Multiple sequence alignment - TraesCS6D01G311700

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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 TraesCS6D01G311700 chr6D 100.000 6467 0 0 1 6467 420963476 420957010 0.000000e+00 11943
1 TraesCS6D01G311700 chr6D 83.099 710 64 22 25 713 141689456 141688782 4.320000e-166 595
2 TraesCS6D01G311700 chr6D 86.771 446 34 10 1876 2312 225663202 225662773 2.110000e-129 473
3 TraesCS6D01G311700 chr6D 92.414 145 11 0 6323 6467 420899766 420899622 2.360000e-49 207
4 TraesCS6D01G311700 chr6D 92.414 145 11 0 6323 6467 420936313 420936169 2.360000e-49 207
5 TraesCS6D01G311700 chr6D 77.561 205 19 14 6143 6326 420936565 420936367 1.480000e-16 99
6 TraesCS6D01G311700 chr6B 94.258 5712 190 53 804 6463 634336016 634330391 0.000000e+00 8604
7 TraesCS6D01G311700 chr6B 84.156 385 40 10 1755 2118 67870673 67870289 2.870000e-93 353
8 TraesCS6D01G311700 chr6B 83.896 385 41 10 1755 2118 124496924 124496540 1.330000e-91 348
9 TraesCS6D01G311700 chr6B 88.750 240 9 10 2074 2312 575573970 575573748 1.780000e-70 278
10 TraesCS6D01G311700 chr6B 86.920 237 15 8 2074 2310 302278438 302278658 1.080000e-62 252
11 TraesCS6D01G311700 chr6B 91.549 142 12 0 6323 6464 634322507 634322366 5.120000e-46 196
12 TraesCS6D01G311700 chr6A 94.508 5226 197 32 811 6008 564274341 564269178 0.000000e+00 7978
13 TraesCS6D01G311700 chr6A 84.229 577 49 16 1755 2310 4928189 4927634 2.070000e-144 523
14 TraesCS6D01G311700 chr6A 91.327 392 19 7 6078 6467 564260854 564260476 7.430000e-144 521
15 TraesCS6D01G311700 chr6A 87.764 237 13 8 2074 2310 463742951 463743171 4.970000e-66 263
16 TraesCS6D01G311700 chr6A 92.254 142 11 0 6323 6464 564118471 564118330 1.100000e-47 202
17 TraesCS6D01G311700 chr6A 91.724 145 12 0 6323 6467 564133019 564132875 1.100000e-47 202
18 TraesCS6D01G311700 chr6A 91.724 145 12 0 6323 6467 564191816 564191672 1.100000e-47 202
19 TraesCS6D01G311700 chr6A 90.476 147 12 2 6323 6467 564239272 564239126 6.620000e-45 193
20 TraesCS6D01G311700 chr5D 85.986 735 75 15 1 712 52253145 52253874 0.000000e+00 761
21 TraesCS6D01G311700 chr5D 83.221 739 82 23 1 713 544788573 544787851 1.970000e-179 640
22 TraesCS6D01G311700 chr5D 86.701 579 40 11 1755 2312 524291921 524292483 5.540000e-170 608
23 TraesCS6D01G311700 chr5D 84.000 575 56 17 1758 2312 289583646 289583088 2.670000e-143 520
24 TraesCS6D01G311700 chr5D 85.010 487 53 16 1 470 82179052 82178569 1.630000e-130 477
25 TraesCS6D01G311700 chr4D 83.863 818 55 24 1 747 483986385 483987196 0.000000e+00 708
26 TraesCS6D01G311700 chr4D 85.944 498 55 10 24 511 495992936 495992444 9.610000e-143 518
27 TraesCS6D01G311700 chr4D 83.902 528 61 16 1 511 364588700 364589220 3.510000e-132 483
28 TraesCS6D01G311700 chr3D 86.782 522 47 15 1 505 554031087 554030571 4.380000e-156 562
29 TraesCS6D01G311700 chr3D 83.938 579 56 20 1755 2312 34545854 34546416 2.670000e-143 520
30 TraesCS6D01G311700 chr3D 87.281 456 33 8 1866 2312 8354496 8354057 1.250000e-136 497
31 TraesCS6D01G311700 chr3D 88.943 407 32 10 1 400 42303646 42304046 2.100000e-134 490
32 TraesCS6D01G311700 chr7A 84.348 575 54 18 1758 2312 627580687 627580129 1.230000e-146 531
33 TraesCS6D01G311700 chr7A 84.000 575 56 15 1758 2312 627554244 627553686 2.670000e-143 520
34 TraesCS6D01G311700 chr7A 82.540 504 61 18 22 511 608895730 608895240 1.000000e-112 418
35 TraesCS6D01G311700 chr5B 84.091 528 62 15 1 511 604173592 604174114 2.100000e-134 490
36 TraesCS6D01G311700 chr5B 85.495 455 52 11 60 506 422119311 422118863 4.570000e-126 462
37 TraesCS6D01G311700 chr5B 85.885 418 41 14 307 713 118505974 118505564 4.630000e-116 429
