Multiple sequence alignment - TraesCS7D01G374700

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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 TraesCS7D01G374700 chr7D 100.000 5676 0 0 1 5676 485024612 485030287 0.000000e+00 10482.0
1 TraesCS7D01G374700 chr7A 95.414 4950 178 28 637 5570 553364669 553369585 0.000000e+00 7838.0
2 TraesCS7D01G374700 chr7A 90.217 276 16 7 1 274 553363928 553364194 3.250000e-92 350.0
3 TraesCS7D01G374700 chr7A 86.853 251 15 9 397 641 553364215 553364453 1.210000e-66 265.0
4 TraesCS7D01G374700 chr7B 89.900 3485 333 12 657 4138 512694816 512698284 0.000000e+00 4468.0
5 TraesCS7D01G374700 chr7B 89.042 3276 330 21 869 4138 512707592 512710844 0.000000e+00 4034.0
6 TraesCS7D01G374700 chr7B 88.504 3201 344 15 961 4138 663120264 663117065 0.000000e+00 3851.0
7 TraesCS7D01G374700 chr7B 94.844 1280 58 7 4230 5505 512710954 512712229 0.000000e+00 1991.0
8 TraesCS7D01G374700 chr7B 92.536 1313 77 12 4231 5538 512698429 512699725 0.000000e+00 1862.0
9 TraesCS7D01G374700 chr7B 82.378 698 88 20 4240 4916 663116698 663116015 4.930000e-160 575.0
10 TraesCS7D01G374700 chr7B 84.746 236 20 5 398 632 512694013 512694233 7.400000e-54 222.0
11 TraesCS7D01G374700 chr7B 85.520 221 15 4 691 911 512693366 512693569 1.240000e-51 215.0
12 TraesCS7D01G374700 chr7B 83.197 244 28 9 46 285 512706469 512706703 1.600000e-50 211.0
13 TraesCS7D01G374700 chr7B 92.913 127 1 3 5491 5617 512712243 512712361 1.630000e-40 178.0
14 TraesCS7D01G374700 chr7B 89.655 116 12 0 283 398 748124182 748124297 1.270000e-31 148.0
15 TraesCS7D01G374700 chr7B 94.643 56 3 0 5529 5584 512701011 512701066 2.820000e-13 87.9
16 TraesCS7D01G374700 chr7B 100.000 29 0 0 880 908 663120325 663120297 3.000000e-03 54.7
17 TraesCS7D01G374700 chr6D 83.452 985 153 6 3153 4135 1413807 1412831 0.000000e+00 907.0
18 TraesCS7D01G374700 chr6D 76.612 1163 248 20 2984 4136 157441343 157440195 2.250000e-173 619.0
19 TraesCS7D01G374700 chr6D 78.476 525 105 8 3533 4053 157666496 157667016 2.530000e-88 337.0
20 TraesCS7D01G374700 chr6D 82.317 164 27 2 4264 4426 157593785 157593947 2.130000e-29 141.0
21 TraesCS7D01G374700 chr6B 81.508 1114 188 14 3028 4135 5731924 5733025 0.000000e+00 900.0
22 TraesCS7D01G374700 chr6B 74.494 988 207 36 3107 4075 715638109 715637148 2.480000e-103 387.0
23 TraesCS7D01G374700 chr6B 86.607 112 15 0 287 398 680549406 680549295 2.150000e-24 124.0
24 TraesCS7D01G374700 chr5B 80.625 320 56 6 3533 3849 516085608 516085924 5.680000e-60 243.0
25 TraesCS7D01G374700 chr5B 85.714 119 17 0 280 398 357108009 357107891 5.970000e-25 126.0
26 TraesCS7D01G374700 chr4D 89.167 120 12 1 279 398 40952391 40952273 1.270000e-31 148.0
27 TraesCS7D01G374700 chr3D 89.655 116 12 0 283 398 442042728 442042613 1.270000e-31 148.0
28 TraesCS7D01G374700 chr3D 88.333 120 13 1 279 398 416394100 416393982 5.930000e-30 143.0
29 TraesCS7D01G374700 chr2A 86.607 112 15 0 287 398 163668020 163667909 2.150000e-24 124.0
30 TraesCS7D01G374700 chr2A 84.167 120 18 1 279 398 763189785 763189667 1.290000e-21 115.0
31 TraesCS7D01G374700 chr4B 85.345 116 17 0 283 398 600423609 600423724 2.780000e-23 121.0
32 TraesCS7D01G374700 chr5D 100.000 44 0 0 4991 5034 22965862 22965905 1.310000e-11 82.4
33 TraesCS7D01G374700 chr2D 95.556 45 1 1 4991 5034 314824032 314824076 2.840000e-08 71.3


