Multiple sequence alignment - TraesCS5D01G535600

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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 TraesCS5D01G535600 chr5D 100.000 3761 0 0 1 3761 549431245 549427485 0.000000e+00 6946.0
1 TraesCS5D01G535600 chr5D 92.244 2063 133 15 848 2903 549548467 549546425 0.000000e+00 2898.0
2 TraesCS5D01G535600 chr5D 82.127 1617 229 35 1178 2743 549262020 549260413 0.000000e+00 1330.0
3 TraesCS5D01G535600 chr5D 79.915 1643 249 39 1178 2768 549229685 549228072 0.000000e+00 1131.0
4 TraesCS5D01G535600 chr5D 88.682 804 77 3 2115 2918 549489367 549488578 0.000000e+00 968.0
5 TraesCS5D01G535600 chr5D 84.178 493 31 21 849 1337 549489822 549489373 5.770000e-118 435.0
6 TraesCS5D01G535600 chr5D 89.691 291 29 1 2455 2745 549358616 549358327 1.650000e-98 370.0
7 TraesCS5D01G535600 chr5D 100.000 32 0 0 5 36 367733262 367733231 4.060000e-05 60.2
8 TraesCS5D01G535600 chr5B 91.871 2079 139 14 848 2918 701052013 701049957 0.000000e+00 2876.0
9 TraesCS5D01G535600 chr5B 85.965 855 105 8 1178 2017 700856493 700855639 0.000000e+00 900.0
10 TraesCS5D01G535600 chr5B 90.578 329 15 4 848 1176 701053309 701052997 4.490000e-114 422.0
11 TraesCS5D01G535600 chr2A 84.701 1608 209 20 1159 2762 107182781 107181207 0.000000e+00 1572.0
12 TraesCS5D01G535600 chr2A 90.945 508 37 8 1 503 653850743 653851246 0.000000e+00 675.0
13 TraesCS5D01G535600 chr2A 97.115 104 3 0 645 748 653857703 653857806 3.860000e-40 176.0
14 TraesCS5D01G535600 chr2D 86.999 1023 102 13 1003 2017 110843361 110842362 0.000000e+00 1123.0
15 TraesCS5D01G535600 chr2D 84.115 661 103 2 2103 2762 110842299 110841640 4.100000e-179 638.0
16 TraesCS5D01G535600 chr2D 88.060 335 16 9 432 762 510208514 510208828 3.550000e-100 375.0
17 TraesCS5D01G535600 chr2D 97.222 36 1 0 1 36 408461836 408461871 1.130000e-05 62.1
18 TraesCS5D01G535600 chr2B 86.413 1023 108 15 1003 2017 159971194 159970195 0.000000e+00 1090.0
19 TraesCS5D01G535600 chr2B 92.298 766 50 1 3005 3761 616487453 616488218 0.000000e+00 1079.0
20 TraesCS5D01G535600 chr2B 90.216 787 40 19 1 762 599807821 599808595 0.000000e+00 992.0
21 TraesCS5D01G535600 chr2B 84.000 650 102 2 2103 2751 159970132 159969484 1.150000e-174 623.0
22 TraesCS5D01G535600 chr7B 89.213 788 61 11 2996 3761 621619987 621619202 0.000000e+00 963.0
23 TraesCS5D01G535600 chr7B 97.222 36 1 0 1 36 578445634 578445599 1.130000e-05 62.1
24 TraesCS5D01G535600 chr7D 90.597 553 38 10 6 555 249487882 249487341 0.000000e+00 721.0
25 TraesCS5D01G535600 chr7D 90.083 242 21 3 593 833 249487357 249487118 1.010000e-80 311.0
26 TraesCS5D01G535600 chr7D 95.652 46 2 0 3157 3202 582058592 582058637 1.450000e-09 75.0
27 TraesCS5D01G535600 chrUn 82.801 814 122 11 1210 2014 75777180 75777984 0.000000e+00 712.0
28 TraesCS5D01G535600 chrUn 82.742 817 123 11 1210 2017 228925104 228924297 0.000000e+00 712.0
29 TraesCS5D01G535600 chrUn 79.407 641 125 7 2091 2728 75745828 75746464 2.670000e-121 446.0
30 TraesCS5D01G535600 chrUn 79.188 591 117 6 2141 2728 228922465 228921878 4.520000e-109 405.0
31 TraesCS5D01G535600 chrUn 79.188 591 117 6 2141 2728 325066151 325065564 4.520000e-109 405.0
32 TraesCS5D01G535600 chr7A 88.827 179 18 2 3517 3695 682158745 682158921 6.320000e-53 219.0
33 TraesCS5D01G535600 chr6B 79.670 182 23 10 3006 3176 86645033 86644855 6.600000e-23 119.0
34 TraesCS5D01G535600 chr4A 100.000 32 0 0 5 36 733590578 733590547 4.060000e-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 TraesCS5D01G535600 chr5D 549427485 549431245 3760 True 6946.0 6946 100.0000 1 3761 1 chr5D.!!$R5 3760
