Multiple sequence alignment - TraesCS5D01G157000

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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 TraesCS5D01G157000 chr5D 100.000 4994 0 0 1 4994 244706069 244701076 0.000000e+00 9223.0
1 TraesCS5D01G157000 chr5D 100.000 152 0 0 5324 5475 244700746 244700595 1.160000e-71 281.0
2 TraesCS5D01G157000 chr5D 85.065 154 19 3 5324 5475 199425277 199425126 2.640000e-33 154.0
3 TraesCS5D01G157000 chr5D 91.379 58 0 1 229 281 459929293 459929350 2.120000e-09 75.0
4 TraesCS5D01G157000 chr5B 97.093 2133 59 3 2863 4994 278226563 278224433 0.000000e+00 3592.0
5 TraesCS5D01G157000 chr5B 95.480 2102 71 12 756 2847 278228636 278226549 0.000000e+00 3334.0
6 TraesCS5D01G157000 chr5B 96.480 483 15 2 278 760 278229070 278228590 0.000000e+00 797.0
7 TraesCS5D01G157000 chr5B 95.708 233 10 0 1 233 278229299 278229067 5.180000e-100 375.0
8 TraesCS5D01G157000 chr5B 92.810 153 10 1 5324 5475 278224361 278224209 2.570000e-53 220.0
9 TraesCS5D01G157000 chr5B 86.719 128 16 1 5324 5451 708039557 708039683 2.060000e-29 141.0
10 TraesCS5D01G157000 chr5B 85.156 128 18 1 5324 5451 186845088 186845214 4.450000e-26 130.0
11 TraesCS5D01G157000 chr5B 88.889 54 3 2 232 282 574906689 574906742 4.580000e-06 63.9
12 TraesCS5D01G157000 chr5A 96.907 2134 62 4 2863 4994 328942216 328940085 0.000000e+00 3572.0
13 TraesCS5D01G157000 chr5A 94.241 1667 53 15 756 2408 328944544 328942907 0.000000e+00 2507.0
14 TraesCS5D01G157000 chr5A 96.847 444 10 3 2406 2847 328942643 328942202 0.000000e+00 739.0
15 TraesCS5D01G157000 chr5A 91.772 474 31 4 293 760 328944969 328944498 0.000000e+00 652.0
16 TraesCS5D01G157000 chr5A 92.735 234 16 1 1 234 328945219 328944987 2.440000e-88 337.0
17 TraesCS5D01G157000 chr5A 91.837 147 12 0 5324 5470 328937062 328936916 7.190000e-49 206.0
18 TraesCS5D01G157000 chr2D 85.235 149 19 2 5324 5472 286025758 286025903 3.420000e-32 150.0
19 TraesCS5D01G157000 chr7A 83.553 152 23 2 5324 5475 690524840 690524691 2.060000e-29 141.0
20 TraesCS5D01G157000 chr2B 82.895 152 24 2 5324 5475 74191984 74191835 9.570000e-28 135.0
21 TraesCS5D01G157000 chr7B 85.938 128 15 2 5324 5451 394813931 394814055 3.440000e-27 134.0
22 TraesCS5D01G157000 chr7B 84.615 65 3 3 224 281 552029510 552029574 2.130000e-04 58.4
23 TraesCS5D01G157000 chr6D 93.478 46 1 2 241 286 100935805 100935848 3.540000e-07 67.6
24 TraesCS5D01G157000 chr6D 97.368 38 1 0 249 286 200436479 200436516 1.270000e-06 65.8
25 TraesCS5D01G157000 chr3B 93.182 44 3 0 249 292 754970305 754970348 1.270000e-06 65.8
26 TraesCS5D01G157000 chr7D 89.796 49 5 0 249 297 155295745 155295697 4.580000e-06 63.9
27 TraesCS5D01G157000 chr1A 90.000 50 4 1 249 297 223997739 223997788 4.580000e-06 63.9
28 TraesCS5D01G157000 chr1A 86.207 58 5 2 227 281 442560258 442560201 5.920000e-05 60.2


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 TraesCS5D01G157000 chr5D 244700595 244706069 5474 True 4752.0 9223 100.0000 1 5475 2 chr5D.!!$R2 5474
1 TraesCS5D01G157000 chr5B 278224209 278229299 5090 True 1663.6 3592 95.5142 1 5475 5 chr5B.!!$R1 5474
2 TraesCS5D01G157000 chr5A 328936916 328945219 8303 True 1335.5 3572 94.0565 1 5470 6 chr5A.!!$R1 5469

