Multiple sequence alignment - TraesCS2A01G055500

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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 TraesCS2A01G055500 chr2A 100.000 2576 0 0 1 2576 23863472 23866047 0.000000e+00 4758.0
1 TraesCS2A01G055500 chr2A 90.060 1006 72 18 896 1901 23826149 23827126 0.000000e+00 1279.0
2 TraesCS2A01G055500 chr2A 87.240 384 30 11 2208 2576 23827305 23827684 1.100000e-113 420.0
3 TraesCS2A01G055500 chr2A 90.041 241 17 4 1984 2217 23827128 23827368 3.220000e-79 305.0
4 TraesCS2A01G055500 chr2A 82.727 330 33 16 521 828 23825491 23825818 3.270000e-69 272.0
5 TraesCS2A01G055500 chr2A 98.305 59 1 0 2208 2266 23865626 23865684 1.260000e-18 104.0
6 TraesCS2A01G055500 chr2D 90.638 1709 117 21 539 2213 21742754 21744453 0.000000e+00 2230.0
7 TraesCS2A01G055500 chr2D 90.451 1707 120 23 539 2213 21770489 21772184 0.000000e+00 2209.0
8 TraesCS2A01G055500 chr2D 88.807 1635 114 21 604 2212 21617163 21618754 0.000000e+00 1941.0
9 TraesCS2A01G055500 chr2D 91.086 1436 100 15 789 2213 21639694 21641112 0.000000e+00 1917.0
10 TraesCS2A01G055500 chr2D 90.362 1380 104 15 843 2213 21662152 21663511 0.000000e+00 1784.0
11 TraesCS2A01G055500 chr2D 90.362 1380 104 15 843 2213 21678567 21679926 0.000000e+00 1784.0
12 TraesCS2A01G055500 chr2D 88.204 373 39 5 2208 2576 21618696 21619067 8.460000e-120 440.0
13 TraesCS2A01G055500 chr2D 87.406 397 21 15 2208 2576 21641054 21641449 1.830000e-116 429.0
14 TraesCS2A01G055500 chr2D 87.406 397 21 15 2208 2576 21663453 21663848 1.830000e-116 429.0
15 TraesCS2A01G055500 chr2D 87.406 397 21 15 2208 2576 21679868 21680263 1.830000e-116 429.0
16 TraesCS2A01G055500 chr2D 86.787 333 30 5 177 496 21659396 21659727 2.440000e-95 359.0
17 TraesCS2A01G055500 chr2D 86.787 333 30 5 177 496 21675800 21676131 2.440000e-95 359.0
18 TraesCS2A01G055500 chr2D 86.567 335 31 5 175 496 21633412 21633745 8.770000e-95 357.0
19 TraesCS2A01G055500 chr2D 88.276 290 18 6 2208 2496 21744395 21744669 1.480000e-87 333.0
20 TraesCS2A01G055500 chr2D 88.276 290 18 6 2208 2496 21772126 21772400 1.480000e-87 333.0
21 TraesCS2A01G055500 chr2D 88.652 282 19 4 175 444 21736790 21737070 5.310000e-87 331.0
22 TraesCS2A01G055500 chr2D 88.652 282 19 4 175 444 21763688 21763968 5.310000e-87 331.0
23 TraesCS2A01G055500 chr2D 89.730 185 11 5 1 177 21631609 21631793 1.990000e-56 230.0
24 TraesCS2A01G055500 chr2D 90.055 181 9 4 1 174 21615019 21615197 2.580000e-55 226.0
25 TraesCS2A01G055500 chr2D 88.043 184 13 6 2 177 21657354 21657536 2.600000e-50 209.0
26 TraesCS2A01G055500 chr2D 88.043 184 13 6 2 177 21673768 21673950 2.600000e-50 209.0
27 TraesCS2A01G055500 chr2D 93.878 98 6 0 521 618 21661843 21661940 5.740000e-32 148.0
28 TraesCS2A01G055500 chr2D 93.878 98 6 0 521 618 21678258 21678355 5.740000e-32 148.0
29 TraesCS2A01G055500 chr2D 80.097 206 20 8 605 807 21661959 21662146 1.610000e-27 134.0
30 TraesCS2A01G055500 chr2D 79.612 206 21 8 605 807 21678374 21678561 7.480000e-26 128.0
31 TraesCS2A01G055500 chr2B 92.802 1306 77 10 782 2077 34867204 34865906 0.000000e+00 1875.0
32 TraesCS2A01G055500 chr2B 91.056 1174 93 9 1048 2212 34954100 34952930 0.000000e+00 1576.0
