Multiple sequence alignment - TraesCS3D01G482900

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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 TraesCS3D01G482900 chr3D 100.000 5239 0 0 1 5239 580538007 580543245 0.000000e+00 9675.0
1 TraesCS3D01G482900 chr3A 93.904 2477 112 19 1612 4070 716067781 716070236 0.000000e+00 3701.0
2 TraesCS3D01G482900 chr3A 88.484 1207 69 33 4069 5237 716070361 716071535 0.000000e+00 1395.0
3 TraesCS3D01G482900 chr3A 94.356 567 32 0 115 681 716043213 716043779 0.000000e+00 870.0
4 TraesCS3D01G482900 chr3A 85.530 698 75 18 2394 3081 465662894 465662213 0.000000e+00 706.0
5 TraesCS3D01G482900 chr3A 85.387 698 76 16 2394 3081 665748588 665749269 0.000000e+00 701.0
6 TraesCS3D01G482900 chr3A 93.151 365 23 2 803 1166 716066953 716067316 7.720000e-148 534.0
7 TraesCS3D01G482900 chr3A 90.634 363 24 6 1613 1968 644734163 644734522 1.710000e-129 473.0
8 TraesCS3D01G482900 chr3A 88.471 399 36 7 1217 1611 716067317 716067709 1.710000e-129 473.0
9 TraesCS3D01G482900 chr3A 95.000 120 5 1 1 119 716033938 716034057 2.490000e-43 187.0
10 TraesCS3D01G482900 chr3A 92.308 65 5 0 683 747 716066881 716066945 5.590000e-15 93.5
11 TraesCS3D01G482900 chr3B 93.037 2025 107 14 1612 3622 775826028 775828032 0.000000e+00 2928.0
12 TraesCS3D01G482900 chr3B 90.786 1031 69 13 3613 4621 775829907 775830933 0.000000e+00 1354.0
13 TraesCS3D01G482900 chr3B 93.174 879 46 4 1 878 775824105 775824970 0.000000e+00 1279.0
14 TraesCS3D01G482900 chr3B 91.516 554 39 3 968 1513 775825323 775825876 0.000000e+00 756.0
15 TraesCS3D01G482900 chr3B 82.045 440 44 24 4650 5069 775830992 775831416 5.020000e-90 342.0
16 TraesCS3D01G482900 chr3B 92.053 151 12 0 4131 4281 775660898 775661048 4.110000e-51 213.0
17 TraesCS3D01G482900 chr6A 86.011 1830 189 36 2138 3947 616816992 616818774 0.000000e+00 1899.0
18 TraesCS3D01G482900 chr6A 85.673 698 74 18 2394 3081 101388562 101389243 0.000000e+00 712.0
19 TraesCS3D01G482900 chr6A 84.521 491 44 18 1633 2111 616816413 616816883 1.720000e-124 457.0
20 TraesCS3D01G482900 chr6A 89.720 107 8 1 1390 1493 616816067 616816173 3.290000e-27 134.0
21 TraesCS3D01G482900 chr6D 85.185 1728 182 37 2245 3947 473085051 473083373 0.000000e+00 1705.0
22 TraesCS3D01G482900 chr6D 92.701 411 21 7 1614 2016 329077203 329076794 7.560000e-163 584.0
23 TraesCS3D01G482900 chr6D 86.179 123 12 3 1390 1507 473086096 473085974 1.530000e-25 128.0
24 TraesCS3D01G482900 chr6B 83.755 1422 160 43 2858 4263 718384553 718383187 0.000000e+00 1280.0
25 TraesCS3D01G482900 chr6B 87.055 703 76 14 2138 2830 718385361 718384664 0.000000e+00 780.0
26 TraesCS3D01G482900 chr6B 86.992 123 10 3 1390 1507 718386252 718386131 3.290000e-27 134.0
27 TraesCS3D01G482900 chr1A 86.246 698 73 15 2394 3081 389948707 389949391 0.000000e+00 736.0
28 TraesCS3D01G482900 chr1A 85.222 697 77 18 2394 3080 115543947 115543267 0.000000e+00 693.0
29 TraesCS3D01G482900 chr2A 85.530 698 75 19 2394 3081 37891942 37891261 0.000000e+00 706.0
30 TraesCS3D01G482900 chr2A 85.551 699 74 19 2394 3081 530935230 530934548 0.000000e+00 706.0
31 TraesCS3D01G482900 chr2A 82.653 490 40 25 1633 2111 579835092 579834637 4.920000e-105 392.0
