Multiple sequence alignment - TraesCS4D01G263000

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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 TraesCS4D01G263000 chr4D 100.000 3683 0 0 1 3683 434148547 434144865 0.000000e+00 6802.0
1 TraesCS4D01G263000 chr4D 79.648 1592 261 47 1031 2592 434031035 434029477 0.000000e+00 1086.0
2 TraesCS4D01G263000 chr4D 73.913 391 74 14 142 529 481880918 481881283 8.300000e-27 132.0
3 TraesCS4D01G263000 chr4A 90.973 3567 219 57 150 3683 35569561 35566065 0.000000e+00 4708.0
4 TraesCS4D01G263000 chr4A 79.924 1589 251 49 1036 2592 35478007 35476455 0.000000e+00 1105.0
5 TraesCS4D01G263000 chr4B 96.103 2643 72 21 492 3121 532721318 532718694 0.000000e+00 4281.0
6 TraesCS4D01G263000 chr4B 80.227 1588 259 46 1031 2592 532582805 532581247 0.000000e+00 1142.0
7 TraesCS4D01G263000 chr4B 93.801 371 22 1 3307 3677 532717481 532717112 1.160000e-154 556.0
8 TraesCS4D01G263000 chr4B 78.310 355 68 7 160 511 125424739 125424391 1.720000e-53 220.0
9 TraesCS4D01G263000 chr1A 72.682 1391 307 59 1236 2594 580988492 580989841 2.670000e-106 396.0
10 TraesCS4D01G263000 chr1D 74.615 973 204 34 1236 2191 483972824 483973770 4.460000e-104 388.0
11 TraesCS4D01G263000 chr1B 72.498 1389 313 52 1236 2594 673992409 673993758 5.770000e-103 385.0
12 TraesCS4D01G263000 chr1B 77.612 268 52 7 256 519 581117605 581117342 4.920000e-34 156.0
13 TraesCS4D01G263000 chr5A 76.000 550 110 15 1247 1785 621540174 621539636 7.840000e-67 265.0
14 TraesCS4D01G263000 chr6A 77.809 356 72 7 146 498 544214712 544214361 2.880000e-51 213.0
15 TraesCS4D01G263000 chr6B 76.880 359 70 13 146 500 688749788 688749439 1.350000e-44 191.0
16 TraesCS4D01G263000 chr7B 74.598 311 68 9 131 432 56515000 56515308 3.860000e-25 126.0
17 TraesCS4D01G263000 chr2B 75.758 231 44 7 159 380 785274946 785275173 5.030000e-19 106.0
18 TraesCS4D01G263000 chr2A 75.455 220 42 9 146 354 28150829 28150611 3.030000e-16 97.1
19 TraesCS4D01G263000 chr2D 76.190 189 31 11 146 322 25752222 25752036 1.820000e-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 TraesCS4D01G263000 chr4D 434144865 434148547 3682 True 6802.0 6802 100.000 1 3683 1 chr4D.!!$R2 3682
1 TraesCS4D01G263000 chr4D 434029477 434031035 1558 True 1086.0 1086 79.648 1031 2592 1 chr4D.!!$R1 1561
2 TraesCS4D01G263000 chr4A 35566065 35569561 3496 True 4708.0 4708 90.973 150 3683 1 chr4A.!!$R2 3533
3 TraesCS4D01G263000 chr4A 35476455 35478007 1552 True 1105.0 1105 79.924 1036 2592 1 chr4A.!!$R1 1556
4 TraesCS4D01G263000 chr4B 532717112 532721318 4206 True 2418.5 4281 94.952 492 3677 2 chr4B.!!$R3 3185
5 TraesCS4D01G263000 chr4B 532581247 532582805 1558 True 1142.0 1142 80.227 1031 2592 1 chr4B.!!$R2 1561
6 TraesCS4D01G263000 chr1A 580988492 580989841 1349 False 396.0 396 72.682 1236 2594 1 chr1A.!!$F1 1358
7 TraesCS4D01G263000 chr1D 483972824 483973770 946 False 388.0 388 74.615 1236 2191 1 chr1D.!!$F1 955
8 TraesCS4D01G263000 chr1B 673992409 673993758 1349 False 385.0 385 72.498 1236 2594 1 chr1B.!!$F1 1358
9 TraesCS4D01G263000 chr5A 621539636 621540174 538 True 265.0 265 76.000 1247 1785 1 chr5A.!!$R1 538

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
61 62 0.027324 GCTTGCTATGCTCGTCTTGC 59.973 55.0 0.00 0.0 0.00 4.01 F
257 258 0.099968 TCTACGCCGAAACTCCATCG 59.900 55.0 0.00 0.0 39.92 3.84 F
529 536 0.323908 AGGTGAGGAAGACGAGAGGG 60.324 60.0 0.00 0.0 0.00 4.30 F
