Multiple sequence alignment - TraesCS6B01G031300

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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 TraesCS6B01G031300 chr6B 100.000 5204 0 0 1 5204 18592030 18597233 0.000000e+00 9611.0
1 TraesCS6B01G031300 chr6B 94.425 1740 76 8 2867 4601 18731295 18729572 0.000000e+00 2656.0
2 TraesCS6B01G031300 chr6B 89.449 1924 155 20 829 2741 18734646 18732760 0.000000e+00 2385.0
3 TraesCS6B01G031300 chr6B 86.546 1323 153 15 1231 2546 18658738 18657434 0.000000e+00 1434.0
4 TraesCS6B01G031300 chr6B 81.740 1632 233 45 1093 2678 18648594 18646982 0.000000e+00 1303.0
5 TraesCS6B01G031300 chr6B 93.453 611 36 3 4597 5204 18729545 18728936 0.000000e+00 904.0
6 TraesCS6B01G031300 chr6B 89.497 676 55 5 124 797 578775651 578776312 0.000000e+00 841.0
7 TraesCS6B01G031300 chr6B 82.523 967 146 17 3251 4202 18656891 18655933 0.000000e+00 828.0
8 TraesCS6B01G031300 chr6B 88.218 679 65 6 124 794 719101713 719102384 0.000000e+00 797.0
9 TraesCS6B01G031300 chr6B 89.899 198 17 3 601 796 578773676 578773480 8.650000e-63 252.0
10 TraesCS6B01G031300 chr6B 90.000 170 14 2 628 796 719099874 719099707 3.160000e-52 217.0
11 TraesCS6B01G031300 chr6B 88.800 125 14 0 2 126 719101544 719101668 2.510000e-33 154.0
12 TraesCS6B01G031300 chr6B 85.185 108 9 4 2732 2832 18731399 18731292 2.560000e-18 104.0
13 TraesCS6B01G031300 chr6B 95.000 40 2 0 5109 5148 18751606 18751567 4.350000e-06 63.9
14 TraesCS6B01G031300 chr6B 100.000 33 0 0 2698 2730 18731373 18731341 1.560000e-05 62.1
15 TraesCS6B01G031300 chr6A 88.267 2199 201 27 829 2987 11591191 11589010 0.000000e+00 2579.0
16 TraesCS6B01G031300 chr6A 92.313 1574 104 10 3033 4601 11588999 11587438 0.000000e+00 2220.0
17 TraesCS6B01G031300 chr6A 84.395 1429 184 24 1126 2542 11571578 11570177 0.000000e+00 1367.0
18 TraesCS6B01G031300 chr6A 83.817 1483 192 33 1093 2545 11557977 11556513 0.000000e+00 1365.0
19 TraesCS6B01G031300 chr6A 94.089 609 29 4 4597 5204 11587407 11586805 0.000000e+00 918.0
20 TraesCS6B01G031300 chr6A 82.240 991 153 16 3251 4227 11569656 11568675 0.000000e+00 833.0
21 TraesCS6B01G031300 chr6A 83.622 751 121 2 3379 4129 11555664 11554916 0.000000e+00 704.0
22 TraesCS6B01G031300 chr6D 87.084 2284 206 32 829 3075 10104507 10102276 0.000000e+00 2501.0
23 TraesCS6B01G031300 chr6D 92.411 1410 82 18 3114 4512 10102285 10100890 0.000000e+00 1988.0
24 TraesCS6B01G031300 chr6D 83.851 1480 197 28 1093 2545 10046125 10044661 0.000000e+00 1371.0
25 TraesCS6B01G031300 chr6D 84.353 1438 179 27 1126 2546 10069053 10067645 0.000000e+00 1367.0
26 TraesCS6B01G031300 chr6D 93.483 844 54 1 3517 4359 10099164 10098321 0.000000e+00 1253.0
27 TraesCS6B01G031300 chr6D 90.285 947 92 0 1599 2545 10121802 10120856 0.000000e+00 1240.0
28 TraesCS6B01G031300 chr6D 89.577 921 89 4 3360 4277 10119943 10119027 0.000000e+00 1162.0
29 TraesCS6B01G031300 chr6D 86.169 723 74 7 864 1566 10122586 10121870 0.000000e+00 758.0
30 TraesCS6B01G031300 chr6D 82.638 743 128 1 3387 4129 10043897 10043156 0.000000e+00 656.0
