Multiple sequence alignment - TraesCS7D01G356000

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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 TraesCS7D01G356000 chr7D 100.000 3867 0 0 1 3867 459607291 459603425 0.000000e+00 7142.0
1 TraesCS7D01G356000 chr7D 93.625 3765 216 12 1 3759 459465869 459462123 0.000000e+00 5602.0
2 TraesCS7D01G356000 chr7D 92.148 2980 219 12 1 2971 459433040 459430067 0.000000e+00 4193.0
3 TraesCS7D01G356000 chr7D 81.146 1501 251 21 1433 2920 459472524 459471043 0.000000e+00 1175.0
4 TraesCS7D01G356000 chr7D 79.545 1364 266 11 79 1435 459746043 459744686 0.000000e+00 961.0
5 TraesCS7D01G356000 chr7D 87.980 782 64 10 2378 3147 459429183 459428420 0.000000e+00 896.0
6 TraesCS7D01G356000 chr7D 79.343 426 38 22 3193 3607 459428431 459428045 1.780000e-63 254.0
7 TraesCS7D01G356000 chr7B 94.160 3613 202 5 1 3609 481617494 481613887 0.000000e+00 5494.0
8 TraesCS7D01G356000 chr7B 80.612 1176 196 23 1433 2594 481623430 481622273 0.000000e+00 880.0
9 TraesCS7D01G356000 chr7B 95.385 65 3 0 3695 3759 481613883 481613819 1.900000e-18 104.0
10 TraesCS7D01G356000 chr7A 93.305 3555 222 8 1 3550 540756088 540759631 0.000000e+00 5232.0
11 TraesCS7D01G356000 chr7A 91.354 2695 222 8 251 2939 540283208 540285897 0.000000e+00 3675.0
12 TraesCS7D01G356000 chr7A 94.342 1679 93 1 1 1677 540771975 540773653 0.000000e+00 2573.0
13 TraesCS7D01G356000 chr7A 86.789 1090 101 24 2378 3453 540776882 540777942 0.000000e+00 1175.0
14 TraesCS7D01G356000 chr7A 93.985 532 19 6 3085 3607 540287382 540287909 0.000000e+00 793.0
15 TraesCS7D01G356000 chr7A 90.287 453 44 0 2487 2939 540775335 540775787 9.250000e-166 593.0
16 TraesCS7D01G356000 chr7A 90.339 383 30 4 2378 2754 540286741 540287122 2.680000e-136 496.0
17 TraesCS7D01G356000 chr7A 93.657 268 15 2 2789 3055 540287122 540287388 2.160000e-107 399.0
18 TraesCS7D01G356000 chr7A 90.361 83 5 3 3606 3687 430771652 430771732 5.280000e-19 106.0
19 TraesCS7D01G356000 chr7A 90.361 83 5 3 3606 3687 541775394 541775314 5.280000e-19 106.0
20 TraesCS7D01G356000 chr6B 89.575 1247 126 3 3 1246 6196361 6197606 0.000000e+00 1580.0
21 TraesCS7D01G356000 chr6B 90.361 83 5 3 3606 3687 519982764 519982844 5.280000e-19 106.0
22 TraesCS7D01G356000 chr6D 89.604 1135 116 1 115 1247 3028787 3029921 0.000000e+00 1441.0
23 TraesCS7D01G356000 chr5A 79.329 1519 262 35 1433 2920 680983258 680984755 0.000000e+00 1018.0
24 TraesCS7D01G356000 chr5A 79.060 1490 258 33 1433 2884 680923349 680924822 0.000000e+00 974.0
25 TraesCS7D01G356000 chr4A 91.566 83 4 3 3606 3687 319196292 319196372 1.140000e-20 111.0
26 TraesCS7D01G356000 chr4A 87.640 89 9 2 3605 3693 64138778 64138864 6.840000e-18 102.0
27 TraesCS7D01G356000 chr4A 84.158 101 11 4 3595 3693 603323599 603323696 4.110000e-15 93.5
28 TraesCS7D01G356000 chr2B 89.655 87 6 3 3606 3692 350306690 350306773 1.470000e-19 108.0
29 TraesCS7D01G356000 chr3A 90.361 83 5 3 3606 3687 171063481 171063401 5.280000e-19 106.0


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 TraesCS7D01G356000 chr7D 459603425 459607291 3866 True 7142.00 7142 100.000000 1 3867 1 chr7D.!!$R3 3866
1 TraesCS7D01G356000 chr7D 459462123 459465869 3746 True 5602.00 5602 93.625000 1 3759 1 chr7D.!!$R1 3758
