Multiple sequence alignment - TraesCS7A01G130800

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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 TraesCS7A01G130800 chr7A 100.000 4879 0 0 1 4879 84249235 84244357 0.000000e+00 9010.0
1 TraesCS7A01G130800 chr7A 78.243 979 139 42 719 1664 78217301 78218238 1.190000e-155 560.0
2 TraesCS7A01G130800 chr7A 76.273 864 132 41 778 1615 78387964 78388780 4.580000e-105 392.0
3 TraesCS7A01G130800 chr7A 75.299 668 109 30 1859 2501 84026351 84025715 8.050000e-68 268.0
4 TraesCS7A01G130800 chr7A 100.000 36 0 0 1825 1860 84026406 84026371 3.150000e-07 67.6
5 TraesCS7A01G130800 chr7D 93.365 2984 106 23 411 3370 82449896 82446981 0.000000e+00 4329.0
6 TraesCS7A01G130800 chr7D 94.703 1548 45 10 3366 4879 82446947 82445403 0.000000e+00 2370.0
7 TraesCS7A01G130800 chr7D 79.529 552 85 17 1069 1612 82349141 82348610 7.720000e-98 368.0
8 TraesCS7A01G130800 chr7D 75.888 676 119 23 1859 2501 82348553 82347889 6.140000e-79 305.0
9 TraesCS7A01G130800 chr7D 81.786 280 29 12 3387 3659 82347819 82347555 1.060000e-51 215.0
10 TraesCS7A01G130800 chr7D 82.949 217 23 5 3401 3617 74393772 74393974 3.000000e-42 183.0
11 TraesCS7A01G130800 chr7D 82.911 158 20 5 2097 2250 73180287 73180441 8.520000e-28 135.0
12 TraesCS7A01G130800 chr7D 83.168 101 12 5 2381 2476 73180527 73180627 2.420000e-13 87.9
13 TraesCS7A01G130800 chr7D 88.525 61 7 0 157 217 388967249 388967189 1.880000e-09 75.0
14 TraesCS7A01G130800 chr7B 91.287 2835 155 40 578 3368 29830479 29827693 0.000000e+00 3783.0
15 TraesCS7A01G130800 chr7B 91.052 2671 148 31 199 2840 31448975 31446367 0.000000e+00 3524.0
16 TraesCS7A01G130800 chr7B 94.675 1521 69 4 1861 3370 30765400 30763881 0.000000e+00 2350.0
17 TraesCS7A01G130800 chr7B 90.464 1552 80 22 3366 4879 30763847 30762326 0.000000e+00 1984.0
18 TraesCS7A01G130800 chr7B 92.703 1069 35 11 3366 4392 31441774 31440707 0.000000e+00 1502.0
19 TraesCS7A01G130800 chr7B 92.596 986 31 10 3923 4879 29827005 29826033 0.000000e+00 1378.0
20 TraesCS7A01G130800 chr7B 90.164 1098 51 9 761 1836 30766456 30765394 0.000000e+00 1376.0
21 TraesCS7A01G130800 chr7B 89.410 1067 66 19 2327 3370 31442850 31441808 0.000000e+00 1301.0
22 TraesCS7A01G130800 chr7B 89.581 979 59 14 2221 3189 31444966 31444021 0.000000e+00 1203.0
23 TraesCS7A01G130800 chr7B 94.241 573 18 3 3366 3925 29827657 29827087 0.000000e+00 861.0
24 TraesCS7A01G130800 chr7B 96.705 516 14 2 2857 3370 31446379 31445865 0.000000e+00 856.0
25 TraesCS7A01G130800 chr7B 87.683 682 29 14 1295 1976 31445681 31445055 0.000000e+00 743.0
26 TraesCS7A01G130800 chr7B 80.182 661 93 20 1012 1664 16950969 16951599 1.240000e-125 460.0
27 TraesCS7A01G130800 chr7B 94.218 294 16 1 4587 4879 31440698 31440405 9.630000e-122 448.0
28 TraesCS7A01G130800 chr7B 79.537 562 87 17 1063 1616 29608521 29607980 4.610000e-100 375.0
29 TraesCS7A01G130800 chr7B 84.521 407 32 10 199 602 30770206 30769828 1.660000e-99 374.0
30 TraesCS7A01G130800 chr7B 75.706 531 86 22 1859 2354 29607933 29607411 4.910000e-55 226.0
31 TraesCS7A01G130800 chr7B 91.975 162 5 2 3366 3527 31445831 31445678 2.290000e-53 220.0
32 TraesCS7A01G130800 chr7B 84.158 101 12 3 3989 4086 30763151 30763052 1.450000e-15 95.3
33 TraesCS7A01G130800 chr7B 100.000 39 0 0 75 113 31449069 31449031 6.770000e-09 73.1
34 TraesCS7A01G130800 chr7B 97.436 39 1 0 75 113 30770300 30770262 3.150000e-07 67.6