1179 1201 0.740868 CACCGTGCATGAAGGTCGAT 60.741 55.0 7.72 0.0 33.51 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1154 1173 0.321210 CTTCATGCACGGTGGTGGTA 60.321 55.000 10.60 0.0 44.54 3.25 R
1299 1333 1.459455 CGGCCAGGATCTCGATCTGT 61.459 60.000 2.24 0.0 37.92 3.41 R
2609 2672 4.318021 CGTCGTGGTCGGTGTCGT 62.318 66.667 0.00 0.0 37.69 4.34 R
2801 2874 0.101939 CGGTCCCTACGTCCTAAAGC 59.898 60.000 0.00 0.0 0.00 3.51 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
18 19 2.273908 AGTAGACGAACATGGGCGT 58.726 52.632 13.78 13.78 44.33 5.68
19 20 0.108804 AGTAGACGAACATGGGCGTG 60.109 55.000 17.86 0.00 41.34 5.34
20 21 1.447140 TAGACGAACATGGGCGTGC 60.447 57.895 17.86 10.45 41.34 5.34
21 22 2.845752 TAGACGAACATGGGCGTGCC 62.846 60.000 17.86 1.16 41.34 5.01
22 23 4.634703 ACGAACATGGGCGTGCCA 62.635 61.111 13.76 0.00 39.56 4.92
23 24 3.803082 CGAACATGGGCGTGCCAG 61.803 66.667 13.76 4.50 37.98 4.85
24 25 4.120331 GAACATGGGCGTGCCAGC 62.120 66.667 13.76 0.00 37.98 4.85
41 42 3.732849 CCACCAAGGCCTCCTCCC 61.733 72.222 5.23 0.00 30.89 4.30
42 43 4.101448 CACCAAGGCCTCCTCCCG 62.101 72.222 5.23 0.00 30.89 5.14
45 46 3.721706 CAAGGCCTCCTCCCGCTT 61.722 66.667 5.23 0.00 30.89 4.68
46 47 3.721706 AAGGCCTCCTCCCGCTTG 61.722 66.667 5.23 0.00 30.89 4.01
49 50 3.470888 GCCTCCTCCCGCTTGCTA 61.471 66.667 0.00 0.00 0.00 3.49
50 51 2.812619 GCCTCCTCCCGCTTGCTAT 61.813 63.158 0.00 0.00 0.00 2.97
51 52 1.070445 CCTCCTCCCGCTTGCTATG 59.930 63.158 0.00 0.00 0.00 2.23
52 53 1.596477 CTCCTCCCGCTTGCTATGC 60.596 63.158 0.00 0.00 0.00 3.14
53 54 2.037620 CTCCTCCCGCTTGCTATGCT 62.038 60.000 0.00 0.00 0.00 3.79
54 55 1.596477 CCTCCCGCTTGCTATGCTC 60.596 63.158 0.00 0.00 0.00 4.26
55 56 1.953138 CTCCCGCTTGCTATGCTCG 60.953 63.158 0.00 0.00 0.00 5.03
56 57 2.202932 CCCGCTTGCTATGCTCGT 60.203 61.111 0.00 0.00 0.00 4.18
57 58 2.240500 CCCGCTTGCTATGCTCGTC 61.241 63.158 0.00 0.00 0.00 4.20
58 59 1.227089 CCGCTTGCTATGCTCGTCT 60.227 57.895 0.00 0.00 0.00 4.18
59 60 0.807667 CCGCTTGCTATGCTCGTCTT 60.808 55.000 0.00 0.00 0.00 3.01
60 61 0.299895 CGCTTGCTATGCTCGTCTTG 59.700 55.000 0.00 0.00 0.00 3.02
61 62 0.027324 GCTTGCTATGCTCGTCTTGC 59.973 55.000 0.00 0.00 0.00 4.01
62 63 0.299895 CTTGCTATGCTCGTCTTGCG 59.700 55.000 0.00 0.00 43.01 4.85
63 64 1.695893 TTGCTATGCTCGTCTTGCGC 61.696 55.000 0.00 0.00 41.07 6.09
64 65 2.167219 GCTATGCTCGTCTTGCGCA 61.167 57.895 5.66 5.66 41.07 6.09
65 66 1.633171 CTATGCTCGTCTTGCGCAC 59.367 57.895 11.12 0.00 41.07 5.34
66 67 2.070890 CTATGCTCGTCTTGCGCACG 62.071 60.000 11.12 11.78 41.07 5.34
86 87 2.429907 CGAGCTCCGCATCGATCC 60.430 66.667 8.47 0.00 41.40 3.36
87 88 2.048690 GAGCTCCGCATCGATCCC 60.049 66.667 0.87 0.00 0.00 3.85
88 89 3.905705 GAGCTCCGCATCGATCCCG 62.906 68.421 0.87 1.01 37.07 5.14
89 90 4.286320 GCTCCGCATCGATCCCGT 62.286 66.667 12.37 0.00 37.05 5.28
90 91 2.049985 CTCCGCATCGATCCCGTC 60.050 66.667 12.37 0.00 37.05 4.79
91 92 3.559657 CTCCGCATCGATCCCGTCC 62.560 68.421 12.37 0.00 37.05 4.79
92 93 3.911698 CCGCATCGATCCCGTCCA 61.912 66.667 12.37 0.00 37.05 4.02
93 94 2.340078 CGCATCGATCCCGTCCAT 59.660 61.111 0.00 0.00 37.05 3.41
94 95 2.023771 CGCATCGATCCCGTCCATG 61.024 63.158 0.00 0.00 37.05 3.66
95 96 1.367471 GCATCGATCCCGTCCATGA 59.633 57.895 0.00 0.00 37.05 3.07
96 97 0.946221 GCATCGATCCCGTCCATGAC 60.946 60.000 0.00 0.00 37.05 3.06
118 119 3.060000 GCGCGGGGCTAAGGTTTT 61.060 61.111 8.83 0.00 39.11 2.43
119 120 2.632544 GCGCGGGGCTAAGGTTTTT 61.633 57.895 8.83 0.00 39.11 1.94
