Multiple sequence alignment - TraesCS6D01G149500

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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 TraesCS6D01G149500 chr6D 100.000 5933 0 0 1 5933 123148574 123154506 0.000000e+00 10957.0
1 TraesCS6D01G149500 chr6D 89.313 131 12 2 1 130 50087174 50087045 4.760000e-36 163.0
2 TraesCS6D01G149500 chr6D 86.076 79 6 5 2467 2540 103006195 103006117 4.930000e-11 80.5
3 TraesCS6D01G149500 chr6D 95.556 45 2 0 3744 3788 56914578 56914622 8.250000e-09 73.1
4 TraesCS6D01G149500 chr6D 89.796 49 3 2 5821 5868 97016181 97016228 1.790000e-05 62.1
5 TraesCS6D01G149500 chr6B 95.888 4402 112 32 1243 5593 217156546 217160929 0.000000e+00 7062.0
6 TraesCS6D01G149500 chr6B 94.122 1259 65 8 1 1253 217154464 217155719 0.000000e+00 1906.0
7 TraesCS6D01G149500 chr6B 82.537 544 64 19 3208 3728 704707897 704707362 3.260000e-122 449.0
8 TraesCS6D01G149500 chr6B 82.869 502 55 21 3867 4346 704707284 704706792 7.110000e-114 422.0
9 TraesCS6D01G149500 chr6B 80.430 419 53 11 3332 3727 157869374 157868962 5.820000e-75 292.0
10 TraesCS6D01G149500 chr6B 87.143 70 7 2 2467 2535 217157851 217157783 1.770000e-10 78.7
11 TraesCS6D01G149500 chr6A 93.973 2323 84 17 1441 3742 158050184 158047897 0.000000e+00 3463.0
12 TraesCS6D01G149500 chr6A 93.810 1454 78 10 1 1449 158051805 158050359 0.000000e+00 2176.0
13 TraesCS6D01G149500 chr6A 94.138 1433 56 13 3738 5152 158047843 158046421 0.000000e+00 2156.0
14 TraesCS6D01G149500 chr6A 93.051 662 24 10 5184 5835 158046425 158045776 0.000000e+00 948.0
15 TraesCS6D01G149500 chr6A 90.000 50 4 1 5833 5881 198073759 198073710 4.960000e-06 63.9
16 TraesCS6D01G149500 chrUn 100.000 386 0 0 2490 2875 480537746 480537361 0.000000e+00 713.0
17 TraesCS6D01G149500 chrUn 81.384 419 50 10 3332 3727 94306612 94306199 3.450000e-82 316.0
18 TraesCS6D01G149500 chrUn 95.238 42 2 0 5833 5874 81901910 81901869 3.840000e-07 67.6
19 TraesCS6D01G149500 chr7D 83.755 554 59 17 3208 3738 403149079 403149624 4.130000e-136 496.0
20 TraesCS6D01G149500 chr7D 83.532 504 49 23 3861 4340 403149686 403150179 1.960000e-119 440.0
21 TraesCS6D01G149500 chr7D 89.313 131 12 2 1 130 569943347 569943218 4.760000e-36 163.0
22 TraesCS6D01G149500 chr7D 90.476 63 5 1 2469 2531 382117471 382117532 1.370000e-11 82.4
23 TraesCS6D01G149500 chr7D 89.655 58 2 4 3733 3786 571261938 571261995 2.970000e-08 71.3
24 TraesCS6D01G149500 chr5B 82.721 544 63 19 3208 3728 325720002 325720537 7.010000e-124 455.0
25 TraesCS6D01G149500 chr5B 97.436 39 1 0 5833 5871 50276813 50276851 3.840000e-07 67.6
26 TraesCS6D01G149500 chr5B 95.238 42 2 0 5833 5874 659712710 659712669 3.840000e-07 67.6
27 TraesCS6D01G149500 chr3A 82.576 528 64 15 3232 3738 125401467 125400947 1.960000e-119 440.0
28 TraesCS6D01G149500 chr1B 82.169 544 66 19 3208 3728 459065766 459065231 7.060000e-119 438.0
29 TraesCS6D01G149500 chr1B 82.143 504 54 25 3867 4346 459065153 459064662 3.330000e-107 399.0
30 TraesCS6D01G149500 chr1B 80.668 419 53 10 3332 3727 456157861 456157448 3.480000e-77 300.0
31 TraesCS6D01G149500 chr1B 97.436 39 1 0 5833 5871 108209378 108209416 3.840000e-07 67.6
32 TraesCS6D01G149500 chr2D 82.738 504 51 26 3861 4340 91116375 91116866 3.310000e-112 416.0
33 TraesCS6D01G149500 chr2D 81.854 507 58 25 3861 4340 43248368 43248867 4.310000e-106 396.0
