Multiple sequence alignment - TraesCS1D01G093200

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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 TraesCS1D01G093200 chr1D 100.000 3047 0 0 1 3047 79114805 79117851 0.000000e+00 5627.0
1 TraesCS1D01G093200 chr1D 77.326 1032 220 13 1046 2071 451941122 451940099 5.620000e-167 597.0
2 TraesCS1D01G093200 chr1A 94.088 1607 80 7 811 2406 97792611 97794213 0.000000e+00 2427.0
3 TraesCS1D01G093200 chr1A 95.518 647 22 5 2403 3047 251337306 251337947 0.000000e+00 1027.0
4 TraesCS1D01G093200 chr1A 90.231 389 25 6 1 389 97789103 97789478 2.110000e-136 496.0
5 TraesCS1D01G093200 chr1B 91.917 1695 83 20 742 2406 130009872 130011542 0.000000e+00 2322.0
6 TraesCS1D01G093200 chr1B 76.612 1039 224 17 1017 2047 621947455 621946428 3.430000e-154 555.0
7 TraesCS1D01G093200 chr1B 83.333 264 24 13 467 713 130007754 130008014 3.060000e-55 226.0
8 TraesCS1D01G093200 chr5B 98.134 643 12 0 2405 3047 656908591 656907949 0.000000e+00 1122.0
9 TraesCS1D01G093200 chr5B 77.838 555 102 16 1505 2049 47127558 47127015 1.050000e-84 324.0
10 TraesCS1D01G093200 chr3A 97.984 645 9 2 2406 3047 170979899 170979256 0.000000e+00 1116.0
11 TraesCS1D01G093200 chr3A 75.973 591 122 17 1469 2046 12117721 12117138 1.380000e-73 287.0
12 TraesCS1D01G093200 chr3A 75.290 603 114 27 1469 2046 11921132 11921724 3.900000e-64 255.0
13 TraesCS1D01G093200 chr3A 87.611 113 14 0 102 214 613377654 613377766 6.850000e-27 132.0
14 TraesCS1D01G093200 chr3D 97.546 652 15 1 2397 3047 338919704 338920355 0.000000e+00 1114.0
15 TraesCS1D01G093200 chr3D 81.188 101 15 2 225 321 401172228 401172328 9.060000e-11 78.7
16 TraesCS1D01G093200 chr7B 97.196 642 18 0 2406 3047 727910686 727910045 0.000000e+00 1086.0
17 TraesCS1D01G093200 chr7B 82.482 137 20 4 374 506 303164644 303164508 1.920000e-22 117.0
18 TraesCS1D01G093200 chr7B 90.244 82 8 0 132 213 407944766 407944685 1.160000e-19 108.0
19 TraesCS1D01G093200 chr7B 85.185 81 3 8 485 556 78323059 78323139 1.170000e-09 75.0
20 TraesCS1D01G093200 chr7B 88.889 45 3 2 521 564 711450345 711450388 2.000000e-03 54.7
21 TraesCS1D01G093200 chr5A 95.963 644 19 5 2406 3047 299776897 299777535 0.000000e+00 1038.0
22 TraesCS1D01G093200 chr5D 95.659 645 21 5 2405 3047 549893036 549893675 0.000000e+00 1029.0
23 TraesCS1D01G093200 chr5D 85.841 113 16 0 102 214 518030184 518030072 1.480000e-23 121.0
24 TraesCS1D01G093200 chr7A 95.497 644 21 6 2406 3047 600552789 600552152 0.000000e+00 1022.0
25 TraesCS1D01G093200 chr7A 95.370 648 18 8 2402 3047 491827682 491828319 0.000000e+00 1020.0
26 TraesCS1D01G093200 chr7A 75.547 548 112 10 1454 1996 10831308 10831838 1.810000e-62 250.0
27 TraesCS1D01G093200 chr7A 75.322 543 110 11 1460 1996 10380944 10381468 3.930000e-59 239.0
