Multiple sequence alignment - TraesCS1A01G061000

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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 TraesCS1A01G061000 chr1A 100.000 2714 0 0 1 2714 41871732 41874445 0.000000e+00 5012.0
1 TraesCS1A01G061000 chr1A 93.370 920 49 4 61 970 452048103 452047186 0.000000e+00 1351.0
2 TraesCS1A01G061000 chr1A 92.216 925 55 11 63 973 300770371 300769450 0.000000e+00 1293.0
3 TraesCS1A01G061000 chr1A 81.106 434 66 10 2290 2714 41831907 41831481 1.560000e-87 333.0
4 TraesCS1A01G061000 chr1A 81.250 112 14 5 1782 1893 41831308 41831412 1.730000e-12 84.2
5 TraesCS1A01G061000 chr1A 73.705 251 43 17 1925 2156 41830492 41830738 2.900000e-10 76.8
6 TraesCS1A01G061000 chr5B 97.919 913 17 2 61 972 406282232 406281321 0.000000e+00 1580.0
7 TraesCS1A01G061000 chr5B 90.130 385 36 2 52 434 565894150 565894534 1.450000e-137 499.0
8 TraesCS1A01G061000 chrUn 96.158 911 34 1 61 970 329813131 329814041 0.000000e+00 1487.0
9 TraesCS1A01G061000 chrUn 95.939 911 36 1 61 970 329821662 329820752 0.000000e+00 1476.0
10 TraesCS1A01G061000 chr5A 93.608 923 45 4 60 970 677745037 677745957 0.000000e+00 1365.0
11 TraesCS1A01G061000 chr4A 92.842 922 52 5 61 970 632867341 632866422 0.000000e+00 1325.0
12 TraesCS1A01G061000 chr4A 92.017 927 47 10 60 974 323531704 323532615 0.000000e+00 1277.0
13 TraesCS1A01G061000 chr3A 92.423 937 43 11 58 983 430396525 430397444 0.000000e+00 1312.0
14 TraesCS1A01G061000 chr3A 81.081 407 67 8 2315 2714 11837214 11836811 1.570000e-82 316.0
15 TraesCS1A01G061000 chr3B 91.883 924 46 11 61 971 766165283 766166190 0.000000e+00 1264.0
16 TraesCS1A01G061000 chr3B 80.000 400 66 9 2319 2711 11620750 11621142 1.590000e-72 283.0
17 TraesCS1A01G061000 chr1B 86.329 1185 117 28 1557 2714 61962722 61963888 0.000000e+00 1249.0
18 TraesCS1A01G061000 chr1B 89.667 600 43 4 971 1558 61962061 61962653 0.000000e+00 747.0
19 TraesCS1A01G061000 chr1B 81.416 113 18 2 1781 1892 62199079 62199189 3.720000e-14 89.8
20 TraesCS1A01G061000 chr1B 80.899 89 14 2 2070 2156 61954189 61954276 1.740000e-07 67.6
21 TraesCS1A01G061000 chr6D 89.936 944 59 14 61 971 445080977 445080037 0.000000e+00 1184.0
22 TraesCS1A01G061000 chr6D 83.158 380 55 9 2338 2712 412631503 412631128 3.350000e-89 339.0
23 TraesCS1A01G061000 chr7B 90.053 935 51 18 59 971 696589124 696588210 0.000000e+00 1173.0
24 TraesCS1A01G061000 chr7A 89.519 935 56 9 61 972 456680582 456681497 0.000000e+00 1146.0
25 TraesCS1A01G061000 chr1D 93.255 593 35 4 971 1558 41820804 41821396 0.000000e+00 869.0
26 TraesCS1A01G061000 chr1D 90.610 639 47 7 1557 2183 41821465 41822102 0.000000e+00 835.0
27 TraesCS1A01G061000 chr1D 82.796 93 13 2 2066 2156 41767267 41767358 2.240000e-11 80.5
28 TraesCS1A01G061000 chr5D 81.140 456 72 12 2263 2714 522762289 522762734 1.200000e-93 353.0
29 TraesCS1A01G061000 chr5D 82.955 352 49 7 2372 2714 232835940 232835591 9.440000e-80 307.0
30 TraesCS1A01G061000 chr3D 78.846 468 85 10 2253 2712 578267590 578267129 1.220000e-78 303.0
31 TraesCS1A01G061000 chr6B 84.615 312 39 7 2408 2714 64965611 64965304 4.390000e-78 302.0
32 TraesCS1A01G061000 chr4B 80.196 409 59 15 2291 2690 48636908 48637303 1.230000e-73 287.0


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 TraesCS1A01G061000 chr1A 41871732 41874445 2713 False 5012 5012 100.0000 1 2714 1 chr1A.!!$F1 2713
1 TraesCS1A01G061000 chr1A 452047186 452048103 917 True 1351 1351 93.3700 61 970 1 chr1A.!!$R3 909
