Multiple sequence alignment - TraesCS3A01G485200

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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 TraesCS3A01G485200 chr3A 100.000 2747 0 0 1 2747 714534198 714536944 0.000000e+00 5073.0
1 TraesCS3A01G485200 chr3A 88.824 1029 91 13 854 1882 714541265 714542269 0.000000e+00 1242.0
2 TraesCS3A01G485200 chr3A 88.557 603 52 13 2157 2747 158166355 158165758 0.000000e+00 715.0
3 TraesCS3A01G485200 chr3A 81.639 305 34 10 14 312 714540964 714541252 1.640000e-57 233.0
4 TraesCS3A01G485200 chr3A 93.333 45 2 1 1 44 25934817 25934773 6.350000e-07 65.8
5 TraesCS3A01G485200 chr3D 92.425 1373 46 15 821 2168 579292542 579293881 0.000000e+00 1906.0
6 TraesCS3A01G485200 chr3D 88.428 916 106 0 967 1882 577657984 577657069 0.000000e+00 1105.0
7 TraesCS3A01G485200 chr3D 87.961 922 111 0 961 1882 578052791 578053712 0.000000e+00 1088.0
8 TraesCS3A01G485200 chr3D 89.085 568 58 4 2 568 579291051 579291615 0.000000e+00 702.0
9 TraesCS3A01G485200 chr3D 87.217 618 57 15 851 1466 579305520 579306117 0.000000e+00 684.0
10 TraesCS3A01G485200 chr3D 87.797 590 61 4 2167 2747 508401327 508400740 0.000000e+00 680.0
11 TraesCS3A01G485200 chr3D 88.435 294 26 5 292 581 579304829 579305118 5.630000e-92 348.0
12 TraesCS3A01G485200 chr3D 92.414 145 7 2 557 697 579291880 579292024 1.290000e-48 204.0
13 TraesCS3A01G485200 chr3D 92.958 71 3 1 657 725 579305451 579305521 4.840000e-18 102.0
14 TraesCS3A01G485200 chr3D 96.226 53 2 0 686 738 579292503 579292555 1.360000e-13 87.9
15 TraesCS3A01G485200 chr3D 97.143 35 1 0 10 44 172583704 172583670 2.950000e-05 60.2
16 TraesCS3A01G485200 chr3B 89.934 1212 72 14 821 2003 773542428 773543618 0.000000e+00 1517.0
17 TraesCS3A01G485200 chr3B 88.663 1032 93 13 851 1882 773568554 773569561 0.000000e+00 1236.0
18 TraesCS3A01G485200 chr3B 87.636 922 114 0 961 1882 771253072 771253993 0.000000e+00 1072.0
19 TraesCS3A01G485200 chr3B 86.609 926 124 0 957 1882 770953540 770952615 0.000000e+00 1024.0
20 TraesCS3A01G485200 chr3B 87.342 553 55 9 2 552 773567486 773568025 1.080000e-173 619.0
21 TraesCS3A01G485200 chr3B 89.366 489 49 2 1 486 773541571 773542059 1.810000e-171 612.0
22 TraesCS3A01G485200 chr3B 88.295 393 44 2 1286 1677 771220738 771221129 1.150000e-128 470.0
23 TraesCS3A01G485200 chr3B 90.541 74 5 2 742 813 389321603 389321676 2.250000e-16 97.1
24 TraesCS3A01G485200 chr6A 88.983 590 54 4 2167 2747 140035505 140034918 0.000000e+00 719.0
25 TraesCS3A01G485200 chr6A 88.795 589 55 4 2168 2747 140057644 140057058 0.000000e+00 712.0
26 TraesCS3A01G485200 chr7A 88.983 590 52 7 2167 2747 118333674 118334259 0.000000e+00 717.0
27 TraesCS3A01G485200 chr7A 88.475 590 57 4 2167 2747 595049342 595048755 0.000000e+00 702.0
28 TraesCS3A01G485200 chr7A 85.329 593 76 5 2164 2747 397780096 397780686 1.090000e-168 603.0
29 TraesCS3A01G485200 chr6D 87.436 589 56 11 2167 2743 47079756 47079174 0.000000e+00 662.0
30 TraesCS3A01G485200 chr6D 90.123 81 5 3 742 820 468881933 468881854 4.840000e-18 102.0
