Multiple sequence alignment - TraesCS5D01G044100

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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 TraesCS5D01G044100 chr5D 100.000 6719 0 0 1 6719 43214906 43208188 0.000000e+00 12408.0
1 TraesCS5D01G044100 chr5D 97.674 43 1 0 2399 2441 408787885 408787927 2.600000e-09 75.0
2 TraesCS5D01G044100 chr5B 94.876 4118 125 34 2030 6124 40788430 40784376 0.000000e+00 6357.0
3 TraesCS5D01G044100 chr5B 93.990 1198 49 10 1 1177 40790985 40789790 0.000000e+00 1792.0
4 TraesCS5D01G044100 chr5B 90.434 899 36 14 1174 2039 40789671 40788790 0.000000e+00 1138.0
5 TraesCS5D01G044100 chr5B 91.590 547 36 4 6154 6700 40784104 40783568 0.000000e+00 747.0
6 TraesCS5D01G044100 chr5B 84.593 344 41 8 1 333 546452614 546452272 1.400000e-86 331.0
7 TraesCS5D01G044100 chr5B 85.484 124 9 8 416 536 163936242 163936125 3.290000e-23 121.0
8 TraesCS5D01G044100 chr5B 85.484 124 9 8 416 536 236809461 236809344 3.290000e-23 121.0
9 TraesCS5D01G044100 chr5B 97.674 43 1 0 2399 2441 706306927 706306885 2.600000e-09 75.0
10 TraesCS5D01G044100 chr5A 95.553 3778 97 28 2399 6148 33007820 33004086 0.000000e+00 5980.0
11 TraesCS5D01G044100 chr5A 91.923 1882 83 28 550 2401 33009691 33007849 0.000000e+00 2569.0
12 TraesCS5D01G044100 chr5A 89.979 469 34 6 6127 6589 33003968 33003507 1.610000e-165 593.0
13 TraesCS5D01G044100 chr5A 86.136 339 37 8 1 329 564551267 564551605 2.300000e-94 357.0
14 TraesCS5D01G044100 chr5A 96.296 135 5 0 6585 6719 33002874 33002740 8.770000e-54 222.0
15 TraesCS5D01G044100 chr5A 87.302 63 2 4 2399 2461 195632235 195632179 4.350000e-07 67.6
16 TraesCS5D01G044100 chr3B 88.822 331 24 4 6389 6719 284008008 284008325 1.760000e-105 394.0
17 TraesCS5D01G044100 chr3B 84.677 124 9 9 416 536 245809517 245809401 1.530000e-21 115.0
18 TraesCS5D01G044100 chr6D 87.356 348 34 5 1 339 423488655 423489001 2.270000e-104 390.0
19 TraesCS5D01G044100 chr6D 93.694 111 7 0 423 533 471320485 471320375 4.170000e-37 167.0
20 TraesCS5D01G044100 chr3D 87.500 344 31 7 1 334 10422380 10422039 2.940000e-103 387.0
21 TraesCS5D01G044100 chr3D 88.485 330 22 6 6390 6719 231727035 231727348 1.060000e-102 385.0
22 TraesCS5D01G044100 chr3A 88.182 330 26 4 6390 6719 296926749 296926433 1.370000e-101 381.0
23 TraesCS5D01G044100 chr3A 86.095 338 38 6 1 329 7620335 7619998 8.290000e-94 355.0
24 TraesCS5D01G044100 chr3A 92.982 114 8 0 423 536 58845950 58845837 4.170000e-37 167.0
25 TraesCS5D01G044100 chr6B 85.714 343 37 7 1 334 676295124 676295463 1.070000e-92 351.0
26 TraesCS5D01G044100 chr6B 94.643 112 5 1 423 533 583281019 583281130 8.960000e-39 172.0
27 TraesCS5D01G044100 chr6B 84.677 124 9 9 416 536 270081674 270081790 1.530000e-21 115.0
28 TraesCS5D01G044100 chr7B 85.799 338 38 5 1 329 539212783 539213119 3.860000e-92 350.0
29 TraesCS5D01G044100 chr7B 94.595 111 5 1 421 531 634848782 634848673 3.220000e-38 171.0
30 TraesCS5D01G044100 chr7B 85.088 114 9 7 416 526 126272620 126272728 7.120000e-20 110.0
31 TraesCS5D01G044100 chr2D 85.546 339 38 7 4 333 557269579 557269243 1.790000e-90 344.0
32 TraesCS5D01G044100 chr2D 97.727 44 1 0 2398 2441 459300606 459300563 7.230000e-10 76.8
33 TraesCS5D01G044100 chr2B 94.737 114 5 1 423 536 47145619 47145507 6.930000e-40 176.0
