Multiple sequence alignment - TraesCS6D01G369000

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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 TraesCS6D01G369000 chr6D 100.000 3933 0 0 1 3933 455908772 455904840 0.000000e+00 7263.0
1 TraesCS6D01G369000 chr6D 86.581 1401 115 32 1004 2380 455899765 455898414 0.000000e+00 1478.0
2 TraesCS6D01G369000 chr6D 86.941 1095 87 29 2386 3429 455898160 455897071 0.000000e+00 1179.0
3 TraesCS6D01G369000 chr6D 81.304 813 88 33 5 778 455900689 455899902 5.620000e-168 601.0
4 TraesCS6D01G369000 chr6D 87.931 522 46 9 1028 1532 455970026 455969505 2.020000e-167 599.0
5 TraesCS6D01G369000 chr6D 81.119 715 86 31 1046 1736 455935638 455934949 9.680000e-146 527.0
6 TraesCS6D01G369000 chr6D 81.162 637 95 16 2412 3045 455968995 455968381 4.570000e-134 488.0
7 TraesCS6D01G369000 chr6D 88.438 320 27 6 2729 3045 455934169 455933857 1.030000e-100 377.0
8 TraesCS6D01G369000 chr6D 88.889 234 26 0 2398 2631 455934488 455934255 4.970000e-74 289.0
9 TraesCS6D01G369000 chr6D 81.707 246 23 15 3416 3649 455897050 455896815 6.710000e-43 185.0
10 TraesCS6D01G369000 chr6D 77.551 147 21 6 294 438 379030877 379030741 1.170000e-10 78.7
11 TraesCS6D01G369000 chr6B 89.953 1702 93 32 1 1679 693303766 693302120 0.000000e+00 2124.0
12 TraesCS6D01G369000 chr6B 92.950 1149 48 12 2221 3346 693300491 693299353 0.000000e+00 1642.0
13 TraesCS6D01G369000 chr6B 88.686 1043 91 18 2386 3403 693131609 693130569 0.000000e+00 1247.0
14 TraesCS6D01G369000 chr6B 83.723 1112 109 30 959 2032 693133218 693132141 0.000000e+00 985.0
15 TraesCS6D01G369000 chr6B 94.494 563 16 8 1682 2242 693301090 693300541 0.000000e+00 854.0
16 TraesCS6D01G369000 chr6B 96.371 496 16 2 3342 3836 693296857 693296363 0.000000e+00 815.0
17 TraesCS6D01G369000 chr6B 87.575 499 42 9 1046 1532 693324353 693323863 9.540000e-156 560.0
18 TraesCS6D01G369000 chr6B 82.663 646 80 21 2408 3045 693323101 693322480 9.610000e-151 544.0
19 TraesCS6D01G369000 chr6B 84.223 431 45 10 1 408 693136143 693135713 7.920000e-107 398.0
20 TraesCS6D01G369000 chr6B 80.282 426 49 20 523 928 693133625 693133215 4.970000e-74 289.0
21 TraesCS6D01G369000 chr6B 87.342 79 8 2 3573 3650 693317959 693317882 5.410000e-14 89.8
22 TraesCS6D01G369000 chr6A 87.311 1718 138 34 1 1670 602718700 602717015 0.000000e+00 1892.0
23 TraesCS6D01G369000 chr6A 91.496 1270 55 20 2377 3633 602715969 602714740 0.000000e+00 1698.0
24 TraesCS6D01G369000 chr6A 93.771 594 25 5 1789 2382 602717013 602716432 0.000000e+00 881.0
25 TraesCS6D01G369000 chr6A 88.732 497 43 7 1046 1532 602740569 602740076 2.620000e-166 595.0
26 TraesCS6D01G369000 chr6A 85.141 498 56 8 1046 1533 602727028 602726539 9.820000e-136 494.0
27 TraesCS6D01G369000 chr6A 88.125 320 28 6 2729 3045 602725542 602725230 4.800000e-99 372.0
28 TraesCS6D01G369000 chr6A 85.479 303 39 2 2743 3045 596486145 596486442 1.060000e-80 311.0
29 TraesCS6D01G369000 chr6A 89.732 224 23 0 2408 2631 602725851 602725628 1.790000e-73 287.0
30 TraesCS6D01G369000 chr6A 83.000 200 34 0 2383 2582 596485833 596486032 8.680000e-42 182.0
31 TraesCS6D01G369000 chr6A 84.211 133 14 6 3517 3648 602725019 602724893 5.340000e-24 122.0
32 TraesCS6D01G369000 chr2D 78.846 676 90 22 1746 2381 484126561 484127223 1.320000e-109 407.0
33 TraesCS6D01G369000 chr3D 86.420 243 29 4 2390 2631 457057231 457057470 3.010000e-66 263.0
