Multiple sequence alignment - TraesCS2A01G593800

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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 TraesCS2A01G593800 chr2A 100.000 2632 0 0 1 2632 780745027 780742396 0.000000e+00 4861.0
1 TraesCS2A01G593800 chr2A 98.387 62 1 0 809 870 90569988 90570049 2.770000e-20 110.0
2 TraesCS2A01G593800 chr2D 91.419 1445 81 13 1170 2573 633593267 633594709 0.000000e+00 1941.0
3 TraesCS2A01G593800 chr2D 93.373 166 8 3 969 1131 633592176 633592341 2.620000e-60 243.0
4 TraesCS2A01G593800 chr2D 86.111 180 17 4 1587 1758 93265478 93265657 1.240000e-43 187.0
5 TraesCS2A01G593800 chr5A 96.790 810 26 0 1 810 512117979 512118788 0.000000e+00 1352.0
6 TraesCS2A01G593800 chr5A 96.420 810 24 1 1 810 663162185 663161381 0.000000e+00 1330.0
7 TraesCS2A01G593800 chr5A 90.026 772 73 4 1170 1939 565941014 565940245 0.000000e+00 996.0
8 TraesCS2A01G593800 chr3A 96.543 810 28 0 1 810 266700495 266701304 0.000000e+00 1341.0
9 TraesCS2A01G593800 chr3A 98.387 62 1 0 809 870 637589238 637589177 2.770000e-20 110.0
10 TraesCS2A01G593800 chr3A 100.000 36 0 0 2251 2286 743974640 743974605 1.690000e-07 67.6
11 TraesCS2A01G593800 chrUn 96.319 815 25 2 1 810 83560472 83561286 0.000000e+00 1334.0
12 TraesCS2A01G593800 chrUn 96.319 815 25 2 1 810 448604952 448604138 0.000000e+00 1334.0
13 TraesCS2A01G593800 chr1B 96.319 815 25 2 1 810 123415701 123414887 0.000000e+00 1334.0
14 TraesCS2A01G593800 chr1B 88.588 701 54 10 1197 1891 572288837 572288157 0.000000e+00 828.0
15 TraesCS2A01G593800 chr1B 84.358 179 23 4 966 1140 572290405 572290228 1.250000e-38 171.0
16 TraesCS2A01G593800 chr1B 87.838 74 6 2 2394 2464 613720015 613720088 1.680000e-12 84.2
17 TraesCS2A01G593800 chr4A 96.420 810 24 1 1 810 210938721 210939525 0.000000e+00 1330.0
18 TraesCS2A01G593800 chr4A 98.387 62 1 0 809 870 585069412 585069351 2.770000e-20 110.0
19 TraesCS2A01G593800 chr4A 98.387 62 1 0 809 870 587163267 587163206 2.770000e-20 110.0
20 TraesCS2A01G593800 chr2B 96.420 810 24 1 1 810 161427502 161426698 0.000000e+00 1330.0
21 TraesCS2A01G593800 chr2B 95.864 677 26 2 1170 1845 776687440 776688115 0.000000e+00 1094.0
22 TraesCS2A01G593800 chr2B 94.620 539 27 1 1836 2372 776689253 776689791 0.000000e+00 833.0
23 TraesCS2A01G593800 chr2B 92.354 497 29 3 1170 1658 138122088 138121593 0.000000e+00 699.0
24 TraesCS2A01G593800 chr2B 86.316 285 27 9 1587 1859 62410269 62410553 1.530000e-77 300.0
25 TraesCS2A01G593800 chr2B 88.400 250 17 8 874 1116 776687172 776687416 9.220000e-75 291.0
26 TraesCS2A01G593800 chr2B 92.079 202 14 1 2368 2569 776691629 776691828 1.540000e-72 283.0
27 TraesCS2A01G593800 chr1A 96.420 810 24 1 1 810 6929566 6930370 0.000000e+00 1330.0
28 TraesCS2A01G593800 chr1A 87.983 699 64 6 1197 1891 518954326 518953644 0.000000e+00 808.0
29 TraesCS2A01G593800 chr1A 92.153 497 30 3 1170 1658 111988670 111988175 0.000000e+00 693.0
30 TraesCS2A01G593800 chr1A 82.597 724 78 15 1210 1923 518952582 518951897 1.740000e-166 595.0
