Multiple sequence alignment - TraesCS3D01G366400

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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 TraesCS3D01G366400 chr3D 100.000 3281 0 0 1 3281 480835933 480839213 0.000000e+00 6059.0
1 TraesCS3D01G366400 chr3D 83.807 704 93 14 888 1583 480357809 480358499 0.000000e+00 649.0
2 TraesCS3D01G366400 chr3D 83.051 708 93 18 888 1583 480375618 480376310 4.650000e-173 617.0
3 TraesCS3D01G366400 chr3D 82.665 698 96 16 888 1583 480366550 480367224 2.180000e-166 595.0
4 TraesCS3D01G366400 chr3D 82.774 685 96 16 902 1573 480125118 480125793 2.820000e-165 592.0
5 TraesCS3D01G366400 chr3D 86.194 536 57 13 1683 2207 480376313 480376842 6.150000e-157 564.0
6 TraesCS3D01G366400 chr3D 86.879 503 65 1 1081 1583 480157917 480158418 2.210000e-156 562.0
7 TraesCS3D01G366400 chr3D 90.074 403 40 0 1683 2085 480158421 480158823 1.040000e-144 523.0
8 TraesCS3D01G366400 chr3D 90.074 403 40 0 1683 2085 480358502 480358904 1.040000e-144 523.0
9 TraesCS3D01G366400 chr3D 85.132 491 70 1 1083 1570 480120544 480121034 1.760000e-137 499.0
10 TraesCS3D01G366400 chr3D 85.749 407 56 2 1682 2087 480125805 480126210 2.340000e-116 429.0
11 TraesCS3D01G366400 chr3D 86.253 371 48 2 1719 2089 480121074 480121441 1.830000e-107 399.0
12 TraesCS3D01G366400 chr3D 85.360 403 40 6 1683 2085 480367227 480367610 1.830000e-107 399.0
13 TraesCS3D01G366400 chr3D 80.223 359 54 10 146 488 403109669 403109312 1.510000e-63 254.0
14 TraesCS3D01G366400 chr3D 77.233 347 50 13 146 477 61771839 61771507 3.360000e-40 176.0
15 TraesCS3D01G366400 chr3D 78.088 251 46 9 145 391 105495524 105495769 2.040000e-32 150.0
16 TraesCS3D01G366400 chr3D 95.604 91 4 0 1 91 506856386 506856476 2.640000e-31 147.0
17 TraesCS3D01G366400 chr3D 94.737 95 4 1 1 95 578430449 578430356 2.640000e-31 147.0
18 TraesCS3D01G366400 chr3D 77.828 221 42 7 146 362 544357217 544357434 2.660000e-26 130.0
19 TraesCS3D01G366400 chr3B 91.331 2884 175 29 146 3002 641653060 641655895 0.000000e+00 3871.0
20 TraesCS3D01G366400 chr3B 84.233 704 87 19 888 1582 640832064 640832752 0.000000e+00 664.0
21 TraesCS3D01G366400 chr3B 86.704 534 57 11 1682 2207 640832755 640833282 6.100000e-162 580.0
22 TraesCS3D01G366400 chr3B 78.551 345 55 14 147 486 54506676 54506346 3.320000e-50 209.0
23 TraesCS3D01G366400 chr3B 76.000 425 81 15 147 558 254492894 254492478 2.000000e-47 200.0
24 TraesCS3D01G366400 chr3A 93.377 2431 135 12 588 3000 623604611 623607033 0.000000e+00 3574.0
25 TraesCS3D01G366400 chr3A 83.167 701 96 18 888 1583 623389445 623390128 3.600000e-174 621.0
26 TraesCS3D01G366400 chr3A 82.578 706 94 22 888 1583 623354308 623354994 2.180000e-166 595.0
27 TraesCS3D01G366400 chr3A 87.189 523 53 11 1683 2197 623390131 623390647 1.700000e-162 582.0
28 TraesCS3D01G366400 chr3A 86.733 505 67 0 1079 1583 623340348 623340852 2.210000e-156 562.0
29 TraesCS3D01G366400 chr3A 90.571 403 38 0 1683 2085 623340855 623341257 4.820000e-148 534.0
30 TraesCS3D01G366400 chr3A 89.330 403 43 0 1683 2085 623354997 623355399 1.050000e-139 507.0
31 TraesCS3D01G366400 chr3A 89.082 403 44 0 1683 2085 623230095 623230497 4.890000e-138 501.0
32 TraesCS3D01G366400 chr3A 92.958 284 19 1 2998 3281 623607086 623607368 2.360000e-111 412.0
33 TraesCS3D01G366400 chr3A 80.952 357 49 13 147 486 326555122 326554768 6.980000e-67 265.0
34 TraesCS3D01G366400 chr6D 79.707 409 57 7 146 538 393927854 393927456 4.170000e-69 272.0
35 TraesCS3D01G366400 chr6D 93.407 91 5 1 1 91 365851776 365851687 2.050000e-27 134.0
36 TraesCS3D01G366400 chr4D 79.277 415 65 11 151 558 472942340 472942740 1.500000e-68 270.0