35 TraesCS7A01G130800 chr7B 100.000 28 0 0 1012 1039 29608558 29608531 9.000000e-03 52.8
36 TraesCS7A01G130800 chr2B 79.127 733 95 38 2596 3302 601733596 601734296 2.070000e-123 453.0
37 TraesCS7A01G130800 chr2B 78.104 749 112 32 2596 3321 675713760 675714479 1.250000e-115 427.0
38 TraesCS7A01G130800 chr2B 78.738 301 39 18 3366 3662 55201808 55201529 1.400000e-40 178.0
39 TraesCS7A01G130800 chr2B 85.507 138 20 0 2105 2242 54786418 54786281 1.420000e-30 145.0
40 TraesCS7A01G130800 chr2B 83.544 158 22 4 2107 2262 122993563 122993718 1.420000e-30 145.0
41 TraesCS7A01G130800 chr2B 78.924 223 37 9 3367 3589 122928865 122929077 5.090000e-30 143.0
42 TraesCS7A01G130800 chr2B 81.250 96 16 2 128 222 701750068 701750162 5.240000e-10 76.8
43 TraesCS7A01G130800 chr2B 100.000 28 0 0 1588 1615 54887355 54887328 9.000000e-03 52.8
44 TraesCS7A01G130800 chr6A 78.075 748 108 36 2596 3317 561602197 561601480 5.840000e-114 422.0
45 TraesCS7A01G130800 chr6A 77.193 228 28 16 3366 3588 31741138 31741346 1.440000e-20 111.0
46 TraesCS7A01G130800 chr4A 77.064 654 97 27 858 1485 648880529 648881155 1.310000e-85 327.0
47 TraesCS7A01G130800 chr4A 88.710 62 3 3 169 227 646820609 646820549 6.770000e-09 73.1
48 TraesCS7A01G130800 chr3B 81.778 225 21 14 3366 3588 229463761 229463967 2.340000e-38 171.0
49 TraesCS7A01G130800 chr2A 83.735 166 26 1 2105 2269 36399233 36399068 6.540000e-34 156.0
50 TraesCS7A01G130800 chr2A 82.822 163 25 3 2105 2265 36410900 36410739 5.090000e-30 143.0
51 TraesCS7A01G130800 chr2A 100.000 28 0 0 1588 1615 36202236 36202209 9.000000e-03 52.8
52 TraesCS7A01G130800 chr2D 76.821 302 40 21 3366 3662 33313608 33313332 5.090000e-30 143.0
53 TraesCS7A01G130800 chr1D 85.859 99 12 2 125 222 28185735 28185638 2.400000e-18 104.0
54 TraesCS7A01G130800 chr5B 86.364 66 9 0 168 233 89029098 89029163 6.770000e-09 73.1
55 TraesCS7A01G130800 chr5B 85.075 67 7 3 173 238 391143620 391143684 1.130000e-06 65.8
56 TraesCS7A01G130800 chr5D 88.333 60 6 1 173 231 420882189 420882130 2.440000e-08 71.3
57 TraesCS7A01G130800 chr5D 85.938 64 9 0 153 216 375409241 375409304 8.760000e-08 69.4
58 TraesCS7A01G130800 chr5D 86.885 61 8 0 157 217 423328400 423328460 8.760000e-08 69.4
59 TraesCS7A01G130800 chr6D 97.222 36 1 0 3582 3617 54481445 54481410 1.470000e-05 62.1
60 TraesCS7A01G130800 chr4D 97.222 36 1 0 3582 3617 459211643 459211608 1.470000e-05 62.1
61 TraesCS7A01G130800 chr3D 97.222 36 1 0 3582 3617 231936362 231936397 1.470000e-05 62.1


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 TraesCS7A01G130800 chr7A 84244357 84249235 4878 True 9010.000000 9010 100.000000 1 4879 1 chr7A.!!$R1 4878
1 TraesCS7A01G130800 chr7A 78217301 78218238 937 False 560.000000 560 78.243000 719 1664 1 chr7A.!!$F1 945
2 TraesCS7A01G130800 chr7A 78387964 78388780 816 False 392.000000 392 76.273000 778 1615 1 chr7A.!!$F2 837
3 TraesCS7A01G130800 chr7D 82445403 82449896 4493 True 3349.500000 4329 94.034000 411 4879 2 chr7D.!!$R3 4468
4 TraesCS7A01G130800 chr7D 82347555 82349141 1586 True 296.000000 368 79.067667 1069 3659 3 chr7D.!!$R2 2590
5 TraesCS7A01G130800 chr7B 29826033 29830479 4446 True 2007.333333 3783 92.708000 578 4879 3 chr7B.!!$R2 4301
6 TraesCS7A01G130800 chr7B 31440405 31449069 8664 True 1096.677778 3524 92.591889 75 4879 9 chr7B.!!$R4 4804
7 TraesCS7A01G130800 chr7B 30762326 30770300 7974 True 1041.150000 2350 90.236333 75 4879 6 chr7B.!!$R3 4804
8 TraesCS7A01G130800 chr7B 16950969 16951599 630 False 460.000000 460 80.182000 1012 1664 1 chr7B.!!$F1 652
