Multiple sequence alignment - TraesCS7D01G250100

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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 TraesCS7D01G250100 chr7D 100.000 8140 0 0 1 8140 222137867 222146006 0.000000e+00 15032.0
1 TraesCS7D01G250100 chr7D 94.662 562 30 0 6 567 38275459 38274898 0.000000e+00 872.0
2 TraesCS7D01G250100 chr7D 90.909 44 4 0 7636 7679 140301309 140301352 8.820000e-05 60.2
3 TraesCS7D01G250100 chr7B 96.668 3631 80 20 3992 7610 174571610 174568009 0.000000e+00 5997.0
4 TraesCS7D01G250100 chr7B 95.832 3431 101 18 568 3990 174575052 174571656 0.000000e+00 5505.0
5 TraesCS7D01G250100 chr7B 90.510 569 52 2 6 573 63778527 63777960 0.000000e+00 750.0
6 TraesCS7D01G250100 chr7B 95.714 70 3 0 1267 1336 174574302 174574371 6.680000e-21 113.0
7 TraesCS7D01G250100 chr7A 96.293 3048 81 15 566 3601 236611650 236614677 0.000000e+00 4974.0
8 TraesCS7D01G250100 chr7A 96.696 2179 48 5 3992 6170 236617083 236619237 0.000000e+00 3603.0
9 TraesCS7D01G250100 chr7A 95.947 1974 72 7 6169 8137 236619320 236621290 0.000000e+00 3195.0
10 TraesCS7D01G250100 chr7A 96.734 398 10 1 3596 3990 236616640 236617037 0.000000e+00 660.0
11 TraesCS7D01G250100 chr1D 94.700 566 30 0 6 571 76952677 76952112 0.000000e+00 880.0
12 TraesCS7D01G250100 chr2D 94.643 560 29 1 6 565 570992982 570992424 0.000000e+00 867.0
13 TraesCS7D01G250100 chr2D 94.139 563 30 2 6 567 608563664 608564224 0.000000e+00 854.0
14 TraesCS7D01G250100 chr5D 94.316 563 29 2 6 567 522500431 522499871 0.000000e+00 859.0
15 TraesCS7D01G250100 chr5B 92.500 560 42 0 6 565 595110501 595111060 0.000000e+00 802.0
16 TraesCS7D01G250100 chr5B 95.455 44 2 0 7636 7679 437185336 437185293 4.080000e-08 71.3
17 TraesCS7D01G250100 chr3A 92.021 564 43 1 6 567 477425837 477425274 0.000000e+00 791.0
18 TraesCS7D01G250100 chr3A 84.615 65 10 0 7611 7675 534539367 534539431 1.900000e-06 65.8
19 TraesCS7D01G250100 chr3B 91.444 561 45 3 6 565 564189173 564188615 0.000000e+00 767.0
20 TraesCS7D01G250100 chr3B 82.692 104 17 1 8035 8137 829293508 829293405 3.130000e-14 91.6
21 TraesCS7D01G250100 chr3B 83.824 68 11 0 7611 7678 542128174 542128107 1.900000e-06 65.8
22 TraesCS7D01G250100 chr3B 84.615 65 10 0 7611 7675 542128952 542128888 1.900000e-06 65.8
23 TraesCS7D01G250100 chr1A 88.703 478 45 3 2749 3225 516368411 516367942 7.090000e-160 575.0
24 TraesCS7D01G250100 chr1A 92.958 71 5 0 3256 3326 516367943 516367873 4.020000e-18 104.0
25 TraesCS7D01G250100 chr1A 93.182 44 3 0 7636 7679 365530832 365530875 1.900000e-06 65.8
26 TraesCS7D01G250100 chr1B 88.968 281 23 2 2749 3021 566600464 566600184 2.810000e-89 340.0
27 TraesCS7D01G250100 chr3D 86.765 68 9 0 7611 7678 415641890 415641823 8.760000e-10 76.8
28 TraesCS7D01G250100 chr3D 83.824 68 11 0 7611 7678 415641616 415641549 1.900000e-06 65.8
29 TraesCS7D01G250100 chr3D 81.081 74 12 2 8065 8137 611538889 611538961 3.170000e-04 58.4
30 TraesCS7D01G250100 chr6B 93.182 44 3 0 7636 7679 550369436 550369393 1.900000e-06 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G250100 chr7D 222137867 222146006 8139 False 15032.0 15032 100.0000 1 8140 1 chr7D.!!$F2 8139