34 TraesCS6D01G149500 chr2D 82.751 458 49 19 3303 3738 43247857 43248306 1.210000e-101 381.0
35 TraesCS6D01G149500 chr2D 91.200 125 10 1 1 124 444860937 444860813 1.020000e-37 169.0
36 TraesCS6D01G149500 chr4A 85.266 414 42 11 3208 3605 176614649 176615059 5.530000e-110 409.0
37 TraesCS6D01G149500 chr4A 82.143 504 55 25 3861 4340 176615238 176615730 3.330000e-107 399.0
38 TraesCS6D01G149500 chr4A 91.803 61 4 1 2472 2532 336064402 336064343 3.810000e-12 84.2
39 TraesCS6D01G149500 chr4A 86.885 61 5 3 5834 5892 32707482 32707541 1.380000e-06 65.8
40 TraesCS6D01G149500 chr7B 86.994 346 36 8 3861 4203 712091831 712092170 1.210000e-101 381.0
41 TraesCS6D01G149500 chr7B 80.328 427 56 19 3332 3739 712091353 712091770 1.250000e-76 298.0
42 TraesCS6D01G149500 chr7B 93.651 63 4 0 2469 2531 376350595 376350657 1.760000e-15 95.3
43 TraesCS6D01G149500 chr7B 95.455 44 2 0 3742 3785 638514052 638514009 2.970000e-08 71.3
44 TraesCS6D01G149500 chr3D 90.076 131 11 2 1 130 314049722 314049851 1.020000e-37 169.0
45 TraesCS6D01G149500 chr3D 93.478 46 3 0 3741 3786 423392166 423392211 1.070000e-07 69.4
46 TraesCS6D01G149500 chr2B 91.057 123 10 1 1 122 9991929 9991807 1.320000e-36 165.0
47 TraesCS6D01G149500 chr2B 90.000 50 5 0 5837 5886 67908182 67908133 1.380000e-06 65.8
48 TraesCS6D01G149500 chr1D 90.400 125 11 1 1 124 49072690 49072566 4.760000e-36 163.0
49 TraesCS6D01G149500 chr1D 89.313 131 12 2 1 130 350369784 350369913 4.760000e-36 163.0
50 TraesCS6D01G149500 chr1D 94.340 53 1 2 3737 3787 221445435 221445487 4.930000e-11 80.5
51 TraesCS6D01G149500 chr1A 95.161 62 3 0 2470 2531 399497076 399497137 1.360000e-16 99.0
52 TraesCS6D01G149500 chr4B 97.674 43 1 0 5832 5874 47495741 47495783 2.290000e-09 75.0
53 TraesCS6D01G149500 chr7A 97.619 42 1 0 3744 3785 84745779 84745820 8.250000e-09 73.1
54 TraesCS6D01G149500 chr7A 95.455 44 2 0 3742 3785 667157783 667157740 2.970000e-08 71.3


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 TraesCS6D01G149500 chr6D 123148574 123154506 5932 False 10957.00 10957 100.0000 1 5933 1 chr6D.!!$F3 5932
1 TraesCS6D01G149500 chr6B 217154464 217160929 6465 False 4484.00 7062 95.0050 1 5593 2 chr6B.!!$F1 5592
2 TraesCS6D01G149500 chr6B 704706792 704707897 1105 True 435.50 449 82.7030 3208 4346 2 chr6B.!!$R3 1138
3 TraesCS6D01G149500 chr6A 158045776 158051805 6029 True 2185.75 3463 93.7430 1 5835 4 chr6A.!!$R2 5834
4 TraesCS6D01G149500 chr7D 403149079 403150179 1100 False 468.00 496 83.6435 3208 4340 2 chr7D.!!$F3 1132
5 TraesCS6D01G149500 chr5B 325720002 325720537 535 False 455.00 455 82.7210 3208 3728 1 chr5B.!!$F2 520
6 TraesCS6D01G149500 chr3A 125400947 125401467 520 True 440.00 440 82.5760 3232 3738 1 chr3A.!!$R1 506
7 TraesCS6D01G149500 chr1B 459064662 459065766 1104 True 418.50 438 82.1560 3208 4346 2 chr1B.!!$R2 1138
8 TraesCS6D01G149500 chr2D 43247857 43248867 1010 False 388.50 396 82.3025 3303 4340 2 chr2D.!!$F2 1037
9 TraesCS6D01G149500 chr4A 176614649 176615730 1081 False 404.00 409 83.7045 3208 4340 2 chr4A.!!$F2 1132
10 TraesCS6D01G149500 chr7B 712091353 712092170 817 False 339.50 381 83.6610 3332 4203 2 chr7B.!!$F2 871

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
492 497 0.248866 CCACACTTTTTCCACGCCAC 60.249 55.000 0.00 0.0 0.00 5.01 F
