Multiple sequence alignment - TraesCS5B01G391900

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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 TraesCS5B01G391900 chr5B 100.000 5283 0 0 1 5283 570935404 570930122 0.000000e+00 9756.0
1 TraesCS5B01G391900 chr5B 85.053 843 93 11 943 1757 571122562 571121725 0.000000e+00 828.0
2 TraesCS5B01G391900 chr5B 89.891 643 61 3 1 643 571123408 571122770 0.000000e+00 824.0
3 TraesCS5B01G391900 chr5B 75.943 212 33 8 702 913 571122761 571122568 5.630000e-15 93.5
4 TraesCS5B01G391900 chr5D 93.667 2921 134 29 1653 4541 464076362 464073461 0.000000e+00 4322.0
5 TraesCS5B01G391900 chr5D 88.745 924 50 14 748 1656 464077276 464076392 0.000000e+00 1081.0
6 TraesCS5B01G391900 chr5D 83.045 1097 175 11 3178 4270 544701288 544702377 0.000000e+00 985.0
7 TraesCS5B01G391900 chr5D 94.755 591 23 3 4613 5203 464073094 464072512 0.000000e+00 913.0
8 TraesCS5B01G391900 chr5D 90.630 651 55 3 1 651 464077955 464077311 0.000000e+00 859.0
9 TraesCS5B01G391900 chr5A 92.184 1612 81 22 2913 4498 584458229 584456637 0.000000e+00 2237.0
10 TraesCS5B01G391900 chr5A 89.784 1576 119 17 960 2512 584491755 584490199 0.000000e+00 1980.0
11 TraesCS5B01G391900 chr5A 93.304 672 27 8 4612 5283 584456134 584455481 0.000000e+00 976.0
12 TraesCS5B01G391900 chr5A 90.448 670 59 3 1 669 584507702 584507037 0.000000e+00 878.0
13 TraesCS5B01G391900 chr5A 85.396 404 38 11 2515 2914 584490156 584489770 2.960000e-107 399.0
14 TraesCS5B01G391900 chr2B 86.142 1436 172 19 2900 4325 752833541 752834959 0.000000e+00 1524.0
15 TraesCS5B01G391900 chr2B 83.677 1213 158 23 940 2145 752831054 752832233 0.000000e+00 1107.0
16 TraesCS5B01G391900 chr2B 78.561 667 108 16 1 647 752830238 752830889 1.770000e-109 407.0
17 TraesCS5B01G391900 chr2A 85.981 1448 175 20 2887 4324 746980925 746982354 0.000000e+00 1524.0
18 TraesCS5B01G391900 chr2A 80.878 1480 207 39 940 2387 746977905 746979340 0.000000e+00 1096.0
19 TraesCS5B01G391900 chr2A 81.495 1097 148 32 940 2027 747144931 747145981 0.000000e+00 850.0
20 TraesCS5B01G391900 chr2A 78.711 667 107 21 1 647 747144115 747144766 3.810000e-111 412.0
21 TraesCS5B01G391900 chr2A 76.840 462 81 16 158 603 746977151 746977602 2.460000e-58 237.0
22 TraesCS5B01G391900 chr2D 85.964 1432 171 22 2896 4315 617076528 617077941 0.000000e+00 1504.0
23 TraesCS5B01G391900 chr2D 82.784 1214 159 26 940 2145 617074045 617075216 0.000000e+00 1038.0
24 TraesCS5B01G391900 chr2D 78.711 667 107 16 1 647 617073230 617073881 3.810000e-111 412.0
25 TraesCS5B01G391900 chr1B 83.668 1096 169 10 3178 4268 10084761 10085851 0.000000e+00 1024.0
26 TraesCS5B01G391900 chr1B 81.038 1329 202 34 2953 4256 9594797 9593494 0.000000e+00 1013.0
27 TraesCS5B01G391900 chrUn 83.164 1081 177 5 3178 4256 238779948 238778871 0.000000e+00 983.0
28 TraesCS5B01G391900 chr3B 79.456 662 108 18 13 660 671746842 671747489 1.350000e-120 444.0


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 TraesCS5B01G391900 chr5B 570930122 570935404 5282 True 9756.000000 9756 100.000000 1 5283 1 chr5B.!!$R1 5282
1 TraesCS5B01G391900 chr5B 571121725 571123408 1683 True 581.833333 828 83.629000 1 1757 3 chr5B.!!$R2 1756
2 TraesCS5B01G391900 chr5D 464072512 464077955 5443 True 1793.750000 4322 91.949250 1 5203 4 chr5D.!!$R1 5202
3 TraesCS5B01G391900 chr5D 544701288 544702377 1089 False 985.000000 985 83.045000 3178 4270 1 chr5D.!!$F1 1092
4 TraesCS5B01G391900 chr5A 584455481 584458229 2748 True 1606.500000 2237 92.744000 2913 5283 2 chr5A.!!$R2 2370
5 TraesCS5B01G391900 chr5A 584489770 584491755 1985 True 1189.500000 1980 87.590000 960 2914 2 chr5A.!!$R3 1954
