Multiple sequence alignment - TraesCS7D01G193900

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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 TraesCS7D01G193900 chr7D 100.000 4328 0 0 1 4328 150839166 150834839 0.000000e+00 7993.0
1 TraesCS7D01G193900 chr4B 91.352 3018 203 25 433 3398 402950619 402947608 0.000000e+00 4074.0
2 TraesCS7D01G193900 chr4B 90.163 1535 135 6 1876 3398 402874707 402873177 0.000000e+00 1984.0
3 TraesCS7D01G193900 chr4B 90.026 1534 140 4 1876 3398 402864615 402863084 0.000000e+00 1973.0
4 TraesCS7D01G193900 chr4B 92.347 1359 103 1 1876 3234 402871378 402870021 0.000000e+00 1932.0
5 TraesCS7D01G193900 chr4B 92.200 1359 105 1 1876 3234 402861284 402859927 0.000000e+00 1921.0
6 TraesCS7D01G193900 chr4B 91.557 758 43 4 3496 4244 402859066 402858321 0.000000e+00 1026.0
7 TraesCS7D01G193900 chr4B 91.173 759 45 5 3496 4244 402869160 402868414 0.000000e+00 1011.0
8 TraesCS7D01G193900 chr4B 89.607 433 38 2 1 431 402951188 402950761 1.060000e-150 544.0
9 TraesCS7D01G193900 chr4B 92.576 229 9 5 3271 3494 402859934 402859709 5.400000e-84 322.0
10 TraesCS7D01G193900 chr4B 92.576 229 9 5 3271 3494 402870028 402869803 5.400000e-84 322.0
11 TraesCS7D01G193900 chr4B 96.296 81 3 0 3945 4025 495566545 495566465 2.720000e-27 134.0
12 TraesCS7D01G193900 chr4B 92.222 90 5 2 4239 4328 211982169 211982082 4.540000e-25 126.0
13 TraesCS7D01G193900 chr7A 93.932 2340 126 13 1072 3398 150445306 150442970 0.000000e+00 3520.0
14 TraesCS7D01G193900 chr7A 88.571 210 17 6 757 965 150446550 150446347 9.290000e-62 248.0
15 TraesCS7D01G193900 chr7A 96.296 81 3 0 3945 4025 211365846 211365926 2.720000e-27 134.0
16 TraesCS7D01G193900 chr7A 97.059 68 1 1 4261 4328 84495397 84495331 3.540000e-21 113.0
17 TraesCS7D01G193900 chr7A 88.298 94 10 1 3418 3510 150442978 150442885 1.270000e-20 111.0
18 TraesCS7D01G193900 chr7A 92.208 77 5 1 4252 4328 587063532 587063607 1.650000e-19 108.0
19 TraesCS7D01G193900 chr7A 100.000 40 0 0 1003 1042 150445345 150445306 1.670000e-09 75.0
20 TraesCS7D01G193900 chr7B 93.207 1899 116 5 1511 3398 113044315 113042419 0.000000e+00 2780.0
21 TraesCS7D01G193900 chr7B 88.346 1536 161 8 1876 3398 112914605 112913075 0.000000e+00 1829.0
22 TraesCS7D01G193900 chr7B 90.368 1360 127 3 1876 3234 112907959 112906603 0.000000e+00 1783.0
23 TraesCS7D01G193900 chr7B 88.787 1088 65 22 433 1482 113045382 113044314 0.000000e+00 1280.0
24 TraesCS7D01G193900 chr7B 92.462 398 10 3 3855 4244 112892163 112891778 6.330000e-153 551.0
25 TraesCS7D01G193900 chr7B 89.145 433 40 2 1 431 113045951 113045524 2.290000e-147 532.0
26 TraesCS7D01G193900 chr7B 92.140 229 10 5 3271 3494 112906610 112906385 2.510000e-82 316.0
27 TraesCS7D01G193900 chr7B 88.186 237 27 1 3494 3729 112892452 112892216 9.160000e-72 281.0
28 TraesCS7D01G193900 chr7B 88.614 202 21 1 3569 3770 248553977 248554176 1.200000e-60 244.0
29 TraesCS7D01G193900 chr7B 100.000 54 0 0 3783 3836 112892214 112892161 2.750000e-17 100.0
30 TraesCS7D01G193900 chr2D 89.500 200 21 0 3571 3770 309155902 309156101 2.000000e-63 254.0
31 TraesCS7D01G193900 chr5D 88.152 211 23 2 3569 3777 404767463 404767253 2.580000e-62 250.0
32 TraesCS7D01G193900 chr3A 88.177 203 23 1 3569 3770 468733697 468733899 1.560000e-59 241.0