31 TraesCS3A01G485200 chr6D 90.000 80 5 3 744 821 294172513 294172591 1.740000e-17 100.0
32 TraesCS3A01G485200 chr6D 89.024 82 5 4 741 821 13673257 13673335 6.260000e-17 99.0
33 TraesCS3A01G485200 chrUn 87.074 557 63 4 2200 2747 98221192 98220636 3.000000e-174 621.0
34 TraesCS3A01G485200 chr1D 94.521 73 2 2 742 813 3263562 3263633 8.040000e-21 111.0
35 TraesCS3A01G485200 chr1B 91.781 73 4 2 742 813 400342806 400342877 1.740000e-17 100.0
36 TraesCS3A01G485200 chr1A 89.024 82 5 4 741 821 589695045 589695123 6.260000e-17 99.0
37 TraesCS3A01G485200 chr5B 90.411 73 5 2 742 813 43450303 43450374 8.100000e-16 95.3
38 TraesCS3A01G485200 chr2B 87.805 82 6 4 741 821 28990513 28990435 2.910000e-15 93.5
39 TraesCS3A01G485200 chr2B 95.455 44 1 1 1 43 315555544 315555587 4.910000e-08 69.4
40 TraesCS3A01G485200 chr5A 94.231 52 3 0 1 52 467062969 467062918 2.270000e-11 80.5
41 TraesCS3A01G485200 chr4B 100.000 29 0 0 15 43 125482339 125482367 1.000000e-03 54.7


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 TraesCS3A01G485200 chr3A 714534198 714536944 2746 False 5073.000 5073 100.000000 1 2747 1 chr3A.!!$F1 2746
1 TraesCS3A01G485200 chr3A 714540964 714542269 1305 False 737.500 1242 85.231500 14 1882 2 chr3A.!!$F2 1868
2 TraesCS3A01G485200 chr3A 158165758 158166355 597 True 715.000 715 88.557000 2157 2747 1 chr3A.!!$R2 590
3 TraesCS3A01G485200 chr3D 577657069 577657984 915 True 1105.000 1105 88.428000 967 1882 1 chr3D.!!$R3 915
4 TraesCS3A01G485200 chr3D 578052791 578053712 921 False 1088.000 1088 87.961000 961 1882 1 chr3D.!!$F1 921
5 TraesCS3A01G485200 chr3D 579291051 579293881 2830 False 724.975 1906 92.537500 2 2168 4 chr3D.!!$F2 2166
6 TraesCS3A01G485200 chr3D 508400740 508401327 587 True 680.000 680 87.797000 2167 2747 1 chr3D.!!$R2 580
7 TraesCS3A01G485200 chr3D 579304829 579306117 1288 False 378.000 684 89.536667 292 1466 3 chr3D.!!$F3 1174
8 TraesCS3A01G485200 chr3B 771253072 771253993 921 False 1072.000 1072 87.636000 961 1882 1 chr3B.!!$F3 921
9 TraesCS3A01G485200 chr3B 773541571 773543618 2047 False 1064.500 1517 89.650000 1 2003 2 chr3B.!!$F4 2002
10 TraesCS3A01G485200 chr3B 770952615 770953540 925 True 1024.000 1024 86.609000 957 1882 1 chr3B.!!$R1 925
11 TraesCS3A01G485200 chr3B 773567486 773569561 2075 False 927.500 1236 88.002500 2 1882 2 chr3B.!!$F5 1880
12 TraesCS3A01G485200 chr6A 140034918 140035505 587 True 719.000 719 88.983000 2167 2747 1 chr6A.!!$R1 580
13 TraesCS3A01G485200 chr6A 140057058 140057644 586 True 712.000 712 88.795000 2168 2747 1 chr6A.!!$R2 579
14 TraesCS3A01G485200 chr7A 118333674 118334259 585 False 717.000 717 88.983000 2167 2747 1 chr7A.!!$F1 580
15 TraesCS3A01G485200 chr7A 595048755 595049342 587 True 702.000 702 88.475000 2167 2747 1 chr7A.!!$R1 580
16 TraesCS3A01G485200 chr7A 397780096 397780686 590 False 603.000 603 85.329000 2164 2747 1 chr7A.!!$F2 583
17 TraesCS3A01G485200 chr6D 47079174 47079756 582 True 662.000 662 87.436000 2167 2743 1 chr6D.!!$R1 576
18 TraesCS3A01G485200 chrUn 98220636 98221192 556 True 621.000 621 87.074000 2200 2747 1 chrUn.!!$R1 547

