Multiple sequence alignment - TraesCS2D01G494500

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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 TraesCS2D01G494500 chr2D 100.000 2408 0 0 1 2408 591574283 591576690 0.000000e+00 4447.0
1 TraesCS2D01G494500 chr2D 92.565 807 42 11 1 792 121768797 121767994 0.000000e+00 1142.0
2 TraesCS2D01G494500 chr2D 90.158 569 35 7 846 1408 591704049 591704602 0.000000e+00 721.0
3 TraesCS2D01G494500 chr2D 92.258 465 21 5 952 1416 591603062 591603511 0.000000e+00 645.0
4 TraesCS2D01G494500 chr2D 80.930 430 43 25 999 1410 592115518 592115926 1.080000e-78 303.0
5 TraesCS2D01G494500 chr2D 88.387 155 14 2 2096 2249 591603915 591604066 1.470000e-42 183.0
6 TraesCS2D01G494500 chr2D 91.781 73 6 0 1417 1489 591603594 591603666 4.240000e-18 102.0
7 TraesCS2D01G494500 chr2D 84.112 107 14 2 2135 2238 591389333 591389439 1.520000e-17 100.0
8 TraesCS2D01G494500 chr2D 90.385 52 4 1 2044 2095 473161371 473161321 1.540000e-07 67.6
9 TraesCS2D01G494500 chr2D 96.875 32 1 0 791 822 209277477 209277446 1.000000e-03 54.7
10 TraesCS2D01G494500 chr1D 93.342 796 40 7 1 790 457137270 457138058 0.000000e+00 1164.0
11 TraesCS2D01G494500 chr7D 90.796 804 49 9 1 791 448516669 448515878 0.000000e+00 1051.0
12 TraesCS2D01G494500 chr7D 89.348 798 74 8 1 791 513326821 513326028 0.000000e+00 992.0
13 TraesCS2D01G494500 chr7D 89.836 305 24 5 1796 2095 376070769 376070467 3.760000e-103 385.0
14 TraesCS2D01G494500 chr7D 88.889 63 5 2 2033 2093 528126365 528126303 2.570000e-10 76.8
15 TraesCS2D01G494500 chr7D 92.453 53 3 1 2045 2097 411020284 411020335 9.230000e-10 75.0
16 TraesCS2D01G494500 chr2A 90.452 796 58 11 4 793 669554950 669555733 0.000000e+00 1033.0
17 TraesCS2D01G494500 chr2A 88.161 870 48 25 822 1646 726322104 726322963 0.000000e+00 985.0
18 TraesCS2D01G494500 chr2A 90.619 533 35 5 877 1408 726387189 726387707 0.000000e+00 693.0
19 TraesCS2D01G494500 chr2A 92.857 70 2 2 2096 2165 726323150 726323216 5.480000e-17 99.0
20 TraesCS2D01G494500 chr2A 92.424 66 3 2 2033 2096 421566084 421566149 2.550000e-15 93.5
21 TraesCS2D01G494500 chr2A 94.595 37 0 1 791 827 136117402 136117436 3.340000e-04 56.5
22 TraesCS2D01G494500 chr6D 89.862 799 65 11 1 790 423800279 423799488 0.000000e+00 1013.0
23 TraesCS2D01G494500 chr6D 89.375 800 69 12 1 789 112937092 112937886 0.000000e+00 992.0
24 TraesCS2D01G494500 chr6A 89.591 807 61 12 1 791 535374079 535373280 0.000000e+00 1003.0
25 TraesCS2D01G494500 chr6A 86.319 307 35 5 1796 2096 447807551 447807246 6.420000e-86 327.0
26 TraesCS2D01G494500 chr1A 88.764 801 76 13 1 792 12594937 12594142 0.000000e+00 968.0
27 TraesCS2D01G494500 chr2B 91.611 596 45 3 822 1416 717237165 717237756 0.000000e+00 819.0
28 TraesCS2D01G494500 chr2B 90.441 544 25 9 875 1408 717345153 717345679 0.000000e+00 691.0
29 TraesCS2D01G494500 chr2B 88.754 578 41 12 846 1416 717327882 717328442 0.000000e+00 686.0
30 TraesCS2D01G494500 chr2B 89.377 546 34 13 890 1416 717131498 717132038 0.000000e+00 665.0
31 TraesCS2D01G494500 chr2B 91.216 296 14 4 1806 2096 232735021 232735309 2.240000e-105 392.0
