Multiple sequence alignment - TraesCS5B01G320000

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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 TraesCS5B01G320000 chr5B 100.000 4569 0 0 1 4569 505377132 505381700 0.000000e+00 8438.0
1 TraesCS5B01G320000 chr5B 92.869 1767 101 12 1871 3619 505276021 505277780 0.000000e+00 2542.0
2 TraesCS5B01G320000 chr5B 86.619 1405 164 14 2068 3455 487438399 487439796 0.000000e+00 1531.0
3 TraesCS5B01G320000 chr5B 91.201 841 50 7 991 1820 505275092 505275919 0.000000e+00 1122.0
4 TraesCS5B01G320000 chr5B 96.536 664 19 1 3620 4279 130613156 130613819 0.000000e+00 1096.0
5 TraesCS5B01G320000 chr5B 96.235 664 21 1 3620 4279 130608132 130608795 0.000000e+00 1085.0
6 TraesCS5B01G320000 chr5B 95.976 671 19 3 3620 4282 130570504 130569834 0.000000e+00 1083.0
7 TraesCS5B01G320000 chr5B 84.116 831 84 28 1204 2010 487437658 487438464 0.000000e+00 760.0
8 TraesCS5B01G320000 chr5B 95.167 269 6 2 4283 4548 505277784 505278048 7.070000e-113 418.0
9 TraesCS5B01G320000 chr5B 92.035 113 9 0 855 967 505268774 505268886 4.730000e-35 159.0
10 TraesCS5B01G320000 chr5D 90.645 2651 165 51 1014 3619 417826914 417829526 0.000000e+00 3445.0
11 TraesCS5B01G320000 chr5D 87.152 1401 153 17 2068 3450 406416187 406417578 0.000000e+00 1565.0
12 TraesCS5B01G320000 chr5D 85.452 818 85 21 1204 2010 406415458 406416252 0.000000e+00 821.0
13 TraesCS5B01G320000 chr5D 97.059 272 6 2 4282 4552 417829526 417829796 1.500000e-124 457.0
14 TraesCS5B01G320000 chr5D 81.707 492 47 22 524 976 417817847 417818334 2.010000e-98 370.0
15 TraesCS5B01G320000 chr5A 91.476 1572 108 15 1948 3512 532740494 532742046 0.000000e+00 2137.0
16 TraesCS5B01G320000 chr5A 86.519 1402 163 16 2068 3450 512060291 512061685 0.000000e+00 1519.0
17 TraesCS5B01G320000 chr5A 86.069 1371 120 35 524 1835 531237892 531239250 0.000000e+00 1408.0
18 TraesCS5B01G320000 chr5A 96.407 668 16 3 3620 4279 238859706 238860373 0.000000e+00 1094.0
19 TraesCS5B01G320000 chr5A 95.976 671 18 4 3620 4282 238829772 238829103 0.000000e+00 1081.0
20 TraesCS5B01G320000 chr5A 84.727 825 81 28 1204 2010 512059559 512060356 0.000000e+00 784.0
21 TraesCS5B01G320000 chr6D 85.961 1389 150 23 2109 3455 36253445 36254830 0.000000e+00 1443.0
22 TraesCS5B01G320000 chr6D 93.277 476 32 0 1301 1776 36252790 36253265 0.000000e+00 702.0
23 TraesCS5B01G320000 chr6D 89.855 69 6 1 722 789 276667518 276667450 2.260000e-13 87.9
24 TraesCS5B01G320000 chr6B 86.142 1335 148 19 2156 3455 75942372 75943704 0.000000e+00 1406.0
25 TraesCS5B01G320000 chr6B 82.723 191 24 7 525 707 704174960 704175149 1.320000e-35 161.0
26 TraesCS5B01G320000 chr6B 78.022 182 38 2 528 707 79845010 79845191 3.740000e-21 113.0
27 TraesCS5B01G320000 chr6A 85.272 1358 158 20 2116 3434 40298756 40300110 0.000000e+00 1362.0
28 TraesCS5B01G320000 chr6A 81.250 528 91 5 1 524 532424923 532425446 1.970000e-113 420.0
29 TraesCS5B01G320000 chr7D 87.113 1001 118 8 2149 3142 509631728 509630732 0.000000e+00 1123.0
30 TraesCS5B01G320000 chr7D 86.482 577 67 8 1204 1776 603583313 603583882 1.400000e-174 623.0
31 TraesCS5B01G320000 chr2D 96.707 668 14 1 3620 4279 644701515 644702182 0.000000e+00 1105.0
32 TraesCS5B01G320000 chr2D 95.181 664 28 2 3620 4279 521221070 521221733 0.000000e+00 1046.0
33 TraesCS5B01G320000 chr2D 94.162 668 26 6 3620 4279 39589453 39590115 0.000000e+00 1005.0
34 TraesCS5B01G320000 chr2D 97.468 395 10 0 3620 4014 635069546 635069152 0.000000e+00 675.0
35 TraesCS5B01G320000 chr2D 83.556 523 73 9 6 524 182812826 182813339 1.150000e-130 477.0