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
246 247 0.038744 AAAGTACTCCCTCCGTCCGA 59.961 55.000 0.00 0.0 0.00 4.55 F
247 248 0.038744 AAGTACTCCCTCCGTCCGAA 59.961 55.000 0.00 0.0 0.00 4.30 F
252 253 0.103208 CTCCCTCCGTCCGAATTGAG 59.897 60.000 0.00 0.0 0.00 3.02 F
740 754 0.179073 CGGCACCTATCAGGGTTCAG 60.179 60.000 0.00 0.0 40.58 3.02 F
1559 1588 0.681175 AGCATTGCAACCCAGAAACC 59.319 50.000 11.91 0.0 0.00 3.27 F
2819 3123 1.296715 CCGAAACAGTGGGAGAGGG 59.703 63.158 0.00 0.0 0.00 4.30 F
4041 4346 0.530288 ACGCTGTTGCTTTTGTGGTT 59.470 45.000 0.00 0.0 36.97 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1429 1454 0.249322 CGGCCTTGTACCATAGTCCG 60.249 60.000 0.00 0.00 0.00 4.79 R
2208 2240 2.593346 ACAAATTGAGCGCCAAAACA 57.407 40.000 13.95 0.78 38.43 2.83 R
2674 2976 6.636666 ATTTAGCGACAAGAAATTGCAATG 57.363 33.333 13.82 3.85 0.00 2.82 R
2811 3115 3.403558 GCACCAGGACCCTCTCCC 61.404 72.222 0.00 0.00 40.53 4.30 R
3779 4084 0.842030 AGTCACCCCTCCAATCTGCA 60.842 55.000 0.00 0.00 0.00 4.41 R
4411 4716 2.035783 GGTCCACCTTTGCTCCCC 59.964 66.667 0.00 0.00 0.00 4.81 R
5355 8354 0.539051 AATCGAAGCTCAGTCCCAGG 59.461 55.000 0.00 0.00 0.00 4.45 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
57 58 3.882444 TGGATTCAAGGCTTCTCTCATG 58.118 45.455 0.00 0.00 0.00 3.07
78 79 1.155042 CTTGTGCTTCTGGACTGCTC 58.845 55.000 0.00 0.00 35.45 4.26
96 97 2.494059 CTCTCCCAAGCTCGTTTTTCA 58.506 47.619 0.00 0.00 0.00 2.69
152 153 6.494893 AAACAGAAAGCATCATTAACGCTA 57.505 33.333 0.00 0.00 34.11 4.26
196 197 7.992180 AAGAACTTGACAAAATGAATGACAC 57.008 32.000 0.00 0.00 0.00 3.67
238 239 3.715638 GGCACCTAAAAAGTACTCCCT 57.284 47.619 0.00 0.00 0.00 4.20
239 240 3.607741 GGCACCTAAAAAGTACTCCCTC 58.392 50.000 0.00 0.00 0.00 4.30
240 241 3.607741 GCACCTAAAAAGTACTCCCTCC 58.392 50.000 0.00 0.00 0.00 4.30
241 242 3.858247 CACCTAAAAAGTACTCCCTCCG 58.142 50.000 0.00 0.00 0.00 4.63
242 243 3.260128 CACCTAAAAAGTACTCCCTCCGT 59.740 47.826 0.00 0.00 0.00 4.69
243 244 3.513119 ACCTAAAAAGTACTCCCTCCGTC 59.487 47.826 0.00 0.00 0.00 4.79
244 245 3.118847 CCTAAAAAGTACTCCCTCCGTCC 60.119 52.174 0.00 0.00 0.00 4.79
245 246 0.893447 AAAAGTACTCCCTCCGTCCG 59.107 55.000 0.00 0.00 0.00 4.79
246 247 0.038744 AAAGTACTCCCTCCGTCCGA 59.961 55.000 0.00 0.00 0.00 4.55
247 248 0.038744 AAGTACTCCCTCCGTCCGAA 59.961 55.000 0.00 0.00 0.00 4.30
248 249 0.258194 AGTACTCCCTCCGTCCGAAT 59.742 55.000 0.00 0.00 0.00 3.34
249 250 1.109609 GTACTCCCTCCGTCCGAATT 58.890 55.000 0.00 0.00 0.00 2.17
250 251 1.108776 TACTCCCTCCGTCCGAATTG 58.891 55.000 0.00 0.00 0.00 2.32
251 252 0.613853 ACTCCCTCCGTCCGAATTGA 60.614 55.000 0.00 0.00 0.00 2.57
252 253 0.103208 CTCCCTCCGTCCGAATTGAG 59.897 60.000 0.00 0.00 0.00 3.02
253 254 1.144057 CCCTCCGTCCGAATTGAGG 59.856 63.158 0.00 0.00 43.29 3.86
254 255 1.144057 CCTCCGTCCGAATTGAGGG 59.856 63.158 0.00 0.00 40.59 4.30
255 256 1.327690 CCTCCGTCCGAATTGAGGGA 61.328 60.000 6.94 6.94 44.68 4.20
260 261 3.551259 TCCGAATTGAGGGACAAGC 57.449 52.632 0.00 0.00 42.02 4.01
261 262 0.984230 TCCGAATTGAGGGACAAGCT 59.016 50.000 0.00 0.00 42.02 3.74
262 263 1.351017 TCCGAATTGAGGGACAAGCTT 59.649 47.619 0.00 0.00 42.02 3.74
263 264 2.162681 CCGAATTGAGGGACAAGCTTT 58.837 47.619 0.00 0.00 42.02 3.51
