Multiple sequence alignment - TraesCS4D01G070300

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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 TraesCS4D01G070300 chr4D 100.000 4573 0 0 1 4573 45668413 45663841 0.000000e+00 8445.0
1 TraesCS4D01G070300 chr4D 89.231 65 6 1 870 933 45667501 45667437 3.790000e-11 80.5
2 TraesCS4D01G070300 chr4A 91.297 3045 205 26 913 3937 553406001 553409005 0.000000e+00 4100.0
3 TraesCS4D01G070300 chr4A 88.394 965 54 20 1 933 553405126 553406064 0.000000e+00 1109.0
4 TraesCS4D01G070300 chr4A 94.068 354 17 2 3798 4147 553426733 553427086 6.730000e-148 534.0
5 TraesCS4D01G070300 chr4A 92.857 280 19 1 3533 3811 553416022 553416301 5.510000e-109 405.0
6 TraesCS4D01G070300 chr4A 83.761 351 39 9 4231 4573 553427142 553427482 2.660000e-82 316.0
7 TraesCS4D01G070300 chr4B 89.043 3021 242 43 967 3957 65988056 65985095 0.000000e+00 3663.0
8 TraesCS4D01G070300 chr4B 87.398 3071 268 50 912 3936 66160587 66157590 0.000000e+00 3417.0
9 TraesCS4D01G070300 chr4B 93.845 1056 54 8 3523 4571 65979087 65978036 0.000000e+00 1580.0
10 TraesCS4D01G070300 chr4B 92.775 692 34 5 3232 3922 65982141 65981465 0.000000e+00 987.0
11 TraesCS4D01G070300 chr4B 83.477 696 56 24 1 680 66166498 66165846 1.100000e-165 593.0
12 TraesCS4D01G070300 chr4B 87.621 412 33 11 3983 4387 65979495 65979095 3.220000e-126 462.0
13 TraesCS4D01G070300 chr4B 84.404 327 30 8 2719 3031 65982774 65982455 7.440000e-78 302.0
14 TraesCS4D01G070300 chr4B 89.189 148 13 3 788 933 66160668 66160522 1.010000e-41 182.0
15 TraesCS4D01G070300 chr4B 78.205 234 35 15 588 809 65988339 65988110 7.980000e-28 135.0


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 TraesCS4D01G070300 chr4D 45663841 45668413 4572 True 4262.750000 8445 94.615500 1 4573 2 chr4D.!!$R1 4572
1 TraesCS4D01G070300 chr4A 553405126 553409005 3879 False 2604.500000 4100 89.845500 1 3937 2 chr4A.!!$F2 3936
2 TraesCS4D01G070300 chr4A 553426733 553427482 749 False 425.000000 534 88.914500 3798 4573 2 chr4A.!!$F3 775
3 TraesCS4D01G070300 chr4B 66157590 66160668 3078 True 1799.500000 3417 88.293500 788 3936 2 chr4B.!!$R3 3148
4 TraesCS4D01G070300 chr4B 65978036 65988339 10303 True 1188.166667 3663 87.648833 588 4571 6 chr4B.!!$R2 3983
5 TraesCS4D01G070300 chr4B 66165846 66166498 652 True 593.000000 593 83.477000 1 680 1 chr4B.!!$R1 679

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
871 915 0.184211 ACGCCCTTGTACCCAAGTTT 59.816 50.0 2.17 0.0 45.49 2.66 F
2180 2234 0.249489 GCTCCATTACGACGGCAGAT 60.249 55.0 0.00 0.0 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2704 2768 0.809385 TCTTCTGTACCGAAGAGGCG 59.191 55.0 21.62 2.05 43.17 5.52 R
4044 10593 0.179127 CTGATCGGTGTGAGCACGAT 60.179 55.0 0.00 0.00 46.13 3.73 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
25 26 5.820926 TTTTATTTGAGCAAACACGATGC 57.179 34.783 0.00 0.00 44.15 3.91
60 61 1.845809 CTGCAGGACAGCAACGGAAC 61.846 60.000 5.57 0.00 45.13 3.62
79 80 6.093082 ACGGAACCAACGGAATTCTAATTTAG 59.907 38.462 5.23 0.00 35.23 1.85
94 95 3.588817 TTAGGGTCGCCGTCCAGGA 62.589 63.158 2.26 0.00 45.00 3.86
133 134 4.309950 GGGCGGGACACGTGTCTT 62.310 66.667 39.01 12.84 46.52 3.01
160 161 2.127118 CGGCTGCAAAGCTGTTCG 60.127 61.111 0.50 0.00 36.49 3.95
183 190 2.281345 GGCATCGGCATCCTCCTG 60.281 66.667 0.00 0.00 43.71 3.86
