Multiple sequence alignment - TraesCS6D01G313400

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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 TraesCS6D01G313400 chr6D 100.000 3047 0 0 1 3047 422192864 422189818 0.000000e+00 5627.0
1 TraesCS6D01G313400 chr6D 88.916 2066 131 51 423 2451 422203732 422205736 0.000000e+00 2457.0
2 TraesCS6D01G313400 chr6D 92.947 1347 80 9 637 1978 409348557 409347221 0.000000e+00 1947.0
3 TraesCS6D01G313400 chr6D 87.943 423 26 6 2471 2871 422205927 422206346 2.750000e-130 475.0
4 TraesCS6D01G313400 chr6D 86.863 373 36 6 1982 2354 409346933 409346574 3.660000e-109 405.0
5 TraesCS6D01G313400 chr6D 89.130 138 13 2 503 640 409348738 409348603 1.450000e-38 171.0
6 TraesCS6D01G313400 chr6B 90.408 2106 113 49 394 2465 636493360 636491310 0.000000e+00 2687.0
7 TraesCS6D01G313400 chr6B 90.645 2063 115 41 410 2442 636584168 636586182 0.000000e+00 2669.0
8 TraesCS6D01G313400 chr6B 91.156 1617 105 23 641 2231 614313236 614311632 0.000000e+00 2159.0
9 TraesCS6D01G313400 chr6B 91.044 1619 105 21 641 2231 614438549 614436943 0.000000e+00 2150.0
10 TraesCS6D01G313400 chr6B 90.999 1622 101 27 641 2231 614583607 614582000 0.000000e+00 2145.0
11 TraesCS6D01G313400 chr6B 94.294 333 17 1 2470 2802 636491150 636490820 2.710000e-140 508.0
12 TraesCS6D01G313400 chr6B 92.063 189 14 1 2790 2978 636490650 636490463 6.480000e-67 265.0
13 TraesCS6D01G313400 chr6B 83.696 184 22 7 459 640 614583834 614583657 1.880000e-37 167.0
14 TraesCS6D01G313400 chr6B 89.286 112 11 1 2867 2978 614434696 614434586 4.100000e-29 139.0
15 TraesCS6D01G313400 chr6B 87.850 107 12 1 2679 2784 614311062 614310956 1.150000e-24 124.0
16 TraesCS6D01G313400 chr6B 87.179 78 10 0 2277 2354 614311616 614311539 4.180000e-14 89.8
17 TraesCS6D01G313400 chr6B 87.179 78 10 0 2277 2354 614436927 614436850 4.180000e-14 89.8
18 TraesCS6D01G313400 chr6B 86.154 65 9 0 2277 2341 614581984 614581920 1.520000e-08 71.3
19 TraesCS6D01G313400 chr6A 93.221 1844 93 19 636 2467 564976339 564974516 0.000000e+00 2684.0
20 TraesCS6D01G313400 chr6A 92.144 1833 97 25 644 2450 564909188 564910999 0.000000e+00 2543.0
21 TraesCS6D01G313400 chr6A 93.820 1343 69 11 642 1978 554826106 554824772 0.000000e+00 2008.0
22 TraesCS6D01G313400 chr6A 91.775 462 26 6 186 640 564976844 564976388 1.540000e-177 632.0
23 TraesCS6D01G313400 chr6A 88.462 442 26 9 2546 2978 564974251 564973826 7.540000e-141 510.0
24 TraesCS6D01G313400 chr6A 85.146 377 39 9 1980 2354 554824473 554824112 1.330000e-98 370.0
25 TraesCS6D01G313400 chr6A 84.000 250 23 13 394 640 564908897 564909132 1.100000e-54 224.0
26 TraesCS6D01G313400 chr6A 96.992 133 4 0 1 133 564976973 564976841 1.100000e-54 224.0
27 TraesCS6D01G313400 chr6A 84.071 226 23 10 406 630 564907618 564907831 3.980000e-49 206.0
28 TraesCS6D01G313400 chr6A 95.385 65 2 1 545 609 554826766 554826703 5.370000e-18 102.0


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 TraesCS6D01G313400 chr6D 422189818 422192864 3046 True 5627.000000 5627 100.000000 1 3047 1 chr6D.!!$R1 3046
1 TraesCS6D01G313400 chr6D 422203732 422206346 2614 False 1466.000000 2457 88.429500 423 2871 2 chr6D.!!$F1 2448
