Multiple sequence alignment - TraesCS2A01G158700

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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 TraesCS2A01G158700 chr2A 100.000 2204 0 0 1 2204 105530860 105533063 0.000000e+00 4071.0
1 TraesCS2A01G158700 chr2A 84.986 706 88 11 1515 2204 105524381 105525084 0.000000e+00 701.0
2 TraesCS2A01G158700 chr2A 85.888 659 70 15 780 1431 105522642 105523284 0.000000e+00 680.0
3 TraesCS2A01G158700 chr2A 86.528 386 33 8 922 1292 105541247 105541628 7.330000e-110 407.0
4 TraesCS2A01G158700 chr2A 83.047 466 58 11 190 654 105540587 105541032 9.480000e-109 403.0
5 TraesCS2A01G158700 chr2A 91.398 186 11 4 291 476 105522175 105522355 1.310000e-62 250.0
6 TraesCS2A01G158700 chr2D 91.373 1020 74 6 833 1844 109830740 109831753 0.000000e+00 1384.0
7 TraesCS2A01G158700 chr2D 87.960 706 48 15 780 1473 109737455 109738135 0.000000e+00 798.0
8 TraesCS2A01G158700 chr2D 86.572 566 55 13 241 799 109803031 109803582 2.420000e-169 604.0
9 TraesCS2A01G158700 chr2D 93.188 367 23 2 1840 2204 109897966 109898332 2.490000e-149 538.0
10 TraesCS2A01G158700 chr2D 91.644 371 28 3 1837 2204 109782724 109783094 5.430000e-141 510.0
11 TraesCS2A01G158700 chr2D 94.225 329 19 0 1513 1841 109740868 109741196 9.080000e-139 503.0
12 TraesCS2A01G158700 chr2D 88.158 380 32 8 933 1304 109793373 109793747 7.220000e-120 440.0
13 TraesCS2A01G158700 chr2D 93.836 292 17 1 1554 1844 109743434 109743725 2.600000e-119 438.0
14 TraesCS2A01G158700 chr2D 88.251 366 30 7 934 1290 109902020 109902381 2.020000e-115 425.0
15 TraesCS2A01G158700 chr2D 84.257 451 49 12 190 638 109901326 109901756 9.410000e-114 420.0
16 TraesCS2A01G158700 chr2D 85.223 291 29 8 190 480 109792818 109793094 9.960000e-74 287.0
17 TraesCS2A01G158700 chr2D 84.647 241 28 7 222 455 109736857 109737095 4.730000e-57 231.0
18 TraesCS2A01G158700 chr2B 91.373 510 35 5 834 1335 159300071 159300579 0.000000e+00 689.0
19 TraesCS2A01G158700 chr2B 87.153 576 56 11 241 811 159299421 159299983 2.390000e-179 638.0
20 TraesCS2A01G158700 chr2B 84.615 442 40 14 869 1292 159319008 159319439 4.380000e-112 414.0
21 TraesCS2A01G158700 chr2B 91.304 138 12 0 1326 1463 159301140 159301277 2.890000e-44 189.0
22 TraesCS2A01G158700 chr7B 91.176 136 12 0 1 136 59948946 59948811 3.740000e-43 185.0
23 TraesCS2A01G158700 chr6D 86.466 133 18 0 1 133 2339043 2338911 1.760000e-31 147.0
24 TraesCS2A01G158700 chr6B 86.260 131 16 2 1 130 27908021 27908150 8.200000e-30 141.0
25 TraesCS2A01G158700 chr6B 85.185 135 17 3 4 136 76005919 76005786 3.820000e-28 135.0
26 TraesCS2A01G158700 chr3D 85.821 134 17 2 1 133 567932958 567932826 8.200000e-30 141.0
27 TraesCS2A01G158700 chr1B 87.273 110 14 0 4 113 40861630 40861521 2.300000e-25 126.0
28 TraesCS2A01G158700 chr5B 83.459 133 19 3 4 135 523760516 523760386 1.070000e-23 121.0
29 TraesCS2A01G158700 chr1A 84.545 110 17 0 4 113 579679093 579678984 2.310000e-20 110.0
30 TraesCS2A01G158700 chr3B 81.061 132 25 0 2 133 627757367 627757236 2.990000e-19 106.0
31 TraesCS2A01G158700 chr6A 100.000 30 0 0 742 771 49754764 49754793 3.060000e-04 56.5


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 TraesCS2A01G158700 chr2A 105530860 105533063 2203 False 4071.000000 4071 100.000000 1 2204 1 chr2A.!!$F1 2203
1 TraesCS2A01G158700 chr2A 105522175 105525084 2909 False 543.666667 701 87.424000 291 2204 3 chr2A.!!$F2 1913