36 TraesCS5B01G320000 chr2D 81.238 533 91 6 1 529 486344555 486345082 5.470000e-114 422.0
37 TraesCS5B01G320000 chr2D 81.250 528 91 5 1 524 498264778 498265301 1.970000e-113 420.0
38 TraesCS5B01G320000 chr2D 81.356 531 86 9 1 524 624910244 624910768 1.970000e-113 420.0
39 TraesCS5B01G320000 chr2D 78.689 183 31 7 524 703 562359844 562360021 1.040000e-21 115.0
40 TraesCS5B01G320000 chr2D 97.826 46 1 0 540 585 159596163 159596118 3.790000e-11 80.5
41 TraesCS5B01G320000 chrUn 96.536 664 19 1 3620 4279 45099047 45099710 0.000000e+00 1096.0
42 TraesCS5B01G320000 chrUn 96.274 671 15 2 3620 4282 261514811 261514143 0.000000e+00 1092.0
43 TraesCS5B01G320000 chrUn 96.108 668 16 4 3620 4279 186162037 186162702 0.000000e+00 1081.0
44 TraesCS5B01G320000 chrUn 81.285 529 90 6 1 524 355158827 355158303 1.970000e-113 420.0
45 TraesCS5B01G320000 chr7B 86.613 1001 123 8 2149 3142 538053046 538052050 0.000000e+00 1096.0
46 TraesCS5B01G320000 chr7B 88.571 595 58 7 1205 1794 538053825 538053236 0.000000e+00 713.0
47 TraesCS5B01G320000 chr3A 96.257 668 20 1 3620 4282 66032059 66031392 0.000000e+00 1090.0
48 TraesCS5B01G320000 chr1A 95.359 668 20 5 3620 4279 334091112 334091776 0.000000e+00 1051.0
49 TraesCS5B01G320000 chr1D 88.316 582 59 5 1204 1776 440718429 440719010 0.000000e+00 689.0
50 TraesCS5B01G320000 chr1D 97.468 395 10 0 3620 4014 493802707 493803101 0.000000e+00 675.0
51 TraesCS5B01G320000 chr1D 81.285 529 90 6 1 524 126217320 126216796 1.970000e-113 420.0
52 TraesCS5B01G320000 chr1B 87.457 582 64 5 1204 1776 598190657 598191238 0.000000e+00 662.0
53 TraesCS5B01G320000 chr3D 81.285 529 89 7 1 524 29930445 29930968 1.970000e-113 420.0
54 TraesCS5B01G320000 chr3D 81.168 531 91 6 1 526 437757141 437756615 7.070000e-113 418.0
55 TraesCS5B01G320000 chr7A 84.024 169 25 2 528 694 63731726 63731894 1.320000e-35 161.0
56 TraesCS5B01G320000 chr2B 81.707 164 24 5 528 689 441104261 441104420 1.030000e-26 132.0
57 TraesCS5B01G320000 chr4D 78.169 142 24 3 525 665 340085110 340085245 2.930000e-12 84.2
58 TraesCS5B01G320000 chr4D 83.784 74 12 0 528 601 436894136 436894063 2.280000e-08 71.3
59 TraesCS5B01G320000 chr4B 84.932 73 11 0 528 600 538708662 538708590 1.760000e-09 75.0


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 TraesCS5B01G320000 chr5B 505377132 505381700 4568 False 8438.000000 8438 100.0000 1 4569 1 chr5B.!!$F4 4568
1 TraesCS5B01G320000 chr5B 505275092 505278048 2956 False 1360.666667 2542 93.0790 991 4548 3 chr5B.!!$F6 3557
2 TraesCS5B01G320000 chr5B 487437658 487439796 2138 False 1145.500000 1531 85.3675 1204 3455 2 chr5B.!!$F5 2251
3 TraesCS5B01G320000 chr5B 130613156 130613819 663 False 1096.000000 1096 96.5360 3620 4279 1 chr5B.!!$F2 659
4 TraesCS5B01G320000 chr5B 130608132 130608795 663 False 1085.000000 1085 96.2350 3620 4279 1 chr5B.!!$F1 659
5 TraesCS5B01G320000 chr5B 130569834 130570504 670 True 1083.000000 1083 95.9760 3620 4282 1 chr5B.!!$R1 662
6 TraesCS5B01G320000 chr5D 417826914 417829796 2882 False 1951.000000 3445 93.8520 1014 4552 2 chr5D.!!$F3 3538
7 TraesCS5B01G320000 chr5D 406415458 406417578 2120 False 1193.000000 1565 86.3020 1204 3450 2 chr5D.!!$F2 2246
8 TraesCS5B01G320000 chr5A 532740494 532742046 1552 False 2137.000000 2137 91.4760 1948 3512 1 chr5A.!!$F3 1564
9 TraesCS5B01G320000 chr5A 531237892 531239250 1358 False 1408.000000 1408 86.0690 524 1835 1 chr5A.!!$F2 1311
10 TraesCS5B01G320000 chr5A 512059559 512061685 2126 False 1151.500000 1519 85.6230 1204 3450 2 chr5A.!!$F4 2246
11 TraesCS5B01G320000 chr5A 238859706 238860373 667 False 1094.000000 1094 96.4070 3620 4279 1 chr5A.!!$F1 659
