Multiple sequence alignment - TraesCS7D01G422100

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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 TraesCS7D01G422100 chr7D 100.000 4484 0 0 1 4484 541967884 541963401 0.000000e+00 8281.0
1 TraesCS7D01G422100 chr7D 90.090 2543 198 21 1174 3694 542099621 542097111 0.000000e+00 3251.0
2 TraesCS7D01G422100 chr7D 87.231 2835 315 28 693 3491 556719926 556717103 0.000000e+00 3186.0
3 TraesCS7D01G422100 chr7D 90.808 1621 140 7 991 2608 541502442 541500828 0.000000e+00 2159.0
4 TraesCS7D01G422100 chr7D 89.664 387 34 4 483 864 542100009 542099624 5.210000e-134 488.0
5 TraesCS7D01G422100 chr7D 88.220 382 36 4 1 379 542123470 542123095 8.850000e-122 448.0
6 TraesCS7D01G422100 chr7D 80.105 191 18 11 3510 3696 556716964 556716790 1.690000e-24 124.0
7 TraesCS7D01G422100 chr7D 87.209 86 10 1 3615 3700 556720333 556720249 3.690000e-16 97.1
8 TraesCS7D01G422100 chr7B 94.970 2624 118 7 1 2614 585516160 585513541 0.000000e+00 4102.0
9 TraesCS7D01G422100 chr7B 87.051 3035 334 32 665 3650 604101177 604098153 0.000000e+00 3373.0
10 TraesCS7D01G422100 chr7B 92.810 1822 105 8 512 2325 585627270 585625467 0.000000e+00 2615.0
11 TraesCS7D01G422100 chr7B 92.900 1338 71 13 57 1387 585573484 585572164 0.000000e+00 1923.0
12 TraesCS7D01G422100 chr7B 92.427 1030 67 8 473 1494 585761229 585760203 0.000000e+00 1459.0
13 TraesCS7D01G422100 chr7B 87.617 428 41 5 1 426 585627682 585627265 1.880000e-133 486.0
14 TraesCS7D01G422100 chr7B 83.293 413 52 10 31 438 585958832 585958432 9.170000e-97 364.0
15 TraesCS7D01G422100 chr7B 76.459 497 68 31 283 769 585632626 585632169 1.620000e-54 224.0
16 TraesCS7D01G422100 chr7B 84.713 157 17 5 4083 4236 604097995 604097843 2.790000e-32 150.0
17 TraesCS7D01G422100 chr7A 87.135 2876 321 32 667 3502 642327793 642324927 0.000000e+00 3216.0
18 TraesCS7D01G422100 chr7A 81.993 2499 380 43 985 3444 625539781 625537314 0.000000e+00 2058.0
19 TraesCS7D01G422100 chr7A 94.824 966 41 3 2820 3777 624821761 624820797 0.000000e+00 1498.0
20 TraesCS7D01G422100 chr7A 87.707 968 103 11 2544 3503 735763340 735762381 0.000000e+00 1114.0
21 TraesCS7D01G422100 chr7A 92.373 590 39 4 1 590 624851699 624851116 0.000000e+00 835.0
22 TraesCS7D01G422100 chr7A 85.056 716 93 11 646 1351 624850732 624850021 0.000000e+00 717.0
23 TraesCS7D01G422100 chr7A 95.320 406 12 4 57 462 624822163 624821765 4.890000e-179 638.0
24 TraesCS7D01G422100 chr7A 84.988 413 46 11 31 438 624853846 624853445 5.400000e-109 405.0
25 TraesCS7D01G422100 chr7A 82.641 409 52 14 31 432 624835648 624835252 1.190000e-90 344.0
26 TraesCS7D01G422100 chr7A 86.463 229 19 1 4248 4476 624820502 624820286 1.610000e-59 241.0
27 TraesCS7D01G422100 chr7A 86.441 118 16 0 472 589 624845797 624845680 3.640000e-26 130.0
28 TraesCS7D01G422100 chr7A 89.535 86 8 1 3615 3700 642328151 642328067 1.710000e-19 108.0
29 TraesCS7D01G422100 chrUn 85.891 2587 340 14 971 3547 88864123 88866694 0.000000e+00 2732.0
30 TraesCS7D01G422100 chrUn 86.582 2042 263 5 971 3008 88843052 88845086 0.000000e+00 2242.0
31 TraesCS7D01G422100 chrUn 86.964 1749 210 13 1764 3503 365696699 365694960 0.000000e+00 1951.0
32 TraesCS7D01G422100 chr1A 85.520 221 29 3 3733 3952 552982285 552982503 1.250000e-55 228.0
33 TraesCS7D01G422100 chr3A 84.091 220 30 4 3734 3951 497647702 497647918 1.630000e-49 207.0