139 140 2.025589 TTTTACGTGTGCCACAGTCA 57.974 45.000 0.00 0.00 33.40 3.41
140 141 2.025589 TTTACGTGTGCCACAGTCAA 57.974 45.000 0.00 0.00 33.40 3.18
141 142 1.292061 TTACGTGTGCCACAGTCAAC 58.708 50.000 0.00 0.00 33.40 3.18
142 143 0.872451 TACGTGTGCCACAGTCAACG 60.872 55.000 0.00 0.00 33.40 4.10
143 144 2.327940 GTGTGCCACAGTCAACGC 59.672 61.111 0.00 0.00 34.08 4.84
144 145 2.180204 GTGTGCCACAGTCAACGCT 61.180 57.895 0.00 0.00 34.08 5.07
145 146 2.179547 TGTGCCACAGTCAACGCTG 61.180 57.895 0.00 0.00 41.92 5.18
147 148 1.451207 TGCCACAGTCAACGCTGTT 60.451 52.632 0.00 0.00 46.45 3.16
148 149 1.009675 GCCACAGTCAACGCTGTTG 60.010 57.895 13.09 13.09 46.45 3.33
164 165 3.841643 CTGTTGAACCCTTGCATTGATC 58.158 45.455 0.00 0.00 0.00 2.92
170 171 2.097825 ACCCTTGCATTGATCTGAAGC 58.902 47.619 0.00 0.00 0.00 3.86
188 189 1.701847 AGCACCTGACACCAAATCTCT 59.298 47.619 0.00 0.00 0.00 3.10
194 195 3.499918 CCTGACACCAAATCTCTTCACAC 59.500 47.826 0.00 0.00 0.00 3.82
198 199 3.748048 ACACCAAATCTCTTCACACGATG 59.252 43.478 0.00 0.00 0.00 3.84
199 200 3.125829 CACCAAATCTCTTCACACGATGG 59.874 47.826 0.00 0.00 0.00 3.51
200 201 3.007940 ACCAAATCTCTTCACACGATGGA 59.992 43.478 0.00 0.00 0.00 3.41
205 206 3.399330 TCTCTTCACACGATGGAAAACC 58.601 45.455 0.00 0.00 0.00 3.27
214 215 2.277084 CGATGGAAAACCCTAACCTCG 58.723 52.381 0.00 0.00 35.38 4.63
215 216 2.014857 GATGGAAAACCCTAACCTCGC 58.985 52.381 0.00 0.00 35.38 5.03
234 235 0.839946 CCACCCCAAGGAGATGGTAG 59.160 60.000 0.00 0.00 38.91 3.18
243 244 4.021894 CCAAGGAGATGGTAGGAATCTACG 60.022 50.000 0.00 0.00 45.10 3.51
246 247 1.887198 AGATGGTAGGAATCTACGCCG 59.113 52.381 0.00 0.00 45.10 6.46
247 248 1.884579 GATGGTAGGAATCTACGCCGA 59.115 52.381 0.00 0.00 45.10 5.54
248 249 1.766494 TGGTAGGAATCTACGCCGAA 58.234 50.000 0.00 0.00 45.10 4.30
252 253 2.580966 AGGAATCTACGCCGAAACTC 57.419 50.000 0.00 0.00 0.00 3.01
254 255 1.134907 GGAATCTACGCCGAAACTCCA 60.135 52.381 0.00 0.00 0.00 3.86
257 258 0.099968 TCTACGCCGAAACTCCATCG 59.900 55.000 0.00 0.00 39.92 3.84
263 264 1.823828 CCGAAACTCCATCGACTACG 58.176 55.000 0.00 0.00 42.76 3.51
266 267 2.790468 CGAAACTCCATCGACTACGTCC 60.790 54.545 0.00 0.00 42.76 4.79
271 272 1.887854 TCCATCGACTACGTCCAAACA 59.112 47.619 0.00 0.00 40.69 2.83
272 273 2.296752 TCCATCGACTACGTCCAAACAA 59.703 45.455 0.00 0.00 40.69 2.83
278 279 4.209703 TCGACTACGTCCAAACAAATGAAC 59.790 41.667 0.00 0.00 40.69 3.18
286 287 6.645415 ACGTCCAAACAAATGAACTAGAGTAG 59.355 38.462 0.00 0.00 0.00 2.57
290 291 8.383175 TCCAAACAAATGAACTAGAGTAGGATT 58.617 33.333 0.00 0.00 0.00 3.01
291 292 8.454106 CCAAACAAATGAACTAGAGTAGGATTG 58.546 37.037 0.00 0.00 0.00 2.67
296 297 3.961408 TGAACTAGAGTAGGATTGGAGCC 59.039 47.826 0.00 0.00 0.00 4.70
324 325 7.857885 AGAAGACAAATTCAATGAAGAAACGTC 59.142 33.333 1.10 4.18 0.00 4.34
325 326 7.026631 AGACAAATTCAATGAAGAAACGTCA 57.973 32.000 1.10 0.00 31.70 4.35
329 330 4.545823 TTCAATGAAGAAACGTCACCAC 57.454 40.909 0.00 0.00 0.00 4.16
330 331 2.875933 TCAATGAAGAAACGTCACCACC 59.124 45.455 0.00 0.00 0.00 4.61
333 334 1.838568 GAAGAAACGTCACCACCCGC 61.839 60.000 0.00 0.00 0.00 6.13
360 361 1.164411 CCGCACATGCAAGGACTAAA 58.836 50.000 4.49 0.00 42.21 1.85
401 407 8.747538 ACTAATAACAAAAGGTAAGGCATAGG 57.252 34.615 0.00 0.00 0.00 2.57
402 408 8.333984 ACTAATAACAAAAGGTAAGGCATAGGT 58.666 33.333 0.00 0.00 0.00 3.08
414 420 3.681311 AGGCATAGGTATTTCCCTTCCT 58.319 45.455 0.00 0.00 35.97 3.36
