Multiple sequence alignment - TraesCS3A01G260300

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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 TraesCS3A01G260300 chr3A 100.000 5458 0 0 1 5458 482978455 482972998 0.000000e+00 10080
1 TraesCS3A01G260300 chr3A 98.709 1472 12 4 2710 4178 718946938 718945471 0.000000e+00 2606
2 TraesCS3A01G260300 chr3A 85.276 163 23 1 5285 5446 637608432 637608594 3.380000e-37 167
3 TraesCS3A01G260300 chr3D 94.872 2730 105 18 1 2718 362433769 362431063 0.000000e+00 4233
4 TraesCS3A01G260300 chr3D 89.147 1161 59 17 4162 5272 362431080 362429937 0.000000e+00 1384
5 TraesCS3A01G260300 chr3D 84.541 207 12 6 5272 5458 362429875 362429669 2.600000e-43 187
6 TraesCS3A01G260300 chr3B 93.614 2662 108 26 1 2653 472325430 472322822 0.000000e+00 3917
7 TraesCS3A01G260300 chr3B 89.453 1024 57 18 4162 5137 472322760 472321740 0.000000e+00 1245
8 TraesCS3A01G260300 chr3B 94.030 134 8 0 5129 5262 472321486 472321353 2.580000e-48 204
9 TraesCS3A01G260300 chr7A 99.244 1455 7 3 2710 4161 265439803 265441256 0.000000e+00 2623
10 TraesCS3A01G260300 chr7A 99.310 1449 7 2 2710 4156 206957491 206958938 0.000000e+00 2617
11 TraesCS3A01G260300 chr7A 99.242 1451 10 1 2710 4160 495454062 495455511 0.000000e+00 2617
12 TraesCS3A01G260300 chr7A 85.625 160 21 2 5290 5448 42596995 42597153 3.380000e-37 167
13 TraesCS3A01G260300 chr2B 99.176 1456 9 2 2710 4163 46598421 46596967 0.000000e+00 2619
14 TraesCS3A01G260300 chr6B 99.242 1451 10 1 2710 4160 606301808 606303257 0.000000e+00 2617
15 TraesCS3A01G260300 chr6B 99.105 1453 12 1 2710 4162 554796080 554797531 0.000000e+00 2610
16 TraesCS3A01G260300 chr6B 90.184 163 8 3 1441 1596 542943513 542943674 7.170000e-49 206
17 TraesCS3A01G260300 chr5B 99.309 1448 9 1 2710 4157 623111705 623113151 0.000000e+00 2617
18 TraesCS3A01G260300 chr5B 85.714 168 21 3 5282 5448 338935128 338934963 2.020000e-39 174
19 TraesCS3A01G260300 chr5B 85.093 161 20 4 5289 5447 45837362 45837520 1.570000e-35 161
20 TraesCS3A01G260300 chr5A 99.173 1451 10 2 2710 4160 174600139 174601587 0.000000e+00 2612
21 TraesCS3A01G260300 chr5A 87.500 184 16 2 1441 1618 162033605 162033423 7.170000e-49 206
22 TraesCS3A01G260300 chr5A 81.522 184 28 5 5272 5452 459753813 459753993 4.410000e-31 147
23 TraesCS3A01G260300 chr1A 90.395 177 15 2 5272 5448 124346813 124346987 1.180000e-56 231
24 TraesCS3A01G260300 chr6A 88.587 184 14 2 1441 1618 265783484 265783302 3.310000e-52 217
25 TraesCS3A01G260300 chr2A 85.083 181 21 4 5272 5447 644251674 644251495 4.340000e-41 180
26 TraesCS3A01G260300 chr7D 84.659 176 26 1 5272 5447 60490567 60490741 2.020000e-39 174
27 TraesCS3A01G260300 chr1B 83.799 179 12 9 1435 1613 280709321 280709160 2.630000e-33 154


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 TraesCS3A01G260300 chr3A 482972998 482978455 5457 True 10080.000000 10080 100.000000 1 5458 1 chr3A.!!$R1 5457
1 TraesCS3A01G260300 chr3A 718945471 718946938 1467 True 2606.000000 2606 98.709000 2710 4178 1 chr3A.!!$R2 1468
2 TraesCS3A01G260300 chr3D 362429669 362433769 4100 True 1934.666667 4233 89.520000 1 5458 3 chr3D.!!$R1 5457
