Multiple sequence alignment - TraesCS7B01G382400

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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 TraesCS7B01G382400 chr7B 100.000 2617 0 0 1 2617 648138017 648140633 0.000000e+00 4833.0
1 TraesCS7B01G382400 chr7B 89.221 770 60 13 1857 2617 648179820 648180575 0.000000e+00 941.0
2 TraesCS7B01G382400 chr7B 96.942 556 16 1 3 558 123689425 123688871 0.000000e+00 931.0
3 TraesCS7B01G382400 chr7B 87.175 538 57 4 1336 1861 648177413 648177950 3.730000e-168 601.0
4 TraesCS7B01G382400 chr7B 73.752 1162 235 38 1420 2555 648365458 648366575 2.440000e-105 392.0
5 TraesCS7B01G382400 chr7B 77.439 164 35 2 1216 1378 649321767 649321929 2.140000e-16 97.1
6 TraesCS7B01G382400 chr7A 88.216 1816 135 20 838 2617 672152643 672154415 0.000000e+00 2095.0
7 TraesCS7B01G382400 chr7A 74.211 1140 223 37 1443 2555 672255418 672256513 6.740000e-111 411.0
8 TraesCS7B01G382400 chr7A 91.892 185 11 2 2437 2617 672155566 672155750 3.340000e-64 255.0
9 TraesCS7B01G382400 chr7A 87.981 208 20 3 558 760 672150953 672151160 9.360000e-60 241.0
10 TraesCS7B01G382400 chr7A 78.947 323 51 11 1088 1397 672148975 672149293 1.230000e-48 204.0
11 TraesCS7B01G382400 chr7A 75.934 241 50 5 1462 1699 673309987 673310222 1.650000e-22 117.0
12 TraesCS7B01G382400 chr7A 77.622 143 29 3 1465 1606 648211584 648211444 1.670000e-12 84.2
13 TraesCS7B01G382400 chr3B 97.482 556 13 1 3 558 520540215 520540769 0.000000e+00 948.0
14 TraesCS7B01G382400 chr1B 96.948 557 15 2 3 558 435922318 435921763 0.000000e+00 933.0
15 TraesCS7B01G382400 chr1B 96.780 559 16 2 1 558 323968709 323969266 0.000000e+00 931.0
16 TraesCS7B01G382400 chr1B 96.768 557 16 2 3 558 50067510 50068065 0.000000e+00 928.0
17 TraesCS7B01G382400 chr1B 95.958 569 20 3 3 570 478699144 478699710 0.000000e+00 920.0
18 TraesCS7B01G382400 chr7D 96.780 559 16 2 2 559 474498823 474499380 0.000000e+00 931.0
19 TraesCS7B01G382400 chr7D 96.774 558 16 2 2 558 474492064 474492620 0.000000e+00 929.0
20 TraesCS7B01G382400 chr7D 74.470 991 194 33 1353 2320 580654351 580655305 8.840000e-100 374.0
21 TraesCS7B01G382400 chr7D 80.471 297 50 7 1107 1397 580576702 580576996 1.220000e-53 220.0
22 TraesCS7B01G382400 chr7D 73.200 500 117 13 1211 1699 582043021 582043514 5.790000e-37 165.0
23 TraesCS7B01G382400 chr7D 71.503 579 135 20 1214 1770 581665537 581666107 7.600000e-26 128.0
24 TraesCS7B01G382400 chr7D 80.723 166 31 1 1232 1397 582085493 582085657 7.600000e-26 128.0
25 TraesCS7B01G382400 chr7D 71.573 496 123 15 1214 1699 581637864 581638351 4.580000e-23 119.0
26 TraesCS7B01G382400 chr4B 96.942 556 16 1 3 558 178777827 178777273 0.000000e+00 931.0
27 TraesCS7B01G382400 chr5D 79.592 147 30 0 1211 1357 289687142 289687288 3.560000e-19 106.0
28 TraesCS7B01G382400 chrUn 83.333 72 12 0 1465 1536 215044929 215044858 1.680000e-07 67.6


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 TraesCS7B01G382400 chr7B 648138017 648140633 2616 False 4833.00 4833 100.000 1 2617 1 chr7B.!!$F1 2616
1 TraesCS7B01G382400 chr7B 123688871 123689425 554 True 931.00 931 96.942 3 558 1 chr7B.!!$R1 555
2 TraesCS7B01G382400 chr7B 648177413 648180575 3162 False 771.00 941 88.198 1336 2617 2 chr7B.!!$F4 1281
