Multiple sequence alignment - TraesCS2A01G446400

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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 TraesCS2A01G446400 chr2A 100.000 3202 0 0 1 3202 695503948 695507149 0.000000e+00 5914.0
1 TraesCS2A01G446400 chr2B 91.098 1494 68 19 634 2096 663123950 663125409 0.000000e+00 1962.0
2 TraesCS2A01G446400 chr2B 88.899 1099 66 17 2134 3199 663126637 663127712 0.000000e+00 1303.0
3 TraesCS2A01G446400 chr2B 90.543 645 41 10 1 641 663109344 663109972 0.000000e+00 835.0
4 TraesCS2A01G446400 chr2B 94.444 54 3 0 2088 2141 663126565 663126618 2.050000e-12 84.2
5 TraesCS2A01G446400 chr2D 90.591 829 47 10 2398 3199 556053381 556054205 0.000000e+00 1070.0
6 TraesCS2A01G446400 chr2D 93.023 86 6 0 2180 2265 11162488 11162573 3.350000e-25 126.0
7 TraesCS2A01G446400 chr4B 94.175 103 6 0 1076 1178 656871080 656871182 1.190000e-34 158.0
8 TraesCS2A01G446400 chr1A 83.893 149 18 5 2833 2976 31176221 31176074 1.550000e-28 137.0
9 TraesCS2A01G446400 chr1B 82.119 151 17 8 2833 2976 49937387 49937240 1.560000e-23 121.0
10 TraesCS2A01G446400 chr6A 91.667 84 7 0 2182 2265 614844564 614844481 2.020000e-22 117.0
11 TraesCS2A01G446400 chr6A 100.000 28 0 0 2240 2267 609002414 609002387 6.000000e-03 52.8
12 TraesCS2A01G446400 chr5B 97.143 35 0 1 2238 2271 261372044 261372010 1.240000e-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 TraesCS2A01G446400 chr2A 695503948 695507149 3201 False 5914.0 5914 100.000000 1 3202 1 chr2A.!!$F1 3201
1 TraesCS2A01G446400 chr2B 663123950 663127712 3762 False 1116.4 1962 91.480333 634 3199 3 chr2B.!!$F2 2565
2 TraesCS2A01G446400 chr2B 663109344 663109972 628 False 835.0 835 90.543000 1 641 1 chr2B.!!$F1 640
3 TraesCS2A01G446400 chr2D 556053381 556054205 824 False 1070.0 1070 90.591000 2398 3199 1 chr2D.!!$F2 801

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
998 1025 0.039346 GCCGGCGAGGAAGATACTAC 60.039 60.0 12.58 0.0 45.0 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2833 4088 0.170339 CATACCGCAGACGACTGACA 59.83 55.0 19.07 0.29 46.03 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
49 50 1.228063 ATCATCGCATCACCAGGCC 60.228 57.895 0.00 0.00 0.00 5.19
62 63 1.591327 CAGGCCAAAAACACGCCAC 60.591 57.895 5.01 0.00 45.56 5.01
65 66 2.237066 GCCAAAAACACGCCACTGC 61.237 57.895 0.00 0.00 0.00 4.40
73 74 1.261938 ACACGCCACTGCATACCCTA 61.262 55.000 0.00 0.00 37.32 3.53
102 103 0.112606 ACTCCCTCCTCGTCAACTCA 59.887 55.000 0.00 0.00 0.00 3.41
136 137 3.027170 CTTGACCACGCCATCACGC 62.027 63.158 0.00 0.00 36.19 5.34
160 161 5.295787 CGAAATGGAAATCCTAATGGAACGA 59.704 40.000 0.44 0.00 46.80 3.85
163 164 7.660030 AATGGAAATCCTAATGGAACGAATT 57.340 32.000 0.44 0.00 46.80 2.17
183 184 1.804151 TGAATAAACGAGCACCACTGC 59.196 47.619 0.00 0.00 44.63 4.40
216 217 2.047560 CGGGAAGAACACGGACCC 60.048 66.667 0.00 0.00 42.25 4.46
217 218 2.350134 GGGAAGAACACGGACCCC 59.650 66.667 0.00 0.00 35.00 4.95
218 219 2.350134 GGAAGAACACGGACCCCC 59.650 66.667 0.00 0.00 0.00 5.40
249 250 3.070302 ACCCACCAAATTGCGTACAAAAT 59.930 39.130 0.00 0.00 39.77 1.82
299 301 0.096454 GAGTTTATCAACGCACCGCC 59.904 55.000 0.00 0.00 38.03 6.13
