Multiple sequence alignment - TraesCS1B01G301500

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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 TraesCS1B01G301500 chr1B 100.000 7391 0 0 1 7391 522016841 522009451 0.000000e+00 13649.0
1 TraesCS1B01G301500 chr1B 91.250 80 5 2 5809 5887 562376881 562376959 2.820000e-19 108.0
2 TraesCS1B01G301500 chr1D 93.734 7453 239 96 1 7391 388644904 388637618 0.000000e+00 10966.0
3 TraesCS1B01G301500 chr1A 90.959 3462 164 58 1 3386 487735139 487731751 0.000000e+00 4521.0
4 TraesCS1B01G301500 chr1A 96.261 1765 38 10 4764 6520 487730278 487728534 0.000000e+00 2868.0
5 TraesCS1B01G301500 chr1A 94.489 1361 28 11 3409 4765 487731757 487730440 0.000000e+00 2054.0
6 TraesCS1B01G301500 chr1A 91.346 520 30 8 6591 7109 487728541 487728036 0.000000e+00 697.0
7 TraesCS1B01G301500 chr1A 94.882 254 12 1 7138 7391 487727780 487727528 5.370000e-106 396.0
8 TraesCS1B01G301500 chr5B 89.524 105 9 2 5788 5890 74996115 74996011 1.670000e-26 132.0
9 TraesCS1B01G301500 chr5D 82.099 162 17 7 5732 5882 69103534 69103374 2.160000e-25 128.0
10 TraesCS1B01G301500 chr5A 87.619 105 9 3 5790 5890 59707982 59707878 1.300000e-22 119.0
11 TraesCS1B01G301500 chr5A 90.476 63 4 2 4504 4565 659340044 659339983 1.710000e-11 82.4
12 TraesCS1B01G301500 chr5A 90.476 63 4 2 4504 4565 709195651 709195712 1.710000e-11 82.4
13 TraesCS1B01G301500 chr2A 81.208 149 24 4 5740 5886 471252609 471252755 4.690000e-22 117.0
14 TraesCS1B01G301500 chr2A 95.652 46 2 0 4503 4548 699526830 699526785 2.860000e-09 75.0
15 TraesCS1B01G301500 chr2B 81.538 130 14 4 5757 5886 419614536 419614655 1.700000e-16 99.0
16 TraesCS1B01G301500 chr2D 79.389 131 16 4 5757 5886 353067865 353067985 1.710000e-11 82.4
17 TraesCS1B01G301500 chr2D 95.745 47 2 0 4505 4551 220563232 220563186 7.950000e-10 76.8
18 TraesCS1B01G301500 chr7A 97.826 46 1 0 4504 4549 77709537 77709492 6.150000e-11 80.5
19 TraesCS1B01G301500 chr6A 95.652 46 2 0 4503 4548 226275660 226275705 2.860000e-09 75.0
20 TraesCS1B01G301500 chr4B 95.745 47 1 1 4502 4548 418517475 418517430 2.860000e-09 75.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G301500 chr1B 522009451 522016841 7390 True 13649.0 13649 100.0000 1 7391 1 chr1B.!!$R1 7390
1 TraesCS1B01G301500 chr1D 388637618 388644904 7286 True 10966.0 10966 93.7340 1 7391 1 chr1D.!!$R1 7390
2 TraesCS1B01G301500 chr1A 487727528 487735139 7611 True 2107.2 4521 93.5874 1 7391 5 chr1A.!!$R1 7390

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
561 599 0.036875 CCGGGAAAGAAAGGTGCTCT 59.963 55.000 0.00 0.0 0.00 4.09 F
568 606 0.321475 AGAAAGGTGCTCTGCTCTGC 60.321 55.000 0.00 0.0 0.00 4.26 F
1666 1777 0.473326 GATCAGGGCTGCTGAATCCT 59.527 55.000 0.00 0.0 34.26 3.24 F
2248 2365 0.036875 ACAGTAAGTGCTTCTGCCCC 59.963 55.000 9.59 0.0 38.71 5.80 F
2378 2495 0.593128 GCACCTGACTGTCGCAATTT 59.407 50.000 2.98 0.0 0.00 1.82 F
3105 3223 1.086067 AGGCACATGATCTTCGCACG 61.086 55.000 0.00 0.0 0.00 5.34 F
3108 3226 1.153369 ACATGATCTTCGCACGGGG 60.153 57.895 0.00 0.0 0.00 5.73 F
4207 4329 3.076621 GGTTTGCATGACATCTGTGAGA 58.923 45.455 0.00 0.0 0.00 3.27 F
4436 4558 3.325135 CCCTTCACAAGTTGAGTAGGACT 59.675 47.826 21.96 0.0 35.02 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2125 2242 0.543749 CTCCACTCCTGGAATCCACC 59.456 60.000 0.00 0.00 46.63 4.61 R