37 TraesCS3D01G366400 chr2D 81.651 327 52 5 149 469 96688673 96688349 6.980000e-67 265.0
38 TraesCS3D01G366400 chr2D 81.369 263 40 5 231 488 183391507 183391249 4.290000e-49 206.0
39 TraesCS3D01G366400 chr2D 81.955 133 17 5 2657 2784 450937269 450937399 4.480000e-19 106.0
40 TraesCS3D01G366400 chr2D 77.059 170 33 6 1388 1554 560399387 560399553 3.490000e-15 93.5
41 TraesCS3D01G366400 chr4B 77.251 422 70 11 147 561 588916056 588915654 1.180000e-54 224.0
42 TraesCS3D01G366400 chr4B 93.407 91 5 1 1 91 322636898 322636987 2.050000e-27 134.0
43 TraesCS3D01G366400 chr4B 92.308 91 7 0 1 91 461996703 461996793 2.660000e-26 130.0
44 TraesCS3D01G366400 chr4B 94.545 55 2 1 3124 3177 140237089 140237143 2.100000e-12 84.2
45 TraesCS3D01G366400 chr4B 92.157 51 4 0 2949 2999 29332607 29332557 4.540000e-09 73.1
46 TraesCS3D01G366400 chr7A 79.240 342 52 17 148 477 197172635 197172301 1.530000e-53 220.0
47 TraesCS3D01G366400 chr7A 83.708 178 19 9 2654 2822 145494651 145494827 3.390000e-35 159.0
48 TraesCS3D01G366400 chr7A 93.333 90 5 1 1 90 690010838 690010926 7.390000e-27 132.0
49 TraesCS3D01G366400 chr2A 82.759 232 32 6 245 471 695186573 695186345 2.000000e-47 200.0
50 TraesCS3D01G366400 chr2A 79.878 164 21 9 2662 2816 695997148 695996988 3.460000e-20 110.0
51 TraesCS3D01G366400 chr7D 86.471 170 19 4 2657 2822 401112860 401113029 2.010000e-42 183.0
52 TraesCS3D01G366400 chr7D 86.986 146 17 2 2656 2801 143990636 143990493 2.620000e-36 163.0
53 TraesCS3D01G366400 chr6A 83.799 179 29 0 2821 2999 1979001 1978823 1.570000e-38 171.0
54 TraesCS3D01G366400 chr4A 86.452 155 19 2 2657 2809 669653980 669654134 5.630000e-38 169.0
55 TraesCS3D01G366400 chr4A 82.967 182 31 0 2821 3002 16213439 16213258 7.280000e-37 165.0
56 TraesCS3D01G366400 chr7B 85.714 154 20 2 2657 2809 410630400 410630552 9.420000e-36 161.0
57 TraesCS3D01G366400 chr7B 84.713 157 21 3 2654 2808 107650306 107650461 1.580000e-33 154.0
58 TraesCS3D01G366400 chr7B 94.505 91 5 0 1 91 159715232 159715142 1.230000e-29 141.0
59 TraesCS3D01G366400 chr1B 85.256 156 18 4 2657 2807 673888670 673888515 4.380000e-34 156.0
60 TraesCS3D01G366400 chr1B 85.393 89 12 1 2701 2788 466944513 466944601 1.250000e-14 91.6
61 TraesCS3D01G366400 chr5A 83.333 174 19 6 2657 2822 566293312 566293141 5.670000e-33 152.0
62 TraesCS3D01G366400 chr5A 79.545 176 24 9 2657 2822 321005545 321005372 7.440000e-22 115.0
63 TraesCS3D01G366400 chr6B 92.473 93 7 0 1 93 412570508 412570600 2.050000e-27 134.0
64 TraesCS3D01G366400 chr5D 81.988 161 21 5 2657 2809 498193538 498193698 2.660000e-26 130.0
65 TraesCS3D01G366400 chr5D 80.588 170 25 7 2659 2822 482534773 482534606 1.240000e-24 124.0
66 TraesCS3D01G366400 chr5B 92.308 91 7 0 1 91 553751753 553751843 2.660000e-26 130.0
67 TraesCS3D01G366400 chr2B 86.726 113 14 1 146 258 749041832 749041943 1.240000e-24 124.0
68 TraesCS3D01G366400 chr1D 87.156 109 13 1 2657 2764 224144861 224144969 4.450000e-24 122.0
69 TraesCS3D01G366400 chr1D 82.576 132 16 5 2657 2783 359475533 359475404 3.460000e-20 110.0


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 TraesCS3D01G366400 chr3D 480835933 480839213 3280 False 6059.00 6059 100.0000 1 3281 1 chr3D.!!$F2 3280
1 TraesCS3D01G366400 chr3D 480375618 480376842 1224 False 590.50 617 84.6225 888 2207 2 chr3D.!!$F9 1319
2 TraesCS3D01G366400 chr3D 480357809 480358904 1095 False 586.00 649 86.9405 888 2085 2 chr3D.!!$F7 1197
3 TraesCS3D01G366400 chr3D 480157917 480158823 906 False 542.50 562 88.4765 1081 2085 2 chr3D.!!$F6 1004
4 TraesCS3D01G366400 chr3D 480366550 480367610 1060 False 497.00 595 84.0125 888 2085 2 chr3D.!!$F8 1197
