Multiple sequence alignment - TraesCS3D01G520100

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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 TraesCS3D01G520100 chr3D 100.000 4858 0 0 1 4858 602728797 602723940 0.000000e+00 8972
1 TraesCS3D01G520100 chr3D 89.796 735 41 17 1883 2589 54627936 54628664 0.000000e+00 911
2 TraesCS3D01G520100 chr3D 86.839 737 38 18 1887 2589 118538437 118537726 0.000000e+00 769
3 TraesCS3D01G520100 chr3D 93.688 301 17 1 2621 2919 118537727 118537427 2.670000e-122 449
4 TraesCS3D01G520100 chr5A 96.512 3698 112 6 1164 4858 31969702 31973385 0.000000e+00 6098
5 TraesCS3D01G520100 chr5A 88.700 1177 41 22 1 1169 31964905 31965997 0.000000e+00 1352
6 TraesCS3D01G520100 chr5A 82.960 223 20 6 4238 4453 31972523 31972734 8.300000e-43 185
7 TraesCS3D01G520100 chr7B 91.516 1049 48 14 1887 2919 368148222 368147199 0.000000e+00 1406
8 TraesCS3D01G520100 chr7B 85.000 180 14 6 1887 2062 285373273 285373443 2.330000e-38 171
9 TraesCS3D01G520100 chr4A 93.988 815 39 6 2117 2922 18305579 18304766 0.000000e+00 1225
10 TraesCS3D01G520100 chr4A 90.116 344 33 1 2378 2721 615518956 615518614 3.450000e-121 446
11 TraesCS3D01G520100 chr5D 89.932 735 40 5 1883 2589 401762051 401762779 0.000000e+00 917
12 TraesCS3D01G520100 chr2D 89.796 735 41 17 1883 2589 623998576 623999304 0.000000e+00 911
13 TraesCS3D01G520100 chr2D 90.407 688 40 13 1927 2589 393688084 393688770 0.000000e+00 881
14 TraesCS3D01G520100 chr1D 94.576 295 15 1 2140 2434 411569321 411569028 5.730000e-124 455
15 TraesCS3D01G520100 chr1D 90.173 173 15 1 2731 2901 393689634 393689806 1.760000e-54 224
16 TraesCS3D01G520100 chr5B 89.459 351 35 2 2372 2721 112184942 112184593 4.460000e-120 442
17 TraesCS3D01G520100 chr5B 84.699 183 16 5 1887 2065 190122006 190121832 6.460000e-39 172
18 TraesCS3D01G520100 chr1A 90.419 334 31 1 2388 2721 181767044 181766712 5.770000e-119 438
19 TraesCS3D01G520100 chr3B 90.816 196 16 1 2727 2920 102756042 102755847 1.340000e-65 261
20 TraesCS3D01G520100 chr2A 89.583 192 18 1 2731 2920 37080786 37080977 4.860000e-60 243
21 TraesCS3D01G520100 chr7D 91.566 166 14 0 2754 2919 280588453 280588618 3.780000e-56 230
22 TraesCS3D01G520100 chr7D 85.714 182 15 4 1884 2062 327403405 327403578 1.070000e-41 182
23 TraesCS3D01G520100 chr1B 86.500 200 25 1 2727 2924 586675198 586675397 8.190000e-53 219
24 TraesCS3D01G520100 chr1B 80.952 231 25 12 1927 2142 2119573 2119347 1.080000e-36 165


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 TraesCS3D01G520100 chr3D 602723940 602728797 4857 True 8972 8972 100.000000 1 4858 1 chr3D.!!$R1 4857
1 TraesCS3D01G520100 chr3D 54627936 54628664 728 False 911 911 89.796000 1883 2589 1 chr3D.!!$F1 706
2 TraesCS3D01G520100 chr3D 118537427 118538437 1010 True 609 769 90.263500 1887 2919 2 chr3D.!!$R2 1032
3 TraesCS3D01G520100 chr5A 31964905 31973385 8480 False 2545 6098 89.390667 1 4858 3 chr5A.!!$F1 4857
4 TraesCS3D01G520100 chr7B 368147199 368148222 1023 True 1406 1406 91.516000 1887 2919 1 chr7B.!!$R1 1032
5 TraesCS3D01G520100 chr4A 18304766 18305579 813 True 1225 1225 93.988000 2117 2922 1 chr4A.!!$R1 805
6 TraesCS3D01G520100 chr5D 401762051 401762779 728 False 917 917 89.932000 1883 2589 1 chr5D.!!$F1 706
7 TraesCS3D01G520100 chr2D 623998576 623999304 728 False 911 911 89.796000 1883 2589 1 chr2D.!!$F2 706
8 TraesCS3D01G520100 chr2D 393688084 393688770 686 False 881 881 90.407000 1927 2589 1 chr2D.!!$F1 662

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
