Multiple sequence alignment - TraesCS1B01G450100

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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 TraesCS1B01G450100 chr1B 100.000 3214 0 0 1 3214 668198849 668202062 0.000000e+00 5936.0
1 TraesCS1B01G450100 chr1B 88.372 1806 151 16 1200 3000 668186381 668188132 0.000000e+00 2117.0
2 TraesCS1B01G450100 chr1B 92.241 1263 91 5 1210 2470 668182985 668184242 0.000000e+00 1783.0
3 TraesCS1B01G450100 chr1B 81.726 892 112 27 1532 2412 668429802 668428951 0.000000e+00 697.0
4 TraesCS1B01G450100 chr1B 87.963 432 44 7 2044 2470 668290242 668289814 1.330000e-138 503.0
5 TraesCS1B01G450100 chr1B 81.295 556 48 26 1220 1753 668540328 668539807 1.800000e-107 399.0
6 TraesCS1B01G450100 chr1B 81.027 448 54 17 583 1011 668182176 668182611 8.600000e-86 327.0
7 TraesCS1B01G450100 chr1B 85.818 275 33 5 1925 2196 668545152 668544881 1.460000e-73 287.0
8 TraesCS1B01G450100 chr1B 83.618 293 35 8 679 966 668185782 668186066 2.460000e-66 263.0
9 TraesCS1B01G450100 chr1B 83.803 284 28 6 2187 2470 668544858 668544593 1.480000e-63 254.0
10 TraesCS1B01G450100 chr1B 95.604 91 3 1 1009 1099 668182893 668182982 9.290000e-31 145.0
11 TraesCS1B01G450100 chr1B 91.463 82 7 0 2581 2662 668544579 668544498 2.620000e-21 113.0
12 TraesCS1B01G450100 chr1D 96.327 1906 44 14 1012 2903 478755906 478754013 0.000000e+00 3109.0
13 TraesCS1B01G450100 chr1D 94.483 1015 46 5 1 1013 480154152 480155158 0.000000e+00 1555.0
14 TraesCS1B01G450100 chr1D 90.217 1196 98 10 1006 2192 480155373 480156558 0.000000e+00 1543.0
15 TraesCS1B01G450100 chr1D 93.763 978 45 6 2031 3000 480099280 480100249 0.000000e+00 1454.0
16 TraesCS1B01G450100 chr1D 93.986 848 43 5 1 848 478727465 478726626 0.000000e+00 1277.0
17 TraesCS1B01G450100 chr1D 91.883 616 32 6 2394 3000 480151877 480152483 0.000000e+00 845.0
18 TraesCS1B01G450100 chr1D 91.234 616 36 8 2394 3000 478729750 478729144 0.000000e+00 822.0
19 TraesCS1B01G450100 chr1D 93.529 510 24 3 2394 2903 478750491 478749991 0.000000e+00 750.0
20 TraesCS1B01G450100 chr1D 93.010 515 27 3 2394 2908 478746396 478745891 0.000000e+00 743.0
21 TraesCS1B01G450100 chr1D 92.750 400 19 2 1644 2033 480076418 480076817 1.290000e-158 569.0
22 TraesCS1B01G450100 chr1D 83.686 472 51 18 1186 1641 480075677 480076138 3.830000e-114 422.0
23 TraesCS1B01G450100 chr1D 93.333 240 15 1 1195 1434 480063671 480063909 1.420000e-93 353.0
24 TraesCS1B01G450100 chr1D 84.639 332 40 8 681 1011 478756503 478756182 1.440000e-83 320.0
25 TraesCS1B01G450100 chr1D 95.294 170 4 2 844 1013 478710775 478710610 1.900000e-67 267.0
26 TraesCS1B01G450100 chr1D 94.595 148 8 0 1 148 480101834 480101981 2.490000e-56 230.0
27 TraesCS1B01G450100 chr1D 93.243 148 10 0 1 148 478751346 478751199 5.400000e-53 219.0
28 TraesCS1B01G450100 chr1D 92.568 148 11 0 1 148 478747252 478747105 2.510000e-51 213.0
29 TraesCS1B01G450100 chr1D 85.789 190 17 6 2963 3145 479957157 479957343 3.270000e-45 193.0
30 TraesCS1B01G450100 chr1D 90.511 137 4 3 1016 1152 478756689 478756562 4.260000e-39 172.0
31 TraesCS1B01G450100 chr1D 90.517 116 10 1 1009 1124 480075575 480075689 5.550000e-33 152.0
32 TraesCS1B01G450100 chr1A 90.435 1035 89 6 1195 2228 576491894 576490869 0.000000e+00 1354.0
33 TraesCS1B01G450100 chr1A 88.539 1047 54 26 1195 2228 576561601 576562594 0.000000e+00 1208.0
34 TraesCS1B01G450100 chr1A 86.220 1016 106 17 1 1012 576493226 576492241 0.000000e+00 1070.0