5 TraesCS3D01G366400 chr3D 480120544 480126210 5666 False 479.75 592 84.9770 902 2089 4 chr3D.!!$F5 1187
6 TraesCS3D01G366400 chr3B 641653060 641655895 2835 False 3871.00 3871 91.3310 146 3002 1 chr3B.!!$F1 2856
7 TraesCS3D01G366400 chr3B 640832064 640833282 1218 False 622.00 664 85.4685 888 2207 2 chr3B.!!$F2 1319
8 TraesCS3D01G366400 chr3A 623604611 623607368 2757 False 1993.00 3574 93.1675 588 3281 2 chr3A.!!$F5 2693
9 TraesCS3D01G366400 chr3A 623389445 623390647 1202 False 601.50 621 85.1780 888 2197 2 chr3A.!!$F4 1309
10 TraesCS3D01G366400 chr3A 623354308 623355399 1091 False 551.00 595 85.9540 888 2085 2 chr3A.!!$F3 1197
11 TraesCS3D01G366400 chr3A 623340348 623341257 909 False 548.00 562 88.6520 1079 2085 2 chr3A.!!$F2 1006

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
134 135 0.171007 CATGCGTCATTTGGGTGGAC 59.829 55.000 0.0 0.0 0.00 4.02 F
412 416 0.541863 CCCGCATATCCTCCCCATAC 59.458 60.000 0.0 0.0 0.00 2.39 F
1134 4853 1.374190 CTTCCAGCTCACTGCCACT 59.626 57.895 0.0 0.0 43.02 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1134 4853 2.676822 AGAAGCGCCACGAGGAGA 60.677 61.111 2.29 0.0 36.74 3.71 R
2216 5950 1.347707 CAACTACACTGGGCTCTCCAA 59.652 52.381 0.00 0.0 46.51 3.53 R
2571 6315 0.808125 CCACATTTTCGCGATTGGGA 59.192 50.000 10.88 0.0 34.90 4.37 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
77 78 9.686683 ATAATACAATATTATTGTCTCCAGGGC 57.313 33.333 22.10 0.00 34.11 5.19
78 79 5.387113 ACAATATTATTGTCTCCAGGGCA 57.613 39.130 14.87 0.00 0.00 5.36
79 80 5.957132 ACAATATTATTGTCTCCAGGGCAT 58.043 37.500 14.87 0.00 0.00 4.40
81 82 7.702785 ACAATATTATTGTCTCCAGGGCATAT 58.297 34.615 14.87 0.00 0.00 1.78
83 84 9.028284 CAATATTATTGTCTCCAGGGCATATTT 57.972 33.333 8.04 0.00 0.00 1.40
85 86 3.297134 TTGTCTCCAGGGCATATTTCC 57.703 47.619 0.00 0.00 0.00 3.13
86 87 2.204463 TGTCTCCAGGGCATATTTCCA 58.796 47.619 0.00 0.00 0.00 3.53
87 88 2.580322 TGTCTCCAGGGCATATTTCCAA 59.420 45.455 0.00 0.00 0.00 3.53
92 93 1.066002 CAGGGCATATTTCCAACAGCG 59.934 52.381 0.00 0.00 0.00 5.18
93 94 1.064758 AGGGCATATTTCCAACAGCGA 60.065 47.619 0.00 0.00 0.00 4.93
96 97 1.663643 GCATATTTCCAACAGCGACGA 59.336 47.619 0.00 0.00 0.00 4.20
97 98 2.536928 GCATATTTCCAACAGCGACGAC 60.537 50.000 0.00 0.00 0.00 4.34
98 99 2.442212 TATTTCCAACAGCGACGACA 57.558 45.000 0.00 0.00 0.00 4.35
99 100 0.865769 ATTTCCAACAGCGACGACAC 59.134 50.000 0.00 0.00 0.00 3.67
100 101 0.460459 TTTCCAACAGCGACGACACA 60.460 50.000 0.00 0.00 0.00 3.72
101 102 1.149361 TTCCAACAGCGACGACACAC 61.149 55.000 0.00 0.00 0.00 3.82
124 125 4.856801 GCGGGACCCATGCGTCAT 62.857 66.667 12.15 0.00 34.24 3.06
125 126 2.124736 CGGGACCCATGCGTCATT 60.125 61.111 12.15 0.00 34.24 2.57
128 129 1.666209 GGGACCCATGCGTCATTTGG 61.666 60.000 12.39 0.00 34.24 3.28
130 131 4.016838 CCCATGCGTCATTTGGGT 57.983 55.556 9.21 0.00 44.30 4.51
131 132 1.512230 CCCATGCGTCATTTGGGTG 59.488 57.895 9.21 0.00 44.30 4.61
132 133 1.512230 CCATGCGTCATTTGGGTGG 59.488 57.895 0.00 0.00 0.00 4.61
133 134 0.964860 CCATGCGTCATTTGGGTGGA 60.965 55.000 0.00 0.00 0.00 4.02
134 135 0.171007 CATGCGTCATTTGGGTGGAC 59.829 55.000 0.00 0.00 0.00 4.02
136 137 2.867472 CGTCATTTGGGTGGACGC 59.133 61.111 0.00 0.00 46.25 5.19
137 138 2.867472 GTCATTTGGGTGGACGCG 59.133 61.111 3.53 3.53 0.00 6.01
139 140 1.024579 GTCATTTGGGTGGACGCGAT 61.025 55.000 15.93 0.00 0.00 4.58
140 141 1.024046 TCATTTGGGTGGACGCGATG 61.024 55.000 15.93 2.14 0.00 3.84
141 142 1.748879 ATTTGGGTGGACGCGATGG 60.749 57.895 15.93 0.00 0.00 3.51
144 145 2.189521 GGGTGGACGCGATGGATT 59.810 61.111 15.93 0.00 0.00 3.01