2 TraesCS6D01G313400 chr6D 409346574 409348738 2164 True 841.000000 1947 89.646667 503 2354 3 chr6D.!!$R2 1851
3 TraesCS6D01G313400 chr6B 636584168 636586182 2014 False 2669.000000 2669 90.645000 410 2442 1 chr6B.!!$F1 2032
4 TraesCS6D01G313400 chr6B 636490463 636493360 2897 True 1153.333333 2687 92.255000 394 2978 3 chr6B.!!$R4 2584
5 TraesCS6D01G313400 chr6B 614581920 614583834 1914 True 794.433333 2145 86.949667 459 2341 3 chr6B.!!$R3 1882
6 TraesCS6D01G313400 chr6B 614434586 614438549 3963 True 792.933333 2150 89.169667 641 2978 3 chr6B.!!$R2 2337
7 TraesCS6D01G313400 chr6B 614310956 614313236 2280 True 790.933333 2159 88.728333 641 2784 3 chr6B.!!$R1 2143
8 TraesCS6D01G313400 chr6A 564973826 564976973 3147 True 1012.500000 2684 92.612500 1 2978 4 chr6A.!!$R2 2977
9 TraesCS6D01G313400 chr6A 564907618 564910999 3381 False 991.000000 2543 86.738333 394 2450 3 chr6A.!!$F1 2056
10 TraesCS6D01G313400 chr6A 554824112 554826766 2654 True 826.666667 2008 91.450333 545 2354 3 chr6A.!!$R1 1809

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
498 504 0.02877 GCCGTGCGCTGCATAATTTA 59.971 50.0 9.73 0.0 41.91 1.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2467 4763 0.320421 GAACCGCTACAGCACTTGGA 60.32 55.0 1.61 0.0 42.21 3.53 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
37 38 3.054802 ACCAGCTACTAGAATTTGCAGCT 60.055 43.478 0.00 0.00 39.86 4.24
41 42 4.081198 AGCTACTAGAATTTGCAGCTCACT 60.081 41.667 0.00 0.00 34.35 3.41
67 68 2.230940 CGCTATCCGTTCGCCACAG 61.231 63.158 0.00 0.00 0.00 3.66
133 134 2.783135 TGAACAGCTTCAGTTCCATCC 58.217 47.619 11.64 0.00 43.57 3.51
134 135 2.106338 TGAACAGCTTCAGTTCCATCCA 59.894 45.455 11.64 0.00 43.57 3.41
135 136 2.957402 ACAGCTTCAGTTCCATCCAA 57.043 45.000 0.00 0.00 0.00 3.53
136 137 2.787994 ACAGCTTCAGTTCCATCCAAG 58.212 47.619 0.00 0.00 0.00 3.61
137 138 2.373169 ACAGCTTCAGTTCCATCCAAGA 59.627 45.455 0.00 0.00 0.00 3.02
138 139 3.181440 ACAGCTTCAGTTCCATCCAAGAA 60.181 43.478 0.00 0.00 0.00 2.52
139 140 4.015084 CAGCTTCAGTTCCATCCAAGAAT 58.985 43.478 0.00 0.00 0.00 2.40
140 141 4.015084 AGCTTCAGTTCCATCCAAGAATG 58.985 43.478 0.00 0.00 0.00 2.67
161 162 1.473278 GTGGTACCACCTCTTCTCTCG 59.527 57.143 31.39 0.00 39.58 4.04
162 163 0.456628 GGTACCACCTCTTCTCTCGC 59.543 60.000 7.15 0.00 34.73 5.03
163 164 0.456628 GTACCACCTCTTCTCTCGCC 59.543 60.000 0.00 0.00 0.00 5.54
164 165 0.683504 TACCACCTCTTCTCTCGCCC 60.684 60.000 0.00 0.00 0.00 6.13
165 166 2.492090 CACCTCTTCTCTCGCCCG 59.508 66.667 0.00 0.00 0.00 6.13
166 167 2.046864 CACCTCTTCTCTCGCCCGA 61.047 63.158 0.00 0.00 0.00 5.14
167 168 1.304217 ACCTCTTCTCTCGCCCGAA 60.304 57.895 0.00 0.00 0.00 4.30
168 169 1.316706 ACCTCTTCTCTCGCCCGAAG 61.317 60.000 0.00 0.00 38.34 3.79
169 170 1.032657 CCTCTTCTCTCGCCCGAAGA 61.033 60.000 8.92 8.92 42.28 2.87
170 171 0.811915 CTCTTCTCTCGCCCGAAGAA 59.188 55.000 10.02 11.70 43.42 2.52
171 172 0.811915 TCTTCTCTCGCCCGAAGAAG 59.188 55.000 22.24 22.24 41.75 2.85
172 173 0.811915 CTTCTCTCGCCCGAAGAAGA 59.188 55.000 23.01 11.91 39.10 2.87
173 174 1.202582 CTTCTCTCGCCCGAAGAAGAA 59.797 52.381 23.01 16.31 39.10 2.52