347 349 2.266055 CCGACCTCACTTGGCCTC 59.734 66.667 3.32 0.00 0.00 4.70
349 351 2.435059 GACCTCACTTGGCCTCGC 60.435 66.667 3.32 0.00 0.00 5.03
370 372 2.881352 CTTCGAGACGCTTCGCCC 60.881 66.667 4.45 0.00 40.29 6.13
371 373 3.343788 CTTCGAGACGCTTCGCCCT 62.344 63.158 4.45 0.00 40.29 5.19
372 374 1.989966 CTTCGAGACGCTTCGCCCTA 61.990 60.000 4.45 0.00 40.29 3.53
387 389 0.458025 CCCTAGGCAGACGTTTCGAC 60.458 60.000 2.05 0.00 0.00 4.20
388 390 0.458025 CCTAGGCAGACGTTTCGACC 60.458 60.000 0.00 0.00 0.00 4.79
389 391 0.797249 CTAGGCAGACGTTTCGACCG 60.797 60.000 0.00 2.35 0.00 4.79
390 392 2.807631 TAGGCAGACGTTTCGACCGC 62.808 60.000 3.74 0.00 0.00 5.68
391 393 2.733593 GCAGACGTTTCGACCGCT 60.734 61.111 3.74 0.44 0.00 5.52
392 394 2.308039 GCAGACGTTTCGACCGCTT 61.308 57.895 3.74 0.00 0.00 4.68
393 395 1.773496 CAGACGTTTCGACCGCTTC 59.227 57.895 3.74 0.00 0.00 3.86
394 396 1.372623 AGACGTTTCGACCGCTTCC 60.373 57.895 3.74 0.00 0.00 3.46
395 397 2.713894 GACGTTTCGACCGCTTCCG 61.714 63.158 3.74 0.00 0.00 4.30
488 491 2.762887 TCACAACACCCAGAAAATGCAA 59.237 40.909 0.00 0.00 0.00 4.08
489 492 2.865551 CACAACACCCAGAAAATGCAAC 59.134 45.455 0.00 0.00 0.00 4.17
510 513 7.762382 GCAACTGCACTAATTAGAATTTAGGT 58.238 34.615 19.38 5.77 41.59 3.08
533 536 3.699538 TCTATAATGTGCTGACAGTCGGT 59.300 43.478 11.22 0.00 34.87 4.69
557 562 4.318760 CCGTACATATGTGCTGCATAACAC 60.319 45.833 18.81 5.84 42.68 3.32
569 574 2.763645 ATAACACCCCCATCCCGGC 61.764 63.158 0.00 0.00 0.00 6.13
615 620 6.664384 TGGATACGGCCTTAAGGTTAAAAATT 59.336 34.615 22.55 1.22 42.51 1.82
620 625 6.664384 ACGGCCTTAAGGTTAAAAATTATCCA 59.336 34.615 22.55 0.00 37.57 3.41
657 663 1.678101 GCACATTCAGGGATTAGGCAC 59.322 52.381 0.00 0.00 0.00 5.01
694 700 5.176592 GTCGAGCTTTACAATCTAAGGGTT 58.823 41.667 0.00 0.00 0.00 4.11
721 727 2.096248 AGGCTTCACTCCTTCTACTCG 58.904 52.381 0.00 0.00 0.00 4.18
834 852 2.359169 TGCTCCTTGGGACTAGGCG 61.359 63.158 0.00 0.00 32.59 5.52
880 898 3.495377 CGAGAAACACATTAACACGGGAA 59.505 43.478 0.00 0.00 0.00 3.97
882 900 3.252458 AGAAACACATTAACACGGGAAGC 59.748 43.478 0.00 0.00 0.00 3.86
884 902 2.151202 ACACATTAACACGGGAAGCAG 58.849 47.619 0.00 0.00 0.00 4.24
906 924 2.021931 GCGCTGGCGATCGAAAAG 59.978 61.111 21.57 13.16 42.83 2.27
907 925 2.703409 CGCTGGCGATCGAAAAGG 59.297 61.111 21.57 4.54 42.83 3.11
908 926 2.405191 GCTGGCGATCGAAAAGGC 59.595 61.111 21.57 10.91 0.00 4.35
909 927 2.109126 GCTGGCGATCGAAAAGGCT 61.109 57.895 21.57 0.00 0.00 4.58
910 928 2.009888 CTGGCGATCGAAAAGGCTC 58.990 57.895 21.57 0.00 0.00 4.70
911 929 0.460987 CTGGCGATCGAAAAGGCTCT 60.461 55.000 21.57 0.00 0.00 4.09
912 930 0.460284 TGGCGATCGAAAAGGCTCTC 60.460 55.000 21.57 0.00 0.00 3.20
913 931 1.483424 GGCGATCGAAAAGGCTCTCG 61.483 60.000 21.57 11.56 36.39 4.04
914 932 1.483424 GCGATCGAAAAGGCTCTCGG 61.483 60.000 21.57 4.80 35.76 4.63
915 933 0.872021 CGATCGAAAAGGCTCTCGGG 60.872 60.000 10.26 5.56 35.76 5.14
938 956 7.309990 CGGGATGCTGGATGGATTTATTAATTT 60.310 37.037 0.00 0.00 0.00 1.82
939 957 9.034800 GGGATGCTGGATGGATTTATTAATTTA 57.965 33.333 0.00 0.00 0.00 1.40
981 1004 0.828677 AAGATATATACCGGCCGGCC 59.171 55.000 43.58 36.69 39.32 6.13
998 1025 0.039346 GCCGGCGAGGAAGATACTAC 60.039 60.000 12.58 0.00 45.00 2.73