1 TraesCS7D01G250100 chr7D 38274898 38275459 561 True 872.0 872 94.6620 6 567 1 chr7D.!!$R1 561
2 TraesCS7D01G250100 chr7B 174568009 174575052 7043 True 5751.0 5997 96.2500 568 7610 2 chr7B.!!$R2 7042
3 TraesCS7D01G250100 chr7B 63777960 63778527 567 True 750.0 750 90.5100 6 573 1 chr7B.!!$R1 567
4 TraesCS7D01G250100 chr7A 236611650 236621290 9640 False 3108.0 4974 96.4175 566 8137 4 chr7A.!!$F1 7571
5 TraesCS7D01G250100 chr1D 76952112 76952677 565 True 880.0 880 94.7000 6 571 1 chr1D.!!$R1 565
6 TraesCS7D01G250100 chr2D 570992424 570992982 558 True 867.0 867 94.6430 6 565 1 chr2D.!!$R1 559
7 TraesCS7D01G250100 chr2D 608563664 608564224 560 False 854.0 854 94.1390 6 567 1 chr2D.!!$F1 561
8 TraesCS7D01G250100 chr5D 522499871 522500431 560 True 859.0 859 94.3160 6 567 1 chr5D.!!$R1 561
9 TraesCS7D01G250100 chr5B 595110501 595111060 559 False 802.0 802 92.5000 6 565 1 chr5B.!!$F1 559
10 TraesCS7D01G250100 chr3A 477425274 477425837 563 True 791.0 791 92.0210 6 567 1 chr3A.!!$R1 561
11 TraesCS7D01G250100 chr3B 564188615 564189173 558 True 767.0 767 91.4440 6 565 1 chr3B.!!$R1 559
12 TraesCS7D01G250100 chr1A 516367873 516368411 538 True 339.5 575 90.8305 2749 3326 2 chr1A.!!$R1 577

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
895 908 1.999071 CTGCTCCGTTCCTCCTCTCG 61.999 65.000 0.00 0.0 0.00 4.04 F
1714 1732 0.544697 ATGATACCCCGGTTGTCACC 59.455 55.000 0.00 0.0 40.16 4.02 F
2052 2070 2.629051 GTCACTATGCAGGTAACCACC 58.371 52.381 0.00 0.0 46.19 4.61 F
3794 5786 1.251251 GCCAAACTGACAAGGCATCT 58.749 50.000 0.00 0.0 46.26 2.90 F
4726 6762 0.032952 CCACATTTGCAGCAACAGCT 59.967 50.000 7.54 0.0 39.75 4.24 F
5645 7702 0.750850 ATGCAGATGCCTTGATTGCC 59.249 50.000 1.72 0.0 41.18 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2266 2284 0.970640 ACCATGGCAGTACACGTACA 59.029 50.000 13.04 0.00 38.48 2.90 R
2741 2759 1.199097 GGCCAAAACAGATACGTGGTG 59.801 52.381 0.00 0.00 0.00 4.17 R
3990 5982 0.318120 TACGTGGTCGGGAGTTTTCC 59.682 55.000 0.00 0.00 43.23 3.13 R
5142 7193 0.681733 ACTGACTGCATTCGACCAGT 59.318 50.000 11.15 11.15 44.43 4.00 R
6037 8094 0.853530 AGCCAGGGGATTTATGACCC 59.146 55.000 0.00 0.00 45.06 4.46 R
7179 9323 0.168128 GAAAAATGTCGGTCCCGCAG 59.832 55.000 0.00 0.00 39.59 5.18 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
34 35 3.684305 TGAGCATATGTGTGTGCAACTAC 59.316 43.478 4.29 0.00 44.06 2.73
36 37 4.264253 AGCATATGTGTGTGCAACTACAT 58.736 39.130 13.38 13.38 44.06 2.29
49 50 6.429692 TGTGCAACTACATTACATTACAAGCT 59.570 34.615 0.00 0.00 38.04 3.74
64 65 2.297033 ACAAGCTAACGAACGAGGGTTA 59.703 45.455 0.14 0.00 36.24 2.85
208 209 6.292381 GGAAAAAGCTGCACGATATAGTACTG 60.292 42.308 5.39 0.00 0.00 2.74
211 212 5.515797 AGCTGCACGATATAGTACTGAAA 57.484 39.130 5.39 0.00 0.00 2.69
439 442 6.488683 TCTGTTCTTTTCGGAATGTGGTAATT 59.511 34.615 0.00 0.00 0.00 1.40
483 486 4.292186 ACAACCACATGCACTAGAAGAT 57.708 40.909 0.00 0.00 0.00 2.40
575 581 9.578439 CAGTGAAGAATTTGGGAATTTTCTATC 57.422 33.333 0.00 0.00 35.65 2.08
578 584 6.149129 AGAATTTGGGAATTTTCTATCGCC 57.851 37.500 0.00 0.00 35.65 5.54
848 861 2.567049 CTCTTTCCGTCGCTCCGT 59.433 61.111 0.00 0.00 0.00 4.69
893 906 2.355193 GCTGCTCCGTTCCTCCTCT 61.355 63.158 0.00 0.00 0.00 3.69
