Multiple sequence alignment - TraesCS7A01G248200

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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 TraesCS7A01G248200 chr7A 100.000 5602 0 0 1 5602 229205572 229199971 0.000000e+00 10346.0
1 TraesCS7A01G248200 chr7A 89.286 56 6 0 5122 5177 229184309 229184254 2.800000e-08 71.3
2 TraesCS7A01G248200 chr7D 95.529 3579 127 15 1625 5179 216097563 216093994 0.000000e+00 5692.0
3 TraesCS7A01G248200 chr7D 90.564 1632 69 28 4 1624 216099165 216097608 0.000000e+00 2082.0
4 TraesCS7A01G248200 chr7D 90.202 347 23 9 5264 5602 216093829 216093486 5.150000e-120 442.0
5 TraesCS7A01G248200 chr7D 79.697 330 43 9 5177 5500 216092315 216092004 3.400000e-52 217.0
6 TraesCS7A01G248200 chr7B 93.787 1368 70 5 1627 2993 184195398 184196751 0.000000e+00 2041.0
7 TraesCS7A01G248200 chr7B 88.717 1613 98 31 4 1576 184193334 184194902 0.000000e+00 1893.0
8 TraesCS7A01G248200 chr7B 90.164 1464 102 21 3456 4892 184197206 184198654 0.000000e+00 1868.0
9 TraesCS7A01G248200 chr7B 93.939 462 23 3 2966 3427 184196755 184197211 0.000000e+00 693.0
10 TraesCS7A01G248200 chr5D 80.345 290 33 12 260 526 445067115 445067403 1.230000e-46 198.0


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 TraesCS7A01G248200 chr7A 229199971 229205572 5601 True 10346.00 10346 100.00000 1 5602 1 chr7A.!!$R2 5601
1 TraesCS7A01G248200 chr7D 216092004 216099165 7161 True 2108.25 5692 88.99800 4 5602 4 chr7D.!!$R1 5598
2 TraesCS7A01G248200 chr7B 184193334 184198654 5320 False 1623.75 2041 91.65175 4 4892 4 chr7B.!!$F1 4888

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
163 175 0.037590 ACCAGCACAAGCCGGAATTA 59.962 50.000 5.05 0.00 40.99 1.40 F
413 448 0.108945 GTCGGTGTACAGTACCCTGC 60.109 60.000 8.30 1.98 42.81 4.85 F
421 456 0.250467 ACAGTACCCTGCTTGCAGTG 60.250 55.000 19.49 12.09 42.81 3.66 F
1450 1499 1.476085 CGTTTGGGCTGCAAATATGGA 59.524 47.619 0.50 0.00 0.00 3.41 F
2180 2683 1.278127 GGATTGGTTCTTGACGAGGGA 59.722 52.381 0.00 0.00 0.00 4.20 F
3767 4307 3.756434 TCATTTGGTGTACTAAAGCCTGC 59.244 43.478 0.00 0.00 29.96 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1869 2372 0.675083 TTGCGAAGGTTACTCGGACA 59.325 50.000 0.00 0.0 0.00 4.02 R
1870 2373 1.458445 GTTTGCGAAGGTTACTCGGAC 59.542 52.381 0.00 0.0 0.00 4.79 R
2138 2641 3.181503 CCACATTCAGCTCCTTGAATTCG 60.182 47.826 0.04 0.0 43.41 3.34 R
2931 3436 2.029020 TCGGAGAATGGACAGAACACAG 60.029 50.000 0.00 0.0 0.00 3.66 R
4039 4579 1.140312 TGTCAAGGACAGAGCCCTTT 58.860 50.000 0.00 0.0 41.79 3.11 R
5213 5843 0.304705 GACCATCTTATGTTGCGCCG 59.695 55.000 4.18 0.0 0.00 6.46 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
53 54 2.026262 TCTATCCAAGCCAACCAAGACC 60.026 50.000 0.00 0.00 0.00 3.85
69 70 1.206610 AGACCGCGTCTACTAGTCAGA 59.793 52.381 4.92 0.00 41.51 3.27
89 90 0.244994 GACTGAGAAGCCGCAGAAGA 59.755 55.000 3.33 0.00 41.89 2.87
120 121 1.189752 AGCGACACTGAGGACATGAT 58.810 50.000 0.00 0.00 0.00 2.45
143 144 0.599558 CCCCACTACGTTTGAGTCGA 59.400 55.000 0.00 0.00 0.00 4.20
150 151 0.179094 ACGTTTGAGTCGAACCAGCA 60.179 50.000 16.17 0.00 0.00 4.41
157 169 2.664851 TCGAACCAGCACAAGCCG 60.665 61.111 0.00 0.00 43.56 5.52
158 170 3.726517 CGAACCAGCACAAGCCGG 61.727 66.667 0.00 0.00 44.21 6.13
159 171 2.281484 GAACCAGCACAAGCCGGA 60.281 61.111 5.05 0.00 40.99 5.14
