Multiple sequence alignment - TraesCS6A01G294000

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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 TraesCS6A01G294000 chr6A 100.000 2953 0 0 1 2953 525993595 525990643 0.000000e+00 5454.0
1 TraesCS6A01G294000 chr6B 89.784 2819 175 50 10 2776 574022447 574019690 0.000000e+00 3506.0
2 TraesCS6A01G294000 chr6D 90.385 2288 118 39 5 2233 383746534 383744290 0.000000e+00 2913.0
3 TraesCS6A01G294000 chr6D 92.388 578 30 9 2224 2798 383744119 383743553 0.000000e+00 811.0
4 TraesCS6A01G294000 chr7D 79.174 605 72 35 993 1549 165634705 165635303 1.290000e-98 370.0
5 TraesCS6A01G294000 chr7B 82.415 381 47 14 999 1361 128822081 128822459 6.140000e-82 315.0
6 TraesCS6A01G294000 chr7A 91.216 148 12 1 992 1138 167179673 167179820 1.790000e-47 200.0
7 TraesCS6A01G294000 chr7A 90.278 144 14 0 1218 1361 167179924 167180067 3.890000e-44 189.0
8 TraesCS6A01G294000 chr5D 90.511 137 11 2 1001 1136 319254271 319254406 2.340000e-41 180.0
9 TraesCS6A01G294000 chr5D 85.821 134 18 1 1425 1558 319254699 319254831 1.100000e-29 141.0
10 TraesCS6A01G294000 chr5B 90.511 137 11 2 1001 1136 369485439 369485574 2.340000e-41 180.0
11 TraesCS6A01G294000 chr5B 100.000 36 0 0 2819 2854 477885230 477885265 1.900000e-07 67.6
12 TraesCS6A01G294000 chr5A 90.511 137 11 2 1001 1136 414934854 414934719 2.340000e-41 180.0
13 TraesCS6A01G294000 chr1B 81.818 121 22 0 1234 1354 487951338 487951218 5.210000e-18 102.0
14 TraesCS6A01G294000 chr3D 89.610 77 7 1 1216 1292 357141490 357141565 2.420000e-16 97.1
15 TraesCS6A01G294000 chr1D 90.769 65 6 0 1437 1501 364624908 364624844 1.460000e-13 87.9


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 TraesCS6A01G294000 chr6A 525990643 525993595 2952 True 5454 5454 100.0000 1 2953 1 chr6A.!!$R1 2952
1 TraesCS6A01G294000 chr6B 574019690 574022447 2757 True 3506 3506 89.7840 10 2776 1 chr6B.!!$R1 2766
2 TraesCS6A01G294000 chr6D 383743553 383746534 2981 True 1862 2913 91.3865 5 2798 2 chr6D.!!$R1 2793
3 TraesCS6A01G294000 chr7D 165634705 165635303 598 False 370 370 79.1740 993 1549 1 chr7D.!!$F1 556

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
243 244 0.108186 GGACATCGCATCACAGTGGA 60.108 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2226 2339 0.238289 AGCGCGTTGAACCAAAGATG 59.762 50.0 8.43 0.0 0.0 2.9 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
95 96 0.803117 GTCGTGACACCGATCTGAGA 59.197 55.000 0.00 0.00 39.34 3.27
163 164 4.052229 CGCCAAGGACGACGGACT 62.052 66.667 0.00 0.00 0.00 3.85
203 204 2.825726 ATCAGACGCTCGCTGGTGTG 62.826 60.000 11.55 0.49 34.20 3.82
204 205 3.606662 AGACGCTCGCTGGTGTGT 61.607 61.111 0.00 0.00 33.45 3.72
233 234 1.374125 CTGAACCGTGGACATCGCA 60.374 57.895 0.00 0.00 0.00 5.10
243 244 0.108186 GGACATCGCATCACAGTGGA 60.108 55.000 0.00 0.00 0.00 4.02
244 245 1.473965 GGACATCGCATCACAGTGGAT 60.474 52.381 0.00 0.00 0.00 3.41
251 252 1.153289 ATCACAGTGGATCGCTGCC 60.153 57.895 13.67 0.00 44.75 4.85
278 279 1.536662 AGCTTCTCTCCGGTTGGGT 60.537 57.895 0.00 0.00 37.00 4.51
302 303 2.477375 GCCCGGAAAATTTCGGTTTTTC 59.523 45.455 14.98 0.00 44.32 2.29
360 362 0.949397 TCGTCGTTGTACTGCTGACT 59.051 50.000 0.00 0.00 0.00 3.41
