Multiple sequence alignment - TraesCS2D01G367800

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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 TraesCS2D01G367800 chr2D 100.000 2483 0 0 2646 5128 472446172 472443690 0.000000e+00 4586.0
1 TraesCS2D01G367800 chr2D 100.000 2283 0 0 1 2283 472448817 472446535 0.000000e+00 4217.0
2 TraesCS2D01G367800 chr2D 81.591 1358 143 67 956 2274 472233959 472232670 0.000000e+00 1024.0
3 TraesCS2D01G367800 chr2D 87.928 497 47 4 3559 4054 472230916 472230432 1.600000e-159 573.0
4 TraesCS2D01G367800 chr2D 88.112 429 41 7 3081 3508 472231649 472231230 7.670000e-138 501.0
5 TraesCS2D01G367800 chr2D 90.598 234 12 5 4900 5126 472230435 472230205 8.340000e-78 302.0
6 TraesCS2D01G367800 chr2B 90.740 1717 113 30 14 1706 551570544 551568850 0.000000e+00 2248.0
7 TraesCS2D01G367800 chr2B 92.857 588 32 8 3547 4128 551566806 551566223 0.000000e+00 845.0
8 TraesCS2D01G367800 chr2B 86.199 826 57 30 2724 3509 551567833 551567025 0.000000e+00 841.0
9 TraesCS2D01G367800 chr2B 89.116 588 52 8 3547 4128 551534621 551534040 0.000000e+00 721.0
10 TraesCS2D01G367800 chr2B 91.829 514 28 7 958 1471 551538523 551538024 0.000000e+00 704.0
11 TraesCS2D01G367800 chr2B 88.739 444 21 11 4683 5121 551566233 551565814 2.740000e-142 516.0
12 TraesCS2D01G367800 chr2B 87.879 429 42 6 3081 3508 551535256 551534837 3.570000e-136 496.0
13 TraesCS2D01G367800 chr2B 90.566 318 24 3 1702 2017 551568739 551568426 2.860000e-112 416.0
14 TraesCS2D01G367800 chr2B 93.585 265 16 1 2016 2279 551568357 551568093 1.340000e-105 394.0
15 TraesCS2D01G367800 chr2B 95.890 73 3 0 4694 4766 551534029 551533957 9.020000e-23 119.0
16 TraesCS2D01G367800 chr2B 74.490 196 39 10 1188 1376 551399549 551399358 1.980000e-09 75.0
17 TraesCS2D01G367800 chr2B 95.455 44 2 0 2935 2978 541012275 541012232 2.560000e-08 71.3
18 TraesCS2D01G367800 chr2B 91.304 46 4 0 2933 2978 338755874 338755919 4.290000e-06 63.9
19 TraesCS2D01G367800 chr2A 92.384 1510 88 21 528 2017 613881118 613879616 0.000000e+00 2126.0
20 TraesCS2D01G367800 chr2A 93.741 1422 64 12 2728 4128 613878902 613877485 0.000000e+00 2109.0
21 TraesCS2D01G367800 chr2A 81.557 1323 143 67 986 2272 613720763 613719506 0.000000e+00 998.0
22 TraesCS2D01G367800 chr2A 87.925 588 57 7 3550 4128 613703427 613702845 0.000000e+00 680.0
23 TraesCS2D01G367800 chr2A 86.712 444 21 17 4683 5121 613877495 613877085 4.680000e-125 459.0
24 TraesCS2D01G367800 chr2A 94.715 246 12 1 3081 3325 613714111 613713866 1.040000e-101 381.0
25 TraesCS2D01G367800 chr2A 83.180 434 37 24 1 425 613881479 613881073 1.050000e-96 364.0
26 TraesCS2D01G367800 chr2A 91.250 240 14 3 2042 2278 613879443 613879208 2.300000e-83 320.0
27 TraesCS2D01G367800 chr2A 91.414 198 11 3 4875 5068 613701060 613700865 3.040000e-67 267.0
28 TraesCS2D01G367800 chr2A 95.122 82 4 0 2646 2727 613879197 613879116 4.170000e-26 130.0
