Multiple sequence alignment - TraesCS2A01G371000

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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 TraesCS2A01G371000 chr2A 100.000 3729 0 0 1 3729 613479022 613475294 0.000000e+00 6887.0
1 TraesCS2A01G371000 chr2A 85.833 480 48 14 125 599 505212736 505212272 3.350000e-135 492.0
2 TraesCS2A01G371000 chr2A 83.065 372 59 4 2360 2729 613699753 613699384 5.970000e-88 335.0
3 TraesCS2A01G371000 chr2A 82.078 385 69 0 2345 2729 613689022 613688638 2.780000e-86 329.0
4 TraesCS2A01G371000 chr2A 94.444 54 3 0 3 56 505212789 505212736 2.390000e-12 84.2
5 TraesCS2A01G371000 chr2D 88.626 2453 168 50 601 2975 472132211 472129792 0.000000e+00 2881.0
6 TraesCS2A01G371000 chr2D 85.832 607 50 15 3 599 562222518 562223098 2.460000e-171 612.0
7 TraesCS2A01G371000 chr2D 82.480 371 63 2 2360 2729 472441952 472441583 1.290000e-84 324.0
8 TraesCS2A01G371000 chr2D 81.989 372 63 4 2360 2729 472229095 472228726 2.800000e-81 313.0
9 TraesCS2A01G371000 chr2D 81.116 233 30 8 5 229 498107839 498107613 1.380000e-39 174.0
10 TraesCS2A01G371000 chr2B 91.275 1318 90 11 1455 2753 551449802 551448491 0.000000e+00 1773.0
11 TraesCS2A01G371000 chr2B 86.405 765 58 17 663 1397 551451652 551450904 0.000000e+00 795.0
12 TraesCS2A01G371000 chr2B 92.537 268 13 2 2397 2664 551446416 551446156 9.780000e-101 377.0
13 TraesCS2A01G371000 chr2B 83.679 386 60 3 2345 2729 551398795 551398412 9.850000e-96 361.0
14 TraesCS2A01G371000 chr2B 82.796 372 64 0 2358 2729 551564619 551564248 2.150000e-87 333.0
15 TraesCS2A01G371000 chr2B 85.507 69 7 3 600 665 551398011 551397943 6.680000e-08 69.4
16 TraesCS2A01G371000 chr6A 94.960 754 36 2 2977 3728 77773682 77774435 0.000000e+00 1181.0
17 TraesCS2A01G371000 chr6A 84.711 242 23 8 1 231 467921511 467921749 2.900000e-56 230.0
18 TraesCS2A01G371000 chr5A 93.891 753 44 2 2977 3728 32195986 32196737 0.000000e+00 1134.0
19 TraesCS2A01G371000 chr5A 84.298 242 24 8 1 231 163504624 163504386 1.350000e-54 224.0
20 TraesCS2A01G371000 chr5A 89.744 117 5 2 242 358 163504315 163504206 3.880000e-30 143.0
21 TraesCS2A01G371000 chr1A 90.849 754 66 3 2977 3728 242698801 242698049 0.000000e+00 1007.0
22 TraesCS2A01G371000 chr1A 89.065 759 70 11 2977 3728 34270154 34270906 0.000000e+00 929.0
23 TraesCS2A01G371000 chr3D 90.716 754 67 3 2977 3728 104126816 104126064 0.000000e+00 1002.0
24 TraesCS2A01G371000 chr6B 90.426 752 68 2 2977 3728 157944761 157945508 0.000000e+00 987.0
25 TraesCS2A01G371000 chr6B 84.519 239 25 8 1 229 507881616 507881852 3.750000e-55 226.0
26 TraesCS2A01G371000 chr6B 89.516 124 4 4 237 358 507881918 507882034 8.340000e-32 148.0
27 TraesCS2A01G371000 chr7B 88.684 760 81 5 2972 3728 479625672 479626429 0.000000e+00 922.0
28 TraesCS2A01G371000 chr6D 88.771 757 76 9 2976 3727 285745527 285746279 0.000000e+00 918.0
29 TraesCS2A01G371000 chr3A 88.669 759 73 11 2976 3728 742367575 742366824 0.000000e+00 913.0
30 TraesCS2A01G371000 chr3A 84.647 241 24 7 1 231 275644007 275644244 1.040000e-55 228.0
31 TraesCS2A01G371000 chr3B 85.417 480 50 13 125 599 829806014 829805550 7.240000e-132 481.0
32 TraesCS2A01G371000 chr3B 85.417 480 50 13 125 599 829809780 829809316 7.240000e-132 481.0
33 TraesCS2A01G371000 chr3B 85.774 239 22 7 1 229 259144224 259144460 3.720000e-60 243.0
34 TraesCS2A01G371000 chr3B 89.516 124 4 4 237 358 259144526 259144642 8.340000e-32 148.0
35 TraesCS2A01G371000 chr3B 94.444 54 3 0 3 56 829806067 829806014 2.390000e-12 84.2
36 TraesCS2A01G371000 chr3B 94.444 54 3 0 3 56 829809833 829809780 2.390000e-12 84.2
