Multiple sequence alignment - TraesCS4D01G264400

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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 TraesCS4D01G264400 chr4D 100.000 6515 0 0 1 6515 435006004 435012518 0.000000e+00 12032.0
1 TraesCS4D01G264400 chr4D 95.266 169 8 0 4363 4531 34661524 34661692 1.080000e-67 268.0
2 TraesCS4D01G264400 chr4D 98.077 52 0 1 2711 2761 46029975 46029924 9.000000e-14 89.8
3 TraesCS4D01G264400 chr4A 93.669 3933 143 39 2649 6506 36386706 36390607 0.000000e+00 5786.0
4 TraesCS4D01G264400 chr4A 94.647 934 31 5 1 923 36385131 36386056 0.000000e+00 1430.0
5 TraesCS4D01G264400 chr4A 92.125 546 27 10 925 1464 36386104 36386639 0.000000e+00 756.0
6 TraesCS4D01G264400 chr4A 94.030 67 4 0 2541 2607 36386632 36386698 1.160000e-17 102.0
7 TraesCS4D01G264400 chr4B 96.703 1274 29 5 3463 4726 535082218 535083488 0.000000e+00 2108.0
8 TraesCS4D01G264400 chr4B 96.727 886 20 5 1 880 535079778 535080660 0.000000e+00 1467.0
9 TraesCS4D01G264400 chr4B 88.996 936 56 23 2541 3434 535081291 535082221 0.000000e+00 1114.0
10 TraesCS4D01G264400 chr4B 89.022 920 67 17 4719 5632 535084304 535085195 0.000000e+00 1109.0
11 TraesCS4D01G264400 chr4B 95.303 511 22 1 954 1464 535080790 535081298 0.000000e+00 809.0
12 TraesCS4D01G264400 chr4B 98.578 422 6 0 6091 6512 535085595 535086016 0.000000e+00 747.0
13 TraesCS4D01G264400 chr4B 99.048 105 1 0 5955 6059 535085492 535085596 8.620000e-44 189.0
14 TraesCS4D01G264400 chr4B 100.000 48 0 0 2714 2761 398249948 398249995 9.000000e-14 89.8
15 TraesCS4D01G264400 chr6D 96.303 1082 10 14 1462 2540 457552126 457553180 0.000000e+00 1749.0
16 TraesCS4D01G264400 chr2B 90.150 934 58 15 1628 2540 28011128 28012048 0.000000e+00 1184.0
17 TraesCS4D01G264400 chr2B 89.667 871 57 14 1692 2541 28078666 28077808 0.000000e+00 1079.0
18 TraesCS4D01G264400 chr2B 94.286 385 12 4 1628 2010 27952004 27952380 1.220000e-161 580.0
19 TraesCS4D01G264400 chr2B 79.478 575 61 26 1987 2540 39938317 39937779 8.030000e-94 355.0
20 TraesCS4D01G264400 chr2B 88.333 300 17 10 1465 1763 39939849 39939567 1.740000e-90 344.0
21 TraesCS4D01G264400 chr2B 93.902 164 10 0 4365 4528 608226724 608226887 1.400000e-61 248.0
22 TraesCS4D01G264400 chr2B 92.442 172 11 2 4356 4527 722081365 722081534 1.810000e-60 244.0
23 TraesCS4D01G264400 chr3A 89.451 948 49 18 1540 2464 652902607 652903526 0.000000e+00 1149.0
24 TraesCS4D01G264400 chr3A 80.621 805 92 33 1770 2540 57560504 57559730 1.230000e-156 564.0
25 TraesCS4D01G264400 chr3A 88.889 306 14 10 1465 1769 60219298 60219012 6.210000e-95 359.0
26 TraesCS4D01G264400 chr3A 88.562 306 15 11 1465 1769 57563233 57562947 2.890000e-93 353.0
27 TraesCS4D01G264400 chr3A 78.165 545 63 28 2019 2540 714380407 714379896 4.940000e-76 296.0
28 TraesCS4D01G264400 chr5A 89.095 807 39 19 1739 2540 562411823 562412585 0.000000e+00 957.0
29 TraesCS4D01G264400 chr5A 80.407 786 89 39 1770 2540 523079486 523078751 7.430000e-149 538.0
30 TraesCS4D01G264400 chr5A 79.449 798 91 42 1770 2541 456679244 456679994 1.260000e-136 497.0
31 TraesCS4D01G264400 chr5A 88.673 309 17 6 1462 1769 523081276 523080985 1.730000e-95 361.0
32 TraesCS4D01G264400 chr5A 96.947 131 4 0 1465 1595 562411667 562411797 3.060000e-53 220.0
33 TraesCS4D01G264400 chr5D 90.794 630 32 8 1540 2168 371067756 371067152 0.000000e+00 819.0
34 TraesCS4D01G264400 chr5D 93.939 165 10 0 4363 4527 529218163 529218327 3.900000e-62 250.0
