Multiple sequence alignment - TraesCS5A01G088800

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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 TraesCS5A01G088800 chr5A 100.000 2515 0 0 1 2515 119064650 119067164 0.000000e+00 4645.0
1 TraesCS5A01G088800 chr5A 85.753 372 22 9 1703 2057 543950463 543950820 5.110000e-97 364.0
2 TraesCS5A01G088800 chr5A 85.797 345 31 2 1704 2030 621680707 621681051 1.430000e-92 350.0
3 TraesCS5A01G088800 chr5A 85.057 348 34 6 1704 2033 371756399 371756052 3.100000e-89 339.0
4 TraesCS5A01G088800 chr5A 92.537 201 15 0 2052 2252 371754264 371754064 3.170000e-74 289.0
5 TraesCS5A01G088800 chr5A 93.671 158 9 1 2358 2515 371754067 371753911 4.180000e-58 235.0
6 TraesCS5A01G088800 chr5A 79.320 353 38 16 1380 1706 555589525 555589868 5.450000e-52 215.0
7 TraesCS5A01G088800 chr5A 94.958 119 6 0 2240 2358 9610211 9610329 1.190000e-43 187.0
8 TraesCS5A01G088800 chr6A 90.724 1919 99 38 366 2251 568060754 568058882 0.000000e+00 2484.0
9 TraesCS5A01G088800 chr6A 92.828 488 32 2 1 487 479396653 479397138 0.000000e+00 704.0
10 TraesCS5A01G088800 chr6A 90.230 522 36 10 1 517 68526374 68526885 0.000000e+00 667.0
11 TraesCS5A01G088800 chr6A 87.368 380 27 3 1699 2060 425737119 425737495 1.390000e-112 416.0
12 TraesCS5A01G088800 chr6A 91.060 302 12 7 148 447 531553362 531553650 6.520000e-106 394.0
13 TraesCS5A01G088800 chr6A 93.467 199 13 0 2052 2250 425740468 425740666 1.890000e-76 296.0
14 TraesCS5A01G088800 chr6A 94.578 166 6 1 2353 2515 568058885 568058720 1.150000e-63 254.0
15 TraesCS5A01G088800 chr6A 94.400 125 6 1 2242 2365 475435048 475435172 9.180000e-45 191.0
16 TraesCS5A01G088800 chr4A 92.829 502 24 7 1 502 16863242 16862753 0.000000e+00 717.0
17 TraesCS5A01G088800 chr4A 97.391 115 3 0 2241 2355 315236464 315236350 1.970000e-46 196.0
18 TraesCS5A01G088800 chr4A 88.000 150 14 3 372 518 374639927 374640075 9.250000e-40 174.0
19 TraesCS5A01G088800 chr4A 86.335 161 14 7 366 520 374638132 374638290 4.300000e-38 169.0
20 TraesCS5A01G088800 chr2B 97.512 402 10 0 1 402 70818992 70819393 0.000000e+00 688.0
21 TraesCS5A01G088800 chr2B 94.000 200 11 1 2052 2251 282451099 282451297 4.070000e-78 302.0
22 TraesCS5A01G088800 chr2B 93.500 200 12 1 2052 2251 609286404 609286206 1.890000e-76 296.0
23 TraesCS5A01G088800 chr3B 93.305 463 30 1 763 1225 198146479 198146018 0.000000e+00 682.0
24 TraesCS5A01G088800 chr3B 95.294 255 9 2 148 402 806992309 806992058 3.900000e-108 401.0
25 TraesCS5A01G088800 chr3B 84.533 375 27 9 1703 2060 145897886 145897526 2.400000e-90 342.0
26 TraesCS5A01G088800 chr3B 96.203 158 6 0 2358 2515 818193618 818193775 2.480000e-65 259.0
27 TraesCS5A01G088800 chr3B 96.203 158 6 0 2358 2515 818229366 818229523 2.480000e-65 259.0
28 TraesCS5A01G088800 chr2A 97.015 402 10 2 1 402 641390934 641390535 0.000000e+00 675.0
29 TraesCS5A01G088800 chr2A 94.355 124 5 2 2242 2364 507071277 507071155 3.300000e-44 189.0
30 TraesCS5A01G088800 chr6B 93.246 459 20 3 1 459 511340898 511340451 0.000000e+00 665.0
31 TraesCS5A01G088800 chr5D 85.940 569 64 7 675 1228 439710508 439711075 5.990000e-166 593.0
32 TraesCS5A01G088800 chr5D 86.207 348 29 3 1704 2033 390802431 390802085 2.380000e-95 359.0
33 TraesCS5A01G088800 chr5D 84.076 314 28 11 1380 1681 439711301 439711604 1.470000e-72 283.0
34 TraesCS5A01G088800 chr5D 93.077 130 7 2 2236 2363 424123670 424123541 3.300000e-44 189.0
35 TraesCS5A01G088800 chr5B 82.662 571 68 18 673 1224 534470716 534471274 6.290000e-131 477.0