1 TraesCS5D01G535600 chr5D 549546425 549548467 2042 True 2898.0 2898 92.2440 848 2903 1 chr5D.!!$R6 2055
2 TraesCS5D01G535600 chr5D 549260413 549262020 1607 True 1330.0 1330 82.1270 1178 2743 1 chr5D.!!$R3 1565
3 TraesCS5D01G535600 chr5D 549228072 549229685 1613 True 1131.0 1131 79.9150 1178 2768 1 chr5D.!!$R2 1590
4 TraesCS5D01G535600 chr5D 549488578 549489822 1244 True 701.5 968 86.4300 849 2918 2 chr5D.!!$R7 2069
5 TraesCS5D01G535600 chr5B 701049957 701053309 3352 True 1649.0 2876 91.2245 848 2918 2 chr5B.!!$R2 2070
6 TraesCS5D01G535600 chr5B 700855639 700856493 854 True 900.0 900 85.9650 1178 2017 1 chr5B.!!$R1 839
7 TraesCS5D01G535600 chr2A 107181207 107182781 1574 True 1572.0 1572 84.7010 1159 2762 1 chr2A.!!$R1 1603
8 TraesCS5D01G535600 chr2A 653850743 653851246 503 False 675.0 675 90.9450 1 503 1 chr2A.!!$F1 502
9 TraesCS5D01G535600 chr2D 110841640 110843361 1721 True 880.5 1123 85.5570 1003 2762 2 chr2D.!!$R1 1759
10 TraesCS5D01G535600 chr2B 616487453 616488218 765 False 1079.0 1079 92.2980 3005 3761 1 chr2B.!!$F2 756
11 TraesCS5D01G535600 chr2B 599807821 599808595 774 False 992.0 992 90.2160 1 762 1 chr2B.!!$F1 761
12 TraesCS5D01G535600 chr2B 159969484 159971194 1710 True 856.5 1090 85.2065 1003 2751 2 chr2B.!!$R1 1748
13 TraesCS5D01G535600 chr7B 621619202 621619987 785 True 963.0 963 89.2130 2996 3761 1 chr7B.!!$R2 765
14 TraesCS5D01G535600 chr7D 249487118 249487882 764 True 516.0 721 90.3400 6 833 2 chr7D.!!$R1 827
15 TraesCS5D01G535600 chrUn 75777180 75777984 804 False 712.0 712 82.8010 1210 2014 1 chrUn.!!$F2 804
16 TraesCS5D01G535600 chrUn 228921878 228925104 3226 True 558.5 712 80.9650 1210 2728 2 chrUn.!!$R2 1518
17 TraesCS5D01G535600 chrUn 75745828 75746464 636 False 446.0 446 79.4070 2091 2728 1 chrUn.!!$F1 637
18 TraesCS5D01G535600 chrUn 325065564 325066151 587 True 405.0 405 79.1880 2141 2728 1 chrUn.!!$R1 587

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
935 2259 0.246635 AACACCCAGCGCTACACTAG 59.753 55.0 10.99 0.32 0.00 2.57 F
1020 2345 0.181114 TGGGGAAGATTGGAGCATCG 59.819 55.0 0.00 0.00 34.37 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2466 5565 0.035152 AATTCATGTGGCGCTCTGGA 60.035 50.0 7.64 0.0 0.0 3.86 R
2907 6006 0.261696 ACTTTGCCCCCTCACACTTT 59.738 50.0 0.00 0.0 0.0 2.66 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
37 38 8.916062 CATAAAAGTTACCGGGGGTATATTTTT 58.084 33.333 6.32 14.09 38.05 1.94
208 211 7.412137 AGTTACCGTGATGTTTGTACTTAAC 57.588 36.000 0.00 0.00 0.00 2.01
334 337 4.391830 CAGACATGTGGTGCGTAAATTACT 59.608 41.667 1.15 0.00 0.00 2.24
344 347 7.428183 GTGGTGCGTAAATTACTGTGATATTTG 59.572 37.037 1.42 0.00 0.00 2.32
361 364 6.824196 TGATATTTGTACAGAAATTACCGGCA 59.176 34.615 0.00 0.00 0.00 5.69
376 379 1.470632 CCGGCAGCAAGTTTCAACAAA 60.471 47.619 0.00 0.00 0.00 2.83
377 380 2.266554 CGGCAGCAAGTTTCAACAAAA 58.733 42.857 0.00 0.00 0.00 2.44
378 381 2.670414 CGGCAGCAAGTTTCAACAAAAA 59.330 40.909 0.00 0.00 0.00 1.94
441 465 2.434336 ACATATCCACTTGCTAGCGGAA 59.566 45.455 10.77 0.00 36.25 4.30
463 488 7.162082 GGAATTGGTAGTCTTGTATGGATAGG 58.838 42.308 0.00 0.00 0.00 2.57
466 491 7.931015 TTGGTAGTCTTGTATGGATAGGATT 57.069 36.000 0.00 0.00 0.00 3.01
467 492 7.931015 TGGTAGTCTTGTATGGATAGGATTT 57.069 36.000 0.00 0.00 0.00 2.17
473 499 5.310594 TCTTGTATGGATAGGATTTGAGGGG 59.689 44.000 0.00 0.00 0.00 4.79
481 507 5.103898 GGATAGGATTTGAGGGGAAGAGTTT 60.104 44.000 0.00 0.00 0.00 2.66
