Multiple sequence alignment - TraesCS2D01G122500

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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 TraesCS2D01G122500 chr2D 100.000 2986 0 0 1 2986 71577337 71580322 0.000000e+00 5515.0
1 TraesCS2D01G122500 chr2D 89.115 2260 152 44 765 2986 71565415 71567618 0.000000e+00 2724.0
2 TraesCS2D01G122500 chr2D 82.826 1380 181 38 1621 2986 71470721 71472058 0.000000e+00 1184.0
3 TraesCS2D01G122500 chr2D 82.316 967 118 31 1062 2014 71598882 71599809 0.000000e+00 789.0
4 TraesCS2D01G122500 chr2D 88.080 646 63 9 2346 2986 71410170 71410806 0.000000e+00 754.0
5 TraesCS2D01G122500 chr2D 77.353 1466 195 82 1230 2672 71455208 71456559 0.000000e+00 741.0
6 TraesCS2D01G122500 chr2D 80.947 950 116 36 1062 1981 70674207 70673293 0.000000e+00 691.0
7 TraesCS2D01G122500 chr2D 91.295 448 34 4 2033 2478 71600086 71600530 9.150000e-170 606.0
8 TraesCS2D01G122500 chr2D 88.378 413 39 5 2073 2478 70672921 70672511 3.460000e-134 488.0
9 TraesCS2D01G122500 chr2D 75.941 611 93 34 836 1440 71594088 71594650 6.350000e-67 265.0
10 TraesCS2D01G122500 chr2D 78.032 437 77 15 1062 1479 71399438 71399874 1.060000e-64 257.0
11 TraesCS2D01G122500 chr2D 76.923 468 84 15 1597 2049 71399891 71400349 8.270000e-61 244.0
12 TraesCS2D01G122500 chr2D 82.215 298 23 19 778 1053 71598635 71598924 2.320000e-56 230.0
13 TraesCS2D01G122500 chr2A 93.714 2259 88 19 765 2986 70643741 70645982 0.000000e+00 3336.0
14 TraesCS2D01G122500 chr2A 84.626 1444 154 40 1062 2478 70655074 70656476 0.000000e+00 1375.0
15 TraesCS2D01G122500 chr2A 84.861 938 101 25 1560 2478 70156029 70155114 0.000000e+00 907.0
16 TraesCS2D01G122500 chr2A 86.842 646 71 9 2346 2986 70278511 70277875 0.000000e+00 710.0
17 TraesCS2D01G122500 chr2A 82.791 645 101 6 2346 2986 70150784 70150146 4.320000e-158 568.0
18 TraesCS2D01G122500 chr2A 89.362 376 36 2 2615 2986 70230600 70230225 1.250000e-128 470.0
19 TraesCS2D01G122500 chr2A 92.698 315 19 2 448 759 156663528 156663841 4.540000e-123 451.0
20 TraesCS2D01G122500 chr2A 78.912 754 85 46 776 1506 70235234 70234532 7.600000e-121 444.0
21 TraesCS2D01G122500 chr2A 83.851 322 22 13 776 1070 70654815 70655133 2.270000e-71 279.0
22 TraesCS2D01G122500 chr2A 92.169 166 13 0 181 346 70643503 70643668 4.980000e-58 235.0
23 TraesCS2D01G122500 chr2A 75.041 605 95 30 903 1485 70153249 70152679 2.320000e-56 230.0
24 TraesCS2D01G122500 chr2A 93.103 145 8 2 1 143 70643265 70643409 8.390000e-51 211.0
25 TraesCS2D01G122500 chr2A 84.906 159 18 4 181 338 70215027 70214874 3.990000e-34 156.0
26 TraesCS2D01G122500 chr2A 97.101 69 2 0 388 456 70643666 70643734 1.880000e-22 117.0
27 TraesCS2D01G122500 chr2B 90.360 2251 128 24 765 2986 107782936 107785126 0.000000e+00 2872.0
28 TraesCS2D01G122500 chr2B 86.146 960 116 14 1528 2478 107793878 107794829 0.000000e+00 1020.0
29 TraesCS2D01G122500 chr2B 87.344 640 72 6 2346 2981 107578248 107578882 0.000000e+00 725.0
30 TraesCS2D01G122500 chr2B 85.289 571 59 14 1914 2478 107023420 107022869 1.550000e-157 566.0
31 TraesCS2D01G122500 chr2B 80.820 610 87 23 1621 2224 107577647 107578232 4.540000e-123 451.0