3 TraesCS7B01G382400 chr7B 648365458 648366575 1117 False 392.00 392 73.752 1420 2555 1 chr7B.!!$F2 1135
4 TraesCS7B01G382400 chr7A 672148975 672155750 6775 False 698.75 2095 86.759 558 2617 4 chr7A.!!$F3 2059
5 TraesCS7B01G382400 chr7A 672255418 672256513 1095 False 411.00 411 74.211 1443 2555 1 chr7A.!!$F1 1112
6 TraesCS7B01G382400 chr3B 520540215 520540769 554 False 948.00 948 97.482 3 558 1 chr3B.!!$F1 555
7 TraesCS7B01G382400 chr1B 435921763 435922318 555 True 933.00 933 96.948 3 558 1 chr1B.!!$R1 555
8 TraesCS7B01G382400 chr1B 323968709 323969266 557 False 931.00 931 96.780 1 558 1 chr1B.!!$F2 557
9 TraesCS7B01G382400 chr1B 50067510 50068065 555 False 928.00 928 96.768 3 558 1 chr1B.!!$F1 555
10 TraesCS7B01G382400 chr1B 478699144 478699710 566 False 920.00 920 95.958 3 570 1 chr1B.!!$F3 567
11 TraesCS7B01G382400 chr7D 474498823 474499380 557 False 931.00 931 96.780 2 559 1 chr7D.!!$F2 557
12 TraesCS7B01G382400 chr7D 474492064 474492620 556 False 929.00 929 96.774 2 558 1 chr7D.!!$F1 556
13 TraesCS7B01G382400 chr7D 580654351 580655305 954 False 374.00 374 74.470 1353 2320 1 chr7D.!!$F4 967
14 TraesCS7B01G382400 chr4B 178777273 178777827 554 True 931.00 931 96.942 3 558 1 chr4B.!!$R1 555

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
709 2136 0.379669 GATCAGATTTGTGCAGGGCG 59.62 55.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1620 4473 0.036732 CTTTGCCTACAGCCTGACCA 59.963 55.0 0.0 0.0 42.71 4.02 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
357 360 7.083858 CCGTTAATCAAATGACAACTCATGTT 58.916 34.615 0.00 0.00 44.12 2.71
383 386 5.887754 TGGCTAGGAAACTTAACCATCTTT 58.112 37.500 0.00 0.00 43.67 2.52
561 564 3.584733 AGGGCATATTTCCTTCACCTC 57.415 47.619 0.00 0.00 0.00 3.85
570 573 1.588239 TCCTTCACCTCCATCATGCT 58.412 50.000 0.00 0.00 0.00 3.79
575 1997 2.190538 TCACCTCCATCATGCTGAAGA 58.809 47.619 0.00 0.00 0.00 2.87
587 2009 2.964740 TGCTGAAGATTTCCTCGACAG 58.035 47.619 0.00 0.00 36.07 3.51
596 2018 6.037786 AGATTTCCTCGACAGACATGTTTA 57.962 37.500 0.00 0.00 40.68 2.01
607 2029 0.796312 ACATGTTTACTCAAGCCGCG 59.204 50.000 0.00 0.00 0.00 6.46
608 2030 1.075542 CATGTTTACTCAAGCCGCGA 58.924 50.000 8.23 0.00 0.00 5.87
609 2031 1.076332 ATGTTTACTCAAGCCGCGAC 58.924 50.000 8.23 0.00 0.00 5.19
612 2034 0.669318 TTTACTCAAGCCGCGACAGG 60.669 55.000 8.23 0.00 0.00 4.00
624 2051 4.410400 GACAGGCCGGGAAGGGTG 62.410 72.222 8.08 0.00 41.48 4.61
638 2065 3.453559 GGGTGTACTCCCATGAACG 57.546 57.895 25.08 0.00 46.30 3.95
640 2067 0.743345 GGTGTACTCCCATGAACGCC 60.743 60.000 2.33 0.00 35.54 5.68
641 2068 0.743345 GTGTACTCCCATGAACGCCC 60.743 60.000 0.00 0.00 0.00 6.13
643 2070 0.743345 GTACTCCCATGAACGCCCAC 60.743 60.000 0.00 0.00 0.00 4.61
661 2088 0.392595 ACAACCTAAAGCTAGCGCCC 60.393 55.000 9.55 0.00 36.60 6.13
680 2107 4.990910 AGGGAGGTGCAGGTGGCT 62.991 66.667 0.00 0.00 45.15 4.75
709 2136 0.379669 GATCAGATTTGTGCAGGGCG 59.620 55.000 0.00 0.00 0.00 6.13
751 2178 8.207545 TGAGGGTTTATACTTTTTGCAAACATT 58.792 29.630 12.39 2.08 32.11 2.71
765 2192 7.655236 TTGCAAACATTAATTGAATCACCTG 57.345 32.000 0.00 0.00 0.00 4.00
768 2195 7.384660 TGCAAACATTAATTGAATCACCTGTTC 59.615 33.333 0.00 0.00 0.00 3.18
769 2196 7.384660 GCAAACATTAATTGAATCACCTGTTCA 59.615 33.333 0.00 0.00 34.01 3.18