999 1026 0.597072 CCGGCGAGGAAGATACTACC 59.403 60.000 9.30 0.00 45.00 3.18
1001 1028 1.887198 CGGCGAGGAAGATACTACCAT 59.113 52.381 0.00 0.00 0.00 3.55
1002 1029 2.351835 CGGCGAGGAAGATACTACCATG 60.352 54.545 0.00 0.00 0.00 3.66
1003 1030 2.891580 GGCGAGGAAGATACTACCATGA 59.108 50.000 0.00 0.00 0.00 3.07
1006 1033 4.320641 GCGAGGAAGATACTACCATGAGAC 60.321 50.000 0.00 0.00 0.00 3.36
1007 1034 4.083749 CGAGGAAGATACTACCATGAGACG 60.084 50.000 0.00 0.00 0.00 4.18
1024 1052 0.807496 ACGAGACCGGCTTGTAGTAC 59.193 55.000 14.79 0.00 39.52 2.73
1052 1080 3.864243 ACTGTTGTTCAACGGACTTGTA 58.136 40.909 25.10 0.97 33.39 2.41
1054 1082 2.610374 TGTTGTTCAACGGACTTGTAGC 59.390 45.455 10.43 0.00 0.00 3.58
1065 1093 1.398390 GACTTGTAGCCGGCAAGAATG 59.602 52.381 31.54 15.95 44.29 2.67
1066 1094 0.734889 CTTGTAGCCGGCAAGAATGG 59.265 55.000 31.54 8.33 44.29 3.16
1073 1101 4.133796 GGCAAGAATGGCGCCACC 62.134 66.667 35.50 26.24 45.52 4.61
1220 1254 1.378778 CCCGTCCGTCTCTCCTTCT 60.379 63.158 0.00 0.00 0.00 2.85
1242 1276 1.596464 CCCGAGCACTAATCGTACGTC 60.596 57.143 16.05 1.56 38.50 4.34
1256 1290 7.975866 AATCGTACGTCGTAACAAGATAAAT 57.024 32.000 16.05 0.00 40.80 1.40
1257 1291 7.600467 ATCGTACGTCGTAACAAGATAAATC 57.400 36.000 16.05 0.00 40.80 2.17
1258 1292 6.775088 TCGTACGTCGTAACAAGATAAATCT 58.225 36.000 16.05 0.00 40.80 2.40
1259 1293 6.684131 TCGTACGTCGTAACAAGATAAATCTG 59.316 38.462 16.05 0.00 40.80 2.90
1583 1617 4.388499 GCCCACTTCGCCGGAGAA 62.388 66.667 19.99 19.99 0.00 2.87
1663 1697 1.006571 ACGGCTTCAACGTCGTCAT 60.007 52.632 0.00 0.00 41.25 3.06
1705 1739 0.037303 CTGCTGTTCCTGGTGATGGT 59.963 55.000 0.00 0.00 0.00 3.55
1717 1751 2.813908 GATGGTGTCGCCCGTGTC 60.814 66.667 0.00 0.00 36.04 3.67
1788 1822 0.587285 CGACGAGATCTTCTACGGGG 59.413 60.000 0.00 0.00 0.00 5.73
1844 1878 1.131315 GGTGAGCGCCTGAAATCTTTC 59.869 52.381 2.29 0.00 37.69 2.62
1893 1927 3.613689 GCCTACCCGATCCCGACC 61.614 72.222 0.00 0.00 38.22 4.79
1952 1986 6.551385 CCATATGAGGCAGAAACTATCAAC 57.449 41.667 3.65 0.00 0.00 3.18
1956 1990 4.517285 TGAGGCAGAAACTATCAACATCC 58.483 43.478 0.00 0.00 0.00 3.51
1974 2008 0.532115 CCAAGCCTGCATTTACACCC 59.468 55.000 0.00 0.00 0.00 4.61
1987 2021 6.542005 TGCATTTACACCCAGATACAGTAATG 59.458 38.462 0.00 0.00 0.00 1.90
1990 2024 8.993121 CATTTACACCCAGATACAGTAATGATC 58.007 37.037 0.00 0.00 0.00 2.92
1996 2030 4.449068 CCAGATACAGTAATGATCCGTTGC 59.551 45.833 0.00 0.00 0.00 4.17
1999 2033 2.009774 ACAGTAATGATCCGTTGCTGC 58.990 47.619 19.05 0.00 43.44 5.25
2002 2036 2.434336 AGTAATGATCCGTTGCTGCCTA 59.566 45.455 0.00 0.00 0.00 3.93
2006 2040 1.136305 TGATCCGTTGCTGCCTACTAC 59.864 52.381 0.00 0.00 0.00 2.73
2007 2041 0.102481 ATCCGTTGCTGCCTACTACG 59.898 55.000 0.00 0.00 36.30 3.51
2010 2044 1.542544 CGTTGCTGCCTACTACGTAC 58.457 55.000 0.00 0.00 32.78 3.67
2012 2046 2.352651 CGTTGCTGCCTACTACGTACTA 59.647 50.000 0.00 0.00 32.78 1.82
2013 2047 3.545624 CGTTGCTGCCTACTACGTACTAG 60.546 52.174 0.00 0.00 32.78 2.57
2014 2048 1.945394 TGCTGCCTACTACGTACTAGC 59.055 52.381 0.00 0.00 0.00 3.42
2015 2049 2.220313 GCTGCCTACTACGTACTAGCT 58.780 52.381 0.00 0.00 0.00 3.32