32 TraesCS3D01G482900 chr2A 91.667 84 6 1 1390 1473 579835413 579835331 1.190000e-21 115.0
33 TraesCS3D01G482900 chr4D 92.927 410 21 6 1614 2016 433631509 433631917 1.620000e-164 590.0
34 TraesCS3D01G482900 chr5A 91.707 410 26 6 1614 2016 610087522 610087114 3.540000e-156 562.0
35 TraesCS3D01G482900 chr7D 88.995 418 30 9 1613 2016 587180167 587180582 2.180000e-138 503.0
36 TraesCS3D01G482900 chr7D 89.256 363 27 5 1613 1968 598005994 598005637 1.340000e-120 444.0
37 TraesCS3D01G482900 chr7D 100.000 30 0 0 4958 4987 89283037 89283008 7.330000e-04 56.5
38 TraesCS3D01G482900 chr2D 89.256 363 27 5 1613 1968 587153246 587152889 1.340000e-120 444.0
39 TraesCS3D01G482900 chr2D 87.059 85 7 2 1936 2016 587152889 587152805 5.590000e-15 93.5
40 TraesCS3D01G482900 chr7A 87.059 85 7 2 1936 2016 484092639 484092555 5.590000e-15 93.5


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 TraesCS3D01G482900 chr3D 580538007 580543245 5238 False 9675.000000 9675 100.000000 1 5239 1 chr3D.!!$F1 5238
1 TraesCS3D01G482900 chr3A 716066881 716071535 4654 False 1239.300000 3701 91.263600 683 5237 5 chr3A.!!$F5 4554
2 TraesCS3D01G482900 chr3A 716043213 716043779 566 False 870.000000 870 94.356000 115 681 1 chr3A.!!$F4 566
3 TraesCS3D01G482900 chr3A 465662213 465662894 681 True 706.000000 706 85.530000 2394 3081 1 chr3A.!!$R1 687
4 TraesCS3D01G482900 chr3A 665748588 665749269 681 False 701.000000 701 85.387000 2394 3081 1 chr3A.!!$F2 687
5 TraesCS3D01G482900 chr3B 775824105 775831416 7311 False 1331.800000 2928 90.111600 1 5069 5 chr3B.!!$F2 5068
6 TraesCS3D01G482900 chr6A 616816067 616818774 2707 False 830.000000 1899 86.750667 1390 3947 3 chr6A.!!$F2 2557
7 TraesCS3D01G482900 chr6A 101388562 101389243 681 False 712.000000 712 85.673000 2394 3081 1 chr6A.!!$F1 687
8 TraesCS3D01G482900 chr6D 473083373 473086096 2723 True 916.500000 1705 85.682000 1390 3947 2 chr6D.!!$R2 2557
9 TraesCS3D01G482900 chr6B 718383187 718386252 3065 True 731.333333 1280 85.934000 1390 4263 3 chr6B.!!$R1 2873
10 TraesCS3D01G482900 chr1A 389948707 389949391 684 False 736.000000 736 86.246000 2394 3081 1 chr1A.!!$F1 687
11 TraesCS3D01G482900 chr1A 115543267 115543947 680 True 693.000000 693 85.222000 2394 3080 1 chr1A.!!$R1 686
12 TraesCS3D01G482900 chr2A 37891261 37891942 681 True 706.000000 706 85.530000 2394 3081 1 chr2A.!!$R1 687
13 TraesCS3D01G482900 chr2A 530934548 530935230 682 True 706.000000 706 85.551000 2394 3081 1 chr2A.!!$R2 687
14 TraesCS3D01G482900 chr2A 579834637 579835413 776 True 253.500000 392 87.160000 1390 2111 2 chr2A.!!$R3 721

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
722 723 0.323542 GAGGGTCGACTGGGAGAGAA 60.324 60.000 16.46 0.00 0.0 2.87 F
1189 1460 0.690192 TCTTCTCCACCCGCAAATCA 59.310 50.000 0.00 0.00 0.0 2.57 F
1246 1517 1.153066 TTTCTGTTCAGGTGCGGCA 60.153 52.632 0.00 0.00 0.0 5.69 F
1254 1525 1.165907 TCAGGTGCGGCACTTTTCTG 61.166 55.000 29.92 25.95 34.4 3.02 F
2623 3265 1.291132 GCCTTGGACGAGCTATTCAC 58.709 55.000 0.00 0.00 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2219 2858 1.298953 ATTGATGCTGTACCAGGGGT 58.701 50.000 0.00 0.0 40.16 4.95 R