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
790 2266 0.107993 TCTTTCTGATGCAGAGGCCG 60.108 55.0 0.0 0.0 41.75 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2711 4279 0.69343 AGCCTGAGATGATGCTCCCA 60.693 55.0 0.0 0.0 33.95 4.37 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
80 84 4.796038 AGCATTGGCATTGATATTAGGC 57.204 40.909 13.23 0.00 44.61 3.93
85 89 6.693466 CATTGGCATTGATATTAGGCATGAA 58.307 36.000 3.31 0.00 36.40 2.57
160 164 3.198068 CACCGTTGGATAGATGAGGTTG 58.802 50.000 0.00 0.00 0.00 3.77
165 170 4.504858 GTTGGATAGATGAGGTTGAACGT 58.495 43.478 0.00 0.00 0.00 3.99
168 173 6.085555 TGGATAGATGAGGTTGAACGTATC 57.914 41.667 0.00 0.00 0.00 2.24
273 280 7.563906 AGATAAGACTGATCTTCTTTTGAGGG 58.436 38.462 13.36 0.00 41.63 4.30
352 359 1.842381 AAGGCCTTGCTCCTACGCTT 61.842 55.000 19.73 0.00 32.65 4.68
366 373 1.213275 CGCTTCACATGGCATTGCA 59.787 52.632 11.39 0.00 0.00 4.08
374 381 2.982643 ATGGCATTGCACCTCGGGA 61.983 57.895 11.39 0.00 0.00 5.14
378 385 1.315257 GCATTGCACCTCGGGATTGT 61.315 55.000 3.15 0.00 0.00 2.71
450 460 9.979578 ATCTTGCAAGTAATCTCAATACTCTAG 57.020 33.333 25.19 0.00 32.54 2.43
543 687 7.447374 TTTCATATGGATTGTAATTAGGGCG 57.553 36.000 2.13 0.00 0.00 6.13
552 974 6.757947 GGATTGTAATTAGGGCGCGTATAATA 59.242 38.462 8.43 0.00 0.00 0.98
553 975 7.440255 GGATTGTAATTAGGGCGCGTATAATAT 59.560 37.037 8.43 1.07 0.00 1.28
554 976 8.726870 ATTGTAATTAGGGCGCGTATAATATT 57.273 30.769 8.43 4.00 0.00 1.28
595 1019 8.485392 TGTCATGTAGGATAATTGATGAGTTCA 58.515 33.333 0.00 0.00 0.00 3.18
617 1041 6.878317 TCAAAGTGAGAGACAGAGAAAAGAA 58.122 36.000 0.00 0.00 0.00 2.52
725 2201 6.466812 GGAACAACATTTTGAGATCCCATTT 58.533 36.000 0.00 0.00 36.48 2.32
726 2202 6.591448 GGAACAACATTTTGAGATCCCATTTC 59.409 38.462 0.00 0.00 36.48 2.17
727 2203 6.669125 ACAACATTTTGAGATCCCATTTCA 57.331 33.333 0.00 0.00 36.48 2.69
728 2204 7.065120 ACAACATTTTGAGATCCCATTTCAA 57.935 32.000 0.00 0.00 36.48 2.69
729 2205 7.682628 ACAACATTTTGAGATCCCATTTCAAT 58.317 30.769 0.00 0.00 36.48 2.57
730 2206 8.158789 ACAACATTTTGAGATCCCATTTCAATT 58.841 29.630 0.00 0.00 36.48 2.32
731 2207 8.662141 CAACATTTTGAGATCCCATTTCAATTC 58.338 33.333 0.00 0.00 34.24 2.17
732 2208 7.037438 ACATTTTGAGATCCCATTTCAATTCG 58.963 34.615 0.00 0.00 31.54 3.34
733 2209 6.588719 TTTTGAGATCCCATTTCAATTCGT 57.411 33.333 0.00 0.00 31.54 3.85
734 2210 6.588719 TTTGAGATCCCATTTCAATTCGTT 57.411 33.333 0.00 0.00 31.54 3.85
735 2211 6.588719 TTGAGATCCCATTTCAATTCGTTT 57.411 33.333 0.00 0.00 0.00 3.60
736 2212 6.588719 TGAGATCCCATTTCAATTCGTTTT 57.411 33.333 0.00 0.00 0.00 2.43
737 2213 6.991938 TGAGATCCCATTTCAATTCGTTTTT 58.008 32.000 0.00 0.00 0.00 1.94
764 2240 8.988064 TTCTTTTGCGTTTTAATAATATGGCA 57.012 26.923 0.00 0.00 0.00 4.92
765 2241 9.593134 TTCTTTTGCGTTTTAATAATATGGCAT 57.407 25.926 4.88 4.88 0.00 4.40
769 2245 8.459521 TTGCGTTTTAATAATATGGCATATGC 57.540 30.769 20.14 19.79 41.14 3.14
770 2246 7.597386 TGCGTTTTAATAATATGGCATATGCA 58.403 30.769 28.07 17.28 44.36 3.96
771 2247 8.249638 TGCGTTTTAATAATATGGCATATGCAT 58.750 29.630 28.07 20.22 44.36 3.96
