraesCS6D01G289600 chr6B 88.568 1592 134 25 1 1568 599447293 599445726 0.000000e+00 1888.0
7 TraesCS6D01G289600 chr6B 91.554 888 53 8 5275 6147 599441936 599441056 0.000000e+00 1205.0
8 TraesCS6D01G289600 chr7D 86.813 182 18 3 1116 1297 152652784 152652609 1.360000e-46 198.0
9 TraesCS6D01G289600 chr7D 77.778 189 34 7 83 267 610795365 610795549 6.530000e-20 110.0
10 TraesCS6D01G289600 chr7A 85.484 186 20 4 1113 1297 153381555 153381376 2.930000e-43 187.0
11 TraesCS6D01G289600 chr7A 75.241 311 58 14 49 347 30719703 30719400 5.020000e-26 130.0
12 TraesCS6D01G289600 chr2D 77.477 222 44 5 42 259 546780238 546780457 1.800000e-25 128.0
13 TraesCS6D01G289600 chr2D 77.540 187 35 7 48 230 595156805 595156988 8.450000e-19 106.0
14 TraesCS6D01G289600 chr2B 73.810 336 74 12 36 363 653584354 653584683 3.020000e-23 121.0
15 TraesCS6D01G289600 chr3B 75.200 250 44 13 33 279 547128343 547128109 1.090000e-17 102.0
16 TraesCS6D01G289600 chr3B 88.235 51 6 0 2981 3031 568570871 568570821 1.860000e-05 62.1
17 TraesCS6D01G289600 chr3B 88.235 51 6 0 2981 3031 568855262 568855212 1.860000e-05 62.1
18 TraesCS6D01G289600 chr4D 73.835 279 61 10 41 313 344128539 344128811 3.930000e-17 100.0
19 TraesCS6D01G289600 chr1D 78.912 147 28 3 86 232 433458996 433458853 5.090000e-16 97.1
20 TraesCS6D01G289600 chr5A 80.328 122 21 3 2981 3100 455084711 455084591 8.510000e-14 89.8
21 TraesCS6D01G289600 chr5D 79.675 123 24 1 2981 3102 257502283 257502161 3.060000e-13 87.9
22 TraesCS6D01G289600 chr5D 85.714 77 11 0 2981 3057 512300873 512300949 1.420000e-11 82.4
23 TraesCS6D01G289600 chr4A 75.301 166 22 13 2981 3131 594142028 594141867 1.860000e-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 TraesCS6D01G289600 chr6D 400545008 400551173 6165 True 11387.000000 11387 100.000000 1 6166 1 chr6D.!!$R1 6165
1 TraesCS6D01G289600 chr6A 546546982 546553813 6831 True 2778.000000 7596 88.598333 87 5856 3 chr6A.!!$R2 5769
2 TraesCS6D01G289600 chr6B 599441056 599447293 6237 True 2969.666667 5816 91.782000 1 6147 3 chr6B.!!$R1 6146

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
620 762 0.249155 CCCGTCACTTACACGTGTGT 60.249 55.000 30.83 18.22 46.87 3.72 F
1475 2634 1.205064 CGCTTCTCGCAACAACAGG 59.795 57.895 0.00 0.00 39.08 4.00 F
2127 3386 0.251916 CCGTATGCAGGAAGGTTGGA 59.748 55.000 0.00 0.00 0.00 3.53 F
2627 3905 2.930040 CACAGTTTGTACTATCTGGCCG 59.070 50.000 16.36 0.00 31.96 6.13 F
3105 4391 2.027192 GTGGGTGCTCACTTTAGGATGA 60.027 50.000 0.00 0.00 34.98 2.92 F
4323 5640 2.151502 TGTGCTGAACCCTTTTCCAA 57.848 45.000 0.00 0.00 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2076 3335 0.540923 GGAGCTGAGCAATCTCCACT 59.459 55.000 7.39 0.00 44.38 4.00 R
2990 4269 0.179000 CTAAGCGTCCAAGGCAGGAT 59.821 55.000 1.91 0.00 40.42 3.24 R
3034 4319 0.605589 TAAGGCGGGCAAAATTGTGG 59.394 50.000 3.78 0.00 0.00 4.17 R
3661 4977 1.981495 CTTCTGGATGGGGGATAGGAC 59.019 57.143 0.00 0.00 0.00 3.85 R
4764 6081 0.170561 CCATCGTCGTCGGACTCTTT 59.829 55.000 6.57 0.00 41.16 2.52 R
6126 7464 1.065418 GGCCACCACTACTGCAGTAAT 60.065 52.381 25.95 15.29 34.98 1.89 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
25 26 2.437413 GTTGTTGAACCCTCCCAGATC 58.563 52.381 0.00 0.00 0.00 2.75
53 54 1.001924 TGCACACGCACGATGAAAAAT 60.002 42.857 0.00 0.00 45.36 1.82
62 63 4.142687 CGCACGATGAAAAATCCTAACCTT 60.143 41.667 0.00 0.00 0.00 3.50
