Multiple sequence alignment - TraesCS7B01G214000

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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 TraesCS7B01G214000 chr7B 100.000 3813 0 0 1 3813 392816759 392812947 0.000000e+00 7042
1 TraesCS7B01G214000 chr7B 93.004 972 66 2 2647 3616 608922037 608921066 0.000000e+00 1417
2 TraesCS7B01G214000 chr7B 94.472 199 11 0 3615 3813 379419071 379419269 1.330000e-79 307
3 TraesCS7B01G214000 chr7B 85.350 157 19 4 2481 2635 25675275 25675429 3.940000e-35 159
4 TraesCS7B01G214000 chr7D 95.597 2657 95 14 1 2647 393108500 393105856 0.000000e+00 4239
5 TraesCS7B01G214000 chr7D 89.949 975 96 2 2648 3621 611640922 611639949 0.000000e+00 1256
6 TraesCS7B01G214000 chr7D 93.500 200 13 0 3614 3813 242795668 242795867 8.010000e-77 298
7 TraesCS7B01G214000 chr7A 94.976 2667 92 12 1 2647 445626608 445623964 0.000000e+00 4145
8 TraesCS7B01G214000 chr2B 97.833 969 21 0 2648 3616 79700736 79699768 0.000000e+00 1674
9 TraesCS7B01G214000 chr2B 80.494 405 62 8 1995 2383 793531041 793530638 1.040000e-75 294
10 TraesCS7B01G214000 chr2B 89.011 182 20 0 2466 2647 793525666 793525485 3.830000e-55 226
11 TraesCS7B01G214000 chr3B 92.213 976 75 1 2647 3621 829502793 829501818 0.000000e+00 1380
12 TraesCS7B01G214000 chr3B 92.622 881 64 1 2742 3621 43598698 43599578 0.000000e+00 1266
13 TraesCS7B01G214000 chr3B 93.532 201 12 1 3614 3813 574269140 574269340 8.010000e-77 298
14 TraesCS7B01G214000 chr3D 88.320 976 109 5 2648 3620 603738823 603737850 0.000000e+00 1166
15 TraesCS7B01G214000 chr6A 88.103 975 115 1 2648 3621 163145897 163146871 0.000000e+00 1157
16 TraesCS7B01G214000 chr1A 87.897 975 116 2 2648 3621 533439658 533440631 0.000000e+00 1146
17 TraesCS7B01G214000 chr3A 88.889 873 96 1 2741 3613 99391475 99392346 0.000000e+00 1074
18 TraesCS7B01G214000 chr4B 74.421 1685 369 50 997 2647 115528711 115530367 0.000000e+00 667
19 TraesCS7B01G214000 chr4D 81.135 652 98 21 2016 2647 81908551 81909197 2.050000e-137 499
20 TraesCS7B01G214000 chr4A 81.773 598 84 18 2072 2647 491688911 491689505 9.580000e-131 477
21 TraesCS7B01G214000 chr4A 93.532 201 13 0 3613 3813 675655813 675656013 2.230000e-77 300
22 TraesCS7B01G214000 chr2D 73.740 1409 279 54 1028 2383 643315485 643316855 5.770000e-128 468
23 TraesCS7B01G214000 chr2D 93.500 200 12 1 3614 3813 88144318 88144120 2.880000e-76 296
24 TraesCS7B01G214000 chr2D 90.110 182 18 0 2466 2647 643322035 643322216 1.770000e-58 237
25 TraesCS7B01G214000 chr2A 81.436 404 58 9 1995 2383 768215159 768215560 7.950000e-82 315
26 TraesCS7B01G214000 chr5D 94.472 199 11 0 3615 3813 550651790 550651988 1.330000e-79 307
27 TraesCS7B01G214000 chr5D 93.500 200 13 0 3614 3813 395719812 395719613 8.010000e-77 298
28 TraesCS7B01G214000 chr6B 94.000 200 12 0 3614 3813 9197125 9197324 1.720000e-78 303
29 TraesCS7B01G214000 chr1B 93.500 200 13 0 3614 3813 616813504 616813305 8.010000e-77 298
30 TraesCS7B01G214000 chrUn 81.306 337 39 9 2079 2393 31725184 31724850 6.320000e-63 252
31 TraesCS7B01G214000 chrUn 88.525 183 21 0 2465 2647 266534759 266534577 4.960000e-54 222
32 TraesCS7B01G214000 chrUn 86.813 182 24 0 2466 2647 31724338 31724157 1.800000e-48 204


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 TraesCS7B01G214000 chr7B 392812947 392816759 3812 True 7042 7042 100.0000 1 3813 1 chr7B.!!$R1 3812
