Multiple sequence alignment - TraesCS2A01G130300

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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 TraesCS2A01G130300 chr2A 100.000 2735 0 0 1 2735 78184585 78181851 0.000000e+00 5051.0
1 TraesCS2A01G130300 chr2A 89.439 606 61 3 1993 2598 440912098 440911496 0.000000e+00 761.0
2 TraesCS2A01G130300 chr2B 91.186 1770 116 22 204 1964 119050793 119049055 0.000000e+00 2368.0
3 TraesCS2A01G130300 chr2B 87.654 162 20 0 2574 2735 539361173 539361334 3.600000e-44 189.0
4 TraesCS2A01G130300 chr2D 90.000 1830 109 34 175 1985 77171986 77170212 0.000000e+00 2298.0
5 TraesCS2A01G130300 chr2D 85.761 611 58 9 1993 2598 555235467 555236053 1.080000e-173 619.0
6 TraesCS2A01G130300 chr2D 90.643 171 13 2 8 175 36803050 36803220 9.860000e-55 224.0
7 TraesCS2A01G130300 chr1A 83.644 752 77 20 1993 2735 50837057 50836343 0.000000e+00 665.0
8 TraesCS2A01G130300 chr1A 78.927 764 109 35 1993 2735 396263419 396264151 3.190000e-129 472.0
9 TraesCS2A01G130300 chr1A 85.057 87 11 2 1541 1626 428664287 428664372 1.350000e-13 87.9
10 TraesCS2A01G130300 chr5A 86.820 607 64 6 1993 2598 359876180 359875589 0.000000e+00 664.0
11 TraesCS2A01G130300 chr5A 91.975 162 13 0 2574 2735 286003759 286003920 7.620000e-56 228.0
12 TraesCS2A01G130300 chr1D 81.915 752 94 22 1988 2735 453301445 453302158 5.040000e-167 597.0
13 TraesCS2A01G130300 chr1D 82.963 405 47 6 1993 2396 9572918 9573301 2.020000e-91 346.0
14 TraesCS2A01G130300 chr1D 90.395 177 13 3 8 181 468312361 468312536 2.120000e-56 230.0
15 TraesCS2A01G130300 chr1D 91.124 169 12 2 12 177 203866370 203866202 2.740000e-55 226.0
16 TraesCS2A01G130300 chr1D 85.057 87 11 2 1541 1626 331506312 331506397 1.350000e-13 87.9
17 TraesCS2A01G130300 chr6D 84.404 545 64 12 2057 2598 355867267 355867793 1.450000e-142 516.0
18 TraesCS2A01G130300 chr6D 81.117 609 84 17 1996 2598 396461548 396462131 2.480000e-125 459.0
19 TraesCS2A01G130300 chr6D 78.628 758 111 29 1993 2733 50608185 50608908 3.210000e-124 455.0
20 TraesCS2A01G130300 chr5D 82.516 612 74 14 1996 2598 243876239 243875652 8.740000e-140 507.0
21 TraesCS2A01G130300 chr5D 77.707 628 97 25 1993 2598 410505080 410504474 7.250000e-91 344.0
22 TraesCS2A01G130300 chr5D 91.195 159 14 0 2577 2735 10652271 10652113 1.650000e-52 217.0
23 TraesCS2A01G130300 chr4D 82.022 623 86 19 1993 2598 480297628 480297015 8.740000e-140 507.0
24 TraesCS2A01G130300 chr4D 90.643 171 13 2 8 175 282512284 282512454 9.860000e-55 224.0
25 TraesCS2A01G130300 chr4D 86.735 196 19 5 8 197 167880985 167880791 7.670000e-51 211.0
26 TraesCS2A01G130300 chr3A 83.784 481 70 5 2258 2735 25285408 25284933 1.490000e-122 449.0
27 TraesCS2A01G130300 chr3A 90.751 173 13 2 8 177 744550659 744550831 7.620000e-56 228.0
28 TraesCS2A01G130300 chrUn 83.942 411 38 10 1993 2396 2383632 2383243 4.300000e-98 368.0
29 TraesCS2A01G130300 chr7D 85.429 350 34 8 1993 2341 620203296 620203629 5.610000e-92 348.0
30 TraesCS2A01G130300 chr7D 74.495 643 114 33 1056 1688 447907577 447908179 1.640000e-57 233.0
31 TraesCS2A01G130300 chr7A 75.659 645 106 32 1056 1688 547758056 547757451 9.650000e-70 274.0
32 TraesCS2A01G130300 chr7A 91.124 169 12 2 12 177 158948787 158948619 2.740000e-55 226.0
33 TraesCS2A01G130300 chr3D 91.228 171 12 2 12 179 283613283 283613113 2.120000e-56 230.0
34 TraesCS2A01G130300 chr6B 91.124 169 12 2 12 177 682836365 682836533 2.740000e-55 226.0