2 TraesCS1A01G061000 chr1A 300769450 300770371 921 True 1293 1293 92.2160 63 973 1 chr1A.!!$R2 910
3 TraesCS1A01G061000 chr5B 406281321 406282232 911 True 1580 1580 97.9190 61 972 1 chr5B.!!$R1 911
4 TraesCS1A01G061000 chrUn 329813131 329814041 910 False 1487 1487 96.1580 61 970 1 chrUn.!!$F1 909
5 TraesCS1A01G061000 chrUn 329820752 329821662 910 True 1476 1476 95.9390 61 970 1 chrUn.!!$R1 909
6 TraesCS1A01G061000 chr5A 677745037 677745957 920 False 1365 1365 93.6080 60 970 1 chr5A.!!$F1 910
7 TraesCS1A01G061000 chr4A 632866422 632867341 919 True 1325 1325 92.8420 61 970 1 chr4A.!!$R1 909
8 TraesCS1A01G061000 chr4A 323531704 323532615 911 False 1277 1277 92.0170 60 974 1 chr4A.!!$F1 914
9 TraesCS1A01G061000 chr3A 430396525 430397444 919 False 1312 1312 92.4230 58 983 1 chr3A.!!$F1 925
10 TraesCS1A01G061000 chr3B 766165283 766166190 907 False 1264 1264 91.8830 61 971 1 chr3B.!!$F2 910
11 TraesCS1A01G061000 chr1B 61962061 61963888 1827 False 998 1249 87.9980 971 2714 2 chr1B.!!$F3 1743
12 TraesCS1A01G061000 chr6D 445080037 445080977 940 True 1184 1184 89.9360 61 971 1 chr6D.!!$R2 910
13 TraesCS1A01G061000 chr7B 696588210 696589124 914 True 1173 1173 90.0530 59 971 1 chr7B.!!$R1 912
14 TraesCS1A01G061000 chr7A 456680582 456681497 915 False 1146 1146 89.5190 61 972 1 chr7A.!!$F1 911
15 TraesCS1A01G061000 chr1D 41820804 41822102 1298 False 852 869 91.9325 971 2183 2 chr1D.!!$F2 1212

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
50 51 0.601046 CGCTGCACCATCGTCCATAT 60.601 55.0 0.00 0.0 0.0 1.78 F
1455 1554 0.983467 TTGCTAGCACTCACCATGGA 59.017 50.0 21.47 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1460 1559 0.171231 GCACCCCAGAAGCGAAATTC 59.829 55.0 0.0 0.0 0.0 2.17 R
2599 2805 0.176910 TGTGTTTCTCGTGACCAGCA 59.823 50.0 0.0 0.0 0.0 4.41 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
22 23 4.556233 CACTAAACAGTAGTAGCAGTGCA 58.444 43.478 19.20 0.00 29.78 4.57
23 24 4.988540 CACTAAACAGTAGTAGCAGTGCAA 59.011 41.667 19.20 0.00 29.78 4.08
24 25 4.989168 ACTAAACAGTAGTAGCAGTGCAAC 59.011 41.667 19.20 9.65 0.00 4.17
25 26 3.469008 AACAGTAGTAGCAGTGCAACA 57.531 42.857 19.20 0.00 41.43 3.33
26 27 2.755650 ACAGTAGTAGCAGTGCAACAC 58.244 47.619 19.20 11.87 41.43 3.32
27 28 2.365617 ACAGTAGTAGCAGTGCAACACT 59.634 45.455 19.20 18.23 46.51 3.55
28 29 3.572682 ACAGTAGTAGCAGTGCAACACTA 59.427 43.478 19.20 17.24 43.43 2.74
29 30 4.038763 ACAGTAGTAGCAGTGCAACACTAA 59.961 41.667 19.20 4.26 43.43 2.24
30 31 4.623167 CAGTAGTAGCAGTGCAACACTAAG 59.377 45.833 19.20 12.54 43.43 2.18
31 32 2.417719 AGTAGCAGTGCAACACTAAGC 58.582 47.619 19.20 1.12 43.43 3.09
32 33 1.126846 GTAGCAGTGCAACACTAAGCG 59.873 52.381 19.20 0.00 43.43 4.68
33 34 1.441016 GCAGTGCAACACTAAGCGC 60.441 57.895 11.09 0.00 43.43 5.92
34 35 4.779475 AGTGCAACACTAAGCGCT 57.221 50.000 2.64 2.64 43.46 5.92
35 36 4.826600 GTGCAACACTAAGCGCTG 57.173 55.556 12.58 0.57 38.19 5.18
36 37 1.441016 GTGCAACACTAAGCGCTGC 60.441 57.895 12.58 10.04 38.19 5.25
37 38 1.891449 TGCAACACTAAGCGCTGCA 60.891 52.632 12.58 13.10 40.54 4.41
38 39 1.441016 GCAACACTAAGCGCTGCAC 60.441 57.895 12.58 0.00 33.19 4.57
39 40 1.207593 CAACACTAAGCGCTGCACC 59.792 57.895 12.58 0.00 0.00 5.01
40 41 1.227823 AACACTAAGCGCTGCACCA 60.228 52.632 12.58 0.00 0.00 4.17
41 42 0.606401 AACACTAAGCGCTGCACCAT 60.606 50.000 12.58 0.00 0.00 3.55
42 43 1.021390 ACACTAAGCGCTGCACCATC 61.021 55.000 12.58 0.00 0.00 3.51
