Multiple sequence alignment - TraesCS2A01G139100

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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 TraesCS2A01G139100 chr2A 100.000 6611 0 0 874 7484 84543585 84550195 0.000000e+00 12209.0
1 TraesCS2A01G139100 chr2A 100.000 468 0 0 1 468 84542712 84543179 0.000000e+00 865.0
2 TraesCS2A01G139100 chr2A 92.308 468 34 2 2 468 84364469 84364935 0.000000e+00 664.0
3 TraesCS2A01G139100 chr2A 93.229 192 12 1 6880 7071 85598672 85598482 1.590000e-71 281.0
4 TraesCS2A01G139100 chr2D 92.212 5932 226 83 1446 7273 83814414 83820213 0.000000e+00 8178.0
5 TraesCS2A01G139100 chr2D 91.297 563 37 8 884 1443 83813459 83814012 0.000000e+00 758.0
6 TraesCS2A01G139100 chr2D 95.385 390 17 1 1 390 83812536 83812924 2.970000e-173 619.0
7 TraesCS2A01G139100 chr2D 93.229 192 12 1 6880 7071 84763516 84763326 1.590000e-71 281.0
8 TraesCS2A01G139100 chr2D 91.803 183 14 1 7303 7484 83820547 83820729 3.470000e-63 254.0
9 TraesCS2A01G139100 chr2B 92.361 4359 182 50 1360 5637 135681393 135685681 0.000000e+00 6065.0
10 TraesCS2A01G139100 chr2B 96.450 845 30 0 5671 6515 135685681 135686525 0.000000e+00 1395.0
11 TraesCS2A01G139100 chr2B 87.733 750 59 19 874 1618 135680730 135681451 0.000000e+00 845.0
12 TraesCS2A01G139100 chr2B 94.295 298 6 7 6578 6870 135686837 135687128 5.330000e-121 446.0
13 TraesCS2A01G139100 chr2B 89.769 303 30 1 166 468 135679901 135680202 3.280000e-103 387.0
14 TraesCS2A01G139100 chr2B 83.117 462 31 12 7070 7484 135689052 135689513 1.970000e-100 377.0
15 TraesCS2A01G139100 chr2B 93.810 210 12 1 6858 7067 135688808 135689016 1.570000e-81 315.0
16 TraesCS2A01G139100 chr2B 93.229 192 12 1 6880 7071 136622658 136622468 1.590000e-71 281.0
17 TraesCS2A01G139100 chr2B 93.714 175 10 1 2 176 135679307 135679480 2.070000e-65 261.0
18 TraesCS2A01G139100 chr1D 84.883 1667 222 18 2749 4399 402129794 402128142 0.000000e+00 1655.0
19 TraesCS2A01G139100 chr1D 87.204 930 102 8 4003 4921 402128132 402127209 0.000000e+00 1042.0
20 TraesCS2A01G139100 chr1D 86.030 859 94 15 3196 4037 401710891 401710042 0.000000e+00 898.0
21 TraesCS2A01G139100 chr1D 83.446 888 122 14 4600 5467 401710034 401709152 0.000000e+00 802.0
22 TraesCS2A01G139100 chr1D 85.012 407 51 3 4003 4399 402128338 402127932 9.040000e-109 405.0
23 TraesCS2A01G139100 chr1D 78.333 600 94 25 6056 6624 401708148 401707554 9.240000e-94 355.0
24 TraesCS2A01G139100 chr1B 84.542 1669 221 22 2749 4399 539661750 539660101 0.000000e+00 1618.0
25 TraesCS2A01G139100 chr1B 87.204 930 102 9 4003 4921 539660091 539659168 0.000000e+00 1042.0
26 TraesCS2A01G139100 chr1B 85.429 851 94 16 3196 4024 539577585 539576743 0.000000e+00 857.0
27 TraesCS2A01G139100 chr1B 81.910 890 132 17 4600 5467 539576719 539575837 0.000000e+00 725.0
28 TraesCS2A01G139100 chr1B 78.333 720 111 26 5840 6520 539575379 539574666 2.500000e-114 424.0
29 TraesCS2A01G139100 chr1B 83.784 407 56 3 4003 4399 539660297 539659891 1.970000e-100 377.0
30 TraesCS2A01G139100 chr1A 84.343 1667 231 16 2749 4399 497622420 497620768 0.000000e+00 1605.0
31 TraesCS2A01G139100 chr1A 87.986 849 95 5 4074 4921 497619831 497618989 0.000000e+00 996.0
32 TraesCS2A01G139100 chr1A 84.901 861 103 17 3196 4037 497541584 497540732 0.000000e+00 845.0
33 TraesCS2A01G139100 chr1A 82.883 888 127 17 4600 5467 497540724 497539842 0.000000e+00 774.0