9 TraesCS7A01G130800 chr7B 29607411 29608558 1147 True 217.933333 375 85.081000 1012 2354 3 chr7B.!!$R1 1342
10 TraesCS7A01G130800 chr2B 601733596 601734296 700 False 453.000000 453 79.127000 2596 3302 1 chr2B.!!$F3 706
11 TraesCS7A01G130800 chr2B 675713760 675714479 719 False 427.000000 427 78.104000 2596 3321 1 chr2B.!!$F4 725
12 TraesCS7A01G130800 chr6A 561601480 561602197 717 True 422.000000 422 78.075000 2596 3317 1 chr6A.!!$R1 721
13 TraesCS7A01G130800 chr4A 648880529 648881155 626 False 327.000000 327 77.064000 858 1485 1 chr4A.!!$F1 627


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
113 114 0.470766 TGGTAAAGGGTGACGCTTGT 59.529 50.000 15.83 8.60 36.76 3.16 F
449 462 0.528684 GCCACTAGCGATGACACTCC 60.529 60.000 0.00 0.00 0.00 3.85 F
455 468 0.534412 AGCGATGACACTCCAGGAAG 59.466 55.000 0.00 0.00 0.00 3.46 F
940 4205 0.968393 TTCAAATACCCCCGCCTTGC 60.968 55.000 0.00 0.00 0.00 4.01 F
1906 5286 1.072159 GGTGACTCAACTGCAGGCT 59.928 57.895 19.93 0.99 0.00 4.58 F
3545 11089 0.030235 CTGCGATACCCGAATGTCGA 59.970 55.000 8.74 0.00 43.74 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1681 5036 0.108615 CGCCCAAGAACTCACTCGAT 60.109 55.000 0.0 0.0 0.00 3.59 R
1687 5042 0.675083 TAACGACGCCCAAGAACTCA 59.325 50.000 0.0 0.0 0.00 3.41 R
1906 5286 1.682684 GAGGTCTTCAGGGAGGCGA 60.683 63.158 0.0 0.0 0.00 5.54 R
2033 5413 2.294536 ACAAGGACCTCCCCCTGATATT 60.295 50.000 0.0 0.0 36.42 1.28 R
3551 11095 2.302260 CGGCTCTGATCCTTCTCTACA 58.698 52.381 0.0 0.0 0.00 2.74 R
4534 12218 0.383949 GAAAACAAACGGAGCTGCCA 59.616 50.000 0.0 0.0 35.94 4.92 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
26 27 8.752766 CAACAAGATCTCAGTTGCAAATTATT 57.247 30.769 21.08 0.00 36.59 1.40
27 28 9.844790 CAACAAGATCTCAGTTGCAAATTATTA 57.155 29.630 21.08 0.00 36.59 0.98
34 35 8.464770 TCTCAGTTGCAAATTATTATTGTTGC 57.535 30.769 0.00 0.40 0.00 4.17
35 36 8.087136 TCTCAGTTGCAAATTATTATTGTTGCA 58.913 29.630 0.00 5.86 0.00 4.08
36 37 8.599055 TCAGTTGCAAATTATTATTGTTGCAA 57.401 26.923 16.28 16.28 38.47 4.08
73 74 9.462174 TTTTGTGAAATGATTCTACAACATGAC 57.538 29.630 0.00 0.00 36.85 3.06
113 114 0.470766 TGGTAAAGGGTGACGCTTGT 59.529 50.000 15.83 8.60 36.76 3.16
114 115 1.134037 TGGTAAAGGGTGACGCTTGTT 60.134 47.619 15.83 3.82 36.76 2.83
115 116 1.534163 GGTAAAGGGTGACGCTTGTTC 59.466 52.381 15.83 8.93 36.76 3.18
116 117 1.534163 GTAAAGGGTGACGCTTGTTCC 59.466 52.381 15.83 1.03 36.76 3.62
117 118 0.822121 AAAGGGTGACGCTTGTTCCC 60.822 55.000 15.83 0.00 36.76 3.97
118 119 1.990160 AAGGGTGACGCTTGTTCCCA 61.990 55.000 14.38 0.00 40.35 4.37
119 120 2.258726 GGGTGACGCTTGTTCCCAC 61.259 63.158 0.00 0.00 38.83 4.61
120 121 1.525077 GGTGACGCTTGTTCCCACA 60.525 57.895 0.00 0.00 0.00 4.17
121 122 1.098712 GGTGACGCTTGTTCCCACAA 61.099 55.000 0.00 0.00 40.82 3.33
122 123 0.736053 GTGACGCTTGTTCCCACAAA 59.264 50.000 0.00 0.00 42.53 2.83
123 124 1.133407 GTGACGCTTGTTCCCACAAAA 59.867 47.619 0.00 0.00 42.53 2.44
124 125 1.819288 TGACGCTTGTTCCCACAAAAA 59.181 42.857 0.00 0.00 42.53 1.94
162 163 2.017559 GCTCACTTAGCCCGATCCGT 62.018 60.000 0.00 0.00 46.25 4.69
169 170 2.327002 TAGCCCGATCCGTCGTTTCG 62.327 60.000 6.99 6.99 46.25 3.46
171 172 3.604202 CCGATCCGTCGTTTCGCG 61.604 66.667 0.00 0.00 46.25 5.87
179 180 4.367023 TCGTTTCGCGAGGTGGGG 62.367 66.667 9.59 0.00 45.68 4.96
181 182 4.011517 GTTTCGCGAGGTGGGGGA 62.012 66.667 9.59 0.00 0.00 4.81
183 184 3.026431 TTTCGCGAGGTGGGGGATC 62.026 63.158 9.59 0.00 0.00 3.36
