Multiple sequence alignment - TraesCS4D01G031500

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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 TraesCS4D01G031500 chr4D 100.000 3945 0 0 1 3945 14833001 14829057 0.000000e+00 7286.0
1 TraesCS4D01G031500 chr4D 91.401 2570 138 35 990 3518 14560414 14562941 0.000000e+00 3445.0
2 TraesCS4D01G031500 chr4D 87.800 959 91 18 1018 1965 14523127 14524070 0.000000e+00 1099.0
3 TraesCS4D01G031500 chr4D 83.333 432 52 16 1 416 14521072 14521499 8.000000e-102 381.0
4 TraesCS4D01G031500 chr4D 94.811 212 9 1 3734 3945 14565089 14565298 2.940000e-86 329.0
5 TraesCS4D01G031500 chr4D 84.314 357 29 18 592 943 14560070 14560404 1.370000e-84 324.0
6 TraesCS4D01G031500 chr4D 86.496 274 25 10 592 858 14522101 14522369 1.390000e-74 291.0
7 TraesCS4D01G031500 chr4D 92.537 134 9 1 2060 2193 14525436 14525568 1.450000e-44 191.0
8 TraesCS4D01G031500 chr4D 95.238 84 2 2 3609 3691 14565007 14565089 8.890000e-27 132.0
9 TraesCS4D01G031500 chr4B 89.223 2431 134 49 652 3039 24666289 24663944 0.000000e+00 2920.0
10 TraesCS4D01G031500 chr4B 90.432 648 51 7 1 641 24675136 24674493 0.000000e+00 843.0
11 TraesCS4D01G031500 chr4B 93.598 328 17 4 3609 3934 24574389 24574064 1.650000e-133 486.0
12 TraesCS4D01G031500 chr4B 84.211 114 16 1 2510 2621 291060810 291060923 4.170000e-20 110.0
13 TraesCS4D01G031500 chr4B 85.047 107 14 1 2510 2614 291099126 291099232 1.500000e-19 108.0
14 TraesCS4D01G031500 chr4B 90.000 50 4 1 487 536 50177264 50177216 3.290000e-06 63.9
15 TraesCS4D01G031500 chr4A 91.851 2123 107 24 993 3068 456473647 456475750 0.000000e+00 2902.0
16 TraesCS4D01G031500 chr4A 91.073 2106 109 28 993 3068 586726816 586728872 0.000000e+00 2774.0
17 TraesCS4D01G031500 chr4A 85.441 261 20 12 669 924 586726535 586726782 5.060000e-64 255.0
18 TraesCS4D01G031500 chr4A 86.638 232 16 10 669 893 456473364 456473587 3.940000e-60 243.0
19 TraesCS4D01G031500 chr4A 93.069 101 5 2 3611 3710 586730664 586730763 3.180000e-31 147.0
20 TraesCS4D01G031500 chr4A 89.535 86 6 3 3609 3692 336029301 336029217 5.390000e-19 106.0
21 TraesCS4D01G031500 chr4A 89.412 85 6 3 3609 3691 609791616 609791533 1.940000e-18 104.0
22 TraesCS4D01G031500 chr4A 92.500 40 3 0 496 535 34671480 34671441 1.530000e-04 58.4
23 TraesCS4D01G031500 chr3B 91.747 2084 127 25 1 2068 452745765 452747819 0.000000e+00 2854.0
24 TraesCS4D01G031500 chr3B 92.531 897 33 16 2060 2930 452754393 452755281 0.000000e+00 1254.0
25 TraesCS4D01G031500 chr3B 90.937 331 30 0 3280 3610 783622270 783621940 2.800000e-121 446.0
26 TraesCS4D01G031500 chr3B 87.356 348 35 8 3268 3610 3087528 3087871 1.330000e-104 390.0
27 TraesCS4D01G031500 chr7D 87.356 348 36 7 3269 3610 629101244 629100899 3.700000e-105 392.0
28 TraesCS4D01G031500 chr7D 92.500 40 3 0 496 535 461939095 461939056 1.530000e-04 58.4
29 TraesCS4D01G031500 chr1D 87.390 341 41 2 3271 3610 476836871 476836532 1.330000e-104 390.0
30 TraesCS4D01G031500 chr1B 86.047 344 44 4 3269 3610 61487809 61488150 2.240000e-97 366.0
31 TraesCS4D01G031500 chr5B 85.965 342 46 2 3270 3610 690404295 690404635 8.060000e-97 364.0
32 TraesCS4D01G031500 chr5B 86.598 97 8 5 3609 3703 699998083 699998176 6.970000e-18 102.0
33 TraesCS4D01G031500 chr5B 87.755 49 5 1 487 535 227895287 227895240 5.510000e-04 56.5
34 TraesCS4D01G031500 chr7A 85.756 344 43 5 3270 3610 669483681 669483341 3.750000e-95 359.0
35 TraesCS4D01G031500 chr6B 85.756 344 43 6 3270 3610 476706347 476706687 3.750000e-95 359.0
