Multiple sequence alignment - TraesCS7B01G181900

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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 TraesCS7B01G181900 chr7B 100.000 9539 0 0 1 9539 278938862 278929324 0.000000e+00 17616.0
1 TraesCS7B01G181900 chr7A 95.711 9092 250 48 536 9539 380184262 380175223 0.000000e+00 14501.0
2 TraesCS7B01G181900 chr7A 100.000 28 0 0 3952 3979 380180940 380180913 1.700000e-02 52.8
3 TraesCS7B01G181900 chr7D 96.998 6530 132 17 2319 8815 339780273 339786771 0.000000e+00 10914.0
4 TraesCS7B01G181900 chr7D 97.104 1243 26 6 1086 2326 339778963 339780197 0.000000e+00 2087.0
5 TraesCS7B01G181900 chr7D 90.734 1090 79 11 32 1117 339777889 339778960 0.000000e+00 1434.0
6 TraesCS7B01G181900 chr7D 96.027 730 26 2 8813 9539 339786929 339787658 0.000000e+00 1184.0
7 TraesCS7B01G181900 chr7D 76.726 391 74 14 255 636 92464607 92464989 1.620000e-47 202.0
8 TraesCS7B01G181900 chr1D 81.818 374 56 8 276 644 312717055 312716689 4.330000e-78 303.0
9 TraesCS7B01G181900 chr1B 79.827 347 62 7 291 632 235004720 235004377 7.400000e-61 246.0
10 TraesCS7B01G181900 chrUn 79.739 306 54 6 233 534 57197578 57197879 2.090000e-51 215.0
11 TraesCS7B01G181900 chrUn 80.319 188 33 4 461 645 249705850 249706036 1.290000e-28 139.0
12 TraesCS7B01G181900 chrUn 80.682 176 27 7 465 636 6001105 6001277 7.770000e-26 130.0
13 TraesCS7B01G181900 chr3A 78.979 333 50 12 256 584 528865995 528866311 9.710000e-50 209.0
14 TraesCS7B01G181900 chr3A 78.443 334 52 12 255 584 528858205 528858522 5.840000e-47 200.0
15 TraesCS7B01G181900 chr3A 80.319 188 33 4 461 645 322904198 322904012 1.290000e-28 139.0
16 TraesCS7B01G181900 chr5B 78.528 326 55 13 262 580 702630728 702630411 5.840000e-47 200.0
17 TraesCS7B01G181900 chr5B 78.505 321 54 13 262 575 702762960 702762648 7.560000e-46 196.0
18 TraesCS7B01G181900 chr1A 82.533 229 30 1 4241 4469 171460328 171460110 9.780000e-45 193.0
19 TraesCS7B01G181900 chr4D 76.203 374 61 23 274 636 230183493 230183849 1.270000e-38 172.0
20 TraesCS7B01G181900 chr6D 84.967 153 16 7 497 645 254214119 254213970 2.150000e-31 148.0


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 TraesCS7B01G181900 chr7B 278929324 278938862 9538 True 17616.00 17616 100.00000 1 9539 1 chr7B.!!$R1 9538
1 TraesCS7B01G181900 chr7A 380175223 380184262 9039 True 7276.90 14501 97.85550 536 9539 2 chr7A.!!$R1 9003
2 TraesCS7B01G181900 chr7D 339777889 339787658 9769 False 3904.75 10914 95.21575 32 9539 4 chr7D.!!$F2 9507

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
477 479 0.106149 GTGGTTGGTCTCAGAACGGT 59.894 55.000 0.00 0.00 0.00 4.83 F
507 509 0.466963 AACGGGGAGAAACGACAACT 59.533 50.000 0.00 0.00 0.00 3.16 F
659 662 0.535553 TACAAAGGTTGTGGACGGGC 60.536 55.000 3.90 0.00 45.03 6.13 F
878 882 1.306141 ATCGAGGCTGAGGGGTTGA 60.306 57.895 0.00 0.00 0.00 3.18 F
1878 1951 1.386412 CGAAACATTTGGATGCGTTGC 59.614 47.619 0.00 0.00 36.72 4.17 F
3164 3324 0.823356 AGGCAAATGCTTGACGTGGT 60.823 50.000 5.25 0.00 46.15 4.16 F
4247 4419 0.106619 ATCTCTAGGAGCCGGACGTT 60.107 55.000 5.05 0.00 0.00 3.99 F
4540 4712 0.179018 GGGCCCGTGCTCTAATCATT 60.179 55.000 5.69 0.00 34.08 2.57 F
5838 6011 0.179004 ATGCGTCCAACTTTGTCCCA 60.179 50.000 0.00 0.00 0.00 4.37 F
6005 6178 1.270147 GGACTGGTGTACGCTTGTCTT 60.270 52.381 21.82 0.00 0.00 3.01 F
7600 7780 0.764369 CCATTCCCATCCTCCGGAGA 60.764 60.000 33.39 18.69 34.05 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1868 1941 1.063649 CATGAGCAGCAACGCATCC 59.936 57.895 0.00 0.0 0.00 3.51 R