184 185 3.976490 TTCGCGAGGTGGGGGATCT 62.976 63.158 9.59 0.00 0.00 2.75
185 186 3.470888 CGCGAGGTGGGGGATCTT 61.471 66.667 0.00 0.00 0.00 2.40
186 187 2.998949 GCGAGGTGGGGGATCTTT 59.001 61.111 0.00 0.00 0.00 2.52
188 189 0.544697 GCGAGGTGGGGGATCTTTTA 59.455 55.000 0.00 0.00 0.00 1.52
189 190 1.064979 GCGAGGTGGGGGATCTTTTAA 60.065 52.381 0.00 0.00 0.00 1.52
190 191 2.619590 GCGAGGTGGGGGATCTTTTAAA 60.620 50.000 0.00 0.00 0.00 1.52
191 192 3.692690 CGAGGTGGGGGATCTTTTAAAA 58.307 45.455 0.00 0.00 0.00 1.52
195 196 5.915628 AGGTGGGGGATCTTTTAAAAAGAT 58.084 37.500 0.00 0.00 39.53 2.40
207 208 2.886730 AAAAAGATCCGCCGGCCGAT 62.887 55.000 30.73 27.17 40.02 4.18
228 229 3.696045 TGTGTAGCAGTGCCCATAAATT 58.304 40.909 12.58 0.00 0.00 1.82
234 235 8.410141 GTGTAGCAGTGCCCATAAATTAATTAA 58.590 33.333 12.58 0.00 0.00 1.40
236 237 9.244799 GTAGCAGTGCCCATAAATTAATTAAAC 57.755 33.333 12.58 0.00 0.00 2.01
238 239 9.196139 AGCAGTGCCCATAAATTAATTAAACTA 57.804 29.630 12.58 0.00 0.00 2.24
286 287 4.160439 TGCTAGTAGAACATCACTCCCTTG 59.840 45.833 0.00 0.00 0.00 3.61
339 340 7.253750 CCGAAACTTCAAAACAGAGTTTTCATG 60.254 37.037 4.99 0.00 33.53 3.07
340 341 7.273381 CGAAACTTCAAAACAGAGTTTTCATGT 59.727 33.333 4.99 0.00 33.53 3.21
341 342 8.831715 AAACTTCAAAACAGAGTTTTCATGTT 57.168 26.923 4.99 5.13 38.76 2.71
343 344 7.378181 ACTTCAAAACAGAGTTTTCATGTTGT 58.622 30.769 4.99 0.00 37.24 3.32
381 382 6.870971 TTATCTTACTTTTGTCACCCACAC 57.129 37.500 0.00 0.00 33.41 3.82
449 462 0.528684 GCCACTAGCGATGACACTCC 60.529 60.000 0.00 0.00 0.00 3.85
450 463 0.817654 CCACTAGCGATGACACTCCA 59.182 55.000 0.00 0.00 0.00 3.86
451 464 1.202348 CCACTAGCGATGACACTCCAG 60.202 57.143 0.00 0.00 0.00 3.86
452 465 1.107114 ACTAGCGATGACACTCCAGG 58.893 55.000 0.00 0.00 0.00 4.45
455 468 0.534412 AGCGATGACACTCCAGGAAG 59.466 55.000 0.00 0.00 0.00 3.46
489 502 2.097038 CAGGCGACAGAAAGGAGCG 61.097 63.158 0.00 0.00 0.00 5.03
613 626 2.683465 GGGCATCCAGGCAAGGAGA 61.683 63.158 4.98 0.00 46.44 3.71
940 4205 0.968393 TTCAAATACCCCCGCCTTGC 60.968 55.000 0.00 0.00 0.00 4.01
1001 4276 2.391389 GCCGGAGCTCCAAGAAACG 61.391 63.158 31.67 15.60 35.50 3.60
1005 4280 1.443802 GGAGCTCCAAGAAACGAAGG 58.556 55.000 28.43 0.00 35.64 3.46
1041 4360 4.704103 AGCGCCCACCTCCTCTGA 62.704 66.667 2.29 0.00 0.00 3.27
1413 4741 1.639298 CTGGCGTGCTGCTCCTAAAC 61.639 60.000 0.00 0.00 45.43 2.01
1414 4742 2.740714 GGCGTGCTGCTCCTAAACG 61.741 63.158 0.00 2.14 45.43 3.60
1415 4743 2.778679 CGTGCTGCTCCTAAACGC 59.221 61.111 0.00 0.00 0.00 4.84
1416 4744 2.740714 CGTGCTGCTCCTAAACGCC 61.741 63.158 0.00 0.00 0.00 5.68
1417 4745 2.434185 TGCTGCTCCTAAACGCCG 60.434 61.111 0.00 0.00 0.00 6.46
1418 4746 3.195698 GCTGCTCCTAAACGCCGG 61.196 66.667 0.00 0.00 0.00 6.13
1662 5017 4.021894 AGCCTACTATCGATTGAGCGAATT 60.022 41.667 13.87 0.00 44.22 2.17
1664 5019 5.461526 CCTACTATCGATTGAGCGAATTGA 58.538 41.667 13.87 4.46 44.22 2.57
1665 5020 6.096036 CCTACTATCGATTGAGCGAATTGAT 58.904 40.000 13.87 14.94 44.44 2.57
1666 5021 7.251281 CCTACTATCGATTGAGCGAATTGATA 58.749 38.462 13.87 15.39 41.65 2.15
1670 5025 5.890110 TCGATTGAGCGAATTGATAGTTC 57.110 39.130 0.00 0.00 37.35 3.01
1680 5035 5.759963 CGAATTGATAGTTCGTAGCCTACT 58.240 41.667 0.00 0.00 42.44 2.57
1681 5036 6.895898 CGAATTGATAGTTCGTAGCCTACTA 58.104 40.000 0.00 0.00 42.44 1.82
1682 5037 7.528307 CGAATTGATAGTTCGTAGCCTACTAT 58.472 38.462 0.00 0.00 42.44 2.12
