Multiple sequence alignment - TraesCS5D01G386600

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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 TraesCS5D01G386600 chr5D 100.000 2961 0 0 1 2961 456572435 456569475 0.000000e+00 5469.0
1 TraesCS5D01G386600 chr5A 91.628 1278 91 9 686 1954 574320026 574318756 0.000000e+00 1753.0
2 TraesCS5D01G386600 chr5A 82.635 668 91 15 2318 2961 574302422 574301756 4.280000e-158 568.0
3 TraesCS5D01G386600 chr5A 84.694 196 20 7 2131 2321 574303258 574303068 1.400000e-43 187.0
4 TraesCS5D01G386600 chr5B 91.491 1281 84 11 594 1857 558261948 558260676 0.000000e+00 1738.0
5 TraesCS5D01G386600 chr5B 87.290 417 39 10 2139 2547 558259013 558258603 5.780000e-127 464.0
6 TraesCS5D01G386600 chr5B 85.000 380 49 5 2585 2961 558258599 558258225 2.150000e-101 379.0
7 TraesCS5D01G386600 chr5B 92.857 42 3 0 1871 1912 558260638 558260597 8.860000e-06 62.1
8 TraesCS5D01G386600 chr2D 97.747 577 13 0 1 577 609656831 609657407 0.000000e+00 994.0
9 TraesCS5D01G386600 chr2D 89.273 578 61 1 1 577 605415593 605415016 0.000000e+00 723.0
10 TraesCS5D01G386600 chr6D 97.574 577 14 0 1 577 113909976 113910552 0.000000e+00 989.0
11 TraesCS5D01G386600 chr6D 96.791 592 19 0 1 592 283807363 283806772 0.000000e+00 989.0
12 TraesCS5D01G386600 chr6D 78.061 196 37 4 595 786 141132817 141132624 5.180000e-23 119.0
13 TraesCS5D01G386600 chr1B 96.230 557 19 2 1 557 629323242 629322688 0.000000e+00 911.0
14 TraesCS5D01G386600 chr2A 94.297 491 27 1 87 576 419186716 419186226 0.000000e+00 750.0
15 TraesCS5D01G386600 chr4B 89.446 578 56 5 1 577 626790209 626790782 0.000000e+00 725.0
16 TraesCS5D01G386600 chr7B 89.520 563 56 3 7 568 629778150 629778710 0.000000e+00 710.0
17 TraesCS5D01G386600 chr2B 88.519 540 60 2 39 577 735823121 735822583 0.000000e+00 652.0
18 TraesCS5D01G386600 chr6A 79.592 196 31 7 595 786 185316340 185316150 6.660000e-27 132.0
19 TraesCS5D01G386600 chr7A 92.683 41 3 0 613 653 719683773 719683813 3.190000e-05 60.2


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 TraesCS5D01G386600 chr5D 456569475 456572435 2960 True 5469.000 5469 100.0000 1 2961 1 chr5D.!!$R1 2960
1 TraesCS5D01G386600 chr5A 574318756 574320026 1270 True 1753.000 1753 91.6280 686 1954 1 chr5A.!!$R1 1268
2 TraesCS5D01G386600 chr5A 574301756 574303258 1502 True 377.500 568 83.6645 2131 2961 2 chr5A.!!$R2 830
3 TraesCS5D01G386600 chr5B 558258225 558261948 3723 True 660.775 1738 89.1595 594 2961 4 chr5B.!!$R1 2367
4 TraesCS5D01G386600 chr2D 609656831 609657407 576 False 994.000 994 97.7470 1 577 1 chr2D.!!$F1 576
5 TraesCS5D01G386600 chr2D 605415016 605415593 577 True 723.000 723 89.2730 1 577 1 chr2D.!!$R1 576
6 TraesCS5D01G386600 chr6D 113909976 113910552 576 False 989.000 989 97.5740 1 577 1 chr6D.!!$F1 576
7 TraesCS5D01G386600 chr6D 283806772 283807363 591 True 989.000 989 96.7910 1 592 1 chr6D.!!$R2 591
8 TraesCS5D01G386600 chr1B 629322688 629323242 554 True 911.000 911 96.2300 1 557 1 chr1B.!!$R1 556
9 TraesCS5D01G386600 chr4B 626790209 626790782 573 False 725.000 725 89.4460 1 577 1 chr4B.!!$F1 576
10 TraesCS5D01G386600 chr7B 629778150 629778710 560 False 710.000 710 89.5200 7 568 1 chr7B.!!$F1 561