264 265 2.558359 CCGAATTGAGGGACAAGCTTTT 59.442 45.455 0.00 0.00 42.02 2.27
265 266 3.005791 CCGAATTGAGGGACAAGCTTTTT 59.994 43.478 0.00 0.00 42.02 1.94
266 267 4.229876 CGAATTGAGGGACAAGCTTTTTC 58.770 43.478 0.00 0.00 42.02 2.29
267 268 3.923017 ATTGAGGGACAAGCTTTTTCG 57.077 42.857 0.00 0.00 42.02 3.46
268 269 1.604604 TGAGGGACAAGCTTTTTCGG 58.395 50.000 0.00 0.00 0.00 4.30
269 270 1.142060 TGAGGGACAAGCTTTTTCGGA 59.858 47.619 0.00 0.00 0.00 4.55
270 271 1.535896 GAGGGACAAGCTTTTTCGGAC 59.464 52.381 0.00 0.00 0.00 4.79
271 272 0.237498 GGGACAAGCTTTTTCGGACG 59.763 55.000 0.00 0.00 0.00 4.79
272 273 0.237498 GGACAAGCTTTTTCGGACGG 59.763 55.000 0.00 0.00 0.00 4.79
273 274 1.223187 GACAAGCTTTTTCGGACGGA 58.777 50.000 0.00 0.00 0.00 4.69
274 275 1.194772 GACAAGCTTTTTCGGACGGAG 59.805 52.381 0.00 0.00 0.00 4.63
275 276 0.517316 CAAGCTTTTTCGGACGGAGG 59.483 55.000 0.00 0.00 0.00 4.30
276 277 0.605589 AAGCTTTTTCGGACGGAGGG 60.606 55.000 0.00 0.00 0.00 4.30
430 439 4.335037 ACTTAACGCTAGAGCTAGGTGTAC 59.665 45.833 0.00 0.00 39.32 2.90
515 529 5.569059 CGATTTCAACCAGCTGATTACAAAC 59.431 40.000 17.39 0.00 0.00 2.93
653 667 1.257750 ACCTCATACGGCACTGCTGA 61.258 55.000 17.08 3.80 38.46 4.26
656 670 1.079197 CATACGGCACTGCTGACCA 60.079 57.895 17.08 1.79 38.46 4.02
711 725 5.450412 CCGTACATCAATTGAATGAAAGGGG 60.450 44.000 13.09 3.33 32.06 4.79
712 726 5.356751 CGTACATCAATTGAATGAAAGGGGA 59.643 40.000 13.09 0.00 32.06 4.81
713 727 5.927281 ACATCAATTGAATGAAAGGGGAG 57.073 39.130 13.09 0.00 32.06 4.30
714 728 5.582953 ACATCAATTGAATGAAAGGGGAGA 58.417 37.500 13.09 0.00 32.06 3.71
715 729 5.655532 ACATCAATTGAATGAAAGGGGAGAG 59.344 40.000 13.09 0.00 32.06 3.20
716 730 5.519183 TCAATTGAATGAAAGGGGAGAGA 57.481 39.130 5.45 0.00 0.00 3.10
717 731 6.083487 TCAATTGAATGAAAGGGGAGAGAT 57.917 37.500 5.45 0.00 0.00 2.75
718 732 6.125029 TCAATTGAATGAAAGGGGAGAGATC 58.875 40.000 5.45 0.00 0.00 2.75
719 733 3.827008 TGAATGAAAGGGGAGAGATCG 57.173 47.619 0.00 0.00 0.00 3.69
720 734 2.158900 TGAATGAAAGGGGAGAGATCGC 60.159 50.000 0.00 0.00 0.00 4.58
721 735 0.761802 ATGAAAGGGGAGAGATCGCC 59.238 55.000 3.30 3.30 42.33 5.54
722 736 1.068250 GAAAGGGGAGAGATCGCCG 59.932 63.158 5.79 0.00 45.99 6.46
723 737 2.370647 GAAAGGGGAGAGATCGCCGG 62.371 65.000 0.00 0.00 45.99 6.13
726 740 4.593864 GGGAGAGATCGCCGGCAC 62.594 72.222 28.98 16.94 36.62 5.01
727 741 4.593864 GGAGAGATCGCCGGCACC 62.594 72.222 28.98 14.50 0.00 5.01
728 742 3.532155 GAGAGATCGCCGGCACCT 61.532 66.667 28.98 19.38 0.00 4.00
729 743 2.123854 AGAGATCGCCGGCACCTA 60.124 61.111 28.98 8.91 0.00 3.08
730 744 1.528292 GAGAGATCGCCGGCACCTAT 61.528 60.000 28.98 16.64 0.00 2.57
731 745 1.080434 GAGATCGCCGGCACCTATC 60.080 63.158 28.98 21.36 0.00 2.08
732 746 1.806461 GAGATCGCCGGCACCTATCA 61.806 60.000 28.98 0.08 0.00 2.15
733 747 1.373497 GATCGCCGGCACCTATCAG 60.373 63.158 28.98 7.38 0.00 2.90
734 748 2.771763 GATCGCCGGCACCTATCAGG 62.772 65.000 28.98 6.54 42.49 3.86
735 749 4.609018 CGCCGGCACCTATCAGGG 62.609 72.222 28.98 0.98 40.58 4.45
736 750 3.480133 GCCGGCACCTATCAGGGT 61.480 66.667 24.80 0.00 40.58 4.34
737 751 3.043999 GCCGGCACCTATCAGGGTT 62.044 63.158 24.80 0.00 40.58 4.11
738 752 1.146263 CCGGCACCTATCAGGGTTC 59.854 63.158 0.00 0.00 40.58 3.62
