Multiple sequence alignment - TraesCS3D01G308600

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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 TraesCS3D01G308600 chr3D 100.000 3612 0 0 1 3612 422550249 422553860 0.000000e+00 6671.0
1 TraesCS3D01G308600 chr3B 94.357 3544 120 28 1 3493 550663906 550667420 0.000000e+00 5363.0
2 TraesCS3D01G308600 chr3B 84.211 190 18 7 87 266 658963306 658963119 1.330000e-39 174.0
3 TraesCS3D01G308600 chr3B 85.625 160 21 2 109 267 659067225 659067067 2.230000e-37 167.0
4 TraesCS3D01G308600 chr3B 78.423 241 33 12 37 260 564762060 564762298 4.860000e-29 139.0
5 TraesCS3D01G308600 chr3B 100.000 32 0 0 34 65 818938523 818938554 3.890000e-05 60.2
6 TraesCS3D01G308600 chr3A 94.567 1988 61 18 410 2368 566334156 566332187 0.000000e+00 3029.0
7 TraesCS3D01G308600 chr3A 94.587 702 27 7 2430 3125 566332103 566331407 0.000000e+00 1075.0
8 TraesCS3D01G308600 chr3A 88.664 247 17 3 3116 3351 566329291 566329045 1.270000e-74 291.0
9 TraesCS3D01G308600 chr6D 80.932 687 91 21 1597 2264 431083266 431083931 1.160000e-139 507.0
10 TraesCS3D01G308600 chr6D 78.721 766 91 35 1577 2324 431159955 431160666 2.560000e-121 446.0
11 TraesCS3D01G308600 chr6B 78.460 766 92 35 1577 2325 650597829 650598538 1.990000e-117 433.0
12 TraesCS3D01G308600 chr6B 88.922 334 31 5 2419 2750 439390485 439390814 1.210000e-109 407.0
13 TraesCS3D01G308600 chr6B 91.860 86 7 0 2353 2438 188673610 188673695 1.760000e-23 121.0
14 TraesCS3D01G308600 chr2D 86.957 391 38 6 1974 2358 210345788 210346171 9.270000e-116 427.0
15 TraesCS3D01G308600 chr2D 85.143 350 31 8 2025 2358 218299057 218299401 4.470000e-89 339.0
16 TraesCS3D01G308600 chr2D 89.370 254 20 3 2440 2692 218299400 218299647 2.710000e-81 313.0
17 TraesCS3D01G308600 chr4B 86.598 388 35 8 1977 2358 625349863 625349487 2.600000e-111 412.0
18 TraesCS3D01G308600 chr4B 91.954 87 6 1 2356 2441 399783160 399783246 1.760000e-23 121.0
19 TraesCS3D01G308600 chr6A 87.988 333 36 3 2419 2750 397523190 397522861 1.220000e-104 390.0
20 TraesCS3D01G308600 chr6A 91.398 93 8 0 2357 2449 101295980 101296072 1.050000e-25 128.0
21 TraesCS3D01G308600 chr6A 89.655 58 4 2 36 92 98985122 98985066 5.000000e-09 73.1
22 TraesCS3D01G308600 chr2B 87.311 331 37 5 2427 2755 47631986 47632313 1.220000e-99 374.0
23 TraesCS3D01G308600 chr2B 94.253 87 5 0 2355 2441 517154300 517154386 2.260000e-27 134.0
24 TraesCS3D01G308600 chr2B 76.190 252 38 13 36 266 783867701 783867951 2.950000e-21 113.0
25 TraesCS3D01G308600 chr2B 90.909 77 6 1 271 346 175422265 175422189 6.380000e-18 102.0
26 TraesCS3D01G308600 chr2B 88.608 79 7 2 585 663 571140974 571141050 1.070000e-15 95.3
27 TraesCS3D01G308600 chr2B 86.250 80 11 0 271 350 691052898 691052977 1.790000e-13 87.9
28 TraesCS3D01G308600 chr1B 84.655 391 43 8 1974 2358 660739275 660739654 1.220000e-99 374.0
29 TraesCS3D01G308600 chr1B 91.429 70 6 0 271 340 322493135 322493066 2.970000e-16 97.1
30 TraesCS3D01G308600 chr1B 87.324 71 7 2 277 347 662451641 662451709 2.990000e-11 80.5
31 TraesCS3D01G308600 chr5B 87.821 312 32 3 2440 2750 142543289 142543595 9.530000e-96 361.0
32 TraesCS3D01G308600 chr5B 86.735 98 4 4 2263 2356 184274101 184274009 2.290000e-17 100.0
33 TraesCS3D01G308600 chr5A 80.328 244 32 11 34 263 547660844 547660603 1.720000e-38 171.0
34 TraesCS3D01G308600 chr5A 100.000 29 0 0 1977 2005 230918809 230918781 2.000000e-03 54.7
35 TraesCS3D01G308600 chr4D 80.321 249 27 14 34 262 504197352 504197106 6.200000e-38 169.0
36 TraesCS3D01G308600 chr5D 83.815 173 24 3 95 266 441401679 441401848 1.040000e-35 161.0