404 407 2.221981 GCTATGCCTCGTAAACATCAGC 59.778 50.000 0.00 0.00 0.00 4.26
430 441 6.858478 GGTCACTTCTCTAAATTTTCAACAGC 59.142 38.462 0.00 0.00 0.00 4.40
509 520 0.250124 AATCCACACGTTTCCGAGCA 60.250 50.000 0.00 0.00 37.88 4.26
510 521 0.250124 ATCCACACGTTTCCGAGCAA 60.250 50.000 0.00 0.00 37.88 3.91
511 522 0.462225 TCCACACGTTTCCGAGCAAA 60.462 50.000 0.00 0.00 37.88 3.68
512 523 0.378962 CCACACGTTTCCGAGCAAAA 59.621 50.000 0.00 0.00 37.88 2.44
513 524 1.202200 CCACACGTTTCCGAGCAAAAA 60.202 47.619 0.00 0.00 37.88 1.94
514 525 2.542824 CCACACGTTTCCGAGCAAAAAT 60.543 45.455 0.00 0.00 37.88 1.82
515 526 2.467305 CACACGTTTCCGAGCAAAAATG 59.533 45.455 0.00 0.00 37.88 2.32
516 527 1.451651 CACGTTTCCGAGCAAAAATGC 59.548 47.619 0.00 0.00 37.88 3.56
518 529 2.550606 ACGTTTCCGAGCAAAAATGCTA 59.449 40.909 2.89 0.00 46.36 3.49
519 530 3.163594 CGTTTCCGAGCAAAAATGCTAG 58.836 45.455 2.89 3.65 46.36 3.42
520 531 3.120338 CGTTTCCGAGCAAAAATGCTAGA 60.120 43.478 11.70 5.86 46.36 2.43
521 532 4.406943 GTTTCCGAGCAAAAATGCTAGAG 58.593 43.478 11.70 3.65 46.36 2.43
522 533 2.009774 TCCGAGCAAAAATGCTAGAGC 58.990 47.619 11.70 0.00 46.36 4.09
552 563 4.378874 CGGTTCATTCAGCCTCTTTCTTTC 60.379 45.833 0.00 0.00 0.00 2.62
567 578 8.463607 CCTCTTTCTTTCCCGATAGATAGATAC 58.536 40.741 6.03 0.00 39.76 2.24
633 644 2.202974 GGTAATCCGTGGCCCGTC 60.203 66.667 0.00 0.00 33.66 4.79
673 684 2.603473 TCGGGTGCACAGCCTAGT 60.603 61.111 20.43 0.00 46.33 2.57
674 685 1.304630 TCGGGTGCACAGCCTAGTA 60.305 57.895 20.43 0.00 46.33 1.82
675 686 1.141881 CGGGTGCACAGCCTAGTAG 59.858 63.158 20.43 0.00 46.33 2.57
687 698 3.614616 CAGCCTAGTAGCAGAAAGAAACG 59.385 47.826 0.00 0.00 34.23 3.60
690 701 1.429463 AGTAGCAGAAAGAAACGCCG 58.571 50.000 0.00 0.00 0.00 6.46
694 705 1.646540 CAGAAAGAAACGCCGTGCA 59.353 52.632 0.00 0.00 0.00 4.57
717 728 3.520862 GCATGCATGGTCCACCCG 61.521 66.667 27.34 0.00 35.15 5.28
718 729 2.045045 CATGCATGGTCCACCCGT 60.045 61.111 19.40 0.00 35.15 5.28
785 802 2.580601 GGCTCACACGTACTGGGGT 61.581 63.158 0.00 0.00 0.00 4.95
791 808 1.375523 CACGTACTGGGGTTCTGCC 60.376 63.158 0.00 0.00 0.00 4.85
889 907 1.352687 AGGCCAAACTTCTTCCTCCTC 59.647 52.381 5.01 0.00 0.00 3.71
898 916 0.323542 TCTTCCTCCTCGGACTGACC 60.324 60.000 0.00 0.00 42.97 4.02
977 995 4.724602 TCGCTCACTGGTGCTCGC 62.725 66.667 0.00 0.00 0.00 5.03
1138 1156 2.659016 CCAAGCTCGCAGGTGAGA 59.341 61.111 13.69 0.00 38.28 3.27
1139 1157 1.220206 CCAAGCTCGCAGGTGAGAT 59.780 57.895 13.69 4.32 38.28 2.75
1143 1161 0.682532 AGCTCGCAGGTGAGATGAGA 60.683 55.000 13.69 0.00 38.28 3.27
1144 1162 0.174389 GCTCGCAGGTGAGATGAGAA 59.826 55.000 13.69 0.00 38.28 2.87
1153 1171 1.457303 GTGAGATGAGAACACACACGC 59.543 52.381 0.00 0.00 35.06 5.34
1168 1193 1.374505 ACGCAAATGCATGGCAACC 60.375 52.632 19.85 0.00 43.62 3.77
1169 1194 1.374378 CGCAAATGCATGGCAACCA 60.374 52.632 19.85 0.00 43.62 3.67
1174 1199 0.683828 AATGCATGGCAACCATCCGA 60.684 50.000 0.00 0.00 43.15 4.55
1177 1202 1.378382 CATGGCAACCATCCGACCA 60.378 57.895 0.00 0.00 43.15 4.02
1179 1204 2.750237 GGCAACCATCCGACCACC 60.750 66.667 0.00 0.00 0.00 4.61
1181 1206 2.435938 CAACCATCCGACCACCCG 60.436 66.667 0.00 0.00 0.00 5.28
