Multiple sequence alignment - TraesCS3B01G199100

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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 TraesCS3B01G199100 chr3B 100.000 3734 0 0 1 3734 227419954 227416221 0.000000e+00 6896.0
1 TraesCS3B01G199100 chr3B 92.384 302 18 2 3081 3382 683323003 683322707 3.450000e-115 425.0
2 TraesCS3B01G199100 chr3B 95.669 254 8 1 356 609 227424588 227424338 4.490000e-109 405.0
3 TraesCS3B01G199100 chr3B 90.813 283 21 2 3081 3363 227411775 227411498 1.270000e-99 374.0
4 TraesCS3B01G199100 chr3B 93.421 152 9 1 3085 3236 683340881 683340731 1.350000e-54 224.0
5 TraesCS3B01G199100 chr3B 93.421 152 9 1 3085 3236 683342174 683342024 1.350000e-54 224.0
6 TraesCS3B01G199100 chr3A 93.979 2425 85 26 610 3006 172629381 172631772 0.000000e+00 3613.0
7 TraesCS3B01G199100 chr3A 95.556 90 1 2 2999 3086 172659087 172659175 1.400000e-29 141.0
8 TraesCS3B01G199100 chr3A 94.444 54 2 1 356 408 647341940 647341993 8.600000e-12 82.4
9 TraesCS3B01G199100 chr3D 95.272 1671 43 15 610 2265 153847858 153849507 0.000000e+00 2615.0
10 TraesCS3B01G199100 chr3D 94.196 827 22 7 2262 3086 153849587 153850389 0.000000e+00 1238.0
11 TraesCS3B01G199100 chr5A 88.993 536 58 1 5 539 338418568 338418033 0.000000e+00 662.0
12 TraesCS3B01G199100 chr5A 84.566 622 79 13 5 613 648776334 648775717 5.340000e-168 601.0
13 TraesCS3B01G199100 chr5A 90.270 185 16 2 356 538 648780916 648780732 1.340000e-59 241.0
14 TraesCS3B01G199100 chr1B 97.019 369 11 0 1 369 58554859 58554491 4.100000e-174 621.0
15 TraesCS3B01G199100 chr1B 83.010 618 83 17 5 613 37729107 37729711 1.180000e-149 540.0
16 TraesCS3B01G199100 chr4A 94.103 407 17 4 1 406 626756657 626757057 2.470000e-171 612.0
17 TraesCS3B01G199100 chr7A 95.935 369 15 0 1 369 603558173 603558541 1.920000e-167 599.0
18 TraesCS3B01G199100 chr1A 95.935 369 15 0 1 369 565131702 565131334 1.920000e-167 599.0
19 TraesCS3B01G199100 chr5B 83.258 663 91 16 3083 3734 212636480 212637133 3.210000e-165 592.0
20 TraesCS3B01G199100 chr5B 75.628 398 91 4 3315 3707 473191891 473191495 3.810000e-45 193.0
21 TraesCS3B01G199100 chr5D 82.380 664 86 16 3083 3734 201852546 201853190 1.960000e-152 549.0
22 TraesCS3B01G199100 chr4B 82.979 611 80 17 13 610 65513885 65513286 7.100000e-147 531.0
23 TraesCS3B01G199100 chr4B 82.815 611 81 15 13 610 65085277 65084678 3.300000e-145 525.0
24 TraesCS3B01G199100 chr6B 80.328 305 34 3 3081 3382 387089707 387089426 1.360000e-49 207.0
25 TraesCS3B01G199100 chr2B 75.570 307 73 2 3402 3707 88416516 88416211 2.320000e-32 150.0
26 TraesCS3B01G199100 chr2B 71.788 397 95 15 3321 3707 411488732 411488343 3.070000e-16 97.1
27 TraesCS3B01G199100 chr6A 90.566 53 5 0 1980 2032 569692348 569692400 1.860000e-08 71.3


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 TraesCS3B01G199100 chr3B 227416221 227419954 3733 True 6896.0 6896 100.000 1 3734 1 chr3B.!!$R2 3733
1 TraesCS3B01G199100 chr3B 683340731 683342174 1443 True 224.0 224 93.421 3085 3236 2 chr3B.!!$R5 151
2 TraesCS3B01G199100 chr3A 172629381 172631772 2391 False 3613.0 3613 93.979 610 3006 1 chr3A.!!$F1 2396
3 TraesCS3B01G199100 chr3D 153847858 153850389 2531 False 1926.5 2615 94.734 610 3086 2 chr3D.!!$F1 2476
4 TraesCS3B01G199100 chr5A 338418033 338418568 535 True 662.0 662 88.993 5 539 1 chr5A.!!$R1 534
5 TraesCS3B01G199100 chr5A 648775717 648776334 617 True 601.0 601 84.566 5 613 1 chr5A.!!$R2 608