165 166 2.503382 GGACGGCCATCTCCTCCTC 61.503 68.421 0.00 0.00 0.00 3.71
166 167 2.835431 ACGGCCATCTCCTCCTCG 60.835 66.667 2.24 0.00 0.00 4.63
171 172 1.075970 CCATCTCCTCCTCGGGACA 60.076 63.158 0.00 0.00 0.00 4.02
172 173 0.687757 CCATCTCCTCCTCGGGACAA 60.688 60.000 0.00 0.00 0.00 3.18
183 184 1.447838 CGGGACAACGTGGGATGAG 60.448 63.158 0.00 0.00 0.00 2.90
196 197 2.362503 ATGAGCCCGGAGTCGACA 60.363 61.111 19.50 0.00 39.00 4.35
198 199 3.827898 GAGCCCGGAGTCGACAGG 61.828 72.222 19.50 16.93 39.00 4.00
203 204 2.701780 CCGGAGTCGACAGGTCTGG 61.702 68.421 19.50 16.71 39.00 3.86
224 225 1.227002 GTGAAGGACTCGGATCCGC 60.227 63.158 29.62 15.32 44.22 5.54
231 232 2.279120 CTCGGATCCGCTGTCAGC 60.279 66.667 29.62 15.22 39.59 4.26
240 241 4.783621 GCTGTCAGCCATGCCGGA 62.784 66.667 14.27 0.00 36.56 5.14
281 282 4.840005 GGCGGAAGGGAGCGAAGG 62.840 72.222 0.00 0.00 0.00 3.46
309 310 1.073923 AGTGAAGTGGCTAGGGTTTGG 59.926 52.381 0.00 0.00 0.00 3.28
313 314 0.770557 AGTGGCTAGGGTTTGGTCCA 60.771 55.000 0.00 0.00 0.00 4.02
316 317 1.378762 GCTAGGGTTTGGTCCAGCA 59.621 57.895 0.00 0.00 32.55 4.41
318 319 1.826385 CTAGGGTTTGGTCCAGCAAG 58.174 55.000 0.00 0.00 0.00 4.01
320 321 1.832167 GGGTTTGGTCCAGCAAGCA 60.832 57.895 7.59 0.00 0.00 3.91
333 334 0.813821 GCAAGCAGATGGGAAGGAAC 59.186 55.000 0.00 0.00 0.00 3.62
338 339 4.096190 AGCAGATGGGAAGGAACATATG 57.904 45.455 0.00 0.00 38.84 1.78
340 341 3.567164 GCAGATGGGAAGGAACATATGTG 59.433 47.826 9.63 0.00 38.28 3.21
344 345 1.569072 GGGAAGGAACATATGTGGGGT 59.431 52.381 9.63 0.00 0.00 4.95
345 346 2.422945 GGGAAGGAACATATGTGGGGTC 60.423 54.545 9.63 2.80 0.00 4.46
346 347 2.561569 GAAGGAACATATGTGGGGTCG 58.438 52.381 9.63 0.00 0.00 4.79
347 348 0.837272 AGGAACATATGTGGGGTCGG 59.163 55.000 9.63 0.00 0.00 4.79
348 349 0.834612 GGAACATATGTGGGGTCGGA 59.165 55.000 9.63 0.00 0.00 4.55
349 350 1.420138 GGAACATATGTGGGGTCGGAT 59.580 52.381 9.63 0.00 0.00 4.18
356 360 3.399181 TGGGGTCGGATGGTCAGC 61.399 66.667 0.00 0.00 0.00 4.26
365 369 1.522092 GATGGTCAGCATGGGTCGA 59.478 57.895 0.00 0.00 36.16 4.20
370 374 2.202797 CAGCATGGGTCGAGTCCG 60.203 66.667 0.00 0.00 37.07 4.79
412 416 0.541863 CCCGCATATCCTCCCCATAC 59.458 60.000 0.00 0.00 0.00 2.39
486 490 2.350964 GCCCGTCTGCGTTGAATTTTTA 60.351 45.455 0.00 0.00 36.15 1.52
488 492 4.437659 GCCCGTCTGCGTTGAATTTTTATA 60.438 41.667 0.00 0.00 36.15 0.98
533 537 1.895231 GGACGTTTGAGGCGGGTTT 60.895 57.895 0.00 0.00 0.00 3.27
539 543 3.740495 TTGAGGCGGGTTTTGGGCA 62.740 57.895 0.00 0.00 0.00 5.36
543 547 2.994417 GCGGGTTTTGGGCATCCA 60.994 61.111 0.00 0.00 42.25 3.41
553 557 2.715749 TGGGCATCCAACTGTAGATG 57.284 50.000 13.57 13.57 40.73 2.90
563 567 8.304202 CATCCAACTGTAGATGCTCTAATTAC 57.696 38.462 7.54 0.00 33.99 1.89
564 568 7.661536 TCCAACTGTAGATGCTCTAATTACT 57.338 36.000 0.00 0.00 29.58 2.24
565 569 8.079211 TCCAACTGTAGATGCTCTAATTACTT 57.921 34.615 0.00 0.00 29.58 2.24
566 570 7.981789 TCCAACTGTAGATGCTCTAATTACTTG 59.018 37.037 0.00 0.00 29.58 3.16
567 571 7.225538 CCAACTGTAGATGCTCTAATTACTTGG 59.774 40.741 0.00 0.00 29.58 3.61
568 572 6.284459 ACTGTAGATGCTCTAATTACTTGGC 58.716 40.000 0.00 0.00 29.58 4.52
570 574 6.889198 TGTAGATGCTCTAATTACTTGGCTT 58.111 36.000 0.00 0.00 29.58 4.35
571 575 6.986817 TGTAGATGCTCTAATTACTTGGCTTC 59.013 38.462 0.00 0.00 29.58 3.86
573 577 4.202245 TGCTCTAATTACTTGGCTTCGT 57.798 40.909 0.00 0.00 0.00 3.85
574 578 4.575885 TGCTCTAATTACTTGGCTTCGTT 58.424 39.130 0.00 0.00 0.00 3.85
577 581 5.220491 GCTCTAATTACTTGGCTTCGTTGAG 60.220 44.000 0.00 0.00 0.00 3.02
965 4642 1.630126 ATGACGCTCCATCAAGGCCT 61.630 55.000 0.00 0.00 37.29 5.19