3 TraesCS3A01G260300 chr3B 472321353 472325430 4077 True 1788.666667 3917 92.365667 1 5262 3 chr3B.!!$R1 5261
4 TraesCS3A01G260300 chr7A 265439803 265441256 1453 False 2623.000000 2623 99.244000 2710 4161 1 chr7A.!!$F3 1451
5 TraesCS3A01G260300 chr7A 206957491 206958938 1447 False 2617.000000 2617 99.310000 2710 4156 1 chr7A.!!$F2 1446
6 TraesCS3A01G260300 chr7A 495454062 495455511 1449 False 2617.000000 2617 99.242000 2710 4160 1 chr7A.!!$F4 1450
7 TraesCS3A01G260300 chr2B 46596967 46598421 1454 True 2619.000000 2619 99.176000 2710 4163 1 chr2B.!!$R1 1453
8 TraesCS3A01G260300 chr6B 606301808 606303257 1449 False 2617.000000 2617 99.242000 2710 4160 1 chr6B.!!$F3 1450
9 TraesCS3A01G260300 chr6B 554796080 554797531 1451 False 2610.000000 2610 99.105000 2710 4162 1 chr6B.!!$F2 1452
10 TraesCS3A01G260300 chr5B 623111705 623113151 1446 False 2617.000000 2617 99.309000 2710 4157 1 chr5B.!!$F2 1447
11 TraesCS3A01G260300 chr5A 174600139 174601587 1448 False 2612.000000 2612 99.173000 2710 4160 1 chr5A.!!$F1 1450

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
108 110 0.825425 TTCGCACCATGAAGGCCAAA 60.825 50.000 5.01 0.0 43.14 3.28 F
243 245 1.074889 GGGGTTGCTGTTCCTCCTTTA 59.925 52.381 0.00 0.0 0.00 1.85 F
577 583 1.075212 TGTTGAACATCCAGGCATCCA 59.925 47.619 0.00 0.0 0.00 3.41 F
1956 1962 1.456705 TTTTGCTGGCCTCGGGTTT 60.457 52.632 3.32 0.0 0.00 3.27 F
2685 2714 0.820871 GTGCCCTTCACACCAAACAA 59.179 50.000 0.00 0.0 44.98 2.83 F
4290 4344 0.250038 TCTGCTCTGTTCGCAAGCTT 60.250 50.000 0.00 0.0 36.88 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1997 2003 2.435437 AGTTTTGCAACATGGCCTCTTT 59.565 40.909 3.32 0.00 35.05 2.52 R
2279 2285 1.428448 CATTTTCGTCAGACGGCAGA 58.572 50.000 22.66 5.99 42.81 4.26 R
2329 2335 1.978580 CCTAACTCTGTGGGGTCTTGT 59.021 52.381 0.00 0.00 0.00 3.16 R
3472 3508 0.844661 TACCACCTGGCCATCAAGGT 60.845 55.000 19.23 19.23 40.61 3.50 R
4427 4487 1.021968 GTTCTGCACCGAGTTTTGGT 58.978 50.000 0.00 0.00 41.47 3.67 R
5134 5221 1.204941 GATTCTCAGTAGCACGGTGGT 59.795 52.381 17.69 17.69 0.00 4.16 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
42 44 2.172717 ACAGGTTTGATCTTATCCCGGG 59.827 50.000 16.85 16.85 0.00 5.73
108 110 0.825425 TTCGCACCATGAAGGCCAAA 60.825 50.000 5.01 0.00 43.14 3.28
243 245 1.074889 GGGGTTGCTGTTCCTCCTTTA 59.925 52.381 0.00 0.00 0.00 1.85
420 426 4.977963 GGTGAATTGTTGATTATGGCATCG 59.022 41.667 1.65 0.00 0.00 3.84
496 502 4.019919 TCTATTTCCGTTCGTACCTTCG 57.980 45.455 0.00 0.00 0.00 3.79
516 522 2.222796 CGGTTGTGTGCTGATAATGACG 60.223 50.000 0.00 0.00 0.00 4.35
547 553 6.938507 TCTAGTTTTGCCTCGTCCTATTTTA 58.061 36.000 0.00 0.00 0.00 1.52
558 564 7.855904 GCCTCGTCCTATTTTATTATGTTTGTG 59.144 37.037 0.00 0.00 0.00 3.33
559 565 8.889717 CCTCGTCCTATTTTATTATGTTTGTGT 58.110 33.333 0.00 0.00 0.00 3.72
570 576 9.689976 TTTATTATGTTTGTGTTGAACATCCAG 57.310 29.630 0.00 0.00 44.26 3.86
572 578 2.100584 TGTTTGTGTTGAACATCCAGGC 59.899 45.455 0.00 0.00 38.99 4.85
573 579 2.064434 TTGTGTTGAACATCCAGGCA 57.936 45.000 0.00 0.00 38.99 4.75
575 581 2.161855 TGTGTTGAACATCCAGGCATC 58.838 47.619 0.00 0.00 32.36 3.91
