Multiple sequence alignment - TraesCS7D01G293600

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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 TraesCS7D01G293600 chr7D 100.000 5158 0 0 1 5158 364412403 364407246 0.000000e+00 9526.0
1 TraesCS7D01G293600 chr7A 95.698 4719 154 23 135 4828 392912570 392917264 0.000000e+00 7544.0
2 TraesCS7D01G293600 chr7A 93.023 301 18 2 4829 5126 392917701 392918001 2.210000e-118 436.0
3 TraesCS7D01G293600 chr7A 92.086 139 11 0 2 140 392912473 392912611 4.070000e-46 196.0
4 TraesCS7D01G293600 chr7A 89.474 133 13 1 1 133 485493461 485493592 3.190000e-37 167.0
5 TraesCS7D01G293600 chr7B 97.269 3259 73 8 1579 4827 323849505 323846253 0.000000e+00 5511.0
6 TraesCS7D01G293600 chr7B 95.147 1051 36 6 507 1550 323850823 323849781 0.000000e+00 1644.0
7 TraesCS7D01G293600 chr7B 85.749 407 47 5 57 456 323878621 323878219 2.220000e-113 420.0
8 TraesCS7D01G293600 chr7B 95.984 249 10 0 4878 5126 323837235 323836987 6.220000e-109 405.0
9 TraesCS7D01G293600 chr7B 93.443 61 3 1 4828 4888 323844379 323844320 7.110000e-14 89.8
10 TraesCS7D01G293600 chr7B 97.959 49 1 0 1547 1595 323849700 323849652 9.200000e-13 86.1
11 TraesCS7D01G293600 chr7B 100.000 29 0 0 5127 5155 323836961 323836933 3.000000e-03 54.7
12 TraesCS7D01G293600 chr2A 82.152 381 55 7 141 508 480027591 480027971 1.080000e-81 315.0
13 TraesCS7D01G293600 chr2A 78.701 385 69 8 137 508 728808033 728807649 1.430000e-60 244.0
14 TraesCS7D01G293600 chr2A 78.215 381 70 7 139 506 728838507 728838127 1.120000e-56 231.0
15 TraesCS7D01G293600 chr1D 81.088 386 50 13 138 508 237809044 237808667 2.350000e-73 287.0
16 TraesCS7D01G293600 chr1D 80.155 388 59 14 135 508 305219708 305220091 1.830000e-69 274.0
17 TraesCS7D01G293600 chr1D 88.571 140 16 0 1 140 468039551 468039412 2.470000e-38 171.0
18 TraesCS7D01G293600 chr1D 76.995 213 27 15 155 355 37415819 37415617 9.140000e-18 102.0
19 TraesCS7D01G293600 chr5D 78.533 368 59 9 2 363 513913644 513913997 1.870000e-54 224.0
20 TraesCS7D01G293600 chr4D 81.579 228 36 3 135 356 94872839 94873066 3.170000e-42 183.0
21 TraesCS7D01G293600 chr1B 91.111 135 12 0 2 136 412252707 412252573 3.170000e-42 183.0
22 TraesCS7D01G293600 chr2D 88.571 140 16 0 1 140 641254378 641254239 2.470000e-38 171.0
23 TraesCS7D01G293600 chr5A 88.889 135 15 0 2 136 690554853 690554987 3.190000e-37 167.0
24 TraesCS7D01G293600 chr1A 88.406 138 14 2 1 137 521879666 521879802 1.150000e-36 165.0


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 TraesCS7D01G293600 chr7D 364407246 364412403 5157 True 9526.000000 9526 100.000000 1 5158 1 chr7D.!!$R1 5157
1 TraesCS7D01G293600 chr7A 392912473 392918001 5528 False 2725.333333 7544 93.602333 2 5126 3 chr7A.!!$F2 5124
2 TraesCS7D01G293600 chr7B 323844320 323850823 6503 True 1832.725000 5511 95.954500 507 4888 4 chr7B.!!$R3 4381

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
132 133 0.034186 TGGAGGTAAGCTGGCCATTG 60.034 55.000 5.51 0.0 0.00 2.82 F
