Multiple sequence alignment - TraesCS5A01G147600

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 TraesCS5A01G147600 chr5A 100.000 7835 0 0 1 7835 325386549 325378715 0.000000e+00 14469.0
1 TraesCS5A01G147600 chr5B 95.389 6571 239 39 1 6547 273729668 273723138 0.000000e+00 10397.0
2 TraesCS5A01G147600 chr5B 90.859 1280 49 22 6607 7835 273723140 273721878 0.000000e+00 1653.0
3 TraesCS5A01G147600 chr5D 98.644 4351 52 6 2201 6547 231736904 231741251 0.000000e+00 7701.0
4 TraesCS5A01G147600 chr5D 93.831 2237 101 20 1 2203 231734548 231736781 0.000000e+00 3332.0
5 TraesCS5A01G147600 chr5D 96.832 1231 31 5 6607 7835 231741249 231742473 0.000000e+00 2050.0
6 TraesCS5A01G147600 chr4A 81.771 768 113 20 3418 4179 476748780 476749526 1.120000e-172 617.0
7 TraesCS5A01G147600 chr4A 82.171 258 40 6 2279 2531 476747549 476747805 4.760000e-52 217.0
8 TraesCS5A01G147600 chr4D 81.769 746 113 16 3438 4179 99662359 99661633 3.130000e-168 603.0
9 TraesCS5A01G147600 chr4D 79.027 329 55 12 2208 2531 99663615 99663296 6.160000e-51 213.0
10 TraesCS5A01G147600 chr4D 93.056 72 3 2 6543 6612 444255078 444255149 3.870000e-18 104.0
11 TraesCS5A01G147600 chr4B 81.380 768 116 20 3418 4179 142056346 142055600 1.120000e-167 601.0
12 TraesCS5A01G147600 chr4B 81.395 258 42 6 2279 2531 142057847 142057591 1.030000e-48 206.0
13 TraesCS5A01G147600 chr4B 93.846 65 3 1 6546 6609 661199895 661199831 6.470000e-16 97.1
14 TraesCS5A01G147600 chr6B 92.857 70 2 3 6542 6609 713975963 713975895 1.800000e-16 99.0
15 TraesCS5A01G147600 chr7B 95.161 62 2 1 6549 6609 328137111 328137050 6.470000e-16 97.1
16 TraesCS5A01G147600 chr6D 91.667 72 3 2 6539 6609 62122730 62122799 6.470000e-16 97.1
17 TraesCS5A01G147600 chr2D 90.909 66 6 0 6544 6609 66821297 66821362 1.080000e-13 89.8
18 TraesCS5A01G147600 chr1B 89.041 73 6 2 6546 6617 24605079 24605008 1.080000e-13 89.8
19 TraesCS5A01G147600 chr2B 88.000 75 5 4 6537 6609 796806444 796806516 1.400000e-12 86.1
20 TraesCS5A01G147600 chr3D 85.882 85 5 4 6525 6609 422648416 422648339 5.040000e-12 84.2


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 TraesCS5A01G147600 chr5A 325378715 325386549 7834 True 14469.0 14469 100.000000 1 7835 1 chr5A.!!$R1 7834
1 TraesCS5A01G147600 chr5B 273721878 273729668 7790 True 6025.0 10397 93.124000 1 7835 2 chr5B.!!$R1 7834
2 TraesCS5A01G147600 chr5D 231734548 231742473 7925 False 4361.0 7701 96.435667 1 7835 3 chr5D.!!$F1 7834
3 TraesCS5A01G147600 chr4A 476747549 476749526 1977 False 417.0 617 81.971000 2279 4179 2 chr4A.!!$F1 1900
4 TraesCS5A01G147600 chr4D 99661633 99663615 1982 True 408.0 603 80.398000 2208 4179 2 chr4D.!!$R1 1971
5 TraesCS5A01G147600 chr4B 142055600 142057847 2247 True 403.5 601 81.387500 2279 4179 2 chr4B.!!$R2 1900

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
188 191 0.035534 TGGTGGTCCGATGATGGTTG 60.036 55.000 0.00 0.00 36.30 3.77 F
328 357 0.253207 AAGACCCGATTTCTCCCCCT 60.253 55.000 0.00 0.00 0.00 4.79 F
1388 1434 0.235665 CGCAGCGTGACAACTTTGAT 59.764 50.000 6.65 0.00 0.00 2.57 F
1389 1435 1.334059 CGCAGCGTGACAACTTTGATT 60.334 47.619 6.65 0.00 0.00 2.57 F
1980 2028 2.025037 TCTTGGATCATTGTTCCCTGGG 60.025 50.000 6.33 6.33 31.87 4.45 F
3436 4444 1.905637 TCAGTCTGCTCGTTACCAGA 58.094 50.000 0.00 0.00 35.84 3.86 F
3731 4742 2.002586 CCTTTAGGATGCACACACTCG 58.997 52.381 0.00 0.00 37.39 4.18 F
4475 5486 1.438651 TCATTGACCTTTTCCGAGCG 58.561 50.000 0.00 0.00 0.00 5.03 F