2170 2287 2.612285 TCTGAAGCTCCTTCTCCAGA 57.388 50.000 6.54 0.00 40.73 3.86 R
3105 3223 1.140312 TAAGGCAGACATCCATCCCC 58.860 55.000 0.00 0.00 0.00 4.81 R
3465 3584 2.291465 TGATTGTTTCAGCTGTCAGCAC 59.709 45.455 26.23 15.65 45.56 4.40 R
3633 3752 2.704572 CTTTGGTAGCAGAACAGGAGG 58.295 52.381 0.00 0.00 0.00 4.30 R
4809 5094 2.239654 AGCACCTGTAACATGTAGCCAT 59.760 45.455 0.00 0.00 0.00 4.40 R
4986 5271 2.693074 AGACAGGCACAAACCGAAAAAT 59.307 40.909 0.00 0.00 33.69 1.82 R
6152 6442 2.278245 TGTCCCCTCCATGTGAAGAAT 58.722 47.619 0.00 0.00 0.00 2.40 R
6419 6718 0.107459 GAGCCCAGGACTGCCTAAAG 60.107 60.000 0.00 0.00 44.80 1.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 0.040425 AAACAGCACGAACGCAATCC 60.040 50.000 0.00 0.00 0.00 3.01
38 39 4.083484 CGAACGCAATCCTTTCCTTTTACT 60.083 41.667 0.00 0.00 0.00 2.24
39 40 5.562113 CGAACGCAATCCTTTCCTTTTACTT 60.562 40.000 0.00 0.00 0.00 2.24
40 41 5.372547 ACGCAATCCTTTCCTTTTACTTC 57.627 39.130 0.00 0.00 0.00 3.01
41 42 4.217767 ACGCAATCCTTTCCTTTTACTTCC 59.782 41.667 0.00 0.00 0.00 3.46
43 44 5.048013 CGCAATCCTTTCCTTTTACTTCCTT 60.048 40.000 0.00 0.00 0.00 3.36
44 45 6.516693 CGCAATCCTTTCCTTTTACTTCCTTT 60.517 38.462 0.00 0.00 0.00 3.11
55 67 8.508875 TCCTTTTACTTCCTTTATTTAAGCACG 58.491 33.333 0.00 0.00 32.19 5.34
115 128 2.027561 CCCGAACTACCATGACAAGGAA 60.028 50.000 3.17 0.00 0.00 3.36
224 241 2.475200 AAACAAACAAGTCGCAGAGC 57.525 45.000 0.00 0.00 36.95 4.09
225 242 1.668419 AACAAACAAGTCGCAGAGCT 58.332 45.000 0.00 0.00 36.95 4.09
227 244 1.599542 ACAAACAAGTCGCAGAGCTTC 59.400 47.619 0.00 0.00 36.95 3.86
228 245 1.599071 CAAACAAGTCGCAGAGCTTCA 59.401 47.619 0.00 0.00 36.95 3.02
229 246 1.221414 AACAAGTCGCAGAGCTTCAC 58.779 50.000 0.00 0.00 36.95 3.18
231 248 1.066914 CAAGTCGCAGAGCTTCACTC 58.933 55.000 0.00 0.00 46.66 3.51
243 271 2.158928 AGCTTCACTCATCTCATCCAGC 60.159 50.000 0.00 0.00 0.00 4.85
245 273 1.767759 TCACTCATCTCATCCAGCGA 58.232 50.000 0.00 0.00 0.00 4.93
308 336 5.356882 TTCTTTCTTCGATCGCACAAAAT 57.643 34.783 11.09 0.00 0.00 1.82
359 387 1.722011 AACGCTCATCTACCAAACCG 58.278 50.000 0.00 0.00 0.00 4.44
360 388 0.892755 ACGCTCATCTACCAAACCGA 59.107 50.000 0.00 0.00 0.00 4.69
363 391 2.416836 CGCTCATCTACCAAACCGAAGA 60.417 50.000 0.00 0.00 0.00 2.87
364 392 3.190874 GCTCATCTACCAAACCGAAGAG 58.809 50.000 0.00 0.00 0.00 2.85
365 393 3.119101 GCTCATCTACCAAACCGAAGAGA 60.119 47.826 0.00 0.00 0.00 3.10
367 395 5.477607 TCATCTACCAAACCGAAGAGAAA 57.522 39.130 0.00 0.00 0.00 2.52
368 396 5.235516 TCATCTACCAAACCGAAGAGAAAC 58.764 41.667 0.00 0.00 0.00 2.78
369 397 4.950205 TCTACCAAACCGAAGAGAAACT 57.050 40.909 0.00 0.00 0.00 2.66
370 398 5.286267 TCTACCAAACCGAAGAGAAACTT 57.714 39.130 0.00 0.00 42.03 2.66
409 442 3.249320 AGCATCATTCGTTGATCCATTCG 59.751 43.478 1.44 0.00 43.40 3.34
462 495 4.789075 CTCCGGCGTGGTGGTACG 62.789 72.222 6.01 0.00 46.28 3.67
464 497 4.137872 CCGGCGTGGTGGTACGAT 62.138 66.667 6.01 0.00 46.46 3.73
465 498 2.581409 CGGCGTGGTGGTACGATC 60.581 66.667 0.00 0.00 46.46 3.69
468 503 2.179767 CGTGGTGGTACGATCGCA 59.820 61.111 16.60 0.00 46.46 5.10
541 579 3.122971 GCGGTTCCAACGGTAGGC 61.123 66.667 0.00 0.00 0.00 3.93
552 590 3.407075 GGTAGGCCCGGGAAAGAA 58.593 61.111 29.31 0.00 0.00 2.52
553 591 1.687014 GGTAGGCCCGGGAAAGAAA 59.313 57.895 29.31 0.00 0.00 2.52