772 2248 8.745837 GCGTTTTAATAATATGGCATATGCATC 58.254 33.333 28.07 13.03 44.36 3.91
779 2255 9.470399 AATAATATGGCATATGCATCTTTCTGA 57.530 29.630 28.07 5.99 44.36 3.27
780 2256 7.956328 AATATGGCATATGCATCTTTCTGAT 57.044 32.000 28.07 8.36 44.36 2.90
789 2265 1.948145 CATCTTTCTGATGCAGAGGCC 59.052 52.381 0.00 0.00 44.96 5.19
790 2266 0.107993 TCTTTCTGATGCAGAGGCCG 60.108 55.000 0.00 0.00 41.75 6.13
791 2267 1.078214 TTTCTGATGCAGAGGCCGG 60.078 57.895 0.00 0.00 41.75 6.13
792 2268 2.541547 TTTCTGATGCAGAGGCCGGG 62.542 60.000 2.18 0.00 41.75 5.73
793 2269 4.559063 CTGATGCAGAGGCCGGGG 62.559 72.222 2.18 0.00 40.13 5.73
795 2271 3.161450 GATGCAGAGGCCGGGGTA 61.161 66.667 2.18 0.00 40.13 3.69
796 2272 2.690881 ATGCAGAGGCCGGGGTAA 60.691 61.111 2.18 0.00 40.13 2.85
797 2273 2.265467 GATGCAGAGGCCGGGGTAAA 62.265 60.000 2.18 0.00 40.13 2.01
798 2274 1.858739 ATGCAGAGGCCGGGGTAAAA 61.859 55.000 2.18 0.00 40.13 1.52
799 2275 2.044555 GCAGAGGCCGGGGTAAAAC 61.045 63.158 2.18 0.00 0.00 2.43
800 2276 1.378119 CAGAGGCCGGGGTAAAACC 60.378 63.158 2.18 0.00 37.60 3.27
813 2289 4.877378 GGTAAAACCCCCTTTTCGAAAT 57.123 40.909 12.12 0.00 33.84 2.17
814 2290 5.981088 GGTAAAACCCCCTTTTCGAAATA 57.019 39.130 12.12 2.24 33.84 1.40
815 2291 5.957798 GGTAAAACCCCCTTTTCGAAATAG 58.042 41.667 12.12 11.43 33.84 1.73
816 2292 5.711506 GGTAAAACCCCCTTTTCGAAATAGA 59.288 40.000 12.12 0.00 33.84 1.98
817 2293 6.209192 GGTAAAACCCCCTTTTCGAAATAGAA 59.791 38.462 12.12 0.00 33.84 2.10
818 2294 6.734502 AAAACCCCCTTTTCGAAATAGAAA 57.265 33.333 12.12 0.00 38.23 2.52
819 2295 6.734502 AAACCCCCTTTTCGAAATAGAAAA 57.265 33.333 12.12 5.04 44.79 2.29
820 2296 6.928348 AACCCCCTTTTCGAAATAGAAAAT 57.072 33.333 12.12 0.00 45.50 1.82
937 2454 6.942163 ATTGACACCTGCTCCTATATATGT 57.058 37.500 0.00 0.00 0.00 2.29
938 2455 8.435931 AATTGACACCTGCTCCTATATATGTA 57.564 34.615 0.00 0.00 0.00 2.29
945 2462 9.190317 CACCTGCTCCTATATATGTACAATCTA 57.810 37.037 0.00 0.00 0.00 1.98
1360 2878 1.351430 CGCCATCAATGTCACGACGT 61.351 55.000 0.00 0.00 0.00 4.34
1377 2895 1.067416 GTCGATATCGCAGGCCACA 59.933 57.895 20.34 0.00 39.60 4.17
1541 3059 2.214216 CCGGTGACCTGGACCTCAA 61.214 63.158 0.00 0.00 0.00 3.02
1590 3108 2.494918 GTGCAGGACGGCGAGTAT 59.505 61.111 16.62 0.00 36.28 2.12
1744 3262 3.348236 ACGCGAGGACGTACAACT 58.652 55.556 15.93 0.00 46.19 3.16
1810 3328 0.731855 GAAGGTGGAGACGTACGTGC 60.732 60.000 28.16 17.00 0.00 5.34
1866 3384 2.759795 GAGCAGAACTGGGGCCTT 59.240 61.111 0.84 0.00 0.00 4.35
1872 3390 2.621668 GCAGAACTGGGGCCTTTTCTAT 60.622 50.000 0.84 0.00 0.00 1.98
1877 3395 1.500736 CTGGGGCCTTTTCTATCCCAT 59.499 52.381 0.84 0.00 45.51 4.00
1956 3501 8.100508 TGGTCACGTAAATGTCAAATAAATGA 57.899 30.769 0.00 0.00 0.00 2.57
1985 3530 1.083806 GTCCGTGCATCGCTTCATGA 61.084 55.000 0.00 0.00 38.35 3.07
1986 3531 1.083806 TCCGTGCATCGCTTCATGAC 61.084 55.000 0.00 0.00 38.35 3.06
1987 3532 1.086067 CCGTGCATCGCTTCATGACT 61.086 55.000 0.00 0.00 38.35 3.41
1988 3533 0.723414 CGTGCATCGCTTCATGACTT 59.277 50.000 0.00 0.00 0.00 3.01
1989 3534 1.926510 CGTGCATCGCTTCATGACTTA 59.073 47.619 0.00 0.00 0.00 2.24