191 198 2.373707 GCATCCTCCTGCCCTCTGT 61.374 63.158 0.00 0.00 36.10 3.41
228 235 1.457643 CCTCCATCGCTCCACCCTA 60.458 63.158 0.00 0.00 0.00 3.53
319 329 2.359169 CGAGGTAAGGCAGCCCTCA 61.359 63.158 8.22 0.00 44.12 3.86
320 330 1.899437 CGAGGTAAGGCAGCCCTCAA 61.899 60.000 8.22 0.00 44.12 3.02
328 344 2.750350 CAGCCCTCAACCGGAACT 59.250 61.111 9.46 0.00 0.00 3.01
465 481 1.648504 CGGGATTCGTAGTTTGTCCC 58.351 55.000 0.00 0.00 44.10 4.46
545 561 1.613437 CTGTGCGGGTTTTGGAATTCT 59.387 47.619 5.23 0.00 0.00 2.40
554 570 5.297547 GGGTTTTGGAATTCTGACCTTTTC 58.702 41.667 5.23 0.00 0.00 2.29
578 594 2.112297 GTGTGGGGTTTCCGCTCA 59.888 61.111 4.62 4.32 46.01 4.26
586 602 1.228657 GGTTTCCGCTCAGTGGTGAC 61.229 60.000 3.58 4.27 34.40 3.67
587 603 0.249911 GTTTCCGCTCAGTGGTGACT 60.250 55.000 3.58 0.00 34.40 3.41
711 730 4.289379 CATGCGTGCGGATGAGCG 62.289 66.667 18.77 0.00 45.01 5.03
712 731 4.512961 ATGCGTGCGGATGAGCGA 62.513 61.111 0.00 0.00 40.67 4.93
716 735 2.887568 GTGCGGATGAGCGAGTGG 60.888 66.667 0.00 0.00 40.67 4.00
717 736 3.068064 TGCGGATGAGCGAGTGGA 61.068 61.111 0.00 0.00 40.67 4.02
718 737 2.583593 GCGGATGAGCGAGTGGAC 60.584 66.667 0.00 0.00 0.00 4.02
730 772 3.702048 GTGGACGTGCTGCCCCTA 61.702 66.667 8.99 0.00 0.00 3.53
786 828 7.482169 AATTGTATCACTAGTCAGGACTTCA 57.518 36.000 7.33 0.00 42.54 3.02
845 889 6.238538 GCACTAGTTACTTGGCAAAACTTGTA 60.239 38.462 22.35 10.58 37.18 2.41
869 913 1.125711 AGACGCCCTTGTACCCAAGT 61.126 55.000 2.17 0.00 45.49 3.16
870 914 0.250597 GACGCCCTTGTACCCAAGTT 60.251 55.000 2.17 0.00 45.49 2.66
871 915 0.184211 ACGCCCTTGTACCCAAGTTT 59.816 50.000 2.17 0.00 45.49 2.66
872 916 1.324383 CGCCCTTGTACCCAAGTTTT 58.676 50.000 2.17 0.00 45.49 2.43
873 917 2.158638 ACGCCCTTGTACCCAAGTTTTA 60.159 45.455 2.17 0.00 45.49 1.52
874 918 2.227149 CGCCCTTGTACCCAAGTTTTAC 59.773 50.000 2.17 0.00 45.49 2.01
875 919 2.559668 GCCCTTGTACCCAAGTTTTACC 59.440 50.000 2.17 0.00 45.49 2.85
876 920 3.752868 GCCCTTGTACCCAAGTTTTACCT 60.753 47.826 2.17 0.00 45.49 3.08
877 921 4.077108 CCCTTGTACCCAAGTTTTACCTC 58.923 47.826 2.17 0.00 45.49 3.85
878 922 4.446600 CCCTTGTACCCAAGTTTTACCTCA 60.447 45.833 2.17 0.00 45.49 3.86
879 923 5.321927 CCTTGTACCCAAGTTTTACCTCAT 58.678 41.667 2.17 0.00 45.49 2.90
880 924 5.414765 CCTTGTACCCAAGTTTTACCTCATC 59.585 44.000 2.17 0.00 45.49 2.92
881 925 5.570205 TGTACCCAAGTTTTACCTCATCA 57.430 39.130 0.00 0.00 0.00 3.07
882 926 6.134535 TGTACCCAAGTTTTACCTCATCAT 57.865 37.500 0.00 0.00 0.00 2.45
883 927 5.943416 TGTACCCAAGTTTTACCTCATCATG 59.057 40.000 0.00 0.00 0.00 3.07
884 928 4.998051 ACCCAAGTTTTACCTCATCATGT 58.002 39.130 0.00 0.00 0.00 3.21
885 929 5.010282 ACCCAAGTTTTACCTCATCATGTC 58.990 41.667 0.00 0.00 0.00 3.06
886 930 5.009631 CCCAAGTTTTACCTCATCATGTCA 58.990 41.667 0.00 0.00 0.00 3.58
887 931 5.653769 CCCAAGTTTTACCTCATCATGTCAT 59.346 40.000 0.00 0.00 0.00 3.06
888 932 6.153340 CCCAAGTTTTACCTCATCATGTCATT 59.847 38.462 0.00 0.00 0.00 2.57
889 933 7.253422 CCAAGTTTTACCTCATCATGTCATTC 58.747 38.462 0.00 0.00 0.00 2.67
890 934 7.253422 CAAGTTTTACCTCATCATGTCATTCC 58.747 38.462 0.00 0.00 0.00 3.01
891 935 6.725364 AGTTTTACCTCATCATGTCATTCCT 58.275 36.000 0.00 0.00 0.00 3.36
892 936 7.177878 AGTTTTACCTCATCATGTCATTCCTT 58.822 34.615 0.00 0.00 0.00 3.36
893 937 7.671398 AGTTTTACCTCATCATGTCATTCCTTT 59.329 33.333 0.00 0.00 0.00 3.11
