Multiple sequence alignment - TraesCS7D01G472900

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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 TraesCS7D01G472900 chr7D 100.000 2999 0 0 1 2999 586028363 586031361 0.000000e+00 5539.0
1 TraesCS7D01G472900 chr7D 89.577 1065 95 11 973 2022 585666909 585667972 0.000000e+00 1338.0
2 TraesCS7D01G472900 chr7D 91.785 353 26 1 1669 2018 585657007 585657359 3.470000e-134 488.0
3 TraesCS7D01G472900 chr7D 78.095 315 27 22 587 899 585666482 585666756 8.600000e-36 161.0
4 TraesCS7D01G472900 chr7D 87.838 74 7 2 709 781 585726942 585727014 5.330000e-13 86.1
5 TraesCS7D01G472900 chr7D 97.368 38 1 0 906 943 585666802 585666839 6.940000e-07 65.8
6 TraesCS7D01G472900 chr7B 93.821 1052 62 3 973 2022 656286792 656287842 0.000000e+00 1580.0
7 TraesCS7D01G472900 chr7B 90.215 1022 83 9 994 1999 656419860 656420880 0.000000e+00 1317.0
8 TraesCS7D01G472900 chr7B 91.493 670 27 19 251 908 656419053 656419704 0.000000e+00 894.0
9 TraesCS7D01G472900 chr7B 87.405 262 23 2 1 252 59609240 59608979 2.920000e-75 292.0
10 TraesCS7D01G472900 chr7B 78.370 319 32 21 587 899 656286347 656286634 3.970000e-39 172.0
11 TraesCS7D01G472900 chr7B 83.871 93 8 6 905 994 656419726 656419814 6.890000e-12 82.4
12 TraesCS7D01G472900 chr7B 84.615 78 6 4 973 1048 656245252 656245325 4.150000e-09 73.1
13 TraesCS7D01G472900 chr7B 97.368 38 1 0 906 943 656286682 656286719 6.940000e-07 65.8
14 TraesCS7D01G472900 chr5B 93.813 986 48 4 2023 2999 61583796 61584777 0.000000e+00 1471.0
15 TraesCS7D01G472900 chr2D 94.209 967 49 2 2040 2999 630314882 630315848 0.000000e+00 1469.0
16 TraesCS7D01G472900 chr2D 92.974 982 63 2 2023 2999 419377932 419376952 0.000000e+00 1426.0
17 TraesCS7D01G472900 chr2D 88.142 253 29 1 2 253 382954601 382954853 1.750000e-77 300.0
18 TraesCS7D01G472900 chr2D 87.218 266 22 4 2 255 543591029 543591294 2.920000e-75 292.0
19 TraesCS7D01G472900 chr2D 87.072 263 23 6 1 253 481281934 481282195 1.360000e-73 287.0
20 TraesCS7D01G472900 chr2D 94.318 88 5 0 2 89 367919815 367919728 5.210000e-28 135.0
21 TraesCS7D01G472900 chr4D 94.450 955 48 1 2050 2999 74409638 74410592 0.000000e+00 1465.0
22 TraesCS7D01G472900 chr4D 93.661 978 53 3 2031 2999 422200068 422199091 0.000000e+00 1454.0
23 TraesCS7D01G472900 chr1D 93.693 983 55 3 2023 2999 434608202 434607221 0.000000e+00 1465.0
24 TraesCS7D01G472900 chr1D 82.031 384 42 14 994 1374 487949066 487949425 4.860000e-78 302.0
25 TraesCS7D01G472900 chr1D 86.538 260 25 4 5 255 466975735 466975477 8.190000e-71 278.0
26 TraesCS7D01G472900 chr1D 85.214 257 27 5 1047 1302 488545533 488545287 1.380000e-63 254.0
27 TraesCS7D01G472900 chr1D 88.608 79 6 3 1 77 441562731 441562654 3.180000e-15 93.5
28 TraesCS7D01G472900 chr7A 95.969 893 36 0 1130 2022 676517623 676518515 0.000000e+00 1450.0
29 TraesCS7D01G472900 chr7A 94.177 893 52 0 1130 2022 676539464 676540356 0.000000e+00 1362.0