2125 2198 2.369860 TGGCAACCAAAATATGCAACCA 59.630 40.909 0.00 0.0 41.80 3.67 R
2334 2493 5.073144 TCCAATCCAGTAATCCCCATAGTTC 59.927 44.000 0.00 0.0 0.00 3.01 R
2833 2992 0.973632 ATAGTCGTTGTGGCAGGACA 59.026 50.000 9.60 0.0 31.93 4.02 R
3305 3465 0.621082 GGCTCCTAGGTTTGGAAGCT 59.379 55.000 15.35 0.0 42.74 3.74 R
4655 4827 0.112218 AGCAAATGTAGCACCCACCA 59.888 50.000 0.00 0.0 0.00 4.17 R
5620 5793 1.016130 CAAGCGTGCTCATCGAAGGT 61.016 55.000 0.00 0.0 0.00 3.50 R
6404 6580 3.962063 TCCCTAACATCGTATGCAGGTAA 59.038 43.478 0.00 0.0 35.22 2.85 R
7600 7780 2.179427 GGGGGCAAAGCTTCTAAATGT 58.821 47.619 0.00 0.0 0.00 2.71 R
7649 7829 3.519913 ACTACCTCCTTGTCCTTGGAATC 59.480 47.826 0.00 0.0 31.23 2.52 R
9510 9883 0.250901 AGCTGTTGACGGATGCCTTT 60.251 50.000 0.00 0.0 0.00 3.11 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
17 18 4.241555 CGGAATCCAGGAGGGCGG 62.242 72.222 0.00 0.00 36.21 6.13
18 19 4.570874 GGAATCCAGGAGGGCGGC 62.571 72.222 0.00 0.00 36.21 6.53
19 20 4.918201 GAATCCAGGAGGGCGGCG 62.918 72.222 0.51 0.51 36.21 6.46
49 50 3.521937 CAGGTAGGTGGAATAGGGTTTCA 59.478 47.826 0.00 0.00 0.00 2.69
88 89 4.202151 GGCCTTCCATTTATAGCAGGTTTG 60.202 45.833 0.00 0.00 0.00 2.93
115 116 2.291024 GGTTTGGGTTTTGGGGTGTTTT 60.291 45.455 0.00 0.00 0.00 2.43
124 125 2.840572 GGGTGTTTTGGGGCCGTT 60.841 61.111 0.00 0.00 0.00 4.44
126 127 2.732016 GTGTTTTGGGGCCGTTCC 59.268 61.111 0.00 0.00 0.00 3.62
135 136 1.301009 GGGCCGTTCCATCTCGATC 60.301 63.158 0.00 0.00 36.21 3.69
136 137 1.661821 GGCCGTTCCATCTCGATCG 60.662 63.158 9.36 9.36 34.01 3.69
144 145 1.360551 CATCTCGATCGGACGGCTT 59.639 57.895 16.41 0.00 0.00 4.35
146 147 1.101635 ATCTCGATCGGACGGCTTCA 61.102 55.000 16.41 0.00 0.00 3.02
162 163 2.685897 GCTTCAGACGAGGAGTAGTGAT 59.314 50.000 0.00 0.00 0.00 3.06
176 177 3.711704 AGTAGTGATGGTGGGTTAGATGG 59.288 47.826 0.00 0.00 0.00 3.51
180 181 2.025416 TGATGGTGGGTTAGATGGGTTG 60.025 50.000 0.00 0.00 0.00 3.77
183 184 3.194620 TGGTGGGTTAGATGGGTTGTAT 58.805 45.455 0.00 0.00 0.00 2.29
187 188 5.131475 GGTGGGTTAGATGGGTTGTATAGAA 59.869 44.000 0.00 0.00 0.00 2.10
209 210 4.316823 AGTGTGGGAGGCCTCGGA 62.317 66.667 26.36 12.46 0.00 4.55
212 213 2.043248 GTGGGAGGCCTCGGACTA 60.043 66.667 26.36 8.09 30.74 2.59
233 234 7.138054 ACTAAGAATAGAGGTAATTGGGTGG 57.862 40.000 0.00 0.00 33.15 4.61
247 248 2.668550 GTGGCCCGACACAGGTTC 60.669 66.667 0.00 0.00 40.99 3.62
252 253 1.369625 GCCCGACACAGGTTCTATTG 58.630 55.000 0.00 0.00 0.00 1.90
253 254 1.066430 GCCCGACACAGGTTCTATTGA 60.066 52.381 0.00 0.00 0.00 2.57
254 255 2.614481 GCCCGACACAGGTTCTATTGAA 60.614 50.000 0.00 0.00 0.00 2.69
281 283 3.502979 TGTCCAACAATTAAACCGGCTAC 59.497 43.478 0.00 0.00 0.00 3.58
300 302 5.107065 GGCTACAATGCCGCTATAGTTTAAG 60.107 44.000 0.84 0.00 43.74 1.85
302 304 4.777463 ACAATGCCGCTATAGTTTAAGGT 58.223 39.130 0.84 0.00 0.00 3.50
308 310 3.881089 CCGCTATAGTTTAAGGTTTGGGG 59.119 47.826 0.84 0.00 0.00 4.96
331 333 0.734942 GAAACGACCTCCGAATGCGA 60.735 55.000 0.00 0.00 41.76 5.10
333 335 1.874345 AACGACCTCCGAATGCGACT 61.874 55.000 0.00 0.00 41.76 4.18
367 369 7.707893 GCAGACGGTCTACCTATAAAATAACAA 59.292 37.037 10.87 0.00 0.00 2.83
406 408 8.190784 ACTTTCAACTCATTTCGAGAATGTTTT 58.809 29.630 15.30 9.69 45.45 2.43
477 479 0.106149 GTGGTTGGTCTCAGAACGGT 59.894 55.000 0.00 0.00 0.00 4.83
506 508 0.584876 CAACGGGGAGAAACGACAAC 59.415 55.000 0.00 0.00 0.00 3.32
507 509 0.466963 AACGGGGAGAAACGACAACT 59.533 50.000 0.00 0.00 0.00 3.16