34 TraesCS2A01G139100 chr1A 86.653 502 58 3 4003 4498 497620758 497620260 1.420000e-151 547.0
35 TraesCS2A01G139100 chr1A 78.286 875 135 37 5838 6676 497539366 497538511 5.180000e-141 512.0
36 TraesCS2A01G139100 chr1A 83.871 403 59 1 4003 4399 497620964 497620562 5.480000e-101 379.0
37 TraesCS2A01G139100 chr1A 75.349 215 30 9 5495 5709 497539847 497539656 1.730000e-11 82.4
38 TraesCS2A01G139100 chr4B 83.459 1197 164 22 2749 3927 360710082 360708902 0.000000e+00 1083.0
39 TraesCS2A01G139100 chr4B 91.626 203 14 2 6870 7070 563624552 563624351 2.060000e-70 278.0
40 TraesCS2A01G139100 chr4B 90.833 120 10 1 7070 7189 563624318 563624200 7.770000e-35 159.0
41 TraesCS2A01G139100 chr7B 82.972 1198 159 25 2749 3927 722942037 722940866 0.000000e+00 1040.0
42 TraesCS2A01G139100 chr4A 91.626 203 14 2 6870 7070 16251334 16251535 2.060000e-70 278.0
43 TraesCS2A01G139100 chr4A 90.833 120 10 1 7070 7189 16251568 16251686 7.770000e-35 159.0
44 TraesCS2A01G139100 chr4D 91.133 203 15 2 6870 7070 450328042 450327841 9.570000e-69 272.0
45 TraesCS2A01G139100 chr4D 90.833 120 10 1 7070 7189 450327808 450327690 7.770000e-35 159.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G139100 chr2A 84542712 84550195 7483 False 6537.000000 12209 100.000000 1 7484 2 chr2A.!!$F2 7483
1 TraesCS2A01G139100 chr2D 83812536 83820729 8193 False 2452.250000 8178 92.674250 1 7484 4 chr2D.!!$F1 7483
2 TraesCS2A01G139100 chr2B 135679307 135689513 10206 False 1261.375000 6065 91.406125 2 7484 8 chr2B.!!$F1 7482
3 TraesCS2A01G139100 chr1D 402127209 402129794 2585 True 1034.000000 1655 85.699667 2749 4921 3 chr1D.!!$R2 2172
4 TraesCS2A01G139100 chr1D 401707554 401710891 3337 True 685.000000 898 82.603000 3196 6624 3 chr1D.!!$R1 3428
5 TraesCS2A01G139100 chr1B 539659168 539661750 2582 True 1012.333333 1618 85.176667 2749 4921 3 chr1B.!!$R2 2172
6 TraesCS2A01G139100 chr1B 539574666 539577585 2919 True 668.666667 857 81.890667 3196 6520 3 chr1B.!!$R1 3324
7 TraesCS2A01G139100 chr1A 497618989 497622420 3431 True 881.750000 1605 85.713250 2749 4921 4 chr1A.!!$R2 2172
8 TraesCS2A01G139100 chr1A 497538511 497541584 3073 True 553.350000 845 80.354750 3196 6676 4 chr1A.!!$R1 3480
9 TraesCS2A01G139100 chr4B 360708902 360710082 1180 True 1083.000000 1083 83.459000 2749 3927 1 chr4B.!!$R1 1178
10 TraesCS2A01G139100 chr7B 722940866 722942037 1171 True 1040.000000 1040 82.972000 2749 3927 1 chr7B.!!$R1 1178

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
436 868 1.000506 TCGGCCCTTTATATGTCTCGC 59.999 52.381 0.00 0.00 0.00 5.03 F
1581 2726 0.036671 GCACACCTACCACTGGTACC 60.037 60.000 4.43 4.43 37.09 3.34 F
1753 2924 0.036732 TTCATGTGGACTGACAGGCC 59.963 55.000 21.54 21.54 46.38 5.19 F
2510 3713 0.179037 CGTGATGGCATGATCCACCT 60.179 55.000 3.81 0.00 39.25 4.00 F
2826 4066 0.110688 CCGACATGCTGTTCAACGTG 60.111 55.000 0.00 0.00 0.00 4.49 F
4171 5893 1.464734 TTTCCGCCGATTGCCAAATA 58.535 45.000 0.00 0.00 36.24 1.40 F
5164 8167 0.872388 AACGCTGGTTTTCGATGTCC 59.128 50.000 0.00 0.00 30.42 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1816 2987 0.109412 AAGTCTCCCTTTACGCGTCG 60.109 55.0 18.63 5.46 0.00 5.12 R
2634 3853 0.398318 GGGTCAGGGCCAGTCATATC 59.602 60.0 6.18 0.00 0.00 1.63 R
2635 3854 1.410850 CGGGTCAGGGCCAGTCATAT 61.411 60.0 6.18 0.00 0.00 1.78 R
