Multiple sequence alignment - TraesCS3D01G106200

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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 TraesCS3D01G106200 chr3D 100.000 5627 0 0 1 5627 58303255 58297629 0.000000e+00 10392
1 TraesCS3D01G106200 chr3D 83.055 1316 148 34 2254 3521 120292024 120290736 0.000000e+00 1125
2 TraesCS3D01G106200 chr3D 87.362 633 53 10 1407 2038 120292835 120292229 0.000000e+00 701
3 TraesCS3D01G106200 chr3D 89.404 453 33 6 3778 4226 120290436 120289995 1.770000e-154 556
4 TraesCS3D01G106200 chr3D 81.447 636 87 21 670 1288 120293466 120292845 5.070000e-135 492
5 TraesCS3D01G106200 chr3D 83.684 190 20 3 1533 1722 58306585 58306763 9.700000e-38 169
6 TraesCS3D01G106200 chr3A 95.000 4420 169 23 608 5015 67314472 67310093 0.000000e+00 6890
7 TraesCS3D01G106200 chr3A 82.096 2290 233 93 2254 4487 127194695 127192527 0.000000e+00 1794
8 TraesCS3D01G106200 chr3A 89.879 662 26 17 1 626 67315309 67314653 0.000000e+00 813
9 TraesCS3D01G106200 chr3A 86.637 666 58 17 1407 2066 127195517 127194877 0.000000e+00 708
10 TraesCS3D01G106200 chr3A 80.851 705 96 26 604 1288 127196212 127195527 8.360000e-143 518
11 TraesCS3D01G106200 chr3B 94.474 2624 95 15 633 3242 92335714 92333127 0.000000e+00 3997
12 TraesCS3D01G106200 chr3B 94.944 2314 84 18 3240 5544 92332822 92330533 0.000000e+00 3594
13 TraesCS3D01G106200 chr3B 83.458 2013 210 70 2254 4203 172318707 172316755 0.000000e+00 1759
14 TraesCS3D01G106200 chr3B 89.577 662 31 7 1 631 92341510 92340856 0.000000e+00 806
15 TraesCS3D01G106200 chr3B 86.289 671 59 16 1407 2070 172319530 172318886 0.000000e+00 699
16 TraesCS3D01G106200 chr3B 80.858 653 90 20 604 1240 172320237 172319604 1.100000e-131 481
17 TraesCS3D01G106200 chr3B 80.000 420 43 16 4555 4952 172316513 172316113 7.180000e-69 272
18 TraesCS3D01G106200 chr3B 88.272 162 14 3 4357 4517 172316747 172316590 7.440000e-44 189
19 TraesCS3D01G106200 chr3B 81.890 127 21 1 5183 5307 821439242 821439116 7.710000e-19 106
20 TraesCS3D01G106200 chr3B 81.102 127 22 1 5183 5307 821289821 821289695 3.590000e-17 100
21 TraesCS3D01G106200 chr2A 94.872 234 12 0 4132 4365 583094876 583095109 3.200000e-97 366
22 TraesCS3D01G106200 chr2A 94.444 234 13 0 4132 4365 583102463 583102696 1.490000e-95 361
23 TraesCS3D01G106200 chrUn 94.372 231 13 0 4132 4362 315294816 315295046 6.930000e-94 355
24 TraesCS3D01G106200 chr7A 86.344 227 27 3 4131 4355 22835172 22834948 1.570000e-60 244
25 TraesCS3D01G106200 chr7A 82.323 198 31 4 3932 4128 20220697 20220891 9.700000e-38 169
26 TraesCS3D01G106200 chr2B 85.333 225 33 0 4131 4355 202916682 202916906 3.390000e-57 233
27 TraesCS3D01G106200 chr7B 77.112 367 78 5 5129 5490 511943272 511943637 2.050000e-49 207
28 TraesCS3D01G106200 chr7D 81.773 203 33 4 3927 4128 262706557 262706756 3.490000e-37 167
29 TraesCS3D01G106200 chr1A 82.000 200 32 4 3930 4128 20996629 20996433 3.490000e-37 167


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 TraesCS3D01G106200 chr3D 58297629 58303255 5626 True 10392.000000 10392 100.000000 1 5627 1 chr3D.!!$R1 5626
1 TraesCS3D01G106200 chr3D 120289995 120293466 3471 True 718.500000 1125 85.317000 670 4226 4 chr3D.!!$R2 3556
2 TraesCS3D01G106200 chr3A 67310093 67315309 5216 True 3851.500000 6890 92.439500 1 5015 2 chr3A.!!$R1 5014
3 TraesCS3D01G106200 chr3A 127192527 127196212 3685 True 1006.666667 1794 83.194667 604 4487 3 chr3A.!!$R2 3883