32 TraesCS2D01G494500 chr2B 81.818 253 25 14 2107 2348 717328933 717329175 2.440000e-45 193.0
33 TraesCS2D01G494500 chr2B 79.100 311 23 19 1492 1774 717132254 717132550 2.460000e-40 176.0
34 TraesCS2D01G494500 chr2B 89.583 48 2 3 1588 1635 717237965 717238009 9.300000e-05 58.4
35 TraesCS2D01G494500 chr4D 91.148 305 21 4 1796 2095 111563763 111563460 2.230000e-110 409.0
36 TraesCS2D01G494500 chr5A 89.869 306 25 3 1796 2096 644156453 644156149 2.900000e-104 388.0
37 TraesCS2D01G494500 chr5A 82.222 90 12 3 2011 2096 395906542 395906631 9.230000e-10 75.0
38 TraesCS2D01G494500 chr3B 89.902 307 22 6 1796 2096 130125398 130125095 1.040000e-103 387.0
39 TraesCS2D01G494500 chr3A 88.746 311 27 5 1796 2100 18568026 18568334 8.130000e-100 374.0
40 TraesCS2D01G494500 chr3A 88.424 311 28 5 1796 2100 18570143 18570451 3.780000e-98 368.0
41 TraesCS2D01G494500 chr3A 88.462 312 27 6 1796 2100 18572260 18572569 3.780000e-98 368.0
42 TraesCS2D01G494500 chr3A 88.462 312 27 6 1796 2100 18574378 18574687 3.780000e-98 368.0
43 TraesCS2D01G494500 chr3A 88.462 312 27 6 1796 2100 18586750 18587059 3.780000e-98 368.0
44 TraesCS2D01G494500 chr3A 88.462 312 27 6 1796 2100 18588868 18589177 3.780000e-98 368.0
45 TraesCS2D01G494500 chr1B 89.262 298 26 3 1806 2097 417017276 417016979 3.780000e-98 368.0
46 TraesCS2D01G494500 chr1B 90.909 44 2 2 791 832 505109502 505109545 9.300000e-05 58.4
47 TraesCS2D01G494500 chr7B 86.711 301 29 6 1807 2097 549923026 549923325 8.300000e-85 324.0
48 TraesCS2D01G494500 chr5D 82.160 213 30 6 1891 2097 489306951 489307161 2.460000e-40 176.0
49 TraesCS2D01G494500 chr5D 92.308 52 3 1 2046 2097 9103939 9103889 3.320000e-09 73.1
50 TraesCS2D01G494500 chr5D 86.765 68 6 2 2031 2096 354536494 354536560 3.320000e-09 73.1
51 TraesCS2D01G494500 chr5D 100.000 30 0 0 2044 2073 242954732 242954761 3.340000e-04 56.5
52 TraesCS2D01G494500 chr5D 96.875 32 1 0 791 822 338563970 338563939 1.000000e-03 54.7
53 TraesCS2D01G494500 chr5B 85.057 87 11 2 2013 2097 608656093 608656007 1.190000e-13 87.9
54 TraesCS2D01G494500 chr4A 81.818 88 13 3 2013 2098 82619188 82619102 1.190000e-08 71.3
55 TraesCS2D01G494500 chr4A 100.000 31 0 0 791 821 511423841 511423811 9.300000e-05 58.4
56 TraesCS2D01G494500 chr4A 100.000 30 0 0 791 820 505422980 505422951 3.340000e-04 56.5
57 TraesCS2D01G494500 chr3D 100.000 30 0 0 791 820 190530790 190530761 3.340000e-04 56.5
58 TraesCS2D01G494500 chr3D 100.000 30 0 0 791 820 335480831 335480802 3.340000e-04 56.5
59 TraesCS2D01G494500 chr3D 96.875 32 1 0 791 822 86847945 86847914 1.000000e-03 54.7


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 TraesCS2D01G494500 chr2D 591574283 591576690 2407 False 4447.0 4447 100.000000 1 2408 1 chr2D.!!$F2 2407
1 TraesCS2D01G494500 chr2D 121767994 121768797 803 True 1142.0 1142 92.565000 1 792 1 chr2D.!!$R1 791
2 TraesCS2D01G494500 chr2D 591704049 591704602 553 False 721.0 721 90.158000 846 1408 1 chr2D.!!$F3 562
3 TraesCS2D01G494500 chr2D 591603062 591604066 1004 False 310.0 645 90.808667 952 2249 3 chr2D.!!$F5 1297
