Multiple sequence alignment - TraesCS6A01G101200

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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 TraesCS6A01G101200 chr6A 100.000 4075 0 0 1 4075 69140537 69136463 0.000000e+00 7526.0
1 TraesCS6A01G101200 chr6A 80.899 178 29 5 259 434 88804031 88804205 7.100000e-28 135.0
2 TraesCS6A01G101200 chr6A 77.778 234 38 9 326 547 56257120 56256889 9.190000e-27 132.0
3 TraesCS6A01G101200 chr6B 90.915 3247 218 39 1 3214 125411804 125408602 0.000000e+00 4290.0
4 TraesCS6A01G101200 chr6B 82.353 476 60 16 2846 3313 125341163 125340704 3.820000e-105 392.0
5 TraesCS6A01G101200 chr6B 84.422 398 46 9 2846 3240 125384114 125383730 1.070000e-100 377.0
6 TraesCS6A01G101200 chr6B 73.551 276 50 8 268 524 182593256 182593527 2.610000e-12 84.2
7 TraesCS6A01G101200 chr6D 91.585 2436 139 28 886 3302 55634972 55632584 0.000000e+00 3302.0
8 TraesCS6A01G101200 chr6D 91.675 1057 52 12 3015 4054 55427250 55426213 0.000000e+00 1432.0
9 TraesCS6A01G101200 chr6D 86.417 854 91 14 1 840 55669661 55668819 0.000000e+00 911.0
10 TraesCS6A01G101200 chr6D 97.768 224 5 0 2756 2979 55427466 55427243 1.780000e-103 387.0
11 TraesCS6A01G101200 chr6D 81.720 465 53 20 2846 3298 55317969 55317525 3.870000e-95 359.0
12 TraesCS6A01G101200 chr6D 80.488 492 63 20 2846 3313 55110071 55109589 3.020000e-91 346.0
13 TraesCS6A01G101200 chr6D 82.484 314 43 10 2929 3240 55407619 55407316 8.680000e-67 265.0
14 TraesCS6A01G101200 chr6D 93.617 141 9 0 2617 2757 55427842 55427702 1.150000e-50 211.0
15 TraesCS6A01G101200 chr6D 76.774 310 56 15 3085 3389 46912396 46912694 4.220000e-35 159.0
16 TraesCS6A01G101200 chr6D 91.139 79 7 0 2543 2621 55432727 55432649 1.550000e-19 108.0
17 TraesCS6A01G101200 chr6D 97.222 36 1 0 4040 4075 55407669 55407634 1.220000e-05 62.1
18 TraesCS6A01G101200 chr6D 82.667 75 8 4 450 522 121800656 121800727 1.220000e-05 62.1
19 TraesCS6A01G101200 chr6D 83.582 67 6 4 450 514 121801422 121801485 1.580000e-04 58.4
20 TraesCS6A01G101200 chr6D 83.582 67 6 4 450 514 121802187 121802250 1.580000e-04 58.4
21 TraesCS6A01G101200 chr5A 79.644 393 53 16 1079 1457 691824209 691824588 1.450000e-64 257.0
22 TraesCS6A01G101200 chr5D 78.161 261 43 9 249 500 328587144 328587399 1.960000e-33 154.0
23 TraesCS6A01G101200 chr1B 76.358 313 52 14 248 546 560254199 560254503 9.130000e-32 148.0
24 TraesCS6A01G101200 chr7D 77.519 258 48 7 257 504 622218395 622218138 3.280000e-31 147.0
25 TraesCS6A01G101200 chr7B 77.323 269 48 6 257 514 719924233 719923967 3.280000e-31 147.0
26 TraesCS6A01G101200 chr2B 76.101 318 51 12 248 555 6254883 6254581 4.250000e-30 143.0
27 TraesCS6A01G101200 chr2B 75.833 240 53 5 300 535 789444962 789444724 2.570000e-22 117.0
28 TraesCS6A01G101200 chr2B 90.909 44 4 0 484 527 526749683 526749640 4.400000e-05 60.2
29 TraesCS6A01G101200 chr3A 74.150 294 54 18 267 545 749726793 749727079 7.210000e-18 102.0
30 TraesCS6A01G101200 chr2D 75.431 232 40 8 328 547 589525098 589524872 3.350000e-16 97.1


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 TraesCS6A01G101200 chr6A 69136463 69140537 4074 True 7526.000000 7526 100.000000 1 4075 1 chr6A.!!$R2 4074
1 TraesCS6A01G101200 chr6B 125408602 125411804 3202 True 4290.000000 4290 90.915000 1 3214 1 chr6B.!!$R3 3213
