Multiple sequence alignment - TraesCS5B01G447600

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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 TraesCS5B01G447600 chr5B 100.000 5715 0 0 1 5715 618469293 618475007 0.000000e+00 10554.0
1 TraesCS5B01G447600 chr5B 89.011 91 10 0 5226 5316 322144419 322144329 4.680000e-21 113.0
2 TraesCS5B01G447600 chr5A 96.389 2908 82 11 2330 5229 623210667 623213559 0.000000e+00 4767.0
3 TraesCS5B01G447600 chr5A 89.145 1824 113 42 1 1783 623206614 623208393 0.000000e+00 2193.0
4 TraesCS5B01G447600 chr5A 88.567 656 62 7 1336 1983 623209720 623210370 0.000000e+00 784.0
5 TraesCS5B01G447600 chr5A 92.683 410 21 7 5310 5711 623213562 623213970 2.970000e-162 582.0
6 TraesCS5B01G447600 chr5A 88.166 169 18 2 2498 2665 623230120 623230287 3.490000e-47 200.0
7 TraesCS5B01G447600 chr5D 95.150 2639 113 10 1778 4407 498773196 498775828 0.000000e+00 4150.0
8 TraesCS5B01G447600 chr5D 90.595 1850 98 18 1 1783 498768837 498770677 0.000000e+00 2383.0
9 TraesCS5B01G447600 chr5D 95.301 830 29 4 4403 5227 498775864 498776688 0.000000e+00 1308.0
10 TraesCS5B01G447600 chr5D 88.608 316 22 4 5412 5713 498776799 498777114 6.990000e-99 372.0
11 TraesCS5B01G447600 chr2D 93.293 820 50 4 2167 2984 513989851 513990667 0.000000e+00 1205.0
12 TraesCS5B01G447600 chr2D 85.682 440 46 10 887 1309 513987768 513988207 1.130000e-121 448.0
13 TraesCS5B01G447600 chr2D 88.660 97 11 0 5223 5319 29166607 29166511 1.010000e-22 119.0
14 TraesCS5B01G447600 chr2D 91.011 89 7 1 5222 5310 29280863 29280950 1.010000e-22 119.0
15 TraesCS5B01G447600 chr7D 95.543 516 20 2 2472 2987 178158530 178158018 0.000000e+00 822.0
16 TraesCS5B01G447600 chr7D 87.679 560 41 14 1929 2475 178171368 178170824 1.350000e-175 627.0
17 TraesCS5B01G447600 chr7D 83.791 364 36 10 846 1193 178175968 178175612 1.990000e-84 324.0
18 TraesCS5B01G447600 chr7D 90.588 85 8 0 5229 5313 535305140 535305056 4.680000e-21 113.0
19 TraesCS5B01G447600 chr7A 91.011 89 8 0 5229 5317 731971235 731971147 2.800000e-23 121.0
20 TraesCS5B01G447600 chr6B 90.217 92 9 0 5229 5320 203686797 203686706 2.800000e-23 121.0
21 TraesCS5B01G447600 chr3A 89.888 89 9 0 5225 5313 698275053 698275141 1.300000e-21 115.0
22 TraesCS5B01G447600 chr1A 90.588 85 8 0 5229 5313 15915249 15915165 4.680000e-21 113.0
23 TraesCS5B01G447600 chr1A 85.294 102 14 1 2843 2943 234546937 234546836 2.820000e-18 104.0
24 TraesCS5B01G447600 chr1A 83.495 103 14 2 2843 2943 234508486 234508385 6.100000e-15 93.5
25 TraesCS5B01G447600 chrUn 88.298 94 9 2 5228 5320 24873915 24874007 1.680000e-20 111.0
26 TraesCS5B01G447600 chr4B 88.235 51 6 0 2870 2920 656241505 656241555 1.720000e-05 62.1
27 TraesCS5B01G447600 chr3B 80.247 81 11 3 2843 2920 570256973 570256895 8.000000e-04 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G447600 chr5B 618469293 618475007 5714 False 10554.00 10554 100.0000 1 5715 1 chr5B.!!$F1 5714
1 TraesCS5B01G447600 chr5A 623206614 623213970 7356 False 2081.50 4767 91.6960 1 5711 4 chr5A.!!$F2 5710
2 TraesCS5B01G447600 chr5D 498768837 498777114 8277 False 2053.25 4150 92.4135 1 5713 4 chr5D.!!$F1 5712
