Multiple sequence alignment - TraesCS1A01G422700

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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 TraesCS1A01G422700 chr1A 100.000 5104 0 0 1 5104 578020942 578026045 0.000000e+00 9426.0
1 TraesCS1A01G422700 chr1A 76.108 812 164 25 2414 3206 578197795 578198595 1.030000e-106 398.0
2 TraesCS1A01G422700 chr1A 79.775 178 36 0 3300 3477 578198664 578198841 4.150000e-26 130.0
3 TraesCS1A01G422700 chr1D 95.654 3129 112 9 1983 5104 481564976 481568087 0.000000e+00 5003.0
4 TraesCS1A01G422700 chr1D 91.755 1989 126 20 1983 3938 481475277 481473294 0.000000e+00 2730.0
5 TraesCS1A01G422700 chr1D 91.257 1098 74 8 881 1968 481476521 481475436 0.000000e+00 1476.0
6 TraesCS1A01G422700 chr1D 91.257 1098 74 8 881 1968 481563732 481564817 0.000000e+00 1476.0
7 TraesCS1A01G422700 chr1D 83.886 844 84 38 2 814 481477545 481476723 0.000000e+00 758.0
8 TraesCS1A01G422700 chr1D 83.886 844 84 38 2 814 481562708 481563530 0.000000e+00 758.0
9 TraesCS1A01G422700 chr1D 74.654 1085 209 49 2417 3478 481465551 481464510 2.200000e-113 420.0
10 TraesCS1A01G422700 chr1D 76.107 745 136 32 1069 1780 481466831 481466096 8.130000e-93 351.0
11 TraesCS1A01G422700 chr1D 94.203 138 6 2 856 991 481476717 481476580 5.180000e-50 209.0
12 TraesCS1A01G422700 chr1D 94.203 138 6 2 856 991 481563536 481563673 5.180000e-50 209.0
13 TraesCS1A01G422700 chr1B 90.915 1585 128 10 1976 3553 670026515 670028090 0.000000e+00 2115.0
14 TraesCS1A01G422700 chr1B 91.730 1439 113 6 2120 3554 670172372 670170936 0.000000e+00 1993.0
15 TraesCS1A01G422700 chr1B 91.678 1442 110 8 2119 3554 670183218 670181781 0.000000e+00 1989.0
16 TraesCS1A01G422700 chr1B 90.881 1294 85 19 857 2142 670184647 670183379 0.000000e+00 1705.0
17 TraesCS1A01G422700 chr1B 91.362 984 69 8 978 1955 670025352 670026325 0.000000e+00 1332.0
18 TraesCS1A01G422700 chr1B 91.766 838 56 9 1314 2142 670173364 670172531 0.000000e+00 1153.0
19 TraesCS1A01G422700 chr1B 88.273 469 35 10 857 1325 670179020 670178572 1.250000e-150 544.0
20 TraesCS1A01G422700 chr1B 89.870 385 39 0 3554 3938 670170909 670170525 3.550000e-136 496.0
21 TraesCS1A01G422700 chr1B 87.597 387 43 2 3554 3935 670028118 670028504 1.300000e-120 444.0
22 TraesCS1A01G422700 chr1B 89.877 326 33 0 3554 3879 670181754 670181429 2.200000e-113 420.0
23 TraesCS1A01G422700 chr1B 75.294 680 135 25 1113 1768 670167589 670166919 1.390000e-75 294.0
24 TraesCS1A01G422700 chr1B 78.571 336 59 10 1073 1397 670034323 670034656 5.180000e-50 209.0
25 TraesCS1A01G422700 chr1B 91.209 91 8 0 647 737 669952141 669952231 1.930000e-24 124.0
26 TraesCS1A01G422700 chr5B 87.200 125 8 3 352 475 664271313 664271430 8.910000e-28 135.0
27 TraesCS1A01G422700 chr5B 86.400 125 9 5 352 475 663333344 663333227 4.150000e-26 130.0
28 TraesCS1A01G422700 chr5B 85.714 126 9 4 351 475 62159204 62159321 1.930000e-24 124.0
29 TraesCS1A01G422700 chr5B 84.058 138 11 6 339 475 62178083 62178210 6.940000e-24 122.0
30 TraesCS1A01G422700 chr7B 92.308 52 3 1 4079 4130 124016793 124016743 7.090000e-09 73.1
31 TraesCS1A01G422700 chr7B 93.023 43 3 0 404 446 365462907 365462949 4.270000e-06 63.9
32 TraesCS1A01G422700 chr6B 93.023 43 3 0 404 446 628588385 628588427 4.270000e-06 63.9


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 TraesCS1A01G422700 chr1A 578020942 578026045 5103 False 9426.00 9426 100.00000 1 5104 1 chr1A.!!$F1 5103
1 TraesCS1A01G422700 chr1A 578197795 578198841 1046 False 264.00 398 77.94150 2414 3477 2 chr1A.!!$F2 1063