160 172 1.896660 GAACCAGCACAAGCCGGAA 60.897 57.895 5.05 0.00 40.99 4.30
161 173 1.228552 AACCAGCACAAGCCGGAAT 60.229 52.632 5.05 0.00 40.99 3.01
162 174 0.827507 AACCAGCACAAGCCGGAATT 60.828 50.000 5.05 0.00 40.99 2.17
163 175 0.037590 ACCAGCACAAGCCGGAATTA 59.962 50.000 5.05 0.00 40.99 1.40
164 176 0.451783 CCAGCACAAGCCGGAATTAC 59.548 55.000 5.05 0.00 40.99 1.89
165 177 1.164411 CAGCACAAGCCGGAATTACA 58.836 50.000 5.05 0.00 43.56 2.41
166 178 1.135689 CAGCACAAGCCGGAATTACAC 60.136 52.381 5.05 0.00 43.56 2.90
167 179 0.170339 GCACAAGCCGGAATTACACC 59.830 55.000 5.05 0.00 33.58 4.16
225 237 0.877649 GCGATCGATCAGCACCACAT 60.878 55.000 26.34 0.00 0.00 3.21
272 285 0.613260 CCCAACGGACTGAGATCCAA 59.387 55.000 0.00 0.00 38.87 3.53
303 321 3.805207 AGTCACCAGTGAAAACAGTACC 58.195 45.455 1.23 0.00 41.85 3.34
322 341 1.903877 CGTGACTTGCCCCTCTCCAT 61.904 60.000 0.00 0.00 0.00 3.41
329 348 1.457831 GCCCCTCTCCATACCGTCT 60.458 63.158 0.00 0.00 0.00 4.18
377 398 4.921515 GCGTGAACAGTACAAGATCTACAA 59.078 41.667 0.00 0.00 0.00 2.41
394 429 2.688507 ACAATGCTCGGTCAACAGTAG 58.311 47.619 0.00 0.00 0.00 2.57
400 435 0.594602 TCGGTCAACAGTAGTCGGTG 59.405 55.000 0.00 0.00 0.00 4.94
412 447 1.542492 AGTCGGTGTACAGTACCCTG 58.458 55.000 8.30 1.87 44.68 4.45
413 448 0.108945 GTCGGTGTACAGTACCCTGC 60.109 60.000 8.30 1.98 42.81 4.85
414 449 0.251474 TCGGTGTACAGTACCCTGCT 60.251 55.000 8.30 0.00 42.81 4.24
418 453 1.052617 TGTACAGTACCCTGCTTGCA 58.947 50.000 8.30 0.00 42.81 4.08
420 455 1.002087 GTACAGTACCCTGCTTGCAGT 59.998 52.381 19.49 7.21 42.81 4.40
421 456 0.250467 ACAGTACCCTGCTTGCAGTG 60.250 55.000 19.49 12.09 42.81 3.66
448 483 4.060900 CTGCTACAGTGTTTGATCTGTGT 58.939 43.478 0.00 0.00 43.46 3.72
450 485 4.058124 GCTACAGTGTTTGATCTGTGTCA 58.942 43.478 0.00 0.00 43.46 3.58
476 512 3.395702 ATCCAACGGCGGGCTACA 61.396 61.111 13.24 0.00 0.00 2.74
545 581 2.569354 GCCCCAACGCACCAAATCA 61.569 57.895 0.00 0.00 0.00 2.57
565 601 4.235762 ACGCGACTGCACCAGGTT 62.236 61.111 15.93 0.00 42.97 3.50
627 665 1.838077 AGGTTAGGGTTTGCTATCGCT 59.162 47.619 1.83 1.83 36.97 4.93
628 666 3.036091 AGGTTAGGGTTTGCTATCGCTA 58.964 45.455 0.11 0.11 36.97 4.26
661 699 2.550208 CCTCGGAAGCAACCTTGTACTT 60.550 50.000 0.00 0.00 0.00 2.24
673 711 7.284489 AGCAACCTTGTACTTCTAATTCACAAA 59.716 33.333 0.00 0.00 0.00 2.83
674 712 7.918562 GCAACCTTGTACTTCTAATTCACAAAA 59.081 33.333 0.00 0.00 0.00 2.44
675 713 9.233232 CAACCTTGTACTTCTAATTCACAAAAC 57.767 33.333 0.00 0.00 0.00 2.43
676 714 8.514330 ACCTTGTACTTCTAATTCACAAAACA 57.486 30.769 0.00 0.00 0.00 2.83
677 715 8.962679 ACCTTGTACTTCTAATTCACAAAACAA 58.037 29.630 0.00 0.00 0.00 2.83
678 716 9.233232 CCTTGTACTTCTAATTCACAAAACAAC 57.767 33.333 0.00 0.00 0.00 3.32
712 750 8.344831 TGCATCTCGGTTATAAATTCAAGATTG 58.655 33.333 0.00 0.00 0.00 2.67
764 802 8.246871 GCTTTCCATTTTCTAGCTAGTTTTCAT 58.753 33.333 20.10 4.59 0.00 2.57
819 857 3.874543 TGTCGTTGTTGCAGAATACAGTT 59.125 39.130 0.00 0.00 0.00 3.16
995 1044 2.093537 GAGGGCTCGATGCGGATTCT 62.094 60.000 0.00 0.00 44.05 2.40
1287 1336 6.183360 CGCTTCCTTCTATACTTCTCAACTCT 60.183 42.308 0.00 0.00 0.00 3.24
1450 1499 1.476085 CGTTTGGGCTGCAAATATGGA 59.524 47.619 0.50 0.00 0.00 3.41
1451 1500 2.101249 CGTTTGGGCTGCAAATATGGAT 59.899 45.455 0.50 0.00 0.00 3.41
1452 1501 3.317711 CGTTTGGGCTGCAAATATGGATA 59.682 43.478 0.50 0.00 0.00 2.59