34 TraesCS6D01G369000 chr3D 74.691 162 28 10 550 702 360591214 360591057 4.240000e-05 60.2
35 TraesCS6D01G369000 chr3D 100.000 28 0 0 674 701 603748062 603748089 7.000000e-03 52.8
36 TraesCS6D01G369000 chr2B 75.772 421 67 26 294 701 22785374 22785772 3.120000e-41 180.0
37 TraesCS6D01G369000 chr2B 74.286 420 58 31 295 701 604992495 604992877 8.870000e-27 132.0
38 TraesCS6D01G369000 chr2A 73.934 422 64 27 294 701 657517230 657517619 1.150000e-25 128.0
39 TraesCS6D01G369000 chr7B 73.239 426 79 32 294 709 539863002 539863402 5.340000e-24 122.0
40 TraesCS6D01G369000 chr4B 74.074 324 50 24 294 602 113959826 113959522 6.950000e-18 102.0
41 TraesCS6D01G369000 chr1D 87.805 82 8 2 293 373 473144860 473144780 1.160000e-15 95.3
42 TraesCS6D01G369000 chr5A 76.562 192 32 10 511 701 31516041 31516220 4.180000e-15 93.5


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 TraesCS6D01G369000 chr6D 455904840 455908772 3932 True 7263.000000 7263 100.000000 1 3933 1 chr6D.!!$R2 3932
1 TraesCS6D01G369000 chr6D 455896815 455900689 3874 True 860.750000 1478 84.133250 5 3649 4 chr6D.!!$R3 3644
2 TraesCS6D01G369000 chr6D 455968381 455970026 1645 True 543.500000 599 84.546500 1028 3045 2 chr6D.!!$R5 2017
3 TraesCS6D01G369000 chr6D 455933857 455935638 1781 True 397.666667 527 86.148667 1046 3045 3 chr6D.!!$R4 1999
4 TraesCS6D01G369000 chr6B 693296363 693303766 7403 True 1358.750000 2124 93.442000 1 3836 4 chr6B.!!$R3 3835
5 TraesCS6D01G369000 chr6B 693130569 693136143 5574 True 729.750000 1247 84.228500 1 3403 4 chr6B.!!$R2 3402
6 TraesCS6D01G369000 chr6B 693322480 693324353 1873 True 552.000000 560 85.119000 1046 3045 2 chr6B.!!$R4 1999
7 TraesCS6D01G369000 chr6A 602714740 602718700 3960 True 1490.333333 1892 90.859333 1 3633 3 chr6A.!!$R2 3632
8 TraesCS6D01G369000 chr6A 602724893 602727028 2135 True 318.750000 494 86.802250 1046 3648 4 chr6A.!!$R3 2602
9 TraesCS6D01G369000 chr6A 596485833 596486442 609 False 246.500000 311 84.239500 2383 3045 2 chr6A.!!$F1 662
10 TraesCS6D01G369000 chr2D 484126561 484127223 662 False 407.000000 407 78.846000 1746 2381 1 chr2D.!!$F1 635

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
256 277 1.888512 TGGAGCTGGCTGACAAATTTC 59.111 47.619 0.00 0.0 0.00 2.17 F
336 358 1.960612 TTTCGGCGGAAACCAATGG 59.039 52.632 14.76 0.0 37.24 3.16 F
729 2739 2.216037 CGTGTACGTTGCGTTGACTTAA 59.784 45.455 0.00 0.0 41.54 1.85 F
1541 3617 0.320508 GGTCCGTTCGCTCTTCCTTT 60.321 55.000 0.00 0.0 0.00 3.11 F
1542 3618 1.069255 GTCCGTTCGCTCTTCCTTTC 58.931 55.000 0.00 0.0 0.00 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1339 3398 0.699577 TGTTGGAGGAGTTTGGGGGA 60.700 55.000 0.00 0.00 0.0 4.81 R
1354 3414 1.303309 GGCCGAGGATGAATCTGTTG 58.697 55.000 0.00 0.00 0.0 3.33 R
1729 4853 2.329267 TCACACTTCACAGGACCATCT 58.671 47.619 0.00 0.00 0.0 2.90 R
2782 6699 1.997311 CTCCAGCTCCATCCACCCA 60.997 63.158 0.00 0.00 0.0 4.51 R
2957 6874 2.742372 CTTTGACCCGGGCGAGTG 60.742 66.667 24.08 4.46 0.0 3.51 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
33 34 8.310406 TGTGAAGAAATGTATGTGTCTGTAAG 57.690 34.615 0.00 0.00 0.00 2.34
182 193 3.548587 GAGCTGACGCGTTATCGTAATA 58.451 45.455 15.53 0.00 43.42 0.98
227 248 4.148825 CCCCTTCGCAGAGACCGG 62.149 72.222 0.00 0.00 38.43 5.28
256 277 1.888512 TGGAGCTGGCTGACAAATTTC 59.111 47.619 0.00 0.00 0.00 2.17
