Multiple sequence alignment - TraesCS7D01G012700

Loading Multiple Alignment...

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 TraesCS7D01G012700 chr7D 100.000 5365 0 0 1 5365 5386112 5391476 0.000000e+00 9908.0
1 TraesCS7D01G012700 chr7D 86.878 1928 180 32 2178 4050 5414954 5416863 0.000000e+00 2091.0
2 TraesCS7D01G012700 chr7D 91.588 1165 79 9 4203 5365 5417048 5418195 0.000000e+00 1591.0
3 TraesCS7D01G012700 chr7D 90.603 1011 64 17 1153 2159 262038 261055 0.000000e+00 1312.0
4 TraesCS7D01G012700 chr7D 88.754 1067 79 20 1101 2159 144158596 144159629 0.000000e+00 1267.0
5 TraesCS7D01G012700 chr7D 87.083 1138 88 32 1 1088 5413768 5414896 0.000000e+00 1232.0
6 TraesCS7D01G012700 chr7D 90.136 953 67 14 1209 2159 606793888 606792961 0.000000e+00 1214.0
7 TraesCS7D01G012700 chr7D 93.902 82 5 0 4137 4218 5417020 5417101 2.030000e-24 124.0
8 TraesCS7D01G012700 chr7D 94.444 54 3 0 4203 4256 5390276 5390329 3.440000e-12 84.2
9 TraesCS7D01G012700 chr7D 94.444 54 3 0 4165 4218 5390314 5390367 3.440000e-12 84.2
10 TraesCS7D01G012700 chr7D 97.368 38 1 0 4048 4085 5416903 5416940 1.250000e-06 65.8
11 TraesCS7D01G012700 chr4A 91.758 2196 110 37 1 2157 737089808 737087645 0.000000e+00 2987.0
12 TraesCS7D01G012700 chr4A 92.975 1637 50 22 2155 3761 737087584 737085983 0.000000e+00 2326.0
13 TraesCS7D01G012700 chr4A 86.788 1930 179 30 2178 4050 736307542 736309452 0.000000e+00 2082.0
14 TraesCS7D01G012700 chr4A 91.409 1164 84 7 4203 5365 736309635 736310783 0.000000e+00 1581.0
15 TraesCS7D01G012700 chr4A 85.377 1484 148 42 2624 4050 737068810 737067339 0.000000e+00 1474.0
16 TraesCS7D01G012700 chr4A 86.731 1138 94 29 1 1088 736306354 736307484 0.000000e+00 1212.0
17 TraesCS7D01G012700 chr4A 84.826 1239 115 31 4135 5365 737085572 737084399 0.000000e+00 1179.0
18 TraesCS7D01G012700 chr4A 85.188 1141 80 42 1 1088 737070523 737069419 0.000000e+00 1088.0
19 TraesCS7D01G012700 chr4A 92.154 701 30 4 4203 4899 737067172 737066493 0.000000e+00 966.0
20 TraesCS7D01G012700 chr4A 92.461 451 34 0 2176 2626 737069363 737068913 0.000000e+00 645.0
21 TraesCS7D01G012700 chr4A 92.689 424 29 2 4931 5353 737066494 737066072 1.280000e-170 610.0
22 TraesCS7D01G012700 chr4A 80.065 612 89 11 4756 5365 737060971 737060391 1.790000e-114 424.0
23 TraesCS7D01G012700 chr4A 92.032 251 18 2 3801 4050 737085976 737085727 8.550000e-93 351.0
24 TraesCS7D01G012700 chr4A 79.357 373 48 18 718 1088 737063983 737063638 8.980000e-58 235.0
25 TraesCS7D01G012700 chr4A 95.238 84 4 0 4135 4218 737067202 737067119 3.370000e-27 134.0
26 TraesCS7D01G012700 chr4A 92.941 85 4 2 4134 4218 736309606 736309688 7.300000e-24 122.0
27 TraesCS7D01G012700 chr4A 97.143 35 1 0 4051 4085 737085684 737085650 5.800000e-05 60.2
