Multiple sequence alignment - TraesCS3B01G467500

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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 TraesCS3B01G467500 chr3B 100.000 4004 0 0 1 4004 710580446 710584449 0.000000e+00 7395.0
1 TraesCS3B01G467500 chr3B 90.966 963 71 8 662 1621 710563367 710564316 0.000000e+00 1282.0
2 TraesCS3B01G467500 chr3B 95.392 217 10 0 1 217 203548256 203548472 2.960000e-91 346.0
3 TraesCS3B01G467500 chr3B 95.266 169 6 2 216 384 203548747 203548913 2.370000e-67 267.0
4 TraesCS3B01G467500 chr3D 95.483 3409 92 36 608 4004 537138907 537142265 0.000000e+00 5385.0
5 TraesCS3B01G467500 chr3D 94.470 217 12 0 1 217 558622778 558622562 6.410000e-88 335.0
6 TraesCS3B01G467500 chr3D 93.452 168 6 3 216 382 558622277 558622114 1.110000e-60 244.0
7 TraesCS3B01G467500 chr3A 94.982 3328 117 29 693 4004 672544730 672548023 0.000000e+00 5175.0
8 TraesCS3B01G467500 chr4B 93.744 1023 37 12 2153 3163 22596592 22595585 0.000000e+00 1509.0
9 TraesCS3B01G467500 chr4B 93.861 505 27 1 1655 2155 22608776 22608272 0.000000e+00 758.0
10 TraesCS3B01G467500 chr4B 94.419 215 12 0 1 215 140869030 140869244 8.290000e-87 331.0
11 TraesCS3B01G467500 chr4B 93.103 145 9 1 216 359 140869526 140869670 1.130000e-50 211.0
12 TraesCS3B01G467500 chr4B 89.412 170 14 3 216 382 167945591 167945423 1.130000e-50 211.0
13 TraesCS3B01G467500 chr1D 85.247 1315 172 15 1699 3008 11413343 11414640 0.000000e+00 1334.0
14 TraesCS3B01G467500 chr1D 82.026 1313 210 15 1690 2995 19309208 19310501 0.000000e+00 1094.0
15 TraesCS3B01G467500 chr7D 94.931 217 11 0 1 217 499906048 499905832 1.380000e-89 340.0
16 TraesCS3B01G467500 chr7D 93.865 163 7 2 216 375 499905547 499905385 4.000000e-60 243.0
17 TraesCS3B01G467500 chr7D 90.419 167 12 3 216 379 607123269 607123434 2.420000e-52 217.0
18 TraesCS3B01G467500 chr7D 84.571 175 25 2 35 207 249081544 249081718 5.320000e-39 172.0
19 TraesCS3B01G467500 chr7D 85.075 134 17 3 1003 1135 84986173 84986304 2.510000e-27 134.0
20 TraesCS3B01G467500 chr7D 82.759 145 14 3 419 563 63005479 63005612 7.030000e-23 119.0
21 TraesCS3B01G467500 chr1B 94.470 217 12 0 1 217 677615183 677614967 6.410000e-88 335.0
22 TraesCS3B01G467500 chr1B 96.250 160 6 0 216 375 677614686 677614527 3.070000e-66 263.0
23 TraesCS3B01G467500 chr1B 89.349 169 15 2 216 382 117210262 117210095 4.050000e-50 209.0
24 TraesCS3B01G467500 chr2B 92.523 214 16 0 1 214 51850060 51850273 1.400000e-79 307.0
25 TraesCS3B01G467500 chr2D 91.053 190 14 3 419 607 47989979 47989792 1.850000e-63 254.0
26 TraesCS3B01G467500 chr5B 90.062 161 14 2 216 375 455346958 455347117 1.460000e-49 207.0
27 TraesCS3B01G467500 chr5B 94.318 88 5 0 59 146 313956230 313956317 6.980000e-28 135.0
28 TraesCS3B01G467500 chr4D 89.091 165 16 2 20 184 391480238 391480400 1.890000e-48 204.0
29 TraesCS3B01G467500 chr6A 85.714 154 18 3 419 570 40607802 40607651 4.140000e-35 159.0
30 TraesCS3B01G467500 chr7B 83.439 157 20 5 1003 1155 34610099 34610253 1.500000e-29 141.0
