Multiple sequence alignment - TraesCS6B01G136900

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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 TraesCS6B01G136900 chr6B 100.000 4586 0 0 1 4586 134766492 134771077 0.000000e+00 8469.0
1 TraesCS6B01G136900 chr6B 92.204 2591 131 28 1109 3671 134488486 134485939 0.000000e+00 3600.0
2 TraesCS6B01G136900 chr6B 98.201 778 14 0 3789 4566 583440692 583439915 0.000000e+00 1360.0
3 TraesCS6B01G136900 chr6B 92.962 341 11 8 756 1093 134488881 134488551 6.900000e-133 484.0
4 TraesCS6B01G136900 chr6B 76.616 727 133 28 2871 3576 54894561 54895271 2.610000e-97 366.0
5 TraesCS6B01G136900 chr6D 92.863 2396 124 22 1416 3787 60494531 60496903 0.000000e+00 3434.0
6 TraesCS6B01G136900 chr6D 88.088 1956 149 44 1108 3013 60391298 60389377 0.000000e+00 2244.0
7 TraesCS6B01G136900 chr6D 94.774 574 25 2 3008 3579 60389282 60388712 0.000000e+00 889.0
8 TraesCS6B01G136900 chr6D 94.071 506 16 5 602 1095 60493503 60494006 0.000000e+00 756.0
9 TraesCS6B01G136900 chr6D 86.364 330 32 8 757 1083 60391692 60391373 9.440000e-92 348.0
10 TraesCS6B01G136900 chr6D 93.642 173 5 1 1249 1421 60494187 60494353 2.120000e-63 254.0
11 TraesCS6B01G136900 chr6D 89.394 132 1 2 1109 1227 60494062 60494193 2.210000e-33 154.0
12 TraesCS6B01G136900 chr6A 88.769 2502 190 55 1108 3579 77010505 77008065 0.000000e+00 2979.0
13 TraesCS6B01G136900 chr6A 94.319 1637 66 13 1109 2730 77158903 77160527 0.000000e+00 2483.0
14 TraesCS6B01G136900 chr6A 92.766 940 48 8 2849 3778 77160597 77161526 0.000000e+00 1341.0
15 TraesCS6B01G136900 chr6A 93.953 430 17 5 672 1095 77158414 77158840 3.870000e-180 641.0
16 TraesCS6B01G136900 chr6A 87.356 348 27 12 749 1093 77010904 77010571 2.590000e-102 383.0
17 TraesCS6B01G136900 chr7A 97.573 783 13 1 3790 4566 14826279 14827061 0.000000e+00 1336.0
18 TraesCS6B01G136900 chr7A 98.930 374 4 0 3790 4163 14822351 14822724 0.000000e+00 669.0
19 TraesCS6B01G136900 chr7A 80.638 878 43 44 3786 4566 675243344 675244191 3.100000e-156 562.0
20 TraesCS6B01G136900 chr5B 98.821 509 3 1 4061 4566 578437882 578438390 0.000000e+00 904.0
21 TraesCS6B01G136900 chr2A 86.555 595 34 6 3790 4340 735585232 735584640 8.430000e-172 614.0
22 TraesCS6B01G136900 chr2A 85.685 496 29 4 3857 4311 60066636 60067130 6.900000e-133 484.0
23 TraesCS6B01G136900 chr2A 94.495 218 7 3 4354 4566 59990097 59990314 9.510000e-87 331.0
24 TraesCS6B01G136900 chr2A 94.495 218 6 4 4354 4566 60067203 60067419 9.510000e-87 331.0
25 TraesCS6B01G136900 chr2A 94.309 123 7 0 4189 4311 59989900 59990022 6.060000e-44 189.0
26 TraesCS6B01G136900 chr2A 78.462 260 45 9 343 598 744918201 744917949 4.750000e-35 159.0
27 TraesCS6B01G136900 chr2B 86.281 605 34 19 3790 4355 74212059 74212653 3.030000e-171 612.0
28 TraesCS6B01G136900 chr2B 94.362 337 14 2 1 337 650423624 650423955 3.160000e-141 512.0
29 TraesCS6B01G136900 chr2B 95.385 260 10 1 343 600 650423990 650424249 3.300000e-111 412.0