577 583 1.075212 TGTTGAACATCCAGGCATCCA 59.925 47.619 0.00 0.00 0.00 3.41
602 608 7.873739 GCAATTGGCATTATAGGTTCATTAC 57.126 36.000 7.72 0.00 43.97 1.89
603 609 6.868339 GCAATTGGCATTATAGGTTCATTACC 59.132 38.462 7.72 0.00 44.68 2.85
624 630 5.801380 ACCTTAACCTTACAATCACGTGAT 58.199 37.500 25.18 25.18 36.07 3.06
666 672 5.011023 TCTCTCTTGAACATCTACAGCACAA 59.989 40.000 0.00 0.00 0.00 3.33
750 756 8.499162 CCTAACAAGATTCTTACTCAAACTGTG 58.501 37.037 0.00 0.00 0.00 3.66
826 832 1.765314 CCTGGGCTGCTAGTCTACAAT 59.235 52.381 0.00 0.00 0.00 2.71
931 937 4.814234 TCTTTGACAAATAGACACGCTTGT 59.186 37.500 0.05 0.00 39.32 3.16
1114 1120 5.186198 ACTGGATTGTGCTGGTTATTCTAC 58.814 41.667 0.00 0.00 0.00 2.59
1127 1133 5.013704 TGGTTATTCTACTTGTGGTGGATGT 59.986 40.000 0.00 0.00 35.40 3.06
1179 1185 3.342377 TTTGTTGGATCGGACATGCTA 57.658 42.857 0.00 0.00 0.00 3.49
1245 1251 3.434299 GGACGGTGCCGGTATATATTTTG 59.566 47.826 15.44 0.00 44.69 2.44
1286 1292 7.396055 CCCTGTTTATTTTCATGAACCTCCTAA 59.604 37.037 7.89 0.00 29.55 2.69
1287 1293 8.462016 CCTGTTTATTTTCATGAACCTCCTAAG 58.538 37.037 7.89 2.10 29.55 2.18
1288 1294 8.934023 TGTTTATTTTCATGAACCTCCTAAGT 57.066 30.769 7.89 0.00 29.55 2.24
1313 1319 9.425893 GTACATTGTCTTGAATTATCGTGATTG 57.574 33.333 0.00 0.00 0.00 2.67
1612 1618 3.059352 ACCTGTAATGTGCTCACCTTC 57.941 47.619 0.00 0.00 0.00 3.46
1673 1679 4.436584 GCACGATTTCATCTGACCTTTCTG 60.437 45.833 0.00 0.00 0.00 3.02
1956 1962 1.456705 TTTTGCTGGCCTCGGGTTT 60.457 52.632 3.32 0.00 0.00 3.27
1997 2003 8.203485 AGCTGGTAAAATCAAAGTTTTTGATCA 58.797 29.630 15.17 9.07 38.11 2.92
2161 2167 8.757789 TGGTTATCTATTAAAGATTACGTTGCG 58.242 33.333 0.00 0.00 42.62 4.85
2180 2186 7.744715 ACGTTGCGAAACAAATAAAGATAGAAG 59.255 33.333 7.15 0.00 40.82 2.85
2291 2297 1.878953 TTTTTCCTCTGCCGTCTGAC 58.121 50.000 0.00 0.00 0.00 3.51
2329 2335 7.822822 GCTTCATACTTCTTTTAGGGTAACTCA 59.177 37.037 0.00 0.00 0.00 3.41
2336 2342 5.861727 TCTTTTAGGGTAACTCACAAGACC 58.138 41.667 0.00 0.00 0.00 3.85
2341 2347 1.418637 GGTAACTCACAAGACCCCACA 59.581 52.381 0.00 0.00 0.00 4.17
2376 2382 4.704965 AGTTCTTAGAAACCACTGGTGTC 58.295 43.478 10.19 10.19 40.12 3.67
2377 2383 3.380479 TCTTAGAAACCACTGGTGTCG 57.620 47.619 12.11 0.00 44.27 4.35
2415 2422 5.004448 TGCAATGTGAAAATTGGCATCAAT 58.996 33.333 0.00 0.00 44.77 2.57
2416 2423 6.171213 TGCAATGTGAAAATTGGCATCAATA 58.829 32.000 0.00 0.00 42.29 1.90
2428 2435 5.308976 TGGCATCAATATCTAGCCTTCAA 57.691 39.130 0.00 0.00 45.42 2.69
2513 2522 7.439955 TCTGTAATATACTTGGGTTGTTATGCG 59.560 37.037 0.00 0.00 0.00 4.73
2514 2523 6.483974 TGTAATATACTTGGGTTGTTATGCGG 59.516 38.462 0.00 0.00 0.00 5.69
2581 2590 4.664150 TTTGTGTCCAATTTCCAGTTCC 57.336 40.909 0.00 0.00 0.00 3.62
2582 2591 2.226330 TGTGTCCAATTTCCAGTTCCG 58.774 47.619 0.00 0.00 0.00 4.30
2583 2592 2.227194 GTGTCCAATTTCCAGTTCCGT 58.773 47.619 0.00 0.00 0.00 4.69
2584 2593 2.225727 GTGTCCAATTTCCAGTTCCGTC 59.774 50.000 0.00 0.00 0.00 4.79
2585 2594 1.463444 GTCCAATTTCCAGTTCCGTCG 59.537 52.381 0.00 0.00 0.00 5.12
2586 2595 1.071071 TCCAATTTCCAGTTCCGTCGT 59.929 47.619 0.00 0.00 0.00 4.34