4955 5966 2.436824 GAGAAACCTCGGCAGGGC 60.437 66.667 7.70 0.00 45.53 5.19 F
5464 6475 2.771688 CCCCTGGTCCTTATTCACCTA 58.228 52.381 0.00 0.00 33.36 3.08 F
5719 6731 7.495934 GCTTGAATTAAAGTGATACTGGAGCTA 59.504 37.037 4.42 0.00 0.00 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1286 1332 0.319211 TCGTAGGGTTTGTCGTGCAG 60.319 55.000 0.00 0.00 0.00 4.41 R
1409 1455 0.764752 ATCCTCCTAAAGGGCTCCCG 60.765 60.000 0.00 0.00 46.23 5.14 R
3122 3485 5.556006 CGGCAACATGTACAACAACAAAATG 60.556 40.000 0.00 0.00 32.02 2.32 R
3345 3799 6.901857 AGGGAATGATAGATGATAGATCTGCA 59.098 38.462 5.18 3.92 0.00 4.41 R
3816 4827 8.598041 AGGAAATAGGACCATGTAAGCTTATAG 58.402 37.037 9.88 2.84 0.00 1.31 R
4421 5432 2.578480 TGGGACAGGCACATATTAACCA 59.422 45.455 0.00 0.00 0.00 3.67 R
4866 5877 3.686726 CAGGAACTTGAAGGATCTTTCCG 59.313 47.826 14.39 8.40 42.46 4.30 R
6031 7043 3.680490 TGCAACAGGAACATAAATCGGA 58.320 40.909 0.00 0.00 0.00 4.55 R
6548 7560 0.462789 GCTATTTTCGGACGGAGGGA 59.537 55.000 0.00 0.00 0.00 4.20 R
6549 7561 0.464452 AGCTATTTTCGGACGGAGGG 59.536 55.000 0.00 0.00 0.00 4.30 R
7492 8553 1.278127 ACGTCATACCACCTTTCCCAG 59.722 52.381 0.00 0.00 0.00 4.45 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
29 30 2.604912 CCTATAAAGGGGAATGGGCC 57.395 55.000 0.00 0.00 39.48 5.80
30 31 1.271926 CCTATAAAGGGGAATGGGCCG 60.272 57.143 0.00 0.00 39.48 6.13
31 32 1.702957 CTATAAAGGGGAATGGGCCGA 59.297 52.381 0.00 0.00 0.00 5.54
32 33 0.478507 ATAAAGGGGAATGGGCCGAG 59.521 55.000 0.00 0.00 0.00 4.63
33 34 0.622154 TAAAGGGGAATGGGCCGAGA 60.622 55.000 0.00 0.00 0.00 4.04
74 76 1.273886 GCGTCCTCACTTCTTCTTCCT 59.726 52.381 0.00 0.00 0.00 3.36
78 80 3.580895 GTCCTCACTTCTTCTTCCTCCTT 59.419 47.826 0.00 0.00 0.00 3.36
79 81 4.041075 GTCCTCACTTCTTCTTCCTCCTTT 59.959 45.833 0.00 0.00 0.00 3.11
80 82 4.660771 TCCTCACTTCTTCTTCCTCCTTTT 59.339 41.667 0.00 0.00 0.00 2.27
81 83 4.759183 CCTCACTTCTTCTTCCTCCTTTTG 59.241 45.833 0.00 0.00 0.00 2.44
83 85 5.368989 TCACTTCTTCTTCCTCCTTTTGTC 58.631 41.667 0.00 0.00 0.00 3.18
90 92 0.108585 TCCTCCTTTTGTCGCTGCTT 59.891 50.000 0.00 0.00 0.00 3.91
102 104 1.515736 GCTGCTTTCTTGCGGATGC 60.516 57.895 0.00 0.00 41.56 3.91
115 117 1.078709 CGGATGCGCTCTTTTCTTCA 58.921 50.000 9.73 0.00 0.00 3.02
116 118 1.201965 CGGATGCGCTCTTTTCTTCAC 60.202 52.381 9.73 0.00 0.00 3.18
118 120 3.262420 GGATGCGCTCTTTTCTTCACTA 58.738 45.455 9.73 0.00 0.00 2.74
119 121 3.873952 GGATGCGCTCTTTTCTTCACTAT 59.126 43.478 9.73 0.00 0.00 2.12
186 189 0.469917 GATGGTGGTCCGATGATGGT 59.530 55.000 0.00 0.00 36.30 3.55
188 191 0.035534 TGGTGGTCCGATGATGGTTG 60.036 55.000 0.00 0.00 36.30 3.77
192 195 0.679640 GGTCCGATGATGGTTGGCAA 60.680 55.000 0.00 0.00 0.00 4.52
200 203 4.559300 CGATGATGGTTGGCAAAGAAAAGT 60.559 41.667 0.00 0.00 0.00 2.66
203 206 3.518634 TGGTTGGCAAAGAAAAGTGAC 57.481 42.857 0.00 0.00 0.00 3.67
225 228 1.203928 CGCTCTTCGTTGCATCTAGG 58.796 55.000 0.00 0.00 0.00 3.02
235 238 1.121407 TGCATCTAGGTCCATCCGGG 61.121 60.000 0.00 0.00 41.99 5.73
261 264 1.287425 GCATGTGAGCGGTTACCTAC 58.713 55.000 7.09 0.00 0.00 3.18
277 280 1.393883 CCTACTTCGCGCCTTCTTTTC 59.606 52.381 0.00 0.00 0.00 2.29
283 311 0.868406 CGCGCCTTCTTTTCACTCTT 59.132 50.000 0.00 0.00 0.00 2.85
292 320 5.363868 CCTTCTTTTCACTCTTTCCCCTTTT 59.636 40.000 0.00 0.00 0.00 2.27
328 357 0.253207 AAGACCCGATTTCTCCCCCT 60.253 55.000 0.00 0.00 0.00 4.79