2 TraesCS7D01G356000 chr7D 459428045 459433040 4995 True 1781.00 4193 86.490333 1 3607 3 chr7D.!!$R5 3606
3 TraesCS7D01G356000 chr7D 459471043 459472524 1481 True 1175.00 1175 81.146000 1433 2920 1 chr7D.!!$R2 1487
4 TraesCS7D01G356000 chr7D 459744686 459746043 1357 True 961.00 961 79.545000 79 1435 1 chr7D.!!$R4 1356
5 TraesCS7D01G356000 chr7B 481613819 481617494 3675 True 2799.00 5494 94.772500 1 3759 2 chr7B.!!$R2 3758
6 TraesCS7D01G356000 chr7B 481622273 481623430 1157 True 880.00 880 80.612000 1433 2594 1 chr7B.!!$R1 1161
7 TraesCS7D01G356000 chr7A 540756088 540759631 3543 False 5232.00 5232 93.305000 1 3550 1 chr7A.!!$F2 3549
8 TraesCS7D01G356000 chr7A 540771975 540777942 5967 False 1447.00 2573 90.472667 1 3453 3 chr7A.!!$F4 3452
9 TraesCS7D01G356000 chr7A 540283208 540287909 4701 False 1340.75 3675 92.333750 251 3607 4 chr7A.!!$F3 3356
10 TraesCS7D01G356000 chr6B 6196361 6197606 1245 False 1580.00 1580 89.575000 3 1246 1 chr6B.!!$F1 1243
11 TraesCS7D01G356000 chr6D 3028787 3029921 1134 False 1441.00 1441 89.604000 115 1247 1 chr6D.!!$F1 1132
12 TraesCS7D01G356000 chr5A 680983258 680984755 1497 False 1018.00 1018 79.329000 1433 2920 1 chr5A.!!$F2 1487
13 TraesCS7D01G356000 chr5A 680923349 680924822 1473 False 974.00 974 79.060000 1433 2884 1 chr5A.!!$F1 1451

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
852 856 1.977854 ACCAGGTTGACTATGCTGACA 59.022 47.619 0.00 0.0 0.00 3.58 F
1776 1786 1.547372 AGGATGCAAGCAAATCCACAC 59.453 47.619 15.02 0.0 44.17 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2084 2409 1.021968 GTTCCCATTCGGCATGTACC 58.978 55.0 0.0 0.0 0.0 3.34 R
3759 7988 0.744874 TCACCCGGTTCGATGATCTC 59.255 55.0 0.0 0.0 0.0 2.75 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
195 196 7.989947 AATAGTTCATCCCTCCAAGTACTTA 57.010 36.000 8.04 0.00 0.00 2.24
237 238 3.910989 AGTGGAAAACTACCAAAGGCTT 58.089 40.909 0.00 0.00 37.36 4.35
374 375 9.533253 CACAATCATATTTCAGGAAAAATACCC 57.467 33.333 0.00 0.00 34.75 3.69
505 506 2.948979 CCTTGACAGCCAACAACTTGTA 59.051 45.455 0.00 0.00 0.00 2.41
631 633 4.585162 ACTCCCGAGTATTCAGACATTAGG 59.415 45.833 0.00 0.00 40.43 2.69
851 855 2.770164 ACCAGGTTGACTATGCTGAC 57.230 50.000 0.00 0.00 0.00 3.51
852 856 1.977854 ACCAGGTTGACTATGCTGACA 59.022 47.619 0.00 0.00 0.00 3.58
1191 1195 3.576648 GATACCTGCAAGTATAGGACGC 58.423 50.000 7.96 0.00 37.52 5.19
1346 1350 5.359009 CAGTGGAAGTTGGCAATCTCATTAT 59.641 40.000 1.92 0.00 0.00 1.28
1616 1620 2.105649 TGTGTACCAGCATTCCAACAGA 59.894 45.455 0.00 0.00 0.00 3.41
1700 1707 5.703310 AGTCCTACGGATAGTAACTCCAAT 58.297 41.667 0.00 0.00 34.45 3.16
1776 1786 1.547372 AGGATGCAAGCAAATCCACAC 59.453 47.619 15.02 0.00 44.17 3.82
1798 1808 4.222145 ACTTGCAGGAATTTGATGAGCATT 59.778 37.500 1.40 0.00 0.00 3.56
2076 2401 2.196319 GGCAGATTTCAAGGCCCTG 58.804 57.895 0.00 0.00 40.55 4.45
2084 2409 2.672996 CAAGGCCCTGGTGTTCCG 60.673 66.667 0.00 0.00 36.30 4.30
2085 2410 3.966543 AAGGCCCTGGTGTTCCGG 61.967 66.667 0.00 0.00 39.70 5.14
2124 3122 3.780294 ACCTAGAAATGTGGCTACATCCA 59.220 43.478 16.73 1.48 46.54 3.41
2251 3250 5.297527 GCATCTCCATTGATACATTGTGACA 59.702 40.000 0.00 0.00 0.00 3.58
2257 3256 8.806429 TCCATTGATACATTGTGACATAAAGT 57.194 30.769 0.00 0.00 0.00 2.66