1990 3535 2.541346 CGTGCATCGCTTCATGACTTAT 59.459 45.455 0.00 0.00 0.00 1.73
1991 3536 3.362401 CGTGCATCGCTTCATGACTTATC 60.362 47.826 0.00 0.00 0.00 1.75
1992 3537 3.557185 GTGCATCGCTTCATGACTTATCA 59.443 43.478 0.00 0.00 39.83 2.15
1994 3539 5.406477 GTGCATCGCTTCATGACTTATCATA 59.594 40.000 0.00 0.00 44.13 2.15
1995 3540 5.406477 TGCATCGCTTCATGACTTATCATAC 59.594 40.000 0.00 0.00 44.13 2.39
1996 3541 5.636965 GCATCGCTTCATGACTTATCATACT 59.363 40.000 0.00 0.00 44.13 2.12
1997 3542 6.146837 GCATCGCTTCATGACTTATCATACTT 59.853 38.462 0.00 0.00 44.13 2.24
1998 3543 7.508134 CATCGCTTCATGACTTATCATACTTG 58.492 38.462 0.00 0.00 44.13 3.16
1999 3544 6.573434 TCGCTTCATGACTTATCATACTTGT 58.427 36.000 0.00 0.00 44.13 3.16
2000 3545 6.476706 TCGCTTCATGACTTATCATACTTGTG 59.523 38.462 0.00 0.00 44.13 3.33
2001 3546 6.425504 GCTTCATGACTTATCATACTTGTGC 58.574 40.000 0.00 0.00 44.13 4.57
2002 3547 6.512415 GCTTCATGACTTATCATACTTGTGCC 60.512 42.308 0.00 0.00 44.13 5.01
2003 3548 6.239217 TCATGACTTATCATACTTGTGCCT 57.761 37.500 0.00 0.00 44.13 4.75
2004 3549 6.283694 TCATGACTTATCATACTTGTGCCTC 58.716 40.000 0.00 0.00 44.13 4.70
2005 3550 4.682787 TGACTTATCATACTTGTGCCTCG 58.317 43.478 0.00 0.00 0.00 4.63
2006 3551 4.401202 TGACTTATCATACTTGTGCCTCGA 59.599 41.667 0.00 0.00 0.00 4.04
2025 3570 2.629051 GAACTTATACTTGTGCCGCCT 58.371 47.619 0.00 0.00 0.00 5.52
2034 3579 2.159000 ACTTGTGCCGCCTACCTATAAC 60.159 50.000 0.00 0.00 0.00 1.89
2037 3582 2.236644 TGTGCCGCCTACCTATAACAAA 59.763 45.455 0.00 0.00 0.00 2.83
2038 3583 2.870411 GTGCCGCCTACCTATAACAAAG 59.130 50.000 0.00 0.00 0.00 2.77
2039 3584 1.871676 GCCGCCTACCTATAACAAAGC 59.128 52.381 0.00 0.00 0.00 3.51
2040 3585 2.743838 GCCGCCTACCTATAACAAAGCA 60.744 50.000 0.00 0.00 0.00 3.91
2041 3586 2.870411 CCGCCTACCTATAACAAAGCAC 59.130 50.000 0.00 0.00 0.00 4.40
2042 3587 3.431766 CCGCCTACCTATAACAAAGCACT 60.432 47.826 0.00 0.00 0.00 4.40
2043 3588 4.202182 CCGCCTACCTATAACAAAGCACTA 60.202 45.833 0.00 0.00 0.00 2.74
2044 3589 5.353938 CGCCTACCTATAACAAAGCACTAA 58.646 41.667 0.00 0.00 0.00 2.24
2082 3627 3.622163 TGCCTTGAAAACAATTTGCAGTG 59.378 39.130 0.00 0.00 0.00 3.66
2086 3631 5.220643 CCTTGAAAACAATTTGCAGTGAACC 60.221 40.000 0.00 0.00 0.00 3.62
2119 3664 8.806429 TCAAATAAATTGATGAGCTTCTGGTA 57.194 30.769 0.00 0.00 43.08 3.25
2160 3708 8.664669 TTCTGGCCTAAAAAGAAAAATATCCT 57.335 30.769 3.32 0.00 0.00 3.24
2266 3820 4.917474 GCGGTAGCGGGAAACTAA 57.083 55.556 17.08 0.00 0.00 2.24
2291 3847 2.178273 GGGAAACGATTGTGCGCC 59.822 61.111 4.18 0.00 33.86 6.53
2314 3874 1.211190 GAAAAAGGCAGCAGCTCGG 59.789 57.895 0.00 0.00 41.70 4.63
2353 3921 0.307760 GCGCGCCTATAAATTGCAGT 59.692 50.000 23.24 0.00 0.00 4.40
2359 3927 2.695147 GCCTATAAATTGCAGTGCCCTT 59.305 45.455 13.72 5.68 0.00 3.95
2377 3945 2.690497 CCTTTGTCGCTCTCTCCATCTA 59.310 50.000 0.00 0.00 0.00 1.98
2393 3961 0.178950 TCTATCCATCGCCCTCTGCT 60.179 55.000 0.00 0.00 38.05 4.24
2498 4066 2.125326 CCGTCCGGCATCTACTCCA 61.125 63.158 0.00 0.00 0.00 3.86
2508 4076 2.362397 GCATCTACTCCACCGAGATTCA 59.638 50.000 0.00 0.00 38.52 2.57