894 938 8.306761 GTTTTACCTCATCATGTCATTCCTTTT 58.693 33.333 0.00 0.00 0.00 2.27
895 939 9.527157 TTTTACCTCATCATGTCATTCCTTTTA 57.473 29.630 0.00 0.00 0.00 1.52
896 940 8.506168 TTACCTCATCATGTCATTCCTTTTAC 57.494 34.615 0.00 0.00 0.00 2.01
897 941 5.888161 ACCTCATCATGTCATTCCTTTTACC 59.112 40.000 0.00 0.00 0.00 2.85
898 942 5.887598 CCTCATCATGTCATTCCTTTTACCA 59.112 40.000 0.00 0.00 0.00 3.25
899 943 6.377996 CCTCATCATGTCATTCCTTTTACCAA 59.622 38.462 0.00 0.00 0.00 3.67
900 944 7.069085 CCTCATCATGTCATTCCTTTTACCAAT 59.931 37.037 0.00 0.00 0.00 3.16
901 945 7.774134 TCATCATGTCATTCCTTTTACCAATG 58.226 34.615 0.00 0.00 0.00 2.82
902 946 7.396907 TCATCATGTCATTCCTTTTACCAATGT 59.603 33.333 0.00 0.00 0.00 2.71
903 947 7.537596 TCATGTCATTCCTTTTACCAATGTT 57.462 32.000 0.00 0.00 0.00 2.71
904 948 7.961351 TCATGTCATTCCTTTTACCAATGTTT 58.039 30.769 0.00 0.00 0.00 2.83
905 949 8.087750 TCATGTCATTCCTTTTACCAATGTTTC 58.912 33.333 0.00 0.00 0.00 2.78
906 950 7.595819 TGTCATTCCTTTTACCAATGTTTCT 57.404 32.000 0.00 0.00 0.00 2.52
907 951 8.017418 TGTCATTCCTTTTACCAATGTTTCTT 57.983 30.769 0.00 0.00 0.00 2.52
908 952 7.925483 TGTCATTCCTTTTACCAATGTTTCTTG 59.075 33.333 0.00 0.00 0.00 3.02
909 953 7.926018 GTCATTCCTTTTACCAATGTTTCTTGT 59.074 33.333 0.00 0.00 0.00 3.16
910 954 8.482128 TCATTCCTTTTACCAATGTTTCTTGTT 58.518 29.630 0.00 0.00 0.00 2.83
949 993 6.811954 TGTCATTCCTTTTACCCAAGTTTTC 58.188 36.000 0.00 0.00 0.00 2.29
954 998 6.459670 TCCTTTTACCCAAGTTTTCAGTTC 57.540 37.500 0.00 0.00 0.00 3.01
963 1007 6.211785 ACCCAAGTTTTCAGTTCTTTTTACCA 59.788 34.615 0.00 0.00 0.00 3.25
993 1038 8.900781 CATGTCATTCTTGTAGATCTTCCATTT 58.099 33.333 0.00 0.00 0.00 2.32
1016 1061 1.546029 TCTCATGGACGACAAGAGTGG 59.454 52.381 13.59 0.00 43.55 4.00
1087 1132 0.868406 GGTGAGTGTTTTCTCCAGCG 59.132 55.000 0.00 0.00 33.93 5.18
1088 1133 1.583054 GTGAGTGTTTTCTCCAGCGT 58.417 50.000 0.00 0.00 33.93 5.07
1108 1153 7.170489 CCAGCGTAATCTGATATGCATATAAGG 59.830 40.741 25.09 15.53 39.71 2.69
1109 1154 6.703607 AGCGTAATCTGATATGCATATAAGGC 59.296 38.462 25.09 20.25 39.71 4.35
1110 1155 6.479990 GCGTAATCTGATATGCATATAAGGCA 59.520 38.462 25.09 15.57 46.66 4.75
1111 1156 7.011389 GCGTAATCTGATATGCATATAAGGCAA 59.989 37.037 25.09 11.15 45.60 4.52
1112 1157 8.546244 CGTAATCTGATATGCATATAAGGCAAG 58.454 37.037 25.09 13.75 45.60 4.01
1205 1250 4.506802 CCCAAGGTGCCTACTAAGAAAACT 60.507 45.833 0.00 0.00 0.00 2.66
1212 1257 6.436261 GTGCCTACTAAGAAAACTCCAAAAC 58.564 40.000 0.00 0.00 0.00 2.43
1233 1278 5.416271 ACGTGTCCCTAAGATGTAATGTT 57.584 39.130 0.00 0.00 32.89 2.71
1270 1315 6.028146 TCTGTTTATGCATGCTTGTTCAAT 57.972 33.333 20.33 4.38 0.00 2.57
1361 1406 1.546476 GAACCAGAAGAGGAGAGCGAA 59.454 52.381 0.00 0.00 0.00 4.70
1368 1413 0.892063 AGAGGAGAGCGAACTTGACC 59.108 55.000 0.00 0.00 0.00 4.02
1424 1470 3.056107 TGCCACAGGTACTTGTATGTCTC 60.056 47.826 10.65 0.00 34.60 3.36
1429 1475 5.184096 CACAGGTACTTGTATGTCTCAGTCT 59.816 44.000 10.65 0.00 34.60 3.24
1547 1596 8.695456 AGAAAAGTGGTCAGTATTTTGATGTTT 58.305 29.630 0.00 0.00 0.00 2.83
1575 1624 6.923508 TGCCTCACAATATCTACTGTATTTCG 59.076 38.462 0.00 0.00 0.00 3.46
1605 1654 3.969976 TCCTGCATTCACTAGCCTATCTT 59.030 43.478 0.00 0.00 0.00 2.40
1611 1660 5.295950 CATTCACTAGCCTATCTTCAGTGG 58.704 45.833 0.00 0.00 37.72 4.00
1622 1671 6.599638 GCCTATCTTCAGTGGAAAATAACTGT 59.400 38.462 3.01 0.00 43.49 3.55
