Multiple sequence alignment - TraesCS3D01G243100

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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 TraesCS3D01G243100 chr3D 100.000 5434 0 0 1 5434 338355084 338349651 0.000000e+00 10035.0
1 TraesCS3D01G243100 chr3D 91.205 307 22 4 443 748 569242261 569242563 3.920000e-111 412.0
2 TraesCS3D01G243100 chr3D 93.889 180 10 1 5256 5434 338321160 338321339 2.490000e-68 270.0
3 TraesCS3D01G243100 chr3D 89.252 214 14 3 171 384 569242056 569242260 5.400000e-65 259.0
4 TraesCS3D01G243100 chr3D 92.683 123 5 2 26 147 569241947 569242066 2.010000e-39 174.0
5 TraesCS3D01G243100 chr3D 97.436 39 1 0 405 443 338354758 338354720 3.510000e-07 67.6
6 TraesCS3D01G243100 chr3B 97.799 1817 38 2 2281 4095 436731002 436729186 0.000000e+00 3133.0
7 TraesCS3D01G243100 chr3B 93.153 1329 60 20 4123 5434 436729189 436727875 0.000000e+00 1921.0
8 TraesCS3D01G243100 chr3B 92.857 1246 61 14 1031 2272 436732259 436731038 0.000000e+00 1783.0
9 TraesCS3D01G243100 chr3B 95.429 175 8 0 5260 5434 436574737 436574911 4.140000e-71 279.0
10 TraesCS3D01G243100 chr3A 93.742 1582 58 16 2571 4121 456704751 456703180 0.000000e+00 2335.0
11 TraesCS3D01G243100 chr3A 94.158 1472 61 10 804 2272 456719141 456717692 0.000000e+00 2218.0
12 TraesCS3D01G243100 chr3A 88.955 1349 78 32 4116 5434 456701779 456700472 0.000000e+00 1600.0
13 TraesCS3D01G243100 chr3A 95.541 314 11 3 2281 2592 456717656 456717344 2.920000e-137 499.0
14 TraesCS3D01G243100 chr3A 94.444 180 9 1 5256 5434 456452188 456452367 5.360000e-70 276.0
15 TraesCS3D01G243100 chr3A 95.833 48 1 1 766 812 456722019 456721972 5.840000e-10 76.8
16 TraesCS3D01G243100 chr4B 90.265 339 32 1 405 743 604701394 604701731 5.000000e-120 442.0
17 TraesCS3D01G243100 chr4B 85.556 360 48 3 1 359 604701070 604701426 1.850000e-99 374.0
18 TraesCS3D01G243100 chr7D 92.508 307 19 3 443 748 458936053 458935750 2.320000e-118 436.0
19 TraesCS3D01G243100 chr7D 89.252 214 14 3 171 384 140818471 140818267 5.400000e-65 259.0
20 TraesCS3D01G243100 chr7D 88.318 214 16 3 171 384 458936258 458936054 1.170000e-61 248.0
21 TraesCS3D01G243100 chr7D 92.405 158 6 4 1 157 458936392 458936240 2.550000e-53 220.0
22 TraesCS3D01G243100 chr7D 90.506 158 9 4 1 157 140818605 140818453 2.570000e-48 204.0
23 TraesCS3D01G243100 chr6D 87.855 387 23 5 364 748 413994648 413994284 3.010000e-117 433.0
24 TraesCS3D01G243100 chr6D 91.857 307 21 3 443 748 437343647 437343950 5.030000e-115 425.0
25 TraesCS3D01G243100 chr6D 89.252 214 14 3 171 384 413994792 413994588 5.400000e-65 259.0
26 TraesCS3D01G243100 chr6D 89.252 214 14 3 171 384 437343442 437343646 5.400000e-65 259.0
27 TraesCS3D01G243100 chr6D 93.919 148 5 2 1 147 437343308 437343452 2.550000e-53 220.0
28 TraesCS3D01G243100 chr6D 91.772 158 7 4 1 157 413994926 413994774 1.190000e-51 215.0
29 TraesCS3D01G243100 chr5D 87.855 387 23 5 364 748 118855792 118855428 3.010000e-117 433.0