37 TraesCS2A01G371000 chrUn 85.774 239 22 7 1 229 22083193 22082957 3.720000e-60 243.0
38 TraesCS2A01G371000 chrUn 94.444 54 3 0 3 56 184606314 184606261 2.390000e-12 84.2
39 TraesCS2A01G371000 chr4A 84.519 239 24 7 3 231 15529385 15529150 1.350000e-54 224.0
40 TraesCS2A01G371000 chr7A 81.008 258 39 9 1120 1369 68211431 68211686 2.940000e-46 196.0
41 TraesCS2A01G371000 chr7A 96.000 50 2 0 3 52 456203992 456204041 8.580000e-12 82.4
42 TraesCS2A01G371000 chr1D 90.598 117 4 2 242 358 249059379 249059270 8.340000e-32 148.0


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 TraesCS2A01G371000 chr2A 613475294 613479022 3728 True 6887.000000 6887 100.000000 1 3729 1 chr2A.!!$R1 3728
1 TraesCS2A01G371000 chr2A 505212272 505212789 517 True 288.100000 492 90.138500 3 599 2 chr2A.!!$R4 596
2 TraesCS2A01G371000 chr2D 472129792 472132211 2419 True 2881.000000 2881 88.626000 601 2975 1 chr2D.!!$R1 2374
3 TraesCS2A01G371000 chr2D 562222518 562223098 580 False 612.000000 612 85.832000 3 599 1 chr2D.!!$F1 596
4 TraesCS2A01G371000 chr2B 551446156 551451652 5496 True 981.666667 1773 90.072333 663 2753 3 chr2B.!!$R3 2090
5 TraesCS2A01G371000 chr2B 551397943 551398795 852 True 215.200000 361 84.593000 600 2729 2 chr2B.!!$R2 2129
6 TraesCS2A01G371000 chr6A 77773682 77774435 753 False 1181.000000 1181 94.960000 2977 3728 1 chr6A.!!$F1 751
7 TraesCS2A01G371000 chr5A 32195986 32196737 751 False 1134.000000 1134 93.891000 2977 3728 1 chr5A.!!$F1 751
8 TraesCS2A01G371000 chr1A 242698049 242698801 752 True 1007.000000 1007 90.849000 2977 3728 1 chr1A.!!$R1 751
9 TraesCS2A01G371000 chr1A 34270154 34270906 752 False 929.000000 929 89.065000 2977 3728 1 chr1A.!!$F1 751
10 TraesCS2A01G371000 chr3D 104126064 104126816 752 True 1002.000000 1002 90.716000 2977 3728 1 chr3D.!!$R1 751
11 TraesCS2A01G371000 chr6B 157944761 157945508 747 False 987.000000 987 90.426000 2977 3728 1 chr6B.!!$F1 751
12 TraesCS2A01G371000 chr7B 479625672 479626429 757 False 922.000000 922 88.684000 2972 3728 1 chr7B.!!$F1 756
13 TraesCS2A01G371000 chr6D 285745527 285746279 752 False 918.000000 918 88.771000 2976 3727 1 chr6D.!!$F1 751
14 TraesCS2A01G371000 chr3A 742366824 742367575 751 True 913.000000 913 88.669000 2976 3728 1 chr3A.!!$R1 752
15 TraesCS2A01G371000 chr3B 829805550 829809833 4283 True 282.600000 481 89.930500 3 599 4 chr3B.!!$R1 596

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
504 4274 0.107081 TCCTTGTTGGTGGTACGGTG 59.893 55.0 0.00 0.00 37.07 4.94 F
505 4275 0.107081 CCTTGTTGGTGGTACGGTGA 59.893 55.0 0.00 0.00 0.00 4.02 F
786 4576 0.166814 CACTCTACAAAAGCTGCGGC 59.833 55.0 10.33 10.33 39.06 6.53 F
2300 7185 0.535102 AGTTCCTCCAACGGCAACAG 60.535 55.0 0.00 0.00 40.32 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2316 7201 0.602905 AGGAAGAAAGTTGGCGTCGG 60.603 55.000 0.00 0.00 0.00 4.79 R
2430 7319 1.075698 TCTCGAAGTCCCTGAGGAACT 59.924 52.381 0.00 0.00 46.38 3.01 R
2691 7580 0.100861 CTCGCCTTCGGAGAAGTACC 59.899 60.000 8.70 0.00 45.90 3.34 R
3394 9405 1.130054 ACCCTCCACATGCAGAGTGT 61.130 55.000 17.64 3.65 35.24 3.55 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
39 40 1.003116 GCAAGTATCAGCTTCCATGCG 60.003 52.381 0.00 0.00 38.13 4.73
59 60 3.431725 GCTTGCGTACCTGCACCC 61.432 66.667 0.00 0.00 46.25 4.61
60 61 2.347490 CTTGCGTACCTGCACCCT 59.653 61.111 0.00 0.00 46.25 4.34
78 79 3.230134 CCCTTCCAGTTTTCATGGTCAA 58.770 45.455 0.00 0.00 39.01 3.18
79 80 3.834231 CCCTTCCAGTTTTCATGGTCAAT 59.166 43.478 0.00 0.00 39.01 2.57
80 81 5.016173 CCCTTCCAGTTTTCATGGTCAATA 58.984 41.667 0.00 0.00 39.01 1.90