6 TraesCS3B01G199100 chr1B 37729107 37729711 604 False 540.0 540 83.010 5 613 1 chr1B.!!$F1 608
7 TraesCS3B01G199100 chr5B 212636480 212637133 653 False 592.0 592 83.258 3083 3734 1 chr5B.!!$F1 651
8 TraesCS3B01G199100 chr5D 201852546 201853190 644 False 549.0 549 82.380 3083 3734 1 chr5D.!!$F1 651
9 TraesCS3B01G199100 chr4B 65513286 65513885 599 True 531.0 531 82.979 13 610 1 chr4B.!!$R2 597
10 TraesCS3B01G199100 chr4B 65084678 65085277 599 True 525.0 525 82.815 13 610 1 chr4B.!!$R1 597

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
454 457 0.257328 TCAAGTCAGGTTGTTGGGCA 59.743 50.0 0.0 0.0 0.00 5.36 F
2093 2122 0.181350 CTGGGTAAGCATCCACCTCC 59.819 60.0 0.0 0.0 35.04 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2341 2459 0.175531 GGTGTACATTGGGCCATTGC 59.824 55.0 24.43 12.30 0.00 3.56 R
3270 3399 0.176680 CAGTGGGCCTAGCTGTACTG 59.823 60.0 4.53 4.12 31.93 2.74 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
26 27 2.093764 GTCAAGCACAGAGGCTGAGTAT 60.094 50.000 0.00 0.00 45.07 2.12
32 33 2.697751 CACAGAGGCTGAGTATAAGGCT 59.302 50.000 0.00 0.00 41.24 4.58
50 51 3.096550 GCTTTAGCCAATGCCACTGCA 62.097 52.381 0.00 0.00 43.40 4.41
65 66 4.019174 CCACTGCAGAGATTATTTGGGTT 58.981 43.478 23.35 0.00 0.00 4.11
68 69 4.946157 ACTGCAGAGATTATTTGGGTTCAG 59.054 41.667 23.35 0.00 0.00 3.02
72 73 6.319658 TGCAGAGATTATTTGGGTTCAGAATC 59.680 38.462 0.00 0.00 0.00 2.52
93 94 2.665165 TGCTGACAGAATTGGGTGTTT 58.335 42.857 6.65 0.00 0.00 2.83
110 111 2.423185 TGTTTATCATCCAAAGGCTGCG 59.577 45.455 0.00 0.00 0.00 5.18
144 145 4.158394 GTGACAATCTTGGTGCCACATATT 59.842 41.667 0.00 0.00 0.00 1.28
161 162 9.401058 GCCACATATTTATCTGCTAATCCTATT 57.599 33.333 0.00 0.00 0.00 1.73
176 177 2.852449 TCCTATTTTCCATGCCAGGACT 59.148 45.455 0.00 0.00 37.42 3.85
179 180 4.823989 CCTATTTTCCATGCCAGGACTAAG 59.176 45.833 0.00 0.00 37.42 2.18
191 192 6.600388 TGCCAGGACTAAGCATATTGAAATA 58.400 36.000 0.00 0.00 0.00 1.40
194 195 7.609532 GCCAGGACTAAGCATATTGAAATAGAT 59.390 37.037 0.00 0.00 0.00 1.98
221 222 0.394488 TTGTTCGTGAAAGGGTGGCA 60.394 50.000 0.00 0.00 0.00 4.92
224 225 0.400213 TTCGTGAAAGGGTGGCAGAT 59.600 50.000 0.00 0.00 0.00 2.90
239 240 6.096846 GGGTGGCAGATAAGTTGTTGAATATT 59.903 38.462 0.00 0.00 0.00 1.28
245 246 9.937175 GCAGATAAGTTGTTGAATATTAGGTTC 57.063 33.333 0.00 0.00 0.00 3.62
287 288 2.507058 TGCAGATGGATTCACTAAGCCT 59.493 45.455 0.00 0.00 41.96 4.58
294 295 5.599999 TGGATTCACTAAGCCTCTTACTC 57.400 43.478 0.00 0.00 41.96 2.59
297 298 6.895756 TGGATTCACTAAGCCTCTTACTCTTA 59.104 38.462 0.00 0.00 41.96 2.10
299 300 7.923878 GGATTCACTAAGCCTCTTACTCTTAAG 59.076 40.741 0.00 0.00 38.19 1.85
305 306 3.517500 AGCCTCTTACTCTTAAGCAGCTT 59.482 43.478 13.46 13.46 38.92 3.74
306 307 3.620821 GCCTCTTACTCTTAAGCAGCTTG 59.379 47.826 18.54 3.17 35.53 4.01
311 312 1.339535 ACTCTTAAGCAGCTTGAGGCC 60.340 52.381 23.11 0.00 43.05 5.19
314 315 2.165998 CTTAAGCAGCTTGAGGCCTTT 58.834 47.619 18.54 0.00 43.05 3.11
422 425 8.098220 ACCGTGTATATTACGTCATATGTGTA 57.902 34.615 11.65 4.71 39.76 2.90
454 457 0.257328 TCAAGTCAGGTTGTTGGGCA 59.743 50.000 0.00 0.00 0.00 5.36
455 458 1.133513 TCAAGTCAGGTTGTTGGGCAT 60.134 47.619 0.00 0.00 0.00 4.40
518 523 3.491342 TGAGATCGATCCTAACCTCCTG 58.509 50.000 21.66 0.00 0.00 3.86
532 537 1.888436 CTCCTGTAACCTCCTGCGCA 61.888 60.000 10.98 10.98 0.00 6.09
535 540 1.453155 CTGTAACCTCCTGCGCATTT 58.547 50.000 12.24 1.92 0.00 2.32