1693 1742 4.020218 TCACAACCTCCTTTGTATCTCTGG 60.020 45.833 0.00 0.00 37.62 3.86
1715 1764 2.417933 GAGCTGCTGAACGATTTGTGAT 59.582 45.455 7.01 0.00 0.00 3.06
1800 1849 9.297037 GAATAGCTATTGGGTAAATGGTAATGT 57.703 33.333 23.51 0.00 0.00 2.71
1806 1855 4.667573 TGGGTAAATGGTAATGTTGAGCA 58.332 39.130 0.00 0.00 0.00 4.26
1813 1862 4.032960 TGGTAATGTTGAGCAGTCCAAT 57.967 40.909 0.00 0.00 0.00 3.16
1924 1975 4.241681 GACTCTGGAGTTGTCTCATGAAC 58.758 47.826 4.67 0.00 42.66 3.18
1931 1982 1.728971 GTTGTCTCATGAACTCGGCAG 59.271 52.381 0.00 0.00 0.00 4.85
2009 2060 5.363101 TGATGCACTTTAGAGGCTTAGATG 58.637 41.667 0.00 0.00 0.00 2.90
2109 2163 9.871238 AATATTTATAACGATCTCAATACCGCT 57.129 29.630 0.00 0.00 0.00 5.52
2129 2183 3.623960 GCTGGTGTAACGGCATTATGTTA 59.376 43.478 0.00 0.00 38.12 2.41
2180 2234 0.249489 GCTCCATTACGACGGCAGAT 60.249 55.000 0.00 0.00 0.00 2.90
2182 2236 1.067060 CTCCATTACGACGGCAGATGA 59.933 52.381 0.00 0.00 0.00 2.92
2242 2296 1.224592 CAAGATCCTTCCCCACCCG 59.775 63.158 0.00 0.00 0.00 5.28
2245 2299 0.398664 AGATCCTTCCCCACCCGTAG 60.399 60.000 0.00 0.00 0.00 3.51
2305 2359 7.124147 ACTCCCATTTGTTCCATATTTACCTTG 59.876 37.037 0.00 0.00 0.00 3.61
2323 2377 9.567776 TTTACCTTGATCTGAACATTTACAGAA 57.432 29.630 0.00 0.00 44.47 3.02
2660 2724 0.818938 TTTTGCCGCATCATGCTCAT 59.181 45.000 8.30 0.00 42.25 2.90
2707 2771 6.785191 TCATTGACATTCTTTTATCTTCGCC 58.215 36.000 0.00 0.00 0.00 5.54
2708 2772 6.599244 TCATTGACATTCTTTTATCTTCGCCT 59.401 34.615 0.00 0.00 0.00 5.52
2736 2800 5.341617 GGTACAGAAGATTTCGACGAAGAT 58.658 41.667 10.61 7.55 34.02 2.40
2738 2802 5.060662 ACAGAAGATTTCGACGAAGATGA 57.939 39.130 10.61 0.00 34.02 2.92
2857 2921 0.599204 TCGAGGAACACCGTTCTTGC 60.599 55.000 6.80 0.00 0.00 4.01
2879 2943 5.704053 TGCTCAGGTATTCATATCAATGCAG 59.296 40.000 0.00 0.00 32.76 4.41
2884 2948 8.623903 TCAGGTATTCATATCAATGCAGAAAAC 58.376 33.333 0.00 0.00 32.76 2.43
2887 2951 8.362639 GGTATTCATATCAATGCAGAAAACCAT 58.637 33.333 0.00 0.00 32.76 3.55
2888 2952 9.188588 GTATTCATATCAATGCAGAAAACCATG 57.811 33.333 0.00 0.00 32.76 3.66
2904 2968 1.407618 CCATGCCACATGTTGATGGAG 59.592 52.381 17.38 0.00 38.34 3.86
2912 2976 3.126514 CACATGTTGATGGAGCTGTCTTC 59.873 47.826 0.00 0.00 33.39 2.87
2952 3016 2.527100 GATGGAACTGTCGGTTACTCG 58.473 52.381 8.27 0.00 39.43 4.18
2962 3026 5.146482 TGTCGGTTACTCGTTTTCTTTTG 57.854 39.130 0.00 0.00 0.00 2.44
2998 3074 9.476202 CTTATATTGATCGAACTGATTGTACCA 57.524 33.333 0.00 0.00 37.47 3.25
3003 3079 1.394917 CGAACTGATTGTACCAGCTGC 59.605 52.381 8.66 0.00 35.14 5.25
3005 3081 1.813513 ACTGATTGTACCAGCTGCAC 58.186 50.000 8.66 8.98 35.14 4.57
3200 3276 8.405531 TGTTGAAACAGAAGAAACCAATAAGAG 58.594 33.333 0.00 0.00 34.30 2.85
3210 3286 5.788014 AGAAACCAATAAGAGGAGGAGACTT 59.212 40.000 0.00 0.00 44.43 3.01
3298 3374 4.757149 ACAAGAGTGGTAAAGTGAAGATGC 59.243 41.667 0.00 0.00 0.00 3.91
3299 3375 4.899352 AGAGTGGTAAAGTGAAGATGCT 57.101 40.909 0.00 0.00 0.00 3.79
3325 3401 4.763073 TGGAGATGCACTCTTTGATGTAG 58.237 43.478 13.59 0.00 44.37 2.74
3336 3412 7.378728 GCACTCTTTGATGTAGGTGTTTAAAAC 59.621 37.037 0.00 0.00 0.00 2.43
3391 3476 2.716504 CGTCTAGTCTTTCGATGATGCG 59.283 50.000 0.00 0.00 0.00 4.73
3408 3493 6.101650 TGATGCGGTACTTGAGATGAATAT 57.898 37.500 0.00 0.00 0.00 1.28
3409 3494 6.524734 TGATGCGGTACTTGAGATGAATATT 58.475 36.000 0.00 0.00 0.00 1.28