43 44 1.811266 ACTAAGCGCTGCACCATCG 60.811 57.895 12.58 0.00 0.00 3.84
44 45 1.811266 CTAAGCGCTGCACCATCGT 60.811 57.895 12.58 0.00 0.00 3.73
45 46 1.756375 CTAAGCGCTGCACCATCGTC 61.756 60.000 12.58 0.00 0.00 4.20
48 49 2.512286 CGCTGCACCATCGTCCAT 60.512 61.111 0.00 0.00 0.00 3.41
49 50 1.227234 CGCTGCACCATCGTCCATA 60.227 57.895 0.00 0.00 0.00 2.74
50 51 0.601046 CGCTGCACCATCGTCCATAT 60.601 55.000 0.00 0.00 0.00 1.78
51 52 1.336795 CGCTGCACCATCGTCCATATA 60.337 52.381 0.00 0.00 0.00 0.86
52 53 2.675032 CGCTGCACCATCGTCCATATAT 60.675 50.000 0.00 0.00 0.00 0.86
53 54 3.428862 CGCTGCACCATCGTCCATATATA 60.429 47.826 0.00 0.00 0.00 0.86
54 55 4.115516 GCTGCACCATCGTCCATATATAG 58.884 47.826 0.00 0.00 0.00 1.31
55 56 4.142160 GCTGCACCATCGTCCATATATAGA 60.142 45.833 0.00 0.00 0.00 1.98
56 57 5.324784 TGCACCATCGTCCATATATAGAC 57.675 43.478 1.55 1.55 0.00 2.59
78 79 8.071177 AGACCATGAAAGAATTCCTTATTTGG 57.929 34.615 0.65 6.27 35.16 3.28
236 238 4.331968 TGACAAATTTACCCCTAGCACTG 58.668 43.478 0.00 0.00 0.00 3.66
495 527 4.041444 AGCAATTAAAAATCCCAAGGCACA 59.959 37.500 0.00 0.00 0.00 4.57
1002 1092 2.354902 GCCAGGCCACATTTCAGTT 58.645 52.632 5.01 0.00 0.00 3.16
1011 1104 4.293415 GCCACATTTCAGTTGAAACAGAG 58.707 43.478 9.29 4.90 45.55 3.35
1014 1107 5.342433 CACATTTCAGTTGAAACAGAGCAA 58.658 37.500 9.29 0.00 45.55 3.91
1021 1114 3.206150 GTTGAAACAGAGCAACTCTCCA 58.794 45.455 0.00 0.00 42.90 3.86
1022 1115 3.777106 TGAAACAGAGCAACTCTCCAT 57.223 42.857 0.00 0.00 42.90 3.41
1032 1125 5.021033 AGCAACTCTCCATAAGATCAGTG 57.979 43.478 0.00 0.00 32.19 3.66
1033 1126 4.713814 AGCAACTCTCCATAAGATCAGTGA 59.286 41.667 0.00 0.00 32.19 3.41
1073 1169 1.671379 GCCTGTCTTCCGTTCCCAC 60.671 63.158 0.00 0.00 0.00 4.61
1230 1329 3.322466 CAGGCTCAAGGGTCCGGT 61.322 66.667 0.00 0.00 0.00 5.28
1232 1331 4.410400 GGCTCAAGGGTCCGGTGG 62.410 72.222 0.00 0.00 0.00 4.61
1356 1455 1.262950 CACATTGAGTTTGGCGACGAA 59.737 47.619 0.00 0.00 0.00 3.85
1380 1479 1.138859 CCGTATGTTGCATCCTCCTCA 59.861 52.381 0.00 0.00 0.00 3.86
1415 1514 7.047891 TCCATGTCCACATACTATTGAACTTC 58.952 38.462 0.00 0.00 34.26 3.01
1442 1541 2.099831 GCGCTGCTTGCTTGCTAG 59.900 61.111 0.00 0.00 40.11 3.42
1454 1553 1.376543 CTTGCTAGCACTCACCATGG 58.623 55.000 19.17 11.19 0.00 3.66
1455 1554 0.983467 TTGCTAGCACTCACCATGGA 59.017 50.000 21.47 0.00 0.00 3.41
1460 1559 3.750130 GCTAGCACTCACCATGGATATTG 59.250 47.826 21.47 11.02 0.00 1.90
1534 1639 1.885388 CACACGTCCAAGGCGAACA 60.885 57.895 9.31 0.00 0.00 3.18
1582 1757 1.618837 AGTGGCTGTCGTGTATCACTT 59.381 47.619 0.00 0.00 32.34 3.16
1640 1817 5.470777 TGTTTTAGTAGCTTGTTATGGCGTT 59.529 36.000 0.00 0.00 0.00 4.84
1666 1843 2.082231 CAGTAGAGTTCGTCCTCGGAA 58.918 52.381 0.00 0.00 36.56 4.30
1674 1851 7.052142 AGAGTTCGTCCTCGGAAATATTATT 57.948 36.000 0.00 0.00 36.56 1.40
1714 1894 5.531634 AGTTGCAGTGATTGTGGTTTATTG 58.468 37.500 0.00 0.00 0.00 1.90
1726 1906 0.388006 GTTTATTGTGCGGTGTGGCC 60.388 55.000 0.00 0.00 0.00 5.36
1729 1909 2.404566 TATTGTGCGGTGTGGCCTGT 62.405 55.000 3.32 0.00 34.25 4.00
1740 1920 1.144708 TGTGGCCTGTTCTCCATTTGA 59.855 47.619 3.32 0.00 34.47 2.69
1741 1921 1.815003 GTGGCCTGTTCTCCATTTGAG 59.185 52.381 3.32 0.00 42.90 3.02
1758 1938 4.630894 TTGAGATTGTGCTCGTTTGTTT 57.369 36.364 0.00 0.00 37.73 2.83
1770 1950 8.447833 TGTGCTCGTTTGTTTCCTAATATAAAG 58.552 33.333 0.00 0.00 0.00 1.85
1775 1955 6.500910 GTTTGTTTCCTAATATAAAGGGGCG 58.499 40.000 4.60 0.00 34.66 6.13