6 TraesCS5B01G391900 chr5A 584507037 584507702 665 True 878.000000 878 90.448000 1 669 1 chr5A.!!$R1 668
7 TraesCS5B01G391900 chr2B 752830238 752834959 4721 False 1012.666667 1524 82.793333 1 4325 3 chr2B.!!$F1 4324
8 TraesCS5B01G391900 chr2A 746977151 746982354 5203 False 952.333333 1524 81.233000 158 4324 3 chr2A.!!$F1 4166
9 TraesCS5B01G391900 chr2A 747144115 747145981 1866 False 631.000000 850 80.103000 1 2027 2 chr2A.!!$F2 2026
10 TraesCS5B01G391900 chr2D 617073230 617077941 4711 False 984.666667 1504 82.486333 1 4315 3 chr2D.!!$F1 4314
11 TraesCS5B01G391900 chr1B 10084761 10085851 1090 False 1024.000000 1024 83.668000 3178 4268 1 chr1B.!!$F1 1090
12 TraesCS5B01G391900 chr1B 9593494 9594797 1303 True 1013.000000 1013 81.038000 2953 4256 1 chr1B.!!$R1 1303
13 TraesCS5B01G391900 chrUn 238778871 238779948 1077 True 983.000000 983 83.164000 3178 4256 1 chrUn.!!$R1 1078
14 TraesCS5B01G391900 chr3B 671746842 671747489 647 False 444.000000 444 79.456000 13 660 1 chr3B.!!$F1 647

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
739 800 0.031178 CAAACACTGCACAAGGGAGC 59.969 55.0 0.0 0.0 38.79 4.70 F
2169 2465 0.039618 ACAAAACCGATGCCATCCCT 59.960 50.0 0.0 0.0 0.00 4.20 F
2673 3053 0.307760 GGACGTGAGCCAACAAGTTG 59.692 55.0 0.0 0.0 40.13 3.16 F
3558 5080 1.172175 GGCTTTTGCTCTGAAGGGAG 58.828 55.0 0.0 0.0 46.54 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2226 2536 0.817013 AAATGCCGCACAGTTATGGG 59.183 50.000 0.00 0.00 34.12 4.00 R
3176 4698 1.458445 CGCCGATGATGTAGCTGAATG 59.542 52.381 0.00 0.00 0.00 2.67 R
4240 5762 0.469494 TGTCTATGGCATGCGGTGAT 59.531 50.000 12.44 3.59 0.00 3.06 R
4826 6793 0.534873 GAGGAGCTGAGGAAGGTGAC 59.465 60.000 0.00 0.00 36.52 3.67 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
97 98 4.699257 AGAAGGCTTAAGCTTCTCAACATG 59.301 41.667 25.88 0.00 41.70 3.21
133 134 2.094417 GCACATAGACGAAAGAAGTGCC 59.906 50.000 0.00 0.00 43.54 5.01
156 157 0.741221 GCTCAGACAATCCACCGGTC 60.741 60.000 2.59 0.00 0.00 4.79
168 169 1.743958 CCACCGGTCTGTAGTCACTAG 59.256 57.143 2.59 0.00 0.00 2.57
177 178 3.572682 TCTGTAGTCACTAGTGTTGGTGG 59.427 47.826 21.99 10.17 36.53 4.61
353 354 4.039973 ACGACCCAGAAGTATGAAAGTTCA 59.960 41.667 0.00 0.00 39.63 3.18
464 465 1.220206 CTCAGCTGGATCGCCTTGT 59.780 57.895 15.13 0.00 34.31 3.16
478 479 0.676782 CCTTGTAGGCGGAAAGGGTG 60.677 60.000 7.11 0.00 37.42 4.61
493 494 2.513259 GGTGGTGGACGTCCTGGAA 61.513 63.158 33.39 12.38 36.82 3.53
496 497 0.768622 TGGTGGACGTCCTGGAAATT 59.231 50.000 33.39 0.00 36.82 1.82
554 570 2.819595 CCCTCAACATCCACGGCG 60.820 66.667 4.80 4.80 0.00 6.46
574 590 3.051392 GAACCGCGGCCAGGAAATG 62.051 63.158 28.58 0.00 0.00 2.32
610 626 1.205655 CCATGGAGGCATCGACGATAT 59.794 52.381 10.57 0.00 0.00 1.63
611 627 2.534298 CATGGAGGCATCGACGATATC 58.466 52.381 10.57 8.90 0.00 1.63
684 700 2.000825 TAGTTGGCTGGGCACAACCA 62.001 55.000 7.09 7.09 46.07 3.67
686 702 2.208619 TTGGCTGGGCACAACCATG 61.209 57.895 12.87 0.00 42.14 3.66
687 703 4.073200 GGCTGGGCACAACCATGC 62.073 66.667 2.71 0.00 45.34 4.06
693 709 4.639824 GCACAACCATGCACAGTG 57.360 55.556 0.00 0.00 45.39 3.66
695 711 0.950836 GCACAACCATGCACAGTGTA 59.049 50.000 1.61 0.00 45.39 2.90
696 712 1.069022 GCACAACCATGCACAGTGTAG 60.069 52.381 1.61 0.00 45.39 2.74
697 713 2.221169 CACAACCATGCACAGTGTAGT 58.779 47.619 1.61 0.00 0.00 2.73
698 714 2.031769 CACAACCATGCACAGTGTAGTG 60.032 50.000 1.61 0.00 42.37 2.74
699 715 1.536766 CAACCATGCACAGTGTAGTGG 59.463 52.381 15.46 15.46 39.87 4.00
700 716 0.036732 ACCATGCACAGTGTAGTGGG 59.963 55.000 19.18 12.88 39.87 4.61
704 720 0.396435 TGCACAGTGTAGTGGGAAGG 59.604 55.000 1.61 0.00 39.87 3.46
