Multiple sequence alignment - TraesCS5D01G297500

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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 TraesCS5D01G297500 chr5D 100.000 2846 0 0 1 2846 394282066 394279221 0.000000e+00 5256.0
1 TraesCS5D01G297500 chr5D 83.623 1380 111 66 426 1785 394549526 394548242 0.000000e+00 1190.0
2 TraesCS5D01G297500 chr5D 83.478 1380 111 66 426 1785 394551537 394550255 0.000000e+00 1177.0
3 TraesCS5D01G297500 chr5D 83.766 887 67 34 1935 2798 394241957 394241125 0.000000e+00 769.0
4 TraesCS5D01G297500 chr5D 85.876 531 31 16 2283 2795 394533554 394533050 2.510000e-145 525.0
5 TraesCS5D01G297500 chr5D 85.124 363 24 15 333 676 394583796 394583445 7.550000e-91 344.0
6 TraesCS5D01G297500 chr5D 85.321 327 21 10 354 657 394563731 394563409 2.130000e-81 313.0
7 TraesCS5D01G297500 chr5D 91.500 200 13 3 1589 1785 394242299 394242101 3.610000e-69 272.0
8 TraesCS5D01G297500 chr5D 77.692 390 43 18 749 1106 394563369 394562992 6.220000e-47 198.0
9 TraesCS5D01G297500 chr5D 81.746 252 16 10 1206 1454 394190509 394190285 1.740000e-42 183.0
10 TraesCS5D01G297500 chr5D 80.345 290 14 19 849 1106 394583347 394583069 2.250000e-41 180.0
11 TraesCS5D01G297500 chr5D 89.437 142 6 4 965 1106 394559709 394559577 1.360000e-38 171.0
12 TraesCS5D01G297500 chr5D 86.400 125 13 2 1457 1581 394163027 394162907 1.780000e-27 134.0
13 TraesCS5D01G297500 chr5D 88.679 53 4 1 2722 2774 394189083 394189033 2.370000e-06 63.9
14 TraesCS5D01G297500 chr5A 83.948 1545 123 61 292 1785 496567286 496565816 0.000000e+00 1363.0
15 TraesCS5D01G297500 chr5A 83.768 844 46 27 978 1785 496205023 496204235 0.000000e+00 715.0
16 TraesCS5D01G297500 chr5A 86.559 372 24 9 2215 2563 496565542 496565174 1.240000e-103 387.0
17 TraesCS5D01G297500 chr5A 90.441 272 14 5 426 693 496284632 496284369 5.840000e-92 348.0
18 TraesCS5D01G297500 chr5A 90.476 189 15 3 2608 2796 496564835 496564650 2.190000e-61 246.0
19 TraesCS5D01G297500 chr5A 83.784 259 26 12 7 257 496285125 496284875 6.130000e-57 231.0
20 TraesCS5D01G297500 chr5A 75.283 619 69 52 1209 1781 496175492 496174912 4.770000e-53 219.0
21 TraesCS5D01G297500 chr5A 80.818 318 24 14 1 288 496569804 496569494 6.180000e-52 215.0
22 TraesCS5D01G297500 chr5A 80.268 299 22 20 2262 2545 496199291 496199015 1.040000e-44 191.0
23 TraesCS5D01G297500 chr5A 80.000 255 18 17 1206 1454 496536466 496536239 1.060000e-34 158.0
24 TraesCS5D01G297500 chr5A 88.119 101 12 0 1457 1557 496134934 496134834 1.380000e-23 121.0
25 TraesCS5D01G297500 chr5A 87.037 54 6 1 2722 2774 496533571 496533518 3.060000e-05 60.2
26 TraesCS5D01G297500 chr5B 81.620 1556 130 72 461 1956 474454165 474452706 0.000000e+00 1146.0
27 TraesCS5D01G297500 chr5B 83.922 877 63 46 944 1783 474279252 474278417 0.000000e+00 767.0
28 TraesCS5D01G297500 chr5B 79.655 1042 93 60 996 2002 428853102 428854059 8.600000e-180 640.0
29 TraesCS5D01G297500 chr5B 81.141 859 79 38 1952 2768 474452610 474451793 1.870000e-171 612.0
30 TraesCS5D01G297500 chr5B 82.391 778 59 40 2010 2771 474274765 474274050 8.720000e-170 606.0
31 TraesCS5D01G297500 chr5B 86.029 544 45 10 2265 2795 474268075 474267550 3.200000e-154 555.0
32 TraesCS5D01G297500 chr5B 85.558 457 32 14 289 723 428851939 428852383 5.590000e-122 448.0
33 TraesCS5D01G297500 chr5B 88.800 250 18 4 426 673 474301330 474301089 5.960000e-77 298.0
34 TraesCS5D01G297500 chr5B 84.058 276 23 7 3 257 428851370 428851645 2.190000e-61 246.0