670 677 0.250338 CCGCTACCTCTATTTGCCCC 60.250 60.000 0.00 0.0 0.00 5.80 F
671 678 0.250338 CGCTACCTCTATTTGCCCCC 60.250 60.000 0.00 0.0 0.00 5.40 F
1033 1042 0.250858 TGGCAGTGAATCCAGTGGTG 60.251 55.000 9.54 0.0 42.56 4.17 F
1289 5007 1.066787 GTTCTGGGAAGAGGTCGAAGG 60.067 57.143 0.00 0.0 0.00 3.46 F
3169 6989 1.265635 CTCTCTTGAGGCGGTATCTCG 59.734 57.143 0.00 0.0 36.70 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1942 5663 0.810031 GCAGTCGACACCACAGTTGT 60.810 55.000 19.5 0.0 0.00 3.32 R
2193 5948 1.139853 CCCAGGAACCAGCAGAGATAC 59.860 57.143 0.0 0.0 0.00 2.24 R
2562 6340 1.670811 AGAGACGTTTTTGCCACACAG 59.329 47.619 0.0 0.0 0.00 3.66 R
3230 7050 0.110328 CAGACTTCAGCTTGCTTGCG 60.110 55.000 0.0 0.0 38.13 4.85 R
4211 8031 0.179134 AGCGACTATTGCGTGAGGAC 60.179 55.000 0.0 0.0 37.44 3.85 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
95 96 4.477975 CCTGTCTCCGGACGCGAC 62.478 72.222 15.93 13.91 44.83 5.19
96 97 4.813526 CTGTCTCCGGACGCGACG 62.814 72.222 15.93 17.33 44.83 5.12
98 99 3.490759 GTCTCCGGACGCGACGTA 61.491 66.667 15.93 2.65 41.37 3.57
99 100 3.490759 TCTCCGGACGCGACGTAC 61.491 66.667 15.93 4.84 41.37 3.67
100 101 3.494336 CTCCGGACGCGACGTACT 61.494 66.667 15.93 0.00 41.37 2.73
101 102 3.713615 CTCCGGACGCGACGTACTG 62.714 68.421 15.93 4.39 41.37 2.74
181 182 3.892284 GAGTCCTCTCCATAGTCAGTCA 58.108 50.000 0.00 0.00 34.87 3.41
182 183 3.882888 GAGTCCTCTCCATAGTCAGTCAG 59.117 52.174 0.00 0.00 34.87 3.51
183 184 2.360801 GTCCTCTCCATAGTCAGTCAGC 59.639 54.545 0.00 0.00 0.00 4.26
184 185 2.024941 TCCTCTCCATAGTCAGTCAGCA 60.025 50.000 0.00 0.00 0.00 4.41
185 186 2.762887 CCTCTCCATAGTCAGTCAGCAA 59.237 50.000 0.00 0.00 0.00 3.91
186 187 3.181477 CCTCTCCATAGTCAGTCAGCAAG 60.181 52.174 0.00 0.00 0.00 4.01
249 250 9.607988 GAAAAGGAAAAATAACAGGGAAAGAAA 57.392 29.630 0.00 0.00 0.00 2.52
408 415 5.709631 CCTTCTCTCTATCATCTCCGATTCA 59.290 44.000 0.00 0.00 0.00 2.57
478 485 1.270839 CCTCGCCGATGGGATTAACAT 60.271 52.381 0.00 0.00 34.06 2.71
497 504 1.298863 GAATTCGTCGCCGATCCGA 60.299 57.895 0.00 0.00 43.80 4.55
501 508 4.702081 CGTCGCCGATCCGATCCC 62.702 72.222 2.69 0.00 39.67 3.85
518 525 3.349006 CGTCCTGCTGCGCAAGTT 61.349 61.111 13.05 0.00 38.41 2.66
544 551 1.195115 TACCAAGCCGCTTCTCATCT 58.805 50.000 1.56 0.00 0.00 2.90
559 566 0.312416 CATCTCCTAAGCCGTCCTCG 59.688 60.000 0.00 0.00 0.00 4.63
616 623 1.873165 GGTGTGTACCAACCATGCG 59.127 57.895 8.77 0.00 46.71 4.73
617 624 0.887387 GGTGTGTACCAACCATGCGT 60.887 55.000 8.77 0.00 46.71 5.24
618 625 0.948678 GTGTGTACCAACCATGCGTT 59.051 50.000 0.00 0.00 33.90 4.84
619 626 1.335496 GTGTGTACCAACCATGCGTTT 59.665 47.619 0.00 0.00 29.93 3.60
620 627 2.025155 TGTGTACCAACCATGCGTTTT 58.975 42.857 0.00 0.00 29.93 2.43
621 628 2.033550 TGTGTACCAACCATGCGTTTTC 59.966 45.455 0.00 0.00 29.93 2.29
622 629 2.292292 GTGTACCAACCATGCGTTTTCT 59.708 45.455 0.00 0.00 29.93 2.52
623 630 2.952978 TGTACCAACCATGCGTTTTCTT 59.047 40.909 0.00 0.00 29.93 2.52
624 631 3.381908 TGTACCAACCATGCGTTTTCTTT 59.618 39.130 0.00 0.00 29.93 2.52
625 632 3.092334 ACCAACCATGCGTTTTCTTTC 57.908 42.857 0.00 0.00 29.93 2.62
667 674 1.867166 GGTCCGCTACCTCTATTTGC 58.133 55.000 0.00 0.00 45.75 3.68
668 675 1.540580 GGTCCGCTACCTCTATTTGCC 60.541 57.143 0.00 0.00 45.75 4.52
669 676 0.756903 TCCGCTACCTCTATTTGCCC 59.243 55.000 0.00 0.00 0.00 5.36
670 677 0.250338 CCGCTACCTCTATTTGCCCC 60.250 60.000 0.00 0.00 0.00 5.80
671 678 0.250338 CGCTACCTCTATTTGCCCCC 60.250 60.000 0.00 0.00 0.00 5.40
672 679 0.843984 GCTACCTCTATTTGCCCCCA 59.156 55.000 0.00 0.00 0.00 4.96