336 358 1.960612 TTTCGGCGGAAACCAATGG 59.039 52.632 14.76 0.00 37.24 3.16
503 529 6.611381 ACAAAATCATCATTGGTTAGTGTCG 58.389 36.000 0.00 0.00 0.00 4.35
544 2542 5.743398 TGAATTTGTTCTTTCAAAGCTCGTG 59.257 36.000 0.00 0.00 40.00 4.35
561 2559 4.203950 TCGTGAACAGTAATGTGTTTGC 57.796 40.909 0.00 0.00 40.83 3.68
594 2592 4.486574 TGCATGGCAATACAATATCACG 57.513 40.909 0.00 0.00 34.76 4.35
704 2714 6.812481 TTTTCATGTGATATTCTCTCGTCG 57.188 37.500 0.00 0.00 0.00 5.12
705 2715 5.500645 TTCATGTGATATTCTCTCGTCGT 57.499 39.130 0.00 0.00 0.00 4.34
706 2716 5.096954 TCATGTGATATTCTCTCGTCGTC 57.903 43.478 0.00 0.00 0.00 4.20
729 2739 2.216037 CGTGTACGTTGCGTTGACTTAA 59.784 45.455 0.00 0.00 41.54 1.85
730 2740 3.657325 CGTGTACGTTGCGTTGACTTAAG 60.657 47.826 0.00 0.00 41.54 1.85
731 2741 3.486841 GTGTACGTTGCGTTGACTTAAGA 59.513 43.478 10.09 0.00 41.54 2.10
732 2742 3.486841 TGTACGTTGCGTTGACTTAAGAC 59.513 43.478 10.09 3.35 41.54 3.01
735 2745 3.371591 ACGTTGCGTTGACTTAAGACAAA 59.628 39.130 19.50 4.53 36.35 2.83
737 2747 3.955771 TGCGTTGACTTAAGACAAACC 57.044 42.857 19.50 14.11 32.18 3.27
739 2749 3.064271 TGCGTTGACTTAAGACAAACCAC 59.936 43.478 19.50 9.09 32.18 4.16
740 2750 3.064271 GCGTTGACTTAAGACAAACCACA 59.936 43.478 19.50 0.00 32.18 4.17
741 2751 4.584394 CGTTGACTTAAGACAAACCACAC 58.416 43.478 19.50 8.16 32.18 3.82
742 2752 4.584394 GTTGACTTAAGACAAACCACACG 58.416 43.478 19.50 0.00 32.18 4.49
743 2753 3.864243 TGACTTAAGACAAACCACACGT 58.136 40.909 10.09 0.00 0.00 4.49
751 2761 3.052036 GACAAACCACACGTACGTATGT 58.948 45.455 23.75 18.46 0.00 2.29
1318 3370 2.676232 CTCCTCCAGGACAAGCTCA 58.324 57.895 0.00 0.00 39.78 4.26
1354 3414 1.615262 CCATCCCCCAAACTCCTCC 59.385 63.158 0.00 0.00 0.00 4.30
1381 3441 3.983494 ATCCTCGGCCGATCGCTG 61.983 66.667 31.19 16.77 46.15 5.18
1387 3447 3.195698 GGCCGATCGCTGACCAAC 61.196 66.667 10.32 0.00 37.74 3.77
1539 3615 1.606889 AGGTCCGTTCGCTCTTCCT 60.607 57.895 0.00 0.00 0.00 3.36
1540 3616 1.186267 AGGTCCGTTCGCTCTTCCTT 61.186 55.000 0.00 0.00 0.00 3.36
1541 3617 0.320508 GGTCCGTTCGCTCTTCCTTT 60.321 55.000 0.00 0.00 0.00 3.11
1542 3618 1.069255 GTCCGTTCGCTCTTCCTTTC 58.931 55.000 0.00 0.00 0.00 2.62
1580 3670 8.936864 ACTTTTATATAGCTTGTGTGTCTGAAC 58.063 33.333 0.00 0.00 0.00 3.18
1831 5016 5.234757 GCACAATGCTTGAAATCAGTTGAAA 59.765 36.000 3.37 0.00 40.96 2.69
1832 5017 6.073440 GCACAATGCTTGAAATCAGTTGAAAT 60.073 34.615 3.37 0.00 40.96 2.17
1840 5027 5.599732 TGAAATCAGTTGAAATGTTGGTGG 58.400 37.500 0.00 0.00 0.00 4.61
1855 5042 4.082463 TGTTGGTGGTCTTGAAACTGTTTC 60.082 41.667 22.94 22.94 40.08 2.78
1868 5055 1.569072 ACTGTTTCAAAGGGACCCAGT 59.431 47.619 14.60 1.20 33.86 4.00
1869 5056 2.024369 ACTGTTTCAAAGGGACCCAGTT 60.024 45.455 14.60 3.15 34.63 3.16
2165 5402 5.611374 TGCTGTTATCTTATCCTTACCTGC 58.389 41.667 0.00 0.00 0.00 4.85
2682 6569 1.434622 GAGGGCGACGACGATGAGTA 61.435 60.000 12.29 0.00 42.66 2.59
2782 6699 0.260230 TCCCTCAGAGAAGAGCCGAT 59.740 55.000 0.00 0.00 34.26 4.18
2957 6874 1.169034 GCGCTCCCAGGATTCATTCC 61.169 60.000 0.00 0.00 45.85 3.01
2975 6893 4.699522 ACTCGCCCGGGTCAAAGC 62.700 66.667 24.63 5.01 0.00 3.51
3070 6995 2.286833 GCGCACAACTTCTTGTACAGAA 59.713 45.455 0.30 1.89 38.66 3.02
3071 6996 3.844943 GCGCACAACTTCTTGTACAGAAC 60.845 47.826 0.30 0.00 38.66 3.01
3195 7152 2.499289 AGATCCTTGTGTCTAGTGGCTG 59.501 50.000 0.00 0.00 0.00 4.85
3463 9970 2.416547 CAGGTGGTGTTGATAGCTTTCG 59.583 50.000 0.00 0.00 0.00 3.46