38 TraesCS6D01G311700 chr5B 87.464 351 35 5 352 701 35970749 35970407 4.700000e-106 396
39 TraesCS6D01G311700 chr1D 84.816 461 52 16 37 483 467037170 467037626 1.280000e-121 448
40 TraesCS6D01G311700 chr1B 84.675 385 38 10 1755 2118 600550168 600549784 1.330000e-96 364
41 TraesCS6D01G311700 chr1B 84.416 385 39 9 1755 2118 64110321 64110705 6.170000e-95 359
42 TraesCS6D01G311700 chr1A 84.416 385 39 10 1755 2118 486126806 486127190 6.170000e-95 359
43 TraesCS6D01G311700 chr1A 84.727 275 19 8 490 747 568124484 568124216 2.990000e-63 254
44 TraesCS6D01G311700 chrUn 88.210 229 22 5 489 713 33347794 33348021 1.070000e-67 268
45 TraesCS6D01G311700 chr5A 87.611 226 22 6 489 712 616441510 616441289 2.310000e-64 257
46 TraesCS6D01G311700 chr4B 87.342 237 14 8 2074 2310 186426300 186426520 2.310000e-64 257
47 TraesCS6D01G311700 chr2D 87.029 239 15 12 2074 2312 229312983 229313205 8.320000e-64 255
48 TraesCS6D01G311700 chr2D 86.957 230 19 6 489 713 644986366 644986589 1.390000e-61 248
49 TraesCS6D01G311700 chr7D 79.433 282 37 14 395 675 183797570 183797831 5.150000e-41 180


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 TraesCS6D01G311700 chr6D 420957010 420963476 6466 True 11943 11943 100.000 1 6467 1 chr6D.!!$R4 6466
1 TraesCS6D01G311700 chr6D 141688782 141689456 674 True 595 595 83.099 25 713 1 chr6D.!!$R1 688
2 TraesCS6D01G311700 chr6B 634330391 634336016 5625 True 8604 8604 94.258 804 6463 1 chr6B.!!$R5 5659
3 TraesCS6D01G311700 chr6A 564269178 564274341 5163 True 7978 7978 94.508 811 6008 1 chr6A.!!$R7 5197
4 TraesCS6D01G311700 chr6A 4927634 4928189 555 True 523 523 84.229 1755 2310 1 chr6A.!!$R1 555
5 TraesCS6D01G311700 chr5D 52253145 52253874 729 False 761 761 85.986 1 712 1 chr5D.!!$F1 711
6 TraesCS6D01G311700 chr5D 544787851 544788573 722 True 640 640 83.221 1 713 1 chr5D.!!$R3 712
7 TraesCS6D01G311700 chr5D 524291921 524292483 562 False 608 608 86.701 1755 2312 1 chr5D.!!$F2 557
8 TraesCS6D01G311700 chr5D 289583088 289583646 558 True 520 520 84.000 1758 2312 1 chr5D.!!$R2 554
9 TraesCS6D01G311700 chr4D 483986385 483987196 811 False 708 708 83.863 1 747 1 chr4D.!!$F2 746
10 TraesCS6D01G311700 chr4D 364588700 364589220 520 False 483 483 83.902 1 511 1 chr4D.!!$F1 510
11 TraesCS6D01G311700 chr3D 554030571 554031087 516 True 562 562 86.782 1 505 1 chr3D.!!$R2 504
12 TraesCS6D01G311700 chr3D 34545854 34546416 562 False 520 520 83.938 1755 2312 1 chr3D.!!$F1 557
13 TraesCS6D01G311700 chr7A 627580129 627580687 558 True 531 531 84.348 1758 2312 1 chr7A.!!$R3 554
14 TraesCS6D01G311700 chr7A 627553686 627554244 558 True 520 520 84.000 1758 2312 1 chr7A.!!$R2 554
15 TraesCS6D01G311700 chr5B 604173592 604174114 522 False 490 490 84.091 1 511 1 chr5B.!!$F1 510

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
751 847 0.767375 AAGCAGTTGCCCTCTGAGAA 59.233 50.000 6.17 0.00 43.38 2.87 F
1987 2112 0.942252 GTTCGGTTCACCACTGTTCC 59.058 55.000 0.00 0.00 35.14 3.62 F
2457 2594 0.549950 AGCTTGGGATGCTGCATACT 59.450 50.000 23.23 8.08 39.56 2.12 F
3513 3651 3.378427 GCAACCTATTTCCAGATGACACC 59.622 47.826 0.00 0.00 0.00 4.16 F
3822 3960 0.094730 GTGAAAAGGATTCGCGTCCG 59.905 55.000 5.77 0.00 43.27 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2229 2366 0.032678 CTGAACAGACCAGCGACAGT 59.967 55.000 0.00 0.0 0.00 3.55 R
3379 3517 0.320073 TTACGACGCTTGGTTCCAGG 60.320 55.000 0.00 0.0 0.00 4.45 R
3822 3960 0.804989 GATGCTGTGCCCACTTGTAC 59.195 55.000 0.00 0.0 0.00 2.90 R
5364 5502 1.334869 GTTCCACTGACTGGTTTGCAG 59.665 52.381 0.00 0.0 41.52 4.41 R
5780 5928 0.963225 TGTTGCTTGATGCTGCATGT 59.037 45.000 21.53 0.0 43.37 3.21 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