30 TraesCS3D01G243100 chr5D 87.855 387 23 5 364 748 518001000 518000636 3.010000e-117 433.0
31 TraesCS3D01G243100 chr5D 90.187 214 12 3 171 384 518001144 518000940 2.490000e-68 270.0
32 TraesCS3D01G243100 chr5D 89.252 214 14 3 171 384 118855936 118855732 5.400000e-65 259.0
33 TraesCS3D01G243100 chr5D 92.405 158 6 4 1 157 518001278 518001126 2.550000e-53 220.0
34 TraesCS3D01G243100 chr5D 90.769 130 6 4 29 157 118856042 118855918 9.360000e-38 169.0
35 TraesCS3D01G243100 chrUn 91.531 307 21 4 443 748 315029799 315029497 8.420000e-113 418.0
36 TraesCS3D01G243100 chrUn 88.785 214 15 3 171 384 315030004 315029800 2.510000e-63 254.0
37 TraesCS3D01G243100 chrUn 91.538 130 5 4 29 157 315030110 315029986 2.010000e-39 174.0
38 TraesCS3D01G243100 chr6B 86.994 346 35 5 405 748 461950565 461950902 1.100000e-101 381.0
39 TraesCS3D01G243100 chr2B 96.429 56 2 0 5379 5434 637775928 637775983 5.800000e-15 93.5


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 TraesCS3D01G243100 chr3D 338349651 338355084 5433 True 5051.300000 10035 98.718000 1 5434 2 chr3D.!!$R1 5433
1 TraesCS3D01G243100 chr3D 569241947 569242563 616 False 281.666667 412 91.046667 26 748 3 chr3D.!!$F2 722
2 TraesCS3D01G243100 chr3B 436727875 436732259 4384 True 2279.000000 3133 94.603000 1031 5434 3 chr3B.!!$R1 4403
3 TraesCS3D01G243100 chr3A 456700472 456704751 4279 True 1967.500000 2335 91.348500 2571 5434 2 chr3A.!!$R1 2863
4 TraesCS3D01G243100 chr3A 456717344 456722019 4675 True 931.266667 2218 95.177333 766 2592 3 chr3A.!!$R2 1826
5 TraesCS3D01G243100 chr4B 604701070 604701731 661 False 408.000000 442 87.910500 1 743 2 chr4B.!!$F1 742
6 TraesCS3D01G243100 chr7D 458935750 458936392 642 True 301.333333 436 91.077000 1 748 3 chr7D.!!$R2 747
7 TraesCS3D01G243100 chr6D 413994284 413994926 642 True 302.333333 433 89.626333 1 748 3 chr6D.!!$R1 747
8 TraesCS3D01G243100 chr6D 437343308 437343950 642 False 301.333333 425 91.676000 1 748 3 chr6D.!!$F1 747
9 TraesCS3D01G243100 chr5D 518000636 518001278 642 True 307.666667 433 90.149000 1 748 3 chr5D.!!$R2 747
10 TraesCS3D01G243100 chr5D 118855428 118856042 614 True 287.000000 433 89.292000 29 748 3 chr5D.!!$R1 719
11 TraesCS3D01G243100 chrUn 315029497 315030110 613 True 282.000000 418 90.618000 29 748 3 chrUn.!!$R1 719

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
474 476 0.036858 GATAGGATCGAGCAAGGGCC 60.037 60.0 1.84 0.0 42.56 5.80 F
1077 3919 0.463295 CGAATCAGCATCCACAGCCT 60.463 55.0 0.00 0.0 0.00 4.58 F
1758 4601 0.102844 TGTTTCTGTTGCTTGGCTGC 59.897 50.0 0.00 0.0 0.00 5.25 F
2964 5850 0.737367 TTCATCAAGTCAGCGAGCGG 60.737 55.0 0.00 0.0 0.00 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1719 4562 0.102300 GCCCGCACACATAAAATCCC 59.898 55.0 0.00 0.0 0.00 3.85 R
2414 5291 0.319986 TCGCAGAATACCGCACAACA 60.320 50.0 0.00 0.0 0.00 3.33 R
3549 6436 0.231279 CTAACACCACGACGTGCAAC 59.769 55.0 22.46 0.0 37.25 4.17 R