3470 9977 5.992829 TGGTGTTGATAGCTTTCGTTCTTAA 59.007 36.000 0.00 0.00 0.00 1.85
3471 9978 6.653320 TGGTGTTGATAGCTTTCGTTCTTAAT 59.347 34.615 0.00 0.00 0.00 1.40
3545 10057 1.955157 CTGGCTGCGAGCATCTAGC 60.955 63.158 0.00 0.00 44.75 3.42
3795 10313 0.321298 CAACTCCCGGGTGTTACCTG 60.321 60.000 34.14 22.10 44.36 4.00
3809 10327 1.948104 TACCTGAATGGAAATCCGCG 58.052 50.000 0.00 0.00 39.43 6.46
3815 10333 2.283472 AATGGAAATCCGCGGCAAGC 62.283 55.000 23.51 9.91 43.95 4.01
3836 10354 4.159506 AGCTACAAGGCTAGACTTCTCTTG 59.840 45.833 8.24 0.00 41.16 3.02
3837 10355 3.971245 ACAAGGCTAGACTTCTCTTGG 57.029 47.619 8.24 0.00 39.10 3.61
3838 10356 2.027653 ACAAGGCTAGACTTCTCTTGGC 60.028 50.000 8.24 2.58 42.70 4.52
3839 10357 2.246091 AGGCTAGACTTCTCTTGGCT 57.754 50.000 0.00 3.05 45.97 4.75
3840 10358 2.307934 GGCTAGACTTCTCTTGGCTG 57.692 55.000 0.00 0.00 40.32 4.85
3841 10359 1.134551 GGCTAGACTTCTCTTGGCTGG 60.135 57.143 0.00 0.00 40.32 4.85
3842 10360 1.552792 GCTAGACTTCTCTTGGCTGGT 59.447 52.381 0.00 0.00 0.00 4.00
3843 10361 2.676463 GCTAGACTTCTCTTGGCTGGTG 60.676 54.545 0.00 0.00 0.00 4.17
3844 10362 0.689623 AGACTTCTCTTGGCTGGTGG 59.310 55.000 0.00 0.00 0.00 4.61
3845 10363 0.957888 GACTTCTCTTGGCTGGTGGC 60.958 60.000 0.00 0.00 40.90 5.01
3852 10370 3.304721 TGGCTGGTGGCATTGTGC 61.305 61.111 0.00 0.00 44.10 4.57
3864 10382 2.878580 GCATTGTGCATCCGAAATTCA 58.121 42.857 0.00 0.00 44.26 2.57
3865 10383 2.855963 GCATTGTGCATCCGAAATTCAG 59.144 45.455 0.00 0.00 44.26 3.02
3866 10384 2.634982 TTGTGCATCCGAAATTCAGC 57.365 45.000 0.00 0.00 0.00 4.26
3867 10385 0.447406 TGTGCATCCGAAATTCAGCG 59.553 50.000 0.00 0.00 0.00 5.18
3868 10386 0.447801 GTGCATCCGAAATTCAGCGT 59.552 50.000 0.00 0.00 0.00 5.07
3869 10387 0.447406 TGCATCCGAAATTCAGCGTG 59.553 50.000 0.00 0.00 0.00 5.34
3870 10388 0.248215 GCATCCGAAATTCAGCGTGG 60.248 55.000 0.00 0.00 0.00 4.94
3871 10389 1.368641 CATCCGAAATTCAGCGTGGA 58.631 50.000 0.00 0.00 0.00 4.02
3872 10390 1.737236 CATCCGAAATTCAGCGTGGAA 59.263 47.619 0.00 0.00 0.00 3.53
3873 10391 1.885560 TCCGAAATTCAGCGTGGAAA 58.114 45.000 0.00 0.00 0.00 3.13
3874 10392 1.804151 TCCGAAATTCAGCGTGGAAAG 59.196 47.619 0.00 0.00 0.00 2.62
3875 10393 1.535462 CCGAAATTCAGCGTGGAAAGT 59.465 47.619 0.00 0.00 0.00 2.66
3876 10394 2.739913 CCGAAATTCAGCGTGGAAAGTA 59.260 45.455 0.00 0.00 0.00 2.24
3877 10395 3.187637 CCGAAATTCAGCGTGGAAAGTAA 59.812 43.478 0.00 0.00 0.00 2.24
3878 10396 4.142687 CCGAAATTCAGCGTGGAAAGTAAT 60.143 41.667 0.00 0.00 0.00 1.89
3879 10397 5.064198 CCGAAATTCAGCGTGGAAAGTAATA 59.936 40.000 0.00 0.00 0.00 0.98
3880 10398 6.402766 CCGAAATTCAGCGTGGAAAGTAATAA 60.403 38.462 0.00 0.00 0.00 1.40
3881 10399 6.464834 CGAAATTCAGCGTGGAAAGTAATAAC 59.535 38.462 0.00 0.00 0.00 1.89
3882 10400 6.811253 AATTCAGCGTGGAAAGTAATAACA 57.189 33.333 0.00 0.00 0.00 2.41
3883 10401 5.856126 TTCAGCGTGGAAAGTAATAACAG 57.144 39.130 0.00 0.00 0.00 3.16
3884 10402 4.250464 TCAGCGTGGAAAGTAATAACAGG 58.750 43.478 0.00 0.00 0.00 4.00
3885 10403 4.000988 CAGCGTGGAAAGTAATAACAGGT 58.999 43.478 0.00 0.00 0.00 4.00
3886 10404 4.454504 CAGCGTGGAAAGTAATAACAGGTT 59.545 41.667 0.00 0.00 0.00 3.50
3887 10405 5.640357 CAGCGTGGAAAGTAATAACAGGTTA 59.360 40.000 0.00 0.00 0.00 2.85
3888 10406 5.873164 AGCGTGGAAAGTAATAACAGGTTAG 59.127 40.000 0.00 0.00 0.00 2.34