34 TraesCS5D01G044100 chr2B 84.677 124 9 9 416 536 118401351 118401235 1.530000e-21 115.0
35 TraesCS5D01G044100 chr2B 84.298 121 11 7 416 533 634975306 634975421 1.980000e-20 111.0
36 TraesCS5D01G044100 chr2B 86.364 66 2 5 2399 2462 764537660 764537600 1.560000e-06 65.8
37 TraesCS5D01G044100 chr4A 94.643 112 5 1 423 533 134210436 134210325 8.960000e-39 172.0
38 TraesCS5D01G044100 chr7A 94.545 110 5 1 423 532 62758295 62758187 1.160000e-37 169.0
39 TraesCS5D01G044100 chr7A 97.674 43 1 0 2399 2441 513221091 513221049 2.600000e-09 75.0
40 TraesCS5D01G044100 chr1B 93.750 112 6 1 423 534 286318690 286318800 4.170000e-37 167.0
41 TraesCS5D01G044100 chr1B 83.871 124 11 8 416 536 497715675 497715558 7.120000e-20 110.0
42 TraesCS5D01G044100 chr1B 97.674 43 1 0 2399 2441 493871928 493871886 2.600000e-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 TraesCS5D01G044100 chr5D 43208188 43214906 6718 True 12408.0 12408 100.00000 1 6719 1 chr5D.!!$R1 6718
1 TraesCS5D01G044100 chr5B 40783568 40790985 7417 True 2508.5 6357 92.72250 1 6700 4 chr5B.!!$R5 6699
2 TraesCS5D01G044100 chr5A 33002740 33009691 6951 True 2341.0 5980 93.43775 550 6719 4 chr5A.!!$R2 6169

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
360 368 0.387878 GGAGCTCGATCGGCATAGTG 60.388 60.000 24.07 6.28 0.00 2.74 F
889 900 1.069090 TCGGTGGCAAGATATCGGC 59.931 57.895 12.37 12.37 0.00 5.54 F
1678 1844 0.104304 AGCGTGTCTCTTTGTCGGTT 59.896 50.000 0.00 0.00 0.00 4.44 F
1679 1845 0.232303 GCGTGTCTCTTTGTCGGTTG 59.768 55.000 0.00 0.00 0.00 3.77 F
1681 1847 0.586802 GTGTCTCTTTGTCGGTTGGC 59.413 55.000 0.00 0.00 0.00 4.52 F
1683 1849 1.134220 TGTCTCTTTGTCGGTTGGCTT 60.134 47.619 0.00 0.00 0.00 4.35 F
1685 1851 1.140052 TCTCTTTGTCGGTTGGCTTCA 59.860 47.619 0.00 0.00 0.00 3.02 F
2187 2745 2.033662 GCATTCGTCAGCGGATCTTAAC 60.034 50.000 0.00 0.00 33.29 2.01 F
3967 4592 1.000739 ACGGTTATCACCCTCGGGA 59.999 57.895 9.43 0.00 40.52 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1629 1795 0.677288 ACCGAACAGAACATGACCGA 59.323 50.000 0.00 0.0 32.08 4.69 R
2432 3029 1.967066 CTACTCCCATTGCTCCGATCT 59.033 52.381 0.00 0.0 0.00 2.75 R
3109 3734 1.460305 ACTCACCACTCCAGGCAGT 60.460 57.895 0.00 0.0 0.00 4.40 R
3450 4075 2.564721 GGCACTGAAGTTGGCACCC 61.565 63.158 0.00 0.0 0.00 4.61 R
3829 4454 1.274703 ATGACCGGGATGCCTCTTGT 61.275 55.000 6.32 0.0 0.00 3.16 R
3894 4519 2.736719 CGTGAGTAGCCATGGTGAAGAG 60.737 54.545 14.67 0.0 0.00 2.85 R
3967 4592 4.155280 GCATACCACAAACTGTCGGTTATT 59.845 41.667 0.00 0.0 37.12 1.40 R
4056 4681 5.300034 CACATACATGGATTGTGCCTGTAAT 59.700 40.000 10.66 0.0 39.48 1.89 R
5786 6419 0.325296 AGCCATAGTGGGAGTTCCGA 60.325 55.000 0.00 0.0 38.19 4.55 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
96 97 7.426410 AGGCATCGATTACCATATTAGTATCG 58.574 38.462 15.00 0.00 0.00 2.92
112 113 2.627515 ATCGTGGGTCATCTGGAATG 57.372 50.000 0.00 0.00 0.00 2.67
180 181 3.811722 TTGCTCAACATCATTGTCGAC 57.188 42.857 9.11 9.11 34.06 4.20
220 222 1.474330 AGCCGGGCAAAGAAATTAGG 58.526 50.000 23.09 0.00 0.00 2.69
317 324 8.829373 ATATATGAGGCAAATATTTTCCCTCC 57.171 34.615 26.73 16.69 41.03 4.30
324 331 6.040247 GGCAAATATTTTCCCTCCGTTTAAG 58.960 40.000 5.63 0.00 0.00 1.85
