Multiple sequence alignment - TraesCS2A01G381800

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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 TraesCS2A01G381800 chr2A 100.000 5516 0 0 1 5516 625024148 625029663 0.000000e+00 10187.0
1 TraesCS2A01G381800 chr2A 88.820 161 16 1 1507 1665 79316165 79316005 4.360000e-46 196.0
2 TraesCS2A01G381800 chr2D 93.403 5154 215 56 2 5122 482660987 482666048 0.000000e+00 7518.0
3 TraesCS2A01G381800 chr2D 90.052 191 15 2 5329 5516 482666189 482666378 1.530000e-60 244.0
4 TraesCS2A01G381800 chr2D 90.683 161 13 1 1507 1665 79056327 79056167 4.330000e-51 213.0
5 TraesCS2A01G381800 chr2B 92.212 5367 283 50 139 5422 566623447 566628761 0.000000e+00 7470.0
6 TraesCS2A01G381800 chr2B 89.796 98 5 3 1 98 566623360 566623452 2.700000e-23 121.0
7 TraesCS2A01G381800 chr2B 90.000 90 5 2 5430 5516 566631149 566631237 4.520000e-21 113.0
8 TraesCS2A01G381800 chr6D 85.388 219 23 7 314 531 298911547 298911337 9.300000e-53 219.0
9 TraesCS2A01G381800 chr3D 91.558 154 12 1 1513 1665 288550458 288550611 1.560000e-50 211.0
10 TraesCS2A01G381800 chr7B 89.375 160 17 0 1506 1665 505937473 505937314 9.370000e-48 202.0
11 TraesCS2A01G381800 chr7B 93.056 72 4 1 1672 1742 638921267 638921338 2.720000e-18 104.0
12 TraesCS2A01G381800 chr3A 89.809 157 14 2 1510 1665 383690929 383691084 3.370000e-47 200.0
13 TraesCS2A01G381800 chr7D 88.889 162 14 2 1507 1665 265692826 265692986 4.360000e-46 196.0
14 TraesCS2A01G381800 chr7D 86.667 90 10 2 1671 1759 99461788 99461876 1.260000e-16 99.0
15 TraesCS2A01G381800 chr3B 88.485 165 13 2 1510 1669 158707496 158707659 1.570000e-45 195.0
16 TraesCS2A01G381800 chr3B 87.324 71 8 1 1687 1756 719446166 719446236 4.580000e-11 80.5
17 TraesCS2A01G381800 chr1B 90.667 75 5 2 1672 1745 156850359 156850432 1.260000e-16 99.0
18 TraesCS2A01G381800 chr4B 85.057 87 11 2 1666 1751 416642524 416642609 2.740000e-13 87.9
19 TraesCS2A01G381800 chr7A 84.444 90 9 4 1675 1761 667224802 667224715 3.540000e-12 84.2
20 TraesCS2A01G381800 chr4D 84.810 79 8 4 1666 1742 337520665 337520741 5.930000e-10 76.8


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 TraesCS2A01G381800 chr2A 625024148 625029663 5515 False 10187 10187 100.000000 1 5516 1 chr2A.!!$F1 5515
1 TraesCS2A01G381800 chr2D 482660987 482666378 5391 False 3881 7518 91.727500 2 5516 2 chr2D.!!$F1 5514
2 TraesCS2A01G381800 chr2B 566623360 566631237 7877 False 2568 7470 90.669333 1 5516 3 chr2B.!!$F1 5515

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
117 159 0.178068 ACCATTCTGCGCGAACCTAT 59.822 50.0 12.1 0.0 33.72 2.57 F
1361 1419 0.035820 GACCAGGATTACGCCCAACA 60.036 55.0 0.0 0.0 0.00 3.33 F
1617 1683 0.035534 AACGTGCCTGCATACATCCA 60.036 50.0 0.0 0.0 0.00 3.41 F
1618 1684 0.181114 ACGTGCCTGCATACATCCAT 59.819 50.0 0.0 0.0 0.00 3.41 F
2761 2834 1.033746 TACCTTCTACTGACGGCCCG 61.034 60.0 0.0 0.0 35.26 6.13 F
3887 3962 1.139439 TGCAGCTAATCATAGGCCCA 58.861 50.0 0.0 0.0 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1424 1490 0.244721 GCACTCCAATTTCAGGTGCC 59.755 55.000 0.00 0.00 44.87 5.01 R
2956 3029 0.105593 CCATGCCGCTACAGATGAGT 59.894 55.000 0.00 0.00 0.00 3.41 R
3430 3504 0.473755 TGGCAGCTCAGTTTTCAGGA 59.526 50.000 0.00 0.00 0.00 3.86 R
3547 3621 4.900635 AGCAAACAAGTCACTAAGGTTG 57.099 40.909 4.04 4.04 0.00 3.77 R
4380 4455 0.248949 GATAGGCGTCGTTCAGGACC 60.249 60.000 0.00 0.00 33.30 4.46 R
5303 5452 0.102120 TGGTTTCAGCAGCCAAAACG 59.898 50.000 11.97 0.00 34.47 3.60 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