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G374700 chr7D 485024612 485030287 5675 False 10482.000000 10482 100.000 1 5676 1 chr7D.!!$F1 5675
1 TraesCS7D01G374700 chr7A 553363928 553369585 5657 False 2817.666667 7838 90.828 1 5570 3 chr7A.!!$F1 5569
2 TraesCS7D01G374700 chr7B 512706469 512712361 5892 False 1603.500000 4034 89.999 46 5617 4 chr7B.!!$F3 5571
3 TraesCS7D01G374700 chr7B 663116015 663120325 4310 True 1493.566667 3851 90.294 880 4916 3 chr7B.!!$R1 4036
4 TraesCS7D01G374700 chr7B 512693366 512701066 7700 False 1370.980000 4468 89.469 398 5584 5 chr7B.!!$F2 5186
5 TraesCS7D01G374700 chr6D 1412831 1413807 976 True 907.000000 907 83.452 3153 4135 1 chr6D.!!$R1 982
6 TraesCS7D01G374700 chr6D 157440195 157441343 1148 True 619.000000 619 76.612 2984 4136 1 chr6D.!!$R2 1152
7 TraesCS7D01G374700 chr6D 157666496 157667016 520 False 337.000000 337 78.476 3533 4053 1 chr6D.!!$F2 520
8 TraesCS7D01G374700 chr6B 5731924 5733025 1101 False 900.000000 900 81.508 3028 4135 1 chr6B.!!$F1 1107
9 TraesCS7D01G374700 chr6B 715637148 715638109 961 True 387.000000 387 74.494 3107 4075 1 chr6B.!!$R2 968

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
389 393 0.108041 TCCGCCAAGTATTTCCGGAC 60.108 55.000 1.83 0.00 42.51 4.79 F
1334 2284 0.252881 ACATTCCTGAGGAGGCTCCA 60.253 55.000 33.86 14.72 39.61 3.86 F
1555 2505 0.175989 CCTGGGTTTACTCGAGCTCC 59.824 60.000 13.61 9.58 0.00 4.70 F
2109 3059 1.557832 TCCATTGGAAACCTACCCTCG 59.442 52.381 1.94 0.00 0.00 4.63 F
3729 4704 2.289882 TGCAGAATGTGAGACCCTGAAG 60.290 50.000 0.00 0.00 39.31 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1389 2339 0.107654 GGTTGAGCCGCTTCAGGTAT 60.108 55.000 0.00 0.0 0.00 2.73 R
2470 3440 1.753073 GCAATTGCTTAGGCTGGACAT 59.247 47.619 23.21 0.0 39.59 3.06 R
2788 3758 4.261280 GCCACCAAGTTTAAGTTCGCTTAA 60.261 41.667 0.00 0.0 45.06 1.85 R
3936 4911 3.328382 TGTTGGTGAAGGTATTCGAGG 57.672 47.619 0.00 0.0 38.34 4.63 R
5348 6627 0.401738 TAGCTGCTTGGCTTGACCTT 59.598 50.000 7.79 0.0 42.97 3.50 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
67 68 5.975693 AGCGACTTCCCAATTATCAAAAA 57.024 34.783 0.00 0.00 0.00 1.94
110 113 3.074390 TCAACAATGGTGACTCCTTCCAT 59.926 43.478 0.00 0.00 42.82 3.41
163 167 2.628178 TGTTGACTGGAGAGAACACGAT 59.372 45.455 0.00 0.00 0.00 3.73
167 171 4.332828 TGACTGGAGAGAACACGATAGAA 58.667 43.478 0.00 0.00 41.38 2.10
208 212 6.645790 AGTTCAGATTCTTCACAAGCAAAT 57.354 33.333 0.00 0.00 0.00 2.32
209 213 7.750229 AGTTCAGATTCTTCACAAGCAAATA 57.250 32.000 0.00 0.00 0.00 1.40
210 214 7.814642 AGTTCAGATTCTTCACAAGCAAATAG 58.185 34.615 0.00 0.00 0.00 1.73
211 215 7.446625 AGTTCAGATTCTTCACAAGCAAATAGT 59.553 33.333 0.00 0.00 0.00 2.12
212 216 8.721478 GTTCAGATTCTTCACAAGCAAATAGTA 58.279 33.333 0.00 0.00 0.00 1.82
213 217 8.484641 TCAGATTCTTCACAAGCAAATAGTAG 57.515 34.615 0.00 0.00 0.00 2.57
235 239 8.610896 AGTAGTACTAGTATGTTTTAGCAGACG 58.389 37.037 8.55 0.00 35.91 4.18
256 260 2.205911 CCTCTCGCCTTTTAGCTAAGC 58.794 52.381 6.24 6.22 0.00 3.09
259 263 2.496070 TCTCGCCTTTTAGCTAAGCAGA 59.504 45.455 14.41 12.52 0.00 4.26
285 289 5.995897 GTCCCCAGCAACGTTAATAAGATAT 59.004 40.000 0.00 0.00 0.00 1.63
286 290 6.485648 GTCCCCAGCAACGTTAATAAGATATT 59.514 38.462 0.00 0.00 0.00 1.28
287 291 6.708949 TCCCCAGCAACGTTAATAAGATATTC 59.291 38.462 0.00 0.00 0.00 1.75
288 292 6.072673 CCCCAGCAACGTTAATAAGATATTCC 60.073 42.308 0.00 0.00 0.00 3.01
