Multiple sequence alignment - TraesCS4D01G348500

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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 TraesCS4D01G348500 chr4D 100.000 4164 0 0 1 4164 502069751 502065588 0.000000e+00 7690.0
1 TraesCS4D01G348500 chr4D 91.575 724 55 5 2435 3153 502063220 502063942 0.000000e+00 994.0
2 TraesCS4D01G348500 chr4D 86.093 942 72 31 3222 4107 502055526 502054588 0.000000e+00 959.0
3 TraesCS4D01G348500 chr4D 96.364 55 2 0 4110 4164 3627930 3627876 1.590000e-14 91.6
4 TraesCS4D01G348500 chr5A 88.159 1706 128 43 1498 3157 661215919 661214242 0.000000e+00 1964.0
5 TraesCS4D01G348500 chr5A 91.319 1198 51 19 2928 4085 684938654 684939838 0.000000e+00 1587.0
6 TraesCS4D01G348500 chr5A 93.194 764 44 6 2397 3157 684942033 684941275 0.000000e+00 1116.0
7 TraesCS4D01G348500 chr5A 88.565 927 66 27 3222 4109 684704700 684703775 0.000000e+00 1088.0
8 TraesCS4D01G348500 chr5A 88.013 901 59 26 525 1408 684944073 684943205 0.000000e+00 1020.0
9 TraesCS4D01G348500 chr5A 94.280 507 27 1 1759 2265 684942811 684942307 0.000000e+00 774.0
10 TraesCS4D01G348500 chr5A 94.631 298 8 3 1463 1760 684943205 684942916 4.910000e-124 455.0
11 TraesCS4D01G348500 chr5A 87.921 356 43 0 2580 2935 684759984 684760339 1.790000e-113 420.0
12 TraesCS4D01G348500 chr5A 81.621 506 67 21 2109 2592 684757823 684758324 3.020000e-106 396.0
13 TraesCS4D01G348500 chr5A 83.210 405 35 17 3 378 684944649 684944249 1.430000e-89 340.0
14 TraesCS4D01G348500 chr5A 84.184 196 20 5 1229 1423 684757422 684757607 3.310000e-41 180.0
15 TraesCS4D01G348500 chr5A 90.833 120 8 2 646 762 684943927 684943808 1.550000e-34 158.0
16 TraesCS4D01G348500 chr5A 96.610 59 2 0 1670 1728 684942866 684942808 9.530000e-17 99.0
17 TraesCS4D01G348500 chr5A 94.286 35 2 0 122 156 21009460 21009426 2.000000e-03 54.7
18 TraesCS4D01G348500 chr4B 87.507 1721 127 40 1482 3157 646188951 646187274 0.000000e+00 1906.0
19 TraesCS4D01G348500 chr4B 89.643 1120 55 23 3001 4085 646182389 646183482 0.000000e+00 1369.0
20 TraesCS4D01G348500 chr4B 84.100 1195 100 57 261 1428 646190173 646189042 0.000000e+00 1072.0
21 TraesCS4D01G348500 chr4B 88.690 893 74 14 3222 4091 646146644 646145756 0.000000e+00 1064.0
22 TraesCS4D01G348500 chr4B 93.310 568 38 0 3222 3789 646175235 646174668 0.000000e+00 839.0
23 TraesCS4D01G348500 chr4B 90.040 251 22 2 2756 3004 646178588 646178837 5.190000e-84 322.0
24 TraesCS4D01G348500 chr4B 78.834 326 27 10 3805 4088 646162631 646162306 9.200000e-42 182.0
25 TraesCS4D01G348500 chr4B 96.364 55 1 1 4111 4164 619456998 619457052 5.730000e-14 89.8
26 TraesCS4D01G348500 chrUn 90.040 251 22 2 2756 3004 391312806 391312557 5.190000e-84 322.0
27 TraesCS4D01G348500 chr3D 89.894 188 12 3 667 854 255227949 255228129 6.960000e-58 235.0
28 TraesCS4D01G348500 chr3D 96.364 55 0 2 4111 4164 11422411 11422358 5.730000e-14 89.8
29 TraesCS4D01G348500 chr2B 84.574 188 22 3 667 854 431265511 431265331 3.310000e-41 180.0
30 TraesCS4D01G348500 chr2B 88.800 125 13 1 671 795 431267149 431267026 7.210000e-33 152.0
31 TraesCS4D01G348500 chr2B 82.143 168 30 0 58 225 87531682 87531515 1.210000e-30 145.0
32 TraesCS4D01G348500 chr2B 96.429 56 2 0 4108 4163 768106354 768106409 4.430000e-15 93.5
33 TraesCS4D01G348500 chr5B 84.247 146 23 0 85 230 250601926 250601781 4.340000e-30 143.0
34 TraesCS4D01G348500 chr5B 92.063 63 4 1 4103 4164 268669707 268669645 2.060000e-13 87.9