186 188 7.943413 ATTTGATCAGTCTCTATCATGTTCG 57.057 36.000 0.00 0.00 32.40 3.95
187 189 4.864633 TGATCAGTCTCTATCATGTTCGC 58.135 43.478 0.00 0.00 0.00 4.70
188 190 4.339247 TGATCAGTCTCTATCATGTTCGCA 59.661 41.667 0.00 0.00 0.00 5.10
197 199 6.486993 TCTCTATCATGTTCGCACTATACTGT 59.513 38.462 0.00 0.00 0.00 3.55
333 4103 3.276857 TCTGCTCTAGGTAACAGTACGG 58.723 50.000 0.00 0.00 41.41 4.02
346 4116 2.811747 TACGGGCATGCGTGAACG 60.812 61.111 12.44 15.03 43.27 3.95
357 4127 1.068895 TGCGTGAACGGTAGAAAAGGA 59.931 47.619 4.84 0.00 40.23 3.36
370 4140 4.779993 AGAAAAGGAGAGGTGTGAAGTT 57.220 40.909 0.00 0.00 0.00 2.66
377 4147 3.141398 GAGAGGTGTGAAGTTCATTGCA 58.859 45.455 9.18 0.00 0.00 4.08
378 4148 3.755378 GAGAGGTGTGAAGTTCATTGCAT 59.245 43.478 9.18 0.17 0.00 3.96
380 4150 2.485426 AGGTGTGAAGTTCATTGCATCG 59.515 45.455 9.18 0.00 0.00 3.84
385 4155 3.058983 GTGAAGTTCATTGCATCGTGACA 60.059 43.478 9.18 0.00 0.00 3.58
461 4231 3.562635 CGAAGCAAAGACGACCCC 58.437 61.111 0.00 0.00 0.00 4.95
504 4274 0.107081 TCCTTGTTGGTGGTACGGTG 59.893 55.000 0.00 0.00 37.07 4.94
505 4275 0.107081 CCTTGTTGGTGGTACGGTGA 59.893 55.000 0.00 0.00 0.00 4.02
506 4276 1.223187 CTTGTTGGTGGTACGGTGAC 58.777 55.000 0.00 0.00 0.00 3.67
551 4321 4.742274 CGGACACGGACAAAGACA 57.258 55.556 0.00 0.00 36.18 3.41
553 4323 1.219522 CGGACACGGACAAAGACACC 61.220 60.000 0.00 0.00 36.18 4.16
554 4324 0.179067 GGACACGGACAAAGACACCA 60.179 55.000 0.00 0.00 0.00 4.17
567 4337 0.242825 GACACCATCCACGTCGAGAA 59.757 55.000 0.00 0.00 0.00 2.87
590 4360 3.494924 CGGTCATATCAAGGCCAAGATCA 60.495 47.826 12.62 2.26 0.00 2.92
599 4369 1.820906 GCCAAGATCATGCGCCTCA 60.821 57.895 4.18 0.00 0.00 3.86
600 4370 1.170919 GCCAAGATCATGCGCCTCAT 61.171 55.000 4.18 0.00 35.31 2.90
601 4371 1.315690 CCAAGATCATGCGCCTCATT 58.684 50.000 4.18 0.00 31.79 2.57
602 4372 1.266175 CCAAGATCATGCGCCTCATTC 59.734 52.381 4.18 0.00 31.79 2.67
603 4373 2.219458 CAAGATCATGCGCCTCATTCT 58.781 47.619 4.18 0.00 31.79 2.40
604 4374 3.396560 CAAGATCATGCGCCTCATTCTA 58.603 45.455 4.18 0.00 31.79 2.10
605 4375 3.037431 AGATCATGCGCCTCATTCTAC 57.963 47.619 4.18 0.00 31.79 2.59
606 4376 2.072298 GATCATGCGCCTCATTCTACC 58.928 52.381 4.18 0.00 31.79 3.18
607 4377 0.249447 TCATGCGCCTCATTCTACCG 60.249 55.000 4.18 0.00 31.79 4.02
608 4378 0.249447 CATGCGCCTCATTCTACCGA 60.249 55.000 4.18 0.00 31.79 4.69
609 4379 0.681733 ATGCGCCTCATTCTACCGAT 59.318 50.000 4.18 0.00 29.16 4.18
621 4391 6.688578 TCATTCTACCGATAATTGTAGCCTC 58.311 40.000 0.00 0.00 35.50 4.70
622 4392 6.266786 TCATTCTACCGATAATTGTAGCCTCA 59.733 38.462 0.00 0.00 35.50 3.86
623 4393 5.707242 TCTACCGATAATTGTAGCCTCAG 57.293 43.478 0.00 0.00 35.50 3.35
625 4395 2.224305 ACCGATAATTGTAGCCTCAGCC 60.224 50.000 0.00 0.00 41.25 4.85
627 4397 3.321497 CGATAATTGTAGCCTCAGCCTC 58.679 50.000 0.00 0.00 41.25 4.70
628 4398 2.890808 TAATTGTAGCCTCAGCCTCG 57.109 50.000 0.00 0.00 41.25 4.63
629 4399 0.905357 AATTGTAGCCTCAGCCTCGT 59.095 50.000 0.00 0.00 41.25 4.18
670 4440 4.367023 ACGCGCCGCTTTGGAGTA 62.367 61.111 5.73 0.00 42.00 2.59
671 4441 3.554692 CGCGCCGCTTTGGAGTAG 61.555 66.667 7.78 0.00 42.00 2.57
673 4443 1.153706 GCGCCGCTTTGGAGTAGTA 60.154 57.895 0.00 0.00 42.00 1.82
709 4496 3.364889 CGCAGTAGGTGGAATCGATAA 57.635 47.619 0.00 0.00 0.00 1.75
722 4509 0.179067 TCGATAATGGTCAACGGCCC 60.179 55.000 0.00 0.00 0.00 5.80
724 4511 1.153046 ATAATGGTCAACGGCCCGG 60.153 57.895 8.57 0.00 0.00 5.73
754 4544 1.039068 CCTCTCGCCACATCTCATCT 58.961 55.000 0.00 0.00 0.00 2.90
761 4551 2.100418 CGCCACATCTCATCTCTTCTCA 59.900 50.000 0.00 0.00 0.00 3.27