33 TraesCS2A01G055500 chr2B 88.657 335 24 4 175 496 35012578 35012245 1.860000e-106 396.0
34 TraesCS2A01G055500 chr2B 91.848 184 14 1 2393 2576 34952843 34952661 3.290000e-64 255.0
35 TraesCS2A01G055500 chr2B 88.636 176 14 3 2 173 34868386 34868213 2.600000e-50 209.0
36 TraesCS2A01G055500 chr2B 90.850 153 12 2 2208 2359 34952987 34952836 1.210000e-48 204.0
37 TraesCS2A01G055500 chr2B 93.204 103 7 0 2111 2213 34865905 34865803 4.440000e-33 152.0
38 TraesCS2A01G055500 chrUn 84.715 386 34 10 607 985 477929003 477928636 1.880000e-96 363.0
39 TraesCS2A01G055500 chrUn 92.500 40 2 1 683 722 97304693 97304731 3.580000e-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 TraesCS2A01G055500 chr2A 23863472 23866047 2575 False 2431.000000 4758 99.152500 1 2576 2 chr2A.!!$F2 2575
1 TraesCS2A01G055500 chr2A 23825491 23827684 2193 False 569.000000 1279 87.517000 521 2576 4 chr2A.!!$F1 2055
2 TraesCS2A01G055500 chr2D 21742754 21744669 1915 False 1281.500000 2230 89.457000 539 2496 2 chr2D.!!$F8 1957
3 TraesCS2A01G055500 chr2D 21770489 21772400 1911 False 1271.000000 2209 89.363500 539 2496 2 chr2D.!!$F9 1957
4 TraesCS2A01G055500 chr2D 21639694 21641449 1755 False 1173.000000 1917 89.246000 789 2576 2 chr2D.!!$F5 1787
5 TraesCS2A01G055500 chr2D 21615019 21619067 4048 False 869.000000 1941 89.022000 1 2576 3 chr2D.!!$F3 2575
6 TraesCS2A01G055500 chr2D 21657354 21663848 6494 False 510.500000 1784 87.762167 2 2576 6 chr2D.!!$F6 2574
7 TraesCS2A01G055500 chr2D 21673768 21680263 6495 False 509.500000 1784 87.681333 2 2576 6 chr2D.!!$F7 2574
8 TraesCS2A01G055500 chr2D 21631609 21633745 2136 False 293.500000 357 88.148500 1 496 2 chr2D.!!$F4 495
9 TraesCS2A01G055500 chr2B 34865803 34868386 2583 True 745.333333 1875 91.547333 2 2213 3 chr2B.!!$R2 2211
10 TraesCS2A01G055500 chr2B 34952661 34954100 1439 True 678.333333 1576 91.251333 1048 2576 3 chr2B.!!$R3 1528

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
164 173 0.666274 CGAGTCGCTGCACCAAGTTA 60.666 55.000 0.00 0.0 0.00 2.24 F
212 2094 1.063469 CCGTCCCATATTGTTTGACGC 59.937 52.381 4.94 0.0 45.37 5.19 F
1290 6207 0.980423 AGGAGAAGCAGGAGTGGAAC 59.020 55.000 0.00 0.0 0.00 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1269 6186 0.115152 TCCACTCCTGCTTCTCCTCA 59.885 55.0 0.00 0.0 0.00 3.86 R
1369 6286 1.006832 ACATCGCTGAACGCCATTAC 58.993 50.0 0.00 0.0 43.23 1.89 R
2241 7174 0.411452 AGGAGAGAACTCTGGAGGCA 59.589 55.0 9.16 0.0 40.61 4.75 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
92 94 2.599082 CGTATTGTGAGAGGTCGCTTTC 59.401 50.000 0.00 0.00 34.00 2.62
96 98 4.330944 TTGTGAGAGGTCGCTTTCTTTA 57.669 40.909 0.00 0.00 34.00 1.85
137 140 1.931841 CTCTCTTGTCATGACCATGCG 59.068 52.381 22.85 8.18 38.65 4.73
164 173 0.666274 CGAGTCGCTGCACCAAGTTA 60.666 55.000 0.00 0.00 0.00 2.24
212 2094 1.063469 CCGTCCCATATTGTTTGACGC 59.937 52.381 4.94 0.00 45.37 5.19
239 2123 4.993028 ACAGATGTCTAGATACTCCCTCC 58.007 47.826 0.00 0.00 0.00 4.30
241 2125 3.653836 AGATGTCTAGATACTCCCTCCGT 59.346 47.826 0.00 0.00 0.00 4.69
243 2127 2.106166 TGTCTAGATACTCCCTCCGTCC 59.894 54.545 0.00 0.00 0.00 4.79
244 2128 2.372837 GTCTAGATACTCCCTCCGTCCT 59.627 54.545 0.00 0.00 0.00 3.85
254 2138 9.638176 GATACTCCCTCCGTCCTATATTATTTA 57.362 37.037 0.00 0.00 0.00 1.40