556 594 0.843343 TAGGCCCGGGAAAGAAAGGT 60.843 55.000 29.31 0.00 0.00 3.50
557 595 1.977009 GGCCCGGGAAAGAAAGGTG 60.977 63.158 29.31 0.00 0.00 4.00
558 596 2.636412 GCCCGGGAAAGAAAGGTGC 61.636 63.158 29.31 0.00 0.00 5.01
559 597 1.074951 CCCGGGAAAGAAAGGTGCT 59.925 57.895 18.48 0.00 0.00 4.40
560 598 0.960861 CCCGGGAAAGAAAGGTGCTC 60.961 60.000 18.48 0.00 0.00 4.26
561 599 0.036875 CCGGGAAAGAAAGGTGCTCT 59.963 55.000 0.00 0.00 0.00 4.09
562 600 1.160137 CGGGAAAGAAAGGTGCTCTG 58.840 55.000 0.00 0.00 0.00 3.35
563 601 0.884514 GGGAAAGAAAGGTGCTCTGC 59.115 55.000 0.00 0.00 0.00 4.26
564 602 1.546548 GGGAAAGAAAGGTGCTCTGCT 60.547 52.381 0.00 0.00 0.00 4.24
565 603 1.809547 GGAAAGAAAGGTGCTCTGCTC 59.190 52.381 0.00 0.00 0.00 4.26
566 604 2.551938 GGAAAGAAAGGTGCTCTGCTCT 60.552 50.000 0.00 0.00 0.00 4.09
567 605 2.181954 AAGAAAGGTGCTCTGCTCTG 57.818 50.000 0.00 0.00 0.00 3.35
568 606 0.321475 AGAAAGGTGCTCTGCTCTGC 60.321 55.000 0.00 0.00 0.00 4.26
648 686 3.702048 GGACGCTGGTGCCTGGTA 61.702 66.667 0.00 0.00 35.36 3.25
649 687 2.125512 GACGCTGGTGCCTGGTAG 60.126 66.667 0.00 0.00 35.36 3.18
650 688 2.923035 ACGCTGGTGCCTGGTAGT 60.923 61.111 0.00 0.00 35.36 2.73
655 693 1.136500 GCTGGTGCCTGGTAGTAGTAC 59.864 57.143 0.00 0.00 0.00 2.73
731 769 2.203082 CCGCAGAGGATCCGGATCA 61.203 63.158 38.29 5.12 44.55 2.92
1088 1179 1.577328 CGCCTCGCTTCAAATGGTGT 61.577 55.000 0.00 0.00 0.00 4.16
1089 1180 0.598065 GCCTCGCTTCAAATGGTGTT 59.402 50.000 0.00 0.00 0.00 3.32
1090 1181 1.666888 GCCTCGCTTCAAATGGTGTTG 60.667 52.381 0.00 0.00 0.00 3.33
1130 1221 2.434185 GGGCGCACGAGTGATTCA 60.434 61.111 10.83 0.00 0.00 2.57
1447 1541 2.293399 CACTAGTTTTTCCCCAGTGTGC 59.707 50.000 0.00 0.00 33.53 4.57
1511 1609 2.040544 GGGGCGTGTGATTGACTGG 61.041 63.158 0.00 0.00 0.00 4.00
1515 1617 1.499056 CGTGTGATTGACTGGCTGC 59.501 57.895 0.00 0.00 0.00 5.25
1571 1675 3.031964 GCATGCTTCAAGCTCGCGT 62.032 57.895 11.57 0.00 42.97 6.01
1626 1737 3.354920 CGAATTTTGTCGCTTCTGTTTCG 59.645 43.478 0.00 0.00 33.66 3.46
1666 1777 0.473326 GATCAGGGCTGCTGAATCCT 59.527 55.000 0.00 0.00 34.26 3.24
1880 1997 3.255379 GCGAGATTGGCGACGACC 61.255 66.667 0.00 0.00 0.00 4.79
1917 2034 2.125673 CAGCAAGGGCAATGCAGC 60.126 61.111 7.79 5.32 46.22 5.25
2107 2224 1.009078 ATGTGAATGACGATGCCACG 58.991 50.000 0.00 0.00 39.31 4.94
2170 2287 2.027377 CCAGGAGTTTGATCTCAGTGCT 60.027 50.000 0.00 0.00 36.30 4.40
2248 2365 0.036875 ACAGTAAGTGCTTCTGCCCC 59.963 55.000 9.59 0.00 38.71 5.80
2252 2369 0.777446 TAAGTGCTTCTGCCCCCTTT 59.223 50.000 0.00 0.00 38.71 3.11
2255 2372 1.228552 TGCTTCTGCCCCCTTTCAC 60.229 57.895 0.00 0.00 38.71 3.18
2282 2399 5.416639 TCCTCAGGATCATTTGTCATGTTTG 59.583 40.000 0.00 0.00 0.00 2.93
2284 2401 4.082081 TCAGGATCATTTGTCATGTTTGGC 60.082 41.667 0.00 0.00 0.00 4.52
2285 2402 3.833650 AGGATCATTTGTCATGTTTGGCA 59.166 39.130 0.00 0.00 35.13 4.92
2286 2403 4.283978 AGGATCATTTGTCATGTTTGGCAA 59.716 37.500 0.00 0.00 45.39 4.52
2378 2495 0.593128 GCACCTGACTGTCGCAATTT 59.407 50.000 2.98 0.00 0.00 1.82
2417 2534 4.152759 TGCTTAAATTACGAACCCAGAACG 59.847 41.667 0.00 0.00 0.00 3.95
2418 2535 4.436451 GCTTAAATTACGAACCCAGAACGG 60.436 45.833 0.00 0.00 0.00 4.44
2435 2552 6.457392 CCAGAACGGACTTGAATTATGATGTG 60.457 42.308 0.00 0.00 36.56 3.21
2451 2568 6.778834 ATGATGTGATTTTGCTGGTTGATA 57.221 33.333 0.00 0.00 0.00 2.15
