Multiple sequence alignment - TraesCS6A01G368500

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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 TraesCS6A01G368500 chr6A 100.000 3004 0 0 1 3004 594660300 594663303 0.000000e+00 5548
1 TraesCS6A01G368500 chr6A 92.450 649 38 9 2362 3004 393556631 393557274 0.000000e+00 917
2 TraesCS6A01G368500 chr6B 89.897 1455 96 18 930 2368 679640772 679642191 0.000000e+00 1825
3 TraesCS6A01G368500 chr2A 92.068 643 41 7 2368 3004 571920112 571920750 0.000000e+00 896
4 TraesCS6A01G368500 chr2A 74.308 759 162 26 1215 1952 19436287 19435541 1.050000e-74 291
5 TraesCS6A01G368500 chr2A 71.870 583 134 24 1123 1694 751093348 751093911 1.120000e-29 141
6 TraesCS6A01G368500 chr6D 88.797 723 66 11 34 755 448611939 448612647 0.000000e+00 872
7 TraesCS6A01G368500 chr6D 95.437 526 22 1 1000 1525 448622796 448623319 0.000000e+00 837
8 TraesCS6A01G368500 chr6D 87.418 763 46 15 1551 2309 448623316 448624032 0.000000e+00 832
9 TraesCS6A01G368500 chr6D 85.829 374 38 9 573 939 448613075 448613440 1.690000e-102 383
10 TraesCS6A01G368500 chr5A 92.749 593 34 7 2368 2955 175786561 175787149 0.000000e+00 848
11 TraesCS6A01G368500 chr5A 91.521 401 28 4 2607 3004 407500757 407500360 5.660000e-152 547
12 TraesCS6A01G368500 chr5A 90.675 311 25 3 2365 2673 407501060 407500752 7.750000e-111 411
13 TraesCS6A01G368500 chr3A 90.217 644 41 6 2367 3004 651510859 651510232 0.000000e+00 821
14 TraesCS6A01G368500 chr7D 88.438 666 42 14 2368 2999 136819733 136819069 0.000000e+00 771
15 TraesCS6A01G368500 chr2B 87.500 640 57 12 2365 2996 661462345 661462969 0.000000e+00 717
16 TraesCS6A01G368500 chr2B 87.031 640 60 12 2365 2996 661473573 661474197 0.000000e+00 701
17 TraesCS6A01G368500 chr2B 73.582 776 164 28 1203 1952 30313387 30312627 2.970000e-65 259
18 TraesCS6A01G368500 chr2B 73.735 415 92 13 1133 1544 759172752 759173152 2.410000e-31 147
19 TraesCS6A01G368500 chr7A 90.503 358 31 2 2650 3004 350478952 350478595 1.260000e-128 470
20 TraesCS6A01G368500 chr7A 92.000 275 20 2 2367 2640 350560751 350560478 4.700000e-103 385
21 TraesCS6A01G368500 chr2D 91.789 341 23 4 2667 3004 641161908 641162246 1.260000e-128 470
22 TraesCS6A01G368500 chr2D 92.532 308 19 3 2369 2674 641132071 641132376 3.560000e-119 438
23 TraesCS6A01G368500 chr2D 74.293 813 169 32 1166 1952 18269669 18268871 1.050000e-79 307
24 TraesCS6A01G368500 chr2D 72.248 854 193 33 1123 1949 13856322 13857158 1.080000e-54 224
25 TraesCS6A01G368500 chr2D 73.861 417 88 19 1133 1544 619598576 619598976 2.410000e-31 147


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 TraesCS6A01G368500 chr6A 594660300 594663303 3003 False 5548.0 5548 100.0000 1 3004 1 chr6A.!!$F2 3003
1 TraesCS6A01G368500 chr6A 393556631 393557274 643 False 917.0 917 92.4500 2362 3004 1 chr6A.!!$F1 642
2 TraesCS6A01G368500 chr6B 679640772 679642191 1419 False 1825.0 1825 89.8970 930 2368 1 chr6B.!!$F1 1438
3 TraesCS6A01G368500 chr2A 571920112 571920750 638 False 896.0 896 92.0680 2368 3004 1 chr2A.!!$F1 636
4 TraesCS6A01G368500 chr2A 19435541 19436287 746 True 291.0 291 74.3080 1215 1952 1 chr2A.!!$R1 737
5 TraesCS6A01G368500 chr6D 448622796 448624032 1236 False 834.5 837 91.4275 1000 2309 2 chr6D.!!$F2 1309
6 TraesCS6A01G368500 chr6D 448611939 448613440 1501 False 627.5 872 87.3130 34 939 2 chr6D.!!$F1 905