31 TraesCS2A01G593800 chr1A 84.615 182 22 4 966 1142 518955846 518955666 2.690000e-40 176.0
32 TraesCS2A01G593800 chr1A 98.387 62 1 0 809 870 234805930 234805991 2.770000e-20 110.0
33 TraesCS2A01G593800 chr1A 82.105 95 13 3 2208 2301 518677973 518677882 7.810000e-11 78.7
34 TraesCS2A01G593800 chr7D 92.362 707 46 5 1871 2574 619663672 619664373 0.000000e+00 1000.0
35 TraesCS2A01G593800 chr1D 88.269 699 60 7 1197 1891 423036034 423035354 0.000000e+00 817.0
36 TraesCS2A01G593800 chr1D 85.475 179 21 4 966 1140 423037579 423037402 5.790000e-42 182.0
37 TraesCS2A01G593800 chr1D 85.556 180 18 4 1587 1758 453667369 453667548 5.790000e-42 182.0
38 TraesCS2A01G593800 chr1D 84.058 138 21 1 989 1126 224139522 224139658 5.910000e-27 132.0
39 TraesCS2A01G593800 chr3B 92.555 497 28 6 1170 1658 646715399 646714904 0.000000e+00 704.0
40 TraesCS2A01G593800 chr3B 98.387 62 1 0 809 870 781747232 781747293 2.770000e-20 110.0
41 TraesCS2A01G593800 chr5D 82.807 285 33 9 1587 1859 520295409 520295689 9.410000e-60 241.0
42 TraesCS2A01G593800 chr4D 82.807 285 33 8 1587 1859 49872913 49872633 9.410000e-60 241.0
43 TraesCS2A01G593800 chr4D 81.139 281 40 7 1587 1859 461529342 461529067 2.050000e-51 213.0
44 TraesCS2A01G593800 chr7B 93.506 154 9 1 1871 2023 611667903 611668056 7.330000e-56 228.0
45 TraesCS2A01G593800 chr7B 94.872 39 2 0 2248 2286 714491461 714491423 7.870000e-06 62.1
46 TraesCS2A01G593800 chr6B 98.387 62 1 0 809 870 147692896 147692957 2.770000e-20 110.0
47 TraesCS2A01G593800 chr4B 98.387 62 1 0 809 870 461687812 461687873 2.770000e-20 110.0
48 TraesCS2A01G593800 chr3D 90.789 76 3 4 812 886 5083701 5083629 6.000000e-17 99.0


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 TraesCS2A01G593800 chr2A 780742396 780745027 2631 True 4861.000000 4861 100.00000 1 2632 1 chr2A.!!$R1 2631
1 TraesCS2A01G593800 chr2D 633592176 633594709 2533 False 1092.000000 1941 92.39600 969 2573 2 chr2D.!!$F2 1604
2 TraesCS2A01G593800 chr5A 512117979 512118788 809 False 1352.000000 1352 96.79000 1 810 1 chr5A.!!$F1 809
3 TraesCS2A01G593800 chr5A 663161381 663162185 804 True 1330.000000 1330 96.42000 1 810 1 chr5A.!!$R2 809
4 TraesCS2A01G593800 chr5A 565940245 565941014 769 True 996.000000 996 90.02600 1170 1939 1 chr5A.!!$R1 769
5 TraesCS2A01G593800 chr3A 266700495 266701304 809 False 1341.000000 1341 96.54300 1 810 1 chr3A.!!$F1 809
6 TraesCS2A01G593800 chrUn 83560472 83561286 814 False 1334.000000 1334 96.31900 1 810 1 chrUn.!!$F1 809
7 TraesCS2A01G593800 chrUn 448604138 448604952 814 True 1334.000000 1334 96.31900 1 810 1 chrUn.!!$R1 809
8 TraesCS2A01G593800 chr1B 123414887 123415701 814 True 1334.000000 1334 96.31900 1 810 1 chr1B.!!$R1 809
9 TraesCS2A01G593800 chr1B 572288157 572290405 2248 True 499.500000 828 86.47300 966 1891 2 chr1B.!!$R2 925
10 TraesCS2A01G593800 chr4A 210938721 210939525 804 False 1330.000000 1330 96.42000 1 810 1 chr4A.!!$F1 809
11 TraesCS2A01G593800 chr2B 161426698 161427502 804 True 1330.000000 1330 96.42000 1 810 1 chr2B.!!$R2 809
12 TraesCS2A01G593800 chr2B 776687172 776691828 4656 False 625.250000 1094 92.74075 874 2569 4 chr2B.!!$F2 1695