673 680 1.425448 GCTACCTCTATTTGCCCCCAT 59.575 52.381 0.00 0.00 0.00 4.00
674 681 2.553247 GCTACCTCTATTTGCCCCCATC 60.553 54.545 0.00 0.00 0.00 3.51
675 682 1.607225 ACCTCTATTTGCCCCCATCA 58.393 50.000 0.00 0.00 0.00 3.07
676 683 1.929494 ACCTCTATTTGCCCCCATCAA 59.071 47.619 0.00 0.00 0.00 2.57
677 684 2.519691 ACCTCTATTTGCCCCCATCAAT 59.480 45.455 0.00 0.00 0.00 2.57
678 685 3.160269 CCTCTATTTGCCCCCATCAATC 58.840 50.000 0.00 0.00 0.00 2.67
679 686 3.436906 CCTCTATTTGCCCCCATCAATCA 60.437 47.826 0.00 0.00 0.00 2.57
705 712 9.967346 ACTTTCTTTTCCTTCTTTATTTACTGC 57.033 29.630 0.00 0.00 0.00 4.40
724 733 1.543429 GCCCATATTCCTACGCTTGCT 60.543 52.381 0.00 0.00 0.00 3.91
744 753 4.522405 TGCTGCAGTGTTGTTTACCATTAT 59.478 37.500 16.64 0.00 0.00 1.28
751 760 7.759433 GCAGTGTTGTTTACCATTATATGCTTT 59.241 33.333 0.00 0.00 0.00 3.51
783 792 3.149196 CACTGTTGTGGGCACTAATTCT 58.851 45.455 0.00 0.00 40.33 2.40
818 827 7.538678 GGGTACAATCATCATTCGATTTTATGC 59.461 37.037 0.00 0.00 30.65 3.14
830 839 9.817365 CATTCGATTTTATGCTATTTAGTGGAG 57.183 33.333 0.00 0.00 0.00 3.86
951 960 7.595311 AAGGTCAAATCAACTTGTTTGTTTC 57.405 32.000 12.55 7.77 36.83 2.78
1033 1042 0.250858 TGGCAGTGAATCCAGTGGTG 60.251 55.000 9.54 0.00 42.56 4.17
1052 1061 2.497273 GTGGGGGAAAAGACAATGATGG 59.503 50.000 0.00 0.00 0.00 3.51
1061 1070 2.625737 AGACAATGATGGCTCAACTCG 58.374 47.619 0.00 0.00 43.21 4.18
1099 1108 8.640091 TCTTCATAGAGTTTTTCGAGATGATG 57.360 34.615 0.00 0.00 29.98 3.07
1103 1112 7.489435 TCATAGAGTTTTTCGAGATGATGACAC 59.511 37.037 0.00 0.00 0.00 3.67
1104 1113 4.932200 AGAGTTTTTCGAGATGATGACACC 59.068 41.667 0.00 0.00 0.00 4.16
1111 1120 2.165234 CGAGATGATGACACCAGTCTGT 59.835 50.000 0.00 0.00 45.20 3.41
1125 1134 5.636965 CACCAGTCTGTGTTCTCTCTATTTG 59.363 44.000 0.00 0.00 0.00 2.32
1148 1157 3.387962 AGATGCCTTCTGGTATGGAAGA 58.612 45.455 5.20 0.00 41.71 2.87
1154 1163 4.742138 GCCTTCTGGTATGGAAGACATCTC 60.742 50.000 5.20 0.00 41.71 2.75
1155 1164 4.202305 CCTTCTGGTATGGAAGACATCTCC 60.202 50.000 5.20 0.00 41.71 3.71
1159 1168 5.250543 TCTGGTATGGAAGACATCTCCAAAA 59.749 40.000 0.00 0.00 40.57 2.44
1160 1169 5.500234 TGGTATGGAAGACATCTCCAAAAG 58.500 41.667 0.00 0.00 39.25 2.27
1161 1170 5.014123 TGGTATGGAAGACATCTCCAAAAGT 59.986 40.000 0.00 0.00 39.25 2.66
1162 1171 5.946377 GGTATGGAAGACATCTCCAAAAGTT 59.054 40.000 0.00 0.00 41.03 2.66
1169 4887 5.790593 AGACATCTCCAAAAGTTACGCTTA 58.209 37.500 0.00 0.00 36.17 3.09
1224 4942 5.833131 AGACAAAAGTCAAAAGGATTGCCTA 59.167 36.000 0.00 0.00 46.28 3.93
1285 5003 1.618837 TGAAGTTCTGGGAAGAGGTCG 59.381 52.381 4.17 0.00 0.00 4.79
1289 5007 1.066787 GTTCTGGGAAGAGGTCGAAGG 60.067 57.143 0.00 0.00 0.00 3.46
1314 5032 2.159057 ACCATACATCCGGGTTTACGTC 60.159 50.000 0.00 0.00 0.00 4.34
1316 5034 1.458398 TACATCCGGGTTTACGTCGA 58.542 50.000 0.00 0.00 0.00 4.20
1369 5087 2.955614 AGAATGCTGAATTTGCTGTGC 58.044 42.857 6.07 0.00 0.00 4.57
1375 5093 2.610976 GCTGAATTTGCTGTGCATCCAA 60.611 45.455 0.00 0.00 38.76 3.53
1376 5094 3.857052 CTGAATTTGCTGTGCATCCAAT 58.143 40.909 0.00 0.00 38.76 3.16
1379 5097 5.979993 TGAATTTGCTGTGCATCCAATAAT 58.020 33.333 0.00 0.00 38.76 1.28
1405 5123 2.767394 TCGGTTCCATCTCGGGATTTTA 59.233 45.455 0.00 0.00 36.67 1.52
1434 5152 8.450578 AAATGGTGTGGTATGTTCATATACTG 57.549 34.615 0.00 0.00 34.65 2.74
1980 5701 5.162075 ACTGCAAATCTCGTGTAGACTAAC 58.838 41.667 0.00 0.00 36.93 2.34
2193 5948 2.202987 GCTGTCCAGATCCAGCCG 60.203 66.667 9.76 0.00 46.55 5.52
2309 6073 1.691196 CTTGTTCCTTGGCTGGTTCA 58.309 50.000 0.00 0.00 0.00 3.18