539 544 4.771903 TGTAACCTCCTGCGCATTTTATA 58.228 39.130 12.24 0.00 0.00 0.98
541 546 2.572290 ACCTCCTGCGCATTTTATACC 58.428 47.619 12.24 0.00 0.00 2.73
542 547 2.172717 ACCTCCTGCGCATTTTATACCT 59.827 45.455 12.24 0.00 0.00 3.08
543 548 2.549754 CCTCCTGCGCATTTTATACCTG 59.450 50.000 12.24 0.00 0.00 4.00
547 552 3.108144 CTGCGCATTTTATACCTGTTGC 58.892 45.455 12.24 0.00 0.00 4.17
552 557 4.261031 CGCATTTTATACCTGTTGCCCTAC 60.261 45.833 0.00 0.00 0.00 3.18
553 558 4.887655 GCATTTTATACCTGTTGCCCTACT 59.112 41.667 0.00 0.00 0.00 2.57
554 559 5.359860 GCATTTTATACCTGTTGCCCTACTT 59.640 40.000 0.00 0.00 0.00 2.24
555 560 6.544564 GCATTTTATACCTGTTGCCCTACTTA 59.455 38.462 0.00 0.00 0.00 2.24
556 561 7.067737 GCATTTTATACCTGTTGCCCTACTTAA 59.932 37.037 0.00 0.00 0.00 1.85
558 563 6.623979 TTATACCTGTTGCCCTACTTAACA 57.376 37.500 0.00 0.00 33.67 2.41
559 564 3.136009 ACCTGTTGCCCTACTTAACAC 57.864 47.619 0.00 0.00 31.64 3.32
560 565 2.073816 CCTGTTGCCCTACTTAACACG 58.926 52.381 0.00 0.00 31.64 4.49
561 566 2.289195 CCTGTTGCCCTACTTAACACGA 60.289 50.000 0.00 0.00 31.64 4.35
562 567 2.993899 CTGTTGCCCTACTTAACACGAG 59.006 50.000 0.00 0.00 31.64 4.18
596 607 1.266718 CCGCATTGGCATACGCTTAAT 59.733 47.619 0.00 0.00 41.24 1.40
598 609 2.665519 CGCATTGGCATACGCTTAATCC 60.666 50.000 0.00 0.00 41.24 3.01
599 610 2.554032 GCATTGGCATACGCTTAATCCT 59.446 45.455 0.00 0.00 40.72 3.24
600 611 3.365364 GCATTGGCATACGCTTAATCCTC 60.365 47.826 0.00 0.00 40.72 3.71
635 646 2.250924 GATTGGGGATAGGCATTTGGG 58.749 52.381 0.00 0.00 0.00 4.12
655 666 2.223947 GGACGGCACCAATCAAAAAGTT 60.224 45.455 0.00 0.00 0.00 2.66
664 675 4.869861 ACCAATCAAAAAGTTGTTGTGCTC 59.130 37.500 5.68 0.00 36.07 4.26
826 838 2.429610 CAAATCCAAAGCATCCTCCCAG 59.570 50.000 0.00 0.00 0.00 4.45
834 846 2.363795 ATCCTCCCAGTCGCCGAA 60.364 61.111 0.00 0.00 0.00 4.30
886 898 4.256983 TCTTCCTAAGCTCAGAGATCCA 57.743 45.455 0.00 0.00 0.00 3.41
887 899 4.614475 TCTTCCTAAGCTCAGAGATCCAA 58.386 43.478 0.00 0.00 0.00 3.53
889 901 5.128499 TCTTCCTAAGCTCAGAGATCCAAAG 59.872 44.000 0.00 0.00 0.00 2.77
890 902 3.133721 TCCTAAGCTCAGAGATCCAAAGC 59.866 47.826 0.00 0.00 0.00 3.51
891 903 3.118482 CCTAAGCTCAGAGATCCAAAGCA 60.118 47.826 0.00 0.00 35.42 3.91
892 904 3.648507 AAGCTCAGAGATCCAAAGCAT 57.351 42.857 0.00 0.00 35.42 3.79
893 905 3.196939 AGCTCAGAGATCCAAAGCATC 57.803 47.619 0.00 0.00 35.42 3.91
895 907 2.158784 GCTCAGAGATCCAAAGCATCCT 60.159 50.000 0.00 0.00 33.21 3.24
1050 1078 6.095440 ACATTACAGTTTGCTCTGTTCTGTTT 59.905 34.615 13.00 0.00 44.92 2.83
1178 1206 7.228308 CCCAAATGAGTTCTTGGATATCTTCTC 59.772 40.741 2.05 3.36 44.16 2.87
1179 1207 7.992033 CCAAATGAGTTCTTGGATATCTTCTCT 59.008 37.037 2.05 0.00 44.16 3.10
1313 1342 0.475475 GGATGATCATGGGGCTGTCA 59.525 55.000 14.30 0.00 0.00 3.58
1337 1366 2.498941 GGACATCATCGGCTCCGGA 61.499 63.158 2.93 2.93 40.25 5.14
1362 1391 1.594833 GGGACGGTGTACATGCTGA 59.405 57.895 0.00 0.00 0.00 4.26
1799 1828 2.278989 CACGTCACCACCGTCGTT 60.279 61.111 0.00 0.00 36.17 3.85
1890 1919 6.478512 ACCTTGAGAATTGAGATCTACTCC 57.521 41.667 0.00 0.00 44.34 3.85
1891 1920 5.068460 ACCTTGAGAATTGAGATCTACTCCG 59.932 44.000 0.00 0.00 44.34 4.63
1892 1921 5.068460 CCTTGAGAATTGAGATCTACTCCGT 59.932 44.000 0.00 0.00 44.34 4.69
1893 1922 6.263392 CCTTGAGAATTGAGATCTACTCCGTA 59.737 42.308 0.00 0.00 44.34 4.02
1894 1923 7.040062 CCTTGAGAATTGAGATCTACTCCGTAT 60.040 40.741 0.00 0.00 44.34 3.06