3425 3510 6.811253 TGAATATTAAACGTGCAGGTTTCT 57.189 33.333 33.63 25.05 40.41 2.52
3474 3560 1.208052 AGGCTGTAGCGATCAACACAT 59.792 47.619 0.00 0.00 43.26 3.21
3566 3659 5.815233 TGGTAGATTCCATCAAGAGGATC 57.185 43.478 0.00 0.00 34.56 3.36
3569 3662 3.312890 AGATTCCATCAAGAGGATCGGT 58.687 45.455 0.00 0.00 42.67 4.69
3577 3670 0.466124 AAGAGGATCGGTTAGCCTGC 59.534 55.000 0.00 0.00 46.71 4.85
3620 3713 7.410120 TCTGATATTAGCTCTGAAAGTGACA 57.590 36.000 0.00 0.00 33.76 3.58
3704 3803 6.757897 AAATTTGCATTAGGAGAATCGTGA 57.242 33.333 0.00 0.00 33.79 4.35
3707 3806 5.801350 TTGCATTAGGAGAATCGTGAAAG 57.199 39.130 0.00 0.00 33.79 2.62
3719 3818 7.307632 GGAGAATCGTGAAAGTTGATATCATGG 60.308 40.741 6.17 0.00 34.37 3.66
3720 3819 7.050377 AGAATCGTGAAAGTTGATATCATGGT 58.950 34.615 6.17 0.00 32.28 3.55
3723 3822 5.937540 TCGTGAAAGTTGATATCATGGTGTT 59.062 36.000 6.17 0.00 32.28 3.32
3727 3826 8.892723 GTGAAAGTTGATATCATGGTGTTGATA 58.107 33.333 6.17 0.00 41.52 2.15
3731 3831 8.387190 AGTTGATATCATGGTGTTGATATGTG 57.613 34.615 6.17 0.00 45.13 3.21
3759 3859 2.671070 GCTAGTGGAAATGTTTTGCCGG 60.671 50.000 0.00 0.00 32.39 6.13
3780 3881 4.142838 CGGTCCTTTAATTTTCACGGTACC 60.143 45.833 0.16 0.16 0.00 3.34
3781 3882 4.761227 GGTCCTTTAATTTTCACGGTACCA 59.239 41.667 13.54 0.00 0.00 3.25
3785 3886 4.705337 TTAATTTTCACGGTACCATGGC 57.295 40.909 13.04 0.00 0.00 4.40
3937 10486 7.240674 TGTTTGTTAGCGCTTTATACAATCAG 58.759 34.615 18.68 0.00 29.82 2.90
3942 10491 2.224314 GCGCTTTATACAATCAGAGGCC 59.776 50.000 0.00 0.00 0.00 5.19
4044 10593 5.845391 TCAACATATGTGATCGGACAGTA 57.155 39.130 9.63 0.00 0.00 2.74
4053 10602 1.333931 GATCGGACAGTATCGTGCTCA 59.666 52.381 0.00 0.00 0.00 4.26
4074 10623 2.721167 CCGATCAGAGGTTGCCGGA 61.721 63.158 5.05 0.00 41.86 5.14
4263 10836 2.756760 GTTCATGGCATGATTGTGGAGT 59.243 45.455 29.22 0.00 39.39 3.85
4290 10863 0.961753 CCCCAAGGACAAGCAAGTTC 59.038 55.000 0.00 0.00 33.47 3.01
4448 11037 3.214328 CTGGGCATGTGTAAATCCCTAC 58.786 50.000 4.25 0.00 37.83 3.18
4459 11048 0.846693 AATCCCTACCCACTGGATGC 59.153 55.000 0.00 0.00 38.85 3.91
4501 11090 6.427150 AGAACAATTGTTGCTACTGTTAACG 58.573 36.000 27.85 0.00 38.56 3.18
4543 11132 4.340617 TGTCCCAAGCCAGTAAATAAAGG 58.659 43.478 0.00 0.00 0.00 3.11
4550 11139 3.513912 AGCCAGTAAATAAAGGTTTGCCC 59.486 43.478 0.00 0.00 34.57 5.36
4551 11140 3.259625 GCCAGTAAATAAAGGTTTGCCCA 59.740 43.478 0.00 0.00 34.66 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 5.007332 CGACCCTAAATTAGAATTCCGTTGG 59.993 44.000 0.65 0.00 0.00 3.77
94 95 1.128188 AGAGGGTCCGCTGGAAAAGT 61.128 55.000 0.00 0.00 31.38 2.66
160 161 3.962421 GATGCCGATGCCTGCAGC 61.962 66.667 8.66 4.57 41.46 5.25
183 190 2.278332 AAGTGGAGAAAACAGAGGGC 57.722 50.000 0.00 0.00 0.00 5.19
191 198 3.329814 GAGGTAGGGGAAAGTGGAGAAAA 59.670 47.826 0.00 0.00 0.00 2.29
328 344 1.080093 GAGCAACACGACGGATCCA 60.080 57.895 13.41 0.00 0.00 3.41
465 481 2.202388 CGGCATTGCAGCAAGACG 60.202 61.111 14.47 15.06 35.83 4.18
545 561 0.253610 ACACCACCACGAAAAGGTCA 59.746 50.000 0.00 0.00 37.23 4.02
554 570 2.124067 AAACCCCACACCACCACG 60.124 61.111 0.00 0.00 0.00 4.94
578 594 2.044806 GCACCTCACCAGTCACCACT 62.045 60.000 0.00 0.00 0.00 4.00
586 602 4.087892 CCTCCCGCACCTCACCAG 62.088 72.222 0.00 0.00 0.00 4.00
590 606 3.916438 TAAGCCCTCCCGCACCTCA 62.916 63.158 0.00 0.00 0.00 3.86
692 708 3.274586 CTCATCCGCACGCATGGG 61.275 66.667 8.44 8.44 38.49 4.00