53 58 8.525290 TTTTTCTTTCAGGAATCTTCTGAACT 57.475 30.769 6.08 0.00 46.84 3.01
54 59 9.627123 TTTTTCTTTCAGGAATCTTCTGAACTA 57.373 29.630 6.08 0.00 46.84 2.24
55 60 8.608844 TTTCTTTCAGGAATCTTCTGAACTAC 57.391 34.615 6.08 0.00 46.84 2.73
56 61 7.303182 TCTTTCAGGAATCTTCTGAACTACA 57.697 36.000 6.08 0.00 46.84 2.74
57 62 7.382110 TCTTTCAGGAATCTTCTGAACTACAG 58.618 38.462 6.08 0.00 46.84 2.74
94 136 7.381323 AGAATGACAAAATTTTCATCCAGGTC 58.619 34.615 0.00 4.61 30.96 3.85
98 140 4.653341 ACAAAATTTTCATCCAGGTCCACA 59.347 37.500 0.00 0.00 0.00 4.17
99 141 4.871933 AAATTTTCATCCAGGTCCACAC 57.128 40.909 0.00 0.00 0.00 3.82
100 142 2.286365 TTTTCATCCAGGTCCACACC 57.714 50.000 0.00 0.00 44.19 4.16
101 143 1.144691 TTTCATCCAGGTCCACACCA 58.855 50.000 0.00 0.00 46.68 4.17
102 144 1.371467 TTCATCCAGGTCCACACCAT 58.629 50.000 0.00 0.00 46.68 3.55
103 145 1.371467 TCATCCAGGTCCACACCATT 58.629 50.000 0.00 0.00 46.68 3.16
104 146 1.281867 TCATCCAGGTCCACACCATTC 59.718 52.381 0.00 0.00 46.68 2.67
105 147 1.283029 CATCCAGGTCCACACCATTCT 59.717 52.381 0.00 0.00 46.68 2.40
106 148 0.692476 TCCAGGTCCACACCATTCTG 59.308 55.000 0.00 0.00 46.68 3.02
107 149 0.962356 CCAGGTCCACACCATTCTGC 60.962 60.000 0.00 0.00 46.68 4.26
108 150 1.003355 AGGTCCACACCATTCTGCG 60.003 57.895 0.00 0.00 46.68 5.18
109 151 2.690778 GGTCCACACCATTCTGCGC 61.691 63.158 0.00 0.00 43.17 6.09
110 152 2.741985 TCCACACCATTCTGCGCG 60.742 61.111 0.00 0.00 0.00 6.86
111 153 2.741985 CCACACCATTCTGCGCGA 60.742 61.111 12.10 0.00 0.00 5.87
112 154 2.324330 CCACACCATTCTGCGCGAA 61.324 57.895 12.10 15.06 35.78 4.70
113 155 1.154413 CACACCATTCTGCGCGAAC 60.154 57.895 12.10 0.00 33.72 3.95
114 156 2.325082 ACACCATTCTGCGCGAACC 61.325 57.895 12.10 0.00 33.72 3.62
115 157 2.034879 CACCATTCTGCGCGAACCT 61.035 57.895 12.10 0.64 33.72 3.50
116 158 0.739462 CACCATTCTGCGCGAACCTA 60.739 55.000 12.10 0.00 33.72 3.08
117 159 0.178068 ACCATTCTGCGCGAACCTAT 59.822 50.000 12.10 0.00 33.72 2.57
118 160 0.861837 CCATTCTGCGCGAACCTATC 59.138 55.000 12.10 0.00 33.72 2.08
119 161 1.570813 CATTCTGCGCGAACCTATCA 58.429 50.000 12.10 0.00 33.72 2.15
120 162 2.138320 CATTCTGCGCGAACCTATCAT 58.862 47.619 12.10 0.00 33.72 2.45
121 163 3.317150 CATTCTGCGCGAACCTATCATA 58.683 45.455 12.10 0.00 33.72 2.15
122 164 3.446310 TTCTGCGCGAACCTATCATAA 57.554 42.857 12.10 0.00 0.00 1.90
123 165 2.739292 TCTGCGCGAACCTATCATAAC 58.261 47.619 12.10 0.00 0.00 1.89
124 166 1.792949 CTGCGCGAACCTATCATAACC 59.207 52.381 12.10 0.00 0.00 2.85
125 167 1.145803 GCGCGAACCTATCATAACCC 58.854 55.000 12.10 0.00 0.00 4.11
126 168 1.539496 GCGCGAACCTATCATAACCCA 60.539 52.381 12.10 0.00 0.00 4.51
127 169 2.870435 GCGCGAACCTATCATAACCCAT 60.870 50.000 12.10 0.00 0.00 4.00
128 170 2.736721 CGCGAACCTATCATAACCCATG 59.263 50.000 0.00 0.00 35.81 3.66
141 183 7.490962 TCATAACCCATGATGAATTTCGTAC 57.509 36.000 0.00 0.00 38.79 3.67
142 184 7.051000 TCATAACCCATGATGAATTTCGTACA 58.949 34.615 0.00 0.00 38.79 2.90
143 185 5.560966 AACCCATGATGAATTTCGTACAC 57.439 39.130 0.00 0.00 0.00 2.90
144 186 4.584874 ACCCATGATGAATTTCGTACACA 58.415 39.130 0.00 0.00 0.00 3.72
147 189 5.528690 CCCATGATGAATTTCGTACACAGAT 59.471 40.000 0.00 0.00 0.00 2.90
264 309 2.611518 CGCTAAAGCTGCTACTTCACT 58.388 47.619 0.90 0.00 39.32 3.41
330 376 0.739112 CAGCAAACCTCGAGGAGCTC 60.739 60.000 37.69 21.49 38.50 4.09
376 422 1.805945 GACGAGCACGACCATGTCC 60.806 63.158 11.40 0.00 42.66 4.02
648 694 2.251409 ATGGTGATCTTCTCATGGCG 57.749 50.000 0.00 0.00 35.97 5.69
