Multiple sequence alignment - TraesCS2B01G389800

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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 TraesCS2B01G389800 chr2B 100.000 6734 0 0 1 6734 553617792 553624525 0.000000e+00 12436.0
1 TraesCS2B01G389800 chr2B 100.000 42 0 0 4362 4403 553622109 553622150 2.010000e-10 78.7
2 TraesCS2B01G389800 chr2B 100.000 42 0 0 4318 4359 553622153 553622194 2.010000e-10 78.7
3 TraesCS2B01G389800 chr2B 90.196 51 5 0 6223 6273 4736025 4736075 4.360000e-07 67.6
4 TraesCS2B01G389800 chr2D 94.440 3903 118 26 508 4362 473281315 473285166 0.000000e+00 5914.0
5 TraesCS2B01G389800 chr2D 91.686 1323 53 28 4721 6027 473285542 473286823 0.000000e+00 1781.0
6 TraesCS2B01G389800 chr2D 95.508 512 18 2 1 508 473280761 473281271 0.000000e+00 813.0
7 TraesCS2B01G389800 chr2D 96.970 363 7 2 4362 4721 473285122 473285483 2.080000e-169 606.0
8 TraesCS2B01G389800 chr2D 99.020 102 1 0 6073 6174 473286817 473286918 4.150000e-42 183.0
9 TraesCS2B01G389800 chr2D 93.750 64 2 1 6158 6221 473286933 473286994 2.000000e-15 95.3
10 TraesCS2B01G389800 chr2A 92.996 1999 100 16 508 2485 615349812 615351791 0.000000e+00 2880.0
11 TraesCS2B01G389800 chr2A 91.967 1917 99 23 2471 4362 615351971 615353857 0.000000e+00 2636.0
12 TraesCS2B01G389800 chr2A 91.181 1372 78 17 4721 6079 615354234 615355575 0.000000e+00 1823.0
13 TraesCS2B01G389800 chr2A 94.531 512 23 4 1 508 615349258 615349768 0.000000e+00 785.0
14 TraesCS2B01G389800 chr2A 93.956 364 15 5 4362 4721 615353813 615354173 1.650000e-150 544.0
15 TraesCS2B01G389800 chr4D 96.491 513 18 0 6222 6734 87554643 87555155 0.000000e+00 848.0
16 TraesCS2B01G389800 chr3A 94.553 514 25 3 6223 6734 660896136 660896648 0.000000e+00 791.0
17 TraesCS2B01G389800 chr5A 94.141 512 29 1 6223 6734 4090507 4091017 0.000000e+00 778.0
18 TraesCS2B01G389800 chrUn 90.196 51 5 0 6223 6273 433958711 433958761 4.360000e-07 67.6
19 TraesCS2B01G389800 chr6B 90.196 51 5 0 6223 6273 558744832 558744882 4.360000e-07 67.6
20 TraesCS2B01G389800 chr6B 90.196 51 5 0 6223 6273 558827415 558827465 4.360000e-07 67.6


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 TraesCS2B01G389800 chr2B 553617792 553624525 6733 False 4197.800000 12436 100.0000 1 6734 3 chr2B.!!$F2 6733
1 TraesCS2B01G389800 chr2D 473280761 473286994 6233 False 1565.383333 5914 95.2290 1 6221 6 chr2D.!!$F1 6220
2 TraesCS2B01G389800 chr2A 615349258 615355575 6317 False 1733.600000 2880 92.9262 1 6079 5 chr2A.!!$F1 6078
3 TraesCS2B01G389800 chr4D 87554643 87555155 512 False 848.000000 848 96.4910 6222 6734 1 chr4D.!!$F1 512
4 TraesCS2B01G389800 chr3A 660896136 660896648 512 False 791.000000 791 94.5530 6223 6734 1 chr3A.!!$F1 511
5 TraesCS2B01G389800 chr5A 4090507 4091017 510 False 778.000000 778 94.1410 6223 6734 1 chr5A.!!$F1 511

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
839 895 0.036294 GGGAGGTTTGGTCGAAGGAG 60.036 60.000 0.00 0.0 0.00 3.69 F
1267 1342 0.451783 GGCAAGTCAAATAGGCGTGG 59.548 55.000 0.00 0.0 31.61 4.94 F
1875 1959 1.669440 CTGCACTGCCCAGCAATTT 59.331 52.632 0.00 0.0 40.73 1.82 F