2605 2618 6.075205 CCGTCGTATAATTTGGTAACTCTTCG 60.075 42.308 0.00 0.00 37.61 3.79
2608 2621 7.485913 GTCGTATAATTTGGTAACTCTTCGACA 59.514 37.037 0.00 0.00 40.25 4.35
2628 2641 4.521146 ACAATATCCCTTGAAGTGCTCAG 58.479 43.478 0.00 0.00 34.81 3.35
2638 2651 5.580297 CCTTGAAGTGCTCAGACTAATCTTC 59.420 44.000 0.00 0.00 34.81 2.87
2641 2654 6.336566 TGAAGTGCTCAGACTAATCTTCATC 58.663 40.000 0.00 0.00 36.16 2.92
2648 2677 7.663081 TGCTCAGACTAATCTTCATCTTTTGTT 59.337 33.333 0.00 0.00 30.42 2.83
2663 2692 8.420222 TCATCTTTTGTTACCACAATTGACAAT 58.580 29.630 13.59 0.00 42.66 2.71
2684 2713 2.499214 GTGCCCTTCACACCAAACA 58.501 52.632 0.00 0.00 44.98 2.83
2685 2714 0.820871 GTGCCCTTCACACCAAACAA 59.179 50.000 0.00 0.00 44.98 2.83
2690 2719 3.944650 GCCCTTCACACCAAACAATTTTT 59.055 39.130 0.00 0.00 0.00 1.94
2691 2720 5.119694 GCCCTTCACACCAAACAATTTTTA 58.880 37.500 0.00 0.00 0.00 1.52
2692 2721 5.007234 GCCCTTCACACCAAACAATTTTTAC 59.993 40.000 0.00 0.00 0.00 2.01
2693 2722 6.345298 CCCTTCACACCAAACAATTTTTACT 58.655 36.000 0.00 0.00 0.00 2.24
2695 2724 7.982354 CCCTTCACACCAAACAATTTTTACTAA 59.018 33.333 0.00 0.00 0.00 2.24
2696 2725 9.541143 CCTTCACACCAAACAATTTTTACTAAT 57.459 29.630 0.00 0.00 0.00 1.73
2703 2732 9.908152 ACCAAACAATTTTTACTAATCTAGTGC 57.092 29.630 0.00 0.00 39.81 4.40
2704 2733 9.353999 CCAAACAATTTTTACTAATCTAGTGCC 57.646 33.333 0.00 0.00 39.81 5.01
2705 2734 9.906660 CAAACAATTTTTACTAATCTAGTGCCA 57.093 29.630 0.00 0.00 39.81 4.92
2708 2737 8.190784 ACAATTTTTACTAATCTAGTGCCATGC 58.809 33.333 0.00 0.00 39.81 4.06
2824 2853 2.879103 TCAAGAACAAGGGGGATGTC 57.121 50.000 0.00 0.00 0.00 3.06
2879 2908 5.872963 TGATGAGCCATACAATGAAGCTAT 58.127 37.500 0.00 0.00 32.97 2.97
3284 3313 3.731431 TGAGGTCACAAGGGGTATACAT 58.269 45.455 5.01 0.00 0.00 2.29
3472 3508 2.327325 AGCTGTGAGGAGGAGGTTAA 57.673 50.000 0.00 0.00 0.00 2.01
3521 3557 2.553685 GGACACCTTTCGGTATTTGGGT 60.554 50.000 0.00 0.00 43.24 4.51
3616 3652 3.272574 CCAAGCTTCTGGCATTCTCTA 57.727 47.619 0.00 0.00 44.79 2.43
3654 3690 4.507756 CACAAAAGCTAAAAGGCAAGTTCC 59.492 41.667 0.00 0.00 34.17 3.62
4165 4202 3.495670 TGTTGTTGTTGTTGTAGTGCC 57.504 42.857 0.00 0.00 0.00 5.01
4193 4230 7.147863 TGCACATGGTGAGAAATGCTTATATTT 60.148 33.333 0.00 0.00 35.23 1.40
4194 4231 7.168637 GCACATGGTGAGAAATGCTTATATTTG 59.831 37.037 0.00 0.00 35.23 2.32
4195 4232 8.407832 CACATGGTGAGAAATGCTTATATTTGA 58.592 33.333 0.00 0.00 35.23 2.69
4196 4233 9.139734 ACATGGTGAGAAATGCTTATATTTGAT 57.860 29.630 0.00 0.00 30.78 2.57
4197 4234 9.406828 CATGGTGAGAAATGCTTATATTTGATG 57.593 33.333 0.00 0.00 30.78 3.07
4198 4235 7.428020 TGGTGAGAAATGCTTATATTTGATGC 58.572 34.615 0.00 0.00 30.78 3.91
4199 4236 7.068470 TGGTGAGAAATGCTTATATTTGATGCA 59.932 33.333 0.00 0.00 38.05 3.96
4260 4314 4.287845 TGATGTTGCAGGGCTATCTCATAT 59.712 41.667 0.00 0.00 0.00 1.78
4261 4315 4.277515 TGTTGCAGGGCTATCTCATATC 57.722 45.455 0.00 0.00 0.00 1.63
4272 4326 7.782644 AGGGCTATCTCATATCCTACTGTAATC 59.217 40.741 0.00 0.00 0.00 1.75
4284 4338 2.611518 ACTGTAATCTGCTCTGTTCGC 58.388 47.619 0.00 0.00 0.00 4.70
4290 4344 0.250038 TCTGCTCTGTTCGCAAGCTT 60.250 50.000 0.00 0.00 36.88 3.74