30 TraesCS6B01G136900 chr2B 78.327 263 49 8 342 600 536637271 536637529 3.670000e-36 163.0
31 TraesCS6B01G136900 chr2B 94.318 88 3 2 4445 4531 74214912 74214998 2.880000e-27 134.0
32 TraesCS6B01G136900 chr1D 97.626 337 8 0 1 337 19353980 19354316 3.080000e-161 579.0
33 TraesCS6B01G136900 chr1D 94.961 258 13 0 343 600 19354351 19354608 5.520000e-109 405.0
34 TraesCS6B01G136900 chr1D 77.692 260 54 4 343 600 242536657 242536400 6.140000e-34 156.0
35 TraesCS6B01G136900 chr7B 93.175 337 23 0 1 337 647740077 647740413 3.190000e-136 496.0
36 TraesCS6B01G136900 chr7B 91.860 258 21 0 343 600 647740448 647740705 1.210000e-95 361.0
37 TraesCS6B01G136900 chr7B 95.714 210 8 1 4358 4566 581250909 581251118 2.040000e-88 337.0
38 TraesCS6B01G136900 chr7B 76.163 344 75 7 1 341 690244612 690244951 1.700000e-39 174.0
39 TraesCS6B01G136900 chr7B 96.040 101 4 0 3789 3889 581250365 581250465 1.020000e-36 165.0
40 TraesCS6B01G136900 chr7B 93.103 87 6 0 4273 4359 581250723 581250809 1.340000e-25 128.0
41 TraesCS6B01G136900 chr3D 81.369 628 84 16 3 600 23807247 23807871 8.920000e-132 481.0
42 TraesCS6B01G136900 chr4D 88.021 384 34 5 3792 4166 30854168 30853788 1.170000e-120 444.0
43 TraesCS6B01G136900 chr4D 83.790 438 57 12 1777 2210 111039659 111040086 1.990000e-108 403.0
44 TraesCS6B01G136900 chr4D 84.351 262 39 2 2871 3131 111040767 111041027 5.890000e-64 255.0
45 TraesCS6B01G136900 chr4D 88.889 153 9 6 4354 4501 30848446 30848297 1.010000e-41 182.0
46 TraesCS6B01G136900 chr4A 87.750 400 18 3 3943 4311 621761434 621761035 5.450000e-119 438.0
47 TraesCS6B01G136900 chr4A 83.643 269 40 3 2871 3136 466108726 466108459 2.740000e-62 250.0
48 TraesCS6B01G136900 chr4A 94.488 127 6 1 4354 4479 621758742 621758616 1.300000e-45 195.0
49 TraesCS6B01G136900 chr4B 88.955 335 36 1 3 337 611700644 611700311 3.300000e-111 412.0
50 TraesCS6B01G136900 chr4B 83.409 440 61 10 1777 2213 171183147 171182717 9.240000e-107 398.0
51 TraesCS6B01G136900 chr4B 81.798 456 79 4 2246 2699 171182600 171182147 3.350000e-101 379.0
52 TraesCS6B01G136900 chr4B 91.473 258 22 0 343 600 611700276 611700019 5.640000e-94 355.0
53 TraesCS6B01G136900 chr4B 79.487 78 16 0 3881 3958 20305059 20305136 6.410000e-04 56.5
54 TraesCS6B01G136900 chrUn 77.685 717 122 25 2871 3574 103503332 103502641 1.990000e-108 403.0
55 TraesCS6B01G136900 chrUn 80.717 446 68 14 1777 2210 103534823 103535262 9.510000e-87 331.0
56 TraesCS6B01G136900 chrUn 75.056 449 69 24 1777 2213 103504448 103504031 7.890000e-38 169.0
57 TraesCS6B01G136900 chrUn 85.833 120 15 2 2576 2694 103503492 103503374 4.820000e-25 126.0
58 TraesCS6B01G136900 chrUn 84.167 120 17 2 2576 2694 103535803 103535921 1.040000e-21 115.0
59 TraesCS6B01G136900 chr5D 85.897 312 41 3 3 312 260385840 260386150 3.420000e-86 329.0
60 TraesCS6B01G136900 chr3A 82.822 163 19 6 343 502 727543372 727543528 2.230000e-28 137.0


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 TraesCS6B01G136900 chr6B 134766492 134771077 4585 False 8469.000000 8469 100.000000 1 4586 1 chr6B.!!$F2 4585