35 TraesCS5D01G297500 chr5B 81.928 249 15 12 1209 1454 474056330 474056109 1.740000e-42 183.0
36 TraesCS5D01G297500 chr5B 91.262 103 8 1 1459 1561 474047667 474047566 3.820000e-29 139.0
37 TraesCS5D01G297500 chr5B 86.792 53 5 1 2722 2774 474054952 474054902 1.100000e-04 58.4
38 TraesCS5D01G297500 chrUn 81.967 976 90 43 827 1785 332176690 332175784 0.000000e+00 749.0
39 TraesCS5D01G297500 chrUn 85.627 327 20 10 354 657 211147911 211147589 4.580000e-83 318.0
40 TraesCS5D01G297500 chrUn 77.949 390 42 18 749 1106 211147549 211147172 1.340000e-48 204.0


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 TraesCS5D01G297500 chr5D 394279221 394282066 2845 True 5256.000000 5256 100.000000 1 2846 1 chr5D.!!$R2 2845
1 TraesCS5D01G297500 chr5D 394548242 394551537 3295 True 1183.500000 1190 83.550500 426 1785 2 chr5D.!!$R6 1359
2 TraesCS5D01G297500 chr5D 394533050 394533554 504 True 525.000000 525 85.876000 2283 2795 1 chr5D.!!$R3 512
3 TraesCS5D01G297500 chr5D 394241125 394242299 1174 True 520.500000 769 87.633000 1589 2798 2 chr5D.!!$R5 1209
4 TraesCS5D01G297500 chr5D 394583069 394583796 727 True 262.000000 344 82.734500 333 1106 2 chr5D.!!$R8 773
5 TraesCS5D01G297500 chr5D 394559577 394563731 4154 True 227.333333 313 84.150000 354 1106 3 chr5D.!!$R7 752
6 TraesCS5D01G297500 chr5A 496204235 496205023 788 True 715.000000 715 83.768000 978 1785 1 chr5A.!!$R4 807
7 TraesCS5D01G297500 chr5A 496564650 496569804 5154 True 552.750000 1363 85.450250 1 2796 4 chr5A.!!$R7 2795
8 TraesCS5D01G297500 chr5A 496284369 496285125 756 True 289.500000 348 87.112500 7 693 2 chr5A.!!$R5 686
9 TraesCS5D01G297500 chr5A 496174912 496175492 580 True 219.000000 219 75.283000 1209 1781 1 chr5A.!!$R2 572
10 TraesCS5D01G297500 chr5B 474451793 474454165 2372 True 879.000000 1146 81.380500 461 2768 2 chr5B.!!$R6 2307
11 TraesCS5D01G297500 chr5B 474274050 474279252 5202 True 686.500000 767 83.156500 944 2771 2 chr5B.!!$R5 1827
12 TraesCS5D01G297500 chr5B 474267550 474268075 525 True 555.000000 555 86.029000 2265 2795 1 chr5B.!!$R2 530
13 TraesCS5D01G297500 chr5B 428851370 428854059 2689 False 444.666667 640 83.090333 3 2002 3 chr5B.!!$F1 1999
14 TraesCS5D01G297500 chrUn 332175784 332176690 906 True 749.000000 749 81.967000 827 1785 1 chrUn.!!$R1 958
15 TraesCS5D01G297500 chrUn 211147172 211147911 739 True 261.000000 318 81.788000 354 1106 2 chrUn.!!$R2 752

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
187 232 0.613260 ATGCCCACAACTAGCTTCGA 59.387 50.0 0.0 0.0 0.00 3.71 F
1140 4162 0.106708 GTGTCCTGTGACCTTGAGCA 59.893 55.0 0.0 0.0 41.01 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1550 4642 0.248215 CGGCCGTACTACGTACCTTG 60.248 60.0 19.5 0.0 40.58 3.61 R
2805 12883 0.037326 TGGTGAACAGAGTGCCGATC 60.037 55.0 0.0 0.0 0.00 3.69 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
82 122 2.579518 CGACGAGCATGTGCGCTA 60.580 61.111 9.73 0.00 44.01 4.26
97 137 1.220749 GCTATGACCAAGTGGCCGA 59.779 57.895 0.00 0.00 39.32 5.54
113 153 1.676635 CGACGTGGGTGAGGACCTA 60.677 63.158 0.00 0.00 42.66 3.08
177 222 2.120053 ATGCCACCATGCCCACAA 59.880 55.556 0.00 0.00 0.00 3.33
187 232 0.613260 ATGCCCACAACTAGCTTCGA 59.387 50.000 0.00 0.00 0.00 3.71
227 293 1.044790 TCATCCAGCTGATCGAGGCA 61.045 55.000 17.39 1.23 0.00 4.75
288 390 3.797353 GAAGGGGATGGCGAGGCA 61.797 66.667 0.88 0.88 0.00 4.75
289 391 3.099170 AAGGGGATGGCGAGGCAT 61.099 61.111 12.04 12.04 0.00 4.40
290 392 3.426309 AAGGGGATGGCGAGGCATG 62.426 63.158 16.91 0.00 0.00 4.06
