Multiple sequence alignment - TraesCS2B01G496700

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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 TraesCS2B01G496700 chr2B 100.000 6515 0 0 1 6515 693320635 693327149 0.000000e+00 12032.0
1 TraesCS2B01G496700 chr2B 84.315 4890 669 56 1001 5849 693723901 693728733 0.000000e+00 4691.0
2 TraesCS2B01G496700 chr2B 80.947 4603 733 94 2000 6515 693366090 693370635 0.000000e+00 3509.0
3 TraesCS2B01G496700 chr2B 79.509 3948 639 90 2022 5890 693738599 693742455 0.000000e+00 2652.0
4 TraesCS2B01G496700 chr2B 76.532 3149 644 69 1607 4706 693892719 693895821 0.000000e+00 1633.0
5 TraesCS2B01G496700 chr2B 83.004 1571 161 54 5006 6515 693849007 693850532 0.000000e+00 1325.0
6 TraesCS2B01G496700 chr2B 86.606 545 38 13 4629 5145 693345989 693346526 2.640000e-158 569.0
7 TraesCS2B01G496700 chr2B 80.661 605 80 16 5214 5810 693346531 693347106 1.000000e-117 435.0
8 TraesCS2B01G496700 chr2B 78.695 521 99 8 3357 3867 8567365 8567883 2.910000e-88 337.0
9 TraesCS2B01G496700 chr2B 87.205 297 35 2 4720 5013 693848586 693848882 1.050000e-87 335.0
10 TraesCS2B01G496700 chr2B 85.366 246 36 0 4403 4648 693848172 693848417 8.380000e-64 255.0
11 TraesCS2B01G496700 chr2B 82.781 302 29 10 5838 6125 693728774 693729066 1.400000e-61 248.0
12 TraesCS2B01G496700 chr2B 79.193 322 47 9 6200 6502 693729183 693729503 8.560000e-49 206.0
13 TraesCS2B01G496700 chr2B 74.542 491 109 14 2452 2933 754921874 754922357 3.980000e-47 200.0
14 TraesCS2B01G496700 chr2B 75.802 343 75 5 1028 1366 693837950 693838288 4.040000e-37 167.0
15 TraesCS2B01G496700 chr2B 74.914 291 69 3 1027 1315 693448015 693448303 5.300000e-26 130.0
16 TraesCS2B01G496700 chr2A 97.279 3601 94 3 733 4332 715274117 715277714 0.000000e+00 6104.0
17 TraesCS2B01G496700 chr2A 88.993 745 43 12 1 735 715273373 715274088 0.000000e+00 885.0
18 TraesCS2B01G496700 chr2A 89.070 613 61 2 4458 5070 715290230 715290836 0.000000e+00 756.0
19 TraesCS2B01G496700 chr2A 81.905 420 55 15 5473 5890 715290830 715291230 1.050000e-87 335.0
20 TraesCS2B01G496700 chr2A 91.204 216 18 1 4251 4465 715277710 715277925 6.390000e-75 292.0
21 TraesCS2B01G496700 chr2D 85.071 5285 692 49 1001 6234 577108616 577113854 0.000000e+00 5299.0
22 TraesCS2B01G496700 chr2D 96.117 1751 62 5 733 2481 577098559 577100305 0.000000e+00 2852.0
23 TraesCS2B01G496700 chr2D 91.745 424 23 3 323 734 577098105 577098528 4.380000e-161 579.0
24 TraesCS2B01G496700 chr2D 93.496 246 10 3 6274 6515 577113856 577114099 1.730000e-95 361.0
25 TraesCS2B01G496700 chr2D 76.207 290 65 4 1018 1305 577126167 577126454 4.070000e-32 150.0
26 TraesCS2B01G496700 chr2D 98.148 54 1 0 147 200 577097924 577097977 1.930000e-15 95.3
27 TraesCS2B01G496700 chr7B 72.584 2670 603 94 1997 4600 744651800 744649194 0.000000e+00 756.0
28 TraesCS2B01G496700 chr7B 73.995 1965 442 52 1994 3928 746386227 746384302 0.000000e+00 734.0
29 TraesCS2B01G496700 chr7B 77.998 809 159 14 3377 4171 746323716 746324519 2.110000e-134 490.0
30 TraesCS2B01G496700 chr6D 74.209 632 128 31 2501 3113 83163693 83164308 1.410000e-56 231.0
31 TraesCS2B01G496700 chr6A 75.000 516 102 19 2501 3005 100264148 100264647 5.120000e-51 213.0
32 TraesCS2B01G496700 chr7A 72.384 688 167 20 2504 3178 708362854 708363531 5.150000e-46 196.0
33 TraesCS2B01G496700 chr5A 73.973 511 104 17 2504 3005 18763990 18764480 5.190000e-41 180.0
34 TraesCS2B01G496700 chr1D 79.032 248 52 0 1028 1275 79142461 79142214 3.120000e-38 171.0
35 TraesCS2B01G496700 chr1D 77.193 285 65 0 1022 1306 86205038 86205322 4.040000e-37 167.0
