Multiple sequence alignment - TraesCS6D01G053300

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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 TraesCS6D01G053300 chr6D 100.000 4800 0 0 1 4800 25651056 25646257 0.000000e+00 8865.0
1 TraesCS6D01G053300 chr6D 83.333 1392 200 19 2543 3912 25641048 25639667 0.000000e+00 1256.0
2 TraesCS6D01G053300 chr6D 88.953 172 16 3 4106 4277 25639659 25639491 4.870000e-50 209.0
3 TraesCS6D01G053300 chr6D 81.982 222 34 3 2143 2359 25641566 25641346 2.950000e-42 183.0
4 TraesCS6D01G053300 chr6D 78.818 203 35 8 4440 4637 355273747 355273548 3.900000e-26 130.0
5 TraesCS6D01G053300 chr6D 80.000 195 22 13 61 245 20389799 20389612 1.400000e-25 128.0
6 TraesCS6D01G053300 chr6D 82.517 143 19 4 3950 4091 350516757 350516620 2.350000e-23 121.0
7 TraesCS6D01G053300 chr6D 97.561 41 1 0 1826 1866 25649190 25649150 2.400000e-08 71.3
8 TraesCS6D01G053300 chr6D 97.561 41 1 0 1867 1907 25649231 25649191 2.400000e-08 71.3
9 TraesCS6D01G053300 chr6A 95.007 2944 126 15 1867 4800 23678870 23675938 0.000000e+00 4602.0
10 TraesCS6D01G053300 chr6A 81.782 1740 246 42 2105 3819 24772327 24770634 0.000000e+00 1391.0
11 TraesCS6D01G053300 chr6A 83.041 1427 210 21 2545 3949 23652890 23651474 0.000000e+00 1266.0
12 TraesCS6D01G053300 chr6A 82.472 1432 220 19 2543 3954 23636878 23635458 0.000000e+00 1225.0
13 TraesCS6D01G053300 chr6A 85.423 933 63 30 1 876 23680886 23679970 0.000000e+00 902.0
14 TraesCS6D01G053300 chr6A 86.472 377 42 3 1494 1866 23679201 23678830 5.780000e-109 405.0
15 TraesCS6D01G053300 chr6A 86.702 188 23 2 4090 4277 23635478 23635293 1.750000e-49 207.0
16 TraesCS6D01G053300 chr6A 82.629 213 24 12 54 257 101366199 101365991 4.940000e-40 176.0
17 TraesCS6D01G053300 chr6A 81.667 120 12 8 1742 1856 23637978 23637864 1.840000e-14 91.6
18 TraesCS6D01G053300 chr6B 95.498 2488 91 9 1251 3734 41457721 41455251 0.000000e+00 3954.0
19 TraesCS6D01G053300 chr6B 82.126 1740 242 38 2105 3819 43223992 43222297 0.000000e+00 1426.0
20 TraesCS6D01G053300 chr6B 82.905 1439 208 29 2543 3954 41448051 41446624 0.000000e+00 1260.0
21 TraesCS6D01G053300 chr6B 95.670 716 26 4 4090 4800 41454777 41454062 0.000000e+00 1146.0
22 TraesCS6D01G053300 chr6B 85.243 637 36 23 625 1242 41458382 41457785 1.910000e-168 603.0
23 TraesCS6D01G053300 chr6B 95.982 224 7 2 3731 3954 41454978 41454757 3.530000e-96 363.0
24 TraesCS6D01G053300 chr6B 88.298 188 20 2 4090 4277 41446644 41446459 1.740000e-54 224.0
25 TraesCS6D01G053300 chr6B 78.571 168 34 2 4440 4605 522421214 522421381 5.080000e-20 110.0
26 TraesCS6D01G053300 chr6B 97.368 38 1 0 1867 1904 41457145 41457108 1.120000e-06 65.8
27 TraesCS6D01G053300 chr6B 94.444 36 2 0 1831 1866 41457107 41457072 6.710000e-04 56.5
28 TraesCS6D01G053300 chrUn 82.051 1716 243 34 2105 3799 94023983 94022312 0.000000e+00 1402.0
29 TraesCS6D01G053300 chrUn 81.302 1690 274 24 2141 3797 93844647 93846327 0.000000e+00 1332.0
30 TraesCS6D01G053300 chrUn 76.636 214 30 17 61 260 48586424 48586631 3.060000e-17 100.0
31 TraesCS6D01G053300 chrUn 75.814 215 36 13 58 260 48607170 48607380 1.420000e-15 95.3
32 TraesCS6D01G053300 chrUn 82.653 98 12 5 3996 4091 119813330 119813424 1.110000e-11 82.4
33 TraesCS6D01G053300 chrUn 100.000 28 0 0 1252 1279 386260205 386260232 9.000000e-03 52.8
34 TraesCS6D01G053300 chr7A 89.091 110 8 4 53 161 512259035 512258929 3.010000e-27 134.0
35 TraesCS6D01G053300 chr5D 79.703 202 23 15 67 258 496954253 496954446 3.900000e-26 130.0
36 TraesCS6D01G053300 chr5D 85.366 82 9 3 4011 4091 27094074 27094153 1.110000e-11 82.4