2630 2925 2.133281 TTCCGTCCGTCTTCTGGATA 57.867 50.000 0.00 0.0 37.93 2.59 F
3975 4294 1.937899 GACCACAACACAGCTACGTTT 59.062 47.619 0.00 0.0 0.00 3.60 F
4865 5250 0.036306 CTGTCTTGGGCCCGTACTTT 59.964 55.000 19.37 0.0 0.00 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1858 1942 0.469070 AAAAATTGCTGGGCAGTGCA 59.531 45.000 18.61 0.0 40.61 4.57 R
2434 2535 3.476552 AGCATGTTTCTTTCTTCCGTGA 58.523 40.909 0.00 0.0 0.00 4.35 R
3288 3606 0.775542 ACCTTGTTTACCCTGACCCC 59.224 55.000 0.00 0.0 0.00 4.95 R
4091 4410 2.325583 TCCGTTGATGGTAAGCATCC 57.674 50.000 0.00 0.0 0.00 3.51 R
4962 5347 0.250901 ATGGCAGTGGTTGAGGTCAC 60.251 55.000 0.00 0.0 0.00 3.67 R
6435 6882 0.969894 CAGGAGAAGAACACGGTCCT 59.030 55.000 0.00 0.0 38.21 3.85 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
120 121 5.982890 AAGGGTAAATCAACAGACAATGG 57.017 39.130 0.00 0.00 0.00 3.16
258 259 0.888619 TCTCAAGCTACACCGACAGG 59.111 55.000 0.00 0.00 45.13 4.00
275 276 3.450904 ACAGGACCCAGCAATTAGACTA 58.549 45.455 0.00 0.00 0.00 2.59
279 280 3.462021 GACCCAGCAATTAGACTAGCAG 58.538 50.000 0.00 0.00 0.00 4.24
301 302 3.312890 CCTCCCACAATCTATCAGGACT 58.687 50.000 0.00 0.00 0.00 3.85
336 337 0.749818 TGCTTTCGGTTCCTGTTGCA 60.750 50.000 0.00 0.00 0.00 4.08
337 338 0.040067 GCTTTCGGTTCCTGTTGCAG 60.040 55.000 0.00 0.00 0.00 4.41
398 399 3.254411 TGATTGCTGCATTTGTAAACGGA 59.746 39.130 1.84 0.00 0.00 4.69
406 407 4.520874 TGCATTTGTAAACGGAGATTTGGA 59.479 37.500 0.00 0.00 0.00 3.53
407 408 5.184864 TGCATTTGTAAACGGAGATTTGGAT 59.815 36.000 0.00 0.00 0.00 3.41
475 480 5.385617 CGACTGCGAAAAGAAGAAATCAAT 58.614 37.500 0.00 0.00 40.82 2.57
630 679 4.222847 GGACCCTCGACATCGCCC 62.223 72.222 0.00 0.00 39.60 6.13
716 765 4.643387 GCGTCAACCCTGCACCCT 62.643 66.667 0.00 0.00 0.00 4.34
833 889 1.003718 GAGGTGGGAGGTTTGGTCG 60.004 63.158 0.00 0.00 0.00 4.79
834 890 1.460689 AGGTGGGAGGTTTGGTCGA 60.461 57.895 0.00 0.00 0.00 4.20
835 891 1.057851 AGGTGGGAGGTTTGGTCGAA 61.058 55.000 0.00 0.00 0.00 3.71
836 892 0.605589 GGTGGGAGGTTTGGTCGAAG 60.606 60.000 0.00 0.00 0.00 3.79
837 893 0.605589 GTGGGAGGTTTGGTCGAAGG 60.606 60.000 0.00 0.00 0.00 3.46
838 894 0.765135 TGGGAGGTTTGGTCGAAGGA 60.765 55.000 0.00 0.00 0.00 3.36
839 895 0.036294 GGGAGGTTTGGTCGAAGGAG 60.036 60.000 0.00 0.00 0.00 3.69
840 896 0.974383 GGAGGTTTGGTCGAAGGAGA 59.026 55.000 0.00 0.00 0.00 3.71
841 897 1.066787 GGAGGTTTGGTCGAAGGAGAG 60.067 57.143 0.00 0.00 0.00 3.20
842 898 0.977395 AGGTTTGGTCGAAGGAGAGG 59.023 55.000 0.00 0.00 0.00 3.69
843 899 0.036294 GGTTTGGTCGAAGGAGAGGG 60.036 60.000 0.00 0.00 0.00 4.30
844 900 0.974383 GTTTGGTCGAAGGAGAGGGA 59.026 55.000 0.00 0.00 0.00 4.20
845 901 1.066787 GTTTGGTCGAAGGAGAGGGAG 60.067 57.143 0.00 0.00 0.00 4.30
846 902 1.258445 TTGGTCGAAGGAGAGGGAGC 61.258 60.000 0.00 0.00 0.00 4.70
1083 1158 4.091939 GCGAAACCCTAGGGCGGT 62.092 66.667 28.88 13.20 39.32 5.68
1146 1221 4.168291 GCAAGGAGGAGGGCGAGG 62.168 72.222 0.00 0.00 0.00 4.63
1147 1222 4.168291 CAAGGAGGAGGGCGAGGC 62.168 72.222 0.00 0.00 0.00 4.70
1199 1274 1.448119 GCAAATCCCTAGAAGCCGCC 61.448 60.000 0.00 0.00 0.00 6.13
1267 1342 0.451783 GGCAAGTCAAATAGGCGTGG 59.548 55.000 0.00 0.00 31.61 4.94