13 TraesCS2A01G593800 chr1A 6929566 6930370 804 False 1330.000000 1330 96.42000 1 810 1 chr1A.!!$F1 809
14 TraesCS2A01G593800 chr1A 518951897 518955846 3949 True 526.333333 808 85.06500 966 1923 3 chr1A.!!$R3 957
15 TraesCS2A01G593800 chr7D 619663672 619664373 701 False 1000.000000 1000 92.36200 1871 2574 1 chr7D.!!$F1 703
16 TraesCS2A01G593800 chr1D 423035354 423037579 2225 True 499.500000 817 86.87200 966 1891 2 chr1D.!!$R1 925

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
554 560 0.107456 GTCGGATCATGGGCTGTCAT 59.893 55.0 0.0 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2378 6177 0.472471 AGGGACACAGAAAGGCGAAA 59.528 50.0 0.0 0.0 0.0 3.46 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
60 61 6.319658 CCATACTGACAATTCAAGGCATAGTT 59.680 38.462 0.00 0.00 0.00 2.24
174 175 4.458989 GCAATTGGAACAGAGGACACAATA 59.541 41.667 7.72 0.00 42.39 1.90
203 204 1.140312 GATCTGGTGGGGGATTGCTA 58.860 55.000 0.00 0.00 0.00 3.49
250 251 7.467675 GCCCATATTGCAATTTCTGAAAAATCC 60.468 37.037 18.75 0.00 0.00 3.01
260 261 2.652348 TCTGAAAAATCCCTAAGGGCCA 59.348 45.455 6.18 0.00 43.94 5.36
299 300 5.735285 ACTAGGTGTAGTGGGAAGTTTAC 57.265 43.478 0.00 0.00 38.14 2.01
323 324 1.918800 CCCCGGAAGTGGAAGGAGT 60.919 63.158 0.73 0.00 0.00 3.85
324 325 1.489560 CCCCGGAAGTGGAAGGAGTT 61.490 60.000 0.73 0.00 0.00 3.01
368 369 6.798427 TTCTCTTCTACATGCTATTGGAGT 57.202 37.500 0.00 0.00 0.00 3.85
493 499 1.259316 GCGCTTATTTTTGCCAGTCG 58.741 50.000 0.00 0.00 0.00 4.18
554 560 0.107456 GTCGGATCATGGGCTGTCAT 59.893 55.000 0.00 0.00 0.00 3.06
568 574 0.891904 TGTCATGGACTCGGACGTGA 60.892 55.000 0.00 0.00 34.32 4.35
714 720 2.052690 CGGTGACTCCATCCCGTCT 61.053 63.158 0.00 0.00 36.77 4.18
763 769 1.599797 CTCCGAAACCACGCCCTTT 60.600 57.895 0.00 0.00 0.00 3.11
772 778 0.250989 CCACGCCCTTTTGGTTCCTA 60.251 55.000 0.00 0.00 38.10 2.94
802 808 1.356398 AGGGGCGAATAGGTTTTTGGA 59.644 47.619 0.00 0.00 0.00 3.53
810 816 4.662145 GAATAGGTTTTTGGACAGCGATG 58.338 43.478 0.00 0.00 0.00 3.84
811 817 0.598065 AGGTTTTTGGACAGCGATGC 59.402 50.000 0.00 0.00 0.00 3.91
812 818 0.388520 GGTTTTTGGACAGCGATGCC 60.389 55.000 0.00 3.60 0.00 4.40
813 819 0.313672 GTTTTTGGACAGCGATGCCA 59.686 50.000 11.87 11.87 0.00 4.92
814 820 1.067635 GTTTTTGGACAGCGATGCCAT 60.068 47.619 15.68 0.00 0.00 4.40
815 821 0.527113 TTTTGGACAGCGATGCCATG 59.473 50.000 15.68 0.00 0.00 3.66
816 822 1.936436 TTTGGACAGCGATGCCATGC 61.936 55.000 15.68 0.00 0.00 4.06
817 823 2.515523 GGACAGCGATGCCATGCT 60.516 61.111 0.00 0.00 43.58 3.79
818 824 1.227645 GGACAGCGATGCCATGCTA 60.228 57.895 0.00 0.00 40.03 3.49
819 825 1.226686 GGACAGCGATGCCATGCTAG 61.227 60.000 0.00 0.00 40.03 3.42
820 826 0.531532 GACAGCGATGCCATGCTAGT 60.532 55.000 0.00 3.77 40.03 2.57
821 827 0.752658 ACAGCGATGCCATGCTAGTA 59.247 50.000 0.00 0.00 40.03 1.82
822 828 1.138859 ACAGCGATGCCATGCTAGTAA 59.861 47.619 0.00 0.00 40.03 2.24
823 829 2.224378 ACAGCGATGCCATGCTAGTAAT 60.224 45.455 0.00 0.00 40.03 1.89