34 TraesCS7D01G422100 chr3A 83.871 186 25 5 3737 3919 46168418 46168235 5.960000e-39 172.0
35 TraesCS7D01G422100 chr3A 77.727 220 44 5 3733 3951 227368017 227367802 3.640000e-26 130.0
36 TraesCS7D01G422100 chr4A 82.700 237 36 5 3685 3919 674435078 674434845 5.880000e-49 206.0
37 TraesCS7D01G422100 chr5A 89.041 146 15 1 3703 3848 39735105 39735249 3.560000e-41 180.0
38 TraesCS7D01G422100 chr5A 80.000 220 38 6 3704 3919 593428900 593428683 1.670000e-34 158.0
39 TraesCS7D01G422100 chr2B 81.915 188 26 6 3752 3937 278440450 278440269 7.770000e-33 152.0
40 TraesCS7D01G422100 chr2A 75.875 257 57 4 3697 3952 596360675 596360927 4.710000e-25 126.0


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 TraesCS7D01G422100 chr7D 541963401 541967884 4483 True 8281.000000 8281 100.000000 1 4484 1 chr7D.!!$R2 4483
1 TraesCS7D01G422100 chr7D 541500828 541502442 1614 True 2159.000000 2159 90.808000 991 2608 1 chr7D.!!$R1 1617
2 TraesCS7D01G422100 chr7D 542097111 542100009 2898 True 1869.500000 3251 89.877000 483 3694 2 chr7D.!!$R4 3211
3 TraesCS7D01G422100 chr7D 556716790 556720333 3543 True 1135.700000 3186 84.848333 693 3700 3 chr7D.!!$R5 3007
4 TraesCS7D01G422100 chr7B 585513541 585516160 2619 True 4102.000000 4102 94.970000 1 2614 1 chr7B.!!$R1 2613
5 TraesCS7D01G422100 chr7B 585572164 585573484 1320 True 1923.000000 1923 92.900000 57 1387 1 chr7B.!!$R2 1330
6 TraesCS7D01G422100 chr7B 604097843 604101177 3334 True 1761.500000 3373 85.882000 665 4236 2 chr7B.!!$R7 3571
7 TraesCS7D01G422100 chr7B 585625467 585627682 2215 True 1550.500000 2615 90.213500 1 2325 2 chr7B.!!$R6 2324
8 TraesCS7D01G422100 chr7B 585760203 585761229 1026 True 1459.000000 1459 92.427000 473 1494 1 chr7B.!!$R4 1021
9 TraesCS7D01G422100 chr7A 625537314 625539781 2467 True 2058.000000 2058 81.993000 985 3444 1 chr7A.!!$R3 2459
10 TraesCS7D01G422100 chr7A 642324927 642328151 3224 True 1662.000000 3216 88.335000 667 3700 2 chr7A.!!$R7 3033
11 TraesCS7D01G422100 chr7A 735762381 735763340 959 True 1114.000000 1114 87.707000 2544 3503 1 chr7A.!!$R4 959
12 TraesCS7D01G422100 chr7A 624820286 624822163 1877 True 792.333333 1498 92.202333 57 4476 3 chr7A.!!$R5 4419
13 TraesCS7D01G422100 chr7A 624850021 624853846 3825 True 652.333333 835 87.472333 1 1351 3 chr7A.!!$R6 1350
14 TraesCS7D01G422100 chrUn 88864123 88866694 2571 False 2732.000000 2732 85.891000 971 3547 1 chrUn.!!$F2 2576
15 TraesCS7D01G422100 chrUn 88843052 88845086 2034 False 2242.000000 2242 86.582000 971 3008 1 chrUn.!!$F1 2037
16 TraesCS7D01G422100 chrUn 365694960 365696699 1739 True 1951.000000 1951 86.964000 1764 3503 1 chrUn.!!$R1 1739

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
716 3199 2.407340 AGACCTCTTCTGACTGGGTT 57.593 50.0 0.00 0.0 31.12 4.11 F
1521 4084 1.847890 GCCTGAAGCGCCGTTTTGTA 61.848 55.0 2.29 0.0 0.00 2.41 F
2205 4795 0.445436 CCTTCAGCGACAACAGATGC 59.555 55.0 0.00 0.0 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2142 4732 1.154093 CAGGCAAATCTGTGCGCAG 60.154 57.895 21.43 21.43 45.91 5.18 R
2808 5406 0.037590 TTGCAACACCTAGGCCGATT 59.962 50.000 9.30 0.00 0.00 3.34 R
3801 6603 0.322456 TGCTAGGAAATTGCCGTGCT 60.322 50.000 19.05 0.06 34.05 4.40 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
253 2403 5.004156 GCAGCGCAATCTCTTCTTTTATTTG 59.996 40.000 11.47 0.00 0.00 2.32