649 695 1.194218 TGGTGATCTTCTCATGGCGA 58.806 50.000 0.00 0.00 35.97 5.54
650 696 1.764723 TGGTGATCTTCTCATGGCGAT 59.235 47.619 0.00 0.00 35.97 4.58
651 697 2.141517 GGTGATCTTCTCATGGCGATG 58.858 52.381 1.66 1.66 35.97 3.84
652 698 2.141517 GTGATCTTCTCATGGCGATGG 58.858 52.381 8.98 0.15 35.97 3.51
653 699 1.764723 TGATCTTCTCATGGCGATGGT 59.235 47.619 8.98 0.00 0.00 3.55
741 791 3.781307 TCGAGGGAATGGGCCGTG 61.781 66.667 0.00 0.00 0.00 4.94
846 896 3.015293 CTCACACGGCGACACATGC 62.015 63.158 16.62 0.00 0.00 4.06
978 1036 1.187087 AAGGAAGAAGACGAGGCGAT 58.813 50.000 0.00 0.00 0.00 4.58
994 1052 3.411418 GATTCCTCTCCGCGTCGCA 62.411 63.158 18.75 0.00 0.00 5.10
1058 1116 1.577242 TCCTTTATCCCTACTCCCCGT 59.423 52.381 0.00 0.00 0.00 5.28
1265 1323 2.474816 GCCGTATCTGTAAGCCTTCTG 58.525 52.381 0.00 0.00 0.00 3.02
1266 1324 2.159085 GCCGTATCTGTAAGCCTTCTGT 60.159 50.000 0.00 0.00 0.00 3.41
1287 1345 7.163441 TCTGTATTTTCCCTTGTGGTTACTAC 58.837 38.462 0.00 0.00 34.77 2.73
1288 1346 7.016858 TCTGTATTTTCCCTTGTGGTTACTACT 59.983 37.037 0.00 0.00 34.77 2.57
1289 1347 6.938030 TGTATTTTCCCTTGTGGTTACTACTG 59.062 38.462 0.00 0.00 34.77 2.74
1290 1348 5.376756 TTTTCCCTTGTGGTTACTACTGT 57.623 39.130 0.00 0.00 34.77 3.55
1291 1349 6.497624 TTTTCCCTTGTGGTTACTACTGTA 57.502 37.500 0.00 0.00 34.77 2.74
1297 1355 6.769341 CCCTTGTGGTTACTACTGTAGTTTTT 59.231 38.462 24.09 3.54 40.14 1.94
1360 1418 1.087771 CGACCAGGATTACGCCCAAC 61.088 60.000 0.00 0.00 0.00 3.77
1361 1419 0.035820 GACCAGGATTACGCCCAACA 60.036 55.000 0.00 0.00 0.00 3.33
1363 1421 1.366111 CCAGGATTACGCCCAACACG 61.366 60.000 0.00 0.00 0.00 4.49
1364 1422 0.390603 CAGGATTACGCCCAACACGA 60.391 55.000 0.00 0.00 0.00 4.35
1365 1423 0.108329 AGGATTACGCCCAACACGAG 60.108 55.000 0.00 0.00 0.00 4.18
1424 1490 5.839517 ATCAGATTAGATTTCCCCCTCTG 57.160 43.478 0.00 0.00 0.00 3.35
1579 1645 3.270877 GGACTGCATACGGACTGAAATT 58.729 45.455 0.00 0.00 0.00 1.82
1608 1674 0.661020 ACACACTAAAACGTGCCTGC 59.339 50.000 0.00 0.00 38.45 4.85
1617 1683 0.035534 AACGTGCCTGCATACATCCA 60.036 50.000 0.00 0.00 0.00 3.41
1618 1684 0.181114 ACGTGCCTGCATACATCCAT 59.819 50.000 0.00 0.00 0.00 3.41
1628 1694 6.684613 GCCTGCATACATCCATTTCAGAAAAT 60.685 38.462 0.00 0.00 35.43 1.82
1699 1765 5.127682 ACCTCCGTACCAAAATATAAGACGT 59.872 40.000 0.00 0.00 0.00 4.34
1806 1873 6.159293 GCGATAGAGACCAACATATCAATCA 58.841 40.000 0.00 0.00 39.76 2.57
2043 2111 6.267471 TCATCTTTGCCCTGAGTGTTATTTTT 59.733 34.615 0.00 0.00 0.00 1.94
2140 2210 7.806409 TGTTCCAATGATACAATGGACTATG 57.194 36.000 7.88 0.00 42.33 2.23
2147 2217 8.562892 CAATGATACAATGGACTATGAACCTTC 58.437 37.037 0.00 0.00 0.00 3.46
2371 2441 6.992715 CCTGTAGGTAAAACTTATCCAGGATG 59.007 42.308 12.80 0.00 39.39 3.51
2670 2743 4.869861 TCGTCATTGGATAATGTGTGTCAG 59.130 41.667 0.00 0.00 43.33 3.51
2683 2756 5.185668 TGTGTGTCAGTTCCATGAATTTG 57.814 39.130 0.00 0.00 0.00 2.32
2761 2834 1.033746 TACCTTCTACTGACGGCCCG 61.034 60.000 0.00 0.00 35.26 6.13
2876 2949 5.423886 ACAGAGATGCTAAAGTTTCTAGCC 58.576 41.667 7.70 0.00 40.95 3.93
2911 2984 5.464168 CGAAACATCTTGGCTGATTTTCTT 58.536 37.500 16.01 0.00 30.55 2.52
3123 3197 3.186001 GCTACATCATCGATGCCTCTTTG 59.814 47.826 20.81 12.16 43.15 2.77
3191 3265 1.877637 TCATTTCACCACTGTGTCCG 58.122 50.000 7.08 0.00 43.26 4.79
3230 3304 1.431496 CAGGCTTGGGAAATTTTGCG 58.569 50.000 0.00 0.00 0.00 4.85
3325 3399 4.797693 TTGCGTGTTTAATTTGTCGAGA 57.202 36.364 0.00 0.00 0.00 4.04
3374 3448 2.079158 CTGCGCCTGATGGTTATATGG 58.921 52.381 4.18 0.00 35.27 2.74