1780 1960 4.431378 TCCTAATATAAAGGGGCGGATCA 58.569 43.478 0.00 0.00 34.66 2.92
1784 1964 0.393077 ATAAAGGGGCGGATCACTCG 59.607 55.000 0.00 0.00 0.00 4.18
1804 1984 6.420604 CACTCGTGCAAATTCCTGTAAAAATT 59.579 34.615 0.00 0.00 0.00 1.82
1893 2076 8.551205 TGAAATCATGTAAAGAGCGATAATGAC 58.449 33.333 0.00 0.00 0.00 3.06
1902 2085 5.490139 AGAGCGATAATGACATGTTTTGG 57.510 39.130 0.00 0.00 0.00 3.28
1909 2092 1.698506 TGACATGTTTTGGGGGACAC 58.301 50.000 0.00 0.00 0.00 3.67
1921 2104 3.430453 TGGGGGACACAATTTGAATCTC 58.570 45.455 2.79 0.03 0.00 2.75
2137 2323 3.568853 AGTACTGACGAGCAACTACAAGT 59.431 43.478 0.00 0.00 0.00 3.16
2159 2347 2.975193 CACATGCATTCAACACACTTCG 59.025 45.455 0.00 0.00 0.00 3.79
2163 2351 2.147958 GCATTCAACACACTTCGGGTA 58.852 47.619 0.00 0.00 0.00 3.69
2196 2391 3.055602 TCATGACATGAGACAGTTGAGGG 60.056 47.826 14.24 0.00 33.59 4.30
2197 2392 1.002430 TGACATGAGACAGTTGAGGGC 59.998 52.381 0.00 0.00 0.00 5.19
2198 2393 1.277557 GACATGAGACAGTTGAGGGCT 59.722 52.381 0.00 0.00 0.00 5.19
2199 2394 1.277557 ACATGAGACAGTTGAGGGCTC 59.722 52.381 0.00 0.00 0.00 4.70
2200 2395 1.277273 CATGAGACAGTTGAGGGCTCA 59.723 52.381 0.00 0.00 39.61 4.26
2201 2396 1.423584 TGAGACAGTTGAGGGCTCAA 58.576 50.000 0.00 0.00 46.27 3.02
2209 2404 2.452600 TTGAGGGCTCAAACCAAAGT 57.547 45.000 0.00 0.00 45.56 2.66
2210 2405 2.452600 TGAGGGCTCAAACCAAAGTT 57.547 45.000 0.00 0.00 36.53 2.66
2211 2406 2.031120 TGAGGGCTCAAACCAAAGTTG 58.969 47.619 0.00 0.00 35.97 3.16
2224 2419 1.873591 CAAAGTTGAAGTAGCGCCAGT 59.126 47.619 2.29 0.00 0.00 4.00
2229 2424 1.725641 TGAAGTAGCGCCAGTGATTG 58.274 50.000 2.29 0.00 0.00 2.67
2242 2437 4.675510 CCAGTGATTGGTAAATGATGTGC 58.324 43.478 0.00 0.00 42.41 4.57
2243 2438 4.158209 CCAGTGATTGGTAAATGATGTGCA 59.842 41.667 0.00 0.00 42.41 4.57
2244 2439 5.337554 CAGTGATTGGTAAATGATGTGCAG 58.662 41.667 0.00 0.00 0.00 4.41
2246 2441 5.711506 AGTGATTGGTAAATGATGTGCAGAA 59.288 36.000 0.00 0.00 0.00 3.02
2250 2447 6.449635 TTGGTAAATGATGTGCAGAATACC 57.550 37.500 0.00 0.00 35.28 2.73
2261 2458 2.675844 TGCAGAATACCACGGAAATTCG 59.324 45.455 0.00 0.00 35.30 3.34
2262 2459 2.031683 GCAGAATACCACGGAAATTCGG 59.968 50.000 0.00 0.00 35.30 4.30
2285 2483 2.033602 AAGTAAGTGCGGGGGCAC 59.966 61.111 11.03 11.03 40.64 5.01
2290 2488 4.101448 AGTGCGGGGGCACTCATC 62.101 66.667 15.40 0.00 46.65 2.92
2291 2489 4.408821 GTGCGGGGGCACTCATCA 62.409 66.667 11.66 0.00 37.68 3.07
2303 2501 1.302285 CTCATCACCTGCCAAGCCT 59.698 57.895 0.00 0.00 0.00 4.58
2304 2502 0.747283 CTCATCACCTGCCAAGCCTC 60.747 60.000 0.00 0.00 0.00 4.70
2322 2520 3.508840 GCCGCCTGGTCGATTTGG 61.509 66.667 11.24 0.00 37.67 3.28
2325 2523 2.464459 CGCCTGGTCGATTTGGCTC 61.464 63.158 18.55 0.00 42.90 4.70
2327 2525 2.464459 CCTGGTCGATTTGGCTCGC 61.464 63.158 0.00 0.00 38.52 5.03
2332 2530 0.373716 GTCGATTTGGCTCGCGATTT 59.626 50.000 10.36 0.00 38.52 2.17
2333 2531 0.373370 TCGATTTGGCTCGCGATTTG 59.627 50.000 10.36 0.00 38.52 2.32
2350 2548 5.398416 GCGATTTGCGAAGTAATTTAATCCC 59.602 40.000 0.00 0.00 44.57 3.85
2351 2549 6.725246 CGATTTGCGAAGTAATTTAATCCCT 58.275 36.000 0.00 0.00 44.57 4.20
2352 2550 6.851330 CGATTTGCGAAGTAATTTAATCCCTC 59.149 38.462 0.00 0.00 44.57 4.30
2353 2551 7.466725 CGATTTGCGAAGTAATTTAATCCCTCA 60.467 37.037 0.00 0.00 44.57 3.86
2355 2553 5.492895 TGCGAAGTAATTTAATCCCTCACA 58.507 37.500 0.00 0.00 0.00 3.58
2357 2555 6.431543 TGCGAAGTAATTTAATCCCTCACAAA 59.568 34.615 0.00 0.00 0.00 2.83
2362 2560 5.405935 AATTTAATCCCTCACAAAGGCAC 57.594 39.130 0.00 0.00 44.71 5.01
