Multiple sequence alignment - TraesCS4D01G102100

Loading Multiple Alignment...

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 TraesCS4D01G102100 chr4D 100.000 4742 0 0 1 4742 80833784 80838525 0.000000e+00 8757.0
1 TraesCS4D01G102100 chr4D 83.333 198 33 0 2789 2986 28881791 28881988 2.910000e-42 183.0
2 TraesCS4D01G102100 chr4A 93.598 3905 153 48 1 3851 504793537 504789676 0.000000e+00 5736.0
3 TraesCS4D01G102100 chr4A 92.047 767 44 8 3977 4742 504789651 504788901 0.000000e+00 1062.0
4 TraesCS4D01G102100 chr4A 100.000 37 0 0 3850 3886 482158360 482158324 8.520000e-08 69.4
5 TraesCS4D01G102100 chr4B 91.182 2234 87 37 2031 4237 112920901 112923051 0.000000e+00 2933.0
6 TraesCS4D01G102100 chr4B 89.445 1459 87 33 610 2032 112919392 112920819 0.000000e+00 1779.0
7 TraesCS4D01G102100 chr4B 97.925 530 9 1 1 528 112918548 112919077 0.000000e+00 917.0
8 TraesCS4D01G102100 chr4B 94.685 508 20 3 4236 4742 112923198 112923699 0.000000e+00 782.0
9 TraesCS4D01G102100 chr4B 83.333 198 33 0 2789 2986 41197715 41197912 2.910000e-42 183.0
10 TraesCS4D01G102100 chr3D 88.095 210 23 2 2789 2997 180470743 180470535 1.020000e-61 248.0
11 TraesCS4D01G102100 chr3D 82.857 210 34 2 2789 2997 546198931 546198723 2.250000e-43 187.0
12 TraesCS4D01G102100 chr3B 87.143 210 25 2 2789 2997 258721283 258721075 2.210000e-58 237.0
13 TraesCS4D01G102100 chr3B 83.333 210 33 2 2789 2997 722590911 722590703 4.840000e-45 193.0
14 TraesCS4D01G102100 chr3A 87.143 210 25 2 2789 2997 225894568 225894360 2.210000e-58 237.0
15 TraesCS4D01G102100 chr5B 90.196 51 5 0 3850 3900 228272257 228272307 3.060000e-07 67.6
16 TraesCS4D01G102100 chrUn 95.122 41 2 0 3846 3886 302070981 302071021 1.100000e-06 65.8
17 TraesCS4D01G102100 chrUn 95.122 41 2 0 3846 3886 302084650 302084690 1.100000e-06 65.8
18 TraesCS4D01G102100 chr2B 100.000 35 0 0 3850 3884 17703892 17703858 1.100000e-06 65.8
19 TraesCS4D01G102100 chr2B 100.000 35 0 0 3851 3885 414774727 414774761 1.100000e-06 65.8
20 TraesCS4D01G102100 chr2A 100.000 35 0 0 3852 3886 66005901 66005935 1.100000e-06 65.8
21 TraesCS4D01G102100 chr2A 95.122 41 2 0 3846 3886 515524347 515524307 1.100000e-06 65.8
22 TraesCS4D01G102100 chr1B 95.122 41 2 0 3846 3886 104479470 104479510 1.100000e-06 65.8


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 TraesCS4D01G102100 chr4D 80833784 80838525 4741 False 8757.00 8757 100.00000 1 4742 1 chr4D.!!$F2 4741
1 TraesCS4D01G102100 chr4A 504788901 504793537 4636 True 3399.00 5736 92.82250 1 4742 2 chr4A.!!$R2 4741
2 TraesCS4D01G102100 chr4B 112918548 112923699 5151 False 1602.75 2933 93.30925 1 4742 4 chr4B.!!$F2 4741

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
827 1072 0.106819 GCATCATTCACAGCCCCTCT 60.107 55.0 0.00 0.0 0.00 3.69 F
1082 1327 0.039617 CGAGCCAGGCTTCGATCTAG 60.040 60.0 17.46 0.0 39.88 2.43 F
1708 1995 0.306228 TTCGTTTGTGTGCACGATGG 59.694 50.0 13.13 0.0 44.52 3.51 F
3045 3451 0.324091 TCCACCTTCCCGTCCTACTC 60.324 60.0 0.00 0.0 0.00 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2418 2797 1.134491 CATGCATGCCTGAGACTGAGA 60.134 52.381 17.08 0.00 0.00 3.27 R
