Multiple sequence alignment - TraesCS4A01G110300

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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 TraesCS4A01G110300 chr4A 100.000 3638 0 0 1 3638 134549128 134552765 0.000000e+00 6719
1 TraesCS4A01G110300 chr4A 86.604 321 28 3 3327 3638 134632927 134632613 1.250000e-89 340
2 TraesCS4A01G110300 chr4D 90.678 1888 94 23 874 2724 337472000 337470158 0.000000e+00 2436
3 TraesCS4A01G110300 chr4D 91.156 588 24 11 1 577 337472870 337472300 0.000000e+00 773
4 TraesCS4A01G110300 chr4D 87.097 589 54 8 2720 3308 111036276 111036842 0.000000e+00 647
5 TraesCS4A01G110300 chr4D 86.426 582 56 8 2719 3298 233108196 233108756 1.860000e-172 616
6 TraesCS4A01G110300 chr4D 82.609 460 56 9 2720 3178 80831454 80831018 5.700000e-103 385
7 TraesCS4A01G110300 chr4D 86.466 266 13 3 616 870 337472300 337472047 1.660000e-68 270
8 TraesCS4A01G110300 chr4B 88.783 1890 113 22 882 2718 416625850 416624007 0.000000e+00 2224
9 TraesCS4A01G110300 chr4B 87.708 903 53 25 1 870 416626784 416625907 0.000000e+00 1000
10 TraesCS4A01G110300 chr7B 87.179 585 54 7 2719 3303 63947835 63948398 0.000000e+00 645
11 TraesCS4A01G110300 chr2D 87.009 585 53 8 2719 3303 65314328 65314889 3.960000e-179 638
12 TraesCS4A01G110300 chr2D 88.652 141 7 4 3327 3458 65314978 65315118 2.910000e-36 163
13 TraesCS4A01G110300 chr6A 86.441 590 58 7 2719 3308 109048519 109047952 8.580000e-176 627
14 TraesCS4A01G110300 chr6A 88.162 321 29 3 3327 3638 109047864 109047544 1.230000e-99 374
15 TraesCS4A01G110300 chr2B 86.130 584 58 10 2720 3303 101238027 101238587 3.110000e-170 608
16 TraesCS4A01G110300 chr2B 84.472 322 35 7 3327 3638 567991388 567991704 1.640000e-78 303
17 TraesCS4A01G110300 chr5B 85.764 576 58 9 2717 3290 264879331 264878778 4.050000e-164 588
18 TraesCS4A01G110300 chr5B 85.324 586 58 11 2721 3303 115366632 115367192 6.770000e-162 580
19 TraesCS4A01G110300 chr5B 86.604 321 33 4 3327 3638 264878308 264877989 2.690000e-91 346
20 TraesCS4A01G110300 chr5B 86.604 321 26 4 3327 3638 115367284 115367596 4.500000e-89 339
21 TraesCS4A01G110300 chr3B 85.229 589 62 9 2719 3303 21170776 21171343 1.880000e-162 582
22 TraesCS4A01G110300 chr3B 80.068 587 93 10 2719 3303 245260149 245259585 7.270000e-112 414
23 TraesCS4A01G110300 chr3B 89.720 321 23 3 3327 3638 245952764 245952445 5.660000e-108 401
24 TraesCS4A01G110300 chr3B 87.850 321 28 2 3327 3638 21171434 21171752 2.060000e-97 366
25 TraesCS4A01G110300 chr3A 84.838 554 60 10 2718 3270 101979023 101978493 1.490000e-148 536
26 TraesCS4A01G110300 chr1B 83.333 600 73 14 2719 3315 584605888 584606463 2.490000e-146 529
27 TraesCS4A01G110300 chr1B 86.218 312 33 4 3336 3638 584568450 584568760 2.710000e-86 329
28 TraesCS4A01G110300 chr1B 86.218 312 33 4 3336 3638 584606559 584606869 2.710000e-86 329
29 TraesCS4A01G110300 chr1B 85.535 318 37 3 3327 3635 322618962 322619279 1.260000e-84 324
30 TraesCS4A01G110300 chr1B 78.819 288 46 6 2719 3006 363460825 363461097 2.890000e-41 180
31 TraesCS4A01G110300 chr6B 83.221 596 74 17 2719 3313 706215111 706214541 1.160000e-144 523