11 TraesCS5D01G386600 chr2B 735822583 735823121 538 True 652.000 652 88.5190 39 577 1 chr2B.!!$R1 538

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
404 407 0.884514 GAGGCTTGCAACTTTCTCCC 59.115 55.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2125 2582 0.32336 GCAGAAACCCATACAGCCCA 60.323 55.0 0.0 0.0 0.0 5.36 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
186 188 4.429212 TGTGGCGACGACGATGGG 62.429 66.667 12.29 0.00 42.66 4.00
404 407 0.884514 GAGGCTTGCAACTTTCTCCC 59.115 55.000 0.00 0.00 0.00 4.30
430 433 1.000955 ACTCGTCAGCAAAATCGGAGT 59.999 47.619 0.00 0.00 0.00 3.85
671 675 9.770503 GAAAATATATACTCTGCAATGCATCTG 57.229 33.333 8.91 4.55 38.13 2.90
684 691 6.647481 TGCAATGCATCTGATATTTATTTGGC 59.353 34.615 2.72 0.00 31.71 4.52
705 712 7.820044 TGGCATTAAAAACGGTGATATTTTC 57.180 32.000 0.00 0.00 0.00 2.29
707 714 7.757624 TGGCATTAAAAACGGTGATATTTTCTC 59.242 33.333 0.00 0.00 0.00 2.87
708 715 7.757624 GGCATTAAAAACGGTGATATTTTCTCA 59.242 33.333 0.00 0.00 0.00 3.27
709 716 9.134734 GCATTAAAAACGGTGATATTTTCTCAA 57.865 29.630 0.00 0.00 0.00 3.02
720 728 9.346725 GGTGATATTTTCTCAACAAACTTGATC 57.653 33.333 0.00 0.00 30.48 2.92
721 729 9.897744 GTGATATTTTCTCAACAAACTTGATCA 57.102 29.630 0.00 0.00 0.00 2.92
754 763 6.749923 AATATTTGACTTCAGTGAAGGCTC 57.250 37.500 33.32 23.21 46.92 4.70
762 771 6.070824 TGACTTCAGTGAAGGCTCATATACAA 60.071 38.462 33.32 12.13 46.92 2.41
764 773 7.168219 ACTTCAGTGAAGGCTCATATACAAAA 58.832 34.615 31.20 0.00 43.25 2.44
813 822 0.935898 GAAGCACGCATCTCATCCAG 59.064 55.000 0.00 0.00 0.00 3.86
845 855 1.068741 CCTACCATTCTAGCCCGTCAC 59.931 57.143 0.00 0.00 0.00 3.67
949 963 1.220206 CTTCCATCACCTGCTCGCT 59.780 57.895 0.00 0.00 0.00 4.93
1046 1060 3.489059 CGCCACATCAGTTCAAACAAGTT 60.489 43.478 0.00 0.00 0.00 2.66
1143 1165 1.682684 GCCTCCTCGTCTTCCTCCA 60.683 63.158 0.00 0.00 0.00 3.86
1146 1168 0.677098 CTCCTCGTCTTCCTCCACGA 60.677 60.000 0.00 0.00 42.61 4.35
1183 1205 3.359523 CGTCCGGTGTCCACGAGA 61.360 66.667 6.79 0.00 35.49 4.04
1186 1208 4.065281 CCGGTGTCCACGAGACCC 62.065 72.222 0.00 7.50 42.14 4.46
1188 1210 4.736896 GGTGTCCACGAGACCCGC 62.737 72.222 7.67 0.12 45.68 6.13
1297 1319 0.464452 GGAAGTGGCTGCCGTACTAT 59.536 55.000 14.98 4.20 0.00 2.12
1353 1375 2.496341 GTACCCGAAGTACCCGGC 59.504 66.667 16.33 2.68 44.85 6.13
1627 1649 1.736586 CGAAGGGACGGAGATGGAG 59.263 63.158 0.00 0.00 0.00 3.86
1630 1652 0.252742 AAGGGACGGAGATGGAGGTT 60.253 55.000 0.00 0.00 0.00 3.50
1760 1784 4.125703 CACTGGCTCAAGACTGGATTATC 58.874 47.826 0.00 0.00 0.00 1.75
1763 1787 3.389329 TGGCTCAAGACTGGATTATCCTC 59.611 47.826 12.91 2.65 37.46 3.71
1775 1799 4.835615 TGGATTATCCTCCTAGTTCTCTGC 59.164 45.833 12.91 0.00 37.46 4.26
1824 1849 1.806542 CCGCAGTCAAGCTTACACAAT 59.193 47.619 0.00 0.00 0.00 2.71
1925 2238 6.432936 TCTGTAAGACTGTAACACGTAGTTG 58.567 40.000 11.90 1.25 36.63 3.16
1930 2243 6.238610 AGACTGTAACACGTAGTTGTAGAG 57.761 41.667 11.90 5.45 41.61 2.43
1978 2291 0.672342 TCTCGGCCGACCTATTTAGC 59.328 55.000 27.28 0.00 0.00 3.09
1979 2292 0.387929 CTCGGCCGACCTATTTAGCA 59.612 55.000 27.28 0.00 0.00 3.49
1981 2294 1.000506 TCGGCCGACCTATTTAGCATC 59.999 52.381 27.28 0.00 0.00 3.91
1982 2295 1.809684 GGCCGACCTATTTAGCATCC 58.190 55.000 0.00 0.00 0.00 3.51
