Multiple sequence alignment - TraesCS7B01G150300

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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 TraesCS7B01G150300 chr7B 100.000 4662 0 0 1 4662 199490671 199495332 0.000000e+00 8610.0
1 TraesCS7B01G150300 chr7D 93.308 4229 224 33 1 4201 228004230 228008427 0.000000e+00 6187.0
2 TraesCS7B01G150300 chr7D 91.866 418 24 6 4248 4662 228009954 228010364 4.050000e-160 575.0
3 TraesCS7B01G150300 chr7D 80.851 282 43 5 649 929 491793092 491792821 1.310000e-50 211.0
4 TraesCS7B01G150300 chr7D 78.378 259 45 11 2 255 161038514 161038766 1.740000e-34 158.0
5 TraesCS7B01G150300 chr7A 94.065 3791 148 39 903 4662 240082004 240085748 0.000000e+00 5683.0
6 TraesCS7B01G150300 chr3B 83.713 614 90 10 2 609 475381673 475382282 5.230000e-159 571.0
7 TraesCS7B01G150300 chr3B 81.564 179 29 4 3 179 825327273 825327449 1.350000e-30 145.0
8 TraesCS7B01G150300 chr3B 89.091 55 5 1 698 751 826655243 826655189 3.010000e-07 67.6
9 TraesCS7B01G150300 chr1B 83.956 455 66 7 160 609 564914992 564915444 3.330000e-116 429.0
10 TraesCS7B01G150300 chr4D 80.460 261 39 11 2 257 358533583 358533836 6.160000e-44 189.0
11 TraesCS7B01G150300 chr5A 77.992 259 48 8 2 257 294873282 294873030 2.250000e-33 154.0
12 TraesCS7B01G150300 chr6B 77.186 263 42 15 1 252 189212309 189212564 2.260000e-28 137.0
13 TraesCS7B01G150300 chrUn 81.212 165 28 3 3 166 41141179 41141017 3.790000e-26 130.0
14 TraesCS7B01G150300 chrUn 81.212 165 28 3 3 166 211776850 211776688 3.790000e-26 130.0
15 TraesCS7B01G150300 chr6A 75.217 230 55 2 698 926 150910879 150910651 1.770000e-19 108.0


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 TraesCS7B01G150300 chr7B 199490671 199495332 4661 False 8610 8610 100.000 1 4662 1 chr7B.!!$F1 4661
1 TraesCS7B01G150300 chr7D 228004230 228010364 6134 False 3381 6187 92.587 1 4662 2 chr7D.!!$F2 4661
2 TraesCS7B01G150300 chr7A 240082004 240085748 3744 False 5683 5683 94.065 903 4662 1 chr7A.!!$F1 3759
3 TraesCS7B01G150300 chr3B 475381673 475382282 609 False 571 571 83.713 2 609 1 chr3B.!!$F1 607


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
82 83 0.105298 GGGGGTACGGATTAGAGGGT 60.105 60.000 0.00 0.00 0.0 4.34 F
556 561 0.317160 CAGTGCACGGTGTCCTTAGA 59.683 55.000 12.01 0.00 0.0 2.10 F
864 869 0.515564 CGCGTTGGACCGATTTTTCT 59.484 50.000 0.00 0.00 0.0 2.52 F
1773 1805 1.079543 CTGAGACAACCGGCCTCTG 60.080 63.158 0.00 3.88 0.0 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1934 1966 0.108138 GGGATCTGTCTCACAACCCG 60.108 60.000 0.00 0.0 30.67 5.28 R
2480 2520 1.695242 ACAACGTCCTGGTAACCATCA 59.305 47.619 0.00 0.0 30.82 3.07 R
2755 2795 4.763793 GCATAGATGTTCCATAATGCTGGT 59.236 41.667 12.98 0.0 37.37 4.00 R
3740 3782 1.169577 TGCCAACAACGACACAAGTT 58.830 45.000 0.00 0.0 0.00 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
19 20 2.925706 TTAGACGCCTGCCCCACA 60.926 61.111 0.00 0.00 0.00 4.17
50 51 1.315690 CTGTCGCGGGAATAGGTCTA 58.684 55.000 6.13 0.00 0.00 2.59
82 83 0.105298 GGGGGTACGGATTAGAGGGT 60.105 60.000 0.00 0.00 0.00 4.34
137 138 4.161001 GGATTTACGAGTTTAGACCCCTCA 59.839 45.833 0.00 0.00 0.00 3.86
139 140 2.005370 ACGAGTTTAGACCCCTCACA 57.995 50.000 0.00 0.00 0.00 3.58
156 157 2.838202 TCACAGAGGAGATAACAACCCC 59.162 50.000 0.00 0.00 0.00 4.95
