Multiple sequence alignment - TraesCS3B01G455700

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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 TraesCS3B01G455700 chr3B 100.000 4976 0 0 1 4976 697168362 697163387 0.000000e+00 9190.0
1 TraesCS3B01G455700 chr3B 99.758 2482 6 0 2343 4824 736480904 736483385 0.000000e+00 4551.0
2 TraesCS3B01G455700 chr3B 88.358 1675 135 16 683 2334 71887343 71888980 0.000000e+00 1958.0
3 TraesCS3B01G455700 chr3B 89.421 397 42 0 44 440 555555304 555554908 7.440000e-138 501.0
4 TraesCS3B01G455700 chr3B 84.936 312 27 11 2025 2334 763300924 763300631 1.050000e-76 298.0
5 TraesCS3B01G455700 chr3B 90.385 208 18 2 2129 2334 819475279 819475486 6.350000e-69 272.0
6 TraesCS3B01G455700 chr1A 99.337 4221 25 2 601 4821 244504208 244499991 0.000000e+00 7637.0
7 TraesCS3B01G455700 chr1A 88.537 1675 138 16 683 2334 474154620 474156263 0.000000e+00 1980.0
8 TraesCS3B01G455700 chr1A 94.410 1288 70 1 3398 4685 529400617 529401902 0.000000e+00 1978.0
9 TraesCS3B01G455700 chr1A 91.667 216 14 3 4728 4939 185849520 185849735 3.770000e-76 296.0
10 TraesCS3B01G455700 chr5A 94.633 3913 164 14 922 4828 381553268 381549396 0.000000e+00 6021.0
11 TraesCS3B01G455700 chr5A 91.852 1755 97 14 601 2334 568064863 568066592 0.000000e+00 2407.0
12 TraesCS3B01G455700 chr5A 99.094 552 5 0 44 595 606398612 606398061 0.000000e+00 992.0
13 TraesCS3B01G455700 chr5A 88.125 320 36 2 601 918 381563752 381563433 3.640000e-101 379.0
14 TraesCS3B01G455700 chr5A 90.643 171 13 2 4769 4936 595922814 595922644 1.800000e-54 224.0
15 TraesCS3B01G455700 chr5A 86.598 97 10 1 601 697 549322017 549321924 2.450000e-18 104.0
16 TraesCS3B01G455700 chr5A 96.875 32 1 0 19 50 504758513 504758544 3.000000e-03 54.7
17 TraesCS3B01G455700 chr6B 99.597 2483 10 0 2343 4825 159797093 159799575 0.000000e+00 4530.0
18 TraesCS3B01G455700 chr6B 90.869 1599 111 19 2331 3901 232748042 232749633 0.000000e+00 2111.0
19 TraesCS3B01G455700 chr6B 90.323 403 37 2 38 439 247039215 247038814 1.230000e-145 527.0
20 TraesCS3B01G455700 chr6B 95.783 166 6 1 431 595 247038874 247038709 2.950000e-67 267.0
21 TraesCS3B01G455700 chr7A 99.597 2483 8 2 2343 4823 56201834 56199352 0.000000e+00 4529.0
22 TraesCS3B01G455700 chr7A 96.147 2362 77 10 2331 4682 630037505 630039862 0.000000e+00 3845.0
23 TraesCS3B01G455700 chr7A 89.582 1747 127 19 601 2334 607420501 607422205 0.000000e+00 2167.0
24 TraesCS3B01G455700 chr7A 90.994 1599 109 19 2331 3901 464232704 464234295 0.000000e+00 2122.0
25 TraesCS3B01G455700 chr7A 89.394 396 42 0 44 439 321638897 321638502 2.670000e-137 499.0
26 TraesCS3B01G455700 chr7A 95.783 166 6 1 431 595 321638562 321638397 2.950000e-67 267.0
27 TraesCS3B01G455700 chr7A 89.706 136 8 6 4685 4814 630042411 630042546 8.570000e-38 169.0
28 TraesCS3B01G455700 chr7A 90.179 112 6 4 4684 4793 464236792 464236900 1.870000e-29 141.0
29 TraesCS3B01G455700 chr1D 97.005 1870 53 2 2816 4685 251295251 251297117 0.000000e+00 3140.0
30 TraesCS3B01G455700 chr4D 96.501 1286 45 0 2331 3616 471711485 471710200 0.000000e+00 2126.0
31 TraesCS3B01G455700 chr7B 88.776 1675 133 17 683 2334 32562477 32560835 0.000000e+00 2001.0
32 TraesCS3B01G455700 chr7B 88.074 1677 141 24 683 2334 161929333 161930975 0.000000e+00 1934.0
33 TraesCS3B01G455700 chr2D 93.393 1347 80 8 3340 4684 267287978 267289317 0.000000e+00 1986.0
34 TraesCS3B01G455700 chr2D 89.595 173 15 3 4771 4942 166155495 166155665 3.020000e-52 217.0
35 TraesCS3B01G455700 chr2B 88.597 1675 136 17 683 2334 54143 55785 0.000000e+00 1984.0
36 TraesCS3B01G455700 chr3A 88.478 1675 137 17 683 2334 704401397 704399756 0.000000e+00 1973.0