4 TraesCS3D01G106200 chr3B 92330533 92335714 5181 True 3795.500000 3997 94.709000 633 5544 2 chr3B.!!$R4 4911
5 TraesCS3D01G106200 chr3B 92340856 92341510 654 True 806.000000 806 89.577000 1 631 1 chr3B.!!$R1 630
6 TraesCS3D01G106200 chr3B 172316113 172320237 4124 True 680.000000 1759 83.775400 604 4952 5 chr3B.!!$R5 4348

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
815 1066 2.300956 TGGGAAAGCTAACATGGCAA 57.699 45.000 0.00 0.0 0.00 4.52 F
1811 2107 0.535102 GGGTGTCCCACACTCTTGTG 60.535 60.000 6.74 0.0 45.87 3.33 F
1921 2217 2.183636 GTTAGGACGCTTTCTACTCGC 58.816 52.381 0.00 0.0 0.00 5.03 F
3025 3397 4.041075 TCTGGTGCAGTTAACAATCTACCA 59.959 41.667 8.61 12.7 35.79 3.25 F
3107 3479 2.201732 CGATGGTTTGTGGTCTATCCG 58.798 52.381 0.00 0.0 39.52 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1921 2217 0.103208 AGCCAGGTTCTATTCTCGCG 59.897 55.000 0.00 0.0 0.00 5.87 R
2787 3149 1.379843 CCCATACCCAGCCAACACC 60.380 63.158 0.00 0.0 0.00 4.16 R
3107 3479 1.656818 CCATTCACCACATGACCGCC 61.657 60.000 0.00 0.0 36.92 6.13 R
4567 5433 0.388134 TCGGCGAAGTACTCAACTGC 60.388 55.000 7.35 0.0 38.88 4.40 R
5057 5943 1.486310 TGCATCCACTGGTCAGGATAC 59.514 52.381 2.87 0.0 42.61 2.24 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
210 217 3.186909 GTTTTCAAAACCAGCGCTCTTT 58.813 40.909 7.13 5.20 0.00 2.52
257 264 8.525316 TGTTAGTCTCGGACTGATATGTTAAAA 58.475 33.333 14.50 0.00 43.30 1.52
417 425 6.049149 CCAGAGTCAAGTTAAGTTCAGTGAA 58.951 40.000 0.08 0.08 0.00 3.18
468 504 3.307762 GGGCACAGTAATCTCAAACCTCT 60.308 47.826 0.00 0.00 0.00 3.69
469 505 4.327680 GGCACAGTAATCTCAAACCTCTT 58.672 43.478 0.00 0.00 0.00 2.85
470 506 4.762251 GGCACAGTAATCTCAAACCTCTTT 59.238 41.667 0.00 0.00 0.00 2.52
613 656 9.937175 GTTCTTATTTAAGCATCCAGTATTGTC 57.063 33.333 0.00 0.00 33.40 3.18
723 968 7.123997 ACTTCATTCTCTCTATGATGTCACTGT 59.876 37.037 0.00 0.00 36.32 3.55
815 1066 2.300956 TGGGAAAGCTAACATGGCAA 57.699 45.000 0.00 0.00 0.00 4.52
969 1225 4.457257 GGCATTGATCCTGGATTTAGCTAC 59.543 45.833 11.17 0.00 0.00 3.58
1213 1478 4.584325 ACCAGAATTTTGCTACAGCTTTCA 59.416 37.500 2.44 0.00 42.66 2.69
1214 1479 5.068987 ACCAGAATTTTGCTACAGCTTTCAA 59.931 36.000 2.44 0.00 42.66 2.69
1331 1614 3.403038 ACTGCTGCGACACTTTCTTTAT 58.597 40.909 0.00 0.00 0.00 1.40
1334 1617 2.742053 GCTGCGACACTTTCTTTATCCA 59.258 45.455 0.00 0.00 0.00 3.41
1738 2034 6.659668 AGATGTCTAGCTGTTGTTCTGTAGTA 59.340 38.462 0.00 0.00 0.00 1.82
1743 2039 9.635520 GTCTAGCTGTTGTTCTGTAGTATTTAA 57.364 33.333 0.00 0.00 0.00 1.52
1745 2041 7.668525 AGCTGTTGTTCTGTAGTATTTAACC 57.331 36.000 0.00 0.00 0.00 2.85
1746 2042 7.450903 AGCTGTTGTTCTGTAGTATTTAACCT 58.549 34.615 0.00 0.00 0.00 3.50
1747 2043 7.937394 AGCTGTTGTTCTGTAGTATTTAACCTT 59.063 33.333 0.00 0.00 0.00 3.50
1748 2044 8.565416 GCTGTTGTTCTGTAGTATTTAACCTTT 58.435 33.333 0.00 0.00 0.00 3.11
1811 2107 0.535102 GGGTGTCCCACACTCTTGTG 60.535 60.000 6.74 0.00 45.87 3.33
1921 2217 2.183636 GTTAGGACGCTTTCTACTCGC 58.816 52.381 0.00 0.00 0.00 5.03
2090 2428 5.165961 ACTACAGTATGCACAAATCCTGT 57.834 39.130 0.00 0.00 42.53 4.00
2611 2950 8.417106 TCTAGTATATGCTGTCTTTTCTCCTTG 58.583 37.037 3.24 0.00 0.00 3.61
2685 3044 7.081526 CTTTCATGTGATTCTACTGAAAGGG 57.918 40.000 17.94 5.03 44.43 3.95
2787 3149 9.797556 CCATATTATCCATCATTTATTGCAGTG 57.202 33.333 0.00 0.00 0.00 3.66
2963 3330 7.770801 TCATCGACTGGTTTAGACATTTATG 57.229 36.000 0.00 0.00 0.00 1.90
3025 3397 4.041075 TCTGGTGCAGTTAACAATCTACCA 59.959 41.667 8.61 12.70 35.79 3.25