174 175 1.475403 TCTCTCGCCCGAAGAAGAAT 58.525 50.000 0.00 0.00 0.00 2.40
175 176 1.135139 TCTCTCGCCCGAAGAAGAATG 59.865 52.381 0.00 0.00 0.00 2.67
176 177 0.460284 TCTCGCCCGAAGAAGAATGC 60.460 55.000 0.00 0.00 0.00 3.56
177 178 0.740868 CTCGCCCGAAGAAGAATGCA 60.741 55.000 0.00 0.00 0.00 3.96
178 179 0.321210 TCGCCCGAAGAAGAATGCAA 60.321 50.000 0.00 0.00 0.00 4.08
179 180 0.179189 CGCCCGAAGAAGAATGCAAC 60.179 55.000 0.00 0.00 0.00 4.17
180 181 0.171231 GCCCGAAGAAGAATGCAACC 59.829 55.000 0.00 0.00 0.00 3.77
181 182 0.447801 CCCGAAGAAGAATGCAACCG 59.552 55.000 0.00 0.00 0.00 4.44
182 183 0.179189 CCGAAGAAGAATGCAACCGC 60.179 55.000 0.00 0.00 39.24 5.68
183 184 0.519175 CGAAGAAGAATGCAACCGCG 60.519 55.000 0.00 0.00 42.97 6.46
184 185 0.179189 GAAGAAGAATGCAACCGCGG 60.179 55.000 26.86 26.86 42.97 6.46
185 186 2.200170 AAGAAGAATGCAACCGCGGC 62.200 55.000 28.58 12.64 42.97 6.53
186 187 2.976840 GAAGAATGCAACCGCGGCA 61.977 57.895 28.58 18.84 46.66 5.69
200 201 1.397190 CGCGGCATTATACTTTGCTCG 60.397 52.381 0.00 0.00 38.88 5.03
202 203 1.069906 CGGCATTATACTTTGCTCGGC 60.070 52.381 0.00 0.00 38.88 5.54
224 225 7.541783 TCGGCACATATTTTGAATGAAAGAAAG 59.458 33.333 0.00 0.00 0.00 2.62
232 233 1.130561 GAATGAAAGAAAGCGTCGGGG 59.869 52.381 0.00 0.00 0.00 5.73
300 306 4.634883 ACATAGCAGCTCTGATCAAAGTTG 59.365 41.667 14.48 8.42 0.00 3.16
318 324 6.981762 AAGTTGATTCAGAACTGATAGCTG 57.018 37.500 5.34 0.00 39.64 4.24
463 469 0.541296 AGCTTGGAGGTTGCATGCTT 60.541 50.000 20.33 1.54 44.40 3.91
498 504 0.028770 GCCGTGCGCTGCATAATTTA 59.971 50.000 9.73 0.00 41.91 1.40
507 1804 4.733230 GCGCTGCATAATTTATGGTCAACA 60.733 41.667 16.22 6.15 36.68 3.33
598 2411 4.254492 GTCCCTCATCCTCACTTTTACAC 58.746 47.826 0.00 0.00 0.00 2.90
622 2436 6.258947 ACGGAGGAAGTACTAAATCGTACTAC 59.741 42.308 0.00 2.05 46.88 2.73
630 2444 5.824904 ACTAAATCGTACTACGTGGACAT 57.175 39.130 5.70 0.00 43.14 3.06
676 2543 7.335924 GCTTATATTTTCTCCCATACGGCATAA 59.664 37.037 0.00 0.00 0.00 1.90
745 2612 0.389391 CATCGTATCTTGGCCCGAGT 59.611 55.000 0.00 0.00 32.26 4.18
762 2629 2.417719 GAGTTTGACGATGACCTTGCT 58.582 47.619 0.00 0.00 0.00 3.91
775 2642 1.140589 CTTGCTGTCGATCTCGGCT 59.859 57.895 15.87 0.00 45.41 5.52
917 2784 6.867550 TGATCGTAGAACTGAAGAATCACAT 58.132 36.000 0.00 0.00 43.58 3.21
921 2788 8.689251 TCGTAGAACTGAAGAATCACATTTAG 57.311 34.615 0.00 0.00 0.00 1.85
946 2820 5.452078 TTCATCAGTTTGGTCATGGTTTC 57.548 39.130 0.00 0.00 0.00 2.78
1087 2972 1.729267 AAGGGAAGGGCCACATGTGT 61.729 55.000 23.79 5.30 38.95 3.72
1126 3011 0.106149 GGTTGTCCACGAAGGTCACT 59.894 55.000 0.00 0.00 35.09 3.41
1705 3590 1.958715 CGTGCGGTGGTTGATGACA 60.959 57.895 0.00 0.00 0.00 3.58
1991 4176 6.030228 CAGAACTCAAAACTCAGTCCAAAAC 58.970 40.000 0.00 0.00 0.00 2.43
2007 4203 3.120923 CCAAAACAAAACATGATCGCAGC 60.121 43.478 0.00 0.00 0.00 5.25
2032 4251 0.784778 GACAGTTCTTGCCGACGAAG 59.215 55.000 0.00 0.00 0.00 3.79
2038 4263 3.192844 AGTTCTTGCCGACGAAGAAGATA 59.807 43.478 10.90 0.00 39.53 1.98
2039 4264 3.861276 TCTTGCCGACGAAGAAGATAA 57.139 42.857 0.00 0.00 0.00 1.75
2054 4279 9.757227 CGAAGAAGATAATACCTGAAAGAGAAT 57.243 33.333 0.00 0.00 34.07 2.40