12 TraesCS5B01G320000 chr5A 238829103 238829772 669 True 1081.000000 1081 95.9760 3620 4282 1 chr5A.!!$R1 662
13 TraesCS5B01G320000 chr6D 36252790 36254830 2040 False 1072.500000 1443 89.6190 1301 3455 2 chr6D.!!$F1 2154
14 TraesCS5B01G320000 chr6B 75942372 75943704 1332 False 1406.000000 1406 86.1420 2156 3455 1 chr6B.!!$F1 1299
15 TraesCS5B01G320000 chr6A 40298756 40300110 1354 False 1362.000000 1362 85.2720 2116 3434 1 chr6A.!!$F1 1318
16 TraesCS5B01G320000 chr6A 532424923 532425446 523 False 420.000000 420 81.2500 1 524 1 chr6A.!!$F2 523
17 TraesCS5B01G320000 chr7D 509630732 509631728 996 True 1123.000000 1123 87.1130 2149 3142 1 chr7D.!!$R1 993
18 TraesCS5B01G320000 chr7D 603583313 603583882 569 False 623.000000 623 86.4820 1204 1776 1 chr7D.!!$F1 572
19 TraesCS5B01G320000 chr2D 644701515 644702182 667 False 1105.000000 1105 96.7070 3620 4279 1 chr2D.!!$F8 659
20 TraesCS5B01G320000 chr2D 521221070 521221733 663 False 1046.000000 1046 95.1810 3620 4279 1 chr2D.!!$F5 659
21 TraesCS5B01G320000 chr2D 39589453 39590115 662 False 1005.000000 1005 94.1620 3620 4279 1 chr2D.!!$F1 659
22 TraesCS5B01G320000 chr2D 182812826 182813339 513 False 477.000000 477 83.5560 6 524 1 chr2D.!!$F2 518
23 TraesCS5B01G320000 chr2D 486344555 486345082 527 False 422.000000 422 81.2380 1 529 1 chr2D.!!$F3 528
24 TraesCS5B01G320000 chr2D 498264778 498265301 523 False 420.000000 420 81.2500 1 524 1 chr2D.!!$F4 523
25 TraesCS5B01G320000 chr2D 624910244 624910768 524 False 420.000000 420 81.3560 1 524 1 chr2D.!!$F7 523
26 TraesCS5B01G320000 chrUn 45099047 45099710 663 False 1096.000000 1096 96.5360 3620 4279 1 chrUn.!!$F1 659
27 TraesCS5B01G320000 chrUn 261514143 261514811 668 True 1092.000000 1092 96.2740 3620 4282 1 chrUn.!!$R1 662
28 TraesCS5B01G320000 chrUn 186162037 186162702 665 False 1081.000000 1081 96.1080 3620 4279 1 chrUn.!!$F2 659
29 TraesCS5B01G320000 chrUn 355158303 355158827 524 True 420.000000 420 81.2850 1 524 1 chrUn.!!$R2 523
30 TraesCS5B01G320000 chr7B 538052050 538053825 1775 True 904.500000 1096 87.5920 1205 3142 2 chr7B.!!$R1 1937
31 TraesCS5B01G320000 chr3A 66031392 66032059 667 True 1090.000000 1090 96.2570 3620 4282 1 chr3A.!!$R1 662
32 TraesCS5B01G320000 chr1A 334091112 334091776 664 False 1051.000000 1051 95.3590 3620 4279 1 chr1A.!!$F1 659
33 TraesCS5B01G320000 chr1D 440718429 440719010 581 False 689.000000 689 88.3160 1204 1776 1 chr1D.!!$F1 572
34 TraesCS5B01G320000 chr1D 126216796 126217320 524 True 420.000000 420 81.2850 1 524 1 chr1D.!!$R1 523
35 TraesCS5B01G320000 chr1B 598190657 598191238 581 False 662.000000 662 87.4570 1204 1776 1 chr1B.!!$F1 572
36 TraesCS5B01G320000 chr3D 29930445 29930968 523 False 420.000000 420 81.2850 1 524 1 chr3D.!!$F1 523
37 TraesCS5B01G320000 chr3D 437756615 437757141 526 True 418.000000 418 81.1680 1 526 1 chr3D.!!$R1 525

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
194 196 0.029989 GGAGGGTGGGGGAGAATAGT 60.030 60.0 0.00 0.0 0.0 2.12 F
714 722 0.179111 CGTTCTGGCGGCTATCTCAA 60.179 55.0 11.43 0.0 0.0 3.02 F
2142 2300 0.249657 GCGATGGAGGTGGATCAGAC 60.250 60.0 0.00 0.0 0.0 3.51 F
2611 2784 0.796312 CCATGACGCGCTACAAGTTT 59.204 50.0 5.73 0.0 0.0 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1765 1852 1.064611 AGATCGTTCTCCTTCCTCCGA 60.065 52.381 0.0 0.0 0.00 4.55 R
2200 2370 0.605860 AGTACGTCTCCAGCGACTGT 60.606 55.000 0.0 0.0 0.00 3.55 R
3190 3399 1.172180 CGGCCCTGAACTTCTTGCAA 61.172 55.000 0.0 0.0 0.00 4.08 R