289 293 6.072673 CCCAGCAACGTTAATAAGATATTCCC 60.073 42.308 0.00 0.00 0.00 3.97
290 294 6.710744 CCAGCAACGTTAATAAGATATTCCCT 59.289 38.462 0.00 0.00 0.00 4.20
291 295 7.095187 CCAGCAACGTTAATAAGATATTCCCTC 60.095 40.741 0.00 0.00 0.00 4.30
292 296 6.935208 AGCAACGTTAATAAGATATTCCCTCC 59.065 38.462 0.00 0.00 0.00 4.30
293 297 6.708949 GCAACGTTAATAAGATATTCCCTCCA 59.291 38.462 0.00 0.00 0.00 3.86
295 299 8.936864 CAACGTTAATAAGATATTCCCTCCATC 58.063 37.037 0.00 0.00 0.00 3.51
296 300 7.621796 ACGTTAATAAGATATTCCCTCCATCC 58.378 38.462 0.00 0.00 0.00 3.51
297 301 7.236847 ACGTTAATAAGATATTCCCTCCATCCA 59.763 37.037 0.00 0.00 0.00 3.41
298 302 7.766278 CGTTAATAAGATATTCCCTCCATCCAG 59.234 40.741 0.00 0.00 0.00 3.86
299 303 8.826765 GTTAATAAGATATTCCCTCCATCCAGA 58.173 37.037 0.00 0.00 0.00 3.86
302 306 6.793518 AAGATATTCCCTCCATCCAGAATT 57.206 37.500 0.00 0.00 31.63 2.17
305 309 7.028131 AGATATTCCCTCCATCCAGAATTACT 58.972 38.462 0.00 0.00 31.63 2.24
306 310 7.519004 AGATATTCCCTCCATCCAGAATTACTT 59.481 37.037 0.00 0.00 31.63 2.24
307 311 4.778213 TCCCTCCATCCAGAATTACTTG 57.222 45.455 0.00 0.00 0.00 3.16
308 312 4.111577 TCCCTCCATCCAGAATTACTTGT 58.888 43.478 0.00 0.00 0.00 3.16
309 313 4.164221 TCCCTCCATCCAGAATTACTTGTC 59.836 45.833 0.00 0.00 0.00 3.18
310 314 4.122776 CCTCCATCCAGAATTACTTGTCG 58.877 47.826 0.00 0.00 0.00 4.35
311 315 3.531538 TCCATCCAGAATTACTTGTCGC 58.468 45.455 0.00 0.00 0.00 5.19
312 316 3.055458 TCCATCCAGAATTACTTGTCGCA 60.055 43.478 0.00 0.00 0.00 5.10
313 317 3.310774 CCATCCAGAATTACTTGTCGCAG 59.689 47.826 0.00 0.00 0.00 5.18
314 318 3.953712 TCCAGAATTACTTGTCGCAGA 57.046 42.857 0.00 0.00 0.00 4.26
315 319 4.265904 TCCAGAATTACTTGTCGCAGAA 57.734 40.909 0.00 0.00 39.69 3.02
317 321 5.245531 TCCAGAATTACTTGTCGCAGAAAT 58.754 37.500 0.00 0.00 39.69 2.17
318 322 6.403049 TCCAGAATTACTTGTCGCAGAAATA 58.597 36.000 0.00 0.00 39.69 1.40
319 323 6.876789 TCCAGAATTACTTGTCGCAGAAATAA 59.123 34.615 0.00 0.00 39.69 1.40
320 324 7.389330 TCCAGAATTACTTGTCGCAGAAATAAA 59.611 33.333 0.00 0.00 39.69 1.40
321 325 8.184192 CCAGAATTACTTGTCGCAGAAATAAAT 58.816 33.333 0.00 0.00 39.69 1.40
364 368 9.406113 AGAACTAAAATACGTCTAGATACACCT 57.594 33.333 0.00 0.00 0.00 4.00
373 377 5.469421 ACGTCTAGATACACCTATTTCTCCG 59.531 44.000 0.00 0.00 0.00 4.63
374 378 5.617308 CGTCTAGATACACCTATTTCTCCGC 60.617 48.000 0.00 0.00 0.00 5.54
375 379 4.765856 TCTAGATACACCTATTTCTCCGCC 59.234 45.833 0.00 0.00 0.00 6.13
376 380 3.305720 AGATACACCTATTTCTCCGCCA 58.694 45.455 0.00 0.00 0.00 5.69
377 381 3.709653 AGATACACCTATTTCTCCGCCAA 59.290 43.478 0.00 0.00 0.00 4.52
378 382 2.403252 ACACCTATTTCTCCGCCAAG 57.597 50.000 0.00 0.00 0.00 3.61
380 384 2.835764 ACACCTATTTCTCCGCCAAGTA 59.164 45.455 0.00 0.00 0.00 2.24
381 385 3.454812 ACACCTATTTCTCCGCCAAGTAT 59.545 43.478 0.00 0.00 0.00 2.12
383 387 4.881850 CACCTATTTCTCCGCCAAGTATTT 59.118 41.667 0.00 0.00 0.00 1.40
384 388 5.007724 CACCTATTTCTCCGCCAAGTATTTC 59.992 44.000 0.00 0.00 0.00 2.17
385 389 4.515567 CCTATTTCTCCGCCAAGTATTTCC 59.484 45.833 0.00 0.00 0.00 3.13
386 390 2.018542 TTCTCCGCCAAGTATTTCCG 57.981 50.000 0.00 0.00 0.00 4.30
387 391 0.177141 TCTCCGCCAAGTATTTCCGG 59.823 55.000 0.00 0.00 40.25 5.14
388 392 0.177141 CTCCGCCAAGTATTTCCGGA 59.823 55.000 0.00 0.00 44.85 5.14
389 393 0.108041 TCCGCCAAGTATTTCCGGAC 60.108 55.000 1.83 0.00 42.51 4.79