31 TraesCS3B01G467500 chr7A 83.439 157 20 5 1003 1155 86048244 86048398 1.500000e-29 141.0
32 TraesCS3B01G467500 chr5D 79.104 134 20 6 1422 1550 440157591 440157721 7.130000e-13 86.1


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 TraesCS3B01G467500 chr3B 710580446 710584449 4003 False 7395.0 7395 100.000 1 4004 1 chr3B.!!$F2 4003
1 TraesCS3B01G467500 chr3B 710563367 710564316 949 False 1282.0 1282 90.966 662 1621 1 chr3B.!!$F1 959
2 TraesCS3B01G467500 chr3B 203548256 203548913 657 False 306.5 346 95.329 1 384 2 chr3B.!!$F3 383
3 TraesCS3B01G467500 chr3D 537138907 537142265 3358 False 5385.0 5385 95.483 608 4004 1 chr3D.!!$F1 3396
4 TraesCS3B01G467500 chr3D 558622114 558622778 664 True 289.5 335 93.961 1 382 2 chr3D.!!$R1 381
5 TraesCS3B01G467500 chr3A 672544730 672548023 3293 False 5175.0 5175 94.982 693 4004 1 chr3A.!!$F1 3311
6 TraesCS3B01G467500 chr4B 22595585 22596592 1007 True 1509.0 1509 93.744 2153 3163 1 chr4B.!!$R1 1010
7 TraesCS3B01G467500 chr4B 22608272 22608776 504 True 758.0 758 93.861 1655 2155 1 chr4B.!!$R2 500
8 TraesCS3B01G467500 chr4B 140869030 140869670 640 False 271.0 331 93.761 1 359 2 chr4B.!!$F1 358
9 TraesCS3B01G467500 chr1D 11413343 11414640 1297 False 1334.0 1334 85.247 1699 3008 1 chr1D.!!$F1 1309
10 TraesCS3B01G467500 chr1D 19309208 19310501 1293 False 1094.0 1094 82.026 1690 2995 1 chr1D.!!$F2 1305
11 TraesCS3B01G467500 chr7D 499905385 499906048 663 True 291.5 340 94.398 1 375 2 chr7D.!!$R1 374
12 TraesCS3B01G467500 chr1B 677614527 677615183 656 True 299.0 335 95.360 1 375 2 chr1B.!!$R2 374

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
392 684 0.033894 GGCGGTAGGGGGAATTTTGA 60.034 55.000 0.00 0.0 0.00 2.69 F
603 895 0.036732 ATTCTTGTCAAGCTCCGCCA 59.963 50.000 7.78 0.0 0.00 5.69 F
868 1172 0.737367 TCAGCAAATCAGCGACTCGG 60.737 55.000 0.00 0.0 40.15 4.63 F
1857 2183 1.066858 GTCGACAAGATGAGCCTGGAA 60.067 52.381 11.55 0.0 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1207 1524 1.000041 TACTCCCCCTCCTCCTCCTC 61.000 65.000 0.0 0.0 0.00 3.71 R
2163 2493 3.069158 CCTTGATGAAATCCCTTGCATCC 59.931 47.826 4.3 0.0 44.73 3.51 R
2577 2915 4.524328 CAGTTATCCCCAAGCAAACTCTTT 59.476 41.667 0.0 0.0 0.00 2.52 R
3313 3659 0.035036 GAGCCTAAATACGAGGGGGC 59.965 60.000 0.0 0.0 39.82 5.80 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
197 198 1.973281 CACACCGCTGCCCATCTTT 60.973 57.895 0.00 0.00 0.00 2.52
387 679 4.485530 TCGGGCGGTAGGGGGAAT 62.486 66.667 0.00 0.00 0.00 3.01
388 680 3.485745 CGGGCGGTAGGGGGAATT 61.486 66.667 0.00 0.00 0.00 2.17
389 681 3.012758 GGGCGGTAGGGGGAATTT 58.987 61.111 0.00 0.00 0.00 1.82
390 682 1.308666 GGGCGGTAGGGGGAATTTT 59.691 57.895 0.00 0.00 0.00 1.82
391 683 1.040893 GGGCGGTAGGGGGAATTTTG 61.041 60.000 0.00 0.00 0.00 2.44
392 684 0.033894 GGCGGTAGGGGGAATTTTGA 60.034 55.000 0.00 0.00 0.00 2.69
393 685 1.411074 GGCGGTAGGGGGAATTTTGAT 60.411 52.381 0.00 0.00 0.00 2.57
394 686 2.384828 GCGGTAGGGGGAATTTTGATT 58.615 47.619 0.00 0.00 0.00 2.57
395 687 2.764010 GCGGTAGGGGGAATTTTGATTT 59.236 45.455 0.00 0.00 0.00 2.17