2293 3292 2.221169 TGGATCTTGATATGGTTGCGC 58.779 47.619 0.00 0.00 0.00 6.09
2328 3327 1.478105 GGCCTGGCAAGGTTTCTATTG 59.522 52.381 22.05 0.00 46.43 1.90
2367 3366 9.587772 GCATACAAAGATAGTTCAAGAAGTCTA 57.412 33.333 0.00 0.00 0.00 2.59
2406 3405 1.071471 CGGATACATCCCACCAGGC 59.929 63.158 2.63 0.00 44.24 4.85
2410 3409 0.691078 ATACATCCCACCAGGCGAGT 60.691 55.000 0.00 0.00 34.51 4.18
2416 3415 0.676782 CCCACCAGGCGAGTTTAAGG 60.677 60.000 0.00 0.00 0.00 2.69
2467 5167 6.315393 GGTCTGTTTGTTCTTTACAGAGTTGA 59.685 38.462 4.55 0.00 46.30 3.18
2530 6721 1.780806 CAGAGTATGGCATGAGCGAG 58.219 55.000 10.98 0.00 43.41 5.03
2825 7016 2.354203 GGACAAGTTTCTGCCGAGATCT 60.354 50.000 0.00 0.00 0.00 2.75
2965 7164 5.841810 TGGCTTTTCCATTTGTTAGTTCAG 58.158 37.500 0.00 0.00 40.72 3.02
3115 7315 3.722082 CGATTTGCGCAGTCAGAGTAAAC 60.722 47.826 11.31 0.00 34.86 2.01
3304 7516 4.697756 CCTGGTTGCCGCGGAAGA 62.698 66.667 33.48 10.85 0.00 2.87
3308 7520 1.375013 GGTTGCCGCGGAAGACTAA 60.375 57.895 33.48 10.25 0.00 2.24
3434 7652 0.528017 GCTTAAGGAGGCAAAGTGGC 59.472 55.000 4.29 0.00 44.10 5.01
3513 7738 0.754472 TACCCTACCCGCATTACTGC 59.246 55.000 0.00 0.00 45.31 4.40
3529 7754 3.540314 ACTGCCTCTGAATAAGCTCTG 57.460 47.619 0.00 0.00 0.00 3.35
3550 7779 5.534654 TCTGTTAAGGTTTCATTTCCCACAG 59.465 40.000 0.00 0.00 32.60 3.66
3556 7785 3.888930 GGTTTCATTTCCCACAGAACAGA 59.111 43.478 0.00 0.00 32.95 3.41
3557 7786 4.261614 GGTTTCATTTCCCACAGAACAGAC 60.262 45.833 0.00 0.00 32.95 3.51
3558 7787 4.437682 TTCATTTCCCACAGAACAGACT 57.562 40.909 0.00 0.00 32.95 3.24
3559 7788 4.008074 TCATTTCCCACAGAACAGACTC 57.992 45.455 0.00 0.00 32.95 3.36
3614 7843 6.692486 ACTGCATCTAAATTATACTCCCTCG 58.308 40.000 0.00 0.00 0.00 4.63
3630 7859 2.290705 CCCTCGGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
3634 7863 3.325425 TCGGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
3638 7867 5.181433 GGTCCCAAAATAAGTGTCTCAACTC 59.819 44.000 0.00 0.00 0.00 3.01
3640 7869 7.159372 GTCCCAAAATAAGTGTCTCAACTCTA 58.841 38.462 0.00 0.00 0.00 2.43
3642 7871 7.016268 TCCCAAAATAAGTGTCTCAACTCTAGT 59.984 37.037 0.00 0.00 0.00 2.57
3643 7872 8.311836 CCCAAAATAAGTGTCTCAACTCTAGTA 58.688 37.037 0.00 0.00 0.00 1.82
3644 7873 9.141400 CCAAAATAAGTGTCTCAACTCTAGTAC 57.859 37.037 0.00 0.00 0.00 2.73
3645 7874 9.692749 CAAAATAAGTGTCTCAACTCTAGTACA 57.307 33.333 0.00 0.00 0.00 2.90
3647 7876 9.694137 AAATAAGTGTCTCAACTCTAGTACAAC 57.306 33.333 0.00 0.00 0.00 3.32
3648 7877 6.963083 AAGTGTCTCAACTCTAGTACAACT 57.037 37.500 0.00 0.00 0.00 3.16
3651 7880 7.203910 AGTGTCTCAACTCTAGTACAACTTTG 58.796 38.462 0.00 0.00 0.00 2.77
3652 7881 6.979238 GTGTCTCAACTCTAGTACAACTTTGT 59.021 38.462 0.00 0.00 44.86 2.83
3653 7882 8.133627 GTGTCTCAACTCTAGTACAACTTTGTA 58.866 37.037 0.00 0.00 42.35 2.41
3654 7883 8.857098 TGTCTCAACTCTAGTACAACTTTGTAT 58.143 33.333 5.16 0.00 44.59 2.29
3687 7916 2.304761 ACACTTATTTTGAGGCGGAGGA 59.695 45.455 0.00 0.00 0.00 3.71
3690 7919 3.009143 ACTTATTTTGAGGCGGAGGAAGT 59.991 43.478 0.00 0.00 0.00 3.01
3691 7920 4.224370 ACTTATTTTGAGGCGGAGGAAGTA 59.776 41.667 0.00 0.00 0.00 2.24
3692 7921 3.933861 ATTTTGAGGCGGAGGAAGTAT 57.066 42.857 0.00 0.00 0.00 2.12
3693 7922 6.099269 ACTTATTTTGAGGCGGAGGAAGTATA 59.901 38.462 0.00 0.00 0.00 1.47