3384 3458 6.652481 CCTGATGGTTATATGGAATGACTGTC 59.348 42.308 0.00 0.00 0.00 3.51
3401 3475 5.585844 TGACTGTCGATTATAGGACGTTGTA 59.414 40.000 2.98 0.00 35.95 2.41
3722 3796 9.581289 TCTGTTTCATTTTATCAGGGAAGTAAA 57.419 29.630 0.00 0.00 0.00 2.01
3723 3797 9.626045 CTGTTTCATTTTATCAGGGAAGTAAAC 57.374 33.333 0.00 0.00 0.00 2.01
3724 3798 8.293867 TGTTTCATTTTATCAGGGAAGTAAACG 58.706 33.333 0.00 0.00 0.00 3.60
3726 3800 8.624367 TTCATTTTATCAGGGAAGTAAACGAA 57.376 30.769 0.00 0.00 0.00 3.85
3727 3801 8.263940 TCATTTTATCAGGGAAGTAAACGAAG 57.736 34.615 0.00 0.00 0.00 3.79
3762 3836 8.581057 AGTGCATTACGTGAATTAGATTAGAG 57.419 34.615 0.00 0.00 0.00 2.43
3766 3840 7.438459 GCATTACGTGAATTAGATTAGAGTGGT 59.562 37.037 0.00 0.00 0.00 4.16
3773 3847 9.817809 GTGAATTAGATTAGAGTGGTCATTACA 57.182 33.333 0.00 0.00 0.00 2.41
3785 3859 6.950842 AGTGGTCATTACATTGAGAATGAGA 58.049 36.000 14.73 6.41 41.51 3.27
3887 3962 1.139439 TGCAGCTAATCATAGGCCCA 58.861 50.000 0.00 0.00 0.00 5.36
4060 4135 9.997482 TTTTCCGAATTACTGCAATACTAATTC 57.003 29.630 11.97 11.97 35.13 2.17
4065 4140 7.792508 CGAATTACTGCAATACTAATTCCGTTC 59.207 37.037 14.32 0.00 35.06 3.95
4148 4223 5.025453 TCTGTTCCCTAACCGGTTAATAGT 58.975 41.667 26.41 3.79 34.49 2.12
4155 4230 5.218139 CCTAACCGGTTAATAGTAGAAGCG 58.782 45.833 26.41 10.96 44.04 4.68
4226 4301 2.685897 GTGTCGAAGAGCTGAGGTCTAT 59.314 50.000 15.24 5.40 39.62 1.98
4242 4317 5.627135 AGGTCTATTTTCCCAAACGAGAAA 58.373 37.500 0.00 0.00 0.00 2.52
4246 4321 7.541091 GGTCTATTTTCCCAAACGAGAAATTTC 59.459 37.037 10.33 10.33 32.33 2.17
4248 4323 8.296713 TCTATTTTCCCAAACGAGAAATTTCTG 58.703 33.333 25.12 17.93 37.73 3.02
4389 4464 3.932289 CGTGACACGGTCCTGAAC 58.068 61.111 20.26 0.00 38.08 3.18
4423 4498 2.907897 GATGGAGAGCGTGTTCCCCG 62.908 65.000 0.00 0.00 32.29 5.73
4537 4616 3.381388 TGCTGGAGGAAGAGCACTA 57.619 52.632 0.00 0.00 40.30 2.74
4574 4655 4.488136 TGCATCCCGCCTGCGATT 62.488 61.111 13.94 0.00 42.62 3.34
4575 4656 3.211963 GCATCCCGCCTGCGATTT 61.212 61.111 13.94 0.00 42.83 2.17
4638 4726 7.764695 AAAAGGAATTGTTTGTAGAAAACCG 57.235 32.000 0.00 0.00 0.00 4.44
4662 4750 3.812156 TCTTTTGTCTTCCGTCACTCA 57.188 42.857 0.00 0.00 0.00 3.41
4674 4762 0.179108 GTCACTCATAGGGTCGCCAC 60.179 60.000 0.00 0.00 0.00 5.01
4739 4827 4.067896 GAGTGGATGCTTTGTCTTCAGAA 58.932 43.478 0.00 0.00 0.00 3.02
4765 4853 5.359756 TCCTGAATCATACACGAAATGGAG 58.640 41.667 0.00 0.00 0.00 3.86
4767 4855 5.464722 CCTGAATCATACACGAAATGGAGAG 59.535 44.000 0.00 0.00 0.00 3.20
4816 4904 2.223433 GGCTGCATCTGTTTGACTATGC 60.223 50.000 0.50 0.00 43.92 3.14
4817 4905 2.681848 GCTGCATCTGTTTGACTATGCT 59.318 45.455 15.05 0.00 43.98 3.79
4848 4937 2.508867 GTTTGACTCGTGCGTATCGTA 58.491 47.619 0.00 0.00 0.00 3.43
4849 4938 2.898181 TTGACTCGTGCGTATCGTAA 57.102 45.000 0.00 0.00 0.00 3.18
4851 4940 1.733912 TGACTCGTGCGTATCGTAAGT 59.266 47.619 0.00 0.00 39.48 2.24
4853 4942 1.733912 ACTCGTGCGTATCGTAAGTGA 59.266 47.619 0.00 0.00 39.48 3.41
4854 4943 2.353889 ACTCGTGCGTATCGTAAGTGAT 59.646 45.455 0.00 0.00 39.48 3.06
4855 4944 2.711885 TCGTGCGTATCGTAAGTGATG 58.288 47.619 0.00 0.00 39.48 3.07
4856 4945 1.779157 CGTGCGTATCGTAAGTGATGG 59.221 52.381 0.00 0.00 39.48 3.51
4858 4947 2.025898 TGCGTATCGTAAGTGATGGGA 58.974 47.619 0.00 0.00 39.48 4.37
4859 4948 2.626266 TGCGTATCGTAAGTGATGGGAT 59.374 45.455 0.00 0.00 39.48 3.85
4892 4981 1.936547 GGCATCTCGATTCCAAGTGAC 59.063 52.381 0.00 0.00 0.00 3.67
4950 5039 2.342651 GGATGACATAATCACGCGATCG 59.657 50.000 15.93 11.69 41.24 3.69
4988 5092 4.124851 CGAAGCCATGTACTAGGTTTCT 57.875 45.455 21.69 5.20 41.32 2.52