2941 3344 1.200839 GTTCTTGACGGCGTTGTCG 59.799 57.895 16.19 3.48 41.87 4.35 R
3280 3686 0.758685 AGGAGAAGGCGATGGAGAGG 60.759 60.000 0.00 0.00 0.00 3.69 R
3945 4359 1.295746 GGGTCTCCGAAGTCCCAAC 59.704 63.158 0.00 0.00 46.73 3.77 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
44 45 1.002251 CCGATCTACTGTTCTCGCTCC 60.002 57.143 0.00 0.00 0.00 4.70
312 313 1.355381 TGGGGATGCACTCAGATGTTT 59.645 47.619 0.00 0.00 0.00 2.83
363 364 5.276461 TCTGGTGTAAATGAGATGCGTAT 57.724 39.130 0.00 0.00 0.00 3.06
421 427 5.000591 TCATAAGAAAGTGCCGTTTGATCA 58.999 37.500 0.00 0.00 0.00 2.92
552 558 5.268118 AGATAGTCGATGATGTCTTTGCA 57.732 39.130 0.00 0.00 0.00 4.08
558 564 3.105937 CGATGATGTCTTTGCATTGCAG 58.894 45.455 11.76 1.32 40.61 4.41
603 621 8.097662 AGGGAAGTTAGAGAAGAAGTACAAATG 58.902 37.037 0.00 0.00 0.00 2.32
740 983 1.099879 ACGGTAGCTAGCCCTACACG 61.100 60.000 16.98 14.97 39.52 4.49
753 998 2.158058 CTACACGCACGCACACAAGG 62.158 60.000 0.00 0.00 0.00 3.61
822 1067 0.458260 TGCATGCATCATTCACAGCC 59.542 50.000 18.46 0.00 0.00 4.85
823 1068 0.249322 GCATGCATCATTCACAGCCC 60.249 55.000 14.21 0.00 0.00 5.19
824 1069 0.387929 CATGCATCATTCACAGCCCC 59.612 55.000 0.00 0.00 0.00 5.80
827 1072 0.106819 GCATCATTCACAGCCCCTCT 60.107 55.000 0.00 0.00 0.00 3.69
849 1094 3.506455 TCCCTCTCTCTTGTCGTGTAAAG 59.494 47.826 0.00 0.00 0.00 1.85
860 1105 8.068893 TCTTGTCGTGTAAAGCTAAACTAAAG 57.931 34.615 0.00 0.00 0.00 1.85
932 1177 2.222445 GTGTGTGTGGGTAAAGCTAACG 59.778 50.000 0.00 0.00 0.00 3.18
1032 1277 2.029380 ACCAAAAACGCATTAGCTTCCC 60.029 45.455 0.00 0.00 39.10 3.97
1064 1309 4.605967 GCTCGGAGCTCTCTCGCG 62.606 72.222 22.32 8.36 40.26 5.87
1065 1310 2.892914 CTCGGAGCTCTCTCGCGA 60.893 66.667 14.64 9.26 40.26 5.87
1080 1325 2.811101 CGAGCCAGGCTTCGATCT 59.189 61.111 17.46 0.00 39.88 2.75
1081 1326 2.033793 CGAGCCAGGCTTCGATCTA 58.966 57.895 17.46 0.00 39.88 1.98
1082 1327 0.039617 CGAGCCAGGCTTCGATCTAG 60.040 60.000 17.46 0.00 39.88 2.43
1083 1328 1.036707 GAGCCAGGCTTCGATCTAGT 58.963 55.000 17.46 0.00 39.88 2.57
1086 1331 1.410882 GCCAGGCTTCGATCTAGTTCT 59.589 52.381 3.29 0.00 0.00 3.01
1087 1332 2.544903 GCCAGGCTTCGATCTAGTTCTC 60.545 54.545 3.29 0.00 0.00 2.87
1090 1335 4.499019 CCAGGCTTCGATCTAGTTCTCTTC 60.499 50.000 0.00 0.00 0.00 2.87
1091 1336 4.338118 CAGGCTTCGATCTAGTTCTCTTCT 59.662 45.833 0.00 0.00 0.00 2.85
1094 1339 5.067283 GGCTTCGATCTAGTTCTCTTCTTCT 59.933 44.000 0.00 0.00 0.00 2.85
1095 1340 6.199393 GCTTCGATCTAGTTCTCTTCTTCTC 58.801 44.000 0.00 0.00 0.00 2.87
1096 1341 6.687081 TTCGATCTAGTTCTCTTCTTCTCC 57.313 41.667 0.00 0.00 0.00 3.71
1206 1459 2.569134 GAGGACGAGAAGCTGCGT 59.431 61.111 8.97 8.97 44.33 5.24
1281 1534 2.273449 GGCAGATCAGGTGGGTGG 59.727 66.667 0.00 0.00 0.00 4.61
1288 1541 1.136329 ATCAGGTGGGTGGAACTGCT 61.136 55.000 0.00 0.00 36.74 4.24
1306 1559 4.713814 ACTGCTGGTCTATCTCTTTGATCA 59.286 41.667 0.00 0.00 36.65 2.92
1307 1560 5.016051 TGCTGGTCTATCTCTTTGATCAC 57.984 43.478 0.00 0.00 36.65 3.06
1356 1609 9.244799 GTTTCTTAATTTTCGTTTTGAGGTGAT 57.755 29.630 0.00 0.00 0.00 3.06
1369 1622 5.761165 TTGAGGTGATGTTGATGCATATG 57.239 39.130 0.00 0.00 0.00 1.78