1983 2296 1.610886 GGCCGACCTATTTAGCATCCC 60.611 57.143 0.00 0.00 0.00 3.85
1984 2297 1.348036 GCCGACCTATTTAGCATCCCT 59.652 52.381 0.00 0.00 0.00 4.20
1985 2298 2.872038 GCCGACCTATTTAGCATCCCTG 60.872 54.545 0.00 0.00 0.00 4.45
1986 2299 2.632996 CCGACCTATTTAGCATCCCTGA 59.367 50.000 0.00 0.00 0.00 3.86
1989 2446 4.692625 CGACCTATTTAGCATCCCTGATTG 59.307 45.833 0.00 0.00 0.00 2.67
1997 2454 4.524802 AGCATCCCTGATTGGAACATTA 57.475 40.909 0.00 0.00 39.30 1.90
2001 2458 4.085357 TCCCTGATTGGAACATTATCGG 57.915 45.455 0.00 0.00 39.30 4.18
2002 2459 2.554032 CCCTGATTGGAACATTATCGGC 59.446 50.000 0.00 0.00 39.30 5.54
2020 2477 2.365820 GCAATTGCCGTGTTGTTTTG 57.634 45.000 20.06 0.00 34.31 2.44
2021 2478 1.663135 GCAATTGCCGTGTTGTTTTGT 59.337 42.857 20.06 0.00 34.31 2.83
2022 2479 2.095053 GCAATTGCCGTGTTGTTTTGTT 59.905 40.909 20.06 0.00 34.31 2.83
2023 2480 3.425492 GCAATTGCCGTGTTGTTTTGTTT 60.425 39.130 20.06 0.00 34.31 2.83
2024 2481 4.330313 CAATTGCCGTGTTGTTTTGTTTC 58.670 39.130 0.00 0.00 0.00 2.78
2025 2482 3.305398 TTGCCGTGTTGTTTTGTTTCT 57.695 38.095 0.00 0.00 0.00 2.52
2026 2483 2.600731 TGCCGTGTTGTTTTGTTTCTG 58.399 42.857 0.00 0.00 0.00 3.02
2027 2484 2.029828 TGCCGTGTTGTTTTGTTTCTGT 60.030 40.909 0.00 0.00 0.00 3.41
2028 2485 2.990514 GCCGTGTTGTTTTGTTTCTGTT 59.009 40.909 0.00 0.00 0.00 3.16
2029 2486 3.060230 GCCGTGTTGTTTTGTTTCTGTTC 59.940 43.478 0.00 0.00 0.00 3.18
2030 2487 4.481463 CCGTGTTGTTTTGTTTCTGTTCT 58.519 39.130 0.00 0.00 0.00 3.01
2031 2488 4.920927 CCGTGTTGTTTTGTTTCTGTTCTT 59.079 37.500 0.00 0.00 0.00 2.52
2032 2489 5.404066 CCGTGTTGTTTTGTTTCTGTTCTTT 59.596 36.000 0.00 0.00 0.00 2.52
2033 2490 6.074034 CCGTGTTGTTTTGTTTCTGTTCTTTT 60.074 34.615 0.00 0.00 0.00 2.27
2034 2491 7.341446 CGTGTTGTTTTGTTTCTGTTCTTTTT 58.659 30.769 0.00 0.00 0.00 1.94
2051 2508 1.726853 TTTTTGTTGTTGTTGCGGGG 58.273 45.000 0.00 0.00 0.00 5.73
2052 2509 0.895530 TTTTGTTGTTGTTGCGGGGA 59.104 45.000 0.00 0.00 0.00 4.81
2053 2510 1.115467 TTTGTTGTTGTTGCGGGGAT 58.885 45.000 0.00 0.00 0.00 3.85
2054 2511 1.115467 TTGTTGTTGTTGCGGGGATT 58.885 45.000 0.00 0.00 0.00 3.01
2055 2512 1.115467 TGTTGTTGTTGCGGGGATTT 58.885 45.000 0.00 0.00 0.00 2.17
2056 2513 1.482593 TGTTGTTGTTGCGGGGATTTT 59.517 42.857 0.00 0.00 0.00 1.82
2057 2514 1.864082 GTTGTTGTTGCGGGGATTTTG 59.136 47.619 0.00 0.00 0.00 2.44
2058 2515 1.115467 TGTTGTTGCGGGGATTTTGT 58.885 45.000 0.00 0.00 0.00 2.83
2059 2516 1.482593 TGTTGTTGCGGGGATTTTGTT 59.517 42.857 0.00 0.00 0.00 2.83
2060 2517 2.093447 TGTTGTTGCGGGGATTTTGTTT 60.093 40.909 0.00 0.00 0.00 2.83
2061 2518 2.517650 TGTTGCGGGGATTTTGTTTC 57.482 45.000 0.00 0.00 0.00 2.78
2062 2519 2.035632 TGTTGCGGGGATTTTGTTTCT 58.964 42.857 0.00 0.00 0.00 2.52
2063 2520 2.223923 TGTTGCGGGGATTTTGTTTCTG 60.224 45.455 0.00 0.00 0.00 3.02
2064 2521 1.698506 TGCGGGGATTTTGTTTCTGT 58.301 45.000 0.00 0.00 0.00 3.41
2065 2522 2.035632 TGCGGGGATTTTGTTTCTGTT 58.964 42.857 0.00 0.00 0.00 3.16
2066 2523 2.035321 TGCGGGGATTTTGTTTCTGTTC 59.965 45.455 0.00 0.00 0.00 3.18
2067 2524 2.296190 GCGGGGATTTTGTTTCTGTTCT 59.704 45.455 0.00 0.00 0.00 3.01
2068 2525 3.243737 GCGGGGATTTTGTTTCTGTTCTT 60.244 43.478 0.00 0.00 0.00 2.52
2069 2526 4.739436 GCGGGGATTTTGTTTCTGTTCTTT 60.739 41.667 0.00 0.00 0.00 2.52