1453 1502 4.022068 CGTTTGGGCTGCAAATATGGATAT 60.022 41.667 0.50 0.00 0.00 1.63
1454 1503 5.182950 CGTTTGGGCTGCAAATATGGATATA 59.817 40.000 0.50 0.00 0.00 0.86
1455 1504 6.389906 GTTTGGGCTGCAAATATGGATATAC 58.610 40.000 0.50 0.00 0.00 1.47
1456 1505 5.519183 TGGGCTGCAAATATGGATATACT 57.481 39.130 0.50 0.00 0.00 2.12
1457 1506 6.634889 TGGGCTGCAAATATGGATATACTA 57.365 37.500 0.50 0.00 0.00 1.82
1458 1507 7.211897 TGGGCTGCAAATATGGATATACTAT 57.788 36.000 0.50 0.00 0.00 2.12
1459 1508 7.282585 TGGGCTGCAAATATGGATATACTATC 58.717 38.462 0.50 0.00 0.00 2.08
1460 1509 7.092489 TGGGCTGCAAATATGGATATACTATCA 60.092 37.037 0.50 0.00 0.00 2.15
1461 1510 7.443575 GGGCTGCAAATATGGATATACTATCAG 59.556 40.741 0.50 0.00 0.00 2.90
1462 1511 7.989741 GGCTGCAAATATGGATATACTATCAGT 59.010 37.037 0.50 0.00 0.00 3.41
1463 1512 9.388506 GCTGCAAATATGGATATACTATCAGTT 57.611 33.333 0.00 0.00 0.00 3.16
1473 1522 9.273016 TGGATATACTATCAGTTTTGCTAAAGC 57.727 33.333 0.00 0.00 42.50 3.51
1595 2050 6.320926 TGGTTGATTTCAGTGTTCTTTCATCA 59.679 34.615 0.00 0.00 0.00 3.07
1670 2169 5.066375 CCAATCACAGTGTTCTCTTTTGTCA 59.934 40.000 0.00 0.00 0.00 3.58
1687 2186 9.500785 TCTTTTGTCACTATTGATGATGTTGTA 57.499 29.630 0.00 0.00 33.11 2.41
1869 2372 7.594351 ATGTATGGCTCGATATACATGATCT 57.406 36.000 20.28 5.94 44.51 2.75
1870 2373 6.799512 TGTATGGCTCGATATACATGATCTG 58.200 40.000 0.00 0.00 35.48 2.90
1878 2381 6.403878 TCGATATACATGATCTGTCCGAGTA 58.596 40.000 0.00 0.00 39.39 2.59
2138 2641 4.340894 TGAGCTATTTGTTGCATCGAAC 57.659 40.909 0.00 0.00 0.00 3.95
2174 2677 3.826157 TGAATGTGGGATTGGTTCTTGAC 59.174 43.478 0.00 0.00 0.00 3.18
2180 2683 1.278127 GGATTGGTTCTTGACGAGGGA 59.722 52.381 0.00 0.00 0.00 4.20
2476 2979 5.240623 CCAAGTTCCTGTTTACAATGTGCTA 59.759 40.000 0.00 0.00 0.00 3.49
2477 2980 6.071952 CCAAGTTCCTGTTTACAATGTGCTAT 60.072 38.462 0.00 0.00 0.00 2.97
2597 3100 9.753674 TGATGTCCTTTTTCTTGATTAACCTAT 57.246 29.630 0.00 0.00 0.00 2.57
2911 3416 9.826574 TTTAGAATTACCATAGTTAATCACGCT 57.173 29.630 0.00 0.00 0.00 5.07
2912 3417 9.826574 TTAGAATTACCATAGTTAATCACGCTT 57.173 29.630 0.00 0.00 0.00 4.68
2913 3418 8.142994 AGAATTACCATAGTTAATCACGCTTG 57.857 34.615 0.00 0.00 0.00 4.01
2931 3436 4.061596 GCTTGCATAGGACCTGATACTTC 58.938 47.826 3.53 0.00 0.00 3.01
2949 3454 4.636249 ACTTCTGTGTTCTGTCCATTCTC 58.364 43.478 0.00 0.00 0.00 2.87
3416 3952 9.851686 TGTGGAGAGCTTACATTATATTTGATT 57.148 29.630 0.00 0.00 0.00 2.57
3767 4307 3.756434 TCATTTGGTGTACTAAAGCCTGC 59.244 43.478 0.00 0.00 29.96 4.85
3836 4376 7.599630 ACAAATACTTTAAAGGCAATGCATG 57.400 32.000 19.14 11.21 0.00 4.06
4133 4673 5.173774 TGTGTTTGAAGAATCTGTGAAGC 57.826 39.130 0.00 0.00 0.00 3.86
4324 4873 2.880890 AGCCATCAACTTATCCGATTGC 59.119 45.455 0.00 0.00 0.00 3.56
4379 4928 1.459592 GACACATCAACGTGCACCTAC 59.540 52.381 12.15 0.00 40.73 3.18
4391 4940 1.893137 TGCACCTACAGTACCTGACAG 59.107 52.381 0.00 0.00 35.18 3.51
4394 4943 3.353557 CACCTACAGTACCTGACAGCTA 58.646 50.000 0.00 0.00 35.18 3.32
4595 5149 0.331954 ACGAGGAGTCTAGGGCAGAA 59.668 55.000 0.00 0.00 34.17 3.02
4627 5187 3.397482 AGATGATCTTATCTTGCCACGC 58.603 45.455 0.00 0.00 33.74 5.34
4644 5204 0.389166 CGCCGGATATCTTGCCTCTC 60.389 60.000 5.05 0.00 0.00 3.20
4655 5216 2.505118 GCCTCTCGACGTGCAGTC 60.505 66.667 0.00 0.00 46.16 3.51