35 TraesCS2A01G130300 chr6B 90.062 161 16 0 2575 2735 646202967 646202807 2.760000e-50 209.0
36 TraesCS2A01G130300 chr7B 73.872 643 118 36 1056 1688 465216549 465217151 7.670000e-51 211.0
37 TraesCS2A01G130300 chr3B 87.037 162 21 0 2574 2735 221150915 221150754 1.670000e-42 183.0
38 TraesCS2A01G130300 chr6A 80.995 221 31 9 2520 2733 596676288 596676072 6.060000e-37 165.0
39 TraesCS2A01G130300 chr1B 85.057 87 11 2 1541 1626 445878424 445878509 1.350000e-13 87.9


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 TraesCS2A01G130300 chr2A 78181851 78184585 2734 True 5051 5051 100.000 1 2735 1 chr2A.!!$R1 2734
1 TraesCS2A01G130300 chr2A 440911496 440912098 602 True 761 761 89.439 1993 2598 1 chr2A.!!$R2 605
2 TraesCS2A01G130300 chr2B 119049055 119050793 1738 True 2368 2368 91.186 204 1964 1 chr2B.!!$R1 1760
3 TraesCS2A01G130300 chr2D 77170212 77171986 1774 True 2298 2298 90.000 175 1985 1 chr2D.!!$R1 1810
4 TraesCS2A01G130300 chr2D 555235467 555236053 586 False 619 619 85.761 1993 2598 1 chr2D.!!$F2 605
5 TraesCS2A01G130300 chr1A 50836343 50837057 714 True 665 665 83.644 1993 2735 1 chr1A.!!$R1 742
6 TraesCS2A01G130300 chr1A 396263419 396264151 732 False 472 472 78.927 1993 2735 1 chr1A.!!$F1 742
7 TraesCS2A01G130300 chr5A 359875589 359876180 591 True 664 664 86.820 1993 2598 1 chr5A.!!$R1 605
8 TraesCS2A01G130300 chr1D 453301445 453302158 713 False 597 597 81.915 1988 2735 1 chr1D.!!$F3 747
9 TraesCS2A01G130300 chr6D 355867267 355867793 526 False 516 516 84.404 2057 2598 1 chr6D.!!$F2 541
10 TraesCS2A01G130300 chr6D 396461548 396462131 583 False 459 459 81.117 1996 2598 1 chr6D.!!$F3 602
11 TraesCS2A01G130300 chr6D 50608185 50608908 723 False 455 455 78.628 1993 2733 1 chr6D.!!$F1 740
12 TraesCS2A01G130300 chr5D 243875652 243876239 587 True 507 507 82.516 1996 2598 1 chr5D.!!$R2 602
13 TraesCS2A01G130300 chr5D 410504474 410505080 606 True 344 344 77.707 1993 2598 1 chr5D.!!$R3 605
14 TraesCS2A01G130300 chr4D 480297015 480297628 613 True 507 507 82.022 1993 2598 1 chr4D.!!$R2 605
15 TraesCS2A01G130300 chr7D 447907577 447908179 602 False 233 233 74.495 1056 1688 1 chr7D.!!$F1 632
16 TraesCS2A01G130300 chr7A 547757451 547758056 605 True 274 274 75.659 1056 1688 1 chr7A.!!$R2 632
17 TraesCS2A01G130300 chr7B 465216549 465217151 602 False 211 211 73.872 1056 1688 1 chr7B.!!$F1 632

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
728 745 0.093026 CGAGAAATCGCGAAAACGCT 59.907 50.0 15.24 6.46 41.67 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1795 1845 0.179084 CACGGTCACTGTTGGTCTGT 60.179 55.0 0.0 0.0 0.0 3.41 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
26 27 9.498307 GGTAGGTTCATTTCATTTATTACGTTG 57.502 33.333 0.00 0.00 0.00 4.10
68 69 9.529325 TTGATATGTGATGTTACAGTAACTAGC 57.471 33.333 21.56 12.59 39.38 3.42
69 70 8.914011 TGATATGTGATGTTACAGTAACTAGCT 58.086 33.333 21.56 6.57 39.38 3.32
73 74 8.063200 TGTGATGTTACAGTAACTAGCTATGT 57.937 34.615 21.56 0.00 39.38 2.29
74 75 8.528643 TGTGATGTTACAGTAACTAGCTATGTT 58.471 33.333 21.56 7.75 39.38 2.71
83 84 8.696374 ACAGTAACTAGCTATGTTATCACATGT 58.304 33.333 14.69 0.00 43.92 3.21
89 90 9.527157 ACTAGCTATGTTATCACATGTATCTCT 57.473 33.333 0.00 0.00 43.92 3.10
92 93 9.703892 AGCTATGTTATCACATGTATCTCTTTC 57.296 33.333 0.00 0.00 43.92 2.62
93 94 9.703892 GCTATGTTATCACATGTATCTCTTTCT 57.296 33.333 0.00 0.00 43.92 2.52
167 168 9.900710 GTTACATCTATATTACTCTCACTGTGG 57.099 37.037 8.11 0.00 0.00 4.17