582 608 5.621329 GCTCATTAAACACGCCAATTAAGGT 60.621 40.000 0.00 0.00 0.00 3.50
583 609 6.403855 GCTCATTAAACACGCCAATTAAGGTA 60.404 38.462 0.00 0.00 0.00 3.08
584 610 6.844254 TCATTAAACACGCCAATTAAGGTAC 58.156 36.000 0.00 0.00 0.00 3.34
585 611 3.817148 AAACACGCCAATTAAGGTACG 57.183 42.857 0.00 0.00 0.00 3.67
586 612 1.729284 ACACGCCAATTAAGGTACGG 58.271 50.000 0.00 0.00 0.00 4.02
587 613 1.275856 ACACGCCAATTAAGGTACGGA 59.724 47.619 0.00 0.00 0.00 4.69
588 614 2.289569 ACACGCCAATTAAGGTACGGAA 60.290 45.455 0.00 0.00 0.00 4.30
589 615 2.350498 CACGCCAATTAAGGTACGGAAG 59.650 50.000 0.00 0.00 0.00 3.46
590 616 2.234414 ACGCCAATTAAGGTACGGAAGA 59.766 45.455 0.00 0.00 0.00 2.87
633 659 3.007723 GGTAAGGAGAAAAACTCGGGTCT 59.992 47.826 0.00 0.00 45.76 3.85
697 723 8.633561 GCTAATTAATGCCCAAGAGAATAAACT 58.366 33.333 0.00 0.00 0.00 2.66
711 737 9.981460 AAGAGAATAAACTGGGTCAATTAAGAT 57.019 29.630 0.00 0.00 0.00 2.40
784 810 3.802418 AAACTTGCGCGAGACCGGT 62.802 57.895 31.19 6.92 36.06 5.28
833 859 1.693627 TCGGATCTCTCCCTAACTGC 58.306 55.000 0.00 0.00 38.45 4.40
834 860 0.676736 CGGATCTCTCCCTAACTGCC 59.323 60.000 0.00 0.00 38.45 4.85
835 861 1.794714 GGATCTCTCCCTAACTGCCA 58.205 55.000 0.00 0.00 35.28 4.92
836 862 2.334023 GGATCTCTCCCTAACTGCCAT 58.666 52.381 0.00 0.00 35.28 4.40
837 863 3.511477 GGATCTCTCCCTAACTGCCATA 58.489 50.000 0.00 0.00 35.28 2.74
838 864 3.513515 GGATCTCTCCCTAACTGCCATAG 59.486 52.174 0.00 0.00 35.28 2.23
839 865 2.320781 TCTCTCCCTAACTGCCATAGC 58.679 52.381 0.00 0.00 40.48 2.97
840 866 2.091055 TCTCTCCCTAACTGCCATAGCT 60.091 50.000 0.00 0.00 40.80 3.32
841 867 2.703007 CTCTCCCTAACTGCCATAGCTT 59.297 50.000 0.00 0.00 40.80 3.74
842 868 3.115390 TCTCCCTAACTGCCATAGCTTT 58.885 45.455 0.00 0.00 40.80 3.51
843 869 3.523564 TCTCCCTAACTGCCATAGCTTTT 59.476 43.478 0.00 0.00 40.80 2.27
844 870 3.879892 CTCCCTAACTGCCATAGCTTTTC 59.120 47.826 0.00 0.00 40.80 2.29
845 871 2.952310 CCCTAACTGCCATAGCTTTTCC 59.048 50.000 0.00 0.00 40.80 3.13
846 872 2.614057 CCTAACTGCCATAGCTTTTCCG 59.386 50.000 0.00 0.00 40.80 4.30
880 2202 3.584848 AGGGGTTAATGCATAGCTAGAGG 59.415 47.826 0.00 0.00 0.00 3.69
922 2246 6.459923 TCATTTGGCAAACTAATTAACACCC 58.540 36.000 16.00 0.00 0.00 4.61
926 2250 3.498082 GCAAACTAATTAACACCCAGCG 58.502 45.455 0.00 0.00 0.00 5.18
929 2253 3.899052 ACTAATTAACACCCAGCGCTA 57.101 42.857 10.99 0.00 0.00 4.26
930 2254 3.528532 ACTAATTAACACCCAGCGCTAC 58.471 45.455 10.99 0.00 0.00 3.58
931 2255 2.483014 AATTAACACCCAGCGCTACA 57.517 45.000 10.99 0.00 0.00 2.74
932 2256 1.734163 ATTAACACCCAGCGCTACAC 58.266 50.000 10.99 0.00 0.00 2.90
934 2258 1.548081 TAACACCCAGCGCTACACTA 58.452 50.000 10.99 0.00 0.00 2.74
935 2259 0.246635 AACACCCAGCGCTACACTAG 59.753 55.000 10.99 0.32 0.00 2.57
936 2260 1.141881 CACCCAGCGCTACACTAGG 59.858 63.158 10.99 5.79 0.00 3.02
937 2261 2.058595 ACCCAGCGCTACACTAGGG 61.059 63.158 22.97 22.97 42.07 3.53
938 2262 2.058595 CCCAGCGCTACACTAGGGT 61.059 63.158 17.89 1.68 40.50 4.34
943 2268 0.664224 GCGCTACACTAGGGTCTCTC 59.336 60.000 0.00 0.00 40.50 3.20
959 2284 4.142271 GGTCTCTCTGATTGATCGAACAGT 60.142 45.833 17.25 0.00 0.00 3.55
969 2294 2.685388 TGATCGAACAGTGGAGAGCTAG 59.315 50.000 0.00 0.00 0.00 3.42
1011 2336 5.089434 AGCTTTCTTTCAATGGGGAAGATT 58.911 37.500 0.00 0.00 0.00 2.40
1020 2345 0.181114 TGGGGAAGATTGGAGCATCG 59.819 55.000 0.00 0.00 34.37 3.84
1032 2357 1.757731 AGCATCGCTCTCCTCTGCT 60.758 57.895 0.00 0.00 38.30 4.24
1053 2390 2.186903 GCCAAGGCGCTACTGCTA 59.813 61.111 7.64 0.00 36.97 3.49