396 688 3.430236 GCGGTAGGGGGAATTTTGATTTG 60.430 47.826 0.00 0.00 0.00 2.32
397 689 4.020543 CGGTAGGGGGAATTTTGATTTGA 58.979 43.478 0.00 0.00 0.00 2.69
398 690 4.097892 CGGTAGGGGGAATTTTGATTTGAG 59.902 45.833 0.00 0.00 0.00 3.02
399 691 5.269189 GGTAGGGGGAATTTTGATTTGAGA 58.731 41.667 0.00 0.00 0.00 3.27
400 692 5.127194 GGTAGGGGGAATTTTGATTTGAGAC 59.873 44.000 0.00 0.00 0.00 3.36
401 693 5.015813 AGGGGGAATTTTGATTTGAGACT 57.984 39.130 0.00 0.00 0.00 3.24
402 694 5.019470 AGGGGGAATTTTGATTTGAGACTC 58.981 41.667 0.00 0.00 0.00 3.36
403 695 4.142381 GGGGGAATTTTGATTTGAGACTCG 60.142 45.833 0.00 0.00 0.00 4.18
404 696 4.142381 GGGGAATTTTGATTTGAGACTCGG 60.142 45.833 0.00 0.00 0.00 4.63
405 697 4.700213 GGGAATTTTGATTTGAGACTCGGA 59.300 41.667 0.00 0.00 0.00 4.55
406 698 5.183140 GGGAATTTTGATTTGAGACTCGGAA 59.817 40.000 0.00 0.00 0.00 4.30
407 699 6.294508 GGGAATTTTGATTTGAGACTCGGAAA 60.295 38.462 0.00 0.00 0.00 3.13
408 700 7.315890 GGAATTTTGATTTGAGACTCGGAAAT 58.684 34.615 0.00 0.00 0.00 2.17
409 701 8.458843 GGAATTTTGATTTGAGACTCGGAAATA 58.541 33.333 0.00 0.00 0.00 1.40
410 702 9.278734 GAATTTTGATTTGAGACTCGGAAATAC 57.721 33.333 0.00 0.00 0.00 1.89
411 703 7.979444 TTTTGATTTGAGACTCGGAAATACT 57.021 32.000 0.00 0.00 0.00 2.12
412 704 9.667107 ATTTTGATTTGAGACTCGGAAATACTA 57.333 29.630 0.00 0.00 0.00 1.82
413 705 8.475331 TTTGATTTGAGACTCGGAAATACTAC 57.525 34.615 0.00 0.00 0.00 2.73
414 706 7.406031 TGATTTGAGACTCGGAAATACTACT 57.594 36.000 0.00 0.00 0.00 2.57
415 707 7.837863 TGATTTGAGACTCGGAAATACTACTT 58.162 34.615 0.00 0.00 0.00 2.24
416 708 7.759886 TGATTTGAGACTCGGAAATACTACTTG 59.240 37.037 0.00 0.00 0.00 3.16
417 709 4.995124 TGAGACTCGGAAATACTACTTGC 58.005 43.478 0.00 0.00 0.00 4.01
418 710 4.030134 AGACTCGGAAATACTACTTGCG 57.970 45.455 0.00 0.00 38.76 4.85
419 711 3.114065 GACTCGGAAATACTACTTGCGG 58.886 50.000 0.00 0.00 38.07 5.69
420 712 2.494870 ACTCGGAAATACTACTTGCGGT 59.505 45.455 0.00 0.00 38.07 5.68
421 713 2.858344 CTCGGAAATACTACTTGCGGTG 59.142 50.000 0.00 0.00 38.07 4.94
422 714 2.231964 TCGGAAATACTACTTGCGGTGT 59.768 45.455 0.00 0.00 38.07 4.16
423 715 2.347452 CGGAAATACTACTTGCGGTGTG 59.653 50.000 0.00 0.00 34.42 3.82
424 716 2.095372 GGAAATACTACTTGCGGTGTGC 59.905 50.000 0.00 0.00 46.70 4.57
425 717 2.762535 AATACTACTTGCGGTGTGCT 57.237 45.000 0.00 0.00 46.63 4.40
426 718 2.762535 ATACTACTTGCGGTGTGCTT 57.237 45.000 0.00 0.00 46.63 3.91
427 719 3.880047 ATACTACTTGCGGTGTGCTTA 57.120 42.857 0.00 0.00 46.63 3.09
428 720 2.080286 ACTACTTGCGGTGTGCTTAG 57.920 50.000 0.00 0.00 46.63 2.18
429 721 1.343465 ACTACTTGCGGTGTGCTTAGT 59.657 47.619 0.00 0.00 46.63 2.24
430 722 2.224209 ACTACTTGCGGTGTGCTTAGTT 60.224 45.455 0.00 0.00 46.63 2.24
431 723 1.226746 ACTTGCGGTGTGCTTAGTTC 58.773 50.000 0.00 0.00 46.63 3.01
432 724 1.202651 ACTTGCGGTGTGCTTAGTTCT 60.203 47.619 0.00 0.00 46.63 3.01
433 725 1.461127 CTTGCGGTGTGCTTAGTTCTC 59.539 52.381 0.00 0.00 46.63 2.87
434 726 0.391228 TGCGGTGTGCTTAGTTCTCA 59.609 50.000 0.00 0.00 46.63 3.27
435 727 1.001974 TGCGGTGTGCTTAGTTCTCAT 59.998 47.619 0.00 0.00 46.63 2.90
