Multiple sequence alignment - TraesCS2A01G238700

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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 TraesCS2A01G238700 chr2A 100.000 3721 0 0 945 4665 323530816 323527096 0.000000e+00 6872
1 TraesCS2A01G238700 chr2A 100.000 730 0 0 1 730 323531760 323531031 0.000000e+00 1349
2 TraesCS2A01G238700 chr2A 95.479 730 32 1 1 730 356525416 356524688 0.000000e+00 1164
3 TraesCS2A01G238700 chr2D 97.549 2897 54 11 963 3854 288228202 288225318 0.000000e+00 4940
4 TraesCS2A01G238700 chr2D 92.847 699 28 1 3853 4551 233430108 233430784 0.000000e+00 994
5 TraesCS2A01G238700 chr2D 88.192 271 22 6 463 730 484384461 484384198 9.740000e-82 315
6 TraesCS2A01G238700 chr2D 86.411 287 33 6 448 730 374815334 374815050 4.530000e-80 309
7 TraesCS2A01G238700 chr2B 96.261 2220 75 8 1609 3825 298326585 298324371 0.000000e+00 3633
8 TraesCS2A01G238700 chr2B 96.224 662 12 5 949 1607 298327323 298326672 0.000000e+00 1072
9 TraesCS2A01G238700 chr2B 84.151 530 60 8 3852 4379 75739300 75738793 4.190000e-135 492
10 TraesCS2A01G238700 chr2B 83.237 173 19 6 3853 4015 39750066 39749894 2.910000e-32 150
11 TraesCS2A01G238700 chr1D 95.499 711 22 1 3851 4551 12002741 12003451 0.000000e+00 1127
12 TraesCS2A01G238700 chr1D 86.885 732 81 12 1 730 306684645 306683927 0.000000e+00 806
13 TraesCS2A01G238700 chr1D 89.219 269 23 2 463 730 357224725 357224462 9.680000e-87 331
14 TraesCS2A01G238700 chr5A 94.655 711 26 3 3852 4551 395901548 395900839 0.000000e+00 1092
15 TraesCS2A01G238700 chr5D 94.142 717 31 2 3845 4551 90769580 90770295 0.000000e+00 1081
16 TraesCS2A01G238700 chr5D 94.819 579 19 2 3851 4419 54817421 54817998 0.000000e+00 893
17 TraesCS2A01G238700 chr5D 83.969 524 67 12 3853 4365 370447602 370448119 1.950000e-133 486
18 TraesCS2A01G238700 chr5D 88.848 269 23 3 463 730 110494111 110493849 1.620000e-84 324
19 TraesCS2A01G238700 chr5D 97.810 137 3 0 4415 4551 54826744 54826880 2.170000e-58 237
20 TraesCS2A01G238700 chr5D 84.653 202 8 8 4374 4553 214062032 214062232 3.710000e-41 180
21 TraesCS2A01G238700 chr6B 90.857 700 29 3 3853 4551 695250311 695249646 0.000000e+00 905
22 TraesCS2A01G238700 chr6B 90.395 708 31 5 3853 4551 371609159 371608480 0.000000e+00 896
23 TraesCS2A01G238700 chr6B 94.010 384 11 1 4168 4551 695233105 695232734 5.240000e-159 571
24 TraesCS2A01G238700 chr6B 81.549 439 59 16 21 457 114974202 114974620 4.470000e-90 342
25 TraesCS2A01G238700 chr6B 90.441 136 13 0 3853 3988 695233773 695233638 3.710000e-41 180
26 TraesCS2A01G238700 chr7B 85.967 734 90 10 1 730 106024655 106025379 0.000000e+00 773
27 TraesCS2A01G238700 chr7B 84.532 737 95 16 1 730 114730457 114731181 0.000000e+00 712
28 TraesCS2A01G238700 chr7B 80.285 421 64 10 52 471 175225014 175224612 2.730000e-77 300
29 TraesCS2A01G238700 chr7B 99.130 115 1 0 4551 4665 674549577 674549463 1.700000e-49 207
30 TraesCS2A01G238700 chr1B 85.034 735 81 12 1 730 168335247 168335957 0.000000e+00 721
31 TraesCS2A01G238700 chr3D 92.193 269 16 4 463 730 391376390 391376654 4.410000e-100 375
32 TraesCS2A01G238700 chr5B 82.045 440 55 18 21 457 677716426 677716008 2.060000e-93 353
33 TraesCS2A01G238700 chr5B 97.391 115 3 0 4551 4665 446139440 446139554 3.680000e-46 196
34 TraesCS2A01G238700 chr7A 82.398 392 48 15 80 469 257357363 257357735 5.820000e-84 322
35 TraesCS2A01G238700 chr7A 75.767 326 61 14 2 323 142394775 142395086 1.050000e-31 148