32 TraesCS2D01G122500 chr2B 83.879 397 47 13 1062 1442 107793295 107793690 2.190000e-96 363.0
33 TraesCS2D01G122500 chr2B 80.714 280 54 0 1148 1427 106962628 106962349 5.010000e-53 219.0
34 TraesCS2D01G122500 chr2B 79.044 272 28 9 181 450 107782029 107782273 3.080000e-35 159.0
35 TraesCS2D01G122500 chr2B 93.651 63 4 0 1444 1506 107793727 107793789 8.810000e-16 95.3
36 TraesCS2D01G122500 chr2B 100.000 28 0 0 1479 1506 107793870 107793897 5.000000e-03 52.8
37 TraesCS2D01G122500 chr6A 92.188 320 22 1 446 762 105585890 105585571 1.630000e-122 449.0
38 TraesCS2D01G122500 chr6A 92.787 305 19 1 458 759 58765458 58765762 3.530000e-119 438.0
39 TraesCS2D01G122500 chr6A 91.987 312 22 1 453 761 297643736 297644047 4.570000e-118 435.0
40 TraesCS2D01G122500 chr4D 92.628 312 20 1 453 761 43651710 43651399 2.110000e-121 446.0
41 TraesCS2D01G122500 chr7A 91.331 323 24 2 445 764 595075744 595075423 3.530000e-119 438.0
42 TraesCS2D01G122500 chr5B 92.013 313 21 2 454 762 416591871 416592183 1.270000e-118 436.0
43 TraesCS2D01G122500 chr1A 92.233 309 20 2 455 759 350489588 350489896 4.570000e-118 435.0
44 TraesCS2D01G122500 chr5A 91.693 313 22 2 453 761 366030808 366030496 5.910000e-117 431.0


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 TraesCS2D01G122500 chr2D 71577337 71580322 2985 False 5515.000000 5515 100.000000 1 2986 1 chr2D.!!$F5 2985
1 TraesCS2D01G122500 chr2D 71565415 71567618 2203 False 2724.000000 2724 89.115000 765 2986 1 chr2D.!!$F4 2221
2 TraesCS2D01G122500 chr2D 71470721 71472058 1337 False 1184.000000 1184 82.826000 1621 2986 1 chr2D.!!$F3 1365
3 TraesCS2D01G122500 chr2D 71410170 71410806 636 False 754.000000 754 88.080000 2346 2986 1 chr2D.!!$F1 640
4 TraesCS2D01G122500 chr2D 71455208 71456559 1351 False 741.000000 741 77.353000 1230 2672 1 chr2D.!!$F2 1442
5 TraesCS2D01G122500 chr2D 70672511 70674207 1696 True 589.500000 691 84.662500 1062 2478 2 chr2D.!!$R1 1416
6 TraesCS2D01G122500 chr2D 71594088 71600530 6442 False 472.500000 789 82.941750 778 2478 4 chr2D.!!$F7 1700
7 TraesCS2D01G122500 chr2D 71399438 71400349 911 False 250.500000 257 77.477500 1062 2049 2 chr2D.!!$F6 987
8 TraesCS2D01G122500 chr2A 70643265 70645982 2717 False 974.750000 3336 94.021750 1 2986 4 chr2A.!!$F2 2985
9 TraesCS2D01G122500 chr2A 70654815 70656476 1661 False 827.000000 1375 84.238500 776 2478 2 chr2A.!!$F3 1702
10 TraesCS2D01G122500 chr2A 70277875 70278511 636 True 710.000000 710 86.842000 2346 2986 1 chr2A.!!$R2 640
11 TraesCS2D01G122500 chr2A 70150146 70156029 5883 True 568.333333 907 80.897667 903 2986 3 chr2A.!!$R3 2083
12 TraesCS2D01G122500 chr2A 70230225 70235234 5009 True 457.000000 470 84.137000 776 2986 2 chr2A.!!$R4 2210
13 TraesCS2D01G122500 chr2B 107782029 107785126 3097 False 1515.500000 2872 84.702000 181 2986 2 chr2B.!!$F2 2805
14 TraesCS2D01G122500 chr2B 107577647 107578882 1235 False 588.000000 725 84.082000 1621 2981 2 chr2B.!!$F1 1360
15 TraesCS2D01G122500 chr2B 107022869 107023420 551 True 566.000000 566 85.289000 1914 2478 1 chr2B.!!$R2 564
16 TraesCS2D01G122500 chr2B 107793295 107794829 1534 False 382.775000 1020 90.919000 1062 2478 4 chr2B.!!$F3 1416

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