739 753 1.622607 CCGGCACCTATCAGGGTTCA 61.623 60.000 0.00 0.00 40.58 3.18
740 754 0.179073 CGGCACCTATCAGGGTTCAG 60.179 60.000 0.00 0.00 40.58 3.02
741 755 1.204146 GGCACCTATCAGGGTTCAGA 58.796 55.000 0.00 0.00 40.58 3.27
742 756 1.139853 GGCACCTATCAGGGTTCAGAG 59.860 57.143 0.00 0.00 40.58 3.35
743 757 1.139853 GCACCTATCAGGGTTCAGAGG 59.860 57.143 0.00 0.00 40.58 3.69
744 758 2.752030 CACCTATCAGGGTTCAGAGGA 58.248 52.381 0.00 0.00 40.58 3.71
745 759 2.697751 CACCTATCAGGGTTCAGAGGAG 59.302 54.545 0.00 0.00 40.58 3.69
746 760 1.691434 CCTATCAGGGTTCAGAGGAGC 59.309 57.143 0.00 0.00 0.00 4.70
747 761 1.339610 CTATCAGGGTTCAGAGGAGCG 59.660 57.143 0.00 0.00 0.00 5.03
748 762 1.333636 ATCAGGGTTCAGAGGAGCGG 61.334 60.000 0.00 0.00 0.00 5.52
749 763 2.120718 AGGGTTCAGAGGAGCGGT 59.879 61.111 0.00 0.00 0.00 5.68
750 764 1.985116 AGGGTTCAGAGGAGCGGTC 60.985 63.158 5.93 5.93 0.00 4.79
751 765 2.182030 GGTTCAGAGGAGCGGTCG 59.818 66.667 8.77 0.00 0.00 4.79
752 766 2.182030 GTTCAGAGGAGCGGTCGG 59.818 66.667 8.77 0.00 0.00 4.79
753 767 3.760035 TTCAGAGGAGCGGTCGGC 61.760 66.667 8.77 2.81 44.05 5.54
895 915 2.281622 CGGGTTGTTACGGCCCAA 60.282 61.111 12.98 0.00 42.44 4.12
896 916 2.329614 CGGGTTGTTACGGCCCAAG 61.330 63.158 12.98 0.00 42.44 3.61
1120 1144 4.711949 CCTGCCGCACTTCTGCCT 62.712 66.667 0.00 0.00 40.73 4.75
1206 1230 4.144703 GACGCTTCCCGGGAGTCC 62.145 72.222 25.26 14.68 42.52 3.85
1248 1272 1.407258 GAGGAAGCTATGACTGCGACT 59.593 52.381 0.00 0.00 35.28 4.18
1385 1410 2.559668 CCTTCGTCGGCCATATAGGTAA 59.440 50.000 2.24 0.00 40.61 2.85
1533 1562 9.935682 CAACCAAATTATGCTACACTAGTATTG 57.064 33.333 0.00 0.00 33.13 1.90
1559 1588 0.681175 AGCATTGCAACCCAGAAACC 59.319 50.000 11.91 0.00 0.00 3.27
1592 1622 2.356069 GCTAGAAATTCCGAGCCTTTGG 59.644 50.000 6.29 0.00 0.00 3.28
1824 1856 4.661993 TTCGATCTTCAATTTGGTGTCG 57.338 40.909 0.00 3.01 0.00 4.35
1857 1889 2.159014 TGTTCCACTGCTTAACGTGACT 60.159 45.455 0.00 0.00 33.04 3.41
2026 2058 7.926555 TCGAAGATTCCCAGATAATAAGTTGAC 59.073 37.037 0.00 0.00 0.00 3.18
2027 2059 7.710907 CGAAGATTCCCAGATAATAAGTTGACA 59.289 37.037 0.00 0.00 0.00 3.58
2100 2132 4.085733 TGGTATTGGGTTGATGGAAACTG 58.914 43.478 0.00 0.00 0.00 3.16
2136 2168 5.133383 TGGATCTGGAACATTGATGGATT 57.867 39.130 0.00 0.00 38.20 3.01
2674 2976 5.063060 CACCTTTGTACGCTATTGGTAAGAC 59.937 44.000 0.00 0.00 0.00 3.01
2757 3060 6.759272 TGAGTATCTGTAACAAGCAAGTCTT 58.241 36.000 0.00 0.00 34.92 3.01
2811 3115 8.899771 AGATATTATTTTTACCCCGAAACAGTG 58.100 33.333 0.00 0.00 0.00 3.66
2819 3123 1.296715 CCGAAACAGTGGGAGAGGG 59.703 63.158 0.00 0.00 0.00 4.30
2825 3129 1.992277 CAGTGGGAGAGGGTCCTGG 60.992 68.421 0.00 0.00 46.06 4.45
2847 3151 8.260114 CCTGGTGCAATATGTACATGAGATATA 58.740 37.037 18.81 0.00 34.53 0.86
2848 3152 9.828039 CTGGTGCAATATGTACATGAGATATAT 57.172 33.333 18.81 0.00 34.53 0.86
2874 3178 8.722480 TTTTTCGATGAAGATGTACATGAGAT 57.278 30.769 14.43 0.00 0.00 2.75
2875 3179 9.816354 TTTTTCGATGAAGATGTACATGAGATA 57.184 29.630 14.43 0.00 0.00 1.98
2876 3180 9.987272 TTTTCGATGAAGATGTACATGAGATAT 57.013 29.630 14.43 1.17 0.00 1.63
2877 3181 9.987272 TTTCGATGAAGATGTACATGAGATATT 57.013 29.630 14.43 0.00 0.00 1.28
3054 3358 3.650942 TGTACTTTCCTCATTGGTGTCCT 59.349 43.478 0.00 0.00 37.07 3.85