2 TraesCS2A01G158700 chr2A 105540587 105541628 1041 False 405.000000 407 84.787500 190 1292 2 chr2A.!!$F3 1102
3 TraesCS2A01G158700 chr2D 109830740 109831753 1013 False 1384.000000 1384 91.373000 833 1844 1 chr2D.!!$F3 1011
4 TraesCS2A01G158700 chr2D 109803031 109803582 551 False 604.000000 604 86.572000 241 799 1 chr2D.!!$F2 558
5 TraesCS2A01G158700 chr2D 109736857 109743725 6868 False 492.500000 798 90.167000 222 1844 4 chr2D.!!$F4 1622
6 TraesCS2A01G158700 chr2D 109897966 109902381 4415 False 461.000000 538 88.565333 190 2204 3 chr2D.!!$F6 2014
7 TraesCS2A01G158700 chr2D 109792818 109793747 929 False 363.500000 440 86.690500 190 1304 2 chr2D.!!$F5 1114
8 TraesCS2A01G158700 chr2B 159299421 159301277 1856 False 505.333333 689 89.943333 241 1463 3 chr2B.!!$F2 1222

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
142 143 0.105593 CCTGGTAGTGATGCGCATCT 59.894 55.0 40.9 28.72 38.6 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1436 6512 1.241315 ACCGCGCATATTATTGGCCC 61.241 55.0 8.75 0.0 0.0 5.8 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
20 21 3.251479 GCATAGATGGACATATGCCGA 57.749 47.619 1.58 0.00 45.51 5.54
21 22 2.932614 GCATAGATGGACATATGCCGAC 59.067 50.000 1.58 3.98 45.51 4.79
22 23 3.182182 CATAGATGGACATATGCCGACG 58.818 50.000 1.58 0.00 0.00 5.12
23 24 0.318441 AGATGGACATATGCCGACGG 59.682 55.000 10.29 10.29 0.00 4.79
61 62 2.521224 GACCTAGGCCGTCGGGAT 60.521 66.667 14.38 0.00 34.06 3.85
62 63 1.228367 GACCTAGGCCGTCGGGATA 60.228 63.158 14.38 0.00 34.06 2.59
64 65 0.700564 ACCTAGGCCGTCGGGATATA 59.299 55.000 14.38 0.00 34.06 0.86
65 66 1.287146 ACCTAGGCCGTCGGGATATAT 59.713 52.381 14.38 0.00 34.06 0.86
66 67 1.955080 CCTAGGCCGTCGGGATATATC 59.045 57.143 14.38 3.96 34.06 1.63
80 81 4.799678 GGATATATCCATCTATGCCGACG 58.200 47.826 24.41 0.00 46.38 5.12
81 82 4.321304 GGATATATCCATCTATGCCGACGG 60.321 50.000 24.41 10.29 46.38 4.79
99 100 4.107029 CCCCCGTCGGCATAGATA 57.893 61.111 5.50 0.00 0.00 1.98
100 101 1.590147 CCCCCGTCGGCATAGATAC 59.410 63.158 5.50 0.00 0.00 2.24
103 104 4.148230 CGTCGGCATAGATACGGC 57.852 61.111 0.00 0.00 0.00 5.68
104 105 1.443872 CGTCGGCATAGATACGGCC 60.444 63.158 0.00 0.00 44.27 6.13
125 126 2.224209 CGTAGGCAATCGGGTAAATCCT 60.224 50.000 0.00 0.00 36.25 3.24
126 127 2.348411 AGGCAATCGGGTAAATCCTG 57.652 50.000 0.00 0.00 43.70 3.86
127 128 1.133792 AGGCAATCGGGTAAATCCTGG 60.134 52.381 0.00 0.00 42.62 4.45
129 130 2.158726 GGCAATCGGGTAAATCCTGGTA 60.159 50.000 0.00 0.00 42.62 3.25
130 131 3.139077 GCAATCGGGTAAATCCTGGTAG 58.861 50.000 0.00 0.00 42.62 3.18
131 132 3.433173 GCAATCGGGTAAATCCTGGTAGT 60.433 47.826 0.00 0.00 42.62 2.73
132 133 4.127171 CAATCGGGTAAATCCTGGTAGTG 58.873 47.826 0.00 0.00 42.62 2.74
134 135 3.649843 TCGGGTAAATCCTGGTAGTGAT 58.350 45.455 0.00 0.00 42.62 3.06
135 136 3.386726 TCGGGTAAATCCTGGTAGTGATG 59.613 47.826 0.00 0.00 42.62 3.07
136 137 3.477530 GGGTAAATCCTGGTAGTGATGC 58.522 50.000 0.00 0.00 36.25 3.91
137 138 3.131396 GGTAAATCCTGGTAGTGATGCG 58.869 50.000 0.00 0.00 0.00 4.73
138 139 1.668419 AAATCCTGGTAGTGATGCGC 58.332 50.000 0.00 0.00 0.00 6.09
139 140 0.541392 AATCCTGGTAGTGATGCGCA 59.459 50.000 14.96 14.96 0.00 6.09
142 143 0.105593 CCTGGTAGTGATGCGCATCT 59.894 55.000 40.90 28.72 38.60 2.90
143 144 1.473965 CCTGGTAGTGATGCGCATCTT 60.474 52.381 40.90 32.03 38.60 2.40
144 145 1.596260 CTGGTAGTGATGCGCATCTTG 59.404 52.381 40.90 22.70 38.60 3.02