799 2226 7.118496 ACTTAAGAGAGAGAGAGAGAGAGAG 57.882 44.000 10.09 0.00 0.00 3.20
800 2227 6.897966 ACTTAAGAGAGAGAGAGAGAGAGAGA 59.102 42.308 10.09 0.00 0.00 3.10
802 2229 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
803 2230 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
804 2231 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
805 2232 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
807 2234 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
808 2235 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
809 2236 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
814 2241 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
815 2242 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
817 2244 4.648762 AGAGAGAGAGAGAGAGAGAGAGTG 59.351 50.000 0.00 0.00 0.00 3.51
818 2245 4.614475 AGAGAGAGAGAGAGAGAGAGTGA 58.386 47.826 0.00 0.00 0.00 3.41
819 2246 4.648762 AGAGAGAGAGAGAGAGAGAGTGAG 59.351 50.000 0.00 0.00 0.00 3.51
820 2247 4.614475 AGAGAGAGAGAGAGAGAGTGAGA 58.386 47.826 0.00 0.00 0.00 3.27
821 2248 4.648762 AGAGAGAGAGAGAGAGAGTGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
823 2250 4.648762 AGAGAGAGAGAGAGAGTGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
825 2252 4.648762 AGAGAGAGAGAGAGTGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
826 2253 4.614475 AGAGAGAGAGAGTGAGAGAGAGA 58.386 47.826 0.00 0.00 0.00 3.10
829 2256 4.648762 AGAGAGAGAGTGAGAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
830 2257 4.614475 AGAGAGAGTGAGAGAGAGAGAGA 58.386 47.826 0.00 0.00 0.00 3.10
831 2258 4.648762 AGAGAGAGTGAGAGAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
832 2259 4.614475 AGAGAGTGAGAGAGAGAGAGAGA 58.386 47.826 0.00 0.00 0.00 3.10
833 2260 4.648762 AGAGAGTGAGAGAGAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
834 2261 4.614475 AGAGTGAGAGAGAGAGAGAGAGA 58.386 47.826 0.00 0.00 0.00 3.10
835 2262 4.648762 AGAGTGAGAGAGAGAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
836 2263 4.614475 AGTGAGAGAGAGAGAGAGAGAGA 58.386 47.826 0.00 0.00 0.00 3.10
843 3675 6.614906 AGAGAGAGAGAGAGAGAGAGAATTCT 59.385 42.308 7.95 7.95 36.01 2.40
863 3695 8.820153 AATTCTTAATCTTTGGCTGAATCTCT 57.180 30.769 0.00 0.00 0.00 3.10
864 3696 9.911788 AATTCTTAATCTTTGGCTGAATCTCTA 57.088 29.630 0.00 0.00 0.00 2.43
865 3697 9.911788 ATTCTTAATCTTTGGCTGAATCTCTAA 57.088 29.630 0.00 0.00 0.00 2.10
870 3702 6.824305 TCTTTGGCTGAATCTCTAAAAAGG 57.176 37.500 0.00 0.00 0.00 3.11
874 3706 6.976934 TGGCTGAATCTCTAAAAAGGTTTT 57.023 33.333 0.00 0.00 0.00 2.43
876 3708 6.159293 GGCTGAATCTCTAAAAAGGTTTTGG 58.841 40.000 0.00 0.00 0.00 3.28
879 3711 7.926018 GCTGAATCTCTAAAAAGGTTTTGGAAA 59.074 33.333 1.92 0.00 0.00 3.13
886 3718 9.078990 CTCTAAAAAGGTTTTGGAAATCCTAGT 57.921 33.333 0.44 0.00 37.17 2.57
894 3726 3.085952 TGGAAATCCTAGTTGGGCAAG 57.914 47.619 0.44 0.00 36.82 4.01
916 3760 4.297891 CATATGGTGCCGTGCGCG 62.298 66.667 13.88 13.88 42.08 6.86
917 3761 4.830765 ATATGGTGCCGTGCGCGT 62.831 61.111 19.61 0.67 42.08 6.01
960 3804 5.774630 AGCCTATTTATTAGACTCTCACGC 58.225 41.667 0.00 0.00 0.00 5.34
961 3805 4.617645 GCCTATTTATTAGACTCTCACGCG 59.382 45.833 3.53 3.53 0.00 6.01
962 3806 5.759963 CCTATTTATTAGACTCTCACGCGT 58.240 41.667 5.58 5.58 0.00 6.01