28 TraesCS7D01G012700 chr7A 94.292 876 40 6 220 1088 6863133 6864005 0.000000e+00 1332.0
29 TraesCS7D01G012700 chr7A 86.210 1240 113 24 4135 5365 6866117 6867307 0.000000e+00 1290.0
30 TraesCS7D01G012700 chr7A 94.492 708 38 1 2176 2882 6864230 6864937 0.000000e+00 1090.0
31 TraesCS7D01G012700 chr7A 92.667 450 29 4 3603 4050 6865515 6865962 0.000000e+00 645.0
32 TraesCS7D01G012700 chr7A 93.291 313 18 3 2936 3246 6864927 6865238 4.900000e-125 459.0
33 TraesCS7D01G012700 chr7A 93.514 185 11 1 3342 3526 6865330 6865513 1.900000e-69 274.0
34 TraesCS7D01G012700 chr7A 92.553 188 11 3 1 186 6862949 6863135 3.190000e-67 267.0
35 TraesCS7D01G012700 chr7A 94.937 79 4 0 3234 3312 6865255 6865333 2.030000e-24 124.0
36 TraesCS7D01G012700 chr7A 94.595 37 2 0 4048 4084 6866002 6866038 2.090000e-04 58.4
37 TraesCS7D01G012700 chr1D 89.493 1066 76 24 1101 2159 457052189 457051153 0.000000e+00 1315.0
38 TraesCS7D01G012700 chr2D 89.573 1055 77 20 1107 2159 209127647 209128670 0.000000e+00 1308.0
39 TraesCS7D01G012700 chr2D 89.380 1064 75 18 1104 2159 461081640 461080607 0.000000e+00 1304.0
40 TraesCS7D01G012700 chr2D 89.108 1065 80 23 1102 2159 55161023 55162058 0.000000e+00 1291.0
41 TraesCS7D01G012700 chr2D 89.395 1009 80 16 1153 2159 143087140 143088123 0.000000e+00 1245.0
42 TraesCS7D01G012700 chr2D 89.631 1003 68 18 1158 2159 626931349 626930382 0.000000e+00 1243.0
43 TraesCS7D01G012700 chr3D 90.486 1009 69 15 1153 2159 535577131 535578114 0.000000e+00 1306.0
44 TraesCS7D01G012700 chr3D 90.208 1011 68 13 1153 2159 120627183 120626200 0.000000e+00 1290.0
45 TraesCS7D01G012700 chr3D 88.649 1066 81 23 1100 2157 553040115 553039082 0.000000e+00 1262.0
46 TraesCS7D01G012700 chr3D 88.555 1066 82 23 1100 2157 553078635 553077602 0.000000e+00 1256.0
47 TraesCS7D01G012700 chr3D 88.262 673 51 16 1494 2160 324422291 324422941 0.000000e+00 780.0
48 TraesCS7D01G012700 chr6D 89.583 1008 78 17 1153 2159 413279250 413278269 0.000000e+00 1254.0
49 TraesCS7D01G012700 chr6D 89.250 800 60 14 1362 2159 137503113 137503888 0.000000e+00 977.0
50 TraesCS7D01G012700 chr6D 89.785 744 49 16 1418 2159 13633644 13632926 0.000000e+00 928.0
51 TraesCS7D01G012700 chr6A 81.146 419 54 10 3649 4050 9484447 9484857 4.030000e-81 313.0
52 TraesCS7D01G012700 chr7B 84.577 201 25 4 4507 4703 286840954 286840756 1.520000e-45 195.0


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 TraesCS7D01G012700 chr7D 5386112 5391476 5364 False 3358.800000 9908 96.296000 1 5365 3 chr7D.!!$F2 5364
1 TraesCS7D01G012700 chr7D 261055 262038 983 True 1312.000000 1312 90.603000 1153 2159 1 chr7D.!!$R1 1006
2 TraesCS7D01G012700 chr7D 144158596 144159629 1033 False 1267.000000 1267 88.754000 1101 2159 1 chr7D.!!$F1 1058