3107 3479 2.201732 CGATGGTTTGTGGTCTATCCG 58.798 52.381 0.00 0.00 39.52 4.18
3311 4008 5.327616 TGTATGCACATTGAAAGATTGGG 57.672 39.130 0.00 0.00 0.00 4.12
3314 4011 2.562298 TGCACATTGAAAGATTGGGACC 59.438 45.455 0.00 0.00 0.00 4.46
3324 4021 8.491045 TTGAAAGATTGGGACCTTTTATCTTT 57.509 30.769 16.40 16.40 44.10 2.52
3399 4097 6.112734 TGAGGTAAGGCACATACAGTTATTG 58.887 40.000 0.00 0.00 33.75 1.90
3644 4445 6.788243 TGTTTCACATGATGTAATCTGATGC 58.212 36.000 0.00 0.00 45.81 3.91
3701 4516 4.990257 AGCTGTTATTGCTGCAAATGTAG 58.010 39.130 20.06 15.46 39.56 2.74
3702 4517 4.107622 GCTGTTATTGCTGCAAATGTAGG 58.892 43.478 20.06 9.25 34.18 3.18
3703 4518 4.142403 GCTGTTATTGCTGCAAATGTAGGA 60.142 41.667 20.06 0.00 34.18 2.94
3722 4537 8.034313 TGTAGGAATTAGGATTGTAGATTGCT 57.966 34.615 0.00 0.00 33.78 3.91
3725 4540 5.532406 GGAATTAGGATTGTAGATTGCTGCA 59.468 40.000 0.00 0.00 34.80 4.41
3751 4566 4.858935 TGACTTGTTGTCTTGCAAATAGC 58.141 39.130 0.00 0.00 45.54 2.97
3754 4569 4.022849 ACTTGTTGTCTTGCAAATAGCCTC 60.023 41.667 0.00 0.00 44.83 4.70
3757 4572 4.523943 TGTTGTCTTGCAAATAGCCTCATT 59.476 37.500 0.00 0.00 44.83 2.57
3758 4573 5.709631 TGTTGTCTTGCAAATAGCCTCATTA 59.290 36.000 0.00 0.00 44.83 1.90
3759 4574 5.818136 TGTCTTGCAAATAGCCTCATTAC 57.182 39.130 0.00 0.00 44.83 1.89
3761 4576 5.945784 TGTCTTGCAAATAGCCTCATTACTT 59.054 36.000 0.00 0.00 44.83 2.24
3762 4577 6.127925 TGTCTTGCAAATAGCCTCATTACTTG 60.128 38.462 0.00 0.00 44.83 3.16
3763 4578 6.094048 GTCTTGCAAATAGCCTCATTACTTGA 59.906 38.462 0.00 0.00 44.83 3.02
3764 4579 6.830324 TCTTGCAAATAGCCTCATTACTTGAT 59.170 34.615 0.00 0.00 44.83 2.57
3767 4582 6.377996 TGCAAATAGCCTCATTACTTGATGTT 59.622 34.615 0.00 0.00 44.83 2.71
3768 4583 6.694411 GCAAATAGCCTCATTACTTGATGTTG 59.306 38.462 0.00 0.00 37.23 3.33
3769 4584 6.382869 AATAGCCTCATTACTTGATGTTGC 57.617 37.500 0.00 0.00 32.72 4.17
3770 4585 3.019564 AGCCTCATTACTTGATGTTGCC 58.980 45.455 0.00 0.00 32.72 4.52
3772 4587 3.181493 GCCTCATTACTTGATGTTGCCTG 60.181 47.826 0.00 0.00 32.72 4.85
3773 4588 4.264253 CCTCATTACTTGATGTTGCCTGA 58.736 43.478 0.00 0.00 32.72 3.86
3776 4593 6.543465 CCTCATTACTTGATGTTGCCTGATTA 59.457 38.462 0.00 0.00 32.72 1.75
3791 4608 4.321527 GCCTGATTACTTTTGCTCTTGCTT 60.322 41.667 0.00 0.00 40.48 3.91
4088 4911 2.273449 CGATCCTTGGGGCAGCTT 59.727 61.111 0.00 0.00 0.00 3.74
4204 5028 7.765695 TTCTTTTGATAACCAGCTCTTTGAT 57.234 32.000 0.00 0.00 0.00 2.57
4327 5153 8.795786 TTTGTACTGTCAGATTTATTTTGTGC 57.204 30.769 6.91 0.00 0.00 4.57
4328 5154 7.503521 TGTACTGTCAGATTTATTTTGTGCA 57.496 32.000 6.91 0.00 0.00 4.57
4329 5155 7.935520 TGTACTGTCAGATTTATTTTGTGCAA 58.064 30.769 6.91 0.00 0.00 4.08
4513 5340 4.460731 TGGTTGTGTTTGTGATTTCTGTCA 59.539 37.500 0.00 0.00 0.00 3.58
4532 5361 2.743664 TCAGCCGAAGTGTCAATTGATG 59.256 45.455 12.12 2.52 0.00 3.07
4542 5377 2.960384 TGTCAATTGATGATCATGCCCC 59.040 45.455 14.30 0.00 40.97 5.80
4601 5467 2.885644 CGACGCCATCAACGGGAG 60.886 66.667 0.00 0.00 34.00 4.30
4699 5566 7.340487 AGAGTGTCATCTCATGTAGTGTAATCA 59.660 37.037 0.00 0.00 36.97 2.57
4779 5657 5.277974 GCTGTCACTGAAGAATTTTGTAGCA 60.278 40.000 0.00 0.00 0.00 3.49
4882 5765 4.342092 AGAAAATTGTGTCAAACCTCAGGG 59.658 41.667 0.00 0.00 38.88 4.45
4952 5838 1.747355 CACCATTCATTGTCTCCCAGC 59.253 52.381 0.00 0.00 0.00 4.85
5072 5958 2.169352 CTCCTTGTATCCTGACCAGTGG 59.831 54.545 7.91 7.91 0.00 4.00
5092 5978 2.289945 GGATGCAGTATGGGGATCTGTC 60.290 54.545 0.00 0.00 35.86 3.51
5106 5992 3.996363 GGATCTGTCCCATTTTGTTTTGC 59.004 43.478 0.00 0.00 38.69 3.68
