Multiple sequence alignment - TraesCS2B01G170500

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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 TraesCS2B01G170500 chr2B 100.000 3107 0 0 1 3107 143482896 143486002 0.000000e+00 5738.0
1 TraesCS2B01G170500 chr2B 75.068 1464 208 98 904 2270 143282138 143280735 1.270000e-148 536.0
2 TraesCS2B01G170500 chr2B 87.898 157 14 2 2385 2538 143485219 143485373 2.460000e-41 180.0
3 TraesCS2B01G170500 chr2B 87.898 157 14 2 2324 2478 143485280 143485433 2.460000e-41 180.0
4 TraesCS2B01G170500 chr2B 93.671 79 2 1 3032 3107 152181157 152181235 7.040000e-22 115.0
5 TraesCS2B01G170500 chr2D 95.217 1589 57 6 895 2478 89216135 89214561 0.000000e+00 2495.0
6 TraesCS2B01G170500 chr2D 96.149 883 34 0 895 1777 104876456 104877338 0.000000e+00 1443.0
7 TraesCS2B01G170500 chr2D 89.947 945 40 25 2163 3092 104886429 104887333 0.000000e+00 1168.0
8 TraesCS2B01G170500 chr2D 88.056 720 45 20 2385 3091 89214711 89214020 0.000000e+00 815.0
9 TraesCS2B01G170500 chr2D 94.647 411 16 2 1774 2178 104885966 104886376 1.570000e-177 632.0
10 TraesCS2B01G170500 chr2D 86.604 530 69 2 14 543 424656307 424655780 4.460000e-163 584.0
11 TraesCS2B01G170500 chr2D 76.022 1272 197 73 1058 2270 90523111 90521889 7.520000e-156 560.0
12 TraesCS2B01G170500 chr2D 93.119 218 9 4 684 896 104876063 104876279 6.470000e-82 315.0
13 TraesCS2B01G170500 chr2D 92.627 217 11 4 684 896 89216528 89216313 1.080000e-79 307.0
14 TraesCS2B01G170500 chr2D 90.789 152 10 2 2327 2478 104886644 104886791 1.890000e-47 200.0
15 TraesCS2B01G170500 chr2D 96.703 91 1 1 2324 2414 89214650 89214562 1.930000e-32 150.0
16 TraesCS2B01G170500 chr2D 94.505 91 3 1 2324 2414 104886702 104886790 4.180000e-29 139.0
17 TraesCS2B01G170500 chr2D 91.892 74 3 2 3032 3105 100320312 100320382 1.970000e-17 100.0
18 TraesCS2B01G170500 chr2D 100.000 28 0 0 3080 3107 89214004 89213977 6.000000e-03 52.8
19 TraesCS2B01G170500 chr2D 100.000 28 0 0 3080 3107 104887347 104887374 6.000000e-03 52.8
20 TraesCS2B01G170500 chr2A 93.949 1570 58 11 923 2478 90509689 90508143 0.000000e+00 2338.0
21 TraesCS2B01G170500 chr2A 91.018 668 48 7 2 658 694464223 694464889 0.000000e+00 891.0
22 TraesCS2B01G170500 chr2A 88.791 678 54 7 2 658 175768606 175767930 0.000000e+00 811.0
23 TraesCS2B01G170500 chr2A 77.588 879 154 20 1058 1898 90428874 90428001 2.780000e-135 492.0
24 TraesCS2B01G170500 chr2A 92.308 169 10 2 2387 2554 90508293 90508127 1.440000e-58 237.0
25 TraesCS2B01G170500 chr2A 95.122 123 3 2 687 806 90511012 90510890 1.140000e-44 191.0
26 TraesCS2B01G170500 chr2A 95.604 91 4 0 2324 2414 90508234 90508144 2.500000e-31 147.0
27 TraesCS2B01G170500 chr2A 92.647 68 5 0 829 896 90509853 90509786 7.090000e-17 99.0
28 TraesCS2B01G170500 chr2A 100.000 30 0 0 2324 2353 90508173 90508144 4.330000e-04 56.5
29 TraesCS2B01G170500 chr5A 90.405 667 50 7 5 658 103389351 103388686 0.000000e+00 865.0
30 TraesCS2B01G170500 chr1A 88.939 669 59 9 2 658 100667685 100667020 0.000000e+00 811.0
31 TraesCS2B01G170500 chr1B 90.694 591 43 6 2 580 536106639 536106049 0.000000e+00 776.0
32 TraesCS2B01G170500 chr1B 90.278 144 10 2 2869 3009 14862320 14862178 5.290000e-43 185.0
33 TraesCS2B01G170500 chr1B 86.826 167 18 2 2869 3032 672428243 672428408 1.900000e-42 183.0
34 TraesCS2B01G170500 chr1B 87.209 86 9 2 571 656 536096921 536096838 2.550000e-16 97.1