708 724 0.905357 CAGTGTAGTGGGAAGGAGGG 59.095 60.000 0.00 0.00 0.00 4.30
734 795 5.844301 AAAGAAAACAAACACTGCACAAG 57.156 34.783 0.00 0.00 0.00 3.16
739 800 0.031178 CAAACACTGCACAAGGGAGC 59.969 55.000 0.00 0.00 38.79 4.70
746 807 2.042831 GCACAAGGGAGCGATGCTT 61.043 57.895 0.00 0.00 39.88 3.91
780 850 7.856145 AAGAAATAGCATGTAGAAAGACCTG 57.144 36.000 0.00 0.00 0.00 4.00
781 851 6.352516 AGAAATAGCATGTAGAAAGACCTGG 58.647 40.000 0.00 0.00 0.00 4.45
782 852 5.700402 AATAGCATGTAGAAAGACCTGGT 57.300 39.130 0.00 0.00 31.81 4.00
783 853 6.808321 AATAGCATGTAGAAAGACCTGGTA 57.192 37.500 0.00 0.00 34.10 3.25
784 854 4.744795 AGCATGTAGAAAGACCTGGTAG 57.255 45.455 0.00 0.00 0.00 3.18
792 862 2.249309 AAGACCTGGTAGTGGTAGGG 57.751 55.000 0.00 0.00 38.03 3.53
813 883 2.422597 GATGGTGAACGTCCACATCAA 58.577 47.619 7.39 0.00 38.74 2.57
829 903 5.458015 CACATCAATGCATCCATATGTCAC 58.542 41.667 0.00 0.00 31.46 3.67
835 909 3.694926 TGCATCCATATGTCACCACAAA 58.305 40.909 1.24 0.00 35.64 2.83
849 923 2.292292 ACCACAAAGAAATACGTGCCAC 59.708 45.455 0.00 0.00 0.00 5.01
853 927 5.163663 CCACAAAGAAATACGTGCCACATAT 60.164 40.000 0.00 0.00 0.00 1.78
864 938 8.763049 ATACGTGCCACATATATATATGATGC 57.237 34.615 30.76 28.35 42.05 3.91
865 939 6.581712 ACGTGCCACATATATATATGATGCA 58.418 36.000 30.76 29.89 42.05 3.96
866 940 7.219322 ACGTGCCACATATATATATGATGCAT 58.781 34.615 32.06 23.56 44.19 3.96
929 1034 3.614399 TGACACACACACACACACA 57.386 47.368 0.00 0.00 0.00 3.72
930 1035 1.152510 TGACACACACACACACACAC 58.847 50.000 0.00 0.00 0.00 3.82
931 1036 1.152510 GACACACACACACACACACA 58.847 50.000 0.00 0.00 0.00 3.72
932 1037 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
933 1038 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
934 1039 1.468127 CACACACACACACACACACAT 59.532 47.619 0.00 0.00 0.00 3.21
935 1040 2.675348 CACACACACACACACACACATA 59.325 45.455 0.00 0.00 0.00 2.29
936 1041 3.312146 CACACACACACACACACACATAT 59.688 43.478 0.00 0.00 0.00 1.78
937 1042 4.509600 CACACACACACACACACACATATA 59.490 41.667 0.00 0.00 0.00 0.86
938 1043 5.179182 CACACACACACACACACACATATAT 59.821 40.000 0.00 0.00 0.00 0.86
1013 1124 2.477845 GCATATGCCGCTGCGATC 59.522 61.111 25.45 14.99 41.78 3.69
1162 1294 2.040412 GACTCATGGACAGGGGAAGTTT 59.960 50.000 0.00 0.00 0.00 2.66
1251 1390 0.541863 ACCTGGCTTACCTTCATCCG 59.458 55.000 0.00 0.00 36.63 4.18
1464 1609 3.303791 CCAGCAACACATCATCATCATCG 60.304 47.826 0.00 0.00 0.00 3.84
1626 1784 1.349627 CGCCTGCACGATGATTCAC 59.650 57.895 0.00 0.00 34.06 3.18
1644 1802 0.664767 ACAAGCTCGTCTCGACAAGC 60.665 55.000 1.85 1.85 0.00 4.01
1707 1898 0.877743 GTGGAGCTGGAAAGCTTGTC 59.122 55.000 0.00 0.00 46.36 3.18
1720 1911 1.004560 CTTGTCGGCTGCTCAAGGA 60.005 57.895 16.99 1.25 36.09 3.36
1722 1913 0.179032 TTGTCGGCTGCTCAAGGAAA 60.179 50.000 0.00 0.00 0.00 3.13
1832 2023 1.035932 CCAATCTCCTGCCTTGGCAG 61.036 60.000 29.11 29.11 33.59 4.85
1914 2105 1.558294 TGCAAGGTCATCTCAGATGCT 59.442 47.619 10.10 0.00 33.66 3.79
1950 2141 1.880027 GGCATAGGGTTTTATGGCTCG 59.120 52.381 11.05 0.00 46.99 5.03
1953 2144 1.209621 TAGGGTTTTATGGCTCGGCT 58.790 50.000 0.00 0.00 0.00 5.52
1954 2145 1.209621 AGGGTTTTATGGCTCGGCTA 58.790 50.000 0.00 0.00 0.00 3.93
1955 2146 1.562475 AGGGTTTTATGGCTCGGCTAA 59.438 47.619 0.00 0.00 0.00 3.09
1966 2157 1.742411 GCTCGGCTAACAAGCATGGTA 60.742 52.381 0.00 0.00 36.06 3.25
2013 2206 0.177604 ACATAGCAGCTGACTGGAGC 59.822 55.000 20.43 0.00 44.63 4.70
2168 2464 0.455815 GACAAAACCGATGCCATCCC 59.544 55.000 0.00 0.00 0.00 3.85
2169 2465 0.039618 ACAAAACCGATGCCATCCCT 59.960 50.000 0.00 0.00 0.00 4.20
2228 2538 8.533569 TGATAATTTCCTTTTAGAATGTCCCC 57.466 34.615 0.00 0.00 0.00 4.81