5107 5993 4.502950 GGATCTGTCCCATTTTGTTTTGCA 60.503 41.667 0.00 0.00 38.69 4.08
5108 5994 4.686191 TCTGTCCCATTTTGTTTTGCAT 57.314 36.364 0.00 0.00 0.00 3.96
5109 5995 4.378774 TCTGTCCCATTTTGTTTTGCATG 58.621 39.130 0.00 0.00 0.00 4.06
5110 5996 4.128643 CTGTCCCATTTTGTTTTGCATGT 58.871 39.130 0.00 0.00 0.00 3.21
5111 5997 3.875727 TGTCCCATTTTGTTTTGCATGTG 59.124 39.130 0.00 0.00 0.00 3.21
5112 5998 4.125703 GTCCCATTTTGTTTTGCATGTGA 58.874 39.130 0.00 0.00 0.00 3.58
5113 5999 4.574013 GTCCCATTTTGTTTTGCATGTGAA 59.426 37.500 0.00 0.00 0.00 3.18
5114 6000 5.239087 GTCCCATTTTGTTTTGCATGTGAAT 59.761 36.000 0.00 0.00 0.00 2.57
5115 6001 6.426328 GTCCCATTTTGTTTTGCATGTGAATA 59.574 34.615 0.00 0.00 0.00 1.75
5116 6002 6.426328 TCCCATTTTGTTTTGCATGTGAATAC 59.574 34.615 0.00 0.00 0.00 1.89
5117 6003 6.204301 CCCATTTTGTTTTGCATGTGAATACA 59.796 34.615 0.00 0.00 41.89 2.29
5118 6004 7.255035 CCCATTTTGTTTTGCATGTGAATACAA 60.255 33.333 9.77 9.77 40.84 2.41
5119 6005 8.291032 CCATTTTGTTTTGCATGTGAATACAAT 58.709 29.630 12.71 2.29 40.84 2.71
5120 6006 9.320406 CATTTTGTTTTGCATGTGAATACAATC 57.680 29.630 12.71 0.15 40.84 2.67
5121 6007 8.659925 TTTTGTTTTGCATGTGAATACAATCT 57.340 26.923 12.71 0.00 40.84 2.40
5122 6008 7.872163 TTGTTTTGCATGTGAATACAATCTC 57.128 32.000 9.77 0.00 40.84 2.75
5172 6058 5.127845 TCTTGGTGTTTATTGTTCAGCCAAA 59.872 36.000 0.00 0.00 34.82 3.28
5175 6061 5.582665 TGGTGTTTATTGTTCAGCCAAAAAC 59.417 36.000 0.00 0.00 32.36 2.43
5177 6063 5.289917 GTGTTTATTGTTCAGCCAAAAACGT 59.710 36.000 0.00 0.00 33.27 3.99
5387 6274 2.765699 GGCTGAAGATCTCCAACTCTCT 59.234 50.000 0.00 0.00 0.00 3.10
5393 6280 5.660417 TGAAGATCTCCAACTCTCTATTGCT 59.340 40.000 0.00 0.00 0.00 3.91
5399 6286 3.008375 TCCAACTCTCTATTGCTTGCACT 59.992 43.478 0.00 0.00 0.00 4.40
5420 6307 3.609853 TGATCAACTCCAAAGAATCGGG 58.390 45.455 0.00 0.00 0.00 5.14
5424 6311 0.108138 ACTCCAAAGAATCGGGCTCG 60.108 55.000 0.00 0.00 37.82 5.03
5425 6312 0.811616 CTCCAAAGAATCGGGCTCGG 60.812 60.000 5.94 0.00 36.95 4.63
5495 6382 2.842058 AGCAAAGGCCTCACTGCT 59.158 55.556 24.24 24.24 42.56 4.24
5496 6383 0.892814 GAGCAAAGGCCTCACTGCTT 60.893 55.000 28.19 17.08 44.93 3.91
5544 6431 3.447586 ACTCACCTATGCTGTTACGTGAT 59.552 43.478 0.00 0.00 30.46 3.06
5545 6432 4.041740 TCACCTATGCTGTTACGTGATC 57.958 45.455 0.00 0.00 0.00 2.92
5546 6433 3.123804 CACCTATGCTGTTACGTGATCC 58.876 50.000 0.00 0.00 0.00 3.36
5547 6434 2.223735 ACCTATGCTGTTACGTGATCCG 60.224 50.000 0.00 2.55 44.03 4.18
5548 6435 2.034179 CCTATGCTGTTACGTGATCCGA 59.966 50.000 0.00 0.00 40.70 4.55
5549 6436 2.890808 ATGCTGTTACGTGATCCGAT 57.109 45.000 0.00 0.00 40.70 4.18
5550 6437 2.665649 TGCTGTTACGTGATCCGATT 57.334 45.000 0.00 0.00 40.70 3.34
5551 6438 2.536365 TGCTGTTACGTGATCCGATTC 58.464 47.619 0.00 1.92 40.70 2.52
5552 6439 2.165641 TGCTGTTACGTGATCCGATTCT 59.834 45.455 0.00 0.00 40.70 2.40
5553 6440 2.789893 GCTGTTACGTGATCCGATTCTC 59.210 50.000 0.00 0.00 40.70 2.87
5554 6441 3.036633 CTGTTACGTGATCCGATTCTCG 58.963 50.000 0.00 7.25 40.70 4.04
5555 6442 2.679336 TGTTACGTGATCCGATTCTCGA 59.321 45.455 0.00 0.00 43.74 4.04
5556 6443 3.314357 TGTTACGTGATCCGATTCTCGAT 59.686 43.478 0.00 0.00 43.74 3.59
5557 6444 2.690173 ACGTGATCCGATTCTCGATC 57.310 50.000 13.39 3.76 43.74 3.69
5558 6445 2.222886 ACGTGATCCGATTCTCGATCT 58.777 47.619 13.39 0.00 43.74 2.75
5559 6446 2.031595 ACGTGATCCGATTCTCGATCTG 60.032 50.000 13.39 6.86 43.74 2.90
5560 6447 2.224314 CGTGATCCGATTCTCGATCTGA 59.776 50.000 0.00 0.00 43.74 3.27