3 TraesCS7D01G012700 chr7D 606792961 606793888 927 True 1214.000000 1214 90.136000 1209 2159 1 chr7D.!!$R2 950
4 TraesCS7D01G012700 chr7D 5413768 5418195 4427 False 1020.760000 2091 91.363800 1 5365 5 chr7D.!!$F3 5364
5 TraesCS7D01G012700 chr4A 737084399 737089808 5409 True 1380.640000 2987 91.746800 1 5365 5 chr4A.!!$R2 5364
6 TraesCS7D01G012700 chr4A 736306354 736310783 4429 False 1249.250000 2082 89.467250 1 5365 4 chr4A.!!$F1 5364
7 TraesCS7D01G012700 chr4A 737060391 737070523 10132 True 697.000000 1474 87.816125 1 5365 8 chr4A.!!$R1 5364
8 TraesCS7D01G012700 chr7A 6862949 6867307 4358 False 615.488889 1332 92.950111 1 5365 9 chr7A.!!$F1 5364
9 TraesCS7D01G012700 chr1D 457051153 457052189 1036 True 1315.000000 1315 89.493000 1101 2159 1 chr1D.!!$R1 1058
10 TraesCS7D01G012700 chr2D 209127647 209128670 1023 False 1308.000000 1308 89.573000 1107 2159 1 chr2D.!!$F3 1052
11 TraesCS7D01G012700 chr2D 461080607 461081640 1033 True 1304.000000 1304 89.380000 1104 2159 1 chr2D.!!$R1 1055
12 TraesCS7D01G012700 chr2D 55161023 55162058 1035 False 1291.000000 1291 89.108000 1102 2159 1 chr2D.!!$F1 1057
13 TraesCS7D01G012700 chr2D 143087140 143088123 983 False 1245.000000 1245 89.395000 1153 2159 1 chr2D.!!$F2 1006
14 TraesCS7D01G012700 chr2D 626930382 626931349 967 True 1243.000000 1243 89.631000 1158 2159 1 chr2D.!!$R2 1001
15 TraesCS7D01G012700 chr3D 535577131 535578114 983 False 1306.000000 1306 90.486000 1153 2159 1 chr3D.!!$F2 1006
16 TraesCS7D01G012700 chr3D 120626200 120627183 983 True 1290.000000 1290 90.208000 1153 2159 1 chr3D.!!$R1 1006
17 TraesCS7D01G012700 chr3D 553039082 553040115 1033 True 1262.000000 1262 88.649000 1100 2157 1 chr3D.!!$R2 1057
18 TraesCS7D01G012700 chr3D 553077602 553078635 1033 True 1256.000000 1256 88.555000 1100 2157 1 chr3D.!!$R3 1057
19 TraesCS7D01G012700 chr3D 324422291 324422941 650 False 780.000000 780 88.262000 1494 2160 1 chr3D.!!$F1 666
20 TraesCS7D01G012700 chr6D 413278269 413279250 981 True 1254.000000 1254 89.583000 1153 2159 1 chr6D.!!$R2 1006
21 TraesCS7D01G012700 chr6D 137503113 137503888 775 False 977.000000 977 89.250000 1362 2159 1 chr6D.!!$F1 797
22 TraesCS7D01G012700 chr6D 13632926 13633644 718 True 928.000000 928 89.785000 1418 2159 1 chr6D.!!$R1 741

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
938 1027 1.995376 ACCACACCACCCTCATTTTC 58.005 50.000 0.00 0.00 0.00 2.29 F
2283 2478 0.110486 ACCCAGACTTCGTTGCCAAT 59.890 50.000 0.00 0.00 0.00 3.16 F
2784 3110 2.099756 GGGCTGATATCAGTTTGGCAAC 59.900 50.000 28.92 12.87 45.45 4.17 F
4282 4896 2.800544 TGAGCTTCGCAACTTACTGAAC 59.199 45.455 0.00 0.00 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2689 3014 0.388520 GAAATTGACCACGCTTGCCC 60.389 55.000 0.00 0.00 0.00 5.36 R