1 TraesCS7B01G214000 chr7B 608921066 608922037 971 True 1417 1417 93.0040 2647 3616 1 chr7B.!!$R2 969
2 TraesCS7B01G214000 chr7D 393105856 393108500 2644 True 4239 4239 95.5970 1 2647 1 chr7D.!!$R1 2646
3 TraesCS7B01G214000 chr7D 611639949 611640922 973 True 1256 1256 89.9490 2648 3621 1 chr7D.!!$R2 973
4 TraesCS7B01G214000 chr7A 445623964 445626608 2644 True 4145 4145 94.9760 1 2647 1 chr7A.!!$R1 2646
5 TraesCS7B01G214000 chr2B 79699768 79700736 968 True 1674 1674 97.8330 2648 3616 1 chr2B.!!$R1 968
6 TraesCS7B01G214000 chr3B 829501818 829502793 975 True 1380 1380 92.2130 2647 3621 1 chr3B.!!$R1 974
7 TraesCS7B01G214000 chr3B 43598698 43599578 880 False 1266 1266 92.6220 2742 3621 1 chr3B.!!$F1 879
8 TraesCS7B01G214000 chr3D 603737850 603738823 973 True 1166 1166 88.3200 2648 3620 1 chr3D.!!$R1 972
9 TraesCS7B01G214000 chr6A 163145897 163146871 974 False 1157 1157 88.1030 2648 3621 1 chr6A.!!$F1 973
10 TraesCS7B01G214000 chr1A 533439658 533440631 973 False 1146 1146 87.8970 2648 3621 1 chr1A.!!$F1 973
11 TraesCS7B01G214000 chr3A 99391475 99392346 871 False 1074 1074 88.8890 2741 3613 1 chr3A.!!$F1 872
12 TraesCS7B01G214000 chr4B 115528711 115530367 1656 False 667 667 74.4210 997 2647 1 chr4B.!!$F1 1650
13 TraesCS7B01G214000 chr4D 81908551 81909197 646 False 499 499 81.1350 2016 2647 1 chr4D.!!$F1 631
14 TraesCS7B01G214000 chr4A 491688911 491689505 594 False 477 477 81.7730 2072 2647 1 chr4A.!!$F1 575
15 TraesCS7B01G214000 chr2D 643315485 643316855 1370 False 468 468 73.7400 1028 2383 1 chr2D.!!$F1 1355
16 TraesCS7B01G214000 chrUn 31724157 31725184 1027 True 228 252 84.0595 2079 2647 2 chrUn.!!$R2 568

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
711 717 0.325933 TCTCATGTTGACAGGCCAGG 59.674 55.0 5.01 0.0 0.0 4.45 F
1830 1867 0.037697 CGGCAACAGTAGTAGCACCA 60.038 55.0 0.00 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1865 1924 0.619255 TCCTGCTATGACCCCGGAAA 60.619 55.0 0.73 0.0 0.00 3.13 R
3705 4247 0.171903 CGTACCACCCGAGTGTTAGG 59.828 60.0 0.00 0.0 42.88 2.69 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
51 52 4.083696 CCGCAGTTCCTTAACGTAATGTTT 60.084 41.667 0.00 0.00 42.09 2.83
57 58 9.719279 CAGTTCCTTAACGTAATGTTTGTTTTA 57.281 29.630 0.00 0.00 42.09 1.52
92 93 7.867921 TGAATCTTAACACTGGGTGGTATTAT 58.132 34.615 2.75 0.00 35.54 1.28
128 129 2.169561 TCCAGCCTTGCGTGTATATTGA 59.830 45.455 0.00 0.00 0.00 2.57
173 174 6.778834 AATTCATCTTATGTGTGCCATTCA 57.221 33.333 0.00 0.00 34.86 2.57
210 211 4.082245 CGCCTACAAATTGAAAAGGTCCAT 60.082 41.667 0.00 0.00 0.00 3.41
224 225 4.927267 AGGTCCATGTCAAAATCCTACA 57.073 40.909 0.00 0.00 0.00 2.74
444 450 7.405292 TCAGGATGGATCTTGTTTATCTGTTT 58.595 34.615 0.00 0.00 35.61 2.83
508 514 2.116827 TGTTTGGTGACTCGGTGTTT 57.883 45.000 0.00 0.00 0.00 2.83
533 539 4.322273 GGTGCGTTCTTTAACTAGTAGGGT 60.322 45.833 0.00 0.00 33.15 4.34
540 546 7.448420 GTTCTTTAACTAGTAGGGTTTCCTGT 58.552 38.462 0.00 0.00 36.99 4.00
558 564 3.305608 CCTGTTGGCTGAAATGTCCTTTC 60.306 47.826 0.00 0.00 43.05 2.62
627 633 7.780008 TCGTTCTTCATGAAGACAAAAGTTA 57.220 32.000 32.80 16.20 46.13 2.24
711 717 0.325933 TCTCATGTTGACAGGCCAGG 59.674 55.000 5.01 0.00 0.00 4.45
713 719 0.478072 TCATGTTGACAGGCCAGGTT 59.522 50.000 5.01 0.00 0.00 3.50
714 720 1.702401 TCATGTTGACAGGCCAGGTTA 59.298 47.619 5.01 0.00 0.00 2.85