28 TraesCS1D01G093200 chr7A 94.595 37 1 1 521 556 66718354 66718390 4.240000e-04 56.5
29 TraesCS1D01G093200 chr4A 76.103 544 110 10 1460 1999 726576664 726576137 1.800000e-67 267.0
30 TraesCS1D01G093200 chr7D 75.547 548 110 11 1460 2001 11261491 11262020 6.520000e-62 248.0
31 TraesCS1D01G093200 chr7D 94.286 35 1 1 523 556 181973443 181973477 5.000000e-03 52.8
32 TraesCS1D01G093200 chr2D 75.502 498 117 5 1503 1999 469226591 469226098 3.930000e-59 239.0
33 TraesCS1D01G093200 chr2D 84.091 132 21 0 1036 1167 621589990 621589859 8.870000e-26 128.0
34 TraesCS1D01G093200 chr2D 84.874 119 18 0 213 331 85926191 85926309 1.480000e-23 121.0
35 TraesCS1D01G093200 chr2D 77.419 124 12 11 459 566 486488483 486488606 3.280000e-05 60.2
36 TraesCS1D01G093200 chr4B 88.496 113 13 0 104 216 139764457 139764345 1.470000e-28 137.0
37 TraesCS1D01G093200 chr2B 81.022 137 21 4 374 506 21919071 21918936 1.490000e-18 104.0
38 TraesCS1D01G093200 chr2A 84.615 104 15 1 220 323 720553253 720553355 5.370000e-18 102.0
39 TraesCS1D01G093200 chr6B 91.837 49 2 2 522 568 686545254 686545206 1.960000e-07 67.6
40 TraesCS1D01G093200 chr4D 89.362 47 4 1 521 566 313885375 313885329 1.180000e-04 58.4
41 TraesCS1D01G093200 chr3B 94.595 37 0 1 521 555 77066788 77066824 4.240000e-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 TraesCS1D01G093200 chr1D 79114805 79117851 3046 False 5627.0 5627 100.0000 1 3047 1 chr1D.!!$F1 3046
1 TraesCS1D01G093200 chr1D 451940099 451941122 1023 True 597.0 597 77.3260 1046 2071 1 chr1D.!!$R1 1025
2 TraesCS1D01G093200 chr1A 97789103 97794213 5110 False 1461.5 2427 92.1595 1 2406 2 chr1A.!!$F2 2405
3 TraesCS1D01G093200 chr1A 251337306 251337947 641 False 1027.0 1027 95.5180 2403 3047 1 chr1A.!!$F1 644
4 TraesCS1D01G093200 chr1B 130007754 130011542 3788 False 1274.0 2322 87.6250 467 2406 2 chr1B.!!$F1 1939
5 TraesCS1D01G093200 chr1B 621946428 621947455 1027 True 555.0 555 76.6120 1017 2047 1 chr1B.!!$R1 1030
6 TraesCS1D01G093200 chr5B 656907949 656908591 642 True 1122.0 1122 98.1340 2405 3047 1 chr5B.!!$R2 642
7 TraesCS1D01G093200 chr5B 47127015 47127558 543 True 324.0 324 77.8380 1505 2049 1 chr5B.!!$R1 544
8 TraesCS1D01G093200 chr3A 170979256 170979899 643 True 1116.0 1116 97.9840 2406 3047 1 chr3A.!!$R2 641
9 TraesCS1D01G093200 chr3A 12117138 12117721 583 True 287.0 287 75.9730 1469 2046 1 chr3A.!!$R1 577
10 TraesCS1D01G093200 chr3A 11921132 11921724 592 False 255.0 255 75.2900 1469 2046 1 chr3A.!!$F1 577
11 TraesCS1D01G093200 chr3D 338919704 338920355 651 False 1114.0 1114 97.5460 2397 3047 1 chr3D.!!$F1 650
12 TraesCS1D01G093200 chr7B 727910045 727910686 641 True 1086.0 1086 97.1960 2406 3047 1 chr7B.!!$R3 641