35 TraesCS2B01G170500 chr4A 87.592 677 62 8 3 658 136947346 136948021 0.000000e+00 765.0
36 TraesCS2B01G170500 chr7B 82.537 670 86 20 14 658 3924342 3923679 7.520000e-156 560.0
37 TraesCS2B01G170500 chr7B 81.439 264 40 9 1472 1732 424537129 424537386 1.130000e-49 207.0
38 TraesCS2B01G170500 chr4B 84.181 531 79 3 13 542 193493378 193493904 7.690000e-141 510.0
39 TraesCS2B01G170500 chr7A 75.415 663 93 50 1633 2270 570183066 570182449 1.110000e-64 257.0
40 TraesCS2B01G170500 chr7A 86.145 166 17 3 2870 3032 673243176 673243014 1.150000e-39 174.0


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 TraesCS2B01G170500 chr2B 143482896 143486002 3106 False 2032.666667 5738 91.932000 1 3107 3 chr2B.!!$F2 3106
1 TraesCS2B01G170500 chr2B 143280735 143282138 1403 True 536.000000 536 75.068000 904 2270 1 chr2B.!!$R1 1366
2 TraesCS2B01G170500 chr2D 104876063 104877338 1275 False 879.000000 1443 94.634000 684 1777 2 chr2D.!!$F2 1093
3 TraesCS2B01G170500 chr2D 89213977 89216528 2551 True 763.960000 2495 94.520600 684 3107 5 chr2D.!!$R3 2423
4 TraesCS2B01G170500 chr2D 424655780 424656307 527 True 584.000000 584 86.604000 14 543 1 chr2D.!!$R2 529
5 TraesCS2B01G170500 chr2D 90521889 90523111 1222 True 560.000000 560 76.022000 1058 2270 1 chr2D.!!$R1 1212
6 TraesCS2B01G170500 chr2D 104885966 104887374 1408 False 438.360000 1168 93.977600 1774 3107 5 chr2D.!!$F3 1333
7 TraesCS2B01G170500 chr2A 694464223 694464889 666 False 891.000000 891 91.018000 2 658 1 chr2A.!!$F1 656
8 TraesCS2B01G170500 chr2A 175767930 175768606 676 True 811.000000 811 88.791000 2 658 1 chr2A.!!$R2 656
9 TraesCS2B01G170500 chr2A 90508127 90511012 2885 True 511.416667 2338 94.938333 687 2554 6 chr2A.!!$R3 1867
10 TraesCS2B01G170500 chr2A 90428001 90428874 873 True 492.000000 492 77.588000 1058 1898 1 chr2A.!!$R1 840
11 TraesCS2B01G170500 chr5A 103388686 103389351 665 True 865.000000 865 90.405000 5 658 1 chr5A.!!$R1 653
12 TraesCS2B01G170500 chr1A 100667020 100667685 665 True 811.000000 811 88.939000 2 658 1 chr1A.!!$R1 656
13 TraesCS2B01G170500 chr1B 536106049 536106639 590 True 776.000000 776 90.694000 2 580 1 chr1B.!!$R3 578
14 TraesCS2B01G170500 chr4A 136947346 136948021 675 False 765.000000 765 87.592000 3 658 1 chr4A.!!$F1 655
15 TraesCS2B01G170500 chr7B 3923679 3924342 663 True 560.000000 560 82.537000 14 658 1 chr7B.!!$R1 644
16 TraesCS2B01G170500 chr4B 193493378 193493904 526 False 510.000000 510 84.181000 13 542 1 chr4B.!!$F1 529
17 TraesCS2B01G170500 chr7A 570182449 570183066 617 True 257.000000 257 75.415000 1633 2270 1 chr7A.!!$R1 637

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
685 729 0.040425 AAAAACATGGCGAGTCGTGC 60.040 50.0 15.08 0.0 0.0 5.34 F
1171 2471 0.257328 TCCAGCCCCGATGCATTTTA 59.743 50.0 0.00 0.0 0.0 1.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2059 3401 0.400594 AGGAACGGCTTAGTGGCTTT 59.599 50.0 0.00 0.0 39.32 3.51 R
2478 3969 0.987294 CCAGGGTCAGGTGACAAGAT 59.013 55.0 12.09 0.0 46.47 2.40 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
50 51 5.895636 AAATCTGGCACGTCATGAATTTA 57.104 34.783 0.00 0.00 0.00 1.40
73 74 4.522405 AGATCCAGATGTCAATAGTCTCCG 59.478 45.833 0.00 0.00 0.00 4.63
129 130 3.826221 GCCATAAGCACCGCATCA 58.174 55.556 0.00 0.00 42.97 3.07