35 TraesCS1B01G450100 chr1A 83.618 293 34 8 679 966 576560968 576561251 2.460000e-66 263.0
36 TraesCS1B01G450100 chr1A 88.889 117 11 2 1009 1124 576561488 576561603 3.340000e-30 143.0
37 TraesCS1B01G450100 chr1A 91.919 99 7 1 1026 1124 576491989 576491892 1.550000e-28 137.0
38 TraesCS1B01G450100 chr2A 97.143 35 1 0 267 301 276567916 276567882 3.460000e-05 60.2


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 TraesCS1B01G450100 chr1B 668198849 668202062 3213 False 5936.000000 5936 100.000000 1 3214 1 chr1B.!!$F1 3213
1 TraesCS1B01G450100 chr1B 668182176 668188132 5956 False 927.000000 2117 88.172400 583 3000 5 chr1B.!!$F2 2417
2 TraesCS1B01G450100 chr1B 668428951 668429802 851 True 697.000000 697 81.726000 1532 2412 1 chr1B.!!$R2 880
3 TraesCS1B01G450100 chr1B 668539807 668540328 521 True 399.000000 399 81.295000 1220 1753 1 chr1B.!!$R3 533
4 TraesCS1B01G450100 chr1B 668544498 668545152 654 True 218.000000 287 87.028000 1925 2662 3 chr1B.!!$R4 737
5 TraesCS1B01G450100 chr1D 480151877 480156558 4681 False 1314.333333 1555 92.194333 1 3000 3 chr1D.!!$F5 2999
6 TraesCS1B01G450100 chr1D 478726626 478729750 3124 True 1049.500000 1277 92.610000 1 3000 2 chr1D.!!$R2 2999
7 TraesCS1B01G450100 chr1D 480099280 480101981 2701 False 842.000000 1454 94.179000 1 3000 2 chr1D.!!$F4 2999
8 TraesCS1B01G450100 chr1D 478745891 478756689 10798 True 789.428571 3109 91.975286 1 2908 7 chr1D.!!$R3 2907
9 TraesCS1B01G450100 chr1D 480075575 480076817 1242 False 381.000000 569 88.984333 1009 2033 3 chr1D.!!$F3 1024
10 TraesCS1B01G450100 chr1A 576490869 576493226 2357 True 853.666667 1354 89.524667 1 2228 3 chr1A.!!$R1 2227
11 TraesCS1B01G450100 chr1A 576560968 576562594 1626 False 538.000000 1208 87.015333 679 2228 3 chr1A.!!$F1 1549

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
100 2376 0.178068 TATGAGGCGGCTGGACTTTC 59.822 55.000 19.63 0.0 29.96 2.62 F
676 2963 1.065401 AGCAAAACATCACACACACCG 59.935 47.619 0.00 0.0 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1817 4893 0.813184 CTGTAGGTCCTTTCCGCGTA 59.187 55.0 4.92 0.0 0.0 4.42 R
2476 8934 0.042131 AGTACCGGTTCTCCATCCCA 59.958 55.0 15.04 0.0 0.0 4.37 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
100 2376 0.178068 TATGAGGCGGCTGGACTTTC 59.822 55.000 19.63 0.00 29.96 2.62
101 2377 2.436824 GAGGCGGCTGGACTTTCC 60.437 66.667 19.63 0.00 29.96 3.13
109 2385 1.301677 GCTGGACTTTCCGCTCAAGG 61.302 60.000 2.92 0.00 40.17 3.61
132 2408 5.368989 GAAAGTACTCCAATATGGGTCCAG 58.631 45.833 0.00 0.00 38.32 3.86
229 2505 2.010145 TGTGGAGATTACGCTTGAGC 57.990 50.000 0.00 0.00 37.78 4.26
265 2542 1.109296 CAAAAACAAAGTCGGTCGCG 58.891 50.000 0.00 0.00 0.00 5.87
312 2589 5.242838 TGTTGAACACTTTCCTGTTTGAAGT 59.757 36.000 0.00 0.00 34.40 3.01
317 2594 4.157840 ACACTTTCCTGTTTGAAGTTGTCC 59.842 41.667 0.00 0.00 31.63 4.02
323 2600 5.200483 TCCTGTTTGAAGTTGTCCTGAAAT 58.800 37.500 0.00 0.00 0.00 2.17
336 2613 4.101585 TGTCCTGAAATCGATATCTGCCTT 59.898 41.667 0.00 0.00 0.00 4.35
363 2640 4.255510 ACAAACATATGCCTCCAGGATT 57.744 40.909 1.58 0.00 37.39 3.01
412 2689 6.096001 AGTTTGCAATTTACCTCAGATCATCC 59.904 38.462 0.00 0.00 0.00 3.51
458 2735 2.969443 AGCAAATCTCGTTGTTTCGG 57.031 45.000 0.00 0.00 0.00 4.30
471 2748 1.403679 TGTTTCGGTGAGGCAAACAAG 59.596 47.619 0.00 0.00 37.14 3.16
561 2838 8.727100 AGACAAGTATCATTATATGTCTGGGA 57.273 34.615 5.51 0.00 44.10 4.37
570 2847 1.344953 TATGTCTGGGATTGGGCGCT 61.345 55.000 7.64 0.00 0.00 5.92