195 196 3.929610 GAGCTTGATTGACTGGAGTGTAC 59.070 47.826 0.00 0.00 0.00 2.90
238 239 1.005924 CTTGTTATGGAGCTGGGGGTT 59.994 52.381 0.00 0.00 0.00 4.11
257 258 4.492611 GGTTGCTTATATAGAGTACGCCC 58.507 47.826 0.00 0.00 0.00 6.13
259 260 3.415212 TGCTTATATAGAGTACGCCCGT 58.585 45.455 0.00 0.00 0.00 5.28
294 296 5.489637 TGCTCCCATAACTAAGGGTTAAAGA 59.510 40.000 0.00 0.00 45.64 2.52
308 310 4.020839 GGGTTAAAGAGGGGTTTTAAAGGC 60.021 45.833 0.00 0.00 33.28 4.35
309 311 4.589798 GGTTAAAGAGGGGTTTTAAAGGCA 59.410 41.667 0.00 0.00 33.28 4.75
313 315 3.648739 AGAGGGGTTTTAAAGGCAACAA 58.351 40.909 0.00 0.00 41.41 2.83
411 413 2.873094 TGGTCTTCTCTGTCCGAGTA 57.127 50.000 0.00 0.00 40.75 2.59
461 464 3.449377 TGGTCGATGGATTGCTTGTACTA 59.551 43.478 0.00 0.00 0.00 1.82
472 475 4.617253 TGCTTGTACTATGAGTGGTTGT 57.383 40.909 0.00 0.00 0.00 3.32
523 526 3.926058 ATTATGAACGGTAACCTGGCT 57.074 42.857 0.00 0.00 0.00 4.75
530 533 2.125106 GTAACCTGGCTCTGGGCG 60.125 66.667 0.00 0.00 42.94 6.13
554 559 1.301401 GCAGTGCACGGTGTCCTTA 60.301 57.895 18.34 0.00 0.00 2.69
556 561 0.317160 CAGTGCACGGTGTCCTTAGA 59.683 55.000 12.01 0.00 0.00 2.10
589 594 2.457598 GTCAGACCAGTGACCCTATCA 58.542 52.381 0.00 0.00 40.96 2.15
592 597 2.035193 CAGACCAGTGACCCTATCATCG 59.965 54.545 0.00 0.00 40.28 3.84
612 617 4.395625 TCGGTATATGTCCTCGTCAAGAT 58.604 43.478 0.00 0.00 0.00 2.40
620 625 4.847516 TCGTCAAGATCGGCGGCG 62.848 66.667 27.15 27.15 0.00 6.46
636 641 3.864686 CGGCATCAAGGTTCGGCG 61.865 66.667 0.00 0.00 41.08 6.46
637 642 3.508840 GGCATCAAGGTTCGGCGG 61.509 66.667 7.21 0.00 0.00 6.13
675 680 3.135027 CGGGAGGGTTTTGGGAAAA 57.865 52.632 0.00 0.00 0.00 2.29
688 693 3.843177 TGGGAAAATGGAGGGAAATGA 57.157 42.857 0.00 0.00 0.00 2.57
693 698 4.471025 GGAAAATGGAGGGAAATGATGGTT 59.529 41.667 0.00 0.00 0.00 3.67
695 700 3.763557 ATGGAGGGAAATGATGGTTGT 57.236 42.857 0.00 0.00 0.00 3.32
757 762 3.547313 GCGCGCGTCCGTTTCATA 61.547 61.111 32.35 0.00 36.67 2.15
762 767 1.563173 GCGTCCGTTTCATATCCGC 59.437 57.895 0.00 0.00 0.00 5.54
781 786 1.714794 CGTCGAGGCAAATGAGACTT 58.285 50.000 0.00 0.00 0.00 3.01
788 793 7.412563 CGTCGAGGCAAATGAGACTTAAATTTA 60.413 37.037 0.00 0.00 0.00 1.40
790 795 7.822334 TCGAGGCAAATGAGACTTAAATTTAGA 59.178 33.333 0.00 0.00 0.00 2.10
792 797 8.056407 AGGCAAATGAGACTTAAATTTAGACC 57.944 34.615 0.00 0.00 0.00 3.85
795 800 7.472543 CAAATGAGACTTAAATTTAGACCGGG 58.527 38.462 6.32 0.00 0.00 5.73
800 805 6.120220 AGACTTAAATTTAGACCGGGAATGG 58.880 40.000 6.32 0.00 0.00 3.16
809 814 2.297895 CCGGGAATGGGTGGACAGA 61.298 63.158 0.00 0.00 0.00 3.41
816 821 2.987547 GGGTGGACAGACGGACGA 60.988 66.667 0.00 0.00 0.00 4.20
822 827 0.599204 GGACAGACGGACGAAAAGCA 60.599 55.000 0.00 0.00 0.00 3.91
852 857 1.944676 GTCTAGATCGGCGCGTTGG 60.945 63.158 8.43 0.00 0.00 3.77
853 858 2.116533 TCTAGATCGGCGCGTTGGA 61.117 57.895 8.43 2.80 0.00 3.53
855 860 3.420214 TAGATCGGCGCGTTGGACC 62.420 63.158 8.43 0.00 0.00 4.46
860 865 3.428282 GGCGCGTTGGACCGATTT 61.428 61.111 8.43 0.00 0.00 2.17
862 867 1.081708 GCGCGTTGGACCGATTTTT 60.082 52.632 8.43 0.00 0.00 1.94
863 868 1.063412 GCGCGTTGGACCGATTTTTC 61.063 55.000 8.43 0.00 0.00 2.29
864 869 0.515564 CGCGTTGGACCGATTTTTCT 59.484 50.000 0.00 0.00 0.00 2.52
865 870 1.727880 CGCGTTGGACCGATTTTTCTA 59.272 47.619 0.00 0.00 0.00 2.10