255 2405 5.098211 GCGCAATCTCTTCTTTTATTTGCT 58.902 37.500 0.30 0.00 0.00 3.91
547 2698 2.478894 ACTTGTCCTCGTTGTAATTGCG 59.521 45.455 0.00 0.00 0.00 4.85
607 2763 2.639286 GCACTTCAGTTGGGTGCG 59.361 61.111 12.45 0.00 44.91 5.34
716 3199 2.407340 AGACCTCTTCTGACTGGGTT 57.593 50.000 0.00 0.00 31.12 4.11
1420 3982 5.344743 ACTGACAGACTCTTCAAACTCAA 57.655 39.130 10.08 0.00 0.00 3.02
1423 3985 5.487433 TGACAGACTCTTCAAACTCAACAA 58.513 37.500 0.00 0.00 0.00 2.83
1521 4084 1.847890 GCCTGAAGCGCCGTTTTGTA 61.848 55.000 2.29 0.00 0.00 2.41
1605 4172 4.320494 GGTGTTGACCAGTTATTGCTTCTG 60.320 45.833 0.00 0.00 42.59 3.02
2205 4795 0.445436 CCTTCAGCGACAACAGATGC 59.555 55.000 0.00 0.00 0.00 3.91
2259 4849 5.539048 AGACAACTACAATGTAGTGACACC 58.461 41.667 24.74 13.11 38.76 4.16
2317 4910 8.224437 GTCTTTCTGCTAAAGATGTACAAAGTC 58.776 37.037 15.01 0.00 38.39 3.01
2344 4938 6.884280 AAAACAACAGAAGAGGGATAGTTG 57.116 37.500 0.00 0.00 41.37 3.16
2373 4967 8.126700 GGAATTGTAATTGGTACAGGTATTTCG 58.873 37.037 0.00 0.00 43.61 3.46
2395 4989 4.033358 CGACTCTAGGCTTATTTGCACTTG 59.967 45.833 0.00 0.00 34.04 3.16
2447 5041 6.727824 AAACAAGAGATCTGGTCAAATACG 57.272 37.500 0.00 0.00 0.00 3.06
2454 5048 5.605534 AGATCTGGTCAAATACGGAATGAG 58.394 41.667 0.00 0.00 0.00 2.90
2516 5110 5.451908 TGATCTTCAACGAGCAACAAATTC 58.548 37.500 0.00 0.00 0.00 2.17
2521 5115 5.947503 TCAACGAGCAACAAATTCTTTTG 57.052 34.783 0.00 0.00 46.27 2.44
2806 5404 4.184629 GTTGAACTGGACTGCTAGGTATG 58.815 47.826 0.00 0.00 0.00 2.39
2808 5406 4.093743 TGAACTGGACTGCTAGGTATGAA 58.906 43.478 0.00 0.00 0.00 2.57
2811 5409 5.283457 ACTGGACTGCTAGGTATGAAATC 57.717 43.478 0.00 0.00 0.00 2.17
2979 5577 6.500336 AGGAAGGGATTATAGCCGAGTATTA 58.500 40.000 0.00 0.00 0.00 0.98
2997 5595 7.330946 CGAGTATTAACAACAATGAGAGGAACA 59.669 37.037 0.00 0.00 0.00 3.18
3119 5717 1.633774 AGGAACTCATGTCCGACAGT 58.366 50.000 7.41 0.00 0.00 3.55
3324 5922 2.616510 GGGACAGGTGGTTCAGATTCTG 60.617 54.545 7.38 7.38 0.00 3.02
3576 6332 1.136891 TGATGTACCCTCACTGCATCG 59.863 52.381 0.00 0.00 38.87 3.84
3586 6342 4.926238 CCCTCACTGCATCGTTATAATCTC 59.074 45.833 0.00 0.00 0.00 2.75
3593 6349 4.177026 GCATCGTTATAATCTCGAGCCAT 58.823 43.478 7.81 3.08 37.04 4.40
3596 6352 6.477033 GCATCGTTATAATCTCGAGCCATATT 59.523 38.462 7.81 4.92 37.04 1.28
3687 6489 6.561519 ACTTGGAAGCTTATCTTAGCCTTA 57.438 37.500 0.00 0.00 42.20 2.69
3690 6492 7.717436 ACTTGGAAGCTTATCTTAGCCTTATTC 59.283 37.037 0.00 0.00 42.20 1.75
3755 6557 2.035321 ACCATGGCAAATCGAACGTTTT 59.965 40.909 13.04 0.00 0.00 2.43
3777 6579 2.919666 ATGGCAATTGTAGTTGACGC 57.080 45.000 7.40 0.00 40.06 5.19
3779 6581 0.793861 GGCAATTGTAGTTGACGCGA 59.206 50.000 15.93 0.00 0.00 5.87
3780 6582 1.201921 GGCAATTGTAGTTGACGCGAG 60.202 52.381 15.93 0.00 0.00 5.03
3781 6583 1.201921 GCAATTGTAGTTGACGCGAGG 60.202 52.381 15.93 0.00 0.00 4.63
3782 6584 2.333926 CAATTGTAGTTGACGCGAGGA 58.666 47.619 15.93 0.00 0.00 3.71
3783 6585 2.930040 CAATTGTAGTTGACGCGAGGAT 59.070 45.455 15.93 0.00 0.00 3.24
3784 6586 1.990799 TTGTAGTTGACGCGAGGATG 58.009 50.000 15.93 0.00 0.00 3.51
3785 6587 1.170442 TGTAGTTGACGCGAGGATGA 58.830 50.000 15.93 0.00 0.00 2.92
3786 6588 1.135489 TGTAGTTGACGCGAGGATGAC 60.135 52.381 15.93 4.44 0.00 3.06
3787 6589 1.135489 GTAGTTGACGCGAGGATGACA 60.135 52.381 15.93 0.00 0.00 3.58