3723 7952 0.309302 CGGCAATTGAACACGACCAA 59.691 50.000 10.34 0.00 0.00 3.67
3730 7959 5.106712 GCAATTGAACACGACCAATCTTCTA 60.107 40.000 10.34 0.00 32.36 2.10
3738 7967 5.171476 CACGACCAATCTTCTACAATCAGT 58.829 41.667 0.00 0.00 0.00 3.41
3759 7988 7.440198 TCAGTAGGAAGAGATAATGAAGCATG 58.560 38.462 0.00 0.00 0.00 4.06
3760 7989 7.288621 TCAGTAGGAAGAGATAATGAAGCATGA 59.711 37.037 0.00 0.00 0.00 3.07
3761 7990 7.599621 CAGTAGGAAGAGATAATGAAGCATGAG 59.400 40.741 0.00 0.00 0.00 2.90
3762 7991 6.744175 AGGAAGAGATAATGAAGCATGAGA 57.256 37.500 0.00 0.00 0.00 3.27
3763 7992 7.319052 AGGAAGAGATAATGAAGCATGAGAT 57.681 36.000 0.00 0.00 0.00 2.75
3764 7993 7.388437 AGGAAGAGATAATGAAGCATGAGATC 58.612 38.462 0.00 0.00 0.00 2.75
3765 7994 7.016366 AGGAAGAGATAATGAAGCATGAGATCA 59.984 37.037 0.00 0.00 0.00 2.92
3766 7995 7.825270 GGAAGAGATAATGAAGCATGAGATCAT 59.175 37.037 0.00 0.00 35.39 2.45
3767 7996 8.780846 AAGAGATAATGAAGCATGAGATCATC 57.219 34.615 0.00 0.00 32.83 2.92
3768 7997 7.036829 AGAGATAATGAAGCATGAGATCATCG 58.963 38.462 0.00 0.00 32.83 3.84
3769 7998 6.932947 AGATAATGAAGCATGAGATCATCGA 58.067 36.000 0.00 0.00 32.83 3.59
3770 7999 7.384477 AGATAATGAAGCATGAGATCATCGAA 58.616 34.615 0.00 0.00 32.83 3.71
3771 8000 5.670149 AATGAAGCATGAGATCATCGAAC 57.330 39.130 0.00 0.00 32.83 3.95
3772 8001 3.461061 TGAAGCATGAGATCATCGAACC 58.539 45.455 0.00 0.00 33.61 3.62
3773 8002 2.145958 AGCATGAGATCATCGAACCG 57.854 50.000 0.00 0.00 33.61 4.44
3774 8003 1.143305 GCATGAGATCATCGAACCGG 58.857 55.000 0.00 0.00 33.61 5.28
3775 8004 1.788258 CATGAGATCATCGAACCGGG 58.212 55.000 6.32 0.00 33.61 5.73
3776 8005 1.069204 CATGAGATCATCGAACCGGGT 59.931 52.381 6.32 0.00 33.61 5.28
3777 8006 0.459899 TGAGATCATCGAACCGGGTG 59.540 55.000 6.32 0.00 0.00 4.61
3778 8007 0.744874 GAGATCATCGAACCGGGTGA 59.255 55.000 6.32 0.00 0.00 4.02
3779 8008 1.341531 GAGATCATCGAACCGGGTGAT 59.658 52.381 6.32 7.32 36.17 3.06
3780 8009 1.762957 AGATCATCGAACCGGGTGATT 59.237 47.619 6.32 0.00 34.69 2.57
3781 8010 2.963101 AGATCATCGAACCGGGTGATTA 59.037 45.455 6.32 0.00 34.69 1.75
3782 8011 3.386726 AGATCATCGAACCGGGTGATTAA 59.613 43.478 6.32 0.00 34.69 1.40
3783 8012 3.830744 TCATCGAACCGGGTGATTAAT 57.169 42.857 6.32 0.00 0.00 1.40
3784 8013 4.145365 TCATCGAACCGGGTGATTAATT 57.855 40.909 6.32 0.00 0.00 1.40
3785 8014 5.279255 TCATCGAACCGGGTGATTAATTA 57.721 39.130 6.32 0.00 0.00 1.40
3786 8015 5.294356 TCATCGAACCGGGTGATTAATTAG 58.706 41.667 6.32 0.00 0.00 1.73
3787 8016 4.741321 TCGAACCGGGTGATTAATTAGT 57.259 40.909 6.32 0.00 0.00 2.24
3788 8017 5.088680 TCGAACCGGGTGATTAATTAGTT 57.911 39.130 6.32 0.00 0.00 2.24
3789 8018 4.871557 TCGAACCGGGTGATTAATTAGTTG 59.128 41.667 6.32 0.00 0.00 3.16
3790 8019 4.034742 CGAACCGGGTGATTAATTAGTTGG 59.965 45.833 6.32 0.00 0.00 3.77
3791 8020 4.579647 ACCGGGTGATTAATTAGTTGGT 57.420 40.909 6.32 0.00 0.00 3.67
3792 8021 5.697082 ACCGGGTGATTAATTAGTTGGTA 57.303 39.130 6.32 0.00 0.00 3.25
3793 8022 5.430886 ACCGGGTGATTAATTAGTTGGTAC 58.569 41.667 6.32 0.00 0.00 3.34
3794 8023 5.190330 ACCGGGTGATTAATTAGTTGGTACT 59.810 40.000 6.32 0.00 38.44 2.73
3795 8024 6.383726 ACCGGGTGATTAATTAGTTGGTACTA 59.616 38.462 6.32 0.00 35.78 1.82
3797 8026 7.440255 CCGGGTGATTAATTAGTTGGTACTAAG 59.560 40.741 0.00 0.00 46.87 2.18