4459 8774 0.466189 ACAACAACTGCCACCTGGAG 60.466 55.0 0.00 0.0 37.39 3.86 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
45 46 2.041485 TCCCTGGATCTGCAACAATCAA 59.959 45.455 0.00 0.00 0.00 2.57
46 47 2.165030 CCCTGGATCTGCAACAATCAAC 59.835 50.000 0.00 0.00 0.00 3.18
72 73 3.632333 TCTACATCATCAGACCGGTCTT 58.368 45.455 34.54 19.01 37.98 3.01
95 97 3.517296 TTGGGGTGCTATTCTGTGAAA 57.483 42.857 0.00 0.00 0.00 2.69
167 169 3.871594 CCCGAGAGCTTGTAATAAACCAG 59.128 47.826 0.00 0.00 0.00 4.00
203 205 3.682292 CTTGGTAGCCGGAGTGCCC 62.682 68.421 5.05 0.00 0.00 5.36
222 224 3.532896 CTGCGAGCCAGGTTTTCTA 57.467 52.632 0.00 0.00 37.93 2.10
238 240 1.458588 CTAGCCTCCAGACCTCCCC 60.459 68.421 0.00 0.00 0.00 4.81
251 253 1.353394 CCTCCCCCTGGATGTAACCC 61.353 65.000 0.00 0.00 40.80 4.11
253 255 1.999002 CCCCCTGGATGTAACCCGT 60.999 63.158 0.00 0.00 0.00 5.28
258 260 0.802494 CTGGATGTAACCCGTGTTGC 59.198 55.000 0.00 0.00 37.56 4.17
324 326 5.474825 GTGTTCCAGTTCCACAAAGAAAAA 58.525 37.500 0.00 0.00 0.00 1.94
352 354 8.840200 ACTACCATAATTGTAGAGAGGAGAAA 57.160 34.615 8.09 0.00 38.34 2.52
353 355 9.440761 ACTACCATAATTGTAGAGAGGAGAAAT 57.559 33.333 8.09 0.00 38.34 2.17
355 357 8.970859 ACCATAATTGTAGAGAGGAGAAATTG 57.029 34.615 0.00 0.00 0.00 2.32
356 358 8.772250 ACCATAATTGTAGAGAGGAGAAATTGA 58.228 33.333 0.00 0.00 0.00 2.57
357 359 9.790344 CCATAATTGTAGAGAGGAGAAATTGAT 57.210 33.333 0.00 0.00 0.00 2.57
362 364 8.830915 TTGTAGAGAGGAGAAATTGATCTAGT 57.169 34.615 0.00 0.00 0.00 2.57
363 365 9.922477 TTGTAGAGAGGAGAAATTGATCTAGTA 57.078 33.333 0.00 0.00 0.00 1.82
439 441 8.961294 ATTGTAGAGAGGAGAAATTGATCAAG 57.039 34.615 14.54 0.00 0.00 3.02
473 475 0.681733 TGATAGGATCGAGCAAGGGC 59.318 55.000 1.84 0.00 41.61 5.19
474 476 0.036858 GATAGGATCGAGCAAGGGCC 60.037 60.000 1.84 0.00 42.56 5.80
475 477 0.764369 ATAGGATCGAGCAAGGGCCA 60.764 55.000 6.18 0.00 42.56 5.36
514 516 1.723542 CTTGCAAGTGCTCACGACTAG 59.276 52.381 18.65 0.00 42.66 2.57
521 523 0.679960 TGCTCACGACTAGCCTGCTA 60.680 55.000 0.00 0.00 39.30 3.49
571 573 4.093261 CAGTTTGTTCAAAAAGCTTGGTGG 59.907 41.667 0.00 0.00 0.00 4.61
579 581 2.902423 AAAGCTTGGTGGTCGTGGCA 62.902 55.000 0.00 0.00 0.00 4.92
595 597 3.141398 GTGGCAAGACAGATTCTTCACA 58.859 45.455 0.00 0.00 43.23 3.58
739 742 6.712095 AGCTGACTTCATCAACATTTTAGACA 59.288 34.615 0.00 0.00 36.69 3.41
745 748 5.630061 TCATCAACATTTTAGACATGCGTG 58.370 37.500 3.82 3.82 0.00 5.34
746 749 3.820689 TCAACATTTTAGACATGCGTGC 58.179 40.909 5.64 0.00 0.00 5.34
747 750 3.251972 TCAACATTTTAGACATGCGTGCA 59.748 39.130 5.64 0.00 0.00 4.57
749 752 3.825308 ACATTTTAGACATGCGTGCAAG 58.175 40.909 5.64 0.00 0.00 4.01
750 753 2.330231 TTTTAGACATGCGTGCAAGC 57.670 45.000 18.28 18.28 37.71 4.01
751 754 1.522668 TTTAGACATGCGTGCAAGCT 58.477 45.000 24.81 5.30 38.13 3.74
752 755 1.522668 TTAGACATGCGTGCAAGCTT 58.477 45.000 24.81 16.31 38.13 3.74
753 756 2.378445 TAGACATGCGTGCAAGCTTA 57.622 45.000 24.81 6.65 38.13 3.09