762 4552 3.719924 GCCACATCTCATCTCTTCTCAG 58.280 50.000 0.00 0.00 0.00 3.35
764 4554 4.382901 GCCACATCTCATCTCTTCTCAGTT 60.383 45.833 0.00 0.00 0.00 3.16
765 4555 5.350633 CCACATCTCATCTCTTCTCAGTTC 58.649 45.833 0.00 0.00 0.00 3.01
766 4556 5.127519 CCACATCTCATCTCTTCTCAGTTCT 59.872 44.000 0.00 0.00 0.00 3.01
767 4557 6.267817 CACATCTCATCTCTTCTCAGTTCTC 58.732 44.000 0.00 0.00 0.00 2.87
768 4558 5.951148 ACATCTCATCTCTTCTCAGTTCTCA 59.049 40.000 0.00 0.00 0.00 3.27
786 4576 0.166814 CACTCTACAAAAGCTGCGGC 59.833 55.000 10.33 10.33 39.06 6.53
823 4613 2.579684 CTACACCCTTCCAGCTCGCC 62.580 65.000 0.00 0.00 0.00 5.54
858 4648 3.372554 GACCACCTCGGCTGCTACC 62.373 68.421 0.00 0.00 39.03 3.18
859 4649 3.077556 CCACCTCGGCTGCTACCT 61.078 66.667 0.00 0.00 0.00 3.08
860 4650 2.185350 CACCTCGGCTGCTACCTG 59.815 66.667 0.00 0.00 0.00 4.00
861 4651 3.775654 ACCTCGGCTGCTACCTGC 61.776 66.667 0.00 0.00 43.25 4.85
874 4664 1.002251 CTACCTGCTAGTGCTAGACGC 60.002 57.143 10.17 0.00 40.48 5.19
912 4702 1.635487 CCTCCTTCCATCAGGGTTTGA 59.365 52.381 0.00 0.00 40.85 2.69
956 4746 4.559502 GCTTTTGGATCCAAGTTCAGGTTC 60.560 45.833 25.69 6.76 37.24 3.62
963 4753 1.734465 CCAAGTTCAGGTTCGATCTGC 59.266 52.381 10.38 0.47 32.63 4.26
964 4754 2.416747 CAAGTTCAGGTTCGATCTGCA 58.583 47.619 10.38 0.00 32.63 4.41
966 4756 2.417719 AGTTCAGGTTCGATCTGCAAC 58.582 47.619 10.38 13.36 32.63 4.17
967 4757 2.037772 AGTTCAGGTTCGATCTGCAACT 59.962 45.455 17.57 17.57 32.86 3.16
968 4758 2.370281 TCAGGTTCGATCTGCAACTC 57.630 50.000 10.38 0.00 32.63 3.01
969 4759 1.066858 TCAGGTTCGATCTGCAACTCC 60.067 52.381 10.38 0.00 32.63 3.85
1009 4816 3.624777 GGAAGCTTGATCATGGAAGGAA 58.375 45.455 2.10 0.00 0.00 3.36
1010 4817 3.631227 GGAAGCTTGATCATGGAAGGAAG 59.369 47.826 2.10 0.00 0.00 3.46
1035 4854 2.028476 TCCCTCGAACACAAGGTACATG 60.028 50.000 0.00 0.00 0.00 3.21
1066 4885 5.635700 GCCGTATCTCCATGTATTTCTTCTC 59.364 44.000 0.00 0.00 0.00 2.87
1077 4896 1.996292 TTTCTTCTCGCCGATCAGTG 58.004 50.000 0.00 0.00 0.00 3.66
1117 4937 2.793946 GCTATGTGCTGGCGTTGG 59.206 61.111 0.00 0.00 38.95 3.77
1118 4938 2.793946 CTATGTGCTGGCGTTGGC 59.206 61.111 0.00 0.00 38.90 4.52
1398 6247 6.493189 TTTCCTATTTGGGGCATTTTATCC 57.507 37.500 0.00 0.00 36.20 2.59
1402 6251 1.384525 TTGGGGCATTTTATCCGTCG 58.615 50.000 0.00 0.00 0.00 5.12
1419 6268 2.032290 CGTCGCTGTCATACTATTCCGA 60.032 50.000 0.00 0.00 0.00 4.55
1422 6271 3.881089 TCGCTGTCATACTATTCCGAAGA 59.119 43.478 0.00 0.00 0.00 2.87
1444 6300 6.037098 AGAATAGCTTGTTTAGTAGACTGCG 58.963 40.000 0.00 0.00 0.00 5.18
1451 6307 6.700520 GCTTGTTTAGTAGACTGCGGTATTAT 59.299 38.462 0.00 0.00 0.00 1.28
1464 6330 3.066481 GCGGTATTATACTCCCTCCGATC 59.934 52.174 2.21 0.00 38.96 3.69
1465 6331 4.525024 CGGTATTATACTCCCTCCGATCT 58.475 47.826 2.21 0.00 38.96 2.75
1478 6344 6.791371 TCCCTCCGATCTATATTAACTGTCT 58.209 40.000 0.00 0.00 0.00 3.41
1644 6512 3.007635 GGTTTAACTCCCGGTGATGAAG 58.992 50.000 0.00 0.00 0.00 3.02
1691 6559 7.375017 CGTTTATTTTCGAGTGTTTAGCTTGTT 59.625 33.333 0.00 0.00 0.00 2.83
1694 6562 3.188159 TCGAGTGTTTAGCTTGTTGGT 57.812 42.857 0.00 0.00 0.00 3.67
1766 6638 2.632512 GTTTCATTGCTCTCCCCCAAAA 59.367 45.455 0.00 0.00 0.00 2.44
1769 6641 2.042842 TCATTGCTCTCCCCCAAAATGA 59.957 45.455 0.00 0.00 33.02 2.57
1770 6642 2.692709 TTGCTCTCCCCCAAAATGAA 57.307 45.000 0.00 0.00 0.00 2.57
1797 6670 7.486407 AAAAAGATGGCCATTTTCAGAGTAT 57.514 32.000 21.84 0.03 0.00 2.12
1808 6681 2.093306 TCAGAGTATTGCCAACCGTG 57.907 50.000 0.00 0.00 0.00 4.94
1822 6695 4.686554 GCCAACCGTGCAATTTTAAACATA 59.313 37.500 0.00 0.00 0.00 2.29
1879 6752 3.544684 GCTGACCCATCAACATGTCATA 58.455 45.455 0.00 0.00 37.14 2.15