1 TraesCS6B01G136900 chr6B 134485939 134488881 2942 True 2042.000000 3600 92.583000 756 3671 2 chr6B.!!$R2 2915
2 TraesCS6B01G136900 chr6B 583439915 583440692 777 True 1360.000000 1360 98.201000 3789 4566 1 chr6B.!!$R1 777
3 TraesCS6B01G136900 chr6B 54894561 54895271 710 False 366.000000 366 76.616000 2871 3576 1 chr6B.!!$F1 705
4 TraesCS6B01G136900 chr6D 60388712 60391692 2980 True 1160.333333 2244 89.742000 757 3579 3 chr6D.!!$R1 2822
5 TraesCS6B01G136900 chr6D 60493503 60496903 3400 False 1149.500000 3434 92.492500 602 3787 4 chr6D.!!$F1 3185
6 TraesCS6B01G136900 chr6A 77008065 77010904 2839 True 1681.000000 2979 88.062500 749 3579 2 chr6A.!!$R1 2830
7 TraesCS6B01G136900 chr6A 77158414 77161526 3112 False 1488.333333 2483 93.679333 672 3778 3 chr6A.!!$F1 3106
8 TraesCS6B01G136900 chr7A 14822351 14827061 4710 False 1002.500000 1336 98.251500 3790 4566 2 chr7A.!!$F2 776
9 TraesCS6B01G136900 chr7A 675243344 675244191 847 False 562.000000 562 80.638000 3786 4566 1 chr7A.!!$F1 780
10 TraesCS6B01G136900 chr5B 578437882 578438390 508 False 904.000000 904 98.821000 4061 4566 1 chr5B.!!$F1 505
11 TraesCS6B01G136900 chr2A 735584640 735585232 592 True 614.000000 614 86.555000 3790 4340 1 chr2A.!!$R1 550
12 TraesCS6B01G136900 chr2A 60066636 60067419 783 False 407.500000 484 90.090000 3857 4566 2 chr2A.!!$F2 709
13 TraesCS6B01G136900 chr2B 650423624 650424249 625 False 462.000000 512 94.873500 1 600 2 chr2B.!!$F3 599
14 TraesCS6B01G136900 chr2B 74212059 74214998 2939 False 373.000000 612 90.299500 3790 4531 2 chr2B.!!$F2 741
15 TraesCS6B01G136900 chr1D 19353980 19354608 628 False 492.000000 579 96.293500 1 600 2 chr1D.!!$F1 599
16 TraesCS6B01G136900 chr7B 647740077 647740705 628 False 428.500000 496 92.517500 1 600 2 chr7B.!!$F3 599
17 TraesCS6B01G136900 chr7B 581250365 581251118 753 False 210.000000 337 94.952333 3789 4566 3 chr7B.!!$F2 777
18 TraesCS6B01G136900 chr3D 23807247 23807871 624 False 481.000000 481 81.369000 3 600 1 chr3D.!!$F1 597
19 TraesCS6B01G136900 chr4D 111039659 111041027 1368 False 329.000000 403 84.070500 1777 3131 2 chr4D.!!$F1 1354
20 TraesCS6B01G136900 chr4A 621758616 621761434 2818 True 316.500000 438 91.119000 3943 4479 2 chr4A.!!$R2 536
21 TraesCS6B01G136900 chr4B 171182147 171183147 1000 True 388.500000 398 82.603500 1777 2699 2 chr4B.!!$R1 922
22 TraesCS6B01G136900 chr4B 611700019 611700644 625 True 383.500000 412 90.214000 3 600 2 chr4B.!!$R2 597
23 TraesCS6B01G136900 chrUn 103502641 103504448 1807 True 232.666667 403 79.524667 1777 3574 3 chrUn.!!$R1 1797
24 TraesCS6B01G136900 chrUn 103534823 103535921 1098 False 223.000000 331 82.442000 1777 2694 2 chrUn.!!$F1 917

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
636 668 1.457303 GCTAGAGTGAACACACAAGCG 59.543 52.381 7.68 0.0 37.04 4.68 F
1008 1056 1.638388 CCGTGTCGTTGATGCTGCAT 61.638 55.000 16.20 16.2 0.00 3.96 F