1182 1207 4.404098 AACCATCCGACCACCCGC 62.404 66.667 0.00 0.00 0.00 6.13
1184 1209 4.402528 CCATCCGACCACCCGCAA 62.403 66.667 0.00 0.00 0.00 4.85
1185 1210 2.359354 CATCCGACCACCCGCAAA 60.359 61.111 0.00 0.00 0.00 3.68
1189 1214 3.055719 CGACCACCCGCAAAGCAT 61.056 61.111 0.00 0.00 0.00 3.79
1190 1215 2.625823 CGACCACCCGCAAAGCATT 61.626 57.895 0.00 0.00 0.00 3.56
1191 1216 1.665442 GACCACCCGCAAAGCATTT 59.335 52.632 0.00 0.00 40.26 2.32
1209 1256 0.390340 TTGGAGTCTCAGTCGCATGC 60.390 55.000 7.91 7.91 0.00 4.06
1210 1257 1.253593 TGGAGTCTCAGTCGCATGCT 61.254 55.000 17.13 0.00 0.00 3.79
1211 1258 0.108424 GGAGTCTCAGTCGCATGCTT 60.108 55.000 17.13 0.00 0.00 3.91
1212 1259 0.997932 GAGTCTCAGTCGCATGCTTG 59.002 55.000 17.13 11.38 0.00 4.01
1213 1260 1.018226 AGTCTCAGTCGCATGCTTGC 61.018 55.000 17.13 14.31 45.78 4.01
1214 1261 1.742880 TCTCAGTCGCATGCTTGCC 60.743 57.895 17.13 5.92 46.57 4.52
1215 1262 2.032376 TCAGTCGCATGCTTGCCA 59.968 55.556 17.13 3.19 46.57 4.92
1216 1263 1.374343 CTCAGTCGCATGCTTGCCAT 61.374 55.000 17.13 2.37 46.57 4.40
1407 1490 1.057636 TGTTCGCGTCGTGAATTCTC 58.942 50.000 22.80 11.40 34.54 2.87
1484 1567 3.600388 GGACAACGAGATCAAGAACCAT 58.400 45.455 0.00 0.00 0.00 3.55
1582 1665 4.444081 CGACCCCCTCGAGGACCT 62.444 72.222 33.39 13.61 46.14 3.85
1607 1693 0.390866 AGGAGCACTGCGATGACAAG 60.391 55.000 0.00 0.00 0.00 3.16
1748 1834 4.095400 TCCCCCTGCTCCTCCTCC 62.095 72.222 0.00 0.00 0.00 4.30
1835 1927 2.636412 CCTCTTCCAGGTCGACGCA 61.636 63.158 9.92 0.00 37.53 5.24
1863 1955 3.065787 ATGGACTGGGCCAGCATCC 62.066 63.158 33.04 30.17 42.15 3.51
1965 2057 2.953020 GGATGTGATCCTGACGATAGC 58.047 52.381 0.00 0.00 46.19 2.97
2036 2140 4.411927 TCTAGCTGTTTTCCTCTCACTCT 58.588 43.478 0.00 0.00 0.00 3.24
2038 2142 2.968574 AGCTGTTTTCCTCTCACTCTCA 59.031 45.455 0.00 0.00 0.00 3.27
2040 2144 3.244044 GCTGTTTTCCTCTCACTCTCACT 60.244 47.826 0.00 0.00 0.00 3.41
2044 2148 3.797559 TTCCTCTCACTCTCACTCTCA 57.202 47.619 0.00 0.00 0.00 3.27
2050 2154 3.326297 TCTCACTCTCACTCTCACTCTCA 59.674 47.826 0.00 0.00 0.00 3.27
2051 2155 3.407698 TCACTCTCACTCTCACTCTCAC 58.592 50.000 0.00 0.00 0.00 3.51
2052 2156 3.072330 TCACTCTCACTCTCACTCTCACT 59.928 47.826 0.00 0.00 0.00 3.41
2053 2157 3.436704 CACTCTCACTCTCACTCTCACTC 59.563 52.174 0.00 0.00 0.00 3.51
2054 2158 3.327757 ACTCTCACTCTCACTCTCACTCT 59.672 47.826 0.00 0.00 0.00 3.24
2055 2159 3.935203 CTCTCACTCTCACTCTCACTCTC 59.065 52.174 0.00 0.00 0.00 3.20
2056 2160 3.582647 TCTCACTCTCACTCTCACTCTCT 59.417 47.826 0.00 0.00 0.00 3.10
2057 2161 4.775253 TCTCACTCTCACTCTCACTCTCTA 59.225 45.833 0.00 0.00 0.00 2.43
2058 2162 5.425217 TCTCACTCTCACTCTCACTCTCTAT 59.575 44.000 0.00 0.00 0.00 1.98
2067 2171 4.198530 CTCTCACTCTCTATGTGCTCTGA 58.801 47.826 0.00 0.00 35.58 3.27
2155 2267 2.159517 ACGAATGAGAAAAATGGCGAGC 60.160 45.455 0.00 0.00 0.00 5.03
2226 2339 3.763902 CTGGATCATCGATCACGGTATC 58.236 50.000 0.00 0.00 40.50 2.24
2241 2534 3.682858 ACGGTATCATCTTTGGTTCAACG 59.317 43.478 0.00 0.00 0.00 4.10
2255 2548 2.971959 AACGCGCTCATGCACACA 60.972 55.556 5.73 0.00 39.64 3.72
2282 2575 3.258722 AGAACAAACATTCCCACCCAT 57.741 42.857 0.00 0.00 0.00 4.00
2283 2576 4.396357 AGAACAAACATTCCCACCCATA 57.604 40.909 0.00 0.00 0.00 2.74