36 TraesCS2A01G238700 chr3A 81.841 391 53 10 80 469 145596188 145595815 3.500000e-81 313
37 TraesCS2A01G238700 chr4D 99.130 115 1 0 4551 4665 468197394 468197280 1.700000e-49 207
38 TraesCS2A01G238700 chr4D 98.261 115 2 0 4551 4665 468172455 468172569 7.910000e-48 202
39 TraesCS2A01G238700 chr3B 99.130 115 1 0 4551 4665 804983215 804983329 1.700000e-49 207
40 TraesCS2A01G238700 chr3B 98.246 114 2 0 4552 4665 826448941 826449054 2.850000e-47 200
41 TraesCS2A01G238700 chr3B 98.246 114 2 0 4552 4665 826510002 826510115 2.850000e-47 200
42 TraesCS2A01G238700 chr3B 98.246 114 2 0 4552 4665 826589379 826589492 2.850000e-47 200
43 TraesCS2A01G238700 chrUn 98.246 114 2 0 4552 4665 320317174 320317287 2.850000e-47 200


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 TraesCS2A01G238700 chr2A 323527096 323531760 4664 True 4110.5 6872 100.0000 1 4665 2 chr2A.!!$R2 4664
1 TraesCS2A01G238700 chr2A 356524688 356525416 728 True 1164.0 1164 95.4790 1 730 1 chr2A.!!$R1 729
2 TraesCS2A01G238700 chr2D 288225318 288228202 2884 True 4940.0 4940 97.5490 963 3854 1 chr2D.!!$R1 2891
3 TraesCS2A01G238700 chr2D 233430108 233430784 676 False 994.0 994 92.8470 3853 4551 1 chr2D.!!$F1 698
4 TraesCS2A01G238700 chr2B 298324371 298327323 2952 True 2352.5 3633 96.2425 949 3825 2 chr2B.!!$R3 2876
5 TraesCS2A01G238700 chr2B 75738793 75739300 507 True 492.0 492 84.1510 3852 4379 1 chr2B.!!$R2 527
6 TraesCS2A01G238700 chr1D 12002741 12003451 710 False 1127.0 1127 95.4990 3851 4551 1 chr1D.!!$F1 700
7 TraesCS2A01G238700 chr1D 306683927 306684645 718 True 806.0 806 86.8850 1 730 1 chr1D.!!$R1 729
8 TraesCS2A01G238700 chr5A 395900839 395901548 709 True 1092.0 1092 94.6550 3852 4551 1 chr5A.!!$R1 699
9 TraesCS2A01G238700 chr5D 90769580 90770295 715 False 1081.0 1081 94.1420 3845 4551 1 chr5D.!!$F3 706
10 TraesCS2A01G238700 chr5D 54817421 54817998 577 False 893.0 893 94.8190 3851 4419 1 chr5D.!!$F1 568
11 TraesCS2A01G238700 chr5D 370447602 370448119 517 False 486.0 486 83.9690 3853 4365 1 chr5D.!!$F5 512
12 TraesCS2A01G238700 chr6B 695249646 695250311 665 True 905.0 905 90.8570 3853 4551 1 chr6B.!!$R2 698
13 TraesCS2A01G238700 chr6B 371608480 371609159 679 True 896.0 896 90.3950 3853 4551 1 chr6B.!!$R1 698
14 TraesCS2A01G238700 chr6B 695232734 695233773 1039 True 375.5 571 92.2255 3853 4551 2 chr6B.!!$R3 698
15 TraesCS2A01G238700 chr7B 106024655 106025379 724 False 773.0 773 85.9670 1 730 1 chr7B.!!$F1 729
16 TraesCS2A01G238700 chr7B 114730457 114731181 724 False 712.0 712 84.5320 1 730 1 chr7B.!!$F2 729
17 TraesCS2A01G238700 chr1B 168335247 168335957 710 False 721.0 721 85.0340 1 730 1 chr1B.!!$F1 729

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
611 620 0.179067 AAACGCCTTTGACTGGACGA 60.179 50.0 0.00 0.0 0.00 4.20 F
1193 1204 0.035056 CAAGAATTGGAGGGCGAGGT 60.035 55.0 0.00 0.0 43.94 3.85 F
1355 1366 2.095718 GCAAGAACTTGTTCCGTCCATC 60.096 50.0 14.62 0.0 42.31 3.51 F
3182 3287 2.472695 TGAATTAGCTTGGTCGTGCT 57.527 45.0 0.00 0.0 42.67 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2169 2273 2.125912 CCTTCAGGGACAGACGCG 60.126 66.667 3.53 3.53 37.23 6.01 R
2438 2542 5.794894 CCCTAGATACCGCAATCAACTAAT 58.205 41.667 0.00 0.00 0.00 1.73 R
3363 3468 7.995488 ACTGAATCTCCATAGGGTCTAAAATTG 59.005 37.037 0.00 0.00 34.93 2.32 R
4246 4707 0.617535 TCTGCGGATTGGAGAAGGGA 60.618 55.000 0.00 0.00 42.70 4.20 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
302 305 2.825836 CTGGATTGGTGCGAGGCC 60.826 66.667 0.00 0.00 0.00 5.19