369 429 0.037790 AGCAAGTCTTCTCTGTCGGC 60.038 55.000 0.0 0.0 0.0 5.54 F
1322 5198 1.402984 CCTCAAGGTCTGCGTCTACAC 60.403 57.143 0.0 0.0 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1872 6048 0.039180 GAACCGACCATTTCCCCCTT 59.961 55.000 0.0 0.0 0.00 3.95 R
2789 10076 1.609072 TGAGTCACAGAACAGAGGACG 59.391 52.381 0.0 0.0 33.84 4.79 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
139 142 1.228367 GGGCCACCATCATAGCTGG 60.228 63.158 4.39 0.00 39.80 4.85
143 146 1.602311 CCACCATCATAGCTGGCTTC 58.398 55.000 0.00 0.00 37.27 3.86
161 192 1.028330 TCGACGACCAAGCTACGGAT 61.028 55.000 9.05 0.00 0.00 4.18
194 253 0.179094 CCTACTTCCCGCGCACAATA 60.179 55.000 8.75 0.00 0.00 1.90
210 269 7.326305 CGCGCACAATACTTAATAGAAGACTAT 59.674 37.037 8.75 0.00 40.58 2.12
250 309 9.956640 ATCTGATCAATCATTAAGAATAGGGAC 57.043 33.333 0.00 0.00 36.02 4.46
310 370 2.193536 GCTTCGCACAACCCAACCT 61.194 57.895 0.00 0.00 0.00 3.50
343 403 4.837860 AGAAGGTTATGAATGCCCAACAAA 59.162 37.500 0.00 0.00 0.00 2.83
344 404 4.806640 AGGTTATGAATGCCCAACAAAG 57.193 40.909 0.00 0.00 0.00 2.77
361 421 2.359230 GCCGCCAGCAAGTCTTCT 60.359 61.111 0.00 0.00 42.97 2.85
362 422 2.394563 GCCGCCAGCAAGTCTTCTC 61.395 63.158 0.00 0.00 42.97 2.87
363 423 1.294780 CCGCCAGCAAGTCTTCTCT 59.705 57.895 0.00 0.00 0.00 3.10
365 425 0.320247 CGCCAGCAAGTCTTCTCTGT 60.320 55.000 9.37 0.00 0.00 3.41
367 427 1.707632 CCAGCAAGTCTTCTCTGTCG 58.292 55.000 9.37 0.00 0.00 4.35
368 428 1.671261 CCAGCAAGTCTTCTCTGTCGG 60.671 57.143 9.37 0.00 0.00 4.79
369 429 0.037790 AGCAAGTCTTCTCTGTCGGC 60.038 55.000 0.00 0.00 0.00 5.54
371 431 1.674221 GCAAGTCTTCTCTGTCGGCAT 60.674 52.381 0.00 0.00 0.00 4.40
372 432 2.417379 GCAAGTCTTCTCTGTCGGCATA 60.417 50.000 0.00 0.00 0.00 3.14
373 433 3.443037 CAAGTCTTCTCTGTCGGCATAG 58.557 50.000 0.00 0.00 0.00 2.23
374 434 1.407258 AGTCTTCTCTGTCGGCATAGC 59.593 52.381 0.00 0.00 0.00 2.97
375 435 1.407258 GTCTTCTCTGTCGGCATAGCT 59.593 52.381 0.00 0.00 0.00 3.32
466 526 5.977731 GCAACAAAGTTTATGCCTCTTTTG 58.022 37.500 12.35 0.00 32.73 2.44
467 527 5.752955 GCAACAAAGTTTATGCCTCTTTTGA 59.247 36.000 12.35 0.00 32.73 2.69
468 528 6.424812 GCAACAAAGTTTATGCCTCTTTTGAT 59.575 34.615 12.35 0.00 32.73 2.57
469 529 7.041848 GCAACAAAGTTTATGCCTCTTTTGATT 60.042 33.333 12.35 0.00 32.73 2.57
470 530 8.490355 CAACAAAGTTTATGCCTCTTTTGATTC 58.510 33.333 2.21 0.00 30.41 2.52
471 531 7.725251 ACAAAGTTTATGCCTCTTTTGATTCA 58.275 30.769 2.21 0.00 30.41 2.57
472 532 8.370182 ACAAAGTTTATGCCTCTTTTGATTCAT 58.630 29.630 2.21 0.00 30.41 2.57
477 537 8.854117 GTTTATGCCTCTTTTGATTCATAGGAT 58.146 33.333 8.33 0.00 30.20 3.24
479 539 9.730705 TTATGCCTCTTTTGATTCATAGGATAG 57.269 33.333 8.33 0.00 30.20 2.08
482 542 7.017950 TGCCTCTTTTGATTCATAGGATAGGAT 59.982 37.037 8.33 0.00 28.27 3.24
483 543 7.887495 GCCTCTTTTGATTCATAGGATAGGATT 59.113 37.037 8.33 0.00 28.27 3.01
491 551 9.355916 TGATTCATAGGATAGGATTATCGTAGG 57.644 37.037 1.23 3.78 39.00 3.18
492 552 9.575868 GATTCATAGGATAGGATTATCGTAGGA 57.424 37.037 7.24 7.24 41.67 2.94
495 555 9.937876 TCATAGGATAGGATTATCGTAGGAATT 57.062 33.333 8.35 0.00 41.04 2.17
497 557 7.425224 AGGATAGGATTATCGTAGGAATTGG 57.575 40.000 1.23 0.00 37.20 3.16