371 402 3.311486 TGAATCATGTAGCGTGTGTCA 57.689 42.857 0.00 0.00 0.00 3.58
418 449 0.704076 TTAATCCACCTGCCCTTGCT 59.296 50.000 0.00 0.00 38.71 3.91
535 566 6.546395 GCAATAAAGATTTGAAAGAGCGAGA 58.454 36.000 0.00 0.00 0.00 4.04
538 569 5.604010 AAAGATTTGAAAGAGCGAGACTG 57.396 39.130 0.00 0.00 0.00 3.51
583 614 8.077991 GGTTGTGTCATAAACCCTAAACTAAAC 58.922 37.037 8.54 0.00 40.03 2.01
630 661 1.066914 GAGAGCTCAAAGCACACTCG 58.933 55.000 17.77 0.00 45.56 4.18
633 664 2.856032 CTCAAAGCACACTCGCCG 59.144 61.111 0.00 0.00 0.00 6.46
654 686 2.980699 AAGAAGAGGGGGAAGAGGAT 57.019 50.000 0.00 0.00 0.00 3.24
661 693 1.220750 AGGGGGAAGAGGATATCGTGT 59.779 52.381 1.92 0.00 0.00 4.49
934 978 3.948719 TCGCCCCAAGCTTCCGTT 61.949 61.111 0.00 0.00 40.39 4.44
1007 1053 3.309436 TTCCAGCGTCCATGGTCGG 62.309 63.158 28.37 15.16 39.01 4.79
1242 1288 3.680754 CGGTACCAGTTACTCCATTTCCC 60.681 52.174 13.54 0.00 0.00 3.97
1286 1332 0.321298 TGCTTTCCTTACTGTCCCGC 60.321 55.000 0.00 0.00 0.00 6.13
1304 1350 1.897398 GCTGCACGACAAACCCTACG 61.897 60.000 0.00 0.00 0.00 3.51
1388 1434 0.235665 CGCAGCGTGACAACTTTGAT 59.764 50.000 6.65 0.00 0.00 2.57
1389 1435 1.334059 CGCAGCGTGACAACTTTGATT 60.334 47.619 6.65 0.00 0.00 2.57
1390 1436 2.046313 GCAGCGTGACAACTTTGATTG 58.954 47.619 0.00 0.00 35.59 2.67
1409 1455 3.788227 TGTCATCCCTGTTATATGCCC 57.212 47.619 0.00 0.00 0.00 5.36
1521 1567 8.148351 GCTACTACTCATTTCATGGTTACCATA 58.852 37.037 17.31 1.82 43.15 2.74
1525 1571 7.865706 ACTCATTTCATGGTTACCATACTTC 57.134 36.000 17.31 0.00 43.15 3.01
1527 1573 5.820423 TCATTTCATGGTTACCATACTTCCG 59.180 40.000 17.31 3.69 43.15 4.30
1781 1828 2.707257 GGGTCGGAGGATTGGGTATAAA 59.293 50.000 0.00 0.00 0.00 1.40
1980 2028 2.025037 TCTTGGATCATTGTTCCCTGGG 60.025 50.000 6.33 6.33 31.87 4.45
2004 2052 8.035984 GGGATATCTGGCTAATGTAGTTAGAAC 58.964 40.741 2.05 0.00 41.99 3.01
2107 2155 5.922739 TGGTATGCTCAATATGCTTTACG 57.077 39.130 0.00 0.00 0.00 3.18
2188 2236 7.814107 GCATTAGAGAAAAACCATGAAATCACA 59.186 33.333 0.00 0.00 0.00 3.58
2189 2237 9.695526 CATTAGAGAAAAACCATGAAATCACAA 57.304 29.630 0.00 0.00 0.00 3.33
2313 2490 5.752892 TTCGACAGCCTATAGAAGTACAG 57.247 43.478 0.00 0.00 0.00 2.74
2561 2743 7.259290 TCGAATTGCTCTCTGTTTTAGTTTT 57.741 32.000 0.00 0.00 0.00 2.43
3111 3474 4.100035 TCAGCGGTCTTATCTCATGTCATT 59.900 41.667 0.00 0.00 0.00 2.57
3122 3485 9.926751 CTTATCTCATGTCATTGTTATGAACAC 57.073 33.333 0.00 0.00 42.23 3.32
3345 3799 6.152831 AGTTACTTGGTTGCTTTCTTGAAACT 59.847 34.615 0.00 0.00 0.00 2.66
3436 4444 1.905637 TCAGTCTGCTCGTTACCAGA 58.094 50.000 0.00 0.00 35.84 3.86
3453 4461 5.514500 ACCAGACATATTTGTAACCACCT 57.486 39.130 0.00 0.00 35.79 4.00
3731 4742 2.002586 CCTTTAGGATGCACACACTCG 58.997 52.381 0.00 0.00 37.39 4.18
3816 4827 4.439253 AGTTTGACTGGGATAATAGGGC 57.561 45.455 0.00 0.00 0.00 5.19
3908 4919 9.499585 CTGATCTTTGTGTATGATTGAATGTTC 57.500 33.333 0.00 0.00 0.00 3.18
4234 5245 5.105063 GGAATTTAGGAAAAGCTGATGTGC 58.895 41.667 0.00 0.00 0.00 4.57
4264 5275 5.519566 TGCTTGTTGTGATGTGAAATTGTTC 59.480 36.000 0.00 0.00 0.00 3.18
4421 5432 2.526888 TCCCACGTCCAGAGTTCTAT 57.473 50.000 0.00 0.00 0.00 1.98
4435 5446 6.428159 CCAGAGTTCTATGGTTAATATGTGCC 59.572 42.308 5.43 0.00 0.00 5.01
4475 5486 1.438651 TCATTGACCTTTTCCGAGCG 58.561 50.000 0.00 0.00 0.00 5.03
4585 5596 3.803715 GCAATTGGCTTCTATCGGCTAGA 60.804 47.826 7.72 0.00 40.25 2.43
4745 5756 5.989777 ACGTAACTTTCTTCTTATGTGCACT 59.010 36.000 19.41 6.22 0.00 4.40