3754 5052 0.327924 ATCCCATCTTGAACCACGCA 59.672 50.0 0.00 0.00 0.00 5.24 R
4431 7419 0.620410 TGGCATACCCAGGCACTACT 60.620 55.0 0.00 0.00 39.18 2.57 R
5333 8338 2.097466 CACACGGATAAATGGAAGTGCC 59.903 50.0 0.00 0.00 33.36 5.01 R
6713 10468 0.762842 ACGGCATCACCCCATAGCTA 60.763 55.0 0.00 0.00 33.26 3.32 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
89 90 8.454570 AAATAAAAGTTAGAAAAGGTCCGTCA 57.545 30.769 0.00 0.00 0.00 4.35
161 162 5.764686 TCAGTTCAGCACACTCATTTTATGT 59.235 36.000 0.00 0.00 0.00 2.29
194 626 2.696707 TGAACTATAGGGCCCAAGTACG 59.303 50.000 27.56 9.45 0.00 3.67
281 713 2.785857 CCTATCTTGTCCCCTTTCCCAT 59.214 50.000 0.00 0.00 0.00 4.00
283 715 2.899303 TCTTGTCCCCTTTCCCATTC 57.101 50.000 0.00 0.00 0.00 2.67
359 791 9.926158 AGAATATGTCATGTGTTTATTTTTGCA 57.074 25.926 0.00 0.00 0.00 4.08
371 803 8.575454 GTGTTTATTTTTGCATTGTAGTCGATC 58.425 33.333 0.00 0.00 0.00 3.69
374 806 5.957842 TTTTTGCATTGTAGTCGATCCTT 57.042 34.783 0.00 0.00 0.00 3.36
393 825 7.254658 CGATCCTTAAACCGTACATTTTGCTAT 60.255 37.037 0.00 0.00 0.00 2.97
401 833 7.173863 ACCGTACATTTTGCTATAAGATTCG 57.826 36.000 0.00 0.00 0.00 3.34
403 835 5.778825 CGTACATTTTGCTATAAGATTCGCG 59.221 40.000 0.00 0.00 0.00 5.87
408 840 5.515548 TTTGCTATAAGATTCGCGCATAG 57.484 39.130 8.75 6.25 0.00 2.23
431 863 2.104281 GTGTCCTCGGCCCTTTATATGT 59.896 50.000 0.00 0.00 0.00 2.29
436 868 1.000506 TCGGCCCTTTATATGTCTCGC 59.999 52.381 0.00 0.00 0.00 5.03
443 875 4.051922 CCTTTATATGTCTCGCTCGCTTT 58.948 43.478 0.00 0.00 0.00 3.51
464 896 4.509412 CCCCCATCCGGTACCCCT 62.509 72.222 6.25 0.00 0.00 4.79
937 1491 4.523173 AGACAACTAGAGAATTCACCGTCA 59.477 41.667 8.44 0.00 0.00 4.35
1051 1605 1.208706 TCTGTGGAGTTGGTGGTCAA 58.791 50.000 0.00 0.00 0.00 3.18
1066 1620 4.760047 CAAGGGTGGTCTCGGCCG 62.760 72.222 22.12 22.12 0.00 6.13
1120 1674 0.673985 CGAAGAGATGGGTATCGCCA 59.326 55.000 0.00 0.00 38.38 5.69
1122 1676 2.484889 GAAGAGATGGGTATCGCCAAC 58.515 52.381 0.00 0.00 38.38 3.77
1135 1689 1.700739 TCGCCAACTCCTCCCTTTTTA 59.299 47.619 0.00 0.00 0.00 1.52
1136 1690 1.810755 CGCCAACTCCTCCCTTTTTAC 59.189 52.381 0.00 0.00 0.00 2.01
1137 1691 2.552373 CGCCAACTCCTCCCTTTTTACT 60.552 50.000 0.00 0.00 0.00 2.24
1138 1692 3.497332 GCCAACTCCTCCCTTTTTACTT 58.503 45.455 0.00 0.00 0.00 2.24
1139 1693 4.659115 GCCAACTCCTCCCTTTTTACTTA 58.341 43.478 0.00 0.00 0.00 2.24
1172 1726 4.820897 TGCATAAACAAGATCTCGTCACT 58.179 39.130 0.00 0.00 0.00 3.41
1193 1747 5.295292 CACTATTTTTGTCCTCGCTCATCAT 59.705 40.000 0.00 0.00 0.00 2.45
1198 1752 2.664185 CCTCGCTCATCATGGCCG 60.664 66.667 0.00 0.00 0.00 6.13
1201 1755 1.289800 CTCGCTCATCATGGCCGATG 61.290 60.000 12.98 12.98 43.50 3.84
1277 1831 2.130272 GGGATTTCTCTCCCGCTTTT 57.870 50.000 0.00 0.00 45.41 2.27
1278 1832 2.447443 GGGATTTCTCTCCCGCTTTTT 58.553 47.619 0.00 0.00 45.41 1.94
1307 1861 4.911390 TCCTGAGAAAGATCTGTTTTCCC 58.089 43.478 0.00 0.00 35.54 3.97
1366 1920 9.455847 AAGAAGAAAATATTTGCTAATCGATGC 57.544 29.630 9.20 0.00 0.00 3.91
1388 1942 4.051922 CGCCCATCTATTACTTGAGTCAC 58.948 47.826 0.00 0.00 0.00 3.67
1435 1989 2.515290 TGCATGCATCCTCGCTGG 60.515 61.111 18.46 0.00 37.10 4.85
1479 2624 2.368548 ACTGCCCCAAAATCAAACCTTC 59.631 45.455 0.00 0.00 0.00 3.46
1524 2669 6.889177 AGATTTTCTTCCAGGGAAAGAGATTC 59.111 38.462 1.90 4.41 34.73 2.52