36 TraesCS5A01G088800 chr5B 88.889 351 29 6 148 497 700056094 700055753 8.320000e-115 424.0
37 TraesCS5A01G088800 chr5B 86.933 375 28 10 1703 2060 239333318 239332948 3.900000e-108 401.0
38 TraesCS5A01G088800 chr5B 83.954 349 34 10 1380 1706 534471492 534471840 5.220000e-82 315.0
39 TraesCS5A01G088800 chr5B 95.570 158 7 0 2358 2515 487464707 487464550 1.150000e-63 254.0
40 TraesCS5A01G088800 chr7A 97.398 269 7 0 1 269 518152211 518152479 2.280000e-125 459.0
41 TraesCS5A01G088800 chr7A 86.316 380 28 9 1699 2060 299381910 299381537 2.350000e-105 392.0
42 TraesCS5A01G088800 chr7A 84.195 348 37 6 1704 2033 498731735 498731388 3.120000e-84 322.0
43 TraesCS5A01G088800 chr7A 93.500 200 13 0 2052 2251 299378441 299378242 5.260000e-77 298.0
44 TraesCS5A01G088800 chr7A 96.203 158 6 0 2358 2515 11043726 11043883 2.480000e-65 259.0
45 TraesCS5A01G088800 chr7A 93.671 158 9 1 2358 2515 498729406 498729250 4.180000e-58 235.0
46 TraesCS5A01G088800 chr6D 87.500 376 30 4 1702 2060 384292769 384292394 3.870000e-113 418.0
47 TraesCS5A01G088800 chr6D 85.215 372 24 7 1703 2057 291654504 291654861 1.110000e-93 353.0
48 TraesCS5A01G088800 chr6D 93.500 200 11 1 2052 2251 210884065 210884262 1.890000e-76 296.0
49 TraesCS5A01G088800 chr6D 94.444 72 4 0 1703 1774 210780357 210780428 7.350000e-21 111.0
50 TraesCS5A01G088800 chr1A 87.368 380 25 4 1699 2060 520852371 520852745 5.010000e-112 414.0
51 TraesCS5A01G088800 chr1A 93.970 199 12 0 2052 2250 520855721 520855919 4.070000e-78 302.0
52 TraesCS5A01G088800 chr1A 99.091 110 1 0 2247 2356 498178704 498178595 5.490000e-47 198.0
53 TraesCS5A01G088800 chr1A 95.798 119 3 2 2249 2365 343396696 343396814 9.180000e-45 191.0
54 TraesCS5A01G088800 chr4B 86.595 373 33 4 1702 2057 159345412 159345784 1.810000e-106 396.0
55 TraesCS5A01G088800 chr1B 85.345 348 33 6 1704 2033 235376746 235376399 6.660000e-91 344.0
56 TraesCS5A01G088800 chr2D 84.677 372 26 6 1703 2057 617518027 617518384 2.400000e-90 342.0
57 TraesCS5A01G088800 chr3A 95.187 187 9 0 2064 2250 703928931 703928745 1.890000e-76 296.0
58 TraesCS5A01G088800 chr3A 96.203 158 6 0 2358 2515 550449011 550449168 2.480000e-65 259.0
59 TraesCS5A01G088800 chr3A 97.391 115 3 0 2249 2363 517028742 517028628 1.970000e-46 196.0
60 TraesCS5A01G088800 chr3A 86.335 161 12 7 363 521 6772095 6772247 1.550000e-37 167.0
61 TraesCS5A01G088800 chr3A 87.179 78 10 0 1699 1776 234510989 234511066 3.450000e-14 89.8
62 TraesCS5A01G088800 chr7D 96.203 158 5 1 2358 2515 560904079 560904235 8.930000e-65 257.0
63 TraesCS5A01G088800 chr7D 91.667 132 8 3 2242 2371 251359478 251359608 1.990000e-41 180.0
64 TraesCS5A01G088800 chr4D 86.061 165 12 3 1903 2057 465051746 465051909 1.550000e-37 167.0


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 TraesCS5A01G088800 chr5A 119064650 119067164 2514 False 4645.000000 4645 100.000000 1 2515 1 chr5A.!!$F2 2514
1 TraesCS5A01G088800 chr5A 371753911 371756399 2488 True 287.666667 339 90.421667 1704 2515 3 chr5A.!!$R1 811
2 TraesCS5A01G088800 chr6A 568058720 568060754 2034 True 1369.000000 2484 92.651000 366 2515 2 chr6A.!!$R1 2149
3 TraesCS5A01G088800 chr6A 68526374 68526885 511 False 667.000000 667 90.230000 1 517 1 chr6A.!!$F1 516
4 TraesCS5A01G088800 chr6A 425737119 425740666 3547 False 356.000000 416 90.417500 1699 2250 2 chr6A.!!$F5 551
5 TraesCS5A01G088800 chr5D 439710508 439711604 1096 False 438.000000 593 85.008000 675 1681 2 chr5D.!!$F1 1006