622 2899 5.585445 AGATGAAGAGCTTTTATGCTGAGTG 59.415 40.000 0.00 0.00 44.17 3.51
623 2900 4.645535 TGAAGAGCTTTTATGCTGAGTGT 58.354 39.130 0.00 0.00 44.17 3.55
625 2902 5.871524 TGAAGAGCTTTTATGCTGAGTGTAG 59.128 40.000 0.00 0.00 44.17 2.74
627 2904 5.799213 AGAGCTTTTATGCTGAGTGTAGTT 58.201 37.500 0.00 0.00 44.17 2.24
629 2906 4.938226 AGCTTTTATGCTGAGTGTAGTTCC 59.062 41.667 0.00 0.00 42.33 3.62
634 2913 7.435068 TTTATGCTGAGTGTAGTTCCTTTTC 57.565 36.000 0.00 0.00 0.00 2.29
651 2938 5.596361 TCCTTTTCTTTGCCATGTCAAACTA 59.404 36.000 0.00 0.00 32.99 2.24
676 2963 1.065401 AGCAAAACATCACACACACCG 59.935 47.619 0.00 0.00 0.00 4.94
739 3058 1.526887 CACATGGTACGGGCTCCAT 59.473 57.895 0.00 0.00 44.15 3.41
799 3118 1.728971 CCTCATCACGTCAAAGACTGC 59.271 52.381 0.00 0.00 0.00 4.40
800 3119 2.407090 CTCATCACGTCAAAGACTGCA 58.593 47.619 0.00 0.00 0.00 4.41
801 3120 2.135139 TCATCACGTCAAAGACTGCAC 58.865 47.619 0.00 0.00 0.00 4.57
1461 4198 3.673599 GCTTCTGCAACCTGGACC 58.326 61.111 0.00 0.00 39.41 4.46
1465 4238 1.708993 TTCTGCAACCTGGACCAGCT 61.709 55.000 16.72 0.00 0.00 4.24
1732 4802 5.199024 ACTCATCTTATGCTCTACTGCAG 57.801 43.478 13.48 13.48 46.71 4.41
1769 4845 2.897326 TGTGAAGATCGGGAGAAACTCA 59.103 45.455 0.00 0.00 45.37 3.41
1807 4883 4.285020 ACATGAGAGAGGAGCTGTATGAA 58.715 43.478 0.00 0.00 0.00 2.57
1817 4893 3.751698 GGAGCTGTATGAAAAGGTTTCGT 59.248 43.478 0.00 1.43 0.00 3.85
1866 4942 2.101783 CAGGGCAGGCAAACATATCAA 58.898 47.619 0.00 0.00 0.00 2.57
1929 5009 1.103398 GGGGACAGCACATGGTATGC 61.103 60.000 0.00 0.00 43.74 3.14
2039 5120 1.003003 TCCACTTGATCGTTGCATGGA 59.997 47.619 0.00 0.00 32.39 3.41
2077 5158 3.339253 TCAGCTTGTATGTGCTCATGT 57.661 42.857 11.46 0.00 37.44 3.21
2196 5599 4.646040 TGATTGAGGGCCATGTTTATGAAG 59.354 41.667 6.18 0.00 36.36 3.02
2348 8805 7.118680 TCCCGTTTCTATGTTTGTTGAAGATAC 59.881 37.037 0.00 0.00 0.00 2.24
2451 8909 2.577563 TCTTCTGGGGAGCATGATGAAA 59.422 45.455 0.00 0.00 0.00 2.69
2470 8928 3.293311 AATGCAGCTCACACAACATTC 57.707 42.857 0.00 0.00 0.00 2.67
2471 8929 1.677942 TGCAGCTCACACAACATTCA 58.322 45.000 0.00 0.00 0.00 2.57
2472 8930 2.022934 TGCAGCTCACACAACATTCAA 58.977 42.857 0.00 0.00 0.00 2.69
2473 8931 2.223548 TGCAGCTCACACAACATTCAAC 60.224 45.455 0.00 0.00 0.00 3.18
2474 8932 2.223548 GCAGCTCACACAACATTCAACA 60.224 45.455 0.00 0.00 0.00 3.33
2475 8933 3.551454 GCAGCTCACACAACATTCAACAT 60.551 43.478 0.00 0.00 0.00 2.71
2476 8934 4.613944 CAGCTCACACAACATTCAACATT 58.386 39.130 0.00 0.00 0.00 2.71
2489 8947 3.085952 TCAACATTGGGATGGAGAACC 57.914 47.619 0.00 0.00 37.60 3.62
2518 8976 3.687698 CCCTACGGTCCAAAATAAGTGTG 59.312 47.826 0.00 0.00 0.00 3.82
2586 13067 2.320781 CATGGATCGGAGGGAGTAGTT 58.679 52.381 0.00 0.00 0.00 2.24
2696 13177 3.857665 TCTGCTTTAGTGTAGCGATTTCG 59.142 43.478 0.00 0.00 41.54 3.46
2741 13225 4.162320 AGTTCTCTTCTTGACCACTCAACA 59.838 41.667 0.00 0.00 32.68 3.33
2785 13269 3.445805 ACCAAACAAGTTGTGGTACCAAG 59.554 43.478 18.31 5.24 43.90 3.61
2876 13360 2.031163 AAGTGACTGGTCTGCCGC 59.969 61.111 2.38 0.00 37.67 6.53
3000 13736 2.919494 GCCACAAAACGGCTGGAGG 61.919 63.158 0.00 0.00 46.56 4.30
3002 13738 1.237285 CCACAAAACGGCTGGAGGAG 61.237 60.000 0.00 0.00 0.00 3.69
3003 13739 1.073199 ACAAAACGGCTGGAGGAGG 59.927 57.895 0.00 0.00 0.00 4.30
3004 13740 1.374947 CAAAACGGCTGGAGGAGGA 59.625 57.895 0.00 0.00 0.00 3.71
3005 13741 0.250727 CAAAACGGCTGGAGGAGGAA 60.251 55.000 0.00 0.00 0.00 3.36
3006 13742 0.250770 AAAACGGCTGGAGGAGGAAC 60.251 55.000 0.00 0.00 0.00 3.62