419 425 1.285078 AGGTATTTCCCTTCCTGCCAC 59.715 52.381 0.00 0.00 36.75 5.01
422 428 1.497309 ATTTCCCTTCCTGCCACCGA 61.497 55.000 0.00 0.00 0.00 4.69
424 430 4.410400 CCCTTCCTGCCACCGACC 62.410 72.222 0.00 0.00 0.00 4.79
446 452 3.695606 GAGCGGCAGACACAGGGA 61.696 66.667 1.45 0.00 0.00 4.20
447 453 3.655810 GAGCGGCAGACACAGGGAG 62.656 68.421 1.45 0.00 0.00 4.30
448 454 3.695606 GCGGCAGACACAGGGAGA 61.696 66.667 0.00 0.00 0.00 3.71
449 455 3.023949 GCGGCAGACACAGGGAGAT 62.024 63.158 0.00 0.00 0.00 2.75
450 456 1.153489 CGGCAGACACAGGGAGATG 60.153 63.158 0.00 0.00 0.00 2.90
451 457 1.607801 CGGCAGACACAGGGAGATGA 61.608 60.000 0.00 0.00 0.00 2.92
453 459 1.211457 GGCAGACACAGGGAGATGAAT 59.789 52.381 0.00 0.00 0.00 2.57
454 460 2.559440 GCAGACACAGGGAGATGAATC 58.441 52.381 0.00 0.00 0.00 2.52
456 462 2.502947 CAGACACAGGGAGATGAATCCA 59.497 50.000 0.00 0.00 41.52 3.41
457 463 3.136077 CAGACACAGGGAGATGAATCCAT 59.864 47.826 0.00 0.00 41.52 3.41
460 466 2.581216 CAGGGAGATGAATCCATGGG 57.419 55.000 13.02 0.00 45.31 4.00
463 470 1.271817 GGGAGATGAATCCATGGGCTC 60.272 57.143 13.02 9.41 41.52 4.70
475 482 4.699522 GGGCTCGCCGGTGAAGTT 62.700 66.667 20.06 0.00 36.85 2.66
477 484 2.556287 GCTCGCCGGTGAAGTTTG 59.444 61.111 20.06 8.03 0.00 2.93
481 488 1.301401 CGCCGGTGAAGTTTGGAGA 60.301 57.895 10.20 0.00 0.00 3.71
482 489 1.291877 CGCCGGTGAAGTTTGGAGAG 61.292 60.000 10.20 0.00 0.00 3.20
483 490 0.955919 GCCGGTGAAGTTTGGAGAGG 60.956 60.000 1.90 0.00 0.00 3.69
485 492 1.338200 CCGGTGAAGTTTGGAGAGGAG 60.338 57.143 0.00 0.00 0.00 3.69
501 508 0.548510 GGAGAGTTTGCCCTAGCCAT 59.451 55.000 0.00 0.00 38.69 4.40
502 509 1.064389 GGAGAGTTTGCCCTAGCCATT 60.064 52.381 0.00 0.00 38.69 3.16
520 527 4.781934 CCATTTAGGGTTAGGTGAGGAAG 58.218 47.826 0.00 0.00 0.00 3.46
529 536 0.323908 AGGTGAGGAAGACGAGAGGG 60.324 60.000 0.00 0.00 0.00 4.30
532 539 2.756283 AGGAAGACGAGAGGGCCG 60.756 66.667 0.00 0.00 0.00 6.13
556 563 7.270047 CGGGAACAACATATACTTCTTCCTTA 58.730 38.462 0.00 0.00 0.00 2.69
570 577 6.660949 ACTTCTTCCTTAGGTCATTGATTTGG 59.339 38.462 0.00 0.00 0.00 3.28
655 662 5.234543 CACTCTATACATCTGAGAACGACGA 59.765 44.000 0.00 0.00 0.00 4.20
657 664 2.800694 TACATCTGAGAACGACGACG 57.199 50.000 5.58 5.58 45.75 5.12
663 670 4.353437 AGAACGACGACGGCCCAC 62.353 66.667 12.58 0.00 44.46 4.61
704 712 4.026640 TCGAATACGTAAATTTGCCGCTAC 60.027 41.667 0.00 0.00 40.69 3.58
739 750 1.639298 ATTGCTTCCGCTCTCGTTGC 61.639 55.000 0.00 0.00 36.97 4.17
994 1008 3.036429 ATCTCCAAGCCGAGCACCC 62.036 63.158 0.00 0.00 0.00 4.61
1154 1173 4.697352 ACGTGCATTTTCAGCTAGATCTTT 59.303 37.500 0.00 0.00 0.00 2.52
1178 1200 1.374125 CACCGTGCATGAAGGTCGA 60.374 57.895 7.72 0.00 33.51 4.20
1179 1201 0.740868 CACCGTGCATGAAGGTCGAT 60.741 55.000 7.72 0.00 33.51 3.59
1299 1333 1.272490 GACCTGAAGATCACGGACACA 59.728 52.381 0.00 0.00 0.00 3.72
1734 1768 4.147449 CTCGCCATGCCGGAGTCA 62.147 66.667 5.05 0.00 36.56 3.41
2609 2672 1.080093 GCAAGGACATGGACGACGA 60.080 57.895 0.00 0.00 0.00 4.20
2618 2681 3.716006 GGACGACGACGACACCGA 61.716 66.667 15.32 0.00 42.66 4.69
2619 2682 2.498466 GACGACGACGACACCGAC 60.498 66.667 15.32 0.00 42.66 4.79
2620 2683 3.918114 GACGACGACGACACCGACC 62.918 68.421 15.32 0.00 42.66 4.79
2741 2805 0.801836 GTGCTTGTGTTGTGTGTGGC 60.802 55.000 0.00 0.00 0.00 5.01
2742 2806 1.226945 GCTTGTGTTGTGTGTGGCC 60.227 57.895 0.00 0.00 0.00 5.36
2743 2807 1.063972 CTTGTGTTGTGTGTGGCCG 59.936 57.895 0.00 0.00 0.00 6.13
