Multiple sequence alignment - TraesCS7D01G236600

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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 TraesCS7D01G236600 chr7D 100.000 3458 0 0 444 3901 199560397 199563854 0.000000e+00 6386.0
1 TraesCS7D01G236600 chr7D 100.000 449 0 0 4162 4610 199564115 199564563 0.000000e+00 830.0
2 TraesCS7D01G236600 chr7D 90.476 147 6 7 4459 4601 199564333 199564475 2.190000e-43 187.0
3 TraesCS7D01G236600 chr7D 90.476 147 6 7 4380 4522 199564412 199564554 2.190000e-43 187.0
4 TraesCS7D01G236600 chr7D 100.000 44 0 0 1 44 199559954 199559997 1.060000e-11 82.4
5 TraesCS7D01G236600 chr7B 90.148 2101 108 51 444 2488 164160881 164162938 0.000000e+00 2641.0
6 TraesCS7D01G236600 chr7B 94.407 751 37 5 2867 3612 164163509 164164259 0.000000e+00 1149.0
7 TraesCS7D01G236600 chr7B 93.976 332 20 0 2492 2823 164162998 164163329 1.910000e-138 503.0
8 TraesCS7D01G236600 chr7B 94.186 258 6 5 3652 3901 164164260 164164516 7.240000e-103 385.0
9 TraesCS7D01G236600 chr7B 88.412 233 19 6 4162 4387 164164589 164164820 1.630000e-69 274.0
10 TraesCS7D01G236600 chr7B 92.683 123 5 3 4492 4610 164164808 164164930 1.700000e-39 174.0
11 TraesCS7D01G236600 chr7B 92.683 123 5 3 4492 4610 164165549 164165671 1.700000e-39 174.0
12 TraesCS7D01G236600 chr7B 92.683 123 5 3 4492 4610 164166290 164166412 1.700000e-39 174.0
13 TraesCS7D01G236600 chr7B 92.683 123 5 3 4492 4610 164167030 164167152 1.700000e-39 174.0
14 TraesCS7D01G236600 chr7B 94.175 103 4 2 4287 4387 164165459 164165561 6.180000e-34 156.0
15 TraesCS7D01G236600 chr7B 94.175 103 4 2 4287 4387 164166200 164166302 6.180000e-34 156.0
16 TraesCS7D01G236600 chr7B 94.175 103 4 2 4287 4387 164166940 164167042 6.180000e-34 156.0
17 TraesCS7D01G236600 chr7B 89.744 117 7 4 4411 4525 164164808 164164921 1.340000e-30 145.0
18 TraesCS7D01G236600 chr7B 89.744 117 7 4 4411 4525 164165549 164165662 1.340000e-30 145.0
19 TraesCS7D01G236600 chr7B 89.744 117 7 4 4411 4525 164166290 164166403 1.340000e-30 145.0
20 TraesCS7D01G236600 chr7B 89.744 117 7 4 4411 4525 164167030 164167143 1.340000e-30 145.0
21 TraesCS7D01G236600 chr7A 89.010 2111 113 50 444 2488 209589290 209591347 0.000000e+00 2503.0
22 TraesCS7D01G236600 chr7A 93.882 997 40 13 2917 3901 209591760 209592747 0.000000e+00 1483.0
23 TraesCS7D01G236600 chr7A 95.000 340 16 1 2492 2831 209591407 209591745 2.440000e-147 532.0
24 TraesCS7D01G236600 chr7A 88.942 208 17 3 4162 4363 209592815 209593022 7.660000e-63 252.0
25 TraesCS7D01G236600 chr5B 78.132 439 77 14 3089 3516 438017653 438017223 1.270000e-65 261.0
26 TraesCS7D01G236600 chr5A 77.489 462 83 16 3089 3538 471724030 471723578 1.650000e-64 257.0
27 TraesCS7D01G236600 chr5D 77.556 450 80 16 3101 3538 369308097 369307657 7.660000e-63 252.0
28 TraesCS7D01G236600 chr5D 77.716 359 69 10 3089 3440 369317934 369317580 4.670000e-50 209.0
29 TraesCS7D01G236600 chr3B 96.703 91 1 2 4274 4362 822106285 822106195 2.870000e-32 150.0
30 TraesCS7D01G236600 chr2A 98.810 84 1 0 4279 4362 601338205 601338122 2.870000e-32 150.0
31 TraesCS7D01G236600 chr2B 96.591 88 3 0 4279 4366 538955353 538955266 3.720000e-31 147.0