145 146 0.305922 GGTAGTGATGCGCATCTTGC 59.694 55.000 40.90 31.73 40.69 4.01
146 147 1.009078 GTAGTGATGCGCATCTTGCA 58.991 50.000 40.90 25.15 45.36 4.08
148 149 1.226491 GTGATGCGCATCTTGCACC 60.226 57.895 40.90 21.27 46.57 5.01
149 150 2.409055 TGATGCGCATCTTGCACCC 61.409 57.895 40.90 20.59 46.57 4.61
150 151 3.129913 GATGCGCATCTTGCACCCC 62.130 63.158 36.92 13.17 46.57 4.95
172 173 3.470888 CCCCGACAAGGCGAGGAT 61.471 66.667 0.00 0.00 39.21 3.24
173 174 2.202932 CCCGACAAGGCGAGGATG 60.203 66.667 0.00 0.00 39.21 3.51
174 175 2.202932 CCGACAAGGCGAGGATGG 60.203 66.667 0.00 0.00 0.00 3.51
175 176 2.579201 CGACAAGGCGAGGATGGT 59.421 61.111 0.00 0.00 0.00 3.55
176 177 1.811266 CGACAAGGCGAGGATGGTG 60.811 63.158 0.00 0.00 0.00 4.17
177 178 2.045926 ACAAGGCGAGGATGGTGC 60.046 61.111 0.00 0.00 0.00 5.01
178 179 3.197790 CAAGGCGAGGATGGTGCG 61.198 66.667 0.00 0.00 0.00 5.34
185 186 3.932580 GAGGATGGTGCGCGTGTGA 62.933 63.158 8.43 0.00 0.00 3.58
186 187 2.819595 GGATGGTGCGCGTGTGAT 60.820 61.111 8.43 0.00 0.00 3.06
187 188 2.400798 GATGGTGCGCGTGTGATG 59.599 61.111 8.43 0.00 0.00 3.07
188 189 2.358615 ATGGTGCGCGTGTGATGT 60.359 55.556 8.43 0.00 0.00 3.06
199 3371 3.545633 GCGTGTGATGTTGTTCTCTTTC 58.454 45.455 0.00 0.00 0.00 2.62
207 3379 4.244425 TGTTGTTCTCTTTCTCTCCTCG 57.756 45.455 0.00 0.00 0.00 4.63
223 3395 3.700038 CTCCTCGTACCCATCACTTAGTT 59.300 47.826 0.00 0.00 0.00 2.24
229 3401 3.508845 ACCCATCACTTAGTTGTTGCT 57.491 42.857 0.00 0.00 0.00 3.91
232 3404 3.120199 CCCATCACTTAGTTGTTGCTTCG 60.120 47.826 0.00 0.00 0.00 3.79
234 3406 4.377431 CCATCACTTAGTTGTTGCTTCGTC 60.377 45.833 0.00 0.00 0.00 4.20
238 3410 1.790755 TAGTTGTTGCTTCGTCGCAT 58.209 45.000 2.53 0.00 40.04 4.73
251 3423 5.051039 GCTTCGTCGCATTGTCTCAAATATA 60.051 40.000 0.00 0.00 0.00 0.86
371 3549 3.366273 CGGGACCTGAAATGTTGACAATG 60.366 47.826 0.00 0.00 0.00 2.82
402 3582 3.061965 TCGAATATGCACGTGAATGTGTG 59.938 43.478 22.23 9.11 41.94 3.82
403 3583 3.181521 CGAATATGCACGTGAATGTGTGT 60.182 43.478 22.23 0.00 41.94 3.72
444 3627 0.232303 CAGACACGGCTTCGAAACAC 59.768 55.000 0.00 0.00 37.63 3.32
485 3781 3.119849 GCATTGCCTATAAATACAGGGCG 60.120 47.826 0.00 0.00 45.06 6.13
486 3782 4.323417 CATTGCCTATAAATACAGGGCGA 58.677 43.478 0.00 0.00 45.06 5.54
500 3798 0.657840 GGGCGACTTCATCCAAATCG 59.342 55.000 0.00 0.00 35.91 3.34
508 3806 4.194640 ACTTCATCCAAATCGACATCTGG 58.805 43.478 0.00 0.00 0.00 3.86
509 3807 4.080919 ACTTCATCCAAATCGACATCTGGA 60.081 41.667 8.55 8.55 42.04 3.86
510 3808 4.486125 TCATCCAAATCGACATCTGGAA 57.514 40.909 9.81 0.00 41.20 3.53
511 3809 4.842574 TCATCCAAATCGACATCTGGAAA 58.157 39.130 9.81 1.35 41.20 3.13
512 3810 4.877823 TCATCCAAATCGACATCTGGAAAG 59.122 41.667 9.81 6.91 41.20 2.62
513 3811 4.286297 TCCAAATCGACATCTGGAAAGT 57.714 40.909 4.58 0.00 35.02 2.66
514 3812 5.414789 TCCAAATCGACATCTGGAAAGTA 57.585 39.130 4.58 0.00 35.02 2.24
555 3853 3.309954 GGAACGACCAAATCACATAGAGC 59.690 47.826 0.00 0.00 38.79 4.09
558 3856 4.938080 ACGACCAAATCACATAGAGCTAG 58.062 43.478 0.00 0.00 0.00 3.42
594 3892 1.485066 AGTACCATGTCATTCGTCCCC 59.515 52.381 0.00 0.00 0.00 4.81
596 3894 0.991920 ACCATGTCATTCGTCCCCTT 59.008 50.000 0.00 0.00 0.00 3.95
623 3921 5.915175 TCTGAGAAGATCATTGTCATCCTG 58.085 41.667 0.00 0.00 37.28 3.86
638 3936 5.655090 TGTCATCCTGTCTATTCTTCCGTTA 59.345 40.000 0.00 0.00 0.00 3.18
748 4156 4.969484 TGTTCTCTCCTTTTTGTACTCCC 58.031 43.478 0.00 0.00 0.00 4.30