168 169 9.862149 TTACATCTATATTACTCTCACTGTGGA 57.138 33.333 8.11 3.58 0.00 4.02
169 170 8.948401 ACATCTATATTACTCTCACTGTGGAT 57.052 34.615 8.11 0.00 0.00 3.41
173 174 9.727859 TCTATATTACTCTCACTGTGGATAGTC 57.272 37.037 8.11 0.00 0.00 2.59
192 193 3.114065 GTCTTATGACGATTCCCGACAC 58.886 50.000 0.00 0.00 44.61 3.67
195 196 0.179145 ATGACGATTCCCGACACGAC 60.179 55.000 0.00 0.00 44.61 4.34
197 198 3.245315 CGATTCCCGACACGACGC 61.245 66.667 0.00 0.00 41.76 5.19
206 207 4.406173 ACACGACGCCTCTGCTCG 62.406 66.667 0.00 0.00 41.09 5.03
219 220 2.125350 GCTCGAGTTGCTCCCAGG 60.125 66.667 15.13 0.00 0.00 4.45
254 270 5.827568 CCATTTTGTTGGTCGATTCAAAG 57.172 39.130 5.86 0.00 32.67 2.77
255 271 4.150451 CCATTTTGTTGGTCGATTCAAAGC 59.850 41.667 5.86 0.00 32.67 3.51
256 272 2.679355 TTGTTGGTCGATTCAAAGCG 57.321 45.000 5.86 0.00 39.51 4.68
257 273 1.872388 TGTTGGTCGATTCAAAGCGA 58.128 45.000 0.00 0.00 45.30 4.93
264 280 2.809446 TCGATTCAAAGCGATCGATGT 58.191 42.857 21.57 4.12 42.38 3.06
265 281 2.535574 TCGATTCAAAGCGATCGATGTG 59.464 45.455 21.57 19.32 42.38 3.21
266 282 2.535574 CGATTCAAAGCGATCGATGTGA 59.464 45.455 21.75 21.75 40.84 3.58
267 283 3.600235 CGATTCAAAGCGATCGATGTGAC 60.600 47.826 25.00 13.98 40.84 3.67
268 284 1.640428 TCAAAGCGATCGATGTGACC 58.360 50.000 21.75 0.05 0.00 4.02
269 285 0.652592 CAAAGCGATCGATGTGACCC 59.347 55.000 18.61 0.00 0.00 4.46
270 286 0.537188 AAAGCGATCGATGTGACCCT 59.463 50.000 21.57 0.00 0.00 4.34
271 287 0.179100 AAGCGATCGATGTGACCCTG 60.179 55.000 21.57 0.00 0.00 4.45
272 288 2.240500 GCGATCGATGTGACCCTGC 61.241 63.158 21.57 0.00 0.00 4.85
273 289 1.141665 CGATCGATGTGACCCTGCA 59.858 57.895 10.26 0.00 0.00 4.41
310 326 5.500645 AGCTATAAATCCAAAAAGCGTCC 57.499 39.130 0.00 0.00 35.17 4.79
336 352 1.899437 AACGGTGCGGATCCAGTCAT 61.899 55.000 13.41 0.00 0.00 3.06
337 353 1.040893 ACGGTGCGGATCCAGTCATA 61.041 55.000 13.41 0.00 0.00 2.15
338 354 0.319040 CGGTGCGGATCCAGTCATAG 60.319 60.000 13.41 0.00 0.00 2.23
339 355 0.753262 GGTGCGGATCCAGTCATAGT 59.247 55.000 13.41 0.00 0.00 2.12
340 356 1.961394 GGTGCGGATCCAGTCATAGTA 59.039 52.381 13.41 0.00 0.00 1.82
348 364 4.947388 GGATCCAGTCATAGTAGCTAGGAG 59.053 50.000 6.95 0.00 27.20 3.69
363 379 3.814268 GAGGCGGCCGTACGTGTA 61.814 66.667 28.70 0.00 35.98 2.90
434 450 1.452145 TTTCCGTGACTTTGGCAGCC 61.452 55.000 3.66 3.66 0.00 4.85
476 492 3.636679 CTCCACAGATCAAGGAGGACTA 58.363 50.000 16.25 0.00 44.10 2.59
477 493 3.366396 TCCACAGATCAAGGAGGACTAC 58.634 50.000 0.00 0.00 0.00 2.73
478 494 3.011821 TCCACAGATCAAGGAGGACTACT 59.988 47.826 0.00 0.00 0.00 2.57
479 495 3.383185 CCACAGATCAAGGAGGACTACTC 59.617 52.174 0.00 0.00 45.84 2.59
480 496 4.277476 CACAGATCAAGGAGGACTACTCT 58.723 47.826 0.00 0.00 45.83 3.24
481 497 5.441500 CACAGATCAAGGAGGACTACTCTA 58.558 45.833 0.00 0.00 45.83 2.43
482 498 5.530915 CACAGATCAAGGAGGACTACTCTAG 59.469 48.000 0.00 0.00 45.83 2.43
483 499 5.430417 ACAGATCAAGGAGGACTACTCTAGA 59.570 44.000 0.00 0.00 45.83 2.43
484 500 5.997746 CAGATCAAGGAGGACTACTCTAGAG 59.002 48.000 18.49 18.49 45.83 2.43
485 501 5.908831 AGATCAAGGAGGACTACTCTAGAGA 59.091 44.000 26.57 9.01 45.83 3.10
486 502 6.562608 AGATCAAGGAGGACTACTCTAGAGAT 59.437 42.308 26.57 12.64 45.83 2.75
487 503 5.935945 TCAAGGAGGACTACTCTAGAGATG 58.064 45.833 26.57 18.47 45.83 2.90
488 504 5.430417 TCAAGGAGGACTACTCTAGAGATGT 59.570 44.000 26.57 21.28 45.83 3.06
489 505 6.616137 TCAAGGAGGACTACTCTAGAGATGTA 59.384 42.308 26.57 8.35 45.83 2.29