1683 5038 7.693120 CGAATTGATAGTTCGTAGCCTACTATC 59.307 40.741 12.32 12.32 45.55 2.08
1686 5041 6.335176 GATAGTTCGTAGCCTACTATCGAG 57.665 45.833 0.00 0.00 40.22 4.04
1687 5042 4.070630 AGTTCGTAGCCTACTATCGAGT 57.929 45.455 0.00 0.00 39.92 4.18
1688 5043 3.808726 AGTTCGTAGCCTACTATCGAGTG 59.191 47.826 0.00 0.00 36.28 3.51
1689 5044 3.740631 TCGTAGCCTACTATCGAGTGA 57.259 47.619 0.00 0.00 36.28 3.41
1765 5120 6.859420 TGTGTTGATTTCATTTTCTCGAGA 57.141 33.333 12.08 12.08 0.00 4.04
1766 5121 7.439157 TGTGTTGATTTCATTTTCTCGAGAT 57.561 32.000 17.44 0.00 0.00 2.75
1788 5143 3.054878 CAATTTCTGGTTCTGCTGTTGC 58.945 45.455 0.00 0.00 40.20 4.17
1810 5165 3.182972 CCAAATTTGCGCTTCTTGACTTG 59.817 43.478 12.92 1.60 0.00 3.16
1906 5286 1.072159 GGTGACTCAACTGCAGGCT 59.928 57.895 19.93 0.99 0.00 4.58
1988 5368 3.723348 GGTTCGTGCAAGCGACCC 61.723 66.667 11.90 5.79 40.85 4.46
1989 5369 3.723348 GTTCGTGCAAGCGACCCC 61.723 66.667 0.00 0.00 40.85 4.95
2063 5443 1.610886 GGAGGTCCTTGTACAACCTGC 60.611 57.143 20.08 18.81 43.43 4.85
2103 5498 4.379243 CGACCTGCAGCCCGACTT 62.379 66.667 17.47 0.00 0.00 3.01
2208 5603 2.937149 TCTACCAGATCGTCGTCTTCAG 59.063 50.000 0.00 0.00 0.00 3.02
2507 5916 0.951558 AATTGTCTGCAACCGGTGTC 59.048 50.000 8.52 3.11 37.44 3.67
2516 5925 2.129146 AACCGGTGTCGTCCTGTCA 61.129 57.895 8.52 0.00 33.95 3.58
2561 5970 9.131791 AGTAACATTTTACACTCAACCTTGATT 57.868 29.630 4.66 0.00 40.25 2.57
2716 6139 6.299141 TGAGGTGATTAATCTTATTCAGCCC 58.701 40.000 16.24 8.49 40.01 5.19
2731 6154 6.814954 ATTCAGCCCTAACAGAGAAGATTA 57.185 37.500 0.00 0.00 0.00 1.75
2962 6390 3.838317 ACTAGAAATGCACTGGTGGTCTA 59.162 43.478 0.00 0.00 0.00 2.59
3190 6625 3.972388 TCGATGCCGTGTGGATCTATCC 61.972 54.545 1.79 1.79 41.08 2.59
3323 6765 4.073293 AGTCGCCAGTAGAAATTATGGG 57.927 45.455 0.00 0.00 33.23 4.00
3383 6864 6.878317 TCATCTTTCAGGTTGTATCCTACAG 58.122 40.000 0.00 0.00 40.24 2.74
3545 11089 0.030235 CTGCGATACCCGAATGTCGA 59.970 55.000 8.74 0.00 43.74 4.20
3604 11148 5.118990 CAGTTCACCTCTTCAGAAGTTTCA 58.881 41.667 10.09 0.00 0.00 2.69
3683 11240 4.314121 ACTCATCAGCTCTTGTGTTTCTC 58.686 43.478 0.00 0.00 0.00 2.87
3931 11575 7.504574 TCTGTTAGGCTATGCATGTAGTAGTTA 59.495 37.037 10.16 0.00 0.00 2.24
3999 11650 3.450904 TCACTGTAGGGGTTCTTGCTAT 58.549 45.455 0.00 0.00 0.00 2.97
4086 11746 4.976224 TGCAATGAGTTGATGATCTTGG 57.024 40.909 0.00 0.00 37.53 3.61
4141 11803 3.923017 AAATGTAGTGGTTCTTGCTGC 57.077 42.857 0.00 0.00 0.00 5.25
4181 11851 2.094286 TGTTGTTTTGAGTGTTGGCCAG 60.094 45.455 5.11 0.00 0.00 4.85
4246 11916 2.106511 TGTTTTCAGGTAAGCTGCCTCT 59.893 45.455 7.10 0.00 33.31 3.69
4265 11935 7.209475 TGCCTCTTTTTCTTTTGTTATCTTGG 58.791 34.615 0.00 0.00 0.00 3.61
4294 11964 6.376299 AGCAAAATGAGATTGTTCATCTGCTA 59.624 34.615 17.12 0.00 45.35 3.49
4409 12092 6.296026 TGAAGCACCTGATAACACTAGTTTT 58.704 36.000 0.00 0.00 39.15 2.43
4458 12141 9.204570 GCACTTGAGTTTATCTGTTTCTAACTA 57.795 33.333 0.00 0.00 0.00 2.24
4502 12186 2.029918 GTGTCCCACTTTCCAATCTTGC 60.030 50.000 0.00 0.00 0.00 4.01
4556 12240 1.333619 GCAGCTCCGTTTGTTTTCAGA 59.666 47.619 0.00 0.00 0.00 3.27
4592 12283 7.631510 TCCCATAAGATCAATCATACTTGGA 57.368 36.000 0.00 0.00 0.00 3.53
4632 12324 5.692115 TCACCCACTCAAGCATAAGAATA 57.308 39.130 0.00 0.00 0.00 1.75
4700 12392 1.066605 GCTGCAGTGGCTATCATTTGG 59.933 52.381 16.64 0.00 41.91 3.28
4835 12527 6.041979 ACAACATTCAGCCTAACAAGGATTTT 59.958 34.615 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.752766 AATAATTTGCAACTGAGATCTTGTTG 57.247 30.769 25.43 25.43 42.55 3.33
