Multiple sequence alignment - TraesCS7D01G360400

Loading Multiple Alignment...

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 TraesCS7D01G360400 chr7D 100.000 4396 0 0 1 4396 463262276 463257881 0.000000e+00 8118
1 TraesCS7D01G360400 chr7A 88.631 3580 237 55 3 3515 536983603 536987079 0.000000e+00 4200
2 TraesCS7D01G360400 chr7A 89.214 547 43 7 3532 4069 536987316 536987855 0.000000e+00 669
3 TraesCS7D01G360400 chr7A 93.564 202 10 1 4170 4368 536987981 536988182 9.240000e-77 298
4 TraesCS7D01G360400 chr7A 100.000 40 0 0 4170 4209 536987943 536987982 1.700000e-09 75
5 TraesCS7D01G360400 chr7B 96.935 2480 68 7 1513 3987 488415324 488417800 0.000000e+00 4152
6 TraesCS7D01G360400 chr7B 89.105 1597 80 25 1 1532 488413748 488415315 0.000000e+00 1899
7 TraesCS7D01G360400 chr7B 93.689 206 9 1 4167 4368 488417835 488418040 5.520000e-79 305


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 TraesCS7D01G360400 chr7D 463257881 463262276 4395 True 8118.000000 8118 100.00000 1 4396 1 chr7D.!!$R1 4395
1 TraesCS7D01G360400 chr7A 536983603 536988182 4579 False 1310.500000 4200 92.85225 3 4368 4 chr7A.!!$F1 4365
2 TraesCS7D01G360400 chr7B 488413748 488418040 4292 False 2118.666667 4152 93.24300 1 4368 3 chr7B.!!$F1 4367

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
331 332 0.112412 AGGAATCAAACGGGTGCCTT 59.888 50.0 0.00 0.0 0.00 4.35 F
520 522 0.754472 GATTAACGGGTGATCGGGGA 59.246 55.0 0.00 0.0 0.00 4.81 F
884 942 0.759436 CGCTAGCCCTCCTTCCCTTA 60.759 60.0 9.66 0.0 0.00 2.69 F
1889 1997 0.323629 TGTGCTGGCCACTAACTACC 59.676 55.0 0.00 0.0 44.92 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1582 1690 2.279582 ACTGATTCCGTTCACGCTAG 57.720 50.000 0.0 0.0 38.18 3.42 R
1681 1789 2.787994 AGAAACATGCTCTCCAGGTTG 58.212 47.619 0.0 0.0 46.70 3.77 R
2572 2693 5.226396 GTGAAGATATGTCCAAGATCCTCG 58.774 45.833 0.0 0.0 0.00 4.63 R
3823 4182 0.404040 GAATGGGTCCACCTTCCACA 59.596 55.000 0.0 0.0 41.11 4.17 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
36 37 1.821136 CCAATTCAACTTCCCCTGAGC 59.179 52.381 0.00 0.00 0.00 4.26
41 42 1.494721 TCAACTTCCCCTGAGCAACTT 59.505 47.619 0.00 0.00 0.00 2.66
77 78 2.338785 GCAACCCTGAAGCTGCTCC 61.339 63.158 1.00 0.00 0.00 4.70
94 95 2.933056 GCTCCTGAGGCTGTTCAAGTAC 60.933 54.545 0.00 0.00 0.00 2.73
149 150 5.898120 TGGAACAATCTTAAAAGGGGATGA 58.102 37.500 0.00 0.00 31.92 2.92
150 151 5.951747 TGGAACAATCTTAAAAGGGGATGAG 59.048 40.000 0.00 0.00 31.92 2.90
151 152 6.187682 GGAACAATCTTAAAAGGGGATGAGA 58.812 40.000 0.00 0.00 0.00 3.27
152 153 6.095580 GGAACAATCTTAAAAGGGGATGAGAC 59.904 42.308 0.00 0.00 0.00 3.36
153 154 6.139679 ACAATCTTAAAAGGGGATGAGACA 57.860 37.500 0.00 0.00 0.00 3.41
154 155 6.552008 ACAATCTTAAAAGGGGATGAGACAA 58.448 36.000 0.00 0.00 0.00 3.18
155 156 7.010160 ACAATCTTAAAAGGGGATGAGACAAA 58.990 34.615 0.00 0.00 0.00 2.83
156 157 7.508977 ACAATCTTAAAAGGGGATGAGACAAAA 59.491 33.333 0.00 0.00 0.00 2.44
157 158 8.367156 CAATCTTAAAAGGGGATGAGACAAAAA 58.633 33.333 0.00 0.00 0.00 1.94
158 159 8.670521 ATCTTAAAAGGGGATGAGACAAAAAT 57.329 30.769 0.00 0.00 0.00 1.82
159 160 8.122472 TCTTAAAAGGGGATGAGACAAAAATC 57.878 34.615 0.00 0.00 0.00 2.17
160 161 7.728083 TCTTAAAAGGGGATGAGACAAAAATCA 59.272 33.333 0.00 0.00 0.00 2.57
161 162 6.745794 AAAAGGGGATGAGACAAAAATCAA 57.254 33.333 0.00 0.00 0.00 2.57
162 163 6.745794 AAAGGGGATGAGACAAAAATCAAA 57.254 33.333 0.00 0.00 0.00 2.69