895 908 1.999071 CTGCTCCGTTCCTCCTCTCG 61.999 65.000 0.00 0.00 0.00 4.04
1316 1332 0.602372 GGGAGGAATCATCAGCGCTC 60.602 60.000 7.13 0.00 0.00 5.03
1401 1417 4.256920 AGACAACCATAGTCAACTCATGC 58.743 43.478 0.00 0.00 38.46 4.06
1487 1504 8.883731 TGATTGAGACGGAAATCTAATTCTTTC 58.116 33.333 0.00 0.00 34.52 2.62
1514 1531 6.261118 CAGTGACCTTTTCTTTTCTTCAGTG 58.739 40.000 0.00 0.00 0.00 3.66
1517 1534 6.317893 GTGACCTTTTCTTTTCTTCAGTGGTA 59.682 38.462 0.00 0.00 0.00 3.25
1527 1544 9.035890 TCTTTTCTTCAGTGGTATGAGAGAATA 57.964 33.333 0.00 0.00 32.02 1.75
1714 1732 0.544697 ATGATACCCCGGTTGTCACC 59.455 55.000 0.00 0.00 40.16 4.02
1764 1782 9.790344 AACTATGATGAAAGAATTAGAGATGGG 57.210 33.333 0.00 0.00 0.00 4.00
2052 2070 2.629051 GTCACTATGCAGGTAACCACC 58.371 52.381 0.00 0.00 46.19 4.61
2266 2284 7.970384 TCAGCGAAATCTTTTTATTACGTGAT 58.030 30.769 0.00 0.00 0.00 3.06
2313 2331 5.128335 AGAATTCTTGCCTGAAAATGGGATC 59.872 40.000 0.88 0.00 0.00 3.36
2334 2352 3.259876 TCGGAATTGTAACTGCTAGGTGT 59.740 43.478 0.00 0.00 0.00 4.16
2504 2522 4.903045 TTTCCCTCGTCTTGTAAGGATT 57.097 40.909 0.00 0.00 31.44 3.01
2741 2759 6.465439 AGTTAGCCAAGCCCATATTTTAAC 57.535 37.500 0.00 0.00 0.00 2.01
2746 2764 4.754322 CCAAGCCCATATTTTAACACCAC 58.246 43.478 0.00 0.00 0.00 4.16
2988 3006 5.527582 CCGAGGTCTCTATTTATTTGTTGGG 59.472 44.000 0.00 0.00 0.00 4.12
3023 3042 5.240891 TCCTGACTTTGTATTGCTCAAGAG 58.759 41.667 0.00 0.00 0.00 2.85
3079 3098 5.551760 ATCAGTGCCACTAAAATTCTTCG 57.448 39.130 0.00 0.00 0.00 3.79
3195 3214 4.706962 AGTGATAGCATGCATATCGGAGTA 59.293 41.667 21.98 0.00 33.20 2.59
3421 3442 2.620115 CCAATTATCTCTTGGCATGCGT 59.380 45.455 12.44 0.00 36.98 5.24
3789 5781 1.402787 AACCTGCCAAACTGACAAGG 58.597 50.000 0.00 0.00 0.00 3.61
3794 5786 1.251251 GCCAAACTGACAAGGCATCT 58.749 50.000 0.00 0.00 46.26 2.90
3830 5822 8.926092 TGCTGAGATTAGTAGTATGTATGAGT 57.074 34.615 0.00 0.00 0.00 3.41
3910 5902 2.895680 GAGCCTGTCATCGCTCCA 59.104 61.111 9.83 0.00 44.70 3.86
3990 5982 1.897802 AGGTAACCACGGAACTACAGG 59.102 52.381 0.00 0.00 37.17 4.00
4006 6042 4.391869 GGGAAAACTCCCGACCAC 57.608 61.111 0.00 0.00 40.59 4.16
4151 6187 1.476471 CCATGGCTTGGTGAGGAGATC 60.476 57.143 11.13 0.00 40.99 2.75
4200 6236 2.571653 AGCATAGTGCCTGGTCTAAACA 59.428 45.455 0.00 0.00 46.52 2.83
4723 6759 1.937278 CAACCACATTTGCAGCAACA 58.063 45.000 7.54 0.00 0.00 3.33
4724 6760 1.862201 CAACCACATTTGCAGCAACAG 59.138 47.619 7.54 5.87 0.00 3.16
4725 6761 0.249573 ACCACATTTGCAGCAACAGC 60.250 50.000 7.54 0.00 0.00 4.40
4726 6762 0.032952 CCACATTTGCAGCAACAGCT 59.967 50.000 7.54 0.00 39.75 4.24
4727 6763 1.270274 CCACATTTGCAGCAACAGCTA 59.730 47.619 7.54 0.00 36.70 3.32
4728 6764 2.322161 CACATTTGCAGCAACAGCTAC 58.678 47.619 7.54 0.00 36.70 3.58
4729 6765 1.955778 ACATTTGCAGCAACAGCTACA 59.044 42.857 7.54 0.00 36.70 2.74
4730 6766 2.361757 ACATTTGCAGCAACAGCTACAA 59.638 40.909 7.54 0.00 39.28 2.41
4823 6874 2.153645 GTTCATGTGTCCAGTGATGCA 58.846 47.619 0.00 0.00 0.00 3.96
5140 7191 2.019984 GGGTGCTAGCTCTTTGAATGG 58.980 52.381 17.23 0.00 0.00 3.16
5142 7193 2.356125 GGTGCTAGCTCTTTGAATGGGA 60.356 50.000 17.23 0.00 0.00 4.37
5342 7399 5.639931 GGAAATGAAGTCTTACCAGAGTGTC 59.360 44.000 0.00 0.00 32.50 3.67
