Multiple sequence alignment - TraesCS2B01G034800

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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 TraesCS2B01G034800 chr2B 100.000 4089 0 0 1 4089 16890749 16894837 0.000000e+00 7552.0
1 TraesCS2B01G034800 chr2B 91.874 2252 131 11 913 3159 17351313 17349109 0.000000e+00 3097.0
2 TraesCS2B01G034800 chr2B 86.628 688 66 9 1 683 17358811 17358145 0.000000e+00 737.0
3 TraesCS2B01G034800 chr2B 86.420 486 47 10 3151 3626 17348805 17348329 7.840000e-142 514.0
4 TraesCS2B01G034800 chr2B 79.966 589 74 20 719 1269 17266576 17265994 1.070000e-105 394.0
5 TraesCS2B01G034800 chr2B 89.701 301 26 4 3630 3929 17348273 17347977 2.980000e-101 379.0
6 TraesCS2B01G034800 chr2B 92.135 178 10 1 723 900 17358142 17357969 8.780000e-62 248.0
7 TraesCS2B01G034800 chr2B 86.869 99 9 4 3642 3739 17434083 17434178 1.550000e-19 108.0
8 TraesCS2B01G034800 chr2A 87.576 2970 268 51 714 3626 11904490 11901565 0.000000e+00 3347.0
9 TraesCS2B01G034800 chr2A 88.682 698 57 13 4 695 11905158 11904477 0.000000e+00 832.0
10 TraesCS2B01G034800 chr2A 86.710 459 42 9 3629 4087 11899489 11899050 3.670000e-135 492.0
11 TraesCS2B01G034800 chr2A 86.779 416 48 4 3216 3626 11899965 11899552 1.340000e-124 457.0
12 TraesCS2B01G034800 chr2A 92.920 226 11 2 3637 3857 11901505 11901280 1.420000e-84 324.0
13 TraesCS2B01G034800 chr2D 89.266 885 69 15 953 1814 11081918 11082799 0.000000e+00 1085.0
14 TraesCS2B01G034800 chr2D 90.601 766 66 4 2442 3202 11083153 11083917 0.000000e+00 1011.0
15 TraesCS2B01G034800 chr2D 86.224 196 17 6 711 900 11081619 11081810 1.930000e-48 204.0
16 TraesCS2B01G034800 chr2D 94.186 86 5 0 3810 3895 591118415 591118500 9.220000e-27 132.0
17 TraesCS2B01G034800 chrUn 85.642 982 94 24 902 1845 248329921 248330893 0.000000e+00 989.0
18 TraesCS2B01G034800 chrUn 91.840 674 51 2 2444 3113 248330979 248331652 0.000000e+00 937.0
19 TraesCS2B01G034800 chrUn 86.612 732 68 18 2412 3127 307586552 307585835 0.000000e+00 782.0
20 TraesCS2B01G034800 chrUn 86.475 732 69 18 2412 3127 307590695 307589978 0.000000e+00 776.0
21 TraesCS2B01G034800 chrUn 88.836 636 51 12 1 630 257522660 257523281 0.000000e+00 763.0
22 TraesCS2B01G034800 chrUn 88.836 636 51 12 1 630 366986603 366987224 0.000000e+00 763.0
23 TraesCS2B01G034800 chrUn 89.713 593 52 7 2563 3148 307584984 307584394 0.000000e+00 749.0
24 TraesCS2B01G034800 chrUn 89.713 593 52 7 2563 3148 307589127 307588537 0.000000e+00 749.0
25 TraesCS2B01G034800 chrUn 89.713 593 52 7 2563 3148 318417431 318416841 0.000000e+00 749.0
26 TraesCS2B01G034800 chrUn 82.615 673 78 20 911 1563 397846114 397845461 3.570000e-155 558.0
27 TraesCS2B01G034800 chrUn 79.265 844 132 31 996 1813 267776218 267777044 2.150000e-152 549.0
28 TraesCS2B01G034800 chrUn 79.221 847 133 31 996 1816 324119869 324119040 2.150000e-152 549.0
29 TraesCS2B01G034800 chrUn 86.646 322 37 6 3223 3541 316353585 316353267 6.500000e-93 351.0
30 TraesCS2B01G034800 chrUn 86.957 207 18 3 1620 1817 307586795 307586589 1.480000e-54 224.0
31 TraesCS2B01G034800 chrUn 86.957 207 18 3 1620 1817 307590938 307590732 1.480000e-54 224.0