2229 2539 8.119246 TGATAATTTCCTTTTAGAATGTCCCCA 58.881 33.333 0.00 0.00 0.00 4.96
2230 2540 9.147732 GATAATTTCCTTTTAGAATGTCCCCAT 57.852 33.333 0.00 0.00 0.00 4.00
2272 2587 9.757227 CCAGGAGTTTTGTTGTCAAATTATTTA 57.243 29.630 0.00 0.00 42.14 1.40
2498 2834 6.988622 AATTATTGCAATGACATGGGTTTG 57.011 33.333 22.27 0.00 0.00 2.93
2500 2836 3.383620 TTGCAATGACATGGGTTTGTC 57.616 42.857 0.00 0.00 45.05 3.18
2673 3053 0.307760 GGACGTGAGCCAACAAGTTG 59.692 55.000 0.00 0.00 40.13 3.16
2817 3865 1.173913 GGGGGTCGGAGTCAAAAATG 58.826 55.000 0.00 0.00 0.00 2.32
2878 4369 4.202631 GGTATATCCTAACCCATTGGCCAA 60.203 45.833 23.00 23.00 33.59 4.52
3173 4685 4.836825 ACCCTAATGAATATGCTGATCCG 58.163 43.478 0.00 0.00 0.00 4.18
3176 4698 4.093998 CCTAATGAATATGCTGATCCGTGC 59.906 45.833 0.00 0.00 0.00 5.34
3535 5057 3.135225 CCACACAAACATTGTCCGACTA 58.865 45.455 0.00 0.00 43.23 2.59
3558 5080 1.172175 GGCTTTTGCTCTGAAGGGAG 58.828 55.000 0.00 0.00 46.54 4.30
3649 5171 9.974980 AATTCTATTATTTCTCGAGAACTCCTC 57.025 33.333 27.03 0.00 38.55 3.71
3877 5399 1.560923 GCACTATGGGCTATATCGCG 58.439 55.000 0.00 0.00 0.00 5.87
4240 5762 3.903090 AGCCATTTGTCCCATCTGAAAAA 59.097 39.130 0.00 0.00 0.00 1.94
4331 5856 9.710900 TGGATATAGTTGATTCATGTGTGTATC 57.289 33.333 0.00 0.00 33.99 2.24
4344 5869 2.597305 GTGTGTATCGCTCTTTACCGTG 59.403 50.000 0.00 0.00 0.00 4.94
4347 5872 0.248743 TATCGCTCTTTACCGTGGCG 60.249 55.000 0.00 0.00 45.93 5.69
4360 5885 2.031314 TGGCGCGGTTTCTAGCAA 59.969 55.556 8.83 0.00 0.00 3.91
4361 5886 1.376683 TGGCGCGGTTTCTAGCAAT 60.377 52.632 8.83 0.00 0.00 3.56
4362 5887 1.062525 GGCGCGGTTTCTAGCAATG 59.937 57.895 8.83 0.00 0.00 2.82
4363 5888 1.644786 GGCGCGGTTTCTAGCAATGT 61.645 55.000 8.83 0.00 0.00 2.71
4364 5889 1.003851 GCGCGGTTTCTAGCAATGTA 58.996 50.000 8.83 0.00 0.00 2.29
4372 5897 7.564988 GCGGTTTCTAGCAATGTAGTATAAAG 58.435 38.462 0.00 0.00 0.00 1.85
4373 5898 7.224167 GCGGTTTCTAGCAATGTAGTATAAAGT 59.776 37.037 0.00 0.00 0.00 2.66
4374 5899 9.095065 CGGTTTCTAGCAATGTAGTATAAAGTT 57.905 33.333 0.00 0.00 0.00 2.66
4397 5922 6.403866 TTCTATTGCCAAGTCAATTGTGTT 57.596 33.333 5.13 0.00 37.75 3.32
4398 5923 7.517614 TTCTATTGCCAAGTCAATTGTGTTA 57.482 32.000 5.13 0.00 37.75 2.41
4401 5926 5.590530 TTGCCAAGTCAATTGTGTTAGTT 57.409 34.783 5.13 0.00 37.17 2.24
4402 5927 6.701145 TTGCCAAGTCAATTGTGTTAGTTA 57.299 33.333 5.13 0.00 37.17 2.24
4403 5928 6.067263 TGCCAAGTCAATTGTGTTAGTTAC 57.933 37.500 5.13 0.00 37.17 2.50
4404 5929 5.009210 TGCCAAGTCAATTGTGTTAGTTACC 59.991 40.000 5.13 0.00 37.17 2.85
4405 5930 5.009210 GCCAAGTCAATTGTGTTAGTTACCA 59.991 40.000 5.13 0.00 37.17 3.25
4407 5932 7.305474 CCAAGTCAATTGTGTTAGTTACCATC 58.695 38.462 5.13 0.00 37.17 3.51
4408 5933 7.040755 CCAAGTCAATTGTGTTAGTTACCATCA 60.041 37.037 5.13 0.00 37.17 3.07
4409 5934 8.514594 CAAGTCAATTGTGTTAGTTACCATCAT 58.485 33.333 5.13 0.00 33.95 2.45
4410 5935 8.044060 AGTCAATTGTGTTAGTTACCATCATG 57.956 34.615 5.13 0.00 0.00 3.07
4411 5936 6.747280 GTCAATTGTGTTAGTTACCATCATGC 59.253 38.462 5.13 0.00 0.00 4.06
4412 5937 5.835113 ATTGTGTTAGTTACCATCATGCC 57.165 39.130 0.00 0.00 0.00 4.40
4420 5963 3.461085 AGTTACCATCATGCCTCCTGATT 59.539 43.478 0.00 0.00 31.00 2.57
4425 5968 4.070716 CCATCATGCCTCCTGATTTAGTC 58.929 47.826 0.00 0.00 31.00 2.59
4464 6009 7.459795 TTGTAATACTGGATTTGATGTGCAA 57.540 32.000 0.00 0.00 33.88 4.08
4469 6014 5.471556 ACTGGATTTGATGTGCAATGAAA 57.528 34.783 0.00 0.00 36.15 2.69
4489 6034 5.642919 TGAAATAGTTGAAAATGCCATTGCC 59.357 36.000 0.00 0.00 36.33 4.52
4498 6043 2.766345 ATGCCATTGCCGTGATTTTT 57.234 40.000 0.00 0.00 36.33 1.94