2358 6122 4.297510 TGCTTGTTTCAATTCAACATCCG 58.702 39.130 1.42 0.00 34.13 4.18
2562 6340 5.591099 ACAAATTGACAATCCAGTGTGTTC 58.409 37.500 0.00 0.00 0.00 3.18
2584 6362 3.271729 TGTGTGGCAAAAACGTCTCTTA 58.728 40.909 0.00 0.00 0.00 2.10
2585 6363 3.064271 TGTGTGGCAAAAACGTCTCTTAC 59.936 43.478 0.00 0.00 0.00 2.34
2586 6364 3.311596 GTGTGGCAAAAACGTCTCTTACT 59.688 43.478 0.00 0.00 0.00 2.24
2587 6365 3.311322 TGTGGCAAAAACGTCTCTTACTG 59.689 43.478 0.00 0.00 0.00 2.74
2588 6366 2.875933 TGGCAAAAACGTCTCTTACTGG 59.124 45.455 0.00 0.00 0.00 4.00
2932 6752 4.461992 AAACATTGAGTACCGTTTGTCG 57.538 40.909 0.00 0.00 39.52 4.35
2940 6760 5.472148 TGAGTACCGTTTGTCGATGTTATT 58.528 37.500 0.00 0.00 42.86 1.40
3039 6859 6.115448 AGCTTGGAAACTAACATACAGTCT 57.885 37.500 0.00 0.00 0.00 3.24
3098 6918 3.243068 ACCTTGTTTGCGTCATTTCAGAC 60.243 43.478 0.00 0.00 35.19 3.51
3133 6953 4.859304 TGCAATGTCAAGCTGAAGATTT 57.141 36.364 0.00 0.00 0.00 2.17
3135 6955 4.278919 TGCAATGTCAAGCTGAAGATTTCA 59.721 37.500 0.00 0.00 38.17 2.69
3143 6963 7.093596 TGTCAAGCTGAAGATTTCATCTCTCTA 60.094 37.037 0.00 0.00 39.08 2.43
3169 6989 1.265635 CTCTCTTGAGGCGGTATCTCG 59.734 57.143 0.00 0.00 36.70 4.04
3185 7005 5.921408 GGTATCTCGACATGTGAGGAATAAC 59.079 44.000 18.91 12.28 34.19 1.89
3192 7012 6.264518 TCGACATGTGAGGAATAACTATGCTA 59.735 38.462 1.15 0.00 0.00 3.49
3194 7014 7.438160 CGACATGTGAGGAATAACTATGCTAAA 59.562 37.037 1.15 0.00 0.00 1.85
3200 7020 8.778358 GTGAGGAATAACTATGCTAAATTCCAG 58.222 37.037 13.29 0.00 45.27 3.86
3221 7041 8.402798 TCCAGAATCAAACTTGTTGCTTAATA 57.597 30.769 0.00 0.00 0.00 0.98
3230 7050 9.713740 CAAACTTGTTGCTTAATAGATGATCTC 57.286 33.333 0.00 0.00 0.00 2.75
3255 7075 2.104792 AGCAAGCTGAAGTCTGTTACCA 59.895 45.455 0.00 0.00 0.00 3.25
3260 7080 4.884247 AGCTGAAGTCTGTTACCAAGTAC 58.116 43.478 0.00 0.00 0.00 2.73
3264 7084 5.045215 TGAAGTCTGTTACCAAGTACGTTG 58.955 41.667 0.00 0.00 35.71 4.10
3268 7088 4.805192 GTCTGTTACCAAGTACGTTGTTGA 59.195 41.667 10.33 0.00 33.87 3.18
3271 7091 6.539464 TCTGTTACCAAGTACGTTGTTGAATT 59.461 34.615 10.33 0.00 33.87 2.17
3308 7128 9.626045 AATCGAGAATTTTCCTTTTGTTGATAC 57.374 29.630 0.00 0.00 0.00 2.24
3375 7195 0.236449 GGTTTTCGGTTGGTACAGCG 59.764 55.000 0.00 0.00 41.73 5.18
3423 7243 4.846779 TTTTTGGGATGAGAAAAGGACG 57.153 40.909 0.00 0.00 0.00 4.79
3466 7286 8.348285 TGAGGTACCCAAGATTTTTAAGAATG 57.652 34.615 8.74 0.00 0.00 2.67
3468 7288 8.950007 AGGTACCCAAGATTTTTAAGAATGAA 57.050 30.769 8.74 0.00 0.00 2.57
3470 7290 7.759886 GGTACCCAAGATTTTTAAGAATGAAGC 59.240 37.037 0.00 0.00 0.00 3.86
3542 7362 4.871933 AAACAAAATGGTCACCTGATCC 57.128 40.909 0.00 0.00 0.00 3.36
3561 7381 6.537355 TGATCCATTATCTGACCCAATTCTC 58.463 40.000 0.00 0.00 35.45 2.87
3567 7387 4.760530 ATCTGACCCAATTCTCATCGAA 57.239 40.909 0.00 0.00 35.78 3.71
3579 7399 7.625553 CAATTCTCATCGAAATGGAGAAGTAC 58.374 38.462 19.72 0.00 34.98 2.73
3601 7421 2.742774 GTGCAAAACATGGACTTGGAC 58.257 47.619 10.83 10.83 46.03 4.02
3617 7437 7.390440 TGGACTTGGACAGTACAATGAAAATAG 59.610 37.037 0.00 0.00 44.19 1.73
3679 7499 6.583806 CACACATGAAAATTTACTCAGGAAGC 59.416 38.462 10.59 0.00 0.00 3.86
3694 7514 3.378427 CAGGAAGCAGGTAATTTGTAGGC 59.622 47.826 0.00 0.00 0.00 3.93
3696 7516 3.128764 GGAAGCAGGTAATTTGTAGGCAC 59.871 47.826 0.00 0.00 0.00 5.01
4036 7856 7.428282 TGCAATGAACGTTGTTAGAGAAATA 57.572 32.000 5.00 0.00 0.00 1.40
4125 7945 4.981647 TCATCTATTTGGTAGGGGGAATGT 59.018 41.667 0.00 0.00 0.00 2.71
4211 8031 2.364970 TGGGTTGAGCCAACTTTGATTG 59.635 45.455 14.91 0.00 43.14 2.67
4216 8036 3.149196 TGAGCCAACTTTGATTGTCCTC 58.851 45.455 0.00 0.00 31.63 3.71