163 164 6.745794 AAGGGGATGAGACAAAAATCAAAA 57.254 33.333 0.00 0.00 0.00 2.44
164 165 6.350629 AGGGGATGAGACAAAAATCAAAAG 57.649 37.500 0.00 0.00 0.00 2.27
165 166 5.246883 AGGGGATGAGACAAAAATCAAAAGG 59.753 40.000 0.00 0.00 0.00 3.11
166 167 5.245977 GGGGATGAGACAAAAATCAAAAGGA 59.754 40.000 0.00 0.00 0.00 3.36
167 168 6.239572 GGGGATGAGACAAAAATCAAAAGGAA 60.240 38.462 0.00 0.00 0.00 3.36
168 169 6.646653 GGGATGAGACAAAAATCAAAAGGAAC 59.353 38.462 0.00 0.00 0.00 3.62
169 170 7.209475 GGATGAGACAAAAATCAAAAGGAACA 58.791 34.615 0.00 0.00 0.00 3.18
170 171 7.710475 GGATGAGACAAAAATCAAAAGGAACAA 59.290 33.333 0.00 0.00 0.00 2.83
171 172 9.097257 GATGAGACAAAAATCAAAAGGAACAAA 57.903 29.630 0.00 0.00 0.00 2.83
172 173 8.839310 TGAGACAAAAATCAAAAGGAACAAAA 57.161 26.923 0.00 0.00 0.00 2.44
173 174 9.277783 TGAGACAAAAATCAAAAGGAACAAAAA 57.722 25.926 0.00 0.00 0.00 1.94
227 228 0.617413 CACCACCAGCAGATCTTCCT 59.383 55.000 0.00 0.00 0.00 3.36
331 332 0.112412 AGGAATCAAACGGGTGCCTT 59.888 50.000 0.00 0.00 0.00 4.35
354 355 2.209064 ATCACAGGACGCGCGTAAGT 62.209 55.000 37.91 29.17 41.68 2.24
357 358 2.126580 AGGACGCGCGTAAGTCAC 60.127 61.111 37.91 22.01 39.01 3.67
358 359 2.429571 GGACGCGCGTAAGTCACA 60.430 61.111 37.91 0.00 39.01 3.58
389 390 2.170607 ACGTCTATGTGGCTAGGCAAAT 59.829 45.455 24.10 24.10 0.00 2.32
391 392 3.741075 CGTCTATGTGGCTAGGCAAATGA 60.741 47.826 27.81 20.05 0.00 2.57
434 435 2.168106 AGCAGCTCACATCTTCTCGATT 59.832 45.455 0.00 0.00 0.00 3.34
520 522 0.754472 GATTAACGGGTGATCGGGGA 59.246 55.000 0.00 0.00 0.00 4.81
522 524 1.205966 TTAACGGGTGATCGGGGATT 58.794 50.000 0.00 0.00 0.00 3.01
523 525 0.754472 TAACGGGTGATCGGGGATTC 59.246 55.000 0.00 0.00 0.00 2.52
524 526 2.029073 CGGGTGATCGGGGATTCG 59.971 66.667 0.00 0.00 0.00 3.34
525 527 2.426023 GGGTGATCGGGGATTCGG 59.574 66.667 0.00 0.00 0.00 4.30
526 528 2.426023 GGTGATCGGGGATTCGGG 59.574 66.667 0.00 0.00 0.00 5.14
527 529 2.426023 GTGATCGGGGATTCGGGG 59.574 66.667 0.00 0.00 0.00 5.73
528 530 3.556306 TGATCGGGGATTCGGGGC 61.556 66.667 0.00 0.00 0.00 5.80
683 714 3.551407 GAGGACATCCCGAGGGCC 61.551 72.222 2.58 0.00 41.55 5.80
725 756 2.949678 CGAATGGTCTCGCGGTCG 60.950 66.667 6.13 0.69 31.04 4.79
726 757 3.255379 GAATGGTCTCGCGGTCGC 61.255 66.667 6.13 5.16 35.26 5.19
884 942 0.759436 CGCTAGCCCTCCTTCCCTTA 60.759 60.000 9.66 0.00 0.00 2.69
924 995 4.266976 ACGAATACAATTTACGCGGAAGAG 59.733 41.667 12.47 4.36 0.00 2.85
945 1016 3.691498 GCGGTGGCTGAATGTAAAATAC 58.309 45.455 0.00 0.00 35.83 1.89
979 1053 1.592939 GGGAATTCGCTCTCGCTCC 60.593 63.158 14.84 0.00 35.26 4.70
980 1054 1.439644 GGAATTCGCTCTCGCTCCT 59.560 57.895 0.00 0.00 35.26 3.69
1165 1242 1.137675 CCTGCTGACGATCCAATCTGA 59.862 52.381 0.00 0.00 0.00 3.27
1344 1421 4.591924 TCCTCCTCTTAGTTTCGGTTTCTT 59.408 41.667 0.00 0.00 0.00 2.52
1478 1556 8.075574 TGTTATCAGTGCTTTGTAAAGATTGTG 58.924 33.333 8.47 0.71 38.28 3.33
1576 1684 8.671921 GCAGGATACCACATAAGATTATTCATG 58.328 37.037 0.00 0.00 37.17 3.07
1582 1690 8.388484 ACCACATAAGATTATTCATGCTTCTC 57.612 34.615 0.00 0.00 0.00 2.87
1601 1709 1.816835 TCTAGCGTGAACGGAATCAGT 59.183 47.619 4.84 0.00 40.23 3.41
1616 1724 6.096987 ACGGAATCAGTATCTGTTGTGTATCT 59.903 38.462 0.00 0.00 32.52 1.98
1623 1731 7.067129 TCAGTATCTGTTGTGTATCTACTGACC 59.933 40.741 5.63 0.00 38.89 4.02
1635 1743 7.769044 GTGTATCTACTGACCACATTTTACCAT 59.231 37.037 0.00 0.00 31.53 3.55