3821 4052 1.377856 GAGTTCCCTTGCTCCTGCC 60.378 63.158 0.0 0.0 38.71 4.85 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 4.465512 GCTGCGGCCAATGACACG 62.466 66.667 6.12 0.00 0.00 4.49
51 53 0.816018 ATGACACGCCGAAAACACCA 60.816 50.000 0.00 0.00 0.00 4.17
60 62 2.101082 GCCGAAAACACCAAGGGTTTTA 59.899 45.455 7.63 0.00 45.56 1.52
70 72 2.302157 CCAAGGGTTTTACCTCGTCTCT 59.698 50.000 0.00 0.00 40.87 3.10
82 84 1.664649 CGTCTCTCAACTTGCGCCA 60.665 57.895 4.18 0.00 0.00 5.69
88 90 1.228094 TCAACTTGCGCCATCACCA 60.228 52.632 4.18 0.00 0.00 4.17
102 104 5.184096 CGCCATCACCATAGTCTACTCTATT 59.816 44.000 0.00 0.00 0.00 1.73
108 110 8.783660 TCACCATAGTCTACTCTATTCCAAAT 57.216 34.615 0.00 0.00 0.00 2.32
149 151 2.510664 GAGAGCAGGTCTCCGGAAT 58.489 57.895 17.60 0.00 45.57 3.01
173 175 3.057969 TCGTCTTTGTGATCCTGCATT 57.942 42.857 0.00 0.00 0.00 3.56
186 188 4.463788 GCATTGGGAGGGTGGGGG 62.464 72.222 0.00 0.00 0.00 5.40
187 189 2.616893 CATTGGGAGGGTGGGGGA 60.617 66.667 0.00 0.00 0.00 4.81
188 190 2.287194 ATTGGGAGGGTGGGGGAG 60.287 66.667 0.00 0.00 0.00 4.30
190 192 2.446337 ATTGGGAGGGTGGGGGAGAA 62.446 60.000 0.00 0.00 0.00 2.87
191 193 2.044620 GGGAGGGTGGGGGAGAAT 59.955 66.667 0.00 0.00 0.00 2.40
192 194 1.320512 GGGAGGGTGGGGGAGAATA 59.679 63.158 0.00 0.00 0.00 1.75
193 195 0.768609 GGGAGGGTGGGGGAGAATAG 60.769 65.000 0.00 0.00 0.00 1.73
194 196 0.029989 GGAGGGTGGGGGAGAATAGT 60.030 60.000 0.00 0.00 0.00 2.12
195 197 1.628327 GGAGGGTGGGGGAGAATAGTT 60.628 57.143 0.00 0.00 0.00 2.24
275 277 1.557099 AGTCGGATGGTGCTACTCAA 58.443 50.000 0.00 0.00 0.00 3.02
280 282 1.204941 GGATGGTGCTACTCAACGTCT 59.795 52.381 0.00 0.00 45.56 4.18
290 292 1.887198 ACTCAACGTCTTCTCCATCGT 59.113 47.619 0.00 0.00 38.15 3.73
293 295 1.135774 CAACGTCTTCTCCATCGTCGA 60.136 52.381 0.00 0.00 35.49 4.20
316 318 2.503331 ACAACAGATCATCGCCAACAA 58.497 42.857 0.00 0.00 0.00 2.83
318 320 2.183478 ACAGATCATCGCCAACAACA 57.817 45.000 0.00 0.00 0.00 3.33
326 328 3.695556 TCATCGCCAACAACATCATCAAT 59.304 39.130 0.00 0.00 0.00 2.57
328 330 5.532032 TCATCGCCAACAACATCATCAATAT 59.468 36.000 0.00 0.00 0.00 1.28
332 334 5.806502 CGCCAACAACATCATCAATATTGTT 59.193 36.000 14.97 4.27 42.63 2.83
358 360 8.279800 TGTTCTTACAACAACTAACGATCAATG 58.720 33.333 0.00 0.00 0.00 2.82
384 386 5.869888 GTCCTTCGTGATCTGTTTATGTCTT 59.130 40.000 0.00 0.00 0.00 3.01
417 419 0.884259 TGTGCCGTGTGAGATGTTGG 60.884 55.000 0.00 0.00 0.00 3.77
465 471 5.292765 GCTAGATTGTTGCATGCTAGTCTA 58.707 41.667 20.33 17.34 33.01 2.59
467 473 7.093354 GCTAGATTGTTGCATGCTAGTCTATA 58.907 38.462 20.33 4.10 33.01 1.31
532 538 5.684704 CCTAATATTCCAACAGGCTTCTCA 58.315 41.667 0.00 0.00 0.00 3.27
535 541 2.099141 TTCCAACAGGCTTCTCATCG 57.901 50.000 0.00 0.00 0.00 3.84
536 542 0.976641 TCCAACAGGCTTCTCATCGT 59.023 50.000 0.00 0.00 0.00 3.73
541 547 1.613630 AGGCTTCTCATCGTGGGGT 60.614 57.895 0.00 0.00 0.00 4.95
556 562 1.073763 TGGGGTGAGATTTGGTGTCAG 59.926 52.381 0.00 0.00 29.63 3.51
560 566 1.537202 GTGAGATTTGGTGTCAGGTGC 59.463 52.381 0.00 0.00 29.63 5.01
563 569 2.485814 GAGATTTGGTGTCAGGTGCTTC 59.514 50.000 0.00 0.00 0.00 3.86
572 578 5.130975 TGGTGTCAGGTGCTTCATATCTATT 59.869 40.000 0.00 0.00 0.00 1.73
578 584 5.704515 CAGGTGCTTCATATCTATTCAAGGG 59.295 44.000 0.00 0.00 0.00 3.95
581 587 6.547510 GGTGCTTCATATCTATTCAAGGGTTT 59.452 38.462 0.00 0.00 0.00 3.27
585 591 9.120538 GCTTCATATCTATTCAAGGGTTTAACA 57.879 33.333 0.00 0.00 0.00 2.41
591 597 6.833041 TCTATTCAAGGGTTTAACAGTGACA 58.167 36.000 0.00 0.00 0.00 3.58
605 611 1.620819 AGTGACAACTGTGGCTCTAGG 59.379 52.381 0.00 0.00 34.77 3.02
608 614 1.448540 CAACTGTGGCTCTAGGGCG 60.449 63.158 8.90 0.00 44.11 6.13