1921 1950 2.425578 TGCATGTGTGTTTGCTGATG 57.574 45.000 0.00 0.00 39.60 3.07
1935 1964 1.870055 CTGATGGGTGGTGTGCTTGC 61.870 60.000 0.00 0.00 0.00 4.01
1939 1968 3.982241 GGTGGTGTGCTTGCTGCC 61.982 66.667 0.00 0.00 42.00 4.85
1966 1995 2.683933 TTCGAGACAGGGAGGGCC 60.684 66.667 0.00 0.00 0.00 5.80
2093 2122 0.181350 CTGGGTAAGCATCCACCTCC 59.819 60.000 0.00 0.00 35.04 4.30
2116 2145 2.391926 TCCTCCTGTACTCACACCAA 57.608 50.000 0.00 0.00 0.00 3.67
2174 2203 7.637229 CAAGATTTGATGCGATGAGTAGAATT 58.363 34.615 0.00 0.00 0.00 2.17
2227 2256 4.579454 ATGCAGTGACCAATTGATATGC 57.421 40.909 7.12 10.05 0.00 3.14
2243 2272 6.135290 TGATATGCTGCTGAAATAACCAAC 57.865 37.500 0.00 0.00 0.00 3.77
2244 2273 3.874392 ATGCTGCTGAAATAACCAACC 57.126 42.857 0.00 0.00 0.00 3.77
2246 2275 2.961741 TGCTGCTGAAATAACCAACCAA 59.038 40.909 0.00 0.00 0.00 3.67
2248 2277 3.860754 GCTGCTGAAATAACCAACCAACC 60.861 47.826 0.00 0.00 0.00 3.77
2249 2278 3.571590 TGCTGAAATAACCAACCAACCT 58.428 40.909 0.00 0.00 0.00 3.50
2347 2465 2.819595 CCACGAGGTCCGCAATGG 60.820 66.667 0.00 0.00 43.32 3.16
2348 2466 3.499737 CACGAGGTCCGCAATGGC 61.500 66.667 0.00 0.00 43.32 4.40
2358 2476 1.318886 CCGCAATGGCCCAATGTACA 61.319 55.000 0.00 0.00 36.38 2.90
2370 2488 2.025416 CCAATGTACACCCAATCTCCCA 60.025 50.000 0.00 0.00 0.00 4.37
2394 2513 4.082733 TGTCAAGATCAACGAGGACTAGTG 60.083 45.833 0.00 0.00 0.00 2.74
2415 2534 2.535984 GCATTACTAGCGCAGTACAGTG 59.464 50.000 11.47 13.73 39.52 3.66
2416 2535 2.273370 TTACTAGCGCAGTACAGTGC 57.727 50.000 15.27 15.27 39.52 4.40
2420 2539 3.782042 GCGCAGTACAGTGCTACC 58.218 61.111 15.72 0.00 41.62 3.18
2482 2603 9.739276 TTTTTGTAGATGTGAAGTAAGGATGAT 57.261 29.630 0.00 0.00 0.00 2.45
2644 2765 2.684001 AGTCAAGTTCGTGTTCACCA 57.316 45.000 0.00 0.00 0.00 4.17
2673 2794 0.042431 AGTGCCTGGAGTCTGATCCT 59.958 55.000 0.00 0.00 40.29 3.24
2742 2863 0.755686 AGCTGGCATAGTACAGGCTC 59.244 55.000 0.00 0.00 35.30 4.70
2877 2998 1.337917 TGTCGGCAAACGCTACCAATA 60.338 47.619 0.00 0.00 43.86 1.90
3134 3259 1.540267 TGAGAGAGAAAGGGACGAACG 59.460 52.381 0.00 0.00 0.00 3.95
3136 3261 0.108756 GAGAGAAAGGGACGAACGGG 60.109 60.000 0.00 0.00 0.00 5.28
3175 3300 2.421619 GGGAGAGAAACAGAGCACAAG 58.578 52.381 0.00 0.00 0.00 3.16
3211 3336 7.973388 AGATTCAGACGTTTCTATTCTTCAGAG 59.027 37.037 0.00 0.00 0.00 3.35
3212 3337 6.576662 TCAGACGTTTCTATTCTTCAGAGT 57.423 37.500 0.00 0.00 0.00 3.24
3213 3338 6.982852 TCAGACGTTTCTATTCTTCAGAGTT 58.017 36.000 0.00 0.00 0.00 3.01
3214 3339 6.863645 TCAGACGTTTCTATTCTTCAGAGTTG 59.136 38.462 0.00 0.00 0.00 3.16
3217 3342 5.927115 ACGTTTCTATTCTTCAGAGTTGTCC 59.073 40.000 0.00 0.00 0.00 4.02
3218 3343 5.061064 CGTTTCTATTCTTCAGAGTTGTCCG 59.939 44.000 0.00 0.00 0.00 4.79
3224 3349 1.344763 CTTCAGAGTTGTCCGGTTCCT 59.655 52.381 0.00 0.00 0.00 3.36
3231 3356 2.370849 AGTTGTCCGGTTCCTTACACAT 59.629 45.455 0.00 0.00 0.00 3.21
3232 3357 3.143728 GTTGTCCGGTTCCTTACACATT 58.856 45.455 0.00 0.00 0.00 2.71
3235 3360 3.579586 TGTCCGGTTCCTTACACATTAGT 59.420 43.478 0.00 0.00 0.00 2.24
3269 3398 4.673298 CACGCCACGCCCTACACA 62.673 66.667 0.00 0.00 0.00 3.72
3270 3399 4.675029 ACGCCACGCCCTACACAC 62.675 66.667 0.00 0.00 0.00 3.82
3272 3401 2.742372 GCCACGCCCTACACACAG 60.742 66.667 0.00 0.00 0.00 3.66
3303 3433 0.877071 CCACTGCCAGTCACACATTC 59.123 55.000 0.00 0.00 0.00 2.67
3304 3434 1.544093 CCACTGCCAGTCACACATTCT 60.544 52.381 0.00 0.00 0.00 2.40