67 68 5.583457 CGATGAAAAATCCTAACCTTACCGT 59.417 40.000 0.00 0.00 0.00 4.83
68 69 6.093082 CGATGAAAAATCCTAACCTTACCGTT 59.907 38.462 0.00 0.00 0.00 4.44
69 70 7.361457 CGATGAAAAATCCTAACCTTACCGTTT 60.361 37.037 0.00 0.00 0.00 3.60
92 93 8.548721 GTTTCAAAGAGACGAAAGAAATCTACA 58.451 33.333 0.00 0.00 32.03 2.74
102 103 4.329462 AAGAAATCTACATCGGAGCTCC 57.671 45.455 23.79 23.79 0.00 4.70
136 137 5.928976 TCCAGACAGACAAATTCAAGAAGA 58.071 37.500 0.00 0.00 0.00 2.87
140 141 7.040892 CCAGACAGACAAATTCAAGAAGAATCA 60.041 37.037 0.00 0.00 46.09 2.57
145 146 6.713903 AGACAAATTCAAGAAGAATCAGAGCA 59.286 34.615 0.00 0.00 46.09 4.26
195 196 4.812476 TCCGTCCGAATGCTGCCG 62.812 66.667 0.00 0.00 0.00 5.69
238 239 1.002033 CGTAAACTACTAGCCGCCGAT 60.002 52.381 0.00 0.00 0.00 4.18
259 375 1.082206 ACCGGAATTCTCCTCCCCA 59.918 57.895 9.46 0.00 39.93 4.96
268 384 1.460305 CTCCTCCCCATCACCGGAT 60.460 63.158 9.46 0.00 0.00 4.18
289 405 0.391130 CCGGAGCGATGGTCAAAAGA 60.391 55.000 0.00 0.00 0.00 2.52
294 410 3.074412 GAGCGATGGTCAAAAGAAAGGA 58.926 45.455 0.00 0.00 0.00 3.36
295 411 3.486383 AGCGATGGTCAAAAGAAAGGAA 58.514 40.909 0.00 0.00 0.00 3.36
303 419 5.423610 TGGTCAAAAGAAAGGAAAATCCACA 59.576 36.000 0.00 0.00 39.61 4.17
309 425 1.826385 AAGGAAAATCCACAGGCTCG 58.174 50.000 0.00 0.00 39.61 5.03
356 476 2.728817 CCTAGCCGTCGCTTAGGG 59.271 66.667 10.75 0.00 45.55 3.53
365 485 2.809696 CCGTCGCTTAGGGAAAAAGAAA 59.190 45.455 0.00 0.00 34.90 2.52
367 487 3.497262 CGTCGCTTAGGGAAAAAGAAAGT 59.503 43.478 0.00 0.00 0.00 2.66
369 489 5.212934 GTCGCTTAGGGAAAAAGAAAGTTG 58.787 41.667 0.00 0.00 0.00 3.16
382 502 8.839947 AAAAAGAAAGTTGCATGCAATTTAAC 57.160 26.923 33.00 28.01 35.35 2.01
408 528 8.998377 CCAAACTTAAATTTCCCAAGGTTTATG 58.002 33.333 0.00 0.00 26.74 1.90
432 552 9.875691 ATGATATTTTTCCTTTAGGCTGTTTTC 57.124 29.630 0.00 0.00 34.44 2.29
498 618 6.986231 GGGTGAATGAAAGTGAAAAGTCAAAT 59.014 34.615 0.00 0.00 34.87 2.32
511 631 9.618410 GTGAAAAGTCAAATGATTTAACGTTTG 57.382 29.630 5.91 0.00 43.72 2.93
543 663 3.774616 TCAGCTGACCTGATGCATC 57.225 52.632 20.14 20.14 45.44 3.91
591 733 1.283613 ACACACAAGGTCACCTTTGGA 59.716 47.619 6.26 0.00 41.69 3.53
620 762 0.249155 CCCGTCACTTACACGTGTGT 60.249 55.000 30.83 18.22 46.87 3.72
865 2012 4.214327 CCTTCTCCGCTCCTCGCC 62.214 72.222 0.00 0.00 36.73 5.54
866 2013 3.144193 CTTCTCCGCTCCTCGCCT 61.144 66.667 0.00 0.00 36.73 5.52
867 2014 3.132481 CTTCTCCGCTCCTCGCCTC 62.132 68.421 0.00 0.00 36.73 4.70
940 2087 2.113351 GCGAAATCCCTAGGGCCC 59.887 66.667 24.42 16.46 34.68 5.80
1142 2301 3.352990 TATGGCGGGCCCCAAGTTC 62.353 63.158 18.66 0.00 38.61 3.01
1422 2581 7.592533 CGTATTTCATATCAAATTTGCTCCTGG 59.407 37.037 13.54 1.37 0.00 4.45
1424 2583 5.840243 TCATATCAAATTTGCTCCTGGTG 57.160 39.130 13.54 5.51 0.00 4.17
1439 2598 2.086869 CTGGTGTGGGAACATTAGCTG 58.913 52.381 0.00 0.00 46.14 4.24
1443 2602 3.378427 GGTGTGGGAACATTAGCTGATTC 59.622 47.826 0.00 0.00 46.14 2.52
1452 2611 6.319658 GGAACATTAGCTGATTCTGGATGAAA 59.680 38.462 0.00 0.00 38.29 2.69
1456 2615 7.341256 ACATTAGCTGATTCTGGATGAAATTGT 59.659 33.333 0.00 0.00 38.29 2.71
1470 2629 1.225855 AATTGTCGCTTCTCGCAACA 58.774 45.000 0.00 0.00 37.16 3.33
1475 2634 1.205064 CGCTTCTCGCAACAACAGG 59.795 57.895 0.00 0.00 39.08 4.00
1532 2691 3.474798 AAGACCAGACCAGGATGTCTA 57.525 47.619 0.00 0.00 43.63 2.59
