Multiple sequence alignment - TraesCS6B01G370100

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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 TraesCS6B01G370100 chr6B 100.000 4355 0 0 1 4355 643821657 643826011 0.000000e+00 8043.0
1 TraesCS6B01G370100 chr6B 87.306 2324 281 8 1099 3413 643639417 643641735 0.000000e+00 2645.0
2 TraesCS6B01G370100 chr6B 85.963 2472 311 26 920 3368 642909408 642906950 0.000000e+00 2610.0
3 TraesCS6B01G370100 chr6B 85.102 2544 338 22 907 3422 642894450 642891920 0.000000e+00 2560.0
4 TraesCS6B01G370100 chr6B 82.801 2378 356 33 993 3342 30457315 30454963 0.000000e+00 2076.0
5 TraesCS6B01G370100 chr6B 80.202 495 79 10 3599 4085 598447357 598446874 1.930000e-93 353.0
6 TraesCS6B01G370100 chr6B 100.000 28 0 0 894 921 643650732 643650759 8.000000e-03 52.8
7 TraesCS6B01G370100 chr6D 93.858 3077 160 9 894 3958 427700751 427697692 0.000000e+00 4608.0
8 TraesCS6B01G370100 chr6D 86.937 2396 278 19 984 3363 427713251 427710875 0.000000e+00 2658.0
9 TraesCS6B01G370100 chr6D 85.423 2497 326 23 907 3376 427072606 427070121 0.000000e+00 2560.0
10 TraesCS6B01G370100 chr6D 92.611 1015 71 2 2355 3369 427894509 427893499 0.000000e+00 1456.0
11 TraesCS6B01G370100 chr6D 80.716 363 53 11 3599 3953 369425253 369425606 2.580000e-67 267.0
12 TraesCS6B01G370100 chr6D 86.905 84 8 3 807 888 427709074 427708992 1.670000e-14 91.6
13 TraesCS6B01G370100 chr6A 94.598 2573 135 1 920 3488 572400340 572402912 0.000000e+00 3978.0
14 TraesCS6B01G370100 chr6A 87.864 2266 270 3 1099 3363 572336161 572338422 0.000000e+00 2656.0
15 TraesCS6B01G370100 chr6A 85.594 2485 323 21 907 3368 571701009 571698537 0.000000e+00 2573.0
16 TraesCS6B01G370100 chr6A 85.222 2497 307 35 894 3362 571791740 571789278 0.000000e+00 2510.0
17 TraesCS6B01G370100 chr6A 83.708 2400 340 31 993 3362 17956096 17958474 0.000000e+00 2218.0
18 TraesCS6B01G370100 chr6A 90.816 98 9 0 801 898 572400167 572400264 9.830000e-27 132.0
19 TraesCS6B01G370100 chr6A 100.000 28 0 0 894 921 572400296 572400323 8.000000e-03 52.8
20 TraesCS6B01G370100 chrUn 97.744 798 18 0 1 798 248920287 248919490 0.000000e+00 1375.0
21 TraesCS6B01G370100 chrUn 97.744 798 18 0 1 798 273988703 273989500 0.000000e+00 1375.0
22 TraesCS6B01G370100 chrUn 97.744 798 18 0 1 798 317744356 317743559 0.000000e+00 1375.0
23 TraesCS6B01G370100 chrUn 97.744 798 18 0 1 798 355330883 355330086 0.000000e+00 1375.0
24 TraesCS6B01G370100 chrUn 78.647 665 116 14 3599 4251 324145056 324145706 6.740000e-113 418.0
25 TraesCS6B01G370100 chr5A 94.661 693 33 4 102 792 567091852 567092542 0.000000e+00 1072.0
26 TraesCS6B01G370100 chr5A 77.705 305 53 13 3813 4109 331811274 331811571 5.790000e-39 172.0
27 TraesCS6B01G370100 chr5A 77.705 305 53 13 3813 4109 331823527 331823824 5.790000e-39 172.0
28 TraesCS6B01G370100 chr2B 88.916 812 62 9 1 797 78090500 78089702 0.000000e+00 976.0
29 TraesCS6B01G370100 chr2B 83.099 213 25 9 11 218 78090625 78090419 2.680000e-42 183.0
30 TraesCS6B01G370100 chr5B 89.070 796 62 7 1 784 56576675 56577457 0.000000e+00 965.0
31 TraesCS6B01G370100 chr1D 84.441 617 39 16 12 609 491591318 491591896 4.920000e-154 555.0
32 TraesCS6B01G370100 chr1D 93.478 46 3 0 622 667 491591967 491592012 7.820000e-08 69.4
33 TraesCS6B01G370100 chr4A 82.951 610 48 20 12 602 37296440 37297012 2.340000e-137 499.0
34 TraesCS6B01G370100 chr3B 78.679 666 111 19 3599 4251 101638221 101638868 8.710000e-112 414.0
35 TraesCS6B01G370100 chr3B 97.143 35 1 0 4277 4311 26810101 26810067 4.700000e-05 60.2