2363 2561 3.517296 TTAATCCCTCACAAAGGCACA 57.483 42.857 0.00 0.00 44.71 4.57
2370 2568 3.243401 CCCTCACAAAGGCACAGTAAAAC 60.243 47.826 0.00 0.00 44.71 2.43
2373 2571 4.992688 TCACAAAGGCACAGTAAAACAAG 58.007 39.130 0.00 0.00 0.00 3.16
2374 2572 4.702612 TCACAAAGGCACAGTAAAACAAGA 59.297 37.500 0.00 0.00 0.00 3.02
2375 2573 5.184096 TCACAAAGGCACAGTAAAACAAGAA 59.816 36.000 0.00 0.00 0.00 2.52
2376 2574 5.288472 CACAAAGGCACAGTAAAACAAGAAC 59.712 40.000 0.00 0.00 0.00 3.01
2377 2575 5.047660 ACAAAGGCACAGTAAAACAAGAACA 60.048 36.000 0.00 0.00 0.00 3.18
2380 2578 4.278419 AGGCACAGTAAAACAAGAACATCC 59.722 41.667 0.00 0.00 0.00 3.51
2381 2579 4.546570 GCACAGTAAAACAAGAACATCCC 58.453 43.478 0.00 0.00 0.00 3.85
2382 2580 4.278419 GCACAGTAAAACAAGAACATCCCT 59.722 41.667 0.00 0.00 0.00 4.20
2383 2581 5.562890 GCACAGTAAAACAAGAACATCCCTC 60.563 44.000 0.00 0.00 0.00 4.30
2384 2582 4.755123 ACAGTAAAACAAGAACATCCCTCG 59.245 41.667 0.00 0.00 0.00 4.63
2385 2583 4.154195 CAGTAAAACAAGAACATCCCTCGG 59.846 45.833 0.00 0.00 0.00 4.63
2386 2584 3.502123 AAAACAAGAACATCCCTCGGA 57.498 42.857 0.00 0.00 35.55 4.55
2387 2585 3.502123 AAACAAGAACATCCCTCGGAA 57.498 42.857 0.00 0.00 34.34 4.30
2390 2588 2.637872 ACAAGAACATCCCTCGGAAAGA 59.362 45.455 0.00 0.00 34.34 2.52
2403 2601 6.206048 TCCCTCGGAAAGATTTAAGTTTCAAC 59.794 38.462 8.46 0.00 34.85 3.18
2404 2602 6.016610 CCCTCGGAAAGATTTAAGTTTCAACA 60.017 38.462 8.46 0.00 34.85 3.33
2454 2654 3.119173 TGCCCAGTTTCAACAAGTTTCAG 60.119 43.478 0.00 0.00 0.00 3.02
2457 2657 4.640201 CCCAGTTTCAACAAGTTTCAGAGA 59.360 41.667 0.00 0.00 0.00 3.10
2461 2661 8.233190 CCAGTTTCAACAAGTTTCAGAGATATC 58.767 37.037 0.00 0.00 0.00 1.63
2470 2670 9.453572 ACAAGTTTCAGAGATATCATTTAAGCA 57.546 29.630 5.32 0.00 0.00 3.91
2501 2705 6.693466 TCTGTCGGTCATAGACACAAAATAA 58.307 36.000 0.00 0.00 42.91 1.40
2618 2824 0.176910 TGCTGGTCACGAGAAACACA 59.823 50.000 0.00 0.00 0.00 3.72
2620 2826 1.873591 GCTGGTCACGAGAAACACAAT 59.126 47.619 0.00 0.00 0.00 2.71
2627 2833 6.429692 TGGTCACGAGAAACACAATTATGAAT 59.570 34.615 0.00 0.00 0.00 2.57
2631 2837 8.994170 TCACGAGAAACACAATTATGAATACAA 58.006 29.630 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.556233 TGCACTGCTACTACTGTTTAGTG 58.444 43.478 1.98 0.00 37.78 2.74
1 2 4.866508 TGCACTGCTACTACTGTTTAGT 57.133 40.909 1.98 0.00 40.99 2.24
2 3 4.988540 TGTTGCACTGCTACTACTGTTTAG 59.011 41.667 15.26 0.00 35.51 1.85
3 4 4.748102 GTGTTGCACTGCTACTACTGTTTA 59.252 41.667 15.26 0.00 35.51 2.01
4 5 3.560068 GTGTTGCACTGCTACTACTGTTT 59.440 43.478 15.26 0.00 35.51 2.83
5 6 3.131396 GTGTTGCACTGCTACTACTGTT 58.869 45.455 15.26 0.00 35.51 3.16
6 7 2.365617 AGTGTTGCACTGCTACTACTGT 59.634 45.455 15.26 0.00 43.63 3.55
7 8 3.032017 AGTGTTGCACTGCTACTACTG 57.968 47.619 15.26 0.00 43.63 2.74
8 9 4.810790 CTTAGTGTTGCACTGCTACTACT 58.189 43.478 15.26 16.59 45.01 2.57
9 10 3.368236 GCTTAGTGTTGCACTGCTACTAC 59.632 47.826 15.26 11.65 45.01 2.73
10 11 3.585862 GCTTAGTGTTGCACTGCTACTA 58.414 45.455 15.26 11.49 45.01 1.82
11 12 2.417719 GCTTAGTGTTGCACTGCTACT 58.582 47.619 15.26 12.31 45.01 2.57
12 13 1.126846 CGCTTAGTGTTGCACTGCTAC 59.873 52.381 11.57 8.48 45.01 3.58
13 14 1.428448 CGCTTAGTGTTGCACTGCTA 58.572 50.000 11.57 0.00 45.01 3.49
14 15 1.845809 GCGCTTAGTGTTGCACTGCT 61.846 55.000 11.57 0.00 45.01 4.24
15 16 1.441016 GCGCTTAGTGTTGCACTGC 60.441 57.895 11.57 6.75 45.01 4.40
16 17 0.110509 CAGCGCTTAGTGTTGCACTG 60.111 55.000 7.50 0.00 45.01 3.66