751 4159 3.838903 TCTCTCCTTTTTGTACTCCCTCC 59.161 47.826 0.00 0.00 0.00 4.30
752 4160 3.583086 CTCTCCTTTTTGTACTCCCTCCA 59.417 47.826 0.00 0.00 0.00 3.86
755 4163 5.074515 TCTCCTTTTTGTACTCCCTCCATTT 59.925 40.000 0.00 0.00 0.00 2.32
756 4164 6.273730 TCTCCTTTTTGTACTCCCTCCATTTA 59.726 38.462 0.00 0.00 0.00 1.40
766 4174 9.238368 TGTACTCCCTCCATTTAAAAATACTTG 57.762 33.333 0.00 0.00 0.00 3.16
811 4219 6.463995 AAGAAAGTGTTTCCTTTACATGCA 57.536 33.333 0.00 0.00 40.54 3.96
812 4220 6.655078 AGAAAGTGTTTCCTTTACATGCAT 57.345 33.333 0.00 0.00 40.54 3.96
813 4221 6.449698 AGAAAGTGTTTCCTTTACATGCATG 58.550 36.000 25.09 25.09 40.54 4.06
814 4222 4.178545 AGTGTTTCCTTTACATGCATGC 57.821 40.909 26.53 11.82 0.00 4.06
822 4230 3.056678 CCTTTACATGCATGCTCCAAACA 60.057 43.478 26.53 0.00 0.00 2.83
828 4236 1.885887 TGCATGCTCCAAACAAGTACC 59.114 47.619 20.33 0.00 0.00 3.34
830 4238 2.095059 GCATGCTCCAAACAAGTACCAG 60.095 50.000 11.37 0.00 0.00 4.00
986 4480 6.807708 CTACTACTTGTAGGCATTTGTACG 57.192 41.667 11.82 0.00 43.63 3.67
991 4486 6.178239 ACTTGTAGGCATTTGTACGATTTC 57.822 37.500 0.00 0.00 0.00 2.17
1026 4530 2.741985 CCATGCGACGCCAAGACA 60.742 61.111 18.69 0.00 0.00 3.41
1135 4642 3.207778 CCGGTAGGAAGTTTTGTGACAA 58.792 45.455 0.00 0.00 41.02 3.18
1256 4765 1.915141 CCCATGCAAGTCTCCACTTT 58.085 50.000 0.00 0.00 41.24 2.66
1308 4821 6.622896 GCATGGGTACAGTCTGAAAAATGTAC 60.623 42.308 6.91 6.18 44.59 2.90
1335 4848 8.240682 GGATGTGCTATGTAATGTTGTTTTGTA 58.759 33.333 0.00 0.00 0.00 2.41
1417 5500 6.737720 ATCTACTTCAGCATTAGGACATGA 57.262 37.500 0.00 0.00 0.00 3.07
1421 6497 6.737720 ACTTCAGCATTAGGACATGATCTA 57.262 37.500 0.00 0.00 0.00 1.98
1436 6512 8.991026 GGACATGATCTATGAATTCTTCTTGAG 58.009 37.037 7.05 0.00 39.21 3.02
1444 6520 5.191727 TGAATTCTTCTTGAGGGCCAATA 57.808 39.130 6.18 0.00 33.68 1.90
1451 6527 3.411446 TCTTGAGGGCCAATAATATGCG 58.589 45.455 6.18 0.00 33.68 4.73
1452 6528 1.533625 TGAGGGCCAATAATATGCGC 58.466 50.000 6.18 0.00 38.13 6.09
1504 8225 5.429130 CAGGAAGACATAACCTTCTTACCC 58.571 45.833 0.00 0.00 39.80 3.69
1587 9377 5.767665 GGATAGAGATGTGAGCAGTCTTCTA 59.232 44.000 0.00 0.00 0.00 2.10
1687 9478 7.649057 AGTAAAAGGTTGTTCATTCTTAGTGC 58.351 34.615 0.00 0.00 0.00 4.40
1709 9500 6.095160 GTGCCATCATTTTCTTCAGAAGAGAT 59.905 38.462 12.74 9.38 39.03 2.75
1725 9516 8.974238 TCAGAAGAGATCCAATGCAAATTTAAT 58.026 29.630 0.00 0.00 0.00 1.40
1782 9574 7.781324 AAGGATGTTATCTTTCACATGGTTT 57.219 32.000 0.00 0.00 33.62 3.27
1865 12183 9.170734 CACAGAGGAAAATCATCAAAGAGAATA 57.829 33.333 0.00 0.00 28.01 1.75
1896 12214 5.104360 ACCATCAAAGAGGCTCTAAGCATAA 60.104 40.000 19.07 0.00 44.75 1.90
1900 12218 6.109359 TCAAAGAGGCTCTAAGCATAAGTTC 58.891 40.000 19.07 0.00 44.75 3.01
1903 12221 4.100808 AGAGGCTCTAAGCATAAGTTCCTG 59.899 45.833 17.09 0.00 44.75 3.86
1907 12225 5.453903 GGCTCTAAGCATAAGTTCCTGATCA 60.454 44.000 0.00 0.00 44.75 2.92
1908 12226 5.695816 GCTCTAAGCATAAGTTCCTGATCAG 59.304 44.000 16.24 16.24 41.89 2.90
1910 12228 6.810911 TCTAAGCATAAGTTCCTGATCAGAC 58.189 40.000 24.62 14.83 0.00 3.51
1913 12231 4.469227 AGCATAAGTTCCTGATCAGACACT 59.531 41.667 24.62 20.09 0.00 3.55
1915 12233 5.625426 GCATAAGTTCCTGATCAGACACTCA 60.625 44.000 24.62 11.43 0.00 3.41
1919 12237 4.101585 AGTTCCTGATCAGACACTCAACAA 59.898 41.667 24.62 0.07 0.00 2.83
1929 12247 6.873997 TCAGACACTCAACAAAAGAGTTAGA 58.126 36.000 0.00 0.00 43.47 2.10