605 629 0.600557 CTCTCCATTCCCGATCCTCG 59.399 60.000 0.00 0.0 40.07 4.63 F
1368 1400 0.451783 GCGCAAGTGGGGTTATTCAG 59.548 55.000 0.30 0.0 41.68 3.02 F
1500 1532 2.239402 TGCTGGTAATGATGCCTTCTGA 59.761 45.455 0.00 0.0 31.58 3.27 F
1845 2126 3.134081 GGGAGGTTCTAAATGGTGATCGA 59.866 47.826 0.00 0.0 0.00 3.59 F
1975 2256 3.199946 TGCCAAGGATTACTACTTCCAGG 59.800 47.826 0.00 0.0 34.27 4.45 F
3796 4085 3.785486 TCTCTTGGACTTGATGCATACG 58.215 45.455 0.00 0.0 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1220 1246 0.107654 AAGCCCTAACTCGTGCATCC 60.108 55.000 0.00 0.0 0.00 3.51 R
1766 2047 0.613853 AGGCCATGCAGCAGTCAATT 60.614 50.000 5.01 0.0 0.00 2.32 R
3116 3398 1.549203 GGCAAGGAGCTTGGAATTCA 58.451 50.000 7.93 0.0 41.31 2.57 R
3168 3450 2.297895 TGCTTCGGTACCAGGGCAT 61.298 57.895 13.54 0.0 0.00 4.40 R
3663 3952 8.429493 AGTGTTTAGTTTAAGTTGTGGTACTC 57.571 34.615 0.00 0.0 0.00 2.59 R
3915 4205 7.874016 AGATCTGCAAATTGAAGCAAAATAACA 59.126 29.630 0.00 0.0 40.73 2.41 R
4824 5116 0.322816 GAAGTGCCTTGAGCCATGGA 60.323 55.000 18.40 0.0 42.71 3.41 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
62 63 5.984725 TGTGAGGTGGTTATTGTATCGATT 58.015 37.500 1.71 0.00 0.00 3.34
68 69 5.332808 GGTGGTTATTGTATCGATTGTACGC 60.333 44.000 1.71 0.00 0.00 4.42
72 73 6.400727 GGTTATTGTATCGATTGTACGCCATC 60.401 42.308 1.71 0.00 0.00 3.51
75 76 1.865865 ATCGATTGTACGCCATCCAC 58.134 50.000 0.00 0.00 0.00 4.02
81 82 1.153429 GTACGCCATCCACACCTCC 60.153 63.158 0.00 0.00 0.00 4.30
87 88 1.079127 CATCCACACCTCCGTCACC 60.079 63.158 0.00 0.00 0.00 4.02
111 112 2.025589 TTTGTGGCGCGGTTGATATA 57.974 45.000 8.83 0.00 0.00 0.86
119 120 1.340248 CGCGGTTGATATACTGGAGGT 59.660 52.381 0.00 0.00 0.00 3.85
120 121 2.555325 CGCGGTTGATATACTGGAGGTA 59.445 50.000 0.00 0.00 34.62 3.08
121 122 3.005050 CGCGGTTGATATACTGGAGGTAA 59.995 47.826 0.00 0.00 33.74 2.85
122 123 4.557205 GCGGTTGATATACTGGAGGTAAG 58.443 47.826 0.00 0.00 33.74 2.34
123 124 4.557205 CGGTTGATATACTGGAGGTAAGC 58.443 47.826 0.00 0.00 33.74 3.09
124 125 4.281182 CGGTTGATATACTGGAGGTAAGCT 59.719 45.833 0.00 0.00 33.74 3.74
125 126 5.542779 GGTTGATATACTGGAGGTAAGCTG 58.457 45.833 0.00 0.00 33.74 4.24
126 127 5.511545 GGTTGATATACTGGAGGTAAGCTGG 60.512 48.000 0.00 0.00 33.74 4.85
127 128 3.578716 TGATATACTGGAGGTAAGCTGGC 59.421 47.826 0.00 0.00 33.74 4.85
128 129 1.132500 ATACTGGAGGTAAGCTGGCC 58.868 55.000 0.00 0.00 33.74 5.36
129 130 0.252513 TACTGGAGGTAAGCTGGCCA 60.253 55.000 4.71 4.71 0.00 5.36
130 131 0.916358 ACTGGAGGTAAGCTGGCCAT 60.916 55.000 5.51 0.00 0.00 4.40
131 132 0.257039 CTGGAGGTAAGCTGGCCATT 59.743 55.000 5.51 0.00 0.00 3.16
132 133 0.034186 TGGAGGTAAGCTGGCCATTG 60.034 55.000 5.51 0.00 0.00 2.82
133 134 1.387295 GGAGGTAAGCTGGCCATTGC 61.387 60.000 5.51 7.56 0.00 3.56
134 135 1.718757 GAGGTAAGCTGGCCATTGCG 61.719 60.000 5.51 0.00 38.85 4.85
135 136 2.102946 GTAAGCTGGCCATTGCGC 59.897 61.111 5.51 6.16 38.85 6.09
136 137 3.507924 TAAGCTGGCCATTGCGCG 61.508 61.111 5.51 0.00 38.85 6.86