31 TraesCS6B01G031300 chr6D 94.186 430 20 2 4780 5204 10100897 10100468 0.000000e+00 651.0
32 TraesCS6B01G031300 chr6D 89.286 84 6 1 864 944 10046408 10046325 9.220000e-18 102.0
33 TraesCS6B01G031300 chr6D 91.489 47 2 2 5120 5165 10065912 10065867 4.350000e-06 63.9
34 TraesCS6B01G031300 chr7B 92.481 798 58 2 1 796 665726238 665727035 0.000000e+00 1140.0
35 TraesCS6B01G031300 chr7B 95.918 49 2 0 4729 4777 504190142 504190094 4.320000e-11 80.5
36 TraesCS6B01G031300 chr2D 92.526 669 46 2 124 791 22816436 22817101 0.000000e+00 955.0
37 TraesCS6B01G031300 chr2D 89.769 303 26 3 124 421 453604642 453604944 2.940000e-102 383.0
38 TraesCS6B01G031300 chr2D 94.444 126 7 0 1 126 22816267 22816392 1.480000e-45 195.0
39 TraesCS6B01G031300 chr2D 90.000 110 10 1 1 110 453570639 453570747 1.950000e-29 141.0
40 TraesCS6B01G031300 chr7D 89.721 681 50 7 125 797 561876215 561876883 0.000000e+00 852.0
41 TraesCS6B01G031300 chr7D 90.404 198 16 3 601 796 561874496 561874300 1.860000e-64 257.0
42 TraesCS6B01G031300 chr7D 88.889 72 6 2 4709 4780 459786340 459786409 2.580000e-13 87.9
43 TraesCS6B01G031300 chr2A 90.210 429 41 1 124 551 596358848 596359276 4.550000e-155 558.0
44 TraesCS6B01G031300 chr2A 91.270 126 11 0 1 126 596358678 596358803 6.930000e-39 172.0
45 TraesCS6B01G031300 chr5D 85.930 199 25 3 600 796 17781672 17781475 5.280000e-50 209.0
46 TraesCS6B01G031300 chr3D 90.435 115 10 1 339 452 594156323 594156209 3.250000e-32 150.0
47 TraesCS6B01G031300 chr2B 97.917 48 1 0 4729 4776 575146519 575146472 3.340000e-12 84.2
48 TraesCS6B01G031300 chr2B 94.231 52 3 0 4726 4777 87922741 87922792 4.320000e-11 80.5
49 TraesCS6B01G031300 chrUn 90.476 63 5 1 4708 4770 115400309 115400248 1.200000e-11 82.4
50 TraesCS6B01G031300 chr5B 90.476 63 5 1 4708 4770 214942883 214942944 1.200000e-11 82.4
51 TraesCS6B01G031300 chr5A 90.476 63 5 1 4708 4770 236879253 236879314 1.200000e-11 82.4


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 TraesCS6B01G031300 chr6B 18592030 18597233 5203 False 9611.000000 9611 100.000000 1 5204 1 chr6B.!!$F1 5203
1 TraesCS6B01G031300 chr6B 18646982 18648594 1612 True 1303.000000 1303 81.740000 1093 2678 1 chr6B.!!$R1 1585
2 TraesCS6B01G031300 chr6B 18728936 18734646 5710 True 1222.220000 2656 92.502400 829 5204 5 chr6B.!!$R6 4375
3 TraesCS6B01G031300 chr6B 18655933 18658738 2805 True 1131.000000 1434 84.534500 1231 4202 2 chr6B.!!$R5 2971
4 TraesCS6B01G031300 chr6B 578775651 578776312 661 False 841.000000 841 89.497000 124 797 1 chr6B.!!$F2 673
5 TraesCS6B01G031300 chr6B 719101544 719102384 840 False 475.500000 797 88.509000 2 794 2 chr6B.!!$F3 792
6 TraesCS6B01G031300 chr6A 11586805 11591191 4386 True 1905.666667 2579 91.556333 829 5204 3 chr6A.!!$R3 4375
7 TraesCS6B01G031300 chr6A 11568675 11571578 2903 True 1100.000000 1367 83.317500 1126 4227 2 chr6A.!!$R2 3101
8 TraesCS6B01G031300 chr6A 11554916 11557977 3061 True 1034.500000 1365 83.719500 1093 4129 2 chr6A.!!$R1 3036
9 TraesCS6B01G031300 chr6D 10098321 10104507 6186 True 1598.250000 2501 91.791000 829 5204 4 chr6D.!!$R3 4375