3007 13743 2.450479 AAACGGCTGGAGGAGGAACG 62.450 60.000 0.00 0.00 0.00 3.95
3008 13744 3.068691 CGGCTGGAGGAGGAACGA 61.069 66.667 0.00 0.00 0.00 3.85
3009 13745 2.579738 GGCTGGAGGAGGAACGAC 59.420 66.667 0.00 0.00 0.00 4.34
3010 13746 2.579738 GCTGGAGGAGGAACGACC 59.420 66.667 0.00 0.00 39.35 4.79
3027 13763 2.432628 CTCGAGGTTCGGCACACC 60.433 66.667 3.91 0.00 40.88 4.16
3070 13806 4.980805 GCCGTCACCGCACCTTGA 62.981 66.667 0.00 0.00 0.00 3.02
3071 13807 2.738521 CCGTCACCGCACCTTGAG 60.739 66.667 0.00 0.00 0.00 3.02
3073 13809 1.594293 CGTCACCGCACCTTGAGTT 60.594 57.895 0.00 0.00 0.00 3.01
3074 13810 1.157870 CGTCACCGCACCTTGAGTTT 61.158 55.000 0.00 0.00 0.00 2.66
3076 13812 0.468226 TCACCGCACCTTGAGTTTCT 59.532 50.000 0.00 0.00 0.00 2.52
3077 13813 0.868406 CACCGCACCTTGAGTTTCTC 59.132 55.000 0.00 0.00 0.00 2.87
3078 13814 0.250338 ACCGCACCTTGAGTTTCTCC 60.250 55.000 0.00 0.00 0.00 3.71
3079 13815 0.250295 CCGCACCTTGAGTTTCTCCA 60.250 55.000 0.00 0.00 0.00 3.86
3083 13819 1.264288 CACCTTGAGTTTCTCCAACGC 59.736 52.381 0.00 0.00 40.75 4.84
3084 13820 0.512952 CCTTGAGTTTCTCCAACGCG 59.487 55.000 3.53 3.53 40.75 6.01
3087 13823 0.320374 TGAGTTTCTCCAACGCGGAT 59.680 50.000 12.47 0.00 45.19 4.18
3088 13824 1.546923 TGAGTTTCTCCAACGCGGATA 59.453 47.619 12.47 0.00 45.19 2.59
3091 13827 0.108041 TTTCTCCAACGCGGATACCC 60.108 55.000 12.47 0.00 45.19 3.69
3093 13829 1.227263 CTCCAACGCGGATACCCTG 60.227 63.158 12.47 0.00 45.19 4.45
3094 13830 2.895372 CCAACGCGGATACCCTGC 60.895 66.667 12.47 0.00 36.56 4.85
3115 15680 1.519751 CCGCCCGTGTTCATGGAAAA 61.520 55.000 12.10 0.00 0.00 2.29
3116 15681 0.525761 CGCCCGTGTTCATGGAAAAT 59.474 50.000 12.10 0.00 0.00 1.82
3117 15682 1.067915 CGCCCGTGTTCATGGAAAATT 60.068 47.619 12.10 0.00 0.00 1.82
3118 15683 2.336667 GCCCGTGTTCATGGAAAATTG 58.663 47.619 12.10 0.00 0.00 2.32
3119 15684 2.288763 GCCCGTGTTCATGGAAAATTGT 60.289 45.455 12.10 0.00 0.00 2.71
3120 15685 3.801983 GCCCGTGTTCATGGAAAATTGTT 60.802 43.478 12.10 0.00 0.00 2.83
3121 15686 3.987220 CCCGTGTTCATGGAAAATTGTTC 59.013 43.478 12.10 0.00 0.00 3.18
3123 15688 4.681025 CCGTGTTCATGGAAAATTGTTCTG 59.319 41.667 5.20 0.00 0.00 3.02
3124 15689 4.681025 CGTGTTCATGGAAAATTGTTCTGG 59.319 41.667 0.00 0.00 0.00 3.86
3125 15690 5.600696 GTGTTCATGGAAAATTGTTCTGGT 58.399 37.500 0.00 0.00 0.00 4.00
3128 15693 4.478203 TCATGGAAAATTGTTCTGGTGGA 58.522 39.130 0.00 0.00 0.00 4.02
3130 15695 4.870123 TGGAAAATTGTTCTGGTGGATG 57.130 40.909 0.00 0.00 0.00 3.51
3132 15697 5.389520 TGGAAAATTGTTCTGGTGGATGTA 58.610 37.500 0.00 0.00 0.00 2.29
3134 15699 5.710099 GGAAAATTGTTCTGGTGGATGTAGA 59.290 40.000 0.00 0.00 0.00 2.59
3135 15700 6.378280 GGAAAATTGTTCTGGTGGATGTAGAT 59.622 38.462 0.00 0.00 0.00 1.98
3137 15702 3.801114 TGTTCTGGTGGATGTAGATCG 57.199 47.619 0.00 0.00 0.00 3.69
3138 15703 3.096852 TGTTCTGGTGGATGTAGATCGT 58.903 45.455 0.00 0.00 0.00 3.73
3139 15704 3.119137 TGTTCTGGTGGATGTAGATCGTG 60.119 47.826 0.00 0.00 0.00 4.35
3140 15705 2.735151 TCTGGTGGATGTAGATCGTGT 58.265 47.619 0.00 0.00 0.00 4.49
3142 15707 3.513912 TCTGGTGGATGTAGATCGTGTTT 59.486 43.478 0.00 0.00 0.00 2.83
3143 15708 4.020573 TCTGGTGGATGTAGATCGTGTTTT 60.021 41.667 0.00 0.00 0.00 2.43
3144 15709 4.647611 TGGTGGATGTAGATCGTGTTTTT 58.352 39.130 0.00 0.00 0.00 1.94
3145 15710 5.795972 TGGTGGATGTAGATCGTGTTTTTA 58.204 37.500 0.00 0.00 0.00 1.52
3147 15712 6.882140 TGGTGGATGTAGATCGTGTTTTTATT 59.118 34.615 0.00 0.00 0.00 1.40
3148 15713 7.065324 TGGTGGATGTAGATCGTGTTTTTATTC 59.935 37.037 0.00 0.00 0.00 1.75