13 TraesCS1D01G093200 chr5A 299776897 299777535 638 False 1038.0 1038 95.9630 2406 3047 1 chr5A.!!$F1 641
14 TraesCS1D01G093200 chr5D 549893036 549893675 639 False 1029.0 1029 95.6590 2405 3047 1 chr5D.!!$F1 642
15 TraesCS1D01G093200 chr7A 600552152 600552789 637 True 1022.0 1022 95.4970 2406 3047 1 chr7A.!!$R1 641
16 TraesCS1D01G093200 chr7A 491827682 491828319 637 False 1020.0 1020 95.3700 2402 3047 1 chr7A.!!$F4 645
17 TraesCS1D01G093200 chr7A 10831308 10831838 530 False 250.0 250 75.5470 1454 1996 1 chr7A.!!$F2 542
18 TraesCS1D01G093200 chr7A 10380944 10381468 524 False 239.0 239 75.3220 1460 1996 1 chr7A.!!$F1 536
19 TraesCS1D01G093200 chr4A 726576137 726576664 527 True 267.0 267 76.1030 1460 1999 1 chr4A.!!$R1 539
20 TraesCS1D01G093200 chr7D 11261491 11262020 529 False 248.0 248 75.5470 1460 2001 1 chr7D.!!$F1 541

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
850 4640 0.32005 GCGAGATTCATCCTCCTCCC 59.68 60.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2729 6579 1.270571 TGAAGTGCAATGTCTACGCCA 60.271 47.619 0.0 0.0 0.0 5.69 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
31 32 1.561542 ACTTTTGGGCGAGATGAGGAT 59.438 47.619 0.00 0.00 0.00 3.24
47 48 1.702957 AGGATTCGGGGAACAAGAACA 59.297 47.619 0.00 0.00 32.65 3.18
82 83 1.526575 CGGGCATTGTGGGCATATCC 61.527 60.000 0.00 0.00 34.52 2.59
124 125 6.440010 TCAGGGGCAAATCATCAAAAATCTAA 59.560 34.615 0.00 0.00 0.00 2.10
127 128 8.162746 AGGGGCAAATCATCAAAAATCTAAAAA 58.837 29.630 0.00 0.00 0.00 1.94
153 154 6.258727 AGGTGTAGCAAATAATCGATGACAAG 59.741 38.462 0.00 0.00 0.00 3.16
155 156 7.201609 GGTGTAGCAAATAATCGATGACAAGAA 60.202 37.037 0.00 0.00 0.00 2.52
157 158 8.726068 TGTAGCAAATAATCGATGACAAGAAAA 58.274 29.630 0.00 0.00 0.00 2.29
158 159 9.554724 GTAGCAAATAATCGATGACAAGAAAAA 57.445 29.630 0.00 0.00 0.00 1.94
217 218 3.334910 AATCCTCAAATTCCCCATCCC 57.665 47.619 0.00 0.00 0.00 3.85
279 280 9.653287 GGTTTTTGGAGGATTAAAATTCTTAGG 57.347 33.333 0.00 0.00 0.00 2.69
309 310 8.786826 TTTTCTACGTTGATCCTTTGATATGT 57.213 30.769 0.00 0.00 0.00 2.29
310 311 9.878667 TTTTCTACGTTGATCCTTTGATATGTA 57.121 29.630 0.00 0.00 0.00 2.29
311 312 9.529325 TTTCTACGTTGATCCTTTGATATGTAG 57.471 33.333 0.00 0.00 33.81 2.74
312 313 7.658261 TCTACGTTGATCCTTTGATATGTAGG 58.342 38.462 0.00 0.00 33.57 3.18
313 314 6.479972 ACGTTGATCCTTTGATATGTAGGA 57.520 37.500 0.00 0.00 41.99 2.94
348 349 4.137543 GGAAATCTGTCACCACTCAAACT 58.862 43.478 0.00 0.00 0.00 2.66
353 354 5.560966 TCTGTCACCACTCAAACTTTTTC 57.439 39.130 0.00 0.00 0.00 2.29
354 355 4.398044 TCTGTCACCACTCAAACTTTTTCC 59.602 41.667 0.00 0.00 0.00 3.13
356 357 4.770010 TGTCACCACTCAAACTTTTTCCTT 59.230 37.500 0.00 0.00 0.00 3.36
358 359 6.163476 GTCACCACTCAAACTTTTTCCTTTT 58.837 36.000 0.00 0.00 0.00 2.27
361 362 7.815549 TCACCACTCAAACTTTTTCCTTTTTAC 59.184 33.333 0.00 0.00 0.00 2.01