436 728 1.661112 GCGGTGTGCTTAGTTCTCATC 59.339 52.381 0.00 0.00 41.73 2.92
437 729 2.675317 GCGGTGTGCTTAGTTCTCATCT 60.675 50.000 0.00 0.00 41.73 2.90
438 730 2.926200 CGGTGTGCTTAGTTCTCATCTG 59.074 50.000 0.00 0.00 0.00 2.90
439 731 3.367395 CGGTGTGCTTAGTTCTCATCTGA 60.367 47.826 0.00 0.00 0.00 3.27
440 732 4.569943 GGTGTGCTTAGTTCTCATCTGAA 58.430 43.478 0.00 0.00 0.00 3.02
441 733 4.629200 GGTGTGCTTAGTTCTCATCTGAAG 59.371 45.833 0.00 0.00 0.00 3.02
442 734 5.233988 GTGTGCTTAGTTCTCATCTGAAGT 58.766 41.667 0.00 0.00 34.41 3.01
443 735 6.390721 GTGTGCTTAGTTCTCATCTGAAGTA 58.609 40.000 0.00 0.00 32.52 2.24
444 736 7.038659 GTGTGCTTAGTTCTCATCTGAAGTAT 58.961 38.462 0.00 0.00 33.48 2.12
445 737 8.191446 GTGTGCTTAGTTCTCATCTGAAGTATA 58.809 37.037 0.00 0.00 33.48 1.47
446 738 8.918116 TGTGCTTAGTTCTCATCTGAAGTATAT 58.082 33.333 0.00 0.00 33.48 0.86
471 763 7.578310 ATTGCTAAATGCTAATCAGACATGT 57.422 32.000 0.00 0.00 43.37 3.21
472 764 8.681486 ATTGCTAAATGCTAATCAGACATGTA 57.319 30.769 0.00 0.00 43.37 2.29
473 765 8.681486 TTGCTAAATGCTAATCAGACATGTAT 57.319 30.769 0.00 0.00 43.37 2.29
474 766 8.681486 TGCTAAATGCTAATCAGACATGTATT 57.319 30.769 0.00 0.00 43.37 1.89
475 767 9.123902 TGCTAAATGCTAATCAGACATGTATTT 57.876 29.630 0.00 0.44 43.37 1.40
476 768 9.956720 GCTAAATGCTAATCAGACATGTATTTT 57.043 29.630 0.00 0.00 38.95 1.82
523 815 8.691661 ACTATATAAGTAAAATTGCCTGGTGG 57.308 34.615 0.00 0.00 36.36 4.61
537 829 3.016736 CCTGGTGGCTACAAGTTTATGG 58.983 50.000 3.65 0.00 0.00 2.74
538 830 3.561313 CCTGGTGGCTACAAGTTTATGGT 60.561 47.826 3.65 0.00 0.00 3.55
539 831 4.079253 CTGGTGGCTACAAGTTTATGGTT 58.921 43.478 1.52 0.00 0.00 3.67
540 832 4.475345 TGGTGGCTACAAGTTTATGGTTT 58.525 39.130 1.52 0.00 0.00 3.27
541 833 4.279671 TGGTGGCTACAAGTTTATGGTTTG 59.720 41.667 1.52 0.00 0.00 2.93
542 834 4.234574 GTGGCTACAAGTTTATGGTTTGC 58.765 43.478 0.00 0.00 0.00 3.68
543 835 4.022329 GTGGCTACAAGTTTATGGTTTGCT 60.022 41.667 0.00 0.00 0.00 3.91
544 836 4.022416 TGGCTACAAGTTTATGGTTTGCTG 60.022 41.667 0.00 0.00 0.00 4.41
545 837 4.217550 GGCTACAAGTTTATGGTTTGCTGA 59.782 41.667 0.00 0.00 0.00 4.26
546 838 5.278758 GGCTACAAGTTTATGGTTTGCTGAA 60.279 40.000 0.00 0.00 0.00 3.02
547 839 5.858581 GCTACAAGTTTATGGTTTGCTGAAG 59.141 40.000 0.00 0.00 0.00 3.02
548 840 5.852282 ACAAGTTTATGGTTTGCTGAAGT 57.148 34.783 0.00 0.00 0.00 3.01
549 841 6.220726 ACAAGTTTATGGTTTGCTGAAGTT 57.779 33.333 0.00 0.00 0.00 2.66
550 842 6.042143 ACAAGTTTATGGTTTGCTGAAGTTG 58.958 36.000 0.00 0.00 34.97 3.16
551 843 4.620982 AGTTTATGGTTTGCTGAAGTTGC 58.379 39.130 0.00 0.00 0.00 4.17
552 844 4.342092 AGTTTATGGTTTGCTGAAGTTGCT 59.658 37.500 0.00 0.00 0.00 3.91
553 845 4.935352 TTATGGTTTGCTGAAGTTGCTT 57.065 36.364 0.00 0.00 0.00 3.91
554 846 2.869233 TGGTTTGCTGAAGTTGCTTC 57.131 45.000 2.22 2.22 40.54 3.86
555 847 2.098614 TGGTTTGCTGAAGTTGCTTCA 58.901 42.857 10.61 10.61 46.50 3.02
577 869 4.304432 TTTTTGTCCTTGGCCCCC 57.696 55.556 0.00 0.00 0.00 5.40
596 888 2.167075 CCCCCATTGATTCTTGTCAAGC 59.833 50.000 7.78 0.00 41.05 4.01