550 567 4.006357 GTACCGACCACCCGCCAA 62.006 66.667 0.00 0.00 0.00 4.52
615 632 1.445582 CTTCCACCTCGTACCACGC 60.446 63.158 0.00 0.00 42.21 5.34
653 670 4.204891 GTCGATTTGACGCCGCGG 62.205 66.667 24.05 24.05 37.96 6.46
685 702 2.361737 GCCCTCCCAACTTGCTCC 60.362 66.667 0.00 0.00 0.00 4.70
697 714 3.429372 TTGCTCCCCGGCAACTTGT 62.429 57.895 0.00 0.00 45.64 3.16
705 722 2.551270 GGCAACTTGTCAGCGTCG 59.449 61.111 0.00 0.00 0.00 5.12
728 745 0.093026 CGAGAAATCGCGAAAACGCT 59.907 50.000 15.24 6.46 41.67 5.07
730 747 0.452784 AGAAATCGCGAAAACGCTGC 60.453 50.000 15.24 0.00 0.00 5.25
752 773 2.355363 TTTGACCACCGACGCGAG 60.355 61.111 15.93 6.19 0.00 5.03
794 815 1.472201 CGACCCATCCATCACTCTGTG 60.472 57.143 0.00 0.00 34.45 3.66
872 894 1.383456 GCTGCCAACTTGTGTCCACA 61.383 55.000 0.00 0.00 39.98 4.17
881 903 2.026945 TTGTGTCCACAGCTCGCTCA 62.027 55.000 0.00 0.00 42.94 4.26
896 918 4.806330 CTCGCTCACCGTGGTTATTATAT 58.194 43.478 0.00 0.00 38.35 0.86
897 919 5.620654 GCTCGCTCACCGTGGTTATTATATA 60.621 44.000 0.00 0.00 38.35 0.86
898 920 6.519679 TCGCTCACCGTGGTTATTATATAT 57.480 37.500 0.00 0.00 38.35 0.86
899 921 7.628769 TCGCTCACCGTGGTTATTATATATA 57.371 36.000 0.00 0.00 38.35 0.86
900 922 7.700505 TCGCTCACCGTGGTTATTATATATAG 58.299 38.462 0.00 0.00 38.35 1.31
901 923 6.417044 CGCTCACCGTGGTTATTATATATAGC 59.583 42.308 0.00 0.00 0.00 2.97
902 924 6.417044 GCTCACCGTGGTTATTATATATAGCG 59.583 42.308 0.00 0.00 0.00 4.26
903 925 6.798482 TCACCGTGGTTATTATATATAGCGG 58.202 40.000 0.00 0.00 40.99 5.52
904 926 5.981315 CACCGTGGTTATTATATATAGCGGG 59.019 44.000 0.00 5.58 39.72 6.13
905 927 5.658190 ACCGTGGTTATTATATATAGCGGGT 59.342 40.000 0.00 6.00 39.72 5.28
935 957 1.715585 CGCGTCAACCAGCCATAAG 59.284 57.895 0.00 0.00 0.00 1.73
956 978 0.455464 TAACGTGCAGATCGTCGTGG 60.455 55.000 1.00 0.00 40.69 4.94
962 984 0.457853 GCAGATCGTCGTGGTTGCTA 60.458 55.000 0.00 0.00 0.00 3.49
966 988 0.179134 ATCGTCGTGGTTGCTAGCTC 60.179 55.000 17.23 9.00 0.00 4.09
967 989 1.805945 CGTCGTGGTTGCTAGCTCC 60.806 63.158 17.23 17.79 0.00 4.70
968 990 1.292223 GTCGTGGTTGCTAGCTCCA 59.708 57.895 21.93 21.93 0.00 3.86
970 992 0.175760 TCGTGGTTGCTAGCTCCATC 59.824 55.000 26.07 19.83 33.68 3.51
971 993 0.108186 CGTGGTTGCTAGCTCCATCA 60.108 55.000 26.07 11.81 33.68 3.07
972 994 1.473965 CGTGGTTGCTAGCTCCATCAT 60.474 52.381 26.07 0.00 33.68 2.45
973 995 2.224042 CGTGGTTGCTAGCTCCATCATA 60.224 50.000 26.07 8.32 33.68 2.15
974 996 3.555795 CGTGGTTGCTAGCTCCATCATAT 60.556 47.826 26.07 0.00 33.68 1.78
977 999 3.999663 GGTTGCTAGCTCCATCATATCAC 59.000 47.826 17.23 0.00 0.00 3.06
978 1000 4.262808 GGTTGCTAGCTCCATCATATCACT 60.263 45.833 17.23 0.00 0.00 3.41
983 1005 2.704596 AGCTCCATCATATCACTGCTGT 59.295 45.455 0.00 0.00 0.00 4.40
984 1006 3.899980 AGCTCCATCATATCACTGCTGTA 59.100 43.478 0.00 0.00 0.00 2.74
985 1007 4.531339 AGCTCCATCATATCACTGCTGTAT 59.469 41.667 0.00 0.00 0.00 2.29
988 1019 4.524328 TCCATCATATCACTGCTGTATCGT 59.476 41.667 0.00 0.00 0.00 3.73
1041 1072 4.135153 CTCTGCGTCGTCCCTGGG 62.135 72.222 6.33 6.33 0.00 4.45
1576 1625 0.528470 GAGGAAGCACTACGAGCTGT 59.472 55.000 0.00 0.00 42.53 4.40
1788 1838 3.681593 TGCAAATTACAGACCCCTACAC 58.318 45.455 0.00 0.00 0.00 2.90
1789 1839 3.329520 TGCAAATTACAGACCCCTACACT 59.670 43.478 0.00 0.00 0.00 3.55
1795 1845 0.976641 CAGACCCCTACACTCTGCAA 59.023 55.000 0.00 0.00 0.00 4.08
1796 1846 0.977395 AGACCCCTACACTCTGCAAC 59.023 55.000 0.00 0.00 0.00 4.17