33 TraesCS7D01G193900 chr3A 87.805 205 19 6 3568 3770 711212034 711212234 7.240000e-58 235.0
34 TraesCS7D01G193900 chr3A 94.444 72 3 1 4257 4328 492755967 492755897 4.580000e-20 110.0
35 TraesCS7D01G193900 chr1A 88.060 201 24 0 3570 3770 588382867 588383067 5.590000e-59 239.0
36 TraesCS7D01G193900 chr1A 96.296 81 3 0 3945 4025 94579474 94579394 2.720000e-27 134.0
37 TraesCS7D01G193900 chr1A 96.296 81 3 0 3945 4025 94665357 94665437 2.720000e-27 134.0
38 TraesCS7D01G193900 chr1A 100.000 32 0 0 4235 4266 508292555 508292586 4.670000e-05 60.2
39 TraesCS7D01G193900 chr1A 100.000 32 0 0 4235 4266 508324768 508324799 4.670000e-05 60.2
40 TraesCS7D01G193900 chr1A 100.000 32 0 0 4235 4266 508345780 508345811 4.670000e-05 60.2
41 TraesCS7D01G193900 chr6B 96.296 81 3 0 3945 4025 307026390 307026310 2.720000e-27 134.0
42 TraesCS7D01G193900 chr6B 96.296 81 3 0 3945 4025 394416458 394416538 2.720000e-27 134.0
43 TraesCS7D01G193900 chr6B 94.444 72 3 1 4257 4328 439395739 439395669 4.580000e-20 110.0
44 TraesCS7D01G193900 chr2A 91.111 90 7 1 4239 4328 89492996 89492908 2.110000e-23 121.0
45 TraesCS7D01G193900 chr5A 90.909 88 6 2 4241 4328 376542024 376541939 2.730000e-22 117.0
46 TraesCS7D01G193900 chr5A 96.875 32 1 0 4235 4266 77990690 77990721 2.000000e-03 54.7
47 TraesCS7D01G193900 chr6D 94.444 72 2 2 4258 4328 248003997 248004067 4.580000e-20 110.0
48 TraesCS7D01G193900 chr5B 94.444 72 2 2 4257 4328 355688828 355688897 4.580000e-20 110.0
49 TraesCS7D01G193900 chr3D 91.139 79 7 0 1 79 393651944 393652022 1.650000e-19 108.0
50 TraesCS7D01G193900 chr3D 100.000 32 0 0 4235 4266 491177441 491177472 4.670000e-05 60.2
51 TraesCS7D01G193900 chr1B 100.000 32 0 0 4235 4266 618002556 618002525 4.670000e-05 60.2


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 TraesCS7D01G193900 chr7D 150834839 150839166 4327 True 7993.000000 7993 100.000000 1 4328 1 chr7D.!!$R1 4327
1 TraesCS7D01G193900 chr4B 402947608 402951188 3580 True 2309.000000 4074 90.479500 1 3398 2 chr4B.!!$R4 3397
2 TraesCS7D01G193900 chr4B 402858321 402874707 16386 True 1311.375000 1984 91.577250 1876 4244 8 chr4B.!!$R3 2368
3 TraesCS7D01G193900 chr7A 150442885 150446550 3665 True 988.500000 3520 92.700250 757 3510 4 chr7A.!!$R2 2753
4 TraesCS7D01G193900 chr7B 112913075 112914605 1530 True 1829.000000 1829 88.346000 1876 3398 1 chr7B.!!$R1 1522
5 TraesCS7D01G193900 chr7B 113042419 113045951 3532 True 1530.666667 2780 90.379667 1 3398 3 chr7B.!!$R4 3397
6 TraesCS7D01G193900 chr7B 112906385 112907959 1574 True 1049.500000 1783 91.254000 1876 3494 2 chr7B.!!$R3 1618
7 TraesCS7D01G193900 chr7B 112891778 112892452 674 True 310.666667 551 93.549333 3494 4244 3 chr7B.!!$R2 750

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
176 177 0.106769 TTGGCAACCTGAACAGCTCA 60.107 50.0 0.0 0.0 0.0 4.26 F
488 631 0.250234 CCGTCTCTTGCCTCATTCCA 59.750 55.0 0.0 0.0 0.0 3.53 F
1851 2999 0.249741 CGACCACCGTCAAGGACTTT 60.250 55.0 0.0 0.0 45.0 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1167 2315 0.176680 CGTGCCAGAGCTTGTAGGAT 59.823 55.0 0.00 0.0 40.8 3.24 R
2131 6608 0.389391 GGATCGACGGTCATGATGGT 59.611 55.0 10.81 0.0 0.0 3.55 R
3611 18787 1.556591 TTAGCGTGTCTGTTGCAGCG 61.557 55.0 0.00 0.0 0.0 5.18 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