2284 2577 4.086457 AGAACAAACATTCCCACCCATAC 58.914 43.478 0.00 0.00 0.00 2.39
2285 2578 2.815158 ACAAACATTCCCACCCATACC 58.185 47.619 0.00 0.00 0.00 2.73
2348 2641 5.281727 AGCCTTTCGTCAAAGAAAAATGTC 58.718 37.500 0.00 0.00 41.60 3.06
2398 2691 2.103538 GCATGCACGCTCCAATGG 59.896 61.111 14.21 0.00 0.00 3.16
2467 2760 2.222027 CCAGTTTGGAAGTGTGAGGAC 58.778 52.381 0.00 0.00 40.96 3.85
2500 2794 8.251721 AGCAATAGTAGTGGAGTACTTAAGTTG 58.748 37.037 14.49 1.72 40.89 3.16
2531 2825 6.594159 GTCTGTTGCTAATATAACCACACACT 59.406 38.462 0.00 0.00 0.00 3.55
2581 2875 3.366273 CGCACAAAAGCATCCTTGTGTAT 60.366 43.478 14.42 0.00 45.56 2.29
2641 2937 6.876257 ACAGTACTCAAAGAAGGATCATTCAC 59.124 38.462 21.18 9.19 0.00 3.18
2724 3020 4.644685 CCAATCACCGGGAACATAATTCTT 59.355 41.667 6.32 0.00 0.00 2.52
2725 3021 5.450412 CCAATCACCGGGAACATAATTCTTG 60.450 44.000 6.32 0.00 0.00 3.02
2747 3043 4.020928 TGTTGATTTGACCGTTAGGCTCTA 60.021 41.667 0.00 0.00 42.76 2.43
2764 3060 4.034975 GGCTCTATTTGAGATTGAGTGTGC 59.965 45.833 0.00 0.00 45.39 4.57
2790 3086 2.420568 CGAAGGGCGTGGCTAGGTA 61.421 63.158 0.00 0.00 34.64 3.08
2794 3090 0.689745 AGGGCGTGGCTAGGTATCAA 60.690 55.000 0.00 0.00 0.00 2.57
2795 3091 0.249911 GGGCGTGGCTAGGTATCAAG 60.250 60.000 0.00 0.00 0.00 3.02
2796 3092 0.464452 GGCGTGGCTAGGTATCAAGT 59.536 55.000 0.00 0.00 0.00 3.16
2797 3093 1.538419 GGCGTGGCTAGGTATCAAGTC 60.538 57.143 0.00 0.00 0.00 3.01
2798 3094 1.409427 GCGTGGCTAGGTATCAAGTCT 59.591 52.381 0.00 0.00 0.00 3.24
2799 3095 2.544069 GCGTGGCTAGGTATCAAGTCTC 60.544 54.545 0.00 0.00 0.00 3.36
2800 3096 2.688446 CGTGGCTAGGTATCAAGTCTCA 59.312 50.000 0.00 0.00 0.00 3.27
2801 3097 3.243234 CGTGGCTAGGTATCAAGTCTCAG 60.243 52.174 0.00 0.00 0.00 3.35
2802 3098 3.702045 GTGGCTAGGTATCAAGTCTCAGT 59.298 47.826 0.00 0.00 0.00 3.41
2803 3099 3.954904 TGGCTAGGTATCAAGTCTCAGTC 59.045 47.826 0.00 0.00 0.00 3.51
2804 3100 3.954904 GGCTAGGTATCAAGTCTCAGTCA 59.045 47.826 0.00 0.00 0.00 3.41
2805 3101 4.402793 GGCTAGGTATCAAGTCTCAGTCAA 59.597 45.833 0.00 0.00 0.00 3.18
2806 3102 5.451242 GGCTAGGTATCAAGTCTCAGTCAAG 60.451 48.000 0.00 0.00 0.00 3.02
2807 3103 5.126384 GCTAGGTATCAAGTCTCAGTCAAGT 59.874 44.000 0.00 0.00 0.00 3.16
2808 3104 5.398603 AGGTATCAAGTCTCAGTCAAGTG 57.601 43.478 0.00 0.00 0.00 3.16
2809 3105 5.080337 AGGTATCAAGTCTCAGTCAAGTGA 58.920 41.667 0.00 0.00 0.00 3.41
2810 3106 5.719085 AGGTATCAAGTCTCAGTCAAGTGAT 59.281 40.000 0.00 0.00 0.00 3.06
2811 3107 6.892456 AGGTATCAAGTCTCAGTCAAGTGATA 59.108 38.462 0.00 0.00 0.00 2.15
2812 3108 7.563188 AGGTATCAAGTCTCAGTCAAGTGATAT 59.437 37.037 0.00 0.00 31.30 1.63
2813 3109 8.851145 GGTATCAAGTCTCAGTCAAGTGATATA 58.149 37.037 0.00 0.00 31.30 0.86
2816 3112 8.122472 TCAAGTCTCAGTCAAGTGATATAACA 57.878 34.615 0.00 0.00 0.00 2.41
2817 3113 8.753133 TCAAGTCTCAGTCAAGTGATATAACAT 58.247 33.333 0.00 0.00 0.00 2.71
2818 3114 9.376075 CAAGTCTCAGTCAAGTGATATAACATT 57.624 33.333 0.00 0.00 0.00 2.71
2819 3115 9.950496 AAGTCTCAGTCAAGTGATATAACATTT 57.050 29.630 0.00 0.00 0.00 2.32
2820 3116 9.950496 AGTCTCAGTCAAGTGATATAACATTTT 57.050 29.630 0.00 0.00 0.00 1.82
2852 3148 5.684550 AAAGCGTCCTTTATCGAAAAAGT 57.315 34.783 0.00 0.00 39.44 2.66