36 TraesCS2B01G496700 chr1B 77.224 281 64 0 1028 1308 130356412 130356132 1.450000e-36 165.0
37 TraesCS2B01G496700 chr3D 74.806 258 59 4 1027 1281 613839633 613839887 1.920000e-20 111.0


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 TraesCS2B01G496700 chr2B 693320635 693327149 6514 False 12032.000000 12032 100.000000 1 6515 1 chr2B.!!$F2 6514
1 TraesCS2B01G496700 chr2B 693366090 693370635 4545 False 3509.000000 3509 80.947000 2000 6515 1 chr2B.!!$F3 4515
2 TraesCS2B01G496700 chr2B 693738599 693742455 3856 False 2652.000000 2652 79.509000 2022 5890 1 chr2B.!!$F5 3868
3 TraesCS2B01G496700 chr2B 693723901 693729503 5602 False 1715.000000 4691 82.096333 1001 6502 3 chr2B.!!$F10 5501
4 TraesCS2B01G496700 chr2B 693892719 693895821 3102 False 1633.000000 1633 76.532000 1607 4706 1 chr2B.!!$F7 3099
5 TraesCS2B01G496700 chr2B 693848172 693850532 2360 False 638.333333 1325 85.191667 4403 6515 3 chr2B.!!$F11 2112
6 TraesCS2B01G496700 chr2B 693345989 693347106 1117 False 502.000000 569 83.633500 4629 5810 2 chr2B.!!$F9 1181
7 TraesCS2B01G496700 chr2B 8567365 8567883 518 False 337.000000 337 78.695000 3357 3867 1 chr2B.!!$F1 510
8 TraesCS2B01G496700 chr2A 715273373 715277925 4552 False 2427.000000 6104 92.492000 1 4465 3 chr2A.!!$F1 4464
9 TraesCS2B01G496700 chr2A 715290230 715291230 1000 False 545.500000 756 85.487500 4458 5890 2 chr2A.!!$F2 1432
10 TraesCS2B01G496700 chr2D 577108616 577114099 5483 False 2830.000000 5299 89.283500 1001 6515 2 chr2D.!!$F3 5514
11 TraesCS2B01G496700 chr2D 577097924 577100305 2381 False 1175.433333 2852 95.336667 147 2481 3 chr2D.!!$F2 2334
12 TraesCS2B01G496700 chr7B 744649194 744651800 2606 True 756.000000 756 72.584000 1997 4600 1 chr7B.!!$R1 2603
13 TraesCS2B01G496700 chr7B 746384302 746386227 1925 True 734.000000 734 73.995000 1994 3928 1 chr7B.!!$R2 1934
14 TraesCS2B01G496700 chr7B 746323716 746324519 803 False 490.000000 490 77.998000 3377 4171 1 chr7B.!!$F1 794
15 TraesCS2B01G496700 chr6D 83163693 83164308 615 False 231.000000 231 74.209000 2501 3113 1 chr6D.!!$F1 612

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
659 701 0.107945 GCTCCTTCTCGACCATTGCT 60.108 55.000 0.00 0.0 0.00 3.91 F
1392 1497 0.320247 AACTGCTCTGCTTCTGTCCG 60.320 55.000 0.00 0.0 0.00 4.79 F
1418 1523 0.870307 CGTGCGGCTGGTCATAGTAC 60.870 60.000 0.00 0.0 0.00 2.73 F
1425 1530 2.029828 GGCTGGTCATAGTACTGATCCG 60.030 54.545 5.39 0.0 0.00 4.18 F
1433 1538 2.130272 AGTACTGATCCGAGTGAGCA 57.870 50.000 0.00 0.0 36.95 4.26 F
2988 3125 2.958818 AGGCCATCTATCCGTCACTTA 58.041 47.619 5.01 0.0 0.00 2.24 F
4420 4666 0.713883 GTCGTCAAATCATCGCGTGT 59.286 50.000 5.77 0.0 0.00 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2988 3125 7.562821 TCATCTGGACCATCTATTATGATCGAT 59.437 37.037 0.00 0.0 0.00 3.59 R
3667 3817 1.296392 CCACTGCTTCCACATCGGA 59.704 57.895 0.00 0.0 44.40 4.55 R
3807 3960 0.750249 CACCCCAAGAAACACCAACC 59.250 55.000 0.00 0.0 0.00 3.77 R
3933 4089 5.779529 TTTCTAAGTCCACGAGTGTAAGT 57.220 39.130 2.36 0.0 0.00 2.24 R
3977 4136 0.482446 AGGGAACAAATGAGTGGCCA 59.518 50.000 0.00 0.0 0.00 5.36 R
4447 4693 0.745486 TCGACAGGATGCTGCCATTG 60.745 55.000 14.95 0.0 42.53 2.82 R
5667 6237 0.449388 GCCAGCTGTACTGTTGATGC 59.551 55.000 13.81 9.4 45.68 3.91 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
17 18 3.479370 GCGAGCAGGCTGTTGTAG 58.521 61.111 17.16 5.12 0.00 2.74
64 67 2.037511 CCTGCAGCATTTGGGAAGAAAA 59.962 45.455 8.66 0.00 0.00 2.29
93 96 6.442952 TGTGAATTGCGCTTTTATTGTTACT 58.557 32.000 9.73 0.00 0.00 2.24