10 TraesCS6B01G031300 chr6D 10119027 10122586 3559 True 1053.333333 1240 88.677000 864 4277 3 chr6D.!!$R4 3413
11 TraesCS6B01G031300 chr6D 10065867 10069053 3186 True 715.450000 1367 87.921000 1126 5165 2 chr6D.!!$R2 4039
12 TraesCS6B01G031300 chr6D 10043156 10046408 3252 True 709.666667 1371 85.258333 864 4129 3 chr6D.!!$R1 3265
13 TraesCS6B01G031300 chr7B 665726238 665727035 797 False 1140.000000 1140 92.481000 1 796 1 chr7B.!!$F1 795
14 TraesCS6B01G031300 chr2D 22816267 22817101 834 False 575.000000 955 93.485000 1 791 2 chr2D.!!$F3 790
15 TraesCS6B01G031300 chr7D 561876215 561876883 668 False 852.000000 852 89.721000 125 797 1 chr7D.!!$F2 672
16 TraesCS6B01G031300 chr2A 596358678 596359276 598 False 365.000000 558 90.740000 1 551 2 chr2A.!!$F1 550

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
594 653 0.176680 GAGAGAGCGAGGGAATTGCA 59.823 55.0 0.00 0.0 41.26 4.08 F
1318 1475 0.179137 GCATCGTCGTCATGTCTGGA 60.179 55.0 0.00 0.0 0.00 3.86 F
2314 2601 0.179205 GACACGACTACTACGCGCTT 60.179 55.0 5.73 0.0 0.00 4.68 F
2329 2616 0.460284 CGCTTGGAAGGTACGATGCT 60.460 55.0 0.00 0.0 0.00 3.79 F
2335 2622 0.645868 GAAGGTACGATGCTGCGAAC 59.354 55.0 5.82 0.0 34.83 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1509 1675 0.392595 GGGGTCGTTCATCCAGTTCC 60.393 60.000 0.00 0.0 0.00 3.62 R
2872 5227 0.329261 TCTTGGCATGCAACTAGGCT 59.671 50.000 21.36 0.0 34.04 4.58 R
3690 6236 0.108472 CATCAGCGAGCACAAGGAGA 60.108 55.000 0.00 0.0 0.00 3.71 R
3745 6291 2.873472 CTCTGGCGACGTAGAAGTAGAT 59.127 50.000 0.00 0.0 0.00 1.98 R
4204 6755 4.507756 TCGATCAGACAACACAGAAAAGTG 59.492 41.667 0.00 0.0 44.93 3.16 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
30 31 4.702274 GGCCTTGGCCACCATGGT 62.702 66.667 24.50 13.00 46.63 3.55
39 40 1.971167 CCACCATGGTGTTCACCGG 60.971 63.158 36.62 20.34 44.02 5.28
113 114 1.254026 CGAGGTACAGTCCCAACTCA 58.746 55.000 0.00 0.00 31.71 3.41
120 121 2.057922 ACAGTCCCAACTCAATGTCCT 58.942 47.619 0.00 0.00 31.71 3.85
209 258 4.643387 GAGGGTGGCGGTGCACTT 62.643 66.667 17.98 0.00 0.00 3.16
242 297 0.544697 AACTCCACCTCCACAAACGT 59.455 50.000 0.00 0.00 0.00 3.99
330 385 2.202878 GTGCCGGCGATCTAGCAA 60.203 61.111 23.90 0.00 36.91 3.91
332 387 2.417516 GCCGGCGATCTAGCAAGA 59.582 61.111 12.58 0.00 39.27 3.02
375 430 2.681778 CGACCTCCAGGAGCCAGT 60.682 66.667 11.57 3.57 38.94 4.00
385 440 4.666253 GAGCCAGTGCAGCCCCAA 62.666 66.667 0.00 0.00 41.13 4.12
435 490 3.492545 GGCAAATGGCGCGTCGTA 61.493 61.111 5.55 0.00 46.16 3.43
440 495 3.642778 AATGGCGCGTCGTAGCTGT 62.643 57.895 5.55 0.00 34.40 4.40
441 496 3.642778 ATGGCGCGTCGTAGCTGTT 62.643 57.895 2.15 0.00 34.40 3.16
496 555 4.619227 CGTGGCCACTGGTTCGGT 62.619 66.667 32.28 0.00 0.00 4.69
594 653 0.176680 GAGAGAGCGAGGGAATTGCA 59.823 55.000 0.00 0.00 41.26 4.08
682 743 1.152963 ACTTGGCAGCGGTTGACTT 60.153 52.632 0.00 0.00 35.09 3.01
686 747 2.594592 GCAGCGGTTGACTTGGGT 60.595 61.111 0.00 0.00 0.00 4.51
705 766 3.181479 GGGTCAGATCAGCATGTACGTAA 60.181 47.826 0.00 0.00 37.40 3.18