1421 1496 3.109240 GAGTCGTCCTACTCGGGC 58.891 66.667 0.00 0.00 36.80 6.13
1757 1833 6.043854 AGTTTTAGGTTTTCACAAGCCAAA 57.956 33.333 0.00 0.00 35.71 3.28
1804 1881 7.718334 TTCTGTCTGGTAGAATTGTATGAGA 57.282 36.000 0.00 0.00 29.68 3.27
1858 1942 2.908940 GTGGTGCTGTGCTTGGCT 60.909 61.111 0.00 0.00 0.00 4.75
1874 1958 3.373226 CTGCACTGCCCAGCAATT 58.627 55.556 0.00 0.00 40.73 2.32
1875 1959 1.669440 CTGCACTGCCCAGCAATTT 59.331 52.632 0.00 0.00 40.73 1.82
1994 2078 7.070571 ACAAACCAATGAAAATCCCTGAAACTA 59.929 33.333 0.00 0.00 0.00 2.24
2001 2085 6.778821 TGAAAATCCCTGAAACTACTGATGA 58.221 36.000 0.00 0.00 0.00 2.92
2054 2144 2.602257 TGTTGATCTATCACTGGCCG 57.398 50.000 0.00 0.00 36.36 6.13
2290 2380 7.060600 TGATTCTTGCCGCTATATAAAATCG 57.939 36.000 0.00 0.00 0.00 3.34
2296 2386 9.297586 TCTTGCCGCTATATAAAATCGTAATAG 57.702 33.333 0.00 0.00 0.00 1.73
2418 2519 7.359514 GCATCAGCCACAAATTAGAAAAAGAAC 60.360 37.037 0.00 0.00 33.58 3.01
2434 2535 8.419442 AGAAAAAGAACTCAAGCAAAAGATGAT 58.581 29.630 0.00 0.00 0.00 2.45
2445 2546 4.761739 AGCAAAAGATGATCACGGAAGAAA 59.238 37.500 0.00 0.00 0.00 2.52
2563 2857 3.321111 AGTGTGTTACTCGAGGACAATGT 59.679 43.478 20.84 9.07 33.17 2.71
2618 2913 3.676093 GGATAATCCTGGAATTCCGTCC 58.324 50.000 19.57 12.85 39.43 4.79
2630 2925 2.133281 TTCCGTCCGTCTTCTGGATA 57.867 50.000 0.00 0.00 37.93 2.59
2697 3012 4.546829 TCTGTGCCTTAAACGTATCCTT 57.453 40.909 0.00 0.00 0.00 3.36
3103 3420 8.565896 AGAGTGCAGACAATCAAATTAATACA 57.434 30.769 0.00 0.00 43.32 2.29
3373 3692 9.314133 GCCCCAAAGGAATATTTATCTAGAAAT 57.686 33.333 0.00 0.00 38.24 2.17
3975 4294 1.937899 GACCACAACACAGCTACGTTT 59.062 47.619 0.00 0.00 0.00 3.60
4362 4681 9.184523 CACTCATTTTGGGTAATAGAATGGTTA 57.815 33.333 0.00 0.00 24.29 2.85
4371 4690 9.715121 TGGGTAATAGAATGGTTATTAATCGAC 57.285 33.333 0.00 0.00 0.00 4.20
4372 4691 9.159364 GGGTAATAGAATGGTTATTAATCGACC 57.841 37.037 12.00 12.00 0.00 4.79
4373 4692 9.939802 GGTAATAGAATGGTTATTAATCGACCT 57.060 33.333 17.23 3.54 34.52 3.85
4379 4698 9.490379 AGAATGGTTATTAATCGACCTATGTTC 57.510 33.333 17.23 15.01 34.52 3.18
4380 4699 8.617290 AATGGTTATTAATCGACCTATGTTCC 57.383 34.615 17.23 0.00 34.52 3.62
4381 4700 7.127012 TGGTTATTAATCGACCTATGTTCCA 57.873 36.000 17.23 0.00 34.52 3.53
4382 4701 6.987992 TGGTTATTAATCGACCTATGTTCCAC 59.012 38.462 17.23 0.00 34.52 4.02
4383 4702 7.147620 TGGTTATTAATCGACCTATGTTCCACT 60.148 37.037 17.23 0.00 34.52 4.00
4384 4703 7.384387 GGTTATTAATCGACCTATGTTCCACTC 59.616 40.741 11.74 0.00 0.00 3.51
4385 4704 5.925506 TTAATCGACCTATGTTCCACTCA 57.074 39.130 0.00 0.00 0.00 3.41
4386 4705 6.479972 TTAATCGACCTATGTTCCACTCAT 57.520 37.500 0.00 0.00 0.00 2.90
4387 4706 5.359194 AATCGACCTATGTTCCACTCATT 57.641 39.130 0.00 0.00 0.00 2.57
4388 4707 4.819105 TCGACCTATGTTCCACTCATTT 57.181 40.909 0.00 0.00 0.00 2.32
4389 4708 5.160607 TCGACCTATGTTCCACTCATTTT 57.839 39.130 0.00 0.00 0.00 1.82
4390 4709 4.935205 TCGACCTATGTTCCACTCATTTTG 59.065 41.667 0.00 0.00 0.00 2.44
4391 4710 4.094887 CGACCTATGTTCCACTCATTTTGG 59.905 45.833 0.00 0.00 35.18 3.28
4392 4711 4.344104 ACCTATGTTCCACTCATTTTGGG 58.656 43.478 0.00 0.00 34.56 4.12