347 355 3.819564 AACAAAACAAAAGGGGAGCTC 57.180 42.857 4.71 4.71 0.00 4.09
353 361 0.811616 CAAAAGGGGAGCTCGATCGG 60.812 60.000 16.41 7.26 0.00 4.18
360 368 0.387878 GGAGCTCGATCGGCATAGTG 60.388 60.000 24.07 6.28 0.00 2.74
384 392 2.420022 GCGATGGAGTTACACAATTGCT 59.580 45.455 5.05 0.00 0.00 3.91
389 397 6.128282 CGATGGAGTTACACAATTGCTACTTT 60.128 38.462 5.05 0.00 0.00 2.66
423 431 1.423845 CGGATTTGCCTGTACGCAC 59.576 57.895 0.00 0.00 38.83 5.34
590 599 2.778299 ACAAAATCTCAGCCGCTGTTA 58.222 42.857 19.77 9.74 32.61 2.41
613 622 6.458232 AGAGTTGATATACGCTTCAGACTT 57.542 37.500 0.00 0.00 0.00 3.01
715 724 5.047590 TGCTCGACTAAATCTTAACCTGTCA 60.048 40.000 0.00 0.00 0.00 3.58
761 770 4.639310 CGCTAAGTAAGTTAGAGGGAGACA 59.361 45.833 2.12 0.00 40.79 3.41
809 820 3.656559 GCGAGTAACCTTCACCTTGTTA 58.343 45.455 0.00 0.00 0.00 2.41
821 832 9.465199 ACCTTCACCTTGTTACTTTTTAGTTTA 57.535 29.630 0.00 0.00 0.00 2.01
889 900 1.069090 TCGGTGGCAAGATATCGGC 59.931 57.895 12.37 12.37 0.00 5.54
1057 1079 4.345257 TGCTACTCCTTGTGTTTCTTCTCT 59.655 41.667 0.00 0.00 0.00 3.10
1093 1115 3.630013 AGCTGTCGCAAGGGCTCA 61.630 61.111 0.00 0.00 39.10 4.26
1220 1377 3.853330 CGAATGTGCTGTCCGGCG 61.853 66.667 0.00 0.00 34.52 6.46
1256 1413 6.758886 AGTGACTAGCTTGTATCTGCAATTAC 59.241 38.462 0.00 0.00 0.00 1.89
1290 1448 8.779354 TTTAGTTGCCAAAAACATGTTAAACT 57.221 26.923 12.39 15.34 32.21 2.66
1347 1505 3.836146 TCCCATTCATTGCTAATCAGGG 58.164 45.455 0.00 0.00 35.09 4.45
1356 1514 1.207089 TGCTAATCAGGGGAGACGTTG 59.793 52.381 0.00 0.00 0.00 4.10
1459 1620 1.610038 CTTTGCACCATGACTTGCTCA 59.390 47.619 13.07 0.87 39.62 4.26
1523 1689 5.153950 ACTCCCTTCGATCCATAATAAGC 57.846 43.478 0.00 0.00 0.00 3.09
1529 1695 5.289675 CCTTCGATCCATAATAAGCGTCATC 59.710 44.000 0.00 0.00 0.00 2.92
1551 1717 9.409312 TCATCAATTTAATACAAAGTTGCACTG 57.591 29.630 0.00 0.00 0.00 3.66
1584 1750 4.422073 TTATACAACATCCTGGCTCCAG 57.578 45.455 8.93 8.93 43.26 3.86
1610 1776 6.785488 TTATACAACACAACTGCTTCTCTG 57.215 37.500 0.00 0.00 0.00 3.35
1626 1792 4.558226 TCTCTGTATGCTTCCATGTTGT 57.442 40.909 0.00 0.00 32.85 3.32
1627 1793 4.256110 TCTCTGTATGCTTCCATGTTGTG 58.744 43.478 0.00 0.00 32.85 3.33
1628 1794 4.005650 CTCTGTATGCTTCCATGTTGTGT 58.994 43.478 0.00 0.00 32.85 3.72
1629 1795 4.397420 TCTGTATGCTTCCATGTTGTGTT 58.603 39.130 0.00 0.00 32.85 3.32
1630 1796 4.455533 TCTGTATGCTTCCATGTTGTGTTC 59.544 41.667 0.00 0.00 32.85 3.18
1631 1797 2.995466 ATGCTTCCATGTTGTGTTCG 57.005 45.000 0.00 0.00 0.00 3.95
1632 1798 0.950836 TGCTTCCATGTTGTGTTCGG 59.049 50.000 0.00 0.00 0.00 4.30
1633 1799 0.951558 GCTTCCATGTTGTGTTCGGT 59.048 50.000 0.00 0.00 0.00 4.69
1634 1800 1.069227 GCTTCCATGTTGTGTTCGGTC 60.069 52.381 0.00 0.00 0.00 4.79
1635 1801 2.217750 CTTCCATGTTGTGTTCGGTCA 58.782 47.619 0.00 0.00 0.00 4.02
1636 1802 2.559698 TCCATGTTGTGTTCGGTCAT 57.440 45.000 0.00 0.00 0.00 3.06
1637 1803 2.150390 TCCATGTTGTGTTCGGTCATG 58.850 47.619 0.00 0.00 36.60 3.07
1638 1804 1.879380 CCATGTTGTGTTCGGTCATGT 59.121 47.619 0.00 0.00 35.54 3.21
1639 1805 2.293122 CCATGTTGTGTTCGGTCATGTT 59.707 45.455 0.00 0.00 35.54 2.71
1640 1806 3.554524 CATGTTGTGTTCGGTCATGTTC 58.445 45.455 0.00 0.00 33.53 3.18
1676 1842 0.318699 TCAGCGTGTCTCTTTGTCGG 60.319 55.000 0.00 0.00 0.00 4.79