3109 3414 5.898972 TGGGGCTCTAATTATCTGCAAAAAT 59.101 36.000 0.00 0.00 0.00 1.82
3344 3649 7.531716 TGTTCTCTTAAACACGTCAAATTGTT 58.468 30.769 0.00 0.00 37.55 2.83
3352 3657 7.876896 AAACACGTCAAATTGTTAACTGTTT 57.123 28.000 7.22 8.71 34.82 2.83
3410 3715 1.620323 CTCCTCACCATGACACTGTCA 59.380 52.381 14.26 14.26 46.90 3.58
3586 3891 8.453238 TGTTAGCTTGGTATGTGTTCTTAAAA 57.547 30.769 0.00 0.00 0.00 1.52
3698 4003 6.942005 TGCAGGTTAGATATACATTTCATGGG 59.058 38.462 0.00 0.00 33.60 4.00
3712 4017 7.738847 ACATTTCATGGGAAAAGAAGTTCATT 58.261 30.769 5.50 0.00 45.52 2.57
3794 4099 1.922447 TGTTATGCAGATTGGAGGGGT 59.078 47.619 0.00 0.00 0.00 4.95
3980 4285 1.871408 GCCATGATACTCACTGCTCCG 60.871 57.143 0.00 0.00 0.00 4.63
4041 4346 0.530288 ACGCTGTTGCTTTTGTGGTT 59.470 45.000 0.00 0.00 36.97 3.67
4138 4443 1.906574 TCTATTCCCCGTCTTGCTGTT 59.093 47.619 0.00 0.00 0.00 3.16
4147 4452 4.569564 CCCCGTCTTGCTGTTAATACTAAC 59.430 45.833 0.00 0.00 38.34 2.34
4290 4595 5.220681 GCCGGTCTCATTCTTTTTATGAGTC 60.221 44.000 1.90 7.02 45.85 3.36
4338 4643 9.585369 GGAGGTAGTGTAGACTATATAGGTTTT 57.415 37.037 14.25 0.00 37.03 2.43
4372 4677 4.739793 TCATGGAAGTTGGAATGGAAACT 58.260 39.130 0.00 0.00 38.25 2.66
4400 4705 7.362401 CCTTGATGACTTCAGGTAATTTTCTGG 60.362 40.741 7.56 0.00 35.27 3.86
4411 4716 3.457610 AATTTTCTGGTGTGCAGGTTG 57.542 42.857 0.00 0.00 0.00 3.77
4488 4793 9.923143 CGACAAAATGTGATACCCTAGATAATA 57.077 33.333 0.00 0.00 0.00 0.98
4571 4876 4.460263 TGGCAAATACATGTACAGATCCC 58.540 43.478 7.96 5.11 0.00 3.85
4681 4986 4.014569 TGCAAATGCTACAGGTAGTTGA 57.985 40.909 6.97 0.00 37.71 3.18
4769 5074 3.766151 ACGTAGATGATGTGTAACCGTG 58.234 45.455 0.00 0.00 34.36 4.94
4802 5107 6.068461 TCCACTTGGTTGTAGCCATTATTA 57.932 37.500 0.00 0.00 38.48 0.98
4918 5223 7.278868 GCAACTTCTACTGTAAATGAGCTATGT 59.721 37.037 0.00 0.00 0.00 2.29
4926 5231 1.742761 AATGAGCTATGTTGTGCGCT 58.257 45.000 9.73 0.00 35.03 5.92
4953 5258 6.594788 TTATGCTCATTTTGGCTTTCTCTT 57.405 33.333 0.00 0.00 0.00 2.85
5355 8354 6.258287 GGATCATATCAATCTGCTATCAGTGC 59.742 42.308 0.00 0.00 41.10 4.40
5452 8452 2.294512 CTGATACACCGAGCAGCATCTA 59.705 50.000 0.00 0.00 0.00 1.98
5453 8453 2.294512 TGATACACCGAGCAGCATCTAG 59.705 50.000 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.082169 GCACAAGCGCGATGAACAA 60.082 52.632 20.68 0.00 0.00 2.83
18 19 2.667874 TGGCACAAGCGCGATGAA 60.668 55.556 20.68 2.51 43.41 2.57
57 58 1.860484 GCAGTCCAGAAGCACAAGCC 61.860 60.000 0.00 0.00 43.56 4.35
78 79 2.224314 GTCTGAAAAACGAGCTTGGGAG 59.776 50.000 5.79 0.00 0.00 4.30
96 97 2.895242 AGGTAACGGTACTGGAGTCT 57.105 50.000 11.05 0.00 46.39 3.24
152 153 4.040217 TCTTTGGCTTGTTTGGTGCATAAT 59.960 37.500 0.00 0.00 0.00 1.28
196 197 6.038825 TGCCCATAGAAATTTACATTGTACCG 59.961 38.462 0.00 0.00 0.00 4.02
229 230 0.258194 ATTCGGACGGAGGGAGTACT 59.742 55.000 0.00 0.00 0.00 2.73
230 231 1.109609 AATTCGGACGGAGGGAGTAC 58.890 55.000 0.00 0.00 0.00 2.73
231 232 1.108776 CAATTCGGACGGAGGGAGTA 58.891 55.000 0.00 0.00 0.00 2.59
232 233 0.613853 TCAATTCGGACGGAGGGAGT 60.614 55.000 0.00 0.00 0.00 3.85
233 234 0.103208 CTCAATTCGGACGGAGGGAG 59.897 60.000 0.00 0.00 0.00 4.30
234 235 1.327690 CCTCAATTCGGACGGAGGGA 61.328 60.000 4.81 0.00 42.55 4.20