29 TraesCS2D01G367800 chr2A 95.714 70 3 0 4823 4892 613702760 613702691 4.200000e-21 113.0
30 TraesCS2D01G367800 chr4A 89.720 749 53 13 1554 2278 395804892 395805640 0.000000e+00 935.0
31 TraesCS2D01G367800 chr4A 91.549 71 6 0 2646 2716 395805651 395805721 1.180000e-16 99.0
32 TraesCS2D01G367800 chr4A 87.755 49 5 1 2884 2932 633353262 633353215 7.170000e-04 56.5
33 TraesCS2D01G367800 chr4A 100.000 29 0 0 2904 2932 472667634 472667662 3.000000e-03 54.7
34 TraesCS2D01G367800 chr4A 90.476 42 3 1 2891 2932 635932324 635932364 3.000000e-03 54.7
35 TraesCS2D01G367800 chr1D 96.403 556 20 0 4127 4682 250741385 250740830 0.000000e+00 917.0
36 TraesCS2D01G367800 chr1D 95.315 555 26 0 4127 4681 19875235 19874681 0.000000e+00 881.0
37 TraesCS2D01G367800 chr5D 96.558 552 19 0 4127 4678 342525686 342526237 0.000000e+00 915.0
38 TraesCS2D01G367800 chr5D 96.377 552 18 2 4127 4678 397029806 397030355 0.000000e+00 907.0
39 TraesCS2D01G367800 chr5D 93.478 46 1 2 2937 2981 550192076 550192120 3.310000e-07 67.6
40 TraesCS2D01G367800 chrUn 95.691 557 23 1 4127 4683 115109770 115110325 0.000000e+00 894.0
41 TraesCS2D01G367800 chr5B 95.652 552 23 1 4127 4678 318172801 318173351 0.000000e+00 885.0
42 TraesCS2D01G367800 chr4D 95.471 552 25 0 4127 4678 108101239 108101790 0.000000e+00 881.0
43 TraesCS2D01G367800 chr4D 90.385 52 4 1 2933 2983 404666199 404666250 3.310000e-07 67.6
44 TraesCS2D01G367800 chr4D 100.000 29 0 0 2904 2932 312868377 312868349 3.000000e-03 54.7
45 TraesCS2D01G367800 chr1B 95.018 562 26 1 4127 4686 305284870 305284309 0.000000e+00 881.0
46 TraesCS2D01G367800 chr1B 100.000 32 0 0 2903 2934 36260857 36260826 5.540000e-05 60.2
47 TraesCS2D01G367800 chr1B 100.000 32 0 0 2903 2934 36263599 36263568 5.540000e-05 60.2
48 TraesCS2D01G367800 chr1B 100.000 31 0 0 2904 2934 497275994 497276024 1.990000e-04 58.4
49 TraesCS2D01G367800 chr7D 95.315 555 25 1 4127 4681 136708145 136707592 0.000000e+00 880.0
50 TraesCS2D01G367800 chr7D 100.000 31 0 0 2904 2934 416626631 416626601 1.990000e-04 58.4
51 TraesCS2D01G367800 chr5A 91.837 49 3 1 2936 2983 449018249 449018297 3.310000e-07 67.6
52 TraesCS2D01G367800 chr5A 83.117 77 6 5 2904 2979 462150465 462150535 4.290000e-06 63.9
53 TraesCS2D01G367800 chr5A 92.683 41 2 1 2892 2932 536890399 536890438 1.990000e-04 58.4
54 TraesCS2D01G367800 chr5A 90.698 43 2 2 2890 2930 552064825 552064867 7.170000e-04 56.5
55 TraesCS2D01G367800 chr6B 93.182 44 3 0 2935 2978 26595592 26595635 1.190000e-06 65.8
56 TraesCS2D01G367800 chr6B 100.000 29 0 0 2904 2932 567471502 567471530 3.000000e-03 54.7
57 TraesCS2D01G367800 chr1A 100.000 33 0 0 2937 2969 259202115 259202147 1.540000e-05 62.1
58 TraesCS2D01G367800 chr1A 79.070 86 12 5 2903 2983 475458706 475458790 3.000000e-03 54.7
59 TraesCS2D01G367800 chr1A 79.310 87 10 5 2903 2983 475483799 475483715 3.000000e-03 54.7
