Multiple sequence alignment - TraesCS4A01G177800

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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 TraesCS4A01G177800 chr4A 100.000 7273 0 0 1 7273 449820126 449812854 0.000000e+00 13431.0
1 TraesCS4A01G177800 chr4A 89.272 261 26 1 1 261 67481724 67481982 7.040000e-85 326.0
2 TraesCS4A01G177800 chr4A 94.805 77 3 1 381 457 67482042 67482117 1.280000e-22 119.0
3 TraesCS4A01G177800 chr4B 96.093 4274 88 17 2430 6678 181690199 181685980 0.000000e+00 6894.0
4 TraesCS4A01G177800 chr4B 93.446 1709 70 24 714 2399 181691892 181690203 0.000000e+00 2497.0
5 TraesCS4A01G177800 chr4B 92.991 214 14 1 7061 7273 181683430 181683217 1.970000e-80 311.0
6 TraesCS4A01G177800 chr4B 91.061 179 14 2 6820 6997 181685740 181685563 2.620000e-59 241.0
7 TraesCS4A01G177800 chr4B 91.045 67 3 1 6698 6761 181685810 181685744 3.610000e-13 87.9
8 TraesCS4A01G177800 chr4B 95.745 47 2 0 2396 2442 181690197 181690243 7.820000e-10 76.8
9 TraesCS4A01G177800 chr4B 97.297 37 1 0 2354 2390 24676260 24676224 6.090000e-06 63.9
10 TraesCS4A01G177800 chr4D 93.657 2617 68 33 4689 7268 119407429 119404874 0.000000e+00 3823.0
11 TraesCS4A01G177800 chr4D 97.370 2205 45 6 2403 4607 119409616 119407425 0.000000e+00 3738.0
12 TraesCS4A01G177800 chr4D 92.662 1608 56 28 713 2282 119411203 119409620 0.000000e+00 2259.0
13 TraesCS4A01G177800 chr4D 89.062 64 3 4 7211 7273 399227073 399227013 7.820000e-10 76.8
14 TraesCS4A01G177800 chr4D 94.000 50 2 1 7225 7273 165888332 165888283 2.810000e-09 75.0
15 TraesCS4A01G177800 chr5D 88.404 733 54 9 2 705 169543702 169542972 0.000000e+00 854.0
16 TraesCS4A01G177800 chr5D 84.821 112 9 7 2353 2462 531995647 531995542 9.980000e-19 106.0
17 TraesCS4A01G177800 chr2B 87.314 741 56 15 1 705 638792234 638792972 0.000000e+00 813.0
18 TraesCS4A01G177800 chr2B 76.545 712 106 41 1 671 710229160 710229851 4.210000e-87 333.0
19 TraesCS4A01G177800 chr2B 95.652 46 2 0 7228 7273 131518240 131518195 2.810000e-09 75.0
20 TraesCS4A01G177800 chr2B 90.244 41 3 1 2339 2379 512119868 512119907 1.300000e-02 52.8
21 TraesCS4A01G177800 chr6B 86.505 741 62 7 1 705 351591564 351592302 0.000000e+00 780.0
22 TraesCS4A01G177800 chr6B 93.333 45 3 0 6804 6848 11584257 11584301 4.710000e-07 67.6
23 TraesCS4A01G177800 chr6B 96.875 32 0 1 2352 2382 486342245 486342214 1.300000e-02 52.8
24 TraesCS4A01G177800 chr5B 83.646 746 58 23 1 715 573830776 573830064 1.710000e-180 643.0
25 TraesCS4A01G177800 chr5B 83.178 107 13 4 2353 2457 671194707 671194604 7.770000e-15 93.5
26 TraesCS4A01G177800 chr3A 82.848 653 101 9 5635 6283 186846071 186845426 6.330000e-160 575.0
27 TraesCS4A01G177800 chr3A 84.971 519 72 5 2475 2990 186848732 186848217 8.360000e-144 521.0
28 TraesCS4A01G177800 chr3A 75.745 738 123 38 4387 5104 186847087 186846386 3.270000e-83 320.0
29 TraesCS4A01G177800 chr3A 90.411 219 21 0 3138 3356 186848218 186848000 9.230000e-74 289.0
30 TraesCS4A01G177800 chr3A 83.832 167 26 1 540 705 580459509 580459343 2.720000e-34 158.0
31 TraesCS4A01G177800 chr3A 85.185 135 18 2 196 328 631504089 631503955 3.540000e-28 137.0
32 TraesCS4A01G177800 chr3A 94.444 36 1 1 6800 6834 222444206 222444171 4.000000e-03 54.7
33 TraesCS4A01G177800 chr3B 82.695 653 102 9 5635 6283 237292012 237291367 2.940000e-158 569.0
34 TraesCS4A01G177800 chr3B 84.423 520 74 6 2474 2990 237294685 237294170 8.420000e-139 505.0
35 TraesCS4A01G177800 chr3B 76.190 735 126 37 4387 5104 237293030 237292328 6.990000e-90 342.0