32 TraesCS7D01G236600 chr3D 91.589 107 4 5 4258 4362 598715492 598715389 4.810000e-30 143.0


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 TraesCS7D01G236600 chr7D 199559954 199564563 4609 False 1534.48 6386 96.190400 1 4610 5 chr7D.!!$F1 4609
1 TraesCS7D01G236600 chr7B 164160881 164167152 6271 False 418.50 2641 92.085125 444 4610 16 chr7B.!!$F1 4166
2 TraesCS7D01G236600 chr7A 209589290 209593022 3732 False 1192.50 2503 91.708500 444 4363 4 chr7A.!!$F1 3919

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
838 882 0.107897 TCGTGCTGAGTGGTTTGTGT 60.108 50.0 0.0 0.0 0.0 3.72 F
839 883 0.732571 CGTGCTGAGTGGTTTGTGTT 59.267 50.0 0.0 0.0 0.0 3.32 F
2351 2459 1.048601 AGCCTCTGAAACACGAAGGA 58.951 50.0 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1896 1994 0.179000 CAAAGGAGGCTATCGGTGCT 59.821 55.0 0.0 0.0 0.0 4.40 R
2562 2727 1.830279 ATTGGTGTGCATCAGTCCAG 58.170 50.0 0.0 0.0 0.0 3.86 R
3621 3927 0.249868 CCCAGACGCAGAGACAACAA 60.250 55.0 0.0 0.0 0.0 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
20 21 2.740121 CATGCATGCCATGGGATGA 58.260 52.632 40.94 28.03 46.09 2.92
21 22 1.044611 CATGCATGCCATGGGATGAA 58.955 50.000 40.94 34.85 46.09 2.57
22 23 1.623311 CATGCATGCCATGGGATGAAT 59.377 47.619 40.94 35.37 46.09 2.57
23 24 1.796017 TGCATGCCATGGGATGAATT 58.204 45.000 40.94 10.56 45.01 2.17
24 25 1.689813 TGCATGCCATGGGATGAATTC 59.310 47.619 40.94 26.47 45.01 2.17
25 26 1.336517 GCATGCCATGGGATGAATTCG 60.337 52.381 40.94 20.08 45.01 3.34
26 27 1.958579 CATGCCATGGGATGAATTCGT 59.041 47.619 35.80 2.85 45.01 3.85
27 28 1.679139 TGCCATGGGATGAATTCGTC 58.321 50.000 17.82 17.82 0.00 4.20
28 29 0.588252 GCCATGGGATGAATTCGTCG 59.412 55.000 19.05 8.04 32.78 5.12
29 30 1.953559 CCATGGGATGAATTCGTCGT 58.046 50.000 19.05 7.17 32.78 4.34
30 31 1.867233 CCATGGGATGAATTCGTCGTC 59.133 52.381 19.05 14.52 41.02 4.20
31 32 1.522676 CATGGGATGAATTCGTCGTCG 59.477 52.381 19.05 6.20 42.45 5.12
32 33 0.812549 TGGGATGAATTCGTCGTCGA 59.187 50.000 19.05 0.00 42.45 4.20
466 468 6.567602 AGTGGAAGCAGGAGTAATCTAATT 57.432 37.500 0.00 0.00 0.00 1.40
478 480 6.311690 GGAGTAATCTAATTCTAATCGGCTGC 59.688 42.308 0.00 0.00 0.00 5.25
480 482 5.931441 AATCTAATTCTAATCGGCTGCAC 57.069 39.130 0.50 0.00 0.00 4.57
513 518 4.963878 GGAGCATTCACCATCCGT 57.036 55.556 0.00 0.00 0.00 4.69
514 519 2.695314 GGAGCATTCACCATCCGTC 58.305 57.895 0.00 0.00 0.00 4.79
515 520 0.815615 GGAGCATTCACCATCCGTCC 60.816 60.000 0.00 0.00 0.00 4.79
516 521 1.153369 AGCATTCACCATCCGTCCG 60.153 57.895 0.00 0.00 0.00 4.79
560 565 0.667184 CTCCCATTTGCGTGCCAAAC 60.667 55.000 0.00 0.00 45.52 2.93
572 577 2.644676 GTGCCAAACTAATCCTCCTCC 58.355 52.381 0.00 0.00 0.00 4.30
573 578 2.239907 GTGCCAAACTAATCCTCCTCCT 59.760 50.000 0.00 0.00 0.00 3.69
574 579 2.239654 TGCCAAACTAATCCTCCTCCTG 59.760 50.000 0.00 0.00 0.00 3.86
575 580 2.924421 CCAAACTAATCCTCCTCCTGC 58.076 52.381 0.00 0.00 0.00 4.85
576 581 2.507471 CCAAACTAATCCTCCTCCTGCT 59.493 50.000 0.00 0.00 0.00 4.24
577 582 3.539604 CAAACTAATCCTCCTCCTGCTG 58.460 50.000 0.00 0.00 0.00 4.41
578 583 1.127343 ACTAATCCTCCTCCTGCTGC 58.873 55.000 0.00 0.00 0.00 5.25