60 TraesCS2D01G367800 chr3B 89.583 48 3 1 2887 2934 752800471 752800516 5.540000e-05 60.2
61 TraesCS2D01G367800 chr3B 94.444 36 2 0 2932 2967 18648456 18648421 7.170000e-04 56.5
62 TraesCS2D01G367800 chr7A 94.737 38 1 1 2893 2930 654781574 654781610 1.990000e-04 58.4


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 TraesCS2D01G367800 chr2D 472443690 472448817 5127 True 4401.500000 4586 100.000000 1 5128 2 chr2D.!!$R2 5127
1 TraesCS2D01G367800 chr2D 472230205 472233959 3754 True 600.000000 1024 87.057250 956 5126 4 chr2D.!!$R1 4170
2 TraesCS2D01G367800 chr2B 551565814 551570544 4730 True 876.666667 2248 90.447667 14 5121 6 chr2B.!!$R4 5107
3 TraesCS2D01G367800 chr2B 551533957 551538523 4566 True 510.000000 721 91.178500 958 4766 4 chr2B.!!$R3 3808
4 TraesCS2D01G367800 chr2A 613719506 613720763 1257 True 998.000000 998 81.557000 986 2272 1 chr2A.!!$R2 1286
5 TraesCS2D01G367800 chr2A 613877085 613881479 4394 True 918.000000 2126 90.398167 1 5121 6 chr2A.!!$R4 5120
6 TraesCS2D01G367800 chr2A 613700865 613703427 2562 True 353.333333 680 91.684333 3550 5068 3 chr2A.!!$R3 1518
7 TraesCS2D01G367800 chr4A 395804892 395805721 829 False 517.000000 935 90.634500 1554 2716 2 chr4A.!!$F3 1162
8 TraesCS2D01G367800 chr1D 250740830 250741385 555 True 917.000000 917 96.403000 4127 4682 1 chr1D.!!$R2 555
9 TraesCS2D01G367800 chr1D 19874681 19875235 554 True 881.000000 881 95.315000 4127 4681 1 chr1D.!!$R1 554
10 TraesCS2D01G367800 chr5D 342525686 342526237 551 False 915.000000 915 96.558000 4127 4678 1 chr5D.!!$F1 551
11 TraesCS2D01G367800 chr5D 397029806 397030355 549 False 907.000000 907 96.377000 4127 4678 1 chr5D.!!$F2 551
12 TraesCS2D01G367800 chrUn 115109770 115110325 555 False 894.000000 894 95.691000 4127 4683 1 chrUn.!!$F1 556
13 TraesCS2D01G367800 chr5B 318172801 318173351 550 False 885.000000 885 95.652000 4127 4678 1 chr5B.!!$F1 551
14 TraesCS2D01G367800 chr4D 108101239 108101790 551 False 881.000000 881 95.471000 4127 4678 1 chr4D.!!$F1 551
15 TraesCS2D01G367800 chr1B 305284309 305284870 561 True 881.000000 881 95.018000 4127 4686 1 chr1B.!!$R1 559
16 TraesCS2D01G367800 chr7D 136707592 136708145 553 True 880.000000 880 95.315000 4127 4681 1 chr7D.!!$R1 554


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
849 883 1.276140 TAACAGGCCGGCCCATTACT 61.276 55.0 41.72 20.42 36.58 2.24 F
1873 3682 1.660560 ATGCAGGCATTTCAGGCGTC 61.661 55.0 0.00 0.00 39.37 5.19 F
3079 5919 0.179004 CCACCTGGCACCTAAACACA 60.179 55.0 0.00 0.00 0.00 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1932 3741 5.106357 TGCAAATAAACACGCAGTACATCAT 60.106 36.0 0.00 0.0 41.61 2.45 R
3511 6355 0.540923 GGCATTCCTCTCTGCTCAGT 59.459 55.0 0.00 0.0 38.45 3.41 R
4556 7704 0.031585 GGCGTCACACTACACTGTGA 59.968 55.0 15.86 0.0 46.69 3.58 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