35 TraesCS4D01G348500 chr2D 96.364 55 1 1 4110 4163 446308469 446308523 5.730000e-14 89.8
36 TraesCS4D01G348500 chr1B 96.364 55 1 1 4111 4164 9983802 9983856 5.730000e-14 89.8
37 TraesCS4D01G348500 chr5D 92.063 63 4 1 4103 4164 236254838 236254900 2.060000e-13 87.9
38 TraesCS4D01G348500 chr4A 93.220 59 2 2 4107 4164 731250717 731250660 7.420000e-13 86.1
39 TraesCS4D01G348500 chr7D 83.607 61 4 6 3457 3517 538603023 538603077 8.000000e-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 TraesCS4D01G348500 chr4D 502065588 502069751 4163 True 7690.0 7690 100.000000 1 4164 1 chr4D.!!$R3 4163
1 TraesCS4D01G348500 chr4D 502063220 502063942 722 False 994.0 994 91.575000 2435 3153 1 chr4D.!!$F1 718
2 TraesCS4D01G348500 chr4D 502054588 502055526 938 True 959.0 959 86.093000 3222 4107 1 chr4D.!!$R2 885
3 TraesCS4D01G348500 chr5A 661214242 661215919 1677 True 1964.0 1964 88.159000 1498 3157 1 chr5A.!!$R2 1659
4 TraesCS4D01G348500 chr5A 684938654 684939838 1184 False 1587.0 1587 91.319000 2928 4085 1 chr5A.!!$F1 1157
5 TraesCS4D01G348500 chr5A 684703775 684704700 925 True 1088.0 1088 88.565000 3222 4109 1 chr5A.!!$R3 887
6 TraesCS4D01G348500 chr5A 684941275 684944649 3374 True 566.0 1116 91.538714 3 3157 7 chr5A.!!$R4 3154
7 TraesCS4D01G348500 chr5A 684757422 684760339 2917 False 332.0 420 84.575333 1229 2935 3 chr5A.!!$F2 1706
8 TraesCS4D01G348500 chr4B 646187274 646190173 2899 True 1489.0 1906 85.803500 261 3157 2 chr4B.!!$R4 2896
9 TraesCS4D01G348500 chr4B 646145756 646146644 888 True 1064.0 1064 88.690000 3222 4091 1 chr4B.!!$R1 869
10 TraesCS4D01G348500 chr4B 646178588 646183482 4894 False 845.5 1369 89.841500 2756 4085 2 chr4B.!!$F2 1329
11 TraesCS4D01G348500 chr4B 646174668 646175235 567 True 839.0 839 93.310000 3222 3789 1 chr4B.!!$R3 567

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
921 1015 0.105039 GTCGAGGCAGATTACAGGGG 59.895 60.0 0.00 0.00 0.0 4.79 F
924 1018 0.464554 GAGGCAGATTACAGGGGCAC 60.465 60.0 0.00 0.00 0.0 5.01 F
2137 2418 0.304705 GAAACGCCGGCATAGATGTG 59.695 55.0 28.98 9.93 0.0 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2137 2418 0.036875 CTTCCTCCACACCAACCCTC 59.963 60.000 0.0 0.0 0.00 4.30 R
2443 2889 1.386748 CAGCGTCACACACTGTATTCG 59.613 52.381 0.0 0.0 0.00 3.34 R
4121 9920 0.035343 CCGGGGTCTTCCTCCTTTTC 60.035 60.000 0.0 0.0 35.33 2.29 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
28 29 0.808755 CTTCCATAAACCCGTGGTGC 59.191 55.000 0.00 0.00 35.34 5.01
52 53 2.676822 TTCCTCGCGAGTGCCTCT 60.677 61.111 32.41 0.00 38.08 3.69
112 123 4.398319 GAACATTTGGAAGGAGAGGAACA 58.602 43.478 0.00 0.00 0.00 3.18
118 129 1.202817 GGAAGGAGAGGAACAGTCGTC 59.797 57.143 0.00 0.00 38.66 4.20
153 164 3.947612 AGGATGACCTACCGAGAAGTA 57.052 47.619 0.00 0.00 45.83 2.24
178 190 2.919228 ACCAAGCCTTGACGGATATTC 58.081 47.619 5.89 0.00 33.16 1.75
179 191 2.238646 ACCAAGCCTTGACGGATATTCA 59.761 45.455 5.89 0.00 33.16 2.57
209 221 8.616076 ACACAGATCTAGTTGTTTTCTCTTTTG 58.384 33.333 0.00 0.00 0.00 2.44
218 231 5.652744 TGTTTTCTCTTTTGCGAGTAGTC 57.347 39.130 0.00 0.00 32.83 2.59
219 232 5.357257 TGTTTTCTCTTTTGCGAGTAGTCT 58.643 37.500 0.00 0.00 32.83 3.24
220 233 5.462398 TGTTTTCTCTTTTGCGAGTAGTCTC 59.538 40.000 0.00 0.00 37.35 3.36
225 238 3.258372 TCTTTTGCGAGTAGTCTCCATGT 59.742 43.478 0.00 0.00 37.40 3.21
228 241 0.592754 GCGAGTAGTCTCCATGTCGC 60.593 60.000 7.22 7.22 45.00 5.19