30 TraesCS7D01G472900 chr7A 88.569 1041 78 18 988 2023 676360608 676359604 0.000000e+00 1225.0
31 TraesCS7D01G472900 chr7A 89.088 669 42 15 251 908 677387154 677387802 0.000000e+00 802.0
32 TraesCS7D01G472900 chr7A 89.368 649 44 8 988 1629 682175803 682175173 0.000000e+00 793.0
33 TraesCS7D01G472900 chr7A 90.867 427 33 5 973 1394 677387927 677388352 4.340000e-158 568.0
34 TraesCS7D01G472900 chr7A 92.068 353 25 1 1669 2018 682175175 682174823 7.470000e-136 494.0
35 TraesCS7D01G472900 chr7A 91.036 357 29 1 1669 2022 682179364 682179008 2.090000e-131 479.0
36 TraesCS7D01G472900 chr7A 83.836 464 27 16 498 951 676514739 676515164 6.020000e-107 398.0
37 TraesCS7D01G472900 chr7A 87.143 350 39 4 1493 1836 677433468 677433817 2.800000e-105 392.0
38 TraesCS7D01G472900 chr7A 85.171 263 26 4 1 252 30454937 30455197 1.070000e-64 257.0
39 TraesCS7D01G472900 chr7A 94.964 139 5 2 1013 1150 676516549 676516686 1.810000e-52 217.0
40 TraesCS7D01G472900 chr7A 77.922 308 27 23 597 902 682176244 682175976 1.440000e-33 154.0
41 TraesCS7D01G472900 chr7A 76.774 310 33 22 587 892 676361061 676360787 1.450000e-28 137.0
42 TraesCS7D01G472900 chr7A 82.143 112 15 5 905 1014 677387825 677387933 1.140000e-14 91.6
43 TraesCS7D01G472900 chr7A 100.000 38 0 0 906 943 676360729 676360692 1.490000e-08 71.3
44 TraesCS7D01G472900 chr2A 92.559 981 66 3 2024 2999 9996053 9997031 0.000000e+00 1400.0
45 TraesCS7D01G472900 chr2A 92.608 974 61 2 2031 2999 566666929 566667896 0.000000e+00 1389.0
46 TraesCS7D01G472900 chr2A 86.742 264 25 2 2 255 29592009 29591746 4.890000e-73 285.0
47 TraesCS7D01G472900 chr4B 92.065 983 68 3 2022 2999 615553920 615552943 0.000000e+00 1375.0
48 TraesCS7D01G472900 chr4B 87.833 263 22 2 2 254 88933652 88933390 1.750000e-77 300.0
49 TraesCS7D01G472900 chr5D 89.328 253 26 1 1 252 286167692 286167944 1.740000e-82 316.0
50 TraesCS7D01G472900 chr6D 87.452 263 23 2 1 253 151317474 151317212 8.130000e-76 294.0
51 TraesCS7D01G472900 chr1A 80.151 398 57 15 994 1374 586950122 586950514 8.190000e-71 278.0
52 TraesCS7D01G472900 chr1A 87.778 90 11 0 1 90 502509173 502509262 4.090000e-19 106.0
53 TraesCS7D01G472900 chr2B 94.382 89 3 2 2 89 436958147 436958060 5.210000e-28 135.0
54 TraesCS7D01G472900 chr3D 89.024 82 5 2 1 78 236634595 236634676 6.840000e-17 99.0
55 TraesCS7D01G472900 chr3B 95.652 46 2 0 393 438 723652722 723652677 1.150000e-09 75.0


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 TraesCS7D01G472900 chr7D 586028363 586031361 2998 False 5539.000000 5539 100.000000 1 2999 1 chr7D.!!$F3 2998
1 TraesCS7D01G472900 chr7D 585666482 585667972 1490 False 521.600000 1338 88.346667 587 2022 3 chr7D.!!$F4 1435
2 TraesCS7D01G472900 chr7B 656419053 656420880 1827 False 764.466667 1317 88.526333 251 1999 3 chr7B.!!$F3 1748
3 TraesCS7D01G472900 chr7B 656286347 656287842 1495 False 605.933333 1580 89.853000 587 2022 3 chr7B.!!$F2 1435
4 TraesCS7D01G472900 chr5B 61583796 61584777 981 False 1471.000000 1471 93.813000 2023 2999 1 chr5B.!!$F1 976