734 740 3.206211 TTTTTCTGCCGGCTTGCCG 62.206 57.895 29.70 25.17 0.00 5.69
788 794 3.568538 GCAGACTGCAACAGGTTTATTG 58.431 45.455 22.62 0.00 44.26 1.90
840 846 8.044908 GTCCTACATAATTACCTGTTCCTTTGA 58.955 37.037 0.00 0.00 0.00 2.69
991 997 0.965439 TGCCATTTGCCAACTACCAC 59.035 50.000 0.00 0.00 40.16 4.16
1065 1084 1.644509 TCTCCTTCACTTGCTGCCTA 58.355 50.000 0.00 0.00 0.00 3.93
1410 1432 1.991121 ACTACAACCTCGGTCTCACA 58.009 50.000 0.00 0.00 0.00 3.58
1583 1605 1.321474 CTGCCAAACTTCAGCCTCAA 58.679 50.000 0.00 0.00 0.00 3.02
1796 1833 4.500375 GCTTTCTTGGCACTTCAACTCATT 60.500 41.667 0.00 0.00 0.00 2.57
1830 1867 0.037697 CGGCAACAGTAGTAGCACCA 60.038 55.000 0.00 0.00 0.00 4.17
1837 1874 2.029623 CAGTAGTAGCACCACCGGTAT 58.970 52.381 6.87 0.00 32.11 2.73
1865 1924 0.966370 CCCTCCTCGAGAACTTCCGT 60.966 60.000 15.71 0.00 0.00 4.69
1993 2055 2.103263 GAGGCAAAGGACGAGGATATGT 59.897 50.000 0.00 0.00 0.00 2.29
2028 2099 2.025887 GGTGGTCATGGAGATGGAGTTT 60.026 50.000 0.00 0.00 0.00 2.66
2238 2333 3.489908 CGTCGGAGATCAATGTCATCAGT 60.490 47.826 0.00 0.00 40.67 3.41
2301 2396 1.204704 CACAACCACGATGAGCTCCTA 59.795 52.381 12.15 0.00 0.00 2.94
2666 3205 4.758692 CTACGGGATCGCAGCAAT 57.241 55.556 10.70 0.00 40.63 3.56
2744 3283 3.513515 GGAAGAAGAAGCAGAGAGGAAGA 59.486 47.826 0.00 0.00 0.00 2.87
2753 3292 7.401246 AGAAGCAGAGAGGAAGAATTGTATTT 58.599 34.615 0.00 0.00 0.00 1.40
2800 3341 1.132849 TCTCTTTCTCCCCTCCACACA 60.133 52.381 0.00 0.00 0.00 3.72
3034 3575 1.487452 TTCAGTTGCTGTCGCGTGTC 61.487 55.000 5.77 0.00 39.65 3.67
3035 3576 2.661866 AGTTGCTGTCGCGTGTCC 60.662 61.111 5.77 0.00 39.65 4.02
3122 3664 0.805322 CATCCAGCGTCTCTGTCTGC 60.805 60.000 0.00 0.00 41.25 4.26
3123 3665 2.276863 ATCCAGCGTCTCTGTCTGCG 62.277 60.000 0.00 0.00 41.25 5.18
3417 3959 0.832135 TGCTCGGAGGAGGTGTTCTT 60.832 55.000 7.20 0.00 40.80 2.52
3545 4087 8.092068 CCATATAATACTTGGAACGGTGTATGA 58.908 37.037 0.00 0.00 31.94 2.15
3613 4155 4.593634 AGGTAGCCAGTATACCCATTTCTC 59.406 45.833 0.00 0.00 43.20 2.87
3616 4158 2.767505 CCAGTATACCCATTTCTCGGC 58.232 52.381 0.00 0.00 0.00 5.54
3621 4163 4.489771 CCCATTTCTCGGCGGCCT 62.490 66.667 18.34 0.00 0.00 5.19
3622 4164 2.438434 CCATTTCTCGGCGGCCTT 60.438 61.111 18.34 0.00 0.00 4.35
3623 4165 2.472909 CCATTTCTCGGCGGCCTTC 61.473 63.158 18.34 0.00 0.00 3.46
3624 4166 2.511600 ATTTCTCGGCGGCCTTCG 60.512 61.111 18.34 4.51 42.76 3.79
3625 4167 4.752879 TTTCTCGGCGGCCTTCGG 62.753 66.667 18.34 0.81 39.69 4.30
3660 4202 3.083997 GTCCTCCTGCCCCGTCAT 61.084 66.667 0.00 0.00 0.00 3.06
3661 4203 2.764128 TCCTCCTGCCCCGTCATC 60.764 66.667 0.00 0.00 0.00 2.92
3662 4204 2.765807 CCTCCTGCCCCGTCATCT 60.766 66.667 0.00 0.00 0.00 2.90
3663 4205 2.503061 CTCCTGCCCCGTCATCTG 59.497 66.667 0.00 0.00 0.00 2.90
3664 4206 3.083349 TCCTGCCCCGTCATCTGG 61.083 66.667 0.00 0.00 0.00 3.86
3665 4207 4.864334 CCTGCCCCGTCATCTGGC 62.864 72.222 0.00 0.00 45.56 4.85
3668 4210 2.825836 GCCCCGTCATCTGGCAAG 60.826 66.667 0.00 0.00 44.70 4.01
3669 4211 2.825836 CCCCGTCATCTGGCAAGC 60.826 66.667 0.00 0.00 0.00 4.01
3670 4212 2.825836 CCCGTCATCTGGCAAGCC 60.826 66.667 3.61 3.61 0.00 4.35
3671 4213 2.825836 CCGTCATCTGGCAAGCCC 60.826 66.667 8.89 0.00 34.56 5.19
3672 4214 3.197790 CGTCATCTGGCAAGCCCG 61.198 66.667 8.89 1.88 35.87 6.13
3673 4215 3.512516 GTCATCTGGCAAGCCCGC 61.513 66.667 8.89 0.00 35.87 6.13