4 TraesCS2D01G494500 chr1D 457137270 457138058 788 False 1164.0 1164 93.342000 1 790 1 chr1D.!!$F1 789
5 TraesCS2D01G494500 chr7D 448515878 448516669 791 True 1051.0 1051 90.796000 1 791 1 chr7D.!!$R2 790
6 TraesCS2D01G494500 chr7D 513326028 513326821 793 True 992.0 992 89.348000 1 791 1 chr7D.!!$R3 790
7 TraesCS2D01G494500 chr2A 669554950 669555733 783 False 1033.0 1033 90.452000 4 793 1 chr2A.!!$F3 789
8 TraesCS2D01G494500 chr2A 726387189 726387707 518 False 693.0 693 90.619000 877 1408 1 chr2A.!!$F4 531
9 TraesCS2D01G494500 chr2A 726322104 726323216 1112 False 542.0 985 90.509000 822 2165 2 chr2A.!!$F5 1343
10 TraesCS2D01G494500 chr6D 423799488 423800279 791 True 1013.0 1013 89.862000 1 790 1 chr6D.!!$R1 789
11 TraesCS2D01G494500 chr6D 112937092 112937886 794 False 992.0 992 89.375000 1 789 1 chr6D.!!$F1 788
12 TraesCS2D01G494500 chr6A 535373280 535374079 799 True 1003.0 1003 89.591000 1 791 1 chr6A.!!$R2 790
13 TraesCS2D01G494500 chr1A 12594142 12594937 795 True 968.0 968 88.764000 1 792 1 chr1A.!!$R1 791
14 TraesCS2D01G494500 chr2B 717345153 717345679 526 False 691.0 691 90.441000 875 1408 1 chr2B.!!$F2 533
15 TraesCS2D01G494500 chr2B 717327882 717329175 1293 False 439.5 686 85.286000 846 2348 2 chr2B.!!$F5 1502
16 TraesCS2D01G494500 chr2B 717237165 717238009 844 False 438.7 819 90.597000 822 1635 2 chr2B.!!$F4 813
17 TraesCS2D01G494500 chr2B 717131498 717132550 1052 False 420.5 665 84.238500 890 1774 2 chr2B.!!$F3 884
18 TraesCS2D01G494500 chr3A 18568026 18574687 6661 False 369.5 374 88.523500 1796 2100 4 chr3A.!!$F1 304
19 TraesCS2D01G494500 chr3A 18586750 18589177 2427 False 368.0 368 88.462000 1796 2100 2 chr3A.!!$F2 304

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
812 848 0.028374 GCTTGCGTTTGTACCGTGTT 59.972 50.0 0.0 0.0 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2294 9025 0.317854 GAACGGCCAAGACAAGTTGC 60.318 55.0 2.24 0.0 0.0 4.17 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
286 300 0.382515 GCGAGTACGAGGAGATGCTT 59.617 55.000 0.00 0.00 42.66 3.91
473 489 1.303806 TCATCGACCTCACGGACCA 60.304 57.895 0.00 0.00 0.00 4.02
723 759 2.680352 ATCCGTGTCCGTCTGGCT 60.680 61.111 0.00 0.00 34.14 4.75
792 828 1.068541 CCCGTTGGAGTTGCTTTAAGC 60.069 52.381 10.38 10.38 42.82 3.09
793 829 1.399727 CCGTTGGAGTTGCTTTAAGCG 60.400 52.381 12.54 0.00 46.26 4.68
794 830 1.686464 GTTGGAGTTGCTTTAAGCGC 58.314 50.000 12.54 0.00 46.26 5.92
795 831 1.266989 GTTGGAGTTGCTTTAAGCGCT 59.733 47.619 2.64 2.64 46.26 5.92
796 832 1.604604 TGGAGTTGCTTTAAGCGCTT 58.395 45.000 27.97 27.97 46.26 4.68
797 833 1.266718 TGGAGTTGCTTTAAGCGCTTG 59.733 47.619 32.23 16.93 46.26 4.01
798 834 1.331241 GAGTTGCTTTAAGCGCTTGC 58.669 50.000 32.23 25.83 46.26 4.01
799 835 0.385974 AGTTGCTTTAAGCGCTTGCG 60.386 50.000 32.23 19.68 46.26 4.85
800 836 0.660300 GTTGCTTTAAGCGCTTGCGT 60.660 50.000 32.23 8.97 46.26 5.24
801 837 0.030101 TTGCTTTAAGCGCTTGCGTT 59.970 45.000 32.23 8.53 46.26 4.84
802 838 0.030101 TGCTTTAAGCGCTTGCGTTT 59.970 45.000 32.23 19.41 46.26 3.60
803 839 0.430858 GCTTTAAGCGCTTGCGTTTG 59.569 50.000 32.23 15.98 45.69 2.93