50 51 2.559440 GGTGTGATGGAGAAGATGAGC 58.441 52.381 0.00 0.00 0.00 4.26
66 67 0.880278 GAGCTGCGAAGACAACACCA 60.880 55.000 0.00 0.00 0.00 4.17
68 69 0.317020 GCTGCGAAGACAACACCAAC 60.317 55.000 0.00 0.00 0.00 3.77
108 109 7.161404 TGTCTGAGTTGTTTAGCATATTCACT 58.839 34.615 0.00 0.00 0.00 3.41
141 142 3.430042 TCAAGCTCCAGATGAAGCTTT 57.570 42.857 3.30 0.00 44.05 3.51
142 143 4.558226 TCAAGCTCCAGATGAAGCTTTA 57.442 40.909 3.30 0.00 44.05 1.85
157 158 7.817418 TGAAGCTTTAGTGTGTTAATTTCCT 57.183 32.000 0.00 0.00 0.00 3.36
158 159 8.232913 TGAAGCTTTAGTGTGTTAATTTCCTT 57.767 30.769 0.00 0.00 0.00 3.36
159 160 8.134895 TGAAGCTTTAGTGTGTTAATTTCCTTG 58.865 33.333 0.00 0.00 0.00 3.61
160 161 6.981722 AGCTTTAGTGTGTTAATTTCCTTGG 58.018 36.000 0.00 0.00 0.00 3.61
161 162 5.633601 GCTTTAGTGTGTTAATTTCCTTGGC 59.366 40.000 0.00 0.00 0.00 4.52
165 166 4.055360 GTGTGTTAATTTCCTTGGCAACC 58.945 43.478 0.00 0.00 0.00 3.77
175 176 0.595095 CTTGGCAACCTGAACAGCTC 59.405 55.000 0.00 0.00 0.00 4.09
176 177 0.106769 TTGGCAACCTGAACAGCTCA 60.107 50.000 0.00 0.00 0.00 4.26
186 187 2.353889 CTGAACAGCTCATGTACATGCC 59.646 50.000 27.71 20.53 43.00 4.40
187 188 1.672881 GAACAGCTCATGTACATGCCC 59.327 52.381 27.71 20.22 43.00 5.36
199 200 1.274703 ACATGCCCGAATCTCCACCT 61.275 55.000 0.00 0.00 0.00 4.00
227 228 3.306780 GGATCAGAAGACCAACCGAAGAA 60.307 47.826 0.00 0.00 0.00 2.52
235 236 1.613437 ACCAACCGAAGAAATGGCAAG 59.387 47.619 0.00 0.00 36.37 4.01
239 240 0.883833 CCGAAGAAATGGCAAGCAGT 59.116 50.000 0.00 0.00 0.00 4.40
265 266 1.079503 GAAAGCACCCTCGTGATCAC 58.920 55.000 16.21 16.21 43.14 3.06
279 280 1.341089 TGATCACGTAGCACTCCTCCT 60.341 52.381 0.00 0.00 0.00 3.69
293 294 1.631071 CCTCCTCCTCCTCCTTTGCC 61.631 65.000 0.00 0.00 0.00 4.52
315 318 5.825151 GCCTCTGTTTAGATAAAGCTCCATT 59.175 40.000 0.00 0.00 31.21 3.16
318 321 5.523916 TCTGTTTAGATAAAGCTCCATTCGC 59.476 40.000 0.00 0.00 0.00 4.70
339 342 2.391678 GTTGGCCTTGATCCATCCATT 58.608 47.619 3.32 0.00 32.92 3.16
342 345 4.038271 TGGCCTTGATCCATCCATTATC 57.962 45.455 3.32 0.00 0.00 1.75
344 347 3.011032 GGCCTTGATCCATCCATTATCCT 59.989 47.826 0.00 0.00 0.00 3.24
352 355 4.168101 TCCATCCATTATCCTGTACCTCC 58.832 47.826 0.00 0.00 0.00 4.30
359 362 1.338136 ATCCTGTACCTCCCAAGCCG 61.338 60.000 0.00 0.00 0.00 5.52
361 364 3.682292 CTGTACCTCCCAAGCCGGC 62.682 68.421 21.89 21.89 0.00 6.13
363 366 2.062177 GTACCTCCCAAGCCGGCTA 61.062 63.158 33.07 13.81 0.00 3.93
426 429 1.906574 TCCCATTCCTTCACGTAAGCT 59.093 47.619 0.00 0.00 45.62 3.74
431 434 4.567159 CCATTCCTTCACGTAAGCTAAGAC 59.433 45.833 0.00 0.00 45.62 3.01
466 609 1.141881 CGTGCCTCGGCTATTCTGT 59.858 57.895 9.65 0.00 42.51 3.41
488 631 0.250234 CCGTCTCTTGCCTCATTCCA 59.750 55.000 0.00 0.00 0.00 3.53
511 654 2.288273 GCTAACCAGAGGCCGTATACTG 60.288 54.545 0.00 3.62 0.00 2.74
547 692 0.603569 TCTCCTCTTCTGTTGCGTCC 59.396 55.000 0.00 0.00 0.00 4.79
549 694 1.006102 CCTCTTCTGTTGCGTCCGT 60.006 57.895 0.00 0.00 0.00 4.69
557 702 1.593209 GTTGCGTCCGTGAACCAGA 60.593 57.895 0.00 0.00 0.00 3.86
571 716 7.283580 TCCGTGAACCAGAAGAAAAGAAAATTA 59.716 33.333 0.00 0.00 0.00 1.40
572 717 7.918562 CCGTGAACCAGAAGAAAAGAAAATTAA 59.081 33.333 0.00 0.00 0.00 1.40
573 718 9.296400 CGTGAACCAGAAGAAAAGAAAATTAAA 57.704 29.630 0.00 0.00 0.00 1.52