4541 6086 7.672983 AATTTCAGTTGTGTAGTATCCACTG 57.327 36.000 0.00 0.00 36.14 3.66
4543 6088 4.157246 TCAGTTGTGTAGTATCCACTGGT 58.843 43.478 0.00 0.00 36.14 4.00
4544 6089 4.591498 TCAGTTGTGTAGTATCCACTGGTT 59.409 41.667 0.00 0.00 36.14 3.67
4545 6090 4.929808 CAGTTGTGTAGTATCCACTGGTTC 59.070 45.833 0.00 0.00 36.14 3.62
4549 6146 2.045326 TGTAGTATCCACTGGTTCCCCT 59.955 50.000 0.00 0.00 36.14 4.79
4550 6147 3.272818 TGTAGTATCCACTGGTTCCCCTA 59.727 47.826 0.00 0.00 36.14 3.53
4553 6150 4.180723 AGTATCCACTGGTTCCCCTAAAA 58.819 43.478 0.00 0.00 32.25 1.52
4566 6163 6.243148 GTTCCCCTAAAACACAAGAGGATTA 58.757 40.000 0.00 0.00 0.00 1.75
4568 6165 7.039722 TCCCCTAAAACACAAGAGGATTATT 57.960 36.000 0.00 0.00 0.00 1.40
4570 6167 8.272173 TCCCCTAAAACACAAGAGGATTATTAG 58.728 37.037 0.00 0.00 0.00 1.73
4572 6169 9.110502 CCCTAAAACACAAGAGGATTATTAGTC 57.889 37.037 0.00 0.00 0.00 2.59
4573 6170 9.110502 CCTAAAACACAAGAGGATTATTAGTCC 57.889 37.037 0.00 0.00 35.94 3.85
4576 6173 5.675538 ACACAAGAGGATTATTAGTCCAGC 58.324 41.667 7.85 0.23 38.25 4.85
4577 6174 5.189736 ACACAAGAGGATTATTAGTCCAGCA 59.810 40.000 7.85 0.00 38.25 4.41
4578 6175 6.115446 CACAAGAGGATTATTAGTCCAGCAA 58.885 40.000 7.85 0.00 38.25 3.91
4606 6327 8.422577 AAAGATACTTGCCTCCTATTTTGTTT 57.577 30.769 0.00 0.00 0.00 2.83
4607 6328 7.396540 AGATACTTGCCTCCTATTTTGTTTG 57.603 36.000 0.00 0.00 0.00 2.93
4608 6329 7.175104 AGATACTTGCCTCCTATTTTGTTTGA 58.825 34.615 0.00 0.00 0.00 2.69
4610 6331 6.029346 ACTTGCCTCCTATTTTGTTTGATG 57.971 37.500 0.00 0.00 0.00 3.07
4618 6585 9.362539 CCTCCTATTTTGTTTGATGAAAATGAG 57.637 33.333 0.00 0.00 34.42 2.90
4629 6596 6.012658 TGATGAAAATGAGAGGAAAAACGG 57.987 37.500 0.00 0.00 0.00 4.44
4630 6597 5.767665 TGATGAAAATGAGAGGAAAAACGGA 59.232 36.000 0.00 0.00 0.00 4.69
4652 6619 2.618709 CCAAAATATCGAAGAGGCCACC 59.381 50.000 5.01 0.00 43.63 4.61
4655 6622 0.759346 ATATCGAAGAGGCCACCCAC 59.241 55.000 5.01 0.00 43.63 4.61
4657 6624 2.185310 ATCGAAGAGGCCACCCACAC 62.185 60.000 5.01 0.00 43.63 3.82
4658 6625 2.836154 GAAGAGGCCACCCACACA 59.164 61.111 5.01 0.00 0.00 3.72
4659 6626 1.600916 GAAGAGGCCACCCACACAC 60.601 63.158 5.01 0.00 0.00 3.82
4661 6628 2.594592 GAGGCCACCCACACACAC 60.595 66.667 5.01 0.00 0.00 3.82
4826 6793 1.645034 CTCATGGAAGCACAGTACCG 58.355 55.000 0.00 0.00 0.00 4.02
4856 6823 0.039617 CAGCTCCTCGAGGCTAATCG 60.040 60.000 27.39 8.68 44.07 3.34
5200 7167 3.706373 ATGGACTTCCGGTGCGCT 61.706 61.111 9.73 0.00 39.22 5.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 98 6.083630 GTCTATGTGCTGATCGACTCTTATC 58.916 44.000 0.00 0.00 0.00 1.75
133 134 1.021390 GGTGGATTGTCTGAGCACCG 61.021 60.000 0.00 0.00 0.00 4.94
156 157 3.321111 ACCACCAACACTAGTGACTACAG 59.679 47.826 29.30 14.83 36.01 2.74
168 169 2.203153 ACAGCCGACCACCAACAC 60.203 61.111 0.00 0.00 0.00 3.32
364 365 1.628340 CAGGGACATACTTGGTCACCA 59.372 52.381 0.00 0.00 39.53 4.17
464 465 2.598787 CCACCACCCTTTCCGCCTA 61.599 63.158 0.00 0.00 0.00 3.93
478 479 1.165270 CAATTTCCAGGACGTCCACC 58.835 55.000 35.00 10.80 38.89 4.61
493 494 2.289010 CCTCCTTTTTCTTGCGGCAATT 60.289 45.455 16.80 0.00 0.00 2.32
496 497 1.178534 CCCTCCTTTTTCTTGCGGCA 61.179 55.000 0.00 0.00 0.00 5.69
554 570 3.894547 TTTCCTGGCCGCGGTTCTC 62.895 63.158 28.70 14.43 0.00 2.87
574 590 4.353437 GGTGGTTGCTGCTGCTGC 62.353 66.667 22.51 22.51 40.48 5.25
575 591 2.273179 ATGGTGGTTGCTGCTGCTG 61.273 57.895 17.00 0.77 40.48 4.41
576 592 2.116772 ATGGTGGTTGCTGCTGCT 59.883 55.556 17.00 0.00 40.48 4.24
610 626 4.112634 CAAGAGCTAAACAATCGATCGGA 58.887 43.478 16.41 2.25 0.00 4.55
611 627 3.302740 GCAAGAGCTAAACAATCGATCGG 60.303 47.826 16.41 1.30 37.91 4.18
684 700 1.003580 CCTTCCCACTACACTGTGCAT 59.996 52.381 7.90 0.00 36.68 3.96