2745 2809 2.826738 GTGTTGTGTGTGGCCGGT 60.827 61.111 1.90 0.00 0.00 5.28
2748 2812 3.798511 TTGTGTGTGGCCGGTCCA 61.799 61.111 12.86 12.86 44.18 4.02
2797 2870 2.480419 CTGGACACGTTGGTCAGATTTC 59.520 50.000 8.15 0.00 39.59 2.17
2801 2874 1.806542 CACGTTGGTCAGATTTCCAGG 59.193 52.381 0.00 0.00 35.05 4.45
2818 2891 1.136500 CAGGCTTTAGGACGTAGGGAC 59.864 57.143 0.00 0.00 0.00 4.46
2819 2892 0.463204 GGCTTTAGGACGTAGGGACC 59.537 60.000 0.00 0.00 0.00 4.46
2880 2953 1.765161 CGCACGCGTGATGAATCCAT 61.765 55.000 41.19 0.00 33.28 3.41
2891 2967 5.586243 CGTGATGAATCCATGTAGAAAGGTT 59.414 40.000 0.00 0.00 32.09 3.50
3040 3124 5.342525 GCTTGTGTTATATATGACCGAGTCG 59.657 44.000 5.29 5.29 34.95 4.18
3054 3138 2.276201 CGAGTCGTCTCTGATCTCTGT 58.724 52.381 3.82 0.00 38.45 3.41
3121 3205 8.993121 CATCTCTGTACTTTTGCTTCTTCTAAA 58.007 33.333 0.00 0.00 0.00 1.85
3122 3206 8.958119 TCTCTGTACTTTTGCTTCTTCTAAAA 57.042 30.769 0.00 0.00 0.00 1.52
3288 4413 7.815068 AGTTCAGCTTGTAATAACTGAGTAGTG 59.185 37.037 0.00 0.00 40.08 2.74
3294 4419 9.635520 GCTTGTAATAACTGAGTAGTGTAGAAA 57.364 33.333 0.00 0.00 37.19 2.52
3301 4426 6.137794 ACTGAGTAGTGTAGAAATCATCCG 57.862 41.667 0.00 0.00 35.34 4.18
3334 4459 3.826729 ACTCTTTTGGCCCACTAATGAAC 59.173 43.478 0.00 0.00 0.00 3.18
3350 4475 5.443185 AATGAACAGGTGATGAGTTGTTG 57.557 39.130 0.00 0.00 34.18 3.33
3399 4524 3.068560 TGTTTATGTGTGCCTACCGAAC 58.931 45.455 0.00 0.00 0.00 3.95
3401 4526 0.173935 TATGTGTGCCTACCGAACCG 59.826 55.000 0.00 0.00 0.00 4.44
3417 4542 3.555518 GAACCGAGACAAACATTGAAGC 58.444 45.455 0.00 0.00 0.00 3.86
3473 4598 1.790623 CTTGTCGACCTTTGTACACGG 59.209 52.381 14.12 1.45 0.00 4.94
3500 4625 7.624134 GCAACTTGAAGAAAAAGAAAAACCTGG 60.624 37.037 0.00 0.00 0.00 4.45
3517 4642 3.508402 ACCTGGTGTTTTGTTTCTTTCGT 59.492 39.130 0.00 0.00 0.00 3.85
3531 4658 9.574458 TTGTTTCTTTCGTGAAATAATGTGAAA 57.426 25.926 0.00 0.00 38.09 2.69
3533 4660 9.993881 GTTTCTTTCGTGAAATAATGTGAAATG 57.006 29.630 7.82 0.00 38.09 2.32
3537 4664 9.605955 CTTTCGTGAAATAATGTGAAATGTGTA 57.394 29.630 0.00 0.00 0.00 2.90
3598 4726 2.475111 AGTTCGTAACGCTGAACATGTG 59.525 45.455 0.00 0.00 45.34 3.21
3603 4731 0.586319 AACGCTGAACATGTGAACGG 59.414 50.000 0.00 0.65 0.00 4.44
3678 4806 5.532557 TGTTGATATCTTAGATGAGCCACG 58.467 41.667 4.78 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.108804 CACGCCCATGTTCGTCTACT 60.109 55.000 6.53 0.00 36.73 2.57
1 2 1.693083 GCACGCCCATGTTCGTCTAC 61.693 60.000 6.53 0.00 36.73 2.59
2 3 1.447140 GCACGCCCATGTTCGTCTA 60.447 57.895 6.53 0.00 36.73 2.59
3 4 2.742372 GCACGCCCATGTTCGTCT 60.742 61.111 6.53 0.00 36.73 4.18
4 5 3.799755 GGCACGCCCATGTTCGTC 61.800 66.667 6.53 3.35 36.73 4.20
5 6 4.634703 TGGCACGCCCATGTTCGT 62.635 61.111 5.42 3.98 39.18 3.85
6 7 3.803082 CTGGCACGCCCATGTTCG 61.803 66.667 5.42 2.79 44.33 3.95
7 8 4.120331 GCTGGCACGCCCATGTTC 62.120 66.667 5.42 0.00 44.33 3.18
24 25 3.732849 GGGAGGAGGCCTTGGTGG 61.733 72.222 6.77 0.00 31.76 4.61
25 26 4.101448 CGGGAGGAGGCCTTGGTG 62.101 72.222 6.77 0.00 31.76 4.17
28 29 3.721706 AAGCGGGAGGAGGCCTTG 61.722 66.667 6.77 0.00 31.76 3.61
29 30 3.721706 CAAGCGGGAGGAGGCCTT 61.722 66.667 6.77 0.00 31.76 4.35
32 33 2.812619 ATAGCAAGCGGGAGGAGGC 61.813 63.158 0.00 0.00 0.00 4.70
33 34 1.070445 CATAGCAAGCGGGAGGAGG 59.930 63.158 0.00 0.00 0.00 4.30
34 35 1.596477 GCATAGCAAGCGGGAGGAG 60.596 63.158 0.00 0.00 0.00 3.69
35 36 2.032860 GAGCATAGCAAGCGGGAGGA 62.033 60.000 0.00 0.00 37.01 3.71