35 TraesCS4D01G264400 chr5D 93.827 162 10 0 4366 4527 377988002 377988163 1.810000e-60 244.0
36 TraesCS4D01G264400 chr5D 100.000 47 0 0 2715 2761 285845272 285845226 3.240000e-13 87.9
37 TraesCS4D01G264400 chr5B 93.010 515 27 4 1602 2115 34883946 34884452 0.000000e+00 743.0
38 TraesCS4D01G264400 chr5B 100.000 48 0 0 2714 2761 278011963 278011916 9.000000e-14 89.8
39 TraesCS4D01G264400 chr3B 81.081 777 90 41 1770 2543 766065832 766065110 9.480000e-158 568.0
40 TraesCS4D01G264400 chr3B 77.455 550 50 43 2019 2540 750995832 750996335 1.800000e-65 261.0
41 TraesCS4D01G264400 chr7A 80.230 784 102 31 1770 2543 68224662 68225402 2.070000e-149 540.0
42 TraesCS4D01G264400 chr1D 85.824 522 50 11 1770 2288 467931997 467932497 3.460000e-147 532.0
43 TraesCS4D01G264400 chr1D 88.608 316 18 6 1455 1769 27681433 27681731 1.030000e-97 368.0
44 TraesCS4D01G264400 chr1D 93.103 58 2 2 2706 2761 473778165 473778108 4.190000e-12 84.2
45 TraesCS4D01G264400 chr1B 89.583 384 19 10 1464 1846 15516135 15515772 9.890000e-128 468.0
46 TraesCS4D01G264400 chr1A 88.562 306 15 10 1465 1769 537447326 537447040 2.890000e-93 353.0
47 TraesCS4D01G264400 chr2D 93.529 170 11 0 4358 4527 134301480 134301649 3.020000e-63 254.0
48 TraesCS4D01G264400 chr2D 98.000 50 1 0 2712 2761 592288513 592288562 3.240000e-13 87.9
49 TraesCS4D01G264400 chr7D 92.814 167 12 0 4366 4532 454079408 454079242 6.530000e-60 243.0
50 TraesCS4D01G264400 chr6A 100.000 48 0 0 2714 2761 610350229 610350276 9.000000e-14 89.8
51 TraesCS4D01G264400 chrUn 96.226 53 2 0 2709 2761 22763206 22763154 3.240000e-13 87.9
52 TraesCS4D01G264400 chr2A 98.000 50 1 0 2712 2761 81785579 81785628 3.240000e-13 87.9


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 TraesCS4D01G264400 chr4D 435006004 435012518 6514 False 12032.000000 12032 100.00000 1 6515 1 chr4D.!!$F2 6514
1 TraesCS4D01G264400 chr4A 36385131 36390607 5476 False 2018.500000 5786 93.61775 1 6506 4 chr4A.!!$F1 6505
2 TraesCS4D01G264400 chr4B 535079778 535086016 6238 False 1077.571429 2108 94.91100 1 6512 7 chr4B.!!$F2 6511
3 TraesCS4D01G264400 chr6D 457552126 457553180 1054 False 1749.000000 1749 96.30300 1462 2540 1 chr6D.!!$F1 1078
4 TraesCS4D01G264400 chr2B 28011128 28012048 920 False 1184.000000 1184 90.15000 1628 2540 1 chr2B.!!$F2 912
5 TraesCS4D01G264400 chr2B 28077808 28078666 858 True 1079.000000 1079 89.66700 1692 2541 1 chr2B.!!$R1 849
6 TraesCS4D01G264400 chr2B 39937779 39939849 2070 True 349.500000 355 83.90550 1465 2540 2 chr2B.!!$R2 1075
7 TraesCS4D01G264400 chr3A 652902607 652903526 919 False 1149.000000 1149 89.45100 1540 2464 1 chr3A.!!$F1 924
8 TraesCS4D01G264400 chr3A 57559730 57563233 3503 True 458.500000 564 84.59150 1465 2540 2 chr3A.!!$R3 1075
9 TraesCS4D01G264400 chr3A 714379896 714380407 511 True 296.000000 296 78.16500 2019 2540 1 chr3A.!!$R2 521
10 TraesCS4D01G264400 chr5A 562411667 562412585 918 False 588.500000 957 93.02100 1465 2540 2 chr5A.!!$F2 1075
11 TraesCS4D01G264400 chr5A 456679244 456679994 750 False 497.000000 497 79.44900 1770 2541 1 chr5A.!!$F1 771
12 TraesCS4D01G264400 chr5A 523078751 523081276 2525 True 449.500000 538 84.54000 1462 2540 2 chr5A.!!$R1 1078
13 TraesCS4D01G264400 chr5D 371067152 371067756 604 True 819.000000 819 90.79400 1540 2168 1 chr5D.!!$R2 628
14 TraesCS4D01G264400 chr5B 34883946 34884452 506 False 743.000000 743 93.01000 1602 2115 1 chr5B.!!$F1 513