231 244 2.792890 CGAGTAGTCTCCATGTCGCTTG 60.793 54.545 0.00 0.00 37.40 4.01
232 245 2.164624 GAGTAGTCTCCATGTCGCTTGT 59.835 50.000 0.00 0.00 34.87 3.16
233 246 2.094494 AGTAGTCTCCATGTCGCTTGTG 60.094 50.000 0.00 0.00 0.00 3.33
234 247 0.969149 AGTCTCCATGTCGCTTGTGA 59.031 50.000 0.00 0.00 0.00 3.58
235 248 1.071605 GTCTCCATGTCGCTTGTGAC 58.928 55.000 7.31 7.31 39.37 3.67
240 253 4.921834 TGTCGCTTGTGACACACA 57.078 50.000 8.05 2.93 43.62 3.72
249 262 4.627788 TGACACACACACACACCC 57.372 55.556 0.00 0.00 0.00 4.61
250 263 1.078072 TGACACACACACACACCCC 60.078 57.895 0.00 0.00 0.00 4.95
251 264 1.078072 GACACACACACACACCCCA 60.078 57.895 0.00 0.00 0.00 4.96
252 265 0.678366 GACACACACACACACCCCAA 60.678 55.000 0.00 0.00 0.00 4.12
253 266 0.963355 ACACACACACACACCCCAAC 60.963 55.000 0.00 0.00 0.00 3.77
255 268 0.963355 ACACACACACACCCCAACAC 60.963 55.000 0.00 0.00 0.00 3.32
256 269 0.962855 CACACACACACCCCAACACA 60.963 55.000 0.00 0.00 0.00 3.72
257 270 0.963355 ACACACACACCCCAACACAC 60.963 55.000 0.00 0.00 0.00 3.82
258 271 0.962855 CACACACACCCCAACACACA 60.963 55.000 0.00 0.00 0.00 3.72
259 272 0.251386 ACACACACCCCAACACACAA 60.251 50.000 0.00 0.00 0.00 3.33
276 305 6.329496 ACACACAACAAATGGTGAAAGTAAG 58.671 36.000 5.28 0.00 38.38 2.34
327 357 7.041107 GTGAAATATCTTCTGAGAGAGCAGTT 58.959 38.462 0.00 0.00 37.20 3.16
331 361 3.495331 TCTTCTGAGAGAGCAGTTGACT 58.505 45.455 0.00 0.00 37.20 3.41
335 365 5.028549 TCTGAGAGAGCAGTTGACTTTTT 57.971 39.130 0.00 0.00 37.20 1.94
336 366 6.161855 TCTGAGAGAGCAGTTGACTTTTTA 57.838 37.500 0.00 0.00 37.20 1.52
403 433 4.380531 TGGAAGCACACAAAACACAAAAA 58.619 34.783 0.00 0.00 0.00 1.94
450 482 3.660970 TTGCTTTACCCCATGAGCATA 57.339 42.857 5.46 0.00 43.83 3.14
461 493 7.530426 ACCCCATGAGCATATTTATTTCTTC 57.470 36.000 0.00 0.00 0.00 2.87
481 513 4.264460 TCGCCAAAATAATGCACCTTTT 57.736 36.364 0.00 0.00 0.00 2.27
570 629 1.357761 CCCACCTGTCAAAATACCCCT 59.642 52.381 0.00 0.00 0.00 4.79
573 632 3.499563 CCACCTGTCAAAATACCCCTGAA 60.500 47.826 0.00 0.00 0.00 3.02
600 659 2.760634 TTCTCTTATGCTGCGGTTCA 57.239 45.000 0.00 0.00 0.00 3.18
738 825 2.203209 GCGCCGGGATTCCTCATT 60.203 61.111 2.18 0.00 0.00 2.57
740 827 1.447643 CGCCGGGATTCCTCATTCT 59.552 57.895 2.18 0.00 0.00 2.40
744 831 1.131638 CGGGATTCCTCATTCTCCCA 58.868 55.000 2.01 0.00 46.54 4.37
745 832 1.071385 CGGGATTCCTCATTCTCCCAG 59.929 57.143 2.01 0.00 46.54 4.45
747 834 2.412591 GGATTCCTCATTCTCCCAGGA 58.587 52.381 0.00 0.00 34.31 3.86
912 1006 4.074526 GCAGGCAGTCGAGGCAGA 62.075 66.667 10.78 0.00 36.37 4.26
921 1015 0.105039 GTCGAGGCAGATTACAGGGG 59.895 60.000 0.00 0.00 0.00 4.79
922 1016 1.227674 CGAGGCAGATTACAGGGGC 60.228 63.158 0.00 0.00 0.00 5.80
923 1017 1.915228 GAGGCAGATTACAGGGGCA 59.085 57.895 0.00 0.00 0.00 5.36
924 1018 0.464554 GAGGCAGATTACAGGGGCAC 60.465 60.000 0.00 0.00 0.00 5.01
1025 1123 2.515991 CTCCTCGCTCCTCTCGCT 60.516 66.667 0.00 0.00 0.00 4.93
1329 1433 2.639839 CCCTCTCACCCTTCTTCTCAAA 59.360 50.000 0.00 0.00 0.00 2.69
1366 1470 4.360951 TTGGGACTACGAAGGATTTGTT 57.639 40.909 0.00 0.00 40.60 2.83
1396 1500 4.183865 GTTTATTGCAAGCCTGGGAATTC 58.816 43.478 4.94 0.00 0.00 2.17
1423 1533 8.715191 ACAACTATCTCATCTGTCAAATCTTC 57.285 34.615 0.00 0.00 0.00 2.87
1425 1535 9.381033 CAACTATCTCATCTGTCAAATCTTCTT 57.619 33.333 0.00 0.00 0.00 2.52
1426 1536 8.945481 ACTATCTCATCTGTCAAATCTTCTTG 57.055 34.615 0.00 0.00 0.00 3.02