1769 3028 2.034878 TCCTCTGGATTCGAGGTGATG 58.965 52.381 10.50 0.00 46.49 3.07
1810 3069 6.212888 AGTTTGAGTTGCTTGTTTCTCATT 57.787 33.333 0.00 0.00 36.91 2.57
1958 3217 9.472361 GGACACGCTGTTTTATTCTCTAATATA 57.528 33.333 0.00 0.00 0.00 0.86
2094 3353 1.206610 TCAGTGGAGATTGCTCAGCTC 59.793 52.381 0.00 0.00 43.14 4.09
2127 3386 0.251916 CCGTATGCAGGAAGGTTGGA 59.748 55.000 0.00 0.00 0.00 3.53
2166 3425 7.028962 CGTTTCATCTCCATGCATTCTTTTTA 58.971 34.615 0.00 0.00 0.00 1.52
2339 3598 4.317418 GCAAACTCGTCGTTAGCATCTATG 60.317 45.833 0.00 0.00 33.90 2.23
2496 3755 3.896122 TGAGTGTTAAGAAATTTGCGGC 58.104 40.909 0.00 0.00 0.00 6.53
2595 3873 8.686334 CCAGCCTACAATAATGTACTGATTTTT 58.314 33.333 9.18 0.00 37.91 1.94
2627 3905 2.930040 CACAGTTTGTACTATCTGGCCG 59.070 50.000 16.36 0.00 31.96 6.13
2682 3960 4.193865 TGATATGTGCACCATCTCAACAG 58.806 43.478 22.14 0.00 34.70 3.16
2881 4159 6.429385 AGTTGCTCTATTTTGAACCTGAAGAG 59.571 38.462 0.00 0.00 33.70 2.85
3034 4319 3.890936 AAGCACGCTGACAGCTCCC 62.891 63.158 24.36 12.03 39.60 4.30
3072 4358 4.202121 CCTTAGGCACTTAGTCATCGCTAA 60.202 45.833 0.00 0.00 41.75 3.09
3094 4380 2.521451 TTAAGGCGGTGGGTGCTCA 61.521 57.895 0.00 0.00 0.00 4.26
3105 4391 2.027192 GTGGGTGCTCACTTTAGGATGA 60.027 50.000 0.00 0.00 34.98 2.92
3106 4392 2.846206 TGGGTGCTCACTTTAGGATGAT 59.154 45.455 0.00 0.00 0.00 2.45
3107 4393 3.209410 GGGTGCTCACTTTAGGATGATG 58.791 50.000 0.00 0.00 0.00 3.07
3108 4394 2.615912 GGTGCTCACTTTAGGATGATGC 59.384 50.000 0.00 0.00 0.00 3.91
3109 4395 2.615912 GTGCTCACTTTAGGATGATGCC 59.384 50.000 0.00 0.00 0.00 4.40
3110 4396 2.507058 TGCTCACTTTAGGATGATGCCT 59.493 45.455 0.00 0.00 42.15 4.75
3135 4421 4.513442 ACCGCATAAGAACATTGCTTCTA 58.487 39.130 0.00 0.00 34.23 2.10
3204 4490 2.818130 TTTGTTTCTTGCCATCAGCC 57.182 45.000 0.00 0.00 42.71 4.85
3225 4512 7.127955 TCAGCCTTTATCTTTCCTAAATCTCCT 59.872 37.037 0.00 0.00 0.00 3.69
3286 4573 3.536956 TTCTAATCATGGGTGTCGGTC 57.463 47.619 0.00 0.00 0.00 4.79
3367 4668 5.423931 ACAACCCTCCTTGTGTTAATGTTTT 59.576 36.000 0.00 0.00 32.95 2.43
3627 4943 2.684843 CCAGGAAGCTGCGTTCTGC 61.685 63.158 17.14 0.00 46.70 4.26
3661 4977 6.451064 AACCTTAACAAAGTCTTCTTGTGG 57.549 37.500 0.00 0.00 33.79 4.17
3758 5074 6.761099 TCTTCTAGTGTGATTGGAGTAGTC 57.239 41.667 0.00 0.00 0.00 2.59
3771 5087 4.798882 TGGAGTAGTCCCAATTTTGTGTT 58.201 39.130 14.26 0.00 43.15 3.32
3822 5138 3.612479 GCCTTGGAAGTATGCTTGTGTTG 60.612 47.826 0.00 0.00 34.61 3.33
3845 5161 9.705290 GTTGGTCCATTTTATAATTTTCAGTGT 57.295 29.630 0.00 0.00 0.00 3.55
3891 5207 7.046652 GCATTATGTCAGCTGATATCTACCAT 58.953 38.462 26.94 20.56 0.00 3.55
4039 5355 6.420903 GTCTATCCTTTTGTTTCTTTGTTGGC 59.579 38.462 0.00 0.00 0.00 4.52
4068 5384 7.189512 CCTCTTTACAAGCTCCAATTATTTCG 58.810 38.462 0.00 0.00 0.00 3.46
4261 5578 7.277174 ACATAAAGCATTTGGTCTATTAGGC 57.723 36.000 0.00 0.00 39.63 3.93
4323 5640 2.151502 TGTGCTGAACCCTTTTCCAA 57.848 45.000 0.00 0.00 0.00 3.53
4433 5750 2.224992 TGCCCTCACCTTTTGCAGATTA 60.225 45.455 0.00 0.00 0.00 1.75
4447 5764 5.592104 TGCAGATTATCTACGGAAACAGA 57.408 39.130 0.00 0.00 0.00 3.41
4536 5853 3.181468 TGACCAGCAGATATGCTCAAGAG 60.181 47.826 12.92 0.29 44.30 2.85
4597 5914 4.072131 GTTCCTTGCCTTGTTCTCACATA 58.928 43.478 0.00 0.00 31.06 2.29
4614 5931 8.969260 TCTCACATAATGTTCTTGCATAGATT 57.031 30.769 0.00 0.00 31.54 2.40
