Multiple sequence alignment - TraesCS6A01G378600

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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 TraesCS6A01G378600 chr6A 100.000 4127 0 0 1 4127 599714112 599718238 0.000000e+00 7622.0
1 TraesCS6A01G378600 chr6A 83.057 1086 127 29 2112 3160 599260604 599261669 0.000000e+00 933.0
2 TraesCS6A01G378600 chr6A 85.109 920 94 24 2294 3172 599622007 599622924 0.000000e+00 900.0
3 TraesCS6A01G378600 chr6A 82.819 518 53 17 1556 2067 599621155 599621642 8.200000e-117 431.0
4 TraesCS6A01G378600 chr6A 95.545 202 8 1 1323 1524 599259532 599259732 5.150000e-84 322.0
5 TraesCS6A01G378600 chr6A 89.222 167 14 3 295 459 599258677 599258841 5.410000e-49 206.0
6 TraesCS6A01G378600 chr6A 76.484 455 47 33 647 1085 599258961 599259371 4.210000e-45 193.0
7 TraesCS6A01G378600 chr6A 78.516 256 37 11 1846 2092 599260310 599260556 7.150000e-33 152.0
8 TraesCS6A01G378600 chr6A 83.230 161 18 4 2966 3117 599215484 599215644 5.560000e-29 139.0
9 TraesCS6A01G378600 chr6A 93.333 60 4 0 2272 2331 599203546 599203605 5.680000e-14 89.8
10 TraesCS6A01G378600 chr6D 90.798 1967 134 31 2095 4045 453346657 453348592 0.000000e+00 2586.0
11 TraesCS6A01G378600 chr6D 89.002 1773 99 55 281 2003 453344803 453346529 0.000000e+00 2106.0
12 TraesCS6A01G378600 chr6D 84.622 1086 101 32 2095 3154 453240119 453241164 0.000000e+00 1020.0
13 TraesCS6A01G378600 chr6D 84.906 583 65 13 2596 3160 453188501 453189078 5.990000e-158 568.0
14 TraesCS6A01G378600 chr6D 85.501 469 38 14 2112 2570 453187924 453188372 2.910000e-126 462.0
15 TraesCS6A01G378600 chr6D 86.413 368 38 6 1160 1525 453186479 453186836 3.870000e-105 392.0
16 TraesCS6A01G378600 chr6D 92.446 278 6 3 1 277 453344237 453344500 2.330000e-102 383.0
17 TraesCS6A01G378600 chr6D 76.289 776 68 59 270 1024 453185716 453186396 1.440000e-79 307.0
18 TraesCS6A01G378600 chr6D 84.062 320 24 8 442 761 453239405 453239697 2.430000e-72 283.0
19 TraesCS6A01G378600 chr6D 84.477 277 30 9 1816 2089 453239821 453240087 1.140000e-65 261.0
20 TraesCS6A01G378600 chr6D 93.878 49 3 0 1037 1085 453186391 453186439 1.590000e-09 75.0
21 TraesCS6A01G378600 chr6B 89.990 1958 154 23 2123 4054 688606700 688604759 0.000000e+00 2492.0
22 TraesCS6A01G378600 chr6B 89.059 1179 60 37 641 1764 688608263 688607099 0.000000e+00 1399.0
23 TraesCS6A01G378600 chr6B 83.544 1106 122 35 2095 3182 688665288 688664225 0.000000e+00 979.0
24 TraesCS6A01G378600 chr6B 89.802 353 26 4 1194 1536 688666422 688666070 1.050000e-120 444.0
25 TraesCS6A01G378600 chr6B 89.744 351 19 5 682 1020 688666782 688666437 2.280000e-117 433.0
26 TraesCS6A01G378600 chr6B 88.920 352 30 3 2238 2584 688757216 688756869 3.810000e-115 425.0
27 TraesCS6A01G378600 chr6B 87.921 356 32 7 1160 1513 688758586 688758240 3.840000e-110 409.0
28 TraesCS6A01G378600 chr6B 86.389 360 25 10 243 594 688667117 688666774 5.040000e-99 372.0
29 TraesCS6A01G378600 chr6B 78.622 566 78 20 2608 3160 688756736 688756201 6.610000e-88 335.0
30 TraesCS6A01G378600 chr6B 83.425 362 16 11 1599 1943 688665993 688665659 3.120000e-76 296.0
31 TraesCS6A01G378600 chr7D 80.081 246 26 12 2302 2546 438368653 438368876 1.190000e-35 161.0


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 TraesCS6A01G378600 chr6A 599714112 599718238 4126 False 7622.000000 7622 100.000000 1 4127 1 chr6A.!!$F3 4126
1 TraesCS6A01G378600 chr6A 599621155 599622924 1769 False 665.500000 900 83.964000 1556 3172 2 chr6A.!!$F5 1616