3149 15714 7.280205 GGTGGATGTAGATCGTGTTTTTATTCT 59.720 37.037 0.00 0.00 0.00 2.40
3150 15715 8.665685 GTGGATGTAGATCGTGTTTTTATTCTT 58.334 33.333 0.00 0.00 0.00 2.52
3152 15717 8.122952 GGATGTAGATCGTGTTTTTATTCTTGG 58.877 37.037 0.00 0.00 0.00 3.61
3153 15718 7.972832 TGTAGATCGTGTTTTTATTCTTGGT 57.027 32.000 0.00 0.00 0.00 3.67
3154 15719 8.385898 TGTAGATCGTGTTTTTATTCTTGGTT 57.614 30.769 0.00 0.00 0.00 3.67
3155 15720 8.842280 TGTAGATCGTGTTTTTATTCTTGGTTT 58.158 29.630 0.00 0.00 0.00 3.27
3156 15721 9.326339 GTAGATCGTGTTTTTATTCTTGGTTTC 57.674 33.333 0.00 0.00 0.00 2.78
3158 15723 7.860872 AGATCGTGTTTTTATTCTTGGTTTCAC 59.139 33.333 0.00 0.00 0.00 3.18
3159 15724 5.966503 TCGTGTTTTTATTCTTGGTTTCACG 59.033 36.000 0.00 0.00 43.60 4.35
3160 15725 5.172411 CGTGTTTTTATTCTTGGTTTCACGG 59.828 40.000 0.00 0.00 40.32 4.94
3161 15726 6.267070 GTGTTTTTATTCTTGGTTTCACGGA 58.733 36.000 0.00 0.00 0.00 4.69
3162 15727 6.752815 GTGTTTTTATTCTTGGTTTCACGGAA 59.247 34.615 0.00 0.00 0.00 4.30
3163 15728 7.275999 GTGTTTTTATTCTTGGTTTCACGGAAA 59.724 33.333 0.00 0.00 0.00 3.13
3164 15729 7.817962 TGTTTTTATTCTTGGTTTCACGGAAAA 59.182 29.630 1.37 0.00 33.14 2.29
3166 15731 8.950208 TTTTATTCTTGGTTTCACGGAAAATT 57.050 26.923 1.37 0.00 33.14 1.82
3168 15733 4.993029 TCTTGGTTTCACGGAAAATTGT 57.007 36.364 1.37 0.00 33.14 2.71
3169 15734 5.331876 TCTTGGTTTCACGGAAAATTGTT 57.668 34.783 1.37 0.00 33.14 2.83
3171 15736 4.993029 TGGTTTCACGGAAAATTGTTCT 57.007 36.364 1.37 0.00 33.14 3.01
3172 15737 4.677584 TGGTTTCACGGAAAATTGTTCTG 58.322 39.130 1.37 0.00 33.14 3.02
3173 15738 4.048504 GGTTTCACGGAAAATTGTTCTGG 58.951 43.478 0.56 0.00 33.14 3.86
3174 15739 4.440940 GGTTTCACGGAAAATTGTTCTGGT 60.441 41.667 0.56 0.00 33.14 4.00
3175 15740 3.980646 TCACGGAAAATTGTTCTGGTG 57.019 42.857 0.56 3.43 0.00 4.17
3176 15741 2.621055 TCACGGAAAATTGTTCTGGTGG 59.379 45.455 0.56 0.00 0.00 4.61
3177 15742 2.621055 CACGGAAAATTGTTCTGGTGGA 59.379 45.455 0.56 0.00 0.00 4.02
3178 15743 3.255642 CACGGAAAATTGTTCTGGTGGAT 59.744 43.478 0.56 0.00 0.00 3.41
3179 15744 3.255642 ACGGAAAATTGTTCTGGTGGATG 59.744 43.478 0.56 0.00 0.00 3.51
3181 15746 4.457603 CGGAAAATTGTTCTGGTGGATGTA 59.542 41.667 0.00 0.00 0.00 2.29
3182 15747 5.619086 CGGAAAATTGTTCTGGTGGATGTAC 60.619 44.000 0.00 0.00 0.00 2.90
3183 15748 5.242838 GGAAAATTGTTCTGGTGGATGTACA 59.757 40.000 0.00 0.00 0.00 2.90
3185 15750 6.515272 AAATTGTTCTGGTGGATGTACATC 57.485 37.500 24.95 24.95 37.11 3.06
3186 15751 3.245518 TGTTCTGGTGGATGTACATCG 57.754 47.619 25.65 13.94 38.69 3.84
3187 15752 1.933853 GTTCTGGTGGATGTACATCGC 59.066 52.381 25.65 20.52 38.69 4.58
3188 15753 1.190643 TCTGGTGGATGTACATCGCA 58.809 50.000 25.65 21.36 38.69 5.10
3189 15754 1.762370 TCTGGTGGATGTACATCGCAT 59.238 47.619 25.65 0.00 38.69 4.73
3190 15755 2.138320 CTGGTGGATGTACATCGCATC 58.862 52.381 25.65 23.23 41.30 3.91
3191 15756 1.762370 TGGTGGATGTACATCGCATCT 59.238 47.619 25.65 0.00 41.63 2.90
3193 15758 3.386402 TGGTGGATGTACATCGCATCTTA 59.614 43.478 25.65 10.35 41.63 2.10
3197 15762 5.753438 GTGGATGTACATCGCATCTTAGAAA 59.247 40.000 25.65 1.75 41.63 2.52
3200 15765 6.425114 GGATGTACATCGCATCTTAGAAACAT 59.575 38.462 25.65 0.00 41.63 2.71
3201 15766 7.041780 GGATGTACATCGCATCTTAGAAACATT 60.042 37.037 25.65 0.00 41.63 2.71
3202 15767 8.887036 ATGTACATCGCATCTTAGAAACATTA 57.113 30.769 1.41 0.00 0.00 1.90
3203 15768 8.126871 TGTACATCGCATCTTAGAAACATTAC 57.873 34.615 0.00 0.00 0.00 1.89