1235 1243 0.725117 GTAGATGTTGTTTCCCGGCG 59.275 55.000 0.00 0.0 0.00 6.46 F
2875 3951 1.077930 AATCATGCGCACTCTGCCT 60.078 52.632 14.90 0.0 41.12 4.75 F
3101 4177 1.941668 GCTGTAGGTGGCTTGTCTGAC 60.942 57.143 0.00 0.0 0.00 3.51 F
3855 5018 3.069016 TCACGTTTGAGCTCCTGTTAGAA 59.931 43.478 12.15 0.0 0.00 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1474 2502 0.179129 CCAGAATTGCCGGCAATGTC 60.179 55.000 45.89 38.60 44.86 3.06 R
3101 4177 1.635487 TCCCTGAGTTCCCTGATTTGG 59.365 52.381 0.00 0.00 0.00 3.28 R
4690 5880 0.749091 CATTGCGAAGATCAGCCCCA 60.749 55.000 0.00 0.00 0.00 4.96 R
4741 5931 1.077930 TACGTAGTCCCGCTCTGCT 60.078 57.895 0.00 0.00 43.93 4.24 R
5280 6478 0.724549 GGTCGCATGTCGTATGCAAA 59.275 50.000 21.06 10.19 44.75 3.68 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
84 85 3.731652 TTGGTCAAATTTGGCACAGAG 57.268 42.857 23.34 0.00 42.39 3.35
104 105 8.576442 CACAGAGTACAAAAGGGACAAATAAAT 58.424 33.333 0.00 0.00 0.00 1.40
147 148 2.597578 ACCCTTAATTCGTGGGCTTT 57.402 45.000 9.46 0.00 44.56 3.51
187 188 4.953940 AGGCTTCTAGAATAAGCTGAGG 57.046 45.455 13.28 0.00 46.81 3.86
195 196 0.704076 AATAAGCTGAGGTGGGGCAA 59.296 50.000 0.00 0.00 0.00 4.52
212 213 4.157840 GGGGCAACTTATTTCTACAACCAG 59.842 45.833 0.00 0.00 0.00 4.00
234 235 5.453587 CAGCTATAAATCGCAAAAGAACTGC 59.546 40.000 0.00 0.00 36.41 4.40
244 245 1.664956 AAAGAACTGCCCCTTGGGGT 61.665 55.000 24.38 5.94 44.57 4.95
246 247 1.908299 GAACTGCCCCTTGGGGTTG 60.908 63.158 24.38 18.75 44.57 3.77
247 248 2.656698 GAACTGCCCCTTGGGGTTGT 62.657 60.000 24.38 19.33 44.57 3.32
259 261 5.515106 CCTTGGGGTTGTTTGGATAGATAA 58.485 41.667 0.00 0.00 0.00 1.75
331 333 6.567050 ACGAAGTTATTCTAACTAATCCGCA 58.433 36.000 0.28 0.00 37.78 5.69
358 360 8.571336 CATGTGAAGAACTTGTTTCTAGGAAAT 58.429 33.333 0.00 0.00 44.41 2.17
405 408 6.206634 TCAGAATTTCACGCTGGTAGAAAAAT 59.793 34.615 0.00 0.00 35.20 1.82
441 445 4.822026 TGTTCCAAAAACCACGATTTTGT 58.178 34.783 9.93 0.00 43.11 2.83
470 474 4.654262 TGGATCCTAACTAACTCCATCACC 59.346 45.833 14.23 0.00 31.19 4.02
492 497 0.248866 CCACACTTTTTCCACGCCAC 60.249 55.000 0.00 0.00 0.00 5.01
503 508 1.280710 TCCACGCCACCATACTTTCAT 59.719 47.619 0.00 0.00 0.00 2.57
551 556 7.148137 GGATTGTTATCCCAACAAGTAAATCGT 60.148 37.037 8.37 0.00 43.98 3.73
702 709 4.142049 CCAAACAACCACTTAGCCTTTCAA 60.142 41.667 0.00 0.00 0.00 2.69
861 869 5.423886 GAAATTCCACCTTCAAAACAACCA 58.576 37.500 0.00 0.00 0.00 3.67
1235 1243 0.725117 GTAGATGTTGTTTCCCGGCG 59.275 55.000 0.00 0.00 0.00 6.46
1331 2176 5.643664 ACTTAGGGTTTTGTTTTTGTCGTC 58.356 37.500 0.00 0.00 0.00 4.20
1399 2244 7.715657 TGATTACTTGATGTGGAATAATTGGC 58.284 34.615 0.00 0.00 0.00 4.52
1522 2550 1.733360 GCCGCGTTGTTATTTAGGTGA 59.267 47.619 4.92 0.00 0.00 4.02
1523 2551 2.353579 GCCGCGTTGTTATTTAGGTGAT 59.646 45.455 4.92 0.00 0.00 3.06
1557 2585 5.827797 TCAAAGTGCTATTTTGTGGACTCTT 59.172 36.000 7.62 0.00 36.97 2.85
1572 2600 6.152154 TGTGGACTCTTACAGATTTATGTCGA 59.848 38.462 0.00 0.00 34.56 4.20
1582 2610 5.937540 ACAGATTTATGTCGACACATTTCCA 59.062 36.000 22.71 1.02 40.66 3.53
1714 2745 6.604171 TCCATGCATAACATCCAGACTAAAT 58.396 36.000 0.00 0.00 36.64 1.40
2022 3062 6.281405 TCCTTCTTAGTGTGAACTTTCAGTC 58.719 40.000 0.00 0.00 37.98 3.51
2101 3141 2.637872 TCCCAAAGACCGAAGATGACTT 59.362 45.455 0.00 0.00 39.24 3.01