3798 8027 8.199449 CGGGTGATTAATTAGTTGGTACTAAGA 58.801 37.037 0.00 0.00 46.87 2.10
3799 8028 9.322773 GGGTGATTAATTAGTTGGTACTAAGAC 57.677 37.037 0.00 0.00 46.87 3.01
3800 8029 9.322773 GGTGATTAATTAGTTGGTACTAAGACC 57.677 37.037 0.00 0.00 46.87 3.85
3801 8030 9.028185 GTGATTAATTAGTTGGTACTAAGACCG 57.972 37.037 0.00 0.00 46.87 4.79
3802 8031 7.707893 TGATTAATTAGTTGGTACTAAGACCGC 59.292 37.037 0.00 0.00 46.87 5.68
3803 8032 5.410355 AATTAGTTGGTACTAAGACCGCA 57.590 39.130 0.00 0.00 46.87 5.69
3804 8033 4.445452 TTAGTTGGTACTAAGACCGCAG 57.555 45.455 0.00 0.00 40.92 5.18
3805 8034 1.549170 AGTTGGTACTAAGACCGCAGG 59.451 52.381 0.00 0.00 44.23 4.85
3806 8035 4.304419 AGTTGGTACTAAGACCGCAGGC 62.304 54.545 0.00 0.00 42.83 4.85
3824 8053 4.179599 GGGGAGGGAGGGAGGGAG 62.180 77.778 0.00 0.00 0.00 4.30
3825 8054 4.179599 GGGAGGGAGGGAGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
3826 8055 4.179599 GGAGGGAGGGAGGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
3827 8056 4.179599 GAGGGAGGGAGGGAGGGG 62.180 77.778 0.00 0.00 0.00 4.79
3828 8057 4.761304 AGGGAGGGAGGGAGGGGA 62.761 72.222 0.00 0.00 0.00 4.81
3829 8058 3.707189 GGGAGGGAGGGAGGGGAA 61.707 72.222 0.00 0.00 0.00 3.97
3830 8059 2.040359 GGAGGGAGGGAGGGGAAG 60.040 72.222 0.00 0.00 0.00 3.46
3831 8060 2.040359 GAGGGAGGGAGGGGAAGG 60.040 72.222 0.00 0.00 0.00 3.46
3832 8061 2.543637 AGGGAGGGAGGGGAAGGA 60.544 66.667 0.00 0.00 0.00 3.36
3833 8062 2.040359 GGGAGGGAGGGGAAGGAG 60.040 72.222 0.00 0.00 0.00 3.69
3834 8063 2.788589 GGAGGGAGGGGAAGGAGT 59.211 66.667 0.00 0.00 0.00 3.85
3835 8064 1.600763 GGGAGGGAGGGGAAGGAGTA 61.601 65.000 0.00 0.00 0.00 2.59
3836 8065 0.105401 GGAGGGAGGGGAAGGAGTAG 60.105 65.000 0.00 0.00 0.00 2.57
3837 8066 0.105401 GAGGGAGGGGAAGGAGTAGG 60.105 65.000 0.00 0.00 0.00 3.18
3838 8067 1.074395 GGGAGGGGAAGGAGTAGGG 60.074 68.421 0.00 0.00 0.00 3.53
3839 8068 1.074395 GGAGGGGAAGGAGTAGGGG 60.074 68.421 0.00 0.00 0.00 4.79
3840 8069 1.710972 GAGGGGAAGGAGTAGGGGT 59.289 63.158 0.00 0.00 0.00 4.95
3841 8070 0.398806 GAGGGGAAGGAGTAGGGGTC 60.399 65.000 0.00 0.00 0.00 4.46
3842 8071 1.160289 AGGGGAAGGAGTAGGGGTCA 61.160 60.000 0.00 0.00 0.00 4.02
3843 8072 0.981801 GGGGAAGGAGTAGGGGTCAC 60.982 65.000 0.00 0.00 0.00 3.67
3844 8073 0.981801 GGGAAGGAGTAGGGGTCACC 60.982 65.000 0.00 0.00 40.67 4.02
3845 8074 0.252558 GGAAGGAGTAGGGGTCACCA 60.253 60.000 0.00 0.00 43.89 4.17
3846 8075 0.903236 GAAGGAGTAGGGGTCACCAC 59.097 60.000 0.00 0.00 43.89 4.16
3847 8076 0.492276 AAGGAGTAGGGGTCACCACT 59.508 55.000 2.67 2.67 43.89 4.00
3848 8077 0.252284 AGGAGTAGGGGTCACCACTG 60.252 60.000 9.67 0.00 43.89 3.66
3849 8078 1.597461 GAGTAGGGGTCACCACTGC 59.403 63.158 9.67 7.73 43.89 4.40
3850 8079 1.900545 GAGTAGGGGTCACCACTGCC 61.901 65.000 9.67 0.00 43.89 4.85
3851 8080 3.000819 TAGGGGTCACCACTGCCG 61.001 66.667 9.67 0.00 43.89 5.69
3856 8085 3.717294 GTCACCACTGCCGGGGAT 61.717 66.667 2.24 0.00 41.64 3.85
3857 8086 3.716195 TCACCACTGCCGGGGATG 61.716 66.667 2.24 0.00 31.82 3.51
3858 8087 4.802051 CACCACTGCCGGGGATGG 62.802 72.222 2.24 12.94 38.26 3.51
3861 8090 3.492353 CACTGCCGGGGATGGGAT 61.492 66.667 2.18 0.00 0.00 3.85
3862 8091 3.171388 ACTGCCGGGGATGGGATC 61.171 66.667 2.18 0.00 0.00 3.36