2016 2050 3.181462 TGCTGCCTACTACGTACTAGCTA 60.181 47.826 0.00 0.00 0.00 3.32
2034 2069 2.921754 GCTAGTGTTACGAATCGCACTT 59.078 45.455 16.80 4.70 41.67 3.16
2035 2070 3.241678 GCTAGTGTTACGAATCGCACTTG 60.242 47.826 16.80 15.65 41.67 3.16
2074 2109 0.310543 TGCCAACGCTGTGTTTCATC 59.689 50.000 3.43 0.00 39.29 2.92
2116 3315 8.924511 AAGTATTTGATTGATATTCCCGTCAT 57.075 30.769 0.00 0.00 0.00 3.06
2121 3320 5.230182 TGATTGATATTCCCGTCATTCGAG 58.770 41.667 0.00 0.00 42.86 4.04
2137 3336 6.316390 GTCATTCGAGTCCTACCAATCAAAAT 59.684 38.462 0.00 0.00 0.00 1.82
2143 3368 6.293081 CGAGTCCTACCAATCAAAATGCTATG 60.293 42.308 0.00 0.00 0.00 2.23
2144 3369 6.662755 AGTCCTACCAATCAAAATGCTATGA 58.337 36.000 0.00 0.00 0.00 2.15
2173 3398 4.090761 TGTCTTTTCACCAGCTCAATCT 57.909 40.909 0.00 0.00 0.00 2.40
2185 3410 7.336931 TCACCAGCTCAATCTTTTTATACTTCC 59.663 37.037 0.00 0.00 0.00 3.46
2204 3429 6.708285 ACTTCCTCTGTTCCAAAATATACGT 58.292 36.000 0.00 0.00 0.00 3.57
2206 3431 5.345702 TCCTCTGTTCCAAAATATACGTCG 58.654 41.667 0.00 0.00 0.00 5.12
2207 3432 5.105635 TCCTCTGTTCCAAAATATACGTCGT 60.106 40.000 2.21 2.21 0.00 4.34
2208 3433 5.579511 CCTCTGTTCCAAAATATACGTCGTT 59.420 40.000 1.78 0.00 0.00 3.85
2209 3434 6.091713 CCTCTGTTCCAAAATATACGTCGTTT 59.908 38.462 1.78 0.00 0.00 3.60
2210 3435 7.360607 CCTCTGTTCCAAAATATACGTCGTTTT 60.361 37.037 1.78 0.00 0.00 2.43
2211 3436 8.531622 TCTGTTCCAAAATATACGTCGTTTTA 57.468 30.769 1.78 0.00 0.00 1.52
2212 3437 8.649841 TCTGTTCCAAAATATACGTCGTTTTAG 58.350 33.333 1.78 0.00 0.00 1.85
2213 3438 7.235777 TGTTCCAAAATATACGTCGTTTTAGC 58.764 34.615 1.78 0.00 0.00 3.09
2214 3439 6.964741 TCCAAAATATACGTCGTTTTAGCA 57.035 33.333 1.78 0.00 0.00 3.49
2215 3440 7.361889 TCCAAAATATACGTCGTTTTAGCAA 57.638 32.000 1.78 0.00 0.00 3.91
2216 3441 7.457868 TCCAAAATATACGTCGTTTTAGCAAG 58.542 34.615 1.78 0.00 0.00 4.01
2217 3442 6.193959 CCAAAATATACGTCGTTTTAGCAAGC 59.806 38.462 1.78 0.00 0.00 4.01
2218 3443 6.657836 AAATATACGTCGTTTTAGCAAGCT 57.342 33.333 1.78 0.00 0.00 3.74
2258 3487 7.941795 AACGACTTATATTATGAAACGGAGG 57.058 36.000 0.00 0.00 0.00 4.30
2268 3497 3.887621 TGAAACGGAGGGAGTATGAAG 57.112 47.619 0.00 0.00 0.00 3.02
2285 3514 5.772825 ATGAAGTAAAGCAAGTGCAAAGA 57.227 34.783 6.00 0.00 45.16 2.52
2334 3566 3.330701 ACTTGGGTGAACTGGATGTGTAT 59.669 43.478 0.00 0.00 0.00 2.29
2356 3588 4.569943 TGTTGCTCTATCAAAGGAGACAC 58.430 43.478 0.00 0.00 0.00 3.67
2360 3592 4.246458 GCTCTATCAAAGGAGACACGTTT 58.754 43.478 0.00 0.00 37.11 3.60
2394 3626 8.077991 CGGCACATTCAACTTAATTCATCATAT 58.922 33.333 0.00 0.00 0.00 1.78
2420 3652 0.662085 TGACGCCACGGGTTAAAAAC 59.338 50.000 0.00 0.00 0.00 2.43
2458 3691 0.375803 ACACGTCAAACTGCCGAAAC 59.624 50.000 0.00 0.00 0.00 2.78
2468 3701 5.705441 TCAAACTGCCGAAACATAGAGAAAT 59.295 36.000 0.00 0.00 0.00 2.17
2543 3778 4.215399 CACAACCACCAGTACCAGTAAATG 59.785 45.833 0.00 0.00 0.00 2.32
2548 3783 5.222048 ACCACCAGTACCAGTAAATGTCAAT 60.222 40.000 0.00 0.00 0.00 2.57
2638 3873 3.817084 TGCAGATTCTTCTCAACAACAGG 59.183 43.478 0.00 0.00 0.00 4.00
2647 3882 1.608590 CTCAACAACAGGCACGGAAAT 59.391 47.619 0.00 0.00 0.00 2.17
2648 3883 1.606668 TCAACAACAGGCACGGAAATC 59.393 47.619 0.00 0.00 0.00 2.17