37 TraesCS3B01G455700 chr3A 91.111 135 7 4 4684 4816 95543376 95543245 1.420000e-40 178.0
38 TraesCS3B01G455700 chr3A 84.663 163 24 1 430 591 640036818 640036656 1.430000e-35 161.0
39 TraesCS3B01G455700 chr1B 88.060 1675 142 18 683 2334 112365207 112363568 0.000000e+00 1932.0
40 TraesCS3B01G455700 chr1B 87.947 1676 145 20 683 2334 569422578 569424220 0.000000e+00 1923.0
41 TraesCS3B01G455700 chr1B 92.063 63 4 1 635 697 39295379 39295318 2.470000e-13 87.9
42 TraesCS3B01G455700 chr2A 88.007 1676 146 17 683 2334 719357127 719355483 0.000000e+00 1930.0
43 TraesCS3B01G455700 chr2A 94.492 236 13 0 2099 2334 424506828 424506593 1.020000e-96 364.0
44 TraesCS3B01G455700 chr2A 86.170 282 34 2 121 401 46326170 46326447 2.910000e-77 300.0
45 TraesCS3B01G455700 chr2A 97.872 141 3 0 44 184 216749496 216749356 1.380000e-60 244.0
46 TraesCS3B01G455700 chr2A 91.515 165 11 2 4786 4947 409161147 409161311 1.800000e-54 224.0
47 TraesCS3B01G455700 chr2A 80.508 118 20 3 28 144 516304996 516304881 2.470000e-13 87.9
48 TraesCS3B01G455700 chr2A 83.146 89 14 1 40 127 348616158 348616246 4.130000e-11 80.5
49 TraesCS3B01G455700 chr4A 90.657 396 37 0 44 439 729649423 729649028 1.230000e-145 527.0
50 TraesCS3B01G455700 chr4A 95.181 166 7 1 431 595 729649088 729648923 1.370000e-65 261.0
51 TraesCS3B01G455700 chr4A 91.411 163 13 1 4812 4974 650392111 650392272 6.480000e-54 222.0
52 TraesCS3B01G455700 chr4B 90.959 365 33 0 76 440 16782265 16782629 4.480000e-135 492.0
53 TraesCS3B01G455700 chr7D 84.519 478 54 16 136 595 446554587 446554112 5.870000e-124 455.0
54 TraesCS3B01G455700 chr7D 93.103 87 6 0 254 340 446554429 446554343 1.450000e-25 128.0
55 TraesCS3B01G455700 chr3D 95.181 166 7 1 431 595 16431812 16431977 1.370000e-65 261.0
56 TraesCS3B01G455700 chrUn 91.444 187 14 2 4755 4939 250550480 250550294 6.390000e-64 255.0
57 TraesCS3B01G455700 chrUn 91.444 187 14 2 4755 4939 261964565 261964379 6.390000e-64 255.0
58 TraesCS3B01G455700 chrUn 91.053 190 15 2 4752 4939 273752490 273752679 6.390000e-64 255.0
59 TraesCS3B01G455700 chr5B 91.411 163 13 1 4781 4942 166654187 166654025 6.480000e-54 222.0
60 TraesCS3B01G455700 chr6A 84.848 132 20 0 308 439 2970523 2970392 3.130000e-27 134.0
61 TraesCS3B01G455700 chr6A 84.848 132 20 0 308 439 107697305 107697436 3.130000e-27 134.0


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 TraesCS3B01G455700 chr3B 697163387 697168362 4975 True 9190.0 9190 100.0000 1 4976 1 chr3B.!!$R2 4975
1 TraesCS3B01G455700 chr3B 736480904 736483385 2481 False 4551.0 4551 99.7580 2343 4824 1 chr3B.!!$F2 2481
2 TraesCS3B01G455700 chr3B 71887343 71888980 1637 False 1958.0 1958 88.3580 683 2334 1 chr3B.!!$F1 1651
3 TraesCS3B01G455700 chr1A 244499991 244504208 4217 True 7637.0 7637 99.3370 601 4821 1 chr1A.!!$R1 4220
4 TraesCS3B01G455700 chr1A 474154620 474156263 1643 False 1980.0 1980 88.5370 683 2334 1 chr1A.!!$F2 1651
5 TraesCS3B01G455700 chr1A 529400617 529401902 1285 False 1978.0 1978 94.4100 3398 4685 1 chr1A.!!$F3 1287
6 TraesCS3B01G455700 chr5A 381549396 381553268 3872 True 6021.0 6021 94.6330 922 4828 1 chr5A.!!$R1 3906
7 TraesCS3B01G455700 chr5A 568064863 568066592 1729 False 2407.0 2407 91.8520 601 2334 1 chr5A.!!$F2 1733
8 TraesCS3B01G455700 chr5A 606398061 606398612 551 True 992.0 992 99.0940 44 595 1 chr5A.!!$R5 551
9 TraesCS3B01G455700 chr6B 159797093 159799575 2482 False 4530.0 4530 99.5970 2343 4825 1 chr6B.!!$F1 2482
10 TraesCS3B01G455700 chr6B 232748042 232749633 1591 False 2111.0 2111 90.8690 2331 3901 1 chr6B.!!$F2 1570
11 TraesCS3B01G455700 chr6B 247038709 247039215 506 True 397.0 527 93.0530 38 595 2 chr6B.!!$R1 557