5 TraesCS7D01G472900 chr2D 630314882 630315848 966 False 1469.000000 1469 94.209000 2040 2999 1 chr2D.!!$F4 959
6 TraesCS7D01G472900 chr2D 419376952 419377932 980 True 1426.000000 1426 92.974000 2023 2999 1 chr2D.!!$R2 976
7 TraesCS7D01G472900 chr4D 74409638 74410592 954 False 1465.000000 1465 94.450000 2050 2999 1 chr4D.!!$F1 949
8 TraesCS7D01G472900 chr4D 422199091 422200068 977 True 1454.000000 1454 93.661000 2031 2999 1 chr4D.!!$R1 968
9 TraesCS7D01G472900 chr1D 434607221 434608202 981 True 1465.000000 1465 93.693000 2023 2999 1 chr1D.!!$R1 976
10 TraesCS7D01G472900 chr7A 676539464 676540356 892 False 1362.000000 1362 94.177000 1130 2022 1 chr7A.!!$F2 892
11 TraesCS7D01G472900 chr7A 676514739 676518515 3776 False 688.333333 1450 91.589667 498 2022 3 chr7A.!!$F4 1524
12 TraesCS7D01G472900 chr7A 677387154 677388352 1198 False 487.200000 802 87.366000 251 1394 3 chr7A.!!$F5 1143
13 TraesCS7D01G472900 chr7A 682174823 682179364 4541 True 480.000000 793 87.598500 597 2022 4 chr7A.!!$R2 1425
14 TraesCS7D01G472900 chr7A 676359604 676361061 1457 True 477.766667 1225 88.447667 587 2023 3 chr7A.!!$R1 1436
15 TraesCS7D01G472900 chr2A 9996053 9997031 978 False 1400.000000 1400 92.559000 2024 2999 1 chr2A.!!$F1 975
16 TraesCS7D01G472900 chr2A 566666929 566667896 967 False 1389.000000 1389 92.608000 2031 2999 1 chr2A.!!$F2 968
17 TraesCS7D01G472900 chr4B 615552943 615553920 977 True 1375.000000 1375 92.065000 2022 2999 1 chr4B.!!$R2 977

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
954 3569 0.038744 CCAACTCATCCCACCAAGCT 59.961 55.0 0.0 0.0 0.0 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2896 7913 0.309302 TTCCGCCAAATGTGACGTTG 59.691 50.0 0.0 0.0 0.0 4.1 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
24 25 5.832539 ACTCCCTCCATTCCATAATGTAG 57.167 43.478 0.00 0.00 40.84 2.74
25 26 5.227593 ACTCCCTCCATTCCATAATGTAGT 58.772 41.667 0.00 0.00 40.84 2.73
26 27 5.072329 ACTCCCTCCATTCCATAATGTAGTG 59.928 44.000 0.00 0.00 40.84 2.74
28 29 4.446167 CCCTCCATTCCATAATGTAGTGCA 60.446 45.833 0.00 0.00 40.84 4.57
29 30 5.319453 CCTCCATTCCATAATGTAGTGCAT 58.681 41.667 0.00 0.00 40.84 3.96
30 31 6.475504 CCTCCATTCCATAATGTAGTGCATA 58.524 40.000 0.00 0.00 40.84 3.14
31 32 7.114754 CCTCCATTCCATAATGTAGTGCATAT 58.885 38.462 0.00 0.00 40.84 1.78
35 36 9.842775 CCATTCCATAATGTAGTGCATATAGAT 57.157 33.333 0.00 0.00 40.84 1.98
49 50 9.453572 AGTGCATATAGATTTTTCTGAAAGTCA 57.546 29.630 15.39 2.26 34.85 3.41
108 109 9.461312 ACATCTACAATACCAAACATGTACATT 57.539 29.630 5.37 0.00 0.00 2.71
143 144 4.154737 ACCGATGATTTATCCAATGATGCG 59.845 41.667 0.00 0.00 31.82 4.73
144 145 4.093514 CGATGATTTATCCAATGATGCGC 58.906 43.478 0.00 0.00 31.82 6.09
145 146 4.378666 CGATGATTTATCCAATGATGCGCA 60.379 41.667 14.96 14.96 31.82 6.09
146 147 5.647589 GATGATTTATCCAATGATGCGCAT 58.352 37.500 25.66 25.66 39.43 4.73
148 149 5.845103 TGATTTATCCAATGATGCGCATTT 58.155 33.333 26.12 13.26 44.68 2.32
