Multiple sequence alignment - TraesCS2D01G029200

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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 TraesCS2D01G029200 chr2D 100.000 5376 0 0 1 5376 11861646 11856271 0.000000e+00 9928.0
1 TraesCS2D01G029200 chr2A 88.939 1537 117 24 2778 4311 12344335 12342849 0.000000e+00 1847.0
2 TraesCS2D01G029200 chr2A 95.426 634 26 2 157 790 12361986 12361356 0.000000e+00 1007.0
3 TraesCS2D01G029200 chr2A 86.696 917 83 17 839 1734 12423983 12423085 0.000000e+00 981.0
4 TraesCS2D01G029200 chr2A 96.797 562 17 1 1995 2556 12360279 12359719 0.000000e+00 937.0
5 TraesCS2D01G029200 chr2A 91.971 548 20 8 803 1350 12360988 12360465 0.000000e+00 747.0
6 TraesCS2D01G029200 chr2A 83.956 642 66 16 4352 4963 12342853 12342219 1.000000e-161 580.0
7 TraesCS2D01G029200 chr2A 88.889 414 26 8 4969 5376 12342248 12341849 4.840000e-135 492.0
8 TraesCS2D01G029200 chr2A 90.852 317 23 4 4101 4414 12446736 12446423 2.320000e-113 420.0
9 TraesCS2D01G029200 chr2A 93.750 240 15 0 2547 2786 12345959 12345720 1.420000e-95 361.0
10 TraesCS2D01G029200 chr2A 97.382 191 5 0 1764 1954 12360465 12360275 5.190000e-85 326.0
11 TraesCS2D01G029200 chr2A 95.333 150 7 0 9 158 12364863 12364714 6.960000e-59 239.0
12 TraesCS2D01G029200 chr2A 87.978 183 14 4 596 778 12424268 12424094 5.460000e-50 209.0
13 TraesCS2D01G029200 chr2A 91.954 87 6 1 72 158 12543542 12543457 2.630000e-23 121.0
14 TraesCS2D01G029200 chr2A 85.586 111 14 1 469 579 12424441 12424333 1.220000e-21 115.0
15 TraesCS2D01G029200 chr2A 85.897 78 10 1 3062 3138 49929547 49929470 1.240000e-11 82.4
16 TraesCS2D01G029200 chr2B 89.146 1124 101 9 3369 4488 18278038 18276932 0.000000e+00 1380.0
17 TraesCS2D01G029200 chr2B 94.783 460 18 6 2541 2996 18278509 18278052 0.000000e+00 712.0
18 TraesCS2D01G029200 chr2B 83.896 770 69 21 4242 4963 18381475 18380713 0.000000e+00 684.0
19 TraesCS2D01G029200 chr2B 90.226 399 22 4 4974 5368 18380737 18380352 6.210000e-139 505.0
20 TraesCS2D01G029200 chr2B 88.925 307 22 7 5070 5376 18276199 18275905 8.510000e-98 368.0
21 TraesCS2D01G029200 chr2B 86.288 299 22 4 4748 5039 18276484 18276198 1.880000e-79 307.0
22 TraesCS2D01G029200 chr2B 81.625 283 33 12 1971 2253 18278929 18278666 3.260000e-52 217.0
23 TraesCS2D01G029200 chr2B 87.342 158 6 3 1 158 18307428 18307285 9.260000e-38 169.0
24 TraesCS2D01G029200 chr4D 87.097 62 8 0 3077 3138 435232876 435232937 2.690000e-08 71.3


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 TraesCS2D01G029200 chr2D 11856271 11861646 5375 True 9928.0 9928 100.000000 1 5376 1 chr2D.!!$R1 5375
1 TraesCS2D01G029200 chr2A 12341849 12345959 4110 True 820.0 1847 88.883500 2547 5376 4 chr2A.!!$R4 2829
2 TraesCS2D01G029200 chr2A 12359719 12364863 5144 True 651.2 1007 95.381800 9 2556 5 chr2A.!!$R5 2547
3 TraesCS2D01G029200 chr2A 12423085 12424441 1356 True 435.0 981 86.753333 469 1734 3 chr2A.!!$R6 1265
4 TraesCS2D01G029200 chr2B 18275905 18278929 3024 True 596.8 1380 88.153400 1971 5376 5 chr2B.!!$R2 3405
5 TraesCS2D01G029200 chr2B 18380352 18381475 1123 True 594.5 684 87.061000 4242 5368 2 chr2B.!!$R3 1126

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
668 3446 1.340697 GGGGCTTACAAACCGGAATCT 60.341 52.381 9.46 0.0 0.00 2.40 F
1060 4292 0.179215 CACCGTGATCTTCTTTGCGC 60.179 55.000 0.00 0.0 0.00 6.09 F
1802 5041 0.601576 TATGCGCGGTGTTGTTCAGT 60.602 50.000 8.83 0.0 0.00 3.41 F