112 115 4.806342 ACTGTAACAACACCGAAATGTC 57.194 40.909 0.00 0.00 30.55 3.06
142 145 7.343057 AGAAATATTTCCTCTTTTAGGCCCTTG 59.657 37.037 21.86 0.00 46.10 3.61
153 156 3.436924 GCCCTTGGCGTTAACCCG 61.437 66.667 0.00 0.00 39.62 5.28
204 237 6.867519 TTCACCCAGTCAAATCTCATACTA 57.132 37.500 0.00 0.00 0.00 1.82
248 282 6.124088 AGGCAAACATCTCGACAAATTATC 57.876 37.500 0.00 0.00 0.00 1.75
277 311 4.279145 TCACCTCACCTACTTATCTCACC 58.721 47.826 0.00 0.00 0.00 4.02
289 323 6.342338 ACTTATCTCACCGTGTCTTTTAGT 57.658 37.500 0.00 0.00 0.00 2.24
290 324 6.756221 ACTTATCTCACCGTGTCTTTTAGTT 58.244 36.000 0.00 0.00 0.00 2.24
291 325 7.215085 ACTTATCTCACCGTGTCTTTTAGTTT 58.785 34.615 0.00 0.00 0.00 2.66
292 326 7.713942 ACTTATCTCACCGTGTCTTTTAGTTTT 59.286 33.333 0.00 0.00 0.00 2.43
295 329 5.987347 TCTCACCGTGTCTTTTAGTTTTAGG 59.013 40.000 0.00 0.00 0.00 2.69
297 331 6.347696 TCACCGTGTCTTTTAGTTTTAGGAA 58.652 36.000 0.00 0.00 0.00 3.36
302 336 9.643693 CCGTGTCTTTTAGTTTTAGGAATACTA 57.356 33.333 0.00 0.00 0.00 1.82
312 346 8.999220 AGTTTTAGGAATACTAGTTACTGCAC 57.001 34.615 0.00 0.00 32.16 4.57
313 347 8.813951 AGTTTTAGGAATACTAGTTACTGCACT 58.186 33.333 0.00 0.00 32.16 4.40
394 428 1.329171 TTGCAGGTGGCTTTGTGCTT 61.329 50.000 0.00 0.00 45.15 3.91
412 446 2.032528 TGCGGAACAGCAAGAGGG 59.967 61.111 0.00 0.00 45.06 4.30
471 512 1.134551 AGAGAGAAAAGCCGATGCCTC 60.135 52.381 0.00 0.00 38.69 4.70
479 520 2.537560 GCCGATGCCTCATTCGGTG 61.538 63.158 12.38 0.00 46.35 4.94
495 537 1.338105 CGGTGACCTTTGATCAGCTCA 60.338 52.381 0.00 0.00 41.42 4.26
523 565 2.115291 GTGCCCGATTCCTTGCCTC 61.115 63.158 0.00 0.00 0.00 4.70
640 682 1.751927 GTGCCCTGAGATGCCTTGG 60.752 63.158 0.00 0.00 0.00 3.61
642 684 3.004951 CCCTGAGATGCCTTGGCT 58.995 61.111 13.18 0.00 0.00 4.75
643 685 1.153005 CCCTGAGATGCCTTGGCTC 60.153 63.158 13.18 7.88 0.00 4.70
644 686 1.153005 CCTGAGATGCCTTGGCTCC 60.153 63.158 13.18 4.67 0.00 4.70
645 687 1.633915 CCTGAGATGCCTTGGCTCCT 61.634 60.000 13.18 9.28 0.00 3.69
646 688 0.255318 CTGAGATGCCTTGGCTCCTT 59.745 55.000 13.18 0.00 0.00 3.36
647 689 0.254178 TGAGATGCCTTGGCTCCTTC 59.746 55.000 13.18 6.22 0.00 3.46
648 690 0.545646 GAGATGCCTTGGCTCCTTCT 59.454 55.000 13.18 9.35 0.00 2.85
649 691 0.545646 AGATGCCTTGGCTCCTTCTC 59.454 55.000 13.18 1.12 0.00 2.87
650 692 0.813210 GATGCCTTGGCTCCTTCTCG 60.813 60.000 13.18 0.00 0.00 4.04
651 693 1.267574 ATGCCTTGGCTCCTTCTCGA 61.268 55.000 13.18 0.00 0.00 4.04
652 694 1.448717 GCCTTGGCTCCTTCTCGAC 60.449 63.158 4.11 0.00 0.00 4.20
653 695 1.219393 CCTTGGCTCCTTCTCGACC 59.781 63.158 0.00 0.00 0.00 4.79
654 696 1.544825 CCTTGGCTCCTTCTCGACCA 61.545 60.000 0.00 0.00 0.00 4.02
655 697 0.539051 CTTGGCTCCTTCTCGACCAT 59.461 55.000 0.00 0.00 0.00 3.55
656 698 0.984230 TTGGCTCCTTCTCGACCATT 59.016 50.000 0.00 0.00 0.00 3.16
657 699 0.250234 TGGCTCCTTCTCGACCATTG 59.750 55.000 0.00 0.00 0.00 2.82
658 700 1.092345 GGCTCCTTCTCGACCATTGC 61.092 60.000 0.00 0.00 0.00 3.56
659 701 0.107945 GCTCCTTCTCGACCATTGCT 60.108 55.000 0.00 0.00 0.00 3.91
660 702 1.137086 GCTCCTTCTCGACCATTGCTA 59.863 52.381 0.00 0.00 0.00 3.49
661 703 2.815478 CTCCTTCTCGACCATTGCTAC 58.185 52.381 0.00 0.00 0.00 3.58
662 704 2.428890 CTCCTTCTCGACCATTGCTACT 59.571 50.000 0.00 0.00 0.00 2.57
663 705 2.832129 TCCTTCTCGACCATTGCTACTT 59.168 45.455 0.00 0.00 0.00 2.24
664 706 3.260884 TCCTTCTCGACCATTGCTACTTT 59.739 43.478 0.00 0.00 0.00 2.66
665 707 3.372206 CCTTCTCGACCATTGCTACTTTG 59.628 47.826 0.00 0.00 0.00 2.77
666 708 3.678056 TCTCGACCATTGCTACTTTGT 57.322 42.857 0.00 0.00 0.00 2.83