12 TraesCS3B01G455700 chr7A 56199352 56201834 2482 True 4529.0 4529 99.5970 2343 4823 1 chr7A.!!$R1 2480
13 TraesCS3B01G455700 chr7A 607420501 607422205 1704 False 2167.0 2167 89.5820 601 2334 1 chr7A.!!$F1 1733
14 TraesCS3B01G455700 chr7A 630037505 630042546 5041 False 2007.0 3845 92.9265 2331 4814 2 chr7A.!!$F3 2483
15 TraesCS3B01G455700 chr7A 464232704 464236900 4196 False 1131.5 2122 90.5865 2331 4793 2 chr7A.!!$F2 2462
16 TraesCS3B01G455700 chr7A 321638397 321638897 500 True 383.0 499 92.5885 44 595 2 chr7A.!!$R2 551
17 TraesCS3B01G455700 chr1D 251295251 251297117 1866 False 3140.0 3140 97.0050 2816 4685 1 chr1D.!!$F1 1869
18 TraesCS3B01G455700 chr4D 471710200 471711485 1285 True 2126.0 2126 96.5010 2331 3616 1 chr4D.!!$R1 1285
19 TraesCS3B01G455700 chr7B 32560835 32562477 1642 True 2001.0 2001 88.7760 683 2334 1 chr7B.!!$R1 1651
20 TraesCS3B01G455700 chr7B 161929333 161930975 1642 False 1934.0 1934 88.0740 683 2334 1 chr7B.!!$F1 1651
21 TraesCS3B01G455700 chr2D 267287978 267289317 1339 False 1986.0 1986 93.3930 3340 4684 1 chr2D.!!$F2 1344
22 TraesCS3B01G455700 chr2B 54143 55785 1642 False 1984.0 1984 88.5970 683 2334 1 chr2B.!!$F1 1651
23 TraesCS3B01G455700 chr3A 704399756 704401397 1641 True 1973.0 1973 88.4780 683 2334 1 chr3A.!!$R3 1651
24 TraesCS3B01G455700 chr1B 112363568 112365207 1639 True 1932.0 1932 88.0600 683 2334 1 chr1B.!!$R2 1651
25 TraesCS3B01G455700 chr1B 569422578 569424220 1642 False 1923.0 1923 87.9470 683 2334 1 chr1B.!!$F1 1651
26 TraesCS3B01G455700 chr2A 719355483 719357127 1644 True 1930.0 1930 88.0070 683 2334 1 chr2A.!!$R4 1651
27 TraesCS3B01G455700 chr4A 729648923 729649423 500 True 394.0 527 92.9190 44 595 2 chr4A.!!$R1 551

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
960 976 0.683504 TTGAGCGGTAGGAGAGACCC 60.684 60.0 0.00 0.00 40.05 4.46 F
1208 1224 0.400213 TCACGGTGAAAATCCCAGCT 59.600 50.0 8.68 0.00 0.00 4.24 F
1209 1225 0.523072 CACGGTGAAAATCCCAGCTG 59.477 55.0 6.78 6.78 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2127 2194 4.379243 CTCTGCCGTTCCGCCAGT 62.379 66.667 0.00 0.0 0.00 4.00 R
3450 3527 0.251354 GCTGGATCTGACAGGAGCAA 59.749 55.000 1.81 0.0 36.48 3.91 R
4831 7850 0.036306 GGTGAACCCACGGAGTCAAT 59.964 55.000 0.00 0.0 41.61 2.57 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
24 25 6.307776 CCCTAATCTTTCCCTAATCTTTCCC 58.692 44.000 0.00 0.00 0.00 3.97
25 26 6.103353 CCCTAATCTTTCCCTAATCTTTCCCT 59.897 42.308 0.00 0.00 0.00 4.20
26 27 7.294958 CCCTAATCTTTCCCTAATCTTTCCCTA 59.705 40.741 0.00 0.00 0.00 3.53
27 28 8.895624 CCTAATCTTTCCCTAATCTTTCCCTAT 58.104 37.037 0.00 0.00 0.00 2.57
28 29 9.952030 CTAATCTTTCCCTAATCTTTCCCTATC 57.048 37.037 0.00 0.00 0.00 2.08
29 30 6.765355 TCTTTCCCTAATCTTTCCCTATCC 57.235 41.667 0.00 0.00 0.00 2.59
30 31 5.611408 TCTTTCCCTAATCTTTCCCTATCCC 59.389 44.000 0.00 0.00 0.00 3.85
31 32 4.871806 TCCCTAATCTTTCCCTATCCCT 57.128 45.455 0.00 0.00 0.00 4.20
32 33 5.980040 TCCCTAATCTTTCCCTATCCCTA 57.020 43.478 0.00 0.00 0.00 3.53
33 34 6.515763 TCCCTAATCTTTCCCTATCCCTAT 57.484 41.667 0.00 0.00 0.00 2.57
34 35 6.513033 TCCCTAATCTTTCCCTATCCCTATC 58.487 44.000 0.00 0.00 0.00 2.08
35 36 5.668080 CCCTAATCTTTCCCTATCCCTATCC 59.332 48.000 0.00 0.00 0.00 2.59
36 37 5.668080 CCTAATCTTTCCCTATCCCTATCCC 59.332 48.000 0.00 0.00 0.00 3.85
595 597 4.640690 AGGGGAGGTGCGGTGTCT 62.641 66.667 0.00 0.00 0.00 3.41
596 598 4.394712 GGGGAGGTGCGGTGTCTG 62.395 72.222 0.00 0.00 0.00 3.51
597 599 3.626924 GGGAGGTGCGGTGTCTGT 61.627 66.667 0.00 0.00 0.00 3.41
598 600 2.426023 GGAGGTGCGGTGTCTGTT 59.574 61.111 0.00 0.00 0.00 3.16
599 601 1.227853 GGAGGTGCGGTGTCTGTTT 60.228 57.895 0.00 0.00 0.00 2.83