2853 3149 4.663636 AGCGTCCTTTATCGAAAAAGTG 57.336 40.909 0.00 0.00 35.16 3.16
2854 3150 4.312443 AGCGTCCTTTATCGAAAAAGTGA 58.688 39.130 0.00 0.00 35.16 3.41
2855 3151 4.935808 AGCGTCCTTTATCGAAAAAGTGAT 59.064 37.500 0.00 0.00 35.16 3.06
2856 3152 6.103997 AGCGTCCTTTATCGAAAAAGTGATA 58.896 36.000 0.00 0.00 35.16 2.15
2857 3153 6.761714 AGCGTCCTTTATCGAAAAAGTGATAT 59.238 34.615 0.00 0.00 35.16 1.63
2858 3154 7.924412 AGCGTCCTTTATCGAAAAAGTGATATA 59.076 33.333 0.00 0.00 35.16 0.86
2859 3155 8.545420 GCGTCCTTTATCGAAAAAGTGATATAA 58.455 33.333 0.00 0.00 35.16 0.98
2860 3156 9.845305 CGTCCTTTATCGAAAAAGTGATATAAC 57.155 33.333 0.00 0.00 35.16 1.89
2933 3229 9.481340 TCTTATTGATATAGCATTGACTGACAC 57.519 33.333 0.00 0.00 0.00 3.67
2934 3230 9.486497 CTTATTGATATAGCATTGACTGACACT 57.514 33.333 0.00 0.00 0.00 3.55
2935 3231 9.836864 TTATTGATATAGCATTGACTGACACTT 57.163 29.630 0.00 0.00 0.00 3.16
2937 3233 9.836864 ATTGATATAGCATTGACTGACACTTAA 57.163 29.630 0.00 0.00 0.00 1.85
2938 3234 8.648557 TGATATAGCATTGACTGACACTTAAC 57.351 34.615 0.00 0.00 0.00 2.01
2939 3235 7.710907 TGATATAGCATTGACTGACACTTAACC 59.289 37.037 0.00 0.00 0.00 2.85
2940 3236 4.085357 AGCATTGACTGACACTTAACCA 57.915 40.909 0.00 0.00 0.00 3.67
2941 3237 4.460263 AGCATTGACTGACACTTAACCAA 58.540 39.130 0.00 0.00 0.00 3.67
2942 3238 4.516698 AGCATTGACTGACACTTAACCAAG 59.483 41.667 0.00 0.00 37.81 3.61
2943 3239 4.275936 GCATTGACTGACACTTAACCAAGT 59.724 41.667 0.00 0.00 46.15 3.16
2944 3240 5.560953 GCATTGACTGACACTTAACCAAGTC 60.561 44.000 0.00 0.00 43.30 3.01
2945 3241 5.353394 TTGACTGACACTTAACCAAGTCT 57.647 39.130 0.00 0.00 43.30 3.24
2946 3242 4.945246 TGACTGACACTTAACCAAGTCTC 58.055 43.478 0.00 0.00 43.30 3.36
2947 3243 4.404394 TGACTGACACTTAACCAAGTCTCA 59.596 41.667 0.00 0.00 43.30 3.27
2949 3245 4.950050 CTGACACTTAACCAAGTCTCAGT 58.050 43.478 12.11 0.00 45.49 3.41
2950 3246 4.945246 TGACACTTAACCAAGTCTCAGTC 58.055 43.478 0.00 0.00 43.30 3.51
2951 3247 3.978687 ACACTTAACCAAGTCTCAGTCG 58.021 45.455 0.00 0.00 43.30 4.18
2952 3248 3.635373 ACACTTAACCAAGTCTCAGTCGA 59.365 43.478 0.00 0.00 43.30 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.369892 GCATCAGAGGAAAAGAGGCACTA 60.370 47.826 0.00 0.00 41.55 2.74
3 4 1.742268 GCATCAGAGGAAAAGAGGCAC 59.258 52.381 0.00 0.00 38.77 5.01
8 9 2.039480 ACTGCAGCATCAGAGGAAAAGA 59.961 45.455 15.27 0.00 37.51 2.52
95 96 2.072298 GATGCACTCTTTCTTGCTCGT 58.928 47.619 0.00 0.00 39.62 4.18
157 158 3.048602 CGACAAGGGTCAGTCCGT 58.951 61.111 0.00 0.00 44.54 4.69
158 159 2.432628 GCGACAAGGGTCAGTCCG 60.433 66.667 0.00 0.00 44.54 4.79
159 160 2.047179 GGCGACAAGGGTCAGTCC 60.047 66.667 0.00 0.00 44.54 3.85
163 164 4.308458 CACCGGCGACAAGGGTCA 62.308 66.667 9.30 0.00 44.54 4.02
182 183 3.260483 CCAGCGAGCGTCTGATGC 61.260 66.667 13.90 13.90 33.54 3.91
203 204 1.294459 GGTTCAGGACACGGGGTAC 59.706 63.158 0.00 0.00 0.00 3.34
204 205 2.277591 CGGTTCAGGACACGGGGTA 61.278 63.158 0.00 0.00 0.00 3.69
233 234 1.153289 GGCAGCGATCCACTGTGAT 60.153 57.895 9.86 0.88 37.47 3.06
278 279 1.968310 CCGAAATTTTCCGGGCCAA 59.032 52.632 4.39 0.00 41.89 4.52
302 303 1.433837 GCGGGCTATGTTAACGTGGG 61.434 60.000 10.68 4.68 0.00 4.61