3 TraesCS5B01G447600 chr2D 513987768 513990667 2899 False 826.50 1205 89.4875 887 2984 2 chr2D.!!$F2 2097
4 TraesCS5B01G447600 chr7D 178158018 178158530 512 True 822.00 822 95.5430 2472 2987 1 chr7D.!!$R1 515
5 TraesCS5B01G447600 chr7D 178170824 178171368 544 True 627.00 627 87.6790 1929 2475 1 chr7D.!!$R2 546

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
347 348 2.413765 GAAGTAGGCGCGGAGGAG 59.586 66.667 8.83 0.00 0.00 3.69 F
1258 1312 2.101575 GACCGTAGCGCGATGTGA 59.898 61.111 12.10 0.00 44.77 3.58 F
1842 6377 0.573279 ATGATAGGGGGCCTAGGTGT 59.427 55.000 11.31 0.00 39.70 4.16 F
1875 6410 1.281899 GTAGTTCATGAGCCTGTCGC 58.718 55.000 5.87 0.00 37.98 5.19 F
3239 8636 1.464687 GCATCAACATCGACTGTGCAC 60.465 52.381 10.75 10.75 38.39 4.57 F
3895 9297 3.508845 TCACTCTGAAGGGGAAAAAGG 57.491 47.619 0.00 0.00 0.00 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1368 1433 0.228742 CGTGGGAAAATATCGACGCG 59.771 55.000 3.53 3.53 34.75 6.01 R
3003 8398 4.017126 AGTAGTCACATAGTGCTGCTACA 58.983 43.478 18.56 0.00 36.51 2.74 R
3400 8797 2.044888 AATTTTAACGGCACTGTGCG 57.955 45.000 24.86 21.17 46.21 5.34 R
3703 9105 3.519510 TCCTCTTCGGAACCTGATTTGAT 59.480 43.478 0.00 0.00 39.40 2.57 R
4196 9598 1.134907 GCAGGCAATTCAACATCCCTG 60.135 52.381 0.00 0.00 42.04 4.45 R
5604 11069 1.066587 CTTCCGATCGCCAGAGTCC 59.933 63.158 10.32 0.00 0.00 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
69 70 4.785453 CCCTGCACGGCCTTCCTC 62.785 72.222 0.00 0.00 0.00 3.71
124 125 2.804828 GAACTCCTTGCTGTCGGGGG 62.805 65.000 0.00 0.00 0.00 5.40
125 126 4.785453 CTCCTTGCTGTCGGGGGC 62.785 72.222 0.00 0.00 0.00 5.80
246 247 4.740822 AAGCGGACCATGTGGCCC 62.741 66.667 0.00 0.00 39.32 5.80
347 348 2.413765 GAAGTAGGCGCGGAGGAG 59.586 66.667 8.83 0.00 0.00 3.69
348 349 3.776659 GAAGTAGGCGCGGAGGAGC 62.777 68.421 8.83 0.00 38.36 4.70
768 775 2.657237 CTCGAGGACTGCGGGTTT 59.343 61.111 3.91 0.00 0.00 3.27
855 867 2.439883 ACGGCGACCTAGACCTCC 60.440 66.667 16.62 0.00 0.00 4.30
922 934 3.274455 CTGTCGCTGTCGCAGAGGT 62.274 63.158 10.46 0.00 40.04 3.85
1258 1312 2.101575 GACCGTAGCGCGATGTGA 59.898 61.111 12.10 0.00 44.77 3.58
1434 1499 4.980805 TGCGCGTGGAAGGTGGAC 62.981 66.667 8.43 0.00 31.91 4.02
1474 1539 6.855914 GTCAGAGAATTTGCAATTTCGTTGTA 59.144 34.615 21.93 13.64 40.07 2.41
1475 1540 7.538678 GTCAGAGAATTTGCAATTTCGTTGTAT 59.461 33.333 21.93 8.92 40.07 2.29
1476 1541 7.538334 TCAGAGAATTTGCAATTTCGTTGTATG 59.462 33.333 21.93 14.74 40.07 2.39
1477 1542 6.808212 AGAGAATTTGCAATTTCGTTGTATGG 59.192 34.615 21.93 0.00 40.07 2.74
1500 1571 7.083628 TGGGTTGTATGGGTTATTATAGAGGA 58.916 38.462 0.00 0.00 0.00 3.71
1501 1572 7.742213 TGGGTTGTATGGGTTATTATAGAGGAT 59.258 37.037 0.00 0.00 0.00 3.24
1602 1673 2.025898 GCGGAGAGGCTAACTTCTACT 58.974 52.381 0.00 0.00 0.00 2.57
1607 1678 6.440436 CGGAGAGGCTAACTTCTACTAATTC 58.560 44.000 0.00 0.00 0.00 2.17
1685 3696 7.173390 GCCCATTTAGGAGATAACATTAGTGAC 59.827 40.741 0.00 0.00 41.22 3.67
1693 3704 2.200373 AACATTAGTGACTGGGTGCC 57.800 50.000 0.00 0.00 0.00 5.01
1698 3709 1.823169 TAGTGACTGGGTGCCCGAAC 61.823 60.000 0.00 0.00 39.42 3.95