1708 1816 5.452356 CCTGGAGAGCATGTTTCTTTTGTTT 60.452 40.000 0.00 0.00 0.00 2.83
1821 1929 2.027385 GAAAGGTCCATGGCCATTCTC 58.973 52.381 24.10 8.84 32.71 2.87
1836 1944 4.456911 GCCATTCTCAACACTTTCATCAGA 59.543 41.667 0.00 0.00 0.00 3.27
1886 1994 3.819245 TTTGTGCTGGCCACTAACT 57.181 47.368 0.00 0.00 44.92 2.24
1887 1995 2.940994 TTTGTGCTGGCCACTAACTA 57.059 45.000 0.00 0.00 44.92 2.24
1888 1996 2.178912 TTGTGCTGGCCACTAACTAC 57.821 50.000 0.00 0.00 44.92 2.73
1889 1997 0.323629 TGTGCTGGCCACTAACTACC 59.676 55.000 0.00 0.00 44.92 3.18
1890 1998 0.323629 GTGCTGGCCACTAACTACCA 59.676 55.000 0.00 0.00 41.35 3.25
1891 1999 1.060729 TGCTGGCCACTAACTACCAA 58.939 50.000 0.00 0.00 0.00 3.67
1892 2000 1.271163 TGCTGGCCACTAACTACCAAC 60.271 52.381 0.00 0.00 0.00 3.77
1983 2103 9.427821 ACTGAGAGATAGTTCAATGGTAGTAAT 57.572 33.333 0.00 0.00 0.00 1.89
2138 2258 6.151648 GGAACACATGATCTTCCTTCATTGAA 59.848 38.462 0.00 0.00 31.50 2.69
2441 2562 6.150307 TGTTCAACCATCTATGTGCGTTATTT 59.850 34.615 0.00 0.00 0.00 1.40
2572 2693 4.063689 CTGATTCTGATATGGCAGTGGTC 58.936 47.826 0.00 0.00 37.20 4.02
2681 2802 2.028020 GGATTTATAGCGGTGAGAGGGG 60.028 54.545 0.00 0.00 0.00 4.79
3000 3121 1.566298 ATTGGACTCCACCTGAGGGC 61.566 60.000 2.38 0.00 46.01 5.19
3012 3133 1.372087 CTGAGGGCGCTGGACAATTC 61.372 60.000 8.56 0.00 0.00 2.17
3257 3393 8.678593 ATGATAGCATGCCAAATCTGATATAG 57.321 34.615 15.66 0.00 32.31 1.31
3338 3474 6.317391 GGGATTTCTACAATTCAACCTCTCAG 59.683 42.308 0.00 0.00 0.00 3.35
3497 3633 9.855021 TGTGCTTTATTTTCCTTAATCTTTAGC 57.145 29.630 0.00 0.00 0.00 3.09
3572 3928 6.907206 TGTATGGCTTATAACGTGTTTACC 57.093 37.500 0.00 0.00 0.00 2.85
3783 4139 0.257039 AGGGTGATCCAGATTGTGCC 59.743 55.000 0.00 0.00 38.24 5.01
3823 4182 1.194781 AGATTGGTGCCACGACTCCT 61.195 55.000 0.00 0.00 0.00 3.69
3921 4280 2.027192 TGGTGATGGTTCTTGGTAGCTC 60.027 50.000 0.00 0.00 0.00 4.09
3989 4354 2.941720 GCTGATGAGGCTACTGGAAAAG 59.058 50.000 0.00 0.00 0.00 2.27
3990 4355 3.539604 CTGATGAGGCTACTGGAAAAGG 58.460 50.000 0.00 0.00 0.00 3.11
3993 4358 3.876309 TGAGGCTACTGGAAAAGGTTT 57.124 42.857 0.00 0.00 0.00 3.27
4058 4423 2.432628 GAGGAACGTCAGGCGGTG 60.433 66.667 0.00 0.00 42.72 4.94
4065 4430 2.887568 GTCAGGCGGTGCTCGATG 60.888 66.667 4.33 2.72 42.43 3.84
4068 4433 4.521062 AGGCGGTGCTCGATGCTC 62.521 66.667 8.07 4.86 43.37 4.26
4073 4438 4.919653 GTGCTCGATGCTCCAGAA 57.080 55.556 8.07 0.00 43.37 3.02
4074 4439 3.376218 GTGCTCGATGCTCCAGAAT 57.624 52.632 8.07 0.00 43.37 2.40
4075 4440 2.515926 GTGCTCGATGCTCCAGAATA 57.484 50.000 8.07 0.00 43.37 1.75
4076 4441 2.131183 GTGCTCGATGCTCCAGAATAC 58.869 52.381 8.07 0.00 43.37 1.89
4077 4442 1.269257 TGCTCGATGCTCCAGAATACG 60.269 52.381 8.07 0.00 43.37 3.06
4078 4443 1.269309 GCTCGATGCTCCAGAATACGT 60.269 52.381 0.00 0.00 38.95 3.57
4079 4444 2.031069 GCTCGATGCTCCAGAATACGTA 60.031 50.000 0.00 0.00 38.95 3.57
4080 4445 3.816091 CTCGATGCTCCAGAATACGTAG 58.184 50.000 0.08 0.00 0.00 3.51
4081 4446 2.031069 TCGATGCTCCAGAATACGTAGC 60.031 50.000 0.08 0.00 0.00 3.58
4082 4447 2.030717 CGATGCTCCAGAATACGTAGCT 60.031 50.000 0.08 0.00 34.28 3.32
4083 4448 2.871182 TGCTCCAGAATACGTAGCTG 57.129 50.000 16.99 16.99 34.28 4.24
4084 4449 1.202417 TGCTCCAGAATACGTAGCTGC 60.202 52.381 18.02 10.63 34.28 5.25
4085 4450 1.067821 GCTCCAGAATACGTAGCTGCT 59.932 52.381 18.02 7.57 0.00 4.24
4086 4451 2.482142 GCTCCAGAATACGTAGCTGCTT 60.482 50.000 7.79 1.00 0.00 3.91