2 TraesCS6A01G378600 chr6A 599258677 599261669 2992 False 361.200000 933 84.564800 295 3160 5 chr6A.!!$F4 2865
3 TraesCS6A01G378600 chr6D 453344237 453348592 4355 False 1691.666667 2586 90.748667 1 4045 3 chr6D.!!$F3 4044
4 TraesCS6A01G378600 chr6D 453239405 453241164 1759 False 521.333333 1020 84.387000 442 3154 3 chr6D.!!$F2 2712
5 TraesCS6A01G378600 chr6D 453185716 453189078 3362 False 360.800000 568 85.397400 270 3160 5 chr6D.!!$F1 2890
6 TraesCS6A01G378600 chr6B 688604759 688608263 3504 True 1945.500000 2492 89.524500 641 4054 2 chr6B.!!$R1 3413
7 TraesCS6A01G378600 chr6B 688664225 688667117 2892 True 504.800000 979 86.580800 243 3182 5 chr6B.!!$R2 2939
8 TraesCS6A01G378600 chr6B 688756201 688758586 2385 True 389.666667 425 85.154333 1160 3160 3 chr6B.!!$R3 2000

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
535 862 0.829990 CTTCTTCTCCCTCTCTGCCC 59.170 60.0 0.00 0.0 0.0 5.36 F
2206 3780 0.107116 TTTGCGTGTACACTTGGGGT 60.107 50.0 23.01 0.0 0.0 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2291 3870 0.178068 ACCACTCGTTTGTGCTCAGT 59.822 50.0 0.0 0.0 36.68 3.41 R
3328 5289 0.250424 CATGACACACCAGCCTCACA 60.250 55.0 0.0 0.0 0.00 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
187 189 2.035632 ACATAAAGGCGGGAGAGAGAG 58.964 52.381 0.00 0.00 0.00 3.20
188 190 2.311463 CATAAAGGCGGGAGAGAGAGA 58.689 52.381 0.00 0.00 0.00 3.10
189 191 2.060050 TAAAGGCGGGAGAGAGAGAG 57.940 55.000 0.00 0.00 0.00 3.20
208 231 5.901853 AGAGAGAGAGAGAGAGAGATCTTGA 59.098 44.000 0.00 0.00 0.00 3.02
229 252 7.816995 TCTTGAACAGAGAGAGAAAATTAGAGC 59.183 37.037 0.00 0.00 0.00 4.09
230 253 7.238486 TGAACAGAGAGAGAAAATTAGAGCT 57.762 36.000 0.00 0.00 0.00 4.09
266 293 7.178573 TGGACAGAGAGAGAAAATTAGAGAGA 58.821 38.462 0.00 0.00 0.00 3.10
267 294 7.339212 TGGACAGAGAGAGAAAATTAGAGAGAG 59.661 40.741 0.00 0.00 0.00 3.20
268 295 7.556275 GGACAGAGAGAGAAAATTAGAGAGAGA 59.444 40.741 0.00 0.00 0.00 3.10
269 296 8.511604 ACAGAGAGAGAAAATTAGAGAGAGAG 57.488 38.462 0.00 0.00 0.00 3.20
270 297 8.328758 ACAGAGAGAGAAAATTAGAGAGAGAGA 58.671 37.037 0.00 0.00 0.00 3.10
271 298 8.834465 CAGAGAGAGAAAATTAGAGAGAGAGAG 58.166 40.741 0.00 0.00 0.00 3.20
347 669 5.125900 GGTGATGATGGAATGATGAACAACA 59.874 40.000 0.00 0.00 0.00 3.33
377 699 3.348647 TGTGGAGTGTGTGATAATGGG 57.651 47.619 0.00 0.00 0.00 4.00
447 774 4.083324 GGCATATATGTTGCTGCGTACATT 60.083 41.667 20.37 12.95 40.03 2.71
517 844 2.018086 CCTCCTCCCTCCCCTCTCT 61.018 68.421 0.00 0.00 0.00 3.10
535 862 0.829990 CTTCTTCTCCCTCTCTGCCC 59.170 60.000 0.00 0.00 0.00 5.36
1024 1407 6.597832 ACCTCATTCATACATACTCTAGCC 57.402 41.667 0.00 0.00 0.00 3.93
1032 1415 5.891551 TCATACATACTCTAGCCTCACACAA 59.108 40.000 0.00 0.00 0.00 3.33
1033 1416 4.727507 ACATACTCTAGCCTCACACAAG 57.272 45.455 0.00 0.00 0.00 3.16
1035 1418 2.016905 ACTCTAGCCTCACACAAGGT 57.983 50.000 0.00 0.00 38.79 3.50
1039 1422 2.703536 TCTAGCCTCACACAAGGTTCAA 59.296 45.455 0.00 0.00 38.79 2.69
1086 1469 3.643792 CTGCCTAATTCCTGCTACCTACT 59.356 47.826 0.00 0.00 0.00 2.57
1087 1470 3.641906 TGCCTAATTCCTGCTACCTACTC 59.358 47.826 0.00 0.00 0.00 2.59
1116 1503 3.885297 CCTAGCTTCTTCTCTCCTCTCTG 59.115 52.174 0.00 0.00 0.00 3.35
1135 1530 5.593909 TCTCTGGAGATCTTGTCAATCTCTC 59.406 44.000 13.41 13.09 45.56 3.20
1154 1549 2.367567 CTCTCTCCTCCGTCTAGCTAGT 59.632 54.545 20.10 0.00 0.00 2.57
1217 1625 2.421775 CGAGATCTCTCATCCATACCCG 59.578 54.545 20.26 0.00 43.00 5.28
1241 1651 5.627499 AGTACACATCGCAATTCACAATT 57.373 34.783 0.00 0.00 0.00 2.32