4866 5877 2.543067 ATCTTGGTGCCCGGAAGCTC 62.543 60.000 0.73 0.00 0.00 4.09
4955 5966 2.436824 GAGAAACCTCGGCAGGGC 60.437 66.667 7.70 0.00 45.53 5.19
5464 6475 2.771688 CCCCTGGTCCTTATTCACCTA 58.228 52.381 0.00 0.00 33.36 3.08
5719 6731 7.495934 GCTTGAATTAAAGTGATACTGGAGCTA 59.504 37.037 4.42 0.00 0.00 3.32
6544 7556 8.402472 TGAAAACCACACTAGAACACTAATTTG 58.598 33.333 0.00 0.00 0.00 2.32
6545 7557 7.875327 AAACCACACTAGAACACTAATTTGT 57.125 32.000 0.00 0.00 0.00 2.83
6546 7558 8.967664 AAACCACACTAGAACACTAATTTGTA 57.032 30.769 0.00 0.00 0.00 2.41
6547 7559 7.958053 ACCACACTAGAACACTAATTTGTAC 57.042 36.000 0.00 0.00 0.00 2.90
6548 7560 7.732996 ACCACACTAGAACACTAATTTGTACT 58.267 34.615 0.00 0.00 0.00 2.73
6549 7561 7.871463 ACCACACTAGAACACTAATTTGTACTC 59.129 37.037 0.00 0.00 0.00 2.59
6550 7562 7.331193 CCACACTAGAACACTAATTTGTACTCC 59.669 40.741 0.00 0.00 0.00 3.85
6551 7563 7.331193 CACACTAGAACACTAATTTGTACTCCC 59.669 40.741 0.00 0.00 0.00 4.30
6552 7564 7.234988 ACACTAGAACACTAATTTGTACTCCCT 59.765 37.037 0.00 0.00 0.00 4.20
6553 7565 7.760340 CACTAGAACACTAATTTGTACTCCCTC 59.240 40.741 0.00 0.00 0.00 4.30
6554 7566 6.051179 AGAACACTAATTTGTACTCCCTCC 57.949 41.667 0.00 0.00 0.00 4.30
6555 7567 4.467198 ACACTAATTTGTACTCCCTCCG 57.533 45.455 0.00 0.00 0.00 4.63
6556 7568 3.836562 ACACTAATTTGTACTCCCTCCGT 59.163 43.478 0.00 0.00 0.00 4.69
6557 7569 4.081807 ACACTAATTTGTACTCCCTCCGTC 60.082 45.833 0.00 0.00 0.00 4.79
6558 7570 3.450096 ACTAATTTGTACTCCCTCCGTCC 59.550 47.826 0.00 0.00 0.00 4.79
6559 7571 0.822164 ATTTGTACTCCCTCCGTCCG 59.178 55.000 0.00 0.00 0.00 4.79
6560 7572 0.251297 TTTGTACTCCCTCCGTCCGA 60.251 55.000 0.00 0.00 0.00 4.55
6561 7573 0.251297 TTGTACTCCCTCCGTCCGAA 60.251 55.000 0.00 0.00 0.00 4.30
6562 7574 0.251297 TGTACTCCCTCCGTCCGAAA 60.251 55.000 0.00 0.00 0.00 3.46
6563 7575 0.890683 GTACTCCCTCCGTCCGAAAA 59.109 55.000 0.00 0.00 0.00 2.29
6564 7576 1.479730 GTACTCCCTCCGTCCGAAAAT 59.520 52.381 0.00 0.00 0.00 1.82
6565 7577 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
6566 7578 1.755380 ACTCCCTCCGTCCGAAAATAG 59.245 52.381 0.00 0.00 0.00 1.73
6567 7579 0.462789 TCCCTCCGTCCGAAAATAGC 59.537 55.000 0.00 0.00 0.00 2.97
6568 7580 0.464452 CCCTCCGTCCGAAAATAGCT 59.536 55.000 0.00 0.00 0.00 3.32
6569 7581 1.684983 CCCTCCGTCCGAAAATAGCTA 59.315 52.381 0.00 0.00 0.00 3.32
6570 7582 2.288273 CCCTCCGTCCGAAAATAGCTAG 60.288 54.545 0.00 0.00 0.00 3.42
6571 7583 2.361438 CCTCCGTCCGAAAATAGCTAGT 59.639 50.000 0.00 0.00 0.00 2.57
6572 7584 3.567164 CCTCCGTCCGAAAATAGCTAGTA 59.433 47.826 0.00 0.00 0.00 1.82
6573 7585 4.535116 CTCCGTCCGAAAATAGCTAGTAC 58.465 47.826 0.00 0.00 0.00 2.73
6574 7586 3.947196 TCCGTCCGAAAATAGCTAGTACA 59.053 43.478 0.00 0.00 0.00 2.90
6575 7587 4.398988 TCCGTCCGAAAATAGCTAGTACAA 59.601 41.667 0.00 0.00 0.00 2.41
6576 7588 5.104374 CCGTCCGAAAATAGCTAGTACAAA 58.896 41.667 0.00 0.00 0.00 2.83
6577 7589 5.231568 CCGTCCGAAAATAGCTAGTACAAAG 59.768 44.000 0.00 0.00 0.00 2.77
6578 7590 5.276254 CGTCCGAAAATAGCTAGTACAAAGC 60.276 44.000 11.24 11.24 40.40 3.51
6587 7599 4.181309 GCTAGTACAAAGCTGAGTCACT 57.819 45.455 11.77 0.00 37.01 3.41
6588 7600 4.561105 GCTAGTACAAAGCTGAGTCACTT 58.439 43.478 11.77 0.00 37.01 3.16
6589 7601 5.710984 GCTAGTACAAAGCTGAGTCACTTA 58.289 41.667 11.77 0.00 37.01 2.24
6590 7602 6.334202 GCTAGTACAAAGCTGAGTCACTTAT 58.666 40.000 11.77 4.10 37.01 1.73