2070 2527 5.356426 CGGGGATTTTGTTTCTGTTCTTTT 58.644 37.500 0.00 0.00 0.00 2.27
2071 2528 5.815222 CGGGGATTTTGTTTCTGTTCTTTTT 59.185 36.000 0.00 0.00 0.00 1.94
2088 2545 1.726853 TTTTTGTTGTTGTTGCGGGG 58.273 45.000 0.00 0.00 0.00 5.73
2089 2546 0.895530 TTTTGTTGTTGTTGCGGGGA 59.104 45.000 0.00 0.00 0.00 4.81
2090 2547 1.115467 TTTGTTGTTGTTGCGGGGAT 58.885 45.000 0.00 0.00 0.00 3.85
2091 2548 1.115467 TTGTTGTTGTTGCGGGGATT 58.885 45.000 0.00 0.00 0.00 3.01
2092 2549 1.115467 TGTTGTTGTTGCGGGGATTT 58.885 45.000 0.00 0.00 0.00 2.17
2093 2550 1.482593 TGTTGTTGTTGCGGGGATTTT 59.517 42.857 0.00 0.00 0.00 1.82
2094 2551 1.864082 GTTGTTGTTGCGGGGATTTTG 59.136 47.619 0.00 0.00 0.00 2.44
2095 2552 1.115467 TGTTGTTGCGGGGATTTTGT 58.885 45.000 0.00 0.00 0.00 2.83
2096 2553 1.482593 TGTTGTTGCGGGGATTTTGTT 59.517 42.857 0.00 0.00 0.00 2.83
2097 2554 2.093447 TGTTGTTGCGGGGATTTTGTTT 60.093 40.909 0.00 0.00 0.00 2.83
2098 2555 2.517650 TGTTGCGGGGATTTTGTTTC 57.482 45.000 0.00 0.00 0.00 2.78
2111 2568 5.010617 GGATTTTGTTTCTGTTCTGGCCTTA 59.989 40.000 3.32 0.00 0.00 2.69
2121 2578 7.301868 TCTGTTCTGGCCTTATTCAATTTTT 57.698 32.000 3.32 0.00 0.00 1.94
2122 2579 7.378181 TCTGTTCTGGCCTTATTCAATTTTTC 58.622 34.615 3.32 0.00 0.00 2.29
2123 2580 7.015098 TCTGTTCTGGCCTTATTCAATTTTTCA 59.985 33.333 3.32 0.00 0.00 2.69
2125 2582 8.156165 TGTTCTGGCCTTATTCAATTTTTCATT 58.844 29.630 3.32 0.00 0.00 2.57
2128 2585 6.179040 TGGCCTTATTCAATTTTTCATTGGG 58.821 36.000 3.32 0.00 0.00 4.12
2129 2586 5.066375 GGCCTTATTCAATTTTTCATTGGGC 59.934 40.000 0.00 0.00 33.52 5.36
2134 2591 9.603921 CTTATTCAATTTTTCATTGGGCTGTAT 57.396 29.630 0.00 0.00 0.00 2.29
2135 2592 7.852971 ATTCAATTTTTCATTGGGCTGTATG 57.147 32.000 0.00 0.00 0.00 2.39
2154 3647 4.590850 ATGGGTTTCTGCTTTCTGTTTC 57.409 40.909 0.00 0.00 0.00 2.78
2172 3665 5.168569 TGTTTCGGCTCTGTGTATTCTAAG 58.831 41.667 0.00 0.00 0.00 2.18
2188 3681 2.087646 CTAAGGGGCTTTCAAGTCAGC 58.912 52.381 0.00 0.00 35.07 4.26
2189 3682 0.480252 AAGGGGCTTTCAAGTCAGCT 59.520 50.000 0.00 0.00 36.20 4.24
2220 3713 6.878923 GGGCCTTTTAGATTGCAGTTTAATTT 59.121 34.615 0.84 0.00 0.00 1.82
2258 3751 8.973182 ACTTTTGTACCTTTTTATGGAGAAACA 58.027 29.630 0.00 0.00 0.00 2.83
2391 4540 8.031864 TCTTTTCACTGTTGCACTTTTTGATAA 58.968 29.630 0.00 0.00 0.00 1.75
2460 4610 0.716108 CGCAAACTCGTCATCTGTCC 59.284 55.000 0.00 0.00 0.00 4.02
2463 4613 1.728971 CAAACTCGTCATCTGTCCTGC 59.271 52.381 0.00 0.00 0.00 4.85
2472 4622 1.137872 CATCTGTCCTGCCTACCTCAC 59.862 57.143 0.00 0.00 0.00 3.51
2501 4652 2.749076 TCATCGGCAAAACCAATGAGAG 59.251 45.455 0.00 0.00 39.03 3.20
2506 4657 4.280677 TCGGCAAAACCAATGAGAGAAAAT 59.719 37.500 0.00 0.00 39.03 1.82
2521 4673 4.515567 AGAGAAAATCAACCACTTCGTTCC 59.484 41.667 0.00 0.00 0.00 3.62
2531 4683 2.544267 CCACTTCGTTCCTGTCAAGTTC 59.456 50.000 0.00 0.00 0.00 3.01
2552 4704 2.600731 CCAACCCACACCCACACT 59.399 61.111 0.00 0.00 0.00 3.55
2561 4713 1.523711 CACCCACACTGACGCTTGT 60.524 57.895 0.00 0.00 0.00 3.16
2583 4735 2.896443 CGACCTCTCTGGCCCTTC 59.104 66.667 0.00 0.00 40.22 3.46
2592 4744 2.121963 TGGCCCTTCCTGGTGAGT 60.122 61.111 0.00 0.00 35.26 3.41
2627 4791 2.224159 ACACGTTCCTGCCTCCCAT 61.224 57.895 0.00 0.00 0.00 4.00