36 TraesCS6B01G370100 chr3B 83.607 61 8 2 4284 4343 817029706 817029647 6.080000e-04 56.5
37 TraesCS6B01G370100 chr3A 78.986 552 93 19 3601 4143 13366371 13366908 5.360000e-94 355.0
38 TraesCS6B01G370100 chr3A 83.607 61 8 2 4284 4343 17668002 17668061 6.080000e-04 56.5
39 TraesCS6B01G370100 chr3A 83.607 61 8 2 4284 4343 17801072 17801013 6.080000e-04 56.5
40 TraesCS6B01G370100 chr2A 76.128 687 126 25 3590 4251 651993822 651993149 4.200000e-85 326.0
41 TraesCS6B01G370100 chr7D 80.495 364 53 11 3599 3953 53739141 53739495 3.340000e-66 263.0
42 TraesCS6B01G370100 chr4D 80.548 365 50 14 3599 3953 64581137 64581490 1.200000e-65 261.0
43 TraesCS6B01G370100 chr7A 81.951 205 26 9 3585 3787 626943909 626943714 3.480000e-36 163.0
44 TraesCS6B01G370100 chr1A 82.812 64 10 1 4279 4342 387177120 387177182 6.080000e-04 56.5


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 TraesCS6B01G370100 chr6B 643821657 643826011 4354 False 8043.0 8043 100.0000 1 4355 1 chr6B.!!$F3 4354
1 TraesCS6B01G370100 chr6B 643639417 643641735 2318 False 2645.0 2645 87.3060 1099 3413 1 chr6B.!!$F1 2314
2 TraesCS6B01G370100 chr6B 642906950 642909408 2458 True 2610.0 2610 85.9630 920 3368 1 chr6B.!!$R4 2448
3 TraesCS6B01G370100 chr6B 642891920 642894450 2530 True 2560.0 2560 85.1020 907 3422 1 chr6B.!!$R3 2515
4 TraesCS6B01G370100 chr6B 30454963 30457315 2352 True 2076.0 2076 82.8010 993 3342 1 chr6B.!!$R1 2349
5 TraesCS6B01G370100 chr6D 427697692 427700751 3059 True 4608.0 4608 93.8580 894 3958 1 chr6D.!!$R2 3064
6 TraesCS6B01G370100 chr6D 427070121 427072606 2485 True 2560.0 2560 85.4230 907 3376 1 chr6D.!!$R1 2469
7 TraesCS6B01G370100 chr6D 427893499 427894509 1010 True 1456.0 1456 92.6110 2355 3369 1 chr6D.!!$R3 1014
8 TraesCS6B01G370100 chr6D 427708992 427713251 4259 True 1374.8 2658 86.9210 807 3363 2 chr6D.!!$R4 2556
9 TraesCS6B01G370100 chr6A 572336161 572338422 2261 False 2656.0 2656 87.8640 1099 3363 1 chr6A.!!$F2 2264
10 TraesCS6B01G370100 chr6A 571698537 571701009 2472 True 2573.0 2573 85.5940 907 3368 1 chr6A.!!$R1 2461
11 TraesCS6B01G370100 chr6A 571789278 571791740 2462 True 2510.0 2510 85.2220 894 3362 1 chr6A.!!$R2 2468
12 TraesCS6B01G370100 chr6A 17956096 17958474 2378 False 2218.0 2218 83.7080 993 3362 1 chr6A.!!$F1 2369
13 TraesCS6B01G370100 chr6A 572400167 572402912 2745 False 1387.6 3978 95.1380 801 3488 3 chr6A.!!$F3 2687
14 TraesCS6B01G370100 chrUn 248919490 248920287 797 True 1375.0 1375 97.7440 1 798 1 chrUn.!!$R1 797
15 TraesCS6B01G370100 chrUn 273988703 273989500 797 False 1375.0 1375 97.7440 1 798 1 chrUn.!!$F1 797
16 TraesCS6B01G370100 chrUn 317743559 317744356 797 True 1375.0 1375 97.7440 1 798 1 chrUn.!!$R2 797
17 TraesCS6B01G370100 chrUn 355330086 355330883 797 True 1375.0 1375 97.7440 1 798 1 chrUn.!!$R3 797
18 TraesCS6B01G370100 chrUn 324145056 324145706 650 False 418.0 418 78.6470 3599 4251 1 chrUn.!!$F2 652
19 TraesCS6B01G370100 chr5A 567091852 567092542 690 False 1072.0 1072 94.6610 102 792 1 chr5A.!!$F3 690
20 TraesCS6B01G370100 chr2B 78089702 78090625 923 True 579.5 976 86.0075 1 797 2 chr2B.!!$R1 796
21 TraesCS6B01G370100 chr5B 56576675 56577457 782 False 965.0 965 89.0700 1 784 1 chr5B.!!$F1 783
22 TraesCS6B01G370100 chr1D 491591318 491592012 694 False 312.2 555 88.9595 12 667 2 chr1D.!!$F1 655
23 TraesCS6B01G370100 chr4A 37296440 37297012 572 False 499.0 499 82.9510 12 602 1 chr4A.!!$F1 590
24 TraesCS6B01G370100 chr3B 101638221 101638868 647 False 414.0 414 78.6790 3599 4251 1 chr3B.!!$F1 652