2551 4119 0.597072 GTCTCGGAACCTTCGACACT 59.403 55.000 0.00 0.00 32.86 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 9.037737 GTAATTATATACCACGTGACACATGTT 57.962 33.333 19.30 5.55 30.47 2.71
127 131 0.713883 CAACGGTGTACATCACTCGC 59.286 55.000 6.97 0.00 45.50 5.03
139 143 3.118775 TCAACCTCATCTATCCAACGGTG 60.119 47.826 0.00 0.00 0.00 4.94
160 164 6.858993 GGAGATCTAACACATCTGATACGTTC 59.141 42.308 0.00 0.00 30.30 3.95
165 170 4.827284 TGCGGAGATCTAACACATCTGATA 59.173 41.667 0.00 0.00 30.30 2.15
168 173 3.443099 TGCGGAGATCTAACACATCTG 57.557 47.619 0.00 0.00 30.30 2.90
273 280 5.066505 ACAATAATCTGATCAAAGGCGGTTC 59.933 40.000 0.00 0.00 0.00 3.62
312 319 0.321564 CACCATTGGCGTCTTCTCCA 60.322 55.000 1.54 0.00 0.00 3.86
352 359 1.307355 CGAGGTGCAATGCCATGTGA 61.307 55.000 1.53 0.00 0.00 3.58
366 373 0.531200 GAAGACGACAATCCCGAGGT 59.469 55.000 0.00 0.00 0.00 3.85
374 381 2.159226 GGATGGAGACGAAGACGACAAT 60.159 50.000 0.00 0.00 42.66 2.71
378 385 1.472878 CAAGGATGGAGACGAAGACGA 59.527 52.381 0.00 0.00 42.66 4.20
467 478 4.311606 TGCTAGACGCACAATGTTTTAGA 58.688 39.130 0.00 0.00 45.47 2.10
552 974 9.486497 CTACATGACACTCAAGATAATAGCAAT 57.514 33.333 0.00 0.00 0.00 3.56
553 975 7.928167 CCTACATGACACTCAAGATAATAGCAA 59.072 37.037 0.00 0.00 0.00 3.91
554 976 7.287696 TCCTACATGACACTCAAGATAATAGCA 59.712 37.037 0.00 0.00 0.00 3.49
595 1019 6.098982 TCCTTCTTTTCTCTGTCTCTCACTTT 59.901 38.462 0.00 0.00 0.00 2.66
738 2214 9.424319 TGCCATATTATTAAAACGCAAAAGAAA 57.576 25.926 0.00 0.00 0.00 2.52
739 2215 8.988064 TGCCATATTATTAAAACGCAAAAGAA 57.012 26.923 0.00 0.00 0.00 2.52
743 2219 8.920665 GCATATGCCATATTATTAAAACGCAAA 58.079 29.630 17.26 0.00 34.31 3.68
744 2220 8.084684 TGCATATGCCATATTATTAAAACGCAA 58.915 29.630 24.54 0.00 41.18 4.85
745 2221 7.597386 TGCATATGCCATATTATTAAAACGCA 58.403 30.769 24.54 0.00 41.18 5.24
746 2222 8.633075 ATGCATATGCCATATTATTAAAACGC 57.367 30.769 24.54 0.00 41.18 4.84
753 2229 9.470399 TCAGAAAGATGCATATGCCATATTATT 57.530 29.630 24.54 10.38 41.18 1.40
754 2230 9.642343 ATCAGAAAGATGCATATGCCATATTAT 57.358 29.630 24.54 10.31 41.18 1.28
755 2231 8.899771 CATCAGAAAGATGCATATGCCATATTA 58.100 33.333 24.54 5.39 46.90 0.98
756 2232 7.772166 CATCAGAAAGATGCATATGCCATATT 58.228 34.615 24.54 16.93 46.90 1.28
757 2233 7.334844 CATCAGAAAGATGCATATGCCATAT 57.665 36.000 24.54 11.81 46.90 1.78
758 2234 6.753107 CATCAGAAAGATGCATATGCCATA 57.247 37.500 24.54 6.97 46.90 2.74
759 2235 5.644977 CATCAGAAAGATGCATATGCCAT 57.355 39.130 24.54 17.02 46.90 4.40
770 2246 1.474677 CGGCCTCTGCATCAGAAAGAT 60.475 52.381 0.00 0.00 40.18 2.40
771 2247 0.107993 CGGCCTCTGCATCAGAAAGA 60.108 55.000 0.00 0.00 40.18 2.52
772 2248 1.094073 CCGGCCTCTGCATCAGAAAG 61.094 60.000 0.00 0.00 40.18 2.62
773 2249 1.078214 CCGGCCTCTGCATCAGAAA 60.078 57.895 0.00 0.00 40.18 2.52
774 2250 2.586245 CCGGCCTCTGCATCAGAA 59.414 61.111 0.00 0.00 40.18 3.02
775 2251 3.473647 CCCGGCCTCTGCATCAGA 61.474 66.667 0.00 0.00 38.25 3.27
776 2252 4.559063 CCCCGGCCTCTGCATCAG 62.559 72.222 0.00 0.00 40.13 2.90
777 2253 3.993865 TACCCCGGCCTCTGCATCA 62.994 63.158 0.00 0.00 40.13 3.07