499 559 7.678598 AGGATAGGATTATCGTAGGAATTGGAA 59.321 37.037 1.23 0.00 37.20 3.53
500 560 8.319146 GGATAGGATTATCGTAGGAATTGGAAA 58.681 37.037 1.23 0.00 37.20 3.13
501 561 9.892130 GATAGGATTATCGTAGGAATTGGAAAT 57.108 33.333 1.23 0.00 0.00 2.17
503 563 8.996651 AGGATTATCGTAGGAATTGGAAATTT 57.003 30.769 0.00 0.00 0.00 1.82
504 564 8.850156 AGGATTATCGTAGGAATTGGAAATTTG 58.150 33.333 0.00 0.00 0.00 2.32
506 566 5.913137 ATCGTAGGAATTGGAAATTTGCA 57.087 34.783 8.47 8.47 0.00 4.08
507 567 5.309323 TCGTAGGAATTGGAAATTTGCAG 57.691 39.130 12.38 0.00 0.00 4.41
508 568 4.157656 TCGTAGGAATTGGAAATTTGCAGG 59.842 41.667 12.38 0.00 0.00 4.85
509 569 4.157656 CGTAGGAATTGGAAATTTGCAGGA 59.842 41.667 12.38 0.00 0.00 3.86
510 570 5.336372 CGTAGGAATTGGAAATTTGCAGGAA 60.336 40.000 12.38 0.00 0.00 3.36
512 572 6.130692 AGGAATTGGAAATTTGCAGGAAAT 57.869 33.333 12.38 0.85 35.65 2.17
513 573 5.941647 AGGAATTGGAAATTTGCAGGAAATG 59.058 36.000 12.38 0.00 34.30 2.32
514 574 5.939296 GGAATTGGAAATTTGCAGGAAATGA 59.061 36.000 12.38 0.00 34.30 2.57
515 575 6.093082 GGAATTGGAAATTTGCAGGAAATGAG 59.907 38.462 12.38 0.00 34.30 2.90
516 576 5.804944 TTGGAAATTTGCAGGAAATGAGA 57.195 34.783 12.38 0.00 34.30 3.27
518 578 5.726397 TGGAAATTTGCAGGAAATGAGATG 58.274 37.500 8.47 0.00 34.30 2.90
519 579 5.481122 TGGAAATTTGCAGGAAATGAGATGA 59.519 36.000 8.47 0.00 34.30 2.92
520 580 5.809051 GGAAATTTGCAGGAAATGAGATGAC 59.191 40.000 4.63 0.00 34.30 3.06
522 582 6.540438 AATTTGCAGGAAATGAGATGACAT 57.460 33.333 0.00 0.00 34.30 3.06
524 584 3.959293 TGCAGGAAATGAGATGACATGT 58.041 40.909 0.00 0.00 0.00 3.21
525 585 5.101648 TGCAGGAAATGAGATGACATGTA 57.898 39.130 0.00 0.00 0.00 2.29
529 589 6.238320 GCAGGAAATGAGATGACATGTAACTC 60.238 42.308 15.13 15.13 0.00 3.01
531 591 7.335171 CAGGAAATGAGATGACATGTAACTCAA 59.665 37.037 23.18 12.95 40.21 3.02
536 596 9.458727 AATGAGATGACATGTAACTCAAATTCT 57.541 29.630 23.18 6.57 40.21 2.40
557 617 8.707796 ATTCTATGAGTAGGAATAGGAAACGA 57.292 34.615 0.00 0.00 0.00 3.85
558 618 7.747155 TCTATGAGTAGGAATAGGAAACGAG 57.253 40.000 0.00 0.00 0.00 4.18
559 619 7.515586 TCTATGAGTAGGAATAGGAAACGAGA 58.484 38.462 0.00 0.00 0.00 4.04
560 620 8.164733 TCTATGAGTAGGAATAGGAAACGAGAT 58.835 37.037 0.00 0.00 0.00 2.75
561 621 6.392625 TGAGTAGGAATAGGAAACGAGATG 57.607 41.667 0.00 0.00 0.00 2.90
562 622 5.892119 TGAGTAGGAATAGGAAACGAGATGT 59.108 40.000 0.00 0.00 0.00 3.06
563 623 6.380274 TGAGTAGGAATAGGAAACGAGATGTT 59.620 38.462 0.00 0.00 44.59 2.71
564 624 7.558807 TGAGTAGGAATAGGAAACGAGATGTTA 59.441 37.037 0.00 0.00 40.84 2.41
566 626 8.925338 AGTAGGAATAGGAAACGAGATGTTATT 58.075 33.333 0.00 0.00 40.84 1.40
567 627 9.543783 GTAGGAATAGGAAACGAGATGTTATTT 57.456 33.333 0.00 0.00 40.84 1.40
569 629 7.499232 AGGAATAGGAAACGAGATGTTATTTGG 59.501 37.037 0.00 0.00 40.84 3.28
573 633 6.001460 AGGAAACGAGATGTTATTTGGTTCA 58.999 36.000 0.00 0.00 40.84 3.18
574 634 6.659242 AGGAAACGAGATGTTATTTGGTTCAT 59.341 34.615 0.00 0.00 40.84 2.57
576 636 7.908601 GGAAACGAGATGTTATTTGGTTCATAC 59.091 37.037 0.00 0.00 40.84 2.39
578 638 6.882140 AACGAGATGTTATTTGGTTCATACCA 59.118 34.615 0.00 0.00 45.57 3.25
620 680 9.975218 TGAGTCTAGGCTTATTTTTATTTTCCT 57.025 29.630 0.00 0.00 0.00 3.36