740 755 3.338250 GCCTCCCACCACATCCCA 61.338 66.667 0.00 0.00 0.00 4.37
784 799 2.444140 CTGCCGCCCCTACCTAGT 60.444 66.667 0.00 0.00 0.00 2.57
870 886 0.904865 AGATCCAACCACCGCAGAGA 60.905 55.000 0.00 0.00 0.00 3.10
960 976 0.683504 TTGAGCGGTAGGAGAGACCC 60.684 60.000 0.00 0.00 40.05 4.46
961 977 1.829096 GAGCGGTAGGAGAGACCCC 60.829 68.421 0.00 0.00 40.05 4.95
1197 1213 2.678580 TCGGCCATCTCACGGTGA 60.679 61.111 10.88 10.88 0.00 4.02
1198 1214 2.225791 CTCGGCCATCTCACGGTGAA 62.226 60.000 12.54 4.09 0.00 3.18
1199 1215 1.375396 CGGCCATCTCACGGTGAAA 60.375 57.895 12.54 0.00 0.00 2.69
1200 1216 0.953471 CGGCCATCTCACGGTGAAAA 60.953 55.000 12.54 3.89 0.00 2.29
1201 1217 1.463674 GGCCATCTCACGGTGAAAAT 58.536 50.000 12.54 6.11 0.00 1.82
1202 1218 1.401905 GGCCATCTCACGGTGAAAATC 59.598 52.381 12.54 1.08 0.00 2.17
1203 1219 1.401905 GCCATCTCACGGTGAAAATCC 59.598 52.381 12.54 0.00 0.00 3.01
1204 1220 2.017049 CCATCTCACGGTGAAAATCCC 58.983 52.381 12.54 0.00 0.00 3.85
1205 1221 2.617788 CCATCTCACGGTGAAAATCCCA 60.618 50.000 12.54 0.00 0.00 4.37
1206 1222 2.472695 TCTCACGGTGAAAATCCCAG 57.527 50.000 12.54 0.00 0.00 4.45
1207 1223 0.804989 CTCACGGTGAAAATCCCAGC 59.195 55.000 12.54 0.00 0.00 4.85
1208 1224 0.400213 TCACGGTGAAAATCCCAGCT 59.600 50.000 8.68 0.00 0.00 4.24
1209 1225 0.523072 CACGGTGAAAATCCCAGCTG 59.477 55.000 6.78 6.78 0.00 4.24
1210 1226 0.609131 ACGGTGAAAATCCCAGCTGG 60.609 55.000 26.87 26.87 0.00 4.85
1211 1227 1.893062 GGTGAAAATCCCAGCTGGC 59.107 57.895 28.39 13.03 0.00 4.85
1212 1228 1.508088 GTGAAAATCCCAGCTGGCG 59.492 57.895 28.39 19.98 0.00 5.69
1213 1229 1.678635 TGAAAATCCCAGCTGGCGG 60.679 57.895 28.39 15.11 0.00 6.13
1214 1230 2.362889 AAAATCCCAGCTGGCGGG 60.363 61.111 28.39 14.71 46.03 6.13
1215 1231 3.224007 AAAATCCCAGCTGGCGGGT 62.224 57.895 28.39 8.26 44.81 5.28
1216 1232 3.944250 AAATCCCAGCTGGCGGGTG 62.944 63.158 28.39 18.40 44.81 4.61
1626 1682 1.218047 GGCATGCGACTCTGTACCA 59.782 57.895 12.44 0.00 0.00 3.25
1936 1996 4.718858 TTTAACAAACACGAGATGACGG 57.281 40.909 0.00 0.00 37.61 4.79
2014 2077 3.093057 TGACAGTCTGATCTGTAGGCT 57.907 47.619 6.91 0.00 46.81 4.58
2127 2194 2.092968 GTGGATCATGGTGGCTTCACTA 60.093 50.000 0.00 0.00 41.00 2.74
3450 3527 2.259818 CTGCTGGTCTTCGTCGCT 59.740 61.111 0.00 0.00 0.00 4.93
4836 7855 9.257651 ACTAGTAATAATAAAGCACGGATTGAC 57.742 33.333 0.00 0.00 0.00 3.18
4837 7856 9.477484 CTAGTAATAATAAAGCACGGATTGACT 57.523 33.333 0.00 0.00 0.00 3.41
4838 7857 8.366671 AGTAATAATAAAGCACGGATTGACTC 57.633 34.615 0.00 0.00 0.00 3.36
4839 7858 6.619801 AATAATAAAGCACGGATTGACTCC 57.380 37.500 0.00 0.00 41.07 3.85
4847 7866 3.154589 GGATTGACTCCGTGGGTTC 57.845 57.895 0.00 0.00 33.29 3.62
4848 7867 0.323629 GGATTGACTCCGTGGGTTCA 59.676 55.000 0.00 0.00 33.29 3.18
4849 7868 1.439679 GATTGACTCCGTGGGTTCAC 58.560 55.000 0.00 0.00 40.36 3.18
4850 7869 0.036306 ATTGACTCCGTGGGTTCACC 59.964 55.000 0.00 0.00 40.65 4.02
4851 7870 2.048503 GACTCCGTGGGTTCACCG 60.049 66.667 0.00 0.00 44.64 4.94
4852 7871 2.841044 ACTCCGTGGGTTCACCGT 60.841 61.111 0.00 0.00 44.64 4.83
4853 7872 2.048503 CTCCGTGGGTTCACCGTC 60.049 66.667 0.00 0.00 44.64 4.79
4854 7873 2.838693 TCCGTGGGTTCACCGTCA 60.839 61.111 0.00 0.00 44.64 4.35
4855 7874 2.663852 CCGTGGGTTCACCGTCAC 60.664 66.667 0.00 0.00 44.64 3.67
4856 7875 2.107343 CGTGGGTTCACCGTCACA 59.893 61.111 6.29 0.00 44.64 3.58
4857 7876 1.521906 CGTGGGTTCACCGTCACAA 60.522 57.895 6.29 0.00 44.64 3.33
4858 7877 0.882927 CGTGGGTTCACCGTCACAAT 60.883 55.000 6.29 0.00 44.64 2.71
4859 7878 1.605968 CGTGGGTTCACCGTCACAATA 60.606 52.381 6.29 0.00 44.64 1.90
4860 7879 1.802365 GTGGGTTCACCGTCACAATAC 59.198 52.381 1.63 0.00 44.64 1.89