3863 8092 2.851102 CTGCCGGGGATGGGATCT 60.851 66.667 2.18 0.00 0.00 2.75
3864 8093 2.368192 TGCCGGGGATGGGATCTT 60.368 61.111 2.18 0.00 0.00 2.40
3865 8094 2.113986 GCCGGGGATGGGATCTTG 59.886 66.667 2.18 0.00 0.00 3.02
3866 8095 2.839098 CCGGGGATGGGATCTTGG 59.161 66.667 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 0.469494 TTGCTGAGGTTGAGCTCACA 59.531 50.000 18.03 10.32 37.35 3.58
237 238 7.172190 GTCAAGAAGAGATGATGTGTTGAAGAA 59.828 37.037 0.00 0.00 0.00 2.52
505 506 1.561542 GAGATGGTGGAACTGTCCCAT 59.438 52.381 0.00 0.00 44.23 4.00
603 605 3.056749 GTCTGAATACTCGGGAGTGTGTT 60.057 47.826 11.47 4.06 42.52 3.32
631 633 4.370364 TCAAACTTGTTTGTTGAGAGGC 57.630 40.909 20.99 0.00 33.82 4.70
851 855 5.394883 CCTTGAAGATTGTTCCCATCCAATG 60.395 44.000 0.00 0.00 31.67 2.82
852 856 4.713321 CCTTGAAGATTGTTCCCATCCAAT 59.287 41.667 0.00 0.00 34.11 3.16
1191 1195 6.369065 GGTTGAGTATTTGGAGTTGAGTACAG 59.631 42.308 0.00 0.00 0.00 2.74
1776 1786 3.861276 TGCTCATCAAATTCCTGCAAG 57.139 42.857 0.00 0.00 0.00 4.01
2076 2401 3.899395 GGCATGTACCGGAACACC 58.101 61.111 9.46 0.00 30.75 4.16
2084 2409 1.021968 GTTCCCATTCGGCATGTACC 58.978 55.000 0.00 0.00 0.00 3.34
2085 2410 1.021968 GGTTCCCATTCGGCATGTAC 58.978 55.000 0.00 0.00 0.00 2.90
2124 3122 3.648067 TCTCACCATGTTCAAGGTCTTCT 59.352 43.478 0.00 0.00 35.52 2.85
2257 3256 8.352137 TCAAGATCCAAAAGAATATTGCTTGA 57.648 30.769 0.00 0.00 34.73 3.02
2293 3292 1.538512 CAGGCCAAAGTCAGTGACATG 59.461 52.381 24.73 20.68 34.60 3.21
2360 3359 3.197983 TCCTTTTAGGCAGGCTAGACTTC 59.802 47.826 0.00 0.00 34.61 3.01
2367 3366 1.298953 TGGATCCTTTTAGGCAGGCT 58.701 50.000 14.23 0.38 34.61 4.58
2416 3415 7.655328 CCAACAATCTAACATACTGAGGAGATC 59.345 40.741 0.00 0.00 0.00 2.75
2530 6721 4.141390 ACATCACCCTTGGTTGATATCTCC 60.141 45.833 3.98 7.33 31.02 3.71
2825 7016 4.202441 GAGGCCAGATGCTTGATTCTAAA 58.798 43.478 5.01 0.00 40.92 1.85
2965 7164 3.304057 GCAGTCTGCAAGTTTCACTAACC 60.304 47.826 20.16 0.00 44.26 2.85
2987 7186 2.424956 GCTATGGCAAAAGAGAAGGGTG 59.575 50.000 0.00 0.00 38.54 4.61
3115 7315 2.517959 TCCAAGTCAGCTTCCCAAATG 58.482 47.619 0.00 0.00 31.49 2.32
3304 7516 2.043349 GGGGCGGGGCAAATTAGT 60.043 61.111 0.00 0.00 0.00 2.24
3308 7520 1.943730 TATCAAGGGGCGGGGCAAAT 61.944 55.000 0.00 0.00 0.00 2.32
3434 7652 5.344743 TCATCTTGTAAGGTAGCTTCAGG 57.655 43.478 11.11 9.60 0.00 3.86
3513 7738 5.983540 ACCTTAACAGAGCTTATTCAGAGG 58.016 41.667 0.00 0.00 0.00 3.69
3529 7754 6.183360 TGTTCTGTGGGAAATGAAACCTTAAC 60.183 38.462 0.00 0.00 35.51 2.01
3550 7779 5.630661 TGCTTACTAGAGTGAGTCTGTTC 57.369 43.478 0.00 0.00 36.64 3.18
3556 7785 5.449107 TTCGTTTGCTTACTAGAGTGAGT 57.551 39.130 0.00 0.00 34.54 3.41
3557 7786 4.859798 CCTTCGTTTGCTTACTAGAGTGAG 59.140 45.833 0.00 0.00 35.08 3.51
3558 7787 4.521639 TCCTTCGTTTGCTTACTAGAGTGA 59.478 41.667 0.00 0.00 0.00 3.41
3559 7788 4.806330 TCCTTCGTTTGCTTACTAGAGTG 58.194 43.478 0.00 0.00 0.00 3.51
3609 7838 2.290705 ACACTTATTTTGGGACCGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
3614 7843 5.070685 AGTTGAGACACTTATTTTGGGACC 58.929 41.667 0.00 0.00 0.00 4.46
3655 7884 8.515414 GCCTCAAAATAAGTGTCTCAACTTTAT 58.485 33.333 0.00 0.00 40.77 1.40
3659 7888 4.452455 CGCCTCAAAATAAGTGTCTCAACT 59.548 41.667 0.00 0.00 0.00 3.16