6 TraesCS5A01G088800 chr5B 534470716 534471840 1124 False 396.000000 477 83.308000 673 1706 2 chr5B.!!$F1 1033
7 TraesCS5A01G088800 chr7A 299378242 299381910 3668 True 345.000000 392 89.908000 1699 2251 2 chr7A.!!$R1 552
8 TraesCS5A01G088800 chr7A 498729250 498731735 2485 True 278.500000 322 88.933000 1704 2515 2 chr7A.!!$R2 811
9 TraesCS5A01G088800 chr1A 520852371 520855919 3548 False 358.000000 414 90.669000 1699 2250 2 chr1A.!!$F2 551

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
146 147 1.001503 GGGGTGGGGATTGAATGCA 59.998 57.895 0.00 0.0 0.00 3.96 F
1132 1171 0.536724 TGCTCTGGCGCTTGATTCTA 59.463 50.000 7.64 0.0 42.25 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1255 1319 0.463620 TGCCAACCAGCCAGAAAAAC 59.536 50.000 0.0 0.0 0.00 2.43 R
2260 5678 1.274167 ACCTGCGACAAGTAATTCGGA 59.726 47.619 0.0 0.0 35.73 4.55 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
43 44 3.960102 AGTCATGGAGAAGAGAGGATGAC 59.040 47.826 0.00 0.00 39.89 3.06
68 69 4.130118 GTGATGGATGTGGATAAGGTCAC 58.870 47.826 0.00 0.00 34.71 3.67
84 85 1.134670 GTCACGGGAGGAGAAAGATGG 60.135 57.143 0.00 0.00 0.00 3.51
146 147 1.001503 GGGGTGGGGATTGAATGCA 59.998 57.895 0.00 0.00 0.00 3.96
167 168 2.378038 TGTTGCAACTGCTCCTTTCTT 58.622 42.857 28.61 0.00 42.66 2.52
168 169 2.760092 TGTTGCAACTGCTCCTTTCTTT 59.240 40.909 28.61 0.00 42.66 2.52
169 170 3.195396 TGTTGCAACTGCTCCTTTCTTTT 59.805 39.130 28.61 0.00 42.66 2.27
170 171 4.183865 GTTGCAACTGCTCCTTTCTTTTT 58.816 39.130 22.36 0.00 42.66 1.94
171 172 4.045636 TGCAACTGCTCCTTTCTTTTTC 57.954 40.909 2.95 0.00 42.66 2.29
174 175 4.742167 GCAACTGCTCCTTTCTTTTTCTTC 59.258 41.667 0.00 0.00 38.21 2.87
179 180 7.615403 ACTGCTCCTTTCTTTTTCTTCTTTTT 58.385 30.769 0.00 0.00 0.00 1.94
181 182 8.926715 TGCTCCTTTCTTTTTCTTCTTTTTAC 57.073 30.769 0.00 0.00 0.00 2.01
184 185 7.485810 TCCTTTCTTTTTCTTCTTTTTACGGG 58.514 34.615 0.00 0.00 0.00 5.28
208 209 1.901650 GCAACTGCTCCTACGTGCAC 61.902 60.000 6.82 6.82 34.86 4.57
229 230 2.346803 GCACTGGCTAAATCAACTCGA 58.653 47.619 0.00 0.00 36.96 4.04
235 236 5.070446 ACTGGCTAAATCAACTCGATCCATA 59.930 40.000 0.00 0.00 31.11 2.74
275 276 2.035961 ACGCGGATGCATCTAAGTGTAT 59.964 45.455 25.28 7.26 42.97 2.29
281 282 6.423905 GCGGATGCATCTAAGTGTATTCTTAA 59.576 38.462 25.28 0.00 42.15 1.85
285 286 9.604626 GATGCATCTAAGTGTATTCTTAAATGC 57.395 33.333 19.70 14.10 46.18 3.56
349 350 3.301794 TTCCCATGATGCACTATGCTT 57.698 42.857 2.02 0.00 45.31 3.91
407 416 7.061752 CACAGGTATTTGTGCTAGTTCTAAC 57.938 40.000 0.00 0.00 41.65 2.34
408 417 6.874134 CACAGGTATTTGTGCTAGTTCTAACT 59.126 38.462 0.39 0.39 41.65 2.24
409 418 8.033038 CACAGGTATTTGTGCTAGTTCTAACTA 58.967 37.037 2.76 2.76 41.65 2.24
410 419 8.591072 ACAGGTATTTGTGCTAGTTCTAACTAA 58.409 33.333 4.27 0.00 40.70 2.24
411 420 9.431887 CAGGTATTTGTGCTAGTTCTAACTAAA 57.568 33.333 4.27 0.00 40.70 1.85
429 438 9.274065 CTAACTAAATTTAAAGCACGGATTGAC 57.726 33.333 0.00 0.00 0.00 3.18
455 464 1.606224 GGGTTCACCGTCACAATACGT 60.606 52.381 0.00 0.00 41.27 3.57
456 465 2.137523 GGTTCACCGTCACAATACGTT 58.862 47.619 0.00 0.00 41.27 3.99
457 466 2.545106 GGTTCACCGTCACAATACGTTT 59.455 45.455 0.00 0.00 41.27 3.60
464 473 6.257411 TCACCGTCACAATACGTTTTTCTTTA 59.743 34.615 0.00 0.00 41.27 1.85
465 474 7.041916 TCACCGTCACAATACGTTTTTCTTTAT 60.042 33.333 0.00 0.00 41.27 1.40
466 475 7.059033 CACCGTCACAATACGTTTTTCTTTATG 59.941 37.037 0.00 0.00 41.27 1.90