4218 8038 2.887152 AGCCAACTTTGATTGTCCTCAC 59.113 45.455 0.00 0.00 0.00 3.51
4221 8041 2.254546 ACTTTGATTGTCCTCACGCA 57.745 45.000 0.00 0.00 0.00 5.24
4234 8054 2.726760 CCTCACGCAATAGTCGCTTATC 59.273 50.000 0.00 0.00 0.00 1.75
4238 8058 3.117507 CACGCAATAGTCGCTTATCGTAC 59.882 47.826 0.00 0.00 39.67 3.67
4289 8109 8.669243 GTTGTTTGAGAAATATACTTAGCAGCT 58.331 33.333 0.00 0.00 0.00 4.24
4304 8124 6.543831 ACTTAGCAGCTGTTAGGAAATTATGG 59.456 38.462 23.40 0.00 0.00 2.74
4391 8211 8.674607 GGTTGTTAGGATATTCACAAACTTAGG 58.325 37.037 0.00 0.00 34.56 2.69
4401 8221 5.055265 TCACAAACTTAGGAATGGTGGAA 57.945 39.130 0.00 0.00 0.00 3.53
4441 8261 8.231007 TCATTTATTTGATAGGGGAATGGCTTA 58.769 33.333 0.00 0.00 0.00 3.09
4501 8321 2.358003 GCTGCTCTTGCACTCCGT 60.358 61.111 0.00 0.00 45.31 4.69
4502 8322 1.963338 GCTGCTCTTGCACTCCGTT 60.963 57.895 0.00 0.00 45.31 4.44
4559 8382 4.246458 GGTTCTGTAGTTAACTGCTGGAG 58.754 47.826 23.51 14.27 0.00 3.86
4606 8429 9.539825 ACATAGTTTCTGCATCTGAAAGTATAG 57.460 33.333 19.18 16.45 41.48 1.31
4658 8481 6.815142 GCATGTCCTTGCTGATCTTAATTTTT 59.185 34.615 0.00 0.00 39.57 1.94
4762 8585 8.779303 TCAGTGATAACGACATGTGTTTTAATT 58.221 29.630 1.15 0.00 0.00 1.40
4801 8624 0.112995 TCCATTGTGCTTCTGCCCTT 59.887 50.000 0.00 0.00 38.71 3.95
4805 8628 1.172180 TTGTGCTTCTGCCCTTTCCG 61.172 55.000 0.00 0.00 38.71 4.30
4818 8641 3.740452 GCCCTTTCCGATTGTACCTCTAC 60.740 52.174 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 96 2.036086 GTGCAAACAAAAACGCAGTACG 60.036 45.455 0.00 0.00 45.00 3.67
96 97 2.917971 TGTGCAAACAAAAACGCAGTAC 59.082 40.909 0.00 0.00 45.00 2.73
97 98 2.917971 GTGTGCAAACAAAAACGCAGTA 59.082 40.909 0.88 0.00 45.00 2.74
98 99 4.166595 ATGTGTGCAAACAAAAACGCAGT 61.167 39.130 15.04 0.00 36.57 4.40
99 100 1.723542 TGTGTGCAAACAAAAACGCAG 59.276 42.857 7.42 0.00 34.49 5.18
100 101 1.783284 TGTGTGCAAACAAAAACGCA 58.217 40.000 7.42 0.00 0.00 5.24
101 102 4.032331 ACTTATGTGTGCAAACAAAAACGC 59.968 37.500 15.04 0.00 32.81 4.84
102 103 5.694674 ACTTATGTGTGCAAACAAAAACG 57.305 34.783 15.04 8.17 32.81 3.60
103 104 7.289587 AGAACTTATGTGTGCAAACAAAAAC 57.710 32.000 15.04 4.22 32.81 2.43
110 111 9.283768 CCCATATATAGAACTTATGTGTGCAAA 57.716 33.333 0.00 0.00 0.00 3.68
111 112 7.390440 GCCCATATATAGAACTTATGTGTGCAA 59.610 37.037 0.00 0.00 27.62 4.08
112 113 6.878923 GCCCATATATAGAACTTATGTGTGCA 59.121 38.462 0.00 0.00 27.62 4.57
130 131 7.062957 GCCCAATGTAATATAAGAGCCCATAT 58.937 38.462 0.00 0.00 0.00 1.78
131 132 6.217487 AGCCCAATGTAATATAAGAGCCCATA 59.783 38.462 0.00 0.00 0.00 2.74
132 133 5.015603 AGCCCAATGTAATATAAGAGCCCAT 59.984 40.000 0.00 0.00 0.00 4.00
133 134 4.353788 AGCCCAATGTAATATAAGAGCCCA 59.646 41.667 0.00 0.00 0.00 5.36
145 146 2.378547 AGGACTCCAAAGCCCAATGTAA 59.621 45.455 0.00 0.00 0.00 2.41
165 166 3.446873 ACTTGCTGACTGACTATGGAGAG 59.553 47.826 0.00 0.00 0.00 3.20
182 183 3.968649 TGAGACAATTTTCAGCACTTGC 58.031 40.909 0.00 0.00 42.49 4.01
183 184 6.890663 TTTTGAGACAATTTTCAGCACTTG 57.109 33.333 0.00 0.00 0.00 3.16
210 211 5.975693 TTTCCTTTTCAACACACTTGTCT 57.024 34.783 0.00 0.00 33.55 3.41
211 212 7.595311 ATTTTTCCTTTTCAACACACTTGTC 57.405 32.000 0.00 0.00 33.55 3.18
212 213 8.931775 GTTATTTTTCCTTTTCAACACACTTGT 58.068 29.630 0.00 0.00 37.67 3.16
215 216 7.763985 CCTGTTATTTTTCCTTTTCAACACACT 59.236 33.333 0.00 0.00 0.00 3.55
216 217 7.011016 CCCTGTTATTTTTCCTTTTCAACACAC 59.989 37.037 0.00 0.00 0.00 3.82
217 218 7.044798 CCCTGTTATTTTTCCTTTTCAACACA 58.955 34.615 0.00 0.00 0.00 3.72