508 510 1.331214 ACGGGGAGAAACGACAACTA 58.669 50.000 0.00 0.00 0.00 2.24
509 511 1.897802 ACGGGGAGAAACGACAACTAT 59.102 47.619 0.00 0.00 0.00 2.12
510 512 2.268298 CGGGGAGAAACGACAACTATG 58.732 52.381 0.00 0.00 0.00 2.23
511 513 2.094390 CGGGGAGAAACGACAACTATGA 60.094 50.000 0.00 0.00 0.00 2.15
512 514 3.615592 CGGGGAGAAACGACAACTATGAA 60.616 47.826 0.00 0.00 0.00 2.57
513 515 3.683340 GGGGAGAAACGACAACTATGAAC 59.317 47.826 0.00 0.00 0.00 3.18
514 516 3.367025 GGGAGAAACGACAACTATGAACG 59.633 47.826 0.00 0.00 36.55 3.95
515 517 3.367025 GGAGAAACGACAACTATGAACGG 59.633 47.826 0.00 0.00 35.53 4.44
516 518 4.232221 GAGAAACGACAACTATGAACGGA 58.768 43.478 0.00 0.00 35.53 4.69
519 521 2.268298 ACGACAACTATGAACGGATGC 58.732 47.619 0.00 0.00 35.53 3.91
600 603 3.398954 ACAATTAATGCGGCTAACACG 57.601 42.857 0.00 0.00 0.00 4.49
617 620 3.417101 ACACGAAAACATGGAAGGCATA 58.583 40.909 0.00 0.00 0.00 3.14
620 623 4.096231 CACGAAAACATGGAAGGCATATGA 59.904 41.667 6.97 0.00 0.00 2.15
635 638 1.721664 TATGAAGCGTCGGTCTCGGG 61.722 60.000 0.00 0.00 36.95 5.14
659 662 0.535553 TACAAAGGTTGTGGACGGGC 60.536 55.000 3.90 0.00 45.03 6.13
687 690 3.621892 AAGTAGGCGACGACGGTGC 62.622 63.158 9.67 2.00 41.32 5.01
742 745 4.856801 GGCCGCCATGGACGATGT 62.857 66.667 24.22 0.00 42.00 3.06
800 803 6.400940 GCACAACGACATCAATAAATTTTGGG 60.401 38.462 0.00 0.00 0.00 4.12
805 808 5.357742 ACATCAATAAATTTTGGGAGGGC 57.642 39.130 0.00 0.00 0.00 5.19
868 872 3.330701 AGAAGAGAGATAGGATCGAGGCT 59.669 47.826 0.00 0.00 0.00 4.58
878 882 1.306141 ATCGAGGCTGAGGGGTTGA 60.306 57.895 0.00 0.00 0.00 3.18
903 907 3.610040 AGATTCGGAAGTGTGTGCATA 57.390 42.857 0.00 0.00 0.00 3.14
904 908 3.937814 AGATTCGGAAGTGTGTGCATAA 58.062 40.909 0.00 0.00 0.00 1.90
909 913 2.805671 CGGAAGTGTGTGCATAAGTTGA 59.194 45.455 0.00 0.00 0.00 3.18
921 925 6.072508 TGTGCATAAGTTGATGAAGTTTCCTC 60.073 38.462 0.00 0.00 0.00 3.71
926 930 9.007901 CATAAGTTGATGAAGTTTCCTCTTTCT 57.992 33.333 0.00 0.00 0.00 2.52
929 933 5.468540 TGATGAAGTTTCCTCTTTCTCGA 57.531 39.130 0.00 0.00 0.00 4.04
1035 1052 4.712476 AGATTGGTAGATTGAGCCATCAC 58.288 43.478 0.00 0.00 34.35 3.06
1126 1197 6.526526 GCCCTTATTTCCAAAACTTTTGGTA 58.473 36.000 25.94 17.66 40.40 3.25
1132 1203 3.648739 TCCAAAACTTTTGGTAGGGCTT 58.351 40.909 25.94 0.00 40.40 4.35
1212 1283 2.418746 CGGGAAAAGGATCACACGATCT 60.419 50.000 0.00 0.00 46.30 2.75
1525 1597 1.596477 GCCCATCATCACCGAGCTC 60.596 63.158 2.73 2.73 0.00 4.09
1540 1612 2.501128 CTCACCATCATCGCGGGT 59.499 61.111 6.13 1.23 34.59 5.28
1783 1856 6.622028 TCAAAGTTGAGAAGTTTCGTGAAACC 60.622 38.462 19.01 7.52 40.64 3.27
1840 1913 5.424252 CACCCTTTGTCCCTAGAATAGTGTA 59.576 44.000 0.00 0.00 36.82 2.90
1878 1951 1.386412 CGAAACATTTGGATGCGTTGC 59.614 47.619 0.00 0.00 36.72 4.17
1989 2062 7.559897 AGTGACTTGGATTTAGGAGTTTTGAAA 59.440 33.333 0.00 0.00 0.00 2.69
2135 2208 3.006110 GCATAGGCATTGTGGTTGCATAT 59.994 43.478 0.00 0.00 45.07 1.78
2366 2525 4.580580 GGATTACTGGATTGGATGTGAACC 59.419 45.833 0.00 0.00 0.00 3.62
2368 2527 2.795329 ACTGGATTGGATGTGAACCAC 58.205 47.619 0.00 0.00 37.13 4.16
2956 3115 3.257624 ACTCAAGAACGGTACCAAGGTAG 59.742 47.826 13.54 2.65 0.00 3.18
3069 3229 2.935740 GCTGGCAACCTTTGAGGCC 61.936 63.158 0.00 0.00 46.58 5.19
3164 3324 0.823356 AGGCAAATGCTTGACGTGGT 60.823 50.000 5.25 0.00 46.15 4.16
3294 3454 6.430925 TGTCATATCTTTTCCTTTGTGTCCTG 59.569 38.462 0.00 0.00 0.00 3.86
3302 3462 1.625818 CCTTTGTGTCCTGCTCCTAGT 59.374 52.381 0.00 0.00 0.00 2.57
3305 3465 3.451402 TTGTGTCCTGCTCCTAGTCTA 57.549 47.619 0.00 0.00 0.00 2.59