597 889 3.094572 CCCCATTGATTCTTGTCAAGCT 58.905 45.455 7.78 0.00 41.05 3.74
598 890 3.129988 CCCCATTGATTCTTGTCAAGCTC 59.870 47.826 7.78 7.69 41.05 4.09
599 891 3.129988 CCCATTGATTCTTGTCAAGCTCC 59.870 47.826 7.78 0.13 41.05 4.70
600 892 3.181503 CCATTGATTCTTGTCAAGCTCCG 60.182 47.826 7.78 0.27 41.05 4.63
601 893 1.442769 TGATTCTTGTCAAGCTCCGC 58.557 50.000 7.78 0.00 0.00 5.54
602 894 0.729690 GATTCTTGTCAAGCTCCGCC 59.270 55.000 7.78 0.00 0.00 6.13
603 895 0.036732 ATTCTTGTCAAGCTCCGCCA 59.963 50.000 7.78 0.00 0.00 5.69
604 896 0.884704 TTCTTGTCAAGCTCCGCCAC 60.885 55.000 7.78 0.00 0.00 5.01
605 897 1.302033 CTTGTCAAGCTCCGCCACT 60.302 57.895 0.00 0.00 0.00 4.00
606 898 1.572085 CTTGTCAAGCTCCGCCACTG 61.572 60.000 0.00 0.00 0.00 3.66
634 926 2.132762 GTGTCTGTACCGTGTTTGGAG 58.867 52.381 0.00 0.00 0.00 3.86
638 930 3.872771 GTCTGTACCGTGTTTGGAGAAAA 59.127 43.478 0.00 0.00 0.00 2.29
642 934 6.938030 TCTGTACCGTGTTTGGAGAAAAATAT 59.062 34.615 0.00 0.00 0.00 1.28
644 936 6.711194 TGTACCGTGTTTGGAGAAAAATATCA 59.289 34.615 0.00 0.00 0.00 2.15
645 937 6.254281 ACCGTGTTTGGAGAAAAATATCAG 57.746 37.500 0.00 0.00 0.00 2.90
646 938 6.001460 ACCGTGTTTGGAGAAAAATATCAGA 58.999 36.000 0.00 0.00 0.00 3.27
647 939 6.488683 ACCGTGTTTGGAGAAAAATATCAGAA 59.511 34.615 0.00 0.00 0.00 3.02
648 940 7.023575 CCGTGTTTGGAGAAAAATATCAGAAG 58.976 38.462 0.00 0.00 0.00 2.85
663 955 9.522804 AAATATCAGAAGAGACGATACAAAGTC 57.477 33.333 0.00 0.00 37.63 3.01
769 1064 4.154737 TGTGATCAAAGCAGGAAAAGATCG 59.845 41.667 0.00 0.00 35.77 3.69
868 1172 0.737367 TCAGCAAATCAGCGACTCGG 60.737 55.000 0.00 0.00 40.15 4.63
886 1190 2.040359 CTCCCTCCCCCTTCCTCC 60.040 72.222 0.00 0.00 0.00 4.30
887 1191 2.543637 TCCCTCCCCCTTCCTCCT 60.544 66.667 0.00 0.00 0.00 3.69
889 1193 2.652113 CCCTCCCCCTTCCTCCTCT 61.652 68.421 0.00 0.00 0.00 3.69
891 1195 1.074850 CTCCCCCTTCCTCCTCTCC 60.075 68.421 0.00 0.00 0.00 3.71
932 1238 4.426313 CTCCCCGCCCCCTTTCAC 62.426 72.222 0.00 0.00 0.00 3.18
966 1272 1.361993 CTCCTCCGATCCAAGAGCG 59.638 63.158 0.00 0.00 41.31 5.03
1077 1394 1.373497 CAAGTCGCTCGCCAACTCT 60.373 57.895 0.00 0.00 0.00 3.24
1857 2183 1.066858 GTCGACAAGATGAGCCTGGAA 60.067 52.381 11.55 0.00 0.00 3.53
2163 2493 1.078848 CGAGGCCTTGTTCTCAGGG 60.079 63.158 6.77 0.00 42.71 4.45
2577 2915 5.453057 GCAGAAGATCAAGGATTCAGAGCTA 60.453 44.000 0.00 0.00 0.00 3.32
3254 3600 7.680310 AGATACTACATAGATTGCACCCCTATT 59.320 37.037 0.00 0.00 0.00 1.73
3313 3659 1.373590 CTCCGCACGGGTTTATTGGG 61.374 60.000 9.58 0.00 37.00 4.12
3489 3840 0.479378 GGCCCCAATAAACCCGGATA 59.521 55.000 0.73 0.00 0.00 2.59
3729 4080 1.284785 CTGGACTGGGCTAATTTGGGA 59.715 52.381 0.00 0.00 0.00 4.37
3804 4155 0.919710 AGGGGTGGGCATAGAAACTC 59.080 55.000 0.00 0.00 0.00 3.01
3828 4179 2.678471 ACCGAATACCGAACCGAAAT 57.322 45.000 0.00 0.00 41.76 2.17
3899 4251 5.941948 ATTCGGTTTTCACTTCCACTAAG 57.058 39.130 0.00 0.00 41.33 2.18
3976 4328 4.637276 TGTATGGCAGGGTGTTATATTCG 58.363 43.478 0.00 0.00 0.00 3.34
3990 4342 6.929049 GTGTTATATTCGAGTGGAATGGATCA 59.071 38.462 10.36 3.06 44.95 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 2.478890 CGCCGGTCACCTACGATCT 61.479 63.158 1.90 0.00 0.00 2.75