1806 1858 1.600957 CACTCTGCAACAGACCAACAG 59.399 52.381 0.00 0.00 35.39 3.16
1825 1877 0.437295 GTGACCGTGCACGTGAATAC 59.563 55.000 34.81 21.87 37.74 1.89
1853 1905 3.064207 TCAACAATGACCTTCGCTGTAC 58.936 45.455 0.00 0.00 0.00 2.90
1857 1909 5.023533 ACAATGACCTTCGCTGTACATAT 57.976 39.130 0.00 0.00 0.00 1.78
1858 1910 6.156748 ACAATGACCTTCGCTGTACATATA 57.843 37.500 0.00 0.00 0.00 0.86
1859 1911 5.983720 ACAATGACCTTCGCTGTACATATAC 59.016 40.000 0.00 0.00 0.00 1.47
1879 1934 2.632028 ACTGCTATGTGGCTCCATCTAG 59.368 50.000 0.00 0.00 0.00 2.43
1905 1960 2.979676 CTTGCCTTGGCTGACGCA 60.980 61.111 13.18 0.00 38.10 5.24
2046 2102 3.788817 CGTAAAATCGCCGCCTGA 58.211 55.556 0.00 0.00 0.00 3.86
2155 2252 6.856135 AAAAGAGTTCGACTAAAATTCGGT 57.144 33.333 0.00 0.00 37.09 4.69
2193 2309 3.047613 GGCTAAAGTTTGGCGATTACG 57.952 47.619 16.58 0.00 38.12 3.18
2199 2315 6.578172 GCTAAAGTTTGGCGATTACGTAAAAA 59.422 34.615 12.81 5.11 41.98 1.94
2211 2358 3.870633 ACGTAAAAACTGGGCAAACAA 57.129 38.095 0.00 0.00 0.00 2.83
2316 2501 4.129737 CGTCACCGCCATCCTCGT 62.130 66.667 0.00 0.00 0.00 4.18
2445 2657 3.966026 GAGGACGACAACGCCTCCG 62.966 68.421 16.08 0.00 46.43 4.63
2566 2787 3.125573 CGTCGTCGAGCTCCTCCA 61.126 66.667 8.47 0.00 39.71 3.86
2607 2882 1.305201 GCTCCGTCTTTGGTTTGACA 58.695 50.000 0.00 0.00 33.18 3.58
2611 2886 4.315803 CTCCGTCTTTGGTTTGACATAGT 58.684 43.478 0.00 0.00 33.18 2.12
2619 2905 1.913419 GGTTTGACATAGTGGGGAGGA 59.087 52.381 0.00 0.00 0.00 3.71
2620 2906 2.092914 GGTTTGACATAGTGGGGAGGAG 60.093 54.545 0.00 0.00 0.00 3.69
2621 2907 1.204146 TTGACATAGTGGGGAGGAGC 58.796 55.000 0.00 0.00 0.00 4.70
2622 2908 0.691078 TGACATAGTGGGGAGGAGCC 60.691 60.000 0.00 0.00 0.00 4.70
2623 2909 0.691078 GACATAGTGGGGAGGAGCCA 60.691 60.000 0.00 0.00 38.95 4.75
2624 2910 0.253160 ACATAGTGGGGAGGAGCCAA 60.253 55.000 0.00 0.00 38.95 4.52
2625 2911 0.471617 CATAGTGGGGAGGAGCCAAG 59.528 60.000 0.00 0.00 38.95 3.61
2626 2912 0.695803 ATAGTGGGGAGGAGCCAAGG 60.696 60.000 0.00 0.00 38.95 3.61
2627 2913 1.821966 TAGTGGGGAGGAGCCAAGGA 61.822 60.000 0.00 0.00 38.95 3.36
2628 2914 2.285668 TGGGGAGGAGCCAAGGAG 60.286 66.667 0.00 0.00 38.95 3.69
2629 2915 3.093172 GGGGAGGAGCCAAGGAGG 61.093 72.222 0.00 0.00 38.95 4.30
2665 2962 1.358877 CTTGTTGATGACGATGCCGA 58.641 50.000 0.00 0.00 39.50 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 9.529325 GCTAGTTACTGTAACATCACATATCAA 57.471 33.333 27.12 3.03 41.07 2.57
43 44 8.914011 AGCTAGTTACTGTAACATCACATATCA 58.086 33.333 27.12 3.99 41.07 2.15
47 48 8.696374 ACATAGCTAGTTACTGTAACATCACAT 58.304 33.333 27.12 14.32 41.07 3.21
48 49 8.063200 ACATAGCTAGTTACTGTAACATCACA 57.937 34.615 27.12 12.96 41.07 3.58
49 50 8.928270 AACATAGCTAGTTACTGTAACATCAC 57.072 34.615 27.12 15.70 41.07 3.06
57 58 8.696374 ACATGTGATAACATAGCTAGTTACTGT 58.304 33.333 14.19 4.91 34.59 3.55
63 64 9.527157 AGAGATACATGTGATAACATAGCTAGT 57.473 33.333 9.11 0.00 0.00 2.57
66 67 9.703892 GAAAGAGATACATGTGATAACATAGCT 57.296 33.333 9.11 0.00 0.00 3.32
67 68 9.703892 AGAAAGAGATACATGTGATAACATAGC 57.296 33.333 9.11 0.00 0.00 2.97
141 142 9.900710 CCACAGTGAGAGTAATATAGATGTAAC 57.099 37.037 0.62 0.00 0.00 2.50
142 143 9.862149 TCCACAGTGAGAGTAATATAGATGTAA 57.138 33.333 0.62 0.00 0.00 2.41
144 145 8.948401 ATCCACAGTGAGAGTAATATAGATGT 57.052 34.615 0.62 0.00 0.00 3.06
147 148 9.727859 GACTATCCACAGTGAGAGTAATATAGA 57.272 37.037 0.62 0.00 36.96 1.98
148 149 9.733556 AGACTATCCACAGTGAGAGTAATATAG 57.266 37.037 0.62 0.00 36.96 1.31