8 9 9.090692 GCAACAATAATAATTTGCAACTGAGAT 57.909 29.630 0.00 0.00 31.76 2.75
9 10 8.087136 TGCAACAATAATAATTTGCAACTGAGA 58.913 29.630 0.00 0.00 36.41 3.27
10 11 8.242085 TGCAACAATAATAATTTGCAACTGAG 57.758 30.769 0.00 0.00 36.41 3.35
11 12 8.599055 TTGCAACAATAATAATTTGCAACTGA 57.401 26.923 14.76 0.00 40.96 3.41
47 48 9.462174 GTCATGTTGTAGAATCATTTCACAAAA 57.538 29.630 0.00 0.00 36.04 2.44
48 49 8.081633 GGTCATGTTGTAGAATCATTTCACAAA 58.918 33.333 0.00 0.00 36.04 2.83
49 50 7.230309 TGGTCATGTTGTAGAATCATTTCACAA 59.770 33.333 0.00 0.00 33.97 3.33
50 51 6.714356 TGGTCATGTTGTAGAATCATTTCACA 59.286 34.615 0.00 0.00 34.08 3.58
51 52 7.144722 TGGTCATGTTGTAGAATCATTTCAC 57.855 36.000 0.00 0.00 34.08 3.18
52 53 7.230309 TGTTGGTCATGTTGTAGAATCATTTCA 59.770 33.333 0.00 0.00 34.08 2.69
53 54 7.538678 GTGTTGGTCATGTTGTAGAATCATTTC 59.461 37.037 0.00 0.00 0.00 2.17
54 55 7.370383 GTGTTGGTCATGTTGTAGAATCATTT 58.630 34.615 0.00 0.00 0.00 2.32
55 56 6.348458 CGTGTTGGTCATGTTGTAGAATCATT 60.348 38.462 0.00 0.00 0.00 2.57
56 57 5.122239 CGTGTTGGTCATGTTGTAGAATCAT 59.878 40.000 0.00 0.00 0.00 2.45
57 58 4.450757 CGTGTTGGTCATGTTGTAGAATCA 59.549 41.667 0.00 0.00 0.00 2.57
58 59 4.688879 TCGTGTTGGTCATGTTGTAGAATC 59.311 41.667 0.00 0.00 34.87 2.52
59 60 4.451096 GTCGTGTTGGTCATGTTGTAGAAT 59.549 41.667 0.00 0.00 34.87 2.40
60 61 3.805422 GTCGTGTTGGTCATGTTGTAGAA 59.195 43.478 0.00 0.00 34.87 2.10
61 62 3.386486 GTCGTGTTGGTCATGTTGTAGA 58.614 45.455 0.00 0.00 34.87 2.59
62 63 2.478894 GGTCGTGTTGGTCATGTTGTAG 59.521 50.000 0.00 0.00 34.87 2.74
63 64 2.103432 AGGTCGTGTTGGTCATGTTGTA 59.897 45.455 0.00 0.00 34.87 2.41
64 65 1.134220 AGGTCGTGTTGGTCATGTTGT 60.134 47.619 0.00 0.00 34.87 3.32
65 66 1.593196 AGGTCGTGTTGGTCATGTTG 58.407 50.000 0.00 0.00 34.87 3.33
66 67 2.341846 AAGGTCGTGTTGGTCATGTT 57.658 45.000 0.00 0.00 34.87 2.71
67 68 1.946768 CAAAGGTCGTGTTGGTCATGT 59.053 47.619 0.00 0.00 34.87 3.21
68 69 1.946768 ACAAAGGTCGTGTTGGTCATG 59.053 47.619 0.00 0.00 34.61 3.07
69 70 2.341846 ACAAAGGTCGTGTTGGTCAT 57.658 45.000 0.00 0.00 0.00 3.06
70 71 2.116827 AACAAAGGTCGTGTTGGTCA 57.883 45.000 0.00 0.00 37.80 4.02
123 124 2.997485 GCTCAAGCGTCATCCTTTTT 57.003 45.000 0.00 0.00 0.00 1.94
135 136 1.712663 GCTAAGTGAGCGCTCAAGC 59.287 57.895 39.63 36.55 42.62 4.01
169 170 0.544697 TAAAAGATCCCCCACCTCGC 59.455 55.000 0.00 0.00 0.00 5.03
171 172 5.330233 TCTTTTTAAAAGATCCCCCACCTC 58.670 41.667 15.24 0.00 0.00 3.85
172 173 5.348259 TCTTTTTAAAAGATCCCCCACCT 57.652 39.130 15.24 0.00 0.00 4.00
173 174 6.222038 GATCTTTTTAAAAGATCCCCCACC 57.778 41.667 33.44 17.82 44.17 4.61
181 182 3.181490 GCCGGCGGATCTTTTTAAAAGAT 60.181 43.478 33.44 26.87 39.53 2.40
183 184 2.526077 GCCGGCGGATCTTTTTAAAAG 58.474 47.619 33.44 10.89 0.00 2.27
184 185 1.202817 GGCCGGCGGATCTTTTTAAAA 59.797 47.619 33.44 0.00 0.00 1.52
185 186 0.812549 GGCCGGCGGATCTTTTTAAA 59.187 50.000 33.44 0.00 0.00 1.52
186 187 1.370587 CGGCCGGCGGATCTTTTTAA 61.371 55.000 33.44 0.00 0.00 1.52
188 189 2.886730 ATCGGCCGGCGGATCTTTTT 62.887 55.000 36.01 19.57 31.70 1.94
189 190 3.400599 ATCGGCCGGCGGATCTTTT 62.401 57.895 36.01 20.25 31.70 2.27
190 191 3.861797 ATCGGCCGGCGGATCTTT 61.862 61.111 36.01 20.61 31.70 2.52
191 192 4.609018 CATCGGCCGGCGGATCTT 62.609 66.667 37.99 22.11 34.46 2.40
207 208 2.869101 TTTATGGGCACTGCTACACA 57.131 45.000 0.00 0.00 0.00 3.72
209 210 8.526667 TTAATTAATTTATGGGCACTGCTACA 57.473 30.769 5.91 1.29 0.00 2.74