290 578 4.465446 CCTCGCCTCCCTCCCTCA 62.465 72.222 0.00 0.00 0.00 3.86
375 667 4.020543 TCAAATCAAAATTCCCCCTACCG 58.979 43.478 0.00 0.00 0.00 4.02
376 668 5.127194 GTCTCAAATCAAAATTCCCCCTACC 59.873 44.000 0.00 0.00 0.00 3.18
377 669 5.952347 AGTCTCAAATCAAAATTCCCCCTAC 59.048 40.000 0.00 0.00 0.00 3.18
378 670 6.152638 AGTCTCAAATCAAAATTCCCCCTA 57.847 37.500 0.00 0.00 0.00 3.53
379 671 5.015813 AGTCTCAAATCAAAATTCCCCCT 57.984 39.130 0.00 0.00 0.00 4.79
380 672 4.142381 CGAGTCTCAAATCAAAATTCCCCC 60.142 45.833 0.00 0.00 0.00 5.40
381 673 4.142381 CCGAGTCTCAAATCAAAATTCCCC 60.142 45.833 0.00 0.00 0.00 4.81
382 674 4.700213 TCCGAGTCTCAAATCAAAATTCCC 59.300 41.667 0.00 0.00 0.00 3.97
383 675 5.880054 TCCGAGTCTCAAATCAAAATTCC 57.120 39.130 0.00 0.00 0.00 3.01
384 676 9.278734 GTATTTCCGAGTCTCAAATCAAAATTC 57.721 33.333 0.00 0.00 0.00 2.17
385 677 9.014297 AGTATTTCCGAGTCTCAAATCAAAATT 57.986 29.630 0.00 0.00 0.00 1.82
386 678 8.567285 AGTATTTCCGAGTCTCAAATCAAAAT 57.433 30.769 0.00 0.00 0.00 1.82
387 679 7.979444 AGTATTTCCGAGTCTCAAATCAAAA 57.021 32.000 0.00 0.00 0.00 2.44
388 680 8.311836 AGTAGTATTTCCGAGTCTCAAATCAAA 58.688 33.333 0.00 0.00 0.00 2.69
389 681 7.837863 AGTAGTATTTCCGAGTCTCAAATCAA 58.162 34.615 0.00 0.00 0.00 2.57
390 682 7.406031 AGTAGTATTTCCGAGTCTCAAATCA 57.594 36.000 0.00 0.00 0.00 2.57
391 683 7.254151 GCAAGTAGTATTTCCGAGTCTCAAATC 60.254 40.741 0.00 0.00 0.00 2.17
392 684 6.535508 GCAAGTAGTATTTCCGAGTCTCAAAT 59.464 38.462 0.00 2.44 0.00 2.32
393 685 5.867716 GCAAGTAGTATTTCCGAGTCTCAAA 59.132 40.000 0.00 0.00 0.00 2.69
394 686 5.408356 GCAAGTAGTATTTCCGAGTCTCAA 58.592 41.667 0.00 0.00 0.00 3.02
395 687 4.438336 CGCAAGTAGTATTTCCGAGTCTCA 60.438 45.833 0.00 0.00 0.00 3.27
396 688 4.036352 CGCAAGTAGTATTTCCGAGTCTC 58.964 47.826 0.00 0.00 0.00 3.36
397 689 3.181489 CCGCAAGTAGTATTTCCGAGTCT 60.181 47.826 0.00 0.00 0.00 3.24
398 690 3.114065 CCGCAAGTAGTATTTCCGAGTC 58.886 50.000 0.00 0.00 0.00 3.36
399 691 2.494870 ACCGCAAGTAGTATTTCCGAGT 59.505 45.455 0.00 0.00 0.00 4.18
400 692 2.858344 CACCGCAAGTAGTATTTCCGAG 59.142 50.000 0.00 0.00 0.00 4.63
401 693 2.231964 ACACCGCAAGTAGTATTTCCGA 59.768 45.455 0.00 0.00 0.00 4.55
402 694 2.347452 CACACCGCAAGTAGTATTTCCG 59.653 50.000 0.00 0.00 0.00 4.30
403 695 2.095372 GCACACCGCAAGTAGTATTTCC 59.905 50.000 0.00 0.00 41.79 3.13
404 696 3.000727 AGCACACCGCAAGTAGTATTTC 58.999 45.455 0.00 0.00 46.13 2.17
405 697 3.053831 AGCACACCGCAAGTAGTATTT 57.946 42.857 0.00 0.00 46.13 1.40
406 698 2.762535 AGCACACCGCAAGTAGTATT 57.237 45.000 0.00 0.00 46.13 1.89
407 699 2.762535 AAGCACACCGCAAGTAGTAT 57.237 45.000 0.00 0.00 46.13 2.12
408 700 2.559668 ACTAAGCACACCGCAAGTAGTA 59.440 45.455 0.00 0.00 46.13 1.82
409 701 1.343465 ACTAAGCACACCGCAAGTAGT 59.657 47.619 0.00 0.00 46.13 2.73
410 702 2.080286 ACTAAGCACACCGCAAGTAG 57.920 50.000 0.00 0.00 46.13 2.57
411 703 2.036733 AGAACTAAGCACACCGCAAGTA 59.963 45.455 0.00 0.00 46.13 2.24
412 704 1.202651 AGAACTAAGCACACCGCAAGT 60.203 47.619 0.00 0.00 46.13 3.16