152 153 8.855110 CATAAGACTATCCACAGTGAGAGTAAT 58.145 37.037 0.62 0.00 36.96 1.89
153 154 8.053355 TCATAAGACTATCCACAGTGAGAGTAA 58.947 37.037 0.62 0.00 36.96 2.24
154 155 7.499563 GTCATAAGACTATCCACAGTGAGAGTA 59.500 40.741 0.62 0.00 36.96 2.59
155 156 6.320164 GTCATAAGACTATCCACAGTGAGAGT 59.680 42.308 0.62 1.83 39.40 3.24
156 157 6.512578 CGTCATAAGACTATCCACAGTGAGAG 60.513 46.154 0.62 0.00 42.73 3.20
157 158 5.297029 CGTCATAAGACTATCCACAGTGAGA 59.703 44.000 0.62 0.00 42.73 3.27
158 159 5.297029 TCGTCATAAGACTATCCACAGTGAG 59.703 44.000 0.62 0.00 42.73 3.51
159 160 5.190677 TCGTCATAAGACTATCCACAGTGA 58.809 41.667 0.62 0.00 42.73 3.41
160 161 5.500645 TCGTCATAAGACTATCCACAGTG 57.499 43.478 0.00 0.00 42.73 3.66
161 162 6.239064 GGAATCGTCATAAGACTATCCACAGT 60.239 42.308 8.10 0.00 42.73 3.55
162 163 6.153067 GGAATCGTCATAAGACTATCCACAG 58.847 44.000 8.10 0.00 42.73 3.66
163 164 5.010719 GGGAATCGTCATAAGACTATCCACA 59.989 44.000 12.62 0.00 42.73 4.17
164 165 5.471257 GGGAATCGTCATAAGACTATCCAC 58.529 45.833 12.62 3.22 42.73 4.02
165 166 4.217767 CGGGAATCGTCATAAGACTATCCA 59.782 45.833 12.62 0.00 42.73 3.41
166 167 4.458295 TCGGGAATCGTCATAAGACTATCC 59.542 45.833 0.00 1.67 42.73 2.59
167 168 5.048921 TGTCGGGAATCGTCATAAGACTATC 60.049 44.000 0.00 0.00 42.73 2.08
168 169 4.825634 TGTCGGGAATCGTCATAAGACTAT 59.174 41.667 0.00 0.00 42.73 2.12
169 170 4.036027 GTGTCGGGAATCGTCATAAGACTA 59.964 45.833 0.00 0.00 42.73 2.59
170 171 3.021695 TGTCGGGAATCGTCATAAGACT 58.978 45.455 0.00 0.00 42.73 3.24
171 172 3.114065 GTGTCGGGAATCGTCATAAGAC 58.886 50.000 0.00 0.00 38.91 3.01
172 173 2.223409 CGTGTCGGGAATCGTCATAAGA 60.223 50.000 0.00 0.00 38.91 2.10
173 174 2.117137 CGTGTCGGGAATCGTCATAAG 58.883 52.381 0.00 0.00 38.91 1.73
219 220 3.123050 ACAAAATGGTTCGCTTCTTTGC 58.877 40.909 0.00 0.00 0.00 3.68
249 265 1.640428 GGTCACATCGATCGCTTTGA 58.360 50.000 11.09 7.00 0.00 2.69
250 266 0.652592 GGGTCACATCGATCGCTTTG 59.347 55.000 11.09 10.35 0.00 2.77
251 267 0.537188 AGGGTCACATCGATCGCTTT 59.463 50.000 11.09 0.00 0.00 3.51
253 269 1.439228 CAGGGTCACATCGATCGCT 59.561 57.895 11.09 0.00 0.00 4.93
254 270 2.240500 GCAGGGTCACATCGATCGC 61.241 63.158 11.09 0.00 0.00 4.58
255 271 1.141665 TGCAGGGTCACATCGATCG 59.858 57.895 9.36 9.36 0.00 3.69
256 272 0.176680 AGTGCAGGGTCACATCGATC 59.823 55.000 0.00 0.00 39.35 3.69
257 273 0.107993 CAGTGCAGGGTCACATCGAT 60.108 55.000 0.00 0.00 39.35 3.59
258 274 1.293179 CAGTGCAGGGTCACATCGA 59.707 57.895 0.00 0.00 39.35 3.59
259 275 2.393768 GCAGTGCAGGGTCACATCG 61.394 63.158 11.09 0.00 39.35 3.84
260 276 1.302752 TGCAGTGCAGGGTCACATC 60.303 57.895 15.37 0.00 39.35 3.06
261 277 1.601759 GTGCAGTGCAGGGTCACAT 60.602 57.895 20.42 0.00 40.08 3.21
262 278 2.203195 GTGCAGTGCAGGGTCACA 60.203 61.111 20.42 0.00 40.08 3.58
263 279 3.349006 CGTGCAGTGCAGGGTCAC 61.349 66.667 26.36 10.15 40.08 3.67
268 284 4.081030 CTTCGCGTGCAGTGCAGG 62.081 66.667 28.91 28.91 45.60 4.85
269 285 4.731503 GCTTCGCGTGCAGTGCAG 62.732 66.667 20.42 13.74 40.08 4.41
271 287 4.312231 TTGCTTCGCGTGCAGTGC 62.312 61.111 22.94 8.58 41.71 4.40
272 288 2.127496 CTTGCTTCGCGTGCAGTG 60.127 61.111 22.94 17.63 41.71 3.66
273 289 4.017877 GCTTGCTTCGCGTGCAGT 62.018 61.111 22.94 0.00 41.71 4.40
310 326 0.168128 GATCCGCACCGTTCCAAAAG 59.832 55.000 0.00 0.00 0.00 2.27
336 352 1.228490 GGCCGCCTCCTAGCTACTA 60.228 63.158 0.71 0.00 0.00 1.82
337 353 2.522193 GGCCGCCTCCTAGCTACT 60.522 66.667 0.71 0.00 0.00 2.57