2597 3239 1.937546 GCTCGTCCAAGGCCCATTTG 61.938 60.000 0.00 0.0 0.00 2.32 R
3220 3976 1.882623 GGTCAAGGAAGAAACAGCTGG 59.117 52.381 19.93 0.0 0.00 4.85 R
3240 3996 7.013655 CCCAATCATCCCAATAAGTAAACTCTG 59.986 40.741 0.00 0.0 0.00 3.35 R
4245 7050 0.112412 AAATTTCCCACCTCGGCACT 59.888 50.000 0.00 0.0 0.00 4.40 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
257 258 4.618460 CGTAGTATGAGCCAAGACACAACT 60.618 45.833 0.00 0.00 0.00 3.16
274 275 4.856487 CACAACTTATAAACATGGTTGGCG 59.144 41.667 6.16 0.00 40.75 5.69
313 314 3.556213 CCCACCTTGTCGATAGTTCACAA 60.556 47.826 0.00 0.00 37.40 3.33
373 374 0.698818 GAAGAAAGGAAGCCCTCCCA 59.301 55.000 0.00 0.00 46.81 4.37
426 427 4.681978 GCCGCCACCACTTCTCGT 62.682 66.667 0.00 0.00 0.00 4.18
487 488 4.043200 GCTGGCCAAAGGTCACGC 62.043 66.667 7.01 0.00 32.12 5.34
608 609 9.393786 ACCCTATATAAGTACCTCATGTTTGAT 57.606 33.333 0.00 0.00 0.00 2.57
654 655 1.340017 GCTCCAAGTAACCATGCAGGA 60.340 52.381 0.00 0.00 41.22 3.86
657 658 2.237143 TCCAAGTAACCATGCAGGAGAG 59.763 50.000 0.00 0.00 41.22 3.20
672 673 2.832129 AGGAGAGGAATTGCAACTACGA 59.168 45.455 0.00 0.00 0.00 3.43
681 682 0.386352 TGCAACTACGACGAACCTCG 60.386 55.000 0.00 0.00 46.93 4.63
722 723 0.323542 GAGGGTCGACTGGGAGAGAA 60.324 60.000 16.46 0.00 0.00 2.87
727 728 2.096248 GTCGACTGGGAGAGAACTCAT 58.904 52.381 8.70 0.00 44.22 2.90
730 731 2.757868 CGACTGGGAGAGAACTCATCTT 59.242 50.000 4.64 0.00 44.22 2.40
761 762 1.738099 CAAACCCGACTCTGCCTCG 60.738 63.158 0.00 0.00 0.00 4.63
850 851 3.235195 CAGTTCGTCGACCTAGTTTCAG 58.765 50.000 10.58 0.00 0.00 3.02
895 896 2.099141 TGTGAAATCCTTCTCGCAGG 57.901 50.000 0.00 0.00 34.86 4.85
978 1243 2.604686 ACTGCTCTTCCTCCGCCA 60.605 61.111 0.00 0.00 0.00 5.69
981 1246 4.070552 GCTCTTCCTCCGCCACGT 62.071 66.667 0.00 0.00 0.00 4.49
1011 1276 1.227853 GCCCGCGATGGTTCCTAAT 60.228 57.895 8.23 0.00 35.15 1.73
1018 1283 1.499049 GATGGTTCCTAATCCGCGTC 58.501 55.000 4.92 0.00 0.00 5.19
1166 1431 1.465200 GGGATCTGGTCGCCTCTACC 61.465 65.000 0.00 0.00 37.53 3.18
1179 1450 2.364002 GCCTCTACCTCATCTTCTCCAC 59.636 54.545 0.00 0.00 0.00 4.02
1189 1460 0.690192 TCTTCTCCACCCGCAAATCA 59.310 50.000 0.00 0.00 0.00 2.57
1194 1465 2.503765 TCTCCACCCGCAAATCAGATTA 59.496 45.455 0.00 0.00 0.00 1.75
1208 1479 7.570324 GCAAATCAGATTAGCCGAGTAGATTTC 60.570 40.741 0.00 0.00 33.60 2.17
1225 1496 3.518992 TTTCCCCTTGATTCGGTTTCT 57.481 42.857 0.00 0.00 0.00 2.52
1246 1517 1.153066 TTTCTGTTCAGGTGCGGCA 60.153 52.632 0.00 0.00 0.00 5.69
1254 1525 1.165907 TCAGGTGCGGCACTTTTCTG 61.166 55.000 29.92 25.95 34.40 3.02
1317 1591 4.095400 GCCCCCTCCTCCTCTCCA 62.095 72.222 0.00 0.00 0.00 3.86
1324 1598 2.593026 CCTCCTCCTCTCCAGTATCAC 58.407 57.143 0.00 0.00 0.00 3.06
1366 1640 3.191371 CCAAGATGTTAACCTGTTCTGCC 59.809 47.826 2.48 0.00 0.00 4.85
1432 1706 1.661112 GCTTGCAATCGACCAGACTAC 59.339 52.381 0.00 0.00 0.00 2.73
1438 1712 2.656560 ATCGACCAGACTACTTGCAC 57.343 50.000 0.00 0.00 0.00 4.57
1467 1741 6.377429 ACAGTTGAATCTATCCTCAAGTACGA 59.623 38.462 0.00 0.00 34.24 3.43
1493 1770 4.006319 GTCTCCATTCCTCTGTTTTCCAG 58.994 47.826 0.00 0.00 42.97 3.86
1509 1786 6.035112 TGTTTTCCAGAAACGAAAATTTTCCG 59.965 34.615 22.15 18.79 40.34 4.30