579 584 1.343884 ACTAATCCTCCTCCTGCTGCT 60.344 52.381 0.00 0.00 0.00 4.24
580 585 1.070445 CTAATCCTCCTCCTGCTGCTG 59.930 57.143 0.00 0.00 0.00 4.41
581 586 2.268167 AATCCTCCTCCTGCTGCTGC 62.268 60.000 8.89 8.89 40.20 5.25
591 596 2.181445 CTGCTGCTGCTCTTCCTCCA 62.181 60.000 17.00 0.00 40.48 3.86
677 696 1.302511 CCACCATATAGCCGCCACC 60.303 63.158 0.00 0.00 0.00 4.61
680 699 2.351276 CATATAGCCGCCACCCCC 59.649 66.667 0.00 0.00 0.00 5.40
681 700 2.122144 ATATAGCCGCCACCCCCA 60.122 61.111 0.00 0.00 0.00 4.96
704 733 3.420482 CCCCACCCCACCATCCTC 61.420 72.222 0.00 0.00 0.00 3.71
705 734 2.286425 CCCACCCCACCATCCTCT 60.286 66.667 0.00 0.00 0.00 3.69
758 792 3.068691 CCCTCCGCGACTCCTTGA 61.069 66.667 8.23 0.00 0.00 3.02
807 843 2.428569 CCGTGAGTCGTCGTGGTG 60.429 66.667 6.75 0.00 37.94 4.17
833 877 0.603707 CCATGTCGTGCTGAGTGGTT 60.604 55.000 0.00 0.00 31.78 3.67
834 878 1.229428 CATGTCGTGCTGAGTGGTTT 58.771 50.000 0.00 0.00 0.00 3.27
838 882 0.107897 TCGTGCTGAGTGGTTTGTGT 60.108 50.000 0.00 0.00 0.00 3.72
839 883 0.732571 CGTGCTGAGTGGTTTGTGTT 59.267 50.000 0.00 0.00 0.00 3.32
840 884 1.132262 CGTGCTGAGTGGTTTGTGTTT 59.868 47.619 0.00 0.00 0.00 2.83
842 886 1.476085 TGCTGAGTGGTTTGTGTTTGG 59.524 47.619 0.00 0.00 0.00 3.28
843 887 1.202405 GCTGAGTGGTTTGTGTTTGGG 60.202 52.381 0.00 0.00 0.00 4.12
844 888 2.374184 CTGAGTGGTTTGTGTTTGGGA 58.626 47.619 0.00 0.00 0.00 4.37
845 889 2.096248 TGAGTGGTTTGTGTTTGGGAC 58.904 47.619 0.00 0.00 0.00 4.46
846 890 2.291282 TGAGTGGTTTGTGTTTGGGACT 60.291 45.455 0.00 0.00 0.00 3.85
847 891 2.758423 GAGTGGTTTGTGTTTGGGACTT 59.242 45.455 0.00 0.00 0.00 3.01
848 892 2.758423 AGTGGTTTGTGTTTGGGACTTC 59.242 45.455 0.00 0.00 0.00 3.01
1166 1210 2.612251 CCTCCTCCCCTCTCCTCC 59.388 72.222 0.00 0.00 0.00 4.30
1222 1276 6.030849 TGTTTGGTTTCTTGTTTGACATACG 58.969 36.000 0.00 0.00 0.00 3.06
1243 1297 1.597854 TCCGGCAAAGCAGAGTGTG 60.598 57.895 0.00 0.00 0.00 3.82
1259 1313 1.216444 GTGTCCTGCTCTGCGATCA 59.784 57.895 0.00 0.00 0.00 2.92
1272 1326 1.966493 GCGATCATTGTTGCGACCGT 61.966 55.000 0.45 0.00 0.00 4.83
1284 1338 1.623973 GCGACCGTGGTTCTTAGTGC 61.624 60.000 0.00 0.00 0.00 4.40
1314 1370 1.947456 AGTTCAGTCGGGTTTTCTTGC 59.053 47.619 0.00 0.00 0.00 4.01
1320 1376 1.533731 GTCGGGTTTTCTTGCGATCAA 59.466 47.619 0.00 0.00 0.00 2.57
1321 1377 1.533731 TCGGGTTTTCTTGCGATCAAC 59.466 47.619 0.00 0.00 0.00 3.18
1322 1378 1.265635 CGGGTTTTCTTGCGATCAACA 59.734 47.619 0.00 0.00 0.00 3.33
1353 1421 1.168714 GTGGTGGCTTGATTCTGTCC 58.831 55.000 0.00 0.00 0.00 4.02
1394 1462 9.860898 GATCAATAGGCTGTTTCTGTTAAAAAT 57.139 29.630 0.00 0.00 0.00 1.82
1403 1471 9.196552 GCTGTTTCTGTTAAAAATATCTTGCTT 57.803 29.630 0.00 0.00 0.00 3.91
1442 1519 3.330701 AGGTTCAGAATTTGGTAGCAGGA 59.669 43.478 0.00 0.00 0.00 3.86
1444 1521 4.706962 GGTTCAGAATTTGGTAGCAGGAAT 59.293 41.667 0.00 0.00 0.00 3.01
1447 1524 4.018506 TCAGAATTTGGTAGCAGGAATGGA 60.019 41.667 0.00 0.00 0.00 3.41
1475 1563 8.712285 TCTTCCGTAAAGTATTATTGAACTGG 57.288 34.615 0.00 0.00 36.31 4.00
1517 1608 7.389053 GGAATCTTTGGTCAGCGATAATATCTT 59.611 37.037 0.00 0.00 0.00 2.40