442 446 0.326618 ATGGAGGTCGGGGATGAGTT 60.327 55.000 0.00 0.00 0.00 3.01
459 464 6.271159 GGATGAGTTGGGTAGGAAGAAGATAT 59.729 42.308 0.00 0.00 0.00 1.63
611 620 0.179067 AAACGCCTTTGACTGGACGA 60.179 50.000 0.00 0.00 0.00 4.20
627 636 0.688487 ACGAAATTGGGACGGAAGGA 59.312 50.000 0.00 0.00 0.00 3.36
629 638 1.084289 GAAATTGGGACGGAAGGACG 58.916 55.000 0.00 0.00 40.31 4.79
667 676 1.198759 ACGCACTTGGGTAGGACCAT 61.199 55.000 0.00 0.00 41.02 3.55
669 678 0.618458 GCACTTGGGTAGGACCATGA 59.382 55.000 0.00 0.00 41.02 3.07
682 692 7.090808 GGTAGGACCATGAGTTTTTCAAATTC 58.909 38.462 0.00 0.00 39.77 2.17
968 978 1.131303 TCCTTCCCCCTCAAAGCGAA 61.131 55.000 0.00 0.00 0.00 4.70
1062 1073 4.849310 GCTACCATGGCGGCGGAA 62.849 66.667 13.04 0.00 39.03 4.30
1193 1204 0.035056 CAAGAATTGGAGGGCGAGGT 60.035 55.000 0.00 0.00 43.94 3.85
1355 1366 2.095718 GCAAGAACTTGTTCCGTCCATC 60.096 50.000 14.62 0.00 42.31 3.51
1359 1370 3.006110 AGAACTTGTTCCGTCCATCGTTA 59.994 43.478 9.58 0.00 37.94 3.18
1360 1371 3.389925 ACTTGTTCCGTCCATCGTTAA 57.610 42.857 0.00 0.00 37.94 2.01
1361 1372 3.934068 ACTTGTTCCGTCCATCGTTAAT 58.066 40.909 0.00 0.00 37.94 1.40
1362 1373 3.930848 ACTTGTTCCGTCCATCGTTAATC 59.069 43.478 0.00 0.00 37.94 1.75
1763 1866 3.032265 AGCTTGAGGGGTTTCTTGTTT 57.968 42.857 0.00 0.00 0.00 2.83
1924 2028 2.706890 GTCGGGTTCTTTAAGCATGGA 58.293 47.619 0.00 0.00 34.70 3.41
2169 2273 3.438434 AGGAAGAAATGAGAGCGCTTTTC 59.562 43.478 19.79 19.79 34.16 2.29
2578 2683 3.295973 TCAAGAACCCCCTGAAAAGTTG 58.704 45.455 0.00 0.00 0.00 3.16
2794 2899 5.710513 AATATTGTGAACGCCATATGCAT 57.289 34.783 3.79 3.79 41.33 3.96
3123 3228 3.227614 GAAGAAGCCACAAAAACCCCTA 58.772 45.455 0.00 0.00 0.00 3.53
3182 3287 2.472695 TGAATTAGCTTGGTCGTGCT 57.527 45.000 0.00 0.00 42.67 4.40
3363 3468 7.649306 GTTGCATAACAATTGGAAGATCCATAC 59.351 37.037 10.83 0.00 40.36 2.39
3392 3497 8.798975 TTTAGACCCTATGGAGATTCAGTTAT 57.201 34.615 0.00 0.00 34.81 1.89
3496 3601 4.039703 GCATGTGTGATGTAATGATGTGC 58.960 43.478 0.00 0.00 0.00 4.57
3642 3747 4.667519 TTCCTCGGAGGCTTTCTTATAC 57.332 45.455 19.48 0.00 34.61 1.47
3754 3861 6.636454 ACTAGTTGATTCCCAGGTAATGAA 57.364 37.500 0.00 0.00 0.00 2.57
3867 3974 1.002069 TAAGTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
3926 4034 1.760613 TGTCGTTCTCCTGACCAAACT 59.239 47.619 0.00 0.00 34.18 2.66
3930 4038 1.048601 TTCTCCTGACCAAACTCGCT 58.951 50.000 0.00 0.00 0.00 4.93
4181 4642 0.526211 CGTCGTGAATCACCTCCTCA 59.474 55.000 7.91 0.00 0.00 3.86
4219 4680 4.096003 CCCTCCATGGACGCCGTT 62.096 66.667 11.44 0.00 38.35 4.44
4246 4707 3.168528 ACTGGGAAGCACGGGTGT 61.169 61.111 0.25 0.00 0.00 4.16
4551 5012 8.533153 GCAATTTTTGTGGAATTTTGAAACATG 58.467 29.630 0.00 0.00 0.00 3.21
4552 5013 9.570488 CAATTTTTGTGGAATTTTGAAACATGT 57.430 25.926 0.00 0.00 0.00 3.21
4553 5014 9.570488 AATTTTTGTGGAATTTTGAAACATGTG 57.430 25.926 0.00 0.00 0.00 3.21
4554 5015 7.678947 TTTTGTGGAATTTTGAAACATGTGT 57.321 28.000 0.00 0.00 0.00 3.72
4555 5016 6.659361 TTGTGGAATTTTGAAACATGTGTG 57.341 33.333 0.00 0.00 0.00 3.82
4556 5017 5.728471 TGTGGAATTTTGAAACATGTGTGT 58.272 33.333 0.00 0.00 41.28 3.72
4557 5018 5.579904 TGTGGAATTTTGAAACATGTGTGTG 59.420 36.000 0.00 0.00 38.92 3.82
4558 5019 5.580297 GTGGAATTTTGAAACATGTGTGTGT 59.420 36.000 0.00 0.00 38.92 3.72
4559 5020 5.579904 TGGAATTTTGAAACATGTGTGTGTG 59.420 36.000 0.00 0.00 38.92 3.82
4560 5021 5.006552 GGAATTTTGAAACATGTGTGTGTGG 59.993 40.000 0.00 0.00 38.92 4.17