2 TraesCS6A01G101200 chr6D 55632584 55634972 2388 True 3302.000000 3302 91.585000 886 3302 1 chr6D.!!$R4 2416
3 TraesCS6A01G101200 chr6D 55668819 55669661 842 True 911.000000 911 86.417000 1 840 1 chr6D.!!$R5 839
4 TraesCS6A01G101200 chr6D 55426213 55427842 1629 True 676.666667 1432 94.353333 2617 4054 3 chr6D.!!$R7 1437

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
536 550 0.110419 GCGTCTGCGTTTGTATTGCA 60.110 50.0 0.0 0.0 40.81 4.08 F
1650 1673 0.464870 CTCAGCAGCAGATGGTAGCT 59.535 55.0 0.0 0.0 42.94 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1817 1846 0.974383 TCCCTGGTCTCGGTTTCTTC 59.026 55.0 0.00 0.0 0.00 2.87 R
3408 3684 0.038251 CTTCAGTAGGCGTGACTGCA 60.038 55.0 11.05 0.0 43.37 4.41 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
52 53 9.466497 TCAGCAAGATCCAAATAAAGAAGTAAT 57.534 29.630 0.00 0.00 0.00 1.89
199 201 9.745323 GCATTTGTCTTGCATATTCTTTTTAAC 57.255 29.630 0.00 0.00 39.90 2.01
276 280 2.262637 TGGTTGGATCGTTAGGAAGGT 58.737 47.619 0.00 0.00 0.00 3.50
298 302 0.485543 TGGTATCCCTAGCCCATCGA 59.514 55.000 0.00 0.00 0.00 3.59
322 326 9.831737 CGAAGTTCAAATCTTAGATTTGACATT 57.168 29.630 35.77 31.52 44.67 2.71
337 341 3.761657 TGACATTGATGCTCGCATTTTC 58.238 40.909 5.79 0.00 36.70 2.29
341 345 1.825090 TGATGCTCGCATTTTCCTGT 58.175 45.000 5.79 0.00 36.70 4.00
350 354 6.751425 TGCTCGCATTTTCCTGTATTTATTTG 59.249 34.615 0.00 0.00 0.00 2.32
358 362 6.773976 TTCCTGTATTTATTTGAGGGCTTG 57.226 37.500 0.00 0.00 0.00 4.01
379 383 1.225855 GGCGATGTGTGTTCAGTGAA 58.774 50.000 0.08 0.08 0.00 3.18
382 386 2.908634 CGATGTGTGTTCAGTGAAAGC 58.091 47.619 7.25 4.14 0.00 3.51
406 410 3.179010 CGTTCTCGTCGACTACAAAGA 57.821 47.619 14.70 5.77 0.00 2.52
438 452 3.057734 GACTTCGTCAATCTCAACGGTT 58.942 45.455 0.00 0.00 39.31 4.44
444 458 2.737252 GTCAATCTCAACGGTTCAGTCC 59.263 50.000 0.00 0.00 0.00 3.85
448 462 0.388649 CTCAACGGTTCAGTCCCTCG 60.389 60.000 0.00 0.00 0.00 4.63
452 466 2.711922 CGGTTCAGTCCCTCGGAGG 61.712 68.421 17.41 17.41 34.30 4.30
463 477 1.365633 CTCGGAGGTGCTCATAGGC 59.634 63.158 0.00 0.00 31.08 3.93
464 478 1.381191 TCGGAGGTGCTCATAGGCA 60.381 57.895 0.00 0.00 40.15 4.75
465 479 0.760567 TCGGAGGTGCTCATAGGCAT 60.761 55.000 0.00 0.00 44.34 4.40
468 482 2.251818 GGAGGTGCTCATAGGCATAGA 58.748 52.381 0.00 0.00 44.34 1.98
469 483 2.233431 GGAGGTGCTCATAGGCATAGAG 59.767 54.545 0.00 0.00 44.34 2.43
479 493 2.322355 AGGCATAGAGTGTGCATGTC 57.678 50.000 0.00 0.00 44.25 3.06
483 497 2.350804 GCATAGAGTGTGCATGTCTGTG 59.649 50.000 12.46 12.46 42.08 3.66
490 504 3.999001 AGTGTGCATGTCTGTGTTCATAG 59.001 43.478 0.00 0.00 0.00 2.23
514 528 5.520632 AGATGAGTGTATGTGCGTATGTAC 58.479 41.667 0.00 0.00 0.00 2.90
515 529 4.705337 TGAGTGTATGTGCGTATGTACA 57.295 40.909 8.38 8.38 44.99 2.90
523 537 1.320555 GTGCGTATGTACAAGCGTCTG 59.679 52.381 18.93 0.81 0.00 3.51
524 538 0.297820 GCGTATGTACAAGCGTCTGC 59.702 55.000 18.93 6.19 43.24 4.26
535 549 2.625488 GCGTCTGCGTTTGTATTGC 58.375 52.632 0.00 0.00 40.81 3.56
536 550 0.110419 GCGTCTGCGTTTGTATTGCA 60.110 50.000 0.00 0.00 40.81 4.08
618 632 9.578576 TCAGGTTCATATATTACCTAGTAACGT 57.421 33.333 13.48 0.00 40.24 3.99
630 644 4.639310 ACCTAGTAACGTCTACCATCACTG 59.361 45.833 0.00 0.00 0.00 3.66
640 654 2.046988 CATCACTGGTGCGAGCCA 60.047 61.111 0.00 0.00 36.97 4.75