1291 1702 1.994463 CAGGGGGAGGTTTCAGAGG 59.006 63.158 0.00 0.00 0.00 3.69
1321 1733 6.389830 AGTGCACAGATAGAGAGATAAGTG 57.610 41.667 21.04 0.00 0.00 3.16
1514 1932 1.271379 GGAGCTGCCAGGTCAGTTTAA 60.271 52.381 23.95 0.00 44.10 1.52
1515 1933 1.807142 GAGCTGCCAGGTCAGTTTAAC 59.193 52.381 18.56 0.00 42.03 2.01
1516 1934 1.421646 AGCTGCCAGGTCAGTTTAACT 59.578 47.619 11.25 0.00 36.49 2.24
1517 1935 2.637872 AGCTGCCAGGTCAGTTTAACTA 59.362 45.455 11.25 0.00 36.49 2.24
1518 1936 2.742589 GCTGCCAGGTCAGTTTAACTAC 59.257 50.000 11.25 0.00 36.49 2.73
1519 1937 3.557264 GCTGCCAGGTCAGTTTAACTACT 60.557 47.826 11.25 0.00 36.49 2.57
1520 1938 3.997021 CTGCCAGGTCAGTTTAACTACTG 59.003 47.826 13.21 13.21 45.46 2.74
1522 1940 4.141574 TGCCAGGTCAGTTTAACTACTGTT 60.142 41.667 16.58 0.00 44.62 3.16
1523 1941 5.070714 TGCCAGGTCAGTTTAACTACTGTTA 59.929 40.000 16.58 7.42 44.62 2.41
1524 1942 5.638234 GCCAGGTCAGTTTAACTACTGTTAG 59.362 44.000 16.58 7.74 44.62 2.34
1527 2025 8.746530 CCAGGTCAGTTTAACTACTGTTAGATA 58.253 37.037 16.58 0.00 44.62 1.98
1554 2076 4.166919 AGTTACTACGTAGTACCCCATCCT 59.833 45.833 30.26 15.91 45.11 3.24
1573 2103 1.206849 CTTCTCTTGTCCCTCTCCAGC 59.793 57.143 0.00 0.00 0.00 4.85
1660 2391 8.119226 CAGCAAGCTACATGTCTCTTAATTAAC 58.881 37.037 0.00 0.00 0.00 2.01
1724 2455 3.056179 CGTTTTATTGGCTCCAATTGGGT 60.056 43.478 24.29 6.64 43.32 4.51
1731 2466 1.272147 GGCTCCAATTGGGTCTTGTCT 60.272 52.381 24.29 0.00 38.11 3.41
1803 3025 7.711339 TGTCATACCGTTTGTATATACATGCAA 59.289 33.333 16.16 5.48 38.10 4.08
1804 3026 8.552865 GTCATACCGTTTGTATATACATGCAAA 58.447 33.333 16.16 5.13 42.29 3.68
1805 3027 9.110502 TCATACCGTTTGTATATACATGCAAAA 57.889 29.630 16.16 4.78 44.82 2.44
1806 3028 9.165014 CATACCGTTTGTATATACATGCAAAAC 57.835 33.333 16.16 14.73 44.82 2.43
1807 3029 7.147143 ACCGTTTGTATATACATGCAAAACA 57.853 32.000 16.16 0.00 44.82 2.83
1808 3030 7.594714 ACCGTTTGTATATACATGCAAAACAA 58.405 30.769 16.16 2.69 44.82 2.83
1809 3031 8.082852 ACCGTTTGTATATACATGCAAAACAAA 58.917 29.630 16.16 3.76 44.82 2.83
1810 3032 8.582930 CCGTTTGTATATACATGCAAAACAAAG 58.417 33.333 16.16 7.34 44.82 2.77
1811 3033 9.335891 CGTTTGTATATACATGCAAAACAAAGA 57.664 29.630 16.16 0.00 44.82 2.52
1839 3077 3.959535 TGCATGCATATACCATCTCGA 57.040 42.857 18.46 0.00 0.00 4.04
1840 3078 4.476628 TGCATGCATATACCATCTCGAT 57.523 40.909 18.46 0.00 0.00 3.59
1841 3079 4.436332 TGCATGCATATACCATCTCGATC 58.564 43.478 18.46 0.00 0.00 3.69
1842 3080 3.806521 GCATGCATATACCATCTCGATCC 59.193 47.826 14.21 0.00 0.00 3.36
1843 3081 4.442612 GCATGCATATACCATCTCGATCCT 60.443 45.833 14.21 0.00 0.00 3.24
1844 3082 5.221322 GCATGCATATACCATCTCGATCCTA 60.221 44.000 14.21 0.00 0.00 2.94
1900 3147 9.301897 AGCACAAGTTTCTCCTAAGAATTTTAT 57.698 29.630 0.00 0.00 41.12 1.40
1901 3148 9.914131 GCACAAGTTTCTCCTAAGAATTTTATT 57.086 29.630 0.00 0.00 41.12 1.40
1969 3407 6.594547 TGTCTAACTCTGCAGTACTGTAGTAG 59.405 42.308 31.82 27.76 42.71 2.57
2023 3469 4.442073 GCAAGTGGCAAATTTATATCAGCG 59.558 41.667 0.00 0.00 43.97 5.18
2046 3497 0.845102 TTTCTCCACCCCTTCCCCTC 60.845 60.000 0.00 0.00 0.00 4.30
2092 3615 8.675705 AACTTAAAATTCCCCAATGTTTTGAG 57.324 30.769 0.00 0.00 34.95 3.02
2093 3616 7.223584 ACTTAAAATTCCCCAATGTTTTGAGG 58.776 34.615 0.00 0.00 33.83 3.86
2145 3712 3.243602 GCCCCTCGACTTCTCTTTCTATC 60.244 52.174 0.00 0.00 0.00 2.08
2206 3780 0.107116 TTTGCGTGTACACTTGGGGT 60.107 50.000 23.01 0.00 0.00 4.95
2207 3781 0.107116 TTGCGTGTACACTTGGGGTT 60.107 50.000 23.01 0.00 0.00 4.11
2208 3782 0.816018 TGCGTGTACACTTGGGGTTG 60.816 55.000 23.01 6.66 0.00 3.77