5358 7415 4.460382 AGAGTGTCAAGCCAACAATAATGG 59.540 41.667 0.00 0.00 41.08 3.16
5580 7637 7.751732 TGAGATTTCAGATCCAACAAATAACG 58.248 34.615 0.00 0.00 0.00 3.18
5640 7697 3.018856 CCACTTAATGCAGATGCCTTGA 58.981 45.455 1.72 0.00 41.18 3.02
5645 7702 0.750850 ATGCAGATGCCTTGATTGCC 59.249 50.000 1.72 0.00 41.18 4.52
5859 7916 1.452651 CCGGCTCCTGCACATCAAT 60.453 57.895 0.00 0.00 41.91 2.57
5886 7943 3.560896 GCGAACTTACACCAAGGTTTGTA 59.439 43.478 0.00 0.00 38.70 2.41
5887 7944 4.214758 GCGAACTTACACCAAGGTTTGTAT 59.785 41.667 0.00 0.00 38.70 2.29
5888 7945 5.409214 GCGAACTTACACCAAGGTTTGTATA 59.591 40.000 0.00 0.00 38.70 1.47
5889 7946 6.073112 GCGAACTTACACCAAGGTTTGTATAA 60.073 38.462 0.00 0.00 38.70 0.98
5890 7947 7.520292 GCGAACTTACACCAAGGTTTGTATAAA 60.520 37.037 0.00 0.00 38.70 1.40
5891 7948 8.344098 CGAACTTACACCAAGGTTTGTATAAAA 58.656 33.333 0.00 0.00 38.70 1.52
6021 8078 6.764877 AAAAGTCACATAGTCTGTTACACG 57.235 37.500 0.00 0.00 34.93 4.49
6037 8094 2.091541 ACACGATAGCCACCCAAATTG 58.908 47.619 0.00 0.00 42.67 2.32
6061 8118 4.566488 GGTCATAAATCCCCTGGCTATCAG 60.566 50.000 0.00 0.00 43.00 2.90
6075 8132 1.969208 CTATCAGCTCCAGCCTCATGA 59.031 52.381 0.00 0.00 43.38 3.07
6097 8154 1.000052 GCCCGTAGTCATAGGCTCTTC 60.000 57.143 0.00 0.00 42.34 2.87
6098 8155 2.588620 CCCGTAGTCATAGGCTCTTCT 58.411 52.381 0.00 0.00 0.00 2.85
6121 8178 4.563061 ACACCACAGGAATACTTCGTTAC 58.437 43.478 0.00 0.00 0.00 2.50
6133 8190 9.362539 GGAATACTTCGTTACAGATAAGAAACA 57.637 33.333 0.00 0.00 0.00 2.83
6238 8379 2.231964 TCCTTGCAAAATGATGACCTGC 59.768 45.455 0.00 0.00 0.00 4.85
6265 8406 7.680442 TTTTATATGCTCACTTTACTGTGCA 57.320 32.000 0.00 0.00 42.96 4.57
6293 8434 8.621286 AGAAAGTCAATGTTCAAAGTCGTTAAT 58.379 29.630 0.00 0.00 0.00 1.40
6361 8502 8.342634 TGTGTTTCTACTTTCTAGCATTGTTTC 58.657 33.333 0.00 0.00 0.00 2.78
6363 8504 8.559536 TGTTTCTACTTTCTAGCATTGTTTCTG 58.440 33.333 0.00 0.00 0.00 3.02
6404 8545 4.769488 TGTCTCACTCTTGCAGTAAGATCT 59.231 41.667 0.87 0.00 44.12 2.75
6462 8603 3.643792 GTGGTGCTGTAGGGAGATCTATT 59.356 47.826 0.00 0.00 0.00 1.73
6705 8846 5.437289 TCTGGAAATGTGCAAAACTACTG 57.563 39.130 0.00 0.00 0.00 2.74
6780 8921 5.014228 GGGGAATGGGTAGCTATCAACTAAT 59.986 44.000 6.30 0.00 0.00 1.73
6856 8999 9.419297 TGTGACAGTATAACTTCAACTGAATAC 57.581 33.333 8.57 5.22 42.59 1.89
6870 9013 7.436118 TCAACTGAATACGTACCTGTAAAAGT 58.564 34.615 0.00 0.00 0.00 2.66
6926 9069 0.039437 CTGCTGCACTTTGGCTTCAG 60.039 55.000 0.00 0.00 34.04 3.02
6987 9131 4.973168 TGAGCCACTCTGATAAACAAAGT 58.027 39.130 0.00 0.00 28.80 2.66
6993 9137 6.349280 GCCACTCTGATAAACAAAGTATTGCA 60.349 38.462 0.00 0.00 40.34 4.08
7159 9303 7.041721 TGGTAACTGAGATCACATGTATGAAC 58.958 38.462 0.00 0.00 37.61 3.18
7177 9321 4.699637 TGAACGACCAATGTAGTTTCTGT 58.300 39.130 0.00 0.00 39.93 3.41
7178 9322 4.509970 TGAACGACCAATGTAGTTTCTGTG 59.490 41.667 0.00 0.00 39.93 3.66
7179 9323 2.806244 ACGACCAATGTAGTTTCTGTGC 59.194 45.455 0.00 0.00 0.00 4.57
7180 9324 3.067106 CGACCAATGTAGTTTCTGTGCT 58.933 45.455 0.00 0.00 0.00 4.40
7181 9325 3.120546 CGACCAATGTAGTTTCTGTGCTG 60.121 47.826 0.00 0.00 0.00 4.41
7182 9326 2.554032 ACCAATGTAGTTTCTGTGCTGC 59.446 45.455 0.00 0.00 0.00 5.25
7206 9352 3.306780 GGACCGACATTTTTCTCCTCTCA 60.307 47.826 0.00 0.00 0.00 3.27