655 669 2.671070 CCAAGGAGGCACCATCGT 59.329 61.111 3.18 0.00 42.04 3.73
656 670 1.450312 CCAAGGAGGCACCATCGTC 60.450 63.158 3.18 0.00 42.04 4.20
661 675 1.154205 GGAGGCACCATCGTCATTCG 61.154 60.000 0.00 0.00 38.79 3.34
671 685 0.895530 TCGTCATTCGCTCCTTCCTT 59.104 50.000 0.00 0.00 39.67 3.36
681 695 2.690497 CGCTCCTTCCTTATCAGAGACA 59.310 50.000 0.00 0.00 0.00 3.41
688 702 6.729100 TCCTTCCTTATCAGAGACAGGTAAAA 59.271 38.462 0.00 0.00 0.00 1.52
744 758 4.697352 AGAAAAACCATGGAAGTCTCGATG 59.303 41.667 21.47 0.00 37.49 3.84
753 769 3.192844 TGGAAGTCTCGATGGTGTAGAAC 59.807 47.826 0.00 0.00 0.00 3.01
774 790 7.746703 AGAACTAGGATTGGTTTAACTTGTCT 58.253 34.615 0.00 0.00 0.00 3.41
856 874 7.972832 TTGGAGTACTGTATTCAAATTCGTT 57.027 32.000 0.00 0.00 0.00 3.85
870 888 5.759273 TCAAATTCGTTCTCTTTTACCCGAA 59.241 36.000 0.00 0.00 38.48 4.30
871 889 6.260493 TCAAATTCGTTCTCTTTTACCCGAAA 59.740 34.615 0.00 0.00 37.77 3.46
872 890 6.622833 AATTCGTTCTCTTTTACCCGAAAA 57.377 33.333 0.00 0.00 37.77 2.29
873 891 6.622833 ATTCGTTCTCTTTTACCCGAAAAA 57.377 33.333 0.00 0.00 36.59 1.94
1007 1027 2.266055 CACGCCTCCCCAGTCTTC 59.734 66.667 0.00 0.00 0.00 2.87
1026 1046 0.933047 CCGATTCAGTTCGCGCGATA 60.933 55.000 35.21 21.11 37.80 2.92
1031 1051 0.734309 TCAGTTCGCGCGATAGGTAA 59.266 50.000 35.21 15.30 0.00 2.85
1069 1089 3.638592 AATCCCAGGGTTTCCGCCG 62.639 63.158 5.01 0.00 38.33 6.46
1077 1097 2.631580 GGTTTCCGCCGCCAAATCA 61.632 57.895 0.00 0.00 0.00 2.57
1185 1205 3.822192 CCCCGATCGACGCACTCA 61.822 66.667 18.66 0.00 41.07 3.41
1187 1207 1.658717 CCCGATCGACGCACTCATC 60.659 63.158 18.66 0.00 41.07 2.92
1389 1409 2.802792 CGCGGATCTACAACCCGA 59.197 61.111 0.00 0.00 45.58 5.14
1558 1581 3.814906 TGGTGGTGGTGGTGGTGG 61.815 66.667 0.00 0.00 0.00 4.61
1559 1582 3.816090 GGTGGTGGTGGTGGTGGT 61.816 66.667 0.00 0.00 0.00 4.16
1570 1593 0.693049 GGTGGTGGTGGTGAGAAGAT 59.307 55.000 0.00 0.00 0.00 2.40
1607 1630 3.976339 GGATGACTCCGATGGTGAG 57.024 57.895 0.00 0.00 35.92 3.51
1614 1637 1.612146 TCCGATGGTGAGCCTTCCA 60.612 57.895 0.00 0.00 36.03 3.53
1650 1673 0.464870 CTCAGCAGCAGATGGTAGCT 59.535 55.000 0.00 0.00 42.94 3.32
1659 1682 2.357009 GCAGATGGTAGCTTCAATGGTG 59.643 50.000 10.10 1.21 0.00 4.17
1683 1706 0.543277 AGAGAATTCTCATGCCGGCA 59.457 50.000 34.80 34.80 45.21 5.69
1701 1724 1.805871 GCAATGGTGGTGTTGTTGTGG 60.806 52.381 0.00 0.00 0.00 4.17
1730 1753 1.636003 GAGGAAGGAGGTCCCAACAAT 59.364 52.381 0.00 0.00 38.59 2.71
1756 1779 8.841300 TGGGGCTTTTAATTTTGAAAACATAAC 58.159 29.630 0.00 0.00 0.00 1.89
1774 1797 7.707774 ACATAACAAAATTCCTTTTTCCACG 57.292 32.000 0.00 0.00 35.31 4.94
1792 1821 3.093574 CACGCAATGATAAAGACAAGCG 58.906 45.455 0.00 0.00 44.66 4.68
1796 1825 4.496341 CGCAATGATAAAGACAAGCGGAAT 60.496 41.667 0.00 0.00 39.88 3.01
1798 1827 6.494842 GCAATGATAAAGACAAGCGGAATAA 58.505 36.000 0.00 0.00 0.00 1.40
1815 1844 4.947388 GGAATAAACCTGTGCACAAGGATA 59.053 41.667 30.11 23.37 0.00 2.59
1816 1845 5.417580 GGAATAAACCTGTGCACAAGGATAA 59.582 40.000 30.11 18.91 0.00 1.75
1817 1846 6.404734 GGAATAAACCTGTGCACAAGGATAAG 60.405 42.308 30.11 15.29 0.00 1.73
1892 1921 5.131142 ACCATCCGAGAAGAAGTTGGATTAT 59.869 40.000 0.00 0.00 37.33 1.28
1906 1935 3.803840 GGATTATTCCAACCCGGCGGT 62.804 57.143 26.32 10.35 42.12 5.68
1964 1993 1.424302 CAGGGGAAGAGCATGATGGAT 59.576 52.381 0.00 0.00 0.00 3.41