4675 5236 3.246936 GTCGTAACGCAGAAGAAGGTTTT 59.753 43.478 0.00 0.00 0.00 2.43
4677 5238 3.606153 CGTAACGCAGAAGAAGGTTTTGG 60.606 47.826 0.00 0.00 0.00 3.28
4706 5268 1.667830 TTCTGTTTCTGCTCCGGCG 60.668 57.895 0.00 0.00 42.25 6.46
4794 5359 1.478510 ACTGCATCTGTAGTTCCTCCG 59.521 52.381 0.00 0.00 37.74 4.63
4819 5384 7.201274 CGCATATTGTACGAGTAATGACATCTC 60.201 40.741 0.00 0.00 0.00 2.75
4826 5391 9.333724 TGTACGAGTAATGACATCTCTGTATAA 57.666 33.333 0.00 0.31 35.14 0.98
4854 5419 2.726821 AGTGATGGCATTTCATCCGTT 58.273 42.857 0.00 0.00 41.97 4.44
4870 5435 5.179368 TCATCCGTTGTTCATCAGTTCTTTC 59.821 40.000 0.00 0.00 0.00 2.62
4874 5439 5.237344 CCGTTGTTCATCAGTTCTTTCTCTT 59.763 40.000 0.00 0.00 0.00 2.85
4879 5444 5.551305 TCATCAGTTCTTTCTCTTGGTGA 57.449 39.130 0.00 0.00 0.00 4.02
4883 5448 2.439507 AGTTCTTTCTCTTGGTGAGGCA 59.560 45.455 0.00 0.00 42.86 4.75
4884 5449 2.550180 GTTCTTTCTCTTGGTGAGGCAC 59.450 50.000 0.00 0.00 42.86 5.01
4902 5467 2.349886 GCACTTCCTCGCTACTTTGATG 59.650 50.000 0.00 0.00 0.00 3.07
4903 5468 2.349886 CACTTCCTCGCTACTTTGATGC 59.650 50.000 0.00 0.00 0.00 3.91
4914 5479 2.408050 ACTTTGATGCGTCAGTGAGAC 58.592 47.619 17.64 0.00 44.02 3.36
4929 5494 0.318762 GAGACACCGTCCTGAAGCTT 59.681 55.000 0.00 0.00 32.18 3.74
4930 5495 0.759346 AGACACCGTCCTGAAGCTTT 59.241 50.000 0.00 0.00 32.18 3.51
4933 5498 0.868406 CACCGTCCTGAAGCTTTGAC 59.132 55.000 0.00 7.48 0.00 3.18
4973 5538 0.036858 ACGCAGCTCCTCTCTTTTCC 60.037 55.000 0.00 0.00 0.00 3.13
4976 5541 1.284313 CAGCTCCTCTCTTTTCCCCT 58.716 55.000 0.00 0.00 0.00 4.79
4978 5543 0.544223 GCTCCTCTCTTTTCCCCTCC 59.456 60.000 0.00 0.00 0.00 4.30
4980 5545 1.836802 CTCCTCTCTTTTCCCCTCCTG 59.163 57.143 0.00 0.00 0.00 3.86
4999 5564 6.871492 CCTCCTGAAGTTCTCTTTCTTTCTAC 59.129 42.308 4.17 0.00 33.64 2.59
5003 5568 4.875561 AGTTCTCTTTCTTTCTACGCCT 57.124 40.909 0.00 0.00 0.00 5.52
5005 5570 2.960819 TCTCTTTCTTTCTACGCCTGC 58.039 47.619 0.00 0.00 0.00 4.85
5022 5587 4.722193 CCTTGGAAGGCACGACAT 57.278 55.556 0.00 0.00 39.76 3.06
5057 5622 5.673337 TTGTGCACAACAGAGATAAACTC 57.327 39.130 27.96 0.00 45.22 3.01
5074 5639 4.426112 CGCTCGTCTCAGCCTGCA 62.426 66.667 0.00 0.00 35.84 4.41
5099 5670 1.755179 CGCTGGATCAGGTGGAATTT 58.245 50.000 0.00 0.00 31.21 1.82
5104 5675 2.027385 GGATCAGGTGGAATTTCTGGC 58.973 52.381 0.00 0.00 0.00 4.85
5166 5737 0.898326 TACACTGCTCTTGCCCTCGA 60.898 55.000 0.00 0.00 38.71 4.04
5170 5741 3.394836 GCTCTTGCCCTCGACCCT 61.395 66.667 0.00 0.00 0.00 4.34
5191 5821 7.242359 ACCCTCAGCTCAGTGTTATATATAGT 58.758 38.462 0.00 0.00 0.00 2.12
5221 5851 3.249605 GCATCAATGCGGCGCAAC 61.250 61.111 39.46 19.17 43.62 4.17
5234 5864 1.331756 GGCGCAACATAAGATGGTCAG 59.668 52.381 10.83 0.00 33.60 3.51
5236 5866 2.632377 CGCAACATAAGATGGTCAGGT 58.368 47.619 0.00 0.00 33.60 4.00
5237 5867 2.352651 CGCAACATAAGATGGTCAGGTG 59.647 50.000 0.00 0.00 33.60 4.00
5238 5868 3.609853 GCAACATAAGATGGTCAGGTGA 58.390 45.455 0.00 0.00 33.60 4.02
5239 5869 4.202441 GCAACATAAGATGGTCAGGTGAT 58.798 43.478 0.00 0.00 33.60 3.06
5240 5870 4.641989 GCAACATAAGATGGTCAGGTGATT 59.358 41.667 0.00 0.00 33.60 2.57
5241 5871 5.822519 GCAACATAAGATGGTCAGGTGATTA 59.177 40.000 0.00 0.00 33.60 1.75
5244 5874 8.347771 CAACATAAGATGGTCAGGTGATTATTG 58.652 37.037 0.00 0.00 33.60 1.90
5245 5875 6.488006 ACATAAGATGGTCAGGTGATTATTGC 59.512 38.462 0.00 0.00 33.60 3.56