4561 5022 4.527509 TTTTGAAACATGTGTGTGTGGT 57.472 36.364 0.00 0.00 38.92 4.16
4562 5023 3.500558 TTGAAACATGTGTGTGTGGTG 57.499 42.857 0.00 0.00 38.92 4.17
4563 5024 2.441410 TGAAACATGTGTGTGTGGTGT 58.559 42.857 0.00 0.00 38.92 4.16
4564 5025 3.610911 TGAAACATGTGTGTGTGGTGTA 58.389 40.909 0.00 0.00 38.92 2.90
4565 5026 3.625313 TGAAACATGTGTGTGTGGTGTAG 59.375 43.478 0.00 0.00 38.92 2.74
4566 5027 2.254546 ACATGTGTGTGTGGTGTAGG 57.745 50.000 0.00 0.00 37.14 3.18
4567 5028 1.765904 ACATGTGTGTGTGGTGTAGGA 59.234 47.619 0.00 0.00 37.14 2.94
4568 5029 2.171659 ACATGTGTGTGTGGTGTAGGAA 59.828 45.455 0.00 0.00 37.14 3.36
4569 5030 3.210227 CATGTGTGTGTGGTGTAGGAAA 58.790 45.455 0.00 0.00 0.00 3.13
4570 5031 3.351794 TGTGTGTGTGGTGTAGGAAAA 57.648 42.857 0.00 0.00 0.00 2.29
4571 5032 3.687125 TGTGTGTGTGGTGTAGGAAAAA 58.313 40.909 0.00 0.00 0.00 1.94
4572 5033 3.692101 TGTGTGTGTGGTGTAGGAAAAAG 59.308 43.478 0.00 0.00 0.00 2.27
4573 5034 2.685897 TGTGTGTGGTGTAGGAAAAAGC 59.314 45.455 0.00 0.00 0.00 3.51
4574 5035 2.949644 GTGTGTGGTGTAGGAAAAAGCT 59.050 45.455 0.00 0.00 0.00 3.74
4575 5036 3.380320 GTGTGTGGTGTAGGAAAAAGCTT 59.620 43.478 0.00 0.00 0.00 3.74
4576 5037 4.577283 GTGTGTGGTGTAGGAAAAAGCTTA 59.423 41.667 0.00 0.00 0.00 3.09
4577 5038 4.819630 TGTGTGGTGTAGGAAAAAGCTTAG 59.180 41.667 0.00 0.00 0.00 2.18
4578 5039 5.061179 GTGTGGTGTAGGAAAAAGCTTAGA 58.939 41.667 0.00 0.00 0.00 2.10
4579 5040 5.049612 GTGTGGTGTAGGAAAAAGCTTAGAC 60.050 44.000 0.00 0.00 0.00 2.59
4580 5041 5.163237 TGTGGTGTAGGAAAAAGCTTAGACT 60.163 40.000 0.00 0.00 0.00 3.24
4581 5042 5.763698 GTGGTGTAGGAAAAAGCTTAGACTT 59.236 40.000 0.00 0.00 0.00 3.01
4582 5043 5.763204 TGGTGTAGGAAAAAGCTTAGACTTG 59.237 40.000 0.00 0.00 0.00 3.16
4583 5044 5.334957 GGTGTAGGAAAAAGCTTAGACTTGC 60.335 44.000 0.00 0.00 0.00 4.01
4584 5045 5.470437 GTGTAGGAAAAAGCTTAGACTTGCT 59.530 40.000 0.00 4.71 41.82 3.91
4585 5046 5.701290 TGTAGGAAAAAGCTTAGACTTGCTC 59.299 40.000 0.00 0.00 38.75 4.26
4586 5047 4.979335 AGGAAAAAGCTTAGACTTGCTCT 58.021 39.130 0.00 0.00 38.75 4.09
4587 5048 5.380900 AGGAAAAAGCTTAGACTTGCTCTT 58.619 37.500 0.00 1.76 38.75 2.85
4588 5049 6.534634 AGGAAAAAGCTTAGACTTGCTCTTA 58.465 36.000 0.00 0.00 38.75 2.10
4589 5050 6.652900 AGGAAAAAGCTTAGACTTGCTCTTAG 59.347 38.462 0.00 0.00 38.75 2.18
4590 5051 6.428465 GGAAAAAGCTTAGACTTGCTCTTAGT 59.572 38.462 0.00 0.00 38.75 2.24
4591 5052 6.793492 AAAAGCTTAGACTTGCTCTTAGTG 57.207 37.500 0.00 0.00 38.75 2.74
4592 5053 4.464069 AGCTTAGACTTGCTCTTAGTGG 57.536 45.455 0.00 0.00 33.90 4.00
4593 5054 4.090090 AGCTTAGACTTGCTCTTAGTGGA 58.910 43.478 0.00 0.00 33.90 4.02
4594 5055 4.714308 AGCTTAGACTTGCTCTTAGTGGAT 59.286 41.667 0.00 0.00 33.90 3.41
4595 5056 5.047188 GCTTAGACTTGCTCTTAGTGGATC 58.953 45.833 0.00 0.00 29.62 3.36
4596 5057 5.394663 GCTTAGACTTGCTCTTAGTGGATCA 60.395 44.000 0.00 0.00 29.62 2.92
4597 5058 4.734398 AGACTTGCTCTTAGTGGATCAG 57.266 45.455 0.00 0.00 0.00 2.90
4598 5059 4.348486 AGACTTGCTCTTAGTGGATCAGA 58.652 43.478 0.00 0.00 0.00 3.27
4599 5060 4.774726 AGACTTGCTCTTAGTGGATCAGAA 59.225 41.667 0.00 0.00 0.00 3.02
4600 5061 4.826556 ACTTGCTCTTAGTGGATCAGAAC 58.173 43.478 0.00 0.00 0.00 3.01
4601 5062 4.284490 ACTTGCTCTTAGTGGATCAGAACA 59.716 41.667 0.00 0.00 0.00 3.18
4602 5063 5.046014 ACTTGCTCTTAGTGGATCAGAACAT 60.046 40.000 0.00 0.00 0.00 2.71
4603 5064 4.763073 TGCTCTTAGTGGATCAGAACATG 58.237 43.478 0.00 0.00 0.00 3.21
4604 5065 3.559242 GCTCTTAGTGGATCAGAACATGC 59.441 47.826 0.00 0.00 0.00 4.06