1664 2021 0.032403 TTGTGTGCGTACGTAGGCTT 59.968 50.000 32.70 0.0 37.90 4.35 F
2750 3408 0.179108 GCTACCACCCGCTGTTCTAG 60.179 60.000 0.00 0.0 0.00 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1651 2008 0.179119 ACCATCAAGCCTACGTACGC 60.179 55.0 16.72 8.32 0.00 4.42 R
2736 3394 0.320374 TTGGACTAGAACAGCGGGTG 59.680 55.0 5.50 5.50 0.00 4.61 R
2783 3473 0.399454 AGTTGCTGGTCATGCAGACT 59.601 50.0 13.59 0.00 46.72 3.24 R
3738 4566 0.468226 GGCTGGTCGATTGTGGGATA 59.532 55.0 0.00 0.00 0.00 2.59 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
64 65 6.378280 GCAAGAATTCCTCCTTAAATTCCTCA 59.622 38.462 0.65 0.00 40.95 3.86
120 121 9.277565 CCATTTACATTTTCTATTCTTGTCACG 57.722 33.333 0.00 0.00 0.00 4.35
312 313 4.177537 TCATGGTTTCTTGAAGACCCAA 57.822 40.909 14.56 0.00 31.58 4.12
337 338 7.512992 AGAAATCTAGGGAATGGTCACTAATG 58.487 38.462 0.00 0.00 39.34 1.90
339 340 7.451731 AATCTAGGGAATGGTCACTAATGAA 57.548 36.000 0.00 0.00 39.34 2.57
340 341 6.485830 TCTAGGGAATGGTCACTAATGAAG 57.514 41.667 0.00 0.00 39.34 3.02
341 342 6.202331 TCTAGGGAATGGTCACTAATGAAGA 58.798 40.000 0.00 0.00 39.34 2.87
435 467 1.685224 CAGGAGGCTTTGTAGGGCA 59.315 57.895 0.00 0.00 0.00 5.36
479 511 7.639113 TTCAACTCTTTCTTTTGGCTTCTAA 57.361 32.000 0.00 0.00 0.00 2.10
590 622 4.216411 TGGTCCAGCCAAGTTAGATTAC 57.784 45.455 0.00 0.00 45.94 1.89
600 632 2.568979 AGTTAGATTACCAGGGGCCAA 58.431 47.619 4.39 0.00 0.00 4.52
605 637 2.091665 AGATTACCAGGGGCCAATCAAG 60.092 50.000 4.39 0.00 32.91 3.02
633 665 3.809279 CACATGCTAGAGTGAACACACAA 59.191 43.478 7.68 0.00 37.97 3.33
636 668 1.457303 GCTAGAGTGAACACACAAGCG 59.543 52.381 7.68 0.00 37.04 4.68
654 686 1.639280 CGCAAGGTTTGTGCAAAGTT 58.361 45.000 0.00 0.00 42.33 2.66
655 687 2.803451 CGCAAGGTTTGTGCAAAGTTA 58.197 42.857 0.00 0.00 42.33 2.24
670 702 4.670221 GCAAAGTTAAGACAAGGCGATCAG 60.670 45.833 0.00 0.00 0.00 2.90
1008 1056 1.638388 CCGTGTCGTTGATGCTGCAT 61.638 55.000 16.20 16.20 0.00 3.96
1084 1135 2.022195 GCGTGGATAGTAGACAGGTGA 58.978 52.381 0.00 0.00 0.00 4.02
1088 1139 3.024547 TGGATAGTAGACAGGTGAGCAC 58.975 50.000 0.00 0.00 0.00 4.40
1095 1146 6.985653 AGTAGACAGGTGAGCACATATATT 57.014 37.500 2.75 0.00 0.00 1.28
1097 1148 5.620738 AGACAGGTGAGCACATATATTGT 57.379 39.130 2.75 0.00 39.91 2.71
1098 1149 5.605534 AGACAGGTGAGCACATATATTGTC 58.394 41.667 2.75 6.32 36.00 3.18
1099 1150 4.371786 ACAGGTGAGCACATATATTGTCG 58.628 43.478 2.75 0.00 36.00 4.35
1101 1152 3.388024 AGGTGAGCACATATATTGTCGGT 59.612 43.478 2.75 0.00 36.00 4.69
1103 1154 4.211374 GGTGAGCACATATATTGTCGGTTC 59.789 45.833 2.75 0.00 36.00 3.62
1105 1156 3.390135 AGCACATATATTGTCGGTTCCG 58.610 45.455 4.74 4.74 36.00 4.30
1227 1350 4.565229 CGTTTTAAGCTGCATGTACGTAG 58.435 43.478 1.02 0.00 0.00 3.51
1229 1352 4.459390 TTTAAGCTGCATGTACGTAGGA 57.541 40.909 1.02 0.00 0.00 2.94
1230 1353 2.586258 AAGCTGCATGTACGTAGGAG 57.414 50.000 1.02 0.00 0.00 3.69
1234 1363 3.253677 AGCTGCATGTACGTAGGAGTATC 59.746 47.826 1.02 0.00 0.00 2.24
1279 1421 8.991243 ATAACTTAGATACTTACGTGTGCAAA 57.009 30.769 0.00 0.00 0.00 3.68