145 147 2.806434 CATCACCCCTGAAATTCCACA 58.194 47.619 0.00 0.00 0.00 4.17
242 244 2.754552 TGAATTTTGCTTCCTGCGCTAT 59.245 40.909 9.73 0.00 46.63 2.97
420 422 3.069300 CCATCATCATCTTCTCCACGTCT 59.931 47.826 0.00 0.00 0.00 4.18
543 552 2.932234 CGGTCCAGTCCAAGAGCGT 61.932 63.158 3.65 0.00 46.03 5.07
544 553 1.079750 GGTCCAGTCCAAGAGCGTC 60.080 63.158 0.00 0.00 0.00 5.19
545 554 1.666011 GTCCAGTCCAAGAGCGTCA 59.334 57.895 0.00 0.00 0.00 4.35
547 556 1.739562 CCAGTCCAAGAGCGTCAGC 60.740 63.158 0.00 0.00 45.58 4.26
597 641 4.360405 GGCGGCAGGGGAGGAAAA 62.360 66.667 3.07 0.00 0.00 2.29
666 710 6.466885 CCTAACGAGAGGGAAGATTCTAAA 57.533 41.667 0.00 0.00 32.39 1.85
667 711 6.875076 CCTAACGAGAGGGAAGATTCTAAAA 58.125 40.000 0.00 0.00 32.39 1.52
668 712 7.328737 CCTAACGAGAGGGAAGATTCTAAAAA 58.671 38.462 0.00 0.00 32.39 1.94
685 729 0.040425 AAAAACATGGCGAGTCGTGC 60.040 50.000 15.08 0.00 0.00 5.34
720 765 0.925466 ACTGGTTCGTTTCGTTCGTG 59.075 50.000 0.00 0.00 0.00 4.35
743 788 4.018409 GCTGGGGCCGAGAAAAAT 57.982 55.556 20.75 0.00 0.00 1.82
822 880 5.301805 CCATTTATAAGCCAACGATCCCTTT 59.698 40.000 0.00 0.00 0.00 3.11
823 881 6.438763 CATTTATAAGCCAACGATCCCTTTC 58.561 40.000 0.00 0.00 0.00 2.62
884 1947 7.888021 ACTATTGTCTCCCAACACAATCAATTA 59.112 33.333 0.67 0.00 41.37 1.40
885 1948 6.968263 TTGTCTCCCAACACAATCAATTAA 57.032 33.333 0.00 0.00 0.00 1.40
896 1959 4.320690 CACAATCAATTAACGAAACCGCTG 59.679 41.667 0.00 0.00 0.00 5.18
906 2148 1.696832 GAAACCGCTGCCAGTCGATC 61.697 60.000 9.57 2.97 0.00 3.69
909 2151 4.498520 CGCTGCCAGTCGATCCGT 62.499 66.667 2.97 0.00 0.00 4.69
991 2243 6.920758 CAGATCTACGAGTAATCCAGGAAAAG 59.079 42.308 0.00 0.00 0.00 2.27
1171 2471 0.257328 TCCAGCCCCGATGCATTTTA 59.743 50.000 0.00 0.00 0.00 1.52
1211 2517 4.838486 GGCGCCTCTCGAGTCGTG 62.838 72.222 22.15 10.57 41.67 4.35
1252 2558 4.155280 GCTCTAAGATTTTGGCGGTGTTTA 59.845 41.667 0.00 0.00 0.00 2.01
1506 2839 1.137086 TCTGAGAAGCCGCCATTCTAC 59.863 52.381 0.00 0.00 37.14 2.59
1762 3095 3.457380 AGTGCCCATCTATGACACTGATT 59.543 43.478 14.14 0.00 40.79 2.57
1898 3234 0.966179 TGCCTCGTACAGTGTGTCAT 59.034 50.000 5.88 0.00 0.00 3.06
2030 3372 1.423541 ACTGACAACTGGCAATACCCA 59.576 47.619 0.00 0.00 37.83 4.51
2059 3401 5.369833 TGCAGTACTACAAAGTGCCTAAAA 58.630 37.500 0.00 0.00 41.64 1.52
2085 3430 2.737252 CACTAAGCCGTTCCTTCAAGAC 59.263 50.000 0.00 0.00 0.00 3.01
2239 3667 8.122952 CGTCTGATTTGTAAATGTATTCCCTTC 58.877 37.037 0.00 0.00 0.00 3.46
2419 3910 1.073025 TTGCACCGTCATTCAGCCT 59.927 52.632 0.00 0.00 0.00 4.58
2420 3911 0.955428 TTGCACCGTCATTCAGCCTC 60.955 55.000 0.00 0.00 0.00 4.70
2421 3912 1.078848 GCACCGTCATTCAGCCTCT 60.079 57.895 0.00 0.00 0.00 3.69
2422 3913 1.086634 GCACCGTCATTCAGCCTCTC 61.087 60.000 0.00 0.00 0.00 3.20
2423 3914 0.247460 CACCGTCATTCAGCCTCTCA 59.753 55.000 0.00 0.00 0.00 3.27
2424 3915 0.247736 ACCGTCATTCAGCCTCTCAC 59.752 55.000 0.00 0.00 0.00 3.51
2425 3916 0.460987 CCGTCATTCAGCCTCTCACC 60.461 60.000 0.00 0.00 0.00 4.02
2426 3917 0.247460 CGTCATTCAGCCTCTCACCA 59.753 55.000 0.00 0.00 0.00 4.17
2427 3918 1.738365 CGTCATTCAGCCTCTCACCAG 60.738 57.143 0.00 0.00 0.00 4.00
2428 3919 1.552337 GTCATTCAGCCTCTCACCAGA 59.448 52.381 0.00 0.00 0.00 3.86
2429 3920 1.552337 TCATTCAGCCTCTCACCAGAC 59.448 52.381 0.00 0.00 0.00 3.51
2430 3921 1.277273 CATTCAGCCTCTCACCAGACA 59.723 52.381 0.00 0.00 0.00 3.41