3788 6590 0.317160 AGTTGACGCGAGGATGACAA 59.683 50.000 15.93 4.53 0.00 3.18
3789 6591 0.716108 GTTGACGCGAGGATGACAAG 59.284 55.000 15.93 0.00 0.00 3.16
3790 6592 0.317160 TTGACGCGAGGATGACAAGT 59.683 50.000 15.93 0.00 0.00 3.16
3791 6593 0.317160 TGACGCGAGGATGACAAGTT 59.683 50.000 15.93 0.00 0.00 2.66
3792 6594 1.270094 TGACGCGAGGATGACAAGTTT 60.270 47.619 15.93 0.00 0.00 2.66
3793 6595 2.029739 TGACGCGAGGATGACAAGTTTA 60.030 45.455 15.93 0.00 0.00 2.01
3794 6596 2.599082 GACGCGAGGATGACAAGTTTAG 59.401 50.000 15.93 0.00 0.00 1.85
3795 6597 2.029290 ACGCGAGGATGACAAGTTTAGT 60.029 45.455 15.93 0.00 0.00 2.24
3796 6598 2.993899 CGCGAGGATGACAAGTTTAGTT 59.006 45.455 0.00 0.00 0.00 2.24
3797 6599 3.181530 CGCGAGGATGACAAGTTTAGTTG 60.182 47.826 0.00 0.00 0.00 3.16
3798 6600 3.125316 GCGAGGATGACAAGTTTAGTTGG 59.875 47.826 2.66 0.00 0.00 3.77
3799 6601 3.125316 CGAGGATGACAAGTTTAGTTGGC 59.875 47.826 2.66 0.00 35.83 4.52
3803 6605 3.708563 TGACAAGTTTAGTTGGCAAGC 57.291 42.857 0.00 0.00 42.70 4.01
3804 6606 3.020274 TGACAAGTTTAGTTGGCAAGCA 58.980 40.909 0.00 0.00 42.70 3.91
3805 6607 3.181491 TGACAAGTTTAGTTGGCAAGCAC 60.181 43.478 0.00 0.00 42.70 4.40
3806 6608 2.223479 ACAAGTTTAGTTGGCAAGCACG 60.223 45.455 0.00 0.00 0.00 5.34
3807 6609 0.951558 AGTTTAGTTGGCAAGCACGG 59.048 50.000 0.00 0.00 0.00 4.94
3808 6610 0.663269 GTTTAGTTGGCAAGCACGGC 60.663 55.000 0.00 0.00 0.00 5.68
3809 6611 1.103987 TTTAGTTGGCAAGCACGGCA 61.104 50.000 0.00 0.00 40.11 5.69
3812 6614 3.136750 TTGGCAAGCACGGCAATT 58.863 50.000 9.84 0.00 45.48 2.32
3813 6615 1.445095 TTGGCAAGCACGGCAATTT 59.555 47.368 9.84 0.00 45.48 1.82
3814 6616 0.599728 TTGGCAAGCACGGCAATTTC 60.600 50.000 9.84 0.00 45.48 2.17
3815 6617 1.737735 GGCAAGCACGGCAATTTCC 60.738 57.895 0.00 0.00 0.00 3.13
3816 6618 1.290009 GCAAGCACGGCAATTTCCT 59.710 52.632 0.00 0.00 0.00 3.36
3817 6619 0.525761 GCAAGCACGGCAATTTCCTA 59.474 50.000 0.00 0.00 0.00 2.94
3818 6620 1.468054 GCAAGCACGGCAATTTCCTAG 60.468 52.381 0.00 0.00 0.00 3.02
3819 6621 0.811281 AAGCACGGCAATTTCCTAGC 59.189 50.000 0.00 0.00 0.00 3.42
3820 6622 0.322456 AGCACGGCAATTTCCTAGCA 60.322 50.000 9.53 0.00 0.00 3.49
3821 6623 0.525761 GCACGGCAATTTCCTAGCAA 59.474 50.000 3.49 0.00 0.00 3.91
3822 6624 1.067915 GCACGGCAATTTCCTAGCAAA 60.068 47.619 3.49 0.00 0.00 3.68
3823 6625 2.609244 GCACGGCAATTTCCTAGCAAAA 60.609 45.455 3.49 0.00 0.00 2.44
3824 6626 3.648009 CACGGCAATTTCCTAGCAAAAA 58.352 40.909 0.00 0.00 0.00 1.94
3842 6644 4.948341 AAAAACAAACTAAGGGCGGAAT 57.052 36.364 0.00 0.00 0.00 3.01
3843 6645 4.948341 AAAACAAACTAAGGGCGGAATT 57.052 36.364 0.00 0.00 0.00 2.17
3844 6646 3.934457 AACAAACTAAGGGCGGAATTG 57.066 42.857 0.00 0.00 0.00 2.32
3845 6647 1.544246 ACAAACTAAGGGCGGAATTGC 59.456 47.619 0.00 0.00 0.00 3.56
3854 6656 3.641031 GCGGAATTGCCATGTTACC 57.359 52.632 0.00 0.00 35.94 2.85
3855 6657 0.814457 GCGGAATTGCCATGTTACCA 59.186 50.000 0.00 0.00 35.94 3.25
3856 6658 1.203523 GCGGAATTGCCATGTTACCAA 59.796 47.619 0.00 0.00 35.94 3.67
3857 6659 2.874849 CGGAATTGCCATGTTACCAAC 58.125 47.619 0.00 0.00 35.94 3.77
3858 6660 2.491693 CGGAATTGCCATGTTACCAACT 59.508 45.455 0.00 0.00 35.94 3.16
3859 6661 3.692101 CGGAATTGCCATGTTACCAACTA 59.308 43.478 0.00 0.00 35.94 2.24
3860 6662 4.156922 CGGAATTGCCATGTTACCAACTAA 59.843 41.667 0.00 0.00 35.94 2.24