149 150 5.692654 TGATTTATCCAATGATGCGCATTTG 59.307 36.000 26.12 23.85 44.68 2.32
151 152 1.184431 TCCAATGATGCGCATTTGGT 58.816 45.000 35.67 15.75 44.68 3.67
153 154 2.957680 TCCAATGATGCGCATTTGGTAT 59.042 40.909 35.67 20.04 44.68 2.73
154 155 3.384146 TCCAATGATGCGCATTTGGTATT 59.616 39.130 35.67 23.26 44.68 1.89
156 157 4.500205 CCAATGATGCGCATTTGGTATTCT 60.500 41.667 32.16 8.88 44.68 2.40
158 159 6.384224 CAATGATGCGCATTTGGTATTCTAT 58.616 36.000 26.12 0.00 44.68 1.98
159 160 7.361971 CCAATGATGCGCATTTGGTATTCTATA 60.362 37.037 32.16 5.31 44.68 1.31
160 161 7.870509 ATGATGCGCATTTGGTATTCTATAT 57.129 32.000 26.12 0.00 31.73 0.86
161 162 7.075674 TGATGCGCATTTGGTATTCTATATG 57.924 36.000 26.12 0.00 0.00 1.78
162 163 6.654582 TGATGCGCATTTGGTATTCTATATGT 59.345 34.615 26.12 0.00 0.00 2.29
163 164 7.821846 TGATGCGCATTTGGTATTCTATATGTA 59.178 33.333 26.12 0.00 0.00 2.29
164 165 7.359262 TGCGCATTTGGTATTCTATATGTAC 57.641 36.000 5.66 0.00 0.00 2.90
166 167 6.594159 GCGCATTTGGTATTCTATATGTACCT 59.406 38.462 0.30 0.00 38.89 3.08
167 168 7.762615 GCGCATTTGGTATTCTATATGTACCTA 59.237 37.037 0.30 0.00 38.89 3.08
168 169 9.817809 CGCATTTGGTATTCTATATGTACCTAT 57.182 33.333 0.00 0.00 38.89 2.57
186 187 8.989131 TGTACCTATTTTTCTCTAAGCTATGGT 58.011 33.333 0.00 0.00 0.00 3.55
187 188 9.478768 GTACCTATTTTTCTCTAAGCTATGGTC 57.521 37.037 0.00 0.00 0.00 4.02
188 189 8.090788 ACCTATTTTTCTCTAAGCTATGGTCA 57.909 34.615 0.00 0.00 0.00 4.02
190 191 9.396022 CCTATTTTTCTCTAAGCTATGGTCAAA 57.604 33.333 0.00 0.00 0.00 2.69
192 193 8.870075 ATTTTTCTCTAAGCTATGGTCAAAGT 57.130 30.769 0.00 0.00 0.00 2.66
193 194 8.691661 TTTTTCTCTAAGCTATGGTCAAAGTT 57.308 30.769 0.00 0.00 0.00 2.66
194 195 8.691661 TTTTCTCTAAGCTATGGTCAAAGTTT 57.308 30.769 0.00 0.00 0.00 2.66
196 197 6.769512 TCTCTAAGCTATGGTCAAAGTTTGT 58.230 36.000 15.08 0.00 0.00 2.83
197 198 7.903145 TCTCTAAGCTATGGTCAAAGTTTGTA 58.097 34.615 15.08 4.30 0.00 2.41
198 199 8.372459 TCTCTAAGCTATGGTCAAAGTTTGTAA 58.628 33.333 15.08 3.22 0.00 2.41
199 200 9.167311 CTCTAAGCTATGGTCAAAGTTTGTAAT 57.833 33.333 15.08 9.74 0.00 1.89
200 201 8.946085 TCTAAGCTATGGTCAAAGTTTGTAATG 58.054 33.333 15.08 4.20 0.00 1.90
201 202 7.524717 AAGCTATGGTCAAAGTTTGTAATGT 57.475 32.000 15.08 2.79 0.00 2.71
202 203 7.524717 AGCTATGGTCAAAGTTTGTAATGTT 57.475 32.000 15.08 0.79 0.00 2.71
203 204 7.951591 AGCTATGGTCAAAGTTTGTAATGTTT 58.048 30.769 15.08 0.00 0.00 2.83
205 206 7.865385 GCTATGGTCAAAGTTTGTAATGTTTGA 59.135 33.333 15.08 0.00 36.74 2.69
248 249 8.731591 AGGAACTATATTATAAAACGGAGGGA 57.268 34.615 0.00 0.00 36.02 4.20
268 269 9.403583 GGAGGGAGTATTATTTTTGATGTAACA 57.596 33.333 0.00 0.00 0.00 2.41
310 311 1.200519 CGTCCAAGGACATTCCCCTA 58.799 55.000 18.57 0.00 44.77 3.53
382 386 7.846644 ACAACAAACATGTGATGTCATTTTT 57.153 28.000 15.58 0.00 44.07 1.94
493 506 1.708027 GCGCTTGCTAAGTGTACGG 59.292 57.895 0.00 0.00 41.04 4.02
704 3247 0.460987 CTTTCTTCGCCTCGCTCCAT 60.461 55.000 0.00 0.00 0.00 3.41
754 3299 1.828660 CCTACCGCACGGAGATCCT 60.829 63.158 17.40 0.00 38.96 3.24