2640 4804 3.217626 GCCTCCCATTTGTTCCTCTATG 58.782 50.000 0.00 0.00 0.00 2.23
2645 4809 5.989477 TCCCATTTGTTCCTCTATGTACAG 58.011 41.667 0.33 0.00 0.00 2.74
2649 4813 5.499004 TTTGTTCCTCTATGTACAGGCTT 57.501 39.130 0.33 0.00 0.00 4.35
2675 4839 2.654877 CACGGGCTACCTCGTTGT 59.345 61.111 0.00 0.00 37.53 3.32
2678 4842 1.005394 CGGGCTACCTCGTTGTTGT 60.005 57.895 0.00 0.00 33.28 3.32
2681 4845 0.319297 GGCTACCTCGTTGTTGTCGT 60.319 55.000 0.00 0.00 0.00 4.34
2685 4849 1.594293 CCTCGTTGTTGTCGTGGCT 60.594 57.895 0.00 0.00 35.72 4.75
2686 4850 1.157870 CCTCGTTGTTGTCGTGGCTT 61.158 55.000 0.00 0.00 35.72 4.35
2707 4871 3.605664 GCTGGCGCAACCCAAGTT 61.606 61.111 10.83 0.00 37.83 2.66
2750 4914 1.741055 GCGATGGAATAACCGGTGTGA 60.741 52.381 8.52 0.00 42.61 3.58
2751 4915 1.931172 CGATGGAATAACCGGTGTGAC 59.069 52.381 8.52 0.02 42.61 3.67
2758 4922 0.899720 TAACCGGTGTGACATCCTCC 59.100 55.000 8.52 0.00 0.00 4.30
2760 4924 1.990060 CCGGTGTGACATCCTCCCT 60.990 63.158 0.00 0.00 0.00 4.20
2762 4926 1.908483 GGTGTGACATCCTCCCTCC 59.092 63.158 0.00 0.00 0.00 4.30
2764 4928 0.539051 GTGTGACATCCTCCCTCCTG 59.461 60.000 0.00 0.00 0.00 3.86
2776 4944 1.519455 CCTCCTGACATTCGCGACC 60.519 63.158 9.15 0.00 0.00 4.79
2777 4945 1.874019 CTCCTGACATTCGCGACCG 60.874 63.158 9.15 5.13 0.00 4.79
2804 4972 0.326264 AGCTTAGGTGCAGACCAAGG 59.674 55.000 0.00 0.00 45.98 3.61
2806 4974 1.065126 GCTTAGGTGCAGACCAAGGAT 60.065 52.381 0.00 0.00 45.98 3.24
2810 4978 0.615331 GGTGCAGACCAAGGATCAGA 59.385 55.000 0.00 0.00 42.59 3.27
2847 5015 4.371786 CTGCGTAGAACATGGTGATGTAT 58.628 43.478 0.00 0.00 42.30 2.29
2848 5016 4.119136 TGCGTAGAACATGGTGATGTATG 58.881 43.478 0.00 0.00 42.30 2.39
2852 5020 1.956477 GAACATGGTGATGTATGGGGC 59.044 52.381 0.00 0.00 42.30 5.80
2916 5085 1.992170 CGCCTAGACGTTGCTTAAGT 58.008 50.000 4.02 0.00 0.00 2.24
2924 5093 2.809696 GACGTTGCTTAAGTGCCCTAAA 59.190 45.455 4.02 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
135 137 2.927856 ACCCACCTCGCATCACCA 60.928 61.111 0.00 0.00 0.00 4.17
253 255 4.160642 TCACAGCCAGAAATCAGCATAT 57.839 40.909 0.00 0.00 0.00 1.78
404 407 2.730183 TTTTGCTGACGAGTTTCACG 57.270 45.000 0.00 0.00 0.00 4.35
430 433 0.317160 AAGCGTCGATGACAGGACAA 59.683 50.000 9.31 0.00 32.74 3.18
494 497 4.085733 CCAAGATTACAAACCCCACATGA 58.914 43.478 0.00 0.00 0.00 3.07
645 649 9.770503 CAGATGCATTGCAGAGTATATATTTTC 57.229 33.333 17.52 4.85 43.65 2.29
655 659 7.997773 ATAAATATCAGATGCATTGCAGAGT 57.002 32.000 17.52 0.00 43.65 3.24
658 662 7.148639 GCCAAATAAATATCAGATGCATTGCAG 60.149 37.037 17.52 3.76 43.65 4.41
678 685 8.785329 AAATATCACCGTTTTTAATGCCAAAT 57.215 26.923 0.00 0.00 0.00 2.32
689 696 8.194769 AGTTTGTTGAGAAAATATCACCGTTTT 58.805 29.630 0.00 0.00 0.00 2.43
733 741 5.227569 TGAGCCTTCACTGAAGTCAAATA 57.772 39.130 16.10 0.00 37.92 1.40
762 771 8.788325 AGTACTCGCTCTGGTTATTTTTATTT 57.212 30.769 0.00 0.00 0.00 1.40
764 773 7.783042 AGAGTACTCGCTCTGGTTATTTTTAT 58.217 34.615 17.07 0.00 43.54 1.40
772 781 3.353370 AGTAGAGTACTCGCTCTGGTT 57.647 47.619 17.07 0.00 44.71 3.67
777 786 3.127203 TGCTTCAAGTAGAGTACTCGCTC 59.873 47.826 17.07 11.20 38.26 5.03
780 789 3.418094 CGTGCTTCAAGTAGAGTACTCG 58.582 50.000 17.07 2.89 38.26 4.18
813 822 0.321298 ATGGTAGGTTGGTCACGCAC 60.321 55.000 0.00 0.00 0.00 5.34