869 874 4.791676 GCGTTGGACCGATTTTTCTATTTC 59.208 41.667 0.00 0.00 0.00 2.17
871 876 5.329493 GTTGGACCGATTTTTCTATTTCCG 58.671 41.667 0.00 0.00 0.00 4.30
873 878 3.242969 GGACCGATTTTTCTATTTCCGGC 60.243 47.826 0.00 0.00 39.09 6.13
907 929 7.956508 GGATACGTATAGATGAAATGAGTCG 57.043 40.000 8.34 0.00 0.00 4.18
916 938 2.777094 TGAAATGAGTCGGTGCATTGA 58.223 42.857 0.00 0.00 35.11 2.57
928 950 3.425359 CGGTGCATTGAAGTTGCTCTTAG 60.425 47.826 0.00 0.00 40.77 2.18
940 962 4.019321 AGTTGCTCTTAGGCTATCCAAACA 60.019 41.667 0.00 0.00 33.74 2.83
949 971 5.649782 AGGCTATCCAAACAGACAAAATG 57.350 39.130 0.00 0.00 33.74 2.32
950 972 4.463891 AGGCTATCCAAACAGACAAAATGG 59.536 41.667 0.00 0.00 33.74 3.16
952 974 4.462483 GCTATCCAAACAGACAAAATGGGA 59.538 41.667 0.00 0.00 0.00 4.37
954 976 6.351286 GCTATCCAAACAGACAAAATGGGAAT 60.351 38.462 0.00 0.00 0.00 3.01
959 981 8.435982 TCCAAACAGACAAAATGGGAATAAAAT 58.564 29.630 0.00 0.00 0.00 1.82
961 983 8.434661 CAAACAGACAAAATGGGAATAAAATCG 58.565 33.333 0.00 0.00 0.00 3.34
962 984 6.099341 ACAGACAAAATGGGAATAAAATCGC 58.901 36.000 0.00 0.00 0.00 4.58
973 995 5.463061 GGGAATAAAATCGCATGTCCATTTG 59.537 40.000 0.00 0.00 32.88 2.32
1159 1188 3.007182 TCCACGAATTAACGAGTTTCCCT 59.993 43.478 0.00 0.00 37.03 4.20
1215 1244 2.892425 CCATCGACCGAAGCCAGC 60.892 66.667 0.00 0.00 0.00 4.85
1251 1280 2.835431 CCGAGCGGAGGGATGACT 60.835 66.667 2.00 0.00 37.50 3.41
1433 1462 2.156098 CTCCGGTGAGTAGCCTATCTC 58.844 57.143 0.00 0.00 33.70 2.75
1480 1509 2.123854 CGGATCGGTCAGGGAGGA 60.124 66.667 0.00 0.00 0.00 3.71
1488 1517 1.338200 CGGTCAGGGAGGAAGTTTCTG 60.338 57.143 0.00 0.00 0.00 3.02
1495 1524 1.478654 GGAGGAAGTTTCTGTGGGCAA 60.479 52.381 0.00 0.00 0.00 4.52
1505 1534 1.133513 TCTGTGGGCAACTTGGTTGAT 60.134 47.619 13.63 0.00 45.28 2.57
1567 1596 2.356069 CACTCGATCGATCAACTGGAGA 59.644 50.000 24.89 13.13 0.00 3.71
1569 1598 2.616376 CTCGATCGATCAACTGGAGAGT 59.384 50.000 24.40 0.00 0.00 3.24
1582 1611 8.589701 TCAACTGGAGAGTAATGTAGAATGTA 57.410 34.615 0.00 0.00 0.00 2.29
1598 1627 4.517453 AGAATGTATGCTCTACGGAGTCTC 59.483 45.833 0.00 0.00 43.93 3.36
1628 1657 3.190079 TGTAGAATGACTCGAATGCTGC 58.810 45.455 0.00 0.00 0.00 5.25
1718 1747 7.566858 GGTAACAATACAATCAAAGCAACTG 57.433 36.000 0.00 0.00 33.45 3.16
1739 1768 6.051717 ACTGGTGATGTAGCAAGTCAATATC 58.948 40.000 0.00 0.00 36.15 1.63
1744 1773 7.096023 GGTGATGTAGCAAGTCAATATCTTACG 60.096 40.741 0.00 0.00 0.00 3.18
1745 1774 7.435488 GTGATGTAGCAAGTCAATATCTTACGT 59.565 37.037 0.00 0.00 0.00 3.57
1746 1775 7.979537 TGATGTAGCAAGTCAATATCTTACGTT 59.020 33.333 0.00 0.00 0.00 3.99
1773 1805 1.079543 CTGAGACAACCGGCCTCTG 60.080 63.158 0.00 3.88 0.00 3.35
1774 1806 1.821061 CTGAGACAACCGGCCTCTGT 61.821 60.000 0.00 0.00 0.00 3.41
1786 1818 3.644606 CTCTGTGCCCTGTGCCCT 61.645 66.667 0.00 0.00 40.16 5.19
1787 1819 3.914579 CTCTGTGCCCTGTGCCCTG 62.915 68.421 0.00 0.00 40.16 4.45
1977 2009 1.767692 GACTCCCTTCCCCAAAGCA 59.232 57.895 0.00 0.00 33.29 3.91
2052 2091 9.342308 ACTACTGGTGATATGGAAATTTATGTG 57.658 33.333 0.00 0.00 0.00 3.21
2169 2208 6.425721 CGTCTTGGGTTCATGAAAACTTACTA 59.574 38.462 10.35 0.00 0.00 1.82
2222 2261 8.443937 GTTACACAGTCCATTCTCATCTTTTAC 58.556 37.037 0.00 0.00 0.00 2.01
2315 2354 6.716628 ACTGGTTGTATTGTTGATTGAGATGT 59.283 34.615 0.00 0.00 0.00 3.06