4737 6054 4.598036 AGGGTCCAAAAGTGATGATGAT 57.402 40.909 0.00 0.00 0.00 2.45
4918 6235 3.118482 ACCCTGCTGAGAGATGTATTGTG 60.118 47.826 0.00 0.00 0.00 3.33
4922 6239 3.193479 TGCTGAGAGATGTATTGTGTCGT 59.807 43.478 0.00 0.00 0.00 4.34
5105 6425 5.416013 GCTAGCCCTGAAAACTCTTATTTGT 59.584 40.000 2.29 0.00 0.00 2.83
5112 6432 9.720769 CCCTGAAAACTCTTATTTGTACTTCTA 57.279 33.333 0.00 0.00 0.00 2.10
5123 6443 9.539825 CTTATTTGTACTTCTAGTCTCATGCAT 57.460 33.333 0.00 0.00 0.00 3.96
5125 6445 8.798859 ATTTGTACTTCTAGTCTCATGCATTT 57.201 30.769 0.00 0.00 0.00 2.32
5231 6551 4.681978 GGGACGCCAGCACGAACT 62.682 66.667 0.00 0.00 36.70 3.01
5240 6560 1.067283 CCAGCACGAACTGTCTGATCT 60.067 52.381 8.28 0.00 35.83 2.75
5244 6564 2.416027 GCACGAACTGTCTGATCTGCTA 60.416 50.000 0.00 0.00 0.00 3.49
5261 6581 5.570320 TCTGCTAAAGCCTGAAAATTACCT 58.430 37.500 0.00 0.00 41.18 3.08
5265 6585 5.183140 GCTAAAGCCTGAAAATTACCTGTCA 59.817 40.000 0.00 0.00 34.31 3.58
5308 6628 4.706035 TCAAGTAGCGTCCTGGTTTTAAA 58.294 39.130 0.00 0.00 0.00 1.52
5389 6709 5.515626 GCTACATGGAGTAAACAGTAACTCG 59.484 44.000 6.84 1.07 42.51 4.18
5413 6733 1.148310 TTAGCGAGCTTGTTCTGCAC 58.852 50.000 1.86 0.00 0.00 4.57
5465 6789 8.279970 TGTGACCTAATTGTCTTATGGATTTG 57.720 34.615 0.00 0.00 36.21 2.32
5466 6790 7.888021 TGTGACCTAATTGTCTTATGGATTTGT 59.112 33.333 0.00 0.00 36.21 2.83
5467 6791 8.739972 GTGACCTAATTGTCTTATGGATTTGTT 58.260 33.333 0.00 0.00 36.21 2.83
5468 6792 8.956426 TGACCTAATTGTCTTATGGATTTGTTC 58.044 33.333 0.00 0.00 36.21 3.18
5470 6794 9.308000 ACCTAATTGTCTTATGGATTTGTTCAA 57.692 29.630 0.00 0.00 0.00 2.69
5549 6876 6.187125 CTAGCATAGCATTGTGAGTTTGTT 57.813 37.500 0.00 0.00 0.00 2.83
5581 6908 9.276590 GGATCATTACATATGATGTTGAACTGA 57.723 33.333 10.38 0.09 41.63 3.41
5592 6919 7.800155 TGATGTTGAACTGAGTTATGTTTCA 57.200 32.000 0.00 0.00 0.00 2.69
5609 6936 7.935338 ATGTTTCAGCTAATTTGACAAGTTG 57.065 32.000 6.21 0.00 0.00 3.16
5614 6941 7.561021 TCAGCTAATTTGACAAGTTGTGTTA 57.439 32.000 14.57 6.44 41.96 2.41
5620 6947 9.515020 CTAATTTGACAAGTTGTGTTAATGTGT 57.485 29.630 14.57 0.00 41.96 3.72
5676 7013 4.972514 TGTCTGCAACAACAACATAACA 57.027 36.364 0.00 0.00 34.03 2.41
5713 7050 8.470040 AGCATCAAAATGAATCACAACATAAC 57.530 30.769 0.00 0.00 34.61 1.89
5750 7087 7.518370 CGAATACCATTATGCTTCACCTTACAC 60.518 40.741 0.00 0.00 0.00 2.90
5825 7163 7.384660 ACAAGCATGTAAAACAACACAATATGG 59.615 33.333 0.00 0.00 38.24 2.74
5829 7167 7.374272 CATGTAAAACAACACAATATGGGACA 58.626 34.615 0.00 0.00 35.43 4.02
5849 7187 7.936847 TGGGACATAACAAGTATCATGGAATAC 59.063 37.037 0.00 0.00 33.18 1.89
5867 7205 7.952671 TGGAATACATAGGTTACTCAGATGAC 58.047 38.462 0.00 0.00 0.00 3.06
5880 7218 0.179127 AGATGACGAGTGGCACATCG 60.179 55.000 26.50 26.50 44.52 3.84
5900 7238 9.897744 CACATCGGCAGAAATATATAACAAAAT 57.102 29.630 0.00 0.00 0.00 1.82
5949 7287 6.791887 AACAATCCATCACGACATGATATC 57.208 37.500 0.00 0.00 46.96 1.63
5953 7291 7.282901 ACAATCCATCACGACATGATATCAAAA 59.717 33.333 9.99 0.00 46.96 2.44
5954 7292 6.603237 TCCATCACGACATGATATCAAAAC 57.397 37.500 9.99 3.22 46.96 2.43
5955 7293 6.112058 TCCATCACGACATGATATCAAAACA 58.888 36.000 9.99 0.00 46.96 2.83
5956 7294 6.597280 TCCATCACGACATGATATCAAAACAA 59.403 34.615 9.99 0.00 46.96 2.83
5981 7319 1.563924 ACGCACACCATAAGAGGGTA 58.436 50.000 0.00 0.00 36.72 3.69