36 TraesCS4A01G177800 chr3B 89.954 219 22 0 3138 3356 237294171 237293953 4.300000e-72 283.0
37 TraesCS4A01G177800 chr3B 85.083 181 26 1 521 700 414473020 414472840 4.480000e-42 183.0
38 TraesCS4A01G177800 chr3B 84.615 169 25 1 540 707 416286883 416286715 4.510000e-37 167.0
39 TraesCS4A01G177800 chr3B 97.297 37 1 0 2354 2390 452744622 452744658 6.090000e-06 63.9
40 TraesCS4A01G177800 chr3B 91.304 46 2 2 6797 6841 136556773 136556817 2.190000e-05 62.1
41 TraesCS4A01G177800 chr3D 82.542 653 103 9 5635 6283 160613209 160612564 1.370000e-156 564.0
42 TraesCS4A01G177800 chr3D 84.418 507 71 7 2488 2990 160615856 160615354 6.560000e-135 492.0
43 TraesCS4A01G177800 chr3D 90.411 219 21 0 3138 3356 160615355 160615137 9.230000e-74 289.0
44 TraesCS4A01G177800 chr3D 86.029 272 28 5 4834 5104 160613786 160613524 4.300000e-72 283.0
45 TraesCS4A01G177800 chr1A 87.013 231 18 3 6064 6292 566584952 566584732 4.360000e-62 250.0
46 TraesCS4A01G177800 chr1A 93.069 101 5 2 6392 6490 566584716 566584616 5.880000e-31 147.0
47 TraesCS4A01G177800 chr1B 84.466 206 12 10 6287 6490 657280588 657280401 1.250000e-42 185.0
48 TraesCS4A01G177800 chr1B 78.857 175 36 1 532 705 100489352 100489526 4.610000e-22 117.0
49 TraesCS4A01G177800 chr1B 78.363 171 33 4 538 705 595158314 595158145 2.770000e-19 108.0
50 TraesCS4A01G177800 chr1B 92.453 53 2 2 6787 6839 48412450 48412500 2.810000e-09 75.0
51 TraesCS4A01G177800 chr1B 92.453 53 2 2 6787 6839 48487921 48487971 2.810000e-09 75.0
52 TraesCS4A01G177800 chr5A 83.929 168 24 3 540 705 599336992 599337158 2.720000e-34 158.0
53 TraesCS4A01G177800 chr2A 82.759 174 28 2 540 711 467115510 467115683 3.510000e-33 154.0
54 TraesCS4A01G177800 chr2A 92.000 50 4 0 7224 7273 628727935 628727984 3.640000e-08 71.3
55 TraesCS4A01G177800 chr2A 91.489 47 2 2 6796 6841 552325769 552325724 6.090000e-06 63.9
56 TraesCS4A01G177800 chr1D 83.962 106 13 3 2353 2458 109479413 109479514 1.670000e-16 99.0
57 TraesCS4A01G177800 chr1D 94.118 34 2 0 2418 2451 30095359 30095326 1.300000e-02 52.8
58 TraesCS4A01G177800 chrUn 84.375 96 11 3 2352 2445 94184266 94184173 2.790000e-14 91.6
59 TraesCS4A01G177800 chr2D 97.826 46 1 0 7228 7273 605457338 605457293 6.050000e-11 80.5
60 TraesCS4A01G177800 chr2D 95.652 46 1 1 7228 7273 79979887 79979843 1.010000e-08 73.1
61 TraesCS4A01G177800 chr6D 97.826 46 0 1 7228 7273 150779906 150779862 2.180000e-10 78.7
62 TraesCS4A01G177800 chr7D 77.670 103 14 7 2353 2455 213385327 213385234 4.000000e-03 54.7


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 TraesCS4A01G177800 chr4A 449812854 449820126 7272 True 13431.000000 13431 100.00000 1 7273 1 chr4A.!!$R1 7272
1 TraesCS4A01G177800 chr4B 181683217 181691892 8675 True 2006.180000 6894 92.92720 714 7273 5 chr4B.!!$R2 6559
2 TraesCS4A01G177800 chr4D 119404874 119411203 6329 True 3273.333333 3823 94.56300 713 7268 3 chr4D.!!$R3 6555
3 TraesCS4A01G177800 chr5D 169542972 169543702 730 True 854.000000 854 88.40400 2 705 1 chr5D.!!$R1 703
4 TraesCS4A01G177800 chr2B 638792234 638792972 738 False 813.000000 813 87.31400 1 705 1 chr2B.!!$F2 704
5 TraesCS4A01G177800 chr2B 710229160 710229851 691 False 333.000000 333 76.54500 1 671 1 chr2B.!!$F3 670
6 TraesCS4A01G177800 chr6B 351591564 351592302 738 False 780.000000 780 86.50500 1 705 1 chr6B.!!$F2 704
7 TraesCS4A01G177800 chr5B 573830064 573830776 712 True 643.000000 643 83.64600 1 715 1 chr5B.!!$R1 714
8 TraesCS4A01G177800 chr3A 186845426 186848732 3306 True 426.250000 575 83.49375 2475 6283 4 chr3A.!!$R4 3808