4605 5066 4.682859 GCTCTTAGTGGATCAGAACATGCT 60.683 45.833 0.00 0.00 0.00 3.79
4606 5067 4.763073 TCTTAGTGGATCAGAACATGCTG 58.237 43.478 0.00 0.00 37.24 4.41
4607 5068 4.223700 TCTTAGTGGATCAGAACATGCTGT 59.776 41.667 0.00 0.00 37.20 4.40
4608 5069 3.430042 AGTGGATCAGAACATGCTGTT 57.570 42.857 0.00 1.82 44.37 3.16
4609 5070 4.558226 AGTGGATCAGAACATGCTGTTA 57.442 40.909 0.00 0.00 41.28 2.41
4610 5071 4.511527 AGTGGATCAGAACATGCTGTTAG 58.488 43.478 0.00 0.13 41.28 2.34
4611 5072 3.624861 GTGGATCAGAACATGCTGTTAGG 59.375 47.826 0.00 0.00 41.28 2.69
4612 5073 3.519107 TGGATCAGAACATGCTGTTAGGA 59.481 43.478 0.00 4.00 41.28 2.94
4613 5074 4.019411 TGGATCAGAACATGCTGTTAGGAA 60.019 41.667 0.00 0.00 41.28 3.36
4614 5075 4.574013 GGATCAGAACATGCTGTTAGGAAG 59.426 45.833 0.00 0.00 41.28 3.46
4615 5076 4.623932 TCAGAACATGCTGTTAGGAAGT 57.376 40.909 0.00 0.00 41.28 3.01
4616 5077 4.569943 TCAGAACATGCTGTTAGGAAGTC 58.430 43.478 0.00 0.00 41.28 3.01
4617 5078 4.284490 TCAGAACATGCTGTTAGGAAGTCT 59.716 41.667 0.00 0.00 41.28 3.24
4618 5079 5.480422 TCAGAACATGCTGTTAGGAAGTCTA 59.520 40.000 0.00 0.00 41.28 2.59
4619 5080 6.014584 TCAGAACATGCTGTTAGGAAGTCTAA 60.015 38.462 0.00 0.00 41.28 2.10
4620 5081 6.312426 CAGAACATGCTGTTAGGAAGTCTAAG 59.688 42.308 0.00 0.00 41.28 2.18
4621 5082 5.746990 ACATGCTGTTAGGAAGTCTAAGT 57.253 39.130 0.00 0.00 38.51 2.24
4622 5083 6.115448 ACATGCTGTTAGGAAGTCTAAGTT 57.885 37.500 0.00 0.00 38.51 2.66
4623 5084 6.534634 ACATGCTGTTAGGAAGTCTAAGTTT 58.465 36.000 0.00 0.00 38.51 2.66
4624 5085 7.676947 ACATGCTGTTAGGAAGTCTAAGTTTA 58.323 34.615 0.00 0.00 38.51 2.01
4625 5086 7.603024 ACATGCTGTTAGGAAGTCTAAGTTTAC 59.397 37.037 0.00 0.00 38.51 2.01
4626 5087 7.299246 TGCTGTTAGGAAGTCTAAGTTTACT 57.701 36.000 0.00 0.00 38.51 2.24
4627 5088 7.376615 TGCTGTTAGGAAGTCTAAGTTTACTC 58.623 38.462 0.00 0.00 38.51 2.59
4628 5089 7.014905 TGCTGTTAGGAAGTCTAAGTTTACTCA 59.985 37.037 0.00 0.00 38.51 3.41
4629 5090 7.871463 GCTGTTAGGAAGTCTAAGTTTACTCAA 59.129 37.037 0.00 0.00 38.51 3.02
4630 5091 9.413048 CTGTTAGGAAGTCTAAGTTTACTCAAG 57.587 37.037 0.00 0.00 38.51 3.02
4631 5092 8.365647 TGTTAGGAAGTCTAAGTTTACTCAAGG 58.634 37.037 0.00 0.00 38.51 3.61
4632 5093 5.795972 AGGAAGTCTAAGTTTACTCAAGGC 58.204 41.667 0.00 0.00 0.00 4.35
4633 5094 4.936411 GGAAGTCTAAGTTTACTCAAGGCC 59.064 45.833 0.00 0.00 0.00 5.19
4634 5095 5.280062 GGAAGTCTAAGTTTACTCAAGGCCT 60.280 44.000 0.00 0.00 0.00 5.19
4635 5096 5.827326 AGTCTAAGTTTACTCAAGGCCTT 57.173 39.130 13.78 13.78 0.00 4.35
4636 5097 5.552178 AGTCTAAGTTTACTCAAGGCCTTG 58.448 41.667 35.52 35.52 41.71 3.61
4637 5098 5.071923 AGTCTAAGTTTACTCAAGGCCTTGT 59.928 40.000 37.97 25.72 41.16 3.16
4638 5099 5.763698 GTCTAAGTTTACTCAAGGCCTTGTT 59.236 40.000 37.97 28.94 41.16 2.83
4639 5100 4.918810 AAGTTTACTCAAGGCCTTGTTG 57.081 40.909 37.97 31.93 41.16 3.33
4640 5101 3.898482 AGTTTACTCAAGGCCTTGTTGT 58.102 40.909 37.97 34.71 41.16 3.32
4641 5102 4.278310 AGTTTACTCAAGGCCTTGTTGTT 58.722 39.130 37.97 24.39 41.16 2.83
4642 5103 5.442391 AGTTTACTCAAGGCCTTGTTGTTA 58.558 37.500 37.97 27.98 41.16 2.41
4643 5104 5.889289 AGTTTACTCAAGGCCTTGTTGTTAA 59.111 36.000 37.97 30.79 41.16 2.01
4644 5105 6.549736 AGTTTACTCAAGGCCTTGTTGTTAAT 59.450 34.615 37.97 24.35 41.16 1.40
4645 5106 4.853924 ACTCAAGGCCTTGTTGTTAATG 57.146 40.909 37.97 21.99 41.16 1.90
4646 5107 3.005791 ACTCAAGGCCTTGTTGTTAATGC 59.994 43.478 37.97 0.00 41.16 3.56