25 TraesCS6B01G370100 chr3A 13366371 13366908 537 False 355.0 355 78.9860 3601 4143 1 chr3A.!!$F1 542
26 TraesCS6B01G370100 chr2A 651993149 651993822 673 True 326.0 326 76.1280 3590 4251 1 chr2A.!!$R1 661

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
955 1221 1.259142 TTATTCGTGCTCCCCGTCCA 61.259 55.0 0.00 0.0 0.00 4.02 F
1219 1517 0.246635 CAATCAACTCCCCGTCGAGT 59.753 55.0 0.00 0.0 45.12 4.18 F
2649 2956 0.596600 TTGACACGAGGCGAGTGAAC 60.597 55.0 19.21 13.3 41.83 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2106 2410 0.251653 TAGTGCCCGTGAAGGTCTCT 60.252 55.0 0.00 0.00 38.74 3.10 R
3012 3319 0.766674 AGGCTGGGTAGTTGTGGTCA 60.767 55.0 0.00 0.00 0.00 4.02 R
4139 5752 0.108851 TGTAGCTGCTGAAATCGCGA 60.109 50.0 13.09 13.09 0.00 5.87 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
213 340 8.177119 TGCTTGGTATTTTCACTGTAATTTCT 57.823 30.769 0.00 0.00 0.00 2.52
389 528 8.403236 GTGTCAGGTTTACACTGTAATTTCTTT 58.597 33.333 2.41 0.00 43.13 2.52
629 834 2.929848 CGCCGCGTCGTTGTGTTTA 61.930 57.895 0.00 0.00 0.00 2.01
677 885 4.057432 CACAATTTTAGCCCAACCAGTTG 58.943 43.478 3.47 3.47 40.13 3.16
754 962 7.330208 CAGAACATTGGTCAGGAAATTTGAATC 59.670 37.037 4.20 0.00 0.00 2.52
798 1006 5.425217 TCAAATGCTAGATAGACACTCCCAA 59.575 40.000 0.00 0.00 0.00 4.12
799 1007 5.543507 AATGCTAGATAGACACTCCCAAG 57.456 43.478 0.00 0.00 0.00 3.61
802 1010 5.211973 TGCTAGATAGACACTCCCAAGAAT 58.788 41.667 0.00 0.00 0.00 2.40
805 1013 7.510685 TGCTAGATAGACACTCCCAAGAATAAT 59.489 37.037 0.00 0.00 0.00 1.28
955 1221 1.259142 TTATTCGTGCTCCCCGTCCA 61.259 55.000 0.00 0.00 0.00 4.02
995 1272 1.893808 CGCCAACACCTCTTGCAGT 60.894 57.895 0.00 0.00 0.00 4.40
1051 1337 2.035442 GTCCTGCTTGGCTTCGTCC 61.035 63.158 0.00 0.00 35.26 4.79
1061 1347 4.099170 CTTCGTCCTCGTCGCCGT 62.099 66.667 0.00 0.00 38.33 5.68
1096 1394 2.034376 AGGTGGAGAGCGAGACGT 59.966 61.111 0.00 0.00 0.00 4.34
1097 1395 2.179517 GGTGGAGAGCGAGACGTG 59.820 66.667 0.00 0.00 0.00 4.49
1219 1517 0.246635 CAATCAACTCCCCGTCGAGT 59.753 55.000 0.00 0.00 45.12 4.18
1896 2200 2.223066 CGACGTTATCTCTGTCTCGCTT 60.223 50.000 0.00 0.00 0.00 4.68
1989 2293 2.437895 ATCGTCGTCTCCGCCTCA 60.438 61.111 0.00 0.00 0.00 3.86
2223 2527 1.073923 GAAGAGGGGAAGCTGAAACCA 59.926 52.381 0.00 0.00 0.00 3.67
2271 2575 1.005394 CGAACTGGGTGTAACGGCT 60.005 57.895 0.00 0.00 38.12 5.52
2448 2752 1.908066 GCACGCAAACTTCCCCTACG 61.908 60.000 0.00 0.00 0.00 3.51
2511 2818 1.123928 CTTCCCCTAGAATGGCGTCT 58.876 55.000 0.00 0.00 32.82 4.18
2649 2956 0.596600 TTGACACGAGGCGAGTGAAC 60.597 55.000 19.21 13.30 41.83 3.18
2861 3168 4.838152 CGGGGCCGGACACATCAG 62.838 72.222 12.00 0.00 35.56 2.90
2946 3253 3.680786 TGCGCACTCGGCTACACT 61.681 61.111 5.66 0.00 41.67 3.55
3369 3710 4.953667 AGATGTGAATGCGATCAGTGTAT 58.046 39.130 0.00 0.00 0.00 2.29
3374 3715 4.093408 GTGAATGCGATCAGTGTATTGTGT 59.907 41.667 0.00 0.00 0.00 3.72
3469 3820 7.329471 TGATTTCAAAGAGAAGTCTCATGTACG 59.671 37.037 10.83 0.00 45.21 3.67
3477 3828 4.636648 AGAAGTCTCATGTACGACTACCTG 59.363 45.833 12.86 0.00 39.44 4.00
3583 4733 8.743714 GGTCATTCCAAGAAAATGAACTAAGAT 58.256 33.333 6.63 0.00 44.06 2.40
3626 4776 6.836242 AGGGTGAATTTTATTGGCTCAAAAA 58.164 32.000 0.00 0.00 0.00 1.94
3691 4843 1.302949 GCACAGGTAGGATGCCCAA 59.697 57.895 0.00 0.00 44.75 4.12
3699 4851 0.679640 TAGGATGCCCAAAGCCAACG 60.680 55.000 0.00 0.00 42.71 4.10
3716 4869 2.081725 ACGTAACACACACACACACA 57.918 45.000 0.00 0.00 0.00 3.72
3717 4870 1.727880 ACGTAACACACACACACACAC 59.272 47.619 0.00 0.00 0.00 3.82