551 569 1.533731 GAAAAATCGGTTCGCTGGACA 59.466 47.619 0.00 0.00 0.00 4.02
1016 1050 2.022240 GAGATGCGGGAGTGGGAGTC 62.022 65.000 0.00 0.00 0.00 3.36
1097 1136 2.158914 AGGTACGGTTCCGTTTGTTTCT 60.159 45.455 21.64 8.17 42.88 2.52
1132 1171 0.536724 TGCTCTGGCGCTTGATTCTA 59.463 50.000 7.64 0.00 42.25 2.10
1203 1250 0.780637 ATAGCTGAGATCCCGGGAGA 59.219 55.000 30.42 6.89 0.00 3.71
1241 1305 2.037144 GGGACCGGTAAATGCTCTCTA 58.963 52.381 7.34 0.00 0.00 2.43
1255 1319 3.928992 TGCTCTCTACTCATCGCTTTTTG 59.071 43.478 0.00 0.00 0.00 2.44
1256 1320 3.929610 GCTCTCTACTCATCGCTTTTTGT 59.070 43.478 0.00 0.00 0.00 2.83
1262 1326 7.226720 TCTCTACTCATCGCTTTTTGTTTTTCT 59.773 33.333 0.00 0.00 0.00 2.52
1263 1327 7.132213 TCTACTCATCGCTTTTTGTTTTTCTG 58.868 34.615 0.00 0.00 0.00 3.02
1264 1328 5.043248 ACTCATCGCTTTTTGTTTTTCTGG 58.957 37.500 0.00 0.00 0.00 3.86
1347 1415 4.521130 ACTCTGCACTTTGATTAGTCGA 57.479 40.909 0.00 0.00 0.00 4.20
1481 1610 1.798813 GCGACACCGACAAGAGAAATT 59.201 47.619 0.00 0.00 38.22 1.82
1556 1699 2.876581 CCTGGTCCAAACTTTTAGGCT 58.123 47.619 0.00 0.00 0.00 4.58
1560 1703 4.794334 TGGTCCAAACTTTTAGGCTTACA 58.206 39.130 0.00 0.00 0.00 2.41
1611 1761 5.047377 TCTGCTTGCGTCCATACATGATATA 60.047 40.000 0.00 0.00 0.00 0.86
1723 1879 2.202610 CTCGATGCAGAACGGCGA 60.203 61.111 16.62 0.00 36.28 5.54
1904 2069 1.341778 GGTAGGAGAAGAAGGACGGGA 60.342 57.143 0.00 0.00 0.00 5.14
1921 2086 1.272704 GGGAAAGAAGGAAGGGTGCAT 60.273 52.381 0.00 0.00 0.00 3.96
1953 2121 1.367840 GTGCGAGGACACTGGTCTT 59.632 57.895 0.00 0.00 43.77 3.01
1955 2123 1.367840 GCGAGGACACTGGTCTTGT 59.632 57.895 0.00 0.00 43.77 3.16
2025 2202 4.262463 CCACTTCAGAGCAAGGTACTGTTA 60.262 45.833 0.00 0.00 40.86 2.41
2035 2212 7.614583 AGAGCAAGGTACTGTTATAGAACTACA 59.385 37.037 1.39 0.00 40.86 2.74
2051 2228 4.078639 ACTACAAAGAAGCAAGCTGACT 57.921 40.909 0.00 0.00 0.00 3.41
2163 5581 6.019748 TGGTCTCAAGGAGAATTCTTACTCT 58.980 40.000 9.87 2.92 40.59 3.24
2251 5669 8.039603 TGTTTTTCGAATGCTTATCATGTACT 57.960 30.769 0.00 0.00 35.13 2.73
2252 5670 8.175069 TGTTTTTCGAATGCTTATCATGTACTC 58.825 33.333 0.00 0.00 35.13 2.59
2253 5671 6.844696 TTTCGAATGCTTATCATGTACTCC 57.155 37.500 0.00 0.00 35.13 3.85
2254 5672 4.883083 TCGAATGCTTATCATGTACTCCC 58.117 43.478 0.00 0.00 35.13 4.30
2255 5673 4.588951 TCGAATGCTTATCATGTACTCCCT 59.411 41.667 0.00 0.00 35.13 4.20
2256 5674 4.926238 CGAATGCTTATCATGTACTCCCTC 59.074 45.833 0.00 0.00 35.13 4.30
2257 5675 4.899352 ATGCTTATCATGTACTCCCTCC 57.101 45.455 0.00 0.00 33.26 4.30
2258 5676 2.628178 TGCTTATCATGTACTCCCTCCG 59.372 50.000 0.00 0.00 0.00 4.63
2259 5677 2.628657 GCTTATCATGTACTCCCTCCGT 59.371 50.000 0.00 0.00 0.00 4.69
2260 5678 3.069729 GCTTATCATGTACTCCCTCCGTT 59.930 47.826 0.00 0.00 0.00 4.44
2261 5679 4.796618 GCTTATCATGTACTCCCTCCGTTC 60.797 50.000 0.00 0.00 0.00 3.95
2262 5680 1.481871 TCATGTACTCCCTCCGTTCC 58.518 55.000 0.00 0.00 0.00 3.62
2263 5681 0.102481 CATGTACTCCCTCCGTTCCG 59.898 60.000 0.00 0.00 0.00 4.30
2264 5682 0.033796 ATGTACTCCCTCCGTTCCGA 60.034 55.000 0.00 0.00 0.00 4.55
2265 5683 0.251297 TGTACTCCCTCCGTTCCGAA 60.251 55.000 0.00 0.00 0.00 4.30
2266 5684 1.109609 GTACTCCCTCCGTTCCGAAT 58.890 55.000 0.00 0.00 0.00 3.34
2267 5685 1.479730 GTACTCCCTCCGTTCCGAATT 59.520 52.381 0.00 0.00 0.00 2.17
2268 5686 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
2269 5687 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
2270 5688 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