17 18 1.845809 GCAGCGCTTAGTGTTGCACT 61.846 55.000 25.29 6.99 46.48 4.40
18 19 1.441016 GCAGCGCTTAGTGTTGCAC 60.441 57.895 25.29 1.18 46.48 4.57
19 20 2.945984 GCAGCGCTTAGTGTTGCA 59.054 55.556 25.29 0.00 46.48 4.08
21 22 1.207593 GGTGCAGCGCTTAGTGTTG 59.792 57.895 7.50 5.27 0.00 3.33
22 23 0.606401 ATGGTGCAGCGCTTAGTGTT 60.606 50.000 7.50 0.00 0.00 3.32
23 24 1.003355 ATGGTGCAGCGCTTAGTGT 60.003 52.632 7.50 0.00 0.00 3.55
24 25 1.717937 GATGGTGCAGCGCTTAGTG 59.282 57.895 7.50 0.00 0.00 2.74
25 26 1.811266 CGATGGTGCAGCGCTTAGT 60.811 57.895 7.50 0.00 36.27 2.24
26 27 3.009140 CGATGGTGCAGCGCTTAG 58.991 61.111 7.50 0.00 36.27 2.18
35 36 4.159693 TGGTCTATATATGGACGATGGTGC 59.840 45.833 19.44 7.51 38.95 5.01
36 37 5.914898 TGGTCTATATATGGACGATGGTG 57.085 43.478 19.44 0.00 38.95 4.17
37 38 6.194967 TCATGGTCTATATATGGACGATGGT 58.805 40.000 33.49 13.90 46.59 3.55
38 39 6.715347 TCATGGTCTATATATGGACGATGG 57.285 41.667 33.49 23.00 46.59 3.51
40 41 8.595362 TCTTTCATGGTCTATATATGGACGAT 57.405 34.615 19.44 18.37 38.95 3.73
41 42 8.417273 TTCTTTCATGGTCTATATATGGACGA 57.583 34.615 19.44 17.10 38.95 4.20
42 43 9.658799 AATTCTTTCATGGTCTATATATGGACG 57.341 33.333 19.44 9.01 38.95 4.79
52 53 9.189156 CCAAATAAGGAATTCTTTCATGGTCTA 57.811 33.333 6.03 0.00 36.93 2.59
53 54 7.364144 GCCAAATAAGGAATTCTTTCATGGTCT 60.364 37.037 20.37 1.65 36.93 3.85
54 55 6.758416 GCCAAATAAGGAATTCTTTCATGGTC 59.242 38.462 20.37 13.59 36.93 4.02
55 56 6.213195 TGCCAAATAAGGAATTCTTTCATGGT 59.787 34.615 20.37 0.00 36.93 3.55
56 57 6.536224 GTGCCAAATAAGGAATTCTTTCATGG 59.464 38.462 17.52 17.52 36.93 3.66
78 79 6.822073 AGGAAACGAAATTTAAAACAGTGC 57.178 33.333 0.00 0.00 0.00 4.40
255 257 5.415701 GGTGAAGCCAATGAGAATGACTTTA 59.584 40.000 0.00 0.00 37.17 1.85
495 527 7.174772 GCCTTTGGATTTATTTTTGACCATGTT 59.825 33.333 0.00 0.00 0.00 2.71
627 681 4.489493 GCACACGCACGTATAAAACAATAC 59.511 41.667 0.00 0.00 38.36 1.89
1002 1092 3.777106 ATGGAGAGTTGCTCTGTTTCA 57.223 42.857 3.12 0.00 41.35 2.69
1011 1104 5.016051 TCACTGATCTTATGGAGAGTTGC 57.984 43.478 0.00 0.00 37.93 4.17
1014 1107 3.640967 GGCTCACTGATCTTATGGAGAGT 59.359 47.826 0.00 0.00 37.93 3.24
1021 1114 4.880696 GCTTCTTTGGCTCACTGATCTTAT 59.119 41.667 0.00 0.00 0.00 1.73
1022 1115 4.256920 GCTTCTTTGGCTCACTGATCTTA 58.743 43.478 0.00 0.00 0.00 2.10
1032 1125 1.012841 CCATCTCGCTTCTTTGGCTC 58.987 55.000 0.00 0.00 0.00 4.70
1033 1126 3.165606 CCATCTCGCTTCTTTGGCT 57.834 52.632 0.00 0.00 0.00 4.75
1059 1155 1.295746 GGAGGTGGGAACGGAAGAC 59.704 63.158 0.00 0.00 0.00 3.01
1073 1169 2.806009 GCTAGCAGCAGGAGGGAGG 61.806 68.421 10.63 0.00 41.89 4.30
1224 1323 2.266055 CTGAAGCCTCCACCGGAC 59.734 66.667 9.46 0.00 0.00 4.79
1230 1329 2.066393 CCGGATCCTGAAGCCTCCA 61.066 63.158 10.75 0.00 0.00 3.86
1232 1331 2.110006 GCCGGATCCTGAAGCCTC 59.890 66.667 5.05 0.00 0.00 4.70
1337 1436 1.263217 GTTCGTCGCCAAACTCAATGT 59.737 47.619 0.00 0.00 0.00 2.71
1341 1440 1.144969 GATGTTCGTCGCCAAACTCA 58.855 50.000 0.00 0.00 0.00 3.41
1380 1479 1.556911 GTGGACATGGATGTGAGGACT 59.443 52.381 0.00 0.00 41.95 3.85
1442 1541 5.779529 AATTCAATATCCATGGTGAGTGC 57.220 39.130 12.58 0.00 0.00 4.40
1454 1553 4.580580 ACCCCAGAAGCGAAATTCAATATC 59.419 41.667 0.00 0.00 0.00 1.63
1455 1554 4.339247 CACCCCAGAAGCGAAATTCAATAT 59.661 41.667 0.00 0.00 0.00 1.28
1460 1559 0.171231 GCACCCCAGAAGCGAAATTC 59.829 55.000 0.00 0.00 0.00 2.17
1582 1757 5.845391 AAAACAAGCTACTAAAACAGGCA 57.155 34.783 0.00 0.00 0.00 4.75