735 807 2.472059 CGCAATGGATGACCCCACG 61.472 63.158 0.00 0.00 39.34 4.94
780 884 1.001974 TCTCCACCCAAACATCGACAG 59.998 52.381 0.00 0.00 0.00 3.51
849 953 1.752310 CTCCCTGCTCTCTCGCTCA 60.752 63.158 0.00 0.00 0.00 4.26
967 1072 7.232534 AGTGGGTAACTGCAAAGAAATGAATTA 59.767 33.333 0.00 0.00 37.88 1.40
1008 1113 2.426024 CCTTGATTTCAGCATGGAGGTG 59.574 50.000 0.00 0.00 46.98 4.00
1012 1117 3.626996 TTCAGCATGGAGGTGGCCG 62.627 63.158 0.00 0.00 45.66 6.13
1131 1236 0.807667 ACGCGCTAAAGATGGAGCTG 60.808 55.000 5.73 0.00 36.50 4.24
1191 1296 0.320771 ACATCGACAACCCTGCACTC 60.321 55.000 0.00 0.00 0.00 3.51
1243 1348 1.739035 CGTACAATGCCGAGGATGTGT 60.739 52.381 0.00 0.00 0.00 3.72
1281 1386 2.513204 CGCATCCAGGACCAGCTG 60.513 66.667 6.78 6.78 0.00 4.24
1287 1392 2.608988 CAGGACCAGCTGGAGGGT 60.609 66.667 39.19 17.35 40.96 4.34
1290 1395 1.306226 GGACCAGCTGGAGGGTACT 60.306 63.158 39.19 15.22 37.57 2.73
1320 1425 2.268920 GACGAGCATGCCAAGGGA 59.731 61.111 15.66 0.00 0.00 4.20
1392 1497 0.320247 AACTGCTCTGCTTCTGTCCG 60.320 55.000 0.00 0.00 0.00 4.79
1413 1518 3.939837 CTCACGTGCGGCTGGTCAT 62.940 63.158 11.67 0.00 0.00 3.06
1414 1519 2.125713 CACGTGCGGCTGGTCATA 60.126 61.111 0.82 0.00 0.00 2.15
1417 1522 1.317431 ACGTGCGGCTGGTCATAGTA 61.317 55.000 0.00 0.00 0.00 1.82
1418 1523 0.870307 CGTGCGGCTGGTCATAGTAC 60.870 60.000 0.00 0.00 0.00 2.73
1425 1530 2.029828 GGCTGGTCATAGTACTGATCCG 60.030 54.545 5.39 0.00 0.00 4.18
1428 1533 4.138290 CTGGTCATAGTACTGATCCGAGT 58.862 47.826 5.39 0.00 0.00 4.18
1433 1538 2.130272 AGTACTGATCCGAGTGAGCA 57.870 50.000 0.00 0.00 36.95 4.26
2988 3125 2.958818 AGGCCATCTATCCGTCACTTA 58.041 47.619 5.01 0.00 0.00 2.24
3421 3568 4.870636 TCTTGCCCAATATGGTGATCTTT 58.129 39.130 0.00 0.00 35.17 2.52
3667 3817 4.156455 AGTGAGCGGTCCAATATTGAAT 57.844 40.909 17.23 0.00 0.00 2.57
4372 4618 5.012239 TGAAGCTGGAGCATTTTCTAATGT 58.988 37.500 0.65 0.00 42.56 2.71
4416 4662 1.595489 GCATGGTCGTCAAATCATCGC 60.595 52.381 0.00 0.00 0.00 4.58
4420 4666 0.713883 GTCGTCAAATCATCGCGTGT 59.286 50.000 5.77 0.00 0.00 4.49
4447 4693 2.365617 TCAGAAGTTCAGAGTGGTGTCC 59.634 50.000 5.50 0.00 0.00 4.02
4482 4728 4.034510 CCTGTCGAGGACATTCTTATTTGC 59.965 45.833 0.00 0.00 42.93 3.68
4489 4738 6.073873 CGAGGACATTCTTATTTGCAGATCTC 60.074 42.308 0.00 0.00 0.00 2.75
4552 4801 5.875098 TCCCAAAGCTATCCAAACTGGGAT 61.875 45.833 2.77 0.00 44.79 3.85
4610 4859 2.137523 GGTGGATTTGCAGCAAACAAG 58.862 47.619 22.92 0.00 36.13 3.16
4679 5012 5.982356 TGATACACTAGCAAAAGATGAGCT 58.018 37.500 0.00 0.00 42.14 4.09
4706 5039 0.639392 ATAGCAGAGGTGGAGGAGGT 59.361 55.000 0.00 0.00 0.00 3.85
4821 5176 2.103263 GGTAGTTCATTCCCTCGATGCT 59.897 50.000 0.00 0.00 0.00 3.79
4825 5180 1.780503 TCATTCCCTCGATGCTCTCA 58.219 50.000 0.00 0.00 0.00 3.27
4842 5197 2.838202 TCTCAAAGCCCTAACTACCCTG 59.162 50.000 0.00 0.00 0.00 4.45
4892 5265 3.541713 CCCGTCCTCCCTGCTAGC 61.542 72.222 8.10 8.10 0.00 3.42
4911 5285 1.176527 CCCTGGAACTTACGTCCGTA 58.823 55.000 0.00 0.00 0.00 4.02
4914 5288 2.989166 CCTGGAACTTACGTCCGTAAAC 59.011 50.000 12.72 7.74 39.69 2.01
4956 5348 1.135915 CTCACCTCTCTCACCCGATTG 59.864 57.143 0.00 0.00 0.00 2.67
4972 5364 3.186205 CCGATTGTGCATATATCGTTGCA 59.814 43.478 19.66 4.33 46.03 4.08
5299 5839 1.814793 GCTCCAGGAACTCCAGTTTC 58.185 55.000 0.00 0.00 38.56 2.78
5311 5851 0.656205 CCAGTTTCGGTTTTGCGACG 60.656 55.000 0.00 0.00 0.00 5.12
5360 5900 2.107204 ACAAGCTGACCAACCTCAAGAT 59.893 45.455 0.00 0.00 0.00 2.40
5440 5983 6.797454 AGTTCACTACGAGAATTAGATGTCC 58.203 40.000 0.00 0.00 0.00 4.02