1936 12254 7.926555 CACTCAACAAAAGAGTTAGAGGTAGAA 59.073 37.037 0.00 0.00 43.47 2.10
1968 12286 6.022107 GGGGTTACCTTACATATCCCTTTT 57.978 41.667 0.00 0.00 33.57 2.27
1970 12288 6.066690 GGGTTACCTTACATATCCCTTTTCC 58.933 44.000 0.00 0.00 31.27 3.13
1971 12289 6.126273 GGGTTACCTTACATATCCCTTTTCCT 60.126 42.308 0.00 0.00 31.27 3.36
1972 12290 7.351952 GGTTACCTTACATATCCCTTTTCCTT 58.648 38.462 0.00 0.00 0.00 3.36
1982 12300 8.053355 ACATATCCCTTTTCCTTGTAAGGTTAG 58.947 37.037 10.28 6.53 46.54 2.34
1984 12302 6.270219 TCCCTTTTCCTTGTAAGGTTAGTT 57.730 37.500 10.28 0.00 46.54 2.24
1991 12309 5.686753 TCCTTGTAAGGTTAGTTGCTTGAA 58.313 37.500 10.28 0.00 46.54 2.69
1992 12310 5.529800 TCCTTGTAAGGTTAGTTGCTTGAAC 59.470 40.000 10.28 0.00 46.54 3.18
1999 12317 3.746492 GGTTAGTTGCTTGAACGATCACT 59.254 43.478 0.00 0.00 39.80 3.41
2004 12322 6.560253 AGTTGCTTGAACGATCACTTTATT 57.440 33.333 0.00 0.00 39.80 1.40
2010 12328 8.551205 TGCTTGAACGATCACTTTATTCATATC 58.449 33.333 0.00 0.00 34.61 1.63
2019 12337 7.003939 TCACTTTATTCATATCGCACAACTG 57.996 36.000 0.00 0.00 0.00 3.16
2032 12350 4.988598 AACTGGGTGCGCCGACAG 62.989 66.667 17.88 17.88 37.01 3.51
2042 12360 1.446792 CGCCGACAGAGCTGAATGT 60.447 57.895 4.21 0.00 0.00 2.71
2044 12362 1.160137 GCCGACAGAGCTGAATGTTT 58.840 50.000 4.21 0.00 0.00 2.83
2045 12363 1.129437 GCCGACAGAGCTGAATGTTTC 59.871 52.381 4.21 0.00 0.00 2.78
2047 12365 2.416747 CGACAGAGCTGAATGTTTCCA 58.583 47.619 4.21 0.00 0.00 3.53
2060 12379 5.830457 TGAATGTTTCCACAACTCCACAATA 59.170 36.000 0.00 0.00 36.16 1.90
2076 12395 6.422333 TCCACAATAATCAAGTGCATAAGGA 58.578 36.000 0.00 0.00 32.09 3.36
2077 12396 6.889177 TCCACAATAATCAAGTGCATAAGGAA 59.111 34.615 0.00 0.00 32.09 3.36
2144 12465 4.102681 CCAGGTAACCAGGGGATTAAGTAG 59.897 50.000 0.00 0.00 37.17 2.57
2153 12478 5.770162 CCAGGGGATTAAGTAGCAAATAAGG 59.230 44.000 0.00 0.00 0.00 2.69
2154 12479 5.770162 CAGGGGATTAAGTAGCAAATAAGGG 59.230 44.000 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.182182 CGTCGGCATATGTCCATCTATG 58.818 50.000 14.11 0.00 0.00 2.23
2 3 2.166459 CCGTCGGCATATGTCCATCTAT 59.834 50.000 14.11 0.00 0.00 1.98
3 4 1.544246 CCGTCGGCATATGTCCATCTA 59.456 52.381 14.11 0.00 0.00 1.98
4 5 0.318441 CCGTCGGCATATGTCCATCT 59.682 55.000 14.11 0.00 0.00 2.90
5 6 2.827604 CCGTCGGCATATGTCCATC 58.172 57.895 14.11 7.05 0.00 3.51
45 46 0.700564 TATATCCCGACGGCCTAGGT 59.299 55.000 8.86 0.00 0.00 3.08
47 48 1.955080 GGATATATCCCGACGGCCTAG 59.045 57.143 19.69 0.00 41.20 3.02
48 49 1.285667 TGGATATATCCCGACGGCCTA 59.714 52.381 25.86 1.99 46.59 3.93
49 50 0.040646 TGGATATATCCCGACGGCCT 59.959 55.000 25.86 0.00 46.59 5.19
50 51 1.068741 GATGGATATATCCCGACGGCC 59.931 57.143 25.86 2.64 46.59 6.13
51 52 2.032620 AGATGGATATATCCCGACGGC 58.967 52.381 25.86 10.69 46.59 5.68
52 53 4.321304 GCATAGATGGATATATCCCGACGG 60.321 50.000 25.86 6.99 46.59 4.79
54 55 4.321304 CGGCATAGATGGATATATCCCGAC 60.321 50.000 25.86 17.16 46.59 4.79
56 57 3.826729 TCGGCATAGATGGATATATCCCG 59.173 47.826 25.86 19.03 46.59 5.14
57 58 4.321304 CGTCGGCATAGATGGATATATCCC 60.321 50.000 25.86 13.42 46.59 3.85
82 83 1.590147 GTATCTATGCCGACGGGGG 59.410 63.158 17.22 0.00 35.78 5.40
83 84 1.211969 CGTATCTATGCCGACGGGG 59.788 63.158 17.22 0.00 39.58 5.73
84 85 4.861883 CGTATCTATGCCGACGGG 57.138 61.111 17.22 0.00 0.00 5.28
86 87 1.443872 GGCCGTATCTATGCCGACG 60.444 63.158 0.00 0.00 35.08 5.12
87 88 4.573162 GGCCGTATCTATGCCGAC 57.427 61.111 0.00 0.00 35.08 4.79