4291 4345 1.000843 TCTGCTCTGTTCGCAAGCTTA 59.999 47.619 0.00 0.00 36.88 3.09
4292 4346 1.800586 CTGCTCTGTTCGCAAGCTTAA 59.199 47.619 0.00 0.00 36.88 1.85
4297 4351 2.923655 TCTGTTCGCAAGCTTAAGATCG 59.076 45.455 6.67 0.58 37.18 3.69
4365 4425 1.227380 GGTCTATGGCCTCACGCAG 60.227 63.158 3.32 0.00 40.31 5.18
4372 4432 2.265739 GCCTCACGCAGACATCCA 59.734 61.111 0.00 0.00 37.47 3.41
4380 4440 0.376152 CGCAGACATCCAGCACATTC 59.624 55.000 0.00 0.00 0.00 2.67
4385 4445 4.277672 GCAGACATCCAGCACATTCATAAT 59.722 41.667 0.00 0.00 0.00 1.28
4427 4487 1.548081 CAACCCACAGCAATGGATCA 58.452 50.000 7.80 0.00 43.02 2.92
4451 4511 0.463116 AACTCGGTGCAGAACGGTTT 60.463 50.000 0.00 0.00 0.00 3.27
4462 4522 3.674955 GCAGAACGGTTTGTTTGAAGGTT 60.675 43.478 0.00 0.00 42.09 3.50
4479 4539 3.283751 AGGTTCTGATGGACTAGAGACG 58.716 50.000 0.00 0.00 0.00 4.18
4488 4548 1.417145 GGACTAGAGACGAGGGCTAGA 59.583 57.143 0.00 0.00 36.12 2.43
4556 4617 7.905604 TGAATAGGATGGTTGCTAAATATCG 57.094 36.000 0.00 0.00 28.80 2.92
4697 4779 8.782137 ATATTGCTTTTAACATGGGGTAGAAT 57.218 30.769 0.00 0.00 0.00 2.40
4743 4825 3.449918 TGATGATCTGTGACCCCTGTTA 58.550 45.455 0.00 0.00 0.00 2.41
4749 4831 3.750371 TCTGTGACCCCTGTTATTTGTG 58.250 45.455 0.00 0.00 0.00 3.33
4831 4915 7.794041 TGTAGTCTTACCCTTGAAGTTAAACA 58.206 34.615 0.00 0.00 0.00 2.83
4971 5058 3.181461 ACTGATCCCGAATAGGCTTTCAG 60.181 47.826 0.00 0.00 41.00 3.02
4981 5068 5.449177 CGAATAGGCTTTCAGATCCCAAAAC 60.449 44.000 0.00 0.00 0.00 2.43
4997 5084 1.021968 AAACGTTTTTGGAGCGAGCT 58.978 45.000 7.96 0.00 0.00 4.09
5029 5116 3.566332 CCCCTCCATCCCAAAAGATTCAA 60.566 47.826 0.00 0.00 0.00 2.69
5059 5146 1.391485 CGAGCGTCAAAATGTCTCCAG 59.609 52.381 0.00 0.00 0.00 3.86
5185 5534 3.879885 CCACCGTGACCCCCACAA 61.880 66.667 0.00 0.00 45.98 3.33
5287 5698 8.243426 CAGGCAAGTGCTTTTGAATATAAAGTA 58.757 33.333 2.85 0.00 41.70 2.24
5414 5845 8.546244 AGTTTTAACTCTTGAAACTTAGTACGC 58.454 33.333 0.38 0.00 44.09 4.42
5415 5846 8.330302 GTTTTAACTCTTGAAACTTAGTACGCA 58.670 33.333 0.00 0.00 36.53 5.24
5417 5848 4.304939 ACTCTTGAAACTTAGTACGCACC 58.695 43.478 0.00 0.00 0.00 5.01
5432 5863 6.044046 AGTACGCACCAACGATAAAATCATA 58.956 36.000 0.00 0.00 36.70 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.135139 TGTAGCAAAGCTAGCTCCTCG 59.865 52.381 19.65 7.94 42.11 4.63
42 44 1.082951 CGCGCATGCACATCAGATC 60.083 57.895 19.57 0.00 42.97 2.75
61 63 1.341531 ACCACAAGTTCACGAGAGGAG 59.658 52.381 0.00 0.00 0.00 3.69
130 132 0.924090 CACAAGGCGCTCGACTATTC 59.076 55.000 7.64 0.00 30.17 1.75
211 213 0.098200 GCAACCCCTTCGCGTTATTC 59.902 55.000 5.77 0.00 0.00 1.75
225 227 4.336280 AGAATAAAGGAGGAACAGCAACC 58.664 43.478 0.00 0.00 0.00 3.77
243 245 6.006449 AGTATCAAGTGGAAGTTGCAAGAAT 58.994 36.000 0.00 0.00 46.75 2.40
496 502 2.095853 CCGTCATTATCAGCACACAACC 59.904 50.000 0.00 0.00 0.00 3.77
516 522 3.751698 ACGAGGCAAAACTAGAACAATCC 59.248 43.478 0.00 0.00 0.00 3.01
547 553 6.690530 CCTGGATGTTCAACACAAACATAAT 58.309 36.000 0.00 0.00 45.02 1.28
558 564 1.747355 CTGGATGCCTGGATGTTCAAC 59.253 52.381 0.00 0.00 0.00 3.18