640 700 9.973661 TTTTCCTATGAAATGTGAAGGATAAGA 57.026 29.630 0.00 0.00 40.08 2.10
641 701 9.973661 TTTCCTATGAAATGTGAAGGATAAGAA 57.026 29.630 0.00 0.00 36.28 2.52
643 703 7.993183 TCCTATGAAATGTGAAGGATAAGAACC 59.007 37.037 0.00 0.00 31.41 3.62
644 704 7.775093 CCTATGAAATGTGAAGGATAAGAACCA 59.225 37.037 0.00 0.00 0.00 3.67
645 705 9.177608 CTATGAAATGTGAAGGATAAGAACCAA 57.822 33.333 0.00 0.00 0.00 3.67
681 741 9.690913 GGAATATGAATCCATTCCTATGAATCA 57.309 33.333 13.43 0.00 44.56 2.57
685 745 7.828508 TGAATCCATTCCTATGAATCAAAGG 57.171 36.000 0.00 0.00 39.20 3.11
686 746 6.779049 TGAATCCATTCCTATGAATCAAAGGG 59.221 38.462 0.00 0.00 39.20 3.95
687 747 4.473444 TCCATTCCTATGAATCAAAGGGC 58.527 43.478 0.00 0.00 39.20 5.19
688 748 4.168675 TCCATTCCTATGAATCAAAGGGCT 59.831 41.667 0.00 0.00 39.20 5.19
690 750 5.383476 CATTCCTATGAATCAAAGGGCTCT 58.617 41.667 0.00 0.00 39.20 4.09
691 751 6.466326 CCATTCCTATGAATCAAAGGGCTCTA 60.466 42.308 0.00 0.00 39.20 2.43
692 752 6.575244 TTCCTATGAATCAAAGGGCTCTAA 57.425 37.500 0.00 0.00 0.00 2.10
693 753 6.575244 TCCTATGAATCAAAGGGCTCTAAA 57.425 37.500 0.00 0.00 0.00 1.85
694 754 6.595682 TCCTATGAATCAAAGGGCTCTAAAG 58.404 40.000 0.00 0.00 0.00 1.85
695 755 6.386927 TCCTATGAATCAAAGGGCTCTAAAGA 59.613 38.462 0.00 0.00 0.00 2.52
696 756 7.056635 CCTATGAATCAAAGGGCTCTAAAGAA 58.943 38.462 0.00 0.00 0.00 2.52
697 757 7.557719 CCTATGAATCAAAGGGCTCTAAAGAAA 59.442 37.037 0.00 0.00 0.00 2.52
698 758 7.781324 ATGAATCAAAGGGCTCTAAAGAAAA 57.219 32.000 0.00 0.00 0.00 2.29
756 816 5.722021 TGAAATTCCTAACCAAAGAAGGC 57.278 39.130 0.00 0.00 0.00 4.35
757 817 4.526650 TGAAATTCCTAACCAAAGAAGGCC 59.473 41.667 0.00 0.00 0.00 5.19
760 820 5.530176 ATTCCTAACCAAAGAAGGCCTTA 57.470 39.130 20.54 0.00 34.00 2.69
761 821 5.327737 TTCCTAACCAAAGAAGGCCTTAA 57.672 39.130 20.54 0.81 34.00 1.85
762 822 4.659115 TCCTAACCAAAGAAGGCCTTAAC 58.341 43.478 20.54 7.09 34.00 2.01
763 823 4.105057 TCCTAACCAAAGAAGGCCTTAACA 59.895 41.667 20.54 0.00 34.00 2.41
856 4641 2.223745 GGTTAGAACTGAACCCGCAAA 58.776 47.619 0.00 0.00 40.51 3.68
1322 5198 1.402984 CCTCAAGGTCTGCGTCTACAC 60.403 57.143 0.00 0.00 0.00 2.90
1363 5239 3.927548 TCGTCCTGCTGCTGTGCA 61.928 61.111 0.00 0.00 41.05 4.57
1442 5329 6.170506 AGAAGGTATCGTGCAAATTAACTCA 58.829 36.000 0.00 0.00 0.00 3.41
1605 5750 6.425721 CCTGATGCTGAGTAGTAGTAGTAGTC 59.574 46.154 11.54 11.54 0.00 2.59
1705 5878 7.221838 CGTATGGTTTTGTTGAAATTGTTGTCT 59.778 33.333 0.00 0.00 0.00 3.41
1872 6048 5.185828 CCACATGTGAAGGGATCGATATCTA 59.814 44.000 27.46 0.00 32.29 1.98
2156 6648 5.630680 CAGTGTTGTTAGTTTGCCATCATTC 59.369 40.000 0.00 0.00 0.00 2.67
2300 6806 7.496529 TGGGATTGACATCGATCTTAAATTC 57.503 36.000 8.67 0.00 37.04 2.17
2312 6819 2.487762 TCTTAAATTCTGCAAGGTGCCG 59.512 45.455 0.00 0.00 44.23 5.69
2342 6861 7.933215 TGCAGTTCTACACTTCTACTGTATA 57.067 36.000 0.00 0.00 38.70 1.47
2494 7237 2.617250 TTGCATGCTTCTAAACTGCG 57.383 45.000 20.33 0.00 35.63 5.18
2578 7322 4.338400 AGACCCAAAGTTTACAAGTCTTGC 59.662 41.667 12.66 0.00 29.06 4.01
2613 7357 5.067153 TGAGTCTACTCTTCTTAGCTGCATC 59.933 44.000 11.22 0.00 43.25 3.91
2698 9983 6.898041 TCATGTAAATAAATAGCATGACGGC 58.102 36.000 0.00 0.00 40.35 5.68