3691 4233 4.530857 CCCGTCCCCTGCATCGAC 62.531 72.222 0.00 0.00 0.00 4.20
3692 4234 4.530857 CCGTCCCCTGCATCGACC 62.531 72.222 0.00 0.00 0.00 4.79
3693 4235 4.530857 CGTCCCCTGCATCGACCC 62.531 72.222 0.00 0.00 0.00 4.46
3694 4236 3.083997 GTCCCCTGCATCGACCCT 61.084 66.667 0.00 0.00 0.00 4.34
3695 4237 1.760875 GTCCCCTGCATCGACCCTA 60.761 63.158 0.00 0.00 0.00 3.53
3696 4238 1.457643 TCCCCTGCATCGACCCTAG 60.458 63.158 0.00 0.00 0.00 3.02
3697 4239 2.511452 CCCCTGCATCGACCCTAGG 61.511 68.421 0.06 0.06 0.00 3.02
3698 4240 1.762460 CCCTGCATCGACCCTAGGT 60.762 63.158 8.29 0.00 39.44 3.08
3699 4241 1.443407 CCTGCATCGACCCTAGGTG 59.557 63.158 8.29 0.00 35.25 4.00
3700 4242 1.443407 CTGCATCGACCCTAGGTGG 59.557 63.158 8.29 0.00 35.25 4.61
3709 4251 2.375173 CCTAGGTGGGGGCCCTAA 59.625 66.667 24.38 8.68 34.22 2.69
3710 4252 2.076803 CCTAGGTGGGGGCCCTAAC 61.077 68.421 24.38 21.28 34.22 2.34
3711 4253 1.307517 CTAGGTGGGGGCCCTAACA 60.308 63.158 27.30 16.01 34.22 2.41
3712 4254 1.617233 TAGGTGGGGGCCCTAACAC 60.617 63.158 27.30 26.46 36.94 3.32
3713 4255 2.127685 TAGGTGGGGGCCCTAACACT 62.128 60.000 30.15 18.85 36.94 3.55
3714 4256 2.675371 GTGGGGGCCCTAACACTC 59.325 66.667 26.86 3.83 36.94 3.51
3715 4257 3.006728 TGGGGGCCCTAACACTCG 61.007 66.667 24.38 0.00 36.94 4.18
3716 4258 3.793888 GGGGGCCCTAACACTCGG 61.794 72.222 24.38 0.00 0.00 4.63
3717 4259 3.793888 GGGGCCCTAACACTCGGG 61.794 72.222 24.38 0.00 43.60 5.14
3718 4260 3.007323 GGGCCCTAACACTCGGGT 61.007 66.667 17.04 0.00 42.67 5.28
3720 4262 2.267961 GCCCTAACACTCGGGTGG 59.732 66.667 21.67 1.69 46.85 4.61
3721 4263 2.590114 GCCCTAACACTCGGGTGGT 61.590 63.158 21.67 17.43 46.85 4.16
3722 4264 1.259840 GCCCTAACACTCGGGTGGTA 61.260 60.000 21.67 17.67 46.85 3.25
3723 4265 0.533951 CCCTAACACTCGGGTGGTAC 59.466 60.000 21.67 0.00 46.85 3.34
3724 4266 0.171903 CCTAACACTCGGGTGGTACG 59.828 60.000 21.67 7.81 46.85 3.67
3725 4267 0.457337 CTAACACTCGGGTGGTACGC 60.457 60.000 21.67 0.00 46.85 4.42
3736 4278 1.520192 TGGTACGCCAGCTATGTGG 59.480 57.895 0.00 0.00 40.46 4.17
3737 4279 1.261938 TGGTACGCCAGCTATGTGGT 61.262 55.000 0.00 0.00 40.46 4.16
3738 4280 0.529992 GGTACGCCAGCTATGTGGTC 60.530 60.000 0.00 0.00 40.09 4.02
3739 4281 0.870307 GTACGCCAGCTATGTGGTCG 60.870 60.000 0.00 0.00 40.09 4.79
3740 4282 1.317431 TACGCCAGCTATGTGGTCGT 61.317 55.000 13.56 13.56 45.74 4.34
3741 4283 2.167219 CGCCAGCTATGTGGTCGTG 61.167 63.158 0.00 0.00 40.09 4.35
3742 4284 1.218047 GCCAGCTATGTGGTCGTGA 59.782 57.895 0.00 0.00 40.09 4.35
3743 4285 0.391130 GCCAGCTATGTGGTCGTGAA 60.391 55.000 0.00 0.00 40.09 3.18
3744 4286 1.359848 CCAGCTATGTGGTCGTGAAC 58.640 55.000 0.00 0.00 32.32 3.18
3745 4287 0.992072 CAGCTATGTGGTCGTGAACG 59.008 55.000 0.00 0.00 41.45 3.95
3746 4288 0.736325 AGCTATGTGGTCGTGAACGC 60.736 55.000 0.00 0.00 39.60 4.84
3747 4289 1.693083 GCTATGTGGTCGTGAACGCC 61.693 60.000 0.00 3.87 39.60 5.68
3748 4290 0.389296 CTATGTGGTCGTGAACGCCA 60.389 55.000 12.78 12.78 40.97 5.69
3749 4291 0.248012 TATGTGGTCGTGAACGCCAT 59.752 50.000 17.61 10.49 43.39 4.40
3750 4292 1.298157 ATGTGGTCGTGAACGCCATG 61.298 55.000 17.61 0.00 43.39 3.66
3751 4293 1.959226 GTGGTCGTGAACGCCATGT 60.959 57.895 17.61 0.00 43.39 3.21
3752 4294 1.666553 TGGTCGTGAACGCCATGTC 60.667 57.895 12.78 0.00 39.37 3.06
3753 4295 2.726691 GGTCGTGAACGCCATGTCG 61.727 63.158 0.00 0.00 39.60 4.35