257 2141 7.179872 ACTCCCTCCGTCCTATATTATTTAACC 59.820 40.741 0.00 0.00 0.00 2.85
280 2164 5.473931 CCTCAAACAGATGGATATAGACCG 58.526 45.833 0.00 0.00 0.00 4.79
282 2166 3.577649 AACAGATGGATATAGACCGCG 57.422 47.619 0.00 0.00 0.00 6.46
290 2174 7.921214 CAGATGGATATAGACCGCGTATTATTT 59.079 37.037 4.92 0.00 0.00 1.40
324 2218 4.083643 CGAACGTAGATACATCCCACGTAT 60.084 45.833 15.71 9.19 43.60 3.06
356 2250 7.867305 TGTTTCATTGTGTACCAGTAAAAGA 57.133 32.000 0.00 0.00 0.00 2.52
357 2251 8.282455 TGTTTCATTGTGTACCAGTAAAAGAA 57.718 30.769 0.00 0.00 0.00 2.52
358 2252 8.402472 TGTTTCATTGTGTACCAGTAAAAGAAG 58.598 33.333 0.00 0.00 0.00 2.85
359 2253 8.617809 GTTTCATTGTGTACCAGTAAAAGAAGA 58.382 33.333 0.00 0.00 0.00 2.87
360 2254 7.962964 TCATTGTGTACCAGTAAAAGAAGAG 57.037 36.000 0.00 0.00 0.00 2.85
361 2255 7.506114 TCATTGTGTACCAGTAAAAGAAGAGT 58.494 34.615 0.00 0.00 0.00 3.24
362 2256 7.441157 TCATTGTGTACCAGTAAAAGAAGAGTG 59.559 37.037 0.00 0.00 0.00 3.51
363 2257 5.054477 TGTGTACCAGTAAAAGAAGAGTGC 58.946 41.667 0.00 0.00 0.00 4.40
364 2258 4.150098 GTGTACCAGTAAAAGAAGAGTGCG 59.850 45.833 0.00 0.00 0.00 5.34
426 2320 4.563184 GCGTGTCTCAAGGTGTATCTTAAG 59.437 45.833 0.00 0.00 0.00 1.85
446 2340 9.607988 TCTTAAGGCTTCGAAATATATGAACAA 57.392 29.630 1.30 0.00 0.00 2.83
470 2364 2.061773 CTGAACGCACGAATCTCAACT 58.938 47.619 0.00 0.00 0.00 3.16
474 2368 2.329379 ACGCACGAATCTCAACTCTTC 58.671 47.619 0.00 0.00 0.00 2.87
482 2376 4.491602 CGAATCTCAACTCTTCGTCAATGC 60.492 45.833 0.00 0.00 37.56 3.56
483 2377 3.385193 TCTCAACTCTTCGTCAATGCA 57.615 42.857 0.00 0.00 0.00 3.96
493 2387 6.818644 ACTCTTCGTCAATGCACACTTTATAT 59.181 34.615 0.00 0.00 0.00 0.86
494 2388 7.003939 TCTTCGTCAATGCACACTTTATATG 57.996 36.000 0.00 0.00 0.00 1.78
497 2391 4.335315 CGTCAATGCACACTTTATATGGGT 59.665 41.667 0.00 0.00 0.00 4.51
498 2392 5.525745 CGTCAATGCACACTTTATATGGGTA 59.474 40.000 0.00 0.00 0.00 3.69
499 2393 6.511121 CGTCAATGCACACTTTATATGGGTAC 60.511 42.308 0.00 0.00 0.00 3.34
546 4544 7.218204 CCAATGAAATTAACGTGCTAGCTTAAC 59.782 37.037 17.23 4.86 32.46 2.01
618 5218 8.043710 CACCTATCTAGAGAGTTCAAACCAATT 58.956 37.037 13.18 0.00 0.00 2.32
667 5306 8.893219 ATACATTATTAGCATATCCCATGTCG 57.107 34.615 0.00 0.00 0.00 4.35
668 5307 5.586243 ACATTATTAGCATATCCCATGTCGC 59.414 40.000 0.00 0.00 0.00 5.19
669 5308 3.988976 ATTAGCATATCCCATGTCGCT 57.011 42.857 0.00 0.00 0.00 4.93
670 5309 3.319137 TTAGCATATCCCATGTCGCTC 57.681 47.619 0.00 0.00 0.00 5.03
671 5310 1.346062 AGCATATCCCATGTCGCTCT 58.654 50.000 0.00 0.00 0.00 4.09
672 5311 2.529632 AGCATATCCCATGTCGCTCTA 58.470 47.619 0.00 0.00 0.00 2.43
686 5325 5.656480 TGTCGCTCTATAGTGTGCAATTAA 58.344 37.500 9.92 0.00 34.68 1.40
699 5338 5.788531 GTGTGCAATTAACGAGACATTGTAC 59.211 40.000 12.11 12.11 41.35 2.90
721 5360 8.884726 TGTACATTAATTTATTTAGCGAGCACA 58.115 29.630 0.00 0.00 0.00 4.57
787 5428 5.240844 GCATGTGTACCTAACTTGGACTTTT 59.759 40.000 0.00 0.00 0.00 2.27
798 5439 5.324784 ACTTGGACTTTTGACTTTGGAAC 57.675 39.130 0.00 0.00 0.00 3.62
834 5476 7.962918 CGGATTAATTGCCTATATAACTGCAAC 59.037 37.037 13.25 4.37 45.44 4.17
859 5501 1.135083 ACATTCCTTAGGACACGAGCG 60.135 52.381 0.00 0.00 0.00 5.03