7 TraesCS6A01G368500 chr5A 175786561 175787149 588 False 848.0 848 92.7490 2368 2955 1 chr5A.!!$F1 587
8 TraesCS6A01G368500 chr5A 407500360 407501060 700 True 479.0 547 91.0980 2365 3004 2 chr5A.!!$R1 639
9 TraesCS6A01G368500 chr3A 651510232 651510859 627 True 821.0 821 90.2170 2367 3004 1 chr3A.!!$R1 637
10 TraesCS6A01G368500 chr7D 136819069 136819733 664 True 771.0 771 88.4380 2368 2999 1 chr7D.!!$R1 631
11 TraesCS6A01G368500 chr2B 661462345 661462969 624 False 717.0 717 87.5000 2365 2996 1 chr2B.!!$F1 631
12 TraesCS6A01G368500 chr2B 661473573 661474197 624 False 701.0 701 87.0310 2365 2996 1 chr2B.!!$F2 631
13 TraesCS6A01G368500 chr2B 30312627 30313387 760 True 259.0 259 73.5820 1203 1952 1 chr2B.!!$R1 749
14 TraesCS6A01G368500 chr2D 18268871 18269669 798 True 307.0 307 74.2930 1166 1952 1 chr2D.!!$R1 786
15 TraesCS6A01G368500 chr2D 13856322 13857158 836 False 224.0 224 72.2480 1123 1949 1 chr2D.!!$F1 826

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
713 1318 0.248134 CCGCTGACGACTAGCACTAC 60.248 60.0 9.99 0.0 43.93 2.73 F
714 1319 0.727970 CGCTGACGACTAGCACTACT 59.272 55.0 9.99 0.0 43.93 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1973 2610 0.179936 GTCCAGATCCCTTGAGCCTG 59.820 60.0 0.0 0.0 0.0 4.85 R
2713 3455 0.105246 AGTGCCTCATAGCCTAGCCT 60.105 55.0 0.0 0.0 0.0 4.58 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 2.193248 GGGGGCTGATACAGTGCC 59.807 66.667 0.00 0.00 45.42 5.01
21 22 2.203070 GGCTGATACAGTGCCCCG 60.203 66.667 0.00 0.00 40.71 5.73
22 23 2.203070 GCTGATACAGTGCCCCGG 60.203 66.667 0.00 0.00 33.43 5.73
23 24 3.031417 GCTGATACAGTGCCCCGGT 62.031 63.158 0.00 0.00 33.43 5.28
24 25 1.153369 CTGATACAGTGCCCCGGTG 60.153 63.158 0.00 0.00 0.00 4.94
25 26 2.189521 GATACAGTGCCCCGGTGG 59.810 66.667 0.00 2.05 37.09 4.61
54 55 5.066375 CAGATGATTTGGCTAATTTCGGTGA 59.934 40.000 0.00 0.00 0.00 4.02
83 84 0.822944 CTTGTGCCCACATGTGACCA 60.823 55.000 27.46 18.97 41.52 4.02
92 93 3.221771 CCACATGTGACCAAGGAAAAGA 58.778 45.455 27.46 0.00 0.00 2.52
110 111 7.394641 AGGAAAAGAAAGACTCCCATCAAATAC 59.605 37.037 0.00 0.00 0.00 1.89
123 124 5.392595 CCCATCAAATACGTTGGTTAGGTTG 60.393 44.000 0.00 0.00 37.85 3.77
147 148 0.610174 TTGCTAGTGTGGCTCAGGAG 59.390 55.000 0.00 0.00 0.00 3.69
164 165 6.236017 TCAGGAGCAAAAATAGTGTAAACG 57.764 37.500 0.00 0.00 0.00 3.60
174 175 2.732844 AGTGTAAACGGGACCCAAAA 57.267 45.000 12.15 0.00 0.00 2.44
178 179 2.553172 TGTAAACGGGACCCAAAATTCG 59.447 45.455 12.15 0.00 0.00 3.34
183 184 2.815503 ACGGGACCCAAAATTCGTTAAG 59.184 45.455 12.15 0.00 0.00 1.85
190 191 6.809689 GGACCCAAAATTCGTTAAGGTAAATG 59.190 38.462 0.00 0.00 0.00 2.32
191 192 6.160684 ACCCAAAATTCGTTAAGGTAAATGC 58.839 36.000 0.00 0.00 0.00 3.56
225 226 8.258007 ACATTCTATGAGAACGAAGGAATAACA 58.742 33.333 0.00 0.00 37.00 2.41
226 227 9.098355 CATTCTATGAGAACGAAGGAATAACAA 57.902 33.333 0.00 0.00 37.00 2.83
235 236 4.039973 ACGAAGGAATAACAACTGTCCTGA 59.960 41.667 0.00 0.00 39.65 3.86
239 240 4.223923 AGGAATAACAACTGTCCTGAGAGG 59.776 45.833 0.00 0.00 39.09 3.69
246 247 2.614259 ACTGTCCTGAGAGGTGACAAT 58.386 47.619 0.00 0.00 38.45 2.71
248 249 2.564504 CTGTCCTGAGAGGTGACAATGA 59.435 50.000 0.00 0.00 38.45 2.57
251 252 4.777366 TGTCCTGAGAGGTGACAATGATAA 59.223 41.667 0.00 0.00 36.16 1.75
265 266 8.279103 GTGACAATGATAACTTTATAGCTGCTC 58.721 37.037 4.91 0.00 0.00 4.26