1424 1749 2.459644 ACACTGGCGGGTTAGTACATA 58.540 47.619 0.00 0.00 0.00 2.29
1464 1789 7.096271 TGCGTGTTAATTAATTTGTTCTTGCAG 60.096 33.333 5.91 0.00 0.00 4.41
1481 1807 5.880054 TTGCAGTTAGTTAAGCAAGATCC 57.120 39.130 0.00 0.00 41.55 3.36
1498 1824 9.587772 AGCAAGATCCGTATATATGATTTGTAC 57.412 33.333 3.36 0.00 0.00 2.90
1587 1936 3.634730 ACGTGATCGCGAATTAACTTG 57.365 42.857 33.43 2.34 41.18 3.16
1641 1998 7.329717 GTGCAAATACTAAGCTAGAATCGCTAT 59.670 37.037 0.00 0.00 36.56 2.97
1642 1999 8.520351 TGCAAATACTAAGCTAGAATCGCTATA 58.480 33.333 0.00 0.00 36.56 1.31
1651 2008 8.694975 AAGCTAGAATCGCTATATATTGTGTG 57.305 34.615 7.45 0.00 36.56 3.82
1664 2021 0.032403 TTGTGTGCGTACGTAGGCTT 59.968 50.000 32.70 0.00 37.90 4.35
1781 2138 1.199327 CTCAACGTCGACAAGAGGCTA 59.801 52.381 17.16 0.00 38.23 3.93
1934 2291 4.450122 TCGGACGACGTACAGCGC 62.450 66.667 11.47 0.00 46.11 5.92
2243 2731 1.595311 TGTTCCATGGGAGGCACTAT 58.405 50.000 13.02 0.00 41.55 2.12
2309 2797 3.264845 AAGGTCATGGGCCCCGTT 61.265 61.111 22.27 8.72 0.00 4.44
2369 2857 3.386237 GTGCTCTGGGAGGACGCT 61.386 66.667 3.68 0.00 40.77 5.07
2675 3333 2.601067 TACGCGTGGGTTCCTGGA 60.601 61.111 24.59 0.00 0.00 3.86
2730 3388 1.135112 CCGTAACACCCGGTTAGTACC 60.135 57.143 0.00 0.00 42.44 3.34
2740 3398 0.461548 GGTTAGTACCGCTACCACCC 59.538 60.000 0.00 0.00 34.01 4.61
2744 3402 3.454573 TACCGCTACCACCCGCTG 61.455 66.667 0.00 0.00 0.00 5.18
2747 3405 2.813908 CGCTACCACCCGCTGTTC 60.814 66.667 0.00 0.00 0.00 3.18
2750 3408 0.179108 GCTACCACCCGCTGTTCTAG 60.179 60.000 0.00 0.00 0.00 2.43
2751 3409 1.183549 CTACCACCCGCTGTTCTAGT 58.816 55.000 0.00 0.00 0.00 2.57
2752 3410 1.134560 CTACCACCCGCTGTTCTAGTC 59.865 57.143 0.00 0.00 0.00 2.59
2777 3467 3.634397 TTTGGTTTGGCATTTGTTCCA 57.366 38.095 0.00 0.00 0.00 3.53
2778 3468 2.906691 TGGTTTGGCATTTGTTCCAG 57.093 45.000 0.00 0.00 33.32 3.86
2780 3470 2.364970 TGGTTTGGCATTTGTTCCAGAG 59.635 45.455 0.00 0.00 33.32 3.35
2781 3471 2.407090 GTTTGGCATTTGTTCCAGAGC 58.593 47.619 0.00 0.00 33.32 4.09
2782 3472 1.999648 TTGGCATTTGTTCCAGAGCT 58.000 45.000 0.00 0.00 33.32 4.09
2783 3473 2.877097 TGGCATTTGTTCCAGAGCTA 57.123 45.000 0.00 0.00 0.00 3.32
2784 3474 2.715046 TGGCATTTGTTCCAGAGCTAG 58.285 47.619 0.00 0.00 0.00 3.42
2785 3475 2.040278 TGGCATTTGTTCCAGAGCTAGT 59.960 45.455 0.00 0.00 0.00 2.57
2786 3476 2.680339 GGCATTTGTTCCAGAGCTAGTC 59.320 50.000 0.00 0.00 0.00 2.59
2787 3477 3.604582 GCATTTGTTCCAGAGCTAGTCT 58.395 45.455 0.00 0.00 35.00 3.24
2795 3485 2.222007 CAGAGCTAGTCTGCATGACC 57.778 55.000 0.00 0.00 46.41 4.02
2796 3486 1.479730 CAGAGCTAGTCTGCATGACCA 59.520 52.381 0.00 0.02 46.41 4.02
2797 3487 1.755959 AGAGCTAGTCTGCATGACCAG 59.244 52.381 0.00 9.12 46.46 4.00
2800 3490 2.391616 CTAGTCTGCATGACCAGCAA 57.608 50.000 0.00 0.00 46.46 3.91
2801 3491 2.005451 CTAGTCTGCATGACCAGCAAC 58.995 52.381 0.00 0.00 46.46 4.17
2802 3492 0.399454 AGTCTGCATGACCAGCAACT 59.601 50.000 0.00 0.00 46.46 3.16