2702 3938 8.656849 CATAAACACTTAAATAACTGAGCGAGT 58.343 33.333 0.00 0.00 35.94 4.18
2763 4018 0.240945 CAAATGCACCTTGGGACGAC 59.759 55.000 0.00 0.00 0.00 4.34
2790 4045 1.350684 TGCACATACAGGGAAGCTTCA 59.649 47.619 27.02 7.35 0.00 3.02
2795 4050 4.946157 CACATACAGGGAAGCTTCAGAAAT 59.054 41.667 27.02 11.00 0.00 2.17
2833 4088 1.055040 GCAGATATGGGAGAGCCTGT 58.945 55.000 0.00 0.00 0.00 4.00
2898 4153 1.285950 CTGCGACGTCTTGAGGACA 59.714 57.895 14.70 0.00 44.70 4.02
2912 4167 1.966451 GGACAACCTTCCGGCACAG 60.966 63.158 0.00 0.00 0.00 3.66
2913 4168 1.070786 GACAACCTTCCGGCACAGA 59.929 57.895 0.00 0.00 0.00 3.41
2992 4247 4.923281 GCACCAAGTTACCAAAGCAAATAG 59.077 41.667 0.00 0.00 0.00 1.73
3007 4262 8.630917 CAAAGCAAATAGAGAATCATGAGGAAT 58.369 33.333 0.09 0.00 37.82 3.01
3011 4266 3.123157 AGAGAATCATGAGGAATGGCG 57.877 47.619 0.09 0.00 37.82 5.69
3012 4267 2.149578 GAGAATCATGAGGAATGGCGG 58.850 52.381 0.09 0.00 36.86 6.13
3013 4268 1.202855 AGAATCATGAGGAATGGCGGG 60.203 52.381 0.09 0.00 36.86 6.13
3025 4281 1.319614 ATGGCGGGGTATTGTGCAAC 61.320 55.000 0.00 0.00 37.35 4.17
3042 4298 5.243507 TGTGCAACATGGTAAGAACAATGAT 59.756 36.000 0.00 0.00 45.67 2.45
3048 4304 9.650371 CAACATGGTAAGAACAATGATATTACG 57.350 33.333 0.00 0.00 39.12 3.18
3088 4345 7.509546 AGATCTATGAATTCACACCCGTAAAT 58.490 34.615 11.07 0.00 0.00 1.40
3147 4405 4.469586 TGGTTATAGCCTGACATCTGTTGA 59.530 41.667 7.19 0.00 0.00 3.18
3157 4415 4.198530 TGACATCTGTTGACTGAAGCAAA 58.801 39.130 0.00 0.00 0.00 3.68
3158 4416 4.639755 TGACATCTGTTGACTGAAGCAAAA 59.360 37.500 0.00 0.00 0.00 2.44
3159 4417 5.125257 TGACATCTGTTGACTGAAGCAAAAA 59.875 36.000 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.609853 TGAATGTGGGATTGCTCTGTAC 58.390 45.455 0.00 0.00 0.00 2.90
49 50 2.050691 GTATGCAGTGGCGTGTTTTTG 58.949 47.619 0.00 0.00 45.35 2.44
62 63 1.686587 TGGTCGATGTAGGGTATGCAG 59.313 52.381 0.00 0.00 0.00 4.41
65 66 3.243771 GGAGTTGGTCGATGTAGGGTATG 60.244 52.174 0.00 0.00 0.00 2.39
73 74 0.252284 AGGAGGGAGTTGGTCGATGT 60.252 55.000 0.00 0.00 0.00 3.06
102 103 3.896272 GGTCAAGGTAGGGTTCTATCGAT 59.104 47.826 2.16 2.16 32.00 3.59
136 137 5.295787 TCGTTCCATTAGGATTTCCATTTCG 59.704 40.000 0.00 0.00 45.26 3.46
160 161 5.046910 CAGTGGTGCTCGTTTATTCAATT 57.953 39.130 0.00 0.00 0.00 2.32
183 184 1.153706 CCGTGCTGGTTAGGGTACG 60.154 63.158 0.00 0.00 40.23 3.67
235 236 9.522804 TTTTCACTCTAAATTTTGTACGCAATT 57.477 25.926 0.00 0.00 34.18 2.32
249 250 3.644738 ACTCCCCTCGTTTTCACTCTAAA 59.355 43.478 0.00 0.00 0.00 1.85
294 296 2.683933 AGGAGATGGTTCGGCGGT 60.684 61.111 7.21 0.00 0.00 5.68
299 301 1.424493 GCTTGCGAGGAGATGGTTCG 61.424 60.000 2.37 0.00 37.40 3.95
370 372 0.797249 CGGTCGAAACGTCTGCCTAG 60.797 60.000 0.00 0.00 0.00 3.02
371 373 1.210931 CGGTCGAAACGTCTGCCTA 59.789 57.895 0.00 0.00 0.00 3.93
372 374 2.049433 CGGTCGAAACGTCTGCCT 60.049 61.111 0.00 0.00 0.00 4.75
376 378 1.372623 GGAAGCGGTCGAAACGTCT 60.373 57.895 11.67 7.11 0.00 4.18
379 381 3.475774 CCGGAAGCGGTCGAAACG 61.476 66.667 0.00 6.42 0.00 3.60
435 438 0.382158 TGAGCCGTCAGATCGATCAC 59.618 55.000 26.47 15.76 0.00 3.06
469 472 2.765699 AGTTGCATTTTCTGGGTGTTGT 59.234 40.909 0.00 0.00 0.00 3.32