693 709 3.945434 GCTCATCCGCACGCATGG 61.945 66.667 0.00 0.00 0.00 3.66
714 733 3.390521 CTAGGGGCAGCACGTCCA 61.391 66.667 0.00 0.00 43.46 4.02
716 735 2.496817 CTCTAGGGGCAGCACGTC 59.503 66.667 0.00 0.00 0.00 4.34
717 736 3.775654 GCTCTAGGGGCAGCACGT 61.776 66.667 0.00 0.00 35.56 4.49
718 737 3.438017 GAGCTCTAGGGGCAGCACG 62.438 68.421 6.43 0.00 38.18 5.34
768 810 6.865834 AATTCTGAAGTCCTGACTAGTGAT 57.134 37.500 0.00 0.00 41.58 3.06
776 818 6.012508 ACTCCCATAAAATTCTGAAGTCCTGA 60.013 38.462 0.00 0.00 0.00 3.86
786 828 7.775561 GTCCATAGTCAACTCCCATAAAATTCT 59.224 37.037 0.00 0.00 0.00 2.40
869 913 8.421249 AAAAGGAATGACATGATGAGGTAAAA 57.579 30.769 0.00 0.00 0.00 1.52
870 914 8.956426 GTAAAAGGAATGACATGATGAGGTAAA 58.044 33.333 0.00 0.00 0.00 2.01
871 915 7.556275 GGTAAAAGGAATGACATGATGAGGTAA 59.444 37.037 0.00 0.00 0.00 2.85
872 916 7.054124 GGTAAAAGGAATGACATGATGAGGTA 58.946 38.462 0.00 0.00 0.00 3.08
873 917 5.888161 GGTAAAAGGAATGACATGATGAGGT 59.112 40.000 0.00 0.00 0.00 3.85
874 918 5.887598 TGGTAAAAGGAATGACATGATGAGG 59.112 40.000 0.00 0.00 0.00 3.86
875 919 7.395190 TTGGTAAAAGGAATGACATGATGAG 57.605 36.000 0.00 0.00 0.00 2.90
876 920 7.396907 ACATTGGTAAAAGGAATGACATGATGA 59.603 33.333 0.00 0.00 32.47 2.92
877 921 7.549839 ACATTGGTAAAAGGAATGACATGATG 58.450 34.615 0.00 0.00 32.47 3.07
878 922 7.722949 ACATTGGTAAAAGGAATGACATGAT 57.277 32.000 0.00 0.00 32.47 2.45
879 923 7.537596 AACATTGGTAAAAGGAATGACATGA 57.462 32.000 0.00 0.00 32.47 3.07
880 924 8.090214 AGAAACATTGGTAAAAGGAATGACATG 58.910 33.333 0.00 0.00 32.47 3.21
881 925 8.193953 AGAAACATTGGTAAAAGGAATGACAT 57.806 30.769 0.00 0.00 32.47 3.06
882 926 7.595819 AGAAACATTGGTAAAAGGAATGACA 57.404 32.000 0.00 0.00 32.47 3.58
883 927 7.926018 ACAAGAAACATTGGTAAAAGGAATGAC 59.074 33.333 0.00 0.00 34.36 3.06
884 928 8.017418 ACAAGAAACATTGGTAAAAGGAATGA 57.983 30.769 0.00 0.00 34.36 2.57
885 929 8.661352 AACAAGAAACATTGGTAAAAGGAATG 57.339 30.769 0.00 0.00 34.36 2.67
886 930 9.679661 AAAACAAGAAACATTGGTAAAAGGAAT 57.320 25.926 0.00 0.00 34.36 3.01
887 931 9.508642 AAAAACAAGAAACATTGGTAAAAGGAA 57.491 25.926 0.00 0.00 34.36 3.36
949 993 6.969366 TGACATGATGTGGTAAAAAGAACTG 58.031 36.000 1.23 0.00 0.00 3.16
954 998 8.084073 ACAAGAATGACATGATGTGGTAAAAAG 58.916 33.333 1.23 0.00 0.00 2.27
963 1007 7.714377 GGAAGATCTACAAGAATGACATGATGT 59.286 37.037 0.00 0.00 0.00 3.06
993 1038 2.628178 ACTCTTGTCGTCCATGAGAACA 59.372 45.455 19.60 0.00 44.29 3.18
1016 1061 3.625853 CCATCCTTCTCTTTCCCCTTTC 58.374 50.000 0.00 0.00 0.00 2.62
1087 1132 8.341173 GCTTGCCTTATATGCATATCAGATTAC 58.659 37.037 23.65 13.16 38.76 1.89
1088 1133 8.270030 AGCTTGCCTTATATGCATATCAGATTA 58.730 33.333 23.65 10.47 38.76 1.75
1108 1153 0.383231 AGCAAACACACTGAGCTTGC 59.617 50.000 6.50 6.50 42.10 4.01
1109 1154 1.862815 GCAGCAAACACACTGAGCTTG 60.863 52.381 0.00 0.00 35.90 4.01
1110 1155 0.383231 GCAGCAAACACACTGAGCTT 59.617 50.000 0.00 0.00 35.90 3.74
1111 1156 0.465097 AGCAGCAAACACACTGAGCT 60.465 50.000 0.00 0.00 35.90 4.09
1112 1157 0.383231 AAGCAGCAAACACACTGAGC 59.617 50.000 0.00 0.00 35.90 4.26
1205 1250 3.071892 ACATCTTAGGGACACGTTTTGGA 59.928 43.478 0.00 0.00 0.00 3.53
1212 1257 5.416083 TGAACATTACATCTTAGGGACACG 58.584 41.667 0.00 0.00 0.00 4.49
1233 1278 6.152492 TGCATAAACAGAGCATTGGTTAATGA 59.848 34.615 4.33 0.00 45.21 2.57