7209 9355 4.202367 ACCGACATTTTTCTCCTCTCAGTT 60.202 41.667 0.00 0.00 0.00 3.16
7238 9384 5.820404 ATGAATACAGATGCTGAGGATGA 57.180 39.130 0.00 0.00 35.18 2.92
7335 9481 8.556213 TTTGTTTCTGTTGTAGTCTTGTAGTT 57.444 30.769 0.00 0.00 0.00 2.24
7405 9551 4.631131 TGCTGCCATGTAGTATATGTCAC 58.369 43.478 6.20 0.00 0.00 3.67
7629 9777 2.774439 GTGCTCAACACGGACAAATT 57.226 45.000 0.00 0.00 40.07 1.82
7642 9790 0.535335 ACAAATTCGCGAGGGCTCTA 59.465 50.000 9.59 0.00 36.88 2.43
7656 9804 1.696884 GGCTCTAAGGCTAAGATGGCT 59.303 52.381 0.00 0.00 45.04 4.75
7680 9828 2.029623 GTATGAGTGGAAGGAGCCGTA 58.970 52.381 0.00 0.00 0.00 4.02
7701 9849 0.768622 AAAATGTGGGTCGGTCTGGA 59.231 50.000 0.00 0.00 0.00 3.86
7710 9858 0.978907 GTCGGTCTGGAAAACCCCTA 59.021 55.000 0.00 0.00 32.89 3.53
7716 9864 3.202151 GGTCTGGAAAACCCCTATGATGA 59.798 47.826 0.00 0.00 0.00 2.92
7741 9889 6.487331 ACAAGGATTACGATCTCTTCTACGAT 59.513 38.462 0.00 0.00 32.66 3.73
7745 9893 6.802834 GGATTACGATCTCTTCTACGATTTCC 59.197 42.308 0.00 0.00 32.66 3.13
7746 9894 6.939132 TTACGATCTCTTCTACGATTTCCT 57.061 37.500 0.00 0.00 0.00 3.36
7785 9933 3.659850 GTGCCCACACACCTTTTTC 57.340 52.632 0.00 0.00 46.61 2.29
7786 9934 0.820871 GTGCCCACACACCTTTTTCA 59.179 50.000 0.00 0.00 46.61 2.69
7792 9940 1.670811 CACACACCTTTTTCAGACGCT 59.329 47.619 0.00 0.00 0.00 5.07
7809 9957 4.738998 TCCATGGGTGCAAGGCCG 62.739 66.667 13.02 0.00 0.00 6.13
7926 10074 6.581171 AATCAAATTGACCAACTCCTTCTC 57.419 37.500 0.00 0.00 0.00 2.87
7927 10075 4.065088 TCAAATTGACCAACTCCTTCTCG 58.935 43.478 0.00 0.00 0.00 4.04
7939 10087 3.196685 ACTCCTTCTCGCTAGCTCATTTT 59.803 43.478 13.93 0.00 0.00 1.82
7941 10089 2.869192 CCTTCTCGCTAGCTCATTTTCC 59.131 50.000 13.93 0.00 0.00 3.13
7955 10103 3.845398 TCATTTTCCCCAATTCCTGCAAT 59.155 39.130 0.00 0.00 0.00 3.56
7961 10109 2.086094 CCCAATTCCTGCAATTTTGGC 58.914 47.619 10.40 0.00 36.37 4.52
8015 10163 1.627864 TGAGGACGAGATTGTGTGGA 58.372 50.000 0.00 0.00 0.00 4.02
8016 10164 1.967779 TGAGGACGAGATTGTGTGGAA 59.032 47.619 0.00 0.00 0.00 3.53
8074 10222 2.405892 ATGCAACGTGAGCAAGAAAC 57.594 45.000 18.20 0.00 46.27 2.78
8120 10269 0.243636 GGTTCACCATTCGGCTTTGG 59.756 55.000 0.00 0.00 39.02 3.28
8137 10286 3.969466 TTGGGGCATGATCAAGGAATA 57.031 42.857 0.00 0.00 0.00 1.75
8138 10287 3.513909 TGGGGCATGATCAAGGAATAG 57.486 47.619 0.00 0.00 0.00 1.73
8139 10288 2.165998 GGGGCATGATCAAGGAATAGC 58.834 52.381 0.00 0.00 0.00 2.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.740868 TATGCTCAGTTGGCTGCGAC 60.741 55.000 0.00 0.00 42.29 5.19
1 2 0.178767 ATATGCTCAGTTGGCTGCGA 59.821 50.000 0.00 0.00 42.29 5.10
2 3 0.306840 CATATGCTCAGTTGGCTGCG 59.693 55.000 0.00 0.00 42.29 5.18
3 4 1.065102 CACATATGCTCAGTTGGCTGC 59.935 52.381 1.58 0.00 42.29 5.25
4 5 2.096980 CACACATATGCTCAGTTGGCTG 59.903 50.000 1.58 0.00 43.87 4.85
34 35 6.985013 TCGTTCGTTAGCTTGTAATGTAATG 58.015 36.000 0.00 0.00 0.00 1.90
36 37 5.574055 CCTCGTTCGTTAGCTTGTAATGTAA 59.426 40.000 0.00 0.00 0.00 2.41
49 50 3.670359 CGATGTGTAACCCTCGTTCGTTA 60.670 47.826 0.00 0.00 36.58 3.18
64 65 4.639310 CCAACTACCTAGTAGTCGATGTGT 59.361 45.833 7.81 0.00 46.96 3.72
88 89 1.134560 GCAACTAGTCTACTGTCCCGG 59.865 57.143 0.00 0.00 0.00 5.73