1371 1624 5.438833 TGAGGTGATGTTGATGCATATGAA 58.561 37.500 6.97 0.00 0.00 2.57
1375 1628 7.056006 AGGTGATGTTGATGCATATGAACTTA 58.944 34.615 6.97 0.00 32.47 2.24
1411 1670 2.097680 TGATGCGATTTGTGCTCAGA 57.902 45.000 0.00 0.00 0.00 3.27
1414 1673 3.441222 TGATGCGATTTGTGCTCAGAAAT 59.559 39.130 4.90 4.90 37.05 2.17
1452 1711 3.573967 CCTTGGTTCAGTTTGCCATACTT 59.426 43.478 0.00 0.00 31.71 2.24
1453 1712 4.321230 CCTTGGTTCAGTTTGCCATACTTC 60.321 45.833 0.00 0.00 31.71 3.01
1602 1885 9.807921 TTGGGTATCTTGAAAATAGAAGAGTTT 57.192 29.630 0.00 0.00 31.83 2.66
1666 1953 7.645402 AGTTTTTCTTCGTGTTATACCCAAAG 58.355 34.615 0.00 0.00 0.00 2.77
1708 1995 0.306228 TTCGTTTGTGTGCACGATGG 59.694 50.000 13.13 0.00 44.52 3.51
1729 2016 2.552315 GCGAGTTGAATCTGTTTTGGGA 59.448 45.455 0.00 0.00 0.00 4.37
1880 2171 9.319143 CTTACACCAAAGATAAATCTAGTCTGG 57.681 37.037 0.00 1.83 35.76 3.86
2028 2321 4.919168 CACAAGGTTACATTTGCATGACTG 59.081 41.667 0.00 0.00 34.11 3.51
2069 2445 3.874392 ACAAGGTGAAATTAGCATGCC 57.126 42.857 15.66 0.00 0.00 4.40
2195 2574 4.765339 AGGTAAAGGGAAGCAACAACATAC 59.235 41.667 0.00 0.00 0.00 2.39
2248 2627 0.470766 TGCGGTAGGGTGTGTTCTTT 59.529 50.000 0.00 0.00 0.00 2.52
2251 2630 2.809299 GCGGTAGGGTGTGTTCTTTCTT 60.809 50.000 0.00 0.00 0.00 2.52
2252 2631 3.555586 GCGGTAGGGTGTGTTCTTTCTTA 60.556 47.826 0.00 0.00 0.00 2.10
2254 2633 4.262335 CGGTAGGGTGTGTTCTTTCTTACT 60.262 45.833 0.00 0.00 0.00 2.24
2256 2635 6.517194 CGGTAGGGTGTGTTCTTTCTTACTAA 60.517 42.308 0.00 0.00 0.00 2.24
2257 2636 6.648310 GGTAGGGTGTGTTCTTTCTTACTAAC 59.352 42.308 0.00 0.00 0.00 2.34
2258 2637 6.243216 AGGGTGTGTTCTTTCTTACTAACA 57.757 37.500 0.00 0.00 0.00 2.41
2259 2638 6.655930 AGGGTGTGTTCTTTCTTACTAACAA 58.344 36.000 0.00 0.00 33.92 2.83
2261 2640 6.541278 GGGTGTGTTCTTTCTTACTAACAAGT 59.459 38.462 0.00 0.00 33.92 3.16
2262 2641 7.712205 GGGTGTGTTCTTTCTTACTAACAAGTA 59.288 37.037 0.00 0.00 33.92 2.24
2263 2642 9.101655 GGTGTGTTCTTTCTTACTAACAAGTAA 57.898 33.333 0.00 0.00 33.92 2.24
2264 2643 9.911980 GTGTGTTCTTTCTTACTAACAAGTAAC 57.088 33.333 0.00 0.00 33.92 2.50
2265 2644 9.656040 TGTGTTCTTTCTTACTAACAAGTAACA 57.344 29.630 0.00 0.00 33.92 2.41
2268 2647 9.926751 GTTCTTTCTTACTAACAAGTAACAACC 57.073 33.333 0.00 0.00 31.74 3.77
2269 2648 8.667076 TCTTTCTTACTAACAAGTAACAACCC 57.333 34.615 0.00 0.00 31.74 4.11
2270 2649 8.488668 TCTTTCTTACTAACAAGTAACAACCCT 58.511 33.333 0.00 0.00 31.74 4.34
2271 2650 9.768662 CTTTCTTACTAACAAGTAACAACCCTA 57.231 33.333 0.00 0.00 31.74 3.53
2420 2799 5.975693 AAGATTTCTTCACTCGTCTCTCT 57.024 39.130 0.00 0.00 0.00 3.10
2421 2800 5.560966 AGATTTCTTCACTCGTCTCTCTC 57.439 43.478 0.00 0.00 0.00 3.20
2422 2801 5.007034 AGATTTCTTCACTCGTCTCTCTCA 58.993 41.667 0.00 0.00 0.00 3.27
2423 2802 4.757799 TTTCTTCACTCGTCTCTCTCAG 57.242 45.455 0.00 0.00 0.00 3.35
2569 2948 4.700213 ACAATCCTACAACATTACACTGCC 59.300 41.667 0.00 0.00 0.00 4.85
2570 2949 3.343941 TCCTACAACATTACACTGCCC 57.656 47.619 0.00 0.00 0.00 5.36
2585 2964 5.815581 ACACTGCCCTATTAGAATTTCACA 58.184 37.500 0.00 0.00 0.00 3.58
2625 3004 7.067494 GCACTACTTAACCATGAATTCTCCATT 59.933 37.037 7.05 0.00 0.00 3.16