292 293 7.194607 TGCAAGTATATATCTTTTGCTGCTC 57.805 36.000 20.31 3.02 43.29 4.26
316 317 5.895636 TGTGGTTACAAATGAAGCTATGG 57.104 39.130 0.00 0.00 32.88 2.74
335 337 2.093288 TGGCCATGAGAGATGACTTGAC 60.093 50.000 0.00 0.00 0.00 3.18
350 352 4.041567 TGACTTGACTTGGCCAATTCTCTA 59.958 41.667 29.51 17.15 0.00 2.43
352 354 4.287067 ACTTGACTTGGCCAATTCTCTAGA 59.713 41.667 29.51 11.92 0.00 2.43
359 361 5.441718 TGGCCAATTCTCTAGAGTTCAAT 57.558 39.130 19.21 9.22 0.00 2.57
360 362 5.188434 TGGCCAATTCTCTAGAGTTCAATG 58.812 41.667 19.21 11.76 0.00 2.82
362 364 5.189180 GCCAATTCTCTAGAGTTCAATGGT 58.811 41.667 19.21 0.00 0.00 3.55
364 366 6.648192 CCAATTCTCTAGAGTTCAATGGTCT 58.352 40.000 19.21 0.00 0.00 3.85
365 367 7.633772 GCCAATTCTCTAGAGTTCAATGGTCTA 60.634 40.741 19.21 0.00 0.00 2.59
366 368 7.925483 CCAATTCTCTAGAGTTCAATGGTCTAG 59.075 40.741 19.21 8.15 40.77 2.43
367 369 8.690884 CAATTCTCTAGAGTTCAATGGTCTAGA 58.309 37.037 19.21 13.44 44.18 2.43
368 370 7.633193 TTCTCTAGAGTTCAATGGTCTAGAC 57.367 40.000 19.21 14.87 42.43 2.59
369 371 6.964464 TCTCTAGAGTTCAATGGTCTAGACT 58.036 40.000 21.88 0.44 42.43 3.24
370 372 7.051623 TCTCTAGAGTTCAATGGTCTAGACTC 58.948 42.308 21.88 12.69 42.43 3.36
371 373 6.964464 TCTAGAGTTCAATGGTCTAGACTCT 58.036 40.000 21.88 15.54 42.43 3.24
377 379 6.096282 AGTTCAATGGTCTAGACTCTAGAAGC 59.904 42.308 21.88 10.96 0.00 3.86
378 380 4.890581 TCAATGGTCTAGACTCTAGAAGCC 59.109 45.833 21.88 14.24 0.00 4.35
398 400 2.799412 CCGAGTCTGATTCTATGCAAGC 59.201 50.000 0.00 0.00 0.00 4.01
409 411 5.627499 TTCTATGCAAGCGATCAACTTTT 57.373 34.783 0.00 0.00 0.00 2.27
419 421 1.880027 GATCAACTTTTGCACCGGACT 59.120 47.619 9.46 0.00 0.00 3.85
431 433 1.825474 CACCGGACTGTCTAGATGGTT 59.175 52.381 9.46 0.00 0.00 3.67
441 443 2.505819 GTCTAGATGGTTGGTGGGATGT 59.494 50.000 0.00 0.00 0.00 3.06
457 459 2.279741 GATGTGACGCCAGCTATTTCA 58.720 47.619 0.00 0.00 0.00 2.69
462 464 1.869767 GACGCCAGCTATTTCATGGAG 59.130 52.381 0.00 0.00 39.51 3.86
468 470 4.769688 CCAGCTATTTCATGGAGTGTGTA 58.230 43.478 0.00 0.00 36.09 2.90
517 519 8.345565 AGATCATCTTTAAACATTGTTATCGGC 58.654 33.333 1.76 0.00 0.00 5.54
518 520 6.791303 TCATCTTTAAACATTGTTATCGGCC 58.209 36.000 1.76 0.00 0.00 6.13
528 530 6.061441 ACATTGTTATCGGCCATCTAATCAA 58.939 36.000 2.24 5.30 0.00 2.57
538 540 3.181503 GCCATCTAATCAAGCGGCATATG 60.182 47.826 1.45 0.00 41.05 1.78
539 541 4.256110 CCATCTAATCAAGCGGCATATGA 58.744 43.478 6.97 4.11 0.00 2.15
545 547 2.759191 TCAAGCGGCATATGAGCTAAG 58.241 47.619 21.22 17.35 40.78 2.18
592 594 1.531149 CTCTTGTTTGGATGAACGCGT 59.469 47.619 5.58 5.58 32.18 6.01
593 595 1.944024 TCTTGTTTGGATGAACGCGTT 59.056 42.857 26.97 26.97 32.18 4.84
594 596 2.043411 CTTGTTTGGATGAACGCGTTG 58.957 47.619 31.89 6.15 32.18 4.10
607 1212 1.291184 CGCGTTGCCTGACATCTTGA 61.291 55.000 0.00 0.00 0.00 3.02
640 1245 7.985184 AGCTCGGAGACAATGTACAATTATTTA 59.015 33.333 9.69 0.00 0.00 1.40
667 1272 6.588719 TTAACAAAACTAGCCATGATTGCT 57.411 33.333 0.00 0.00 42.81 3.91
701 1306 3.887335 TTACCCGGTTGCCGCTGAC 62.887 63.158 0.00 0.00 46.86 3.51
707 1312 1.805945 GGTTGCCGCTGACGACTAG 60.806 63.158 0.00 0.00 43.93 2.57
708 1313 2.126071 TTGCCGCTGACGACTAGC 60.126 61.111 0.00 0.00 43.93 3.42
710 1315 2.881352 GCCGCTGACGACTAGCAC 60.881 66.667 9.99 0.00 43.93 4.40
711 1316 2.878429 CCGCTGACGACTAGCACT 59.122 61.111 9.99 0.00 43.93 4.40
712 1317 1.989966 GCCGCTGACGACTAGCACTA 61.990 60.000 9.99 0.00 43.93 2.74