383 384 6.731292 ACAATTCTTTTGCTTTTAGACCCT 57.269 33.333 0.00 0.00 0.00 4.34
384 385 6.515832 ACAATTCTTTTGCTTTTAGACCCTG 58.484 36.000 0.00 0.00 0.00 4.45
385 386 6.323739 ACAATTCTTTTGCTTTTAGACCCTGA 59.676 34.615 0.00 0.00 0.00 3.86
386 387 7.015584 ACAATTCTTTTGCTTTTAGACCCTGAT 59.984 33.333 0.00 0.00 0.00 2.90
388 389 8.650143 ATTCTTTTGCTTTTAGACCCTGATAA 57.350 30.769 0.00 0.00 0.00 1.75
389 390 8.472007 TTCTTTTGCTTTTAGACCCTGATAAA 57.528 30.769 0.00 0.00 0.00 1.40
390 391 8.650143 TCTTTTGCTTTTAGACCCTGATAAAT 57.350 30.769 0.00 0.00 0.00 1.40
391 392 8.522830 TCTTTTGCTTTTAGACCCTGATAAATG 58.477 33.333 0.00 0.00 0.00 2.32
393 394 4.644685 TGCTTTTAGACCCTGATAAATGCC 59.355 41.667 10.93 0.00 39.46 4.40
394 395 4.644685 GCTTTTAGACCCTGATAAATGCCA 59.355 41.667 0.00 0.00 36.66 4.92
395 396 5.450550 GCTTTTAGACCCTGATAAATGCCAC 60.451 44.000 0.00 0.00 36.66 5.01
396 397 4.853468 TTAGACCCTGATAAATGCCACA 57.147 40.909 0.00 0.00 0.00 4.17
397 398 3.004752 AGACCCTGATAAATGCCACAC 57.995 47.619 0.00 0.00 0.00 3.82
399 400 1.004277 ACCCTGATAAATGCCACACGT 59.996 47.619 0.00 0.00 0.00 4.49
400 401 1.401552 CCCTGATAAATGCCACACGTG 59.598 52.381 15.48 15.48 0.00 4.49
401 402 2.083774 CCTGATAAATGCCACACGTGT 58.916 47.619 17.22 17.22 0.00 4.49
402 403 2.159531 CCTGATAAATGCCACACGTGTG 60.160 50.000 36.13 36.13 45.23 3.82
416 417 6.156932 CACACGTGTGGCATGAATATATAG 57.843 41.667 35.65 8.80 42.10 1.31
417 418 4.690748 ACACGTGTGGCATGAATATATAGC 59.309 41.667 22.71 0.00 34.19 2.97
418 419 4.690280 CACGTGTGGCATGAATATATAGCA 59.310 41.667 7.58 0.00 0.00 3.49
419 420 5.179182 CACGTGTGGCATGAATATATAGCAA 59.821 40.000 7.58 0.00 0.00 3.91
420 421 5.179368 ACGTGTGGCATGAATATATAGCAAC 59.821 40.000 0.00 0.00 0.00 4.17
421 422 5.409520 CGTGTGGCATGAATATATAGCAACT 59.590 40.000 0.00 0.00 30.59 3.16
422 423 6.401474 CGTGTGGCATGAATATATAGCAACTC 60.401 42.308 0.00 0.00 30.59 3.01
423 424 5.939883 TGTGGCATGAATATATAGCAACTCC 59.060 40.000 0.00 4.21 30.59 3.85
424 425 5.063944 GTGGCATGAATATATAGCAACTCCG 59.936 44.000 0.00 0.00 0.00 4.63
425 426 5.046663 TGGCATGAATATATAGCAACTCCGA 60.047 40.000 0.00 0.00 0.00 4.55
426 427 6.051717 GGCATGAATATATAGCAACTCCGAT 58.948 40.000 0.00 0.00 0.00 4.18
427 428 6.540189 GGCATGAATATATAGCAACTCCGATT 59.460 38.462 0.00 0.00 0.00 3.34
428 429 7.710907 GGCATGAATATATAGCAACTCCGATTA 59.289 37.037 0.00 0.00 0.00 1.75
454 455 5.783100 TTTATGGGAAGTTTAGTAACGCG 57.217 39.130 3.53 3.53 39.31 6.01
456 457 2.676076 TGGGAAGTTTAGTAACGCGAC 58.324 47.619 15.93 0.00 39.31 5.19
461 462 3.476295 AGTTTAGTAACGCGACGATGA 57.524 42.857 15.93 0.00 39.31 2.92
469 470 0.782384 ACGCGACGATGACAACTTTC 59.218 50.000 15.93 0.00 0.00 2.62
470 471 1.060713 CGCGACGATGACAACTTTCT 58.939 50.000 0.00 0.00 0.00 2.52