3754 4296 3.109547 TCGTGAACGCCATGTCGC 61.110 61.111 0.00 0.00 39.60 5.19
3755 4297 4.147322 CGTGAACGCCATGTCGCC 62.147 66.667 0.00 0.00 0.00 5.54
3756 4298 2.742372 GTGAACGCCATGTCGCCT 60.742 61.111 0.00 0.00 0.00 5.52
3757 4299 2.434185 TGAACGCCATGTCGCCTC 60.434 61.111 0.00 0.00 0.00 4.70
3758 4300 3.195698 GAACGCCATGTCGCCTCC 61.196 66.667 0.00 0.00 0.00 4.30
3759 4301 3.950794 GAACGCCATGTCGCCTCCA 62.951 63.158 0.00 0.00 0.00 3.86
3760 4302 3.545124 AACGCCATGTCGCCTCCAA 62.545 57.895 0.00 0.00 0.00 3.53
3761 4303 3.197790 CGCCATGTCGCCTCCAAG 61.198 66.667 0.00 0.00 0.00 3.61
3762 4304 2.045926 GCCATGTCGCCTCCAAGT 60.046 61.111 0.00 0.00 0.00 3.16
3763 4305 2.401766 GCCATGTCGCCTCCAAGTG 61.402 63.158 0.00 0.00 0.00 3.16
3764 4306 1.003355 CCATGTCGCCTCCAAGTGT 60.003 57.895 0.00 0.00 0.00 3.55
3765 4307 1.021390 CCATGTCGCCTCCAAGTGTC 61.021 60.000 0.00 0.00 0.00 3.67
3766 4308 0.320683 CATGTCGCCTCCAAGTGTCA 60.321 55.000 0.00 0.00 0.00 3.58
3767 4309 0.320771 ATGTCGCCTCCAAGTGTCAC 60.321 55.000 0.00 0.00 0.00 3.67
3768 4310 1.668151 GTCGCCTCCAAGTGTCACC 60.668 63.158 0.00 0.00 0.00 4.02
3769 4311 2.738521 CGCCTCCAAGTGTCACCG 60.739 66.667 0.00 0.00 0.00 4.94
3770 4312 3.050275 GCCTCCAAGTGTCACCGC 61.050 66.667 0.00 0.00 0.00 5.68
3771 4313 2.358737 CCTCCAAGTGTCACCGCC 60.359 66.667 0.00 0.00 0.00 6.13
3772 4314 2.738521 CTCCAAGTGTCACCGCCG 60.739 66.667 0.00 0.00 0.00 6.46
3773 4315 4.980805 TCCAAGTGTCACCGCCGC 62.981 66.667 0.00 0.00 0.00 6.53
3774 4316 4.988598 CCAAGTGTCACCGCCGCT 62.989 66.667 0.00 0.00 0.00 5.52
3775 4317 2.972505 CAAGTGTCACCGCCGCTT 60.973 61.111 0.00 0.00 33.11 4.68
3776 4318 2.203153 AAGTGTCACCGCCGCTTT 60.203 55.556 0.00 0.00 28.61 3.51
3777 4319 2.251642 AAGTGTCACCGCCGCTTTC 61.252 57.895 0.00 0.00 28.61 2.62
3778 4320 2.933878 AAGTGTCACCGCCGCTTTCA 62.934 55.000 0.00 0.00 28.61 2.69
3779 4321 2.664851 TGTCACCGCCGCTTTCAG 60.665 61.111 0.00 0.00 0.00 3.02
3780 4322 2.357034 GTCACCGCCGCTTTCAGA 60.357 61.111 0.00 0.00 0.00 3.27
3781 4323 2.048222 TCACCGCCGCTTTCAGAG 60.048 61.111 0.00 0.00 0.00 3.35
3782 4324 3.121030 CACCGCCGCTTTCAGAGG 61.121 66.667 0.00 0.00 38.30 3.69
3783 4325 3.311110 ACCGCCGCTTTCAGAGGA 61.311 61.111 0.00 0.00 37.36 3.71
3784 4326 2.510238 CCGCCGCTTTCAGAGGAG 60.510 66.667 0.00 0.00 37.36 3.69
3785 4327 3.191539 CGCCGCTTTCAGAGGAGC 61.192 66.667 0.00 0.00 37.36 4.70
3786 4328 2.267324 GCCGCTTTCAGAGGAGCT 59.733 61.111 0.00 0.00 37.36 4.09
3787 4329 1.376553 GCCGCTTTCAGAGGAGCTT 60.377 57.895 0.00 0.00 37.36 3.74
3788 4330 1.365368 GCCGCTTTCAGAGGAGCTTC 61.365 60.000 0.00 0.00 37.36 3.86
3789 4331 0.742635 CCGCTTTCAGAGGAGCTTCC 60.743 60.000 0.00 0.00 37.36 3.46
3798 4340 1.222936 AGGAGCTTCCTTGGCATCG 59.777 57.895 0.00 0.00 46.91 3.84
3799 4341 1.821332 GGAGCTTCCTTGGCATCGG 60.821 63.158 0.00 0.00 32.53 4.18
3800 4342 2.439156 AGCTTCCTTGGCATCGGC 60.439 61.111 0.00 0.00 40.13 5.54
3801 4343 2.751436 GCTTCCTTGGCATCGGCA 60.751 61.111 0.00 0.00 43.71 5.69
3802 4344 2.342650 GCTTCCTTGGCATCGGCAA 61.343 57.895 2.83 2.83 45.54 4.52
3803 4345 1.508088 CTTCCTTGGCATCGGCAAC 59.492 57.895 0.00 0.00 42.98 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 6.480320 GGTAACTCTGTTATTGCATAGAGTGG 59.520 42.308 14.61 2.71 46.61 4.00
51 52 8.573035 GTTAAGATTCAAGGTGTCCATAAAACA 58.427 33.333 0.00 0.00 0.00 2.83