1976 2005 3.126514 GCATGATGGATAAGGATGAAGCG 59.873 47.826 0.00 0.00 0.00 4.68
2036 2065 1.279496 TCAGGAGCATTGCAGGTAGT 58.721 50.000 11.91 0.00 0.00 2.73
2150 2179 0.605083 AGCTCTGTGAATCAGTCGCA 59.395 50.000 0.00 0.00 44.57 5.10
2153 2182 4.284123 TGTGAATCAGTCGCAGCC 57.716 55.556 0.00 0.00 41.89 4.85
2177 2206 1.556911 CTCCTAGGCAAGAAGCTTGGA 59.443 52.381 2.10 0.00 44.79 3.53
2231 2260 1.488393 GCTATGGAAGAGGCTCTGGTT 59.512 52.381 19.53 1.50 0.00 3.67
2558 2587 1.076332 CCCGGAACAAATCAGACGTC 58.924 55.000 7.70 7.70 0.00 4.34
2645 2674 4.703897 TCATCAATCTCAATAACCCGGAC 58.296 43.478 0.73 0.00 0.00 4.79
3007 3273 8.882415 AATATCCATTACTTTGTCGTTATCGT 57.118 30.769 0.00 0.00 38.33 3.73
3011 3277 7.952339 TCCATTACTTTGTCGTTATCGTTAAC 58.048 34.615 6.35 6.35 38.33 2.01
3056 3322 6.569127 TGATACTTATGTAAGGGCTGGAAA 57.431 37.500 4.92 0.00 37.62 3.13
3187 3454 4.085357 TGGCGCAAGAAGATTATGGTAT 57.915 40.909 10.83 0.00 43.02 2.73
3192 3459 6.347725 GGCGCAAGAAGATTATGGTATAAGTG 60.348 42.308 10.83 0.00 43.02 3.16
3195 3462 8.700644 CGCAAGAAGATTATGGTATAAGTGTAC 58.299 37.037 0.00 0.00 43.02 2.90
3229 3497 1.094785 ACAGTTGGTGTGCTGTTCAC 58.905 50.000 0.00 0.00 42.61 3.18
3240 3508 3.627577 TGTGCTGTTCACTTCTTTCCTTC 59.372 43.478 0.00 0.00 45.81 3.46
3246 3514 4.096382 TGTTCACTTCTTTCCTTCAAGTGC 59.904 41.667 6.22 0.00 44.49 4.40
3249 3517 5.057149 TCACTTCTTTCCTTCAAGTGCTAC 58.943 41.667 6.22 0.00 44.49 3.58
3258 3530 7.435068 TTCCTTCAAGTGCTACAGTAAAATC 57.565 36.000 0.00 0.00 0.00 2.17
3427 3703 0.038251 TGCAGTCACGCCTACTGAAG 60.038 55.000 14.52 0.00 45.89 3.02
3466 3743 6.708949 TCTGGTACTTTATCGCTTCAGTTTTT 59.291 34.615 0.00 0.00 0.00 1.94
3485 3762 0.380378 TTGGTGCTTTGTCGCTTCAC 59.620 50.000 0.00 0.00 0.00 3.18
3533 3810 5.347342 TCTGTACAATTTTGGTGCTTTGTG 58.653 37.500 0.00 0.00 34.39 3.33
3578 3855 7.201591 CCTCTTCTGCACATACTAAATTGTCTG 60.202 40.741 0.00 0.00 0.00 3.51
3579 3856 6.595326 TCTTCTGCACATACTAAATTGTCTGG 59.405 38.462 0.00 0.00 0.00 3.86
3592 3869 1.126948 TGTCTGGTGAGGATGCCACA 61.127 55.000 7.82 0.00 36.31 4.17
3613 3890 7.121759 GCCACATGTAAGATATAGCAAATGGAT 59.878 37.037 0.00 0.00 0.00 3.41
3690 3976 3.771160 CCTTCACCCGACTCCCCG 61.771 72.222 0.00 0.00 0.00 5.73
3718 4004 8.568794 CATGATTGCTTTATCTTCATCATCACT 58.431 33.333 0.00 0.00 0.00 3.41
3719 4005 8.151141 TGATTGCTTTATCTTCATCATCACTC 57.849 34.615 0.00 0.00 0.00 3.51
3722 4008 6.647229 TGCTTTATCTTCATCATCACTCTGT 58.353 36.000 0.00 0.00 0.00 3.41
3741 4027 3.475575 TGTCAGCTGCATTTCACTGTAA 58.524 40.909 9.47 0.00 0.00 2.41
3772 4058 8.668510 ACTTTATGACTTGGTATATCAGCTTG 57.331 34.615 0.00 0.00 0.00 4.01
3896 4182 2.806745 CGTTCTCCTGGCTGTTTTCTCA 60.807 50.000 0.00 0.00 0.00 3.27
3909 4195 6.038356 GCTGTTTTCTCATCATATGGTTTGG 58.962 40.000 2.13 0.00 0.00 3.28
3913 4199 8.646004 TGTTTTCTCATCATATGGTTTGGAAAA 58.354 29.630 2.13 9.05 0.00 2.29
3914 4200 9.657419 GTTTTCTCATCATATGGTTTGGAAAAT 57.343 29.630 16.57 0.00 34.35 1.82
3917 4203 9.656040 TTCTCATCATATGGTTTGGAAAATTTG 57.344 29.630 2.13 0.00 0.00 2.32
3918 4204 8.259411 TCTCATCATATGGTTTGGAAAATTTGG 58.741 33.333 2.13 0.00 0.00 3.28
3919 4205 7.337167 TCATCATATGGTTTGGAAAATTTGGG 58.663 34.615 2.13 0.00 0.00 4.12
3920 4206 5.495640 TCATATGGTTTGGAAAATTTGGGC 58.504 37.500 2.13 0.00 0.00 5.36