2316 2355 7.231317 ACTGGTTGTATTGTTGATTGAGATGTT 59.769 33.333 0.00 0.00 0.00 2.71
2399 2439 4.911610 GCAGTTGTTATATTATTGCCAGCG 59.088 41.667 0.00 0.00 0.00 5.18
2411 2451 4.519540 ATTGCCAGCGTGTTTATTCTTT 57.480 36.364 0.00 0.00 0.00 2.52
2737 2777 7.148540 GCTGTTATTGACAAAGGTATCGTTACA 60.149 37.037 6.02 0.00 37.93 2.41
3296 3338 4.684724 ACAATGTCCTACTCTTGACCCTA 58.315 43.478 0.00 0.00 0.00 3.53
3554 3596 5.525378 GTCATAATCATCCGAACTTGCTTCT 59.475 40.000 0.00 0.00 0.00 2.85
3557 3599 3.401033 TCATCCGAACTTGCTTCTTGA 57.599 42.857 0.00 0.00 0.00 3.02
3628 3670 0.032678 ACGACAGTGCAAGAGTGGAG 59.967 55.000 0.00 0.00 0.00 3.86
3636 3678 1.490490 TGCAAGAGTGGAGTTGAAGGT 59.510 47.619 0.00 0.00 0.00 3.50
3641 3683 1.887198 GAGTGGAGTTGAAGGTCGAGA 59.113 52.381 0.00 0.00 0.00 4.04
3669 3711 4.034394 TGAAGCAGACAAATGATCGCATAC 59.966 41.667 0.00 0.00 33.44 2.39
3804 3847 4.521146 AGGATGTTGCTTCTTCGATCATT 58.479 39.130 0.00 0.00 0.00 2.57
3823 3866 9.188588 CGATCATTGAATTTGGAATAGAAATGG 57.811 33.333 0.00 0.00 0.00 3.16
3829 3872 8.592529 TGAATTTGGAATAGAAATGGATGTGA 57.407 30.769 0.00 0.00 0.00 3.58
3837 3880 7.922811 GGAATAGAAATGGATGTGATGTTTTCC 59.077 37.037 0.00 0.00 0.00 3.13
3980 4023 1.835531 GGGACGGGAAAGTATCTTGGA 59.164 52.381 0.00 0.00 0.00 3.53
3983 4027 4.524053 GGACGGGAAAGTATCTTGGAAAT 58.476 43.478 0.00 0.00 0.00 2.17
4135 4182 9.803315 GAGAAACTTGAACTTTTTAGGATTGTT 57.197 29.630 0.00 0.00 0.00 2.83
4171 4218 2.592102 ACATTCACAATGCTCCCTGT 57.408 45.000 0.00 0.00 42.69 4.00
4172 4219 2.880443 ACATTCACAATGCTCCCTGTT 58.120 42.857 0.00 0.00 42.69 3.16
4173 4220 3.233507 ACATTCACAATGCTCCCTGTTT 58.766 40.909 0.00 0.00 42.69 2.83
4174 4221 3.642848 ACATTCACAATGCTCCCTGTTTT 59.357 39.130 0.00 0.00 42.69 2.43
4175 4222 4.101430 ACATTCACAATGCTCCCTGTTTTT 59.899 37.500 0.00 0.00 42.69 1.94
4203 4250 6.676237 TTTTTGAAACTTCTGAATTTGGCC 57.324 33.333 0.00 0.00 0.00 5.36
4204 4251 5.350504 TTTGAAACTTCTGAATTTGGCCA 57.649 34.783 0.00 0.00 0.00 5.36
4207 4254 5.927819 TGAAACTTCTGAATTTGGCCATTT 58.072 33.333 6.09 3.13 0.00 2.32
4209 4256 7.504403 TGAAACTTCTGAATTTGGCCATTTTA 58.496 30.769 6.09 0.00 0.00 1.52
4210 4257 7.656948 TGAAACTTCTGAATTTGGCCATTTTAG 59.343 33.333 6.09 10.23 0.00 1.85
4211 4258 6.041423 ACTTCTGAATTTGGCCATTTTAGG 57.959 37.500 6.09 1.36 0.00 2.69
4212 4259 5.779771 ACTTCTGAATTTGGCCATTTTAGGA 59.220 36.000 6.09 3.87 0.00 2.94
4213 4260 6.269769 ACTTCTGAATTTGGCCATTTTAGGAA 59.730 34.615 6.09 7.34 0.00 3.36
4214 4261 6.872585 TCTGAATTTGGCCATTTTAGGAAT 57.127 33.333 6.09 0.00 0.00 3.01
4215 4262 7.256494 TCTGAATTTGGCCATTTTAGGAATT 57.744 32.000 6.09 7.74 0.00 2.17
4216 4263 7.104939 TCTGAATTTGGCCATTTTAGGAATTG 58.895 34.615 6.09 0.00 0.00 2.32
4217 4264 6.777782 TGAATTTGGCCATTTTAGGAATTGT 58.222 32.000 6.09 0.00 0.00 2.71
4218 4265 7.230027 TGAATTTGGCCATTTTAGGAATTGTT 58.770 30.769 6.09 0.00 0.00 2.83
4219 4266 7.174599 TGAATTTGGCCATTTTAGGAATTGTTG 59.825 33.333 6.09 0.00 0.00 3.33
4220 4267 5.815233 TTGGCCATTTTAGGAATTGTTGA 57.185 34.783 6.09 0.00 0.00 3.18
4221 4268 5.146010 TGGCCATTTTAGGAATTGTTGAC 57.854 39.130 0.00 0.00 0.00 3.18
4222 4269 4.590647 TGGCCATTTTAGGAATTGTTGACA 59.409 37.500 0.00 0.00 0.00 3.58
4223 4270 4.929211 GGCCATTTTAGGAATTGTTGACAC 59.071 41.667 0.00 0.00 0.00 3.67