3718 4871 1.727335 CGTAACACACACACACACACA 59.273 47.619 0.00 0.00 0.00 3.72
3719 4872 2.222707 CGTAACACACACACACACACAG 60.223 50.000 0.00 0.00 0.00 3.66
3720 4873 2.177394 AACACACACACACACACAGA 57.823 45.000 0.00 0.00 0.00 3.41
3721 4874 1.725641 ACACACACACACACACAGAG 58.274 50.000 0.00 0.00 0.00 3.35
3779 4938 3.062763 CAAAGCTATGCGTAGATGAGGG 58.937 50.000 17.35 0.00 0.00 4.30
3780 4939 1.261480 AGCTATGCGTAGATGAGGGG 58.739 55.000 17.35 0.00 0.00 4.79
3841 5299 2.231964 GACCGTACTCACACCAACCATA 59.768 50.000 0.00 0.00 0.00 2.74
3845 5303 3.863424 CGTACTCACACCAACCATATCAC 59.137 47.826 0.00 0.00 0.00 3.06
3871 5330 2.878406 CCACATGGACAACGAGTTCTTT 59.122 45.455 0.00 0.00 37.39 2.52
3919 5378 1.153086 GCCCAAGCCTCGATGTCAT 60.153 57.895 0.00 0.00 0.00 3.06
3940 5399 1.076549 GATCCAACCACCCAAGGCA 59.923 57.895 0.00 0.00 0.00 4.75
3958 5417 6.462909 CCAAGGCAAAAATCTAGGTTTTCACT 60.463 38.462 14.00 9.63 31.29 3.41
3959 5418 7.255801 CCAAGGCAAAAATCTAGGTTTTCACTA 60.256 37.037 14.00 0.00 31.29 2.74
3973 5432 5.998363 GGTTTTCACTATGAAGAACCAGTCT 59.002 40.000 19.57 0.00 41.58 3.24
3983 5442 6.798427 TGAAGAACCAGTCTAAGCATATCT 57.202 37.500 0.00 0.00 34.56 1.98
3986 5445 6.798427 AGAACCAGTCTAAGCATATCTGAA 57.202 37.500 0.00 0.00 33.56 3.02
3995 5454 6.931281 GTCTAAGCATATCTGAACAATGCCTA 59.069 38.462 15.21 9.02 45.66 3.93
4002 5461 7.682741 GCATATCTGAACAATGCCTACAACAAT 60.683 37.037 10.27 0.00 40.06 2.71
4007 5466 7.176515 TCTGAACAATGCCTACAACAATGTAAT 59.823 33.333 0.00 0.00 41.36 1.89
4032 5516 6.127111 TGACATAAAAACATAGCCATTGCCAT 60.127 34.615 0.00 0.00 38.69 4.40
4049 5533 2.218603 CCATGTATAACCAACTCGGGC 58.781 52.381 0.00 0.00 40.22 6.13
4052 5538 1.208535 TGTATAACCAACTCGGGCCAG 59.791 52.381 4.39 0.00 40.22 4.85
4110 5663 3.827505 AGTTGCACCACCATCAACT 57.172 47.368 1.47 1.47 43.73 3.16
4111 5664 2.949177 AGTTGCACCACCATCAACTA 57.051 45.000 5.20 0.00 45.82 2.24
4165 5778 5.154222 CGATTTCAGCAGCTACATACGATA 58.846 41.667 0.00 0.00 0.00 2.92
4177 5790 3.990092 ACATACGATATGCGACCATTGT 58.010 40.909 0.00 0.00 44.57 2.71
4180 5793 2.473816 ACGATATGCGACCATTGTCAG 58.526 47.619 0.00 0.00 44.57 3.51
4183 5796 2.760634 TATGCGACCATTGTCAGTGT 57.239 45.000 0.00 0.00 41.85 3.55
4205 5820 3.073735 CTCCCTCTGCGTCAGGCT 61.074 66.667 6.95 0.00 44.05 4.58
4226 5841 5.237344 GGCTATCGTTCATAGTTTGCATCTT 59.763 40.000 0.00 0.00 37.41 2.40
4227 5842 6.238484 GGCTATCGTTCATAGTTTGCATCTTT 60.238 38.462 0.00 0.00 37.41 2.52
4228 5843 7.189512 GCTATCGTTCATAGTTTGCATCTTTT 58.810 34.615 0.00 0.00 37.41 2.27
4229 5844 7.698130 GCTATCGTTCATAGTTTGCATCTTTTT 59.302 33.333 0.00 0.00 37.41 1.94
4232 5847 8.894409 TCGTTCATAGTTTGCATCTTTTTATG 57.106 30.769 0.00 0.00 0.00 1.90
4233 5848 8.726068 TCGTTCATAGTTTGCATCTTTTTATGA 58.274 29.630 0.00 0.00 0.00 2.15
4251 5866 3.773418 TGAAAGTTAACCACCGGATCA 57.227 42.857 9.46 0.00 0.00 2.92
4252 5867 3.404899 TGAAAGTTAACCACCGGATCAC 58.595 45.455 9.46 0.00 0.00 3.06
4253 5868 3.181453 TGAAAGTTAACCACCGGATCACA 60.181 43.478 9.46 0.00 0.00 3.58
4255 5870 1.975680 AGTTAACCACCGGATCACAGT 59.024 47.619 9.46 0.00 0.00 3.55
4256 5871 2.028385 AGTTAACCACCGGATCACAGTC 60.028 50.000 9.46 0.00 0.00 3.51
4257 5872 0.899720 TAACCACCGGATCACAGTCC 59.100 55.000 9.46 0.00 34.82 3.85
4265 5880 0.895530 GGATCACAGTCCGGAGTGAA 59.104 55.000 39.51 27.70 46.62 3.18
4268 5883 0.827925 TCACAGTCCGGAGTGAAGCT 60.828 55.000 39.51 19.00 41.42 3.74
4269 5884 0.888619 CACAGTCCGGAGTGAAGCTA 59.111 55.000 39.51 0.00 37.97 3.32
4270 5885 1.478510 CACAGTCCGGAGTGAAGCTAT 59.521 52.381 39.51 17.91 37.97 2.97