187 205 2.625695 TTTTTCGTTTCCGAGGAGGT 57.374 45.000 0.00 0.00 45.24 3.85
201 219 2.282674 AGGTACGGCCGTGACTCA 60.283 61.111 40.02 18.25 43.70 3.41
572 645 4.553330 ATCGAAAAGCTAAGGAAGACCA 57.447 40.909 0.00 0.00 38.94 4.02
587 660 4.100963 GGAAGACCAGTGGAAAACCAAAAT 59.899 41.667 18.40 0.00 35.97 1.82
625 709 2.600122 AAAAGCCGAAAACGCGTGCA 62.600 50.000 14.98 0.00 32.44 4.57
697 783 2.202797 GAATGGCTGAGAGCGCGA 60.203 61.111 12.10 0.00 43.62 5.87
734 830 2.279469 CGAAGGAGCGCTCGTTAAG 58.721 57.895 36.96 29.66 37.75 1.85
747 843 0.798776 CGTTAAGCAGTTGCCCTCTG 59.201 55.000 0.00 0.00 43.38 3.35
748 844 1.608025 CGTTAAGCAGTTGCCCTCTGA 60.608 52.381 0.00 0.00 43.38 3.27
749 845 2.079925 GTTAAGCAGTTGCCCTCTGAG 58.920 52.381 0.00 0.00 43.38 3.35
750 846 1.644509 TAAGCAGTTGCCCTCTGAGA 58.355 50.000 6.17 0.00 43.38 3.27
751 847 0.767375 AAGCAGTTGCCCTCTGAGAA 59.233 50.000 6.17 0.00 43.38 2.87
752 848 0.990374 AGCAGTTGCCCTCTGAGAAT 59.010 50.000 6.17 0.00 43.38 2.40
753 849 1.353694 AGCAGTTGCCCTCTGAGAATT 59.646 47.619 6.17 0.00 43.38 2.17
754 850 1.742268 GCAGTTGCCCTCTGAGAATTC 59.258 52.381 6.17 0.00 35.20 2.17
755 851 2.617532 GCAGTTGCCCTCTGAGAATTCT 60.618 50.000 7.95 7.95 35.20 2.40
756 852 3.269178 CAGTTGCCCTCTGAGAATTCTC 58.731 50.000 25.68 25.68 43.15 2.87
757 853 6.905027 GCAGTTGCCCTCTGAGAATTCTCA 62.905 50.000 31.10 31.10 41.92 3.27
830 926 2.281208 TTTGTCGGCCGGTTCCTG 60.281 61.111 27.83 0.00 0.00 3.86
1089 1189 2.282462 CCAAAGCCACGCTCCCTT 60.282 61.111 0.00 0.00 38.25 3.95
1507 1608 1.446366 GAAGCACCCGGGGATAGAC 59.554 63.158 27.92 7.78 0.00 2.59
1564 1665 1.337260 GCTGACATCCGTGACAAGACT 60.337 52.381 0.00 0.00 30.00 3.24
1573 1674 2.876645 GACAAGACTCTCGCGGCG 60.877 66.667 17.70 17.70 0.00 6.46
1662 1763 2.280457 GCCACTCGCATAGGAGCC 60.280 66.667 0.00 0.00 37.57 4.70
1700 1801 5.506686 TGAATTTGATGTGGTTTGTTCGA 57.493 34.783 0.00 0.00 0.00 3.71
1701 1802 6.083098 TGAATTTGATGTGGTTTGTTCGAT 57.917 33.333 0.00 0.00 0.00 3.59
1702 1803 5.919707 TGAATTTGATGTGGTTTGTTCGATG 59.080 36.000 0.00 0.00 0.00 3.84
1723 1824 6.923508 CGATGATTGCTGGTCTAATGTAGTTA 59.076 38.462 0.00 0.00 0.00 2.24
1733 1841 6.127793 GGTCTAATGTAGTTAGTGGAGAGGA 58.872 44.000 0.00 0.00 40.58 3.71
1779 1887 7.332678 GCATGAAAAACCTAAATTCAGCTTGAT 59.667 33.333 0.00 0.00 36.59 2.57
1780 1888 8.653338 CATGAAAAACCTAAATTCAGCTTGATG 58.347 33.333 0.00 0.00 36.59 3.07
1790 1898 1.558294 TCAGCTTGATGGAGAGCACAT 59.442 47.619 0.00 0.00 41.31 3.21
1815 1929 7.715657 TGAATGGTTTCATATCATGTTTAGGC 58.284 34.615 0.00 0.00 36.94 3.93
1818 1932 5.593909 TGGTTTCATATCATGTTTAGGCTGG 59.406 40.000 0.00 0.00 0.00 4.85
1831 1947 5.168569 GTTTAGGCTGGGAAACTTAATTGC 58.831 41.667 0.00 0.00 33.62 3.56
1852 1968 7.466746 TTGCAAGGATTAGAAAATGTAAGCT 57.533 32.000 0.00 0.00 0.00 3.74
1860 1976 8.893727 GGATTAGAAAATGTAAGCTGAGCTAAA 58.106 33.333 7.68 0.00 38.25 1.85
1950 2075 5.590259 GGTTCCTGCTGCTTATTAGAATCAA 59.410 40.000 0.00 0.00 0.00 2.57
1951 2076 6.095440 GGTTCCTGCTGCTTATTAGAATCAAA 59.905 38.462 0.00 0.00 0.00 2.69
1985 2110 1.339247 TGTGTTCGGTTCACCACTGTT 60.339 47.619 0.00 0.00 35.25 3.16
1987 2112 0.942252 GTTCGGTTCACCACTGTTCC 59.058 55.000 0.00 0.00 35.14 3.62
2029 2166 4.446371 ACTAGAATACAATGTCTGCTGGC 58.554 43.478 0.00 0.00 0.00 4.85
2087 2224 4.876107 CCAGGCCAGTTTGTGTACTATTAG 59.124 45.833 5.01 0.00 0.00 1.73
2174 2311 9.631452 GATTTTTCATCCTGCTATAAAATAGCC 57.369 33.333 14.59 0.51 39.69 3.93
2229 2366 6.451064 TTGCTAGTCAGAAGTCGATTATCA 57.549 37.500 0.00 0.00 0.00 2.15
2230 2367 5.822278 TGCTAGTCAGAAGTCGATTATCAC 58.178 41.667 0.00 0.00 0.00 3.06