1699 3710 3.948719 TGACTGGGTGCCCGAACC 61.949 66.667 2.44 0.00 39.42 3.62
1706 3717 2.203153 GTGCCCGAACCACAGTGT 60.203 61.111 0.00 0.00 33.50 3.55
1731 3742 1.890979 GAGCATGGCCAGTGATCCG 60.891 63.158 13.05 0.00 0.00 4.18
1823 6358 3.737559 ATGGTTGCTAGGGATTTGTGA 57.262 42.857 0.00 0.00 0.00 3.58
1825 6360 3.355378 TGGTTGCTAGGGATTTGTGATG 58.645 45.455 0.00 0.00 0.00 3.07
1831 6366 4.042062 TGCTAGGGATTTGTGATGATAGGG 59.958 45.833 0.00 0.00 0.00 3.53
1842 6377 0.573279 ATGATAGGGGGCCTAGGTGT 59.427 55.000 11.31 0.00 39.70 4.16
1855 6390 5.466819 GGCCTAGGTGTTATTTTTGTGTTC 58.533 41.667 11.31 0.00 0.00 3.18
1860 6395 6.930667 AGGTGTTATTTTTGTGTTCGTAGT 57.069 33.333 0.00 0.00 0.00 2.73
1875 6410 1.281899 GTAGTTCATGAGCCTGTCGC 58.718 55.000 5.87 0.00 37.98 5.19
1878 6413 2.942796 TTCATGAGCCTGTCGCGGT 61.943 57.895 6.13 0.00 44.76 5.68
2054 7302 3.900966 TGGAGTGGATGATGAAGACTG 57.099 47.619 0.00 0.00 0.00 3.51
2115 7374 8.561738 AGGAAATTGTTCGTGTGAGTATTATT 57.438 30.769 0.00 0.00 34.28 1.40
2116 7375 8.450964 AGGAAATTGTTCGTGTGAGTATTATTG 58.549 33.333 0.00 0.00 34.28 1.90
2121 7380 7.285783 TGTTCGTGTGAGTATTATTGTTAGC 57.714 36.000 0.00 0.00 0.00 3.09
2171 7433 7.232127 ACCAGCTAACTGTACAGAAAGTTACTA 59.768 37.037 29.30 6.29 42.81 1.82
2202 7522 8.274322 TGTATAAAGATTGTGATTGGTGGATCT 58.726 33.333 0.00 0.00 0.00 2.75
2227 7547 7.559590 ACTATGGCATCTTCAACTTCATTAC 57.440 36.000 1.65 0.00 0.00 1.89
2240 7561 7.930217 TCAACTTCATTACTTGTCAGGAAAAG 58.070 34.615 0.00 0.00 0.00 2.27
2243 7564 7.707104 ACTTCATTACTTGTCAGGAAAAGTTG 58.293 34.615 9.96 4.34 37.74 3.16
2249 7570 8.795842 TTACTTGTCAGGAAAAGTTGTTTAGA 57.204 30.769 9.96 0.00 37.74 2.10
2266 7587 6.073314 TGTTTAGACTGGTTAGGTGTAGACT 58.927 40.000 0.00 0.00 0.00 3.24
2406 7800 6.591834 CAGTTCGTCATCTATCTTTGGAAAGT 59.408 38.462 0.00 0.00 37.31 2.66
2492 7887 8.909671 GTGAAAAACAGCTCTTCAGAAATTATG 58.090 33.333 0.00 0.00 30.00 1.90
2839 8234 1.942657 CAAGAAGCCATATCACCGGTG 59.057 52.381 29.26 29.26 0.00 4.94
3045 8441 4.850680 ACTTTGGGGCTAAAACATATCGA 58.149 39.130 0.00 0.00 0.00 3.59
3050 8446 5.063204 TGGGGCTAAAACATATCGATTGAG 58.937 41.667 1.71 0.00 0.00 3.02
3132 8528 5.936686 TGCTAAATGAATAGAGCATGAGC 57.063 39.130 0.00 0.00 39.93 4.26
3134 8530 5.002516 GCTAAATGAATAGAGCATGAGCCT 58.997 41.667 0.00 0.00 43.56 4.58
3239 8636 1.464687 GCATCAACATCGACTGTGCAC 60.465 52.381 10.75 10.75 38.39 4.57
3298 8695 6.484288 TCAATCAACCATGGTGAGATTTACT 58.516 36.000 29.51 15.58 34.02 2.24
3351 8748 5.744171 ACATTAGGATAGATGCACAACACA 58.256 37.500 0.00 0.00 0.00 3.72
3478 8876 4.789012 ATGCAATAACTGTTTGTGAGGG 57.211 40.909 0.00 0.00 0.00 4.30
3895 9297 3.508845 TCACTCTGAAGGGGAAAAAGG 57.491 47.619 0.00 0.00 0.00 3.11
3909 9311 5.428253 GGGAAAAAGGAAATATTCAAGGCC 58.572 41.667 0.00 0.00 0.00 5.19
3938 9340 5.880901 ACCTAGGAAAAAGAGAAGATTGCA 58.119 37.500 17.98 0.00 0.00 4.08
4014 9416 6.803807 ACTTCTCTTACGACGTTTATTGTACC 59.196 38.462 5.50 0.00 0.00 3.34
4086 9488 3.545724 GGGACAACCTCCTTTACCG 57.454 57.895 0.00 0.00 39.39 4.02
4194 9596 3.696051 ACTTGCGCCTTTATCACATTGAT 59.304 39.130 4.18 0.00 40.72 2.57
4196 9598 2.618241 TGCGCCTTTATCACATTGATCC 59.382 45.455 4.18 0.00 38.26 3.36