2271 5689 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
2272 5690 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
2273 5691 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
2274 5692 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2275 5693 2.597305 CTCCGTTCCGAATTACTTGTCG 59.403 50.000 0.00 0.00 37.01 4.35
2276 5694 1.060122 CCGTTCCGAATTACTTGTCGC 59.940 52.381 0.00 0.00 35.93 5.19
2277 5695 1.722464 CGTTCCGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 35.93 5.10
2278 5696 2.222508 CGTTCCGAATTACTTGTCGCAG 60.223 50.000 0.00 0.00 35.93 5.18
2279 5697 2.004583 TCCGAATTACTTGTCGCAGG 57.995 50.000 0.00 0.00 35.93 4.85
2280 5698 1.274167 TCCGAATTACTTGTCGCAGGT 59.726 47.619 0.00 0.91 35.93 4.00
2281 5699 2.492881 TCCGAATTACTTGTCGCAGGTA 59.507 45.455 0.00 0.00 35.93 3.08
2282 5700 3.131577 TCCGAATTACTTGTCGCAGGTAT 59.868 43.478 3.46 0.00 35.93 2.73
2283 5701 3.245284 CCGAATTACTTGTCGCAGGTATG 59.755 47.826 3.46 0.00 35.93 2.39
2284 5702 3.245284 CGAATTACTTGTCGCAGGTATGG 59.755 47.826 3.46 0.00 0.00 2.74
2285 5703 4.439057 GAATTACTTGTCGCAGGTATGGA 58.561 43.478 3.46 0.00 0.00 3.41
2286 5704 4.689612 ATTACTTGTCGCAGGTATGGAT 57.310 40.909 3.46 0.00 0.00 3.41
2287 5705 2.315925 ACTTGTCGCAGGTATGGATG 57.684 50.000 0.00 0.00 0.00 3.51
2288 5706 1.555075 ACTTGTCGCAGGTATGGATGT 59.445 47.619 0.00 0.00 0.00 3.06
2289 5707 2.764010 ACTTGTCGCAGGTATGGATGTA 59.236 45.455 0.00 0.00 0.00 2.29
2290 5708 3.388024 ACTTGTCGCAGGTATGGATGTAT 59.612 43.478 0.00 0.00 0.00 2.29
2291 5709 3.660501 TGTCGCAGGTATGGATGTATC 57.339 47.619 0.00 0.00 0.00 2.24
2292 5710 3.230976 TGTCGCAGGTATGGATGTATCT 58.769 45.455 0.00 0.00 0.00 1.98
2293 5711 4.403734 TGTCGCAGGTATGGATGTATCTA 58.596 43.478 0.00 0.00 0.00 1.98
2294 5712 4.459337 TGTCGCAGGTATGGATGTATCTAG 59.541 45.833 0.00 0.00 0.00 2.43
2295 5713 4.700692 GTCGCAGGTATGGATGTATCTAGA 59.299 45.833 0.00 0.00 0.00 2.43
2296 5714 5.358442 GTCGCAGGTATGGATGTATCTAGAT 59.642 44.000 10.73 10.73 0.00 1.98
2297 5715 5.358160 TCGCAGGTATGGATGTATCTAGATG 59.642 44.000 15.79 0.00 0.00 2.90
2298 5716 5.126222 CGCAGGTATGGATGTATCTAGATGT 59.874 44.000 15.79 1.25 0.00 3.06
2299 5717 6.318900 CGCAGGTATGGATGTATCTAGATGTA 59.681 42.308 15.79 4.44 0.00 2.29
2300 5718 7.013750 CGCAGGTATGGATGTATCTAGATGTAT 59.986 40.741 15.79 9.11 0.00 2.29
2301 5719 8.700051 GCAGGTATGGATGTATCTAGATGTATT 58.300 37.037 15.79 0.00 0.00 1.89
2331 5749 9.347934 GTTCTAGATACATCCATTTCTATGACG 57.652 37.037 0.00 0.00 33.37 4.35
2332 5750 8.863872 TCTAGATACATCCATTTCTATGACGA 57.136 34.615 0.00 0.00 33.37 4.20
2333 5751 8.951243 TCTAGATACATCCATTTCTATGACGAG 58.049 37.037 0.00 0.00 33.37 4.18
2334 5752 7.531857 AGATACATCCATTTCTATGACGAGT 57.468 36.000 0.00 0.00 33.37 4.18
2335 5753 8.637196 AGATACATCCATTTCTATGACGAGTA 57.363 34.615 0.00 0.00 33.37 2.59
2336 5754 9.078990 AGATACATCCATTTCTATGACGAGTAA 57.921 33.333 0.00 0.00 33.37 2.24
2337 5755 9.862371 GATACATCCATTTCTATGACGAGTAAT 57.138 33.333 0.00 0.00 33.37 1.89
2339 5757 8.964476 ACATCCATTTCTATGACGAGTAATTT 57.036 30.769 0.00 0.00 33.37 1.82
2340 5758 8.830580 ACATCCATTTCTATGACGAGTAATTTG 58.169 33.333 0.00 0.00 33.37 2.32
2341 5759 7.786178 TCCATTTCTATGACGAGTAATTTGG 57.214 36.000 0.00 0.00 33.37 3.28
2342 5760 7.561251 TCCATTTCTATGACGAGTAATTTGGA 58.439 34.615 0.00 0.00 33.37 3.53
2343 5761 8.044309 TCCATTTCTATGACGAGTAATTTGGAA 58.956 33.333 0.00 0.00 33.37 3.53
2344 5762 8.122952 CCATTTCTATGACGAGTAATTTGGAAC 58.877 37.037 0.00 0.00 33.37 3.62