738 799 2.176247 ATGGACCGTAGATGACCCTT 57.824 50.000 0.00 0.00 0.00 3.95
743 804 4.210331 GGACCGTAGATGACCCTTTAGTA 58.790 47.826 0.00 0.00 0.00 1.82
797 859 8.905660 TGTAACCACATAACTAAAGCTAACAA 57.094 30.769 0.00 0.00 0.00 2.83
798 860 9.509956 TGTAACCACATAACTAAAGCTAACAAT 57.490 29.630 0.00 0.00 0.00 2.71
799 861 9.769093 GTAACCACATAACTAAAGCTAACAATG 57.231 33.333 0.00 0.00 0.00 2.82
800 862 7.996098 ACCACATAACTAAAGCTAACAATGT 57.004 32.000 0.00 0.00 0.00 2.71
801 863 7.816640 ACCACATAACTAAAGCTAACAATGTG 58.183 34.615 14.85 14.85 41.50 3.21
803 865 8.039603 CACATAACTAAAGCTAACAATGTGGA 57.960 34.615 14.34 0.00 39.34 4.02
804 866 7.962918 CACATAACTAAAGCTAACAATGTGGAC 59.037 37.037 14.34 0.00 39.34 4.02
805 867 5.959618 AACTAAAGCTAACAATGTGGACC 57.040 39.130 0.00 0.00 0.00 4.46
806 868 5.242795 ACTAAAGCTAACAATGTGGACCT 57.757 39.130 0.00 0.00 0.00 3.85
807 869 5.003804 ACTAAAGCTAACAATGTGGACCTG 58.996 41.667 0.00 0.00 0.00 4.00
808 870 3.508845 AAGCTAACAATGTGGACCTGT 57.491 42.857 0.00 0.00 0.00 4.00
809 871 4.634012 AAGCTAACAATGTGGACCTGTA 57.366 40.909 0.00 0.00 0.00 2.74
810 872 4.207891 AGCTAACAATGTGGACCTGTAG 57.792 45.455 0.00 0.00 0.00 2.74
811 873 3.583086 AGCTAACAATGTGGACCTGTAGT 59.417 43.478 0.00 0.00 0.00 2.73
812 874 3.684788 GCTAACAATGTGGACCTGTAGTG 59.315 47.826 0.00 0.00 0.00 2.74
813 875 4.562757 GCTAACAATGTGGACCTGTAGTGA 60.563 45.833 0.00 0.00 0.00 3.41
814 876 4.431416 AACAATGTGGACCTGTAGTGAA 57.569 40.909 0.00 0.00 0.00 3.18
815 877 4.640771 ACAATGTGGACCTGTAGTGAAT 57.359 40.909 0.00 0.00 0.00 2.57
816 878 4.985538 ACAATGTGGACCTGTAGTGAATT 58.014 39.130 0.00 0.00 0.00 2.17
817 879 5.385198 ACAATGTGGACCTGTAGTGAATTT 58.615 37.500 0.00 0.00 0.00 1.82
818 880 5.833131 ACAATGTGGACCTGTAGTGAATTTT 59.167 36.000 0.00 0.00 0.00 1.82
819 881 6.323739 ACAATGTGGACCTGTAGTGAATTTTT 59.676 34.615 0.00 0.00 0.00 1.94
820 882 6.575162 ATGTGGACCTGTAGTGAATTTTTC 57.425 37.500 0.00 0.00 0.00 2.29
821 883 5.690865 TGTGGACCTGTAGTGAATTTTTCT 58.309 37.500 0.00 0.00 0.00 2.52
822 884 5.763204 TGTGGACCTGTAGTGAATTTTTCTC 59.237 40.000 0.00 0.00 0.00 2.87
823 885 5.998363 GTGGACCTGTAGTGAATTTTTCTCT 59.002 40.000 0.00 0.00 37.31 3.10
824 886 6.486993 GTGGACCTGTAGTGAATTTTTCTCTT 59.513 38.462 0.00 0.00 35.37 2.85
825 887 6.710744 TGGACCTGTAGTGAATTTTTCTCTTC 59.289 38.462 0.00 0.00 35.37 2.87
826 888 6.710744 GGACCTGTAGTGAATTTTTCTCTTCA 59.289 38.462 0.00 0.00 35.37 3.02
827 889 7.095017 GGACCTGTAGTGAATTTTTCTCTTCAG 60.095 40.741 14.08 14.08 42.87 3.02
849 911 1.125021 GAACAATGAGTGAGTGCGACG 59.875 52.381 0.00 0.00 0.00 5.12
862 924 3.500642 CGACGAGGCTCGAGCTGA 61.501 66.667 40.35 0.00 43.74 4.26
1009 1094 1.810606 CTCCTCGGCAGACACACACT 61.811 60.000 0.00 0.00 0.00 3.55
1010 1095 1.373497 CCTCGGCAGACACACACTC 60.373 63.158 0.00 0.00 0.00 3.51
1018 1104 2.295909 GCAGACACACACTCTCTCTTCT 59.704 50.000 0.00 0.00 0.00 2.85
1073 1160 5.392380 GCTAATTGACCAATCACTTCCACTG 60.392 44.000 0.00 0.00 33.38 3.66
1080 1219 4.202503 ACCAATCACTTCCACTGATCACTT 60.203 41.667 0.00 0.00 0.00 3.16