978 4655 4.938575 TCAAGGCCTCTATAAAACCCAA 57.061 40.909 5.23 0.00 0.00 4.12
1105 4824 3.818787 CAGCCATGGCAAGCCGAC 61.819 66.667 37.18 6.56 44.88 4.79
1114 4833 1.605058 GGCAAGCCGACCTCTCACTA 61.605 60.000 0.00 0.00 0.00 2.74
1134 4853 1.374190 CTTCCAGCTCACTGCCACT 59.626 57.895 0.00 0.00 43.02 4.00
1149 4868 2.992114 ACTCTCCTCGTGGCGCTT 60.992 61.111 7.64 0.00 0.00 4.68
1305 5024 4.379243 ACGCCGGAGCTGAACCTG 62.379 66.667 5.05 0.00 36.60 4.00
1437 5156 4.051167 TACGGCCTCTCGTCCCCA 62.051 66.667 0.00 0.00 42.82 4.96
2144 5875 4.006989 TGTGGGCATTTGTGTACTATGTC 58.993 43.478 0.00 0.00 0.00 3.06
2150 5884 5.334569 GGCATTTGTGTACTATGTCGTTTGT 60.335 40.000 0.00 0.00 0.00 2.83
2156 5890 5.693104 TGTGTACTATGTCGTTTGTCCTTTC 59.307 40.000 0.00 0.00 0.00 2.62
2167 5901 4.676723 CGTTTGTCCTTTCCATGTTTGTGT 60.677 41.667 0.00 0.00 0.00 3.72
2169 5903 4.383850 TGTCCTTTCCATGTTTGTGTTG 57.616 40.909 0.00 0.00 0.00 3.33
2170 5904 3.766591 TGTCCTTTCCATGTTTGTGTTGT 59.233 39.130 0.00 0.00 0.00 3.32
2171 5905 4.950475 TGTCCTTTCCATGTTTGTGTTGTA 59.050 37.500 0.00 0.00 0.00 2.41
2172 5906 5.596361 TGTCCTTTCCATGTTTGTGTTGTAT 59.404 36.000 0.00 0.00 0.00 2.29
2174 5908 6.640907 GTCCTTTCCATGTTTGTGTTGTATTC 59.359 38.462 0.00 0.00 0.00 1.75
2208 5942 5.505286 CATATTCTTTGTTGATGTCTCGGC 58.495 41.667 0.00 0.00 0.00 5.54
2216 5950 4.260985 TGTTGATGTCTCGGCATTGTTAT 58.739 39.130 0.00 0.00 0.00 1.89
2418 6152 2.635714 TGATGCACACACATCCATCTC 58.364 47.619 0.00 0.00 44.84 2.75
2516 6260 4.591038 CCCGTTTGGTTCAAGGGT 57.409 55.556 0.00 0.00 37.36 4.34
2528 6272 0.119155 TCAAGGGTGAGGAGGGACAT 59.881 55.000 0.00 0.00 0.00 3.06
2555 6299 3.182967 GCTAGATGCTCCGAATATTCCG 58.817 50.000 9.87 3.75 38.95 4.30
2556 6300 3.367498 GCTAGATGCTCCGAATATTCCGT 60.367 47.826 9.87 0.00 38.95 4.69
2557 6301 3.032017 AGATGCTCCGAATATTCCGTG 57.968 47.619 9.87 5.80 0.00 4.94
2562 6306 3.372822 TGCTCCGAATATTCCGTGAAAAC 59.627 43.478 9.87 0.00 0.00 2.43
2571 6315 2.871096 TCCGTGAAAACCAGGCTATT 57.129 45.000 0.00 0.00 0.00 1.73
2586 6330 2.293399 GGCTATTCCCAATCGCGAAAAT 59.707 45.455 15.24 10.66 30.91 1.82
2836 6583 3.073678 TCAAATTGATGTCACCTCCACG 58.926 45.455 0.00 0.00 0.00 4.94
2881 6628 7.362920 GCAATTCTCTTCCAAAACATAGCCTTA 60.363 37.037 0.00 0.00 0.00 2.69
2889 6636 7.391148 TCCAAAACATAGCCTTAGTTTGATC 57.609 36.000 0.00 0.00 35.79 2.92
2899 6646 5.476945 AGCCTTAGTTTGATCCGTTTCAATT 59.523 36.000 0.00 0.00 35.64 2.32
2906 6653 3.899734 TGATCCGTTTCAATTGTTGCAG 58.100 40.909 5.13 0.00 0.00 4.41
2940 6687 5.163269 TGTTCATCCAAGCATAGCATAGAGT 60.163 40.000 0.00 0.00 0.00 3.24
2951 6698 6.071447 AGCATAGCATAGAGTAACATCCTCAG 60.071 42.308 0.00 0.00 0.00 3.35
2984 6731 1.478916 TGTGAGTTCGTGACCTTGACA 59.521 47.619 0.00 0.00 0.00 3.58
3021 6823 4.275689 TCCGAATGATCCCAAATTGAATCG 59.724 41.667 0.00 0.00 0.00 3.34
3048 6850 2.490115 GAGACCATCTAGCCCATCGTAG 59.510 54.545 0.00 0.00 0.00 3.51
3049 6851 2.158445 AGACCATCTAGCCCATCGTAGT 60.158 50.000 0.00 0.00 0.00 2.73
3079 6881 2.914838 CCAAAGACGCTAAAAATTCGGC 59.085 45.455 0.00 0.00 0.00 5.54
3086 6888 1.982913 GCTAAAAATTCGGCCGTGTTG 59.017 47.619 27.15 9.99 0.00 3.33
3091 6893 1.369625 AATTCGGCCGTGTTGATCTC 58.630 50.000 27.15 0.00 0.00 2.75
3095 6897 1.003839 GGCCGTGTTGATCTCCACA 60.004 57.895 13.38 3.29 0.00 4.17
3111 6913 2.604011 TCCACACTACGACAACAAAACG 59.396 45.455 0.00 0.00 0.00 3.60
3121 6923 3.609175 CGACAACAAAACGAATGAGCCAT 60.609 43.478 0.00 0.00 0.00 4.40
3169 6971 1.550524 GGAGCTTTTTCATCCCCAACC 59.449 52.381 0.00 0.00 0.00 3.77
3189 6991 3.223854 TTTTTCGACGCGGACGAC 58.776 55.556 24.81 5.08 43.93 4.34
