Multiple sequence alignment - TraesCS2D01G531900

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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 TraesCS2D01G531900 chr2D 100.000 2836 0 0 1 2836 617462861 617465696 0.000000e+00 5238.0
1 TraesCS2D01G531900 chr2D 85.017 1762 218 34 560 2303 617511163 617512896 0.000000e+00 1749.0
2 TraesCS2D01G531900 chr2D 100.000 40 0 0 2405 2444 617465226 617465265 1.090000e-09 75.0
3 TraesCS2D01G531900 chr2D 100.000 40 0 0 2366 2405 617465265 617465304 1.090000e-09 75.0
4 TraesCS2D01G531900 chr2A 92.857 2044 115 21 373 2404 748079561 748081585 0.000000e+00 2937.0
5 TraesCS2D01G531900 chr2A 86.124 1290 153 16 905 2187 748165834 748167104 0.000000e+00 1367.0
6 TraesCS2D01G531900 chr2A 85.814 1290 158 15 905 2187 748124841 748126112 0.000000e+00 1345.0
7 TraesCS2D01G531900 chr2A 85.659 1290 160 15 905 2187 748190194 748191465 0.000000e+00 1334.0
8 TraesCS2D01G531900 chr2A 89.095 431 40 5 2406 2833 748081549 748081975 1.930000e-146 529.0
9 TraesCS2D01G531900 chr2A 88.251 366 38 5 1 366 747696175 747696535 1.560000e-117 433.0
10 TraesCS2D01G531900 chr2A 85.792 366 48 4 1 366 747837539 747837900 4.430000e-103 385.0
11 TraesCS2D01G531900 chr2A 85.519 366 50 3 1 366 747722893 747723255 2.060000e-101 379.0
12 TraesCS2D01G531900 chr2A 85.519 366 50 3 1 366 747732356 747732718 2.060000e-101 379.0
13 TraesCS2D01G531900 chr2A 85.519 366 49 3 1 366 747873723 747874084 2.060000e-101 379.0
14 TraesCS2D01G531900 chr2A 85.246 366 51 3 1 366 747735493 747735855 9.590000e-100 374.0
15 TraesCS2D01G531900 chr2A 85.246 366 50 4 1 366 747775952 747776313 9.590000e-100 374.0
16 TraesCS2D01G531900 chr2A 85.246 366 50 4 1 366 747812120 747812481 9.590000e-100 374.0
17 TraesCS2D01G531900 chr2A 82.075 106 15 3 2713 2815 748959293 748959189 1.400000e-13 87.9
18 TraesCS2D01G531900 chr2B 83.662 1824 230 39 560 2366 753749239 753751011 0.000000e+00 1655.0
19 TraesCS2D01G531900 chr2B 85.292 1455 176 23 561 1995 753765626 753767062 0.000000e+00 1467.0
20 TraesCS2D01G531900 chr2B 85.065 1453 182 19 561 1995 753828704 753827269 0.000000e+00 1448.0
21 TraesCS2D01G531900 chr2B 95.245 715 33 1 976 1689 753701936 753702650 0.000000e+00 1131.0
22 TraesCS2D01G531900 chr2B 93.882 474 25 2 1687 2160 753705286 753705755 0.000000e+00 712.0
23 TraesCS2D01G531900 chr2B 93.033 244 15 2 2161 2404 753705964 753706205 3.470000e-94 355.0
24 TraesCS2D01G531900 chr2B 85.000 100 14 1 924 1022 753854611 753854512 1.800000e-17 100.0
25 TraesCS2D01G531900 chrUn 85.519 366 50 3 1 366 420896625 420896263 2.060000e-101 379.0
26 TraesCS2D01G531900 chr4D 88.000 75 8 1 381 455 449380932 449380859 1.400000e-13 87.9
27 TraesCS2D01G531900 chr3B 77.236 123 22 5 2707 2825 223700603 223700723 1.820000e-07 67.6
28 TraesCS2D01G531900 chr7A 84.058 69 10 1 2713 2781 41808886 41808953 6.560000e-07 65.8
29 TraesCS2D01G531900 chr1B 76.336 131 22 8 2712 2836 621063460 621063587 8.480000e-06 62.1


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 TraesCS2D01G531900 chr2D 617462861 617465696 2835 False 1796.000000 5238 100.000000 1 2836 3 chr2D.!!$F2 2835
1 TraesCS2D01G531900 chr2D 617511163 617512896 1733 False 1749.000000 1749 85.017000 560 2303 1 chr2D.!!$F1 1743
2 TraesCS2D01G531900 chr2A 748079561 748081975 2414 False 1733.000000 2937 90.976000 373 2833 2 chr2A.!!$F11 2460