36 37 1.596477 GAGCATAGCAAGCGGGAGG 60.596 63.158 0.00 0.00 37.01 4.30
37 38 1.953138 CGAGCATAGCAAGCGGGAG 60.953 63.158 0.00 0.00 37.01 4.30
38 39 2.106938 CGAGCATAGCAAGCGGGA 59.893 61.111 0.00 0.00 37.01 5.14
39 40 2.202932 ACGAGCATAGCAAGCGGG 60.203 61.111 0.00 0.00 37.01 6.13
40 41 0.807667 AAGACGAGCATAGCAAGCGG 60.808 55.000 0.00 0.00 37.01 5.52
41 42 0.299895 CAAGACGAGCATAGCAAGCG 59.700 55.000 0.00 0.00 37.01 4.68
42 43 0.027324 GCAAGACGAGCATAGCAAGC 59.973 55.000 0.00 0.00 0.00 4.01
45 46 2.834034 TGCGCAAGACGAGCATAGCA 62.834 55.000 8.16 0.00 46.30 3.49
46 47 2.167219 TGCGCAAGACGAGCATAGC 61.167 57.895 8.16 0.00 46.30 2.97
47 48 4.093115 TGCGCAAGACGAGCATAG 57.907 55.556 8.16 0.00 46.30 2.23
73 74 2.049985 GACGGGATCGATGCGGAG 60.050 66.667 27.00 15.66 40.11 4.63
74 75 3.602677 GGACGGGATCGATGCGGA 61.603 66.667 27.00 0.00 40.11 5.54
75 76 3.226429 ATGGACGGGATCGATGCGG 62.226 63.158 20.37 20.37 40.11 5.69
76 77 2.023771 CATGGACGGGATCGATGCG 61.024 63.158 11.02 8.78 36.82 4.73
77 78 0.946221 GTCATGGACGGGATCGATGC 60.946 60.000 8.63 8.63 41.90 3.91
78 79 3.201342 GTCATGGACGGGATCGATG 57.799 57.895 0.54 0.00 43.13 3.84
101 102 2.632544 AAAAACCTTAGCCCCGCGC 61.633 57.895 0.00 0.00 37.98 6.86
102 103 3.676216 AAAAACCTTAGCCCCGCG 58.324 55.556 0.00 0.00 0.00 6.46
127 128 2.179547 CAGCGTTGACTGTGGCACA 61.180 57.895 20.76 20.76 32.78 4.57
128 129 2.633657 CAGCGTTGACTGTGGCAC 59.366 61.111 11.55 11.55 32.78 5.01
134 135 0.307760 GGGTTCAACAGCGTTGACTG 59.692 55.000 19.07 2.99 43.59 3.51
135 136 0.180406 AGGGTTCAACAGCGTTGACT 59.820 50.000 19.07 12.62 0.00 3.41
136 137 1.021968 AAGGGTTCAACAGCGTTGAC 58.978 50.000 19.07 14.76 29.85 3.18
137 138 1.021202 CAAGGGTTCAACAGCGTTGA 58.979 50.000 16.54 16.54 46.95 3.18
138 139 0.594796 GCAAGGGTTCAACAGCGTTG 60.595 55.000 13.09 13.09 46.79 4.10
139 140 1.034838 TGCAAGGGTTCAACAGCGTT 61.035 50.000 0.00 0.00 0.00 4.84
140 141 0.823356 ATGCAAGGGTTCAACAGCGT 60.823 50.000 0.00 0.00 0.00 5.07
141 142 0.314935 AATGCAAGGGTTCAACAGCG 59.685 50.000 0.00 0.00 0.00 5.18
142 143 1.340889 TCAATGCAAGGGTTCAACAGC 59.659 47.619 0.00 0.00 0.00 4.40
143 144 3.508793 AGATCAATGCAAGGGTTCAACAG 59.491 43.478 0.00 0.00 0.00 3.16
144 145 3.256383 CAGATCAATGCAAGGGTTCAACA 59.744 43.478 0.00 0.00 0.00 3.33
145 146 3.507233 TCAGATCAATGCAAGGGTTCAAC 59.493 43.478 0.00 0.00 0.00 3.18
146 147 3.765381 TCAGATCAATGCAAGGGTTCAA 58.235 40.909 0.00 0.00 0.00 2.69
147 148 3.438216 TCAGATCAATGCAAGGGTTCA 57.562 42.857 0.00 0.00 0.00 3.18
148 149 3.428589 GCTTCAGATCAATGCAAGGGTTC 60.429 47.826 0.00 0.00 0.00 3.62
164 165 1.679139 TTTGGTGTCAGGTGCTTCAG 58.321 50.000 0.00 0.00 0.00 3.02
170 171 3.499918 GTGAAGAGATTTGGTGTCAGGTG 59.500 47.826 0.00 0.00 0.00 4.00
188 189 2.649531 AGGGTTTTCCATCGTGTGAA 57.350 45.000 0.00 0.00 42.91 3.18
194 195 2.277084 CGAGGTTAGGGTTTTCCATCG 58.723 52.381 0.00 0.00 42.91 3.84
198 199 0.037160 TGGCGAGGTTAGGGTTTTCC 59.963 55.000 0.00 0.00 39.75 3.13
199 200 1.162698 GTGGCGAGGTTAGGGTTTTC 58.837 55.000 0.00 0.00 0.00 2.29
200 201 0.251033 GGTGGCGAGGTTAGGGTTTT 60.251 55.000 0.00 0.00 0.00 2.43
205 206 2.536997 CTTGGGGTGGCGAGGTTAGG 62.537 65.000 0.00 0.00 0.00 2.69
214 215 1.279025 TACCATCTCCTTGGGGTGGC 61.279 60.000 0.00 0.00 41.35 5.01
215 216 0.839946 CTACCATCTCCTTGGGGTGG 59.160 60.000 0.00 0.00 41.35 4.61
234 235 1.134907 TGGAGTTTCGGCGTAGATTCC 60.135 52.381 6.85 10.21 0.00 3.01
243 244 1.557651 GTAGTCGATGGAGTTTCGGC 58.442 55.000 0.00 0.00 41.35 5.54