973 3817 4.101790 CACGCGTGGACCATTGGC 62.102 66.667 31.15 0.94 0.00 4.52
1014 3858 2.241430 AGGCTCCATGGTTAGGTTTACC 59.759 50.000 12.58 0.00 36.17 2.85
1028 3872 0.183014 TTTACCCTTGTTCGTGGCCA 59.817 50.000 0.00 0.00 0.00 5.36
1040 3884 1.091771 CGTGGCCATCTTCGCTTCAT 61.092 55.000 9.72 0.00 0.00 2.57
1042 3886 0.749091 TGGCCATCTTCGCTTCATGG 60.749 55.000 0.00 0.00 40.24 3.66
1043 3887 0.749454 GGCCATCTTCGCTTCATGGT 60.749 55.000 0.00 0.00 39.55 3.55
1048 3892 2.745884 TTCGCTTCATGGTGGCCG 60.746 61.111 0.00 0.00 0.00 6.13
1086 3930 3.046870 GGCATGTCCGTTTTGGCA 58.953 55.556 0.00 0.00 37.80 4.92
1119 3963 2.391389 GCAGGCTCGTGCAAGGTAC 61.391 63.158 12.07 0.00 43.41 3.34
1122 3966 3.838795 GCTCGTGCAAGGTACGCG 61.839 66.667 3.53 3.53 41.08 6.01
1137 3981 4.820744 GCGGGGCATCACCACCAT 62.821 66.667 0.00 0.00 39.56 3.55
1138 3982 2.516930 CGGGGCATCACCACCATC 60.517 66.667 0.00 0.00 39.56 3.51
1139 3983 2.516930 GGGGCATCACCACCATCG 60.517 66.667 0.00 0.00 42.05 3.84
1140 3984 2.589540 GGGCATCACCACCATCGA 59.410 61.111 0.00 0.00 42.05 3.59
1141 3985 1.149174 GGGCATCACCACCATCGAT 59.851 57.895 0.00 0.00 42.05 3.59
1142 3986 0.886490 GGGCATCACCACCATCGATC 60.886 60.000 0.00 0.00 42.05 3.69
1143 3987 0.179048 GGCATCACCACCATCGATCA 60.179 55.000 0.00 0.00 38.86 2.92
1183 4027 1.534595 GCCATCTTCGCTGATCCATTC 59.465 52.381 0.00 0.00 0.00 2.67
1188 4032 3.535561 TCTTCGCTGATCCATTCTTTCC 58.464 45.455 0.00 0.00 0.00 3.13
1189 4033 3.055167 TCTTCGCTGATCCATTCTTTCCA 60.055 43.478 0.00 0.00 0.00 3.53
1190 4034 3.565764 TCGCTGATCCATTCTTTCCAT 57.434 42.857 0.00 0.00 0.00 3.41
1191 4035 4.687901 TCGCTGATCCATTCTTTCCATA 57.312 40.909 0.00 0.00 0.00 2.74
1199 4043 2.355756 CCATTCTTTCCATACGTGCAGG 59.644 50.000 4.53 4.53 0.00 4.85
1200 4044 1.448985 TTCTTTCCATACGTGCAGGC 58.551 50.000 6.26 0.00 0.00 4.85
1247 4091 3.053849 GCTCACCGACGACCTCCTC 62.054 68.421 0.00 0.00 0.00 3.71
1262 4106 0.179043 TCCTCGTCCAGATCCTCTCG 60.179 60.000 0.00 0.00 0.00 4.04
1266 4110 2.440247 TCCAGATCCTCTCGCGCA 60.440 61.111 8.75 0.00 0.00 6.09
1288 4132 4.641645 CGCCAAGGTGGTCTGCCA 62.642 66.667 0.00 0.00 40.46 4.92
1309 4153 2.032528 CAAGGCCGTCTCCAAGCA 59.967 61.111 0.00 0.00 0.00 3.91
1310 4154 1.377725 CAAGGCCGTCTCCAAGCAT 60.378 57.895 0.00 0.00 0.00 3.79
1361 4205 1.078848 CAAGAGGCTCTCCCAACCG 60.079 63.158 19.03 0.00 35.39 4.44
1365 4210 3.706373 GGCTCTCCCAACCGCTGA 61.706 66.667 0.00 0.00 0.00 4.26
1395 4240 1.946768 TCTACAACAGCACCAACAAGC 59.053 47.619 0.00 0.00 0.00 4.01
1437 4282 1.565156 GCACTTCGTCAATGCGTCCA 61.565 55.000 0.00 0.00 0.00 4.02
1439 4284 0.033504 ACTTCGTCAATGCGTCCAGT 59.966 50.000 0.00 0.00 0.00 4.00
1517 4362 0.403271 ACCTCTTGGACTGCTGCAAT 59.597 50.000 3.02 0.00 37.04 3.56
1569 4414 3.744719 CCGGAGGCGACGAGTTCA 61.745 66.667 0.00 0.00 46.14 3.18
1570 4415 2.504244 CGGAGGCGACGAGTTCAC 60.504 66.667 0.00 0.00 0.00 3.18
1578 4423 2.993130 GACGAGTTCACGTACGTCC 58.007 57.895 19.94 9.50 46.52 4.79
1611 4456 4.760047 CGGAGGAGTGGGCGGTTG 62.760 72.222 0.00 0.00 0.00 3.77
1706 4568 1.614903 CCATGTGTTTGTGCTGGATGT 59.385 47.619 0.00 0.00 0.00 3.06
1709 4574 2.585330 TGTGTTTGTGCTGGATGTGAT 58.415 42.857 0.00 0.00 0.00 3.06
1737 4602 5.946942 ACTTCATCTGAGTGGATGTGTAT 57.053 39.130 0.00 0.00 42.45 2.29