37 TraesCS6D01G053300 chr5A 82.353 153 19 7 3944 4091 17438238 17438089 5.040000e-25 126.0
38 TraesCS6D01G053300 chr3B 81.757 148 17 10 3948 4091 377108265 377108406 1.090000e-21 115.0
39 TraesCS6D01G053300 chr2D 81.457 151 17 6 98 241 144457562 144457416 3.930000e-21 113.0
40 TraesCS6D01G053300 chr2D 81.119 143 15 9 3951 4088 62556580 62556715 2.360000e-18 104.0
41 TraesCS6D01G053300 chr2D 89.873 79 6 2 4013 4091 483870933 483871009 3.060000e-17 100.0
42 TraesCS6D01G053300 chr2D 96.970 33 1 0 1512 1544 630427849 630427817 6.710000e-04 56.5
43 TraesCS6D01G053300 chr1B 79.630 162 21 9 53 208 642732662 642732507 6.570000e-19 106.0
44 TraesCS6D01G053300 chr3D 80.420 143 22 6 3950 4089 255393316 255393455 2.360000e-18 104.0
45 TraesCS6D01G053300 chr2B 81.395 86 9 5 2860 2940 761279920 761279837 4.010000e-06 63.9
46 TraesCS6D01G053300 chr2B 100.000 28 0 0 1252 1279 714254249 714254222 9.000000e-03 52.8
47 TraesCS6D01G053300 chr2B 100.000 28 0 0 1252 1279 714254647 714254620 9.000000e-03 52.8
48 TraesCS6D01G053300 chr2B 100.000 28 0 0 1252 1279 714255963 714255936 9.000000e-03 52.8
49 TraesCS6D01G053300 chr2B 100.000 28 0 0 1252 1279 714309643 714309616 9.000000e-03 52.8
50 TraesCS6D01G053300 chr2B 100.000 28 0 0 1252 1279 714310958 714310931 9.000000e-03 52.8
51 TraesCS6D01G053300 chr1A 100.000 29 0 0 1251 1279 39184715 39184743 2.000000e-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 TraesCS6D01G053300 chr6D 25646257 25651056 4799 True 3002.533333 8865 98.374000 1 4800 3 chr6D.!!$R5 4799
1 TraesCS6D01G053300 chr6D 25639491 25641566 2075 True 549.333333 1256 84.756000 2143 4277 3 chr6D.!!$R4 2134
2 TraesCS6D01G053300 chr6A 23675938 23680886 4948 True 1969.666667 4602 88.967333 1 4800 3 chr6A.!!$R5 4799
3 TraesCS6D01G053300 chr6A 24770634 24772327 1693 True 1391.000000 1391 81.782000 2105 3819 1 chr6A.!!$R2 1714
4 TraesCS6D01G053300 chr6A 23651474 23652890 1416 True 1266.000000 1266 83.041000 2545 3949 1 chr6A.!!$R1 1404
5 TraesCS6D01G053300 chr6A 23635293 23637978 2685 True 507.866667 1225 83.613667 1742 4277 3 chr6A.!!$R4 2535
6 TraesCS6D01G053300 chr6B 43222297 43223992 1695 True 1426.000000 1426 82.126000 2105 3819 1 chr6B.!!$R1 1714
7 TraesCS6D01G053300 chr6B 41454062 41458382 4320 True 1031.383333 3954 94.034167 625 4800 6 chr6B.!!$R3 4175
8 TraesCS6D01G053300 chr6B 41446459 41448051 1592 True 742.000000 1260 85.601500 2543 4277 2 chr6B.!!$R2 1734
9 TraesCS6D01G053300 chrUn 94022312 94023983 1671 True 1402.000000 1402 82.051000 2105 3799 1 chrUn.!!$R1 1694
10 TraesCS6D01G053300 chrUn 93844647 93846327 1680 False 1332.000000 1332 81.302000 2141 3797 1 chrUn.!!$F3 1656

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
764 794 0.034616 GATCTGGAGGAGGGCAATCG 59.965 60.0 0.0 0.0 0.0 3.34 F
1839 2313 0.036010 CCTGCTTCGATCACAACCCT 60.036 55.0 0.0 0.0 0.0 4.34 F
1849 2323 0.843309 TCACAACCCTCTCCAAAGCA 59.157 50.0 0.0 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1872 2346 0.036010 ATGCTTTGGAGAGGGTCGTG 60.036 55.0 0.0 0.0 0.0 4.35 R
3338 4292 0.659957 GATCGGATGACTTTGCAGGC 59.340 55.0 0.0 0.0 0.0 4.85 R
3882 5119 7.831691 TGTCCATCCAAGATTGAACTAAAAA 57.168 32.0 0.0 0.0 0.0 1.94 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
275 282 2.656069 GCAGGAGGGGTTGTCGCTA 61.656 63.158 0.00 0.00 38.88 4.26
290 297 0.877649 CGCTATTCGATGTGCCAGCT 60.878 55.000 0.00 0.00 41.67 4.24
321 328 2.236893 TCGGCTTTTTCCTACCGGTAAT 59.763 45.455 16.65 0.00 45.65 1.89
348 355 2.550180 GCTTCCGAGCTTTTTCTTCTGT 59.450 45.455 0.00 0.00 45.65 3.41