612 618 2.731374 GTGGCTCTAGGGCGCTAG 59.269 66.667 27.36 27.36 45.80 3.42
621 627 3.951765 GGGCGCTAGTCCTTAGGT 58.048 61.111 7.64 0.00 39.58 3.08
625 631 0.806492 GCGCTAGTCCTTAGGTGCAC 60.806 60.000 8.80 8.80 35.59 4.57
639 645 4.238385 GCACGTGCACGAAGACTA 57.762 55.556 42.94 0.00 43.02 2.59
641 647 0.640768 GCACGTGCACGAAGACTATC 59.359 55.000 42.94 18.01 43.02 2.08
643 649 1.135373 CACGTGCACGAAGACTATCCT 60.135 52.381 42.94 16.00 43.02 3.24
645 651 1.281899 GTGCACGAAGACTATCCTGC 58.718 55.000 0.00 0.00 33.61 4.85
646 652 0.894835 TGCACGAAGACTATCCTGCA 59.105 50.000 0.00 0.00 38.46 4.41
652 658 3.067461 ACGAAGACTATCCTGCAGTCATC 59.933 47.826 13.81 5.64 44.03 2.92
673 679 1.340248 GACAAGGTCAAGTCGACTCCA 59.660 52.381 20.33 5.33 44.70 3.86
677 683 4.177026 CAAGGTCAAGTCGACTCCAATAG 58.823 47.826 20.33 5.25 44.70 1.73
680 686 2.758979 GTCAAGTCGACTCCAATAGGGA 59.241 50.000 20.33 4.06 45.20 4.20
681 687 2.758979 TCAAGTCGACTCCAATAGGGAC 59.241 50.000 20.33 0.00 42.15 4.46
682 688 2.496070 CAAGTCGACTCCAATAGGGACA 59.504 50.000 20.33 0.00 42.15 4.02
708 716 4.143333 GGCTCGTTCTGGCGGCTA 62.143 66.667 11.43 0.00 0.00 3.93
710 718 1.951631 GCTCGTTCTGGCGGCTATC 60.952 63.158 11.43 0.00 0.00 2.08
711 719 1.736586 CTCGTTCTGGCGGCTATCT 59.263 57.895 11.43 0.00 0.00 1.98
712 720 0.318275 CTCGTTCTGGCGGCTATCTC 60.318 60.000 11.43 0.00 0.00 2.75
713 721 1.035385 TCGTTCTGGCGGCTATCTCA 61.035 55.000 11.43 0.00 0.00 3.27
714 722 0.179111 CGTTCTGGCGGCTATCTCAA 60.179 55.000 11.43 0.00 0.00 3.02
716 724 1.869767 GTTCTGGCGGCTATCTCAATG 59.130 52.381 11.43 0.00 0.00 2.82
717 725 1.123077 TCTGGCGGCTATCTCAATGT 58.877 50.000 11.43 0.00 0.00 2.71
718 726 2.316108 TCTGGCGGCTATCTCAATGTA 58.684 47.619 11.43 0.00 0.00 2.29
720 728 3.324846 TCTGGCGGCTATCTCAATGTATT 59.675 43.478 11.43 0.00 0.00 1.89
757 789 9.204570 GTTTAAGATGCTTTGTACTTCTACTGA 57.795 33.333 0.00 0.00 0.00 3.41
852 894 7.640597 AGTGTTTTCTACAAAGTAAAAGCCT 57.359 32.000 0.00 0.00 38.80 4.58
906 948 7.428472 GCTTGATATATGCATTCATGATGTTCG 59.572 37.037 3.54 0.00 38.07 3.95
972 1018 9.591792 AAAAGATAGCCTTATTTCTTTGATTGC 57.408 29.630 0.00 0.00 38.18 3.56
973 1019 7.886629 AGATAGCCTTATTTCTTTGATTGCA 57.113 32.000 0.00 0.00 0.00 4.08
975 1021 8.921205 AGATAGCCTTATTTCTTTGATTGCAAT 58.079 29.630 12.83 12.83 33.25 3.56
976 1022 9.189723 GATAGCCTTATTTCTTTGATTGCAATC 57.810 33.333 28.83 28.83 33.25 2.67
977 1023 6.938507 AGCCTTATTTCTTTGATTGCAATCA 58.061 32.000 33.08 33.08 43.28 2.57
1085 1133 2.577059 GAACGACGGCCCAGATCA 59.423 61.111 0.00 0.00 0.00 2.92
1426 1513 1.517913 GGCCACGTACGCTAACTCC 60.518 63.158 16.72 4.57 0.00 3.85
1588 1675 1.301401 CGGCAAGTCGGACAAGGAA 60.301 57.895 11.27 0.00 0.00 3.36
1780 1867 0.973496 AGGCTCGGAGGAAGGAGAAC 60.973 60.000 7.20 0.00 31.90 3.01
1783 1870 1.394618 CTCGGAGGAAGGAGAACGAT 58.605 55.000 0.00 0.00 31.90 3.73
1824 1928 4.263572 CACCTGGTTGGCCGGTCA 62.264 66.667 3.51 3.51 38.81 4.02
1838 1942 2.781911 GGTCAGCCGAAAAGATCCC 58.218 57.895 0.00 0.00 0.00 3.85
1840 1944 1.449601 TCAGCCGAAAAGATCCCGC 60.450 57.895 0.00 0.00 0.00 6.13
1847 1951 1.003839 AAAAGATCCCGCTGCGTCA 60.004 52.632 21.59 6.97 0.00 4.35
1859 1963 4.719369 GCGTCAGCGAACCGGTCT 62.719 66.667 8.04 0.00 41.33 3.85
1891 2046 3.966543 CCCAAGGCCACCTTCGGT 61.967 66.667 5.01 0.00 42.67 4.69
1922 2077 2.534903 GCCGCGCTCTACAAATCCC 61.535 63.158 5.56 0.00 0.00 3.85
1950 2105 4.265056 GGCCGTGGTGGTTGAGGT 62.265 66.667 0.00 0.00 41.21 3.85
1987 2142 2.360475 GTCCAGGAGGCAGCCAAC 60.360 66.667 15.80 5.65 33.74 3.77
1995 2150 2.598394 GGCAGCCAACCAGAAGCA 60.598 61.111 6.55 0.00 0.00 3.91
2142 2300 0.249657 GCGATGGAGGTGGATCAGAC 60.250 60.000 0.00 0.00 0.00 3.51