3400 3560 1.097232 TGCTTCCATGCTTTCATCCG 58.903 50.000 0.00 0.00 0.00 4.18
3404 3564 3.128589 GCTTCCATGCTTTCATCCGTAAA 59.871 43.478 0.00 0.00 0.00 2.01
3575 3736 7.942341 TGGGGCTTCCAACTTACATTATTATAG 59.058 37.037 0.00 0.00 43.84 1.31
3605 3766 4.267349 AGCATAACAGTGTAAACCGAGT 57.733 40.909 0.00 0.00 0.00 4.18
3678 3839 4.699257 AGTCTCATCATTCCAAGTTCTTGC 59.301 41.667 7.00 0.00 0.00 4.01
3820 3981 2.118683 CACATGTGCTTTCCAAACACG 58.881 47.619 13.94 0.00 37.11 4.49
3889 4061 8.414629 AAAAGCTCTTCCAAAACATCTAAGAT 57.585 30.769 0.00 0.00 0.00 2.40
4031 4203 3.520569 CAAAGCTCTCTCAAGGTCTAGC 58.479 50.000 0.00 0.00 0.00 3.42
4061 4233 5.627968 GCTTTGCTAACTCTAATGGGAGTCT 60.628 44.000 0.00 0.00 44.67 3.24
4178 4350 0.250338 GGTTGGATGGCGGATAGTCC 60.250 60.000 0.00 0.00 0.00 3.85
4247 4419 0.106619 ATCTCTAGGAGCCGGACGTT 60.107 55.000 5.05 0.00 0.00 3.99
4270 4442 3.181526 CTGGAAGCTGGATTGTCCC 57.818 57.895 0.00 0.00 35.03 4.46
4277 4449 1.915228 CTGGATTGTCCCGGGTCAT 59.085 57.895 21.46 11.21 35.03 3.06
4309 4481 1.598130 GTTGGAGGCTGCAGTCGTT 60.598 57.895 16.64 0.00 0.00 3.85
4359 4531 3.072915 TGCATTTCTTCCTTGTCTCCTCA 59.927 43.478 0.00 0.00 0.00 3.86
4403 4575 0.608640 TTCTCCCCTCGCTTCTTCAC 59.391 55.000 0.00 0.00 0.00 3.18
4465 4637 3.211865 TGTAGGTAGTAGCCATGTCTCG 58.788 50.000 0.00 0.00 0.00 4.04
4539 4711 1.451936 GGGCCCGTGCTCTAATCAT 59.548 57.895 5.69 0.00 34.08 2.45
4540 4712 0.179018 GGGCCCGTGCTCTAATCATT 60.179 55.000 5.69 0.00 34.08 2.57
4584 4756 0.468226 TTGGCGTAGGATCCATGGTC 59.532 55.000 15.82 8.64 31.54 4.02
4589 4761 2.759191 CGTAGGATCCATGGTCATGTG 58.241 52.381 15.82 0.64 37.11 3.21
4655 4827 7.094205 GGAAGTATTTGAGTTGGTGATGATTGT 60.094 37.037 0.00 0.00 0.00 2.71
4689 4861 2.151502 TTGCTCTCTCACCTCCTAGG 57.848 55.000 0.82 0.82 42.49 3.02
4755 4927 5.606348 AAAACCTCCTAACAAACATGCAA 57.394 34.783 0.00 0.00 0.00 4.08
4965 5138 3.187700 CCTGCTTTAGGCTAGTTACGTG 58.812 50.000 0.00 0.00 40.38 4.49
5008 5181 3.931468 CAGTAGTCTGATTGTGCTCCTTG 59.069 47.826 0.00 0.00 43.76 3.61
5009 5182 2.486472 AGTCTGATTGTGCTCCTTGG 57.514 50.000 0.00 0.00 0.00 3.61
5620 5793 3.394674 TTTGAGGATAGTGCACAACGA 57.605 42.857 21.04 1.01 0.00 3.85
5838 6011 0.179004 ATGCGTCCAACTTTGTCCCA 60.179 50.000 0.00 0.00 0.00 4.37
5843 6016 3.638484 CGTCCAACTTTGTCCCAAAATC 58.362 45.455 0.00 0.00 0.00 2.17
5929 6102 3.250617 TGGGCAGCTGGATTCTGATATA 58.749 45.455 17.12 0.00 33.54 0.86
6005 6178 1.270147 GGACTGGTGTACGCTTGTCTT 60.270 52.381 21.82 0.00 0.00 3.01
6057 6231 6.291377 ACATTGACACAACACTTCTCATACT 58.709 36.000 0.00 0.00 0.00 2.12
6119 6293 5.332743 TGATCTTTTAACCCCTGCTTTGAT 58.667 37.500 0.00 0.00 0.00 2.57
6404 6580 7.788026 ACATATTTGTCCAAATGCATCTTCAT 58.212 30.769 14.02 0.00 40.83 2.57
6416 6592 3.809279 TGCATCTTCATTACCTGCATACG 59.191 43.478 0.00 0.00 37.88 3.06
6530 6706 4.574599 ATTCTGTCTGCCAACAAGTTTC 57.425 40.909 0.00 0.00 0.00 2.78
6532 6708 4.415881 TCTGTCTGCCAACAAGTTTCTA 57.584 40.909 0.00 0.00 0.00 2.10
6579 6755 5.909621 TGCGTAGTAGATTCCAAAGTAGT 57.090 39.130 0.00 0.00 0.00 2.73
6580 6756 5.647589 TGCGTAGTAGATTCCAAAGTAGTG 58.352 41.667 0.00 0.00 0.00 2.74
6612 6788 7.588512 AGTTTGAATTCTGAATAGTGCACTTC 58.411 34.615 27.06 18.01 0.00 3.01
6753 6930 6.669278 AGAAAGGAAACGACTTTTAGCAATC 58.331 36.000 0.00 0.00 38.21 2.67
6845 7022 5.189736 GGATGGTGCAGTCCTGGAATATATA 59.810 44.000 0.00 0.00 31.21 0.86
6846 7023 6.126652 GGATGGTGCAGTCCTGGAATATATAT 60.127 42.308 0.00 0.00 31.21 0.86