4299 9701 1.194781 TCCCTTCTCCCAGTGTCAGC 61.195 60.000 0.00 0.00 0.00 4.26
4713 10155 1.171308 CCTGAAAGTCACCATGGCTG 58.829 55.000 13.04 9.79 29.54 4.85
4715 10157 1.808945 CTGAAAGTCACCATGGCTGAC 59.191 52.381 26.88 26.88 38.70 3.51
4760 10202 2.435059 GTTCGGCCTCACTCCAGC 60.435 66.667 0.00 0.00 0.00 4.85
4771 10213 2.166459 CTCACTCCAGCCGTCTATTTCA 59.834 50.000 0.00 0.00 0.00 2.69
4831 10273 2.977178 CTCAGCTCGGCTCACCTT 59.023 61.111 0.00 0.00 36.40 3.50
4943 10386 1.955080 GGAGTAGCTGTACCTATGCGT 59.045 52.381 0.00 0.00 0.00 5.24
5104 10552 6.701145 ATATATGGAGTAGCGTATGGAGTG 57.299 41.667 0.00 0.00 0.00 3.51
5155 10603 7.692908 TGCAAGTTACAAGTAATTTCTTTGC 57.307 32.000 8.94 8.94 0.00 3.68
5157 10605 6.923508 GCAAGTTACAAGTAATTTCTTTGCCT 59.076 34.615 5.91 0.00 0.00 4.75
5231 10680 8.459911 AACCTTGCATTTAAACAACTACTACT 57.540 30.769 0.00 0.00 0.00 2.57
5232 10681 8.459911 ACCTTGCATTTAAACAACTACTACTT 57.540 30.769 0.00 0.00 0.00 2.24
5233 10682 8.565416 ACCTTGCATTTAAACAACTACTACTTC 58.435 33.333 0.00 0.00 0.00 3.01
5234 10683 8.021396 CCTTGCATTTAAACAACTACTACTTCC 58.979 37.037 0.00 0.00 0.00 3.46
5236 10685 8.319143 TGCATTTAAACAACTACTACTTCCTC 57.681 34.615 0.00 0.00 0.00 3.71
5238 10687 7.412672 GCATTTAAACAACTACTACTTCCTCCG 60.413 40.741 0.00 0.00 0.00 4.63
5239 10688 6.655078 TTAAACAACTACTACTTCCTCCGT 57.345 37.500 0.00 0.00 0.00 4.69
5242 10691 6.655078 AACAACTACTACTTCCTCCGTAAA 57.345 37.500 0.00 0.00 0.00 2.01
5243 10692 6.264841 ACAACTACTACTTCCTCCGTAAAG 57.735 41.667 0.00 0.00 0.00 1.85
5244 10693 6.006449 ACAACTACTACTTCCTCCGTAAAGA 58.994 40.000 0.00 0.00 0.00 2.52
5245 10694 6.491403 ACAACTACTACTTCCTCCGTAAAGAA 59.509 38.462 0.00 0.00 0.00 2.52
5246 10695 7.014615 ACAACTACTACTTCCTCCGTAAAGAAA 59.985 37.037 0.00 0.00 0.00 2.52
5247 10696 7.715266 ACTACTACTTCCTCCGTAAAGAAAT 57.285 36.000 0.00 0.00 0.00 2.17
5248 10697 7.545489 ACTACTACTTCCTCCGTAAAGAAATG 58.455 38.462 0.00 0.00 0.00 2.32
5249 10698 6.356186 ACTACTTCCTCCGTAAAGAAATGT 57.644 37.500 0.00 0.00 0.00 2.71
5250 10699 7.472334 ACTACTTCCTCCGTAAAGAAATGTA 57.528 36.000 0.00 0.00 0.00 2.29
5252 10701 8.033626 ACTACTTCCTCCGTAAAGAAATGTAAG 58.966 37.037 0.00 0.00 0.00 2.34
5253 10702 7.001099 ACTTCCTCCGTAAAGAAATGTAAGA 57.999 36.000 0.00 0.00 0.00 2.10
5254 10703 7.097834 ACTTCCTCCGTAAAGAAATGTAAGAG 58.902 38.462 0.00 0.00 0.00 2.85
5255 10704 5.416947 TCCTCCGTAAAGAAATGTAAGAGC 58.583 41.667 0.00 0.00 0.00 4.09
5257 10706 4.813027 TCCGTAAAGAAATGTAAGAGCGT 58.187 39.130 0.00 0.00 0.00 5.07
5258 10707 5.232463 TCCGTAAAGAAATGTAAGAGCGTT 58.768 37.500 0.00 0.00 0.00 4.84
5259 10708 5.697633 TCCGTAAAGAAATGTAAGAGCGTTT 59.302 36.000 0.00 0.00 0.00 3.60
5260 10709 6.867816 TCCGTAAAGAAATGTAAGAGCGTTTA 59.132 34.615 0.00 0.00 0.00 2.01
5261 10710 7.062605 TCCGTAAAGAAATGTAAGAGCGTTTAG 59.937 37.037 0.00 0.00 0.00 1.85
5263 10712 8.592998 CGTAAAGAAATGTAAGAGCGTTTAGAT 58.407 33.333 0.00 0.00 0.00 1.98
5264 10713 9.903185 GTAAAGAAATGTAAGAGCGTTTAGATC 57.097 33.333 0.00 0.00 35.01 2.75
5265 10714 8.547967 AAAGAAATGTAAGAGCGTTTAGATCA 57.452 30.769 0.00 0.00 37.82 2.92