9 TraesCS4A01G177800 chr3B 237291367 237294685 3318 True 424.750000 569 83.31550 2474 6283 4 chr3B.!!$R3 3809
10 TraesCS4A01G177800 chr3D 160612564 160615856 3292 True 407.000000 564 85.85000 2488 6283 4 chr3D.!!$R1 3795

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
782 848 0.322906 GGTCCCAAGAGGCCAAAGAG 60.323 60.000 5.01 0.00 33.37 2.85 F
1045 1119 0.043334 CCCTCCTCTCCTTTCCCTCA 59.957 60.000 0.00 0.00 0.00 3.86 F
1766 1874 0.398696 TTGGTGCTACATCAACCGGT 59.601 50.000 0.00 0.00 28.74 5.28 F
2938 3046 0.603707 TCAGCAGCTGCAACTGGTAC 60.604 55.000 38.24 7.79 46.21 3.34 F
3802 3916 0.745468 CCCGCAACTACTACCTCCTC 59.255 60.000 0.00 0.00 0.00 3.71 F
4969 5306 3.651803 GTGGATCCTCACCTTCTATCG 57.348 52.381 14.23 0.00 0.00 2.92 F
5734 6076 2.688666 ATCAAGCGAGCCTGGGGA 60.689 61.111 0.00 0.00 0.00 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2290 2398 0.610232 AGCAAAGGGACAGCATGGAC 60.610 55.000 0.00 0.00 43.62 4.02 R
2938 3046 0.035458 AGTTGTTCCGAAGAGGCTGG 59.965 55.000 0.00 0.00 40.77 4.85 R
3230 3341 0.816825 CCACTTGCAGCAGTGTCAGT 60.817 55.000 15.60 7.37 42.45 3.41 R
4827 5164 2.694628 TCAAGAATGCAACAGGCTGTTT 59.305 40.909 29.32 15.83 38.77 2.83 R
5734 6076 2.156917 CATTCATATGCCGAGCCACAT 58.843 47.619 0.00 0.00 0.00 3.21 R
5996 6339 0.179006 CTGGGGGCTTCTTGCTATCC 60.179 60.000 0.00 0.00 42.39 2.59 R
7245 9838 0.454196 TGTATGAGCGCTTGCGTCTA 59.546 50.000 13.26 3.62 45.69 2.59 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
28 29 3.707793 GATGTCTCGAACCGAATTAGCT 58.292 45.455 0.00 0.00 34.74 3.32
29 30 4.856664 GATGTCTCGAACCGAATTAGCTA 58.143 43.478 0.00 0.00 34.74 3.32
69 70 3.133362 ACCGAAACTGAGTACTTTGGTGA 59.867 43.478 7.91 0.00 0.00 4.02
87 88 4.393680 TGGTGATAAGTTCGGTTTGCATAC 59.606 41.667 0.00 0.00 0.00 2.39
89 90 3.062909 TGATAAGTTCGGTTTGCATACGC 59.937 43.478 1.02 0.00 39.24 4.42
155 156 1.301401 CTGAGCGGACCGAAAACCA 60.301 57.895 20.50 6.04 0.00 3.67
157 158 1.161563 TGAGCGGACCGAAAACCAAC 61.162 55.000 20.50 0.00 0.00 3.77
162 163 2.227149 GCGGACCGAAAACCAACTAAAT 59.773 45.455 20.50 0.00 0.00 1.40
169 170 5.704053 ACCGAAAACCAACTAAATAGAGGTG 59.296 40.000 9.09 0.00 36.15 4.00
187 188 2.048597 CGACCTGTGCGCCTGTTA 60.049 61.111 4.18 0.00 0.00 2.41
247 263 2.164422 CCTATCTGACAAGTGCGTGAGA 59.836 50.000 0.00 0.00 33.53 3.27
261 277 2.821366 GAGACCCACAGCCGCATG 60.821 66.667 0.00 0.00 0.00 4.06
263 279 4.408821 GACCCACAGCCGCATGGA 62.409 66.667 13.88 0.00 38.34 3.41
268 284 2.110967 CACAGCCGCATGGAGAAGG 61.111 63.158 0.00 0.00 37.49 3.46
273 289 3.197790 CGCATGGAGAAGGCACGG 61.198 66.667 0.00 0.00 0.00 4.94
281 297 1.066430 GGAGAAGGCACGGACATAACA 60.066 52.381 0.00 0.00 0.00 2.41
283 299 0.719465 GAAGGCACGGACATAACACG 59.281 55.000 0.00 0.00 0.00 4.49
375 418 1.833630 TGCATGGAGTAGTTAGCTGCT 59.166 47.619 7.57 7.57 40.41 4.24
484 544 4.578871 AGCTACATGCACTGTACATTCAA 58.421 39.130 0.00 0.00 45.94 2.69
519 582 5.523916 CGACTGCTGCTAATACAGGTAAAAT 59.476 40.000 0.00 0.00 38.16 1.82
538 603 7.012044 GGTAAAATGTAGCGATTCCAGTACATT 59.988 37.037 0.00 0.00 44.29 2.71
571 636 0.531311 GTGGAACCGACGACCAAACT 60.531 55.000 0.00 0.00 35.40 2.66
588 653 5.300792 ACCAAACTGAAATTTCGGTACACAT 59.699 36.000 28.48 13.14 45.62 3.21
591 656 7.863375 CCAAACTGAAATTTCGGTACACATAAA 59.137 33.333 28.48 0.24 45.62 1.40
612 677 9.704098 CATAAACTTCGGTTAGCTAATCTTTTC 57.296 33.333 14.67 0.00 37.14 2.29
671 737 8.953368 ATTTTAAATATACCGAAGAACCGACT 57.047 30.769 0.00 0.00 0.00 4.18
676 742 0.886563 ACCGAAGAACCGACTCGAAT 59.113 50.000 0.00 0.00 0.00 3.34
738 804 2.866762 GCGTTGTTCCTAAGCTATCCTG 59.133 50.000 0.00 0.00 0.00 3.86