3861 6663 5.336055 CGGAATTGCCATGTTACCAACTAAA 60.336 40.000 0.00 0.00 35.94 1.85
3862 6664 5.867174 GGAATTGCCATGTTACCAACTAAAC 59.133 40.000 0.00 0.00 36.34 2.01
3863 6665 6.295067 GGAATTGCCATGTTACCAACTAAACT 60.295 38.462 0.00 0.00 36.34 2.66
3864 6666 6.664428 ATTGCCATGTTACCAACTAAACTT 57.336 33.333 0.00 0.00 0.00 2.66
3870 6672 7.094549 GCCATGTTACCAACTAAACTTGTCATA 60.095 37.037 0.00 0.00 32.02 2.15
3873 6675 8.373048 TGTTACCAACTAAACTTGTCATAGTG 57.627 34.615 0.00 0.00 30.61 2.74
3876 6678 7.730364 ACCAACTAAACTTGTCATAGTGAAG 57.270 36.000 0.00 0.00 30.61 3.02
3910 6712 5.101628 TGCCATAAAAGATGTTCGATTTGC 58.898 37.500 0.00 0.00 0.00 3.68
3915 6717 3.788333 AAGATGTTCGATTTGCCATGG 57.212 42.857 7.63 7.63 0.00 3.66
3919 6721 1.811965 TGTTCGATTTGCCATGGTCAG 59.188 47.619 14.67 0.66 0.00 3.51
3923 6725 2.093021 TCGATTTGCCATGGTCAGATCA 60.093 45.455 25.29 16.24 0.00 2.92
3924 6726 2.032550 CGATTTGCCATGGTCAGATCAC 59.967 50.000 25.29 11.31 0.00 3.06
3928 6730 1.009829 GCCATGGTCAGATCACGAAC 58.990 55.000 14.67 0.00 0.00 3.95
3929 6731 1.406069 GCCATGGTCAGATCACGAACT 60.406 52.381 14.67 0.00 0.00 3.01
3946 6748 0.737219 ACTCGTTCGGGACTTATCGG 59.263 55.000 0.00 0.00 0.00 4.18
3955 6757 0.458669 GGACTTATCGGCGTCCTTCA 59.541 55.000 6.85 0.00 44.90 3.02
3980 6782 3.923017 TTTGAAAGAGCTTAGCCTTGC 57.077 42.857 0.00 3.62 0.00 4.01
3981 6783 2.566833 TGAAAGAGCTTAGCCTTGCA 57.433 45.000 10.64 10.64 0.00 4.08
3996 6802 2.092968 CCTTGCATAACACCTAGCAGGA 60.093 50.000 8.91 0.00 37.67 3.86
4019 6825 5.039920 TGCTGCACAATCTACATCCTTAT 57.960 39.130 0.00 0.00 0.00 1.73
4105 6920 0.464870 ATGCAACTGCCAAAACAGCA 59.535 45.000 0.00 0.00 41.60 4.41
4167 6984 2.590007 CGCAGGCTCTGGTATGGC 60.590 66.667 4.65 0.00 31.21 4.40
4191 7008 2.191375 CATGCAGGCGGTGATCCT 59.809 61.111 0.00 0.00 0.00 3.24
4192 7009 1.452651 CATGCAGGCGGTGATCCTT 60.453 57.895 0.00 0.00 0.00 3.36
4193 7010 1.452651 ATGCAGGCGGTGATCCTTG 60.453 57.895 0.00 0.00 0.00 3.61
4194 7011 3.512516 GCAGGCGGTGATCCTTGC 61.513 66.667 0.00 0.00 0.00 4.01
4201 7018 1.699656 CGGTGATCCTTGCTTGCTCG 61.700 60.000 0.00 0.00 0.00 5.03
4206 7023 0.674895 ATCCTTGCTTGCTCGGTGAC 60.675 55.000 0.00 0.00 0.00 3.67
4240 7058 3.716006 CGGCGTGGCTGAACACTG 61.716 66.667 0.00 0.00 39.19 3.66
4241 7059 2.591715 GGCGTGGCTGAACACTGT 60.592 61.111 0.00 0.00 39.19 3.55
4242 7060 2.633657 GCGTGGCTGAACACTGTG 59.366 61.111 6.19 6.19 39.19 3.66
4243 7061 1.887242 GCGTGGCTGAACACTGTGA 60.887 57.895 15.86 0.00 39.19 3.58
4244 7062 1.230635 GCGTGGCTGAACACTGTGAT 61.231 55.000 15.86 1.59 39.19 3.06
4245 7063 1.939381 GCGTGGCTGAACACTGTGATA 60.939 52.381 15.86 0.00 39.19 2.15
4246 7064 1.995484 CGTGGCTGAACACTGTGATAG 59.005 52.381 15.86 10.06 39.19 2.08
4297 7115 2.690653 TTTGAGCCGGAGTTGGTGGG 62.691 60.000 5.05 0.00 0.00 4.61
4306 7124 1.460689 AGTTGGTGGGGAAGACGGA 60.461 57.895 0.00 0.00 0.00 4.69
4320 7138 1.134068 AGACGGACATCTCGATCTCCA 60.134 52.381 2.80 0.00 0.00 3.86
4326 7144 1.039068 CATCTCGATCTCCAGTGCCT 58.961 55.000 0.00 0.00 0.00 4.75
4328 7146 2.666272 TCTCGATCTCCAGTGCCTAT 57.334 50.000 0.00 0.00 0.00 2.57
4333 7151 2.094803 CGATCTCCAGTGCCTATAGCTG 60.095 54.545 0.00 0.00 44.23 4.24
4348 7166 2.044123 AGCTGGAAATTAAGCGAGGG 57.956 50.000 0.00 0.00 44.34 4.30
4360 7178 9.436957 GAAATTAAGCGAGGGAAATATCAGATA 57.563 33.333 0.00 0.00 0.00 1.98
4361 7179 9.442047 AAATTAAGCGAGGGAAATATCAGATAG 57.558 33.333 0.00 0.00 0.00 2.08