713 1318 0.248134 CCGCTGACGACTAGCACTAC 60.248 60.000 9.99 0.00 43.93 2.73
714 1319 0.727970 CGCTGACGACTAGCACTACT 59.272 55.000 9.99 0.00 43.93 2.57
715 1320 1.931841 CGCTGACGACTAGCACTACTA 59.068 52.381 9.99 0.00 43.93 1.82
716 1321 2.544686 CGCTGACGACTAGCACTACTAT 59.455 50.000 9.99 0.00 43.93 2.12
717 1322 3.739810 CGCTGACGACTAGCACTACTATA 59.260 47.826 9.99 0.00 43.93 1.31
758 1363 1.197036 GCACTAACACGCCTTTTCCTC 59.803 52.381 0.00 0.00 0.00 3.71
759 1364 1.459592 CACTAACACGCCTTTTCCTCG 59.540 52.381 0.00 0.00 0.00 4.63
780 1385 3.728845 GTAAAATAGGGCAGCTCGATCA 58.271 45.455 0.00 0.00 0.00 2.92
783 1388 3.601443 AATAGGGCAGCTCGATCATAC 57.399 47.619 0.00 0.00 0.00 2.39
784 1389 0.881796 TAGGGCAGCTCGATCATACG 59.118 55.000 0.00 0.00 0.00 3.06
815 1420 2.125512 GCTGTACCTGGCGGTCAG 60.126 66.667 1.75 1.75 44.21 3.51
816 1421 2.646175 GCTGTACCTGGCGGTCAGA 61.646 63.158 11.97 0.00 46.18 3.27
830 1435 1.609320 GGTCAGAGGAGTTTCAGTGGC 60.609 57.143 0.00 0.00 0.00 5.01
837 1448 1.610886 GGAGTTTCAGTGGCTGTACCC 60.611 57.143 0.00 0.00 37.83 3.69
843 1454 4.394712 GTGGCTGTACCCGCTGCT 62.395 66.667 0.00 0.00 37.83 4.24
849 1460 1.571919 CTGTACCCGCTGCTCATAAC 58.428 55.000 0.00 0.00 0.00 1.89
850 1461 0.899019 TGTACCCGCTGCTCATAACA 59.101 50.000 0.00 0.00 0.00 2.41
858 1469 3.429085 CGCTGCTCATAACAAAACCATC 58.571 45.455 0.00 0.00 0.00 3.51
866 1477 6.458206 GCTCATAACAAAACCATCTAATGCGA 60.458 38.462 0.00 0.00 0.00 5.10
870 1481 6.811253 AACAAAACCATCTAATGCGAGTTA 57.189 33.333 0.00 0.00 0.00 2.24
871 1482 6.422776 ACAAAACCATCTAATGCGAGTTAG 57.577 37.500 0.00 0.00 33.85 2.34
888 1499 4.359105 AGTTAGGTATCCAGTTGCCACTA 58.641 43.478 0.00 0.00 0.00 2.74
904 1515 6.012658 TGCCACTAACTGCAATTTAGAAAG 57.987 37.500 17.65 9.10 33.87 2.62
909 1520 9.696917 CCACTAACTGCAATTTAGAAAGAAAAT 57.303 29.630 17.65 0.00 31.92 1.82
957 1568 1.575419 ACCACGCCTTGTCCCTATAA 58.425 50.000 0.00 0.00 0.00 0.98
965 1578 4.010349 GCCTTGTCCCTATAATATGGCAC 58.990 47.826 0.00 0.00 37.91 5.01
1014 1627 2.373707 GGACATGGCTCAGGCTCCT 61.374 63.158 0.00 0.00 38.73 3.69
1394 2019 1.129058 GGGACCATACCGACCTCAAT 58.871 55.000 0.00 0.00 0.00 2.57
1412 2037 2.817396 GCACTTGCCTCTCCTCGC 60.817 66.667 0.00 0.00 34.31 5.03
1710 2347 4.671831 AGAGATCAAGGAAGACTCTGTGA 58.328 43.478 0.00 0.00 36.72 3.58
1721 2358 3.873805 CTCTGTGAGAGTCGTGCAA 57.126 52.632 0.00 0.00 37.57 4.08
1742 2379 2.357517 CTTGCAGCGTTCCTCCGT 60.358 61.111 0.00 0.00 0.00 4.69
1748 2385 3.692406 GCGTTCCTCCGTGTCCCT 61.692 66.667 0.00 0.00 0.00 4.20
1952 2589 0.748367 GCCGAGAGATGGGGGAAAAC 60.748 60.000 0.00 0.00 0.00 2.43
1973 2610 4.521146 ACATGGATCAGATCACCAAAGAC 58.479 43.478 12.66 0.00 37.24 3.01
1975 2612 4.212143 TGGATCAGATCACCAAAGACAG 57.788 45.455 12.66 0.00 0.00 3.51
2016 2653 4.883585 TCGCCTTCTGATTTGCATTTCTAT 59.116 37.500 0.00 0.00 0.00 1.98
2050 2687 4.617530 GCACACCTCTGTTTCGTACTCATA 60.618 45.833 0.00 0.00 0.00 2.15
2051 2688 5.096169 CACACCTCTGTTTCGTACTCATAG 58.904 45.833 0.00 0.00 0.00 2.23
2052 2689 4.765856 ACACCTCTGTTTCGTACTCATAGT 59.234 41.667 0.00 0.00 0.00 2.12
2053 2690 5.106237 ACACCTCTGTTTCGTACTCATAGTC 60.106 44.000 0.00 0.00 0.00 2.59
2054 2691 5.124138 CACCTCTGTTTCGTACTCATAGTCT 59.876 44.000 0.00 0.00 0.00 3.24
2055 2692 5.354792 ACCTCTGTTTCGTACTCATAGTCTC 59.645 44.000 0.00 0.00 0.00 3.36