782 848 0.322906 GGTCCCAAGAGGCCAAAGAG 60.323 60.000 5.01 0.00 33.37 2.85
790 856 1.004440 AGGCCAAAGAGACAGACGC 60.004 57.895 5.01 0.00 0.00 5.19
834 905 1.314875 ATCCAGATCCCCCTCCTCCA 61.315 60.000 0.00 0.00 0.00 3.86
836 907 1.316266 CAGATCCCCCTCCTCCACT 59.684 63.158 0.00 0.00 0.00 4.00
906 977 4.083862 GACAGCGACCCCCACCTC 62.084 72.222 0.00 0.00 0.00 3.85
1039 1113 1.909986 GTAAGCACCCTCCTCTCCTTT 59.090 52.381 0.00 0.00 0.00 3.11
1040 1114 0.988063 AAGCACCCTCCTCTCCTTTC 59.012 55.000 0.00 0.00 0.00 2.62
1042 1116 1.916206 GCACCCTCCTCTCCTTTCCC 61.916 65.000 0.00 0.00 0.00 3.97
1043 1117 0.252927 CACCCTCCTCTCCTTTCCCT 60.253 60.000 0.00 0.00 0.00 4.20
1044 1118 0.043485 ACCCTCCTCTCCTTTCCCTC 59.957 60.000 0.00 0.00 0.00 4.30
1045 1119 0.043334 CCCTCCTCTCCTTTCCCTCA 59.957 60.000 0.00 0.00 0.00 3.86
1094 1168 4.397832 GTTTCCCCGTGCGCCCTA 62.398 66.667 4.18 0.00 0.00 3.53
1095 1169 4.397832 TTTCCCCGTGCGCCCTAC 62.398 66.667 4.18 0.00 0.00 3.18
1212 1291 4.020218 GTCGAGATCCCCCATTTGATGATA 60.020 45.833 0.00 0.00 0.00 2.15
1255 1334 4.878439 TCACGCTACAGTGTTGATAAACT 58.122 39.130 9.00 0.00 42.40 2.66
1280 1363 2.452600 TCAAGTTTTTCTGCCTGGGT 57.547 45.000 0.00 0.00 0.00 4.51
1285 1368 5.652014 TCAAGTTTTTCTGCCTGGGTATATG 59.348 40.000 0.00 0.00 0.00 1.78
1304 1387 9.899226 GGTATATGATTCTTCTATTGTTTTGCC 57.101 33.333 0.00 0.00 0.00 4.52
1307 1390 6.325919 TGATTCTTCTATTGTTTTGCCGTT 57.674 33.333 0.00 0.00 0.00 4.44
1332 1440 3.745799 TGCGGATTTCAGTCCAGTTTTA 58.254 40.909 0.00 0.00 38.21 1.52
1346 1454 9.280174 CAGTCCAGTTTTACCTATGAAAGTTAA 57.720 33.333 0.00 0.00 0.00 2.01
1412 1520 2.747460 GCAGCATTCGGGCAGTCA 60.747 61.111 0.00 0.00 35.83 3.41
1676 1784 4.065281 GGCGCTACGTCCACTGGT 62.065 66.667 7.64 0.00 0.00 4.00
1766 1874 0.398696 TTGGTGCTACATCAACCGGT 59.601 50.000 0.00 0.00 28.74 5.28
1916 2024 3.197434 GGTTTGTACCATTCTCGCAAC 57.803 47.619 0.00 0.00 44.36 4.17
1993 2101 8.318412 TGCATTTACTGAATCTTTACCTGTCTA 58.682 33.333 0.00 0.00 0.00 2.59
2026 2134 5.543507 TGTGTTTAATTGCCAACCTTGAT 57.456 34.783 0.00 0.00 0.00 2.57
2165 2273 8.467402 ACTTTGAAATATCTCTGTCAAGTACG 57.533 34.615 0.00 0.00 31.98 3.67
2166 2274 8.088981 ACTTTGAAATATCTCTGTCAAGTACGT 58.911 33.333 0.00 0.00 31.98 3.57
2167 2275 9.569167 CTTTGAAATATCTCTGTCAAGTACGTA 57.431 33.333 0.00 0.00 31.98 3.57
2213 2321 9.666626 CTACTAGTTGAAGTTTATGATCGGTAG 57.333 37.037 0.00 0.00 0.00 3.18
2214 2322 7.490000 ACTAGTTGAAGTTTATGATCGGTAGG 58.510 38.462 0.00 0.00 0.00 3.18
2257 2365 6.120905 TCATCAGTAGGAGTGTAGGACTAAC 58.879 44.000 0.00 0.00 33.83 2.34
2290 2398 6.205101 ACTGTCACCCTATAAACTCGTTAG 57.795 41.667 0.00 0.00 0.00 2.34
2376 2484 6.604795 GCTACTACCTCCGTCCCATAATATAA 59.395 42.308 0.00 0.00 0.00 0.98
2382 2490 6.154706 ACCTCCGTCCCATAATATAAGATGTC 59.845 42.308 0.00 0.00 0.00 3.06
2399 2507 7.953158 AAGATGTCATTACAACCGAGATATG 57.047 36.000 0.00 0.00 39.58 1.78
2400 2508 7.290110 AGATGTCATTACAACCGAGATATGA 57.710 36.000 0.00 0.00 39.58 2.15
2401 2509 7.901029 AGATGTCATTACAACCGAGATATGAT 58.099 34.615 0.00 0.00 39.58 2.45
2491 2599 8.711457 CGTTTCCTTTTTAGACCGATAGTTTTA 58.289 33.333 0.00 0.00 0.00 1.52
2577 2685 1.691434 GCTTTGGTGGGTTTGGATCAA 59.309 47.619 0.00 0.00 0.00 2.57
2938 3046 0.603707 TCAGCAGCTGCAACTGGTAC 60.604 55.000 38.24 7.79 46.21 3.34
3085 3196 3.127548 CCTGTGTTACATTCCATGTGCTC 59.872 47.826 0.00 0.00 44.60 4.26
3230 3341 6.112734 CAGCCTTATGTACAAACACCTGATA 58.887 40.000 0.00 0.00 38.78 2.15
3337 3448 6.973642 TGAAGAATTGAGGTGGGAAGATTAT 58.026 36.000 0.00 0.00 0.00 1.28