235 236 1.144057 CCTCAATTCGGACGGAGGG 59.856 63.158 4.81 0.00 42.55 4.30
236 237 1.144057 CCCTCAATTCGGACGGAGG 59.856 63.158 5.64 5.64 45.20 4.30
237 238 0.179108 GTCCCTCAATTCGGACGGAG 60.179 60.000 1.20 0.00 39.29 4.63
238 239 1.895238 GTCCCTCAATTCGGACGGA 59.105 57.895 1.20 0.00 39.29 4.69
239 240 4.515404 GTCCCTCAATTCGGACGG 57.485 61.111 1.20 0.00 39.29 4.79
242 243 0.984230 AGCTTGTCCCTCAATTCGGA 59.016 50.000 0.00 0.00 35.35 4.55
243 244 1.826385 AAGCTTGTCCCTCAATTCGG 58.174 50.000 0.00 0.00 35.35 4.30
244 245 3.923017 AAAAGCTTGTCCCTCAATTCG 57.077 42.857 0.00 0.00 35.35 3.34
245 246 4.229876 CGAAAAAGCTTGTCCCTCAATTC 58.770 43.478 0.00 0.00 35.35 2.17
246 247 3.005791 CCGAAAAAGCTTGTCCCTCAATT 59.994 43.478 0.00 0.00 35.35 2.32
247 248 2.558359 CCGAAAAAGCTTGTCCCTCAAT 59.442 45.455 0.00 0.00 35.35 2.57
248 249 1.953686 CCGAAAAAGCTTGTCCCTCAA 59.046 47.619 0.00 0.00 34.61 3.02
249 250 1.142060 TCCGAAAAAGCTTGTCCCTCA 59.858 47.619 0.00 0.00 0.00 3.86
250 251 1.535896 GTCCGAAAAAGCTTGTCCCTC 59.464 52.381 0.00 0.00 0.00 4.30
251 252 1.605753 GTCCGAAAAAGCTTGTCCCT 58.394 50.000 0.00 0.00 0.00 4.20
252 253 0.237498 CGTCCGAAAAAGCTTGTCCC 59.763 55.000 0.00 0.00 0.00 4.46
253 254 0.237498 CCGTCCGAAAAAGCTTGTCC 59.763 55.000 0.00 0.00 0.00 4.02
254 255 1.194772 CTCCGTCCGAAAAAGCTTGTC 59.805 52.381 0.00 0.00 0.00 3.18
255 256 1.226746 CTCCGTCCGAAAAAGCTTGT 58.773 50.000 0.00 0.00 0.00 3.16
256 257 0.517316 CCTCCGTCCGAAAAAGCTTG 59.483 55.000 0.00 0.00 0.00 4.01
257 258 0.605589 CCCTCCGTCCGAAAAAGCTT 60.606 55.000 0.00 0.00 0.00 3.74
258 259 1.003718 CCCTCCGTCCGAAAAAGCT 60.004 57.895 0.00 0.00 0.00 3.74
259 260 1.004200 TCCCTCCGTCCGAAAAAGC 60.004 57.895 0.00 0.00 0.00 3.51
260 261 0.320697 ACTCCCTCCGTCCGAAAAAG 59.679 55.000 0.00 0.00 0.00 2.27
261 262 1.547372 CTACTCCCTCCGTCCGAAAAA 59.453 52.381 0.00 0.00 0.00 1.94
262 263 1.180029 CTACTCCCTCCGTCCGAAAA 58.820 55.000 0.00 0.00 0.00 2.29
263 264 0.329261 TCTACTCCCTCCGTCCGAAA 59.671 55.000 0.00 0.00 0.00 3.46
264 265 0.329261 TTCTACTCCCTCCGTCCGAA 59.671 55.000 0.00 0.00 0.00 4.30
265 266 0.107312 CTTCTACTCCCTCCGTCCGA 60.107 60.000 0.00 0.00 0.00 4.55
266 267 0.394080 ACTTCTACTCCCTCCGTCCG 60.394 60.000 0.00 0.00 0.00 4.79
267 268 1.849977 AACTTCTACTCCCTCCGTCC 58.150 55.000 0.00 0.00 0.00 4.79
268 269 2.561858 ACAAACTTCTACTCCCTCCGTC 59.438 50.000 0.00 0.00 0.00 4.79
269 270 2.299297 CACAAACTTCTACTCCCTCCGT 59.701 50.000 0.00 0.00 0.00 4.69
270 271 2.561419 TCACAAACTTCTACTCCCTCCG 59.439 50.000 0.00 0.00 0.00 4.63
271 272 4.020128 ACATCACAAACTTCTACTCCCTCC 60.020 45.833 0.00 0.00 0.00 4.30
272 273 5.153950 ACATCACAAACTTCTACTCCCTC 57.846 43.478 0.00 0.00 0.00 4.30
273 274 5.568620 AACATCACAAACTTCTACTCCCT 57.431 39.130 0.00 0.00 0.00 4.20
274 275 6.369065 CAGTAACATCACAAACTTCTACTCCC 59.631 42.308 0.00 0.00 0.00 4.30
275 276 7.152645 TCAGTAACATCACAAACTTCTACTCC 58.847 38.462 0.00 0.00 0.00 3.85
276 277 8.651588 CATCAGTAACATCACAAACTTCTACTC 58.348 37.037 0.00 0.00 0.00 2.59
430 439 4.776743 CGTGTCAAGTCTCCTCAAAATTG 58.223 43.478 0.00 0.00 0.00 2.32
515 529 1.745087 CCTCCATTCAACATCCAACCG 59.255 52.381 0.00 0.00 0.00 4.44
653 667 1.975407 GGATGCAGCAGCTTGTGGT 60.975 57.895 11.16 0.00 42.74 4.16