2056 2693 5.354513 CCTCTGTTTCGTACTCATAGTCTCA 59.645 44.000 0.00 0.00 0.00 3.27
2057 2694 6.038825 CCTCTGTTTCGTACTCATAGTCTCAT 59.961 42.308 0.00 0.00 0.00 2.90
2058 2695 7.226918 CCTCTGTTTCGTACTCATAGTCTCATA 59.773 40.741 0.00 0.00 0.00 2.15
2059 2696 7.917597 TCTGTTTCGTACTCATAGTCTCATAC 58.082 38.462 0.00 0.00 0.00 2.39
2078 2715 7.759886 TCTCATACACATTTCGGACTAAAGAAG 59.240 37.037 0.00 0.00 0.00 2.85
2105 2742 7.375106 TCTTTAAACGGTGTTGTCTTTTGTA 57.625 32.000 0.00 0.00 0.00 2.41
2106 2743 7.814642 TCTTTAAACGGTGTTGTCTTTTGTAA 58.185 30.769 0.00 0.00 0.00 2.41
2108 2745 8.807667 TTTAAACGGTGTTGTCTTTTGTAAAA 57.192 26.923 0.00 0.00 0.00 1.52
2154 2792 4.142665 CCATGAGCATCTTGAAAGTCTGTG 60.143 45.833 0.00 0.00 42.34 3.66
2190 2836 9.209175 GATAACACTTTGTCTGAGTACAAGAAT 57.791 33.333 0.00 0.00 40.29 2.40
2257 2903 7.202016 TCATAATTTTGGGATCTCGTAATGC 57.798 36.000 0.00 0.00 0.00 3.56
2261 2907 0.673985 TGGGATCTCGTAATGCGGAG 59.326 55.000 0.00 0.00 41.72 4.63
2276 2922 6.625873 AATGCGGAGAAAATAAAGGATCTC 57.374 37.500 0.00 0.00 38.04 2.75
2290 2936 4.927978 AGGATCTCGTAACATTCAGAGG 57.072 45.455 0.00 0.00 0.00 3.69
2309 2955 8.589701 TCAGAGGTAACACTAAGACATAATCA 57.410 34.615 0.00 0.00 34.91 2.57
2312 2958 8.470805 AGAGGTAACACTAAGACATAATCAGTG 58.529 37.037 0.00 0.00 41.83 3.66
2332 2978 4.574828 AGTGCACCTTGTACTAAAACTGTG 59.425 41.667 14.63 0.00 41.50 3.66
2342 2988 4.385358 ACTAAAACTGTGGTTTGGCTTG 57.615 40.909 0.00 0.00 43.90 4.01
2468 3118 9.064706 AGAAGTGATAATCCATAGCAATCAAAG 57.935 33.333 0.00 0.00 30.36 2.77
2647 3319 1.509644 CCATGTGATTCGCATCCCGG 61.510 60.000 9.73 5.36 37.59 5.73
2709 3451 7.327214 GTCACTTGAATGGTCTTCTCTCTAAT 58.673 38.462 0.00 0.00 0.00 1.73
2710 3452 7.821846 GTCACTTGAATGGTCTTCTCTCTAATT 59.178 37.037 0.00 0.00 0.00 1.40
2711 3453 7.821359 TCACTTGAATGGTCTTCTCTCTAATTG 59.179 37.037 0.00 0.00 0.00 2.32
2713 3455 8.816894 ACTTGAATGGTCTTCTCTCTAATTGTA 58.183 33.333 0.00 0.00 0.00 2.41
2714 3456 9.311916 CTTGAATGGTCTTCTCTCTAATTGTAG 57.688 37.037 0.00 0.00 0.00 2.74
2726 3471 6.552932 TCTCTAATTGTAGGCTAGGCTATGA 58.447 40.000 26.90 18.73 0.00 2.15
2728 3473 4.899352 AATTGTAGGCTAGGCTATGAGG 57.101 45.455 26.90 0.00 0.00 3.86
2820 3567 3.953775 CACCCCACAACCGCCTCT 61.954 66.667 0.00 0.00 0.00 3.69
2905 3652 3.237741 CGCCTCCATCTCTCCCCC 61.238 72.222 0.00 0.00 0.00 5.40
2906 3653 2.040464 GCCTCCATCTCTCCCCCA 60.040 66.667 0.00 0.00 0.00 4.96
2999 3746 1.229984 CCCACCCCCTCTTCTTCCT 60.230 63.158 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.193248 GGCACTGTATCAGCCCCC 59.807 66.667 0.00 0.00 42.58 5.40
5 6 2.203070 CCGGGGCACTGTATCAGC 60.203 66.667 0.00 0.00 34.37 4.26
6 7 1.153369 CACCGGGGCACTGTATCAG 60.153 63.158 6.32 0.00 37.52 2.90
7 8 2.665089 CCACCGGGGCACTGTATCA 61.665 63.158 6.32 0.00 0.00 2.15
8 9 2.189521 CCACCGGGGCACTGTATC 59.810 66.667 6.32 0.00 0.00 2.24
21 22 2.301346 CCAAATCATCTGGTAGCCACC 58.699 52.381 0.00 0.00 46.00 4.61
22 23 1.678101 GCCAAATCATCTGGTAGCCAC 59.322 52.381 0.00 0.00 36.24 5.01
23 24 1.565759 AGCCAAATCATCTGGTAGCCA 59.434 47.619 0.00 0.00 36.24 4.75
24 25 2.355010 AGCCAAATCATCTGGTAGCC 57.645 50.000 0.00 0.00 36.24 3.93
25 26 6.396829 AAATTAGCCAAATCATCTGGTAGC 57.603 37.500 0.00 0.00 36.24 3.58
26 27 6.293626 CCGAAATTAGCCAAATCATCTGGTAG 60.294 42.308 0.00 0.00 36.24 3.18
27 28 5.530915 CCGAAATTAGCCAAATCATCTGGTA 59.469 40.000 0.00 0.00 36.24 3.25