1612 1706 4.843728 AGTTTCACTTTCTCCAACACTCA 58.156 39.130 0.00 0.00 0.00 3.41
1691 1785 7.797819 ACGTTTACTTCTTCAAATCTCATCAC 58.202 34.615 0.00 0.00 0.00 3.06
1827 1925 2.367567 GTGAAGGTACCTGTCTGTGGAA 59.632 50.000 17.14 0.00 0.00 3.53
1896 1994 2.203480 GCCAAGAACACAGCCCCA 60.203 61.111 0.00 0.00 0.00 4.96
2113 2220 7.497595 TGCTTGTTCTTAGTTCATACGGATAT 58.502 34.615 0.00 0.00 0.00 1.63
2155 2262 2.787601 AGTGTCATGCAAAAGCAGTG 57.212 45.000 0.00 0.00 0.00 3.66
2266 2374 4.122776 GTTGAGTTCTCCACGCATATCAT 58.877 43.478 0.00 0.00 34.81 2.45
2351 2459 1.048601 AGCCTCTGAAACACGAAGGA 58.951 50.000 0.00 0.00 0.00 3.36
2482 2591 7.257722 ACTTCTGTTTTGTCAATGTTTGGTAG 58.742 34.615 0.00 0.00 0.00 3.18
2488 2597 8.037758 TGTTTTGTCAATGTTTGGTAGAACAAT 58.962 29.630 0.00 0.00 42.29 2.71
2489 2598 8.878769 GTTTTGTCAATGTTTGGTAGAACAATT 58.121 29.630 0.00 0.00 42.29 2.32
2521 2686 2.907892 TCTTGACTCACCTGGAATCCT 58.092 47.619 0.00 0.00 0.00 3.24
2562 2727 7.172190 AGCTGCACACTATATTAACATGACATC 59.828 37.037 0.00 0.00 0.00 3.06
2635 2800 5.720041 AGGTGTCTATAGTTGCTTTCTACCA 59.280 40.000 0.00 0.00 0.00 3.25
2637 2802 7.048512 GGTGTCTATAGTTGCTTTCTACCATT 58.951 38.462 0.00 0.00 0.00 3.16
2735 2900 6.430451 CACAACAGAAACCTAAATCAGACAC 58.570 40.000 0.00 0.00 0.00 3.67
2771 2936 3.069586 TCAGTAATTGCTCGATCCGGATT 59.930 43.478 20.22 2.83 0.00 3.01
2778 2943 3.601435 TGCTCGATCCGGATTAAAAACA 58.399 40.909 20.22 9.83 0.00 2.83
2839 3017 4.939509 AATGACTGTAAATTCCGAACGG 57.060 40.909 6.94 6.94 0.00 4.44
2841 3019 3.731089 TGACTGTAAATTCCGAACGGTT 58.269 40.909 12.93 0.00 32.96 4.44
2859 3037 5.985911 ACGGTTAGTGCTAATACTTTCCAT 58.014 37.500 0.00 0.00 32.19 3.41
2860 3038 5.815740 ACGGTTAGTGCTAATACTTTCCATG 59.184 40.000 0.00 0.00 32.19 3.66
2861 3039 6.046593 CGGTTAGTGCTAATACTTTCCATGA 58.953 40.000 0.00 0.00 32.19 3.07
2868 3170 6.094048 GTGCTAATACTTTCCATGAGAGCAAA 59.906 38.462 0.00 0.00 38.97 3.68
2881 3183 4.923893 TGAGAGCAAAACAACACATGAAG 58.076 39.130 0.00 0.00 0.00 3.02
2883 3185 2.796593 GAGCAAAACAACACATGAAGCC 59.203 45.455 0.00 0.00 0.00 4.35
2900 3202 4.949856 TGAAGCCCTTCAATAATCACTTCC 59.050 41.667 8.19 0.00 45.56 3.46
2913 3215 2.497138 TCACTTCCTGCACATGTTCAG 58.503 47.619 17.41 17.41 0.00 3.02
2937 3239 6.769341 AGGACCGTTTCAAACTTACAGTTAAT 59.231 34.615 0.00 0.00 37.47 1.40
2941 3243 8.340443 ACCGTTTCAAACTTACAGTTAATTCTC 58.660 33.333 0.00 0.00 37.47 2.87
2943 3245 9.582223 CGTTTCAAACTTACAGTTAATTCTCTC 57.418 33.333 0.00 0.00 37.47 3.20
2967 3273 3.836365 TTTTGGCTTTTGGAAGGAAGG 57.164 42.857 0.00 0.00 33.34 3.46
2969 3275 0.831711 TGGCTTTTGGAAGGAAGGCC 60.832 55.000 0.00 0.00 46.18 5.19
2988 3294 5.186198 AGGCCTACAGTTAACTTATTGCTG 58.814 41.667 1.29 0.00 0.00 4.41
3036 3342 4.292178 GCCTCGATCTGGGCCTCG 62.292 72.222 4.53 6.16 42.30 4.63
3522 3828 0.818296 AGGTGTACGAGATGCAGGAC 59.182 55.000 0.00 0.00 0.00 3.85
3582 3888 1.352622 TGGCAGAGGTGTTTCAGGGT 61.353 55.000 0.00 0.00 0.00 4.34
3625 3931 1.524961 TGAGCGTGGGTCACTTGTT 59.475 52.632 0.00 0.00 35.04 2.83
3633 3942 1.230324 GGGTCACTTGTTGTCTCTGC 58.770 55.000 0.00 0.00 0.00 4.26
3636 3945 1.523095 GTCACTTGTTGTCTCTGCGTC 59.477 52.381 0.00 0.00 0.00 5.19