6879 7056 7.593875 TGCCATAATGTTTAAATGCAACTTC 57.406 32.000 0.00 0.00 0.00 3.01
7026 7203 5.136105 AGATATCCAGGCAATTTTGGTCTC 58.864 41.667 0.00 0.00 35.89 3.36
7175 7352 5.491982 ACCTTCATCAACACTGAATAGGTC 58.508 41.667 0.00 0.00 36.62 3.85
7600 7780 0.764369 CCATTCCCATCCTCCGGAGA 60.764 60.000 33.39 18.69 34.05 3.71
7701 7881 1.203994 CCACCAGTTACACCTCTACCG 59.796 57.143 0.00 0.00 0.00 4.02
8121 8307 0.249238 GGCAATGCAAAACGTGTGGA 60.249 50.000 7.79 0.00 0.00 4.02
8229 8415 9.605955 CAATCTTCACGTAAATATTTTGTCACA 57.394 29.630 5.91 0.00 0.00 3.58
8244 8430 0.856982 TCACAGTGGGGGAATGGTTT 59.143 50.000 0.00 0.00 0.00 3.27
8508 8694 2.310538 GGGCCTATTGTCCATTCCAAG 58.689 52.381 0.84 0.00 0.00 3.61
8771 8979 3.786635 ACGCTGAATGTGATACTCCTTC 58.213 45.455 0.00 0.00 0.00 3.46
8777 8985 7.172190 CGCTGAATGTGATACTCCTTCATTATT 59.828 37.037 0.00 0.00 0.00 1.40
8921 9290 2.299867 CCTTTTGGTTGGGGACATTCTG 59.700 50.000 0.00 0.00 42.32 3.02
8923 9292 2.765689 TTGGTTGGGGACATTCTGTT 57.234 45.000 0.00 0.00 42.32 3.16
8939 9308 5.713792 TTCTGTTTGTTGTGTTTGAAGGA 57.286 34.783 0.00 0.00 0.00 3.36
8982 9351 2.880890 AGTGTTTCTGTCACTTCCATGC 59.119 45.455 0.00 0.00 42.50 4.06
8986 9355 3.334583 TTCTGTCACTTCCATGCTACC 57.665 47.619 0.00 0.00 0.00 3.18
9323 9692 1.887242 GCAGTCGCCACAGTTGTCA 60.887 57.895 0.00 0.00 0.00 3.58
9377 9750 6.327365 TCCTCTTAATCTAGGATGACATGCAA 59.673 38.462 9.80 0.00 36.97 4.08
9386 9759 2.094545 GGATGACATGCAAACCCTTCAC 60.095 50.000 1.50 0.00 0.00 3.18
9489 9862 1.000506 TGAGTGCTGGTAACTTCCGAC 59.999 52.381 0.00 0.00 37.61 4.79
9510 9883 4.721132 ACAAAACCCAGGACGAAAGAATA 58.279 39.130 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.241555 CCGCCCTCCTGGATTCCG 62.242 72.222 0.00 0.00 35.39 4.30
1 2 4.570874 GCCGCCCTCCTGGATTCC 62.571 72.222 0.00 0.00 35.39 3.01
21 22 2.257409 ATTCCACCTACCTGCAGCCG 62.257 60.000 8.66 0.00 0.00 5.52
22 23 0.837272 TATTCCACCTACCTGCAGCC 59.163 55.000 8.66 0.00 0.00 4.85
23 24 1.202698 CCTATTCCACCTACCTGCAGC 60.203 57.143 8.66 0.00 0.00 5.25
24 25 1.417890 CCCTATTCCACCTACCTGCAG 59.582 57.143 6.78 6.78 0.00 4.41
25 26 1.274184 ACCCTATTCCACCTACCTGCA 60.274 52.381 0.00 0.00 0.00 4.41
26 27 1.508256 ACCCTATTCCACCTACCTGC 58.492 55.000 0.00 0.00 0.00 4.85
27 28 3.521937 TGAAACCCTATTCCACCTACCTG 59.478 47.826 0.00 0.00 0.00 4.00
28 29 3.810623 TGAAACCCTATTCCACCTACCT 58.189 45.455 0.00 0.00 0.00 3.08
29 30 4.579647 TTGAAACCCTATTCCACCTACC 57.420 45.455 0.00 0.00 0.00 3.18
30 31 6.904463 TTTTTGAAACCCTATTCCACCTAC 57.096 37.500 0.00 0.00 0.00 3.18
31 32 6.439058 CCATTTTTGAAACCCTATTCCACCTA 59.561 38.462 0.00 0.00 0.00 3.08
32 33 5.248248 CCATTTTTGAAACCCTATTCCACCT 59.752 40.000 0.00 0.00 0.00 4.00
33 34 5.247337 TCCATTTTTGAAACCCTATTCCACC 59.753 40.000 0.00 0.00 0.00 4.61
34 35 6.353404 TCCATTTTTGAAACCCTATTCCAC 57.647 37.500 0.00 0.00 0.00 4.02
35 36 6.013812 CCTTCCATTTTTGAAACCCTATTCCA 60.014 38.462 0.00 0.00 0.00 3.53
36 37 6.406370 CCTTCCATTTTTGAAACCCTATTCC 58.594 40.000 0.00 0.00 0.00 3.01
49 50 3.560357 AGGCCTAACCCTTCCATTTTT 57.440 42.857 1.29 0.00 40.58 1.94
88 89 0.973632 CCAAAACCCAAACCCTAGCC 59.026 55.000 0.00 0.00 0.00 3.93
115 116 3.781307 CGAGATGGAACGGCCCCA 61.781 66.667 1.28 1.28 38.19 4.96
124 125 2.552819 GCCGTCCGATCGAGATGGA 61.553 63.158 31.94 15.34 42.15 3.41
126 127 0.661780 GAAGCCGTCCGATCGAGATG 60.662 60.000 18.66 16.34 0.00 2.90
135 136 2.202492 CTCGTCTGAAGCCGTCCG 60.202 66.667 0.00 0.00 0.00 4.79
136 137 2.182030 CCTCGTCTGAAGCCGTCC 59.818 66.667 0.00 0.00 0.00 4.79