2 TraesCS1A01G422700 chr1D 481562708 481568087 5379 False 1861.50 5003 91.25000 2 5104 4 chr1D.!!$F1 5102
3 TraesCS1A01G422700 chr1D 481473294 481477545 4251 True 1293.25 2730 90.27525 2 3938 4 chr1D.!!$R2 3936
4 TraesCS1A01G422700 chr1D 481464510 481466831 2321 True 385.50 420 75.38050 1069 3478 2 chr1D.!!$R1 2409
5 TraesCS1A01G422700 chr1B 670025352 670028504 3152 False 1297.00 2115 89.95800 978 3935 3 chr1B.!!$F3 2957
6 TraesCS1A01G422700 chr1B 670178572 670184647 6075 True 1164.50 1989 90.17725 857 3879 4 chr1B.!!$R2 3022
7 TraesCS1A01G422700 chr1B 670166919 670173364 6445 True 984.00 1993 87.16500 1113 3938 4 chr1B.!!$R1 2825

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
993 1212 0.179215 CGTTCCAACATCTTGCTCGC 60.179 55.0 0.00 0.0 0.0 5.03 F
1042 1261 0.110147 GATATCTCACCGGCTCGTCG 60.110 60.0 0.00 0.0 0.0 5.12 F
2299 2913 0.466124 GAGAAGGAAGCGGCCACTAT 59.534 55.0 2.24 0.0 0.0 2.12 F
3525 4145 0.826062 TTACCACTTAGTAGGCCGCC 59.174 55.0 0.00 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1817 2066 0.040781 CAAAACCGTTGGTACCGCAG 60.041 55.0 7.57 0.13 33.12 5.18 R
2660 3279 0.245266 TCACTGCTATTTCGTCGCCA 59.755 50.0 0.00 0.00 0.00 5.69 R
3687 4342 0.030638 CCGCTCTCTGAGAAGCTAGC 59.969 60.0 6.62 6.62 0.00 3.42 R
4389 5393 1.388547 TTCCTGCTCGCTGTTTGTTT 58.611 45.0 0.00 0.00 0.00 2.83 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
111 114 8.757307 ATCTGGTAGAGGATATTTTATCCCAA 57.243 34.615 9.44 0.00 38.98 4.12
113 116 7.570982 TCTGGTAGAGGATATTTTATCCCAACA 59.429 37.037 9.44 4.62 38.98 3.33
140 143 7.936847 TGAAGCACTAACTAAAGAAAGAATCCA 59.063 33.333 0.00 0.00 0.00 3.41
143 146 8.103305 AGCACTAACTAAAGAAAGAATCCATGA 58.897 33.333 0.00 0.00 0.00 3.07
146 149 9.620259 ACTAACTAAAGAAAGAATCCATGATCC 57.380 33.333 0.00 0.00 0.00 3.36
147 150 9.844257 CTAACTAAAGAAAGAATCCATGATCCT 57.156 33.333 0.00 0.00 0.00 3.24
148 151 8.744568 AACTAAAGAAAGAATCCATGATCCTC 57.255 34.615 0.00 0.00 0.00 3.71
149 152 7.865820 ACTAAAGAAAGAATCCATGATCCTCA 58.134 34.615 0.00 0.00 0.00 3.86
150 153 8.331740 ACTAAAGAAAGAATCCATGATCCTCAA 58.668 33.333 0.00 0.00 0.00 3.02
151 154 9.182214 CTAAAGAAAGAATCCATGATCCTCAAA 57.818 33.333 0.00 0.00 0.00 2.69
152 155 8.426569 AAAGAAAGAATCCATGATCCTCAAAA 57.573 30.769 0.00 0.00 0.00 2.44
153 156 8.605325 AAGAAAGAATCCATGATCCTCAAAAT 57.395 30.769 0.00 0.00 0.00 1.82
154 157 9.705103 AAGAAAGAATCCATGATCCTCAAAATA 57.295 29.630 0.00 0.00 0.00 1.40
155 158 9.705103 AGAAAGAATCCATGATCCTCAAAATAA 57.295 29.630 0.00 0.00 0.00 1.40
217 241 5.277393 GGACTTTCTTTTTGTTCTCGGACTC 60.277 44.000 0.00 0.00 0.00 3.36
237 261 0.688087 TTTTGGTGGGGTGTTGGGAC 60.688 55.000 0.00 0.00 0.00 4.46
252 276 1.280457 GGGACTCTCACATGGGAGTT 58.720 55.000 24.11 12.80 42.06 3.01
257 281 1.808945 CTCTCACATGGGAGTTGTTGC 59.191 52.381 24.11 0.00 36.30 4.17
281 305 5.577945 CCTGCTGTATTTTGCAATACCAAAG 59.422 40.000 0.00 0.00 43.00 2.77
284 308 6.423302 TGCTGTATTTTGCAATACCAAAGTTG 59.577 34.615 0.00 0.00 43.00 3.16
291 315 5.720371 TGCAATACCAAAGTTGTGCTTAT 57.280 34.783 6.09 0.00 36.17 1.73
380 407 4.526970 AGGAGACATGTCAAACTGTTTGT 58.473 39.130 27.02 12.82 41.36 2.83
388 415 5.764487 TGTCAAACTGTTTGTGCATGATA 57.236 34.783 27.06 7.83 41.36 2.15
438 465 9.582223 GTAACGCTACATATTTTAAATCTCAGC 57.418 33.333 0.00 0.00 0.00 4.26
446 473 9.337396 ACATATTTTAAATCTCAGCCGTCAATA 57.663 29.630 0.00 0.00 0.00 1.90
447 474 9.817365 CATATTTTAAATCTCAGCCGTCAATAG 57.183 33.333 0.00 0.00 0.00 1.73