1795 4660 2.170607 GGATTGGACCGAGATTTCAGGA 59.829 50.000 2.05 0.00 0.00 3.86
1797 4662 4.040461 GGATTGGACCGAGATTTCAGGATA 59.960 45.833 2.05 0.00 0.00 2.59
1919 6658 5.862845 AGAATCATGGTTGAGCTTCGATAT 58.137 37.500 0.00 0.00 34.73 1.63
1929 6677 3.005897 TGAGCTTCGATATCCCTTGTAGC 59.994 47.826 0.00 0.00 0.00 3.58
1965 6713 9.734620 TTTCTTGATTTCATTCAACAGTTACAG 57.265 29.630 0.00 0.00 32.39 2.74
1971 6719 3.149196 CATTCAACAGTTACAGCAGGGT 58.851 45.455 0.00 0.00 0.00 4.34
2044 6792 8.870879 GTGATATTCAACTAGAAGTTTACGCTT 58.129 33.333 0.00 0.00 40.15 4.68
2073 6821 2.459555 ATCCCGGCAAAGATTGGAAT 57.540 45.000 0.00 0.00 0.00 3.01
2134 6885 0.763035 AGGGGTTGCTCAACGTTACT 59.237 50.000 0.00 0.47 42.02 2.24
2135 6886 1.142262 AGGGGTTGCTCAACGTTACTT 59.858 47.619 0.00 0.00 42.02 2.24
2136 6887 1.951602 GGGGTTGCTCAACGTTACTTT 59.048 47.619 0.00 0.00 42.02 2.66
2137 6888 2.287368 GGGGTTGCTCAACGTTACTTTG 60.287 50.000 0.00 0.00 42.02 2.77
2138 6889 2.614983 GGGTTGCTCAACGTTACTTTGA 59.385 45.455 0.00 4.30 42.02 2.69
2139 6890 3.065648 GGGTTGCTCAACGTTACTTTGAA 59.934 43.478 0.00 0.00 42.02 2.69
2140 6891 4.439016 GGGTTGCTCAACGTTACTTTGAAA 60.439 41.667 0.00 0.00 42.02 2.69
2201 6952 4.228210 TCTTCTTCATAGATGGGCCACTTT 59.772 41.667 9.28 0.00 0.00 2.66
2202 6953 3.889815 TCTTCATAGATGGGCCACTTTG 58.110 45.455 9.28 13.49 0.00 2.77
2257 7008 4.331168 CGGAAAGTGAGAAAGATCATCACC 59.669 45.833 13.49 0.00 43.47 4.02
2260 7011 4.751767 AGTGAGAAAGATCATCACCCTC 57.248 45.455 13.49 0.00 43.47 4.30
2327 7079 5.798934 TCGAGTTAGAATCTTTGCGTTAGTC 59.201 40.000 0.00 0.00 0.00 2.59
2385 7138 4.223923 AGGTGGTTCTTTGATAGGAGTCAG 59.776 45.833 0.00 0.00 0.00 3.51
2386 7139 3.935828 GTGGTTCTTTGATAGGAGTCAGC 59.064 47.826 0.00 0.00 0.00 4.26
2458 8549 1.001378 CGGCTTTTTGAACAGGAGTGG 60.001 52.381 0.00 0.00 0.00 4.00
2571 8665 3.813166 TGCACTAAACTTTCAGTACTGGC 59.187 43.478 22.48 13.59 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
166 167 6.067217 AGGAACACTTTATCTGCTACCAAT 57.933 37.500 0.00 0.00 0.00 3.16
176 177 6.038356 TCGTTTATCGGAGGAACACTTTATC 58.962 40.000 6.95 0.00 40.32 1.75
357 360 7.208064 AGATGGTTAAGTTTCCTAGCCATAA 57.792 36.000 0.00 0.00 35.64 1.90
383 386 4.883083 ACTTGACTAGCTCGTTGAATCAA 58.117 39.130 0.00 0.00 0.00 2.57
570 573 4.021104 ACATGTCTGTCGAGGAAATCTTCA 60.021 41.667 0.00 0.00 0.00 3.02
575 1997 5.794894 AGTAAACATGTCTGTCGAGGAAAT 58.205 37.500 0.00 0.00 33.36 2.17
587 2009 1.201921 CGCGGCTTGAGTAAACATGTC 60.202 52.381 0.00 0.00 0.00 3.06
607 2029 4.410400 CACCCTTCCCGGCCTGTC 62.410 72.222 0.00 0.00 0.00 3.51
608 2030 3.857521 TACACCCTTCCCGGCCTGT 62.858 63.158 0.00 0.00 0.00 4.00
609 2031 3.006728 TACACCCTTCCCGGCCTG 61.007 66.667 0.00 0.00 0.00 4.85
612 2034 2.582978 GAGTACACCCTTCCCGGC 59.417 66.667 0.00 0.00 0.00 6.13
614 2036 3.306379 GGGAGTACACCCTTCCCG 58.694 66.667 20.23 0.00 45.90 5.14
624 2051 0.743345 GTGGGCGTTCATGGGAGTAC 60.743 60.000 0.00 0.00 0.00 2.73
631 2058 1.529226 TTAGGTTGTGGGCGTTCATG 58.471 50.000 0.00 0.00 0.00 3.07
638 2065 1.095600 GCTAGCTTTAGGTTGTGGGC 58.904 55.000 7.70 0.00 0.00 5.36
640 2067 0.727398 GCGCTAGCTTTAGGTTGTGG 59.273 55.000 13.93 0.00 41.01 4.17
641 2068 0.727398 GGCGCTAGCTTTAGGTTGTG 59.273 55.000 13.93 0.00 44.37 3.33