1146 2485 4.008933 GCCGGTGGTCACAGCTCT 62.009 66.667 1.90 0.00 42.79 4.09
1152 2491 1.065854 GGTGGTCACAGCTCTAGCATT 60.066 52.381 4.54 0.00 45.16 3.56
1444 2783 0.942410 GTACAAGAACGCCGTGCTCA 60.942 55.000 0.00 0.00 0.00 4.26
1579 2918 2.178890 CGCTACGTCTACGCCCTCT 61.179 63.158 1.74 0.00 44.43 3.69
1755 3109 1.301401 CGTGTTCACGTCCATGGGT 60.301 57.895 13.02 0.00 0.00 4.51
1791 3145 0.468400 GCATCTCCGACTACCTCCCT 60.468 60.000 0.00 0.00 0.00 4.20
1828 3188 2.282958 TCGACGGCCAGGAGAAGT 60.283 61.111 2.24 0.00 0.00 3.01
1908 3268 2.526873 AGGCAGTGGAAGTCCGGT 60.527 61.111 0.00 0.00 39.43 5.28
2054 3506 2.500369 GCGCACGTCAAGCATGTG 60.500 61.111 0.30 0.00 44.05 3.21
2136 3601 0.732571 AGGACATAACATTTGCGGCG 59.267 50.000 0.51 0.51 0.00 6.46
2203 5297 0.745845 GAATGCGCCAGAGGTGATGT 60.746 55.000 4.18 0.00 34.74 3.06
2204 5298 0.322816 AATGCGCCAGAGGTGATGTT 60.323 50.000 4.18 0.00 34.74 2.71
2228 5322 1.402896 GCGATGGAGGAGATGGACCA 61.403 60.000 0.00 0.00 36.83 4.02
2340 5434 0.391927 CGGTCGCCCCTTTCAATGTA 60.392 55.000 0.00 0.00 0.00 2.29
2363 5462 0.464373 CATGTTGCCCTAGCCGACAT 60.464 55.000 8.09 8.09 42.26 3.06
2407 5506 1.452651 AAGGGCAGCCACATCATCG 60.453 57.895 15.19 0.00 0.00 3.84
2481 5580 0.745486 TCAATCCAGAGCGCCACATG 60.745 55.000 2.29 0.00 0.00 3.21
2485 5584 0.035152 TCCAGAGCGCCACATGAATT 60.035 50.000 2.29 0.00 0.00 2.17
2674 5773 2.897436 CCATTGATCTCAGCGAGTCAA 58.103 47.619 16.82 16.82 35.74 3.18
2746 5845 0.676184 GCCGATGCATCTCTACTCCA 59.324 55.000 23.73 0.00 37.47 3.86
2752 5851 1.195115 GCATCTCTACTCCACCACCA 58.805 55.000 0.00 0.00 0.00 4.17
2774 5873 6.841229 ACCAACATCTAATAGATCTCTGGTCA 59.159 38.462 16.08 0.00 35.01 4.02
2778 5877 6.434028 ACATCTAATAGATCTCTGGTCAGCTC 59.566 42.308 0.00 0.00 31.32 4.09
2826 5925 8.821686 ATTATGACAAATAACCAGTTCCATCA 57.178 30.769 0.00 0.00 0.00 3.07
2828 5927 6.968263 TGACAAATAACCAGTTCCATCAAA 57.032 33.333 0.00 0.00 0.00 2.69
2880 5979 9.965824 CTTTACATGGTGTAACAATTCTTCTTT 57.034 29.630 0.00 0.00 41.97 2.52
2882 5981 9.743057 TTACATGGTGTAACAATTCTTCTTTTG 57.257 29.630 0.00 0.00 37.86 2.44
2903 6002 9.437045 CTTTTGAATTGGTTAATTTCTGTTTGC 57.563 29.630 0.00 0.00 36.66 3.68
2907 6006 4.902443 TGGTTAATTTCTGTTTGCGTGA 57.098 36.364 0.00 0.00 0.00 4.35
2915 6014 2.351455 TCTGTTTGCGTGAAAGTGTGA 58.649 42.857 0.00 0.00 0.00 3.58
2918 6017 1.021202 TTTGCGTGAAAGTGTGAGGG 58.979 50.000 0.00 0.00 0.00 4.30
2919 6018 0.817634 TTGCGTGAAAGTGTGAGGGG 60.818 55.000 0.00 0.00 0.00 4.79
2920 6019 1.966451 GCGTGAAAGTGTGAGGGGG 60.966 63.158 0.00 0.00 0.00 5.40
2921 6020 1.966451 CGTGAAAGTGTGAGGGGGC 60.966 63.158 0.00 0.00 0.00 5.80
2922 6021 1.150536 GTGAAAGTGTGAGGGGGCA 59.849 57.895 0.00 0.00 0.00 5.36
2923 6022 0.467290 GTGAAAGTGTGAGGGGGCAA 60.467 55.000 0.00 0.00 0.00 4.52
2924 6023 0.260230 TGAAAGTGTGAGGGGGCAAA 59.740 50.000 0.00 0.00 0.00 3.68
2925 6024 0.961753 GAAAGTGTGAGGGGGCAAAG 59.038 55.000 0.00 0.00 0.00 2.77
2926 6025 0.261696 AAAGTGTGAGGGGGCAAAGT 59.738 50.000 0.00 0.00 0.00 2.66
2927 6026 1.145571 AAGTGTGAGGGGGCAAAGTA 58.854 50.000 0.00 0.00 0.00 2.24
2928 6027 1.372501 AGTGTGAGGGGGCAAAGTAT 58.627 50.000 0.00 0.00 0.00 2.12
2929 6028 1.004745 AGTGTGAGGGGGCAAAGTATG 59.995 52.381 0.00 0.00 0.00 2.39
2930 6029 1.004277 GTGTGAGGGGGCAAAGTATGA 59.996 52.381 0.00 0.00 0.00 2.15
2931 6030 1.707989 TGTGAGGGGGCAAAGTATGAA 59.292 47.619 0.00 0.00 0.00 2.57
2932 6031 2.290896 TGTGAGGGGGCAAAGTATGAAG 60.291 50.000 0.00 0.00 0.00 3.02
2933 6032 1.992557 TGAGGGGGCAAAGTATGAAGT 59.007 47.619 0.00 0.00 0.00 3.01