2231 2368 5.590663 TGCTAGTCAGAAGTCGATTATCACT 59.409 40.000 0.00 0.00 0.00 3.41
2232 2369 5.912396 GCTAGTCAGAAGTCGATTATCACTG 59.088 44.000 0.00 0.00 0.00 3.66
2233 2370 5.906113 AGTCAGAAGTCGATTATCACTGT 57.094 39.130 0.00 0.00 0.00 3.55
2234 2371 5.885881 AGTCAGAAGTCGATTATCACTGTC 58.114 41.667 0.00 0.00 0.00 3.51
2421 2558 6.889301 TTGAAATCACTGAAGAAAGCATCT 57.111 33.333 0.00 0.00 41.32 2.90
2457 2594 0.549950 AGCTTGGGATGCTGCATACT 59.450 50.000 23.23 8.08 39.56 2.12
2728 2866 6.922957 TGTTCCTTTATTGCATTTCTCAACAC 59.077 34.615 0.00 0.00 0.00 3.32
2833 2971 7.111466 ACCTTGGACGTATCCTATATAGTCTC 58.889 42.308 8.92 0.00 46.43 3.36
3081 3219 5.710513 TGCTGCTTTGTTCATCTTTACAT 57.289 34.783 0.00 0.00 0.00 2.29
3097 3235 7.750229 TCTTTACATTTGAGTTTCTGAGCAT 57.250 32.000 0.00 0.00 0.00 3.79
3110 3248 3.774066 TCTGAGCATATGAACACAGTCG 58.226 45.455 6.97 0.00 0.00 4.18
3146 3284 9.283768 TGATTATGTGACAGTTTGTAAGTCATT 57.716 29.630 0.00 0.00 43.35 2.57
3224 3362 6.732154 CAGGTACTTTGGCAAATGATGATAG 58.268 40.000 13.89 1.23 34.60 2.08
3237 3375 8.887717 GCAAATGATGATAGTAATAGGATGGAC 58.112 37.037 0.00 0.00 0.00 4.02
3240 3378 8.774546 ATGATGATAGTAATAGGATGGACGAT 57.225 34.615 0.00 0.00 0.00 3.73
3513 3651 3.378427 GCAACCTATTTCCAGATGACACC 59.622 47.826 0.00 0.00 0.00 4.16
3753 3891 8.840321 CCATACAATCTAAAAAGGTGACCTATG 58.160 37.037 3.68 0.00 31.13 2.23
3822 3960 0.094730 GTGAAAAGGATTCGCGTCCG 59.905 55.000 5.77 0.00 43.27 4.79
4117 4255 6.564499 GCATTGTACTTTGGCTGACAATTTTG 60.564 38.462 0.00 0.00 39.81 2.44
4362 4500 4.759693 TGTCATTTACAGGTGGCAACTTAG 59.240 41.667 0.00 0.00 33.01 2.18
4610 4748 2.887152 GAGCTTCCAATTGTGGTTCACT 59.113 45.455 4.43 0.00 46.11 3.41
4648 4786 6.988580 CAGATGATTCTAAAGTATCACAGGCA 59.011 38.462 1.91 0.00 35.24 4.75
5093 5231 1.266989 GCTGGTTTCTGAAAAGACCGG 59.733 52.381 12.30 12.30 40.69 5.28
5298 5436 2.571653 AGTTCTGTGCCTGGCTATGTTA 59.428 45.455 21.03 0.00 0.00 2.41
5364 5502 1.134699 TCAGTGATTGATGTCGGGCTC 60.135 52.381 0.00 0.00 0.00 4.70
5491 5629 1.880027 GGTTGATCGCCAGTTGAGTTT 59.120 47.619 1.69 0.00 0.00 2.66
5493 5631 2.542020 TGATCGCCAGTTGAGTTTGA 57.458 45.000 0.00 0.00 0.00 2.69
5494 5632 2.844946 TGATCGCCAGTTGAGTTTGAA 58.155 42.857 0.00 0.00 0.00 2.69
5503 5646 5.163581 GCCAGTTGAGTTTGAATGCATATCT 60.164 40.000 0.00 0.00 0.00 1.98
5510 5653 7.022979 TGAGTTTGAATGCATATCTTTTGTCG 58.977 34.615 0.00 0.00 0.00 4.35
5565 5712 1.542915 CCATGGCACTGAGAAACCTTG 59.457 52.381 0.00 0.00 0.00 3.61
5596 5743 4.102524 ACTGGAACTAACATGGTCTGACAA 59.897 41.667 10.38 0.00 0.00 3.18
5654 5801 0.034670 GAGATGCTTCCCTGTTGCCT 60.035 55.000 0.00 0.00 0.00 4.75
5722 5869 5.550981 CAATCACAAGAATACCGAAACTCG 58.449 41.667 0.00 0.00 40.07 4.18
5780 5928 1.270839 GCAACTCCAGCAGACTTGGTA 60.271 52.381 0.00 0.00 37.02 3.25
5843 5992 2.639327 GCCTTGATGGTGGTGGTGC 61.639 63.158 0.00 0.00 38.35 5.01
5869 6018 2.843701 CTGGTCAGACTTGCTTGTTCT 58.156 47.619 0.00 0.00 0.00 3.01
5969 6120 7.972832 TGTTTAATCTGAACTACCAAATCGT 57.027 32.000 0.00 0.00 0.00 3.73
5980 6132 5.227152 ACTACCAAATCGTTGCATTTTTCC 58.773 37.500 0.00 0.00 33.01 3.13
6010 6162 8.658840 TTTTTGGTGCCTTCTAACCTATATTT 57.341 30.769 0.00 0.00 37.36 1.40
6011 6163 7.639113 TTTGGTGCCTTCTAACCTATATTTG 57.361 36.000 0.00 0.00 37.36 2.32
6019 6171 9.163899 GCCTTCTAACCTATATTTGGCTATAAC 57.836 37.037 0.00 0.00 35.44 1.89
6022 6174 8.426569 TCTAACCTATATTTGGCTATAACGGT 57.573 34.615 0.00 0.00 0.00 4.83
6051 6203 6.764877 ACAACAGACTCGTACAATACTTTG 57.235 37.500 0.00 0.00 38.86 2.77
6067 6219 9.113838 ACAATACTTTGCTATCAAACATAGGAG 57.886 33.333 0.00 0.00 37.28 3.69
6068 6220 7.736447 ATACTTTGCTATCAAACATAGGAGC 57.264 36.000 0.00 0.00 37.28 4.70
