Multiple sequence alignment - TraesCS6D01G349600

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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 TraesCS6D01G349600 chr6D 100.000 2456 0 0 1 2456 447277276 447279731 0.000000e+00 4536.0
1 TraesCS6D01G349600 chr6D 83.012 883 72 30 1 824 447739233 447738370 0.000000e+00 728.0
2 TraesCS6D01G349600 chr6D 86.220 537 56 13 1205 1734 447213406 447213931 1.270000e-157 566.0
3 TraesCS6D01G349600 chr6D 85.424 295 36 4 244 534 446935801 446935510 1.430000e-77 300.0
4 TraesCS6D01G349600 chr6D 90.090 111 6 5 855 963 447278015 447278122 3.290000e-29 139.0
5 TraesCS6D01G349600 chr6D 90.090 111 6 5 740 847 447278130 447278238 3.290000e-29 139.0
6 TraesCS6D01G349600 chr6D 78.539 219 26 14 2150 2355 447737408 447737198 9.220000e-25 124.0
7 TraesCS6D01G349600 chr6D 80.435 184 14 13 1806 1979 447214033 447214204 1.190000e-23 121.0
8 TraesCS6D01G349600 chr6D 97.727 44 1 0 1690 1733 447445086 447445129 2.620000e-10 76.8
9 TraesCS6D01G349600 chr6D 100.000 30 0 0 1758 1787 447445217 447445246 3.410000e-04 56.5
10 TraesCS6D01G349600 chr6B 84.657 1473 136 52 851 2300 677044903 677046308 0.000000e+00 1386.0
11 TraesCS6D01G349600 chr6B 88.539 890 63 22 851 1738 678092026 678092878 0.000000e+00 1042.0
12 TraesCS6D01G349600 chr6B 88.383 835 66 10 14 828 678176163 678175340 0.000000e+00 976.0
13 TraesCS6D01G349600 chr6B 87.058 904 66 24 847 1738 678357695 678356831 0.000000e+00 974.0
14 TraesCS6D01G349600 chr6B 87.925 853 54 21 851 1691 678175432 678174617 0.000000e+00 959.0
15 TraesCS6D01G349600 chr6B 88.674 777 63 11 978 1746 677087709 677088468 0.000000e+00 924.0
16 TraesCS6D01G349600 chr6B 88.860 763 40 20 860 1613 678543348 678542622 0.000000e+00 896.0
17 TraesCS6D01G349600 chr6B 84.624 904 65 37 851 1738 676865137 676865982 0.000000e+00 832.0
18 TraesCS6D01G349600 chr6B 83.077 845 83 20 25 847 678358386 678357580 0.000000e+00 713.0
19 TraesCS6D01G349600 chr6B 87.606 589 54 9 169 739 677087101 677087688 0.000000e+00 665.0
20 TraesCS6D01G349600 chr6B 87.350 585 51 13 1 572 678091241 678091815 0.000000e+00 649.0
21 TraesCS6D01G349600 chr6B 87.365 554 50 11 169 704 677777303 677777854 3.470000e-173 617.0
22 TraesCS6D01G349600 chr6B 87.365 554 51 9 169 704 677909583 677910135 3.470000e-173 617.0
23 TraesCS6D01G349600 chr6B 78.932 674 61 41 188 824 676729554 676730183 1.380000e-102 383.0
24 TraesCS6D01G349600 chr6B 78.014 705 88 40 191 847 678543934 678543249 4.960000e-102 381.0
25 TraesCS6D01G349600 chr6B 80.360 555 48 26 1758 2302 678174507 678174004 4.990000e-97 364.0
26 TraesCS6D01G349600 chr6B 80.402 398 47 19 311 701 676491607 676491980 8.650000e-70 274.0
27 TraesCS6D01G349600 chr6B 81.851 281 35 11 577 847 678091863 678092137 3.180000e-54 222.0
28 TraesCS6D01G349600 chr6B 93.277 119 8 0 11 129 677335758 677335876 2.510000e-40 176.0
29 TraesCS6D01G349600 chr6B 91.935 124 10 0 1 124 677044411 677044534 9.030000e-40 174.0
30 TraesCS6D01G349600 chr6B 87.826 115 11 2 1 112 677079592 677079706 5.510000e-27 132.0
31 TraesCS6D01G349600 chr6B 90.722 97 7 1 16 112 677906656 677906750 7.130000e-26 128.0
32 TraesCS6D01G349600 chr6B 86.957 115 12 3 1 112 676859309 676859423 2.560000e-25 126.0
33 TraesCS6D01G349600 chr6B 83.333 144 12 7 1748 1891 677337031 677337162 3.320000e-24 122.0
34 TraesCS6D01G349600 chr6B 90.426 94 7 1 16 109 677774548 677774639 3.320000e-24 122.0