2241 4482 1.527611 CAGGATGCATCATGCCGGT 60.528 57.895 26.48 0.40 44.23 5.28
2242 4483 1.527611 AGGATGCATCATGCCGGTG 60.528 57.895 27.25 0.00 44.23 4.94
2243 4484 1.526686 GGATGCATCATGCCGGTGA 60.527 57.895 27.25 0.00 44.23 4.02
2244 4485 0.892358 GGATGCATCATGCCGGTGAT 60.892 55.000 27.25 1.83 44.23 3.06
2245 4486 0.520404 GATGCATCATGCCGGTGATC 59.480 55.000 21.92 0.00 44.23 2.92
2335 4592 0.108041 GGAGTTTGTTATCGGCCGGA 60.108 55.000 27.83 12.89 0.00 5.14
2336 4593 1.676615 GGAGTTTGTTATCGGCCGGAA 60.677 52.381 27.83 17.38 0.00 4.30
2360 4630 0.793250 GAGCTCAAAAGGCGAGTGAC 59.207 55.000 9.40 0.00 32.83 3.67
2366 4636 2.100879 AAAAGGCGAGTGACGGAGCT 62.101 55.000 0.00 0.00 42.83 4.09
2377 4653 1.681793 TGACGGAGCTAGCCTTGTATC 59.318 52.381 12.13 0.38 0.00 2.24
2420 4701 1.009829 GCCAGTTATCCTGCTGAACG 58.990 55.000 0.00 0.00 40.06 3.95
2450 4731 1.939934 CTCAGAACTCACACGCCAAAA 59.060 47.619 0.00 0.00 0.00 2.44
2452 4733 2.290367 TCAGAACTCACACGCCAAAATG 59.710 45.455 0.00 0.00 0.00 2.32
2467 4763 5.627968 CGCCAAAATGGGGGTAAATAAACAT 60.628 40.000 5.60 0.00 45.66 2.71
2482 5075 1.442769 AACATCCAAGTGCTGTAGCG 58.557 50.000 0.00 0.00 45.83 4.26
2517 5139 1.601166 GGGCAACTGACGGTTACTTT 58.399 50.000 0.00 0.00 36.23 2.66
2522 5144 2.450609 ACTGACGGTTACTTTCGCAT 57.549 45.000 0.00 0.00 0.00 4.73
2523 5145 2.762745 ACTGACGGTTACTTTCGCATT 58.237 42.857 0.00 0.00 0.00 3.56
2565 5187 0.811281 CCGGGTCAGAAAATTCCTGC 59.189 55.000 0.00 0.00 0.00 4.85
2598 5220 0.810031 ATAACGTGGATGAGGTGCGC 60.810 55.000 0.00 0.00 0.00 6.09
2644 5270 5.047164 ACATAAATCTGCCAGCATTGTTCAA 60.047 36.000 0.00 0.00 0.00 2.69
2665 5291 2.833631 AACTTTCTGGTGAGTACCCG 57.166 50.000 0.00 0.00 46.96 5.28
2725 5379 1.005975 CCGAGCATTCATTCGTTCGAC 60.006 52.381 0.00 0.00 35.14 4.20
2798 5452 5.714806 TGTTCACCCATTTTATCCCTTCTTC 59.285 40.000 0.00 0.00 0.00 2.87
2811 5653 5.024803 TCCCTTCTTCTTATATCCCCGAT 57.975 43.478 0.00 0.00 0.00 4.18
2932 7315 0.034616 GATAAGCGCTGGCCAGAGAT 59.965 55.000 37.11 30.37 41.24 2.75
2945 7328 1.413382 CAGAGATGTTATCGCGAGGC 58.587 55.000 16.66 7.69 34.06 4.70
2978 7361 3.863424 TCGAACTGACTCAACAGAACAAC 59.137 43.478 0.00 0.00 40.63 3.32
2979 7362 3.865745 CGAACTGACTCAACAGAACAACT 59.134 43.478 0.00 0.00 40.63 3.16
2980 7363 4.330074 CGAACTGACTCAACAGAACAACTT 59.670 41.667 0.00 0.00 40.63 2.66
2981 7364 5.551760 AACTGACTCAACAGAACAACTTG 57.448 39.130 0.00 0.00 40.63 3.16
2982 7365 4.832248 ACTGACTCAACAGAACAACTTGA 58.168 39.130 0.00 0.00 40.63 3.02
2983 7366 4.631813 ACTGACTCAACAGAACAACTTGAC 59.368 41.667 0.00 0.00 40.63 3.18
2984 7367 4.574892 TGACTCAACAGAACAACTTGACA 58.425 39.130 0.00 0.00 0.00 3.58
2985 7368 5.000591 TGACTCAACAGAACAACTTGACAA 58.999 37.500 0.00 0.00 0.00 3.18
2986 7369 5.122239 TGACTCAACAGAACAACTTGACAAG 59.878 40.000 13.77 13.77 0.00 3.16
2987 7370 5.245531 ACTCAACAGAACAACTTGACAAGA 58.754 37.500 21.95 0.00 0.00 3.02
2988 7371 5.352569 ACTCAACAGAACAACTTGACAAGAG 59.647 40.000 21.95 14.94 0.00 2.85
2989 7372 5.245531 TCAACAGAACAACTTGACAAGAGT 58.754 37.500 21.95 15.54 0.00 3.24
2990 7373 5.122239 TCAACAGAACAACTTGACAAGAGTG 59.878 40.000 21.95 18.91 0.00 3.51