2773 2890 1.202290 GGCCAGCGGATACAAATGTTG 60.202 52.381 0.00 0.00 0.00 3.33
3105 3223 1.086067 AGGCACATGATCTTCGCACG 61.086 55.000 0.00 0.00 0.00 5.34
3108 3226 1.153369 ACATGATCTTCGCACGGGG 60.153 57.895 0.00 0.00 0.00 5.73
3279 3397 6.334237 AGGTATTGATATGGGGATACAAACCA 59.666 38.462 0.00 0.00 38.88 3.67
3283 3401 6.272953 TGATATGGGGATACAAACCATTGA 57.727 37.500 0.30 0.00 42.08 2.57
3385 3503 8.854614 ATCTTAACACTTATGAGCTGTTCTTT 57.145 30.769 0.00 0.00 32.87 2.52
3465 3584 7.398746 TCTATTTCATTTTTGACGTCGCATAG 58.601 34.615 11.62 5.90 0.00 2.23
3508 3627 7.111247 TCAACAGGAACATCTTTTCATTGTT 57.889 32.000 0.00 0.00 36.26 2.83
4207 4329 3.076621 GGTTTGCATGACATCTGTGAGA 58.923 45.455 0.00 0.00 0.00 3.27
4220 4342 4.391405 TCTGTGAGACGCATCAACATAT 57.609 40.909 0.00 0.00 0.00 1.78
4436 4558 3.325135 CCCTTCACAAGTTGAGTAGGACT 59.675 47.826 21.96 0.00 35.02 3.85
4479 4601 6.122277 TGAACAGGAGAGTGAATTCAAAAGT 58.878 36.000 10.35 0.00 0.00 2.66
4487 4609 5.300034 AGAGTGAATTCAAAAGTGCATGACA 59.700 36.000 10.35 0.00 0.00 3.58
4601 4723 6.707290 ACCTTCTAGTAACATTGCACATACA 58.293 36.000 0.00 0.00 0.00 2.29
4658 4780 9.605275 TGAAGATAATGTGTCTAGAATCTTTGG 57.395 33.333 13.68 0.00 34.67 3.28
4809 5094 5.708736 AGAGAAGTAGAGACTGAGGATGA 57.291 43.478 0.00 0.00 35.52 2.92
4986 5271 3.997762 ACGAGGTACATGCTTGTTTACA 58.002 40.909 10.85 0.00 37.28 2.41
5542 5832 5.540337 TGTTTTGTGCAAGGGATATGGTTTA 59.460 36.000 0.00 0.00 0.00 2.01
5684 5974 4.641989 ACTTCTTTGTCATCACTGCAAAGT 59.358 37.500 13.58 0.00 41.73 2.66
5781 6071 5.431765 CTGTGCTCTAGGTGATACCAAAAT 58.568 41.667 0.28 0.00 41.95 1.82
5908 6198 5.065988 ACTTTGATCACCACACAAGTGTTAC 59.934 40.000 2.55 0.00 44.39 2.50
6152 6442 1.202915 TGAGCTGCCAATCAAAGACCA 60.203 47.619 0.00 0.00 0.00 4.02
6198 6488 1.736681 GCAGTTCCTCAGCTCATGAAC 59.263 52.381 0.00 0.00 37.52 3.18
6199 6489 1.998315 CAGTTCCTCAGCTCATGAACG 59.002 52.381 0.41 0.00 41.43 3.95
6200 6490 1.895798 AGTTCCTCAGCTCATGAACGA 59.104 47.619 0.41 0.00 41.43 3.85
6201 6491 1.996191 GTTCCTCAGCTCATGAACGAC 59.004 52.381 0.00 0.00 37.52 4.34
6202 6492 1.256812 TCCTCAGCTCATGAACGACA 58.743 50.000 0.00 0.00 37.52 4.35
6203 6493 1.067565 TCCTCAGCTCATGAACGACAC 60.068 52.381 0.00 0.00 37.52 3.67
6204 6494 0.987715 CTCAGCTCATGAACGACACG 59.012 55.000 0.00 0.00 37.52 4.49
6205 6495 0.313987 TCAGCTCATGAACGACACGT 59.686 50.000 0.00 0.00 43.97 4.49
6377 6676 9.174166 TCTGATGGAGCTTTTTAAAATACTACC 57.826 33.333 0.55 6.80 0.00 3.18
6437 6736 1.994463 CTTTAGGCAGTCCTGGGCT 59.006 57.895 0.00 0.00 44.08 5.19
6446 6745 2.744494 GCAGTCCTGGGCTCTATCTTTG 60.744 54.545 0.00 0.00 0.00 2.77
6548 6848 5.898972 AGCAAAGCTCCAAAAATATATCCCA 59.101 36.000 0.00 0.00 30.62 4.37
6549 6849 5.985530 GCAAAGCTCCAAAAATATATCCCAC 59.014 40.000 0.00 0.00 0.00 4.61
6553 6853 6.012745 AGCTCCAAAAATATATCCCACATCC 58.987 40.000 0.00 0.00 0.00 3.51
6638 6938 2.838736 CTTAGTTGCCATGCTACCGAT 58.161 47.619 0.00 0.00 35.09 4.18
6646 6946 2.223572 GCCATGCTACCGATTTCTTTGG 60.224 50.000 0.00 0.00 34.63 3.28
6739 7039 5.542635 ACACAGGAGAAGGTTTACAGACATA 59.457 40.000 0.00 0.00 0.00 2.29
6754 7054 5.668471 ACAGACATATGATGTGAGTTCTGG 58.332 41.667 10.38 0.00 45.03 3.86
6790 7090 9.525409 GAAGTTACTCTATGTAAAAGCGGAATA 57.475 33.333 0.00 0.00 42.12 1.75