3206 15771 8.942338 ACATCGCATCTTAGAAACATTACTAA 57.058 30.769 0.00 0.00 0.00 2.24
3209 15774 8.589335 TCGCATCTTAGAAACATTACTAATCC 57.411 34.615 0.00 0.00 0.00 3.01
3210 15775 8.201464 TCGCATCTTAGAAACATTACTAATCCA 58.799 33.333 0.00 0.00 0.00 3.41
3211 15776 8.276325 CGCATCTTAGAAACATTACTAATCCAC 58.724 37.037 0.00 0.00 0.00 4.02
3212 15777 9.109393 GCATCTTAGAAACATTACTAATCCACA 57.891 33.333 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 2376 1.275291 TGGAGTACTTTCCTTGAGCGG 59.725 52.381 0.00 0.00 38.12 5.52
101 2377 2.743636 TGGAGTACTTTCCTTGAGCG 57.256 50.000 0.00 0.00 38.12 5.03
109 2385 5.130477 TCTGGACCCATATTGGAGTACTTTC 59.870 44.000 0.00 0.00 40.96 2.62
132 2408 9.247126 GTTCGAATTAAGGTAGGTTTAGAGATC 57.753 37.037 0.00 0.00 0.00 2.75
265 2542 0.386985 AAGTTCTTCGCCTCGTCGAC 60.387 55.000 5.18 5.18 38.30 4.20
312 2589 4.101585 AGGCAGATATCGATTTCAGGACAA 59.898 41.667 16.66 0.00 0.00 3.18
317 2594 4.063689 AGCAAGGCAGATATCGATTTCAG 58.936 43.478 16.66 10.55 0.00 3.02
323 2600 5.722021 TTGTATAGCAAGGCAGATATCGA 57.278 39.130 0.00 0.00 32.52 3.59
336 2613 5.303259 TGGAGGCATATGTTTGTATAGCA 57.697 39.130 4.29 0.00 0.00 3.49
363 2640 8.262227 ACTCGGTCAACAAGGAAATACATATAA 58.738 33.333 0.00 0.00 0.00 0.98
384 2661 3.751175 TCTGAGGTAAATTGCAAACTCGG 59.249 43.478 1.71 11.31 33.71 4.63
458 2735 4.045636 ACATGAAACTTGTTTGCCTCAC 57.954 40.909 0.00 0.00 0.00 3.51
471 2748 4.783242 TCAAAAGCTCGCTAACATGAAAC 58.217 39.130 0.00 0.00 0.00 2.78
561 2838 3.399440 TTCAAAATTTGAGCGCCCAAT 57.601 38.095 4.79 0.00 41.38 3.16
622 2899 5.009610 TGACATGGCAAAGAAAAGGAACTAC 59.990 40.000 0.00 0.00 38.49 2.73
623 2900 5.136828 TGACATGGCAAAGAAAAGGAACTA 58.863 37.500 0.00 0.00 38.49 2.24
625 2902 4.320608 TGACATGGCAAAGAAAAGGAAC 57.679 40.909 0.00 0.00 0.00 3.62
627 2904 4.405358 AGTTTGACATGGCAAAGAAAAGGA 59.595 37.500 27.04 0.00 38.33 3.36
629 2906 7.147312 TCATAGTTTGACATGGCAAAGAAAAG 58.853 34.615 27.04 15.35 38.33 2.27
634 2913 6.183360 TGCTATCATAGTTTGACATGGCAAAG 60.183 38.462 27.04 15.13 38.33 2.77
651 2938 5.335897 GGTGTGTGTGATGTTTTGCTATCAT 60.336 40.000 0.00 0.00 35.91 2.45
714 3029 1.451927 CCGTACCATGTGCATGCCT 60.452 57.895 16.68 0.00 37.49 4.75
799 3118 4.123497 TCTAGATTCATTGTCGGTGGTG 57.877 45.455 0.00 0.00 0.00 4.17
800 3119 4.499865 CGATCTAGATTCATTGTCGGTGGT 60.500 45.833 6.70 0.00 0.00 4.16
801 3120 3.983988 CGATCTAGATTCATTGTCGGTGG 59.016 47.826 6.70 0.00 0.00 4.61
1465 4238 4.322080 ACGAGCTATTAGCACAGCATAA 57.678 40.909 17.59 0.00 45.56 1.90
1607 4391 4.450419 GCTATTCGGTCCTCTGATTGATTG 59.550 45.833 0.00 0.00 0.00 2.67
1769 4845 7.240167 TCTCTCATGTTATGGATCTCTCTCAT 58.760 38.462 0.00 0.00 0.00 2.90
1807 4883 1.528161 CTTTCCGCGTACGAAACCTTT 59.472 47.619 21.65 0.00 43.93 3.11
1817 4893 0.813184 CTGTAGGTCCTTTCCGCGTA 59.187 55.000 4.92 0.00 0.00 4.42
1866 4942 4.521062 GCTCCTCACGCAGCCGAT 62.521 66.667 0.00 0.00 38.29 4.18
2039 5120 3.550842 GCTGAAGGTCAAAGTCGCAAATT 60.551 43.478 0.00 0.00 0.00 1.82
2077 5158 4.488136 CCTACCAGCGGCCATGCA 62.488 66.667 2.24 0.00 37.31 3.96
2348 8805 5.793026 GAGCTGTGAACTCCTTATTTCAG 57.207 43.478 0.00 0.00 32.40 3.02
2451 8909 2.232399 TGAATGTTGTGTGAGCTGCAT 58.768 42.857 1.02 0.00 0.00 3.96
2470 8928 1.745087 CGGTTCTCCATCCCAATGTTG 59.255 52.381 0.00 0.00 0.00 3.33
2471 8929 1.340991 CCGGTTCTCCATCCCAATGTT 60.341 52.381 0.00 0.00 0.00 2.71
2472 8930 0.255890 CCGGTTCTCCATCCCAATGT 59.744 55.000 0.00 0.00 0.00 2.71
2473 8931 0.255890 ACCGGTTCTCCATCCCAATG 59.744 55.000 0.00 0.00 0.00 2.82