1567 2712 1.277326 TGATAAGCATCGACGCACAC 58.723 50.000 6.14 0.00 33.51 3.82
1572 2717 2.165301 GCATCGACGCACACCTACC 61.165 63.158 0.00 0.00 0.00 3.18
1581 2726 0.036671 GCACACCTACCACTGGTACC 60.037 60.000 4.43 4.43 37.09 3.34
1582 2727 0.611714 CACACCTACCACTGGTACCC 59.388 60.000 10.07 0.00 37.09 3.69
1629 2792 0.887933 GGATTTTCTTTGCTCGCCCA 59.112 50.000 0.00 0.00 0.00 5.36
1645 2808 1.136891 GCCCACAATTAATCACTGCCC 59.863 52.381 0.00 0.00 0.00 5.36
1753 2924 0.036732 TTCATGTGGACTGACAGGCC 59.963 55.000 21.54 21.54 46.38 5.19
1791 2962 0.246086 CAGCCAGTCAGAGGAGTGAC 59.754 60.000 1.24 0.00 45.56 3.67
1799 2970 2.101380 GAGGAGTGACGAGCGAGC 59.899 66.667 0.00 0.00 0.00 5.03
1802 2973 2.276994 GAGTGACGAGCGAGCGAG 60.277 66.667 4.36 0.00 34.83 5.03
1816 2987 2.020287 CGAGACGAGACGAGACGC 59.980 66.667 0.00 0.00 0.00 5.19
1923 3108 3.775654 CTCCCGCCCACTCCACTC 61.776 72.222 0.00 0.00 0.00 3.51
1926 3111 4.394712 CCGCCCACTCCACTCCAC 62.395 72.222 0.00 0.00 0.00 4.02
2017 3202 2.358125 CATGACACCGCCGTCCAA 60.358 61.111 0.00 0.00 34.88 3.53
2103 3288 2.202518 ATAACGTCGTCGCCACCG 60.203 61.111 0.00 0.00 41.18 4.94
2183 3374 2.444140 GCTCGCCCCCTTCTCCTA 60.444 66.667 0.00 0.00 0.00 2.94
2234 3425 2.866156 GTTCATTGCTCCGATCGAATCA 59.134 45.455 18.66 7.85 0.00 2.57
2239 3430 3.950087 TGCTCCGATCGAATCATTTTG 57.050 42.857 18.66 0.00 0.00 2.44
2255 3446 2.781681 TTTGTCTCCTTCCCGATTCC 57.218 50.000 0.00 0.00 0.00 3.01
2276 3467 0.539669 CCAACTCCAAACCCCTGTCC 60.540 60.000 0.00 0.00 0.00 4.02
2355 3548 0.648958 GTGCGCGTGACCTAATTACC 59.351 55.000 8.43 0.00 0.00 2.85
2388 3581 1.141881 AGTTCCTAGGATGCGCGTG 59.858 57.895 13.57 0.00 0.00 5.34
2482 3685 1.656095 GACGCGTCAAAGATTCAGAGG 59.344 52.381 33.09 0.00 0.00 3.69
2498 3701 2.438434 GGTGCCTTCCCGTGATGG 60.438 66.667 0.00 0.00 38.53 3.51
2510 3713 0.179037 CGTGATGGCATGATCCACCT 60.179 55.000 3.81 0.00 39.25 4.00
2569 3773 3.245875 TGTGCTACTCTACCTACCCCTTT 60.246 47.826 0.00 0.00 0.00 3.11
2570 3774 3.773667 GTGCTACTCTACCTACCCCTTTT 59.226 47.826 0.00 0.00 0.00 2.27
2571 3775 4.958581 GTGCTACTCTACCTACCCCTTTTA 59.041 45.833 0.00 0.00 0.00 1.52
2572 3776 4.958581 TGCTACTCTACCTACCCCTTTTAC 59.041 45.833 0.00 0.00 0.00 2.01
2573 3777 4.958581 GCTACTCTACCTACCCCTTTTACA 59.041 45.833 0.00 0.00 0.00 2.41
2574 3778 5.068855 GCTACTCTACCTACCCCTTTTACAG 59.931 48.000 0.00 0.00 0.00 2.74
2575 3779 5.020941 ACTCTACCTACCCCTTTTACAGT 57.979 43.478 0.00 0.00 0.00 3.55
2626 3845 7.280205 CCTAGGCAGGTAGTAATAACTTGTTTG 59.720 40.741 0.00 0.00 37.15 2.93
2644 3863 8.950210 ACTTGTTTGTGAATAAGATATGACTGG 58.050 33.333 3.21 0.00 37.41 4.00
2653 3893 0.398318 GATATGACTGGCCCTGACCC 59.602 60.000 0.00 0.00 0.00 4.46
2692 3932 7.941238 AGGCTGCACTGAAATATTATTATGTCT 59.059 33.333 0.50 0.00 0.00 3.41
2792 4032 3.947834 GCTTTGATGCTTGTAGGTACCAT 59.052 43.478 15.94 1.66 0.00 3.55
2826 4066 0.110688 CCGACATGCTGTTCAACGTG 60.111 55.000 0.00 0.00 0.00 4.49
2869 4109 4.527944 TGATCCTGAGTCTCTACGACATT 58.472 43.478 0.65 0.00 45.32 2.71
2908 4152 7.967303 GTGCATTCCTTTCTTCTTTGAGATAAG 59.033 37.037 0.00 0.00 0.00 1.73
2974 4219 4.983215 TCGGTGCACTATTATTTATGCG 57.017 40.909 17.98 7.09 41.07 4.73
3100 4354 8.224389 TCCTTGATGAATTACATACATTGTGG 57.776 34.615 0.00 0.00 39.48 4.17
3206 4469 3.256383 TGATGCAACCAAAGGTGAATCAG 59.744 43.478 0.00 0.00 35.34 2.90