4087 4452 3.786635 CTCCAGAATACGTAGCTGCTTT 58.213 45.455 7.79 0.00 0.00 3.51
4088 4453 4.184629 CTCCAGAATACGTAGCTGCTTTT 58.815 43.478 7.79 0.00 0.00 2.27
4089 4454 3.932710 TCCAGAATACGTAGCTGCTTTTG 59.067 43.478 7.79 0.26 0.00 2.44
4090 4455 3.063997 CCAGAATACGTAGCTGCTTTTGG 59.936 47.826 7.79 10.54 0.00 3.28
4091 4456 3.063997 CAGAATACGTAGCTGCTTTTGGG 59.936 47.826 7.79 0.00 0.00 4.12
4092 4457 2.781681 ATACGTAGCTGCTTTTGGGT 57.218 45.000 7.79 1.87 0.00 4.51
4093 4458 1.803334 TACGTAGCTGCTTTTGGGTG 58.197 50.000 7.79 0.00 0.00 4.61
4094 4459 1.210155 CGTAGCTGCTTTTGGGTGC 59.790 57.895 7.79 0.00 0.00 5.01
4095 4460 1.237285 CGTAGCTGCTTTTGGGTGCT 61.237 55.000 7.79 0.00 37.72 4.40
4096 4461 0.961753 GTAGCTGCTTTTGGGTGCTT 59.038 50.000 7.79 0.00 35.47 3.91
4097 4462 2.159382 GTAGCTGCTTTTGGGTGCTTA 58.841 47.619 7.79 0.00 35.47 3.09
4098 4463 1.928868 AGCTGCTTTTGGGTGCTTAT 58.071 45.000 0.00 0.00 0.00 1.73
4099 4464 2.250924 AGCTGCTTTTGGGTGCTTATT 58.749 42.857 0.00 0.00 0.00 1.40
4100 4465 3.430453 AGCTGCTTTTGGGTGCTTATTA 58.570 40.909 0.00 0.00 0.00 0.98
4101 4466 4.026052 AGCTGCTTTTGGGTGCTTATTAT 58.974 39.130 0.00 0.00 0.00 1.28
4102 4467 4.467438 AGCTGCTTTTGGGTGCTTATTATT 59.533 37.500 0.00 0.00 0.00 1.40
4103 4468 4.567959 GCTGCTTTTGGGTGCTTATTATTG 59.432 41.667 0.00 0.00 0.00 1.90
4104 4469 5.624281 GCTGCTTTTGGGTGCTTATTATTGA 60.624 40.000 0.00 0.00 0.00 2.57
4105 4470 5.719173 TGCTTTTGGGTGCTTATTATTGAC 58.281 37.500 0.00 0.00 0.00 3.18
4106 4471 5.480073 TGCTTTTGGGTGCTTATTATTGACT 59.520 36.000 0.00 0.00 0.00 3.41
4107 4472 6.661377 TGCTTTTGGGTGCTTATTATTGACTA 59.339 34.615 0.00 0.00 0.00 2.59
4108 4473 6.972901 GCTTTTGGGTGCTTATTATTGACTAC 59.027 38.462 0.00 0.00 0.00 2.73
4109 4474 7.148069 GCTTTTGGGTGCTTATTATTGACTACT 60.148 37.037 0.00 0.00 0.00 2.57
4110 4475 7.859325 TTTGGGTGCTTATTATTGACTACTC 57.141 36.000 0.00 0.00 0.00 2.59
4111 4476 5.925509 TGGGTGCTTATTATTGACTACTCC 58.074 41.667 0.00 0.00 0.00 3.85
4112 4477 5.665812 TGGGTGCTTATTATTGACTACTCCT 59.334 40.000 0.00 0.00 0.00 3.69
4113 4478 6.842280 TGGGTGCTTATTATTGACTACTCCTA 59.158 38.462 0.00 0.00 0.00 2.94
4114 4479 7.015292 TGGGTGCTTATTATTGACTACTCCTAG 59.985 40.741 0.00 0.00 0.00 3.02
4115 4480 7.379750 GGTGCTTATTATTGACTACTCCTAGG 58.620 42.308 0.82 0.82 0.00 3.02
4116 4481 7.015389 GGTGCTTATTATTGACTACTCCTAGGT 59.985 40.741 9.08 0.00 0.00 3.08
4117 4482 7.868415 GTGCTTATTATTGACTACTCCTAGGTG 59.132 40.741 9.08 9.22 0.00 4.00
4118 4483 7.563924 TGCTTATTATTGACTACTCCTAGGTGT 59.436 37.037 19.80 19.80 0.00 4.16
4119 4484 8.422566 GCTTATTATTGACTACTCCTAGGTGTT 58.577 37.037 20.98 4.85 0.00 3.32
4122 4487 7.549147 TTATTGACTACTCCTAGGTGTTTGT 57.451 36.000 20.98 18.55 0.00 2.83
4123 4488 5.881923 TTGACTACTCCTAGGTGTTTGTT 57.118 39.130 20.98 4.24 0.00 2.83
4124 4489 5.464030 TGACTACTCCTAGGTGTTTGTTC 57.536 43.478 20.98 12.47 0.00 3.18
4125 4490 4.897076 TGACTACTCCTAGGTGTTTGTTCA 59.103 41.667 20.98 14.51 0.00 3.18
4126 4491 5.010719 TGACTACTCCTAGGTGTTTGTTCAG 59.989 44.000 20.98 13.36 0.00 3.02
4146 4511 7.552687 TGTTCAGCTTATCCTGTAGTTTTATGG 59.447 37.037 0.00 0.00 34.47 2.74
4154 4519 4.764823 TCCTGTAGTTTTATGGTGGCTTTG 59.235 41.667 0.00 0.00 0.00 2.77
4155 4520 4.522789 CCTGTAGTTTTATGGTGGCTTTGT 59.477 41.667 0.00 0.00 0.00 2.83
4156 4521 5.708230 CCTGTAGTTTTATGGTGGCTTTGTA 59.292 40.000 0.00 0.00 0.00 2.41