331 2699 3.945285 TGGGTTAAGATCAAATTCCTCGC 59.055 43.478 0.00 0.00 0.00 5.03
379 2747 8.708742 GCTGATTAAAGTAACCAAACAAATTCC 58.291 33.333 0.00 0.00 0.00 3.01
398 2766 3.981212 TCCCATTTTTCTCCATTCCCTC 58.019 45.455 0.00 0.00 0.00 4.30
423 2791 4.628333 ACAGTAACGGTGTAAATCGATTGG 59.372 41.667 12.25 0.23 0.00 3.16
424 2792 4.865925 CAGTAACGGTGTAAATCGATTGGA 59.134 41.667 12.25 0.00 0.00 3.53
443 2830 2.422945 GGAAACCAAACACCTCAGTCCT 60.423 50.000 0.00 0.00 0.00 3.85
444 2831 3.181448 GGAAACCAAACACCTCAGTCCTA 60.181 47.826 0.00 0.00 0.00 2.94
445 2832 3.487120 AACCAAACACCTCAGTCCTAC 57.513 47.619 0.00 0.00 0.00 3.18
598 2986 0.810648 GCCTGTGATGATGCCGAAAA 59.189 50.000 0.00 0.00 0.00 2.29
712 3113 1.722464 CGATGGTTCGTCGCAGTAAAA 59.278 47.619 0.00 0.00 40.53 1.52
819 3251 2.124570 CCCGCTGCAGGCTACAAT 60.125 61.111 17.12 0.00 39.13 2.71
820 3252 2.475466 CCCGCTGCAGGCTACAATG 61.475 63.158 17.12 0.00 39.13 2.82
821 3253 1.450134 CCGCTGCAGGCTACAATGA 60.450 57.895 17.12 0.00 39.13 2.57
833 3266 5.412594 CAGGCTACAATGAGCTACTGAAAAA 59.587 40.000 0.00 0.00 42.43 1.94
837 3270 5.695851 ACAATGAGCTACTGAAAAAGGTG 57.304 39.130 0.00 0.00 0.00 4.00
873 3328 1.808945 CTTGCTCGCTCCTTGTCAAAT 59.191 47.619 0.00 0.00 0.00 2.32
905 3360 3.706373 GCCCCACTCCTCGCTTCA 61.706 66.667 0.00 0.00 0.00 3.02
915 3428 2.202946 TCGCTTCAACGCCACACA 60.203 55.556 0.00 0.00 0.00 3.72
916 3429 2.052237 CGCTTCAACGCCACACAC 60.052 61.111 0.00 0.00 0.00 3.82
917 3430 2.331451 GCTTCAACGCCACACACC 59.669 61.111 0.00 0.00 0.00 4.16
918 3431 2.631428 CTTCAACGCCACACACCG 59.369 61.111 0.00 0.00 0.00 4.94
919 3432 2.892334 CTTCAACGCCACACACCGG 61.892 63.158 0.00 0.00 0.00 5.28
920 3433 4.920112 TCAACGCCACACACCGGG 62.920 66.667 6.32 0.00 0.00 5.73
929 3442 4.690719 CACACCGGGCCGTGCTTA 62.691 66.667 26.32 0.00 37.25 3.09
930 3443 4.692475 ACACCGGGCCGTGCTTAC 62.692 66.667 26.32 0.00 37.25 2.34
931 3444 4.388499 CACCGGGCCGTGCTTACT 62.388 66.667 26.32 0.00 0.00 2.24
932 3445 4.388499 ACCGGGCCGTGCTTACTG 62.388 66.667 26.32 9.20 0.00 2.74
984 3510 2.025037 TCCATTGGAGGAGGTTCCATTG 60.025 50.000 0.00 9.03 46.22 2.82
1047 4056 2.837591 AGCTTCCCTTCTTCTTCCTCTC 59.162 50.000 0.00 0.00 0.00 3.20
1048 4057 2.093181 GCTTCCCTTCTTCTTCCTCTCC 60.093 54.545 0.00 0.00 0.00 3.71
1049 4058 3.449918 CTTCCCTTCTTCTTCCTCTCCT 58.550 50.000 0.00 0.00 0.00 3.69
1050 4059 3.569135 TCCCTTCTTCTTCCTCTCCTT 57.431 47.619 0.00 0.00 0.00 3.36
1051 4060 3.445987 TCCCTTCTTCTTCCTCTCCTTC 58.554 50.000 0.00 0.00 0.00 3.46
1060 4069 1.018226 TCCTCTCCTTCGTCGTCGTC 61.018 60.000 1.33 0.00 38.33 4.20
1061 4070 1.020333 CCTCTCCTTCGTCGTCGTCT 61.020 60.000 1.33 0.00 38.33 4.18
1062 4071 1.638133 CTCTCCTTCGTCGTCGTCTA 58.362 55.000 1.33 0.00 38.33 2.59
1076 4094 4.686091 TCGTCGTCTACTTCTTCTTCGTAA 59.314 41.667 0.00 0.00 0.00 3.18
1098 4116 3.119531 ACTCATTCTGTCTGCTCTTCTCG 60.120 47.826 0.00 0.00 0.00 4.04
1140 4162 0.106708 GTGTCCTGTGACCTTGAGCA 59.893 55.000 0.00 0.00 41.01 4.26
1152 4191 0.606604 CTTGAGCAAGGCAAGGCATT 59.393 50.000 2.30 0.00 39.18 3.56
1199 4243 3.490419 CGGAGTCCTAGTTATCGTTTGGG 60.490 52.174 7.77 0.00 0.00 4.12
1201 4245 3.105283 AGTCCTAGTTATCGTTTGGGCT 58.895 45.455 0.00 0.00 0.00 5.19
1214 4258 0.829333 TTGGGCTTTGCTTGCAGAAA 59.171 45.000 0.00 0.00 0.00 2.52
1418 4471 3.958860 ACGCCCAAGAAGCAGGCT 61.959 61.111 0.00 0.00 44.84 4.58
1574 4670 2.581409 CGTAGTACGGCCGCCAAG 60.581 66.667 28.58 8.41 38.08 3.61
1585 4682 1.339929 GGCCGCCAAGAAAGAAAGAAA 59.660 47.619 3.91 0.00 0.00 2.52