845 855 0.321671 ACCGGTCACAGGTGATTCAG 59.678 55.000 0.00 0.00 42.18 3.02
1168 1190 2.987547 GGTCTCGTGGACACCGGA 60.988 66.667 9.46 0.00 46.16 5.14
1188 1210 4.180946 CAGACGTCCCGGAGCTCG 62.181 72.222 13.01 4.40 38.88 5.03
1745 1769 6.031964 ACTAGGAGGATAATCCAGTCTTGA 57.968 41.667 0.00 0.00 42.26 3.02
1760 1784 0.741915 GACGGCAGAGAACTAGGAGG 59.258 60.000 0.00 0.00 0.00 4.30
1763 1787 0.809385 TTCGACGGCAGAGAACTAGG 59.191 55.000 0.00 0.00 0.00 3.02
1775 1799 1.772182 GAGGCACATCTATTCGACGG 58.228 55.000 0.00 0.00 0.00 4.79
1804 1829 1.225855 TTGTGTAAGCTTGACTGCGG 58.774 50.000 9.86 0.00 38.13 5.69
1806 1831 5.173854 GTCAAAATTGTGTAAGCTTGACTGC 59.826 40.000 9.86 2.64 37.82 4.40
1840 1865 9.388506 ACAATGTTGTTTCCATGTCAAAATTTA 57.611 25.926 0.00 0.00 38.47 1.40
1925 2238 7.600752 GCATGTTTATCCTGTAATCCTCTCTAC 59.399 40.741 0.00 0.00 0.00 2.59
1930 2243 7.445945 AGTAGCATGTTTATCCTGTAATCCTC 58.554 38.462 0.00 0.00 0.00 3.71
1978 2291 4.456911 CCGATAATGTTCCAATCAGGGATG 59.543 45.833 0.00 0.00 36.67 3.51
1979 2292 4.655963 CCGATAATGTTCCAATCAGGGAT 58.344 43.478 0.00 0.00 36.67 3.85
1981 2294 2.554032 GCCGATAATGTTCCAATCAGGG 59.446 50.000 0.00 0.00 38.24 4.45
1982 2295 3.213506 TGCCGATAATGTTCCAATCAGG 58.786 45.455 0.00 0.00 39.47 3.86
1983 2296 4.898829 TTGCCGATAATGTTCCAATCAG 57.101 40.909 0.00 0.00 0.00 2.90
1984 2297 5.590145 CAATTGCCGATAATGTTCCAATCA 58.410 37.500 0.00 0.00 0.00 2.57
1985 2298 4.445385 GCAATTGCCGATAATGTTCCAATC 59.555 41.667 20.06 0.00 34.31 2.67
1986 2299 4.370917 GCAATTGCCGATAATGTTCCAAT 58.629 39.130 20.06 0.00 34.31 3.16
2001 2458 1.663135 ACAAAACAACACGGCAATTGC 59.337 42.857 22.47 22.47 41.14 3.56
2002 2459 4.092675 AGAAACAAAACAACACGGCAATTG 59.907 37.500 0.00 0.00 0.00 2.32
2032 2489 1.275291 TCCCCGCAACAACAACAAAAA 59.725 42.857 0.00 0.00 0.00 1.94
2033 2490 0.895530 TCCCCGCAACAACAACAAAA 59.104 45.000 0.00 0.00 0.00 2.44
2034 2491 1.115467 ATCCCCGCAACAACAACAAA 58.885 45.000 0.00 0.00 0.00 2.83
2035 2492 1.115467 AATCCCCGCAACAACAACAA 58.885 45.000 0.00 0.00 0.00 2.83
2036 2493 1.115467 AAATCCCCGCAACAACAACA 58.885 45.000 0.00 0.00 0.00 3.33
2037 2494 1.864082 CAAAATCCCCGCAACAACAAC 59.136 47.619 0.00 0.00 0.00 3.32
2038 2495 1.482593 ACAAAATCCCCGCAACAACAA 59.517 42.857 0.00 0.00 0.00 2.83
2039 2496 1.115467 ACAAAATCCCCGCAACAACA 58.885 45.000 0.00 0.00 0.00 3.33
2040 2497 2.232756 AACAAAATCCCCGCAACAAC 57.767 45.000 0.00 0.00 0.00 3.32
2041 2498 2.432510 AGAAACAAAATCCCCGCAACAA 59.567 40.909 0.00 0.00 0.00 2.83
2042 2499 2.035632 AGAAACAAAATCCCCGCAACA 58.964 42.857 0.00 0.00 0.00 3.33
2043 2500 2.223947 ACAGAAACAAAATCCCCGCAAC 60.224 45.455 0.00 0.00 0.00 4.17
2044 2501 2.035632 ACAGAAACAAAATCCCCGCAA 58.964 42.857 0.00 0.00 0.00 4.85
2045 2502 1.698506 ACAGAAACAAAATCCCCGCA 58.301 45.000 0.00 0.00 0.00 5.69
2046 2503 2.296190 AGAACAGAAACAAAATCCCCGC 59.704 45.455 0.00 0.00 0.00 6.13
2047 2504 4.584327 AAGAACAGAAACAAAATCCCCG 57.416 40.909 0.00 0.00 0.00 5.73
2069 2526 1.275291 TCCCCGCAACAACAACAAAAA 59.725 42.857 0.00 0.00 0.00 1.94
2070 2527 0.895530 TCCCCGCAACAACAACAAAA 59.104 45.000 0.00 0.00 0.00 2.44
2071 2528 1.115467 ATCCCCGCAACAACAACAAA 58.885 45.000 0.00 0.00 0.00 2.83
2072 2529 1.115467 AATCCCCGCAACAACAACAA 58.885 45.000 0.00 0.00 0.00 2.83