2431 3922 1.423584 TTCAGCCTCTCACCAGACAA 58.576 50.000 0.00 0.00 0.00 3.18
2432 3923 1.649321 TCAGCCTCTCACCAGACAAT 58.351 50.000 0.00 0.00 0.00 2.71
2433 3924 1.277273 TCAGCCTCTCACCAGACAATG 59.723 52.381 0.00 0.00 0.00 2.82
2468 3959 8.746922 TGCATTTAAAATTTGTTTTTGTTGCA 57.253 23.077 0.00 0.00 40.91 4.08
2469 3960 8.642020 TGCATTTAAAATTTGTTTTTGTTGCAC 58.358 25.926 0.00 0.00 39.77 4.57
2470 3961 8.106956 GCATTTAAAATTTGTTTTTGTTGCACC 58.893 29.630 0.00 0.00 38.03 5.01
2471 3962 7.781763 TTTAAAATTTGTTTTTGTTGCACCG 57.218 28.000 0.00 0.00 38.03 4.94
2472 3963 5.363979 AAAATTTGTTTTTGTTGCACCGT 57.636 30.435 0.00 0.00 36.18 4.83
2473 3964 4.591998 AATTTGTTTTTGTTGCACCGTC 57.408 36.364 0.00 0.00 0.00 4.79
2474 3965 2.724977 TTGTTTTTGTTGCACCGTCA 57.275 40.000 0.00 0.00 0.00 4.35
2475 3966 2.949451 TGTTTTTGTTGCACCGTCAT 57.051 40.000 0.00 0.00 0.00 3.06
2476 3967 3.238108 TGTTTTTGTTGCACCGTCATT 57.762 38.095 0.00 0.00 0.00 2.57
2477 3968 3.589988 TGTTTTTGTTGCACCGTCATTT 58.410 36.364 0.00 0.00 0.00 2.32
2478 3969 4.744570 TGTTTTTGTTGCACCGTCATTTA 58.255 34.783 0.00 0.00 0.00 1.40
2479 3970 5.352284 TGTTTTTGTTGCACCGTCATTTAT 58.648 33.333 0.00 0.00 0.00 1.40
2480 3971 5.460419 TGTTTTTGTTGCACCGTCATTTATC 59.540 36.000 0.00 0.00 0.00 1.75
2481 3972 5.446143 TTTTGTTGCACCGTCATTTATCT 57.554 34.783 0.00 0.00 0.00 1.98
2529 4021 9.530633 AAATGCATTTAATTGTTTTTGTTGCAT 57.469 22.222 22.95 0.00 46.80 3.96
2570 4062 1.558741 AGTACACGCGTTTCACGAAA 58.441 45.000 10.22 0.00 46.05 3.46
2609 4101 9.203421 CTGTACAGTGATGTGTTTTATACTCAA 57.797 33.333 15.06 0.00 34.25 3.02
2626 4118 1.154073 AAAGAGCGCGGTCGTAGTC 60.154 57.895 30.16 8.51 38.14 2.59
2747 4239 1.755977 CGATAGTCCCCTCTTGCTCCT 60.756 57.143 0.00 0.00 0.00 3.69
2748 4240 1.967779 GATAGTCCCCTCTTGCTCCTC 59.032 57.143 0.00 0.00 0.00 3.71
2749 4241 0.032017 TAGTCCCCTCTTGCTCCTCC 60.032 60.000 0.00 0.00 0.00 4.30
2752 4244 3.080121 CCCTCTTGCTCCTCCGCT 61.080 66.667 0.00 0.00 0.00 5.52
2753 4245 2.186384 CCTCTTGCTCCTCCGCTG 59.814 66.667 0.00 0.00 0.00 5.18
2754 4246 2.354401 CCTCTTGCTCCTCCGCTGA 61.354 63.158 0.00 0.00 0.00 4.26
2755 4247 1.153667 CTCTTGCTCCTCCGCTGAC 60.154 63.158 0.00 0.00 0.00 3.51
2756 4248 1.603236 CTCTTGCTCCTCCGCTGACT 61.603 60.000 0.00 0.00 0.00 3.41
2757 4249 1.188219 TCTTGCTCCTCCGCTGACTT 61.188 55.000 0.00 0.00 0.00 3.01
2759 4251 0.320771 TTGCTCCTCCGCTGACTTTC 60.321 55.000 0.00 0.00 0.00 2.62
2761 4253 1.807573 CTCCTCCGCTGACTTTCGC 60.808 63.158 0.00 0.00 0.00 4.70
2762 4254 2.048222 CCTCCGCTGACTTTCGCA 60.048 61.111 0.00 0.00 0.00 5.10
2764 4256 1.424493 CCTCCGCTGACTTTCGCATC 61.424 60.000 0.00 0.00 0.00 3.91
2765 4257 1.746727 CTCCGCTGACTTTCGCATCG 61.747 60.000 0.00 0.00 0.00 3.84
2766 4258 2.697425 CGCTGACTTTCGCATCGG 59.303 61.111 0.00 0.00 0.00 4.18
2767 4259 2.401195 GCTGACTTTCGCATCGGC 59.599 61.111 0.00 0.00 39.89 5.54
2768 4260 3.093278 CTGACTTTCGCATCGGCC 58.907 61.111 0.00 0.00 36.38 6.13
2769 4261 1.448540 CTGACTTTCGCATCGGCCT 60.449 57.895 0.00 0.00 36.38 5.19
2770 4262 1.424493 CTGACTTTCGCATCGGCCTC 61.424 60.000 0.00 0.00 36.38 4.70
2771 4263 1.153549 GACTTTCGCATCGGCCTCT 60.154 57.895 0.00 0.00 36.38 3.69
2772 4264 1.148759 GACTTTCGCATCGGCCTCTC 61.149 60.000 0.00 0.00 36.38 3.20
2773 4265 2.202743 TTTCGCATCGGCCTCTCG 60.203 61.111 0.00 0.00 36.38 4.04
2774 4266 4.873129 TTCGCATCGGCCTCTCGC 62.873 66.667 0.00 0.00 36.38 5.03