656 670 0.824595 TTGTGGATGCAGCAGCTTGT 60.825 50.000 11.16 0.00 42.74 3.16
711 725 1.528292 ATAGGTGCCGGCGATCTCTC 61.528 60.000 23.90 5.66 0.00 3.20
712 726 1.528292 GATAGGTGCCGGCGATCTCT 61.528 60.000 23.90 15.92 0.00 3.10
713 727 1.080434 GATAGGTGCCGGCGATCTC 60.080 63.158 23.90 10.93 0.00 2.75
714 728 1.810606 CTGATAGGTGCCGGCGATCT 61.811 60.000 23.90 20.24 0.00 2.75
715 729 1.373497 CTGATAGGTGCCGGCGATC 60.373 63.158 23.90 20.54 0.00 3.69
716 730 2.737180 CTGATAGGTGCCGGCGAT 59.263 61.111 23.90 12.42 0.00 4.58
717 731 3.536917 CCTGATAGGTGCCGGCGA 61.537 66.667 23.90 8.37 0.00 5.54
718 732 4.609018 CCCTGATAGGTGCCGGCG 62.609 72.222 23.90 0.00 31.93 6.46
719 733 2.942648 GAACCCTGATAGGTGCCGGC 62.943 65.000 22.73 22.73 40.05 6.13
720 734 1.146263 GAACCCTGATAGGTGCCGG 59.854 63.158 0.00 0.00 40.05 6.13
721 735 0.179073 CTGAACCCTGATAGGTGCCG 60.179 60.000 0.00 0.00 40.05 5.69
722 736 1.139853 CTCTGAACCCTGATAGGTGCC 59.860 57.143 0.00 0.00 40.05 5.01
723 737 1.139853 CCTCTGAACCCTGATAGGTGC 59.860 57.143 0.00 0.00 40.05 5.01
724 738 2.697751 CTCCTCTGAACCCTGATAGGTG 59.302 54.545 0.00 0.00 40.05 4.00
725 739 2.957312 GCTCCTCTGAACCCTGATAGGT 60.957 54.545 0.00 0.00 44.00 3.08
726 740 1.691434 GCTCCTCTGAACCCTGATAGG 59.309 57.143 0.00 0.00 34.30 2.57
727 741 1.339610 CGCTCCTCTGAACCCTGATAG 59.660 57.143 0.00 0.00 0.00 2.08
728 742 1.403814 CGCTCCTCTGAACCCTGATA 58.596 55.000 0.00 0.00 0.00 2.15
729 743 1.333636 CCGCTCCTCTGAACCCTGAT 61.334 60.000 0.00 0.00 0.00 2.90
730 744 1.984570 CCGCTCCTCTGAACCCTGA 60.985 63.158 0.00 0.00 0.00 3.86
731 745 2.232298 GACCGCTCCTCTGAACCCTG 62.232 65.000 0.00 0.00 0.00 4.45
732 746 1.985116 GACCGCTCCTCTGAACCCT 60.985 63.158 0.00 0.00 0.00 4.34
733 747 2.579738 GACCGCTCCTCTGAACCC 59.420 66.667 0.00 0.00 0.00 4.11
734 748 2.182030 CGACCGCTCCTCTGAACC 59.818 66.667 0.00 0.00 0.00 3.62
735 749 2.182030 CCGACCGCTCCTCTGAAC 59.818 66.667 0.00 0.00 0.00 3.18
736 750 3.760035 GCCGACCGCTCCTCTGAA 61.760 66.667 0.00 0.00 0.00 3.02
747 761 2.646143 GCTATCTCTCGGCCGACC 59.354 66.667 27.28 2.67 0.00 4.79
748 762 2.646143 GGCTATCTCTCGGCCGAC 59.354 66.667 27.28 12.88 36.37 4.79
751 765 1.602888 TACCGGCTATCTCTCGGCC 60.603 63.158 0.00 0.00 46.87 6.13
752 766 1.580437 GTACCGGCTATCTCTCGGC 59.420 63.158 0.00 0.00 46.87 5.54
754 768 0.875728 CAGGTACCGGCTATCTCTCG 59.124 60.000 6.18 0.00 0.00 4.04
820 834 2.503382 GCCACGATCCTCCTCCTCC 61.503 68.421 0.00 0.00 0.00 4.30
821 835 1.758514 TGCCACGATCCTCCTCCTC 60.759 63.158 0.00 0.00 0.00 3.71
822 836 2.060980 GTGCCACGATCCTCCTCCT 61.061 63.158 0.00 0.00 0.00 3.69
863 883 0.323178 ACCCGCTACCTCTTCTTCGA 60.323 55.000 0.00 0.00 0.00 3.71
1206 1230 0.250513 CCTCCTTCCTTTCAGGGTCG 59.749 60.000 0.00 0.00 35.59 4.79
1209 1233 0.915364 CCTCCTCCTTCCTTTCAGGG 59.085 60.000 0.00 0.00 35.59 4.45
1226 1250 0.749649 CGCAGTCATAGCTTCCTCCT 59.250 55.000 0.00 0.00 0.00 3.69
1248 1272 4.155733 CATCCCGGCAGCGTACCA 62.156 66.667 0.00 0.00 0.00 3.25
1385 1410 4.078980 AGGATGGCAAGAAAGAACCCATAT 60.079 41.667 0.00 0.00 36.48 1.78
1429 1454 0.249322 CGGCCTTGTACCATAGTCCG 60.249 60.000 0.00 0.00 0.00 4.79
1559 1588 7.083858 TCGGAATTTCTAGCACAAAATCTTTG 58.916 34.615 0.00 0.00 0.00 2.77
1592 1622 4.095334 TGCAGATTGACTACACATGAATGC 59.905 41.667 0.00 0.00 0.00 3.56