191 192 6.200854 TGCAATTTCAGTACTATATCGTGCAG 59.799 38.462 12.59 0.00 33.53 4.41
208 209 9.893305 AACTTTAGTACTGTATTGTGCAATTTC 57.107 29.630 5.39 0.00 32.50 2.17
211 212 7.040755 TGCAACTTTAGTACTGTATTGTGCAAT 60.041 33.333 5.39 2.83 34.93 3.56
300 301 3.245797 TCTTGCGACGAGATCTTTGAAG 58.754 45.455 0.00 0.00 0.00 3.02
522 528 0.810648 GCATCATCTGGGCAAAACGA 59.189 50.000 0.00 0.00 0.00 3.85
550 556 8.462016 CGATAGAAAATTCCCAAATTCTTCACT 58.538 33.333 0.00 0.00 33.69 3.41
552 558 7.257722 GCGATAGAAAATTCCCAAATTCTTCA 58.742 34.615 0.00 0.00 33.69 3.02
575 581 0.173255 AAATGAAAATCTGCGGGGCG 59.827 50.000 0.00 0.00 0.00 6.13
578 584 2.919666 ACGAAATGAAAATCTGCGGG 57.080 45.000 0.00 0.00 0.00 6.13
643 649 0.091344 CGTGCGTACAAGCTTTCGAG 59.909 55.000 16.20 0.42 38.13 4.04
1166 1182 0.033228 GATCAGCAGGAGTCATCGGG 59.967 60.000 0.00 0.00 0.00 5.14
1285 1301 2.992114 CCTCCCTCCCCGCGATAG 60.992 72.222 8.23 0.83 0.00 2.08
1487 1504 5.590259 TGAAGAAAAGAAAAGGTCACTGGAG 59.410 40.000 0.00 0.00 0.00 3.86
1541 1558 5.010012 CCCAAATTTCCCATCTTCTATTCGG 59.990 44.000 0.00 0.00 0.00 4.30
1555 1572 3.771479 AGAAATCCAGCTCCCAAATTTCC 59.229 43.478 10.08 0.00 37.14 3.13
1637 1655 2.507407 TCAAGTATGAACCAAGCCCC 57.493 50.000 0.00 0.00 30.99 5.80
1714 1732 1.526887 GTCCAACATGACAGTGACACG 59.473 52.381 0.00 0.00 35.29 4.49
1764 1782 0.999406 TCGCGCTAAATCAGAAGCAC 59.001 50.000 5.56 0.00 38.70 4.40
1809 1827 4.693283 TCTCAACTGAACTTGTACACAGG 58.307 43.478 13.84 2.92 35.08 4.00
2052 2070 2.097466 GTGGTGTCTGTTCAAAGTGGTG 59.903 50.000 0.00 0.00 0.00 4.17
2054 2072 2.643551 AGTGGTGTCTGTTCAAAGTGG 58.356 47.619 0.00 0.00 0.00 4.00
2266 2284 0.970640 ACCATGGCAGTACACGTACA 59.029 50.000 13.04 0.00 38.48 2.90
2313 2331 3.596214 ACACCTAGCAGTTACAATTCCG 58.404 45.455 0.00 0.00 0.00 4.30
2334 2352 5.482006 CAATATCTCCTTGTCACACTGTGA 58.518 41.667 15.86 7.84 40.50 3.58
2741 2759 1.199097 GGCCAAAACAGATACGTGGTG 59.801 52.381 0.00 0.00 0.00 4.17
2746 2764 3.596214 ACTGTAGGCCAAAACAGATACG 58.404 45.455 29.16 11.74 44.79 3.06
2826 2844 8.223177 AGAGGAAGAGAAGCAATCATAAAATG 57.777 34.615 0.00 0.00 0.00 2.32
3079 3098 2.368439 TGCATCCCTACAATCACAAGC 58.632 47.619 0.00 0.00 0.00 4.01
3298 3319 8.983724 GCAGTCCAATTGAAACTCTAGTATATC 58.016 37.037 7.12 0.00 0.00 1.63
3421 3442 8.625651 TCTTCGGTTTCAAACATCATTCTAAAA 58.374 29.630 1.93 0.00 0.00 1.52
3682 5674 5.614308 TCCAGATCACTTATGCCAGTTATG 58.386 41.667 0.00 0.00 0.00 1.90
3789 5781 6.199937 TCTCAGCAAAAATAAAGGAGATGC 57.800 37.500 0.00 0.00 0.00 3.91
3794 5786 9.959721 ACTACTAATCTCAGCAAAAATAAAGGA 57.040 29.630 0.00 0.00 0.00 3.36
3830 5822 1.284491 TGCTTCATCCCATGCAACCTA 59.716 47.619 0.00 0.00 32.12 3.08
3910 5902 5.919348 ATGGTGTGGGATAGATGAAGAAT 57.081 39.130 0.00 0.00 0.00 2.40
3990 5982 0.318120 TACGTGGTCGGGAGTTTTCC 59.682 55.000 0.00 0.00 43.23 3.13
4151 6187 8.883954 TCTGAGTATTCATATCTTTCTTGCAG 57.116 34.615 0.00 0.00 31.68 4.41
4200 6236 8.995998 ATTCATCCACTGAAGTGACTGAGCTAT 61.996 40.741 12.05 3.11 46.71 2.97
4442 6478 4.551702 AATATTTCCCAGTTGGTTTGGC 57.448 40.909 0.00 0.00 34.26 4.52
4725 6761 3.376859 TGTTGAGGTTGTTGCTGTTGTAG 59.623 43.478 0.00 0.00 0.00 2.74
4726 6762 3.348119 TGTTGAGGTTGTTGCTGTTGTA 58.652 40.909 0.00 0.00 0.00 2.41