473 474 3.603857 CGCGACGATGACAACTTTCTTTT 60.604 43.478 0.00 0.00 0.00 2.27
474 475 3.900703 GCGACGATGACAACTTTCTTTTC 59.099 43.478 0.00 0.00 0.00 2.29
475 476 4.134546 CGACGATGACAACTTTCTTTTCG 58.865 43.478 0.00 0.00 0.00 3.46
476 477 4.455124 GACGATGACAACTTTCTTTTCGG 58.545 43.478 0.00 0.00 0.00 4.30
478 479 4.755123 ACGATGACAACTTTCTTTTCGGAT 59.245 37.500 0.00 0.00 0.00 4.18
479 480 5.082059 CGATGACAACTTTCTTTTCGGATG 58.918 41.667 0.00 0.00 0.00 3.51
480 481 4.829064 TGACAACTTTCTTTTCGGATGG 57.171 40.909 0.00 0.00 0.00 3.51
481 482 3.004315 TGACAACTTTCTTTTCGGATGGC 59.996 43.478 0.00 0.00 0.00 4.40
482 483 2.955660 ACAACTTTCTTTTCGGATGGCA 59.044 40.909 0.00 0.00 0.00 4.92
487 535 5.610398 ACTTTCTTTTCGGATGGCAATTTT 58.390 33.333 0.00 0.00 0.00 1.82
511 559 6.668541 TTTTCGAATGGCAATTTTTGTTGA 57.331 29.167 0.00 0.00 0.00 3.18
517 565 8.279103 TCGAATGGCAATTTTTGTTGAAAATAC 58.721 29.630 0.00 0.00 44.98 1.89
520 568 6.709643 TGGCAATTTTTGTTGAAAATACGTG 58.290 32.000 0.00 0.00 44.98 4.49
522 570 7.062848 GGCAATTTTTGTTGAAAATACGTGAG 58.937 34.615 0.00 0.00 44.98 3.51
523 571 7.254286 GGCAATTTTTGTTGAAAATACGTGAGT 60.254 33.333 0.00 0.00 44.98 3.41
560 617 8.227119 CACGTGTGACACTTATCATTTGAATTA 58.773 33.333 14.42 0.00 31.34 1.40
582 639 9.814899 AATTATTTTTCTGACACATCAAACACA 57.185 25.926 0.00 0.00 33.30 3.72
586 644 9.814899 ATTTTTCTGACACATCAAACACATTTA 57.185 25.926 0.00 0.00 33.30 1.40
630 688 9.950496 AATGGATATGTCACTTCAATCCTATAC 57.050 33.333 0.00 0.00 37.57 1.47
660 722 7.186570 TCTATTCATGTGTTCTGAGAATCCA 57.813 36.000 0.00 0.00 31.89 3.41
664 726 3.744238 TGTGTTCTGAGAATCCAACGA 57.256 42.857 0.00 0.00 31.43 3.85
674 736 3.574614 AGAATCCAACGAATTTTTGGCG 58.425 40.909 12.80 0.00 42.96 5.69
689 999 2.121538 GGCGGAGAAAATGGAGGCC 61.122 63.158 0.00 0.00 0.00 5.19
694 1004 1.657751 GAGAAAATGGAGGCCGCCAC 61.658 60.000 32.15 18.02 41.56 5.01
729 1097 4.595986 TGACCTTAACCCCAAATCTAAGC 58.404 43.478 0.00 0.00 0.00 3.09
730 1098 4.043561 TGACCTTAACCCCAAATCTAAGCA 59.956 41.667 0.00 0.00 0.00 3.91
731 1099 5.201243 GACCTTAACCCCAAATCTAAGCAT 58.799 41.667 0.00 0.00 0.00 3.79
732 1100 5.589831 ACCTTAACCCCAAATCTAAGCATT 58.410 37.500 0.00 0.00 0.00 3.56
734 1102 6.070824 ACCTTAACCCCAAATCTAAGCATTTG 60.071 38.462 1.26 1.26 41.59 2.32
735 1103 6.154363 CCTTAACCCCAAATCTAAGCATTTGA 59.846 38.462 8.40 0.00 43.70 2.69
738 1106 4.026052 CCCCAAATCTAAGCATTTGACCT 58.974 43.478 8.40 0.00 43.70 3.85
739 1107 4.098501 CCCCAAATCTAAGCATTTGACCTC 59.901 45.833 8.40 0.00 43.70 3.85
740 1108 4.201950 CCCAAATCTAAGCATTTGACCTCG 60.202 45.833 8.40 0.00 43.70 4.63
850 4640 0.320050 GCGAGATTCATCCTCCTCCC 59.680 60.000 0.00 0.00 0.00 4.30
903 4701 1.348775 AATCCCCTACTGGCCTGCTC 61.349 60.000 9.95 0.00 0.00 4.26