2777 4269 3.910490 GCATCGGCCTCTCGCTCT 61.910 66.667 0.00 0.00 37.74 4.09
2778 4270 2.334653 CATCGGCCTCTCGCTCTC 59.665 66.667 0.00 0.00 37.74 3.20
2779 4271 2.909965 ATCGGCCTCTCGCTCTCC 60.910 66.667 0.00 0.00 37.74 3.71
2780 4272 3.429372 ATCGGCCTCTCGCTCTCCT 62.429 63.158 0.00 0.00 37.74 3.69
2781 4273 3.898509 CGGCCTCTCGCTCTCCTG 61.899 72.222 0.00 0.00 37.74 3.86
2782 4274 4.219999 GGCCTCTCGCTCTCCTGC 62.220 72.222 0.00 0.00 37.74 4.85
2783 4275 4.219999 GCCTCTCGCTCTCCTGCC 62.220 72.222 0.00 0.00 0.00 4.85
2784 4276 2.757508 CCTCTCGCTCTCCTGCCA 60.758 66.667 0.00 0.00 0.00 4.92
2785 4277 2.132996 CCTCTCGCTCTCCTGCCAT 61.133 63.158 0.00 0.00 0.00 4.40
2786 4278 1.067749 CTCTCGCTCTCCTGCCATG 59.932 63.158 0.00 0.00 0.00 3.66
2821 4313 3.880040 TGGACATGTACATGCCCAG 57.120 52.632 32.70 13.21 44.68 4.45
2827 4319 3.564027 GTACATGCCCAGCGCGAC 61.564 66.667 12.10 0.04 42.08 5.19
2859 4351 1.393539 CGGACGCACGAGATCAATTTT 59.606 47.619 0.00 0.00 35.47 1.82
2862 4354 3.125316 GGACGCACGAGATCAATTTTCTT 59.875 43.478 0.00 0.00 0.00 2.52
2868 4360 5.335191 GCACGAGATCAATTTTCTTGTCCTT 60.335 40.000 0.00 0.00 35.99 3.36
2941 4443 5.337554 TCGTTCGTGAGGAATAGTACAATG 58.662 41.667 0.00 0.00 36.92 2.82
2969 4471 5.569355 TCATAAGCTCCTCAAACCAATCAA 58.431 37.500 0.00 0.00 0.00 2.57
2973 4475 2.352127 GCTCCTCAAACCAATCAACAGC 60.352 50.000 0.00 0.00 0.00 4.40
2984 4486 5.776744 ACCAATCAACAGCAGAAGAAAATC 58.223 37.500 0.00 0.00 0.00 2.17
2988 4490 5.869753 TCAACAGCAGAAGAAAATCTAGC 57.130 39.130 0.00 0.00 0.00 3.42
3015 4517 0.937304 ACATCGTGCGCAACCATATC 59.063 50.000 14.00 0.00 0.00 1.63
3016 4518 0.936600 CATCGTGCGCAACCATATCA 59.063 50.000 14.00 0.00 0.00 2.15
3017 4519 1.330213 CATCGTGCGCAACCATATCAA 59.670 47.619 14.00 0.00 0.00 2.57
3075 4577 8.383175 ACCTCAGAGGATAAAAATTGTAGTTGA 58.617 33.333 24.45 0.00 37.67 3.18
3076 4578 8.669243 CCTCAGAGGATAAAAATTGTAGTTGAC 58.331 37.037 11.62 0.00 37.67 3.18
3077 4579 8.561738 TCAGAGGATAAAAATTGTAGTTGACC 57.438 34.615 0.00 0.00 0.00 4.02
3078 4580 8.383175 TCAGAGGATAAAAATTGTAGTTGACCT 58.617 33.333 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 4.522405 CGGAGACTATTGACATCTGGATCT 59.478 45.833 0.00 0.00 0.00 2.75
73 74 2.109425 AAACCATCTACGGTCAAGCC 57.891 50.000 0.00 0.00 38.76 4.35
129 130 0.251787 GGCTGTGGAATTTCAGGGGT 60.252 55.000 0.00 0.00 32.94 4.95
145 147 2.285969 AGTCATGCAGGAGGGGCT 60.286 61.111 0.00 0.00 0.00 5.19
252 254 2.433868 TCTACCGGAATATGCGCTTC 57.566 50.000 9.46 3.82 0.00 3.86
253 255 2.480845 GTTCTACCGGAATATGCGCTT 58.519 47.619 9.46 4.59 36.24 4.68
369 371 1.407258 CTTCGTGAGGAGGATCTGGAC 59.593 57.143 0.00 0.00 31.14 4.02
420 422 1.536073 CGGGCTCCTCTGAACTCACA 61.536 60.000 0.00 0.00 0.00 3.58
590 632 2.092882 CCGCCGTCGAGTTTTCCTC 61.093 63.158 0.00 0.00 38.10 3.71
666 710 0.040425 GCACGACTCGCCATGTTTTT 60.040 50.000 0.00 0.00 0.00 1.94
667 711 0.884704 AGCACGACTCGCCATGTTTT 60.885 50.000 0.00 0.00 0.00 2.43
668 712 1.301716 AGCACGACTCGCCATGTTT 60.302 52.632 0.00 0.00 0.00 2.83
669 713 2.029288 CAGCACGACTCGCCATGTT 61.029 57.895 0.00 0.00 0.00 2.71
670 714 2.433145 CAGCACGACTCGCCATGT 60.433 61.111 0.00 0.00 0.00 3.21
671 715 3.857854 GCAGCACGACTCGCCATG 61.858 66.667 0.00 0.00 0.00 3.66
672 716 3.596066 AAGCAGCACGACTCGCCAT 62.596 57.895 0.00 0.00 0.00 4.40
673 717 4.299547 AAGCAGCACGACTCGCCA 62.300 61.111 0.00 0.00 0.00 5.69