824 830 2.810274 CAGCGATGCCATGCTAGTAATT 59.190 45.455 0.00 0.00 40.03 1.40
825 831 3.251729 CAGCGATGCCATGCTAGTAATTT 59.748 43.478 0.00 0.00 40.03 1.82
826 832 4.452114 CAGCGATGCCATGCTAGTAATTTA 59.548 41.667 0.00 0.00 40.03 1.40
827 833 4.452455 AGCGATGCCATGCTAGTAATTTAC 59.548 41.667 0.00 0.00 40.28 2.01
828 834 4.452455 GCGATGCCATGCTAGTAATTTACT 59.548 41.667 13.36 13.36 42.68 2.24
829 835 5.389935 GCGATGCCATGCTAGTAATTTACTC 60.390 44.000 12.26 0.88 40.14 2.59
830 836 5.696270 CGATGCCATGCTAGTAATTTACTCA 59.304 40.000 12.26 6.41 40.14 3.41
831 837 6.369890 CGATGCCATGCTAGTAATTTACTCAT 59.630 38.462 12.26 8.31 40.14 2.90
832 838 6.866010 TGCCATGCTAGTAATTTACTCATG 57.134 37.500 20.80 20.80 39.15 3.07
868 874 9.860898 AATCAAGAAATTGCCTATTTACTCAAC 57.139 29.630 0.00 0.00 36.59 3.18
869 875 8.402798 TCAAGAAATTGCCTATTTACTCAACA 57.597 30.769 0.00 0.00 36.59 3.33
870 876 9.023962 TCAAGAAATTGCCTATTTACTCAACAT 57.976 29.630 0.00 0.00 36.59 2.71
871 877 9.079833 CAAGAAATTGCCTATTTACTCAACATG 57.920 33.333 0.00 0.00 36.59 3.21
872 878 8.579850 AGAAATTGCCTATTTACTCAACATGA 57.420 30.769 0.00 0.00 36.59 3.07
918 928 4.647853 TCGGAGTACAGCCACAGTATATTT 59.352 41.667 0.00 0.00 0.00 1.40
932 942 7.381408 CCACAGTATATTTATAGACACACCACG 59.619 40.741 0.00 0.00 0.00 4.94
937 947 0.966875 TATAGACACACCACGCCCGT 60.967 55.000 0.00 0.00 0.00 5.28
938 948 2.221906 ATAGACACACCACGCCCGTC 62.222 60.000 0.00 0.00 0.00 4.79
1014 1035 6.095432 AGAGCGAATATGTCTTATCTGCTT 57.905 37.500 0.00 0.00 33.31 3.91
1132 1162 1.341913 TATGCAGGTACGGTGCCCAT 61.342 55.000 11.90 11.19 40.43 4.00
1137 1167 3.404438 GTACGGTGCCCATCCCCA 61.404 66.667 0.00 0.00 0.00 4.96
1138 1168 2.611172 TACGGTGCCCATCCCCAA 60.611 61.111 0.00 0.00 0.00 4.12
1139 1169 2.974041 TACGGTGCCCATCCCCAAC 61.974 63.158 0.00 0.00 0.00 3.77
1140 1170 4.047125 CGGTGCCCATCCCCAACT 62.047 66.667 0.00 0.00 0.00 3.16
1141 1171 2.675242 CGGTGCCCATCCCCAACTA 61.675 63.158 0.00 0.00 0.00 2.24
1143 1173 1.571773 GGTGCCCATCCCCAACTAGT 61.572 60.000 0.00 0.00 0.00 2.57
1144 1174 0.107165 GTGCCCATCCCCAACTAGTC 60.107 60.000 0.00 0.00 0.00 2.59
1145 1175 1.279025 TGCCCATCCCCAACTAGTCC 61.279 60.000 0.00 0.00 0.00 3.85
1146 1176 0.988678 GCCCATCCCCAACTAGTCCT 60.989 60.000 0.00 0.00 0.00 3.85
1147 1177 1.596496 CCCATCCCCAACTAGTCCTT 58.404 55.000 0.00 0.00 0.00 3.36
1148 1178 2.771688 CCCATCCCCAACTAGTCCTTA 58.228 52.381 0.00 0.00 0.00 2.69
1149 1179 3.120108 CCCATCCCCAACTAGTCCTTAA 58.880 50.000 0.00 0.00 0.00 1.85
1156 1186 6.301486 TCCCCAACTAGTCCTTAAAGTTTTC 58.699 40.000 0.00 0.00 31.21 2.29
1177 2682 9.872757 GTTTTCTCGTATCTGAAATTGTACAAA 57.127 29.630 13.23 0.00 33.04 2.83
1219 2724 7.326063 GCGGTTTTATATTATTGATTGCAGACC 59.674 37.037 0.00 0.00 0.00 3.85
1292 2805 4.274705 TGCATGTTGTTGACTTCATTACGT 59.725 37.500 0.00 0.00 0.00 3.57
1724 3237 3.044059 GCGCTGTGACCCTTGATGC 62.044 63.158 0.00 0.00 0.00 3.91
1868 5631 4.869861 AGATGTTTGGTTTGAACTTTGTGC 59.130 37.500 0.00 0.00 0.00 4.57
1907 5672 2.030805 GGGCTCGATTTATCATGTTGGC 60.031 50.000 0.00 0.00 0.00 4.52
1978 5743 8.352201 CAGGTTCATGTTCAGTGAAAGAAAATA 58.648 33.333 7.25 0.00 37.34 1.40