32 TraesCS2B01G034800 chrUn 83.756 197 21 7 711 900 248329690 248329882 4.200000e-40 176.0
33 TraesCS2B01G034800 chrUn 84.828 145 17 3 757 900 397846300 397846160 1.530000e-29 141.0
34 TraesCS2B01G034800 chr1D 79.929 847 125 31 996 1813 2505655 2506485 7.620000e-162 580.0
35 TraesCS2B01G034800 chr1D 89.796 98 6 2 3810 3905 451257337 451257242 5.550000e-24 122.0
36 TraesCS2B01G034800 chr6B 81.452 496 72 11 1326 1811 25571301 25571786 4.960000e-104 388.0
37 TraesCS2B01G034800 chr6B 90.426 94 9 0 3810 3903 682539836 682539929 1.540000e-24 124.0
38 TraesCS2B01G034800 chr6B 81.538 130 16 6 2165 2288 550323246 550323373 2.600000e-17 100.0
39 TraesCS2B01G034800 chr3B 78.215 381 64 14 1088 1455 176783464 176783090 4.110000e-55 226.0
40 TraesCS2B01G034800 chr1B 93.023 86 6 0 3810 3895 169117416 169117331 4.290000e-25 126.0
41 TraesCS2B01G034800 chr5D 84.328 134 14 6 2165 2292 109938314 109938446 1.540000e-24 124.0
42 TraesCS2B01G034800 chr5D 88.889 99 7 2 3810 3906 413675888 413675792 7.180000e-23 119.0
43 TraesCS2B01G034800 chr3A 84.615 130 13 2 2165 2288 220639339 220639467 5.550000e-24 122.0
44 TraesCS2B01G034800 chr7D 89.583 96 8 1 3810 3905 538519050 538519143 2.000000e-23 121.0
45 TraesCS2B01G034800 chr7B 87.255 102 11 1 3810 3909 504211115 504211216 9.290000e-22 115.0
46 TraesCS2B01G034800 chr4A 82.946 129 14 4 2165 2287 575005187 575005061 4.320000e-20 110.0
47 TraesCS2B01G034800 chr6A 83.478 115 17 2 2178 2290 154048638 154048524 5.590000e-19 106.0
48 TraesCS2B01G034800 chr7A 81.203 133 17 5 2165 2290 171374671 171374540 2.600000e-17 100.0
49 TraesCS2B01G034800 chr5A 80.620 129 18 3 2165 2287 643370943 643371070 4.350000e-15 93.5
50 TraesCS2B01G034800 chr3D 96.774 31 1 0 2950 2980 109965887 109965857 7.000000e-03 52.8


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 TraesCS2B01G034800 chr2B 16890749 16894837 4088 False 7552.000000 7552 100.000000 1 4089 1 chr2B.!!$F1 4088
1 TraesCS2B01G034800 chr2B 17347977 17351313 3336 True 1330.000000 3097 89.331667 913 3929 3 chr2B.!!$R2 3016
2 TraesCS2B01G034800 chr2B 17357969 17358811 842 True 492.500000 737 89.381500 1 900 2 chr2B.!!$R3 899
3 TraesCS2B01G034800 chr2B 17265994 17266576 582 True 394.000000 394 79.966000 719 1269 1 chr2B.!!$R1 550
4 TraesCS2B01G034800 chr2A 11899050 11905158 6108 True 1090.400000 3347 88.533400 4 4087 5 chr2A.!!$R1 4083
5 TraesCS2B01G034800 chr2D 11081619 11083917 2298 False 766.666667 1085 88.697000 711 3202 3 chr2D.!!$F2 2491
6 TraesCS2B01G034800 chrUn 257522660 257523281 621 False 763.000000 763 88.836000 1 630 1 chrUn.!!$F1 629
7 TraesCS2B01G034800 chrUn 366986603 366987224 621 False 763.000000 763 88.836000 1 630 1 chrUn.!!$F3 629
8 TraesCS2B01G034800 chrUn 318416841 318417431 590 True 749.000000 749 89.713000 2563 3148 1 chrUn.!!$R2 585
9 TraesCS2B01G034800 chrUn 248329690 248331652 1962 False 700.666667 989 87.079333 711 3113 3 chrUn.!!$F4 2402
10 TraesCS2B01G034800 chrUn 307584394 307590938 6544 True 584.000000 782 87.737833 1620 3148 6 chrUn.!!$R4 1528
11 TraesCS2B01G034800 chrUn 267776218 267777044 826 False 549.000000 549 79.265000 996 1813 1 chrUn.!!$F2 817