2626 3005 8.616076 CACTACTTAACCATGAATTCTCCATTC 58.384 37.037 7.05 0.00 41.76 2.67
2637 3037 6.563422 TGAATTCTCCATTCGCCAAAATAAG 58.437 36.000 7.05 0.00 44.07 1.73
2744 3146 2.979678 TCCCTGACCTGCTAAGTTTTCT 59.020 45.455 0.00 0.00 0.00 2.52
2941 3344 3.365265 CACTTTCCTGGCCGCACC 61.365 66.667 0.00 0.00 39.84 5.01
3045 3451 0.324091 TCCACCTTCCCGTCCTACTC 60.324 60.000 0.00 0.00 0.00 2.59
3046 3452 1.328430 CCACCTTCCCGTCCTACTCC 61.328 65.000 0.00 0.00 0.00 3.85
3047 3453 0.324460 CACCTTCCCGTCCTACTCCT 60.324 60.000 0.00 0.00 0.00 3.69
3185 3591 2.165845 GCGCCTTCTTCTACTCCAGTAA 59.834 50.000 0.00 0.00 0.00 2.24
3250 3656 3.752359 AGGTACAGTAGCTACCTGGAA 57.248 47.619 20.31 8.03 42.15 3.53
3357 3763 2.124983 CAGCCCTGACCATCACCG 60.125 66.667 0.00 0.00 0.00 4.94
3631 4037 4.844884 AGGGCCTTAATTAGAACTGTGAC 58.155 43.478 0.00 0.00 0.00 3.67
3756 4169 1.798223 GTGTTGTGTGCTAATCGCTGA 59.202 47.619 0.00 0.00 40.11 4.26
3762 4175 6.019075 TGTTGTGTGCTAATCGCTGATTATAC 60.019 38.462 10.13 11.78 40.11 1.47
3770 4183 3.838244 TCGCTGATTATACAAAGGCCT 57.162 42.857 0.00 0.00 0.00 5.19
3791 4204 2.772568 TTGTTGAGACGCCAATTGTG 57.227 45.000 4.43 0.00 0.00 3.33
3794 4207 2.685388 TGTTGAGACGCCAATTGTGAAA 59.315 40.909 4.43 0.00 0.00 2.69
3795 4208 3.243035 TGTTGAGACGCCAATTGTGAAAG 60.243 43.478 4.43 0.00 0.00 2.62
3839 4253 9.265938 CATCAGACGTGTAAATTGTGATAAAAG 57.734 33.333 0.00 0.00 0.00 2.27
3840 4254 7.802738 TCAGACGTGTAAATTGTGATAAAAGG 58.197 34.615 0.00 0.00 0.00 3.11
3851 4265 3.572255 TGTGATAAAAGGGGCAACAAGAC 59.428 43.478 0.00 0.00 39.74 3.01
3852 4266 3.572255 GTGATAAAAGGGGCAACAAGACA 59.428 43.478 0.00 0.00 39.74 3.41
3854 4268 1.859302 AAAAGGGGCAACAAGACACA 58.141 45.000 0.00 0.00 39.74 3.72
3855 4269 2.086610 AAAGGGGCAACAAGACACAT 57.913 45.000 0.00 0.00 39.74 3.21
3856 4270 1.331214 AAGGGGCAACAAGACACATG 58.669 50.000 0.00 0.00 39.74 3.21
3857 4271 0.185901 AGGGGCAACAAGACACATGT 59.814 50.000 0.00 0.00 39.74 3.21
3858 4272 0.314935 GGGGCAACAAGACACATGTG 59.685 55.000 24.25 24.25 39.74 3.21
3859 4273 0.314935 GGGCAACAAGACACATGTGG 59.685 55.000 28.64 13.84 39.74 4.17
3860 4274 1.032014 GGCAACAAGACACATGTGGT 58.968 50.000 28.64 14.49 34.19 4.16
3863 4277 3.304659 GGCAACAAGACACATGTGGTAAG 60.305 47.826 28.64 17.60 34.19 2.34
3864 4278 3.853307 GCAACAAGACACATGTGGTAAGC 60.853 47.826 28.64 18.50 34.19 3.09
3866 4280 3.550820 ACAAGACACATGTGGTAAGCAA 58.449 40.909 28.64 0.00 34.19 3.91
3867 4281 4.144297 ACAAGACACATGTGGTAAGCAAT 58.856 39.130 28.64 5.90 34.19 3.56
3868 4282 4.584325 ACAAGACACATGTGGTAAGCAATT 59.416 37.500 28.64 5.13 34.19 2.32
3869 4283 5.156355 CAAGACACATGTGGTAAGCAATTC 58.844 41.667 28.64 13.92 34.19 2.17
3870 4284 4.397420 AGACACATGTGGTAAGCAATTCA 58.603 39.130 28.64 0.00 34.19 2.57
3873 4287 5.288804 ACACATGTGGTAAGCAATTCAAAC 58.711 37.500 28.64 0.00 34.19 2.93
3875 4289 5.752472 CACATGTGGTAAGCAATTCAAACAA 59.248 36.000 18.51 0.00 0.00 2.83
3876 4290 6.424509 CACATGTGGTAAGCAATTCAAACAAT 59.575 34.615 18.51 0.00 0.00 2.71
3877 4291 6.991531 ACATGTGGTAAGCAATTCAAACAATT 59.008 30.769 0.00 0.00 0.00 2.32