884 5783 1.914051 CTGATCAAGCACAGACGTACG 59.086 52.381 15.01 15.01 36.38 3.67
889 5788 1.976728 CAAGCACAGACGTACGTACAG 59.023 52.381 22.87 15.97 0.00 2.74
908 5825 4.070716 ACAGTGGCATCTTCTTCTTCTTG 58.929 43.478 0.00 0.00 0.00 3.02
910 5827 4.153835 CAGTGGCATCTTCTTCTTCTTGTC 59.846 45.833 0.00 0.00 0.00 3.18
913 5830 2.095053 GCATCTTCTTCTTCTTGTCGGC 59.905 50.000 0.00 0.00 0.00 5.54
968 5885 3.775202 ACAACGATGACAGTGAGATAGC 58.225 45.455 0.00 0.00 0.00 2.97
969 5886 3.445450 ACAACGATGACAGTGAGATAGCT 59.555 43.478 0.00 0.00 0.00 3.32
977 5894 1.678627 CAGTGAGATAGCTGCTACCGT 59.321 52.381 12.26 0.00 0.00 4.83
1026 5943 2.027073 GGTCATGTCAAGCGTCGCA 61.027 57.895 21.09 0.00 0.00 5.10
1050 5967 4.792804 GCTCAGCTCCTGCCCACC 62.793 72.222 0.00 0.00 40.80 4.61
1096 6013 1.682344 GCCCCATCCTTCACCAACC 60.682 63.158 0.00 0.00 0.00 3.77
1145 6062 4.690719 TACCACGGCGCTGGTTGG 62.691 66.667 29.34 22.68 42.29 3.77
1157 6074 2.397413 CTGGTTGGTGTCCTCGCCTT 62.397 60.000 0.00 0.00 43.94 4.35
1183 6100 1.625818 GCCTCTTCTTCTCCTTCACCA 59.374 52.381 0.00 0.00 0.00 4.17
1269 6186 2.417719 GTGTTCAACTTCTCCAGCGAT 58.582 47.619 0.00 0.00 0.00 4.58
1290 6207 0.980423 AGGAGAAGCAGGAGTGGAAC 59.020 55.000 0.00 0.00 0.00 3.62
1338 6255 3.867771 CAGCTGCTGGACTTCGTC 58.132 61.111 21.71 0.00 0.00 4.20
1369 6286 3.419759 CGGCGGTGGTTTTCCTCG 61.420 66.667 0.00 0.00 41.38 4.63
1401 6318 1.213537 CGATGTGGGGCTGCAAAAG 59.786 57.895 0.50 0.00 0.00 2.27
1420 6337 2.897350 GCTTCTTCCCGGATGGCG 60.897 66.667 0.73 0.00 0.00 5.69
1440 6357 1.593196 GCAGGAACACACAACAGCTA 58.407 50.000 0.00 0.00 0.00 3.32
1578 6496 5.697633 CCATCCCTTGAACAAAGTTTGATTG 59.302 40.000 22.23 3.87 33.66 2.67
1586 6504 7.236674 TGAACAAAGTTTGATTGCAAGAATG 57.763 32.000 22.23 0.00 35.04 2.67
1750 6668 2.078849 TTCGCTCCATAGTGTGTGTG 57.921 50.000 0.00 0.00 34.68 3.82
1818 6740 6.417258 TGCATGAATTCACTATTCTCTTCCA 58.583 36.000 11.07 0.00 42.63 3.53
1822 6744 9.605275 CATGAATTCACTATTCTCTTCCAGTAA 57.395 33.333 11.07 0.00 42.63 2.24
1827 6749 7.718334 TCACTATTCTCTTCCAGTAACATCA 57.282 36.000 0.00 0.00 0.00 3.07
2109 7041 1.765314 CATCCCAACCTCCTAGGACTG 59.235 57.143 7.62 4.60 37.67 3.51
2131 7063 4.756642 TGTCACAGTCATCCATTCACTTTC 59.243 41.667 0.00 0.00 0.00 2.62
2213 7146 6.440647 TGCCTCAAGAGTTCTCTCCTATTTTA 59.559 38.462 2.69 0.00 41.26 1.52
2214 7147 6.759356 GCCTCAAGAGTTCTCTCCTATTTTAC 59.241 42.308 2.69 0.00 41.26 2.01
2215 7148 7.579723 GCCTCAAGAGTTCTCTCCTATTTTACA 60.580 40.741 2.69 0.00 41.26 2.41
2216 7149 8.314751 CCTCAAGAGTTCTCTCCTATTTTACAA 58.685 37.037 2.69 0.00 41.26 2.41
2217 7150 9.712305 CTCAAGAGTTCTCTCCTATTTTACAAA 57.288 33.333 2.69 0.00 41.26 2.83
2237 7170 9.605275 TTACAAAAATGTCATGAACAAAATCCA 57.395 25.926 0.00 0.00 42.37 3.41
2238 7171 8.145316 ACAAAAATGTCATGAACAAAATCCAG 57.855 30.769 0.00 0.00 42.37 3.86
2239 7172 7.769970 ACAAAAATGTCATGAACAAAATCCAGT 59.230 29.630 0.00 0.00 42.37 4.00
2240 7173 8.614346 CAAAAATGTCATGAACAAAATCCAGTT 58.386 29.630 0.00 0.00 42.37 3.16
2241 7174 8.735692 AAAATGTCATGAACAAAATCCAGTTT 57.264 26.923 0.00 0.00 42.37 2.66
2242 7175 7.718272 AATGTCATGAACAAAATCCAGTTTG 57.282 32.000 0.00 0.00 42.37 2.93
2243 7176 5.049167 TGTCATGAACAAAATCCAGTTTGC 58.951 37.500 0.00 0.00 41.33 3.68