5443 5986 5.886474 TCACTACGAGAATTAGATGTCCAGT 59.114 40.000 0.00 0.00 0.00 4.00
5538 6084 7.924541 AGACCAATCCAAGGTAACAAATACTA 58.075 34.615 0.00 0.00 40.09 1.82
5539 6085 7.827729 AGACCAATCCAAGGTAACAAATACTAC 59.172 37.037 0.00 0.00 40.09 2.73
5540 6086 7.696017 ACCAATCCAAGGTAACAAATACTACT 58.304 34.615 0.00 0.00 37.67 2.57
5546 6094 8.534496 TCCAAGGTAACAAATACTACTACCTTC 58.466 37.037 8.51 0.00 45.57 3.46
5561 6109 4.850386 ACTACCTTCCTTGTACCAATTCCT 59.150 41.667 0.00 0.00 0.00 3.36
5571 6119 7.454380 TCCTTGTACCAATTCCTGATTTCAATT 59.546 33.333 0.00 0.00 0.00 2.32
5583 6143 6.894654 TCCTGATTTCAATTATTACCCTTGCA 59.105 34.615 0.00 0.00 0.00 4.08
5584 6144 6.980397 CCTGATTTCAATTATTACCCTTGCAC 59.020 38.462 0.00 0.00 0.00 4.57
5600 6160 1.168714 GCACTTTCCTGATCCCACAC 58.831 55.000 0.00 0.00 0.00 3.82
5602 6162 2.862541 CACTTTCCTGATCCCACACAA 58.137 47.619 0.00 0.00 0.00 3.33
5632 6202 6.312672 ACTCATTTTTCTTTCGGTTTGGTTTG 59.687 34.615 0.00 0.00 0.00 2.93
5675 6249 4.039151 ACATCGTTTGTTTGCATCAACA 57.961 36.364 0.00 0.00 33.74 3.33
5678 6252 4.884458 TCGTTTGTTTGCATCAACAGTA 57.116 36.364 4.28 0.00 0.00 2.74
5692 6266 1.519719 CAGTACAGCTGGCCTCTCC 59.480 63.158 19.93 0.00 41.42 3.71
5726 6300 2.019984 GCATTCTTCTAGCCTTGTGGG 58.980 52.381 0.00 0.00 38.36 4.61
5783 6358 5.123979 GGTCCTGTGTGGTATTTTCTTCATC 59.876 44.000 0.00 0.00 37.07 2.92
5803 6399 9.689976 CTTCATCTCAATACATCTGGTAAGTAG 57.310 37.037 0.00 0.00 35.14 2.57
5832 6428 7.750903 GCAAATCGTCTAAAAAGTATCTGCTTT 59.249 33.333 0.00 0.00 40.07 3.51
5880 6528 8.927675 TGCTCCCAGTTCTATTACTTTAAAAA 57.072 30.769 0.00 0.00 0.00 1.94
5896 6544 6.039717 ACTTTAAAAATCACTGCTCTTGAGCA 59.960 34.615 21.90 21.90 43.22 4.26
5935 6584 3.146618 ACGAGTATGTGACGGACAATC 57.853 47.619 0.00 0.00 38.36 2.67
5987 6636 9.912634 AATTATTACCATTATGCTTATGTGCAC 57.087 29.630 10.75 10.75 46.33 4.57
5988 6637 5.766150 TTACCATTATGCTTATGTGCACC 57.234 39.130 15.69 0.00 46.33 5.01
5991 6640 4.142182 ACCATTATGCTTATGTGCACCAAC 60.142 41.667 15.69 0.00 46.33 3.77
6068 6758 4.298332 CTTTCGCCTGTGCAAAATTAACT 58.702 39.130 0.00 0.00 37.32 2.24
6131 6826 7.223584 TCTTTCCAGATATCATGGCGAATTTA 58.776 34.615 5.32 0.00 37.76 1.40
6147 6842 9.698309 TGGCGAATTTAAATTATTCTCAAAACA 57.302 25.926 13.34 0.24 31.35 2.83
6261 7050 3.202151 TCAAGGAAACAAGTGAAGGGAGT 59.798 43.478 0.00 0.00 0.00 3.85
6309 7106 0.586802 GAGTCACGCAAGGTTGAACC 59.413 55.000 6.16 6.16 46.39 3.62
6342 7145 5.871396 ACTTCAGTGTTAGTTCAGAGGAA 57.129 39.130 0.00 0.00 0.00 3.36
6392 7200 0.179045 AGCAGTTTCAGAACACCGCT 60.179 50.000 0.00 2.22 38.26 5.52
6409 7217 1.596954 CGCTGTTTTGACAAAGGACCG 60.597 52.381 0.10 0.60 0.00 4.79
6433 7241 3.472652 TGAGCGGTGAAAACAGTGTTAT 58.527 40.909 9.37 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 8.754080 GGGACTGTAATATCATATGAGTAAGCT 58.246 37.037 11.78 0.00 0.00 3.74
17 18 7.982354 GGGGACTGTAATATCATATGAGTAAGC 59.018 40.741 11.78 2.49 0.00 3.09
18 19 8.478877 GGGGGACTGTAATATCATATGAGTAAG 58.521 40.741 11.78 5.53 0.00 2.34
38 41 2.353610 CCAAATGCTGCAGGGGGAC 61.354 63.158 17.12 0.00 0.00 4.46
40 43 3.078836 CCCAAATGCTGCAGGGGG 61.079 66.667 22.33 20.21 37.66 5.40
64 67 7.638134 ACAATAAAAGCGCAATTCACAATTTT 58.362 26.923 11.47 6.81 0.00 1.82
66 69 6.783892 ACAATAAAAGCGCAATTCACAATT 57.216 29.167 11.47 0.00 0.00 2.32
67 70 6.783892 AACAATAAAAGCGCAATTCACAAT 57.216 29.167 11.47 0.00 0.00 2.71
69 72 6.362016 CAGTAACAATAAAAGCGCAATTCACA 59.638 34.615 11.47 0.00 0.00 3.58
70 73 6.362283 ACAGTAACAATAAAAGCGCAATTCAC 59.638 34.615 11.47 2.18 0.00 3.18