969 4767 0.948678 GCCGCCGCCATTAATTTCTA 59.051 50.000 0.00 0.00 0.00 2.10
1219 5017 2.074547 TTTCCTCGACCTTGTTAGCG 57.925 50.000 0.00 0.00 0.00 4.26
1232 5030 2.707849 TTAGCGAGGACACCGAGGC 61.708 63.158 0.00 0.00 0.00 4.70
1264 5062 1.802337 CGAGGTCAGGTTGGTCGACA 61.802 60.000 18.91 0.27 32.32 4.35
1325 5123 1.126113 GACGCCGTATGTGTTCAACAG 59.874 52.381 0.00 0.00 43.64 3.16
1331 5129 3.491356 CGTATGTGTTCAACAGCAATGG 58.509 45.455 0.00 0.00 43.64 3.16
1334 5132 1.333308 TGTGTTCAACAGCAATGGACG 59.667 47.619 0.00 0.00 33.78 4.79
1340 5138 2.002586 CAACAGCAATGGACGTAGGAG 58.997 52.381 0.00 0.00 0.00 3.69
1344 5142 0.530870 GCAATGGACGTAGGAGCTCC 60.531 60.000 26.22 26.22 0.00 4.70
1424 5222 1.723542 GTGCGATGTCACAGTTCTGAG 59.276 52.381 6.83 0.00 36.97 3.35
1908 5721 0.034616 ACTGCAGCAACCTCAGAGAC 59.965 55.000 15.27 0.00 0.00 3.36
1933 5746 5.643777 GCTTGCCTTGAGTTTATCACTTCTA 59.356 40.000 0.00 0.00 37.77 2.10
2014 5827 5.221722 TGCCCTTCTATTGTCATAGATGTCC 60.222 44.000 0.00 0.00 40.97 4.02
2021 5834 8.007405 TCTATTGTCATAGATGTCCTCGAAAA 57.993 34.615 0.00 0.00 37.13 2.29
2058 5871 5.391097 CCGCAAAATTTAGTACGTTCATCCA 60.391 40.000 0.00 0.00 0.00 3.41
2145 5960 5.175859 TGGCTTCTCAGTTATTAGTTTCCG 58.824 41.667 0.00 0.00 0.00 4.30
2217 6062 7.185565 AGGCTCCTCTTGCTATATCTTGTATA 58.814 38.462 0.00 0.00 0.00 1.47
2235 6080 7.538678 TCTTGTATATGATGACGATTGACGATG 59.461 37.037 0.00 0.00 45.77 3.84
2236 6081 6.908825 TGTATATGATGACGATTGACGATGA 58.091 36.000 0.00 0.00 45.77 2.92
2290 6135 2.151202 GTTCTCGAAAATGCCCTGACA 58.849 47.619 0.00 0.00 0.00 3.58
2366 6211 8.829612 CCTTAATTTCTCAATGCTGTTTGTTTT 58.170 29.630 0.00 0.00 0.00 2.43
2464 6309 7.339721 TCGAAGGTTGAGACTCATAGACTAATT 59.660 37.037 5.87 0.00 0.00 1.40
2607 6456 4.631377 CGTCAATTTGTCCTGCAGATTAGA 59.369 41.667 17.39 0.00 31.63 2.10
2729 6579 9.453572 TGCTGAAACAATACTTGAGATATTTCT 57.546 29.630 0.00 0.00 33.88 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 1.213430 ACCTTGTTCTTGTTCCCCGAA 59.787 47.619 0.00 0.00 0.00 4.30
47 48 1.450211 CCGTGTGAGACCCAACCTT 59.550 57.895 0.00 0.00 0.00 3.50
82 83 0.752658 TGACGACATGAGCCCATAGG 59.247 55.000 0.00 0.00 0.00 2.57
85 86 1.524002 CCTGACGACATGAGCCCAT 59.476 57.895 0.00 0.00 0.00 4.00
124 125 7.968405 GTCATCGATTATTTGCTACACCTTTTT 59.032 33.333 0.00 0.00 0.00 1.94
127 128 6.112734 TGTCATCGATTATTTGCTACACCTT 58.887 36.000 0.00 0.00 0.00 3.50
153 154 3.876274 GAGGATTTGCCCCTCTTTTTC 57.124 47.619 0.00 0.00 45.18 2.29
178 179 4.021544 GGATTTGCCACAAGTTTGATGGTA 60.022 41.667 0.00 0.47 34.21 3.25
217 218 5.890424 TTAAATCAAAGGAGCCCTAAACG 57.110 39.130 0.00 0.00 31.13 3.60
302 303 6.873605 CCTACGAAATGCAATCCTACATATCA 59.126 38.462 0.00 0.00 0.00 2.15
304 305 7.004555 TCCTACGAAATGCAATCCTACATAT 57.995 36.000 0.00 0.00 0.00 1.78