3921 4207 2.647683 TGGTTTGGAAAATTTGGGCC 57.352 45.000 0.00 0.00 0.00 5.80
3922 4208 1.846439 TGGTTTGGAAAATTTGGGCCA 59.154 42.857 0.00 0.00 0.00 5.36
3923 4209 2.242196 TGGTTTGGAAAATTTGGGCCAA 59.758 40.909 16.66 16.66 38.54 4.52
3924 4210 3.291584 GGTTTGGAAAATTTGGGCCAAA 58.708 40.909 32.12 32.12 45.29 3.28
3926 4212 2.947127 TGGAAAATTTGGGCCAAAGG 57.053 45.000 32.84 0.00 36.76 3.11
3927 4213 2.412591 TGGAAAATTTGGGCCAAAGGA 58.587 42.857 32.84 14.52 36.76 3.36
3928 4214 2.780010 TGGAAAATTTGGGCCAAAGGAA 59.220 40.909 32.84 14.14 36.76 3.36
3929 4215 3.146066 GGAAAATTTGGGCCAAAGGAAC 58.854 45.455 32.84 23.11 36.76 3.62
3930 4216 8.508415 TTTGGAAAATTTGGGCCAAAGGAACT 62.508 38.462 32.84 16.16 43.34 3.01
3931 4217 3.490439 AAATTTGGGCCAAAGGAACTG 57.510 42.857 32.84 0.00 40.86 3.16
3932 4218 1.351076 ATTTGGGCCAAAGGAACTGG 58.649 50.000 32.84 0.00 40.86 4.00
3933 4219 0.031616 TTTGGGCCAAAGGAACTGGT 60.032 50.000 27.28 0.00 40.86 4.00
3934 4220 0.031616 TTGGGCCAAAGGAACTGGTT 60.032 50.000 18.51 0.00 40.86 3.67
3988 4274 2.735151 AGGTACATGGATCAGTCGTGA 58.265 47.619 0.00 0.00 37.02 4.35
4035 4321 8.879342 ACTATCACTAGCATGAAACTGTTATC 57.121 34.615 0.00 0.00 30.82 1.75
4064 4350 9.617975 GAGTGAGAATTTTAGAATGTTTTGAGG 57.382 33.333 0.00 0.00 0.00 3.86
4065 4351 9.354673 AGTGAGAATTTTAGAATGTTTTGAGGA 57.645 29.630 0.00 0.00 0.00 3.71
4066 4352 9.399403 GTGAGAATTTTAGAATGTTTTGAGGAC 57.601 33.333 0.00 0.00 0.00 3.85
4067 4353 8.289618 TGAGAATTTTAGAATGTTTTGAGGACG 58.710 33.333 0.00 0.00 0.00 4.79
4068 4354 7.084486 AGAATTTTAGAATGTTTTGAGGACGC 58.916 34.615 0.00 0.00 0.00 5.19
4069 4355 5.759506 TTTTAGAATGTTTTGAGGACGCA 57.240 34.783 0.00 0.00 0.00 5.24
4070 4356 5.356882 TTTAGAATGTTTTGAGGACGCAG 57.643 39.130 0.00 0.00 0.00 5.18
4071 4357 1.537202 AGAATGTTTTGAGGACGCAGC 59.463 47.619 0.00 0.00 0.00 5.25
4072 4358 1.266718 GAATGTTTTGAGGACGCAGCA 59.733 47.619 0.00 0.00 0.00 4.41
4073 4359 1.317613 ATGTTTTGAGGACGCAGCAA 58.682 45.000 0.00 0.00 0.00 3.91
4074 4360 0.662619 TGTTTTGAGGACGCAGCAAG 59.337 50.000 0.00 0.00 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 9.777297 AAACATGGTTGTTATTTGCTTCTTATT 57.223 25.926 0.00 0.00 45.30 1.40
173 175 9.745323 GTTAAAAAGAATATGCAAGACAAATGC 57.255 29.630 0.00 0.00 44.08 3.56
199 201 3.824414 AGTTTGGAAGTATTTTCCGCG 57.176 42.857 0.00 0.00 41.43 6.46
265 269 4.581077 GGATACCACTACCTTCCTAACG 57.419 50.000 0.00 0.00 0.00 3.18
322 326 1.825090 ACAGGAAAATGCGAGCATCA 58.175 45.000 11.26 0.00 35.31 3.07
337 341 4.498009 CGCAAGCCCTCAAATAAATACAGG 60.498 45.833 0.00 0.00 0.00 4.00
341 345 2.360801 GCCGCAAGCCCTCAAATAAATA 59.639 45.455 0.00 0.00 34.35 1.40
358 362 2.317609 ACTGAACACACATCGCCGC 61.318 57.895 0.00 0.00 0.00 6.53
395 399 2.316792 CCACAGACGTCTTTGTAGTCG 58.683 52.381 25.61 11.49 39.65 4.18
402 406 0.104304 AAGTCGCCACAGACGTCTTT 59.896 50.000 17.26 6.93 45.26 2.52
406 410 2.050351 CGAAGTCGCCACAGACGT 60.050 61.111 0.00 0.00 45.26 4.34
438 452 2.680352 GCACCTCCGAGGGACTGA 60.680 66.667 18.99 0.00 41.55 3.41
444 458 2.045280 CCTATGAGCACCTCCGAGG 58.955 63.158 13.31 13.31 42.49 4.63
463 477 3.593096 ACACAGACATGCACACTCTATG 58.407 45.455 0.00 0.00 0.00 2.23
464 478 3.969287 ACACAGACATGCACACTCTAT 57.031 42.857 0.00 0.00 0.00 1.98
465 479 3.069443 TGAACACAGACATGCACACTCTA 59.931 43.478 0.00 0.00 0.00 2.43