2291 3870 1.017177 GGTATGCAGACGTGGCGAAA 61.017 55.000 5.22 0.00 0.00 3.46
2546 4245 2.092291 GCACGAGTTCCGCATCGAA 61.092 57.895 1.13 0.00 41.40 3.71
2556 4255 1.419922 CGCATCGAAAACCCTCACG 59.580 57.895 0.00 0.00 0.00 4.35
2594 4297 5.653507 TGTTTAATTGGCATCTGATCTTGC 58.346 37.500 7.16 7.16 38.14 4.01
2601 4499 2.613133 GGCATCTGATCTTGCTTGAGTC 59.387 50.000 13.15 0.00 38.88 3.36
2606 4504 6.544622 CATCTGATCTTGCTTGAGTCTTTTC 58.455 40.000 0.00 0.00 0.00 2.29
2701 4601 5.067023 CAGAGTTTTCCACAAGAAGAAAGCT 59.933 40.000 2.13 2.13 43.48 3.74
2743 4646 4.719997 GAGCAAGAGATCGTCGGG 57.280 61.111 0.00 0.00 0.00 5.14
2797 4721 0.173708 CCAACTACGTCAGCTCCTCC 59.826 60.000 0.00 0.00 0.00 4.30
2798 4722 0.179161 CAACTACGTCAGCTCCTCCG 60.179 60.000 0.00 0.00 0.00 4.63
2963 4896 4.758251 CGGACATGCCACCGCTGA 62.758 66.667 12.25 0.00 42.55 4.26
2964 4897 3.127533 GGACATGCCACCGCTGAC 61.128 66.667 0.00 0.00 36.34 3.51
3067 5012 1.229951 TGGGGAGCTGATGGACCTT 60.230 57.895 0.00 0.00 0.00 3.50
3263 5220 7.781219 TGTAGTGTAGGGTAGAAGCATAATACA 59.219 37.037 0.00 0.00 0.00 2.29
3264 5221 7.857404 AGTGTAGGGTAGAAGCATAATACAT 57.143 36.000 0.00 0.00 0.00 2.29
3265 5222 8.951614 AGTGTAGGGTAGAAGCATAATACATA 57.048 34.615 0.00 0.00 0.00 2.29
3266 5223 8.804204 AGTGTAGGGTAGAAGCATAATACATAC 58.196 37.037 0.00 0.00 0.00 2.39
3267 5224 8.804204 GTGTAGGGTAGAAGCATAATACATACT 58.196 37.037 0.00 0.00 0.00 2.12
3328 5289 7.667635 TCTCGATTGATTAGGATATGTGAGAGT 59.332 37.037 0.00 0.00 0.00 3.24
3338 5299 0.612229 ATGTGAGAGTGTGAGGCTGG 59.388 55.000 0.00 0.00 0.00 4.85
3391 5354 5.598005 TCATTTCTGTTGTTGGAGAATGGTT 59.402 36.000 0.00 0.00 0.00 3.67
3516 5479 3.698040 GACTTAGTTGATGTAGGACGGGA 59.302 47.826 0.00 0.00 0.00 5.14
3530 5493 5.422214 AGGACGGGATATCCATTATGTTC 57.578 43.478 23.27 11.30 38.86 3.18
3581 5544 4.773149 AGGAAGTCTTAAATCAGAGTCCGT 59.227 41.667 0.00 0.00 34.95 4.69
3582 5545 4.865365 GGAAGTCTTAAATCAGAGTCCGTG 59.135 45.833 0.00 0.00 0.00 4.94
3599 5562 1.076332 GTGGGTGTGAGCATTACGAC 58.924 55.000 0.00 0.00 0.00 4.34
3609 5572 5.576774 TGTGAGCATTACGACATTACTCTTG 59.423 40.000 0.00 0.00 0.00 3.02
3686 5652 9.450807 CTCTAAGTTTCAAGTTACAATTTGTGG 57.549 33.333 12.30 0.00 0.00 4.17
3740 5707 7.493367 TCCAAAATACCCCATTAATTTAAGCG 58.507 34.615 0.00 0.00 0.00 4.68
3746 5713 4.160814 ACCCCATTAATTTAAGCGGGTTTC 59.839 41.667 17.44 0.00 39.06 2.78
3753 5720 9.150348 CATTAATTTAAGCGGGTTTCTTCAATT 57.850 29.630 0.00 0.00 34.04 2.32
3757 5724 9.549078 AATTTAAGCGGGTTTCTTCAATTTTTA 57.451 25.926 0.00 0.00 28.51 1.52
3758 5725 9.719355 ATTTAAGCGGGTTTCTTCAATTTTTAT 57.281 25.926 0.00 0.00 0.00 1.40
3827 5795 0.755698 AGGACGTGGCTATCGATGGT 60.756 55.000 8.54 0.00 0.00 3.55
3830 5798 2.302952 CGTGGCTATCGATGGTGCG 61.303 63.158 8.54 7.67 0.00 5.34
3841 5809 3.272364 ATGGTGCGCTCATGTGGGT 62.272 57.895 9.73 0.00 0.00 4.51
3848 5817 2.665000 CTCATGTGGGTGCGTCCT 59.335 61.111 0.00 0.00 36.25 3.85
3995 5965 0.692756 TGGTGGTGGTGGAGTCTTGA 60.693 55.000 0.00 0.00 0.00 3.02
4006 5976 1.000955 GGAGTCTTGAAGTCGAAGCCA 59.999 52.381 0.00 0.00 0.00 4.75
4008 5978 1.149148 GTCTTGAAGTCGAAGCCACC 58.851 55.000 0.00 0.00 0.00 4.61
4012 5982 1.959226 GAAGTCGAAGCCACCGCAA 60.959 57.895 0.00 0.00 37.52 4.85
4045 6015 2.184830 GGGTTAGCGCCGGGATTTC 61.185 63.158 2.29 0.00 0.00 2.17
4047 6017 0.105408 GGTTAGCGCCGGGATTTCTA 59.895 55.000 2.29 0.00 0.00 2.10
4051 6021 1.153429 GCGCCGGGATTTCTACTGT 60.153 57.895 2.18 0.00 0.00 3.55