2345 5763 6.880822 TTCTATGACGAGTAATTTGGAACG 57.119 37.500 0.00 0.00 0.00 3.95
2346 5764 5.345702 TCTATGACGAGTAATTTGGAACGG 58.654 41.667 0.00 0.00 0.00 4.44
2347 5765 3.663995 TGACGAGTAATTTGGAACGGA 57.336 42.857 0.00 0.00 0.00 4.69
2348 5766 3.992643 TGACGAGTAATTTGGAACGGAA 58.007 40.909 0.00 0.00 0.00 4.30
2349 5767 3.991773 TGACGAGTAATTTGGAACGGAAG 59.008 43.478 0.00 0.00 0.00 3.46
2350 5768 3.332034 ACGAGTAATTTGGAACGGAAGG 58.668 45.455 0.00 0.00 0.00 3.46
2351 5769 3.007182 ACGAGTAATTTGGAACGGAAGGA 59.993 43.478 0.00 0.00 0.00 3.36
2352 5770 3.617263 CGAGTAATTTGGAACGGAAGGAG 59.383 47.826 0.00 0.00 0.00 3.69
2353 5771 4.576879 GAGTAATTTGGAACGGAAGGAGT 58.423 43.478 0.00 0.00 0.00 3.85
2354 5772 5.622914 CGAGTAATTTGGAACGGAAGGAGTA 60.623 44.000 0.00 0.00 0.00 2.59
2462 5883 7.820872 GGTACAGAATAGTTGCCACTTAGTTAA 59.179 37.037 0.00 0.00 34.06 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 2.550855 CCTTATCCACATCCATCACGGG 60.551 54.545 0.00 0.00 34.36 5.28
68 69 0.755686 CCTCCATCTTTCTCCTCCCG 59.244 60.000 0.00 0.00 0.00 5.14
84 85 3.755628 TACGTGCCTCACCGCCTC 61.756 66.667 0.00 0.00 0.00 4.70
146 147 2.590821 AGAAAGGAGCAGTTGCAACAT 58.409 42.857 30.11 16.15 45.16 2.71
154 155 6.782082 AAAGAAGAAAAAGAAAGGAGCAGT 57.218 33.333 0.00 0.00 0.00 4.40
167 168 5.103687 GCAACACCCGTAAAAAGAAGAAAA 58.896 37.500 0.00 0.00 0.00 2.29
168 169 4.158025 TGCAACACCCGTAAAAAGAAGAAA 59.842 37.500 0.00 0.00 0.00 2.52
169 170 3.695060 TGCAACACCCGTAAAAAGAAGAA 59.305 39.130 0.00 0.00 0.00 2.52
170 171 3.280295 TGCAACACCCGTAAAAAGAAGA 58.720 40.909 0.00 0.00 0.00 2.87
171 172 3.701532 TGCAACACCCGTAAAAAGAAG 57.298 42.857 0.00 0.00 0.00 2.85
174 175 3.112580 CAGTTGCAACACCCGTAAAAAG 58.887 45.455 30.11 2.77 0.00 2.27
179 180 0.882927 GAGCAGTTGCAACACCCGTA 60.883 55.000 30.11 0.00 45.16 4.02
181 182 2.639286 GAGCAGTTGCAACACCCG 59.361 61.111 30.11 16.37 45.16 5.28
184 185 0.512952 CGTAGGAGCAGTTGCAACAC 59.487 55.000 30.11 21.22 45.16 3.32
208 209 1.061131 CGAGTTGATTTAGCCAGTGCG 59.939 52.381 0.00 0.00 44.33 5.34
235 236 6.987992 TCCGCGTCCATACTTTCTATATTTTT 59.012 34.615 4.92 0.00 0.00 1.94
275 276 8.138712 ACGTGATAAAAAGTTGGCATTTAAGAA 58.861 29.630 0.00 0.00 0.00 2.52
281 282 4.447389 GCAACGTGATAAAAAGTTGGCATT 59.553 37.500 8.87 0.00 42.80 3.56
285 286 5.289675 TGTTTGCAACGTGATAAAAAGTTGG 59.710 36.000 0.00 0.00 42.80 3.77
402 411 9.221933 TCAATCCGTGCTTTAAATTTAGTTAGA 57.778 29.630 0.00 0.00 0.00 2.10
403 412 9.274065 GTCAATCCGTGCTTTAAATTTAGTTAG 57.726 33.333 0.00 0.00 0.00 2.34
407 416 6.967199 GGAGTCAATCCGTGCTTTAAATTTAG 59.033 38.462 0.00 0.00 38.67 1.85
408 417 6.848451 GGAGTCAATCCGTGCTTTAAATTTA 58.152 36.000 0.00 0.00 38.67 1.40
409 418 5.709966 GGAGTCAATCCGTGCTTTAAATTT 58.290 37.500 0.00 0.00 38.67 1.82
410 419 5.310720 GGAGTCAATCCGTGCTTTAAATT 57.689 39.130 0.00 0.00 38.67 1.82
411 420 4.965119 GGAGTCAATCCGTGCTTTAAAT 57.035 40.909 0.00 0.00 38.67 1.40
429 438 2.048503 GACGGTGAACCCACGGAG 60.049 66.667 9.54 0.00 43.69 4.63
433 442 1.802365 GTATTGTGACGGTGAACCCAC 59.198 52.381 2.84 2.84 42.46 4.61
456 465 9.737427 TGAAAGCGTAAATTCACATAAAGAAAA 57.263 25.926 0.00 0.00 30.94 2.29
457 466 9.393249 CTGAAAGCGTAAATTCACATAAAGAAA 57.607 29.630 0.00 0.00 32.46 2.52
464 473 9.691362 ATTTAAACTGAAAGCGTAAATTCACAT 57.309 25.926 0.00 0.00 34.42 3.21
465 474 9.522804 AATTTAAACTGAAAGCGTAAATTCACA 57.477 25.926 0.00 0.00 39.80 3.58
501 511 9.646427 GCACATTAAATTTAATACCACCTTGAA 57.354 29.630 20.32 0.00 32.39 2.69