3 TraesCS2D01G531900 chr2A 748165834 748167104 1270 False 1367.000000 1367 86.124000 905 2187 1 chr2A.!!$F8 1282
4 TraesCS2D01G531900 chr2A 748124841 748126112 1271 False 1345.000000 1345 85.814000 905 2187 1 chr2A.!!$F7 1282
5 TraesCS2D01G531900 chr2A 748190194 748191465 1271 False 1334.000000 1334 85.659000 905 2187 1 chr2A.!!$F9 1282
6 TraesCS2D01G531900 chr2A 747732356 747735855 3499 False 376.500000 379 85.382500 1 366 2 chr2A.!!$F10 365
7 TraesCS2D01G531900 chr2B 753749239 753751011 1772 False 1655.000000 1655 83.662000 560 2366 1 chr2B.!!$F1 1806
8 TraesCS2D01G531900 chr2B 753765626 753767062 1436 False 1467.000000 1467 85.292000 561 1995 1 chr2B.!!$F2 1434
9 TraesCS2D01G531900 chr2B 753827269 753828704 1435 True 1448.000000 1448 85.065000 561 1995 1 chr2B.!!$R1 1434
10 TraesCS2D01G531900 chr2B 753701936 753706205 4269 False 732.666667 1131 94.053333 976 2404 3 chr2B.!!$F3 1428

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
77 78 0.107456 ACTCCATTGGATGCTAGGCG 59.893 55.0 5.70 0.0 0.00 5.52 F
96 97 0.108186 GTCTGGCACGATGTGATGGA 60.108 55.0 0.24 0.0 35.23 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1584 1614 1.429463 ACAACGAAGCGAGGATCAAC 58.571 50.00 0.0 0.0 33.17 3.18 R
1846 4516 3.938963 AGTGCGAGAAAGTCAAGTTTTCA 59.061 39.13 0.0 0.0 37.08 2.69 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
32 33 3.608506 CGACAGAGTTACGTTGGATCTTG 59.391 47.826 0.00 0.00 0.00 3.02
33 34 3.326747 ACAGAGTTACGTTGGATCTTGC 58.673 45.455 0.00 0.00 0.00 4.01
42 43 2.633488 GTTGGATCTTGCACCTAGGTC 58.367 52.381 12.84 7.92 0.00 3.85
46 47 2.159028 GGATCTTGCACCTAGGTCTGAC 60.159 54.545 12.84 2.48 0.00 3.51
48 49 1.618837 TCTTGCACCTAGGTCTGACAC 59.381 52.381 12.84 0.00 0.00 3.67
59 60 1.522806 TCTGACACCGTTGGCACAC 60.523 57.895 0.00 0.00 34.98 3.82
73 74 1.408683 GGCACACTCCATTGGATGCTA 60.409 52.381 22.65 0.00 36.04 3.49
75 76 2.569059 CACACTCCATTGGATGCTAGG 58.431 52.381 5.70 0.00 0.00 3.02
77 78 0.107456 ACTCCATTGGATGCTAGGCG 59.893 55.000 5.70 0.00 0.00 5.52
81 82 1.224075 CATTGGATGCTAGGCGTCTG 58.776 55.000 0.00 0.00 43.35 3.51
96 97 0.108186 GTCTGGCACGATGTGATGGA 60.108 55.000 0.24 0.00 35.23 3.41
99 100 1.332686 CTGGCACGATGTGATGGATTG 59.667 52.381 0.24 0.00 35.23 2.67
103 104 2.223112 GCACGATGTGATGGATTGTCAC 60.223 50.000 0.24 0.00 44.77 3.67
105 106 1.594397 CGATGTGATGGATTGTCACCG 59.406 52.381 4.06 0.00 44.10 4.94
108 109 1.346068 TGTGATGGATTGTCACCGTCA 59.654 47.619 0.00 0.00 46.85 4.35
119 120 3.882131 CACCGTCAGGGGATTCATT 57.118 52.632 0.00 0.00 46.39 2.57
120 121 2.128771 CACCGTCAGGGGATTCATTT 57.871 50.000 0.00 0.00 46.39 2.32
133 134 5.392703 GGGGATTCATTTTTACGTGAGGTTC 60.393 44.000 0.00 0.00 0.00 3.62
173 174 6.400940 GGTTCAAGTTTGTCACATTGTTGTTG 60.401 38.462 0.00 0.00 32.34 3.33
175 176 6.092092 TCAAGTTTGTCACATTGTTGTTGAG 58.908 36.000 0.00 0.00 32.34 3.02
182 183 6.295249 TGTCACATTGTTGTTGAGGAATCTA 58.705 36.000 0.00 0.00 32.34 1.98
187 188 8.517878 CACATTGTTGTTGAGGAATCTAGAATT 58.482 33.333 0.00 0.00 32.34 2.17
193 194 9.823647 GTTGTTGAGGAATCTAGAATTCAGATA 57.176 33.333 16.01 3.49 32.40 1.98
208 209 8.680001 AGAATTCAGATATGATCATCTCTCTCG 58.320 37.037 18.11 9.67 32.83 4.04
211 212 8.491331 TTCAGATATGATCATCTCTCTCGTAG 57.509 38.462 18.11 8.49 32.83 3.51
213 214 7.548780 TCAGATATGATCATCTCTCTCGTAGTG 59.451 40.741 18.11 8.03 32.83 2.74