2991 7374 3.941483 ACAGAACAACTTGACAAGAGTGG 59.059 43.478 21.95 13.52 0.00 4.00
2992 7375 2.945668 AGAACAACTTGACAAGAGTGGC 59.054 45.455 21.95 13.73 0.00 5.01
2993 7376 2.418368 ACAACTTGACAAGAGTGGCA 57.582 45.000 21.95 0.00 42.77 4.92
3001 7384 4.760530 TGACAAGAGTGGCAAGCTATAT 57.239 40.909 0.00 0.00 40.96 0.86
3002 7385 4.697514 TGACAAGAGTGGCAAGCTATATC 58.302 43.478 0.00 0.00 40.96 1.63
3003 7386 4.162131 TGACAAGAGTGGCAAGCTATATCA 59.838 41.667 0.00 0.00 40.96 2.15
3004 7387 5.102953 ACAAGAGTGGCAAGCTATATCAA 57.897 39.130 0.00 0.00 0.00 2.57
3005 7388 5.500234 ACAAGAGTGGCAAGCTATATCAAA 58.500 37.500 0.00 0.00 0.00 2.69
3006 7389 5.945784 ACAAGAGTGGCAAGCTATATCAAAA 59.054 36.000 0.00 0.00 0.00 2.44
3007 7390 6.127897 ACAAGAGTGGCAAGCTATATCAAAAC 60.128 38.462 0.00 0.00 0.00 2.43
3008 7391 5.500234 AGAGTGGCAAGCTATATCAAAACA 58.500 37.500 0.00 0.00 0.00 2.83
3009 7392 5.945784 AGAGTGGCAAGCTATATCAAAACAA 59.054 36.000 0.00 0.00 0.00 2.83
3010 7393 6.434028 AGAGTGGCAAGCTATATCAAAACAAA 59.566 34.615 0.00 0.00 0.00 2.83
3011 7394 6.991938 AGTGGCAAGCTATATCAAAACAAAA 58.008 32.000 0.00 0.00 0.00 2.44
3012 7395 7.441017 AGTGGCAAGCTATATCAAAACAAAAA 58.559 30.769 0.00 0.00 0.00 1.94
3013 7396 7.384932 AGTGGCAAGCTATATCAAAACAAAAAC 59.615 33.333 0.00 0.00 0.00 2.43
3014 7397 7.170658 GTGGCAAGCTATATCAAAACAAAAACA 59.829 33.333 0.00 0.00 0.00 2.83
3015 7398 7.712639 TGGCAAGCTATATCAAAACAAAAACAA 59.287 29.630 0.00 0.00 0.00 2.83
3016 7399 8.555361 GGCAAGCTATATCAAAACAAAAACAAA 58.445 29.630 0.00 0.00 0.00 2.83
3017 7400 9.928236 GCAAGCTATATCAAAACAAAAACAAAA 57.072 25.926 0.00 0.00 0.00 2.44
3035 7418 1.601166 AAAAACCGGCAGAGTGTACC 58.399 50.000 0.00 0.00 0.00 3.34
3036 7419 0.250597 AAAACCGGCAGAGTGTACCC 60.251 55.000 0.00 0.00 0.00 3.69
3037 7420 1.125711 AAACCGGCAGAGTGTACCCT 61.126 55.000 0.00 0.00 0.00 4.34
3038 7421 1.125711 AACCGGCAGAGTGTACCCTT 61.126 55.000 0.00 0.00 0.00 3.95
3039 7422 1.125711 ACCGGCAGAGTGTACCCTTT 61.126 55.000 0.00 0.00 0.00 3.11
3040 7423 0.391263 CCGGCAGAGTGTACCCTTTC 60.391 60.000 0.00 0.00 0.00 2.62
3041 7424 0.320374 CGGCAGAGTGTACCCTTTCA 59.680 55.000 0.00 0.00 0.00 2.69
3042 7425 1.270625 CGGCAGAGTGTACCCTTTCAA 60.271 52.381 0.00 0.00 0.00 2.69
3043 7426 2.427506 GGCAGAGTGTACCCTTTCAAG 58.572 52.381 0.00 0.00 0.00 3.02
3044 7427 2.038557 GGCAGAGTGTACCCTTTCAAGA 59.961 50.000 0.00 0.00 0.00 3.02
3045 7428 3.330267 GCAGAGTGTACCCTTTCAAGAG 58.670 50.000 0.00 0.00 0.00 2.85
3046 7429 3.866449 GCAGAGTGTACCCTTTCAAGAGG 60.866 52.174 0.00 0.00 36.52 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 1.611977 CGGATAGCGGTGGATTAGTGA 59.388 52.381 0.00 0.00 0.00 3.41
41 42 1.001048 CGAACGGATAGCGGTGGATTA 60.001 52.381 0.00 0.00 0.00 1.75
67 68 2.044135 GTTGCAGCTAAGTTTGAACGC 58.956 47.619 0.00 0.00 0.00 4.84
109 110 4.890158 TGGAACTGAAGCTGTTCATCTA 57.110 40.909 15.08 0.00 41.96 1.98
141 142 1.473278 CGAGAGAAGAGGTGGTACCAC 59.527 57.143 33.15 33.15 41.95 4.16
142 143 1.835494 CGAGAGAAGAGGTGGTACCA 58.165 55.000 11.60 11.60 41.95 3.25
143 144 0.456628 GCGAGAGAAGAGGTGGTACC 59.543 60.000 4.43 4.43 38.99 3.34
144 145 0.456628 GGCGAGAGAAGAGGTGGTAC 59.543 60.000 0.00 0.00 0.00 3.34