1609 1786 9.922305 CATAACAAGCTACTAAAACAGATTAGC 57.078 33.333 0.00 0.00 36.54 3.09
1640 1817 2.209064 GACGAACTCTACTGGCCGCA 62.209 60.000 0.00 0.00 0.00 5.69
1652 1829 6.812998 TCAATAATATTTCCGAGGACGAACT 58.187 36.000 0.00 0.00 42.66 3.01
1674 1851 7.493645 CACTGCAACTACTAGATGATGAATTCA 59.506 37.037 11.26 11.26 39.12 2.57
1714 1894 3.660111 GAACAGGCCACACCGCAC 61.660 66.667 5.01 0.00 46.52 5.34
1740 1920 3.214328 AGGAAACAAACGAGCACAATCT 58.786 40.909 0.00 0.00 0.00 2.40
1741 1921 3.626028 AGGAAACAAACGAGCACAATC 57.374 42.857 0.00 0.00 0.00 2.67
1750 1930 6.500910 GCCCCTTTATATTAGGAAACAAACG 58.499 40.000 5.39 0.00 34.56 3.60
1758 1938 4.224370 GTGATCCGCCCCTTTATATTAGGA 59.776 45.833 5.39 0.00 34.56 2.94
1775 1955 2.096496 CAGGAATTTGCACGAGTGATCC 59.904 50.000 7.50 6.01 0.00 3.36
1780 1960 5.508200 TTTTTACAGGAATTTGCACGAGT 57.492 34.783 0.00 0.00 0.00 4.18
1854 2034 8.755696 TTACATGATTTCACATTTGCTTTACC 57.244 30.769 0.00 0.00 0.00 2.85
1893 2076 3.767902 AATTGTGTCCCCCAAAACATG 57.232 42.857 0.00 0.00 0.00 3.21
1902 2085 4.335416 TCTGAGATTCAAATTGTGTCCCC 58.665 43.478 0.00 0.00 0.00 4.81
1909 2092 9.472361 AAACTTGACATTCTGAGATTCAAATTG 57.528 29.630 4.05 0.00 0.00 2.32
1921 2104 5.126061 CCCTCCCATAAAACTTGACATTCTG 59.874 44.000 0.00 0.00 0.00 3.02
2137 2323 3.303924 CGAAGTGTGTTGAATGCATGTGA 60.304 43.478 0.00 0.00 0.00 3.58
2159 2347 3.767673 TGTCATGAGAAGTACCACTACCC 59.232 47.826 0.00 0.00 0.00 3.69
2196 2391 4.290969 GCTACTTCAACTTTGGTTTGAGC 58.709 43.478 0.00 0.00 32.73 4.26
2197 2392 4.527564 CGCTACTTCAACTTTGGTTTGAG 58.472 43.478 0.00 0.00 32.73 3.02
2198 2393 3.242936 GCGCTACTTCAACTTTGGTTTGA 60.243 43.478 0.00 0.00 32.73 2.69
2199 2394 3.042887 GCGCTACTTCAACTTTGGTTTG 58.957 45.455 0.00 0.00 32.73 2.93
2200 2395 2.034179 GGCGCTACTTCAACTTTGGTTT 59.966 45.455 7.64 0.00 32.73 3.27
2201 2396 1.607148 GGCGCTACTTCAACTTTGGTT 59.393 47.619 7.64 0.00 35.86 3.67
2202 2397 1.235724 GGCGCTACTTCAACTTTGGT 58.764 50.000 7.64 0.00 0.00 3.67
2203 2398 1.197721 CTGGCGCTACTTCAACTTTGG 59.802 52.381 7.64 0.00 0.00 3.28
2206 2401 1.070134 TCACTGGCGCTACTTCAACTT 59.930 47.619 7.64 0.00 0.00 2.66
2207 2402 0.679505 TCACTGGCGCTACTTCAACT 59.320 50.000 7.64 0.00 0.00 3.16
2208 2403 1.726853 ATCACTGGCGCTACTTCAAC 58.273 50.000 7.64 0.00 0.00 3.18
2209 2404 2.076100 CAATCACTGGCGCTACTTCAA 58.924 47.619 7.64 0.00 0.00 2.69
2210 2405 1.675714 CCAATCACTGGCGCTACTTCA 60.676 52.381 7.64 0.00 38.76 3.02
2211 2406 1.009829 CCAATCACTGGCGCTACTTC 58.990 55.000 7.64 0.00 38.76 3.01
2224 2419 6.778834 ATTCTGCACATCATTTACCAATCA 57.221 33.333 0.00 0.00 0.00 2.57
2229 2424 5.504010 CGTGGTATTCTGCACATCATTTACC 60.504 44.000 0.00 0.00 0.00 2.85
2235 2430 1.552792 TCCGTGGTATTCTGCACATCA 59.447 47.619 0.00 0.00 0.00 3.07
2236 2431 2.309528 TCCGTGGTATTCTGCACATC 57.690 50.000 0.00 0.00 0.00 3.06
2240 2435 2.675844 CGAATTTCCGTGGTATTCTGCA 59.324 45.455 11.72 0.00 0.00 4.41
2241 2436 2.031683 CCGAATTTCCGTGGTATTCTGC 59.968 50.000 11.72 0.00 0.00 4.26
2242 2437 2.612212 CCCGAATTTCCGTGGTATTCTG 59.388 50.000 11.72 7.43 0.00 3.02
2243 2438 2.420967 CCCCGAATTTCCGTGGTATTCT 60.421 50.000 11.72 0.00 0.00 2.40
2244 2439 1.944709 CCCCGAATTTCCGTGGTATTC 59.055 52.381 0.00 6.49 0.00 1.75
2246 2441 0.181824 CCCCCGAATTTCCGTGGTAT 59.818 55.000 0.00 0.00 0.00 2.73
2250 2447 0.606944 TTGTCCCCCGAATTTCCGTG 60.607 55.000 0.00 0.00 0.00 4.94
2261 2458 1.376812 CCGCACTTACTTGTCCCCC 60.377 63.158 0.00 0.00 0.00 5.40