686 702 0.685097 TCCTTCCCACTACACTGTGC 59.315 55.000 7.90 0.00 36.68 4.57
687 703 1.276421 CCTCCTTCCCACTACACTGTG 59.724 57.143 6.19 6.19 37.66 3.66
688 704 1.645710 CCTCCTTCCCACTACACTGT 58.354 55.000 0.00 0.00 0.00 3.55
689 705 0.905357 CCCTCCTTCCCACTACACTG 59.095 60.000 0.00 0.00 0.00 3.66
690 706 0.492276 ACCCTCCTTCCCACTACACT 59.508 55.000 0.00 0.00 0.00 3.55
691 707 0.613777 CACCCTCCTTCCCACTACAC 59.386 60.000 0.00 0.00 0.00 2.90
692 708 0.490017 TCACCCTCCTTCCCACTACA 59.510 55.000 0.00 0.00 0.00 2.74
693 709 1.652947 TTCACCCTCCTTCCCACTAC 58.347 55.000 0.00 0.00 0.00 2.73
695 711 1.425448 CTTTTCACCCTCCTTCCCACT 59.575 52.381 0.00 0.00 0.00 4.00
696 712 1.423921 TCTTTTCACCCTCCTTCCCAC 59.576 52.381 0.00 0.00 0.00 4.61
697 713 1.827792 TCTTTTCACCCTCCTTCCCA 58.172 50.000 0.00 0.00 0.00 4.37
698 714 2.971901 TTCTTTTCACCCTCCTTCCC 57.028 50.000 0.00 0.00 0.00 3.97
699 715 3.958147 TGTTTTCTTTTCACCCTCCTTCC 59.042 43.478 0.00 0.00 0.00 3.46
700 716 5.592104 TTGTTTTCTTTTCACCCTCCTTC 57.408 39.130 0.00 0.00 0.00 3.46
704 720 5.576774 CAGTGTTTGTTTTCTTTTCACCCTC 59.423 40.000 0.00 0.00 0.00 4.30
708 724 5.176590 TGTGCAGTGTTTGTTTTCTTTTCAC 59.823 36.000 0.00 0.00 0.00 3.18
734 795 1.453155 TCTTTTCAAGCATCGCTCCC 58.547 50.000 0.00 0.00 38.25 4.30
739 800 8.951969 GCTATTTCTTAATCTTTTCAAGCATCG 58.048 33.333 0.00 0.00 0.00 3.84
756 817 6.825721 CCAGGTCTTTCTACATGCTATTTCTT 59.174 38.462 0.00 0.00 29.97 2.52
758 819 6.116126 ACCAGGTCTTTCTACATGCTATTTC 58.884 40.000 0.00 0.00 29.97 2.17
762 823 5.127194 CACTACCAGGTCTTTCTACATGCTA 59.873 44.000 0.00 0.00 29.97 3.49
779 849 0.720232 ACCATCCCCTACCACTACCA 59.280 55.000 0.00 0.00 0.00 3.25
780 850 1.129058 CACCATCCCCTACCACTACC 58.871 60.000 0.00 0.00 0.00 3.18
781 851 2.169978 GTTCACCATCCCCTACCACTAC 59.830 54.545 0.00 0.00 0.00 2.73
782 852 2.474112 GTTCACCATCCCCTACCACTA 58.526 52.381 0.00 0.00 0.00 2.74
783 853 1.286248 GTTCACCATCCCCTACCACT 58.714 55.000 0.00 0.00 0.00 4.00
784 854 0.107848 CGTTCACCATCCCCTACCAC 60.108 60.000 0.00 0.00 0.00 4.16
792 862 1.338674 TGATGTGGACGTTCACCATCC 60.339 52.381 24.06 10.65 39.69 3.51
813 883 3.581265 TGTGGTGACATATGGATGCAT 57.419 42.857 7.80 4.68 46.14 3.96
829 903 2.292016 TGTGGCACGTATTTCTTTGTGG 59.708 45.455 13.77 0.00 33.04 4.17
859 933 7.229907 AGCAGTGATGTTTTCATATATGCATCA 59.770 33.333 20.72 20.72 40.80 3.07
860 934 7.537649 CAGCAGTGATGTTTTCATATATGCATC 59.462 37.037 17.48 17.48 40.80 3.91
861 935 7.368059 CAGCAGTGATGTTTTCATATATGCAT 58.632 34.615 3.79 3.79 40.80 3.96
862 936 6.731164 CAGCAGTGATGTTTTCATATATGCA 58.269 36.000 7.92 0.74 40.80 3.96
863 937 5.628193 GCAGCAGTGATGTTTTCATATATGC 59.372 40.000 10.56 0.00 41.05 3.14
864 938 6.147581 GGCAGCAGTGATGTTTTCATATATG 58.852 40.000 10.56 6.36 41.05 1.78
865 939 5.829391 TGGCAGCAGTGATGTTTTCATATAT 59.171 36.000 10.56 0.00 41.05 0.86
866 940 5.192176 TGGCAGCAGTGATGTTTTCATATA 58.808 37.500 10.56 0.00 41.05 0.86
913 1018 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1013 1124 3.181475 ACATGTATCAACTACCTCGGCAG 60.181 47.826 0.00 0.00 0.00 4.85
1018 1129 5.967088 ACACTGACATGTATCAACTACCTC 58.033 41.667 0.00 0.00 0.00 3.85
1269 1408 9.464714 GCGACAAGAAATATACTCATCTTTCTA 57.535 33.333 0.00 0.00 36.87 2.10
1355 1494 7.174599 AGTTTCTGAAGAAATCTTGGTCATCTG 59.825 37.037 8.64 0.00 44.69 2.90
1356 1495 7.174599 CAGTTTCTGAAGAAATCTTGGTCATCT 59.825 37.037 8.64 0.00 44.69 2.90
1388 1527 1.109609 ATCTCTGCTGCATCGAGACA 58.890 50.000 19.84 3.87 36.70 3.41
1602 1760 4.148825 ATCGTGCAGGCGGAGGTC 62.149 66.667 0.35 0.00 0.00 3.85
1707 1898 1.135575 GTGAATTTCCTTGAGCAGCCG 60.136 52.381 0.00 0.00 0.00 5.52