3415 3824 1.839994 TGCTAAAGGAGAGGGTGATGG 59.160 52.381 0.00 0.00 0.00 3.51 R
4294 4908 0.604780 CAGTGTCTTCAGGCACCTGG 60.605 60.000 16.52 1.86 43.75 4.45 R
5341 6000 2.245582 ACCACTATAGTCCATACGCCC 58.754 52.381 1.26 0.00 0.00 6.13 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
507 510 7.843490 TGAGACAAGGAAATAAAAGGTATCG 57.157 36.000 0.00 0.00 0.00 2.92
510 513 8.857694 AGACAAGGAAATAAAAGGTATCGAAA 57.142 30.769 0.00 0.00 0.00 3.46
638 672 8.421249 TGAAAGGTATCCAATGAAACAATTCT 57.579 30.769 0.00 0.00 36.48 2.40
814 868 4.616181 AAAGACGAAATAAATGAGGGCG 57.384 40.909 0.00 0.00 0.00 6.13
938 1027 1.995376 ACCACACCACCCTCATTTTC 58.005 50.000 0.00 0.00 0.00 2.29
967 1056 3.248024 TCACTTAGCTTTTCTCCTCCCA 58.752 45.455 0.00 0.00 0.00 4.37
968 1057 3.261897 TCACTTAGCTTTTCTCCTCCCAG 59.738 47.826 0.00 0.00 0.00 4.45
969 1058 2.026729 ACTTAGCTTTTCTCCTCCCAGC 60.027 50.000 0.00 0.00 0.00 4.85
1039 1128 0.466189 CCAACTCAGCACCCTTGTGT 60.466 55.000 0.00 0.00 44.65 3.72
1111 1201 1.631071 CCTTTGCTCCTCCTCCTCCC 61.631 65.000 0.00 0.00 0.00 4.30
1125 1215 1.082954 CTCCCTCCTCCCTCCCAAA 59.917 63.158 0.00 0.00 0.00 3.28
1140 1230 3.253838 AAACCTAGCCGCCCCACA 61.254 61.111 0.00 0.00 0.00 4.17
1253 1345 2.284331 TCGGTTGCCCTGCCTCTA 60.284 61.111 0.00 0.00 0.00 2.43
1342 1434 3.170672 TGGATCTGGCATCCCGGG 61.171 66.667 16.85 16.85 38.11 5.73
1501 1593 1.258445 CCGGTTCTGTACAGGAGGCT 61.258 60.000 22.48 0.00 44.02 4.58
1628 1720 2.940514 TGGACTGATCCCCTCACTTA 57.059 50.000 0.00 0.00 45.59 2.24
1651 1749 3.436028 CCCCTAGGTCTCCCGGGA 61.436 72.222 25.06 25.06 37.04 5.14
1809 1907 1.005037 ATCTGCGTCCGTTGCTTGA 60.005 52.632 0.00 0.00 0.00 3.02
1859 1970 2.438254 GGCATCATGGTGGCGTCA 60.438 61.111 17.60 0.00 34.85 4.35
1906 2032 3.604582 GCACCTTAATCTGCTCTGAAGT 58.395 45.455 0.00 0.00 0.00 3.01
1913 2039 1.302033 CTGCTCTGAAGTTGGCGGT 60.302 57.895 0.00 0.00 0.00 5.68
1968 2094 4.540735 CGGACCCGGTATGTGCCC 62.541 72.222 0.00 0.00 35.56 5.36
1969 2095 4.185286 GGACCCGGTATGTGCCCC 62.185 72.222 0.00 0.00 0.00 5.80
1970 2096 4.540735 GACCCGGTATGTGCCCCG 62.541 72.222 0.00 0.00 43.82 5.73
1974 2100 4.540735 CGGTATGTGCCCCGGACC 62.541 72.222 0.73 0.00 40.54 4.46
1975 2101 4.185286 GGTATGTGCCCCGGACCC 62.185 72.222 0.73 0.00 0.00 4.46
1976 2102 4.540735 GTATGTGCCCCGGACCCG 62.541 72.222 0.73 0.66 39.44 5.28
2039 2165 6.465035 CCTCTGGCTTTAGATGTTAGGCTTAT 60.465 42.308 0.00 0.00 35.66 1.73
2128 2254 3.483954 CCAAGATGGCGGATTCAGT 57.516 52.632 0.00 0.00 0.00 3.41
2154 2280 4.561735 TTGTTGTGCTACTTTGTAAGGC 57.438 40.909 0.00 0.00 0.00 4.35
2199 2394 6.976636 TGATGTTTTTCCTTTTGTGTTTCC 57.023 33.333 0.00 0.00 0.00 3.13
2283 2478 0.110486 ACCCAGACTTCGTTGCCAAT 59.890 50.000 0.00 0.00 0.00 3.16
2404 2599 5.278808 GGGTGGTTTGATTTGACTTCTTACC 60.279 44.000 0.00 0.00 0.00 2.85