144 145 2.026169 ACCATCACTACTCCTCGTCTGA 60.026 50.000 0.00 0.00 0.00 3.27
146 147 2.370349 CACCATCACTACTCCTCGTCT 58.630 52.381 0.00 0.00 0.00 4.18
154 155 3.711704 CCATCTAACCCACCATCACTACT 59.288 47.826 0.00 0.00 0.00 2.57
162 163 1.451449 ACAACCCATCTAACCCACCA 58.549 50.000 0.00 0.00 0.00 4.17
176 177 3.627577 CCACACTGCCATTCTATACAACC 59.372 47.826 0.00 0.00 0.00 3.77
180 181 3.495100 CCTCCCACACTGCCATTCTATAC 60.495 52.174 0.00 0.00 0.00 1.47
183 184 0.911769 CCTCCCACACTGCCATTCTA 59.088 55.000 0.00 0.00 0.00 2.10
187 188 4.052518 GGCCTCCCACACTGCCAT 62.053 66.667 0.00 0.00 43.46 4.40
209 210 6.409349 GCCACCCAATTACCTCTATTCTTAGT 60.409 42.308 0.00 0.00 0.00 2.24
212 213 4.386424 GGCCACCCAATTACCTCTATTCTT 60.386 45.833 0.00 0.00 0.00 2.52
233 234 1.066430 TCAATAGAACCTGTGTCGGGC 60.066 52.381 0.00 0.00 32.02 6.13
254 255 5.237561 GCCGGTTTAATTGTTGGACATTTTT 59.762 36.000 1.90 0.00 0.00 1.94
259 260 2.588620 AGCCGGTTTAATTGTTGGACA 58.411 42.857 1.90 0.00 0.00 4.02
264 266 4.490743 GCATTGTAGCCGGTTTAATTGTT 58.509 39.130 1.90 0.00 0.00 2.83
281 283 5.751243 AACCTTAAACTATAGCGGCATTG 57.249 39.130 1.45 0.00 0.00 2.82
300 302 1.814394 GGTCGTTTCATACCCCAAACC 59.186 52.381 0.00 0.00 0.00 3.27
302 304 2.290450 GGAGGTCGTTTCATACCCCAAA 60.290 50.000 0.00 0.00 36.34 3.28
308 310 2.284417 GCATTCGGAGGTCGTTTCATAC 59.716 50.000 0.00 0.00 40.32 2.39
331 333 3.418684 AGACCGTCTGCCAAATTTAGT 57.581 42.857 0.00 0.00 0.00 2.24
333 335 3.602483 GGTAGACCGTCTGCCAAATTTA 58.398 45.455 25.92 0.00 46.79 1.40
367 369 2.203153 AAAGTTGGCGTGCGGTCT 60.203 55.556 0.00 0.00 0.00 3.85
419 421 7.273659 GTCGCGCCATCATTAAAAATTATTTC 58.726 34.615 0.00 0.00 0.00 2.17
426 428 1.202087 CGGTCGCGCCATCATTAAAAA 60.202 47.619 17.57 0.00 36.97 1.94
427 429 0.375454 CGGTCGCGCCATCATTAAAA 59.625 50.000 17.57 0.00 36.97 1.52
477 479 0.531090 CTCCCCGTTGTTGTCGTTGA 60.531 55.000 0.00 0.00 0.00 3.18
506 508 6.958255 TCATAAAACATGCATCCGTTCATAG 58.042 36.000 0.00 0.00 0.00 2.23
507 509 6.934048 TCATAAAACATGCATCCGTTCATA 57.066 33.333 0.00 0.00 0.00 2.15
508 510 5.833406 TCATAAAACATGCATCCGTTCAT 57.167 34.783 0.00 0.00 0.00 2.57
509 511 5.635417 TTCATAAAACATGCATCCGTTCA 57.365 34.783 0.00 0.00 0.00 3.18
510 512 6.942886 TTTTCATAAAACATGCATCCGTTC 57.057 33.333 0.00 0.00 0.00 3.95
580 583 3.004171 TCGTGTTAGCCGCATTAATTGT 58.996 40.909 0.00 0.00 0.00 2.71
588 591 1.069568 CATGTTTTCGTGTTAGCCGCA 60.070 47.619 0.00 0.00 32.61 5.69
589 592 1.602191 CATGTTTTCGTGTTAGCCGC 58.398 50.000 0.00 0.00 32.61 6.53
600 603 5.045872 GCTTCATATGCCTTCCATGTTTTC 58.954 41.667 0.00 0.00 35.34 2.29
617 620 2.490217 CCGAGACCGACGCTTCAT 59.510 61.111 0.00 0.00 38.22 2.57
620 623 3.745803 GACCCGAGACCGACGCTT 61.746 66.667 0.00 0.00 38.22 4.68
635 638 3.058501 CCGTCCACAACCTTTGTAATGAC 60.059 47.826 0.00 0.00 43.23 3.06
638 641 2.510613 CCCGTCCACAACCTTTGTAAT 58.489 47.619 0.00 0.00 43.23 1.89
659 662 2.592308 GCCTACTTGCAGGGGGAG 59.408 66.667 12.85 2.19 36.10 4.30
667 670 2.879462 CCGTCGTCGCCTACTTGC 60.879 66.667 0.00 0.00 35.54 4.01
687 690 5.255710 ACGGAGAAGTAGTCATCATTCAG 57.744 43.478 0.00 0.00 0.00 3.02
690 693 3.489398 GCGACGGAGAAGTAGTCATCATT 60.489 47.826 0.00 0.00 34.80 2.57
742 745 0.093535 CACTCGCGTCTTACGTACGA 59.906 55.000 24.41 5.56 44.73 3.43
751 754 3.432588 CCGACTCCACTCGCGTCT 61.433 66.667 5.77 0.00 31.98 4.18
857 861 2.123077 CCCCTCAGCCTCGATCCT 60.123 66.667 0.00 0.00 0.00 3.24
868 872 1.004745 GAATCTTGCCTCAACCCCTCA 59.995 52.381 0.00 0.00 0.00 3.86
878 882 1.072331 ACACACTTCCGAATCTTGCCT 59.928 47.619 0.00 0.00 0.00 4.75