2068 5834 4.465660 AGTGATGTATGCACTCTGAGTCTT 59.534 41.667 7.49 4.51 42.62 3.01
2106 5875 7.698836 AAATTCAAACTAATCTTGTGTGTGC 57.301 32.000 0.00 0.00 0.00 4.57
2130 5918 6.968904 GCCATACTTTGTTGATACATGAACTG 59.031 38.462 0.00 0.00 33.44 3.16
2269 6067 4.328025 TGGCGCAGTTGGCTAGCA 62.328 61.111 18.24 0.00 41.67 3.49
2301 6100 2.881266 GCTGCACGACGTGAGCAAA 61.881 57.895 31.08 9.46 43.75 3.68
2306 6105 1.321743 GCACGACGTGAGCAAATCTAG 59.678 52.381 31.08 0.45 35.23 2.43
2372 6171 1.284785 CCTCCATGGGTTCAGCCTTAA 59.715 52.381 13.02 0.00 37.43 1.85
2373 6172 2.369394 CTCCATGGGTTCAGCCTTAAC 58.631 52.381 13.02 0.00 37.43 2.01
2374 6173 1.992557 TCCATGGGTTCAGCCTTAACT 59.007 47.619 13.02 0.00 37.43 2.24
2375 6174 2.094675 CCATGGGTTCAGCCTTAACTG 58.905 52.381 2.85 0.00 39.12 3.16
2376 6175 1.474077 CATGGGTTCAGCCTTAACTGC 59.526 52.381 0.00 0.00 37.59 4.40
2378 6177 1.144913 TGGGTTCAGCCTTAACTGCTT 59.855 47.619 0.00 0.00 36.81 3.91
2380 6179 2.628178 GGGTTCAGCCTTAACTGCTTTT 59.372 45.455 0.00 0.00 36.81 2.27
2387 8026 2.288213 GCCTTAACTGCTTTTCGCCTTT 60.288 45.455 0.00 0.00 38.05 3.11
2519 8158 2.563179 GTCCTCTTCAGTTACCAGCTGA 59.437 50.000 17.39 0.00 40.76 4.26
2574 8213 6.884472 TTGGAGGAATATGAGTACCTTCAA 57.116 37.500 0.00 0.00 43.21 2.69
2575 8214 6.485830 TGGAGGAATATGAGTACCTTCAAG 57.514 41.667 0.00 0.00 35.40 3.02
2576 8215 5.163301 TGGAGGAATATGAGTACCTTCAAGC 60.163 44.000 0.00 0.00 35.40 4.01
2577 8216 5.071115 GGAGGAATATGAGTACCTTCAAGCT 59.929 44.000 0.00 0.00 32.53 3.74
2578 8217 6.408662 GGAGGAATATGAGTACCTTCAAGCTT 60.409 42.308 0.00 0.00 32.53 3.74
2579 8218 6.587273 AGGAATATGAGTACCTTCAAGCTTC 58.413 40.000 0.00 0.00 0.00 3.86
2580 8219 6.156949 AGGAATATGAGTACCTTCAAGCTTCA 59.843 38.462 0.00 0.00 0.00 3.02
2581 8220 6.481644 GGAATATGAGTACCTTCAAGCTTCAG 59.518 42.308 0.00 0.00 0.00 3.02
2582 8221 6.798427 ATATGAGTACCTTCAAGCTTCAGA 57.202 37.500 0.00 0.00 0.00 3.27
2583 8222 5.690464 ATGAGTACCTTCAAGCTTCAGAT 57.310 39.130 0.00 0.00 0.00 2.90
2584 8223 6.798427 ATGAGTACCTTCAAGCTTCAGATA 57.202 37.500 0.00 0.00 0.00 1.98
2585 8224 6.605471 TGAGTACCTTCAAGCTTCAGATAA 57.395 37.500 0.00 0.00 0.00 1.75
2586 8225 6.634805 TGAGTACCTTCAAGCTTCAGATAAG 58.365 40.000 0.00 0.00 0.00 1.73
2587 8226 5.983540 AGTACCTTCAAGCTTCAGATAAGG 58.016 41.667 14.77 14.77 39.50 2.69
2588 8227 4.917906 ACCTTCAAGCTTCAGATAAGGT 57.082 40.909 15.69 15.69 41.36 3.50
2589 8228 6.668283 AGTACCTTCAAGCTTCAGATAAGGTA 59.332 38.462 19.81 19.81 43.65 3.08
2590 8229 5.735766 ACCTTCAAGCTTCAGATAAGGTAC 58.264 41.667 18.20 0.00 43.65 3.34
2591 8230 5.248477 ACCTTCAAGCTTCAGATAAGGTACA 59.752 40.000 18.20 0.00 43.65 2.90
2592 8231 6.069963 ACCTTCAAGCTTCAGATAAGGTACAT 60.070 38.462 18.20 0.00 43.65 2.29
2593 8232 6.259608 CCTTCAAGCTTCAGATAAGGTACATG 59.740 42.308 0.00 0.00 30.97 3.21
2594 8233 6.544928 TCAAGCTTCAGATAAGGTACATGA 57.455 37.500 0.00 0.00 0.00 3.07
2595 8234 6.946340 TCAAGCTTCAGATAAGGTACATGAA 58.054 36.000 0.00 0.00 0.00 2.57
2596 8235 7.044181 TCAAGCTTCAGATAAGGTACATGAAG 58.956 38.462 0.00 8.50 46.12 3.02