3637 3946 1.409064 TCACTTGTTGTCTCTGCGTCT 59.591 47.619 0.00 0.00 0.00 4.18
3638 3947 1.524355 CACTTGTTGTCTCTGCGTCTG 59.476 52.381 0.00 0.00 0.00 3.51
3652 3961 1.529796 GTCTGGGTGGTGGTGTTCA 59.470 57.895 0.00 0.00 0.00 3.18
3653 3962 0.818040 GTCTGGGTGGTGGTGTTCAC 60.818 60.000 0.00 0.00 45.34 3.18
3664 3974 0.823356 GGTGTTCACTGGTGGTGCAT 60.823 55.000 0.00 0.00 44.98 3.96
3687 3997 0.604578 TTTGCTGGATTCTTGCTGGC 59.395 50.000 0.00 0.00 0.00 4.85
4194 4516 5.297547 TCACAACAGTTCTGTACCTGATTC 58.702 41.667 5.87 0.00 0.00 2.52
4210 4532 4.084328 CCTGATTCGAAGTGTTGTGAAGAC 60.084 45.833 3.35 0.00 0.00 3.01
4212 4534 4.745125 TGATTCGAAGTGTTGTGAAGACTC 59.255 41.667 3.35 0.00 33.33 3.36
4213 4535 3.793797 TCGAAGTGTTGTGAAGACTCA 57.206 42.857 0.00 0.00 33.33 3.41
4216 4538 5.116180 TCGAAGTGTTGTGAAGACTCATTT 58.884 37.500 0.00 0.00 33.33 2.32
4220 4542 5.810525 AGTGTTGTGAAGACTCATTTTTCG 58.189 37.500 0.00 0.00 33.05 3.46
4225 4551 5.498159 TGTGAAGACTCATTTTTCGAAACG 58.502 37.500 10.79 2.42 33.05 3.60
4235 4561 0.733729 TTTCGAAACGGGTGTTGTGG 59.266 50.000 6.47 0.00 38.62 4.17
4237 4563 0.107800 TCGAAACGGGTGTTGTGGAA 60.108 50.000 0.00 0.00 38.62 3.53
4252 4578 8.138712 GGTGTTGTGGAAACTTGAATATGTAAA 58.861 33.333 0.00 0.00 0.00 2.01
4253 4579 8.964150 GTGTTGTGGAAACTTGAATATGTAAAC 58.036 33.333 0.00 0.00 0.00 2.01
4272 4598 8.682128 TGTAAACCCTAAATAGTAAACGTACG 57.318 34.615 15.01 15.01 35.20 3.67
4384 5453 3.568538 CCCACAGCTTCAAATCTTTTCG 58.431 45.455 0.00 0.00 0.00 3.46
4387 5456 3.004734 CACAGCTTCAAATCTTTTCGGGT 59.995 43.478 0.00 0.00 0.00 5.28
4388 5457 3.004734 ACAGCTTCAAATCTTTTCGGGTG 59.995 43.478 0.00 0.00 0.00 4.61
4397 5513 3.672767 TCTTTTCGGGTGTTCTAGTCC 57.327 47.619 0.00 0.00 0.00 3.85
4434 6209 5.708736 TCTTTTCAGGGAATAGGTGCATA 57.291 39.130 0.00 0.00 0.00 3.14
4435 6210 6.266131 TCTTTTCAGGGAATAGGTGCATAT 57.734 37.500 0.00 0.00 0.00 1.78
4463 6239 2.423185 TCAGCATGGCCAGTATTTTTCG 59.577 45.455 13.05 0.00 36.16 3.46
4516 6951 2.905415 TTCAGGGAAAGGTGCATGAT 57.095 45.000 0.00 0.00 35.73 2.45
4544 6979 2.423185 TCAGCATGGCCAGTATTTTTCG 59.577 45.455 13.05 0.00 36.16 3.46
4557 6992 5.064834 CAGTATTTTTCGGGGAGTTTCTAGC 59.935 44.000 0.00 0.00 0.00 3.42
4594 7029 5.139727 CAATTTAGGGGAATAGGTGCATGA 58.860 41.667 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.830023 TCATCCCATGGCATGCATGG 60.830 55.000 28.27 28.27 46.82 3.66
2 3 1.044611 TTCATCCCATGGCATGCATG 58.955 50.000 22.70 22.70 0.00 4.06
3 4 2.024176 ATTCATCCCATGGCATGCAT 57.976 45.000 22.02 12.53 0.00 3.96
4 5 1.689813 GAATTCATCCCATGGCATGCA 59.310 47.619 22.02 10.70 0.00 3.96
5 6 1.336517 CGAATTCATCCCATGGCATGC 60.337 52.381 22.02 9.90 0.00 4.06
6 7 1.958579 ACGAATTCATCCCATGGCATG 59.041 47.619 20.56 20.56 0.00 4.06
7 8 2.233271 GACGAATTCATCCCATGGCAT 58.767 47.619 6.09 0.00 0.00 4.40
8 9 1.679139 GACGAATTCATCCCATGGCA 58.321 50.000 6.09 0.00 0.00 4.92
9 10 0.588252 CGACGAATTCATCCCATGGC 59.412 55.000 6.09 0.00 0.00 4.40
10 11 1.867233 GACGACGAATTCATCCCATGG 59.133 52.381 4.14 4.14 0.00 3.66
11 12 1.522676 CGACGACGAATTCATCCCATG 59.477 52.381 0.00 0.00 42.66 3.66