5266 10715 7.527084 AGAAATGTAAGAGCGTTTAGATCAC 57.473 36.000 0.00 0.00 37.82 3.06
5267 10716 7.324178 AGAAATGTAAGAGCGTTTAGATCACT 58.676 34.615 0.00 0.00 37.82 3.41
5268 10717 6.893958 AATGTAAGAGCGTTTAGATCACTG 57.106 37.500 0.00 0.00 37.82 3.66
5269 10718 4.174009 TGTAAGAGCGTTTAGATCACTGC 58.826 43.478 0.00 0.00 37.82 4.40
5270 10719 3.601443 AAGAGCGTTTAGATCACTGCT 57.399 42.857 0.00 0.00 37.82 4.24
5271 10720 3.601443 AGAGCGTTTAGATCACTGCTT 57.399 42.857 0.00 0.00 37.82 3.91
5272 10721 3.931578 AGAGCGTTTAGATCACTGCTTT 58.068 40.909 0.00 0.00 37.82 3.51
5273 10722 5.073311 AGAGCGTTTAGATCACTGCTTTA 57.927 39.130 0.00 0.00 37.82 1.85
5274 10723 5.105752 AGAGCGTTTAGATCACTGCTTTAG 58.894 41.667 0.00 0.00 37.82 1.85
5275 10724 4.822026 AGCGTTTAGATCACTGCTTTAGT 58.178 39.130 0.00 0.00 41.36 2.24
5276 10725 5.962433 AGCGTTTAGATCACTGCTTTAGTA 58.038 37.500 0.00 0.00 37.60 1.82
5277 10726 6.395629 AGCGTTTAGATCACTGCTTTAGTAA 58.604 36.000 0.00 0.00 37.60 2.24
5278 10727 7.042335 AGCGTTTAGATCACTGCTTTAGTAAT 58.958 34.615 0.00 0.00 37.60 1.89
5279 10728 7.222999 AGCGTTTAGATCACTGCTTTAGTAATC 59.777 37.037 0.00 0.00 37.60 1.75
5280 10729 7.222999 GCGTTTAGATCACTGCTTTAGTAATCT 59.777 37.037 0.00 0.00 44.81 2.40
5281 10730 9.731819 CGTTTAGATCACTGCTTTAGTAATCTA 57.268 33.333 0.00 0.00 41.67 1.98
5286 10735 9.372369 AGATCACTGCTTTAGTAATCTAAACAC 57.628 33.333 0.00 0.00 41.67 3.32
5287 10736 9.372369 GATCACTGCTTTAGTAATCTAAACACT 57.628 33.333 0.00 0.00 40.05 3.55
5288 10737 8.758633 TCACTGCTTTAGTAATCTAAACACTC 57.241 34.615 0.00 0.00 40.05 3.51
5289 10738 8.364894 TCACTGCTTTAGTAATCTAAACACTCA 58.635 33.333 0.00 0.00 40.05 3.41
5290 10739 9.155975 CACTGCTTTAGTAATCTAAACACTCAT 57.844 33.333 0.00 0.00 40.05 2.90
5308 10757 9.838339 AACACTCATATATTTCTTTACAGAGGG 57.162 33.333 0.00 0.00 0.00 4.30
5309 10758 9.213777 ACACTCATATATTTCTTTACAGAGGGA 57.786 33.333 0.00 0.00 0.00 4.20
5310 10759 9.703892 CACTCATATATTTCTTTACAGAGGGAG 57.296 37.037 0.00 0.00 0.00 4.30
5311 10760 9.440761 ACTCATATATTTCTTTACAGAGGGAGT 57.559 33.333 0.00 0.00 0.00 3.85
5383 10833 2.426522 CCGTTACATCTGGCATATGGG 58.573 52.381 16.10 4.97 0.00 4.00
5402 10855 3.263425 TGGGAACTGGACTGTTTATCCTC 59.737 47.826 0.00 0.00 37.13 3.71
5422 10875 1.537814 TTGCTGCCCCATTGCTGAAG 61.538 55.000 0.00 0.00 32.50 3.02
5565 11029 1.133668 GCCTCCATACCCTGCTTCAAT 60.134 52.381 0.00 0.00 0.00 2.57
5579 11043 5.335740 CCTGCTTCAATTCCATATCATCAGC 60.336 44.000 0.00 0.00 0.00 4.26
5604 11069 2.361610 AGCACCTTGCCCATTCCG 60.362 61.111 0.00 0.00 46.52 4.30
5669 11137 1.827399 TTCCAGGAACTCCGCTGTCC 61.827 60.000 0.00 0.00 42.08 4.02
5693 11161 4.460382 GGTGTTTGATCATCATCCACACTT 59.540 41.667 18.21 0.00 39.78 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 2.046892 CTGGTGAGGAAGGCCGTG 60.047 66.667 0.00 0.00 39.96 4.94
86 87 1.544691 TCGTCAGGTACAAGAAGAGGC 59.455 52.381 0.00 0.00 0.00 4.70
124 125 2.202946 GAAGCTCTACAGGGCCGC 60.203 66.667 0.00 0.00 0.00 6.53
125 126 0.531532 CATGAAGCTCTACAGGGCCG 60.532 60.000 0.00 0.00 0.00 6.13
131 132 2.234661 CAGGACACCATGAAGCTCTACA 59.765 50.000 0.00 0.00 0.00 2.74
246 247 2.358737 GTGCTCCACCCCTTCACG 60.359 66.667 0.00 0.00 0.00 4.35