1593 4694 7.253983 CCGCCAAGAAAGAAAGAAAGTTTTTAC 60.254 37.037 0.00 0.00 0.00 2.01
1642 4745 3.555518 GACTCTGTTTGAATGCGGTTTC 58.444 45.455 0.00 0.00 0.00 2.78
1760 4882 4.806571 GCGTCTTCATCGCCAGTA 57.193 55.556 0.00 0.00 46.61 2.74
1785 4907 6.524101 TTATTTGCCCTTTCTGTTGGATAC 57.476 37.500 0.00 0.00 0.00 2.24
1914 8373 4.461198 TGTGTACAGTTCTGTCTCTCTCA 58.539 43.478 8.80 4.20 0.00 3.27
1939 8398 1.080298 ATGCGCTTTCTTGGCTTGC 60.080 52.632 9.73 0.00 0.00 4.01
1974 9095 1.290203 CATGGCTAGTACTGGCAACG 58.710 55.000 29.41 10.53 43.05 4.10
2073 10494 1.128692 GCTAGTAGTGCCTTTGTTGCG 59.871 52.381 0.00 0.00 0.00 4.85
2078 10499 0.814457 AGTGCCTTTGTTGCGTGAAA 59.186 45.000 0.00 0.00 0.00 2.69
2124 10769 1.739067 AGCGAGTTTATTGGAGGTGC 58.261 50.000 0.00 0.00 0.00 5.01
2126 10771 1.666189 GCGAGTTTATTGGAGGTGCTC 59.334 52.381 0.00 0.00 0.00 4.26
2127 10772 2.678190 GCGAGTTTATTGGAGGTGCTCT 60.678 50.000 0.00 0.00 0.00 4.09
2174 10820 0.179137 TGGCAACTGATAGACGAGCG 60.179 55.000 0.00 0.00 37.61 5.03
2175 10821 0.100682 GGCAACTGATAGACGAGCGA 59.899 55.000 0.00 0.00 0.00 4.93
2177 10823 1.471964 CAACTGATAGACGAGCGAGC 58.528 55.000 0.00 0.00 0.00 5.03
2180 10826 0.655915 CTGATAGACGAGCGAGCACG 60.656 60.000 12.88 12.88 42.93 5.34
2182 10828 0.580578 GATAGACGAGCGAGCACGTA 59.419 55.000 19.16 6.75 42.66 3.57
2183 10829 0.304098 ATAGACGAGCGAGCACGTAC 59.696 55.000 19.16 12.97 42.66 3.67
2184 10830 1.015607 TAGACGAGCGAGCACGTACA 61.016 55.000 19.16 8.42 42.66 2.90
2187 10833 1.071019 ACGAGCGAGCACGTACATTG 61.071 55.000 17.90 0.00 41.03 2.82
2188 10834 0.796870 CGAGCGAGCACGTACATTGA 60.797 55.000 5.23 0.00 41.98 2.57
2189 10835 1.560923 GAGCGAGCACGTACATTGAT 58.439 50.000 5.23 0.00 41.98 2.57
2205 10851 0.400213 TGATTCCCACCGTTCTGCTT 59.600 50.000 0.00 0.00 0.00 3.91
2208 10854 0.250295 TTCCCACCGTTCTGCTTCTG 60.250 55.000 0.00 0.00 0.00 3.02
2210 10856 1.302033 CCACCGTTCTGCTTCTGCT 60.302 57.895 0.00 0.00 40.48 4.24
2213 10885 1.962822 CCGTTCTGCTTCTGCTGCA 60.963 57.895 0.88 0.88 40.48 4.41
2245 10925 2.526432 AGTCTGGTGAATCTGGTACGT 58.474 47.619 0.00 0.00 0.00 3.57
2260 10940 0.107897 TACGTGCATTGATTCCCGCT 60.108 50.000 0.00 0.00 0.00 5.52
2380 11104 4.710695 CACCGTCGCAGCCGTGTA 62.711 66.667 0.00 0.00 35.54 2.90
2518 12292 1.754745 GAAGACCTGTGGCTGTGGA 59.245 57.895 0.00 0.00 0.00 4.02
2522 12296 1.985159 AGACCTGTGGCTGTGGATTTA 59.015 47.619 0.00 0.00 0.00 1.40
2535 12309 6.116126 GCTGTGGATTTAGTAGTCCTTGAAT 58.884 40.000 5.55 0.00 35.49 2.57
2541 12315 7.067372 TGGATTTAGTAGTCCTTGAATTGCATG 59.933 37.037 0.00 0.00 35.49 4.06
2594 12382 3.376935 CTACCGCCCCAGTCTGCTG 62.377 68.421 0.00 0.00 42.22 4.41
2599 12387 4.031129 CCCCAGTCTGCTGCTGCT 62.031 66.667 17.00 0.00 41.26 4.24
2600 12388 2.663075 CCCCAGTCTGCTGCTGCTA 61.663 63.158 17.00 2.17 41.26 3.49
2601 12389 1.449246 CCCAGTCTGCTGCTGCTAC 60.449 63.158 17.00 14.00 41.26 3.58
2605 12393 1.476085 CAGTCTGCTGCTGCTACTACT 59.524 52.381 17.00 11.03 40.48 2.57
2606 12394 2.685388 CAGTCTGCTGCTGCTACTACTA 59.315 50.000 17.00 0.00 40.48 1.82
2610 12398 3.878103 TCTGCTGCTGCTACTACTACTAC 59.122 47.826 17.00 0.00 40.48 2.73
2629 12702 0.108615 CGTAGCTAGGTGCAACAGCT 60.109 55.000 25.10 25.10 46.91 4.24
2640 12713 2.555757 GTGCAACAGCTGATCCTTCTTT 59.444 45.455 23.35 0.00 36.32 2.52
2707 12782 6.455045 TTTTGGTTCAAAGTTCAAACGAAC 57.545 33.333 0.00 0.00 42.66 3.95
2788 12866 2.338984 GGACAAGTCTGCCGACGT 59.661 61.111 2.37 0.00 44.93 4.34
2792 12870 2.338984 AAGTCTGCCGACGTGACC 59.661 61.111 0.00 0.00 44.93 4.02