1883 6756 5.944135 TGACCCATCAACATGTCATATCAT 58.056 37.500 0.00 0.00 33.09 2.45
1886 6759 4.521256 CCCATCAACATGTCATATCATGCA 59.479 41.667 0.00 0.00 46.15 3.96
1892 6765 7.641760 TCAACATGTCATATCATGCACATAAC 58.358 34.615 0.00 0.00 46.15 1.89
1971 6844 3.000041 TGCTTAACTAATCAGTGCGGTG 59.000 45.455 0.00 0.00 34.36 4.94
1984 6857 3.308053 CAGTGCGGTGTCATCTATTCAAG 59.692 47.826 0.00 0.00 0.00 3.02
2002 6875 7.814264 ATTCAAGATTATCCTTAAGCACCAG 57.186 36.000 0.00 0.00 0.00 4.00
2003 6876 5.126067 TCAAGATTATCCTTAAGCACCAGC 58.874 41.667 0.00 0.00 42.56 4.85
2017 6890 2.150424 CCAGCTGGTACAAACGACG 58.850 57.895 25.53 0.00 38.70 5.12
2023 6896 2.066262 CTGGTACAAACGACGCTGAAT 58.934 47.619 4.68 0.00 38.70 2.57
2150 7023 2.281761 AAACAGGGCCTGCAGACG 60.282 61.111 33.04 9.27 34.37 4.18
2293 7178 4.868171 TCGATCAAATAAGTTCCTCCAACG 59.132 41.667 0.00 0.00 40.32 4.10
2300 7185 0.535102 AGTTCCTCCAACGGCAACAG 60.535 55.000 0.00 0.00 40.32 3.16
2316 7201 4.142513 GGCAACAGAAAAGAGGTCATGATC 60.143 45.833 0.00 0.00 0.00 2.92
2358 7247 1.581447 GGCCGCAGTTTTTCAGGAG 59.419 57.895 0.00 0.00 0.00 3.69
2395 7284 2.254350 CTGAACGGCGTCGACAGA 59.746 61.111 26.55 5.50 41.91 3.41
2399 7288 3.553437 AACGGCGTCGACAGACTGG 62.553 63.158 20.03 0.00 44.93 4.00
2773 7673 2.658325 CTGTTTTGTTGCGCTTATCTGC 59.342 45.455 9.73 0.00 0.00 4.26
2774 7674 1.985684 GTTTTGTTGCGCTTATCTGCC 59.014 47.619 9.73 0.00 0.00 4.85
2775 7675 1.242989 TTTGTTGCGCTTATCTGCCA 58.757 45.000 9.73 0.00 0.00 4.92
2777 7677 0.804364 TGTTGCGCTTATCTGCCAAG 59.196 50.000 9.73 0.00 0.00 3.61
2850 8790 2.100631 GGACTTCGCATGTGACGGG 61.101 63.158 16.15 9.05 0.00 5.28
2892 8859 4.717233 TTGTGATGTGAAAACTGTTGCT 57.283 36.364 0.00 0.00 0.00 3.91
2898 8865 1.338020 GTGAAAACTGTTGCTCTGGGG 59.662 52.381 0.00 0.00 0.00 4.96
2932 8899 0.740737 AGTGGCTGGCGCATAATTTC 59.259 50.000 17.32 0.00 38.10 2.17
3035 9042 7.394077 TCATTGATCAGAAAGAGGCATTACAAA 59.606 33.333 0.00 0.00 0.00 2.83
3071 9081 4.999212 TGCACCGCATAAGACGAA 57.001 50.000 0.00 0.00 31.71 3.85
3106 9116 6.268387 AGAAGAAATGAAAAGGGATTGCTCAA 59.732 34.615 0.00 0.00 0.00 3.02
3145 9155 1.778334 CAAAAACCTAAACAGCGCCC 58.222 50.000 2.29 0.00 0.00 6.13
3215 9225 1.869824 AACACCCCACAACACACCCT 61.870 55.000 0.00 0.00 0.00 4.34
3217 9228 2.313427 ACCCCACAACACACCCTGT 61.313 57.895 0.00 0.00 32.89 4.00
3251 9262 0.108992 CTCACGCCGCTACCAAAGTA 60.109 55.000 0.00 0.00 0.00 2.24
3319 9330 3.613563 GCAAAACTCGACGACATCAAAA 58.386 40.909 0.00 0.00 0.00 2.44
3326 9337 3.459145 TCGACGACATCAAAAAGGAACA 58.541 40.909 0.00 0.00 0.00 3.18
3394 9405 1.404181 GCTGACATAACTCGCCTGACA 60.404 52.381 0.00 0.00 0.00 3.58
3466 9477 1.301087 CGTCGCCAACCACCTACAA 60.301 57.895 0.00 0.00 0.00 2.41
3539 9551 2.350522 GAGACATGACACCGAGCAAAT 58.649 47.619 0.00 0.00 0.00 2.32
3540 9552 2.744202 GAGACATGACACCGAGCAAATT 59.256 45.455 0.00 0.00 0.00 1.82
3563 9575 1.235724 TAGCATCGTCATCGTCCGAT 58.764 50.000 0.00 0.00 44.07 4.18
3565 9577 0.039978 GCATCGTCATCGTCCGATCT 60.040 55.000 0.00 0.00 41.54 2.75
3567 9579 1.264288 CATCGTCATCGTCCGATCTGA 59.736 52.381 0.00 0.00 41.54 3.27
3586 9598 7.412563 CGATCTGATAGACCGAATCTAGAGTTC 60.413 44.444 0.00 2.14 43.35 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 6.573664 TGTATTGACCATGAAAACTGGAAG 57.426 37.500 0.00 0.00 37.22 3.46
60 61 6.071447 CCATGTATTGACCATGAAAACTGGAA 60.071 38.462 0.00 0.00 41.78 3.53
78 79 4.174704 ACCATTCACTCATGCCATGTAT 57.825 40.909 4.31 0.00 0.00 2.29
79 80 3.650281 ACCATTCACTCATGCCATGTA 57.350 42.857 4.31 0.00 0.00 2.29
80 81 2.519771 ACCATTCACTCATGCCATGT 57.480 45.000 4.31 0.00 0.00 3.21