6809 7109 6.093495 CGGAATAAGAGGCATTGTAACTTCAA 59.907 38.462 0.00 0.00 0.00 2.69
6838 7138 3.442273 ACTTTCGTCAGCAACCAAAAAGA 59.558 39.130 0.00 0.00 0.00 2.52
6841 7141 1.334869 CGTCAGCAACCAAAAAGAGCT 59.665 47.619 0.00 0.00 35.63 4.09
6842 7142 2.548057 CGTCAGCAACCAAAAAGAGCTA 59.452 45.455 0.00 0.00 33.59 3.32
6850 7150 7.912250 CAGCAACCAAAAAGAGCTATATACAAG 59.088 37.037 0.00 0.00 33.59 3.16
6884 7184 2.708861 ACTGATGTACAACCCTGACCAA 59.291 45.455 0.00 0.00 0.00 3.67
6895 7195 0.595095 CCTGACCAAGCTTTGCAGAC 59.405 55.000 17.20 1.29 0.00 3.51
6907 7207 2.859165 TTGCAGACCTTTACTCCCTG 57.141 50.000 0.00 0.00 0.00 4.45
6927 7227 3.666274 TGGTACACGTAAAACCATCAGG 58.334 45.455 10.79 0.00 38.36 3.86
7014 7314 5.647225 AGAAAGAAAAATCTGCCAGAGCTAG 59.353 40.000 0.00 0.00 40.80 3.42
7016 7316 3.521126 AGAAAAATCTGCCAGAGCTAGGA 59.479 43.478 8.81 0.00 40.80 2.94
7017 7317 4.165758 AGAAAAATCTGCCAGAGCTAGGAT 59.834 41.667 8.81 0.00 40.80 3.24
7018 7318 5.367937 AGAAAAATCTGCCAGAGCTAGGATA 59.632 40.000 8.81 0.00 40.80 2.59
7019 7319 5.839517 AAAATCTGCCAGAGCTAGGATAT 57.160 39.130 8.81 0.00 40.80 1.63
7020 7320 5.839517 AAATCTGCCAGAGCTAGGATATT 57.160 39.130 8.81 2.34 40.80 1.28
7021 7321 6.942163 AAATCTGCCAGAGCTAGGATATTA 57.058 37.500 8.81 0.00 40.80 0.98
7022 7322 5.930837 ATCTGCCAGAGCTAGGATATTAC 57.069 43.478 8.81 0.00 40.80 1.89
7023 7323 4.740902 TCTGCCAGAGCTAGGATATTACA 58.259 43.478 8.81 0.00 40.80 2.41
7024 7324 4.769488 TCTGCCAGAGCTAGGATATTACAG 59.231 45.833 8.81 5.41 40.80 2.74
7046 7346 1.625818 ACATCTTTCTTCTCTGCGGGT 59.374 47.619 0.00 0.00 0.00 5.28
7117 7417 8.579863 ACGAATATAACTGTACAAGTATACCCC 58.420 37.037 0.00 0.00 38.56 4.95
7134 7434 1.763770 CCCCAGAGGAACAACAGCT 59.236 57.895 0.00 0.00 38.24 4.24
7168 7695 6.825721 AGCTTTCACCTACTAATCCAATTCAG 59.174 38.462 0.00 0.00 0.00 3.02
7197 7724 5.400485 CAGAGTTGCTGCAAAACTTACATTC 59.600 40.000 17.80 0.31 37.98 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 9.026074 CAAAAGAAACGTGCTTAAATAAAGGAA 57.974 29.630 4.58 0.00 37.28 3.36
39 40 8.192110 ACAAAAGAAACGTGCTTAAATAAAGGA 58.808 29.630 4.58 0.00 35.58 3.36
40 41 8.347729 ACAAAAGAAACGTGCTTAAATAAAGG 57.652 30.769 4.58 0.00 35.58 3.11
44 45 9.355215 TGAAAACAAAAGAAACGTGCTTAAATA 57.645 25.926 4.58 0.00 0.00 1.40
55 67 9.888878 GTATAGTAGGGTGAAAACAAAAGAAAC 57.111 33.333 0.00 0.00 0.00 2.78
69 81 6.190346 ACTGACTAGGAGTATAGTAGGGTG 57.810 45.833 0.00 0.00 36.13 4.61
115 128 2.955402 GACGTCGCACTGGAGACT 59.045 61.111 0.00 0.00 41.12 3.24
224 241 2.100418 TCGCTGGATGAGATGAGTGAAG 59.900 50.000 0.00 0.00 0.00 3.02
225 242 2.102578 TCGCTGGATGAGATGAGTGAA 58.897 47.619 0.00 0.00 0.00 3.18
227 244 1.537776 GGTCGCTGGATGAGATGAGTG 60.538 57.143 0.00 0.00 0.00 3.51
228 245 0.749649 GGTCGCTGGATGAGATGAGT 59.250 55.000 0.00 0.00 0.00 3.41
229 246 0.033228 GGGTCGCTGGATGAGATGAG 59.967 60.000 0.00 0.00 0.00 2.90
231 248 1.300465 CGGGTCGCTGGATGAGATG 60.300 63.158 0.00 0.00 0.00 2.90
232 249 1.330655 AACGGGTCGCTGGATGAGAT 61.331 55.000 0.00 0.00 0.00 2.75
233 250 1.541310 AAACGGGTCGCTGGATGAGA 61.541 55.000 0.00 0.00 0.00 3.27
234 251 0.673644 AAAACGGGTCGCTGGATGAG 60.674 55.000 0.00 0.00 0.00 2.90
237 265 2.332654 GCAAAACGGGTCGCTGGAT 61.333 57.895 0.00 0.00 0.00 3.41
243 271 1.278637 GACAGTGCAAAACGGGTCG 59.721 57.895 0.00 0.00 31.39 4.79
245 273 0.454196 GTTGACAGTGCAAAACGGGT 59.546 50.000 0.00 0.00 0.00 5.28