468 482 2.330440 TGAACACAGACATGCACACT 57.670 45.000 0.00 0.00 0.00 3.55
469 483 3.996363 TCTATGAACACAGACATGCACAC 59.004 43.478 0.00 0.00 0.00 3.82
479 493 7.434602 CACATACACTCATCTCTATGAACACAG 59.565 40.741 0.00 0.00 41.57 3.66
483 497 5.400782 CGCACATACACTCATCTCTATGAAC 59.599 44.000 0.00 0.00 41.57 3.18
490 504 4.611943 ACATACGCACATACACTCATCTC 58.388 43.478 0.00 0.00 0.00 2.75
515 529 1.399727 GCAATACAAACGCAGACGCTT 60.400 47.619 0.00 0.00 45.53 4.68
555 569 8.717821 TGTTACTTCTGATGTTATTTGTACTGC 58.282 33.333 1.28 0.00 0.00 4.40
605 619 6.317140 CAGTGATGGTAGACGTTACTAGGTAA 59.683 42.308 0.00 0.00 33.58 2.85
606 620 5.819379 CAGTGATGGTAGACGTTACTAGGTA 59.181 44.000 0.00 0.00 33.58 3.08
618 632 0.817654 CTCGCACCAGTGATGGTAGA 59.182 55.000 0.99 2.59 40.85 2.59
640 654 0.620556 AATGACGATGGTGCCTCCTT 59.379 50.000 0.00 0.00 37.07 3.36
648 662 0.537188 AAGGAGCGAATGACGATGGT 59.463 50.000 0.00 0.00 41.91 3.55
649 663 1.212616 GAAGGAGCGAATGACGATGG 58.787 55.000 0.00 0.00 41.91 3.51
650 664 1.202463 AGGAAGGAGCGAATGACGATG 60.202 52.381 0.00 0.00 41.91 3.84
651 665 1.115467 AGGAAGGAGCGAATGACGAT 58.885 50.000 0.00 0.00 45.46 3.73
652 666 0.895530 AAGGAAGGAGCGAATGACGA 59.104 50.000 0.00 0.00 45.77 4.20
653 667 2.579207 TAAGGAAGGAGCGAATGACG 57.421 50.000 0.00 0.00 45.66 4.35
654 668 4.054671 CTGATAAGGAAGGAGCGAATGAC 58.945 47.826 0.00 0.00 0.00 3.06
655 669 3.960755 TCTGATAAGGAAGGAGCGAATGA 59.039 43.478 0.00 0.00 0.00 2.57
656 670 4.038522 TCTCTGATAAGGAAGGAGCGAATG 59.961 45.833 0.00 0.00 0.00 2.67
661 675 3.069443 CCTGTCTCTGATAAGGAAGGAGC 59.931 52.174 0.00 0.00 30.92 4.70
744 758 7.392418 AGTTAAACCAATCCTAGTTCTACACC 58.608 38.462 0.00 0.00 0.00 4.16
745 761 8.718734 CAAGTTAAACCAATCCTAGTTCTACAC 58.281 37.037 0.00 0.00 0.00 2.90
1007 1027 0.933047 TATCGCGCGAACTGAATCGG 60.933 55.000 38.07 0.00 42.93 4.18
1026 1046 1.153429 GGCGGCGAACTGATTACCT 60.153 57.895 12.98 0.00 0.00 3.08
1049 1069 1.304134 GCGGAAACCCTGGGATTGT 60.304 57.895 22.23 0.29 0.00 2.71
1077 1097 2.579201 CTCCAACATCTCGCCGGT 59.421 61.111 1.90 0.00 0.00 5.28
1181 1201 0.688087 GGAGGAAGGACCGGATGAGT 60.688 60.000 9.46 0.00 44.74 3.41
1185 1205 1.455959 CGAGGAGGAAGGACCGGAT 60.456 63.158 9.46 0.00 44.74 4.18
1187 1207 2.044252 TCGAGGAGGAAGGACCGG 60.044 66.667 0.00 0.00 44.74 5.28
1365 1385 1.326548 GTTGTAGATCCGCGCGAATTT 59.673 47.619 34.63 15.84 0.00 1.82
1538 1561 4.947147 CCACCACCACCACCACCG 62.947 72.222 0.00 0.00 0.00 4.94
1539 1562 3.816090 ACCACCACCACCACCACC 61.816 66.667 0.00 0.00 0.00 4.61
1540 1563 2.518349 CACCACCACCACCACCAC 60.518 66.667 0.00 0.00 0.00 4.16
1541 1564 3.814906 CCACCACCACCACCACCA 61.815 66.667 0.00 0.00 0.00 4.17
1558 1581 2.237143 TCATCACCCATCTTCTCACCAC 59.763 50.000 0.00 0.00 0.00 4.16
1559 1582 2.502947 CTCATCACCCATCTTCTCACCA 59.497 50.000 0.00 0.00 0.00 4.17
1570 1593 1.279496 CTTCCCAGACTCATCACCCA 58.721 55.000 0.00 0.00 0.00 4.51
1621 1644 2.979197 GCTGCTGAGCTGTGCTTGG 61.979 63.158 12.89 0.00 42.52 3.61
1622 1645 2.188849 CTGCTGCTGAGCTGTGCTTG 62.189 60.000 12.89 5.38 46.39 4.01
1650 1673 5.634118 AGAATTCTCTTCCACACCATTGAA 58.366 37.500 0.88 0.00 0.00 2.69
1659 1682 2.611292 CGGCATGAGAATTCTCTTCCAC 59.389 50.000 30.45 17.52 43.25 4.02
1683 1706 2.151502 TCCACAACAACACCACCATT 57.848 45.000 0.00 0.00 0.00 3.16