2102 3142 2.744202 CCCAAAGACCGAAGATGACTTG 59.256 50.000 0.00 0.00 36.39 3.16
2103 3143 3.557054 CCCAAAGACCGAAGATGACTTGA 60.557 47.826 0.00 0.00 36.39 3.02
2104 3144 4.065088 CCAAAGACCGAAGATGACTTGAA 58.935 43.478 0.00 0.00 36.39 2.69
2105 3145 4.153117 CCAAAGACCGAAGATGACTTGAAG 59.847 45.833 0.00 0.00 36.39 3.02
2106 3146 4.873746 AAGACCGAAGATGACTTGAAGA 57.126 40.909 0.00 0.00 36.39 2.87
2107 3147 4.448537 AGACCGAAGATGACTTGAAGAG 57.551 45.455 0.00 0.00 36.39 2.85
2108 3148 3.829601 AGACCGAAGATGACTTGAAGAGT 59.170 43.478 0.00 0.00 42.70 3.24
2203 3244 3.473113 AGAGCCCTCTCTCTCTCTTTT 57.527 47.619 0.00 0.00 46.32 2.27
2204 3245 3.790126 AGAGCCCTCTCTCTCTCTTTTT 58.210 45.455 0.00 0.00 46.32 1.94
2328 3398 1.772836 AGCTCCCCAAGAAATCATGC 58.227 50.000 0.00 0.00 0.00 4.06
2333 3403 3.765511 CTCCCCAAGAAATCATGCTTCAA 59.234 43.478 9.27 0.00 0.00 2.69
2444 3515 2.063156 TGTCACGAATTTTGGCATGC 57.937 45.000 9.90 9.90 0.00 4.06
2445 3516 1.339291 TGTCACGAATTTTGGCATGCA 59.661 42.857 21.36 2.54 0.00 3.96
2488 3559 6.522946 ACAAGTACTCCCTCTGTAAAGAAAC 58.477 40.000 0.00 0.00 0.00 2.78
2875 3951 1.077930 AATCATGCGCACTCTGCCT 60.078 52.632 14.90 0.00 41.12 4.75
2934 4010 5.391312 ACTCCTTTTGTTGGTGCATTATC 57.609 39.130 0.00 0.00 0.00 1.75
3101 4177 1.941668 GCTGTAGGTGGCTTGTCTGAC 60.942 57.143 0.00 0.00 0.00 3.51
3729 4831 3.239449 TGTTCCTGTCCACACACTATCT 58.761 45.455 0.00 0.00 0.00 1.98
3730 4832 3.646162 TGTTCCTGTCCACACACTATCTT 59.354 43.478 0.00 0.00 0.00 2.40
3855 5018 3.069016 TCACGTTTGAGCTCCTGTTAGAA 59.931 43.478 12.15 0.00 0.00 2.10
4183 5348 9.880157 CAATGGATTTGATTGAAGTAATTTCCT 57.120 29.630 0.00 0.00 37.53 3.36
4188 5353 9.428097 GATTTGATTGAAGTAATTTCCTTTGCT 57.572 29.630 0.00 0.00 34.77 3.91
4389 5578 3.641434 ATGGATTCCTCTTGACAGTGG 57.359 47.619 3.95 0.00 35.27 4.00
4395 5585 6.214615 TGGATTCCTCTTGACAGTGGTATTTA 59.785 38.462 3.95 0.00 35.45 1.40
4617 5807 7.505923 TGGCTGAAGTGAGTATATCTTAGCTAA 59.494 37.037 5.94 5.94 0.00 3.09
4618 5808 7.810759 GGCTGAAGTGAGTATATCTTAGCTAAC 59.189 40.741 0.86 0.00 0.00 2.34
4619 5809 7.535940 GCTGAAGTGAGTATATCTTAGCTAACG 59.464 40.741 0.86 0.00 0.00 3.18
4690 5880 3.203710 TCATCTGGCTTCAGGGATTCAAT 59.796 43.478 0.00 0.00 38.96 2.57
4785 5975 1.066573 CGAGGACTTCATGAAGGTGCT 60.067 52.381 33.11 27.20 42.53 4.40
4938 6135 2.843401 TTGGCAAAGACTAAGGCGTA 57.157 45.000 0.00 0.00 0.00 4.42
4939 6136 2.380084 TGGCAAAGACTAAGGCGTAG 57.620 50.000 5.89 5.89 35.75 3.51
4940 6137 1.621814 TGGCAAAGACTAAGGCGTAGT 59.378 47.619 13.00 13.00 46.23 2.73
5001 6198 1.815840 GCCCCTTCTCTGTAAGCGC 60.816 63.158 0.00 0.00 0.00 5.92
5143 6340 0.235665 CTTTGCTCGTGCGTTCACAT 59.764 50.000 4.84 0.00 43.28 3.21
5198 6395 7.521099 CGACACTAGTCTTGTTAGTAACTTGGA 60.521 40.741 14.00 6.79 42.73 3.53
5225 6422 4.705023 GGCTGTACCATTCCATGTACTTTT 59.295 41.667 0.00 0.00 38.86 2.27
5229 6426 5.410132 TGTACCATTCCATGTACTTTTGACG 59.590 40.000 0.00 0.00 0.00 4.35
5233 6430 4.678509 TTCCATGTACTTTTGACGATGC 57.321 40.909 0.00 0.00 0.00 3.91
5238 6435 2.096466 TGTACTTTTGACGATGCGCTTG 60.096 45.455 9.73 0.00 0.00 4.01
5245 6443 0.239879 GACGATGCGCTTGGGAAAAA 59.760 50.000 9.73 0.00 0.00 1.94
5280 6478 5.654650 TGTTCACCTTTGAGTTGTGGTTTAT 59.345 36.000 0.00 0.00 31.71 1.40