2527 2722 4.022762 GGCCTCTTTTCTTCTTCTTTCACC 60.023 45.833 0.00 0.00 0.00 4.02
2621 2816 7.784470 AACTAGGTATTTAGATCCCAGCTAG 57.216 40.000 0.00 11.32 41.08 3.42
2624 2819 8.847816 ACTAGGTATTTAGATCCCAGCTAGATA 58.152 37.037 16.35 0.00 38.83 1.98
2629 2824 8.972127 GTATTTAGATCCCAGCTAGATACATCA 58.028 37.037 0.00 0.00 36.60 3.07
2632 2827 9.547279 TTTAGATCCCAGCTAGATACATCATAA 57.453 33.333 0.00 0.00 0.00 1.90
2784 3110 2.099756 GGGCTGATATCAGTTTGGCAAC 59.900 50.000 28.92 12.87 45.45 4.17
2941 3268 8.880878 TTTTATGATTTAGATCCGACAATCGA 57.119 30.769 0.00 0.00 43.74 3.59
3177 3546 9.314321 CTGTTGTACCGTTCTATGAATTAGATT 57.686 33.333 0.00 0.00 36.81 2.40
3256 3634 4.862371 TCCACCTTGTTAAGTGGTTCTTT 58.138 39.130 10.46 0.00 38.11 2.52
3415 3824 5.187687 TCGTACAATTAATTTGGGGAGGAC 58.812 41.667 0.00 0.00 39.80 3.85
3444 3853 4.162320 CCCTCTCCTTTAGCATCACAACTA 59.838 45.833 0.00 0.00 0.00 2.24
3460 3869 5.067805 TCACAACTATGCATGACGTAGATCT 59.932 40.000 10.16 0.00 39.87 2.75
3724 4191 5.665812 TGGTACATCTATTTGCTTAGGAGGT 59.334 40.000 0.00 0.00 0.00 3.85
3749 4216 4.513406 AGTGAAGGGAAAACACTACCAA 57.487 40.909 0.00 0.00 42.01 3.67
3897 4364 5.043737 AGAGCAAAGTTGGGTTAGTAACA 57.956 39.130 14.81 0.00 0.00 2.41
3902 4369 5.009210 GCAAAGTTGGGTTAGTAACATGTGA 59.991 40.000 14.81 0.00 0.00 3.58
4079 4589 8.946523 AGACATATTTGGCTAACTCCACTGAGT 61.947 40.741 0.00 0.00 43.39 3.41
4222 4791 8.752005 ATAACATGTCCATTAGCATTTGTAGT 57.248 30.769 0.00 0.00 0.00 2.73
4223 4792 9.845740 ATAACATGTCCATTAGCATTTGTAGTA 57.154 29.630 0.00 0.00 0.00 1.82
4224 4793 7.792374 ACATGTCCATTAGCATTTGTAGTAG 57.208 36.000 0.00 0.00 0.00 2.57
4225 4794 7.338710 ACATGTCCATTAGCATTTGTAGTAGT 58.661 34.615 0.00 0.00 0.00 2.73
4226 4795 7.829211 ACATGTCCATTAGCATTTGTAGTAGTT 59.171 33.333 0.00 0.00 0.00 2.24
4227 4796 9.325198 CATGTCCATTAGCATTTGTAGTAGTTA 57.675 33.333 0.00 0.00 0.00 2.24
4269 4883 3.181517 TGAGCATTTCGAAATGAGCTTCG 60.182 43.478 41.10 21.68 46.72 3.79
4282 4896 2.800544 TGAGCTTCGCAACTTACTGAAC 59.199 45.455 0.00 0.00 0.00 3.18
4318 4932 2.027192 GGTGCCTGAAGACACTGGATTA 60.027 50.000 0.00 0.00 36.99 1.75
4555 5198 5.028549 AGGCTATGGATTCAGTTAGTGTG 57.971 43.478 0.00 0.00 0.00 3.82
4605 5248 7.463544 TGTTAATGAAATGAATGCGACTAGTG 58.536 34.615 0.00 0.00 0.00 2.74
4657 5301 6.018016 GCTAATTGTGGAAAACAAACAAGCAT 60.018 34.615 13.42 0.00 44.97 3.79
4663 5307 4.141756 TGGAAAACAAACAAGCATGGACAT 60.142 37.500 0.00 0.00 0.00 3.06
4745 5390 7.533222 CAGAAATCTCAGTTGAAAATCTTCGTG 59.467 37.037 0.00 0.00 33.94 4.35
4754 5399 5.784750 TGAAAATCTTCGTGCACAGATAG 57.215 39.130 18.64 13.61 33.94 2.08
4880 5538 5.460091 GGACTTCATGTTTTGCTTTCTTGTC 59.540 40.000 0.00 0.00 0.00 3.18
4881 5539 6.212888 ACTTCATGTTTTGCTTTCTTGTCT 57.787 33.333 0.00 0.00 0.00 3.41