235 236 4.082081 TGAAATAAACAGAGCATGGCCAAG 60.082 41.667 10.96 6.55 0.00 3.61
236 237 1.176527 TAAACAGAGCATGGCCAAGC 58.823 50.000 25.22 25.22 0.00 4.01
247 248 1.153509 GGCCAAGCACATGCAATCC 60.154 57.895 6.64 0.00 45.16 3.01
249 250 1.105457 GCCAAGCACATGCAATCCTA 58.895 50.000 6.64 0.00 45.16 2.94
260 261 3.370840 TGCAATCCTAGCTTTGGTGAT 57.629 42.857 0.00 0.00 0.00 3.06
263 264 3.565902 GCAATCCTAGCTTTGGTGATACC 59.434 47.826 0.00 0.00 39.22 2.73
277 278 6.385649 TGGTGATACCACAAACTTTTCTTC 57.614 37.500 0.00 0.00 44.79 2.87
278 279 5.008217 TGGTGATACCACAAACTTTTCTTCG 59.992 40.000 0.00 0.00 44.79 3.79
279 280 5.008316 GGTGATACCACAAACTTTTCTTCGT 59.992 40.000 0.00 0.00 44.93 3.85
280 281 6.203338 GGTGATACCACAAACTTTTCTTCGTA 59.797 38.462 0.00 0.00 44.93 3.43
282 283 4.888038 ACCACAAACTTTTCTTCGTACC 57.112 40.909 0.00 0.00 0.00 3.34
287 288 7.121020 ACCACAAACTTTTCTTCGTACCTTTTA 59.879 33.333 0.00 0.00 0.00 1.52
302 303 5.977489 ACCTTTTAGCATGTTAAACCTCC 57.023 39.130 13.58 0.00 0.00 4.30
327 328 3.740115 TGAGGCAGTTTTCTAAGACCAC 58.260 45.455 0.00 0.00 0.00 4.16
329 330 2.441750 AGGCAGTTTTCTAAGACCACCA 59.558 45.455 0.00 0.00 0.00 4.17
334 335 2.552743 GTTTTCTAAGACCACCAGCACC 59.447 50.000 0.00 0.00 0.00 5.01
338 339 0.396435 TAAGACCACCAGCACCACAG 59.604 55.000 0.00 0.00 0.00 3.66
353 354 3.360867 ACCACAGGTGTTTTGTCATCAA 58.639 40.909 0.00 0.00 32.98 2.57
360 361 3.380142 GTGTTTTGTCATCAAATGGCGT 58.620 40.909 0.00 0.00 42.14 5.68
366 367 4.614555 TGTCATCAAATGGCGTATTGTC 57.385 40.909 0.00 0.00 37.81 3.18
367 368 3.376859 TGTCATCAAATGGCGTATTGTCC 59.623 43.478 0.00 0.00 37.81 4.02
368 369 3.627577 GTCATCAAATGGCGTATTGTCCT 59.372 43.478 0.00 0.00 0.00 3.85
369 370 4.814234 GTCATCAAATGGCGTATTGTCCTA 59.186 41.667 0.00 0.00 0.00 2.94
371 372 5.700832 TCATCAAATGGCGTATTGTCCTATC 59.299 40.000 0.00 0.00 0.00 2.08
383 384 7.376866 GCGTATTGTCCTATCACATTGATTTTG 59.623 37.037 0.00 0.00 38.26 2.44
393 394 4.269603 TCACATTGATTTTGTTTTGCCACG 59.730 37.500 0.00 0.00 0.00 4.94
394 395 4.269603 CACATTGATTTTGTTTTGCCACGA 59.730 37.500 0.00 0.00 0.00 4.35
410 411 0.611062 ACGACCTCCTCGAATGTCCA 60.611 55.000 0.00 0.00 46.14 4.02
422 423 5.277683 CCTCGAATGTCCAAACATCATGATC 60.278 44.000 4.86 0.00 45.48 2.92
431 432 5.010820 TCCAAACATCATGATCTTTTGCACA 59.989 36.000 23.01 12.63 0.00 4.57
437 438 5.050644 TCATGATCTTTTGCACACACATC 57.949 39.130 0.00 0.00 0.00 3.06
448 449 2.411935 GCACACACATCACACATTCGAG 60.412 50.000 0.00 0.00 0.00 4.04
449 450 1.800586 ACACACATCACACATTCGAGC 59.199 47.619 0.00 0.00 0.00 5.03
456 457 2.621338 TCACACATTCGAGCATCTTCC 58.379 47.619 0.00 0.00 0.00 3.46
460 461 1.945394 ACATTCGAGCATCTTCCATGC 59.055 47.619 0.00 0.00 44.85 4.06
516 518 0.813610 TGCATATACACCTGCGCACC 60.814 55.000 5.66 0.00 41.32 5.01
517 519 1.831389 GCATATACACCTGCGCACCG 61.831 60.000 5.66 1.12 0.00 4.94
530 532 2.223456 TGCGCACCGAATCAAATATTGG 60.223 45.455 5.66 0.00 0.00 3.16
532 534 3.002862 GCGCACCGAATCAAATATTGGTA 59.997 43.478 0.30 0.00 0.00 3.25
536 538 5.564651 GCACCGAATCAAATATTGGTATGGG 60.565 44.000 0.00 0.00 0.00 4.00
589 591 5.913137 ATCCACTCTACTGATGCTATAGC 57.087 43.478 18.18 18.18 42.50 2.97
605 607 6.292389 GCTATAGCAACCACTAACAATGAG 57.708 41.667 20.01 0.00 41.59 2.90
738 755 2.440409 CACCAGTGGGATTTTCCTCTG 58.560 52.381 15.21 6.11 43.95 3.35
792 809 9.898152 TTCCAATGTTCTTCCTTTGTTTAAAAT 57.102 25.926 0.00 0.00 0.00 1.82