2798 12876 4.719369 GCCGACGTGACCGCTCTT 62.719 66.667 0.00 0.00 37.70 2.85
2799 12877 2.504244 CCGACGTGACCGCTCTTC 60.504 66.667 0.00 0.00 37.70 2.87
2800 12878 2.561885 CGACGTGACCGCTCTTCT 59.438 61.111 0.00 0.00 37.70 2.85
2801 12879 1.797933 CGACGTGACCGCTCTTCTG 60.798 63.158 0.00 0.00 37.70 3.02
2802 12880 1.579932 GACGTGACCGCTCTTCTGA 59.420 57.895 0.00 0.00 37.70 3.27
2803 12881 0.039437 GACGTGACCGCTCTTCTGAA 60.039 55.000 0.00 0.00 37.70 3.02
2804 12882 0.039074 ACGTGACCGCTCTTCTGAAG 60.039 55.000 11.18 11.18 37.70 3.02
2805 12883 0.734253 CGTGACCGCTCTTCTGAAGG 60.734 60.000 16.83 9.10 0.00 3.46
2806 12884 0.603569 GTGACCGCTCTTCTGAAGGA 59.396 55.000 16.83 3.90 0.00 3.36
2807 12885 1.205893 GTGACCGCTCTTCTGAAGGAT 59.794 52.381 16.83 0.00 0.00 3.24
2808 12886 1.478510 TGACCGCTCTTCTGAAGGATC 59.521 52.381 16.83 8.42 0.00 3.36
2809 12887 0.457851 ACCGCTCTTCTGAAGGATCG 59.542 55.000 16.83 15.68 0.00 3.69
2810 12888 0.249238 CCGCTCTTCTGAAGGATCGG 60.249 60.000 21.54 21.54 0.00 4.18
2811 12889 0.873743 CGCTCTTCTGAAGGATCGGC 60.874 60.000 16.83 11.94 31.55 5.54
2812 12890 0.176680 GCTCTTCTGAAGGATCGGCA 59.823 55.000 16.83 0.00 31.55 5.69
2813 12891 1.933247 CTCTTCTGAAGGATCGGCAC 58.067 55.000 16.83 0.00 31.55 5.01
2814 12892 1.480137 CTCTTCTGAAGGATCGGCACT 59.520 52.381 16.83 0.00 31.55 4.40
2815 12893 1.478510 TCTTCTGAAGGATCGGCACTC 59.521 52.381 16.83 0.00 31.55 3.51
2816 12894 1.480137 CTTCTGAAGGATCGGCACTCT 59.520 52.381 9.57 0.00 31.55 3.24
2817 12895 0.820226 TCTGAAGGATCGGCACTCTG 59.180 55.000 0.00 0.00 31.55 3.35
2818 12896 0.534412 CTGAAGGATCGGCACTCTGT 59.466 55.000 0.00 0.00 0.00 3.41
2819 12897 0.976641 TGAAGGATCGGCACTCTGTT 59.023 50.000 0.00 0.00 0.00 3.16
2820 12898 1.066858 TGAAGGATCGGCACTCTGTTC 60.067 52.381 0.00 0.00 0.00 3.18
2821 12899 0.976641 AAGGATCGGCACTCTGTTCA 59.023 50.000 0.00 0.00 0.00 3.18
2822 12900 0.247736 AGGATCGGCACTCTGTTCAC 59.752 55.000 0.00 0.00 0.00 3.18
2823 12901 0.741221 GGATCGGCACTCTGTTCACC 60.741 60.000 0.00 0.00 0.00 4.02
2824 12902 0.037326 GATCGGCACTCTGTTCACCA 60.037 55.000 0.00 0.00 0.00 4.17
2825 12903 0.320771 ATCGGCACTCTGTTCACCAC 60.321 55.000 0.00 0.00 0.00 4.16
2826 12904 1.069765 CGGCACTCTGTTCACCACT 59.930 57.895 0.00 0.00 0.00 4.00
2827 12905 0.532862 CGGCACTCTGTTCACCACTT 60.533 55.000 0.00 0.00 0.00 3.16
2828 12906 1.230324 GGCACTCTGTTCACCACTTC 58.770 55.000 0.00 0.00 0.00 3.01
2829 12907 1.202698 GGCACTCTGTTCACCACTTCT 60.203 52.381 0.00 0.00 0.00 2.85
2830 12908 2.565841 GCACTCTGTTCACCACTTCTT 58.434 47.619 0.00 0.00 0.00 2.52
2831 12909 2.945668 GCACTCTGTTCACCACTTCTTT 59.054 45.455 0.00 0.00 0.00 2.52
2832 12910 3.242870 GCACTCTGTTCACCACTTCTTTG 60.243 47.826 0.00 0.00 0.00 2.77
2833 12911 4.191544 CACTCTGTTCACCACTTCTTTGA 58.808 43.478 0.00 0.00 0.00 2.69
2834 12912 4.034510 CACTCTGTTCACCACTTCTTTGAC 59.965 45.833 0.00 0.00 0.00 3.18
2835 12913 4.191544 CTCTGTTCACCACTTCTTTGACA 58.808 43.478 0.00 0.00 0.00 3.58
2836 12914 4.780815 TCTGTTCACCACTTCTTTGACAT 58.219 39.130 0.00 0.00 0.00 3.06
2837 12915 4.576053 TCTGTTCACCACTTCTTTGACATG 59.424 41.667 0.00 0.00 0.00 3.21
2838 12916 4.522114 TGTTCACCACTTCTTTGACATGA 58.478 39.130 0.00 0.00 0.00 3.07
2839 12917 5.132502 TGTTCACCACTTCTTTGACATGAT 58.867 37.500 0.00 0.00 0.00 2.45
2840 12918 5.239306 TGTTCACCACTTCTTTGACATGATC 59.761 40.000 0.00 0.00 0.00 2.92
2841 12919 5.233083 TCACCACTTCTTTGACATGATCT 57.767 39.130 0.00 0.00 0.00 2.75
2842 12920 5.624159 TCACCACTTCTTTGACATGATCTT 58.376 37.500 0.00 0.00 0.00 2.40