5246 5876 4.508551 AGATGGTCAGGTGATTATTGCA 57.491 40.909 0.00 0.00 0.00 4.08
5247 5877 4.202441 AGATGGTCAGGTGATTATTGCAC 58.798 43.478 0.00 0.00 35.56 4.57
5248 5878 2.355197 TGGTCAGGTGATTATTGCACG 58.645 47.619 0.00 0.00 37.13 5.34
5249 5879 1.670811 GGTCAGGTGATTATTGCACGG 59.329 52.381 0.00 0.00 37.13 4.94
5252 5882 2.746904 TCAGGTGATTATTGCACGGTTG 59.253 45.455 0.00 0.00 37.13 3.77
5253 5883 2.091541 AGGTGATTATTGCACGGTTGG 58.908 47.619 0.00 0.00 37.13 3.77
5254 5884 2.088423 GGTGATTATTGCACGGTTGGA 58.912 47.619 0.00 0.00 37.13 3.53
5256 5886 3.130340 GGTGATTATTGCACGGTTGGATT 59.870 43.478 0.00 0.00 37.13 3.01
5257 5887 4.336993 GGTGATTATTGCACGGTTGGATTA 59.663 41.667 0.00 0.00 37.13 1.75
5258 5888 5.009610 GGTGATTATTGCACGGTTGGATTAT 59.990 40.000 0.00 0.00 37.13 1.28
5259 5889 6.460953 GGTGATTATTGCACGGTTGGATTATT 60.461 38.462 0.00 0.00 37.13 1.40
5260 5890 6.978080 GTGATTATTGCACGGTTGGATTATTT 59.022 34.615 0.00 0.00 0.00 1.40
5261 5891 7.491048 GTGATTATTGCACGGTTGGATTATTTT 59.509 33.333 0.00 0.00 0.00 1.82
5262 5892 8.037758 TGATTATTGCACGGTTGGATTATTTTT 58.962 29.630 0.00 0.00 0.00 1.94
5301 5951 1.625616 CTTGTTACGAGCCACCTACG 58.374 55.000 0.00 0.00 0.00 3.51
5304 5954 1.336148 TGTTACGAGCCACCTACGTTG 60.336 52.381 0.00 0.00 40.61 4.10
5371 6021 1.205064 CTGTGCCGCGAACTCTTTG 59.795 57.895 8.23 0.00 0.00 2.77
5380 6030 2.599848 CGCGAACTCTTTGTCCTTTGTG 60.600 50.000 0.00 0.00 0.00 3.33
5385 6035 4.772886 ACTCTTTGTCCTTTGTGGTAGT 57.227 40.909 0.00 0.00 37.07 2.73
5401 6052 8.809468 TTGTGGTAGTGGCAATTATACAATTA 57.191 30.769 0.00 0.00 32.96 1.40
5495 6150 3.325870 ACATCACGTGTACAACTCCATG 58.674 45.455 16.51 10.66 39.91 3.66
5501 6156 4.512198 CACGTGTACAACTCCATGGTAAAA 59.488 41.667 12.58 0.00 0.00 1.52
5506 6161 7.527457 GTGTACAACTCCATGGTAAAAGAATC 58.473 38.462 12.58 0.00 0.00 2.52
5531 6186 0.462759 GTACCTGAGCACAGATGGGC 60.463 60.000 13.19 0.00 46.03 5.36
5551 6206 2.381911 CACCTCAAAGGGATTGGGATG 58.618 52.381 0.00 0.00 42.54 3.51
5553 6208 3.053693 CACCTCAAAGGGATTGGGATGTA 60.054 47.826 0.00 0.00 42.54 2.29
5555 6210 4.981647 ACCTCAAAGGGATTGGGATGTATA 59.018 41.667 0.00 0.00 42.54 1.47
5557 6212 6.104691 ACCTCAAAGGGATTGGGATGTATAAT 59.895 38.462 0.00 0.00 42.54 1.28
5560 6215 6.714810 TCAAAGGGATTGGGATGTATAATTCG 59.285 38.462 0.00 0.00 39.62 3.34
5561 6216 6.448369 AAGGGATTGGGATGTATAATTCGA 57.552 37.500 0.00 0.00 0.00 3.71
5581 6238 5.607477 TCGATTATAAAGGTACTGGCCAAG 58.393 41.667 7.01 3.48 40.86 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.140375 CAGCGACGTAGGGGTTACC 59.860 63.158 0.00 0.00 40.67 2.85
2 3 1.517913 GCAGCGACGTAGGGGTTAC 60.518 63.158 0.00 0.00 0.00 2.50
53 54 2.283086 CAGTCTCTGACTAGTAGACGCG 59.717 54.545 15.40 3.53 41.37 6.01
69 70 0.246086 CTTCTGCGGCTTCTCAGTCT 59.754 55.000 0.00 0.00 0.00 3.24
89 90 2.047179 GTCGCTTTCGCCCTCCTT 60.047 61.111 0.00 0.00 35.26 3.36
108 109 2.052468 TGGGGATGATCATGTCCTCAG 58.948 52.381 14.30 0.00 40.03 3.35
109 110 1.770658 GTGGGGATGATCATGTCCTCA 59.229 52.381 14.30 13.58 42.61 3.86
120 121 2.232941 GACTCAAACGTAGTGGGGATGA 59.767 50.000 4.24 0.00 45.00 2.92
150 151 1.530323 GTGGTGTAATTCCGGCTTGT 58.470 50.000 0.00 0.00 0.00 3.16
246 258 3.953775 AGTCCGTTGGGGCAGTGG 61.954 66.667 0.00 0.00 41.80 4.00
248 260 2.847234 TCAGTCCGTTGGGGCAGT 60.847 61.111 0.00 0.00 41.80 4.40