793 810 9.898152 TCCAATGTTCTTCCTTTGTTTAAAATT 57.102 25.926 0.00 0.00 0.00 1.82
820 837 7.132213 ACCTTGTGATATTTTATCGCATTTCG 58.868 34.615 10.58 3.52 38.21 3.46
848 865 2.963101 TCCACCATAACCCTCTGTATCG 59.037 50.000 0.00 0.00 0.00 2.92
857 874 1.409064 CCCTCTGTATCGCTGCACTTA 59.591 52.381 0.00 0.00 0.00 2.24
885 903 5.269505 ACGTGTGAAAAATGGGAAATTGA 57.730 34.783 0.00 0.00 0.00 2.57
901 919 1.909700 TTGAGTCAGGAACAATGGCC 58.090 50.000 0.00 0.00 0.00 5.36
910 928 4.721776 TCAGGAACAATGGCCTCTACTATT 59.278 41.667 3.32 0.00 30.41 1.73
922 940 5.590259 GGCCTCTACTATTCTGCAATGAAAA 59.410 40.000 0.00 0.00 0.00 2.29
1305 1335 7.222872 CCTATCTCCAAGCTGTCATAAAAGAT 58.777 38.462 0.00 0.00 0.00 2.40
1524 1554 2.356125 GGGTGCTGATTTTGAGCTCCTA 60.356 50.000 12.15 0.00 45.49 2.94
1584 1614 2.309528 TGGCTATTAGAACGGTGCAG 57.690 50.000 0.00 0.00 0.00 4.41
1642 1672 4.438148 GAGTCTCCCTATTGAGCTTGAAC 58.562 47.826 0.00 0.00 32.22 3.18
1676 1706 4.466015 TGATATGGAAGAAAAGTTTGGCCC 59.534 41.667 0.00 0.00 0.00 5.80
2071 4991 7.582352 TCATTCACATGCGATACTAGTAGTAC 58.418 38.462 12.25 6.11 32.84 2.73
2073 4993 5.370679 TCACATGCGATACTAGTAGTACCA 58.629 41.667 12.25 10.12 32.84 3.25
2106 5031 9.988815 GATGAGATAGTATTGAGAGCCTTAAAA 57.011 33.333 0.00 0.00 0.00 1.52
2381 7441 8.815912 AGTTCATAAATTTAATATGGATGGGGC 58.184 33.333 1.21 0.00 32.73 5.80
2382 7442 8.592809 GTTCATAAATTTAATATGGATGGGGCA 58.407 33.333 1.21 0.00 32.73 5.36
2383 7443 8.365060 TCATAAATTTAATATGGATGGGGCAG 57.635 34.615 1.21 0.00 32.73 4.85
2384 7444 7.955185 TCATAAATTTAATATGGATGGGGCAGT 59.045 33.333 1.21 0.00 32.73 4.40
2386 7446 6.423776 AATTTAATATGGATGGGGCAGTTG 57.576 37.500 0.00 0.00 0.00 3.16
2387 7447 1.708341 AATATGGATGGGGCAGTTGC 58.292 50.000 0.00 0.00 41.14 4.17
2398 7458 1.302192 GCAGTTGCCAGGAACGGTA 60.302 57.895 4.37 0.00 34.31 4.02
2400 7460 1.821216 CAGTTGCCAGGAACGGTAAT 58.179 50.000 0.00 0.00 32.95 1.89
2401 7461 2.937873 GCAGTTGCCAGGAACGGTAATA 60.938 50.000 4.37 0.00 32.95 0.98
2402 7462 2.936498 CAGTTGCCAGGAACGGTAATAG 59.064 50.000 0.00 0.00 32.95 1.73
2403 7463 2.093128 AGTTGCCAGGAACGGTAATAGG 60.093 50.000 0.00 0.00 32.95 2.57
2404 7464 1.575419 TGCCAGGAACGGTAATAGGT 58.425 50.000 0.00 0.00 0.00 3.08
2405 7465 1.910671 TGCCAGGAACGGTAATAGGTT 59.089 47.619 0.00 0.00 0.00 3.50
2407 7467 3.518705 TGCCAGGAACGGTAATAGGTTTA 59.481 43.478 0.00 0.00 0.00 2.01
2408 7468 4.019501 TGCCAGGAACGGTAATAGGTTTAA 60.020 41.667 0.00 0.00 0.00 1.52
2409 7469 5.128205 GCCAGGAACGGTAATAGGTTTAAT 58.872 41.667 0.00 0.00 0.00 1.40
2410 7470 6.126825 TGCCAGGAACGGTAATAGGTTTAATA 60.127 38.462 0.00 0.00 0.00 0.98
2411 7471 6.938596 GCCAGGAACGGTAATAGGTTTAATAT 59.061 38.462 0.00 0.00 0.00 1.28
2413 7473 7.389607 CCAGGAACGGTAATAGGTTTAATATGG 59.610 40.741 0.00 0.00 0.00 2.74
2414 7474 8.152246 CAGGAACGGTAATAGGTTTAATATGGA 58.848 37.037 0.00 0.00 0.00 3.41
2415 7475 8.887393 AGGAACGGTAATAGGTTTAATATGGAT 58.113 33.333 0.00 0.00 0.00 3.41
2416 7476 8.943002 GGAACGGTAATAGGTTTAATATGGATG 58.057 37.037 0.00 0.00 0.00 3.51
2417 7477 8.857694 AACGGTAATAGGTTTAATATGGATGG 57.142 34.615 0.00 0.00 0.00 3.51
2418 7478 7.399634 ACGGTAATAGGTTTAATATGGATGGG 58.600 38.462 0.00 0.00 0.00 4.00
2419 7479 6.826741 CGGTAATAGGTTTAATATGGATGGGG 59.173 42.308 0.00 0.00 0.00 4.96
2443 7503 1.575419 TGCCAGGAACGGTAATAGGT 58.425 50.000 0.00 0.00 0.00 3.08
2448 7508 3.307199 CCAGGAACGGTAATAGGTGTGTT 60.307 47.826 0.00 0.00 0.00 3.32