755 3300 1.360551 CTACCGCACGGAGATCCTG 59.639 63.158 17.40 0.00 38.96 3.86
761 3306 0.179081 GCACGGAGATCCTGTAACCC 60.179 60.000 0.00 0.00 0.00 4.11
767 3312 3.116174 GGAGATCCTGTAACCCTTCCTT 58.884 50.000 0.00 0.00 0.00 3.36
892 3444 6.086371 CGATTTCCTTCTTTTACAAGTTTCGC 59.914 38.462 0.00 0.00 0.00 4.70
945 3558 1.839424 CCAACCTTCCCAACTCATCC 58.161 55.000 0.00 0.00 0.00 3.51
950 3563 0.698238 CTTCCCAACTCATCCCACCA 59.302 55.000 0.00 0.00 0.00 4.17
951 3564 1.075374 CTTCCCAACTCATCCCACCAA 59.925 52.381 0.00 0.00 0.00 3.67
952 3565 0.698238 TCCCAACTCATCCCACCAAG 59.302 55.000 0.00 0.00 0.00 3.61
954 3569 0.038744 CCAACTCATCCCACCAAGCT 59.961 55.000 0.00 0.00 0.00 3.74
955 3570 1.457346 CAACTCATCCCACCAAGCTC 58.543 55.000 0.00 0.00 0.00 4.09
958 3573 1.202330 CTCATCCCACCAAGCTCTCT 58.798 55.000 0.00 0.00 0.00 3.10
960 3575 0.179936 CATCCCACCAAGCTCTCTCC 59.820 60.000 0.00 0.00 0.00 3.71
961 3576 0.985490 ATCCCACCAAGCTCTCTCCC 60.985 60.000 0.00 0.00 0.00 4.30
962 3585 2.674220 CCCACCAAGCTCTCTCCCC 61.674 68.421 0.00 0.00 0.00 4.81
987 3629 0.540365 ACAACCACCAGCCAATCCAG 60.540 55.000 0.00 0.00 0.00 3.86
991 3633 1.607178 CACCAGCCAATCCAGCCAA 60.607 57.895 0.00 0.00 0.00 4.52
1233 6210 1.614824 CTTCCAGCTCCCCTCCACT 60.615 63.158 0.00 0.00 0.00 4.00
1423 6412 1.144969 GCGAACCAAAGATGTCGACA 58.855 50.000 22.48 22.48 0.00 4.35
1434 6423 2.094494 AGATGTCGACAGCAACGAGAAT 60.094 45.455 32.88 9.27 40.37 2.40
1446 6435 1.745115 CGAGAATGAGGCGGCCAAA 60.745 57.895 23.09 9.12 0.00 3.28
1602 6597 1.610522 CAGCAAAAGCTAGCACCAACT 59.389 47.619 18.83 5.62 0.00 3.16
1805 6800 1.538687 GCTGCCATGGAAGCCAAAGT 61.539 55.000 32.20 0.00 40.87 2.66
1932 6927 2.488347 GGCAAGGAACAACAAGGAGGTA 60.488 50.000 0.00 0.00 0.00 3.08
1935 6930 4.461198 CAAGGAACAACAAGGAGGTAGTT 58.539 43.478 0.00 0.00 0.00 2.24
1947 6942 0.464373 AGGTAGTTGCCATCGCCATG 60.464 55.000 0.00 0.00 0.00 3.66
2075 7074 6.724893 AAAAGTTTAAGCATTACACCTGGT 57.275 33.333 0.00 0.00 31.81 4.00
2115 7114 1.597027 ACCGCCAACAAAGTCCTCG 60.597 57.895 0.00 0.00 0.00 4.63
2133 7134 3.311322 CCTCGCGACAAGCCAATATAAAA 59.689 43.478 3.71 0.00 44.76 1.52
2290 7294 2.530701 ACAGGTCTCGATTCTCCACTT 58.469 47.619 0.00 0.00 0.00 3.16
2311 7315 6.655003 CACTTGTTGTAGACAGGACCATAAAT 59.345 38.462 0.00 0.00 39.94 1.40
2408 7412 5.018809 ACATAGCCAAAGTGACCAAATCAT 58.981 37.500 0.00 0.00 40.28 2.45
2431 7435 1.684386 AAGCGCTCCCATCCTGAGAG 61.684 60.000 12.06 0.00 33.41 3.20
2456 7460 6.603201 GGAATTCTAAACCTGTGATCAATCCA 59.397 38.462 5.23 0.00 0.00 3.41
2556 7560 8.773645 CATATAGAACGAGCCAATTTACAATGA 58.226 33.333 0.00 0.00 0.00 2.57
2679 7688 6.019075 CGACGAAGATACCATGCAAAGATTTA 60.019 38.462 0.00 0.00 0.00 1.40
2742 7755 5.675684 TTATCAACTGGCATGTCTGACTA 57.324 39.130 11.50 0.00 0.00 2.59
2775 7788 7.611467 AGCTCTATACATAGAATCCACTGAGAG 59.389 40.741 0.87 0.00 38.80 3.20
2811 7824 6.370442 CCATGTAAGTTCCAACGAAAGACATA 59.630 38.462 0.00 0.00 30.99 2.29