4224 4271 5.510520 GGCCATTTTAGGAATTGTTGACACA 60.511 40.000 0.00 0.00 0.00 3.72
4225 4272 6.165577 GCCATTTTAGGAATTGTTGACACAT 58.834 36.000 0.00 0.00 31.06 3.21
4226 4273 7.319646 GCCATTTTAGGAATTGTTGACACATA 58.680 34.615 0.00 0.00 31.06 2.29
4227 4274 7.981225 GCCATTTTAGGAATTGTTGACACATAT 59.019 33.333 0.00 0.00 31.06 1.78
4244 4291 4.456911 CACATATGTTGGGAGCATGGTATC 59.543 45.833 5.37 0.00 0.00 2.24
4285 5830 1.490910 GGATACTTTCCACTCCTGGGG 59.509 57.143 0.00 0.00 44.74 4.96
4286 5831 0.919710 ATACTTTCCACTCCTGGGGC 59.080 55.000 0.00 0.00 38.25 5.80
4339 5884 9.097257 CCGTATGCAATTTTCCTTTATTTTCAT 57.903 29.630 0.00 0.00 0.00 2.57
4454 6004 4.270834 GGGAAAGTGGAAGAATCCCTTAC 58.729 47.826 1.89 0.00 45.95 2.34
4466 6016 2.241281 TCCCTTACTGGAACGGATCA 57.759 50.000 0.00 0.00 38.67 2.92
4487 6037 3.703001 ACGTCCATCTTCAATCCAACT 57.297 42.857 0.00 0.00 0.00 3.16
4491 6041 3.944015 GTCCATCTTCAATCCAACTCCTG 59.056 47.826 0.00 0.00 0.00 3.86
4506 6056 0.388520 TCCTGCAGATTCGACACGTG 60.389 55.000 17.39 15.48 0.00 4.49
4510 6060 1.352156 GCAGATTCGACACGTGTCCC 61.352 60.000 36.01 23.93 41.86 4.46
4623 6174 0.606673 GTGTGCCCCTCCTTTCTGTC 60.607 60.000 0.00 0.00 0.00 3.51
4624 6175 1.002011 GTGCCCCTCCTTTCTGTCC 60.002 63.158 0.00 0.00 0.00 4.02
4630 6181 1.199615 CCTCCTTTCTGTCCCTCTCC 58.800 60.000 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 4.988598 CGACAGTTGGCGCCCACT 62.989 66.667 26.54 26.54 40.91 4.00
37 38 4.643784 ACACTACTGTTAGACCTATTCCCG 59.356 45.833 0.00 0.00 0.00 5.14
50 51 2.762327 CGTACCCCCATACACTACTGTT 59.238 50.000 0.00 0.00 0.00 3.16
82 83 1.445871 TGCGTCGTAGCAAGACTCTA 58.554 50.000 5.20 0.00 45.06 2.43
137 138 2.572104 GTGGGGTTGTTATCTCCTCTGT 59.428 50.000 0.00 0.00 0.00 3.41
139 140 1.831736 CGTGGGGTTGTTATCTCCTCT 59.168 52.381 0.00 0.00 0.00 3.69
146 147 0.248289 CCGAGACGTGGGGTTGTTAT 59.752 55.000 0.00 0.00 0.00 1.89
156 157 2.126307 CCAGAGCACCGAGACGTG 60.126 66.667 0.00 0.00 36.80 4.49
195 196 5.765182 AGGGTTCACAATCTCTTGTTAACTG 59.235 40.000 7.22 0.14 43.88 3.16
200 201 4.536765 ACAAGGGTTCACAATCTCTTGTT 58.463 39.130 4.84 0.00 43.05 2.83
238 239 3.415212 ACGGGCGTACTCTATATAAGCA 58.585 45.455 0.00 0.00 0.00 3.91
257 258 0.533755 GGGAGCATTCATCAGGGACG 60.534 60.000 0.00 0.00 0.00 4.79
259 260 1.526315 ATGGGAGCATTCATCAGGGA 58.474 50.000 0.00 0.00 0.00 4.20
294 296 5.605069 AGTAATTGTTGCCTTTAAAACCCCT 59.395 36.000 0.00 0.00 0.00 4.79
313 315 8.910944 ACAGTCAATATAGACGTTACCAGTAAT 58.089 33.333 0.00 0.00 43.24 1.89
366 368 2.002586 CTCATCAAGATCGCAACGGTT 58.997 47.619 0.00 0.00 0.00 4.44
411 413 3.008157 TCTCACTCGGAGTACTTGAGTCT 59.992 47.826 22.04 6.20 44.40 3.24
461 464 2.104111 TCGGAAGACAACAACCACTCAT 59.896 45.455 0.00 0.00 33.31 2.90
472 475 2.814280 GAGAACCACTCGGAAGACAA 57.186 50.000 0.00 0.00 35.84 3.18
523 526 1.005037 CACTGCAACTACGCCCAGA 60.005 57.895 0.00 0.00 0.00 3.86
530 533 1.157870 ACACCGTGCACTGCAACTAC 61.158 55.000 16.19 0.00 41.47 2.73
577 582 5.580998 ACATATACCGATGATAGGGTCACT 58.419 41.667 0.00 0.00 40.28 3.41
589 594 4.395625 TCTTGACGAGGACATATACCGAT 58.604 43.478 0.00 0.00 0.00 4.18
592 597 4.379603 CCGATCTTGACGAGGACATATACC 60.380 50.000 0.00 0.00 0.00 2.73
620 625 3.508840 CCGCCGAACCTTGATGCC 61.509 66.667 0.00 0.00 0.00 4.40
621 626 3.508840 CCCGCCGAACCTTGATGC 61.509 66.667 0.00 0.00 0.00 3.91