36 TraesCS4D01G031500 chr6D 83.735 166 26 1 2405 2570 429945116 429944952 5.280000e-34 156.0
37 TraesCS4D01G031500 chr6D 77.844 167 24 10 2398 2558 141591117 141591276 1.510000e-14 91.6
38 TraesCS4D01G031500 chr2D 79.630 162 25 7 2445 2602 584898264 584898421 4.170000e-20 110.0
39 TraesCS4D01G031500 chr3A 89.655 87 6 3 3608 3692 557617859 557617944 1.500000e-19 108.0
40 TraesCS4D01G031500 chr3A 92.683 41 1 2 496 535 425378446 425378407 1.530000e-04 58.4
41 TraesCS4D01G031500 chr1A 89.412 85 8 1 3608 3691 588682034 588681950 5.390000e-19 106.0
42 TraesCS4D01G031500 chr5A 89.412 85 6 3 3609 3691 33893566 33893483 1.940000e-18 104.0
43 TraesCS4D01G031500 chr6A 78.443 167 23 10 2398 2558 186529699 186529858 3.240000e-16 97.1
44 TraesCS4D01G031500 chr5D 93.182 44 3 0 493 536 335051197 335051240 9.150000e-07 65.8
45 TraesCS4D01G031500 chr3D 93.182 44 1 2 493 535 608334821 608334863 3.290000e-06 63.9
46 TraesCS4D01G031500 chr2B 92.308 39 3 0 22 60 518754534 518754572 5.510000e-04 56.5


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 TraesCS4D01G031500 chr4D 14829057 14833001 3944 True 7286.000000 7286 100.0000 1 3945 1 chr4D.!!$R1 3944
1 TraesCS4D01G031500 chr4D 14560070 14565298 5228 False 1057.500000 3445 91.4410 592 3945 4 chr4D.!!$F2 3353
2 TraesCS4D01G031500 chr4D 14521072 14525568 4496 False 490.500000 1099 87.5415 1 2193 4 chr4D.!!$F1 2192
3 TraesCS4D01G031500 chr4B 24663944 24666289 2345 True 2920.000000 2920 89.2230 652 3039 1 chr4B.!!$R2 2387
4 TraesCS4D01G031500 chr4B 24674493 24675136 643 True 843.000000 843 90.4320 1 641 1 chr4B.!!$R3 640
5 TraesCS4D01G031500 chr4A 456473364 456475750 2386 False 1572.500000 2902 89.2445 669 3068 2 chr4A.!!$F1 2399
6 TraesCS4D01G031500 chr4A 586726535 586730763 4228 False 1058.666667 2774 89.8610 669 3710 3 chr4A.!!$F2 3041
7 TraesCS4D01G031500 chr3B 452745765 452747819 2054 False 2854.000000 2854 91.7470 1 2068 1 chr3B.!!$F2 2067
8 TraesCS4D01G031500 chr3B 452754393 452755281 888 False 1254.000000 1254 92.5310 2060 2930 1 chr3B.!!$F3 870

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
958 1436 0.308993 GCATAAGGAGATTGCGCACC 59.691 55.0 11.12 8.44 0.0 5.01 F
1062 2209 0.461135 GCCACATAAACCCCATGCTG 59.539 55.0 0.00 0.00 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2738 5213 0.527817 AGTTTCTTATCGGAGGCGCG 60.528 55.000 0.0 0.0 0.0 6.86 R
3010 5485 1.065109 GCAAAACCACACCACGACC 59.935 57.895 0.0 0.0 0.0 4.79 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
33 35 9.883142 CCATTTTTATTAATAAGAGGTTGGCAA 57.117 29.630 7.91 0.00 0.00 4.52
171 177 3.980646 TCAATGGCACGGCATATTTAC 57.019 42.857 6.51 0.00 0.00 2.01
176 184 3.348119 TGGCACGGCATATTTACTGAAA 58.652 40.909 0.00 0.00 0.00 2.69
179 187 5.590663 TGGCACGGCATATTTACTGAAATTA 59.409 36.000 0.00 0.00 36.62 1.40
184 192 7.809331 CACGGCATATTTACTGAAATTATGCAT 59.191 33.333 18.65 3.79 39.97 3.96
369 385 6.660521 GTGAAATGATATCTATGGGCCAATCA 59.339 38.462 17.64 17.64 0.00 2.57
394 410 3.246112 CCTGGACCCCGACCACAA 61.246 66.667 0.00 0.00 33.57 3.33
430 582 2.098607 AGGATGAAACGTTCGCTCGATA 59.901 45.455 0.00 0.00 34.70 2.92
487 909 2.288666 GGTCCAAAATCTATGCGCTCA 58.711 47.619 9.73 0.00 0.00 4.26
493 915 5.048083 TCCAAAATCTATGCGCTCAAACTTT 60.048 36.000 9.73 0.00 0.00 2.66
503 925 6.554334 TGCGCTCAAACTTTCTACTAAAAT 57.446 33.333 9.73 0.00 0.00 1.82
533 955 6.443849 ACACTTATTTTGAGATGGAGGGAGTA 59.556 38.462 0.00 0.00 0.00 2.59