413 705 1.461127 GAGAACTAAGCACACCGCAAG 59.539 52.381 0.00 0.00 46.13 4.01
414 706 1.202592 TGAGAACTAAGCACACCGCAA 60.203 47.619 0.00 0.00 46.13 4.85
415 707 0.391228 TGAGAACTAAGCACACCGCA 59.609 50.000 0.00 0.00 46.13 5.69
416 708 1.661112 GATGAGAACTAAGCACACCGC 59.339 52.381 0.00 0.00 42.91 5.68
417 709 2.926200 CAGATGAGAACTAAGCACACCG 59.074 50.000 0.00 0.00 0.00 4.94
418 710 4.193826 TCAGATGAGAACTAAGCACACC 57.806 45.455 0.00 0.00 0.00 4.16
419 711 5.233988 ACTTCAGATGAGAACTAAGCACAC 58.766 41.667 0.00 0.00 0.00 3.82
420 712 5.474578 ACTTCAGATGAGAACTAAGCACA 57.525 39.130 0.00 0.00 0.00 4.57
450 742 9.956720 AAAATACATGTCTGATTAGCATTTAGC 57.043 29.630 0.00 0.00 46.19 3.09
497 789 9.131791 CCACCAGGCAATTTTACTTATATAGTT 57.868 33.333 0.00 0.00 38.33 2.24
498 790 8.691661 CCACCAGGCAATTTTACTTATATAGT 57.308 34.615 0.00 0.00 41.04 2.12
516 808 3.016736 CCATAAACTTGTAGCCACCAGG 58.983 50.000 0.00 0.00 38.23 4.45
517 809 3.686016 ACCATAAACTTGTAGCCACCAG 58.314 45.455 0.00 0.00 0.00 4.00
518 810 3.799432 ACCATAAACTTGTAGCCACCA 57.201 42.857 0.00 0.00 0.00 4.17
519 811 4.805219 CAAACCATAAACTTGTAGCCACC 58.195 43.478 0.00 0.00 0.00 4.61
520 812 4.022329 AGCAAACCATAAACTTGTAGCCAC 60.022 41.667 0.00 0.00 0.00 5.01
521 813 4.022416 CAGCAAACCATAAACTTGTAGCCA 60.022 41.667 0.00 0.00 0.00 4.75
522 814 4.217550 TCAGCAAACCATAAACTTGTAGCC 59.782 41.667 0.00 0.00 0.00 3.93
523 815 5.371115 TCAGCAAACCATAAACTTGTAGC 57.629 39.130 0.00 0.00 0.00 3.58
524 816 6.970484 ACTTCAGCAAACCATAAACTTGTAG 58.030 36.000 0.00 0.00 0.00 2.74
525 817 6.952773 ACTTCAGCAAACCATAAACTTGTA 57.047 33.333 0.00 0.00 0.00 2.41
526 818 5.852282 ACTTCAGCAAACCATAAACTTGT 57.148 34.783 0.00 0.00 0.00 3.16
527 819 5.050837 GCAACTTCAGCAAACCATAAACTTG 60.051 40.000 0.00 0.00 0.00 3.16
528 820 5.049828 GCAACTTCAGCAAACCATAAACTT 58.950 37.500 0.00 0.00 0.00 2.66
529 821 4.342092 AGCAACTTCAGCAAACCATAAACT 59.658 37.500 0.00 0.00 0.00 2.66
530 822 4.620982 AGCAACTTCAGCAAACCATAAAC 58.379 39.130 0.00 0.00 0.00 2.01
531 823 4.935352 AGCAACTTCAGCAAACCATAAA 57.065 36.364 0.00 0.00 0.00 1.40
532 824 4.340666 TGAAGCAACTTCAGCAAACCATAA 59.659 37.500 5.94 0.00 44.27 1.90
533 825 3.888323 TGAAGCAACTTCAGCAAACCATA 59.112 39.130 5.94 0.00 44.27 2.74
534 826 2.694628 TGAAGCAACTTCAGCAAACCAT 59.305 40.909 5.94 0.00 44.27 3.55
535 827 2.098614 TGAAGCAACTTCAGCAAACCA 58.901 42.857 5.94 0.00 44.27 3.67
536 828 2.869233 TGAAGCAACTTCAGCAAACC 57.131 45.000 5.94 0.00 44.27 3.27
560 852 4.304432 GGGGGCCAAGGACAAAAA 57.696 55.556 4.39 0.00 0.00 1.94
575 867 2.167075 GCTTGACAAGAATCAATGGGGG 59.833 50.000 19.51 0.00 37.93 5.40
576 868 3.094572 AGCTTGACAAGAATCAATGGGG 58.905 45.455 19.51 0.00 37.93 4.96
577 869 3.129988 GGAGCTTGACAAGAATCAATGGG 59.870 47.826 19.51 0.00 37.93 4.00
578 870 3.181503 CGGAGCTTGACAAGAATCAATGG 60.182 47.826 19.51 3.58 37.93 3.16
579 871 4.012319 CGGAGCTTGACAAGAATCAATG 57.988 45.455 19.51 6.12 37.93 2.82
600 892 4.664677 ACACGAGACGCCAGTGGC 62.665 66.667 25.07 25.07 46.75 5.01
601 893 2.430921 GACACGAGACGCCAGTGG 60.431 66.667 4.20 4.20 39.95 4.00