144 145 4.178214 CCATTGCGCGCGGTTGAT 62.178 61.111 33.06 11.97 0.00 2.57
145 146 2.706432 CATTGCGCGCGGTTGATA 59.294 55.556 33.06 3.19 0.00 2.15
146 147 1.279539 CATTGCGCGCGGTTGATAT 59.720 52.632 33.06 7.73 0.00 1.63
147 148 0.993251 CATTGCGCGCGGTTGATATG 60.993 55.000 33.06 15.55 0.00 1.78
148 149 2.715864 ATTGCGCGCGGTTGATATGC 62.716 55.000 33.06 11.78 0.00 3.14
149 150 4.666532 GCGCGCGGTTGATATGCC 62.667 66.667 33.06 6.44 0.00 4.40
187 191 4.498520 ACGCGGCAGAGGACATCG 62.499 66.667 12.47 0.00 0.00 3.84
197 201 3.746492 GCAGAGGACATCGTAAGTTTTGT 59.254 43.478 0.00 0.00 39.48 2.83
226 230 9.734620 TTTCTTACTCAACTTGTTGATTGATTG 57.265 29.630 15.35 6.63 34.43 2.67
227 231 8.675705 TCTTACTCAACTTGTTGATTGATTGA 57.324 30.769 15.35 7.83 34.43 2.57
230 234 9.681692 TTACTCAACTTGTTGATTGATTGATTG 57.318 29.630 15.35 4.20 34.43 2.67
234 238 9.198837 TCAACTTGTTGATTGATTGATTGATTG 57.801 29.630 11.62 0.00 29.89 2.67
240 244 9.581099 TGTTGATTGATTGATTGATTGATTCAG 57.419 29.630 0.00 0.00 35.27 3.02
242 246 9.581099 TTGATTGATTGATTGATTGATTCAGTG 57.419 29.630 0.00 0.00 35.27 3.66
243 247 8.962679 TGATTGATTGATTGATTGATTCAGTGA 58.037 29.630 0.00 0.00 35.27 3.41
259 263 4.248058 TCAGTGATGCTCTACACATTGTG 58.752 43.478 15.18 15.18 39.18 3.33
289 293 1.683790 GCGCTGTCGTGATGTACCAC 61.684 60.000 0.00 0.00 38.14 4.16
305 309 1.103398 CCACGGGATGAAGGAATGGC 61.103 60.000 0.00 0.00 0.00 4.40
340 344 5.437289 TGCACTGTTGGATGAAGTTAAAG 57.563 39.130 0.00 0.00 0.00 1.85
350 354 2.361789 TGAAGTTAAAGGGCGGTATGC 58.638 47.619 0.00 0.00 45.38 3.14
411 421 7.125792 ACTATTACTGTACTATTTGCAGGCT 57.874 36.000 0.00 0.00 42.06 4.58
413 423 8.871125 ACTATTACTGTACTATTTGCAGGCTAT 58.129 33.333 0.00 0.00 42.06 2.97
428 438 4.763793 GCAGGCTATATGGATGATTTGTGT 59.236 41.667 0.00 0.00 0.00 3.72
429 439 5.106396 GCAGGCTATATGGATGATTTGTGTC 60.106 44.000 0.00 0.00 0.00 3.67
435 445 9.754382 GCTATATGGATGATTTGTGTCATTTTT 57.246 29.630 0.00 0.00 38.88 1.94
467 477 6.611381 ACTATGATGAAATTCACCGTGTTTG 58.389 36.000 0.00 0.00 0.00 2.93
469 479 2.112475 TGAAATTCACCGTGTTTGCG 57.888 45.000 0.00 0.00 0.00 4.85
482 492 2.097925 GTGTTTGCGCGAATTTTGTCTG 60.098 45.455 14.34 0.00 0.00 3.51
494 504 7.280769 GCGAATTTTGTCTGGTTAATTGAAAC 58.719 34.615 0.00 0.00 0.00 2.78
504 514 3.006003 GGTTAATTGAAACCCGGCTTCAA 59.994 43.478 24.04 24.04 44.55 2.69
507 517 2.810439 TTGAAACCCGGCTTCAAATG 57.190 45.000 21.26 0.00 39.28 2.32
508 518 1.988293 TGAAACCCGGCTTCAAATGA 58.012 45.000 13.21 0.00 29.93 2.57
510 520 2.035321 TGAAACCCGGCTTCAAATGAAC 59.965 45.455 13.21 0.00 29.93 3.18
511 521 1.995376 AACCCGGCTTCAAATGAACT 58.005 45.000 0.00 0.00 0.00 3.01
512 522 1.995376 ACCCGGCTTCAAATGAACTT 58.005 45.000 0.00 0.00 0.00 2.66
513 523 2.316108 ACCCGGCTTCAAATGAACTTT 58.684 42.857 0.00 0.00 0.00 2.66
514 524 2.698274 ACCCGGCTTCAAATGAACTTTT 59.302 40.909 0.00 0.00 0.00 2.27
557 581 3.588057 AAATTTGCGCCCTTGCCCG 62.588 57.895 4.18 0.00 0.00 6.13
605 629 0.600557 CTCTCCATTCCCGATCCTCG 59.399 60.000 0.00 0.00 40.07 4.63