2771 10058 4.642885 GCTATGCCCACTACATTTTGGTAA 59.357 41.667 0.00 0.00 0.00 2.85
2772 10059 5.301805 GCTATGCCCACTACATTTTGGTAAT 59.698 40.000 0.00 0.00 0.00 1.89
2789 10076 4.099266 TGGTAATATTGCCATTGTGCCTTC 59.901 41.667 20.09 0.00 38.05 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 88 6.664428 AAGTGTTGCCTAATTTGGTTATGT 57.336 33.333 7.77 0.00 0.00 2.29
143 146 0.866061 CATCCGTAGCTTGGTCGTCG 60.866 60.000 0.00 0.00 0.00 5.12
161 192 0.549950 AGTAGGGCTAGCGGTACTCA 59.450 55.000 17.66 0.00 0.00 3.41
250 309 7.390718 AGTGAGGGTTTGTTAGTTTAATAGCAG 59.609 37.037 0.00 0.00 0.00 4.24
261 320 7.148239 GGATGAAATGTAGTGAGGGTTTGTTAG 60.148 40.741 0.00 0.00 0.00 2.34
343 403 2.359230 GAAGACTTGCTGGCGGCT 60.359 61.111 20.66 0.00 42.39 5.52
344 404 2.359230 AGAAGACTTGCTGGCGGC 60.359 61.111 12.43 12.43 42.22 6.53
353 413 2.159170 GCTATGCCGACAGAGAAGACTT 60.159 50.000 0.00 0.00 37.30 3.01
354 414 1.407258 GCTATGCCGACAGAGAAGACT 59.593 52.381 0.00 0.00 37.30 3.24
355 415 1.407258 AGCTATGCCGACAGAGAAGAC 59.593 52.381 0.00 0.00 37.30 3.01
356 416 1.769026 AGCTATGCCGACAGAGAAGA 58.231 50.000 0.00 0.00 37.30 2.87
357 417 2.159184 TGAAGCTATGCCGACAGAGAAG 60.159 50.000 0.00 0.00 37.30 2.85
359 419 1.406898 CTGAAGCTATGCCGACAGAGA 59.593 52.381 0.00 0.00 37.30 3.10
361 421 0.179100 GCTGAAGCTATGCCGACAGA 60.179 55.000 0.00 0.00 38.21 3.41
362 422 2.305405 GCTGAAGCTATGCCGACAG 58.695 57.895 0.00 0.00 38.21 3.51
363 423 4.521075 GCTGAAGCTATGCCGACA 57.479 55.556 0.00 0.00 38.21 4.35
466 526 9.575868 TCCTACGATAATCCTATCCTATGAATC 57.424 37.037 0.00 0.00 31.68 2.52
467 527 9.937876 TTCCTACGATAATCCTATCCTATGAAT 57.062 33.333 0.00 0.00 31.68 2.57
468 528 9.937876 ATTCCTACGATAATCCTATCCTATGAA 57.062 33.333 0.00 0.00 31.68 2.57
469 529 9.937876 AATTCCTACGATAATCCTATCCTATGA 57.062 33.333 0.00 0.00 31.68 2.15
470 530 9.973450 CAATTCCTACGATAATCCTATCCTATG 57.027 37.037 0.00 0.00 31.68 2.23
471 531 9.148879 CCAATTCCTACGATAATCCTATCCTAT 57.851 37.037 0.00 0.00 31.68 2.57
472 532 8.341513 TCCAATTCCTACGATAATCCTATCCTA 58.658 37.037 0.00 0.00 31.68 2.94
474 534 7.419711 TCCAATTCCTACGATAATCCTATCC 57.580 40.000 0.00 0.00 31.68 2.59
478 538 8.850156 CAAATTTCCAATTCCTACGATAATCCT 58.150 33.333 0.00 0.00 0.00 3.24
479 539 7.595130 GCAAATTTCCAATTCCTACGATAATCC 59.405 37.037 0.00 0.00 0.00 3.01
482 542 7.397892 TGCAAATTTCCAATTCCTACGATAA 57.602 32.000 0.00 0.00 0.00 1.75
483 543 6.039270 CCTGCAAATTTCCAATTCCTACGATA 59.961 38.462 0.00 0.00 0.00 2.92
485 545 4.157656 CCTGCAAATTTCCAATTCCTACGA 59.842 41.667 0.00 0.00 0.00 3.43
486 546 4.157656 TCCTGCAAATTTCCAATTCCTACG 59.842 41.667 0.00 0.00 0.00 3.51
490 550 5.939296 TCATTTCCTGCAAATTTCCAATTCC 59.061 36.000 0.00 0.00 31.79 3.01
491 551 6.875195 TCTCATTTCCTGCAAATTTCCAATTC 59.125 34.615 0.00 0.00 31.79 2.17
492 552 6.771573 TCTCATTTCCTGCAAATTTCCAATT 58.228 32.000 0.00 0.00 31.79 2.32
493 553 6.363167 TCTCATTTCCTGCAAATTTCCAAT 57.637 33.333 0.00 0.00 31.79 3.16
495 555 5.481122 TCATCTCATTTCCTGCAAATTTCCA 59.519 36.000 0.00 0.00 31.79 3.53
497 557 6.392354 TGTCATCTCATTTCCTGCAAATTTC 58.608 36.000 0.00 0.00 31.79 2.17
499 559 5.988310 TGTCATCTCATTTCCTGCAAATT 57.012 34.783 0.00 0.00 31.79 1.82