643 2070 0.392461 TGGGCGCTAGCTTTAGGTTG 60.392 55.000 13.93 0.00 44.37 3.77
661 2088 2.034687 CCACCTGCACCTCCCTTG 59.965 66.667 0.00 0.00 0.00 3.61
680 2107 2.535485 AAATCTGATCCACCGCGGCA 62.535 55.000 28.58 14.10 33.14 5.69
693 2120 2.180017 GCGCCCTGCACAAATCTG 59.820 61.111 0.00 0.00 45.45 2.90
709 2136 2.743928 CACCTCAAGCTCACCGGC 60.744 66.667 0.00 0.00 0.00 6.13
772 2199 9.877222 TCTCTCTCTCTCTCTCTCTTAAGTATA 57.123 37.037 1.63 0.00 0.00 1.47
774 2201 8.059461 TCTCTCTCTCTCTCTCTCTCTTAAGTA 58.941 40.741 1.63 0.00 0.00 2.24
776 2203 7.286546 TCTCTCTCTCTCTCTCTCTCTCTTAAG 59.713 44.444 0.00 0.00 0.00 1.85
777 2204 7.126061 TCTCTCTCTCTCTCTCTCTCTCTTAA 58.874 42.308 0.00 0.00 0.00 1.85
778 2205 6.673583 TCTCTCTCTCTCTCTCTCTCTCTTA 58.326 44.000 0.00 0.00 0.00 2.10
779 2206 5.523588 TCTCTCTCTCTCTCTCTCTCTCTT 58.476 45.833 0.00 0.00 0.00 2.85
780 2207 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
781 2208 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
782 2209 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
783 2210 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
785 2212 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
786 2213 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
787 2214 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
788 2215 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
789 2216 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
790 2217 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
791 2218 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
792 2219 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
794 2221 4.648762 CACTCTCTCTCTCTCTCTCTCTCT 59.351 50.000 0.00 0.00 0.00 3.10
795 2222 4.646945 TCACTCTCTCTCTCTCTCTCTCTC 59.353 50.000 0.00 0.00 0.00 3.20
796 2223 4.614475 TCACTCTCTCTCTCTCTCTCTCT 58.386 47.826 0.00 0.00 0.00 3.10
797 2224 4.646945 TCTCACTCTCTCTCTCTCTCTCTC 59.353 50.000 0.00 0.00 0.00 3.20
799 2226 4.646945 TCTCTCACTCTCTCTCTCTCTCTC 59.353 50.000 0.00 0.00 0.00 3.20
800 2227 4.614475 TCTCTCACTCTCTCTCTCTCTCT 58.386 47.826 0.00 0.00 0.00 3.10
802 2229 4.614475 TCTCTCTCACTCTCTCTCTCTCT 58.386 47.826 0.00 0.00 0.00 3.10
803 2230 4.646945 TCTCTCTCTCACTCTCTCTCTCTC 59.353 50.000 0.00 0.00 0.00 3.20
804 2231 4.614475 TCTCTCTCTCACTCTCTCTCTCT 58.386 47.826 0.00 0.00 0.00 3.10
805 2232 4.646945 TCTCTCTCTCTCACTCTCTCTCTC 59.353 50.000 0.00 0.00 0.00 3.20
807 2234 4.646945 TCTCTCTCTCTCTCACTCTCTCTC 59.353 50.000 0.00 0.00 0.00 3.20
808 2235 4.614475 TCTCTCTCTCTCTCACTCTCTCT 58.386 47.826 0.00 0.00 0.00 3.10
809 2236 4.646945 TCTCTCTCTCTCTCTCACTCTCTC 59.353 50.000 0.00 0.00 0.00 3.20
814 2241 4.614475 TCTCTCTCTCTCTCTCTCTCACT 58.386 47.826 0.00 0.00 0.00 3.41
815 2242 4.646945 TCTCTCTCTCTCTCTCTCTCTCAC 59.353 50.000 0.00 0.00 0.00 3.51
817 2244 5.860941 TTCTCTCTCTCTCTCTCTCTCTC 57.139 47.826 0.00 0.00 0.00 3.20
818 2245 6.614906 AGAATTCTCTCTCTCTCTCTCTCTCT 59.385 42.308 0.88 0.00 0.00 3.10
819 2246 6.825610 AGAATTCTCTCTCTCTCTCTCTCTC 58.174 44.000 0.88 0.00 0.00 3.20
820 2247 6.821616 AGAATTCTCTCTCTCTCTCTCTCT 57.178 41.667 0.88 0.00 0.00 3.10
821 2248 8.964476 TTAAGAATTCTCTCTCTCTCTCTCTC 57.036 38.462 8.78 0.00 0.00 3.20
823 2250 9.566432 AGATTAAGAATTCTCTCTCTCTCTCTC 57.434 37.037 8.78 0.00 0.00 3.20