450 477 8.780846 TTTTAAATCTCAGCCGTCAATAGTTA 57.219 30.769 0.00 0.00 0.00 2.24
459 486 6.930164 TCAGCCGTCAATAGTTAAAACTAACA 59.070 34.615 6.66 0.00 44.03 2.41
493 535 8.995419 AATTTAACAACAACAACAACAACAAC 57.005 26.923 0.00 0.00 0.00 3.32
496 538 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
504 546 7.715265 ACAACAACAACAACAACAACAATAA 57.285 28.000 0.00 0.00 0.00 1.40
508 550 9.862371 AACAACAACAACAACAACAATAATAGA 57.138 25.926 0.00 0.00 0.00 1.98
584 627 3.722123 CATAAACTTTGACTCGACGCAC 58.278 45.455 0.00 0.00 0.00 5.34
585 628 0.575390 AAACTTTGACTCGACGCACG 59.425 50.000 0.00 0.00 44.09 5.34
586 629 0.526954 AACTTTGACTCGACGCACGT 60.527 50.000 0.00 0.00 43.13 4.49
603 659 2.558594 CGTACGTACGGTTTGGTTTG 57.441 50.000 34.54 7.76 45.30 2.93
604 660 1.397065 CGTACGTACGGTTTGGTTTGC 60.397 52.381 34.54 0.72 45.30 3.68
605 661 1.866601 GTACGTACGGTTTGGTTTGCT 59.133 47.619 21.06 0.00 0.00 3.91
606 662 1.381522 ACGTACGGTTTGGTTTGCTT 58.618 45.000 21.06 0.00 0.00 3.91
607 663 1.064357 ACGTACGGTTTGGTTTGCTTG 59.936 47.619 21.06 0.00 0.00 4.01
608 664 1.331138 CGTACGGTTTGGTTTGCTTGA 59.669 47.619 7.57 0.00 0.00 3.02
609 665 2.223294 CGTACGGTTTGGTTTGCTTGAA 60.223 45.455 7.57 0.00 0.00 2.69
610 666 2.577449 ACGGTTTGGTTTGCTTGAAG 57.423 45.000 0.00 0.00 0.00 3.02
611 667 1.208259 CGGTTTGGTTTGCTTGAAGC 58.792 50.000 10.84 10.84 42.82 3.86
623 679 1.200948 GCTTGAAGCATTCCACTCCAC 59.799 52.381 13.09 0.00 46.93 4.02
648 704 1.302366 TGCGGAATGATGAGTCATGC 58.698 50.000 11.20 7.13 44.20 4.06
715 771 3.252215 CCACCTTTTGCGACTACATTCAA 59.748 43.478 0.00 0.00 0.00 2.69
739 795 1.064825 ATGGAGAAGGTTCACCCGTT 58.935 50.000 4.02 0.00 37.16 4.44
758 814 5.215160 CCGTTCAGTTTTCTCCTTTCATTG 58.785 41.667 0.00 0.00 0.00 2.82
768 824 4.759782 TCTCCTTTCATTGACGGAAGATC 58.240 43.478 5.63 0.00 0.00 2.75
784 840 2.751671 GATCGCTACTCTCGCCGTCG 62.752 65.000 0.00 0.00 0.00 5.12
785 841 4.592936 CGCTACTCTCGCCGTCGG 62.593 72.222 6.99 6.99 36.13 4.79
795 851 4.094590 ACTCTCGCCGTCGGATAATATAAG 59.905 45.833 17.49 3.16 36.13 1.73
798 854 3.376234 TCGCCGTCGGATAATATAAGAGG 59.624 47.826 17.49 0.00 36.13 3.69
799 855 3.128242 CGCCGTCGGATAATATAAGAGGT 59.872 47.826 17.49 0.00 0.00 3.85
838 894 8.649973 AAACTAAAAGTACTTCTCAGTCACAG 57.350 34.615 8.95 0.00 34.06 3.66
839 895 6.750148 ACTAAAAGTACTTCTCAGTCACAGG 58.250 40.000 8.95 0.00 34.06 4.00
840 896 3.669251 AAGTACTTCTCAGTCACAGGC 57.331 47.619 1.12 0.00 34.06 4.85
841 897 1.542030 AGTACTTCTCAGTCACAGGCG 59.458 52.381 0.00 0.00 34.06 5.52
842 898 1.540267 GTACTTCTCAGTCACAGGCGA 59.460 52.381 0.00 0.00 34.06 5.54
843 899 1.261480 ACTTCTCAGTCACAGGCGAT 58.739 50.000 0.00 0.00 0.00 4.58
844 900 1.067283 ACTTCTCAGTCACAGGCGATG 60.067 52.381 0.00 0.00 0.00 3.84
845 901 0.247460 TTCTCAGTCACAGGCGATGG 59.753 55.000 0.00 0.00 0.00 3.51
846 902 1.153489 CTCAGTCACAGGCGATGGG 60.153 63.158 0.00 0.00 0.00 4.00
847 903 2.124983 CAGTCACAGGCGATGGGG 60.125 66.667 0.00 0.00 30.96 4.96
848 904 2.284625 AGTCACAGGCGATGGGGA 60.285 61.111 0.00 0.00 30.96 4.81
849 905 2.125106 GTCACAGGCGATGGGGAC 60.125 66.667 0.00 0.00 30.96 4.46
850 906 3.770040 TCACAGGCGATGGGGACG 61.770 66.667 0.00 0.00 30.96 4.79
851 907 4.082523 CACAGGCGATGGGGACGT 62.083 66.667 0.00 0.00 0.00 4.34
852 908 4.082523 ACAGGCGATGGGGACGTG 62.083 66.667 0.00 0.00 0.00 4.49
853 909 3.770040 CAGGCGATGGGGACGTGA 61.770 66.667 0.00 0.00 0.00 4.35
854 910 3.000819 AGGCGATGGGGACGTGAA 61.001 61.111 0.00 0.00 0.00 3.18