92 93 3.715854 GCCTACGGCCGTATCTATG 57.284 57.895 36.37 23.97 44.06 2.23
104 105 2.140717 GGATTTACCCGATTGCCTACG 58.859 52.381 0.00 0.00 0.00 3.51
105 106 3.139077 CAGGATTTACCCGATTGCCTAC 58.861 50.000 0.00 0.00 40.05 3.18
106 107 2.105821 CCAGGATTTACCCGATTGCCTA 59.894 50.000 0.00 0.00 40.05 3.93
107 108 1.133792 CCAGGATTTACCCGATTGCCT 60.134 52.381 0.00 0.00 40.05 4.75
110 111 4.127171 CACTACCAGGATTTACCCGATTG 58.873 47.826 0.00 0.00 40.05 2.67
111 112 4.035112 TCACTACCAGGATTTACCCGATT 58.965 43.478 0.00 0.00 40.05 3.34
113 114 3.104519 TCACTACCAGGATTTACCCGA 57.895 47.619 0.00 0.00 40.05 5.14
115 116 3.477530 GCATCACTACCAGGATTTACCC 58.522 50.000 0.00 0.00 40.05 3.69
116 117 3.131396 CGCATCACTACCAGGATTTACC 58.869 50.000 0.00 0.00 39.35 2.85
117 118 2.544267 GCGCATCACTACCAGGATTTAC 59.456 50.000 0.30 0.00 0.00 2.01
118 119 2.169561 TGCGCATCACTACCAGGATTTA 59.830 45.455 5.66 0.00 0.00 1.40
120 121 0.541392 TGCGCATCACTACCAGGATT 59.459 50.000 5.66 0.00 0.00 3.01
125 126 1.655484 CAAGATGCGCATCACTACCA 58.345 50.000 42.35 6.97 40.22 3.25
126 127 0.305922 GCAAGATGCGCATCACTACC 59.694 55.000 42.35 25.30 40.22 3.18
127 128 3.814049 GCAAGATGCGCATCACTAC 57.186 52.632 42.35 27.91 40.22 2.73
156 157 2.202932 CATCCTCGCCTTGTCGGG 60.203 66.667 0.00 0.00 0.00 5.14
158 159 1.811266 CACCATCCTCGCCTTGTCG 60.811 63.158 0.00 0.00 0.00 4.35
159 160 2.109126 GCACCATCCTCGCCTTGTC 61.109 63.158 0.00 0.00 0.00 3.18
160 161 2.045926 GCACCATCCTCGCCTTGT 60.046 61.111 0.00 0.00 0.00 3.16
161 162 3.197790 CGCACCATCCTCGCCTTG 61.198 66.667 0.00 0.00 0.00 3.61
167 168 3.490759 CACACGCGCACCATCCTC 61.491 66.667 5.73 0.00 0.00 3.71
168 169 3.315142 ATCACACGCGCACCATCCT 62.315 57.895 5.73 0.00 0.00 3.24
169 170 2.819595 ATCACACGCGCACCATCC 60.820 61.111 5.73 0.00 0.00 3.51
170 171 1.911293 AACATCACACGCGCACCATC 61.911 55.000 5.73 0.00 0.00 3.51
171 172 1.965930 AACATCACACGCGCACCAT 60.966 52.632 5.73 0.00 0.00 3.55
172 173 2.590291 AACATCACACGCGCACCA 60.590 55.556 5.73 0.00 0.00 4.17
173 174 2.127270 CAACATCACACGCGCACC 60.127 61.111 5.73 0.00 0.00 5.01
174 175 0.991770 GAACAACATCACACGCGCAC 60.992 55.000 5.73 0.00 0.00 5.34
175 176 1.157257 AGAACAACATCACACGCGCA 61.157 50.000 5.73 0.00 0.00 6.09
176 177 0.451135 GAGAACAACATCACACGCGC 60.451 55.000 5.73 0.00 0.00 6.86
177 178 1.139989 AGAGAACAACATCACACGCG 58.860 50.000 3.53 3.53 0.00 6.01
178 179 3.248602 AGAAAGAGAACAACATCACACGC 59.751 43.478 0.00 0.00 0.00 5.34
179 180 4.747108 AGAGAAAGAGAACAACATCACACG 59.253 41.667 0.00 0.00 0.00 4.49
181 182 5.070981 AGGAGAGAAAGAGAACAACATCACA 59.929 40.000 0.00 0.00 0.00 3.58
185 186 4.282195 ACGAGGAGAGAAAGAGAACAACAT 59.718 41.667 0.00 0.00 0.00 2.71
186 187 3.637229 ACGAGGAGAGAAAGAGAACAACA 59.363 43.478 0.00 0.00 0.00 3.33
187 188 4.245845 ACGAGGAGAGAAAGAGAACAAC 57.754 45.455 0.00 0.00 0.00 3.32
188 189 4.217983 GGTACGAGGAGAGAAAGAGAACAA 59.782 45.833 0.00 0.00 0.00 2.83
199 3371 2.060050 AGTGATGGGTACGAGGAGAG 57.940 55.000 0.00 0.00 0.00 3.20
207 3379 4.324267 AGCAACAACTAAGTGATGGGTAC 58.676 43.478 0.00 0.00 0.00 3.34
229 3401 7.477144 AATATATTTGAGACAATGCGACGAA 57.523 32.000 0.00 0.00 0.00 3.85
251 3423 9.336171 ACATAAAAATACAACCAACTTGCAAAT 57.664 25.926 0.00 0.00 32.41 2.32
276 3451 7.928706 ACCTTATCATCTTGTAGCAGTGAATAC 59.071 37.037 0.00 0.00 0.00 1.89
353 3531 2.964464 TGCCATTGTCAACATTTCAGGT 59.036 40.909 0.00 0.00 0.00 4.00