501 504 9.109393 TGTCAGCACATTATAGAACCTAAATTC 57.891 33.333 0.00 0.00 0.00 2.17
509 512 4.504461 CCGACTGTCAGCACATTATAGAAC 59.496 45.833 8.73 0.00 0.00 3.01
510 513 4.159693 ACCGACTGTCAGCACATTATAGAA 59.840 41.667 8.73 0.00 0.00 2.10
514 517 2.418746 GGACCGACTGTCAGCACATTAT 60.419 50.000 8.73 0.00 46.38 1.28
519 522 1.859427 TACGGACCGACTGTCAGCAC 61.859 60.000 23.38 0.00 46.38 4.40
533 536 2.908688 ATGCAGCACATATGTACGGA 57.091 45.000 8.32 1.55 37.17 4.69
557 562 4.603535 GAATGGCCGGGATGGGGG 62.604 72.222 2.18 0.00 38.63 5.40
582 587 0.974010 AGGCCGTATCCAAACGAGGA 60.974 55.000 0.00 0.00 45.68 3.71
615 620 7.147567 TGTGCCTTGTTCTCTGTAATATGGATA 60.148 37.037 0.00 0.00 0.00 2.59
620 625 7.112122 TGAATGTGCCTTGTTCTCTGTAATAT 58.888 34.615 0.00 0.00 0.00 1.28
628 633 1.815003 CCCTGAATGTGCCTTGTTCTC 59.185 52.381 0.00 0.00 0.00 2.87
637 642 1.678101 GTGCCTAATCCCTGAATGTGC 59.322 52.381 0.00 0.00 0.00 4.57
657 663 4.067016 CGACGCAAACGAACCCCG 62.067 66.667 0.00 0.00 43.93 5.73
671 677 4.756502 ACCCTTAGATTGTAAAGCTCGAC 58.243 43.478 0.00 0.00 38.98 4.20
672 678 5.416271 AACCCTTAGATTGTAAAGCTCGA 57.584 39.130 0.00 0.00 38.98 4.04
673 679 7.605410 TTAAACCCTTAGATTGTAAAGCTCG 57.395 36.000 0.00 0.00 38.98 5.03
688 694 5.715279 GGAGTGAAGCCTATTTTAAACCCTT 59.285 40.000 0.00 0.00 0.00 3.95
694 700 8.147244 AGTAGAAGGAGTGAAGCCTATTTTAA 57.853 34.615 0.00 0.00 33.76 1.52
703 709 1.135333 CCCGAGTAGAAGGAGTGAAGC 59.865 57.143 0.00 0.00 0.00 3.86
766 772 5.991606 CCCTGCGACTCTCATATTCATAAAA 59.008 40.000 0.00 0.00 0.00 1.52
834 852 0.939419 GTGTCCCAACCAACACGTAC 59.061 55.000 0.00 0.00 36.73 3.67
896 914 0.872021 CCCGAGAGCCTTTTCGATCG 60.872 60.000 9.36 9.36 39.06 3.69
897 915 0.460311 TCCCGAGAGCCTTTTCGATC 59.540 55.000 1.71 0.00 39.06 3.69
898 916 1.123928 ATCCCGAGAGCCTTTTCGAT 58.876 50.000 1.71 0.00 39.06 3.59
899 917 0.175760 CATCCCGAGAGCCTTTTCGA 59.824 55.000 1.71 0.00 39.06 3.71
900 918 1.432270 GCATCCCGAGAGCCTTTTCG 61.432 60.000 0.00 0.00 36.62 3.46
901 919 0.107459 AGCATCCCGAGAGCCTTTTC 60.107 55.000 0.00 0.00 0.00 2.29
902 920 0.393537 CAGCATCCCGAGAGCCTTTT 60.394 55.000 0.00 0.00 0.00 2.27
903 921 1.222936 CAGCATCCCGAGAGCCTTT 59.777 57.895 0.00 0.00 0.00 3.11
904 922 2.739996 CCAGCATCCCGAGAGCCTT 61.740 63.158 0.00 0.00 0.00 4.35
905 923 2.961559 ATCCAGCATCCCGAGAGCCT 62.962 60.000 0.00 0.00 0.00 4.58
906 924 2.515071 ATCCAGCATCCCGAGAGCC 61.515 63.158 0.00 0.00 0.00 4.70
907 925 1.301558 CATCCAGCATCCCGAGAGC 60.302 63.158 0.00 0.00 0.00 4.09
908 926 1.117749 TCCATCCAGCATCCCGAGAG 61.118 60.000 0.00 0.00 0.00 3.20
909 927 0.472543 ATCCATCCAGCATCCCGAGA 60.473 55.000 0.00 0.00 0.00 4.04
910 928 0.399454 AATCCATCCAGCATCCCGAG 59.601 55.000 0.00 0.00 0.00 4.63
911 929 0.846015 AAATCCATCCAGCATCCCGA 59.154 50.000 0.00 0.00 0.00 5.14
912 930 2.566833 TAAATCCATCCAGCATCCCG 57.433 50.000 0.00 0.00 0.00 5.14
913 931 7.486407 AATTAATAAATCCATCCAGCATCCC 57.514 36.000 0.00 0.00 0.00 3.85
938 956 5.295045 TGTGTCACTCGTCTCGCTAATAATA 59.705 40.000 4.27 0.00 0.00 0.98
939 957 4.095932 TGTGTCACTCGTCTCGCTAATAAT 59.904 41.667 4.27 0.00 0.00 1.28
940 958 3.437741 TGTGTCACTCGTCTCGCTAATAA 59.562 43.478 4.27 0.00 0.00 1.40
941 959 3.004862 TGTGTCACTCGTCTCGCTAATA 58.995 45.455 4.27 0.00 0.00 0.98