1677 1843 0.597637 CAGCGTGTCTCTTTGTCGGT 60.598 55.000 0.00 0.00 0.00 4.69
1678 1844 0.104304 AGCGTGTCTCTTTGTCGGTT 59.896 50.000 0.00 0.00 0.00 4.44
1679 1845 0.232303 GCGTGTCTCTTTGTCGGTTG 59.768 55.000 0.00 0.00 0.00 3.77
1680 1846 0.859232 CGTGTCTCTTTGTCGGTTGG 59.141 55.000 0.00 0.00 0.00 3.77
1681 1847 0.586802 GTGTCTCTTTGTCGGTTGGC 59.413 55.000 0.00 0.00 0.00 4.52
1683 1849 1.134220 TGTCTCTTTGTCGGTTGGCTT 60.134 47.619 0.00 0.00 0.00 4.35
1684 1850 1.531578 GTCTCTTTGTCGGTTGGCTTC 59.468 52.381 0.00 0.00 0.00 3.86
1685 1851 1.140052 TCTCTTTGTCGGTTGGCTTCA 59.860 47.619 0.00 0.00 0.00 3.02
1720 1896 8.613922 TTAGTTAGGTACTTATTAGGTGGCTT 57.386 34.615 0.00 0.00 41.75 4.35
1846 2035 2.751806 GGAGCTTCCAGTCATTTTGAGG 59.248 50.000 0.00 0.00 36.28 3.86
1966 2155 4.130118 TCACTTTCTGCACCTCTCTTTTC 58.870 43.478 0.00 0.00 0.00 2.29
1968 2157 4.578105 CACTTTCTGCACCTCTCTTTTCTT 59.422 41.667 0.00 0.00 0.00 2.52
2007 2196 7.663827 TCTCAAACAAGAATCAAATGCAGAAT 58.336 30.769 0.00 0.00 0.00 2.40
2187 2745 2.033662 GCATTCGTCAGCGGATCTTAAC 60.034 50.000 0.00 0.00 33.29 2.01
2216 2774 5.940470 CAGGTTAACTAAGGATGACAAGCTT 59.060 40.000 5.42 0.00 0.00 3.74
2321 2883 6.607019 TCTCCTCTATTCTTCCTCCTTAGTC 58.393 44.000 0.00 0.00 0.00 2.59
2331 2893 2.655407 TCCTCCTTAGTCTCCACTCCTT 59.345 50.000 0.00 0.00 33.62 3.36
2374 2940 7.715249 AGAACACTACTTGCAGAAACTTAATCA 59.285 33.333 0.00 0.00 0.00 2.57
2392 2958 4.708726 ATCAAGCTATTTGCAGAACACC 57.291 40.909 0.00 0.00 45.94 4.16
2432 3029 9.107177 TGAACTAAAACCACGACACTTATTTTA 57.893 29.630 0.00 0.00 0.00 1.52
2548 3145 8.531982 TCCCGTCATATGGAATCTTATAAGAAG 58.468 37.037 18.79 0.00 38.77 2.85
2777 3383 5.515106 TCTCAAAAGTTCCTTTCCTCCAAA 58.485 37.500 0.00 0.00 31.99 3.28
2822 3431 9.575868 TTATACCATTTCTCAAGTTGGTTTACA 57.424 29.630 2.34 0.00 42.35 2.41
2896 3509 5.395657 CCACAGCTACAGATATGGTTTCTCA 60.396 44.000 0.00 0.00 0.00 3.27
3292 3917 2.983433 CATCGACTCAGGTGGATGC 58.017 57.895 7.86 0.00 46.11 3.91
3829 4454 2.280797 GAACGCTGGGTGCTGTGA 60.281 61.111 0.00 0.00 40.11 3.58
3967 4592 1.000739 ACGGTTATCACCCTCGGGA 59.999 57.895 9.43 0.00 40.52 5.14
4056 4681 5.508567 TCTCACAATGGGATGCTTAATTGA 58.491 37.500 12.27 0.00 34.75 2.57
4095 4720 3.265737 TGTATGTGGCAGATAAAGGTGGT 59.734 43.478 5.85 0.00 0.00 4.16
4496 5123 5.748872 CTGCAAGTACGTAGAGAAAGTTC 57.251 43.478 0.00 0.00 0.00 3.01
4497 5124 5.449107 TGCAAGTACGTAGAGAAAGTTCT 57.551 39.130 0.00 0.00 41.00 3.01
4498 5125 5.839621 TGCAAGTACGTAGAGAAAGTTCTT 58.160 37.500 0.00 0.00 37.73 2.52
4499 5126 6.973843 TGCAAGTACGTAGAGAAAGTTCTTA 58.026 36.000 0.00 0.00 37.73 2.10
4500 5127 7.082602 TGCAAGTACGTAGAGAAAGTTCTTAG 58.917 38.462 0.00 0.00 37.73 2.18
4501 5128 7.040892 TGCAAGTACGTAGAGAAAGTTCTTAGA 60.041 37.037 0.00 0.00 37.73 2.10
4502 5129 7.969508 GCAAGTACGTAGAGAAAGTTCTTAGAT 59.030 37.037 0.00 0.00 37.73 1.98
4509 5136 9.227490 CGTAGAGAAAGTTCTTAGATGTACATG 57.773 37.037 14.43 0.00 37.73 3.21
4540 5167 2.751259 TCTACTTTCTGGACGTACGCAT 59.249 45.455 16.72 0.00 0.00 4.73
4660 5287 1.264288 GAACAACCAGCGGAAGTGAAG 59.736 52.381 1.50 0.00 0.00 3.02
4664 5291 0.180406 ACCAGCGGAAGTGAAGTTGT 59.820 50.000 1.50 0.00 0.00 3.32
4715 5342 2.315155 GGGGGCCTAGTCCTATCTATCA 59.685 54.545 0.84 0.00 0.00 2.15
4761 5388 4.279671 GCACCTCTAGCTAGCAATCTCTTA 59.720 45.833 18.83 0.00 0.00 2.10