2843 12921 6.064060 TCACCACTTCTTTGACATGATCTTT 58.936 36.000 0.00 0.00 0.00 2.52
2844 12922 6.205464 TCACCACTTCTTTGACATGATCTTTC 59.795 38.462 0.00 0.00 0.00 2.62
2845 12923 5.474876 ACCACTTCTTTGACATGATCTTTCC 59.525 40.000 0.00 0.00 0.00 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 1.805869 CTATACCAGCATGCTCCAGC 58.194 55.000 19.68 0.00 42.50 4.85
76 116 1.745115 GCCACTTGGTCATAGCGCA 60.745 57.895 11.47 0.00 37.57 6.09
82 122 2.047274 CGTCGGCCACTTGGTCAT 60.047 61.111 2.24 0.00 40.62 3.06
97 137 1.411216 CCTATAGGTCCTCACCCACGT 60.411 57.143 10.96 0.00 45.12 4.49
113 153 3.797353 CCAGTGTGCCCGGCCTAT 61.797 66.667 7.03 0.00 0.00 2.57
132 172 1.687146 TCAGCCGCTCTCCATCCTT 60.687 57.895 0.00 0.00 0.00 3.36
161 204 2.074113 TAGTTGTGGGCATGGTGGCA 62.074 55.000 5.86 0.00 45.76 4.92
177 222 2.885861 CCCGCAGTCGAAGCTAGT 59.114 61.111 9.14 0.00 38.10 2.57
187 232 1.453015 TGTTGTTGAAGCCCGCAGT 60.453 52.632 0.00 0.00 0.00 4.40
227 293 3.707793 GACGATAGCAACGAGAATTCCT 58.292 45.455 0.65 0.00 42.67 3.36
288 390 4.023193 CCACGCTTTACTCCAAACTTTCAT 60.023 41.667 0.00 0.00 0.00 2.57
289 391 3.314080 CCACGCTTTACTCCAAACTTTCA 59.686 43.478 0.00 0.00 0.00 2.69
290 392 3.304458 CCCACGCTTTACTCCAAACTTTC 60.304 47.826 0.00 0.00 0.00 2.62
331 2699 4.360563 CTGTAACGTAATCAGCCCTACAG 58.639 47.826 4.43 4.43 31.68 2.74
379 2747 5.509498 TGTAGAGGGAATGGAGAAAAATGG 58.491 41.667 0.00 0.00 0.00 3.16
398 2766 6.020121 CCAATCGATTTACACCGTTACTGTAG 60.020 42.308 8.21 0.00 0.00 2.74
423 2791 2.932261 AGGACTGAGGTGTTTGGTTTC 58.068 47.619 0.00 0.00 0.00 2.78
424 2792 3.434596 GGTAGGACTGAGGTGTTTGGTTT 60.435 47.826 0.00 0.00 0.00 3.27
443 2830 6.016527 CACAGATTAAGGAGCATACGTAGGTA 60.017 42.308 9.23 0.00 0.00 3.08
444 2831 4.894114 ACAGATTAAGGAGCATACGTAGGT 59.106 41.667 9.23 2.95 0.00 3.08
445 2832 5.223382 CACAGATTAAGGAGCATACGTAGG 58.777 45.833 2.16 2.16 0.00 3.18
598 2986 2.756025 CCCGCGTGTGTGTGTGTTT 61.756 57.895 4.92 0.00 0.00 2.83
627 3027 4.463879 CAGCAGACCCTGGAGGCG 62.464 72.222 0.00 0.00 40.58 5.52
699 3100 1.057636 CGAGCTTTTTACTGCGACGA 58.942 50.000 0.00 0.00 36.59 4.20
805 3237 0.747283 AGCTCATTGTAGCCTGCAGC 60.747 55.000 8.66 3.91 43.86 5.25
806 3238 2.158986 AGTAGCTCATTGTAGCCTGCAG 60.159 50.000 6.78 6.78 43.86 4.41
807 3239 1.833630 AGTAGCTCATTGTAGCCTGCA 59.166 47.619 0.00 0.00 43.86 4.41
808 3240 2.159043 TCAGTAGCTCATTGTAGCCTGC 60.159 50.000 0.00 0.00 43.86 4.85
809 3241 3.808466 TCAGTAGCTCATTGTAGCCTG 57.192 47.619 0.00 0.00 43.86 4.85
810 3242 4.826274 TTTCAGTAGCTCATTGTAGCCT 57.174 40.909 0.00 0.00 43.86 4.58
811 3243 5.163713 CCTTTTTCAGTAGCTCATTGTAGCC 60.164 44.000 0.00 0.00 43.86 3.93
812 3244 5.412904 ACCTTTTTCAGTAGCTCATTGTAGC 59.587 40.000 0.00 0.00 43.11 3.58
813 3245 6.128172 CCACCTTTTTCAGTAGCTCATTGTAG 60.128 42.308 0.00 0.00 0.00 2.74
814 3246 5.705441 CCACCTTTTTCAGTAGCTCATTGTA 59.295 40.000 0.00 0.00 0.00 2.41
815 3247 4.520492 CCACCTTTTTCAGTAGCTCATTGT 59.480 41.667 0.00 0.00 0.00 2.71
816 3248 4.082571 CCCACCTTTTTCAGTAGCTCATTG 60.083 45.833 0.00 0.00 0.00 2.82
817 3249 4.082125 CCCACCTTTTTCAGTAGCTCATT 58.918 43.478 0.00 0.00 0.00 2.57
818 3250 3.690460 CCCACCTTTTTCAGTAGCTCAT 58.310 45.455 0.00 0.00 0.00 2.90
819 3251 2.814097 GCCCACCTTTTTCAGTAGCTCA 60.814 50.000 0.00 0.00 0.00 4.26
820 3252 1.813178 GCCCACCTTTTTCAGTAGCTC 59.187 52.381 0.00 0.00 0.00 4.09
821 3253 1.547901 GGCCCACCTTTTTCAGTAGCT 60.548 52.381 0.00 0.00 0.00 3.32
837 3270 0.182299 CAAGAGAGGATGGAAGGCCC 59.818 60.000 0.00 0.00 0.00 5.80