35 TraesCS6D01G349600 chr6B 83.333 144 12 6 1748 1891 678092927 678093058 3.320000e-24 122.0
36 TraesCS6D01G349600 chr6B 89.888 89 9 0 2214 2302 677090468 677090556 5.550000e-22 115.0
37 TraesCS6D01G349600 chr6B 91.781 73 3 2 1806 1877 676730875 676730945 5.590000e-17 99.0
38 TraesCS6D01G349600 chr6B 96.296 54 1 1 2303 2356 677046336 677046388 1.210000e-13 87.9
39 TraesCS6D01G349600 chr6B 95.745 47 2 0 1831 1877 678356719 678356673 2.620000e-10 76.8
40 TraesCS6D01G349600 chr6B 85.714 77 4 3 1758 1834 677129635 677129704 9.420000e-10 75.0
41 TraesCS6D01G349600 chr6B 97.619 42 1 0 2372 2413 677585281 677585322 3.390000e-09 73.1
42 TraesCS6D01G349600 chr6A 88.670 812 63 16 59 847 593990983 593991788 0.000000e+00 963.0
43 TraesCS6D01G349600 chr6A 86.946 858 66 21 851 1696 594366415 594365592 0.000000e+00 922.0
44 TraesCS6D01G349600 chr6A 84.972 885 79 29 855 1734 593991682 593992517 0.000000e+00 848.0
45 TraesCS6D01G349600 chr6A 85.240 874 66 22 855 1725 594253537 594254350 0.000000e+00 841.0
46 TraesCS6D01G349600 chr6A 82.986 864 82 37 1 824 594320735 594319897 0.000000e+00 721.0
47 TraesCS6D01G349600 chr6A 87.783 442 30 15 420 847 594253212 594253643 1.700000e-136 496.0
48 TraesCS6D01G349600 chr6A 79.079 760 99 37 1205 1924 593929554 593930293 3.700000e-128 468.0
49 TraesCS6D01G349600 chr6A 85.294 374 41 10 1932 2302 594217117 594217479 8.290000e-100 374.0
50 TraesCS6D01G349600 chr6A 82.487 394 43 13 222 602 569677938 569678318 3.050000e-84 322.0
51 TraesCS6D01G349600 chr6A 79.250 400 50 20 191 572 594366879 594366495 5.240000e-62 248.0
52 TraesCS6D01G349600 chr6A 84.519 239 29 4 2044 2281 594254928 594255159 1.900000e-56 230.0
53 TraesCS6D01G349600 chr6A 89.167 120 12 1 1758 1876 594319024 594318905 5.470000e-32 148.0
54 TraesCS6D01G349600 chr6A 78.235 170 15 15 1831 1978 594365051 594364882 3.360000e-14 89.8
55 TraesCS6D01G349600 chr6A 92.157 51 4 0 2306 2356 593776496 593776446 3.390000e-09 73.1
56 TraesCS6D01G349600 chr7A 80.090 221 21 9 617 824 19013050 19012840 2.550000e-30 143.0


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 TraesCS6D01G349600 chr6D 447277276 447279731 2455 False 1604.666667 4536 93.393333 1 2456 3 chr6D.!!$F2 2455
1 TraesCS6D01G349600 chr6D 447737198 447739233 2035 True 426.000000 728 80.775500 1 2355 2 chr6D.!!$R2 2354
2 TraesCS6D01G349600 chr6D 447213406 447214204 798 False 343.500000 566 83.327500 1205 1979 2 chr6D.!!$F1 774
3 TraesCS6D01G349600 chr6B 676865137 676865982 845 False 832.000000 832 84.624000 851 1738 1 chr6B.!!$F3 887
4 TraesCS6D01G349600 chr6B 678174004 678176163 2159 True 766.333333 976 85.556000 14 2302 3 chr6B.!!$R1 2288
5 TraesCS6D01G349600 chr6B 678542622 678543934 1312 True 638.500000 896 83.437000 191 1613 2 chr6B.!!$R3 1422
6 TraesCS6D01G349600 chr6B 678356673 678358386 1713 True 587.933333 974 88.626667 25 1877 3 chr6B.!!$R2 1852
7 TraesCS6D01G349600 chr6B 677087101 677090556 3455 False 568.000000 924 88.722667 169 2302 3 chr6B.!!$F9 2133
8 TraesCS6D01G349600 chr6B 677044411 677046388 1977 False 549.300000 1386 90.962667 1 2356 3 chr6B.!!$F8 2355
9 TraesCS6D01G349600 chr6B 678091241 678093058 1817 False 508.750000 1042 85.268250 1 1891 4 chr6B.!!$F13 1890
10 TraesCS6D01G349600 chr6B 677906656 677910135 3479 False 372.500000 617 89.043500 16 704 2 chr6B.!!$F12 688
11 TraesCS6D01G349600 chr6B 677774548 677777854 3306 False 369.500000 617 88.895500 16 704 2 chr6B.!!$F11 688