2244 7177 4.448732 GTCATGAACAAAATCCAGTTTGCC 59.551 41.667 0.00 0.00 41.33 4.52
2245 7178 4.344679 TCATGAACAAAATCCAGTTTGCCT 59.655 37.500 0.00 0.00 41.33 4.75
2246 7179 4.320608 TGAACAAAATCCAGTTTGCCTC 57.679 40.909 0.00 0.00 41.33 4.70
2247 7180 3.069443 TGAACAAAATCCAGTTTGCCTCC 59.931 43.478 0.00 0.00 41.33 4.30
2248 7181 2.676748 ACAAAATCCAGTTTGCCTCCA 58.323 42.857 0.00 0.00 41.33 3.86
2249 7182 2.629617 ACAAAATCCAGTTTGCCTCCAG 59.370 45.455 0.00 0.00 41.33 3.86
2250 7183 2.892852 CAAAATCCAGTTTGCCTCCAGA 59.107 45.455 0.00 0.00 32.10 3.86
2251 7184 2.503895 AATCCAGTTTGCCTCCAGAG 57.496 50.000 0.00 0.00 0.00 3.35
2252 7185 1.366319 ATCCAGTTTGCCTCCAGAGT 58.634 50.000 0.00 0.00 0.00 3.24
2253 7186 1.140312 TCCAGTTTGCCTCCAGAGTT 58.860 50.000 0.00 0.00 0.00 3.01
2254 7187 1.072331 TCCAGTTTGCCTCCAGAGTTC 59.928 52.381 0.00 0.00 0.00 3.01
2255 7188 1.072965 CCAGTTTGCCTCCAGAGTTCT 59.927 52.381 0.00 0.00 0.00 3.01
2256 7189 2.421619 CAGTTTGCCTCCAGAGTTCTC 58.578 52.381 0.00 0.00 0.00 2.87
2257 7190 2.038295 CAGTTTGCCTCCAGAGTTCTCT 59.962 50.000 0.00 0.00 0.00 3.10
2258 7191 2.301583 AGTTTGCCTCCAGAGTTCTCTC 59.698 50.000 0.00 0.00 40.70 3.20
2259 7192 1.270907 TTGCCTCCAGAGTTCTCTCC 58.729 55.000 0.00 0.00 41.26 3.71
2260 7193 0.411452 TGCCTCCAGAGTTCTCTCCT 59.589 55.000 0.00 0.00 41.26 3.69
2261 7194 1.641192 TGCCTCCAGAGTTCTCTCCTA 59.359 52.381 0.00 0.00 41.26 2.94
2262 7195 2.246067 TGCCTCCAGAGTTCTCTCCTAT 59.754 50.000 0.00 0.00 41.26 2.57
2304 7238 5.531122 TTCTTACCCCTCTTCATCATACG 57.469 43.478 0.00 0.00 0.00 3.06
2305 7239 4.543689 TCTTACCCCTCTTCATCATACGT 58.456 43.478 0.00 0.00 0.00 3.57
2463 7429 2.485903 TGTTCCGCTCGTGTAAAACAT 58.514 42.857 0.00 0.00 0.00 2.71
2519 7485 2.414612 ACAACCAACCTCCAACCTCTA 58.585 47.619 0.00 0.00 0.00 2.43
2545 7512 4.210331 GCATGGTTAGGAGAATGGATGTT 58.790 43.478 0.00 0.00 0.00 2.71
2553 7520 2.024941 GGAGAATGGATGTTCCCCAACT 60.025 50.000 0.00 0.00 37.22 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 50 1.648467 GGCTGTTCGACAAGGCATCC 61.648 60.000 13.48 0.00 0.00 3.51
92 94 3.369756 ACGTATGCATTGACACGGTAAAG 59.630 43.478 20.43 0.00 38.67 1.85
96 98 1.067142 AGACGTATGCATTGACACGGT 60.067 47.619 20.43 8.88 38.67 4.83
137 140 3.084579 CAGCGACTCGTGCCAATC 58.915 61.111 0.00 0.00 0.00 2.67
150 159 2.546368 TGTAAAGTAACTTGGTGCAGCG 59.454 45.455 11.91 0.00 0.00 5.18
164 173 7.041848 GGGTGTAACAAACTTCGTATGTAAAGT 60.042 37.037 0.00 0.00 39.98 2.66
187 2069 1.591768 AACAATATGGGACGGAGGGT 58.408 50.000 0.00 0.00 0.00 4.34
212 2094 6.549364 AGGGAGTATCTAGACATCTGTTTGAG 59.451 42.308 0.00 0.00 33.73 3.02
219 2101 3.653836 ACGGAGGGAGTATCTAGACATCT 59.346 47.826 0.00 0.00 33.73 2.90
239 2123 9.550406 TGTTTGAGGGTTAAATAATATAGGACG 57.450 33.333 0.00 0.00 0.00 4.79
254 2138 6.183361 GGTCTATATCCATCTGTTTGAGGGTT 60.183 42.308 0.00 0.00 46.03 4.11
257 2141 5.473931 CGGTCTATATCCATCTGTTTGAGG 58.526 45.833 0.00 0.00 0.00 3.86
282 2166 5.443763 CGTTCGTTTGAGCGTCAAATAATAC 59.556 40.000 13.63 9.91 46.55 1.89
301 2185 2.032550 ACGTGGGATGTATCTACGTTCG 59.967 50.000 16.20 0.00 42.82 3.95
356 2250 2.088674 AACCTGACGAGCGCACTCTT 62.089 55.000 11.47 0.00 41.09 2.85
357 2251 2.088674 AAACCTGACGAGCGCACTCT 62.089 55.000 11.47 0.00 41.09 3.24