57 58 5.707298 CAGTGTTAAGATTCAAGGTGTCCAT 59.293 40.000 0.00 0.00 0.00 3.41
92 93 2.842208 CTGGAAAACGACAAACAGCA 57.158 45.000 0.00 0.00 0.00 4.41
128 129 1.828979 AAACACACAAACGACCCACT 58.171 45.000 0.00 0.00 0.00 4.00
173 174 6.380095 TTTGTAGGCGTTTTTGTCTTGTAT 57.620 33.333 0.00 0.00 0.00 2.29
210 211 4.698201 TCACCACTGTAGGATTTTGACA 57.302 40.909 3.76 0.00 0.00 3.58
224 225 6.248433 AGGAATTGTAAACATGATCACCACT 58.752 36.000 0.00 0.00 0.00 4.00
262 263 6.896860 TGAATATCCCAACCAATGAAGAACAT 59.103 34.615 0.00 0.00 41.45 2.71
444 450 4.081185 TCGCCAAGCCGAGCATCA 62.081 61.111 0.00 0.00 33.17 3.07
508 514 3.756933 ACTAGTTAAAGAACGCACCCA 57.243 42.857 0.00 0.00 40.76 4.51
533 539 2.627699 GGACATTTCAGCCAACAGGAAA 59.372 45.455 0.00 0.00 35.27 3.13
774 780 8.495148 CCAAATAGAAAACAATAAACCTGTTGC 58.505 33.333 0.00 0.00 37.10 4.17
776 782 7.659799 GGCCAAATAGAAAACAATAAACCTGTT 59.340 33.333 0.00 0.00 38.65 3.16
777 783 7.158697 GGCCAAATAGAAAACAATAAACCTGT 58.841 34.615 0.00 0.00 0.00 4.00
788 794 4.142249 ACATAAGCCGGCCAAATAGAAAAC 60.142 41.667 26.15 0.00 0.00 2.43
1065 1084 0.043940 AGGATCCAGCAAGAGGAGGT 59.956 55.000 15.82 0.00 38.83 3.85
1410 1432 1.412343 ACAGCGCCATCTTTTTGGTTT 59.588 42.857 2.29 0.00 39.11 3.27
1583 1605 2.291209 TGTGGCAGTCATGTTTCCAT 57.709 45.000 0.00 0.00 0.00 3.41
1600 1622 7.231317 ACTTGAAATGTTGTCATACTGGATTGT 59.769 33.333 0.00 0.00 33.49 2.71
1796 1833 4.020617 CCGTCTTGCCCTCCAGCA 62.021 66.667 0.00 0.00 42.17 4.41
1830 1867 0.619543 AGGGTGGTGCTAATACCGGT 60.620 55.000 13.98 13.98 43.87 5.28
1837 1874 0.970937 CTCGAGGAGGGTGGTGCTAA 60.971 60.000 3.91 0.00 0.00 3.09
1865 1924 0.619255 TCCTGCTATGACCCCGGAAA 60.619 55.000 0.73 0.00 0.00 3.13
1872 1931 0.811616 CAACGGCTCCTGCTATGACC 60.812 60.000 0.00 0.00 39.59 4.02
2301 2396 1.676014 GGCATGAGCTCGTAAACCAGT 60.676 52.381 8.44 0.00 41.70 4.00
2753 3292 7.611467 ACTGGCATTGTAAACATTATTCTCTGA 59.389 33.333 0.00 0.00 0.00 3.27
2800 3341 8.413309 TGTAATGGAACCGTTATATAGCTAGT 57.587 34.615 8.48 0.00 31.18 2.57
2850 3391 1.133181 TGCCTTGAGTGGGTGGATGA 61.133 55.000 0.00 0.00 0.00 2.92
3034 3575 3.747521 TTGGTGCAGGTTGGTGGGG 62.748 63.158 0.00 0.00 0.00 4.96
3035 3576 1.760086 TTTGGTGCAGGTTGGTGGG 60.760 57.895 0.00 0.00 0.00 4.61
3122 3664 2.433838 CCAGACCAGACTGCAGCG 60.434 66.667 15.27 2.10 36.67 5.18
3123 3665 2.046507 CCCAGACCAGACTGCAGC 60.047 66.667 15.27 6.85 36.67 5.25
3417 3959 5.999205 ACAATGATGCAAGGGTTAATTCA 57.001 34.783 0.00 0.00 0.00 2.57
3545 4087 5.020132 ACAAACTATCACTCAGCTCTAGGT 58.980 41.667 0.00 0.00 0.00 3.08
3593 4135 3.576982 CCGAGAAATGGGTATACTGGCTA 59.423 47.826 2.25 0.00 0.00 3.93
3643 4185 3.083997 ATGACGGGGCAGGAGGAC 61.084 66.667 0.00 0.00 0.00 3.85
3644 4186 2.764128 GATGACGGGGCAGGAGGA 60.764 66.667 0.00 0.00 0.00 3.71
3645 4187 2.765807 AGATGACGGGGCAGGAGG 60.766 66.667 0.00 0.00 0.00 4.30
3646 4188 2.503061 CAGATGACGGGGCAGGAG 59.497 66.667 0.00 0.00 0.00 3.69
3647 4189 3.083349 CCAGATGACGGGGCAGGA 61.083 66.667 0.00 0.00 0.00 3.86
3648 4190 4.864334 GCCAGATGACGGGGCAGG 62.864 72.222 0.00 0.00 46.92 4.85
3652 4194 2.825836 GCTTGCCAGATGACGGGG 60.826 66.667 0.00 0.00 32.13 5.73
3653 4195 2.825836 GGCTTGCCAGATGACGGG 60.826 66.667 6.79 0.00 34.56 5.28
3654 4196 2.825836 GGGCTTGCCAGATGACGG 60.826 66.667 14.04 0.00 0.00 4.79