2821 7834 3.798202 ACGAAAGACATAGGATCCTTGC 58.202 45.455 22.03 13.08 0.00 4.01
2822 7835 3.197766 ACGAAAGACATAGGATCCTTGCA 59.802 43.478 22.03 1.44 0.00 4.08
2826 7839 4.148128 AGACATAGGATCCTTGCAACAG 57.852 45.455 22.03 5.01 0.00 3.16
2896 7913 6.993308 GTCTAGGTCCAATTAAATCCCTTCTC 59.007 42.308 0.00 0.00 0.00 2.87
2950 7967 4.724798 ACCTTGGCAATAGTATCACCCTTA 59.275 41.667 0.00 0.00 0.00 2.69
2973 7990 5.066968 TGACGCACAACATTGTATAGAGA 57.933 39.130 0.00 0.00 39.91 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 5.832539 CTACATTATGGAATGGAGGGAGT 57.167 43.478 2.44 0.00 46.58 3.85
8 9 9.045745 TCTATATGCACTACATTATGGAATGGA 57.954 33.333 0.00 0.00 45.83 3.41
9 10 9.842775 ATCTATATGCACTACATTATGGAATGG 57.157 33.333 0.00 0.00 45.83 3.16
23 24 9.453572 TGACTTTCAGAAAAATCTATATGCACT 57.546 29.630 0.00 0.00 0.00 4.40
79 80 9.811995 GTACATGTTTGGTATTGTAGATGTAGA 57.188 33.333 2.30 0.00 0.00 2.59
80 81 9.594478 TGTACATGTTTGGTATTGTAGATGTAG 57.406 33.333 2.30 0.00 0.00 2.74
82 83 9.461312 AATGTACATGTTTGGTATTGTAGATGT 57.539 29.630 9.63 0.00 31.34 3.06
116 117 8.892723 GCATCATTGGATAAATCATCGGTTATA 58.107 33.333 0.00 0.00 34.12 0.98
117 118 7.414429 CGCATCATTGGATAAATCATCGGTTAT 60.414 37.037 0.00 0.00 34.12 1.89
118 119 6.128309 CGCATCATTGGATAAATCATCGGTTA 60.128 38.462 0.00 0.00 34.12 2.85
119 120 5.335113 CGCATCATTGGATAAATCATCGGTT 60.335 40.000 0.00 0.00 34.12 4.44
120 121 4.154737 CGCATCATTGGATAAATCATCGGT 59.845 41.667 0.00 0.00 34.12 4.69
121 122 4.655027 CGCATCATTGGATAAATCATCGG 58.345 43.478 0.00 0.00 34.12 4.18
123 124 5.050644 TGCGCATCATTGGATAAATCATC 57.949 39.130 5.66 0.00 30.87 2.92
127 128 4.992319 CCAAATGCGCATCATTGGATAAAT 59.008 37.500 35.13 11.75 44.23 1.40
128 129 4.141981 ACCAAATGCGCATCATTGGATAAA 60.142 37.500 40.59 9.05 44.23 1.40
129 130 3.384146 ACCAAATGCGCATCATTGGATAA 59.616 39.130 40.59 9.24 44.23 1.75
130 131 2.957680 ACCAAATGCGCATCATTGGATA 59.042 40.909 40.59 9.75 44.23 2.59
131 132 1.758280 ACCAAATGCGCATCATTGGAT 59.242 42.857 40.59 28.30 44.23 3.41
132 133 1.184431 ACCAAATGCGCATCATTGGA 58.816 45.000 40.59 11.18 44.23 3.53
133 134 2.867287 TACCAAATGCGCATCATTGG 57.133 45.000 35.84 35.84 44.23 3.16
134 135 4.613944 AGAATACCAAATGCGCATCATTG 58.386 39.130 25.53 23.59 44.23 2.82
136 137 7.337689 ACATATAGAATACCAAATGCGCATCAT 59.662 33.333 25.53 13.30 36.87 2.45
137 138 6.654582 ACATATAGAATACCAAATGCGCATCA 59.345 34.615 25.53 7.19 0.00 3.07
139 140 7.065803 GGTACATATAGAATACCAAATGCGCAT 59.934 37.037 19.28 19.28 38.61 4.73
160 161 8.989131 ACCATAGCTTAGAGAAAAATAGGTACA 58.011 33.333 0.00 0.00 0.00 2.90
161 162 9.478768 GACCATAGCTTAGAGAAAAATAGGTAC 57.521 37.037 0.00 0.00 0.00 3.34
162 163 9.209048 TGACCATAGCTTAGAGAAAAATAGGTA 57.791 33.333 0.00 0.00 0.00 3.08
163 164 8.090788 TGACCATAGCTTAGAGAAAAATAGGT 57.909 34.615 0.00 0.00 0.00 3.08
164 165 8.964476 TTGACCATAGCTTAGAGAAAAATAGG 57.036 34.615 0.00 0.00 0.00 2.57
166 167 9.959721 ACTTTGACCATAGCTTAGAGAAAAATA 57.040 29.630 0.00 0.00 0.00 1.40