915 3428 4.388499 CAGTAAGCACGGCCCGGT 62.388 66.667 8.57 0.00 0.00 5.28
920 3433 3.788766 CACGCCAGTAAGCACGGC 61.789 66.667 0.00 0.00 39.47 5.68
921 3434 3.788766 GCACGCCAGTAAGCACGG 61.789 66.667 0.00 0.00 0.00 4.94
922 3435 2.738521 AGCACGCCAGTAAGCACG 60.739 61.111 0.00 0.00 0.00 5.34
923 3436 2.863153 CAGCACGCCAGTAAGCAC 59.137 61.111 0.00 0.00 0.00 4.40
924 3437 3.049674 GCAGCACGCCAGTAAGCA 61.050 61.111 0.00 0.00 32.94 3.91
925 3438 4.152625 CGCAGCACGCCAGTAAGC 62.153 66.667 0.00 0.00 37.30 3.09
984 3510 1.929836 CTACGAGGCTGAACAGAATGC 59.070 52.381 5.97 0.00 42.53 3.56
1047 4056 1.731160 AGAAGTAGACGACGACGAAGG 59.269 52.381 15.32 0.00 42.66 3.46
1048 4057 3.123284 AGAAGAAGTAGACGACGACGAAG 59.877 47.826 15.32 0.00 42.66 3.79
1049 4058 3.062763 AGAAGAAGTAGACGACGACGAA 58.937 45.455 15.32 0.00 42.66 3.85
1050 4059 2.681706 AGAAGAAGTAGACGACGACGA 58.318 47.619 15.32 0.00 42.66 4.20
1051 4060 3.406355 GAAGAAGAAGTAGACGACGACG 58.594 50.000 5.58 5.58 45.75 5.12
1060 4069 8.024285 ACAGAATGAGTTACGAAGAAGAAGTAG 58.976 37.037 0.00 0.00 39.69 2.57
1061 4070 7.883217 ACAGAATGAGTTACGAAGAAGAAGTA 58.117 34.615 0.00 0.00 39.69 2.24
1062 4071 6.750148 ACAGAATGAGTTACGAAGAAGAAGT 58.250 36.000 0.00 0.00 39.69 3.01
1076 4094 3.119531 CGAGAAGAGCAGACAGAATGAGT 60.120 47.826 0.00 0.00 39.69 3.41
1152 4191 1.702401 TGGGTGAACTTACTGGCATGA 59.298 47.619 0.00 0.00 0.00 3.07
1398 4451 3.741476 CTGCTTCTTGGGCGTGGC 61.741 66.667 0.00 0.00 0.00 5.01
1550 4642 0.248215 CGGCCGTACTACGTACCTTG 60.248 60.000 19.50 0.00 40.58 3.61
1569 4665 8.703604 AGTAAAAACTTTCTTTCTTTCTTGGC 57.296 30.769 0.00 0.00 0.00 4.52
1585 4682 4.099824 CCACGCGACAAAAAGTAAAAACT 58.900 39.130 15.93 0.00 0.00 2.66
1593 4694 0.378962 TCCAACCACGCGACAAAAAG 59.621 50.000 15.93 0.00 0.00 2.27
1760 4882 6.625532 ATCCAACAGAAAGGGCAAATAAAT 57.374 33.333 0.00 0.00 0.00 1.40
1821 8266 3.988379 AGTACAAAGCACACCAACATG 57.012 42.857 0.00 0.00 0.00 3.21
1827 8273 0.872388 CCGGAAGTACAAAGCACACC 59.128 55.000 0.00 0.00 0.00 4.16
1828 8274 1.263217 CACCGGAAGTACAAAGCACAC 59.737 52.381 9.46 0.00 0.00 3.82
1861 8308 9.778741 TTGCGGAAATGATTTAGATCTATTAGT 57.221 29.630 2.58 0.00 33.28 2.24
1892 8346 4.461198 TGAGAGAGACAGAACTGTACACA 58.539 43.478 7.46 3.23 45.05 3.72
1898 8355 3.366273 GCACTCTGAGAGAGACAGAACTG 60.366 52.174 17.71 1.45 45.07 3.16
1914 8373 0.520404 CAAGAAAGCGCATGCACTCT 59.480 50.000 19.57 10.02 46.23 3.24
1939 8398 2.606308 GCCATGTACTACCATCGTACCG 60.606 54.545 0.00 0.00 37.11 4.02
1974 9095 4.269363 ACGAATGTTAATTACACGGCTAGC 59.731 41.667 6.04 6.04 40.19 3.42
2008 9129 8.446273 ACATTACACAAGATGAAGAGAAATTCG 58.554 33.333 0.00 0.00 31.52 3.34
2078 10499 6.529125 GCACGTCAAAATTGATCAGAAATGAT 59.471 34.615 0.00 0.00 39.73 2.45
2124 10769 7.764901 TGAATCTCTGAAGTGAATGATGAAGAG 59.235 37.037 0.00 0.00 32.92 2.85
2126 10771 7.764901 TCTGAATCTCTGAAGTGAATGATGAAG 59.235 37.037 0.00 0.00 0.00 3.02
2127 10772 7.618137 TCTGAATCTCTGAAGTGAATGATGAA 58.382 34.615 0.00 0.00 0.00 2.57
2174 10820 2.351726 GTGGGAATCAATGTACGTGCTC 59.648 50.000 4.97 0.00 0.00 4.26
2175 10821 2.356135 GTGGGAATCAATGTACGTGCT 58.644 47.619 4.97 0.00 0.00 4.40
2177 10823 1.663643 CGGTGGGAATCAATGTACGTG 59.336 52.381 0.00 0.00 0.00 4.49
2180 10826 3.374058 CAGAACGGTGGGAATCAATGTAC 59.626 47.826 0.00 0.00 0.00 2.90
2182 10828 2.436417 CAGAACGGTGGGAATCAATGT 58.564 47.619 0.00 0.00 0.00 2.71
2183 10829 1.133025 GCAGAACGGTGGGAATCAATG 59.867 52.381 0.00 0.00 0.00 2.82
2184 10830 1.004745 AGCAGAACGGTGGGAATCAAT 59.995 47.619 0.00 0.00 0.00 2.57