2600 8239 6.798427 TTCAGATAAGGTACATGAAGCTCT 57.202 37.500 0.00 0.00 0.00 4.09
2601 8240 6.398234 TCAGATAAGGTACATGAAGCTCTC 57.602 41.667 0.00 0.00 0.00 3.20
2602 8241 5.009110 TCAGATAAGGTACATGAAGCTCTCG 59.991 44.000 0.00 0.00 0.00 4.04
2603 8242 2.969628 AAGGTACATGAAGCTCTCGG 57.030 50.000 0.00 0.00 0.00 4.63
2604 8243 0.461961 AGGTACATGAAGCTCTCGGC 59.538 55.000 0.00 0.00 42.19 5.54
2621 8260 4.988598 CGGCGAACCACCTGTGCT 62.989 66.667 0.00 0.00 34.57 4.40
2622 8261 3.050275 GGCGAACCACCTGTGCTC 61.050 66.667 0.00 0.00 35.26 4.26
2623 8262 3.050275 GCGAACCACCTGTGCTCC 61.050 66.667 0.00 0.00 0.00 4.70
2624 8263 2.358737 CGAACCACCTGTGCTCCC 60.359 66.667 0.00 0.00 0.00 4.30
2625 8264 2.034221 GAACCACCTGTGCTCCCC 59.966 66.667 0.00 0.00 0.00 4.81
2626 8265 3.901797 GAACCACCTGTGCTCCCCG 62.902 68.421 0.00 0.00 0.00 5.73
2627 8266 4.954118 ACCACCTGTGCTCCCCGA 62.954 66.667 0.00 0.00 0.00 5.14
2628 8267 4.394712 CCACCTGTGCTCCCCGAC 62.395 72.222 0.00 0.00 0.00 4.79
2629 8268 3.314331 CACCTGTGCTCCCCGACT 61.314 66.667 0.00 0.00 0.00 4.18
2630 8269 2.526873 ACCTGTGCTCCCCGACTT 60.527 61.111 0.00 0.00 0.00 3.01
2631 8270 2.147387 ACCTGTGCTCCCCGACTTT 61.147 57.895 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 6.913873 TGGTGTAAAGAAGTTTCACTACAC 57.086 37.500 18.56 18.56 41.64 2.90
34 35 4.032960 TGCCTTGAATTGTCAGTATGGT 57.967 40.909 0.00 0.00 34.49 3.55
38 39 6.472016 TGAACTATGCCTTGAATTGTCAGTA 58.528 36.000 0.00 0.00 34.49 2.74
60 61 4.576053 CACTCCTTCACAACTGAACAATGA 59.424 41.667 0.00 0.00 32.68 2.57
174 175 1.760086 CACCAGATCTCGAGGGCCT 60.760 63.158 5.25 5.25 0.00 5.19
203 204 3.181446 GCCTAGAGCCCATCTCAGATTTT 60.181 47.826 0.00 0.00 44.35 1.82
250 251 0.041090 AACCCACATTGGCCCTTAGG 59.959 55.000 0.00 0.00 35.79 2.69
260 261 4.415512 ACCTAGTGCCATATAACCCACATT 59.584 41.667 0.00 0.00 0.00 2.71
323 324 7.070629 AGAAACCCTTATAAACCACTCCAAAA 58.929 34.615 0.00 0.00 0.00 2.44
324 325 6.616577 AGAAACCCTTATAAACCACTCCAAA 58.383 36.000 0.00 0.00 0.00 3.28
368 369 2.569404 GAGGGCCTCTTCTCTTCTCAAA 59.431 50.000 26.44 0.00 0.00 2.69
493 499 3.650139 TGTCAGAAAACTCTCCGTTAGC 58.350 45.455 0.00 0.00 33.90 3.09
543 549 1.524002 CGAGTCCATGACAGCCCAT 59.476 57.895 0.00 0.00 34.60 4.00
568 574 2.034376 AGAGACGTGGGCTCGACT 59.966 61.111 0.00 8.12 38.32 4.18
763 769 2.112998 CTCACCCCGTATAGGAACCAA 58.887 52.381 0.00 0.00 45.00 3.67
772 778 3.853183 TATTCGCCCCTCACCCCGTAT 62.853 57.143 0.00 0.00 0.00 3.06
802 808 0.752658 TACTAGCATGGCATCGCTGT 59.247 50.000 24.89 21.77 39.30 4.40
810 816 6.246420 CCATGAGTAAATTACTAGCATGGC 57.754 41.667 26.79 8.95 45.81 4.40
842 848 9.860898 GTTGAGTAAATAGGCAATTTCTTGATT 57.139 29.630 0.00 0.00 38.71 2.57
843 849 9.023962 TGTTGAGTAAATAGGCAATTTCTTGAT 57.976 29.630 0.00 0.00 38.71 2.57
844 850 8.402798 TGTTGAGTAAATAGGCAATTTCTTGA 57.597 30.769 0.00 0.00 38.71 3.02
845 851 9.079833 CATGTTGAGTAAATAGGCAATTTCTTG 57.920 33.333 0.00 0.00 38.71 3.02
846 852 9.023962 TCATGTTGAGTAAATAGGCAATTTCTT 57.976 29.630 0.00 0.00 38.71 2.52