4950 5581 2.128853 TTAGCCGCTGCAGCACAAAC 62.129 55.000 36.03 20.08 42.21 2.93
5577 6208 1.202818 AGGAGGGTGCAGAGTTTCAAC 60.203 52.381 0.00 0.00 0.00 3.18
5592 6223 0.878523 TCAACGTGACTTTCAGGGCG 60.879 55.000 0.00 0.00 36.65 6.13
5736 6367 0.398696 AAGTGGGGACGTTACATGCA 59.601 50.000 0.00 0.00 0.00 3.96
5741 6372 0.719465 GGGACGTTACATGCAGTTCG 59.281 55.000 0.00 2.86 34.31 3.95
5806 6439 1.063492 TCGGAACTCCCACTATGGCTA 60.063 52.381 0.00 0.00 35.79 3.93
5834 6471 4.989279 TTAGTGTCCGTTCCTATGGTAC 57.011 45.455 0.00 0.00 0.00 3.34
5853 6490 5.407084 TGGTACGTGAACATTTATGTCAGTG 59.593 40.000 0.00 0.00 40.80 3.66
5854 6491 5.407387 GGTACGTGAACATTTATGTCAGTGT 59.593 40.000 0.00 0.00 40.80 3.55
5889 6529 4.193865 ACATAAGTTTGTATGGTACCGGC 58.806 43.478 7.57 0.12 36.04 6.13
5890 6530 1.729284 AAGTTTGTATGGTACCGGCG 58.271 50.000 7.57 0.00 0.00 6.46
5891 6531 0.108041 AGTTTGTATGGTACCGGCGG 60.108 55.000 27.06 27.06 0.00 6.13
5917 6557 1.065709 GGAAATCCACCCGCAACTAGA 60.066 52.381 0.00 0.00 35.64 2.43
5958 6598 2.945668 GCTAGCAATGGTAACTCCCTTG 59.054 50.000 10.63 0.00 42.25 3.61
5979 6619 9.231297 CCCTTGATGTTAAAATTCTTCAGACTA 57.769 33.333 0.00 0.00 0.00 2.59
6066 6706 2.125912 CGCACAGGGAAGAGACGG 60.126 66.667 0.00 0.00 0.00 4.79
6071 6711 0.250513 ACAGGGAAGAGACGGAATGC 59.749 55.000 0.00 0.00 0.00 3.56
6142 6785 2.993545 TGCGAGGAACAAAACATTTCG 58.006 42.857 0.00 0.00 0.00 3.46
6162 7047 2.989422 CTTTACCGACCCAAAAGCAG 57.011 50.000 0.00 0.00 0.00 4.24
6165 7050 0.978151 TACCGACCCAAAAGCAGCTA 59.022 50.000 0.00 0.00 0.00 3.32
6218 7103 5.645929 TCAAGTACACACAAGACACAACAAT 59.354 36.000 0.00 0.00 0.00 2.71
6235 7120 2.259917 CAATGGAGGCCCCTTTTCTTT 58.740 47.619 0.00 0.00 35.38 2.52
6260 7145 5.421056 TCCTCACGTACAGATAATTTGAGGT 59.579 40.000 13.90 0.00 45.94 3.85
6266 7151 7.064609 CACGTACAGATAATTTGAGGTGTCAAT 59.935 37.037 0.00 0.00 42.41 2.57
6290 7175 1.081376 CGAGACGCTGTCGACCTTT 60.081 57.895 14.12 0.00 39.92 3.11
6333 7218 0.320374 TGGAAGGCACGTAGTCCTTG 59.680 55.000 17.31 0.00 44.02 3.61
6366 7254 6.206634 GGATCTTGTTTGATGGTGTACAGAAA 59.793 38.462 0.00 0.00 0.00 2.52
6380 7268 4.399934 TGTACAGAAACCAAAAACCCAGAC 59.600 41.667 0.00 0.00 0.00 3.51
6397 7287 3.055530 CCAGACTCAAGGCATACAGAAGT 60.056 47.826 0.00 0.00 0.00 3.01
6405 7295 6.003326 TCAAGGCATACAGAAGTCAAAATGA 58.997 36.000 0.00 0.00 0.00 2.57
6425 7315 9.768662 AAAATGAAAATCTGATGCTTGTACTTT 57.231 25.926 0.00 0.00 0.00 2.66
6427 7317 7.275888 TGAAAATCTGATGCTTGTACTTTGT 57.724 32.000 0.00 0.00 0.00 2.83
6468 7358 5.595133 AGCCTAAACTCTATGACTGTAGTCC 59.405 44.000 9.37 0.00 44.15 3.85
6480 7370 3.522553 ACTGTAGTCCTTTTATCGCAGC 58.477 45.455 0.00 0.00 0.00 5.25
6509 7399 5.005299 GGTTGTCGAAACAAATGAAACAAGG 59.995 40.000 10.99 0.00 46.56 3.61
6578 7468 4.202274 GGGAAGAGAGGTCATTTAGGCTAC 60.202 50.000 0.00 0.00 0.00 3.58
6608 8136 3.319972 CAGCCTGGGAATTTCCACATATG 59.680 47.826 17.08 0.00 38.64 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 97 1.673168 GCTCATTCCAGATGACCCAC 58.327 55.000 0.00 0.00 0.00 4.61
130 131 0.386478 GTTGCGCTCTTTTGGCTGAG 60.386 55.000 9.73 0.00 0.00 3.35
144 145 1.858719 CAAAATTTGCGGGGTTGCG 59.141 52.632 0.00 0.00 37.81 4.85
154 155 6.144241 TCGACAATGATGTTGAGCAAAATTTG 59.856 34.615 0.57 0.57 43.57 2.32