804 840 1.753956 CTTTAAGCGCTTGCGTTTGT 58.246 45.000 32.23 6.01 45.69 2.83
805 841 2.911120 CTTTAAGCGCTTGCGTTTGTA 58.089 42.857 32.23 6.92 45.69 2.41
806 842 2.303707 TTAAGCGCTTGCGTTTGTAC 57.696 45.000 32.23 4.00 45.69 2.90
807 843 0.513820 TAAGCGCTTGCGTTTGTACC 59.486 50.000 32.23 3.33 45.69 3.34
808 844 2.438385 AAGCGCTTGCGTTTGTACCG 62.438 55.000 24.40 0.00 45.69 4.02
809 845 2.932905 CGCTTGCGTTTGTACCGT 59.067 55.556 6.86 0.00 0.00 4.83
810 846 1.438059 CGCTTGCGTTTGTACCGTG 60.438 57.895 6.86 0.00 0.00 4.94
811 847 1.644913 GCTTGCGTTTGTACCGTGT 59.355 52.632 0.00 0.00 0.00 4.49
812 848 0.028374 GCTTGCGTTTGTACCGTGTT 59.972 50.000 0.00 0.00 0.00 3.32
813 849 1.261089 GCTTGCGTTTGTACCGTGTTA 59.739 47.619 0.00 0.00 0.00 2.41
814 850 2.286301 GCTTGCGTTTGTACCGTGTTAA 60.286 45.455 0.00 0.00 0.00 2.01
815 851 3.788135 GCTTGCGTTTGTACCGTGTTAAA 60.788 43.478 0.00 0.00 0.00 1.52
816 852 4.341099 CTTGCGTTTGTACCGTGTTAAAA 58.659 39.130 0.00 0.00 0.00 1.52
817 853 4.346734 TGCGTTTGTACCGTGTTAAAAA 57.653 36.364 0.00 0.00 0.00 1.94
883 926 3.412386 GAAACCAAGCATCGGCCTATAT 58.588 45.455 0.00 0.00 42.56 0.86
983 1030 0.111253 AAAGCAGAACACCCCTCAGG 59.889 55.000 0.00 0.00 43.78 3.86
985 1032 3.160585 CAGAACACCCCTCAGGCA 58.839 61.111 0.00 0.00 40.58 4.75
1024 1071 0.101759 CAAATGCGGCAAGATCCAGG 59.898 55.000 6.82 0.00 0.00 4.45
1392 1484 4.489771 CAGGGGATGGCGGTGGAC 62.490 72.222 0.00 0.00 0.00 4.02
1410 1502 1.227527 CAAGCTCGTGTGGTGACCA 60.228 57.895 0.00 0.00 0.00 4.02
1434 1657 2.434884 AACATCTCGCGTGCCTGG 60.435 61.111 5.77 0.00 0.00 4.45
1489 1712 3.865011 ACACAACAAGCAATGACACAA 57.135 38.095 0.00 0.00 0.00 3.33
1490 1713 4.389890 ACACAACAAGCAATGACACAAT 57.610 36.364 0.00 0.00 0.00 2.71
1709 2054 4.278513 CACCGCCCAAGACCCCAA 62.279 66.667 0.00 0.00 0.00 4.12
1737 2083 3.335729 GGAACCCGTGGGACCCAT 61.336 66.667 18.51 0.00 35.28 4.00
1738 2084 2.045340 GAACCCGTGGGACCCATG 60.045 66.667 24.15 24.15 40.02 3.66
1758 2104 6.705381 CCCATGTCTATTTGCTTTTTGAACAA 59.295 34.615 0.00 0.00 0.00 2.83
1790 2136 4.310769 GGATCATTAGCACTGCGAGTAAT 58.689 43.478 0.00 0.00 0.00 1.89
1791 2137 4.151335 GGATCATTAGCACTGCGAGTAATG 59.849 45.833 12.28 12.28 0.00 1.90
1792 2138 3.457234 TCATTAGCACTGCGAGTAATGG 58.543 45.455 15.99 4.45 28.02 3.16
1793 2139 1.651987 TTAGCACTGCGAGTAATGGC 58.348 50.000 0.00 0.00 0.00 4.40
1794 2140 0.534873 TAGCACTGCGAGTAATGGCA 59.465 50.000 0.00 0.00 37.63 4.92
1798 2144 3.889227 TGCGAGTAATGGCAGTGC 58.111 55.556 6.55 6.55 33.52 4.40
1799 2145 2.100031 TGCGAGTAATGGCAGTGCG 61.100 57.895 9.45 0.00 33.52 5.34
1800 2146 2.100631 GCGAGTAATGGCAGTGCGT 61.101 57.895 9.45 0.00 0.00 5.24
1801 2147 1.635663 GCGAGTAATGGCAGTGCGTT 61.636 55.000 9.45 9.20 0.00 4.84
1802 2148 0.095245 CGAGTAATGGCAGTGCGTTG 59.905 55.000 9.45 0.00 0.00 4.10
1803 2149 1.438651 GAGTAATGGCAGTGCGTTGA 58.561 50.000 9.45 0.00 0.00 3.18
1804 2150 2.009774 GAGTAATGGCAGTGCGTTGAT 58.990 47.619 9.45 0.25 0.00 2.57
1810 2156 2.562912 CAGTGCGTTGATGTGGCC 59.437 61.111 0.00 0.00 0.00 5.36
1812 2158 1.968017 AGTGCGTTGATGTGGCCTG 60.968 57.895 3.32 0.00 0.00 4.85