3660 7889 4.378459 CCGCCTCAAAATAAGTGTCTCAAC 60.378 45.833 0.00 0.00 0.00 3.18
3661 7890 3.751175 CCGCCTCAAAATAAGTGTCTCAA 59.249 43.478 0.00 0.00 0.00 3.02
3662 7891 3.007506 TCCGCCTCAAAATAAGTGTCTCA 59.992 43.478 0.00 0.00 0.00 3.27
3663 7892 3.596214 TCCGCCTCAAAATAAGTGTCTC 58.404 45.455 0.00 0.00 0.00 3.36
3666 7895 2.304761 TCCTCCGCCTCAAAATAAGTGT 59.695 45.455 0.00 0.00 0.00 3.55
3678 7907 3.459710 AGCTATATACTTCCTCCGCCT 57.540 47.619 0.00 0.00 0.00 5.52
3680 7909 6.911511 CGTTATTAGCTATATACTTCCTCCGC 59.088 42.308 0.00 0.00 0.00 5.54
3687 7916 9.938280 TCAATTGCCGTTATTAGCTATATACTT 57.062 29.630 0.00 0.00 0.00 2.24
3690 7919 9.713713 TGTTCAATTGCCGTTATTAGCTATATA 57.286 29.630 0.00 0.00 0.00 0.86
3691 7920 8.504005 GTGTTCAATTGCCGTTATTAGCTATAT 58.496 33.333 0.00 0.00 0.00 0.86
3692 7921 7.306925 CGTGTTCAATTGCCGTTATTAGCTATA 60.307 37.037 0.00 0.00 0.00 1.31
3693 7922 6.511121 CGTGTTCAATTGCCGTTATTAGCTAT 60.511 38.462 0.00 0.00 0.00 2.97
3730 7959 7.930865 GCTTCATTATCTCTTCCTACTGATTGT 59.069 37.037 0.00 0.00 0.00 2.71
3738 7967 7.846101 TCTCATGCTTCATTATCTCTTCCTA 57.154 36.000 0.00 0.00 0.00 2.94
3759 7988 0.744874 TCACCCGGTTCGATGATCTC 59.255 55.000 0.00 0.00 0.00 2.75
3760 7989 1.414158 ATCACCCGGTTCGATGATCT 58.586 50.000 0.00 0.00 0.00 2.75
3761 7990 2.240493 AATCACCCGGTTCGATGATC 57.760 50.000 0.00 0.00 31.41 2.92
3762 7991 3.830744 TTAATCACCCGGTTCGATGAT 57.169 42.857 0.00 0.00 33.18 2.45
3763 7992 3.830744 ATTAATCACCCGGTTCGATGA 57.169 42.857 0.00 0.00 0.00 2.92
3764 7993 5.054477 ACTAATTAATCACCCGGTTCGATG 58.946 41.667 0.00 0.00 0.00 3.84
3765 7994 5.286267 ACTAATTAATCACCCGGTTCGAT 57.714 39.130 0.00 0.00 0.00 3.59
3766 7995 4.741321 ACTAATTAATCACCCGGTTCGA 57.259 40.909 0.00 0.00 0.00 3.71
3767 7996 4.034742 CCAACTAATTAATCACCCGGTTCG 59.965 45.833 0.00 0.00 0.00 3.95
3768 7997 4.945543 ACCAACTAATTAATCACCCGGTTC 59.054 41.667 0.00 0.00 0.00 3.62
3769 7998 4.925836 ACCAACTAATTAATCACCCGGTT 58.074 39.130 0.00 0.00 0.00 4.44
3770 7999 4.579647 ACCAACTAATTAATCACCCGGT 57.420 40.909 0.00 0.00 0.00 5.28
3771 8000 5.677567 AGTACCAACTAATTAATCACCCGG 58.322 41.667 0.00 0.00 32.84 5.73
3772 8001 8.199449 TCTTAGTACCAACTAATTAATCACCCG 58.801 37.037 0.00 0.00 45.03 5.28
3773 8002 9.322773 GTCTTAGTACCAACTAATTAATCACCC 57.677 37.037 0.00 0.00 45.03 4.61
3774 8003 9.322773 GGTCTTAGTACCAACTAATTAATCACC 57.677 37.037 0.00 0.00 45.03 4.02
3775 8004 9.028185 CGGTCTTAGTACCAACTAATTAATCAC 57.972 37.037 0.00 0.00 45.03 3.06
3776 8005 7.707893 GCGGTCTTAGTACCAACTAATTAATCA 59.292 37.037 0.00 0.00 45.03 2.57
3777 8006 7.707893 TGCGGTCTTAGTACCAACTAATTAATC 59.292 37.037 0.00 0.00 45.03 1.75
3778 8007 7.558604 TGCGGTCTTAGTACCAACTAATTAAT 58.441 34.615 0.00 0.00 45.03 1.40
3779 8008 6.934056 TGCGGTCTTAGTACCAACTAATTAA 58.066 36.000 0.00 0.00 45.03 1.40
3780 8009 6.406177 CCTGCGGTCTTAGTACCAACTAATTA 60.406 42.308 0.00 0.00 45.03 1.40
3781 8010 5.410355 TGCGGTCTTAGTACCAACTAATT 57.590 39.130 0.00 0.00 45.03 1.40
3782 8011 4.142004 CCTGCGGTCTTAGTACCAACTAAT 60.142 45.833 0.00 0.00 45.03 1.73
3783 8012 3.194116 CCTGCGGTCTTAGTACCAACTAA 59.806 47.826 0.00 0.00 44.19 2.24
3784 8013 2.756760 CCTGCGGTCTTAGTACCAACTA 59.243 50.000 0.00 0.00 39.71 2.24
3785 8014 1.549170 CCTGCGGTCTTAGTACCAACT 59.451 52.381 0.00 0.00 39.71 3.16