6095 6249 0.304705 CCAATACTGAACGCGATGGC 59.695 55.000 15.93 0.00 0.00 4.40
6168 6324 2.355756 CCAGATTACGTGCCTTTGATGG 59.644 50.000 0.00 0.00 0.00 3.51
6169 6325 3.270027 CAGATTACGTGCCTTTGATGGA 58.730 45.455 0.00 0.00 0.00 3.41
6170 6326 3.063997 CAGATTACGTGCCTTTGATGGAC 59.936 47.826 0.00 0.00 0.00 4.02
6171 6327 2.552599 TTACGTGCCTTTGATGGACA 57.447 45.000 0.00 0.00 0.00 4.02
6172 6328 2.779755 TACGTGCCTTTGATGGACAT 57.220 45.000 0.00 0.00 0.00 3.06
6173 6329 2.779755 ACGTGCCTTTGATGGACATA 57.220 45.000 0.00 0.00 0.00 2.29
6178 6334 4.858692 CGTGCCTTTGATGGACATAAAAAG 59.141 41.667 10.66 10.66 0.00 2.27
6186 6342 6.839124 TGATGGACATAAAAAGCTGTCATT 57.161 33.333 4.20 0.00 33.35 2.57
6187 6343 6.623486 TGATGGACATAAAAAGCTGTCATTG 58.377 36.000 4.20 0.00 33.35 2.82
6190 6346 4.379394 GGACATAAAAAGCTGTCATTGCGA 60.379 41.667 4.20 0.00 35.28 5.10
6191 6347 4.475944 ACATAAAAAGCTGTCATTGCGAC 58.524 39.130 0.00 0.00 45.61 5.19
6192 6348 4.216257 ACATAAAAAGCTGTCATTGCGACT 59.784 37.500 0.00 0.00 45.60 4.18
6193 6349 5.411361 ACATAAAAAGCTGTCATTGCGACTA 59.589 36.000 0.00 0.00 45.60 2.59
6194 6350 6.094048 ACATAAAAAGCTGTCATTGCGACTAT 59.906 34.615 0.00 0.00 45.60 2.12
6195 6351 4.606457 AAAAGCTGTCATTGCGACTATC 57.394 40.909 0.00 0.00 45.60 2.08
6196 6352 1.845266 AGCTGTCATTGCGACTATCG 58.155 50.000 0.00 0.00 45.60 2.92
6197 6353 1.405463 AGCTGTCATTGCGACTATCGA 59.595 47.619 1.69 0.00 43.74 3.59
6198 6354 2.035193 AGCTGTCATTGCGACTATCGAT 59.965 45.455 2.16 2.16 43.74 3.59
6199 6355 2.797156 GCTGTCATTGCGACTATCGATT 59.203 45.455 1.71 0.00 43.74 3.34
6200 6356 3.981416 GCTGTCATTGCGACTATCGATTA 59.019 43.478 1.71 0.00 43.74 1.75
6201 6357 4.623167 GCTGTCATTGCGACTATCGATTAT 59.377 41.667 1.71 0.00 43.74 1.28
6202 6358 5.443824 GCTGTCATTGCGACTATCGATTATG 60.444 44.000 1.71 0.00 43.74 1.90
6203 6359 5.768317 TGTCATTGCGACTATCGATTATGA 58.232 37.500 1.71 4.68 43.74 2.15
6204 6360 5.858581 TGTCATTGCGACTATCGATTATGAG 59.141 40.000 1.71 0.00 43.74 2.90
6205 6361 5.859114 GTCATTGCGACTATCGATTATGAGT 59.141 40.000 1.71 0.00 43.74 3.41
6206 6362 6.363626 GTCATTGCGACTATCGATTATGAGTT 59.636 38.462 1.71 0.00 43.74 3.01
6238 6394 6.475727 TGACGAGATATTCAGAATCGGAAAAC 59.524 38.462 0.00 0.00 37.69 2.43
6250 6406 0.098025 CGGAAAACAACACGTGCTGT 59.902 50.000 18.50 18.50 32.89 4.40
6256 6412 1.301716 CAACACGTGCTGTAGGCCT 60.302 57.895 17.22 11.78 40.92 5.19
6268 6424 3.304794 GCTGTAGGCCTCGAGTAGTATTG 60.305 52.174 9.68 0.00 34.27 1.90
6294 6450 3.496884 TCGACTGCGTTTTATTTCTTGCT 59.503 39.130 0.00 0.00 38.98 3.91
6313 6469 1.496429 CTGGGGCTACTGATTTCCCAT 59.504 52.381 0.00 0.00 45.51 4.00
6465 6621 4.446413 CCACCCTCGCCACCGTAC 62.446 72.222 0.00 0.00 35.54 3.67
6466 6622 4.789075 CACCCTCGCCACCGTACG 62.789 72.222 8.69 8.69 35.54 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
133 138 3.372795 TTTTTCCGCGAGTGTCACT 57.627 47.368 8.23 4.81 0.00 3.41
201 219 1.719117 CACGGTTGTGCTTTCACGT 59.281 52.632 0.00 0.00 46.01 4.49
425 485 2.743636 TTTCCTTTCGCGAGACTCAT 57.256 45.000 9.59 0.00 41.84 2.90
697 783 1.078848 GGAGATCAGCGCCACTTGT 60.079 57.895 2.29 0.00 36.33 3.16
734 830 1.742268 GAATTCTCAGAGGGCAACTGC 59.258 52.381 0.00 0.00 41.14 4.40
735 831 3.269178 GAGAATTCTCAGAGGGCAACTG 58.731 50.000 27.08 4.22 42.42 3.16
777 873 9.343539 GCCCTTTGTCTCAATAATAGAAGTTAT 57.656 33.333 0.00 0.00 0.00 1.89
778 874 7.773690 GGCCCTTTGTCTCAATAATAGAAGTTA 59.226 37.037 0.00 0.00 0.00 2.24
779 875 6.603599 GGCCCTTTGTCTCAATAATAGAAGTT 59.396 38.462 0.00 0.00 0.00 2.66
780 876 6.122964 GGCCCTTTGTCTCAATAATAGAAGT 58.877 40.000 0.00 0.00 0.00 3.01