28 29 4.339247 CCGAAATTAGCCAAATCATCTGGT 59.661 41.667 0.00 0.00 36.24 4.00
29 30 4.339247 ACCGAAATTAGCCAAATCATCTGG 59.661 41.667 0.00 0.00 36.99 3.86
30 31 5.066375 TCACCGAAATTAGCCAAATCATCTG 59.934 40.000 0.00 0.00 0.00 2.90
31 32 5.192927 TCACCGAAATTAGCCAAATCATCT 58.807 37.500 0.00 0.00 0.00 2.90
32 33 5.499139 TCACCGAAATTAGCCAAATCATC 57.501 39.130 0.00 0.00 0.00 2.92
39 40 2.752354 CAACCATCACCGAAATTAGCCA 59.248 45.455 0.00 0.00 0.00 4.75
54 55 0.480690 TGGGCACAAGGTACAACCAT 59.519 50.000 0.00 0.00 41.95 3.55
83 84 5.324832 TGATGGGAGTCTTTCTTTTCCTT 57.675 39.130 0.00 0.00 0.00 3.36
92 93 4.700213 CCAACGTATTTGATGGGAGTCTTT 59.300 41.667 0.00 0.00 37.39 2.52
110 111 1.167781 AACCGGCAACCTAACCAACG 61.168 55.000 0.00 0.00 0.00 4.10
123 124 3.431725 GCCACACTAGCAACCGGC 61.432 66.667 0.00 0.00 45.30 6.13
147 148 4.478699 GGTCCCGTTTACACTATTTTTGC 58.521 43.478 0.00 0.00 0.00 3.68
155 156 2.732844 TTTTGGGTCCCGTTTACACT 57.267 45.000 2.65 0.00 0.00 3.55
164 165 3.159472 ACCTTAACGAATTTTGGGTCCC 58.841 45.455 0.00 0.00 0.00 4.46
174 175 4.261031 GCATCCGCATTTACCTTAACGAAT 60.261 41.667 0.00 0.00 38.36 3.34
190 191 3.133691 TCTCATAGAATGTTGCATCCGC 58.866 45.455 0.00 0.00 39.24 5.54
191 192 4.318333 CGTTCTCATAGAATGTTGCATCCG 60.318 45.833 0.00 0.00 36.50 4.18
225 226 2.088104 TGTCACCTCTCAGGACAGTT 57.912 50.000 0.00 0.00 37.67 3.16
226 227 2.088104 TTGTCACCTCTCAGGACAGT 57.912 50.000 0.00 0.00 41.99 3.55
235 236 8.709308 AGCTATAAAGTTATCATTGTCACCTCT 58.291 33.333 0.00 0.00 0.00 3.69
239 240 8.147642 AGCAGCTATAAAGTTATCATTGTCAC 57.852 34.615 0.00 0.00 0.00 3.67
246 247 7.194607 GCATTGAGCAGCTATAAAGTTATCA 57.805 36.000 0.00 0.00 44.79 2.15
265 266 8.080417 AGCAGCAAAAGATATATACTTGCATTG 58.920 33.333 19.92 14.25 43.77 2.82
292 293 6.267817 CCATAGCTTCATTTGTAACCACATG 58.732 40.000 0.00 0.00 33.76 3.21
312 313 3.969312 TCAAGTCATCTCTCATGGCCATA 59.031 43.478 20.30 1.93 0.00 2.74
316 317 3.540314 AGTCAAGTCATCTCTCATGGC 57.460 47.619 0.00 0.00 0.00 4.40
335 337 4.836825 TGAACTCTAGAGAATTGGCCAAG 58.163 43.478 26.57 8.26 0.00 3.61
350 352 6.964464 TCTAGAGTCTAGACCATTGAACTCT 58.036 40.000 23.38 14.31 37.18 3.24
352 354 6.096282 GCTTCTAGAGTCTAGACCATTGAACT 59.904 42.308 26.28 9.65 0.00 3.01
359 361 2.504585 TCGGCTTCTAGAGTCTAGACCA 59.495 50.000 26.28 13.99 0.00 4.02
360 362 3.135994 CTCGGCTTCTAGAGTCTAGACC 58.864 54.545 26.28 22.74 0.00 3.85
368 370 3.882888 AGAATCAGACTCGGCTTCTAGAG 59.117 47.826 0.00 0.00 40.16 2.43
369 371 3.892284 AGAATCAGACTCGGCTTCTAGA 58.108 45.455 0.00 0.00 0.00 2.43
370 372 5.698832 CATAGAATCAGACTCGGCTTCTAG 58.301 45.833 8.03 0.00 33.35 2.43
371 373 4.022762 GCATAGAATCAGACTCGGCTTCTA 60.023 45.833 5.36 5.36 34.09 2.10
377 379 2.799412 GCTTGCATAGAATCAGACTCGG 59.201 50.000 0.00 0.00 0.00 4.63
378 380 2.470628 CGCTTGCATAGAATCAGACTCG 59.529 50.000 0.00 0.00 0.00 4.18
385 387 5.415415 AAGTTGATCGCTTGCATAGAATC 57.585 39.130 0.00 0.00 0.00 2.52
398 400 0.871722 TCCGGTGCAAAAGTTGATCG 59.128 50.000 0.00 0.00 0.00 3.69
409 411 0.817654 CATCTAGACAGTCCGGTGCA 59.182 55.000 0.00 0.00 0.00 4.57
419 421 2.335681 TCCCACCAACCATCTAGACA 57.664 50.000 0.00 0.00 0.00 3.41
431 433 3.245346 TGGCGTCACATCCCACCA 61.245 61.111 0.00 0.00 0.00 4.17
441 443 1.209261 TCCATGAAATAGCTGGCGTCA 59.791 47.619 0.00 0.00 0.00 4.35
462 464 8.366930 CCTATTGACATAGCTGTGTCTACACAC 61.367 44.444 34.37 15.07 46.70 3.82