253 254 8.883731 GTGATGTTCTACTAGCATGTAAATTGT 58.116 33.333 0.00 0.00 0.00 2.71
254 255 9.102757 AGTGATGTTCTACTAGCATGTAAATTG 57.897 33.333 0.00 0.00 0.00 2.32
255 256 9.319143 GAGTGATGTTCTACTAGCATGTAAATT 57.681 33.333 0.00 0.00 0.00 1.82
305 306 7.316640 TCTGTTTTGAAGTTTCGGAAAAATCA 58.683 30.769 4.46 9.60 0.00 2.57
308 309 6.683715 ACTCTGTTTTGAAGTTTCGGAAAAA 58.316 32.000 4.46 0.00 0.00 1.94
314 315 7.273381 ACATGAAAACTCTGTTTTGAAGTTTCG 59.727 33.333 12.32 0.00 32.39 3.46
359 360 5.310451 GGTGTGGGTGACAAAAGTAAGATA 58.690 41.667 0.00 0.00 35.91 1.98
360 361 4.142038 GGTGTGGGTGACAAAAGTAAGAT 58.858 43.478 0.00 0.00 35.91 2.40
362 363 2.289547 CGGTGTGGGTGACAAAAGTAAG 59.710 50.000 0.00 0.00 35.91 2.34
402 412 3.250744 CTTTGCTGTCATTGGCTCATTG 58.749 45.455 0.00 0.00 0.00 2.82
403 413 2.353406 GCTTTGCTGTCATTGGCTCATT 60.353 45.455 0.00 0.00 0.00 2.57
404 414 1.203994 GCTTTGCTGTCATTGGCTCAT 59.796 47.619 0.00 0.00 0.00 2.90
405 415 0.599558 GCTTTGCTGTCATTGGCTCA 59.400 50.000 0.00 0.00 0.00 4.26
406 416 0.599558 TGCTTTGCTGTCATTGGCTC 59.400 50.000 0.00 0.00 0.00 4.70
407 417 0.601558 CTGCTTTGCTGTCATTGGCT 59.398 50.000 0.00 0.00 0.00 4.75
408 418 0.389426 CCTGCTTTGCTGTCATTGGC 60.389 55.000 0.00 0.00 0.00 4.52
409 419 0.963962 ACCTGCTTTGCTGTCATTGG 59.036 50.000 0.00 0.00 0.00 3.16
472 485 2.219325 CTCGCTCCTTTCTGTCGCCT 62.219 60.000 0.00 0.00 0.00 5.52
473 486 1.807573 CTCGCTCCTTTCTGTCGCC 60.808 63.158 0.00 0.00 0.00 5.54
489 502 2.202987 CATGGGGTGCGAGCTCTC 60.203 66.667 12.85 4.04 0.00 3.20
948 4213 0.881600 GTTGGTTCAGGCGGTTACGT 60.882 55.000 0.00 0.00 43.45 3.57
1001 4276 4.475135 GTGGAGAGCGGGGCCTTC 62.475 72.222 0.84 0.00 0.00 3.46
1071 4390 0.171903 CGTCGTAGAACCGGTCCATT 59.828 55.000 8.04 0.00 39.69 3.16
1394 4722 1.375908 TTTAGGAGCAGCACGCCAG 60.376 57.895 0.00 0.00 44.04 4.85
1662 5017 5.787380 TCGATAGTAGGCTACGAACTATCA 58.213 41.667 24.39 14.45 46.52 2.15
1664 5019 5.638657 CACTCGATAGTAGGCTACGAACTAT 59.361 44.000 18.41 12.53 38.75 2.12
1665 5020 4.987285 CACTCGATAGTAGGCTACGAACTA 59.013 45.833 18.41 8.10 33.70 2.24
1666 5021 3.808726 CACTCGATAGTAGGCTACGAACT 59.191 47.826 18.41 5.96 33.70 3.01
1667 5022 3.806521 TCACTCGATAGTAGGCTACGAAC 59.193 47.826 18.41 11.47 33.70 3.95
1668 5023 4.056740 CTCACTCGATAGTAGGCTACGAA 58.943 47.826 18.41 11.57 33.70 3.85
1669 5024 3.069300 ACTCACTCGATAGTAGGCTACGA 59.931 47.826 18.41 14.29 33.48 3.43
1670 5025 3.391965 ACTCACTCGATAGTAGGCTACG 58.608 50.000 18.41 7.43 33.48 3.51
1671 5026 5.058490 AGAACTCACTCGATAGTAGGCTAC 58.942 45.833 16.93 16.93 33.48 3.58
1672 5027 5.293319 AGAACTCACTCGATAGTAGGCTA 57.707 43.478 0.00 0.00 33.48 3.93
1673 5028 4.159244 AGAACTCACTCGATAGTAGGCT 57.841 45.455 0.00 0.00 33.48 4.58
1674 5029 4.498345 CCAAGAACTCACTCGATAGTAGGC 60.498 50.000 0.00 0.00 33.48 3.93
1675 5030 4.036971 CCCAAGAACTCACTCGATAGTAGG 59.963 50.000 0.00 0.00 33.48 3.18
1676 5031 4.498345 GCCCAAGAACTCACTCGATAGTAG 60.498 50.000 0.00 0.00 33.48 2.57
1677 5032 3.380637 GCCCAAGAACTCACTCGATAGTA 59.619 47.826 0.00 0.00 33.48 1.82
1678 5033 2.166664 GCCCAAGAACTCACTCGATAGT 59.833 50.000 0.00 0.00 35.91 2.12
1679 5034 2.796383 CGCCCAAGAACTCACTCGATAG 60.796 54.545 0.00 0.00 0.00 2.08
1680 5035 1.134367 CGCCCAAGAACTCACTCGATA 59.866 52.381 0.00 0.00 0.00 2.92
1681 5036 0.108615 CGCCCAAGAACTCACTCGAT 60.109 55.000 0.00 0.00 0.00 3.59
1682 5037 1.289066 CGCCCAAGAACTCACTCGA 59.711 57.895 0.00 0.00 0.00 4.04
1683 5038 1.006102 ACGCCCAAGAACTCACTCG 60.006 57.895 0.00 0.00 0.00 4.18