502 512 7.971168 CGCACATTAAATTTAATACCACCTTGA 59.029 33.333 20.32 0.00 32.39 3.02
513 531 8.359409 CGATTTTTCGTCGCACATTAAATTTAA 58.641 29.630 12.85 12.85 31.85 1.52
524 542 1.587991 GAACCGATTTTTCGTCGCAC 58.412 50.000 0.00 0.00 37.75 5.34
537 555 3.082165 TTTTTGTCCAGCGAACCGA 57.918 47.368 0.00 0.00 0.00 4.69
596 614 1.928714 TAGGGGGATTTGGTTCGGCC 61.929 60.000 0.00 0.00 37.90 6.13
726 744 2.636412 TTGTCGTCCCTCGGCTGAG 61.636 63.158 16.14 16.14 45.15 3.35
823 853 2.801631 GCTGGCATAGGACCTCGCT 61.802 63.158 13.90 0.00 0.00 4.93
1132 1171 0.478072 TCAGCACCCCACAGACATTT 59.522 50.000 0.00 0.00 0.00 2.32
1203 1250 3.073209 GTCCCCTGTTTCCTCTTTCTCTT 59.927 47.826 0.00 0.00 0.00 2.85
1235 1299 6.473397 AAACAAAAAGCGATGAGTAGAGAG 57.527 37.500 0.00 0.00 0.00 3.20
1236 1300 6.861065 AAAACAAAAAGCGATGAGTAGAGA 57.139 33.333 0.00 0.00 0.00 3.10
1241 1305 5.043248 CCAGAAAAACAAAAAGCGATGAGT 58.957 37.500 0.00 0.00 0.00 3.41
1255 1319 0.463620 TGCCAACCAGCCAGAAAAAC 59.536 50.000 0.00 0.00 0.00 2.43
1256 1320 1.198713 TTGCCAACCAGCCAGAAAAA 58.801 45.000 0.00 0.00 0.00 1.94
1262 1326 0.835941 ACATTTTTGCCAACCAGCCA 59.164 45.000 0.00 0.00 0.00 4.75
1263 1327 1.228533 CACATTTTTGCCAACCAGCC 58.771 50.000 0.00 0.00 0.00 4.85
1264 1328 1.866601 GACACATTTTTGCCAACCAGC 59.133 47.619 0.00 0.00 0.00 4.85
1347 1415 5.389859 TCAAAATCAAGCATTTCGTCCAT 57.610 34.783 0.00 0.00 33.16 3.41
1481 1610 1.672363 CTTTCGATTGCTGCTGCCATA 59.328 47.619 13.47 0.00 38.71 2.74
1540 1675 7.430441 TCATTTGTAAGCCTAAAAGTTTGGAC 58.570 34.615 0.00 0.00 0.00 4.02
1556 1699 8.674263 AACAAGCCATTTGATTTCATTTGTAA 57.326 26.923 0.00 0.00 39.21 2.41
1560 1703 6.546772 ACCAAACAAGCCATTTGATTTCATTT 59.453 30.769 6.52 0.00 39.01 2.32
1611 1761 5.471556 TGCTGAACATTCAAAACCATCAT 57.528 34.783 0.00 0.00 36.64 2.45
1904 2069 2.519013 GTGATGCACCCTTCCTTCTTT 58.481 47.619 0.00 0.00 0.00 2.52
2025 2202 6.370166 GTCAGCTTGCTTCTTTGTAGTTCTAT 59.630 38.462 0.00 0.00 0.00 1.98
2035 2212 3.688673 GCATCTAGTCAGCTTGCTTCTTT 59.311 43.478 0.00 0.00 31.57 2.52
2051 2228 3.475575 TGACAAAACTGCAGTGCATCTA 58.524 40.909 22.49 3.45 38.13 1.98
2258 5676 2.093783 CCTGCGACAAGTAATTCGGAAC 59.906 50.000 0.00 0.00 35.02 3.62
2259 5677 2.289195 ACCTGCGACAAGTAATTCGGAA 60.289 45.455 0.00 0.00 35.02 4.30
2260 5678 1.274167 ACCTGCGACAAGTAATTCGGA 59.726 47.619 0.00 0.00 35.73 4.55
2261 5679 1.722011 ACCTGCGACAAGTAATTCGG 58.278 50.000 0.00 0.00 35.73 4.30
2262 5680 3.245284 CCATACCTGCGACAAGTAATTCG 59.755 47.826 0.00 0.00 38.31 3.34
2263 5681 4.439057 TCCATACCTGCGACAAGTAATTC 58.561 43.478 0.00 0.00 0.00 2.17
2264 5682 4.481368 TCCATACCTGCGACAAGTAATT 57.519 40.909 0.00 0.00 0.00 1.40
2265 5683 4.141711 ACATCCATACCTGCGACAAGTAAT 60.142 41.667 0.00 0.00 0.00 1.89
2266 5684 3.196901 ACATCCATACCTGCGACAAGTAA 59.803 43.478 0.00 0.00 0.00 2.24
2267 5685 2.764010 ACATCCATACCTGCGACAAGTA 59.236 45.455 0.00 0.00 0.00 2.24
2268 5686 1.555075 ACATCCATACCTGCGACAAGT 59.445 47.619 0.00 0.00 0.00 3.16
2269 5687 2.315925 ACATCCATACCTGCGACAAG 57.684 50.000 0.00 0.00 0.00 3.16
2270 5688 3.641436 AGATACATCCATACCTGCGACAA 59.359 43.478 0.00 0.00 0.00 3.18
2271 5689 3.230976 AGATACATCCATACCTGCGACA 58.769 45.455 0.00 0.00 0.00 4.35
2272 5690 3.944055 AGATACATCCATACCTGCGAC 57.056 47.619 0.00 0.00 0.00 5.19
2273 5691 4.918588 TCTAGATACATCCATACCTGCGA 58.081 43.478 0.00 0.00 0.00 5.10
2274 5692 5.126222 ACATCTAGATACATCCATACCTGCG 59.874 44.000 4.54 0.00 0.00 5.18