468 470 5.939764 TTCCTATTGACATAGCTGTGTCT 57.060 39.130 34.37 22.54 46.70 3.41
475 477 8.845413 AAGATGATCTTTCCTATTGACATAGC 57.155 34.615 0.97 0.00 31.57 2.97
516 518 1.242076 ATGCCGCTTGATTAGATGGC 58.758 50.000 0.00 0.00 43.48 4.40
517 519 4.256110 TCATATGCCGCTTGATTAGATGG 58.744 43.478 0.00 0.00 0.00 3.51
518 520 4.201792 GCTCATATGCCGCTTGATTAGATG 60.202 45.833 0.00 0.00 0.00 2.90
528 530 4.021104 TGATTACTTAGCTCATATGCCGCT 60.021 41.667 18.92 18.92 37.77 5.52
563 565 7.257722 GTTCATCCAAACAAGAGAAAGTTCAA 58.742 34.615 0.00 0.00 0.00 2.69
567 569 4.261197 GCGTTCATCCAAACAAGAGAAAGT 60.261 41.667 0.00 0.00 0.00 2.66
592 594 2.290450 TGCTGATCAAGATGTCAGGCAA 60.290 45.455 0.00 0.00 41.62 4.52
593 595 1.279846 TGCTGATCAAGATGTCAGGCA 59.720 47.619 0.00 0.00 41.62 4.75
594 596 2.034104 TGCTGATCAAGATGTCAGGC 57.966 50.000 0.00 0.00 41.62 4.85
607 1212 0.610174 TTGTCTCCGAGCTTGCTGAT 59.390 50.000 0.00 0.00 0.00 2.90
640 1245 8.720562 GCAATCATGGCTAGTTTTGTTAAAATT 58.279 29.630 0.00 0.00 32.22 1.82
652 1257 7.466746 TTCTTAAAAAGCAATCATGGCTAGT 57.533 32.000 0.00 0.00 41.66 2.57
690 1295 2.445438 GCTAGTCGTCAGCGGCAAC 61.445 63.158 1.45 0.00 46.51 4.17
696 1301 5.866335 ATATAGTAGTGCTAGTCGTCAGC 57.134 43.478 0.00 0.00 39.56 4.26
717 1322 8.962884 AGTGCACTTTTCTTTTTCCAAATTAT 57.037 26.923 15.25 0.00 0.00 1.28
758 1363 2.218953 TCGAGCTGCCCTATTTTACG 57.781 50.000 0.00 0.00 0.00 3.18
759 1364 3.728845 TGATCGAGCTGCCCTATTTTAC 58.271 45.455 0.90 0.00 0.00 2.01
815 1420 2.613223 GGTACAGCCACTGAAACTCCTC 60.613 54.545 0.78 0.00 35.18 3.71
816 1421 1.348036 GGTACAGCCACTGAAACTCCT 59.652 52.381 0.78 0.00 35.18 3.69
830 1435 1.134818 TGTTATGAGCAGCGGGTACAG 60.135 52.381 0.00 0.00 0.00 2.74
837 1448 2.987413 TGGTTTTGTTATGAGCAGCG 57.013 45.000 0.00 0.00 0.00 5.18
843 1454 6.597672 ACTCGCATTAGATGGTTTTGTTATGA 59.402 34.615 0.00 0.00 0.00 2.15
849 1460 5.354234 ACCTAACTCGCATTAGATGGTTTTG 59.646 40.000 6.99 0.00 34.59 2.44
850 1461 5.497474 ACCTAACTCGCATTAGATGGTTTT 58.503 37.500 6.99 0.00 34.59 2.43
858 1469 5.455056 ACTGGATACCTAACTCGCATTAG 57.545 43.478 0.00 0.00 32.78 1.73
866 1477 3.182152 AGTGGCAACTGGATACCTAACT 58.818 45.455 0.00 0.00 34.48 2.24
870 1481 3.182152 AGTTAGTGGCAACTGGATACCT 58.818 45.455 3.21 0.00 37.37 3.08
871 1482 3.629142 AGTTAGTGGCAACTGGATACC 57.371 47.619 3.21 0.00 37.37 2.73
932 1543 2.631545 AGGGACAAGGCGTGGTATATAC 59.368 50.000 5.22 4.14 0.00 1.47
965 1578 1.982395 TACGGTGAGGCAGTGGAGG 60.982 63.158 0.00 0.00 0.00 4.30
1014 1627 1.001633 GCACCGTCTTCTACCTTGGAA 59.998 52.381 0.00 0.00 0.00 3.53
1131 1747 4.149598 TCAGCCAGTAGTTCTTGTACAGA 58.850 43.478 0.00 0.00 0.00 3.41
1192 1808 4.820744 CCCGGGGCTTGATGGTGG 62.821 72.222 14.71 0.00 0.00 4.61
1394 2019 2.659016 CGAGGAGAGGCAAGTGCA 59.341 61.111 5.52 0.00 44.36 4.57
1412 2037 1.363744 GAATGTGCGTGGAGAGAAGG 58.636 55.000 0.00 0.00 0.00 3.46
1662 2299 6.596497 TCGTACTTCAAGAAAAGAACCTTGTT 59.404 34.615 0.00 0.00 40.32 2.83
1732 2369 0.669625 GAAAGGGACACGGAGGAACG 60.670 60.000 0.00 0.00 40.31 3.95
1740 2377 1.672356 CCTGGCTGAAAGGGACACG 60.672 63.158 0.00 0.00 0.00 4.49
1742 2379 1.492133 CCTCCTGGCTGAAAGGGACA 61.492 60.000 0.00 0.00 35.35 4.02
1748 2385 1.352352 CTTTCCTCCTCCTGGCTGAAA 59.648 52.381 0.00 0.00 34.11 2.69
1952 2589 4.520179 TGTCTTTGGTGATCTGATCCATG 58.480 43.478 14.71 4.46 0.00 3.66
1973 2610 0.179936 GTCCAGATCCCTTGAGCCTG 59.820 60.000 0.00 0.00 0.00 4.85