544 966 3.919834 TGGAGGGAGTATTACCAGTACC 58.080 50.000 0.00 0.00 0.00 3.34
571 1010 0.836400 TTCCGGCAGAAGAGGGTTCT 60.836 55.000 0.00 0.00 34.29 3.01
573 1012 0.902531 CCGGCAGAAGAGGGTTCTTA 59.097 55.000 0.00 0.00 43.63 2.10
574 1013 1.278127 CCGGCAGAAGAGGGTTCTTAA 59.722 52.381 0.00 0.00 43.63 1.85
604 1047 2.294512 GGAGTCAGAAAAACCCAGCAAG 59.705 50.000 0.00 0.00 0.00 4.01
763 1215 8.523915 TGCATGGATAAACTCTTTGTCAATAT 57.476 30.769 0.00 0.00 33.05 1.28
819 1288 2.752354 TGGAATTAATGGTGCCAGAACG 59.248 45.455 0.00 0.00 0.00 3.95
826 1296 2.617274 GGTGCCAGAACGGAGCAAC 61.617 63.158 0.00 0.00 38.45 4.17
838 1308 0.955919 GGAGCAACAAACCTCCTCCG 60.956 60.000 0.00 0.00 43.42 4.63
923 1401 1.686587 TGATCCGATCCGCAGTAACAT 59.313 47.619 5.91 0.00 0.00 2.71
924 1402 2.888414 TGATCCGATCCGCAGTAACATA 59.112 45.455 5.91 0.00 0.00 2.29
925 1403 3.319689 TGATCCGATCCGCAGTAACATAA 59.680 43.478 5.91 0.00 0.00 1.90
926 1404 3.088194 TCCGATCCGCAGTAACATAAC 57.912 47.619 0.00 0.00 0.00 1.89
927 1405 2.427812 TCCGATCCGCAGTAACATAACA 59.572 45.455 0.00 0.00 0.00 2.41
958 1436 0.308993 GCATAAGGAGATTGCGCACC 59.691 55.000 11.12 8.44 0.00 5.01
965 1443 2.965831 AGGAGATTGCGCACCTTCTATA 59.034 45.455 11.12 0.00 0.00 1.31
966 1444 3.580458 AGGAGATTGCGCACCTTCTATAT 59.420 43.478 11.12 0.00 0.00 0.86
967 1445 4.772624 AGGAGATTGCGCACCTTCTATATA 59.227 41.667 11.12 0.00 0.00 0.86
968 1446 5.423610 AGGAGATTGCGCACCTTCTATATAT 59.576 40.000 11.12 0.00 0.00 0.86
969 1447 6.070538 AGGAGATTGCGCACCTTCTATATATT 60.071 38.462 11.12 0.00 0.00 1.28
972 1450 7.038659 AGATTGCGCACCTTCTATATATTCTC 58.961 38.462 11.12 0.00 0.00 2.87
974 1452 4.081642 TGCGCACCTTCTATATATTCTCCC 60.082 45.833 5.66 0.00 0.00 4.30
975 1453 4.673441 CGCACCTTCTATATATTCTCCCG 58.327 47.826 0.00 0.00 0.00 5.14
976 1454 4.440250 CGCACCTTCTATATATTCTCCCGG 60.440 50.000 0.00 0.00 0.00 5.73
977 1455 4.680975 GCACCTTCTATATATTCTCCCGGC 60.681 50.000 0.00 0.00 0.00 6.13
978 1456 4.031611 ACCTTCTATATATTCTCCCGGCC 58.968 47.826 0.00 0.00 0.00 6.13
979 1457 3.388350 CCTTCTATATATTCTCCCGGCCC 59.612 52.174 0.00 0.00 0.00 5.80
980 1458 2.662866 TCTATATATTCTCCCGGCCCG 58.337 52.381 0.00 0.00 0.00 6.13
981 1459 1.068741 CTATATATTCTCCCGGCCCGC 59.931 57.143 0.00 0.00 0.00 6.13
982 1460 0.907704 ATATATTCTCCCGGCCCGCA 60.908 55.000 0.00 0.00 0.00 5.69
983 1461 1.541310 TATATTCTCCCGGCCCGCAG 61.541 60.000 0.00 0.00 0.00 5.18
984 1462 3.906400 TATATTCTCCCGGCCCGCAGA 62.906 57.143 0.00 0.00 0.00 4.26
986 1464 3.906400 TATTCTCCCGGCCCGCAGATA 62.906 57.143 0.00 0.00 0.00 1.98
987 1465 4.301027 CTCCCGGCCCGCAGATAC 62.301 72.222 0.00 0.00 0.00 2.24
988 1466 4.853142 TCCCGGCCCGCAGATACT 62.853 66.667 0.00 0.00 0.00 2.12
994 1472 0.601311 GGCCCGCAGATACTAGCAAG 60.601 60.000 0.00 0.00 0.00 4.01
1037 2184 4.078516 GCTCGTGCCCTACCCGTT 62.079 66.667 0.00 0.00 0.00 4.44
1062 2209 0.461135 GCCACATAAACCCCATGCTG 59.539 55.000 0.00 0.00 0.00 4.41
1235 2382 2.223502 GCATCGACGAGTATGTGGAGAA 60.224 50.000 3.01 0.00 29.93 2.87
1245 2392 0.534412 ATGTGGAGAAGCTGGAGTCG 59.466 55.000 0.00 0.00 0.00 4.18
1263 2410 2.603776 AGTGGGTCGGTGTCCCTC 60.604 66.667 2.65 0.00 44.84 4.30
1380 2527 0.490017 TACCCTTCTCCACCCAGTCA 59.510 55.000 0.00 0.00 0.00 3.41
1641 2791 5.363562 TGGAGTACGAGGTAGTAAGATCA 57.636 43.478 0.00 0.00 0.00 2.92
1752 2912 9.563748 AACATGATCCATGAAAATTGAACTTTT 57.436 25.926 13.22 0.00 43.81 2.27
2117 4565 1.048724 CAAGGTCCGAGCCATAGGGA 61.049 60.000 0.00 0.00 35.59 4.20