778 2254 2.265467 TTTACCCCGGCCTCTGCATC 62.265 60.000 0.00 0.00 40.13 3.91
779 2255 1.858739 TTTTACCCCGGCCTCTGCAT 61.859 55.000 0.00 0.00 40.13 3.96
780 2256 2.530672 TTTTACCCCGGCCTCTGCA 61.531 57.895 0.00 0.00 40.13 4.41
781 2257 2.044555 GTTTTACCCCGGCCTCTGC 61.045 63.158 0.00 0.00 0.00 4.26
782 2258 1.378119 GGTTTTACCCCGGCCTCTG 60.378 63.158 0.00 0.00 30.04 3.35
783 2259 3.084304 GGTTTTACCCCGGCCTCT 58.916 61.111 0.00 0.00 30.04 3.69
792 2268 4.877378 ATTTCGAAAAGGGGGTTTTACC 57.123 40.909 15.66 0.00 38.54 2.85
793 2269 6.822667 TCTATTTCGAAAAGGGGGTTTTAC 57.177 37.500 15.66 0.00 38.54 2.01
794 2270 7.836479 TTTCTATTTCGAAAAGGGGGTTTTA 57.164 32.000 15.66 0.00 38.54 1.52
795 2271 6.734502 TTTCTATTTCGAAAAGGGGGTTTT 57.265 33.333 15.66 0.00 41.29 2.43
796 2272 6.734502 TTTTCTATTTCGAAAAGGGGGTTT 57.265 33.333 15.66 0.00 37.81 3.27
797 2273 6.928348 ATTTTCTATTTCGAAAAGGGGGTT 57.072 33.333 15.66 0.00 43.65 4.11
798 2274 6.495526 TGAATTTTCTATTTCGAAAAGGGGGT 59.504 34.615 15.66 0.00 43.65 4.95
799 2275 6.930731 TGAATTTTCTATTTCGAAAAGGGGG 58.069 36.000 15.66 3.96 43.65 5.40
800 2276 9.435688 AATTGAATTTTCTATTTCGAAAAGGGG 57.564 29.630 15.66 5.66 43.65 4.79
804 2280 9.685828 ACCGAATTGAATTTTCTATTTCGAAAA 57.314 25.926 15.66 3.81 44.28 2.29
805 2281 9.685828 AACCGAATTGAATTTTCTATTTCGAAA 57.314 25.926 13.91 13.91 33.83 3.46
806 2282 9.685828 AAACCGAATTGAATTTTCTATTTCGAA 57.314 25.926 16.75 0.00 33.83 3.71
807 2283 9.685828 AAAACCGAATTGAATTTTCTATTTCGA 57.314 25.926 16.75 0.00 33.83 3.71
814 2290 9.594478 ACTTTGTAAAACCGAATTGAATTTTCT 57.406 25.926 0.00 0.00 0.00 2.52
816 2292 9.980780 CAACTTTGTAAAACCGAATTGAATTTT 57.019 25.926 0.00 0.00 0.00 1.82
817 2293 9.372369 TCAACTTTGTAAAACCGAATTGAATTT 57.628 25.926 0.00 0.00 0.00 1.82
818 2294 8.813282 GTCAACTTTGTAAAACCGAATTGAATT 58.187 29.630 0.00 0.00 0.00 2.17
819 2295 8.194769 AGTCAACTTTGTAAAACCGAATTGAAT 58.805 29.630 0.00 0.00 0.00 2.57
820 2296 7.540299 AGTCAACTTTGTAAAACCGAATTGAA 58.460 30.769 0.00 0.00 0.00 2.69
935 2452 6.881065 AGTAGTCGTACCTTGTAGATTGTACA 59.119 38.462 0.00 0.00 0.00 2.90
936 2453 7.313951 AGTAGTCGTACCTTGTAGATTGTAC 57.686 40.000 0.00 0.00 0.00 2.90
937 2454 8.260818 AGTAGTAGTCGTACCTTGTAGATTGTA 58.739 37.037 0.00 0.00 0.00 2.41
938 2455 7.108847 AGTAGTAGTCGTACCTTGTAGATTGT 58.891 38.462 0.00 0.00 0.00 2.71
945 2462 4.633565 GCAGTAGTAGTAGTCGTACCTTGT 59.366 45.833 0.00 0.00 0.00 3.16
1360 2878 0.392706 ATTGTGGCCTGCGATATCGA 59.607 50.000 28.63 12.43 43.02 3.59
1537 3055 2.096069 CCGTGAACAGCATGAAGTTGAG 60.096 50.000 7.79 0.73 39.69 3.02
1541 3059 1.568612 CGCCGTGAACAGCATGAAGT 61.569 55.000 0.00 0.00 39.69 3.01
1590 3108 1.972075 TCGAACATGTTCTGGTACCCA 59.028 47.619 30.45 0.00 37.44 4.51
1638 3156 4.400251 ACCCCTAGCCGCTCCACT 62.400 66.667 0.00 0.00 0.00 4.00
1668 3186 2.852180 CGTCTCCGACACCACCACA 61.852 63.158 0.00 0.00 35.63 4.17
1785 3303 3.692406 GTCTCCACCTTCCGCGGT 61.692 66.667 27.15 1.49 37.93 5.68
1866 3384 9.540538 TTTAAAATGAAGGTGATGGGATAGAAA 57.459 29.630 0.00 0.00 0.00 2.52