2878 7513 0.892358 AAGACGAGGTGGACGTGCTA 60.892 55.000 8.99 0.0 43.97 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1777 5016 1.003108 CAACACCGCGCATACACATA 58.997 50.0 8.75 0.0 0.0 2.29 R
3010 7646 0.039764 AGGAGGTGACGGATGACTGA 59.960 55.0 0.00 0.0 0.0 3.41 R
3180 7816 0.034616 GCATTCCTCATCCTCTCCGG 59.965 60.0 0.00 0.0 0.0 5.14 R
4646 9493 0.817013 TTTTGATGATGAAGGCCCGC 59.183 50.0 0.00 0.0 0.0 6.13 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
28 29 2.105930 GCAGCAGAGCGTCTAGGG 59.894 66.667 0.00 0.00 0.00 3.53
36 37 4.208686 GCGTCTAGGGTGGGCTCG 62.209 72.222 0.00 0.00 0.00 5.03
90 91 2.631062 ACTTTCGACACACTGGGTATGA 59.369 45.455 0.00 0.00 0.00 2.15
97 98 3.696051 GACACACTGGGTATGAAATGCAT 59.304 43.478 0.00 0.00 41.08 3.96
98 99 4.854173 ACACACTGGGTATGAAATGCATA 58.146 39.130 0.00 0.00 38.44 3.14
207 2937 7.434013 ACTGTTGAAATAATTTGACCGAAACAC 59.566 33.333 0.00 0.00 0.00 3.32
225 2955 7.858382 CCGAAACACAAAATTTCAGTACATACA 59.142 33.333 0.00 0.00 36.09 2.29
252 2982 8.016497 CAATTACTGAAATTGCCGAAAATTCA 57.984 30.769 0.00 0.00 45.87 2.57
298 3028 2.629137 ACAACATTGCCTGCTGATTGAA 59.371 40.909 0.00 0.00 0.00 2.69
325 3055 3.695060 TCCGCTTTTGTGAACCAACTAAA 59.305 39.130 0.00 0.00 31.20 1.85
326 3056 3.794564 CCGCTTTTGTGAACCAACTAAAC 59.205 43.478 0.00 0.00 31.20 2.01
359 3089 5.235850 TCATGCTTGTACTAACCAAAGGA 57.764 39.130 0.00 0.00 0.00 3.36
363 3093 5.790593 TGCTTGTACTAACCAAAGGAGTAG 58.209 41.667 0.00 0.00 0.00 2.57
456 3186 7.288810 TGTAAATTTGTGGAGAAAATGAGCT 57.711 32.000 0.00 0.00 0.00 4.09
529 3259 9.887629 TTATACGACAAAAACTATACATTGGGA 57.112 29.630 0.00 0.00 0.00 4.37
530 3260 8.795842 ATACGACAAAAACTATACATTGGGAA 57.204 30.769 0.00 0.00 0.00 3.97
565 3295 8.959548 TCGAACACTAATCTAACACAGGTATAA 58.040 33.333 0.00 0.00 0.00 0.98
668 3446 1.340697 GGGGCTTACAAACCGGAATCT 60.341 52.381 9.46 0.00 0.00 2.40
790 3568 7.333672 ACAGCAAAGTTAATTACTGGCTACTAC 59.666 37.037 0.00 0.00 42.90 2.73
791 3569 7.549488 CAGCAAAGTTAATTACTGGCTACTACT 59.451 37.037 0.00 0.00 42.90 2.57
792 3570 7.764901 AGCAAAGTTAATTACTGGCTACTACTC 59.235 37.037 0.00 0.00 42.93 2.59
793 3571 7.764901 GCAAAGTTAATTACTGGCTACTACTCT 59.235 37.037 0.00 0.00 37.12 3.24
800 3578 8.550710 AATTACTGGCTACTACTCTAGATACG 57.449 38.462 0.00 0.00 0.00 3.06
801 3579 5.804944 ACTGGCTACTACTCTAGATACGA 57.195 43.478 0.00 0.00 0.00 3.43
873 4088 1.956170 CGCGGCAGAACACAGAAGT 60.956 57.895 0.00 0.00 0.00 3.01
944 4161 2.524306 TCCGTTGCCATTTTTCCATCT 58.476 42.857 0.00 0.00 0.00 2.90
958 4175 3.407424 TCCATCTATCGGGCATCAAAG 57.593 47.619 0.00 0.00 0.00 2.77
959 4176 2.705658 TCCATCTATCGGGCATCAAAGT 59.294 45.455 0.00 0.00 0.00 2.66
960 4177 3.136443 TCCATCTATCGGGCATCAAAGTT 59.864 43.478 0.00 0.00 0.00 2.66
961 4178 3.885297 CCATCTATCGGGCATCAAAGTTT 59.115 43.478 0.00 0.00 0.00 2.66
962 4179 4.339247 CCATCTATCGGGCATCAAAGTTTT 59.661 41.667 0.00 0.00 0.00 2.43
963 4180 5.163519 CCATCTATCGGGCATCAAAGTTTTT 60.164 40.000 0.00 0.00 0.00 1.94
964 4181 6.039270 CCATCTATCGGGCATCAAAGTTTTTA 59.961 38.462 0.00 0.00 0.00 1.52
965 4182 6.677781 TCTATCGGGCATCAAAGTTTTTAG 57.322 37.500 0.00 0.00 0.00 1.85
966 4183 4.718940 ATCGGGCATCAAAGTTTTTAGG 57.281 40.909 0.00 0.00 0.00 2.69
977 4194 2.944129 AGTTTTTAGGCTTCCTGCACA 58.056 42.857 0.00 0.00 45.15 4.57
981 4202 3.780804 TTTAGGCTTCCTGCACAGTTA 57.219 42.857 0.00 0.00 45.15 2.24