330 358 0.384669 GATGAGCGTTACGGGCTACT 59.615 55.000 6.94 0.00 41.72 2.57
397 430 2.354821 GCTGGTTACCGAATGGATCAAC 59.645 50.000 0.00 0.00 39.21 3.18
409 442 2.325082 CGTGCACTGGCTGGTTACC 61.325 63.158 16.19 0.00 41.91 2.85
445 478 4.789075 CGTACCACCACGCCGGAG 62.789 72.222 5.05 3.72 38.63 4.63
447 480 4.137872 ATCGTACCACCACGCCGG 62.138 66.667 0.00 0.00 41.67 6.13
448 481 2.581409 GATCGTACCACCACGCCG 60.581 66.667 0.00 0.00 41.67 6.46
449 482 2.581409 CGATCGTACCACCACGCC 60.581 66.667 7.03 0.00 41.67 5.68
450 483 3.252484 GCGATCGTACCACCACGC 61.252 66.667 17.81 0.00 41.67 5.34
451 484 2.156446 GTGCGATCGTACCACCACG 61.156 63.158 23.72 0.00 43.28 4.94
452 485 2.156446 CGTGCGATCGTACCACCAC 61.156 63.158 27.08 18.25 0.00 4.16
453 486 2.179767 CGTGCGATCGTACCACCA 59.820 61.111 27.08 8.64 0.00 4.17
454 487 2.581409 CCGTGCGATCGTACCACC 60.581 66.667 27.08 6.15 0.00 4.61
455 488 3.252484 GCCGTGCGATCGTACCAC 61.252 66.667 27.08 19.54 0.00 4.16
456 489 4.501714 GGCCGTGCGATCGTACCA 62.502 66.667 27.08 10.10 0.00 3.25
541 579 0.960861 GAGCACCTTTCTTTCCCGGG 60.961 60.000 16.85 16.85 0.00 5.73
545 583 1.809547 GAGCAGAGCACCTTTCTTTCC 59.190 52.381 0.00 0.00 0.00 3.13
547 585 2.502295 CAGAGCAGAGCACCTTTCTTT 58.498 47.619 0.00 0.00 0.00 2.52
548 586 1.881498 GCAGAGCAGAGCACCTTTCTT 60.881 52.381 0.00 0.00 0.00 2.52
549 587 0.321475 GCAGAGCAGAGCACCTTTCT 60.321 55.000 0.00 0.00 0.00 2.52
550 588 0.321475 AGCAGAGCAGAGCACCTTTC 60.321 55.000 0.00 0.00 0.00 2.62
551 589 0.605860 CAGCAGAGCAGAGCACCTTT 60.606 55.000 0.00 0.00 0.00 3.11
552 590 1.003597 CAGCAGAGCAGAGCACCTT 60.004 57.895 0.00 0.00 0.00 3.50
553 591 2.663796 CAGCAGAGCAGAGCACCT 59.336 61.111 0.00 0.00 0.00 4.00
556 594 3.230522 TTCGCAGCAGAGCAGAGCA 62.231 57.895 0.00 0.00 0.00 4.26
557 595 2.433838 TTCGCAGCAGAGCAGAGC 60.434 61.111 0.00 0.00 0.00 4.09
558 596 1.810441 CCTTCGCAGCAGAGCAGAG 60.810 63.158 0.00 0.00 0.00 3.35
559 597 2.263852 CCTTCGCAGCAGAGCAGA 59.736 61.111 0.00 0.00 0.00 4.26
560 598 2.793160 TTCCCTTCGCAGCAGAGCAG 62.793 60.000 0.00 0.00 0.00 4.24
561 599 2.793160 CTTCCCTTCGCAGCAGAGCA 62.793 60.000 0.00 0.00 0.00 4.26
562 600 2.046892 TTCCCTTCGCAGCAGAGC 60.047 61.111 0.00 0.00 0.00 4.09
563 601 1.449246 CCTTCCCTTCGCAGCAGAG 60.449 63.158 0.00 0.00 0.00 3.35
564 602 2.665000 CCTTCCCTTCGCAGCAGA 59.335 61.111 0.00 0.00 0.00 4.26
565 603 3.130160 GCCTTCCCTTCGCAGCAG 61.130 66.667 0.00 0.00 0.00 4.24
566 604 4.722700 GGCCTTCCCTTCGCAGCA 62.723 66.667 0.00 0.00 0.00 4.41
647 685 5.367937 CCACTCCTACCAGGTAGTACTACTA 59.632 48.000 27.71 14.18 36.53 1.82
648 686 4.165758 CCACTCCTACCAGGTAGTACTACT 59.834 50.000 27.71 13.83 36.53 2.57
649 687 4.080072 ACCACTCCTACCAGGTAGTACTAC 60.080 50.000 22.53 22.53 36.53 2.73
650 688 4.114597 ACCACTCCTACCAGGTAGTACTA 58.885 47.826 23.04 0.00 36.53 1.82
851 927 4.796231 GGTGCCGCTGTCGTCGAT 62.796 66.667 0.00 0.00 0.00 3.59
1343 1434 2.364842 GAGGAGGAGCTGGAGGCA 60.365 66.667 0.00 0.00 44.79 4.75
1488 1586 3.706373 AATCACACGCCCCGCTCT 61.706 61.111 0.00 0.00 0.00 4.09
1511 1609 2.806856 CGAGATTCACAGCGGCAGC 61.807 63.158 0.00 0.00 45.58 5.25
1515 1617 1.601663 GGAGATCGAGATTCACAGCGG 60.602 57.143 0.00 0.00 0.00 5.52
1547 1649 1.334243 GAGCTTGAAGCATGCATCTCC 59.666 52.381 22.26 11.12 45.56 3.71
1552 1654 2.872557 GCGAGCTTGAAGCATGCA 59.127 55.556 21.98 0.00 45.56 3.96