167 168 8.870075 ACTTTGACCATAGCTTAGAGAAAAAT 57.130 30.769 0.00 0.00 0.00 1.82
168 169 8.691661 AACTTTGACCATAGCTTAGAGAAAAA 57.308 30.769 0.00 0.00 0.00 1.94
169 170 8.567948 CAAACTTTGACCATAGCTTAGAGAAAA 58.432 33.333 0.00 0.00 0.00 2.29
170 171 7.719633 ACAAACTTTGACCATAGCTTAGAGAAA 59.280 33.333 8.55 0.00 0.00 2.52
171 172 7.224297 ACAAACTTTGACCATAGCTTAGAGAA 58.776 34.615 8.55 0.00 0.00 2.87
173 174 8.547967 TTACAAACTTTGACCATAGCTTAGAG 57.452 34.615 8.55 0.00 0.00 2.43
174 175 8.946085 CATTACAAACTTTGACCATAGCTTAGA 58.054 33.333 8.55 0.00 0.00 2.10
175 176 8.730680 ACATTACAAACTTTGACCATAGCTTAG 58.269 33.333 8.55 0.00 0.00 2.18
176 177 8.630054 ACATTACAAACTTTGACCATAGCTTA 57.370 30.769 8.55 0.00 0.00 3.09
178 179 7.524717 AACATTACAAACTTTGACCATAGCT 57.475 32.000 8.55 0.00 0.00 3.32
179 180 7.865385 TCAAACATTACAAACTTTGACCATAGC 59.135 33.333 8.55 0.00 29.66 2.97
180 181 9.180678 GTCAAACATTACAAACTTTGACCATAG 57.819 33.333 8.55 0.00 43.35 2.23
185 186 8.911247 AGAAGTCAAACATTACAAACTTTGAC 57.089 30.769 8.55 12.19 46.84 3.18
222 223 9.827198 TCCCTCCGTTTTATAATATAGTTCCTA 57.173 33.333 0.00 0.00 0.00 2.94
223 224 8.731591 TCCCTCCGTTTTATAATATAGTTCCT 57.268 34.615 0.00 0.00 0.00 3.36
224 225 8.591940 ACTCCCTCCGTTTTATAATATAGTTCC 58.408 37.037 0.00 0.00 0.00 3.62
235 236 9.689501 TCAAAAATAATACTCCCTCCGTTTTAT 57.310 29.630 0.00 0.00 0.00 1.40
237 238 8.466798 CATCAAAAATAATACTCCCTCCGTTTT 58.533 33.333 0.00 0.00 0.00 2.43
238 239 7.614192 ACATCAAAAATAATACTCCCTCCGTTT 59.386 33.333 0.00 0.00 0.00 3.60
240 241 6.659824 ACATCAAAAATAATACTCCCTCCGT 58.340 36.000 0.00 0.00 0.00 4.69
241 242 8.557029 GTTACATCAAAAATAATACTCCCTCCG 58.443 37.037 0.00 0.00 0.00 4.63
242 243 9.403583 TGTTACATCAAAAATAATACTCCCTCC 57.596 33.333 0.00 0.00 0.00 4.30
244 245 9.975218 ACTGTTACATCAAAAATAATACTCCCT 57.025 29.630 0.00 0.00 0.00 4.20
268 269 7.422399 ACGCACTTTATTAACATCAAACAACT 58.578 30.769 0.00 0.00 0.00 3.16
379 383 7.599245 AGTTTGGTTTCATTTACGTGACAAAAA 59.401 29.630 0.00 0.00 29.28 1.94
382 386 6.197364 AGTTTGGTTTCATTTACGTGACAA 57.803 33.333 0.00 0.00 0.00 3.18
399 403 8.330466 ACTCATCTAGACGAGATATAGTTTGG 57.670 38.462 22.00 0.00 43.52 3.28
754 3299 4.595781 AGTCATGTGTAAGGAAGGGTTACA 59.404 41.667 0.00 0.00 37.91 2.41
755 3300 5.161943 AGTCATGTGTAAGGAAGGGTTAC 57.838 43.478 0.00 0.00 0.00 2.50
761 3306 3.056821 TCGTGGAGTCATGTGTAAGGAAG 60.057 47.826 0.00 0.00 0.00 3.46
767 3312 3.181490 GCATACTCGTGGAGTCATGTGTA 60.181 47.826 0.85 0.00 42.40 2.90
892 3444 5.874261 TCGTGTATATATGGCATGGTTGATG 59.126 40.000 10.98 0.00 34.84 3.07
945 3558 1.492133 TTGGGGAGAGAGCTTGGTGG 61.492 60.000 0.00 0.00 0.00 4.61
950 3563 1.988107 TGTGATTTGGGGAGAGAGCTT 59.012 47.619 0.00 0.00 0.00 3.74
951 3564 1.661463 TGTGATTTGGGGAGAGAGCT 58.339 50.000 0.00 0.00 0.00 4.09
952 3565 2.087646 GTTGTGATTTGGGGAGAGAGC 58.912 52.381 0.00 0.00 0.00 4.09
954 3569 2.061848 TGGTTGTGATTTGGGGAGAGA 58.938 47.619 0.00 0.00 0.00 3.10
955 3570 2.162681 GTGGTTGTGATTTGGGGAGAG 58.837 52.381 0.00 0.00 0.00 3.20