12 13 1.407618 TCGACGACGAATTCATCCCAT 59.592 47.619 7.68 0.00 45.74 4.00
13 14 0.812549 TCGACGACGAATTCATCCCA 59.187 50.000 7.68 0.00 45.74 4.37
14 15 3.635433 TCGACGACGAATTCATCCC 57.365 52.632 7.68 0.00 45.74 3.85
466 468 2.778299 ACTTTTGTGCAGCCGATTAGA 58.222 42.857 0.00 0.00 0.00 2.10
478 480 4.083003 TGCTCCGGCTTAATTACTTTTGTG 60.083 41.667 0.00 0.00 39.59 3.33
480 482 4.695217 TGCTCCGGCTTAATTACTTTTG 57.305 40.909 0.00 0.00 39.59 2.44
513 518 2.915659 ACGCCAGTGGAAGACGGA 60.916 61.111 15.20 0.00 0.00 4.69
514 519 2.738521 CACGCCAGTGGAAGACGG 60.739 66.667 15.20 0.00 44.34 4.79
560 565 1.070445 CAGCAGCAGGAGGAGGATTAG 59.930 57.143 0.00 0.00 0.00 1.73
572 577 1.449956 GGAGGAAGAGCAGCAGCAG 60.450 63.158 3.17 0.00 45.49 4.24
573 578 2.219164 TGGAGGAAGAGCAGCAGCA 61.219 57.895 3.17 0.00 45.49 4.41
574 579 1.744741 GTGGAGGAAGAGCAGCAGC 60.745 63.158 0.00 0.00 42.56 5.25
575 580 1.078567 GGTGGAGGAAGAGCAGCAG 60.079 63.158 0.00 0.00 0.00 4.24
576 581 2.947532 CGGTGGAGGAAGAGCAGCA 61.948 63.158 0.00 0.00 0.00 4.41
577 582 2.125350 CGGTGGAGGAAGAGCAGC 60.125 66.667 0.00 0.00 0.00 5.25
578 583 2.125350 GCGGTGGAGGAAGAGCAG 60.125 66.667 0.00 0.00 0.00 4.24
579 584 2.515979 TTGCGGTGGAGGAAGAGCA 61.516 57.895 0.00 0.00 0.00 4.26
580 585 2.035442 GTTGCGGTGGAGGAAGAGC 61.035 63.158 0.00 0.00 0.00 4.09
581 586 0.671781 CTGTTGCGGTGGAGGAAGAG 60.672 60.000 0.00 0.00 0.00 2.85
591 596 2.413963 TTGCTGTTGCTGTTGCGGT 61.414 52.632 0.00 0.00 43.34 5.68
614 619 4.035102 GTGGGACTGTGGGAGGGC 62.035 72.222 0.00 0.00 0.00 5.19
713 742 2.351276 CGGTTCTTGGGGAGTGGG 59.649 66.667 0.00 0.00 0.00 4.61
807 843 3.005261 ACTCAGCACGACATGGATAGATC 59.995 47.826 0.00 0.00 0.00 2.75
833 877 0.256464 ACCCGAAGTCCCAAACACAA 59.744 50.000 0.00 0.00 0.00 3.33
834 878 0.256464 AACCCGAAGTCCCAAACACA 59.744 50.000 0.00 0.00 0.00 3.72
838 882 1.110518 GCCAAACCCGAAGTCCCAAA 61.111 55.000 0.00 0.00 0.00 3.28
839 883 1.529713 GCCAAACCCGAAGTCCCAA 60.530 57.895 0.00 0.00 0.00 4.12
840 884 2.114411 GCCAAACCCGAAGTCCCA 59.886 61.111 0.00 0.00 0.00 4.37
868 912 2.901281 ATGTACTGCCGCCAACCCA 61.901 57.895 0.00 0.00 0.00 4.51
1182 1236 1.961793 AACAGGTAGCGAGCAACAAA 58.038 45.000 0.00 0.00 0.00 2.83
1222 1276 1.598130 ACTCTGCTTTGCCGGACAC 60.598 57.895 5.05 0.00 0.00 3.67
1228 1282 0.536006 AGGACACACTCTGCTTTGCC 60.536 55.000 0.00 0.00 0.00 4.52
1259 1313 0.534203 AGAACCACGGTCGCAACAAT 60.534 50.000 0.00 0.00 0.00 2.71
1272 1326 5.221843 ACTCATAAACCAGCACTAAGAACCA 60.222 40.000 0.00 0.00 0.00 3.67
1284 1338 3.262420 CCCGACTGAACTCATAAACCAG 58.738 50.000 0.00 0.00 0.00 4.00
1314 1370 4.378770 CCACTGAAAACCTCATGTTGATCG 60.379 45.833 0.00 0.00 37.23 3.69
1320 1376 2.586425 CCACCACTGAAAACCTCATGT 58.414 47.619 0.00 0.00 32.14 3.21
1321 1377 1.270550 GCCACCACTGAAAACCTCATG 59.729 52.381 0.00 0.00 32.14 3.07
1322 1378 1.145738 AGCCACCACTGAAAACCTCAT 59.854 47.619 0.00 0.00 32.14 2.90
1353 1421 0.251297 TGATCCCCTTTGCACTGGTG 60.251 55.000 0.00 0.00 0.00 4.17
1394 1462 7.984422 TTCTCAGAATCAAACAAGCAAGATA 57.016 32.000 0.00 0.00 0.00 1.98
1403 1471 6.828273 TCTGAACCTTTTCTCAGAATCAAACA 59.172 34.615 0.00 0.00 43.90 2.83