1701 1724 1.208706 CCTCCTTCCTCCTCCCTTTC 58.791 60.000 0.00 0.00 0.00 2.62
1730 1753 8.841300 GTTATGTTTTCAAAATTAAAAGCCCCA 58.159 29.630 0.00 0.00 0.00 4.96
1756 1779 5.236047 TCATTGCGTGGAAAAAGGAATTTTG 59.764 36.000 0.00 0.00 41.27 2.44
1760 1783 4.806640 ATCATTGCGTGGAAAAAGGAAT 57.193 36.364 0.00 0.00 0.00 3.01
1761 1784 5.713792 TTATCATTGCGTGGAAAAAGGAA 57.286 34.783 0.00 0.00 0.00 3.36
1772 1795 2.095853 CCGCTTGTCTTTATCATTGCGT 59.904 45.455 0.00 0.00 36.88 5.24
1774 1797 4.355543 TTCCGCTTGTCTTTATCATTGC 57.644 40.909 0.00 0.00 0.00 3.56
1792 1821 3.153919 TCCTTGTGCACAGGTTTATTCC 58.846 45.455 25.26 0.00 0.00 3.01
1796 1825 5.235850 TCTTATCCTTGTGCACAGGTTTA 57.764 39.130 25.26 14.36 0.00 2.01
1798 1827 3.788227 TCTTATCCTTGTGCACAGGTT 57.212 42.857 25.26 20.69 0.00 3.50
1815 1844 1.348036 CCCTGGTCTCGGTTTCTTCTT 59.652 52.381 0.00 0.00 0.00 2.52
1816 1845 0.977395 CCCTGGTCTCGGTTTCTTCT 59.023 55.000 0.00 0.00 0.00 2.85
1817 1846 0.974383 TCCCTGGTCTCGGTTTCTTC 59.026 55.000 0.00 0.00 0.00 2.87
1906 1935 4.113815 CAGCCCCTCCGCCATGAA 62.114 66.667 0.00 0.00 0.00 2.57
1964 1993 1.757118 CTCCTCACCGCTTCATCCTTA 59.243 52.381 0.00 0.00 0.00 2.69
1976 2005 1.239968 CCTTTGCTGTGCTCCTCACC 61.240 60.000 0.00 0.00 45.03 4.02
2036 2065 4.528206 TCAGACTCCTTCAGTTCTGCATTA 59.472 41.667 0.00 0.00 34.41 1.90
2177 2206 3.223435 AGAGGATATCCGTGTGAACGAT 58.777 45.455 16.21 0.00 42.08 3.73
2231 2260 1.531739 GCCTTGGGGTCAAAATGCGA 61.532 55.000 0.00 0.00 31.77 5.10
2303 2332 3.374058 CCCCAACAAAGACGATGACATAC 59.626 47.826 0.00 0.00 0.00 2.39
2558 2587 1.876453 CTGCGGTGTCGACAAGAACG 61.876 60.000 21.95 21.55 39.00 3.95
2645 2674 2.383855 TCTCCCACAAACAAAACCAGG 58.616 47.619 0.00 0.00 0.00 4.45
2985 3251 8.598075 GTTAACGATAACGACAAAGTAATGGAT 58.402 33.333 0.00 0.00 42.66 3.41
3035 3301 8.506196 TCTATTTCCAGCCCTTACATAAGTAT 57.494 34.615 0.00 0.00 0.00 2.12
3154 3421 1.606668 CTTGCGCCAAAGGTCAAGTAA 59.393 47.619 4.18 0.00 33.87 2.24
3187 3454 6.489022 TGTTACTCTGAGCTCAAGTACACTTA 59.511 38.462 25.42 15.12 34.28 2.24
3192 3459 5.379732 ACTGTTACTCTGAGCTCAAGTAC 57.620 43.478 25.42 21.42 0.00 2.73
3195 3462 3.993081 CCAACTGTTACTCTGAGCTCAAG 59.007 47.826 18.85 18.65 0.00 3.02
3229 3497 5.059833 ACTGTAGCACTTGAAGGAAAGAAG 58.940 41.667 0.00 0.00 0.00 2.85
3269 3541 7.365840 ACATCGGAGAGAAGATTACAAAAAC 57.634 36.000 0.00 0.00 43.63 2.43
3271 3543 7.386851 AGAACATCGGAGAGAAGATTACAAAA 58.613 34.615 0.00 0.00 43.63 2.44
3285 3557 3.189080 TCATGCACAAAAGAACATCGGAG 59.811 43.478 0.00 0.00 0.00 4.63
3346 3618 8.792830 TCGTCATTTCCATAGAGAAAGAAAAT 57.207 30.769 0.00 0.00 39.04 1.82
3367 3642 3.764885 AAACCTTATGCAATGCTCGTC 57.235 42.857 6.82 0.00 0.00 4.20
3408 3684 0.038251 CTTCAGTAGGCGTGACTGCA 60.038 55.000 11.05 0.00 43.37 4.41
3427 3703 1.583054 ACCAGAACTGAAGCGACAAC 58.417 50.000 3.19 0.00 0.00 3.32
3442 3718 6.481954 AAAACTGAAGCGATAAAGTACCAG 57.518 37.500 0.00 0.00 0.00 4.00
3466 3743 0.380378 GTGAAGCGACAAAGCACCAA 59.620 50.000 0.00 0.00 40.15 3.67
3533 3810 2.067013 GGTACGACTGAAACTGAAGCC 58.933 52.381 0.00 0.00 0.00 4.35
3578 3855 2.092968 TCTTACATGTGGCATCCTCACC 60.093 50.000 9.11 0.00 34.46 4.02
3579 3856 3.266510 TCTTACATGTGGCATCCTCAC 57.733 47.619 9.11 0.00 35.82 3.51
3690 3976 6.080648 TGATGAAGATAAAGCAATCATGGC 57.919 37.500 0.00 0.00 31.24 4.40