390 394 1.426041 CCGCCAAGTATTTCCGGACG 61.426 60.000 1.83 0.00 41.34 4.79
392 396 0.108041 GCCAAGTATTTCCGGACGGA 60.108 55.000 1.83 9.76 43.52 4.69
393 397 1.935933 CCAAGTATTTCCGGACGGAG 58.064 55.000 13.64 0.46 46.06 4.63
394 398 1.472728 CCAAGTATTTCCGGACGGAGG 60.473 57.143 13.64 6.09 46.06 4.30
395 399 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
414 665 2.093921 GGGAGAGGAGCACAAAGTCTAC 60.094 54.545 0.00 0.00 0.00 2.59
440 691 0.607489 CTGGAGGAGCACTGGGTTTG 60.607 60.000 0.00 0.00 0.00 2.93
453 704 4.638421 CACTGGGTTTGTTACAAGAGACAA 59.362 41.667 0.00 0.00 34.22 3.18
454 705 5.299279 CACTGGGTTTGTTACAAGAGACAAT 59.701 40.000 0.00 0.00 35.85 2.71
455 706 5.299279 ACTGGGTTTGTTACAAGAGACAATG 59.701 40.000 0.00 0.00 35.85 2.82
456 707 5.197451 TGGGTTTGTTACAAGAGACAATGT 58.803 37.500 0.00 0.00 35.85 2.71
457 708 6.358178 TGGGTTTGTTACAAGAGACAATGTA 58.642 36.000 0.00 0.00 35.85 2.29
458 709 7.001674 TGGGTTTGTTACAAGAGACAATGTAT 58.998 34.615 0.00 0.00 35.85 2.29
459 710 7.040755 TGGGTTTGTTACAAGAGACAATGTATG 60.041 37.037 0.00 0.00 35.85 2.39
480 753 5.159273 TGTATGTATCCTTTCACACAGCA 57.841 39.130 0.00 0.00 0.00 4.41
525 798 6.270927 ACAGCACCAGGATAATCACATATACT 59.729 38.462 0.00 0.00 0.00 2.12
526 799 7.454694 ACAGCACCAGGATAATCACATATACTA 59.545 37.037 0.00 0.00 0.00 1.82
527 800 7.761704 CAGCACCAGGATAATCACATATACTAC 59.238 40.741 0.00 0.00 0.00 2.73
544 817 9.162764 CATATACTACCAATATAAACACAGGCC 57.837 37.037 0.00 0.00 0.00 5.19
579 852 3.861341 CCGAGAATTTGGCAGAGGA 57.139 52.632 0.00 0.00 0.00 3.71
588 861 2.276732 TTGGCAGAGGAACAAAGAGG 57.723 50.000 0.00 0.00 0.00 3.69
609 888 2.158798 GGTTACTCCCTTATCCTGGCAC 60.159 54.545 0.00 0.00 0.00 5.01
616 895 4.508331 TCCCTTATCCTGGCACCATATTA 58.492 43.478 0.00 0.00 0.00 0.98
632 911 7.030165 CACCATATTACATCTAGCTCCGTTAG 58.970 42.308 0.00 0.00 0.00 2.34
672 1332 8.970859 ATATTTCTTCTTAGTGGAATGGACAG 57.029 34.615 0.00 0.00 0.00 3.51
673 1333 4.207891 TCTTCTTAGTGGAATGGACAGC 57.792 45.455 0.00 0.00 0.00 4.40
717 1571 2.921754 GCAGATTCTCAATTGCACAAGC 59.078 45.455 0.00 0.00 42.57 4.01
749 1603 5.300034 GCATAAATCAACCATGGATGACTCA 59.700 40.000 25.38 13.85 29.96 3.41
774 1631 2.280797 TGCGTTGACCAGAGCACC 60.281 61.111 0.00 0.00 34.39 5.01
778 1635 1.069090 GTTGACCAGAGCACCGACA 59.931 57.895 0.00 0.00 0.00 4.35
871 1819 9.331282 ACAGATAATTAAGTTCACTAAGCCATC 57.669 33.333 0.00 0.00 0.00 3.51
908 1856 5.533903 ACTTGCCTTGCTCAATCCATTATAG 59.466 40.000 0.00 0.00 0.00 1.31
909 1857 5.052693 TGCCTTGCTCAATCCATTATAGT 57.947 39.130 0.00 0.00 0.00 2.12
910 1858 6.186420 TGCCTTGCTCAATCCATTATAGTA 57.814 37.500 0.00 0.00 0.00 1.82
911 1859 6.782986 TGCCTTGCTCAATCCATTATAGTAT 58.217 36.000 0.00 0.00 0.00 2.12
912 1860 7.917003 TGCCTTGCTCAATCCATTATAGTATA 58.083 34.615 0.00 0.00 0.00 1.47
913 1861 8.551440 TGCCTTGCTCAATCCATTATAGTATAT 58.449 33.333 0.00 0.00 0.00 0.86
936 1884 5.726980 AAACAATGCATAGAAGGAAAGCA 57.273 34.783 0.00 0.00 39.79 3.91
940 1888 3.423539 TGCATAGAAGGAAAGCACACT 57.576 42.857 0.00 0.00 0.00 3.55
941 1889 3.754965 TGCATAGAAGGAAAGCACACTT 58.245 40.909 0.00 0.00 37.90 3.16
942 1890 3.503363 TGCATAGAAGGAAAGCACACTTG 59.497 43.478 0.00 0.00 35.85 3.16
985 1933 0.386478 GAAGTGAGCAAAAGCAGCCG 60.386 55.000 0.00 0.00 0.00 5.52
1006 1956 2.554344 GGCCTTGGTAGAAACATGGTGA 60.554 50.000 0.00 0.00 36.02 4.02