3365 3476 4.591498 GTGGGGACAAAGGTAAAGGAAATT 59.409 41.667 0.00 0.00 46.06 1.82
3564 3675 9.598517 TCTATTTCAAATGTCCCATTATTTTGC 57.401 29.630 0.00 0.00 0.00 3.68
3800 3914 1.143401 GCCCGCAACTACTACCTCC 59.857 63.158 0.00 0.00 0.00 4.30
3801 3915 1.328430 GCCCGCAACTACTACCTCCT 61.328 60.000 0.00 0.00 0.00 3.69
3802 3916 0.745468 CCCGCAACTACTACCTCCTC 59.255 60.000 0.00 0.00 0.00 3.71
3872 3986 9.847224 TCTTCTCTATTTGGAAATAATACCACC 57.153 33.333 0.00 0.00 35.81 4.61
3907 4030 5.130145 TCAACAACCCAAATCCTTTCAATGT 59.870 36.000 0.00 0.00 0.00 2.71
4339 4635 9.448587 AGTATTCAGACCCCTAATACTTAATGT 57.551 33.333 0.00 0.00 41.41 2.71
4553 4882 7.043059 ACGTAAATATGGTGCAACAAACAAAAG 60.043 33.333 9.38 1.15 39.98 2.27
4644 4977 5.848036 GTCAATTGTATATGCTAGCTTTGCG 59.152 40.000 17.23 0.00 0.00 4.85
4969 5306 3.651803 GTGGATCCTCACCTTCTATCG 57.348 52.381 14.23 0.00 0.00 2.92
5090 5431 9.220767 CAAGGAGGGTATTATTTATAGCAGTTC 57.779 37.037 0.00 0.00 38.66 3.01
5265 5606 5.402270 GCCACGAAAATATAATGCAACATCC 59.598 40.000 0.00 0.00 0.00 3.51
5266 5607 6.502652 CCACGAAAATATAATGCAACATCCA 58.497 36.000 0.00 0.00 0.00 3.41
5455 5797 3.841255 CCCTAGAGAGAACCCAAGAAGTT 59.159 47.826 0.00 0.00 0.00 2.66
5734 6076 2.688666 ATCAAGCGAGCCTGGGGA 60.689 61.111 0.00 0.00 0.00 4.81
5748 6090 2.818169 GGGGATGTGGCTCGGCATA 61.818 63.158 0.00 0.00 0.00 3.14
5996 6339 4.150627 CGTGAAGTGATTGTGTACAAGGAG 59.849 45.833 0.00 0.00 39.47 3.69
6149 6492 2.957402 TGTTGGTGAAGAAGGCTGAT 57.043 45.000 0.00 0.00 0.00 2.90
6234 6577 2.232941 CACTTCAGCTCCTACGGGTTTA 59.767 50.000 0.00 0.00 0.00 2.01
6347 6690 2.888594 TGTAGCTTTGGTCGATGTAGC 58.111 47.619 0.00 0.00 0.00 3.58
6348 6691 2.496070 TGTAGCTTTGGTCGATGTAGCT 59.504 45.455 15.37 15.37 43.93 3.32
6349 6692 2.015736 AGCTTTGGTCGATGTAGCTG 57.984 50.000 11.77 0.00 40.45 4.24
6350 6693 1.009829 GCTTTGGTCGATGTAGCTGG 58.990 55.000 0.00 0.00 0.00 4.85
6351 6694 1.676014 GCTTTGGTCGATGTAGCTGGT 60.676 52.381 0.00 0.00 0.00 4.00
6352 6695 2.271800 CTTTGGTCGATGTAGCTGGTC 58.728 52.381 0.00 0.00 0.00 4.02
6353 6696 1.557099 TTGGTCGATGTAGCTGGTCT 58.443 50.000 0.00 0.00 0.00 3.85
6354 6697 0.817654 TGGTCGATGTAGCTGGTCTG 59.182 55.000 0.00 0.00 0.00 3.51
6355 6698 0.103208 GGTCGATGTAGCTGGTCTGG 59.897 60.000 0.00 0.00 0.00 3.86
6356 6699 0.818296 GTCGATGTAGCTGGTCTGGT 59.182 55.000 0.00 0.00 0.00 4.00
6381 6724 4.200092 GGTCTGGGAGAATATTGGTTGTC 58.800 47.826 0.00 0.00 0.00 3.18
6386 6729 3.319122 GGGAGAATATTGGTTGTCATGCC 59.681 47.826 0.00 0.00 0.00 4.40
6514 6874 9.154847 CAATGAACTGACATCTGTACAAATCTA 57.845 33.333 0.00 0.00 0.00 1.98
6540 6900 8.470805 AGTCGATGAATAATCTTGTTACTGTCT 58.529 33.333 0.00 0.00 32.61 3.41
6642 7004 8.223769 CGTAATGTAATCATCATTAGCCAAGTC 58.776 37.037 0.00 0.00 38.08 3.01
6663 7025 7.918536 AGTCTCATAACAGTACGAAGAACTA 57.081 36.000 0.00 0.00 0.00 2.24
6714 7226 4.589908 ACCTCTGCTCGGAATTAATTGTT 58.410 39.130 5.17 0.00 0.00 2.83
6811 7327 6.387041 TCCATCGTCTACTACAAACTATGG 57.613 41.667 0.00 0.00 37.51 2.74
6812 7328 5.889853 TCCATCGTCTACTACAAACTATGGT 59.110 40.000 0.00 0.00 37.46 3.55
6813 7329 7.056006 TCCATCGTCTACTACAAACTATGGTA 58.944 38.462 0.00 0.00 37.46 3.25
6814 7330 7.012704 TCCATCGTCTACTACAAACTATGGTAC 59.987 40.741 0.00 0.00 37.46 3.34
6815 7331 6.349973 TCGTCTACTACAAACTATGGTACG 57.650 41.667 0.00 0.00 0.00 3.67
6816 7332 4.966366 CGTCTACTACAAACTATGGTACGC 59.034 45.833 0.00 0.00 0.00 4.42
6817 7333 5.447683 CGTCTACTACAAACTATGGTACGCA 60.448 44.000 0.00 0.00 0.00 5.24
6818 7334 6.324819 GTCTACTACAAACTATGGTACGCAA 58.675 40.000 0.00 0.00 0.00 4.85