145 146 0.683504 GGGCGAGAGAAGAGGTGGTA 60.684 60.000 0.00 0.00 0.00 3.25
146 147 1.985116 GGGCGAGAGAAGAGGTGGT 60.985 63.158 0.00 0.00 0.00 4.16
147 148 2.896443 GGGCGAGAGAAGAGGTGG 59.104 66.667 0.00 0.00 0.00 4.61
148 149 1.595993 TTCGGGCGAGAGAAGAGGTG 61.596 60.000 0.00 0.00 0.00 4.00
149 150 1.304217 TTCGGGCGAGAGAAGAGGT 60.304 57.895 0.00 0.00 0.00 3.85
150 151 1.032657 TCTTCGGGCGAGAGAAGAGG 61.033 60.000 11.18 0.00 45.33 3.69
151 152 2.483441 TCTTCGGGCGAGAGAAGAG 58.517 57.895 11.18 0.00 45.33 2.85
153 154 0.811915 TCTTCTTCGGGCGAGAGAAG 59.188 55.000 13.11 13.11 43.70 2.85
154 155 1.254026 TTCTTCTTCGGGCGAGAGAA 58.746 50.000 0.00 0.00 0.00 2.87
155 156 1.135139 CATTCTTCTTCGGGCGAGAGA 59.865 52.381 0.00 0.00 0.00 3.10
156 157 1.565305 CATTCTTCTTCGGGCGAGAG 58.435 55.000 0.00 0.00 0.00 3.20
157 158 0.460284 GCATTCTTCTTCGGGCGAGA 60.460 55.000 0.00 0.00 0.00 4.04
158 159 0.740868 TGCATTCTTCTTCGGGCGAG 60.741 55.000 0.00 0.00 0.00 5.03
159 160 0.321210 TTGCATTCTTCTTCGGGCGA 60.321 50.000 0.00 0.00 0.00 5.54
160 161 0.179189 GTTGCATTCTTCTTCGGGCG 60.179 55.000 0.00 0.00 0.00 6.13
161 162 0.171231 GGTTGCATTCTTCTTCGGGC 59.829 55.000 0.00 0.00 0.00 6.13
162 163 0.447801 CGGTTGCATTCTTCTTCGGG 59.552 55.000 0.00 0.00 0.00 5.14
163 164 0.179189 GCGGTTGCATTCTTCTTCGG 60.179 55.000 0.00 0.00 42.15 4.30
164 165 0.519175 CGCGGTTGCATTCTTCTTCG 60.519 55.000 0.00 0.00 42.97 3.79
165 166 0.179189 CCGCGGTTGCATTCTTCTTC 60.179 55.000 19.50 0.00 42.97 2.87
166 167 1.875963 CCGCGGTTGCATTCTTCTT 59.124 52.632 19.50 0.00 42.97 2.52
167 168 2.690778 GCCGCGGTTGCATTCTTCT 61.691 57.895 28.70 0.00 42.97 2.85
168 169 2.202479 GCCGCGGTTGCATTCTTC 60.202 61.111 28.70 0.93 42.97 2.87
169 170 2.342650 ATGCCGCGGTTGCATTCTT 61.343 52.632 28.70 2.94 46.91 2.52
170 171 2.751436 ATGCCGCGGTTGCATTCT 60.751 55.556 28.70 0.36 46.91 2.40
174 175 0.462937 AGTATAATGCCGCGGTTGCA 60.463 50.000 28.70 19.32 42.97 4.08
175 176 0.661020 AAGTATAATGCCGCGGTTGC 59.339 50.000 28.70 13.41 37.91 4.17
176 177 2.715268 CAAAGTATAATGCCGCGGTTG 58.285 47.619 28.70 15.67 0.00 3.77
177 178 1.064952 GCAAAGTATAATGCCGCGGTT 59.935 47.619 28.70 16.89 36.56 4.44
178 179 0.661020 GCAAAGTATAATGCCGCGGT 59.339 50.000 28.70 9.89 36.56 5.68
179 180 0.944386 AGCAAAGTATAATGCCGCGG 59.056 50.000 24.05 24.05 43.57 6.46
180 181 1.397190 CGAGCAAAGTATAATGCCGCG 60.397 52.381 0.00 0.00 43.57 6.46
181 182 1.069906 CCGAGCAAAGTATAATGCCGC 60.070 52.381 3.52 0.00 43.57 6.53
182 183 1.069906 GCCGAGCAAAGTATAATGCCG 60.070 52.381 3.52 6.57 43.57 5.69
183 184 1.946768 TGCCGAGCAAAGTATAATGCC 59.053 47.619 0.00 0.00 43.57 4.40
184 185 2.354510 TGTGCCGAGCAAAGTATAATGC 59.645 45.455 0.00 0.00 41.47 3.56
185 186 4.818534 ATGTGCCGAGCAAAGTATAATG 57.181 40.909 0.00 0.00 41.47 1.90
186 187 7.510549 AAATATGTGCCGAGCAAAGTATAAT 57.489 32.000 0.00 0.00 41.47 1.28
187 188 6.935741 AAATATGTGCCGAGCAAAGTATAA 57.064 33.333 0.00 0.00 41.47 0.98
188 189 6.540551 TCAAAATATGTGCCGAGCAAAGTATA 59.459 34.615 0.00 0.00 41.47 1.47
200 201 7.458677 GCTTTCTTTCATTCAAAATATGTGCC 58.541 34.615 0.00 0.00 0.00 5.01
202 203 8.231304 ACGCTTTCTTTCATTCAAAATATGTG 57.769 30.769 0.00 0.00 0.00 3.21