4054 6024 1.404986 CGCCGGGATTTCTACTGTTGA 60.405 52.381 2.18 0.00 0.00 3.18
4055 6025 2.007608 GCCGGGATTTCTACTGTTGAC 58.992 52.381 2.18 0.00 0.00 3.18
4056 6026 2.614481 GCCGGGATTTCTACTGTTGACA 60.614 50.000 2.18 0.00 0.00 3.58
4057 6027 3.670625 CCGGGATTTCTACTGTTGACAA 58.329 45.455 0.00 0.00 0.00 3.18
4058 6028 4.261801 CCGGGATTTCTACTGTTGACAAT 58.738 43.478 0.00 0.00 0.00 2.71
4059 6029 4.332819 CCGGGATTTCTACTGTTGACAATC 59.667 45.833 0.00 13.21 0.00 2.67
4060 6030 5.178797 CGGGATTTCTACTGTTGACAATCT 58.821 41.667 17.16 0.00 0.00 2.40
4061 6031 6.338146 CGGGATTTCTACTGTTGACAATCTA 58.662 40.000 17.16 0.00 0.00 1.98
4062 6032 6.477033 CGGGATTTCTACTGTTGACAATCTAG 59.523 42.308 17.16 0.00 0.00 2.43
4063 6033 7.556844 GGGATTTCTACTGTTGACAATCTAGA 58.443 38.462 17.16 0.00 0.00 2.43
4064 6034 8.041323 GGGATTTCTACTGTTGACAATCTAGAA 58.959 37.037 17.16 0.36 0.00 2.10
4065 6035 9.436957 GGATTTCTACTGTTGACAATCTAGAAA 57.563 33.333 18.03 18.03 34.49 2.52
4069 6039 9.698309 TTCTACTGTTGACAATCTAGAAAGAAG 57.302 33.333 0.00 0.00 34.73 2.85
4070 6040 8.307483 TCTACTGTTGACAATCTAGAAAGAAGG 58.693 37.037 0.00 0.00 34.73 3.46
4071 6041 7.067496 ACTGTTGACAATCTAGAAAGAAGGA 57.933 36.000 0.00 0.00 34.73 3.36
4072 6042 7.509546 ACTGTTGACAATCTAGAAAGAAGGAA 58.490 34.615 0.00 0.00 34.73 3.36
4073 6043 7.993183 ACTGTTGACAATCTAGAAAGAAGGAAA 59.007 33.333 0.00 0.00 34.73 3.13
4074 6044 8.924511 TGTTGACAATCTAGAAAGAAGGAAAT 57.075 30.769 0.00 0.00 34.73 2.17
4075 6045 9.354673 TGTTGACAATCTAGAAAGAAGGAAATT 57.645 29.630 0.00 0.00 34.73 1.82
4098 6068 9.780186 AATTTAGAAATATCTACCTAGTGTGCC 57.220 33.333 0.00 0.00 37.88 5.01
4099 6069 8.548880 TTTAGAAATATCTACCTAGTGTGCCT 57.451 34.615 0.00 0.00 37.88 4.75
4100 6070 9.650714 TTTAGAAATATCTACCTAGTGTGCCTA 57.349 33.333 0.00 0.00 37.88 3.93
4101 6071 9.650714 TTAGAAATATCTACCTAGTGTGCCTAA 57.349 33.333 0.00 0.00 37.88 2.69
4102 6072 8.728596 AGAAATATCTACCTAGTGTGCCTAAT 57.271 34.615 0.00 0.00 32.88 1.73
4103 6073 8.808092 AGAAATATCTACCTAGTGTGCCTAATC 58.192 37.037 0.00 0.00 32.88 1.75
4104 6074 8.728596 AAATATCTACCTAGTGTGCCTAATCT 57.271 34.615 0.00 0.00 0.00 2.40
4105 6075 8.728596 AATATCTACCTAGTGTGCCTAATCTT 57.271 34.615 0.00 0.00 0.00 2.40
4106 6076 6.658188 ATCTACCTAGTGTGCCTAATCTTC 57.342 41.667 0.00 0.00 0.00 2.87
4107 6077 4.894114 TCTACCTAGTGTGCCTAATCTTCC 59.106 45.833 0.00 0.00 0.00 3.46
4108 6078 3.725634 ACCTAGTGTGCCTAATCTTCCT 58.274 45.455 0.00 0.00 0.00 3.36
4109 6079 4.104831 ACCTAGTGTGCCTAATCTTCCTT 58.895 43.478 0.00 0.00 0.00 3.36
4110 6080 4.162509 ACCTAGTGTGCCTAATCTTCCTTC 59.837 45.833 0.00 0.00 0.00 3.46
4111 6081 3.636153 AGTGTGCCTAATCTTCCTTCC 57.364 47.619 0.00 0.00 0.00 3.46
4112 6082 2.093447 AGTGTGCCTAATCTTCCTTCCG 60.093 50.000 0.00 0.00 0.00 4.30
4113 6083 1.906574 TGTGCCTAATCTTCCTTCCGT 59.093 47.619 0.00 0.00 0.00 4.69
4114 6084 2.280628 GTGCCTAATCTTCCTTCCGTG 58.719 52.381 0.00 0.00 0.00 4.94
4115 6085 2.093658 GTGCCTAATCTTCCTTCCGTGA 60.094 50.000 0.00 0.00 0.00 4.35
4116 6086 2.771943 TGCCTAATCTTCCTTCCGTGAT 59.228 45.455 0.00 0.00 0.00 3.06
4117 6087 3.181465 TGCCTAATCTTCCTTCCGTGATC 60.181 47.826 0.00 0.00 0.00 2.92
4118 6088 3.181465 GCCTAATCTTCCTTCCGTGATCA 60.181 47.826 0.00 0.00 0.00 2.92
4119 6089 4.372656 CCTAATCTTCCTTCCGTGATCAC 58.627 47.826 16.21 16.21 0.00 3.06
4120 6090 2.990066 ATCTTCCTTCCGTGATCACC 57.010 50.000 20.03 2.90 0.00 4.02
4121 6091 1.938585 TCTTCCTTCCGTGATCACCT 58.061 50.000 20.03 0.00 0.00 4.00
4122 6092 1.825474 TCTTCCTTCCGTGATCACCTC 59.175 52.381 20.03 0.00 0.00 3.85