249 261 1.903877 ATCTCAGTCCGTTGGGGCAG 61.904 60.000 0.00 0.00 41.80 4.85
250 262 1.899437 GATCTCAGTCCGTTGGGGCA 61.899 60.000 0.00 0.00 41.80 5.36
292 305 2.032290 GGCAAGTCACGGTACTGTTTTC 60.032 50.000 4.06 0.00 0.00 2.29
294 307 1.589803 GGCAAGTCACGGTACTGTTT 58.410 50.000 4.06 0.00 0.00 2.83
303 321 1.903877 ATGGAGAGGGGCAAGTCACG 61.904 60.000 0.00 0.00 0.00 4.35
322 341 3.549423 CGCCGATTTTAGATCAGACGGTA 60.549 47.826 0.00 0.00 40.76 4.02
329 348 2.429250 TCTGTCCGCCGATTTTAGATCA 59.571 45.455 0.00 0.00 0.00 2.92
377 398 1.135373 CGACTACTGTTGACCGAGCAT 60.135 52.381 0.00 0.00 0.00 3.79
394 429 0.108945 GCAGGGTACTGTACACCGAC 60.109 60.000 16.24 9.74 46.62 4.79
400 435 1.726853 CTGCAAGCAGGGTACTGTAC 58.273 55.000 14.10 9.46 46.62 2.90
418 453 3.560636 AACACTGTAGCAGGAAACACT 57.439 42.857 1.08 0.00 35.51 3.55
420 455 3.879998 TCAAACACTGTAGCAGGAAACA 58.120 40.909 1.08 0.00 35.51 2.83
421 456 4.757149 AGATCAAACACTGTAGCAGGAAAC 59.243 41.667 0.00 0.00 35.51 2.78
448 483 2.763215 GTTGGATGCAGGGGGTGA 59.237 61.111 0.00 0.00 0.00 4.02
450 485 4.047125 CCGTTGGATGCAGGGGGT 62.047 66.667 0.00 0.00 0.00 4.95
479 515 2.036604 TGCCAAGTCACATCGTAACTGA 59.963 45.455 0.00 0.00 0.00 3.41
487 523 2.475666 GCCTCTGCCAAGTCACATC 58.524 57.895 0.00 0.00 0.00 3.06
488 524 4.730487 GCCTCTGCCAAGTCACAT 57.270 55.556 0.00 0.00 0.00 3.21
545 581 2.967076 CTGGTGCAGTCGCGTGTT 60.967 61.111 5.77 0.00 42.97 3.32
565 601 3.569277 CACACACACCCAAAATCAGATGA 59.431 43.478 0.00 0.00 0.00 2.92
661 699 8.867935 CATGTTGTTGTTGTTTTGTGAATTAGA 58.132 29.630 0.00 0.00 0.00 2.10
673 711 3.550639 CCGAGATGCATGTTGTTGTTGTT 60.551 43.478 2.46 0.00 0.00 2.83
674 712 2.030893 CCGAGATGCATGTTGTTGTTGT 60.031 45.455 2.46 0.00 0.00 3.32
675 713 2.030893 ACCGAGATGCATGTTGTTGTTG 60.031 45.455 2.46 0.00 0.00 3.33
676 714 2.229792 ACCGAGATGCATGTTGTTGTT 58.770 42.857 2.46 0.00 0.00 2.83
677 715 1.896220 ACCGAGATGCATGTTGTTGT 58.104 45.000 2.46 0.00 0.00 3.32
678 716 2.995466 AACCGAGATGCATGTTGTTG 57.005 45.000 2.46 0.00 0.00 3.33
720 758 7.725251 TGGAAAGCTAAATTGAGAATGTTTGT 58.275 30.769 0.00 0.00 0.00 2.83
721 759 8.767478 ATGGAAAGCTAAATTGAGAATGTTTG 57.233 30.769 0.00 0.00 0.00 2.93
819 857 5.297527 TCAACTGACGTAGAAGAGTTGTACA 59.702 40.000 16.79 0.00 43.75 2.90
832 879 4.729227 TCATAAGGCATCAACTGACGTA 57.271 40.909 0.00 0.00 38.25 3.57
995 1044 0.615331 GGTGAGTCCAGCCATGAGAA 59.385 55.000 0.00 0.00 34.88 2.87
1287 1336 4.634133 GGCACGACGTCGGTGTGA 62.634 66.667 37.89 0.00 44.95 3.58
1595 2050 3.866651 AGATTACTCAAGCATGCTCGTT 58.133 40.909 22.93 1.73 0.00 3.85
1670 2169 9.283768 TCACAAGTTTACAACATCATCAATAGT 57.716 29.630 0.00 0.00 0.00 2.12
1687 2186 8.450578 TGAATCTAGTCACAATTCACAAGTTT 57.549 30.769 0.84 0.00 35.17 2.66
1718 2217 7.040132 TGCACATGGAGTATAGATCTCTACAAG 60.040 40.741 17.69 8.06 33.06 3.16
1869 2372 0.675083 TTGCGAAGGTTACTCGGACA 59.325 50.000 0.00 0.00 0.00 4.02
1870 2373 1.458445 GTTTGCGAAGGTTACTCGGAC 59.542 52.381 0.00 0.00 0.00 4.79
1969 2472 4.041567 TGTCCTACATTCATGAACCACAGT 59.958 41.667 11.07 7.33 0.00 3.55
2138 2641 3.181503 CCACATTCAGCTCCTTGAATTCG 60.182 47.826 0.04 0.00 43.41 3.34
2909 3414 3.760580 AGTATCAGGTCCTATGCAAGC 57.239 47.619 0.00 0.00 0.00 4.01
2910 3415 5.163364 ACAGAAGTATCAGGTCCTATGCAAG 60.163 44.000 0.00 0.00 0.00 4.01
2911 3416 4.716784 ACAGAAGTATCAGGTCCTATGCAA 59.283 41.667 0.00 0.00 0.00 4.08