4393 4712 4.202673 ACCTATGTTCCACTCATTTTGGGT 60.203 41.667 0.00 0.00 34.56 4.51
4394 4713 5.014755 ACCTATGTTCCACTCATTTTGGGTA 59.985 40.000 0.00 0.00 34.56 3.69
4395 4714 5.949354 CCTATGTTCCACTCATTTTGGGTAA 59.051 40.000 0.00 0.00 34.56 2.85
4396 4715 6.607198 CCTATGTTCCACTCATTTTGGGTAAT 59.393 38.462 0.00 0.00 34.56 1.89
4397 4716 7.777910 CCTATGTTCCACTCATTTTGGGTAATA 59.222 37.037 0.00 0.00 34.56 0.98
4398 4717 7.645058 ATGTTCCACTCATTTTGGGTAATAG 57.355 36.000 0.00 0.00 34.56 1.73
4399 4718 6.785076 TGTTCCACTCATTTTGGGTAATAGA 58.215 36.000 0.00 0.00 34.56 1.98
4400 4719 7.235079 TGTTCCACTCATTTTGGGTAATAGAA 58.765 34.615 0.00 0.00 34.56 2.10
4401 4720 7.893302 TGTTCCACTCATTTTGGGTAATAGAAT 59.107 33.333 0.00 0.00 34.56 2.40
4402 4721 7.880160 TCCACTCATTTTGGGTAATAGAATG 57.120 36.000 0.00 0.00 34.56 2.67
4403 4722 7.410174 TCCACTCATTTTGGGTAATAGAATGT 58.590 34.615 0.00 0.00 34.56 2.71
4455 4774 4.469657 ACTCCAAATTGTGAGCCTGTTAA 58.530 39.130 10.11 0.00 31.65 2.01
4666 4985 7.902920 AACTGGAATGGTTAGAATATTGCAT 57.097 32.000 0.00 0.00 32.89 3.96
4743 5127 5.255687 TCATTGACAGCATAGGTTTGACAT 58.744 37.500 0.00 0.00 0.00 3.06
4744 5128 5.124297 TCATTGACAGCATAGGTTTGACATG 59.876 40.000 0.00 0.00 0.00 3.21
4745 5129 4.284829 TGACAGCATAGGTTTGACATGA 57.715 40.909 0.00 0.00 0.00 3.07
4746 5130 4.002982 TGACAGCATAGGTTTGACATGAC 58.997 43.478 0.00 0.00 0.00 3.06
4747 5131 4.002982 GACAGCATAGGTTTGACATGACA 58.997 43.478 0.00 0.00 0.00 3.58
4814 5198 9.739276 TTCTTTCATGTATCCTAGATGTTGTTT 57.261 29.630 0.00 0.00 31.89 2.83
4856 5241 4.092968 CGTAGTTGTAATTCTGTCTTGGGC 59.907 45.833 0.00 0.00 0.00 5.36
4865 5250 0.036306 CTGTCTTGGGCCCGTACTTT 59.964 55.000 19.37 0.00 0.00 2.66
4866 5251 0.475044 TGTCTTGGGCCCGTACTTTT 59.525 50.000 19.37 0.00 0.00 2.27
4870 5255 2.372837 TCTTGGGCCCGTACTTTTACTT 59.627 45.455 19.37 0.00 0.00 2.24
4999 5392 1.002142 CATGTGCTCGGCCATTATGTG 60.002 52.381 2.24 0.00 0.00 3.21
5081 5477 6.462347 CCCAAGTGTTGCTTTGTAAGGTTTAT 60.462 38.462 0.00 0.00 34.69 1.40
5090 5486 8.506168 TGCTTTGTAAGGTTTATCTAATCCAG 57.494 34.615 1.09 0.00 0.00 3.86
5130 5526 4.436332 TGCTACTGAACATATGACTGCAG 58.564 43.478 13.48 13.48 0.00 4.41
5136 5532 4.388485 TGAACATATGACTGCAGTTGTGT 58.612 39.130 22.65 17.22 0.00 3.72
5140 5536 6.875948 ACATATGACTGCAGTTGTGTTTAA 57.124 33.333 22.65 1.60 0.00 1.52
5151 5547 5.181245 GCAGTTGTGTTTAAATCCTGCTAGA 59.819 40.000 14.74 0.00 40.39 2.43
5321 5721 1.811679 GCAGCAGTCCCTTCTACGC 60.812 63.158 0.00 0.00 0.00 4.42
5367 5767 3.358111 TGGGCAATTTCGAGGTAATGA 57.642 42.857 0.00 0.00 0.00 2.57
5434 5834 3.506067 ACGCTACTTATGCCAAGCTTTTT 59.494 39.130 0.00 0.00 32.73 1.94
5484 5888 1.755179 AAAGGTTGGATCCTGATGCG 58.245 50.000 14.23 0.00 37.93 4.73
5623 6027 0.390735 GCTGGCTTGGAAAATGCTGG 60.391 55.000 0.00 0.00 0.00 4.85
5682 6086 5.050363 GCTCGTTAGATTCAACAAGTTGTGA 60.050 40.000 9.79 6.66 41.16 3.58
5691 6095 5.107109 TCAACAAGTTGTGATGTATGCAC 57.893 39.130 9.79 0.00 41.16 4.57
5720 6124 6.985188 TGGTACATTGAGCTGTAAGATTTC 57.015 37.500 0.00 0.00 34.07 2.17
5752 6156 7.859325 TTTTCTATTACTGTTCCATAGGCAC 57.141 36.000 0.00 0.00 0.00 5.01
5855 6267 2.089980 CTCATGAGTTGGGGCTTTCAG 58.910 52.381 14.95 0.00 0.00 3.02