12 TraesCS2B01G034800 chrUn 324119040 324119869 829 True 549.000000 549 79.221000 996 1816 1 chrUn.!!$R3 820
13 TraesCS2B01G034800 chrUn 397845461 397846300 839 True 349.500000 558 83.721500 757 1563 2 chrUn.!!$R5 806
14 TraesCS2B01G034800 chr1D 2505655 2506485 830 False 580.000000 580 79.929000 996 1813 1 chr1D.!!$F1 817

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
908 967 0.318762 GGCGGGCGAGATTAGAGATT 59.681 55.000 0.0 0.0 0.0 2.40 F
2170 2574 1.202031 GGTTCTTATGCAAGTTCGGCG 60.202 52.381 0.0 0.0 33.2 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2556 2976 0.182775 AGACAGCCGGTTTTGGAGTT 59.817 50.0 1.90 0.0 0.0 3.01 R
3500 5896 0.174845 CCAAGTTAGTCGCGATCCCA 59.825 55.0 14.06 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
55 56 6.371809 TGACATGTAACTGAGGTTTGAAAC 57.628 37.500 0.00 0.00 36.92 2.78
59 60 5.728351 TGTAACTGAGGTTTGAAACTTCG 57.272 39.130 14.20 11.44 40.08 3.79
63 64 3.442273 ACTGAGGTTTGAAACTTCGCAAA 59.558 39.130 14.20 0.00 40.08 3.68
78 79 9.862585 AAACTTCGCAAATAAATGTTGAAAATC 57.137 25.926 0.00 0.00 0.00 2.17
240 245 9.448438 TGCCTAAAATATAGCGAATCAATACAT 57.552 29.630 0.00 0.00 0.00 2.29
356 361 9.054922 CATTTCACATTGTTCCTTAATTTGGTT 57.945 29.630 0.00 0.00 0.00 3.67
424 431 2.579684 GAACCCTCAGGATTCGCGCT 62.580 60.000 5.56 0.00 36.73 5.92
426 433 1.884926 CCCTCAGGATTCGCGCTTC 60.885 63.158 5.56 0.00 33.47 3.86
433 440 1.812571 AGGATTCGCGCTTCAATTTGT 59.187 42.857 5.56 0.00 0.00 2.83
444 451 4.025896 CGCTTCAATTTGTTGTTTCATGCA 60.026 37.500 0.00 0.00 0.00 3.96
557 564 5.246203 AGGATTTGAACCCTTAGGCTTTTTC 59.754 40.000 0.00 0.00 36.11 2.29
560 568 2.178106 TGAACCCTTAGGCTTTTTCCCA 59.822 45.455 0.00 0.00 36.11 4.37
583 591 2.954318 AGGGATTGCATTGCACTATGTC 59.046 45.455 11.66 4.94 38.71 3.06
593 601 5.163854 GCATTGCACTATGTCTAAACGAACT 60.164 40.000 3.15 0.00 0.00 3.01
630 638 8.621286 ACAACTATACTTTGTTTTTCCTGTGAG 58.379 33.333 0.00 0.00 33.23 3.51
631 639 8.836413 CAACTATACTTTGTTTTTCCTGTGAGA 58.164 33.333 0.00 0.00 0.00 3.27
635 643 6.149129 ACTTTGTTTTTCCTGTGAGATTCC 57.851 37.500 0.00 0.00 0.00 3.01
659 667 7.440856 TCCAAACAGTCTTTAATGCAAATTTCC 59.559 33.333 0.00 0.00 0.00 3.13
678 686 1.529226 CGTGGCTTTCCAACCATACA 58.471 50.000 0.00 0.00 45.53 2.29
679 687 1.468520 CGTGGCTTTCCAACCATACAG 59.531 52.381 0.00 0.00 45.53 2.74
680 688 2.514803 GTGGCTTTCCAACCATACAGT 58.485 47.619 0.00 0.00 45.53 3.55
681 689 3.681593 GTGGCTTTCCAACCATACAGTA 58.318 45.455 0.00 0.00 45.53 2.74
682 690 4.270008 GTGGCTTTCCAACCATACAGTAT 58.730 43.478 0.00 0.00 45.53 2.12
683 691 4.705023 GTGGCTTTCCAACCATACAGTATT 59.295 41.667 0.00 0.00 45.53 1.89
684 692 4.947388 TGGCTTTCCAACCATACAGTATTC 59.053 41.667 0.00 0.00 39.99 1.75
685 693 4.947388 GGCTTTCCAACCATACAGTATTCA 59.053 41.667 0.00 0.00 0.00 2.57
686 694 5.417580 GGCTTTCCAACCATACAGTATTCAA 59.582 40.000 0.00 0.00 0.00 2.69
687 695 6.322491 GCTTTCCAACCATACAGTATTCAAC 58.678 40.000 0.00 0.00 0.00 3.18
688 696 6.072175 GCTTTCCAACCATACAGTATTCAACA 60.072 38.462 0.00 0.00 0.00 3.33
689 697 6.811253 TTCCAACCATACAGTATTCAACAC 57.189 37.500 0.00 0.00 0.00 3.32