847 853 8.579850 TCATGTTGAGTAAATAGGCAATTTCT 57.420 30.769 0.00 0.00 38.71 2.52
848 854 8.847444 CTCATGTTGAGTAAATAGGCAATTTC 57.153 34.615 0.00 0.00 39.58 2.17
863 869 4.552448 TGGCTGTCCGACTCATGTTGAG 62.552 54.545 3.03 3.03 42.04 3.02
864 870 0.037326 GGCTGTCCGACTCATGTTGA 60.037 55.000 0.00 0.00 0.00 3.18
865 871 0.320683 TGGCTGTCCGACTCATGTTG 60.321 55.000 0.00 0.00 34.14 3.33
866 872 0.396435 TTGGCTGTCCGACTCATGTT 59.604 50.000 0.00 0.00 34.14 2.71
867 873 0.615331 ATTGGCTGTCCGACTCATGT 59.385 50.000 0.00 0.00 34.14 3.21
868 874 1.293924 GATTGGCTGTCCGACTCATG 58.706 55.000 0.00 0.00 34.14 3.07
869 875 0.179000 GGATTGGCTGTCCGACTCAT 59.821 55.000 0.00 0.00 34.14 2.90
870 876 0.904865 AGGATTGGCTGTCCGACTCA 60.905 55.000 0.00 0.00 40.76 3.41
871 877 0.250513 AAGGATTGGCTGTCCGACTC 59.749 55.000 0.00 0.00 40.76 3.36
872 878 0.693049 AAAGGATTGGCTGTCCGACT 59.307 50.000 0.00 0.00 40.76 4.18
918 928 0.966875 ACGGGCGTGGTGTGTCTATA 60.967 55.000 0.00 0.00 0.00 1.31
938 948 4.517703 GAGAGTCGACGACGGCCG 62.518 72.222 26.86 26.86 45.89 6.13
939 949 4.517703 CGAGAGTCGACGACGGCC 62.518 72.222 21.44 14.56 45.89 6.13
941 951 4.847585 CGCGAGAGTCGACGACGG 62.848 72.222 21.44 13.29 43.74 4.79
942 952 3.344836 TTCGCGAGAGTCGACGACG 62.345 63.158 21.44 20.83 43.59 5.12
943 953 1.858280 GTTCGCGAGAGTCGACGAC 60.858 63.158 20.25 20.25 43.59 4.34
944 954 2.473378 GTTCGCGAGAGTCGACGA 59.527 61.111 9.59 8.62 43.74 4.20
1071 1092 0.248498 CGAAGCGGATTAGCACGAGA 60.248 55.000 0.00 0.00 39.82 4.04
1097 1118 2.037902 TGCATACAAGTTTCGTCCCAGA 59.962 45.455 0.00 0.00 0.00 3.86
1132 1162 5.917545 AAACTTTAAGGACTAGTTGGGGA 57.082 39.130 0.00 0.00 32.76 4.81
1137 1167 9.636879 GATACGAGAAAACTTTAAGGACTAGTT 57.363 33.333 0.00 0.00 33.76 2.24
1138 1168 9.022884 AGATACGAGAAAACTTTAAGGACTAGT 57.977 33.333 0.00 0.00 0.00 2.57
1139 1169 9.291664 CAGATACGAGAAAACTTTAAGGACTAG 57.708 37.037 0.00 0.00 0.00 2.57
1140 1170 9.017509 TCAGATACGAGAAAACTTTAAGGACTA 57.982 33.333 0.00 0.00 0.00 2.59
1141 1171 7.893658 TCAGATACGAGAAAACTTTAAGGACT 58.106 34.615 0.00 0.00 0.00 3.85
1143 1173 9.720769 ATTTCAGATACGAGAAAACTTTAAGGA 57.279 29.630 0.00 0.00 37.30 3.36
1149 1179 9.268268 TGTACAATTTCAGATACGAGAAAACTT 57.732 29.630 0.00 0.00 37.30 2.66
1173 2678 5.476945 ACCGCTAGGAAATTGAATTCTTTGT 59.523 36.000 7.05 0.00 41.02 2.83
1177 2682 6.590234 AAAACCGCTAGGAAATTGAATTCT 57.410 33.333 7.05 0.00 41.02 2.40
1190 2695 9.546909 CTGCAATCAATAATATAAAACCGCTAG 57.453 33.333 0.00 0.00 0.00 3.42
1219 2724 4.022849 AGCCTGCTAAAAGTTAAACTGCAG 60.023 41.667 13.48 13.48 39.68 4.41
1271 2783 5.747565 ACACGTAATGAAGTCAACAACATG 58.252 37.500 0.00 0.00 0.00 3.21
1292 2805 8.367911 ACATGAACAAGTAGATAGTCAGAAACA 58.632 33.333 0.00 0.00 0.00 2.83
1468 2981 3.887110 TGTCCCAAGATCAATCATGATGC 59.113 43.478 9.46 0.00 46.30 3.91
1637 3150 2.708051 CACATGAAGAGACAGGCACAT 58.292 47.619 0.00 0.00 0.00 3.21
1724 3237 3.809832 ACTCCGAAAGTTGACAGACATTG 59.190 43.478 0.00 0.00 33.03 2.82
1907 5672 9.160496 AGATAAAAGAAGAGCAGTAACATTCTG 57.840 33.333 0.00 0.00 36.18 3.02
1961 5726 5.241728 AGCCTGGTATTTTCTTTCACTGAAC 59.758 40.000 0.00 0.00 0.00 3.18