371 3549 2.348872 CGTGCATATTCGAGATGTTGCC 60.349 50.000 10.15 1.17 0.00 4.52
385 3563 1.803555 CCACACACATTCACGTGCATA 59.196 47.619 11.67 0.00 40.73 3.14
402 3582 1.166531 AAGCTTCTCACGGCAACCAC 61.167 55.000 0.00 0.00 0.00 4.16
403 3583 1.148273 AAGCTTCTCACGGCAACCA 59.852 52.632 0.00 0.00 0.00 3.67
485 3781 4.272018 CCAGATGTCGATTTGGATGAAGTC 59.728 45.833 0.00 0.00 36.14 3.01
486 3782 4.080919 TCCAGATGTCGATTTGGATGAAGT 60.081 41.667 6.18 0.00 37.82 3.01
500 3798 5.391416 GCTTGCTTTCTACTTTCCAGATGTC 60.391 44.000 0.00 0.00 0.00 3.06
508 3806 3.610349 GCACTGGCTTGCTTTCTACTTTC 60.610 47.826 4.63 0.00 39.59 2.62
509 3807 2.294512 GCACTGGCTTGCTTTCTACTTT 59.705 45.455 4.63 0.00 39.59 2.66
510 3808 1.882623 GCACTGGCTTGCTTTCTACTT 59.117 47.619 4.63 0.00 39.59 2.24
511 3809 1.528129 GCACTGGCTTGCTTTCTACT 58.472 50.000 4.63 0.00 39.59 2.57
555 3853 3.561143 ACTCACCACCAGCTCTATCTAG 58.439 50.000 0.00 0.00 0.00 2.43
558 3856 2.362717 GGTACTCACCACCAGCTCTATC 59.637 54.545 0.00 0.00 45.04 2.08
596 3894 7.886970 AGGATGACAATGATCTTCTCAGAAAAA 59.113 33.333 0.00 0.00 37.28 1.94
601 3899 5.672503 ACAGGATGACAATGATCTTCTCAG 58.327 41.667 0.00 0.00 39.69 3.35
612 3910 5.129485 ACGGAAGAATAGACAGGATGACAAT 59.871 40.000 0.00 0.00 39.69 2.71
638 3936 1.086696 CCGCGACAAATGACATTCCT 58.913 50.000 8.23 0.00 0.00 3.36
734 4102 7.533289 TTTAAATGGAGGGAGTACAAAAAGG 57.467 36.000 0.00 0.00 0.00 3.11
735 4103 9.996554 ATTTTTAAATGGAGGGAGTACAAAAAG 57.003 29.630 0.00 0.00 0.00 2.27
740 4148 9.238368 CAAGTATTTTTAAATGGAGGGAGTACA 57.762 33.333 0.00 0.00 0.00 2.90
785 4193 9.290988 TGCATGTAAAGGAAACACTTTCTTATA 57.709 29.630 0.00 0.00 40.82 0.98
786 4194 8.177119 TGCATGTAAAGGAAACACTTTCTTAT 57.823 30.769 0.00 0.00 40.82 1.73
811 4219 3.508845 ACTGGTACTTGTTTGGAGCAT 57.491 42.857 0.00 0.00 0.00 3.79
812 4220 3.389983 AGTACTGGTACTTGTTTGGAGCA 59.610 43.478 7.51 0.00 43.35 4.26
813 4221 4.004196 AGTACTGGTACTTGTTTGGAGC 57.996 45.455 7.51 0.00 43.35 4.70
984 4478 3.820467 TGCTCATGTTGGAAAGAAATCGT 59.180 39.130 0.00 0.00 0.00 3.73
986 4480 4.624452 GCTTGCTCATGTTGGAAAGAAATC 59.376 41.667 7.60 0.00 0.00 2.17
991 4486 1.614903 TGGCTTGCTCATGTTGGAAAG 59.385 47.619 0.00 0.00 0.00 2.62
1026 4530 2.203907 ACCAGCTCAGGCCACTCT 60.204 61.111 5.01 0.00 39.73 3.24
1047 4551 2.125512 GCCTCCTTGATCGTGCGT 60.126 61.111 0.00 0.00 0.00 5.24
1126 4630 2.281140 TCGACGTCTGTTGTCACAAA 57.719 45.000 14.70 0.00 36.11 2.83
1135 4642 1.415374 CGGTTCAAATCGACGTCTGT 58.585 50.000 14.70 0.00 33.50 3.41
1256 4765 6.576662 TTTATTCGGCCAATTAACTGAACA 57.423 33.333 2.24 0.00 34.15 3.18
1308 4821 5.484173 AACAACATTACATAGCACATCCG 57.516 39.130 0.00 0.00 0.00 4.18
1335 4848 9.618890 AATATTACTGATGCTTACAACTCACAT 57.381 29.630 0.00 0.00 0.00 3.21
1436 6512 1.241315 ACCGCGCATATTATTGGCCC 61.241 55.000 8.75 0.00 0.00 5.80
1444 6520 6.985188 ATTAGAAATCATACCGCGCATATT 57.015 33.333 8.75 0.00 0.00 1.28
1451 6527 7.291567 GCTGAACTTATTAGAAATCATACCGC 58.708 38.462 0.00 0.00 0.00 5.68
1452 6528 7.381408 TCGCTGAACTTATTAGAAATCATACCG 59.619 37.037 0.00 0.00 0.00 4.02
1504 8225 2.827921 CCAAAAGATTTGTCCAGGGGAG 59.172 50.000 2.53 0.00 29.39 4.30
1587 9377 2.096248 CTCGACTTCTAACCAGGAGCT 58.904 52.381 0.00 0.00 29.18 4.09
1687 9478 6.827251 TGGATCTCTTCTGAAGAAAATGATGG 59.173 38.462 19.73 7.05 37.02 3.51
1709 9500 9.956640 ATAAAACTCCATTAAATTTGCATTGGA 57.043 25.926 0.00 6.94 0.00 3.53
1782 9574 2.095853 GCTAGCTGCTAAAATCGCAACA 59.904 45.455 11.02 0.00 36.88 3.33