12 TraesCS6D01G349600 chr6B 676729554 676730945 1391 False 241.000000 383 85.356500 188 1877 2 chr6B.!!$F7 1689
13 TraesCS6D01G349600 chr6A 593990983 593992517 1534 False 905.500000 963 86.821000 59 1734 2 chr6A.!!$F4 1675
14 TraesCS6D01G349600 chr6A 594253212 594255159 1947 False 522.333333 841 85.847333 420 2281 3 chr6A.!!$F5 1861
15 TraesCS6D01G349600 chr6A 593929554 593930293 739 False 468.000000 468 79.079000 1205 1924 1 chr6A.!!$F2 719
16 TraesCS6D01G349600 chr6A 594318905 594320735 1830 True 434.500000 721 86.076500 1 1876 2 chr6A.!!$R2 1875
17 TraesCS6D01G349600 chr6A 594364882 594366879 1997 True 419.933333 922 81.477000 191 1978 3 chr6A.!!$R3 1787

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
875 3897 0.250081 GATCCCCACCGATCTTCTGC 60.25 60.0 0.0 0.0 36.51 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2378 7923 0.109342 CCATGATCCCTTCCTTCCCG 59.891 60.0 0.0 0.0 0.0 5.14 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
66 71 3.126000 CAGGACGAAGAAAAATCCTCAGC 59.874 47.826 0.00 0.00 39.66 4.26
207 3003 6.348622 GGAAAGAAGAAGAAAAATCCTCGGTC 60.349 42.308 0.00 0.00 0.00 4.79
240 3037 2.350522 GCGTCATGAAACTCCACAGAT 58.649 47.619 0.00 0.00 0.00 2.90
293 3090 0.964358 GCAAGTTGCTGGCCTGATCT 60.964 55.000 20.71 4.94 40.96 2.75
430 3261 3.627577 TCCAGAAACAGAAACAGAAGCAC 59.372 43.478 0.00 0.00 0.00 4.40
518 3412 4.591202 CATGTATGCGTGTCTCCAATTTC 58.409 43.478 0.00 0.00 0.00 2.17
572 3479 5.329399 ACCAAAATCAAGGGCTATACACAA 58.671 37.500 0.00 0.00 0.00 3.33
831 3853 9.903185 CAGTATGTTCAGTATATACGTATCTCG 57.097 37.037 12.24 0.00 46.00 4.04
832 3854 8.602328 AGTATGTTCAGTATATACGTATCTCGC 58.398 37.037 12.24 1.57 44.19 5.03
833 3855 7.612668 ATGTTCAGTATATACGTATCTCGCT 57.387 36.000 12.24 3.89 44.19 4.93
834 3856 7.058298 TGTTCAGTATATACGTATCTCGCTC 57.942 40.000 12.24 0.00 44.19 5.03
835 3857 6.091849 TGTTCAGTATATACGTATCTCGCTCC 59.908 42.308 12.24 0.00 44.19 4.70
836 3858 5.975282 TCAGTATATACGTATCTCGCTCCT 58.025 41.667 12.24 0.00 44.19 3.69
837 3859 7.105241 TCAGTATATACGTATCTCGCTCCTA 57.895 40.000 12.24 0.00 44.19 2.94
838 3860 7.724287 TCAGTATATACGTATCTCGCTCCTAT 58.276 38.462 12.24 0.00 44.19 2.57
839 3861 7.652507 TCAGTATATACGTATCTCGCTCCTATG 59.347 40.741 12.24 0.00 44.19 2.23
840 3862 6.930164 AGTATATACGTATCTCGCTCCTATGG 59.070 42.308 12.24 0.00 44.19 2.74
841 3863 0.882474 ACGTATCTCGCTCCTATGGC 59.118 55.000 0.00 0.00 44.19 4.40
842 3864 0.881796 CGTATCTCGCTCCTATGGCA 59.118 55.000 0.00 0.00 0.00 4.92
843 3865 1.474478 CGTATCTCGCTCCTATGGCAT 59.526 52.381 4.88 4.88 0.00 4.40
844 3866 2.733542 CGTATCTCGCTCCTATGGCATG 60.734 54.545 10.98 0.00 0.00 4.06
845 3867 1.346062 ATCTCGCTCCTATGGCATGT 58.654 50.000 10.98 0.00 0.00 3.21
846 3868 0.676184 TCTCGCTCCTATGGCATGTC 59.324 55.000 10.98 0.00 0.00 3.06
847 3869 0.320247 CTCGCTCCTATGGCATGTCC 60.320 60.000 10.98 0.00 0.00 4.02
848 3870 1.665916 CGCTCCTATGGCATGTCCG 60.666 63.158 10.98 2.05 37.80 4.79
849 3871 1.302033 GCTCCTATGGCATGTCCGG 60.302 63.158 10.98 0.00 37.80 5.14
873 3895 1.418334 CTGATCCCCACCGATCTTCT 58.582 55.000 0.00 0.00 39.57 2.85
874 3896 1.069823 CTGATCCCCACCGATCTTCTG 59.930 57.143 0.00 0.00 39.57 3.02
875 3897 0.250081 GATCCCCACCGATCTTCTGC 60.250 60.000 0.00 0.00 36.51 4.26
876 3898 0.982852 ATCCCCACCGATCTTCTGCA 60.983 55.000 0.00 0.00 0.00 4.41
879 3901 1.541233 CCCCACCGATCTTCTGCATAC 60.541 57.143 0.00 0.00 0.00 2.39
881 3903 2.477825 CCACCGATCTTCTGCATACAG 58.522 52.381 0.00 0.00 45.95 2.74