4885 5543 4.637483 TGTTTTGCTTTCTTGTCTGGAG 57.363 40.909 0.00 0.00 0.00 3.86
4946 5604 2.537143 TGGGTCCTCCTTCTGAGTAAC 58.463 52.381 0.00 0.00 39.65 2.50
4947 5605 2.158219 TGGGTCCTCCTTCTGAGTAACA 60.158 50.000 0.00 0.00 39.65 2.41
4975 5633 6.120157 GTGGTTTACGAAACTAACGTGTTAC 58.880 40.000 0.00 0.00 43.73 2.50
5022 5680 3.838317 AGCATGTCCTAAACTGTAGACCA 59.162 43.478 0.00 0.00 0.00 4.02
5068 5726 5.042593 TGTTCTGATTGCACATTGTGTTTC 58.957 37.500 17.64 12.13 35.75 2.78
5089 5747 3.740832 TCAAGTCGTACAACATGCTCAAG 59.259 43.478 0.00 0.00 0.00 3.02
5146 5804 3.451178 GGGGTCTATAGTTCTGTCAAGCA 59.549 47.826 0.00 0.00 0.00 3.91
5198 5856 3.818210 TGGTACTGTCCGTAGTTTCGTTA 59.182 43.478 0.00 0.00 32.19 3.18
5209 5867 8.810427 GTCCGTAGTTTCGTTATGAATTATTGA 58.190 33.333 0.00 0.00 36.22 2.57
5236 5894 4.813697 TCAAATAACAATCATCCGCGATCA 59.186 37.500 8.23 0.00 0.00 2.92
5243 5901 0.662619 TCATCCGCGATCATTTTGCC 59.337 50.000 8.23 0.00 0.00 4.52
5251 5909 3.155998 GCGATCATTTTGCCGATTATCG 58.844 45.455 7.74 7.74 40.07 2.92
5311 5969 2.346803 TCGTAGAAATTCAGTGGCAGC 58.653 47.619 0.00 0.00 0.00 5.25
5320 5978 1.186200 TCAGTGGCAGCGTAATCTCT 58.814 50.000 0.00 0.00 0.00 3.10
5341 6000 6.427853 TCTCTACAAAATCATGTGTCTTGGTG 59.572 38.462 0.00 0.00 34.75 4.17
5356 11684 2.385135 TGGTGGGCGTATGGACTATA 57.615 50.000 0.00 0.00 0.00 1.31
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
507 510 7.993183 TGATGGGATGTAGGAATAGTTTCTTTC 59.007 37.037 0.00 0.00 32.16 2.62
510 513 7.451731 TTGATGGGATGTAGGAATAGTTTCT 57.548 36.000 0.00 0.00 32.16 2.52
587 591 3.812167 GCCTCTCACTTTCCAGGATGTTT 60.812 47.826 0.00 0.00 0.00 2.83
636 670 6.785337 TGATTTTACTGGTTAGATCCGAGA 57.215 37.500 0.00 0.00 0.00 4.04
638 672 6.942976 ACTTGATTTTACTGGTTAGATCCGA 58.057 36.000 0.00 0.00 0.00 4.55
814 868 6.350629 AGGGCTGCCATTCATATTTTTATC 57.649 37.500 22.05 0.00 0.00 1.75
938 1027 3.517500 AGAAAAGCTAAGTGAGGAGAGGG 59.482 47.826 0.00 0.00 0.00 4.30
968 1057 1.668237 GCAAGGAGTTAAGCTAGCAGC 59.332 52.381 18.83 0.00 42.84 5.25
969 1058 2.284190 GGCAAGGAGTTAAGCTAGCAG 58.716 52.381 18.83 0.00 0.00 4.24
1039 1128 2.324330 CCGCAGCGAACATGTTGGA 61.324 57.895 22.97 0.00 0.00 3.53
1111 1201 1.501582 CTAGGTTTGGGAGGGAGGAG 58.498 60.000 0.00 0.00 0.00 3.69
1140 1230 2.122954 GAGGGGTCAGGAGGTGGT 59.877 66.667 0.00 0.00 0.00 4.16
1320 1412 2.969238 GATGCCAGATCCACCGCG 60.969 66.667 0.00 0.00 0.00 6.46
1480 1572 1.541310 CCTCCTGTACAGAACCGGCA 61.541 60.000 24.68 0.00 32.70 5.69
1628 1720 1.710972 GGAGACCTAGGGGAAGGGT 59.289 63.158 14.81 0.00 41.32 4.34
1651 1749 3.230976 CCCAACAAAGTTAGGGCTTTCT 58.769 45.455 0.00 0.00 36.64 2.52
1686 1784 0.963962 AAGAAGGGAACAGCGTCGTA 59.036 50.000 0.00 0.00 0.00 3.43
1690 1788 1.884235 CTTCAAGAAGGGAACAGCGT 58.116 50.000 1.86 0.00 34.87 5.07