903 907 6.203723 CGAGAAAGAGGAAACTTCATCAACTT 59.796 38.462 6.85 0.00 44.43 2.66
904 908 5.698545 CGAGAAAGAGGAAACTTCATCAACT 59.301 40.000 6.85 3.11 44.43 3.16
909 913 5.476091 ACTCGAGAAAGAGGAAACTTCAT 57.524 39.130 21.68 0.00 44.43 2.57
921 925 1.532868 CAAGGGCACAACTCGAGAAAG 59.467 52.381 21.68 10.56 0.00 2.62
926 930 1.891919 GCACAAGGGCACAACTCGA 60.892 57.895 0.00 0.00 0.00 4.04
929 933 1.147376 TACGCACAAGGGCACAACT 59.853 52.632 0.00 0.00 0.00 3.16
1101 1139 4.450757 CCAAAAGTTTTGGAAATAAGGGCG 59.549 41.667 34.61 9.40 42.06 6.13
1160 1231 2.882761 GACCTGCCGTAATTTAATCCCC 59.117 50.000 0.00 0.00 0.00 4.81
1212 1283 2.953284 TGGGATTTGTAACACGGGAA 57.047 45.000 0.00 0.00 0.00 3.97
1525 1597 1.884464 CTGACCCGCGATGATGGTG 60.884 63.158 8.23 0.00 30.97 4.17
1783 1856 4.647424 TCAAGCCCAAACTTTAACAGTG 57.353 40.909 0.00 0.00 35.12 3.66
1840 1913 4.386652 GTTTCGCATGAAAATGCAGTGAAT 59.613 37.500 10.96 0.00 45.22 2.57
1868 1941 1.063649 CATGAGCAGCAACGCATCC 59.936 57.895 0.00 0.00 0.00 3.51
2062 2135 8.859090 CCAATTATGCACCCTATATCAGAAAAA 58.141 33.333 0.00 0.00 0.00 1.94
2063 2136 8.004215 ACCAATTATGCACCCTATATCAGAAAA 58.996 33.333 0.00 0.00 0.00 2.29
2125 2198 2.369860 TGGCAACCAAAATATGCAACCA 59.630 40.909 0.00 0.00 41.80 3.67
2334 2493 5.073144 TCCAATCCAGTAATCCCCATAGTTC 59.927 44.000 0.00 0.00 0.00 3.01
2366 2525 7.928167 TCATATCTGCCAAGTAACATCTAAGTG 59.072 37.037 0.00 0.00 0.00 3.16
2368 2527 9.499479 AATCATATCTGCCAAGTAACATCTAAG 57.501 33.333 0.00 0.00 0.00 2.18
2833 2992 0.973632 ATAGTCGTTGTGGCAGGACA 59.026 50.000 9.60 0.00 31.93 4.02
2911 3070 3.117046 GGTGTTGCGCTTCTAGATACTC 58.883 50.000 9.73 0.00 0.00 2.59
3107 3267 7.814264 AGCTGATCCACCTGATTATTAAAAG 57.186 36.000 0.00 0.00 32.41 2.27
3164 3324 8.051468 TGTTAACCCATTAATATGATCCTCCA 57.949 34.615 2.48 0.00 32.91 3.86
3294 3454 3.431068 GGTTTGGAAGCTAGACTAGGAGC 60.431 52.174 11.48 0.00 39.08 4.70
3305 3465 0.621082 GGCTCCTAGGTTTGGAAGCT 59.379 55.000 15.35 0.00 42.74 3.74
3468 3629 3.138304 GGGTGAAAAATGCAAAAGGTCC 58.862 45.455 0.00 0.00 0.00 4.46
3575 3736 7.753580 GGTTTACACTGTTATGCTACCAAAATC 59.246 37.037 0.00 0.00 0.00 2.17
3605 3766 4.334552 TGCTTTGCTTATGACCTTGATGA 58.665 39.130 0.00 0.00 0.00 2.92
3678 3839 3.367806 CCCACATCATATGCTCTCCTACG 60.368 52.174 0.00 0.00 0.00 3.51
3820 3981 7.148255 TGTGGATCTATGTGTATCTTTGTTTGC 60.148 37.037 0.00 0.00 0.00 3.68
4031 4203 8.097038 TCCCATTAGAGTTAGCAAAGCATATAG 58.903 37.037 0.00 0.00 0.00 1.31
4048 4220 4.481280 ACTGTACCCTAGACTCCCATTAGA 59.519 45.833 0.00 0.00 0.00 2.10
4061 4233 6.297243 GCCCCTACACTATATACTGTACCCTA 60.297 46.154 0.00 0.00 0.00 3.53
4150 4322 0.753111 GCCATCCAACCCAGATGTCC 60.753 60.000 0.00 0.00 39.62 4.02
4154 4326 1.355718 ATCCGCCATCCAACCCAGAT 61.356 55.000 0.00 0.00 0.00 2.90
4247 4419 2.300967 AATCCAGCTTCCAGCCCGA 61.301 57.895 0.00 0.00 43.77 5.14
4270 4442 2.202570 GACGTCCGACATGACCCG 60.203 66.667 3.51 0.00 31.35 5.28
4359 4531 3.772025 CCAAGTCATAGTGGAGGAGAAGT 59.228 47.826 0.00 0.00 37.03 3.01
4403 4575 2.027561 TCAGGTACCAAGGAATTGACCG 60.028 50.000 15.94 0.00 34.73 4.79
4465 4637 2.644676 GAACTTCCTATGCCTTCCCAC 58.355 52.381 0.00 0.00 0.00 4.61
4535 4707 4.847990 ATGCCAATTGGACCAAAATGAT 57.152 36.364 29.02 4.56 37.39 2.45
4539 4711 3.397482 CGAAATGCCAATTGGACCAAAA 58.603 40.909 29.02 5.82 37.39 2.44
4540 4712 2.289320 CCGAAATGCCAATTGGACCAAA 60.289 45.455 29.02 7.62 37.39 3.28
4584 4756 2.442236 ACCTTTAGCCCATCCACATG 57.558 50.000 0.00 0.00 0.00 3.21