260 266 6.182627 TGCTATGTGTTGGAGAAAATCTGAT 58.817 36.000 0.00 0.00 0.00 2.90
272 278 2.391616 TCAGAGCTGCTATGTGTTGG 57.608 50.000 22.14 0.00 0.00 3.77
281 287 3.413846 TCAACTTTGATCAGAGCTGCT 57.586 42.857 12.97 0.00 31.01 4.24
300 306 4.057432 GCTCCAGCTATCAGTTCTGAATC 58.943 47.826 6.60 0.12 38.21 2.52
318 324 7.382759 GTCTGTAGCTTAGTTATACAATGCTCC 59.617 40.741 0.00 0.00 0.00 4.70
378 384 4.712476 AGGGCTCTACATAAGAAAGCATG 58.288 43.478 0.00 0.00 32.46 4.06
463 469 4.357947 GCCAGTGACTCGTGCGGA 62.358 66.667 0.00 0.00 0.00 5.54
498 504 5.048991 GGTTTACTCGATGTTTGTTGACCAT 60.049 40.000 0.00 0.00 0.00 3.55
507 1804 5.581085 GCTACTCATGGTTTACTCGATGTTT 59.419 40.000 0.00 0.00 0.00 2.83
622 2436 0.873312 CGGAGCTCATGATGTCCACG 60.873 60.000 17.19 1.45 0.00 4.94
630 2444 2.682856 GCAAAATTACCGGAGCTCATGA 59.317 45.455 17.19 0.00 0.00 3.07
676 2543 3.788766 GTCGCGCACGGCAAAGAT 61.789 61.111 8.75 0.00 45.32 2.40
745 2612 2.143122 GACAGCAAGGTCATCGTCAAA 58.857 47.619 0.00 0.00 37.73 2.69
762 2629 2.336945 TTACCTAGCCGAGATCGACA 57.663 50.000 3.31 0.00 43.02 4.35
775 2642 0.813184 CTGACGCCGACCTTTACCTA 59.187 55.000 0.00 0.00 0.00 3.08
917 2784 7.069331 ACCATGACCAAACTGATGAAAACTAAA 59.931 33.333 0.00 0.00 0.00 1.85
921 2788 5.200368 ACCATGACCAAACTGATGAAAAC 57.800 39.130 0.00 0.00 0.00 2.43
934 2801 3.944650 CCGTTCATATGAAACCATGACCA 59.055 43.478 19.55 0.00 35.58 4.02
985 2870 2.009774 AGTCATCGTGCTATTGCCAAC 58.990 47.619 0.00 0.00 38.71 3.77
994 2879 0.803768 GCATCGTGAGTCATCGTGCT 60.804 55.000 20.77 7.74 34.28 4.40
1087 2972 4.980805 GACACCGGCTCCACGCAA 62.981 66.667 0.00 0.00 41.67 4.85
1210 3095 0.032813 CCACCAAGGGCATCCTCAAT 60.033 55.000 0.00 0.00 44.07 2.57
1991 4176 1.469703 TCAGGCTGCGATCATGTTTTG 59.530 47.619 10.34 0.00 0.00 2.44
2007 4203 1.151668 CGGCAAGAACTGTCTTCAGG 58.848 55.000 0.47 0.00 42.45 3.86
2038 4263 5.648092 CCGGTCAAATTCTCTTTCAGGTATT 59.352 40.000 0.00 0.00 0.00 1.89
2039 4264 5.045869 TCCGGTCAAATTCTCTTTCAGGTAT 60.046 40.000 0.00 0.00 0.00 2.73
2238 4479 1.291184 TGCAAGTTGCTCGATCACCG 61.291 55.000 27.17 0.00 45.31 4.94
2239 4480 0.874390 TTGCAAGTTGCTCGATCACC 59.126 50.000 27.17 0.00 45.31 4.02
2241 4482 1.800586 GTCTTGCAAGTTGCTCGATCA 59.199 47.619 27.17 4.26 45.31 2.92
2242 4483 1.800586 TGTCTTGCAAGTTGCTCGATC 59.199 47.619 27.17 16.45 45.31 3.69
2243 4484 1.882912 TGTCTTGCAAGTTGCTCGAT 58.117 45.000 27.17 0.00 45.31 3.59
2244 4485 1.532437 CATGTCTTGCAAGTTGCTCGA 59.468 47.619 27.17 19.59 45.31 4.04
2245 4486 1.265095 ACATGTCTTGCAAGTTGCTCG 59.735 47.619 27.17 17.77 45.31 5.03
2335 4592 1.507141 CGCCTTTTGAGCTCACCGTT 61.507 55.000 18.03 0.00 0.00 4.44
2336 4593 1.961277 CGCCTTTTGAGCTCACCGT 60.961 57.895 18.03 0.00 0.00 4.83
2360 4630 1.957177 TCTGATACAAGGCTAGCTCCG 59.043 52.381 15.72 5.49 0.00 4.63
2420 4701 4.688413 GTGTGAGTTCTGAGGAATTCTCAC 59.312 45.833 15.96 15.96 46.71 3.51
2450 4731 5.660864 CACTTGGATGTTTATTTACCCCCAT 59.339 40.000 0.00 0.00 0.00 4.00
2452 4733 4.142026 GCACTTGGATGTTTATTTACCCCC 60.142 45.833 0.00 0.00 0.00 5.40
2457 4751 6.183360 CGCTACAGCACTTGGATGTTTATTTA 60.183 38.462 1.61 0.00 45.58 1.40