1880 1991 2.040278 AGAGCAGATTAAGGTGCCAACA 59.960 45.455 7.95 0.00 40.81 3.33
1906 2032 1.958715 CATGTGTCGTCACCGCCAA 60.959 57.895 10.28 0.00 43.26 4.52
1913 2039 0.939106 CGCACTCACATGTGTCGTCA 60.939 55.000 24.63 4.88 39.89 4.35
1958 2084 4.185286 GGGTCCGGGGCACATACC 62.185 72.222 0.00 0.00 0.00 2.73
1959 2085 4.540735 CGGGTCCGGGGCACATAC 62.541 72.222 0.01 0.00 35.56 2.39
1969 2095 4.540735 GGGCACATACCGGGTCCG 62.541 72.222 6.32 1.86 39.44 4.79
1970 2096 4.185286 GGGGCACATACCGGGTCC 62.185 72.222 6.32 0.00 0.00 4.46
1971 2097 4.540735 CGGGGCACATACCGGGTC 62.541 72.222 6.32 0.00 46.08 4.46
1976 2102 4.185286 GGGTCCGGGGCACATACC 62.185 72.222 0.00 0.00 0.00 2.73
1977 2103 4.540735 CGGGTCCGGGGCACATAC 62.541 72.222 0.01 0.00 35.56 2.39
2039 2165 2.571653 CCAAATACCCAGACCTCTCACA 59.428 50.000 0.00 0.00 0.00 3.58
2128 2254 7.361713 GCCTTACAAAGTAGCACAACAATATGA 60.362 37.037 0.00 0.00 0.00 2.15
2199 2394 0.966179 GCAAACCCTAACCCACCAAG 59.034 55.000 0.00 0.00 0.00 3.61
2283 2478 2.931969 CTCGCAGAATAGCATGACAACA 59.068 45.455 0.00 0.00 34.09 3.33
2338 2533 3.426159 CCTGACATGGCAACGTACAATTC 60.426 47.826 1.11 0.00 42.51 2.17
2404 2599 0.734889 GACATGAACCGAATGCCCAG 59.265 55.000 0.00 0.00 0.00 4.45
2527 2722 3.123621 GCACAAACACATACGAAGAGGAG 59.876 47.826 0.00 0.00 0.00 3.69
2621 2816 8.209584 ACATGATAGGATGCCTTATGATGTATC 58.790 37.037 0.00 0.00 34.61 2.24
2624 2819 6.384342 ACATGATAGGATGCCTTATGATGT 57.616 37.500 0.00 0.00 34.61 3.06
2629 2824 4.264083 CCCCAACATGATAGGATGCCTTAT 60.264 45.833 0.00 0.00 34.61 1.73
2632 2827 1.426598 CCCCAACATGATAGGATGCCT 59.573 52.381 0.00 0.00 37.71 4.75
2688 3013 0.827507 AAATTGACCACGCTTGCCCT 60.828 50.000 0.00 0.00 0.00 5.19
2689 3014 0.388520 GAAATTGACCACGCTTGCCC 60.389 55.000 0.00 0.00 0.00 5.36
2784 3110 9.566530 CGGATCTAGATGATAAATCACTACAAG 57.433 37.037 10.74 0.00 40.03 3.16
2980 3307 3.306472 ACAGTAAAACAGCCAAAGGGA 57.694 42.857 0.00 0.00 35.59 4.20
3177 3546 5.739959 TGGGAAGTGATTGATATTTGTCGA 58.260 37.500 0.00 0.00 0.00 4.20
3256 3634 5.362143 TGTCAACCTCCAAAACATCAATTGA 59.638 36.000 11.26 11.26 0.00 2.57
3415 3824 1.839994 TGCTAAAGGAGAGGGTGATGG 59.160 52.381 0.00 0.00 0.00 3.51
3444 3853 3.388308 GCAAGAGATCTACGTCATGCAT 58.612 45.455 0.00 0.00 0.00 3.96
3453 3862 7.387397 CCAAGATTCATTAGGCAAGAGATCTAC 59.613 40.741 0.00 0.00 0.00 2.59
3460 3869 6.603201 CCTAAACCAAGATTCATTAGGCAAGA 59.397 38.462 0.00 0.00 37.05 3.02
3724 4191 3.662759 AGTGTTTTCCCTTCACTTCCA 57.337 42.857 0.00 0.00 39.00 3.53
3749 4216 9.860898 AATCGCTTTAATGAAAGAAAAATAGCT 57.139 25.926 6.75 0.00 44.23 3.32
3849 4316 2.810274 CTGACAACACTCATGGAACTGG 59.190 50.000 0.00 0.00 0.00 4.00
3902 4369 6.882610 AAACAATAGTGTGTGACATGATGT 57.117 33.333 0.00 0.00 38.27 3.06