4362 7180 7.776618 TTAAGCGAGGGAAATATCAGATAGA 57.223 36.000 0.00 0.00 0.00 1.98
4363 7181 6.672266 AAGCGAGGGAAATATCAGATAGAA 57.328 37.500 0.00 0.00 0.00 2.10
4364 7182 6.865834 AGCGAGGGAAATATCAGATAGAAT 57.134 37.500 0.00 0.00 0.00 2.40
4365 7183 7.251321 AGCGAGGGAAATATCAGATAGAATT 57.749 36.000 0.00 0.00 0.00 2.17
4366 7184 7.327214 AGCGAGGGAAATATCAGATAGAATTC 58.673 38.462 0.00 0.00 0.00 2.17
4367 7185 6.536941 GCGAGGGAAATATCAGATAGAATTCC 59.463 42.308 16.99 16.99 37.07 3.01
4368 7186 7.615403 CGAGGGAAATATCAGATAGAATTCCA 58.385 38.462 22.21 0.00 38.39 3.53
4369 7187 7.547370 CGAGGGAAATATCAGATAGAATTCCAC 59.453 40.741 22.21 17.09 38.39 4.02
4370 7188 8.280258 AGGGAAATATCAGATAGAATTCCACA 57.720 34.615 22.21 0.00 38.39 4.17
4371 7189 8.898728 AGGGAAATATCAGATAGAATTCCACAT 58.101 33.333 22.21 12.15 38.39 3.21
4412 7230 2.415843 GCGAATGGGATCGGACGA 59.584 61.111 0.00 0.00 42.93 4.20
4421 7239 2.362503 ATCGGACGAGGCTCACCA 60.363 61.111 21.75 12.55 39.06 4.17
4439 7257 3.195698 GTGAGGTCAATCGGCGGC 61.196 66.667 7.21 0.00 0.00 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
255 2405 6.519679 AATACAATTCTGCTGCTTTCATCA 57.480 33.333 0.00 0.00 0.00 3.07
459 2609 9.531158 AAAACTAGTGAAGTACTACCTCTGTAT 57.469 33.333 0.00 0.00 40.89 2.29
607 2763 3.454375 TGAGACCGACACTGTTCTTTTC 58.546 45.455 0.00 0.00 0.00 2.29
880 3377 7.439108 ACTAGTATAGGCAGATTCAAAGGTT 57.561 36.000 0.00 0.00 44.97 3.50
881 3378 7.439108 AACTAGTATAGGCAGATTCAAAGGT 57.561 36.000 0.00 0.00 44.97 3.50
882 3379 7.227512 CCAAACTAGTATAGGCAGATTCAAAGG 59.772 40.741 0.00 0.00 44.97 3.11
883 3380 7.987458 TCCAAACTAGTATAGGCAGATTCAAAG 59.013 37.037 0.00 0.00 44.97 2.77
895 3392 4.040952 AGCCCAGCATCCAAACTAGTATAG 59.959 45.833 0.00 0.00 46.50 1.31
1322 3883 2.654749 TGCTTGTGTAGTCCAGATCG 57.345 50.000 0.00 0.00 0.00 3.69
1420 3982 1.136891 GCTCTGCCACAAAACCTTTGT 59.863 47.619 0.00 0.00 0.00 2.83
1423 3985 1.780503 AAGCTCTGCCACAAAACCTT 58.219 45.000 0.00 0.00 0.00 3.50
1521 4084 4.100963 GGGTTGACCAAGTTTTTCCAAGAT 59.899 41.667 2.12 0.00 39.85 2.40
1605 4172 2.092968 TGGTATGGATGAGTTCAGTGCC 60.093 50.000 0.00 0.00 0.00 5.01
2142 4732 1.154093 CAGGCAAATCTGTGCGCAG 60.154 57.895 21.43 21.43 45.91 5.18
2177 4767 1.281899 GTCGCTGAAGGAGTATGCAC 58.718 55.000 0.00 0.00 0.00 4.57
2205 4795 6.206048 TGAGCAATTCATTATGCCACATAGAG 59.794 38.462 0.00 0.00 43.57 2.43
2259 4849 8.611654 AAAGAATTTCTCCATTTGAATTGGTG 57.388 30.769 6.06 4.28 27.08 4.17
2317 4910 6.712547 ACTATCCCTCTTCTGTTGTTTTTCAG 59.287 38.462 0.00 0.00 0.00 3.02
2344 4938 4.705023 ACCTGTACCAATTACAATTCCAGC 59.295 41.667 0.00 0.00 40.33 4.85
2373 4967 4.938226 ACAAGTGCAAATAAGCCTAGAGTC 59.062 41.667 0.00 0.00 0.00 3.36
2395 4989 6.732896 TCTCCAAATCATTAGTAGGAGGAC 57.267 41.667 0.00 0.00 42.20 3.85
2447 5041 5.106396 CCATCACAAACTTCAGACTCATTCC 60.106 44.000 0.00 0.00 0.00 3.01
2454 5048 5.947228 TGATTCCATCACAAACTTCAGAC 57.053 39.130 0.00 0.00 33.59 3.51
2516 5110 3.874392 CCCCCAACTTATCTGCAAAAG 57.126 47.619 0.00 0.00 0.00 2.27
2790 5388 4.302455 CGATTTCATACCTAGCAGTCCAG 58.698 47.826 0.00 0.00 0.00 3.86
2806 5404 0.733150 GCAACACCTAGGCCGATTTC 59.267 55.000 9.30 0.00 0.00 2.17
2808 5406 0.037590 TTGCAACACCTAGGCCGATT 59.962 50.000 9.30 0.00 0.00 3.34
2811 5409 1.003839 TCTTGCAACACCTAGGCCG 60.004 57.895 9.30 2.47 0.00 6.13