1571 1675 1.330521 GAACTCGAGCAAAAGCACACA 59.669 47.619 13.61 0.00 0.00 3.72
1586 1690 6.917217 AATTCGGATCAGAATTCAGAACTC 57.083 37.500 23.08 0.73 44.76 3.01
1587 1691 7.175641 ACAAAATTCGGATCAGAATTCAGAACT 59.824 33.333 26.99 12.74 46.55 3.01
1588 1692 7.308435 ACAAAATTCGGATCAGAATTCAGAAC 58.692 34.615 26.99 3.85 46.55 3.01
1589 1693 7.452880 ACAAAATTCGGATCAGAATTCAGAA 57.547 32.000 26.99 0.29 46.55 3.02
1590 1694 6.183360 CGACAAAATTCGGATCAGAATTCAGA 60.183 38.462 26.99 5.51 46.55 3.27
1591 1695 5.961843 CGACAAAATTCGGATCAGAATTCAG 59.038 40.000 26.99 23.46 46.55 3.02
1592 1696 5.673568 GCGACAAAATTCGGATCAGAATTCA 60.674 40.000 26.99 1.21 46.55 2.57
1626 1737 0.597377 CCAAGCGAAACAGCCAAACC 60.597 55.000 0.00 0.00 38.01 3.27
1666 1777 4.006357 GGCGACCACACCCCGTAA 62.006 66.667 0.00 0.00 0.00 3.18
1856 1973 2.813908 GCCAATCTCGCCGACGTT 60.814 61.111 0.00 0.00 41.18 3.99
1917 2034 2.915685 GCGGTTTCGTATACGCCG 59.084 61.111 27.78 27.78 45.70 6.46
2107 2224 4.699522 AACGGACCGCCCTTGAGC 62.700 66.667 15.39 0.00 0.00 4.26
2125 2242 0.543749 CTCCACTCCTGGAATCCACC 59.456 60.000 0.00 0.00 46.63 4.61
2170 2287 2.612285 TCTGAAGCTCCTTCTCCAGA 57.388 50.000 6.54 0.00 40.73 3.86
2248 2365 4.226427 TGATCCTGAGGAATGTGAAAGG 57.774 45.455 4.76 0.00 34.34 3.11
2252 2369 5.183530 ACAAATGATCCTGAGGAATGTGA 57.816 39.130 4.76 0.00 34.34 3.58
2255 2372 5.593095 ACATGACAAATGATCCTGAGGAATG 59.407 40.000 4.76 3.79 34.34 2.67
2282 2399 6.843069 TCAAGCTTGTTAAAGAATTTTGCC 57.157 33.333 25.19 0.00 40.09 4.52
2284 2401 8.591312 TCGTTTCAAGCTTGTTAAAGAATTTTG 58.409 29.630 25.19 0.00 40.09 2.44
2285 2402 8.696410 TCGTTTCAAGCTTGTTAAAGAATTTT 57.304 26.923 25.19 0.00 40.09 1.82
2286 2403 8.871686 ATCGTTTCAAGCTTGTTAAAGAATTT 57.128 26.923 25.19 10.99 43.42 1.82
2287 2404 8.871686 AATCGTTTCAAGCTTGTTAAAGAATT 57.128 26.923 25.19 16.40 35.19 2.17
2288 2405 8.134895 TGAATCGTTTCAAGCTTGTTAAAGAAT 58.865 29.630 25.19 18.83 38.90 2.40
2289 2406 7.431084 GTGAATCGTTTCAAGCTTGTTAAAGAA 59.569 33.333 25.19 9.01 43.29 2.52
2290 2407 6.910433 GTGAATCGTTTCAAGCTTGTTAAAGA 59.090 34.615 25.19 23.81 43.29 2.52
2399 2516 3.069289 GTCCGTTCTGGGTTCGTAATTT 58.931 45.455 0.00 0.00 38.76 1.82
2417 2534 7.977853 AGCAAAATCACATCATAATTCAAGTCC 59.022 33.333 0.00 0.00 0.00 3.85
2418 2535 8.804743 CAGCAAAATCACATCATAATTCAAGTC 58.195 33.333 0.00 0.00 0.00 3.01
2435 2552 7.934457 ACTACATCATATCAACCAGCAAAATC 58.066 34.615 0.00 0.00 0.00 2.17
2451 2568 6.947733 TGGATCAACCAGAAAAACTACATCAT 59.052 34.615 0.00 0.00 44.64 2.45
2481 2598 4.407496 TTTGGAATTACAAAGGTACGCG 57.593 40.909 11.95 3.53 35.57 6.01
2773 2890 7.745972 TCATCGATATTATGAGCAGCATTTTC 58.254 34.615 0.00 0.00 38.44 2.29
3105 3223 1.140312 TAAGGCAGACATCCATCCCC 58.860 55.000 0.00 0.00 0.00 4.81
3279 3397 6.010219 AGGTATGGTGTAAAAGCAAGTCAAT 58.990 36.000 0.00 0.00 40.33 2.57
3283 3401 6.300703 TGTAAGGTATGGTGTAAAAGCAAGT 58.699 36.000 0.00 0.00 40.33 3.16
3385 3503 5.009911 ACTGAAGCACACATCTTGCATAAAA 59.990 36.000 0.00 0.00 42.83 1.52
3443 3561 5.794945 CACTATGCGACGTCAAAAATGAAAT 59.205 36.000 17.16 0.00 0.00 2.17
3465 3584 2.291465 TGATTGTTTCAGCTGTCAGCAC 59.709 45.455 26.23 15.65 45.56 4.40
3508 3627 4.840168 GCCCGTAGCAATTCGGTA 57.160 55.556 3.00 0.00 44.51 4.02
3633 3752 2.704572 CTTTGGTAGCAGAACAGGAGG 58.295 52.381 0.00 0.00 0.00 4.30