559 565 1.956636 GCTGGATGCCTGGATGTTCAA 60.957 52.381 0.00 0.00 35.15 2.69
561 567 0.394762 TGCTGGATGCCTGGATGTTC 60.395 55.000 0.00 0.00 42.00 3.18
562 568 0.040058 TTGCTGGATGCCTGGATGTT 59.960 50.000 0.00 0.00 42.00 2.71
563 569 0.260816 ATTGCTGGATGCCTGGATGT 59.739 50.000 0.00 0.00 42.00 3.06
564 570 1.068588 CAATTGCTGGATGCCTGGATG 59.931 52.381 0.00 0.00 42.00 3.51
565 571 1.410004 CAATTGCTGGATGCCTGGAT 58.590 50.000 0.00 0.00 42.00 3.41
566 572 2.890612 CAATTGCTGGATGCCTGGA 58.109 52.632 0.00 0.00 42.00 3.86
577 583 6.736110 AATGAACCTATAATGCCAATTGCT 57.264 33.333 0.00 0.00 42.00 3.91
594 600 8.173130 CGTGATTGTAAGGTTAAGGTAATGAAC 58.827 37.037 0.00 0.00 0.00 3.18
595 601 7.879160 ACGTGATTGTAAGGTTAAGGTAATGAA 59.121 33.333 0.00 0.00 0.00 2.57
596 602 7.332430 CACGTGATTGTAAGGTTAAGGTAATGA 59.668 37.037 10.90 0.00 0.00 2.57
597 603 7.332430 TCACGTGATTGTAAGGTTAAGGTAATG 59.668 37.037 15.76 0.00 0.00 1.90
598 604 7.388437 TCACGTGATTGTAAGGTTAAGGTAAT 58.612 34.615 15.76 0.00 0.00 1.89
599 605 6.757237 TCACGTGATTGTAAGGTTAAGGTAA 58.243 36.000 15.76 0.00 0.00 2.85
600 606 6.343716 TCACGTGATTGTAAGGTTAAGGTA 57.656 37.500 15.76 0.00 0.00 3.08
601 607 5.217978 TCACGTGATTGTAAGGTTAAGGT 57.782 39.130 15.76 0.00 0.00 3.50
602 608 6.737254 AATCACGTGATTGTAAGGTTAAGG 57.263 37.500 36.26 0.00 42.66 2.69
624 630 6.358178 AGAGAGATATCGTGTCCTAGAACAA 58.642 40.000 0.00 0.00 0.00 2.83
638 644 7.594758 GTGCTGTAGATGTTCAAGAGAGATATC 59.405 40.741 0.00 0.00 0.00 1.63
666 672 0.957395 CTCACAGAACATGCGCCCTT 60.957 55.000 4.18 0.00 0.00 3.95
723 729 8.211629 ACAGTTTGAGTAAGAATCTTGTTAGGT 58.788 33.333 5.64 0.00 0.00 3.08
812 818 8.634444 ACCTGTTTCTATATTGTAGACTAGCAG 58.366 37.037 0.00 0.00 0.00 4.24
922 928 9.997482 CCACTAAATAAATTATAACAAGCGTGT 57.003 29.630 0.00 0.00 40.75 4.49
945 951 6.596497 TCCACCGAATAGATTTAAGAAACCAC 59.404 38.462 0.00 0.00 0.00 4.16
947 953 7.255139 CCATCCACCGAATAGATTTAAGAAACC 60.255 40.741 0.00 0.00 0.00 3.27
992 998 1.599240 GGAGATGGCATCGCTTCCC 60.599 63.158 26.59 17.04 0.00 3.97
1114 1120 9.661563 TTTATTTAGTACTACATCCACCACAAG 57.338 33.333 0.91 0.00 0.00 3.16
1286 1292 8.948631 ATCACGATAATTCAAGACAATGTACT 57.051 30.769 0.00 0.00 0.00 2.73
1287 1293 9.425893 CAATCACGATAATTCAAGACAATGTAC 57.574 33.333 0.00 0.00 0.00 2.90
1288 1294 9.161629 ACAATCACGATAATTCAAGACAATGTA 57.838 29.630 0.00 0.00 0.00 2.29
1289 1295 7.964559 CACAATCACGATAATTCAAGACAATGT 59.035 33.333 0.00 0.00 0.00 2.71
1313 1319 6.540189 GGTCCAATGATACCATATATCTGCAC 59.460 42.308 0.71 0.00 35.73 4.57
1424 1430 8.565896 AGAATAAGATATCACAAACTTGCACA 57.434 30.769 5.32 0.00 0.00 4.57
1462 1468 5.344743 TGGTAGGACAAGCTAGATTTCAG 57.655 43.478 0.00 0.00 0.00 3.02
1956 1962 3.916035 ACCAGCTAGATACCATGACAGA 58.084 45.455 0.00 0.00 0.00 3.41
1997 2003 2.435437 AGTTTTGCAACATGGCCTCTTT 59.565 40.909 3.32 0.00 35.05 2.52
2279 2285 1.428448 CATTTTCGTCAGACGGCAGA 58.572 50.000 22.66 5.99 42.81 4.26
2291 2297 7.251704 AGAAGTATGAAGCATACCATTTTCG 57.748 36.000 12.53 0.00 45.37 3.46
2329 2335 1.978580 CCTAACTCTGTGGGGTCTTGT 59.021 52.381 0.00 0.00 0.00 3.16
2336 2342 4.717280 AGAACTATTCCCTAACTCTGTGGG 59.283 45.833 0.00 0.00 42.20 4.61