4861 7880 1.073177 GGGTTCACCGTCACAATACG 58.927 55.000 0.00 0.00 42.49 3.06
4862 7881 0.441145 GGTTCACCGTCACAATACGC 59.559 55.000 0.00 0.00 41.51 4.42
4863 7882 1.425412 GTTCACCGTCACAATACGCT 58.575 50.000 0.00 0.00 41.51 5.07
4864 7883 1.796459 GTTCACCGTCACAATACGCTT 59.204 47.619 0.00 0.00 41.51 4.68
4865 7884 2.157834 TCACCGTCACAATACGCTTT 57.842 45.000 0.00 0.00 41.51 3.51
4866 7885 2.063266 TCACCGTCACAATACGCTTTC 58.937 47.619 0.00 0.00 41.51 2.62
4867 7886 2.066262 CACCGTCACAATACGCTTTCT 58.934 47.619 0.00 0.00 41.51 2.52
4868 7887 2.478894 CACCGTCACAATACGCTTTCTT 59.521 45.455 0.00 0.00 41.51 2.52
4869 7888 2.735134 ACCGTCACAATACGCTTTCTTC 59.265 45.455 0.00 0.00 41.51 2.87
4870 7889 2.993899 CCGTCACAATACGCTTTCTTCT 59.006 45.455 0.00 0.00 41.51 2.85
4871 7890 3.060895 CCGTCACAATACGCTTTCTTCTC 59.939 47.826 0.00 0.00 41.51 2.87
4872 7891 3.241364 CGTCACAATACGCTTTCTTCTCG 60.241 47.826 0.00 0.00 35.87 4.04
4873 7892 3.673809 GTCACAATACGCTTTCTTCTCGT 59.326 43.478 0.00 0.00 39.88 4.18
4874 7893 3.673338 TCACAATACGCTTTCTTCTCGTG 59.327 43.478 0.00 0.00 37.61 4.35
4875 7894 3.428870 CACAATACGCTTTCTTCTCGTGT 59.571 43.478 0.00 0.00 37.61 4.49
4876 7895 3.673809 ACAATACGCTTTCTTCTCGTGTC 59.326 43.478 0.00 0.00 37.61 3.67
4877 7896 3.570926 ATACGCTTTCTTCTCGTGTCA 57.429 42.857 0.00 0.00 37.61 3.58
4878 7897 2.440539 ACGCTTTCTTCTCGTGTCAT 57.559 45.000 0.00 0.00 34.92 3.06
4879 7898 3.570926 ACGCTTTCTTCTCGTGTCATA 57.429 42.857 0.00 0.00 34.92 2.15
4880 7899 3.909430 ACGCTTTCTTCTCGTGTCATAA 58.091 40.909 0.00 0.00 34.92 1.90
4881 7900 4.495422 ACGCTTTCTTCTCGTGTCATAAT 58.505 39.130 0.00 0.00 34.92 1.28
4882 7901 5.647589 ACGCTTTCTTCTCGTGTCATAATA 58.352 37.500 0.00 0.00 34.92 0.98
4883 7902 5.515626 ACGCTTTCTTCTCGTGTCATAATAC 59.484 40.000 0.00 0.00 34.92 1.89
4884 7903 5.330866 CGCTTTCTTCTCGTGTCATAATACG 60.331 44.000 0.00 0.00 40.91 3.06
4885 7904 5.554696 GCTTTCTTCTCGTGTCATAATACGC 60.555 44.000 0.00 0.00 39.56 4.42
4886 7905 4.895224 TCTTCTCGTGTCATAATACGCT 57.105 40.909 0.00 0.00 39.56 5.07
4887 7906 5.244785 TCTTCTCGTGTCATAATACGCTT 57.755 39.130 0.00 0.00 39.56 4.68
4888 7907 5.647589 TCTTCTCGTGTCATAATACGCTTT 58.352 37.500 0.00 0.00 39.56 3.51
4889 7908 6.097356 TCTTCTCGTGTCATAATACGCTTTT 58.903 36.000 0.00 0.00 39.56 2.27
4890 7909 7.252708 TCTTCTCGTGTCATAATACGCTTTTA 58.747 34.615 0.00 0.00 39.56 1.52
4891 7910 7.919091 TCTTCTCGTGTCATAATACGCTTTTAT 59.081 33.333 0.00 0.00 39.56 1.40
4892 7911 7.389603 TCTCGTGTCATAATACGCTTTTATG 57.610 36.000 6.35 6.35 39.56 1.90
4893 7912 7.197703 TCTCGTGTCATAATACGCTTTTATGA 58.802 34.615 9.82 9.82 41.45 2.15
4894 7913 7.865889 TCTCGTGTCATAATACGCTTTTATGAT 59.134 33.333 14.55 0.00 43.93 2.45
4895 7914 8.360325 TCGTGTCATAATACGCTTTTATGATT 57.640 30.769 14.55 0.00 43.93 2.57
4896 7915 8.822855 TCGTGTCATAATACGCTTTTATGATTT 58.177 29.630 14.55 0.00 43.93 2.17
4897 7916 8.882199 CGTGTCATAATACGCTTTTATGATTTG 58.118 33.333 14.55 7.18 43.93 2.32
4898 7917 9.716507 GTGTCATAATACGCTTTTATGATTTGT 57.283 29.630 14.55 0.00 43.93 2.83
4928 7947 9.498307 GACAAAATTGTAATATAAACGAGGTGG 57.502 33.333 0.00 0.00 42.43 4.61
4929 7948 9.016438 ACAAAATTGTAATATAAACGAGGTGGT 57.984 29.630 0.00 0.00 40.16 4.16
4932 7951 9.895138 AAATTGTAATATAAACGAGGTGGTACT 57.105 29.630 0.00 0.00 0.00 2.73
4939 7958 8.897872 ATATAAACGAGGTGGTACTAATTTGG 57.102 34.615 0.00 0.00 0.00 3.28
4940 7959 3.622166 ACGAGGTGGTACTAATTTGGG 57.378 47.619 0.00 0.00 0.00 4.12
4941 7960 2.237893 ACGAGGTGGTACTAATTTGGGG 59.762 50.000 0.00 0.00 0.00 4.96
4942 7961 2.420967 CGAGGTGGTACTAATTTGGGGG 60.421 54.545 0.00 0.00 0.00 5.40
4943 7962 2.579400 GAGGTGGTACTAATTTGGGGGT 59.421 50.000 0.00 0.00 0.00 4.95