2934 6033 3.054655 GTGAGGGGGCAAAGTATGAAGTA 60.055 47.826 0.00 0.00 0.00 2.24
2935 6034 3.054655 TGAGGGGGCAAAGTATGAAGTAC 60.055 47.826 0.00 0.00 0.00 2.73
2936 6035 3.190439 AGGGGGCAAAGTATGAAGTACT 58.810 45.455 0.00 0.00 45.56 2.73
2947 6046 6.448207 AGTATGAAGTACTTCCTCCGTTAC 57.552 41.667 28.43 19.14 40.80 2.50
2948 6047 6.186234 AGTATGAAGTACTTCCTCCGTTACT 58.814 40.000 28.43 20.54 40.80 2.24
2949 6048 7.341805 AGTATGAAGTACTTCCTCCGTTACTA 58.658 38.462 28.43 9.77 40.80 1.82
2950 6049 7.831193 AGTATGAAGTACTTCCTCCGTTACTAA 59.169 37.037 28.43 9.30 40.80 2.24
2951 6050 6.506500 TGAAGTACTTCCTCCGTTACTAAG 57.493 41.667 28.43 0.00 38.77 2.18
2952 6051 6.006449 TGAAGTACTTCCTCCGTTACTAAGT 58.994 40.000 28.43 0.00 38.77 2.24
2953 6052 7.168219 TGAAGTACTTCCTCCGTTACTAAGTA 58.832 38.462 28.43 5.28 38.77 2.24
2954 6053 7.831193 TGAAGTACTTCCTCCGTTACTAAGTAT 59.169 37.037 28.43 0.00 38.77 2.12
2955 6054 9.331282 GAAGTACTTCCTCCGTTACTAAGTATA 57.669 37.037 22.74 0.00 35.69 1.47
2956 6055 9.686683 AAGTACTTCCTCCGTTACTAAGTATAA 57.313 33.333 1.12 0.00 35.69 0.98
2957 6056 9.336171 AGTACTTCCTCCGTTACTAAGTATAAG 57.664 37.037 0.00 0.00 35.69 1.73
2958 6057 9.114952 GTACTTCCTCCGTTACTAAGTATAAGT 57.885 37.037 0.00 0.00 35.69 2.24
2960 6059 9.859152 ACTTCCTCCGTTACTAAGTATAAGTAT 57.141 33.333 0.00 0.00 29.86 2.12
3003 6102 8.557592 TGAATTACATACGGACGTATCTCTAT 57.442 34.615 13.86 4.11 39.07 1.98
3053 6152 6.528537 TCGTTAAGTACACCAAGCCTAATA 57.471 37.500 0.00 0.00 0.00 0.98
3082 6190 6.205784 CAAAACAACACAGACCAATACGATT 58.794 36.000 0.00 0.00 0.00 3.34
3131 6239 8.413229 GCATTAAGATTTTATTAACCTCAGCCA 58.587 33.333 0.00 0.00 0.00 4.75
3178 6286 0.511653 GGACGAAAACTCTGCCGAAC 59.488 55.000 0.00 0.00 0.00 3.95
3247 6357 7.606456 TCGCTTCCCTGATAATAATCCATTAAC 59.394 37.037 0.00 0.00 32.84 2.01
3304 6414 0.899720 TAAACGCATCTCCCCGACTT 59.100 50.000 0.00 0.00 0.00 3.01
3358 6468 4.724697 CTCGCTTGCACAACGCCG 62.725 66.667 0.00 0.00 41.33 6.46
3382 6492 3.710722 CCAGCGCAACCTCCCTCT 61.711 66.667 11.47 0.00 0.00 3.69
3386 6496 3.764466 CGCAACCTCCCTCTCGCT 61.764 66.667 0.00 0.00 0.00 4.93
3469 6585 2.897972 GTCCGCCTTACCATCGGT 59.102 61.111 0.00 0.00 43.35 4.69
3496 6612 2.203640 ACCGTCTCTCCTGTGGCA 60.204 61.111 0.00 0.00 0.00 4.92
3535 6651 4.699522 GTCCCCCACACAGCCGAC 62.700 72.222 0.00 0.00 0.00 4.79
3556 6672 1.677966 CGACTCCTCCGTCCTCCAA 60.678 63.158 0.00 0.00 0.00 3.53
3611 6727 1.187087 ACGTAGAAGCTCCTCCCTTG 58.813 55.000 0.00 0.00 0.00 3.61
3617 6733 1.846712 AAGCTCCTCCCTTGGCAGAC 61.847 60.000 0.00 0.00 0.00 3.51
3633 6749 1.372997 GACGCGTTCTTCCTCTGCA 60.373 57.895 15.53 0.00 0.00 4.41
3662 6778 2.117941 GAACAGTTCGTGCACCCAGC 62.118 60.000 12.15 0.00 45.96 4.85
3707 6828 3.997681 GGTAAGAACTGCTTCCTTGAGTC 59.002 47.826 0.00 0.00 38.05 3.36
3748 6869 3.991367 ACGAGGTTCTTGTTTCCTACTG 58.009 45.455 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 6.350906 CCCCGGTAACTTTTATGTGAATAGA 58.649 40.000 0.00 0.00 0.00 1.98
103 104 7.817478 TGATAACATACACACAACAGACCTAAG 59.183 37.037 0.00 0.00 0.00 2.18
139 140 9.189723 GTTAAAACACACTCGATAACTTCTACT 57.810 33.333 0.00 0.00 0.00 2.57
226 229 7.351981 GCACGAAAATAGCATGATAACATACA 58.648 34.615 0.00 0.00 35.09 2.29
334 337 7.201661 GCCGGTAATTTCTGTACAAATATCACA 60.202 37.037 1.90 0.00 0.00 3.58
344 347 2.352388 TGCTGCCGGTAATTTCTGTAC 58.648 47.619 1.90 0.00 0.00 2.90
402 426 7.011950 TGGATATGTATTTGTTCCAACTAAGCG 59.988 37.037 0.00 0.00 33.66 4.68
404 428 9.396022 AGTGGATATGTATTTGTTCCAACTAAG 57.604 33.333 0.00 0.00 38.16 2.18