4727 6763 2.166829 TGTTGAGGTTGTTGCTGTTGT 58.833 42.857 0.00 0.00 0.00 3.32
4728 6764 2.937469 TGTTGAGGTTGTTGCTGTTG 57.063 45.000 0.00 0.00 0.00 3.33
4729 6765 3.023119 TGATGTTGAGGTTGTTGCTGTT 58.977 40.909 0.00 0.00 0.00 3.16
4730 6766 2.653726 TGATGTTGAGGTTGTTGCTGT 58.346 42.857 0.00 0.00 0.00 4.40
4823 6874 9.671279 TGATCAGATAGTTGTGTATTCATGTTT 57.329 29.630 0.00 0.00 0.00 2.83
5012 7063 3.266636 CGTTGCATACTGGATGGTGTTA 58.733 45.455 1.35 0.00 35.91 2.41
5142 7193 0.681733 ACTGACTGCATTCGACCAGT 59.318 50.000 11.15 11.15 44.43 4.00
5358 7415 4.082026 CCCTTGTTCAATCATCTTGGGAAC 60.082 45.833 0.00 0.00 38.59 3.62
5580 7637 5.975693 TCAATGTTCACCCCAAATAGAAC 57.024 39.130 0.00 0.00 40.45 3.01
5810 7867 8.766994 TGGAATTTCTATTTAAGAATGAGGGG 57.233 34.615 0.00 0.00 43.75 4.79
5859 7916 1.535028 CTTGGTGTAAGTTCGCATGCA 59.465 47.619 19.57 1.73 0.00 3.96
5886 7943 8.421002 ACACACTGGAGCAAAAGTTATTTTTAT 58.579 29.630 0.00 0.00 36.87 1.40
5887 7944 7.777095 ACACACTGGAGCAAAAGTTATTTTTA 58.223 30.769 0.00 0.00 36.87 1.52
5888 7945 6.639563 ACACACTGGAGCAAAAGTTATTTTT 58.360 32.000 0.00 0.00 39.55 1.94
5889 7946 6.127479 TGACACACTGGAGCAAAAGTTATTTT 60.127 34.615 0.00 0.00 39.22 1.82
5890 7947 5.359576 TGACACACTGGAGCAAAAGTTATTT 59.640 36.000 0.00 0.00 0.00 1.40
5891 7948 4.887071 TGACACACTGGAGCAAAAGTTATT 59.113 37.500 0.00 0.00 0.00 1.40
5892 7949 4.460263 TGACACACTGGAGCAAAAGTTAT 58.540 39.130 0.00 0.00 0.00 1.89
5893 7950 3.879998 TGACACACTGGAGCAAAAGTTA 58.120 40.909 0.00 0.00 0.00 2.24
5894 7951 2.722094 TGACACACTGGAGCAAAAGTT 58.278 42.857 0.00 0.00 0.00 2.66
5895 7952 2.418368 TGACACACTGGAGCAAAAGT 57.582 45.000 0.00 0.00 0.00 2.66
5896 7953 3.996150 AATGACACACTGGAGCAAAAG 57.004 42.857 0.00 0.00 0.00 2.27
6037 8094 0.853530 AGCCAGGGGATTTATGACCC 59.146 55.000 0.00 0.00 45.06 4.46
6061 8118 2.894387 GCGTCATGAGGCTGGAGC 60.894 66.667 28.47 8.08 38.98 4.70
6075 8132 3.126528 GCCTATGACTACGGGCGT 58.873 61.111 0.00 0.00 35.08 5.68
6097 8154 4.451629 ACGAAGTATTCCTGTGGTGTAG 57.548 45.455 0.00 0.00 43.81 2.74
6098 8155 4.877378 AACGAAGTATTCCTGTGGTGTA 57.123 40.909 0.00 0.00 45.00 2.90
6198 8339 9.295825 TGCAAGGAAATTAGTCAGAGAAAATTA 57.704 29.630 0.00 0.00 0.00 1.40
6238 8379 9.013490 GCACAGTAAAGTGAGCATATAAAATTG 57.987 33.333 2.81 0.00 42.05 2.32
6265 8406 5.354234 ACGACTTTGAACATTGACTTTCTGT 59.646 36.000 0.00 0.00 0.00 3.41
6268 8409 8.682016 CATTAACGACTTTGAACATTGACTTTC 58.318 33.333 0.00 0.00 0.00 2.62
6293 8434 7.620094 AGAGCCTAAGGATAAACTCTTCTAACA 59.380 37.037 0.00 0.00 30.52 2.41
6361 8502 3.987868 ACAGTGCACTCGTATGTAAACAG 59.012 43.478 18.64 3.22 0.00 3.16
6363 8504 4.235360 AGACAGTGCACTCGTATGTAAAC 58.765 43.478 18.64 5.35 0.00 2.01
6404 8545 6.953101 TGCATATAGTACTTTGGTCAGGAAA 58.047 36.000 0.00 0.00 0.00 3.13
6462 8603 3.008594 ACCCTGAATAACGGTTCATGTCA 59.991 43.478 0.00 0.00 37.47 3.58
6705 8846 3.067320 GCCACCCATCAGCTTTATCTTTC 59.933 47.826 0.00 0.00 0.00 2.62
6780 8921 2.363306 AGCAACCAGTGAATGAACCA 57.637 45.000 0.00 0.00 0.00 3.67
6926 9069 8.470002 AGAGAGTAAATGAATGGGCATTAAAAC 58.530 33.333 0.00 0.00 37.50 2.43
6987 9131 6.422333 TCAGAAAATCCCTACACATGCAATA 58.578 36.000 0.00 0.00 0.00 1.90