3220 7022 2.485795 TTTTCGGCGGCAACAAGCT 61.486 52.632 10.53 0.00 44.79 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 9.686683 GCCCTGGAGACAATAATATTGTATTAT 57.313 33.333 17.54 5.67 42.06 1.28
52 53 8.664992 TGCCCTGGAGACAATAATATTGTATTA 58.335 33.333 17.54 8.13 42.06 0.98
53 54 7.526041 TGCCCTGGAGACAATAATATTGTATT 58.474 34.615 17.54 9.85 42.06 1.89
54 55 7.090319 TGCCCTGGAGACAATAATATTGTAT 57.910 36.000 17.54 15.00 42.06 2.29
55 56 6.508030 TGCCCTGGAGACAATAATATTGTA 57.492 37.500 17.54 2.84 42.06 2.41
56 57 5.387113 TGCCCTGGAGACAATAATATTGT 57.613 39.130 17.55 17.55 42.06 2.71
57 58 8.585471 AATATGCCCTGGAGACAATAATATTG 57.415 34.615 11.14 11.14 42.06 1.90
58 59 9.247861 GAAATATGCCCTGGAGACAATAATATT 57.752 33.333 0.00 0.00 42.06 1.28
59 60 7.836183 GGAAATATGCCCTGGAGACAATAATAT 59.164 37.037 0.00 0.00 42.06 1.28
61 62 6.012745 GGAAATATGCCCTGGAGACAATAAT 58.987 40.000 0.00 0.00 42.06 1.28
62 63 5.103728 TGGAAATATGCCCTGGAGACAATAA 60.104 40.000 0.00 0.00 42.06 1.40
63 64 4.415179 TGGAAATATGCCCTGGAGACAATA 59.585 41.667 0.00 0.00 42.06 1.90
64 65 3.205056 TGGAAATATGCCCTGGAGACAAT 59.795 43.478 0.00 0.00 42.06 2.71
65 66 2.580322 TGGAAATATGCCCTGGAGACAA 59.420 45.455 0.00 0.00 42.06 3.18
67 68 2.952310 GTTGGAAATATGCCCTGGAGAC 59.048 50.000 0.00 0.00 0.00 3.36
69 70 2.954318 CTGTTGGAAATATGCCCTGGAG 59.046 50.000 0.00 0.00 0.00 3.86
70 71 2.949963 GCTGTTGGAAATATGCCCTGGA 60.950 50.000 0.00 0.00 0.00 3.86
71 72 1.410153 GCTGTTGGAAATATGCCCTGG 59.590 52.381 0.00 0.00 0.00 4.45
72 73 1.066002 CGCTGTTGGAAATATGCCCTG 59.934 52.381 0.00 0.00 0.00 4.45
73 74 1.064758 TCGCTGTTGGAAATATGCCCT 60.065 47.619 0.00 0.00 0.00 5.19
74 75 1.065551 GTCGCTGTTGGAAATATGCCC 59.934 52.381 0.00 0.00 0.00 5.36
75 76 1.268032 CGTCGCTGTTGGAAATATGCC 60.268 52.381 0.00 0.00 0.00 4.40
77 78 2.670905 TGTCGTCGCTGTTGGAAATATG 59.329 45.455 0.00 0.00 0.00 1.78
78 79 2.671396 GTGTCGTCGCTGTTGGAAATAT 59.329 45.455 0.00 0.00 0.00 1.28
79 80 2.063266 GTGTCGTCGCTGTTGGAAATA 58.937 47.619 0.00 0.00 0.00 1.40
81 82 0.460459 TGTGTCGTCGCTGTTGGAAA 60.460 50.000 0.00 0.00 0.00 3.13
83 84 1.590525 GTGTGTCGTCGCTGTTGGA 60.591 57.895 0.00 0.00 0.00 3.53
85 86 2.539503 CGTGTGTCGTCGCTGTTG 59.460 61.111 0.00 0.00 34.52 3.33
96 97 4.712425 GTCCCGCGCTACGTGTGT 62.712 66.667 5.56 0.00 41.42 3.72
108 109 1.748879 AAATGACGCATGGGTCCCG 60.749 57.895 32.59 13.45 36.07 5.14
109 110 1.666209 CCAAATGACGCATGGGTCCC 61.666 60.000 32.59 15.82 36.07 4.46
110 111 1.809207 CCAAATGACGCATGGGTCC 59.191 57.895 32.59 18.92 36.07 4.46
114 115 0.964860 TCCACCCAAATGACGCATGG 60.965 55.000 0.00 0.00 0.00 3.66
116 117 1.305219 CGTCCACCCAAATGACGCAT 61.305 55.000 0.00 0.00 44.29 4.73
117 118 1.963855 CGTCCACCCAAATGACGCA 60.964 57.895 0.00 0.00 44.29 5.24
118 119 2.867472 CGTCCACCCAAATGACGC 59.133 61.111 0.00 0.00 44.29 5.19
121 122 1.024046 CATCGCGTCCACCCAAATGA 61.024 55.000 5.77 0.00 0.00 2.57
122 123 1.429021 CATCGCGTCCACCCAAATG 59.571 57.895 5.77 0.00 0.00 2.32
124 125 2.191786 ATCCATCGCGTCCACCCAAA 62.192 55.000 5.77 0.00 0.00 3.28
125 126 2.191786 AATCCATCGCGTCCACCCAA 62.192 55.000 5.77 0.00 0.00 4.12
128 129 1.887707 GGAATCCATCGCGTCCACC 60.888 63.158 5.77 0.00 0.00 4.61
129 130 2.237751 CGGAATCCATCGCGTCCAC 61.238 63.158 5.77 0.00 0.00 4.02
130 131 2.106131 CGGAATCCATCGCGTCCA 59.894 61.111 5.77 0.00 0.00 4.02
131 132 2.661866 CCGGAATCCATCGCGTCC 60.662 66.667 5.77 3.13 0.00 4.79
132 133 1.949631 GTCCGGAATCCATCGCGTC 60.950 63.158 5.23 0.00 0.00 5.19
133 134 2.106332 GTCCGGAATCCATCGCGT 59.894 61.111 5.23 0.00 0.00 6.01
134 135 3.030308 CGTCCGGAATCCATCGCG 61.030 66.667 5.23 0.00 0.00 5.87
135 136 2.661866 CCGTCCGGAATCCATCGC 60.662 66.667 5.23 0.00 37.50 4.58