15 TraesCS4D01G264400 chr3B 766065110 766065832 722 True 568.000000 568 81.08100 1770 2543 1 chr3B.!!$R1 773
16 TraesCS4D01G264400 chr3B 750995832 750996335 503 False 261.000000 261 77.45500 2019 2540 1 chr3B.!!$F1 521
17 TraesCS4D01G264400 chr7A 68224662 68225402 740 False 540.000000 540 80.23000 1770 2543 1 chr7A.!!$F1 773
18 TraesCS4D01G264400 chr1D 467931997 467932497 500 False 532.000000 532 85.82400 1770 2288 1 chr1D.!!$F2 518

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
942 1006 0.117140 TCTCAGGGCTTCCTCTCCAA 59.883 55.000 0.00 0.00 39.29 3.53 F
1107 1180 0.535797 GGTAACTCCACTTCCTCCGG 59.464 60.000 0.00 0.00 35.97 5.14 F
1197 1270 1.153842 GCTCGAATTTTTGGGCCGG 60.154 57.895 0.00 0.00 31.59 6.13 F
1204 1277 1.422977 ATTTTTGGGCCGGGGCTTTT 61.423 50.000 20.88 0.00 41.60 2.27 F
1412 1485 2.711542 AGGCAGGAAGGTACAAATTCG 58.288 47.619 0.00 0.00 0.00 3.34 F
3133 5811 2.756840 AACCGAGGTACCTGCTAAAC 57.243 50.000 22.10 2.05 0.00 2.01 F
4563 7252 2.168313 TGTGACATATCCAGCGTGTGAT 59.832 45.455 0.00 0.00 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2752 5407 0.530744 TTGACCGCAGCCTACACTAG 59.469 55.000 0.0 0.0 0.00 2.57 R
2753 5408 0.970640 TTTGACCGCAGCCTACACTA 59.029 50.000 0.0 0.0 0.00 2.74 R
3002 5680 2.096496 AGTGCATCTTTTAGCATCGCAC 59.904 45.455 0.0 0.0 46.52 5.34 R
3096 5774 3.496160 CGGTTTTGAGAGGAGGGAAAGAA 60.496 47.826 0.0 0.0 0.00 2.52 R
3316 5994 8.873215 ATCTTATACATTACCTGAGAACAACG 57.127 34.615 0.0 0.0 0.00 4.10 R
4656 7345 1.337703 ACTTGAATTTCGCAAGCAGCA 59.662 42.857 0.0 0.0 45.00 4.41 R
5730 9253 0.742505 CGTCCCACGAGCCTGTATTA 59.257 55.000 0.0 0.0 46.05 0.98 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 1.757118 ACCATGACCATCGTGTAGAGG 59.243 52.381 0.00 0.00 31.62 3.69
37 38 0.537188 CCATCGTGTAGAGGCTGGTT 59.463 55.000 0.00 0.00 0.00 3.67
49 50 1.439644 GCTGGTTAGCGAGGAGAGG 59.560 63.158 0.00 0.00 40.67 3.69
143 144 1.293498 GCCTCGAAGTCCTGCAGAA 59.707 57.895 17.39 0.00 0.00 3.02
145 146 1.878102 GCCTCGAAGTCCTGCAGAAAA 60.878 52.381 17.39 0.00 0.00 2.29
229 230 4.774503 GCCGCAGCCTCTGAAGCT 62.775 66.667 0.00 0.00 42.70 3.74
231 232 1.520342 CCGCAGCCTCTGAAGCTAC 60.520 63.158 0.00 0.00 38.95 3.58
235 236 1.414181 GCAGCCTCTGAAGCTACCATA 59.586 52.381 0.00 0.00 38.95 2.74
236 237 2.804933 GCAGCCTCTGAAGCTACCATAC 60.805 54.545 0.00 0.00 38.95 2.39
661 663 0.830648 TCTCTCGCGAATGGGGATTT 59.169 50.000 11.33 0.00 36.94 2.17
664 666 1.447317 CTCGCGAATGGGGATTTGGG 61.447 60.000 11.33 0.00 36.94 4.12
722 727 0.393077 CCACCTGATATGACGGGACC 59.607 60.000 0.00 0.00 39.41 4.46
846 853 1.559682 GTGGAATGGGCTGGAGAACTA 59.440 52.381 0.00 0.00 0.00 2.24
880 887 2.116125 GCCCACAGCCCAACTTCT 59.884 61.111 0.00 0.00 34.35 2.85
883 890 1.151450 CCACAGCCCAACTTCTGGT 59.849 57.895 0.00 0.00 44.76 4.00
884 891 0.890996 CCACAGCCCAACTTCTGGTC 60.891 60.000 0.00 0.00 44.76 4.02
941 1005 0.325110 CTCTCAGGGCTTCCTCTCCA 60.325 60.000 0.00 0.00 39.29 3.86
942 1006 0.117140 TCTCAGGGCTTCCTCTCCAA 59.883 55.000 0.00 0.00 39.29 3.53
1107 1180 0.535797 GGTAACTCCACTTCCTCCGG 59.464 60.000 0.00 0.00 35.97 5.14
1190 1263 6.389906 CCTGTAGGATTTTGCTCGAATTTTT 58.610 36.000 0.00 0.00 37.39 1.94
1197 1270 1.153842 GCTCGAATTTTTGGGCCGG 60.154 57.895 0.00 0.00 31.59 6.13
1204 1277 1.422977 ATTTTTGGGCCGGGGCTTTT 61.423 50.000 20.88 0.00 41.60 2.27
1314 1387 6.252599 TGGATAGTGATACCAGCATCTTTT 57.747 37.500 0.00 0.00 0.00 2.27
1315 1388 7.373617 TGGATAGTGATACCAGCATCTTTTA 57.626 36.000 0.00 0.00 0.00 1.52