1978 5743 4.965532 ACTCTAATATGTCTGAAGCCTGGT 59.034 41.667 0.00 0.00 0.00 4.00
2106 5875 8.177663 GTCAGTTCATGTATCAACAAAGTATGG 58.822 37.037 0.00 0.00 39.58 2.74
2142 5930 2.749621 CCTGCAAGTATCAACAAGGGAC 59.250 50.000 0.00 0.00 0.00 4.46
2269 6067 1.405821 GTGCAGCTATGAGACCTACGT 59.594 52.381 0.00 0.00 0.00 3.57
2301 6100 6.943899 AGAAAAAGAAGACCAGGTCTAGAT 57.056 37.500 23.24 7.32 42.59 1.98
2306 6105 6.701145 AGAAAAGAAAAAGAAGACCAGGTC 57.299 37.500 12.25 12.25 0.00 3.85
2376 6175 1.266989 GGGACACAGAAAGGCGAAAAG 59.733 52.381 0.00 0.00 0.00 2.27
2378 6177 0.472471 AGGGACACAGAAAGGCGAAA 59.528 50.000 0.00 0.00 0.00 3.46
2380 6179 1.671742 GAGGGACACAGAAAGGCGA 59.328 57.895 0.00 0.00 0.00 5.54
2387 8026 2.601666 AGCAGCGAGGGACACAGA 60.602 61.111 0.00 0.00 0.00 3.41
2519 8158 1.352352 CCAGACCATGAACCCAGAACT 59.648 52.381 0.00 0.00 0.00 3.01
2576 8215 6.815089 AGAGCTTCATGTACCTTATCTGAAG 58.185 40.000 6.30 6.30 43.51 3.02
2577 8216 6.460261 CGAGAGCTTCATGTACCTTATCTGAA 60.460 42.308 0.00 0.00 0.00 3.02
2578 8217 5.009110 CGAGAGCTTCATGTACCTTATCTGA 59.991 44.000 0.00 0.00 0.00 3.27
2579 8218 5.218885 CGAGAGCTTCATGTACCTTATCTG 58.781 45.833 0.00 0.00 0.00 2.90
2580 8219 4.279671 CCGAGAGCTTCATGTACCTTATCT 59.720 45.833 0.00 0.00 0.00 1.98
2581 8220 4.551388 CCGAGAGCTTCATGTACCTTATC 58.449 47.826 0.00 0.00 0.00 1.75
2582 8221 3.243907 GCCGAGAGCTTCATGTACCTTAT 60.244 47.826 0.00 0.00 38.99 1.73
2583 8222 2.100916 GCCGAGAGCTTCATGTACCTTA 59.899 50.000 0.00 0.00 38.99 2.69
2584 8223 1.134670 GCCGAGAGCTTCATGTACCTT 60.135 52.381 0.00 0.00 38.99 3.50
2585 8224 0.461961 GCCGAGAGCTTCATGTACCT 59.538 55.000 0.00 0.00 38.99 3.08
2586 8225 0.872021 CGCCGAGAGCTTCATGTACC 60.872 60.000 0.00 0.00 40.39 3.34
2587 8226 0.872021 CCGCCGAGAGCTTCATGTAC 60.872 60.000 0.00 0.00 40.39 2.90
2588 8227 1.437573 CCGCCGAGAGCTTCATGTA 59.562 57.895 0.00 0.00 40.39 2.29
2589 8228 2.185350 CCGCCGAGAGCTTCATGT 59.815 61.111 0.00 0.00 40.39 3.21
2590 8229 3.267860 GCCGCCGAGAGCTTCATG 61.268 66.667 0.00 0.00 40.39 3.07
2591 8230 4.880537 CGCCGCCGAGAGCTTCAT 62.881 66.667 0.00 0.00 40.39 2.57
2593 8232 4.796231 TTCGCCGCCGAGAGCTTC 62.796 66.667 0.00 0.00 45.35 3.86
2604 8243 4.988598 AGCACAGGTGGTTCGCCG 62.989 66.667 0.00 0.00 38.24 6.46
2605 8244 3.050275 GAGCACAGGTGGTTCGCC 61.050 66.667 5.52 0.00 41.93 5.54
2606 8245 3.050275 GGAGCACAGGTGGTTCGC 61.050 66.667 5.52 0.00 41.93 4.70
2607 8246 2.358737 GGGAGCACAGGTGGTTCG 60.359 66.667 5.52 0.00 41.93 3.95
2608 8247 2.034221 GGGGAGCACAGGTGGTTC 59.966 66.667 5.52 3.35 41.93 3.62
2609 8248 3.953775 CGGGGAGCACAGGTGGTT 61.954 66.667 5.52 0.00 41.93 3.67
2610 8249 4.954118 TCGGGGAGCACAGGTGGT 62.954 66.667 3.45 3.45 44.89 4.16
2611 8250 4.394712 GTCGGGGAGCACAGGTGG 62.395 72.222 1.10 0.00 0.00 4.61
2612 8251 2.397413 AAAGTCGGGGAGCACAGGTG 62.397 60.000 0.00 0.00 0.00 4.00
2613 8252 2.147387 AAAGTCGGGGAGCACAGGT 61.147 57.895 0.00 0.00 0.00 4.00
2614 8253 2.750350 AAAGTCGGGGAGCACAGG 59.250 61.111 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.