4271 5886 2.093973 CACAGTCCGGAGTGAAGCTATT 60.094 50.000 39.51 17.20 37.97 1.73
4272 5887 2.093973 ACAGTCCGGAGTGAAGCTATTG 60.094 50.000 39.51 15.09 35.75 1.90
4275 5890 1.134367 TCCGGAGTGAAGCTATTGTCG 59.866 52.381 0.00 0.00 0.00 4.35
4276 5891 1.135083 CCGGAGTGAAGCTATTGTCGT 60.135 52.381 0.00 0.00 0.00 4.34
4277 5892 2.098607 CCGGAGTGAAGCTATTGTCGTA 59.901 50.000 0.00 0.00 0.00 3.43
4278 5893 3.364062 CGGAGTGAAGCTATTGTCGTAG 58.636 50.000 0.00 0.00 0.00 3.51
4279 5894 3.707793 GGAGTGAAGCTATTGTCGTAGG 58.292 50.000 0.00 0.00 0.00 3.18
4280 5895 3.117046 GAGTGAAGCTATTGTCGTAGGC 58.883 50.000 0.00 0.00 0.00 3.93
4281 5896 2.159085 AGTGAAGCTATTGTCGTAGGCC 60.159 50.000 0.00 0.00 0.00 5.19
4283 5898 2.159099 TGAAGCTATTGTCGTAGGCCAG 60.159 50.000 5.01 0.00 0.00 4.85
4284 5899 1.776662 AGCTATTGTCGTAGGCCAGA 58.223 50.000 5.01 0.00 0.00 3.86
4286 5901 1.409427 GCTATTGTCGTAGGCCAGAGT 59.591 52.381 5.01 0.00 0.00 3.24
4287 5902 2.799917 GCTATTGTCGTAGGCCAGAGTG 60.800 54.545 5.01 0.00 0.00 3.51
4290 5905 1.248785 TGTCGTAGGCCAGAGTGGTC 61.249 60.000 5.01 0.00 44.07 4.02
4291 5906 1.076014 TCGTAGGCCAGAGTGGTCA 59.924 57.895 5.01 0.00 46.77 4.02
4292 5907 1.215647 CGTAGGCCAGAGTGGTCAC 59.784 63.158 5.01 0.00 46.77 3.67
4293 5908 1.597461 GTAGGCCAGAGTGGTCACC 59.403 63.158 5.01 0.00 46.77 4.02
4294 5909 1.157513 TAGGCCAGAGTGGTCACCA 59.842 57.895 5.01 0.00 46.77 4.17
4306 5921 3.487576 GTCACCACAAGGACCAACA 57.512 52.632 0.00 0.00 38.69 3.33
4307 5922 1.021968 GTCACCACAAGGACCAACAC 58.978 55.000 0.00 0.00 38.69 3.32
4308 5923 0.106918 TCACCACAAGGACCAACACC 60.107 55.000 0.00 0.00 38.69 4.16
4309 5924 1.153046 ACCACAAGGACCAACACCG 60.153 57.895 0.00 0.00 38.69 4.94
4311 5926 0.884704 CCACAAGGACCAACACCGAG 60.885 60.000 0.00 0.00 36.89 4.63
4312 5927 0.884704 CACAAGGACCAACACCGAGG 60.885 60.000 0.00 0.00 0.00 4.63
4313 5928 1.052124 ACAAGGACCAACACCGAGGA 61.052 55.000 0.00 0.00 0.00 3.71
4314 5929 0.324943 CAAGGACCAACACCGAGGAT 59.675 55.000 0.00 0.00 0.00 3.24
4315 5930 0.324943 AAGGACCAACACCGAGGATG 59.675 55.000 0.00 0.00 0.00 3.51
4316 5931 0.544357 AGGACCAACACCGAGGATGA 60.544 55.000 0.00 0.00 0.00 2.92
4317 5932 0.323629 GGACCAACACCGAGGATGAA 59.676 55.000 0.00 0.00 0.00 2.57
4318 5933 1.676014 GGACCAACACCGAGGATGAAG 60.676 57.143 0.00 0.00 0.00 3.02
4319 5934 0.321653 ACCAACACCGAGGATGAAGC 60.322 55.000 0.00 0.00 0.00 3.86
4320 5935 0.321564 CCAACACCGAGGATGAAGCA 60.322 55.000 0.00 0.00 0.00 3.91
4321 5936 0.798776 CAACACCGAGGATGAAGCAC 59.201 55.000 0.00 0.00 0.00 4.40
4322 5937 0.396435 AACACCGAGGATGAAGCACA 59.604 50.000 0.00 0.00 0.00 4.57
4323 5938 0.615331 ACACCGAGGATGAAGCACAT 59.385 50.000 0.00 0.00 42.47 3.21
4334 5949 3.044235 TGAAGCACATCAACGATGACT 57.956 42.857 10.81 5.01 42.09 3.41
4335 5950 4.186856 TGAAGCACATCAACGATGACTA 57.813 40.909 10.81 0.00 42.09 2.59
4336 5951 3.926527 TGAAGCACATCAACGATGACTAC 59.073 43.478 10.81 0.00 42.09 2.73
4337 5952 2.893637 AGCACATCAACGATGACTACC 58.106 47.619 10.81 0.00 42.09 3.18
4338 5953 2.233676 AGCACATCAACGATGACTACCA 59.766 45.455 10.81 0.00 42.09 3.25
4339 5954 2.348666 GCACATCAACGATGACTACCAC 59.651 50.000 10.81 0.00 42.09 4.16
4340 5955 2.930040 CACATCAACGATGACTACCACC 59.070 50.000 10.81 0.00 42.09 4.61
4341 5956 2.832129 ACATCAACGATGACTACCACCT 59.168 45.455 10.81 0.00 42.09 4.00
4342 5957 3.119101 ACATCAACGATGACTACCACCTC 60.119 47.826 10.81 0.00 42.09 3.85
4343 5958 2.521126 TCAACGATGACTACCACCTCA 58.479 47.619 0.00 0.00 0.00 3.86
4344 5959 2.230508 TCAACGATGACTACCACCTCAC 59.769 50.000 0.00 0.00 0.00 3.51