754 757 0.798776 AGACATGCGTGCAAGCTTAC 59.201 50.000 24.81 15.09 38.13 2.34
755 758 0.798776 GACATGCGTGCAAGCTTACT 59.201 50.000 24.81 7.74 38.13 2.24
756 759 1.999735 GACATGCGTGCAAGCTTACTA 59.000 47.619 24.81 5.08 38.13 1.82
757 760 2.002586 ACATGCGTGCAAGCTTACTAG 58.997 47.619 24.81 9.62 38.13 2.57
758 761 2.002586 CATGCGTGCAAGCTTACTAGT 58.997 47.619 24.81 0.00 38.13 2.57
759 762 2.163818 TGCGTGCAAGCTTACTAGTT 57.836 45.000 24.81 0.00 38.13 2.24
760 763 2.489971 TGCGTGCAAGCTTACTAGTTT 58.510 42.857 24.81 0.00 38.13 2.66
761 764 2.478894 TGCGTGCAAGCTTACTAGTTTC 59.521 45.455 24.81 0.00 38.13 2.78
762 765 2.737252 GCGTGCAAGCTTACTAGTTTCT 59.263 45.455 17.84 0.00 0.00 2.52
763 766 3.181529 GCGTGCAAGCTTACTAGTTTCTC 60.182 47.826 17.84 0.00 0.00 2.87
764 767 3.987868 CGTGCAAGCTTACTAGTTTCTCA 59.012 43.478 0.00 0.00 0.00 3.27
765 768 4.447724 CGTGCAAGCTTACTAGTTTCTCAA 59.552 41.667 0.00 0.00 0.00 3.02
766 769 5.050363 CGTGCAAGCTTACTAGTTTCTCAAA 60.050 40.000 0.00 0.00 0.00 2.69
767 770 6.511121 CGTGCAAGCTTACTAGTTTCTCAAAA 60.511 38.462 0.00 0.00 0.00 2.44
768 771 6.853362 GTGCAAGCTTACTAGTTTCTCAAAAG 59.147 38.462 0.00 0.00 0.00 2.27
769 772 6.765989 TGCAAGCTTACTAGTTTCTCAAAAGA 59.234 34.615 0.00 0.00 0.00 2.52
866 3708 1.214175 TGGACTTTTGACTTCAGCCCA 59.786 47.619 0.00 0.00 0.00 5.36
867 3709 1.609072 GGACTTTTGACTTCAGCCCAC 59.391 52.381 0.00 0.00 0.00 4.61
868 3710 2.297701 GACTTTTGACTTCAGCCCACA 58.702 47.619 0.00 0.00 0.00 4.17
869 3711 2.291741 GACTTTTGACTTCAGCCCACAG 59.708 50.000 0.00 0.00 0.00 3.66
870 3712 1.610522 CTTTTGACTTCAGCCCACAGG 59.389 52.381 0.00 0.00 0.00 4.00
1014 3856 1.153568 CGCCATGATGTCGTCACCT 60.154 57.895 0.00 0.00 40.28 4.00
1016 3858 1.091771 GCCATGATGTCGTCACCTGG 61.092 60.000 9.52 9.52 40.28 4.45
1077 3919 0.463295 CGAATCAGCATCCACAGCCT 60.463 55.000 0.00 0.00 0.00 4.58
1079 3921 0.917533 AATCAGCATCCACAGCCTCT 59.082 50.000 0.00 0.00 0.00 3.69
1372 4214 6.238103 CCACAAGTACGTCCACAATTATCATC 60.238 42.308 0.00 0.00 0.00 2.92
1389 4231 8.945195 ATTATCATCCTTATGGCATTTCTTCA 57.055 30.769 4.78 0.00 33.61 3.02
1407 4249 4.588951 TCTTCAGTGTGATTGTAGACTGGT 59.411 41.667 0.00 0.00 41.02 4.00
1456 4298 8.553459 AGAATTACTTAATCAATCCTATGGCG 57.447 34.615 0.00 0.00 0.00 5.69
1467 4309 1.003851 CCTATGGCGTACCGTTTGTG 58.996 55.000 0.00 0.00 39.70 3.33
1477 4319 4.388469 GCGTACCGTTTGTGAAGGTATTAA 59.612 41.667 0.00 0.00 41.84 1.40
1485 4327 7.371936 CGTTTGTGAAGGTATTAAATTCCCAA 58.628 34.615 0.00 0.00 0.00 4.12
1486 4328 8.032451 CGTTTGTGAAGGTATTAAATTCCCAAT 58.968 33.333 0.00 0.00 0.00 3.16
1489 4331 8.760980 TGTGAAGGTATTAAATTCCCAATAGG 57.239 34.615 0.00 0.00 0.00 2.57
1535 4377 4.131596 GAGACTAAGTAGCCGTGATCTCT 58.868 47.826 0.00 0.00 0.00 3.10
1536 4378 5.293319 AGACTAAGTAGCCGTGATCTCTA 57.707 43.478 0.00 0.00 0.00 2.43
1537 4379 5.871834 AGACTAAGTAGCCGTGATCTCTAT 58.128 41.667 0.00 0.00 0.00 1.98
1538 4380 7.006865 AGACTAAGTAGCCGTGATCTCTATA 57.993 40.000 0.00 0.00 0.00 1.31