1318 1475 0.179137 GCATCGTCGTCATGTCTGGA 60.179 55.000 0.00 0.00 0.00 3.86
1322 1479 1.065572 CGTCGTCATGTCTGGACACG 61.066 60.000 5.52 5.84 45.05 4.49
1332 1489 3.948086 CTGGACACGAGACGACGGC 62.948 68.421 0.00 0.00 37.61 5.68
1509 1675 1.544825 TTCCACTTCCAGCCCGAGAG 61.545 60.000 0.00 0.00 0.00 3.20
1559 1732 2.911819 ACATTTCCGCCATTGTTACG 57.088 45.000 0.00 0.00 0.00 3.18
1611 1836 7.211573 TCTTGTTGATGATGCAAAACTCATTT 58.788 30.769 2.21 0.00 32.36 2.32
1675 1962 2.901839 GTGGTACCACCTCTTCTACCAA 59.098 50.000 31.39 0.00 40.23 3.67
1882 2169 1.963855 CACCAACGCATCGGTCCAA 60.964 57.895 0.00 0.00 31.41 3.53
1892 2179 1.480212 ATCGGTCCAAGTCCAGTGCA 61.480 55.000 0.00 0.00 0.00 4.57
2231 2518 0.607217 CATGACAGAGGCAGTGGCAA 60.607 55.000 20.04 0.00 43.71 4.52
2314 2601 0.179205 GACACGACTACTACGCGCTT 60.179 55.000 5.73 0.00 0.00 4.68
2329 2616 0.460284 CGCTTGGAAGGTACGATGCT 60.460 55.000 0.00 0.00 0.00 3.79
2335 2622 0.645868 GAAGGTACGATGCTGCGAAC 59.354 55.000 5.82 0.00 34.83 3.95
2555 2897 7.514784 TTCATCATCTTGTTCAAGTGATTGT 57.485 32.000 18.36 6.19 0.00 2.71
2663 3143 1.067425 TGGGTTTCATAGACACGTCGG 60.067 52.381 0.00 0.00 34.09 4.79
2664 3144 0.997196 GGTTTCATAGACACGTCGGC 59.003 55.000 0.00 0.00 34.09 5.54
2665 3145 1.670674 GGTTTCATAGACACGTCGGCA 60.671 52.381 0.00 0.00 34.09 5.69
2666 3146 2.268298 GTTTCATAGACACGTCGGCAT 58.732 47.619 0.00 0.00 34.09 4.40
2667 3147 1.921243 TTCATAGACACGTCGGCATG 58.079 50.000 0.00 0.00 34.09 4.06
2668 3148 1.099689 TCATAGACACGTCGGCATGA 58.900 50.000 0.00 7.59 34.09 3.07
2669 3149 1.681264 TCATAGACACGTCGGCATGAT 59.319 47.619 0.00 0.00 34.09 2.45
2670 3150 2.100749 TCATAGACACGTCGGCATGATT 59.899 45.455 0.00 0.00 34.09 2.57
2671 3151 1.921243 TAGACACGTCGGCATGATTG 58.079 50.000 0.00 0.00 34.09 2.67
2872 5227 0.981183 AACTCTTCACGCCCCATGTA 59.019 50.000 0.00 0.00 0.00 2.29
2880 5235 0.981277 ACGCCCCATGTAGCCTAGTT 60.981 55.000 0.00 0.00 0.00 2.24
3050 5455 4.743151 GGGTTCTAAAAGGAAAAGCAAACG 59.257 41.667 0.00 0.00 0.00 3.60
3112 5517 7.528996 TGGATGATGAAGAAGTTCAATTGTT 57.471 32.000 5.13 0.00 45.88 2.83
3137 5543 6.991938 ACAGTTGCTAATGCCTTTTATTTGA 58.008 32.000 0.00 0.00 38.71 2.69
3138 5544 7.614494 ACAGTTGCTAATGCCTTTTATTTGAT 58.386 30.769 0.00 0.00 38.71 2.57
3150 5556 9.859427 TGCCTTTTATTTGATATATATTGCAGC 57.141 29.630 0.00 0.00 0.00 5.25
3170 5576 5.296780 GCAGCAGTACATTATACACCAATGT 59.703 40.000 6.04 6.04 45.90 2.71
3396 5942 9.116067 AGTTGCTAATGTTTTCTGTTGTTACTA 57.884 29.630 0.00 0.00 0.00 1.82
3573 6119 2.821366 GCCACCCAGCTCGACATG 60.821 66.667 0.00 0.00 0.00 3.21
3745 6291 2.363276 ACATGGAGCGGACCGGTA 60.363 61.111 20.28 4.52 37.83 4.02
3895 6441 1.270358 GCGAGGAGTTTTCAGTGAGGT 60.270 52.381 0.00 0.00 0.00 3.85
4020 6566 0.180406 ACCTCTTCAACAACGCCACT 59.820 50.000 0.00 0.00 0.00 4.00
4204 6755 1.130561 CGCTCCCATTTCTTCGTTTCC 59.869 52.381 0.00 0.00 0.00 3.13
4399 6953 1.133513 AGCAAGGAACAACCACATCCA 60.134 47.619 0.00 0.00 42.04 3.41
4458 7012 1.419762 ACACTGCTGATTACCACCACA 59.580 47.619 0.00 0.00 0.00 4.17
4459 7013 2.158682 ACACTGCTGATTACCACCACAA 60.159 45.455 0.00 0.00 0.00 3.33