630 635 4.444838 CATGGACGACCCGCCGAA 62.445 66.667 0.34 0.00 37.93 4.30
655 660 3.516949 TTCCCAAAACCCTCCCGGC 62.517 63.158 0.00 0.00 33.26 6.13
675 680 3.635591 GACAACCATCATTTCCCTCCAT 58.364 45.455 0.00 0.00 0.00 3.41
688 693 2.668212 CGGTGGCACGACAACCAT 60.668 61.111 12.17 0.00 38.46 3.55
715 720 1.228613 CGCCTACTCCTCCCCCTAG 60.229 68.421 0.00 0.00 0.00 3.02
754 759 0.874175 TTTGCCTCGACGCGGATATG 60.874 55.000 12.47 0.00 0.00 1.78
757 762 2.173669 CATTTGCCTCGACGCGGAT 61.174 57.895 12.47 0.00 0.00 4.18
762 767 1.714794 AAGTCTCATTTGCCTCGACG 58.285 50.000 0.00 0.00 0.00 5.12
781 786 4.528920 CACCCATTCCCGGTCTAAATTTA 58.471 43.478 0.00 0.00 0.00 1.40
788 793 2.124085 TCCACCCATTCCCGGTCT 59.876 61.111 0.00 0.00 0.00 3.85
790 795 2.530661 TGTCCACCCATTCCCGGT 60.531 61.111 0.00 0.00 0.00 5.28
792 797 1.078426 GTCTGTCCACCCATTCCCG 60.078 63.158 0.00 0.00 0.00 5.14
795 800 0.391263 GTCCGTCTGTCCACCCATTC 60.391 60.000 0.00 0.00 0.00 2.67
800 805 0.249573 TTTTCGTCCGTCTGTCCACC 60.250 55.000 0.00 0.00 0.00 4.61
809 814 2.308039 GCGTCTGCTTTTCGTCCGT 61.308 57.895 0.00 0.00 38.39 4.69
816 821 2.022129 CGGACTCGCGTCTGCTTTT 61.022 57.895 5.77 0.00 39.50 2.27
822 827 0.179078 ATCTAGACGGACTCGCGTCT 60.179 55.000 17.65 17.65 45.78 4.18
836 841 1.944676 GTCCAACGCGCCGATCTAG 60.945 63.158 5.73 0.00 0.00 2.43
838 843 4.814294 GGTCCAACGCGCCGATCT 62.814 66.667 5.73 0.00 0.00 2.75
852 857 3.545426 CGCCGGAAATAGAAAAATCGGTC 60.545 47.826 5.05 0.00 38.41 4.79
853 858 2.353579 CGCCGGAAATAGAAAAATCGGT 59.646 45.455 5.05 0.00 38.41 4.69
855 860 3.545426 GGTCGCCGGAAATAGAAAAATCG 60.545 47.826 5.05 0.00 0.00 3.34
856 861 3.242969 GGGTCGCCGGAAATAGAAAAATC 60.243 47.826 5.05 0.00 0.00 2.17
857 862 2.686405 GGGTCGCCGGAAATAGAAAAAT 59.314 45.455 5.05 0.00 0.00 1.82
858 863 2.086094 GGGTCGCCGGAAATAGAAAAA 58.914 47.619 5.05 0.00 0.00 1.94
860 865 0.614294 TGGGTCGCCGGAAATAGAAA 59.386 50.000 5.05 0.00 0.00 2.52
862 867 0.614294 TTTGGGTCGCCGGAAATAGA 59.386 50.000 5.05 0.00 0.00 1.98
863 868 0.730840 GTTTGGGTCGCCGGAAATAG 59.269 55.000 5.05 0.00 0.00 1.73
864 869 1.020333 CGTTTGGGTCGCCGGAAATA 61.020 55.000 5.05 0.00 0.00 1.40
865 870 2.329614 CGTTTGGGTCGCCGGAAAT 61.330 57.895 5.05 0.00 0.00 2.17
869 874 3.374012 TATCCGTTTGGGTCGCCGG 62.374 63.158 0.00 0.00 41.75 6.13
871 876 2.169146 CGTATCCGTTTGGGTCGCC 61.169 63.158 0.00 0.00 37.00 5.54
884 906 7.482113 CACCGACTCATTTCATCTATACGTATC 59.518 40.741 12.24 0.00 0.00 2.24
886 908 6.665465 CACCGACTCATTTCATCTATACGTA 58.335 40.000 0.00 0.00 0.00 3.57
889 911 5.289595 TGCACCGACTCATTTCATCTATAC 58.710 41.667 0.00 0.00 0.00 1.47
891 913 4.406648 TGCACCGACTCATTTCATCTAT 57.593 40.909 0.00 0.00 0.00 1.98
892 914 3.885724 TGCACCGACTCATTTCATCTA 57.114 42.857 0.00 0.00 0.00 1.98
894 916 3.374988 TCAATGCACCGACTCATTTCATC 59.625 43.478 0.00 0.00 31.15 2.92
895 917 3.346315 TCAATGCACCGACTCATTTCAT 58.654 40.909 0.00 0.00 31.15 2.57
896 918 2.777094 TCAATGCACCGACTCATTTCA 58.223 42.857 0.00 0.00 31.15 2.69
897 919 3.189287 ACTTCAATGCACCGACTCATTTC 59.811 43.478 0.00 0.00 31.15 2.17
899 921 2.783135 ACTTCAATGCACCGACTCATT 58.217 42.857 0.00 0.00 33.56 2.57
900 922 2.479566 ACTTCAATGCACCGACTCAT 57.520 45.000 0.00 0.00 0.00 2.90
901 923 1.872952 CAACTTCAATGCACCGACTCA 59.127 47.619 0.00 0.00 0.00 3.41