3786 8015 2.005560 GCCTGCGGTCTTAGTACCAAC 61.006 57.143 0.00 0.00 39.71 3.77
3787 8016 0.248289 GCCTGCGGTCTTAGTACCAA 59.752 55.000 0.00 0.00 39.71 3.67
3788 8017 1.895238 GCCTGCGGTCTTAGTACCA 59.105 57.895 0.00 0.00 39.71 3.25
3789 8018 1.226888 CGCCTGCGGTCTTAGTACC 60.227 63.158 3.07 0.00 36.08 3.34
3790 8019 4.396854 CGCCTGCGGTCTTAGTAC 57.603 61.111 3.07 0.00 35.56 2.73
3807 8036 4.179599 CTCCCTCCCTCCCTCCCC 62.180 77.778 0.00 0.00 0.00 4.81
3808 8037 4.179599 CCTCCCTCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
3809 8038 4.179599 CCCTCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
3810 8039 4.179599 CCCCTCCCTCCCTCCCTC 62.180 77.778 0.00 0.00 0.00 4.30
3811 8040 4.761304 TCCCCTCCCTCCCTCCCT 62.761 72.222 0.00 0.00 0.00 4.20
3812 8041 3.707189 TTCCCCTCCCTCCCTCCC 61.707 72.222 0.00 0.00 0.00 4.30
3813 8042 2.040359 CTTCCCCTCCCTCCCTCC 60.040 72.222 0.00 0.00 0.00 4.30
3814 8043 2.040359 CCTTCCCCTCCCTCCCTC 60.040 72.222 0.00 0.00 0.00 4.30
3815 8044 2.543637 TCCTTCCCCTCCCTCCCT 60.544 66.667 0.00 0.00 0.00 4.20
3816 8045 1.600763 TACTCCTTCCCCTCCCTCCC 61.601 65.000 0.00 0.00 0.00 4.30
3817 8046 0.105401 CTACTCCTTCCCCTCCCTCC 60.105 65.000 0.00 0.00 0.00 4.30
3818 8047 0.105401 CCTACTCCTTCCCCTCCCTC 60.105 65.000 0.00 0.00 0.00 4.30
3819 8048 1.604592 CCCTACTCCTTCCCCTCCCT 61.605 65.000 0.00 0.00 0.00 4.20
3820 8049 1.074395 CCCTACTCCTTCCCCTCCC 60.074 68.421 0.00 0.00 0.00 4.30
3821 8050 1.074395 CCCCTACTCCTTCCCCTCC 60.074 68.421 0.00 0.00 0.00 4.30
3822 8051 0.398806 GACCCCTACTCCTTCCCCTC 60.399 65.000 0.00 0.00 0.00 4.30
3823 8052 1.160289 TGACCCCTACTCCTTCCCCT 61.160 60.000 0.00 0.00 0.00 4.79
3824 8053 0.981801 GTGACCCCTACTCCTTCCCC 60.982 65.000 0.00 0.00 0.00 4.81
3825 8054 0.981801 GGTGACCCCTACTCCTTCCC 60.982 65.000 0.00 0.00 0.00 3.97
3826 8055 0.252558 TGGTGACCCCTACTCCTTCC 60.253 60.000 0.00 0.00 0.00 3.46
3827 8056 0.903236 GTGGTGACCCCTACTCCTTC 59.097 60.000 0.00 0.00 0.00 3.46
3828 8057 0.492276 AGTGGTGACCCCTACTCCTT 59.508 55.000 0.00 0.00 0.00 3.36
3829 8058 0.252284 CAGTGGTGACCCCTACTCCT 60.252 60.000 0.00 0.00 0.00 3.69
3830 8059 1.900545 GCAGTGGTGACCCCTACTCC 61.901 65.000 0.00 0.00 0.00 3.85
3831 8060 1.597461 GCAGTGGTGACCCCTACTC 59.403 63.158 0.00 0.00 0.00 2.59
3832 8061 1.918800 GGCAGTGGTGACCCCTACT 60.919 63.158 0.00 0.00 0.00 2.57
3833 8062 2.669240 GGCAGTGGTGACCCCTAC 59.331 66.667 0.00 0.00 0.00 3.18
3834 8063 3.000819 CGGCAGTGGTGACCCCTA 61.001 66.667 0.00 0.00 0.00 3.53
3839 8068 3.717294 ATCCCCGGCAGTGGTGAC 61.717 66.667 0.00 0.00 0.00 3.67
3840 8069 3.716195 CATCCCCGGCAGTGGTGA 61.716 66.667 0.00 0.00 0.00 4.02
3841 8070 4.802051 CCATCCCCGGCAGTGGTG 62.802 72.222 0.00 0.00 0.00 4.17
3844 8073 3.482232 GATCCCATCCCCGGCAGTG 62.482 68.421 0.00 0.00 0.00 3.66
3845 8074 3.171388 GATCCCATCCCCGGCAGT 61.171 66.667 0.00 0.00 0.00 4.40
3846 8075 2.455565 AAGATCCCATCCCCGGCAG 61.456 63.158 0.00 0.00 0.00 4.85
3847 8076 2.368192 AAGATCCCATCCCCGGCA 60.368 61.111 0.00 0.00 0.00 5.69
3848 8077 2.113986 CAAGATCCCATCCCCGGC 59.886 66.667 0.00 0.00 0.00 6.13
3849 8078 2.839098 CCAAGATCCCATCCCCGG 59.161 66.667 0.00 0.00 0.00 5.73


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

AutoCloner maintained by Alex Coulton.