638 663 0.971386 TACCTCCCTCACAAACGACC 59.029 55.000 0.00 0.00 0.00 4.79
827 853 2.851104 GTCGCCGTTTCCGTTCTG 59.149 61.111 0.00 0.00 0.00 3.02
836 862 1.464997 GTTTCCGTTCTGCATCACCTC 59.535 52.381 0.00 0.00 0.00 3.85
874 900 4.018609 CGCGATCTCGGAGCATTT 57.981 55.556 0.00 0.00 40.23 2.32
899 925 3.271729 TCTGAGGTACTACGAGCTTCTG 58.728 50.000 0.00 0.00 41.55 3.02
947 973 4.383444 GGCGTACTAACCCTCCACTAATTT 60.383 45.833 0.00 0.00 0.00 1.82
1220 1246 2.993899 GTCCCGTTGTCTGTCTACAATG 59.006 50.000 0.00 0.00 43.15 2.82
1253 1279 0.815734 GGGCTTCGTACTGCTGTCTA 59.184 55.000 0.00 0.00 0.00 2.59
1368 1400 0.451783 GCGCAAGTGGGGTTATTCAG 59.548 55.000 0.30 0.00 41.68 3.02
1400 1432 4.023021 GGGAGGCAAGAGTAGTTAGTATCG 60.023 50.000 0.00 0.00 0.00 2.92
1499 1531 2.617308 CTGCTGGTAATGATGCCTTCTG 59.383 50.000 0.00 0.00 31.58 3.02
1500 1532 2.239402 TGCTGGTAATGATGCCTTCTGA 59.761 45.455 0.00 0.00 31.58 3.27
1517 1551 6.599638 GCCTTCTGAACTATGGTAATTTGACT 59.400 38.462 0.00 0.00 0.00 3.41
1537 1571 3.316308 ACTGTTCAAGCATCACTTCAACC 59.684 43.478 0.00 0.00 38.50 3.77
1708 1989 5.075493 AGAGATGTCACATGCCTTTTCTTT 58.925 37.500 0.00 0.00 0.00 2.52
1766 2047 4.219115 TGCCCAAGTCAATTTTCCTTGTA 58.781 39.130 0.00 0.00 35.02 2.41
1845 2126 3.134081 GGGAGGTTCTAAATGGTGATCGA 59.866 47.826 0.00 0.00 0.00 3.59
1975 2256 3.199946 TGCCAAGGATTACTACTTCCAGG 59.800 47.826 0.00 0.00 34.27 4.45
2405 2686 9.880254 TCTTAATCATTTCATTCCATTCCCATA 57.120 29.630 0.00 0.00 0.00 2.74
2433 2714 9.774742 CATGGAAGCTTTACTAAATACAGTTTC 57.225 33.333 0.00 0.00 32.73 2.78
3116 3398 7.665974 GGTATAGCTGGGAAAAATAGCAATACT 59.334 37.037 0.00 0.00 39.84 2.12
3458 3740 4.807304 TCCTCGTCTGTTACTGTTTTTGTC 59.193 41.667 0.00 0.00 0.00 3.18
3663 3952 7.558161 TGGAAATGCTTCAAGTCATACATAG 57.442 36.000 0.00 0.00 32.75 2.23
3690 3979 9.889128 AGTACCACAACTTAAACTAAACACTTA 57.111 29.630 0.00 0.00 0.00 2.24
3796 4085 3.785486 TCTCTTGGACTTGATGCATACG 58.215 45.455 0.00 0.00 0.00 3.06
3817 4106 4.054671 CGTATTGGGCATGTTGTGTTTTT 58.945 39.130 0.00 0.00 0.00 1.94
3895 4185 5.984926 GTGCAATTGTCAATATACCATTGGG 59.015 40.000 7.78 0.00 34.62 4.12
3915 4205 5.494390 GGGACGTGGTAATATCCCTAAAT 57.506 43.478 0.00 0.00 46.43 1.40
4061 4351 1.557099 TCTTCGGCTACATGACCTGT 58.443 50.000 0.00 0.00 42.13 4.00
4192 4482 3.200605 TGGTGACATCAGACATGGCTATT 59.799 43.478 0.00 0.00 33.40 1.73
4193 4483 4.408596 TGGTGACATCAGACATGGCTATTA 59.591 41.667 0.00 0.00 33.40 0.98
4194 4484 4.752101 GGTGACATCAGACATGGCTATTAC 59.248 45.833 0.00 0.00 0.00 1.89
4195 4485 4.752101 GTGACATCAGACATGGCTATTACC 59.248 45.833 0.00 0.00 0.00 2.85
4196 4486 4.202357 TGACATCAGACATGGCTATTACCC 60.202 45.833 0.00 0.00 0.00 3.69
4197 4487 3.716353 ACATCAGACATGGCTATTACCCA 59.284 43.478 0.00 0.00 36.66 4.51
4278 4568 3.554934 TGCATGTCCTCAATATGAACCC 58.445 45.455 0.00 0.00 0.00 4.11
4350 4640 5.330455 TGTGTAGAACAGATTAGAGCCAG 57.670 43.478 0.00 0.00 33.78 4.85
4358 4648 3.070734 ACAGATTAGAGCCAGCACTATGG 59.929 47.826 0.00 0.00 43.72 2.74