4647 5108 2.961741 TCAAGGCCTTGTTGTTAATGCA 59.038 40.909 37.97 17.27 41.16 3.96
4648 5109 3.577848 TCAAGGCCTTGTTGTTAATGCAT 59.422 39.130 37.97 1.24 41.16 3.96
4649 5110 3.874392 AGGCCTTGTTGTTAATGCATC 57.126 42.857 0.00 0.00 0.00 3.91
4650 5111 3.434309 AGGCCTTGTTGTTAATGCATCT 58.566 40.909 0.00 0.00 0.00 2.90
4651 5112 3.834231 AGGCCTTGTTGTTAATGCATCTT 59.166 39.130 0.00 0.00 0.00 2.40
4652 5113 4.284234 AGGCCTTGTTGTTAATGCATCTTT 59.716 37.500 0.00 0.00 0.00 2.52
4653 5114 5.480073 AGGCCTTGTTGTTAATGCATCTTTA 59.520 36.000 0.00 0.00 0.00 1.85
4654 5115 6.014669 AGGCCTTGTTGTTAATGCATCTTTAA 60.015 34.615 0.00 0.00 0.00 1.52
4655 5116 6.090763 GGCCTTGTTGTTAATGCATCTTTAAC 59.909 38.462 12.48 12.48 39.11 2.01
4656 5117 6.868339 GCCTTGTTGTTAATGCATCTTTAACT 59.132 34.615 17.76 0.00 39.29 2.24
4657 5118 7.148755 GCCTTGTTGTTAATGCATCTTTAACTG 60.149 37.037 17.76 10.62 39.29 3.16
4658 5119 8.081633 CCTTGTTGTTAATGCATCTTTAACTGA 58.918 33.333 17.76 7.87 39.29 3.41
4659 5120 9.462174 CTTGTTGTTAATGCATCTTTAACTGAA 57.538 29.630 17.76 6.56 39.29 3.02
4660 5121 9.979578 TTGTTGTTAATGCATCTTTAACTGAAT 57.020 25.926 17.76 0.00 39.29 2.57
4661 5122 9.979578 TGTTGTTAATGCATCTTTAACTGAATT 57.020 25.926 17.76 0.00 39.29 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.408821 GTGGATGTGGCCGAGGCA 62.409 66.667 16.65 0.00 44.11 4.75
232 234 3.706373 AGGATCAGTGCCGCCGTT 61.706 61.111 0.00 0.00 0.00 4.44
302 305 2.027625 GTCTTTGTCGCGTCCCCAG 61.028 63.158 5.77 0.00 0.00 4.45
442 446 5.841237 CCTCTTCATATCTTCTTCCTACCCA 59.159 44.000 0.00 0.00 0.00 4.51
459 464 3.884037 AAAAGAAGCCTTCCCTCTTCA 57.116 42.857 0.00 0.00 40.72 3.02
545 554 2.102578 CCATTTTGCCCCTCCTTACAG 58.897 52.381 0.00 0.00 0.00 2.74
611 620 0.688487 TCGTCCTTCCGTCCCAATTT 59.312 50.000 0.00 0.00 0.00 1.82
627 636 0.256464 TGGTCCCCTTGTGTTTTCGT 59.744 50.000 0.00 0.00 0.00 3.85
629 638 2.480587 CGTTTGGTCCCCTTGTGTTTTC 60.481 50.000 0.00 0.00 0.00 2.29
659 668 7.039784 CCTGAATTTGAAAAACTCATGGTCCTA 60.040 37.037 0.00 0.00 32.78 2.94
667 676 3.708631 TGCCCCTGAATTTGAAAAACTCA 59.291 39.130 0.00 0.00 0.00 3.41
669 678 4.769345 TTGCCCCTGAATTTGAAAAACT 57.231 36.364 0.00 0.00 0.00 2.66
682 692 0.036010 ACTCGACTGATTTGCCCCTG 60.036 55.000 0.00 0.00 0.00 4.45
944 954 1.283321 CTTTGAGGGGGAAGGAGAAGG 59.717 57.143 0.00 0.00 0.00 3.46
945 955 1.340502 GCTTTGAGGGGGAAGGAGAAG 60.341 57.143 0.00 0.00 0.00 2.85
946 956 0.698818 GCTTTGAGGGGGAAGGAGAA 59.301 55.000 0.00 0.00 0.00 2.87
947 957 1.553690 CGCTTTGAGGGGGAAGGAGA 61.554 60.000 0.00 0.00 0.00 3.71
992 1003 2.664402 ATCTTTGGGATTGGATCGGG 57.336 50.000 0.00 0.00 0.00 5.14
1062 1073 1.589414 CATCCTTCTTGTCCTCCCCT 58.411 55.000 0.00 0.00 0.00 4.79
1110 1121 3.649277 CTCCAGGGTGTTCTCGCCG 62.649 68.421 0.00 0.00 44.47 6.46
1111 1122 2.266055 CTCCAGGGTGTTCTCGCC 59.734 66.667 0.00 0.00 42.95 5.54
1112 1123 2.266055 CCTCCAGGGTGTTCTCGC 59.734 66.667 0.00 0.00 0.00 5.03
1193 1204 2.484928 CGATCTGCGCTCTCCTCCA 61.485 63.158 9.73 0.00 0.00 3.86
1355 1366 6.111862 GAAAAGTTTCTTGCGTGATTAACG 57.888 37.500 0.00 0.00 43.24 3.18
1359 1370 5.036737 CACAGAAAAGTTTCTTGCGTGATT 58.963 37.500 13.52 0.00 44.70 2.57
1360 1371 4.601019 CACAGAAAAGTTTCTTGCGTGAT 58.399 39.130 13.52 0.00 44.70 3.06
1361 1372 3.730662 GCACAGAAAAGTTTCTTGCGTGA 60.731 43.478 19.24 0.00 44.70 4.35
1362 1373 2.531508 GCACAGAAAAGTTTCTTGCGTG 59.468 45.455 17.26 15.75 44.70 5.34
1677 1780 8.729805 TCAAACAGCCATAAAGAAACAAAAAT 57.270 26.923 0.00 0.00 0.00 1.82