1322 1367 2.858644 TCCCTGTAGAATCCCACCATT 58.141 47.619 0.00 0.00 0.00 3.16
1323 1368 2.509964 GTTCCCTGTAGAATCCCACCAT 59.490 50.000 0.00 0.00 0.00 3.55
1324 1369 1.913419 GTTCCCTGTAGAATCCCACCA 59.087 52.381 0.00 0.00 0.00 4.17
1346 1391 2.230266 GTCAAGTTCGCTCTCCTCTTCT 59.770 50.000 0.00 0.00 0.00 2.85
1361 1406 6.125029 CAGATCCTTATCAATTGGGTCAAGT 58.875 40.000 5.42 0.00 33.64 3.16
1368 1413 6.359804 TCCTCAACAGATCCTTATCAATTGG 58.640 40.000 5.42 0.00 33.35 3.16
1424 1470 2.926200 CAGGCACGTAGAAATCAGACTG 59.074 50.000 0.00 0.00 0.00 3.51
1429 1475 5.116180 CCTAAATCAGGCACGTAGAAATCA 58.884 41.667 0.00 0.00 37.70 2.57
1547 1596 9.461312 AAATACAGTAGATATTGTGAGGCAAAA 57.539 29.630 0.00 0.00 40.91 2.44
1575 1624 2.350522 AGTGAATGCAGGATCGAACAC 58.649 47.619 0.00 0.00 0.00 3.32
1622 1671 3.278574 ACAGCAACTGCAGTTAACTGAA 58.721 40.909 40.68 25.69 45.37 3.02
1693 1742 1.135859 CACAAATCGTTCAGCAGCTCC 60.136 52.381 0.00 0.00 0.00 4.70
1800 1849 1.614903 CCTTGCAATTGGACTGCTCAA 59.385 47.619 7.72 0.16 40.59 3.02
1931 1982 8.053026 TCCAGTCGAATTATATCTTAGGCTAC 57.947 38.462 0.00 0.00 0.00 3.58
1939 1990 7.565680 ACAAAACCTCCAGTCGAATTATATCT 58.434 34.615 0.00 0.00 0.00 1.98
1994 2045 6.179756 TGCAACAATCATCTAAGCCTCTAAA 58.820 36.000 0.00 0.00 0.00 1.85
2095 2149 2.604046 ACACCAGCGGTATTGAGATC 57.396 50.000 0.00 0.00 32.11 2.75
2109 2163 6.761099 AAATAACATAATGCCGTTACACCA 57.239 33.333 0.00 0.00 30.79 4.17
2180 2234 2.346766 ATGCAACCTGAACACAGTCA 57.653 45.000 0.00 0.00 0.00 3.41
2182 2236 2.101249 CCAAATGCAACCTGAACACAGT 59.899 45.455 0.00 0.00 0.00 3.55
2242 2296 7.067737 AGCTACTACCTGATGAAGAACTTCTAC 59.932 40.741 14.31 9.31 40.14 2.59
2245 2299 6.215495 AGCTACTACCTGATGAAGAACTTC 57.785 41.667 7.51 7.51 39.91 3.01
2323 2377 5.948162 ACTGGCAGAAGAAATGATACATTGT 59.052 36.000 23.66 0.00 0.00 2.71
2375 2429 3.431233 CGCCAGACATCATATACTTGCTG 59.569 47.826 0.00 0.00 0.00 4.41
2458 2512 5.773176 CCCCACCCCTTATGTTATTATTGTC 59.227 44.000 0.00 0.00 0.00 3.18
2463 2517 3.464080 CCACCCCACCCCTTATGTTATTA 59.536 47.826 0.00 0.00 0.00 0.98
2648 2712 2.621998 AGGCAAACTATGAGCATGATGC 59.378 45.455 9.89 9.89 45.46 3.91
2660 2724 7.155328 TGAAAGTGTTTTTGAAAGGCAAACTA 58.845 30.769 0.00 0.00 45.64 2.24
2704 2768 0.809385 TCTTCTGTACCGAAGAGGCG 59.191 55.000 21.62 2.05 43.17 5.52
2727 2791 1.397343 TCTCCGAACTCATCTTCGTCG 59.603 52.381 1.11 0.00 41.24 5.12
2736 2800 3.386726 TGGAAGAAAACTCTCCGAACTCA 59.613 43.478 0.00 0.00 0.00 3.41
2738 2802 3.804063 GCTGGAAGAAAACTCTCCGAACT 60.804 47.826 0.00 0.00 34.07 3.01
2802 2866 9.964354 ATGCAACATGATATACATACCATTAGT 57.036 29.630 0.00 0.00 37.46 2.24
2857 2921 7.974482 TTCTGCATTGATATGAATACCTGAG 57.026 36.000 0.00 0.00 33.37 3.35
2879 2943 3.383620 TCAACATGTGGCATGGTTTTC 57.616 42.857 12.87 0.00 0.00 2.29
2884 2948 1.407618 CTCCATCAACATGTGGCATGG 59.592 52.381 18.73 18.73 36.15 3.66
2887 2951 0.038599 AGCTCCATCAACATGTGGCA 59.961 50.000 0.00 0.00 35.43 4.92
2888 2952 0.454600 CAGCTCCATCAACATGTGGC 59.545 55.000 0.00 0.00 35.43 5.01
2919 2983 0.251916 TTCCATCGACATCCCACCAC 59.748 55.000 0.00 0.00 0.00 4.16
2920 2984 0.251916 GTTCCATCGACATCCCACCA 59.748 55.000 0.00 0.00 0.00 4.17
2921 2985 0.541863 AGTTCCATCGACATCCCACC 59.458 55.000 0.00 0.00 0.00 4.61
2922 2986 1.066143 ACAGTTCCATCGACATCCCAC 60.066 52.381 0.00 0.00 0.00 4.61
2923 2987 1.207089 GACAGTTCCATCGACATCCCA 59.793 52.381 0.00 0.00 0.00 4.37