6591 7603 6.814146 GCTAGTACAAAGCTGAGTCACTTATT 59.186 38.462 11.77 2.93 37.01 1.40
6592 7604 7.332182 GCTAGTACAAAGCTGAGTCACTTATTT 59.668 37.037 11.77 0.00 37.01 1.40
6593 7605 9.209175 CTAGTACAAAGCTGAGTCACTTATTTT 57.791 33.333 7.95 0.00 0.00 1.82
6594 7606 7.865707 AGTACAAAGCTGAGTCACTTATTTTG 58.134 34.615 7.95 5.60 0.00 2.44
6595 7607 6.076981 ACAAAGCTGAGTCACTTATTTTGG 57.923 37.500 9.89 0.00 0.00 3.28
6596 7608 5.010012 ACAAAGCTGAGTCACTTATTTTGGG 59.990 40.000 9.89 0.00 0.00 4.12
6597 7609 4.640771 AGCTGAGTCACTTATTTTGGGA 57.359 40.909 0.00 0.00 0.00 4.37
6598 7610 4.327680 AGCTGAGTCACTTATTTTGGGAC 58.672 43.478 0.00 0.00 0.00 4.46
6599 7611 3.125316 GCTGAGTCACTTATTTTGGGACG 59.875 47.826 0.00 0.00 33.84 4.79
6600 7612 3.670625 TGAGTCACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 33.84 4.79
6601 7613 3.325425 TGAGTCACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 33.84 4.69
6602 7614 3.933332 GAGTCACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 33.84 4.63
6603 7615 3.007635 GTCACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
6604 7616 2.026636 TCACTTATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
6605 7617 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
6637 7649 5.450826 GGAAACCGTCCATTTTGTTAGTGTT 60.451 40.000 0.00 0.00 46.97 3.32
6645 7657 6.921307 GTCCATTTTGTTAGTGTTAACCTTGG 59.079 38.462 2.48 3.43 38.71 3.61
6900 7914 6.549736 TCTGATTCAACCGGAAGATACTGATA 59.450 38.462 9.46 0.00 39.30 2.15
6956 7970 4.564769 GGTTTCTCTTCTAGTCAAGCATCG 59.435 45.833 0.00 0.00 0.00 3.84
7257 8271 0.811219 TGAGCATTCGAGGATTGCCG 60.811 55.000 8.40 0.00 39.00 5.69
7427 8469 1.299316 CGTGTTGTGCCTTGCCTTG 60.299 57.895 0.00 0.00 0.00 3.61
7492 8553 5.171476 TCTACTGTTAGCTCTGTTTCATGC 58.829 41.667 0.00 0.00 0.00 4.06
7510 8571 1.004277 TGCTGGGAAAGGTGGTATGAC 59.996 52.381 0.00 0.00 0.00 3.06
7550 8611 5.940192 TGTGATTTTGCATAGAAACGAGT 57.060 34.783 0.00 0.00 0.00 4.18
7552 8613 5.238432 TGTGATTTTGCATAGAAACGAGTGT 59.762 36.000 0.00 0.00 0.00 3.55
7632 8693 5.923733 ACTAGAAGAATCCGAGTCATGTT 57.076 39.130 0.00 0.00 0.00 2.71
7673 8738 5.349817 GGATAGGATGCAACGATATGTTCAG 59.650 44.000 0.00 0.00 39.29 3.02
7677 8742 2.267426 TGCAACGATATGTTCAGTCGG 58.733 47.619 12.40 1.37 39.29 4.79
7683 8748 3.698040 ACGATATGTTCAGTCGGGTAGTT 59.302 43.478 12.40 0.00 39.53 2.24
7699 8764 5.921976 CGGGTAGTTGGTCAAAAATAAAACC 59.078 40.000 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.490902 GGCCCATTCCCCTTTATAGGTG 60.491 54.545 0.00 0.00 40.19 4.00
9 10 1.787058 GGCCCATTCCCCTTTATAGGT 59.213 52.381 0.00 0.00 40.19 3.08
27 28 2.584873 TAACCTCTCCCCCTCTCGGC 62.585 65.000 0.00 0.00 0.00 5.54
29 30 1.102222 CGTAACCTCTCCCCCTCTCG 61.102 65.000 0.00 0.00 0.00 4.04
30 31 1.393487 GCGTAACCTCTCCCCCTCTC 61.393 65.000 0.00 0.00 0.00 3.20
31 32 1.381463 GCGTAACCTCTCCCCCTCT 60.381 63.158 0.00 0.00 0.00 3.69
32 33 1.381463 AGCGTAACCTCTCCCCCTC 60.381 63.158 0.00 0.00 0.00 4.30
33 34 1.381463 GAGCGTAACCTCTCCCCCT 60.381 63.158 0.00 0.00 0.00 4.79
36 37 0.460459 GCAAGAGCGTAACCTCTCCC 60.460 60.000 0.00 0.00 41.19 4.30
56 57 3.169908 AGGAGGAAGAAGAAGTGAGGAC 58.830 50.000 0.00 0.00 0.00 3.85
74 76 1.967319 AGAAAGCAGCGACAAAAGGA 58.033 45.000 0.00 0.00 0.00 3.36
78 80 3.549997 GCAAGAAAGCAGCGACAAA 57.450 47.368 0.00 0.00 0.00 2.83
102 104 3.484886 GCAGCATAGTGAAGAAAAGAGCG 60.485 47.826 0.00 0.00 0.00 5.03
132 134 2.098233 GTGTATCGTGGTGGTGCGG 61.098 63.158 0.00 0.00 0.00 5.69