1070 2020 3.989698 CTAGCACGGGGTCAGCACG 62.990 68.421 0.00 0.00 0.00 5.34
1181 2131 1.525923 CTCTGGAGTCATGGGGCAG 59.474 63.158 0.00 0.00 0.00 4.85
1334 2284 0.252881 ACATTCCTGAGGAGGCTCCA 60.253 55.000 33.86 14.72 39.61 3.86
1513 2463 3.117738 CAGGCTGAAAGGGAAGATACCAT 60.118 47.826 9.42 0.00 0.00 3.55
1516 2466 3.117888 GCTGAAAGGGAAGATACCATGGA 60.118 47.826 21.47 2.01 0.00 3.41
1521 2471 2.708325 AGGGAAGATACCATGGAAGCTC 59.292 50.000 21.47 8.98 0.00 4.09
1555 2505 0.175989 CCTGGGTTTACTCGAGCTCC 59.824 60.000 13.61 9.58 0.00 4.70
1670 2620 3.390639 ACCATCCCTTCAGAGATAAGCAG 59.609 47.826 0.00 0.00 0.00 4.24
1674 2624 2.224257 CCCTTCAGAGATAAGCAGCCTC 60.224 54.545 0.00 0.00 0.00 4.70
2056 3006 4.946157 ACATGCTTGAACTCCTTTATCTGG 59.054 41.667 6.60 0.00 0.00 3.86
2105 3055 3.610911 CTCACTCCATTGGAAACCTACC 58.389 50.000 6.88 0.00 0.00 3.18
2109 3059 1.557832 TCCATTGGAAACCTACCCTCG 59.442 52.381 1.94 0.00 0.00 4.63
2143 3093 9.757227 AAATTGACCTCGAAAACAATGAATTAA 57.243 25.926 10.02 0.00 34.02 1.40
2144 3094 8.970691 ATTGACCTCGAAAACAATGAATTAAG 57.029 30.769 8.93 0.00 32.79 1.85
2178 3128 5.731686 GCCTCCTTTGCTATTCAATCTTTCG 60.732 44.000 0.00 0.00 34.12 3.46
2435 3405 2.708386 TTAACCATTGCCGAAAACCG 57.292 45.000 0.00 0.00 38.18 4.44
2607 3577 6.513806 AACATGCAAGATAACAGCATAACA 57.486 33.333 0.00 0.00 46.39 2.41
2788 3758 4.142403 CCACATTCGGCAATCTTACACAAT 60.142 41.667 0.00 0.00 0.00 2.71
3729 4704 2.289882 TGCAGAATGTGAGACCCTGAAG 60.290 50.000 0.00 0.00 39.31 3.02
3936 4911 4.841443 TGCAATTGATGTAGCATCATCC 57.159 40.909 10.34 3.37 42.24 3.51
4228 5285 9.391006 CACCACTCTTAAGTTAAATATGGCTAA 57.609 33.333 14.39 0.00 31.71 3.09
4330 5583 2.430694 TGATGTCTACAGCTACGGCATT 59.569 45.455 0.00 0.00 41.70 3.56
4543 5796 4.006780 TGCTTGCATCACTTCAGTTCTA 57.993 40.909 0.00 0.00 0.00 2.10
4572 5825 3.626670 GGGATTTCATGCTCACAAGAGAG 59.373 47.826 0.00 0.00 44.98 3.20
4881 6151 9.110502 GTATAAACCATATGCCCTAGAATAAGC 57.889 37.037 0.00 0.00 0.00 3.09
4892 6162 4.505039 CCCTAGAATAAGCCCATGGTGTAC 60.505 50.000 11.73 0.00 0.00 2.90
5041 6314 3.043999 ATACGCTTCCAGCCCCACC 62.044 63.158 0.00 0.00 38.18 4.61
5064 6338 9.191995 CACCTTTTACTTTAATAAACTGCCTTG 57.808 33.333 0.00 0.00 0.00 3.61
5085 6359 3.064207 GTGTATTCTCCACGACTGCAAA 58.936 45.455 0.00 0.00 0.00 3.68
5087 6361 3.684305 TGTATTCTCCACGACTGCAAATG 59.316 43.478 0.00 0.00 0.00 2.32
5102 6376 9.244799 CGACTGCAAATGTTTACTGAGTATATA 57.755 33.333 0.00 0.00 0.00 0.86
5206 6485 6.183359 GCTTATTCGCTTACATCCTCGATTAC 60.183 42.308 0.00 0.00 0.00 1.89
5324 6603 5.592587 TTGGTAAGAATGGAAGGAAGGAA 57.407 39.130 0.00 0.00 0.00 3.36
5348 6627 3.299977 CCTCCGTCGTGGTGGTCA 61.300 66.667 8.71 0.00 44.87 4.02
5352 6631 2.420043 CGTCGTGGTGGTCAAGGT 59.580 61.111 0.00 0.00 0.00 3.50
5584 8186 0.110295 ACACACTGGTATTGGCTGCA 59.890 50.000 0.50 0.00 0.00 4.41
5585 8187 1.272092 ACACACTGGTATTGGCTGCAT 60.272 47.619 0.50 0.00 0.00 3.96
5586 8188 1.820519 CACACTGGTATTGGCTGCATT 59.179 47.619 0.50 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 4.802248 GCTCAAGTGTTGAATGAGGTCTCT 60.802 45.833 4.39 0.00 40.68 3.10
10 11 3.434984 GCTCAAGTGTTGAATGAGGTCTC 59.565 47.826 4.39 0.00 40.68 3.36
11 12 3.181451 TGCTCAAGTGTTGAATGAGGTCT 60.181 43.478 4.39 0.00 40.68 3.85
67 68 0.773644 ATGGCTGGTCTTGTCAGGTT 59.226 50.000 0.00 0.00 33.16 3.50
209 213 8.610896 CGTCTGCTAAAACATACTAGTACTACT 58.389 37.037 4.31 0.00 0.00 2.57