1510 1787 5.502153 TTCCAGAAACGAAAATTTTCCGA 57.498 34.783 22.15 6.49 34.07 4.55
1511 1788 5.699097 TCCAGAAACGAAAATTTTCCGAT 57.301 34.783 22.15 10.23 34.07 4.18
1512 1789 5.457140 TCCAGAAACGAAAATTTTCCGATG 58.543 37.500 22.15 12.29 34.07 3.84
1513 1790 4.089923 CCAGAAACGAAAATTTTCCGATGC 59.910 41.667 22.15 12.17 34.07 3.91
1514 1791 4.917415 CAGAAACGAAAATTTTCCGATGCT 59.083 37.500 22.15 13.84 34.07 3.79
1515 1792 4.917415 AGAAACGAAAATTTTCCGATGCTG 59.083 37.500 22.15 10.73 34.07 4.41
1516 1793 3.915437 ACGAAAATTTTCCGATGCTGT 57.085 38.095 22.15 11.30 33.68 4.40
1518 1795 5.365403 ACGAAAATTTTCCGATGCTGTTA 57.635 34.783 22.15 0.00 33.68 2.41
1519 1796 5.151389 ACGAAAATTTTCCGATGCTGTTAC 58.849 37.500 22.15 0.00 33.68 2.50
1554 1857 2.092323 CCACTCAGTCGATGACACCTA 58.908 52.381 0.00 0.00 34.60 3.08
1558 1861 3.764434 ACTCAGTCGATGACACCTATGTT 59.236 43.478 0.00 0.00 39.95 2.71
1560 1863 5.417894 ACTCAGTCGATGACACCTATGTTTA 59.582 40.000 0.00 0.00 39.95 2.01
1562 1865 6.873997 TCAGTCGATGACACCTATGTTTATT 58.126 36.000 0.00 0.00 39.95 1.40
1563 1866 8.002984 TCAGTCGATGACACCTATGTTTATTA 57.997 34.615 0.00 0.00 39.95 0.98
1564 1867 8.135529 TCAGTCGATGACACCTATGTTTATTAG 58.864 37.037 0.00 0.00 39.95 1.73
2018 2566 7.264373 AGTAGCCATATGAGTGCAAAAATAC 57.736 36.000 3.65 0.00 0.00 1.89
2024 2572 9.311916 GCCATATGAGTGCAAAAATACAAATAA 57.688 29.630 3.65 0.00 0.00 1.40
2075 2623 3.810310 AGCTGTAGATGTACCAAGAGC 57.190 47.619 0.00 0.10 0.00 4.09
2206 2844 2.684881 GAGCGATGTCAATGGTCCAAAT 59.315 45.455 0.00 0.00 0.00 2.32
2219 2858 4.940483 TGGTCCAAATATGAAATGGTCCA 58.060 39.130 6.00 6.00 45.85 4.02
2328 2968 6.041296 GGATCTGGATGATTGCACCTTTTATT 59.959 38.462 0.00 0.00 35.14 1.40
2554 3196 7.526608 CGTGTTTTCTTAAGGCTGATGAAATA 58.473 34.615 12.35 4.42 0.00 1.40
2597 3239 6.183360 CGATGTTTCTCAATTCAGACCACTAC 60.183 42.308 0.00 0.00 0.00 2.73
2612 3254 1.818674 CACTACAAATGGGCCTTGGAC 59.181 52.381 4.53 0.00 0.00 4.02
2623 3265 1.291132 GCCTTGGACGAGCTATTCAC 58.709 55.000 0.00 0.00 0.00 3.18
2629 3271 2.223502 TGGACGAGCTATTCACTAAGCG 60.224 50.000 0.00 0.00 43.63 4.68
2668 3310 5.972327 ATCATTCTGGAAGGTCTGATCTT 57.028 39.130 2.11 2.11 0.00 2.40
2699 3343 6.641314 TGATTCTTCGACTGTCTTGTTCTTAC 59.359 38.462 6.21 0.00 0.00 2.34
2896 3645 8.033626 GTCTAATTAGGCTACTGTAACTGTTGT 58.966 37.037 9.90 0.00 0.00 3.32
2897 3646 8.591072 TCTAATTAGGCTACTGTAACTGTTGTT 58.409 33.333 12.54 0.00 39.98 2.83
2898 3647 7.435068 AATTAGGCTACTGTAACTGTTGTTG 57.565 36.000 2.69 0.00 37.59 3.33
2899 3648 4.417426 AGGCTACTGTAACTGTTGTTGT 57.583 40.909 2.69 1.84 37.59 3.32
2900 3649 4.777463 AGGCTACTGTAACTGTTGTTGTT 58.223 39.130 2.69 0.00 37.59 2.83
2901 3650 4.574828 AGGCTACTGTAACTGTTGTTGTTG 59.425 41.667 2.69 1.88 37.59 3.33
2902 3651 4.334481 GGCTACTGTAACTGTTGTTGTTGT 59.666 41.667 2.69 0.00 37.59 3.32
2903 3652 5.163693 GGCTACTGTAACTGTTGTTGTTGTT 60.164 40.000 2.69 0.00 37.59 2.83
2904 3653 5.737290 GCTACTGTAACTGTTGTTGTTGTTG 59.263 40.000 2.69 0.00 37.59 3.33
2905 3654 5.699097 ACTGTAACTGTTGTTGTTGTTGT 57.301 34.783 2.69 0.00 37.59 3.32
2906 3655 6.079424 ACTGTAACTGTTGTTGTTGTTGTT 57.921 33.333 2.69 0.00 37.59 2.83
2907 3656 6.146898 ACTGTAACTGTTGTTGTTGTTGTTC 58.853 36.000 2.69 0.00 37.59 3.18