882 3904 1.863454 CACCGATCTTCTGCATACAGC 59.137 52.381 0.00 0.00 44.10 4.40
910 3942 4.579340 GGGATTATTCGGGGAACTTCTTTC 59.421 45.833 0.00 0.00 0.00 2.62
1338 4405 3.127533 GTCGGGGAGCACATGCAC 61.128 66.667 6.64 0.00 45.16 4.57
1341 4408 2.821366 GGGGAGCACATGCACGAG 60.821 66.667 6.64 0.00 45.16 4.18
1359 4426 3.781307 CGACGGATCTTGGGGGCA 61.781 66.667 0.00 0.00 0.00 5.36
1389 4465 2.438795 GAGGGGCGAGACGAGACT 60.439 66.667 0.00 0.00 0.00 3.24
1535 4629 5.162892 ACATGATGAGAGATTAGAGGAGGGA 60.163 44.000 0.00 0.00 0.00 4.20
1536 4630 4.996793 TGATGAGAGATTAGAGGAGGGAG 58.003 47.826 0.00 0.00 0.00 4.30
1537 4631 3.893753 TGAGAGATTAGAGGAGGGAGG 57.106 52.381 0.00 0.00 0.00 4.30
1538 4632 3.135279 TGAGAGATTAGAGGAGGGAGGT 58.865 50.000 0.00 0.00 0.00 3.85
1539 4633 3.139397 TGAGAGATTAGAGGAGGGAGGTC 59.861 52.174 0.00 0.00 0.00 3.85
1571 4695 4.779733 GGACTCAGGAGGGGGCGA 62.780 72.222 0.83 0.00 0.00 5.54
1668 4811 0.249398 CCTCGATTTATAGGCCCGGG 59.751 60.000 19.09 19.09 0.00 5.73
1756 5450 2.042404 AACTCGGGTTGTGGGCGTAA 62.042 55.000 0.00 0.00 33.96 3.18
1798 5493 2.509569 TGCGATTCAAGGCAGGTAAAA 58.490 42.857 0.00 0.00 33.52 1.52
1810 5676 2.571212 CAGGTAAAATAGGGCGCATGA 58.429 47.619 10.83 0.00 0.00 3.07
1834 5708 8.359642 TGACAGCTTGCTTTGAATACTAATTTT 58.640 29.630 0.00 0.00 0.00 1.82
1881 5755 6.167685 TCTTGCATTACAAACCAGTACGTAT 58.832 36.000 0.00 0.00 37.96 3.06
1906 5928 6.868864 TCTTGCTAGTCATGTGAAAGAAGTAC 59.131 38.462 0.00 0.00 0.00 2.73
1992 6164 7.148722 GGACTGATTCGTAAGTTTCTCTTCTTG 60.149 40.741 0.00 0.00 37.56 3.02
1994 6166 7.382759 ACTGATTCGTAAGTTTCTCTTCTTGAC 59.617 37.037 0.00 0.00 37.56 3.18
2070 6242 4.465512 CGCGCATGTGCCAGTTCC 62.466 66.667 24.76 0.00 37.91 3.62
2071 6243 3.364441 GCGCATGTGCCAGTTCCA 61.364 61.111 20.70 0.00 37.91 3.53
2088 6260 2.607499 TCCACTGGAATTTGGCAATGT 58.393 42.857 0.00 0.00 32.37 2.71
2146 6323 3.096092 GCCTGGACCCATCACATTTTTA 58.904 45.455 0.00 0.00 0.00 1.52
2161 6338 9.715121 ATCACATTTTTAAGATGTTGCTTTCAT 57.285 25.926 0.00 0.00 35.64 2.57
2200 6378 0.685097 TGAAAGGACGGTCCCAGAAG 59.315 55.000 23.21 0.00 37.19 2.85
2224 7743 1.136500 AGGGAACTTATCTCCGAACGC 59.864 52.381 0.00 0.00 37.44 4.84
2281 7800 0.456221 ATGACCTGATCGACGTGACC 59.544 55.000 0.00 0.00 0.00 4.02
2283 7802 1.592400 GACCTGATCGACGTGACCCA 61.592 60.000 0.00 0.00 0.00 4.51
2356 7901 0.596600 TCTGAACGTTCGACACAGCC 60.597 55.000 22.48 0.00 0.00 4.85
2357 7902 1.557443 CTGAACGTTCGACACAGCCC 61.557 60.000 22.48 0.00 0.00 5.19
2358 7903 1.593209 GAACGTTCGACACAGCCCA 60.593 57.895 13.36 0.00 0.00 5.36
2359 7904 0.949105 GAACGTTCGACACAGCCCAT 60.949 55.000 13.36 0.00 0.00 4.00
2360 7905 1.227999 AACGTTCGACACAGCCCATG 61.228 55.000 0.00 0.00 0.00 3.66
2361 7906 1.667830 CGTTCGACACAGCCCATGT 60.668 57.895 0.00 0.00 45.43 3.21
2362 7907 0.389296 CGTTCGACACAGCCCATGTA 60.389 55.000 0.00 0.00 41.41 2.29
2363 7908 1.739035 CGTTCGACACAGCCCATGTAT 60.739 52.381 0.00 0.00 41.41 2.29
2364 7909 1.665679 GTTCGACACAGCCCATGTATG 59.334 52.381 0.00 0.00 41.41 2.39
2365 7910 0.901827 TCGACACAGCCCATGTATGT 59.098 50.000 0.00 0.00 41.41 2.29
2366 7911 1.277842 TCGACACAGCCCATGTATGTT 59.722 47.619 0.00 0.00 41.41 2.71
2367 7912 2.083774 CGACACAGCCCATGTATGTTT 58.916 47.619 0.00 0.00 41.41 2.83
2368 7913 2.159531 CGACACAGCCCATGTATGTTTG 60.160 50.000 0.00 0.00 41.41 2.93
2369 7914 1.545582 ACACAGCCCATGTATGTTTGC 59.454 47.619 0.00 0.00 41.41 3.68
2370 7915 1.820519 CACAGCCCATGTATGTTTGCT 59.179 47.619 0.00 0.00 41.41 3.91