1843 2189 0.034337 AGCAAAGAAACGCGAGGGTA 59.966 50.000 15.93 0.00 0.00 3.69
1870 2216 6.804295 TCAACCGGATAAATCAACAAAAATCG 59.196 34.615 9.46 0.00 0.00 3.34
1873 2219 5.741982 CCGGATAAATCAACAAAAATCGGTC 59.258 40.000 0.00 0.00 0.00 4.79
1924 4387 2.514458 TCAAAGAATGGAAGGAGGCC 57.486 50.000 0.00 0.00 0.00 5.19
1935 4398 1.984288 AAGGAGGCCGGATTAGGTGC 61.984 60.000 5.05 0.00 0.00 5.01
1937 4400 1.227674 GAGGCCGGATTAGGTGCTG 60.228 63.158 5.05 0.00 0.00 4.41
1940 4403 1.451936 GCCGGATTAGGTGCTGGAT 59.548 57.895 5.05 0.00 0.00 3.41
1941 4404 0.886490 GCCGGATTAGGTGCTGGATG 60.886 60.000 5.05 0.00 0.00 3.51
1942 4405 0.469917 CCGGATTAGGTGCTGGATGT 59.530 55.000 0.00 0.00 0.00 3.06
1947 4410 4.137543 GGATTAGGTGCTGGATGTTTAGG 58.862 47.826 0.00 0.00 0.00 2.69
1949 4412 5.163237 GGATTAGGTGCTGGATGTTTAGGTA 60.163 44.000 0.00 0.00 0.00 3.08
1952 4415 3.587506 AGGTGCTGGATGTTTAGGTAGTT 59.412 43.478 0.00 0.00 0.00 2.24
1955 4418 5.106277 GGTGCTGGATGTTTAGGTAGTTTTC 60.106 44.000 0.00 0.00 0.00 2.29
1962 8661 6.819146 GGATGTTTAGGTAGTTTTCTGGAGAG 59.181 42.308 0.00 0.00 0.00 3.20
1975 8674 2.234908 TCTGGAGAGTAGGCTTTGCTTC 59.765 50.000 0.00 0.00 0.00 3.86
1976 8675 1.977854 TGGAGAGTAGGCTTTGCTTCA 59.022 47.619 0.00 0.00 0.00 3.02
1993 8696 1.563924 TCATAGGTGTGTAGGCGGTT 58.436 50.000 0.00 0.00 0.00 4.44
1996 8699 2.934886 TAGGTGTGTAGGCGGTTTTT 57.065 45.000 0.00 0.00 0.00 1.94
2073 8776 7.880713 TGCCTTCTATAAAAATATGATACGCCA 59.119 33.333 0.00 0.00 0.00 5.69
2125 8831 7.307632 GCAGTGCGAATATATTTCAGACTTCAT 60.308 37.037 0.00 0.00 0.00 2.57
2126 8832 8.219769 CAGTGCGAATATATTTCAGACTTCATC 58.780 37.037 0.00 0.00 0.00 2.92
2127 8833 7.928167 AGTGCGAATATATTTCAGACTTCATCA 59.072 33.333 0.00 0.00 0.00 3.07
2128 8834 8.006590 GTGCGAATATATTTCAGACTTCATCAC 58.993 37.037 0.00 0.00 0.00 3.06
2129 8835 7.928167 TGCGAATATATTTCAGACTTCATCACT 59.072 33.333 0.00 0.00 0.00 3.41
2130 8836 8.431593 GCGAATATATTTCAGACTTCATCACTC 58.568 37.037 0.00 0.00 0.00 3.51
2131 8837 9.689976 CGAATATATTTCAGACTTCATCACTCT 57.310 33.333 0.00 0.00 0.00 3.24
2185 8892 6.699575 TTTTGGGACTCTTTTCTCTGAAAG 57.300 37.500 0.00 0.00 37.85 2.62
2221 8928 1.377725 CAACTCCTTGCCGAGCCAT 60.378 57.895 0.00 0.00 32.79 4.40
2223 8930 0.618458 AACTCCTTGCCGAGCCATAA 59.382 50.000 0.00 0.00 32.79 1.90
2270 9001 3.432252 ACTCGTCGTTTGTGATTCATTCC 59.568 43.478 0.00 0.00 0.00 3.01
2277 9008 3.829886 TTGTGATTCATTCCTGCGTTC 57.170 42.857 0.00 0.00 0.00 3.95
2278 9009 2.777094 TGTGATTCATTCCTGCGTTCA 58.223 42.857 0.00 0.00 0.00 3.18
2279 9010 3.346315 TGTGATTCATTCCTGCGTTCAT 58.654 40.909 0.00 0.00 0.00 2.57
2280 9011 3.374988 TGTGATTCATTCCTGCGTTCATC 59.625 43.478 0.00 0.00 0.00 2.92
2281 9012 3.374988 GTGATTCATTCCTGCGTTCATCA 59.625 43.478 0.00 0.00 0.00 3.07
2282 9013 4.036027 GTGATTCATTCCTGCGTTCATCAT 59.964 41.667 0.00 0.00 0.00 2.45
2283 9014 4.035909 TGATTCATTCCTGCGTTCATCATG 59.964 41.667 0.00 0.00 0.00 3.07
2284 9015 2.989909 TCATTCCTGCGTTCATCATGT 58.010 42.857 0.00 0.00 0.00 3.21
2285 9016 3.346315 TCATTCCTGCGTTCATCATGTT 58.654 40.909 0.00 0.00 0.00 2.71