602 894 1.730902 CAGACACGAGACGCCAGTG 60.731 63.158 0.00 0.00 41.28 3.66
603 895 0.887836 TACAGACACGAGACGCCAGT 60.888 55.000 0.00 0.00 0.00 4.00
604 896 0.454620 GTACAGACACGAGACGCCAG 60.455 60.000 0.00 0.00 0.00 4.85
605 897 1.577922 GTACAGACACGAGACGCCA 59.422 57.895 0.00 0.00 0.00 5.69
606 898 1.154073 GGTACAGACACGAGACGCC 60.154 63.158 0.00 0.00 0.00 5.68
638 930 7.858382 CGACTTTGTATCGTCTCTTCTGATATT 59.142 37.037 0.00 0.00 34.84 1.28
642 934 4.694037 TCGACTTTGTATCGTCTCTTCTGA 59.306 41.667 0.00 0.00 40.50 3.27
644 936 4.696402 ACTCGACTTTGTATCGTCTCTTCT 59.304 41.667 0.00 0.00 40.50 2.85
645 937 4.789119 CACTCGACTTTGTATCGTCTCTTC 59.211 45.833 0.00 0.00 40.50 2.87
646 938 4.724303 CACTCGACTTTGTATCGTCTCTT 58.276 43.478 0.00 0.00 40.50 2.85
647 939 3.426426 GCACTCGACTTTGTATCGTCTCT 60.426 47.826 0.00 0.00 40.50 3.10
648 940 2.847133 GCACTCGACTTTGTATCGTCTC 59.153 50.000 0.00 0.00 40.50 3.36
681 974 4.495422 CGACCATACACTAGCTCACTTTT 58.505 43.478 0.00 0.00 0.00 2.27
761 1054 3.771577 AGGTTGGACTGACGATCTTTT 57.228 42.857 0.00 0.00 0.00 2.27
868 1172 2.770475 GAGGAAGGGGGAGGGAGC 60.770 72.222 0.00 0.00 0.00 4.70
1077 1394 3.736100 TCGTCCGCGGCGTTCTTA 61.736 61.111 30.84 15.86 38.89 2.10
1194 1511 4.798682 TCCTCTTCCCCCTCCGGC 62.799 72.222 0.00 0.00 0.00 6.13
1196 1513 2.444895 CCTCCTCTTCCCCCTCCG 60.445 72.222 0.00 0.00 0.00 4.63
1205 1522 1.550374 TCCCCCTCCTCCTCCTCTT 60.550 63.158 0.00 0.00 0.00 2.85
1207 1524 1.000041 TACTCCCCCTCCTCCTCCTC 61.000 65.000 0.00 0.00 0.00 3.71
1208 1525 1.088896 TACTCCCCCTCCTCCTCCT 59.911 63.158 0.00 0.00 0.00 3.69
1209 1526 1.233659 GTACTCCCCCTCCTCCTCC 59.766 68.421 0.00 0.00 0.00 4.30
1210 1527 1.152715 CGTACTCCCCCTCCTCCTC 60.153 68.421 0.00 0.00 0.00 3.71
2163 2493 3.069158 CCTTGATGAAATCCCTTGCATCC 59.931 47.826 4.30 0.00 44.73 3.51
2577 2915 4.524328 CAGTTATCCCCAAGCAAACTCTTT 59.476 41.667 0.00 0.00 0.00 2.52
3141 3486 6.936968 AGGTAGAAGGTACCATTATGATCC 57.063 41.667 15.94 6.02 39.99 3.36
3238 3584 6.542821 CAGGATAAAATAGGGGTGCAATCTA 58.457 40.000 0.00 0.00 0.00 1.98
3254 3600 9.944663 GATGTATTTTTACAATCGCAGGATAAA 57.055 29.630 0.00 0.00 33.21 1.40
3276 3622 4.503296 GCGGAGGGAGTATATTTGTGATGT 60.503 45.833 0.00 0.00 0.00 3.06
3313 3659 0.035036 GAGCCTAAATACGAGGGGGC 59.965 60.000 0.00 0.00 39.82 5.80
3428 3774 7.106239 ACTTTGACCATCTAGACTAACAATGG 58.894 38.462 13.13 13.13 42.12 3.16
3429 3775 8.553459 AACTTTGACCATCTAGACTAACAATG 57.447 34.615 0.00 5.47 0.00 2.82
3430 3776 9.003658 CAAACTTTGACCATCTAGACTAACAAT 57.996 33.333 0.00 0.00 0.00 2.71
3729 4080 1.270147 GCTTTCGCGGATGTATAGGGT 60.270 52.381 6.13 0.00 0.00 4.34
3780 4131 0.764369 TCTATGCCCACCCCTAGCTG 60.764 60.000 0.00 0.00 0.00 4.24
3804 4155 1.648504 GGTTCGGTATTCGGTTCCTG 58.351 55.000 0.00 0.00 39.77 3.86
3899 4251 5.296035 CACCGAACCAACCTTATCTAATTCC 59.704 44.000 0.00 0.00 0.00 3.01
3914 4266 0.680618 ACCGATGTAACACCGAACCA 59.319 50.000 0.00 0.00 0.00 3.67
3976 4328 1.576356 GAGCGTGATCCATTCCACTC 58.424 55.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.