2193 4641 4.680237 CGCCAACCTGCTCGACCA 62.680 66.667 0.00 0.00 0.00 4.02
2766 5241 3.700038 TCCGATAAGAAACTGGGAGAGTC 59.300 47.826 0.00 0.00 31.73 3.36
2967 5442 2.949451 AAGTCTCACTGTATCTGGCG 57.051 50.000 0.00 0.00 0.00 5.69
2968 5443 1.107114 AGTCTCACTGTATCTGGCGG 58.893 55.000 0.00 0.00 0.00 6.13
2973 5448 0.392706 CACTGTATCTGGCGGGCATA 59.607 55.000 4.16 0.00 0.00 3.14
2974 5449 1.002430 CACTGTATCTGGCGGGCATAT 59.998 52.381 4.16 6.16 0.00 1.78
2975 5450 2.233676 CACTGTATCTGGCGGGCATATA 59.766 50.000 4.16 5.06 0.00 0.86
2976 5451 3.107601 ACTGTATCTGGCGGGCATATAT 58.892 45.455 4.16 2.23 0.00 0.86
2977 5452 3.118629 ACTGTATCTGGCGGGCATATATG 60.119 47.826 8.45 8.45 0.00 1.78
2978 5453 2.170397 TGTATCTGGCGGGCATATATGG 59.830 50.000 14.51 0.00 0.00 2.74
2979 5454 1.289160 ATCTGGCGGGCATATATGGT 58.711 50.000 14.51 0.00 0.00 3.55
2980 5455 1.064003 TCTGGCGGGCATATATGGTT 58.936 50.000 14.51 0.00 0.00 3.67
2981 5456 1.423541 TCTGGCGGGCATATATGGTTT 59.576 47.619 14.51 0.00 0.00 3.27
2982 5457 2.158534 TCTGGCGGGCATATATGGTTTT 60.159 45.455 14.51 0.00 0.00 2.43
2983 5458 2.627699 CTGGCGGGCATATATGGTTTTT 59.372 45.455 14.51 0.00 0.00 1.94
2991 5466 5.505654 GGGCATATATGGTTTTTGTCTCGTG 60.506 44.000 14.51 0.00 0.00 4.35
2999 5474 2.542020 TTTTGTCTCGTGGATCTGCA 57.458 45.000 0.00 0.00 0.00 4.41
3000 5475 2.768253 TTTGTCTCGTGGATCTGCAT 57.232 45.000 0.00 0.00 0.00 3.96
3001 5476 3.885724 TTTGTCTCGTGGATCTGCATA 57.114 42.857 0.00 0.00 0.00 3.14
3002 5477 4.406648 TTTGTCTCGTGGATCTGCATAT 57.593 40.909 0.00 0.00 0.00 1.78
3010 5485 7.274468 GTCTCGTGGATCTGCATATATTACTTG 59.726 40.741 0.00 0.00 0.00 3.16
3026 5501 1.099689 CTTGGTCGTGGTGTGGTTTT 58.900 50.000 0.00 0.00 0.00 2.43
3039 5514 2.204237 GTGGTTTTGCTGGAGCTTTTG 58.796 47.619 0.00 0.00 42.66 2.44
3067 5542 1.074752 GAGTCCTTGCTTGCTTCTCG 58.925 55.000 0.00 0.00 0.00 4.04
3068 5543 0.681733 AGTCCTTGCTTGCTTCTCGA 59.318 50.000 0.00 0.00 0.00 4.04
3069 5544 1.277557 AGTCCTTGCTTGCTTCTCGAT 59.722 47.619 0.00 0.00 0.00 3.59
3070 5545 1.663135 GTCCTTGCTTGCTTCTCGATC 59.337 52.381 0.00 0.00 0.00 3.69
3095 5570 2.715046 TGATAGGCTTTTGTGCTGAGG 58.285 47.619 0.00 0.00 0.00 3.86
3096 5571 2.305635 TGATAGGCTTTTGTGCTGAGGA 59.694 45.455 0.00 0.00 0.00 3.71
3097 5572 2.479566 TAGGCTTTTGTGCTGAGGAG 57.520 50.000 0.00 0.00 0.00 3.69
3127 5602 0.321298 TAGGGTCGTGGCTTTTGAGC 60.321 55.000 0.00 0.00 0.00 4.26
3128 5603 1.896660 GGGTCGTGGCTTTTGAGCA 60.897 57.895 0.47 0.00 36.33 4.26
3129 5604 1.576421 GGTCGTGGCTTTTGAGCAG 59.424 57.895 0.47 0.00 36.33 4.24
3130 5605 1.081840 GTCGTGGCTTTTGAGCAGC 60.082 57.895 0.47 0.00 36.33 5.25
3131 5606 1.227943 TCGTGGCTTTTGAGCAGCT 60.228 52.632 0.00 0.00 37.43 4.24
3133 5608 1.089920 CGTGGCTTTTGAGCAGCTAT 58.910 50.000 0.00 0.00 37.43 2.97
3134 5609 2.093711 TCGTGGCTTTTGAGCAGCTATA 60.094 45.455 0.00 0.00 37.43 1.31
3159 5637 3.321111 TCTTCTTGTTCTTCTAGTGCGGT 59.679 43.478 0.00 0.00 0.00 5.68
3160 5638 4.521639 TCTTCTTGTTCTTCTAGTGCGGTA 59.478 41.667 0.00 0.00 0.00 4.02
3161 5639 4.436242 TCTTGTTCTTCTAGTGCGGTAG 57.564 45.455 0.00 0.00 0.00 3.18
3182 5660 1.812686 GCCGCGTCCCATATCACCTA 61.813 60.000 4.92 0.00 0.00 3.08
3190 5668 2.299013 TCCCATATCACCTATGTCGTGC 59.701 50.000 0.00 0.00 36.27 5.34
3247 5725 4.459685 ACTTGATCTGTAGCGTTGTAGTCT 59.540 41.667 0.00 0.00 0.00 3.24
3261 5739 4.635833 TGTAGTCTGTGTCGTTTGTGTA 57.364 40.909 0.00 0.00 0.00 2.90
3311 5789 1.528309 CACCCGTGCCCTTTCTGTT 60.528 57.895 0.00 0.00 0.00 3.16