1475 1563 9.154847 CCAAAGATTCCAAATCCAACTTAAATC 57.845 33.333 0.00 0.00 0.00 2.17
1517 1608 7.915293 ATATGGTTAAGAAAACATGTCGACA 57.085 32.000 22.48 22.48 43.02 4.35
1550 1641 5.578005 TGGTTCCACGTCTCTCTTAATAG 57.422 43.478 0.00 0.00 0.00 1.73
1612 1706 9.785982 AATAGTAGAAAAGAAAGAGCTGAAAGT 57.214 29.630 0.00 0.00 35.30 2.66
1746 1844 3.122480 TCATGTGGTGGACCCTCATAAT 58.878 45.455 0.00 0.00 43.86 1.28
1896 1994 0.179000 CAAAGGAGGCTATCGGTGCT 59.821 55.000 0.00 0.00 0.00 4.40
2090 2197 9.186323 CTCATATCCGTATGAACTAAGAACAAG 57.814 37.037 0.46 0.00 44.48 3.16
2113 2220 9.208022 CACTTGATCTCTACACAAATTAACTCA 57.792 33.333 0.00 0.00 0.00 3.41
2183 2290 3.092403 CATGTGTGCCCGATCACG 58.908 61.111 0.00 0.00 39.73 4.35
2184 2291 2.793946 GCATGTGTGCCCGATCAC 59.206 61.111 0.00 0.00 45.76 3.06
2296 2404 4.797471 TGTGTTCATGCAAATTAGCTGAC 58.203 39.130 0.00 0.00 34.99 3.51
2351 2459 6.640518 ACTACTATCAATCGTCCACACAAAT 58.359 36.000 0.00 0.00 0.00 2.32
2482 2591 7.389053 AGTCAAGAATGTCACTCCTAATTGTTC 59.611 37.037 0.00 0.00 0.00 3.18
2488 2597 5.279506 GGTGAGTCAAGAATGTCACTCCTAA 60.280 44.000 0.00 0.00 39.45 2.69
2489 2598 4.220821 GGTGAGTCAAGAATGTCACTCCTA 59.779 45.833 0.00 0.00 39.45 2.94
2521 2686 5.582269 GTGTGCAGCTGTCTAAAATCAGATA 59.418 40.000 16.64 0.00 34.02 1.98
2562 2727 1.830279 ATTGGTGTGCATCAGTCCAG 58.170 50.000 0.00 0.00 0.00 3.86
2635 2800 5.310331 ACAATCAGGGGGTTTTCAATTCAAT 59.690 36.000 0.00 0.00 0.00 2.57
2637 2802 4.040217 CACAATCAGGGGGTTTTCAATTCA 59.960 41.667 0.00 0.00 0.00 2.57
2673 2838 5.863935 CACGTCTCTGATCAAAGAACATGTA 59.136 40.000 0.00 0.00 0.00 2.29
2778 2943 9.268268 TCTCAAAGACGTTGTTCTTATATTGTT 57.732 29.630 0.98 0.00 38.47 2.83
2832 3010 4.037858 AGTATTAGCACTAACCGTTCGG 57.962 45.455 9.81 9.81 0.00 4.30
2833 3011 5.005107 GGAAAGTATTAGCACTAACCGTTCG 59.995 44.000 0.00 0.00 0.00 3.95
2836 3014 5.410355 TGGAAAGTATTAGCACTAACCGT 57.590 39.130 0.00 0.00 30.98 4.83
2839 3017 7.042389 GCTCTCATGGAAAGTATTAGCACTAAC 60.042 40.741 0.00 0.00 0.00 2.34
2841 3019 6.098266 TGCTCTCATGGAAAGTATTAGCACTA 59.902 38.462 0.00 0.00 32.88 2.74
2859 3037 4.734402 GCTTCATGTGTTGTTTTGCTCTCA 60.734 41.667 0.00 0.00 0.00 3.27
2860 3038 3.732721 GCTTCATGTGTTGTTTTGCTCTC 59.267 43.478 0.00 0.00 0.00 3.20
2861 3039 3.491447 GGCTTCATGTGTTGTTTTGCTCT 60.491 43.478 0.00 0.00 0.00 4.09
2868 3170 2.665165 TGAAGGGCTTCATGTGTTGTT 58.335 42.857 0.00 0.00 43.90 2.83
2881 3183 3.067320 GCAGGAAGTGATTATTGAAGGGC 59.933 47.826 0.00 0.00 0.00 5.19
2883 3185 4.701651 TGTGCAGGAAGTGATTATTGAAGG 59.298 41.667 0.00 0.00 0.00 3.46
2900 3202 0.603707 ACGGTCCTGAACATGTGCAG 60.604 55.000 25.02 25.02 0.00 4.41
2953 3255 3.084786 CTGTAGGCCTTCCTTCCAAAAG 58.915 50.000 12.58 0.00 40.66 2.27
2954 3256 2.445525 ACTGTAGGCCTTCCTTCCAAAA 59.554 45.455 12.58 0.00 40.66 2.44
2955 3257 2.062636 ACTGTAGGCCTTCCTTCCAAA 58.937 47.619 12.58 0.00 40.66 3.28
2956 3258 1.742308 ACTGTAGGCCTTCCTTCCAA 58.258 50.000 12.58 0.00 40.66 3.53
2959 3265 4.554960 AGTTAACTGTAGGCCTTCCTTC 57.445 45.455 12.58 0.00 40.66 3.46
2967 3273 5.411669 ACACAGCAATAAGTTAACTGTAGGC 59.588 40.000 9.34 11.14 39.48 3.93
2988 3294 3.129287 CACCCTGGAATGCAGAATTACAC 59.871 47.826 2.50 0.00 33.90 2.90