5561 6448 3.120025 CGTGATCCGATTCTCGATCTGAT 60.120 47.826 0.00 0.00 43.74 2.90
5562 6449 4.614764 CGTGATCCGATTCTCGATCTGATT 60.615 45.833 0.00 0.00 43.74 2.57
5563 6450 4.856487 GTGATCCGATTCTCGATCTGATTC 59.144 45.833 0.00 0.00 43.74 2.52
5564 6451 4.764308 TGATCCGATTCTCGATCTGATTCT 59.236 41.667 0.00 0.00 43.74 2.40
5565 6452 4.757799 TCCGATTCTCGATCTGATTCTC 57.242 45.455 0.00 0.00 43.74 2.87
5566 6453 4.393834 TCCGATTCTCGATCTGATTCTCT 58.606 43.478 0.00 0.00 43.74 3.10
5567 6454 5.552178 TCCGATTCTCGATCTGATTCTCTA 58.448 41.667 0.00 0.00 43.74 2.43
5568 6455 5.641636 TCCGATTCTCGATCTGATTCTCTAG 59.358 44.000 0.00 0.00 43.74 2.43
5569 6456 5.411361 CCGATTCTCGATCTGATTCTCTAGT 59.589 44.000 0.00 0.00 43.74 2.57
5570 6457 6.402118 CCGATTCTCGATCTGATTCTCTAGTC 60.402 46.154 0.00 0.00 43.74 2.59
5571 6458 5.915812 TTCTCGATCTGATTCTCTAGTCG 57.084 43.478 0.00 0.00 0.00 4.18
5572 6459 3.743911 TCTCGATCTGATTCTCTAGTCGC 59.256 47.826 0.00 0.00 0.00 5.19
5573 6460 2.809119 TCGATCTGATTCTCTAGTCGCC 59.191 50.000 0.00 0.00 0.00 5.54
5574 6461 2.550180 CGATCTGATTCTCTAGTCGCCA 59.450 50.000 0.00 0.00 0.00 5.69
5575 6462 3.608241 CGATCTGATTCTCTAGTCGCCAC 60.608 52.174 0.00 0.00 0.00 5.01
5576 6463 1.671328 TCTGATTCTCTAGTCGCCACG 59.329 52.381 0.00 0.00 0.00 4.94
5577 6464 1.402259 CTGATTCTCTAGTCGCCACGT 59.598 52.381 0.00 0.00 0.00 4.49
5578 6465 2.612672 CTGATTCTCTAGTCGCCACGTA 59.387 50.000 0.00 0.00 0.00 3.57
5579 6466 3.011818 TGATTCTCTAGTCGCCACGTAA 58.988 45.455 0.00 0.00 0.00 3.18
5580 6467 3.441222 TGATTCTCTAGTCGCCACGTAAA 59.559 43.478 0.00 0.00 0.00 2.01
5581 6468 3.921119 TTCTCTAGTCGCCACGTAAAA 57.079 42.857 0.00 0.00 0.00 1.52
5582 6469 3.207474 TCTCTAGTCGCCACGTAAAAC 57.793 47.619 0.00 0.00 0.00 2.43
5592 6479 3.402185 CGTAAAACGGCCCCGATC 58.598 61.111 14.44 0.00 42.83 3.69
5593 6480 1.153509 CGTAAAACGGCCCCGATCT 60.154 57.895 14.44 0.00 42.83 2.75
5594 6481 1.426041 CGTAAAACGGCCCCGATCTG 61.426 60.000 14.44 0.00 42.83 2.90
5595 6482 0.392060 GTAAAACGGCCCCGATCTGT 60.392 55.000 14.44 0.00 42.83 3.41
5596 6483 0.325602 TAAAACGGCCCCGATCTGTT 59.674 50.000 14.44 0.00 42.83 3.16
5597 6484 0.325602 AAAACGGCCCCGATCTGTTA 59.674 50.000 14.44 0.00 42.83 2.41
5598 6485 0.392060 AAACGGCCCCGATCTGTTAC 60.392 55.000 14.44 0.00 42.83 2.50
5599 6486 2.108362 CGGCCCCGATCTGTTACC 59.892 66.667 0.00 0.00 42.83 2.85
5600 6487 2.727392 CGGCCCCGATCTGTTACCA 61.727 63.158 0.00 0.00 42.83 3.25
5601 6488 1.146263 GGCCCCGATCTGTTACCAG 59.854 63.158 0.00 0.00 40.25 4.00
5602 6489 1.146263 GCCCCGATCTGTTACCAGG 59.854 63.158 0.00 0.00 39.31 4.45
5603 6490 1.335132 GCCCCGATCTGTTACCAGGA 61.335 60.000 0.00 0.00 39.31 3.86
5604 6491 1.200519 CCCCGATCTGTTACCAGGAA 58.799 55.000 0.00 0.00 39.31 3.36
5605 6492 1.557832 CCCCGATCTGTTACCAGGAAA 59.442 52.381 0.00 0.00 39.31 3.13
5606 6493 2.026636 CCCCGATCTGTTACCAGGAAAA 60.027 50.000 0.00 0.00 39.31 2.29
5607 6494 3.560453 CCCCGATCTGTTACCAGGAAAAA 60.560 47.826 0.00 0.00 39.31 1.94
5608 6495 4.270008 CCCGATCTGTTACCAGGAAAAAT 58.730 43.478 0.00 0.00 39.31 1.82
5609 6496 5.433526 CCCGATCTGTTACCAGGAAAAATA 58.566 41.667 0.00 0.00 39.31 1.40
5610 6497 6.062095 CCCGATCTGTTACCAGGAAAAATAT 58.938 40.000 0.00 0.00 39.31 1.28
5611 6498 6.546034 CCCGATCTGTTACCAGGAAAAATATT 59.454 38.462 0.00 0.00 39.31 1.28
5612 6499 7.417612 CCGATCTGTTACCAGGAAAAATATTG 58.582 38.462 0.00 0.00 39.31 1.90
5613 6500 7.067008 CCGATCTGTTACCAGGAAAAATATTGT 59.933 37.037 0.00 0.00 39.31 2.71