3013 3767 5.241506 TCTGATAGGCCTTTGTTCAACTTTG 59.758 40.000 12.58 0.00 0.00 2.77
3240 3996 1.882623 CCAGCTGTTTCTTCCTTGACC 59.117 52.381 13.81 0.00 0.00 4.02
3288 4044 3.007614 GTGAGGCTAAAGGAGGTACACAA 59.992 47.826 0.00 0.00 0.00 3.33
3295 4051 4.884668 AAAGGAGGTACACAAAGATCGA 57.115 40.909 0.00 0.00 0.00 3.59
3379 4135 9.888878 CTACTCTATGACAATGCAAATTTATGG 57.111 33.333 0.00 0.00 0.00 2.74
3395 4152 2.483014 ATGGCTGCATTTTTGCATGT 57.517 40.000 0.50 0.00 44.47 3.21
3430 4188 4.276926 GCTGATTAGCCCTTGACTATTTGG 59.723 45.833 0.00 0.00 44.33 3.28
3432 4190 4.229582 TGATTAGCCCTTGACTATTTGGGT 59.770 41.667 0.00 0.00 41.59 4.51
3441 4199 6.414732 CCTTGACTATTTGGGTCATTGACTA 58.585 40.000 16.02 3.80 42.26 2.59
3448 4206 8.061304 ACTATTTGGGTCATTGACTATGGATTT 58.939 33.333 16.02 0.00 34.85 2.17
3456 4214 5.533528 TCATTGACTATGGATTTCTGGCATG 59.466 40.000 0.00 0.00 34.85 4.06
3565 4339 5.826208 TGATGCTCATGTATGCAAATCTTCT 59.174 36.000 12.82 0.00 42.74 2.85
3674 6331 0.106918 CGAGGACCTGAGCTACCTCT 60.107 60.000 0.00 0.00 44.47 3.69
3716 6376 4.141620 TGTTCCTCAGAGAGAAAGTTGCTT 60.142 41.667 0.00 0.00 0.00 3.91
3743 6407 7.418337 TCCATAAGAGTGTCTAATGCTTGTA 57.582 36.000 0.00 0.00 0.00 2.41
3844 6508 1.133513 TGTTGAAGGCCCACAATCTGT 60.134 47.619 13.90 0.00 0.00 3.41
4097 6899 4.279671 TCTTCCGGTGCAAAACATTATTGT 59.720 37.500 0.00 0.00 37.82 2.71
4102 6904 5.407995 CCGGTGCAAAACATTATTGTTCATT 59.592 36.000 3.60 0.00 45.30 2.57
4103 6905 6.587990 CCGGTGCAAAACATTATTGTTCATTA 59.412 34.615 3.60 0.00 45.30 1.90
4178 6983 2.610976 CGTGGTGGTCTTCCGATACAAA 60.611 50.000 0.00 0.00 36.30 2.83
4245 7050 3.153919 CAACTTGGGGTTTAGCTTAGCA 58.846 45.455 7.07 0.00 35.74 3.49
4275 7081 6.394345 AGGTGGGAAATTTCTCTATTGACT 57.606 37.500 18.69 5.51 0.00 3.41
4327 7141 5.585047 ACTGAGGTAATTAATTGTTCTCCGC 59.415 40.000 11.05 7.63 0.00 5.54
4328 7142 5.741011 TGAGGTAATTAATTGTTCTCCGCT 58.259 37.500 11.05 0.00 0.00 5.52
4333 7147 4.600012 ATTAATTGTTCTCCGCTTGTCG 57.400 40.909 0.00 0.00 38.08 4.35
4371 7185 3.319755 CATGCTGTGTGGTTGAAAATCC 58.680 45.455 0.00 0.00 0.00 3.01
4437 7251 8.833493 CAGATTTTCAGATACATGTCAGCAATA 58.167 33.333 0.00 0.00 0.00 1.90
4503 7317 0.396556 TGATACCTGGAGCTACGGCA 60.397 55.000 0.00 0.00 41.70 5.69
4590 7404 2.743928 GTGCTGGACTGGGCGAAG 60.744 66.667 0.00 0.00 0.00 3.79
4725 7587 1.043022 TGACAGTCTGCAGCTTCAGA 58.957 50.000 12.33 12.33 40.50 3.27
4734 7596 4.394300 GTCTGCAGCTTCAGATGTAAATGT 59.606 41.667 19.13 0.00 44.04 2.71
4997 7886 7.081349 TGTAGAAATATTTTTGAACAGTGCCG 58.919 34.615 1.43 0.00 0.00 5.69
5121 8010 3.361917 GCATGAACATTTTGTGAACGTGC 60.362 43.478 0.00 0.00 39.68 5.34
5124 8018 1.821336 ACATTTTGTGAACGTGCACG 58.179 45.000 35.99 35.99 41.63 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 5.753438 GTCAGTATGTGGAATATTCGCTCAA 59.247 40.000 9.32 0.00 37.40 3.02
16 17 4.377021 TGGTCAGTATGTGGAATATTCGC 58.623 43.478 9.32 5.67 37.40 4.70
74 75 0.816373 GTAAGGTGGAGACGGGACTC 59.184 60.000 0.00 0.00 36.31 3.36
76 77 0.816373 GAGTAAGGTGGAGACGGGAC 59.184 60.000 0.00 0.00 0.00 4.46
247 248 7.657336 CCAACCATGTTTATAAGTTGTGTCTT 58.343 34.615 11.43 0.00 36.85 3.01