4944 7963 2.579400 AGGTGGTACTAATTTGGGGGTC 59.421 50.000 0.00 0.00 0.00 4.46
4945 7964 2.635714 GTGGTACTAATTTGGGGGTCG 58.364 52.381 0.00 0.00 0.00 4.79
4946 7965 2.026915 GTGGTACTAATTTGGGGGTCGT 60.027 50.000 0.00 0.00 0.00 4.34
4947 7966 2.236893 TGGTACTAATTTGGGGGTCGTC 59.763 50.000 0.00 0.00 0.00 4.20
4948 7967 2.236893 GGTACTAATTTGGGGGTCGTCA 59.763 50.000 0.00 0.00 0.00 4.35
4949 7968 3.118149 GGTACTAATTTGGGGGTCGTCAT 60.118 47.826 0.00 0.00 0.00 3.06
4950 7969 3.277142 ACTAATTTGGGGGTCGTCATC 57.723 47.619 0.00 0.00 0.00 2.92
4951 7970 2.844348 ACTAATTTGGGGGTCGTCATCT 59.156 45.455 0.00 0.00 0.00 2.90
4952 7971 4.035112 ACTAATTTGGGGGTCGTCATCTA 58.965 43.478 0.00 0.00 0.00 1.98
4953 7972 3.277142 AATTTGGGGGTCGTCATCTAC 57.723 47.619 0.00 0.00 0.00 2.59
4954 7973 1.646912 TTTGGGGGTCGTCATCTACA 58.353 50.000 0.00 0.00 0.00 2.74
4955 7974 1.874129 TTGGGGGTCGTCATCTACAT 58.126 50.000 0.00 0.00 0.00 2.29
4956 7975 1.874129 TGGGGGTCGTCATCTACATT 58.126 50.000 0.00 0.00 0.00 2.71
4957 7976 1.760613 TGGGGGTCGTCATCTACATTC 59.239 52.381 0.00 0.00 0.00 2.67
4958 7977 1.070289 GGGGGTCGTCATCTACATTCC 59.930 57.143 0.00 0.00 0.00 3.01
4959 7978 1.269621 GGGGTCGTCATCTACATTCCG 60.270 57.143 0.00 0.00 0.00 4.30
4960 7979 1.407979 GGGTCGTCATCTACATTCCGT 59.592 52.381 0.00 0.00 0.00 4.69
4961 7980 2.159142 GGGTCGTCATCTACATTCCGTT 60.159 50.000 0.00 0.00 0.00 4.44
4962 7981 3.114065 GGTCGTCATCTACATTCCGTTC 58.886 50.000 0.00 0.00 0.00 3.95
4963 7982 3.114065 GTCGTCATCTACATTCCGTTCC 58.886 50.000 0.00 0.00 0.00 3.62
4964 7983 2.117137 CGTCATCTACATTCCGTTCCG 58.883 52.381 0.00 0.00 0.00 4.30
4965 7984 2.479049 CGTCATCTACATTCCGTTCCGT 60.479 50.000 0.00 0.00 0.00 4.69
4966 7985 3.114065 GTCATCTACATTCCGTTCCGTC 58.886 50.000 0.00 0.00 0.00 4.79
4967 7986 2.756207 TCATCTACATTCCGTTCCGTCA 59.244 45.455 0.00 0.00 0.00 4.35
4968 7987 3.193903 TCATCTACATTCCGTTCCGTCAA 59.806 43.478 0.00 0.00 0.00 3.18
4969 7988 2.950433 TCTACATTCCGTTCCGTCAAC 58.050 47.619 0.00 0.00 0.00 3.18
4970 7989 2.559668 TCTACATTCCGTTCCGTCAACT 59.440 45.455 0.00 0.00 32.09 3.16
4971 7990 1.508632 ACATTCCGTTCCGTCAACTG 58.491 50.000 0.00 0.00 32.09 3.16
4972 7991 1.202604 ACATTCCGTTCCGTCAACTGT 60.203 47.619 0.00 0.00 32.09 3.55
4973 7992 1.459592 CATTCCGTTCCGTCAACTGTC 59.540 52.381 0.00 0.00 32.09 3.51
4974 7993 0.748450 TTCCGTTCCGTCAACTGTCT 59.252 50.000 0.00 0.00 32.09 3.41
4975 7994 1.608055 TCCGTTCCGTCAACTGTCTA 58.392 50.000 0.00 0.00 32.09 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.103353 AGGGAAAGATTAGGGAAAGATTAGGG 59.897 42.308 0.00 0.00 0.00 3.53
1 2 7.155442 AGGGAAAGATTAGGGAAAGATTAGG 57.845 40.000 0.00 0.00 0.00 2.69
3 4 8.891501 GGATAGGGAAAGATTAGGGAAAGATTA 58.108 37.037 0.00 0.00 0.00 1.75
4 5 7.202326 GGGATAGGGAAAGATTAGGGAAAGATT 60.202 40.741 0.00 0.00 0.00 2.40
5 6 6.275855 GGGATAGGGAAAGATTAGGGAAAGAT 59.724 42.308 0.00 0.00 0.00 2.40
6 7 5.611408 GGGATAGGGAAAGATTAGGGAAAGA 59.389 44.000 0.00 0.00 0.00 2.52
7 8 5.613116 AGGGATAGGGAAAGATTAGGGAAAG 59.387 44.000 0.00 0.00 0.00 2.62
8 9 5.558379 AGGGATAGGGAAAGATTAGGGAAA 58.442 41.667 0.00 0.00 0.00 3.13
9 10 5.185475 AGGGATAGGGAAAGATTAGGGAA 57.815 43.478 0.00 0.00 0.00 3.97
10 11 4.871806 AGGGATAGGGAAAGATTAGGGA 57.128 45.455 0.00 0.00 0.00 4.20
11 12 5.668080 GGATAGGGATAGGGAAAGATTAGGG 59.332 48.000 0.00 0.00 0.00 3.53
12 13 5.668080 GGGATAGGGATAGGGAAAGATTAGG 59.332 48.000 0.00 0.00 0.00 2.69
13 14 6.516696 AGGGATAGGGATAGGGAAAGATTAG 58.483 44.000 0.00 0.00 0.00 1.73
14 15 6.515763 AGGGATAGGGATAGGGAAAGATTA 57.484 41.667 0.00 0.00 0.00 1.75
15 16 5.391855 AGGGATAGGGATAGGGAAAGATT 57.608 43.478 0.00 0.00 0.00 2.40
16 17 6.715353 ATAGGGATAGGGATAGGGAAAGAT 57.285 41.667 0.00 0.00 0.00 2.40