4400 4690 8.268850 ACTGTGTTATTTAGTCCAATGTGATC 57.731 34.615 0.00 0.00 0.00 2.92
4471 4761 1.347707 TGCTTACCTGGTGGAGAACAG 59.652 52.381 10.23 0.00 37.04 3.16
4484 4774 4.636206 GTGGAGAACAGAGTTTGTGAAAGT 59.364 41.667 0.00 0.00 40.74 2.66
4565 4855 6.484288 AGTCATTGTCACATCCCAGATTTTA 58.516 36.000 0.00 0.00 0.00 1.52
4580 4870 9.527157 TCCCAGATTTTATCAAAACTGAATGTA 57.473 29.630 10.31 0.00 34.43 2.29
4635 4926 9.559958 CTAGAAATACTTATGTTTGTTTGCCTG 57.440 33.333 0.00 0.00 0.00 4.85
4819 5111 1.691434 GGAATCAAACCCCACAAAGCA 59.309 47.619 0.00 0.00 0.00 3.91
4824 5116 0.325203 AAACCCCACAAAGCACCACT 60.325 50.000 0.00 0.00 0.00 4.00
4895 7063 6.500049 ACAATGGTCTTAAAATCCAATTCCCA 59.500 34.615 0.00 0.00 34.80 4.37
4896 7064 6.796785 ATGGTCTTAAAATCCAATTCCCAG 57.203 37.500 0.00 0.00 34.80 4.45
4901 7069 7.614192 GGTCTTAAAATCCAATTCCCAGAGTTA 59.386 37.037 0.00 0.00 0.00 2.24
4926 7094 5.720202 TCTCTTTAGCTGTTAATTGCTCGA 58.280 37.500 8.17 0.00 40.35 4.04
4928 7096 6.818644 TCTCTTTAGCTGTTAATTGCTCGATT 59.181 34.615 8.17 0.00 40.35 3.34
4961 7129 9.613957 GAATAGGTTTTTGACTCTAAAAGCTTC 57.386 33.333 25.14 17.69 45.71 3.86
4970 7138 5.163602 TGACTCTAAAAGCTTCGAGGATCTC 60.164 44.000 18.70 10.94 30.42 2.75
4978 7146 3.380004 AGCTTCGAGGATCTCTTACACAG 59.620 47.826 0.00 0.00 0.00 3.66
4987 7155 1.275291 TCTCTTACACAGCCCCTTTCG 59.725 52.381 0.00 0.00 0.00 3.46
5017 7185 5.795766 GCTTTGGCTCAGTTTTAACAAAAC 58.204 37.500 6.43 6.43 41.91 2.43
5039 7207 5.486526 ACCAGATGATCTTGACTCAAACTC 58.513 41.667 0.01 0.00 0.00 3.01
5082 7250 9.474920 TGACAAATTGAACTATTGTTGGAATTC 57.525 29.630 0.00 0.00 37.41 2.17
5126 7294 6.206829 GCCAAACTCTACAAGGTTTTGATACT 59.793 38.462 0.00 0.00 37.73 2.12
5127 7295 7.389607 GCCAAACTCTACAAGGTTTTGATACTA 59.610 37.037 0.00 0.00 37.73 1.82
5128 7296 9.449719 CCAAACTCTACAAGGTTTTGATACTAT 57.550 33.333 0.00 0.00 37.73 2.12
5132 7300 9.877178 ACTCTACAAGGTTTTGATACTATGAAG 57.123 33.333 0.00 0.00 37.73 3.02
5138 7306 9.793252 CAAGGTTTTGATACTATGAAGATTTGG 57.207 33.333 0.00 0.00 36.36 3.28
5139 7307 9.753674 AAGGTTTTGATACTATGAAGATTTGGA 57.246 29.630 0.00 0.00 0.00 3.53
5140 7308 9.753674 AGGTTTTGATACTATGAAGATTTGGAA 57.246 29.630 0.00 0.00 0.00 3.53
5146 7314 9.060347 TGATACTATGAAGATTTGGAAATCAGC 57.940 33.333 13.30 6.21 45.59 4.26
5147 7315 8.985315 ATACTATGAAGATTTGGAAATCAGCA 57.015 30.769 13.30 10.63 45.59 4.41
5148 7316 7.330900 ACTATGAAGATTTGGAAATCAGCAG 57.669 36.000 13.30 6.38 45.59 4.24
5149 7317 6.888632 ACTATGAAGATTTGGAAATCAGCAGT 59.111 34.615 13.30 6.85 45.59 4.40
5150 7318 8.049117 ACTATGAAGATTTGGAAATCAGCAGTA 58.951 33.333 13.30 5.95 45.59 2.74
5151 7319 6.500684 TGAAGATTTGGAAATCAGCAGTAC 57.499 37.500 13.30 0.00 45.59 2.73
5152 7320 6.240894 TGAAGATTTGGAAATCAGCAGTACT 58.759 36.000 13.30 0.00 45.59 2.73
5153 7321 6.372659 TGAAGATTTGGAAATCAGCAGTACTC 59.627 38.462 13.30 0.00 45.59 2.59
5154 7322 5.189180 AGATTTGGAAATCAGCAGTACTCC 58.811 41.667 13.30 0.00 45.59 3.85
5155 7323 3.350219 TTGGAAATCAGCAGTACTCCC 57.650 47.619 0.00 0.00 0.00 4.30