360 362 1.146041 ACTGGTGAACTTGCTCGCA 59.854 52.632 0.00 0.00 0.00 5.10
404 407 6.954944 TGTTGAAAATTTAGAGAAGTGACCG 58.045 36.000 0.00 0.00 0.00 4.79
430 441 1.687563 GGATTTGAACCCGGGGTATG 58.312 55.000 27.92 0.00 33.12 2.39
451 462 0.040425 GTGCCCAACACGTGAACATC 60.040 55.000 25.01 8.62 40.07 3.06
509 520 2.728007 GTGGGAGGCTCTAGCATTTTT 58.272 47.619 15.23 0.00 44.36 1.94
510 521 1.407437 CGTGGGAGGCTCTAGCATTTT 60.407 52.381 15.23 0.00 44.36 1.82
511 522 0.179000 CGTGGGAGGCTCTAGCATTT 59.821 55.000 15.23 0.00 44.36 2.32
512 523 1.690219 CCGTGGGAGGCTCTAGCATT 61.690 60.000 15.23 0.00 44.36 3.56
513 524 2.136878 CCGTGGGAGGCTCTAGCAT 61.137 63.158 15.23 0.00 44.36 3.79
514 525 2.759973 CCGTGGGAGGCTCTAGCA 60.760 66.667 15.23 0.00 44.36 3.49
515 526 2.299503 GAACCGTGGGAGGCTCTAGC 62.300 65.000 15.23 3.75 41.14 3.42
516 527 0.970937 TGAACCGTGGGAGGCTCTAG 60.971 60.000 15.23 3.49 33.69 2.43
517 528 0.325296 ATGAACCGTGGGAGGCTCTA 60.325 55.000 15.23 0.88 33.69 2.43
518 529 1.201429 AATGAACCGTGGGAGGCTCT 61.201 55.000 15.23 0.00 33.69 4.09
519 530 0.744771 GAATGAACCGTGGGAGGCTC 60.745 60.000 5.78 5.78 33.69 4.70
520 531 1.299976 GAATGAACCGTGGGAGGCT 59.700 57.895 0.00 0.00 33.69 4.58
521 532 1.002624 TGAATGAACCGTGGGAGGC 60.003 57.895 0.00 0.00 33.69 4.70
522 533 1.026718 GCTGAATGAACCGTGGGAGG 61.027 60.000 0.00 0.00 37.30 4.30
552 563 5.695816 GCGGTACTAGTATCTATCTATCGGG 59.304 48.000 11.35 0.00 0.00 5.14
633 644 1.137872 ACGGATTAGCAGCAGGAGAAG 59.862 52.381 0.00 0.00 0.00 2.85
666 677 3.851098 CGTTTCTTTCTGCTACTAGGCT 58.149 45.455 0.00 0.00 0.00 4.58
673 684 1.144969 CACGGCGTTTCTTTCTGCTA 58.855 50.000 11.19 0.00 0.00 3.49
674 685 1.941812 CACGGCGTTTCTTTCTGCT 59.058 52.632 11.19 0.00 0.00 4.24
675 686 1.725973 GCACGGCGTTTCTTTCTGC 60.726 57.895 11.19 4.09 0.00 4.26
694 705 3.359033 GGTGGACCATGCATGCATATAT 58.641 45.455 31.73 19.82 34.91 0.86
717 728 2.750350 CCTCACCCTCACCCACAC 59.250 66.667 0.00 0.00 0.00 3.82
718 729 3.249189 GCCTCACCCTCACCCACA 61.249 66.667 0.00 0.00 0.00 4.17
719 730 4.035102 GGCCTCACCCTCACCCAC 62.035 72.222 0.00 0.00 0.00 4.61
722 733 3.775654 CTCGGCCTCACCCTCACC 61.776 72.222 0.00 0.00 33.26 4.02
747 758 1.592131 GCCTCTGCTCGCTCTGATG 60.592 63.158 0.00 0.00 33.53 3.07
1138 1156 2.605338 GCATTTGCGTGTGTGTTCTCAT 60.605 45.455 0.00 0.00 0.00 2.90
1139 1157 1.268488 GCATTTGCGTGTGTGTTCTCA 60.268 47.619 0.00 0.00 0.00 3.27
1143 1161 3.963676 ATGCATTTGCGTGTGTGTT 57.036 42.105 0.00 0.00 45.83 3.32
1168 1193 2.359354 TTTGCGGGTGGTCGGATG 60.359 61.111 0.00 0.00 0.00 3.51
1169 1194 2.046314 CTTTGCGGGTGGTCGGAT 60.046 61.111 0.00 0.00 0.00 4.18
1174 1199 1.367102 CAAATGCTTTGCGGGTGGT 59.633 52.632 0.00 0.00 33.36 4.16
1177 1202 0.827507 ACTCCAAATGCTTTGCGGGT 60.828 50.000 3.86 1.92 39.31 5.28
1179 1204 0.883833 AGACTCCAAATGCTTTGCGG 59.116 50.000 3.86 0.31 39.31 5.69
1181 1206 2.555757 ACTGAGACTCCAAATGCTTTGC 59.444 45.455 0.00 0.00 39.31 3.68
1182 1207 3.120408 CGACTGAGACTCCAAATGCTTTG 60.120 47.826 0.00 2.70 40.32 2.77
1183 1208 3.070018 CGACTGAGACTCCAAATGCTTT 58.930 45.455 0.00 0.00 0.00 3.51
1184 1209 2.693069 CGACTGAGACTCCAAATGCTT 58.307 47.619 0.00 0.00 0.00 3.91
1185 1210 1.674221 GCGACTGAGACTCCAAATGCT 60.674 52.381 0.00 0.00 0.00 3.79