665 814 5.896073 AAGAGAAAGGAAAGACCAGAAGA 57.104 39.130 0.00 0.00 42.04 2.87
708 883 2.039418 AGGGACTATGCGCTGAATACA 58.961 47.619 9.73 0.00 36.02 2.29
784 959 1.824230 TGCATATCTGGCCCAACAAAC 59.176 47.619 0.00 0.00 0.00 2.93
846 1022 4.154347 CCGACTGCAGCCCTCCTC 62.154 72.222 15.27 1.15 0.00 3.71
861 1038 1.540267 CTCCTCGAAGAACCGACTTCA 59.460 52.381 13.89 4.57 44.28 3.02
992 1796 1.826096 GCCGACCTAGGAGAAGAAAGT 59.174 52.381 17.98 0.00 0.00 2.66
999 1803 4.015084 CCTAGGAGAAGAAAGTGTCGGTA 58.985 47.826 1.05 0.00 0.00 4.02
1071 2219 2.435059 GACGTCCTGCCCTTCAGC 60.435 66.667 3.51 0.00 41.50 4.26
1446 2594 4.214327 CTCCGCCTCGCTTCCCTC 62.214 72.222 0.00 0.00 0.00 4.30
1684 2832 2.363018 CTCCAGAGGAGGTCGCCA 60.363 66.667 5.13 0.00 45.43 5.69
1749 2897 4.143333 GAGGAAGCCGGCGTGCTA 62.143 66.667 33.85 0.00 41.80 3.49
1851 2999 0.249741 CGACCACCGTCAAGGACTTT 60.250 55.000 0.00 0.00 45.00 2.66
1932 3080 3.284449 GGGCAAGCGAACACCGTT 61.284 61.111 0.00 0.00 41.15 4.44
1933 3081 1.962306 GGGCAAGCGAACACCGTTA 60.962 57.895 0.00 0.00 41.15 3.18
2093 6570 2.897350 GCGGGCCAAGATCTTCCG 60.897 66.667 23.13 23.13 43.13 4.30
2096 6573 1.152881 GGGCCAAGATCTTCCGCAT 60.153 57.895 20.36 0.00 0.00 4.73
2134 6611 2.338015 GCGACCTACGTGGAGACCA 61.338 63.158 0.00 0.00 44.60 4.02
2138 6615 2.032620 GACCTACGTGGAGACCATCAT 58.967 52.381 0.00 0.00 39.71 2.45
2398 6875 2.355126 CATCGATCGAGGCCACGG 60.355 66.667 23.84 6.86 0.00 4.94
2528 7005 2.577112 CTGCGCCGTCTACGACAG 60.577 66.667 4.18 5.11 43.02 3.51
2659 7136 2.594303 CCTTCAAGCACCCGCACA 60.594 61.111 0.00 0.00 42.27 4.57
3146 14387 0.179234 TGGAACGACTTTGAGGTGCA 59.821 50.000 0.00 0.00 0.00 4.57
3150 14391 0.463654 ACGACTTTGAGGTGCAGCAA 60.464 50.000 19.63 5.56 0.00 3.91
3223 14464 0.674581 CGTTGCCAGAGATGGAGCAA 60.675 55.000 0.00 0.00 42.60 3.91
3310 14560 1.859427 CGGTGCTCAGCAATGCAAGT 61.859 55.000 0.00 0.00 41.47 3.16
3514 18689 6.620877 TTAGTTATCTGCCCTCTCTTTTCA 57.379 37.500 0.00 0.00 0.00 2.69
3546 18722 1.527034 GAGCATCTTCAACAGCCACA 58.473 50.000 0.00 0.00 0.00 4.17
3551 18727 1.013596 TCTTCAACAGCCACACAACG 58.986 50.000 0.00 0.00 0.00 4.10
3607 18783 2.727798 GCTGCAAAATATAATGCGCCTG 59.272 45.455 4.18 0.00 45.47 4.85
3611 18787 3.568538 CAAAATATAATGCGCCTGAGCC 58.431 45.455 4.18 0.00 36.02 4.70
3680 18856 6.105333 GCTTGCCATATGTTACATTTTGGAA 58.895 36.000 22.78 14.36 0.00 3.53
3755 18931 5.473162 TCACCCAAACAAGTTCATGACATAG 59.527 40.000 0.00 0.00 0.00 2.23
3761 18937 7.805071 CCAAACAAGTTCATGACATAGAAGTTC 59.195 37.037 13.35 0.00 35.75 3.01
3781 18957 8.884124 AAGTTCAAATTCATATCCCAAGAAGA 57.116 30.769 0.00 0.00 0.00 2.87
3852 19028 3.023119 ACCAAACAACAAGCACATCTGA 58.977 40.909 0.00 0.00 0.00 3.27
3871 19047 1.134753 GATCAACATCATTGCGGGCAA 59.865 47.619 8.72 8.72 40.47 4.52
3883 19059 1.748493 TGCGGGCAACTTAATGGAATC 59.252 47.619 0.00 0.00 0.00 2.52
3912 19088 4.693095 ACAAATCAAAACAAAAACGGCTGT 59.307 33.333 0.00 0.00 0.00 4.40
3986 19164 0.716108 CGTAACCAGCTCTGCTTTCG 59.284 55.000 0.00 0.00 36.40 3.46
4018 19196 2.358247 GAAGCCCCGAACGCTTGA 60.358 61.111 8.09 0.00 46.37 3.02
4051 19229 4.180057 CTGTGATCTAAGAGGCAAGACAC 58.820 47.826 0.00 0.00 0.00 3.67
4052 19230 3.834813 TGTGATCTAAGAGGCAAGACACT 59.165 43.478 0.00 0.00 31.16 3.55
4053 19231 4.180057 GTGATCTAAGAGGCAAGACACTG 58.820 47.826 0.00 0.00 0.00 3.66