2341 2347 8.760735 GGTTTCTAAGAACTATTCCCTAACTCT 58.239 37.037 0.00 0.00 0.00 3.24
2376 2382 2.420628 TGCAAAGCACTTTCCAATCG 57.579 45.000 0.00 0.00 31.71 3.34
2377 2383 4.060205 ACATTGCAAAGCACTTTCCAATC 58.940 39.130 8.91 0.00 38.48 2.67
2415 2422 7.878127 GTGGTTATAATGCTTGAAGGCTAGATA 59.122 37.037 0.00 0.00 0.00 1.98
2416 2423 6.712547 GTGGTTATAATGCTTGAAGGCTAGAT 59.287 38.462 0.00 0.00 0.00 1.98
2428 2435 7.609918 TGTACAAATGAGTGTGGTTATAATGCT 59.390 33.333 0.00 0.00 32.75 3.79
2513 2522 3.459232 TGCTACTGTATCATCAGTGCC 57.541 47.619 9.21 1.91 46.36 5.01
2514 2523 4.375272 ACATGCTACTGTATCATCAGTGC 58.625 43.478 9.21 10.44 46.36 4.40
2581 2590 6.688385 TCGAAGAGTTACCAAATTATACGACG 59.312 38.462 0.00 0.00 0.00 5.12
2582 2591 7.485913 TGTCGAAGAGTTACCAAATTATACGAC 59.514 37.037 0.00 0.00 42.20 4.34
2583 2592 7.537715 TGTCGAAGAGTTACCAAATTATACGA 58.462 34.615 0.00 0.00 36.95 3.43
2584 2593 7.745022 TGTCGAAGAGTTACCAAATTATACG 57.255 36.000 0.00 0.00 36.95 3.06
2605 2618 4.517285 TGAGCACTTCAAGGGATATTGTC 58.483 43.478 0.00 0.00 31.34 3.18
2608 2621 4.472833 AGTCTGAGCACTTCAAGGGATATT 59.527 41.667 0.00 0.00 34.81 1.28
2648 2677 2.560542 GCACCCATTGTCAATTGTGGTA 59.439 45.455 19.36 0.00 0.00 3.25
2682 2711 8.190784 GCATGGCACTAGATTAGTAAAAATTGT 58.809 33.333 0.00 0.00 37.23 2.71
2683 2712 8.190122 TGCATGGCACTAGATTAGTAAAAATTG 58.810 33.333 0.00 0.00 37.23 2.32
2684 2713 8.292444 TGCATGGCACTAGATTAGTAAAAATT 57.708 30.769 0.00 0.00 37.23 1.82
2685 2714 7.880160 TGCATGGCACTAGATTAGTAAAAAT 57.120 32.000 0.00 0.00 37.23 1.82
2701 2730 1.070601 ACTATCGCTATGTGCATGGCA 59.929 47.619 18.08 7.83 44.30 4.92
2702 2731 1.800805 ACTATCGCTATGTGCATGGC 58.199 50.000 9.97 9.97 43.06 4.40
2703 2732 3.867493 CCATACTATCGCTATGTGCATGG 59.133 47.826 0.00 0.00 43.06 3.66
2704 2733 3.308053 GCCATACTATCGCTATGTGCATG 59.692 47.826 0.00 0.00 43.06 4.06
2705 2734 3.196469 AGCCATACTATCGCTATGTGCAT 59.804 43.478 0.00 0.00 43.06 3.96
2706 2735 2.562738 AGCCATACTATCGCTATGTGCA 59.437 45.455 0.00 0.00 43.06 4.57
2707 2736 3.238108 AGCCATACTATCGCTATGTGC 57.762 47.619 0.00 0.00 38.57 4.57
2708 2737 5.103000 GGTTAGCCATACTATCGCTATGTG 58.897 45.833 0.00 0.00 35.17 3.21
2824 2853 5.105635 TCCACGGTAATTAGTACAACTCTGG 60.106 44.000 0.00 0.00 34.01 3.86
2879 2908 2.027745 GTGCTCAATGACTCTCTCCCAA 60.028 50.000 0.00 0.00 0.00 4.12
3284 3313 3.264193 GCATACACCATGGGATATCTCCA 59.736 47.826 18.09 13.34 44.08 3.86
3472 3508 0.844661 TACCACCTGGCCATCAAGGT 60.845 55.000 19.23 19.23 40.61 3.50
3521 3557 2.449464 CCATCCTCCTGCAACATTGAA 58.551 47.619 0.00 0.00 0.00 2.69
3616 3652 2.936919 TTGTGGCACTCTCTTGTCAT 57.063 45.000 19.83 0.00 32.63 3.06
3654 3690 4.351938 TCGAACCGCCGTCCTGTG 62.352 66.667 0.00 0.00 0.00 3.66
4165 4202 2.165641 AGCATTTCTCACCATGTGCATG 59.834 45.455 5.26 5.26 38.51 4.06
4220 4257 9.158233 TGCAACATCAACCTAGTAGTTTATAAC 57.842 33.333 0.00 0.00 0.00 1.89
4237 4274 1.839354 TGAGATAGCCCTGCAACATCA 59.161 47.619 0.00 0.00 0.00 3.07
4238 4275 2.627515 TGAGATAGCCCTGCAACATC 57.372 50.000 0.00 0.00 0.00 3.06
4239 4276 4.324099 GGATATGAGATAGCCCTGCAACAT 60.324 45.833 0.00 0.00 35.28 2.71