855 911 2.189521 GGCGATGGGGACGTGAAT 59.810 61.111 0.00 0.00 0.00 2.57
886 942 0.661020 AAAACGGACAAGGACTTGCG 59.339 50.000 11.73 10.46 44.03 4.85
909 966 1.667830 CAGTTGCCATGGTCGTCGT 60.668 57.895 14.67 0.00 0.00 4.34
993 1212 0.179215 CGTTCCAACATCTTGCTCGC 60.179 55.000 0.00 0.00 0.00 5.03
1026 1245 0.758734 CCACAAGGCCGAGGATGATA 59.241 55.000 0.00 0.00 0.00 2.15
1042 1261 0.110147 GATATCTCACCGGCTCGTCG 60.110 60.000 0.00 0.00 0.00 5.12
1305 1533 3.714001 TCCTGCCTCAGCTGCCTG 61.714 66.667 9.47 0.30 40.80 4.85
1471 1714 2.035449 ACAAATGTCACGTCGGAGAAGA 59.965 45.455 0.00 0.00 38.59 2.87
1629 1872 4.003788 CCAGACCTGACCGCGGTT 62.004 66.667 34.65 17.52 34.19 4.44
1832 2081 3.876589 CTGCTGCGGTACCAACGGT 62.877 63.158 13.54 0.00 40.16 4.83
1843 2092 1.368374 CCAACGGTTTTGACGTCGC 60.368 57.895 11.62 0.93 44.83 5.19
1847 2096 4.379143 GGTTTTGACGTCGCCGCC 62.379 66.667 11.62 7.15 37.70 6.13
1848 2097 4.712873 GTTTTGACGTCGCCGCCG 62.713 66.667 11.62 0.00 37.70 6.46
1873 2122 2.889617 CGGCATCCACACGAGGTA 59.110 61.111 0.00 0.00 0.00 3.08
1890 2139 5.106830 ACGAGGTAAGCTTTAATTTTCACCG 60.107 40.000 3.20 0.00 0.00 4.94
1900 2149 6.403855 GCTTTAATTTTCACCGTACCATGCTA 60.404 38.462 0.00 0.00 0.00 3.49
1901 2150 7.450124 TTTAATTTTCACCGTACCATGCTAA 57.550 32.000 0.00 0.00 0.00 3.09
2013 2434 7.930325 ACTTTTCTGTACCTACCTTCTAACAAC 59.070 37.037 0.00 0.00 0.00 3.32
2024 2445 4.288626 ACCTTCTAACAACAAGGAGCCATA 59.711 41.667 4.71 0.00 41.74 2.74
2109 2534 8.552296 AGTGAGATACCAATCCAAATTTAGAGT 58.448 33.333 0.00 0.00 31.98 3.24
2299 2913 0.466124 GAGAAGGAAGCGGCCACTAT 59.534 55.000 2.24 0.00 0.00 2.12
2305 2919 1.401905 GGAAGCGGCCACTATCAAAAG 59.598 52.381 2.24 0.00 0.00 2.27
2324 2938 5.852282 AAAGCAAAACAGTCAGGTATGTT 57.148 34.783 0.00 0.00 41.28 2.71
2337 2951 6.207417 AGTCAGGTATGTTCAAAATTCACCAG 59.793 38.462 0.00 0.00 0.00 4.00
2357 2971 5.942325 CAGTTTACAACGGGAAAGTTTTG 57.058 39.130 0.00 0.00 36.23 2.44
2370 2984 5.116180 GGAAAGTTTTGAAAGGACCCAAAG 58.884 41.667 0.00 0.00 34.29 2.77
2375 2989 0.882927 TGAAAGGACCCAAAGCGACG 60.883 55.000 0.00 0.00 0.00 5.12
2379 2993 1.447314 GGACCCAAAGCGACGTAGG 60.447 63.158 0.00 0.00 0.00 3.18
2380 2994 1.291272 GACCCAAAGCGACGTAGGT 59.709 57.895 0.00 0.00 0.00 3.08
2384 2998 2.199236 CCCAAAGCGACGTAGGTTATC 58.801 52.381 13.46 0.00 0.00 1.75
2400 3016 7.042187 CGTAGGTTATCTATACTCGTTGTGACT 60.042 40.741 0.00 0.00 0.00 3.41
2401 3017 7.261829 AGGTTATCTATACTCGTTGTGACTC 57.738 40.000 0.00 0.00 0.00 3.36
2404 3020 7.012138 GGTTATCTATACTCGTTGTGACTCTGA 59.988 40.741 0.00 0.00 0.00 3.27
2409 3025 4.280101 ACTCGTTGTGACTCTGATATCG 57.720 45.455 0.00 0.00 0.00 2.92
2458 3074 3.664107 CTGACGAGGAGGACAATGAAAA 58.336 45.455 0.00 0.00 0.00 2.29
2549 3165 1.603236 TTGGTGATGGCGGATTTGGC 61.603 55.000 0.00 0.00 0.00 4.52
2577 3193 6.598064 GGTGTACAAGGTGCTAAATAGACATT 59.402 38.462 0.00 0.00 0.00 2.71
2579 3195 8.175716 GTGTACAAGGTGCTAAATAGACATTTC 58.824 37.037 0.00 0.00 35.88 2.17
2586 3202 8.200792 AGGTGCTAAATAGACATTTCTCTACTG 58.799 37.037 0.00 0.00 35.88 2.74
2598 3217 4.537135 TTCTCTACTGAAATCGCCAACT 57.463 40.909 0.00 0.00 0.00 3.16
2660 3279 8.337118 TGATCTTTTAGGGTATTCTTCCAGAT 57.663 34.615 0.00 0.00 0.00 2.90
2865 3484 3.255888 CCTCTTCCTTTTTGGTACTTGCC 59.744 47.826 0.00 0.00 37.07 4.52
2907 3526 4.346418 TCAATTATGGCCTCCTTCTCTCTC 59.654 45.833 3.32 0.00 0.00 3.20
2915 3534 5.029474 GGCCTCCTTCTCTCTCCATATTAT 58.971 45.833 0.00 0.00 0.00 1.28
3153 3772 3.011949 TGGAATTGCGAGACTTTTTGC 57.988 42.857 0.00 0.00 0.00 3.68