1598 4440 2.645838 TGGATCATCTTTAGGGCAGC 57.354 50.000 0.00 0.00 0.00 5.25
1599 4441 1.845791 TGGATCATCTTTAGGGCAGCA 59.154 47.619 0.00 0.00 0.00 4.41
1623 4465 5.065988 ACAAACTACAAAAGCAGGTGTACAG 59.934 40.000 0.00 0.00 0.00 2.74
1666 4509 3.478509 TCTACTCCTTGCCGATCTAGAC 58.521 50.000 0.00 0.00 0.00 2.59
1668 4511 1.025812 CTCCTTGCCGATCTAGACGT 58.974 55.000 0.00 0.00 0.00 4.34
1719 4562 0.371989 TTAACGCGGCGATCAACATG 59.628 50.000 30.94 0.00 0.00 3.21
1758 4601 0.102844 TGTTTCTGTTGCTTGGCTGC 59.897 50.000 0.00 0.00 0.00 5.25
1787 4630 5.952698 TGCAATGCACGAATTAATGAATG 57.047 34.783 2.72 0.00 31.71 2.67
1828 4671 7.599245 GCACACAGTAGACAAGTTAAGATAACT 59.401 37.037 0.00 0.00 0.00 2.24
1835 4678 7.426929 AGACAAGTTAAGATAACTGCACTTG 57.573 36.000 16.82 16.82 44.24 3.16
1883 4726 6.509418 TGTATGTAGTGAAATTTTCCAGCC 57.491 37.500 6.68 0.00 0.00 4.85
1912 4755 4.151883 ACCAGGCAACACAAATAGTTCAT 58.848 39.130 0.00 0.00 41.41 2.57
1938 4781 7.441157 TGGAAGATAATATTCACCGTTGATCAC 59.559 37.037 0.00 0.00 0.00 3.06
2036 4882 1.070604 CCTGATATGGAGGGGTGCAT 58.929 55.000 0.00 0.00 0.00 3.96
2127 4975 2.645838 ACTTGGCTGTATAGGGCATG 57.354 50.000 11.00 11.00 38.95 4.06
2135 4983 3.750130 GCTGTATAGGGCATGAGATGTTG 59.250 47.826 0.00 0.00 0.00 3.33
2155 5003 7.120923 TGTTGGTTACTCTAATATGAGGACC 57.879 40.000 0.00 0.00 41.04 4.46
2220 5068 3.328505 GCACCATTTTATGTGCTTTGCT 58.671 40.909 7.33 0.00 39.48 3.91
2414 5291 5.997746 AGTGAACTGTTACATGTGCTTGTAT 59.002 36.000 9.11 0.00 32.39 2.29
2597 5474 9.862371 CTTGTACCATGAGTATACCATAGAATC 57.138 37.037 0.00 0.00 32.28 2.52
2964 5850 0.737367 TTCATCAAGTCAGCGAGCGG 60.737 55.000 0.00 0.00 0.00 5.52
3032 5918 5.528043 AATGAGAGTGTCGATTCTATGCT 57.472 39.130 0.00 0.00 0.00 3.79
3046 5932 4.090761 TCTATGCTAAATCCCAAGCCAG 57.909 45.455 0.00 0.00 37.97 4.85
3223 6109 2.169561 ACAAAATTGGAACTGGCGGTTT 59.830 40.909 13.88 0.00 38.41 3.27
3383 6270 4.858680 TCACGTGTTGCGCCCCAA 62.859 61.111 16.51 0.00 46.11 4.12
3477 6364 4.732285 AAATCTGTACAAGCTGTGTTCG 57.268 40.909 0.00 0.00 41.98 3.95
3501 6388 5.394224 GGCTGCTTCATGTACAGACTAACTA 60.394 44.000 13.93 0.00 36.47 2.24
3549 6436 4.495422 ACTGTTTTGTAGTATGAGGAGCG 58.505 43.478 0.00 0.00 0.00 5.03
3574 6461 1.670083 GTCGTGGTGTTAGGTGGGC 60.670 63.158 0.00 0.00 0.00 5.36
3884 6783 2.027192 GTGGCCTTGTATGGAGAGACAA 60.027 50.000 3.32 0.00 32.42 3.18
4027 6934 2.673523 GTGCTCCAGCCTCCATGT 59.326 61.111 0.00 0.00 41.18 3.21
4094 7001 9.606631 ATTCAAATTTAAAACTGGTGCTTTGTA 57.393 25.926 0.00 0.00 0.00 2.41
4149 8462 7.083062 AGATCCCTTGATTGCATACTATCAA 57.917 36.000 10.34 10.34 42.97 2.57
4459 8774 6.643770 TCGAGGTTTTGTATGTCTTACTTGTC 59.356 38.462 0.00 0.00 0.00 3.18
4460 8775 6.645415 CGAGGTTTTGTATGTCTTACTTGTCT 59.355 38.462 0.00 0.00 0.00 3.41
4488 8803 4.513692 GTGGCAGTTGTTGTAGTTCATGTA 59.486 41.667 0.00 0.00 0.00 2.29
4535 8850 6.135290 TGAGAAGATTTGTCTTGTTTGTGG 57.865 37.500 0.00 0.00 0.00 4.17