441 465 8.511748 AATCCTATCCATACAAGACTACCAAT 57.488 34.615 0.00 0.00 0.00 3.16
463 488 5.126222 GGAATCAAACTCTTCCCCTCAAATC 59.874 44.000 0.00 0.00 35.83 2.17
466 491 3.657727 AGGAATCAAACTCTTCCCCTCAA 59.342 43.478 0.00 0.00 41.59 3.02
467 492 3.260205 AGGAATCAAACTCTTCCCCTCA 58.740 45.455 0.00 0.00 41.59 3.86
473 499 6.254589 CGTGTCATAGAGGAATCAAACTCTTC 59.745 42.308 0.00 0.00 41.05 2.87
481 507 1.536072 GCGCGTGTCATAGAGGAATCA 60.536 52.381 8.43 0.00 0.00 2.57
531 557 8.050325 TCCTAATTAGTACTGCCATTTAAAGCA 58.950 33.333 11.50 2.55 37.46 3.91
582 608 7.707464 TCATTAGCACGATTTAATTCTTCCGTA 59.293 33.333 0.00 0.00 0.00 4.02
583 609 6.537301 TCATTAGCACGATTTAATTCTTCCGT 59.463 34.615 0.00 0.00 0.00 4.69
584 610 6.943981 TCATTAGCACGATTTAATTCTTCCG 58.056 36.000 0.00 0.00 0.00 4.30
585 611 9.173939 CATTCATTAGCACGATTTAATTCTTCC 57.826 33.333 0.00 0.00 0.00 3.46
586 612 9.173939 CCATTCATTAGCACGATTTAATTCTTC 57.826 33.333 0.00 0.00 0.00 2.87
587 613 8.686334 ACCATTCATTAGCACGATTTAATTCTT 58.314 29.630 0.00 0.00 0.00 2.52
588 614 8.225603 ACCATTCATTAGCACGATTTAATTCT 57.774 30.769 0.00 0.00 0.00 2.40
589 615 9.944663 TTACCATTCATTAGCACGATTTAATTC 57.055 29.630 0.00 0.00 0.00 2.17
590 616 9.950680 CTTACCATTCATTAGCACGATTTAATT 57.049 29.630 0.00 0.00 0.00 1.40
715 741 8.410141 CCTTAATTAGCGGGATTTAATTGTTCA 58.590 33.333 0.00 0.00 33.06 3.18
765 791 2.470286 CGGTCTCGCGCAAGTTTC 59.530 61.111 8.75 0.00 41.68 2.78
808 834 1.611519 AGGGAGAGATCCGAACGATC 58.388 55.000 0.00 0.00 46.86 3.69
814 840 1.693627 GCAGTTAGGGAGAGATCCGA 58.306 55.000 0.00 0.00 0.00 4.55
825 851 2.614057 CGGAAAAGCTATGGCAGTTAGG 59.386 50.000 3.10 0.00 41.70 2.69
833 859 7.730364 ATTTATAGTGTCGGAAAAGCTATGG 57.270 36.000 0.00 0.00 0.00 2.74
834 860 8.926710 CCTATTTATAGTGTCGGAAAAGCTATG 58.073 37.037 0.00 0.00 0.00 2.23
835 861 8.095169 CCCTATTTATAGTGTCGGAAAAGCTAT 58.905 37.037 0.00 0.00 0.00 2.97
836 862 7.439381 CCCTATTTATAGTGTCGGAAAAGCTA 58.561 38.462 0.00 0.00 0.00 3.32
837 863 6.289064 CCCTATTTATAGTGTCGGAAAAGCT 58.711 40.000 0.00 0.00 0.00 3.74
838 864 5.469084 CCCCTATTTATAGTGTCGGAAAAGC 59.531 44.000 0.00 0.00 0.00 3.51
839 865 6.589135 ACCCCTATTTATAGTGTCGGAAAAG 58.411 40.000 0.00 0.00 0.00 2.27
840 866 6.564557 ACCCCTATTTATAGTGTCGGAAAA 57.435 37.500 0.00 0.00 0.00 2.29
841 867 6.564557 AACCCCTATTTATAGTGTCGGAAA 57.435 37.500 0.00 0.00 0.00 3.13
842 868 7.673641 TTAACCCCTATTTATAGTGTCGGAA 57.326 36.000 0.00 0.00 0.00 4.30
843 869 7.673180 CATTAACCCCTATTTATAGTGTCGGA 58.327 38.462 0.00 0.00 0.00 4.55
844 870 6.370718 GCATTAACCCCTATTTATAGTGTCGG 59.629 42.308 0.00 0.00 0.00 4.79
845 871 6.932400 TGCATTAACCCCTATTTATAGTGTCG 59.068 38.462 0.00 0.00 0.00 4.35
846 872 8.863872 ATGCATTAACCCCTATTTATAGTGTC 57.136 34.615 0.00 0.00 0.00 3.67
880 2202 0.742635 GAGGCTAGCTTGGTGTGCTC 60.743 60.000 15.72 6.15 41.46 4.26
919 2243 2.058595 CCCTAGTGTAGCGCTGGGT 61.059 63.158 22.90 4.26 40.31 4.51
922 2246 0.382515 GAGACCCTAGTGTAGCGCTG 59.617 60.000 22.90 2.27 0.00 5.18
926 2250 3.284793 TCAGAGAGACCCTAGTGTAGC 57.715 52.381 0.00 0.00 0.00 3.58
929 2253 4.323569 TCAATCAGAGAGACCCTAGTGT 57.676 45.455 0.00 0.00 0.00 3.55
930 2254 4.023279 CGATCAATCAGAGAGACCCTAGTG 60.023 50.000 0.00 0.00 0.00 2.74
931 2255 4.141287 CGATCAATCAGAGAGACCCTAGT 58.859 47.826 0.00 0.00 0.00 2.57
932 2256 4.393834 TCGATCAATCAGAGAGACCCTAG 58.606 47.826 0.00 0.00 0.00 3.02
934 2258 3.304911 TCGATCAATCAGAGAGACCCT 57.695 47.619 0.00 0.00 0.00 4.34
935 2259 3.131223 TGTTCGATCAATCAGAGAGACCC 59.869 47.826 0.00 0.00 0.00 4.46