71 74 6.442952 ACAGTAACAATAAAAGCGCAATTCA 58.557 32.000 11.47 0.00 0.00 2.57
93 96 3.245754 GTCGACATTTCGGTGTTGTTACA 59.754 43.478 11.55 0.00 45.90 2.41
107 110 8.567285 AAAGAGGAAATATTTCTGTCGACATT 57.433 30.769 20.40 8.45 37.35 2.71
142 145 0.320160 AGAACAGTCGGGTTAACGCC 60.320 55.000 16.20 9.60 0.00 5.68
145 148 3.725490 AGTTCAGAACAGTCGGGTTAAC 58.275 45.455 15.85 0.00 0.00 2.01
153 156 5.755375 TCACAATCAGAAGTTCAGAACAGTC 59.245 40.000 15.85 11.65 0.00 3.51
204 237 1.312815 GTTGCTTGTGGCTCAACTCT 58.687 50.000 0.00 0.00 42.39 3.24
248 282 0.737715 GTAGGTGAGGTGAAGCGCTG 60.738 60.000 12.58 0.00 0.00 5.18
290 324 9.246670 TGTAGTGCAGTAACTAGTATTCCTAAA 57.753 33.333 1.96 0.00 33.35 1.85
291 325 8.812513 TGTAGTGCAGTAACTAGTATTCCTAA 57.187 34.615 1.96 0.00 33.35 2.69
292 326 8.847196 CATGTAGTGCAGTAACTAGTATTCCTA 58.153 37.037 1.96 0.00 33.35 2.94
310 344 4.033358 GCAGCAGTAACTTAGCATGTAGTG 59.967 45.833 0.00 0.00 0.00 2.74
312 346 4.183865 TGCAGCAGTAACTTAGCATGTAG 58.816 43.478 0.00 0.00 0.00 2.74
313 347 4.200838 TGCAGCAGTAACTTAGCATGTA 57.799 40.909 0.00 0.00 0.00 2.29
394 428 1.600636 CCCTCTTGCTGTTCCGCAA 60.601 57.895 0.00 0.00 46.73 4.85
418 459 3.119137 CCTTATCCCTTTCCCGCTTTTTG 60.119 47.826 0.00 0.00 0.00 2.44
419 460 3.096852 CCTTATCCCTTTCCCGCTTTTT 58.903 45.455 0.00 0.00 0.00 1.94
471 512 2.096496 GCTGATCAAAGGTCACCGAATG 59.904 50.000 0.00 0.00 0.00 2.67
479 520 1.363744 CGGTGAGCTGATCAAAGGTC 58.636 55.000 0.00 7.10 43.50 3.85
523 565 6.447162 GTGAACAACAAGGAAAGGAATTAGG 58.553 40.000 0.00 0.00 0.00 2.69
640 682 0.107945 AGCAATGGTCGAGAAGGAGC 60.108 55.000 0.00 0.00 35.07 4.70
642 684 2.457598 AGTAGCAATGGTCGAGAAGGA 58.542 47.619 0.00 0.00 0.00 3.36
643 685 2.969628 AGTAGCAATGGTCGAGAAGG 57.030 50.000 0.00 0.00 0.00 3.46
644 686 3.997021 ACAAAGTAGCAATGGTCGAGAAG 59.003 43.478 0.00 0.00 0.00 2.85
645 687 4.002906 ACAAAGTAGCAATGGTCGAGAA 57.997 40.909 0.00 0.00 0.00 2.87
646 688 3.678056 ACAAAGTAGCAATGGTCGAGA 57.322 42.857 0.00 0.00 0.00 4.04
647 689 4.466828 CAAACAAAGTAGCAATGGTCGAG 58.533 43.478 0.00 0.00 0.00 4.04
648 690 3.304391 GCAAACAAAGTAGCAATGGTCGA 60.304 43.478 0.00 0.00 0.00 4.20
649 691 2.979813 GCAAACAAAGTAGCAATGGTCG 59.020 45.455 0.00 0.00 0.00 4.79
650 692 3.735746 GTGCAAACAAAGTAGCAATGGTC 59.264 43.478 0.00 0.00 38.91 4.02
651 693 3.492482 GGTGCAAACAAAGTAGCAATGGT 60.492 43.478 0.00 0.00 38.91 3.55
652 694 3.059166 GGTGCAAACAAAGTAGCAATGG 58.941 45.455 0.00 0.00 38.91 3.16
653 695 3.715495 TGGTGCAAACAAAGTAGCAATG 58.285 40.909 0.00 0.00 38.91 2.82
654 696 4.119136 GTTGGTGCAAACAAAGTAGCAAT 58.881 39.130 6.65 0.00 40.22 3.56
655 697 3.056536 TGTTGGTGCAAACAAAGTAGCAA 60.057 39.130 6.65 0.00 37.12 3.91
656 698 2.493675 TGTTGGTGCAAACAAAGTAGCA 59.506 40.909 6.65 0.00 37.12 3.49
657 699 3.157932 TGTTGGTGCAAACAAAGTAGC 57.842 42.857 6.65 0.00 37.12 3.58
658 700 5.009610 ACCTATGTTGGTGCAAACAAAGTAG 59.990 40.000 7.98 11.21 42.98 2.57
659 701 4.890581 ACCTATGTTGGTGCAAACAAAGTA 59.109 37.500 7.98 3.80 42.98 2.24
660 702 3.704061 ACCTATGTTGGTGCAAACAAAGT 59.296 39.130 7.98 3.85 42.98 2.66
661 703 4.320608 ACCTATGTTGGTGCAAACAAAG 57.679 40.909 7.98 2.66 42.98 2.77
662 704 4.688021 GAACCTATGTTGGTGCAAACAAA 58.312 39.130 7.98 0.36 42.98 2.83
663 705 3.243234 CGAACCTATGTTGGTGCAAACAA 60.243 43.478 7.98 4.62 42.98 2.83
664 706 2.292016 CGAACCTATGTTGGTGCAAACA 59.708 45.455 6.43 6.43 43.82 2.83
665 707 2.351350 CCGAACCTATGTTGGTGCAAAC 60.351 50.000 0.00 0.00 40.73 2.93
666 708 1.883275 CCGAACCTATGTTGGTGCAAA 59.117 47.619 0.00 0.00 40.73 3.68