1188 1213 2.625737 CATGCGACTGAGACTCCAAAT 58.374 47.619 0.00 0.00 0.00 2.32
1189 1214 1.941209 GCATGCGACTGAGACTCCAAA 60.941 52.381 0.00 0.00 0.00 3.28
1190 1215 0.390340 GCATGCGACTGAGACTCCAA 60.390 55.000 0.00 0.00 0.00 3.53
1191 1216 1.216444 GCATGCGACTGAGACTCCA 59.784 57.895 0.00 0.00 0.00 3.86
1256 1303 1.078426 GCGCAGGTAGTTGGTCCAT 60.078 57.895 0.30 0.00 0.00 3.41
1407 1490 4.748679 GCGCCGCAGCACAAGAAG 62.749 66.667 3.15 0.00 39.83 2.85
1592 1675 2.482374 GCCTTGTCATCGCAGTGC 59.518 61.111 4.58 4.58 0.00 4.40
1601 1687 2.525629 TGGGACGAGGCCTTGTCA 60.526 61.111 41.20 27.15 44.02 3.58
1603 1689 3.322466 CCTGGGACGAGGCCTTGT 61.322 66.667 26.51 26.51 0.00 3.16
1607 1693 2.506472 GATTCCTGGGACGAGGCC 59.494 66.667 0.00 0.00 32.51 5.19
1835 1927 1.475751 GCCCAGTCCATGTCGATGATT 60.476 52.381 0.00 0.00 0.00 2.57
1965 2057 5.577164 CACAATCTACTCTAACCCTCAAACG 59.423 44.000 0.00 0.00 0.00 3.60
1967 2059 5.488341 GCACAATCTACTCTAACCCTCAAA 58.512 41.667 0.00 0.00 0.00 2.69
1969 2069 3.451178 GGCACAATCTACTCTAACCCTCA 59.549 47.826 0.00 0.00 0.00 3.86
2036 2140 5.045942 ACATAGAGAGTGAGAGTGAGAGTGA 60.046 44.000 0.00 0.00 0.00 3.41
2038 2142 5.185454 CACATAGAGAGTGAGAGTGAGAGT 58.815 45.833 0.00 0.00 39.30 3.24
2040 2144 3.944650 GCACATAGAGAGTGAGAGTGAGA 59.055 47.826 0.00 0.00 39.30 3.27
2044 2148 3.947196 CAGAGCACATAGAGAGTGAGAGT 59.053 47.826 0.00 0.00 39.30 3.24
2050 2154 6.543430 AAGAAATCAGAGCACATAGAGAGT 57.457 37.500 0.00 0.00 0.00 3.24
2051 2155 6.258287 CCAAAGAAATCAGAGCACATAGAGAG 59.742 42.308 0.00 0.00 0.00 3.20
2052 2156 6.111382 CCAAAGAAATCAGAGCACATAGAGA 58.889 40.000 0.00 0.00 0.00 3.10
2053 2157 5.879223 ACCAAAGAAATCAGAGCACATAGAG 59.121 40.000 0.00 0.00 0.00 2.43
2054 2158 5.809001 ACCAAAGAAATCAGAGCACATAGA 58.191 37.500 0.00 0.00 0.00 1.98
2055 2159 7.714377 AGATACCAAAGAAATCAGAGCACATAG 59.286 37.037 0.00 0.00 0.00 2.23
2056 2160 7.568349 AGATACCAAAGAAATCAGAGCACATA 58.432 34.615 0.00 0.00 0.00 2.29
2057 2161 6.421485 AGATACCAAAGAAATCAGAGCACAT 58.579 36.000 0.00 0.00 0.00 3.21
2058 2162 5.809001 AGATACCAAAGAAATCAGAGCACA 58.191 37.500 0.00 0.00 0.00 4.57
2067 2171 6.642733 TCTCTCCCAAGATACCAAAGAAAT 57.357 37.500 0.00 0.00 0.00 2.17
2155 2267 2.032302 TCACGGATTTTCACAAACCACG 59.968 45.455 0.00 0.00 0.00 4.94
2226 2339 0.238289 AGCGCGTTGAACCAAAGATG 59.762 50.000 8.43 0.00 0.00 2.90
2255 2548 5.175127 GTGGGAATGTTTGTTCTTTTGTGT 58.825 37.500 0.00 0.00 0.00 3.72
2283 2576 8.960064 AGAATTGAATATGTTTATAGGGGAGGT 58.040 33.333 0.00 0.00 0.00 3.85
2284 2577 9.236006 CAGAATTGAATATGTTTATAGGGGAGG 57.764 37.037 0.00 0.00 0.00 4.30
2348 2641 8.246180 ACTATTCAGCCATGTTCATAAAACAAG 58.754 33.333 0.00 0.00 33.42 3.16
2398 2691 2.433318 GTCTCTGCCGCAGTCCAC 60.433 66.667 19.77 10.98 32.61 4.02
2467 2760 7.416890 AGTACTCCACTACTATTGCTAAAGCAG 60.417 40.741 4.63 0.00 43.83 4.24
2500 2794 8.552034 GTGGTTATATTAGCAACAGACATCTTC 58.448 37.037 0.00 0.00 0.00 2.87
2559 2853 1.411394 CACAAGGATGCTTTTGTGCG 58.589 50.000 6.17 0.00 45.09 5.34
2641 2937 1.812571 AGGCTGCGACCATAAAAGTTG 59.187 47.619 0.00 0.00 0.00 3.16
2724 3020 3.071479 GAGCCTAACGGTCAAATCAACA 58.929 45.455 0.00 0.00 38.92 3.33