2371 7916 1.820519 ACAGCCCATGTATGTTTGCTG 59.179 47.619 18.53 18.53 41.60 4.41
2372 7917 2.093890 CAGCCCATGTATGTTTGCTGA 58.906 47.619 16.65 0.00 41.48 4.26
2373 7918 2.098607 CAGCCCATGTATGTTTGCTGAG 59.901 50.000 16.65 0.00 41.48 3.35
2374 7919 2.094675 GCCCATGTATGTTTGCTGAGT 58.905 47.619 0.00 0.00 0.00 3.41
2375 7920 2.098117 GCCCATGTATGTTTGCTGAGTC 59.902 50.000 0.00 0.00 0.00 3.36
2376 7921 2.684881 CCCATGTATGTTTGCTGAGTCC 59.315 50.000 0.00 0.00 0.00 3.85
2377 7922 2.352651 CCATGTATGTTTGCTGAGTCCG 59.647 50.000 0.00 0.00 0.00 4.79
2378 7923 1.438651 TGTATGTTTGCTGAGTCCGC 58.561 50.000 0.00 0.00 0.00 5.54
2379 7924 0.370273 GTATGTTTGCTGAGTCCGCG 59.630 55.000 0.00 0.00 0.00 6.46
2380 7925 0.739462 TATGTTTGCTGAGTCCGCGG 60.739 55.000 22.12 22.12 0.00 6.46
2381 7926 3.423154 GTTTGCTGAGTCCGCGGG 61.423 66.667 27.83 10.00 0.00 6.13
2382 7927 3.621805 TTTGCTGAGTCCGCGGGA 61.622 61.111 27.83 9.51 0.00 5.14
2383 7928 3.171828 TTTGCTGAGTCCGCGGGAA 62.172 57.895 27.83 3.06 31.38 3.97
2384 7929 3.589654 TTGCTGAGTCCGCGGGAAG 62.590 63.158 27.83 17.96 31.38 3.46
2385 7930 4.821589 GCTGAGTCCGCGGGAAGG 62.822 72.222 27.83 13.06 31.38 3.46
2386 7931 3.068691 CTGAGTCCGCGGGAAGGA 61.069 66.667 27.83 1.12 31.38 3.36
2387 7932 2.602267 TGAGTCCGCGGGAAGGAA 60.602 61.111 27.83 0.17 39.84 3.36
2388 7933 2.184579 GAGTCCGCGGGAAGGAAG 59.815 66.667 27.83 0.00 39.84 3.46
2389 7934 3.372554 GAGTCCGCGGGAAGGAAGG 62.373 68.421 27.83 0.00 39.84 3.46
2390 7935 4.468689 GTCCGCGGGAAGGAAGGG 62.469 72.222 27.83 0.00 39.84 3.95
2391 7936 4.707768 TCCGCGGGAAGGAAGGGA 62.708 66.667 27.83 0.00 34.33 4.20
2392 7937 3.480133 CCGCGGGAAGGAAGGGAT 61.480 66.667 20.10 0.00 0.00 3.85
2393 7938 2.109181 CGCGGGAAGGAAGGGATC 59.891 66.667 0.00 0.00 0.00 3.36
2394 7939 2.731571 CGCGGGAAGGAAGGGATCA 61.732 63.158 0.00 0.00 0.00 2.92
2395 7940 1.839894 GCGGGAAGGAAGGGATCAT 59.160 57.895 0.00 0.00 0.00 2.45
2396 7941 0.536006 GCGGGAAGGAAGGGATCATG 60.536 60.000 0.00 0.00 0.00 3.07
2397 7942 0.109342 CGGGAAGGAAGGGATCATGG 59.891 60.000 0.00 0.00 0.00 3.66
2398 7943 1.522900 GGGAAGGAAGGGATCATGGA 58.477 55.000 0.00 0.00 0.00 3.41
2399 7944 1.423161 GGGAAGGAAGGGATCATGGAG 59.577 57.143 0.00 0.00 0.00 3.86
2400 7945 2.131023 GGAAGGAAGGGATCATGGAGT 58.869 52.381 0.00 0.00 0.00 3.85
2401 7946 2.158696 GGAAGGAAGGGATCATGGAGTG 60.159 54.545 0.00 0.00 0.00 3.51
2402 7947 1.516110 AGGAAGGGATCATGGAGTGG 58.484 55.000 0.00 0.00 0.00 4.00
2403 7948 1.010046 AGGAAGGGATCATGGAGTGGA 59.990 52.381 0.00 0.00 0.00 4.02
2404 7949 1.419387 GGAAGGGATCATGGAGTGGAG 59.581 57.143 0.00 0.00 0.00 3.86
2405 7950 0.842635 AAGGGATCATGGAGTGGAGC 59.157 55.000 0.00 0.00 0.00 4.70
2406 7951 1.059006 AGGGATCATGGAGTGGAGCC 61.059 60.000 0.00 0.00 38.84 4.70
2407 7952 1.070445 GGATCATGGAGTGGAGCCG 59.930 63.158 0.00 0.00 28.87 5.52
2408 7953 1.070445 GATCATGGAGTGGAGCCGG 59.930 63.158 0.00 0.00 0.00 6.13
2409 7954 3.112205 ATCATGGAGTGGAGCCGGC 62.112 63.158 21.89 21.89 0.00 6.13
2413 7958 3.224324 GGAGTGGAGCCGGCGATA 61.224 66.667 23.20 8.27 0.00 2.92
2414 7959 2.792947 GGAGTGGAGCCGGCGATAA 61.793 63.158 23.20 5.29 0.00 1.75
2415 7960 1.367840 GAGTGGAGCCGGCGATAAT 59.632 57.895 23.20 10.38 0.00 1.28
2416 7961 0.667792 GAGTGGAGCCGGCGATAATC 60.668 60.000 23.20 15.63 0.00 1.75
2417 7962 2.022129 GTGGAGCCGGCGATAATCG 61.022 63.158 23.20 0.00 43.89 3.34
2443 7988 3.315521 CGCCATCGCTCTCGTTCG 61.316 66.667 0.00 0.00 36.96 3.95
2444 7989 2.202623 GCCATCGCTCTCGTTCGT 60.203 61.111 0.00 0.00 36.96 3.85