3291 3910 7.067737 TGACTAAATATGACGTACCTCATCACA 59.932 37.037 10.18 0.00 32.86 3.58
3451 4070 5.821470 GGAATCTCAAGATCTTCTGAATGCA 59.179 40.000 4.57 0.00 32.75 3.96
3525 4145 0.826062 TTACCACTTAGTAGGCCGCC 59.174 55.000 0.00 0.00 0.00 6.13
3687 4342 1.143305 GATGGATCCGAGCATGAACG 58.857 55.000 7.39 0.35 0.00 3.95
3735 4390 4.942363 AGATGCATCCATATAGGGCTTT 57.058 40.909 23.06 0.00 38.24 3.51
3829 4484 3.509575 GTGTCTCTATCTGCCCCATCTAG 59.490 52.174 0.00 0.00 0.00 2.43
4056 4713 7.402811 TGCGTGTTGCTATGTATAGATAAAC 57.597 36.000 3.15 4.90 46.63 2.01
4121 4778 3.560896 GCCCGACTTTATAAATAACGCCA 59.439 43.478 0.00 0.00 0.00 5.69
4140 4797 0.321653 ATCACGGCAAGGTCCAGAAC 60.322 55.000 0.00 0.00 0.00 3.01
4186 4843 9.463443 GATAAAACAGTTCATAACAAACAAGCT 57.537 29.630 0.00 0.00 0.00 3.74
4202 5166 7.092846 ACAAACAAGCTAGGTACAGATCCTAAT 60.093 37.037 0.00 0.00 37.15 1.73
4317 5281 2.159240 GGAGGTGCGGATTTTGGAAATC 60.159 50.000 5.12 5.12 0.00 2.17
4367 5371 3.366396 CTTTAGTGAGAGGGCTCCACTA 58.634 50.000 0.72 0.72 40.55 2.74
4389 5393 9.868277 CACTATTGAATAAAGGCAACCATTTTA 57.132 29.630 0.00 0.00 37.17 1.52
4509 7154 4.142381 GCAATCCAAAACACCCTAGCTAAG 60.142 45.833 0.00 0.00 0.00 2.18
4604 7324 0.391661 GAACGCTGCTCCATCCAAGA 60.392 55.000 0.00 0.00 0.00 3.02
4609 7329 1.809651 GCTGCTCCATCCAAGACTAGC 60.810 57.143 0.00 0.00 0.00 3.42
4611 7331 2.961741 CTGCTCCATCCAAGACTAGCTA 59.038 50.000 0.00 0.00 0.00 3.32
4787 7507 1.038681 TTATAGCGAGGACGTGGCCA 61.039 55.000 0.00 0.00 41.98 5.36
4816 8028 7.931407 ACTTGGTGAGTTAATGGAAAATTTTCC 59.069 33.333 33.92 33.92 45.68 3.13
4871 8083 0.882927 CTCCGAGAGCGTAGGAGGAG 60.883 65.000 9.53 6.13 45.77 3.69
4942 9679 0.178990 GCAGTCCAAGGTCCCAGTTT 60.179 55.000 0.00 0.00 0.00 2.66
5034 10124 1.351017 ACATATGGTTATGCTCCCCCG 59.649 52.381 7.80 0.00 39.09 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 0.972883 GCAAAAACTGTGGGGCCATA 59.027 50.000 4.39 0.00 0.00 2.74
38 39 0.763986 AGCAAAAACTGTGGGGCCAT 60.764 50.000 4.39 0.00 0.00 4.40
91 94 9.793259 TTCATGTTGGGATAAAATATCCTCTAC 57.207 33.333 14.36 11.75 38.26 2.59
96 99 7.014615 AGTGCTTCATGTTGGGATAAAATATCC 59.985 37.037 7.71 7.71 37.47 2.59
97 100 7.945134 AGTGCTTCATGTTGGGATAAAATATC 58.055 34.615 0.00 0.00 0.00 1.63
111 114 8.677148 TTCTTTCTTTAGTTAGTGCTTCATGT 57.323 30.769 0.00 0.00 0.00 3.21
113 116 8.951243 GGATTCTTTCTTTAGTTAGTGCTTCAT 58.049 33.333 0.00 0.00 0.00 2.57
178 181 6.259550 AGAAAGTCCAAGCACAATACATTC 57.740 37.500 0.00 0.00 0.00 2.67
181 184 6.463995 AAAAGAAAGTCCAAGCACAATACA 57.536 33.333 0.00 0.00 0.00 2.29
217 241 0.397816 TCCCAACACCCCACCAAAAG 60.398 55.000 0.00 0.00 0.00 2.27
237 261 1.808945 GCAACAACTCCCATGTGAGAG 59.191 52.381 12.50 7.57 36.22 3.20
252 276 1.685517 TGCAAAATACAGCAGGCAACA 59.314 42.857 0.00 0.00 35.51 3.33
257 281 4.717233 TGGTATTGCAAAATACAGCAGG 57.283 40.909 1.71 0.00 42.39 4.85
281 305 5.503031 CGAGACAATCATCCATAAGCACAAC 60.503 44.000 0.00 0.00 0.00 3.32
284 308 4.122776 ACGAGACAATCATCCATAAGCAC 58.877 43.478 0.00 0.00 0.00 4.40
291 315 3.096852 AGGTGTACGAGACAATCATCCA 58.903 45.455 0.00 0.00 40.66 3.41
417 444 7.042051 TGACGGCTGAGATTTAAAATATGTAGC 60.042 37.037 0.00 0.00 0.00 3.58
438 465 8.767085 TCAGTTGTTAGTTTTAACTATTGACGG 58.233 33.333 3.37 4.32 40.87 4.79
475 502 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
478 505 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
481 508 9.898806 CTATTATTGTTGTTGTTGTTGTTGTTG 57.101 29.630 0.00 0.00 0.00 3.33