500 560 5.421056 ACATGTCATCTCATTTCCTGCAAAT 59.579 36.000 0.00 0.00 34.79 2.32
501 561 4.768448 ACATGTCATCTCATTTCCTGCAAA 59.232 37.500 0.00 0.00 0.00 3.68
502 562 4.338012 ACATGTCATCTCATTTCCTGCAA 58.662 39.130 0.00 0.00 0.00 4.08
503 563 3.959293 ACATGTCATCTCATTTCCTGCA 58.041 40.909 0.00 0.00 0.00 4.41
504 564 5.587844 AGTTACATGTCATCTCATTTCCTGC 59.412 40.000 0.00 0.00 0.00 4.85
506 566 6.950842 TGAGTTACATGTCATCTCATTTCCT 58.049 36.000 17.59 0.00 31.51 3.36
507 567 7.615582 TTGAGTTACATGTCATCTCATTTCC 57.384 36.000 20.32 2.26 35.54 3.13
510 570 9.458727 AGAATTTGAGTTACATGTCATCTCATT 57.541 29.630 20.32 15.27 35.54 2.57
531 591 9.144298 TCGTTTCCTATTCCTACTCATAGAATT 57.856 33.333 0.00 0.00 0.00 2.17
534 594 7.515586 TCTCGTTTCCTATTCCTACTCATAGA 58.484 38.462 0.00 0.00 0.00 1.98
536 596 7.724506 ACATCTCGTTTCCTATTCCTACTCATA 59.275 37.037 0.00 0.00 0.00 2.15
537 597 6.551601 ACATCTCGTTTCCTATTCCTACTCAT 59.448 38.462 0.00 0.00 0.00 2.90
538 598 5.892119 ACATCTCGTTTCCTATTCCTACTCA 59.108 40.000 0.00 0.00 0.00 3.41
540 600 6.793505 AACATCTCGTTTCCTATTCCTACT 57.206 37.500 0.00 0.00 32.35 2.57
541 601 9.543783 AAATAACATCTCGTTTCCTATTCCTAC 57.456 33.333 0.00 0.00 39.14 3.18
543 603 7.499232 CCAAATAACATCTCGTTTCCTATTCCT 59.501 37.037 0.00 0.00 39.14 3.36
544 604 7.282450 ACCAAATAACATCTCGTTTCCTATTCC 59.718 37.037 0.00 0.00 39.14 3.01
545 605 8.209917 ACCAAATAACATCTCGTTTCCTATTC 57.790 34.615 0.00 0.00 39.14 1.75
546 606 8.575649 AACCAAATAACATCTCGTTTCCTATT 57.424 30.769 0.00 0.00 39.14 1.73
547 607 7.827236 TGAACCAAATAACATCTCGTTTCCTAT 59.173 33.333 0.00 0.00 39.14 2.57
548 608 7.162761 TGAACCAAATAACATCTCGTTTCCTA 58.837 34.615 0.00 0.00 39.14 2.94
551 611 7.908601 GGTATGAACCAAATAACATCTCGTTTC 59.091 37.037 0.00 0.00 45.98 2.78
552 612 7.758495 GGTATGAACCAAATAACATCTCGTTT 58.242 34.615 0.00 0.00 45.98 3.60
553 613 7.316544 GGTATGAACCAAATAACATCTCGTT 57.683 36.000 0.00 0.00 45.98 3.85
594 654 9.975218 AGGAAAATAAAAATAAGCCTAGACTCA 57.025 29.630 0.00 0.00 0.00 3.41
617 677 7.993183 GGTTCTTATCCTTCACATTTCATAGGA 59.007 37.037 0.00 0.00 39.21 2.94
618 678 7.775093 TGGTTCTTATCCTTCACATTTCATAGG 59.225 37.037 0.00 0.00 0.00 2.57
620 680 9.699410 ATTGGTTCTTATCCTTCACATTTCATA 57.301 29.630 0.00 0.00 0.00 2.15
621 681 8.599624 ATTGGTTCTTATCCTTCACATTTCAT 57.400 30.769 0.00 0.00 0.00 2.57
625 685 6.735556 AGGATTGGTTCTTATCCTTCACATT 58.264 36.000 0.00 0.00 46.64 2.71
626 686 6.332976 AGGATTGGTTCTTATCCTTCACAT 57.667 37.500 0.00 0.00 46.64 3.21
628 688 7.283329 ACATAGGATTGGTTCTTATCCTTCAC 58.717 38.462 8.77 0.00 46.64 3.18
629 689 7.451731 ACATAGGATTGGTTCTTATCCTTCA 57.548 36.000 8.77 0.00 46.64 3.02
630 690 8.097662 CCTACATAGGATTGGTTCTTATCCTTC 58.902 40.741 8.77 0.00 46.64 3.46
631 691 7.794683 TCCTACATAGGATTGGTTCTTATCCTT 59.205 37.037 8.77 0.00 46.64 3.36
661 721 6.779049 CCCTTTGATTCATAGGAATGGATTCA 59.221 38.462 20.87 0.00 43.69 2.57
662 722 6.294955 GCCCTTTGATTCATAGGAATGGATTC 60.295 42.308 20.87 0.00 43.69 2.52
663 723 5.541484 GCCCTTTGATTCATAGGAATGGATT 59.459 40.000 20.87 0.00 43.69 3.01
664 724 5.082425 GCCCTTTGATTCATAGGAATGGAT 58.918 41.667 20.87 0.00 43.69 3.41
665 725 4.168675 AGCCCTTTGATTCATAGGAATGGA 59.831 41.667 20.87 0.00 43.69 3.41