2465 7552 3.823304 TGTGTTATTGCAGTTGTATGCCA 59.177 39.130 0.00 0.00 45.91 4.92
2519 7606 5.353111 TGCTGTGAATTCGAATTATACGGA 58.647 37.500 31.07 22.16 29.95 4.69
2542 7629 3.507233 TGATTGTCCAGCACCTTTCAATC 59.493 43.478 0.00 0.00 40.47 2.67
2546 7633 1.089920 CCAGCACCTTTCAATCCTCG 58.910 55.000 0.00 0.00 0.00 4.63
2547 7634 0.449388 CAGCACCTTTCAATCCTCGC 59.551 55.000 0.00 0.00 0.00 5.03
2548 7635 0.036732 AGCACCTTTCAATCCTCGCA 59.963 50.000 0.00 0.00 0.00 5.10
2565 7652 2.159099 TCGCAGCAATCACTTAGGGTAG 60.159 50.000 0.00 0.00 0.00 3.18
2587 7674 2.820787 CGAAGGAGAACCACACTAGTCT 59.179 50.000 0.00 0.00 38.94 3.24
2605 7692 8.535690 ACTAGTCTAAGTGATTGCTAAAACAC 57.464 34.615 0.00 0.00 38.88 3.32
2615 7702 8.143193 AGTGATTGCTAAAACACAAATGAATGA 58.857 29.630 0.00 0.00 40.52 2.57
2617 7704 7.384660 TGATTGCTAAAACACAAATGAATGACC 59.615 33.333 0.00 0.00 0.00 4.02
2619 7706 6.757237 TGCTAAAACACAAATGAATGACCAT 58.243 32.000 0.00 0.00 0.00 3.55
2632 7719 6.734502 TGAATGACCATCCATGCAAATAAT 57.265 33.333 0.00 0.00 29.43 1.28
2663 7750 2.669364 GTTCTGCAATTGAACTGGCTG 58.331 47.619 10.34 0.00 40.23 4.85
2681 7768 7.606349 ACTGGCTGAAATTCTAAAGGAAAATC 58.394 34.615 0.00 0.00 37.49 2.17
2696 7783 0.984230 AAATCCTGCTCCGAGAACCA 59.016 50.000 0.00 0.00 0.00 3.67
2706 7793 0.032952 CCGAGAACCAACCGAGTCAA 59.967 55.000 0.00 0.00 0.00 3.18
2753 7840 1.412937 GCCCCAAACCCCACATCATAT 60.413 52.381 0.00 0.00 0.00 1.78
2765 7852 3.254024 ATCATATGCCCGGGCGGAC 62.254 63.158 39.00 15.31 45.51 4.79
2766 7853 4.248842 CATATGCCCGGGCGGACA 62.249 66.667 39.00 23.69 45.51 4.02
2768 7855 3.767630 ATATGCCCGGGCGGACAAC 62.768 63.158 39.00 13.26 45.51 3.32
2776 7863 2.668550 GGCGGACAACCCAGTCAC 60.669 66.667 0.00 0.00 40.29 3.67
2785 7872 4.394712 CCCAGTCACTGACCGGCC 62.395 72.222 6.30 0.00 32.44 6.13
2786 7873 3.625897 CCAGTCACTGACCGGCCA 61.626 66.667 6.30 0.00 32.44 5.36
2829 7917 1.830847 AAACCGGCCTCAAACACCC 60.831 57.895 0.00 0.00 0.00 4.61
2834 7922 1.152546 GGCCTCAAACACCCAGGTT 60.153 57.895 0.00 0.00 0.00 3.50
2835 7923 1.463553 GGCCTCAAACACCCAGGTTG 61.464 60.000 0.00 0.00 46.56 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.571571 TCCAACGTAACTCTGTCGAATG 58.428 45.455 0.00 0.00 0.00 2.67
10 11 3.489180 AGATCCAACGTAACTCTGTCG 57.511 47.619 0.00 0.00 0.00 4.35
11 12 3.368236 GCAAGATCCAACGTAACTCTGTC 59.632 47.826 0.00 0.00 0.00 3.51
12 13 3.244078 TGCAAGATCCAACGTAACTCTGT 60.244 43.478 0.00 0.00 0.00 3.41
32 33 1.215647 CGGTGTCAGACCTAGGTGC 59.784 63.158 22.10 11.15 43.55 5.01
33 34 0.966920 AACGGTGTCAGACCTAGGTG 59.033 55.000 22.10 6.03 43.55 4.00
42 43 1.498865 GAGTGTGCCAACGGTGTCAG 61.499 60.000 0.00 0.00 0.00 3.51
46 47 1.172180 AATGGAGTGTGCCAACGGTG 61.172 55.000 0.00 0.00 42.16 4.94
48 49 1.580942 CAATGGAGTGTGCCAACGG 59.419 57.895 0.00 0.00 42.16 4.44
59 60 0.107456 ACGCCTAGCATCCAATGGAG 59.893 55.000 8.40 1.23 34.05 3.86
77 78 0.108186 TCCATCACATCGTGCCAGAC 60.108 55.000 0.00 0.00 32.98 3.51
81 82 1.331756 GACAATCCATCACATCGTGCC 59.668 52.381 0.00 0.00 32.98 5.01
96 97 0.991920 AATCCCCTGACGGTGACAAT 59.008 50.000 0.00 0.00 0.00 2.71
99 100 0.541863 ATGAATCCCCTGACGGTGAC 59.458 55.000 0.00 0.00 0.00 3.67
103 104 3.064820 CGTAAAAATGAATCCCCTGACGG 59.935 47.826 0.00 0.00 0.00 4.79
105 106 4.698304 TCACGTAAAAATGAATCCCCTGAC 59.302 41.667 0.00 0.00 0.00 3.51