3878 4292 7.171337 ACATGTGGTAAGCAATTCAAACAATTC 59.829 33.333 0.00 0.00 0.00 2.17
3879 4293 6.577103 TGTGGTAAGCAATTCAAACAATTCA 58.423 32.000 0.00 0.00 0.00 2.57
3880 4294 7.044181 TGTGGTAAGCAATTCAAACAATTCAA 58.956 30.769 0.00 0.00 0.00 2.69
3881 4295 7.550551 TGTGGTAAGCAATTCAAACAATTCAAA 59.449 29.630 0.00 0.00 0.00 2.69
3882 4296 8.394121 GTGGTAAGCAATTCAAACAATTCAAAA 58.606 29.630 0.00 0.00 0.00 2.44
3883 4297 8.950210 TGGTAAGCAATTCAAACAATTCAAAAA 58.050 25.926 0.00 0.00 0.00 1.94
3945 4359 2.129607 GCAGTTTGCCAATGTTGTGAG 58.870 47.619 0.00 0.00 37.42 3.51
3955 4369 3.004734 CCAATGTTGTGAGTTGGGACTTC 59.995 47.826 0.00 0.00 38.93 3.01
3997 4411 9.412460 AGTAAATCACATTCACATGGAATACAT 57.588 29.630 8.52 0.00 44.41 2.29
4009 4423 8.309656 TCACATGGAATACATATTTTGCAAACA 58.690 29.630 12.39 3.01 37.84 2.83
4010 4424 9.100554 CACATGGAATACATATTTTGCAAACAT 57.899 29.630 12.39 11.09 37.84 2.71
4126 4540 9.750783 AGACTATATAGGGCTAAATCGACTTAA 57.249 33.333 14.25 0.00 0.00 1.85
4178 4592 6.857777 AGCCATAAGATCAAGATTTTCTCG 57.142 37.500 0.00 0.00 0.00 4.04
4188 4602 9.149225 AGATCAAGATTTTCTCGTCATATATGC 57.851 33.333 7.92 2.83 0.00 3.14
4189 4603 7.338440 TCAAGATTTTCTCGTCATATATGCG 57.662 36.000 17.83 17.83 0.00 4.73
4299 4861 4.290155 CAGCTTTTGTCCACACATAACAC 58.710 43.478 0.00 0.00 30.55 3.32
4328 4890 7.903995 AAAATGTTGGCCTGTTTTATACATG 57.096 32.000 3.32 0.00 35.85 3.21
4329 4891 6.849085 AATGTTGGCCTGTTTTATACATGA 57.151 33.333 3.32 0.00 35.85 3.07
4365 4927 7.167468 GCAACACAGAACTTCGATTGTAATTTT 59.833 33.333 0.00 0.00 0.00 1.82
4383 4945 8.868916 TGTAATTTTCTTTTTGAGTTTGTCAGC 58.131 29.630 0.00 0.00 36.21 4.26
4388 4950 2.730183 TTTGAGTTTGTCAGCGAACG 57.270 45.000 0.00 0.00 42.41 3.95
4565 5128 5.289675 GGACAAATCTACATTGACGACTGAG 59.710 44.000 0.00 0.00 0.00 3.35
4573 5136 5.652744 ACATTGACGACTGAGTGTTAAAC 57.347 39.130 0.00 0.00 0.00 2.01
4583 5146 6.523893 CGACTGAGTGTTAAACTTACTCTAGC 59.476 42.308 0.00 0.00 40.07 3.42
4584 5147 7.527568 ACTGAGTGTTAAACTTACTCTAGCT 57.472 36.000 0.00 0.00 40.07 3.32
4585 5148 8.632906 ACTGAGTGTTAAACTTACTCTAGCTA 57.367 34.615 0.00 0.00 40.07 3.32
4586 5149 8.732531 ACTGAGTGTTAAACTTACTCTAGCTAG 58.267 37.037 15.01 15.01 40.07 3.42
4607 5170 7.329717 AGCTAGAAAGAAAATAGTGTGAAGTCG 59.670 37.037 0.00 0.00 0.00 4.18
4608 5171 7.116519 GCTAGAAAGAAAATAGTGTGAAGTCGT 59.883 37.037 0.00 0.00 0.00 4.34
4666 5229 1.892209 AGACAAACCATCCAACCGTC 58.108 50.000 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 5.999600 TGGAGTAACATGCATATCTTGATGG 59.000 40.000 0.00 0.00 0.00 3.51
297 298 6.179756 TGTTATGGTAAACATCTGAGTGCAT 58.820 36.000 0.00 0.00 41.03 3.96
303 304 7.016153 AGAGGTTGTTATGGTAAACATCTGA 57.984 36.000 1.60 0.00 41.77 3.27
312 313 6.681729 AAGTTGAGAGAGGTTGTTATGGTA 57.318 37.500 0.00 0.00 0.00 3.25
385 386 9.604626 GCACTTTCTTATGATCTTATGTTATGC 57.395 33.333 0.00 1.99 0.00 3.14
533 539 4.034394 GCAATGCAAAGACATCATCGACTA 59.966 41.667 0.00 0.00 0.00 2.59
537 543 3.105937 CTGCAATGCAAAGACATCATCG 58.894 45.455 9.92 0.00 38.41 3.84
552 558 5.950023 ACAATATTCTCCTCCATCTGCAAT 58.050 37.500 0.00 0.00 0.00 3.56
558 564 6.688073 TCCCTAACAATATTCTCCTCCATC 57.312 41.667 0.00 0.00 0.00 3.51