554 597 7.167801 GTCGAGTCAAAGTTTATGCTACCTATC 59.832 40.741 0.00 0.00 0.00 2.08
555 598 6.979238 GTCGAGTCAAAGTTTATGCTACCTAT 59.021 38.462 0.00 0.00 0.00 2.57
559 602 4.490479 GCGTCGAGTCAAAGTTTATGCTAC 60.490 45.833 0.00 0.00 0.00 3.58
563 606 3.718036 CGTGCGTCGAGTCAAAGTTTATG 60.718 47.826 0.00 0.00 42.86 1.90
564 607 2.407361 CGTGCGTCGAGTCAAAGTTTAT 59.593 45.455 0.00 0.00 42.86 1.40
565 608 1.782569 CGTGCGTCGAGTCAAAGTTTA 59.217 47.619 0.00 0.00 42.86 2.01
566 609 0.575390 CGTGCGTCGAGTCAAAGTTT 59.425 50.000 0.00 0.00 42.86 2.66
585 628 1.866601 AGCAAACCAAACCGTACGTAC 59.133 47.619 15.90 15.90 0.00 3.67
586 629 2.237393 AGCAAACCAAACCGTACGTA 57.763 45.000 15.21 0.00 0.00 3.57
590 646 2.223618 GCTTCAAGCAAACCAAACCGTA 60.224 45.455 3.89 0.00 41.89 4.02
603 659 1.200948 GTGGAGTGGAATGCTTCAAGC 59.799 52.381 1.04 1.04 42.82 4.01
604 660 1.466167 CGTGGAGTGGAATGCTTCAAG 59.534 52.381 0.00 0.00 0.00 3.02
605 661 1.522668 CGTGGAGTGGAATGCTTCAA 58.477 50.000 0.00 0.00 0.00 2.69
606 662 0.321564 CCGTGGAGTGGAATGCTTCA 60.322 55.000 0.00 0.00 0.00 3.02
607 663 1.648467 GCCGTGGAGTGGAATGCTTC 61.648 60.000 0.00 0.00 0.00 3.86
608 664 1.675641 GCCGTGGAGTGGAATGCTT 60.676 57.895 0.00 0.00 0.00 3.91
609 665 2.045926 GCCGTGGAGTGGAATGCT 60.046 61.111 0.00 0.00 0.00 3.79
610 666 1.244019 AAAGCCGTGGAGTGGAATGC 61.244 55.000 0.00 0.00 0.00 3.56
611 667 0.523072 CAAAGCCGTGGAGTGGAATG 59.477 55.000 0.00 0.00 0.00 2.67
612 668 1.244019 GCAAAGCCGTGGAGTGGAAT 61.244 55.000 0.00 0.00 0.00 3.01
613 669 1.896660 GCAAAGCCGTGGAGTGGAA 60.897 57.895 0.00 0.00 0.00 3.53
614 670 2.281484 GCAAAGCCGTGGAGTGGA 60.281 61.111 0.00 0.00 0.00 4.02
615 671 3.726517 CGCAAAGCCGTGGAGTGG 61.727 66.667 0.00 0.00 0.00 4.00
616 672 3.726517 CCGCAAAGCCGTGGAGTG 61.727 66.667 0.00 0.00 38.98 3.51
617 673 2.748058 ATTCCGCAAAGCCGTGGAGT 62.748 55.000 1.48 0.00 45.95 3.85
618 674 2.040544 ATTCCGCAAAGCCGTGGAG 61.041 57.895 1.48 0.00 45.95 3.86
623 679 0.028505 CTCATCATTCCGCAAAGCCG 59.971 55.000 0.00 0.00 0.00 5.52
648 704 3.428862 GGGATTTTACCAGTTTGGATGCG 60.429 47.826 1.40 0.00 40.96 4.73
715 771 2.024941 GGGTGAACCTTCTCCATTCCAT 60.025 50.000 8.11 0.00 41.43 3.41
725 781 1.963172 AACTGAACGGGTGAACCTTC 58.037 50.000 0.00 0.00 36.97 3.46
739 795 4.515191 CCGTCAATGAAAGGAGAAAACTGA 59.485 41.667 0.39 0.00 0.00 3.41
758 814 1.070443 CGAGAGTAGCGATCTTCCGTC 60.070 57.143 0.00 0.00 0.00 4.79
768 824 4.592936 CCGACGGCGAGAGTAGCG 62.593 72.222 15.16 5.14 40.82 4.26
813 869 7.711339 CCTGTGACTGAGAAGTACTTTTAGTTT 59.289 37.037 10.02 0.00 0.00 2.66
814 870 7.210873 CCTGTGACTGAGAAGTACTTTTAGTT 58.789 38.462 10.02 0.00 0.00 2.24
818 874 4.381411 GCCTGTGACTGAGAAGTACTTTT 58.619 43.478 10.02 3.52 0.00 2.27
819 875 3.553096 CGCCTGTGACTGAGAAGTACTTT 60.553 47.826 10.02 0.00 0.00 2.66
820 876 2.029828 CGCCTGTGACTGAGAAGTACTT 60.030 50.000 8.13 8.13 0.00 2.24
821 877 1.542030 CGCCTGTGACTGAGAAGTACT 59.458 52.381 0.00 0.00 0.00 2.73
822 878 1.540267 TCGCCTGTGACTGAGAAGTAC 59.460 52.381 0.00 0.00 0.00 2.73
823 879 1.905637 TCGCCTGTGACTGAGAAGTA 58.094 50.000 0.00 0.00 0.00 2.24
824 880 1.067283 CATCGCCTGTGACTGAGAAGT 60.067 52.381 0.00 0.00 0.00 3.01
825 881 1.638133 CATCGCCTGTGACTGAGAAG 58.362 55.000 0.00 0.00 0.00 2.85
826 882 0.247460 CCATCGCCTGTGACTGAGAA 59.753 55.000 0.00 0.00 0.00 2.87
827 883 1.607801 CCCATCGCCTGTGACTGAGA 61.608 60.000 0.00 0.00 0.00 3.27
828 884 1.153489 CCCATCGCCTGTGACTGAG 60.153 63.158 0.00 0.00 0.00 3.35
829 885 2.659063 CCCCATCGCCTGTGACTGA 61.659 63.158 0.00 0.00 0.00 3.41