3344 4607 5.100344 TCAAACACCAACCGGCTTATATA 57.900 39.130 0.00 0.00 34.57 0.86
3502 4789 2.821366 CAGGTGCATGGTCCGCTC 60.821 66.667 0.00 0.00 0.00 5.03
3507 4794 2.183300 GCATGGTCCGCTCGTACA 59.817 61.111 0.00 0.00 0.00 2.90
3572 4860 4.267349 ACTAACGCCATATATGTCCACC 57.733 45.455 11.73 0.00 0.00 4.61
3591 4879 2.848691 CCACAAATGCATGGTTTGGTT 58.151 42.857 14.11 0.00 40.08 3.67
3740 5038 2.791004 CGACGGTACTTTTGAGAACGTT 59.209 45.455 0.00 0.00 32.84 3.99
3754 5052 3.978687 AGAACGTTGAGAGTGAAATCGT 58.021 40.909 5.00 0.00 0.00 3.73
4156 5878 6.159293 CCAAAGTCCAGCTAAAGAAATTTCC 58.841 40.000 14.61 0.00 0.00 3.13
4171 5893 1.464734 TTTCCGCCGATTGCCAAATA 58.535 45.000 0.00 0.00 36.24 1.40
4370 7152 5.960105 CAGCTAAAGAAATTTCCGTCGATTC 59.040 40.000 14.61 0.00 0.00 2.52
4423 7411 5.063204 TCGTCACATCAAATTCTCCTTTGT 58.937 37.500 0.00 0.00 37.39 2.83
4430 7418 5.310409 TCAAATTCTCCTTTGTCTGGACT 57.690 39.130 2.38 0.00 37.39 3.85
4431 7419 6.433847 TCAAATTCTCCTTTGTCTGGACTA 57.566 37.500 2.38 0.00 37.39 2.59
4432 7420 6.467677 TCAAATTCTCCTTTGTCTGGACTAG 58.532 40.000 2.38 0.00 37.39 2.57
5163 8166 2.223377 AGAAACGCTGGTTTTCGATGTC 59.777 45.455 0.00 0.00 46.04 3.06
5164 8167 0.872388 AACGCTGGTTTTCGATGTCC 59.128 50.000 0.00 0.00 30.42 4.02
5218 8221 1.496857 TGGGAAATGGGTTGTCACAGA 59.503 47.619 0.00 0.00 0.00 3.41
5220 8223 2.582052 GGAAATGGGTTGTCACAGACA 58.418 47.619 0.00 0.00 41.09 3.41
5235 8238 8.349568 TGTCACAGACAGATGTTAGTATTAGT 57.650 34.615 0.00 0.00 37.67 2.24
5251 8254 9.877222 TTAGTATTAGTCCATCTTACATCTCCA 57.123 33.333 0.00 0.00 0.00 3.86
5333 8338 4.002982 TGTAACAAGCTGCTGGTCTATTG 58.997 43.478 10.68 1.71 0.00 1.90
5363 8368 6.280643 TCCATTTATCCGTGTGTCATCTAAG 58.719 40.000 0.00 0.00 0.00 2.18
5399 8405 6.235231 TCGGCAGAGAATATTATTATCCCC 57.765 41.667 7.29 7.51 0.00 4.81
5530 8536 7.702348 CGGAAATTTCTTATGAGGTGAAATTCC 59.298 37.037 17.42 12.38 44.53 3.01
5531 8537 7.702348 GGAAATTTCTTATGAGGTGAAATTCCG 59.298 37.037 17.42 0.00 44.53 4.30
5712 8718 2.101415 GCATAAGTTCAGGGAATTGGCC 59.899 50.000 0.00 0.00 0.00 5.36
6178 9667 1.012086 CTGCTTCAGCGCATACATGT 58.988 50.000 11.47 2.69 45.83 3.21
6237 9726 0.693049 CTGGTGGAGGGCAACTACTT 59.307 55.000 0.00 0.00 0.00 2.24
6354 9843 3.396260 TCGGATTTCGAACCTGAGTTT 57.604 42.857 0.00 0.00 45.86 2.66
6638 10392 2.539972 ATGTCGTCGTCGTCGTCGTC 62.540 60.000 18.44 14.46 45.27 4.20
6713 10468 2.238084 TCACATACTCTGCTCACCCT 57.762 50.000 0.00 0.00 0.00 4.34
6720 10478 2.315176 ACTCTGCTCACCCTAGCTATG 58.685 52.381 0.00 0.00 43.19 2.23
6771 10529 1.892474 GGATTGCTTGTTTACTGGCCA 59.108 47.619 4.71 4.71 0.00 5.36
6901 12353 1.018910 TGTCTTCGATATGCCGACGA 58.981 50.000 0.00 0.00 38.39 4.20
6935 12387 1.259142 CCATGTTGCCAGAATGCCCA 61.259 55.000 0.00 0.00 31.97 5.36
6993 12445 1.620323 GGCCAGGAAGCTTTGAACAAT 59.380 47.619 0.00 0.00 0.00 2.71
7055 12507 2.104963 GCTAGAATACAACCTCCAGGGG 59.895 54.545 0.00 0.00 40.27 4.79
7128 12613 3.398318 TTGATAGAGCACCAGGGACTA 57.602 47.619 0.00 0.00 36.02 2.59
7134 12619 1.205893 GAGCACCAGGGACTACTTGAG 59.794 57.143 0.00 0.00 36.02 3.02
7147 12632 6.239458 GGGACTACTTGAGGAATTATCTCCTG 60.239 46.154 0.00 2.66 46.33 3.86
7225 12729 3.441572 GCTGCTGCAAGAAAGAGGAAATA 59.558 43.478 11.11 0.00 39.41 1.40
7264 12768 8.633561 CCACTGATAAGGAAAATAAAGGGAATC 58.366 37.037 0.00 0.00 0.00 2.52