257 258 4.590918 TCTTCCGCCAACCATGTTTATAA 58.409 39.130 0.00 0.00 0.00 0.98
274 275 0.108089 GGGAGCCGTCTCTTTCTTCC 60.108 60.000 0.00 0.00 39.31 3.46
313 314 4.660168 ACTTTGGAGAAGAAGATGCATGT 58.340 39.130 2.46 0.00 0.00 3.21
395 396 2.804912 GCGGCTAGGGTTACCTCCC 61.805 68.421 0.00 0.00 46.95 4.30
426 427 2.747686 GGAAGCCAGGGACGACAA 59.252 61.111 0.00 0.00 0.00 3.18
467 468 1.675641 GTGACCTTTGGCCAGCGAT 60.676 57.895 5.11 0.00 0.00 4.58
487 488 4.752879 CCGCCACCACCTACACCG 62.753 72.222 0.00 0.00 0.00 4.94
608 609 1.283029 AGCTCCTATGCCTTCTTTGCA 59.717 47.619 0.00 0.00 43.97 4.08
654 655 2.230508 TCGTCGTAGTTGCAATTCCTCT 59.769 45.455 0.59 0.00 0.00 3.69
657 658 2.159747 GGTTCGTCGTAGTTGCAATTCC 60.160 50.000 0.59 0.00 0.00 3.01
672 673 3.446570 CGCCCTACCGAGGTTCGT 61.447 66.667 0.00 0.00 41.95 3.85
681 682 4.509737 GTGACGCCTCGCCCTACC 62.510 72.222 0.00 0.00 0.00 3.18
722 723 4.028131 TGGTTGGACCGTATAAGATGAGT 58.972 43.478 0.00 0.00 42.58 3.41
727 728 3.307621 GGGTTTGGTTGGACCGTATAAGA 60.308 47.826 0.00 0.00 42.58 2.10
730 731 1.066286 CGGGTTTGGTTGGACCGTATA 60.066 52.381 0.00 0.00 42.58 1.47
850 851 5.294799 GGAAATTACACAAAAACCCCACAAC 59.705 40.000 0.00 0.00 0.00 3.32
905 907 2.031245 CACTGCTTTGCGTTACAATGGA 60.031 45.455 0.00 0.00 38.31 3.41
915 917 1.063321 TGTAACACACACTGCTTTGCG 59.937 47.619 0.00 0.00 30.04 4.85
996 1261 1.557443 GCGGATTAGGAACCATCGCG 61.557 60.000 0.00 0.00 0.00 5.87
1004 1269 1.202486 GGATGTGACGCGGATTAGGAA 60.202 52.381 12.47 0.00 0.00 3.36
1007 1272 2.506544 CGGATGTGACGCGGATTAG 58.493 57.895 12.47 0.00 0.00 1.73
1018 1283 4.899239 GAGGAGGCGGCGGATGTG 62.899 72.222 9.78 0.00 0.00 3.21
1155 1420 2.292292 GAGAAGATGAGGTAGAGGCGAC 59.708 54.545 0.00 0.00 0.00 5.19
1156 1421 2.577700 GAGAAGATGAGGTAGAGGCGA 58.422 52.381 0.00 0.00 0.00 5.54
1166 1431 0.250234 TTGCGGGTGGAGAAGATGAG 59.750 55.000 0.00 0.00 0.00 2.90
1179 1450 0.588252 CGGCTAATCTGATTTGCGGG 59.412 55.000 25.23 17.98 40.99 6.13
1189 1460 3.579151 GGGGAAATCTACTCGGCTAATCT 59.421 47.826 0.00 0.00 0.00 2.40
1194 1465 1.486726 CAAGGGGAAATCTACTCGGCT 59.513 52.381 0.00 0.00 0.00 5.52
1208 1479 1.282157 AGGAGAAACCGAATCAAGGGG 59.718 52.381 0.00 0.00 44.74 4.79
1225 1496 0.250295 CCGCACCTGAACAGAAAGGA 60.250 55.000 3.19 0.00 37.01 3.36
1246 1517 2.373169 TCATGAGACTGGGCAGAAAAGT 59.627 45.455 0.00 0.00 0.00 2.66
1254 1525 2.512515 GGCGTCATGAGACTGGGC 60.513 66.667 0.00 0.00 42.73 5.36
1291 1565 1.690985 AGGAGGGGGCTTACTGCTC 60.691 63.158 0.00 0.00 42.70 4.26
1317 1591 1.414181 CCCTGGAATGAGCGTGATACT 59.586 52.381 0.00 0.00 0.00 2.12
1324 1598 1.808945 GATTATGCCCTGGAATGAGCG 59.191 52.381 0.00 0.00 0.00 5.03
1378 1652 0.809241 CGGCAACAGAGAGATCAGGC 60.809 60.000 0.00 0.00 0.00 4.85
1388 1662 0.534877 ATGACAACAGCGGCAACAGA 60.535 50.000 1.45 0.00 0.00 3.41
1390 1664 1.598882 TTATGACAACAGCGGCAACA 58.401 45.000 1.45 0.00 0.00 3.33
1432 1706 3.144506 AGATTCAACTGTCCTGTGCAAG 58.855 45.455 0.00 0.00 0.00 4.01
1493 1770 4.679654 ACAGCATCGGAAAATTTTCGTTTC 59.320 37.500 21.53 9.24 38.06 2.78
1497 1774 5.150683 TGTAACAGCATCGGAAAATTTTCG 58.849 37.500 21.53 16.99 38.06 3.46
1509 1786 5.503683 GCTCTCATCAACATGTAACAGCATC 60.504 44.000 0.00 0.00 0.00 3.91