108 109 4.263771 ACCTCACGTAAAAATGAATCCCCT 60.264 41.667 0.00 0.00 0.00 4.79
113 114 6.715264 AGAAGGAACCTCACGTAAAAATGAAT 59.285 34.615 0.00 0.00 0.00 2.57
119 120 7.177216 TGTCTATAGAAGGAACCTCACGTAAAA 59.823 37.037 3.40 0.00 0.00 1.52
120 121 6.660521 TGTCTATAGAAGGAACCTCACGTAAA 59.339 38.462 3.40 0.00 0.00 2.01
133 134 8.454106 CAAACTTGAACCATTGTCTATAGAAGG 58.546 37.037 3.40 7.08 0.00 3.46
182 183 8.680001 CGAGAGAGATGATCATATCTGAATTCT 58.320 37.037 32.01 22.94 39.27 2.40
187 188 7.548780 CACTACGAGAGAGATGATCATATCTGA 59.451 40.741 32.01 13.83 39.27 3.27
193 194 6.951062 TTTCACTACGAGAGAGATGATCAT 57.049 37.500 8.25 8.25 0.00 2.45
196 197 8.687242 TGTTTATTTCACTACGAGAGAGATGAT 58.313 33.333 0.00 0.00 0.00 2.45
208 209 5.449177 GGCCATGCTCTGTTTATTTCACTAC 60.449 44.000 0.00 0.00 0.00 2.73
211 212 3.193267 TGGCCATGCTCTGTTTATTTCAC 59.807 43.478 0.00 0.00 0.00 3.18
213 214 4.427312 CTTGGCCATGCTCTGTTTATTTC 58.573 43.478 6.09 0.00 0.00 2.17
235 236 2.480759 CCAAAGCTAGGATTGCATGTGC 60.481 50.000 0.00 0.00 42.50 4.57
236 237 2.756760 ACCAAAGCTAGGATTGCATGTG 59.243 45.455 11.80 0.00 0.00 3.21
260 261 5.673514 AGGTACGAAGAAAAGTTTGTGGTA 58.326 37.500 0.00 0.00 0.00 3.25
263 264 7.165318 GCTAAAAGGTACGAAGAAAAGTTTGTG 59.835 37.037 0.00 0.00 0.00 3.33
274 275 7.019418 GGTTTAACATGCTAAAAGGTACGAAG 58.981 38.462 2.93 0.00 0.00 3.79
276 277 6.232692 AGGTTTAACATGCTAAAAGGTACGA 58.767 36.000 2.93 0.00 0.00 3.43
277 278 6.402875 GGAGGTTTAACATGCTAAAAGGTACG 60.403 42.308 2.93 0.00 0.00 3.67
278 279 6.431852 TGGAGGTTTAACATGCTAAAAGGTAC 59.568 38.462 2.93 0.00 0.00 3.34
279 280 6.544650 TGGAGGTTTAACATGCTAAAAGGTA 58.455 36.000 2.93 0.00 0.00 3.08
280 281 5.390387 TGGAGGTTTAACATGCTAAAAGGT 58.610 37.500 2.93 0.00 0.00 3.50
282 283 8.902806 TCATATGGAGGTTTAACATGCTAAAAG 58.097 33.333 2.13 0.00 0.00 2.27
302 303 6.037610 GTGGTCTTAGAAAACTGCCTCATATG 59.962 42.308 0.00 0.00 0.00 1.78
311 312 3.251004 GTGCTGGTGGTCTTAGAAAACTG 59.749 47.826 0.00 0.00 0.00 3.16
317 318 0.685097 GTGGTGCTGGTGGTCTTAGA 59.315 55.000 0.00 0.00 0.00 2.10
334 335 4.746115 CCATTTGATGACAAAACACCTGTG 59.254 41.667 0.00 0.00 46.77 3.66
338 339 2.730928 CGCCATTTGATGACAAAACACC 59.269 45.455 0.00 0.00 46.77 4.16
351 352 4.574421 TGTGATAGGACAATACGCCATTTG 59.426 41.667 0.00 0.00 0.00 2.32
353 354 4.415881 TGTGATAGGACAATACGCCATT 57.584 40.909 0.00 0.00 0.00 3.16
366 367 6.649973 TGGCAAAACAAAATCAATGTGATAGG 59.350 34.615 0.00 0.00 35.76 2.57
367 368 7.512297 GTGGCAAAACAAAATCAATGTGATAG 58.488 34.615 0.00 0.00 35.76 2.08
368 369 6.145209 CGTGGCAAAACAAAATCAATGTGATA 59.855 34.615 0.00 0.00 35.76 2.15
369 370 5.050227 CGTGGCAAAACAAAATCAATGTGAT 60.050 36.000 0.00 0.00 39.09 3.06
371 372 4.269603 TCGTGGCAAAACAAAATCAATGTG 59.730 37.500 0.00 0.00 0.00 3.21
383 384 1.566018 CGAGGAGGTCGTGGCAAAAC 61.566 60.000 0.00 0.00 44.20 2.43
393 394 2.289444 TGTTTGGACATTCGAGGAGGTC 60.289 50.000 0.00 0.00 0.00 3.85
394 395 1.697432 TGTTTGGACATTCGAGGAGGT 59.303 47.619 0.00 0.00 0.00 3.85
410 411 5.693104 GTGTGTGCAAAAGATCATGATGTTT 59.307 36.000 21.67 21.67 36.06 2.83
422 423 3.148026 TGTGTGATGTGTGTGCAAAAG 57.852 42.857 0.00 0.00 0.00 2.27
431 432 2.168326 TGCTCGAATGTGTGATGTGT 57.832 45.000 0.00 0.00 0.00 3.72
437 438 2.349590 TGGAAGATGCTCGAATGTGTG 58.650 47.619 0.00 0.00 0.00 3.82
478 480 2.878406 GCACCTGTGTGTGAACAGTAAT 59.122 45.455 3.85 0.00 45.08 1.89
496 498 0.304705 GTGCGCAGGTGTATATGCAC 59.695 55.000 12.22 14.90 44.72 4.57