358 2252 1.222115 AAAACCTGACGAGCGCACTC 61.222 55.000 11.47 3.71 39.75 3.51
359 2253 0.814010 AAAAACCTGACGAGCGCACT 60.814 50.000 11.47 0.00 0.00 4.40
360 2254 0.863144 TAAAAACCTGACGAGCGCAC 59.137 50.000 11.47 0.96 0.00 5.34
361 2255 0.863144 GTAAAAACCTGACGAGCGCA 59.137 50.000 11.47 0.00 0.00 6.09
362 2256 1.145803 AGTAAAAACCTGACGAGCGC 58.854 50.000 0.00 0.00 0.00 5.92
363 2257 3.181533 GCTTAGTAAAAACCTGACGAGCG 60.182 47.826 0.00 0.00 0.00 5.03
364 2258 3.995048 AGCTTAGTAAAAACCTGACGAGC 59.005 43.478 0.00 0.00 0.00 5.03
426 2320 9.173939 CAGATTTTGTTCATATATTTCGAAGCC 57.826 33.333 0.00 0.00 0.00 4.35
444 2338 4.070581 AGATTCGTGCGTTCAGATTTTG 57.929 40.909 0.00 0.00 0.00 2.44
446 2340 3.325870 TGAGATTCGTGCGTTCAGATTT 58.674 40.909 0.00 0.00 0.00 2.17
448 2342 2.654749 TGAGATTCGTGCGTTCAGAT 57.345 45.000 0.00 0.00 0.00 2.90
470 2364 6.037062 CCATATAAAGTGTGCATTGACGAAGA 59.963 38.462 0.00 0.00 0.00 2.87
474 2368 4.335315 ACCCATATAAAGTGTGCATTGACG 59.665 41.667 0.00 0.00 0.00 4.35
480 2374 4.846168 TGGTACCCATATAAAGTGTGCA 57.154 40.909 10.07 0.00 0.00 4.57
482 2376 7.873719 TTCATTGGTACCCATATAAAGTGTG 57.126 36.000 10.07 0.00 31.53 3.82
483 2377 8.887264 TTTTCATTGGTACCCATATAAAGTGT 57.113 30.769 10.07 0.00 31.53 3.55
515 4513 7.010738 GCTAGCACGTTAATTTCATTGGTACTA 59.989 37.037 10.63 0.00 0.00 1.82
516 4514 6.183360 GCTAGCACGTTAATTTCATTGGTACT 60.183 38.462 10.63 0.00 0.00 2.73
517 4515 5.963586 GCTAGCACGTTAATTTCATTGGTAC 59.036 40.000 10.63 0.00 0.00 3.34
518 4516 5.878116 AGCTAGCACGTTAATTTCATTGGTA 59.122 36.000 18.83 0.00 0.00 3.25
519 4517 4.700213 AGCTAGCACGTTAATTTCATTGGT 59.300 37.500 18.83 0.00 0.00 3.67
659 5298 2.864097 GCACACTATAGAGCGACATGGG 60.864 54.545 6.78 0.00 0.00 4.00
661 5300 3.084070 TGCACACTATAGAGCGACATG 57.916 47.619 6.78 0.00 0.00 3.21
662 5301 3.801114 TTGCACACTATAGAGCGACAT 57.199 42.857 6.78 0.00 0.00 3.06
663 5302 3.801114 ATTGCACACTATAGAGCGACA 57.199 42.857 6.78 0.00 0.00 4.35
664 5303 5.331607 CGTTAATTGCACACTATAGAGCGAC 60.332 44.000 6.78 0.00 0.00 5.19
665 5304 4.738252 CGTTAATTGCACACTATAGAGCGA 59.262 41.667 6.78 7.74 0.00 4.93
666 5305 4.738252 TCGTTAATTGCACACTATAGAGCG 59.262 41.667 6.78 0.00 0.00 5.03
667 5306 5.977725 TCTCGTTAATTGCACACTATAGAGC 59.022 40.000 6.78 8.06 0.00 4.09
668 5307 6.972901 TGTCTCGTTAATTGCACACTATAGAG 59.027 38.462 6.78 0.31 0.00 2.43
669 5308 6.859017 TGTCTCGTTAATTGCACACTATAGA 58.141 36.000 6.78 0.00 0.00 1.98
670 5309 7.700322 ATGTCTCGTTAATTGCACACTATAG 57.300 36.000 0.00 0.00 0.00 1.31
671 5310 7.547722 ACAATGTCTCGTTAATTGCACACTATA 59.452 33.333 0.00 0.00 35.20 1.31
672 5311 6.371548 ACAATGTCTCGTTAATTGCACACTAT 59.628 34.615 0.00 0.00 35.20 2.12
699 5338 7.910162 AGTGTGTGCTCGCTAAATAAATTAATG 59.090 33.333 0.56 0.00 0.00 1.90
776 5417 4.159693 GGTTCCAAAGTCAAAAGTCCAAGT 59.840 41.667 0.00 0.00 0.00 3.16
787 5428 0.109532 TGCGGATGGTTCCAAAGTCA 59.890 50.000 0.00 0.00 42.74 3.41
807 5448 6.093495 TGCAGTTATATAGGCAATTAATCCGC 59.907 38.462 4.04 2.00 32.54 5.54
834 5476 4.566004 TCGTGTCCTAAGGAATGTTCAAG 58.434 43.478 0.00 0.00 31.38 3.02
859 5501 1.751927 CTGTGCTTGATCAGGGGGC 60.752 63.158 6.99 6.10 0.00 5.80
884 5783 4.826556 AGAAGAAGAAGATGCCACTGTAC 58.173 43.478 0.00 0.00 0.00 2.90