5867 6279 1.666189 GGCTTTCAGTGATTCGTAGCC 59.334 52.381 12.15 12.15 39.79 3.93
5900 6312 2.695359 CCGTAGGCTGTCAGCTTTTAA 58.305 47.619 23.68 0.00 46.14 1.52
5902 6314 3.120304 CCGTAGGCTGTCAGCTTTTAAAC 60.120 47.826 23.68 10.65 46.14 2.01
5904 6316 4.143094 CGTAGGCTGTCAGCTTTTAAACTC 60.143 45.833 23.68 4.43 41.99 3.01
5907 6319 4.036852 AGGCTGTCAGCTTTTAAACTCAAC 59.963 41.667 23.68 3.00 41.99 3.18
5908 6320 4.036852 GGCTGTCAGCTTTTAAACTCAACT 59.963 41.667 23.68 0.00 41.99 3.16
5909 6321 5.238650 GGCTGTCAGCTTTTAAACTCAACTA 59.761 40.000 23.68 0.00 41.99 2.24
5910 6322 6.366630 GCTGTCAGCTTTTAAACTCAACTAG 58.633 40.000 17.89 0.00 38.45 2.57
5937 6352 1.863662 ATCTACGAGGGTATGCGCGG 61.864 60.000 8.83 0.00 0.00 6.46
5959 6374 3.403038 GACTCTTGGCTTTTAGTGCTGA 58.597 45.455 0.00 0.00 0.00 4.26
6036 6451 2.866156 GCAAAAAGCAACCACCTTTCTC 59.134 45.455 0.00 0.00 44.79 2.87
6043 6458 2.422597 CAACCACCTTTCTCATGCGTA 58.577 47.619 0.00 0.00 0.00 4.42
6050 6465 5.235186 CCACCTTTCTCATGCGTAAATAGAG 59.765 44.000 0.00 0.00 0.00 2.43
6064 6479 6.455246 GCGTAAATAGAGTAAACAGGAAGTGC 60.455 42.308 0.00 0.00 0.00 4.40
6160 6606 1.470098 GCTGTGAACGCCAGATGAAAT 59.530 47.619 0.00 0.00 31.38 2.17
6162 6608 3.313526 GCTGTGAACGCCAGATGAAATAT 59.686 43.478 0.00 0.00 31.38 1.28
6250 6696 2.355837 TTCTGGTCGCGAGCACAC 60.356 61.111 34.84 11.84 34.78 3.82
6297 6743 3.709987 CATGTCATCGAGATGTGTAGCA 58.290 45.455 12.22 6.34 39.72 3.49
6346 6793 2.875094 TTTTTAATCGGGGGAACGGA 57.125 45.000 0.00 0.00 0.00 4.69
6580 7029 3.694043 TGTTTGGATCTCCATTGACGA 57.306 42.857 0.00 0.00 46.97 4.20
6582 7031 2.293677 TTGGATCTCCATTGACGACG 57.706 50.000 0.00 0.00 46.97 5.12
6585 7034 0.460311 GATCTCCATTGACGACGGGT 59.540 55.000 0.00 0.00 0.00 5.28
6608 7057 2.060383 CCCTGAGCACCGGAGATCA 61.060 63.158 18.80 18.80 0.00 2.92
6616 7065 2.365635 CCGGAGATCAGTGGGGGT 60.366 66.667 0.00 0.00 0.00 4.95
6626 7075 2.759355 TCAGTGGGGGTAGGAATACAG 58.241 52.381 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 7.226325 GCTAGATGATTCTTTGTGACAATAGCT 59.774 37.037 12.09 0.00 33.17 3.32
78 79 4.829492 CCTTTCTCCTTGTTTGAGGATTGT 59.171 41.667 0.00 0.00 44.56 2.71
100 101 5.253330 TCTCCATTGTCTGTTGATTTACCC 58.747 41.667 0.00 0.00 0.00 3.69
120 121 8.713271 CATGAAGTAAGTTTCAACCTTACTCTC 58.287 37.037 7.75 8.32 41.37 3.20
258 259 3.462021 CTGCTAGTCTAATTGCTGGGTC 58.538 50.000 0.00 0.00 0.00 4.46
275 276 1.419387 GATAGATTGTGGGAGGCTGCT 59.581 52.381 5.84 0.00 0.00 4.24
279 280 2.050144 TCCTGATAGATTGTGGGAGGC 58.950 52.381 0.00 0.00 0.00 4.70
336 337 3.882888 TCTTTCGCCATTCTGTTTTGACT 59.117 39.130 0.00 0.00 0.00 3.41
337 338 4.222114 CTCTTTCGCCATTCTGTTTTGAC 58.778 43.478 0.00 0.00 0.00 3.18
350 351 2.263945 GTAGAACTCTGCTCTTTCGCC 58.736 52.381 0.00 0.00 0.00 5.54
398 399 1.743772 CGGAAGCCGTCATCCAAATCT 60.744 52.381 0.00 0.00 42.73 2.40
406 407 0.250038 CATCATCCGGAAGCCGTCAT 60.250 55.000 9.01 0.00 46.80 3.06
407 408 1.143838 CATCATCCGGAAGCCGTCA 59.856 57.895 9.01 0.00 46.80 4.35
475 480 7.653311 CAGTCTCATCATTTACGATCCATTGTA 59.347 37.037 0.00 0.00 0.00 2.41
716 765 1.474330 TGCTCACCTTATCAGCTCGA 58.526 50.000 0.00 0.00 34.03 4.04