690 698 6.121776 TCCAACCATACAGTATTCAACACT 57.878 37.500 0.00 0.00 0.00 3.55
691 699 7.247456 TCCAACCATACAGTATTCAACACTA 57.753 36.000 0.00 0.00 0.00 2.74
692 700 7.101054 TCCAACCATACAGTATTCAACACTAC 58.899 38.462 0.00 0.00 0.00 2.73
693 701 6.876789 CCAACCATACAGTATTCAACACTACA 59.123 38.462 0.00 0.00 0.00 2.74
694 702 7.552687 CCAACCATACAGTATTCAACACTACAT 59.447 37.037 0.00 0.00 0.00 2.29
695 703 8.946085 CAACCATACAGTATTCAACACTACATT 58.054 33.333 0.00 0.00 0.00 2.71
696 704 9.515226 AACCATACAGTATTCAACACTACATTT 57.485 29.630 0.00 0.00 0.00 2.32
697 705 9.515226 ACCATACAGTATTCAACACTACATTTT 57.485 29.630 0.00 0.00 0.00 1.82
776 789 3.137533 GCTAGTGGCCAATTTTGCAAAA 58.862 40.909 25.76 25.76 34.27 2.44
795 808 2.231215 AGCATCTGTGGACGATTAGC 57.769 50.000 0.00 0.00 0.00 3.09
796 809 1.759445 AGCATCTGTGGACGATTAGCT 59.241 47.619 0.00 0.00 0.00 3.32
797 810 2.959030 AGCATCTGTGGACGATTAGCTA 59.041 45.455 0.00 0.00 0.00 3.32
798 811 3.005261 AGCATCTGTGGACGATTAGCTAG 59.995 47.826 0.00 0.00 0.00 3.42
908 967 0.318762 GGCGGGCGAGATTAGAGATT 59.681 55.000 0.00 0.00 0.00 2.40
976 1056 2.238521 TCTTCTGCCCATGTTTCAACC 58.761 47.619 0.00 0.00 0.00 3.77
1307 1421 2.076100 CTGGAAAACGCAGCAGTCATA 58.924 47.619 0.00 0.00 0.00 2.15
1322 1436 9.910511 GCAGCAGTCATAAATTTTATGATTTTG 57.089 29.630 26.45 23.69 36.48 2.44
1373 1491 4.467084 CGTATGTGCCGCCCACCT 62.467 66.667 2.58 0.00 44.01 4.00
1385 1503 3.215568 CCACCTTGGCGCACAACA 61.216 61.111 10.83 0.00 34.76 3.33
1782 1939 4.709886 TCAGATCCTTCGTTCCAGATGTTA 59.290 41.667 0.00 0.00 0.00 2.41
2022 2426 6.929625 TGAGAAAACATTTGAACCTGAAACA 58.070 32.000 0.00 0.00 0.00 2.83
2075 2479 9.382275 ACTATGTGCAGAATTGTTTTTCTTTTT 57.618 25.926 0.00 0.00 33.69 1.94
2161 2565 2.279741 GCATCGACTGGTTCTTATGCA 58.720 47.619 0.00 0.00 39.42 3.96
2162 2566 2.677836 GCATCGACTGGTTCTTATGCAA 59.322 45.455 0.00 0.00 39.42 4.08
2163 2567 3.242543 GCATCGACTGGTTCTTATGCAAG 60.243 47.826 0.00 0.00 39.42 4.01
2170 2574 1.202031 GGTTCTTATGCAAGTTCGGCG 60.202 52.381 0.00 0.00 33.20 6.46
2194 2598 3.501445 ACTCTAGTGCTTTTACTCGTCGT 59.499 43.478 0.00 0.00 32.19 4.34
2230 2640 5.508153 CGGACCTGGATGTTACTTCTGATAG 60.508 48.000 0.00 0.00 0.00 2.08
2238 2648 7.819415 TGGATGTTACTTCTGATAGTCTTTGTG 59.181 37.037 0.00 0.00 0.00 3.33
2279 2689 6.762108 TGAATAGATCGAAAGTTTTTCTCGC 58.238 36.000 0.00 0.00 32.66 5.03
2535 2955 1.619654 CATCCTGACCAAGTTTGCCA 58.380 50.000 0.00 0.00 0.00 4.92
2556 2976 2.986290 CCCCACCGTCAGCATACA 59.014 61.111 0.00 0.00 0.00 2.29
2612 3032 2.032071 GGGCTGTACCACAACGCT 59.968 61.111 0.00 0.00 42.05 5.07
2711 3131 2.252535 TCATGGAGATGGTGGAGTCA 57.747 50.000 0.00 0.00 0.00 3.41
2734 3154 1.804151 GCACAAGTTCGGTTAGCATCA 59.196 47.619 0.00 0.00 0.00 3.07
2757 4591 4.287067 ACCAACTCTGCTGGAAGAATCTAA 59.713 41.667 0.00 0.00 37.40 2.10
2763 4597 7.278875 ACTCTGCTGGAAGAATCTAAATTAGG 58.721 38.462 0.00 0.00 34.07 2.69
2791 4637 3.065786 AGCACATAGGCAAAATGTCATCG 59.934 43.478 0.00 0.00 35.39 3.84
2845 4705 1.264288 GCAGGTTTTGAAGAGGACGTG 59.736 52.381 0.00 0.00 0.00 4.49
2851 4711 4.933400 GGTTTTGAAGAGGACGTGCTTATA 59.067 41.667 12.08 0.00 0.00 0.98
2893 4753 0.739561 GGTACGGAATGAGCTCGACT 59.260 55.000 9.64 0.00 0.00 4.18