32 TraesCS4A01G110300 chr6B 83.529 510 60 15 2721 3229 706017613 706017127 4.280000e-124 455
33 TraesCS4A01G110300 chr3D 81.864 590 83 11 2715 3303 103625613 103626179 3.290000e-130 475
34 TraesCS4A01G110300 chr5A 85.893 319 35 4 3327 3636 577748491 577748174 7.530000e-87 331
35 TraesCS4A01G110300 chr1D 81.350 311 48 2 3332 3633 62578543 62578852 1.010000e-60 244
36 TraesCS4A01G110300 chr6D 81.013 316 50 2 3327 3633 119965855 119966169 3.630000e-60 243
37 TraesCS4A01G110300 chr5D 81.395 215 31 5 2719 2932 404253744 404253538 2.250000e-37 167


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 TraesCS4A01G110300 chr4A 134549128 134552765 3637 False 6719.000000 6719 100.000000 1 3638 1 chr4A.!!$F1 3637
1 TraesCS4A01G110300 chr4D 337470158 337472870 2712 True 1159.666667 2436 89.433333 1 2724 3 chr4D.!!$R2 2723
2 TraesCS4A01G110300 chr4D 111036276 111036842 566 False 647.000000 647 87.097000 2720 3308 1 chr4D.!!$F1 588
3 TraesCS4A01G110300 chr4D 233108196 233108756 560 False 616.000000 616 86.426000 2719 3298 1 chr4D.!!$F2 579
4 TraesCS4A01G110300 chr4B 416624007 416626784 2777 True 1612.000000 2224 88.245500 1 2718 2 chr4B.!!$R1 2717
5 TraesCS4A01G110300 chr7B 63947835 63948398 563 False 645.000000 645 87.179000 2719 3303 1 chr7B.!!$F1 584
6 TraesCS4A01G110300 chr2D 65314328 65315118 790 False 400.500000 638 87.830500 2719 3458 2 chr2D.!!$F1 739
7 TraesCS4A01G110300 chr6A 109047544 109048519 975 True 500.500000 627 87.301500 2719 3638 2 chr6A.!!$R1 919
8 TraesCS4A01G110300 chr2B 101238027 101238587 560 False 608.000000 608 86.130000 2720 3303 1 chr2B.!!$F1 583
9 TraesCS4A01G110300 chr5B 264877989 264879331 1342 True 467.000000 588 86.184000 2717 3638 2 chr5B.!!$R1 921
10 TraesCS4A01G110300 chr5B 115366632 115367596 964 False 459.500000 580 85.964000 2721 3638 2 chr5B.!!$F1 917
11 TraesCS4A01G110300 chr3B 21170776 21171752 976 False 474.000000 582 86.539500 2719 3638 2 chr3B.!!$F1 919
12 TraesCS4A01G110300 chr3B 245259585 245260149 564 True 414.000000 414 80.068000 2719 3303 1 chr3B.!!$R1 584
13 TraesCS4A01G110300 chr3A 101978493 101979023 530 True 536.000000 536 84.838000 2718 3270 1 chr3A.!!$R1 552
14 TraesCS4A01G110300 chr1B 584605888 584606869 981 False 429.000000 529 84.775500 2719 3638 2 chr1B.!!$F4 919
15 TraesCS4A01G110300 chr6B 706214541 706215111 570 True 523.000000 523 83.221000 2719 3313 1 chr6B.!!$R2 594
16 TraesCS4A01G110300 chr3D 103625613 103626179 566 False 475.000000 475 81.864000 2715 3303 1 chr3D.!!$F1 588

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
742 787 0.250467 CACCCGTCCATCCATCCATC 60.25 60.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2669 2819 0.108615 CCAACTAGTGTCTGGCCGAG 60.109 60.0 0.0 0.0 0.0 4.63 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
136 141 2.728817 GAGTCGTATCCCAGCCCG 59.271 66.667 0.00 0.00 0.00 6.13
230 235 2.612115 CTCCCCTCCTTGGCACCT 60.612 66.667 0.00 0.00 0.00 4.00
231 236 2.610859 TCCCCTCCTTGGCACCTC 60.611 66.667 0.00 0.00 0.00 3.85
265 284 0.400213 TTCCATGTCACCACACCCTC 59.600 55.000 0.00 0.00 34.48 4.30
277 296 4.681978 ACCCTCGTGTGCTTCGGC 62.682 66.667 0.00 0.00 42.19 5.54
365 384 3.319137 TTGTGCTGCTCTCGTTTATCT 57.681 42.857 0.00 0.00 0.00 1.98