1026 4258 2.821366 CCGTGCTGCCATGGTCTC 60.821 66.667 14.67 2.96 42.18 3.36
1060 4292 0.179215 CACCGTGATCTTCTTTGCGC 60.179 55.000 0.00 0.00 0.00 6.09
1120 4352 1.669115 GTCGATGATCATGGCGGGG 60.669 63.158 14.30 0.00 0.00 5.73
1221 4453 1.872234 CGCGACGTGGTACCATGAG 60.872 63.158 35.58 27.69 36.80 2.90
1256 4488 4.183101 GCACAGGAGAAGAAGAAGATGAG 58.817 47.826 0.00 0.00 0.00 2.90
1350 4582 3.145228 GCTCTACAGCTTCCACCAC 57.855 57.895 0.00 0.00 43.09 4.16
1353 4585 1.741770 CTACAGCTTCCACCACGCC 60.742 63.158 0.00 0.00 0.00 5.68
1354 4586 3.583276 TACAGCTTCCACCACGCCG 62.583 63.158 0.00 0.00 0.00 6.46
1410 4642 3.456365 GCGGCTGAGAGGCTGAGA 61.456 66.667 0.00 0.00 40.74 3.27
1524 4763 1.298339 GCGGCATAAACACGATGGC 60.298 57.895 0.00 0.00 44.26 4.40
1736 4975 4.500116 GCTCCCGCTCGACACCTC 62.500 72.222 0.00 0.00 0.00 3.85
1737 4976 4.180946 CTCCCGCTCGACACCTCG 62.181 72.222 0.00 0.00 41.65 4.63
1757 4996 4.394078 CGACCTGTCGCCGTTCGA 62.394 66.667 6.77 0.00 46.50 3.71
1787 5026 0.937304 CACGGCAGGTATGTGTATGC 59.063 55.000 0.00 0.00 37.95 3.14
1802 5041 0.601576 TATGCGCGGTGTTGTTCAGT 60.602 50.000 8.83 0.00 0.00 3.41
1990 5229 7.355017 TGAATCTCTGAAAGTTTTGACAATCG 58.645 34.615 0.00 0.00 33.76 3.34
1991 5230 6.867662 ATCTCTGAAAGTTTTGACAATCGT 57.132 33.333 0.00 0.00 33.76 3.73
1993 5232 5.815222 TCTCTGAAAGTTTTGACAATCGTGA 59.185 36.000 0.00 0.00 33.76 4.35
1996 5235 7.309177 TCTGAAAGTTTTGACAATCGTGAAAA 58.691 30.769 0.00 0.00 36.11 2.29
1997 5236 7.973388 TCTGAAAGTTTTGACAATCGTGAAAAT 59.027 29.630 0.00 0.00 39.80 1.82
2039 5278 3.552890 GGCAAGAATTTTCTGAAAGCGGT 60.553 43.478 2.75 0.00 37.65 5.68
2066 5305 9.651718 GTACTACATTTTCTGAAAGTGTCAAAG 57.348 33.333 27.44 22.22 35.22 2.77
2090 5329 3.818961 AAACTTGACATGATCAGTGCG 57.181 42.857 0.00 0.00 38.99 5.34
2168 5407 2.180769 CGTCGGAAGTGATCGGCA 59.819 61.111 0.00 0.00 0.00 5.69
2255 5494 6.367969 GGCGTTTAGAGTCTTGACTTTTATGA 59.632 38.462 0.00 0.00 0.00 2.15
2361 5603 5.412526 AAAACGACTTCGATGTTGCTTTA 57.587 34.783 16.51 0.00 43.02 1.85
2396 5638 7.599621 TCTTGGTTAAACTTGCATTCATGATTG 59.400 33.333 12.30 12.30 0.00 2.67
2414 5656 5.912892 TGATTGCTCGAGACCAATACAATA 58.087 37.500 18.75 1.69 32.20 1.90
2478 5720 4.410400 CGTGGGGAACAGGGGAGC 62.410 72.222 0.00 0.00 0.00 4.70
2617 5859 8.417106 TGCAACTTGAATTTTATTCACCACTAA 58.583 29.630 1.77 0.00 0.00 2.24
2627 5869 8.586570 TTTTATTCACCACTAAAATGTTGCAG 57.413 30.769 0.00 0.00 0.00 4.41
2638 5880 8.660373 CACTAAAATGTTGCAGTTTAACCAAAA 58.340 29.630 3.91 0.00 34.37 2.44
2639 5881 8.661257 ACTAAAATGTTGCAGTTTAACCAAAAC 58.339 29.630 3.91 0.00 46.61 2.43
2688 5930 6.107343 TCGCTACGATATACTCAGATTAGCT 58.893 40.000 0.00 0.00 0.00 3.32
2751 5994 5.334182 CGATCTGATTTCTGCCATTGATCAG 60.334 44.000 0.00 5.52 43.05 2.90
2816 7451 9.520515 AGAAGTAGGAACATGTATGATTTTTGT 57.479 29.630 0.00 0.00 0.00 2.83
2878 7513 0.892358 AAGACGAGGTGGACGTGCTA 60.892 55.000 8.99 0.00 43.97 3.49
2882 7517 1.446272 GAGGTGGACGTGCTAGTGC 60.446 63.158 8.99 0.00 40.20 4.40
3019 7655 4.554036 GGCCCGGCTCAGTCATCC 62.554 72.222 9.86 0.00 0.00 3.51
3037 7673 2.893398 GTCACCTCCTACAGCCCG 59.107 66.667 0.00 0.00 0.00 6.13
3042 7678 2.683933 CTCCTACAGCCCGTGGGT 60.684 66.667 6.82 0.00 46.24 4.51
3077 7713 4.643387 GCACCACTGGCCGAACCT 62.643 66.667 0.00 0.00 40.22 3.50
3105 7741 2.281484 GCTGGTCCTCGGCAACAA 60.281 61.111 0.00 0.00 46.73 2.83
3196 7832 2.127869 CGCCGGAGAGGATGAGGAA 61.128 63.158 5.05 0.00 45.00 3.36