4992 5096 6.472686 AAGCCATGTACTAGGTTTCTCTAG 57.527 41.667 0.00 0.00 41.72 2.43
5051 5157 2.897969 ACTATCCTGCGATCGGGTTAAT 59.102 45.455 18.30 3.11 39.81 1.40
5082 5189 2.012948 GTGAACCACGTCGTCGACC 61.013 63.158 19.29 5.06 40.62 4.79
5084 5191 4.332637 AACCACGTCGTCGACCCG 62.333 66.667 19.29 17.68 40.62 5.28
5156 5305 3.902162 TTCAGCGTACGTGACCGGC 62.902 63.158 17.90 0.00 38.78 6.13
5222 5371 1.257155 GCGATCGAAATTACCGTGGAC 59.743 52.381 21.57 0.00 0.00 4.02
5225 5374 1.717194 TCGAAATTACCGTGGACTGC 58.283 50.000 0.00 0.00 0.00 4.40
5248 5397 6.583912 CATGCTCTGCTAAATCCAAATTTG 57.416 37.500 11.40 11.40 35.84 2.32
5276 5425 3.121030 CTGAGGTTCGGGCGCAAG 61.121 66.667 10.83 1.50 43.44 4.01
5293 5442 3.774702 GAACGGACGAAGGCACGC 61.775 66.667 0.00 0.00 36.70 5.34
5329 5478 0.109597 GCTGCTGAAACCATCAACGG 60.110 55.000 0.00 0.00 37.67 4.44
5333 5482 0.523072 CTGAAACCATCAACGGCTGG 59.477 55.000 0.00 0.00 37.67 4.85
5351 5510 3.169099 CTGGGAGAGGATATTGGACGAT 58.831 50.000 0.00 0.00 0.00 3.73
5405 5564 2.113860 TGCTAAGACCAATCACAGCC 57.886 50.000 0.00 0.00 34.56 4.85
5428 7967 5.181433 CCTTTTCTCTGGCCTAACAAGTTAC 59.819 44.000 3.32 0.00 0.00 2.50
5432 7971 5.081728 TCTCTGGCCTAACAAGTTACTACA 58.918 41.667 3.32 0.00 0.00 2.74
5452 7991 8.948401 ACTACATCCTACTTGATGATCACTAT 57.052 34.615 0.00 0.00 43.94 2.12
5453 7992 9.019656 ACTACATCCTACTTGATGATCACTATC 57.980 37.037 0.00 0.00 43.94 2.08
5455 7994 7.665690 ACATCCTACTTGATGATCACTATCAC 58.334 38.462 0.00 0.00 44.79 3.06
5456 7995 7.508636 ACATCCTACTTGATGATCACTATCACT 59.491 37.037 0.00 0.00 44.79 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 58 8.510243 TTGTCATTCTAGTCCGTATTACTGTA 57.490 34.615 0.00 0.00 0.00 2.74
54 59 7.400599 TTGTCATTCTAGTCCGTATTACTGT 57.599 36.000 0.00 0.00 0.00 3.55
55 60 8.697846 TTTTGTCATTCTAGTCCGTATTACTG 57.302 34.615 0.00 0.00 0.00 2.74
56 61 9.886132 AATTTTGTCATTCTAGTCCGTATTACT 57.114 29.630 0.00 0.00 0.00 2.24
94 136 2.324330 TTCGCGCAGAATGGTGTGG 61.324 57.895 8.75 0.00 35.86 4.17
98 140 0.178068 ATAGGTTCGCGCAGAATGGT 59.822 50.000 8.75 3.99 41.49 3.55
99 141 0.861837 GATAGGTTCGCGCAGAATGG 59.138 55.000 8.75 0.00 41.49 3.16
100 142 1.570813 TGATAGGTTCGCGCAGAATG 58.429 50.000 8.75 0.00 41.49 2.67
101 143 2.533266 ATGATAGGTTCGCGCAGAAT 57.467 45.000 8.75 0.96 41.49 2.40
102 144 3.120792 GTTATGATAGGTTCGCGCAGAA 58.879 45.455 8.75 9.50 36.31 3.02
103 145 2.545113 GGTTATGATAGGTTCGCGCAGA 60.545 50.000 8.75 2.49 0.00 4.26
104 146 1.792949 GGTTATGATAGGTTCGCGCAG 59.207 52.381 8.75 0.00 0.00 5.18
105 147 1.539496 GGGTTATGATAGGTTCGCGCA 60.539 52.381 8.75 0.00 0.00 6.09
106 148 1.145803 GGGTTATGATAGGTTCGCGC 58.854 55.000 0.00 0.00 0.00 6.86
107 149 2.519377 TGGGTTATGATAGGTTCGCG 57.481 50.000 0.00 0.00 0.00 5.87
108 150 4.002906 TCATGGGTTATGATAGGTTCGC 57.997 45.455 0.00 0.00 40.82 4.70
118 160 7.132213 GTGTACGAAATTCATCATGGGTTATG 58.868 38.462 0.00 0.00 38.17 1.90
119 161 6.826231 TGTGTACGAAATTCATCATGGGTTAT 59.174 34.615 0.00 0.00 0.00 1.89
120 162 6.174049 TGTGTACGAAATTCATCATGGGTTA 58.826 36.000 0.00 0.00 0.00 2.85
121 163 5.007034 TGTGTACGAAATTCATCATGGGTT 58.993 37.500 0.00 0.00 0.00 4.11
122 164 4.584874 TGTGTACGAAATTCATCATGGGT 58.415 39.130 0.00 0.00 0.00 4.51
123 165 4.875536 TCTGTGTACGAAATTCATCATGGG 59.124 41.667 0.00 0.00 0.00 4.00
124 166 6.609237 ATCTGTGTACGAAATTCATCATGG 57.391 37.500 0.00 0.00 0.00 3.66
125 167 8.981647 TGATATCTGTGTACGAAATTCATCATG 58.018 33.333 3.98 0.00 0.00 3.07
126 168 8.982685 GTGATATCTGTGTACGAAATTCATCAT 58.017 33.333 3.98 0.00 0.00 2.45