781 877 5.532779 GGGCCCTTTGTCTCAATAATAGAAG 59.467 44.000 17.04 0.00 0.00 2.85
782 878 5.044476 TGGGCCCTTTGTCTCAATAATAGAA 60.044 40.000 25.70 0.00 0.00 2.10
783 879 4.476846 TGGGCCCTTTGTCTCAATAATAGA 59.523 41.667 25.70 0.00 0.00 1.98
784 880 4.792068 TGGGCCCTTTGTCTCAATAATAG 58.208 43.478 25.70 0.00 0.00 1.73
785 881 4.871871 TGGGCCCTTTGTCTCAATAATA 57.128 40.909 25.70 0.00 0.00 0.98
786 882 3.756082 TGGGCCCTTTGTCTCAATAAT 57.244 42.857 25.70 0.00 0.00 1.28
787 883 3.245586 ACATGGGCCCTTTGTCTCAATAA 60.246 43.478 25.70 0.00 0.00 1.40
788 884 2.311542 ACATGGGCCCTTTGTCTCAATA 59.688 45.455 25.70 0.00 0.00 1.90
789 885 1.077663 ACATGGGCCCTTTGTCTCAAT 59.922 47.619 25.70 0.54 0.00 2.57
790 886 0.482446 ACATGGGCCCTTTGTCTCAA 59.518 50.000 25.70 0.00 0.00 3.02
791 887 1.281867 CTACATGGGCCCTTTGTCTCA 59.718 52.381 27.69 14.21 0.00 3.27
792 888 2.019156 GCTACATGGGCCCTTTGTCTC 61.019 57.143 27.69 18.68 0.00 3.36
793 889 0.034089 GCTACATGGGCCCTTTGTCT 60.034 55.000 27.69 12.29 0.00 3.41
794 890 0.034089 AGCTACATGGGCCCTTTGTC 60.034 55.000 27.69 17.54 0.00 3.18
795 891 0.409484 AAGCTACATGGGCCCTTTGT 59.591 50.000 27.20 27.20 0.00 2.83
796 892 1.205417 CAAAGCTACATGGGCCCTTTG 59.795 52.381 25.70 22.36 37.23 2.77
797 893 1.203174 ACAAAGCTACATGGGCCCTTT 60.203 47.619 25.70 10.44 0.00 3.11
798 894 0.409484 ACAAAGCTACATGGGCCCTT 59.591 50.000 25.70 15.22 0.00 3.95
799 895 0.034089 GACAAAGCTACATGGGCCCT 60.034 55.000 25.70 5.02 0.00 5.19
800 896 1.376609 CGACAAAGCTACATGGGCCC 61.377 60.000 17.59 17.59 0.00 5.80
801 897 1.376609 CCGACAAAGCTACATGGGCC 61.377 60.000 0.00 0.00 0.00 5.80
802 898 1.993369 GCCGACAAAGCTACATGGGC 61.993 60.000 0.00 0.72 0.00 5.36
830 926 0.472471 TATCCGGCCCAAATCAGGAC 59.528 55.000 0.00 0.00 33.37 3.85
856 952 3.644966 ATCGAGACCAGCCCAATTTTA 57.355 42.857 0.00 0.00 0.00 1.52
1322 1423 2.025441 GTTCACCTGCGCGCAAAA 59.975 55.556 35.50 22.25 0.00 2.44
1323 1424 3.179869 CTGTTCACCTGCGCGCAAA 62.180 57.895 35.50 23.27 0.00 3.68
1324 1425 3.648982 CTGTTCACCTGCGCGCAA 61.649 61.111 35.50 18.10 0.00 4.85
1411 1512 2.974148 TTGTGCAGCCTCAGCGTG 60.974 61.111 0.00 0.00 46.67 5.34
1513 1614 2.038975 TGGAACTCCTCCTCGGGG 59.961 66.667 0.00 0.00 45.64 5.73
1555 1656 2.258591 GCCGCGAGAGTCTTGTCA 59.741 61.111 8.23 0.00 0.00 3.58
1700 1801 7.712639 CACTAACTACATTAGACCAGCAATCAT 59.287 37.037 0.81 0.00 42.75 2.45
1701 1802 7.041721 CACTAACTACATTAGACCAGCAATCA 58.958 38.462 0.81 0.00 42.75 2.57
1702 1803 6.480320 CCACTAACTACATTAGACCAGCAATC 59.520 42.308 0.81 0.00 42.75 2.67
1723 1824 1.274069 ACCATGGACATCCTCTCCACT 60.274 52.381 21.47 0.00 40.73 4.00
1733 1841 2.682856 GCATGTACGAAACCATGGACAT 59.317 45.455 21.47 13.67 39.06 3.06
1779 1887 2.885135 AACCATTCATGTGCTCTCCA 57.115 45.000 0.00 0.00 0.00 3.86
1780 1888 3.084039 TGAAACCATTCATGTGCTCTCC 58.916 45.455 0.00 0.00 40.59 3.71
1804 1918 3.806949 AGTTTCCCAGCCTAAACATGA 57.193 42.857 0.00 0.00 37.92 3.07
1805 1919 5.975693 TTAAGTTTCCCAGCCTAAACATG 57.024 39.130 0.00 0.00 37.92 3.21
1806 1920 6.574269 GCAATTAAGTTTCCCAGCCTAAACAT 60.574 38.462 0.00 0.00 37.92 2.71
1815 1929 5.665916 ATCCTTGCAATTAAGTTTCCCAG 57.334 39.130 0.00 0.00 0.00 4.45
1818 1932 9.705290 TTTTCTAATCCTTGCAATTAAGTTTCC 57.295 29.630 0.00 0.00 0.00 3.13
1831 1947 7.066766 AGCTCAGCTTACATTTTCTAATCCTTG 59.933 37.037 0.00 0.00 33.89 3.61
1848 1964 8.622948 AAGTTACTTAACATTTAGCTCAGCTT 57.377 30.769 3.31 0.00 38.11 3.74
1902 2027 7.832685 ACCTCCCTACTTTTGTGATATAAAACC 59.167 37.037 0.00 0.00 0.00 3.27
1950 2075 7.696992 ACCGAACACAGTAATAATCCAAATT 57.303 32.000 0.00 0.00 0.00 1.82
1951 2076 7.392113 TGAACCGAACACAGTAATAATCCAAAT 59.608 33.333 0.00 0.00 0.00 2.32