4578 8893 6.975196 TCAAATTCAGAAAATGGTCTTGGA 57.025 33.333 0.00 0.00 0.00 3.53
4640 8982 3.181454 ACTGACGAGGTGTTTTGATCCTT 60.181 43.478 0.00 0.00 0.00 3.36
4803 9145 4.949856 CCACCAGTTCTAATTTAGCATGGT 59.050 41.667 15.56 15.56 36.60 3.55
4804 9146 6.069905 TCCACCAGTTCTAATTTAGCATGGTA 60.070 38.462 18.57 0.00 35.36 3.25
4813 9155 9.982651 TTCTAATTTAGCATGGTATACAGAGAC 57.017 33.333 5.28 0.00 0.00 3.36
4947 9289 3.553828 CGGAAGCTTAACCATTCCCTA 57.446 47.619 0.00 0.00 39.50 3.53
4949 9291 3.370103 CGGAAGCTTAACCATTCCCTACA 60.370 47.826 0.00 0.00 39.50 2.74
4951 9293 4.822350 GGAAGCTTAACCATTCCCTACATC 59.178 45.833 0.00 0.00 37.17 3.06
4952 9294 5.398012 GGAAGCTTAACCATTCCCTACATCT 60.398 44.000 0.00 0.00 37.17 2.90
4953 9295 5.041191 AGCTTAACCATTCCCTACATCTG 57.959 43.478 0.00 0.00 0.00 2.90
4954 9296 3.565902 GCTTAACCATTCCCTACATCTGC 59.434 47.826 0.00 0.00 0.00 4.26
4955 9297 2.332063 AACCATTCCCTACATCTGCG 57.668 50.000 0.00 0.00 0.00 5.18
4957 9299 1.224069 CCATTCCCTACATCTGCGCG 61.224 60.000 0.00 0.00 0.00 6.86
4959 9301 2.383245 ATTCCCTACATCTGCGCGGG 62.383 60.000 17.88 12.39 36.21 6.13
5119 9472 2.671177 CCGCAAGCTGTCCTTCACG 61.671 63.158 0.00 0.00 32.61 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 3.201290 CAGATCCAGGGAATCAGTTTCG 58.799 50.000 0.00 0.00 34.98 3.46
45 46 4.138290 CGGTCTGATGATGTAGAGGTAGT 58.862 47.826 0.00 0.00 0.00 2.73
46 47 3.504134 CCGGTCTGATGATGTAGAGGTAG 59.496 52.174 0.00 0.00 0.00 3.18
72 73 2.575735 TCACAGAATAGCACCCCAATGA 59.424 45.455 0.00 0.00 0.00 2.57
95 97 9.134055 GAAACCTAACTGTAGTAGATATCTGGT 57.866 37.037 15.79 6.84 0.00 4.00
109 111 3.844211 TGGCCTCTATGAAACCTAACTGT 59.156 43.478 3.32 0.00 0.00 3.55
176 178 0.527817 CGGCTACCAAGGTTCGCTAG 60.528 60.000 0.00 0.00 0.00 3.42
178 180 2.264794 CGGCTACCAAGGTTCGCT 59.735 61.111 0.00 0.00 0.00 4.93
203 205 0.036388 TAGAAAACCTGGCTCGCAGG 60.036 55.000 5.99 5.99 45.06 4.85
222 224 4.423209 GGGGGAGGTCTGGAGGCT 62.423 72.222 0.00 0.00 0.00 4.58
238 240 1.448985 CAACACGGGTTACATCCAGG 58.551 55.000 0.85 0.00 34.87 4.45
251 253 2.667318 AATCAGCGGTCGCAACACG 61.667 57.895 17.71 0.95 44.88 4.49
253 255 1.596752 ACAATCAGCGGTCGCAACA 60.597 52.632 17.71 0.97 44.88 3.33
258 260 3.072598 CGACACAATCAGCGGTCG 58.927 61.111 0.00 0.00 45.62 4.79
456 458 0.764369 TGGCCCTTGCTCGATCCTAT 60.764 55.000 0.00 0.00 37.74 2.57
500 502 1.886585 CAGGCTAGTCGTGAGCACT 59.113 57.895 7.94 0.00 41.98 4.40
514 516 4.157656 TGAATTTACACATGGTTAGCAGGC 59.842 41.667 0.00 0.00 0.00 4.85
571 573 2.086054 AGAATCTGTCTTGCCACGAC 57.914 50.000 0.00 0.00 29.66 4.34
579 581 5.380043 ACAACCATGTGAAGAATCTGTCTT 58.620 37.500 0.00 0.00 39.93 3.01
595 597 3.258872 CACCATTGTGATCCAACAACCAT 59.741 43.478 1.03 0.00 45.76 3.55
715 718 6.902341 TGTCTAAAATGTTGATGAAGTCAGC 58.098 36.000 0.00 0.00 38.29 4.26
718 721 6.467047 CGCATGTCTAAAATGTTGATGAAGTC 59.533 38.462 0.00 0.00 0.00 3.01
739 742 2.386661 ACTAGTAAGCTTGCACGCAT 57.613 45.000 18.25 8.16 0.00 4.73