1510 1787 4.334759 GCTCTCATCAACATGTAACAGCAT 59.665 41.667 0.00 0.00 0.00 3.79
1511 1788 3.686241 GCTCTCATCAACATGTAACAGCA 59.314 43.478 0.00 0.00 0.00 4.41
1512 1789 3.064545 GGCTCTCATCAACATGTAACAGC 59.935 47.826 0.00 0.17 0.00 4.40
1513 1790 3.624861 GGGCTCTCATCAACATGTAACAG 59.375 47.826 0.00 0.00 0.00 3.16
1514 1791 3.008923 TGGGCTCTCATCAACATGTAACA 59.991 43.478 0.00 0.00 0.00 2.41
1515 1792 3.375299 GTGGGCTCTCATCAACATGTAAC 59.625 47.826 0.00 0.00 0.00 2.50
1516 1793 3.264193 AGTGGGCTCTCATCAACATGTAA 59.736 43.478 0.00 0.00 0.00 2.41
1518 1795 1.632409 AGTGGGCTCTCATCAACATGT 59.368 47.619 0.00 0.00 0.00 3.21
1519 1796 2.286872 GAGTGGGCTCTCATCAACATG 58.713 52.381 0.00 0.00 38.66 3.21
1563 1866 9.182214 AGAGTGCATTTTGATTTCACATATACT 57.818 29.630 0.00 0.00 0.00 2.12
1564 1867 9.793252 AAGAGTGCATTTTGATTTCACATATAC 57.207 29.630 0.00 0.00 0.00 1.47
1581 1891 1.696336 AGTGAGGTGACAAGAGTGCAT 59.304 47.619 0.00 0.00 0.00 3.96
2029 2577 6.997476 TCTTGCAGGCCAAATTTTCTATTTTT 59.003 30.769 5.01 0.00 31.94 1.94
2030 2578 6.532826 TCTTGCAGGCCAAATTTTCTATTTT 58.467 32.000 5.01 0.00 31.94 1.82
2031 2579 6.112927 TCTTGCAGGCCAAATTTTCTATTT 57.887 33.333 5.01 0.00 31.94 1.40
2033 2581 5.727434 CTTCTTGCAGGCCAAATTTTCTAT 58.273 37.500 5.01 0.00 31.94 1.98
2034 2582 4.561326 GCTTCTTGCAGGCCAAATTTTCTA 60.561 41.667 5.01 0.00 42.31 2.10
2035 2583 3.804759 GCTTCTTGCAGGCCAAATTTTCT 60.805 43.478 5.01 0.00 42.31 2.52
2075 2623 3.192422 CCTCCATCTAGATTCGCTACCAG 59.808 52.174 1.33 0.00 0.00 4.00
2206 2844 1.568597 CCAGGGGTGGACCATTTCATA 59.431 52.381 0.00 0.00 42.91 2.15
2219 2858 1.298953 ATTGATGCTGTACCAGGGGT 58.701 50.000 0.00 0.00 40.16 4.95
2483 3123 9.212641 ACTAGCTATCTTGTAATATGCAATGTG 57.787 33.333 0.00 0.00 0.00 3.21
2597 3239 1.937546 GCTCGTCCAAGGCCCATTTG 61.938 60.000 0.00 0.00 0.00 2.32
2612 3254 6.512177 AAATTACGCTTAGTGAATAGCTCG 57.488 37.500 0.00 0.00 35.25 5.03
2623 3265 6.544620 TTACTCGACGAAAATTACGCTTAG 57.455 37.500 0.00 3.44 0.00 2.18
2629 3271 8.056571 CCAGAATGATTACTCGACGAAAATTAC 58.943 37.037 0.00 0.00 39.69 1.89
2668 3310 8.378172 ACAAGACAGTCGAAGAATCATAAAAA 57.622 30.769 0.00 0.00 39.69 1.94
2672 3316 6.925211 AGAACAAGACAGTCGAAGAATCATA 58.075 36.000 0.00 0.00 39.69 2.15
2699 3343 9.353999 CATGGAAATGAGATGCACAAATATATG 57.646 33.333 0.00 0.00 0.00 1.78
2707 3351 3.090210 ACCATGGAAATGAGATGCACA 57.910 42.857 21.47 0.00 0.00 4.57
2708 3352 4.460948 AAACCATGGAAATGAGATGCAC 57.539 40.909 21.47 0.00 0.00 4.57
2709 3353 6.151663 CATAAACCATGGAAATGAGATGCA 57.848 37.500 21.47 0.00 0.00 3.96
2881 3618 6.837992 ACAACAACAACAACAGTTACAGTAG 58.162 36.000 0.00 0.00 0.00 2.57
2896 3645 6.123651 ACCTACAATACCAGAACAACAACAA 58.876 36.000 0.00 0.00 0.00 2.83
2897 3646 5.686753 ACCTACAATACCAGAACAACAACA 58.313 37.500 0.00 0.00 0.00 3.33
2898 3647 5.107220 CGACCTACAATACCAGAACAACAAC 60.107 44.000 0.00 0.00 0.00 3.32
2899 3648 4.992319 CGACCTACAATACCAGAACAACAA 59.008 41.667 0.00 0.00 0.00 2.83
2900 3649 4.281435 TCGACCTACAATACCAGAACAACA 59.719 41.667 0.00 0.00 0.00 3.33
2901 3650 4.813027 TCGACCTACAATACCAGAACAAC 58.187 43.478 0.00 0.00 0.00 3.32
2902 3651 5.670792 ATCGACCTACAATACCAGAACAA 57.329 39.130 0.00 0.00 0.00 2.83