497 499 0.813610 GGTGCGCAGGTGTATATGCA 60.814 55.000 12.22 0.00 42.68 3.96
498 500 1.831389 CGGTGCGCAGGTGTATATGC 61.831 60.000 12.22 0.00 39.09 3.14
499 501 0.249280 TCGGTGCGCAGGTGTATATG 60.249 55.000 12.22 0.00 0.00 1.78
500 502 0.462375 TTCGGTGCGCAGGTGTATAT 59.538 50.000 12.22 0.00 0.00 0.86
501 503 0.462375 ATTCGGTGCGCAGGTGTATA 59.538 50.000 12.22 0.00 0.00 1.47
504 506 2.742372 GATTCGGTGCGCAGGTGT 60.742 61.111 12.22 0.00 0.00 4.16
516 518 8.816144 CAAAAACCCATACCAATATTTGATTCG 58.184 33.333 0.00 0.00 0.00 3.34
517 519 9.665719 ACAAAAACCCATACCAATATTTGATTC 57.334 29.630 0.00 0.00 32.45 2.52
530 532 2.101582 TGTGTGCCACAAAAACCCATAC 59.898 45.455 0.00 0.00 41.69 2.39
532 534 1.198713 TGTGTGCCACAAAAACCCAT 58.801 45.000 0.00 0.00 41.69 4.00
589 591 6.558771 TGATGTTCTCATTGTTAGTGGTTG 57.441 37.500 0.00 0.00 34.06 3.77
605 607 9.906660 TGTATCCAAATGTTACTTTTGATGTTC 57.093 29.630 20.50 10.15 36.40 3.18
681 692 3.118261 TGAGTAACCTGCCATGATTCCTC 60.118 47.826 0.00 0.00 0.00 3.71
793 810 9.944663 GAAATGCGATAAAATATCACAAGGTTA 57.055 29.630 0.00 0.00 0.00 2.85
795 812 7.011950 TCGAAATGCGATAAAATATCACAAGGT 59.988 33.333 0.00 0.00 45.59 3.50
820 837 4.399303 CAGAGGGTTATGGTGGAATTGTTC 59.601 45.833 0.00 0.00 0.00 3.18
848 865 1.535462 ACACGTTGGATTAAGTGCAGC 59.465 47.619 0.00 0.00 38.08 5.25
857 874 3.639094 TCCCATTTTTCACACGTTGGATT 59.361 39.130 0.20 0.00 0.00 3.01
885 903 1.366319 AGAGGCCATTGTTCCTGACT 58.634 50.000 5.01 0.00 31.71 3.41
969 988 2.002586 CAGCGGTACTGTTTGGATGAG 58.997 52.381 3.10 0.00 41.86 2.90
1043 1069 7.165485 AGATACACTAAACAAGCACCACATAA 58.835 34.615 0.00 0.00 0.00 1.90
1110 1137 5.614887 GCAGAGAACAAATCCTAACGTGAAC 60.615 44.000 0.00 0.00 0.00 3.18
1112 1139 3.994392 GCAGAGAACAAATCCTAACGTGA 59.006 43.478 0.00 0.00 0.00 4.35
1113 1140 3.997021 AGCAGAGAACAAATCCTAACGTG 59.003 43.478 0.00 0.00 0.00 4.49
1114 1141 3.997021 CAGCAGAGAACAAATCCTAACGT 59.003 43.478 0.00 0.00 0.00 3.99
1115 1142 3.372206 CCAGCAGAGAACAAATCCTAACG 59.628 47.826 0.00 0.00 0.00 3.18
1172 1201 2.349912 GGTTTTCGAGCAGCTCTTTCAC 60.350 50.000 20.39 11.16 0.00 3.18
1187 1216 3.614870 GCTGGACATTGATGTGGGTTTTC 60.615 47.826 0.57 0.00 41.95 2.29
1305 1335 3.119245 CGGGAGGATGAAGTCGAAAAGTA 60.119 47.826 0.00 0.00 0.00 2.24
1584 1614 1.429463 ACAACGAAGCGAGGATCAAC 58.571 50.000 0.00 0.00 33.17 3.18
1642 1672 4.910195 TCTTCCATATCAATTCCATCCCG 58.090 43.478 0.00 0.00 0.00 5.14
1846 4516 3.938963 AGTGCGAGAAAGTCAAGTTTTCA 59.061 39.130 0.00 0.00 37.08 2.69
2071 4991 8.518702 TCTCAATACTATCTCATCGAAATCTGG 58.481 37.037 0.00 0.00 0.00 3.86
2073 4993 8.243426 GCTCTCAATACTATCTCATCGAAATCT 58.757 37.037 0.00 0.00 0.00 2.40
2380 7440 0.887387 TTACCGTTCCTGGCAACTGC 60.887 55.000 0.00 0.00 41.14 4.40
2381 7441 1.821216 ATTACCGTTCCTGGCAACTG 58.179 50.000 0.00 0.00 37.61 3.16
2382 7442 2.093128 CCTATTACCGTTCCTGGCAACT 60.093 50.000 0.00 0.00 37.61 3.16
2383 7443 2.285977 CCTATTACCGTTCCTGGCAAC 58.714 52.381 0.00 0.00 0.00 4.17
2384 7444 1.910671 ACCTATTACCGTTCCTGGCAA 59.089 47.619 0.00 0.00 0.00 4.52
2386 7446 2.704464 AACCTATTACCGTTCCTGGC 57.296 50.000 0.00 0.00 0.00 4.85
2387 7447 7.389607 CCATATTAAACCTATTACCGTTCCTGG 59.610 40.741 0.00 0.00 0.00 4.45
2389 7449 8.266363 TCCATATTAAACCTATTACCGTTCCT 57.734 34.615 0.00 0.00 0.00 3.36
2390 7450 8.943002 CATCCATATTAAACCTATTACCGTTCC 58.057 37.037 0.00 0.00 0.00 3.62