603 621 1.398390 CGGATTACTTCCAGCTGCAAC 59.602 52.381 8.66 0.00 45.78 4.17
740 983 3.357079 CCTCCCTTGTGTGCGTGC 61.357 66.667 0.00 0.00 0.00 5.34
753 998 3.772025 TCAACATCTCTCTTTCTCCCTCC 59.228 47.826 0.00 0.00 0.00 4.30
822 1067 1.775385 GACAAGAGAGAGGGAGAGGG 58.225 60.000 0.00 0.00 0.00 4.30
823 1068 1.340600 ACGACAAGAGAGAGGGAGAGG 60.341 57.143 0.00 0.00 0.00 3.69
824 1069 1.742831 CACGACAAGAGAGAGGGAGAG 59.257 57.143 0.00 0.00 0.00 3.20
827 1072 2.873094 TACACGACAAGAGAGAGGGA 57.127 50.000 0.00 0.00 0.00 4.20
849 1094 4.515361 GGAAGAGGTCCCTTTAGTTTAGC 58.485 47.826 0.00 0.00 41.10 3.09
932 1177 1.065854 AGAGAAGGCTATGGTGTGTGC 60.066 52.381 0.00 0.00 0.00 4.57
1032 1277 1.519013 GAGCTGCGCTTGAGAGAGG 60.519 63.158 9.73 0.00 39.88 3.69
1063 1308 0.039617 CTAGATCGAAGCCTGGCTCG 60.040 60.000 23.61 24.37 38.25 5.03
1064 1309 1.036707 ACTAGATCGAAGCCTGGCTC 58.963 55.000 23.61 14.20 38.25 4.70
1065 1310 1.410882 GAACTAGATCGAAGCCTGGCT 59.589 52.381 17.22 17.22 42.56 4.75
1080 1325 2.100989 GGCCGGAGAAGAAGAGAACTA 58.899 52.381 5.05 0.00 0.00 2.24
1081 1326 0.899019 GGCCGGAGAAGAAGAGAACT 59.101 55.000 5.05 0.00 0.00 3.01
1082 1327 0.458716 CGGCCGGAGAAGAAGAGAAC 60.459 60.000 20.10 0.00 0.00 3.01
1083 1328 0.611062 TCGGCCGGAGAAGAAGAGAA 60.611 55.000 27.83 0.00 0.00 2.87
1086 1331 1.676678 CCATCGGCCGGAGAAGAAGA 61.677 60.000 27.83 1.69 0.00 2.87
1087 1332 1.227380 CCATCGGCCGGAGAAGAAG 60.227 63.158 27.83 0.67 0.00 2.85
1206 1459 0.803117 CGTACTTCTCCACGAGCTGA 59.197 55.000 0.00 0.00 40.56 4.26
1281 1534 5.078411 TCAAAGAGATAGACCAGCAGTTC 57.922 43.478 0.00 0.00 0.00 3.01
1288 1541 4.278310 TCGGTGATCAAAGAGATAGACCA 58.722 43.478 0.00 0.00 38.45 4.02
1342 1595 3.058293 GCATCAACATCACCTCAAAACGA 60.058 43.478 0.00 0.00 0.00 3.85
1344 1597 4.241590 TGCATCAACATCACCTCAAAAC 57.758 40.909 0.00 0.00 0.00 2.43
1349 1602 5.530171 AGTTCATATGCATCAACATCACCTC 59.470 40.000 0.19 0.00 0.00 3.85
1352 1605 8.615211 TCTTAAGTTCATATGCATCAACATCAC 58.385 33.333 0.19 0.00 0.00 3.06
1371 1624 8.031277 GCATCATCCAAAGTCAATTTCTTAAGT 58.969 33.333 1.63 0.00 0.00 2.24
1375 1628 5.183713 TCGCATCATCCAAAGTCAATTTCTT 59.816 36.000 0.00 0.00 0.00 2.52
1391 1650 2.635714 TCTGAGCACAAATCGCATCAT 58.364 42.857 0.00 0.00 0.00 2.45
1411 1670 5.760253 CCAAGGTGCGTAGATCATCTAATTT 59.240 40.000 0.00 0.00 29.58 1.82
1414 1673 3.704566 ACCAAGGTGCGTAGATCATCTAA 59.295 43.478 0.00 0.00 29.58 2.10
1648 1931 5.699458 ACTGTTCTTTGGGTATAACACGAAG 59.301 40.000 3.30 3.30 42.98 3.79
1695 1982 2.738139 CTCGCCATCGTGCACACA 60.738 61.111 18.64 2.29 36.96 3.72
1708 1995 2.552315 TCCCAAAACAGATTCAACTCGC 59.448 45.455 0.00 0.00 0.00 5.03
1729 2016 7.453126 AGCACAGCAAGAGAACTATATAGGTAT 59.547 37.037 14.25 4.51 0.00 2.73
1858 2145 6.540189 CCACCAGACTAGATTTATCTTTGGTG 59.460 42.308 22.35 22.35 43.72 4.17
2028 2321 4.984161 TGTTCTTGAATTTTGCAAGCTAGC 59.016 37.500 6.62 6.62 41.83 3.42
2069 2445 9.558396 AAGAGGAGATTTAGAATAAAGATGCAG 57.442 33.333 0.00 0.00 0.00 4.41
2159 2537 5.925509 TCCCTTTACCTCATACTATGCAAC 58.074 41.667 0.00 0.00 0.00 4.17
2160 2538 6.569127 TTCCCTTTACCTCATACTATGCAA 57.431 37.500 0.00 0.00 0.00 4.08