249 250 2.995574 CGAGTGGGGAACGAGGGT 60.996 66.667 0.00 0.00 0.00 4.34
360 367 1.240256 CGAGGGATAGGAGAGTTCGG 58.760 60.000 0.00 0.00 0.00 4.30
533 540 1.601663 CGGCTTAGGAGATGAGAAGCG 60.602 57.143 0.00 0.00 44.21 4.68
544 551 1.001764 TGTCGAGGACGGCTTAGGA 60.002 57.895 0.00 0.00 44.93 2.94
608 615 5.262588 AGAAAGAAAGAAAACGCATGGTT 57.737 34.783 0.00 0.00 41.76 3.67
609 616 4.918810 AGAAAGAAAGAAAACGCATGGT 57.081 36.364 0.00 0.00 0.00 3.55
610 617 5.979517 AGAAAGAAAGAAAGAAAACGCATGG 59.020 36.000 0.00 0.00 0.00 3.66
611 618 7.455331 AAGAAAGAAAGAAAGAAAACGCATG 57.545 32.000 0.00 0.00 0.00 4.06
612 619 7.976175 AGAAAGAAAGAAAGAAAGAAAACGCAT 59.024 29.630 0.00 0.00 0.00 4.73
613 620 7.312899 AGAAAGAAAGAAAGAAAGAAAACGCA 58.687 30.769 0.00 0.00 0.00 5.24
614 621 7.742019 AGAAAGAAAGAAAGAAAGAAAACGC 57.258 32.000 0.00 0.00 0.00 4.84
624 631 9.799106 ACCATGATCTAAAGAAAGAAAGAAAGA 57.201 29.630 0.00 0.00 0.00 2.52
658 665 3.571401 GTGATTGATGGGGGCAAATAGAG 59.429 47.826 0.00 0.00 0.00 2.43
661 668 3.686227 AGTGATTGATGGGGGCAAATA 57.314 42.857 0.00 0.00 0.00 1.40
664 671 2.178580 GAAAGTGATTGATGGGGGCAA 58.821 47.619 0.00 0.00 0.00 4.52
665 672 1.358787 AGAAAGTGATTGATGGGGGCA 59.641 47.619 0.00 0.00 0.00 5.36
666 673 2.149973 AGAAAGTGATTGATGGGGGC 57.850 50.000 0.00 0.00 0.00 5.80
667 674 4.081476 GGAAAAGAAAGTGATTGATGGGGG 60.081 45.833 0.00 0.00 0.00 5.40
668 675 4.774200 AGGAAAAGAAAGTGATTGATGGGG 59.226 41.667 0.00 0.00 0.00 4.96
669 676 5.990120 AGGAAAAGAAAGTGATTGATGGG 57.010 39.130 0.00 0.00 0.00 4.00
670 677 7.224522 AGAAGGAAAAGAAAGTGATTGATGG 57.775 36.000 0.00 0.00 0.00 3.51
679 686 9.967346 GCAGTAAATAAAGAAGGAAAAGAAAGT 57.033 29.630 0.00 0.00 0.00 2.66
705 712 2.146342 CAGCAAGCGTAGGAATATGGG 58.854 52.381 0.00 0.00 0.00 4.00
724 733 6.376864 AGCATATAATGGTAAACAACACTGCA 59.623 34.615 0.00 0.00 39.58 4.41
744 753 6.839124 ACAGTGGATGAATCAAAAAGCATA 57.161 33.333 0.00 0.00 0.00 3.14
783 792 5.491323 TGATGATTGTACCCACAGTAACA 57.509 39.130 0.00 0.00 35.67 2.41
818 827 9.751542 ATTCGATACAAGTTCTCCACTAAATAG 57.248 33.333 0.00 0.00 32.94 1.73
830 839 9.456797 CGTACAAGTAAAATTCGATACAAGTTC 57.543 33.333 0.00 0.00 0.00 3.01
854 863 6.014584 TGCATGGACCTTAGAATCATATACGT 60.015 38.462 0.00 0.00 0.00 3.57
855 864 6.398095 TGCATGGACCTTAGAATCATATACG 58.602 40.000 0.00 0.00 0.00 3.06
860 869 4.164796 TGTCTGCATGGACCTTAGAATCAT 59.835 41.667 3.85 0.00 35.54 2.45
1009 1018 1.421268 ACTGGATTCACTGCCACTTGA 59.579 47.619 0.00 0.00 0.00 3.02
1033 1042 1.482182 GCCATCATTGTCTTTTCCCCC 59.518 52.381 0.00 0.00 0.00 5.40
1052 1061 1.480954 TGAAGGGGATACGAGTTGAGC 59.519 52.381 0.00 0.00 37.60 4.26
1055 1064 2.761208 AGAGTGAAGGGGATACGAGTTG 59.239 50.000 0.00 0.00 37.60 3.16
1061 1070 6.339587 CTCTATGAAGAGTGAAGGGGATAC 57.660 45.833 0.00 0.00 43.75 2.24
1085 1094 4.641396 ACTGGTGTCATCATCTCGAAAAA 58.359 39.130 0.00 0.00 0.00 1.94
1086 1095 4.021104 AGACTGGTGTCATCATCTCGAAAA 60.021 41.667 0.00 0.00 45.20 2.29
1087 1096 3.511540 AGACTGGTGTCATCATCTCGAAA 59.488 43.478 0.00 0.00 45.20 3.46
1088 1097 3.092301 AGACTGGTGTCATCATCTCGAA 58.908 45.455 0.00 0.00 45.20 3.71
1089 1098 2.424956 CAGACTGGTGTCATCATCTCGA 59.575 50.000 0.00 0.00 45.20 4.04
1090 1099 2.165234 ACAGACTGGTGTCATCATCTCG 59.835 50.000 7.51 0.00 45.20 4.04
1091 1100 3.519579 CACAGACTGGTGTCATCATCTC 58.480 50.000 7.51 0.00 45.20 2.75
1092 1101 3.606595 CACAGACTGGTGTCATCATCT 57.393 47.619 7.51 0.00 45.20 2.90
1103 1112 5.047021 TCCAAATAGAGAGAACACAGACTGG 60.047 44.000 7.51 0.00 0.00 4.00
1104 1113 6.030548 TCCAAATAGAGAGAACACAGACTG 57.969 41.667 0.00 0.00 0.00 3.51