3333 5811 2.101783 AGCCATTCATTTTCCGCATCA 58.898 42.857 0.00 0.00 0.00 3.07
3357 5835 4.386049 CGATTCGTGCAAGTAGTTTTCTCT 59.614 41.667 0.00 0.00 0.00 3.10
3445 5923 9.667107 TCTAACTAGAATGTGGGATAAAACTTG 57.333 33.333 0.00 0.00 0.00 3.16
3455 5933 7.666623 TGTGGGATAAAACTTGGAGATTTTTC 58.333 34.615 0.00 0.00 30.80 2.29
3559 8022 9.973661 TCTGAAAATTTTATCCCACATTCTAGA 57.026 29.630 2.75 0.00 0.00 2.43
3593 8056 5.280945 TGTTATGCTGCAAAGTTTGAAGTC 58.719 37.500 22.18 15.47 38.65 3.01
3682 8189 4.383335 CCAGGGTGCATATGCTCAAAAATT 60.383 41.667 27.13 5.43 42.66 1.82
3701 8208 1.946745 TCTGCATTCGTTGTGTGTCA 58.053 45.000 0.00 0.00 0.00 3.58
3710 8217 6.036083 GCATTCGTTGTGTGTCACTATAATCT 59.964 38.462 4.27 0.00 35.11 2.40
3711 8218 6.944557 TTCGTTGTGTGTCACTATAATCTG 57.055 37.500 4.27 0.00 35.11 2.90
3712 8219 6.020971 TCGTTGTGTGTCACTATAATCTGT 57.979 37.500 4.27 0.00 35.11 3.41
3713 8220 6.452242 TCGTTGTGTGTCACTATAATCTGTT 58.548 36.000 4.27 0.00 35.11 3.16
3714 8221 6.364976 TCGTTGTGTGTCACTATAATCTGTTG 59.635 38.462 4.27 0.00 35.11 3.33
3715 8222 6.145534 CGTTGTGTGTCACTATAATCTGTTGT 59.854 38.462 4.27 0.00 35.11 3.32
3716 8223 7.327518 CGTTGTGTGTCACTATAATCTGTTGTA 59.672 37.037 4.27 0.00 35.11 2.41
3717 8224 8.648097 GTTGTGTGTCACTATAATCTGTTGTAG 58.352 37.037 4.27 0.00 35.75 2.74
3718 8225 6.811665 TGTGTGTCACTATAATCTGTTGTAGC 59.188 38.462 4.27 0.00 33.68 3.58
3719 8226 6.255887 GTGTGTCACTATAATCTGTTGTAGCC 59.744 42.308 4.27 0.00 33.68 3.93
3720 8227 6.154534 TGTGTCACTATAATCTGTTGTAGCCT 59.845 38.462 4.27 0.00 33.68 4.58
3721 8228 6.477033 GTGTCACTATAATCTGTTGTAGCCTG 59.523 42.308 0.00 0.00 33.68 4.85
3722 8229 5.986135 GTCACTATAATCTGTTGTAGCCTGG 59.014 44.000 0.00 0.00 33.68 4.45
3723 8230 5.661312 TCACTATAATCTGTTGTAGCCTGGT 59.339 40.000 0.00 0.00 33.68 4.00
3724 8231 6.156256 TCACTATAATCTGTTGTAGCCTGGTT 59.844 38.462 0.00 0.00 33.68 3.67
3725 8232 6.258727 CACTATAATCTGTTGTAGCCTGGTTG 59.741 42.308 0.00 0.00 33.68 3.77
3726 8233 3.508845 AATCTGTTGTAGCCTGGTTGT 57.491 42.857 0.00 0.00 0.00 3.32
3727 8234 4.634012 AATCTGTTGTAGCCTGGTTGTA 57.366 40.909 0.00 0.00 0.00 2.41
3728 8235 4.634012 ATCTGTTGTAGCCTGGTTGTAA 57.366 40.909 0.00 0.00 0.00 2.41
3729 8236 4.002906 TCTGTTGTAGCCTGGTTGTAAG 57.997 45.455 0.00 0.00 0.00 2.34
3730 8237 2.484264 CTGTTGTAGCCTGGTTGTAAGC 59.516 50.000 0.00 0.00 0.00 3.09
3731 8238 2.105821 TGTTGTAGCCTGGTTGTAAGCT 59.894 45.455 0.00 0.00 39.37 3.74
3732 8239 2.742589 GTTGTAGCCTGGTTGTAAGCTC 59.257 50.000 0.00 0.00 36.79 4.09
3733 8240 1.278127 TGTAGCCTGGTTGTAAGCTCC 59.722 52.381 0.00 0.00 36.79 4.70
3756 8263 3.565902 AGCTTGTCAACTTAGTTCCTTGC 59.434 43.478 0.00 0.00 0.00 4.01
3760 8267 3.820467 TGTCAACTTAGTTCCTTGCATGG 59.180 43.478 12.41 12.41 0.00 3.66
3786 8293 6.476380 TCATGTTCTTTCATTTTCTGTTGCAC 59.524 34.615 0.00 0.00 0.00 4.57
3799 8306 2.548057 CTGTTGCACGCTCTTTTCCTTA 59.452 45.455 0.00 0.00 0.00 2.69
3844 8351 6.071952 GGTGTGTTTTGTCTACCATGATGATT 60.072 38.462 0.00 0.00 0.00 2.57
3856 8363 4.823442 ACCATGATGATTATCGTGCAATGT 59.177 37.500 12.99 4.38 45.11 2.71
3916 8423 0.256752 TGAGCAACATGAGGATGGGG 59.743 55.000 0.00 0.00 33.39 4.96
3917 8424 0.257039 GAGCAACATGAGGATGGGGT 59.743 55.000 0.00 0.00 33.39 4.95
3923 8430 1.386485 ATGAGGATGGGGTGGAGGG 60.386 63.158 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
171 177 7.830940 TTTGGTTTGCTATGCATAATTTCAG 57.169 32.000 8.00 0.00 38.76 3.02
176 184 9.889128 AACTTTATTTGGTTTGCTATGCATAAT 57.111 25.926 8.00 0.00 38.76 1.28