2245 2415 2.558286 CCGCGCCTACCGATTCCTA 61.558 63.158 0.00 0.00 40.02 2.94
2293 2463 3.522731 CTCCTCGCCTCGGACCTG 61.523 72.222 0.00 0.00 0.00 4.00
2380 2553 3.598715 TCGTTCGACCGCACCACT 61.599 61.111 0.00 0.00 0.00 4.00
2381 2554 2.660552 CGTTCGACCGCACCACTT 60.661 61.111 0.00 0.00 0.00 3.16
2527 2700 1.079127 GCGCAAGGTCCTGAAGCTA 60.079 57.895 0.30 0.00 33.60 3.32
2611 2784 0.796312 CCATGACGCGCTACAAGTTT 59.204 50.000 5.73 0.00 0.00 2.66
2662 2835 1.108776 GCAGGTACCTGGATGACGTA 58.891 55.000 36.91 0.00 43.77 3.57
2715 2888 2.202797 CCTGCCACACGAGATCGG 60.203 66.667 7.22 0.00 44.95 4.18
2844 3017 3.190849 CGTGTCCGGCAGCATGAG 61.191 66.667 0.00 0.00 39.69 2.90
2942 3115 2.420022 GTGATCACGTTCCATTCAAGGG 59.580 50.000 10.69 0.00 0.00 3.95
3032 3207 0.821711 CGGGAGCACCAACTTCCAAA 60.822 55.000 1.58 0.00 40.22 3.28
3055 3231 1.002087 GTGTTTGACCAGATCCTCCGT 59.998 52.381 0.00 0.00 0.00 4.69
3190 3399 2.492484 GGACAGTGACTACGAGGTGATT 59.508 50.000 0.00 0.00 0.00 2.57
3351 3560 2.005451 CAAGATCTTCCTGCAGAACGG 58.995 52.381 17.39 0.00 0.00 4.44
3451 3671 2.188837 TCGATTGTCGGTTCTCATCG 57.811 50.000 0.00 0.00 40.88 3.84
3455 3675 0.108804 TTGTCGGTTCTCATCGGCTC 60.109 55.000 0.00 0.00 31.68 4.70
3457 3677 0.108804 GTCGGTTCTCATCGGCTCAA 60.109 55.000 0.00 0.00 0.00 3.02
3465 3686 4.801330 TCTCATCGGCTCAACTTCTTTA 57.199 40.909 0.00 0.00 0.00 1.85
3529 3757 2.227194 GAACGTTGTTCCCTTGGTCAT 58.773 47.619 5.00 0.00 0.00 3.06
3552 3780 4.123506 GGGAAGTAAGCTATGAGAGTTGC 58.876 47.826 0.00 0.00 0.00 4.17
3553 3781 4.383118 GGGAAGTAAGCTATGAGAGTTGCA 60.383 45.833 0.00 0.00 0.00 4.08
3585 3816 3.643159 AAGAAGAAATTGGCGGTTCAC 57.357 42.857 0.00 0.00 0.00 3.18
3670 3901 2.492088 GTGGGTTGGCTTGGATTACTTC 59.508 50.000 0.00 0.00 0.00 3.01
3725 3956 0.528470 GCGGAGGAGCTATTATCGCT 59.472 55.000 11.79 0.00 41.15 4.93
3741 3972 0.671251 CGCTCAGCTCCCTAACCTAG 59.329 60.000 0.00 0.00 0.00 3.02
3821 4052 3.392440 GCCGGCTAATCGTACGCG 61.392 66.667 22.15 3.53 39.92 6.01
3867 4098 0.325933 CAGGAAGGCACATGAGTCCA 59.674 55.000 0.00 0.00 0.00 4.02
3921 4152 1.263356 ACGTAGGTACCTGTGCATGT 58.737 50.000 25.33 12.82 0.00 3.21
4006 4237 1.204146 GCAACCTAGGGATCACCAGA 58.796 55.000 14.81 0.00 43.89 3.86
4024 4263 5.126869 CACCAGACAGCTCTATAGGGATATG 59.873 48.000 2.98 1.09 0.00 1.78
4107 4352 3.104512 CCCTGCCATAATATACTCCCGA 58.895 50.000 0.00 0.00 0.00 5.14
4279 4525 6.443849 AGACAAGATACAACTATTGGGAAGGA 59.556 38.462 0.00 0.00 34.12 3.36
4319 4565 3.308473 GGGCTTTCTGACCCATCTTACTT 60.308 47.826 0.00 0.00 46.22 2.24
4505 4754 6.277605 TGTACCTATACAACATTGTCCATCG 58.722 40.000 0.00 0.00 42.35 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 1.025113 TTGGTGTTTTCGGCGTGTCA 61.025 50.000 6.85 0.00 0.00 3.58
39 40 0.462375 AAACCCTTGGTGTTTTCGGC 59.538 50.000 0.00 0.00 35.34 5.54
51 53 3.236896 TGAGAGACGAGGTAAAACCCTT 58.763 45.455 0.00 0.00 39.75 3.95
60 62 0.039074 CGCAAGTTGAGAGACGAGGT 60.039 55.000 7.16 0.00 0.00 3.85
70 72 0.608856 ATGGTGATGGCGCAAGTTGA 60.609 50.000 10.83 0.00 41.68 3.18
82 84 8.783660 TTTGGAATAGAGTAGACTATGGTGAT 57.216 34.615 0.00 0.00 33.96 3.06
88 90 6.493802 TCGGCATTTGGAATAGAGTAGACTAT 59.506 38.462 0.00 0.00 34.98 2.12
102 104 2.281139 TGCACGTCGGCATTTGGA 60.281 55.556 4.55 0.00 39.25 3.53
122 124 3.699894 CCTGCTCTCCCGCACACT 61.700 66.667 0.00 0.00 35.74 3.55
124 126 3.695606 GACCTGCTCTCCCGCACA 61.696 66.667 0.00 0.00 35.74 4.57
149 151 2.672714 CAGGATCACAAAGACGAACGA 58.327 47.619 0.14 0.00 0.00 3.85
173 175 1.542093 TATTCTCCCCCACCCTCCCA 61.542 60.000 0.00 0.00 0.00 4.37