2474 8932 1.489230 GTACCGGTTCTCCATCCCAAT 59.511 52.381 15.04 0.00 0.00 3.16
2475 8933 0.906775 GTACCGGTTCTCCATCCCAA 59.093 55.000 15.04 0.00 0.00 4.12
2476 8934 0.042131 AGTACCGGTTCTCCATCCCA 59.958 55.000 15.04 0.00 0.00 4.37
2503 8961 4.584327 AACTGCCACACTTATTTTGGAC 57.416 40.909 0.00 0.00 31.39 4.02
2518 8976 3.068165 AGGTTGCTTAGTTCAAAACTGCC 59.932 43.478 2.65 0.00 42.84 4.85
2586 13067 2.362397 TCTTTATGGTGGCGCAAAAACA 59.638 40.909 10.83 2.90 0.00 2.83
2696 13177 5.641209 ACTTGTCTCATAGAGTGTGAATTGC 59.359 40.000 0.00 0.00 32.59 3.56
2741 13225 4.641989 GTGCCTGACATATTTGACCTTCAT 59.358 41.667 0.00 0.00 0.00 2.57
2785 13269 1.448013 GTTAGCGGCTCACCCACTC 60.448 63.158 5.39 0.00 0.00 3.51
2876 13360 0.685131 TCAAATGCAGCCTGGATGGG 60.685 55.000 14.61 0.00 36.00 4.00
2909 13393 1.343821 GGCAACGATTACAGCGTCG 59.656 57.895 0.00 0.00 41.75 5.12
2924 13408 4.641645 CAACCTGGACAGCCGGCA 62.642 66.667 31.54 6.15 39.39 5.69
3009 13745 2.432628 GTGTGCCGAACCTCGAGG 60.433 66.667 30.11 30.11 43.74 4.63
3010 13746 2.432628 GGTGTGCCGAACCTCGAG 60.433 66.667 5.13 5.13 43.74 4.04
3057 13793 0.468226 AGAAACTCAAGGTGCGGTGA 59.532 50.000 0.00 0.00 0.00 4.02
3058 13794 0.868406 GAGAAACTCAAGGTGCGGTG 59.132 55.000 0.00 0.00 0.00 4.94
3060 13796 0.250295 TGGAGAAACTCAAGGTGCGG 60.250 55.000 0.00 0.00 31.08 5.69
3061 13797 1.264288 GTTGGAGAAACTCAAGGTGCG 59.736 52.381 0.00 0.00 35.75 5.34
3062 13798 1.264288 CGTTGGAGAAACTCAAGGTGC 59.736 52.381 0.00 0.00 36.56 5.01
3063 13799 1.264288 GCGTTGGAGAAACTCAAGGTG 59.736 52.381 0.00 0.00 36.56 4.00
3064 13800 1.594331 GCGTTGGAGAAACTCAAGGT 58.406 50.000 0.00 0.00 36.56 3.50
3065 13801 0.512952 CGCGTTGGAGAAACTCAAGG 59.487 55.000 0.00 0.00 36.56 3.61
3066 13802 0.512952 CCGCGTTGGAGAAACTCAAG 59.487 55.000 4.92 0.00 42.00 3.02
3067 13803 0.105224 TCCGCGTTGGAGAAACTCAA 59.895 50.000 4.92 0.00 43.74 3.02
3069 13805 4.667420 TCCGCGTTGGAGAAACTC 57.333 55.556 4.92 0.00 43.74 3.01
3077 13813 2.895372 GCAGGGTATCCGCGTTGG 60.895 66.667 4.92 0.00 38.33 3.77
3078 13814 3.261951 CGCAGGGTATCCGCGTTG 61.262 66.667 18.93 0.00 44.58 4.10
3096 13832 1.519751 TTTTCCATGAACACGGGCGG 61.520 55.000 0.00 0.00 0.00 6.13
3098 13834 2.288763 ACAATTTTCCATGAACACGGGC 60.289 45.455 0.00 0.00 0.00 6.13
3102 15667 5.463061 CACCAGAACAATTTTCCATGAACAC 59.537 40.000 0.00 0.00 0.00 3.32
3104 15669 4.990426 CCACCAGAACAATTTTCCATGAAC 59.010 41.667 0.00 0.00 0.00 3.18
3115 15680 4.162320 ACGATCTACATCCACCAGAACAAT 59.838 41.667 0.00 0.00 0.00 2.71
3116 15681 3.513912 ACGATCTACATCCACCAGAACAA 59.486 43.478 0.00 0.00 0.00 2.83
3117 15682 3.096852 ACGATCTACATCCACCAGAACA 58.903 45.455 0.00 0.00 0.00 3.18
3118 15683 3.119101 ACACGATCTACATCCACCAGAAC 60.119 47.826 0.00 0.00 0.00 3.01
3119 15684 3.096852 ACACGATCTACATCCACCAGAA 58.903 45.455 0.00 0.00 0.00 3.02
3120 15685 2.735151 ACACGATCTACATCCACCAGA 58.265 47.619 0.00 0.00 0.00 3.86
3121 15686 3.526931 AACACGATCTACATCCACCAG 57.473 47.619 0.00 0.00 0.00 4.00
3123 15688 6.920569 ATAAAAACACGATCTACATCCACC 57.079 37.500 0.00 0.00 0.00 4.61
3124 15689 8.197988 AGAATAAAAACACGATCTACATCCAC 57.802 34.615 0.00 0.00 0.00 4.02
3125 15690 8.664798 CAAGAATAAAAACACGATCTACATCCA 58.335 33.333 0.00 0.00 0.00 3.41
3128 15693 8.561738 ACCAAGAATAAAAACACGATCTACAT 57.438 30.769 0.00 0.00 0.00 2.29
3130 15695 9.326339 GAAACCAAGAATAAAAACACGATCTAC 57.674 33.333 0.00 0.00 0.00 2.59
3132 15697 7.860872 GTGAAACCAAGAATAAAAACACGATCT 59.139 33.333 0.00 0.00 0.00 2.75
3134 15699 6.635239 CGTGAAACCAAGAATAAAAACACGAT 59.365 34.615 0.00 0.00 46.10 3.73