338 354 3.979739 CGGCCGCCTCCTAGCTAC 61.980 72.222 14.67 0.00 0.00 3.58
339 355 3.124051 TACGGCCGCCTCCTAGCTA 62.124 63.158 28.58 3.16 0.00 3.32
340 356 4.517934 TACGGCCGCCTCCTAGCT 62.518 66.667 28.58 4.37 0.00 3.32
348 364 3.340953 TTCTACACGTACGGCCGCC 62.341 63.158 28.58 15.84 0.00 6.13
363 379 1.315690 TCGACTGTCCAGAACGTTCT 58.684 50.000 24.93 24.93 38.25 3.01
434 450 3.803082 CTTGTGGACGGCGCATGG 61.803 66.667 10.83 0.00 0.00 3.66
440 456 2.435059 GAGGAGCTTGTGGACGGC 60.435 66.667 0.00 0.00 0.00 5.68
472 488 5.343058 CGCGTACTACATCTCTAGAGTAGTC 59.657 48.000 20.61 13.80 43.50 2.59
476 492 2.801679 GCGCGTACTACATCTCTAGAGT 59.198 50.000 19.21 4.03 0.00 3.24
477 493 2.159947 CGCGCGTACTACATCTCTAGAG 60.160 54.545 24.19 13.98 0.00 2.43
478 494 1.791204 CGCGCGTACTACATCTCTAGA 59.209 52.381 24.19 0.00 0.00 2.43
479 495 1.791204 TCGCGCGTACTACATCTCTAG 59.209 52.381 30.98 0.00 0.00 2.43
480 496 1.856802 TCGCGCGTACTACATCTCTA 58.143 50.000 30.98 1.54 0.00 2.43
481 497 1.012086 TTCGCGCGTACTACATCTCT 58.988 50.000 30.98 0.00 0.00 3.10
482 498 1.110876 GTTCGCGCGTACTACATCTC 58.889 55.000 30.98 1.23 0.00 2.75
483 499 0.248377 GGTTCGCGCGTACTACATCT 60.248 55.000 32.97 0.00 0.00 2.90
484 500 1.204856 GGGTTCGCGCGTACTACATC 61.205 60.000 32.97 18.99 0.00 3.06
485 501 1.226773 GGGTTCGCGCGTACTACAT 60.227 57.895 32.97 0.00 0.00 2.29
486 502 2.179018 GGGTTCGCGCGTACTACA 59.821 61.111 32.97 11.07 0.00 2.74
487 503 1.584742 GAGGGTTCGCGCGTACTAC 60.585 63.158 32.97 26.11 34.97 2.73
488 504 2.793946 GAGGGTTCGCGCGTACTA 59.206 61.111 32.97 12.26 34.97 1.82
489 505 4.471726 CGAGGGTTCGCGCGTACT 62.472 66.667 32.97 23.99 40.36 2.73
685 702 3.726517 CGCTGACAAGTTGCCGGG 61.727 66.667 2.18 0.00 0.00 5.73
728 745 2.280524 CGGTGGTCAAAGTCCGCA 60.281 61.111 0.00 0.00 37.22 5.69
730 747 2.019951 CGTCGGTGGTCAAAGTCCG 61.020 63.158 0.00 0.00 43.65 4.79
755 776 2.033448 GGGTGGCGGTTGACATGA 59.967 61.111 0.00 0.00 33.95 3.07
872 894 1.605058 ATAACCACGGTGAGCGAGCT 61.605 55.000 12.27 0.00 0.00 4.09
881 903 5.658190 ACCCGCTATATATAATAACCACGGT 59.342 40.000 0.00 0.00 35.26 4.83
896 918 1.663739 CGGCTGCTAACCCGCTATA 59.336 57.895 0.00 0.00 37.85 1.31
897 919 2.421739 CGGCTGCTAACCCGCTAT 59.578 61.111 0.00 0.00 37.85 2.97
926 948 1.665679 CTGCACGTTACCTTATGGCTG 59.334 52.381 0.00 0.00 36.63 4.85
935 957 0.455633 ACGACGATCTGCACGTTACC 60.456 55.000 0.00 0.00 43.97 2.85
956 978 4.689812 CAGTGATATGATGGAGCTAGCAAC 59.310 45.833 18.83 9.66 0.00 4.17
962 984 2.704596 ACAGCAGTGATATGATGGAGCT 59.295 45.455 0.00 0.00 40.87 4.09
966 988 4.624452 CACGATACAGCAGTGATATGATGG 59.376 45.833 0.00 0.00 40.87 3.51
967 989 4.091075 GCACGATACAGCAGTGATATGATG 59.909 45.833 0.00 0.00 42.25 3.07
968 990 4.240888 GCACGATACAGCAGTGATATGAT 58.759 43.478 0.00 0.00 38.06 2.45
970 992 2.406357 CGCACGATACAGCAGTGATATG 59.594 50.000 0.00 0.00 38.06 1.78
971 993 2.666026 CGCACGATACAGCAGTGATAT 58.334 47.619 0.00 0.00 38.06 1.63
972 994 1.864029 GCGCACGATACAGCAGTGATA 60.864 52.381 0.30 0.00 38.06 2.15
973 995 1.148157 GCGCACGATACAGCAGTGAT 61.148 55.000 0.30 0.00 38.06 3.06
974 996 1.805539 GCGCACGATACAGCAGTGA 60.806 57.895 0.30 0.00 38.06 3.41
977 999 4.271170 GCGCGCACGATACAGCAG 62.271 66.667 29.10 0.00 43.93 4.24
996 1027 3.669344 ACGCCGTTTGCCATGGTG 61.669 61.111 14.67 3.73 46.48 4.17
1323 1354 4.347096 CCGTTGTGGCTGTCGTAA 57.653 55.556 0.00 0.00 0.00 3.18
1611 1660 2.437895 TCGATCGTCTCCAGCCGT 60.438 61.111 15.94 0.00 0.00 5.68