1412 1485 2.711542 AGGCAGGAAGGTACAAATTCG 58.288 47.619 0.00 0.00 0.00 3.34
1598 1671 8.206189 TCACATTGAATACAAGATGAGCAGATA 58.794 33.333 0.00 0.00 39.46 1.98
1599 1672 9.000486 CACATTGAATACAAGATGAGCAGATAT 58.000 33.333 0.00 0.00 39.46 1.63
2566 5195 8.610896 GGCTTATGATTGATAGATTGCTATGTC 58.389 37.037 0.00 0.00 37.45 3.06
2575 5204 8.387190 TGATAGATTGCTATGTCAAATTGAGG 57.613 34.615 0.00 0.00 37.45 3.86
2628 5257 6.791887 AAGTGTCATGAAACATACAGTGAG 57.208 37.500 18.32 0.00 0.00 3.51
2634 5263 8.581578 TGTCATGAAACATACAGTGAGTTAGTA 58.418 33.333 0.00 0.00 0.00 1.82
2709 5364 7.859325 TTCATAGGTTACAATTTACAGGAGC 57.141 36.000 0.00 0.00 0.00 4.70
2717 5372 9.392259 GGTTACAATTTACAGGAGCTTAATACT 57.608 33.333 0.00 0.00 0.00 2.12
2726 5381 4.545208 GGAGCTTAATACTCCCTCCATC 57.455 50.000 11.87 0.00 46.81 3.51
2727 5382 3.262151 GGAGCTTAATACTCCCTCCATCC 59.738 52.174 11.87 0.00 46.81 3.51
2728 5383 3.252351 AGCTTAATACTCCCTCCATCCC 58.748 50.000 0.00 0.00 0.00 3.85
2730 5385 3.589288 GCTTAATACTCCCTCCATCCCAT 59.411 47.826 0.00 0.00 0.00 4.00
2731 5386 4.783227 GCTTAATACTCCCTCCATCCCATA 59.217 45.833 0.00 0.00 0.00 2.74
2732 5387 5.250774 GCTTAATACTCCCTCCATCCCATAA 59.749 44.000 0.00 0.00 0.00 1.90
2733 5388 6.069381 GCTTAATACTCCCTCCATCCCATAAT 60.069 42.308 0.00 0.00 0.00 1.28
2734 5389 7.127339 GCTTAATACTCCCTCCATCCCATAATA 59.873 40.741 0.00 0.00 0.00 0.98
2735 5390 9.230477 CTTAATACTCCCTCCATCCCATAATAT 57.770 37.037 0.00 0.00 0.00 1.28
2740 5395 6.905776 ACTCCCTCCATCCCATAATATAAGAG 59.094 42.308 0.00 0.00 0.00 2.85
2741 5396 5.667626 TCCCTCCATCCCATAATATAAGAGC 59.332 44.000 0.00 0.00 0.00 4.09
2742 5397 5.453903 CCCTCCATCCCATAATATAAGAGCG 60.454 48.000 0.00 0.00 0.00 5.03
2744 5399 6.352222 CCTCCATCCCATAATATAAGAGCGTT 60.352 42.308 0.00 0.00 0.00 4.84
2745 5400 7.016153 TCCATCCCATAATATAAGAGCGTTT 57.984 36.000 0.00 0.00 0.00 3.60
2937 5615 7.093988 TGTGGGTAGGTATGATGTTTTCAATTG 60.094 37.037 0.00 0.00 38.03 2.32
2962 5640 5.005740 TCTTATGCTGCTCATTTGACAGTT 58.994 37.500 0.00 4.16 36.63 3.16
2979 5657 5.414454 TGACAGTTTGTGTAAGCTCTTTGTT 59.586 36.000 0.00 0.00 40.56 2.83
3002 5680 8.527810 TGTTTTTATTTATAGGACTTTGGGCAG 58.472 33.333 0.00 0.00 0.00 4.85
3061 5739 6.551601 TCAAGATTTGGGCTGTTAAAGGTAAA 59.448 34.615 0.00 0.00 0.00 2.01
3096 5774 9.829507 TGGTTCACAACATCTAAAATTCAAAAT 57.170 25.926 0.00 0.00 0.00 1.82
3133 5811 2.756840 AACCGAGGTACCTGCTAAAC 57.243 50.000 22.10 2.05 0.00 2.01
3316 5994 4.379082 CGAGTTACTAATGGTTTTGGTGGC 60.379 45.833 0.00 0.00 0.00 5.01
3976 6654 5.803967 GGCATGCTTTCATAGAAAGTCTTTG 59.196 40.000 18.92 12.11 0.00 2.77
3985 6663 8.533569 TTCATAGAAAGTCTTTGTTTCCCTTT 57.466 30.769 1.60 0.00 34.93 3.11
4183 6871 6.660949 AGCAGCCCTCATAATATGGTAAATTC 59.339 38.462 0.00 0.00 0.00 2.17
4201 6889 7.870445 GGTAAATTCTCTAGCCTCACTTATCTG 59.130 40.741 0.00 0.00 0.00 2.90
4476 7165 3.745975 TCACTTCTTTTGCTCCGTATGTG 59.254 43.478 0.00 0.00 0.00 3.21
4563 7252 2.168313 TGTGACATATCCAGCGTGTGAT 59.832 45.455 0.00 0.00 0.00 3.06
4656 7345 2.558800 GGGAGGAAGAGACAGGAGAACT 60.559 54.545 0.00 0.00 0.00 3.01
4721 7410 8.041323 CACTTAACAGGTCAGTCCACTAAATAT 58.959 37.037 0.00 0.00 39.02 1.28
4754 8265 8.988934 CGTATTGCATATAGGTTTGTAGTGAAT 58.011 33.333 0.00 0.00 0.00 2.57
4777 8288 9.431887 GAATTTTAGACTGTGTACACCATTCTA 57.568 33.333 22.91 19.86 0.00 2.10
4778 8289 8.773404 ATTTTAGACTGTGTACACCATTCTAC 57.227 34.615 22.91 7.70 0.00 2.59