3243 7879 4.885270 CGTTGGTGGGGTGGTGCA 62.885 66.667 0.00 0.00 0.00 4.57
3245 7881 4.885270 TTGGTGGGGTGGTGCACG 62.885 66.667 11.45 0.00 34.83 5.34
3272 7908 1.515304 GTCCTCTGCTCGTTCTCGC 60.515 63.158 0.00 0.00 36.96 5.03
3284 7920 0.594284 GTTCTCGCGGGGATTCTACG 60.594 60.000 5.94 0.00 0.00 3.51
3291 7927 1.749033 GGGGATTCTACGAGGGCAG 59.251 63.158 0.00 0.00 0.00 4.85
3365 8001 1.590259 GTCCTTCTCGCCGATGCTC 60.590 63.158 0.00 0.00 34.43 4.26
3461 8097 0.169672 CCTGGTGTGGTCGTACTACG 59.830 60.000 1.93 1.93 44.19 3.51
3462 8098 0.455633 CTGGTGTGGTCGTACTACGC 60.456 60.000 3.57 6.54 42.21 4.42
3467 8103 0.801251 GTGGTCGTACTACGCAGAGT 59.199 55.000 3.57 0.00 42.21 3.24
3469 8105 0.522915 GGTCGTACTACGCAGAGTGC 60.523 60.000 3.57 0.00 42.21 4.40
3472 8108 1.126421 CGTACTACGCAGAGTGCACG 61.126 60.000 12.01 0.95 45.36 5.34
3474 8110 1.092348 TACTACGCAGAGTGCACGAT 58.908 50.000 12.01 0.34 45.36 3.73
3481 8117 0.667487 CAGAGTGCACGATGTTCGGT 60.667 55.000 12.01 0.00 45.59 4.69
3484 8120 1.959226 GTGCACGATGTTCGGTGGT 60.959 57.895 0.00 0.00 45.59 4.16
3487 8123 1.352156 GCACGATGTTCGGTGGTCTC 61.352 60.000 1.69 0.00 45.59 3.36
3836 8473 1.210155 GCGTTGAGGCATGACAACC 59.790 57.895 18.13 11.26 41.95 3.77
3866 8503 3.466791 ATCATGGCGGAGGGCTTCG 62.467 63.158 0.00 0.00 42.94 3.79
3880 8517 1.712081 CTTCGAGCTTGGCATGTCG 59.288 57.895 0.00 14.52 0.00 4.35
3991 8628 2.425312 CGACTACATCAGCTTCCTCTGT 59.575 50.000 0.00 0.00 35.63 3.41
4023 8660 4.873129 CAGCCCCGACGATGTCCG 62.873 72.222 0.00 0.00 45.44 4.79
4234 8871 0.605319 GGTGGTTCGACATTGCTCCA 60.605 55.000 0.00 0.00 0.00 3.86
4306 8943 2.101582 GGCTTTCAGCTTCGGAGAGATA 59.898 50.000 0.00 0.00 41.99 1.98
4540 9353 5.621193 ACAAGTTACAGGCAGTAAATCACT 58.379 37.500 3.91 0.00 43.90 3.41
4572 9385 3.758554 GAGAATGTGTTTACATGGCACCT 59.241 43.478 0.00 0.00 46.54 4.00
4574 9387 2.949177 TGTGTTTACATGGCACCTCT 57.051 45.000 0.00 0.00 32.62 3.69
4575 9388 4.568072 ATGTGTTTACATGGCACCTCTA 57.432 40.909 0.00 0.00 45.54 2.43
4576 9389 4.359434 TGTGTTTACATGGCACCTCTAA 57.641 40.909 0.00 0.00 32.62 2.10
4577 9390 4.720046 TGTGTTTACATGGCACCTCTAAA 58.280 39.130 0.00 0.00 32.62 1.85
4578 9391 5.321102 TGTGTTTACATGGCACCTCTAAAT 58.679 37.500 0.00 0.00 32.62 1.40
4579 9392 5.414454 TGTGTTTACATGGCACCTCTAAATC 59.586 40.000 0.00 0.00 32.62 2.17
4580 9393 5.648092 GTGTTTACATGGCACCTCTAAATCT 59.352 40.000 0.00 0.00 0.00 2.40
4581 9394 5.880332 TGTTTACATGGCACCTCTAAATCTC 59.120 40.000 0.00 0.00 0.00 2.75
4582 9395 5.957771 TTACATGGCACCTCTAAATCTCT 57.042 39.130 0.00 0.00 0.00 3.10
4583 9396 4.148128 ACATGGCACCTCTAAATCTCTG 57.852 45.455 0.00 0.00 0.00 3.35
4584 9397 3.776969 ACATGGCACCTCTAAATCTCTGA 59.223 43.478 0.00 0.00 0.00 3.27
4585 9398 4.225942 ACATGGCACCTCTAAATCTCTGAA 59.774 41.667 0.00 0.00 0.00 3.02
4586 9399 5.104193 ACATGGCACCTCTAAATCTCTGAAT 60.104 40.000 0.00 0.00 0.00 2.57
4587 9400 5.028549 TGGCACCTCTAAATCTCTGAATC 57.971 43.478 0.00 0.00 0.00 2.52
4588 9401 4.718774 TGGCACCTCTAAATCTCTGAATCT 59.281 41.667 0.00 0.00 0.00 2.40
4589 9402 5.163364 TGGCACCTCTAAATCTCTGAATCTC 60.163 44.000 0.00 0.00 0.00 2.75
4590 9403 5.070313 GGCACCTCTAAATCTCTGAATCTCT 59.930 44.000 0.00 0.00 0.00 3.10
4591 9404 6.407979 GGCACCTCTAAATCTCTGAATCTCTT 60.408 42.308 0.00 0.00 0.00 2.85
4592 9405 7.047271 GCACCTCTAAATCTCTGAATCTCTTT 58.953 38.462 0.00 0.00 0.00 2.52
4593 9406 7.552330 GCACCTCTAAATCTCTGAATCTCTTTT 59.448 37.037 0.00 0.00 0.00 2.27