1872 3390 7.789202 TCAATTTAAAATGAAGGTGATGGGA 57.211 32.000 3.42 0.00 0.00 4.37
1877 3395 8.335532 ACGAGATCAATTTAAAATGAAGGTGA 57.664 30.769 9.91 0.00 0.00 4.02
1956 3501 3.411351 GCACGGACATGCGAACGT 61.411 61.111 0.00 0.00 40.60 3.99
1985 3530 5.105310 AGTTCGAGGCACAAGTATGATAAGT 60.105 40.000 0.00 0.00 0.00 2.24
1986 3531 5.352284 AGTTCGAGGCACAAGTATGATAAG 58.648 41.667 0.00 0.00 0.00 1.73
1987 3532 5.339008 AGTTCGAGGCACAAGTATGATAA 57.661 39.130 0.00 0.00 0.00 1.75
1988 3533 5.339008 AAGTTCGAGGCACAAGTATGATA 57.661 39.130 0.00 0.00 0.00 2.15
1989 3534 3.895232 AGTTCGAGGCACAAGTATGAT 57.105 42.857 0.00 0.00 0.00 2.45
1990 3535 3.678056 AAGTTCGAGGCACAAGTATGA 57.322 42.857 0.00 0.00 0.00 2.15
1991 3536 6.273825 AGTATAAGTTCGAGGCACAAGTATG 58.726 40.000 0.00 0.00 0.00 2.39
1992 3537 6.466885 AGTATAAGTTCGAGGCACAAGTAT 57.533 37.500 0.00 0.00 0.00 2.12
1993 3538 5.909621 AGTATAAGTTCGAGGCACAAGTA 57.090 39.130 0.00 0.00 0.00 2.24
1994 3539 4.803098 AGTATAAGTTCGAGGCACAAGT 57.197 40.909 0.00 0.00 0.00 3.16
1995 3540 4.929808 ACAAGTATAAGTTCGAGGCACAAG 59.070 41.667 0.00 0.00 0.00 3.16
1996 3541 4.688879 CACAAGTATAAGTTCGAGGCACAA 59.311 41.667 0.00 0.00 0.00 3.33
1997 3542 4.242475 CACAAGTATAAGTTCGAGGCACA 58.758 43.478 0.00 0.00 0.00 4.57
1998 3543 3.062234 GCACAAGTATAAGTTCGAGGCAC 59.938 47.826 0.00 0.00 0.00 5.01
1999 3544 3.259064 GCACAAGTATAAGTTCGAGGCA 58.741 45.455 0.00 0.00 0.00 4.75
2000 3545 2.608090 GGCACAAGTATAAGTTCGAGGC 59.392 50.000 0.00 0.00 0.00 4.70
2001 3546 2.858344 CGGCACAAGTATAAGTTCGAGG 59.142 50.000 0.00 0.00 0.00 4.63
2002 3547 2.281762 GCGGCACAAGTATAAGTTCGAG 59.718 50.000 0.00 0.00 0.00 4.04
2003 3548 2.264813 GCGGCACAAGTATAAGTTCGA 58.735 47.619 0.00 0.00 0.00 3.71
2004 3549 1.326548 GGCGGCACAAGTATAAGTTCG 59.673 52.381 3.07 0.00 0.00 3.95
2005 3550 2.629051 AGGCGGCACAAGTATAAGTTC 58.371 47.619 13.08 0.00 0.00 3.01
2006 3551 2.781681 AGGCGGCACAAGTATAAGTT 57.218 45.000 13.08 0.00 0.00 2.66
2025 3570 5.808540 CGTGCTTAGTGCTTTGTTATAGGTA 59.191 40.000 0.00 0.00 43.37 3.08
2034 3579 1.793613 GCGCGTGCTTAGTGCTTTG 60.794 57.895 15.02 0.00 43.37 2.77
2037 3582 2.664851 TTGCGCGTGCTTAGTGCT 60.665 55.556 23.16 0.00 44.60 4.40
2038 3583 2.202222 CTTGCGCGTGCTTAGTGC 60.202 61.111 23.16 5.48 44.57 4.40
2039 3584 1.154599 CACTTGCGCGTGCTTAGTG 60.155 57.895 28.79 28.79 43.09 2.74
2040 3585 3.244105 CACTTGCGCGTGCTTAGT 58.756 55.556 23.16 20.75 43.34 2.24
2205 3755 3.498082 CGCGCTAAAAAGCCAATTTACT 58.502 40.909 5.56 0.00 0.00 2.24
2270 3824 2.961669 GCACAATCGTTTCCCGCGT 61.962 57.895 4.92 0.00 36.19 6.01
2291 3847 2.600173 TGCTGCCTTTTTCCCCGG 60.600 61.111 0.00 0.00 0.00 5.73
2297 3857 2.270986 CCCGAGCTGCTGCCTTTTT 61.271 57.895 7.01 0.00 40.80 1.94
2353 3921 1.293498 GAGAGAGCGACAAAGGGCA 59.707 57.895 0.00 0.00 0.00 5.36
2359 3927 2.887783 GGATAGATGGAGAGAGCGACAA 59.112 50.000 0.00 0.00 0.00 3.18
2490 4058 3.280295 GACTGAATCTCGGTGGAGTAGA 58.720 50.000 0.00 0.00 41.26 2.59
2711 4279 0.693430 AGCCTGAGATGATGCTCCCA 60.693 55.000 0.00 0.00 33.95 4.37


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

AutoCloner maintained by Alex Coulton.