17 18 7.821713 ATATAGGGATAGGGATAGGGAAAGA 57.178 40.000 0.00 0.00 0.00 2.52
20 21 9.962862 AGTATATATAGGGATAGGGATAGGGAA 57.037 37.037 0.00 0.00 0.00 3.97
33 34 9.925545 TCCGTGCTTTATTAGTATATATAGGGA 57.074 33.333 0.00 0.00 0.00 4.20
595 597 1.602237 GAGCCGGATCTGGGAAACA 59.398 57.895 22.38 0.00 0.00 2.83
596 598 1.521681 CGAGCCGGATCTGGGAAAC 60.522 63.158 22.38 5.26 0.00 2.78
597 599 2.900273 CGAGCCGGATCTGGGAAA 59.100 61.111 22.38 0.00 0.00 3.13
598 600 3.849951 GCGAGCCGGATCTGGGAA 61.850 66.667 22.38 0.00 0.00 3.97
784 799 0.322816 AAGTAGTCGGGGTCGTGCTA 60.323 55.000 0.00 0.00 37.69 3.49
870 886 2.672996 GTGGTTGGCGATGCAGGT 60.673 61.111 0.00 0.00 0.00 4.00
1203 1219 1.937546 GATTTTCACCCGCCAGCTGG 61.938 60.000 29.34 29.34 38.53 4.85
1204 1220 1.508088 GATTTTCACCCGCCAGCTG 59.492 57.895 6.78 6.78 0.00 4.24
1205 1221 1.678970 GGATTTTCACCCGCCAGCT 60.679 57.895 0.00 0.00 0.00 4.24
1206 1222 2.710902 GGGATTTTCACCCGCCAGC 61.711 63.158 0.00 0.00 37.85 4.85
1207 1223 3.603365 GGGATTTTCACCCGCCAG 58.397 61.111 0.00 0.00 37.85 4.85
1212 1228 2.052104 CCGGCTGGGATTTTCACCC 61.052 63.158 2.57 0.00 46.87 4.61
1213 1229 2.710902 GCCGGCTGGGATTTTCACC 61.711 63.158 22.15 0.00 38.47 4.02
1214 1230 2.885113 GCCGGCTGGGATTTTCAC 59.115 61.111 22.15 0.00 38.47 3.18
1215 1231 2.749839 CGCCGGCTGGGATTTTCA 60.750 61.111 26.68 0.00 38.47 2.69
1216 1232 4.193334 GCGCCGGCTGGGATTTTC 62.193 66.667 26.68 0.00 38.47 2.29
2127 2194 4.379243 CTCTGCCGTTCCGCCAGT 62.379 66.667 0.00 0.00 0.00 4.00
3450 3527 0.251354 GCTGGATCTGACAGGAGCAA 59.749 55.000 1.81 0.00 36.48 3.91
4829 7848 0.323629 TGAACCCACGGAGTCAATCC 59.676 55.000 0.00 0.00 41.61 3.01
4830 7849 1.439679 GTGAACCCACGGAGTCAATC 58.560 55.000 0.00 0.00 41.61 2.67
4831 7850 0.036306 GGTGAACCCACGGAGTCAAT 59.964 55.000 0.00 0.00 41.61 2.57
4832 7851 1.448497 GGTGAACCCACGGAGTCAA 59.552 57.895 0.00 0.00 41.61 3.18
4833 7852 2.863346 CGGTGAACCCACGGAGTCA 61.863 63.158 0.00 0.00 41.61 3.41
4834 7853 2.048503 CGGTGAACCCACGGAGTC 60.049 66.667 0.00 0.00 41.61 3.36
4836 7855 2.048503 GACGGTGAACCCACGGAG 60.049 66.667 9.54 0.00 43.69 4.63
4837 7856 2.838693 TGACGGTGAACCCACGGA 60.839 61.111 9.54 0.00 43.69 4.69
4838 7857 2.663852 GTGACGGTGAACCCACGG 60.664 66.667 0.00 0.00 44.09 4.94
4839 7858 0.882927 ATTGTGACGGTGAACCCACG 60.883 55.000 0.00 0.00 44.09 4.94
4840 7859 1.802365 GTATTGTGACGGTGAACCCAC 59.198 52.381 2.84 2.84 42.46 4.61
4841 7860 1.605968 CGTATTGTGACGGTGAACCCA 60.606 52.381 0.00 0.00 39.19 4.51
4842 7861 1.073177 CGTATTGTGACGGTGAACCC 58.927 55.000 0.00 0.00 39.19 4.11
4843 7862 0.441145 GCGTATTGTGACGGTGAACC 59.559 55.000 0.00 0.00 43.13 3.62
4844 7863 3.941194 GCGTATTGTGACGGTGAAC 57.059 52.632 0.00 0.00 43.13 3.18
4849 7868 2.993899 AGAAGAAAGCGTATTGTGACGG 59.006 45.455 0.00 0.00 43.13 4.79
4850 7869 3.241364 CGAGAAGAAAGCGTATTGTGACG 60.241 47.826 0.00 0.00 45.70 4.35
4851 7870 3.673809 ACGAGAAGAAAGCGTATTGTGAC 59.326 43.478 0.00 0.00 36.37 3.67
4852 7871 3.673338 CACGAGAAGAAAGCGTATTGTGA 59.327 43.478 0.00 0.00 32.89 3.58
4853 7872 3.428870 ACACGAGAAGAAAGCGTATTGTG 59.571 43.478 0.00 0.00 35.89 3.33
4854 7873 3.650139 ACACGAGAAGAAAGCGTATTGT 58.350 40.909 0.00 0.00 36.37 2.71
4855 7874 3.673338 TGACACGAGAAGAAAGCGTATTG 59.327 43.478 0.00 0.00 36.37 1.90
4856 7875 3.909430 TGACACGAGAAGAAAGCGTATT 58.091 40.909 0.00 0.00 36.37 1.89
4857 7876 3.570926 TGACACGAGAAGAAAGCGTAT 57.429 42.857 0.00 0.00 36.37 3.06
4858 7877 3.570926 ATGACACGAGAAGAAAGCGTA 57.429 42.857 0.00 0.00 36.37 4.42
4859 7878 2.440539 ATGACACGAGAAGAAAGCGT 57.559 45.000 0.00 0.00 39.04 5.07
4860 7879 5.330866 CGTATTATGACACGAGAAGAAAGCG 60.331 44.000 0.00 0.00 40.56 4.68