4158 4523 6.300703 TGTAGTTTTATGGTGGCTTTGTACT 58.699 36.000 0.00 0.00 0.00 2.73
4159 4524 5.705609 AGTTTTATGGTGGCTTTGTACTG 57.294 39.130 0.00 0.00 0.00 2.74
4160 4525 4.022329 AGTTTTATGGTGGCTTTGTACTGC 60.022 41.667 0.00 0.00 0.00 4.40
4161 4526 1.732941 TATGGTGGCTTTGTACTGCG 58.267 50.000 0.00 0.00 0.00 5.18
4162 4527 0.036164 ATGGTGGCTTTGTACTGCGA 59.964 50.000 0.00 0.00 0.00 5.10
4163 4528 0.036164 TGGTGGCTTTGTACTGCGAT 59.964 50.000 0.00 0.00 0.00 4.58
4164 4529 1.165270 GGTGGCTTTGTACTGCGATT 58.835 50.000 0.00 0.00 0.00 3.34
4165 4530 1.130561 GGTGGCTTTGTACTGCGATTC 59.869 52.381 0.00 0.00 0.00 2.52
4368 4824 2.959516 TGACAAGACCATGCTAACTCG 58.040 47.619 0.00 0.00 0.00 4.18
4369 4825 2.299013 TGACAAGACCATGCTAACTCGT 59.701 45.455 0.00 0.00 0.00 4.18
4370 4826 2.924290 GACAAGACCATGCTAACTCGTC 59.076 50.000 0.00 0.00 0.00 4.20
4371 4827 2.299013 ACAAGACCATGCTAACTCGTCA 59.701 45.455 0.00 0.00 0.00 4.35
4372 4828 2.656560 AGACCATGCTAACTCGTCAC 57.343 50.000 0.00 0.00 0.00 3.67
4373 4829 2.171840 AGACCATGCTAACTCGTCACT 58.828 47.619 0.00 0.00 0.00 3.41
4374 4830 2.094494 AGACCATGCTAACTCGTCACTG 60.094 50.000 0.00 0.00 0.00 3.66
4375 4831 1.002366 CCATGCTAACTCGTCACTGC 58.998 55.000 0.00 0.00 0.00 4.40
4376 4832 1.672737 CCATGCTAACTCGTCACTGCA 60.673 52.381 0.00 0.00 34.88 4.41
4377 4833 2.274437 CATGCTAACTCGTCACTGCAT 58.726 47.619 0.00 0.00 41.08 3.96
4378 4834 1.996292 TGCTAACTCGTCACTGCATC 58.004 50.000 0.00 0.00 0.00 3.91
4379 4835 1.272212 TGCTAACTCGTCACTGCATCA 59.728 47.619 0.00 0.00 0.00 3.07
4380 4836 1.656095 GCTAACTCGTCACTGCATCAC 59.344 52.381 0.00 0.00 0.00 3.06
4381 4837 2.672478 GCTAACTCGTCACTGCATCACT 60.672 50.000 0.00 0.00 0.00 3.41
4382 4838 3.427638 GCTAACTCGTCACTGCATCACTA 60.428 47.826 0.00 0.00 0.00 2.74
4383 4839 2.929531 ACTCGTCACTGCATCACTAG 57.070 50.000 0.00 0.00 0.00 2.57
4384 4840 1.474478 ACTCGTCACTGCATCACTAGG 59.526 52.381 0.00 0.00 0.00 3.02
4385 4841 1.474478 CTCGTCACTGCATCACTAGGT 59.526 52.381 0.00 0.00 0.00 3.08
4386 4842 2.683362 CTCGTCACTGCATCACTAGGTA 59.317 50.000 0.00 0.00 0.00 3.08
4387 4843 2.683362 TCGTCACTGCATCACTAGGTAG 59.317 50.000 0.00 0.00 0.00 3.18
4388 4844 2.796383 CGTCACTGCATCACTAGGTAGC 60.796 54.545 0.00 0.00 0.00 3.58
4389 4845 2.428890 GTCACTGCATCACTAGGTAGCT 59.571 50.000 0.00 0.00 0.00 3.32
4390 4846 3.632604 GTCACTGCATCACTAGGTAGCTA 59.367 47.826 0.99 0.99 0.00 3.32
4391 4847 4.279671 GTCACTGCATCACTAGGTAGCTAT 59.720 45.833 1.35 0.00 0.00 2.97
4392 4848 4.279420 TCACTGCATCACTAGGTAGCTATG 59.721 45.833 1.35 0.08 0.00 2.23
4393 4849 3.576118 ACTGCATCACTAGGTAGCTATGG 59.424 47.826 1.35 0.00 0.00 2.74
4394 4850 3.576118 CTGCATCACTAGGTAGCTATGGT 59.424 47.826 1.35 0.00 0.00 3.55
4395 4851 4.736473 TGCATCACTAGGTAGCTATGGTA 58.264 43.478 1.35 0.00 0.00 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.970640 GGGGAAGTTGAATTGGTTGCT 59.029 47.619 0.00 0.00 0.00 3.91
14 15 3.500343 CTCAGGGGAAGTTGAATTGGTT 58.500 45.455 0.00 0.00 0.00 3.67
41 42 1.905894 TGCAGCCATTGTAGAGGTACA 59.094 47.619 0.00 0.00 37.38 2.90
77 78 1.071605 GCGTACTTGAACAGCCTCAG 58.928 55.000 0.00 0.00 0.00 3.35
94 95 2.738521 CAGGTTCACACGGAGGCG 60.739 66.667 0.00 0.00 0.00 5.52
134 135 7.728083 TGATTTTTGTCTCATCCCCTTTTAAGA 59.272 33.333 0.00 0.00 0.00 2.10
141 142 5.246883 CCTTTTGATTTTTGTCTCATCCCCT 59.753 40.000 0.00 0.00 0.00 4.79
144 145 7.209475 TGTTCCTTTTGATTTTTGTCTCATCC 58.791 34.615 0.00 0.00 0.00 3.51