833 889 0.684805 TCCTTCGCTCCCTCTCCTTC 60.685 60.000 0.00 0.00 0.00 3.46
834 890 0.686112 CTCCTTCGCTCCCTCTCCTT 60.686 60.000 0.00 0.00 0.00 3.36
835 891 1.076339 CTCCTTCGCTCCCTCTCCT 60.076 63.158 0.00 0.00 0.00 3.69
836 892 1.076632 TCTCCTTCGCTCCCTCTCC 60.077 63.158 0.00 0.00 0.00 3.71
837 893 1.106944 CCTCTCCTTCGCTCCCTCTC 61.107 65.000 0.00 0.00 0.00 3.20
838 894 1.076339 CCTCTCCTTCGCTCCCTCT 60.076 63.158 0.00 0.00 0.00 3.69
839 895 2.131067 CCCTCTCCTTCGCTCCCTC 61.131 68.421 0.00 0.00 0.00 4.30
840 896 2.042435 CCCTCTCCTTCGCTCCCT 60.042 66.667 0.00 0.00 0.00 4.20
841 897 2.042843 TCCCTCTCCTTCGCTCCC 60.043 66.667 0.00 0.00 0.00 4.30
842 898 1.076632 TCTCCCTCTCCTTCGCTCC 60.077 63.158 0.00 0.00 0.00 4.70
843 899 0.681564 TGTCTCCCTCTCCTTCGCTC 60.682 60.000 0.00 0.00 0.00 5.03
844 900 0.682855 CTGTCTCCCTCTCCTTCGCT 60.683 60.000 0.00 0.00 0.00 4.93
845 901 0.681564 TCTGTCTCCCTCTCCTTCGC 60.682 60.000 0.00 0.00 0.00 4.70
846 902 1.099689 GTCTGTCTCCCTCTCCTTCG 58.900 60.000 0.00 0.00 0.00 3.79
952 1016 0.541863 AGATAGCCTGGTTTCCACGG 59.458 55.000 0.00 0.00 0.00 4.94
953 1017 1.802880 CGAGATAGCCTGGTTTCCACG 60.803 57.143 0.00 0.00 0.00 4.94
955 1019 1.568504 ACGAGATAGCCTGGTTTCCA 58.431 50.000 0.00 0.00 28.86 3.53
1259 1334 4.435970 TCCTCCTCGCCACGCCTA 62.436 66.667 0.00 0.00 0.00 3.93
1267 1342 3.591835 CGCTCTCCTCCTCCTCGC 61.592 72.222 0.00 0.00 0.00 5.03
1436 1511 1.209383 CGACTCCGACTCGCTTTCA 59.791 57.895 0.00 0.00 38.22 2.69
1482 1557 1.398799 TCCTTCTCCTTCCTCCTCCT 58.601 55.000 0.00 0.00 0.00 3.69
1710 1785 9.545105 ACTAAGAAATGATGATCTAGAAGCAAG 57.455 33.333 0.00 0.00 0.00 4.01
1828 1905 0.947180 GCACCACCGTAACACGACAT 60.947 55.000 0.00 0.00 46.05 3.06
1858 1942 0.469070 AAAAATTGCTGGGCAGTGCA 59.531 45.000 18.61 0.00 40.61 4.57
1885 1969 3.138798 GCTGCAGGCTGGGACATG 61.139 66.667 17.12 0.00 38.20 3.21
1904 1988 1.398692 AAGGCGAAAAAGAAGGTGCA 58.601 45.000 0.00 0.00 0.00 4.57
1916 2000 2.787473 ATCCACTCATCAAAGGCGAA 57.213 45.000 0.00 0.00 0.00 4.70
1994 2078 2.433604 AGATCAGTCCGCAATCATCAGT 59.566 45.455 0.00 0.00 0.00 3.41
2001 2085 1.833630 TGGAGAAGATCAGTCCGCAAT 59.166 47.619 0.00 0.00 32.51 3.56
2290 2380 6.985188 TCTGTCATTTTGCTCCACTATTAC 57.015 37.500 0.00 0.00 0.00 1.89
2296 2386 6.749118 GTGATTTATCTGTCATTTTGCTCCAC 59.251 38.462 0.00 0.00 0.00 4.02
2418 2519 3.686241 TCCGTGATCATCTTTTGCTTGAG 59.314 43.478 0.00 0.00 0.00 3.02
2434 2535 3.476552 AGCATGTTTCTTTCTTCCGTGA 58.523 40.909 0.00 0.00 0.00 4.35
2630 2925 6.149973 CACCATATCATAAGATTTGCGTCCAT 59.850 38.462 0.00 0.00 35.67 3.41
2697 3012 5.692115 TCAGTATCCAACTTTCAGGCATA 57.308 39.130 0.00 0.00 35.76 3.14
2945 3262 8.589629 GTGTTTGCATATGACAATTCAAAGATC 58.410 33.333 6.97 0.00 34.61 2.75
3036 3353 7.121168 GTCACAGGGATTCATCACTTAAATCAA 59.879 37.037 0.00 0.00 38.84 2.57
3288 3606 0.775542 ACCTTGTTTACCCTGACCCC 59.224 55.000 0.00 0.00 0.00 4.95
3373 3692 5.362717 TCAACTGAAAGAACACTAGTCCTCA 59.637 40.000 0.00 0.00 37.43 3.86
3697 4016 2.926838 GAGAGTAAAAAGCCTGAGAGCG 59.073 50.000 0.00 0.00 38.01 5.03
3936 4255 5.704515 GTGGTCTTCCATGAATCTGATATGG 59.295 44.000 11.62 11.62 46.20 2.74