686 693 3.041946 ACTAATCCACACTCCCAGATCC 58.958 50.000 0.00 0.00 0.00 3.36
1258 1312 1.663695 CTTCCACGCCATAATTCGGT 58.336 50.000 0.00 0.00 0.00 4.69
1368 1433 0.228742 CGTGGGAAAATATCGACGCG 59.771 55.000 3.53 3.53 34.75 6.01
1434 1499 3.470567 GACGAGACAGCCAACGCG 61.471 66.667 3.53 3.53 41.18 6.01
1474 1539 7.742213 TCCTCTATAATAACCCATACAACCCAT 59.258 37.037 0.00 0.00 0.00 4.00
1475 1540 7.083628 TCCTCTATAATAACCCATACAACCCA 58.916 38.462 0.00 0.00 0.00 4.51
1476 1541 7.563724 TCCTCTATAATAACCCATACAACCC 57.436 40.000 0.00 0.00 0.00 4.11
1500 1571 5.047021 AGACGAGCATACCTGTTGCATATAT 60.047 40.000 0.00 0.00 42.62 0.86
1501 1572 4.280929 AGACGAGCATACCTGTTGCATATA 59.719 41.667 0.00 0.00 42.62 0.86
1602 1673 1.208844 TTGCGGTCCTGGGGGAATTA 61.209 55.000 0.00 0.00 44.15 1.40
1607 1678 2.375345 ATACTTGCGGTCCTGGGGG 61.375 63.158 0.00 0.00 0.00 5.40
1666 3677 6.323996 CACCCAGTCACTAATGTTATCTCCTA 59.676 42.308 0.00 0.00 0.00 2.94
1693 3704 2.616376 TCAAAATCACACTGTGGTTCGG 59.384 45.455 13.09 4.28 35.67 4.30
1698 3709 3.571571 CATGCTCAAAATCACACTGTGG 58.428 45.455 13.09 1.42 33.87 4.17
1699 3710 3.571571 CCATGCTCAAAATCACACTGTG 58.428 45.455 6.19 6.19 34.45 3.66
1706 3717 1.546923 CACTGGCCATGCTCAAAATCA 59.453 47.619 5.51 0.00 0.00 2.57
1731 3742 9.512435 CAAACCATAATTCATCTGATTTCACTC 57.488 33.333 0.00 0.00 0.00 3.51
1761 3772 1.059913 ACAAGTTGCCTACAGCCTCT 58.940 50.000 1.81 0.00 42.71 3.69
1823 6358 0.573279 ACACCTAGGCCCCCTATCAT 59.427 55.000 9.30 0.00 35.36 2.45
1825 6360 2.410790 TAACACCTAGGCCCCCTATC 57.589 55.000 9.30 0.00 35.36 2.08
1831 6366 3.830178 ACACAAAAATAACACCTAGGCCC 59.170 43.478 9.30 0.00 0.00 5.80
1842 6377 7.801315 GCTCATGAACTACGAACACAAAAATAA 59.199 33.333 0.00 0.00 0.00 1.40
1855 6390 1.550065 CGACAGGCTCATGAACTACG 58.450 55.000 0.00 4.54 0.00 3.51
1860 6395 1.600511 TACCGCGACAGGCTCATGAA 61.601 55.000 8.23 0.00 40.44 2.57
1875 6410 2.470983 TTTAACCCTTTCCGGTACCG 57.529 50.000 27.68 27.68 33.98 4.02
1878 6413 6.517027 GCTGAAAATTTTAACCCTTTCCGGTA 60.517 38.462 2.75 0.00 33.98 4.02
2090 7349 8.450964 CAATAATACTCACACGAACAATTTCCT 58.549 33.333 0.00 0.00 0.00 3.36
2180 7442 7.861629 AGTAGATCCACCAATCACAATCTTTA 58.138 34.615 0.00 0.00 0.00 1.85
2202 7522 8.486210 AGTAATGAAGTTGAAGATGCCATAGTA 58.514 33.333 0.00 0.00 0.00 1.82
2227 7547 7.189512 CAGTCTAAACAACTTTTCCTGACAAG 58.810 38.462 0.00 0.00 0.00 3.16
2240 7561 6.644181 GTCTACACCTAACCAGTCTAAACAAC 59.356 42.308 0.00 0.00 0.00 3.32
2243 7564 6.587206 AGTCTACACCTAACCAGTCTAAAC 57.413 41.667 0.00 0.00 0.00 2.01
2249 7570 4.043812 TGGTCTAGTCTACACCTAACCAGT 59.956 45.833 5.96 0.00 32.12 4.00
2344 7738 7.971168 TCCAATACGCAACTTTAACCATTATTG 59.029 33.333 0.00 0.00 0.00 1.90
2345 7739 8.057536 TCCAATACGCAACTTTAACCATTATT 57.942 30.769 0.00 0.00 0.00 1.40
2406 7800 6.341316 AGAAGATAACTGAAAATGCTCGCTA 58.659 36.000 0.00 0.00 0.00 4.26
2839 8234 5.308825 TCTTTTCTCTTGACAGGTGATTCC 58.691 41.667 0.00 0.00 0.00 3.01
3003 8398 4.017126 AGTAGTCACATAGTGCTGCTACA 58.983 43.478 18.56 0.00 36.51 2.74
3045 8441 5.324409 TGTGCCCAAGAGAATAAACTCAAT 58.676 37.500 0.00 0.00 39.14 2.57