263 264 7.159372 TCCTACTCTAGTTCATTTGTTTGGAC 58.841 38.462 0.00 0.00 0.00 4.02
266 267 8.454106 CCAATCCTACTCTAGTTCATTTGTTTG 58.546 37.037 0.00 0.00 0.00 2.93
271 272 6.408662 GGCTCCAATCCTACTCTAGTTCATTT 60.409 42.308 0.00 0.00 0.00 2.32
272 273 5.071115 GGCTCCAATCCTACTCTAGTTCATT 59.929 44.000 0.00 0.00 0.00 2.57
278 279 5.249780 TCTAGGCTCCAATCCTACTCTAG 57.750 47.826 0.00 0.00 35.21 2.43
286 287 3.914426 TTGTCTTCTAGGCTCCAATCC 57.086 47.619 0.00 0.00 0.00 3.01
290 291 4.908601 TGAATTTGTCTTCTAGGCTCCA 57.091 40.909 0.00 0.00 0.00 3.86
291 292 5.882557 TCATTGAATTTGTCTTCTAGGCTCC 59.117 40.000 0.00 0.00 0.00 4.70
296 297 9.322776 CGTTTCTTCATTGAATTTGTCTTCTAG 57.677 33.333 0.00 0.00 0.00 2.43
341 342 1.164411 TTTAGTCCTTGCATGTGCGG 58.836 50.000 0.01 0.00 45.83 5.69
370 371 9.017509 GCCTTACCTTTTGTTATTAGTTTAGGT 57.982 33.333 0.00 0.00 38.28 3.08
376 382 8.333984 ACCTATGCCTTACCTTTTGTTATTAGT 58.666 33.333 0.00 0.00 0.00 2.24
386 392 5.435373 AGGGAAATACCTATGCCTTACCTTT 59.565 40.000 0.00 0.00 39.65 3.11
387 393 4.982302 AGGGAAATACCTATGCCTTACCTT 59.018 41.667 0.00 0.00 39.65 3.50
395 401 3.149981 GCAGGAAGGGAAATACCTATGC 58.850 50.000 1.91 1.91 40.87 3.14
398 404 2.508300 GTGGCAGGAAGGGAAATACCTA 59.492 50.000 0.00 0.00 40.87 3.08
401 407 1.763968 GGTGGCAGGAAGGGAAATAC 58.236 55.000 0.00 0.00 0.00 1.89
402 408 0.254747 CGGTGGCAGGAAGGGAAATA 59.745 55.000 0.00 0.00 0.00 1.40
429 435 3.655810 CTCCCTGTGTCTGCCGCTC 62.656 68.421 0.00 0.00 0.00 5.03
433 439 0.615331 TTCATCTCCCTGTGTCTGCC 59.385 55.000 0.00 0.00 0.00 4.85
434 440 2.559440 GATTCATCTCCCTGTGTCTGC 58.441 52.381 0.00 0.00 0.00 4.26
437 443 3.474600 CATGGATTCATCTCCCTGTGTC 58.525 50.000 0.00 0.00 34.12 3.67
438 444 2.174210 CCATGGATTCATCTCCCTGTGT 59.826 50.000 5.56 0.00 34.12 3.72
439 445 2.488528 CCCATGGATTCATCTCCCTGTG 60.489 54.545 15.22 0.00 34.12 3.66
441 447 1.547223 GCCCATGGATTCATCTCCCTG 60.547 57.143 15.22 0.00 34.12 4.45
446 452 0.250640 GCGAGCCCATGGATTCATCT 60.251 55.000 15.22 0.00 0.00 2.90
447 453 1.239968 GGCGAGCCCATGGATTCATC 61.240 60.000 15.22 2.51 0.00 2.92
448 454 1.228367 GGCGAGCCCATGGATTCAT 60.228 57.895 15.22 0.00 0.00 2.57
449 455 2.192979 GGCGAGCCCATGGATTCA 59.807 61.111 15.22 0.00 0.00 2.57
450 456 2.974698 CGGCGAGCCCATGGATTC 60.975 66.667 15.22 9.34 0.00 2.52
451 457 4.569180 CCGGCGAGCCCATGGATT 62.569 66.667 15.22 0.00 0.00 3.01
456 462 4.473520 CTTCACCGGCGAGCCCAT 62.474 66.667 9.30 0.00 0.00 4.00
458 464 4.699522 AACTTCACCGGCGAGCCC 62.700 66.667 9.30 0.00 0.00 5.19
459 465 2.668550 AAACTTCACCGGCGAGCC 60.669 61.111 9.30 3.59 0.00 4.70
460 466 2.556287 CAAACTTCACCGGCGAGC 59.444 61.111 9.30 0.00 0.00 5.03
463 470 1.291877 CTCTCCAAACTTCACCGGCG 61.292 60.000 0.00 0.00 0.00 6.46
475 482 0.693049 GGGCAAACTCTCCTCTCCAA 59.307 55.000 0.00 0.00 0.00 3.53
477 484 1.760029 CTAGGGCAAACTCTCCTCTCC 59.240 57.143 0.00 0.00 32.46 3.71
481 488 0.547712 TGGCTAGGGCAAACTCTCCT 60.548 55.000 0.00 0.00 40.87 3.69
482 489 0.548510 ATGGCTAGGGCAAACTCTCC 59.451 55.000 0.00 0.00 42.43 3.71
483 490 2.426842 AATGGCTAGGGCAAACTCTC 57.573 50.000 0.00 0.00 42.43 3.20
485 492 2.952310 CCTAAATGGCTAGGGCAAACTC 59.048 50.000 0.00 0.00 42.43 3.01
501 508 3.512724 CGTCTTCCTCACCTAACCCTAAA 59.487 47.826 0.00 0.00 0.00 1.85
502 509 3.094572 CGTCTTCCTCACCTAACCCTAA 58.905 50.000 0.00 0.00 0.00 2.69
507 514 2.424246 CCTCTCGTCTTCCTCACCTAAC 59.576 54.545 0.00 0.00 0.00 2.34
513 520 1.682684 GGCCCTCTCGTCTTCCTCA 60.683 63.158 0.00 0.00 0.00 3.86