4035 4503 4.067192 TGTCTATCCATGCAATTCCATCG 58.933 43.478 0.00 0.00 0.00 3.84
4100 4610 2.938956 ACCCAAGAAACTCAGTGGAG 57.061 50.000 0.00 0.00 46.96 3.86
4101 4611 3.072476 CCTAACCCAAGAAACTCAGTGGA 59.928 47.826 0.00 0.00 32.54 4.02
4102 4612 3.072476 TCCTAACCCAAGAAACTCAGTGG 59.928 47.826 0.00 0.00 0.00 4.00
4103 4613 4.351874 TCCTAACCCAAGAAACTCAGTG 57.648 45.455 0.00 0.00 0.00 3.66
4104 4614 5.584551 ATTCCTAACCCAAGAAACTCAGT 57.415 39.130 0.00 0.00 0.00 3.41
4105 4615 9.110502 GTTATATTCCTAACCCAAGAAACTCAG 57.889 37.037 0.00 0.00 0.00 3.35
4106 4616 8.832735 AGTTATATTCCTAACCCAAGAAACTCA 58.167 33.333 0.00 0.00 33.02 3.41
4107 4617 9.682465 AAGTTATATTCCTAACCCAAGAAACTC 57.318 33.333 0.00 0.00 33.02 3.01
4226 4795 9.306777 TGCTCATGGCCATGTTATTAATTAATA 57.693 29.630 38.18 17.97 40.92 0.98
4227 4796 8.192743 TGCTCATGGCCATGTTATTAATTAAT 57.807 30.769 38.18 14.86 40.92 1.40
4228 4797 7.594351 TGCTCATGGCCATGTTATTAATTAA 57.406 32.000 38.18 18.63 40.92 1.40
4294 4908 0.604780 CAGTGTCTTCAGGCACCTGG 60.605 60.000 16.52 1.86 43.75 4.45
4341 4955 2.512705 TGGTATGAACATGCTGCACAA 58.487 42.857 3.57 0.00 0.00 3.33
4499 5142 7.971722 ACTGTTTAGTTCTACGTTTTGCATTTT 59.028 29.630 0.00 0.00 31.66 1.82
4555 5198 5.091431 GTCTTTCATCTGTTGTAATGCAGC 58.909 41.667 0.00 0.00 33.09 5.25
4605 5248 8.023128 ACAAGTAATTTAATGTCTGACATGCAC 58.977 33.333 22.91 13.80 37.97 4.57
4754 5399 7.661437 TCAGATGTCATATATACCCAAAACAGC 59.339 37.037 0.00 0.00 0.00 4.40
4880 5538 6.830912 TGTAAAGATTATGTCCATCCTCCAG 58.169 40.000 0.00 0.00 0.00 3.86
4881 5539 6.823286 TGTAAAGATTATGTCCATCCTCCA 57.177 37.500 0.00 0.00 0.00 3.86
4913 5571 4.354087 AGGAGGACCCAAAGAGTTAAACAT 59.646 41.667 0.00 0.00 37.41 2.71
4946 5604 6.139482 CACGTTAGTTTCGTAAACCACAAATG 59.861 38.462 0.00 5.62 42.34 2.32
4947 5605 6.183360 ACACGTTAGTTTCGTAAACCACAAAT 60.183 34.615 0.00 0.00 42.34 2.32
4975 5633 5.517770 GCTGCAGCTGTATTTGAAAATAAGG 59.482 40.000 31.33 0.00 38.21 2.69
5068 5726 3.494626 ACTTGAGCATGTTGTACGACTTG 59.505 43.478 19.97 19.97 0.00 3.16
5089 5747 5.765182 ACAACTCCAAGCCATATATGCTAAC 59.235 40.000 7.24 0.00 38.34 2.34
5146 5804 3.406764 GACACCAGATGAGAAGCTTGTT 58.593 45.455 2.10 0.00 0.00 2.83
5154 5812 3.511540 ACAGAAATCGACACCAGATGAGA 59.488 43.478 0.00 0.00 0.00 3.27
5209 5867 4.261155 CGCGGATGATTGTTATTTGACCAT 60.261 41.667 0.00 0.00 0.00 3.55
5243 5901 4.447724 CACCAGATTAACCACCGATAATCG 59.552 45.833 0.00 0.00 41.33 3.34
5251 5909 2.556622 CCACAACACCAGATTAACCACC 59.443 50.000 0.00 0.00 0.00 4.61
5311 5969 8.412608 AGACACATGATTTTGTAGAGATTACG 57.587 34.615 0.00 0.00 0.00 3.18
5320 5978 4.522405 CCCACCAAGACACATGATTTTGTA 59.478 41.667 0.00 0.00 0.00 2.41
5341 6000 2.245582 ACCACTATAGTCCATACGCCC 58.754 52.381 1.26 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.