830 886 2.124983 CCCCATCGCCTGTGACTG 60.125 66.667 0.00 0.00 0.00 3.51
831 887 2.284625 TCCCCATCGCCTGTGACT 60.285 61.111 0.00 0.00 0.00 3.41
832 888 2.125106 GTCCCCATCGCCTGTGAC 60.125 66.667 0.00 0.00 0.00 3.67
833 889 3.770040 CGTCCCCATCGCCTGTGA 61.770 66.667 0.00 0.00 0.00 3.58
834 890 4.082523 ACGTCCCCATCGCCTGTG 62.083 66.667 0.00 0.00 0.00 3.66
835 891 4.082523 CACGTCCCCATCGCCTGT 62.083 66.667 0.00 0.00 0.00 4.00
836 892 2.593468 ATTCACGTCCCCATCGCCTG 62.593 60.000 0.00 0.00 0.00 4.85
837 893 2.367202 ATTCACGTCCCCATCGCCT 61.367 57.895 0.00 0.00 0.00 5.52
838 894 2.180204 CATTCACGTCCCCATCGCC 61.180 63.158 0.00 0.00 0.00 5.54
839 895 2.823829 GCATTCACGTCCCCATCGC 61.824 63.158 0.00 0.00 0.00 4.58
840 896 0.104120 TAGCATTCACGTCCCCATCG 59.896 55.000 0.00 0.00 0.00 3.84
841 897 1.139058 ACTAGCATTCACGTCCCCATC 59.861 52.381 0.00 0.00 0.00 3.51
842 898 1.204146 ACTAGCATTCACGTCCCCAT 58.796 50.000 0.00 0.00 0.00 4.00
843 899 0.981183 AACTAGCATTCACGTCCCCA 59.019 50.000 0.00 0.00 0.00 4.96
844 900 1.369625 CAACTAGCATTCACGTCCCC 58.630 55.000 0.00 0.00 0.00 4.81
845 901 0.727398 GCAACTAGCATTCACGTCCC 59.273 55.000 0.00 0.00 44.79 4.46
909 966 1.292223 GCCTAGTGCACGTCCTTGA 59.708 57.895 12.01 0.00 40.77 3.02
919 976 1.144936 CCTAGTGCCTGCCTAGTGC 59.855 63.158 11.28 0.00 41.77 4.40
1026 1245 2.750637 ACGACGAGCCGGTGAGAT 60.751 61.111 1.90 0.00 0.00 2.75
1176 1404 2.269241 GAGGCGTTCTTGGGGAGG 59.731 66.667 0.00 0.00 0.00 4.30
1234 1462 2.928396 CCAGACCTTGTCCGGGGT 60.928 66.667 0.00 0.00 38.70 4.95
1335 1563 0.602638 CCACCTTGCTGTAGTCGCAA 60.603 55.000 0.00 0.00 44.36 4.85
1627 1870 4.030452 GCACTGCCGGCACTGAAC 62.030 66.667 32.30 16.40 0.00 3.18
1817 2066 0.040781 CAAAACCGTTGGTACCGCAG 60.041 55.000 7.57 0.13 33.12 5.18
1827 2076 3.016499 GGCGACGTCAAAACCGTT 58.984 55.556 17.16 0.00 38.92 4.44
1855 2104 2.845752 TTACCTCGTGTGGATGCCGC 62.846 60.000 0.00 0.00 34.12 6.53
1868 2117 6.250344 ACGGTGAAAATTAAAGCTTACCTC 57.750 37.500 0.00 0.00 0.00 3.85
1873 2122 6.386654 CATGGTACGGTGAAAATTAAAGCTT 58.613 36.000 0.00 0.00 0.00 3.74
1890 2139 4.423732 CAAGGCAAATGTTAGCATGGTAC 58.576 43.478 3.60 1.17 35.15 3.34
1900 2149 0.749649 TCGTTGGCAAGGCAAATGTT 59.250 45.000 14.76 0.00 31.06 2.71
1901 2150 0.968405 ATCGTTGGCAAGGCAAATGT 59.032 45.000 14.76 0.00 31.06 2.71
2013 2434 5.829924 ACAGTATTTTCCATATGGCTCCTTG 59.170 40.000 17.58 10.94 34.44 3.61
2024 2445 6.407074 CCCTCTAACTCGACAGTATTTTCCAT 60.407 42.308 0.00 0.00 30.14 3.41
2073 2498 6.093633 GGATTGGTATCTCACTTGGTTTGTAC 59.906 42.308 0.00 0.00 0.00 2.90
2144 2758 7.440255 AGAAAAATGTCAGCTCAAATGGAAAAG 59.560 33.333 0.00 0.00 0.00 2.27
2299 2913 5.359576 ACATACCTGACTGTTTTGCTTTTGA 59.640 36.000 0.00 0.00 0.00 2.69
2305 2919 4.829064 TGAACATACCTGACTGTTTTGC 57.171 40.909 0.00 0.00 35.80 3.68
2324 2938 5.450688 CCCGTTGTAAACTGGTGAATTTTGA 60.451 40.000 0.00 0.00 46.99 2.69
2337 2951 6.035220 CCTTTCAAAACTTTCCCGTTGTAAAC 59.965 38.462 0.00 0.00 45.31 2.01
2353 2967 2.100087 GTCGCTTTGGGTCCTTTCAAAA 59.900 45.455 0.00 0.00 33.24 2.44
2357 2971 0.883370 ACGTCGCTTTGGGTCCTTTC 60.883 55.000 0.00 0.00 0.00 2.62
2370 2984 4.387256 ACGAGTATAGATAACCTACGTCGC 59.613 45.833 0.00 0.00 33.70 5.19
2375 2989 8.152309 AGTCACAACGAGTATAGATAACCTAC 57.848 38.462 0.00 0.00 0.00 3.18
2379 2993 7.917597 TCAGAGTCACAACGAGTATAGATAAC 58.082 38.462 0.00 0.00 0.00 1.89
2380 2994 8.678593 ATCAGAGTCACAACGAGTATAGATAA 57.321 34.615 0.00 0.00 0.00 1.75