3036 3342 2.294233 TGAAGACTGCTTGATTTGGTGC 59.706 45.455 0.00 0.00 33.61 5.01
3267 3573 3.381908 CGTAGATGTAGTTGAGGAAGCCT 59.618 47.826 0.00 0.00 36.03 4.58
3522 3828 1.945776 GAAGGAACGCGCTGAACTCG 61.946 60.000 5.73 0.00 0.00 4.18
3567 3873 2.127708 AGAACACCCTGAAACACCTCT 58.872 47.619 0.00 0.00 0.00 3.69
3582 3888 2.664851 CTCCACGCCGCAAGAACA 60.665 61.111 0.00 0.00 43.02 3.18
3614 3920 1.230324 GCAGAGACAACAAGTGACCC 58.770 55.000 0.00 0.00 0.00 4.46
3615 3921 0.861837 CGCAGAGACAACAAGTGACC 59.138 55.000 0.00 0.00 0.00 4.02
3617 3923 1.409064 AGACGCAGAGACAACAAGTGA 59.591 47.619 0.00 0.00 0.00 3.41
3618 3924 1.524355 CAGACGCAGAGACAACAAGTG 59.476 52.381 0.00 0.00 0.00 3.16
3619 3925 1.539065 CCAGACGCAGAGACAACAAGT 60.539 52.381 0.00 0.00 0.00 3.16
3621 3927 0.249868 CCCAGACGCAGAGACAACAA 60.250 55.000 0.00 0.00 0.00 2.83
3622 3928 1.367471 CCCAGACGCAGAGACAACA 59.633 57.895 0.00 0.00 0.00 3.33
3623 3929 0.946221 CACCCAGACGCAGAGACAAC 60.946 60.000 0.00 0.00 0.00 3.32
3625 3931 2.574018 CCACCCAGACGCAGAGACA 61.574 63.158 0.00 0.00 0.00 3.41
3633 3942 1.597027 GAACACCACCACCCAGACG 60.597 63.158 0.00 0.00 0.00 4.18
3636 3945 0.819259 CAGTGAACACCACCACCCAG 60.819 60.000 1.11 0.00 46.87 4.45
3637 3946 1.225983 CAGTGAACACCACCACCCA 59.774 57.895 1.11 0.00 46.87 4.51
3638 3947 1.528309 CCAGTGAACACCACCACCC 60.528 63.158 1.11 0.00 46.87 4.61
3652 3961 1.473080 GCAAACAAATGCACCACCAGT 60.473 47.619 0.00 0.00 45.70 4.00
3653 3962 1.219646 GCAAACAAATGCACCACCAG 58.780 50.000 0.00 0.00 45.70 4.00
3664 3974 3.493002 CCAGCAAGAATCCAGCAAACAAA 60.493 43.478 0.00 0.00 0.00 2.83
3687 3997 3.133814 GCGCTATTTACAAGCTGCG 57.866 52.632 0.00 6.45 45.12 5.18
3794 4110 1.616374 TCACCAAGACGCACTACATCA 59.384 47.619 0.00 0.00 0.00 3.07
4165 4485 6.146184 CAGGTACAGAACTGTTGTGAGTTATG 59.854 42.308 22.53 6.35 46.20 1.90
4194 4516 5.409643 AAATGAGTCTTCACAACACTTCG 57.590 39.130 0.00 0.00 35.83 3.79
4210 4532 3.619233 ACACCCGTTTCGAAAAATGAG 57.381 42.857 13.10 5.82 33.93 2.90
4212 4534 3.241784 CACAACACCCGTTTCGAAAAATG 59.758 43.478 13.10 10.69 31.13 2.32
4213 4535 3.440228 CACAACACCCGTTTCGAAAAAT 58.560 40.909 13.10 0.00 31.13 1.82
4216 4538 0.733729 CCACAACACCCGTTTCGAAA 59.266 50.000 6.47 6.47 31.13 3.46
4220 4542 1.746787 AGTTTCCACAACACCCGTTTC 59.253 47.619 0.00 0.00 31.13 2.78
4225 4551 5.010617 ACATATTCAAGTTTCCACAACACCC 59.989 40.000 0.00 0.00 0.00 4.61
4252 4578 6.509418 TGACGTACGTTTACTATTTAGGGT 57.491 37.500 23.70 0.00 0.00 4.34
4253 4579 7.009540 CCTTTGACGTACGTTTACTATTTAGGG 59.990 40.741 23.70 8.55 0.00 3.53
4272 4598 2.875317 GCTGAGCTAATAGGCCTTTGAC 59.125 50.000 12.58 0.00 0.00 3.18
4434 6209 1.822990 CTGGCCATGCTGAAGAACAAT 59.177 47.619 5.51 0.00 0.00 2.71
4435 6210 1.250328 CTGGCCATGCTGAAGAACAA 58.750 50.000 5.51 0.00 0.00 2.83
4516 6951 1.250328 CTGGCCATGCTGAAGAACAA 58.750 50.000 5.51 0.00 0.00 2.83
4544 6979 2.195741 AAAACGGCTAGAAACTCCCC 57.804 50.000 0.00 0.00 0.00 4.81
4586 7021 2.295885 CTCCAGGAAGAATCATGCACC 58.704 52.381 0.00 0.00 36.05 5.01


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

AutoCloner maintained by Alex Coulton.