210 214 7.375544 GCGTCTGCTAAAACATACTAGTACTAC 59.624 40.741 4.31 0.00 38.39 2.73
211 215 7.412853 GCGTCTGCTAAAACATACTAGTACTA 58.587 38.462 4.31 1.89 38.39 1.82
212 216 6.264088 GCGTCTGCTAAAACATACTAGTACT 58.736 40.000 4.31 0.00 38.39 2.73
213 217 5.458126 GGCGTCTGCTAAAACATACTAGTAC 59.542 44.000 4.31 0.00 42.25 2.73
256 260 0.606401 AACGTTGCTGGGGACATCTG 60.606 55.000 0.00 0.00 41.51 2.90
259 263 2.507407 ATTAACGTTGCTGGGGACAT 57.493 45.000 11.99 0.00 41.51 3.06
285 289 4.540099 ACAAGTAATTCTGGATGGAGGGAA 59.460 41.667 0.00 0.00 0.00 3.97
286 290 4.111577 ACAAGTAATTCTGGATGGAGGGA 58.888 43.478 0.00 0.00 0.00 4.20
287 291 4.455606 GACAAGTAATTCTGGATGGAGGG 58.544 47.826 0.00 0.00 0.00 4.30
288 292 4.122776 CGACAAGTAATTCTGGATGGAGG 58.877 47.826 0.00 0.00 0.00 4.30
289 293 3.557595 GCGACAAGTAATTCTGGATGGAG 59.442 47.826 0.00 0.00 0.00 3.86
290 294 3.055458 TGCGACAAGTAATTCTGGATGGA 60.055 43.478 0.00 0.00 0.00 3.41
291 295 3.270027 TGCGACAAGTAATTCTGGATGG 58.730 45.455 0.00 0.00 0.00 3.51
292 296 4.183865 TCTGCGACAAGTAATTCTGGATG 58.816 43.478 0.00 0.00 0.00 3.51
293 297 4.471904 TCTGCGACAAGTAATTCTGGAT 57.528 40.909 0.00 0.00 0.00 3.41
295 299 5.551760 ATTTCTGCGACAAGTAATTCTGG 57.448 39.130 0.00 0.00 0.00 3.86
338 342 9.406113 AGGTGTATCTAGACGTATTTTAGTTCT 57.594 33.333 0.00 0.00 0.00 3.01
347 351 7.333921 CGGAGAAATAGGTGTATCTAGACGTAT 59.666 40.741 0.00 0.00 33.68 3.06
348 352 6.648310 CGGAGAAATAGGTGTATCTAGACGTA 59.352 42.308 0.00 0.00 0.00 3.57
350 354 5.617308 GCGGAGAAATAGGTGTATCTAGACG 60.617 48.000 0.00 0.00 0.00 4.18
351 355 5.335819 GGCGGAGAAATAGGTGTATCTAGAC 60.336 48.000 0.00 0.00 0.00 2.59
352 356 4.765856 GGCGGAGAAATAGGTGTATCTAGA 59.234 45.833 0.00 0.00 0.00 2.43
353 357 4.523173 TGGCGGAGAAATAGGTGTATCTAG 59.477 45.833 0.00 0.00 0.00 2.43
354 358 4.476297 TGGCGGAGAAATAGGTGTATCTA 58.524 43.478 0.00 0.00 0.00 1.98
355 359 3.305720 TGGCGGAGAAATAGGTGTATCT 58.694 45.455 0.00 0.00 0.00 1.98
356 360 3.746045 TGGCGGAGAAATAGGTGTATC 57.254 47.619 0.00 0.00 0.00 2.24
357 361 3.454812 ACTTGGCGGAGAAATAGGTGTAT 59.545 43.478 0.00 0.00 0.00 2.29
358 362 2.835764 ACTTGGCGGAGAAATAGGTGTA 59.164 45.455 0.00 0.00 0.00 2.90
359 363 1.628846 ACTTGGCGGAGAAATAGGTGT 59.371 47.619 0.00 0.00 0.00 4.16
362 366 4.515567 GGAAATACTTGGCGGAGAAATAGG 59.484 45.833 0.00 0.00 0.00 2.57
363 367 4.211374 CGGAAATACTTGGCGGAGAAATAG 59.789 45.833 0.00 0.00 0.00 1.73
364 368 4.124238 CGGAAATACTTGGCGGAGAAATA 58.876 43.478 0.00 0.00 0.00 1.40
365 369 2.943033 CGGAAATACTTGGCGGAGAAAT 59.057 45.455 0.00 0.00 0.00 2.17
366 370 2.352388 CGGAAATACTTGGCGGAGAAA 58.648 47.619 0.00 0.00 0.00 2.52
367 371 1.406341 CCGGAAATACTTGGCGGAGAA 60.406 52.381 0.00 0.00 0.00 2.87
368 372 0.177141 CCGGAAATACTTGGCGGAGA 59.823 55.000 0.00 0.00 0.00 3.71
370 374 0.108041 GTCCGGAAATACTTGGCGGA 60.108 55.000 5.23 0.00 0.00 5.54
371 375 1.426041 CGTCCGGAAATACTTGGCGG 61.426 60.000 5.23 0.00 0.00 6.13
373 377 0.108041 TCCGTCCGGAAATACTTGGC 60.108 55.000 5.23 0.00 42.05 4.52
374 378 1.472728 CCTCCGTCCGGAAATACTTGG 60.473 57.143 5.23 1.90 44.66 3.61
375 379 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
376 380 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
377 381 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
378 382 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