4594 9407 9.447157 CACCTCTAAATCTCTGAATCTCTTTTT 57.553 33.333 0.00 0.00 0.00 1.94
4631 9476 9.610705 TTAAATCTCTGAATCTCTTCTGAATGG 57.389 33.333 0.00 0.00 38.42 3.16
4646 9493 3.107601 TGAATGGAAGGGTAGACAGAGG 58.892 50.000 0.00 0.00 0.00 3.69
4662 9509 2.192979 GGCGGGCCTTCATCATCA 59.807 61.111 0.84 0.00 0.00 3.07
4684 9531 4.769345 AAATCTCTTCTCCATGTCCCTC 57.231 45.455 0.00 0.00 0.00 4.30
4700 9547 1.289066 CTCGACAACCTCGCCAAGA 59.711 57.895 0.00 0.00 42.62 3.02
4710 9557 2.224523 ACCTCGCCAAGAATGAAGTTCA 60.225 45.455 8.27 8.27 39.39 3.18
4713 9560 1.536766 CGCCAAGAATGAAGTTCAGCA 59.463 47.619 11.91 0.00 39.39 4.41
4757 9631 1.588082 GGCAATTGCAGACCACCTG 59.412 57.895 30.32 0.00 45.67 4.00
4795 9675 7.318141 CAAATTCTGTGTCTTATGATTTGGCT 58.682 34.615 0.00 0.00 0.00 4.75
4957 9839 9.331282 AGATAGCTTGTTACCATAACAAAGATC 57.669 33.333 13.53 14.18 39.36 2.75
4958 9840 9.109393 GATAGCTTGTTACCATAACAAAGATCA 57.891 33.333 13.53 1.49 39.36 2.92
4959 9841 7.383102 AGCTTGTTACCATAACAAAGATCAG 57.617 36.000 13.53 4.28 39.36 2.90
4960 9842 6.375455 AGCTTGTTACCATAACAAAGATCAGG 59.625 38.462 13.53 3.89 39.36 3.86
4961 9843 6.374333 GCTTGTTACCATAACAAAGATCAGGA 59.626 38.462 13.53 0.00 39.36 3.86
4962 9844 7.626452 GCTTGTTACCATAACAAAGATCAGGAC 60.626 40.741 13.53 0.00 39.36 3.85
4963 9845 6.177610 TGTTACCATAACAAAGATCAGGACC 58.822 40.000 0.00 0.00 0.00 4.46
4964 9846 6.012858 TGTTACCATAACAAAGATCAGGACCT 60.013 38.462 0.00 0.00 0.00 3.85
4965 9847 5.104259 ACCATAACAAAGATCAGGACCTC 57.896 43.478 0.00 0.00 0.00 3.85
4966 9848 4.122776 CCATAACAAAGATCAGGACCTCG 58.877 47.826 0.00 0.00 0.00 4.63
4967 9849 4.383118 CCATAACAAAGATCAGGACCTCGT 60.383 45.833 0.00 0.00 0.00 4.18
5049 9932 9.760926 TTATGAGTTGGCAGTAGATAGATAGAT 57.239 33.333 0.00 0.00 0.00 1.98
5051 9934 8.800370 TGAGTTGGCAGTAGATAGATAGATAG 57.200 38.462 0.00 0.00 0.00 2.08
5052 9935 8.606830 TGAGTTGGCAGTAGATAGATAGATAGA 58.393 37.037 0.00 0.00 0.00 1.98
5053 9936 9.627123 GAGTTGGCAGTAGATAGATAGATAGAT 57.373 37.037 0.00 0.00 0.00 1.98
5103 9988 9.019764 TCAACTAAAAGCTTCAATTTTTCGAAG 57.980 29.630 0.00 0.00 41.31 3.79
5187 10073 4.658901 AGGACCGGACCTTCAATTATACAT 59.341 41.667 20.47 0.00 36.86 2.29
5246 10132 5.186198 GGCCAGACCATCCAATATACATAC 58.814 45.833 0.00 0.00 38.86 2.39
5267 10153 8.258007 ACATACCCTGATATCCATATTAACACG 58.742 37.037 0.00 0.00 0.00 4.49
5290 10176 7.277319 CACGCTGATACTATATGAAGATGCAAT 59.723 37.037 0.00 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.175302 CTCTGCTGCTCGATCAGGTT 59.825 55.000 17.36 0.00 34.74 3.50
1 2 1.815196 CTCTGCTGCTCGATCAGGT 59.185 57.895 17.36 0.00 34.74 4.00
2 3 1.592131 GCTCTGCTGCTCGATCAGG 60.592 63.158 17.36 2.61 34.74 3.86
3 4 1.945169 CGCTCTGCTGCTCGATCAG 60.945 63.158 11.90 11.90 37.15 2.90
4 5 2.103736 CGCTCTGCTGCTCGATCA 59.896 61.111 0.00 0.00 0.00 2.92
5 6 1.943693 GACGCTCTGCTGCTCGATC 60.944 63.158 0.00 0.00 0.00 3.69
6 7 1.098129 TAGACGCTCTGCTGCTCGAT 61.098 55.000 0.00 0.00 0.00 3.59
7 8 1.710103 CTAGACGCTCTGCTGCTCGA 61.710 60.000 0.00 0.00 0.00 4.04
90 91 5.835113 AAACTATGAAGCCGTATGCATTT 57.165 34.783 3.54 0.00 44.83 2.32
262 2992 6.098679 GCAATGTTGTATGCAGTATGGAAAA 58.901 36.000 0.00 0.00 42.43 2.29
264 2994 4.097741 GGCAATGTTGTATGCAGTATGGAA 59.902 41.667 0.00 0.00 42.43 3.53
298 3028 1.886542 GGTTCACAAAAGCGGATTCCT 59.113 47.619 0.30 0.00 0.00 3.36
325 3055 6.893583 AGTACAAGCATGATTCTGAATAGGT 58.106 36.000 2.28 0.00 0.00 3.08