7273 12783 7.614192 AGGAAAATAAAGGGAATCGCTCTTTTA 59.386 33.333 0.00 0.00 33.44 1.52
7329 13141 7.622713 TGAATTTGAATTGCATCCCAGTAAAT 58.377 30.769 0.00 0.00 0.00 1.40
7357 13173 7.996385 TCTTTTAAACAGAGAAAAGGTGGAAG 58.004 34.615 7.13 0.00 41.15 3.46
7360 13176 7.712204 TTAAACAGAGAAAAGGTGGAAGTTT 57.288 32.000 0.00 0.00 0.00 2.66
7369 13185 8.542497 AGAAAAGGTGGAAGTTTAAACAAAAC 57.458 30.769 20.06 11.74 46.61 2.43
7385 13201 4.969816 ACAAAACTCAACTGTTTCAGTCG 58.030 39.130 2.86 0.00 44.62 4.18
7451 13267 8.131847 TGATTCTTCTATCAATCATCGAGGAT 57.868 34.615 6.78 6.78 34.71 3.24
7478 13294 9.834628 GAATAACCGATGAACTAAATTTGAACA 57.165 29.630 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 90 4.514816 GCTATGCAAATTTGGTTGTTTGGT 59.485 37.500 19.47 0.00 36.19 3.67
161 162 5.629133 GCCCTATAGTTCATCAACCACAAGA 60.629 44.000 0.00 0.00 32.22 3.02
281 713 2.950309 GCTGAGGTACGAGACTATGGAA 59.050 50.000 0.00 0.00 0.00 3.53
283 715 2.298610 TGCTGAGGTACGAGACTATGG 58.701 52.381 0.00 0.00 0.00 2.74
344 776 7.418408 TCGACTACAATGCAAAAATAAACACA 58.582 30.769 0.00 0.00 0.00 3.72
359 791 5.334724 ACGGTTTAAGGATCGACTACAAT 57.665 39.130 0.00 0.00 0.00 2.71
360 792 4.789012 ACGGTTTAAGGATCGACTACAA 57.211 40.909 0.00 0.00 0.00 2.41
371 803 8.885722 TCTTATAGCAAAATGTACGGTTTAAGG 58.114 33.333 0.00 0.00 0.00 2.69
393 825 3.550233 GGACACTCTATGCGCGAATCTTA 60.550 47.826 12.10 0.00 0.00 2.10
401 833 1.299468 CCGAGGACACTCTATGCGC 60.299 63.158 0.00 0.00 41.71 6.09
403 835 1.068250 GGCCGAGGACACTCTATGC 59.932 63.158 0.00 0.00 41.71 3.14
408 840 0.831307 ATAAAGGGCCGAGGACACTC 59.169 55.000 0.00 0.00 40.44 3.51
431 863 2.711922 GGGGAGAAAGCGAGCGAGA 61.712 63.158 0.00 0.00 0.00 4.04
928 1482 0.605319 GGCAAGGATGTGACGGTGAA 60.605 55.000 0.00 0.00 0.00 3.18
931 1485 2.351276 GGGCAAGGATGTGACGGT 59.649 61.111 0.00 0.00 0.00 4.83
937 1491 3.411517 CGGAGGGGGCAAGGATGT 61.412 66.667 0.00 0.00 0.00 3.06
1031 1585 1.208706 TGACCACCAACTCCACAGAA 58.791 50.000 0.00 0.00 0.00 3.02
1096 1650 2.602456 CGATACCCATCTCTTCGTCGTG 60.602 54.545 0.00 0.00 0.00 4.35
1101 1655 0.673985 TGGCGATACCCATCTCTTCG 59.326 55.000 0.00 0.00 37.83 3.79
1149 1703 5.237815 AGTGACGAGATCTTGTTTATGCAA 58.762 37.500 16.92 0.00 0.00 4.08
1150 1704 4.820897 AGTGACGAGATCTTGTTTATGCA 58.179 39.130 16.92 7.15 0.00 3.96
1157 1711 6.369065 GGACAAAAATAGTGACGAGATCTTGT 59.631 38.462 15.83 15.83 0.00 3.16
1159 1713 6.702329 AGGACAAAAATAGTGACGAGATCTT 58.298 36.000 0.00 0.00 0.00 2.40
1160 1714 6.287589 AGGACAAAAATAGTGACGAGATCT 57.712 37.500 0.00 0.00 0.00 2.75
1164 1718 3.060895 GCGAGGACAAAAATAGTGACGAG 59.939 47.826 0.00 0.00 0.00 4.18
1172 1726 4.576053 CCATGATGAGCGAGGACAAAAATA 59.424 41.667 0.00 0.00 0.00 1.40
1193 1747 2.359850 AAAAGAGCGCATCGGCCA 60.360 55.556 11.47 0.00 36.38 5.36
1198 1752 1.853646 GCGTGATGAAAAGAGCGCATC 60.854 52.381 11.47 4.24 43.62 3.91
1201 1755 1.578618 CGCGTGATGAAAAGAGCGC 60.579 57.895 0.00 0.00 41.08 5.92
1345 1899 5.059710 GGCGCATCGATTAGCAAATATTTTC 59.940 40.000 19.56 0.00 0.00 2.29
1346 1900 4.917415 GGCGCATCGATTAGCAAATATTTT 59.083 37.500 19.56 0.00 0.00 1.82
1347 1901 4.475944 GGCGCATCGATTAGCAAATATTT 58.524 39.130 19.56 0.00 0.00 1.40
1366 1920 4.051922 GTGACTCAAGTAATAGATGGGCG 58.948 47.826 0.00 0.00 0.00 6.13
1413 1967 1.153309 CGAGGATGCATGCACAGGA 60.153 57.895 25.37 0.00 0.00 3.86
1435 1989 0.324275 TAATTGGGGGCCAGCAAGAC 60.324 55.000 4.39 0.00 33.81 3.01