305 306 6.413783 TCCTACGAAATGCAATCCTACATA 57.586 37.500 0.00 0.00 0.00 2.29
306 307 5.290493 TCCTACGAAATGCAATCCTACAT 57.710 39.130 0.00 0.00 0.00 2.29
307 308 4.746535 TCCTACGAAATGCAATCCTACA 57.253 40.909 0.00 0.00 0.00 2.74
308 309 6.483640 AGATTTCCTACGAAATGCAATCCTAC 59.516 38.462 4.66 0.00 46.48 3.18
309 310 6.483307 CAGATTTCCTACGAAATGCAATCCTA 59.517 38.462 4.66 0.00 46.48 2.94
310 311 5.297776 CAGATTTCCTACGAAATGCAATCCT 59.702 40.000 4.66 0.00 46.48 3.24
311 312 5.066505 ACAGATTTCCTACGAAATGCAATCC 59.933 40.000 4.66 0.00 46.48 3.01
312 313 6.124088 ACAGATTTCCTACGAAATGCAATC 57.876 37.500 4.66 0.00 46.48 2.67
313 314 5.647658 TGACAGATTTCCTACGAAATGCAAT 59.352 36.000 4.66 0.00 46.48 3.56
334 335 4.983671 AGGAAAAAGTTTGAGTGGTGAC 57.016 40.909 0.00 0.00 0.00 3.67
335 336 5.993748 AAAGGAAAAAGTTTGAGTGGTGA 57.006 34.783 0.00 0.00 0.00 4.02
356 357 9.320352 GGGTCTAAAAGCAAAAGAATTGTAAAA 57.680 29.630 0.00 0.00 0.00 1.52
358 359 8.141268 CAGGGTCTAAAAGCAAAAGAATTGTAA 58.859 33.333 0.00 0.00 0.00 2.41
361 362 6.748132 TCAGGGTCTAAAAGCAAAAGAATTG 58.252 36.000 0.00 0.00 0.00 2.32
367 368 7.096551 GCATTTATCAGGGTCTAAAAGCAAAA 58.903 34.615 0.00 0.00 33.82 2.44
372 373 5.652014 TGTGGCATTTATCAGGGTCTAAAAG 59.348 40.000 0.00 0.00 0.00 2.27
377 378 2.680805 CGTGTGGCATTTATCAGGGTCT 60.681 50.000 0.00 0.00 0.00 3.85
393 394 5.389830 GCTATATATTCATGCCACACGTGTG 60.390 44.000 36.13 36.13 45.23 3.82
394 395 4.690748 GCTATATATTCATGCCACACGTGT 59.309 41.667 17.22 17.22 36.60 4.49
395 396 4.690280 TGCTATATATTCATGCCACACGTG 59.310 41.667 15.48 15.48 36.55 4.49
396 397 4.893608 TGCTATATATTCATGCCACACGT 58.106 39.130 0.00 0.00 0.00 4.49
397 398 5.409520 AGTTGCTATATATTCATGCCACACG 59.590 40.000 0.00 0.00 0.00 4.49
399 400 5.939883 GGAGTTGCTATATATTCATGCCACA 59.060 40.000 0.00 0.00 0.00 4.17
400 401 5.063944 CGGAGTTGCTATATATTCATGCCAC 59.936 44.000 0.00 0.00 0.00 5.01
401 402 5.046663 TCGGAGTTGCTATATATTCATGCCA 60.047 40.000 0.00 0.00 0.00 4.92
402 403 5.419542 TCGGAGTTGCTATATATTCATGCC 58.580 41.667 0.00 0.00 0.00 4.40
403 404 7.545362 AATCGGAGTTGCTATATATTCATGC 57.455 36.000 0.00 0.00 0.00 4.06
438 439 2.584791 TCGTCGCGTTACTAAACTTCC 58.415 47.619 5.77 0.00 33.15 3.46
439 440 3.848019 TCATCGTCGCGTTACTAAACTTC 59.152 43.478 5.77 0.00 33.15 3.01
453 454 4.134546 CGAAAAGAAAGTTGTCATCGTCG 58.865 43.478 0.00 0.00 0.00 5.12
454 455 4.210537 TCCGAAAAGAAAGTTGTCATCGTC 59.789 41.667 0.00 0.00 0.00 4.20
456 457 4.725556 TCCGAAAAGAAAGTTGTCATCG 57.274 40.909 0.00 0.00 0.00 3.84
461 462 2.955660 TGCCATCCGAAAAGAAAGTTGT 59.044 40.909 0.00 0.00 0.00 3.32
487 535 7.076842 TCAACAAAAATTGCCATTCGAAAAA 57.923 28.000 0.00 0.00 0.00 1.94
511 559 5.122554 TGTGACACAAACACTCACGTATTTT 59.877 36.000 5.62 0.00 37.69 1.82
515 563 2.924926 GTGTGACACAAACACTCACGTA 59.075 45.455 10.50 0.00 43.69 3.57