2803 3493 0.801251 GTCTGCATGACCAGCAACTC 59.199 55.000 0.00 0.00 42.17 3.01
2804 3494 0.689055 TCTGCATGACCAGCAACTCT 59.311 50.000 0.00 0.00 42.17 3.24
2805 3495 0.803117 CTGCATGACCAGCAACTCTG 59.197 55.000 0.00 0.00 42.17 3.35
3005 3696 4.464008 TCAACAAGCTCTTCCAGAACAAT 58.536 39.130 0.00 0.00 0.00 2.71
3138 3929 4.024893 CACATGTCACAAGGTAAGACACAC 60.025 45.833 0.00 0.00 44.15 3.82
3144 3935 2.224769 ACAAGGTAAGACACACCCATGG 60.225 50.000 4.14 4.14 36.67 3.66
3145 3936 0.991920 AGGTAAGACACACCCATGGG 59.008 55.000 30.23 30.23 36.67 4.00
3456 4270 0.946221 CGCAGTGGAGCTTCGAGTTT 60.946 55.000 0.00 0.00 35.93 2.66
3590 4404 0.461961 CCCGGCTCTTCCTAGAACAG 59.538 60.000 0.00 0.00 0.00 3.16
3594 4408 2.159310 CGGCTCTTCCTAGAACAGAGTG 60.159 54.545 12.00 4.73 37.06 3.51
3715 4543 9.844257 TTCCTTTTTCATCAAATTGTTAATGGT 57.156 25.926 0.00 0.00 0.00 3.55
3730 4558 0.895100 ATGGTTGCCATTGTGCGACT 60.895 50.000 13.70 0.00 42.23 4.18
3738 4566 1.167851 CATTGTGCGACTGTCCCATT 58.832 50.000 1.55 0.00 0.00 3.16
3740 4568 2.779755 TTGTGCGACTGTCCCATTAT 57.220 45.000 1.55 0.00 0.00 1.28
3782 4610 1.593196 TGCACACAGCTAAGGTCAAC 58.407 50.000 0.00 0.00 45.94 3.18
3787 4615 2.037772 ACACAGCTAAGGTCAACTCCAG 59.962 50.000 0.00 0.00 0.00 3.86
4019 8810 6.093771 AGTATCGACTGAGACATAACGAAGTT 59.906 38.462 0.00 0.00 45.94 2.66
4092 8886 2.341846 ATCAACCGTTGACCAACTGT 57.658 45.000 16.15 7.57 43.48 3.55
4566 13983 0.818938 TAACATAGCTCCGCCGTTGA 59.181 50.000 0.00 0.00 0.00 3.18
4567 13984 0.739813 AACATAGCTCCGCCGTTGAC 60.740 55.000 0.00 0.00 0.00 3.18
4568 13985 1.141881 CATAGCTCCGCCGTTGACT 59.858 57.895 0.00 0.00 0.00 3.41
4569 13986 0.872021 CATAGCTCCGCCGTTGACTC 60.872 60.000 0.00 0.00 0.00 3.36
4570 13987 2.017559 ATAGCTCCGCCGTTGACTCC 62.018 60.000 0.00 0.00 0.00 3.85
4571 13988 4.373116 GCTCCGCCGTTGACTCCA 62.373 66.667 0.00 0.00 0.00 3.86
4572 13989 2.125912 CTCCGCCGTTGACTCCAG 60.126 66.667 0.00 0.00 0.00 3.86
4573 13990 2.915659 TCCGCCGTTGACTCCAGT 60.916 61.111 0.00 0.00 0.00 4.00
4574 13991 2.738521 CCGCCGTTGACTCCAGTG 60.739 66.667 0.00 0.00 0.00 3.66
4575 13992 3.414700 CGCCGTTGACTCCAGTGC 61.415 66.667 0.00 0.00 0.00 4.40
4576 13993 3.050275 GCCGTTGACTCCAGTGCC 61.050 66.667 0.00 0.00 0.00 5.01
4577 13994 2.738521 CCGTTGACTCCAGTGCCG 60.739 66.667 0.00 0.00 0.00 5.69
4578 13995 3.414700 CGTTGACTCCAGTGCCGC 61.415 66.667 0.00 0.00 0.00 6.53
4579 13996 3.414700 GTTGACTCCAGTGCCGCG 61.415 66.667 0.00 0.00 0.00 6.46
4585 14002 4.695993 TCCAGTGCCGCGCATCAA 62.696 61.111 8.75 0.00 41.91 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 121 7.201652 GCAAGTACATTCTCCAAGTTATCCTTC 60.202 40.741 0.00 0.00 0.00 3.46
312 313 7.348274 TCATTAGTGACCATTCCCTAGATTTCT 59.652 37.037 0.00 0.00 0.00 2.52
337 338 2.190488 CTGCAGAGGGGTGGGTCTTC 62.190 65.000 8.42 0.00 0.00 2.87
339 340 2.608988 CTGCAGAGGGGTGGGTCT 60.609 66.667 8.42 0.00 0.00 3.85
340 341 2.470938 GAACTGCAGAGGGGTGGGTC 62.471 65.000 23.35 0.00 0.00 4.46
341 342 2.450502 AACTGCAGAGGGGTGGGT 60.451 61.111 23.35 0.00 0.00 4.51