262 264 2.563179 AGAAGACGTTGAGTAGCACCAT 59.437 45.455 0.00 0.00 0.00 3.55
263 265 1.961394 AGAAGACGTTGAGTAGCACCA 59.039 47.619 0.00 0.00 0.00 4.17
275 277 0.447011 GTCGACGATGGAGAAGACGT 59.553 55.000 0.00 0.00 41.57 4.34
280 282 2.223852 TGTTGTTGTCGACGATGGAGAA 60.224 45.455 9.14 0.00 0.00 2.87
290 292 1.992667 GCGATGATCTGTTGTTGTCGA 59.007 47.619 0.00 0.00 0.00 4.20
293 295 2.183478 TGGCGATGATCTGTTGTTGT 57.817 45.000 0.00 0.00 0.00 3.32
332 334 7.773864 TTGATCGTTAGTTGTTGTAAGAACA 57.226 32.000 7.28 0.00 34.89 3.18
334 336 7.295201 GCATTGATCGTTAGTTGTTGTAAGAA 58.705 34.615 0.00 0.00 0.00 2.52
337 339 5.177881 ACGCATTGATCGTTAGTTGTTGTAA 59.822 36.000 0.00 0.00 36.72 2.41
358 360 1.429463 AAACAGATCACGAAGGACGC 58.571 50.000 0.00 0.00 46.94 5.19
384 386 2.490115 ACGGCACAACAACTTCAAAGAA 59.510 40.909 0.00 0.00 0.00 2.52
433 435 4.529897 TGCAACAATCTAGCCAGATGAAT 58.470 39.130 0.00 0.00 40.81 2.57
441 443 3.209410 ACTAGCATGCAACAATCTAGCC 58.791 45.455 21.98 0.00 32.23 3.93
526 532 1.186200 TCTCACCCCACGATGAGAAG 58.814 55.000 1.52 0.00 46.47 2.85
532 538 0.991920 ACCAAATCTCACCCCACGAT 59.008 50.000 0.00 0.00 0.00 3.73
535 541 1.202879 TGACACCAAATCTCACCCCAC 60.203 52.381 0.00 0.00 0.00 4.61
536 542 1.073763 CTGACACCAAATCTCACCCCA 59.926 52.381 0.00 0.00 0.00 4.96
541 547 1.421268 AGCACCTGACACCAAATCTCA 59.579 47.619 0.00 0.00 0.00 3.27
556 562 5.625150 ACCCTTGAATAGATATGAAGCACC 58.375 41.667 0.00 0.00 0.00 5.01
563 569 9.613428 TCACTGTTAAACCCTTGAATAGATATG 57.387 33.333 0.00 0.00 0.00 1.78
572 578 4.638421 CAGTTGTCACTGTTAAACCCTTGA 59.362 41.667 0.00 0.00 44.96 3.02
585 591 1.620819 CCTAGAGCCACAGTTGTCACT 59.379 52.381 0.00 0.00 0.00 3.41
591 597 2.982130 CGCCCTAGAGCCACAGTT 59.018 61.111 0.00 0.00 0.00 3.16
595 601 2.077821 GACTAGCGCCCTAGAGCCAC 62.078 65.000 12.38 0.00 43.07 5.01
596 602 1.828660 GACTAGCGCCCTAGAGCCA 60.829 63.158 12.38 0.00 43.07 4.75
597 603 2.566570 GGACTAGCGCCCTAGAGCC 61.567 68.421 12.38 8.91 43.07 4.70
603 609 1.043673 CACCTAAGGACTAGCGCCCT 61.044 60.000 2.29 0.00 0.00 5.19
605 611 1.227292 GCACCTAAGGACTAGCGCC 60.227 63.158 2.29 0.00 0.00 6.53
608 614 0.531200 ACGTGCACCTAAGGACTAGC 59.469 55.000 12.15 0.00 0.00 3.42
612 618 3.562635 GCACGTGCACCTAAGGAC 58.437 61.111 34.52 0.76 41.59 3.85
625 631 1.550065 CAGGATAGTCTTCGTGCACG 58.450 55.000 32.76 32.76 41.45 5.34
631 637 3.637432 GATGACTGCAGGATAGTCTTCG 58.363 50.000 19.93 0.00 43.79 3.79
632 638 3.316588 TCGATGACTGCAGGATAGTCTTC 59.683 47.826 19.93 12.73 43.79 2.87
639 645 1.134580 CCTTGTCGATGACTGCAGGAT 60.135 52.381 19.93 9.55 31.33 3.24
641 647 0.036952 ACCTTGTCGATGACTGCAGG 60.037 55.000 19.93 0.00 33.91 4.85
643 649 0.678950 TGACCTTGTCGATGACTGCA 59.321 50.000 0.00 0.00 34.95 4.41
645 651 2.989840 GACTTGACCTTGTCGATGACTG 59.010 50.000 0.00 0.00 34.95 3.51
646 652 3.305398 GACTTGACCTTGTCGATGACT 57.695 47.619 0.00 0.00 34.95 3.41
673 679 1.141881 CGCTGTCGCTGTCCCTATT 59.858 57.895 0.00 0.00 0.00 1.73
694 702 1.035385 TGAGATAGCCGCCAGAACGA 61.035 55.000 0.00 0.00 34.06 3.85
729 761 9.726438 AGTAGAAGTACAAAGCATCTTAAACAT 57.274 29.630 0.00 0.00 0.00 2.71
735 767 8.854614 AATTCAGTAGAAGTACAAAGCATCTT 57.145 30.769 0.00 0.00 37.14 2.40
825 865 9.791820 GGCTTTTACTTTGTAGAAAACACTTTA 57.208 29.630 0.00 0.00 38.00 1.85
848 890 3.181450 CGGATGGGAAATTCTAGAAGGCT 60.181 47.826 11.53 0.00 0.00 4.58
852 894 7.832187 ACAAATAACGGATGGGAAATTCTAGAA 59.168 33.333 7.82 7.82 0.00 2.10
906 948 2.468915 AGGCTACTTAACTCAGGGGAC 58.531 52.381 0.00 0.00 0.00 4.46
997 1045 6.647067 GCCGACTTACTTGATCTTTATATGCT 59.353 38.462 0.00 0.00 0.00 3.79
1000 1048 8.421784 TCAAGCCGACTTACTTGATCTTTATAT 58.578 33.333 1.49 0.00 45.48 0.86