4477 7031 0.732571 AACCACAACACAGTTCAGCG 59.267 50.000 0.00 0.00 0.00 5.18
4482 7036 3.120546 CCACAACACAGTTCAGCGAATAG 60.121 47.826 0.00 0.00 0.00 1.73
4537 7091 6.481984 TGCGTTCAAATTCAAATTTTCAACC 58.518 32.000 0.00 1.91 36.52 3.77
4724 7409 2.043227 CTTCTACTCCCTCCCATCCAC 58.957 57.143 0.00 0.00 0.00 4.02
4917 7603 4.551509 CGATCGACGATCAATCTGTACATC 59.448 45.833 31.15 7.31 45.77 3.06
5010 7697 3.061322 CGGTGATTCGGTGAACAACTTA 58.939 45.455 0.00 0.00 0.00 2.24
5077 7764 3.738791 GGTAAACAAACAAGCGGGAATTG 59.261 43.478 0.00 0.00 0.00 2.32
5156 7847 1.134907 GTCAATGATGCCAAGCCCAAG 60.135 52.381 0.00 0.00 0.00 3.61
5166 7857 2.948924 AGCCCAAGCCCAGGGATT 60.949 61.111 10.89 6.35 43.93 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 4.228567 TGCTGACGCCGGTGAACA 62.229 61.111 24.59 19.08 34.43 3.18
39 40 4.175489 CCATGCTGCTGCTGACGC 62.175 66.667 17.00 4.01 40.48 5.19
64 65 2.491152 GGGACGGTGATCGCGTTA 59.509 61.111 5.77 0.00 43.89 3.18
113 114 1.254026 TGAAGTCGTCCGAGGACATT 58.746 50.000 20.75 12.28 44.77 2.71
127 175 2.683933 ACGCTCCCCCGATGAAGT 60.684 61.111 0.00 0.00 0.00 3.01
166 214 0.689623 CCCAGAGAGCAACAGGTTCT 59.310 55.000 0.00 0.00 40.09 3.01
206 255 1.003839 TTCGATGGGAAGCGCAAGT 60.004 52.632 11.47 0.00 41.68 3.16
209 258 1.447838 GAGTTCGATGGGAAGCGCA 60.448 57.895 11.47 0.00 34.69 6.09
219 274 1.348064 TTGTGGAGGTGGAGTTCGAT 58.652 50.000 0.00 0.00 0.00 3.59
330 385 2.282040 GGCTGCTGCTGGTTGTCT 60.282 61.111 15.64 0.00 39.59 3.41
375 430 4.776322 CGACGGATTGGGGCTGCA 62.776 66.667 0.50 0.00 0.00 4.41
421 476 2.125673 AGCTACGACGCGCCATTT 60.126 55.556 5.73 0.00 34.40 2.32
422 477 2.885644 CAGCTACGACGCGCCATT 60.886 61.111 5.73 0.00 34.40 3.16
435 490 0.751643 AAAGCACGGGAACAACAGCT 60.752 50.000 0.00 0.00 0.00 4.24
440 495 0.532573 TTTGCAAAGCACGGGAACAA 59.467 45.000 8.05 0.00 38.71 2.83
441 496 0.532573 TTTTGCAAAGCACGGGAACA 59.467 45.000 12.41 0.00 38.71 3.18
496 555 0.035725 CCAGACATGAGCCTGCTTCA 60.036 55.000 0.00 0.00 0.00 3.02
594 653 4.505390 CCAGGGGTCTTTTGCAAAAATGAT 60.505 41.667 23.92 7.05 0.00 2.45
682 743 1.136891 CGTACATGCTGATCTGACCCA 59.863 52.381 3.42 0.00 0.00 4.51
686 747 4.081917 TGGTTTACGTACATGCTGATCTGA 60.082 41.667 3.42 0.00 0.00 3.27
705 766 3.272581 CGGTCCATTATACGGTTTGGTT 58.727 45.455 0.00 0.00 0.00 3.67
743 804 6.775629 ACCAATAATACAGTCACCAAACTTGT 59.224 34.615 0.00 0.00 0.00 3.16
797 859 6.306987 AGAAAAATTCACTACAGGTCCACAT 58.693 36.000 0.00 0.00 0.00 3.21
798 860 5.690865 AGAAAAATTCACTACAGGTCCACA 58.309 37.500 0.00 0.00 0.00 4.17
799 861 5.998363 AGAGAAAAATTCACTACAGGTCCAC 59.002 40.000 0.00 0.00 0.00 4.02
800 862 6.187727 AGAGAAAAATTCACTACAGGTCCA 57.812 37.500 0.00 0.00 0.00 4.02
801 863 6.710744 TGAAGAGAAAAATTCACTACAGGTCC 59.289 38.462 0.00 0.00 30.67 4.46
802 864 7.095017 CCTGAAGAGAAAAATTCACTACAGGTC 60.095 40.741 0.00 1.48 36.50 3.85
803 865 6.712547 CCTGAAGAGAAAAATTCACTACAGGT 59.287 38.462 0.00 0.00 36.50 4.00
804 866 6.150140 CCCTGAAGAGAAAAATTCACTACAGG 59.850 42.308 0.00 0.00 38.57 4.00