3693 3979 8.693120 AGTGATGATGAAGATAAAGCAATCAT 57.307 30.769 0.00 0.00 33.64 2.45
3718 4004 2.148768 CAGTGAAATGCAGCTGACAGA 58.851 47.619 20.43 0.00 31.48 3.41
3719 4005 1.878088 ACAGTGAAATGCAGCTGACAG 59.122 47.619 20.43 4.81 33.06 3.51
3722 4008 5.352293 CAGTATTACAGTGAAATGCAGCTGA 59.648 40.000 20.43 2.70 33.06 4.26
3772 4058 2.091588 CACAATGTACTACCGTTGTCGC 59.908 50.000 0.00 0.00 41.43 5.19
3875 4161 1.801178 GAGAAAACAGCCAGGAGAACG 59.199 52.381 0.00 0.00 0.00 3.95
3896 4182 6.121590 GCCCAAATTTTCCAAACCATATGAT 58.878 36.000 3.65 0.00 0.00 2.45
3909 4195 3.814842 CAGTTCCTTTGGCCCAAATTTTC 59.185 43.478 9.81 1.85 32.70 2.29
3913 4199 1.351076 CCAGTTCCTTTGGCCCAAAT 58.649 50.000 9.81 0.00 32.70 2.32
3914 4200 0.031616 ACCAGTTCCTTTGGCCCAAA 60.032 50.000 8.93 8.93 39.39 3.28
3916 4202 0.758685 CAACCAGTTCCTTTGGCCCA 60.759 55.000 0.00 0.00 39.39 5.36
3917 4203 1.471829 CCAACCAGTTCCTTTGGCCC 61.472 60.000 0.00 0.00 39.39 5.80
3918 4204 2.049435 CCAACCAGTTCCTTTGGCC 58.951 57.895 0.00 0.00 39.39 5.36
3920 4206 0.469892 AGGCCAACCAGTTCCTTTGG 60.470 55.000 5.01 0.00 42.43 3.28
3921 4207 1.069049 CAAGGCCAACCAGTTCCTTTG 59.931 52.381 5.01 0.00 36.85 2.77
3922 4208 1.413118 CAAGGCCAACCAGTTCCTTT 58.587 50.000 5.01 0.00 36.85 3.11
3923 4209 0.469892 CCAAGGCCAACCAGTTCCTT 60.470 55.000 5.01 0.00 39.35 3.36
3924 4210 1.153756 CCAAGGCCAACCAGTTCCT 59.846 57.895 5.01 0.00 39.06 3.36
3925 4211 1.908299 CCCAAGGCCAACCAGTTCC 60.908 63.158 5.01 0.00 39.06 3.62
3926 4212 1.152546 ACCCAAGGCCAACCAGTTC 60.153 57.895 5.01 0.00 39.06 3.01
3927 4213 1.152546 GACCCAAGGCCAACCAGTT 60.153 57.895 5.01 0.00 39.06 3.16
3928 4214 1.655114 AAGACCCAAGGCCAACCAGT 61.655 55.000 5.01 0.00 39.06 4.00
3929 4215 0.895559 GAAGACCCAAGGCCAACCAG 60.896 60.000 5.01 0.00 39.06 4.00
3930 4216 1.152830 GAAGACCCAAGGCCAACCA 59.847 57.895 5.01 0.00 39.06 3.67
3931 4217 0.895559 CTGAAGACCCAAGGCCAACC 60.896 60.000 5.01 0.00 0.00 3.77
3932 4218 0.178990 ACTGAAGACCCAAGGCCAAC 60.179 55.000 5.01 0.00 0.00 3.77
3933 4219 1.440618 TACTGAAGACCCAAGGCCAA 58.559 50.000 5.01 0.00 0.00 4.52
3934 4220 1.440618 TTACTGAAGACCCAAGGCCA 58.559 50.000 5.01 0.00 0.00 5.36
4010 4296 8.478066 TGATAACAGTTTCATGCTAGTGATAGT 58.522 33.333 8.23 0.00 0.00 2.12
4011 4297 8.877808 TGATAACAGTTTCATGCTAGTGATAG 57.122 34.615 8.23 0.00 0.00 2.08
4012 4298 9.264719 CATGATAACAGTTTCATGCTAGTGATA 57.735 33.333 17.89 2.77 41.82 2.15
4013 4299 7.989170 TCATGATAACAGTTTCATGCTAGTGAT 59.011 33.333 21.67 0.95 45.67 3.06
4014 4300 7.330262 TCATGATAACAGTTTCATGCTAGTGA 58.670 34.615 21.67 10.56 45.67 3.41
4015 4301 7.279536 ACTCATGATAACAGTTTCATGCTAGTG 59.720 37.037 21.67 15.06 45.67 2.74
4016 4302 7.279536 CACTCATGATAACAGTTTCATGCTAGT 59.720 37.037 21.67 19.02 45.67 2.57
4017 4303 7.493645 TCACTCATGATAACAGTTTCATGCTAG 59.506 37.037 21.67 18.64 45.67 3.42
4018 4304 7.330262 TCACTCATGATAACAGTTTCATGCTA 58.670 34.615 21.67 12.26 45.67 3.49
4019 4305 6.175471 TCACTCATGATAACAGTTTCATGCT 58.825 36.000 21.67 12.95 45.67 3.79
4020 4306 6.314648 TCTCACTCATGATAACAGTTTCATGC 59.685 38.462 21.67 0.00 45.67 4.06
4054 4340 1.267806 CTTGCTGCGTCCTCAAAACAT 59.732 47.619 0.00 0.00 0.00 2.71
4055 4341 0.662619 CTTGCTGCGTCCTCAAAACA 59.337 50.000 0.00 0.00 0.00 2.83
4056 4342 3.461843 CTTGCTGCGTCCTCAAAAC 57.538 52.632 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.