4810 8321 6.747414 ATGGGTAGTGTAAGCAATGAGATA 57.253 37.500 0.00 0.00 0.00 1.98
4914 8428 2.159085 ACGCTAACTGCTGACCTAATCC 60.159 50.000 0.00 0.00 40.11 3.01
4926 8440 5.036117 TGACCTAATCCCTAACAATCAGC 57.964 43.478 0.00 0.00 0.00 4.26
4927 8441 4.473196 TGACCTAATCCCTAACAATCAGCA 59.527 41.667 0.00 0.00 0.00 4.41
4963 8477 3.131046 AGGGCACTTTGCTGCATATTTAC 59.869 43.478 1.84 0.00 44.28 2.01
5016 8530 2.289320 TGCAATACCCAAATTGTGCACC 60.289 45.455 15.69 0.00 38.78 5.01
5052 8566 6.037610 CACATTAACTAGCCTGGATTCTTCAC 59.962 42.308 0.00 0.00 0.00 3.18
5151 8668 3.754188 CTGAAAGCATACTCCAAGTGC 57.246 47.619 0.00 0.00 39.10 4.40
5187 8704 5.078411 AGATAATCAACGTGCAGAACTCT 57.922 39.130 0.00 0.00 0.00 3.24
5243 8760 3.002553 CCTGTAAACGGTAACAACCACAC 59.997 47.826 0.00 0.00 0.00 3.82
5253 8770 2.346766 ACAACCACACTGCATCTCAA 57.653 45.000 0.00 0.00 0.00 3.02
5286 8804 9.205513 AGAATTTTGGCAAAATCTATCCATACT 57.794 29.630 31.79 16.32 40.05 2.12
5312 8830 7.446931 TCAAATTGTACTAAGATTGGTTCTGCA 59.553 33.333 0.00 0.00 33.93 4.41
5333 8852 8.845227 TCTGCAGACATTGATTTTACTTTGTTA 58.155 29.630 13.74 0.00 0.00 2.41
5448 8970 2.568623 ACATGAACCACTTGGACCTC 57.431 50.000 0.00 0.00 38.94 3.85
5517 9039 3.548014 GGATTACCGACGCAAAATGATGG 60.548 47.826 0.00 0.00 0.00 3.51
5527 9049 4.050553 CGCAAAATGATGGTTGTTTGTCT 58.949 39.130 0.00 0.00 34.24 3.41
5558 9081 3.197927 AGATCCAGGTCTCTTGAGGTT 57.802 47.619 0.00 0.00 0.00 3.50
5561 9084 4.352298 AGATCCAGGTCTCTTGAGGTTTTT 59.648 41.667 0.00 0.00 0.00 1.94
5562 9085 5.548056 AGATCCAGGTCTCTTGAGGTTTTTA 59.452 40.000 0.00 0.00 0.00 1.52
5613 9136 1.980844 CACTTGTATTGCTTGCTTGCG 59.019 47.619 0.00 0.00 35.36 4.85
5621 9144 1.154654 GCTTGCTTGCGTCGTGTAC 60.155 57.895 0.00 0.00 0.00 2.90
5626 9149 1.615107 GCTTGCGTCGTGTACCAGTC 61.615 60.000 0.00 0.00 0.00 3.51
5627 9150 0.318360 CTTGCGTCGTGTACCAGTCA 60.318 55.000 0.00 0.00 0.00 3.41
5628 9151 0.315886 TTGCGTCGTGTACCAGTCAT 59.684 50.000 0.00 0.00 0.00 3.06
5658 9181 7.519032 TTTTTCTTTTGAGGGATTCGTGTAT 57.481 32.000 0.00 0.00 0.00 2.29
5659 9182 6.737254 TTTCTTTTGAGGGATTCGTGTATC 57.263 37.500 0.00 0.00 0.00 2.24
5660 9183 5.414789 TCTTTTGAGGGATTCGTGTATCA 57.585 39.130 0.00 0.00 0.00 2.15
5661 9184 5.419542 TCTTTTGAGGGATTCGTGTATCAG 58.580 41.667 0.00 0.00 0.00 2.90
5662 9185 5.186992 TCTTTTGAGGGATTCGTGTATCAGA 59.813 40.000 0.00 0.00 0.00 3.27
5663 9186 5.614324 TTTGAGGGATTCGTGTATCAGAT 57.386 39.130 0.00 0.00 0.00 2.90
5718 9241 2.101582 AGTCTTTGAGAACACGAGTGCT 59.898 45.455 2.76 0.00 35.88 4.40
5730 9253 6.929606 AGAACACGAGTGCTTTTATTTAGACT 59.070 34.615 2.76 0.00 24.49 3.24
5732 9255 8.597662 AACACGAGTGCTTTTATTTAGACTAA 57.402 30.769 2.76 0.00 0.00 2.24
5733 9256 8.773404 ACACGAGTGCTTTTATTTAGACTAAT 57.227 30.769 2.76 0.00 0.00 1.73
5734 9257 9.865321 ACACGAGTGCTTTTATTTAGACTAATA 57.135 29.630 2.76 0.00 0.00 0.98
5736 9259 9.865321 ACGAGTGCTTTTATTTAGACTAATACA 57.135 29.630 0.00 0.00 0.00 2.29
5739 9262 9.110502 AGTGCTTTTATTTAGACTAATACAGGC 57.889 33.333 0.00 0.00 0.00 4.85
5741 9264 9.326413 TGCTTTTATTTAGACTAATACAGGCTC 57.674 33.333 0.00 0.00 38.86 4.70
5742 9265 8.488764 GCTTTTATTTAGACTAATACAGGCTCG 58.511 37.037 0.00 0.00 38.86 5.03
5744 9267 8.867112 TTTATTTAGACTAATACAGGCTCGTG 57.133 34.615 0.00 0.00 38.86 4.35
5745 9268 4.913335 TTAGACTAATACAGGCTCGTGG 57.087 45.455 0.00 0.00 38.86 4.94
5746 9269 2.032620 AGACTAATACAGGCTCGTGGG 58.967 52.381 0.00 0.00 38.86 4.61