2073 2530 1.115467 AAATCCCCGCAACAACAACA 58.885 45.000 0.00 0.00 0.00 3.33
2074 2531 1.864082 CAAAATCCCCGCAACAACAAC 59.136 47.619 0.00 0.00 0.00 3.32
2075 2532 1.482593 ACAAAATCCCCGCAACAACAA 59.517 42.857 0.00 0.00 0.00 2.83
2076 2533 1.115467 ACAAAATCCCCGCAACAACA 58.885 45.000 0.00 0.00 0.00 3.33
2077 2534 2.232756 AACAAAATCCCCGCAACAAC 57.767 45.000 0.00 0.00 0.00 3.32
2078 2535 2.432510 AGAAACAAAATCCCCGCAACAA 59.567 40.909 0.00 0.00 0.00 2.83
2079 2536 2.035632 AGAAACAAAATCCCCGCAACA 58.964 42.857 0.00 0.00 0.00 3.33
2080 2537 2.223947 ACAGAAACAAAATCCCCGCAAC 60.224 45.455 0.00 0.00 0.00 4.17
2081 2538 2.035632 ACAGAAACAAAATCCCCGCAA 58.964 42.857 0.00 0.00 0.00 4.85
2082 2539 1.698506 ACAGAAACAAAATCCCCGCA 58.301 45.000 0.00 0.00 0.00 5.69
2083 2540 2.296190 AGAACAGAAACAAAATCCCCGC 59.704 45.455 0.00 0.00 0.00 6.13
2084 2541 3.305335 CCAGAACAGAAACAAAATCCCCG 60.305 47.826 0.00 0.00 0.00 5.73
2085 2542 3.554960 GCCAGAACAGAAACAAAATCCCC 60.555 47.826 0.00 0.00 0.00 4.81
2086 2543 3.554960 GGCCAGAACAGAAACAAAATCCC 60.555 47.826 0.00 0.00 0.00 3.85
2087 2544 3.321968 AGGCCAGAACAGAAACAAAATCC 59.678 43.478 5.01 0.00 0.00 3.01
2088 2545 4.590850 AGGCCAGAACAGAAACAAAATC 57.409 40.909 5.01 0.00 0.00 2.17
2089 2546 6.670695 ATAAGGCCAGAACAGAAACAAAAT 57.329 33.333 5.01 0.00 0.00 1.82
2090 2547 6.097554 TGAATAAGGCCAGAACAGAAACAAAA 59.902 34.615 5.01 0.00 0.00 2.44
2091 2548 5.596361 TGAATAAGGCCAGAACAGAAACAAA 59.404 36.000 5.01 0.00 0.00 2.83
2092 2549 5.136828 TGAATAAGGCCAGAACAGAAACAA 58.863 37.500 5.01 0.00 0.00 2.83
2093 2550 4.724399 TGAATAAGGCCAGAACAGAAACA 58.276 39.130 5.01 0.00 0.00 2.83
2094 2551 5.705609 TTGAATAAGGCCAGAACAGAAAC 57.294 39.130 5.01 0.00 0.00 2.78
2095 2552 6.916360 AATTGAATAAGGCCAGAACAGAAA 57.084 33.333 5.01 0.00 0.00 2.52
2096 2553 6.916360 AAATTGAATAAGGCCAGAACAGAA 57.084 33.333 5.01 0.00 0.00 3.02
2097 2554 6.916360 AAAATTGAATAAGGCCAGAACAGA 57.084 33.333 5.01 0.00 0.00 3.41
2098 2555 7.153985 TGAAAAATTGAATAAGGCCAGAACAG 58.846 34.615 5.01 0.00 0.00 3.16
2111 2568 6.824704 CCATACAGCCCAATGAAAAATTGAAT 59.175 34.615 0.00 0.00 0.00 2.57
2121 2578 2.311542 AGAAACCCATACAGCCCAATGA 59.688 45.455 0.00 0.00 0.00 2.57
2122 2579 2.428171 CAGAAACCCATACAGCCCAATG 59.572 50.000 0.00 0.00 0.00 2.82
2123 2580 2.738743 CAGAAACCCATACAGCCCAAT 58.261 47.619 0.00 0.00 0.00 3.16
2125 2582 0.323360 GCAGAAACCCATACAGCCCA 60.323 55.000 0.00 0.00 0.00 5.36
2128 2585 3.084786 AGAAAGCAGAAACCCATACAGC 58.915 45.455 0.00 0.00 0.00 4.40
2129 2586 4.074970 ACAGAAAGCAGAAACCCATACAG 58.925 43.478 0.00 0.00 0.00 2.74
2134 2591 2.357637 CGAAACAGAAAGCAGAAACCCA 59.642 45.455 0.00 0.00 0.00 4.51
2135 2592 2.287608 CCGAAACAGAAAGCAGAAACCC 60.288 50.000 0.00 0.00 0.00 4.11
2154 3647 2.224066 CCCCTTAGAATACACAGAGCCG 60.224 54.545 0.00 0.00 0.00 5.52
2172 3665 1.270826 GAAAGCTGACTTGAAAGCCCC 59.729 52.381 0.00 0.00 40.42 5.80
2188 3681 4.949856 TGCAATCTAAAAGGCCCTAGAAAG 59.050 41.667 0.00 2.41 0.00 2.62
2189 3682 4.929479 TGCAATCTAAAAGGCCCTAGAAA 58.071 39.130 0.00 0.00 0.00 2.52
2230 3723 8.754991 TTCTCCATAAAAAGGTACAAAAGTCA 57.245 30.769 0.00 0.00 0.00 3.41
2231 3724 9.459640 GTTTCTCCATAAAAAGGTACAAAAGTC 57.540 33.333 0.00 0.00 0.00 3.01