145 146 8.647143 TTGTTCCTTTTGATTTTTGTCTCATC 57.353 30.769 0.00 0.00 0.00 2.92
146 147 9.447157 TTTTGTTCCTTTTGATTTTTGTCTCAT 57.553 25.926 0.00 0.00 0.00 2.90
147 148 8.839310 TTTTGTTCCTTTTGATTTTTGTCTCA 57.161 26.923 0.00 0.00 0.00 3.27
178 179 8.553459 ACAATCTGTTTTCACTAGGTTCATAG 57.447 34.615 0.00 0.00 0.00 2.23
208 209 0.617413 AGGAAGATCTGCTGGTGGTG 59.383 55.000 0.00 0.00 0.00 4.17
253 254 2.125912 CACCTGGAGAAGACGCGG 60.126 66.667 12.47 0.00 0.00 6.46
256 257 1.831652 AAGGCCACCTGGAGAAGACG 61.832 60.000 5.01 0.00 37.39 4.18
257 258 0.035915 GAAGGCCACCTGGAGAAGAC 60.036 60.000 5.01 0.00 37.39 3.01
331 332 2.432456 GCGCGTCCTGTGATGTGA 60.432 61.111 8.43 0.00 39.84 3.58
354 355 1.080772 GACGTGCATCGGACTGTGA 60.081 57.895 12.18 0.00 44.69 3.58
357 358 1.202302 ACATAGACGTGCATCGGACTG 60.202 52.381 12.18 7.19 44.69 3.51
358 359 1.103803 ACATAGACGTGCATCGGACT 58.896 50.000 12.18 12.11 44.69 3.85
389 390 0.617535 TTCCCGCCTCTTCTCCATCA 60.618 55.000 0.00 0.00 0.00 3.07
391 392 1.977293 GCTTCCCGCCTCTTCTCCAT 61.977 60.000 0.00 0.00 0.00 3.41
434 435 2.771639 CGACATCGCCTTCCTCGGA 61.772 63.158 0.00 0.00 0.00 4.55
498 499 1.217882 CCGATCACCCGTTAATCTGC 58.782 55.000 0.00 0.00 0.00 4.26
500 501 0.756903 CCCCGATCACCCGTTAATCT 59.243 55.000 0.00 0.00 0.00 2.40
525 527 4.162690 ATGCTCCTCCGTTCGCCC 62.163 66.667 0.00 0.00 0.00 6.13
526 528 2.586357 GATGCTCCTCCGTTCGCC 60.586 66.667 0.00 0.00 0.00 5.54
527 529 1.590259 GAGATGCTCCTCCGTTCGC 60.590 63.158 0.00 0.00 0.00 4.70
528 530 1.066587 GGAGATGCTCCTCCGTTCG 59.933 63.158 6.23 0.00 46.41 3.95
662 675 2.491022 CCTCGGGATGTCCTCGTCC 61.491 68.421 0.00 0.00 46.10 4.79
822 880 3.931578 AGCACTCTCTCGCAAAAAGTAT 58.068 40.909 0.00 0.00 0.00 2.12
847 905 4.297299 AGCGATGCAAATATCCAACTTG 57.703 40.909 0.00 0.00 0.00 3.16
884 942 0.532862 CGTGTGCTCCAAACTCCAGT 60.533 55.000 0.00 0.00 0.00 4.00
924 995 2.939460 ATTTTACATTCAGCCACCGC 57.061 45.000 0.00 0.00 0.00 5.68
1344 1421 4.136051 TGAGAATCACAAGTCACAATGCA 58.864 39.130 0.00 0.00 42.56 3.96
1478 1556 6.034256 GTCAATTTACATTCAGAACAGCATGC 59.966 38.462 10.51 10.51 42.53 4.06
1582 1690 2.279582 ACTGATTCCGTTCACGCTAG 57.720 50.000 0.00 0.00 38.18 3.42
1601 1709 6.661805 TGTGGTCAGTAGATACACAACAGATA 59.338 38.462 0.00 0.00 39.74 1.98
1616 1724 8.472007 AGAAAAATGGTAAAATGTGGTCAGTA 57.528 30.769 0.00 0.00 0.00 2.74
1623 1731 8.143835 AGTCCTGAAGAAAAATGGTAAAATGTG 58.856 33.333 0.00 0.00 0.00 3.21
1635 1743 6.601613 TCACAGCTTTAAGTCCTGAAGAAAAA 59.398 34.615 6.60 0.00 0.00 1.94
1681 1789 2.787994 AGAAACATGCTCTCCAGGTTG 58.212 47.619 0.00 0.00 46.70 3.77
1708 1816 6.665992 AGAACTGTAGGTTGTGAATACTGA 57.334 37.500 0.00 0.00 38.41 3.41
1821 1929 7.120285 ACCTGTATGAATCTGATGAAAGTGTTG 59.880 37.037 0.00 0.00 0.00 3.33
1836 1944 5.983333 AAGGAAGATCCACCTGTATGAAT 57.017 39.130 8.73 0.00 39.61 2.57
1983 2103 9.862371 GTCTTCACTGTAATTTCTTCTCTATCA 57.138 33.333 0.00 0.00 0.00 2.15
2138 2258 6.262273 ACGTTAAACAAACATCCTCACAATCT 59.738 34.615 0.00 0.00 38.03 2.40
2441 2562 9.311916 CACAAACATATCAGTTTTCTGGAAAAA 57.688 29.630 9.65 0.00 46.94 1.94
2572 2693 5.226396 GTGAAGATATGTCCAAGATCCTCG 58.774 45.833 0.00 0.00 0.00 4.63
3018 3139 3.018423 ACCTTAACATCCAAGGGCATC 57.982 47.619 6.12 0.00 45.81 3.91
3219 3353 9.695526 TGGCATGCTATCATATTTAATGAAAAC 57.304 29.630 18.92 0.00 0.00 2.43
3257 3393 7.435192 CCTTTGAAATGAACAACCTAAGAACAC 59.565 37.037 0.00 0.00 0.00 3.32