517 565 1.266842 CGTGTGACACAAACACTCACG 60.267 52.381 16.74 3.17 44.64 4.35
520 568 1.730064 ACACGTGTGACACAAACACTC 59.270 47.619 22.71 0.00 44.64 3.51
560 617 8.721019 AAATGTGTTTGATGTGTCAGAAAAAT 57.279 26.923 0.00 0.00 35.39 1.82
660 722 3.719173 TTTCTCCGCCAAAAATTCGTT 57.281 38.095 0.00 0.00 0.00 3.85
664 726 4.563374 CCTCCATTTTCTCCGCCAAAAATT 60.563 41.667 0.00 0.00 33.86 1.82
674 736 2.121538 GGCGGCCTCCATTTTCTCC 61.122 63.158 12.87 0.00 0.00 3.71
694 1004 1.954362 AAGGTCAGAGCTAGCGGCAG 61.954 60.000 9.55 2.89 44.79 4.85
729 1097 1.363744 GACAGGAGCGAGGTCAAATG 58.636 55.000 4.64 2.93 0.00 2.32
730 1098 0.108615 CGACAGGAGCGAGGTCAAAT 60.109 55.000 4.64 0.00 0.00 2.32
731 1099 1.289066 CGACAGGAGCGAGGTCAAA 59.711 57.895 4.64 0.00 0.00 2.69
732 1100 2.636412 CCGACAGGAGCGAGGTCAA 61.636 63.158 4.64 0.00 41.02 3.18
734 1102 4.500116 GCCGACAGGAGCGAGGTC 62.500 72.222 0.00 0.00 41.02 3.85
740 1108 4.500116 GAGGTCGCCGACAGGAGC 62.500 72.222 20.08 0.57 41.02 4.70
837 4627 0.552848 GCAATGGGGAGGAGGATGAA 59.447 55.000 0.00 0.00 0.00 2.57
850 4640 1.992519 CTGGGGAGAGGGAGCAATGG 61.993 65.000 0.00 0.00 0.00 3.16
884 4682 1.308216 AGCAGGCCAGTAGGGGATT 60.308 57.895 5.01 0.00 37.04 3.01
903 4701 3.064545 GGAAAAGTGATCTCAAGGCATCG 59.935 47.826 0.00 0.00 0.00 3.84
969 4767 1.210155 GAAATTGGAGCTTGCGCGT 59.790 52.632 8.43 0.00 42.32 6.01
1219 5017 3.827898 CCTCGCCTCGGTGTCCTC 61.828 72.222 0.00 0.00 0.00 3.71
1232 5030 2.202623 CCTCGAAGAACGCCCTCG 60.203 66.667 0.00 0.00 42.26 4.63
1264 5062 0.955919 GGCGGCAGCTTGTTAGTCTT 60.956 55.000 9.17 0.00 44.37 3.01
1325 5123 0.530870 GGAGCTCCTACGTCCATTGC 60.531 60.000 26.25 0.00 0.00 3.56
1334 5132 4.208686 CGCCCACGGAGCTCCTAC 62.209 72.222 29.73 13.23 34.97 3.18
1908 5721 2.744202 AGTGATAAACTCAAGGCAAGCG 59.256 45.455 0.00 0.00 31.64 4.68
1933 5746 5.485620 CATGACATCATCCATTCTATCCGT 58.514 41.667 0.00 0.00 33.61 4.69
2049 5862 6.603237 TCATAAGCTAAACATGGATGAACG 57.397 37.500 0.00 0.00 0.00 3.95
2119 5932 6.655425 GGAAACTAATAACTGAGAAGCCAACT 59.345 38.462 0.00 0.00 0.00 3.16
2145 5960 3.441500 ACCCTTCTCCAAAAGATCACC 57.558 47.619 0.00 0.00 32.82 4.02
2217 6062 5.536260 AGATTCATCGTCAATCGTCATCAT 58.464 37.500 0.00 0.00 40.80 2.45
2290 6135 6.879458 CAGTAACCTAATTGTTTAGCCAGACT 59.121 38.462 0.00 0.00 34.62 3.24
2366 6211 9.565090 CATCTCTTTCCAATAATGAGAATGGTA 57.435 33.333 7.23 0.00 37.34 3.25
2367 6212 7.504911 CCATCTCTTTCCAATAATGAGAATGGT 59.495 37.037 7.23 0.00 37.34 3.55
2464 6309 6.326843 TCCAGCAGTAGTCTAGACTAGTCATA 59.673 42.308 29.63 11.31 43.63 2.15
2607 6456 5.360714 CCAACATGGAAATATGCTTACTGGT 59.639 40.000 0.00 0.00 40.96 4.00
2729 6579 1.270571 TGAAGTGCAATGTCTACGCCA 60.271 47.619 0.00 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.