4589 4761 4.373156 ACATCATACCTTTAGCCCATCC 57.627 45.455 0.00 0.00 0.00 3.51
4649 4821 0.767998 TGTAGCACCCACCACAATCA 59.232 50.000 0.00 0.00 0.00 2.57
4655 4827 0.112218 AGCAAATGTAGCACCCACCA 59.888 50.000 0.00 0.00 0.00 4.17
4689 4861 3.454082 AGAGATCACCAAGGGAGATTGAC 59.546 47.826 0.00 0.00 33.39 3.18
4779 4951 3.758300 CCCTCGTCAATATTTGTTGTGC 58.242 45.455 0.00 0.00 0.00 4.57
5008 5181 2.633481 AGTCTCCTTGTGTCTACCAACC 59.367 50.000 0.00 0.00 0.00 3.77
5009 5182 3.069729 ACAGTCTCCTTGTGTCTACCAAC 59.930 47.826 0.00 0.00 0.00 3.77
5334 5507 7.094205 CCAGGAAAGATTATAAGCAACACTTGT 60.094 37.037 3.17 0.00 39.58 3.16
5620 5793 1.016130 CAAGCGTGCTCATCGAAGGT 61.016 55.000 0.00 0.00 0.00 3.50
5838 6011 5.432885 AGACGGAATGTTGTTTCGATTTT 57.567 34.783 0.00 0.00 0.00 1.82
5843 6016 4.212636 AGGTAAAGACGGAATGTTGTTTCG 59.787 41.667 0.00 0.00 0.00 3.46
6057 6231 8.094548 TCATCGAAAAAGGAGAAGTGATAGAAA 58.905 33.333 0.00 0.00 0.00 2.52
6303 6479 6.380079 AGACAGATACCCTTTTCAGTCATT 57.620 37.500 0.00 0.00 32.57 2.57
6404 6580 3.962063 TCCCTAACATCGTATGCAGGTAA 59.038 43.478 0.00 0.00 35.22 2.85
6416 6592 6.817765 TTTGTTCAAGTGATCCCTAACATC 57.182 37.500 0.00 0.00 0.00 3.06
6579 6755 9.342308 ACTATTCAGAATTCAAACTTCAGAACA 57.658 29.630 8.44 0.00 32.99 3.18
6580 6756 9.604626 CACTATTCAGAATTCAAACTTCAGAAC 57.395 33.333 8.44 0.00 32.99 3.01
6740 6917 3.950395 AGCCCATGAGATTGCTAAAAGTC 59.050 43.478 0.00 0.00 30.97 3.01
6753 6930 3.565764 TCAAATGAGGTAGCCCATGAG 57.434 47.619 0.00 0.00 0.00 2.90
6846 7023 9.814899 CATTTAAACATTATGGCAATGGAGTAA 57.185 29.630 4.33 0.00 32.14 2.24
7026 7203 4.521146 ACTCTGAAATAGCTCCATTGTGG 58.479 43.478 0.00 0.00 39.43 4.17
7600 7780 2.179427 GGGGGCAAAGCTTCTAAATGT 58.821 47.619 0.00 0.00 0.00 2.71
7649 7829 3.519913 ACTACCTCCTTGTCCTTGGAATC 59.480 47.826 0.00 0.00 31.23 2.52
7701 7881 6.018180 CAGTAGGTGTTACAGAAAAGGTGTTC 60.018 42.308 0.00 0.00 34.56 3.18
7746 7926 3.809832 GCAGAGCAAAACTAGACACTGAA 59.190 43.478 0.00 0.00 0.00 3.02
8059 8245 5.748402 AGCATTAATGACAGACTCATTCCA 58.252 37.500 19.73 0.00 45.08 3.53
8064 8250 5.411831 ACAGAGCATTAATGACAGACTCA 57.588 39.130 19.73 0.00 0.00 3.41
8229 8415 1.285078 GCTCTAAACCATTCCCCCACT 59.715 52.381 0.00 0.00 0.00 4.00
8244 8430 3.431415 TCCTACTGTTTCTGCTGCTCTA 58.569 45.455 0.00 0.00 0.00 2.43
8508 8694 1.327690 TACTGGGGCCAGATCGACAC 61.328 60.000 4.39 0.00 46.30 3.67
8650 8858 5.340439 ACGGTCTCAGTTCCTTTTATAGG 57.660 43.478 0.00 0.00 46.27 2.57
8656 8864 5.374071 ACAAATTACGGTCTCAGTTCCTTT 58.626 37.500 0.00 0.00 0.00 3.11
8669 8877 9.537192 TGTATTAGAATACAGGACAAATTACGG 57.463 33.333 10.39 0.00 44.52 4.02
8832 9200 4.393062 ACGGAAGCAGTATTTGATGAACTG 59.607 41.667 0.00 0.00 42.80 3.16
8870 9238 9.373750 CAGTATTTGATGAACAATATTGCTACG 57.626 33.333 15.48 0.00 38.36 3.51
8921 9290 5.866633 TCACAATCCTTCAAACACAACAAAC 59.133 36.000 0.00 0.00 0.00 2.93
8923 9292 5.651387 TCACAATCCTTCAAACACAACAA 57.349 34.783 0.00 0.00 0.00 2.83
8986 9355 4.707030 TGAAGCAGGCTAACAATGAATG 57.293 40.909 0.00 0.00 0.00 2.67
9323 9692 8.796475 CCATATATTAATGTAAAAGCAGCAGGT 58.204 33.333 0.00 0.00 0.00 4.00
9377 9750 1.597027 CGCCTGTTCGTGAAGGGTT 60.597 57.895 0.00 0.00 33.87 4.11
9386 9759 2.043411 CATGTTTGTTTCGCCTGTTCG 58.957 47.619 0.00 0.00 0.00 3.95
9489 9862 5.699097 TTATTCTTTCGTCCTGGGTTTTG 57.301 39.130 0.00 0.00 0.00 2.44
9510 9883 0.250901 AGCTGTTGACGGATGCCTTT 60.251 50.000 0.00 0.00 0.00 3.11


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

AutoCloner maintained by Alex Coulton.