981 1004 1.315690 TGGTAGTATCTTCCTCGCCG 58.684 55.000 0.00 0.00 0.00 6.46
998 1025 1.949847 AAGCCGGTCTCGTCTCATGG 61.950 60.000 1.90 0.00 33.95 3.66
999 1026 0.803768 CAAGCCGGTCTCGTCTCATG 60.804 60.000 1.90 0.00 33.95 3.07
1001 1028 0.607217 TACAAGCCGGTCTCGTCTCA 60.607 55.000 1.90 0.00 33.95 3.27
1002 1029 0.099082 CTACAAGCCGGTCTCGTCTC 59.901 60.000 1.90 0.00 33.95 3.36
1003 1030 0.608582 ACTACAAGCCGGTCTCGTCT 60.609 55.000 1.90 0.00 33.95 4.18
1006 1033 0.806868 TGTACTACAAGCCGGTCTCG 59.193 55.000 1.90 0.00 0.00 4.04
1007 1034 1.134560 CCTGTACTACAAGCCGGTCTC 59.865 57.143 1.90 0.00 0.00 3.36
1122 1150 2.645567 CAGACACCGCAGTCGAGT 59.354 61.111 0.00 0.00 43.24 4.18
1229 1263 5.530519 TCTTGTTACGACGTACGATTAGT 57.469 39.130 24.41 16.80 45.77 2.24
1242 1276 4.260784 GGCAGGCAGATTTATCTTGTTACG 60.261 45.833 0.00 0.00 34.22 3.18
1256 1290 2.993008 GGAGACATGGCAGGCAGA 59.007 61.111 0.00 0.00 0.00 4.26
1257 1291 2.513204 CGGAGACATGGCAGGCAG 60.513 66.667 0.00 0.00 0.00 4.85
1258 1292 4.100084 CCGGAGACATGGCAGGCA 62.100 66.667 0.00 0.00 0.00 4.75
1316 1350 4.143333 GAGGCCAGCTTACCGCGA 62.143 66.667 8.23 0.00 45.59 5.87
1340 1374 3.036084 CGACACACGTGGCAGGTC 61.036 66.667 21.57 18.63 38.95 3.85
1550 1584 2.894387 GCCAGCAGCATCTCCGTC 60.894 66.667 0.00 0.00 42.97 4.79
1772 1806 0.587285 CGACCCCGTAGAAGATCTCG 59.413 60.000 0.00 0.00 0.00 4.04
1893 1927 1.376037 GGAGGAACTGGAAGCGGTG 60.376 63.158 0.00 0.00 41.55 4.94
1940 1974 4.946157 CAGGCTTGGATGTTGATAGTTTCT 59.054 41.667 0.00 0.00 0.00 2.52
1942 1976 3.445096 GCAGGCTTGGATGTTGATAGTTT 59.555 43.478 0.00 0.00 0.00 2.66
1952 1986 2.159198 GGTGTAAATGCAGGCTTGGATG 60.159 50.000 2.96 0.00 35.34 3.51
1956 1990 1.203052 CTGGGTGTAAATGCAGGCTTG 59.797 52.381 0.00 0.00 0.00 4.01
1974 2008 5.176406 CAGCAACGGATCATTACTGTATCTG 59.824 44.000 0.00 0.00 33.16 2.90
1987 2021 1.854227 GTAGTAGGCAGCAACGGATC 58.146 55.000 0.00 0.00 0.00 3.36
1990 2024 0.452987 TACGTAGTAGGCAGCAACGG 59.547 55.000 0.00 0.00 45.11 4.44
2006 2040 5.129151 CGATTCGTAACACTAGCTAGTACG 58.871 45.833 29.32 29.32 37.22 3.67
2007 2041 4.903016 GCGATTCGTAACACTAGCTAGTAC 59.097 45.833 25.63 18.68 34.13 2.73
2010 2044 3.724751 GTGCGATTCGTAACACTAGCTAG 59.275 47.826 19.44 19.44 0.00 3.42
2012 2046 2.163815 AGTGCGATTCGTAACACTAGCT 59.836 45.455 13.76 0.00 41.41 3.32
2013 2047 2.527100 AGTGCGATTCGTAACACTAGC 58.473 47.619 13.76 0.00 41.41 3.42
2014 2048 3.303495 CCAAGTGCGATTCGTAACACTAG 59.697 47.826 15.14 8.62 42.34 2.57
2015 2049 3.247442 CCAAGTGCGATTCGTAACACTA 58.753 45.455 15.14 0.00 42.34 2.74
2016 2050 2.066262 CCAAGTGCGATTCGTAACACT 58.934 47.619 8.03 9.60 44.96 3.55
2034 2069 4.015406 AATGCAGCCCGACGACCA 62.015 61.111 0.00 0.00 0.00 4.02
2035 2070 3.499737 CAATGCAGCCCGACGACC 61.500 66.667 0.00 0.00 0.00 4.79
2063 2098 3.057315 GGTTCACCATGGATGAAACACAG 60.057 47.826 26.78 5.64 42.32 3.66
2116 3315 4.394920 GCATTTTGATTGGTAGGACTCGAA 59.605 41.667 0.00 0.00 0.00 3.71
2121 3320 6.942532 TCATAGCATTTTGATTGGTAGGAC 57.057 37.500 0.00 0.00 34.22 3.85
2137 3336 7.094805 GGTGAAAAGACAACATACTTCATAGCA 60.095 37.037 0.00 0.00 0.00 3.49
2143 3368 5.239525 AGCTGGTGAAAAGACAACATACTTC 59.760 40.000 0.00 0.00 36.86 3.01