3889 10407 5.064325 GCGTGGAAAGTAATAACAGGTTAGG 59.936 44.000 0.00 0.00 0.00 2.69
3890 10408 5.583457 CGTGGAAAGTAATAACAGGTTAGGG 59.417 44.000 0.00 0.00 0.00 3.53
3891 10409 6.574859 CGTGGAAAGTAATAACAGGTTAGGGA 60.575 42.308 0.00 0.00 0.00 4.20
3892 10410 7.170277 GTGGAAAGTAATAACAGGTTAGGGAA 58.830 38.462 0.00 0.00 0.00 3.97
3893 10411 7.666804 GTGGAAAGTAATAACAGGTTAGGGAAA 59.333 37.037 0.00 0.00 0.00 3.13
3894 10412 7.666804 TGGAAAGTAATAACAGGTTAGGGAAAC 59.333 37.037 0.00 0.00 37.36 2.78
3895 10413 7.886970 GGAAAGTAATAACAGGTTAGGGAAACT 59.113 37.037 0.00 0.00 38.23 2.66
3896 10414 8.859236 AAAGTAATAACAGGTTAGGGAAACTC 57.141 34.615 0.00 0.00 38.23 3.01
3897 10415 6.955364 AGTAATAACAGGTTAGGGAAACTCC 58.045 40.000 0.00 0.00 38.23 3.85
3898 10416 5.853572 AATAACAGGTTAGGGAAACTCCA 57.146 39.130 0.00 0.00 38.64 3.86
3899 10417 5.853572 ATAACAGGTTAGGGAAACTCCAA 57.146 39.130 0.00 0.00 38.64 3.53
3900 10418 4.741928 AACAGGTTAGGGAAACTCCAAT 57.258 40.909 0.00 0.00 38.64 3.16
3901 10419 5.853572 AACAGGTTAGGGAAACTCCAATA 57.146 39.130 0.00 0.00 38.64 1.90
3902 10420 6.402981 AACAGGTTAGGGAAACTCCAATAT 57.597 37.500 0.00 0.00 38.64 1.28
3903 10421 7.519347 AACAGGTTAGGGAAACTCCAATATA 57.481 36.000 0.00 0.00 38.64 0.86
3904 10422 7.138054 ACAGGTTAGGGAAACTCCAATATAG 57.862 40.000 0.00 0.00 38.64 1.31
3905 10423 6.906901 ACAGGTTAGGGAAACTCCAATATAGA 59.093 38.462 0.00 0.00 38.64 1.98
3906 10424 7.572861 ACAGGTTAGGGAAACTCCAATATAGAT 59.427 37.037 0.00 0.00 38.64 1.98
3907 10425 8.097662 CAGGTTAGGGAAACTCCAATATAGATC 58.902 40.741 0.00 0.00 38.64 2.75
3908 10426 7.794683 AGGTTAGGGAAACTCCAATATAGATCA 59.205 37.037 0.00 0.00 38.64 2.92
3909 10427 8.606830 GGTTAGGGAAACTCCAATATAGATCAT 58.393 37.037 0.00 0.00 38.64 2.45
3910 10428 9.660180 GTTAGGGAAACTCCAATATAGATCATC 57.340 37.037 0.00 0.00 38.64 2.92
3911 10429 7.878621 AGGGAAACTCCAATATAGATCATCA 57.121 36.000 0.00 0.00 38.64 3.07
3912 10430 8.280258 AGGGAAACTCCAATATAGATCATCAA 57.720 34.615 0.00 0.00 38.64 2.57
3913 10431 8.727149 AGGGAAACTCCAATATAGATCATCAAA 58.273 33.333 0.00 0.00 38.64 2.69
3914 10432 9.525826 GGGAAACTCCAATATAGATCATCAAAT 57.474 33.333 0.00 0.00 38.64 2.32
3917 10435 8.783833 AACTCCAATATAGATCATCAAATCGG 57.216 34.615 0.00 0.00 0.00 4.18
3918 10436 8.138928 ACTCCAATATAGATCATCAAATCGGA 57.861 34.615 0.00 0.00 0.00 4.55
3919 10437 8.037758 ACTCCAATATAGATCATCAAATCGGAC 58.962 37.037 0.00 0.00 0.00 4.79
3920 10438 7.906327 TCCAATATAGATCATCAAATCGGACA 58.094 34.615 0.00 0.00 0.00 4.02
3921 10439 7.819415 TCCAATATAGATCATCAAATCGGACAC 59.181 37.037 0.00 0.00 0.00 3.67
3922 10440 7.603784 CCAATATAGATCATCAAATCGGACACA 59.396 37.037 0.00 0.00 0.00 3.72
3923 10441 8.438513 CAATATAGATCATCAAATCGGACACAC 58.561 37.037 0.00 0.00 0.00 3.82
3924 10442 3.190079 AGATCATCAAATCGGACACACG 58.810 45.455 0.00 0.00 0.00 4.49
3926 10444 3.033368 TCATCAAATCGGACACACGAA 57.967 42.857 0.00 0.00 46.92 3.85
3927 10445 3.394719 TCATCAAATCGGACACACGAAA 58.605 40.909 0.00 0.00 46.92 3.46
3928 10446 4.000325 TCATCAAATCGGACACACGAAAT 59.000 39.130 0.00 0.00 46.92 2.17
3929 10447 3.804518 TCAAATCGGACACACGAAATG 57.195 42.857 0.00 0.00 46.92 2.32
3930 10448 3.135225 TCAAATCGGACACACGAAATGT 58.865 40.909 0.00 0.00 46.92 2.71
3931 10449 3.185594 TCAAATCGGACACACGAAATGTC 59.814 43.478 9.11 9.11 46.92 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 8.995906 GTGTGCAATTAATCTACGAAAACATAC 58.004 33.333 0.00 0.00 0.00 2.39