2232 3725 8.973182 TGTTTCTCCATAAAAAGGTACAAAAGT 58.027 29.630 0.00 0.00 0.00 2.66
2233 3726 9.810545 TTGTTTCTCCATAAAAAGGTACAAAAG 57.189 29.630 0.00 0.00 0.00 2.27
2235 3728 9.757227 CATTGTTTCTCCATAAAAAGGTACAAA 57.243 29.630 0.00 0.00 0.00 2.83
2238 3731 9.758651 AAACATTGTTTCTCCATAAAAAGGTAC 57.241 29.630 8.97 0.00 0.00 3.34
2240 3733 9.679661 AAAAACATTGTTTCTCCATAAAAAGGT 57.320 25.926 14.80 0.00 0.00 3.50
2241 3734 9.934190 CAAAAACATTGTTTCTCCATAAAAAGG 57.066 29.630 14.80 0.00 0.00 3.11
2362 4511 7.225538 TCAAAAAGTGCAACAGTGAAAAGAAAA 59.774 29.630 0.00 0.00 41.43 2.29
2373 4522 9.301153 ACTTTAGTTTATCAAAAAGTGCAACAG 57.699 29.630 0.00 0.00 39.89 3.16
2374 4523 9.646427 AACTTTAGTTTATCAAAAAGTGCAACA 57.354 25.926 0.00 0.00 40.35 3.33
2391 4540 8.798859 AGATTGAGATATGTGCAACTTTAGTT 57.201 30.769 0.00 0.00 38.04 2.24
2429 4578 4.181578 ACGAGTTTGCGCATTATTCTAGT 58.818 39.130 12.75 9.05 33.86 2.57
2472 4622 2.666022 GGTTTTGCCGATGATTTTTCCG 59.334 45.455 0.00 0.00 0.00 4.30
2501 4652 4.036380 ACAGGAACGAAGTGGTTGATTTTC 59.964 41.667 0.00 0.00 45.00 2.29
2506 4657 1.483004 TGACAGGAACGAAGTGGTTGA 59.517 47.619 0.00 0.00 45.00 3.18
2521 4673 1.338020 GGGTTGGCTTGAACTTGACAG 59.662 52.381 0.00 0.00 0.00 3.51
2531 4683 2.123511 TGGGTGTGGGTTGGCTTG 60.124 61.111 0.00 0.00 0.00 4.01
2572 4724 1.908340 CTCACCAGGAAGGGCCAGAG 61.908 65.000 6.18 0.00 43.89 3.35
2577 4729 0.178990 ACAAACTCACCAGGAAGGGC 60.179 55.000 0.00 0.00 43.89 5.19
2578 4730 1.956477 CAACAAACTCACCAGGAAGGG 59.044 52.381 0.00 0.00 43.89 3.95
2583 4735 1.008538 GCGCAACAAACTCACCAGG 60.009 57.895 0.30 0.00 0.00 4.45
2627 4791 5.012664 TGAAGCCTGTACATAGAGGAACAAA 59.987 40.000 6.29 0.00 38.96 2.83
2660 4824 1.005394 ACAACAACGAGGTAGCCCG 60.005 57.895 0.00 0.00 35.12 6.13
2706 4870 2.495270 ACAATGGTGTTGTGCAAGACAA 59.505 40.909 13.00 3.48 42.55 3.18
2707 4871 2.098614 ACAATGGTGTTGTGCAAGACA 58.901 42.857 13.00 0.00 36.43 3.41
2750 4914 2.122768 GAATGTCAGGAGGGAGGATGT 58.877 52.381 0.00 0.00 0.00 3.06
2751 4915 1.069823 CGAATGTCAGGAGGGAGGATG 59.930 57.143 0.00 0.00 0.00 3.51
2758 4922 1.519455 GGTCGCGAATGTCAGGAGG 60.519 63.158 12.06 0.00 0.00 4.30
2760 4924 2.180769 CGGTCGCGAATGTCAGGA 59.819 61.111 12.06 0.00 0.00 3.86
2762 4926 1.695893 ATTGCGGTCGCGAATGTCAG 61.696 55.000 12.06 0.00 45.51 3.51
2764 4928 1.296867 CATTGCGGTCGCGAATGTC 60.297 57.895 12.06 0.00 45.51 3.06
2776 4944 1.430632 CACCTAAGCTGCCATTGCG 59.569 57.895 0.00 0.00 41.78 4.85
2777 4945 1.140375 GCACCTAAGCTGCCATTGC 59.860 57.895 0.00 0.00 38.26 3.56
2797 4965 3.244700 CCATGGGTATCTGATCCTTGGTC 60.245 52.174 16.31 0.33 39.57 4.02
2810 4978 0.035881 CGCAGCAGATCCATGGGTAT 59.964 55.000 13.02 0.00 0.00 2.73
2860 5029 0.953003 GCCTCGTCTACGCCTATCTT 59.047 55.000 0.00 0.00 39.60 2.40
2861 5030 0.179026 TGCCTCGTCTACGCCTATCT 60.179 55.000 0.00 0.00 39.60 1.98
2873 5042 0.598065 GCAAAGGTCAATTGCCTCGT 59.402 50.000 18.02 9.42 45.73 4.18
2881 5050 2.639327 GCGCTGGGCAAAGGTCAAT 61.639 57.895 12.19 0.00 42.87 2.57
2894 5063 0.457853 TAAGCAACGTCTAGGCGCTG 60.458 55.000 18.32 16.80 32.76 5.18
2916 5085 1.745232 CATAGGTTGCGTTTAGGGCA 58.255 50.000 0.00 0.00 38.93 5.36


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

AutoCloner maintained by Alex Coulton.