3309 3439 2.221169 GCCAGTCACACATTCTTGTCA 58.779 47.619 0.00 0.00 32.34 3.58
3310 3440 2.816087 GCCAGTCACACATTCTTGTCAT 59.184 45.455 0.00 0.00 32.34 3.06
3313 3443 4.067192 CAGTCACACATTCTTGTCATCCA 58.933 43.478 0.00 0.00 32.34 3.41
3318 3448 3.181440 ACACATTCTTGTCATCCACCTGT 60.181 43.478 0.00 0.00 32.34 4.00
3320 3450 2.859165 TTCTTGTCATCCACCTGTCC 57.141 50.000 0.00 0.00 0.00 4.02
3394 3528 1.276421 CCGTGACATTCTCCCTTGAGT 59.724 52.381 0.00 0.00 39.75 3.41
3399 3533 5.006386 GTGACATTCTCCCTTGAGTTTGAT 58.994 41.667 0.00 0.00 39.75 2.57
3419 3553 0.324091 CCTCCTCCCAAATTGCAGCT 60.324 55.000 0.00 0.00 0.00 4.24
3424 3558 0.250684 TCCCAAATTGCAGCTGACGA 60.251 50.000 20.43 9.28 0.00 4.20
3470 3604 1.634973 TCTTCCCAGGTTGCATGATCA 59.365 47.619 0.00 0.00 0.00 2.92
3473 3607 1.721664 CCCAGGTTGCATGATCAGCG 61.722 60.000 0.09 0.00 33.85 5.18
3475 3609 2.117156 AGGTTGCATGATCAGCGGC 61.117 57.895 0.09 5.71 33.85 6.53
3478 3612 1.524393 TTGCATGATCAGCGGCGAT 60.524 52.632 12.98 0.00 33.85 4.58
3503 3637 3.058016 CGTGCCATTGAACTTTGATCTGT 60.058 43.478 0.00 0.00 0.00 3.41
3509 3643 6.127647 GCCATTGAACTTTGATCTGTGGAATA 60.128 38.462 0.00 0.00 0.00 1.75
3527 3661 5.779771 TGGAATAGCATTGTTTCCCTTCTTT 59.220 36.000 10.61 0.00 38.51 2.52
3528 3662 6.101997 GGAATAGCATTGTTTCCCTTCTTTG 58.898 40.000 0.00 0.00 34.15 2.77
3533 3667 4.322650 GCATTGTTTCCCTTCTTTGCCATA 60.323 41.667 0.00 0.00 0.00 2.74
3536 3670 2.817844 GTTTCCCTTCTTTGCCATACGT 59.182 45.455 0.00 0.00 0.00 3.57
3545 3679 0.529773 TTGCCATACGTCGATCCAGC 60.530 55.000 0.00 0.00 0.00 4.85
3547 3681 1.215655 GCCATACGTCGATCCAGCAC 61.216 60.000 0.00 0.00 0.00 4.40
3549 3683 1.470805 CCATACGTCGATCCAGCACAA 60.471 52.381 0.00 0.00 0.00 3.33
3593 3727 3.309121 CCAATAAATCAGGTGGGTCTGGT 60.309 47.826 0.00 0.00 35.58 4.00
3641 3775 1.541588 GCAGTGAAGGGTTTTAGCTGG 59.458 52.381 0.00 0.00 0.00 4.85
3656 3790 1.021968 GCTGGGAAACGTGAAACACT 58.978 50.000 0.00 0.00 35.74 3.55
3672 3806 5.248248 TGAAACACTGGATGGATCAGACTTA 59.752 40.000 0.00 0.00 36.22 2.24
3680 3814 6.565036 TGGATGGATCAGACTTATATCAGGA 58.435 40.000 0.00 0.00 0.00 3.86
3698 3832 3.246226 CAGGAAAATCCAGACGATAAGCG 59.754 47.826 0.00 0.00 42.30 4.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.061220 CCTCTGTGCTTGACCTGGA 58.939 57.895 0.00 0.00 0.00 3.86
1 2 1.673665 GCCTCTGTGCTTGACCTGG 60.674 63.158 0.00 0.00 0.00 4.45
2 3 0.954449 CAGCCTCTGTGCTTGACCTG 60.954 60.000 0.00 0.00 40.32 4.00
3 4 1.123861 TCAGCCTCTGTGCTTGACCT 61.124 55.000 0.00 0.00 40.32 3.85
8 9 3.133721 CCTTATACTCAGCCTCTGTGCTT 59.866 47.826 0.00 0.00 40.32 3.91
11 12 2.697751 AGCCTTATACTCAGCCTCTGTG 59.302 50.000 0.00 0.00 32.61 3.66
44 45 4.701651 TGAACCCAAATAATCTCTGCAGTG 59.298 41.667 14.67 11.96 0.00 3.66
50 51 6.545298 GCAGATTCTGAACCCAAATAATCTCT 59.455 38.462 17.87 0.00 32.76 3.10
53 54 6.319658 TCAGCAGATTCTGAACCCAAATAATC 59.680 38.462 17.87 0.00 39.89 1.75
72 73 1.901591 ACACCCAATTCTGTCAGCAG 58.098 50.000 0.00 0.00 43.87 4.24
93 94 1.209261 TGACGCAGCCTTTGGATGATA 59.791 47.619 6.00 0.00 42.34 2.15
125 126 7.143340 CAGATAAATATGTGGCACCAAGATTG 58.857 38.462 16.26 0.00 0.00 2.67
144 145 7.394359 GGCATGGAAAATAGGATTAGCAGATAA 59.606 37.037 0.00 0.00 0.00 1.75
161 162 1.354031 TGCTTAGTCCTGGCATGGAAA 59.646 47.619 7.17 0.29 37.93 3.13
164 165 2.936919 TATGCTTAGTCCTGGCATGG 57.063 50.000 15.10 0.00 44.83 3.66
191 192 7.176690 ACCCTTTCACGAACAAAATGATAATCT 59.823 33.333 0.00 0.00 0.00 2.40