5360 6558 9.199982 GTTCATTGTCATTTGTCAATCAATCTT 57.800 29.630 0.93 0.00 35.84 2.40
5388 6586 5.259632 CACCCAGGAATTTTGAAGAGATCT 58.740 41.667 0.00 0.00 0.00 2.75
5612 6825 2.778299 TGGTTGTTTGCTACAGCTAGG 58.222 47.619 2.44 0.00 42.66 3.02
5613 6826 2.084546 GGTTGTTTGCTACAGCTAGGG 58.915 52.381 2.44 0.00 42.66 3.53
5614 6827 2.552373 GGTTGTTTGCTACAGCTAGGGT 60.552 50.000 2.44 0.00 42.66 4.34
5615 6828 3.146847 GTTGTTTGCTACAGCTAGGGTT 58.853 45.455 2.44 0.00 42.66 4.11
5635 6857 1.990160 TTGCTGTCGGTTCCCCTTGT 61.990 55.000 0.00 0.00 0.00 3.16
5673 6895 3.221222 CCATCGAGGTGGGGAGTC 58.779 66.667 0.00 0.00 35.55 3.36
5805 7027 3.255395 AGAGATGCTGACTGGTATCGATG 59.745 47.826 8.54 0.00 34.36 3.84
5808 7030 2.107366 TGCTGACTGGTATCGATGGAA 58.893 47.619 8.54 0.00 0.00 3.53
5811 7033 1.412710 TGACTGGTATCGATGGAAGGC 59.587 52.381 8.54 5.08 0.00 4.35
5835 7057 0.179000 CGAGCTTTGGTCAGGGCTAT 59.821 55.000 0.00 0.00 35.01 2.97
5836 7058 1.407437 CGAGCTTTGGTCAGGGCTATT 60.407 52.381 0.00 0.00 35.01 1.73
5837 7059 2.293170 GAGCTTTGGTCAGGGCTATTC 58.707 52.381 0.00 0.00 35.01 1.75
5838 7060 1.064389 AGCTTTGGTCAGGGCTATTCC 60.064 52.381 0.00 0.00 32.94 3.01
5849 7071 2.413310 GGCTATTCCCTCCGTTTCAA 57.587 50.000 0.00 0.00 0.00 2.69
5850 7072 2.718563 GGCTATTCCCTCCGTTTCAAA 58.281 47.619 0.00 0.00 0.00 2.69
5851 7073 3.086282 GGCTATTCCCTCCGTTTCAAAA 58.914 45.455 0.00 0.00 0.00 2.44
5852 7074 3.699538 GGCTATTCCCTCCGTTTCAAAAT 59.300 43.478 0.00 0.00 0.00 1.82
5853 7075 4.885325 GGCTATTCCCTCCGTTTCAAAATA 59.115 41.667 0.00 0.00 0.00 1.40
5854 7076 5.008712 GGCTATTCCCTCCGTTTCAAAATAG 59.991 44.000 0.00 0.00 0.00 1.73
5855 7077 5.820947 GCTATTCCCTCCGTTTCAAAATAGA 59.179 40.000 0.00 0.00 30.43 1.98
5856 7078 6.486993 GCTATTCCCTCCGTTTCAAAATAGAT 59.513 38.462 0.00 0.00 30.43 1.98
5857 7079 6.699575 ATTCCCTCCGTTTCAAAATAGATG 57.300 37.500 0.00 0.00 0.00 2.90
5858 7080 5.429681 TCCCTCCGTTTCAAAATAGATGA 57.570 39.130 0.00 0.00 0.00 2.92
5859 7081 5.183228 TCCCTCCGTTTCAAAATAGATGAC 58.817 41.667 0.00 0.00 0.00 3.06
5860 7082 5.045869 TCCCTCCGTTTCAAAATAGATGACT 60.046 40.000 0.00 0.00 0.00 3.41
5861 7083 5.648092 CCCTCCGTTTCAAAATAGATGACTT 59.352 40.000 0.00 0.00 0.00 3.01
5862 7084 6.821665 CCCTCCGTTTCAAAATAGATGACTTA 59.178 38.462 0.00 0.00 0.00 2.24
5863 7085 7.335924 CCCTCCGTTTCAAAATAGATGACTTAA 59.664 37.037 0.00 0.00 0.00 1.85
5864 7086 8.175716 CCTCCGTTTCAAAATAGATGACTTAAC 58.824 37.037 0.00 0.00 0.00 2.01
5865 7087 8.842358 TCCGTTTCAAAATAGATGACTTAACT 57.158 30.769 0.00 0.00 0.00 2.24
5866 7088 9.280174 TCCGTTTCAAAATAGATGACTTAACTT 57.720 29.630 0.00 0.00 0.00 2.66
5867 7089 9.893305 CCGTTTCAAAATAGATGACTTAACTTT 57.107 29.630 0.00 0.00 0.00 2.66
5909 7131 7.631717 ATGACTTAACTTTTGGATCTTAGGC 57.368 36.000 0.00 0.00 0.00 3.93
5910 7132 5.944007 TGACTTAACTTTTGGATCTTAGGCC 59.056 40.000 0.00 0.00 0.00 5.19
5911 7133 5.262009 ACTTAACTTTTGGATCTTAGGCCC 58.738 41.667 0.00 0.00 0.00 5.80
5912 7134 2.828661 ACTTTTGGATCTTAGGCCCC 57.171 50.000 0.00 0.00 0.00 5.80
5913 7135 1.064685 ACTTTTGGATCTTAGGCCCCG 60.065 52.381 0.00 0.00 0.00 5.73
5914 7136 0.996583 TTTTGGATCTTAGGCCCCGT 59.003 50.000 0.00 0.00 0.00 5.28
5915 7137 0.996583 TTTGGATCTTAGGCCCCGTT 59.003 50.000 0.00 0.00 0.00 4.44
5916 7138 1.882308 TTGGATCTTAGGCCCCGTTA 58.118 50.000 0.00 0.00 0.00 3.18