4123 6093 0.530744 TTCCTTCCGTGATCACCTCG 59.469 55.000 20.03 8.69 0.00 4.63
4124 6094 0.323087 TCCTTCCGTGATCACCTCGA 60.323 55.000 20.03 10.17 33.99 4.04
4125 6095 0.747255 CCTTCCGTGATCACCTCGAT 59.253 55.000 20.03 0.00 36.91 3.59
4126 6096 1.536922 CCTTCCGTGATCACCTCGATG 60.537 57.143 20.03 13.58 33.17 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
187 189 6.115446 TGTTCAAGATCTCTCTCTCTCTCTC 58.885 44.000 0.00 0.00 0.00 3.20
188 190 6.065976 TGTTCAAGATCTCTCTCTCTCTCT 57.934 41.667 0.00 0.00 0.00 3.10
189 191 6.115446 TCTGTTCAAGATCTCTCTCTCTCTC 58.885 44.000 0.00 0.00 0.00 3.20
208 231 8.588290 TCTAGCTCTAATTTTCTCTCTCTGTT 57.412 34.615 0.00 0.00 0.00 3.16
229 252 5.928976 TCTCTCTGTCCAAGATCTCTCTAG 58.071 45.833 0.00 0.00 33.29 2.43
230 253 5.665360 TCTCTCTCTGTCCAAGATCTCTCTA 59.335 44.000 0.00 0.00 33.29 2.43
266 293 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
267 294 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
268 295 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
269 296 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
270 297 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
271 298 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
347 669 7.661536 ATCACACACTCCACATATAGTTAGT 57.338 36.000 0.00 0.00 0.00 2.24
447 774 2.682494 GTCCGGAGCCCCACAGTA 60.682 66.667 3.06 0.00 0.00 2.74
517 844 0.117140 TGGGCAGAGAGGGAGAAGAA 59.883 55.000 0.00 0.00 0.00 2.52
535 862 0.537143 TGTGGTGGTGGCTTTAGCTG 60.537 55.000 0.00 0.00 41.70 4.24
633 968 2.044551 AGGGGGAGGACGTACGAC 60.045 66.667 24.41 16.49 0.00 4.34
634 969 2.273449 GAGGGGGAGGACGTACGA 59.727 66.667 24.41 0.00 0.00 3.43
635 970 2.832201 GGAGGGGGAGGACGTACG 60.832 72.222 15.01 15.01 0.00 3.67
636 971 1.455402 GAGGAGGGGGAGGACGTAC 60.455 68.421 0.00 0.00 0.00 3.67
637 972 2.698075 GGAGGAGGGGGAGGACGTA 61.698 68.421 0.00 0.00 0.00 3.57
638 973 4.077180 GGAGGAGGGGGAGGACGT 62.077 72.222 0.00 0.00 0.00 4.34
731 1071 0.825840 GGACGGATCCAGAGCTAGCT 60.826 60.000 19.45 19.45 45.47 3.32
848 1208 5.470368 CGGGGTGATGATACAATAGTACAG 58.530 45.833 0.00 0.00 31.96 2.74
849 1209 4.282449 CCGGGGTGATGATACAATAGTACA 59.718 45.833 0.00 0.00 31.96 2.90
1024 1407 3.466836 TGTAGCTTGAACCTTGTGTGAG 58.533 45.455 0.00 0.00 0.00 3.51
1032 1415 2.638480 TGTTGCTGTAGCTTGAACCT 57.362 45.000 5.38 0.00 42.66 3.50
1033 1416 4.253685 TCTATGTTGCTGTAGCTTGAACC 58.746 43.478 5.38 0.00 42.66 3.62
1035 1418 9.428097 CATATATCTATGTTGCTGTAGCTTGAA 57.572 33.333 5.38 0.00 35.07 2.69
1039 1422 6.344500 GGCATATATCTATGTTGCTGTAGCT 58.656 40.000 5.38 0.00 38.45 3.32
1086 1469 6.102027 AGGAGAGAAGAAGCTAGGTATGTAGA 59.898 42.308 0.00 0.00 0.00 2.59
1087 1470 6.303839 AGGAGAGAAGAAGCTAGGTATGTAG 58.696 44.000 0.00 0.00 0.00 2.74
1116 1503 5.010012 GGAGAGAGAGATTGACAAGATCTCC 59.990 48.000 20.69 16.76 46.88 3.71
1135 1530 2.922740 ACTAGCTAGACGGAGGAGAG 57.077 55.000 27.45 0.00 0.00 3.20
1154 1549 3.535561 GCACCAATTGAGCTAGCTCTAA 58.464 45.455 37.42 29.56 43.12 2.10
1189 1594 4.468713 TGGATGAGAGATCTCGATGAACT 58.531 43.478 16.97 0.00 45.72 3.01
1190 1595 4.844998 TGGATGAGAGATCTCGATGAAC 57.155 45.455 16.97 8.01 45.72 3.18
1192 1597 4.946772 GGTATGGATGAGAGATCTCGATGA 59.053 45.833 16.97 3.05 45.72 2.92
1217 1625 5.524511 TTGTGAATTGCGATGTGTACTAC 57.475 39.130 0.00 0.00 0.00 2.73
1241 1651 4.702612 AGCTCGACTCTCTCTACAATTTGA 59.297 41.667 2.79 0.00 0.00 2.69
1291 1702 5.767665 TCTCTCTATCTGTGCACTATCTTCC 59.232 44.000 19.41 0.00 0.00 3.46
1321 1733 1.380380 CCCTCAGCCCCATGGAAAC 60.380 63.158 15.22 1.40 0.00 2.78