829 2256 7.986889 AGCCAAAGATTAAGAATTCTCTCTCTC 59.013 37.037 8.78 2.36 0.00 3.20
830 2257 7.769970 CAGCCAAAGATTAAGAATTCTCTCTCT 59.230 37.037 8.78 7.96 0.00 3.10
831 2258 7.768120 TCAGCCAAAGATTAAGAATTCTCTCTC 59.232 37.037 8.78 5.79 0.00 3.20
832 2259 7.628234 TCAGCCAAAGATTAAGAATTCTCTCT 58.372 34.615 8.78 8.65 0.00 3.10
833 2260 7.856145 TCAGCCAAAGATTAAGAATTCTCTC 57.144 36.000 8.78 6.49 0.00 3.20
834 2261 8.820153 ATTCAGCCAAAGATTAAGAATTCTCT 57.180 30.769 8.78 0.00 0.00 3.10
835 2262 8.901793 AGATTCAGCCAAAGATTAAGAATTCTC 58.098 33.333 8.78 0.00 0.00 2.87
836 2263 8.820153 AGATTCAGCCAAAGATTAAGAATTCT 57.180 30.769 0.88 0.88 0.00 2.40
851 3683 6.239289 CCAAAACCTTTTTAGAGATTCAGCCA 60.239 38.462 0.00 0.00 0.00 4.75
863 3695 8.425703 CCAACTAGGATTTCCAAAACCTTTTTA 58.574 33.333 6.21 0.00 40.96 1.52
864 3696 7.279615 CCAACTAGGATTTCCAAAACCTTTTT 58.720 34.615 6.21 0.00 40.96 1.94
865 3697 6.183361 CCCAACTAGGATTTCCAAAACCTTTT 60.183 38.462 6.21 0.00 40.96 2.27
870 3702 3.576550 TGCCCAACTAGGATTTCCAAAAC 59.423 43.478 0.00 0.00 41.22 2.43
874 3706 2.378547 ACTTGCCCAACTAGGATTTCCA 59.621 45.455 0.00 0.00 41.22 3.53
876 3708 4.336280 AGAACTTGCCCAACTAGGATTTC 58.664 43.478 0.00 0.00 41.22 2.17
879 3711 2.912956 TGAGAACTTGCCCAACTAGGAT 59.087 45.455 0.00 0.00 41.22 3.24
886 3718 3.355378 CACCATATGAGAACTTGCCCAA 58.645 45.455 3.65 0.00 0.00 4.12
894 3726 0.657840 GCACGGCACCATATGAGAAC 59.342 55.000 3.65 0.00 0.00 3.01
916 3760 5.088739 GCTAAATTGTAGCATGTCACACAC 58.911 41.667 0.72 0.00 40.14 3.82
917 3761 4.155826 GGCTAAATTGTAGCATGTCACACA 59.844 41.667 8.12 0.00 42.06 3.72
933 3777 9.915629 CGTGAGAGTCTAATAAATAGGCTAAAT 57.084 33.333 0.00 0.00 46.59 1.40
961 3805 2.282180 ACGTGGCCAATGGTCCAC 60.282 61.111 25.72 25.72 42.32 4.02
962 3806 2.033448 GACGTGGCCAATGGTCCA 59.967 61.111 7.24 10.64 0.00 4.02
973 3817 1.278637 GAACTTTGCCGTGACGTGG 59.721 57.895 3.64 0.00 0.00 4.94
977 3821 1.949257 CCTGGAACTTTGCCGTGAC 59.051 57.895 0.00 0.00 0.00 3.67
985 3829 0.779997 ACCATGGAGCCTGGAACTTT 59.220 50.000 21.47 0.00 37.22 2.66
1014 3858 0.804989 GAAGATGGCCACGAACAAGG 59.195 55.000 8.16 0.00 0.00 3.61
1028 3872 0.749454 GGCCACCATGAAGCGAAGAT 60.749 55.000 0.00 0.00 0.00 2.40
1081 3925 4.961511 AGCGCGACGAACTGCCAA 62.962 61.111 12.10 0.00 0.00 4.52
1103 3947 2.261671 CGTACCTTGCACGAGCCT 59.738 61.111 1.39 0.00 41.91 4.58
1105 3949 3.838795 CGCGTACCTTGCACGAGC 61.839 66.667 0.00 0.00 41.91 5.03
1122 3966 2.343475 ATCGATGGTGGTGATGCCCC 62.343 60.000 0.00 0.00 36.04 5.80
1135 3979 2.477825 AGGTTCTTGCGATGATCGATG 58.522 47.619 20.25 7.38 43.74 3.84
1137 3981 2.672874 CAAAGGTTCTTGCGATGATCGA 59.327 45.455 20.25 0.69 43.74 3.59
1138 3982 2.789092 GCAAAGGTTCTTGCGATGATCG 60.789 50.000 11.02 11.02 42.09 3.69
1139 3983 2.790387 GCAAAGGTTCTTGCGATGATC 58.210 47.619 0.00 0.00 42.09 2.92
1140 3984 2.927553 GCAAAGGTTCTTGCGATGAT 57.072 45.000 0.00 0.00 42.09 2.45
1183 4027 0.392998 AGGCCTGCACGTATGGAAAG 60.393 55.000 3.11 0.00 0.00 2.62
1188 4032 0.532862 CCCTTAGGCCTGCACGTATG 60.533 60.000 17.99 0.00 0.00 2.39
1189 4033 1.830145 CCCTTAGGCCTGCACGTAT 59.170 57.895 17.99 0.00 0.00 3.06
1190 4034 3.305314 CCCTTAGGCCTGCACGTA 58.695 61.111 17.99 0.00 0.00 3.57
1200 4044 2.903855 CATGCGGCTGCCCTTAGG 60.904 66.667 16.57 0.00 41.78 2.69