5614 6501 8.458843 CGATCTGTTACCAGGAAAAATATTGTT 58.541 33.333 0.00 0.00 39.31 2.83
5615 6502 9.788960 GATCTGTTACCAGGAAAAATATTGTTC 57.211 33.333 9.57 9.57 39.31 3.18
5616 6503 8.698973 TCTGTTACCAGGAAAAATATTGTTCA 57.301 30.769 18.11 0.00 39.31 3.18
5617 6504 8.792633 TCTGTTACCAGGAAAAATATTGTTCAG 58.207 33.333 18.11 10.67 39.31 3.02
5618 6505 8.698973 TGTTACCAGGAAAAATATTGTTCAGA 57.301 30.769 18.11 0.00 0.00 3.27
5619 6506 9.137459 TGTTACCAGGAAAAATATTGTTCAGAA 57.863 29.630 18.11 3.96 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
219 226 3.362693 CGAGACTAACACTTTCGTTTGCC 60.363 47.826 0.00 0.00 0.00 4.52
220 227 3.362693 CCGAGACTAACACTTTCGTTTGC 60.363 47.826 0.00 0.00 0.00 3.68
221 228 4.046462 TCCGAGACTAACACTTTCGTTTG 58.954 43.478 0.00 0.00 0.00 2.93
224 231 2.883386 AGTCCGAGACTAACACTTTCGT 59.117 45.455 4.93 0.00 41.51 3.85
225 232 3.058432 TCAGTCCGAGACTAACACTTTCG 60.058 47.826 6.28 0.00 41.37 3.46
226 233 4.500603 TCAGTCCGAGACTAACACTTTC 57.499 45.455 6.28 0.00 41.37 2.62
257 264 9.601217 GACAGTAGGTACTCAATTAACATCAAT 57.399 33.333 0.00 0.00 41.75 2.57
417 425 7.372260 AGTACCATTCATAAGCTGAGAGAAT 57.628 36.000 0.00 0.00 34.68 2.40
509 548 5.657474 AGCTCAAAGGAAATGCATAATGTG 58.343 37.500 0.00 0.00 0.00 3.21
613 656 5.048224 GGCATTCTGACATTCATAAGATGGG 60.048 44.000 0.00 0.00 0.00 4.00
681 923 4.207891 TGAAGTATGAGGTCCTTCAAGC 57.792 45.455 0.00 0.00 41.03 4.01
742 987 5.462034 TTTTCAAATTTGTTGCTCCGTTG 57.538 34.783 17.47 0.00 0.00 4.10
743 988 5.814705 TGATTTTCAAATTTGTTGCTCCGTT 59.185 32.000 17.47 0.00 0.00 4.44
749 994 9.321590 GAAGCTAATGATTTTCAAATTTGTTGC 57.678 29.630 17.47 8.41 0.00 4.17
815 1066 6.037610 CGCTCTAAAATAGTCTTGCTGGAAAT 59.962 38.462 0.00 0.00 0.00 2.17
876 1127 1.964933 TGGTGTTACATGTCAGACGGA 59.035 47.619 0.00 0.00 0.00 4.69
885 1139 3.586892 TGCATGCAAATGGTGTTACATG 58.413 40.909 20.30 0.00 38.30 3.21
946 1202 3.494332 AGCTAAATCCAGGATCAATGCC 58.506 45.455 1.11 0.00 0.00 4.40
1094 1355 7.126421 ACCATCTGATTAGACTAACCAGACAAT 59.874 37.037 19.65 6.90 36.80 2.71
1177 1441 6.314400 GCAAAATTCTGGTTCATATGCAATGT 59.686 34.615 0.00 0.00 0.00 2.71
1213 1478 5.818857 AGACGTGTTGTGTTACCAATTACTT 59.181 36.000 0.00 0.00 0.00 2.24
1214 1479 5.362263 AGACGTGTTGTGTTACCAATTACT 58.638 37.500 0.00 0.00 0.00 2.24
1240 1523 7.494952 GCTTAATCCTATATTCACCCGATAACC 59.505 40.741 0.00 0.00 0.00 2.85
1433 1722 9.371136 TCAGTTATGAGTGCTATTAACAAGAAG 57.629 33.333 0.00 0.00 0.00 2.85
1434 1723 9.151471 GTCAGTTATGAGTGCTATTAACAAGAA 57.849 33.333 0.00 0.00 35.66 2.52
1816 2112 9.401058 AGGAGGATGTCAAGTTTCATTAATTAG 57.599 33.333 0.00 0.00 0.00 1.73
1840 2136 2.205022 TCAAATTCTGGACCTGCAGG 57.795 50.000 31.60 31.60 42.17 4.85
1921 2217 0.103208 AGCCAGGTTCTATTCTCGCG 59.897 55.000 0.00 0.00 0.00 5.87
2325 2664 5.580691 CGAGTTTCTGCCATACTGAAATACA 59.419 40.000 1.88 0.00 44.76 2.29
2326 2665 5.810587 TCGAGTTTCTGCCATACTGAAATAC 59.189 40.000 1.88 0.28 44.76 1.89
2327 2666 5.972935 TCGAGTTTCTGCCATACTGAAATA 58.027 37.500 1.88 0.00 44.76 1.40
2328 2667 4.832248 TCGAGTTTCTGCCATACTGAAAT 58.168 39.130 1.88 0.00 44.76 2.17
2438 2777 8.623903 GCTGGATATTTCATCAAATTACACTGA 58.376 33.333 0.00 0.00 33.95 3.41
2685 3044 7.761409 TGATATAAGATGTGGACTTGCAAAAC 58.239 34.615 0.00 0.00 0.00 2.43
2787 3149 1.379843 CCCATACCCAGCCAACACC 60.380 63.158 0.00 0.00 0.00 4.16
3025 3397 2.704065 CTGAAGTACCGGATACCCCATT 59.296 50.000 9.46 0.00 33.85 3.16
3037 3409 3.265791 CATCAGAGGTTGCTGAAGTACC 58.734 50.000 0.00 0.00 46.94 3.34