391 398 2.023673 TGTTGCTCTGTTTTCTGTGGG 58.976 47.619 0.00 0.00 0.00 4.61
396 403 3.513515 TGCTCTGTTTTCTGTGGGTTTTT 59.486 39.130 0.00 0.00 0.00 1.94
499 507 6.937436 TTTTGACTAGTCCTTTTTCCAGAC 57.063 37.500 20.11 0.00 0.00 3.51
501 509 5.623956 TGACTAGTCCTTTTTCCAGACAA 57.376 39.130 20.11 0.00 32.82 3.18
504 512 7.741785 TGACTAGTCCTTTTTCCAGACAATTA 58.258 34.615 20.11 0.00 32.82 1.40
538 547 1.754745 GTGTGGGAAGAGCAGACCA 59.245 57.895 0.00 0.00 0.00 4.02
545 554 3.335356 AAGAGCAGACCATGGGCCG 62.335 63.158 16.13 4.74 0.00 6.13
571 580 1.202521 TCGCATACCGCACAATCATCT 60.203 47.619 0.00 0.00 42.60 2.90
642 663 4.142469 CCCCTAAAAATTACTCGCACTTGG 60.142 45.833 0.00 0.00 0.00 3.61
744 774 1.759445 GCAGAGCTGGATAGGAGTTGA 59.241 52.381 0.00 0.00 0.00 3.18
751 781 3.006752 GCTGGATAGGAGTTGAGATCTGG 59.993 52.174 0.00 0.00 0.00 3.86
759 789 0.467804 GTTGAGATCTGGAGGAGGGC 59.532 60.000 0.00 0.00 0.00 5.19
760 790 0.043183 TTGAGATCTGGAGGAGGGCA 59.957 55.000 0.00 0.00 0.00 5.36
761 791 0.043183 TGAGATCTGGAGGAGGGCAA 59.957 55.000 0.00 0.00 0.00 4.52
762 792 1.344803 TGAGATCTGGAGGAGGGCAAT 60.345 52.381 0.00 0.00 0.00 3.56
763 793 1.347378 GAGATCTGGAGGAGGGCAATC 59.653 57.143 0.00 0.00 0.00 2.67
764 794 0.034616 GATCTGGAGGAGGGCAATCG 59.965 60.000 0.00 0.00 0.00 3.34
765 795 0.399091 ATCTGGAGGAGGGCAATCGA 60.399 55.000 0.00 0.00 0.00 3.59
767 797 2.110006 GGAGGAGGGCAATCGAGC 59.890 66.667 0.00 0.00 0.00 5.03
768 798 2.439104 GGAGGAGGGCAATCGAGCT 61.439 63.158 0.00 0.00 34.17 4.09
770 800 2.899339 GGAGGGCAATCGAGCTGC 60.899 66.667 12.66 12.66 39.16 5.25
781 820 2.588439 GAGCTGCTGCCAGATCCA 59.412 61.111 7.01 0.00 46.20 3.41
798 837 1.700042 CCAATCCGAGGGAGGAAGGG 61.700 65.000 0.00 0.00 44.50 3.95
802 841 2.722201 CCGAGGGAGGAAGGGTTCG 61.722 68.421 0.00 0.00 0.00 3.95
817 856 3.884581 TTCGTTCGTCGGCCACTCG 62.885 63.158 2.24 4.00 40.32 4.18
822 861 4.498520 CGTCGGCCACTCGCTCAT 62.499 66.667 2.24 0.00 37.74 2.90
823 862 2.125512 GTCGGCCACTCGCTCATT 60.126 61.111 2.24 0.00 37.74 2.57
824 863 1.141019 GTCGGCCACTCGCTCATTA 59.859 57.895 2.24 0.00 37.74 1.90
825 864 0.872021 GTCGGCCACTCGCTCATTAG 60.872 60.000 2.24 0.00 37.74 1.73
892 950 1.299648 GTGACACCCTGCCTGCATA 59.700 57.895 0.00 0.00 0.00 3.14
899 957 5.129320 TGACACCCTGCCTGCATATATATAG 59.871 44.000 0.00 0.00 0.00 1.31
900 958 4.410228 ACACCCTGCCTGCATATATATAGG 59.590 45.833 7.06 7.06 0.00 2.57
901 959 4.410228 CACCCTGCCTGCATATATATAGGT 59.590 45.833 11.58 0.00 32.85 3.08
902 960 5.039645 ACCCTGCCTGCATATATATAGGTT 58.960 41.667 11.58 0.00 32.85 3.50
903 961 5.492524 ACCCTGCCTGCATATATATAGGTTT 59.507 40.000 11.58 0.00 32.85 3.27
904 962 6.676632 ACCCTGCCTGCATATATATAGGTTTA 59.323 38.462 11.58 1.55 32.85 2.01
905 963 6.992715 CCCTGCCTGCATATATATAGGTTTAC 59.007 42.308 11.58 0.00 32.85 2.01
906 964 7.147479 CCCTGCCTGCATATATATAGGTTTACT 60.147 40.741 11.58 0.00 32.85 2.24
907 965 7.928706 CCTGCCTGCATATATATAGGTTTACTC 59.071 40.741 11.58 0.00 32.85 2.59
908 966 8.374184 TGCCTGCATATATATAGGTTTACTCA 57.626 34.615 11.58 0.56 32.85 3.41
909 967 8.258007 TGCCTGCATATATATAGGTTTACTCAC 58.742 37.037 11.58 0.00 32.85 3.51
910 968 7.435488 GCCTGCATATATATAGGTTTACTCACG 59.565 40.741 11.58 0.00 32.85 4.35
911 969 8.683615 CCTGCATATATATAGGTTTACTCACGA 58.316 37.037 6.30 0.00 0.00 4.35
974 1032 3.076079 TCCATAACGACCCCCTTTTTC 57.924 47.619 0.00 0.00 0.00 2.29
1058 1116 3.936203 TGGAGAACAAGGCGGCGT 61.936 61.111 9.37 0.00 0.00 5.68
1077 1135 0.385751 TCGATGGCGATTCTCAGTCC 59.614 55.000 0.00 0.00 42.51 3.85