936 2260 4.142271 ACTGTTCGATCAATCAGAGAGACC 60.142 45.833 12.73 0.00 0.00 3.85
937 2261 4.797868 CACTGTTCGATCAATCAGAGAGAC 59.202 45.833 12.73 0.00 0.00 3.36
938 2262 4.142293 CCACTGTTCGATCAATCAGAGAGA 60.142 45.833 12.73 0.00 0.00 3.10
943 2268 4.111198 CTCTCCACTGTTCGATCAATCAG 58.889 47.826 0.00 0.14 0.00 2.90
982 2307 4.578105 CCCCATTGAAAGAAAGCTAGCTAG 59.422 45.833 19.70 16.84 0.00 3.42
983 2308 4.227300 TCCCCATTGAAAGAAAGCTAGCTA 59.773 41.667 19.70 0.00 0.00 3.32
984 2309 3.010584 TCCCCATTGAAAGAAAGCTAGCT 59.989 43.478 12.68 12.68 0.00 3.32
985 2310 3.356290 TCCCCATTGAAAGAAAGCTAGC 58.644 45.455 6.62 6.62 0.00 3.42
986 2311 5.256474 TCTTCCCCATTGAAAGAAAGCTAG 58.744 41.667 0.00 0.00 0.00 3.42
987 2312 5.255397 TCTTCCCCATTGAAAGAAAGCTA 57.745 39.130 0.00 0.00 0.00 3.32
988 2313 4.118168 TCTTCCCCATTGAAAGAAAGCT 57.882 40.909 0.00 0.00 0.00 3.74
989 2314 5.173664 CAATCTTCCCCATTGAAAGAAAGC 58.826 41.667 0.00 0.00 33.69 3.51
990 2315 5.481473 TCCAATCTTCCCCATTGAAAGAAAG 59.519 40.000 0.00 0.00 33.69 2.62
991 2316 5.401750 TCCAATCTTCCCCATTGAAAGAAA 58.598 37.500 0.00 0.00 33.69 2.52
992 2317 5.009436 TCCAATCTTCCCCATTGAAAGAA 57.991 39.130 0.00 0.00 33.69 2.52
993 2318 4.603131 CTCCAATCTTCCCCATTGAAAGA 58.397 43.478 0.00 0.00 33.69 2.52
994 2319 3.131755 GCTCCAATCTTCCCCATTGAAAG 59.868 47.826 0.00 0.00 33.69 2.62
1020 2345 2.512057 GCAGCAGCAGAGGAGAGC 60.512 66.667 0.00 0.00 41.58 4.09
1032 2357 4.020617 AGTAGCGCCTTGGCAGCA 62.021 61.111 22.59 11.29 34.64 4.41
1053 2390 1.912043 AGGTTGATGAAGGCTAGCACT 59.088 47.619 18.24 8.50 0.00 4.40
1139 2478 5.878406 ACCATTAGTAATGCTAGAGCTGT 57.122 39.130 16.17 4.71 42.66 4.40
1146 2485 4.557296 GCCGACGTACCATTAGTAATGCTA 60.557 45.833 16.17 5.69 37.57 3.49
1152 2491 0.662619 CCGCCGACGTACCATTAGTA 59.337 55.000 0.00 0.00 37.70 1.82
1221 2560 2.743664 CGGCTTGTTGAACATCATCTCA 59.256 45.455 0.00 0.00 0.00 3.27
1674 3025 1.511305 CTGAGGCTCGCCGAAGTAA 59.489 57.895 10.42 0.00 41.95 2.24
1755 3109 3.217242 GCAGAACGCAAAGAGGAGA 57.783 52.632 0.00 0.00 41.79 3.71
1828 3188 1.452145 GCGTTTGCCTCCTTGACCAA 61.452 55.000 0.00 0.00 33.98 3.67
1908 3268 1.077357 GTCGAGCTCCCTCCTCTCA 60.077 63.158 8.47 0.00 34.49 3.27
2156 5250 4.263572 CCAACGCCCACTCCACCA 62.264 66.667 0.00 0.00 0.00 4.17
2203 5297 1.139654 CATCTCCTCCATCGCCTTCAA 59.860 52.381 0.00 0.00 0.00 2.69
2204 5298 0.755079 CATCTCCTCCATCGCCTTCA 59.245 55.000 0.00 0.00 0.00 3.02
2272 5366 4.392047 CATGCCTTGGCATAGTTGAGATA 58.608 43.478 24.53 0.00 0.00 1.98
2340 5434 1.000896 GGCTAGGGCAACATGTGGT 60.001 57.895 0.00 0.00 40.87 4.16
2363 5462 2.652530 GGTAACCGGCGACTGTGA 59.347 61.111 9.30 0.00 0.00 3.58
2452 5551 0.742281 TCTGGATTGAAGCAGAGCGC 60.742 55.000 0.00 0.00 42.91 5.92
2466 5565 0.035152 AATTCATGTGGCGCTCTGGA 60.035 50.000 7.64 0.00 0.00 3.86
2481 5580 1.227060 GCCGCCATCAGCCAAATTC 60.227 57.895 0.00 0.00 38.78 2.17
2517 5616 1.798813 GAGATGAACCGCAACTCGTTT 59.201 47.619 0.00 0.00 36.80 3.60
2746 5845 6.042552 CCAGAGATCTATTAGATGTTGGTGGT 59.957 42.308 10.93 0.00 34.53 4.16
2752 5851 6.782000 AGCTGACCAGAGATCTATTAGATGTT 59.218 38.462 10.93 0.00 34.53 2.71
2801 5900 8.821686 TGATGGAACTGGTTATTTGTCATAAT 57.178 30.769 0.00 0.00 0.00 1.28
2806 5905 7.433680 ACTTTTGATGGAACTGGTTATTTGTC 58.566 34.615 0.00 0.00 0.00 3.18
2826 5925 6.590068 AGAGCTCATGCATGACTATACTTTT 58.410 36.000 25.42 7.79 42.74 2.27
2828 5927 5.804944 AGAGCTCATGCATGACTATACTT 57.195 39.130 25.42 5.98 42.74 2.24
2856 5955 9.743057 CAAAAGAAGAATTGTTACACCATGTAA 57.257 29.630 0.00 0.00 40.21 2.41
2880 5979 6.758886 ACGCAAACAGAAATTAACCAATTCAA 59.241 30.769 0.00 0.00 33.09 2.69