2162 2540 4.998033 GCTTCCCTTTACCTCATACTATGC 59.002 45.833 0.00 0.00 0.00 3.14
2195 2574 3.999046 AGGAACTGTACACGGTTTTAGG 58.001 45.455 7.94 0.00 44.81 2.69
2248 2627 9.546428 GTTTAGGGTTGTTACTTGTTAGTAAGA 57.454 33.333 0.00 0.00 45.12 2.10
2251 2630 7.442062 GCTGTTTAGGGTTGTTACTTGTTAGTA 59.558 37.037 0.00 0.00 35.78 1.82
2252 2631 6.261603 GCTGTTTAGGGTTGTTACTTGTTAGT 59.738 38.462 0.00 0.00 38.44 2.24
2254 2633 6.120905 TGCTGTTTAGGGTTGTTACTTGTTA 58.879 36.000 0.00 0.00 0.00 2.41
2256 2635 4.528920 TGCTGTTTAGGGTTGTTACTTGT 58.471 39.130 0.00 0.00 0.00 3.16
2257 2636 5.705609 ATGCTGTTTAGGGTTGTTACTTG 57.294 39.130 0.00 0.00 0.00 3.16
2258 2637 7.826918 TTAATGCTGTTTAGGGTTGTTACTT 57.173 32.000 0.00 0.00 0.00 2.24
2259 2638 8.417273 AATTAATGCTGTTTAGGGTTGTTACT 57.583 30.769 0.00 0.00 0.00 2.24
2261 2640 9.523168 ACTAATTAATGCTGTTTAGGGTTGTTA 57.477 29.630 0.00 0.00 0.00 2.41
2262 2641 8.417273 ACTAATTAATGCTGTTTAGGGTTGTT 57.583 30.769 0.00 0.00 0.00 2.83
2263 2642 8.417273 AACTAATTAATGCTGTTTAGGGTTGT 57.583 30.769 0.00 0.00 0.00 3.32
2272 2651 8.686334 CCTGGTGATTAACTAATTAATGCTGTT 58.314 33.333 0.00 0.00 40.42 3.16
2418 2797 1.134491 CATGCATGCCTGAGACTGAGA 60.134 52.381 17.08 0.00 0.00 3.27
2419 2798 1.300481 CATGCATGCCTGAGACTGAG 58.700 55.000 17.08 0.00 0.00 3.35
2420 2799 3.471354 CATGCATGCCTGAGACTGA 57.529 52.632 17.08 0.00 0.00 3.41
2526 2905 8.203485 GGATTGTGGAAAAATAATAATCAGGCA 58.797 33.333 0.00 0.00 0.00 4.75
2538 2917 8.865090 TGTAATGTTGTAGGATTGTGGAAAAAT 58.135 29.630 0.00 0.00 0.00 1.82
2542 2921 6.429692 CAGTGTAATGTTGTAGGATTGTGGAA 59.570 38.462 0.00 0.00 0.00 3.53
2545 2924 5.391950 GGCAGTGTAATGTTGTAGGATTGTG 60.392 44.000 0.00 0.00 0.00 3.33
2546 2925 4.700213 GGCAGTGTAATGTTGTAGGATTGT 59.300 41.667 0.00 0.00 0.00 2.71
2547 2926 4.096382 GGGCAGTGTAATGTTGTAGGATTG 59.904 45.833 0.00 0.00 0.00 2.67
2569 2948 7.572523 TGCAAGGATGTGAAATTCTAATAGG 57.427 36.000 0.00 0.00 0.00 2.57
2570 2949 9.859427 TTTTGCAAGGATGTGAAATTCTAATAG 57.141 29.630 0.00 0.00 0.00 1.73
2625 3004 6.542574 TCGTAGTTTTTCTTATTTTGGCGA 57.457 33.333 0.00 0.00 0.00 5.54
2626 3005 7.790861 ATTCGTAGTTTTTCTTATTTTGGCG 57.209 32.000 0.00 0.00 0.00 5.69
2707 3109 7.287927 CAGGTCAGGGAAATACATTCTAGTAGA 59.712 40.741 0.00 0.00 38.18 2.59
2708 3110 7.437748 CAGGTCAGGGAAATACATTCTAGTAG 58.562 42.308 0.00 0.00 38.18 2.57
2709 3111 6.183360 GCAGGTCAGGGAAATACATTCTAGTA 60.183 42.308 0.00 0.00 38.18 1.82
2710 3112 5.396884 GCAGGTCAGGGAAATACATTCTAGT 60.397 44.000 0.00 0.00 38.18 2.57
2766 3168 9.429359 TGCCTACAATTAATTACCACAAATTTG 57.571 29.630 16.67 16.67 31.63 2.32
2926 3329 4.697756 TCGGTGCGGCCAGGAAAG 62.698 66.667 2.24 0.00 36.97 2.62
2941 3344 1.200839 GTTCTTGACGGCGTTGTCG 59.799 57.895 16.19 3.48 41.87 4.35
3115 3521 0.834687 AGAAACCGCCACCACTAGGA 60.835 55.000 0.00 0.00 38.69 2.94
3185 3591 1.714899 GCGCCGTAGCCATTGAACAT 61.715 55.000 0.00 0.00 34.57 2.71
3280 3686 0.758685 AGGAGAAGGCGATGGAGAGG 60.759 60.000 0.00 0.00 0.00 3.69
3341 3747 4.101448 GCGGTGATGGTCAGGGCT 62.101 66.667 0.00 0.00 0.00 5.19
3357 3763 1.653151 GACGTGGTAATCCTTCCTGC 58.347 55.000 0.00 0.00 34.23 4.85