2275 5693 6.537453 ACATCTAGATACATCCATACCTGC 57.463 41.667 4.54 0.00 0.00 4.85
2305 5723 9.347934 CGTCATAGAAATGGATGTATCTAGAAC 57.652 37.037 0.00 0.00 33.61 3.01
2306 5724 9.297037 TCGTCATAGAAATGGATGTATCTAGAA 57.703 33.333 0.00 0.00 33.61 2.10
2307 5725 8.863872 TCGTCATAGAAATGGATGTATCTAGA 57.136 34.615 0.00 0.00 33.61 2.43
2308 5726 8.735315 ACTCGTCATAGAAATGGATGTATCTAG 58.265 37.037 0.00 0.00 33.61 2.43
2309 5727 8.637196 ACTCGTCATAGAAATGGATGTATCTA 57.363 34.615 0.00 0.00 33.61 1.98
2310 5728 7.531857 ACTCGTCATAGAAATGGATGTATCT 57.468 36.000 0.00 0.00 33.61 1.98
2311 5729 9.862371 ATTACTCGTCATAGAAATGGATGTATC 57.138 33.333 0.00 0.00 33.61 2.24
2314 5732 8.830580 CAAATTACTCGTCATAGAAATGGATGT 58.169 33.333 0.00 0.00 33.61 3.06
2315 5733 8.285394 CCAAATTACTCGTCATAGAAATGGATG 58.715 37.037 0.00 0.00 33.61 3.51
2316 5734 8.210946 TCCAAATTACTCGTCATAGAAATGGAT 58.789 33.333 0.00 0.00 33.61 3.41
2317 5735 7.561251 TCCAAATTACTCGTCATAGAAATGGA 58.439 34.615 0.00 0.00 33.61 3.41
2318 5736 7.786178 TCCAAATTACTCGTCATAGAAATGG 57.214 36.000 0.00 0.00 33.61 3.16
2319 5737 7.846107 CGTTCCAAATTACTCGTCATAGAAATG 59.154 37.037 0.00 0.00 0.00 2.32
2320 5738 7.011109 CCGTTCCAAATTACTCGTCATAGAAAT 59.989 37.037 0.00 0.00 0.00 2.17
2321 5739 6.311935 CCGTTCCAAATTACTCGTCATAGAAA 59.688 38.462 0.00 0.00 0.00 2.52
2322 5740 5.808540 CCGTTCCAAATTACTCGTCATAGAA 59.191 40.000 0.00 0.00 0.00 2.10
2323 5741 5.125900 TCCGTTCCAAATTACTCGTCATAGA 59.874 40.000 0.00 0.00 0.00 1.98
2324 5742 5.345702 TCCGTTCCAAATTACTCGTCATAG 58.654 41.667 0.00 0.00 0.00 2.23
2325 5743 5.327616 TCCGTTCCAAATTACTCGTCATA 57.672 39.130 0.00 0.00 0.00 2.15
2326 5744 4.196626 TCCGTTCCAAATTACTCGTCAT 57.803 40.909 0.00 0.00 0.00 3.06
2327 5745 3.663995 TCCGTTCCAAATTACTCGTCA 57.336 42.857 0.00 0.00 0.00 4.35
2328 5746 3.370061 CCTTCCGTTCCAAATTACTCGTC 59.630 47.826 0.00 0.00 0.00 4.20
2329 5747 3.007182 TCCTTCCGTTCCAAATTACTCGT 59.993 43.478 0.00 0.00 0.00 4.18
2330 5748 3.592059 TCCTTCCGTTCCAAATTACTCG 58.408 45.455 0.00 0.00 0.00 4.18
2331 5749 4.576879 ACTCCTTCCGTTCCAAATTACTC 58.423 43.478 0.00 0.00 0.00 2.59
2332 5750 4.635699 ACTCCTTCCGTTCCAAATTACT 57.364 40.909 0.00 0.00 0.00 2.24
2333 5751 5.240121 TGTACTCCTTCCGTTCCAAATTAC 58.760 41.667 0.00 0.00 0.00 1.89
2334 5752 5.486735 TGTACTCCTTCCGTTCCAAATTA 57.513 39.130 0.00 0.00 0.00 1.40
2335 5753 4.360951 TGTACTCCTTCCGTTCCAAATT 57.639 40.909 0.00 0.00 0.00 1.82
2336 5754 4.569719 ATGTACTCCTTCCGTTCCAAAT 57.430 40.909 0.00 0.00 0.00 2.32
2337 5755 4.529377 AGTATGTACTCCTTCCGTTCCAAA 59.471 41.667 0.00 0.00 0.00 3.28
2338 5756 4.091549 AGTATGTACTCCTTCCGTTCCAA 58.908 43.478 0.00 0.00 0.00 3.53
2339 5757 3.705051 AGTATGTACTCCTTCCGTTCCA 58.295 45.455 0.00 0.00 0.00 3.53
2340 5758 5.841957 TTAGTATGTACTCCTTCCGTTCC 57.158 43.478 0.00 0.00 37.73 3.62
2341 5759 6.861144 AGTTTAGTATGTACTCCTTCCGTTC 58.139 40.000 0.00 0.00 37.73 3.95
2342 5760 6.847421 AGTTTAGTATGTACTCCTTCCGTT 57.153 37.500 0.00 0.00 37.73 4.44
2343 5761 6.448207 GAGTTTAGTATGTACTCCTTCCGT 57.552 41.667 0.00 0.00 37.73 4.69
2350 5768 4.202233 GGGCAGGGAGTTTAGTATGTACTC 60.202 50.000 0.00 0.00 37.73 2.59
2351 5769 3.710165 GGGCAGGGAGTTTAGTATGTACT 59.290 47.826 0.00 0.00 40.24 2.73
2352 5770 3.181457 GGGGCAGGGAGTTTAGTATGTAC 60.181 52.174 0.00 0.00 0.00 2.90
2353 5771 3.043418 GGGGCAGGGAGTTTAGTATGTA 58.957 50.000 0.00 0.00 0.00 2.29
2354 5772 1.844497 GGGGCAGGGAGTTTAGTATGT 59.156 52.381 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.