121 123 9.434275 TTCATCTACTTATATTCTTCAGGGTCA 57.566 33.333 0.00 0.00 0.00 4.02
333 4103 1.017177 TTCTACCGTTCACGCATGCC 61.017 55.000 13.15 0.00 38.18 4.40
346 4116 4.040584 ACTTCACACCTCTCCTTTTCTACC 59.959 45.833 0.00 0.00 0.00 3.18
357 4127 3.213206 TGCAATGAACTTCACACCTCT 57.787 42.857 0.00 0.00 0.00 3.69
370 4140 1.360931 CCGCTGTCACGATGCAATGA 61.361 55.000 0.00 0.00 34.06 2.57
377 4147 1.215647 GAAGGACCGCTGTCACGAT 59.784 57.895 10.60 0.00 43.65 3.73
378 4148 1.863662 GAGAAGGACCGCTGTCACGA 61.864 60.000 10.60 0.00 43.65 4.35
380 4150 0.667792 GTGAGAAGGACCGCTGTCAC 60.668 60.000 10.60 9.98 43.65 3.67
385 4155 2.286523 CCCAGTGAGAAGGACCGCT 61.287 63.158 0.00 0.00 0.00 5.52
458 4228 2.697644 ATGGCCTCTCCTTGGGGG 60.698 66.667 3.32 0.00 35.26 5.40
459 4229 2.922234 GATGGCCTCTCCTTGGGG 59.078 66.667 3.32 0.00 35.26 4.96
461 4231 2.507944 CCGATGGCCTCTCCTTGG 59.492 66.667 3.32 0.00 35.26 3.61
504 4274 1.406447 GTTCCGTCTTCTGTGTCGTC 58.594 55.000 0.00 0.00 0.00 4.20
505 4275 0.031721 GGTTCCGTCTTCTGTGTCGT 59.968 55.000 0.00 0.00 0.00 4.34
506 4276 0.031585 TGGTTCCGTCTTCTGTGTCG 59.968 55.000 0.00 0.00 0.00 4.35
508 4278 0.106149 GGTGGTTCCGTCTTCTGTGT 59.894 55.000 0.00 0.00 0.00 3.72
509 4279 2.914379 GGTGGTTCCGTCTTCTGTG 58.086 57.895 0.00 0.00 0.00 3.66
543 4313 1.872237 CGACGTGGATGGTGTCTTTGT 60.872 52.381 0.00 0.00 0.00 2.83
547 4317 0.608308 TCTCGACGTGGATGGTGTCT 60.608 55.000 0.00 0.00 0.00 3.41
548 4318 0.242825 TTCTCGACGTGGATGGTGTC 59.757 55.000 0.00 0.00 0.00 3.67
549 4319 0.038526 GTTCTCGACGTGGATGGTGT 60.039 55.000 0.00 0.00 0.00 4.16
550 4320 1.071019 CGTTCTCGACGTGGATGGTG 61.071 60.000 0.00 0.00 46.49 4.17
551 4321 1.211969 CGTTCTCGACGTGGATGGT 59.788 57.895 0.00 0.00 46.49 3.55
567 4337 1.837439 TCTTGGCCTTGATATGACCGT 59.163 47.619 3.32 0.00 0.00 4.83
574 4344 2.497138 CGCATGATCTTGGCCTTGATA 58.503 47.619 3.32 0.00 0.00 2.15
590 4360 0.681733 ATCGGTAGAATGAGGCGCAT 59.318 50.000 10.83 0.00 39.43 4.73
599 4369 6.665992 TGAGGCTACAATTATCGGTAGAAT 57.334 37.500 5.17 0.00 39.43 2.40
600 4370 5.509163 GCTGAGGCTACAATTATCGGTAGAA 60.509 44.000 5.17 0.00 39.43 2.10
601 4371 4.022242 GCTGAGGCTACAATTATCGGTAGA 60.022 45.833 5.17 0.00 39.43 2.59
602 4372 4.238514 GCTGAGGCTACAATTATCGGTAG 58.761 47.826 0.00 0.00 39.92 3.18
603 4373 3.006537 GGCTGAGGCTACAATTATCGGTA 59.993 47.826 0.00 0.00 38.73 4.02
604 4374 2.224305 GGCTGAGGCTACAATTATCGGT 60.224 50.000 0.00 0.00 38.73 4.69
605 4375 2.037772 AGGCTGAGGCTACAATTATCGG 59.962 50.000 6.79 0.00 36.44 4.18
606 4376 3.321497 GAGGCTGAGGCTACAATTATCG 58.679 50.000 9.08 0.00 38.98 2.92
607 4377 3.243907 ACGAGGCTGAGGCTACAATTATC 60.244 47.826 9.08 0.00 38.98 1.75
608 4378 2.700897 ACGAGGCTGAGGCTACAATTAT 59.299 45.455 9.08 0.00 38.98 1.28
609 4379 2.108168 ACGAGGCTGAGGCTACAATTA 58.892 47.619 9.08 0.00 38.98 1.40
621 4391 0.445436 GCAGAACAATCACGAGGCTG 59.555 55.000 0.00 0.00 0.00 4.85
622 4392 0.035317 TGCAGAACAATCACGAGGCT 59.965 50.000 0.00 0.00 0.00 4.58
623 4393 1.089920 ATGCAGAACAATCACGAGGC 58.910 50.000 0.00 0.00 0.00 4.70
625 4395 6.588348 TTACATATGCAGAACAATCACGAG 57.412 37.500 1.58 0.00 0.00 4.18
627 4397 6.192682 CGTTTTACATATGCAGAACAATCACG 59.807 38.462 1.58 0.00 0.00 4.35
628 4398 7.216317 GTCGTTTTACATATGCAGAACAATCAC 59.784 37.037 1.58 0.00 0.00 3.06
629 4399 7.240674 GTCGTTTTACATATGCAGAACAATCA 58.759 34.615 1.58 0.00 0.00 2.57
666 4436 3.550678 GTGCGGCAACAAGTATACTACTC 59.449 47.826 3.23 0.00 38.26 2.59
667 4437 3.518590 GTGCGGCAACAAGTATACTACT 58.481 45.455 3.23 0.00 41.73 2.57
669 4439 2.736081 CGGTGCGGCAACAAGTATACTA 60.736 50.000 19.35 0.00 0.00 1.82