1134 1192 1.066918 GGTACCCACTACCGATGCG 59.933 63.158 0.00 0.00 35.70 4.73
1147 1205 3.009723 ACCGATGCGTTGAATTCTGATT 58.990 40.909 7.05 0.00 0.00 2.57
1158 1216 7.439490 CGTTGAATTCTGATTATTGCAACAAC 58.561 34.615 0.00 6.20 35.40 3.32
1159 1217 7.114670 CGTTGAATTCTGATTATTGCAACAACA 59.885 33.333 0.00 0.00 35.40 3.33
1160 1218 8.763356 GTTGAATTCTGATTATTGCAACAACAA 58.237 29.630 0.00 0.00 35.66 2.83
1178 1236 5.824097 ACAACAATAGTAGCATGCATCATGA 59.176 36.000 21.98 0.00 43.81 3.07
1182 1240 6.148976 ACAATAGTAGCATGCATCATGACATC 59.851 38.462 21.98 0.00 43.81 3.06
1230 1288 3.497640 ACTAATTCTCGATCGGGACTACG 59.502 47.826 19.33 9.49 0.00 3.51
1242 1300 4.074259 TCGGGACTACGCTAAGCATAATA 58.926 43.478 0.00 0.00 0.00 0.98
1243 1301 4.083110 TCGGGACTACGCTAAGCATAATAC 60.083 45.833 0.00 0.00 0.00 1.89
1244 1302 4.492611 GGGACTACGCTAAGCATAATACC 58.507 47.826 0.00 0.00 0.00 2.73
1245 1303 4.164294 GGACTACGCTAAGCATAATACCG 58.836 47.826 0.00 0.00 0.00 4.02
1246 1304 3.572584 ACTACGCTAAGCATAATACCGC 58.427 45.455 0.00 0.00 0.00 5.68
1248 1306 1.069513 ACGCTAAGCATAATACCGCCA 59.930 47.619 0.00 0.00 0.00 5.69
1249 1307 2.139917 CGCTAAGCATAATACCGCCAA 58.860 47.619 0.00 0.00 0.00 4.52
1289 1402 0.040692 GCGACAAGTTTTTCCGGACC 60.041 55.000 1.83 0.00 0.00 4.46
1297 1410 1.833787 TTTTTCCGGACCGAGGGAGG 61.834 60.000 17.49 0.00 33.01 4.30
1317 1430 9.424906 AGGGAGGGATTTATAAATAGAGGAAAT 57.575 33.333 10.68 0.00 0.00 2.17
1348 1494 0.719465 CGCATCCTAACGTTGACACC 59.281 55.000 11.99 0.00 0.00 4.16
1360 1509 1.332686 GTTGACACCAAAAGGACGGTC 59.667 52.381 0.00 0.00 33.49 4.79
1409 1558 7.138692 ACGATTCGTTCTAGTAACTGTAACT 57.861 36.000 5.75 0.00 36.35 2.24
1410 1559 7.239972 ACGATTCGTTCTAGTAACTGTAACTC 58.760 38.462 5.75 0.00 36.35 3.01
1427 1576 9.593134 ACTGTAACTCTTCTATCTGCTAATTTG 57.407 33.333 0.00 0.00 0.00 2.32
1457 1607 6.698766 CCTACTACTGTAACTCGTGTGTTTTT 59.301 38.462 0.00 0.00 0.00 1.94
1493 1893 5.531287 TCTTTTCTTAGAAGGTGCAACTTCC 59.469 40.000 35.21 20.32 46.24 3.46
1589 2053 5.003778 GTCATGTGCTTCAAAATTGATACGC 59.996 40.000 0.00 1.98 37.00 4.42
1616 2080 4.495844 GGTTCGTATTCATAAGCACTTGCC 60.496 45.833 0.00 0.00 43.38 4.52
1638 2102 6.038161 TGCCGACCATTATGATTTTCTAACTG 59.962 38.462 0.00 0.00 0.00 3.16
1683 2151 5.531634 TGATGGTCAAAACTCTGATTTTGC 58.468 37.500 14.79 11.61 45.30 3.68
1838 2312 0.321653 ACCTGCTTCGATCACAACCC 60.322 55.000 0.00 0.00 0.00 4.11
1839 2313 0.036010 CCTGCTTCGATCACAACCCT 60.036 55.000 0.00 0.00 0.00 4.34
1840 2314 1.363744 CTGCTTCGATCACAACCCTC 58.636 55.000 0.00 0.00 0.00 4.30
1841 2315 0.976641 TGCTTCGATCACAACCCTCT 59.023 50.000 0.00 0.00 0.00 3.69
1842 2316 1.066858 TGCTTCGATCACAACCCTCTC 60.067 52.381 0.00 0.00 0.00 3.20
1843 2317 1.740718 GCTTCGATCACAACCCTCTCC 60.741 57.143 0.00 0.00 0.00 3.71
1844 2318 1.550524 CTTCGATCACAACCCTCTCCA 59.449 52.381 0.00 0.00 0.00 3.86
1845 2319 1.639722 TCGATCACAACCCTCTCCAA 58.360 50.000 0.00 0.00 0.00 3.53
1846 2320 1.974957 TCGATCACAACCCTCTCCAAA 59.025 47.619 0.00 0.00 0.00 3.28
1847 2321 2.028112 TCGATCACAACCCTCTCCAAAG 60.028 50.000 0.00 0.00 0.00 2.77
1848 2322 2.087646 GATCACAACCCTCTCCAAAGC 58.912 52.381 0.00 0.00 0.00 3.51
1849 2323 0.843309 TCACAACCCTCTCCAAAGCA 59.157 50.000 0.00 0.00 0.00 3.91
1850 2324 1.425066 TCACAACCCTCTCCAAAGCAT 59.575 47.619 0.00 0.00 0.00 3.79
1851 2325 2.158475 TCACAACCCTCTCCAAAGCATT 60.158 45.455 0.00 0.00 0.00 3.56
1852 2326 2.029649 CACAACCCTCTCCAAAGCATTG 60.030 50.000 0.00 0.00 36.25 2.82
1853 2327 2.158475 ACAACCCTCTCCAAAGCATTGA 60.158 45.455 2.61 0.00 38.94 2.57
1854 2328 3.094572 CAACCCTCTCCAAAGCATTGAT 58.905 45.455 2.61 0.00 38.94 2.57