3098 4958 3.650942 TCACAGAATATAGGGGCCGAAAT 59.349 43.478 0.00 0.00 0.00 2.17
3107 4967 1.417890 AGGGGCCGAAATAGTGATGAG 59.582 52.381 0.00 0.00 0.00 2.90
3131 4992 7.562135 AGGTAAGTGAGCCGAAAGATAATTTA 58.438 34.615 0.00 0.00 0.00 1.40
3138 4999 7.656137 GTGAGCCGAAAGATAATTTATCCAGTA 59.344 37.037 11.89 0.00 35.79 2.74
3154 5015 6.605471 ATCCAGTAGATAGTTTGACACACA 57.395 37.500 0.00 0.00 31.60 3.72
3241 5422 9.279904 TCAAGTTTTAATTGTTTACTGTCGTTG 57.720 29.630 0.00 0.00 0.00 4.10
3303 5698 5.284079 GTTCAGCTTCATGTTTGTGTTCAT 58.716 37.500 0.00 0.00 0.00 2.57
3309 5704 2.551887 TCATGTTTGTGTTCATGGTCCG 59.448 45.455 0.00 0.00 40.94 4.79
3312 5707 1.070175 GTTTGTGTTCATGGTCCGACG 60.070 52.381 0.00 0.00 0.00 5.12
3350 5746 1.593196 CACGGGTGAGCTTTCTTTGA 58.407 50.000 0.00 0.00 0.00 2.69
3394 5790 2.679716 GACTGGCAAGCCCTGGAT 59.320 61.111 8.89 0.00 36.90 3.41
3397 5793 1.153005 CTGGCAAGCCCTGGATCTC 60.153 63.158 8.89 0.00 34.56 2.75
3402 5798 0.907486 CAAGCCCTGGATCTCACAGA 59.093 55.000 0.00 0.00 38.20 3.41
3431 5827 3.199071 TCAAACCCGTGCTAACCAGATAT 59.801 43.478 0.00 0.00 0.00 1.63
3435 5831 2.555325 CCCGTGCTAACCAGATATACGA 59.445 50.000 0.00 0.00 32.36 3.43
3458 5854 9.877178 ACGAACTTCTGACTATATCTTCAAATT 57.123 29.630 0.00 0.00 0.00 1.82
3486 5882 4.039004 TGCATTTTTGTAGCATTGACACCT 59.961 37.500 0.00 0.00 32.55 4.00
3499 5895 2.441410 TGACACCTGCTCTCTAGACAG 58.559 52.381 2.55 2.55 0.00 3.51
3500 5896 2.224892 TGACACCTGCTCTCTAGACAGT 60.225 50.000 7.77 0.00 0.00 3.55
3507 5903 1.606668 GCTCTCTAGACAGTGGGATCG 59.393 57.143 0.00 0.00 0.00 3.69
3513 5909 0.393944 AGACAGTGGGATCGCGACTA 60.394 55.000 12.93 0.00 0.00 2.59
3518 5914 1.135083 AGTGGGATCGCGACTAACTTG 60.135 52.381 12.93 0.00 0.00 3.16
3529 5925 5.062934 TCGCGACTAACTTGGTCATAAAATG 59.937 40.000 3.71 0.00 33.73 2.32
3532 5928 6.674760 GCGACTAACTTGGTCATAAAATGGAC 60.675 42.308 6.15 0.00 33.73 4.02
3534 5930 6.235664 ACTAACTTGGTCATAAAATGGACGT 58.764 36.000 0.00 0.00 34.87 4.34
3542 5938 6.315144 TGGTCATAAAATGGACGTGATAACTG 59.685 38.462 0.00 0.00 34.87 3.16
3546 5942 3.610040 AATGGACGTGATAACTGCTGA 57.390 42.857 0.00 0.00 0.00 4.26
3550 5946 0.038618 ACGTGATAACTGCTGACGCA 60.039 50.000 0.00 0.00 45.60 5.24
3578 5974 1.017387 CACTTAGCCGCAGATTTCCC 58.983 55.000 0.00 0.00 0.00 3.97
3594 5990 1.507140 TCCCGATCTACTGGCCATTT 58.493 50.000 5.51 0.00 0.00 2.32
3612 6008 5.427378 CCATTTGGTGGTCTTTTTCACTTT 58.573 37.500 0.00 0.00 43.44 2.66
3618 6014 6.394809 TGGTGGTCTTTTTCACTTTCTTTTC 58.605 36.000 0.00 0.00 34.57 2.29
3640 6077 8.710835 TTTCATAGTTGAACTTGTCGCATATA 57.289 30.769 1.97 0.00 41.50 0.86
3702 6147 0.867086 CCCAAAAGGCACGCAATTTG 59.133 50.000 10.22 10.22 33.62 2.32
3708 6158 0.238289 AGGCACGCAATTTGAGAACG 59.762 50.000 7.16 0.20 0.00 3.95
3709 6159 0.237235 GGCACGCAATTTGAGAACGA 59.763 50.000 7.16 0.00 0.00 3.85
3719 6169 6.290026 CGCAATTTGAGAACGATTTGTATTCG 60.290 38.462 0.00 0.00 42.20 3.34
3732 6182 3.822594 TGTATTCGCGTGAAAAAGCAT 57.177 38.095 16.40 0.15 37.71 3.79
3755 6205 9.054922 GCATGGCCATTTATAAAATGTTAATGT 57.945 29.630 17.92 0.00 0.00 2.71
3775 6225 4.667262 TGTATTTAATCCGTGTGCATTGC 58.333 39.130 0.46 0.46 0.00 3.56