889 5788 3.124297 CGACAAGAAGAAGAAGATGCCAC 59.876 47.826 0.00 0.00 0.00 5.01
913 5830 0.680921 ATCTGGTTTGCCGTGGATGG 60.681 55.000 0.00 0.00 37.67 3.51
924 5841 6.496565 TGTTGATTGGTGGAATTATCTGGTTT 59.503 34.615 0.00 0.00 0.00 3.27
1026 5943 0.892814 GCAGGAGCTGAGCAAGGTTT 60.893 55.000 7.39 0.00 36.52 3.27
1050 5967 2.125713 TATGTCAGCACCGTGCCG 60.126 61.111 19.96 10.30 46.52 5.69
1083 6000 1.303317 GCCGTGGTTGGTGAAGGAT 60.303 57.895 0.00 0.00 0.00 3.24
1096 6013 3.414700 GGTCTCGCACTTGCCGTG 61.415 66.667 0.00 0.00 46.58 4.94
1145 6062 4.021925 AGGCCAAGGCGAGGACAC 62.022 66.667 5.01 0.00 43.06 3.67
1157 6074 1.557269 GGAGAAGAAGAGGCAGGCCA 61.557 60.000 13.63 0.00 38.92 5.36
1236 6153 0.741574 TGAACACGTTGAAGCCACGT 60.742 50.000 0.00 0.00 41.01 4.49
1269 6186 0.115152 TCCACTCCTGCTTCTCCTCA 59.885 55.000 0.00 0.00 0.00 3.86
1290 6207 2.120232 CTCCGAAATTGGTCGAGATCG 58.880 52.381 1.10 0.00 43.86 3.69
1338 6255 3.423154 GCCGTGAAGAAGGCGTGG 61.423 66.667 0.00 0.00 44.22 4.94
1369 6286 1.006832 ACATCGCTGAACGCCATTAC 58.993 50.000 0.00 0.00 43.23 1.89
1401 6318 2.115291 GCCATCCGGGAAGAAGCAC 61.115 63.158 0.00 0.00 40.01 4.40
1420 6337 1.103398 AGCTGTTGTGTGTTCCTGCC 61.103 55.000 0.00 0.00 0.00 4.85
1440 6357 1.548582 CCCAATGGCAGGTTCTTGAGT 60.549 52.381 0.00 0.00 0.00 3.41
1578 6496 6.919662 TGATCTTTTGTTCTTCACATTCTTGC 59.080 34.615 0.00 0.00 34.43 4.01
1586 6504 6.416161 GCTTTCACTGATCTTTTGTTCTTCAC 59.584 38.462 0.00 0.00 0.00 3.18
1750 6668 1.217001 TGTCTGCAATCGACACACAC 58.783 50.000 3.31 0.00 36.54 3.82
1818 6740 7.041098 GGAAGTTGAACACTCATTGATGTTACT 60.041 37.037 11.77 10.44 39.13 2.24
1822 6744 5.132502 TGGAAGTTGAACACTCATTGATGT 58.867 37.500 0.00 0.00 32.94 3.06
1947 6870 9.838975 CAGTCAAGCAACATTTATTACACATTA 57.161 29.630 0.00 0.00 0.00 1.90
2109 7041 4.999950 AGAAAGTGAATGGATGACTGTGAC 59.000 41.667 0.00 0.00 0.00 3.67
2116 7048 6.409524 AAAGCAAAGAAAGTGAATGGATGA 57.590 33.333 0.00 0.00 0.00 2.92
2177 7110 4.218312 ACTCTTGAGGCAAACTGGATTTT 58.782 39.130 2.55 0.00 0.00 1.82
2213 7146 7.769970 ACTGGATTTTGTTCATGACATTTTTGT 59.230 29.630 0.00 0.00 38.26 2.83
2214 7147 8.145316 ACTGGATTTTGTTCATGACATTTTTG 57.855 30.769 0.00 0.00 38.26 2.44
2215 7148 8.735692 AACTGGATTTTGTTCATGACATTTTT 57.264 26.923 0.00 0.00 38.26 1.94
2216 7149 8.614346 CAAACTGGATTTTGTTCATGACATTTT 58.386 29.630 0.00 0.00 38.26 1.82
2217 7150 7.254863 GCAAACTGGATTTTGTTCATGACATTT 60.255 33.333 0.00 0.00 38.51 2.32
2218 7151 6.203338 GCAAACTGGATTTTGTTCATGACATT 59.797 34.615 0.00 0.00 38.51 2.71
2219 7152 5.697633 GCAAACTGGATTTTGTTCATGACAT 59.302 36.000 0.00 0.00 38.51 3.06
2220 7153 5.049167 GCAAACTGGATTTTGTTCATGACA 58.951 37.500 0.00 0.00 38.51 3.58
2221 7154 4.448732 GGCAAACTGGATTTTGTTCATGAC 59.551 41.667 0.00 0.00 38.51 3.06
2222 7155 4.344679 AGGCAAACTGGATTTTGTTCATGA 59.655 37.500 0.00 0.00 38.51 3.07
2223 7156 4.634199 AGGCAAACTGGATTTTGTTCATG 58.366 39.130 0.00 0.00 38.51 3.07
2224 7157 4.262592 GGAGGCAAACTGGATTTTGTTCAT 60.263 41.667 0.00 0.00 38.51 2.57
2225 7158 3.069443 GGAGGCAAACTGGATTTTGTTCA 59.931 43.478 0.00 0.00 38.51 3.18
2226 7159 3.069443 TGGAGGCAAACTGGATTTTGTTC 59.931 43.478 0.00 0.00 38.51 3.18
2227 7160 3.037549 TGGAGGCAAACTGGATTTTGTT 58.962 40.909 0.00 0.00 38.51 2.83