1975 2612 0.467804 GAGTCCAGATCCCTTGAGCC 59.532 60.000 0.00 0.00 0.00 4.70
2016 2653 4.973168 ACAGAGGTGTGCAGATAAGAAAA 58.027 39.130 0.00 0.00 34.75 2.29
2023 2660 1.070758 ACGAAACAGAGGTGTGCAGAT 59.929 47.619 0.00 0.00 36.84 2.90
2026 2663 1.411246 AGTACGAAACAGAGGTGTGCA 59.589 47.619 0.00 0.00 36.84 4.57
2050 2687 6.525578 TTAGTCCGAAATGTGTATGAGACT 57.474 37.500 0.00 0.00 37.18 3.24
2051 2688 7.033791 TCTTTAGTCCGAAATGTGTATGAGAC 58.966 38.462 0.00 0.00 0.00 3.36
2052 2689 7.165460 TCTTTAGTCCGAAATGTGTATGAGA 57.835 36.000 0.00 0.00 0.00 3.27
2053 2690 7.545965 ACTTCTTTAGTCCGAAATGTGTATGAG 59.454 37.037 0.00 0.00 28.23 2.90
2054 2691 7.383687 ACTTCTTTAGTCCGAAATGTGTATGA 58.616 34.615 0.00 0.00 28.23 2.15
2055 2692 7.596749 ACTTCTTTAGTCCGAAATGTGTATG 57.403 36.000 0.00 0.00 28.23 2.39
2056 2693 8.617290 AAACTTCTTTAGTCCGAAATGTGTAT 57.383 30.769 0.00 0.00 35.54 2.29
2057 2694 7.929785 AGAAACTTCTTTAGTCCGAAATGTGTA 59.070 33.333 0.00 0.00 35.54 2.90
2058 2695 6.766467 AGAAACTTCTTTAGTCCGAAATGTGT 59.234 34.615 0.00 0.00 35.54 3.72
2059 2696 7.190920 AGAAACTTCTTTAGTCCGAAATGTG 57.809 36.000 0.00 0.00 35.54 3.21
2078 2715 7.115236 ACAAAAGACAACACCGTTTAAAGAAAC 59.885 33.333 0.00 0.00 41.40 2.78
2163 2801 7.952671 TCTTGTACTCAGACAAAGTGTTATCT 58.047 34.615 0.00 0.00 38.80 1.98
2169 2807 9.226345 GAAAAATTCTTGTACTCAGACAAAGTG 57.774 33.333 0.00 0.00 38.80 3.16
2180 2818 9.793259 TGTGAATAGGAGAAAAATTCTTGTACT 57.207 29.630 0.00 0.00 40.87 2.73
2257 2903 6.755141 TGTTACGAGATCCTTTATTTTCTCCG 59.245 38.462 0.00 0.00 32.73 4.63
2261 2907 9.922305 CTGAATGTTACGAGATCCTTTATTTTC 57.078 33.333 0.00 0.00 0.00 2.29
2276 2922 7.272948 GTCTTAGTGTTACCTCTGAATGTTACG 59.727 40.741 0.00 0.00 0.00 3.18
2290 2936 7.201530 GGTGCACTGATTATGTCTTAGTGTTAC 60.202 40.741 17.98 0.00 40.52 2.50
2309 2955 4.574828 CACAGTTTTAGTACAAGGTGCACT 59.425 41.667 17.98 0.00 0.00 4.40
2312 2958 3.881089 ACCACAGTTTTAGTACAAGGTGC 59.119 43.478 0.00 0.00 0.00 5.01
2332 2978 0.673985 GACCAGAACCAAGCCAAACC 59.326 55.000 0.00 0.00 0.00 3.27
2342 2988 0.613777 ATGTTCTCCGGACCAGAACC 59.386 55.000 24.44 12.33 46.35 3.62
2453 3103 4.710865 TCAATTGCCTTTGATTGCTATGGA 59.289 37.500 0.00 0.00 34.15 3.41
2692 3434 6.385467 AGCCTACAATTAGAGAGAAGACCATT 59.615 38.462 0.00 0.00 0.00 3.16
2709 3451 1.971357 GCCTCATAGCCTAGCCTACAA 59.029 52.381 0.00 0.00 0.00 2.41
2710 3452 1.133167 TGCCTCATAGCCTAGCCTACA 60.133 52.381 0.00 0.00 0.00 2.74
2711 3453 1.273886 GTGCCTCATAGCCTAGCCTAC 59.726 57.143 0.00 0.00 0.00 3.18
2713 3455 0.105246 AGTGCCTCATAGCCTAGCCT 60.105 55.000 0.00 0.00 0.00 4.58
2714 3456 0.761802 AAGTGCCTCATAGCCTAGCC 59.238 55.000 0.00 0.00 0.00 3.93
2726 3471 3.181461 GCTATGAGGTGACATAAGTGCCT 60.181 47.826 0.00 0.00 33.26 4.75
2728 3473 3.797039 TGCTATGAGGTGACATAAGTGC 58.203 45.455 0.00 0.00 33.26 4.40
2783 3530 2.362397 TGAGTGAGTGAGAGGTGTGAAC 59.638 50.000 0.00 0.00 0.00 3.18
2789 3536 0.543174 GGGGTGAGTGAGTGAGAGGT 60.543 60.000 0.00 0.00 0.00 3.85
2820 3567 1.372683 GGCTGTGTGAGGAGAGCAA 59.627 57.895 0.00 0.00 33.91 3.91
2892 3639 0.914417 GGTGTTGGGGGAGAGATGGA 60.914 60.000 0.00 0.00 0.00 3.41
2905 3652 2.738521 CGTGGAGCGGAGGTGTTG 60.739 66.667 0.00 0.00 39.88 3.33
2906 3653 4.681978 GCGTGGAGCGGAGGTGTT 62.682 66.667 0.00 0.00 39.88 3.32


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

AutoCloner maintained by Alex Coulton.