3107 3479 1.656818 CCATTCACCACATGACCGCC 61.657 60.000 0.00 0.00 36.92 6.13
3264 3961 5.319453 AGAGAGAAAATGATTTGCCAGACA 58.681 37.500 0.00 0.00 0.00 3.41
3311 4008 7.540055 CAGAAGCAACATCAAAGATAAAAGGTC 59.460 37.037 0.00 0.00 0.00 3.85
3314 4011 7.540055 GGACAGAAGCAACATCAAAGATAAAAG 59.460 37.037 0.00 0.00 0.00 2.27
3324 4021 2.636647 TGTGGACAGAAGCAACATCA 57.363 45.000 0.00 0.00 0.00 3.07
3399 4097 2.276472 TTGACAAGTGCAGCAACAAC 57.724 45.000 0.00 0.00 0.00 3.32
3701 4516 5.532406 TGCAGCAATCTACAATCCTAATTCC 59.468 40.000 0.00 0.00 0.00 3.01
3702 4517 6.624352 TGCAGCAATCTACAATCCTAATTC 57.376 37.500 0.00 0.00 0.00 2.17
3703 4518 7.504911 AGAATGCAGCAATCTACAATCCTAATT 59.495 33.333 11.54 0.00 0.00 1.40
3725 4540 7.998329 GCTATTTGCAAGACAACAAGTCAGAAT 60.998 37.037 0.00 0.00 44.97 2.40
3751 4566 4.264253 TCAGGCAACATCAAGTAATGAGG 58.736 43.478 0.00 0.00 45.24 3.86
3754 4569 7.325660 AGTAATCAGGCAACATCAAGTAATG 57.674 36.000 0.00 0.00 41.41 1.90
3757 4572 7.592938 CAAAAGTAATCAGGCAACATCAAGTA 58.407 34.615 0.00 0.00 41.41 2.24
3758 4573 6.449698 CAAAAGTAATCAGGCAACATCAAGT 58.550 36.000 0.00 0.00 41.41 3.16
3759 4574 5.346822 GCAAAAGTAATCAGGCAACATCAAG 59.653 40.000 0.00 0.00 41.41 3.02
3761 4576 4.523943 AGCAAAAGTAATCAGGCAACATCA 59.476 37.500 0.00 0.00 41.41 3.07
3762 4577 5.064441 AGCAAAAGTAATCAGGCAACATC 57.936 39.130 0.00 0.00 41.41 3.06
3763 4578 4.768968 AGAGCAAAAGTAATCAGGCAACAT 59.231 37.500 0.00 0.00 41.41 2.71
3764 4579 4.144297 AGAGCAAAAGTAATCAGGCAACA 58.856 39.130 0.00 0.00 41.41 3.33
3767 4582 3.057315 GCAAGAGCAAAAGTAATCAGGCA 60.057 43.478 0.00 0.00 41.58 4.75
3768 4583 3.192212 AGCAAGAGCAAAAGTAATCAGGC 59.808 43.478 0.00 0.00 45.49 4.85
3769 4584 5.382618 AAGCAAGAGCAAAAGTAATCAGG 57.617 39.130 0.00 0.00 45.49 3.86
3770 4585 6.919662 TGAAAAGCAAGAGCAAAAGTAATCAG 59.080 34.615 0.00 0.00 45.49 2.90
3772 4587 6.697019 TGTGAAAAGCAAGAGCAAAAGTAATC 59.303 34.615 0.00 0.00 45.49 1.75
3773 4588 6.572519 TGTGAAAAGCAAGAGCAAAAGTAAT 58.427 32.000 0.00 0.00 45.49 1.89
3776 4593 4.454728 TGTGAAAAGCAAGAGCAAAAGT 57.545 36.364 0.00 0.00 45.49 2.66
4204 5028 8.134202 TCCTGAGTAGATCACAGTTTCATTTA 57.866 34.615 0.00 0.00 33.89 1.40
4327 5153 6.757897 TTAGAATGACAGGCAAATAGGTTG 57.242 37.500 0.00 0.00 40.50 3.77
4328 5154 7.961326 ATTTAGAATGACAGGCAAATAGGTT 57.039 32.000 0.00 0.00 0.00 3.50
4329 5155 7.961326 AATTTAGAATGACAGGCAAATAGGT 57.039 32.000 0.00 0.00 0.00 3.08
4513 5340 3.057969 TCATCAATTGACACTTCGGCT 57.942 42.857 11.07 0.00 0.00 5.52
4532 5361 5.069516 ACAAATCATTAAGTGGGGCATGATC 59.930 40.000 0.00 0.00 35.70 2.92
4542 5377 9.669353 GCAGATAATACCACAAATCATTAAGTG 57.331 33.333 0.00 0.00 0.00 3.16
4567 5433 0.388134 TCGGCGAAGTACTCAACTGC 60.388 55.000 7.35 0.00 38.88 4.40
4601 5467 8.412456 TCTATGACTTCTCTTCATCTGATTGAC 58.588 37.037 0.00 0.00 35.31 3.18
4757 5635 6.882610 ATGCTACAAAATTCTTCAGTGACA 57.117 33.333 0.00 0.00 0.00 3.58
4758 5636 6.521133 CGAATGCTACAAAATTCTTCAGTGAC 59.479 38.462 0.00 0.00 31.83 3.67
5057 5943 1.486310 TGCATCCACTGGTCAGGATAC 59.514 52.381 2.87 0.00 42.61 2.24
5072 5958 2.289945 GGACAGATCCCCATACTGCATC 60.290 54.545 0.00 0.00 39.39 3.91
5092 5978 5.692613 ATTCACATGCAAAACAAAATGGG 57.307 34.783 0.00 0.00 0.00 4.00
5100 5986 6.749118 GGAGAGATTGTATTCACATGCAAAAC 59.251 38.462 0.00 0.00 38.36 2.43
5101 5987 6.660521 AGGAGAGATTGTATTCACATGCAAAA 59.339 34.615 0.00 0.00 38.36 2.44
5105 5991 6.690194 AAAGGAGAGATTGTATTCACATGC 57.310 37.500 0.00 0.00 33.76 4.06