2979 5577 4.339247 CCTGTTGTTCCTCTCATTGTTGTT 59.661 41.667 0.00 0.00 0.00 2.83
2997 5595 2.033602 GGCGCAAGGTACCCTGTT 59.966 61.111 10.83 0.00 32.13 3.16
3119 5717 1.302192 GTGTTGCCACCGCTAGGAA 60.302 57.895 0.00 0.00 41.02 3.36
3324 5922 2.284190 GTGATCTCAACTAGCCCTTGC 58.716 52.381 0.00 0.00 37.95 4.01
3508 6242 4.276926 AGAACACAGCTGTTTCTTCAATCC 59.723 41.667 25.62 9.75 40.93 3.01
3586 6342 3.067106 ACGCCTATTTCAATATGGCTCG 58.933 45.455 13.56 0.00 41.25 5.03
3596 6352 8.367911 ACTGAAATATCTATGACGCCTATTTCA 58.632 33.333 12.73 12.73 42.25 2.69
3636 6392 7.864882 GGATCTTAAAAGCTAGAAATTCCATGC 59.135 37.037 0.00 0.00 0.00 4.06
3731 6533 1.202065 CGTTCGATTTGCCATGGTCAG 60.202 52.381 14.67 0.66 0.00 3.51
3755 6557 4.670478 CGCGTCAACTACAATTGCCATAAA 60.670 41.667 5.05 0.00 0.00 1.40
3767 6569 1.135489 TGTCATCCTCGCGTCAACTAC 60.135 52.381 5.77 0.00 0.00 2.73
3777 6579 3.125316 GCCAACTAAACTTGTCATCCTCG 59.875 47.826 0.00 0.00 0.00 4.63
3779 6581 4.098914 TGCCAACTAAACTTGTCATCCT 57.901 40.909 0.00 0.00 0.00 3.24
3780 6582 4.798574 CTTGCCAACTAAACTTGTCATCC 58.201 43.478 0.00 0.00 0.00 3.51
3781 6583 4.229876 GCTTGCCAACTAAACTTGTCATC 58.770 43.478 0.00 0.00 0.00 2.92
3782 6584 3.636300 TGCTTGCCAACTAAACTTGTCAT 59.364 39.130 0.00 0.00 0.00 3.06
3783 6585 3.020274 TGCTTGCCAACTAAACTTGTCA 58.980 40.909 0.00 0.00 0.00 3.58
3784 6586 3.372060 GTGCTTGCCAACTAAACTTGTC 58.628 45.455 0.00 0.00 0.00 3.18
3785 6587 2.223479 CGTGCTTGCCAACTAAACTTGT 60.223 45.455 0.00 0.00 0.00 3.16
3786 6588 2.384382 CGTGCTTGCCAACTAAACTTG 58.616 47.619 0.00 0.00 0.00 3.16
3787 6589 1.336755 CCGTGCTTGCCAACTAAACTT 59.663 47.619 0.00 0.00 0.00 2.66
3788 6590 0.951558 CCGTGCTTGCCAACTAAACT 59.048 50.000 0.00 0.00 0.00 2.66
3789 6591 0.663269 GCCGTGCTTGCCAACTAAAC 60.663 55.000 0.00 0.00 0.00 2.01
3790 6592 1.103987 TGCCGTGCTTGCCAACTAAA 61.104 50.000 0.00 0.00 0.00 1.85
3791 6593 1.103987 TTGCCGTGCTTGCCAACTAA 61.104 50.000 0.00 0.00 0.00 2.24
3792 6594 0.893270 ATTGCCGTGCTTGCCAACTA 60.893 50.000 0.00 0.00 0.00 2.24
3793 6595 1.747325 AATTGCCGTGCTTGCCAACT 61.747 50.000 0.00 0.00 0.00 3.16
3794 6596 0.879839 AAATTGCCGTGCTTGCCAAC 60.880 50.000 0.00 0.00 0.00 3.77
3795 6597 0.599728 GAAATTGCCGTGCTTGCCAA 60.600 50.000 0.00 0.00 0.00 4.52
3796 6598 1.006337 GAAATTGCCGTGCTTGCCA 60.006 52.632 0.00 0.00 0.00 4.92
3797 6599 1.737735 GGAAATTGCCGTGCTTGCC 60.738 57.895 0.00 0.00 0.00 4.52
3798 6600 0.525761 TAGGAAATTGCCGTGCTTGC 59.474 50.000 0.00 0.00 0.00 4.01
3799 6601 1.468054 GCTAGGAAATTGCCGTGCTTG 60.468 52.381 13.41 0.00 0.00 4.01
3800 6602 0.811281 GCTAGGAAATTGCCGTGCTT 59.189 50.000 13.41 0.00 0.00 3.91
3801 6603 0.322456 TGCTAGGAAATTGCCGTGCT 60.322 50.000 19.05 0.06 34.05 4.40
3802 6604 0.525761 TTGCTAGGAAATTGCCGTGC 59.474 50.000 13.70 13.70 0.00 5.34
3803 6605 3.296322 TTTTGCTAGGAAATTGCCGTG 57.704 42.857 10.45 0.00 0.00 4.94
3821 6623 4.948341 ATTCCGCCCTTAGTTTGTTTTT 57.052 36.364 0.00 0.00 0.00 1.94
3822 6624 4.627058 CAATTCCGCCCTTAGTTTGTTTT 58.373 39.130 0.00 0.00 0.00 2.43
3823 6625 3.554129 GCAATTCCGCCCTTAGTTTGTTT 60.554 43.478 0.00 0.00 0.00 2.83
3824 6626 2.029380 GCAATTCCGCCCTTAGTTTGTT 60.029 45.455 0.00 0.00 0.00 2.83
3825 6627 1.544246 GCAATTCCGCCCTTAGTTTGT 59.456 47.619 0.00 0.00 0.00 2.83
3826 6628 2.278026 GCAATTCCGCCCTTAGTTTG 57.722 50.000 0.00 0.00 0.00 2.93