134 136 0.037697 TGAGTGTATCGTGGTGGTGC 60.038 55.000 0.00 0.00 0.00 5.01
141 143 1.066858 AGCCAAGGTGAGTGTATCGTG 60.067 52.381 0.00 0.00 0.00 4.35
186 189 2.159310 CGTGGTCACTTTTCTTTGCCAA 60.159 45.455 0.00 0.00 0.00 4.52
188 191 1.864029 GCGTGGTCACTTTTCTTTGCC 60.864 52.381 0.00 0.00 0.00 4.52
192 195 2.622064 AGAGCGTGGTCACTTTTCTT 57.378 45.000 1.55 0.00 0.00 2.52
261 264 0.868406 AGTGAAAAGAAGGCGCGAAG 59.132 50.000 12.10 0.00 0.00 3.79
277 280 4.100279 AGGTACAAAAGGGGAAAGAGTG 57.900 45.455 0.00 0.00 0.00 3.51
283 311 6.768641 AAAGTACTAGGTACAAAAGGGGAA 57.231 37.500 0.00 0.00 41.03 3.97
292 320 7.573710 TCGGGTCTTATAAAGTACTAGGTACA 58.426 38.462 0.00 0.00 41.03 2.90
328 357 2.924302 TGTCTACAAGGTAGGGGAGAGA 59.076 50.000 3.77 0.00 0.00 3.10
391 422 2.952310 GGCAGGTGGATTAATGAAGGAC 59.048 50.000 0.00 0.00 0.00 3.85
401 432 1.304713 CAGCAAGGGCAGGTGGATT 60.305 57.895 0.00 0.00 44.61 3.01
418 449 1.952102 GAGGGCGGTGATCGGTAACA 61.952 60.000 0.00 0.00 39.69 2.41
469 500 2.169769 TCGGTATTGTCCCTGGTGATTC 59.830 50.000 0.00 0.00 0.00 2.52
535 566 4.250305 AAGGGCACGAACCGCAGT 62.250 61.111 0.00 0.00 0.00 4.40
630 661 0.393132 CTTCCCCCTCTTCTTTCGGC 60.393 60.000 0.00 0.00 0.00 5.54
633 664 2.552367 TCCTCTTCCCCCTCTTCTTTC 58.448 52.381 0.00 0.00 0.00 2.62
654 686 1.548719 CACACCTCTTCCCACACGATA 59.451 52.381 0.00 0.00 0.00 2.92
661 693 0.545309 CCTCCTCACACCTCTTCCCA 60.545 60.000 0.00 0.00 0.00 4.37
934 978 2.742372 GCGCCGCTGGAGAAGAAA 60.742 61.111 0.00 0.00 0.00 2.52
1242 1288 3.100817 CGAGTAAAAATTGGAGCATGCG 58.899 45.455 13.01 0.00 0.00 4.73
1286 1332 0.319211 TCGTAGGGTTTGTCGTGCAG 60.319 55.000 0.00 0.00 0.00 4.41
1299 1345 2.476185 CGCAAAGCAAAGGAATCGTAGG 60.476 50.000 0.00 0.00 0.00 3.18
1388 1434 3.495983 CGGGCATATAACAGGGATGACAA 60.496 47.826 0.00 0.00 29.51 3.18
1389 1435 2.038426 CGGGCATATAACAGGGATGACA 59.962 50.000 0.00 0.00 29.51 3.58
1390 1436 2.615493 CCGGGCATATAACAGGGATGAC 60.615 54.545 0.00 0.00 0.00 3.06
1409 1455 0.764752 ATCCTCCTAAAGGGCTCCCG 60.765 60.000 0.00 0.00 46.23 5.14
1432 1478 7.270779 ACCTAAAGGATAAATCAGAACCGTAC 58.729 38.462 2.23 0.00 38.94 3.67
1433 1479 7.124599 TGACCTAAAGGATAAATCAGAACCGTA 59.875 37.037 2.23 0.00 38.94 4.02
1436 1482 7.229506 CCATGACCTAAAGGATAAATCAGAACC 59.770 40.741 2.23 0.00 38.94 3.62
1521 1567 2.874086 CACCTAAAACGAAACCGGAAGT 59.126 45.455 9.46 0.00 0.00 3.01
1525 1571 3.392882 AGTACACCTAAAACGAAACCGG 58.607 45.455 0.00 0.00 0.00 5.28
1527 1573 4.450080 CCAGAGTACACCTAAAACGAAACC 59.550 45.833 0.00 0.00 0.00 3.27
1781 1828 5.186992 GGCCCAAAATGGTCACTAAGTTAAT 59.813 40.000 0.00 0.00 35.17 1.40
1903 1950 4.658901 ACATAACCCTTCCTCGGATACAAT 59.341 41.667 0.00 0.00 0.00 2.71
2004 2052 6.128795 GCGCCAAGTAGACTATTTATAGCAAG 60.129 42.308 0.00 0.00 33.68 4.01
2133 2181 7.618117 TCTCCAGAAGTGACAGTATTATTACCA 59.382 37.037 0.00 0.00 0.00 3.25
2134 2182 8.008513 TCTCCAGAAGTGACAGTATTATTACC 57.991 38.462 0.00 0.00 0.00 2.85
2196 2244 7.458038 CCAACTTTGGTACACAATTACAAAC 57.542 36.000 0.00 0.00 43.43 2.93
2313 2490 8.617809 GTTTGAAAAAGGGAAAAGGGTTAATTC 58.382 33.333 0.00 0.00 0.00 2.17
2652 2841 5.621197 TTGGTTAAATCACAGGAATGTCG 57.379 39.130 0.00 0.00 0.00 4.35
2970 3333 7.806180 ACTCTGGCCAATAGTATGAATAAAGT 58.194 34.615 16.86 0.00 0.00 2.66
3122 3485 5.556006 CGGCAACATGTACAACAACAAAATG 60.556 40.000 0.00 0.00 32.02 2.32
3345 3799 6.901857 AGGGAATGATAGATGATAGATCTGCA 59.098 38.462 5.18 3.92 0.00 4.41