2903 3652 6.778834 TTATCGACCTACAATACCAGAACA 57.221 37.500 0.00 0.00 0.00 3.18
2904 3653 6.645415 CCATTATCGACCTACAATACCAGAAC 59.355 42.308 0.00 0.00 0.00 3.01
2905 3654 6.740401 GCCATTATCGACCTACAATACCAGAA 60.740 42.308 0.00 0.00 0.00 3.02
2906 3655 5.279306 GCCATTATCGACCTACAATACCAGA 60.279 44.000 0.00 0.00 0.00 3.86
2907 3656 4.929808 GCCATTATCGACCTACAATACCAG 59.070 45.833 0.00 0.00 0.00 4.00
3013 3767 3.694566 ACTTTCCCTATCAATGCGGAAAC 59.305 43.478 0.00 0.00 39.01 2.78
3209 3965 3.901844 AGAAACAGCTGGTACAAGGTAGA 59.098 43.478 19.93 0.00 38.70 2.59
3220 3976 1.882623 GGTCAAGGAAGAAACAGCTGG 59.117 52.381 19.93 0.00 0.00 4.85
3240 3996 7.013655 CCCAATCATCCCAATAAGTAAACTCTG 59.986 40.741 0.00 0.00 0.00 3.35
3288 4044 6.338146 TCTGGTCGAATAAATTGTCGATCTT 58.662 36.000 16.23 0.00 46.91 2.40
3295 4051 6.597672 TGCATACTTCTGGTCGAATAAATTGT 59.402 34.615 0.00 0.00 0.00 2.71
3430 4188 4.276926 GCCAGAAATCCATAGTCAATGACC 59.723 45.833 10.12 0.00 37.86 4.02
3432 4190 5.114764 TGCCAGAAATCCATAGTCAATGA 57.885 39.130 0.00 0.00 37.86 2.57
3441 4199 4.603131 AGTGTTACATGCCAGAAATCCAT 58.397 39.130 0.00 0.00 0.00 3.41
3448 4206 3.207265 ACACAAGTGTTACATGCCAGA 57.793 42.857 0.00 0.00 41.83 3.86
3674 6331 5.126707 GGAACAGATTAACTCTTACCTCCGA 59.873 44.000 0.00 0.00 29.16 4.55
3716 6376 7.665559 ACAAGCATTAGACACTCTTATGGAAAA 59.334 33.333 1.59 0.00 34.94 2.29
3743 6407 7.942341 TCAAGAACTTGTCCTAATGTTACCAAT 59.058 33.333 13.15 0.00 41.16 3.16
3844 6508 6.971726 ATACTGAATCCTTACGTCCACATA 57.028 37.500 0.00 0.00 0.00 2.29
3971 6636 7.212976 TCAGAGATTTATCACTTGCCATACTC 58.787 38.462 0.00 0.00 0.00 2.59
4040 6716 3.502211 CAGGTTCTTACGCATTTCCAGTT 59.498 43.478 0.00 0.00 0.00 3.16
4102 6904 8.046107 CCTTGGAAAATGGCAGGAAAAATAATA 58.954 33.333 0.00 0.00 0.00 0.98
4103 6905 6.885918 CCTTGGAAAATGGCAGGAAAAATAAT 59.114 34.615 0.00 0.00 0.00 1.28
4106 6908 4.350520 TCCTTGGAAAATGGCAGGAAAAAT 59.649 37.500 0.00 0.00 30.33 1.82
4178 6983 4.338682 AGGTATATTCGTCTTCGACTGCTT 59.661 41.667 0.00 0.00 46.03 3.91
4205 7010 1.228894 ACGAAGAGAGTCAGGGCCA 60.229 57.895 6.18 0.00 0.00 5.36
4245 7050 0.112412 AAATTTCCCACCTCGGCACT 59.888 50.000 0.00 0.00 0.00 4.40
4275 7081 1.485124 ATGACAGCGATACACAGGGA 58.515 50.000 0.00 0.00 0.00 4.20
4328 7142 3.002246 GCTGTGTGAATCTTGAACGACAA 59.998 43.478 0.00 0.00 36.97 3.18
4333 7147 3.057736 AGCATGCTGTGTGAATCTTGAAC 60.058 43.478 21.98 0.00 0.00 3.18
4371 7185 1.428448 TGCCACGACTTGAAGAATCG 58.572 50.000 0.00 0.96 41.60 3.34
4548 7362 1.965219 CTCGTCCTCTGGTCGGTTT 59.035 57.895 3.77 0.00 35.20 3.27
4554 7368 1.254284 CCTTCTGCTCGTCCTCTGGT 61.254 60.000 0.00 0.00 0.00 4.00
4590 7404 3.728076 TCAACACCTAGACGATATGGC 57.272 47.619 0.00 0.00 0.00 4.40
4646 7505 7.342284 AGCACATATACTAGTGTAGGTTCAACT 59.658 37.037 13.41 7.07 38.02 3.16
4752 7636 3.557577 TGCATCGAGTTGTTTGGATTG 57.442 42.857 0.00 0.00 0.00 2.67
4992 7881 4.495422 TCTCTAGAAAATCTTCACGGCAC 58.505 43.478 0.00 0.00 33.64 5.01
5074 7963 7.326063 GCAGTGTTAGAAAAATGTTGTGTATCC 59.674 37.037 0.00 0.00 0.00 2.59
5078 7967 5.960113 TGCAGTGTTAGAAAAATGTTGTGT 58.040 33.333 0.00 0.00 0.00 3.72
5083 7972 6.804677 TGTTCATGCAGTGTTAGAAAAATGT 58.195 32.000 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.