2384 2998 7.116519 TCGATATCAGAGTCACAACGAGTATAG 59.883 40.741 3.12 0.00 0.00 1.31
2400 3016 7.378966 GGATCTGTTTAATGGTCGATATCAGA 58.621 38.462 3.12 0.00 34.68 3.27
2401 3017 6.591834 GGGATCTGTTTAATGGTCGATATCAG 59.408 42.308 3.12 0.00 0.00 2.90
2404 3020 6.043243 ACTGGGATCTGTTTAATGGTCGATAT 59.957 38.462 0.00 0.00 0.00 1.63
2409 3025 7.881775 AATAACTGGGATCTGTTTAATGGTC 57.118 36.000 0.00 0.00 36.61 4.02
2458 3074 5.965922 TGTCAATCAACATCGAGTCTACAT 58.034 37.500 0.00 0.00 0.00 2.29
2549 3165 0.668096 TTAGCACCTTGTACACCGCG 60.668 55.000 0.00 0.00 0.00 6.46
2577 3193 4.537135 AGTTGGCGATTTCAGTAGAGAA 57.463 40.909 0.00 0.00 0.00 2.87
2579 3195 7.867909 TCAATATAGTTGGCGATTTCAGTAGAG 59.132 37.037 0.00 0.00 0.00 2.43
2586 3202 7.484035 AACTCTCAATATAGTTGGCGATTTC 57.516 36.000 0.00 0.00 34.70 2.17
2591 3210 4.360563 ACGAACTCTCAATATAGTTGGCG 58.639 43.478 0.00 0.00 36.10 5.69
2598 3217 9.817809 AAGCTCAATTAACGAACTCTCAATATA 57.182 29.630 0.00 0.00 0.00 0.86
2660 3279 0.245266 TCACTGCTATTTCGTCGCCA 59.755 50.000 0.00 0.00 0.00 5.69
2865 3484 7.827819 AATTGACTTTGAGCATGATTCAATG 57.172 32.000 17.30 17.30 33.57 2.82
3017 3636 4.361253 TTGCAGTCCTCGAGCAAC 57.639 55.556 6.99 7.50 42.71 4.17
3153 3772 1.746615 CCATGGGTCTGGTCTTGCG 60.747 63.158 2.85 0.00 0.00 4.85
3291 3910 5.230942 GCGCCATATATCCGCTATAAGAAT 58.769 41.667 16.14 0.00 43.95 2.40
3425 4044 6.543100 GCATTCAGAAGATCTTGAGATTCCTT 59.457 38.462 14.00 0.00 34.37 3.36
3451 4070 6.600822 AGATATTCAAACAGCAAGCACATACT 59.399 34.615 0.00 0.00 0.00 2.12
3579 4230 4.813296 AAAGTCTAAGTGCAGGTTTTCG 57.187 40.909 0.00 0.00 0.00 3.46
3687 4342 0.030638 CCGCTCTCTGAGAAGCTAGC 59.969 60.000 6.62 6.62 0.00 3.42
3735 4390 2.164624 CCGGGTTTTCTTGAACACACAA 59.835 45.455 0.00 0.00 32.42 3.33
3964 4621 1.725641 TCATCGAGTGCACCACAATC 58.274 50.000 14.63 2.78 40.01 2.67
3995 4652 6.266786 AGTCAATAAAAACACCCTTTACCAGG 59.733 38.462 0.00 0.00 43.49 4.45
4056 4713 0.238289 GAACACGGTGGCTCAACATG 59.762 55.000 13.48 0.00 0.00 3.21
4093 4750 6.364435 CGTTATTTATAAAGTCGGGCTCCTAC 59.636 42.308 3.94 0.00 0.00 3.18
4121 4778 0.321653 GTTCTGGACCTTGCCGTGAT 60.322 55.000 0.00 0.00 0.00 3.06
4140 4797 4.292186 TCTCTTTCCCTGATGAACCTTG 57.708 45.455 0.00 0.00 0.00 3.61
4184 4841 6.246919 TCACCTATTAGGATCTGTACCTAGC 58.753 44.000 16.80 0.00 40.46 3.42
4186 4843 6.720288 GCTTCACCTATTAGGATCTGTACCTA 59.280 42.308 16.80 0.00 37.67 3.08
4202 5166 1.519408 GCGTCCTTTTGCTTCACCTA 58.481 50.000 0.00 0.00 0.00 3.08
4317 5281 4.428615 TGTTGATGCTGTCATGTTGATG 57.571 40.909 0.00 0.00 36.54 3.07
4367 5371 9.566432 TGTTTAAAATGGTTGCCTTTATTCAAT 57.434 25.926 0.00 0.00 0.00 2.57
4389 5393 1.388547 TTCCTGCTCGCTGTTTGTTT 58.611 45.000 0.00 0.00 0.00 2.83
4509 7154 3.934068 TCCTTGAAATTACTCCGGACAC 58.066 45.455 0.00 0.00 0.00 3.67
4551 7196 2.501723 GCATCTCCTGGAACCTGACTAA 59.498 50.000 0.00 0.00 0.00 2.24
4604 7324 6.070767 TCCTCTTTAATTGTGTGCTAGCTAGT 60.071 38.462 21.62 2.20 0.00 2.57
4609 7329 6.037610 GGACATCCTCTTTAATTGTGTGCTAG 59.962 42.308 0.00 0.00 0.00 3.42
4611 7331 4.702131 GGACATCCTCTTTAATTGTGTGCT 59.298 41.667 0.00 0.00 0.00 4.40
4725 7445 2.026262 TCTTCCTTTGGTAGGCCATCAC 60.026 50.000 5.01 0.00 45.56 3.06
4816 8028 1.691196 TTTGCCCCACTTGTCTTCTG 58.309 50.000 0.00 0.00 0.00 3.02
4871 8083 2.360475 GCAACCTCTCACTGCCCC 60.360 66.667 0.00 0.00 0.00 5.80
5034 10124 6.310711 ACAATATCGAACTTCGGAAAGAGAAC 59.689 38.462 11.21 0.00 40.88 3.01


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

AutoCloner maintained by Alex Coulton.