366 385 4.450082 TTGTGCTGCTCTCGTTTATCTA 57.550 40.909 0.00 0.00 0.00 1.98
386 405 3.623906 ATATCCATCCTCTCGCCAATG 57.376 47.619 0.00 0.00 0.00 2.82
405 424 1.801771 TGTATTTTTGGAGGCACGTCG 59.198 47.619 0.00 0.00 0.00 5.12
415 434 1.660575 GGCACGTCGGATATCACGG 60.661 63.158 17.00 9.08 40.43 4.94
463 483 1.139734 TCTCTTGGATGCGAGCGTC 59.860 57.895 8.68 8.68 0.00 5.19
520 540 9.871299 CATATAGCGTGATGTGTATAGATAGAC 57.129 37.037 0.00 0.00 0.00 2.59
548 568 1.672030 CGGTGCTCAAGGACATGCA 60.672 57.895 4.02 0.00 38.19 3.96
550 570 0.524862 GGTGCTCAAGGACATGCAAG 59.475 55.000 4.02 0.00 38.19 4.01
551 571 1.527034 GTGCTCAAGGACATGCAAGA 58.473 50.000 0.00 0.00 37.17 3.02
555 581 3.575256 TGCTCAAGGACATGCAAGATTTT 59.425 39.130 0.00 0.00 32.12 1.82
557 583 4.624452 GCTCAAGGACATGCAAGATTTTTC 59.376 41.667 0.00 0.00 0.00 2.29
585 611 9.502091 TTTACAAGATCAAACACTACATTAGCT 57.498 29.630 0.00 0.00 0.00 3.32
587 613 8.396272 ACAAGATCAAACACTACATTAGCTTT 57.604 30.769 0.00 0.00 0.00 3.51
588 614 8.850156 ACAAGATCAAACACTACATTAGCTTTT 58.150 29.630 0.00 0.00 0.00 2.27
589 615 9.683069 CAAGATCAAACACTACATTAGCTTTTT 57.317 29.630 0.00 0.00 0.00 1.94
627 653 4.204978 GTCACAATTGTTTGCTTCAAGTCG 59.795 41.667 8.77 0.00 36.22 4.18
671 708 1.682854 AGGGAAACATATGGCAATGCG 59.317 47.619 7.80 0.00 0.00 4.73
718 763 1.231221 AATCAAAGGTGCGTGCGTTA 58.769 45.000 0.00 0.00 0.00 3.18
728 773 1.418367 CGTGCGTTAATGACACCCG 59.582 57.895 13.23 3.60 0.00 5.28
738 783 0.469917 ATGACACCCGTCCATCCATC 59.530 55.000 0.00 0.00 41.85 3.51
742 787 0.250467 CACCCGTCCATCCATCCATC 60.250 60.000 0.00 0.00 0.00 3.51
743 788 1.376466 CCCGTCCATCCATCCATCC 59.624 63.158 0.00 0.00 0.00 3.51
744 789 1.418097 CCCGTCCATCCATCCATCCA 61.418 60.000 0.00 0.00 0.00 3.41
813 858 2.751436 CCATGTGGCCTCAACGGG 60.751 66.667 12.26 10.04 0.00 5.28
871 916 3.842923 CCGCTCGCTCTCCCACAT 61.843 66.667 0.00 0.00 0.00 3.21
872 917 2.279120 CGCTCGCTCTCCCACATC 60.279 66.667 0.00 0.00 0.00 3.06
880 970 0.312416 CTCTCCCACATCGTCGATCC 59.688 60.000 4.34 0.00 0.00 3.36
909 1002 5.491323 TCCGTGATATTATATGCAACCCA 57.509 39.130 0.00 0.00 0.00 4.51
1051 1165 4.335647 CCACCCTCACGCTTGCCT 62.336 66.667 0.00 0.00 0.00 4.75
1074 1200 0.836606 TCTTGCAACTCCTCACACCA 59.163 50.000 0.00 0.00 0.00 4.17
1113 1247 2.740055 CCTCCGCACACACTCTGC 60.740 66.667 0.00 0.00 0.00 4.26
1159 1297 2.597805 ACTGCCCACTCGTCGTCT 60.598 61.111 0.00 0.00 0.00 4.18
1160 1298 2.179517 CTGCCCACTCGTCGTCTC 59.820 66.667 0.00 0.00 0.00 3.36
1162 1300 3.371063 GCCCACTCGTCGTCTCCA 61.371 66.667 0.00 0.00 0.00 3.86
1163 1301 2.878429 CCCACTCGTCGTCTCCAG 59.122 66.667 0.00 0.00 0.00 3.86
1164 1302 2.179517 CCACTCGTCGTCTCCAGC 59.820 66.667 0.00 0.00 0.00 4.85
1166 1304 4.104417 ACTCGTCGTCTCCAGCGC 62.104 66.667 0.00 0.00 0.00 5.92
1180 1318 2.912744 GCGCGCGCATAAAAATGG 59.087 55.556 46.11 12.36 41.49 3.16
1181 1319 1.585002 GCGCGCGCATAAAAATGGA 60.585 52.632 46.11 0.00 41.49 3.41
1182 1320 1.531522 GCGCGCGCATAAAAATGGAG 61.532 55.000 46.11 10.98 41.49 3.86
1183 1321 0.929824 CGCGCGCATAAAAATGGAGG 60.930 55.000 32.61 5.56 0.00 4.30
1184 1322 0.594796 GCGCGCATAAAAATGGAGGG 60.595 55.000 29.10 0.00 0.00 4.30