194 195 6.442952 CACCCTTTCACGAACAAAATGATAA 58.557 36.000 0.00 0.00 0.00 1.75
213 214 2.375174 TCAACAACTTATCTGCCACCCT 59.625 45.455 0.00 0.00 0.00 4.34
245 246 6.108687 TGCAACTTGATCTTCAGTAGGTATG 58.891 40.000 0.00 0.00 0.00 2.39
251 252 5.046376 TCCATCTGCAACTTGATCTTCAGTA 60.046 40.000 0.00 0.00 0.00 2.74
256 257 5.125097 GTGAATCCATCTGCAACTTGATCTT 59.875 40.000 0.00 0.00 0.00 2.40
257 258 4.639310 GTGAATCCATCTGCAACTTGATCT 59.361 41.667 0.00 0.00 0.00 2.75
287 288 4.621747 GCCTCAAGCTGCTTAAGAGTAAGA 60.622 45.833 21.28 10.42 37.76 2.10
294 295 1.831580 AAGGCCTCAAGCTGCTTAAG 58.168 50.000 15.51 10.34 43.05 1.85
297 298 1.352352 TCTAAAGGCCTCAAGCTGCTT 59.648 47.619 5.23 9.53 43.05 3.91
299 300 1.090728 GTCTAAAGGCCTCAAGCTGC 58.909 55.000 5.23 0.00 43.05 5.25
305 306 1.555075 AGATTGCGTCTAAAGGCCTCA 59.445 47.619 5.23 0.00 34.69 3.86
306 307 2.205911 GAGATTGCGTCTAAAGGCCTC 58.794 52.381 5.23 0.00 37.29 4.70
311 312 4.690748 TCCAAGTTGAGATTGCGTCTAAAG 59.309 41.667 3.87 0.00 37.29 1.85
314 315 3.953712 TCCAAGTTGAGATTGCGTCTA 57.046 42.857 3.87 0.00 37.29 2.59
422 425 1.269361 TGACTTGATACACACGCACGT 60.269 47.619 0.00 0.00 0.00 4.49
518 523 4.024302 GGTATAAAATGCGCAGGAGGTTAC 60.024 45.833 18.32 12.66 0.00 2.50
532 537 8.110908 TGTTAAGTAGGGCAACAGGTATAAAAT 58.889 33.333 0.00 0.00 39.74 1.82
535 540 6.408869 GTGTTAAGTAGGGCAACAGGTATAA 58.591 40.000 0.00 0.00 33.10 0.98
539 544 2.549349 CGTGTTAAGTAGGGCAACAGGT 60.549 50.000 0.00 0.00 34.81 4.00
541 546 2.993899 CTCGTGTTAAGTAGGGCAACAG 59.006 50.000 0.00 0.00 33.10 3.16
542 547 2.289195 CCTCGTGTTAAGTAGGGCAACA 60.289 50.000 0.00 0.00 39.74 3.33
543 548 2.289257 ACCTCGTGTTAAGTAGGGCAAC 60.289 50.000 0.00 0.00 33.16 4.17
547 552 2.478539 GCGTACCTCGTGTTAAGTAGGG 60.479 54.545 0.00 0.00 42.13 3.53
558 563 3.437795 CAGGGACGCGTACCTCGT 61.438 66.667 40.11 18.47 40.91 4.18
559 564 4.849329 GCAGGGACGCGTACCTCG 62.849 72.222 40.11 31.89 40.91 4.63
560 565 4.509737 GGCAGGGACGCGTACCTC 62.510 72.222 40.11 30.49 40.91 3.85
578 588 2.554032 AGGATTAAGCGTATGCCAATGC 59.446 45.455 12.67 12.67 44.31 3.56
579 589 4.067896 AGAGGATTAAGCGTATGCCAATG 58.932 43.478 2.51 0.00 44.31 2.82
581 591 3.838244 AGAGGATTAAGCGTATGCCAA 57.162 42.857 2.51 0.00 44.31 4.52
596 607 6.015180 CCCAATCAATTCTTGTGAAAAGAGGA 60.015 38.462 0.00 0.00 35.63 3.71
598 609 6.015180 TCCCCAATCAATTCTTGTGAAAAGAG 60.015 38.462 0.00 0.00 35.63 2.85
599 610 5.837979 TCCCCAATCAATTCTTGTGAAAAGA 59.162 36.000 0.00 0.00 35.63 2.52
600 611 6.100404 TCCCCAATCAATTCTTGTGAAAAG 57.900 37.500 0.00 0.00 35.63 2.27
635 646 2.793278 ACTTTTTGATTGGTGCCGTC 57.207 45.000 0.00 0.00 0.00 4.79
655 666 2.280797 GCAGACCCGAGCACAACA 60.281 61.111 0.00 0.00 0.00 3.33
664 675 0.392863 TCATGTGAATGGCAGACCCG 60.393 55.000 0.00 0.00 35.87 5.28
826 838 3.963383 ATATGTTTTGGATTCGGCGAC 57.037 42.857 10.16 0.00 0.00 5.19
834 846 5.270853 GCGAACGCTAAATATGTTTTGGAT 58.729 37.500 11.97 0.00 38.26 3.41
889 901 0.915364 ACCCAGAAGAAGGAGGATGC 59.085 55.000 0.00 0.00 0.00 3.91
890 902 3.777522 ACTTACCCAGAAGAAGGAGGATG 59.222 47.826 0.00 0.00 0.00 3.51
891 903 4.081695 ACTTACCCAGAAGAAGGAGGAT 57.918 45.455 0.00 0.00 0.00 3.24
892 904 3.562108 ACTTACCCAGAAGAAGGAGGA 57.438 47.619 0.00 0.00 0.00 3.71
893 905 4.383226 GCTTACTTACCCAGAAGAAGGAGG 60.383 50.000 0.00 0.00 0.00 4.30
895 907 4.223032 CAGCTTACTTACCCAGAAGAAGGA 59.777 45.833 0.00 0.00 0.00 3.36