5917 7139 1.882308 TGGATCTTAGGCCCCGTTAA 58.118 50.000 0.00 0.00 0.00 2.01
5918 7140 2.198336 TGGATCTTAGGCCCCGTTAAA 58.802 47.619 0.00 0.00 0.00 1.52
5919 7141 2.781174 TGGATCTTAGGCCCCGTTAAAT 59.219 45.455 0.00 0.00 0.00 1.40
5920 7142 3.181448 TGGATCTTAGGCCCCGTTAAATC 60.181 47.826 0.00 0.00 0.00 2.17
5921 7143 3.072622 GGATCTTAGGCCCCGTTAAATCT 59.927 47.826 0.00 0.00 0.00 2.40
5922 7144 4.445879 GGATCTTAGGCCCCGTTAAATCTT 60.446 45.833 0.00 0.00 0.00 2.40
5923 7145 5.221783 GGATCTTAGGCCCCGTTAAATCTTA 60.222 44.000 0.00 0.00 0.00 2.10
5924 7146 5.286267 TCTTAGGCCCCGTTAAATCTTAG 57.714 43.478 0.00 0.00 0.00 2.18
5925 7147 4.102054 TCTTAGGCCCCGTTAAATCTTAGG 59.898 45.833 0.00 0.00 0.00 2.69
5926 7148 2.202707 AGGCCCCGTTAAATCTTAGGT 58.797 47.619 0.00 0.00 0.00 3.08
5927 7149 2.172082 AGGCCCCGTTAAATCTTAGGTC 59.828 50.000 0.00 0.00 0.00 3.85
5928 7150 2.092807 GGCCCCGTTAAATCTTAGGTCA 60.093 50.000 0.00 0.00 0.00 4.02
5929 7151 2.941064 GCCCCGTTAAATCTTAGGTCAC 59.059 50.000 0.00 0.00 0.00 3.67
5930 7152 3.538591 CCCCGTTAAATCTTAGGTCACC 58.461 50.000 0.00 0.00 0.00 4.02
5931 7153 3.199289 CCCCGTTAAATCTTAGGTCACCT 59.801 47.826 0.00 0.00 37.71 4.00
5932 7154 4.324022 CCCCGTTAAATCTTAGGTCACCTT 60.324 45.833 0.00 0.00 34.61 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 6.641169 TGCATGTCAACAAAAGTTATACCA 57.359 33.333 0.00 0.00 0.00 3.25
84 85 8.027189 GTCCTGATTTATTTGTCCCTTTTGTAC 58.973 37.037 0.00 0.00 0.00 2.90
104 105 4.942363 ACTAGTACTACCTTGGTCCTGA 57.058 45.455 0.00 0.00 0.00 3.86
187 188 4.082408 GGTTGTAGAAATAAGTTGCCCCAC 60.082 45.833 0.00 0.00 0.00 4.61
212 213 4.735338 GGCAGTTCTTTTGCGATTTATAGC 59.265 41.667 0.00 0.00 42.42 2.97
284 286 8.457261 TCGTCTGGTTAGATACTTTTTCTAGTC 58.543 37.037 0.00 0.00 34.94 2.59
306 308 6.694411 TGCGGATTAGTTAGAATAACTTCGTC 59.306 38.462 7.45 4.52 36.45 4.20
308 310 6.474427 TGTGCGGATTAGTTAGAATAACTTCG 59.526 38.462 7.45 8.15 36.45 3.79
331 333 6.591935 TCCTAGAAACAAGTTCTTCACATGT 58.408 36.000 0.00 0.00 44.64 3.21
430 433 6.055588 AGGATCCAGTATTACAAAATCGTGG 58.944 40.000 15.82 0.00 32.70 4.94
441 445 9.310449 GATGGAGTTAGTTAGGATCCAGTATTA 57.690 37.037 15.82 0.00 42.99 0.98
470 474 2.037871 CGTGGAAAAAGTGTGGGGG 58.962 57.895 0.00 0.00 0.00 5.40
492 497 5.902681 TCTCCGTGAGTTATGAAAGTATGG 58.097 41.667 1.60 0.00 0.00 2.74
503 508 4.779113 CCCCCTCTCCGTGAGTTA 57.221 61.111 1.60 0.00 41.11 2.24
708 715 9.673454 CGCACATATACACTCTGTACTTATAAA 57.327 33.333 0.00 0.00 35.42 1.40
718 725 2.539476 TGCACGCACATATACACTCTG 58.461 47.619 0.00 0.00 0.00 3.35
861 869 6.149807 ACCGAATACGTAAATTGTGGATGTTT 59.850 34.615 0.00 0.00 37.88 2.83
1235 1243 2.159517 CGTCCAAACCAGCAGATTTAGC 60.160 50.000 0.00 0.00 0.00 3.09
1331 2176 2.985139 GTTTTCTAAGGAGTCGACCACG 59.015 50.000 13.01 0.00 41.26 4.94
1399 2244 1.017387 GCAAATCTACTGAAGGGCCG 58.983 55.000 0.00 0.00 0.00 6.13
1470 2498 0.896923 AATTGCCGGCAATGTCACAT 59.103 45.000 45.89 30.63 44.86 3.21
1474 2502 0.179129 CCAGAATTGCCGGCAATGTC 60.179 55.000 45.89 38.60 44.86 3.06
1522 2550 9.643693 CAAAATAGCACTTTGAACCAGAATTAT 57.356 29.630 0.28 0.00 36.12 1.28
1523 2551 8.637986 ACAAAATAGCACTTTGAACCAGAATTA 58.362 29.630 10.91 0.00 37.25 1.40
1557 2585 7.100409 TGGAAATGTGTCGACATAAATCTGTA 58.900 34.615 23.12 9.31 42.30 2.74
1582 2610 2.840511 TCCCATACGCCATACCCATAT 58.159 47.619 0.00 0.00 0.00 1.78