1428 1538 9.767228 CTATCTCATCTGTCAAATCTTCTTGAT 57.233 33.333 0.00 0.00 37.63 2.57
1429 1539 7.845066 TCTCATCTGTCAAATCTTCTTGATG 57.155 36.000 0.00 0.00 37.63 3.07
1430 1540 7.392418 TCTCATCTGTCAAATCTTCTTGATGT 58.608 34.615 0.00 0.00 37.63 3.06
1431 1541 8.534496 TCTCATCTGTCAAATCTTCTTGATGTA 58.466 33.333 0.00 0.00 37.63 2.29
1432 1542 8.484641 TCATCTGTCAAATCTTCTTGATGTAC 57.515 34.615 0.00 0.00 37.63 2.90
1434 1544 8.602328 CATCTGTCAAATCTTCTTGATGTACTC 58.398 37.037 0.00 0.00 37.63 2.59
1436 1546 8.316946 TCTGTCAAATCTTCTTGATGTACTCAT 58.683 33.333 0.00 0.00 37.63 2.90
1489 1641 1.589716 GCCTGGCCTGTTAGCAGTTG 61.590 60.000 7.66 0.00 41.02 3.16
1522 1674 9.739276 TTCATATGATCCCTAATTTCACATACC 57.261 33.333 6.17 0.00 0.00 2.73
1612 1770 8.902540 TGTCATAAATTGTTCACTTCTACTGT 57.097 30.769 0.00 0.00 0.00 3.55
1661 1819 9.855021 ACATCTAACACCAAACAAATATTTAGC 57.145 29.630 0.00 0.00 0.00 3.09
1730 1897 7.754924 GGTTTTCAGTCATACACAACAATATGG 59.245 37.037 0.00 0.00 30.98 2.74
1771 2044 5.811399 TGAAGAAATAATAACCAGCACCG 57.189 39.130 0.00 0.00 0.00 4.94
1821 2094 6.276832 ACGTACAGGTAACAGAACATATGT 57.723 37.500 1.41 1.41 41.41 2.29
1822 2095 6.694447 ACGTACAGGTAACAGAACATATGTT 58.306 36.000 20.93 20.93 43.15 2.71
1849 2122 1.821136 GCTTGCATAAGAACTTGGGCT 59.179 47.619 0.00 0.00 35.92 5.19
1850 2123 2.416431 GCTTGCATAAGAACTTGGGCTG 60.416 50.000 0.00 7.24 35.92 4.85
1886 2162 4.457257 GGTGCTGATAATTTCATAGGCTCC 59.543 45.833 0.00 0.00 32.78 4.70
1918 2199 4.495690 TGGTGTTGCTAATATGTGGCTA 57.504 40.909 0.00 0.00 0.00 3.93
1933 2214 2.614057 GTGGCTATGTGTGCAGGTATTC 59.386 50.000 0.00 0.00 0.00 1.75
2026 2307 2.936032 AGAACCCCTCCCTGCACC 60.936 66.667 0.00 0.00 0.00 5.01
2098 2379 5.132648 TGACCCAAATCCTATTGTAGCATCT 59.867 40.000 0.00 0.00 0.00 2.90
2137 2418 0.304705 GAAACGCCGGCATAGATGTG 59.695 55.000 28.98 9.93 0.00 3.21
2164 2445 1.678101 GGTGTGGAGGAAGCATTATGC 59.322 52.381 9.46 9.46 45.46 3.14
2209 2490 2.016318 CATCGCATGCTTACTGGGAAA 58.984 47.619 17.13 0.00 38.79 3.13
2256 2537 9.765795 AATATCCAACTACAAGTATCTTGCTAC 57.234 33.333 9.06 0.00 0.00 3.58
2270 2551 3.066900 TCTTGCTACGATTCTAGACTGGC 59.933 47.826 0.00 0.00 0.00 4.85
2279 2562 5.303078 ACGATTCTAGACTGGCAATATCAGT 59.697 40.000 0.00 0.00 46.82 3.41
2291 2574 6.851609 TGGCAATATCAGTACACACATTTTC 58.148 36.000 0.00 0.00 0.00 2.29
2361 2772 6.475076 TGCACAATATGTTCAAACTTTGTGTC 59.525 34.615 22.61 18.42 41.46 3.67
2375 2813 4.881273 ACTTTGTGTCACACTCATTGCTTA 59.119 37.500 9.90 0.00 35.11 3.09
2376 2814 5.008019 ACTTTGTGTCACACTCATTGCTTAG 59.992 40.000 9.90 0.00 35.11 2.18
2377 2815 4.071961 TGTGTCACACTCATTGCTTAGT 57.928 40.909 9.90 0.00 35.11 2.24
2427 2873 2.406596 ACCATTGCATGCCATTTTCC 57.593 45.000 16.68 0.00 0.00 3.13
2443 2889 6.455647 CCATTTTCCTTAGTCCTTTTTGTCC 58.544 40.000 0.00 0.00 0.00 4.02
2700 4820 2.327325 TAGTGCAGGGAGAAGGTTCT 57.673 50.000 0.00 0.00 41.00 3.01
2701 4821 0.689623 AGTGCAGGGAGAAGGTTCTG 59.310 55.000 0.00 0.00 37.73 3.02
2745 4865 1.135139 GAGGAGTCTGCATCTAACGCA 59.865 52.381 0.00 0.00 37.88 5.24
2769 4889 2.432300 CCTGGCCGATAGTCCCGTT 61.432 63.158 0.00 0.00 0.00 4.44
3069 8750 2.352127 GGTGAATGGAACTTTGCTGCTC 60.352 50.000 0.00 0.00 0.00 4.26
3106 8790 6.788598 AGCATCTTATCTTCTCTGTCTGAA 57.211 37.500 0.00 0.00 0.00 3.02
3122 8806 2.376518 TCTGAAGATTTGTGGCCTCCTT 59.623 45.455 3.32 0.00 0.00 3.36
3202 8905 2.647356 GCTCCTGCGCTCTCCTATA 58.353 57.895 9.73 0.00 0.00 1.31