1865 12183 9.566432 CTTAGAGCCTCTTTGATGGTTATTAAT 57.434 33.333 0.00 0.00 0.00 1.40
1883 12201 4.408182 TCAGGAACTTATGCTTAGAGCC 57.592 45.455 0.00 0.00 37.07 4.70
1887 12205 6.478344 GTGTCTGATCAGGAACTTATGCTTAG 59.522 42.308 22.42 0.00 34.60 2.18
1896 12214 3.643320 TGTTGAGTGTCTGATCAGGAACT 59.357 43.478 23.22 23.22 43.88 3.01
1900 12218 5.059161 TCTTTTGTTGAGTGTCTGATCAGG 58.941 41.667 22.42 4.43 0.00 3.86
1903 12221 6.610741 AACTCTTTTGTTGAGTGTCTGATC 57.389 37.500 0.00 0.00 43.16 2.92
1907 12225 6.127026 ACCTCTAACTCTTTTGTTGAGTGTCT 60.127 38.462 0.00 0.00 43.16 3.41
1908 12226 6.049790 ACCTCTAACTCTTTTGTTGAGTGTC 58.950 40.000 0.00 0.00 43.16 3.67
1910 12228 7.434492 TCTACCTCTAACTCTTTTGTTGAGTG 58.566 38.462 0.00 0.00 43.16 3.51
1913 12231 8.019656 ACTTCTACCTCTAACTCTTTTGTTGA 57.980 34.615 0.00 0.00 0.00 3.18
1915 12233 8.483758 TCAACTTCTACCTCTAACTCTTTTGTT 58.516 33.333 0.00 0.00 0.00 2.83
1919 12237 9.549078 CTTTTCAACTTCTACCTCTAACTCTTT 57.451 33.333 0.00 0.00 0.00 2.52
1929 12247 4.808767 AACCCCTTTTCAACTTCTACCT 57.191 40.909 0.00 0.00 0.00 3.08
1968 12286 5.529800 GTTCAAGCAACTAACCTTACAAGGA 59.470 40.000 14.94 0.00 39.07 3.36
1970 12288 5.235616 TCGTTCAAGCAACTAACCTTACAAG 59.764 40.000 0.00 0.00 32.09 3.16
1971 12289 5.117584 TCGTTCAAGCAACTAACCTTACAA 58.882 37.500 0.00 0.00 32.09 2.41
1972 12290 4.695396 TCGTTCAAGCAACTAACCTTACA 58.305 39.130 0.00 0.00 32.09 2.41
1982 12300 6.370593 TGAATAAAGTGATCGTTCAAGCAAC 58.629 36.000 0.00 0.00 32.48 4.17
1984 12302 6.741992 ATGAATAAAGTGATCGTTCAAGCA 57.258 33.333 0.00 0.00 33.12 3.91
1991 12309 5.983118 TGTGCGATATGAATAAAGTGATCGT 59.017 36.000 0.00 0.00 38.67 3.73
1992 12310 6.452244 TGTGCGATATGAATAAAGTGATCG 57.548 37.500 0.00 0.00 39.26 3.69
1999 12317 5.065859 CACCCAGTTGTGCGATATGAATAAA 59.934 40.000 0.00 0.00 0.00 1.40
2004 12322 2.022764 CACCCAGTTGTGCGATATGA 57.977 50.000 0.00 0.00 0.00 2.15
2032 12350 3.057946 GGAGTTGTGGAAACATTCAGCTC 60.058 47.826 0.00 0.00 46.14 4.09
2034 12352 2.622942 TGGAGTTGTGGAAACATTCAGC 59.377 45.455 0.00 0.00 46.14 4.26
2036 12354 3.625853 TGTGGAGTTGTGGAAACATTCA 58.374 40.909 0.00 0.00 46.14 2.57
2042 12360 6.549364 ACTTGATTATTGTGGAGTTGTGGAAA 59.451 34.615 0.00 0.00 0.00 3.13
2044 12362 5.473162 CACTTGATTATTGTGGAGTTGTGGA 59.527 40.000 0.00 0.00 0.00 4.02
2045 12363 5.702865 CACTTGATTATTGTGGAGTTGTGG 58.297 41.667 0.00 0.00 0.00 4.17
2047 12365 4.826733 TGCACTTGATTATTGTGGAGTTGT 59.173 37.500 0.00 0.00 32.85 3.32
2099 12418 8.539544 CCTGGTTCAATCCCTTAAAAATAATGT 58.460 33.333 0.00 0.00 0.00 2.71
2100 12419 8.539544 ACCTGGTTCAATCCCTTAAAAATAATG 58.460 33.333 0.00 0.00 0.00 1.90
2101 12420 8.679344 ACCTGGTTCAATCCCTTAAAAATAAT 57.321 30.769 0.00 0.00 0.00 1.28
2102 12421 9.603189 TTACCTGGTTCAATCCCTTAAAAATAA 57.397 29.630 3.84 0.00 0.00 1.40
2103 12422 9.027202 GTTACCTGGTTCAATCCCTTAAAAATA 57.973 33.333 3.84 0.00 0.00 1.40
2104 12423 7.038587 GGTTACCTGGTTCAATCCCTTAAAAAT 60.039 37.037 3.84 0.00 0.00 1.82
2109 12430 3.917629 TGGTTACCTGGTTCAATCCCTTA 59.082 43.478 3.84 0.00 0.00 2.69
2124 12445 3.457012 TGCTACTTAATCCCCTGGTTACC 59.543 47.826 0.00 0.00 0.00 2.85
2144 12465 2.128771 TGAGTCTGGCCCTTATTTGC 57.871 50.000 0.00 0.00 0.00 3.68
2153 12478 2.424956 GTCATGGAAATTGAGTCTGGCC 59.575 50.000 0.00 0.00 0.00 5.36
2154 12479 3.084039 TGTCATGGAAATTGAGTCTGGC 58.916 45.455 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.