805 867 6.936900 TCCCTGAAGAGAAAAATTCACTACAG 59.063 38.462 0.00 0.00 32.25 2.74
806 868 6.837312 TCCCTGAAGAGAAAAATTCACTACA 58.163 36.000 0.00 0.00 32.25 2.74
807 869 7.228706 TGTTCCCTGAAGAGAAAAATTCACTAC 59.771 37.037 0.00 0.00 32.25 2.73
808 870 7.287061 TGTTCCCTGAAGAGAAAAATTCACTA 58.713 34.615 0.00 0.00 32.25 2.74
809 871 6.129179 TGTTCCCTGAAGAGAAAAATTCACT 58.871 36.000 0.00 0.00 32.25 3.41
810 872 6.391227 TGTTCCCTGAAGAGAAAAATTCAC 57.609 37.500 0.00 0.00 32.25 3.18
811 873 7.287466 TCATTGTTCCCTGAAGAGAAAAATTCA 59.713 33.333 0.00 0.00 29.31 2.57
812 874 7.661040 TCATTGTTCCCTGAAGAGAAAAATTC 58.339 34.615 0.00 0.00 29.31 2.17
813 875 7.288621 ACTCATTGTTCCCTGAAGAGAAAAATT 59.711 33.333 0.00 0.00 29.31 1.82
814 876 6.779539 ACTCATTGTTCCCTGAAGAGAAAAAT 59.220 34.615 0.00 0.00 31.45 1.82
815 877 6.039717 CACTCATTGTTCCCTGAAGAGAAAAA 59.960 38.462 0.00 0.00 0.00 1.94
816 878 5.532406 CACTCATTGTTCCCTGAAGAGAAAA 59.468 40.000 0.00 0.00 0.00 2.29
817 879 5.065914 CACTCATTGTTCCCTGAAGAGAAA 58.934 41.667 0.00 0.00 0.00 2.52
818 880 4.347876 TCACTCATTGTTCCCTGAAGAGAA 59.652 41.667 0.00 0.00 0.00 2.87
819 881 3.903714 TCACTCATTGTTCCCTGAAGAGA 59.096 43.478 0.00 0.00 0.00 3.10
820 882 4.252073 CTCACTCATTGTTCCCTGAAGAG 58.748 47.826 0.00 0.00 0.00 2.85
821 883 3.648067 ACTCACTCATTGTTCCCTGAAGA 59.352 43.478 0.00 0.00 0.00 2.87
822 884 3.750130 CACTCACTCATTGTTCCCTGAAG 59.250 47.826 0.00 0.00 0.00 3.02
823 885 3.743521 CACTCACTCATTGTTCCCTGAA 58.256 45.455 0.00 0.00 0.00 3.02
824 886 2.550855 GCACTCACTCATTGTTCCCTGA 60.551 50.000 0.00 0.00 0.00 3.86
825 887 1.808945 GCACTCACTCATTGTTCCCTG 59.191 52.381 0.00 0.00 0.00 4.45
826 888 1.609061 CGCACTCACTCATTGTTCCCT 60.609 52.381 0.00 0.00 0.00 4.20
827 889 0.798776 CGCACTCACTCATTGTTCCC 59.201 55.000 0.00 0.00 0.00 3.97
849 911 1.886777 GCCATTCAGCTCGAGCCTC 60.887 63.158 32.94 7.14 43.38 4.70
862 924 1.784593 TCATCATCCATCCAGGCCATT 59.215 47.619 5.01 0.00 37.29 3.16
949 1023 0.907704 TCTCCATGCCACCCGTTAGT 60.908 55.000 0.00 0.00 0.00 2.24
1009 1094 8.254508 GCTAATCTTAACAAGGAAGAAGAGAGA 58.745 37.037 0.00 0.00 36.54 3.10
1010 1095 8.037758 TGCTAATCTTAACAAGGAAGAAGAGAG 58.962 37.037 0.00 0.00 36.54 3.20
1018 1104 6.121776 TCCACTGCTAATCTTAACAAGGAA 57.878 37.500 0.00 0.00 0.00 3.36
1073 1160 3.079960 TGGCGTAGAATCGAAGTGATC 57.920 47.619 0.00 0.00 35.84 2.92
1080 1219 1.068588 CCTCCATTGGCGTAGAATCGA 59.931 52.381 0.00 0.00 0.00 3.59
1237 1394 4.357947 GCGACCACGAGGAGCACA 62.358 66.667 5.68 0.00 42.66 4.57
1318 1475 2.976350 TCAGCCGTCGTCTCGTGT 60.976 61.111 0.00 0.00 0.00 4.49
1509 1675 0.392595 GGGGTCGTTCATCCAGTTCC 60.393 60.000 0.00 0.00 0.00 3.62
1538 1704 3.676540 CGTAACAATGGCGGAAATGTAC 58.323 45.455 0.00 0.00 0.00 2.90
1580 1763 5.581126 TTGCATCATCAACAAGATTACCC 57.419 39.130 0.00 0.00 33.72 3.69
1581 1764 7.092716 AGTTTTGCATCATCAACAAGATTACC 58.907 34.615 0.00 0.00 33.72 2.85
1675 1962 4.825252 GCGCCGTCCGGGTTGTAT 62.825 66.667 7.97 0.00 38.44 2.29
1892 2179 2.696125 ATCGGTGGGGAAGGCCAT 60.696 61.111 5.01 0.00 35.15 4.40
1981 2268 0.547712 CCCTGAAGTCCTTCTCCCCA 60.548 60.000 8.40 0.00 40.14 4.96