1001 1049 7.778083 TCAAGCCGACTTACTTGATCTTTATA 58.222 34.615 1.49 0.00 45.48 0.98
1011 1059 6.039382 AGTTCAAATTTCAAGCCGACTTACTT 59.961 34.615 0.00 0.00 33.74 2.24
1029 1077 2.351447 CGACGTGCTAGAGGAGTTCAAA 60.351 50.000 0.00 0.00 0.00 2.69
1085 1133 3.647771 GGGGGAACAACGAGGGCT 61.648 66.667 0.00 0.00 0.00 5.19
1387 1474 3.175240 CAGTTCTCGGTGAGCGCG 61.175 66.667 0.00 0.00 0.00 6.86
1765 1852 1.064611 AGATCGTTCTCCTTCCTCCGA 60.065 52.381 0.00 0.00 0.00 4.55
1780 1867 3.534970 CTCCTGCTCGCCGAGATCG 62.535 68.421 20.05 4.53 39.44 3.69
1822 1926 1.449601 GCGGGATCTTTTCGGCTGA 60.450 57.895 0.00 0.00 0.00 4.26
1824 1928 1.450312 CAGCGGGATCTTTTCGGCT 60.450 57.895 0.00 0.00 35.80 5.52
1827 1931 2.025359 GACGCAGCGGGATCTTTTCG 62.025 60.000 21.15 0.00 0.00 3.46
1830 1934 1.448540 CTGACGCAGCGGGATCTTT 60.449 57.895 21.15 0.00 0.00 2.52
1922 2077 4.093952 CACGGCCTTGCTCTTGCG 62.094 66.667 0.00 0.00 43.34 4.85
1985 2140 1.557269 ATCGCCTCCTGCTTCTGGTT 61.557 55.000 0.00 0.00 38.05 3.67
1987 2142 1.523258 CATCGCCTCCTGCTTCTGG 60.523 63.158 0.00 0.00 38.05 3.86
2060 2215 4.593864 GACGGCCTCCATCGCCTC 62.594 72.222 0.00 0.00 44.73 4.70
2118 2273 2.896677 ATCCACCTCCATCGCCTCCA 62.897 60.000 0.00 0.00 0.00 3.86
2142 2300 2.818274 GCCGCTTACTTGGGGTCG 60.818 66.667 0.00 0.00 41.45 4.79
2194 2364 1.153745 CTCCAGCGACTGTACAGCC 60.154 63.158 22.90 11.28 0.00 4.85
2197 2367 0.887836 ACGTCTCCAGCGACTGTACA 60.888 55.000 0.00 0.00 0.00 2.90
2200 2370 0.605860 AGTACGTCTCCAGCGACTGT 60.606 55.000 0.00 0.00 0.00 3.55
2293 2463 3.060615 CTGTGGGCAAGCTGCTCC 61.061 66.667 1.00 0.00 45.08 4.70
2527 2700 1.295423 GCACATGTACACCTCCGGT 59.705 57.895 0.00 0.00 35.62 5.28
2553 2726 2.623450 TAGGGGAGCTCGGACCACT 61.623 63.158 19.06 10.68 42.96 4.00
2598 2771 1.525197 TGAACAGAAACTTGTAGCGCG 59.475 47.619 0.00 0.00 0.00 6.86
2611 2784 1.066454 TCGTCGTGCTTCTTGAACAGA 59.934 47.619 0.00 0.00 0.00 3.41
2695 2868 1.893786 GATCTCGTGTGGCAGGAGT 59.106 57.895 15.45 6.30 43.91 3.85
3032 3207 1.630878 GAGGATCTGGTCAAACACCCT 59.369 52.381 0.00 0.00 46.18 4.34
3083 3259 2.167281 ACACGGTCCTGATCATCTTCTG 59.833 50.000 0.00 0.00 0.00 3.02
3190 3399 1.172180 CGGCCCTGAACTTCTTGCAA 61.172 55.000 0.00 0.00 0.00 4.08
3451 3671 4.691216 ACGATTCAGTAAAGAAGTTGAGCC 59.309 41.667 0.00 0.00 0.00 4.70
3455 3675 8.708742 TCACAATACGATTCAGTAAAGAAGTTG 58.291 33.333 0.00 0.00 0.00 3.16
3457 3677 8.709646 GTTCACAATACGATTCAGTAAAGAAGT 58.290 33.333 0.00 0.00 0.00 3.01
3465 3686 4.569943 AGCTGTTCACAATACGATTCAGT 58.430 39.130 0.00 0.00 0.00 3.41
3529 3757 4.383118 GCAACTCTCATAGCTTACTTCCCA 60.383 45.833 0.00 0.00 0.00 4.37
3553 3781 9.191995 CGCCAATTTCTTCTTTTAAATAACTGT 57.808 29.630 0.00 0.00 0.00 3.55
3618 3849 9.326413 CTAACTAACGGTGGATAATCATCTTTT 57.674 33.333 0.00 0.00 0.00 2.27
3725 3956 1.486211 GCACTAGGTTAGGGAGCTGA 58.514 55.000 0.00 0.00 37.30 4.26
3821 4052 1.377856 GAGTTCCCTTGCTCCTGCC 60.378 63.158 0.00 0.00 38.71 4.85
3867 4098 4.260620 GGTCGCACATTCATAATAGCGTTT 60.261 41.667 14.26 0.00 41.97 3.60
3921 4152 3.129502 CGACCGACGCCTCACCTA 61.130 66.667 0.00 0.00 34.51 3.08
4006 4237 3.310954 CCCCCATATCCCTATAGAGCTGT 60.311 52.174 0.00 0.00 0.00 4.40
4086 4331 3.104512 TCGGGAGTATATTATGGCAGGG 58.895 50.000 0.00 0.00 0.00 4.45
4107 4352 1.832883 TGCCGGTGCAATAGAATTGT 58.167 45.000 1.90 0.00 46.66 2.71
4319 4565 7.057894 GGGTAATGGTTAAGGATTACATCACA 58.942 38.462 14.30 0.00 36.95 3.58
4505 4754 6.738114 TGGAATGATTTGTTGTCTCACTTTC 58.262 36.000 0.00 0.00 0.00 2.62


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

AutoCloner maintained by Alex Coulton.