5992 7330 4.640201 CCATAAGAGGGTACATGTGTTTGG 59.360 45.833 9.11 0.00 0.00 3.28
5997 7335 3.634910 GAGGGTACATGTGTTTGGTGTTT 59.365 43.478 9.11 0.00 0.00 2.83
6005 7343 4.935885 TGTGTTTGGTGTTTCAAAATGC 57.064 36.364 0.00 0.00 38.21 3.56
6033 7371 6.639671 TCAAAACAACACACAAACATTAGC 57.360 33.333 0.00 0.00 0.00 3.09
6066 7404 5.854010 AACTTTCTGGTTTTTCTTCTCCC 57.146 39.130 0.00 0.00 0.00 4.30
6067 7405 4.867086 ACTTTCTGGTTTTTCTTCTCCCA 58.133 39.130 0.00 0.00 0.00 4.37
6077 7415 4.788925 TTTCTTCTCCCAGGAAAGTGAA 57.211 40.909 0.00 0.00 0.00 3.18
6093 7431 6.258947 GGAAAGTGAAGATCATAGCAACCTAC 59.741 42.308 0.00 0.00 0.00 3.18
6119 7457 5.221342 CCTCCTAGTTGTAGACATAGGCAAG 60.221 48.000 4.94 0.24 35.71 4.01
6145 7483 2.403252 ATTACTGCAGTAGTGGTGGC 57.597 50.000 24.79 0.00 40.65 5.01
6146 7484 0.323629 TTACTGCAGTAGTGGTGGCC 59.676 55.000 24.79 0.00 40.65 5.36
6147 7485 1.884075 TACTGCAGTAGTGGTGGCCG 61.884 60.000 22.67 0.00 40.65 6.13
6148 7486 3.958147 CTGCAGTAGTGGTGGCCGG 62.958 68.421 5.25 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.630369 CAGATCTGGGAGGGTTCAACA 59.370 52.381 15.38 0.00 0.00 3.33
48 49 7.585579 TTGAAACGGTAAGGTTAGGATTTTT 57.414 32.000 0.00 0.00 0.00 1.94
53 54 5.305128 TCTCTTTGAAACGGTAAGGTTAGGA 59.695 40.000 0.00 0.00 0.00 2.94
62 63 4.935702 TCTTTCGTCTCTTTGAAACGGTA 58.064 39.130 0.00 0.00 37.05 4.02
67 68 8.657074 TGTAGATTTCTTTCGTCTCTTTGAAA 57.343 30.769 0.00 0.00 33.38 2.69
68 69 8.833231 ATGTAGATTTCTTTCGTCTCTTTGAA 57.167 30.769 0.00 0.00 0.00 2.69
69 70 7.273598 CGATGTAGATTTCTTTCGTCTCTTTGA 59.726 37.037 0.00 0.00 0.00 2.69
102 103 0.099613 CTGTCTGGATGGAGTCGACG 59.900 60.000 10.46 0.00 0.00 5.12
108 109 4.582869 TGAATTTGTCTGTCTGGATGGAG 58.417 43.478 0.00 0.00 0.00 3.86
136 137 3.009916 AGTTGGTCTTCCATGCTCTGATT 59.990 43.478 0.00 0.00 43.91 2.57
140 141 1.066573 CGAGTTGGTCTTCCATGCTCT 60.067 52.381 13.20 1.97 43.91 4.09
145 146 3.578716 TCTTCTTCGAGTTGGTCTTCCAT 59.421 43.478 0.00 0.00 43.91 3.41
195 196 0.803117 GGGTTTTTAGTCCTCGCAGC 59.197 55.000 0.00 0.00 0.00 5.25
196 197 2.474410 AGGGTTTTTAGTCCTCGCAG 57.526 50.000 0.00 0.00 0.00 5.18
206 207 7.817478 GGCTAGTAGTTTACGTTAGGGTTTTTA 59.183 37.037 0.00 0.00 0.00 1.52
268 384 2.739849 TTTTGACCATCGCTCCGGCA 62.740 55.000 0.00 0.00 38.60 5.69
279 395 5.423610 TGTGGATTTTCCTTTCTTTTGACCA 59.576 36.000 0.00 0.00 37.46 4.02
280 396 5.912892 TGTGGATTTTCCTTTCTTTTGACC 58.087 37.500 0.00 0.00 37.46 4.02
281 397 5.985530 CCTGTGGATTTTCCTTTCTTTTGAC 59.014 40.000 0.00 0.00 37.46 3.18
289 405 2.162681 CGAGCCTGTGGATTTTCCTTT 58.837 47.619 0.00 0.00 37.46 3.11
294 410 2.040544 CGGCGAGCCTGTGGATTTT 61.041 57.895 12.70 0.00 0.00 1.82
295 411 2.436646 CGGCGAGCCTGTGGATTT 60.437 61.111 12.70 0.00 0.00 2.17
309 425 1.376609 CCCATCTAAGCAACACCGGC 61.377 60.000 0.00 0.00 0.00 6.13
356 476 8.946935 GTTAAATTGCATGCAACTTTCTTTTTC 58.053 29.630 34.10 19.60 38.88 2.29
365 485 5.367302 AGTTTGGTTAAATTGCATGCAACT 58.633 33.333 34.10 22.76 38.88 3.16
367 487 7.792374 TTAAGTTTGGTTAAATTGCATGCAA 57.208 28.000 33.57 33.57 40.47 4.08
369 489 9.676195 AAATTTAAGTTTGGTTAAATTGCATGC 57.324 25.926 11.82 11.82 45.49 4.06
382 502 8.998377 CATAAACCTTGGGAAATTTAAGTTTGG 58.002 33.333 0.06 0.00 0.00 3.28
408 528 7.488150 CCGAAAACAGCCTAAAGGAAAAATATC 59.512 37.037 0.00 0.00 37.39 1.63
418 538 3.751175 TCACATCCGAAAACAGCCTAAAG 59.249 43.478 0.00 0.00 0.00 1.85