182 193 4.959596 TCTAGTCGATTCGTTACAGCTT 57.040 40.909 5.89 0.00 0.00 3.74
227 248 3.365265 CCAGCTCCAACCAACCGC 61.365 66.667 0.00 0.00 0.00 5.68
256 277 2.527100 GTCCAAGTCTCCGTCGTTATG 58.473 52.381 0.00 0.00 0.00 1.90
289 310 3.576861 TCCATGTGATATTCTCTCCGGT 58.423 45.455 0.00 0.00 0.00 5.28
323 344 0.676736 TGGTTTCCATTGGTTTCCGC 59.323 50.000 1.86 0.00 0.00 5.54
394 417 6.072893 ACGTCACACTTTTAACAACCCATATC 60.073 38.462 0.00 0.00 0.00 1.63
402 427 8.277713 GCTAATAGAACGTCACACTTTTAACAA 58.722 33.333 0.00 0.00 0.00 2.83
561 2559 2.768698 TGCCATGCAAAATTCCAAGTG 58.231 42.857 0.00 0.00 34.76 3.16
585 2583 8.929746 ACATGATGTTATAAGAGCGTGATATTG 58.070 33.333 22.52 0.39 30.26 1.90
704 2714 0.158096 CAACGCAACGTACACGAGAC 59.842 55.000 9.04 0.00 39.99 3.36
705 2715 0.029167 TCAACGCAACGTACACGAGA 59.971 50.000 9.04 6.29 39.99 4.04
706 2716 0.158096 GTCAACGCAACGTACACGAG 59.842 55.000 9.04 1.92 39.99 4.18
729 2739 3.243501 ACATACGTACGTGTGGTTTGTCT 60.244 43.478 37.12 19.39 40.75 3.41
730 2740 3.052036 ACATACGTACGTGTGGTTTGTC 58.948 45.455 37.12 0.00 40.75 3.18
731 2741 2.796031 CACATACGTACGTGTGGTTTGT 59.204 45.455 37.12 23.42 41.46 2.83
732 2742 3.051327 TCACATACGTACGTGTGGTTTG 58.949 45.455 37.12 28.69 44.41 2.93
735 2745 2.553602 TCTTCACATACGTACGTGTGGT 59.446 45.455 37.12 25.67 44.41 4.16
737 2747 4.074466 TCTCTTCACATACGTACGTGTG 57.926 45.455 34.41 34.41 45.37 3.82
739 2749 4.093115 AGACTCTCTTCACATACGTACGTG 59.907 45.833 30.25 15.33 34.34 4.49
740 2750 4.252073 AGACTCTCTTCACATACGTACGT 58.748 43.478 25.98 25.98 0.00 3.57
741 2751 4.861389 AGACTCTCTTCACATACGTACG 57.139 45.455 15.01 15.01 0.00 3.67
797 2814 4.785453 CAGTTGGAGGAGGGCCGC 62.785 72.222 0.00 0.00 39.96 6.53
1339 3398 0.699577 TGTTGGAGGAGTTTGGGGGA 60.700 55.000 0.00 0.00 0.00 4.81
1354 3414 1.303309 GGCCGAGGATGAATCTGTTG 58.697 55.000 0.00 0.00 0.00 3.33
1383 3443 2.637025 CGCGGACAACCAAGTTGG 59.363 61.111 20.76 20.76 46.50 3.77
1580 3670 2.872557 CATCACCAGGCAGCAACG 59.127 61.111 0.00 0.00 0.00 4.10
1716 4840 5.421374 ACAGGACCATCTTACCAGTTACTAC 59.579 44.000 0.00 0.00 0.00 2.73
1717 4841 5.421056 CACAGGACCATCTTACCAGTTACTA 59.579 44.000 0.00 0.00 0.00 1.82
1729 4853 2.329267 TCACACTTCACAGGACCATCT 58.671 47.619 0.00 0.00 0.00 2.90
1831 5016 3.631250 ACAGTTTCAAGACCACCAACAT 58.369 40.909 0.00 0.00 0.00 2.71
1832 5017 3.080300 ACAGTTTCAAGACCACCAACA 57.920 42.857 0.00 0.00 0.00 3.33
1855 5042 2.965147 ACATCAAAACTGGGTCCCTTTG 59.035 45.455 10.00 11.73 0.00 2.77
1868 5055 8.087750 GGTATCCAAATGAAAGTGACATCAAAA 58.912 33.333 0.00 0.00 0.00 2.44
1869 5056 7.574779 CGGTATCCAAATGAAAGTGACATCAAA 60.575 37.037 0.00 0.00 0.00 2.69
1979 5168 5.163205 ACAAATTTGAAAAGGCCCTTAGCTT 60.163 36.000 24.64 0.00 43.05 3.74
1980 5169 4.347876 ACAAATTTGAAAAGGCCCTTAGCT 59.652 37.500 24.64 0.00 43.05 3.32
2682 6569 2.436292 CCTCGTCCTCCTCGTCGT 60.436 66.667 0.00 0.00 0.00 4.34
2738 6652 5.096169 CGTGACATTCTCTTCGTGAACTAT 58.904 41.667 0.00 0.00 0.00 2.12
2782 6699 1.997311 CTCCAGCTCCATCCACCCA 60.997 63.158 0.00 0.00 0.00 4.51
2957 6874 2.742372 CTTTGACCCGGGCGAGTG 60.742 66.667 24.08 4.46 0.00 3.51
3070 6995 5.012893 TGTCACTCATGAGTCATCTGTAGT 58.987 41.667 25.58 2.20 40.20 2.73
3071 6996 5.356470 TCTGTCACTCATGAGTCATCTGTAG 59.644 44.000 25.58 15.39 40.20 2.74
3195 7152 2.754552 TCAACATAACCAGATGCCAAGC 59.245 45.455 0.00 0.00 0.00 4.01