4054 19232 3.196469 TGATCTAAGAGGCAAGACACTGG 59.804 47.826 0.00 0.00 0.00 4.00
4055 19233 2.609747 TCTAAGAGGCAAGACACTGGT 58.390 47.619 0.00 0.00 0.00 4.00
4056 19234 2.972713 TCTAAGAGGCAAGACACTGGTT 59.027 45.455 0.00 0.00 0.00 3.67
4057 19235 1.972872 AAGAGGCAAGACACTGGTTG 58.027 50.000 0.00 0.00 0.00 3.77
4058 19236 1.131638 AGAGGCAAGACACTGGTTGA 58.868 50.000 0.00 0.00 0.00 3.18
4059 19237 1.701847 AGAGGCAAGACACTGGTTGAT 59.298 47.619 0.00 0.00 0.00 2.57
4060 19238 1.808945 GAGGCAAGACACTGGTTGATG 59.191 52.381 0.00 0.00 0.00 3.07
4061 19239 1.421268 AGGCAAGACACTGGTTGATGA 59.579 47.619 0.00 0.00 0.00 2.92
4062 19240 2.158623 AGGCAAGACACTGGTTGATGAA 60.159 45.455 0.00 0.00 0.00 2.57
4067 19245 5.243981 CAAGACACTGGTTGATGAATCTCT 58.756 41.667 0.00 0.00 0.00 3.10
4244 19428 5.867174 ACAGCAAAACCTGTTTCAAAACTAC 59.133 36.000 7.12 0.00 43.19 2.73
4245 19429 6.099341 CAGCAAAACCTGTTTCAAAACTACT 58.901 36.000 7.12 0.00 39.59 2.57
4246 19430 6.253512 CAGCAAAACCTGTTTCAAAACTACTC 59.746 38.462 7.12 0.00 39.59 2.59
4247 19431 5.518847 GCAAAACCTGTTTCAAAACTACTCC 59.481 40.000 7.12 0.00 39.59 3.85
4248 19432 5.847111 AAACCTGTTTCAAAACTACTCCC 57.153 39.130 7.12 0.00 39.59 4.30
4249 19433 4.790718 ACCTGTTTCAAAACTACTCCCT 57.209 40.909 7.12 0.00 39.59 4.20
4250 19434 4.715713 ACCTGTTTCAAAACTACTCCCTC 58.284 43.478 7.12 0.00 39.59 4.30
4251 19435 4.072839 CCTGTTTCAAAACTACTCCCTCC 58.927 47.826 7.12 0.00 39.59 4.30
4252 19436 3.735591 TGTTTCAAAACTACTCCCTCCG 58.264 45.455 7.12 0.00 39.59 4.63
4253 19437 3.135167 TGTTTCAAAACTACTCCCTCCGT 59.865 43.478 7.12 0.00 39.59 4.69
4254 19438 4.132336 GTTTCAAAACTACTCCCTCCGTT 58.868 43.478 0.00 0.00 36.03 4.44
4255 19439 3.672767 TCAAAACTACTCCCTCCGTTC 57.327 47.619 0.00 0.00 0.00 3.95
4256 19440 2.301009 TCAAAACTACTCCCTCCGTTCC 59.699 50.000 0.00 0.00 0.00 3.62
4257 19441 2.019807 AAACTACTCCCTCCGTTCCA 57.980 50.000 0.00 0.00 0.00 3.53
4258 19442 2.019807 AACTACTCCCTCCGTTCCAA 57.980 50.000 0.00 0.00 0.00 3.53
4259 19443 2.019807 ACTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
4260 19444 2.547990 ACTACTCCCTCCGTTCCAAAT 58.452 47.619 0.00 0.00 0.00 2.32
4261 19445 2.910977 ACTACTCCCTCCGTTCCAAATT 59.089 45.455 0.00 0.00 0.00 1.82
4262 19446 4.098894 ACTACTCCCTCCGTTCCAAATTA 58.901 43.478 0.00 0.00 0.00 1.40
4263 19447 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
4264 19448 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
4265 19449 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
4266 19450 2.237893 TCCCTCCGTTCCAAATTACTCC 59.762 50.000 0.00 0.00 0.00 3.85
4267 19451 2.640184 CCTCCGTTCCAAATTACTCCC 58.360 52.381 0.00 0.00 0.00 4.30
4268 19452 2.238898 CCTCCGTTCCAAATTACTCCCT 59.761 50.000 0.00 0.00 0.00 4.20
4269 19453 3.532542 CTCCGTTCCAAATTACTCCCTC 58.467 50.000 0.00 0.00 0.00 4.30
4270 19454 3.178865 TCCGTTCCAAATTACTCCCTCT 58.821 45.455 0.00 0.00 0.00 3.69
4271 19455 3.055385 TCCGTTCCAAATTACTCCCTCTG 60.055 47.826 0.00 0.00 0.00 3.35
4272 19456 3.307480 CCGTTCCAAATTACTCCCTCTGT 60.307 47.826 0.00 0.00 0.00 3.41
4273 19457 4.081309 CCGTTCCAAATTACTCCCTCTGTA 60.081 45.833 0.00 0.00 0.00 2.74
4274 19458 5.484715 CGTTCCAAATTACTCCCTCTGTAA 58.515 41.667 0.00 0.00 34.87 2.41
4275 19459 5.935789 CGTTCCAAATTACTCCCTCTGTAAA 59.064 40.000 0.00 0.00 34.20 2.01