127 169 7.978975 TGTGATATCTGTGTACGAAATTCATCA 59.021 33.333 3.98 0.00 0.00 3.07
128 170 8.352752 TGTGATATCTGTGTACGAAATTCATC 57.647 34.615 3.98 0.00 0.00 2.92
129 171 7.981789 ACTGTGATATCTGTGTACGAAATTCAT 59.018 33.333 3.98 0.00 0.00 2.57
130 172 7.275560 CACTGTGATATCTGTGTACGAAATTCA 59.724 37.037 0.32 0.00 34.27 2.57
131 173 7.488150 TCACTGTGATATCTGTGTACGAAATTC 59.512 37.037 6.36 0.00 38.07 2.17
132 174 7.320399 TCACTGTGATATCTGTGTACGAAATT 58.680 34.615 6.36 0.00 38.07 1.82
133 175 6.863275 TCACTGTGATATCTGTGTACGAAAT 58.137 36.000 6.36 0.00 38.07 2.17
134 176 6.262193 TCACTGTGATATCTGTGTACGAAA 57.738 37.500 6.36 2.56 38.07 3.46
135 177 5.676331 GCTCACTGTGATATCTGTGTACGAA 60.676 44.000 11.45 4.41 38.07 3.85
136 178 4.201920 GCTCACTGTGATATCTGTGTACGA 60.202 45.833 11.45 4.65 38.07 3.43
137 179 4.038361 GCTCACTGTGATATCTGTGTACG 58.962 47.826 11.45 0.00 38.07 3.67
138 180 4.800993 GTGCTCACTGTGATATCTGTGTAC 59.199 45.833 11.45 3.91 38.07 2.90
139 181 4.142160 GGTGCTCACTGTGATATCTGTGTA 60.142 45.833 11.45 0.00 38.07 2.90
140 182 3.368843 GGTGCTCACTGTGATATCTGTGT 60.369 47.826 11.45 6.61 38.07 3.72
141 183 3.193263 GGTGCTCACTGTGATATCTGTG 58.807 50.000 11.45 10.24 38.18 3.66
142 184 2.169352 GGGTGCTCACTGTGATATCTGT 59.831 50.000 11.45 0.00 0.00 3.41
143 185 2.484417 GGGGTGCTCACTGTGATATCTG 60.484 54.545 11.45 0.14 0.00 2.90
144 186 1.765314 GGGGTGCTCACTGTGATATCT 59.235 52.381 11.45 0.00 0.00 1.98
147 189 2.543037 TAGGGGTGCTCACTGTGATA 57.457 50.000 11.45 0.82 0.00 2.15
264 309 3.056107 AGCGGTAGATTAAGTGTGCTTCA 60.056 43.478 0.00 0.00 36.22 3.02
648 694 2.868583 CGAACACATCTCCATCACCATC 59.131 50.000 0.00 0.00 0.00 3.51
649 695 2.420547 CCGAACACATCTCCATCACCAT 60.421 50.000 0.00 0.00 0.00 3.55
650 696 1.066215 CCGAACACATCTCCATCACCA 60.066 52.381 0.00 0.00 0.00 4.17
651 697 1.066143 ACCGAACACATCTCCATCACC 60.066 52.381 0.00 0.00 0.00 4.02
652 698 2.271800 GACCGAACACATCTCCATCAC 58.728 52.381 0.00 0.00 0.00 3.06
653 699 1.899142 TGACCGAACACATCTCCATCA 59.101 47.619 0.00 0.00 0.00 3.07
715 761 1.676635 ATTCCCTCGACGACCGTCA 60.677 57.895 20.43 8.44 44.77 4.35
846 896 3.516615 GATTCCAACTCCTCTTCTGTCG 58.483 50.000 0.00 0.00 0.00 4.35
978 1036 4.415332 GTGCGACGCGGAGAGGAA 62.415 66.667 16.14 0.00 0.00 3.36
994 1052 0.326238 ACGAGTATGTCCATGGGGGT 60.326 55.000 13.02 0.14 38.11 4.95
1032 1090 3.067833 GAGTAGGGATAAAGGATTGCGC 58.932 50.000 0.00 0.00 0.00 6.09
1244 1302 1.413077 AGAAGGCTTACAGATACGGCC 59.587 52.381 0.00 0.00 42.74 6.13
1246 1304 3.802948 ACAGAAGGCTTACAGATACGG 57.197 47.619 0.00 0.00 0.00 4.02
1265 1323 6.938596 ACAGTAGTAACCACAAGGGAAAATAC 59.061 38.462 0.00 0.00 41.15 1.89
1266 1324 7.081857 ACAGTAGTAACCACAAGGGAAAATA 57.918 36.000 0.00 0.00 41.15 1.40
1297 1355 4.142622 CGATGCAAGCCTGAAAGTTCATAA 60.143 41.667 0.00 0.00 36.46 1.90
1327 1385 2.040544 GGTCGGCACACCAAGGATG 61.041 63.158 0.00 0.00 36.32 3.51
1334 1392 0.743345 GTAATCCTGGTCGGCACACC 60.743 60.000 0.00 0.00 36.90 4.16
1360 1418 4.639135 TTCACTGTCATCCTATCTCGTG 57.361 45.455 0.00 0.00 0.00 4.35
1361 1419 5.661056 TTTTCACTGTCATCCTATCTCGT 57.339 39.130 0.00 0.00 0.00 4.18
1363 1421 7.856145 ACATTTTTCACTGTCATCCTATCTC 57.144 36.000 0.00 0.00 0.00 2.75
1364 1422 7.667219 ACAACATTTTTCACTGTCATCCTATCT 59.333 33.333 0.00 0.00 0.00 1.98
1365 1423 7.820648 ACAACATTTTTCACTGTCATCCTATC 58.179 34.615 0.00 0.00 0.00 2.08
1399 1465 5.311913 AGAGGGGGAAATCTAATCTGATTCC 59.688 44.000 6.10 1.57 35.82 3.01
1424 1490 0.244721 GCACTCCAATTTCAGGTGCC 59.755 55.000 0.00 0.00 44.87 5.01