4241 4278 3.262915 AGGATATGAGATAGCCCTGCAAC 59.737 47.826 0.00 0.00 42.21 4.17
4242 4279 3.524826 AGGATATGAGATAGCCCTGCAA 58.475 45.455 0.00 0.00 42.21 4.08
4243 4280 3.196415 AGGATATGAGATAGCCCTGCA 57.804 47.619 0.00 0.00 42.21 4.41
4260 4314 4.096532 CGAACAGAGCAGATTACAGTAGGA 59.903 45.833 0.00 0.00 0.00 2.94
4261 4315 4.355437 CGAACAGAGCAGATTACAGTAGG 58.645 47.826 0.00 0.00 0.00 3.18
4272 4326 1.432514 TAAGCTTGCGAACAGAGCAG 58.567 50.000 9.86 0.00 46.01 4.24
4292 4346 9.092876 GACAAAGATGAAAGAAGATAACGATCT 57.907 33.333 0.00 0.00 44.79 2.75
4331 4385 5.649395 CCATAGACCTGTCAATGAACAATGT 59.351 40.000 0.00 0.00 0.00 2.71
4332 4386 5.449588 GCCATAGACCTGTCAATGAACAATG 60.450 44.000 0.00 0.00 0.00 2.82
4333 4387 4.641989 GCCATAGACCTGTCAATGAACAAT 59.358 41.667 0.00 0.00 0.00 2.71
4336 4390 2.945668 GGCCATAGACCTGTCAATGAAC 59.054 50.000 0.00 0.00 0.00 3.18
4337 4391 2.846206 AGGCCATAGACCTGTCAATGAA 59.154 45.455 5.01 0.00 35.72 2.57
4338 4392 2.435805 GAGGCCATAGACCTGTCAATGA 59.564 50.000 5.01 0.00 37.77 2.57
4339 4393 2.171237 TGAGGCCATAGACCTGTCAATG 59.829 50.000 5.01 0.00 37.77 2.82
4340 4394 2.171448 GTGAGGCCATAGACCTGTCAAT 59.829 50.000 5.01 0.00 37.77 2.57
4342 4396 1.195115 GTGAGGCCATAGACCTGTCA 58.805 55.000 5.01 0.00 37.77 3.58
4365 4425 4.083643 CGGATTATGAATGTGCTGGATGTC 60.084 45.833 0.00 0.00 0.00 3.06
4372 4432 3.480470 CCTTCCGGATTATGAATGTGCT 58.520 45.455 4.15 0.00 0.00 4.40
4380 4440 1.136828 TGTCCCCCTTCCGGATTATG 58.863 55.000 4.15 0.00 0.00 1.90
4385 4445 2.926242 GTGTGTCCCCCTTCCGGA 60.926 66.667 0.00 0.00 0.00 5.14
4418 4478 2.819608 ACCGAGTTTTGGTGATCCATTG 59.180 45.455 0.00 0.00 43.91 2.82
4419 4479 3.154827 ACCGAGTTTTGGTGATCCATT 57.845 42.857 0.00 0.00 43.91 3.16
4427 4487 1.021968 GTTCTGCACCGAGTTTTGGT 58.978 50.000 0.00 0.00 41.47 3.67
4442 4502 4.014406 AGAACCTTCAAACAAACCGTTCT 58.986 39.130 0.00 0.00 36.59 3.01
4451 4511 4.437682 AGTCCATCAGAACCTTCAAACA 57.562 40.909 0.00 0.00 0.00 2.83
4462 4522 2.158740 CCCTCGTCTCTAGTCCATCAGA 60.159 54.545 0.00 0.00 0.00 3.27
4479 4539 2.334023 ACCTCATGGAATCTAGCCCTC 58.666 52.381 0.00 0.00 37.04 4.30
4488 4548 3.104512 TCTACGACCAACCTCATGGAAT 58.895 45.455 0.00 0.00 43.54 3.01
4556 4617 6.817765 TCAGGTTCTATTGAAAACACATCC 57.182 37.500 0.00 0.00 33.52 3.51
4743 4825 5.047802 CAGGATAAAAGGTGCAGTCACAAAT 60.048 40.000 0.00 0.00 44.87 2.32
4749 4831 3.274288 CTCCAGGATAAAAGGTGCAGTC 58.726 50.000 0.00 0.00 0.00 3.51
4930 5017 6.890979 TCAGTCAGATGGATATAGTGACAG 57.109 41.667 3.81 0.00 40.03 3.51
4971 5058 3.057019 GCTCCAAAAACGTTTTGGGATC 58.943 45.455 37.90 32.35 46.38 3.36
4981 5068 0.586319 TTCAGCTCGCTCCAAAAACG 59.414 50.000 0.00 0.00 0.00 3.60
4997 5084 2.919602 GGGATGGAGGGGCTATATTTCA 59.080 50.000 0.00 0.00 0.00 2.69
5029 5116 2.280592 GACGCTCGTGGGTTTGGT 60.281 61.111 8.65 0.00 39.55 3.67
5059 5146 2.777692 TCCCACTAGGAATCATGGAACC 59.222 50.000 0.00 0.00 43.78 3.62
5134 5221 1.204941 GATTCTCAGTAGCACGGTGGT 59.795 52.381 17.69 17.69 0.00 4.16
5311 5722 1.538512 TCCTAGTCACGAGAAACACGG 59.461 52.381 0.00 0.00 34.93 4.94


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

AutoCloner maintained by Alex Coulton.