2391 7451 8.943002 CCATCCATATTAAACCTATTACCGTTC 58.057 37.037 0.00 0.00 0.00 3.95
2392 7452 7.886446 CCCATCCATATTAAACCTATTACCGTT 59.114 37.037 0.00 0.00 0.00 4.44
2393 7453 7.399634 CCCATCCATATTAAACCTATTACCGT 58.600 38.462 0.00 0.00 0.00 4.83
2395 7455 6.605995 GCCCCATCCATATTAAACCTATTACC 59.394 42.308 0.00 0.00 0.00 2.85
2396 7456 7.179269 TGCCCCATCCATATTAAACCTATTAC 58.821 38.462 0.00 0.00 0.00 1.89
2398 7458 6.183361 ACTGCCCCATCCATATTAAACCTATT 60.183 38.462 0.00 0.00 0.00 1.73
2400 7460 4.667858 ACTGCCCCATCCATATTAAACCTA 59.332 41.667 0.00 0.00 0.00 3.08
2401 7461 3.467103 ACTGCCCCATCCATATTAAACCT 59.533 43.478 0.00 0.00 0.00 3.50
2402 7462 3.844640 ACTGCCCCATCCATATTAAACC 58.155 45.455 0.00 0.00 0.00 3.27
2403 7463 4.501400 GCAACTGCCCCATCCATATTAAAC 60.501 45.833 0.00 0.00 34.31 2.01
2404 7464 3.640967 GCAACTGCCCCATCCATATTAAA 59.359 43.478 0.00 0.00 34.31 1.52
2405 7465 3.230134 GCAACTGCCCCATCCATATTAA 58.770 45.455 0.00 0.00 34.31 1.40
2407 7467 1.708341 GCAACTGCCCCATCCATATT 58.292 50.000 0.00 0.00 34.31 1.28
2408 7468 3.444850 GCAACTGCCCCATCCATAT 57.555 52.632 0.00 0.00 34.31 1.78
2419 7479 0.887387 TTACCGTTCCTGGCAACTGC 60.887 55.000 0.00 0.00 41.14 4.40
2443 7503 3.823304 TGGCATACAACTGCAATAACACA 59.177 39.130 0.00 0.00 44.12 3.72
2448 7508 3.643199 TCCTGGCATACAACTGCAATA 57.357 42.857 0.00 0.00 44.12 1.90
2519 7606 3.159213 TGAAAGGTGCTGGACAATCAT 57.841 42.857 0.77 0.00 0.00 2.45
2542 7629 1.293924 CCTAAGTGATTGCTGCGAGG 58.706 55.000 0.00 0.00 0.00 4.63
2546 7633 1.943340 GCTACCCTAAGTGATTGCTGC 59.057 52.381 0.00 0.00 0.00 5.25
2547 7634 2.159099 TCGCTACCCTAAGTGATTGCTG 60.159 50.000 0.00 0.00 31.19 4.41
2548 7635 2.108168 TCGCTACCCTAAGTGATTGCT 58.892 47.619 0.00 0.00 31.19 3.91
2565 7652 1.272769 ACTAGTGTGGTTCTCCTTCGC 59.727 52.381 0.00 0.00 34.23 4.70
2587 7674 9.979578 ATTCATTTGTGTTTTAGCAATCACTTA 57.020 25.926 0.00 0.00 34.76 2.24
2605 7692 4.394439 TGCATGGATGGTCATTCATTTG 57.606 40.909 2.13 0.00 34.87 2.32
2658 7745 6.725834 AGGATTTTCCTTTAGAATTTCAGCCA 59.274 34.615 0.00 0.00 46.91 4.75
2663 7750 7.261325 GGAGCAGGATTTTCCTTTAGAATTTC 58.739 38.462 0.00 0.00 46.91 2.17
2681 7768 1.376037 GGTTGGTTCTCGGAGCAGG 60.376 63.158 0.00 0.00 0.00 4.85
2688 7775 1.269621 ACTTGACTCGGTTGGTTCTCG 60.270 52.381 0.00 0.00 0.00 4.04
2696 7783 3.799232 GCTCTAACACACTTGACTCGGTT 60.799 47.826 0.00 0.00 0.00 4.44
2706 7793 3.766591 AGCTGTAGATGCTCTAACACACT 59.233 43.478 0.00 0.00 35.67 3.55
2731 7818 2.203773 ATGTGGGGTTTGGGGCAC 60.204 61.111 0.00 0.00 0.00 5.01
2732 7819 2.104359 ATGATGTGGGGTTTGGGGCA 62.104 55.000 0.00 0.00 0.00 5.36
2745 7832 2.032528 CGCCCGGGCATATGATGT 59.967 61.111 42.78 0.00 42.06 3.06
2765 7852 4.361253 CGGTCAGTGACTGGGTTG 57.639 61.111 22.38 3.56 35.49 3.77
2791 7878 2.746277 GCTGCCCGTTTGGATCGT 60.746 61.111 0.00 0.00 37.49 3.73
2792 7879 2.436646 AGCTGCCCGTTTGGATCG 60.437 61.111 0.00 0.00 37.49 3.69
2793 7880 0.960364 TTGAGCTGCCCGTTTGGATC 60.960 55.000 0.00 0.00 37.49 3.36
2796 7883 1.007387 GTTTGAGCTGCCCGTTTGG 60.007 57.895 0.00 0.00 37.09 3.28
2797 7884 1.007387 GGTTTGAGCTGCCCGTTTG 60.007 57.895 0.00 0.00 0.00 2.93
2798 7885 2.551912 CGGTTTGAGCTGCCCGTTT 61.552 57.895 0.00 0.00 35.78 3.60
2799 7886 2.978010 CGGTTTGAGCTGCCCGTT 60.978 61.111 0.00 0.00 35.78 4.44


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

AutoCloner maintained by Alex Coulton.