5156 7324 2.265367 TGGAAATCAGCAGTACTCCCA 58.735 47.619 0.00 0.00 0.00 4.37
5157 7325 2.642311 TGGAAATCAGCAGTACTCCCAA 59.358 45.455 0.00 0.00 0.00 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.039798 GCATGTCATAGGGCGCAATG 60.040 55.000 10.83 10.06 0.00 2.82
62 63 1.594833 GAGGTGTGGATGGCGTACA 59.405 57.895 0.00 0.00 0.00 2.90
68 69 1.079127 GTGACGGAGGTGTGGATGG 60.079 63.158 0.00 0.00 0.00 3.51
72 73 1.301716 CTTGGTGACGGAGGTGTGG 60.302 63.158 0.00 0.00 0.00 4.17
75 76 1.333619 CAAAACTTGGTGACGGAGGTG 59.666 52.381 0.00 0.00 0.00 4.00
81 82 0.591236 CGCCACAAAACTTGGTGACG 60.591 55.000 0.00 0.00 45.99 4.35
87 88 1.226831 AACCGCGCCACAAAACTTG 60.227 52.632 0.00 0.00 0.00 3.16
111 112 0.916358 ATGGCCAGCTTACCTCCAGT 60.916 55.000 13.05 0.00 0.00 4.00
119 120 3.507924 CGCGCAATGGCCAGCTTA 61.508 61.111 13.05 0.00 36.38 3.09
127 128 2.116736 ATATCAACCGCGCGCAATGG 62.117 55.000 32.61 25.83 0.00 3.16
128 129 0.993251 CATATCAACCGCGCGCAATG 60.993 55.000 32.61 24.56 0.00 2.82
129 130 1.279539 CATATCAACCGCGCGCAAT 59.720 52.632 32.61 15.86 0.00 3.56
130 131 2.706432 CATATCAACCGCGCGCAA 59.294 55.556 32.61 10.78 0.00 4.85
131 132 3.935872 GCATATCAACCGCGCGCA 61.936 61.111 32.61 11.88 0.00 6.09
132 133 4.666532 GGCATATCAACCGCGCGC 62.667 66.667 27.36 23.91 0.00 6.86
133 134 4.354212 CGGCATATCAACCGCGCG 62.354 66.667 25.67 25.67 43.44 6.86
147 148 4.056125 GGCCACTTTGCTTCCGGC 62.056 66.667 0.00 0.00 42.21 6.13
148 149 1.535204 AATGGCCACTTTGCTTCCGG 61.535 55.000 8.16 0.00 0.00 5.14
149 150 0.388907 CAATGGCCACTTTGCTTCCG 60.389 55.000 8.16 0.00 0.00 4.30
150 151 3.520187 CAATGGCCACTTTGCTTCC 57.480 52.632 8.16 0.00 0.00 3.46
170 171 4.498520 CGATGTCCTCTGCCGCGT 62.499 66.667 4.92 0.00 0.00 6.01
211 215 9.938280 AATCAATCAATCAATCAATCAACAAGT 57.062 25.926 0.00 0.00 0.00 3.16
220 224 7.704899 GCATCACTGAATCAATCAATCAATCAA 59.295 33.333 0.00 0.00 37.67 2.57
221 225 7.068226 AGCATCACTGAATCAATCAATCAATCA 59.932 33.333 0.00 0.00 37.67 2.57
226 230 6.621316 AGAGCATCACTGAATCAATCAATC 57.379 37.500 0.00 0.00 35.67 2.67
227 231 7.012138 GTGTAGAGCATCACTGAATCAATCAAT 59.988 37.037 0.00 0.00 35.67 2.57
230 234 5.814188 TGTGTAGAGCATCACTGAATCAATC 59.186 40.000 0.00 0.00 37.82 2.67
234 238 5.583854 ACAATGTGTAGAGCATCACTGAATC 59.416 40.000 0.00 0.00 37.82 2.52
259 263 3.000080 GACAGCGCGTGTGCACTAC 62.000 63.158 19.41 13.21 40.56 2.73
269 273 2.505498 GGTACATCACGACAGCGCG 61.505 63.158 0.00 0.00 42.48 6.86
280 284 1.760613 TCCTTCATCCCGTGGTACATC 59.239 52.381 0.00 0.00 44.52 3.06
289 293 0.178981 ATGGCCATTCCTTCATCCCG 60.179 55.000 14.09 0.00 35.26 5.14
335 339 0.745128 CCACGCATACCGCCCTTTAA 60.745 55.000 0.00 0.00 41.76 1.52
337 341 2.437716 CCACGCATACCGCCCTTT 60.438 61.111 0.00 0.00 41.76 3.11
350 354 2.885644 CGAATCTGTCGCCCCACG 60.886 66.667 0.00 0.00 44.14 4.94
385 389 7.495934 AGCCTGCAAATAGTACAGTAATAGTTG 59.504 37.037 19.09 19.09 37.36 3.16
394 398 6.701340 TCCATATAGCCTGCAAATAGTACAG 58.299 40.000 0.00 0.00 0.00 2.74