4276 19460 6.128363 CGTTCCAAATTACTCCCTCTGTAAAC 60.128 42.308 0.00 0.00 34.20 2.01
4277 19461 6.697641 TCCAAATTACTCCCTCTGTAAACT 57.302 37.500 0.00 0.00 34.20 2.66
4278 19462 7.801893 TCCAAATTACTCCCTCTGTAAACTA 57.198 36.000 0.00 0.00 34.20 2.24
4279 19463 8.209802 TCCAAATTACTCCCTCTGTAAACTAA 57.790 34.615 0.00 0.00 34.20 2.24
4280 19464 8.662255 TCCAAATTACTCCCTCTGTAAACTAAA 58.338 33.333 0.00 0.00 34.20 1.85
4281 19465 9.462606 CCAAATTACTCCCTCTGTAAACTAAAT 57.537 33.333 0.00 0.00 34.20 1.40
4289 19473 9.699703 CTCCCTCTGTAAACTAAATATAAGAGC 57.300 37.037 0.00 0.00 0.00 4.09
4290 19474 8.358148 TCCCTCTGTAAACTAAATATAAGAGCG 58.642 37.037 0.00 0.00 0.00 5.03
4291 19475 8.142551 CCCTCTGTAAACTAAATATAAGAGCGT 58.857 37.037 0.00 0.00 0.00 5.07
4292 19476 9.530633 CCTCTGTAAACTAAATATAAGAGCGTT 57.469 33.333 0.00 0.00 0.00 4.84
4323 19507 7.811117 ACTAAAATAGTGATCTAGACGCTCT 57.189 36.000 10.41 7.61 37.69 4.09
4324 19508 8.228035 ACTAAAATAGTGATCTAGACGCTCTT 57.772 34.615 10.41 6.31 37.69 2.85
4325 19509 9.339850 ACTAAAATAGTGATCTAGACGCTCTTA 57.660 33.333 10.41 7.60 37.69 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 1.299541 AGTTGGTGTTGTCTTCGCAG 58.700 50.000 0.00 0.00 0.00 5.18
108 109 2.106511 GGAGCTTGATAACCTGGGCATA 59.893 50.000 0.00 0.00 0.00 3.14
141 142 5.010213 GGTTGCCAAGGAAATTAACACACTA 59.990 40.000 0.00 0.00 0.00 2.74
142 143 4.202212 GGTTGCCAAGGAAATTAACACACT 60.202 41.667 0.00 0.00 0.00 3.55
157 158 0.106769 TGAGCTGTTCAGGTTGCCAA 60.107 50.000 5.99 0.00 0.00 4.52
158 159 0.111061 ATGAGCTGTTCAGGTTGCCA 59.889 50.000 5.99 0.95 39.68 4.92
159 160 0.524862 CATGAGCTGTTCAGGTTGCC 59.475 55.000 5.99 0.00 39.68 4.52
165 166 2.353889 GGCATGTACATGAGCTGTTCAG 59.646 50.000 34.65 8.84 38.37 3.02
175 176 2.146342 GGAGATTCGGGCATGTACATG 58.854 52.381 28.07 28.07 41.60 3.21
176 177 1.768275 TGGAGATTCGGGCATGTACAT 59.232 47.619 1.41 1.41 0.00 2.29
186 187 1.137872 CCAGAGAAGGTGGAGATTCGG 59.862 57.143 0.00 0.00 37.23 4.30
187 188 2.103373 TCCAGAGAAGGTGGAGATTCG 58.897 52.381 0.00 0.00 39.28 3.34
199 200 3.261897 GGTTGGTCTTCTGATCCAGAGAA 59.738 47.826 0.00 0.00 41.75 2.87
247 248 3.233355 GTGATCACGAGGGTGCTTT 57.767 52.632 10.69 0.00 44.03 3.51
258 259 1.202313 GGAGGAGTGCTACGTGATCAC 60.202 57.143 16.21 16.21 0.00 3.06
265 266 1.104577 GGAGGAGGAGGAGTGCTACG 61.105 65.000 0.00 0.00 27.63 3.51
269 270 1.760480 GGAGGAGGAGGAGGAGTGC 60.760 68.421 0.00 0.00 0.00 4.40
274 275 1.631071 GGCAAAGGAGGAGGAGGAGG 61.631 65.000 0.00 0.00 0.00 4.30
279 280 0.178891 ACAGAGGCAAAGGAGGAGGA 60.179 55.000 0.00 0.00 0.00 3.71
293 294 6.292596 GCGAATGGAGCTTTATCTAAACAGAG 60.293 42.308 0.00 0.00 0.00 3.35
315 318 2.435938 GGATCAAGGCCAACGCGA 60.436 61.111 15.93 0.00 35.02 5.87
318 321 0.394216 TGGATGGATCAAGGCCAACG 60.394 55.000 5.01 0.00 39.21 4.10
339 342 1.802553 GGCTTGGGAGGTACAGGATA 58.197 55.000 0.00 0.00 0.00 2.59
342 345 2.584608 CGGCTTGGGAGGTACAGG 59.415 66.667 0.00 0.00 0.00 4.00
344 347 2.808761 TAGCCGGCTTGGGAGGTACA 62.809 60.000 37.74 9.65 38.63 2.90
352 355 1.450312 CAAGGTCTAGCCGGCTTGG 60.450 63.158 37.74 26.70 43.70 3.61
359 362 1.271379 TGAGCAAACCAAGGTCTAGCC 60.271 52.381 0.00 0.00 34.73 3.93
361 364 3.007398 AGAGTGAGCAAACCAAGGTCTAG 59.993 47.826 0.00 0.00 34.73 2.43