3990 4309 5.050091 ACAGTCTATGAAAAGAAACGTGCAG 60.050 40.000 0.00 0.00 0.00 4.41
4037 4356 6.839134 GGGGGAGAAACATAAATTCCATTAGT 59.161 38.462 0.00 0.00 0.00 2.24
4091 4410 2.325583 TCCGTTGATGGTAAGCATCC 57.674 50.000 0.00 0.00 0.00 3.51
4323 4642 4.819105 AAATGAGTGGAACATAGGTCGA 57.181 40.909 0.00 0.00 44.52 4.20
4362 4681 6.479972 TGAGTGGAACATAGGTCGATTAAT 57.520 37.500 0.00 0.00 44.52 1.40
4365 4684 5.359194 AATGAGTGGAACATAGGTCGATT 57.641 39.130 0.00 0.00 44.52 3.34
4366 4685 5.359194 AAATGAGTGGAACATAGGTCGAT 57.641 39.130 0.00 0.00 44.52 3.59
4367 4686 4.819105 AAATGAGTGGAACATAGGTCGA 57.181 40.909 0.00 0.00 44.52 4.20
4368 4687 4.094887 CCAAAATGAGTGGAACATAGGTCG 59.905 45.833 0.00 0.00 44.52 4.79
4369 4688 4.399303 CCCAAAATGAGTGGAACATAGGTC 59.601 45.833 0.00 0.00 44.52 3.85
4370 4689 4.202673 ACCCAAAATGAGTGGAACATAGGT 60.203 41.667 0.00 0.00 44.52 3.08
4371 4690 4.344104 ACCCAAAATGAGTGGAACATAGG 58.656 43.478 0.00 0.00 44.52 2.57
4372 4691 7.645058 ATTACCCAAAATGAGTGGAACATAG 57.355 36.000 0.00 0.00 44.52 2.23
4373 4692 8.553153 TCTATTACCCAAAATGAGTGGAACATA 58.447 33.333 0.00 0.00 44.52 2.29
4374 4693 7.410174 TCTATTACCCAAAATGAGTGGAACAT 58.590 34.615 0.00 0.00 44.52 2.71
4375 4694 6.785076 TCTATTACCCAAAATGAGTGGAACA 58.215 36.000 0.00 0.00 41.43 3.18
4376 4695 7.696992 TTCTATTACCCAAAATGAGTGGAAC 57.303 36.000 0.00 0.00 38.54 3.62
4377 4696 7.893302 ACATTCTATTACCCAAAATGAGTGGAA 59.107 33.333 0.00 0.00 38.54 3.53
4378 4697 7.410174 ACATTCTATTACCCAAAATGAGTGGA 58.590 34.615 0.00 0.00 38.54 4.02
4379 4698 7.645058 ACATTCTATTACCCAAAATGAGTGG 57.355 36.000 0.00 0.00 35.77 4.00
4380 4699 9.927668 AAAACATTCTATTACCCAAAATGAGTG 57.072 29.630 0.00 0.00 32.86 3.51
4455 4774 3.054679 TGTGGAACATTGCATGGCT 57.945 47.368 0.00 0.00 45.67 4.75
4534 4853 8.856153 TTACAGAAAACTGTAAGCCAATGATA 57.144 30.769 15.69 0.00 42.68 2.15
4743 5127 4.648626 GGGCAGCCTGCACTGTCA 62.649 66.667 19.95 0.00 45.01 3.58
4814 5198 6.931838 ACTACGTTTCATTCATGGAAGACTA 58.068 36.000 0.00 0.00 0.00 2.59
4856 5241 5.990996 TCAAGTAACCAAGTAAAAGTACGGG 59.009 40.000 0.00 0.00 36.30 5.28
4962 5347 0.250901 ATGGCAGTGGTTGAGGTCAC 60.251 55.000 0.00 0.00 0.00 3.67
4999 5392 6.759497 AAAACAGGAAGATGCACCTATAAC 57.241 37.500 0.00 0.00 34.87 1.89
5025 5421 6.115446 CAGCTATTGTACAAGGGAAGATTCA 58.885 40.000 14.65 0.00 0.00 2.57
5113 5509 4.453478 ACACAACTGCAGTCATATGTTCAG 59.547 41.667 21.95 11.14 0.00 3.02
5130 5526 6.204882 ACAGTCTAGCAGGATTTAAACACAAC 59.795 38.462 0.00 0.00 0.00 3.32
5136 5532 4.695455 GTGCACAGTCTAGCAGGATTTAAA 59.305 41.667 13.17 0.00 42.14 1.52
5140 5536 1.905215 AGTGCACAGTCTAGCAGGATT 59.095 47.619 21.04 0.00 42.14 3.01
5151 5547 5.611128 ATCATCAGAAGATAGTGCACAGT 57.389 39.130 21.04 6.66 31.88 3.55
5321 5721 6.590292 ACTTGTACTGTAACATCATTTCCTCG 59.410 38.462 0.00 0.00 0.00 4.63
5367 5767 4.463050 TTTGTAAGGGTTGGAATGAGGT 57.537 40.909 0.00 0.00 0.00 3.85
5407 5807 0.804544 TGGCATAAGTAGCGTGCGTC 60.805 55.000 0.00 0.00 39.69 5.19
5434 5834 1.094785 GCTGCGGCCTGATAAAGAAA 58.905 50.000 6.12 0.00 0.00 2.52
5435 5835 0.253044 AGCTGCGGCCTGATAAAGAA 59.747 50.000 15.55 0.00 39.73 2.52
5436 5836 0.462581 CAGCTGCGGCCTGATAAAGA 60.463 55.000 15.55 0.00 39.73 2.52