3385 3791 0.875059 CCTTCGTTTTCAGTGGCTCC 59.125 55.000 0.00 0.00 0.00 4.70
3631 4037 4.730600 TCAACAGTTCAACACATGATCG 57.269 40.909 0.00 0.00 38.03 3.69
3756 4169 7.226720 CGTCTCAACAATAGGCCTTTGTATAAT 59.773 37.037 24.38 12.47 36.32 1.28
3762 4175 2.159517 GCGTCTCAACAATAGGCCTTTG 60.160 50.000 12.58 17.56 0.00 2.77
3770 4183 4.068599 TCACAATTGGCGTCTCAACAATA 58.931 39.130 10.83 0.00 34.00 1.90
3839 4253 0.314935 CACATGTGTCTTGTTGCCCC 59.685 55.000 18.03 0.00 0.00 5.80
3840 4254 0.314935 CCACATGTGTCTTGTTGCCC 59.685 55.000 23.79 0.00 0.00 5.36
3851 4265 5.288015 TGTTTGAATTGCTTACCACATGTG 58.712 37.500 19.31 19.31 0.00 3.21
3852 4266 5.528043 TGTTTGAATTGCTTACCACATGT 57.472 34.783 0.00 0.00 0.00 3.21
3854 4268 7.215789 TGAATTGTTTGAATTGCTTACCACAT 58.784 30.769 0.00 0.00 0.00 3.21
3855 4269 6.577103 TGAATTGTTTGAATTGCTTACCACA 58.423 32.000 0.00 0.00 0.00 4.17
3856 4270 7.475771 TTGAATTGTTTGAATTGCTTACCAC 57.524 32.000 0.00 0.00 0.00 4.16
3857 4271 8.498054 TTTTGAATTGTTTGAATTGCTTACCA 57.502 26.923 0.00 0.00 0.00 3.25
3883 4297 9.976255 GCCTTAAACAAATTTTCTTTTACGTTT 57.024 25.926 0.00 0.00 0.00 3.60
3884 4298 9.373603 AGCCTTAAACAAATTTTCTTTTACGTT 57.626 25.926 0.00 0.00 0.00 3.99
3885 4299 8.813282 CAGCCTTAAACAAATTTTCTTTTACGT 58.187 29.630 0.00 0.00 0.00 3.57
3894 4308 6.475402 CGACTTGACAGCCTTAAACAAATTTT 59.525 34.615 0.00 0.00 0.00 1.82
3907 4321 1.853319 CACGTTCGACTTGACAGCC 59.147 57.895 0.00 0.00 0.00 4.85
3945 4359 1.295746 GGGTCTCCGAAGTCCCAAC 59.704 63.158 0.00 0.00 46.73 3.77
4009 4423 3.257624 GGGACGACGATATTCACCCTTAT 59.742 47.826 0.00 0.00 32.23 1.73
4010 4424 2.624838 GGGACGACGATATTCACCCTTA 59.375 50.000 0.00 0.00 32.23 2.69
4097 4511 7.771826 AGTCGATTTAGCCCTATATAGTCTCTC 59.228 40.741 8.92 3.84 0.00 3.20
4098 4512 7.635648 AGTCGATTTAGCCCTATATAGTCTCT 58.364 38.462 8.92 5.25 0.00 3.10
4099 4513 7.868906 AGTCGATTTAGCCCTATATAGTCTC 57.131 40.000 8.92 0.00 0.00 3.36
4110 4524 6.250344 ACTGTTTTTAAGTCGATTTAGCCC 57.750 37.500 0.45 0.00 0.00 5.19
4188 4602 4.541085 TCTTTCATGAGTTATGCATGCG 57.459 40.909 14.09 0.00 42.13 4.73
4189 4603 5.049886 TCGATCTTTCATGAGTTATGCATGC 60.050 40.000 11.82 11.82 42.13 4.06
4246 4808 7.994194 AGCAATTTTGTTATTTCAAAAAGGCA 58.006 26.923 21.00 0.97 45.87 4.75
4365 4927 4.658071 GTTCGCTGACAAACTCAAAAAGA 58.342 39.130 0.00 0.00 0.00 2.52
4383 4945 8.905103 AATATTTCTGGAATTTAAACCGTTCG 57.095 30.769 0.00 0.00 0.00 3.95
4504 5067 9.178758 AGACAGTAAAATTCTTTATCATGGACC 57.821 33.333 0.00 0.00 29.86 4.46
4583 5146 8.428536 CACGACTTCACACTATTTTCTTTCTAG 58.571 37.037 0.00 0.00 0.00 2.43
4584 5147 7.924412 ACACGACTTCACACTATTTTCTTTCTA 59.076 33.333 0.00 0.00 0.00 2.10
4585 5148 6.761714 ACACGACTTCACACTATTTTCTTTCT 59.238 34.615 0.00 0.00 0.00 2.52
4586 5149 6.945072 ACACGACTTCACACTATTTTCTTTC 58.055 36.000 0.00 0.00 0.00 2.62
4607 5170 3.678056 TGTAGTTCCATCCTGTGACAC 57.322 47.619 0.00 0.00 0.00 3.67
4608 5171 3.837731 TCATGTAGTTCCATCCTGTGACA 59.162 43.478 0.00 0.00 0.00 3.58
4666 5229 5.051240 GGCGATCACTACATAAGTTAAACCG 60.051 44.000 0.00 0.00 35.76 4.44


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

AutoCloner maintained by Alex Coulton.