2024 2311 1.374252 GCCATGTGTCGTCCGAACT 60.374 57.895 0.00 0.00 0.00 3.01
2231 2518 0.680921 CCACCATTCTTGGATGCCGT 60.681 55.000 0.00 0.00 46.92 5.68
2314 2601 1.153647 CGCAGCATCGTACCTTCCA 60.154 57.895 0.00 0.00 0.00 3.53
2329 2616 1.938125 CGTCCATGTGTTGTTCGCA 59.062 52.632 0.00 0.00 40.97 5.10
2335 2622 1.078709 CTAGTGGCGTCCATGTGTTG 58.921 55.000 1.90 0.00 35.28 3.33
2573 2915 9.790389 AACAAAGAGATAGTGTACTAAGAATCG 57.210 33.333 0.00 0.00 31.39 3.34
2672 3152 6.028146 TGCTATTATTATTTGCATGCCCTG 57.972 37.500 16.68 0.00 0.00 4.45
2673 3153 5.337009 GCTGCTATTATTATTTGCATGCCCT 60.337 40.000 16.68 1.84 33.02 5.19
2674 3154 4.866486 GCTGCTATTATTATTTGCATGCCC 59.134 41.667 16.68 0.00 33.02 5.36
2836 5191 3.255642 AGAGTTTGTTTGTTGCACACAGT 59.744 39.130 0.00 0.00 36.48 3.55
2843 5198 2.278875 GCGTGAAGAGTTTGTTTGTTGC 59.721 45.455 0.00 0.00 0.00 4.17
2872 5227 0.329261 TCTTGGCATGCAACTAGGCT 59.671 50.000 21.36 0.00 34.04 4.58
2880 5235 0.403655 TAGGTGGTTCTTGGCATGCA 59.596 50.000 21.36 2.54 0.00 3.96
3050 5455 3.004106 GCAACTGCCACCATTCTATCATC 59.996 47.826 0.00 0.00 34.31 2.92
3112 5517 8.116651 TCAAATAAAAGGCATTAGCAACTGTA 57.883 30.769 0.00 0.00 44.61 2.74
3144 5550 4.837972 TGGTGTATAATGTACTGCTGCAA 58.162 39.130 3.02 0.00 0.00 4.08
3157 5563 9.811995 CAACTAGCTAGTTACATTGGTGTATAA 57.188 33.333 33.06 0.00 44.19 0.98
3170 5576 4.831155 AGGACACACACAACTAGCTAGTTA 59.169 41.667 33.06 0.00 44.19 2.24
3396 5942 1.227380 GCGAGGGATCGACTGCAAT 60.227 57.895 1.17 0.00 34.64 3.56
3515 6061 3.822192 CGGAGCCATGGTCGACGA 61.822 66.667 14.67 5.99 0.00 4.20
3573 6119 1.066143 TCAAGACGAAATGAGGCCTCC 60.066 52.381 29.95 13.34 0.00 4.30
3690 6236 0.108472 CATCAGCGAGCACAAGGAGA 60.108 55.000 0.00 0.00 0.00 3.71
3745 6291 2.873472 CTCTGGCGACGTAGAAGTAGAT 59.127 50.000 0.00 0.00 0.00 1.98
4204 6755 4.507756 TCGATCAGACAACACAGAAAAGTG 59.492 41.667 0.00 0.00 44.93 3.16
4370 6924 2.949644 GTTGTTCCTTGCTGTAACACCT 59.050 45.455 0.00 0.00 33.10 4.00
4399 6953 5.046304 TCCTGAGATCGAAAATCTCCAACTT 60.046 40.000 11.10 0.00 42.83 2.66
4458 7012 0.732571 CGCTGAACTGTGTTGTGGTT 59.267 50.000 0.00 0.00 0.00 3.67
4459 7013 0.107897 TCGCTGAACTGTGTTGTGGT 60.108 50.000 0.00 0.00 0.00 4.16
4560 7114 1.151908 CCGGTCCACCCCAAGAAAA 59.848 57.895 0.00 0.00 0.00 2.29
4663 7347 9.449719 ACACCTACTCAAAATTAGAATTAGTGG 57.550 33.333 0.00 0.00 0.00 4.00
4707 7392 1.123928 GTGTGGATGGGAGGGAGTAG 58.876 60.000 0.00 0.00 0.00 2.57
4724 7409 3.242155 TGTCGCAGTTTTGAACTAACGTG 60.242 43.478 12.24 1.55 40.46 4.49
4810 7495 7.254227 GTTGACCACAAGTCTACAAACATTA 57.746 36.000 3.14 0.00 46.58 1.90
4865 7551 1.761449 ACAACAAGACCACATGCACA 58.239 45.000 0.00 0.00 0.00 4.57
4917 7603 1.973138 CCTCGAGTGCAAAAGCAATG 58.027 50.000 12.31 0.00 0.00 2.82
4977 7664 2.535984 CGAATCACCGATAGTGCACTTC 59.464 50.000 27.06 19.60 46.81 3.01
5010 7697 4.637534 GCAGGAGATGTGTTTGTATGTGAT 59.362 41.667 0.00 0.00 0.00 3.06
5156 7847 8.689972 CATCTAATATAATCAAAATCCCTGGGC 58.310 37.037 8.22 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.