1282 1420 3.562779 TTCGCGGTCAAGTCGGTCC 62.563 63.158 6.13 0.00 0.00 4.46
1355 1493 1.522580 GGATCTTGAGGCGGCTGTC 60.523 63.158 19.63 3.13 0.00 3.51
1366 1504 3.755628 GGCTGTCCTCGCCGTACA 61.756 66.667 0.00 0.00 37.87 2.90
1398 1536 4.760047 GGTGATGACGCCACGGCT 62.760 66.667 6.48 0.00 45.14 5.52
1399 1537 2.742372 GTGATGACGCCACGGCTT 60.742 61.111 6.48 0.00 35.04 4.35
1402 1540 3.982372 GATGACGCCACGGCTTCGA 62.982 63.158 9.70 0.65 41.49 3.71
1404 1542 4.719369 GACGCCACGGCTTCGACT 62.719 66.667 6.48 0.00 39.32 4.18
1524 1674 4.840005 GCCGCCCTGCACTACCTC 62.840 72.222 0.00 0.00 0.00 3.85
1644 1794 3.353836 GCGGCGAGGCTTGTTTCA 61.354 61.111 12.98 0.00 0.00 2.69
1791 1941 4.473520 AAGCGGCCATGGTCGGAG 62.474 66.667 37.47 13.18 44.14 4.63
1794 1944 2.280389 CGGCCATGGTCGGAGATG 60.280 66.667 31.05 0.85 40.67 2.90
1844 1994 2.125832 CCACATCGGTTACGGCGT 60.126 61.111 19.64 19.64 41.39 5.68
2075 2225 2.202756 GTCGTCCGACTGCCATCC 60.203 66.667 12.31 0.00 41.57 3.51
2243 2393 2.349886 GTCTTGAGATGTCAACCGATGC 59.650 50.000 0.23 0.00 37.79 3.91
2247 2397 1.662629 GAGATGTCAACCGATGCAGTG 59.337 52.381 0.00 0.00 0.00 3.66
2248 2398 0.097674 GATGTCAACCGATGCAGTGC 59.902 55.000 8.58 8.58 0.00 4.40
2452 2602 1.303282 GGGTTTGATCGGCCTCCTT 59.697 57.895 0.00 0.00 0.00 3.36
2499 2649 3.430236 CCGTGCTGGTGTCATGTATTCTA 60.430 47.826 0.00 0.00 0.00 2.10
2540 2690 4.652421 TGATTTTGTTTCAGCAAGCAGA 57.348 36.364 0.00 0.00 0.00 4.26
2542 2692 2.473530 TTTGTTTCAGCAAGCAGACG 57.526 45.000 0.00 0.00 0.00 4.18
2553 2703 2.677836 GCAAGCAGACGGTGAATTGATA 59.322 45.455 8.61 0.00 29.85 2.15
2554 2704 3.485877 GCAAGCAGACGGTGAATTGATAC 60.486 47.826 8.61 0.00 29.85 2.24
2555 2705 3.895232 AGCAGACGGTGAATTGATACT 57.105 42.857 0.00 0.00 0.00 2.12
2556 2706 5.109210 CAAGCAGACGGTGAATTGATACTA 58.891 41.667 0.00 0.00 29.85 1.82
2582 2732 3.838244 TGCTACAGTTTCTGGTTCTGT 57.162 42.857 0.00 0.00 43.46 3.41
2610 2760 0.179045 ACAGCGCAGTTTCTGGTTCT 60.179 50.000 11.47 0.00 34.76 3.01
2638 2788 5.474825 TCTTTGGTGGTTTTGACTTTTGAC 58.525 37.500 0.00 0.00 0.00 3.18
2639 2789 5.245075 TCTTTGGTGGTTTTGACTTTTGACT 59.755 36.000 0.00 0.00 0.00 3.41
2641 2791 5.066968 TGGTGGTTTTGACTTTTGACTTC 57.933 39.130 0.00 0.00 0.00 3.01
2642 2792 4.770010 TGGTGGTTTTGACTTTTGACTTCT 59.230 37.500 0.00 0.00 0.00 2.85
2643 2793 5.102313 GGTGGTTTTGACTTTTGACTTCTG 58.898 41.667 0.00 0.00 0.00 3.02
2644 2794 5.105917 GGTGGTTTTGACTTTTGACTTCTGA 60.106 40.000 0.00 0.00 0.00 3.27
2669 2819 0.737715 CTGCTAGTTGGGTGAGCGAC 60.738 60.000 0.00 0.00 39.14 5.19
2679 2829 3.749064 TGAGCGACTCGGCCAGAC 61.749 66.667 2.24 0.00 32.35 3.51
2698 2848 0.319900 CACTAGTTGGTCAGCAGCGT 60.320 55.000 0.00 0.00 0.00 5.07
2759 2909 6.091441 GGCGTAAGATTTGCCTCATCTATTAG 59.909 42.308 0.00 0.00 45.40 1.73
2760 2910 6.091441 GCGTAAGATTTGCCTCATCTATTAGG 59.909 42.308 0.00 0.00 43.02 2.69
2761 2911 7.155328 CGTAAGATTTGCCTCATCTATTAGGT 58.845 38.462 0.00 0.00 43.02 3.08
2762 2912 7.657761 CGTAAGATTTGCCTCATCTATTAGGTT 59.342 37.037 0.00 0.00 43.02 3.50
2763 2913 9.998106 GTAAGATTTGCCTCATCTATTAGGTTA 57.002 33.333 0.00 0.00 35.16 2.85