5748 9271 1.755380 ACTAATACAGGCTCGTGGGAC 59.245 52.381 0.00 0.00 0.00 4.46
5749 9272 0.742505 TAATACAGGCTCGTGGGACG 59.257 55.000 0.00 0.00 44.19 4.79
5750 9273 1.255667 AATACAGGCTCGTGGGACGT 61.256 55.000 0.00 0.00 43.14 4.34
5753 9276 1.597027 CAGGCTCGTGGGACGTTTT 60.597 57.895 0.00 0.00 43.14 2.43
5754 9277 1.301479 AGGCTCGTGGGACGTTTTC 60.301 57.895 0.00 0.00 43.14 2.29
5770 9293 1.717194 TTTCGCTGACGTATGTTCCC 58.283 50.000 0.00 0.00 41.18 3.97
5785 9308 7.881232 ACGTATGTTCCCTATATTAACCAATGG 59.119 37.037 0.00 0.00 0.00 3.16
5849 9380 0.179137 TAGTTGATCAGCACGAGCCG 60.179 55.000 12.41 0.00 43.56 5.52
5850 9381 1.738099 GTTGATCAGCACGAGCCGT 60.738 57.895 4.47 0.00 43.56 5.68
5906 9486 7.226523 TGCGTATACATGAATGAGTAAGCAAAT 59.773 33.333 0.00 0.00 35.21 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 1.439644 CCTCTCCTCGCTAACCAGC 59.560 63.158 0.00 0.00 44.90 4.85
37 38 1.142060 CTCTCTTCCCTCTCCTCGCTA 59.858 57.143 0.00 0.00 0.00 4.26
49 50 0.829333 TCATCCTGCTGCTCTCTTCC 59.171 55.000 0.00 0.00 0.00 3.46
145 146 4.142469 GCCTGAAACTAACTGTGTGTTTGT 60.142 41.667 13.55 0.00 44.14 2.83
629 631 3.743091 GAGAGAGAACCGGCGAGCG 62.743 68.421 9.30 0.00 0.00 5.03
630 632 2.103340 GAGAGAGAACCGGCGAGC 59.897 66.667 9.30 0.00 0.00 5.03
631 633 2.405594 CGAGAGAGAACCGGCGAG 59.594 66.667 9.30 0.06 0.00 5.03
664 666 3.091850 TAGCTAAACCCCGGCCCC 61.092 66.667 0.00 0.00 0.00 5.80
668 673 0.622136 AAACCCTAGCTAAACCCCGG 59.378 55.000 0.00 0.00 0.00 5.73
722 727 1.758906 GGTTCCCCTCCTCCTCTCG 60.759 68.421 0.00 0.00 0.00 4.04
817 824 1.830145 CCCATTCCACCGTAGAGGG 59.170 63.158 0.00 0.00 46.96 4.30
846 853 2.052104 GCCCAATTTAGCAGGCCGT 61.052 57.895 0.00 0.00 39.60 5.68
934 998 1.001378 CGTTGTTTGGCTTTGGAGAGG 60.001 52.381 0.00 0.00 0.00 3.69
941 1005 2.279186 GCGGCGTTGTTTGGCTTT 60.279 55.556 9.37 0.00 0.00 3.51
942 1006 4.279043 GGCGGCGTTGTTTGGCTT 62.279 61.111 9.37 0.00 0.00 4.35
984 1057 0.622665 CCATCCTGGAAGACTTGCCT 59.377 55.000 0.00 0.00 40.96 4.75
1107 1180 1.197036 GACTGGAAACAAACTAGCGCC 59.803 52.381 2.29 0.00 42.06 6.53
1197 1270 3.010420 CCTAGTCTAACTGCAAAAGCCC 58.990 50.000 0.00 0.00 0.00 5.19
1204 1277 4.321008 CGAGTGAAACCTAGTCTAACTGCA 60.321 45.833 0.00 0.00 37.80 4.41
1412 1485 1.692411 AACAACCAGGAAGTTCCAGC 58.308 50.000 23.87 0.00 39.61 4.85
1598 1671 8.969260 TCTGCTCATCTTGTATTCAATGTTAT 57.031 30.769 0.00 0.00 32.82 1.89
1599 1672 8.969260 ATCTGCTCATCTTGTATTCAATGTTA 57.031 30.769 0.00 0.00 32.82 2.41
2553 5182 6.038603 GCACCTCAATTTGACATAGCAATCTA 59.961 38.462 0.00 0.00 0.00 1.98
2555 5184 5.039333 GCACCTCAATTTGACATAGCAATC 58.961 41.667 0.00 0.00 0.00 2.67
2566 5195 3.479006 CGTCTAAACGCACCTCAATTTG 58.521 45.455 0.00 0.00 42.82 2.32
2628 5257 4.628333 TGGCGAGTACAAGCAAATACTAAC 59.372 41.667 13.33 0.00 31.69 2.34
2634 5263 1.165270 GGTGGCGAGTACAAGCAAAT 58.835 50.000 13.33 0.00 34.54 2.32
2709 5364 6.952605 TTATGGGATGGAGGGAGTATTAAG 57.047 41.667 0.00 0.00 0.00 1.85
2717 5372 5.667626 GCTCTTATATTATGGGATGGAGGGA 59.332 44.000 0.00 0.00 0.00 4.20
2718 5373 5.453903 CGCTCTTATATTATGGGATGGAGGG 60.454 48.000 0.00 0.00 0.00 4.30
2719 5374 5.129485 ACGCTCTTATATTATGGGATGGAGG 59.871 44.000 0.00 0.00 0.00 4.30
2720 5375 6.227298 ACGCTCTTATATTATGGGATGGAG 57.773 41.667 0.00 0.00 0.00 3.86
2721 5376 6.620877 AACGCTCTTATATTATGGGATGGA 57.379 37.500 0.00 0.00 0.00 3.41
2722 5377 7.687941 AAAACGCTCTTATATTATGGGATGG 57.312 36.000 0.00 0.00 0.00 3.51
2744 5399 3.991773 CGCAGCCTACACTAGTGTAAAAA 59.008 43.478 30.31 15.08 44.47 1.94