2187 10833 1.087501 GAAGCAGAACGGTGGGAATC 58.912 55.000 0.00 0.00 0.00 2.52
2188 10834 0.693049 AGAAGCAGAACGGTGGGAAT 59.307 50.000 0.00 0.00 0.00 3.01
2189 10835 0.250295 CAGAAGCAGAACGGTGGGAA 60.250 55.000 0.00 0.00 0.00 3.97
2210 10856 3.918253 GACTTCACGGCCCCATGCA 62.918 63.158 0.00 0.00 43.89 3.96
2213 10885 2.671070 CAGACTTCACGGCCCCAT 59.329 61.111 0.00 0.00 0.00 4.00
2245 10925 0.527113 CAACAGCGGGAATCAATGCA 59.473 50.000 0.00 0.00 0.00 3.96
2319 11007 1.512926 GAGTTGAATGACACGGCTGT 58.487 50.000 0.00 0.00 0.00 4.40
2380 11104 0.973632 TCACTTACTGCGGTGGACAT 59.026 50.000 8.92 0.00 34.57 3.06
2444 11780 1.484038 TGTGACTTTTGGCCTTGCTT 58.516 45.000 3.32 0.00 0.00 3.91
2518 12292 6.891908 ACCATGCAATTCAAGGACTACTAAAT 59.108 34.615 0.00 0.00 37.03 1.40
2522 12296 4.307032 ACCATGCAATTCAAGGACTACT 57.693 40.909 0.00 0.00 37.03 2.57
2535 12309 7.039574 TGTTCTTGTACTACTACTACCATGCAA 60.040 37.037 0.00 0.00 0.00 4.08
2541 12315 5.352569 TCGCTGTTCTTGTACTACTACTACC 59.647 44.000 0.00 0.00 0.00 3.18
2606 12394 2.935481 GTTGCACCTAGCTACGTAGT 57.065 50.000 22.98 12.59 45.94 2.73
2629 12702 6.039270 ACGACATGTTTTTCAAAGAAGGATCA 59.961 34.615 0.00 0.00 0.00 2.92
2640 12713 4.505922 GGAAAATGCACGACATGTTTTTCA 59.494 37.500 22.89 11.71 40.56 2.69
2725 12803 0.542805 GCAGGGTAACATTCCCCGTA 59.457 55.000 0.00 0.00 46.17 4.02
2788 12866 1.478510 GATCCTTCAGAAGAGCGGTCA 59.521 52.381 18.15 0.00 0.00 4.02
2792 12870 0.873743 GCCGATCCTTCAGAAGAGCG 60.874 60.000 12.14 11.54 0.00 5.03
2798 12876 0.820226 CAGAGTGCCGATCCTTCAGA 59.180 55.000 0.00 0.00 0.00 3.27
2799 12877 0.534412 ACAGAGTGCCGATCCTTCAG 59.466 55.000 0.00 0.00 0.00 3.02
2800 12878 0.976641 AACAGAGTGCCGATCCTTCA 59.023 50.000 0.00 0.00 0.00 3.02
2801 12879 1.066858 TGAACAGAGTGCCGATCCTTC 60.067 52.381 0.00 0.00 0.00 3.46
2802 12880 0.976641 TGAACAGAGTGCCGATCCTT 59.023 50.000 0.00 0.00 0.00 3.36
2803 12881 0.247736 GTGAACAGAGTGCCGATCCT 59.752 55.000 0.00 0.00 0.00 3.24
2804 12882 0.741221 GGTGAACAGAGTGCCGATCC 60.741 60.000 0.00 0.00 0.00 3.36
2805 12883 0.037326 TGGTGAACAGAGTGCCGATC 60.037 55.000 0.00 0.00 0.00 3.69
2806 12884 0.320771 GTGGTGAACAGAGTGCCGAT 60.321 55.000 0.00 0.00 0.00 4.18
2807 12885 1.069090 GTGGTGAACAGAGTGCCGA 59.931 57.895 0.00 0.00 0.00 5.54
2808 12886 0.532862 AAGTGGTGAACAGAGTGCCG 60.533 55.000 0.00 0.00 0.00 5.69
2809 12887 1.202698 AGAAGTGGTGAACAGAGTGCC 60.203 52.381 0.00 0.00 0.00 5.01
2810 12888 2.246719 AGAAGTGGTGAACAGAGTGC 57.753 50.000 0.00 0.00 0.00 4.40
2811 12889 4.034510 GTCAAAGAAGTGGTGAACAGAGTG 59.965 45.833 0.00 0.00 0.00 3.51
2812 12890 4.192317 GTCAAAGAAGTGGTGAACAGAGT 58.808 43.478 0.00 0.00 0.00 3.24
2813 12891 4.191544 TGTCAAAGAAGTGGTGAACAGAG 58.808 43.478 0.00 0.00 0.00 3.35
2814 12892 4.214986 TGTCAAAGAAGTGGTGAACAGA 57.785 40.909 0.00 0.00 0.00 3.41
2815 12893 4.576053 TCATGTCAAAGAAGTGGTGAACAG 59.424 41.667 0.00 0.00 0.00 3.16
2816 12894 4.522114 TCATGTCAAAGAAGTGGTGAACA 58.478 39.130 0.00 0.00 0.00 3.18
2817 12895 5.471456 AGATCATGTCAAAGAAGTGGTGAAC 59.529 40.000 0.00 0.00 0.00 3.18
2818 12896 5.624159 AGATCATGTCAAAGAAGTGGTGAA 58.376 37.500 0.00 0.00 0.00 3.18
2819 12897 5.233083 AGATCATGTCAAAGAAGTGGTGA 57.767 39.130 0.00 0.00 0.00 4.02
2820 12898 5.954296 AAGATCATGTCAAAGAAGTGGTG 57.046 39.130 0.00 0.00 0.00 4.17
2821 12899 5.474876 GGAAAGATCATGTCAAAGAAGTGGT 59.525 40.000 0.00 0.00 0.00 4.16
2822 12900 5.947443 GGAAAGATCATGTCAAAGAAGTGG 58.053 41.667 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.