1313 1342 0.254178 AGCCGATGATGTCCTTGCTT 59.746 50.000 0.00 0.00 0.00 3.91
1337 1366 1.678970 GTACACCGTCCCGTACCCT 60.679 63.158 0.00 0.00 33.39 4.34
1362 1391 2.344203 CCGACTTCTCGTCCAGCCT 61.344 63.158 0.00 0.00 39.56 4.58
1883 1912 6.378280 ACATGCATGATGATATACGGAGTAGA 59.622 38.462 32.75 0.00 40.25 2.59
1884 1913 6.474751 CACATGCATGATGATATACGGAGTAG 59.525 42.308 32.75 0.00 40.25 2.57
1885 1914 6.071391 ACACATGCATGATGATATACGGAGTA 60.071 38.462 32.75 0.00 40.80 2.59
1886 1915 5.173664 CACATGCATGATGATATACGGAGT 58.826 41.667 32.75 2.07 39.26 3.85
1887 1916 5.063060 CACACATGCATGATGATATACGGAG 59.937 44.000 32.75 1.29 35.80 4.63
1888 1917 4.931002 CACACATGCATGATGATATACGGA 59.069 41.667 32.75 0.00 35.80 4.69
1889 1918 4.692155 ACACACATGCATGATGATATACGG 59.308 41.667 32.75 11.40 35.80 4.02
1890 1919 5.851047 ACACACATGCATGATGATATACG 57.149 39.130 32.75 11.88 35.80 3.06
1891 1920 6.361481 GCAAACACACATGCATGATGATATAC 59.639 38.462 32.75 15.57 42.12 1.47
1892 1921 6.263617 AGCAAACACACATGCATGATGATATA 59.736 34.615 32.75 0.00 44.95 0.86
1893 1922 5.068591 AGCAAACACACATGCATGATGATAT 59.931 36.000 32.75 16.88 44.95 1.63
1894 1923 4.399934 AGCAAACACACATGCATGATGATA 59.600 37.500 32.75 0.00 44.95 2.15
1921 1950 3.982241 GCAGCAAGCACACCACCC 61.982 66.667 0.00 0.00 44.79 4.61
1935 1964 2.096819 GTCTCGAAGTACTCTGAGGCAG 59.903 54.545 18.82 0.00 32.79 4.85
1939 1968 2.680841 CCCTGTCTCGAAGTACTCTGAG 59.319 54.545 14.98 14.98 0.00 3.35
1966 1995 1.227999 ACACATCGCCTTTGGTCGTG 61.228 55.000 0.00 0.00 0.00 4.35
2093 2122 2.093447 GGTGTGAGTACAGGAGGAATGG 60.093 54.545 0.00 0.00 37.52 3.16
2227 2256 3.573967 AGGTTGGTTGGTTATTTCAGCAG 59.426 43.478 0.00 0.00 0.00 4.24
2243 2272 6.702282 GCTAAGTAGTTGATAGCTAAGGTTGG 59.298 42.308 0.00 0.00 39.12 3.77
2244 2273 7.265673 TGCTAAGTAGTTGATAGCTAAGGTTG 58.734 38.462 0.00 0.00 41.97 3.77
2246 2275 7.419711 TTGCTAAGTAGTTGATAGCTAAGGT 57.580 36.000 0.00 0.00 41.97 3.50
2248 2277 9.190858 CAGATTGCTAAGTAGTTGATAGCTAAG 57.809 37.037 0.00 0.00 41.97 2.18
2249 2278 8.696374 ACAGATTGCTAAGTAGTTGATAGCTAA 58.304 33.333 0.00 0.35 41.97 3.09
2341 2459 0.175531 GGTGTACATTGGGCCATTGC 59.824 55.000 24.43 12.30 0.00 3.56
2342 2460 0.823460 GGGTGTACATTGGGCCATTG 59.177 55.000 23.25 23.25 0.00 2.82
2343 2461 0.411452 TGGGTGTACATTGGGCCATT 59.589 50.000 7.26 0.00 0.00 3.16
2344 2462 0.411452 TTGGGTGTACATTGGGCCAT 59.589 50.000 7.26 0.00 0.00 4.40
2345 2463 0.411452 ATTGGGTGTACATTGGGCCA 59.589 50.000 0.00 0.00 0.00 5.36
2346 2464 1.111277 GATTGGGTGTACATTGGGCC 58.889 55.000 0.00 0.00 0.00 5.80
2347 2465 2.024414 GAGATTGGGTGTACATTGGGC 58.976 52.381 0.00 0.00 0.00 5.36
2348 2466 2.654863 GGAGATTGGGTGTACATTGGG 58.345 52.381 0.00 0.00 0.00 4.12
2358 2476 2.278245 TCTTGACATGGGAGATTGGGT 58.722 47.619 0.00 0.00 0.00 4.51
2370 2488 4.707448 ACTAGTCCTCGTTGATCTTGACAT 59.293 41.667 0.00 0.00 0.00 3.06
2394 2513 2.535984 CACTGTACTGCGCTAGTAATGC 59.464 50.000 17.41 9.11 43.24 3.56
2416 2535 4.645136 TCAGACCATGCTACTGTTAGGTAG 59.355 45.833 10.26 0.00 41.31 3.18
2419 2538 4.679373 ATCAGACCATGCTACTGTTAGG 57.321 45.455 10.26 0.00 33.93 2.69
2420 2539 6.648310 CCATTATCAGACCATGCTACTGTTAG 59.352 42.308 10.26 0.00 33.93 2.34
2430 2551 5.702670 GGTACATGTCCATTATCAGACCATG 59.297 44.000 0.00 0.00 32.54 3.66
2482 2603 3.071312 GGGATGCATGCCCAATTAATTCA 59.929 43.478 25.86 0.00 45.31 2.57
2673 2794 1.227527 CATGGTTGGCCTATCGCGA 60.228 57.895 13.09 13.09 38.94 5.87