2768 2918 9.965902 ATTTGCCTCATCTATTAGGTTATTAGG 57.034 33.333 0.00 0.00 35.16 2.69
2831 2985 3.486708 CGCAAGCGGCATGAAAATTACTA 60.487 43.478 9.71 0.00 45.17 1.82
2880 3034 0.534203 CGCCGGCAGTAACCCATAAT 60.534 55.000 28.98 0.00 0.00 1.28
2917 3071 5.542251 AGAATAGATCTAAGGAGAACAGGCC 59.458 44.000 6.52 0.00 36.32 5.19
2924 3078 2.283529 GGAGAACAGGCCGTGGAGA 61.284 63.158 0.00 0.00 0.00 3.71
2926 3080 0.250513 GAGAACAGGCCGTGGAGAAT 59.749 55.000 0.00 0.00 0.00 2.40
2928 3082 1.073923 AGAACAGGCCGTGGAGAATTT 59.926 47.619 0.00 0.00 0.00 1.82
2929 3083 1.886542 GAACAGGCCGTGGAGAATTTT 59.113 47.619 0.00 0.00 0.00 1.82
2930 3084 1.995376 ACAGGCCGTGGAGAATTTTT 58.005 45.000 0.00 0.00 0.00 1.94
2973 3127 2.177173 GCATTCCGCTCGTTTCAAATC 58.823 47.619 0.00 0.00 37.77 2.17
2981 3135 2.159627 GCTCGTTTCAAATCGTCCATGT 59.840 45.455 0.00 0.00 0.00 3.21
3024 3178 1.053264 TGGCATGCCAGTTTGGGTTT 61.053 50.000 35.59 0.00 41.89 3.27
3025 3179 0.320683 GGCATGCCAGTTTGGGTTTC 60.321 55.000 32.08 0.00 38.19 2.78
3026 3180 0.667184 GCATGCCAGTTTGGGTTTCG 60.667 55.000 6.36 0.00 38.19 3.46
3027 3181 0.038343 CATGCCAGTTTGGGTTTCGG 60.038 55.000 0.00 0.00 38.19 4.30
3028 3182 0.469144 ATGCCAGTTTGGGTTTCGGT 60.469 50.000 0.00 0.00 38.19 4.69
3029 3183 0.684805 TGCCAGTTTGGGTTTCGGTT 60.685 50.000 0.00 0.00 38.19 4.44
3030 3184 1.320507 GCCAGTTTGGGTTTCGGTTA 58.679 50.000 0.00 0.00 38.19 2.85
3061 3215 0.834612 TTCGTTTGTCCCACCACTCT 59.165 50.000 0.00 0.00 0.00 3.24
3136 3290 4.458989 AGCTTCTCGATGATAGATCTCCAC 59.541 45.833 0.00 0.00 0.00 4.02
3169 3323 1.686587 TGCCGACACTTGAAGAAGAGA 59.313 47.619 0.00 0.00 32.98 3.10
3186 3340 3.454858 AGAGATGAGGCCCTGTTTCTTA 58.545 45.455 0.00 0.00 0.00 2.10
3235 3389 3.532155 TTTGCCAAACCGCGCCTT 61.532 55.556 0.00 0.00 0.00 4.35
3237 3391 2.579684 TTTGCCAAACCGCGCCTTTT 62.580 50.000 0.00 0.00 0.00 2.27
3242 3396 0.248866 CAAACCGCGCCTTTTCAACT 60.249 50.000 0.00 0.00 0.00 3.16
3243 3397 0.458260 AAACCGCGCCTTTTCAACTT 59.542 45.000 0.00 0.00 0.00 2.66
3270 3424 3.587923 CGGTCCAAATACGGTCTTGTAA 58.412 45.455 0.00 0.00 0.00 2.41
3281 3435 4.453751 ACGGTCTTGTAAAGCTAACCAAA 58.546 39.130 0.00 0.00 45.70 3.28
3303 3466 5.195848 ACGAATAATTTAACCTTGGGGGA 57.804 39.130 0.00 0.00 38.76 4.81
3433 4029 0.387565 GAATGTGGCCAACGGTGTTT 59.612 50.000 7.24 0.00 0.00 2.83
3447 4043 5.269505 ACGGTGTTTGGATTGATTTTGAA 57.730 34.783 0.00 0.00 0.00 2.69
3461 4057 9.902196 GATTGATTTTGAAAATCCAAGCATTTT 57.098 25.926 23.43 6.27 38.43 1.82
3537 4135 3.004752 ACAGTGCAATATCCTTGGACC 57.995 47.619 6.06 0.00 40.92 4.46
3548 4146 4.689549 TTGGACCTCCGCCCGAGA 62.690 66.667 0.00 0.00 41.63 4.04
3562 4160 1.612395 CCGAGAAGCCAAGGAGAGCT 61.612 60.000 0.00 0.00 42.40 4.09
3623 4221 4.859304 TGTAGAGGCGTAGAAAAACTCA 57.141 40.909 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 101 4.554036 GGATCGGTGGCTCCTGGC 62.554 72.222 3.83 0.00 40.90 4.85
136 141 2.563427 GCGAAAAGCTGTGGCCTC 59.437 61.111 3.32 0.00 44.04 4.70
178 183 1.653151 GCTACGCGGAGGAAAGAAAT 58.347 50.000 22.20 0.00 0.00 2.17
179 184 0.390735 GGCTACGCGGAGGAAAGAAA 60.391 55.000 22.20 0.00 0.00 2.52
180 185 1.217244 GGCTACGCGGAGGAAAGAA 59.783 57.895 22.20 0.00 0.00 2.52