136 137 2.661866 GCCGTCCGGAATCCATCG 60.662 66.667 5.23 3.90 37.50 3.84
137 138 2.280865 GGCCGTCCGGAATCCATC 60.281 66.667 5.23 0.00 37.50 3.51
139 140 3.087253 ATGGCCGTCCGGAATCCA 61.087 61.111 19.09 19.09 37.50 3.41
140 141 2.280865 GATGGCCGTCCGGAATCC 60.281 66.667 14.58 8.45 37.50 3.01
141 142 1.301009 GAGATGGCCGTCCGGAATC 60.301 63.158 21.73 5.16 37.50 2.52
144 145 4.458829 AGGAGATGGCCGTCCGGA 62.459 66.667 21.73 0.00 37.97 5.14
165 166 1.447838 CTCATCCCACGTTGTCCCG 60.448 63.158 0.00 0.00 0.00 5.14
166 167 1.745489 GCTCATCCCACGTTGTCCC 60.745 63.158 0.00 0.00 0.00 4.46
183 184 4.131088 GACCTGTCGACTCCGGGC 62.131 72.222 17.92 12.77 36.24 6.13
187 188 1.316706 CCTCCAGACCTGTCGACTCC 61.317 65.000 17.92 3.20 34.09 3.85
196 197 0.489567 AGTCCTTCACCTCCAGACCT 59.510 55.000 0.00 0.00 0.00 3.85
198 199 0.528470 CGAGTCCTTCACCTCCAGAC 59.472 60.000 0.00 0.00 0.00 3.51
203 204 0.747852 GGATCCGAGTCCTTCACCTC 59.252 60.000 0.00 0.00 35.32 3.85
224 225 2.321263 ATCTCCGGCATGGCTGACAG 62.321 60.000 18.09 5.70 37.02 3.51
240 241 0.608640 AAACTCCTGTTCGGCGATCT 59.391 50.000 11.76 0.00 34.96 2.75
249 250 1.528309 CGCCACCCAAACTCCTGTT 60.528 57.895 0.00 0.00 38.16 3.16
278 279 2.224548 GCCACTTCACTCCACTAACCTT 60.225 50.000 0.00 0.00 0.00 3.50
281 282 2.841442 AGCCACTTCACTCCACTAAC 57.159 50.000 0.00 0.00 0.00 2.34
309 310 0.322816 TTCCCATCTGCTTGCTGGAC 60.323 55.000 1.59 0.00 33.99 4.02
313 314 0.700564 TTCCTTCCCATCTGCTTGCT 59.299 50.000 0.00 0.00 0.00 3.91
316 317 4.079558 ACATATGTTCCTTCCCATCTGCTT 60.080 41.667 1.41 0.00 0.00 3.91
318 319 3.567164 CACATATGTTCCTTCCCATCTGC 59.433 47.826 5.37 0.00 0.00 4.26
320 321 3.139025 CCCACATATGTTCCTTCCCATCT 59.861 47.826 5.37 0.00 0.00 2.90
333 334 0.764890 ACCATCCGACCCCACATATG 59.235 55.000 0.00 0.00 0.00 1.78
338 339 2.584608 CTGACCATCCGACCCCAC 59.415 66.667 0.00 0.00 0.00 4.61
340 341 2.746375 ATGCTGACCATCCGACCCC 61.746 63.158 0.00 0.00 0.00 4.95
344 345 1.971505 GACCCATGCTGACCATCCGA 61.972 60.000 0.00 0.00 29.71 4.55
345 346 1.524621 GACCCATGCTGACCATCCG 60.525 63.158 0.00 0.00 29.71 4.18
346 347 1.524621 CGACCCATGCTGACCATCC 60.525 63.158 0.00 0.00 29.71 3.51
347 348 0.531532 CTCGACCCATGCTGACCATC 60.532 60.000 0.00 0.00 29.71 3.51
348 349 1.267574 ACTCGACCCATGCTGACCAT 61.268 55.000 0.00 0.00 33.39 3.55
349 350 1.888436 GACTCGACCCATGCTGACCA 61.888 60.000 0.00 0.00 0.00 4.02
412 416 0.403271 CCCCTCATATCCAGCCCAAG 59.597 60.000 0.00 0.00 0.00 3.61
486 490 8.308931 TGAACGGTCTAGTCATTAACTGTTTAT 58.691 33.333 0.33 0.00 40.38 1.40
488 492 6.423001 GTGAACGGTCTAGTCATTAACTGTTT 59.577 38.462 0.33 0.00 40.38 2.83
553 557 4.630069 TCAACGAAGCCAAGTAATTAGAGC 59.370 41.667 0.00 0.00 0.00 4.09
555 559 5.175859 CCTCAACGAAGCCAAGTAATTAGA 58.824 41.667 0.00 0.00 0.00 2.10
556 560 4.201822 GCCTCAACGAAGCCAAGTAATTAG 60.202 45.833 0.00 0.00 0.00 1.73
558 562 2.488153 GCCTCAACGAAGCCAAGTAATT 59.512 45.455 0.00 0.00 0.00 1.40
559 563 2.084546 GCCTCAACGAAGCCAAGTAAT 58.915 47.619 0.00 0.00 0.00 1.89
560 564 1.071699 AGCCTCAACGAAGCCAAGTAA 59.928 47.619 0.00 0.00 0.00 2.24
561 565 0.685097 AGCCTCAACGAAGCCAAGTA 59.315 50.000 0.00 0.00 0.00 2.24
562 566 0.603975 GAGCCTCAACGAAGCCAAGT 60.604 55.000 0.00 0.00 0.00 3.16
563 567 0.321122 AGAGCCTCAACGAAGCCAAG 60.321 55.000 0.00 0.00 0.00 3.61
564 568 0.973632 TAGAGCCTCAACGAAGCCAA 59.026 50.000 0.00 0.00 0.00 4.52
565 569 0.973632 TTAGAGCCTCAACGAAGCCA 59.026 50.000 0.00 0.00 0.00 4.75
566 570 2.317530 ATTAGAGCCTCAACGAAGCC 57.682 50.000 0.00 0.00 0.00 4.35
567 571 4.434520 AGTAATTAGAGCCTCAACGAAGC 58.565 43.478 0.00 0.00 0.00 3.86
568 572 5.292101 CCAAGTAATTAGAGCCTCAACGAAG 59.708 44.000 0.00 0.00 0.00 3.79