745 748 7.190920 TCTTTTGAGAAACTAGTAAGCTTGC 57.809 36.000 9.86 8.07 0.00 4.01
774 777 5.522456 TCGTGACGTGTATAACTCTGTTTT 58.478 37.500 4.40 0.00 0.00 2.43
777 780 4.754372 TTCGTGACGTGTATAACTCTGT 57.246 40.909 4.40 0.00 0.00 3.41
846 3688 1.214175 TGGGCTGAAGTCAAAAGTCCA 59.786 47.619 0.00 0.00 43.30 4.02
866 3708 0.250338 GAACCTTGACTTCGGCCTGT 60.250 55.000 0.00 0.00 0.00 4.00
867 3709 0.955919 GGAACCTTGACTTCGGCCTG 60.956 60.000 0.00 0.00 0.00 4.85
868 3710 1.375326 GGAACCTTGACTTCGGCCT 59.625 57.895 0.00 0.00 0.00 5.19
869 3711 3.982829 GGAACCTTGACTTCGGCC 58.017 61.111 0.00 0.00 0.00 6.13
1014 3856 3.896133 GACGGCGCGGTATCTCCA 61.896 66.667 21.33 0.00 35.57 3.86
1016 3858 1.729838 GATGACGGCGCGGTATCTC 60.730 63.158 21.33 13.33 0.00 2.75
1056 3898 2.020131 CTGTGGATGCTGATTCGGC 58.980 57.895 10.66 10.66 36.10 5.54
1344 4186 2.025418 GTGGACGTACTTGTGGGCG 61.025 63.158 0.00 0.00 0.00 6.13
1372 4214 4.701651 TCACACTGAAGAAATGCCATAAGG 59.298 41.667 0.00 0.00 38.23 2.69
1389 4231 8.691661 AAAAATAACCAGTCTACAATCACACT 57.308 30.769 0.00 0.00 0.00 3.55
1456 4298 7.964559 GGAATTTAATACCTTCACAAACGGTAC 59.035 37.037 0.00 0.00 36.22 3.34
1489 4331 3.611530 GCTCTTAGTGCAGAGGATCGATC 60.612 52.174 17.36 17.36 42.67 3.69
1556 4398 9.530040 TCCATGTTGGGAATCCATATTGGGATT 62.530 40.741 7.13 7.13 46.82 3.01
1557 4399 5.992447 CCATGTTGGGAATCCATATTGGGAT 60.992 44.000 0.09 0.00 43.63 3.85
1558 4400 4.482030 CATGTTGGGAATCCATATTGGGA 58.518 43.478 0.09 0.00 43.63 4.37
1559 4401 3.579586 CCATGTTGGGAATCCATATTGGG 59.420 47.826 0.09 0.00 43.63 4.12
1598 4440 4.370364 ACACCTGCTTTTGTAGTTTGTG 57.630 40.909 0.00 0.00 31.85 3.33
1599 4441 4.944930 TGTACACCTGCTTTTGTAGTTTGT 59.055 37.500 0.00 0.00 33.44 2.83
1623 4465 3.761752 AGAGAAACAGCTGACTCTACCTC 59.238 47.826 27.16 19.02 37.85 3.85
1666 4509 4.801891 TGTTAGTTGCCTCTAGTGTTACG 58.198 43.478 0.00 0.00 0.00 3.18
1668 4511 7.985184 CCATTATGTTAGTTGCCTCTAGTGTTA 59.015 37.037 0.00 0.00 0.00 2.41
1719 4562 0.102300 GCCCGCACACATAAAATCCC 59.898 55.000 0.00 0.00 0.00 3.85
1758 4601 1.837648 TTCGTGCATTGCAACTGTTG 58.162 45.000 13.94 15.98 41.47 3.33
1763 4606 5.760193 TTCATTAATTCGTGCATTGCAAC 57.240 34.783 13.94 7.00 41.47 4.17
1787 4630 4.424061 TGTGTGCATAATTCACAGCTTC 57.576 40.909 3.17 0.00 44.11 3.86
1828 4671 6.106003 AGTACGATTGATTCATACAAGTGCA 58.894 36.000 0.00 0.00 0.00 4.57
1912 4755 7.441157 GTGATCAACGGTGAATATTATCTTCCA 59.559 37.037 7.51 0.00 37.30 3.53
1995 4841 3.623510 GCGGAGAGAATAGGAAAACAAGG 59.376 47.826 0.00 0.00 0.00 3.61
2127 4975 8.861086 TCCTCATATTAGAGTAACCAACATCTC 58.139 37.037 0.00 0.00 33.75 2.75
2135 4983 6.645790 TTCGGTCCTCATATTAGAGTAACC 57.354 41.667 0.00 0.00 36.74 2.85
2155 5003 8.715998 AGATTGAGCTTATGCAGTTATAATTCG 58.284 33.333 3.16 0.00 42.74 3.34
2220 5068 5.163174 ACAAGGGTAACACAAACTAGGCTTA 60.163 40.000 0.00 0.00 39.74 3.09
2272 5120 9.255029 ACCACCTTCTAAAATAATTAGCATGTT 57.745 29.630 0.00 0.00 0.00 2.71
2273 5121 8.823220 ACCACCTTCTAAAATAATTAGCATGT 57.177 30.769 0.00 0.00 0.00 3.21