4345 5960 1.183549 ACGATGACTACCACCTCACC 58.816 55.000 0.00 0.00 0.00 4.02
4346 5961 1.182667 CGATGACTACCACCTCACCA 58.817 55.000 0.00 0.00 0.00 4.17
4347 5962 1.135139 CGATGACTACCACCTCACCAG 59.865 57.143 0.00 0.00 0.00 4.00
4348 5963 2.457598 GATGACTACCACCTCACCAGA 58.542 52.381 0.00 0.00 0.00 3.86
4349 5964 1.924731 TGACTACCACCTCACCAGAG 58.075 55.000 0.00 0.00 41.72 3.35
4350 5965 1.427753 TGACTACCACCTCACCAGAGA 59.572 52.381 0.00 0.00 44.98 3.10
4351 5966 2.096248 GACTACCACCTCACCAGAGAG 58.904 57.143 0.00 0.00 44.98 3.20
4352 5967 1.711375 ACTACCACCTCACCAGAGAGA 59.289 52.381 0.00 0.00 44.98 3.10
4353 5968 2.291282 ACTACCACCTCACCAGAGAGAG 60.291 54.545 0.00 0.00 44.98 3.20
4354 5969 0.902516 ACCACCTCACCAGAGAGAGC 60.903 60.000 0.00 0.00 44.98 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
213 340 6.899393 AATTACACTGGCAAAAATCTGAGA 57.101 33.333 0.00 0.00 0.00 3.27
389 528 4.733077 TGGAAATTACCCTCAAGAACCA 57.267 40.909 0.00 0.00 0.00 3.67
629 834 5.989777 CCCGGTTCTCAACTAATCGAAATAT 59.010 40.000 0.00 0.00 32.17 1.28
677 885 8.234546 ACCGATCTTTGTGTGTATTTCAATAAC 58.765 33.333 0.00 0.00 0.00 1.89
825 1033 2.699073 CAGCGAGGCACTGCATTAT 58.301 52.632 2.82 0.00 41.55 1.28
826 1034 4.206958 CAGCGAGGCACTGCATTA 57.793 55.556 2.82 0.00 41.55 1.90
924 1190 0.460311 ACGAATAAGTAGGCAGCGCT 59.540 50.000 2.64 2.64 0.00 5.92
980 1253 1.667236 TGTCACTGCAAGAGGTGTTG 58.333 50.000 4.00 0.00 37.43 3.33
981 1254 2.418368 TTGTCACTGCAAGAGGTGTT 57.582 45.000 4.00 0.00 37.43 3.32
995 1272 1.552337 GTCTGAGGAGCTCCATTGTCA 59.448 52.381 33.90 25.39 38.89 3.58
1112 1410 2.987593 CGACGTGCACGATGTAGC 59.012 61.111 42.94 22.20 43.02 3.58
1201 1499 2.667348 ACTCGACGGGGAGTTGATT 58.333 52.632 0.00 0.00 44.65 2.57
1519 1820 2.594592 GCGGAACTTGCTGGGTGT 60.595 61.111 0.00 0.00 0.00 4.16
1647 1951 1.957562 CGACAACGAGTCCTCACCT 59.042 57.895 0.00 0.00 44.66 4.00
1989 2293 4.035102 GGGCCAGAGTTTCCCGCT 62.035 66.667 4.39 0.00 0.00 5.52
2106 2410 0.251653 TAGTGCCCGTGAAGGTCTCT 60.252 55.000 0.00 0.00 38.74 3.10
2223 2527 2.609610 TTCCCGGCTACCTTGGCT 60.610 61.111 0.00 0.00 0.00 4.75
2271 2575 1.229428 CTTGTCCTTTCGCTGCTTGA 58.771 50.000 0.00 0.00 0.00 3.02
2448 2752 2.303676 GCGGAAGATGATCGTCGCC 61.304 63.158 15.83 15.83 0.00 5.54
2649 2956 2.731451 CGTGCCCGATATGATGTTGTAG 59.269 50.000 0.00 0.00 35.63 2.74
2745 3052 1.412710 GTCATCAGGGCGGACTTGATA 59.587 52.381 8.26 0.00 0.00 2.15
2805 3112 2.994995 TCGCCGGTGGACATGTCT 60.995 61.111 24.50 0.00 0.00 3.41
3012 3319 0.766674 AGGCTGGGTAGTTGTGGTCA 60.767 55.000 0.00 0.00 0.00 4.02
3242 3549 0.520827 GTACTTCTCCGTGACGCTCG 60.521 60.000 0.00 0.00 0.00 5.03
3342 3649 1.217585 ATCGCATTCACATCTCCGCG 61.218 55.000 0.00 0.00 43.80 6.46
3369 3710 7.542890 ACAACAAATGACATAAACTCACACAA 58.457 30.769 0.00 0.00 0.00 3.33
3583 4733 8.243961 TCACCCTTTGTAAAAGAAAATGATGA 57.756 30.769 1.31 0.00 0.00 2.92
3691 4843 1.399089 GTGTGTGTGTTACGTTGGCTT 59.601 47.619 0.00 0.00 0.00 4.35
3699 4851 2.997303 TCTGTGTGTGTGTGTGTGTTAC 59.003 45.455 0.00 0.00 0.00 2.50
3716 4869 1.782028 GCCGGCGTGTTTTTCTCTGT 61.782 55.000 12.58 0.00 0.00 3.41
3717 4870 1.082104 GCCGGCGTGTTTTTCTCTG 60.082 57.895 12.58 0.00 0.00 3.35
3718 4871 1.098712 TTGCCGGCGTGTTTTTCTCT 61.099 50.000 23.90 0.00 0.00 3.10
3719 4872 0.248702 TTTGCCGGCGTGTTTTTCTC 60.249 50.000 23.90 0.00 0.00 2.87
3720 4873 0.387565 ATTTGCCGGCGTGTTTTTCT 59.612 45.000 23.90 0.00 0.00 2.52
3721 4874 1.982913 CTATTTGCCGGCGTGTTTTTC 59.017 47.619 23.90 0.00 0.00 2.29
3748 4901 7.667557 TCTACGCATAGCTTTGGTCTTATATT 58.332 34.615 6.29 0.00 0.00 1.28