674 718 3.482783 GAAGCAGCACGACTCGCC 61.483 66.667 0.00 0.00 0.00 5.54
675 719 3.482783 GGAAGCAGCACGACTCGC 61.483 66.667 0.00 0.00 0.00 5.03
676 720 1.803519 GAGGAAGCAGCACGACTCG 60.804 63.158 0.00 0.00 0.00 4.18
677 721 1.803519 CGAGGAAGCAGCACGACTC 60.804 63.158 0.00 0.00 0.00 3.36
678 722 2.259818 CGAGGAAGCAGCACGACT 59.740 61.111 0.00 0.00 0.00 4.18
679 723 2.811317 CCGAGGAAGCAGCACGAC 60.811 66.667 0.00 0.00 0.00 4.34
680 724 4.742201 GCCGAGGAAGCAGCACGA 62.742 66.667 0.00 0.00 0.00 4.35
681 725 4.749310 AGCCGAGGAAGCAGCACG 62.749 66.667 0.00 0.00 0.00 5.34
682 726 2.817396 GAGCCGAGGAAGCAGCAC 60.817 66.667 0.00 0.00 0.00 4.40
683 727 4.441695 CGAGCCGAGGAAGCAGCA 62.442 66.667 0.00 0.00 0.00 4.41
684 728 4.135153 TCGAGCCGAGGAAGCAGC 62.135 66.667 0.00 0.00 0.00 5.25
685 729 2.202676 GTCGAGCCGAGGAAGCAG 60.203 66.667 0.00 0.00 36.23 4.24
822 880 0.034380 CGGTGGGAGACAGAGTAGGA 60.034 60.000 0.00 0.00 0.00 2.94
823 881 1.668101 GCGGTGGGAGACAGAGTAGG 61.668 65.000 0.00 0.00 0.00 3.18
860 1923 8.519526 GTTAATTGATTGTGTTGGGAGACAATA 58.480 33.333 0.00 0.00 46.26 1.90
884 1947 2.203153 ACTGGCAGCGGTTTCGTT 60.203 55.556 15.89 0.00 38.89 3.85
885 1948 2.665185 GACTGGCAGCGGTTTCGT 60.665 61.111 15.89 0.00 38.89 3.85
896 1959 2.158959 CGAACACGGATCGACTGGC 61.159 63.158 0.00 0.00 42.76 4.85
906 2148 5.086058 CCTGTAATTTGAATTCGAACACGG 58.914 41.667 10.38 14.57 0.00 4.94
909 2151 6.657117 TGATCCCTGTAATTTGAATTCGAACA 59.343 34.615 10.38 4.59 0.00 3.18
954 2196 7.681939 ACTCGTAGATCTGATTCCTTAGATC 57.318 40.000 5.18 0.00 46.11 2.75
991 2243 2.125106 GGCGGACATGGTCTGACC 60.125 66.667 19.96 19.96 40.84 4.02
1162 2453 3.196254 CAGAAAGGCTGGGTAAAATGCAT 59.804 43.478 0.00 0.00 41.07 3.96
1211 2517 1.576421 CCAAAGGCTGACGTGAAGC 59.424 57.895 10.67 10.67 40.06 3.86
1252 2558 0.324738 TCAGCTTCGGGATCTCTGGT 60.325 55.000 0.00 0.00 0.00 4.00
1444 2777 1.941294 CATGCTGCAAGACTGATCCTC 59.059 52.381 6.36 0.00 34.07 3.71
1762 3095 1.692749 GGGGAGGGCACAGACCATA 60.693 63.158 0.00 0.00 29.21 2.74
2030 3372 2.233922 ACTTTGTAGTACTGCAGCCGAT 59.766 45.455 15.27 0.00 31.21 4.18
2059 3401 0.400594 AGGAACGGCTTAGTGGCTTT 59.599 50.000 0.00 0.00 39.32 3.51
2085 3430 1.257055 ACATCCAAAATGCCACCGGG 61.257 55.000 6.32 0.00 37.18 5.73
2112 3459 5.240183 AGGAAGTGACTCATGACACAATTTG 59.760 40.000 16.30 0.00 40.37 2.32
2194 3619 7.604549 TCAGACGTCCACACATTATTACTAAA 58.395 34.615 13.01 0.00 0.00 1.85
2195 3620 7.160547 TCAGACGTCCACACATTATTACTAA 57.839 36.000 13.01 0.00 0.00 2.24
2196 3621 6.762702 TCAGACGTCCACACATTATTACTA 57.237 37.500 13.01 0.00 0.00 1.82
2197 3622 5.654603 TCAGACGTCCACACATTATTACT 57.345 39.130 13.01 0.00 0.00 2.24
2198 3623 6.903883 AATCAGACGTCCACACATTATTAC 57.096 37.500 13.01 0.00 0.00 1.89
2199 3624 6.876789 ACAAATCAGACGTCCACACATTATTA 59.123 34.615 13.01 0.00 0.00 0.98
2200 3625 5.705441 ACAAATCAGACGTCCACACATTATT 59.295 36.000 13.01 0.00 0.00 1.40
2211 3636 7.280205 AGGGAATACATTTACAAATCAGACGTC 59.720 37.037 7.70 7.70 0.00 4.34
2239 3667 4.923893 TGCAAACTCACAGATGAAAACAG 58.076 39.130 0.00 0.00 33.30 3.16
2296 3727 4.390297 GCAACTGAAGCTACTTACAGGAAG 59.610 45.833 0.00 0.00 41.37 3.46
2297 3728 4.202315 TGCAACTGAAGCTACTTACAGGAA 60.202 41.667 0.00 0.00 35.08 3.36
2298 3729 3.323691 TGCAACTGAAGCTACTTACAGGA 59.676 43.478 0.00 0.00 35.08 3.86