180 181 1.533625 TGATCCAAAGGTTTGCCTCG 58.466 50.000 0.00 0.00 46.33 4.63
306 313 7.820578 TGTTTTCTTAAACGGAGGGAAAATA 57.179 32.000 0.00 0.00 45.29 1.40
307 314 6.718522 TGTTTTCTTAAACGGAGGGAAAAT 57.281 33.333 0.00 0.00 45.29 1.82
310 317 6.071503 TGTTTTGTTTTCTTAAACGGAGGGAA 60.072 34.615 0.00 0.00 45.29 3.97
312 319 5.652518 TGTTTTGTTTTCTTAAACGGAGGG 58.347 37.500 0.00 0.00 45.29 4.30
317 324 7.117956 TCCCCTTTTGTTTTGTTTTCTTAAACG 59.882 33.333 0.00 0.00 45.29 3.60
324 331 4.513442 AGCTCCCCTTTTGTTTTGTTTTC 58.487 39.130 0.00 0.00 0.00 2.29
347 355 2.357517 GCCCCACTATGCCGATCG 60.358 66.667 8.51 8.51 0.00 3.69
353 361 1.302033 CTCCATCGCCCCACTATGC 60.302 63.158 0.00 0.00 0.00 3.14
360 368 0.035820 TTGTGTAACTCCATCGCCCC 60.036 55.000 0.00 0.00 38.04 5.80
384 392 3.674138 CGCAGCGGAAGGTTACTAAAGTA 60.674 47.826 7.00 0.00 41.81 2.24
423 431 1.290203 AGCGGCATGACAATTACTCG 58.710 50.000 0.00 0.00 0.00 4.18
546 554 7.652105 TGTAAAGTGAAAAGACTGTAGCTACTG 59.348 37.037 24.46 24.46 0.00 2.74
590 599 6.095580 TCAAGTCTGAAGCGTATATCAACTCT 59.904 38.462 0.00 0.00 0.00 3.24
642 651 6.937392 AGTAGAGTCCCAAAATAAGTGTCTC 58.063 40.000 0.00 0.00 0.00 3.36
715 724 4.923281 GCTTGTAGCCGTTGAATGAAAAAT 59.077 37.500 0.00 0.00 34.48 1.82
761 770 4.996122 GCTTGTCTGATATGCTGAAGCTAT 59.004 41.667 3.61 0.00 42.66 2.97
821 832 7.336396 GGGATTAACCTGTAGTACAAATGAGT 58.664 38.462 4.21 0.00 38.98 3.41
1093 1115 3.072211 GCTAGCTTACCCGTCTTTGTTT 58.928 45.455 7.70 0.00 0.00 2.83
1220 1377 4.116747 AGCTAGTCACTAACATCAGTGC 57.883 45.455 0.00 0.00 44.62 4.40
1347 1505 8.365938 GTTTACGTATTAACTAACAACGTCTCC 58.634 37.037 12.51 2.85 44.79 3.71
1523 1689 8.365210 GTGCAACTTTGTATTAAATTGATGACG 58.635 33.333 0.00 0.00 0.00 4.35
1551 1717 8.598924 CAGGATGTTGTATAATATCGCTGATTC 58.401 37.037 15.35 0.00 36.27 2.52
1584 1750 8.383619 CAGAGAAGCAGTTGTGTTGTATAATAC 58.616 37.037 0.00 0.00 0.00 1.89
1610 1776 3.426159 CCGAACACAACATGGAAGCATAC 60.426 47.826 0.00 0.00 0.00 2.39
1626 1792 2.131972 CGAACAGAACATGACCGAACA 58.868 47.619 0.00 0.00 32.08 3.18
1627 1793 1.459592 CCGAACAGAACATGACCGAAC 59.540 52.381 0.00 0.00 32.08 3.95
1628 1794 1.069513 ACCGAACAGAACATGACCGAA 59.930 47.619 0.00 0.00 32.08 4.30
1629 1795 0.677288 ACCGAACAGAACATGACCGA 59.323 50.000 0.00 0.00 32.08 4.69
1630 1796 1.194547 CAACCGAACAGAACATGACCG 59.805 52.381 0.00 0.00 0.00 4.79
1631 1797 1.535462 CCAACCGAACAGAACATGACC 59.465 52.381 0.00 0.00 0.00 4.02
1632 1798 1.069227 GCCAACCGAACAGAACATGAC 60.069 52.381 0.00 0.00 0.00 3.06
1633 1799 1.202758 AGCCAACCGAACAGAACATGA 60.203 47.619 0.00 0.00 0.00 3.07
1634 1800 1.238439 AGCCAACCGAACAGAACATG 58.762 50.000 0.00 0.00 0.00 3.21
1635 1801 1.880027 GAAGCCAACCGAACAGAACAT 59.120 47.619 0.00 0.00 0.00 2.71
1636 1802 1.305201 GAAGCCAACCGAACAGAACA 58.695 50.000 0.00 0.00 0.00 3.18
1637 1803 1.305201 TGAAGCCAACCGAACAGAAC 58.695 50.000 0.00 0.00 0.00 3.01
1638 1804 2.151202 GATGAAGCCAACCGAACAGAA 58.849 47.619 0.00 0.00 0.00 3.02
1639 1805 1.071542 TGATGAAGCCAACCGAACAGA 59.928 47.619 0.00 0.00 0.00 3.41
1640 1806 1.466167 CTGATGAAGCCAACCGAACAG 59.534 52.381 0.00 0.00 0.00 3.16
1677 1843 7.606456 CCTAACTAAAGTAGATGTTGAAGCCAA 59.394 37.037 0.00 0.00 0.00 4.52
1678 1844 7.103641 CCTAACTAAAGTAGATGTTGAAGCCA 58.896 38.462 0.00 0.00 0.00 4.75