432 552 3.820557 ACCTTGGGAAATATCACATCCG 58.179 45.455 0.00 0.00 39.17 4.18
498 618 6.415702 CAGACTTTCGACAAACGTTAAATCA 58.584 36.000 0.00 0.00 43.13 2.57
511 631 0.664767 AGCTGACGCAGACTTTCGAC 60.665 55.000 10.46 0.00 39.10 4.20
573 693 1.564348 ACTCCAAAGGTGACCTTGTGT 59.436 47.619 19.04 10.32 43.92 3.72
579 699 4.321718 GGTTAAGTACTCCAAAGGTGACC 58.678 47.826 0.00 0.00 0.00 4.02
591 733 4.021981 GTGTAAGTGACGGGGTTAAGTACT 60.022 45.833 0.00 0.00 0.00 2.73
869 2016 3.622060 ATTTGGGACGGTGGCGAGG 62.622 63.158 0.00 0.00 0.00 4.63
922 2069 2.752807 GGGCCCTAGGGATTTCGCA 61.753 63.158 33.21 0.00 37.50 5.10
1072 2231 2.263540 CTAACCCCGGACCACACG 59.736 66.667 0.73 0.00 0.00 4.49
1073 2232 2.666812 CCTAACCCCGGACCACAC 59.333 66.667 0.73 0.00 0.00 3.82
1074 2233 2.608368 CCCTAACCCCGGACCACA 60.608 66.667 0.73 0.00 0.00 4.17
1075 2234 1.782201 AAACCCTAACCCCGGACCAC 61.782 60.000 0.73 0.00 0.00 4.16
1076 2235 1.463804 AAACCCTAACCCCGGACCA 60.464 57.895 0.73 0.00 0.00 4.02
1111 2270 4.647615 CCATAGACGCCGCCTCCG 62.648 72.222 0.00 0.00 0.00 4.63
1142 2301 1.443872 CTCCGACTTGAACGACCCG 60.444 63.158 0.00 0.00 0.00 5.28
1320 2479 0.469494 TGAGGAGCACAACAAGAGCA 59.531 50.000 0.00 0.00 36.17 4.26
1347 2506 2.251818 GTATCATCCTGGCTAGCTGGA 58.748 52.381 24.53 24.53 0.00 3.86
1422 2581 4.095483 CAGAATCAGCTAATGTTCCCACAC 59.905 45.833 0.00 0.00 35.03 3.82
1424 2583 3.629398 CCAGAATCAGCTAATGTTCCCAC 59.371 47.826 0.00 0.00 0.00 4.61
1439 2598 4.889832 AGCGACAATTTCATCCAGAATC 57.110 40.909 0.00 0.00 35.83 2.52
1443 2602 3.242220 CGAGAAGCGACAATTTCATCCAG 60.242 47.826 0.00 0.00 44.57 3.86
1470 2629 2.102925 CCCAAGAAATTGTGTGCCTGTT 59.897 45.455 0.00 0.00 0.00 3.16
1475 2634 1.963515 AGGTCCCAAGAAATTGTGTGC 59.036 47.619 0.00 0.00 0.00 4.57
1501 2660 2.673368 GGTCTGGTCTTAACAAGCGATG 59.327 50.000 0.00 0.00 0.00 3.84
1548 2707 9.747898 ACTACTATACTAATCAAGCTAGCTGAT 57.252 33.333 20.16 19.00 0.00 2.90
1604 2863 8.115490 AGCATTAACAGAAAATTACTCAAGCT 57.885 30.769 0.00 0.00 0.00 3.74
1679 2938 1.801178 GTGGCTTCTTGGAACTTCTCG 59.199 52.381 0.00 0.00 0.00 4.04
1769 3028 7.119846 ACTCAAACTACTCAAATCAAGCCATAC 59.880 37.037 0.00 0.00 0.00 2.39
1961 3220 9.920946 ACATAACCTCATAACCAGACAAATATT 57.079 29.630 0.00 0.00 0.00 1.28
1964 3223 8.548877 ACTACATAACCTCATAACCAGACAAAT 58.451 33.333 0.00 0.00 0.00 2.32
1965 3224 7.822334 CACTACATAACCTCATAACCAGACAAA 59.178 37.037 0.00 0.00 0.00 2.83
2076 3335 0.540923 GGAGCTGAGCAATCTCCACT 59.459 55.000 7.39 0.00 44.38 4.00
2094 3353 1.881973 CATACGGATTTGCCCAGATGG 59.118 52.381 0.00 0.00 37.09 3.51
2127 3386 3.202829 TGAAACGAAGGCAGGTAGTTT 57.797 42.857 0.00 0.00 37.68 2.66
2135 3394 2.358957 CATGGAGATGAAACGAAGGCA 58.641 47.619 0.00 0.00 0.00 4.75
2339 3598 8.280497 AGTTAAGTTATCAAATGAACGTGACAC 58.720 33.333 0.00 0.00 29.91 3.67
2493 3752 3.793492 CAGTGCATATCAGTATATCGCCG 59.207 47.826 0.00 0.00 0.00 6.46
2496 3755 4.747810 TGCCAGTGCATATCAGTATATCG 58.252 43.478 0.00 0.00 44.23 2.92
2553 3823 6.719370 TGTAGGCTGGACTTCATGTAATTTTT 59.281 34.615 0.00 0.00 0.00 1.94
2554 3824 6.245408 TGTAGGCTGGACTTCATGTAATTTT 58.755 36.000 0.00 0.00 0.00 1.82
2595 3873 6.845758 AGTACAAACTGTGCTACCATACTA 57.154 37.500 0.00 0.00 41.50 1.82
2597 3875 7.435488 CAGATAGTACAAACTGTGCTACCATAC 59.565 40.741 6.74 0.00 45.69 2.39