1594 2622 2.260844 ATGAACAGGCATCCCATACG 57.739 50.000 0.00 0.00 0.00 3.06
1662 2690 1.202976 GGGGATGAGAATGGGTGGATG 60.203 57.143 0.00 0.00 0.00 3.51
1714 2745 8.800370 TTAACAGTGGAGATGTAAAATGCATA 57.200 30.769 0.00 0.00 0.00 3.14
1731 2763 5.737290 CGGACAAACACTCTTTTTAACAGTG 59.263 40.000 0.00 0.00 42.80 3.66
1815 2847 2.301346 CTAATTGCCCCTGTTAGCTGG 58.699 52.381 0.00 0.00 0.00 4.85
2022 3062 2.959507 TGGAGATGTACCATGTGTCG 57.040 50.000 0.00 0.00 32.03 4.35
2082 3122 3.664107 TCAAGTCATCTTCGGTCTTTGG 58.336 45.455 0.00 0.00 0.00 3.28
2090 3130 5.694006 ACTTCAACTCTTCAAGTCATCTTCG 59.306 40.000 0.00 0.00 37.17 3.79
2101 3141 3.541996 TGCAGTGACTTCAACTCTTCA 57.458 42.857 0.00 0.00 0.00 3.02
2102 3142 4.333926 ACTTTGCAGTGACTTCAACTCTTC 59.666 41.667 0.00 0.00 0.00 2.87
2103 3143 4.265073 ACTTTGCAGTGACTTCAACTCTT 58.735 39.130 0.00 0.00 0.00 2.85
2104 3144 3.878778 ACTTTGCAGTGACTTCAACTCT 58.121 40.909 0.00 0.00 0.00 3.24
2225 3295 6.477688 AGTGTCCGTTCAAAATATATGTACCG 59.522 38.462 0.00 0.00 0.00 4.02
2295 3365 2.740447 GGGGAGCTTTTGTAAGTGTACG 59.260 50.000 0.00 0.00 33.74 3.67
2875 3951 7.733047 TCAGCATTACTAAATCATACCTCCCTA 59.267 37.037 0.00 0.00 0.00 3.53
3101 4177 1.635487 TCCCTGAGTTCCCTGATTTGG 59.365 52.381 0.00 0.00 0.00 3.28
4183 5348 4.652421 ATCACACACACATTCAAGCAAA 57.348 36.364 0.00 0.00 0.00 3.68
4188 5353 5.045668 GTGCATATCACACACACATTCAA 57.954 39.130 0.00 0.00 44.98 2.69
4617 5807 2.273370 ATGTGCGATAAGAACGTCGT 57.727 45.000 0.00 0.00 39.87 4.34
4618 5808 4.748503 TTTATGTGCGATAAGAACGTCG 57.251 40.909 0.00 0.00 40.62 5.12
4619 5809 6.934210 AGATTTTATGTGCGATAAGAACGTC 58.066 36.000 0.00 0.00 0.00 4.34
4690 5880 0.749091 CATTGCGAAGATCAGCCCCA 60.749 55.000 0.00 0.00 0.00 4.96
4741 5931 1.077930 TACGTAGTCCCGCTCTGCT 60.078 57.895 0.00 0.00 43.93 4.24
4785 5975 3.052036 GGTTTTAAGCGTGTACGACAGA 58.948 45.455 8.82 0.00 43.02 3.41
4938 6135 5.656859 TGCTATTACATCAGTGACCACTACT 59.343 40.000 1.95 0.00 40.20 2.57
4939 6136 5.902681 TGCTATTACATCAGTGACCACTAC 58.097 41.667 1.95 0.00 40.20 2.73
4940 6137 5.891551 TCTGCTATTACATCAGTGACCACTA 59.108 40.000 1.95 0.00 40.20 2.74
5001 6198 3.181967 CGAAGCTGAACTCCCGCG 61.182 66.667 0.00 0.00 0.00 6.46
5058 6255 1.654954 GCACAGCATGAAGGGAGCAG 61.655 60.000 0.00 0.00 39.69 4.24
5080 6277 4.584325 TGAATGGTCCTCTTTTGACTTTGG 59.416 41.667 0.00 0.00 33.22 3.28
5151 6348 4.153957 GGAAGCTCTCCAGGGGAA 57.846 61.111 9.31 0.00 44.67 3.97
5173 6370 7.655490 TCCAAGTTACTAACAAGACTAGTGTC 58.345 38.462 0.00 0.00 43.22 3.67
5225 6422 0.886938 TTTTCCCAAGCGCATCGTCA 60.887 50.000 11.47 0.00 0.00 4.35
5229 6426 2.438868 AACTTTTTCCCAAGCGCATC 57.561 45.000 11.47 0.00 0.00 3.91
5245 6443 8.293699 ACTCAAAGGTGAACAAAAGAATAACT 57.706 30.769 0.00 0.00 31.88 2.24
5260 6458 5.234116 GCAAATAAACCACAACTCAAAGGTG 59.766 40.000 0.00 0.00 39.30 4.00
5280 6478 0.724549 GGTCGCATGTCGTATGCAAA 59.275 50.000 21.06 10.19 44.75 3.68
5310 6508 3.498397 ACAAAGAGCACAGATGGTAAACG 59.502 43.478 0.00 0.00 36.44 3.60
5360 6558 4.163078 TCTTCAAAATTCCTGGGTGCAAAA 59.837 37.500 0.00 0.00 0.00 2.44
5612 6825 1.658114 GGGAACCGACAGCAAAACC 59.342 57.895 0.00 0.00 40.86 3.27
5797 7019 1.488527 GACACGCCTTCCATCGATAC 58.511 55.000 0.00 0.00 0.00 2.24
5799 7021 1.226974 CGACACGCCTTCCATCGAT 60.227 57.895 0.00 0.00 34.77 3.59