35 36 3.358707 GCCAAACGCACCGCCTTA 61.359 61.111 0.00 0.00 37.47 2.69
83 86 3.230990 GGTGGCGCCCCTGTTTTT 61.231 61.111 26.77 0.00 0.00 1.94
391 411 7.200778 TCATGAGTTCGAAAATGTTCATGAA 57.799 32.000 23.48 3.38 44.47 2.57
486 509 9.188588 CGATCCAGAAAATATTCATGAATTTGG 57.811 33.333 25.26 20.02 38.06 3.28
499 522 4.377839 TGAATTTGGAAACAGTTTGCGA 57.622 36.364 12.40 8.13 44.54 5.10
849 883 1.276140 TAACAGGCCGGCCCATTACT 61.276 55.000 41.72 20.42 36.58 2.24
1290 1332 4.493747 GACGGCGAGGAACGAGGG 62.494 72.222 16.62 0.00 45.77 4.30
1443 1485 6.697395 TCGATATCCTGGTATGTGTTAATGG 58.303 40.000 0.00 0.00 0.00 3.16
1493 1695 2.267642 CTCGCGGATTTGGGGTCA 59.732 61.111 6.13 0.00 0.00 4.02
1512 1718 4.130118 GTCAGGCAAGTGGGTATTCATAG 58.870 47.826 0.00 0.00 0.00 2.23
1523 1729 3.181443 GGGTATTCATAGGGTTCCACTGG 60.181 52.174 0.00 0.00 0.00 4.00
1672 3346 7.715266 AGAGTTCCGTTTAGAAGTATAGGTT 57.285 36.000 0.00 0.00 29.43 3.50
1720 3509 6.204108 TGGCTTGTACTAGTTAAAGCTGAAAC 59.796 38.462 27.69 17.73 43.58 2.78
1830 3639 1.807139 TCGTCACCATGAATGTGTGG 58.193 50.000 0.00 0.00 41.35 4.17
1841 3650 7.869937 CACCATGAATGTGTGGTTTTTGTTATA 59.130 33.333 0.00 0.00 46.22 0.98
1873 3682 1.660560 ATGCAGGCATTTCAGGCGTC 61.661 55.000 0.00 0.00 39.37 5.19
1974 3783 4.227512 TGCAGTTTGTCAGCAGTTAATG 57.772 40.909 0.00 0.00 33.75 1.90
1976 3785 4.222114 GCAGTTTGTCAGCAGTTAATGTC 58.778 43.478 0.00 0.00 0.00 3.06
2021 3914 8.082242 AGGTTGAGTCAACAAAATAATAGTTGC 58.918 33.333 31.52 12.99 45.11 4.17
2099 4076 5.593679 TCTTGTAACTACTGGAGCATACC 57.406 43.478 0.00 0.00 0.00 2.73
2161 4138 7.849804 ACATGATGTACATAGAAGTTTGGAC 57.150 36.000 8.71 0.00 37.46 4.02
2279 4257 8.905850 TGATGTTGCAATACAAGATGACAATAT 58.094 29.630 0.59 0.00 42.02 1.28
2686 4665 9.492973 CCATCAAAGTTGACAATCCTAAAATTT 57.507 29.630 0.00 0.00 40.49 1.82
2930 5745 5.359576 TCCCTCCAATCCAAATTAATTGACG 59.640 40.000 0.39 0.00 41.85 4.35
2953 5790 4.853743 GCAAAGTTGTACTAAAGCTGCATC 59.146 41.667 1.02 0.00 0.00 3.91
2954 5791 5.562696 GCAAAGTTGTACTAAAGCTGCATCA 60.563 40.000 1.02 0.00 0.00 3.07
2955 5792 6.437928 CAAAGTTGTACTAAAGCTGCATCAA 58.562 36.000 1.02 0.00 0.00 2.57
2956 5793 6.824305 AAGTTGTACTAAAGCTGCATCAAT 57.176 33.333 1.02 0.00 0.00 2.57
2957 5794 6.824305 AGTTGTACTAAAGCTGCATCAATT 57.176 33.333 1.02 0.00 0.00 2.32
2958 5795 7.921786 AGTTGTACTAAAGCTGCATCAATTA 57.078 32.000 1.02 0.00 0.00 1.40
2959 5796 8.335532 AGTTGTACTAAAGCTGCATCAATTAA 57.664 30.769 1.02 0.00 0.00 1.40
2960 5797 8.960591 AGTTGTACTAAAGCTGCATCAATTAAT 58.039 29.630 1.02 0.00 0.00 1.40
2969 5806 5.068198 AGCTGCATCAATTAATTTGGATCGT 59.932 36.000 1.02 0.00 35.92 3.73
2973 5810 6.770303 TGCATCAATTAATTTGGATCGTAGGA 59.230 34.615 0.00 0.00 35.92 2.94
2986 5826 6.604171 TGGATCGTAGGAAGTAGTATTGGTA 58.396 40.000 0.00 0.00 0.00 3.25
3026 5866 7.550196 CCATTTAATTGGATCTTTTCACCAAGG 59.450 37.037 10.33 0.00 44.95 3.61