3338 3474 7.880195 AGGATTAGGCACAACATATCAGATAAC 59.120 37.037 0.00 0.00 0.00 1.89
3409 3545 5.019470 AGACTACCAGATGTCACTTCATCA 58.981 41.667 8.93 0.00 44.46 3.07
3572 3928 3.963383 AAGCACACTTTGTAGAAACCG 57.037 42.857 0.00 0.00 29.41 4.44
3823 4182 0.404040 GAATGGGTCCACCTTCCACA 59.596 55.000 0.00 0.00 41.11 4.17
3921 4280 5.089970 TGAATAGTGATGAAGGGTGACAG 57.910 43.478 0.00 0.00 0.00 3.51
3989 4354 2.706555 GCCTGTGCTGAAAGTAAACC 57.293 50.000 0.00 0.00 35.30 3.27
4002 4367 5.375417 TCATTTGTCAATAACAGCCTGTG 57.625 39.130 0.00 0.00 39.58 3.66
4013 4378 4.895668 AAAGGCACCATCATTTGTCAAT 57.104 36.364 0.00 0.00 0.00 2.57
4058 4423 1.269309 ACGTATTCTGGAGCATCGAGC 60.269 52.381 0.00 0.00 41.12 5.03
4065 4430 1.067821 AGCAGCTACGTATTCTGGAGC 59.932 52.381 19.92 10.61 0.00 4.70
4068 4433 3.063997 CCAAAAGCAGCTACGTATTCTGG 59.936 47.826 19.92 5.72 0.00 3.86
4069 4434 3.063997 CCCAAAAGCAGCTACGTATTCTG 59.936 47.826 16.30 16.30 0.00 3.02
4070 4435 3.270877 CCCAAAAGCAGCTACGTATTCT 58.729 45.455 0.00 0.00 0.00 2.40
4071 4436 3.007635 ACCCAAAAGCAGCTACGTATTC 58.992 45.455 0.00 0.00 0.00 1.75
4072 4437 2.747446 CACCCAAAAGCAGCTACGTATT 59.253 45.455 0.00 0.00 0.00 1.89
4073 4438 2.356135 CACCCAAAAGCAGCTACGTAT 58.644 47.619 0.00 0.00 0.00 3.06
4074 4439 1.803334 CACCCAAAAGCAGCTACGTA 58.197 50.000 0.00 0.00 0.00 3.57
4075 4440 1.515521 GCACCCAAAAGCAGCTACGT 61.516 55.000 0.00 0.00 0.00 3.57
4076 4441 1.210155 GCACCCAAAAGCAGCTACG 59.790 57.895 0.00 0.00 0.00 3.51
4077 4442 0.961753 AAGCACCCAAAAGCAGCTAC 59.038 50.000 0.00 0.00 34.66 3.58
4078 4443 2.577606 TAAGCACCCAAAAGCAGCTA 57.422 45.000 0.00 0.00 34.66 3.32
4079 4444 1.928868 ATAAGCACCCAAAAGCAGCT 58.071 45.000 0.00 0.00 37.08 4.24
4080 4445 2.749280 AATAAGCACCCAAAAGCAGC 57.251 45.000 0.00 0.00 0.00 5.25
4081 4446 5.807011 GTCAATAATAAGCACCCAAAAGCAG 59.193 40.000 0.00 0.00 0.00 4.24
4082 4447 5.480073 AGTCAATAATAAGCACCCAAAAGCA 59.520 36.000 0.00 0.00 0.00 3.91
4083 4448 5.965922 AGTCAATAATAAGCACCCAAAAGC 58.034 37.500 0.00 0.00 0.00 3.51
4084 4449 8.281212 AGTAGTCAATAATAAGCACCCAAAAG 57.719 34.615 0.00 0.00 0.00 2.27
4085 4450 7.338449 GGAGTAGTCAATAATAAGCACCCAAAA 59.662 37.037 0.00 0.00 0.00 2.44
4086 4451 6.826741 GGAGTAGTCAATAATAAGCACCCAAA 59.173 38.462 0.00 0.00 0.00 3.28
4087 4452 6.157994 AGGAGTAGTCAATAATAAGCACCCAA 59.842 38.462 0.00 0.00 0.00 4.12
4088 4453 5.665812 AGGAGTAGTCAATAATAAGCACCCA 59.334 40.000 0.00 0.00 0.00 4.51
4089 4454 6.176014 AGGAGTAGTCAATAATAAGCACCC 57.824 41.667 0.00 0.00 0.00 4.61
4090 4455 7.015389 ACCTAGGAGTAGTCAATAATAAGCACC 59.985 40.741 17.98 0.00 0.00 5.01
4091 4456 7.868415 CACCTAGGAGTAGTCAATAATAAGCAC 59.132 40.741 17.98 0.00 0.00 4.40
4092 4457 7.563924 ACACCTAGGAGTAGTCAATAATAAGCA 59.436 37.037 17.98 0.00 0.00 3.91
4093 4458 7.953752 ACACCTAGGAGTAGTCAATAATAAGC 58.046 38.462 17.98 0.00 0.00 3.09
4096 4461 9.263446 ACAAACACCTAGGAGTAGTCAATAATA 57.737 33.333 17.98 0.00 0.00 0.98
4097 4462 8.147244 ACAAACACCTAGGAGTAGTCAATAAT 57.853 34.615 17.98 0.00 0.00 1.28
4098 4463 7.549147 ACAAACACCTAGGAGTAGTCAATAA 57.451 36.000 17.98 0.00 0.00 1.40
4099 4464 7.233962 TGAACAAACACCTAGGAGTAGTCAATA 59.766 37.037 17.98 1.98 0.00 1.90
4100 4465 6.042781 TGAACAAACACCTAGGAGTAGTCAAT 59.957 38.462 17.98 1.81 0.00 2.57
4101 4466 5.364446 TGAACAAACACCTAGGAGTAGTCAA 59.636 40.000 17.98 5.71 0.00 3.18