3204 8907 0.885196 CTCCTGCGCTCTCCTATACC 59.115 60.000 9.73 0.00 0.00 2.73
3555 9273 3.154584 AACTTGTTCGTCGCCGGGA 62.155 57.895 2.18 0.00 33.95 5.14
3590 9308 0.996762 TGGTCCACCAACTCCCCTTT 60.997 55.000 0.00 0.00 44.35 3.11
3594 9312 0.184933 CCACCAACTCCCCTTTGACA 59.815 55.000 0.00 0.00 0.00 3.58
3766 9484 3.425713 CGACGTCGACGAGGGGAA 61.426 66.667 41.52 0.00 43.02 3.97
3839 9557 2.668550 GTCAGGGTGCCCGTTGTC 60.669 66.667 0.98 0.00 41.95 3.18
3859 9583 3.055580 GCTATCAGCGGGAGAGGG 58.944 66.667 5.44 0.00 35.35 4.30
3869 9593 0.105778 CGGGAGAGGGAGAAGAATGC 59.894 60.000 0.00 0.00 0.00 3.56
3923 9679 2.232298 CTGCGGAGGAGGAGGTTGAC 62.232 65.000 0.00 0.00 44.33 3.18
3939 9695 0.249953 TGACGCCGAAGCTGGTAAAA 60.250 50.000 0.00 0.00 36.60 1.52
3998 9759 4.336433 CACCAGCCATGTGGAATTAACTAG 59.664 45.833 9.25 0.00 40.44 2.57
3999 9760 3.316308 CCAGCCATGTGGAATTAACTAGC 59.684 47.826 2.55 0.00 40.44 3.42
4000 9761 4.202441 CAGCCATGTGGAATTAACTAGCT 58.798 43.478 2.55 0.00 37.39 3.32
4001 9762 5.368145 CAGCCATGTGGAATTAACTAGCTA 58.632 41.667 2.55 0.00 37.39 3.32
4002 9763 6.000219 CAGCCATGTGGAATTAACTAGCTAT 59.000 40.000 2.55 0.00 37.39 2.97
4004 9765 6.043706 AGCCATGTGGAATTAACTAGCTATCT 59.956 38.462 2.55 0.00 37.39 1.98
4005 9766 6.712547 GCCATGTGGAATTAACTAGCTATCTT 59.287 38.462 2.55 0.00 37.39 2.40
4006 9767 7.308229 GCCATGTGGAATTAACTAGCTATCTTG 60.308 40.741 2.55 0.00 37.39 3.02
4007 9768 7.308229 CCATGTGGAATTAACTAGCTATCTTGC 60.308 40.741 0.00 0.00 37.39 4.01
4063 9857 4.401022 TGCTGTGAAGGAGAAACAATGAT 58.599 39.130 0.00 0.00 0.00 2.45
4078 9872 9.507329 AGAAACAATGATAATACACACAGTTCT 57.493 29.630 0.00 0.00 0.00 3.01
4138 9937 4.652679 TTTAGAAAAGGAGGAAGACCCC 57.347 45.455 0.00 0.00 36.73 4.95
4139 9938 0.984995 AGAAAAGGAGGAAGACCCCG 59.015 55.000 0.00 0.00 36.73 5.73
4140 9939 0.035343 GAAAAGGAGGAAGACCCCGG 60.035 60.000 0.00 0.00 36.73 5.73
4141 9940 2.138453 AAAAGGAGGAAGACCCCGGC 62.138 60.000 0.00 0.00 36.73 6.13
4144 9943 3.471806 GAGGAAGACCCCGGCCTC 61.472 72.222 7.66 7.66 40.04 4.70
4145 9944 3.986116 GAGGAAGACCCCGGCCTCT 62.986 68.421 14.36 4.99 42.81 3.69
4146 9945 3.787001 GGAAGACCCCGGCCTCTG 61.787 72.222 0.00 0.00 0.00 3.35
4147 9946 4.475135 GAAGACCCCGGCCTCTGC 62.475 72.222 0.00 0.00 0.00 4.26
4150 9949 4.554036 GACCCCGGCCTCTGCATC 62.554 72.222 0.00 0.00 40.13 3.91
4152 9951 4.559063 CCCCGGCCTCTGCATCTG 62.559 72.222 0.00 0.00 40.13 2.90
4153 9952 4.559063 CCCGGCCTCTGCATCTGG 62.559 72.222 0.00 0.00 40.13 3.86
4154 9953 3.473647 CCGGCCTCTGCATCTGGA 61.474 66.667 0.00 0.00 40.13 3.86
4155 9954 2.815945 CCGGCCTCTGCATCTGGAT 61.816 63.158 0.00 0.00 40.13 3.41
4156 9955 1.597302 CGGCCTCTGCATCTGGATG 60.597 63.158 0.00 6.24 41.60 3.51
4157 9956 1.834996 GGCCTCTGCATCTGGATGA 59.165 57.895 13.96 0.04 41.20 2.92
4158 9957 0.400975 GGCCTCTGCATCTGGATGAT 59.599 55.000 13.96 0.00 41.20 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.885297 CGGGTTTATGGAAGAATCAGCAT 59.115 43.478 0.00 0.00 0.00 3.79
1 2 3.278574 CGGGTTTATGGAAGAATCAGCA 58.721 45.455 0.00 0.00 0.00 4.41
28 29 2.809601 CTCGCGAGGAACCCAACG 60.810 66.667 28.40 0.00 0.00 4.10
52 53 0.748367 ATCTCACTACGCTCCGCTCA 60.748 55.000 0.00 0.00 0.00 4.26
118 129 4.363999 GTCATCCTCTTGTCGGTGAATAG 58.636 47.826 0.00 0.00 0.00 1.73
144 155 2.541556 GCTTGGTTAGCTACTTCTCGG 58.458 52.381 0.00 0.00 46.77 4.63
168 179 6.740110 AGATCTGTGTAAGTGAATATCCGTC 58.260 40.000 0.00 0.00 0.00 4.79