380 384 1.001248 TCTCCCTCCGTCCGGAAAT 59.999 57.895 5.23 0.00 44.66 2.17
381 385 1.681327 CTCTCCCTCCGTCCGGAAA 60.681 63.158 5.23 0.00 44.66 3.13
383 387 4.124943 CCTCTCCCTCCGTCCGGA 62.125 72.222 0.00 0.00 42.90 5.14
384 388 4.124943 TCCTCTCCCTCCGTCCGG 62.125 72.222 0.00 0.00 0.00 5.14
385 389 2.517402 CTCCTCTCCCTCCGTCCG 60.517 72.222 0.00 0.00 0.00 4.79
386 390 2.835895 GCTCCTCTCCCTCCGTCC 60.836 72.222 0.00 0.00 0.00 4.79
387 391 2.043852 TGCTCCTCTCCCTCCGTC 60.044 66.667 0.00 0.00 0.00 4.79
388 392 2.363147 GTGCTCCTCTCCCTCCGT 60.363 66.667 0.00 0.00 0.00 4.69
389 393 1.544825 TTTGTGCTCCTCTCCCTCCG 61.545 60.000 0.00 0.00 0.00 4.63
390 394 0.251634 CTTTGTGCTCCTCTCCCTCC 59.748 60.000 0.00 0.00 0.00 4.30
392 396 0.980423 GACTTTGTGCTCCTCTCCCT 59.020 55.000 0.00 0.00 0.00 4.20
393 397 0.980423 AGACTTTGTGCTCCTCTCCC 59.020 55.000 0.00 0.00 0.00 4.30
394 398 2.563179 TGTAGACTTTGTGCTCCTCTCC 59.437 50.000 0.00 0.00 0.00 3.71
395 399 3.944055 TGTAGACTTTGTGCTCCTCTC 57.056 47.619 0.00 0.00 0.00 3.20
453 704 7.442364 GCTGTGTGAAAGGATACATACATACAT 59.558 37.037 0.00 0.00 37.46 2.29
454 705 6.761242 GCTGTGTGAAAGGATACATACATACA 59.239 38.462 0.00 0.00 37.46 2.29
455 706 6.761242 TGCTGTGTGAAAGGATACATACATAC 59.239 38.462 0.00 0.00 37.46 2.39
456 707 6.761242 GTGCTGTGTGAAAGGATACATACATA 59.239 38.462 0.00 0.00 37.46 2.29
457 708 5.586243 GTGCTGTGTGAAAGGATACATACAT 59.414 40.000 0.00 0.00 37.46 2.29
458 709 4.935205 GTGCTGTGTGAAAGGATACATACA 59.065 41.667 0.00 0.00 36.85 2.29
459 710 4.032900 CGTGCTGTGTGAAAGGATACATAC 59.967 45.833 0.00 0.00 41.41 2.39
460 711 4.081917 TCGTGCTGTGTGAAAGGATACATA 60.082 41.667 0.00 0.00 41.41 2.29
480 753 0.671796 TTCATCCGTGTCACTGTCGT 59.328 50.000 0.65 0.00 0.00 4.34
525 798 4.204012 GCTGGCCTGTGTTTATATTGGTA 58.796 43.478 11.69 0.00 0.00 3.25
526 799 3.023832 GCTGGCCTGTGTTTATATTGGT 58.976 45.455 11.69 0.00 0.00 3.67
527 800 2.362077 GGCTGGCCTGTGTTTATATTGG 59.638 50.000 11.69 0.00 0.00 3.16
588 861 2.124411 TGCCAGGATAAGGGAGTAACC 58.876 52.381 0.00 0.00 38.08 2.85
601 875 4.020218 GCTAGATGTAATATGGTGCCAGGA 60.020 45.833 0.00 0.00 0.00 3.86
663 1323 2.747460 TGCTGCCGCTGTCCATTC 60.747 61.111 0.70 0.00 36.97 2.67
664 1324 3.058160 GTGCTGCCGCTGTCCATT 61.058 61.111 0.70 0.00 36.97 3.16
665 1325 4.025858 AGTGCTGCCGCTGTCCAT 62.026 61.111 0.70 0.00 36.97 3.41
666 1326 4.994471 CAGTGCTGCCGCTGTCCA 62.994 66.667 11.55 0.00 43.06 4.02
717 1571 5.294799 CCATGGTTGATTTATGCATTGTTGG 59.705 40.000 3.54 0.00 0.00 3.77
749 1603 0.532862 CTGGTCAACGCAGGACTTGT 60.533 55.000 0.00 0.00 35.61 3.16
774 1631 2.611751 TGTGAACCAACATGACTTGTCG 59.388 45.455 0.00 0.00 37.68 4.35
778 1635 4.269183 TGACTTGTGAACCAACATGACTT 58.731 39.130 0.00 0.00 0.00 3.01
786 1643 2.653726 AGTGCATGACTTGTGAACCAA 58.346 42.857 0.00 0.00 0.00 3.67
815 1672 2.685388 TGCCGACAAATTGAGTCAACAA 59.315 40.909 7.96 0.00 35.77 2.83
871 1819 5.773239 CAAGGCAAGTTGCTCAATAATTG 57.227 39.130 26.16 14.96 44.28 2.32
910 1858 9.135189 TGCTTTCCTTCTATGCATTGTTTATAT 57.865 29.630 3.54 0.00 0.00 0.86
911 1859 8.405531 GTGCTTTCCTTCTATGCATTGTTTATA 58.594 33.333 3.54 0.00 36.04 0.98
912 1860 7.093814 TGTGCTTTCCTTCTATGCATTGTTTAT 60.094 33.333 3.54 0.00 36.04 1.40
913 1861 6.208402 TGTGCTTTCCTTCTATGCATTGTTTA 59.792 34.615 3.54 0.00 36.04 2.01
914 1862 5.010922 TGTGCTTTCCTTCTATGCATTGTTT 59.989 36.000 3.54 0.00 36.04 2.83