406 416 5.999600 TGACACAAATCATCCATATAGCCTG 59.000 40.000 0.00 0.00 0.00 4.85
439 449 6.429692 ACACGGTGAATTTCATCATAGTTTGA 59.570 34.615 16.29 0.00 39.12 2.69
441 451 6.817765 ACACGGTGAATTTCATCATAGTTT 57.182 33.333 16.29 0.00 0.00 2.66
459 469 0.158511 CAAAATTCGCGCAAACACGG 59.841 50.000 8.75 0.00 0.00 4.94
467 477 2.604969 TAACCAGACAAAATTCGCGC 57.395 45.000 0.00 0.00 0.00 6.86
469 479 7.280769 GTTTCAATTAACCAGACAAAATTCGC 58.719 34.615 0.00 0.00 0.00 4.70
482 492 2.559231 TGAAGCCGGGTTTCAATTAACC 59.441 45.455 21.96 4.63 45.56 2.85
494 504 3.385193 AAAAGTTCATTTGAAGCCGGG 57.615 42.857 2.18 0.00 34.27 5.73
557 581 4.415881 ACCCATTTTCTTTCCCAAACAC 57.584 40.909 0.00 0.00 0.00 3.32
583 607 1.666234 GATCGGGAATGGAGAGCGC 60.666 63.158 0.00 0.00 0.00 5.92
605 629 3.074094 AGGGAGGTAGGTTTTCTTTCACC 59.926 47.826 0.00 0.00 0.00 4.02
638 663 3.270877 CGGTATGGTGGAGAGGAAAAAG 58.729 50.000 0.00 0.00 0.00 2.27
827 853 2.512515 GCAGGGACGAGGTGATGC 60.513 66.667 0.00 0.00 0.00 3.91
836 862 2.041115 TCGAGAGACAGCAGGGACG 61.041 63.158 0.00 0.00 33.31 4.79
874 900 3.418995 AGCTCGTAGTACCTCAGAAACA 58.581 45.455 0.00 0.00 0.00 2.83
1220 1246 0.107654 AAGCCCTAACTCGTGCATCC 60.108 55.000 0.00 0.00 0.00 3.51
1253 1279 7.739825 TCTCATTTAGCCTTAGTTAGCATCAT 58.260 34.615 0.00 0.00 0.00 2.45
1368 1400 1.691434 CTCTTGCCTCCCTCCTATCAC 59.309 57.143 0.00 0.00 0.00 3.06
1400 1432 7.698970 TGAAGTGAAATTCGAGTTACAAAAACC 59.301 33.333 0.00 0.00 31.52 3.27
1460 1492 6.950619 ACCAGCAGAGATTTCTTTTCCTTATT 59.049 34.615 0.00 0.00 0.00 1.40
1499 1531 7.750903 GCTTGAACAGTCAAATTACCATAGTTC 59.249 37.037 0.00 0.00 43.18 3.01
1500 1532 7.230510 TGCTTGAACAGTCAAATTACCATAGTT 59.769 33.333 0.00 0.00 43.18 2.24
1537 1571 9.210426 CAAAGCTGCTATTTAGTAACATAAACG 57.790 33.333 0.90 0.00 0.00 3.60
1766 2047 0.613853 AGGCCATGCAGCAGTCAATT 60.614 50.000 5.01 0.00 0.00 2.32
1975 2256 7.094634 CCATAAAGGCAGGTCATCATAATACAC 60.095 40.741 0.00 0.00 0.00 2.90
2405 2686 7.112779 ACTGTATTTAGTAAAGCTTCCATGCT 58.887 34.615 0.00 0.00 46.40 3.79
2461 2743 1.550524 TCAAGGGACTCGTCTTCATGG 59.449 52.381 0.00 0.00 38.49 3.66
2897 3179 4.724399 TCACCTGAAACATTAAGGCAGAA 58.276 39.130 0.00 0.00 34.18 3.02
3116 3398 1.549203 GGCAAGGAGCTTGGAATTCA 58.451 50.000 7.93 0.00 41.31 2.57
3168 3450 2.297895 TGCTTCGGTACCAGGGCAT 61.298 57.895 13.54 0.00 0.00 4.40
3637 3926 9.276590 CTATGTATGACTTGAAGCATTTCCATA 57.723 33.333 7.26 9.70 32.09 2.74
3663 3952 8.429493 AGTGTTTAGTTTAAGTTGTGGTACTC 57.571 34.615 0.00 0.00 0.00 2.59
3817 4106 9.693739 TCCCAAACTCTTATTGATAAGCATAAA 57.306 29.630 5.98 0.00 39.60 1.40
3895 4185 9.498176 AATAACATTTAGGGATATTACCACGTC 57.502 33.333 0.00 0.00 0.00 4.34
3915 4205 7.874016 AGATCTGCAAATTGAAGCAAAATAACA 59.126 29.630 0.00 0.00 40.73 2.41
4192 4482 2.623418 TCTCTTGAGCTTCCTGGGTA 57.377 50.000 0.00 0.00 0.00 3.69
4193 4483 1.627834 CTTCTCTTGAGCTTCCTGGGT 59.372 52.381 0.00 0.00 0.00 4.51
4194 4484 1.678425 GCTTCTCTTGAGCTTCCTGGG 60.678 57.143 0.00 0.00 0.00 4.45
4195 4485 1.002888 TGCTTCTCTTGAGCTTCCTGG 59.997 52.381 0.00 0.00 0.00 4.45