2442 3933 9.362539 TGCAACAAAAACAAATTTTAAATGCAT 57.637 22.222 0.00 0.00 42.13 3.96
2443 3934 8.642020 GTGCAACAAAAACAAATTTTAAATGCA 58.358 25.926 12.24 12.24 43.30 3.96
2444 3935 8.106956 GGTGCAACAAAAACAAATTTTAAATGC 58.893 29.630 0.00 0.00 39.20 3.56
2445 3936 8.309718 CGGTGCAACAAAAACAAATTTTAAATG 58.690 29.630 0.98 0.00 39.20 2.32
2446 3937 8.023706 ACGGTGCAACAAAAACAAATTTTAAAT 58.976 25.926 0.98 0.00 39.20 1.40
2447 3938 7.360361 ACGGTGCAACAAAAACAAATTTTAAA 58.640 26.923 0.98 0.00 39.20 1.52
2448 3939 6.899114 ACGGTGCAACAAAAACAAATTTTAA 58.101 28.000 0.98 0.00 39.20 1.52
2449 3940 6.147164 TGACGGTGCAACAAAAACAAATTTTA 59.853 30.769 0.98 0.00 39.20 1.52
2450 3941 5.049405 TGACGGTGCAACAAAAACAAATTTT 60.049 32.000 0.98 0.00 41.93 1.82
2451 3942 4.452455 TGACGGTGCAACAAAAACAAATTT 59.548 33.333 0.98 0.00 39.98 1.82
2452 3943 3.997021 TGACGGTGCAACAAAAACAAATT 59.003 34.783 0.98 0.00 39.98 1.82
2453 3944 3.589988 TGACGGTGCAACAAAAACAAAT 58.410 36.364 0.98 0.00 39.98 2.32
2454 3945 3.026630 TGACGGTGCAACAAAAACAAA 57.973 38.095 0.98 0.00 39.98 2.83
2455 3946 2.724977 TGACGGTGCAACAAAAACAA 57.275 40.000 0.98 0.00 39.98 2.83
2456 3947 2.949451 ATGACGGTGCAACAAAAACA 57.051 40.000 0.98 0.00 39.98 2.83
2457 3948 5.689961 AGATAAATGACGGTGCAACAAAAAC 59.310 36.000 0.98 0.00 39.98 2.43
2458 3949 5.837437 AGATAAATGACGGTGCAACAAAAA 58.163 33.333 0.98 0.00 39.98 1.94
2459 3950 5.446143 AGATAAATGACGGTGCAACAAAA 57.554 34.783 0.98 0.00 39.98 2.44
2460 3951 5.218885 CAAGATAAATGACGGTGCAACAAA 58.781 37.500 0.98 0.00 39.98 2.83
2461 3952 4.277174 ACAAGATAAATGACGGTGCAACAA 59.723 37.500 0.98 0.00 39.98 2.83
2462 3953 3.818210 ACAAGATAAATGACGGTGCAACA 59.182 39.130 0.98 0.00 39.98 3.33
2463 3954 4.083537 TGACAAGATAAATGACGGTGCAAC 60.084 41.667 0.00 0.00 0.00 4.17
2464 3955 4.068599 TGACAAGATAAATGACGGTGCAA 58.931 39.130 0.00 0.00 0.00 4.08
2465 3956 3.435327 GTGACAAGATAAATGACGGTGCA 59.565 43.478 0.00 0.00 0.00 4.57
2466 3957 3.181510 GGTGACAAGATAAATGACGGTGC 60.182 47.826 0.00 0.00 0.00 5.01
2467 3958 4.093408 CAGGTGACAAGATAAATGACGGTG 59.907 45.833 0.00 0.00 0.00 4.94
2468 3959 4.020573 TCAGGTGACAAGATAAATGACGGT 60.021 41.667 0.00 0.00 0.00 4.83
2469 3960 4.330074 GTCAGGTGACAAGATAAATGACGG 59.670 45.833 5.21 0.00 44.18 4.79
2470 3961 4.330074 GGTCAGGTGACAAGATAAATGACG 59.670 45.833 12.09 0.00 46.47 4.35
2471 3962 4.636206 GGGTCAGGTGACAAGATAAATGAC 59.364 45.833 12.09 0.00 46.47 3.06
2472 3963 4.536090 AGGGTCAGGTGACAAGATAAATGA 59.464 41.667 12.09 0.00 46.47 2.57
2473 3964 4.637534 CAGGGTCAGGTGACAAGATAAATG 59.362 45.833 12.09 0.00 46.47 2.32
2474 3965 4.324563 CCAGGGTCAGGTGACAAGATAAAT 60.325 45.833 12.09 0.00 46.47 1.40
2475 3966 3.009033 CCAGGGTCAGGTGACAAGATAAA 59.991 47.826 12.09 0.00 46.47 1.40
2476 3967 2.571653 CCAGGGTCAGGTGACAAGATAA 59.428 50.000 12.09 0.00 46.47 1.75
2477 3968 2.187958 CCAGGGTCAGGTGACAAGATA 58.812 52.381 12.09 0.00 46.47 1.98
2478 3969 0.987294 CCAGGGTCAGGTGACAAGAT 59.013 55.000 12.09 0.00 46.47 2.40
2479 3970 1.768684 GCCAGGGTCAGGTGACAAGA 61.769 60.000 12.09 0.00 46.47 3.02
2480 3971 1.302832 GCCAGGGTCAGGTGACAAG 60.303 63.158 12.09 1.37 46.47 3.16
2481 3972 1.426251 ATGCCAGGGTCAGGTGACAA 61.426 55.000 12.09 0.00 46.47 3.18
2570 4062 4.517832 TCACTGTACAGTATTGTCACGACT 59.482 41.667 27.48 0.00 40.20 4.18
2586 4078 9.990360 TCTTTGAGTATAAAACACATCACTGTA 57.010 29.630 0.00 0.00 33.14 2.74