1855 2329 3.463048 ACCCTCTCCAAAGCATTGATT 57.537 42.857 2.61 0.00 38.94 2.57
1856 2330 3.359950 ACCCTCTCCAAAGCATTGATTC 58.640 45.455 2.61 0.00 38.94 2.52
1857 2331 3.011032 ACCCTCTCCAAAGCATTGATTCT 59.989 43.478 2.61 0.00 38.94 2.40
1858 2332 3.380637 CCCTCTCCAAAGCATTGATTCTG 59.619 47.826 2.61 0.00 38.94 3.02
1859 2333 3.181489 CCTCTCCAAAGCATTGATTCTGC 60.181 47.826 2.61 0.00 38.94 4.26
1867 2341 3.764885 GCATTGATTCTGCTACCGTTT 57.235 42.857 0.00 0.00 36.68 3.60
1868 2342 3.685058 GCATTGATTCTGCTACCGTTTC 58.315 45.455 0.00 0.00 36.68 2.78
1869 2343 3.785505 GCATTGATTCTGCTACCGTTTCG 60.786 47.826 0.00 0.00 36.68 3.46
1870 2344 3.306917 TTGATTCTGCTACCGTTTCGA 57.693 42.857 0.00 0.00 0.00 3.71
1871 2345 3.520290 TGATTCTGCTACCGTTTCGAT 57.480 42.857 0.00 0.00 0.00 3.59
1872 2346 3.444916 TGATTCTGCTACCGTTTCGATC 58.555 45.455 0.00 0.00 0.00 3.69
1873 2347 3.119280 TGATTCTGCTACCGTTTCGATCA 60.119 43.478 0.00 0.00 0.00 2.92
1874 2348 2.273370 TCTGCTACCGTTTCGATCAC 57.727 50.000 0.00 0.00 0.00 3.06
1875 2349 0.914551 CTGCTACCGTTTCGATCACG 59.085 55.000 10.02 10.02 41.26 4.35
1927 2441 6.427853 ACCGTGGTATCTAAAACCTGTAAAAC 59.572 38.462 0.00 0.00 37.91 2.43
1966 2482 5.830457 ACAGCTGTGCTCTAGATGTTATAGA 59.170 40.000 20.97 0.00 41.56 1.98
1970 2486 9.083422 AGCTGTGCTCTAGATGTTATAGATTTA 57.917 33.333 0.00 0.00 30.62 1.40
1971 2487 9.698309 GCTGTGCTCTAGATGTTATAGATTTAA 57.302 33.333 0.00 0.00 0.00 1.52
2020 2539 5.698545 GTGCTACCTGAATCCAGAATACATC 59.301 44.000 0.00 0.00 43.02 3.06
2068 2587 5.984233 ATTTTTCGACTTTTTCTTTGCCC 57.016 34.783 0.00 0.00 0.00 5.36
2308 3111 4.023291 GCATATCTCCCACCTTTTTCCAA 58.977 43.478 0.00 0.00 0.00 3.53
2366 3235 4.054671 GGATACGATTGGCTTGAAGAGAG 58.945 47.826 0.00 0.00 0.00 3.20
2592 3512 1.002033 CCCATGCTCGCTTTTATCTGC 60.002 52.381 0.00 0.00 0.00 4.26
2888 3808 1.399791 GCAAAGCTCCAAATCTCTCCG 59.600 52.381 0.00 0.00 0.00 4.63
3089 4023 2.746277 GGTGTTGTAGGCCAGCGG 60.746 66.667 5.01 0.00 0.00 5.52
3111 4053 8.158789 AGCGGTATATTTGGTTAAATTAGGCTA 58.841 33.333 0.00 0.00 37.64 3.93
3321 4275 7.534723 TGATATTAGATGTAAGGCGGTAACT 57.465 36.000 0.00 0.00 0.00 2.24
3324 4278 8.874744 ATATTAGATGTAAGGCGGTAACTCTA 57.125 34.615 0.00 0.00 0.00 2.43
3338 4292 8.283291 GGCGGTAACTCTATTCATTTATTTCAG 58.717 37.037 0.00 0.00 0.00 3.02
3882 5119 5.061179 GTGTGACCCTACTGTACAACAAAT 58.939 41.667 0.00 0.00 0.00 2.32
3888 5125 8.842280 TGACCCTACTGTACAACAAATTTTTAG 58.158 33.333 0.00 0.00 0.00 1.85
4042 5282 3.058293 TGAACCTTTGATGTTGTCGCATC 60.058 43.478 0.00 0.00 43.97 3.91
4044 5284 3.149196 ACCTTTGATGTTGTCGCATCTT 58.851 40.909 7.45 0.00 44.02 2.40
4188 5430 5.505780 ACTATATTGTTACTGGCAGCCAAA 58.494 37.500 17.03 6.79 30.80 3.28
4269 5511 4.010349 CCAAGGAATACAACTCTTGACCC 58.990 47.826 0.00 0.00 38.96 4.46
4274 5518 6.133356 AGGAATACAACTCTTGACCCAAAAA 58.867 36.000 0.00 0.00 0.00 1.94
4357 5603 1.867233 TGAGACGCTTCAAAAGAGCAC 59.133 47.619 0.00 0.00 40.13 4.40
4467 5713 2.019249 CTGTGTCCCATCGCATGAATT 58.981 47.619 0.00 0.00 0.00 2.17
4485 5731 6.363167 TGAATTTGGCCTTGATTTTGAGAT 57.637 33.333 3.32 0.00 0.00 2.75
4500 5746 7.673504 TGATTTTGAGATGGGTTTGAAGGATTA 59.326 33.333 0.00 0.00 0.00 1.75
4511 5757 4.402056 TTGAAGGATTATCAGGGACGAC 57.598 45.455 0.00 0.00 0.00 4.34
4563 5809 6.867697 CCAAGTACTTGCAAGGCTACCCTT 62.868 50.000 29.18 16.92 43.44 3.95
4584 5830 4.316205 TTTCTCACTTGTGAGCGTAGAA 57.684 40.909 21.95 10.85 35.97 2.10
4773 6021 1.552792 GGCTAGATCTATGGCTGGGAC 59.447 57.143 12.30 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