2144 3369 5.133221 AGCTGGTGAAAAGACAACATACTT 58.867 37.500 0.00 0.00 36.86 2.24
2185 3410 6.642683 AACGACGTATATTTTGGAACAGAG 57.357 37.500 0.00 0.00 42.39 3.35
2202 3427 2.663279 AACAGCTTGCTAAAACGACG 57.337 45.000 0.00 0.00 0.00 5.12
2258 3487 4.695455 TGCACTTGCTTTACTTCATACTCC 59.305 41.667 2.33 0.00 42.66 3.85
2268 3497 4.229876 GGATGTCTTTGCACTTGCTTTAC 58.770 43.478 2.33 0.00 42.66 2.01
2310 3539 0.883833 CATCCAGTTCACCCAAGTGC 59.116 55.000 0.00 0.00 44.16 4.40
2311 3540 1.881973 CACATCCAGTTCACCCAAGTG 59.118 52.381 0.00 0.00 46.00 3.16
2312 3541 1.494721 ACACATCCAGTTCACCCAAGT 59.505 47.619 0.00 0.00 0.00 3.16
2313 3542 2.276732 ACACATCCAGTTCACCCAAG 57.723 50.000 0.00 0.00 0.00 3.61
2314 3543 3.073798 ACATACACATCCAGTTCACCCAA 59.926 43.478 0.00 0.00 0.00 4.12
2315 3544 2.642311 ACATACACATCCAGTTCACCCA 59.358 45.455 0.00 0.00 0.00 4.51
2316 3545 3.350219 ACATACACATCCAGTTCACCC 57.650 47.619 0.00 0.00 0.00 4.61
2317 3546 3.119849 GCAACATACACATCCAGTTCACC 60.120 47.826 0.00 0.00 0.00 4.02
2318 3547 3.753272 AGCAACATACACATCCAGTTCAC 59.247 43.478 0.00 0.00 0.00 3.18
2334 3566 4.569943 GTGTCTCCTTTGATAGAGCAACA 58.430 43.478 0.00 0.00 0.00 3.33
2360 3592 0.466372 TTGAATGTGCCGTGGTTGGA 60.466 50.000 0.00 0.00 0.00 3.53
2394 3626 2.632544 CCCGTGGCGTCAGTGTCTA 61.633 63.158 0.00 0.00 0.00 2.59
2395 3627 3.991051 CCCGTGGCGTCAGTGTCT 61.991 66.667 0.00 0.00 0.00 3.41
2396 3628 2.424705 TAACCCGTGGCGTCAGTGTC 62.425 60.000 0.00 0.00 0.00 3.67
2420 3652 2.100749 TGTGTACGAGTATGATGCCCTG 59.899 50.000 0.00 0.00 0.00 4.45
2543 3778 6.258507 AGTGAAACCTTGCAAAAATCATTGAC 59.741 34.615 0.00 0.00 37.80 3.18
2548 3783 3.870419 GCAGTGAAACCTTGCAAAAATCA 59.130 39.130 0.00 0.14 37.80 2.57
2638 3873 4.394920 TCTTTAGTCCATTGATTTCCGTGC 59.605 41.667 0.00 0.00 0.00 5.34
2647 3882 3.953712 TCTGCGTCTTTAGTCCATTGA 57.046 42.857 0.00 0.00 0.00 2.57
2648 3883 5.551760 AAATCTGCGTCTTTAGTCCATTG 57.448 39.130 0.00 0.00 0.00 2.82
2815 4070 2.036992 GACACAGGCTCTCCCATATCTG 59.963 54.545 0.00 0.00 35.39 2.90
2833 4088 0.170339 CATACCGCAGACGACTGACA 59.830 55.000 19.07 0.29 46.03 3.58
2992 4247 2.149578 CCGCCATTCCTCATGATTCTC 58.850 52.381 0.00 0.00 34.31 2.87
3007 4262 1.974343 GTTGCACAATACCCCGCCA 60.974 57.895 0.00 0.00 0.00 5.69
3011 4266 1.555967 ACCATGTTGCACAATACCCC 58.444 50.000 0.00 0.00 0.00 4.95
3012 4267 4.013728 TCTTACCATGTTGCACAATACCC 58.986 43.478 0.00 0.00 0.00 3.69
3013 4268 5.048364 TGTTCTTACCATGTTGCACAATACC 60.048 40.000 0.00 0.00 0.00 2.73
3027 4283 9.476202 CAGATCGTAATATCATTGTTCTTACCA 57.524 33.333 0.00 0.00 0.00 3.25
3028 4284 9.692749 TCAGATCGTAATATCATTGTTCTTACC 57.307 33.333 0.00 0.00 0.00 2.85
3030 4286 9.914131 CCTCAGATCGTAATATCATTGTTCTTA 57.086 33.333 0.00 0.00 0.00 2.10
3036 4292 6.861329 CGACCTCAGATCGTAATATCATTG 57.139 41.667 0.00 0.00 34.84 2.82
3048 4304 7.441890 TCATAGATCTTAACGACCTCAGATC 57.558 40.000 0.00 0.00 41.36 2.75
3055 4312 7.042658 GGTGTGAATTCATAGATCTTAACGACC 60.043 40.741 12.12 0.00 0.00 4.79
3114 4371 2.174854 AGGCTATAACCATTCCCCACAC 59.825 50.000 0.00 0.00 0.00 3.82


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

AutoCloner maintained by Alex Coulton.