3050 5890 3.870538 TGAATCTTAGATGGGCATGCT 57.129 42.857 18.92 0.00 0.00 3.79
3079 5919 0.179004 CCACCTGGCACCTAAACACA 60.179 55.000 0.00 0.00 0.00 3.72
3098 5939 5.212194 ACACATGCATTTTAACAAGACGTC 58.788 37.500 7.70 7.70 0.00 4.34
3104 5945 6.754206 TGCATTTTAACAAGACGTCGTATAC 58.246 36.000 10.46 0.00 0.00 1.47
3333 6174 6.091034 GGCTTTTCACTGCTAAGAGTAAGTAC 59.909 42.308 0.00 0.00 0.00 2.73
3375 6216 6.646240 GGTCGTACAAGACAAATTACCAGTTA 59.354 38.462 3.73 0.00 42.62 2.24
3528 6372 9.770097 TTATTATTTACTGAGCAGAGAGGAATG 57.230 33.333 4.21 0.00 0.00 2.67
3640 6781 4.260985 TGAGCAGAACTTCAACAGTGAAA 58.739 39.130 0.00 0.00 43.18 2.69
3661 6802 9.567848 GTGAAAAACTGAAGAATGAGTTTAACA 57.432 29.630 0.00 0.00 40.68 2.41
3665 6806 5.748592 ACTGAAGAATGAGTTTAACAACGC 58.251 37.500 0.00 0.00 38.03 4.84
3672 6813 5.689383 ATGAGTTTAACAACGCTGACAAT 57.311 34.783 0.00 0.00 38.03 2.71
4028 7169 3.499537 TGACTCTGTCGTACGTGTAATGT 59.500 43.478 16.05 8.50 36.06 2.71
4046 7187 4.737353 ATGTTTTCGTCCGGTTTTACTC 57.263 40.909 0.00 0.00 0.00 2.59
4214 7362 1.661509 GCGGCTGACCTTTTTGTGC 60.662 57.895 0.00 0.00 0.00 4.57
4678 7826 9.039870 GTCCACATGTCAATTTTGTCAAATTTA 57.960 29.630 0.00 0.00 40.09 1.40
4683 7831 8.759641 CATGTCAATTTTGTCAAATTTACCGAA 58.240 29.630 0.00 0.00 40.09 4.30
4684 7832 8.879342 TGTCAATTTTGTCAAATTTACCGAAT 57.121 26.923 0.00 0.00 40.09 3.34
4685 7833 8.973378 TGTCAATTTTGTCAAATTTACCGAATC 58.027 29.630 0.00 0.00 40.09 2.52
4686 7834 8.153411 GTCAATTTTGTCAAATTTACCGAATCG 58.847 33.333 0.00 0.00 40.09 3.34
4687 7835 8.076781 TCAATTTTGTCAAATTTACCGAATCGA 58.923 29.630 3.36 0.00 40.09 3.59
4688 7836 7.790861 ATTTTGTCAAATTTACCGAATCGAC 57.209 32.000 3.36 0.00 0.00 4.20
4689 7837 5.926214 TTGTCAAATTTACCGAATCGACA 57.074 34.783 3.36 0.00 0.00 4.35
4690 7838 6.489127 TTGTCAAATTTACCGAATCGACAT 57.511 33.333 3.36 0.00 32.65 3.06
4691 7839 5.863898 TGTCAAATTTACCGAATCGACATG 58.136 37.500 3.36 0.00 0.00 3.21
4692 7840 4.728608 GTCAAATTTACCGAATCGACATGC 59.271 41.667 3.36 0.00 0.00 4.06
4726 7874 4.523173 TCCATATTGGTCGATGAGGTCTAC 59.477 45.833 0.00 0.00 39.03 2.59
4727 7875 4.476862 CATATTGGTCGATGAGGTCTACG 58.523 47.826 0.00 0.00 0.00 3.51
4737 7885 1.476891 TGAGGTCTACGGATCTTGTGC 59.523 52.381 0.00 0.00 32.26 4.57
4778 7926 1.296577 CGACAACACACACACACGC 60.297 57.895 0.00 0.00 0.00 5.34
4779 7927 1.296577 GACAACACACACACACGCG 60.297 57.895 3.53 3.53 0.00 6.01
4780 7928 2.647481 CAACACACACACACGCGC 60.647 61.111 5.73 0.00 0.00 6.86
4781 7929 4.217111 AACACACACACACGCGCG 62.217 61.111 30.96 30.96 0.00 6.86
4783 7931 3.919386 CACACACACACGCGCGAA 61.919 61.111 39.36 0.00 0.00 4.70
4784 7932 2.964925 ACACACACACGCGCGAAT 60.965 55.556 39.36 21.26 0.00 3.34
4785 7933 1.662133 ACACACACACGCGCGAATA 60.662 52.632 39.36 0.00 0.00 1.75
4786 7934 1.225368 CACACACACGCGCGAATAC 60.225 57.895 39.36 0.00 0.00 1.89
4787 7935 1.662133 ACACACACGCGCGAATACA 60.662 52.632 39.36 0.00 0.00 2.29