1579 1645 6.074195 GCACGTTTTAGTGTGTATGTTCACTA 60.074 38.462 0.00 0.00 43.39 2.74
2043 2111 7.870954 CCAAACTATGTACTACACTTTCTGTCA 59.129 37.037 0.00 0.00 33.91 3.58
2061 2129 8.458573 TCAGTTAAACAATCACACCAAACTAT 57.541 30.769 0.00 0.00 0.00 2.12
2140 2210 6.976636 TTCAAACAACAATTTGGAAGGTTC 57.023 33.333 0.78 0.00 39.57 3.62
2371 2441 3.813443 ACTTATCATGTGCCATCCTGTC 58.187 45.455 0.00 0.00 0.00 3.51
2670 2743 1.474077 AGCGGCTCAAATTCATGGAAC 59.526 47.619 0.00 0.00 0.00 3.62
2683 2756 7.716768 AATTTAAGTATCTAGAAAGCGGCTC 57.283 36.000 1.45 0.00 0.00 4.70
2956 3029 0.105593 CCATGCCGCTACAGATGAGT 59.894 55.000 0.00 0.00 0.00 3.41
3043 3117 8.199449 ACAAGCATAAATATCAGAAAATGGGTG 58.801 33.333 0.00 0.00 0.00 4.61
3123 3197 0.675633 ACATCAGCTGGCACCAAAAC 59.324 50.000 15.13 0.00 0.00 2.43
3191 3265 3.520569 TGCCACTTCAAGAAAAAGTTGC 58.479 40.909 0.00 5.42 42.59 4.17
3230 3304 3.896122 TGCAAGTTAAATTCGCACCTTC 58.104 40.909 8.12 0.00 0.00 3.46
3325 3399 6.929606 ACAGTCGTTTTATCTTTGAGTAAGCT 59.070 34.615 0.00 0.00 33.66 3.74
3374 3448 5.759963 ACGTCCTATAATCGACAGTCATTC 58.240 41.667 0.41 0.00 0.00 2.67
3384 3458 9.417284 GTTCATTTTTACAACGTCCTATAATCG 57.583 33.333 0.00 0.00 0.00 3.34
3430 3504 0.473755 TGGCAGCTCAGTTTTCAGGA 59.526 50.000 0.00 0.00 0.00 3.86
3547 3621 4.900635 AGCAAACAAGTCACTAAGGTTG 57.099 40.909 4.04 4.04 0.00 3.77
3644 3718 5.130292 TGTACCTTTCCTTGAGTCGTTAG 57.870 43.478 0.00 0.00 0.00 2.34
3645 3719 5.733620 ATGTACCTTTCCTTGAGTCGTTA 57.266 39.130 0.00 0.00 0.00 3.18
3738 3812 8.269424 CACTCTAATCTAATTCACGTAATGCAC 58.731 37.037 0.00 0.00 0.00 4.57
3739 3813 7.438160 CCACTCTAATCTAATTCACGTAATGCA 59.562 37.037 0.00 0.00 0.00 3.96
3740 3814 7.438459 ACCACTCTAATCTAATTCACGTAATGC 59.562 37.037 0.00 0.00 0.00 3.56
3741 3815 8.873215 ACCACTCTAATCTAATTCACGTAATG 57.127 34.615 0.00 0.00 0.00 1.90
3747 3821 9.817809 TGTAATGACCACTCTAATCTAATTCAC 57.182 33.333 0.00 0.00 0.00 3.18
3762 3836 7.467623 GTTCTCATTCTCAATGTAATGACCAC 58.532 38.462 8.80 6.17 37.23 4.16
3766 3840 6.535150 GGTCGTTCTCATTCTCAATGTAATGA 59.465 38.462 11.23 11.23 39.24 2.57
3773 3847 5.089970 TGATGGTCGTTCTCATTCTCAAT 57.910 39.130 0.00 0.00 0.00 2.57
3785 3859 1.191535 TCCGGATTCTGATGGTCGTT 58.808 50.000 0.00 0.00 0.00 3.85
3829 3903 8.685838 AGTAATTAGAAGCTTGTACCAAACAA 57.314 30.769 2.10 0.00 45.90 2.83
3869 3944 2.490903 CAATGGGCCTATGATTAGCTGC 59.509 50.000 0.67 0.00 0.00 5.25
4060 4135 1.737363 GCTCTGCAGAGTAAGGAACGG 60.737 57.143 37.25 15.38 43.85 4.44
4065 4140 0.532573 TTCCGCTCTGCAGAGTAAGG 59.467 55.000 37.25 33.91 43.85 2.69
4148 4223 0.319083 TTTCACGCTTCCCGCTTCTA 59.681 50.000 0.00 0.00 41.76 2.10
4155 4230 2.033194 CCCGACTTTCACGCTTCCC 61.033 63.158 0.00 0.00 0.00 3.97
4226 4301 5.047188 GCAGAAATTTCTCGTTTGGGAAAA 58.953 37.500 17.91 0.00 34.74 2.29
4380 4455 0.248949 GATAGGCGTCGTTCAGGACC 60.249 60.000 0.00 0.00 33.30 4.46
4386 4461 2.846039 TCTTCTGATAGGCGTCGTTC 57.154 50.000 0.00 0.00 0.00 3.95
4389 4464 1.609072 TCCATCTTCTGATAGGCGTCG 59.391 52.381 0.00 0.00 0.00 5.12
4423 4498 2.861935 TCTTGACTTCCGAAACGAACAC 59.138 45.455 0.00 0.00 0.00 3.32
4575 4656 5.895636 TTGAACTCTGCAACTCTGAAAAA 57.104 34.783 0.00 0.00 0.00 1.94
4617 4705 6.459670 AACGGTTTTCTACAAACAATTCCT 57.540 33.333 0.25 0.00 32.04 3.36
4618 4706 7.528481 AAAACGGTTTTCTACAAACAATTCC 57.472 32.000 12.86 0.00 32.04 3.01
4637 4725 4.026407 GTGACGGAAGACAAAAGAAAACG 58.974 43.478 0.00 0.00 37.55 3.60
4638 4726 5.163794 TGAGTGACGGAAGACAAAAGAAAAC 60.164 40.000 0.00 0.00 37.55 2.43