363 366 1.771255 AGAGTGAGCAAACCAAGGTCT 59.229 47.619 0.00 0.00 34.73 3.85
426 429 4.746611 CGCAATATCATGCAGTCAGTCTTA 59.253 41.667 0.00 0.00 46.76 2.10
431 434 2.601504 GCACGCAATATCATGCAGTCAG 60.602 50.000 0.00 0.00 46.76 3.51
452 595 0.249073 CGGACACAGAATAGCCGAGG 60.249 60.000 0.00 0.00 44.43 4.63
466 609 0.976641 AATGAGGCAAGAGACGGACA 59.023 50.000 0.00 0.00 0.00 4.02
488 631 1.041447 ATACGGCCTCTGGTTAGCGT 61.041 55.000 0.00 0.00 0.00 5.07
547 692 8.850454 TTAATTTTCTTTTCTTCTGGTTCACG 57.150 30.769 0.00 0.00 0.00 4.35
595 743 9.500785 TCTTTTTCTGTTTTTCATGGTCTTTTT 57.499 25.926 0.00 0.00 0.00 1.94
634 783 8.630037 TGGTCTTTCCTTTCTCTTACATTTTTC 58.370 33.333 0.00 0.00 37.07 2.29
636 785 7.998964 TCTGGTCTTTCCTTTCTCTTACATTTT 59.001 33.333 0.00 0.00 37.07 1.82
708 883 3.857038 AACCACACGACACGGCCT 61.857 61.111 0.00 0.00 0.00 5.19
746 921 1.371635 AACGCGGCGTAACGTAACT 60.372 52.632 29.63 7.42 42.68 2.24
806 982 4.521062 GCCCACGAGATCGCTGCT 62.521 66.667 1.39 0.00 44.43 4.24
835 1011 1.448717 GTTCTTCGAGGAGGGCTGC 60.449 63.158 0.00 0.00 0.00 5.25
844 1020 2.917971 GTCATGAAGTCGGTTCTTCGAG 59.082 50.000 0.00 6.39 44.53 4.04
845 1021 2.667448 CGTCATGAAGTCGGTTCTTCGA 60.667 50.000 0.00 0.00 44.53 3.71
846 1022 1.649171 CGTCATGAAGTCGGTTCTTCG 59.351 52.381 0.00 0.00 44.53 3.79
861 1038 2.260434 CACGTCCGAACCCGTCAT 59.740 61.111 0.00 0.00 34.59 3.06
965 1143 0.821711 CTCCTAGGTCGGCTCCTCAG 60.822 65.000 9.08 0.00 38.86 3.35
971 1149 2.104170 CTTTCTTCTCCTAGGTCGGCT 58.896 52.381 9.08 0.00 0.00 5.52
975 1779 3.119424 CCGACACTTTCTTCTCCTAGGTC 60.119 52.174 9.08 0.00 0.00 3.85
979 1783 5.105473 CCATTACCGACACTTTCTTCTCCTA 60.105 44.000 0.00 0.00 0.00 2.94
992 1796 4.823419 CCGCCGCCATTACCGACA 62.823 66.667 0.00 0.00 0.00 4.35
1167 2315 0.176680 CGTGCCAGAGCTTGTAGGAT 59.823 55.000 0.00 0.00 40.80 3.24
1440 2588 2.610859 GGGCAGTCAGGGAGGGAA 60.611 66.667 0.00 0.00 0.00 3.97
1668 2816 2.363018 CTGGCGACCTCCTCTGGA 60.363 66.667 0.00 0.00 0.00 3.86
1671 2819 1.760086 CATCCTGGCGACCTCCTCT 60.760 63.158 0.00 0.00 0.00 3.69
1701 2849 4.923942 ATGCTGCCGCGGAGGATG 62.924 66.667 33.48 13.94 45.00 3.51
1749 2897 2.277737 CTGGCCAGGCATGTCCAT 59.722 61.111 26.14 0.00 37.29 3.41
1851 2999 2.126228 GCGTCGAACACCATCCGA 60.126 61.111 0.00 0.00 0.00 4.55
1924 3072 2.370849 AGTCCTGGATGTTAACGGTGTT 59.629 45.455 0.00 0.00 0.00 3.32
2131 6608 0.389391 GGATCGACGGTCATGATGGT 59.611 55.000 10.81 0.00 0.00 3.55
2196 6673 1.043673 GGTCCTCGTACATCCTGGCT 61.044 60.000 0.00 0.00 0.00 4.75
2659 7136 1.843376 CCTCCCATATGGCCTCGGT 60.843 63.158 16.97 0.00 0.00 4.69
2710 7187 4.154347 CCTCTCCGGCCTGCACTC 62.154 72.222 0.00 0.00 0.00 3.51
3074 14314 4.683721 TGAAGGCCGCCGCGTAAA 62.684 61.111 12.58 0.00 35.02 2.01
3146 14387 2.678934 TACCCTCGTCGCCTTGCT 60.679 61.111 0.00 0.00 0.00 3.91
3150 14391 2.674380 AACGTACCCTCGTCGCCT 60.674 61.111 0.00 0.00 43.38 5.52
3279 14529 1.740043 GAGCACCGTCGTATCGTTGC 61.740 60.000 10.35 10.35 46.48 4.17
3287 14537 2.029288 CATTGCTGAGCACCGTCGT 61.029 57.895 6.64 0.00 38.71 4.34
3334 14584 9.436957 GTCATGTCAAGTTAATTAAGAGGAGAA 57.563 33.333 0.00 0.00 0.00 2.87
3335 14585 8.593679 TGTCATGTCAAGTTAATTAAGAGGAGA 58.406 33.333 0.00 0.00 0.00 3.71
3413 17941 4.517285 ACGATCTGGTGATAGCACATTTT 58.483 39.130 13.97 0.00 46.96 1.82