1479 2624 3.187637 TCTTCCGTGTTAATTTTCTGGCG 59.812 43.478 0.00 0.00 0.00 5.69
1524 2669 4.106197 CGAAGTATTCTTCCTGGAAGACG 58.894 47.826 33.10 27.01 46.54 4.18
1596 2741 8.173130 GCAAAGAAAATCCAGCAAAGATAATTG 58.827 33.333 0.00 0.00 0.00 2.32
1629 2792 1.283613 TCGGGGGCAGTGATTAATTGT 59.716 47.619 0.00 0.00 0.00 2.71
1645 2808 0.320421 TTCTCTCGCAAAGGTTCGGG 60.320 55.000 0.00 0.00 0.00 5.14
1722 2888 5.012893 AGTCCACATGAAGAAAGATTTCCC 58.987 41.667 0.00 0.00 37.92 3.97
1768 2939 4.463879 CCTCTGACTGGCTGGCCG 62.464 72.222 7.14 4.75 39.42 6.13
1769 2940 3.005539 TCCTCTGACTGGCTGGCC 61.006 66.667 4.43 4.43 0.00 5.36
1770 2941 2.289532 ACTCCTCTGACTGGCTGGC 61.290 63.158 0.00 0.00 0.00 4.85
1771 2942 0.902048 TCACTCCTCTGACTGGCTGG 60.902 60.000 0.00 0.00 0.00 4.85
1791 2962 3.555619 TCTCGTCTCGCTCGCTCG 61.556 66.667 0.00 0.00 0.00 5.03
1799 2970 2.020287 GCGTCTCGTCTCGTCTCG 59.980 66.667 0.00 0.00 0.00 4.04
1802 2973 2.275935 GTCGCGTCTCGTCTCGTC 60.276 66.667 5.77 0.00 39.67 4.20
1816 2987 0.109412 AAGTCTCCCTTTACGCGTCG 60.109 55.000 18.63 5.46 0.00 5.12
1850 3022 2.437359 GCGATTGGCCAGCACTCT 60.437 61.111 5.11 0.00 34.80 3.24
2234 3425 3.267031 AGGAATCGGGAAGGAGACAAAAT 59.733 43.478 0.00 0.00 0.00 1.82
2239 3430 0.753867 GGAGGAATCGGGAAGGAGAC 59.246 60.000 0.00 0.00 0.00 3.36
2255 3446 0.478507 ACAGGGGTTTGGAGTTGGAG 59.521 55.000 0.00 0.00 0.00 3.86
2318 3511 2.278013 CGAACGAGTAGGCCGCTC 60.278 66.667 17.10 17.10 0.00 5.03
2355 3548 1.807142 GGAACTGAGAAAAGGAAGGCG 59.193 52.381 0.00 0.00 0.00 5.52
2427 3624 2.108700 CGCCAACTTTGAAACACGAAG 58.891 47.619 0.00 0.00 43.57 3.79
2510 3713 2.444706 AGCTATCGCTCCCCAGCA 60.445 61.111 0.00 0.00 45.15 4.41
2575 3779 9.444600 GGAATTACATACTTGAGGAACAGTAAA 57.555 33.333 0.00 0.00 0.00 2.01
2626 3845 4.999950 CAGGGCCAGTCATATCTTATTCAC 59.000 45.833 6.18 0.00 0.00 3.18
2634 3853 0.398318 GGGTCAGGGCCAGTCATATC 59.602 60.000 6.18 0.00 0.00 1.63
2635 3854 1.410850 CGGGTCAGGGCCAGTCATAT 61.411 60.000 6.18 0.00 0.00 1.78
2636 3855 2.063979 CGGGTCAGGGCCAGTCATA 61.064 63.158 6.18 0.00 0.00 2.15
2637 3856 3.402681 CGGGTCAGGGCCAGTCAT 61.403 66.667 6.18 0.00 0.00 3.06
2644 3863 2.552231 ATTTACAGGCGGGTCAGGGC 62.552 60.000 0.00 0.00 0.00 5.19
2869 4109 3.964031 AGGAATGCACAAAGTACCCAAAA 59.036 39.130 0.00 0.00 0.00 2.44
2908 4152 6.361748 AGAACTACGTCGAAAACTGAACATAC 59.638 38.462 0.00 0.00 0.00 2.39
2955 4200 6.090898 CCTCTACGCATAAATAATAGTGCACC 59.909 42.308 14.63 0.00 37.44 5.01
2974 4219 5.701290 AGCATGAAACTGTGTTTACCTCTAC 59.299 40.000 0.00 0.00 0.00 2.59
3206 4469 4.497473 TGTTACTTGCATTAACACCTGC 57.503 40.909 14.45 0.00 35.07 4.85
3443 4717 8.802267 ACATGTTTTAGTGCCAGTACAAATAAT 58.198 29.630 0.00 0.00 0.00 1.28
3502 4789 5.006153 TCCTTCCATTGTGATACTGTACG 57.994 43.478 0.00 0.00 0.00 3.67
3572 4860 4.630111 ACTAACCAAACCATGCATTTGTG 58.370 39.130 15.54 11.09 35.65 3.33
3740 5038 1.418373 CACGCACGATTTCACTCTCA 58.582 50.000 0.00 0.00 0.00 3.27
3754 5052 0.327924 ATCCCATCTTGAACCACGCA 59.672 50.000 0.00 0.00 0.00 5.24
4120 5842 1.200020 GGACTTTGGCTGAAATGACCG 59.800 52.381 0.00 0.00 0.00 4.79
4156 5878 1.939934 TCTTCTATTTGGCAATCGGCG 59.060 47.619 0.00 0.00 46.16 6.46
4171 5893 9.205513 AGCAATGGATTAATTTGGTTATCTTCT 57.794 29.630 0.00 0.00 0.00 2.85
4423 7411 1.342076 CCCAGGCACTACTAGTCCAGA 60.342 57.143 0.00 0.00 36.02 3.86