3050 8446 5.393461 CCAAGATGTGCCCAAGAGAATAAAC 60.393 44.000 0.00 0.00 0.00 2.01
3132 8528 5.754890 CCAAACAAACAAAGGATCAAAGAGG 59.245 40.000 0.00 0.00 0.00 3.69
3134 8530 6.293004 ACCAAACAAACAAAGGATCAAAGA 57.707 33.333 0.00 0.00 0.00 2.52
3239 8636 5.673337 AAATCGATGTTTGTATGATCCCG 57.327 39.130 0.00 0.00 0.00 5.14
3351 8748 5.940470 AGAGTTCAAGACAAACACAAAGACT 59.060 36.000 0.00 0.00 0.00 3.24
3400 8797 2.044888 AATTTTAACGGCACTGTGCG 57.955 45.000 24.86 21.17 46.21 5.34
3478 8876 4.003648 CTGAAGGGTGTGGACAATACTTC 58.996 47.826 10.26 10.26 35.02 3.01
3703 9105 3.519510 TCCTCTTCGGAACCTGATTTGAT 59.480 43.478 0.00 0.00 39.40 2.57
3895 9297 5.793817 AGGTTGTTTGGCCTTGAATATTTC 58.206 37.500 3.32 0.00 0.00 2.17
3909 9311 7.568199 TCTTCTCTTTTTCCTAGGTTGTTTG 57.432 36.000 9.08 0.00 0.00 2.93
3938 9340 6.043706 AGCCACTAGATAGAACCATAATGCTT 59.956 38.462 0.00 0.00 0.00 3.91
4014 9416 7.306983 GCATGATTTCTGTGTTTCCTTCAAAAG 60.307 37.037 0.00 0.00 0.00 2.27
4086 9488 5.863935 CCTCAAAAATTTTGTAGGTAGCTGC 59.136 40.000 16.83 3.46 0.00 5.25
4194 9596 1.358787 AGGCAATTCAACATCCCTGGA 59.641 47.619 0.00 0.00 0.00 3.86
4196 9598 1.134907 GCAGGCAATTCAACATCCCTG 60.135 52.381 0.00 0.00 42.04 4.45
4299 9701 5.759506 TTTCTCTCAGGTCTAGCTTATCG 57.240 43.478 0.00 0.00 0.00 2.92
4534 9976 1.379916 CAGGGTGATTGCTGGGTCA 59.620 57.895 0.00 0.00 0.00 4.02
4642 10084 2.094659 CGGCCTGCTGTAGAACACG 61.095 63.158 0.00 0.00 0.00 4.49
4760 10202 2.035632 AGAGGGCTCTGAAATAGACGG 58.964 52.381 0.00 0.00 38.75 4.79
4771 10213 2.900106 GCACCAACCAGAGGGCTCT 61.900 63.158 0.00 0.00 41.37 4.09
4791 10233 3.415297 TCGCAAGGTTGGCATCAATGC 62.415 52.381 6.42 6.42 46.02 3.56
4831 10273 7.544804 ACATCTATCTACATATCACAAGGCA 57.455 36.000 0.00 0.00 0.00 4.75
4943 10386 5.650266 ACAACTCAACACAGGATTACAAACA 59.350 36.000 0.00 0.00 0.00 2.83
5104 10552 7.823310 AGACAGTATCCATCAATCAATATCAGC 59.177 37.037 0.00 0.00 0.00 4.26
5155 10603 1.478105 GGCCATTTGGAGCTACAAAGG 59.522 52.381 27.31 26.50 42.91 3.11
5157 10605 2.300956 TGGCCATTTGGAGCTACAAA 57.699 45.000 25.97 25.97 43.69 2.83
5230 10679 6.036191 GCTCTTACATTTCTTTACGGAGGAAG 59.964 42.308 0.00 0.00 0.00 3.46
5231 10680 5.873164 GCTCTTACATTTCTTTACGGAGGAA 59.127 40.000 0.00 0.00 0.00 3.36
5232 10681 5.416947 GCTCTTACATTTCTTTACGGAGGA 58.583 41.667 0.00 0.00 0.00 3.71
5233 10682 4.267928 CGCTCTTACATTTCTTTACGGAGG 59.732 45.833 0.00 0.00 0.00 4.30
5234 10683 4.863131 ACGCTCTTACATTTCTTTACGGAG 59.137 41.667 0.00 0.00 0.00 4.63
5236 10685 5.526010 AACGCTCTTACATTTCTTTACGG 57.474 39.130 0.00 0.00 0.00 4.02
5238 10687 9.903185 GATCTAAACGCTCTTACATTTCTTTAC 57.097 33.333 0.00 0.00 0.00 2.01
5239 10688 9.647797 TGATCTAAACGCTCTTACATTTCTTTA 57.352 29.630 0.00 0.00 0.00 1.85
5242 10691 7.276658 CAGTGATCTAAACGCTCTTACATTTCT 59.723 37.037 0.00 0.00 0.00 2.52
5243 10692 7.394872 CAGTGATCTAAACGCTCTTACATTTC 58.605 38.462 0.00 0.00 0.00 2.17
5244 10693 6.183360 GCAGTGATCTAAACGCTCTTACATTT 60.183 38.462 0.00 0.00 0.00 2.32
5245 10694 5.292101 GCAGTGATCTAAACGCTCTTACATT 59.708 40.000 0.00 0.00 0.00 2.71
5246 10695 4.806247 GCAGTGATCTAAACGCTCTTACAT 59.194 41.667 0.00 0.00 0.00 2.29
5247 10696 4.082190 AGCAGTGATCTAAACGCTCTTACA 60.082 41.667 0.00 0.00 0.00 2.41