3778 6228 1.819928 TAATCCGTGTGCATTGCAGT 58.180 45.000 12.53 0.00 40.08 4.40
3895 8443 7.801716 ATAAGACACGTATTACCATGCAAAT 57.198 32.000 0.00 0.00 0.00 2.32
3896 8444 5.484173 AGACACGTATTACCATGCAAATG 57.516 39.130 0.00 0.00 0.00 2.32
3897 8445 5.182487 AGACACGTATTACCATGCAAATGA 58.818 37.500 0.00 0.00 0.00 2.57
3898 8446 5.645929 AGACACGTATTACCATGCAAATGAA 59.354 36.000 0.00 0.00 0.00 2.57
3940 8488 3.118665 TGCTCTGCTACACAATGCTGATA 60.119 43.478 0.00 0.00 36.75 2.15
3967 8515 5.181009 TGGTCAATTCTAGATGCTTCACTG 58.819 41.667 2.07 0.00 0.00 3.66
3989 8537 1.699656 GCACATTGCAGTCGAGCGAT 61.700 55.000 0.00 0.00 44.26 4.58
4010 8558 1.162698 CACCATCAGCTCACCACTTG 58.837 55.000 0.00 0.00 0.00 3.16
4017 8565 2.623915 GCTCACCACTTGCAGCAGG 61.624 63.158 2.26 2.26 31.99 4.85
4088 9454 3.425014 AACCACACTGCCCCCACA 61.425 61.111 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 5.620206 TCAAACCTCAGTTACATGTCATGT 58.380 37.500 21.70 21.70 46.92 3.21
41 42 2.639065 TGCGAAGTTTCAAACCTCAGT 58.361 42.857 0.00 0.00 0.00 3.41
42 43 3.691049 TTGCGAAGTTTCAAACCTCAG 57.309 42.857 0.00 0.00 0.00 3.35
45 46 6.983890 ACATTTATTTGCGAAGTTTCAAACCT 59.016 30.769 0.00 0.00 35.34 3.50
55 56 9.731519 GAAGATTTTCAACATTTATTTGCGAAG 57.268 29.630 0.00 0.00 33.38 3.79
59 60 9.269415 GCATGAAGATTTTCAACATTTATTTGC 57.731 29.630 2.39 1.74 45.82 3.68
237 242 8.907222 AAGATCAAAGTTTGGCATTTTTATGT 57.093 26.923 15.47 0.00 0.00 2.29
376 383 5.339990 CAACGGACCAAATAAATGATGTCC 58.660 41.667 0.00 0.00 39.07 4.02
392 399 1.810755 GAGGGTTCAAATCCAACGGAC 59.189 52.381 0.00 0.00 32.98 4.79
394 401 1.812571 CTGAGGGTTCAAATCCAACGG 59.187 52.381 0.00 0.00 31.69 4.44
424 431 4.272991 GCCTGCATGAAACAACAAATTGAA 59.727 37.500 0.00 0.00 39.30 2.69
426 433 3.810941 AGCCTGCATGAAACAACAAATTG 59.189 39.130 0.00 0.00 41.98 2.32
433 440 4.405116 AAAAGAAGCCTGCATGAAACAA 57.595 36.364 0.00 0.00 0.00 2.83
557 564 1.342174 GTGCAATGCAATCCCTATGGG 59.658 52.381 10.44 0.00 42.14 4.00
560 568 4.733165 ACATAGTGCAATGCAATCCCTAT 58.267 39.130 12.63 10.65 41.47 2.57
630 638 7.945033 TTTGCATTAAAGACTGTTTGGAATC 57.055 32.000 0.00 0.00 0.00 2.52
631 639 8.907222 AATTTGCATTAAAGACTGTTTGGAAT 57.093 26.923 0.00 0.00 0.00 3.01
634 642 7.569226 CGGAAATTTGCATTAAAGACTGTTTGG 60.569 37.037 10.49 0.00 0.00 3.28
635 643 7.042791 ACGGAAATTTGCATTAAAGACTGTTTG 60.043 33.333 10.49 0.00 0.00 2.93
659 667 1.468520 CTGTATGGTTGGAAAGCCACG 59.531 52.381 0.00 0.00 45.94 4.94
699 707 6.371809 AGTGTTGAATACTTCTCGCAAAAA 57.628 33.333 0.00 0.00 0.00 1.94
700 708 6.480651 TGTAGTGTTGAATACTTCTCGCAAAA 59.519 34.615 0.00 0.00 0.00 2.44
701 709 5.986741 TGTAGTGTTGAATACTTCTCGCAAA 59.013 36.000 0.00 0.00 0.00 3.68
702 710 5.534407 TGTAGTGTTGAATACTTCTCGCAA 58.466 37.500 0.00 0.00 0.00 4.85
703 711 5.128992 TGTAGTGTTGAATACTTCTCGCA 57.871 39.130 0.00 0.00 0.00 5.10
704 712 7.274904 TGTTATGTAGTGTTGAATACTTCTCGC 59.725 37.037 0.00 0.00 0.00 5.03
705 713 8.584600 GTGTTATGTAGTGTTGAATACTTCTCG 58.415 37.037 0.00 0.00 0.00 4.04
706 714 9.640963 AGTGTTATGTAGTGTTGAATACTTCTC 57.359 33.333 0.00 0.00 0.00 2.87
707 715 9.640963 GAGTGTTATGTAGTGTTGAATACTTCT 57.359 33.333 0.00 0.00 0.00 2.85