169 180 6.716934 AGATCTGTGTAAGTGAATATCCGT 57.283 37.500 0.00 0.00 0.00 4.69
178 190 8.594881 AGAAAACAACTAGATCTGTGTAAGTG 57.405 34.615 5.18 2.91 0.00 3.16
179 191 8.643324 AGAGAAAACAACTAGATCTGTGTAAGT 58.357 33.333 5.18 0.00 0.00 2.24
209 221 0.592754 GCGACATGGAGACTACTCGC 60.593 60.000 4.27 4.27 43.44 5.03
218 231 0.792640 GTGTCACAAGCGACATGGAG 59.207 55.000 0.00 0.00 46.98 3.86
219 232 0.105778 TGTGTCACAAGCGACATGGA 59.894 50.000 2.31 0.00 46.98 3.41
220 233 0.235665 GTGTGTCACAAGCGACATGG 59.764 55.000 7.38 0.00 46.98 3.66
231 244 1.373590 GGGGTGTGTGTGTGTGTCAC 61.374 60.000 0.00 0.00 46.31 3.67
232 245 1.078072 GGGGTGTGTGTGTGTGTCA 60.078 57.895 0.00 0.00 0.00 3.58
233 246 0.678366 TTGGGGTGTGTGTGTGTGTC 60.678 55.000 0.00 0.00 0.00 3.67
234 247 0.963355 GTTGGGGTGTGTGTGTGTGT 60.963 55.000 0.00 0.00 0.00 3.72
235 248 0.962855 TGTTGGGGTGTGTGTGTGTG 60.963 55.000 0.00 0.00 0.00 3.82
237 250 0.962855 TGTGTTGGGGTGTGTGTGTG 60.963 55.000 0.00 0.00 0.00 3.82
239 252 0.962855 TGTGTGTTGGGGTGTGTGTG 60.963 55.000 0.00 0.00 0.00 3.82
240 253 0.251386 TTGTGTGTTGGGGTGTGTGT 60.251 50.000 0.00 0.00 0.00 3.72
243 256 0.891373 TTGTTGTGTGTTGGGGTGTG 59.109 50.000 0.00 0.00 0.00 3.82
244 257 1.633774 TTTGTTGTGTGTTGGGGTGT 58.366 45.000 0.00 0.00 0.00 4.16
245 258 2.548875 CATTTGTTGTGTGTTGGGGTG 58.451 47.619 0.00 0.00 0.00 4.61
246 259 1.484240 CCATTTGTTGTGTGTTGGGGT 59.516 47.619 0.00 0.00 0.00 4.95
247 260 1.484240 ACCATTTGTTGTGTGTTGGGG 59.516 47.619 0.00 0.00 0.00 4.96
249 262 3.516981 TCACCATTTGTTGTGTGTTGG 57.483 42.857 0.00 0.00 34.14 3.77
250 263 4.928615 ACTTTCACCATTTGTTGTGTGTTG 59.071 37.500 0.00 0.00 34.14 3.33
251 264 5.146010 ACTTTCACCATTTGTTGTGTGTT 57.854 34.783 0.00 0.00 34.14 3.32
252 265 4.799564 ACTTTCACCATTTGTTGTGTGT 57.200 36.364 0.00 0.00 34.14 3.72
253 266 6.559810 TCTTACTTTCACCATTTGTTGTGTG 58.440 36.000 0.00 0.00 34.14 3.82
255 268 7.257722 ACTTCTTACTTTCACCATTTGTTGTG 58.742 34.615 0.00 0.00 0.00 3.33
256 269 7.339466 AGACTTCTTACTTTCACCATTTGTTGT 59.661 33.333 0.00 0.00 0.00 3.32
257 270 7.707104 AGACTTCTTACTTTCACCATTTGTTG 58.293 34.615 0.00 0.00 0.00 3.33
258 271 7.881775 AGACTTCTTACTTTCACCATTTGTT 57.118 32.000 0.00 0.00 0.00 2.83
259 272 7.775561 AGAAGACTTCTTACTTTCACCATTTGT 59.224 33.333 12.12 0.00 36.36 2.83
293 323 3.199946 AGAAGATATTTCACTTCCCCGCA 59.800 43.478 0.00 0.00 42.09 5.69
450 482 8.603181 GTGCATTATTTTGGCGAAGAAATAAAT 58.397 29.630 11.57 0.00 39.65 1.40
461 493 6.476896 CAATAAAAGGTGCATTATTTTGGCG 58.523 36.000 13.56 0.00 31.17 5.69
473 505 3.793797 ATAACGGGCAATAAAAGGTGC 57.206 42.857 0.00 0.00 40.14 5.01
912 1006 2.045340 GTGCGGTGCCCCTGTAAT 60.045 61.111 0.00 0.00 0.00 1.89
921 1015 3.615536 GATTGCCTGTGTGCGGTGC 62.616 63.158 0.00 0.00 0.00 5.01
922 1016 2.562912 GATTGCCTGTGTGCGGTG 59.437 61.111 0.00 0.00 0.00 4.94
923 1017 2.672996 GGATTGCCTGTGTGCGGT 60.673 61.111 0.00 0.00 0.00 5.68
924 1018 1.804396 TTTGGATTGCCTGTGTGCGG 61.804 55.000 0.00 0.00 34.31 5.69
925 1019 0.031857 TTTTGGATTGCCTGTGTGCG 59.968 50.000 0.00 0.00 34.31 5.34
926 1020 1.787012 CTTTTGGATTGCCTGTGTGC 58.213 50.000 0.00 0.00 34.31 4.57
927 1021 1.606224 GGCTTTTGGATTGCCTGTGTG 60.606 52.381 0.00 0.00 43.05 3.82
928 1022 0.681175 GGCTTTTGGATTGCCTGTGT 59.319 50.000 0.00 0.00 43.05 3.72
929 1023 0.680618 TGGCTTTTGGATTGCCTGTG 59.319 50.000 0.00 0.00 46.23 3.66
930 1024 0.971386 CTGGCTTTTGGATTGCCTGT 59.029 50.000 0.00 0.00 46.23 4.00