3135 15700 5.966503 CGTGAAACCAAGAATAAAAACACGA 59.033 36.000 0.00 0.00 46.10 4.35
3137 15702 6.267070 TCCGTGAAACCAAGAATAAAAACAC 58.733 36.000 0.00 0.00 0.00 3.32
3138 15703 6.452494 TCCGTGAAACCAAGAATAAAAACA 57.548 33.333 0.00 0.00 0.00 2.83
3139 15704 7.758613 TTTCCGTGAAACCAAGAATAAAAAC 57.241 32.000 0.00 0.00 0.00 2.43
3140 15705 8.950208 ATTTTCCGTGAAACCAAGAATAAAAA 57.050 26.923 0.00 0.00 30.83 1.94
3142 15707 7.982354 ACAATTTTCCGTGAAACCAAGAATAAA 59.018 29.630 0.00 0.00 30.83 1.40
3143 15708 7.493367 ACAATTTTCCGTGAAACCAAGAATAA 58.507 30.769 0.00 0.00 30.83 1.40
3144 15709 7.045126 ACAATTTTCCGTGAAACCAAGAATA 57.955 32.000 0.00 0.00 30.83 1.75
3145 15710 5.912892 ACAATTTTCCGTGAAACCAAGAAT 58.087 33.333 0.00 0.00 30.83 2.40
3147 15712 4.993029 ACAATTTTCCGTGAAACCAAGA 57.007 36.364 0.00 0.00 30.83 3.02
3148 15713 5.231991 CAGAACAATTTTCCGTGAAACCAAG 59.768 40.000 0.00 0.00 30.83 3.61
3149 15714 5.105752 CAGAACAATTTTCCGTGAAACCAA 58.894 37.500 0.00 0.00 30.83 3.67
3150 15715 4.440802 CCAGAACAATTTTCCGTGAAACCA 60.441 41.667 0.00 0.00 30.83 3.67
3152 15717 4.502645 CACCAGAACAATTTTCCGTGAAAC 59.497 41.667 0.00 0.00 30.83 2.78
3153 15718 4.440802 CCACCAGAACAATTTTCCGTGAAA 60.441 41.667 13.61 0.00 0.00 2.69
3154 15719 3.067461 CCACCAGAACAATTTTCCGTGAA 59.933 43.478 13.61 0.00 0.00 3.18
3155 15720 2.621055 CCACCAGAACAATTTTCCGTGA 59.379 45.455 13.61 0.00 0.00 4.35
3156 15721 2.621055 TCCACCAGAACAATTTTCCGTG 59.379 45.455 9.10 9.10 0.00 4.94
3158 15723 3.255642 ACATCCACCAGAACAATTTTCCG 59.744 43.478 0.00 0.00 0.00 4.30
3159 15724 4.871933 ACATCCACCAGAACAATTTTCC 57.128 40.909 0.00 0.00 0.00 3.13
3160 15725 6.325919 TGTACATCCACCAGAACAATTTTC 57.674 37.500 0.00 0.00 0.00 2.29
3161 15726 6.349280 CGATGTACATCCACCAGAACAATTTT 60.349 38.462 26.33 0.00 34.40 1.82
3162 15727 5.123820 CGATGTACATCCACCAGAACAATTT 59.876 40.000 26.33 0.00 34.40 1.82
3163 15728 4.635765 CGATGTACATCCACCAGAACAATT 59.364 41.667 26.33 0.00 34.40 2.32
3164 15729 4.191544 CGATGTACATCCACCAGAACAAT 58.808 43.478 26.33 0.00 34.40 2.71
3166 15731 2.676750 GCGATGTACATCCACCAGAACA 60.677 50.000 26.33 0.00 34.40 3.18
3168 15733 1.552792 TGCGATGTACATCCACCAGAA 59.447 47.619 26.33 7.20 34.40 3.02
3169 15734 1.190643 TGCGATGTACATCCACCAGA 58.809 50.000 26.33 4.54 34.40 3.86
3171 15736 1.762370 AGATGCGATGTACATCCACCA 59.238 47.619 26.33 20.73 44.08 4.17
3172 15737 2.533266 AGATGCGATGTACATCCACC 57.467 50.000 26.33 17.39 44.08 4.61
3173 15738 4.871513 TCTAAGATGCGATGTACATCCAC 58.128 43.478 26.33 19.76 44.08 4.02
3174 15739 5.529581 TTCTAAGATGCGATGTACATCCA 57.470 39.130 26.33 23.70 44.08 3.41
3175 15740 5.753438 TGTTTCTAAGATGCGATGTACATCC 59.247 40.000 26.33 19.67 44.08 3.51
3176 15741 6.828502 TGTTTCTAAGATGCGATGTACATC 57.171 37.500 23.47 23.47 43.49 3.06
3177 15742 7.792374 AATGTTTCTAAGATGCGATGTACAT 57.208 32.000 8.43 8.43 0.00 2.29
3178 15743 7.979537 AGTAATGTTTCTAAGATGCGATGTACA 59.020 33.333 0.00 0.00 0.00 2.90
3179 15744 8.354011 AGTAATGTTTCTAAGATGCGATGTAC 57.646 34.615 0.00 0.00 0.00 2.90
3181 15746 8.942338 TTAGTAATGTTTCTAAGATGCGATGT 57.058 30.769 0.00 0.00 0.00 3.06
3183 15748 9.209175 GGATTAGTAATGTTTCTAAGATGCGAT 57.791 33.333 0.00 0.00 31.16 4.58
3185 15750 8.276325 GTGGATTAGTAATGTTTCTAAGATGCG 58.724 37.037 0.00 0.00 31.16 4.73
3186 15751 9.109393 TGTGGATTAGTAATGTTTCTAAGATGC 57.891 33.333 0.00 0.00 31.16 3.91


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

AutoCloner maintained by Alex Coulton.