520 527 4.144703 GTTCCCGGCCCTCTCGTC 62.145 72.222 0.00 0.00 0.00 4.20
529 536 3.805207 AGAAGTATATGTTGTTCCCGGC 58.195 45.455 0.00 0.00 0.00 6.13
532 539 7.715686 CCTAAGGAAGAAGTATATGTTGTTCCC 59.284 40.741 17.96 7.10 44.65 3.97
556 563 4.235079 TCGATTCCCAAATCAATGACCT 57.765 40.909 0.00 0.00 41.22 3.85
570 577 5.517054 GTCATGAACTAGTGACTTCGATTCC 59.483 44.000 0.00 0.00 41.10 3.01
655 662 0.970427 GGGAAATTGATGTGGGCCGT 60.970 55.000 0.00 0.00 0.00 5.68
657 664 1.499368 ATGGGAAATTGATGTGGGCC 58.501 50.000 0.00 0.00 0.00 5.80
663 670 9.117145 CGTATTCGAATTAATGGGAAATTGATG 57.883 33.333 17.19 0.00 39.71 3.07
704 712 0.247419 CAATAAGTGCACGCTCGCTG 60.247 55.000 12.01 1.86 0.00 5.18
739 750 1.079612 TGCTGGTGATCACTGAGCG 60.080 57.895 29.24 15.83 38.63 5.03
741 752 0.036671 TGCTGCTGGTGATCACTGAG 60.037 55.000 24.50 20.00 0.00 3.35
768 779 2.102588 TCTGCTCGGCCCTCTTTTATAC 59.897 50.000 0.00 0.00 0.00 1.47
930 944 3.651803 AGCTCACTGTCACAGTACTTC 57.348 47.619 10.98 0.36 43.43 3.01
963 977 0.684535 TGGAGATGAGGCGTTTGTGA 59.315 50.000 0.00 0.00 0.00 3.58
994 1008 2.887568 GTCCGTGCTCATGGCGAG 60.888 66.667 3.27 0.00 45.43 5.03
1154 1173 0.321210 CTTCATGCACGGTGGTGGTA 60.321 55.000 10.60 0.00 44.54 3.25
1178 1200 2.691409 ACGTGTTAGCCACAGCATAT 57.309 45.000 0.00 0.00 44.78 1.78
1179 1201 2.465860 AACGTGTTAGCCACAGCATA 57.534 45.000 0.00 0.00 44.78 3.14
1299 1333 1.459455 CGGCCAGGATCTCGATCTGT 61.459 60.000 2.24 0.00 37.92 3.41
2609 2672 4.318021 CGTCGTGGTCGGTGTCGT 62.318 66.667 0.00 0.00 37.69 4.34
2752 2825 3.280295 TCTAGAGATTCACGTCCAGGAC 58.720 50.000 9.92 9.92 0.00 3.85
2797 2870 0.464452 CCCTACGTCCTAAAGCCTGG 59.536 60.000 0.00 0.00 0.00 4.45
2801 2874 0.101939 CGGTCCCTACGTCCTAAAGC 59.898 60.000 0.00 0.00 0.00 3.51
2818 2891 3.449227 TAGAGCGCTGGGTGTCGG 61.449 66.667 18.48 0.00 0.00 4.79
2819 2892 2.202623 GTAGAGCGCTGGGTGTCG 60.203 66.667 18.48 0.00 0.00 4.35
2880 2953 3.116079 GGTGAACCGAACCTTTCTACA 57.884 47.619 0.00 0.00 34.66 2.74
3040 3124 5.719173 AGCAAAAGTACAGAGATCAGAGAC 58.281 41.667 0.00 0.00 0.00 3.36
3054 3138 7.575414 TTAACCAACAGATGAAGCAAAAGTA 57.425 32.000 0.00 0.00 0.00 2.24
3160 4118 6.656902 TCCGAAGTAGAGTAGTCAGGAATTA 58.343 40.000 0.00 0.00 0.00 1.40
3215 4173 7.994894 CGAATTTACGACGATATTAGTTTGTCC 59.005 37.037 0.00 0.00 35.09 4.02
3279 4403 4.979197 GCGGATGATTTCTACACTACTCAG 59.021 45.833 0.00 0.00 0.00 3.35
3288 4413 4.537135 TCATAGGGCGGATGATTTCTAC 57.463 45.455 0.00 0.00 0.00 2.59
3294 4419 4.357325 AGAGTAATCATAGGGCGGATGAT 58.643 43.478 6.87 6.87 44.21 2.45
3301 4426 3.570125 GGCCAAAAGAGTAATCATAGGGC 59.430 47.826 0.00 7.22 36.98 5.19
3334 4459 3.668757 CGAATGCAACAACTCATCACCTG 60.669 47.826 0.00 0.00 0.00 4.00
3385 4510 1.445582 CTCGGTTCGGTAGGCACAC 60.446 63.158 0.00 0.00 0.00 3.82
3399 4524 2.807967 TGAGCTTCAATGTTTGTCTCGG 59.192 45.455 0.00 0.00 0.00 4.63
3401 4526 5.429957 ACTTGAGCTTCAATGTTTGTCTC 57.570 39.130 0.00 0.00 35.59 3.36
3473 4598 6.371548 AGGTTTTTCTTTTTCTTCAAGTTGCC 59.628 34.615 0.00 0.00 0.00 4.52
3500 4625 9.618410 CATTATTTCACGAAAGAAACAAAACAC 57.382 29.630 3.91 0.00 40.03 3.32
3531 4658 5.557514 CGCAAGTGAAAACTACGTTACACAT 60.558 40.000 0.00 5.14 36.36 3.21
3533 4660 4.198584 CGCAAGTGAAAACTACGTTACAC 58.801 43.478 0.00 0.00 35.20 2.90
3537 4664 1.666700 TGCGCAAGTGAAAACTACGTT 59.333 42.857 8.16 0.00 41.68 3.99


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

AutoCloner maintained by Alex Coulton.