2286 9017 3.127376 TCATTCCTGCGTTCATCATGTTG 59.873 43.478 0.00 0.00 0.00 3.33
2287 9018 2.470983 TCCTGCGTTCATCATGTTGA 57.529 45.000 2.22 2.22 0.00 3.18
2288 9019 2.989909 TCCTGCGTTCATCATGTTGAT 58.010 42.857 7.29 0.00 37.65 2.57
2289 9020 4.135747 TCCTGCGTTCATCATGTTGATA 57.864 40.909 7.29 0.00 34.28 2.15
2290 9021 4.707105 TCCTGCGTTCATCATGTTGATAT 58.293 39.130 7.29 0.00 34.28 1.63
2291 9022 4.751600 TCCTGCGTTCATCATGTTGATATC 59.248 41.667 7.29 0.00 34.28 1.63
2292 9023 4.753610 CCTGCGTTCATCATGTTGATATCT 59.246 41.667 7.29 0.00 34.28 1.98
2293 9024 5.107182 CCTGCGTTCATCATGTTGATATCTC 60.107 44.000 7.29 0.00 34.28 2.75
2294 9025 4.445385 TGCGTTCATCATGTTGATATCTCG 59.555 41.667 7.29 8.59 34.28 4.04
2299 9030 5.604565 TCATCATGTTGATATCTCGCAACT 58.395 37.500 3.98 0.00 43.52 3.16
2318 9049 0.394488 TTGTCTTGGCCGTTCACCAA 60.394 50.000 0.00 0.00 44.86 3.67
2347 9080 4.545823 TTTTGCGAGACTTGATCGTTTT 57.454 36.364 0.00 0.00 42.13 2.43
2348 9081 4.545823 TTTGCGAGACTTGATCGTTTTT 57.454 36.364 0.00 0.00 42.13 1.94
2402 9135 3.092334 GAGAGCTCTCTTCCCGATTTC 57.908 52.381 32.25 5.99 40.61 2.17
2403 9136 2.693074 GAGAGCTCTCTTCCCGATTTCT 59.307 50.000 32.25 0.00 40.61 2.52
2404 9137 3.886505 GAGAGCTCTCTTCCCGATTTCTA 59.113 47.826 32.25 0.00 40.61 2.10
2405 9138 4.479158 AGAGCTCTCTTCCCGATTTCTAT 58.521 43.478 11.45 0.00 36.31 1.98
2406 9139 4.898861 AGAGCTCTCTTCCCGATTTCTATT 59.101 41.667 11.45 0.00 36.31 1.73
2407 9140 6.071984 AGAGCTCTCTTCCCGATTTCTATTA 58.928 40.000 11.45 0.00 36.31 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
450 466 3.352447 CGTGAGGTCGATGAGCATT 57.648 52.632 0.00 0.00 31.89 3.56
473 489 1.739196 TCATCGTCGTCGTCCTCGT 60.739 57.895 1.33 0.00 38.33 4.18
792 828 1.438059 CACGGTACAAACGCAAGCG 60.438 57.895 13.50 13.50 46.03 4.68
793 829 0.028374 AACACGGTACAAACGCAAGC 59.972 50.000 0.00 0.00 45.62 4.01
795 831 4.346734 TTTTAACACGGTACAAACGCAA 57.653 36.364 0.00 0.00 34.00 4.85
796 832 4.346734 TTTTTAACACGGTACAAACGCA 57.653 36.364 0.00 0.00 34.00 5.24
817 853 9.923143 CCTCGGGTTTAATTTCTTTTCTTAATT 57.077 29.630 0.00 0.00 0.00 1.40
818 854 9.304335 TCCTCGGGTTTAATTTCTTTTCTTAAT 57.696 29.630 0.00 0.00 0.00 1.40
819 855 8.694581 TCCTCGGGTTTAATTTCTTTTCTTAA 57.305 30.769 0.00 0.00 0.00 1.85
820 856 8.570488 GTTCCTCGGGTTTAATTTCTTTTCTTA 58.430 33.333 0.00 0.00 0.00 2.10
828 864 4.905269 CGATGTTCCTCGGGTTTAATTTC 58.095 43.478 0.00 0.00 35.03 2.17
855 892 1.808411 GATGCTTGGTTTCGTCCAGA 58.192 50.000 0.00 0.00 38.80 3.86
883 926 4.367023 AGCGCGGCGTGGAGTTTA 62.367 61.111 24.46 0.00 0.00 2.01
905 948 2.079158 TGAGAATGCTCTGCTTTTCCG 58.921 47.619 1.43 0.00 41.84 4.30
948 992 2.299582 TGCTTTTGGTGGGTTGATGATG 59.700 45.455 0.00 0.00 0.00 3.07
949 993 2.564062 CTGCTTTTGGTGGGTTGATGAT 59.436 45.455 0.00 0.00 0.00 2.45
950 994 1.962807 CTGCTTTTGGTGGGTTGATGA 59.037 47.619 0.00 0.00 0.00 2.92
983 1030 4.760047 TCGCTCCCTTTCCGCTGC 62.760 66.667 0.00 0.00 0.00 5.25
985 1032 2.187946 CATCGCTCCCTTTCCGCT 59.812 61.111 0.00 0.00 0.00 5.52
989 1036 0.965363 TTTGGCCATCGCTCCCTTTC 60.965 55.000 6.09 0.00 34.44 2.62
1392 1484 1.227527 TGGTCACCACACGAGCTTG 60.228 57.895 0.00 0.00 0.00 4.01