4861 7880 5.554696 GCGTATTATGACACGAGAAGAAAGC 60.555 44.000 0.00 0.00 40.56 3.51
4862 7881 5.744345 AGCGTATTATGACACGAGAAGAAAG 59.256 40.000 0.00 0.00 40.56 2.62
4863 7882 5.647589 AGCGTATTATGACACGAGAAGAAA 58.352 37.500 0.00 0.00 40.56 2.52
4864 7883 5.244785 AGCGTATTATGACACGAGAAGAA 57.755 39.130 0.00 0.00 40.56 2.52
4865 7884 4.895224 AGCGTATTATGACACGAGAAGA 57.105 40.909 0.00 0.00 40.56 2.87
4866 7885 5.950965 AAAGCGTATTATGACACGAGAAG 57.049 39.130 0.00 0.00 40.56 2.85
4867 7886 7.703197 TCATAAAAGCGTATTATGACACGAGAA 59.297 33.333 14.08 0.00 42.09 2.87
4868 7887 7.197703 TCATAAAAGCGTATTATGACACGAGA 58.802 34.615 14.08 0.00 42.09 4.04
4869 7888 7.389603 TCATAAAAGCGTATTATGACACGAG 57.610 36.000 14.08 0.00 42.09 4.18
4870 7889 7.940178 ATCATAAAAGCGTATTATGACACGA 57.060 32.000 18.01 3.46 46.71 4.35
4871 7890 8.882199 CAAATCATAAAAGCGTATTATGACACG 58.118 33.333 18.01 9.64 46.71 4.49
4872 7891 9.716507 ACAAATCATAAAAGCGTATTATGACAC 57.283 29.630 18.01 0.00 46.71 3.67
4902 7921 9.498307 CCACCTCGTTTATATTACAATTTTGTC 57.502 33.333 0.00 0.00 42.35 3.18
4903 7922 9.016438 ACCACCTCGTTTATATTACAATTTTGT 57.984 29.630 1.08 1.08 44.86 2.83
4906 7925 9.895138 AGTACCACCTCGTTTATATTACAATTT 57.105 29.630 0.00 0.00 0.00 1.82
4913 7932 9.333724 CCAAATTAGTACCACCTCGTTTATATT 57.666 33.333 0.00 0.00 0.00 1.28
4914 7933 7.935210 CCCAAATTAGTACCACCTCGTTTATAT 59.065 37.037 0.00 0.00 0.00 0.86
4915 7934 7.274447 CCCAAATTAGTACCACCTCGTTTATA 58.726 38.462 0.00 0.00 0.00 0.98
4916 7935 6.117488 CCCAAATTAGTACCACCTCGTTTAT 58.883 40.000 0.00 0.00 0.00 1.40
4917 7936 5.490159 CCCAAATTAGTACCACCTCGTTTA 58.510 41.667 0.00 0.00 0.00 2.01
4918 7937 4.329392 CCCAAATTAGTACCACCTCGTTT 58.671 43.478 0.00 0.00 0.00 3.60
4919 7938 3.307904 CCCCAAATTAGTACCACCTCGTT 60.308 47.826 0.00 0.00 0.00 3.85
4920 7939 2.237893 CCCCAAATTAGTACCACCTCGT 59.762 50.000 0.00 0.00 0.00 4.18
4921 7940 2.420967 CCCCCAAATTAGTACCACCTCG 60.421 54.545 0.00 0.00 0.00 4.63
4922 7941 2.579400 ACCCCCAAATTAGTACCACCTC 59.421 50.000 0.00 0.00 0.00 3.85
4923 7942 2.579400 GACCCCCAAATTAGTACCACCT 59.421 50.000 0.00 0.00 0.00 4.00
4924 7943 2.681682 CGACCCCCAAATTAGTACCACC 60.682 54.545 0.00 0.00 0.00 4.61
4925 7944 2.026915 ACGACCCCCAAATTAGTACCAC 60.027 50.000 0.00 0.00 0.00 4.16
4926 7945 2.236893 GACGACCCCCAAATTAGTACCA 59.763 50.000 0.00 0.00 0.00 3.25
4927 7946 2.236893 TGACGACCCCCAAATTAGTACC 59.763 50.000 0.00 0.00 0.00 3.34
4928 7947 3.615224 TGACGACCCCCAAATTAGTAC 57.385 47.619 0.00 0.00 0.00 2.73
4929 7948 4.035112 AGATGACGACCCCCAAATTAGTA 58.965 43.478 0.00 0.00 0.00 1.82
4930 7949 2.844348 AGATGACGACCCCCAAATTAGT 59.156 45.455 0.00 0.00 0.00 2.24
4931 7950 3.560636 AGATGACGACCCCCAAATTAG 57.439 47.619 0.00 0.00 0.00 1.73
4932 7951 3.775866 TGTAGATGACGACCCCCAAATTA 59.224 43.478 0.00 0.00 0.00 1.40
4933 7952 2.574369 TGTAGATGACGACCCCCAAATT 59.426 45.455 0.00 0.00 0.00 1.82
4934 7953 2.193127 TGTAGATGACGACCCCCAAAT 58.807 47.619 0.00 0.00 0.00 2.32
4935 7954 1.646912 TGTAGATGACGACCCCCAAA 58.353 50.000 0.00 0.00 0.00 3.28
4936 7955 1.874129 ATGTAGATGACGACCCCCAA 58.126 50.000 0.00 0.00 0.00 4.12
4937 7956 1.760613 GAATGTAGATGACGACCCCCA 59.239 52.381 0.00 0.00 0.00 4.96
4938 7957 1.070289 GGAATGTAGATGACGACCCCC 59.930 57.143 0.00 0.00 0.00 5.40
4939 7958 1.269621 CGGAATGTAGATGACGACCCC 60.270 57.143 0.00 0.00 0.00 4.95
4940 7959 1.407979 ACGGAATGTAGATGACGACCC 59.592 52.381 0.00 0.00 0.00 4.46
4941 7960 2.865343 ACGGAATGTAGATGACGACC 57.135 50.000 0.00 0.00 0.00 4.79
4942 7961 3.114065 GGAACGGAATGTAGATGACGAC 58.886 50.000 0.00 0.00 0.00 4.34
4943 7962 3.431922 GGAACGGAATGTAGATGACGA 57.568 47.619 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.