326 3056 8.768955 GTTAGTACAAGCATGATTCTGAATAGG 58.231 37.037 2.28 0.00 0.00 2.57
456 3186 2.731571 GGTGCTCGGGCTACATGGA 61.732 63.158 9.62 0.00 39.59 3.41
819 3952 9.465199 TCTTTTACCAAGTAACCCCATTTATAC 57.535 33.333 0.00 0.00 0.00 1.47
873 4088 0.465824 TTCCCGCTTCCGTTTTCCAA 60.466 50.000 0.00 0.00 0.00 3.53
944 4161 4.097286 GCCTAAAAACTTTGATGCCCGATA 59.903 41.667 0.00 0.00 0.00 2.92
958 4175 2.623416 ACTGTGCAGGAAGCCTAAAAAC 59.377 45.455 4.11 0.00 44.83 2.43
959 4176 2.944129 ACTGTGCAGGAAGCCTAAAAA 58.056 42.857 4.11 0.00 44.83 1.94
960 4177 2.656947 ACTGTGCAGGAAGCCTAAAA 57.343 45.000 4.11 0.00 44.83 1.52
961 4178 2.656947 AACTGTGCAGGAAGCCTAAA 57.343 45.000 4.11 0.00 44.83 1.85
962 4179 2.290071 GGTAACTGTGCAGGAAGCCTAA 60.290 50.000 4.11 0.00 44.83 2.69
963 4180 1.278127 GGTAACTGTGCAGGAAGCCTA 59.722 52.381 4.11 0.00 44.83 3.93
964 4181 0.036875 GGTAACTGTGCAGGAAGCCT 59.963 55.000 4.11 0.00 44.83 4.58
965 4182 0.960861 GGGTAACTGTGCAGGAAGCC 60.961 60.000 4.11 6.38 44.83 4.35
966 4183 0.036875 AGGGTAACTGTGCAGGAAGC 59.963 55.000 4.11 1.23 45.96 3.86
977 4194 2.679930 GCAGGTTAATCGCAGGGTAACT 60.680 50.000 0.00 0.00 31.20 2.24
981 4202 0.037590 TTGCAGGTTAATCGCAGGGT 59.962 50.000 5.61 0.00 36.91 4.34
1022 4254 1.487976 TGGCCAAGATGAGGATGAGAC 59.512 52.381 0.61 0.00 0.00 3.36
1026 4258 0.816825 CGGTGGCCAAGATGAGGATG 60.817 60.000 7.24 0.00 0.00 3.51
1371 4603 4.864334 GAGCCCTCCGCCACATGG 62.864 72.222 0.00 0.00 38.78 3.66
1435 4667 1.229529 TGGTCCCCTTGTCCTCCTC 60.230 63.158 0.00 0.00 0.00 3.71
1455 4687 1.084370 GCGTGTAGGTGGTCATGAGC 61.084 60.000 18.01 18.01 0.00 4.26
1507 4746 1.011242 CGCCATCGTGTTTATGCCG 60.011 57.895 0.00 0.00 0.00 5.69
1510 4749 1.011242 CGCCGCCATCGTGTTTATG 60.011 57.895 0.00 0.00 0.00 1.90
1511 4750 2.177580 CCGCCGCCATCGTGTTTAT 61.178 57.895 0.00 0.00 0.00 1.40
1512 4751 2.223200 TACCGCCGCCATCGTGTTTA 62.223 55.000 0.00 0.00 0.00 2.01
1513 4752 3.592856 TACCGCCGCCATCGTGTTT 62.593 57.895 0.00 0.00 0.00 2.83
1514 4753 4.071875 TACCGCCGCCATCGTGTT 62.072 61.111 0.00 0.00 0.00 3.32
1515 4754 4.508128 CTACCGCCGCCATCGTGT 62.508 66.667 0.00 0.00 0.00 4.49
1620 4859 4.969196 CTGCAGACACCCGTGCGT 62.969 66.667 8.42 0.00 42.96 5.24
1679 4918 1.915614 GAAGTACCTCGCCGTGACGA 61.916 60.000 6.54 0.00 40.36 4.20
1761 5000 3.460672 ATACCTGCCGTGGCCATCG 62.461 63.158 9.72 14.81 41.09 3.84
1762 5001 1.893808 CATACCTGCCGTGGCCATC 60.894 63.158 9.72 1.29 41.09 3.51
1763 5002 2.192979 CATACCTGCCGTGGCCAT 59.807 61.111 9.72 0.00 41.09 4.40
1764 5003 3.326578 ACATACCTGCCGTGGCCA 61.327 61.111 0.00 0.00 41.09 5.36
1765 5004 2.246761 TACACATACCTGCCGTGGCC 62.247 60.000 8.69 0.00 41.09 5.36
1777 5016 1.003108 CAACACCGCGCATACACATA 58.997 50.000 8.75 0.00 0.00 2.29
1787 5026 1.151777 ACTGACTGAACAACACCGCG 61.152 55.000 0.00 0.00 0.00 6.46
1879 5118 9.614792 AAAGAAAAGCTAGTAAGAAGAAACAGA 57.385 29.630 0.00 0.00 0.00 3.41
1964 5203 8.019669 CGATTGTCAAAACTTTCAGAGATTCAT 58.980 33.333 0.00 0.00 0.00 2.57
1965 5204 7.012327 ACGATTGTCAAAACTTTCAGAGATTCA 59.988 33.333 0.00 0.00 0.00 2.57
1966 5205 7.322222 CACGATTGTCAAAACTTTCAGAGATTC 59.678 37.037 0.00 0.00 0.00 2.52
1967 5206 7.012327 TCACGATTGTCAAAACTTTCAGAGATT 59.988 33.333 0.00 0.00 0.00 2.40
1968 5207 6.483307 TCACGATTGTCAAAACTTTCAGAGAT 59.517 34.615 0.00 0.00 0.00 2.75
1969 5208 5.815222 TCACGATTGTCAAAACTTTCAGAGA 59.185 36.000 0.00 0.00 0.00 3.10