2912 3417 4.100035 CACAGAAGTATCAGGTCCTATGCA 59.900 45.833 0.00 0.00 0.00 3.96
2913 3418 4.100189 ACACAGAAGTATCAGGTCCTATGC 59.900 45.833 0.00 0.00 0.00 3.14
2931 3436 2.029020 TCGGAGAATGGACAGAACACAG 60.029 50.000 0.00 0.00 0.00 3.66
2949 3454 5.060662 TGACTTACAATTCTCTGACTCGG 57.939 43.478 0.00 0.00 0.00 4.63
3416 3952 6.847400 TGACAAAGAACACGATTCAAGAAAA 58.153 32.000 0.00 0.00 0.00 2.29
3767 4307 5.551760 ATCAGTTTTCACCAATAGAAGCG 57.448 39.130 0.00 0.00 0.00 4.68
3836 4376 1.460743 GCCTTTCGCAAATTTTCAGCC 59.539 47.619 0.00 0.00 37.47 4.85
4039 4579 1.140312 TGTCAAGGACAGAGCCCTTT 58.860 50.000 0.00 0.00 41.79 3.11
4133 4673 1.283793 CAAGTTTGCCACCAGCTCG 59.716 57.895 0.00 0.00 44.23 5.03
4219 4759 1.077068 CGCCATAGGGGAAAAGCCA 60.077 57.895 0.00 0.00 40.01 4.75
4316 4857 6.419484 TTCTATATGAGAAAGGCAATCGGA 57.581 37.500 0.00 0.00 41.39 4.55
4394 4943 7.069085 AGAGCATGACCAATATGTTGCTATTTT 59.931 33.333 0.00 0.00 40.29 1.82
4559 5113 1.402613 TCGTCGATGCCGTCATCTTTA 59.597 47.619 4.76 0.00 45.32 1.85
4595 5149 7.673641 AGATAAGATCATCTTTCCTCACAGT 57.326 36.000 4.90 0.00 37.89 3.55
4627 5187 1.068194 GTCGAGAGGCAAGATATCCGG 60.068 57.143 0.00 0.00 34.40 5.14
4655 5216 3.541711 CAAAACCTTCTTCTGCGTTACG 58.458 45.455 0.00 0.00 0.00 3.18
4659 5220 0.668535 GCCAAAACCTTCTTCTGCGT 59.331 50.000 0.00 0.00 0.00 5.24
4675 5236 5.771469 CAGAAACAGAACATGTATTTGCCA 58.229 37.500 0.00 0.00 43.00 4.92
4677 5238 5.464168 AGCAGAAACAGAACATGTATTTGC 58.536 37.500 0.00 1.63 43.00 3.68
4706 5268 0.463620 TCTGTGGTTTTGCTTTGGCC 59.536 50.000 0.00 0.00 37.74 5.36
4794 5359 7.810282 AGAGATGTCATTACTCGTACAATATGC 59.190 37.037 0.00 0.00 36.03 3.14
4826 5391 8.084073 CGGATGAAATGCCATCACTTATTTAAT 58.916 33.333 0.00 0.00 43.49 1.40
4854 5419 5.528690 CACCAAGAGAAAGAACTGATGAACA 59.471 40.000 0.00 0.00 0.00 3.18
4870 5435 0.689623 AGGAAGTGCCTCACCAAGAG 59.310 55.000 0.00 0.00 46.97 2.85
4883 5448 2.622436 GCATCAAAGTAGCGAGGAAGT 58.378 47.619 0.00 0.00 0.00 3.01
4914 5479 0.868406 GTCAAAGCTTCAGGACGGTG 59.132 55.000 0.00 0.00 0.00 4.94
4920 5485 2.393271 AGATCCGTCAAAGCTTCAGG 57.607 50.000 0.00 1.06 0.00 3.86
4929 5494 2.897326 TCCAAGTCTCAAGATCCGTCAA 59.103 45.455 0.00 0.00 0.00 3.18
4930 5495 2.525368 TCCAAGTCTCAAGATCCGTCA 58.475 47.619 0.00 0.00 0.00 4.35
4933 5498 3.104843 GGATCCAAGTCTCAAGATCCG 57.895 52.381 6.95 0.00 43.88 4.18
4955 5520 0.742635 GGGAAAAGAGAGGAGCTGCG 60.743 60.000 0.00 0.00 0.00 5.18
4973 5538 4.632327 AAGAAAGAGAACTTCAGGAGGG 57.368 45.455 0.00 0.00 35.05 4.30
4976 5541 6.448006 CGTAGAAAGAAAGAGAACTTCAGGA 58.552 40.000 0.00 0.00 35.05 3.86
4978 5543 5.119434 GGCGTAGAAAGAAAGAGAACTTCAG 59.881 44.000 0.00 0.00 35.05 3.02
4980 5545 5.119434 CAGGCGTAGAAAGAAAGAGAACTTC 59.881 44.000 0.00 0.00 35.05 3.01
5022 5587 2.858862 GCACAACACATGCCTGGCA 61.859 57.895 25.65 25.65 44.86 4.92
5045 5610 3.064134 TGAGACGAGCGAGTTTATCTCTG 59.936 47.826 0.00 0.00 40.75 3.35
5052 5617 1.080434 GGCTGAGACGAGCGAGTTT 60.080 57.895 0.00 0.00 40.13 2.66
5053 5618 1.974343 AGGCTGAGACGAGCGAGTT 60.974 57.895 0.00 0.00 40.13 3.01
5057 5622 4.426112 TGCAGGCTGAGACGAGCG 62.426 66.667 20.86 0.00 40.13 5.03
5061 5626 1.864862 CAAACTGCAGGCTGAGACG 59.135 57.895 20.86 4.97 0.00 4.18
5074 5639 0.957395 CACCTGATCCAGCGCAAACT 60.957 55.000 11.47 0.00 0.00 2.66
5082 5653 3.285484 CCAGAAATTCCACCTGATCCAG 58.715 50.000 0.00 0.00 0.00 3.86