1857 1889 4.754372 CTGCTCAGCAACAAAAGATGTA 57.246 40.909 0.00 0.00 42.99 2.29
2008 2040 7.733773 TCTTCTGTCAACTTATTATCTGGGA 57.266 36.000 0.00 0.00 0.00 4.37
2100 2132 4.462483 TCCAGATCCAAAAATAAGTGCCAC 59.538 41.667 0.00 0.00 0.00 5.01
2136 2168 4.897076 ACATACCACTGGTATACCGATGAA 59.103 41.667 18.70 12.25 45.97 2.57
2208 2240 2.593346 ACAAATTGAGCGCCAAAACA 57.407 40.000 13.95 0.78 38.43 2.83
2674 2976 6.636666 ATTTAGCGACAAGAAATTGCAATG 57.363 33.333 13.82 3.85 0.00 2.82
2757 3060 6.213397 AGTGCATATAGGCATATGTGTTCCTA 59.787 38.462 16.01 6.91 46.92 2.94
2811 3115 3.403558 GCACCAGGACCCTCTCCC 61.404 72.222 0.00 0.00 40.53 4.30
2819 3123 4.450976 TCATGTACATATTGCACCAGGAC 58.549 43.478 8.32 0.00 0.00 3.85
2850 3154 9.987272 ATATCTCATGTACATCTTCATCGAAAA 57.013 29.630 5.07 0.00 0.00 2.29
2851 3155 9.987272 AATATCTCATGTACATCTTCATCGAAA 57.013 29.630 5.07 0.00 0.00 3.46
2875 3179 9.504708 TGCAAAACATCCAAATCAAGAAATAAT 57.495 25.926 0.00 0.00 0.00 1.28
2876 3180 8.899427 TGCAAAACATCCAAATCAAGAAATAA 57.101 26.923 0.00 0.00 0.00 1.40
2877 3181 8.937884 CATGCAAAACATCCAAATCAAGAAATA 58.062 29.630 0.00 0.00 36.64 1.40
2878 3182 7.574217 GCATGCAAAACATCCAAATCAAGAAAT 60.574 33.333 14.21 0.00 36.64 2.17
2879 3183 6.293516 GCATGCAAAACATCCAAATCAAGAAA 60.294 34.615 14.21 0.00 36.64 2.52
3054 3358 6.634805 CAGATGACTAAAAGTAAGAGCTGGA 58.365 40.000 0.00 0.00 0.00 3.86
3268 3573 6.080969 TGGATAAGGTAGGCAAAACCAATA 57.919 37.500 6.48 0.75 43.14 1.90
3344 3649 2.948979 CAGTCCACCTGCAAAACAGTTA 59.051 45.455 0.00 0.00 45.68 2.24
3410 3715 1.074405 TCCCTTGCAGCAAGAGATGTT 59.926 47.619 32.94 0.00 43.42 2.71
3586 3891 6.015688 CAGAGCCTGCATTGTTTTATGGATAT 60.016 38.462 0.00 0.00 0.00 1.63
3698 4003 7.086376 TCAGCAGCATTAATGAACTTCTTTTC 58.914 34.615 19.73 0.00 0.00 2.29
3712 4017 3.988976 AAGAGAACCTCAGCAGCATTA 57.011 42.857 0.00 0.00 32.06 1.90
3779 4084 0.842030 AGTCACCCCTCCAATCTGCA 60.842 55.000 0.00 0.00 0.00 4.41
3794 4099 2.959372 CGAGTGCCGTACCAGTCA 59.041 61.111 7.47 0.00 35.39 3.41
3935 4240 7.596248 GCATCAAAACTTCACTTGTCACATTAT 59.404 33.333 0.00 0.00 0.00 1.28
3980 4285 5.841296 GCGACGAACTGCAAGATTTAATATC 59.159 40.000 0.00 0.00 37.43 1.63
4041 4346 3.046283 ACACCATAGTAGAGCCCATCA 57.954 47.619 0.00 0.00 0.00 3.07
4138 4443 9.667107 AGTTATTTTGCAGCTCAGTTAGTATTA 57.333 29.630 0.00 0.00 0.00 0.98
4147 4452 9.793252 AATATTGTTAGTTATTTTGCAGCTCAG 57.207 29.630 0.00 0.00 0.00 3.35
4372 4677 8.383175 AGAAAATTACCTGAAGTCATCAAGGTA 58.617 33.333 0.00 0.00 39.11 3.08
4400 4705 2.985847 GCTCCCCAACCTGCACAC 60.986 66.667 0.00 0.00 0.00 3.82
4411 4716 2.035783 GGTCCACCTTTGCTCCCC 59.964 66.667 0.00 0.00 0.00 4.81
4538 4843 5.185635 ACATGTATTTGCCAAGTAACTGCAT 59.814 36.000 0.00 0.00 34.51 3.96
4540 4845 5.059404 ACATGTATTTGCCAAGTAACTGC 57.941 39.130 0.00 0.00 0.00 4.40
4769 5074 2.206576 ACCAAGTGGAGAATGCTTCC 57.793 50.000 3.83 0.00 38.94 3.46
4802 5107 5.400066 AACCAACTTTTTGTAGCACTTGT 57.600 34.783 0.00 0.00 0.00 3.16
4918 5223 2.150390 TGAGCATAAAAGAGCGCACAA 58.850 42.857 11.47 0.00 35.66 3.33
4926 5231 6.996509 AGAAAGCCAAAATGAGCATAAAAGA 58.003 32.000 0.00 0.00 0.00 2.52
5355 8354 0.539051 AATCGAAGCTCAGTCCCAGG 59.461 55.000 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.