2262 2459 1.376812 CCCGCACTTACTTGTCCCC 60.377 63.158 0.00 0.00 0.00 4.81
2266 2464 2.033602 GCCCCCGCACTTACTTGT 59.966 61.111 0.00 0.00 34.03 3.16
2285 2483 0.747283 GAGGCTTGGCAGGTGATGAG 60.747 60.000 0.00 0.00 0.00 2.90
2289 2487 4.704833 GCGAGGCTTGGCAGGTGA 62.705 66.667 3.44 0.00 0.00 4.02
2303 2501 4.077184 AAATCGACCAGGCGGCGA 62.077 61.111 12.98 13.37 42.35 5.54
2304 2502 3.864686 CAAATCGACCAGGCGGCG 61.865 66.667 0.51 0.51 34.57 6.46
2309 2507 2.464459 GCGAGCCAAATCGACCAGG 61.464 63.158 0.00 0.00 45.56 4.45
2311 2509 2.572095 ATCGCGAGCCAAATCGACCA 62.572 55.000 16.66 0.00 45.56 4.02
2313 2511 0.373716 AAATCGCGAGCCAAATCGAC 59.626 50.000 16.66 0.00 45.56 4.20
2327 2525 6.725246 AGGGATTAAATTACTTCGCAAATCG 58.275 36.000 0.00 0.00 40.15 3.34
2332 2530 5.492895 TGTGAGGGATTAAATTACTTCGCA 58.507 37.500 0.00 0.00 0.00 5.10
2333 2531 6.431198 TTGTGAGGGATTAAATTACTTCGC 57.569 37.500 0.00 0.00 0.00 4.70
2350 2548 4.630894 TGTTTTACTGTGCCTTTGTGAG 57.369 40.909 0.00 0.00 0.00 3.51
2351 2549 4.702612 TCTTGTTTTACTGTGCCTTTGTGA 59.297 37.500 0.00 0.00 0.00 3.58
2352 2550 4.992688 TCTTGTTTTACTGTGCCTTTGTG 58.007 39.130 0.00 0.00 0.00 3.33
2353 2551 5.047660 TGTTCTTGTTTTACTGTGCCTTTGT 60.048 36.000 0.00 0.00 0.00 2.83
2355 2553 5.652994 TGTTCTTGTTTTACTGTGCCTTT 57.347 34.783 0.00 0.00 0.00 3.11
2357 2555 4.278419 GGATGTTCTTGTTTTACTGTGCCT 59.722 41.667 0.00 0.00 0.00 4.75
2362 2560 4.154195 CCGAGGGATGTTCTTGTTTTACTG 59.846 45.833 0.00 0.00 0.00 2.74
2363 2561 4.041198 TCCGAGGGATGTTCTTGTTTTACT 59.959 41.667 0.00 0.00 0.00 2.24
2370 2568 3.334583 TCTTTCCGAGGGATGTTCTTG 57.665 47.619 0.00 0.00 0.00 3.02
2373 2571 5.880887 ACTTAAATCTTTCCGAGGGATGTTC 59.119 40.000 0.00 0.00 0.00 3.18
2374 2572 5.816682 ACTTAAATCTTTCCGAGGGATGTT 58.183 37.500 0.00 0.00 0.00 2.71
2375 2573 5.437191 ACTTAAATCTTTCCGAGGGATGT 57.563 39.130 0.00 0.00 0.00 3.06
2376 2574 6.374333 TGAAACTTAAATCTTTCCGAGGGATG 59.626 38.462 0.00 0.00 0.00 3.51
2377 2575 6.481643 TGAAACTTAAATCTTTCCGAGGGAT 58.518 36.000 0.00 0.00 0.00 3.85
2380 2578 6.966021 TGTTGAAACTTAAATCTTTCCGAGG 58.034 36.000 0.00 0.00 0.00 4.63
2427 2625 5.606348 ACTTGTTGAAACTGGGCATTTAA 57.394 34.783 0.00 0.00 0.00 1.52
2478 2678 6.961359 TTATTTTGTGTCTATGACCGACAG 57.039 37.500 0.00 0.00 41.62 3.51
2482 2682 9.787532 AAATCAATTATTTTGTGTCTATGACCG 57.212 29.630 0.00 0.00 33.91 4.79
2501 2705 4.253685 ACGAGTGACCGATCAAAATCAAT 58.746 39.130 0.00 0.00 36.31 2.57
2510 2714 4.612932 AACTTAGTACGAGTGACCGATC 57.387 45.455 5.83 0.00 0.00 3.69
2515 2719 7.168637 TCAATGTTGAAACTTAGTACGAGTGAC 59.831 37.037 5.83 4.68 33.55 3.67
2517 2721 7.402811 TCAATGTTGAAACTTAGTACGAGTG 57.597 36.000 5.83 0.00 33.55 3.51
2598 2804 0.582005 GTGTTTCTCGTGACCAGCAC 59.418 55.000 0.00 0.00 44.21 4.40
2599 2805 0.176910 TGTGTTTCTCGTGACCAGCA 59.823 50.000 0.00 0.00 0.00 4.41
2601 2807 5.408299 TCATAATTGTGTTTCTCGTGACCAG 59.592 40.000 1.86 0.00 0.00 4.00
2657 2863 7.383102 TCCAATTTGCAAAGTTCTAGATCTC 57.617 36.000 18.19 0.00 0.00 2.75
2658 2864 7.576477 GCTTCCAATTTGCAAAGTTCTAGATCT 60.576 37.037 18.19 0.00 0.00 2.75
2662 2868 4.925646 GGCTTCCAATTTGCAAAGTTCTAG 59.074 41.667 18.19 11.61 0.00 2.43
2673 2879 6.862608 GGCTTTTAATTTTGGCTTCCAATTTG 59.137 34.615 0.00 0.00 43.55 2.32
2678 2884 3.556004 CCGGCTTTTAATTTTGGCTTCCA 60.556 43.478 0.00 0.00 0.00 3.53
2691 2897 0.891904 GTCCCTTGTGCCGGCTTTTA 60.892 55.000 29.70 3.37 0.00 1.52


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

AutoCloner maintained by Alex Coulton.