1938 2129 3.730963 GCTTGTTAGCCGAGCCATAAAAC 60.731 47.826 0.00 0.00 43.79 2.43
1940 2131 2.014128 GCTTGTTAGCCGAGCCATAAA 58.986 47.619 0.00 0.00 43.79 1.40
1953 2144 5.045213 TCCTTCTTCCATACCATGCTTGTTA 60.045 40.000 0.00 0.00 0.00 2.41
1954 2145 4.019174 CCTTCTTCCATACCATGCTTGTT 58.981 43.478 0.00 0.00 0.00 2.83
1955 2146 3.266772 TCCTTCTTCCATACCATGCTTGT 59.733 43.478 0.00 0.00 0.00 3.16
1966 2157 0.912486 CGGAGGGTTCCTTCTTCCAT 59.088 55.000 1.26 0.00 41.67 3.41
1990 2183 2.159000 TCCAGTCAGCTGCTATGTCATG 60.159 50.000 9.47 0.00 41.26 3.07
2013 2206 1.519455 GGATGACGGCTCCTGTTCG 60.519 63.158 0.00 0.00 0.00 3.95
2226 2536 0.817013 AAATGCCGCACAGTTATGGG 59.183 50.000 0.00 0.00 34.12 4.00
2228 2538 1.472082 TGGAAATGCCGCACAGTTATG 59.528 47.619 0.00 0.00 36.53 1.90
2229 2539 1.745087 CTGGAAATGCCGCACAGTTAT 59.255 47.619 0.00 0.00 36.53 1.89
2230 2540 1.164411 CTGGAAATGCCGCACAGTTA 58.836 50.000 0.00 0.00 36.53 2.24
2231 2541 1.526575 CCTGGAAATGCCGCACAGTT 61.527 55.000 0.00 0.00 39.79 3.16
2275 2590 4.148128 ACCCAAATGTTTTGTCATGCAA 57.852 36.364 0.00 0.00 34.87 4.08
2498 2834 5.718649 TGCTAAACGCTAATTGATCAGAC 57.281 39.130 0.00 0.00 40.11 3.51
2500 2836 7.697710 TGAAAATGCTAAACGCTAATTGATCAG 59.302 33.333 0.00 0.00 40.11 2.90
2551 2929 4.878971 GCTTGTGTTTACCCCAAATGTTTT 59.121 37.500 0.00 0.00 0.00 2.43
2552 2930 4.080863 TGCTTGTGTTTACCCCAAATGTTT 60.081 37.500 0.00 0.00 0.00 2.83
2673 3053 7.210174 AGGGAAAATAGAAACAAAAAGTCTGC 58.790 34.615 0.00 0.00 0.00 4.26
2750 3161 6.412362 TTTTCTGTATGCTTTAGCCCAAAA 57.588 33.333 0.00 0.00 41.18 2.44
2797 3489 1.073098 ATTTTTGACTCCGACCCCCT 58.927 50.000 0.00 0.00 0.00 4.79
2817 3865 3.961849 AGAGGAAGAAGCAAAGAATCCC 58.038 45.455 0.00 0.00 0.00 3.85
2871 4361 6.926630 AGGTAAGATGTTTTAATTGGCCAA 57.073 33.333 23.00 23.00 0.00 4.52
3086 4594 8.558973 AGTTAAGAGCGAGAGTAACTAGTAAA 57.441 34.615 0.00 0.00 35.54 2.01
3173 4685 2.222678 CCGATGATGTAGCTGAATGCAC 59.777 50.000 0.00 0.00 45.94 4.57
3176 4698 1.458445 CGCCGATGATGTAGCTGAATG 59.542 52.381 0.00 0.00 0.00 2.67
3517 5039 4.319477 CCAAGTAGTCGGACAATGTTTGTG 60.319 45.833 11.27 0.00 45.52 3.33
3535 5057 1.959282 CCTTCAGAGCAAAAGCCAAGT 59.041 47.619 0.00 0.00 0.00 3.16
3558 5080 7.709613 TGAATTCGTAAATAAGAGCCCTTCTAC 59.290 37.037 0.04 0.00 34.14 2.59
3649 5171 7.567571 CAATATCTAGCATTTTGTCTGGTACG 58.432 38.462 0.00 0.00 0.00 3.67
4120 5642 3.506067 GGTTCCACTGAATACACCAAAGG 59.494 47.826 0.00 0.00 31.98 3.11
4240 5762 0.469494 TGTCTATGGCATGCGGTGAT 59.531 50.000 12.44 3.59 0.00 3.06
4305 5830 9.710900 GATACACACATGAATCAACTATATCCA 57.289 33.333 0.00 0.00 0.00 3.41
4344 5869 1.062525 CATTGCTAGAAACCGCGCC 59.937 57.895 0.00 0.00 0.00 6.53
4347 5872 7.224167 ACTTTATACTACATTGCTAGAAACCGC 59.776 37.037 0.00 0.00 0.00 5.68
4361 5886 9.953565 ACTTGGCAATAGAAACTTTATACTACA 57.046 29.630 0.00 0.00 0.00 2.74
4364 5889 9.515226 TTGACTTGGCAATAGAAACTTTATACT 57.485 29.630 0.00 0.00 0.00 2.12
4372 5897 6.215845 ACACAATTGACTTGGCAATAGAAAC 58.784 36.000 13.59 0.00 37.50 2.78
4373 5898 6.403866 ACACAATTGACTTGGCAATAGAAA 57.596 33.333 13.59 0.00 37.50 2.52
4374 5899 6.403866 AACACAATTGACTTGGCAATAGAA 57.596 33.333 13.59 0.00 37.50 2.10
4375 5900 6.714810 ACTAACACAATTGACTTGGCAATAGA 59.285 34.615 13.59 0.00 37.50 1.98
4376 5901 6.913170 ACTAACACAATTGACTTGGCAATAG 58.087 36.000 13.59 0.00 37.50 1.73
4391 5916 4.917385 AGGCATGATGGTAACTAACACAA 58.083 39.130 0.00 0.00 37.61 3.33
4397 5922 3.653164 TCAGGAGGCATGATGGTAACTA 58.347 45.455 0.00 0.00 37.61 2.24
4398 5923 2.481441 TCAGGAGGCATGATGGTAACT 58.519 47.619 0.00 0.00 37.61 2.24
4401 5926 4.660303 ACTAAATCAGGAGGCATGATGGTA 59.340 41.667 0.00 0.00 37.46 3.25