570 574 4.755411 CCAAGTAATTAGAGCCTCAACGA 58.245 43.478 0.00 0.00 0.00 3.85
571 575 3.309954 GCCAAGTAATTAGAGCCTCAACG 59.690 47.826 0.00 0.00 0.00 4.10
573 577 4.844349 AGCCAAGTAATTAGAGCCTCAA 57.156 40.909 0.00 0.00 0.00 3.02
574 578 4.680708 CGAAGCCAAGTAATTAGAGCCTCA 60.681 45.833 0.00 0.00 0.00 3.86
577 581 3.532542 ACGAAGCCAAGTAATTAGAGCC 58.467 45.455 0.00 0.00 0.00 4.70
965 4642 5.354792 GCGTATGGTGTTTGGGTTTTATAGA 59.645 40.000 0.00 0.00 0.00 1.98
978 4655 2.411628 TGGCTATTGCGTATGGTGTT 57.588 45.000 0.00 0.00 40.82 3.32
1134 4853 2.676822 AGAAGCGCCACGAGGAGA 60.677 61.111 2.29 0.00 36.74 3.71
2144 5875 3.796178 CACAAACATGGAAAGGACAAACG 59.204 43.478 0.00 0.00 0.00 3.60
2150 5884 6.549364 AGAATACAACACAAACATGGAAAGGA 59.451 34.615 0.00 0.00 0.00 3.36
2208 5942 3.379372 CACTGGGCTCTCCAATAACAATG 59.621 47.826 0.00 0.00 46.51 2.82
2216 5950 1.347707 CAACTACACTGGGCTCTCCAA 59.652 52.381 0.00 0.00 46.51 3.53
2516 6260 1.997311 CTGCCCATGTCCCTCCTCA 60.997 63.158 0.00 0.00 0.00 3.86
2544 6288 3.064820 CCTGGTTTTCACGGAATATTCGG 59.935 47.826 18.53 18.53 0.00 4.30
2555 6299 2.802719 TGGGAATAGCCTGGTTTTCAC 58.197 47.619 0.00 0.00 36.66 3.18
2556 6300 3.534357 TTGGGAATAGCCTGGTTTTCA 57.466 42.857 0.00 0.00 36.66 2.69
2557 6301 3.066760 CGATTGGGAATAGCCTGGTTTTC 59.933 47.826 0.00 0.00 36.66 2.29
2562 6306 1.230635 CGCGATTGGGAATAGCCTGG 61.231 60.000 0.00 0.00 36.33 4.45
2571 6315 0.808125 CCACATTTTCGCGATTGGGA 59.192 50.000 10.88 0.00 34.90 4.37
2641 6385 5.184287 GGCTAGGTGCACCTATAAACAAAAA 59.816 40.000 39.06 19.75 46.71 1.94
2642 6386 4.703093 GGCTAGGTGCACCTATAAACAAAA 59.297 41.667 39.06 20.45 46.71 2.44
2643 6387 4.266714 GGCTAGGTGCACCTATAAACAAA 58.733 43.478 39.06 21.15 46.71 2.83
2644 6388 3.680475 CGGCTAGGTGCACCTATAAACAA 60.680 47.826 39.06 21.85 46.71 2.83
2699 6444 3.626930 TGCAAGTAGGACACAAAACCTT 58.373 40.909 0.00 0.00 37.68 3.50
2836 6583 2.029649 TGCGGACTACTACAACAACTCC 60.030 50.000 0.00 0.00 0.00 3.85
2881 6628 4.744631 GCAACAATTGAAACGGATCAAACT 59.255 37.500 13.59 0.00 42.22 2.66
2889 6636 1.139163 GGCTGCAACAATTGAAACGG 58.861 50.000 13.59 6.63 0.00 4.44
2899 6646 1.913778 ACATCTTCATGGCTGCAACA 58.086 45.000 0.50 0.00 33.82 3.33
2906 6653 3.490419 GCTTGGATGAACATCTTCATGGC 60.490 47.826 13.34 8.37 45.55 4.40
2940 6687 8.486210 ACAACTATAATCAAGCTGAGGATGTTA 58.514 33.333 0.00 0.00 0.00 2.41
2951 6698 6.310467 TCACGAACTCACAACTATAATCAAGC 59.690 38.462 0.00 0.00 0.00 4.01
2984 6731 0.963962 TTCGGAGCAAGTACGAGGTT 59.036 50.000 0.00 0.00 37.95 3.50
3021 6823 3.031736 TGGGCTAGATGGTCTCAGTTAC 58.968 50.000 0.00 0.00 0.00 2.50
3048 6850 0.992802 GCGTCTTTGGAGTCATCGAC 59.007 55.000 0.00 0.00 0.00 4.20
3049 6851 0.888619 AGCGTCTTTGGAGTCATCGA 59.111 50.000 0.00 0.00 0.00 3.59
3053 6855 5.333798 CGAATTTTTAGCGTCTTTGGAGTCA 60.334 40.000 0.00 0.00 0.00 3.41
3058 6860 2.914838 GCCGAATTTTTAGCGTCTTTGG 59.085 45.455 0.00 0.00 0.00 3.28
3079 6881 2.607187 GTAGTGTGGAGATCAACACGG 58.393 52.381 13.49 0.00 40.39 4.94
3086 6888 3.570926 TGTTGTCGTAGTGTGGAGATC 57.429 47.619 0.00 0.00 0.00 2.75
3091 6893 2.604011 TCGTTTTGTTGTCGTAGTGTGG 59.396 45.455 0.00 0.00 0.00 4.17
3095 6897 4.318546 GCTCATTCGTTTTGTTGTCGTAGT 60.319 41.667 0.00 0.00 0.00 2.73
3147 6949 2.833943 GTTGGGGATGAAAAAGCTCCAT 59.166 45.455 0.00 0.00 0.00 3.41
3189 6991 3.666253 GAAAACCACCCCGCACCG 61.666 66.667 0.00 0.00 0.00 4.94
3197 6999 3.597728 TTGCCGCCGAAAACCACC 61.598 61.111 0.00 0.00 0.00 4.61
3246 7048 3.938963 GGAATGGATTGTCAAGACGCTTA 59.061 43.478 0.00 0.00 0.00 3.09


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

AutoCloner maintained by Alex Coulton.