735 807 8.485162 AGGATAGGGAGATATATATAGACCCC 57.515 42.308 19.31 16.81 36.84 4.95
745 849 4.482772 GGGTGGAGAGGATAGGGAGATATA 59.517 50.000 0.00 0.00 0.00 0.86
749 853 0.861155 GGGTGGAGAGGATAGGGAGA 59.139 60.000 0.00 0.00 0.00 3.71
763 867 0.888736 TGCTGTCGATGTTTGGGTGG 60.889 55.000 0.00 0.00 0.00 4.61
849 953 5.012239 ACAATACCAGATGATTGCAGTTGT 58.988 37.500 0.00 0.00 36.67 3.32
967 1072 1.744368 CGCTGCATGCAGGAAGAGT 60.744 57.895 40.59 0.00 43.77 3.24
1020 1125 4.033776 CCCACCACCCATCGTGCT 62.034 66.667 0.00 0.00 41.53 4.40
1077 1182 3.694058 CTCCTTGCTCGCAGCCCAT 62.694 63.158 5.82 0.00 41.51 4.00
1131 1236 1.227380 CATCCCCTGCACGTAGAGC 60.227 63.158 0.00 0.00 46.44 4.09
1170 1275 0.320771 GTGCAGGGTTGTCGATGTCT 60.321 55.000 0.00 0.00 0.00 3.41
1243 1348 1.467734 GAAGTAGTCGAGCTCGTCCAA 59.532 52.381 33.33 17.39 40.80 3.53
1281 1386 0.745468 CAGCCTCGTAAGTACCCTCC 59.255 60.000 0.00 0.00 39.48 4.30
1284 1389 1.143401 GGCAGCCTCGTAAGTACCC 59.857 63.158 3.29 0.00 39.48 3.69
1287 1392 1.805254 GTCGGCAGCCTCGTAAGTA 59.195 57.895 10.54 0.00 39.48 2.24
1290 1395 3.047718 CTCGTCGGCAGCCTCGTAA 62.048 63.158 20.18 6.49 0.00 3.18
1404 1509 2.029828 CGGATCAGTACTATGACCAGCC 60.030 54.545 0.00 0.00 30.46 4.85
1409 1514 4.319911 GCTCACTCGGATCAGTACTATGAC 60.320 50.000 0.00 0.00 30.46 3.06
1411 1516 3.565902 TGCTCACTCGGATCAGTACTATG 59.434 47.826 0.00 0.00 0.00 2.23
1413 1518 3.277142 TGCTCACTCGGATCAGTACTA 57.723 47.619 0.00 0.00 0.00 1.82
1414 1519 2.130272 TGCTCACTCGGATCAGTACT 57.870 50.000 0.00 0.00 0.00 2.73
1417 1522 1.066573 CCTTTGCTCACTCGGATCAGT 60.067 52.381 0.00 0.00 0.00 3.41
1418 1523 1.649664 CCTTTGCTCACTCGGATCAG 58.350 55.000 0.00 0.00 0.00 2.90
1425 1530 3.409026 TCTTCTTCCCTTTGCTCACTC 57.591 47.619 0.00 0.00 0.00 3.51
1428 1533 4.908601 TGTATCTTCTTCCCTTTGCTCA 57.091 40.909 0.00 0.00 0.00 4.26
1433 1538 4.657814 TGCCTTGTATCTTCTTCCCTTT 57.342 40.909 0.00 0.00 0.00 3.11
2988 3125 7.562821 TCATCTGGACCATCTATTATGATCGAT 59.437 37.037 0.00 0.00 0.00 3.59
3421 3568 7.479352 TCCCGACATTATAAATACCCGAATA 57.521 36.000 0.00 0.00 0.00 1.75
3667 3817 1.296392 CCACTGCTTCCACATCGGA 59.704 57.895 0.00 0.00 44.40 4.55
3807 3960 0.750249 CACCCCAAGAAACACCAACC 59.250 55.000 0.00 0.00 0.00 3.77
3933 4089 5.779529 TTTCTAAGTCCACGAGTGTAAGT 57.220 39.130 2.36 0.00 0.00 2.24
3977 4136 0.482446 AGGGAACAAATGAGTGGCCA 59.518 50.000 0.00 0.00 0.00 5.36
4009 4174 9.998106 GAGTTTAGGGCAATCTATAATAGTCAA 57.002 33.333 0.00 0.00 0.00 3.18
4013 4178 7.976734 CCGAGAGTTTAGGGCAATCTATAATAG 59.023 40.741 0.00 0.00 0.00 1.73
4256 4502 3.755378 GCTATGCATACCATCCTTTCCAG 59.245 47.826 1.16 0.00 35.34 3.86
4330 4576 1.407258 CAAAGGTGGGCACTTTTCGAA 59.593 47.619 0.00 0.00 38.34 3.71
4372 4618 5.945784 CCCACAATCTCTTCAATGAGGTTAA 59.054 40.000 0.00 0.00 35.43 2.01
4420 4666 3.405831 CACTCTGAACTTCTGATGGCAA 58.594 45.455 0.00 0.00 0.00 4.52
4447 4693 0.745486 TCGACAGGATGCTGCCATTG 60.745 55.000 14.95 0.00 42.53 2.82
4474 4720 6.199908 CCACTAGAACGAGATCTGCAAATAAG 59.800 42.308 0.00 0.00 0.00 1.73
4482 4728 4.399618 TCCTTTCCACTAGAACGAGATCTG 59.600 45.833 0.00 0.00 32.95 2.90
4489 4738 4.994852 TGTCAATTCCTTTCCACTAGAACG 59.005 41.667 0.00 0.00 32.95 3.95
4610 4859 3.315470 TGACGATGATACTACTGGTGCTC 59.685 47.826 0.00 0.00 0.00 4.26
4679 5012 2.305635 TCCACCTCTGCTATTTCTTGCA 59.694 45.455 0.00 0.00 37.63 4.08
4706 5039 4.904590 CCACCGTGTTTGCCCCCA 62.905 66.667 0.00 0.00 0.00 4.96
4821 5176 2.838202 CAGGGTAGTTAGGGCTTTGAGA 59.162 50.000 0.00 0.00 0.00 3.27
4825 5180 2.197465 CTCCAGGGTAGTTAGGGCTTT 58.803 52.381 0.00 0.00 0.00 3.51