227 232 3.681835 GACACGAGTGGCCGAGGT 61.682 66.667 8.19 0.00 30.68 3.85
365 384 4.096681 ACATTGGCGAGAGGATGGATATA 58.903 43.478 0.00 0.00 0.00 0.86
366 385 2.909006 ACATTGGCGAGAGGATGGATAT 59.091 45.455 0.00 0.00 0.00 1.63
386 405 1.129811 CCGACGTGCCTCCAAAAATAC 59.870 52.381 0.00 0.00 0.00 1.89
405 424 5.185056 CCCCAAAATATTTCCCGTGATATCC 59.815 44.000 0.10 0.00 0.00 2.59
415 434 2.093181 GGTGTGGCCCCAAAATATTTCC 60.093 50.000 0.00 0.00 0.00 3.13
477 497 2.717639 ATGGTGTATTGGACTCAGGC 57.282 50.000 0.00 0.00 0.00 4.85
520 540 0.241749 TTGAGCACCGGTACAGTACG 59.758 55.000 6.87 0.00 0.00 3.67
587 613 2.177654 GACGCCGATCCACGCAAAAA 62.178 55.000 0.00 0.00 41.07 1.94
588 614 2.666862 ACGCCGATCCACGCAAAA 60.667 55.556 0.00 0.00 41.07 2.44
589 615 3.115892 GACGCCGATCCACGCAAA 61.116 61.111 0.00 0.00 41.07 3.68
590 616 4.365505 TGACGCCGATCCACGCAA 62.366 61.111 0.00 0.00 41.07 4.85
593 619 1.358725 AATTGTGACGCCGATCCACG 61.359 55.000 0.00 0.77 42.18 4.94
594 620 0.096976 CAATTGTGACGCCGATCCAC 59.903 55.000 0.00 0.00 0.00 4.02
595 621 0.321210 ACAATTGTGACGCCGATCCA 60.321 50.000 11.07 0.00 0.00 3.41
596 622 0.802494 AACAATTGTGACGCCGATCC 59.198 50.000 12.82 0.00 0.00 3.36
597 623 2.241722 CAAACAATTGTGACGCCGATC 58.758 47.619 12.82 0.00 0.00 3.69
598 624 1.665735 GCAAACAATTGTGACGCCGAT 60.666 47.619 12.82 0.00 38.85 4.18
599 625 0.317436 GCAAACAATTGTGACGCCGA 60.317 50.000 12.82 0.00 38.85 5.54
652 685 1.269726 CCGCATTGCCATATGTTTCCC 60.270 52.381 2.41 0.00 0.00 3.97
671 708 0.179081 GGAATAGTCGAGGGTGCACC 60.179 60.000 28.57 28.57 40.67 5.01
728 773 5.370584 TGGATATATGGATGGATGGATGGAC 59.629 44.000 0.00 0.00 0.00 4.02
738 783 4.700213 GGTTCCGTTTGGATATATGGATGG 59.300 45.833 0.00 0.00 45.91 3.51
742 787 3.496884 CACGGTTCCGTTTGGATATATGG 59.503 47.826 14.42 0.00 45.91 2.74
743 788 4.373527 TCACGGTTCCGTTTGGATATATG 58.626 43.478 14.42 0.00 45.91 1.78
744 789 4.675976 TCACGGTTCCGTTTGGATATAT 57.324 40.909 14.42 0.00 45.91 0.86
856 901 2.279120 CGATGTGGGAGAGCGAGC 60.279 66.667 0.00 0.00 0.00 5.03
870 915 3.987868 CACGGAATAAATGGATCGACGAT 59.012 43.478 10.78 10.78 0.00 3.73
871 916 3.067040 TCACGGAATAAATGGATCGACGA 59.933 43.478 0.00 0.00 0.00 4.20
872 917 3.377439 TCACGGAATAAATGGATCGACG 58.623 45.455 0.00 0.00 0.00 5.12
903 996 7.029563 CCGAATATTTCTTTCTTTCTGGGTTG 58.970 38.462 0.00 0.00 0.00 3.77
909 1002 5.358160 CCTGCCCGAATATTTCTTTCTTTCT 59.642 40.000 0.00 0.00 0.00 2.52
1051 1165 3.206150 GTGTGAGGAGTTGCAAGAAGAA 58.794 45.455 0.00 0.00 0.00 2.52
1074 1200 4.410555 GGTGAGGAGTGAATAAAGGGAGAT 59.589 45.833 0.00 0.00 0.00 2.75
1113 1247 4.130118 GAGTAGAGGAGCTCAGAGAGAAG 58.870 52.174 17.19 0.00 32.06 2.85
1163 1301 1.531522 CTCCATTTTTATGCGCGCGC 61.532 55.000 45.02 45.02 42.35 6.86
1164 1302 0.929824 CCTCCATTTTTATGCGCGCG 60.930 55.000 28.44 28.44 0.00 6.86
1166 1304 0.030638 CCCCTCCATTTTTATGCGCG 59.969 55.000 0.00 0.00 0.00 6.86
1167 1305 1.111277 ACCCCTCCATTTTTATGCGC 58.889 50.000 0.00 0.00 0.00 6.09
1168 1306 1.408702 CCACCCCTCCATTTTTATGCG 59.591 52.381 0.00 0.00 0.00 4.73
1169 1307 2.430694 GTCCACCCCTCCATTTTTATGC 59.569 50.000 0.00 0.00 0.00 3.14
1170 1308 2.687935 CGTCCACCCCTCCATTTTTATG 59.312 50.000 0.00 0.00 0.00 1.90