2445 7990 2.224885 GCCATCGCTCTCGTTCGTC 61.225 63.158 0.00 0.00 36.96 4.20
2446 7991 1.586564 CCATCGCTCTCGTTCGTCC 60.587 63.158 0.00 0.00 36.96 4.79
2447 7992 1.934956 CATCGCTCTCGTTCGTCCG 60.935 63.158 0.00 0.00 36.96 4.79
2448 7993 3.109612 ATCGCTCTCGTTCGTCCGG 62.110 63.158 0.00 0.00 36.96 5.14
2449 7994 4.099170 CGCTCTCGTTCGTCCGGT 62.099 66.667 0.00 0.00 0.00 5.28
2450 7995 2.504244 GCTCTCGTTCGTCCGGTG 60.504 66.667 0.00 0.00 0.00 4.94
2451 7996 2.952245 CTCTCGTTCGTCCGGTGT 59.048 61.111 0.00 0.00 0.00 4.16
2452 7997 1.915614 GCTCTCGTTCGTCCGGTGTA 61.916 60.000 0.00 0.00 0.00 2.90
2453 7998 0.731417 CTCTCGTTCGTCCGGTGTAT 59.269 55.000 0.00 0.00 0.00 2.29
2454 7999 0.448990 TCTCGTTCGTCCGGTGTATG 59.551 55.000 0.00 0.00 0.00 2.39
2455 8000 1.138047 CTCGTTCGTCCGGTGTATGC 61.138 60.000 0.00 0.00 0.00 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
179 2975 6.879458 CGAGGATTTTTCTTCTTCTTTCCCTA 59.121 38.462 0.00 0.00 0.00 3.53
240 3037 1.071228 TCCTCCGATTCCGACGAGATA 59.929 52.381 0.00 0.00 38.22 1.98
430 3261 2.200067 TGATTTGCCGCAACAACTTTG 58.800 42.857 4.98 0.00 0.00 2.77
572 3479 2.752238 CTCGTCCTCTCTGCCCGT 60.752 66.667 0.00 0.00 0.00 5.28
602 3552 2.826128 TCGTCTCTGCTCCACTTGTAAT 59.174 45.455 0.00 0.00 0.00 1.89
603 3553 2.030185 GTCGTCTCTGCTCCACTTGTAA 60.030 50.000 0.00 0.00 0.00 2.41
652 3619 1.829849 CAGTGAGCCTCATCTTCCTCA 59.170 52.381 0.00 0.00 32.35 3.86
820 3842 2.683867 GCCATAGGAGCGAGATACGTAT 59.316 50.000 8.05 8.05 44.60 3.06
824 3846 2.232452 ACATGCCATAGGAGCGAGATAC 59.768 50.000 0.00 0.00 0.00 2.24
825 3847 2.493675 GACATGCCATAGGAGCGAGATA 59.506 50.000 0.00 0.00 0.00 1.98
826 3848 1.274728 GACATGCCATAGGAGCGAGAT 59.725 52.381 0.00 0.00 0.00 2.75
827 3849 0.676184 GACATGCCATAGGAGCGAGA 59.324 55.000 0.00 0.00 0.00 4.04
828 3850 0.320247 GGACATGCCATAGGAGCGAG 60.320 60.000 0.00 0.00 36.34 5.03
829 3851 1.748403 GGACATGCCATAGGAGCGA 59.252 57.895 0.00 0.00 36.34 4.93
830 3852 1.665916 CGGACATGCCATAGGAGCG 60.666 63.158 0.00 0.00 35.94 5.03
831 3853 1.302033 CCGGACATGCCATAGGAGC 60.302 63.158 0.00 0.00 35.94 4.70
832 3854 1.302033 GCCGGACATGCCATAGGAG 60.302 63.158 5.05 0.00 35.94 3.69
833 3855 2.828868 GCCGGACATGCCATAGGA 59.171 61.111 5.05 0.00 35.94 2.94
834 3856 2.666190 CGCCGGACATGCCATAGG 60.666 66.667 5.05 0.00 35.94 2.57
835 3857 2.666190 CCGCCGGACATGCCATAG 60.666 66.667 5.05 0.00 35.94 2.23
836 3858 4.927782 GCCGCCGGACATGCCATA 62.928 66.667 7.68 0.00 35.94 2.74
841 3863 4.552365 ATCAGGCCGCCGGACATG 62.552 66.667 13.69 8.94 29.21 3.21
842 3864 4.241555 GATCAGGCCGCCGGACAT 62.242 66.667 13.69 0.00 29.21 3.06
873 3895 0.107897 AATCCCGTTCGCTGTATGCA 60.108 50.000 0.00 0.00 43.06 3.96
874 3896 1.860676 TAATCCCGTTCGCTGTATGC 58.139 50.000 0.00 0.00 38.57 3.14
875 3897 3.121279 CGAATAATCCCGTTCGCTGTATG 59.879 47.826 0.00 0.00 40.39 2.39
876 3898 3.314553 CGAATAATCCCGTTCGCTGTAT 58.685 45.455 0.00 0.00 40.39 2.29
879 3901 0.859232 CCGAATAATCCCGTTCGCTG 59.141 55.000 2.28 0.00 44.19 5.18
881 3903 1.226030 CCCCGAATAATCCCGTTCGC 61.226 60.000 2.28 0.00 44.19 4.70
882 3904 0.390124 TCCCCGAATAATCCCGTTCG 59.610 55.000 0.91 0.91 44.89 3.95
883 3905 2.158856 AGTTCCCCGAATAATCCCGTTC 60.159 50.000 0.00 0.00 0.00 3.95
884 3906 1.841919 AGTTCCCCGAATAATCCCGTT 59.158 47.619 0.00 0.00 0.00 4.44
887 3919 3.859061 AGAAGTTCCCCGAATAATCCC 57.141 47.619 0.00 0.00 0.00 3.85
910 3942 5.689383 ACTGCACAAAAACTGTACATAGG 57.311 39.130 0.00 0.00 36.10 2.57