670 4440 1.734163 GGTGCGGCAACAAGTATACT 58.266 50.000 14.23 0.00 0.00 2.12
671 4441 0.372334 CGGTGCGGCAACAAGTATAC 59.628 55.000 19.35 0.00 0.00 1.47
673 4443 2.686816 GCGGTGCGGCAACAAGTAT 61.687 57.895 19.35 0.00 0.00 2.12
687 4471 0.968901 TCGATTCCACCTACTGCGGT 60.969 55.000 2.42 2.42 37.93 5.68
722 4509 2.122369 AGAGGGGAATAGGGGCCG 60.122 66.667 0.00 0.00 0.00 6.13
724 4511 2.884980 GCGAGAGGGGAATAGGGGC 61.885 68.421 0.00 0.00 0.00 5.80
727 4514 1.048724 TGTGGCGAGAGGGGAATAGG 61.049 60.000 0.00 0.00 0.00 2.57
754 4544 6.961360 TTTGTAGAGTGAGAACTGAGAAGA 57.039 37.500 0.00 0.00 0.00 2.87
761 4551 4.061596 GCAGCTTTTGTAGAGTGAGAACT 58.938 43.478 0.00 0.00 0.00 3.01
762 4552 3.120854 CGCAGCTTTTGTAGAGTGAGAAC 60.121 47.826 0.00 0.00 0.00 3.01
764 4554 2.610479 CCGCAGCTTTTGTAGAGTGAGA 60.610 50.000 0.00 0.00 0.00 3.27
765 4555 1.728971 CCGCAGCTTTTGTAGAGTGAG 59.271 52.381 0.00 0.00 0.00 3.51
766 4556 1.795768 CCGCAGCTTTTGTAGAGTGA 58.204 50.000 0.00 0.00 0.00 3.41
767 4557 0.166814 GCCGCAGCTTTTGTAGAGTG 59.833 55.000 0.00 0.00 35.50 3.51
768 4558 0.955919 GGCCGCAGCTTTTGTAGAGT 60.956 55.000 0.00 0.00 39.73 3.24
805 4595 2.656069 GGCGAGCTGGAAGGGTGTA 61.656 63.158 0.00 0.00 0.00 2.90
823 4613 2.047844 CAGGTCTCAGGTGGCGTG 60.048 66.667 0.00 0.00 0.00 5.34
895 4685 3.054139 TGAGATCAAACCCTGATGGAAGG 60.054 47.826 0.00 0.00 45.23 3.46
963 4753 1.009829 GGAATAGCACTGCGGAGTTG 58.990 55.000 6.93 4.44 0.00 3.16
964 4754 0.460284 CGGAATAGCACTGCGGAGTT 60.460 55.000 6.93 0.00 0.00 3.01
966 4756 0.179111 TTCGGAATAGCACTGCGGAG 60.179 55.000 0.85 0.85 0.00 4.63
967 4757 0.464036 ATTCGGAATAGCACTGCGGA 59.536 50.000 0.00 0.00 0.00 5.54
968 4758 0.861837 GATTCGGAATAGCACTGCGG 59.138 55.000 2.65 0.00 0.00 5.69
969 4759 0.504384 CGATTCGGAATAGCACTGCG 59.496 55.000 2.65 0.00 0.00 5.18
1009 4816 0.034059 CTTGTGTTCGAGGGAGTGCT 59.966 55.000 0.00 0.00 0.00 4.40
1010 4817 0.951040 CCTTGTGTTCGAGGGAGTGC 60.951 60.000 0.00 0.00 40.63 4.40
1035 4854 2.289072 ACATGGAGATACGGCATGTAGC 60.289 50.000 0.00 0.00 39.79 3.58
1066 4885 0.800683 TTTAGCGACACTGATCGGCG 60.801 55.000 0.00 0.00 42.49 6.46
1077 4896 2.029365 GCGGAGTTCAGATTTTAGCGAC 59.971 50.000 0.00 0.00 0.00 5.19
1199 5019 1.966451 CCTGGCCGTCAGAACAACC 60.966 63.158 0.18 0.00 46.18 3.77
1272 5092 4.035324 GTCCAGCTGATGAAAGATGACATG 59.965 45.833 17.39 0.00 35.57 3.21
1381 5202 2.360801 CGACGGATAAAATGCCCCAAAT 59.639 45.455 0.00 0.00 0.00 2.32
1385 5206 0.818040 AGCGACGGATAAAATGCCCC 60.818 55.000 0.00 0.00 0.00 5.80
1398 6247 2.032290 TCGGAATAGTATGACAGCGACG 60.032 50.000 0.00 0.00 0.00 5.12
1419 6268 6.531948 CGCAGTCTACTAAACAAGCTATTCTT 59.468 38.462 0.00 0.00 34.78 2.52
1422 6271 5.109903 CCGCAGTCTACTAAACAAGCTATT 58.890 41.667 0.00 0.00 0.00 1.73
1444 6300 9.810870 AATATAGATCGGAGGGAGTATAATACC 57.189 37.037 0.00 0.00 0.00 2.73
1451 6307 7.696981 ACAGTTAATATAGATCGGAGGGAGTA 58.303 38.462 0.00 0.00 0.00 2.59
1528 6394 8.650143 ATCAATAACTTGTCATACCAAGGTTT 57.350 30.769 0.00 0.00 39.29 3.27
1566 6434 1.017177 GCGGCGTTATTCACCTGTGA 61.017 55.000 9.37 0.00 37.91 3.58
1625 6493 2.706890 GCTTCATCACCGGGAGTTAAA 58.293 47.619 6.32 0.00 0.00 1.52
1631 6499 1.259142 TTACCGCTTCATCACCGGGA 61.259 55.000 6.32 0.00 45.93 5.14
1660 6528 7.058016 GCTAAACACTCGAAAATAAACGTCAAG 59.942 37.037 0.00 0.00 0.00 3.02
1740 6611 3.274288 GGGGAGAGCAATGAAACAGTAG 58.726 50.000 0.00 0.00 0.00 2.57
1741 6612 2.026262 GGGGGAGAGCAATGAAACAGTA 60.026 50.000 0.00 0.00 0.00 2.74
1777 6649 4.340381 GCAATACTCTGAAAATGGCCATCT 59.660 41.667 21.08 9.62 0.00 2.90