2275 5123 9.474313 TGAACCACCTTCTAAAATAATTAGCAT 57.526 29.630 0.00 0.00 0.00 3.79
2276 5124 8.871629 TGAACCACCTTCTAAAATAATTAGCA 57.128 30.769 0.00 0.00 0.00 3.49
2414 5291 0.319986 TCGCAGAATACCGCACAACA 60.320 50.000 0.00 0.00 0.00 3.33
2614 5491 5.460646 CCACACGAAAAGCAGAACAAATAT 58.539 37.500 0.00 0.00 0.00 1.28
3046 5932 1.966451 CAGTTCGTCCAAGGCCCAC 60.966 63.158 0.00 0.00 0.00 4.61
3133 6019 2.740981 GCACAGAAGTTCAGTGGATCAG 59.259 50.000 24.57 4.17 34.88 2.90
3223 6109 5.238432 AGCGTCAAATGATTACAAGTGTTGA 59.762 36.000 0.00 0.00 0.00 3.18
3383 6270 1.145738 AGGGGCATGACTCTGTTGTTT 59.854 47.619 0.00 0.00 0.00 2.83
3477 6364 2.393271 AGTCTGTACATGAAGCAGCC 57.607 50.000 0.00 0.00 0.00 4.85
3549 6436 0.231279 CTAACACCACGACGTGCAAC 59.769 55.000 22.46 0.00 37.25 4.17
3574 6461 8.428536 CGAGAATTCAGAGTGTAGTTTTGTAAG 58.571 37.037 8.44 0.00 0.00 2.34
3724 6623 8.133024 ACCAAGGCACATTTTAATTAGATCAA 57.867 30.769 0.00 0.00 0.00 2.57
3804 6703 7.117241 AGTTTGTACGACTAATTGTGTCATG 57.883 36.000 11.96 0.00 34.37 3.07
3884 6783 3.072086 TCTCCTGGGGTATCAGTATCCT 58.928 50.000 0.00 0.00 31.28 3.24
4010 6917 0.471617 ATACATGGAGGCTGGAGCAC 59.528 55.000 0.00 0.00 44.36 4.40
4027 6934 5.485353 ACTGTCATTCCCACTCAAGAGAATA 59.515 40.000 3.73 0.00 0.00 1.75
4085 6992 9.329913 CTTCACATTTTATACTGTACAAAGCAC 57.670 33.333 0.00 0.00 0.00 4.40
4094 7001 5.354234 CCTTCGCCTTCACATTTTATACTGT 59.646 40.000 0.00 0.00 0.00 3.55
4149 8462 6.239120 GCAAATTCAATGGTAGCATCTGGTAT 60.239 38.462 8.07 4.53 0.00 2.73
4224 8537 2.869101 TGCCATGGTGCAAGTTAGTA 57.131 45.000 14.67 0.00 38.56 1.82
4459 8774 0.466189 ACAACAACTGCCACCTGGAG 60.466 55.000 0.00 0.00 37.39 3.86
4460 8775 0.840617 TACAACAACTGCCACCTGGA 59.159 50.000 0.00 0.00 37.39 3.86
4488 8803 1.068333 GCAGTTGCATGAACCGTGATT 60.068 47.619 0.00 0.00 41.59 2.57
4535 8850 1.821216 TTTCGCCAGATCAAGGGAAC 58.179 50.000 12.21 0.00 35.02 3.62
4578 8893 4.816392 TCTACATTGCGTGACTGTACATT 58.184 39.130 0.00 0.00 0.00 2.71
4640 8982 0.537143 AACGCCCAGCAAATCAGTCA 60.537 50.000 0.00 0.00 0.00 3.41
4777 9119 6.016777 CCATGCTAAATTAGAACTGGTGGATC 60.017 42.308 3.88 0.00 0.00 3.36
4803 9145 5.066634 CCTGCTTCTTTCTCGTCTCTGTATA 59.933 44.000 0.00 0.00 0.00 1.47
4804 9146 4.142271 CCTGCTTCTTTCTCGTCTCTGTAT 60.142 45.833 0.00 0.00 0.00 2.29
4813 9155 2.169832 TGGAACCTGCTTCTTTCTCG 57.830 50.000 0.00 0.00 0.00 4.04
4955 9297 4.430765 TTCTCGGTTCTCGCCCGC 62.431 66.667 0.00 0.00 45.09 6.13
4957 9299 2.184579 CCTTCTCGGTTCTCGCCC 59.815 66.667 0.00 0.00 39.05 6.13
4959 9301 2.881352 CGCCTTCTCGGTTCTCGC 60.881 66.667 0.00 0.00 39.05 5.03
4960 9302 1.801913 CACGCCTTCTCGGTTCTCG 60.802 63.158 0.00 0.00 40.90 4.04
4961 9303 1.446272 CCACGCCTTCTCGGTTCTC 60.446 63.158 0.00 0.00 34.25 2.87
5119 9472 3.891366 AGCTAAGAAGATCTCTCCAGCTC 59.109 47.826 13.29 0.00 43.82 4.09


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

AutoCloner maintained by Alex Coulton.