1438 1661 2.182030 CAGTCGGTCTTCTCGGCC 59.818 66.667 0.00 0.00 31.99 6.13
1503 1776 4.760047 CCCTCGCCCGTTCACTGG 62.760 72.222 0.00 0.00 0.00 4.00
1668 2006 2.356278 GGAAGGACCATGCAGCCA 59.644 61.111 0.00 0.00 38.79 4.75
1700 2045 1.066143 CACGATAGCACTTGGGGTCTT 60.066 52.381 0.00 0.00 42.67 3.01
1701 2046 0.537188 CACGATAGCACTTGGGGTCT 59.463 55.000 0.00 0.00 42.67 3.85
1702 2047 0.462047 CCACGATAGCACTTGGGGTC 60.462 60.000 0.00 0.00 42.67 4.46
1709 2054 1.255667 ACGGGTTCCACGATAGCACT 61.256 55.000 0.00 0.00 42.67 4.40
1737 2083 7.542477 TCGTTTTGTTCAAAAAGCAAATAGACA 59.458 29.630 15.27 0.00 33.00 3.41
1738 2084 7.839358 GTCGTTTTGTTCAAAAAGCAAATAGAC 59.161 33.333 15.27 5.19 34.84 2.59
1758 2104 1.474498 GCTAATGATCCGGGGTCGTTT 60.474 52.381 19.34 9.87 33.95 3.60
1790 2136 2.260154 CCACATCAACGCACTGCCA 61.260 57.895 0.00 0.00 0.00 4.92
1791 2137 2.562912 CCACATCAACGCACTGCC 59.437 61.111 0.00 0.00 0.00 4.85
1792 2138 2.126734 GCCACATCAACGCACTGC 60.127 61.111 0.00 0.00 0.00 4.40
1793 2139 1.968017 AGGCCACATCAACGCACTG 60.968 57.895 5.01 0.00 0.00 3.66
1794 2140 1.968017 CAGGCCACATCAACGCACT 60.968 57.895 5.01 0.00 0.00 4.40
1795 2141 2.562912 CAGGCCACATCAACGCAC 59.437 61.111 5.01 0.00 0.00 5.34
1796 2142 2.672651 CCAGGCCACATCAACGCA 60.673 61.111 5.01 0.00 0.00 5.24
1797 2143 2.672996 ACCAGGCCACATCAACGC 60.673 61.111 5.01 0.00 0.00 4.84
1798 2144 2.390599 CGACCAGGCCACATCAACG 61.391 63.158 5.01 0.00 0.00 4.10
1799 2145 2.690778 GCGACCAGGCCACATCAAC 61.691 63.158 5.01 0.00 0.00 3.18
1800 2146 1.549243 TAGCGACCAGGCCACATCAA 61.549 55.000 5.01 0.00 0.00 2.57
1801 2147 1.337384 ATAGCGACCAGGCCACATCA 61.337 55.000 5.01 0.00 0.00 3.07
1802 2148 0.882042 CATAGCGACCAGGCCACATC 60.882 60.000 5.01 0.00 0.00 3.06
1803 2149 1.146930 CATAGCGACCAGGCCACAT 59.853 57.895 5.01 0.00 0.00 3.21
1804 2150 2.584064 CATAGCGACCAGGCCACA 59.416 61.111 5.01 0.00 0.00 4.17
1843 2189 9.150348 GATTTTTGTTGATTTATCCGGTTGAAT 57.850 29.630 0.00 0.95 0.00 2.57
1873 2219 0.858583 TGTGTTTGTGTCGCTCATCG 59.141 50.000 0.00 0.00 40.15 3.84
1881 2227 2.805671 TCGTCCATGATGTGTTTGTGTC 59.194 45.455 0.00 0.00 0.00 3.67
1924 4387 2.332063 AACATCCAGCACCTAATCCG 57.668 50.000 0.00 0.00 0.00 4.18
1935 4398 6.472887 TCCAGAAAACTACCTAAACATCCAG 58.527 40.000 0.00 0.00 0.00 3.86
1937 4400 6.708285 TCTCCAGAAAACTACCTAAACATCC 58.292 40.000 0.00 0.00 0.00 3.51
1940 4403 6.742559 ACTCTCCAGAAAACTACCTAAACA 57.257 37.500 0.00 0.00 0.00 2.83
1941 4404 7.321908 CCTACTCTCCAGAAAACTACCTAAAC 58.678 42.308 0.00 0.00 0.00 2.01
1942 4405 6.070938 GCCTACTCTCCAGAAAACTACCTAAA 60.071 42.308 0.00 0.00 0.00 1.85
1947 4410 5.408880 AAGCCTACTCTCCAGAAAACTAC 57.591 43.478 0.00 0.00 0.00 2.73
1949 4412 4.646572 CAAAGCCTACTCTCCAGAAAACT 58.353 43.478 0.00 0.00 0.00 2.66
1952 4415 2.639839 AGCAAAGCCTACTCTCCAGAAA 59.360 45.455 0.00 0.00 0.00 2.52
1955 4418 2.027745 TGAAGCAAAGCCTACTCTCCAG 60.028 50.000 0.00 0.00 0.00 3.86
1962 8661 3.375299 CACACCTATGAAGCAAAGCCTAC 59.625 47.826 0.00 0.00 0.00 3.18
1975 8674 2.396590 AAACCGCCTACACACCTATG 57.603 50.000 0.00 0.00 0.00 2.23