708 716 9.640963 AGAGTGTTATGTAGTGTTGAATACTTC 57.359 33.333 0.00 0.00 0.00 3.01
739 747 8.217799 TGGCCACTAGCACTAAGAAAAATATAT 58.782 33.333 0.00 0.00 46.50 0.86
750 762 3.056891 GCAAAATTGGCCACTAGCACTAA 60.057 43.478 3.88 0.00 46.50 2.24
776 789 1.759445 AGCTAATCGTCCACAGATGCT 59.241 47.619 0.00 0.00 0.00 3.79
795 808 0.242825 TTGTCGAACCGCAGTCCTAG 59.757 55.000 0.00 0.00 0.00 3.02
796 809 0.675083 TTTGTCGAACCGCAGTCCTA 59.325 50.000 0.00 0.00 0.00 2.94
797 810 0.878961 GTTTGTCGAACCGCAGTCCT 60.879 55.000 0.00 0.00 31.85 3.85
798 811 1.155424 TGTTTGTCGAACCGCAGTCC 61.155 55.000 0.31 0.00 37.45 3.85
900 922 8.585881 ACAAACAACTACTCTGCTAATCTCTAA 58.414 33.333 0.00 0.00 0.00 2.10
908 967 9.555727 AAGAATAAACAAACAACTACTCTGCTA 57.444 29.630 0.00 0.00 0.00 3.49
976 1056 3.186909 TGACCGTTTAATGATGAGCGAG 58.813 45.455 0.00 0.00 0.00 5.03
1322 1436 1.538047 TCAGCTGCTCCCACAAATTC 58.462 50.000 9.47 0.00 0.00 2.17
1373 1491 4.268939 GCTGCTGTTGTGCGCCAA 62.269 61.111 4.18 6.02 35.36 4.52
1577 1705 0.767375 AGCTACGGATGCCCATGAAT 59.233 50.000 0.00 0.00 0.00 2.57
1782 1939 0.244994 GCGATGGAGATGGTAGCGAT 59.755 55.000 0.00 0.00 0.00 4.58
2022 2426 4.038282 ACTTGTGTGATGTTGATGTGCAAT 59.962 37.500 0.00 0.00 39.03 3.56
2075 2479 7.006187 TCGTTTTATATATTTCTGTTGCGCA 57.994 32.000 5.66 5.66 0.00 6.09
2161 2565 0.388649 CACTAGAGTGCGCCGAACTT 60.389 55.000 4.18 0.00 39.39 2.66
2162 2566 1.213013 CACTAGAGTGCGCCGAACT 59.787 57.895 4.18 0.00 39.39 3.01
2163 2567 3.768632 CACTAGAGTGCGCCGAAC 58.231 61.111 4.18 0.00 39.39 3.95
2230 2640 5.932303 TCAACTATCAAGGTAGCACAAAGAC 59.068 40.000 0.00 0.00 0.00 3.01
2238 2648 9.364989 GATCTATTCATCAACTATCAAGGTAGC 57.635 37.037 0.00 0.00 0.00 3.58
2468 2888 4.830573 GGAACCAGCAGGCTTCTT 57.169 55.556 0.00 0.00 39.06 2.52
2547 2967 2.811431 CGGTTTTGGAGTTGTATGCTGA 59.189 45.455 0.00 0.00 0.00 4.26
2556 2976 0.182775 AGACAGCCGGTTTTGGAGTT 59.817 50.000 1.90 0.00 0.00 3.01
2631 3051 4.351054 CTTGGCCCGGAGCTTGGT 62.351 66.667 0.73 0.00 43.05 3.67
2690 3110 2.702478 TGACTCCACCATCTCCATGATC 59.298 50.000 0.00 0.00 32.05 2.92
2734 3154 2.641815 AGATTCTTCCAGCAGAGTTGGT 59.358 45.455 0.00 0.00 37.02 3.67
2778 4617 2.228822 ACCTTCCACGATGACATTTTGC 59.771 45.455 0.00 0.00 0.00 3.68
2791 4637 0.661020 CAACGTCAACCACCTTCCAC 59.339 55.000 0.00 0.00 0.00 4.02
2845 4705 2.555199 CCTCCACAGCACACTATAAGC 58.445 52.381 0.00 0.00 0.00 3.09
2851 4711 3.958860 GGCCCTCCACAGCACACT 61.959 66.667 0.00 0.00 0.00 3.55
2869 4729 0.460311 AGCTCATTCCGTACCTTCCG 59.540 55.000 0.00 0.00 0.00 4.30
3098 4958 2.688446 CGGCTCACTTACCTCATCACTA 59.312 50.000 0.00 0.00 0.00 2.74
3107 4967 6.679327 AAATTATCTTTCGGCTCACTTACC 57.321 37.500 0.00 0.00 0.00 2.85
3131 4992 6.605471 TGTGTGTCAAACTATCTACTGGAT 57.395 37.500 0.00 0.00 38.38 3.41
3138 4999 3.059884 CACGCTGTGTGTCAAACTATCT 58.940 45.455 13.01 0.00 43.88 1.98
3154 5015 1.616159 ACAAATTACTTGGCCACGCT 58.384 45.000 3.88 0.00 39.56 5.07
3159 5332 5.336451 CCTTCAGGTAACAAATTACTTGGCC 60.336 44.000 0.00 0.00 44.52 5.36
3241 5422 9.452065 GAAAAGAAAATGACAGGACTCTAAAAC 57.548 33.333 0.00 0.00 0.00 2.43