1684 5039 1.009389 CGACGCCCAAGAACTCACTC 61.009 60.000 0.00 0.00 0.00 3.51
1685 5040 1.006102 CGACGCCCAAGAACTCACT 60.006 57.895 0.00 0.00 0.00 3.41
1686 5041 0.878961 AACGACGCCCAAGAACTCAC 60.879 55.000 0.00 0.00 0.00 3.51
1687 5042 0.675083 TAACGACGCCCAAGAACTCA 59.325 50.000 0.00 0.00 0.00 3.41
1688 5043 1.787012 TTAACGACGCCCAAGAACTC 58.213 50.000 0.00 0.00 0.00 3.01
1689 5044 2.467566 ATTAACGACGCCCAAGAACT 57.532 45.000 0.00 0.00 0.00 3.01
1765 5120 4.560108 GCAACAGCAGAACCAGAAATTGAT 60.560 41.667 0.00 0.00 0.00 2.57
1766 5121 3.243501 GCAACAGCAGAACCAGAAATTGA 60.244 43.478 0.00 0.00 0.00 2.57
1788 5143 3.017265 AGTCAAGAAGCGCAAATTTGG 57.983 42.857 19.47 10.66 0.00 3.28
1810 5165 2.695646 GAATCTCGACGGCGCAAC 59.304 61.111 5.31 0.00 37.46 4.17
1906 5286 1.682684 GAGGTCTTCAGGGAGGCGA 60.683 63.158 0.00 0.00 0.00 5.54
1997 5377 3.782443 CTGGGCCTCGGGGTACAC 61.782 72.222 1.62 0.00 34.45 2.90
2033 5413 2.294536 ACAAGGACCTCCCCCTGATATT 60.295 50.000 0.00 0.00 36.42 1.28
2421 5830 8.920509 ACAATTTCAGTTAACTGTTTTACCAC 57.079 30.769 29.83 0.00 44.12 4.16
2459 5868 9.321562 CAACTCCTAACAGTTTCAGTTAACTTA 57.678 33.333 5.07 0.00 36.24 2.24
2507 5916 3.775661 AACCAAAAAGTTGACAGGACG 57.224 42.857 0.00 0.00 36.83 4.79
2561 5970 2.818751 ACCAACACTTTCCAGTCCAA 57.181 45.000 0.00 0.00 0.00 3.53
2827 6250 9.643693 CAAAACCTGAAAACAATATAGCTCATT 57.356 29.630 0.00 0.00 0.00 2.57
2986 6414 7.413000 GCAGTAAACAGTATCTACACAACCATG 60.413 40.741 0.00 0.00 0.00 3.66
3221 6663 4.885325 AGTAGTTCCTACTAGCTTCAGAGC 59.115 45.833 2.15 0.00 44.35 4.09
3323 6765 8.406297 ACTGAACTTGATTTGACTTTTTAGGTC 58.594 33.333 0.00 0.00 0.00 3.85
3383 6864 9.043079 GGAACTAAGCTTTTATGTACCATCTAC 57.957 37.037 3.20 0.00 0.00 2.59
3545 11089 3.054287 TCTGATCCTTCTCTACACTCCGT 60.054 47.826 0.00 0.00 0.00 4.69
3551 11095 2.302260 CGGCTCTGATCCTTCTCTACA 58.698 52.381 0.00 0.00 0.00 2.74
3683 11240 3.129871 GCATCAGAGTTTAGCTAGCAGG 58.870 50.000 18.83 0.00 0.00 4.85
3999 11650 3.421919 TGTTGCAGGATCATTGACTCA 57.578 42.857 0.00 0.00 0.00 3.41
4051 11711 1.610038 CATTGCAAGAACCACTGCAGA 59.390 47.619 23.35 0.00 35.43 4.26
4086 11746 7.975616 TGACAAATGCATAGCCTAAAAGAAATC 59.024 33.333 0.00 0.00 0.00 2.17
4141 11803 1.069703 CACAACACAATCACCAGCTCG 60.070 52.381 0.00 0.00 0.00 5.03
4181 11851 3.767711 ACTTTGTTCCTTTCCTGATCCC 58.232 45.455 0.00 0.00 0.00 3.85
4246 11916 9.877178 TGCTAAACCAAGATAACAAAAGAAAAA 57.123 25.926 0.00 0.00 0.00 1.94
4265 11935 8.857216 CAGATGAACAATCTCATTTTGCTAAAC 58.143 33.333 0.00 0.00 44.24 2.01
4409 12092 2.418368 ACTCACAAGCAAGAACCACA 57.582 45.000 0.00 0.00 0.00 4.17
4458 12141 4.342092 CCCTTCATTGGACTGAAACTTGTT 59.658 41.667 0.00 0.00 34.86 2.83
4459 12142 3.891366 CCCTTCATTGGACTGAAACTTGT 59.109 43.478 0.00 0.00 34.86 3.16
4488 12172 6.654582 ACAAAACAAAAGCAAGATTGGAAAGT 59.345 30.769 0.00 0.00 0.00 2.66
4534 12218 0.383949 GAAAACAAACGGAGCTGCCA 59.616 50.000 0.00 0.00 35.94 4.92
4556 12240 9.981460 ATTGATCTTATGGGAAAGAGTAAACTT 57.019 29.630 0.00 0.00 38.81 2.66
4592 12283 7.234166 AGTGGGTGATTTTTCATGAAATCTCTT 59.766 33.333 21.10 5.33 43.28 2.85
4632 12324 2.224606 CAAAGTGTGCCTCACAGACAT 58.775 47.619 10.84 0.00 45.43 3.06
4700 12392 5.705609 TGGGAAGAAGAAAACACTTATGC 57.294 39.130 0.00 0.00 0.00 3.14
4835 12527 5.126869 TCTCATTTGCCAAGTTTTCTGTCAA 59.873 36.000 0.00 0.00 0.00 3.18



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

AutoCloner maintained by Alex Coulton.