6819 7335 6.976925 GTCTACTACAAACTATGGTACGCAAT 59.023 38.462 0.00 0.00 0.00 3.56
6820 7336 7.490402 GTCTACTACAAACTATGGTACGCAATT 59.510 37.037 0.00 0.00 0.00 2.32
6821 7337 8.036575 TCTACTACAAACTATGGTACGCAATTT 58.963 33.333 0.00 0.00 0.00 1.82
6822 7338 6.837992 ACTACAAACTATGGTACGCAATTTG 58.162 36.000 12.38 12.38 0.00 2.32
6823 7339 4.481463 ACAAACTATGGTACGCAATTTGC 58.519 39.130 11.42 11.42 40.69 3.68
6824 7340 4.022762 ACAAACTATGGTACGCAATTTGCA 60.023 37.500 20.56 1.59 45.36 4.08
6864 7380 5.762825 ATAGACAATGGTAGCATGCTTTG 57.237 39.130 28.02 24.60 0.00 2.77
6909 7426 3.023119 TCTTTGAACAGGTTGTGCACAT 58.977 40.909 22.39 3.78 35.19 3.21
6910 7427 4.203226 TCTTTGAACAGGTTGTGCACATA 58.797 39.130 22.39 9.00 35.19 2.29
6986 7505 1.899437 GCCCAGGTGGACGAGAATCA 61.899 60.000 0.00 0.00 37.39 2.57
7052 8362 9.334947 GATCAAGTCCAATCTTCAGATCAATTA 57.665 33.333 0.00 0.00 32.24 1.40
7087 9675 1.067635 CCTTTCCATCGCAAGGTTTGG 60.068 52.381 0.00 0.00 35.67 3.28
7112 9700 2.228822 CCTCCAAAAACATCCTGTTCCG 59.771 50.000 0.00 0.00 40.14 4.30
7119 9707 2.683933 ATCCTGTTCCGACCGCCT 60.684 61.111 0.00 0.00 0.00 5.52
7168 9759 0.179045 CCCTCTTAATCCCGCACCTG 60.179 60.000 0.00 0.00 0.00 4.00
7226 9818 2.100252 CGCTCCCGGTATTCTTGTAGAA 59.900 50.000 0.00 0.00 38.78 2.10
7268 9861 0.159554 CGCAAGCGCTCATACATACG 59.840 55.000 12.06 0.00 35.30 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.480759 GGTGCTAGCTAATTCGGTTCGA 60.481 50.000 17.23 0.00 0.00 3.71
42 43 5.347907 CCAAAGTACTCAGTTTCGGTGTATC 59.652 44.000 0.00 0.00 0.00 2.24
55 56 5.011329 ACCGAACTTATCACCAAAGTACTCA 59.989 40.000 0.00 0.00 36.17 3.41
69 70 3.063452 CAGCGTATGCAAACCGAACTTAT 59.937 43.478 10.11 0.00 46.23 1.73
87 88 3.795659 GAACTTAGTTCGGTTTTCAGCG 58.204 45.455 9.47 0.00 45.61 5.18
138 139 1.146485 TTGGTTTTCGGTCCGCTCA 59.854 52.632 6.34 0.00 0.00 4.26
247 263 4.415150 CTCCATGCGGCTGTGGGT 62.415 66.667 19.79 0.00 36.15 4.51
261 277 1.066430 TGTTATGTCCGTGCCTTCTCC 60.066 52.381 0.00 0.00 0.00 3.71
263 279 1.671850 CGTGTTATGTCCGTGCCTTCT 60.672 52.381 0.00 0.00 0.00 2.85
268 284 0.668096 TCACCGTGTTATGTCCGTGC 60.668 55.000 0.00 0.00 0.00 5.34
269 285 1.458064 GTTCACCGTGTTATGTCCGTG 59.542 52.381 0.00 0.00 0.00 4.94
375 418 9.459640 CTTTATTACTCTGTACAATTAGCGCTA 57.540 33.333 14.45 14.45 0.00 4.26
507 567 6.588204 TGGAATCGCTACATTTTACCTGTAT 58.412 36.000 0.00 0.00 0.00 2.29
519 582 4.109766 CGAAATGTACTGGAATCGCTACA 58.890 43.478 0.00 0.00 0.00 2.74
538 603 2.280524 CCACCGAACAGCACCGAA 60.281 61.111 0.00 0.00 0.00 4.30
567 632 8.626526 AGTTTATGTGTACCGAAATTTCAGTTT 58.373 29.630 17.99 1.66 0.00 2.66
571 636 7.292292 CGAAGTTTATGTGTACCGAAATTTCA 58.708 34.615 17.99 0.00 30.95 2.69
588 653 9.498176 AAGAAAAGATTAGCTAACCGAAGTTTA 57.502 29.630 8.70 0.00 37.42 2.01
591 656 7.117956 GTCAAGAAAAGATTAGCTAACCGAAGT 59.882 37.037 8.70 0.00 0.00 3.01
648 714 6.692681 CGAGTCGGTTCTTCGGTATATTTAAA 59.307 38.462 4.10 0.00 0.00 1.52
705 771 3.663176 CAACGCCACAGCCCACAG 61.663 66.667 0.00 0.00 34.57 3.66
706 772 4.497984 ACAACGCCACAGCCCACA 62.498 61.111 0.00 0.00 34.57 4.17
707 773 3.194272 GAACAACGCCACAGCCCAC 62.194 63.158 0.00 0.00 34.57 4.61
710 776 0.887387 TTAGGAACAACGCCACAGCC 60.887 55.000 0.00 0.00 34.57 4.85
738 804 1.437986 CGGCTCTATATAGCGGGGC 59.562 63.158 4.75 8.73 43.74 5.80
775 841 1.738099 CCGGCGTCTGTCTCTTTGG 60.738 63.158 6.01 0.00 0.00 3.28
834 905 7.097834 AGGAGACGAAAAGATAATCGAAAAGT 58.902 34.615 1.84 0.00 41.43 2.66
836 907 6.534079 GGAGGAGACGAAAAGATAATCGAAAA 59.466 38.462 1.84 0.00 41.43 2.29