3303 5698 1.399440 CGAGAATAAGACGTCGGACCA 59.601 52.381 10.46 0.00 0.00 4.02
3334 5729 2.713895 GCTTCAAAGAAAGCTCACCC 57.286 50.000 1.51 0.00 46.51 4.61
3350 5746 3.131046 CCAGAACCTCACAAACAAAGCTT 59.869 43.478 0.00 0.00 0.00 3.74
3394 5790 4.994852 CGGGTTTGAATAAACTCTGTGAGA 59.005 41.667 1.25 0.00 43.62 3.27
3397 5793 4.783242 CACGGGTTTGAATAAACTCTGTG 58.217 43.478 13.59 13.59 43.62 3.66
3402 5798 4.216902 GGTTAGCACGGGTTTGAATAAACT 59.783 41.667 0.00 0.00 44.39 2.66
3435 5831 9.620259 GGGAATTTGAAGATATAGTCAGAAGTT 57.380 33.333 0.00 0.00 0.00 2.66
3458 5854 4.282957 TCAATGCTACAAAAATGCAAGGGA 59.717 37.500 0.00 0.00 40.24 4.20
3486 5882 2.660572 GATCCCACTGTCTAGAGAGCA 58.339 52.381 16.49 0.00 0.00 4.26
3499 5895 1.278238 CAAGTTAGTCGCGATCCCAC 58.722 55.000 14.06 7.35 0.00 4.61
3500 5896 0.174845 CCAAGTTAGTCGCGATCCCA 59.825 55.000 14.06 0.00 0.00 4.37
3507 5903 5.353123 TCCATTTTATGACCAAGTTAGTCGC 59.647 40.000 0.00 0.00 37.04 5.19
3513 5909 5.067273 TCACGTCCATTTTATGACCAAGTT 58.933 37.500 0.00 0.00 0.00 2.66
3518 5914 6.715464 CAGTTATCACGTCCATTTTATGACC 58.285 40.000 0.00 0.00 0.00 4.02
3529 5925 1.269166 CGTCAGCAGTTATCACGTCC 58.731 55.000 0.00 0.00 0.00 4.79
3546 5942 2.544685 GCTAAGTGAGATGACATGCGT 58.455 47.619 0.00 0.00 0.00 5.24
3550 5946 1.482182 TGCGGCTAAGTGAGATGACAT 59.518 47.619 0.00 0.00 0.00 3.06
3564 5960 1.227674 GATCGGGAAATCTGCGGCT 60.228 57.895 0.00 0.00 0.00 5.52
3578 5974 1.942657 CACCAAATGGCCAGTAGATCG 59.057 52.381 13.05 0.00 39.32 3.69
3594 5990 5.993748 AAAGAAAGTGAAAAAGACCACCA 57.006 34.783 0.00 0.00 34.00 4.17
3612 6008 5.525745 TGCGACAAGTTCAACTATGAAAAGA 59.474 36.000 0.00 0.00 46.66 2.52
3618 6014 9.373750 CAATTATATGCGACAAGTTCAACTATG 57.626 33.333 0.00 0.00 0.00 2.23
3700 6145 3.676172 ACGCGAATACAAATCGTTCTCAA 59.324 39.130 15.93 0.00 42.15 3.02
3702 6147 3.302434 TCACGCGAATACAAATCGTTCTC 59.698 43.478 15.93 0.00 42.15 2.87
3708 6158 4.615121 TGCTTTTTCACGCGAATACAAATC 59.385 37.500 15.93 1.49 0.00 2.17
3709 6159 4.541779 TGCTTTTTCACGCGAATACAAAT 58.458 34.783 15.93 0.00 0.00 2.32
3719 6169 0.390209 ATGGCCATGCTTTTTCACGC 60.390 50.000 20.04 0.00 0.00 5.34
3755 6205 4.397730 ACTGCAATGCACACGGATTAAATA 59.602 37.500 2.72 0.00 33.79 1.40
3767 6217 1.081892 ATCACTCGACTGCAATGCAC 58.918 50.000 2.72 0.00 33.79 4.57
3775 6225 2.802247 TGCTTGACAAATCACTCGACTG 59.198 45.455 0.00 0.00 33.38 3.51
3778 6228 2.832563 TGTGCTTGACAAATCACTCGA 58.167 42.857 16.46 0.00 34.27 4.04
3898 8446 9.107177 CAGAGCATCATCTAGAACTATGTTTTT 57.893 33.333 0.00 0.00 37.82 1.94
3905 8453 6.016693 GTGTAGCAGAGCATCATCTAGAACTA 60.017 42.308 0.00 0.00 37.82 2.24
3917 8465 2.014857 CAGCATTGTGTAGCAGAGCAT 58.985 47.619 0.00 0.00 33.14 3.79
3940 8488 8.216423 AGTGAAGCATCTAGAATTGACCATTAT 58.784 33.333 0.00 0.00 0.00 1.28
3989 8537 0.837691 AGTGGTGAGCTGATGGTGGA 60.838 55.000 0.00 0.00 0.00 4.02
4010 8558 1.275856 CTCCTAGATCCATCCTGCTGC 59.724 57.143 0.00 0.00 0.00 5.25
4017 8565 2.301583 GGCTTCACCTCCTAGATCCATC 59.698 54.545 0.00 0.00 34.51 3.51
4062 9428 1.904865 CAGTGTGGTTGCCAGCCAT 60.905 57.895 2.78 0.00 38.40 4.40


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

AutoCloner maintained by Alex Coulton.