2725 3021 3.335579 AGAGCCTAACGGTCAAATCAAC 58.664 45.455 0.00 0.00 41.71 3.18
2747 3043 5.916883 CGAAAAAGCACACTCAATCTCAAAT 59.083 36.000 0.00 0.00 0.00 2.32
2784 3080 6.375736 TCACTTGACTGAGACTTGATACCTAG 59.624 42.308 0.00 0.00 0.00 3.02
2790 3086 8.753133 TGTTATATCACTTGACTGAGACTTGAT 58.247 33.333 0.00 0.00 0.00 2.57
2794 3090 9.950496 AAAATGTTATATCACTTGACTGAGACT 57.050 29.630 0.00 0.00 0.00 3.24
2820 3116 9.585099 TCGATAAAGGACGCTTTATTACTTAAA 57.415 29.630 8.76 0.00 38.98 1.52
2821 3117 9.585099 TTCGATAAAGGACGCTTTATTACTTAA 57.415 29.630 8.76 0.49 38.98 1.85
2822 3118 9.585099 TTTCGATAAAGGACGCTTTATTACTTA 57.415 29.630 8.76 0.00 38.98 2.24
2823 3119 8.483307 TTTCGATAAAGGACGCTTTATTACTT 57.517 30.769 8.76 0.00 38.98 2.24
2824 3120 8.483307 TTTTCGATAAAGGACGCTTTATTACT 57.517 30.769 8.76 0.00 38.98 2.24
2825 3121 9.207042 CTTTTTCGATAAAGGACGCTTTATTAC 57.793 33.333 17.56 0.00 38.98 1.89
2826 3122 8.938906 ACTTTTTCGATAAAGGACGCTTTATTA 58.061 29.630 25.54 0.86 38.98 0.98
2827 3123 7.749126 CACTTTTTCGATAAAGGACGCTTTATT 59.251 33.333 25.54 4.69 38.98 1.40
2828 3124 7.118680 TCACTTTTTCGATAAAGGACGCTTTAT 59.881 33.333 25.54 7.50 40.84 1.40
2829 3125 6.424509 TCACTTTTTCGATAAAGGACGCTTTA 59.575 34.615 25.54 0.00 39.02 1.85
2830 3126 5.237779 TCACTTTTTCGATAAAGGACGCTTT 59.762 36.000 25.54 6.47 39.02 3.51
2831 3127 4.753107 TCACTTTTTCGATAAAGGACGCTT 59.247 37.500 25.54 7.06 39.02 4.68
2832 3128 4.312443 TCACTTTTTCGATAAAGGACGCT 58.688 39.130 25.54 7.65 39.02 5.07
2833 3129 4.657075 TCACTTTTTCGATAAAGGACGC 57.343 40.909 25.54 0.00 39.02 5.19
2834 3130 9.845305 GTTATATCACTTTTTCGATAAAGGACG 57.155 33.333 25.54 16.28 39.02 4.79
2907 3203 9.481340 GTGTCAGTCAATGCTATATCAATAAGA 57.519 33.333 0.00 0.00 0.00 2.10
2908 3204 9.486497 AGTGTCAGTCAATGCTATATCAATAAG 57.514 33.333 0.00 0.00 0.00 1.73
2909 3205 9.836864 AAGTGTCAGTCAATGCTATATCAATAA 57.163 29.630 0.00 0.00 0.00 1.40
2911 3207 9.836864 TTAAGTGTCAGTCAATGCTATATCAAT 57.163 29.630 0.00 0.00 0.00 2.57
2912 3208 9.098355 GTTAAGTGTCAGTCAATGCTATATCAA 57.902 33.333 0.00 0.00 0.00 2.57
2913 3209 7.710907 GGTTAAGTGTCAGTCAATGCTATATCA 59.289 37.037 0.00 0.00 0.00 2.15
2914 3210 7.710907 TGGTTAAGTGTCAGTCAATGCTATATC 59.289 37.037 0.00 0.00 0.00 1.63
2915 3211 7.564793 TGGTTAAGTGTCAGTCAATGCTATAT 58.435 34.615 0.00 0.00 0.00 0.86
2916 3212 6.941857 TGGTTAAGTGTCAGTCAATGCTATA 58.058 36.000 0.00 0.00 0.00 1.31
2917 3213 5.804639 TGGTTAAGTGTCAGTCAATGCTAT 58.195 37.500 0.00 0.00 0.00 2.97
2918 3214 5.222079 TGGTTAAGTGTCAGTCAATGCTA 57.778 39.130 0.00 0.00 0.00 3.49
2919 3215 4.085357 TGGTTAAGTGTCAGTCAATGCT 57.915 40.909 0.00 0.00 0.00 3.79
2920 3216 4.275936 ACTTGGTTAAGTGTCAGTCAATGC 59.724 41.667 0.00 0.00 45.17 3.56
2921 3217 5.760253 AGACTTGGTTAAGTGTCAGTCAATG 59.240 40.000 0.00 0.00 46.79 2.82
2922 3218 5.930135 AGACTTGGTTAAGTGTCAGTCAAT 58.070 37.500 0.00 0.00 46.79 2.57
2923 3219 5.353394 AGACTTGGTTAAGTGTCAGTCAA 57.647 39.130 0.00 0.00 46.79 3.18
2930 3226 3.635373 TCGACTGAGACTTGGTTAAGTGT 59.365 43.478 0.00 0.00 46.79 3.55
2931 3227 4.238761 TCGACTGAGACTTGGTTAAGTG 57.761 45.455 0.00 0.00 46.79 3.16


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

AutoCloner maintained by Alex Coulton.