2682 3960 5.903810 AGAGAAACGACCAGTTATATGTCC 58.096 41.667 0.00 0.00 43.37 4.02
2881 4159 0.879090 CAAGGCTTAACCCACCGTTC 59.121 55.000 0.00 0.00 40.58 3.95
2990 4269 0.179000 CTAAGCGTCCAAGGCAGGAT 59.821 55.000 1.91 0.00 40.42 3.24
3026 4311 0.681175 GCAAAATTGTGGGGAGCTGT 59.319 50.000 0.00 0.00 0.00 4.40
3034 4319 0.605589 TAAGGCGGGCAAAATTGTGG 59.394 50.000 3.78 0.00 0.00 4.17
3072 4358 3.633116 ACCCACCGCCTTAACGCT 61.633 61.111 0.00 0.00 0.00 5.07
3094 4380 4.451900 CGGTAAAGGCATCATCCTAAAGT 58.548 43.478 0.00 0.00 34.82 2.66
3106 4392 3.060736 TGTTCTTATGCGGTAAAGGCA 57.939 42.857 0.00 0.00 45.71 4.75
3107 4393 4.351192 CAATGTTCTTATGCGGTAAAGGC 58.649 43.478 0.00 0.00 0.00 4.35
3108 4394 4.096382 AGCAATGTTCTTATGCGGTAAAGG 59.904 41.667 0.00 0.00 44.60 3.11
3109 4395 5.235305 AGCAATGTTCTTATGCGGTAAAG 57.765 39.130 0.00 0.00 44.60 1.85
3110 4396 5.414454 AGAAGCAATGTTCTTATGCGGTAAA 59.586 36.000 0.00 0.00 44.60 2.01
3135 4421 7.511268 TGGTAGGTGACAAACTAGTTACAAAT 58.489 34.615 8.92 5.10 30.34 2.32
3225 4512 5.104693 TGACACACCCTTTTCAGTAAGAAGA 60.105 40.000 0.00 0.00 37.57 2.87
3367 4668 8.632679 AGCTCAAGTTCAAAAATTCACATAAGA 58.367 29.630 0.00 0.00 0.00 2.10
3432 4741 8.650143 AAGTTCCAACCATATCAACAAAGTAT 57.350 30.769 0.00 0.00 0.00 2.12
3611 4927 2.715532 TTCGCAGAACGCAGCTTCCT 62.716 55.000 0.00 0.00 45.90 3.36
3627 4943 5.048294 ACTTTGTTAAGGTTTAGGCCATTCG 60.048 40.000 5.01 0.00 35.61 3.34
3661 4977 1.981495 CTTCTGGATGGGGGATAGGAC 59.019 57.143 0.00 0.00 0.00 3.85
3721 5037 2.270434 AGAAGATCTGGTTAGGCCCA 57.730 50.000 0.00 0.00 36.04 5.36
3758 5074 7.081526 TCAAATTTGACAACACAAAATTGGG 57.918 32.000 16.91 0.00 44.15 4.12
3845 5161 5.373222 TGCTCAAAGCCTCAAAAACTAGTA 58.627 37.500 0.00 0.00 41.51 1.82
3846 5162 4.207165 TGCTCAAAGCCTCAAAAACTAGT 58.793 39.130 0.00 0.00 41.51 2.57
3891 5207 3.244526 TGCACTATCTTCCTGCAACAGAA 60.245 43.478 0.00 0.00 37.97 3.02
4238 5555 6.204688 TCGCCTAATAGACCAAATGCTTTATG 59.795 38.462 0.00 0.00 0.00 1.90
4261 5578 6.863126 AGGTTGCACTTTTGAAGAAATTATCG 59.137 34.615 0.00 0.00 0.00 2.92
4323 5640 3.576648 CTTCGTAGCTTCTCCTTTTCGT 58.423 45.455 0.00 0.00 0.00 3.85
4425 5742 5.127194 AGTCTGTTTCCGTAGATAATCTGCA 59.873 40.000 0.00 0.00 0.00 4.41
4433 5750 7.439381 TCACTTAAAAGTCTGTTTCCGTAGAT 58.561 34.615 0.00 0.00 37.08 1.98
4536 5853 4.085884 CAAATACACGTACCGTTTGCATC 58.914 43.478 0.00 0.00 38.32 3.91
4597 5914 6.546403 AGCTCATCAATCTATGCAAGAACATT 59.454 34.615 0.00 0.00 37.89 2.71
4614 5931 3.006859 TCCTTTCGTTGAGAAGCTCATCA 59.993 43.478 0.00 0.00 40.39 3.07
4764 6081 0.170561 CCATCGTCGTCGGACTCTTT 59.829 55.000 6.57 0.00 41.16 2.52
4918 6235 9.262472 GACACAAAATAATACATTCAGAACGAC 57.738 33.333 0.00 0.00 0.00 4.34
4922 6239 9.986833 CATCGACACAAAATAATACATTCAGAA 57.013 29.630 0.00 0.00 0.00 3.02
5139 6459 8.143835 GGGCAAGATTATATAAGTGCAAATGTT 58.856 33.333 21.08 1.53 0.00 2.71
5231 6551 2.833943 TCAGGCTTTAGCAGATCAGACA 59.166 45.455 3.88 0.00 44.36 3.41
5240 6560 5.076873 ACAGGTAATTTTCAGGCTTTAGCA 58.923 37.500 3.88 0.00 44.36 3.49
5244 6564 4.023193 CGTGACAGGTAATTTTCAGGCTTT 60.023 41.667 0.00 0.00 0.00 3.51
5389 6709 3.848582 GCAGAACAAGCTCGCTAATTTTC 59.151 43.478 0.00 0.00 0.00 2.29
5475 6799 9.709495 ACACTTGAATTAAATGTTATGCACAAT 57.291 25.926 0.00 0.00 39.50 2.71
5476 6800 9.190858 GACACTTGAATTAAATGTTATGCACAA 57.809 29.630 0.00 0.00 39.50 3.33