3704 3826 4.970662 ATGGTGCTACTAATTGCAAGTG 57.029 40.909 10.14 2.29 41.10 3.16
4292 4414 6.734104 AAAATCGAGATTGAAGAGGACAAG 57.266 37.500 0.00 0.00 0.00 3.16
4479 4601 5.673514 TCTGCAGAAATATACTGTCATGCA 58.326 37.500 15.67 0.00 39.89 3.96
4487 4609 8.808092 GGGAGTAGTATTCTGCAGAAATATACT 58.192 37.037 30.82 30.82 37.61 2.12
4809 5094 2.239654 AGCACCTGTAACATGTAGCCAT 59.760 45.455 0.00 0.00 0.00 4.40
4986 5271 2.693074 AGACAGGCACAAACCGAAAAAT 59.307 40.909 0.00 0.00 33.69 1.82
5684 5974 6.248433 ACAGCTGAAATCCTTATGGAAAGAA 58.752 36.000 23.35 0.00 46.80 2.52
5760 6050 4.035675 GCATTTTGGTATCACCTAGAGCAC 59.964 45.833 0.00 0.00 39.58 4.40
5853 6143 2.420022 ACTAGGCATTCATTGTGCGTTC 59.580 45.455 0.00 0.00 43.40 3.95
5908 6198 7.098477 TGGAAAAATGAATGCCATGTTCTAAG 58.902 34.615 0.00 0.00 31.58 2.18
6152 6442 2.278245 TGTCCCCTCCATGTGAAGAAT 58.722 47.619 0.00 0.00 0.00 2.40
6265 6559 0.322816 CCTAGCAAAGCAGGCCAAGA 60.323 55.000 5.01 0.00 0.00 3.02
6419 6718 0.107459 GAGCCCAGGACTGCCTAAAG 60.107 60.000 0.00 0.00 44.80 1.85
6437 6736 5.188434 CAATCTTCCAGTGCCAAAGATAGA 58.812 41.667 11.67 0.00 38.47 1.98
6446 6745 2.238521 TCCAAACAATCTTCCAGTGCC 58.761 47.619 0.00 0.00 0.00 5.01
6548 6848 9.699410 TTGATTAATTAGGTGAAATGAGGATGT 57.301 29.630 0.00 0.00 0.00 3.06
6635 6935 1.511887 CACCGCGCCAAAGAAATCG 60.512 57.895 0.00 0.00 0.00 3.34
6790 7090 5.507985 GCTTGTTGAAGTTACAATGCCTCTT 60.508 40.000 0.00 0.00 35.18 2.85
6872 7172 0.032540 GCAAAGCTTGGTCAGGGTTG 59.967 55.000 0.00 0.00 0.00 3.77
6884 7184 2.553247 GGGAGTAAAGGTCTGCAAAGCT 60.553 50.000 0.00 0.00 0.00 3.74
6895 7195 1.897802 ACGTGTACCAGGGAGTAAAGG 59.102 52.381 0.00 0.00 0.00 3.11
6907 7207 3.929094 TCCTGATGGTTTTACGTGTACC 58.071 45.455 0.00 3.30 34.23 3.34
6981 7281 7.867403 TGGCAGATTTTTCTTTCTGTAATGAAC 59.133 33.333 2.30 0.00 41.16 3.18
6995 7295 3.878778 TCCTAGCTCTGGCAGATTTTTC 58.121 45.455 19.11 5.32 41.70 2.29
6999 7299 5.782331 TGTAATATCCTAGCTCTGGCAGATT 59.218 40.000 19.11 11.97 41.70 2.40
7000 7300 5.336945 TGTAATATCCTAGCTCTGGCAGAT 58.663 41.667 19.11 6.77 41.70 2.90
7016 7316 9.757227 GCAGAGAAGAAAGATGTACTGTAATAT 57.243 33.333 0.00 0.00 0.00 1.28
7017 7317 7.915923 CGCAGAGAAGAAAGATGTACTGTAATA 59.084 37.037 0.00 0.00 0.00 0.98
7018 7318 6.754209 CGCAGAGAAGAAAGATGTACTGTAAT 59.246 38.462 0.00 0.00 0.00 1.89
7019 7319 6.093404 CGCAGAGAAGAAAGATGTACTGTAA 58.907 40.000 0.00 0.00 0.00 2.41
7020 7320 5.393135 CCGCAGAGAAGAAAGATGTACTGTA 60.393 44.000 0.00 0.00 0.00 2.74
7021 7321 4.489810 CGCAGAGAAGAAAGATGTACTGT 58.510 43.478 0.00 0.00 0.00 3.55
7022 7322 3.862267 CCGCAGAGAAGAAAGATGTACTG 59.138 47.826 0.00 0.00 0.00 2.74
7023 7323 3.118956 CCCGCAGAGAAGAAAGATGTACT 60.119 47.826 0.00 0.00 0.00 2.73
7024 7324 3.190874 CCCGCAGAGAAGAAAGATGTAC 58.809 50.000 0.00 0.00 0.00 2.90
7046 7346 5.570205 TTGTTCAACATGGAGTAACCCTA 57.430 39.130 0.00 0.00 38.00 3.53
7117 7417 1.677217 GCTAGCTGTTGTTCCTCTGGG 60.677 57.143 7.70 0.00 0.00 4.45
7123 7423 3.610349 GCTCAAAAGCTAGCTGTTGTTCC 60.610 47.826 35.69 24.42 45.55 3.62
7125 7425 3.632855 GCTCAAAAGCTAGCTGTTGTT 57.367 42.857 35.69 18.38 45.55 2.83
7197 7724 2.102578 GATCCCACAAATTGACCAGGG 58.897 52.381 0.00 5.68 37.65 4.45
7268 7795 5.095145 TCTCTCTCCAAAATGATGTGAGG 57.905 43.478 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.