958 3573 0.558220 TGGTGGTTGTGATTTGGGGA 59.442 50.000 0.00 0.00 0.00 4.81
960 3575 0.318120 GCTGGTGGTTGTGATTTGGG 59.682 55.000 0.00 0.00 0.00 4.12
961 3576 0.318120 GGCTGGTGGTTGTGATTTGG 59.682 55.000 0.00 0.00 0.00 3.28
962 3585 1.039068 TGGCTGGTGGTTGTGATTTG 58.961 50.000 0.00 0.00 0.00 2.32
987 3629 3.608432 GCCATGAGGAAGGTTGGC 58.392 61.111 0.00 0.00 46.94 4.52
991 3633 4.115199 GGCCGCCATGAGGAAGGT 62.115 66.667 3.91 0.00 36.82 3.50
1233 6210 3.356639 GATGTCGTCGAGGCTGGCA 62.357 63.158 3.38 0.00 0.00 4.92
1406 6395 2.143122 TGCTGTCGACATCTTTGGTTC 58.857 47.619 20.40 1.03 0.00 3.62
1423 6412 1.448540 CCGCCTCATTCTCGTTGCT 60.449 57.895 0.00 0.00 0.00 3.91
1446 6435 4.626081 GTGGTGCTGTCGTGGCCT 62.626 66.667 3.32 0.00 0.00 5.19
1450 6439 1.291877 GGCTTAGTGGTGCTGTCGTG 61.292 60.000 0.00 0.00 0.00 4.35
1566 6555 1.419762 TGCTGTTCTTCCTTGTGCCTA 59.580 47.619 0.00 0.00 0.00 3.93
1602 6597 6.567687 TTCACTTCTTGTTCTTTGTTCACA 57.432 33.333 0.00 0.00 0.00 3.58
1805 6800 1.376466 GCCTTCTTCTCCAGCACCA 59.624 57.895 0.00 0.00 0.00 4.17
1837 6832 2.740055 CACGCGCTCTTTCCAGCT 60.740 61.111 5.73 0.00 37.25 4.24
1900 6895 0.850100 TTCCTTGCCTTCTCCACCAA 59.150 50.000 0.00 0.00 0.00 3.67
1947 6942 3.191539 CCGAGCGAGAAAGCAGCC 61.192 66.667 0.00 0.00 40.15 4.85
2055 7054 5.013183 AGAGACCAGGTGTAATGCTTAAACT 59.987 40.000 0.00 0.00 0.00 2.66
2072 7071 5.818136 GCATTTTAGTTATGCAGAGACCA 57.182 39.130 0.00 0.00 45.93 4.02
2099 7098 2.556287 GCGAGGACTTTGTTGGCG 59.444 61.111 0.00 0.00 0.00 5.69
2115 7114 6.119144 TCTTCTTTTATATTGGCTTGTCGC 57.881 37.500 0.00 0.00 38.13 5.19
2133 7134 6.173339 TCATCTTTGTATTTCGCCTTCTTCT 58.827 36.000 0.00 0.00 0.00 2.85
2290 7294 6.367374 TCATTTATGGTCCTGTCTACAACA 57.633 37.500 0.00 0.00 36.18 3.33
2311 7315 7.079568 ATCTATAGATGTATCGGGACGCTTCA 61.080 42.308 14.60 0.00 42.54 3.02
2431 7435 6.603201 TGGATTGATCACAGGTTTAGAATTCC 59.397 38.462 0.65 0.00 0.00 3.01
2556 7560 7.514435 CGCACGACAATAAAACATTTGTTCTTT 60.514 33.333 0.00 0.00 37.25 2.52
2578 7582 2.476185 GCAATGTGTATTCTGTCCGCAC 60.476 50.000 0.00 0.00 0.00 5.34
2587 7596 5.501715 CATGGAAGTACGCAATGTGTATTC 58.498 41.667 10.02 13.02 31.13 1.75
2742 7755 9.319060 TGGATTCTATGTATAGAGCTTTGATCT 57.681 33.333 2.21 0.00 40.23 2.75
2775 7788 4.157840 GGAACTTACATGGGAATGGACAAC 59.842 45.833 0.00 0.00 0.00 3.32
2811 7824 0.403271 ACAGCTGTTGCAAGGATCCT 59.597 50.000 15.25 9.02 42.74 3.24
2821 7834 2.157834 TAACCACGGTACAGCTGTTG 57.842 50.000 27.06 16.85 33.66 3.33
2822 7835 2.486918 GTTAACCACGGTACAGCTGTT 58.513 47.619 27.06 9.41 33.66 3.16
2826 7839 1.629345 GCGGTTAACCACGGTACAGC 61.629 60.000 24.14 12.59 35.14 4.40
2896 7913 0.309302 TTCCGCCAAATGTGACGTTG 59.691 50.000 0.00 0.00 0.00 4.10
2950 7967 5.660460 TCTCTATACAATGTTGTGCGTCAT 58.340 37.500 8.57 0.00 42.31 3.06
2973 7990 5.511545 GCTACTCTCCGGAAACAATATCCAT 60.512 44.000 5.23 0.00 36.74 3.41


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

AutoCloner maintained by Alex Coulton.