1679 1845 7.104290 ACCTAACTAAAGTAGATGTTGAAGCC 58.896 38.462 0.00 0.00 0.00 4.35
1680 1846 9.085250 GTACCTAACTAAAGTAGATGTTGAAGC 57.915 37.037 0.00 0.00 0.00 3.86
1720 1896 5.299279 GTGAAAATCTCAACAAGACCAAGGA 59.701 40.000 0.00 0.00 36.65 3.36
1846 2035 6.202762 CCCTGCAACTTTATTTTTGGAGAAAC 59.797 38.462 4.60 0.00 42.15 2.78
1968 2157 8.839310 TCTTGTTTGAGATTTTTGGTTCAAAA 57.161 26.923 2.14 2.14 40.14 2.44
2187 2745 5.046591 TGTCATCCTTAGTTAACCTGGACAG 60.047 44.000 12.20 9.24 0.00 3.51
2216 2774 3.780294 ACCACCTCAGCTACCATTTATCA 59.220 43.478 0.00 0.00 0.00 2.15
2277 2839 5.438761 AGAAAATGAAGGGACAAAAGACG 57.561 39.130 0.00 0.00 0.00 4.18
2278 2840 5.536538 AGGAGAAAATGAAGGGACAAAAGAC 59.463 40.000 0.00 0.00 0.00 3.01
2352 2915 6.798959 GCTTGATTAAGTTTCTGCAAGTAGTG 59.201 38.462 0.00 0.00 36.16 2.74
2354 2917 7.138692 AGCTTGATTAAGTTTCTGCAAGTAG 57.861 36.000 0.00 0.00 36.16 2.57
2356 2919 7.693969 ATAGCTTGATTAAGTTTCTGCAAGT 57.306 32.000 0.00 0.00 36.16 3.16
2357 2920 8.857216 CAAATAGCTTGATTAAGTTTCTGCAAG 58.143 33.333 0.00 0.00 37.17 4.01
2359 2922 6.808212 GCAAATAGCTTGATTAAGTTTCTGCA 59.192 34.615 0.00 0.00 41.15 4.41
2360 2923 6.808212 TGCAAATAGCTTGATTAAGTTTCTGC 59.192 34.615 0.00 4.08 45.94 4.26
2361 2924 8.239314 TCTGCAAATAGCTTGATTAAGTTTCTG 58.761 33.333 0.00 0.00 45.94 3.02
2374 2940 3.490348 AGTGGTGTTCTGCAAATAGCTT 58.510 40.909 0.00 0.00 45.94 3.74
2392 2958 7.978975 TGGTTTTAGTTCAAATTTGAAGGAGTG 59.021 33.333 29.34 0.00 46.80 3.51
2432 3029 1.967066 CTACTCCCATTGCTCCGATCT 59.033 52.381 0.00 0.00 0.00 2.75
2548 3145 6.091169 CCAGTTAATGATGTCCATGTTTTTGC 59.909 38.462 0.00 0.00 35.24 3.68
2822 3431 5.360591 GCTTCATAGCCAGTACATACTTGT 58.639 41.667 0.00 0.00 41.74 3.16
2896 3509 3.057033 CAGTAAGCATTGCAGAAAAGCCT 60.057 43.478 11.91 0.00 30.97 4.58
3035 3652 2.293170 TGGTCAACAAGCATTTGTCGA 58.707 42.857 0.00 0.00 46.54 4.20
3109 3734 1.460305 ACTCACCACTCCAGGCAGT 60.460 57.895 0.00 0.00 0.00 4.40
3450 4075 2.564721 GGCACTGAAGTTGGCACCC 61.565 63.158 0.00 0.00 0.00 4.61
3829 4454 1.274703 ATGACCGGGATGCCTCTTGT 61.275 55.000 6.32 0.00 0.00 3.16
3894 4519 2.736719 CGTGAGTAGCCATGGTGAAGAG 60.737 54.545 14.67 0.00 0.00 2.85
3967 4592 4.155280 GCATACCACAAACTGTCGGTTATT 59.845 41.667 0.00 0.00 37.12 1.40
4056 4681 5.300034 CACATACATGGATTGTGCCTGTAAT 59.700 40.000 10.66 0.00 39.48 1.89
4488 5115 9.307121 CGATTCATGTACATCTAAGAACTTTCT 57.693 33.333 5.07 0.00 39.74 2.52
4489 5116 9.302345 TCGATTCATGTACATCTAAGAACTTTC 57.698 33.333 5.07 1.38 0.00 2.62
4490 5117 9.823647 ATCGATTCATGTACATCTAAGAACTTT 57.176 29.630 5.07 0.00 0.00 2.66
4491 5118 9.823647 AATCGATTCATGTACATCTAAGAACTT 57.176 29.630 5.07 0.00 0.00 2.66
4492 5119 9.823647 AAATCGATTCATGTACATCTAAGAACT 57.176 29.630 11.83 0.00 0.00 3.01
4499 5126 9.823647 AAGTAGAAAATCGATTCATGTACATCT 57.176 29.630 22.25 14.11 0.00 2.90
4502 5129 9.653287 AGAAAGTAGAAAATCGATTCATGTACA 57.347 29.630 22.25 0.00 0.00 2.90
4509 5136 6.310711 ACGTCCAGAAAGTAGAAAATCGATTC 59.689 38.462 11.83 0.22 0.00 2.52
4660 5287 1.892474 TGCTATTCTTGGGGCAACAAC 59.108 47.619 0.00 0.00 39.74 3.32
4664 5291 0.332632 AGCTGCTATTCTTGGGGCAA 59.667 50.000 0.00 0.00 34.21 4.52
4715 5342 1.992557 TGCTTACCTTGAGAACCCCAT 59.007 47.619 0.00 0.00 0.00 4.00