435 467 6.126863 TGAATTCTGAGGTGTTGATAGGTT 57.873 37.500 7.05 0.00 0.00 3.50
479 511 4.530161 AGTCAAGCTTTCTAGACCTGTGAT 59.470 41.667 10.20 0.00 0.00 3.06
590 622 2.761213 GCCTTGATTGGCCCCTGG 60.761 66.667 0.00 0.00 46.82 4.45
600 632 3.612251 GCATGTGCTGGCCTTGAT 58.388 55.556 3.32 0.00 38.21 2.57
633 665 0.528249 CTTTGCACAAACCTTGCGCT 60.528 50.000 9.73 0.00 43.34 5.92
636 668 4.267690 GTCTTAACTTTGCACAAACCTTGC 59.732 41.667 0.00 0.00 40.63 4.01
654 686 1.195115 AGCCTGATCGCCTTGTCTTA 58.805 50.000 0.00 0.00 0.00 2.10
655 687 0.326264 AAGCCTGATCGCCTTGTCTT 59.674 50.000 0.00 0.00 0.00 3.01
670 702 5.007136 CGGATCTCTGTTCTTTAATGAAGCC 59.993 44.000 4.14 0.00 35.24 4.35
673 705 5.805486 CGTCGGATCTCTGTTCTTTAATGAA 59.195 40.000 0.00 0.00 0.00 2.57
799 833 1.261938 TATGTGGTGCTACGGCCTGT 61.262 55.000 0.00 2.95 37.74 4.00
935 978 2.494059 CCATCGTGAGGTGTCAAAGTT 58.506 47.619 0.00 0.00 41.83 2.66
936 979 1.878102 GCCATCGTGAGGTGTCAAAGT 60.878 52.381 0.00 0.00 41.83 2.66
938 981 0.107643 TGCCATCGTGAGGTGTCAAA 59.892 50.000 0.00 0.00 41.83 2.69
1084 1135 3.069016 TCGGAACCGACAATATATGTGCT 59.931 43.478 12.04 0.00 44.12 4.40
1098 1149 1.443872 CTGTCGGAAGTCGGAACCG 60.444 63.158 6.94 6.94 46.71 4.44
1099 1150 1.737008 GCTGTCGGAAGTCGGAACC 60.737 63.158 0.00 0.00 39.77 3.62
1101 1152 0.809385 CTAGCTGTCGGAAGTCGGAA 59.191 55.000 0.00 0.00 39.77 4.30
1103 1154 1.226717 GCTAGCTGTCGGAAGTCGG 60.227 63.158 7.70 0.00 39.77 4.79
1105 1156 3.337398 CAGCTAGCTGTCGGAAGTC 57.663 57.895 32.46 0.00 39.10 3.01
1229 1352 6.462500 ACGTACGGAGTCATATGTAGATACT 58.538 40.000 21.06 0.00 43.93 2.12
1230 1353 6.718454 ACGTACGGAGTCATATGTAGATAC 57.282 41.667 21.06 0.00 43.93 2.24
1234 1363 8.249327 AGTTATACGTACGGAGTCATATGTAG 57.751 38.462 21.06 0.00 43.93 2.74
1279 1421 1.980232 CACCACCACCTGCATGCAT 60.980 57.895 22.97 3.95 0.00 3.96
1373 1515 2.343758 GGAGTGCAGCAGGTTCGA 59.656 61.111 0.00 0.00 0.00 3.71
1498 1824 4.339247 CCATATCCCAGTACCTGCAAAAAG 59.661 45.833 0.00 0.00 0.00 2.27
1587 1936 8.929746 TCATATATTTCTCAAGACAATGCGATC 58.070 33.333 0.00 0.00 0.00 3.69
1641 1998 3.316029 AGCCTACGTACGCACACAATATA 59.684 43.478 16.72 0.00 0.00 0.86
1642 1999 2.100252 AGCCTACGTACGCACACAATAT 59.900 45.455 16.72 0.00 0.00 1.28
1651 2008 0.179119 ACCATCAAGCCTACGTACGC 60.179 55.000 16.72 8.32 0.00 4.42
1664 2021 0.613260 CCCTGAACTCCGAACCATCA 59.387 55.000 0.00 0.00 0.00 3.07
2024 2381 1.427072 CCACCTCCCCCTTGAACTGT 61.427 60.000 0.00 0.00 0.00 3.55
2243 2731 0.462375 CCACAATGTCGTCCCCGATA 59.538 55.000 0.00 0.00 46.30 2.92
2309 2797 5.106791 CGAGTTAGAGTTGAGGTAGACGAAA 60.107 44.000 0.00 0.00 0.00 3.46
2353 2841 1.304962 TTAGCGTCCTCCCAGAGCA 60.305 57.895 0.00 0.00 0.00 4.26
2606 3264 1.588082 GGTGAACTCGCCGGAAGTA 59.412 57.895 5.05 0.00 36.72 2.24
2675 3333 3.187700 GTTCATGTAATCGCCGAGAACT 58.812 45.455 7.23 0.00 33.16 3.01
2730 3388 1.940883 TAGAACAGCGGGTGGTAGCG 61.941 60.000 12.33 0.00 38.61 4.26