2745 5400 3.581755 CGCAGCCTACACTAGTGTAAAA 58.418 45.455 30.31 15.41 44.47 1.52
2748 5403 1.100510 CCGCAGCCTACACTAGTGTA 58.899 55.000 29.21 29.21 44.42 2.90
2749 5404 0.898789 ACCGCAGCCTACACTAGTGT 60.899 55.000 30.13 30.13 46.87 3.55
2751 5406 0.611062 TGACCGCAGCCTACACTAGT 60.611 55.000 0.00 0.00 0.00 2.57
2752 5407 0.530744 TTGACCGCAGCCTACACTAG 59.469 55.000 0.00 0.00 0.00 2.57
2753 5408 0.970640 TTTGACCGCAGCCTACACTA 59.029 50.000 0.00 0.00 0.00 2.74
2937 5615 5.106396 ACTGTCAAATGAGCAGCATAAGAAC 60.106 40.000 0.00 0.00 35.78 3.01
2979 5657 7.363443 GCACTGCCCAAAGTCCTATAAATAAAA 60.363 37.037 0.00 0.00 0.00 1.52
3002 5680 2.096496 AGTGCATCTTTTAGCATCGCAC 59.904 45.455 0.00 0.00 46.52 5.34
3096 5774 3.496160 CGGTTTTGAGAGGAGGGAAAGAA 60.496 47.826 0.00 0.00 0.00 2.52
3316 5994 8.873215 ATCTTATACATTACCTGAGAACAACG 57.127 34.615 0.00 0.00 0.00 4.10
3422 6100 4.965762 GCTTCACAGTAACCAACGTTTTAC 59.034 41.667 12.83 12.83 33.17 2.01
3976 6654 7.728148 TGAACCTAATTTTGGTAAAGGGAAAC 58.272 34.615 2.89 0.00 36.69 2.78
4183 6871 6.183360 ACAATTCCAGATAAGTGAGGCTAGAG 60.183 42.308 0.00 0.00 0.00 2.43
4201 6889 8.986477 ACATCAATAGCTTAACAAACAATTCC 57.014 30.769 0.00 0.00 0.00 3.01
4459 7148 2.346803 GAGCACATACGGAGCAAAAGA 58.653 47.619 0.00 0.00 0.00 2.52
4460 7149 1.398390 GGAGCACATACGGAGCAAAAG 59.602 52.381 0.00 0.00 0.00 2.27
4563 7252 7.661536 ACTAGCACTATCCTGAACTATGAAA 57.338 36.000 0.00 0.00 0.00 2.69
4656 7345 1.337703 ACTTGAATTTCGCAAGCAGCA 59.662 42.857 0.00 0.00 45.00 4.41
4728 7417 7.940178 TCACTACAAACCTATATGCAATACG 57.060 36.000 0.00 0.00 0.00 3.06
4749 8260 6.854496 TGGTGTACACAGTCTAAAATTCAC 57.146 37.500 26.51 5.38 0.00 3.18
4754 8265 7.728148 TGTAGAATGGTGTACACAGTCTAAAA 58.272 34.615 26.51 16.82 44.11 1.52
4778 8289 8.500753 TTGCTTACACTACCCATAAATAAGTG 57.499 34.615 0.00 0.00 42.53 3.16
4914 8428 3.155093 GCACCATTGCTGATTGTTAGG 57.845 47.619 0.00 0.00 46.17 2.69
4926 8440 2.706636 CCCTATCGTGGCACCATTG 58.293 57.895 12.86 5.85 0.00 2.82
4963 8477 9.064706 ACTAAGATGATTGAATGCTGGATAAAG 57.935 33.333 0.00 0.00 0.00 1.85
5016 8530 4.274459 GCTAGTTAATGTGAAGGGCAGATG 59.726 45.833 0.00 0.00 29.77 2.90
5052 8566 8.839914 CATTACGTAAATGAAACATGTTCTGTG 58.160 33.333 12.39 0.00 46.81 3.66
5151 8668 3.559655 TGATTATCTCGGTGCCATTTTCG 59.440 43.478 0.00 0.00 0.00 3.46
5187 8704 0.250252 TCGATGCACTTGACAGCCAA 60.250 50.000 0.00 0.00 0.00 4.52
5199 8716 3.002246 GTGACTTTGAAACACTCGATGCA 59.998 43.478 0.00 0.00 0.00 3.96
5243 8760 7.010183 CCAAAATTCTAATGCTTTGAGATGCAG 59.990 37.037 0.00 0.00 42.74 4.41
5253 8770 9.895138 ATAGATTTTGCCAAAATTCTAATGCTT 57.105 25.926 16.03 3.05 40.97 3.91
5286 8804 7.446931 TGCAGAACCAATCTTAGTACAATTTGA 59.553 33.333 2.79 0.00 35.73 2.69
5333 8852 2.480073 GCCACTGCGATGCACAAATAAT 60.480 45.455 0.00 0.00 33.79 1.28
5448 8970 2.744768 GCTTTCTTCGCCCTCGCTG 61.745 63.158 0.00 0.00 35.26 5.18
5456 8978 1.429463 TTCCTCTTCGCTTTCTTCGC 58.571 50.000 0.00 0.00 0.00 4.70
5517 9039 7.905493 GGATCTTATTTCGATCAGACAAACAAC 59.095 37.037 0.00 0.00 39.17 3.32
5527 9049 5.835819 AGAGACCTGGATCTTATTTCGATCA 59.164 40.000 0.00 0.00 39.17 2.92
5558 9081 8.335532 AGATTGTTTTCAGATCCACGATAAAA 57.664 30.769 0.00 0.00 0.00 1.52
5561 9084 8.642432 AGATAGATTGTTTTCAGATCCACGATA 58.358 33.333 0.00 0.00 0.00 2.92
5562 9085 7.504403 AGATAGATTGTTTTCAGATCCACGAT 58.496 34.615 0.00 0.00 0.00 3.73
5613 9136 7.766219 AAAATACATATGACTGGTACACGAC 57.234 36.000 10.38 0.00 0.00 4.34