921 3953 7.661127 AAGATACGTACATACTGCACAAAAA 57.339 32.000 0.00 0.00 0.00 1.94
922 3954 7.514805 CAAAGATACGTACATACTGCACAAAA 58.485 34.615 0.00 0.00 0.00 2.44
1338 4405 2.278857 CCCAAGATCCGTCGCTCG 60.279 66.667 0.00 0.00 39.52 5.03
1378 4454 0.736672 TCCGTCAGAGTCTCGTCTCG 60.737 60.000 0.00 0.00 39.21 4.04
1503 4594 0.101219 CTCTCATCATGTCGACGGCA 59.899 55.000 3.85 3.85 0.00 5.69
1535 4629 1.757306 CAACTGCTCCACCTGACCT 59.243 57.895 0.00 0.00 0.00 3.85
1536 4630 1.302832 CCAACTGCTCCACCTGACC 60.303 63.158 0.00 0.00 0.00 4.02
1537 4631 1.302832 CCCAACTGCTCCACCTGAC 60.303 63.158 0.00 0.00 0.00 3.51
1538 4632 1.461268 TCCCAACTGCTCCACCTGA 60.461 57.895 0.00 0.00 0.00 3.86
1539 4633 1.302832 GTCCCAACTGCTCCACCTG 60.303 63.158 0.00 0.00 0.00 4.00
1571 4695 4.012374 CTCAACTGACATACCAAAGCCAT 58.988 43.478 0.00 0.00 0.00 4.40
1622 4763 1.473434 GGCTCCCATCTCAGTTTACCG 60.473 57.143 0.00 0.00 0.00 4.02
1668 4811 2.123033 GCCCCTCCTCTCTCCCTC 60.123 72.222 0.00 0.00 0.00 4.30
1673 4816 1.204113 CCAAACTGCCCCTCCTCTCT 61.204 60.000 0.00 0.00 0.00 3.10
1747 5410 3.431725 GTGCTGCCTTACGCCCAC 61.432 66.667 0.00 0.00 36.24 4.61
1756 5450 2.045926 GATTCCGGTGTGCTGCCT 60.046 61.111 0.00 0.00 0.00 4.75
1793 5487 2.287009 GCTGTCATGCGCCCTATTTTAC 60.287 50.000 4.18 0.00 0.00 2.01
1794 5488 1.946768 GCTGTCATGCGCCCTATTTTA 59.053 47.619 4.18 0.00 0.00 1.52
1798 5493 0.816825 CAAGCTGTCATGCGCCCTAT 60.817 55.000 4.18 0.00 38.13 2.57
1810 5676 9.846248 CTAAAATTAGTATTCAAAGCAAGCTGT 57.154 29.630 0.00 0.00 0.00 4.40
1834 5708 8.463930 AGAAATTGACCAGAATTTTGACACTA 57.536 30.769 0.00 0.00 36.00 2.74
1881 5755 5.858381 ACTTCTTTCACATGACTAGCAAGA 58.142 37.500 0.00 0.00 0.00 3.02
1925 6088 6.537355 ACCATATGTTCCGATTCATTGATCT 58.463 36.000 1.24 0.00 0.00 2.75
1926 6089 6.808008 ACCATATGTTCCGATTCATTGATC 57.192 37.500 1.24 0.00 0.00 2.92
1994 6166 4.154918 GCTCCTCCTGTATGACACTTTTTG 59.845 45.833 0.00 0.00 0.00 2.44
2070 6242 2.228582 TCGACATTGCCAAATTCCAGTG 59.771 45.455 0.00 0.00 0.00 3.66
2071 6243 2.228822 GTCGACATTGCCAAATTCCAGT 59.771 45.455 11.55 0.00 0.00 4.00
2080 6252 0.742990 GAATCGGGTCGACATTGCCA 60.743 55.000 18.91 1.04 39.18 4.92
2088 6260 3.066190 ACGCAGGAATCGGGTCGA 61.066 61.111 0.00 0.00 41.13 4.20
2119 6296 0.409092 TGATGGGTCCAGGCACAAAT 59.591 50.000 0.00 0.00 0.00 2.32
2120 6297 0.539438 GTGATGGGTCCAGGCACAAA 60.539 55.000 16.05 0.00 36.14 2.83
2146 6323 5.010617 ACCGGTTTAATGAAAGCAACATCTT 59.989 36.000 0.00 0.00 42.10 2.40
2200 6378 4.329256 CGTTCGGAGATAAGTTCCCTTTTC 59.671 45.833 0.00 0.00 35.04 2.29
2224 7743 1.674764 ATCACCTGCCTCGCTCTGAG 61.675 60.000 0.00 0.00 44.83 3.35
2356 7901 2.352651 CGGACTCAGCAAACATACATGG 59.647 50.000 0.00 0.00 0.00 3.66
2357 7902 2.223112 GCGGACTCAGCAAACATACATG 60.223 50.000 0.00 0.00 34.19 3.21
2358 7903 2.009774 GCGGACTCAGCAAACATACAT 58.990 47.619 0.00 0.00 34.19 2.29
2359 7904 1.438651 GCGGACTCAGCAAACATACA 58.561 50.000 0.00 0.00 34.19 2.29
2360 7905 0.370273 CGCGGACTCAGCAAACATAC 59.630 55.000 0.00 0.00 34.19 2.39
2361 7906 0.739462 CCGCGGACTCAGCAAACATA 60.739 55.000 24.07 0.00 34.19 2.29
2362 7907 2.034879 CCGCGGACTCAGCAAACAT 61.035 57.895 24.07 0.00 34.19 2.71
2363 7908 2.664851 CCGCGGACTCAGCAAACA 60.665 61.111 24.07 0.00 34.19 2.83
2364 7909 3.423154 CCCGCGGACTCAGCAAAC 61.423 66.667 30.73 0.00 34.19 2.93
2365 7910 3.171828 TTCCCGCGGACTCAGCAAA 62.172 57.895 30.73 4.44 34.19 3.68
2366 7911 3.589654 CTTCCCGCGGACTCAGCAA 62.590 63.158 30.73 6.19 34.19 3.91