2609 4101 2.484203 GACTACGACCGCGCTCTT 59.516 61.111 5.56 0.00 42.48 2.85
2676 4168 3.649986 GCTGTGCCGTGACCACAC 61.650 66.667 0.85 0.00 38.21 3.82
2677 4169 4.927782 GGCTGTGCCGTGACCACA 62.928 66.667 0.85 0.00 39.62 4.17
2747 4239 1.805539 CGATGCGAAAGTCAGCGGA 60.806 57.895 0.00 0.00 41.04 5.54
2748 4240 2.697425 CGATGCGAAAGTCAGCGG 59.303 61.111 0.00 0.00 41.04 5.52
2749 4241 2.697425 CCGATGCGAAAGTCAGCG 59.303 61.111 0.00 0.00 43.08 5.18
2752 4244 1.447838 GAGGCCGATGCGAAAGTCA 60.448 57.895 0.00 0.00 38.85 3.41
2753 4245 1.148759 GAGAGGCCGATGCGAAAGTC 61.149 60.000 0.00 0.00 38.85 3.01
2754 4246 1.153549 GAGAGGCCGATGCGAAAGT 60.154 57.895 0.00 0.00 38.85 2.66
2755 4247 2.233654 CGAGAGGCCGATGCGAAAG 61.234 63.158 0.00 0.00 38.85 2.62
2756 4248 2.202743 CGAGAGGCCGATGCGAAA 60.203 61.111 0.00 0.00 38.85 3.46
2757 4249 4.873129 GCGAGAGGCCGATGCGAA 62.873 66.667 13.15 0.00 38.85 4.70
2761 4253 2.334653 GAGAGCGAGAGGCCGATG 59.665 66.667 0.00 0.00 45.17 3.84
2762 4254 2.909965 GGAGAGCGAGAGGCCGAT 60.910 66.667 0.00 0.00 45.17 4.18
2764 4256 3.898509 CAGGAGAGCGAGAGGCCG 61.899 72.222 0.00 0.00 45.17 6.13
2765 4257 4.219999 GCAGGAGAGCGAGAGGCC 62.220 72.222 0.00 0.00 45.17 5.19
2766 4258 4.219999 GGCAGGAGAGCGAGAGGC 62.220 72.222 0.00 0.00 44.05 4.70
2767 4259 2.132996 ATGGCAGGAGAGCGAGAGG 61.133 63.158 0.00 0.00 34.64 3.69
2768 4260 1.067749 CATGGCAGGAGAGCGAGAG 59.932 63.158 0.00 0.00 34.64 3.20
2769 4261 2.429767 CCATGGCAGGAGAGCGAGA 61.430 63.158 0.00 0.00 34.64 4.04
2770 4262 2.108566 CCATGGCAGGAGAGCGAG 59.891 66.667 0.00 0.00 34.64 5.03
2771 4263 2.364186 TCCATGGCAGGAGAGCGA 60.364 61.111 6.96 0.00 32.77 4.93
2772 4264 2.202987 GTCCATGGCAGGAGAGCG 60.203 66.667 6.96 0.00 38.64 5.03
2773 4265 1.153208 CAGTCCATGGCAGGAGAGC 60.153 63.158 6.96 0.00 38.64 4.09
2774 4266 1.525923 CCAGTCCATGGCAGGAGAG 59.474 63.158 6.96 0.00 43.83 3.20
2775 4267 3.731547 CCAGTCCATGGCAGGAGA 58.268 61.111 6.96 0.00 43.83 3.71
2783 4275 2.040544 GGTTGCGTCCCAGTCCATG 61.041 63.158 0.00 0.00 0.00 3.66
2784 4276 2.351276 GGTTGCGTCCCAGTCCAT 59.649 61.111 0.00 0.00 0.00 3.41
2785 4277 4.308458 CGGTTGCGTCCCAGTCCA 62.308 66.667 0.00 0.00 0.00 4.02
2786 4278 4.309950 ACGGTTGCGTCCCAGTCC 62.310 66.667 0.00 0.00 0.00 3.85
2809 4301 4.075854 TCGCGCTGGGCATGTACA 62.076 61.111 17.13 0.00 43.84 2.90
2910 4412 1.332686 TCCTCACGAACGATGTATCCG 59.667 52.381 0.14 0.00 0.00 4.18
2941 4443 4.943705 TGGTTTGAGGAGCTTATGATTGAC 59.056 41.667 0.00 0.00 0.00 3.18
2951 4453 3.152341 CTGTTGATTGGTTTGAGGAGCT 58.848 45.455 0.00 0.00 0.00 4.09
2969 4471 4.292186 TGGCTAGATTTTCTTCTGCTGT 57.708 40.909 0.00 0.00 0.00 4.40
2973 4475 6.655003 TGTTAGGTTGGCTAGATTTTCTTCTG 59.345 38.462 0.00 0.00 0.00 3.02
2984 4486 1.933853 GCACGATGTTAGGTTGGCTAG 59.066 52.381 0.00 0.00 0.00 3.42
2988 4490 1.295357 TGCGCACGATGTTAGGTTGG 61.295 55.000 5.66 0.00 0.00 3.77
3015 4517 6.817765 TTGCTCTTTGTAATAGGGAAGTTG 57.182 37.500 0.00 0.00 0.00 3.16
3047 4549 7.918076 ACTACAATTTTTATCCTCTGAGGTCA 58.082 34.615 22.50 9.46 36.53 4.02
3048 4550 8.669243 CAACTACAATTTTTATCCTCTGAGGTC 58.331 37.037 22.50 0.00 36.53 3.85
3075 4577 4.883021 TGATCAACCCTAGACTAGAGGT 57.117 45.455 11.27 12.81 32.85 3.85
3076 4578 8.429237 AATTATGATCAACCCTAGACTAGAGG 57.571 38.462 11.27 12.21 0.00 3.69


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

AutoCloner maintained by Alex Coulton.