4788 7936 1.057208 CACACACGCGCGAATACAG 59.943 57.895 39.36 20.56 0.00 2.74
4803 7951 4.500887 CGAATACAGGATGACGTATGGGTT 60.501 45.833 0.00 0.00 39.69 4.11
4887 9683 3.230743 ACAAAATTAGCCAACCATCGC 57.769 42.857 0.00 0.00 0.00 4.58
4932 9728 4.948847 ACTTGCCAAAAGTTGATCCTTTC 58.051 39.130 0.00 0.00 33.62 2.62
4945 9743 3.706594 TGATCCTTTCGAGAGGTTGCTAT 59.293 43.478 20.59 7.31 38.04 2.97
5029 9834 3.262420 AGCCGTTATAAGTGTCTTGCTG 58.738 45.455 0.00 0.00 0.00 4.41
5085 9890 7.011857 GTCTCAGATAGCTTTAGGATTTTGGTG 59.988 40.741 0.00 0.00 0.00 4.17
5089 9896 7.121168 CAGATAGCTTTAGGATTTTGGTGTCAA 59.879 37.037 0.00 0.00 0.00 3.18
5090 9897 5.712152 AGCTTTAGGATTTTGGTGTCAAG 57.288 39.130 0.00 0.00 33.98 3.02
5091 9898 5.385198 AGCTTTAGGATTTTGGTGTCAAGA 58.615 37.500 0.00 0.00 33.98 3.02
5093 9900 6.494835 AGCTTTAGGATTTTGGTGTCAAGATT 59.505 34.615 0.00 0.00 33.98 2.40
5094 9901 6.587608 GCTTTAGGATTTTGGTGTCAAGATTG 59.412 38.462 0.00 0.00 33.98 2.67
5095 9902 7.595819 TTTAGGATTTTGGTGTCAAGATTGT 57.404 32.000 0.00 0.00 33.98 2.71
5106 9913 1.144057 AAGATTGTAGGAGCGGCCG 59.856 57.895 24.05 24.05 43.43 6.13
5107 9914 1.614241 AAGATTGTAGGAGCGGCCGT 61.614 55.000 28.70 13.92 43.43 5.68
5108 9915 1.591863 GATTGTAGGAGCGGCCGTC 60.592 63.158 28.70 21.54 43.43 4.79
5121 9928 4.436998 CCGTCCGACCTCTGCCAC 62.437 72.222 0.00 0.00 0.00 5.01
5126 9933 2.357517 CGACCTCTGCCACCACAC 60.358 66.667 0.00 0.00 0.00 3.82
5127 9934 2.357517 GACCTCTGCCACCACACG 60.358 66.667 0.00 0.00 0.00 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
126 140 6.449635 TTGATATTTGTTCGAAATCCCTGG 57.550 37.500 0.00 0.00 0.00 4.45
459 479 9.740239 CAAATTCATGAATATTTTCTGGATCGT 57.260 29.630 21.00 0.00 32.78 3.73
460 480 9.188588 CCAAATTCATGAATATTTTCTGGATCG 57.811 33.333 21.00 0.52 32.78 3.69
478 501 4.377839 TCGCAAACTGTTTCCAAATTCA 57.622 36.364 2.13 0.00 0.00 2.57
714 744 8.972458 TCAATCCTCAAATCCGTCATTATTTA 57.028 30.769 0.00 0.00 0.00 1.40
849 883 3.781926 CTTGACGTTTGTGCGCGCA 62.782 57.895 33.09 33.09 34.88 6.09
1105 1147 2.041596 TACGGGAAAGGGGAGGGG 59.958 66.667 0.00 0.00 0.00 4.79
1290 1332 3.541713 CCGCCTCTAGTCCCCTGC 61.542 72.222 0.00 0.00 0.00 4.85
1493 1695 2.443255 CCCTATGAATACCCACTTGCCT 59.557 50.000 0.00 0.00 0.00 4.75
1523 1729 6.736123 TGCATACTTCTATCTAACGAGTTCC 58.264 40.000 0.00 0.00 0.00 3.62
1672 3346 7.390718 GCCAGGTAAAAGAAAGAAATCTACAGA 59.609 37.037 0.00 0.00 0.00 3.41
1841 3650 6.720112 AATGCCTGCATTGTTTATCTACAT 57.280 33.333 16.07 0.00 44.05 2.29
1932 3741 5.106357 TGCAAATAAACACGCAGTACATCAT 60.106 36.000 0.00 0.00 41.61 2.45
1974 3783 9.039870 CAACCTGATTCTGAAATAGATGTAGAC 57.960 37.037 0.00 0.00 34.80 2.59
1976 3785 9.258826 CTCAACCTGATTCTGAAATAGATGTAG 57.741 37.037 0.00 0.00 34.80 2.74
2021 3914 7.426929 AGATAGCAACAAACAACTACAGAAG 57.573 36.000 0.00 0.00 0.00 2.85