1171 1309 2.948600 GCGTCCACCCCTCCATTTTTAT 60.949 50.000 0.00 0.00 0.00 1.40
1172 1310 1.614850 GCGTCCACCCCTCCATTTTTA 60.615 52.381 0.00 0.00 0.00 1.52
1174 1312 1.304134 GCGTCCACCCCTCCATTTT 60.304 57.895 0.00 0.00 0.00 1.82
1175 1313 2.355115 GCGTCCACCCCTCCATTT 59.645 61.111 0.00 0.00 0.00 2.32
1176 1314 4.096003 CGCGTCCACCCCTCCATT 62.096 66.667 0.00 0.00 0.00 3.16
1383 1521 2.434185 GAAGCCGTGGCGTCATCA 60.434 61.111 19.80 0.00 46.16 3.07
1398 1536 1.334160 TGTGCAGGTTCCTAGTCGAA 58.666 50.000 0.00 0.00 0.00 3.71
1399 1537 1.204704 CATGTGCAGGTTCCTAGTCGA 59.795 52.381 0.00 0.00 0.00 4.20
1402 1540 1.556911 CTCCATGTGCAGGTTCCTAGT 59.443 52.381 0.00 0.00 0.00 2.57
1404 1542 0.253044 GCTCCATGTGCAGGTTCCTA 59.747 55.000 0.00 0.00 0.00 2.94
1595 1745 2.266055 GCTTGGAGCTGCCGTACT 59.734 61.111 1.53 0.00 38.45 2.73
1782 1932 3.550431 CCGCCCATCTCCGACCAT 61.550 66.667 0.00 0.00 0.00 3.55
1844 1994 3.760035 GGAGCTCCGGTCGCTTCA 61.760 66.667 19.06 0.00 37.96 3.02
2078 2228 4.907034 CGTCCTCGATGTCGGCCG 62.907 72.222 22.12 22.12 40.29 6.13
2226 2376 1.276138 ACTGCATCGGTTGACATCTCA 59.724 47.619 0.00 0.00 0.00 3.27
2247 2397 0.541863 ATGGTACCAGTGGCAGTAGC 59.458 55.000 21.41 4.77 37.45 3.58
2248 2398 1.202417 CGATGGTACCAGTGGCAGTAG 60.202 57.143 21.41 0.00 0.00 2.57
2403 2553 0.756070 TATGGTACCCACGGCGATCA 60.756 55.000 16.62 0.00 35.80 2.92
2410 2560 2.294074 CCCACATTTATGGTACCCACG 58.706 52.381 10.07 0.00 38.16 4.94
2519 2669 4.362279 GTCTGCTTGCTGAAACAAAATCA 58.638 39.130 3.85 0.00 0.00 2.57
2563 2713 5.500645 AAAACAGAACCAGAAACTGTAGC 57.499 39.130 0.00 0.00 42.81 3.58
2596 2746 4.639135 AGAAACAAGAACCAGAAACTGC 57.361 40.909 0.00 0.00 0.00 4.40
2610 2760 5.476091 AGTCAAAACCACCAAAGAAACAA 57.524 34.783 0.00 0.00 0.00 2.83
2638 2788 3.126514 CCAACTAGCAGCAACATCAGAAG 59.873 47.826 0.00 0.00 0.00 2.85
2639 2789 3.076621 CCAACTAGCAGCAACATCAGAA 58.923 45.455 0.00 0.00 0.00 3.02
2641 2791 1.741706 CCCAACTAGCAGCAACATCAG 59.258 52.381 0.00 0.00 0.00 2.90
2642 2792 1.073763 ACCCAACTAGCAGCAACATCA 59.926 47.619 0.00 0.00 0.00 3.07
2643 2793 1.470098 CACCCAACTAGCAGCAACATC 59.530 52.381 0.00 0.00 0.00 3.06
2644 2794 1.073763 TCACCCAACTAGCAGCAACAT 59.926 47.619 0.00 0.00 0.00 2.71
2669 2819 0.108615 CCAACTAGTGTCTGGCCGAG 60.109 60.000 0.00 0.00 0.00 4.63
2679 2829 0.319900 ACGCTGCTGACCAACTAGTG 60.320 55.000 0.00 0.00 0.00 2.74
2698 2848 1.034838 GGGAGCAAACACACCACACA 61.035 55.000 0.00 0.00 0.00 3.72
2737 2887 8.910351 AACCTAATAGATGAGGCAAATCTTAC 57.090 34.615 7.18 0.00 36.17 2.34
2766 2916 9.549984 ACTCTAAACTCTATTCTTTCCTTACCT 57.450 33.333 0.00 0.00 0.00 3.08
2797 2947 1.787057 CGCTTGCGTGGGGTGTTTTA 61.787 55.000 6.86 0.00 0.00 1.52
2799 2949 3.591835 CGCTTGCGTGGGGTGTTT 61.592 61.111 6.86 0.00 0.00 2.83
2831 2985 6.358974 AACTTGGGCTTATAATTTTGTGCT 57.641 33.333 0.00 0.00 0.00 4.40
2898 3052 2.035632 CGGCCTGTTCTCCTTAGATCT 58.964 52.381 0.00 0.00 0.00 2.75
2928 3082 7.483691 GCTAGAGTGTTTCGTCAAAAAGAAAAA 59.516 33.333 0.00 0.00 37.98 1.94
2929 3083 6.964934 GCTAGAGTGTTTCGTCAAAAAGAAAA 59.035 34.615 0.00 0.00 37.98 2.29
2930 3084 6.092944 TGCTAGAGTGTTTCGTCAAAAAGAAA 59.907 34.615 0.00 0.00 34.40 2.52