3376 9850 9.627395 GTAACATCTATTCTTACAGATACGCAT 57.373 33.333 0.00 0.00 30.32 4.73
3470 9977 9.660180 GTTACAAAGATCTTTCCTGACTCTTAT 57.340 33.333 17.91 0.00 0.00 1.73
3471 9978 8.647796 TGTTACAAAGATCTTTCCTGACTCTTA 58.352 33.333 17.91 0.00 0.00 2.10
3545 10057 2.481952 CACAGAAGGCCGAAGAAGAAAG 59.518 50.000 0.00 0.00 0.00 2.62
3731 10249 2.158726 AGAAAACCGTTTCCTACAGGCA 60.159 45.455 0.00 0.00 43.65 4.75
3795 10313 0.248621 CTTGCCGCGGATTTCCATTC 60.249 55.000 33.48 8.18 35.14 2.67
3796 10314 1.809207 CTTGCCGCGGATTTCCATT 59.191 52.632 33.48 0.00 35.14 3.16
3809 10327 1.208293 AGTCTAGCCTTGTAGCTTGCC 59.792 52.381 0.00 0.00 41.41 4.52
3815 10333 4.679372 GCCAAGAGAAGTCTAGCCTTGTAG 60.679 50.000 0.00 0.00 34.14 2.74
3836 10354 2.567564 GATGCACAATGCCACCAGCC 62.568 60.000 0.00 0.00 44.23 4.85
3837 10355 1.153706 GATGCACAATGCCACCAGC 60.154 57.895 0.00 0.00 44.23 4.85
3838 10356 1.514087 GGATGCACAATGCCACCAG 59.486 57.895 0.00 0.00 44.23 4.00
3839 10357 2.341875 CGGATGCACAATGCCACCA 61.342 57.895 11.79 0.00 44.23 4.17
3840 10358 1.594194 TTCGGATGCACAATGCCACC 61.594 55.000 0.00 1.30 44.23 4.61
3841 10359 0.243365 TTTCGGATGCACAATGCCAC 59.757 50.000 0.00 0.00 44.23 5.01
3842 10360 1.184431 ATTTCGGATGCACAATGCCA 58.816 45.000 0.00 0.00 44.23 4.92
3843 10361 2.195922 GAATTTCGGATGCACAATGCC 58.804 47.619 0.00 0.00 44.23 4.40
3844 10362 2.855963 CTGAATTTCGGATGCACAATGC 59.144 45.455 0.00 0.00 45.29 3.56
3845 10363 2.855963 GCTGAATTTCGGATGCACAATG 59.144 45.455 9.46 0.00 0.00 2.82
3846 10364 2.478370 CGCTGAATTTCGGATGCACAAT 60.478 45.455 9.46 0.00 0.00 2.71
3847 10365 1.135717 CGCTGAATTTCGGATGCACAA 60.136 47.619 9.46 0.00 0.00 3.33
3848 10366 0.447406 CGCTGAATTTCGGATGCACA 59.553 50.000 9.46 0.00 0.00 4.57
3849 10367 0.447801 ACGCTGAATTTCGGATGCAC 59.552 50.000 9.46 0.00 0.00 4.57
3850 10368 0.447406 CACGCTGAATTTCGGATGCA 59.553 50.000 9.46 0.00 0.00 3.96
3851 10369 0.248215 CCACGCTGAATTTCGGATGC 60.248 55.000 9.46 2.13 0.00 3.91
3852 10370 1.368641 TCCACGCTGAATTTCGGATG 58.631 50.000 9.46 6.24 0.00 3.51
3853 10371 2.107950 TTCCACGCTGAATTTCGGAT 57.892 45.000 9.46 0.00 0.00 4.18
3854 10372 1.804151 CTTTCCACGCTGAATTTCGGA 59.196 47.619 9.46 0.00 0.00 4.55
3855 10373 1.535462 ACTTTCCACGCTGAATTTCGG 59.465 47.619 0.56 0.56 0.00 4.30
3856 10374 2.969443 ACTTTCCACGCTGAATTTCG 57.031 45.000 0.00 0.00 0.00 3.46
3857 10375 7.302524 TGTTATTACTTTCCACGCTGAATTTC 58.697 34.615 0.00 0.00 0.00 2.17
3858 10376 7.209471 TGTTATTACTTTCCACGCTGAATTT 57.791 32.000 0.00 0.00 0.00 1.82
3859 10377 6.128007 CCTGTTATTACTTTCCACGCTGAATT 60.128 38.462 0.00 0.00 0.00 2.17
3860 10378 5.354234 CCTGTTATTACTTTCCACGCTGAAT 59.646 40.000 0.00 0.00 0.00 2.57
3861 10379 4.693566 CCTGTTATTACTTTCCACGCTGAA 59.306 41.667 0.00 0.00 0.00 3.02
3862 10380 4.250464 CCTGTTATTACTTTCCACGCTGA 58.750 43.478 0.00 0.00 0.00 4.26
3863 10381 4.000988 ACCTGTTATTACTTTCCACGCTG 58.999 43.478 0.00 0.00 0.00 5.18
3864 10382 4.281898 ACCTGTTATTACTTTCCACGCT 57.718 40.909 0.00 0.00 0.00 5.07
3865 10383 5.064325 CCTAACCTGTTATTACTTTCCACGC 59.936 44.000 0.00 0.00 0.00 5.34
3866 10384 5.583457 CCCTAACCTGTTATTACTTTCCACG 59.417 44.000 0.00 0.00 0.00 4.94
3867 10385 6.714278 TCCCTAACCTGTTATTACTTTCCAC 58.286 40.000 0.00 0.00 0.00 4.02
3868 10386 6.956102 TCCCTAACCTGTTATTACTTTCCA 57.044 37.500 0.00 0.00 0.00 3.53
3869 10387 7.886970 AGTTTCCCTAACCTGTTATTACTTTCC 59.113 37.037 0.00 0.00 37.46 3.13