1091 1165 5.064314 AGGGAAAGCTACTACTAGGTAGG 57.936 47.826 9.14 0.00 40.13 3.18
1092 1166 4.756135 CGAGGGAAAGCTACTACTAGGTAG 59.244 50.000 0.00 3.50 41.43 3.18
1093 1167 4.410228 TCGAGGGAAAGCTACTACTAGGTA 59.590 45.833 0.00 0.00 30.15 3.08
1094 1168 3.201708 TCGAGGGAAAGCTACTACTAGGT 59.798 47.826 0.00 0.00 31.70 3.08
1095 1169 3.818180 TCGAGGGAAAGCTACTACTAGG 58.182 50.000 0.00 0.00 0.00 3.02
1096 1170 5.764131 CAATCGAGGGAAAGCTACTACTAG 58.236 45.833 0.00 0.00 0.00 2.57
1212 1291 8.060090 GCGTGAAAGCATTATTATTAGTAACGT 58.940 33.333 0.00 0.00 37.05 3.99
1255 1334 3.318839 CAGGCAGAAAAACTTGATGGACA 59.681 43.478 0.00 0.00 0.00 4.02
1256 1335 3.305608 CCAGGCAGAAAAACTTGATGGAC 60.306 47.826 0.00 0.00 0.00 4.02
1280 1363 9.337396 ACGGCAAAACAATAGAAGAATCATATA 57.663 29.630 0.00 0.00 0.00 0.86
1285 1368 5.572896 CCAACGGCAAAACAATAGAAGAATC 59.427 40.000 0.00 0.00 0.00 2.52
1304 1387 0.591170 ACTGAAATCCGCAACCAACG 59.409 50.000 0.00 0.00 0.00 4.10
1307 1390 0.109532 TGGACTGAAATCCGCAACCA 59.890 50.000 0.00 0.00 42.24 3.67
1332 1440 7.554835 TGGCGTCAATAATTAACTTTCATAGGT 59.445 33.333 0.00 0.00 0.00 3.08
1346 1454 2.378038 AGCAACCATGGCGTCAATAAT 58.622 42.857 13.04 0.00 36.08 1.28
1394 1502 2.747460 GACTGCCCGAATGCTGCA 60.747 61.111 4.13 4.13 33.92 4.41
1912 2020 5.473039 ACAGAAATTAAATGCTGAGGTTGC 58.527 37.500 5.46 0.00 32.86 4.17
1916 2024 7.754027 CAGAAGAACAGAAATTAAATGCTGAGG 59.246 37.037 5.46 0.00 32.86 3.86
2026 2134 9.631257 TTCATTGCCAGATTCTTCTTTGATATA 57.369 29.630 0.00 0.00 0.00 0.86
2164 2272 9.845305 GTAGCAGCAGTTACTATTTTTAATACG 57.155 33.333 0.00 0.00 0.00 3.06
2214 2322 7.768120 ACTGATGAAGTGATGAAGGAAATAGTC 59.232 37.037 0.00 0.00 37.88 2.59
2257 2365 8.665685 GTTTATAGGGTGACAGTATTTCAAGTG 58.334 37.037 0.00 0.00 0.00 3.16
2290 2398 0.610232 AGCAAAGGGACAGCATGGAC 60.610 55.000 0.00 0.00 43.62 4.02
2376 2484 7.290110 TCATATCTCGGTTGTAATGACATCT 57.710 36.000 0.00 0.00 34.86 2.90
2639 2747 1.407258 GTTGTGGTGCCAAAAGTGCTA 59.593 47.619 0.00 0.00 0.00 3.49
2733 2841 2.102578 AGCACCACCAAATAAGGATGC 58.897 47.619 0.00 0.00 0.00 3.91
2938 3046 0.035458 AGTTGTTCCGAAGAGGCTGG 59.965 55.000 0.00 0.00 40.77 4.85
3085 3196 3.000041 TCCGCAATTACACAACTGCTAG 59.000 45.455 0.00 0.00 32.52 3.42
3230 3341 0.816825 CCACTTGCAGCAGTGTCAGT 60.817 55.000 15.60 7.37 42.45 3.41
3337 3448 1.122632 TACCTTTGTCCCCACGCTGA 61.123 55.000 0.00 0.00 0.00 4.26
3365 3476 7.371159 CAATAGCATACTACTCGATTCCAGAA 58.629 38.462 0.00 0.00 0.00 3.02
3419 3530 5.417580 AGAAAATAAGAACCATTAGCCGCAA 59.582 36.000 0.00 0.00 0.00 4.85
3745 3856 3.614150 CGGAGTAGTAGCAAAAGCACTCA 60.614 47.826 7.62 0.00 35.26 3.41
3872 3986 5.766150 TTGGGTTGTTGAATAGTGAAGTG 57.234 39.130 0.00 0.00 0.00 3.16
4577 4906 6.042208 AGTTTCTTTCTCTACAAGCCTACACT 59.958 38.462 0.00 0.00 0.00 3.55
4644 4977 4.453819 AGAGATAAACAAGAACACAGCAGC 59.546 41.667 0.00 0.00 0.00 5.25
4823 5160 2.704725 ATGCAACAGGCTGTTTTACG 57.295 45.000 29.32 18.92 38.77 3.18
4826 5163 3.132646 TCAAGAATGCAACAGGCTGTTTT 59.867 39.130 29.32 21.06 38.77 2.43
4827 5164 2.694628 TCAAGAATGCAACAGGCTGTTT 59.305 40.909 29.32 15.83 38.77 2.83
4969 5306 5.106157 CCGGCAAACTTGATATCCCATATTC 60.106 44.000 0.00 0.00 0.00 1.75
5038 5378 3.215151 TCTCTACTATCCTTCCACGCTG 58.785 50.000 0.00 0.00 0.00 5.18
5041 5381 4.083003 GCTCATCTCTACTATCCTTCCACG 60.083 50.000 0.00 0.00 0.00 4.94
5090 5431 3.187637 GCTCTAGATACCTCAGTAGCACG 59.812 52.174 0.00 0.00 37.33 5.34
5265 5606 2.795329 ACAGTCCTAACCTTGCCATTG 58.205 47.619 0.00 0.00 0.00 2.82
5266 5607 3.525800 AACAGTCCTAACCTTGCCATT 57.474 42.857 0.00 0.00 0.00 3.16