1778 6650 4.500375 GGCAATACTCTGAAAATGGCCATC 60.500 45.833 21.08 8.50 39.22 3.51
1779 6651 3.385755 GGCAATACTCTGAAAATGGCCAT 59.614 43.478 14.09 14.09 39.22 4.40
1780 6652 2.760092 GGCAATACTCTGAAAATGGCCA 59.240 45.455 8.56 8.56 39.22 5.36
1808 6681 7.951706 AAATTGCGCATATGTTTAAAATTGC 57.048 28.000 12.75 0.00 0.00 3.56
1822 6695 3.428045 GCTCCTGAAACTAAATTGCGCAT 60.428 43.478 12.75 0.00 0.00 4.73
1879 6752 5.521906 AGTCGACTAGTTATGTGCATGAT 57.478 39.130 18.46 0.00 0.00 2.45
1883 6756 8.626526 TCAATAATAGTCGACTAGTTATGTGCA 58.373 33.333 28.23 10.90 0.00 4.57
2002 6875 0.942410 TCAGCGTCGTTTGTACCAGC 60.942 55.000 0.00 0.00 0.00 4.85
2003 6876 1.493772 TTCAGCGTCGTTTGTACCAG 58.506 50.000 0.00 0.00 0.00 4.00
2011 6884 6.385630 AAATGACATGCATTCAGCGTCGTT 62.386 41.667 13.15 13.15 46.25 3.85
2017 6890 4.110482 GAGGAAAATGACATGCATTCAGC 58.890 43.478 13.40 7.78 46.25 4.26
2023 6896 2.761767 CCATGGAGGAAAATGACATGCA 59.238 45.455 5.56 0.00 41.22 3.96
2150 7023 1.266466 GCTTCGTGCCGTAGTAGTTC 58.734 55.000 3.91 0.00 35.15 3.01
2267 7140 4.081862 TGGAGGAACTTATTTGATCGACGT 60.082 41.667 0.00 0.00 41.55 4.34
2293 7178 3.149196 TCATGACCTCTTTTCTGTTGCC 58.851 45.455 0.00 0.00 0.00 4.52
2300 7185 2.860735 CGTCGGATCATGACCTCTTTTC 59.139 50.000 0.00 0.00 32.68 2.29
2316 7201 0.602905 AGGAAGAAAGTTGGCGTCGG 60.603 55.000 0.00 0.00 0.00 4.79
2358 7247 2.511145 CCTGCTTCAGCTCCTCGC 60.511 66.667 0.00 0.00 42.66 5.03
2395 7284 4.390556 AGCCTCTCCTCCGCCAGT 62.391 66.667 0.00 0.00 0.00 4.00
2399 7288 3.844090 GTCCAGCCTCTCCTCCGC 61.844 72.222 0.00 0.00 0.00 5.54
2401 7290 2.043852 TCGTCCAGCCTCTCCTCC 60.044 66.667 0.00 0.00 0.00 4.30
2430 7319 1.075698 TCTCGAAGTCCCTGAGGAACT 59.924 52.381 0.00 0.00 46.38 3.01
2691 7580 0.100861 CTCGCCTTCGGAGAAGTACC 59.899 60.000 8.70 0.00 45.90 3.34
2773 7673 6.599244 TCAACATAGCCTTATTCTTGACTTGG 59.401 38.462 0.00 0.00 0.00 3.61
2774 7674 7.335422 ACTCAACATAGCCTTATTCTTGACTTG 59.665 37.037 0.00 0.00 0.00 3.16
2775 7675 7.398024 ACTCAACATAGCCTTATTCTTGACTT 58.602 34.615 0.00 0.00 0.00 3.01
2777 7677 7.334421 TGAACTCAACATAGCCTTATTCTTGAC 59.666 37.037 0.00 0.00 0.00 3.18
2821 8761 2.277969 TGCGAAGTCCAAACAAACGTA 58.722 42.857 0.00 0.00 0.00 3.57
2850 8790 1.040646 TAGGCGGTGACATCCATCTC 58.959 55.000 0.00 0.00 0.00 2.75
2898 8865 1.961277 CACTGGTCACGGGTGCTTC 60.961 63.158 0.00 0.00 0.00 3.86
2932 8899 7.549134 TCATTGTACTTTGACTACCTATTGCTG 59.451 37.037 0.00 0.00 0.00 4.41
3035 9042 2.358195 GCATTCCTCCTTGGGGTGTTAT 60.358 50.000 0.00 0.00 36.20 1.89
3071 9081 7.443272 CCCTTTTCATTTCTTCTTTTTCAGCAT 59.557 33.333 0.00 0.00 0.00 3.79
3106 9116 5.975693 TTGCTCGGTTTTCCTTGATAAAT 57.024 34.783 0.00 0.00 37.95 1.40
3145 9155 4.299978 GTGCTTTAGGCCTAGTCTTATCG 58.700 47.826 13.36 0.00 40.92 2.92
3251 9262 2.110901 TACAACGGTTTGTGGTGTGT 57.889 45.000 1.90 0.00 45.91 3.72
3319 9330 4.038162 GCTCTATCGGACATAGTGTTCCTT 59.962 45.833 0.00 0.00 0.00 3.36
3326 9337 5.537300 ATGTTTGCTCTATCGGACATAGT 57.463 39.130 0.00 0.00 0.00 2.12
3394 9405 1.130054 ACCCTCCACATGCAGAGTGT 61.130 55.000 17.64 3.65 35.24 3.55
3525 9537 2.093306 ATCGAATTTGCTCGGTGTCA 57.907 45.000 0.00 0.00 39.35 3.58
3563 9575 5.998981 GGAACTCTAGATTCGGTCTATCAGA 59.001 44.000 0.00 2.79 38.71 3.27
3565 9577 5.071370 GGGAACTCTAGATTCGGTCTATCA 58.929 45.833 0.00 0.00 38.71 2.15
3567 9579 4.409187 GGGGAACTCTAGATTCGGTCTAT 58.591 47.826 0.00 0.00 38.71 1.98
3586 9598 1.284785 TGCCTGACATTCTTTAGGGGG 59.715 52.381 0.00 0.00 0.00 5.40
3672 9957 1.971167 GTTGTGGCCGGAGCAATCA 60.971 57.895 5.05 0.00 42.56 2.57


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

AutoCloner maintained by Alex Coulton.