2228 7161 2.629617 CTGGAGGCAAACTGGATTTTGT 59.370 45.455 0.00 0.00 38.51 2.83
2229 7162 2.892852 TCTGGAGGCAAACTGGATTTTG 59.107 45.455 0.00 0.00 39.15 2.44
2230 7163 3.160269 CTCTGGAGGCAAACTGGATTTT 58.840 45.455 0.00 0.00 0.00 1.82
2231 7164 2.108952 ACTCTGGAGGCAAACTGGATTT 59.891 45.455 2.58 0.00 0.00 2.17
2232 7165 1.707427 ACTCTGGAGGCAAACTGGATT 59.293 47.619 2.58 0.00 0.00 3.01
2233 7166 1.366319 ACTCTGGAGGCAAACTGGAT 58.634 50.000 2.58 0.00 0.00 3.41
2234 7167 1.072331 GAACTCTGGAGGCAAACTGGA 59.928 52.381 2.58 0.00 0.00 3.86
2235 7168 1.072965 AGAACTCTGGAGGCAAACTGG 59.927 52.381 2.58 0.00 0.00 4.00
2236 7169 2.038295 AGAGAACTCTGGAGGCAAACTG 59.962 50.000 3.39 0.00 38.75 3.16
2237 7170 2.301583 GAGAGAACTCTGGAGGCAAACT 59.698 50.000 9.16 0.00 40.61 2.66
2238 7171 2.614229 GGAGAGAACTCTGGAGGCAAAC 60.614 54.545 9.16 0.00 40.61 2.93
2239 7172 1.625818 GGAGAGAACTCTGGAGGCAAA 59.374 52.381 9.16 0.00 40.61 3.68
2240 7173 1.203237 AGGAGAGAACTCTGGAGGCAA 60.203 52.381 9.16 0.00 40.61 4.52
2241 7174 0.411452 AGGAGAGAACTCTGGAGGCA 59.589 55.000 9.16 0.00 40.61 4.75
2242 7175 2.445682 TAGGAGAGAACTCTGGAGGC 57.554 55.000 9.16 0.00 40.61 4.70
2243 7176 5.669477 CAAAATAGGAGAGAACTCTGGAGG 58.331 45.833 9.16 0.00 40.61 4.30
2244 7177 5.115480 GCAAAATAGGAGAGAACTCTGGAG 58.885 45.833 9.16 0.00 40.61 3.86
2245 7178 4.382040 CGCAAAATAGGAGAGAACTCTGGA 60.382 45.833 9.16 0.00 40.61 3.86
2246 7179 3.868077 CGCAAAATAGGAGAGAACTCTGG 59.132 47.826 9.16 0.00 40.61 3.86
2247 7180 4.564769 GTCGCAAAATAGGAGAGAACTCTG 59.435 45.833 9.16 0.00 40.61 3.35
2248 7181 4.220821 TGTCGCAAAATAGGAGAGAACTCT 59.779 41.667 3.87 3.87 43.78 3.24
2249 7182 4.327627 GTGTCGCAAAATAGGAGAGAACTC 59.672 45.833 0.00 0.00 41.94 3.01
2250 7183 4.246458 GTGTCGCAAAATAGGAGAGAACT 58.754 43.478 0.00 0.00 0.00 3.01
2251 7184 3.994392 TGTGTCGCAAAATAGGAGAGAAC 59.006 43.478 0.00 0.00 0.00 3.01
2252 7185 4.265904 TGTGTCGCAAAATAGGAGAGAA 57.734 40.909 0.00 0.00 0.00 2.87
2253 7186 3.953712 TGTGTCGCAAAATAGGAGAGA 57.046 42.857 0.00 0.00 0.00 3.10
2254 7187 3.745975 TGTTGTGTCGCAAAATAGGAGAG 59.254 43.478 0.00 0.00 39.03 3.20
2255 7188 3.496884 GTGTTGTGTCGCAAAATAGGAGA 59.503 43.478 0.00 0.00 39.03 3.71
2256 7189 3.498397 AGTGTTGTGTCGCAAAATAGGAG 59.502 43.478 0.00 0.00 39.03 3.69
2257 7190 3.472652 AGTGTTGTGTCGCAAAATAGGA 58.527 40.909 0.00 0.00 39.03 2.94
2258 7191 3.896648 AGTGTTGTGTCGCAAAATAGG 57.103 42.857 0.00 0.00 39.03 2.57
2259 7192 5.095691 AGAAGTGTTGTGTCGCAAAATAG 57.904 39.130 0.00 0.00 39.03 1.73
2260 7193 5.493133 AAGAAGTGTTGTGTCGCAAAATA 57.507 34.783 0.00 0.00 39.03 1.40
2261 7194 4.370364 AAGAAGTGTTGTGTCGCAAAAT 57.630 36.364 0.00 0.00 39.03 1.82
2262 7195 3.840890 AAGAAGTGTTGTGTCGCAAAA 57.159 38.095 0.00 0.00 39.03 2.44
2438 7400 2.554806 TACACGAGCGGAACATGTAG 57.445 50.000 0.00 0.00 0.00 2.74
2496 7462 3.203487 AGAGGTTGGAGGTTGGTTGTTAA 59.797 43.478 0.00 0.00 0.00 2.01
2519 7485 4.870636 TCCATTCTCCTAACCATGCAATT 58.129 39.130 0.00 0.00 0.00 2.32
2545 7512 1.059584 TGCTCTTGGTGAGTTGGGGA 61.060 55.000 0.00 0.00 44.41 4.81
2553 7520 1.768275 TCTGGAGTTTGCTCTTGGTGA 59.232 47.619 0.00 0.00 41.38 4.02


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

AutoCloner maintained by Alex Coulton.