6993 9137 4.702131 GCAGTTCAGAAAATCCCTACACAT 59.298 41.667 0.00 0.00 0.00 3.21
7159 9303 3.067106 AGCACAGAAACTACATTGGTCG 58.933 45.455 0.00 0.00 0.00 4.79
7177 9321 3.545124 AAATGTCGGTCCCGCAGCA 62.545 57.895 0.00 0.69 39.59 4.41
7178 9322 1.862602 AAAAATGTCGGTCCCGCAGC 61.863 55.000 0.00 0.00 39.59 5.25
7179 9323 0.168128 GAAAAATGTCGGTCCCGCAG 59.832 55.000 0.00 0.00 39.59 5.18
7180 9324 0.250553 AGAAAAATGTCGGTCCCGCA 60.251 50.000 0.00 3.17 39.59 5.69
7181 9325 0.446616 GAGAAAAATGTCGGTCCCGC 59.553 55.000 0.00 0.00 39.59 6.13
7182 9326 1.084289 GGAGAAAAATGTCGGTCCCG 58.916 55.000 0.00 0.00 41.35 5.14
7206 9352 8.918116 TCAGCATCTGTATTCATAAGACTAACT 58.082 33.333 0.00 0.00 32.61 2.24
7209 9355 7.725844 TCCTCAGCATCTGTATTCATAAGACTA 59.274 37.037 0.00 0.00 32.61 2.59
7238 9384 5.812642 CAGAGCCTAAATTATCGTCAACTGT 59.187 40.000 0.00 0.00 0.00 3.55
7315 9461 7.342769 TGAGAACTACAAGACTACAACAGAA 57.657 36.000 0.00 0.00 0.00 3.02
7335 9481 2.224018 GCAAGGCCAACAAAACATGAGA 60.224 45.455 5.01 0.00 0.00 3.27
7627 9775 1.742768 CCTTAGAGCCCTCGCGAAT 59.257 57.895 11.33 0.00 41.18 3.34
7629 9777 2.619941 TAGCCTTAGAGCCCTCGCGA 62.620 60.000 9.26 9.26 41.18 5.87
7642 9790 2.907458 ACCAAAGCCATCTTAGCCTT 57.093 45.000 0.00 0.00 31.02 4.35
7656 9804 2.026262 GGCTCCTTCCACTCATACCAAA 60.026 50.000 0.00 0.00 0.00 3.28
7662 9810 1.568504 TTACGGCTCCTTCCACTCAT 58.431 50.000 0.00 0.00 0.00 2.90
7701 9849 4.946160 TCCTTGTCATCATAGGGGTTTT 57.054 40.909 0.00 0.00 0.00 2.43
7710 9858 6.662865 AGAGATCGTAATCCTTGTCATCAT 57.337 37.500 0.00 0.00 31.78 2.45
7716 9864 5.821470 TCGTAGAAGAGATCGTAATCCTTGT 59.179 40.000 0.00 0.00 31.78 3.16
7741 9889 2.562298 GCCAACATTGATGGTCAGGAAA 59.438 45.455 13.78 0.00 40.23 3.13
7745 9893 3.517602 CATTGCCAACATTGATGGTCAG 58.482 45.455 13.78 0.04 40.23 3.51
7746 9894 2.234168 CCATTGCCAACATTGATGGTCA 59.766 45.455 13.78 9.61 40.23 4.02
7773 9921 1.940613 GAGCGTCTGAAAAAGGTGTGT 59.059 47.619 0.00 0.00 0.00 3.72
7783 9931 1.296392 CACCCATGGAGCGTCTGAA 59.704 57.895 15.22 0.00 0.00 3.02
7785 9933 2.821366 GCACCCATGGAGCGTCTG 60.821 66.667 15.22 0.00 28.62 3.51
7786 9934 2.809861 CTTGCACCCATGGAGCGTCT 62.810 60.000 15.22 0.00 42.08 4.18
7792 9940 4.738998 CGGCCTTGCACCCATGGA 62.739 66.667 15.22 0.00 38.26 3.41
7809 9957 2.092323 GAGCAATGTCCCTGGGTTTAC 58.908 52.381 13.56 4.21 0.00 2.01
7878 10026 4.030913 AGATATCCAAGAACCGTCCTTCA 58.969 43.478 0.00 0.00 0.00 3.02
7926 10074 1.750193 TTGGGGAAAATGAGCTAGCG 58.250 50.000 9.55 0.00 0.00 4.26
7927 10075 3.068732 GGAATTGGGGAAAATGAGCTAGC 59.931 47.826 6.62 6.62 0.00 3.42
7939 10087 2.305343 CCAAAATTGCAGGAATTGGGGA 59.695 45.455 10.46 0.00 37.47 4.81
7941 10089 2.086094 GCCAAAATTGCAGGAATTGGG 58.914 47.619 18.40 11.82 40.65 4.12
7961 10109 3.133003 AGATGGAAGTCGTGAATGGTAGG 59.867 47.826 0.00 0.00 0.00 3.18
8015 10163 0.034574 TGCCCACTGACAGTGTGTTT 60.035 50.000 29.09 0.00 44.50 2.83
8016 10164 0.034574 TTGCCCACTGACAGTGTGTT 60.035 50.000 29.09 0.00 44.50 3.32
8055 10203 1.334059 CGTTTCTTGCTCACGTTGCAT 60.334 47.619 12.87 0.00 40.34 3.96
8074 10222 7.090173 ACATTTGAATTAAAGGTGGTCAATCG 58.910 34.615 0.00 0.00 41.31 3.34


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

AutoCloner maintained by Alex Coulton.