1651 1700 1.517257 GGCTGATCACGACGTCCAG 60.517 63.158 10.58 11.85 0.00 3.86
1788 1838 1.600957 CACTGTTGGTCTGTTGCAGAG 59.399 52.381 0.00 0.00 41.46 3.35
1789 1839 1.209261 TCACTGTTGGTCTGTTGCAGA 59.791 47.619 0.00 0.00 38.25 4.26
1795 1845 0.179084 CACGGTCACTGTTGGTCTGT 60.179 55.000 0.00 0.00 0.00 3.41
1796 1846 1.498865 GCACGGTCACTGTTGGTCTG 61.499 60.000 0.00 0.00 0.00 3.51
1806 1858 0.437295 GTATTCACGTGCACGGTCAC 59.563 55.000 39.21 24.94 44.95 3.67
1825 1877 4.726416 CGAAGGTCATTGTTGAGAAATGG 58.274 43.478 0.00 0.00 36.01 3.16
1853 1905 4.541973 TGGAGCCACATAGCAGTATATG 57.458 45.455 0.00 0.00 38.79 1.78
1857 1909 2.682594 AGATGGAGCCACATAGCAGTA 58.317 47.619 0.00 0.00 34.23 2.74
1858 1910 1.504912 AGATGGAGCCACATAGCAGT 58.495 50.000 0.00 0.00 34.23 4.40
1859 1911 2.632028 ACTAGATGGAGCCACATAGCAG 59.368 50.000 0.00 0.00 34.23 4.24
1879 1934 1.615392 AGCCAAGGCAAGTTCATTCAC 59.385 47.619 14.40 0.00 44.88 3.18
1905 1960 7.807977 ATTAAGCAAAATGTACAGATCGGAT 57.192 32.000 0.33 0.00 0.00 4.18
1967 2022 7.728083 AGTCTGGTTGTAGATGCTCTTATAGAT 59.272 37.037 0.00 0.00 0.00 1.98
1968 2023 7.063593 AGTCTGGTTGTAGATGCTCTTATAGA 58.936 38.462 0.00 0.00 0.00 1.98
1977 2032 4.116238 GCTCTAAGTCTGGTTGTAGATGC 58.884 47.826 0.00 0.00 0.00 3.91
1978 2033 5.330455 TGCTCTAAGTCTGGTTGTAGATG 57.670 43.478 0.00 0.00 0.00 2.90
1979 2034 5.896678 AGATGCTCTAAGTCTGGTTGTAGAT 59.103 40.000 0.00 0.00 0.00 1.98
1980 2035 5.265191 AGATGCTCTAAGTCTGGTTGTAGA 58.735 41.667 0.00 0.00 0.00 2.59
1981 2036 5.451242 GGAGATGCTCTAAGTCTGGTTGTAG 60.451 48.000 0.00 0.00 0.00 2.74
1982 2037 4.402793 GGAGATGCTCTAAGTCTGGTTGTA 59.597 45.833 0.00 0.00 0.00 2.41
1983 2038 3.196685 GGAGATGCTCTAAGTCTGGTTGT 59.803 47.826 0.00 0.00 0.00 3.32
1984 2039 3.196469 TGGAGATGCTCTAAGTCTGGTTG 59.804 47.826 0.00 0.00 0.00 3.77
1985 2040 3.445008 TGGAGATGCTCTAAGTCTGGTT 58.555 45.455 0.00 0.00 0.00 3.67
1986 2041 3.030291 CTGGAGATGCTCTAAGTCTGGT 58.970 50.000 0.00 0.00 0.00 4.00
1987 2042 2.224018 GCTGGAGATGCTCTAAGTCTGG 60.224 54.545 0.00 0.00 0.00 3.86
1988 2043 2.224018 GGCTGGAGATGCTCTAAGTCTG 60.224 54.545 0.00 0.00 0.00 3.51
1989 2044 2.038659 GGCTGGAGATGCTCTAAGTCT 58.961 52.381 0.00 0.00 0.00 3.24
1990 2045 1.269517 CGGCTGGAGATGCTCTAAGTC 60.270 57.143 0.00 0.00 0.00 3.01
1991 2046 0.749649 CGGCTGGAGATGCTCTAAGT 59.250 55.000 0.00 0.00 0.00 2.24
2138 2235 6.146021 TCCAGTTTACCGAATTTTAGTCGAAC 59.854 38.462 0.00 0.00 41.02 3.95
2155 2252 7.608761 ACTTTAGCCGAATATTTGTCCAGTTTA 59.391 33.333 1.99 0.00 0.00 2.01
2193 2309 4.749976 TGTCTTGTTTGCCCAGTTTTTAC 58.250 39.130 0.00 0.00 0.00 2.01
2199 2315 3.561143 TGTAATGTCTTGTTTGCCCAGT 58.439 40.909 0.00 0.00 0.00 4.00
2246 2427 5.363562 TCGACCCATAGTAGTAGTTGAGA 57.636 43.478 0.00 0.00 0.00 3.27
2288 2473 2.355481 GGTGACGTCGGCGACTTT 60.355 61.111 33.90 22.48 42.00 2.66
2316 2501 3.515286 GGCCGATGAGGACGACGA 61.515 66.667 0.00 0.00 45.00 4.20
2462 2674 2.166270 GAGCAGTTTGAAGCTCGGG 58.834 57.895 0.00 0.00 46.53 5.14
2607 2882 0.695803 CCTTGGCTCCTCCCCACTAT 60.696 60.000 0.00 0.00 30.65 2.12
2611 2886 2.285668 CTCCTTGGCTCCTCCCCA 60.286 66.667 0.00 0.00 0.00 4.96
2642 2939 1.452110 CATCGTCATCAACAAGGGCA 58.548 50.000 0.00 0.00 0.00 5.36
2648 2945 1.075979 CGTCGGCATCGTCATCAACA 61.076 55.000 0.00 0.00 37.69 3.33
2711 3008 2.660552 CGGTGTTCGGCGTCAAGT 60.661 61.111 6.85 0.00 34.75 3.16


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

AutoCloner maintained by Alex Coulton.