4196 4486 2.469274 TGCTTCTCTTGAGCTTCCTG 57.531 50.000 0.00 0.00 0.00 3.86
4197 4487 3.145286 GTTTGCTTCTCTTGAGCTTCCT 58.855 45.455 0.00 0.00 0.00 3.36
4278 4568 7.015226 TGCACGATAATGTAATTTGAGAAGG 57.985 36.000 0.00 0.00 37.87 3.46
4400 4690 4.641989 CAGGATCCAGGAACAAACTAATGG 59.358 45.833 15.82 0.00 0.00 3.16
4536 4826 4.728772 TGGGATGTGACAATGACTCTTTT 58.271 39.130 0.00 0.00 0.00 2.27
4610 4901 9.073475 ACAGGCAAACAAACATAAGTATTTCTA 57.927 29.630 0.00 0.00 0.00 2.10
4663 4954 3.973305 TGGGCCACACTATCAATCTATCA 59.027 43.478 0.00 0.00 0.00 2.15
4664 4955 4.623932 TGGGCCACACTATCAATCTATC 57.376 45.455 0.00 0.00 0.00 2.08
4676 4967 2.871633 CAAAAGTTCAATTGGGCCACAC 59.128 45.455 5.23 0.00 0.00 3.82
4731 5023 9.981114 CTCCACATTTGGTTTTATAATTATCCC 57.019 33.333 0.00 0.00 44.35 3.85
4824 5116 0.322816 GAAGTGCCTTGAGCCATGGA 60.323 55.000 18.40 0.00 42.71 3.41
4896 7064 9.709600 GCAATTAACAGCTAAAGAGAATAACTC 57.290 33.333 0.00 0.00 45.22 3.01
4901 7069 6.818644 TCGAGCAATTAACAGCTAAAGAGAAT 59.181 34.615 3.67 0.00 42.04 2.40
4910 7078 6.017605 CCATAGAAATCGAGCAATTAACAGCT 60.018 38.462 3.33 3.33 45.25 4.24
4911 7079 6.017934 TCCATAGAAATCGAGCAATTAACAGC 60.018 38.462 0.00 0.00 0.00 4.40
4912 7080 7.482654 TCCATAGAAATCGAGCAATTAACAG 57.517 36.000 0.00 0.00 0.00 3.16
4926 7094 9.981460 AGAGTCAAAAACCTATTCCATAGAAAT 57.019 29.630 0.00 0.00 35.09 2.17
4961 7129 1.067821 GGGCTGTGTAAGAGATCCTCG 59.932 57.143 0.00 0.00 35.36 4.63
4970 7138 2.280628 GATCGAAAGGGGCTGTGTAAG 58.719 52.381 0.00 0.00 0.00 2.34
4978 7146 0.681243 AAGCTTGGATCGAAAGGGGC 60.681 55.000 0.00 1.13 0.00 5.80
5012 7180 6.564709 TTGAGTCAAGATCATCTGGTTTTG 57.435 37.500 0.08 0.00 0.00 2.44
5017 7185 5.485620 TGAGTTTGAGTCAAGATCATCTGG 58.514 41.667 14.70 0.00 0.00 3.86
5039 7207 2.358582 TGTCATTGTTTGTGGTGAGCTG 59.641 45.455 0.00 0.00 0.00 4.24
5082 7250 3.567164 TGGCAGAAGAGAAAGAAAAGCAG 59.433 43.478 0.00 0.00 0.00 4.24
5126 7294 8.049117 AGTACTGCTGATTTCCAAATCTTCATA 58.951 33.333 12.22 4.29 43.97 2.15
5127 7295 6.888632 AGTACTGCTGATTTCCAAATCTTCAT 59.111 34.615 12.22 4.94 43.97 2.57
5128 7296 6.240894 AGTACTGCTGATTTCCAAATCTTCA 58.759 36.000 12.22 9.06 43.97 3.02
5129 7297 6.183360 GGAGTACTGCTGATTTCCAAATCTTC 60.183 42.308 7.20 5.70 43.97 2.87
5130 7298 5.649831 GGAGTACTGCTGATTTCCAAATCTT 59.350 40.000 7.20 0.00 43.97 2.40
5131 7299 5.189180 GGAGTACTGCTGATTTCCAAATCT 58.811 41.667 7.20 0.00 43.97 2.40
5132 7300 4.336713 GGGAGTACTGCTGATTTCCAAATC 59.663 45.833 14.52 5.25 43.91 2.17
5133 7301 4.263905 TGGGAGTACTGCTGATTTCCAAAT 60.264 41.667 14.52 0.00 0.00 2.32
5134 7302 3.073798 TGGGAGTACTGCTGATTTCCAAA 59.926 43.478 14.52 0.00 0.00 3.28
5135 7303 2.642311 TGGGAGTACTGCTGATTTCCAA 59.358 45.455 14.52 0.00 0.00 3.53
5136 7304 2.265367 TGGGAGTACTGCTGATTTCCA 58.735 47.619 14.52 0.00 0.00 3.53
5137 7305 3.350219 TTGGGAGTACTGCTGATTTCC 57.650 47.619 14.52 0.00 0.00 3.13


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

AutoCloner maintained by Alex Coulton.