4950 5581 4.452455 CACCTAGACTTTTGTAAGCACCAG 59.548 45.833 0.00 0.00 34.60 4.00
5014 5645 5.761205 AGAGCGACTATCCCAGATATATGT 58.239 41.667 0.00 0.00 0.00 2.29
5135 5766 7.973388 TGTGCTTTGCATAAATAAATACTCCAC 59.027 33.333 0.00 0.00 41.91 4.02
5137 5768 8.925161 TTGTGCTTTGCATAAATAAATACTCC 57.075 30.769 0.00 0.00 41.91 3.85
5507 6138 1.672356 ACAGCCATCTTGACGCCAC 60.672 57.895 0.00 0.00 0.00 5.01
5577 6208 2.027625 GGTCGCCCTGAAAGTCACG 61.028 63.158 0.00 0.00 0.00 4.35
5592 6223 3.108288 GCCCTGGATCCTTCGGGTC 62.108 68.421 25.51 17.78 38.97 4.46
5736 6367 7.650903 AGTCGTCTTTTATTTTACAGTCGAACT 59.349 33.333 0.00 0.00 30.55 3.01
5741 6372 7.647907 TCCAGTCGTCTTTTATTTTACAGTC 57.352 36.000 0.00 0.00 0.00 3.51
5785 6418 0.539986 GCCATAGTGGGAGTTCCGAA 59.460 55.000 0.00 0.00 38.19 4.30
5786 6419 0.325296 AGCCATAGTGGGAGTTCCGA 60.325 55.000 0.00 0.00 38.19 4.55
5787 6420 1.410004 TAGCCATAGTGGGAGTTCCG 58.590 55.000 0.00 0.00 38.19 4.30
5788 6421 2.039084 CCATAGCCATAGTGGGAGTTCC 59.961 54.545 0.00 0.00 38.19 3.62
5789 6422 2.706190 ACCATAGCCATAGTGGGAGTTC 59.294 50.000 0.00 0.00 38.19 3.01
5806 6439 2.838202 AGGAACGGACACTAATCACCAT 59.162 45.455 0.00 0.00 0.00 3.55
5834 6471 7.738345 TCAATACACTGACATAAATGTTCACG 58.262 34.615 0.00 0.00 41.95 4.35
5889 6529 2.218603 CGGGTGGATTTCCTTATTCCG 58.781 52.381 0.00 0.00 36.82 4.30
5890 6530 1.954382 GCGGGTGGATTTCCTTATTCC 59.046 52.381 0.00 0.00 36.82 3.01
5891 6531 2.650322 TGCGGGTGGATTTCCTTATTC 58.350 47.619 0.00 0.00 36.82 1.75
5917 6557 2.288640 GCAGCAAGGCAGAAAATCTTGT 60.289 45.455 0.00 0.00 39.80 3.16
5979 6619 2.161855 TGCGATGCTTTCCATTCACTT 58.838 42.857 0.00 0.00 33.29 3.16
6034 6674 3.006430 CCTGTGCGGGGTTTCTTTTAAAT 59.994 43.478 0.00 0.00 0.00 1.40
6035 6675 2.362717 CCTGTGCGGGGTTTCTTTTAAA 59.637 45.455 0.00 0.00 0.00 1.52
6066 6706 7.435488 TCGACTTATAAAACTAGCTCTGCATTC 59.565 37.037 0.00 0.00 0.00 2.67
6071 6711 9.601971 GTCTATCGACTTATAAAACTAGCTCTG 57.398 37.037 0.00 0.00 37.19 3.35
6142 6785 3.786809 GCTTTTGGGTCGGTAAAGC 57.213 52.632 0.00 0.00 44.57 3.51
6162 7047 2.388310 ACGAGAAAAAGGCCTCTAGC 57.612 50.000 5.23 0.00 42.60 3.42
6165 7050 3.493767 AGAAACGAGAAAAAGGCCTCT 57.506 42.857 5.23 0.00 0.00 3.69
6218 7103 1.482365 GGAAAAGAAAAGGGGCCTCCA 60.482 52.381 0.00 0.00 38.24 3.86
6260 7145 1.749063 AGCGTCTCGATGGTATTGACA 59.251 47.619 0.00 0.00 0.00 3.58
6299 7184 2.878406 CCTTCCAGTCGCAAAGAAAAGA 59.122 45.455 0.00 0.00 0.00 2.52
6327 7212 4.646572 ACAAGATCCAAGAGAACAAGGAC 58.353 43.478 0.00 0.00 32.04 3.85
6333 7218 5.474876 ACCATCAAACAAGATCCAAGAGAAC 59.525 40.000 0.00 0.00 0.00 3.01
6366 7254 2.666317 CCTTGAGTCTGGGTTTTTGGT 58.334 47.619 0.00 0.00 0.00 3.67
6380 7268 5.947228 TTTTGACTTCTGTATGCCTTGAG 57.053 39.130 0.00 0.00 0.00 3.02
6397 7287 8.579006 AGTACAAGCATCAGATTTTCATTTTGA 58.421 29.630 0.00 0.00 0.00 2.69
6405 7295 8.292448 CACTACAAAGTACAAGCATCAGATTTT 58.708 33.333 0.00 0.00 33.48 1.82
6468 7358 3.181397 CAACCCATTGCTGCGATAAAAG 58.819 45.455 1.23 0.00 0.00 2.27
6475 7365 1.851021 TTCGACAACCCATTGCTGCG 61.851 55.000 0.00 0.00 39.66 5.18
6480 7370 4.615949 TCATTTGTTTCGACAACCCATTG 58.384 39.130 7.64 0.00 41.98 2.82
6578 7468 2.348411 ATTCCCAGGCTGTTAATCCG 57.652 50.000 14.43 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.