2099 4076 6.912591 GGTGTGATGTGTTTTCTCAAAGTAAG 59.087 38.462 0.00 0.00 0.00 2.34
2131 4108 8.803201 AACTTCTATGTACATCATGTATCGTG 57.197 34.615 12.68 0.00 35.05 4.35
2133 4110 8.703336 CCAAACTTCTATGTACATCATGTATCG 58.297 37.037 12.68 0.00 35.05 2.92
2161 4138 5.939883 TGTGGTTGATGAATGGTTTCTAGAG 59.060 40.000 0.00 0.00 32.78 2.43
2686 4665 7.661127 AATAAACACACTGTCGCTAATGTAA 57.339 32.000 0.00 0.00 0.00 2.41
2930 5745 4.223320 TGCAGCTTTAGTACAACTTTGC 57.777 40.909 0.00 0.00 0.00 3.68
2953 5790 9.326413 ACTACTTCCTACGATCCAAATTAATTG 57.674 33.333 0.39 0.00 38.84 2.32
2957 5794 9.976511 CAATACTACTTCCTACGATCCAAATTA 57.023 33.333 0.00 0.00 0.00 1.40
2958 5795 7.931948 CCAATACTACTTCCTACGATCCAAATT 59.068 37.037 0.00 0.00 0.00 1.82
2959 5796 7.070821 ACCAATACTACTTCCTACGATCCAAAT 59.929 37.037 0.00 0.00 0.00 2.32
2960 5797 6.381994 ACCAATACTACTTCCTACGATCCAAA 59.618 38.462 0.00 0.00 0.00 3.28
2986 5826 7.777910 TCCAATTAAATGGATACGAGGTGAATT 59.222 33.333 8.25 0.00 44.52 2.17
3014 5854 8.796475 TCTAAGATTCATTTCCTTGGTGAAAAG 58.204 33.333 0.00 0.00 37.74 2.27
3019 5859 6.040166 CCCATCTAAGATTCATTTCCTTGGTG 59.960 42.308 0.00 0.00 0.00 4.17
3026 5866 5.243283 AGCATGCCCATCTAAGATTCATTTC 59.757 40.000 15.66 0.00 0.00 2.17
3079 5919 4.742438 ACGACGTCTTGTTAAAATGCAT 57.258 36.364 14.70 0.00 0.00 3.96
3098 5939 6.926826 TGCATAGACAGGTTAATTGGTATACG 59.073 38.462 0.00 0.00 0.00 3.06
3104 5945 5.132502 TCCATGCATAGACAGGTTAATTGG 58.867 41.667 0.00 0.00 0.00 3.16
3333 6174 2.095768 CGACCTGCAACATGGTTAACAG 60.096 50.000 8.10 0.00 36.59 3.16
3408 6252 9.921637 AGAGAAAGCTATAGCAGAAACATATAC 57.078 33.333 26.07 5.93 45.16 1.47
3467 6311 4.146058 TGCAAGGCCGCATAGATG 57.854 55.556 0.59 0.00 36.86 2.90
3511 6355 0.540923 GGCATTCCTCTCTGCTCAGT 59.459 55.000 0.00 0.00 38.45 3.41
3519 6363 7.227156 TCAATAAAGGATAAGGCATTCCTCTC 58.773 38.462 3.75 0.00 43.40 3.20
3640 6781 6.691388 GCGTTGTTAAACTCATTCTTCAGTTT 59.309 34.615 2.84 2.84 43.65 2.66
3661 6802 5.758296 TCTTTTCAGTAAGATTGTCAGCGTT 59.242 36.000 0.00 0.00 0.00 4.84
3665 6806 9.352784 CTAGTCTCTTTTCAGTAAGATTGTCAG 57.647 37.037 0.00 0.00 33.89 3.51
3672 6813 6.376018 GCTCCTCTAGTCTCTTTTCAGTAAGA 59.624 42.308 0.00 0.00 33.33 2.10
4028 7169 4.053295 CTGAGAGTAAAACCGGACGAAAA 58.947 43.478 9.46 0.00 0.00 2.29
4116 7264 6.450845 TTTGTCAATTTTGCATGTCGATTC 57.549 33.333 0.00 0.00 0.00 2.52
4120 7268 6.647569 TCAAATTTGTCAATTTTGCATGTCG 58.352 32.000 20.61 4.08 40.09 4.35
4268 7416 3.390521 CCTGGCCAGGCGTGTAGA 61.391 66.667 38.39 0.00 42.44 2.59
4286 7434 1.758936 TCAGATCACACGGGTACGAT 58.241 50.000 0.00 0.00 44.60 3.73
4290 7438 6.045072 AGTAATTTTCAGATCACACGGGTA 57.955 37.500 0.00 0.00 0.00 3.69
4545 7693 0.178068 ACACTGTGAAACGCCTCACT 59.822 50.000 15.86 0.00 45.03 3.41
4556 7704 0.031585 GGCGTCACACTACACTGTGA 59.968 55.000 15.86 0.00 46.69 3.58
4588 7736 1.608590 CGGCTGACCTTTTTGTGTGAT 59.391 47.619 0.00 0.00 0.00 3.06