3655 4197 3.197790 CGGGCTTGCCAGATGACG 61.198 66.667 14.04 2.82 0.00 4.35
3656 4198 3.512516 GCGGGCTTGCCAGATGAC 61.513 66.667 15.54 0.00 0.00 3.06
3674 4216 4.530857 GTCGATGCAGGGGACGGG 62.531 72.222 0.00 0.00 0.00 5.28
3675 4217 4.530857 GGTCGATGCAGGGGACGG 62.531 72.222 0.00 0.00 0.00 4.79
3676 4218 4.530857 GGGTCGATGCAGGGGACG 62.531 72.222 0.00 0.00 0.00 4.79
3677 4219 1.749334 CTAGGGTCGATGCAGGGGAC 61.749 65.000 0.00 0.00 0.00 4.46
3678 4220 1.457643 CTAGGGTCGATGCAGGGGA 60.458 63.158 0.00 0.00 0.00 4.81
3679 4221 2.511452 CCTAGGGTCGATGCAGGGG 61.511 68.421 0.00 0.00 0.00 4.79
3680 4222 1.762460 ACCTAGGGTCGATGCAGGG 60.762 63.158 14.81 3.54 0.00 4.45
3681 4223 1.443407 CACCTAGGGTCGATGCAGG 59.557 63.158 14.81 0.00 31.02 4.85
3682 4224 1.443407 CCACCTAGGGTCGATGCAG 59.557 63.158 14.81 0.00 31.02 4.41
3683 4225 3.628989 CCACCTAGGGTCGATGCA 58.371 61.111 14.81 0.00 31.02 3.96
3692 4234 2.076803 GTTAGGGCCCCCACCTAGG 61.077 68.421 21.43 7.41 41.35 3.02
3693 4235 1.307517 TGTTAGGGCCCCCACCTAG 60.308 63.158 21.43 0.00 41.35 3.02
3694 4236 1.617233 GTGTTAGGGCCCCCACCTA 60.617 63.158 21.43 0.00 39.54 3.08
3695 4237 2.939353 GTGTTAGGGCCCCCACCT 60.939 66.667 21.43 0.62 42.15 4.00
3696 4238 2.939353 AGTGTTAGGGCCCCCACC 60.939 66.667 25.48 14.30 38.92 4.61
3697 4239 2.675371 GAGTGTTAGGGCCCCCAC 59.325 66.667 21.43 22.44 38.92 4.61
3698 4240 3.006728 CGAGTGTTAGGGCCCCCA 61.007 66.667 21.43 10.66 38.92 4.96
3699 4241 3.793888 CCGAGTGTTAGGGCCCCC 61.794 72.222 21.43 7.57 0.00 5.40
3700 4242 3.793888 CCCGAGTGTTAGGGCCCC 61.794 72.222 21.43 3.22 41.34 5.80
3705 4247 0.171903 CGTACCACCCGAGTGTTAGG 59.828 60.000 0.00 0.00 42.88 2.69
3706 4248 0.457337 GCGTACCACCCGAGTGTTAG 60.457 60.000 0.00 0.00 42.88 2.34
3707 4249 1.586028 GCGTACCACCCGAGTGTTA 59.414 57.895 0.00 0.00 42.88 2.41
3708 4250 2.341176 GCGTACCACCCGAGTGTT 59.659 61.111 0.00 0.00 42.88 3.32
3709 4251 3.688159 GGCGTACCACCCGAGTGT 61.688 66.667 0.00 0.00 42.88 3.55
3710 4252 3.642778 CTGGCGTACCACCCGAGTG 62.643 68.421 0.00 0.00 42.67 3.51
3711 4253 3.379445 CTGGCGTACCACCCGAGT 61.379 66.667 0.00 0.00 42.67 4.18
3712 4254 4.814294 GCTGGCGTACCACCCGAG 62.814 72.222 0.00 0.00 42.67 4.63
3713 4255 3.942377 TAGCTGGCGTACCACCCGA 62.942 63.158 0.00 0.00 42.67 5.14
3714 4256 2.792947 ATAGCTGGCGTACCACCCG 61.793 63.158 0.00 0.00 42.67 5.28
3715 4257 1.227556 CATAGCTGGCGTACCACCC 60.228 63.158 0.00 0.00 42.67 4.61
3716 4258 0.810031 CACATAGCTGGCGTACCACC 60.810 60.000 0.00 0.00 42.67 4.61
3717 4259 0.810031 CCACATAGCTGGCGTACCAC 60.810 60.000 0.00 0.00 42.67 4.16
3718 4260 1.261938 ACCACATAGCTGGCGTACCA 61.262 55.000 0.00 0.00 46.51 3.25
3719 4261 0.529992 GACCACATAGCTGGCGTACC 60.530 60.000 0.00 0.00 34.20 3.34
3720 4262 0.870307 CGACCACATAGCTGGCGTAC 60.870 60.000 0.00 0.00 34.20 3.67
3721 4263 1.317431 ACGACCACATAGCTGGCGTA 61.317 55.000 0.00 0.00 40.18 4.42
3722 4264 2.184322 CGACCACATAGCTGGCGT 59.816 61.111 0.00 0.00 34.20 5.68
3723 4265 2.167219 CACGACCACATAGCTGGCG 61.167 63.158 0.00 0.00 37.07 5.69
3724 4266 0.391130 TTCACGACCACATAGCTGGC 60.391 55.000 0.00 0.00 34.20 4.85
3725 4267 1.359848 GTTCACGACCACATAGCTGG 58.640 55.000 0.00 0.00 37.33 4.85
3726 4268 0.992072 CGTTCACGACCACATAGCTG 59.008 55.000 0.00 0.00 43.02 4.24
3727 4269 0.736325 GCGTTCACGACCACATAGCT 60.736 55.000 2.87 0.00 43.02 3.32
3728 4270 1.693083 GGCGTTCACGACCACATAGC 61.693 60.000 2.87 0.00 42.67 2.97