5455 5797 3.262151 TGGTCTGTTGGACGGATTATCAA 59.738 43.478 0.00 0.00 45.35 2.57
5555 5897 9.660180 GGAGAAAGAATACAGACAGTTCTAAAT 57.340 33.333 0.00 0.00 32.26 1.40
5734 6076 2.156917 CATTCATATGCCGAGCCACAT 58.843 47.619 0.00 0.00 0.00 3.21
5748 6090 2.236146 TCTCAACGGTAGCACCATTCAT 59.764 45.455 6.21 0.00 38.47 2.57
5996 6339 0.179006 CTGGGGGCTTCTTGCTATCC 60.179 60.000 0.00 0.00 42.39 2.59
6149 6492 0.474854 TAAACTCCACCCCCTGCTCA 60.475 55.000 0.00 0.00 0.00 4.26
6158 6501 3.367025 CGTCAAACGAGATAAACTCCACC 59.633 47.826 0.00 0.00 46.05 4.61
6234 6577 2.048127 GTCGGCTTCGGCTTCACT 60.048 61.111 0.00 0.00 41.44 3.41
6347 6690 1.548357 CCCAGACCAGACCAGACCAG 61.548 65.000 0.00 0.00 0.00 4.00
6348 6691 1.536418 CCCAGACCAGACCAGACCA 60.536 63.158 0.00 0.00 0.00 4.02
6349 6692 1.229209 TCCCAGACCAGACCAGACC 60.229 63.158 0.00 0.00 0.00 3.85
6350 6693 0.251832 TCTCCCAGACCAGACCAGAC 60.252 60.000 0.00 0.00 0.00 3.51
6351 6694 0.487325 TTCTCCCAGACCAGACCAGA 59.513 55.000 0.00 0.00 0.00 3.86
6352 6695 1.577736 ATTCTCCCAGACCAGACCAG 58.422 55.000 0.00 0.00 0.00 4.00
6353 6696 2.940514 TATTCTCCCAGACCAGACCA 57.059 50.000 0.00 0.00 0.00 4.02
6354 6697 3.181450 CCAATATTCTCCCAGACCAGACC 60.181 52.174 0.00 0.00 0.00 3.85
6355 6698 3.456277 ACCAATATTCTCCCAGACCAGAC 59.544 47.826 0.00 0.00 0.00 3.51
6356 6699 3.736094 ACCAATATTCTCCCAGACCAGA 58.264 45.455 0.00 0.00 0.00 3.86
6381 6724 3.695060 AGCATTCAGAGAAGAAAGGCATG 59.305 43.478 0.00 0.00 35.56 4.06
6386 6729 5.816258 TCATAGCAGCATTCAGAGAAGAAAG 59.184 40.000 0.00 0.00 0.00 2.62
6514 6874 8.470805 AGACAGTAACAAGATTATTCATCGACT 58.529 33.333 0.00 0.00 36.93 4.18
6540 6900 4.099881 GCCAAAAGGATGCATTCTATCCAA 59.900 41.667 8.25 0.00 45.28 3.53
6546 6906 2.532843 ACTGCCAAAAGGATGCATTCT 58.467 42.857 0.01 0.01 33.97 2.40
6627 6989 6.765036 ACTGTTATGAGACTTGGCTAATGATG 59.235 38.462 0.00 0.00 0.00 3.07
6628 6990 6.893583 ACTGTTATGAGACTTGGCTAATGAT 58.106 36.000 0.00 0.00 0.00 2.45
6629 6991 6.299805 ACTGTTATGAGACTTGGCTAATGA 57.700 37.500 0.00 0.00 0.00 2.57
6630 6992 6.199154 CGTACTGTTATGAGACTTGGCTAATG 59.801 42.308 0.00 0.00 0.00 1.90
6642 7004 8.912787 ATGTTAGTTCTTCGTACTGTTATGAG 57.087 34.615 0.00 0.00 0.00 2.90
6683 7045 2.950309 TCCGAGCAGAGGTAGTACAATC 59.050 50.000 2.06 0.00 0.00 2.67
6684 7046 3.014304 TCCGAGCAGAGGTAGTACAAT 57.986 47.619 2.06 0.00 0.00 2.71
6714 7226 6.934083 TCTGTGTGAATACATTAGTTTGAGCA 59.066 34.615 0.00 0.00 39.39 4.26
6750 7265 2.231964 TGAAATGCCAGAAATGCCTCAC 59.768 45.455 0.00 0.00 0.00 3.51
6815 7331 4.864916 TTCTCGAGAGTATGCAAATTGC 57.135 40.909 15.94 11.58 45.29 3.56
6841 7357 5.653769 ACAAAGCATGCTACCATTGTCTATT 59.346 36.000 23.50 8.08 0.00 1.73
6850 7366 2.293122 GTGAACACAAAGCATGCTACCA 59.707 45.455 23.00 8.36 0.00 3.25
6864 7380 4.278975 AGGATTGGAGAAGAGTGAACAC 57.721 45.455 0.00 0.00 0.00 3.32
6921 7438 1.162698 CTGCACAACATGTCCTCTGG 58.837 55.000 0.00 0.00 0.00 3.86
7003 7522 3.833070 AGACGTCTCATACCTCCAAAACT 59.167 43.478 13.58 0.00 0.00 2.66
7052 8362 5.261040 TGGAAAGGAATTTGACAGGAGAT 57.739 39.130 0.00 0.00 0.00 2.75
7087 9675 1.821136 CAGGATGTTTTTGGAGGCTCC 59.179 52.381 26.95 26.95 36.96 4.70
7112 9700 2.981859 TTTGGAGATAGAAGGCGGTC 57.018 50.000 0.00 0.00 0.00 4.79
7136 9727 2.044946 GAGGGATTTGGGCGTGCT 60.045 61.111 0.00 0.00 0.00 4.40
7168 9759 1.477295 ACCGAGCAAACTAGACTAGGC 59.523 52.381 14.03 7.64 30.07 3.93
7245 9838 0.454196 TGTATGAGCGCTTGCGTCTA 59.546 50.000 13.26 3.62 45.69 2.59


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

AutoCloner maintained by Alex Coulton.