1527 2025 8.049721 GGATGGGGTACTACGTAGTAACTATAT 58.950 40.741 36.85 29.15 45.13 0.86
1549 2071 2.433970 GGAGAGGGACAAGAGAAGGATG 59.566 54.545 0.00 0.00 0.00 3.51
1554 2076 1.270907 GCTGGAGAGGGACAAGAGAA 58.729 55.000 0.00 0.00 0.00 2.87
1619 2340 1.561643 TGCTGGAGAGGGACTAACAG 58.438 55.000 0.00 0.00 41.55 3.16
1724 2455 9.710979 CACTAATTAACAAAAACGAAGACAAGA 57.289 29.630 0.00 0.00 0.00 3.02
1731 2466 9.784680 TTTAGTGCACTAATTAACAAAAACGAA 57.215 25.926 33.72 15.11 38.16 3.85
1820 3042 3.806521 GGATCGAGATGGTATATGCATGC 59.193 47.826 11.82 11.82 0.00 4.06
1832 3070 4.244066 CAGGAATTGCTAGGATCGAGATG 58.756 47.826 0.00 0.00 0.00 2.90
1833 3071 4.533919 CAGGAATTGCTAGGATCGAGAT 57.466 45.455 0.00 0.00 0.00 2.75
2046 3497 6.402222 AGTTTCTTGGTAGAAGTGCTCATAG 58.598 40.000 0.00 0.00 41.25 2.23
2092 3615 5.183228 TGTATGCACTAGTCCTTTTAAGCC 58.817 41.667 0.00 0.00 0.00 4.35
2093 3616 6.927294 ATGTATGCACTAGTCCTTTTAAGC 57.073 37.500 0.00 0.00 0.00 3.09
2145 3712 9.770097 AGATCATATCCTGTTGTACAATTACAG 57.230 33.333 12.26 14.59 39.44 2.74
2194 3768 4.587262 AGGATTTTTCAACCCCAAGTGTAC 59.413 41.667 0.00 0.00 0.00 2.90
2206 3780 6.488683 AGTGGACGTTGATTAGGATTTTTCAA 59.511 34.615 0.00 0.00 0.00 2.69
2207 3781 6.001460 AGTGGACGTTGATTAGGATTTTTCA 58.999 36.000 0.00 0.00 0.00 2.69
2208 3782 6.148811 TCAGTGGACGTTGATTAGGATTTTTC 59.851 38.462 0.00 0.00 0.00 2.29
2291 3870 0.178068 ACCACTCGTTTGTGCTCAGT 59.822 50.000 0.00 0.00 36.68 3.41
2546 4245 4.280019 GGTGGGGCGTGAGGGTTT 62.280 66.667 0.00 0.00 0.00 3.27
2556 4255 2.656698 AAACAGACCTTGGGTGGGGC 62.657 60.000 0.00 0.00 35.25 5.80
2606 4504 9.961265 ACACATATTAGCATCTCAAATCAATTG 57.039 29.630 0.00 0.00 40.58 2.32
2701 4601 1.214325 CATGGCGTACTCCGTGTCA 59.786 57.895 14.82 0.00 38.13 3.58
2797 4721 4.147449 TGAGGATCGTGGCAGGCG 62.147 66.667 1.51 0.00 38.61 5.52
2798 4722 1.676678 TACTGAGGATCGTGGCAGGC 61.677 60.000 1.51 0.00 38.61 4.85
2927 4860 2.124695 GAAGGGGTCCATGTCGGC 60.125 66.667 0.00 0.00 33.14 5.54
3328 5289 0.250424 CATGACACACCAGCCTCACA 60.250 55.000 0.00 0.00 0.00 3.58
3391 5354 3.505386 ACATCAAATGCCCCAACTTGTA 58.495 40.909 0.00 0.00 0.00 2.41
3472 5435 8.311650 AGTCTCAACTTGTTCACAATATACAC 57.688 34.615 0.00 0.00 35.02 2.90
3478 5441 7.552687 TCAACTAAGTCTCAACTTGTTCACAAT 59.447 33.333 1.17 0.00 45.37 2.71
3500 5463 3.576982 TGGATATCCCGTCCTACATCAAC 59.423 47.826 19.34 0.00 37.93 3.18
3516 5479 8.489676 AGACACTCAGAGAACATAATGGATAT 57.510 34.615 3.79 0.00 0.00 1.63
3530 5493 4.734398 ATTGAGCCTTAGACACTCAGAG 57.266 45.455 0.00 0.00 41.21 3.35
3561 5524 4.322801 CCCACGGACTCTGATTTAAGACTT 60.323 45.833 0.00 0.00 0.00 3.01
3581 5544 0.682292 TGTCGTAATGCTCACACCCA 59.318 50.000 0.00 0.00 0.00 4.51
3582 5545 2.024176 ATGTCGTAATGCTCACACCC 57.976 50.000 0.00 0.00 0.00 4.61
3622 5585 7.539436 GGATTCACCCTTTCTTCTAAAATGTC 58.461 38.462 0.00 0.00 0.00 3.06
3686 5652 8.507524 ACTTCTACTAAATGGGTAAGAAATGC 57.492 34.615 0.00 0.00 0.00 3.56
3802 5770 3.748083 TCGATAGCCACGTCCTACTAAT 58.252 45.455 0.00 0.00 0.00 1.73
3809 5777 0.597637 CACCATCGATAGCCACGTCC 60.598 60.000 0.00 0.00 0.00 4.79
3811 5779 1.227263 GCACCATCGATAGCCACGT 60.227 57.895 0.00 0.00 0.00 4.49
3830 5798 3.127533 GGACGCACCCACATGAGC 61.128 66.667 0.00 0.00 0.00 4.26
3848 5817 2.203112 GCCTCATCTGCCGCATCA 60.203 61.111 0.00 0.00 0.00 3.07
3856 5825 1.065701 GCTTGCTTGATGCCTCATCTG 59.934 52.381 8.11 3.21 41.06 2.90
3914 5883 2.741092 GGACTTGCTCGGGTGTGA 59.259 61.111 0.00 0.00 0.00 3.58