4102 4467 4.897076 TGAACAAACACCTAGGAGTAGTCA 59.103 41.667 17.98 12.06 0.00 3.41
4103 4468 5.464030 TGAACAAACACCTAGGAGTAGTC 57.536 43.478 17.98 9.70 0.00 2.59
4104 4469 4.262506 GCTGAACAAACACCTAGGAGTAGT 60.263 45.833 17.98 13.21 0.00 2.73
4105 4470 4.021016 AGCTGAACAAACACCTAGGAGTAG 60.021 45.833 17.98 12.55 0.00 2.57
4106 4471 3.901844 AGCTGAACAAACACCTAGGAGTA 59.098 43.478 17.98 0.00 0.00 2.59
4107 4472 2.706190 AGCTGAACAAACACCTAGGAGT 59.294 45.455 17.98 11.68 0.00 3.85
4108 4473 3.409026 AGCTGAACAAACACCTAGGAG 57.591 47.619 17.98 10.85 0.00 3.69
4109 4474 3.857157 AAGCTGAACAAACACCTAGGA 57.143 42.857 17.98 0.00 0.00 2.94
4110 4475 4.636206 GGATAAGCTGAACAAACACCTAGG 59.364 45.833 7.41 7.41 0.00 3.02
4111 4476 5.352569 CAGGATAAGCTGAACAAACACCTAG 59.647 44.000 0.00 0.00 0.00 3.02
4112 4477 5.221843 ACAGGATAAGCTGAACAAACACCTA 60.222 40.000 0.00 0.00 0.00 3.08
4113 4478 4.074970 CAGGATAAGCTGAACAAACACCT 58.925 43.478 0.00 0.00 0.00 4.00
4114 4479 3.821033 ACAGGATAAGCTGAACAAACACC 59.179 43.478 0.00 0.00 0.00 4.16
4115 4480 5.701290 ACTACAGGATAAGCTGAACAAACAC 59.299 40.000 0.00 0.00 0.00 3.32
4116 4481 5.865085 ACTACAGGATAAGCTGAACAAACA 58.135 37.500 0.00 0.00 0.00 2.83
4117 4482 6.803154 AACTACAGGATAAGCTGAACAAAC 57.197 37.500 0.00 0.00 0.00 2.93
4118 4483 7.817418 AAAACTACAGGATAAGCTGAACAAA 57.183 32.000 0.00 0.00 0.00 2.83
4119 4484 8.946085 CATAAAACTACAGGATAAGCTGAACAA 58.054 33.333 0.00 0.00 0.00 2.83
4120 4485 7.552687 CCATAAAACTACAGGATAAGCTGAACA 59.447 37.037 0.00 0.00 0.00 3.18
4121 4486 7.553044 ACCATAAAACTACAGGATAAGCTGAAC 59.447 37.037 0.00 0.00 0.00 3.18
4122 4487 7.552687 CACCATAAAACTACAGGATAAGCTGAA 59.447 37.037 0.00 0.00 0.00 3.02
4123 4488 7.047891 CACCATAAAACTACAGGATAAGCTGA 58.952 38.462 0.00 0.00 0.00 4.26
4124 4489 6.260936 CCACCATAAAACTACAGGATAAGCTG 59.739 42.308 0.00 0.00 0.00 4.24
4125 4490 6.357367 CCACCATAAAACTACAGGATAAGCT 58.643 40.000 0.00 0.00 0.00 3.74
4126 4491 5.008712 GCCACCATAAAACTACAGGATAAGC 59.991 44.000 0.00 0.00 0.00 3.09
4146 4511 1.804151 TGAATCGCAGTACAAAGCCAC 59.196 47.619 0.00 0.00 0.00 5.01
4154 4519 7.785197 ATTCTTTGGAAAACTGAATCGCAGTAC 60.785 37.037 0.00 0.00 44.21 2.73
4155 4520 6.206634 ATTCTTTGGAAAACTGAATCGCAGTA 59.793 34.615 0.00 0.00 44.21 2.74
4156 4521 5.010012 ATTCTTTGGAAAACTGAATCGCAGT 59.990 36.000 0.00 0.00 45.22 4.40
4158 4523 4.909696 TTCTTTGGAAAACTGAATCGCA 57.090 36.364 0.00 0.00 0.00 5.10
4159 4524 5.703876 AGATTCTTTGGAAAACTGAATCGC 58.296 37.500 0.00 0.00 44.28 4.58
4160 4525 9.677567 TTAAAGATTCTTTGGAAAACTGAATCG 57.322 29.630 19.60 0.00 44.28 3.34
4162 4527 9.764363 GGTTAAAGATTCTTTGGAAAACTGAAT 57.236 29.630 19.60 0.00 34.90 2.57
4163 4528 8.754080 TGGTTAAAGATTCTTTGGAAAACTGAA 58.246 29.630 19.60 2.27 34.90 3.02
4164 4529 8.299990 TGGTTAAAGATTCTTTGGAAAACTGA 57.700 30.769 19.60 6.39 34.90 3.41
4165 4530 8.817100 GTTGGTTAAAGATTCTTTGGAAAACTG 58.183 33.333 19.60 0.00 34.90 3.16
4368 4824 2.428890 AGCTACCTAGTGATGCAGTGAC 59.571 50.000 0.00 0.00 0.00 3.67
4369 4825 2.739943 AGCTACCTAGTGATGCAGTGA 58.260 47.619 0.00 0.00 0.00 3.41
4370 4826 4.554292 CATAGCTACCTAGTGATGCAGTG 58.446 47.826 0.00 0.00 0.00 3.66
4371 4827 3.576118 CCATAGCTACCTAGTGATGCAGT 59.424 47.826 0.00 0.00 0.00 4.40
4372 4828 3.576118 ACCATAGCTACCTAGTGATGCAG 59.424 47.826 0.00 0.00 0.00 4.41
4373 4829 3.576861 ACCATAGCTACCTAGTGATGCA 58.423 45.455 0.00 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.