2367 7912 4.069232 CTTCCCGCGGACTCAGCA 62.069 66.667 30.73 0.00 34.19 4.41
2368 7913 4.821589 CCTTCCCGCGGACTCAGC 62.822 72.222 30.73 0.00 0.00 4.26
2369 7914 2.564553 CTTCCTTCCCGCGGACTCAG 62.565 65.000 30.73 15.89 0.00 3.35
2370 7915 2.602267 TTCCTTCCCGCGGACTCA 60.602 61.111 30.73 3.99 0.00 3.41
2371 7916 2.184579 CTTCCTTCCCGCGGACTC 59.815 66.667 30.73 0.00 0.00 3.36
2372 7917 3.391382 CCTTCCTTCCCGCGGACT 61.391 66.667 30.73 0.00 0.00 3.85
2373 7918 4.468689 CCCTTCCTTCCCGCGGAC 62.469 72.222 30.73 0.00 0.00 4.79
2374 7919 3.995809 ATCCCTTCCTTCCCGCGGA 62.996 63.158 30.73 10.38 0.00 5.54
2375 7920 3.462199 GATCCCTTCCTTCCCGCGG 62.462 68.421 21.04 21.04 0.00 6.46
2376 7921 2.044806 ATGATCCCTTCCTTCCCGCG 62.045 60.000 0.00 0.00 0.00 6.46
2377 7922 0.536006 CATGATCCCTTCCTTCCCGC 60.536 60.000 0.00 0.00 0.00 6.13
2378 7923 0.109342 CCATGATCCCTTCCTTCCCG 59.891 60.000 0.00 0.00 0.00 5.14
2379 7924 1.423161 CTCCATGATCCCTTCCTTCCC 59.577 57.143 0.00 0.00 0.00 3.97
2380 7925 2.131023 ACTCCATGATCCCTTCCTTCC 58.869 52.381 0.00 0.00 0.00 3.46
2381 7926 2.158696 CCACTCCATGATCCCTTCCTTC 60.159 54.545 0.00 0.00 0.00 3.46
2382 7927 1.849039 CCACTCCATGATCCCTTCCTT 59.151 52.381 0.00 0.00 0.00 3.36
2383 7928 1.010046 TCCACTCCATGATCCCTTCCT 59.990 52.381 0.00 0.00 0.00 3.36
2384 7929 1.419387 CTCCACTCCATGATCCCTTCC 59.581 57.143 0.00 0.00 0.00 3.46
2385 7930 1.202746 GCTCCACTCCATGATCCCTTC 60.203 57.143 0.00 0.00 0.00 3.46
2386 7931 0.842635 GCTCCACTCCATGATCCCTT 59.157 55.000 0.00 0.00 0.00 3.95
2387 7932 1.059006 GGCTCCACTCCATGATCCCT 61.059 60.000 0.00 0.00 0.00 4.20
2388 7933 1.453669 GGCTCCACTCCATGATCCC 59.546 63.158 0.00 0.00 0.00 3.85
2389 7934 1.070445 CGGCTCCACTCCATGATCC 59.930 63.158 0.00 0.00 0.00 3.36
2390 7935 1.070445 CCGGCTCCACTCCATGATC 59.930 63.158 0.00 0.00 0.00 2.92
2391 7936 3.112205 GCCGGCTCCACTCCATGAT 62.112 63.158 22.15 0.00 0.00 2.45
2392 7937 3.785859 GCCGGCTCCACTCCATGA 61.786 66.667 22.15 0.00 0.00 3.07
2396 7941 2.100879 ATTATCGCCGGCTCCACTCC 62.101 60.000 26.68 0.00 0.00 3.85
2397 7942 0.667792 GATTATCGCCGGCTCCACTC 60.668 60.000 26.68 11.97 0.00 3.51
2398 7943 1.367840 GATTATCGCCGGCTCCACT 59.632 57.895 26.68 6.09 0.00 4.00
2399 7944 2.022129 CGATTATCGCCGGCTCCAC 61.022 63.158 26.68 9.80 31.14 4.02
2400 7945 2.338620 CGATTATCGCCGGCTCCA 59.661 61.111 26.68 8.65 31.14 3.86
2409 7954 4.059459 GCGGTGGCGCGATTATCG 62.059 66.667 12.10 10.56 43.89 2.92
2426 7971 3.315521 CGAACGAGAGCGATGGCG 61.316 66.667 0.00 0.00 46.35 5.69
2427 7972 2.202623 ACGAACGAGAGCGATGGC 60.203 61.111 0.14 0.00 41.64 4.40
2428 7973 1.586564 GGACGAACGAGAGCGATGG 60.587 63.158 0.14 0.00 41.64 3.51
2429 7974 1.934956 CGGACGAACGAGAGCGATG 60.935 63.158 0.14 0.00 41.64 3.84
2430 7975 2.403987 CGGACGAACGAGAGCGAT 59.596 61.111 0.14 0.00 41.64 4.58
2431 7976 3.796443 CCGGACGAACGAGAGCGA 61.796 66.667 0.00 0.00 41.64 4.93
2432 7977 4.099170 ACCGGACGAACGAGAGCG 62.099 66.667 9.46 0.00 44.79 5.03
2433 7978 1.915614 TACACCGGACGAACGAGAGC 61.916 60.000 9.46 0.00 35.47 4.09
2434 7979 0.731417 ATACACCGGACGAACGAGAG 59.269 55.000 9.46 0.00 35.47 3.20
2435 7980 0.448990 CATACACCGGACGAACGAGA 59.551 55.000 9.46 0.00 35.47 4.04
2436 7981 1.138047 GCATACACCGGACGAACGAG 61.138 60.000 9.46 0.00 35.47 4.18
2437 7982 1.153978 GCATACACCGGACGAACGA 60.154 57.895 9.46 0.00 35.47 3.85
2438 7983 3.380671 GCATACACCGGACGAACG 58.619 61.111 9.46 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.