3426 17959 5.359860 TGAGTACATACATCAACGATCTGGT 59.640 40.000 0.00 0.00 0.00 4.00
3535 18710 2.818487 CGCGTTGTGTGGCTGTTGA 61.818 57.895 0.00 0.00 0.00 3.18
3536 18711 2.352229 CGCGTTGTGTGGCTGTTG 60.352 61.111 0.00 0.00 0.00 3.33
3539 18714 2.111932 TTTAGCGCGTTGTGTGGCTG 62.112 55.000 8.43 0.00 36.97 4.85
3580 18756 2.861462 TTATATTTTGCAGCGGCCAC 57.139 45.000 6.32 0.00 40.13 5.01
3581 18757 2.545532 GCATTATATTTTGCAGCGGCCA 60.546 45.455 6.32 0.00 40.13 5.36
3607 18783 2.666190 TGTCTGTTGCAGCGGCTC 60.666 61.111 10.92 4.08 41.91 4.70
3611 18787 1.556591 TTAGCGTGTCTGTTGCAGCG 61.557 55.000 0.00 0.00 0.00 5.18
3615 18791 1.660333 GCAGTTTAGCGTGTCTGTTGC 60.660 52.381 0.00 0.00 0.00 4.17
3691 18867 8.545229 TGTCTTGTTTTGATGTTTGAAATGTT 57.455 26.923 0.00 0.00 0.00 2.71
3755 18931 8.960591 TCTTCTTGGGATATGAATTTGAACTTC 58.039 33.333 0.00 0.00 0.00 3.01
3761 18937 9.618890 TTAGTCTCTTCTTGGGATATGAATTTG 57.381 33.333 0.00 0.00 0.00 2.32
3781 18957 5.479124 AGTCCCGTGTGTTTATTTAGTCT 57.521 39.130 0.00 0.00 0.00 3.24
3852 19028 1.135024 GTTGCCCGCAATGATGTTGAT 60.135 47.619 5.25 0.00 38.28 2.57
3871 19047 6.947733 TGATTTGTCCACAGATTCCATTAAGT 59.052 34.615 0.00 0.00 0.00 2.24
3883 19059 6.239945 CGTTTTTGTTTTGATTTGTCCACAG 58.760 36.000 0.00 0.00 0.00 3.66
3912 19088 2.356125 GGACAAATCAGGCCTTCTAGCA 60.356 50.000 0.00 0.00 0.00 3.49
3993 19171 0.391793 GTTCGGGGCTTCTCCTCTTG 60.392 60.000 0.00 0.00 31.12 3.02
4018 19196 4.225942 TCTTAGATCACAGGATGGCAACTT 59.774 41.667 0.00 0.00 43.62 2.66
4051 19229 8.037758 AGTTTACTGTAGAGATTCATCAACCAG 58.962 37.037 0.00 0.00 0.00 4.00
4052 19230 7.907389 AGTTTACTGTAGAGATTCATCAACCA 58.093 34.615 0.00 0.00 0.00 3.67
4053 19231 8.779354 AAGTTTACTGTAGAGATTCATCAACC 57.221 34.615 0.00 0.00 0.00 3.77
4192 19376 6.257849 GCGTGAGTTAATTCCATCAGTAATCA 59.742 38.462 0.00 0.00 0.00 2.57
4244 19428 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
4245 19429 2.237893 GGAGTAATTTGGAACGGAGGGA 59.762 50.000 0.00 0.00 0.00 4.20
4246 19430 2.640184 GGAGTAATTTGGAACGGAGGG 58.360 52.381 0.00 0.00 0.00 4.30
4247 19431 2.238898 AGGGAGTAATTTGGAACGGAGG 59.761 50.000 0.00 0.00 0.00 4.30
4248 19432 3.197983 AGAGGGAGTAATTTGGAACGGAG 59.802 47.826 0.00 0.00 0.00 4.63
4249 19433 3.055385 CAGAGGGAGTAATTTGGAACGGA 60.055 47.826 0.00 0.00 0.00 4.69
4250 19434 3.270877 CAGAGGGAGTAATTTGGAACGG 58.729 50.000 0.00 0.00 0.00 4.44
4251 19435 3.939066 ACAGAGGGAGTAATTTGGAACG 58.061 45.455 0.00 0.00 0.00 3.95
4252 19436 6.940867 AGTTTACAGAGGGAGTAATTTGGAAC 59.059 38.462 0.00 0.00 32.07 3.62
4253 19437 7.086685 AGTTTACAGAGGGAGTAATTTGGAA 57.913 36.000 0.00 0.00 32.07 3.53
4254 19438 6.697641 AGTTTACAGAGGGAGTAATTTGGA 57.302 37.500 0.00 0.00 32.07 3.53
4255 19439 8.857694 TTTAGTTTACAGAGGGAGTAATTTGG 57.142 34.615 0.00 0.00 32.07 3.28
4263 19447 9.699703 GCTCTTATATTTAGTTTACAGAGGGAG 57.300 37.037 0.00 0.00 0.00 4.30
4264 19448 8.358148 CGCTCTTATATTTAGTTTACAGAGGGA 58.642 37.037 0.00 0.00 40.65 4.20
4265 19449 8.142551 ACGCTCTTATATTTAGTTTACAGAGGG 58.857 37.037 8.01 8.01 42.67 4.30
4266 19450 9.530633 AACGCTCTTATATTTAGTTTACAGAGG 57.469 33.333 0.00 0.00 0.00 3.69
4299 19483 7.811117 AGAGCGTCTAGATCACTATTTTAGT 57.189 36.000 0.00 0.00 37.82 2.24


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

AutoCloner maintained by Alex Coulton.