903 925 0.593128 GCAACTTCAATGCACCGACT 59.407 50.000 0.00 0.00 43.29 4.18
904 926 0.593128 AGCAACTTCAATGCACCGAC 59.407 50.000 0.00 0.00 46.22 4.79
905 927 0.874390 GAGCAACTTCAATGCACCGA 59.126 50.000 0.00 0.00 46.22 4.69
906 928 0.877071 AGAGCAACTTCAATGCACCG 59.123 50.000 0.00 0.00 46.22 4.94
907 929 3.119708 CCTAAGAGCAACTTCAATGCACC 60.120 47.826 0.00 0.00 46.22 5.01
916 938 4.844349 TTGGATAGCCTAAGAGCAACTT 57.156 40.909 0.00 2.10 42.04 2.66
928 950 4.381932 CCCATTTTGTCTGTTTGGATAGCC 60.382 45.833 0.00 0.00 0.00 3.93
940 962 6.279513 TGCGATTTTATTCCCATTTTGTCT 57.720 33.333 0.00 0.00 0.00 3.41
949 971 4.853924 ATGGACATGCGATTTTATTCCC 57.146 40.909 0.00 0.00 0.00 3.97
950 972 5.463061 CCAAATGGACATGCGATTTTATTCC 59.537 40.000 0.00 0.00 33.35 3.01
952 974 5.358922 CCCAAATGGACATGCGATTTTATT 58.641 37.500 0.00 0.00 33.35 1.40
954 976 3.131933 CCCCAAATGGACATGCGATTTTA 59.868 43.478 0.00 0.00 33.35 1.52
959 981 0.621082 TACCCCAAATGGACATGCGA 59.379 50.000 0.00 0.00 37.39 5.10
961 983 2.143876 ACTACCCCAAATGGACATGC 57.856 50.000 0.00 0.00 37.39 4.06
962 984 2.760092 CCAACTACCCCAAATGGACATG 59.240 50.000 0.00 0.00 37.39 3.21
973 995 3.496870 GATCATGGTGATCCAACTACCCC 60.497 52.174 8.41 0.00 45.66 4.95
995 1017 2.351726 GACGATGGGGAGAACATTTTCG 59.648 50.000 0.00 0.00 36.78 3.46
1433 1462 2.513204 CATGGGCGAGTGGAGCAG 60.513 66.667 0.00 0.00 36.08 4.24
1463 1492 1.739338 CTTCCTCCCTGACCGATCCG 61.739 65.000 0.00 0.00 0.00 4.18
1470 1499 2.551071 CCACAGAAACTTCCTCCCTGAC 60.551 54.545 0.00 0.00 0.00 3.51
1480 1509 1.756538 CCAAGTTGCCCACAGAAACTT 59.243 47.619 0.00 0.00 43.18 2.66
1488 1517 1.270550 CAGATCAACCAAGTTGCCCAC 59.729 52.381 0.00 0.00 42.55 4.61
1495 1524 1.612726 GCTGGAGCAGATCAACCAAGT 60.613 52.381 0.00 0.00 41.59 3.16
1505 1534 3.282271 CAGAGACGCTGGAGCAGA 58.718 61.111 0.00 0.00 41.07 4.26
1567 1596 7.447545 TCCGTAGAGCATACATTCTACATTACT 59.552 37.037 11.01 0.00 43.74 2.24
1569 1598 7.447545 ACTCCGTAGAGCATACATTCTACATTA 59.552 37.037 11.01 0.00 43.74 1.90
1582 1611 2.158928 ACGTAGAGACTCCGTAGAGCAT 60.159 50.000 5.13 0.00 44.65 3.79
1598 1627 6.922980 TCGAGTCATTCTACAAAAACGTAG 57.077 37.500 0.00 0.00 40.26 3.51
1617 1646 2.284263 TGTGTCTAGCAGCATTCGAG 57.716 50.000 0.00 0.00 0.00 4.04
1628 1657 5.997746 TGATTGAGGAAACCTTTGTGTCTAG 59.002 40.000 0.00 0.00 31.76 2.43
1718 1747 7.096023 CGTAAGATATTGACTTGCTACATCACC 60.096 40.741 0.00 0.00 43.02 4.02
1744 1773 4.083484 CCGGTTGTCTCAGATTGGTAAAAC 60.083 45.833 0.00 0.00 0.00 2.43
1745 1774 4.069304 CCGGTTGTCTCAGATTGGTAAAA 58.931 43.478 0.00 0.00 0.00 1.52
1746 1775 3.670625 CCGGTTGTCTCAGATTGGTAAA 58.329 45.455 0.00 0.00 0.00 2.01
1934 1966 0.108138 GGGATCTGTCTCACAACCCG 60.108 60.000 0.00 0.00 30.67 5.28
1977 2009 3.830536 ATCCATTGACTACAAGGGGTCCT 60.831 47.826 12.44 0.00 46.43 3.85
2052 2091 8.782144 TCAAAATTTGATTAAAGGAAATGTGGC 58.218 29.630 4.03 0.00 34.08 5.01
2169 2208 6.127814 CGCCAATTCCATGCTAATTATCAGAT 60.128 38.462 4.50 0.00 0.00 2.90
2273 2312 6.265422 ACAACCAGTTTCAAAAGGGATAAGAG 59.735 38.462 0.00 0.00 0.00 2.85
2480 2520 1.695242 ACAACGTCCTGGTAACCATCA 59.305 47.619 0.00 0.00 30.82 3.07
2737 2777 7.710676 TGCTGGTAACCATTACATTTACATT 57.289 32.000 1.47 0.00 37.88 2.71
2755 2795 4.763793 GCATAGATGTTCCATAATGCTGGT 59.236 41.667 12.98 0.00 37.37 4.00