1985 2110 5.181622 AGTTATTAAACAAATGTTCGCCGGA 59.818 36.000 5.05 0.00 37.25 5.14
1987 2112 7.457868 TCTAGTTATTAAACAAATGTTCGCCG 58.542 34.615 0.00 0.00 37.25 6.46
2087 2224 2.568623 AGGACCCTCACACACATTTC 57.431 50.000 0.00 0.00 0.00 2.17
2171 2308 1.696336 AGAACACATGAGACACAGGCT 59.304 47.619 0.00 0.00 33.22 4.58
2174 2311 5.120363 CAGATTCAGAACACATGAGACACAG 59.880 44.000 0.00 0.00 0.00 3.66
2229 2366 0.032678 CTGAACAGACCAGCGACAGT 59.967 55.000 0.00 0.00 0.00 3.55
2230 2367 0.668706 CCTGAACAGACCAGCGACAG 60.669 60.000 3.19 0.00 0.00 3.51
2231 2368 1.112916 TCCTGAACAGACCAGCGACA 61.113 55.000 3.19 0.00 0.00 4.35
2232 2369 0.247736 ATCCTGAACAGACCAGCGAC 59.752 55.000 3.19 0.00 0.00 5.19
2233 2370 0.976641 AATCCTGAACAGACCAGCGA 59.023 50.000 3.19 0.00 0.00 4.93
2234 2371 1.466167 CAAATCCTGAACAGACCAGCG 59.534 52.381 3.19 0.00 0.00 5.18
2457 2594 5.047448 TGCATGGTGCTGCTTTAATTTCTTA 60.047 36.000 0.00 0.00 45.31 2.10
2619 2756 8.045720 ACAGATATAACATACCCATTTCCTGT 57.954 34.615 0.00 0.00 0.00 4.00
2691 2829 0.111253 AAGGAACAAGTGCAGGGAGG 59.889 55.000 0.00 0.00 0.00 4.30
2728 2866 5.289675 CCACTCGTCTATTAAGAAACAGCAG 59.710 44.000 0.00 0.00 32.16 4.24
2864 3002 1.944024 CACGTCCCTTTTGCACTGTTA 59.056 47.619 0.00 0.00 0.00 2.41
2879 3017 1.016130 CCTCACATGACCAGCACGTC 61.016 60.000 0.00 0.00 0.00 4.34
3081 3219 6.486320 TGTGTTCATATGCTCAGAAACTCAAA 59.514 34.615 0.00 0.00 0.00 2.69
3097 3235 6.652900 TCAATTTGATTCCGACTGTGTTCATA 59.347 34.615 0.00 0.00 0.00 2.15
3110 3248 9.643693 AAACTGTCACATAATCAATTTGATTCC 57.356 29.630 24.14 9.96 43.03 3.01
3224 3362 4.820897 TGCATCATCGTCCATCCTATTAC 58.179 43.478 0.00 0.00 0.00 1.89
3237 3375 4.514066 TCTTCCTCATCAATTGCATCATCG 59.486 41.667 0.00 0.00 0.00 3.84
3240 3378 5.503002 TCTTCTTCCTCATCAATTGCATCA 58.497 37.500 0.00 0.00 0.00 3.07
3379 3517 0.320073 TTACGACGCTTGGTTCCAGG 60.320 55.000 0.00 0.00 0.00 4.45
3597 3735 6.463995 AAAGGACAAAAGCATGTAAACTGA 57.536 33.333 0.00 0.00 32.57 3.41
3626 3764 5.688807 ACTAAATGCTGCCTATGAAGACAT 58.311 37.500 0.00 0.00 40.16 3.06
3627 3765 5.102953 ACTAAATGCTGCCTATGAAGACA 57.897 39.130 0.00 0.00 0.00 3.41
3628 3766 6.017852 GGTAACTAAATGCTGCCTATGAAGAC 60.018 42.308 0.00 0.00 0.00 3.01
3629 3767 6.055588 GGTAACTAAATGCTGCCTATGAAGA 58.944 40.000 0.00 0.00 0.00 2.87
3753 3891 6.081872 AGCTTAGCCATCTGCATAAAATTC 57.918 37.500 0.00 0.00 44.83 2.17
3822 3960 0.804989 GATGCTGTGCCCACTTGTAC 59.195 55.000 0.00 0.00 0.00 2.90
4117 4255 1.098050 AGCAAAAGCATCATCCGACC 58.902 50.000 0.00 0.00 0.00 4.79
4199 4337 4.578928 AGCTTTAAACGAGGTGTTCACAAT 59.421 37.500 5.32 0.00 40.84 2.71
4362 4500 5.066117 GGCCACCTCAGCTTAGTTAAATAAC 59.934 44.000 0.00 0.00 36.46 1.89
4390 4528 5.463392 CCATGGTGTATTCTCGTGTTCTATG 59.537 44.000 2.57 0.00 0.00 2.23
4610 4748 6.683312 AGAATCATCTGGCATATCTTCAGA 57.317 37.500 0.00 0.00 41.09 3.27
5093 5231 6.570692 AGATCATTGTGCCATTTCAAATCTC 58.429 36.000 0.00 0.00 0.00 2.75
5298 5436 5.132502 TCCTCGTCCAAATGCATATCAAAT 58.867 37.500 0.00 0.00 0.00 2.32
5364 5502 1.334869 GTTCCACTGACTGGTTTGCAG 59.665 52.381 0.00 0.00 41.52 4.41
5491 5629 6.072230 TCCAAACGACAAAAGATATGCATTCA 60.072 34.615 3.54 0.00 0.00 2.57
5493 5631 6.266168 TCCAAACGACAAAAGATATGCATT 57.734 33.333 3.54 0.00 0.00 3.56
5494 5632 5.163622 CCTCCAAACGACAAAAGATATGCAT 60.164 40.000 3.79 3.79 0.00 3.96
5510 5653 3.253432 AGCATCTTCGTTTTCCTCCAAAC 59.747 43.478 0.00 0.00 33.90 2.93
5525 5668 2.560105 GGAAAGGCAGTTTCAGCATCTT 59.440 45.455 11.62 0.00 45.75 2.40
5554 5701 4.124238 CAGTACCGAAACAAGGTTTCTCA 58.876 43.478 16.92 2.75 42.81 3.27
5565 5712 4.390909 CCATGTTAGTTCCAGTACCGAAAC 59.609 45.833 0.00 0.00 0.00 2.78
5596 5743 3.239861 GCTTGGCAGCTTCTACTGT 57.760 52.632 0.00 0.00 43.51 3.55