1111 1120 4.718774 AGGCATCTCCAAATAGAGAGAACA 59.281 41.667 0.00 0.00 45.77 3.18
1115 1124 5.299148 CAGAAGGCATCTCCAAATAGAGAG 58.701 45.833 0.00 0.00 45.77 3.20
1125 1134 2.050144 TCCATACCAGAAGGCATCTCC 58.950 52.381 0.00 0.00 35.73 3.71
1148 1157 5.585047 GGATAAGCGTAACTTTTGGAGATGT 59.415 40.000 0.00 0.00 39.97 3.06
1154 1163 5.048294 ACCTTTGGATAAGCGTAACTTTTGG 60.048 40.000 0.00 0.00 39.97 3.28
1155 1164 6.009115 ACCTTTGGATAAGCGTAACTTTTG 57.991 37.500 0.00 0.00 39.97 2.44
1159 1168 6.489022 AGAAAAACCTTTGGATAAGCGTAACT 59.511 34.615 0.00 0.00 0.00 2.24
1160 1169 6.675026 AGAAAAACCTTTGGATAAGCGTAAC 58.325 36.000 0.00 0.00 0.00 2.50
1161 1170 6.887626 AGAAAAACCTTTGGATAAGCGTAA 57.112 33.333 0.00 0.00 0.00 3.18
1162 1171 6.887626 AAGAAAAACCTTTGGATAAGCGTA 57.112 33.333 0.00 0.00 0.00 4.42
1169 4887 9.546428 CATTCACTAAAAGAAAAACCTTTGGAT 57.454 29.630 0.00 0.00 36.57 3.41
1224 4942 9.297037 TCATGAATGAGATTATGCATCATCTTT 57.703 29.630 21.38 14.08 32.59 2.52
1285 5003 2.561569 CCGGATGTATGGTTCACCTTC 58.438 52.381 0.00 0.00 36.82 3.46
1289 5007 2.413310 AACCCGGATGTATGGTTCAC 57.587 50.000 0.73 0.00 37.88 3.18
1314 5032 1.739466 ACAAATGCAGTGTATGGCTCG 59.261 47.619 4.06 0.00 0.00 5.03
1316 5034 3.573538 TGAAACAAATGCAGTGTATGGCT 59.426 39.130 6.27 0.00 0.00 4.75
1369 5087 5.364778 TGGAACCGAGTGTATTATTGGATG 58.635 41.667 0.00 0.00 0.00 3.51
1375 5093 4.022242 CCGAGATGGAACCGAGTGTATTAT 60.022 45.833 0.00 0.00 42.00 1.28
1376 5094 3.317149 CCGAGATGGAACCGAGTGTATTA 59.683 47.826 0.00 0.00 42.00 0.98
1379 5097 1.100510 CCGAGATGGAACCGAGTGTA 58.899 55.000 0.00 0.00 42.00 2.90
1405 5123 6.916360 ATGAACATACCACACCATTTTTCT 57.084 33.333 0.00 0.00 0.00 2.52
1462 5180 9.632807 TTAATTGTGTATAATGGCAAACTGAAC 57.367 29.630 0.00 0.00 0.00 3.18
1650 5368 6.634805 TGGAGTTCAGCTCTAGAGTTATTTG 58.365 40.000 20.75 11.47 43.62 2.32
1942 5663 0.810031 GCAGTCGACACCACAGTTGT 60.810 55.000 19.50 0.00 0.00 3.32
2092 5847 3.181423 ACCTAGCCACAAAATTTCCCTCA 60.181 43.478 0.00 0.00 0.00 3.86
2193 5948 1.139853 CCCAGGAACCAGCAGAGATAC 59.860 57.143 0.00 0.00 0.00 2.24
2309 6073 4.724279 AAACCAGGAACCAACAGTAGAT 57.276 40.909 0.00 0.00 0.00 1.98
2358 6122 3.445805 ACTCTAGCTCTGCTCAAACCTAC 59.554 47.826 0.00 0.00 40.44 3.18
2528 6306 2.743664 TGTCAATTTGTCCTGCAGATCG 59.256 45.455 17.39 0.00 0.00 3.69
2562 6340 1.670811 AGAGACGTTTTTGCCACACAG 59.329 47.619 0.00 0.00 0.00 3.66
2584 6362 3.445008 TCTTCATCCTTAGCACTCCAGT 58.555 45.455 0.00 0.00 0.00 4.00
2585 6363 4.440880 CTTCTTCATCCTTAGCACTCCAG 58.559 47.826 0.00 0.00 0.00 3.86
2586 6364 3.369892 GCTTCTTCATCCTTAGCACTCCA 60.370 47.826 0.00 0.00 0.00 3.86
2587 6365 3.202097 GCTTCTTCATCCTTAGCACTCC 58.798 50.000 0.00 0.00 0.00 3.85
2588 6366 3.866651 TGCTTCTTCATCCTTAGCACTC 58.133 45.455 0.00 0.00 36.96 3.51
2805 6625 1.736126 CATGGCACTGTAGCACTGAAG 59.264 52.381 0.00 0.00 35.83 3.02
2972 6792 5.868043 TTCTATGATGTTGCACAAGACTG 57.132 39.130 0.00 0.00 0.00 3.51
3081 6901 2.548057 TGGAGTCTGAAATGACGCAAAC 59.452 45.455 0.00 0.00 41.47 2.93
3098 6918 4.202040 TGACATTGCAACAGAGTTTTGGAG 60.202 41.667 0.00 0.00 0.00 3.86
3133 6953 3.326521 AGAGAGGCTCCTAGAGAGATGA 58.673 50.000 11.71 0.00 46.50 2.92
3135 6955 3.721575 TCAAGAGAGGCTCCTAGAGAGAT 59.278 47.826 11.71 0.00 46.50 2.75
3169 6989 8.662781 TTTAGCATAGTTATTCCTCACATGTC 57.337 34.615 0.00 0.00 0.00 3.06
3185 7005 9.512435 CAAGTTTGATTCTGGAATTTAGCATAG 57.488 33.333 0.00 0.00 0.00 2.23
3192 7012 6.585416 AGCAACAAGTTTGATTCTGGAATTT 58.415 32.000 0.00 0.00 0.00 1.82
3194 7014 5.796424 AGCAACAAGTTTGATTCTGGAAT 57.204 34.783 0.00 0.00 0.00 3.01