2951 2991 2.239907 GTTCACCTCCCCTAGCATCTTT 59.760 50.000 0.00 0.00 0.00 2.52
3628 3670 4.201763 GCTTCATTGATCTCGACCTTCAAC 60.202 45.833 0.00 0.00 32.61 3.18
3636 3678 3.874392 TGTCTGCTTCATTGATCTCGA 57.126 42.857 0.00 0.00 0.00 4.04
3641 3683 5.732528 GCGATCATTTGTCTGCTTCATTGAT 60.733 40.000 0.00 0.00 0.00 2.57
3669 3711 7.553881 ACACGATGATCCAAAAAGGTTATAG 57.446 36.000 0.00 0.00 39.02 1.31
3740 3782 1.169577 TGCCAACAACGACACAAGTT 58.830 45.000 0.00 0.00 0.00 2.66
3804 3847 8.592529 TCACATCCATTTCTATTCCAAATTCA 57.407 30.769 0.00 0.00 0.00 2.57
3823 3866 5.179368 TCGAAAGACAGGAAAACATCACATC 59.821 40.000 0.00 0.00 33.31 3.06
3829 3872 6.697019 CACAAAATCGAAAGACAGGAAAACAT 59.303 34.615 0.00 0.00 46.97 2.71
3882 3925 2.439883 ACTCCGAGCGGGTCCTAC 60.440 66.667 9.29 0.00 37.00 3.18
4201 4248 5.537188 TGTGTCAACAATTCCTAAAATGGC 58.463 37.500 0.00 0.00 31.82 4.40
4203 4250 9.859427 ACATATGTGTCAACAATTCCTAAAATG 57.141 29.630 7.78 0.00 40.46 2.32
4207 4254 7.093988 CCCAACATATGTGTCAACAATTCCTAA 60.094 37.037 9.63 0.00 40.46 2.69
4209 4256 5.185635 CCCAACATATGTGTCAACAATTCCT 59.814 40.000 9.63 0.00 40.46 3.36
4210 4257 5.184864 TCCCAACATATGTGTCAACAATTCC 59.815 40.000 9.63 0.00 40.46 3.01
4211 4258 6.266168 TCCCAACATATGTGTCAACAATTC 57.734 37.500 9.63 0.00 40.46 2.17
4212 4259 5.336690 GCTCCCAACATATGTGTCAACAATT 60.337 40.000 9.63 0.00 40.46 2.32
4213 4260 4.158394 GCTCCCAACATATGTGTCAACAAT 59.842 41.667 9.63 0.00 40.46 2.71
4214 4261 3.505680 GCTCCCAACATATGTGTCAACAA 59.494 43.478 9.63 0.00 40.46 2.83
4215 4262 3.081061 GCTCCCAACATATGTGTCAACA 58.919 45.455 9.63 0.00 37.67 3.33
4216 4263 3.081061 TGCTCCCAACATATGTGTCAAC 58.919 45.455 9.63 0.00 37.67 3.18
4217 4264 3.431673 TGCTCCCAACATATGTGTCAA 57.568 42.857 9.63 0.00 37.67 3.18
4218 4265 3.281158 CATGCTCCCAACATATGTGTCA 58.719 45.455 9.63 2.23 37.67 3.58
4219 4266 2.620115 CCATGCTCCCAACATATGTGTC 59.380 50.000 9.63 0.00 37.67 3.67
4220 4267 2.025037 ACCATGCTCCCAACATATGTGT 60.025 45.455 9.63 0.00 41.28 3.72
4221 4268 2.658285 ACCATGCTCCCAACATATGTG 58.342 47.619 9.63 3.84 0.00 3.21
4222 4269 4.655963 GATACCATGCTCCCAACATATGT 58.344 43.478 1.41 1.41 0.00 2.29
4223 4270 3.686241 CGATACCATGCTCCCAACATATG 59.314 47.826 0.00 0.00 0.00 1.78
4224 4271 3.327757 ACGATACCATGCTCCCAACATAT 59.672 43.478 0.00 0.00 0.00 1.78
4225 4272 2.703536 ACGATACCATGCTCCCAACATA 59.296 45.455 0.00 0.00 0.00 2.29
4226 4273 1.490490 ACGATACCATGCTCCCAACAT 59.510 47.619 0.00 0.00 0.00 2.71
4227 4274 0.908910 ACGATACCATGCTCCCAACA 59.091 50.000 0.00 0.00 0.00 3.33
4244 4291 2.408704 CGGTGCTTTCAAGACTTAGACG 59.591 50.000 0.00 0.00 0.00 4.18
4306 5851 1.459450 AAATTGCATACGGGTTCGCT 58.541 45.000 0.00 0.00 40.63 4.93
4454 6004 0.037697 TGGACGTTGATCCGTTCCAG 60.038 55.000 0.00 0.00 41.98 3.86
4466 6016 4.003648 GAGTTGGATTGAAGATGGACGTT 58.996 43.478 0.00 0.00 0.00 3.99
4487 6037 0.388520 CACGTGTCGAATCTGCAGGA 60.389 55.000 15.13 0.00 0.00 3.86
4491 6041 1.352156 GGGACACGTGTCGAATCTGC 61.352 60.000 35.21 22.27 45.65 4.26
4506 6056 0.906066 GAGGTGGGAAAGAGAGGGAC 59.094 60.000 0.00 0.00 0.00 4.46
4510 6060 1.199615 GGAGGAGGTGGGAAAGAGAG 58.800 60.000 0.00 0.00 0.00 3.20
4581 6131 1.384525 CGACGGTGAGGAGAGAGAAT 58.615 55.000 0.00 0.00 0.00 2.40



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

AutoCloner maintained by Alex Coulton.