179 187 9.369904 CTTAACTTTATTTGGTTTGCTATGCAT 57.630 29.630 3.79 3.79 38.76 3.96
346 361 6.320672 CCTGATTGGCCCATAGATATCATTTC 59.679 42.308 0.00 0.00 0.00 2.17
387 403 0.515564 CCCGATTGTTCGTTGTGGTC 59.484 55.000 0.00 0.00 43.97 4.02
394 410 2.498481 TCATCCTTACCCGATTGTTCGT 59.502 45.455 0.00 0.00 43.97 3.85
407 423 2.095110 TCGAGCGAACGTTTCATCCTTA 60.095 45.455 0.46 0.00 34.70 2.69
454 852 1.591768 TTGGACCCCAATAGGAGGAC 58.408 55.000 0.00 0.00 38.75 3.85
480 902 5.994887 TTTTAGTAGAAAGTTTGAGCGCA 57.005 34.783 11.47 0.00 0.00 6.09
503 925 6.816640 CCTCCATCTCAAAATAAGTGTCGTTA 59.183 38.462 0.00 0.00 0.00 3.18
514 936 6.389869 TGGTAATACTCCCTCCATCTCAAAAT 59.610 38.462 0.00 0.00 0.00 1.82
533 955 4.758165 CGGAAACAAAGTGGTACTGGTAAT 59.242 41.667 0.00 0.00 0.00 1.89
544 966 1.946768 TCTTCTGCCGGAAACAAAGTG 59.053 47.619 5.05 0.00 33.07 3.16
571 1010 3.254093 TCTGACTCCTGACCTGGTTAA 57.746 47.619 0.00 0.00 0.00 2.01
573 1012 2.103153 TTCTGACTCCTGACCTGGTT 57.897 50.000 0.00 0.00 0.00 3.67
574 1013 2.103153 TTTCTGACTCCTGACCTGGT 57.897 50.000 0.00 0.00 0.00 4.00
580 1019 2.487265 GCTGGGTTTTTCTGACTCCTGA 60.487 50.000 0.00 0.00 0.00 3.86
784 1253 8.971073 ACCATTAATTCCAATAACTCCTTTCTG 58.029 33.333 0.00 0.00 0.00 3.02
789 1258 5.598417 GGCACCATTAATTCCAATAACTCCT 59.402 40.000 0.00 0.00 0.00 3.69
819 1288 0.955919 CGGAGGAGGTTTGTTGCTCC 60.956 60.000 3.05 3.05 46.31 4.70
826 1296 1.607148 GGTGAAAACGGAGGAGGTTTG 59.393 52.381 0.00 0.00 37.64 2.93
838 1308 3.847542 TGCATGCATATGTGGTGAAAAC 58.152 40.909 18.46 0.00 36.65 2.43
923 1401 9.679661 TCTCCTTATGCTAAATTGACAATGTTA 57.320 29.630 0.34 2.79 0.00 2.41
924 1402 8.579850 TCTCCTTATGCTAAATTGACAATGTT 57.420 30.769 0.34 1.78 0.00 2.71
925 1403 8.757982 ATCTCCTTATGCTAAATTGACAATGT 57.242 30.769 0.34 0.00 0.00 2.71
926 1404 9.459640 CAATCTCCTTATGCTAAATTGACAATG 57.540 33.333 0.34 0.00 0.00 2.82
927 1405 8.139989 GCAATCTCCTTATGCTAAATTGACAAT 58.860 33.333 0.00 0.00 37.12 2.71
946 1424 7.038659 AGAATATATAGAAGGTGCGCAATCTC 58.961 38.462 20.76 13.66 0.00 2.75
958 1436 3.068307 CGGGCCGGGAGAATATATAGAAG 59.932 52.174 20.56 0.00 0.00 2.85
965 1443 2.847234 TGCGGGCCGGGAGAATAT 60.847 61.111 29.48 0.00 0.00 1.28
966 1444 3.546543 CTGCGGGCCGGGAGAATA 61.547 66.667 29.48 0.00 0.00 1.75
969 1447 4.533124 TATCTGCGGGCCGGGAGA 62.533 66.667 31.61 31.61 38.80 3.71
972 1450 2.915659 TAGTATCTGCGGGCCGGG 60.916 66.667 29.48 0.00 0.00 5.73
974 1452 2.049063 GCTAGTATCTGCGGGCCG 60.049 66.667 24.35 24.35 0.00 6.13
975 1453 0.601311 CTTGCTAGTATCTGCGGGCC 60.601 60.000 0.00 0.00 0.00 5.80
976 1454 1.224722 GCTTGCTAGTATCTGCGGGC 61.225 60.000 0.00 0.00 0.00 6.13
977 1455 0.104855 TGCTTGCTAGTATCTGCGGG 59.895 55.000 0.00 0.00 0.00 6.13
978 1456 1.594862 GTTGCTTGCTAGTATCTGCGG 59.405 52.381 0.00 0.00 0.00 5.69
979 1457 1.594862 GGTTGCTTGCTAGTATCTGCG 59.405 52.381 0.00 0.00 0.00 5.18
980 1458 2.632377 TGGTTGCTTGCTAGTATCTGC 58.368 47.619 0.00 0.00 0.00 4.26
981 1459 4.194640 ACATGGTTGCTTGCTAGTATCTG 58.805 43.478 0.00 0.00 0.00 2.90
982 1460 4.446371 GACATGGTTGCTTGCTAGTATCT 58.554 43.478 0.00 0.00 0.00 1.98
983 1461 3.561725 GGACATGGTTGCTTGCTAGTATC 59.438 47.826 0.00 0.00 0.00 2.24
984 1462 3.054434 TGGACATGGTTGCTTGCTAGTAT 60.054 43.478 0.00 0.00 0.00 2.12
985 1463 2.304470 TGGACATGGTTGCTTGCTAGTA 59.696 45.455 0.00 0.00 0.00 1.82
986 1464 1.073763 TGGACATGGTTGCTTGCTAGT 59.926 47.619 0.00 0.00 0.00 2.57
987 1465 1.825090 TGGACATGGTTGCTTGCTAG 58.175 50.000 0.00 0.00 0.00 3.42