2008 2112 5.034554 ACATAAAGACAACAATGACAGCG 57.965 39.130 0.00 0.00 0.00 5.18
2169 2273 2.125912 CCTTCAGGGACAGACGCG 60.126 66.667 3.53 3.53 37.23 6.01
2438 2542 5.794894 CCCTAGATACCGCAATCAACTAAT 58.205 41.667 0.00 0.00 0.00 1.73
3363 3468 7.995488 ACTGAATCTCCATAGGGTCTAAAATTG 59.005 37.037 0.00 0.00 34.93 2.32
3496 3601 8.562892 CAAAACATCCTTAGCAGTATCCATTAG 58.437 37.037 0.00 0.00 0.00 1.73
3599 3704 6.205270 GGAATTCAACCATGCAAACTGAAATT 59.795 34.615 7.93 0.00 30.37 1.82
3720 3825 4.202284 GGAATCAACTAGTACCGGGCATAA 60.202 45.833 6.32 0.00 0.00 1.90
3722 3827 2.104281 GGAATCAACTAGTACCGGGCAT 59.896 50.000 6.32 0.00 0.00 4.40
3788 3895 4.341806 TCTTTCAATGCAACCACATGTCTT 59.658 37.500 0.00 0.00 0.00 3.01
3926 4034 2.341101 GGAAGGACGAGGACAGCGA 61.341 63.158 0.00 0.00 0.00 4.93
3930 4038 1.251527 GCTGAGGAAGGACGAGGACA 61.252 60.000 0.00 0.00 0.00 4.02
4136 4304 2.494530 GCGGAAGGAGAGCGAGGAT 61.495 63.158 0.00 0.00 0.00 3.24
4181 4642 3.822607 GAGCTTCATGGTCGACAGT 57.177 52.632 18.91 1.51 33.25 3.55
4219 4680 2.525629 TTCCCAGTGCTCGGGTCA 60.526 61.111 13.06 2.56 44.81 4.02
4246 4707 0.617535 TCTGCGGATTGGAGAAGGGA 60.618 55.000 0.00 0.00 42.70 4.20
4551 5012 3.488553 GCTTTTTCCTACACCACACACAC 60.489 47.826 0.00 0.00 0.00 3.82
4552 5013 2.685897 GCTTTTTCCTACACCACACACA 59.314 45.455 0.00 0.00 0.00 3.72
4553 5014 2.949644 AGCTTTTTCCTACACCACACAC 59.050 45.455 0.00 0.00 0.00 3.82
4554 5015 3.290948 AGCTTTTTCCTACACCACACA 57.709 42.857 0.00 0.00 0.00 3.72
4555 5016 5.049612 GTCTAAGCTTTTTCCTACACCACAC 60.050 44.000 3.20 0.00 0.00 3.82
4556 5017 5.061179 GTCTAAGCTTTTTCCTACACCACA 58.939 41.667 3.20 0.00 0.00 4.17
4557 5018 5.306394 AGTCTAAGCTTTTTCCTACACCAC 58.694 41.667 3.20 0.00 0.00 4.16
4558 5019 5.562298 AGTCTAAGCTTTTTCCTACACCA 57.438 39.130 3.20 0.00 0.00 4.17
4559 5020 5.334957 GCAAGTCTAAGCTTTTTCCTACACC 60.335 44.000 3.20 0.00 0.00 4.16
4560 5021 5.470437 AGCAAGTCTAAGCTTTTTCCTACAC 59.530 40.000 3.20 0.00 38.01 2.90
4561 5022 5.621193 AGCAAGTCTAAGCTTTTTCCTACA 58.379 37.500 3.20 0.00 38.01 2.74
4562 5023 5.935206 AGAGCAAGTCTAAGCTTTTTCCTAC 59.065 40.000 3.20 0.00 42.04 3.18
4563 5024 6.115448 AGAGCAAGTCTAAGCTTTTTCCTA 57.885 37.500 3.20 0.00 42.04 2.94
4564 5025 4.979335 AGAGCAAGTCTAAGCTTTTTCCT 58.021 39.130 3.20 0.00 42.04 3.36
4565 5026 5.697473 AAGAGCAAGTCTAAGCTTTTTCC 57.303 39.130 3.20 0.00 42.04 3.13
4566 5027 7.294473 CACTAAGAGCAAGTCTAAGCTTTTTC 58.706 38.462 3.20 0.00 42.04 2.29
4567 5028 6.205658 CCACTAAGAGCAAGTCTAAGCTTTTT 59.794 38.462 3.20 6.01 42.04 1.94
4568 5029 5.703130 CCACTAAGAGCAAGTCTAAGCTTTT 59.297 40.000 3.20 7.74 42.04 2.27
4569 5030 5.012148 TCCACTAAGAGCAAGTCTAAGCTTT 59.988 40.000 3.20 0.00 42.04 3.51
4570 5031 4.528596 TCCACTAAGAGCAAGTCTAAGCTT 59.471 41.667 3.48 3.48 42.04 3.74
4571 5032 4.090090 TCCACTAAGAGCAAGTCTAAGCT 58.910 43.478 0.00 0.00 45.25 3.74
4572 5033 4.457834 TCCACTAAGAGCAAGTCTAAGC 57.542 45.455 0.00 0.00 32.65 3.09
4573 5034 6.096141 TCTGATCCACTAAGAGCAAGTCTAAG 59.904 42.308 0.00 0.00 32.65 2.18
4574 5035 5.952347 TCTGATCCACTAAGAGCAAGTCTAA 59.048 40.000 0.00 0.00 32.65 2.10
4575 5036 5.510430 TCTGATCCACTAAGAGCAAGTCTA 58.490 41.667 0.00 0.00 32.65 2.59
4576 5037 4.348486 TCTGATCCACTAAGAGCAAGTCT 58.652 43.478 0.00 0.00 36.94 3.24
4577 5038 4.727507 TCTGATCCACTAAGAGCAAGTC 57.272 45.455 0.00 0.00 30.54 3.01
4578 5039 4.284490 TGTTCTGATCCACTAAGAGCAAGT 59.716 41.667 0.00 0.00 30.54 3.16
4579 5040 4.825422 TGTTCTGATCCACTAAGAGCAAG 58.175 43.478 0.00 0.00 30.54 4.01