2467 4763 0.320421 GAACCGCTACAGCACTTGGA 60.320 55.000 1.61 0.00 42.21 3.53
2482 5075 1.152383 GCCCGCAGATCTTACGAACC 61.152 60.000 14.89 1.53 0.00 3.62
2517 5139 5.651530 TGTTTGTTAACCTGAAAAATGCGA 58.348 33.333 2.48 0.00 33.15 5.10
2522 5144 7.489757 CGGATTTCTGTTTGTTAACCTGAAAAA 59.510 33.333 14.56 2.91 38.24 1.94
2523 5145 6.975772 CGGATTTCTGTTTGTTAACCTGAAAA 59.024 34.615 14.56 3.21 38.24 2.29
2565 5187 4.461081 TCCACGTTATCCAGGAAATTTTGG 59.539 41.667 0.00 2.89 35.74 3.28
2598 5220 1.409427 AGTTTTATCCGCCTCGAGGAG 59.591 52.381 35.69 30.98 41.66 3.69
2725 5379 1.328680 CCCTCACGAATTCAATGCTCG 59.671 52.381 6.22 0.00 38.53 5.03
2798 5452 3.838317 TGGGAAGTCATCGGGGATATAAG 59.162 47.826 0.00 0.00 0.00 1.73
2811 5653 0.961019 GCAACTGCATTGGGAAGTCA 59.039 50.000 9.81 0.00 41.59 3.41
2841 7221 3.242316 GGTGAATAAAATGACGTCGAGGC 60.242 47.826 11.62 0.00 0.00 4.70
2886 7269 1.094785 CTGCTTATCCAACCCAACGG 58.905 55.000 0.00 0.00 0.00 4.44
2895 7278 1.526686 CATGGCGCCTGCTTATCCA 60.527 57.895 29.70 3.35 42.25 3.41
2932 7315 0.742990 CTTTGGGCCTCGCGATAACA 60.743 55.000 10.36 3.84 0.00 2.41
2945 7328 2.554032 AGTCAGTTCGATTTGCTTTGGG 59.446 45.455 0.00 0.00 0.00 4.12
2978 7361 1.602311 AGCTTGCCACTCTTGTCAAG 58.398 50.000 6.21 6.21 39.00 3.02
2979 7362 2.928801 TAGCTTGCCACTCTTGTCAA 57.071 45.000 0.00 0.00 0.00 3.18
2980 7363 4.162131 TGATATAGCTTGCCACTCTTGTCA 59.838 41.667 0.00 0.00 0.00 3.58
2981 7364 4.697514 TGATATAGCTTGCCACTCTTGTC 58.302 43.478 0.00 0.00 0.00 3.18
2982 7365 4.760530 TGATATAGCTTGCCACTCTTGT 57.239 40.909 0.00 0.00 0.00 3.16
2983 7366 6.127925 TGTTTTGATATAGCTTGCCACTCTTG 60.128 38.462 0.00 0.00 0.00 3.02
2984 7367 5.945784 TGTTTTGATATAGCTTGCCACTCTT 59.054 36.000 0.00 0.00 0.00 2.85
2985 7368 5.500234 TGTTTTGATATAGCTTGCCACTCT 58.500 37.500 0.00 0.00 0.00 3.24
2986 7369 5.818136 TGTTTTGATATAGCTTGCCACTC 57.182 39.130 0.00 0.00 0.00 3.51
2987 7370 6.588719 TTTGTTTTGATATAGCTTGCCACT 57.411 33.333 0.00 0.00 0.00 4.00
2988 7371 7.170658 TGTTTTTGTTTTGATATAGCTTGCCAC 59.829 33.333 0.00 0.00 0.00 5.01
2989 7372 7.212976 TGTTTTTGTTTTGATATAGCTTGCCA 58.787 30.769 0.00 0.00 0.00 4.92
2990 7373 7.650834 TGTTTTTGTTTTGATATAGCTTGCC 57.349 32.000 0.00 0.00 0.00 4.52
2991 7374 9.928236 TTTTGTTTTTGTTTTGATATAGCTTGC 57.072 25.926 0.00 0.00 0.00 4.01
3016 7399 1.601166 GGTACACTCTGCCGGTTTTT 58.399 50.000 1.90 0.00 0.00 1.94
3017 7400 0.250597 GGGTACACTCTGCCGGTTTT 60.251 55.000 1.90 0.00 0.00 2.43
3018 7401 1.125711 AGGGTACACTCTGCCGGTTT 61.126 55.000 1.90 0.00 0.00 3.27
3019 7402 1.125711 AAGGGTACACTCTGCCGGTT 61.126 55.000 1.90 0.00 0.00 4.44
3020 7403 1.125711 AAAGGGTACACTCTGCCGGT 61.126 55.000 1.90 0.00 0.00 5.28
3021 7404 0.391263 GAAAGGGTACACTCTGCCGG 60.391 60.000 0.00 0.00 0.00 6.13
3022 7405 0.320374 TGAAAGGGTACACTCTGCCG 59.680 55.000 0.00 0.00 0.00 5.69
3023 7406 2.038557 TCTTGAAAGGGTACACTCTGCC 59.961 50.000 0.00 0.00 0.00 4.85
3024 7407 3.330267 CTCTTGAAAGGGTACACTCTGC 58.670 50.000 0.00 0.00 0.00 4.26
3025 7408 3.931578 CCTCTTGAAAGGGTACACTCTG 58.068 50.000 0.00 0.00 32.35 3.35


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

AutoCloner maintained by Alex Coulton.