5248 10697 4.425520 AGCAGTGATCTAAACGCTCTTAC 58.574 43.478 0.00 0.00 0.00 2.34
5249 10698 4.720649 AGCAGTGATCTAAACGCTCTTA 57.279 40.909 0.00 0.00 0.00 2.10
5250 10699 3.601443 AGCAGTGATCTAAACGCTCTT 57.399 42.857 0.00 0.00 0.00 2.85
5252 10701 4.865365 ACTAAAGCAGTGATCTAAACGCTC 59.135 41.667 0.00 0.00 35.62 5.03
5253 10702 4.822026 ACTAAAGCAGTGATCTAAACGCT 58.178 39.130 0.00 0.00 35.62 5.07
5254 10703 6.642683 TTACTAAAGCAGTGATCTAAACGC 57.357 37.500 0.00 0.00 38.24 4.84
5261 10710 9.372369 AGTGTTTAGATTACTAAAGCAGTGATC 57.628 33.333 0.00 1.98 45.99 2.92
5263 10712 8.364894 TGAGTGTTTAGATTACTAAAGCAGTGA 58.635 33.333 0.00 0.00 45.42 3.41
5264 10713 8.534333 TGAGTGTTTAGATTACTAAAGCAGTG 57.466 34.615 0.00 0.00 45.42 3.66
5282 10731 9.838339 CCCTCTGTAAAGAAATATATGAGTGTT 57.162 33.333 0.00 0.00 0.00 3.32
5283 10732 9.213777 TCCCTCTGTAAAGAAATATATGAGTGT 57.786 33.333 0.00 0.00 0.00 3.55
5284 10733 9.703892 CTCCCTCTGTAAAGAAATATATGAGTG 57.296 37.037 0.00 0.00 0.00 3.51
5285 10734 9.440761 ACTCCCTCTGTAAAGAAATATATGAGT 57.559 33.333 0.00 0.00 0.00 3.41
5291 10740 9.268282 TGAACTACTCCCTCTGTAAAGAAATAT 57.732 33.333 0.00 0.00 0.00 1.28
5292 10741 8.660295 TGAACTACTCCCTCTGTAAAGAAATA 57.340 34.615 0.00 0.00 0.00 1.40
5293 10742 7.554959 TGAACTACTCCCTCTGTAAAGAAAT 57.445 36.000 0.00 0.00 0.00 2.17
5294 10743 6.989155 TGAACTACTCCCTCTGTAAAGAAA 57.011 37.500 0.00 0.00 0.00 2.52
5295 10744 8.114102 TCTATGAACTACTCCCTCTGTAAAGAA 58.886 37.037 0.00 0.00 0.00 2.52
5296 10745 7.640313 TCTATGAACTACTCCCTCTGTAAAGA 58.360 38.462 0.00 0.00 0.00 2.52
5297 10746 7.469456 GCTCTATGAACTACTCCCTCTGTAAAG 60.469 44.444 0.00 0.00 0.00 1.85
5298 10747 6.321690 GCTCTATGAACTACTCCCTCTGTAAA 59.678 42.308 0.00 0.00 0.00 2.01
5299 10748 5.828859 GCTCTATGAACTACTCCCTCTGTAA 59.171 44.000 0.00 0.00 0.00 2.41
5300 10749 5.132985 AGCTCTATGAACTACTCCCTCTGTA 59.867 44.000 0.00 0.00 0.00 2.74
5301 10750 4.079443 AGCTCTATGAACTACTCCCTCTGT 60.079 45.833 0.00 0.00 0.00 3.41
5302 10751 4.469657 AGCTCTATGAACTACTCCCTCTG 58.530 47.826 0.00 0.00 0.00 3.35
5303 10752 4.806952 AGCTCTATGAACTACTCCCTCT 57.193 45.455 0.00 0.00 0.00 3.69
5304 10753 6.963083 TTTAGCTCTATGAACTACTCCCTC 57.037 41.667 0.00 0.00 0.00 4.30
5305 10754 7.688083 GCAATTTAGCTCTATGAACTACTCCCT 60.688 40.741 0.00 0.00 0.00 4.20
5306 10755 6.425417 GCAATTTAGCTCTATGAACTACTCCC 59.575 42.308 0.00 0.00 0.00 4.30
5307 10756 7.213678 AGCAATTTAGCTCTATGAACTACTCC 58.786 38.462 0.00 0.00 42.18 3.85
5383 10833 4.393371 GCAAGAGGATAAACAGTCCAGTTC 59.607 45.833 0.00 0.00 38.25 3.01
5402 10855 1.537814 TTCAGCAATGGGGCAGCAAG 61.538 55.000 0.00 0.00 35.83 4.01
5422 10875 1.200948 GTTGCTCATGACCTTTCAGGC 59.799 52.381 0.00 0.00 39.63 4.85
5565 11029 3.975982 TCCTGGAAGCTGATGATATGGAA 59.024 43.478 0.00 0.00 0.00 3.53
5579 11043 1.676967 GGCAAGGTGCTCCTGGAAG 60.677 63.158 13.63 3.28 44.35 3.46
5604 11069 1.066587 CTTCCGATCGCCAGAGTCC 59.933 63.158 10.32 0.00 0.00 3.85
5669 11137 3.009026 TGTGGATGATGATCAAACACCG 58.991 45.455 21.87 0.00 36.72 4.94


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

AutoCloner maintained by Alex Coulton.