4653 4741 1.065928 GCGACCCTATGAGTGACGG 59.934 63.158 0.00 0.00 0.00 4.79
4662 4750 2.982339 AGATAGAGTGGCGACCCTAT 57.018 50.000 2.51 2.51 0.00 2.57
4674 4762 6.127479 ACTGCACTGAAGGTAGAAAGATAGAG 60.127 42.308 0.00 0.00 0.00 2.43
4739 4827 5.586243 CCATTTCGTGTATGATTCAGGAAGT 59.414 40.000 7.14 2.92 39.58 3.01
4774 4862 3.307691 CCTCCTTTCAAGTACCAGCATCA 60.308 47.826 0.00 0.00 0.00 3.07
4816 4904 2.271800 GAGTCAAACCATACGGCAGAG 58.728 52.381 0.00 0.00 34.57 3.35
4817 4905 1.403647 CGAGTCAAACCATACGGCAGA 60.404 52.381 0.00 0.00 34.57 4.26
4848 4937 2.091665 GGTTCCATCCATCCCATCACTT 60.092 50.000 0.00 0.00 0.00 3.16
4849 4938 1.496429 GGTTCCATCCATCCCATCACT 59.504 52.381 0.00 0.00 0.00 3.41
4851 4940 0.473755 CGGTTCCATCCATCCCATCA 59.526 55.000 0.00 0.00 0.00 3.07
4853 4942 1.151450 GCGGTTCCATCCATCCCAT 59.849 57.895 0.00 0.00 0.00 4.00
4854 4943 2.595095 GCGGTTCCATCCATCCCA 59.405 61.111 0.00 0.00 0.00 4.37
4855 4944 2.591715 CGCGGTTCCATCCATCCC 60.592 66.667 0.00 0.00 0.00 3.85
4856 4945 2.591715 CCGCGGTTCCATCCATCC 60.592 66.667 19.50 0.00 0.00 3.51
4858 4947 3.420206 ATGCCGCGGTTCCATCCAT 62.420 57.895 28.70 16.47 0.00 3.41
4859 4948 4.108299 ATGCCGCGGTTCCATCCA 62.108 61.111 28.70 14.71 0.00 3.41
4988 5092 3.981375 TCACCCTACTCTGATAGGCTAGA 59.019 47.826 0.00 0.00 40.56 2.43
4992 5096 2.667470 TGTCACCCTACTCTGATAGGC 58.333 52.381 7.32 0.00 40.56 3.93
5051 5157 3.127895 CGTGGTTCACTCAAACTTGGAAA 59.872 43.478 0.00 0.00 31.34 3.13
5082 5189 3.175240 CGCTCTGCAAGACGACGG 61.175 66.667 0.00 0.00 38.67 4.79
5084 5191 3.832171 CGCGCTCTGCAAGACGAC 61.832 66.667 5.56 0.00 46.97 4.34
5130 5273 1.058748 CGTACGCTGAATTGCACCG 59.941 57.895 0.52 0.00 0.00 4.94
5136 5285 0.734942 CCGGTCACGTACGCTGAATT 60.735 55.000 16.72 0.00 38.78 2.17
5192 5341 1.632422 TTTCGATCGCCTTTCGGTAC 58.368 50.000 11.09 0.00 39.05 3.34
5222 5371 9.046091 CAAATTTGGATTTAGCAGAGCATGCAG 62.046 40.741 21.98 10.46 44.35 4.41
5225 5374 5.006358 GCAAATTTGGATTTAGCAGAGCATG 59.994 40.000 19.47 0.00 33.78 4.06
5264 5413 4.084888 CCGTTCTTGCGCCCGAAC 62.085 66.667 21.91 21.91 36.92 3.95
5276 5425 3.774702 GCGTGCCTTCGTCCGTTC 61.775 66.667 0.00 0.00 0.00 3.95
5302 5451 1.215014 GGTTTCAGCAGCCAAAACGC 61.215 55.000 11.97 4.51 34.47 4.84
5303 5452 0.102120 TGGTTTCAGCAGCCAAAACG 59.898 50.000 11.97 0.00 34.47 3.60
5307 5456 1.340889 GTTGATGGTTTCAGCAGCCAA 59.659 47.619 0.00 0.00 40.62 4.52
5310 5459 0.109597 CCGTTGATGGTTTCAGCAGC 60.110 55.000 0.00 0.00 40.62 5.25
5311 5460 0.109597 GCCGTTGATGGTTTCAGCAG 60.110 55.000 0.00 0.00 40.62 4.24
5312 5461 0.537143 AGCCGTTGATGGTTTCAGCA 60.537 50.000 0.00 0.00 37.53 4.41
5329 5478 1.001406 CGTCCAATATCCTCTCCCAGC 59.999 57.143 0.00 0.00 0.00 4.85
5333 5482 4.873746 TTCATCGTCCAATATCCTCTCC 57.126 45.455 0.00 0.00 0.00 3.71
5384 5543 2.357009 GGCTGTGATTGGTCTTAGCATG 59.643 50.000 0.00 0.00 36.43 4.06
5405 5564 5.998363 AGTAACTTGTTAGGCCAGAGAAAAG 59.002 40.000 5.01 3.38 0.00 2.27
5428 7967 9.018582 TGATAGTGATCATCAAGTAGGATGTAG 57.981 37.037 0.00 0.00 44.00 2.74
5432 7971 8.489676 AAGTGATAGTGATCATCAAGTAGGAT 57.510 34.615 0.00 0.00 43.95 3.24
5452 7991 6.566079 ATCCACCATCAATTCTCTAAGTGA 57.434 37.500 0.00 0.00 43.23 3.41
5453 7992 6.825213 TCAATCCACCATCAATTCTCTAAGTG 59.175 38.462 0.00 0.00 31.98 3.16
5455 7994 6.261826 GGTCAATCCACCATCAATTCTCTAAG 59.738 42.308 0.00 0.00 36.32 2.18
5456 7995 6.122277 GGTCAATCCACCATCAATTCTCTAA 58.878 40.000 0.00 0.00 36.32 2.10


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

AutoCloner maintained by Alex Coulton.