4678 7826 1.080093 ACACGCATGTCGATTCGGT 60.080 52.632 14.88 0.00 41.67 4.69
4683 7831 2.577449 TCATACACACGCATGTCGAT 57.423 45.000 14.88 2.01 41.67 3.59
4684 7832 2.459934 GATCATACACACGCATGTCGA 58.540 47.619 14.88 0.00 41.67 4.20
4685 7833 1.522676 GGATCATACACACGCATGTCG 59.477 52.381 7.79 7.79 45.38 4.35
4686 7834 2.549926 TGGATCATACACACGCATGTC 58.450 47.619 0.00 0.00 36.72 3.06
4687 7835 2.689553 TGGATCATACACACGCATGT 57.310 45.000 0.00 0.00 40.80 3.21
4688 7836 5.391203 CCAATATGGATCATACACACGCATG 60.391 44.000 0.00 0.00 40.96 4.06
4689 7837 4.696877 CCAATATGGATCATACACACGCAT 59.303 41.667 0.00 0.00 40.96 4.73
4690 7838 4.064388 CCAATATGGATCATACACACGCA 58.936 43.478 0.00 0.00 40.96 5.24
4691 7839 4.065088 ACCAATATGGATCATACACACGC 58.935 43.478 2.85 0.00 40.96 5.34
4692 7840 4.385748 CGACCAATATGGATCATACACACG 59.614 45.833 2.85 0.00 40.96 4.49
4726 7874 1.640428 ACACATACGCACAAGATCCG 58.360 50.000 0.00 0.00 0.00 4.18
4727 7875 3.123804 CCTACACATACGCACAAGATCC 58.876 50.000 0.00 0.00 0.00 3.36
4737 7885 4.436852 GCATTGTTTGACCCTACACATACG 60.437 45.833 0.00 0.00 0.00 3.06
4778 7926 2.394545 TACGTCATCCTGTATTCGCG 57.605 50.000 0.00 0.00 0.00 5.87
4779 7927 2.987149 CCATACGTCATCCTGTATTCGC 59.013 50.000 0.00 0.00 0.00 4.70
4780 7928 3.005472 ACCCATACGTCATCCTGTATTCG 59.995 47.826 0.00 0.00 0.00 3.34
4781 7929 4.602340 ACCCATACGTCATCCTGTATTC 57.398 45.455 0.00 0.00 0.00 1.75
4782 7930 5.367945 AAACCCATACGTCATCCTGTATT 57.632 39.130 0.00 0.00 0.00 1.89
4783 7931 5.123227 CAAAACCCATACGTCATCCTGTAT 58.877 41.667 0.00 0.00 0.00 2.29
4784 7932 4.509616 CAAAACCCATACGTCATCCTGTA 58.490 43.478 0.00 0.00 0.00 2.74
4785 7933 3.343617 CAAAACCCATACGTCATCCTGT 58.656 45.455 0.00 0.00 0.00 4.00
4786 7934 2.097466 GCAAAACCCATACGTCATCCTG 59.903 50.000 0.00 0.00 0.00 3.86
4787 7935 2.026262 AGCAAAACCCATACGTCATCCT 60.026 45.455 0.00 0.00 0.00 3.24
4788 7936 2.097466 CAGCAAAACCCATACGTCATCC 59.903 50.000 0.00 0.00 0.00 3.51
4887 9683 8.188531 AGTTTGAAACATTCACACATCAAAAG 57.811 30.769 11.02 0.00 41.57 2.27
4932 9728 4.172505 GAGCATGATATAGCAACCTCTCG 58.827 47.826 11.72 0.00 0.00 4.04
4945 9743 2.613595 GGCACAAACATCGAGCATGATA 59.386 45.455 0.00 0.00 36.21 2.15
5029 9834 4.445879 GGTTATGGTTATGGGAGGAAGGAC 60.446 50.000 0.00 0.00 0.00 3.85
5085 9890 1.291132 GCCGCTCCTACAATCTTGAC 58.709 55.000 0.00 0.00 0.00 3.18
5089 9896 2.017559 GACGGCCGCTCCTACAATCT 62.018 60.000 28.58 0.00 0.00 2.40
5090 9897 1.591863 GACGGCCGCTCCTACAATC 60.592 63.158 28.58 8.12 0.00 2.67
5091 9898 2.499685 GACGGCCGCTCCTACAAT 59.500 61.111 28.58 0.57 0.00 2.71
5106 9913 3.311110 TGGTGGCAGAGGTCGGAC 61.311 66.667 0.00 0.00 0.00 4.79
5107 9914 3.311110 GTGGTGGCAGAGGTCGGA 61.311 66.667 0.00 0.00 0.00 4.55
5108 9915 3.625897 TGTGGTGGCAGAGGTCGG 61.626 66.667 0.00 0.00 0.00 4.79



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

AutoCloner maintained by Alex Coulton.