666 726 4.477249 AGCCCTTTGATTCATAGGAATGG 58.523 43.478 20.87 3.33 43.69 3.16
668 728 5.659849 AGAGCCCTTTGATTCATAGGAAT 57.340 39.130 20.87 1.48 46.27 3.01
670 730 6.386927 TCTTTAGAGCCCTTTGATTCATAGGA 59.613 38.462 20.87 1.95 35.14 2.94
672 732 8.511604 TTTCTTTAGAGCCCTTTGATTCATAG 57.488 34.615 0.00 0.00 0.00 2.23
729 789 9.243105 CCTTCTTTGGTTAGGAATTTCATAGAA 57.757 33.333 0.00 0.00 0.00 2.10
730 790 7.339466 GCCTTCTTTGGTTAGGAATTTCATAGA 59.661 37.037 0.00 0.00 0.00 1.98
731 791 7.416777 GGCCTTCTTTGGTTAGGAATTTCATAG 60.417 40.741 0.00 0.00 0.00 2.23
733 793 5.187772 GGCCTTCTTTGGTTAGGAATTTCAT 59.812 40.000 0.00 0.00 0.00 2.57
737 797 4.404185 AGGCCTTCTTTGGTTAGGAATT 57.596 40.909 0.00 0.00 0.00 2.17
739 799 3.895704 AAGGCCTTCTTTGGTTAGGAA 57.104 42.857 13.78 0.00 29.99 3.36
741 801 4.217767 GTGTTAAGGCCTTCTTTGGTTAGG 59.782 45.833 24.49 0.00 36.93 2.69
742 802 4.825085 TGTGTTAAGGCCTTCTTTGGTTAG 59.175 41.667 24.49 0.00 36.93 2.34
744 804 3.383505 GTGTGTTAAGGCCTTCTTTGGTT 59.616 43.478 24.49 0.00 36.93 3.67
745 805 2.956333 GTGTGTTAAGGCCTTCTTTGGT 59.044 45.455 24.49 0.00 36.93 3.67
747 807 2.296190 GGGTGTGTTAAGGCCTTCTTTG 59.704 50.000 24.49 0.00 36.93 2.77
748 808 2.594131 GGGTGTGTTAAGGCCTTCTTT 58.406 47.619 24.49 0.00 36.93 2.52
749 809 1.544759 CGGGTGTGTTAAGGCCTTCTT 60.545 52.381 24.49 0.00 39.40 2.52
750 810 0.036306 CGGGTGTGTTAAGGCCTTCT 59.964 55.000 24.49 0.27 0.00 2.85
751 811 0.958876 CCGGGTGTGTTAAGGCCTTC 60.959 60.000 24.49 9.55 0.00 3.46
752 812 1.074248 CCGGGTGTGTTAAGGCCTT 59.926 57.895 24.18 24.18 0.00 4.35
754 814 1.969589 CACCGGGTGTGTTAAGGCC 60.970 63.158 19.15 0.00 40.26 5.19
756 816 1.969589 GCCACCGGGTGTGTTAAGG 60.970 63.158 24.70 9.58 43.85 2.69
757 817 0.953960 GAGCCACCGGGTGTGTTAAG 60.954 60.000 24.70 10.12 43.85 1.85
760 820 4.619227 CGAGCCACCGGGTGTGTT 62.619 66.667 24.70 14.35 43.85 3.32
762 822 3.605749 ATTCGAGCCACCGGGTGTG 62.606 63.158 24.70 16.92 45.01 3.82
763 823 3.310860 GATTCGAGCCACCGGGTGT 62.311 63.158 24.70 8.24 36.17 4.16
1322 5198 1.154035 GCGAAAACGGCAAGGATGG 60.154 57.895 0.00 0.00 0.00 3.51
1363 5239 4.016706 GTAGGCCACGCACTGGGT 62.017 66.667 5.01 0.00 41.02 4.51
1442 5329 4.730949 TTCGATCGGAATAAAGGTCACT 57.269 40.909 16.41 0.00 0.00 3.41
1872 6048 0.039180 GAACCGACCATTTCCCCCTT 59.961 55.000 0.00 0.00 0.00 3.95
2001 6187 1.344438 ACCTCAACAGAACTGCGATGA 59.656 47.619 1.46 4.10 0.00 2.92
2090 6558 5.500234 AGAGGCTACACAAAATATGCAGAA 58.500 37.500 0.00 0.00 0.00 3.02
2156 6648 9.823647 AACACCAATAGTCACTAAGATAAGATG 57.176 33.333 0.00 0.00 0.00 2.90
2312 6819 5.931441 AGAAGTGTAGAACTGCAACAATC 57.069 39.130 0.00 0.00 39.81 2.67
2342 6861 4.696877 TGATCATCACTTCGCAACAAAGAT 59.303 37.500 0.00 0.00 0.00 2.40
2578 7322 6.663093 AGAAGAGTAGACTCATATGCCATAGG 59.337 42.308 12.09 0.00 45.21 2.57
2698 9983 2.749621 GGACTAGAGGTGTGCCATTTTG 59.250 50.000 0.00 0.00 37.19 2.44
2771 10058 2.358898 GACGAAGGCACAATGGCAATAT 59.641 45.455 5.10 0.00 46.46 1.28
2772 10059 1.742831 GACGAAGGCACAATGGCAATA 59.257 47.619 5.10 0.00 46.46 1.90
2789 10076 1.609072 TGAGTCACAGAACAGAGGACG 59.391 52.381 0.00 0.00 33.84 4.79


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

AutoCloner maintained by Alex Coulton.