2882 5981 6.419413 TCACGCAAACAGAAATTAACCAATTC 59.581 34.615 0.00 0.00 33.09 2.17
2903 6002 1.966451 GCCCCCTCACACTTTCACG 60.966 63.158 0.00 0.00 0.00 4.35
2907 6006 0.261696 ACTTTGCCCCCTCACACTTT 59.738 50.000 0.00 0.00 0.00 2.66
2915 6014 3.190439 AGTACTTCATACTTTGCCCCCT 58.810 45.455 0.00 0.00 41.71 4.79
2924 6023 6.186234 AGTAACGGAGGAAGTACTTCATACT 58.814 40.000 31.30 22.29 46.75 2.12
2925 6024 6.448207 AGTAACGGAGGAAGTACTTCATAC 57.552 41.667 31.30 26.06 41.20 2.39
2926 6025 7.831193 ACTTAGTAACGGAGGAAGTACTTCATA 59.169 37.037 31.30 11.15 41.20 2.15
2927 6026 6.662663 ACTTAGTAACGGAGGAAGTACTTCAT 59.337 38.462 31.30 27.09 41.20 2.57
2928 6027 6.006449 ACTTAGTAACGGAGGAAGTACTTCA 58.994 40.000 31.30 11.05 41.20 3.02
2929 6028 6.507958 ACTTAGTAACGGAGGAAGTACTTC 57.492 41.667 24.73 24.73 38.80 3.01
2930 6029 9.686683 TTATACTTAGTAACGGAGGAAGTACTT 57.313 33.333 8.13 8.13 35.91 2.24
2931 6030 9.336171 CTTATACTTAGTAACGGAGGAAGTACT 57.664 37.037 0.00 0.00 35.91 2.73
2932 6031 9.114952 ACTTATACTTAGTAACGGAGGAAGTAC 57.885 37.037 0.00 0.00 35.91 2.73
2934 6033 9.859152 ATACTTATACTTAGTAACGGAGGAAGT 57.141 33.333 0.00 1.64 32.28 3.01
2969 6068 9.268268 ACGTCCGTATGTAATTCATATTGAAAT 57.732 29.630 0.00 0.00 40.12 2.17
2970 6069 8.651391 ACGTCCGTATGTAATTCATATTGAAA 57.349 30.769 0.00 0.00 40.12 2.69
2971 6070 9.917129 ATACGTCCGTATGTAATTCATATTGAA 57.083 29.630 11.25 0.00 40.54 2.69
2972 6071 9.563898 GATACGTCCGTATGTAATTCATATTGA 57.436 33.333 16.33 0.00 40.93 2.57
2973 6072 9.569167 AGATACGTCCGTATGTAATTCATATTG 57.431 33.333 16.33 0.00 40.93 1.90
2974 6073 9.784680 GAGATACGTCCGTATGTAATTCATATT 57.215 33.333 16.33 0.00 40.93 1.28
2975 6074 9.175312 AGAGATACGTCCGTATGTAATTCATAT 57.825 33.333 16.33 0.00 40.93 1.78
2976 6075 8.557592 AGAGATACGTCCGTATGTAATTCATA 57.442 34.615 16.33 0.00 40.93 2.15
2977 6076 7.450124 AGAGATACGTCCGTATGTAATTCAT 57.550 36.000 16.33 0.00 40.93 2.57
2978 6077 6.872628 AGAGATACGTCCGTATGTAATTCA 57.127 37.500 16.33 0.00 40.93 2.57
2981 6080 9.664332 ACTAATAGAGATACGTCCGTATGTAAT 57.336 33.333 16.33 7.53 40.93 1.89
2984 6083 9.664332 AATACTAATAGAGATACGTCCGTATGT 57.336 33.333 16.33 12.60 40.93 2.29
3028 6127 6.528537 TTAGGCTTGGTGTACTTAACGATA 57.471 37.500 0.00 0.00 0.00 2.92
3039 6138 3.830744 TGCGTATATTAGGCTTGGTGT 57.169 42.857 0.00 0.00 40.06 4.16
3044 6143 6.072397 TGTGTTGTTTTGCGTATATTAGGCTT 60.072 34.615 0.00 0.00 40.06 4.35
3053 6152 2.946329 TGGTCTGTGTTGTTTTGCGTAT 59.054 40.909 0.00 0.00 0.00 3.06
3105 6213 8.413229 TGGCTGAGGTTAATAAAATCTTAATGC 58.587 33.333 0.00 0.00 0.00 3.56
3131 6239 5.464057 GGGCAAATTGCTAAACGTACTTTTT 59.536 36.000 18.04 0.00 44.28 1.94
3211 6319 1.334869 CAGGGAAGCGATGTATTTGGC 59.665 52.381 0.00 0.00 0.00 4.52
3247 6357 5.160641 CACTAAACACGGAATCAATTTGGG 58.839 41.667 0.00 0.00 0.00 4.12
3304 6414 1.005748 GAGATGGATGCCGATGCGA 60.006 57.895 0.00 0.00 41.78 5.10
3402 6512 2.280186 GGATAGCCGGACAAGCGG 60.280 66.667 5.05 0.00 34.64 5.52
3413 6523 3.264897 CGTGCGCCACAGGATAGC 61.265 66.667 4.18 0.00 36.20 2.97
3556 6672 2.517402 TCTTTGTTGCCGGCCGTT 60.517 55.556 26.77 0.00 0.00 4.44
3564 6680 0.654472 CGTCGTGCAGTCTTTGTTGC 60.654 55.000 0.00 0.00 40.67 4.17
3587 6703 1.544691 GGAGGAGCTTCTACGTTGTCA 59.455 52.381 0.00 0.00 0.00 3.58
3617 6733 2.383527 GGTGCAGAGGAAGAACGCG 61.384 63.158 3.53 3.53 0.00 6.01
3707 6828 0.599558 TGTAGGACGGACCGAAAGTG 59.400 55.000 23.38 0.00 44.74 3.16


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

AutoCloner maintained by Alex Coulton.