3841 5299 3.674997 GTTGTCCATGTGGTGTAGTGAT 58.325 45.455 0.00 0.00 36.34 3.06
3845 5303 2.288825 ACTCGTTGTCCATGTGGTGTAG 60.289 50.000 0.00 0.00 36.34 2.74
3871 5330 3.751175 CCTTCCTGAAAGCGTTGATGTTA 59.249 43.478 0.00 0.00 33.29 2.41
3919 5378 0.114168 CCTTGGGTGGTTGGATCCAA 59.886 55.000 23.63 23.63 39.34 3.53
3958 5417 8.363390 CAGATATGCTTAGACTGGTTCTTCATA 58.637 37.037 0.00 0.00 35.55 2.15
3959 5418 7.070447 TCAGATATGCTTAGACTGGTTCTTCAT 59.930 37.037 12.91 0.00 35.55 2.57
3967 5426 6.293298 GCATTGTTCAGATATGCTTAGACTGG 60.293 42.308 12.91 2.76 41.04 4.00
3973 5432 6.591001 TGTAGGCATTGTTCAGATATGCTTA 58.409 36.000 0.00 0.00 43.17 3.09
3983 5442 6.641169 TTACATTGTTGTAGGCATTGTTCA 57.359 33.333 0.00 0.00 39.43 3.18
3986 5445 6.208402 TGTCATTACATTGTTGTAGGCATTGT 59.792 34.615 0.00 0.00 39.43 2.71
4002 5461 9.800433 CAATGGCTATGTTTTTATGTCATTACA 57.200 29.630 0.00 0.00 40.69 2.41
4007 5466 5.186603 TGGCAATGGCTATGTTTTTATGTCA 59.813 36.000 8.59 0.00 40.87 3.58
4021 5505 3.311167 TGGTTATACATGGCAATGGCT 57.689 42.857 8.59 0.00 40.87 4.75
4032 5516 1.208535 CTGGCCCGAGTTGGTTATACA 59.791 52.381 0.00 0.00 35.15 2.29
4049 5533 1.077429 GGTGAAAGCCTAGGCCTGG 60.077 63.158 30.42 13.68 43.17 4.45
4091 5577 1.609208 AGTTGATGGTGGTGCAACTC 58.391 50.000 2.04 0.00 46.60 3.01
4110 5663 5.429130 TGGTGACAACAACACATAACTGTA 58.571 37.500 0.00 0.00 38.94 2.74
4111 5664 4.265893 TGGTGACAACAACACATAACTGT 58.734 39.130 0.00 0.00 38.94 3.55
4139 5752 0.108851 TGTAGCTGCTGAAATCGCGA 60.109 50.000 13.09 13.09 0.00 5.87
4146 5759 4.237724 GCATATCGTATGTAGCTGCTGAA 58.762 43.478 13.43 0.00 0.00 3.02
4147 5760 3.670627 CGCATATCGTATGTAGCTGCTGA 60.671 47.826 13.43 0.00 0.00 4.26
4177 5790 1.618837 GCAGAGGGAGTTGTACACTGA 59.381 52.381 10.60 0.00 35.01 3.41
4180 5793 0.317479 ACGCAGAGGGAGTTGTACAC 59.683 55.000 0.00 0.00 0.00 2.90
4183 5796 0.888619 CTGACGCAGAGGGAGTTGTA 59.111 55.000 1.18 0.00 32.44 2.41
4226 5841 6.715718 TGATCCGGTGGTTAACTTTCATAAAA 59.284 34.615 0.00 0.00 0.00 1.52
4227 5842 6.149807 GTGATCCGGTGGTTAACTTTCATAAA 59.850 38.462 0.00 0.00 0.00 1.40
4228 5843 5.644636 GTGATCCGGTGGTTAACTTTCATAA 59.355 40.000 0.00 0.00 0.00 1.90
4229 5844 5.180271 GTGATCCGGTGGTTAACTTTCATA 58.820 41.667 0.00 0.00 0.00 2.15
4230 5845 4.007659 GTGATCCGGTGGTTAACTTTCAT 58.992 43.478 0.00 0.00 0.00 2.57
4232 5847 3.404899 TGTGATCCGGTGGTTAACTTTC 58.595 45.455 0.00 0.00 0.00 2.62
4233 5848 3.181448 ACTGTGATCCGGTGGTTAACTTT 60.181 43.478 0.00 0.00 0.00 2.66
4251 5866 1.853963 ATAGCTTCACTCCGGACTGT 58.146 50.000 0.00 0.00 0.00 3.55
4252 5867 2.093973 ACAATAGCTTCACTCCGGACTG 60.094 50.000 0.00 1.48 0.00 3.51
4253 5868 2.166664 GACAATAGCTTCACTCCGGACT 59.833 50.000 0.00 0.00 0.00 3.85
4255 5870 1.134367 CGACAATAGCTTCACTCCGGA 59.866 52.381 2.93 2.93 0.00 5.14
4256 5871 1.135083 ACGACAATAGCTTCACTCCGG 60.135 52.381 0.00 0.00 0.00 5.14
4257 5872 2.279582 ACGACAATAGCTTCACTCCG 57.720 50.000 0.00 0.00 0.00 4.63
4259 5874 3.117046 GCCTACGACAATAGCTTCACTC 58.883 50.000 0.00 0.00 0.00 3.51
4260 5875 2.159085 GGCCTACGACAATAGCTTCACT 60.159 50.000 0.00 0.00 0.00 3.41
4261 5876 2.202566 GGCCTACGACAATAGCTTCAC 58.797 52.381 0.00 0.00 0.00 3.18
4264 5879 2.101582 CTCTGGCCTACGACAATAGCTT 59.898 50.000 3.32 0.00 0.00 3.74
4265 5880 1.683917 CTCTGGCCTACGACAATAGCT 59.316 52.381 3.32 0.00 0.00 3.32
4268 5883 1.754803 CCACTCTGGCCTACGACAATA 59.245 52.381 3.32 0.00 0.00 1.90
4269 5884 0.537188 CCACTCTGGCCTACGACAAT 59.463 55.000 3.32 0.00 0.00 2.71
4270 5885 0.830444 ACCACTCTGGCCTACGACAA 60.830 55.000 3.32 0.00 42.67 3.18