1973 5212 8.472683 AATTTTCACGATTGTCAAAACTTTCA 57.527 26.923 0.00 0.00 0.00 2.69
1996 5235 9.374838 CTTGCCATAGCTTTTAGAATTTGAAAT 57.625 29.630 0.00 0.00 40.80 2.17
1997 5236 8.584157 TCTTGCCATAGCTTTTAGAATTTGAAA 58.416 29.630 0.00 0.00 40.80 2.69
2039 5278 8.725405 TTGACACTTTCAGAAAATGTAGTACA 57.275 30.769 9.92 5.24 34.94 2.90
2066 5305 4.913924 GCACTGATCATGTCAAGTTTTCAC 59.086 41.667 0.00 0.00 36.14 3.18
2090 5329 1.543802 CTCGAGATAGCCCTGTCCATC 59.456 57.143 6.58 0.00 0.00 3.51
2255 5494 7.687941 AACCGAACATAAGATTCAGTTCAAT 57.312 32.000 0.00 0.00 40.14 2.57
2279 5518 7.988937 AGCAGGGTTCAATTATCATAAGGATA 58.011 34.615 0.00 0.00 37.44 2.59
2294 5533 2.890311 CACCAACATTTAGCAGGGTTCA 59.110 45.455 0.00 0.00 0.00 3.18
2361 5603 6.267471 TGCAAGTTTAACCAAGATGAAGGATT 59.733 34.615 0.00 0.00 0.00 3.01
2396 5638 7.438459 ACTTATGTTATTGTATTGGTCTCGAGC 59.562 37.037 7.81 2.69 0.00 5.03
2414 5656 9.474313 ACAATAATAATCCACACCACTTATGTT 57.526 29.630 0.00 0.00 0.00 2.71
2490 5732 2.715005 CATACATTGCGCCACCGG 59.285 61.111 4.18 0.00 34.32 5.28
2617 5859 7.622893 ATGTTTTGGTTAAACTGCAACATTT 57.377 28.000 8.75 0.00 45.18 2.32
2623 5865 5.734720 TCCAAATGTTTTGGTTAAACTGCA 58.265 33.333 16.38 0.00 45.18 4.41
2627 5869 9.110502 TGGTTATTCCAAATGTTTTGGTTAAAC 57.889 29.630 16.38 16.55 44.12 2.01
2751 5994 8.986477 ACAAGAAAAATGTGCATATCTTTACC 57.014 30.769 0.00 0.00 0.00 2.85
2878 7513 4.101448 GGCCCGATGGACAGCACT 62.101 66.667 0.00 0.00 40.65 4.40
2908 7543 1.423794 GGAAGGTGACCTTGGTGGGA 61.424 60.000 23.60 0.00 44.82 4.37
2911 7546 0.320771 CGAGGAAGGTGACCTTGGTG 60.321 60.000 23.60 4.87 44.82 4.17
3010 7646 0.039764 AGGAGGTGACGGATGACTGA 59.960 55.000 0.00 0.00 0.00 3.41
3016 7652 1.043673 GGCTGTAGGAGGTGACGGAT 61.044 60.000 0.00 0.00 0.00 4.18
3019 7655 2.893398 GGGCTGTAGGAGGTGACG 59.107 66.667 0.00 0.00 0.00 4.35
3067 7703 4.382320 GGCGTGTAGGTTCGGCCA 62.382 66.667 2.24 0.00 44.62 5.36
3085 7721 4.329545 TTGCCGAGGACCAGCCAC 62.330 66.667 0.00 0.00 40.02 5.01
3177 7813 3.610669 CCTCATCCTCTCCGGCGG 61.611 72.222 22.51 22.51 0.00 6.13
3180 7816 0.034616 GCATTCCTCATCCTCTCCGG 59.965 60.000 0.00 0.00 0.00 5.14
3184 7820 1.138568 CCTGGCATTCCTCATCCTCT 58.861 55.000 0.00 0.00 0.00 3.69
3228 7864 4.885270 CGTGCACCACCCCACCAA 62.885 66.667 12.15 0.00 0.00 3.67
3245 7881 3.112709 GCAGAGGACGACGTTGCC 61.113 66.667 10.55 5.43 0.00 4.52
3249 7885 2.185103 GAACGAGCAGAGGACGACGT 62.185 60.000 0.00 0.00 35.56 4.34
3257 7893 2.578178 CCGCGAGAACGAGCAGAG 60.578 66.667 8.23 0.00 42.66 3.35
3272 7908 2.088674 CTGCCCTCGTAGAATCCCCG 62.089 65.000 0.00 0.00 34.09 5.73
3284 7920 4.436998 CACCGTCGACCTGCCCTC 62.437 72.222 10.58 0.00 0.00 4.30
3335 7971 2.358737 AAGGACAAAGCCGGCGAG 60.359 61.111 23.20 17.39 0.00 5.03
3442 8078 0.169672 CGTAGTACGACCACACCAGG 59.830 60.000 17.85 0.00 46.05 4.45
3443 8079 0.455633 GCGTAGTACGACCACACCAG 60.456 60.000 26.29 0.00 46.05 4.00
3461 8097 1.417592 CGAACATCGTGCACTCTGC 59.582 57.895 16.19 0.00 45.29 4.26
3462 8098 0.667487 ACCGAACATCGTGCACTCTG 60.667 55.000 16.19 13.99 38.40 3.35
3467 8103 1.666553 GACCACCGAACATCGTGCA 60.667 57.895 0.00 0.00 38.40 4.57
3469 8105 1.071019 CGAGACCACCGAACATCGTG 61.071 60.000 0.00 0.00 38.40 4.35
3472 8108 1.810030 GGCGAGACCACCGAACATC 60.810 63.158 0.00 0.00 38.86 3.06
3474 8110 3.228017 TGGCGAGACCACCGAACA 61.228 61.111 0.00 0.00 46.36 3.18
3553 8189 3.525545 GGCCCCCGAGACGAGTAC 61.526 72.222 0.00 0.00 0.00 2.73