4402 5927 3.461085 ACTAAATCAGGAGGCATGATGGT 59.539 43.478 0.00 0.00 37.46 3.55
4403 5928 4.070716 GACTAAATCAGGAGGCATGATGG 58.929 47.826 0.00 0.00 37.46 3.51
4404 5929 4.070716 GGACTAAATCAGGAGGCATGATG 58.929 47.826 0.00 0.00 37.46 3.07
4405 5930 3.718434 TGGACTAAATCAGGAGGCATGAT 59.282 43.478 0.00 0.00 39.06 2.45
4407 5932 3.565764 TGGACTAAATCAGGAGGCATG 57.434 47.619 0.00 0.00 0.00 4.06
4408 5933 3.718434 TCATGGACTAAATCAGGAGGCAT 59.282 43.478 0.00 0.00 0.00 4.40
4409 5934 3.114606 TCATGGACTAAATCAGGAGGCA 58.885 45.455 0.00 0.00 0.00 4.75
4410 5935 3.737850 CTCATGGACTAAATCAGGAGGC 58.262 50.000 0.00 0.00 37.92 4.70
4411 5936 3.495806 GGCTCATGGACTAAATCAGGAGG 60.496 52.174 7.03 0.00 40.73 4.30
4412 5937 3.135348 TGGCTCATGGACTAAATCAGGAG 59.865 47.826 0.00 0.00 42.53 3.69
4425 5968 8.896744 CCAGTATTACAATATAATGGCTCATGG 58.103 37.037 0.00 0.00 38.81 3.66
4464 6009 6.316890 GGCAATGGCATTTTCAACTATTTCAT 59.683 34.615 10.65 0.00 43.71 2.57
4469 6014 3.195396 ACGGCAATGGCATTTTCAACTAT 59.805 39.130 10.65 0.00 43.71 2.12
4498 6043 9.462174 CTGAAATTAATAACTGCACAAGTCAAA 57.538 29.630 0.00 0.00 38.56 2.69
4499 6044 8.629158 ACTGAAATTAATAACTGCACAAGTCAA 58.371 29.630 0.00 0.00 38.56 3.18
4503 6048 8.693504 CACAACTGAAATTAATAACTGCACAAG 58.306 33.333 0.00 0.00 0.00 3.16
4504 6049 8.194104 ACACAACTGAAATTAATAACTGCACAA 58.806 29.630 0.00 0.00 0.00 3.33
4506 6051 9.329913 CTACACAACTGAAATTAATAACTGCAC 57.670 33.333 0.00 0.00 0.00 4.57
4514 6059 9.959721 AGTGGATACTACACAACTGAAATTAAT 57.040 29.630 0.00 0.00 41.21 1.40
4515 6060 9.214957 CAGTGGATACTACACAACTGAAATTAA 57.785 33.333 0.00 0.00 41.21 1.40
4516 6061 7.822334 CCAGTGGATACTACACAACTGAAATTA 59.178 37.037 1.68 0.00 41.21 1.40
4517 6062 6.655003 CCAGTGGATACTACACAACTGAAATT 59.345 38.462 1.68 0.00 41.21 1.82
4518 6063 6.173339 CCAGTGGATACTACACAACTGAAAT 58.827 40.000 1.68 0.00 41.21 2.17
4543 6088 5.333566 AATCCTCTTGTGTTTTAGGGGAA 57.666 39.130 0.00 0.00 44.01 3.97
4544 6089 6.652205 ATAATCCTCTTGTGTTTTAGGGGA 57.348 37.500 0.00 0.00 44.87 4.81
4545 6090 8.053355 ACTAATAATCCTCTTGTGTTTTAGGGG 58.947 37.037 0.00 0.00 33.01 4.79
4549 6146 9.667107 CTGGACTAATAATCCTCTTGTGTTTTA 57.333 33.333 0.00 0.00 37.13 1.52
4550 6147 7.121315 GCTGGACTAATAATCCTCTTGTGTTTT 59.879 37.037 0.00 0.00 37.13 2.43
4553 6150 5.189736 TGCTGGACTAATAATCCTCTTGTGT 59.810 40.000 0.00 0.00 37.13 3.72
4598 6319 9.835389 TTTCCTCTCATTTTCATCAAACAAAAT 57.165 25.926 0.00 0.00 33.37 1.82
4599 6320 9.664332 TTTTCCTCTCATTTTCATCAAACAAAA 57.336 25.926 0.00 0.00 0.00 2.44
4601 6322 9.097257 GTTTTTCCTCTCATTTTCATCAAACAA 57.903 29.630 0.00 0.00 0.00 2.83
4603 6324 7.096065 CCGTTTTTCCTCTCATTTTCATCAAAC 60.096 37.037 0.00 0.00 0.00 2.93
4606 6327 5.767665 TCCGTTTTTCCTCTCATTTTCATCA 59.232 36.000 0.00 0.00 0.00 3.07
4607 6328 6.086871 GTCCGTTTTTCCTCTCATTTTCATC 58.913 40.000 0.00 0.00 0.00 2.92
4608 6329 5.048013 GGTCCGTTTTTCCTCTCATTTTCAT 60.048 40.000 0.00 0.00 0.00 2.57
4610 6331 4.277423 TGGTCCGTTTTTCCTCTCATTTTC 59.723 41.667 0.00 0.00 0.00 2.29
4618 6585 5.122711 TCGATATTTTGGTCCGTTTTTCCTC 59.877 40.000 0.00 0.00 0.00 3.71
4629 6596 3.312697 GTGGCCTCTTCGATATTTTGGTC 59.687 47.826 3.32 0.00 0.00 4.02
4630 6597 3.279434 GTGGCCTCTTCGATATTTTGGT 58.721 45.455 3.32 0.00 0.00 3.67
4692 6659 2.237143 AGCCTTATCTGCACTGCAACTA 59.763 45.455 4.99 0.00 38.41 2.24
4801 6768 2.124983 TGCTTCCATGAGCTCGGC 60.125 61.111 9.64 6.91 43.11 5.54
4826 6793 0.534873 GAGGAGCTGAGGAAGGTGAC 59.465 60.000 0.00 0.00 36.52 3.67
4984 6951 2.915659 ACGGCCTCGAAGGTGACA 60.916 61.111 0.00 0.00 37.80 3.58


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

AutoCloner maintained by Alex Coulton.