931 1025 0.248289 CCTGGCTTTTGGATTGCCTG 59.752 55.000 0.00 0.00 46.23 4.85
932 1026 1.547472 GCCTGGCTTTTGGATTGCCT 61.547 55.000 12.43 0.00 46.23 4.75
933 1027 1.078918 GCCTGGCTTTTGGATTGCC 60.079 57.895 12.43 0.00 46.26 4.52
934 1028 0.108472 GAGCCTGGCTTTTGGATTGC 60.108 55.000 24.26 2.24 39.88 3.56
935 1029 0.171903 CGAGCCTGGCTTTTGGATTG 59.828 55.000 24.26 0.00 39.88 2.67
1149 1247 1.927210 CATGTAGTGCGCGTCCATC 59.073 57.895 8.43 0.00 0.00 3.51
1366 1470 4.025360 AGGCTTGCAATAAACATCATCCA 58.975 39.130 0.00 0.00 0.00 3.41
1396 1500 8.489990 AGATTTGACAGATGAGATAGTTGTTG 57.510 34.615 0.00 0.00 0.00 3.33
1426 1536 8.328864 GGAAATTCTGTTAACGATGAGTACATC 58.671 37.037 0.26 0.00 46.50 3.06
1428 1538 6.592607 GGGAAATTCTGTTAACGATGAGTACA 59.407 38.462 0.26 0.00 0.00 2.90
1429 1539 6.036844 GGGGAAATTCTGTTAACGATGAGTAC 59.963 42.308 0.26 0.00 0.00 2.73
1430 1540 6.070424 AGGGGAAATTCTGTTAACGATGAGTA 60.070 38.462 0.26 0.00 0.00 2.59
1431 1541 4.941873 GGGGAAATTCTGTTAACGATGAGT 59.058 41.667 0.26 0.00 0.00 3.41
1432 1542 5.186198 AGGGGAAATTCTGTTAACGATGAG 58.814 41.667 0.26 0.00 0.00 2.90
1434 1544 6.995511 TTAGGGGAAATTCTGTTAACGATG 57.004 37.500 0.26 0.00 0.00 3.84
1436 1546 6.954232 AGATTAGGGGAAATTCTGTTAACGA 58.046 36.000 0.26 0.00 0.00 3.85
1437 1547 7.625828 AAGATTAGGGGAAATTCTGTTAACG 57.374 36.000 0.26 0.00 0.00 3.18
1439 1549 9.470399 GGTAAAGATTAGGGGAAATTCTGTTAA 57.530 33.333 0.00 0.00 0.00 2.01
1440 1550 8.616598 TGGTAAAGATTAGGGGAAATTCTGTTA 58.383 33.333 0.00 0.00 0.00 2.41
1441 1551 7.475299 TGGTAAAGATTAGGGGAAATTCTGTT 58.525 34.615 0.00 0.00 0.00 3.16
1443 1553 7.119387 ACTGGTAAAGATTAGGGGAAATTCTG 58.881 38.462 0.00 0.00 0.00 3.02
1444 1554 7.285340 ACTGGTAAAGATTAGGGGAAATTCT 57.715 36.000 0.00 0.00 0.00 2.40
1446 1556 7.061054 GCTACTGGTAAAGATTAGGGGAAATT 58.939 38.462 0.00 0.00 0.00 1.82
1449 1559 4.411212 GGCTACTGGTAAAGATTAGGGGAA 59.589 45.833 0.00 0.00 0.00 3.97
1533 1686 2.231235 AGCGCTGGTTTTTCCTAAATGG 59.769 45.455 10.39 0.00 37.07 3.16
1614 1772 8.184968 AGATGTATCTATCATCTGCTGGACAGT 61.185 40.741 7.49 0.00 46.61 3.55
1661 1819 7.849804 ACTGGCTACAAGTGATAGTTATTTG 57.150 36.000 0.00 0.00 0.00 2.32
1667 1825 5.656859 TGACATACTGGCTACAAGTGATAGT 59.343 40.000 0.00 0.00 0.00 2.12
1771 2044 6.094193 AGGGTAATAGCCGAATACTACAAC 57.906 41.667 2.53 0.00 41.56 3.32
1849 2122 4.014569 TCAGCACCATTGTACTTTAGCA 57.985 40.909 0.00 0.00 0.00 3.49
1850 2123 6.677781 TTATCAGCACCATTGTACTTTAGC 57.322 37.500 0.00 0.00 0.00 3.09
1918 2199 2.113860 AAGCGAATACCTGCACACAT 57.886 45.000 0.00 0.00 0.00 3.21
1933 2214 2.097038 CCCTGCGTCTCTCAAAGCG 61.097 63.158 0.00 0.00 0.00 4.68
2026 2307 1.159285 TGGCTTTGATGAGTGCTTCG 58.841 50.000 0.00 0.00 0.00 3.79
2098 2379 7.422399 CGTTTCTGAGTTTTTCAATCCCTTTA 58.578 34.615 0.00 0.00 34.81 1.85
2137 2418 0.036875 CTTCCTCCACACCAACCCTC 59.963 60.000 0.00 0.00 0.00 4.30
2209 2490 1.780503 ACCTCAAAGTTGCAAAGGCT 58.219 45.000 13.02 0.00 41.91 4.58
2256 2537 5.777802 ACTGATATTGCCAGTCTAGAATCG 58.222 41.667 0.00 0.00 40.55 3.34
2270 2551 5.965334 GGCGAAAATGTGTGTACTGATATTG 59.035 40.000 0.00 0.00 0.00 1.90
2279 2562 3.472652 AGAACTGGCGAAAATGTGTGTA 58.527 40.909 0.00 0.00 0.00 2.90
2291 2574 8.095169 ACCTATTCCTATATTTAAGAACTGGCG 58.905 37.037 0.00 0.00 0.00 5.69
2361 2772 6.017109 ACCAAAGTAACTAAGCAATGAGTGTG 60.017 38.462 0.00 0.00 0.00 3.82
2411 2857 4.141869 GGACTAAGGAAAATGGCATGCAAT 60.142 41.667 21.36 11.73 0.00 3.56