5621 9144 9.793252 CCTCAAAAGAAAAATACATATGACTGG 57.207 33.333 10.38 0.00 0.00 4.00
5628 9151 9.238368 ACGAATCCCTCAAAAGAAAAATACATA 57.762 29.630 0.00 0.00 0.00 2.29
5644 9167 4.279671 ACTGATCTGATACACGAATCCCTC 59.720 45.833 6.60 0.00 0.00 4.30
5660 9183 9.854668 ACAGTCTACACTTACATATACTGATCT 57.145 33.333 0.00 0.00 37.22 2.75
5692 9215 2.135933 CGTGTTCTCAAAGACTGACCC 58.864 52.381 0.00 0.00 0.00 4.46
5693 9216 3.053455 CTCGTGTTCTCAAAGACTGACC 58.947 50.000 0.00 0.00 0.00 4.02
5694 9217 3.487574 CACTCGTGTTCTCAAAGACTGAC 59.512 47.826 0.00 0.00 0.00 3.51
5695 9218 3.706698 CACTCGTGTTCTCAAAGACTGA 58.293 45.455 0.00 0.00 0.00 3.41
5698 9221 2.474816 AGCACTCGTGTTCTCAAAGAC 58.525 47.619 0.00 0.00 0.00 3.01
5718 9241 9.309516 CACGAGCCTGTATTAGTCTAAATAAAA 57.690 33.333 0.00 0.00 0.00 1.52
5730 9253 0.742505 CGTCCCACGAGCCTGTATTA 59.257 55.000 0.00 0.00 46.05 0.98
5732 9255 1.255667 AACGTCCCACGAGCCTGTAT 61.256 55.000 2.48 0.00 46.05 2.29
5733 9256 1.466025 AAACGTCCCACGAGCCTGTA 61.466 55.000 2.48 0.00 46.05 2.74
5734 9257 2.319890 AAAACGTCCCACGAGCCTGT 62.320 55.000 2.48 0.00 46.05 4.00
5735 9258 1.566018 GAAAACGTCCCACGAGCCTG 61.566 60.000 2.48 0.00 46.05 4.85
5736 9259 1.301479 GAAAACGTCCCACGAGCCT 60.301 57.895 2.48 0.00 46.05 4.58
5737 9260 2.664436 CGAAAACGTCCCACGAGCC 61.664 63.158 2.48 0.00 46.05 4.70
5738 9261 2.851104 CGAAAACGTCCCACGAGC 59.149 61.111 2.48 0.00 46.05 5.03
5739 9262 1.663702 AGCGAAAACGTCCCACGAG 60.664 57.895 2.48 0.00 46.05 4.18
5742 9265 1.568025 GTCAGCGAAAACGTCCCAC 59.432 57.895 0.00 0.00 0.00 4.61
5744 9267 2.851104 CGTCAGCGAAAACGTCCC 59.149 61.111 0.00 0.00 41.33 4.46
5748 9271 2.471749 GGAACATACGTCAGCGAAAACG 60.472 50.000 0.00 0.00 44.22 3.60
5749 9272 2.159747 GGGAACATACGTCAGCGAAAAC 60.160 50.000 0.00 0.00 42.00 2.43
5750 9273 2.070783 GGGAACATACGTCAGCGAAAA 58.929 47.619 0.00 0.00 42.00 2.29
5753 9276 1.753930 TAGGGAACATACGTCAGCGA 58.246 50.000 0.00 0.00 42.00 4.93
5754 9277 2.795175 ATAGGGAACATACGTCAGCG 57.205 50.000 0.00 0.00 44.93 5.18
5755 9278 6.589139 GGTTAATATAGGGAACATACGTCAGC 59.411 42.308 0.00 0.00 0.00 4.26
5757 9280 7.600231 TGGTTAATATAGGGAACATACGTCA 57.400 36.000 0.00 0.00 0.00 4.35
5759 9282 7.881232 CCATTGGTTAATATAGGGAACATACGT 59.119 37.037 0.00 0.00 0.00 3.57
5760 9283 7.335924 CCCATTGGTTAATATAGGGAACATACG 59.664 40.741 1.20 0.00 31.66 3.06
5761 9284 7.122204 GCCCATTGGTTAATATAGGGAACATAC 59.878 40.741 1.20 0.00 31.66 2.39
5762 9285 7.179269 GCCCATTGGTTAATATAGGGAACATA 58.821 38.462 1.20 0.00 31.66 2.29
5763 9286 6.016555 GCCCATTGGTTAATATAGGGAACAT 58.983 40.000 1.20 0.00 31.66 2.71
5764 9287 5.103473 TGCCCATTGGTTAATATAGGGAACA 60.103 40.000 1.20 0.00 31.66 3.18
5765 9288 5.390387 TGCCCATTGGTTAATATAGGGAAC 58.610 41.667 1.20 0.00 31.66 3.62
5766 9289 5.671463 TGCCCATTGGTTAATATAGGGAA 57.329 39.130 1.20 0.00 31.66 3.97
5785 9308 9.551734 TCATATATGTATGCTCTAATGAATGCC 57.448 33.333 12.42 0.00 38.05 4.40
5849 9380 1.068474 ACAATAACGCTGCGAGACAC 58.932 50.000 30.47 0.00 0.00 3.67
5850 9381 2.256174 GTACAATAACGCTGCGAGACA 58.744 47.619 30.47 10.40 0.00 3.41
5851 9382 1.252015 CGTACAATAACGCTGCGAGAC 59.748 52.381 30.47 13.02 35.87 3.36
5879 9459 6.223120 TGCTTACTCATTCATGTATACGCAT 58.777 36.000 0.00 0.00 0.00 4.73
5944 9525 2.186125 GCCTAAACCCTCCGTCGG 59.814 66.667 4.39 4.39 0.00 4.79


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

AutoCloner maintained by Alex Coulton.