2998 3074 3.034635 AGGCTACTAATACTGTGCAGCT 58.965 45.455 0.00 0.00 0.00 4.24
3003 3079 8.997621 TCAGTTTTTAGGCTACTAATACTGTG 57.002 34.615 19.76 6.19 43.64 3.66
3005 3081 9.601217 ACATCAGTTTTTAGGCTACTAATACTG 57.399 33.333 16.83 16.83 44.02 2.74
3034 3110 9.200817 AGTGCCCTGTCAAACAATTAATATAAT 57.799 29.630 0.00 0.00 0.00 1.28
3035 3111 8.465999 CAGTGCCCTGTCAAACAATTAATATAA 58.534 33.333 0.00 0.00 33.80 0.98
3056 3132 4.331168 GTGTATTCATCTTGTCCTCAGTGC 59.669 45.833 0.00 0.00 0.00 4.40
3200 3276 0.812549 GACCGACTCAAGTCTCCTCC 59.187 60.000 8.43 0.00 42.66 4.30
3210 3286 1.174078 TACAGCCGTTGACCGACTCA 61.174 55.000 0.00 0.00 39.56 3.41
3217 3293 3.744426 TCTTTTAGCTTACAGCCGTTGAC 59.256 43.478 0.00 0.00 43.77 3.18
3298 3374 2.110901 AAGAGTGCATCTCCAAGCAG 57.889 50.000 11.24 0.00 43.71 4.24
3299 3375 2.156917 CAAAGAGTGCATCTCCAAGCA 58.843 47.619 11.24 0.00 43.71 3.91
3325 3401 5.891451 AGAAGTGCAGAAGTTTTAAACACC 58.109 37.500 10.60 1.43 0.00 4.16
3336 3412 3.189910 TGCAGCATAAAGAAGTGCAGAAG 59.810 43.478 0.00 0.00 43.63 2.85
3391 3476 8.062448 GCACGTTTAATATTCATCTCAAGTACC 58.938 37.037 0.00 0.00 0.00 3.34
3425 3510 0.467844 ATGTGCAGTCCAAACCAGCA 60.468 50.000 0.00 0.00 35.36 4.41
3577 3670 1.804748 GAAGTTACTTGCAGTTCCCCG 59.195 52.381 0.93 0.00 0.00 5.73
3590 3683 9.810545 ACTTTCAGAGCTAATATCAGAAGTTAC 57.189 33.333 0.00 0.00 0.00 2.50
3606 3699 2.219674 CACTTCGTGTCACTTTCAGAGC 59.780 50.000 0.65 0.00 0.00 4.09
3620 3713 5.762218 AGTAGTAAGTAGTGACACACTTCGT 59.238 40.000 19.81 13.68 42.59 3.85
3704 3803 9.412460 ACATATCAACACCATGATATCAACTTT 57.588 29.630 9.99 0.00 45.48 2.66
3707 3806 7.229306 ACCACATATCAACACCATGATATCAAC 59.771 37.037 9.99 0.00 45.48 3.18
3719 3818 6.036083 CACTAGCTGTTACCACATATCAACAC 59.964 42.308 0.00 0.00 30.39 3.32
3720 3819 6.106003 CACTAGCTGTTACCACATATCAACA 58.894 40.000 0.00 0.00 30.39 3.33
3723 3822 4.959839 TCCACTAGCTGTTACCACATATCA 59.040 41.667 0.00 0.00 30.39 2.15
3727 3826 4.634012 TTTCCACTAGCTGTTACCACAT 57.366 40.909 0.00 0.00 30.39 3.21
3731 3831 5.959618 AAACATTTCCACTAGCTGTTACC 57.040 39.130 0.00 0.00 30.33 2.85
3747 3847 4.882842 ATTAAAGGACCGGCAAAACATT 57.117 36.364 0.00 0.00 0.00 2.71
3759 3859 5.945466 TGGTACCGTGAAAATTAAAGGAC 57.055 39.130 7.57 0.00 0.00 3.85
3780 3881 3.581755 CAATTGAGACAAACCAGCCATG 58.418 45.455 0.00 0.00 0.00 3.66
3781 3882 2.028748 GCAATTGAGACAAACCAGCCAT 60.029 45.455 10.34 0.00 0.00 4.40
3937 10486 1.398692 TTTGTTGTTCCTGTGGCCTC 58.601 50.000 3.32 0.00 0.00 4.70
3942 10491 3.906998 TGTGTGTTTTGTTGTTCCTGTG 58.093 40.909 0.00 0.00 0.00 3.66
4044 10593 0.179127 CTGATCGGTGTGAGCACGAT 60.179 55.000 0.00 0.00 46.13 3.73
4053 10602 1.296715 GGCAACCTCTGATCGGTGT 59.703 57.895 0.42 0.00 34.33 4.16
4074 10623 0.403271 AAGTGAACCTGCTGATGGCT 59.597 50.000 0.00 0.00 42.39 4.75
4263 10836 2.696187 GCTTGTCCTTGGGGTTTTACAA 59.304 45.455 0.00 0.00 0.00 2.41
4290 10863 5.245531 TCTGGCAGTTCTACATTTTACAGG 58.754 41.667 15.27 0.00 0.00 4.00
4428 11017 2.092103 GGTAGGGATTTACACATGCCCA 60.092 50.000 0.00 0.00 41.34 5.36
4459 11048 6.990341 TGTTCTATTCATCAATCACCAGTG 57.010 37.500 0.00 0.00 0.00 3.66
4501 11090 6.372937 GGGACAGGCATATATAGCTTTCTTTC 59.627 42.308 0.00 1.21 0.00 2.62
4543 11132 1.416030 ACTGGTTTTGGATGGGCAAAC 59.584 47.619 0.00 0.00 0.00 2.93


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

AutoCloner maintained by Alex Coulton.