5478 6802 8.638565 GTGACACTTGAATTAAATGTTATGCAC 58.361 33.333 0.00 0.00 0.00 4.57
5534 6861 6.012658 TCCATCTTAACAAACTCACAATGC 57.987 37.500 0.00 0.00 0.00 3.56
5581 6908 8.850156 ACTTGTCAAATTAGCTGAAACATAACT 58.150 29.630 0.00 0.00 0.00 2.24
5592 6919 8.413229 ACATTAACACAACTTGTCAAATTAGCT 58.587 29.630 0.00 0.00 37.51 3.32
5609 6936 9.061610 GCATAACAAATAGTCACACATTAACAC 57.938 33.333 0.00 0.00 0.00 3.32
5614 6941 7.466746 AAGGCATAACAAATAGTCACACATT 57.533 32.000 0.00 0.00 0.00 2.71
5620 6947 9.255304 GTTTTTCAAAGGCATAACAAATAGTCA 57.745 29.630 0.00 0.00 0.00 3.41
5676 7013 5.716228 TCATTTTGATGCTTTGTGGGATAGT 59.284 36.000 0.00 0.00 0.00 2.12
5713 7050 8.939929 AGCATAATGGTATTCGTTTGATCATAG 58.060 33.333 0.00 0.00 0.00 2.23
5779 7116 8.992073 TGCTTGTGTGCTATATAAATCATGTAG 58.008 33.333 0.00 0.00 32.83 2.74
5825 7163 8.902540 TGTATTCCATGATACTTGTTATGTCC 57.097 34.615 0.00 0.00 34.36 4.02
5849 7187 5.506483 CCACTCGTCATCTGAGTAACCTATG 60.506 48.000 0.00 0.00 44.60 2.23
5867 7205 3.190849 CTGCCGATGTGCCACTCG 61.191 66.667 8.95 8.95 34.73 4.18
5919 7257 6.918892 TGTCGTGATGGATTGTTAATTAGG 57.081 37.500 0.00 0.00 0.00 2.69
5921 7259 8.675705 ATCATGTCGTGATGGATTGTTAATTA 57.324 30.769 6.75 0.00 45.76 1.40
5927 7265 5.857268 TGATATCATGTCGTGATGGATTGT 58.143 37.500 16.44 0.00 46.85 2.71
5933 7271 8.672214 TTTTGTTTTGATATCATGTCGTGATG 57.328 30.769 16.44 0.00 46.85 3.07
5949 7287 3.921021 TGGTGTGCGTACTTTTTGTTTTG 59.079 39.130 4.97 0.00 0.00 2.44
5953 7291 4.817464 TCTTATGGTGTGCGTACTTTTTGT 59.183 37.500 4.97 0.00 0.00 2.83
5954 7292 5.351233 TCTTATGGTGTGCGTACTTTTTG 57.649 39.130 4.97 0.00 0.00 2.44
5955 7293 4.454504 CCTCTTATGGTGTGCGTACTTTTT 59.545 41.667 4.97 0.00 0.00 1.94
5956 7294 4.000988 CCTCTTATGGTGTGCGTACTTTT 58.999 43.478 4.97 0.00 0.00 2.27
5981 7319 5.163774 GCATTTTGAAACACCAAACACATGT 60.164 36.000 0.00 0.00 35.95 3.21
5992 7330 5.793026 TTTGAAGTGGCATTTTGAAACAC 57.207 34.783 0.00 0.00 0.00 3.32
5997 7335 5.121454 GTGTTGTTTTGAAGTGGCATTTTGA 59.879 36.000 0.00 0.00 0.00 2.69
6005 7343 4.747108 TGTTTGTGTGTTGTTTTGAAGTGG 59.253 37.500 0.00 0.00 0.00 4.00
6033 7371 4.918810 ACCAGAAAGTTTTGGTTAGCAG 57.081 40.909 13.48 0.00 45.16 4.24
6066 7404 5.065731 GGTTGCTATGATCTTCACTTTCCTG 59.934 44.000 0.00 0.00 0.00 3.86
6067 7405 5.045286 AGGTTGCTATGATCTTCACTTTCCT 60.045 40.000 0.00 0.00 0.00 3.36
6077 7415 2.297597 GAGGCGTAGGTTGCTATGATCT 59.702 50.000 0.00 0.00 0.00 2.75
6093 7431 3.253677 CCTATGTCTACAACTAGGAGGCG 59.746 52.174 4.42 0.00 33.77 5.52
6126 7464 1.065418 GGCCACCACTACTGCAGTAAT 60.065 52.381 25.95 15.29 34.98 1.89
6129 7467 2.750350 GGCCACCACTACTGCAGT 59.250 61.111 25.12 25.12 38.32 4.40
6130 7468 2.434884 CGGCCACCACTACTGCAG 60.435 66.667 13.48 13.48 0.00 4.41
6132 7470 3.665675 CTCCGGCCACCACTACTGC 62.666 68.421 2.24 0.00 0.00 4.40
6133 7471 2.283529 ACTCCGGCCACCACTACTG 61.284 63.158 2.24 0.00 0.00 2.74
6134 7472 2.119832 ACTCCGGCCACCACTACT 59.880 61.111 2.24 0.00 0.00 2.57
6135 7473 2.264794 CACTCCGGCCACCACTAC 59.735 66.667 2.24 0.00 0.00 2.73
6136 7474 3.000819 CCACTCCGGCCACCACTA 61.001 66.667 2.24 0.00 0.00 2.74
6138 7476 4.265056 AACCACTCCGGCCACCAC 62.265 66.667 2.24 0.00 39.03 4.16
6139 7477 4.263572 CAACCACTCCGGCCACCA 62.264 66.667 2.24 0.00 39.03 4.17


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

AutoCloner maintained by Alex Coulton.