940 1888 2.171659 TGGTTCTGGTAGACACAAGCAA 59.828 45.455 0.00 0.00 33.51 3.91
941 1889 1.765904 TGGTTCTGGTAGACACAAGCA 59.234 47.619 0.00 0.00 33.93 3.91
942 1890 2.037251 TCTGGTTCTGGTAGACACAAGC 59.963 50.000 0.00 0.00 0.00 4.01
943 1891 4.336889 TTCTGGTTCTGGTAGACACAAG 57.663 45.455 0.00 0.00 0.00 3.16
985 1933 1.818674 CACCATGTTTCTACCAAGGCC 59.181 52.381 0.00 0.00 0.00 5.19
1017 1967 3.194062 GAGCAGAGAAACTAGCATGGAC 58.806 50.000 0.00 0.00 0.00 4.02
1018 1968 2.169352 GGAGCAGAGAAACTAGCATGGA 59.831 50.000 0.00 0.00 0.00 3.41
1070 2020 3.053291 TTCCGGCGTGTGGAATGC 61.053 61.111 6.01 0.00 40.51 3.56
1389 2339 0.107654 GGTTGAGCCGCTTCAGGTAT 60.108 55.000 0.00 0.00 0.00 2.73
1555 2505 4.735132 TTGGAGCTCGTTCCGGCG 62.735 66.667 7.83 0.00 40.27 6.46
1617 2567 0.175760 TGTTGTGGCCTAGATCGAGC 59.824 55.000 3.32 0.00 0.00 5.03
1665 2615 0.392193 CCAGATTCACGAGGCTGCTT 60.392 55.000 0.00 0.00 0.00 3.91
1670 2620 1.734465 CAAACTCCAGATTCACGAGGC 59.266 52.381 0.00 0.00 0.00 4.70
1674 2624 2.480419 GTCCACAAACTCCAGATTCACG 59.520 50.000 0.00 0.00 0.00 4.35
1709 2659 2.158652 GGGGGTATTTCTCCTGTTAGCC 60.159 54.545 0.00 0.00 36.78 3.93
2035 2985 3.950395 GCCAGATAAAGGAGTTCAAGCAT 59.050 43.478 0.00 0.00 0.00 3.79
2056 3006 7.792374 TGAGACCTGTAAGATTATTGAATGC 57.208 36.000 0.00 0.00 34.07 3.56
2105 3055 0.371645 GTCAATTTCAGCGAGCGAGG 59.628 55.000 0.00 0.00 0.00 4.63
2109 3059 0.371645 CGAGGTCAATTTCAGCGAGC 59.628 55.000 0.00 0.00 0.00 5.03
2178 3128 8.556213 TTTGTACATTGATAACTTGGAGGTAC 57.444 34.615 0.00 0.00 0.00 3.34
2435 3405 3.485877 GGCATCTTGTGTTGCTCGAATAC 60.486 47.826 0.00 0.00 38.54 1.89
2470 3440 1.753073 GCAATTGCTTAGGCTGGACAT 59.247 47.619 23.21 0.00 39.59 3.06
2788 3758 4.261280 GCCACCAAGTTTAAGTTCGCTTAA 60.261 41.667 0.00 0.00 45.06 1.85
2822 3792 5.830991 AGTAGACTAGAAGGTATGCTTCCAG 59.169 44.000 0.00 0.00 0.00 3.86
2844 3814 8.387813 TCTAATTTTTGTAATGGACACCCTAGT 58.612 33.333 0.00 0.00 37.96 2.57
2845 3815 8.674607 GTCTAATTTTTGTAATGGACACCCTAG 58.325 37.037 0.00 0.00 37.96 3.02
3729 4704 6.978659 TCATAAGATTCCTATGTCGAACACAC 59.021 38.462 2.92 0.00 38.04 3.82
3936 4911 3.328382 TGTTGGTGAAGGTATTCGAGG 57.672 47.619 0.00 0.00 38.34 4.63
4228 5285 6.704310 AGCAAAATGAAATGAGCAGGTTAAT 58.296 32.000 0.00 0.00 0.00 1.40
4330 5583 2.369860 AGTGAACATCTCCAGCAACAGA 59.630 45.455 0.00 0.00 0.00 3.41
4543 5796 2.029623 GAGCATGAAATCCCAGTGCAT 58.970 47.619 0.00 0.00 38.23 3.96
4572 5825 3.719214 GGATGCGATCCGTTGGTC 58.281 61.111 0.00 0.00 40.13 4.02
4788 6058 6.463995 ACGGCAATACAACAAATATTCCAT 57.536 33.333 0.00 0.00 0.00 3.41
4881 6151 2.480610 GCATGCGGTACACCATGGG 61.481 63.158 18.09 7.72 39.30 4.00
4892 6162 0.998226 CAACAAACAGACGCATGCGG 60.998 55.000 39.95 26.21 44.69 5.69
5041 6314 9.744468 ACACAAGGCAGTTTATTAAAGTAAAAG 57.256 29.630 0.00 0.00 0.00 2.27
5064 6338 2.363788 TGCAGTCGTGGAGAATACAC 57.636 50.000 0.00 0.00 35.55 2.90
5102 6376 5.813383 AGATGAGTTCATTGTTCTGGTCAT 58.187 37.500 0.00 0.00 36.57 3.06
5103 6377 5.233083 AGATGAGTTCATTGTTCTGGTCA 57.767 39.130 0.00 0.00 36.57 4.02
5324 6603 2.564975 CACGACGGAGGTAACGCT 59.435 61.111 0.00 0.00 46.39 5.07
5348 6627 0.401738 TAGCTGCTTGGCTTGACCTT 59.598 50.000 7.79 0.00 42.97 3.50
5352 6631 1.300971 CGCTTAGCTGCTTGGCTTGA 61.301 55.000 7.79 0.00 42.97 3.02


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

AutoCloner maintained by Alex Coulton.