5271 6157 1.605058 GAGGCCAACCGAGTAGCTCA 61.605 60.000 5.01 0.00 42.76 4.26
5320 6207 2.890474 CGAAGGCCCGGTTCATCG 60.890 66.667 0.00 2.44 0.00 3.84
5328 6215 2.255252 CTGTTTTGCGAAGGCCCG 59.745 61.111 0.00 0.00 38.85 6.13
5387 6274 3.691118 GGAGTTGATCAGTGCAAGCAATA 59.309 43.478 0.00 0.00 0.00 1.90
5393 6280 3.819368 TCTTTGGAGTTGATCAGTGCAA 58.181 40.909 9.22 9.22 34.50 4.08
5399 6286 3.609853 CCCGATTCTTTGGAGTTGATCA 58.390 45.455 0.00 0.00 0.00 2.92
5420 6307 2.287308 TGCACAAATGTTAACACCGAGC 60.287 45.455 11.22 12.33 0.00 5.03
5424 6311 2.547007 GGGGTGCACAAATGTTAACACC 60.547 50.000 20.43 16.35 40.48 4.16
5425 6312 2.101582 TGGGGTGCACAAATGTTAACAC 59.898 45.455 20.43 0.00 0.00 3.32
5522 6409 2.823747 TCACGTAACAGCATAGGTGAGT 59.176 45.455 12.66 0.00 42.51 3.41
5547 6434 6.534059 CGACTAGAGAATCAGATCGAGAATC 58.466 44.000 0.00 0.00 37.82 2.52
5548 6435 5.106712 GCGACTAGAGAATCAGATCGAGAAT 60.107 44.000 0.00 0.00 37.82 2.40
5549 6436 4.212425 GCGACTAGAGAATCAGATCGAGAA 59.788 45.833 0.00 0.00 37.82 2.87
5550 6437 3.743911 GCGACTAGAGAATCAGATCGAGA 59.256 47.826 0.00 0.00 37.82 4.04
5551 6438 3.120338 GGCGACTAGAGAATCAGATCGAG 60.120 52.174 0.00 0.00 37.82 4.04
5552 6439 2.809119 GGCGACTAGAGAATCAGATCGA 59.191 50.000 0.00 0.00 37.82 3.59
5553 6440 2.550180 TGGCGACTAGAGAATCAGATCG 59.450 50.000 0.00 0.00 37.82 3.69
5554 6441 3.608241 CGTGGCGACTAGAGAATCAGATC 60.608 52.174 0.00 0.00 37.82 2.75
5555 6442 2.292016 CGTGGCGACTAGAGAATCAGAT 59.708 50.000 0.00 0.00 37.82 2.90
5556 6443 1.671328 CGTGGCGACTAGAGAATCAGA 59.329 52.381 0.00 0.00 37.82 3.27
5557 6444 1.402259 ACGTGGCGACTAGAGAATCAG 59.598 52.381 0.00 0.00 37.82 2.90
5558 6445 1.460504 ACGTGGCGACTAGAGAATCA 58.539 50.000 0.00 0.00 37.82 2.57
5559 6446 3.687572 TTACGTGGCGACTAGAGAATC 57.312 47.619 0.00 0.00 0.00 2.52
5560 6447 4.171754 GTTTTACGTGGCGACTAGAGAAT 58.828 43.478 0.00 0.00 0.00 2.40
5561 6448 3.568538 GTTTTACGTGGCGACTAGAGAA 58.431 45.455 0.00 0.00 0.00 2.87
5562 6449 2.413239 CGTTTTACGTGGCGACTAGAGA 60.413 50.000 0.00 0.00 36.74 3.10
5563 6450 1.909532 CGTTTTACGTGGCGACTAGAG 59.090 52.381 0.00 0.00 36.74 2.43
5564 6451 1.401409 CCGTTTTACGTGGCGACTAGA 60.401 52.381 0.00 0.00 40.58 2.43
5565 6452 0.986992 CCGTTTTACGTGGCGACTAG 59.013 55.000 0.00 0.00 40.58 2.57
5566 6453 1.008361 GCCGTTTTACGTGGCGACTA 61.008 55.000 0.00 0.00 40.58 2.59
5567 6454 2.312436 GCCGTTTTACGTGGCGACT 61.312 57.895 0.00 0.00 40.58 4.18
5568 6455 2.171701 GCCGTTTTACGTGGCGAC 59.828 61.111 0.00 0.00 40.58 5.19
5572 6459 3.424859 CGGGGCCGTTTTACGTGG 61.425 66.667 0.00 0.00 40.58 4.94
5573 6460 1.698714 GATCGGGGCCGTTTTACGTG 61.699 60.000 0.00 0.00 40.58 4.49
5574 6461 1.448365 GATCGGGGCCGTTTTACGT 60.448 57.895 0.00 0.00 40.58 3.57
5575 6462 1.153509 AGATCGGGGCCGTTTTACG 60.154 57.895 0.00 0.00 42.11 3.18
5576 6463 0.392060 ACAGATCGGGGCCGTTTTAC 60.392 55.000 0.00 0.00 40.74 2.01
5577 6464 0.325602 AACAGATCGGGGCCGTTTTA 59.674 50.000 0.00 0.00 40.74 1.52
5578 6465 0.325602 TAACAGATCGGGGCCGTTTT 59.674 50.000 0.00 0.00 40.74 2.43
5579 6466 0.392060 GTAACAGATCGGGGCCGTTT 60.392 55.000 0.00 0.00 40.74 3.60
5580 6467 1.219935 GTAACAGATCGGGGCCGTT 59.780 57.895 0.00 0.00 40.74 4.44
5581 6468 2.728435 GGTAACAGATCGGGGCCGT 61.728 63.158 0.00 0.00 40.74 5.68
5582 6469 2.108362 GGTAACAGATCGGGGCCG 59.892 66.667 0.00 0.00 41.35 6.13
5583 6470 3.316029 TGGTAACAGATCGGGGCC 58.684 61.111 0.00 0.00 46.17 5.80


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

AutoCloner maintained by Alex Coulton.