142 143 9.121517 GTTTCATGACTTTTCTCATACACATTG 57.878 33.333 0.00 0.00 29.28 2.82
146 147 9.760660 GTATGTTTCATGACTTTTCTCATACAC 57.239 33.333 0.00 0.00 36.72 2.90
250 257 1.341080 CAACCCCTCCTGCACATTTT 58.659 50.000 0.00 0.00 0.00 1.82
252 259 0.251341 GACAACCCCTCCTGCACATT 60.251 55.000 0.00 0.00 0.00 2.71
275 282 1.306148 CATGAGCTGGCACATCGAAT 58.694 50.000 0.00 0.00 38.20 3.34
290 297 1.730064 GAAAAAGCCGAGCGTACATGA 59.270 47.619 0.00 0.00 0.00 3.07
367 374 4.928615 CCACAGAAAACAGAGCAACAAAAA 59.071 37.500 0.00 0.00 0.00 1.94
372 379 2.024414 ACCCACAGAAAACAGAGCAAC 58.976 47.619 0.00 0.00 0.00 4.17
375 382 3.801114 AAAACCCACAGAAAACAGAGC 57.199 42.857 0.00 0.00 0.00 4.09
398 405 1.488393 CCCAGCCCCAAAGAAACAAAA 59.512 47.619 0.00 0.00 0.00 2.44
400 407 0.031616 ACCCAGCCCCAAAGAAACAA 60.032 50.000 0.00 0.00 0.00 2.83
402 409 1.128200 AAACCCAGCCCCAAAGAAAC 58.872 50.000 0.00 0.00 0.00 2.78
404 411 1.127343 CAAAACCCAGCCCCAAAGAA 58.873 50.000 0.00 0.00 0.00 2.52
405 412 0.031616 ACAAAACCCAGCCCCAAAGA 60.032 50.000 0.00 0.00 0.00 2.52
406 413 0.392706 GACAAAACCCAGCCCCAAAG 59.607 55.000 0.00 0.00 0.00 2.77
407 414 1.051556 GGACAAAACCCAGCCCCAAA 61.052 55.000 0.00 0.00 0.00 3.28
408 415 1.458588 GGACAAAACCCAGCCCCAA 60.459 57.895 0.00 0.00 0.00 4.12
445 452 8.764524 TCAAAATTTTCGAAAAAGTTCAGGAA 57.235 26.923 25.77 0.65 32.89 3.36
494 502 7.413000 CCACGACTAGTCAAAATAATTGTCTGG 60.413 40.741 22.37 4.30 0.00 3.86
495 503 7.117812 ACCACGACTAGTCAAAATAATTGTCTG 59.882 37.037 22.37 3.69 0.00 3.51
496 504 7.117812 CACCACGACTAGTCAAAATAATTGTCT 59.882 37.037 22.37 0.00 0.00 3.41
497 505 7.095355 ACACCACGACTAGTCAAAATAATTGTC 60.095 37.037 22.37 0.00 0.00 3.18
498 506 6.708949 ACACCACGACTAGTCAAAATAATTGT 59.291 34.615 22.37 10.44 0.00 2.71
499 507 7.015289 CACACCACGACTAGTCAAAATAATTG 58.985 38.462 22.37 9.89 0.00 2.32
501 509 5.642063 CCACACCACGACTAGTCAAAATAAT 59.358 40.000 22.37 0.00 0.00 1.28
504 512 3.399330 CCACACCACGACTAGTCAAAAT 58.601 45.455 22.37 2.47 0.00 1.82
557 566 1.278985 TCTTCCAGATGATTGTGCGGT 59.721 47.619 0.00 0.00 0.00 5.68
621 642 5.622770 ACCAAGTGCGAGTAATTTTTAGG 57.377 39.130 0.00 0.00 0.00 2.69
670 691 2.707849 TACTCACCTTCGAGCCGGC 61.708 63.158 21.89 21.89 36.42 6.13
671 692 1.139095 GTACTCACCTTCGAGCCGG 59.861 63.158 0.00 0.00 36.42 6.13
672 693 0.242825 TTGTACTCACCTTCGAGCCG 59.757 55.000 0.00 0.00 36.42 5.52
673 694 2.450609 TTTGTACTCACCTTCGAGCC 57.549 50.000 0.00 0.00 36.42 4.70
676 697 2.361757 TCCGTTTTGTACTCACCTTCGA 59.638 45.455 0.00 0.00 0.00 3.71
677 698 2.729882 CTCCGTTTTGTACTCACCTTCG 59.270 50.000 0.00 0.00 0.00 3.79
679 700 2.490991 GCTCCGTTTTGTACTCACCTT 58.509 47.619 0.00 0.00 0.00 3.50
680 701 1.270678 GGCTCCGTTTTGTACTCACCT 60.271 52.381 0.00 0.00 0.00 4.00
683 704 1.689813 TCTGGCTCCGTTTTGTACTCA 59.310 47.619 0.00 0.00 0.00 3.41
744 774 1.433121 GATTGCCCTCCTCCAGATCT 58.567 55.000 0.00 0.00 0.00 2.75
751 781 1.227497 CAGCTCGATTGCCCTCCTC 60.227 63.158 0.00 0.00 0.00 3.71
759 789 0.814410 ATCTGGCAGCAGCTCGATTG 60.814 55.000 10.34 0.00 41.70 2.67
760 790 0.532417 GATCTGGCAGCAGCTCGATT 60.532 55.000 10.34 0.00 41.70 3.34
761 791 1.069427 GATCTGGCAGCAGCTCGAT 59.931 57.895 10.34 3.28 41.70 3.59
762 792 2.498248 GATCTGGCAGCAGCTCGA 59.502 61.111 10.34 0.00 41.70 4.04
763 793 2.588314 GGATCTGGCAGCAGCTCG 60.588 66.667 10.34 0.00 41.70 5.03
764 794 0.465824 ATTGGATCTGGCAGCAGCTC 60.466 55.000 10.34 3.78 41.70 4.09
765 795 0.465824 GATTGGATCTGGCAGCAGCT 60.466 55.000 10.34 0.00 41.70 4.24
767 797 1.164662 CGGATTGGATCTGGCAGCAG 61.165 60.000 10.34 0.00 31.92 4.24