1976 8675 3.428413 AAAAACCGCCTACACACCTAT 57.572 42.857 0.00 0.00 0.00 2.57
1993 8696 6.034470 GCGAACATCACACAAAAGAAGAAAAA 59.966 34.615 0.00 0.00 0.00 1.94
1996 8699 4.095632 TGCGAACATCACACAAAAGAAGAA 59.904 37.500 0.00 0.00 0.00 2.52
2125 8831 8.507524 TCTTCGATCAATTAGTAGAAGAGTGA 57.492 34.615 9.32 0.00 39.07 3.41
2126 8832 9.232082 CTTCTTCGATCAATTAGTAGAAGAGTG 57.768 37.037 10.73 7.89 42.98 3.51
2127 8833 8.410141 CCTTCTTCGATCAATTAGTAGAAGAGT 58.590 37.037 15.77 0.00 42.98 3.24
2128 8834 7.381139 GCCTTCTTCGATCAATTAGTAGAAGAG 59.619 40.741 15.77 9.22 42.98 2.85
2129 8835 7.203910 GCCTTCTTCGATCAATTAGTAGAAGA 58.796 38.462 15.77 12.06 41.26 2.87
2130 8836 6.143118 CGCCTTCTTCGATCAATTAGTAGAAG 59.857 42.308 9.67 9.67 37.78 2.85
2131 8837 5.977725 CGCCTTCTTCGATCAATTAGTAGAA 59.022 40.000 0.00 0.00 0.00 2.10
2170 8877 9.974980 AGAGTAAACTACTTTCAGAGAAAAGAG 57.025 33.333 3.56 0.93 39.59 2.85
2182 8889 7.048512 AGTTGCACAGAAGAGTAAACTACTTT 58.951 34.615 0.00 0.00 39.59 2.66
2185 8892 5.405873 GGAGTTGCACAGAAGAGTAAACTAC 59.594 44.000 0.00 0.00 31.54 2.73
2249 8956 3.679980 AGGAATGAATCACAAACGACGAG 59.320 43.478 0.00 0.00 0.00 4.18
2252 8983 3.492313 GCAGGAATGAATCACAAACGAC 58.508 45.455 0.00 0.00 0.00 4.34
2270 9001 5.388164 CGAGATATCAACATGATGAACGCAG 60.388 44.000 9.94 0.00 37.70 5.18
2277 9008 5.919272 AGTTGCGAGATATCAACATGATG 57.081 39.130 5.32 0.00 43.55 3.07
2278 9009 5.819379 ACAAGTTGCGAGATATCAACATGAT 59.181 36.000 14.49 0.00 41.59 2.45
2279 9010 5.178061 ACAAGTTGCGAGATATCAACATGA 58.822 37.500 14.49 0.00 41.59 3.07
2280 9011 5.292834 AGACAAGTTGCGAGATATCAACATG 59.707 40.000 5.32 7.03 43.42 3.21
2281 9012 5.423015 AGACAAGTTGCGAGATATCAACAT 58.577 37.500 5.32 0.00 43.55 2.71
2282 9013 4.820897 AGACAAGTTGCGAGATATCAACA 58.179 39.130 5.32 0.00 43.55 3.33
2283 9014 5.446473 CCAAGACAAGTTGCGAGATATCAAC 60.446 44.000 5.32 1.26 41.97 3.18
2284 9015 4.631377 CCAAGACAAGTTGCGAGATATCAA 59.369 41.667 5.32 0.00 0.00 2.57
2285 9016 4.183865 CCAAGACAAGTTGCGAGATATCA 58.816 43.478 5.32 0.00 0.00 2.15
2286 9017 3.001736 GCCAAGACAAGTTGCGAGATATC 59.998 47.826 1.81 0.00 0.00 1.63
2287 9018 2.939103 GCCAAGACAAGTTGCGAGATAT 59.061 45.455 1.81 0.00 0.00 1.63
2288 9019 2.346803 GCCAAGACAAGTTGCGAGATA 58.653 47.619 1.81 0.00 0.00 1.98
2289 9020 1.160137 GCCAAGACAAGTTGCGAGAT 58.840 50.000 1.81 0.00 0.00 2.75
2290 9021 0.884704 GGCCAAGACAAGTTGCGAGA 60.885 55.000 1.81 0.00 0.00 4.04
2291 9022 1.576421 GGCCAAGACAAGTTGCGAG 59.424 57.895 1.81 0.00 0.00 5.03
2292 9023 2.250939 CGGCCAAGACAAGTTGCGA 61.251 57.895 2.24 0.00 0.00 5.10
2293 9024 2.058829 AACGGCCAAGACAAGTTGCG 62.059 55.000 2.24 0.00 0.00 4.85
2294 9025 0.317854 GAACGGCCAAGACAAGTTGC 60.318 55.000 2.24 0.00 0.00 4.17
2299 9030 0.394488 TTGGTGAACGGCCAAGACAA 60.394 50.000 2.24 0.00 40.69 3.18
2382 9115 2.693074 AGAAATCGGGAAGAGAGCTCTC 59.307 50.000 32.45 32.45 39.39 3.20
2383 9116 2.745968 AGAAATCGGGAAGAGAGCTCT 58.254 47.619 18.28 18.28 42.75 4.09
2384 9117 4.864704 ATAGAAATCGGGAAGAGAGCTC 57.135 45.455 5.27 5.27 0.00 4.09


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

AutoCloner maintained by Alex Coulton.