3816 4827 8.598041 AGGAAATAGGACCATGTAAGCTTATAG 58.402 37.037 9.88 2.84 0.00 1.31
3908 4919 9.817365 GCTATGTGATTAGCAATTATAACACAG 57.183 33.333 0.00 2.85 43.33 3.66
4234 5245 5.422666 TCACATCACAACAAGCAAGTTAG 57.577 39.130 0.00 0.00 0.00 2.34
4421 5432 2.578480 TGGGACAGGCACATATTAACCA 59.422 45.455 0.00 0.00 0.00 3.67
4435 5446 4.584325 TGAAGGAACAGAAAATTGGGACAG 59.416 41.667 0.00 0.00 42.39 3.51
4585 5596 8.919145 TGTACACAAACCTTAAAATGAAATCCT 58.081 29.630 0.00 0.00 0.00 3.24
4745 5756 4.439057 GACTATGTCCATGAAGCGGTTTA 58.561 43.478 0.00 0.00 0.00 2.01
4866 5877 3.686726 CAGGAACTTGAAGGATCTTTCCG 59.313 47.826 14.39 8.40 42.46 4.30
5464 6475 4.538746 ACGGCTTTAAGAAGAAGTAGCT 57.461 40.909 0.00 0.00 34.71 3.32
5625 6637 8.945481 TGATACATGGAATAAAAAGGCATTTG 57.055 30.769 0.00 0.00 0.00 2.32
6031 7043 3.680490 TGCAACAGGAACATAAATCGGA 58.320 40.909 0.00 0.00 0.00 4.55
6210 7222 8.341173 CAGAATATGGTCTGTTAGCTTGATTTC 58.659 37.037 0.00 0.00 40.22 2.17
6523 7535 7.732996 AGTACAAATTAGTGTTCTAGTGTGGT 58.267 34.615 0.00 0.00 32.75 4.16
6544 7556 0.890683 TTTTCGGACGGAGGGAGTAC 59.109 55.000 0.00 0.00 0.00 2.73
6545 7557 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
6546 7558 1.755380 CTATTTTCGGACGGAGGGAGT 59.245 52.381 0.00 0.00 0.00 3.85
6547 7559 1.538419 GCTATTTTCGGACGGAGGGAG 60.538 57.143 0.00 0.00 0.00 4.30
6548 7560 0.462789 GCTATTTTCGGACGGAGGGA 59.537 55.000 0.00 0.00 0.00 4.20
6549 7561 0.464452 AGCTATTTTCGGACGGAGGG 59.536 55.000 0.00 0.00 0.00 4.30
6550 7562 2.361438 ACTAGCTATTTTCGGACGGAGG 59.639 50.000 0.00 0.00 0.00 4.30
6551 7563 3.712091 ACTAGCTATTTTCGGACGGAG 57.288 47.619 0.00 0.00 0.00 4.63
6552 7564 3.947196 TGTACTAGCTATTTTCGGACGGA 59.053 43.478 0.00 0.00 0.00 4.69
6553 7565 4.297299 TGTACTAGCTATTTTCGGACGG 57.703 45.455 0.00 0.00 0.00 4.79
6554 7566 5.276254 GCTTTGTACTAGCTATTTTCGGACG 60.276 44.000 11.72 0.00 35.74 4.79
6555 7567 5.811100 AGCTTTGTACTAGCTATTTTCGGAC 59.189 40.000 17.78 0.00 46.66 4.79
6556 7568 5.810587 CAGCTTTGTACTAGCTATTTTCGGA 59.189 40.000 18.51 0.00 46.80 4.55
6557 7569 5.810587 TCAGCTTTGTACTAGCTATTTTCGG 59.189 40.000 18.51 8.36 46.80 4.30
6558 7570 6.531948 ACTCAGCTTTGTACTAGCTATTTTCG 59.468 38.462 18.51 8.89 46.80 3.46
6559 7571 7.545965 TGACTCAGCTTTGTACTAGCTATTTTC 59.454 37.037 18.51 13.79 46.80 2.29
6560 7572 7.332182 GTGACTCAGCTTTGTACTAGCTATTTT 59.668 37.037 18.51 7.44 46.80 1.82
6561 7573 6.814146 GTGACTCAGCTTTGTACTAGCTATTT 59.186 38.462 18.51 8.78 46.80 1.40
6562 7574 6.153680 AGTGACTCAGCTTTGTACTAGCTATT 59.846 38.462 18.51 9.05 46.80 1.73
6563 7575 5.654650 AGTGACTCAGCTTTGTACTAGCTAT 59.345 40.000 18.51 10.22 46.80 2.97
6564 7576 5.010933 AGTGACTCAGCTTTGTACTAGCTA 58.989 41.667 18.51 0.00 46.80 3.32
6566 7578 4.181309 AGTGACTCAGCTTTGTACTAGC 57.819 45.455 11.22 11.22 38.93 3.42
6567 7579 8.764524 AAATAAGTGACTCAGCTTTGTACTAG 57.235 34.615 0.00 0.00 0.00 2.57
6568 7580 8.988934 CAAAATAAGTGACTCAGCTTTGTACTA 58.011 33.333 0.00 0.00 0.00 1.82
6569 7581 7.041098 CCAAAATAAGTGACTCAGCTTTGTACT 60.041 37.037 0.00 0.00 0.00 2.73
6570 7582 7.078228 CCAAAATAAGTGACTCAGCTTTGTAC 58.922 38.462 0.00 0.00 0.00 2.90
6571 7583 6.206634 CCCAAAATAAGTGACTCAGCTTTGTA 59.793 38.462 0.00 0.00 0.00 2.41
6572 7584 5.010012 CCCAAAATAAGTGACTCAGCTTTGT 59.990 40.000 0.00 0.00 0.00 2.83
6573 7585 5.241506 TCCCAAAATAAGTGACTCAGCTTTG 59.758 40.000 0.00 0.00 0.00 2.77
6574 7586 5.241728 GTCCCAAAATAAGTGACTCAGCTTT 59.758 40.000 0.00 0.00 0.00 3.51