2735 3393 1.218316 GGACTAGAACAGCGGGTGG 59.782 63.158 12.33 0.00 0.00 4.61
2736 3394 0.320374 TTGGACTAGAACAGCGGGTG 59.680 55.000 5.50 5.50 0.00 4.61
2737 3395 1.053424 TTTGGACTAGAACAGCGGGT 58.947 50.000 0.00 0.00 0.00 5.28
2738 3396 2.403252 ATTTGGACTAGAACAGCGGG 57.597 50.000 0.00 0.00 0.00 6.13
2761 3426 2.036346 AGCTCTGGAACAAATGCCAAAC 59.964 45.455 0.00 0.00 38.70 2.93
2771 3461 1.632589 TGCAGACTAGCTCTGGAACA 58.367 50.000 18.15 9.27 43.91 3.18
2775 3465 1.202510 GGTCATGCAGACTAGCTCTGG 60.203 57.143 18.15 7.25 46.08 3.86
2777 3467 1.755959 CTGGTCATGCAGACTAGCTCT 59.244 52.381 13.66 0.00 46.76 4.09
2778 3468 2.222007 CTGGTCATGCAGACTAGCTC 57.778 55.000 13.66 1.66 46.76 4.09
2782 3472 1.625315 AGTTGCTGGTCATGCAGACTA 59.375 47.619 13.59 8.55 46.72 2.59
2783 3473 0.399454 AGTTGCTGGTCATGCAGACT 59.601 50.000 13.59 0.00 46.72 3.24
2784 3474 0.801251 GAGTTGCTGGTCATGCAGAC 59.199 55.000 4.68 7.52 46.83 3.51
2785 3475 0.689055 AGAGTTGCTGGTCATGCAGA 59.311 50.000 4.68 0.00 41.71 4.26
2786 3476 0.803117 CAGAGTTGCTGGTCATGCAG 59.197 55.000 0.00 0.00 41.71 4.41
2787 3477 2.936928 CAGAGTTGCTGGTCATGCA 58.063 52.632 0.00 0.00 41.07 3.96
2795 3485 2.550830 AACAGTACCCAGAGTTGCTG 57.449 50.000 0.00 0.00 44.49 4.41
2796 3486 3.214328 CAAAACAGTACCCAGAGTTGCT 58.786 45.455 0.00 0.00 0.00 3.91
2797 3487 2.287608 GCAAAACAGTACCCAGAGTTGC 60.288 50.000 0.00 0.00 34.05 4.17
2798 3488 3.003689 CAGCAAAACAGTACCCAGAGTTG 59.996 47.826 0.00 0.00 0.00 3.16
2799 3489 3.118038 TCAGCAAAACAGTACCCAGAGTT 60.118 43.478 0.00 0.00 0.00 3.01
2800 3490 2.438021 TCAGCAAAACAGTACCCAGAGT 59.562 45.455 0.00 0.00 0.00 3.24
2801 3491 2.808543 GTCAGCAAAACAGTACCCAGAG 59.191 50.000 0.00 0.00 0.00 3.35
2802 3492 2.805295 CGTCAGCAAAACAGTACCCAGA 60.805 50.000 0.00 0.00 0.00 3.86
2803 3493 1.531149 CGTCAGCAAAACAGTACCCAG 59.469 52.381 0.00 0.00 0.00 4.45
2804 3494 1.588674 CGTCAGCAAAACAGTACCCA 58.411 50.000 0.00 0.00 0.00 4.51
2805 3495 0.872388 CCGTCAGCAAAACAGTACCC 59.128 55.000 0.00 0.00 0.00 3.69
2806 3496 1.529865 GACCGTCAGCAAAACAGTACC 59.470 52.381 0.00 0.00 0.00 3.34
3005 3696 0.885879 CGTACTGCCTGTACCTGTCA 59.114 55.000 6.34 0.00 46.49 3.58
3144 3935 1.988956 TGGAAATGCACCCATGGCC 60.989 57.895 6.09 0.00 0.00 5.36
3145 3936 1.218854 GTGGAAATGCACCCATGGC 59.781 57.895 6.09 0.00 34.58 4.40
3186 3985 2.161808 CAGATCAACGTCGGTCAGTACT 59.838 50.000 0.00 0.00 0.00 2.73
3715 4543 1.514678 GGACAGTCGCACAATGGCAA 61.515 55.000 0.00 0.00 0.00 4.52
3738 4566 0.468226 GGCTGGTCGATTGTGGGATA 59.532 55.000 0.00 0.00 0.00 2.59
3740 4568 0.616395 TAGGCTGGTCGATTGTGGGA 60.616 55.000 0.00 0.00 0.00 4.37
3782 4610 2.575993 CTCCGCCACTGACTGGAG 59.424 66.667 0.00 0.00 43.95 3.86
3787 4615 1.139947 GTCTAGCTCCGCCACTGAC 59.860 63.158 0.00 0.00 0.00 3.51
4019 8810 5.611796 TTACTAAGTCTGCGTCGACTAAA 57.388 39.130 14.70 0.00 43.14 1.85
4568 13985 4.695993 TTGATGCGCGGCACTGGA 62.696 61.111 8.83 0.00 43.04 3.86


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

AutoCloner maintained by Alex Coulton.