5800 7022 2.180769 CGACACGCCTTCCATCGA 59.819 61.111 0.00 0.00 34.77 3.59
5801 7023 1.874019 CTCGACACGCCTTCCATCG 60.874 63.158 0.00 0.00 0.00 3.84
5802 7024 2.167861 GCTCGACACGCCTTCCATC 61.168 63.158 0.00 0.00 0.00 3.51
5805 7027 1.668151 AAAGCTCGACACGCCTTCC 60.668 57.895 0.00 0.00 0.00 3.46
5808 7030 2.357517 CCAAAGCTCGACACGCCT 60.358 61.111 0.00 0.00 0.00 5.52
5811 7033 1.284982 CCTGACCAAAGCTCGACACG 61.285 60.000 0.00 0.00 0.00 4.49
5835 7057 5.646360 GTCATCTATTTTGAAACGGAGGGAA 59.354 40.000 0.00 0.00 0.00 3.97
5836 7058 5.045869 AGTCATCTATTTTGAAACGGAGGGA 60.046 40.000 0.00 0.00 0.00 4.20
5837 7059 5.186198 AGTCATCTATTTTGAAACGGAGGG 58.814 41.667 0.00 0.00 0.00 4.30
5838 7060 6.743575 AAGTCATCTATTTTGAAACGGAGG 57.256 37.500 0.00 0.00 0.00 4.30
5839 7061 8.936864 AGTTAAGTCATCTATTTTGAAACGGAG 58.063 33.333 0.00 0.00 0.00 4.63
5840 7062 8.842358 AGTTAAGTCATCTATTTTGAAACGGA 57.158 30.769 0.00 0.00 0.00 4.69
5841 7063 9.893305 AAAGTTAAGTCATCTATTTTGAAACGG 57.107 29.630 0.00 0.00 0.00 4.44
5883 7105 8.523658 GCCTAAGATCCAAAAGTTAAGTCATTT 58.476 33.333 0.00 0.00 0.00 2.32
5884 7106 7.122799 GGCCTAAGATCCAAAAGTTAAGTCATT 59.877 37.037 0.00 0.00 0.00 2.57
5885 7107 6.603599 GGCCTAAGATCCAAAAGTTAAGTCAT 59.396 38.462 0.00 0.00 0.00 3.06
5886 7108 5.944007 GGCCTAAGATCCAAAAGTTAAGTCA 59.056 40.000 0.00 0.00 0.00 3.41
5887 7109 5.357314 GGGCCTAAGATCCAAAAGTTAAGTC 59.643 44.000 0.84 0.00 0.00 3.01
5888 7110 5.262009 GGGCCTAAGATCCAAAAGTTAAGT 58.738 41.667 0.84 0.00 0.00 2.24
5889 7111 4.645136 GGGGCCTAAGATCCAAAAGTTAAG 59.355 45.833 0.84 0.00 0.00 1.85
5890 7112 4.606210 GGGGCCTAAGATCCAAAAGTTAA 58.394 43.478 0.84 0.00 0.00 2.01
5891 7113 3.371166 CGGGGCCTAAGATCCAAAAGTTA 60.371 47.826 0.84 0.00 0.00 2.24
5892 7114 2.620627 CGGGGCCTAAGATCCAAAAGTT 60.621 50.000 0.84 0.00 0.00 2.66
5893 7115 1.064685 CGGGGCCTAAGATCCAAAAGT 60.065 52.381 0.84 0.00 0.00 2.66
5894 7116 1.064685 ACGGGGCCTAAGATCCAAAAG 60.065 52.381 0.84 0.00 0.00 2.27
5895 7117 0.996583 ACGGGGCCTAAGATCCAAAA 59.003 50.000 0.84 0.00 0.00 2.44
5896 7118 0.996583 AACGGGGCCTAAGATCCAAA 59.003 50.000 0.84 0.00 0.00 3.28
5897 7119 1.882308 TAACGGGGCCTAAGATCCAA 58.118 50.000 0.84 0.00 0.00 3.53
5898 7120 1.882308 TTAACGGGGCCTAAGATCCA 58.118 50.000 0.84 0.00 0.00 3.41
5899 7121 3.072622 AGATTTAACGGGGCCTAAGATCC 59.927 47.826 0.84 0.00 0.00 3.36
5900 7122 4.353383 AGATTTAACGGGGCCTAAGATC 57.647 45.455 0.84 0.43 0.00 2.75
5901 7123 4.790718 AAGATTTAACGGGGCCTAAGAT 57.209 40.909 0.84 0.00 0.00 2.40
5902 7124 4.102054 CCTAAGATTTAACGGGGCCTAAGA 59.898 45.833 0.84 0.00 0.00 2.10
5903 7125 4.141551 ACCTAAGATTTAACGGGGCCTAAG 60.142 45.833 0.84 0.00 0.00 2.18
5904 7126 3.781965 ACCTAAGATTTAACGGGGCCTAA 59.218 43.478 0.84 0.00 0.00 2.69
5905 7127 3.387012 ACCTAAGATTTAACGGGGCCTA 58.613 45.455 0.84 0.00 0.00 3.93
5906 7128 2.172082 GACCTAAGATTTAACGGGGCCT 59.828 50.000 0.84 0.00 0.00 5.19
5907 7129 2.092807 TGACCTAAGATTTAACGGGGCC 60.093 50.000 0.00 0.00 0.00 5.80
5908 7130 2.941064 GTGACCTAAGATTTAACGGGGC 59.059 50.000 0.00 0.00 0.00 5.80
5909 7131 3.199289 AGGTGACCTAAGATTTAACGGGG 59.801 47.826 0.07 0.00 28.47 5.73
5910 7132 4.482952 AGGTGACCTAAGATTTAACGGG 57.517 45.455 0.07 0.00 28.47 5.28


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

AutoCloner maintained by Alex Coulton.