4580 5041 4.890158 TGTTCTGATCCACTAAGAGCAA 57.110 40.909 0.00 0.00 30.54 3.91
4581 5042 4.763073 CATGTTCTGATCCACTAAGAGCA 58.237 43.478 0.17 0.17 35.93 4.26
4582 5043 3.559242 GCATGTTCTGATCCACTAAGAGC 59.441 47.826 0.00 0.00 0.00 4.09
4583 5044 4.809958 CAGCATGTTCTGATCCACTAAGAG 59.190 45.833 0.00 0.00 36.19 2.85
4584 5045 4.763073 CAGCATGTTCTGATCCACTAAGA 58.237 43.478 0.00 0.00 36.19 2.10
4600 5061 7.819900 AGTAAACTTAGACTTCCTAACAGCATG 59.180 37.037 0.00 0.00 46.00 4.06
4601 5062 7.908453 AGTAAACTTAGACTTCCTAACAGCAT 58.092 34.615 0.00 0.00 33.95 3.79
4602 5063 7.014905 TGAGTAAACTTAGACTTCCTAACAGCA 59.985 37.037 0.00 0.00 33.95 4.41
4603 5064 7.376615 TGAGTAAACTTAGACTTCCTAACAGC 58.623 38.462 0.00 0.00 33.95 4.40
4604 5065 9.413048 CTTGAGTAAACTTAGACTTCCTAACAG 57.587 37.037 0.00 0.00 33.95 3.16
4605 5066 8.365647 CCTTGAGTAAACTTAGACTTCCTAACA 58.634 37.037 0.00 0.00 33.95 2.41
4606 5067 7.331440 GCCTTGAGTAAACTTAGACTTCCTAAC 59.669 40.741 0.00 0.00 33.95 2.34
4607 5068 7.384477 GCCTTGAGTAAACTTAGACTTCCTAA 58.616 38.462 0.00 0.00 36.07 2.69
4608 5069 6.070938 GGCCTTGAGTAAACTTAGACTTCCTA 60.071 42.308 0.00 0.00 0.00 2.94
4609 5070 5.280062 GGCCTTGAGTAAACTTAGACTTCCT 60.280 44.000 0.00 0.00 0.00 3.36
4610 5071 4.936411 GGCCTTGAGTAAACTTAGACTTCC 59.064 45.833 0.00 0.00 0.00 3.46
4611 5072 5.795972 AGGCCTTGAGTAAACTTAGACTTC 58.204 41.667 0.00 0.00 0.00 3.01
4612 5073 5.827326 AGGCCTTGAGTAAACTTAGACTT 57.173 39.130 0.00 0.00 0.00 3.01
4613 5074 5.071923 ACAAGGCCTTGAGTAAACTTAGACT 59.928 40.000 44.50 19.41 42.93 3.24
4614 5075 5.306394 ACAAGGCCTTGAGTAAACTTAGAC 58.694 41.667 44.50 0.00 42.93 2.59
4615 5076 5.562298 ACAAGGCCTTGAGTAAACTTAGA 57.438 39.130 44.50 0.00 42.93 2.10
4616 5077 5.531287 ACAACAAGGCCTTGAGTAAACTTAG 59.469 40.000 44.50 23.60 42.93 2.18
4617 5078 5.442391 ACAACAAGGCCTTGAGTAAACTTA 58.558 37.500 44.50 0.00 42.93 2.24
4618 5079 4.278310 ACAACAAGGCCTTGAGTAAACTT 58.722 39.130 44.50 26.67 42.93 2.66
4619 5080 3.898482 ACAACAAGGCCTTGAGTAAACT 58.102 40.909 44.50 22.71 42.93 2.66
4620 5081 4.649088 AACAACAAGGCCTTGAGTAAAC 57.351 40.909 44.50 0.00 42.93 2.01
4621 5082 6.737346 GCATTAACAACAAGGCCTTGAGTAAA 60.737 38.462 44.50 30.16 42.93 2.01
4622 5083 5.278758 GCATTAACAACAAGGCCTTGAGTAA 60.279 40.000 44.50 32.16 42.93 2.24
4623 5084 4.217550 GCATTAACAACAAGGCCTTGAGTA 59.782 41.667 44.50 28.08 42.93 2.59
4624 5085 3.005791 GCATTAACAACAAGGCCTTGAGT 59.994 43.478 44.50 36.21 42.93 3.41
4625 5086 3.005684 TGCATTAACAACAAGGCCTTGAG 59.994 43.478 44.50 35.63 42.93 3.02
4626 5087 2.961741 TGCATTAACAACAAGGCCTTGA 59.038 40.909 44.50 25.82 42.93 3.02
4627 5088 3.383620 TGCATTAACAACAAGGCCTTG 57.616 42.857 38.30 38.30 45.58 3.61
4628 5089 3.834231 AGATGCATTAACAACAAGGCCTT 59.166 39.130 13.78 13.78 34.40 4.35
4629 5090 3.434309 AGATGCATTAACAACAAGGCCT 58.566 40.909 0.00 0.00 34.40 5.19
4630 5091 3.874392 AGATGCATTAACAACAAGGCC 57.126 42.857 0.00 0.00 34.40 5.19
4631 5092 6.868339 AGTTAAAGATGCATTAACAACAAGGC 59.132 34.615 18.75 0.00 42.80 4.35
4632 5093 8.081633 TCAGTTAAAGATGCATTAACAACAAGG 58.918 33.333 18.75 8.56 42.80 3.61
4633 5094 9.462174 TTCAGTTAAAGATGCATTAACAACAAG 57.538 29.630 18.75 10.52 42.80 3.16
4634 5095 9.979578 ATTCAGTTAAAGATGCATTAACAACAA 57.020 25.926 18.75 10.86 42.80 2.83
4635 5096 9.979578 AATTCAGTTAAAGATGCATTAACAACA 57.020 25.926 18.75 6.57 42.80 3.33


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

AutoCloner maintained by Alex Coulton.