5654 5801 7.225931 GCCATAATGGTTAGAAAACTATCGTCA 59.774 37.037 0.00 0.00 40.46 4.35
5722 5869 3.253188 TCAAGCAAGATAAAGTGCACCAC 59.747 43.478 14.63 0.68 43.42 4.16
5780 5928 0.963225 TGTTGCTTGATGCTGCATGT 59.037 45.000 21.53 0.00 43.37 3.21
5843 5992 1.575576 GCAAGTCTGACCAGCAGCAG 61.576 60.000 14.75 0.00 44.52 4.24
5869 6018 2.559668 CTGGCTTGGAAGATTTCAGCAA 59.440 45.455 0.00 0.00 32.15 3.91
5949 6100 5.935206 TGCAACGATTTGGTAGTTCAGATTA 59.065 36.000 0.00 0.00 32.81 1.75
5990 6142 4.519350 GCCAAATATAGGTTAGAAGGCACC 59.481 45.833 0.00 0.00 39.35 5.01
6010 6162 3.965379 TGTTTCTCACCGTTATAGCCA 57.035 42.857 0.00 0.00 0.00 4.75
6011 6163 3.998341 TGTTGTTTCTCACCGTTATAGCC 59.002 43.478 0.00 0.00 0.00 3.93
6019 6171 1.787155 CGAGTCTGTTGTTTCTCACCG 59.213 52.381 0.00 0.00 0.00 4.94
6022 6174 4.642445 TGTACGAGTCTGTTGTTTCTCA 57.358 40.909 0.00 0.00 0.00 3.27
6051 6203 3.717707 TGACGCTCCTATGTTTGATAGC 58.282 45.455 0.00 0.00 0.00 2.97
6065 6217 4.464112 GTTCAGTATTGGTTTTGACGCTC 58.536 43.478 0.00 0.00 0.00 5.03
6066 6218 3.059188 CGTTCAGTATTGGTTTTGACGCT 60.059 43.478 0.00 0.00 0.00 5.07
6067 6219 3.223157 CGTTCAGTATTGGTTTTGACGC 58.777 45.455 0.00 0.00 0.00 5.19
6068 6220 3.223157 GCGTTCAGTATTGGTTTTGACG 58.777 45.455 0.00 0.00 0.00 4.35
6095 6249 1.959899 CTTCAGCAAGTAGGCGCGTG 61.960 60.000 13.84 0.00 39.27 5.34
6168 6324 4.722194 TCGCAATGACAGCTTTTTATGTC 58.278 39.130 0.00 0.00 0.00 3.06
6169 6325 4.764679 TCGCAATGACAGCTTTTTATGT 57.235 36.364 0.00 0.00 0.00 2.29
6186 6342 6.308371 TGTAACTCATAATCGATAGTCGCA 57.692 37.500 0.00 0.00 40.21 5.10
6187 6343 7.021790 TCATGTAACTCATAATCGATAGTCGC 58.978 38.462 0.00 0.00 35.93 5.19
6190 6346 9.847706 GTCATCATGTAACTCATAATCGATAGT 57.152 33.333 0.00 0.00 34.67 2.12
6191 6347 9.004146 CGTCATCATGTAACTCATAATCGATAG 57.996 37.037 0.00 0.00 34.67 2.08
6192 6348 8.726988 TCGTCATCATGTAACTCATAATCGATA 58.273 33.333 0.00 0.00 34.67 2.92
6193 6349 7.593825 TCGTCATCATGTAACTCATAATCGAT 58.406 34.615 0.00 0.00 34.67 3.59
6194 6350 6.966021 TCGTCATCATGTAACTCATAATCGA 58.034 36.000 0.00 0.00 34.67 3.59
6195 6351 7.078228 TCTCGTCATCATGTAACTCATAATCG 58.922 38.462 0.00 0.00 34.67 3.34
6196 6352 8.978564 ATCTCGTCATCATGTAACTCATAATC 57.021 34.615 0.00 0.00 34.67 1.75
6200 6356 8.579863 TGAATATCTCGTCATCATGTAACTCAT 58.420 33.333 0.00 0.00 37.22 2.90
6201 6357 7.940850 TGAATATCTCGTCATCATGTAACTCA 58.059 34.615 0.00 0.00 0.00 3.41
6202 6358 8.293157 TCTGAATATCTCGTCATCATGTAACTC 58.707 37.037 0.00 0.00 0.00 3.01
6203 6359 8.171164 TCTGAATATCTCGTCATCATGTAACT 57.829 34.615 0.00 0.00 0.00 2.24
6204 6360 8.803201 TTCTGAATATCTCGTCATCATGTAAC 57.197 34.615 0.00 0.00 0.00 2.50
6205 6361 9.631452 GATTCTGAATATCTCGTCATCATGTAA 57.369 33.333 2.28 0.00 0.00 2.41
6206 6362 7.965107 CGATTCTGAATATCTCGTCATCATGTA 59.035 37.037 2.28 0.00 0.00 2.29
6238 6394 1.291877 GAGGCCTACAGCACGTGTTG 61.292 60.000 27.99 27.99 46.50 3.33
6250 6406 5.048921 CGAAATCAATACTACTCGAGGCCTA 60.049 44.000 18.41 2.54 0.00 3.93
6256 6412 5.271625 GCAGTCGAAATCAATACTACTCGA 58.728 41.667 0.00 0.00 33.29 4.04
6268 6424 6.451183 GCAAGAAATAAAACGCAGTCGAAATC 60.451 38.462 0.00 0.00 45.00 2.17
6294 6450 3.112878 TGGGAAATCAGTAGCCCCA 57.887 52.632 0.00 0.00 44.21 4.96
6313 6469 1.541147 GCTGCCAAGACTAAATGTGCA 59.459 47.619 0.00 0.00 0.00 4.57
6385 6541 1.078759 GTTCCAGCAGATCGACACCG 61.079 60.000 0.00 0.00 37.07 4.94
6410 6566 4.070552 GGGCTCGACCTTGACGCT 62.071 66.667 4.41 0.00 39.10 5.07
6431 6587 2.672996 GTGGACCAGTGCGCCAAT 60.673 61.111 4.18 0.00 32.68 3.16


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

AutoCloner maintained by Alex Coulton.