988 1466 2.093890 CATGGACATGGTTGCTTGCTA 58.906 47.619 4.39 0.00 35.24 3.49
1037 2184 1.148027 TGGGGTTTATGTGGCTTTGGA 59.852 47.619 0.00 0.00 0.00 3.53
1165 2312 1.832912 GGCCATCGGAGATGGACTT 59.167 57.895 27.62 0.00 43.87 3.01
1216 2363 2.033550 GCTTCTCCACATACTCGTCGAT 59.966 50.000 0.00 0.00 0.00 3.59
1235 2382 1.979693 GACCCACTCGACTCCAGCT 60.980 63.158 0.00 0.00 0.00 4.24
1276 2423 1.600916 GCGTGAAGTGGCCTTCCTT 60.601 57.895 3.32 3.14 45.45 3.36
1356 2503 2.288025 GGTGGAGAAGGGTACGGCA 61.288 63.158 0.00 0.00 0.00 5.69
1752 2912 7.148018 GGGCTAGAAATGAAATCTCACAAATCA 60.148 37.037 0.00 0.00 33.30 2.57
2193 4641 0.617413 CTTGATGCAGGTGTCCTCCT 59.383 55.000 0.00 0.00 38.51 3.69
2738 5213 0.527817 AGTTTCTTATCGGAGGCGCG 60.528 55.000 0.00 0.00 0.00 6.86
2749 5224 3.583086 CCAAGGACTCTCCCAGTTTCTTA 59.417 47.826 0.00 0.00 37.19 2.10
2766 5241 3.777925 CGCACGCGAACTCCAAGG 61.778 66.667 15.93 0.00 42.83 3.61
2967 5442 4.578928 ACGAGACAAAAACCATATATGCCC 59.421 41.667 7.24 0.00 0.00 5.36
2968 5443 5.505654 CCACGAGACAAAAACCATATATGCC 60.506 44.000 7.24 0.00 0.00 4.40
2973 5448 5.586243 CAGATCCACGAGACAAAAACCATAT 59.414 40.000 0.00 0.00 0.00 1.78
2974 5449 4.935205 CAGATCCACGAGACAAAAACCATA 59.065 41.667 0.00 0.00 0.00 2.74
2975 5450 3.753272 CAGATCCACGAGACAAAAACCAT 59.247 43.478 0.00 0.00 0.00 3.55
2976 5451 3.138304 CAGATCCACGAGACAAAAACCA 58.862 45.455 0.00 0.00 0.00 3.67
2977 5452 2.095718 GCAGATCCACGAGACAAAAACC 60.096 50.000 0.00 0.00 0.00 3.27
2978 5453 2.548057 TGCAGATCCACGAGACAAAAAC 59.452 45.455 0.00 0.00 0.00 2.43
2979 5454 2.844946 TGCAGATCCACGAGACAAAAA 58.155 42.857 0.00 0.00 0.00 1.94
2980 5455 2.542020 TGCAGATCCACGAGACAAAA 57.458 45.000 0.00 0.00 0.00 2.44
2981 5456 2.768253 ATGCAGATCCACGAGACAAA 57.232 45.000 0.00 0.00 0.00 2.83
2982 5457 5.728637 ATATATGCAGATCCACGAGACAA 57.271 39.130 0.00 0.00 0.00 3.18
2983 5458 5.728637 AATATATGCAGATCCACGAGACA 57.271 39.130 0.00 0.00 0.00 3.41
2991 5466 6.311445 CACGACCAAGTAATATATGCAGATCC 59.689 42.308 0.00 0.00 0.00 3.36
2999 5474 5.129815 ACCACACCACGACCAAGTAATATAT 59.870 40.000 0.00 0.00 0.00 0.86
3000 5475 4.467082 ACCACACCACGACCAAGTAATATA 59.533 41.667 0.00 0.00 0.00 0.86
3001 5476 3.262405 ACCACACCACGACCAAGTAATAT 59.738 43.478 0.00 0.00 0.00 1.28
3002 5477 2.633967 ACCACACCACGACCAAGTAATA 59.366 45.455 0.00 0.00 0.00 0.98
3010 5485 1.065109 GCAAAACCACACCACGACC 59.935 57.895 0.00 0.00 0.00 4.79
3026 5501 1.290955 GCATGCAAAAGCTCCAGCA 59.709 52.632 14.21 9.00 45.16 4.41
3039 5514 1.436336 GCAAGGACTCCATGCATGC 59.564 57.895 21.69 11.82 46.03 4.06
3067 5542 2.945668 ACAAAAGCCTATCAAGCCGATC 59.054 45.455 0.00 0.00 35.39 3.69
3068 5543 2.684881 CACAAAAGCCTATCAAGCCGAT 59.315 45.455 0.00 0.00 38.21 4.18
3069 5544 2.083774 CACAAAAGCCTATCAAGCCGA 58.916 47.619 0.00 0.00 0.00 5.54
3070 5545 1.468054 GCACAAAAGCCTATCAAGCCG 60.468 52.381 0.00 0.00 0.00 5.52
3095 5570 4.701171 CCACGACCCTAGATAGATAACCTC 59.299 50.000 0.00 0.00 0.00 3.85
3096 5571 4.664392 CCACGACCCTAGATAGATAACCT 58.336 47.826 0.00 0.00 0.00 3.50
3097 5572 3.193056 GCCACGACCCTAGATAGATAACC 59.807 52.174 0.00 0.00 0.00 2.85
3133 5608 7.068348 ACCGCACTAGAAGAACAAGAAGATATA 59.932 37.037 0.00 0.00 0.00 0.86
3134 5609 6.127310 ACCGCACTAGAAGAACAAGAAGATAT 60.127 38.462 0.00 0.00 0.00 1.63
3159 5637 3.277211 GATATGGGACGCGGCGCTA 62.277 63.158 30.10 18.89 0.00 4.26
3160 5638 4.664677 GATATGGGACGCGGCGCT 62.665 66.667 30.10 17.32 0.00 5.92
3161 5639 4.961511 TGATATGGGACGCGGCGC 62.962 66.667 23.92 23.92 0.00 6.53