3729 4271 2.369870 GGCGTTCACGACCACATAG 58.630 57.895 2.87 0.00 42.67 2.23
3730 4272 4.582760 GGCGTTCACGACCACATA 57.417 55.556 2.87 0.00 42.67 2.29
3737 4279 3.109547 GCGACATGGCGTTCACGA 61.110 61.111 24.28 0.00 43.02 4.35
3738 4280 4.147322 GGCGACATGGCGTTCACG 62.147 66.667 24.28 4.85 43.27 4.35
3745 4287 2.045926 ACTTGGAGGCGACATGGC 60.046 61.111 0.00 0.00 45.27 4.40
3746 4288 1.003355 ACACTTGGAGGCGACATGG 60.003 57.895 0.00 0.00 0.00 3.66
3747 4289 0.320683 TGACACTTGGAGGCGACATG 60.321 55.000 0.00 0.00 0.00 3.21
3748 4290 0.320771 GTGACACTTGGAGGCGACAT 60.321 55.000 0.00 0.00 0.00 3.06
3749 4291 1.069090 GTGACACTTGGAGGCGACA 59.931 57.895 0.00 0.00 0.00 4.35
3750 4292 1.668151 GGTGACACTTGGAGGCGAC 60.668 63.158 5.39 0.00 0.00 5.19
3751 4293 2.741092 GGTGACACTTGGAGGCGA 59.259 61.111 5.39 0.00 0.00 5.54
3752 4294 2.738521 CGGTGACACTTGGAGGCG 60.739 66.667 5.39 0.00 0.00 5.52
3753 4295 3.050275 GCGGTGACACTTGGAGGC 61.050 66.667 5.39 0.00 0.00 4.70
3754 4296 2.358737 GGCGGTGACACTTGGAGG 60.359 66.667 5.39 0.00 0.00 4.30
3755 4297 2.738521 CGGCGGTGACACTTGGAG 60.739 66.667 5.39 0.00 0.00 3.86
3756 4298 4.980805 GCGGCGGTGACACTTGGA 62.981 66.667 9.78 0.00 0.00 3.53
3757 4299 4.988598 AGCGGCGGTGACACTTGG 62.989 66.667 12.25 0.00 0.00 3.61
3758 4300 2.443957 GAAAGCGGCGGTGACACTTG 62.444 60.000 14.17 0.00 0.00 3.16
3759 4301 2.203153 AAAGCGGCGGTGACACTT 60.203 55.556 14.17 0.00 0.00 3.16
3760 4302 2.665185 GAAAGCGGCGGTGACACT 60.665 61.111 14.17 0.00 0.00 3.55
3761 4303 2.954753 CTGAAAGCGGCGGTGACAC 61.955 63.158 14.17 5.26 0.00 3.67
3762 4304 2.664851 CTGAAAGCGGCGGTGACA 60.665 61.111 14.17 14.82 0.00 3.58
3763 4305 2.357034 TCTGAAAGCGGCGGTGAC 60.357 61.111 14.17 10.61 0.00 3.67
3764 4306 2.048222 CTCTGAAAGCGGCGGTGA 60.048 61.111 14.17 4.30 0.00 4.02
3765 4307 3.121030 CCTCTGAAAGCGGCGGTG 61.121 66.667 14.17 0.00 28.45 4.94
3766 4308 3.302347 CTCCTCTGAAAGCGGCGGT 62.302 63.158 5.44 5.44 39.16 5.68
3767 4309 2.510238 CTCCTCTGAAAGCGGCGG 60.510 66.667 9.78 0.00 39.16 6.13
3768 4310 3.191539 GCTCCTCTGAAAGCGGCG 61.192 66.667 0.51 0.51 39.16 6.46
3769 4311 1.365368 GAAGCTCCTCTGAAAGCGGC 61.365 60.000 0.00 0.00 39.16 6.53
3770 4312 0.742635 GGAAGCTCCTCTGAAAGCGG 60.743 60.000 6.18 0.00 41.22 5.52
3771 4313 0.248843 AGGAAGCTCCTCTGAAAGCG 59.751 55.000 6.18 0.00 45.66 4.68
3781 4323 1.821332 CCGATGCCAAGGAAGCTCC 60.821 63.158 0.00 0.00 36.58 4.70
3782 4324 2.476320 GCCGATGCCAAGGAAGCTC 61.476 63.158 0.00 0.00 0.00 4.09
3783 4325 2.439156 GCCGATGCCAAGGAAGCT 60.439 61.111 0.00 0.00 0.00 3.74
3784 4326 2.342650 TTGCCGATGCCAAGGAAGC 61.343 57.895 0.00 0.00 36.33 3.86
3785 4327 1.508088 GTTGCCGATGCCAAGGAAG 59.492 57.895 0.00 0.00 36.33 3.46
3786 4328 2.331893 CGTTGCCGATGCCAAGGAA 61.332 57.895 0.00 0.00 36.33 3.36
3787 4329 2.745884 CGTTGCCGATGCCAAGGA 60.746 61.111 0.00 0.00 36.33 3.36
3788 4330 2.745884 TCGTTGCCGATGCCAAGG 60.746 61.111 0.00 0.00 38.40 3.61
3789 4331 2.480555 GTCGTTGCCGATGCCAAG 59.519 61.111 0.00 0.00 46.30 3.61
3790 4332 3.418913 CGTCGTTGCCGATGCCAA 61.419 61.111 0.00 0.00 46.30 4.52
3794 4336 3.367051 CTTGCCGTCGTTGCCGATG 62.367 63.158 0.00 0.00 46.30 3.84
3795 4337 3.118454 CTTGCCGTCGTTGCCGAT 61.118 61.111 0.00 0.00 46.30 4.18


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

AutoCloner maintained by Alex Coulton.