3221 7041 1.134461 AGCTTGCTTGCGAGATCATCT 60.134 47.619 13.56 0.00 38.13 2.90
3230 7050 0.110328 CAGACTTCAGCTTGCTTGCG 60.110 55.000 0.00 0.00 38.13 4.85
3255 7075 3.378742 TGGCACAATTCAACAACGTACTT 59.621 39.130 0.00 0.00 31.92 2.24
3268 7088 8.776376 AAATTCTCGATTTTAATGGCACAATT 57.224 26.923 0.00 0.00 36.79 2.32
3271 7091 6.811170 GGAAAATTCTCGATTTTAATGGCACA 59.189 34.615 0.00 0.00 45.54 4.57
3308 7128 9.888878 CTATAAGATGTCAGGCATAAACAAATG 57.111 33.333 0.00 0.00 38.06 2.32
3402 7222 4.465886 TCGTCCTTTTCTCATCCCAAAAA 58.534 39.130 0.00 0.00 0.00 1.94
3423 7243 5.189180 ACCTCATAGGCAAAGAACATCTTC 58.811 41.667 0.00 0.00 39.63 2.87
3465 7285 7.499232 GCCCTAAATCTATTCTTAACTGCTTCA 59.501 37.037 0.00 0.00 0.00 3.02
3466 7286 7.307455 CGCCCTAAATCTATTCTTAACTGCTTC 60.307 40.741 0.00 0.00 0.00 3.86
3468 7288 5.992217 CGCCCTAAATCTATTCTTAACTGCT 59.008 40.000 0.00 0.00 0.00 4.24
3470 7290 5.992217 AGCGCCCTAAATCTATTCTTAACTG 59.008 40.000 2.29 0.00 0.00 3.16
3542 7362 6.226052 TCGATGAGAATTGGGTCAGATAATG 58.774 40.000 0.00 0.00 0.00 1.90
3561 7381 3.551890 CACGGTACTTCTCCATTTCGATG 59.448 47.826 0.00 0.00 0.00 3.84
3567 7387 2.851263 TTGCACGGTACTTCTCCATT 57.149 45.000 0.00 0.00 0.00 3.16
3579 7399 1.602668 CCAAGTCCATGTTTTGCACGG 60.603 52.381 0.00 0.00 0.00 4.94
3594 7414 8.691661 AACTATTTTCATTGTACTGTCCAAGT 57.308 30.769 0.00 0.00 43.40 3.16
3601 7421 9.530129 GTCTTCGAAACTATTTTCATTGTACTG 57.470 33.333 0.00 0.00 41.22 2.74
3679 7499 3.190535 GTGTGGTGCCTACAAATTACCTG 59.809 47.826 0.00 0.00 32.68 4.00
3694 7514 4.101942 GTGTATTGTGTTTGTGTGTGGTG 58.898 43.478 0.00 0.00 0.00 4.17
3696 7516 4.362932 TGTGTATTGTGTTTGTGTGTGG 57.637 40.909 0.00 0.00 0.00 4.17
3771 7591 1.529438 TGCATCAACGACGAGGTTTTC 59.471 47.619 0.00 0.00 0.00 2.29
3834 7654 0.393077 GCAGCACCCCGTATGATAGT 59.607 55.000 0.00 0.00 0.00 2.12
3847 7667 1.425428 GCATCACCTTACGCAGCAC 59.575 57.895 0.00 0.00 0.00 4.40
3922 7742 8.515473 AATCTGTTTGTAAAATTTTCGCCTAC 57.485 30.769 6.72 0.17 0.00 3.18
4036 7856 3.281727 ACAATCACCATTGCTCGGTAT 57.718 42.857 0.00 0.00 43.03 2.73
4125 7945 4.771903 TGCTAAGTTTGTGAGTACCAACA 58.228 39.130 0.00 0.00 35.51 3.33
4211 8031 0.179134 AGCGACTATTGCGTGAGGAC 60.179 55.000 0.00 0.00 37.44 3.85
4216 8036 2.117137 ACGATAAGCGACTATTGCGTG 58.883 47.619 0.00 0.00 44.57 5.34
4218 8038 3.294102 TGTACGATAAGCGACTATTGCG 58.706 45.455 0.00 0.00 44.57 4.85
4221 8041 5.888105 AGTGTTGTACGATAAGCGACTATT 58.112 37.500 0.00 0.00 44.57 1.73
4234 8054 7.960195 TCATTGCATGTTTAATAGTGTTGTACG 59.040 33.333 0.00 0.00 0.00 3.67
4238 8058 9.142515 ACATTCATTGCATGTTTAATAGTGTTG 57.857 29.630 0.00 0.00 30.22 3.33
4289 8109 7.177568 TGCTAAGTTTGCCATAATTTCCTAACA 59.822 33.333 6.84 0.00 0.00 2.41
4304 8124 2.484264 ACTCGACCATTGCTAAGTTTGC 59.516 45.455 2.06 2.06 0.00 3.68
4441 8261 1.115326 GGGGACAGCAAAGTTGGCTT 61.115 55.000 0.61 0.00 40.23 4.35
4463 8283 0.796927 GTAGGACAAGCGAAAGTGGC 59.203 55.000 0.00 0.00 0.00 5.01
4559 8382 6.000891 TGTCATTCTTACAGCATGAAACAC 57.999 37.500 0.00 0.00 39.69 3.32
4606 8429 4.511527 TCCAGCAATGATTCTTCAGAGAC 58.488 43.478 0.00 0.00 34.73 3.36
4658 8481 6.121776 TGACTCCTAAATTAAGACCAGCAA 57.878 37.500 0.00 0.00 0.00 3.91
4659 8482 5.755409 TGACTCCTAAATTAAGACCAGCA 57.245 39.130 0.00 0.00 0.00 4.41
4801 8624 4.246712 AGGAGTAGAGGTACAATCGGAA 57.753 45.455 0.00 0.00 0.00 4.30
4805 8628 7.362802 ACCAAATAGGAGTAGAGGTACAATC 57.637 40.000 0.00 0.00 41.22 2.67


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

AutoCloner maintained by Alex Coulton.