2721 2842 1.561542 AGCCTGTACTATGCCAGCTTT 59.438 47.619 0.00 0.00 0.00 3.51
2742 2863 4.032445 AGTTACACATACTGCGCGTTAATG 59.968 41.667 8.43 9.48 0.00 1.90
2948 3069 3.134623 TGTCTACCCAGCAGTATTGGATG 59.865 47.826 0.00 0.00 37.96 3.51
3134 3259 3.277715 CCTTTCTCTGCAATCTCTTCCC 58.722 50.000 0.00 0.00 0.00 3.97
3136 3261 3.054802 TCCCCTTTCTCTGCAATCTCTTC 60.055 47.826 0.00 0.00 0.00 2.87
3175 3300 3.492337 ACGTCTGAATCTATCTCTCCCC 58.508 50.000 0.00 0.00 0.00 4.81
3211 3336 2.243602 TGTGTAAGGAACCGGACAAC 57.756 50.000 9.46 1.50 0.00 3.32
3212 3337 3.495434 AATGTGTAAGGAACCGGACAA 57.505 42.857 9.46 0.00 0.00 3.18
3213 3338 3.579586 ACTAATGTGTAAGGAACCGGACA 59.420 43.478 9.46 0.00 0.00 4.02
3214 3339 3.930848 CACTAATGTGTAAGGAACCGGAC 59.069 47.826 9.46 0.76 39.24 4.79
3217 3342 3.934068 ACCACTAATGTGTAAGGAACCG 58.066 45.455 0.00 0.00 42.34 4.44
3235 3360 2.823984 CGTGCGTGGGTTTATATACCA 58.176 47.619 13.55 1.14 40.09 3.25
3261 3390 2.427453 CCTAGCTGTACTGTGTGTAGGG 59.573 54.545 0.00 0.00 0.00 3.53
3263 3392 2.159226 GGCCTAGCTGTACTGTGTGTAG 60.159 54.545 0.00 0.00 0.00 2.74
3269 3398 0.252284 AGTGGGCCTAGCTGTACTGT 60.252 55.000 4.53 0.00 0.00 3.55
3270 3399 0.176680 CAGTGGGCCTAGCTGTACTG 59.823 60.000 4.53 4.12 31.93 2.74
3272 3401 1.153349 GCAGTGGGCCTAGCTGTAC 60.153 63.158 19.00 3.06 36.11 2.90
3303 3433 1.349026 ACTGGACAGGTGGATGACAAG 59.651 52.381 4.14 0.00 0.00 3.16
3304 3434 1.072173 CACTGGACAGGTGGATGACAA 59.928 52.381 4.14 0.00 0.00 3.18
3318 3448 2.203938 GACCCTGGGTCCACTGGA 60.204 66.667 31.73 0.00 46.19 3.86
3360 3490 0.738975 TCACGGCTCCATCTCTAACG 59.261 55.000 0.00 0.00 0.00 3.18
3363 3493 2.073252 ATGTCACGGCTCCATCTCTA 57.927 50.000 0.00 0.00 0.00 2.43
3365 3495 1.137872 AGAATGTCACGGCTCCATCTC 59.862 52.381 0.00 0.00 0.00 2.75
3366 3496 1.137872 GAGAATGTCACGGCTCCATCT 59.862 52.381 0.00 0.00 0.00 2.90
3394 3528 3.099141 GCAATTTGGGAGGAGGATCAAA 58.901 45.455 0.00 0.00 36.25 2.69
3399 3533 0.323725 GCTGCAATTTGGGAGGAGGA 60.324 55.000 0.00 0.00 0.00 3.71
3419 3553 2.542409 CGCGCTCGTTTTTCGTCA 59.458 55.556 5.56 0.00 40.80 4.35
3424 3558 1.937362 GTGTTGCGCGCTCGTTTTT 60.937 52.632 33.29 0.00 38.14 1.94
3475 3609 1.651987 AGTTCAATGGCACGGTATCG 58.348 50.000 0.00 0.00 43.02 2.92
3478 3612 2.852449 TCAAAGTTCAATGGCACGGTA 58.148 42.857 0.00 0.00 0.00 4.02
3503 3637 4.934356 AGAAGGGAAACAATGCTATTCCA 58.066 39.130 12.86 0.00 43.56 3.53
3509 3643 2.037641 GGCAAAGAAGGGAAACAATGCT 59.962 45.455 0.00 0.00 33.29 3.79
3527 3661 1.067416 GCTGGATCGACGTATGGCA 59.933 57.895 0.00 0.00 0.00 4.92
3528 3662 1.067416 TGCTGGATCGACGTATGGC 59.933 57.895 0.00 0.00 0.00 4.40
3533 3667 1.374252 GGTTGTGCTGGATCGACGT 60.374 57.895 0.00 0.00 0.00 4.34
3536 3670 0.247460 CAGAGGTTGTGCTGGATCGA 59.753 55.000 0.00 0.00 0.00 3.59
3549 3683 1.343069 GTCACTCTCCAACCAGAGGT 58.657 55.000 2.68 0.00 43.89 3.85
3573 3707 4.385310 GCTACCAGACCCACCTGATTTATT 60.385 45.833 0.00 0.00 36.29 1.40
3593 3727 2.828520 CTCTCCAGTGTTTCAGGAGCTA 59.171 50.000 0.00 0.00 45.67 3.32
3641 3775 2.031157 CCATCCAGTGTTTCACGTTTCC 60.031 50.000 0.00 0.00 39.64 3.13
3656 3790 6.565036 TCCTGATATAAGTCTGATCCATCCA 58.435 40.000 0.00 0.00 0.00 3.41
3672 3806 6.876257 GCTTATCGTCTGGATTTTCCTGATAT 59.124 38.462 6.43 6.49 44.56 1.63
3680 3814 1.940613 GCCGCTTATCGTCTGGATTTT 59.059 47.619 0.00 0.00 36.55 1.82


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

AutoCloner maintained by Alex Coulton.