3692 8328 2.213499 GGAGATCATCGCGAAATGGTT 58.787 47.619 15.24 0.00 0.00 3.67
3757 8393 2.124736 GGGTGCCGCTGCTTGATA 60.125 61.111 0.70 0.00 38.71 2.15
3821 8457 2.324330 CGCGGTTGTCATGCCTCAA 61.324 57.895 0.00 0.00 0.00 3.02
3866 8503 2.789917 CTGCGACATGCCAAGCTC 59.210 61.111 0.00 0.00 45.60 4.09
4023 8660 2.043852 TCTCTCCGGTGGCTCCTC 60.044 66.667 0.00 0.00 0.00 3.71
4038 8675 2.360852 GTGCAGCCTGGCATGTCT 60.361 61.111 22.65 0.00 46.92 3.41
4234 8871 1.133009 ACAACCTCCTGTGTCTCTCCT 60.133 52.381 0.00 0.00 0.00 3.69
4306 8943 1.007238 TCTAGGCTGCCAGTAAGGACT 59.993 52.381 22.65 0.00 41.22 3.85
4357 8997 3.443045 CATGTGGTTGAGGGCGCC 61.443 66.667 21.18 21.18 0.00 6.53
4362 9002 3.415212 ACACTTGATCATGTGGTTGAGG 58.585 45.455 32.93 15.50 39.80 3.86
4363 9003 4.996758 TGTACACTTGATCATGTGGTTGAG 59.003 41.667 32.93 16.06 39.80 3.02
4595 9408 8.055279 AGATTCAGAGATTTAATCCGCAAAAA 57.945 30.769 0.78 0.00 31.35 1.94
4596 9409 7.554118 AGAGATTCAGAGATTTAATCCGCAAAA 59.446 33.333 0.78 0.00 31.35 2.44
4597 9410 7.050377 AGAGATTCAGAGATTTAATCCGCAAA 58.950 34.615 0.78 0.00 31.35 3.68
4598 9411 6.586344 AGAGATTCAGAGATTTAATCCGCAA 58.414 36.000 0.78 0.00 31.35 4.85
4599 9412 6.166984 AGAGATTCAGAGATTTAATCCGCA 57.833 37.500 0.78 0.00 31.35 5.69
4600 9413 6.928492 AGAAGAGATTCAGAGATTTAATCCGC 59.072 38.462 0.78 0.00 31.35 5.54
4601 9414 8.140628 TCAGAAGAGATTCAGAGATTTAATCCG 58.859 37.037 0.78 0.00 31.35 4.18
4602 9415 9.829507 TTCAGAAGAGATTCAGAGATTTAATCC 57.170 33.333 0.78 0.00 31.35 3.01
4605 9418 9.610705 CCATTCAGAAGAGATTCAGAGATTTAA 57.389 33.333 0.00 0.00 0.00 1.52
4631 9476 1.677637 CCCGCCTCTGTCTACCCTTC 61.678 65.000 0.00 0.00 0.00 3.46
4646 9493 0.817013 TTTTGATGATGAAGGCCCGC 59.183 50.000 0.00 0.00 0.00 6.13
4662 9509 4.383552 CGAGGGACATGGAGAAGAGATTTT 60.384 45.833 0.00 0.00 0.00 1.82
4700 9547 4.280174 ACTTGAGCAATGCTGAACTTCATT 59.720 37.500 14.48 0.00 39.88 2.57
4710 9557 2.432146 TCTCGGATACTTGAGCAATGCT 59.568 45.455 7.79 7.79 43.88 3.79
4713 9560 5.986135 GTGTAATCTCGGATACTTGAGCAAT 59.014 40.000 0.00 0.00 32.20 3.56
4757 9631 8.284693 AGACACAGAATTTGCATTTTATTTTGC 58.715 29.630 0.00 0.00 39.33 3.68
4795 9675 3.243737 CCATACCGTGCAAGCTATCTACA 60.244 47.826 0.00 0.00 0.00 2.74
4957 9839 0.393077 ACAAAGGTGACGAGGTCCTG 59.607 55.000 0.00 0.00 0.00 3.86
4958 9840 1.129058 AACAAAGGTGACGAGGTCCT 58.871 50.000 0.00 0.00 0.00 3.85
4959 9841 2.410939 GTAACAAAGGTGACGAGGTCC 58.589 52.381 0.00 0.00 0.00 4.46
4960 9842 2.410939 GGTAACAAAGGTGACGAGGTC 58.589 52.381 0.00 0.00 0.00 3.85
4961 9843 2.538512 GGTAACAAAGGTGACGAGGT 57.461 50.000 0.00 0.00 0.00 3.85
5049 9932 6.433093 TGGTTATCGTGCAAGCTATCTATCTA 59.567 38.462 0.00 0.00 0.00 1.98
5050 9933 5.243954 TGGTTATCGTGCAAGCTATCTATCT 59.756 40.000 0.00 0.00 0.00 1.98
5051 9934 5.470368 TGGTTATCGTGCAAGCTATCTATC 58.530 41.667 0.00 0.00 0.00 2.08
5052 9935 5.468540 TGGTTATCGTGCAAGCTATCTAT 57.531 39.130 0.00 0.00 0.00 1.98
5053 9936 4.929819 TGGTTATCGTGCAAGCTATCTA 57.070 40.909 0.00 0.00 0.00 1.98
5054 9937 3.819564 TGGTTATCGTGCAAGCTATCT 57.180 42.857 0.00 0.00 0.00 1.98
5055 9938 5.007626 TGAAATGGTTATCGTGCAAGCTATC 59.992 40.000 0.00 0.00 0.00 2.08
5056 9939 4.881273 TGAAATGGTTATCGTGCAAGCTAT 59.119 37.500 0.00 0.00 0.00 2.97
5116 10001 5.403897 TGAAACACGAGAAATGAACTGAC 57.596 39.130 0.00 0.00 0.00 3.51
5246 10132 5.582269 CAGCGTGTTAATATGGATATCAGGG 59.418 44.000 4.83 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.