5087 5658 1.075601 AGGCCAGAAATTCCACCTGA 58.924 50.000 5.01 0.00 0.00 3.86
5099 5670 1.055849 TGTTTGCTACTCAGGCCAGA 58.944 50.000 5.01 0.00 0.00 3.86
5104 5675 3.370978 CGGTAACATGTTTGCTACTCAGG 59.629 47.826 17.78 0.00 0.00 3.86
5166 5737 7.242359 ACTATATATAACACTGAGCTGAGGGT 58.758 38.462 0.66 0.66 0.00 4.34
5170 5741 9.746457 AGATGACTATATATAACACTGAGCTGA 57.254 33.333 0.00 0.00 0.00 4.26
5213 5843 0.304705 GACCATCTTATGTTGCGCCG 59.695 55.000 4.18 0.00 0.00 6.46
5216 5846 2.352651 CACCTGACCATCTTATGTTGCG 59.647 50.000 0.00 0.00 0.00 4.85
5221 5851 6.487668 TGCAATAATCACCTGACCATCTTATG 59.512 38.462 0.00 0.00 0.00 1.90
5234 5864 2.088423 TCCAACCGTGCAATAATCACC 58.912 47.619 0.00 0.00 0.00 4.02
5236 5866 6.707440 AATAATCCAACCGTGCAATAATCA 57.293 33.333 0.00 0.00 0.00 2.57
5237 5867 8.419076 AAAAATAATCCAACCGTGCAATAATC 57.581 30.769 0.00 0.00 0.00 1.75
5260 5890 3.242936 GCCTTACGTGCAGTTCTCAAAAA 60.243 43.478 0.00 0.00 0.00 1.94
5261 5891 2.289547 GCCTTACGTGCAGTTCTCAAAA 59.710 45.455 0.00 0.00 0.00 2.44
5262 5892 1.871039 GCCTTACGTGCAGTTCTCAAA 59.129 47.619 0.00 0.00 0.00 2.69
5263 5893 1.070134 AGCCTTACGTGCAGTTCTCAA 59.930 47.619 0.00 0.00 0.00 3.02
5264 5894 0.679505 AGCCTTACGTGCAGTTCTCA 59.320 50.000 0.00 0.00 0.00 3.27
5265 5895 1.461127 CAAGCCTTACGTGCAGTTCTC 59.539 52.381 0.00 0.00 0.00 2.87
5266 5896 1.202651 ACAAGCCTTACGTGCAGTTCT 60.203 47.619 0.00 0.00 0.00 3.01
5267 5897 1.226746 ACAAGCCTTACGTGCAGTTC 58.773 50.000 0.00 0.00 0.00 3.01
5269 5899 2.140717 GTAACAAGCCTTACGTGCAGT 58.859 47.619 0.00 0.00 0.00 4.40
5272 5902 1.389106 CTCGTAACAAGCCTTACGTGC 59.611 52.381 14.90 0.00 45.98 5.34
5273 5903 1.389106 GCTCGTAACAAGCCTTACGTG 59.611 52.381 14.90 13.85 45.98 4.49
5301 5951 4.260375 GGCGTGAATGTAGATGATGTCAAC 60.260 45.833 0.00 0.00 0.00 3.18
5304 5954 3.492383 CAGGCGTGAATGTAGATGATGTC 59.508 47.826 0.00 0.00 0.00 3.06
5356 6006 1.959226 GGACAAAGAGTTCGCGGCA 60.959 57.895 6.13 0.00 0.00 5.69
5371 6021 1.975660 TTGCCACTACCACAAAGGAC 58.024 50.000 0.00 0.00 41.22 3.85
5401 6052 8.674263 TTTGTGCTATTTGAAATTCAATTGGT 57.326 26.923 9.41 0.00 36.11 3.67
5443 6098 6.456501 GGTGTTCCATCCATGTAGTATACTC 58.543 44.000 9.12 2.17 43.54 2.59
5452 6107 0.690192 TGACGGTGTTCCATCCATGT 59.310 50.000 0.00 0.00 0.00 3.21
5472 6127 3.386486 TGGAGTTGTACACGTGATGTTC 58.614 45.455 25.01 11.18 43.19 3.18
5473 6128 3.462483 TGGAGTTGTACACGTGATGTT 57.538 42.857 25.01 1.30 43.19 2.71
5495 6150 2.862536 GGTACTCGCCGATTCTTTTACC 59.137 50.000 0.00 0.00 0.00 2.85
5501 6156 1.025812 CTCAGGTACTCGCCGATTCT 58.974 55.000 0.00 0.00 34.60 2.40
5506 6161 2.202623 GTGCTCAGGTACTCGCCG 60.203 66.667 0.00 0.00 34.60 6.46
5531 6186 2.291800 ACATCCCAATCCCTTTGAGGTG 60.292 50.000 0.00 0.00 37.53 4.00
5553 6208 8.380099 TGGCCAGTACCTTTATAATCGAATTAT 58.620 33.333 0.00 0.00 38.83 1.28
5555 6210 6.597562 TGGCCAGTACCTTTATAATCGAATT 58.402 36.000 0.00 0.00 0.00 2.17
5557 6212 5.617528 TGGCCAGTACCTTTATAATCGAA 57.382 39.130 0.00 0.00 0.00 3.71
5560 6215 5.008712 GTGCTTGGCCAGTACCTTTATAATC 59.991 44.000 5.11 0.00 32.05 1.75
5561 6216 4.887655 GTGCTTGGCCAGTACCTTTATAAT 59.112 41.667 5.11 0.00 32.05 1.28
5581 6238 3.564235 TCAATGCAGTCATCTTTGTGC 57.436 42.857 0.00 0.00 36.42 4.57


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

AutoCloner maintained by Alex Coulton.