768 798 1.153107 CGGATTGGATCTGGCAGCA 60.153 57.895 10.34 0.00 31.92 4.41
770 800 0.250209 CCTCGGATTGGATCTGGCAG 60.250 60.000 8.58 8.58 36.31 4.85
781 820 0.253207 AACCCTTCCTCCCTCGGATT 60.253 55.000 0.00 0.00 32.02 3.01
798 837 2.355481 AGTGGCCGACGAACGAAC 60.355 61.111 0.00 0.00 45.77 3.95
802 841 4.719369 AGCGAGTGGCCGACGAAC 62.719 66.667 17.62 1.16 45.17 3.95
910 968 1.666234 GAAGGCGCCCGATCTGATC 60.666 63.158 26.15 7.60 0.00 2.92
911 969 2.093537 GAGAAGGCGCCCGATCTGAT 62.094 60.000 26.20 7.85 0.00 2.90
912 970 2.759973 AGAAGGCGCCCGATCTGA 60.760 61.111 26.15 0.00 0.00 3.27
913 971 2.279784 GAGAAGGCGCCCGATCTG 60.280 66.667 26.20 0.00 0.00 2.90
964 1022 0.958876 CGACGGAAGGAAAAAGGGGG 60.959 60.000 0.00 0.00 0.00 5.40
1009 1067 2.874086 CCTTTCTTTTACCCGTTGTCGT 59.126 45.455 0.00 0.00 35.01 4.34
1011 1069 3.479489 TCCCTTTCTTTTACCCGTTGTC 58.521 45.455 0.00 0.00 0.00 3.18
1044 1102 3.296709 ATCGACGCCGCCTTGTTCT 62.297 57.895 0.00 0.00 35.37 3.01
1077 1135 4.741781 CTCCGCGTTGCTTTGCCG 62.742 66.667 4.92 0.00 0.00 5.69
1134 1192 8.296799 TGTTGTTGCAATAATCAGAATTCAAC 57.703 30.769 12.01 11.91 34.76 3.18
1147 1205 6.127786 TGCATGCTACTATTGTTGTTGCAATA 60.128 34.615 20.33 0.00 45.55 1.90
1158 1216 5.934935 TGTCATGATGCATGCTACTATTG 57.065 39.130 20.33 9.11 41.18 1.90
1159 1217 5.350640 CGATGTCATGATGCATGCTACTATT 59.649 40.000 20.33 0.00 41.18 1.73
1160 1218 4.868734 CGATGTCATGATGCATGCTACTAT 59.131 41.667 20.33 3.20 41.18 2.12
1230 1288 3.670627 GCATTGGCGGTATTATGCTTAGC 60.671 47.826 0.00 0.00 40.08 3.09
1245 1303 1.734465 GCGGATGTATCTAGCATTGGC 59.266 52.381 7.58 0.00 41.61 4.52
1246 1304 3.325293 AGCGGATGTATCTAGCATTGG 57.675 47.619 12.56 0.00 34.59 3.16
1248 1306 4.564041 CTCAAGCGGATGTATCTAGCATT 58.436 43.478 12.56 4.81 34.59 3.56
1249 1307 3.616076 GCTCAAGCGGATGTATCTAGCAT 60.616 47.826 12.56 0.00 34.59 3.79
1289 1402 6.668283 TCCTCTATTTATAAATCCCTCCCTCG 59.332 42.308 13.95 0.00 0.00 4.63
1317 1430 5.010314 ACGTTAGGATGCGACCAGAAATATA 59.990 40.000 2.00 0.00 0.00 0.86
1330 1476 1.803334 TGGTGTCAACGTTAGGATGC 58.197 50.000 0.00 0.00 0.00 3.91
1348 1494 5.468746 TCATTCAGTAAAGACCGTCCTTTTG 59.531 40.000 4.89 0.23 37.52 2.44
1360 1509 8.165428 GTCGAATTTCTCACTCATTCAGTAAAG 58.835 37.037 0.00 0.00 32.21 1.85
1409 1558 8.540507 AGGAGTACAAATTAGCAGATAGAAGA 57.459 34.615 0.00 0.00 0.00 2.87
1410 1559 9.685828 GTAGGAGTACAAATTAGCAGATAGAAG 57.314 37.037 0.00 0.00 0.00 2.85
1427 1576 5.872070 ACACGAGTTACAGTAGTAGGAGTAC 59.128 44.000 0.00 0.00 0.00 2.73
1479 1879 0.034896 TCTCCGGAAGTTGCACCTTC 59.965 55.000 15.16 15.16 40.11 3.46
1488 1888 0.314302 CGTCACTTGTCTCCGGAAGT 59.686 55.000 5.23 2.51 32.48 3.01
1489 1889 0.314302 ACGTCACTTGTCTCCGGAAG 59.686 55.000 5.23 1.72 0.00 3.46
1493 1893 1.567504 AACAACGTCACTTGTCTCCG 58.432 50.000 0.00 0.00 33.03 4.63
1525 1989 5.183140 CCCTTTGTTCGGAAATAAGTGATGT 59.817 40.000 10.41 0.00 0.00 3.06
1527 1991 5.566469 TCCCTTTGTTCGGAAATAAGTGAT 58.434 37.500 10.41 0.00 0.00 3.06
1589 2053 3.560068 GTGCTTATGAATACGAACCCAGG 59.440 47.826 0.00 0.00 0.00 4.45
1616 2080 8.196802 TGACAGTTAGAAAATCATAATGGTCG 57.803 34.615 0.00 0.00 0.00 4.79
1638 2102 1.865865 TTTCAGCTCCGTCTGTTGAC 58.134 50.000 0.00 0.00 39.70 3.18
1683 2151 7.993183 TCCTTCTGTTAATTTCTATAAGCCCTG 59.007 37.037 0.00 0.00 0.00 4.45
1838 2312 4.030134 GCAGAATCAATGCTTTGGAGAG 57.970 45.455 11.99 1.64 40.59 3.20
1847 2321 3.685058 GAAACGGTAGCAGAATCAATGC 58.315 45.455 0.00 0.00 44.18 3.56
1848 2322 3.616821 TCGAAACGGTAGCAGAATCAATG 59.383 43.478 0.00 0.00 0.00 2.82
1849 2323 3.857052 TCGAAACGGTAGCAGAATCAAT 58.143 40.909 0.00 0.00 0.00 2.57