3836 6638 0.814457 TGGTAACATGGCAATTCCGC 59.186 50.000 0.00 0.00 46.17 5.54
3849 6651 8.597662 TCACTATGACAAGTTTAGTTGGTAAC 57.402 34.615 2.66 0.00 0.00 2.50
3850 6652 9.268268 CTTCACTATGACAAGTTTAGTTGGTAA 57.732 33.333 2.66 0.00 0.00 2.85
3851 6653 8.644216 TCTTCACTATGACAAGTTTAGTTGGTA 58.356 33.333 2.66 0.00 0.00 3.25
3852 6654 7.506114 TCTTCACTATGACAAGTTTAGTTGGT 58.494 34.615 2.66 0.00 0.00 3.67
3853 6655 7.962964 TCTTCACTATGACAAGTTTAGTTGG 57.037 36.000 2.66 0.00 0.00 3.77
3892 6694 5.184864 ACCATGGCAAATCGAACATCTTTTA 59.815 36.000 13.04 0.00 0.00 1.52
3893 6695 4.021192 ACCATGGCAAATCGAACATCTTTT 60.021 37.500 13.04 0.00 0.00 2.27
3910 6712 2.544685 GAGTTCGTGATCTGACCATGG 58.455 52.381 11.19 11.19 0.00 3.66
3928 6730 0.594284 GCCGATAAGTCCCGAACGAG 60.594 60.000 0.00 0.00 0.00 4.18
3929 6731 1.434696 GCCGATAAGTCCCGAACGA 59.565 57.895 0.00 0.00 0.00 3.85
3996 6802 3.572632 AGGATGTAGATTGTGCAGCAT 57.427 42.857 0.00 0.00 0.00 3.79
4019 6825 2.038033 GCCGGCCATTTACAGTATCCTA 59.962 50.000 18.11 0.00 0.00 2.94
4029 6835 2.373335 ACCATTATGCCGGCCATTTA 57.627 45.000 26.77 4.49 35.34 1.40
4105 6920 1.432251 CGTAGGCGAAGATGACCGT 59.568 57.895 0.00 0.00 41.33 4.83
4191 7008 2.664851 CCGTCACCGAGCAAGCAA 60.665 61.111 0.00 0.00 35.63 3.91
4192 7009 4.680237 CCCGTCACCGAGCAAGCA 62.680 66.667 0.00 0.00 35.63 3.91
4194 7011 4.003788 ACCCCGTCACCGAGCAAG 62.004 66.667 0.00 0.00 35.63 4.01
4224 7042 2.591715 ACAGTGTTCAGCCACGCC 60.592 61.111 0.00 0.00 40.33 5.68
4227 7045 3.257393 CTCTATCACAGTGTTCAGCCAC 58.743 50.000 0.00 0.00 35.53 5.01
4236 7054 0.457443 TGCTCGGCTCTATCACAGTG 59.543 55.000 0.00 0.00 0.00 3.66
4237 7055 0.743688 CTGCTCGGCTCTATCACAGT 59.256 55.000 0.00 0.00 0.00 3.55
4238 7056 0.031857 CCTGCTCGGCTCTATCACAG 59.968 60.000 0.00 0.00 0.00 3.66
4239 7057 2.119009 CCTGCTCGGCTCTATCACA 58.881 57.895 0.00 0.00 0.00 3.58
4281 7099 4.410400 CCCCACCAACTCCGGCTC 62.410 72.222 0.00 0.00 0.00 4.70
4283 7101 3.920093 CTTCCCCACCAACTCCGGC 62.920 68.421 0.00 0.00 0.00 6.13
4297 7115 1.950909 AGATCGAGATGTCCGTCTTCC 59.049 52.381 0.00 0.00 0.00 3.46
4306 7124 0.749649 GGCACTGGAGATCGAGATGT 59.250 55.000 0.00 0.00 0.00 3.06
4320 7138 5.066593 GCTTAATTTCCAGCTATAGGCACT 58.933 41.667 1.04 0.00 44.79 4.40
4326 7144 4.591498 TCCCTCGCTTAATTTCCAGCTATA 59.409 41.667 0.00 0.00 33.52 1.31
4328 7146 2.769663 TCCCTCGCTTAATTTCCAGCTA 59.230 45.455 0.00 0.00 33.52 3.32
4333 7151 6.710744 TCTGATATTTCCCTCGCTTAATTTCC 59.289 38.462 0.00 0.00 0.00 3.13
4362 7180 5.888161 GGGACACTGAATTCTATGTGGAATT 59.112 40.000 21.46 4.31 45.19 2.17
4363 7181 5.044919 TGGGACACTGAATTCTATGTGGAAT 60.045 40.000 21.46 8.73 37.51 3.01
4364 7182 4.288366 TGGGACACTGAATTCTATGTGGAA 59.712 41.667 21.46 7.31 35.02 3.53
4365 7183 3.843619 TGGGACACTGAATTCTATGTGGA 59.156 43.478 21.46 6.39 35.02 4.02
4366 7184 4.220693 TGGGACACTGAATTCTATGTGG 57.779 45.455 21.46 10.51 35.02 4.17
4385 7203 2.390599 CCCATTCGCGTCACAGTGG 61.391 63.158 5.77 2.70 0.00 4.00
4421 7239 2.579201 CCGCCGATTGACCTCACT 59.421 61.111 0.00 0.00 0.00 3.41
4444 7262 0.106967 GCTTGGAATGGAGTCCCCTC 60.107 60.000 6.74 2.75 36.80 4.30
4445 7263 0.551131 AGCTTGGAATGGAGTCCCCT 60.551 55.000 6.74 0.00 36.80 4.79
4446 7264 0.106967 GAGCTTGGAATGGAGTCCCC 60.107 60.000 6.74 0.83 36.80 4.81


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

AutoCloner maintained by Alex Coulton.