3870 10388 8.859236 AGTTTCCCTAACCTGTTATTACTTTC 57.141 34.615 0.00 0.00 37.46 2.62
3871 10389 7.886970 GGAGTTTCCCTAACCTGTTATTACTTT 59.113 37.037 0.00 0.00 37.46 2.66
3872 10390 7.017850 TGGAGTTTCCCTAACCTGTTATTACTT 59.982 37.037 0.00 0.00 37.46 2.24
3873 10391 6.502863 TGGAGTTTCCCTAACCTGTTATTACT 59.497 38.462 0.00 0.00 37.46 2.24
3874 10392 6.714278 TGGAGTTTCCCTAACCTGTTATTAC 58.286 40.000 0.00 0.00 37.46 1.89
3875 10393 6.956102 TGGAGTTTCCCTAACCTGTTATTA 57.044 37.500 0.00 0.00 37.46 0.98
3876 10394 5.853572 TGGAGTTTCCCTAACCTGTTATT 57.146 39.130 0.00 0.00 37.46 1.40
3877 10395 5.853572 TTGGAGTTTCCCTAACCTGTTAT 57.146 39.130 0.00 0.00 37.46 1.89
3878 10396 5.853572 ATTGGAGTTTCCCTAACCTGTTA 57.146 39.130 0.00 0.00 37.46 2.41
3879 10397 4.741928 ATTGGAGTTTCCCTAACCTGTT 57.258 40.909 0.00 0.00 37.46 3.16
3880 10398 6.906901 TCTATATTGGAGTTTCCCTAACCTGT 59.093 38.462 0.00 0.00 37.46 4.00
3881 10399 7.374975 TCTATATTGGAGTTTCCCTAACCTG 57.625 40.000 0.00 0.00 37.46 4.00
3882 10400 7.794683 TGATCTATATTGGAGTTTCCCTAACCT 59.205 37.037 0.00 0.00 37.46 3.50
3883 10401 7.974504 TGATCTATATTGGAGTTTCCCTAACC 58.025 38.462 0.00 0.00 37.46 2.85
3884 10402 9.660180 GATGATCTATATTGGAGTTTCCCTAAC 57.340 37.037 0.00 0.00 35.03 2.34
3885 10403 9.392506 TGATGATCTATATTGGAGTTTCCCTAA 57.607 33.333 0.00 0.00 35.03 2.69
3886 10404 8.972662 TGATGATCTATATTGGAGTTTCCCTA 57.027 34.615 0.00 0.00 35.03 3.53
3887 10405 7.878621 TGATGATCTATATTGGAGTTTCCCT 57.121 36.000 0.00 0.00 35.03 4.20
3888 10406 8.924511 TTTGATGATCTATATTGGAGTTTCCC 57.075 34.615 0.00 0.00 35.03 3.97
3891 10409 9.224267 CCGATTTGATGATCTATATTGGAGTTT 57.776 33.333 0.00 0.00 0.00 2.66
3892 10410 8.597167 TCCGATTTGATGATCTATATTGGAGTT 58.403 33.333 0.00 0.00 0.00 3.01
3893 10411 8.037758 GTCCGATTTGATGATCTATATTGGAGT 58.962 37.037 9.65 0.00 0.00 3.85
3894 10412 8.037166 TGTCCGATTTGATGATCTATATTGGAG 58.963 37.037 9.65 0.00 0.00 3.86
3895 10413 7.819415 GTGTCCGATTTGATGATCTATATTGGA 59.181 37.037 0.00 1.16 0.00 3.53
3896 10414 7.603784 TGTGTCCGATTTGATGATCTATATTGG 59.396 37.037 0.00 0.00 0.00 3.16
3897 10415 8.438513 GTGTGTCCGATTTGATGATCTATATTG 58.561 37.037 0.00 0.00 0.00 1.90
3898 10416 7.329471 CGTGTGTCCGATTTGATGATCTATATT 59.671 37.037 0.00 0.00 0.00 1.28
3899 10417 6.808704 CGTGTGTCCGATTTGATGATCTATAT 59.191 38.462 0.00 0.00 0.00 0.86
3900 10418 6.016610 TCGTGTGTCCGATTTGATGATCTATA 60.017 38.462 0.00 0.00 30.63 1.31
3901 10419 4.984785 CGTGTGTCCGATTTGATGATCTAT 59.015 41.667 0.00 0.00 0.00 1.98
3902 10420 4.097286 TCGTGTGTCCGATTTGATGATCTA 59.903 41.667 0.00 0.00 30.63 1.98
3903 10421 3.119137 TCGTGTGTCCGATTTGATGATCT 60.119 43.478 0.00 0.00 30.63 2.75
3904 10422 3.186909 TCGTGTGTCCGATTTGATGATC 58.813 45.455 0.00 0.00 30.63 2.92
3905 10423 3.245518 TCGTGTGTCCGATTTGATGAT 57.754 42.857 0.00 0.00 30.63 2.45
3906 10424 2.734276 TCGTGTGTCCGATTTGATGA 57.266 45.000 0.00 0.00 30.63 2.92
3907 10425 3.804518 TTTCGTGTGTCCGATTTGATG 57.195 42.857 0.00 0.00 36.62 3.07
3908 10426 3.751175 ACATTTCGTGTGTCCGATTTGAT 59.249 39.130 0.00 0.00 40.28 2.57
3909 10427 3.135225 ACATTTCGTGTGTCCGATTTGA 58.865 40.909 0.00 0.00 40.28 2.69
3910 10428 3.479006 GACATTTCGTGTGTCCGATTTG 58.521 45.455 6.39 0.00 42.36 2.32
3911 10429 3.806316 GACATTTCGTGTGTCCGATTT 57.194 42.857 6.39 0.00 42.36 2.17


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

AutoCloner maintained by Alex Coulton.