3163 5641 1.812686 TAGGTGATATGGGACGCGGC 61.813 60.000 12.47 7.53 0.00 6.53
3164 5642 0.895530 ATAGGTGATATGGGACGCGG 59.104 55.000 12.47 0.00 0.00 6.46
3165 5643 1.272490 ACATAGGTGATATGGGACGCG 59.728 52.381 3.53 3.53 44.86 6.01
3166 5644 2.671351 CGACATAGGTGATATGGGACGC 60.671 54.545 0.00 0.00 44.86 5.19
3167 5645 2.557056 ACGACATAGGTGATATGGGACG 59.443 50.000 0.00 0.00 44.86 4.79
3168 5646 3.861131 GCACGACATAGGTGATATGGGAC 60.861 52.174 0.00 0.00 44.86 4.46
3169 5647 2.299013 GCACGACATAGGTGATATGGGA 59.701 50.000 0.00 0.00 44.86 4.37
3170 5648 2.688507 GCACGACATAGGTGATATGGG 58.311 52.381 0.00 0.00 44.86 4.00
3171 5649 2.030274 TCGCACGACATAGGTGATATGG 60.030 50.000 0.00 0.00 44.86 2.74
3182 5660 4.796231 GCCGGACTCGCACGACAT 62.796 66.667 5.05 0.00 34.56 3.06
3210 5688 2.385013 TCAAGTGATCGACCACATGG 57.615 50.000 14.84 2.41 39.42 3.66
3247 5725 2.924926 GACACACTACACAAACGACACA 59.075 45.455 0.00 0.00 0.00 3.72
3261 5739 4.712122 AAAACATGTTTTCGGACACACT 57.288 36.364 27.01 5.01 38.27 3.55
3311 5789 3.698539 TGATGCGGAAAATGAATGGCTAA 59.301 39.130 0.00 0.00 0.00 3.09
3333 5811 4.056050 AGAAAACTACTTGCACGAATCGT 58.944 39.130 0.96 0.96 42.36 3.73
3383 5861 4.864247 GCTGCAAAGTTTGAAGTTCAAGAA 59.136 37.500 22.18 2.25 38.65 2.52
3445 5923 5.890424 TTATGTTGGACGGAAAAATCTCC 57.110 39.130 0.00 0.00 0.00 3.71
3455 5933 9.663904 CTCATTTTGTATATTTATGTTGGACGG 57.336 33.333 0.00 0.00 0.00 4.79
3559 8022 5.902613 TGCAGCATAACAAAGCTTTCTAT 57.097 34.783 9.23 6.61 39.50 1.98
3593 8056 7.962918 GCTACACAACTATAAAACATGTCTTGG 59.037 37.037 0.00 0.00 0.00 3.61
3682 8189 1.597195 GTGACACACAACGAATGCAGA 59.403 47.619 0.00 0.00 34.08 4.26
3701 8208 6.070194 ACAACCAGGCTACAACAGATTATAGT 60.070 38.462 0.00 0.00 0.00 2.12
3710 8217 2.105821 AGCTTACAACCAGGCTACAACA 59.894 45.455 0.00 0.00 32.94 3.33
3711 8218 2.742589 GAGCTTACAACCAGGCTACAAC 59.257 50.000 0.00 0.00 35.01 3.32
3712 8219 2.290071 GGAGCTTACAACCAGGCTACAA 60.290 50.000 0.00 0.00 35.85 2.41
3713 8220 1.278127 GGAGCTTACAACCAGGCTACA 59.722 52.381 0.00 0.00 35.85 2.74
3714 8221 1.278127 TGGAGCTTACAACCAGGCTAC 59.722 52.381 0.00 0.00 36.30 3.58
3715 8222 1.555075 CTGGAGCTTACAACCAGGCTA 59.445 52.381 9.98 0.00 44.96 3.93
3716 8223 0.326264 CTGGAGCTTACAACCAGGCT 59.674 55.000 9.98 0.00 44.96 4.58
3717 8224 2.859992 CTGGAGCTTACAACCAGGC 58.140 57.895 9.98 0.00 44.96 4.85
3729 8236 2.772287 ACTAAGTTGACAAGCTGGAGC 58.228 47.619 0.00 0.00 42.49 4.70
3730 8237 3.748568 GGAACTAAGTTGACAAGCTGGAG 59.251 47.826 0.00 0.00 0.00 3.86
3731 8238 3.391296 AGGAACTAAGTTGACAAGCTGGA 59.609 43.478 0.00 0.00 36.02 3.86
3732 8239 3.744660 AGGAACTAAGTTGACAAGCTGG 58.255 45.455 0.00 0.00 36.02 4.85
3733 8240 4.555511 GCAAGGAACTAAGTTGACAAGCTG 60.556 45.833 0.00 0.00 38.49 4.24
3739 8246 3.821033 ACCATGCAAGGAACTAAGTTGAC 59.179 43.478 16.33 0.00 38.49 3.18
3756 8263 7.149973 ACAGAAAATGAAAGAACATGACCATG 58.850 34.615 0.00 8.34 44.15 3.66
3760 8267 6.476380 TGCAACAGAAAATGAAAGAACATGAC 59.524 34.615 0.00 0.00 0.00 3.06
3786 8293 3.485877 CGAAGCCAATAAGGAAAAGAGCG 60.486 47.826 0.00 0.00 41.22 5.03
3844 8351 3.190327 CCTTGTTCCAACATTGCACGATA 59.810 43.478 0.00 0.00 38.95 2.92
3856 8363 1.391157 GCAGCACCACCTTGTTCCAA 61.391 55.000 0.00 0.00 0.00 3.53
3907 8414 1.768077 CTCCCTCCACCCCATCCTC 60.768 68.421 0.00 0.00 0.00 3.71
3916 8423 0.251634 CTTCTCCTTGCTCCCTCCAC 59.748 60.000 0.00 0.00 0.00 4.02
3917 8424 0.117140 TCTTCTCCTTGCTCCCTCCA 59.883 55.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.