4430 7418 1.343580 TGGCATACCCAGGCACTACTA 60.344 52.381 0.00 0.00 39.18 1.82
4431 7419 0.620410 TGGCATACCCAGGCACTACT 60.620 55.000 0.00 0.00 39.18 2.57
4432 7420 1.912220 TGGCATACCCAGGCACTAC 59.088 57.895 0.00 0.00 39.18 2.73
4738 7727 6.200878 TGGTAGAAATTCCTTCTTTGTCCT 57.799 37.500 0.00 0.00 41.97 3.85
5155 8158 4.221482 CCTCATATGATCTGGGACATCGAA 59.779 45.833 5.72 0.00 38.20 3.71
5163 8166 3.514539 TCTGGACCTCATATGATCTGGG 58.485 50.000 5.72 6.53 0.00 4.45
5164 8167 4.081031 CCATCTGGACCTCATATGATCTGG 60.081 50.000 5.72 6.90 37.39 3.86
5235 8238 5.013079 ACAAACACTGGAGATGTAAGATGGA 59.987 40.000 0.00 0.00 0.00 3.41
5333 8338 2.097466 CACACGGATAAATGGAAGTGCC 59.903 50.000 0.00 0.00 33.36 5.01
5363 8368 2.227865 CTCTGCCGAGCTAGGATAAGTC 59.772 54.545 18.16 0.00 0.00 3.01
5399 8405 4.926860 TGACATGAACTGATTTAGTGCG 57.073 40.909 0.00 0.00 37.83 5.34
5765 8771 7.714813 TCAAACAGTCTCTGTATGAACATTTCA 59.285 33.333 2.80 0.00 44.62 2.69
6008 9390 9.926158 TTGAAGTGCATCATAAAATAAACACAT 57.074 25.926 0.00 0.00 0.00 3.21
6144 9633 2.574006 AGCAGAAATGCAGTCCTGAA 57.426 45.000 3.98 0.00 37.25 3.02
6178 9667 3.583228 TGTCCTTTCTGTCTTCTGGGTA 58.417 45.455 0.00 0.00 0.00 3.69
6237 9726 1.617018 CGTCTGGGCTGATTCCCTCA 61.617 60.000 0.12 0.00 46.67 3.86
6268 9757 6.118170 CCTCTGCTGGATTTCTTTTCAGATA 58.882 40.000 0.00 0.00 0.00 1.98
6347 9836 2.564771 TGTTGCACTCCTGAAACTCAG 58.435 47.619 0.00 0.00 43.91 3.35
6350 9839 3.004752 ACTTGTTGCACTCCTGAAACT 57.995 42.857 0.00 0.00 0.00 2.66
6351 9840 3.303132 CGTACTTGTTGCACTCCTGAAAC 60.303 47.826 0.00 0.00 0.00 2.78
6352 9841 2.869801 CGTACTTGTTGCACTCCTGAAA 59.130 45.455 0.00 0.00 0.00 2.69
6354 9843 1.411246 ACGTACTTGTTGCACTCCTGA 59.589 47.619 0.00 0.00 0.00 3.86
6638 10392 1.142778 CCGGCACCAAAACAACAACG 61.143 55.000 0.00 0.00 0.00 4.10
6713 10468 0.762842 ACGGCATCACCCCATAGCTA 60.763 55.000 0.00 0.00 33.26 3.32
6720 10478 1.460273 AACAACAACGGCATCACCCC 61.460 55.000 0.00 0.00 33.26 4.95
6771 10529 3.639094 AGTCTGACACAAGCACTAGAAGT 59.361 43.478 10.88 0.00 0.00 3.01
6901 12353 4.320494 GCAACATGGAGAACAGAATTCGTT 60.320 41.667 13.14 13.14 0.00 3.85
6935 12387 5.083953 AGGCCATTGATTATCCTTCCAAT 57.916 39.130 5.01 0.00 0.00 3.16
7055 12507 4.154918 CCTCACCAAGCAGATAAGAACAAC 59.845 45.833 0.00 0.00 0.00 3.32
7128 12613 5.966935 TCCTTCAGGAGATAATTCCTCAAGT 59.033 40.000 5.22 0.00 45.86 3.16
7214 12718 6.072199 AGCCACATCTCTTATTTCCTCTTT 57.928 37.500 0.00 0.00 0.00 2.52
7295 12805 8.677300 GGATGCAATTCAAATTCAGACTAAGTA 58.323 33.333 0.00 0.00 0.00 2.24
7296 12806 7.363268 GGGATGCAATTCAAATTCAGACTAAGT 60.363 37.037 0.00 0.00 0.00 2.24
7297 12807 6.976925 GGGATGCAATTCAAATTCAGACTAAG 59.023 38.462 0.00 0.00 0.00 2.18
7305 13117 8.496707 AATTTACTGGGATGCAATTCAAATTC 57.503 30.769 0.00 0.00 0.00 2.17
7314 13126 6.916360 AAAAGAGAATTTACTGGGATGCAA 57.084 33.333 0.00 0.00 0.00 4.08
7357 13173 8.974408 ACTGAAACAGTTGAGTTTTGTTTAAAC 58.026 29.630 11.54 11.54 42.59 2.01
7360 13176 7.018826 CGACTGAAACAGTTGAGTTTTGTTTA 58.981 34.615 12.23 0.00 45.84 2.01
7378 13194 7.079182 ACATGTGTTTTAACTTTCGACTGAA 57.921 32.000 0.00 0.00 0.00 3.02
7385 13201 7.923878 ACACCCATTACATGTGTTTTAACTTTC 59.076 33.333 9.11 0.00 40.12 2.62
7451 13267 9.834628 GTTCAAATTTAGTTCATCGGTTATTCA 57.165 29.630 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.