2427 2873 6.649557 ACTGTATTCGGACAAAAAGGACTAAG 59.350 38.462 0.00 0.00 0.00 2.18
2443 2889 1.386748 CAGCGTCACACACTGTATTCG 59.613 52.381 0.00 0.00 0.00 3.34
2638 4758 1.432270 GCGCCAGCCTCTTGTGATAC 61.432 60.000 0.00 0.00 37.42 2.24
2700 4820 3.930229 CGAGAAACGGGATGTGTAATTCA 59.070 43.478 0.00 0.00 38.46 2.57
2701 4821 4.032558 GTCGAGAAACGGGATGTGTAATTC 59.967 45.833 0.00 0.00 42.82 2.17
2745 4865 2.249139 GGACTATCGGCCAGGACTATT 58.751 52.381 2.24 0.00 0.00 1.73
2769 4889 3.151710 CCCGATGGCTCCACGGTA 61.152 66.667 20.30 0.00 44.34 4.02
3069 8750 7.551585 AGATAAGATGCTACAAATATCCCTCG 58.448 38.462 0.00 0.00 0.00 4.63
3106 8790 2.962859 ACAAAAGGAGGCCACAAATCT 58.037 42.857 5.01 0.00 0.00 2.40
3122 8806 2.672098 ACATGGCTGGGTGTTTACAAA 58.328 42.857 0.00 0.00 0.00 2.83
3199 8902 1.152504 TCCGACGCCATGGGGTATA 60.153 57.895 32.26 18.32 41.41 1.47
3590 9308 2.522436 AACCCGTCGGAGGTGTCA 60.522 61.111 14.39 0.00 37.78 3.58
3594 9312 3.308705 GTGGAACCCGTCGGAGGT 61.309 66.667 14.39 0.51 40.14 3.85
3766 9484 3.688159 GGTACGTGCCGGTCCACT 61.688 66.667 7.01 0.00 33.60 4.00
3859 9583 2.553172 GCATCATCCTGGCATTCTTCTC 59.447 50.000 0.00 0.00 0.00 2.87
3869 9593 2.537560 GGCGTTCGCATCATCCTGG 61.538 63.158 18.46 0.00 0.00 4.45
3939 9695 2.483188 GGGACAACGCCGAGATCTAATT 60.483 50.000 0.00 0.00 0.00 1.40
3994 9755 5.174395 CAACACTTGAGCAAGATAGCTAGT 58.826 41.667 16.47 0.00 46.75 2.57
3998 9759 2.485426 TGCAACACTTGAGCAAGATAGC 59.515 45.455 16.47 13.50 40.79 2.97
3999 9760 4.754372 TTGCAACACTTGAGCAAGATAG 57.246 40.909 16.47 8.42 42.71 2.08
4005 9766 5.512753 TCTTTTATTGCAACACTTGAGCA 57.487 34.783 0.00 0.00 36.32 4.26
4006 9767 7.412137 AAATCTTTTATTGCAACACTTGAGC 57.588 32.000 0.00 0.00 0.00 4.26
4115 9914 5.391256 GGGGTCTTCCTCCTTTTCTAAAAA 58.609 41.667 0.00 0.00 35.33 1.94
4116 9915 4.506095 CGGGGTCTTCCTCCTTTTCTAAAA 60.506 45.833 0.00 0.00 35.33 1.52
4117 9916 3.008704 CGGGGTCTTCCTCCTTTTCTAAA 59.991 47.826 0.00 0.00 35.33 1.85
4118 9917 2.570302 CGGGGTCTTCCTCCTTTTCTAA 59.430 50.000 0.00 0.00 35.33 2.10
4119 9918 2.185387 CGGGGTCTTCCTCCTTTTCTA 58.815 52.381 0.00 0.00 35.33 2.10
4120 9919 0.984995 CGGGGTCTTCCTCCTTTTCT 59.015 55.000 0.00 0.00 35.33 2.52
4121 9920 0.035343 CCGGGGTCTTCCTCCTTTTC 60.035 60.000 0.00 0.00 35.33 2.29
4122 9921 2.075837 CCGGGGTCTTCCTCCTTTT 58.924 57.895 0.00 0.00 35.33 2.27
4123 9922 2.603652 GCCGGGGTCTTCCTCCTTT 61.604 63.158 2.18 0.00 35.33 3.11
4124 9923 3.009714 GCCGGGGTCTTCCTCCTT 61.010 66.667 2.18 0.00 35.33 3.36
4127 9926 3.471806 GAGGCCGGGGTCTTCCTC 61.472 72.222 2.18 5.59 38.40 3.71
4128 9927 4.012721 AGAGGCCGGGGTCTTCCT 62.013 66.667 2.18 0.00 35.33 3.36
4129 9928 3.787001 CAGAGGCCGGGGTCTTCC 61.787 72.222 2.18 0.00 0.00 3.46
4130 9929 4.475135 GCAGAGGCCGGGGTCTTC 62.475 72.222 2.18 0.00 0.00 2.87
4133 9932 4.554036 GATGCAGAGGCCGGGGTC 62.554 72.222 2.18 0.00 40.13 4.46
4135 9934 4.559063 CAGATGCAGAGGCCGGGG 62.559 72.222 2.18 0.00 40.13 5.73
4136 9935 4.559063 CCAGATGCAGAGGCCGGG 62.559 72.222 2.18 0.00 40.13 5.73
4137 9936 2.815945 ATCCAGATGCAGAGGCCGG 61.816 63.158 0.00 0.00 40.13 6.13
4138 9937 1.597302 CATCCAGATGCAGAGGCCG 60.597 63.158 0.00 0.00 40.13 6.13
4139 9938 0.400975 ATCATCCAGATGCAGAGGCC 59.599 55.000 0.00 0.00 40.13 5.19
4140 9939 1.524848 CATCATCCAGATGCAGAGGC 58.475 55.000 2.63 0.00 46.90 4.70


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

AutoCloner maintained by Alex Coulton.