5437 5837 2.020131 CAGCTGCGGCCTGATAAAG 58.980 57.895 15.55 0.00 39.73 1.85
5544 5948 4.871993 CAGTATGTTGCTCATGAAGGTC 57.128 45.455 0.00 0.00 37.91 3.85
5667 6071 6.151691 GTGCATACATCACAACTTGTTGAAT 58.848 36.000 18.82 9.57 34.73 2.57
5691 6095 3.149196 ACAGCTCAATGTACCAAACTGG 58.851 45.455 0.00 0.00 45.02 4.00
5720 6124 8.306680 TGGAACAGTAATAGAAAAACTTCGAG 57.693 34.615 0.00 0.00 0.00 4.04
5776 6180 9.358406 ACAATGAGATGCCTATGAATTCAAATA 57.642 29.630 13.09 0.17 0.00 1.40
5777 6181 8.246430 ACAATGAGATGCCTATGAATTCAAAT 57.754 30.769 13.09 0.00 0.00 2.32
5778 6182 7.649533 ACAATGAGATGCCTATGAATTCAAA 57.350 32.000 13.09 0.00 0.00 2.69
5779 6183 7.649533 AACAATGAGATGCCTATGAATTCAA 57.350 32.000 13.09 0.00 0.00 2.69
5867 6279 2.125592 TACGGGTTAAAGCGCCGG 60.126 61.111 2.29 0.00 0.00 6.13
5882 6294 4.755123 TGAGTTTAAAAGCTGACAGCCTAC 59.245 41.667 23.74 12.22 43.77 3.18
5902 6314 8.670135 CCCTCGTAGATGAATATACTAGTTGAG 58.330 40.741 0.00 0.00 33.89 3.02
5904 6316 8.338072 ACCCTCGTAGATGAATATACTAGTTG 57.662 38.462 0.00 0.00 33.89 3.16
5907 6319 8.561212 GCATACCCTCGTAGATGAATATACTAG 58.439 40.741 0.00 0.00 33.89 2.57
5908 6320 7.226128 CGCATACCCTCGTAGATGAATATACTA 59.774 40.741 0.00 0.00 33.89 1.82
5909 6321 6.038382 CGCATACCCTCGTAGATGAATATACT 59.962 42.308 0.00 0.00 33.89 2.12
5910 6322 6.200100 CGCATACCCTCGTAGATGAATATAC 58.800 44.000 0.00 0.00 33.89 1.47
5920 6335 2.050351 CCGCGCATACCCTCGTAG 60.050 66.667 8.75 0.00 0.00 3.51
5937 6352 2.485814 CAGCACTAAAAGCCAAGAGTCC 59.514 50.000 0.00 0.00 0.00 3.85
5959 6374 1.064166 ACAAGCCAATCTATGCTGCCT 60.064 47.619 0.00 0.00 38.00 4.75
5970 6385 3.553917 GCACAACGTTAAAACAAGCCAAT 59.446 39.130 0.00 0.00 0.00 3.16
6036 6451 7.277981 ACTTCCTGTTTACTCTATTTACGCATG 59.722 37.037 0.00 0.00 0.00 4.06
6043 6458 9.167311 CTAATGCACTTCCTGTTTACTCTATTT 57.833 33.333 0.00 0.00 0.00 1.40
6050 6465 6.402658 GCTTCTCTAATGCACTTCCTGTTTAC 60.403 42.308 0.00 0.00 0.00 2.01
6064 6479 3.341823 AGCCACTGTTGCTTCTCTAATG 58.658 45.455 0.00 0.00 34.87 1.90
6183 6629 4.935702 TCTGTCCGTTTCGTAGAAAAAGA 58.064 39.130 0.00 0.00 45.90 2.52
6184 6630 5.840940 ATCTGTCCGTTTCGTAGAAAAAG 57.159 39.130 0.00 0.00 45.90 2.27
6250 6696 1.226974 CCCAGATACCACGAGCACG 60.227 63.158 0.76 0.76 45.75 5.34
6275 6721 2.474359 GCTACACATCTCGATGACATGC 59.526 50.000 13.45 8.37 41.20 4.06
6297 6743 5.434408 GACTGGTTCCCTCGGTAATTTAAT 58.566 41.667 0.00 0.00 0.00 1.40
6338 6784 3.451526 CTCTACCGTATTTTCCGTTCCC 58.548 50.000 0.00 0.00 0.00 3.97
6346 6793 4.322499 CGCCATATCCCTCTACCGTATTTT 60.322 45.833 0.00 0.00 0.00 1.82
6395 6842 2.125326 CCCGTCACGGCAGGATCTA 61.125 63.158 12.05 0.00 46.86 1.98
6435 6882 0.969894 CAGGAGAAGAACACGGTCCT 59.030 55.000 0.00 0.00 38.21 3.85
6585 7034 2.111999 CTCCGGTGCTCAGGGTTTCA 62.112 60.000 0.00 0.00 0.00 2.69
6608 7057 1.345112 CCCTGTATTCCTACCCCCACT 60.345 57.143 0.00 0.00 0.00 4.00
6616 7065 3.134879 CGCCGCCCTGTATTCCTA 58.865 61.111 0.00 0.00 0.00 2.94
6682 7131 1.146041 CGCAATCAGGATTCGGGGA 59.854 57.895 0.00 0.00 0.00 4.81


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

AutoCloner maintained by Alex Coulton.