6575 7587 4.762251 GTCCCAAAATAAGTGACTCAGCTT 59.238 41.667 0.00 0.00 0.00 3.74
6576 7588 4.327680 GTCCCAAAATAAGTGACTCAGCT 58.672 43.478 0.00 0.00 0.00 4.24
6577 7589 3.125316 CGTCCCAAAATAAGTGACTCAGC 59.875 47.826 0.00 0.00 0.00 4.26
6578 7590 3.684788 CCGTCCCAAAATAAGTGACTCAG 59.315 47.826 0.00 0.00 0.00 3.35
6579 7591 3.325425 TCCGTCCCAAAATAAGTGACTCA 59.675 43.478 0.00 0.00 0.00 3.41
6580 7592 3.933332 CTCCGTCCCAAAATAAGTGACTC 59.067 47.826 0.00 0.00 0.00 3.36
6581 7593 3.307480 CCTCCGTCCCAAAATAAGTGACT 60.307 47.826 0.00 0.00 0.00 3.41
6582 7594 3.007635 CCTCCGTCCCAAAATAAGTGAC 58.992 50.000 0.00 0.00 0.00 3.67
6583 7595 2.026636 CCCTCCGTCCCAAAATAAGTGA 60.027 50.000 0.00 0.00 0.00 3.41
6584 7596 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
6585 7597 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
6586 7598 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
6587 7599 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
6588 7600 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
6589 7601 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
6590 7602 1.732117 TTACTCCCTCCGTCCCAAAA 58.268 50.000 0.00 0.00 0.00 2.44
6591 7603 1.961133 ATTACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
6592 7604 2.852714 TATTACTCCCTCCGTCCCAA 57.147 50.000 0.00 0.00 0.00 4.12
6593 7605 2.605257 CATATTACTCCCTCCGTCCCA 58.395 52.381 0.00 0.00 0.00 4.37
6594 7606 1.900486 CCATATTACTCCCTCCGTCCC 59.100 57.143 0.00 0.00 0.00 4.46
6595 7607 2.885616 TCCATATTACTCCCTCCGTCC 58.114 52.381 0.00 0.00 0.00 4.79
6596 7608 4.502777 GGTTTCCATATTACTCCCTCCGTC 60.503 50.000 0.00 0.00 0.00 4.79
6597 7609 3.390311 GGTTTCCATATTACTCCCTCCGT 59.610 47.826 0.00 0.00 0.00 4.69
6598 7610 3.554337 CGGTTTCCATATTACTCCCTCCG 60.554 52.174 0.00 0.00 0.00 4.63
6599 7611 3.390311 ACGGTTTCCATATTACTCCCTCC 59.610 47.826 0.00 0.00 0.00 4.30
6600 7612 4.502777 GGACGGTTTCCATATTACTCCCTC 60.503 50.000 0.00 0.00 45.10 4.30
6601 7613 3.390311 GGACGGTTTCCATATTACTCCCT 59.610 47.826 0.00 0.00 45.10 4.20
6602 7614 3.736720 GGACGGTTTCCATATTACTCCC 58.263 50.000 0.00 0.00 45.10 4.30
6637 7649 5.491070 CTGAACAGATGTGATCCAAGGTTA 58.509 41.667 0.00 0.00 0.00 2.85
6645 7657 5.618056 TTTCAAGCTGAACAGATGTGATC 57.382 39.130 5.97 0.00 35.89 2.92
6900 7914 4.314440 ACCGAGTGTGCGCCACAT 62.314 61.111 24.48 13.38 46.32 3.21
6915 7929 1.525535 CCTCTGCTATGGCTGCACC 60.526 63.158 1.68 0.00 39.59 5.01
6956 7970 6.407202 AGAACCAAGTTAGGATGTACATGAC 58.593 40.000 14.43 6.05 0.00 3.06
7257 8271 1.324005 ACTACAAGAGCGAGCTCCCC 61.324 60.000 20.15 0.00 43.70 4.81
7492 8553 1.278127 ACGTCATACCACCTTTCCCAG 59.722 52.381 0.00 0.00 0.00 4.45
7510 8571 5.281693 TCACAAGCAAATCATACTCAACG 57.718 39.130 0.00 0.00 0.00 4.10
7550 8611 2.503331 CACACATTTCTGCCCTACACA 58.497 47.619 0.00 0.00 0.00 3.72
7552 8613 1.423541 ACCACACATTTCTGCCCTACA 59.576 47.619 0.00 0.00 0.00 2.74
7673 8738 5.945466 TTATTTTTGACCAACTACCCGAC 57.055 39.130 0.00 0.00 0.00 4.79
7677 8742 7.494211 AGTGGTTTTATTTTTGACCAACTACC 58.506 34.615 0.00 0.00 43.25 3.18
7683 8748 9.974980 GAAAGATAGTGGTTTTATTTTTGACCA 57.025 29.630 0.00 0.00 39.72 4.02
7738 8803 9.092757 GCAAAAATAATTGTCATCCGCATGGAG 62.093 40.741 0.00 0.00 39.01 3.86
7779 8844 5.009610 TCAAAACAGCCAGAATTCAAGGTAC 59.990 40.000 15.72 3.58 0.00 3.34


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

AutoCloner maintained by Alex Coulton.