3976 5946 0.692756 TCAAGACTCCACCACCACCA 60.693 55.000 0.00 0.00 0.00 4.17
3995 5965 2.110213 TTGCGGTGGCTTCGACTT 59.890 55.556 4.42 0.00 40.82 3.01
4006 5976 3.323979 CCCTCTATAATACCAGTTGCGGT 59.676 47.826 0.00 0.00 43.46 5.68
4008 5978 3.323979 ACCCCTCTATAATACCAGTTGCG 59.676 47.826 0.00 0.00 0.00 4.85
4012 5982 4.771054 CGCTAACCCCTCTATAATACCAGT 59.229 45.833 0.00 0.00 0.00 4.00
4045 6015 8.307483 TCCTTCTTTCTAGATTGTCAACAGTAG 58.693 37.037 0.00 0.00 0.00 2.57
4047 6017 7.067496 TCCTTCTTTCTAGATTGTCAACAGT 57.933 36.000 0.00 0.00 0.00 3.55
4072 6042 9.780186 GGCACACTAGGTAGATATTTCTAAATT 57.220 33.333 0.00 0.00 36.23 1.82
4073 6043 9.160412 AGGCACACTAGGTAGATATTTCTAAAT 57.840 33.333 0.00 0.00 36.23 1.40
4074 6044 8.548880 AGGCACACTAGGTAGATATTTCTAAA 57.451 34.615 0.00 0.00 36.23 1.85
4075 6045 9.650714 TTAGGCACACTAGGTAGATATTTCTAA 57.349 33.333 0.00 0.00 33.03 2.10
4076 6046 9.824216 ATTAGGCACACTAGGTAGATATTTCTA 57.176 33.333 0.00 0.00 31.28 2.10
4077 6047 8.728596 ATTAGGCACACTAGGTAGATATTTCT 57.271 34.615 0.00 0.00 32.70 2.52
4078 6048 8.808092 AGATTAGGCACACTAGGTAGATATTTC 58.192 37.037 0.00 0.00 32.16 2.17
4079 6049 8.728596 AGATTAGGCACACTAGGTAGATATTT 57.271 34.615 0.00 0.00 32.16 1.40
4080 6050 8.728596 AAGATTAGGCACACTAGGTAGATATT 57.271 34.615 0.00 0.00 32.16 1.28
4081 6051 7.397761 GGAAGATTAGGCACACTAGGTAGATAT 59.602 40.741 0.00 0.00 32.16 1.63
4082 6052 6.720288 GGAAGATTAGGCACACTAGGTAGATA 59.280 42.308 0.00 0.00 32.16 1.98
4083 6053 5.540719 GGAAGATTAGGCACACTAGGTAGAT 59.459 44.000 0.00 0.00 32.16 1.98
4084 6054 4.894114 GGAAGATTAGGCACACTAGGTAGA 59.106 45.833 0.00 0.00 32.16 2.59
4085 6055 4.896482 AGGAAGATTAGGCACACTAGGTAG 59.104 45.833 0.00 0.00 32.16 3.18
4086 6056 4.880164 AGGAAGATTAGGCACACTAGGTA 58.120 43.478 0.00 0.00 32.16 3.08
4087 6057 3.725634 AGGAAGATTAGGCACACTAGGT 58.274 45.455 0.00 0.00 32.16 3.08
4088 6058 4.443598 GGAAGGAAGATTAGGCACACTAGG 60.444 50.000 0.00 0.00 32.16 3.02
4089 6059 4.698575 GGAAGGAAGATTAGGCACACTAG 58.301 47.826 0.00 0.00 32.16 2.57
4090 6060 3.132289 CGGAAGGAAGATTAGGCACACTA 59.868 47.826 0.00 0.00 0.00 2.74
4091 6061 2.093447 CGGAAGGAAGATTAGGCACACT 60.093 50.000 0.00 0.00 0.00 3.55
4092 6062 2.280628 CGGAAGGAAGATTAGGCACAC 58.719 52.381 0.00 0.00 0.00 3.82
4093 6063 1.906574 ACGGAAGGAAGATTAGGCACA 59.093 47.619 0.00 0.00 0.00 4.57
4094 6064 2.093658 TCACGGAAGGAAGATTAGGCAC 60.094 50.000 0.00 0.00 0.00 5.01
4095 6065 2.184533 TCACGGAAGGAAGATTAGGCA 58.815 47.619 0.00 0.00 0.00 4.75
4096 6066 2.981859 TCACGGAAGGAAGATTAGGC 57.018 50.000 0.00 0.00 0.00 3.93
4097 6067 4.372656 GTGATCACGGAAGGAAGATTAGG 58.627 47.826 10.69 0.00 0.00 2.69
4098 6068 4.100189 AGGTGATCACGGAAGGAAGATTAG 59.900 45.833 19.33 0.00 0.00 1.73
4099 6069 4.030913 AGGTGATCACGGAAGGAAGATTA 58.969 43.478 19.33 0.00 0.00 1.75
4100 6070 2.840651 AGGTGATCACGGAAGGAAGATT 59.159 45.455 19.33 0.00 0.00 2.40
4101 6071 2.432510 GAGGTGATCACGGAAGGAAGAT 59.567 50.000 19.33 0.00 0.00 2.40
4102 6072 1.825474 GAGGTGATCACGGAAGGAAGA 59.175 52.381 19.33 0.00 0.00 2.87
4103 6073 1.469940 CGAGGTGATCACGGAAGGAAG 60.470 57.143 19.33 1.72 0.00 3.46
4104 6074 0.530744 CGAGGTGATCACGGAAGGAA 59.469 55.000 19.33 0.00 0.00 3.36
4105 6075 0.323087 TCGAGGTGATCACGGAAGGA 60.323 55.000 19.33 9.24 0.00 3.36
4106 6076 0.747255 ATCGAGGTGATCACGGAAGG 59.253 55.000 19.33 7.14 28.49 3.46
4107 6077 1.845266 CATCGAGGTGATCACGGAAG 58.155 55.000 19.33 10.66 34.13 3.46


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

AutoCloner maintained by Alex Coulton.