4911 5285 3.767630 AAGGGTCAGCACGCCGTTT 62.768 57.895 0.00 0.00 36.07 3.60
4914 5288 3.423154 GAAAGGGTCAGCACGCCG 61.423 66.667 0.00 0.00 36.07 6.46
4972 5364 4.455606 CCCTCGCATCTTAAATCCTCTTT 58.544 43.478 0.00 0.00 0.00 2.52
4973 5365 3.745797 GCCCTCGCATCTTAAATCCTCTT 60.746 47.826 0.00 0.00 34.03 2.85
5225 5765 2.202797 TGAAGCGCGCCATCTCTC 60.203 61.111 30.33 14.97 0.00 3.20
5299 5839 1.083015 CCAACTCGTCGCAAAACCG 60.083 57.895 0.00 0.00 0.00 4.44
5360 5900 3.208922 TGGACACCTCCAGATCCCTAATA 59.791 47.826 0.00 0.00 42.15 0.98
5440 5983 1.058748 CGTCGTTGCCGCAATACTG 59.941 57.895 9.46 0.48 0.00 2.74
5443 5986 2.449525 GCTCGTCGTTGCCGCAATA 61.450 57.895 9.46 0.00 0.00 1.90
5507 6050 7.504926 TGTTACCTTGGATTGGTCTATAGTT 57.495 36.000 0.00 0.00 38.88 2.24
5561 6109 7.716799 AGTGCAAGGGTAATAATTGAAATCA 57.283 32.000 0.00 0.00 0.00 2.57
5571 6119 4.919774 TCAGGAAAGTGCAAGGGTAATA 57.080 40.909 0.00 0.00 0.00 0.98
5583 6143 3.222603 GTTTGTGTGGGATCAGGAAAGT 58.777 45.455 0.00 0.00 0.00 2.66
5584 6144 2.558359 GGTTTGTGTGGGATCAGGAAAG 59.442 50.000 0.00 0.00 0.00 2.62
5600 6160 5.810074 ACCGAAAGAAAAATGAGTTGGTTTG 59.190 36.000 0.00 0.00 0.00 2.93
5602 6162 5.592104 ACCGAAAGAAAAATGAGTTGGTT 57.408 34.783 0.00 0.00 0.00 3.67
5658 6228 4.346970 TGTACTGTTGATGCAAACAAACG 58.653 39.130 10.46 7.77 39.47 3.60
5667 6237 0.449388 GCCAGCTGTACTGTTGATGC 59.551 55.000 13.81 9.40 45.68 3.91
5675 6249 2.055042 CGGAGAGGCCAGCTGTACT 61.055 63.158 13.81 10.12 35.94 2.73
5692 6266 2.262471 GAATGCACAGCTCCAAGGCG 62.262 60.000 0.00 0.00 37.29 5.52
5702 6276 3.126514 CACAAGGCTAGAAGAATGCACAG 59.873 47.826 0.00 0.00 0.00 3.66
5745 6319 0.749454 AGGACCTCATGCGCCAATTC 60.749 55.000 4.18 0.00 0.00 2.17
5747 6321 1.452651 CAGGACCTCATGCGCCAAT 60.453 57.895 4.18 0.00 0.00 3.16
5803 6399 7.374491 GCAGATACTTTTTAGACGATTTGCATC 59.626 37.037 0.00 0.00 0.00 3.91
5928 6577 2.190578 CAGGCCCTCCGATTGTCC 59.809 66.667 0.00 0.00 37.47 4.02
5929 6578 1.153349 GACAGGCCCTCCGATTGTC 60.153 63.158 0.00 0.25 37.47 3.18
5935 6584 0.830648 TTGAATAGACAGGCCCTCCG 59.169 55.000 0.00 0.00 37.47 4.63
5984 6633 1.269621 ACACACTCTCGTAGTTGGTGC 60.270 52.381 9.43 0.00 36.19 5.01
5985 6634 2.795175 ACACACTCTCGTAGTTGGTG 57.205 50.000 8.51 8.51 37.85 4.17
5986 6635 2.035576 GGAACACACTCTCGTAGTTGGT 59.964 50.000 0.00 0.00 35.76 3.67
5987 6636 2.296471 AGGAACACACTCTCGTAGTTGG 59.704 50.000 0.00 0.00 35.76 3.77
5988 6637 3.644884 AGGAACACACTCTCGTAGTTG 57.355 47.619 0.00 0.00 35.76 3.16
5991 6640 5.417811 TCTACTAGGAACACACTCTCGTAG 58.582 45.833 0.00 0.00 36.54 3.51
6052 6742 6.073819 GGCTAACAAAGTTAATTTTGCACAGG 60.074 38.462 19.86 9.48 40.80 4.00
6068 6758 6.560003 TTATCCTCAGATCAGGCTAACAAA 57.440 37.500 0.00 0.00 33.67 2.83
6109 6804 7.815840 TTTAAATTCGCCATGATATCTGGAA 57.184 32.000 19.48 9.94 35.70 3.53
6147 6842 5.823861 ATGCCAAAAAGGAAACAAGGTAT 57.176 34.783 0.00 0.00 41.22 2.73
6261 7050 4.158025 GTCGACTTGATGGGACTTTCTCTA 59.842 45.833 8.70 0.00 0.00 2.43
6309 7106 7.730364 ACTAACACTGAAGTACAAATTCCAG 57.270 36.000 0.00 0.00 0.00 3.86
6312 7109 9.042008 TCTGAACTAACACTGAAGTACAAATTC 57.958 33.333 0.00 0.00 0.00 2.17
6342 7145 1.136329 AATCCCTGCAGGTCCAGTGT 61.136 55.000 30.63 6.27 36.75 3.55
6392 7200 3.506455 TCAAACGGTCCTTTGTCAAAACA 59.494 39.130 0.00 0.00 33.54 2.83
6409 7217 2.159435 ACACTGTTTTCACCGCTCAAAC 60.159 45.455 0.00 0.00 0.00 2.93
6433 7241 8.103935 TGTTGTACAACCTATAATGTTCCATGA 58.896 33.333 30.68 7.66 40.46 3.07


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

AutoCloner maintained by Alex Coulton.