1266 4110 1.615424 AGACCACCTTGGCGGGTAT 60.615 57.895 1.70 0.00 42.67 2.73
1288 4132 0.962356 CTTGGAGACGGCCTTGCAAT 60.962 55.000 0.00 0.00 0.00 3.56
1289 4133 1.600636 CTTGGAGACGGCCTTGCAA 60.601 57.895 0.00 0.00 0.00 4.08
1318 4162 1.076265 TCGGGGTGGTCGATGAGAT 60.076 57.895 0.00 0.00 0.00 2.75
1319 4163 2.050350 GTCGGGGTGGTCGATGAGA 61.050 63.158 0.00 0.00 38.93 3.27
1347 4191 3.710722 CAGCGGTTGGGAGAGCCT 61.711 66.667 0.00 0.00 0.00 4.58
1361 4205 0.246635 TGTAGAAGAAGCCGGTCAGC 59.753 55.000 1.90 0.00 0.00 4.26
1365 4210 1.608283 GCTGTTGTAGAAGAAGCCGGT 60.608 52.381 1.90 0.00 0.00 5.28
1395 4240 0.946221 GCTGATATCGGGAAGCGGTG 60.946 60.000 13.48 0.00 0.00 4.94
1497 4342 0.183492 TTGCAGCAGTCCAAGAGGTT 59.817 50.000 0.00 0.00 35.89 3.50
1569 4414 1.300388 GGTTGCACAGGACGTACGT 60.300 57.895 23.04 23.04 0.00 3.57
1570 4415 2.025418 GGGTTGCACAGGACGTACG 61.025 63.158 15.01 15.01 0.00 3.67
1620 4473 0.036732 CTTTGCCTACAGCCTGACCA 59.963 55.000 0.00 0.00 42.71 4.02
1631 4484 0.250124 CACCGTGTCCACTTTGCCTA 60.250 55.000 0.00 0.00 0.00 3.93
1672 4528 1.077501 CATGGAAGTGGGCGGACAT 60.078 57.895 0.00 0.00 0.00 3.06
1706 4568 4.892345 CCACTCAGATGAAGTAGAGGATCA 59.108 45.833 0.00 0.00 37.82 2.92
1709 4574 4.592997 TCCACTCAGATGAAGTAGAGGA 57.407 45.455 0.00 0.00 32.52 3.71
1712 4577 5.019470 ACACATCCACTCAGATGAAGTAGA 58.981 41.667 8.44 0.00 45.43 2.59
1723 4588 2.159296 CCGACGAATACACATCCACTCA 60.159 50.000 0.00 0.00 0.00 3.41
1737 4602 3.744719 CCGCCAGTCTCCGACGAA 61.745 66.667 0.00 0.00 37.67 3.85
1817 4682 5.239744 TGCAAATAGCCGTTAAGAAAGACAA 59.760 36.000 0.00 0.00 44.83 3.18
1919 6658 5.129815 AGAAATACATTACCGCTACAAGGGA 59.870 40.000 0.00 0.00 0.00 4.20
1963 6711 2.309528 TAATGTAAGCGACCCTGCTG 57.690 50.000 0.00 0.00 46.60 4.41
1965 6713 2.544267 GACATAATGTAAGCGACCCTGC 59.456 50.000 0.00 0.00 0.00 4.85
2073 6821 4.202141 CCATCTTGACCTTTGTGCTTCAAA 60.202 41.667 7.25 7.25 42.79 2.69
2134 6885 5.193663 TCGCAGTCCATTCAAATTTCAAA 57.806 34.783 0.00 0.00 0.00 2.69
2135 6886 4.844998 TCGCAGTCCATTCAAATTTCAA 57.155 36.364 0.00 0.00 0.00 2.69
2136 6887 5.048154 TCAATCGCAGTCCATTCAAATTTCA 60.048 36.000 0.00 0.00 0.00 2.69
2137 6888 5.401550 TCAATCGCAGTCCATTCAAATTTC 58.598 37.500 0.00 0.00 0.00 2.17
2138 6889 5.389859 TCAATCGCAGTCCATTCAAATTT 57.610 34.783 0.00 0.00 0.00 1.82
2139 6890 5.587388 ATCAATCGCAGTCCATTCAAATT 57.413 34.783 0.00 0.00 0.00 1.82
2140 6891 5.589855 TGTATCAATCGCAGTCCATTCAAAT 59.410 36.000 0.00 0.00 0.00 2.32
2175 6926 3.975982 TGGCCCATCTATGAAGAAGATCA 59.024 43.478 0.00 0.00 34.73 2.92
2267 7018 1.131638 GGCAGATATGGTGTCTGGGA 58.868 55.000 5.71 0.00 42.58 4.37
2327 7079 0.102120 GGAGGTCTCAGACTGATGCG 59.898 60.000 5.42 0.00 32.47 4.73
2360 7113 3.195825 ACTCCTATCAAAGAACCACCTCG 59.804 47.826 0.00 0.00 0.00 4.63
2385 7138 0.878416 TGTTCCATAGCACAAACGGC 59.122 50.000 0.00 0.00 0.00 5.68
2386 7139 2.095768 CACTGTTCCATAGCACAAACGG 60.096 50.000 0.00 0.00 34.80 4.44
2585 8683 4.642885 GGTAGCAGTGCCATTTACCATTTA 59.357 41.667 20.74 0.00 35.09 1.40
2587 8685 3.023832 GGTAGCAGTGCCATTTACCATT 58.976 45.455 20.74 0.00 35.09 3.16
2598 8696 1.738099 CACGTGGAGGTAGCAGTGC 60.738 63.158 7.13 7.13 0.00 4.40


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

AutoCloner maintained by Alex Coulton.