1850 2324 3.306917 TCGAAACGGTAGCAGAATCAA 57.693 42.857 0.00 0.00 0.00 2.57
1851 2325 3.119280 TGATCGAAACGGTAGCAGAATCA 60.119 43.478 0.00 0.00 0.00 2.57
1852 2326 3.243177 GTGATCGAAACGGTAGCAGAATC 59.757 47.826 0.00 0.00 0.00 2.52
1853 2327 3.187700 GTGATCGAAACGGTAGCAGAAT 58.812 45.455 0.00 0.00 0.00 2.40
1854 2328 2.602878 GTGATCGAAACGGTAGCAGAA 58.397 47.619 0.00 0.00 0.00 3.02
1855 2329 1.466866 CGTGATCGAAACGGTAGCAGA 60.467 52.381 14.33 0.00 39.71 4.26
1856 2330 0.914551 CGTGATCGAAACGGTAGCAG 59.085 55.000 14.33 0.00 39.71 4.24
1857 2331 0.522626 TCGTGATCGAAACGGTAGCA 59.477 50.000 19.87 2.18 43.34 3.49
1858 2332 3.317608 TCGTGATCGAAACGGTAGC 57.682 52.632 19.87 0.00 43.34 3.58
1867 2341 0.323087 TTGGAGAGGGTCGTGATCGA 60.323 55.000 0.00 0.00 44.12 3.59
1868 2342 0.530744 TTTGGAGAGGGTCGTGATCG 59.469 55.000 0.00 0.00 38.55 3.69
1869 2343 1.740718 GCTTTGGAGAGGGTCGTGATC 60.741 57.143 0.00 0.00 0.00 2.92
1870 2344 0.250513 GCTTTGGAGAGGGTCGTGAT 59.749 55.000 0.00 0.00 0.00 3.06
1871 2345 1.118965 TGCTTTGGAGAGGGTCGTGA 61.119 55.000 0.00 0.00 0.00 4.35
1872 2346 0.036010 ATGCTTTGGAGAGGGTCGTG 60.036 55.000 0.00 0.00 0.00 4.35
1873 2347 0.693049 AATGCTTTGGAGAGGGTCGT 59.307 50.000 0.00 0.00 0.00 4.34
1874 2348 1.089920 CAATGCTTTGGAGAGGGTCG 58.910 55.000 4.44 0.00 0.00 4.79
1875 2349 2.496899 TCAATGCTTTGGAGAGGGTC 57.503 50.000 11.99 0.00 33.44 4.46
1876 2350 3.011032 AGAATCAATGCTTTGGAGAGGGT 59.989 43.478 11.99 0.00 33.44 4.34
1877 2351 3.380637 CAGAATCAATGCTTTGGAGAGGG 59.619 47.826 11.99 0.00 33.44 4.30
1878 2352 3.181489 GCAGAATCAATGCTTTGGAGAGG 60.181 47.826 11.99 2.21 40.59 3.69
1904 2411 6.427547 TGGTTTTACAGGTTTTAGATACCACG 59.572 38.462 0.00 0.00 38.16 4.94
1927 2441 5.633830 ACAGCTGTGAAATCTTGTTATGG 57.366 39.130 20.97 0.00 0.00 2.74
2035 2554 9.159470 GAAAAAGTCGAAAAATACAGAGTTCAG 57.841 33.333 0.00 0.00 0.00 3.02
2068 2587 7.880160 TGGGTTAATTGATCAAGACCATAAG 57.120 36.000 26.61 0.00 0.00 1.73
2308 3111 4.664064 AGATTGGAATGACATCTCCAGGAT 59.336 41.667 14.81 9.68 42.61 3.24
2333 3136 4.985409 GCCAATCGTATCCTTAGTGAAGAG 59.015 45.833 0.00 0.00 34.25 2.85
2366 3235 1.523758 AAATTCTCTCCACACGCACC 58.476 50.000 0.00 0.00 0.00 5.01
2472 3341 2.222953 CGGTCAAAATAACTAGTGCCGC 60.223 50.000 0.00 0.00 0.00 6.53
2592 3512 0.250166 AAGTGAGTTTCGAACCCCGG 60.250 55.000 0.00 0.00 39.14 5.73
2842 3762 2.423926 TCACTTTCAGTCTCTCGCAC 57.576 50.000 0.00 0.00 0.00 5.34
3321 4275 7.643569 TTGCAGGCTGAAATAAATGAATAGA 57.356 32.000 20.86 0.00 0.00 1.98
3324 4278 6.704310 ACTTTGCAGGCTGAAATAAATGAAT 58.296 32.000 20.86 0.00 0.00 2.57
3338 4292 0.659957 GATCGGATGACTTTGCAGGC 59.340 55.000 0.00 0.00 0.00 4.85
3882 5119 7.831691 TGTCCATCCAAGATTGAACTAAAAA 57.168 32.000 0.00 0.00 0.00 1.94
4042 5282 3.840890 TTATAAAGCAACCGCACCAAG 57.159 42.857 0.00 0.00 42.27 3.61
4044 5284 7.569639 TTTATATTATAAAGCAACCGCACCA 57.430 32.000 5.01 0.00 42.27 4.17
4188 5430 5.875359 GGTTGTAGCAGATTAAGCACTAAGT 59.125 40.000 0.00 0.00 0.00 2.24
4467 5713 2.833338 CCCATCTCAAAATCAAGGCCAA 59.167 45.455 5.01 0.00 0.00 4.52
4485 5731 3.855599 TCCCTGATAATCCTTCAAACCCA 59.144 43.478 0.00 0.00 0.00 4.51
4517 5763 4.418392 CTTTAATAAGCTGCAGCCACAAG 58.582 43.478 34.39 21.83 43.38 3.16
4541 5787 2.084546 GGGTAGCCTTGCAAGTACTTG 58.915 52.381 27.85 27.85 43.14 3.16
4584 5830 2.136026 GACTTCCATAATGGGACCCCT 58.864 52.381 8.45 0.00 38.32 4.79
4773 6021 0.389817 TCGGCACAAAGTGGAGATCG 60.390 55.000 0.00 0.00 33.64 3.69


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

AutoCloner maintained by Alex Coulton.