2931 3085 5.583061 TGCTAGAGTGTTTCGTCAAAAAGAA 59.417 36.000 0.00 0.00 0.00 2.52
2932 3086 5.113383 TGCTAGAGTGTTTCGTCAAAAAGA 58.887 37.500 0.00 0.00 0.00 2.52
2933 3087 5.403897 TGCTAGAGTGTTTCGTCAAAAAG 57.596 39.130 0.00 0.00 0.00 2.27
2967 3121 2.938451 GCTCATCACATGGACGATTTGA 59.062 45.455 0.00 0.00 0.00 2.69
2981 3135 0.835276 CTCCCTCACCATGCTCATCA 59.165 55.000 0.00 0.00 0.00 3.07
3024 3178 2.286950 CGAACCGATAACCGATAACCGA 60.287 50.000 0.00 0.00 41.76 4.69
3025 3179 2.046313 CGAACCGATAACCGATAACCG 58.954 52.381 0.00 0.00 41.76 4.44
3026 3180 3.084070 ACGAACCGATAACCGATAACC 57.916 47.619 0.00 0.00 41.76 2.85
3027 3181 4.327087 ACAAACGAACCGATAACCGATAAC 59.673 41.667 0.00 0.00 41.76 1.89
3028 3182 4.493547 ACAAACGAACCGATAACCGATAA 58.506 39.130 0.00 0.00 41.76 1.75
3029 3183 4.104776 GACAAACGAACCGATAACCGATA 58.895 43.478 0.00 0.00 41.76 2.92
3030 3184 2.925563 GACAAACGAACCGATAACCGAT 59.074 45.455 0.00 0.00 41.76 4.18
3061 3215 3.378112 GGCATCTTGATGAATCCGTCAAA 59.622 43.478 14.09 0.00 44.87 2.69
3136 3290 3.490759 CGGCACACGCTTAGGCTG 61.491 66.667 0.00 0.00 38.60 4.85
3169 3323 4.476479 AGAGAATAAGAAACAGGGCCTCAT 59.524 41.667 0.95 0.00 0.00 2.90
3186 3340 4.226427 TGCCAACTATGCAAGAGAGAAT 57.774 40.909 6.02 0.00 35.40 2.40
3224 3378 0.458260 AAGTTGAAAAGGCGCGGTTT 59.542 45.000 8.83 3.62 0.00 3.27
3235 3389 1.002201 TGGACCGCCGATAAGTTGAAA 59.998 47.619 0.00 0.00 36.79 2.69
3237 3391 0.609151 TTGGACCGCCGATAAGTTGA 59.391 50.000 0.00 0.00 36.79 3.18
3242 3396 1.538634 CCGTATTTGGACCGCCGATAA 60.539 52.381 0.00 0.00 36.79 1.75
3243 3397 0.032403 CCGTATTTGGACCGCCGATA 59.968 55.000 0.00 0.00 36.79 2.92
3270 3424 8.799367 AGGTTAAATTATTCGTTTGGTTAGCTT 58.201 29.630 0.00 0.00 0.00 3.74
3281 3435 5.195848 TCCCCCAAGGTTAAATTATTCGT 57.804 39.130 0.00 0.00 36.75 3.85
3318 3482 3.809013 ATGCGGATGACCACCCCC 61.809 66.667 0.00 0.00 35.59 5.40
3319 3483 2.516930 CATGCGGATGACCACCCC 60.517 66.667 12.09 0.00 35.59 4.95
3320 3484 3.211963 GCATGCGGATGACCACCC 61.212 66.667 22.14 0.00 35.59 4.61
3321 3485 1.718757 GAAGCATGCGGATGACCACC 61.719 60.000 22.14 1.98 35.59 4.61
3322 3486 1.718757 GGAAGCATGCGGATGACCAC 61.719 60.000 22.14 8.02 35.59 4.16
3323 3487 1.451927 GGAAGCATGCGGATGACCA 60.452 57.895 22.14 0.00 35.59 4.02
3324 3488 1.031571 TTGGAAGCATGCGGATGACC 61.032 55.000 22.14 18.71 0.00 4.02
3325 3489 0.810648 TTTGGAAGCATGCGGATGAC 59.189 50.000 22.14 11.85 0.00 3.06
3330 3917 3.253921 TGATATCATTTGGAAGCATGCGG 59.746 43.478 13.01 0.00 0.00 5.69
3373 3960 4.202441 GGATGCTTGTACATGACTTCCAT 58.798 43.478 12.65 5.86 35.44 3.41
3385 3972 5.227569 TCTTCACTCTTTGGATGCTTGTA 57.772 39.130 0.00 0.00 0.00 2.41
3447 4043 5.930569 GCTCTCAAAGAAAATGCTTGGATTT 59.069 36.000 0.00 0.00 27.94 2.17
3461 4057 1.913262 TGCGGGAGGCTCTCAAAGA 60.913 57.895 15.97 0.00 44.05 2.52
3537 4135 4.082523 TTGGCTTCTCGGGCGGAG 62.083 66.667 15.31 15.31 44.58 4.63
3545 4143 0.177836 GGAGCTCTCCTTGGCTTCTC 59.822 60.000 14.64 0.00 46.16 2.87
3562 4160 1.214589 GCTAAGACGCCGTTCTGGA 59.785 57.895 0.00 0.00 42.00 3.86


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

AutoCloner maintained by Alex Coulton.