4271 5886 1.228769 ACCACTCTGGCCTACGACA 60.229 57.895 3.32 0.00 42.67 4.35
4272 5887 1.248785 TGACCACTCTGGCCTACGAC 61.249 60.000 3.32 0.00 42.67 4.34
4275 5890 1.192146 TGGTGACCACTCTGGCCTAC 61.192 60.000 0.00 0.00 42.67 3.18
4276 5891 1.157513 TGGTGACCACTCTGGCCTA 59.842 57.895 0.00 0.00 42.67 3.93
4277 5892 2.122413 TGGTGACCACTCTGGCCT 60.122 61.111 0.00 0.00 42.67 5.19
4290 5905 1.444119 CGGTGTTGGTCCTTGTGGTG 61.444 60.000 0.00 0.00 34.23 4.17
4291 5906 1.153046 CGGTGTTGGTCCTTGTGGT 60.153 57.895 0.00 0.00 34.23 4.16
4292 5907 0.884704 CTCGGTGTTGGTCCTTGTGG 60.885 60.000 0.00 0.00 0.00 4.17
4293 5908 0.884704 CCTCGGTGTTGGTCCTTGTG 60.885 60.000 0.00 0.00 0.00 3.33
4294 5909 1.052124 TCCTCGGTGTTGGTCCTTGT 61.052 55.000 0.00 0.00 0.00 3.16
4295 5910 0.324943 ATCCTCGGTGTTGGTCCTTG 59.675 55.000 0.00 0.00 0.00 3.61
4297 5912 0.544357 TCATCCTCGGTGTTGGTCCT 60.544 55.000 0.00 0.00 0.00 3.85
4298 5913 0.323629 TTCATCCTCGGTGTTGGTCC 59.676 55.000 0.00 0.00 0.00 4.46
4299 5914 1.726853 CTTCATCCTCGGTGTTGGTC 58.273 55.000 0.00 0.00 0.00 4.02
4300 5915 0.321653 GCTTCATCCTCGGTGTTGGT 60.322 55.000 0.00 0.00 0.00 3.67
4301 5916 0.321564 TGCTTCATCCTCGGTGTTGG 60.322 55.000 0.00 0.00 0.00 3.77
4302 5917 0.798776 GTGCTTCATCCTCGGTGTTG 59.201 55.000 0.00 0.00 0.00 3.33
4303 5918 0.396435 TGTGCTTCATCCTCGGTGTT 59.604 50.000 0.00 0.00 0.00 3.32
4304 5919 0.615331 ATGTGCTTCATCCTCGGTGT 59.385 50.000 0.00 0.00 29.76 4.16
4305 5920 1.293924 GATGTGCTTCATCCTCGGTG 58.706 55.000 10.03 0.00 45.05 4.94
4306 5921 3.768633 GATGTGCTTCATCCTCGGT 57.231 52.632 10.03 0.00 45.05 4.69
4313 5928 3.603532 AGTCATCGTTGATGTGCTTCAT 58.396 40.909 6.68 0.00 40.55 2.57
4314 5929 3.044235 AGTCATCGTTGATGTGCTTCA 57.956 42.857 6.68 0.00 40.55 3.02
4315 5930 3.307242 GGTAGTCATCGTTGATGTGCTTC 59.693 47.826 6.68 5.04 40.55 3.86
4316 5931 3.262420 GGTAGTCATCGTTGATGTGCTT 58.738 45.455 6.68 0.00 40.55 3.91
4317 5932 2.233676 TGGTAGTCATCGTTGATGTGCT 59.766 45.455 6.68 8.59 40.55 4.40
4318 5933 2.348666 GTGGTAGTCATCGTTGATGTGC 59.651 50.000 6.68 2.36 40.55 4.57
4319 5934 2.930040 GGTGGTAGTCATCGTTGATGTG 59.070 50.000 6.68 0.00 40.55 3.21
4320 5935 2.832129 AGGTGGTAGTCATCGTTGATGT 59.168 45.455 6.68 0.00 40.55 3.06
4321 5936 3.119137 TGAGGTGGTAGTCATCGTTGATG 60.119 47.826 0.00 0.32 41.00 3.07
4322 5937 3.096852 TGAGGTGGTAGTCATCGTTGAT 58.903 45.455 0.00 0.00 33.56 2.57
4323 5938 2.230508 GTGAGGTGGTAGTCATCGTTGA 59.769 50.000 0.00 0.00 0.00 3.18
4324 5939 2.607187 GTGAGGTGGTAGTCATCGTTG 58.393 52.381 0.00 0.00 0.00 4.10
4325 5940 1.549170 GGTGAGGTGGTAGTCATCGTT 59.451 52.381 0.00 0.00 0.00 3.85
4326 5941 1.183549 GGTGAGGTGGTAGTCATCGT 58.816 55.000 0.00 0.00 0.00 3.73
4327 5942 1.135139 CTGGTGAGGTGGTAGTCATCG 59.865 57.143 0.00 0.00 0.00 3.84
4328 5943 2.428890 CTCTGGTGAGGTGGTAGTCATC 59.571 54.545 0.00 0.00 36.70 2.92
4329 5944 2.043115 TCTCTGGTGAGGTGGTAGTCAT 59.957 50.000 0.00 0.00 40.58 3.06
4330 5945 1.427753 TCTCTGGTGAGGTGGTAGTCA 59.572 52.381 0.00 0.00 40.58 3.41
4331 5946 2.096248 CTCTCTGGTGAGGTGGTAGTC 58.904 57.143 0.00 0.00 40.58 2.59
4332 5947 1.711375 TCTCTCTGGTGAGGTGGTAGT 59.289 52.381 0.00 0.00 40.58 2.73
4333 5948 2.374184 CTCTCTCTGGTGAGGTGGTAG 58.626 57.143 0.00 0.00 40.58 3.18
4334 5949 1.617263 GCTCTCTCTGGTGAGGTGGTA 60.617 57.143 0.00 0.00 40.58 3.25
4335 5950 0.902516 GCTCTCTCTGGTGAGGTGGT 60.903 60.000 0.00 0.00 40.58 4.16
4336 5951 1.896694 GCTCTCTCTGGTGAGGTGG 59.103 63.158 0.00 0.00 40.58 4.61


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

AutoCloner maintained by Alex Coulton.