37 TraesCS3D01G308600 chr5D 84.615 65 7 3 3261 3323 36759349 36759412 1.080000e-05 62.1
38 TraesCS3D01G308600 chrUn 88.462 130 13 2 123 251 315895311 315895439 4.830000e-34 156.0
39 TraesCS3D01G308600 chrUn 88.462 130 13 2 123 251 315906138 315906266 4.830000e-34 156.0
40 TraesCS3D01G308600 chrUn 87.970 133 14 2 123 254 323249413 323249282 4.830000e-34 156.0
41 TraesCS3D01G308600 chr7B 84.177 158 22 3 108 264 138038024 138037869 2.250000e-32 150.0
42 TraesCS3D01G308600 chr7B 90.000 100 8 2 2353 2450 536662518 536662419 1.050000e-25 128.0
43 TraesCS3D01G308600 chr7A 90.909 88 8 0 2357 2444 580665274 580665361 6.340000e-23 119.0
44 TraesCS3D01G308600 chr7A 90.110 91 8 1 2357 2447 594413589 594413678 2.280000e-22 117.0
45 TraesCS3D01G308600 chr7A 84.810 79 12 0 272 350 101787869 101787791 2.990000e-11 80.5
46 TraesCS3D01G308600 chr7D 85.981 107 13 2 2356 2460 382119459 382119353 2.950000e-21 113.0
47 TraesCS3D01G308600 chr2A 88.750 80 9 0 271 350 646626945 646627024 8.250000e-17 99.0
48 TraesCS3D01G308600 chr2A 91.429 70 6 0 271 340 713219021 713219090 2.970000e-16 97.1
49 TraesCS3D01G308600 chr2A 85.714 84 6 3 585 663 631657286 631657368 2.310000e-12 84.2
50 TraesCS3D01G308600 chr2A 85.000 80 11 1 271 350 31006579 31006501 2.990000e-11 80.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G308600 chr3D 422550249 422553860 3611 False 6671 6671 100.0000 1 3612 1 chr3D.!!$F1 3611
1 TraesCS3D01G308600 chr3B 550663906 550667420 3514 False 5363 5363 94.3570 1 3493 1 chr3B.!!$F1 3492
2 TraesCS3D01G308600 chr3A 566329045 566334156 5111 True 1465 3029 92.6060 410 3351 3 chr3A.!!$R1 2941
3 TraesCS3D01G308600 chr6D 431083266 431083931 665 False 507 507 80.9320 1597 2264 1 chr6D.!!$F1 667
4 TraesCS3D01G308600 chr6D 431159955 431160666 711 False 446 446 78.7210 1577 2324 1 chr6D.!!$F2 747
5 TraesCS3D01G308600 chr6B 650597829 650598538 709 False 433 433 78.4600 1577 2325 1 chr6B.!!$F3 748
6 TraesCS3D01G308600 chr2D 218299057 218299647 590 False 326 339 87.2565 2025 2692 2 chr2D.!!$F2 667

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
170 179 0.040958 GTCGCAGTTGCTGTTTCTGG 60.041 55.000 2.29 0.00 39.32 3.86 F
395 408 0.097150 GCACCGCGATTTTTCCTCTC 59.903 55.000 8.23 0.00 0.00 3.20 F
729 749 1.745087 CCCAGTGATCAATTGAACCGG 59.255 52.381 13.09 8.74 0.00 5.28 F
1065 1086 2.893489 AGGACAGCAAAGAAACCCAATC 59.107 45.455 0.00 0.00 0.00 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2012 2097 0.457851 CAACAGGAGAGCTAGTCCCG 59.542 60.000 10.44 3.97 34.21 5.14 R
2361 2464 4.960469 ACTTCTTATATTGTGGGACGGAGA 59.040 41.667 0.00 0.00 0.00 3.71 R
2599 2724 2.238898 AGGTCGCAACTAAAATAGCCCT 59.761 45.455 0.00 0.00 0.00 5.19 R
2785 2911 3.244215 ACTCGATTTCAACAGCCAGAAGA 60.244 43.478 0.00 0.00 0.00 2.87 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
33 34 1.219393 GCGCCTAGCCTTGTCTTCT 59.781 57.895 0.00 0.00 40.81 2.85
34 35 1.086634 GCGCCTAGCCTTGTCTTCTG 61.087 60.000 0.00 0.00 40.81 3.02
69 70 1.660917 GGATCTCGTGGGATCGGTC 59.339 63.158 3.75 0.00 41.99 4.79
72 73 4.570663 CTCGTGGGATCGGTCGGC 62.571 72.222 0.00 0.00 0.00 5.54
81 82 1.963190 GATCGGTCGGCGTTTTGTCC 61.963 60.000 6.85 0.68 0.00 4.02
84 85 1.595929 GGTCGGCGTTTTGTCCTCA 60.596 57.895 6.85 0.00 0.00 3.86
99 100 0.905357 CCTCAGTGGATCCGGTCTTT 59.095 55.000 7.39 0.00 38.35 2.52
105 106 0.672401 TGGATCCGGTCTTTGTTCGC 60.672 55.000 7.39 0.00 0.00 4.70
125 134 5.773575 TCGCCTGTGTCTGAATATTAGATC 58.226 41.667 0.00 0.00 0.00 2.75
126 135 4.926238 CGCCTGTGTCTGAATATTAGATCC 59.074 45.833 0.00 0.00 0.00 3.36
130 139 7.172361 GCCTGTGTCTGAATATTAGATCCTTTC 59.828 40.741 0.00 0.00 0.00 2.62
131 140 7.383572 CCTGTGTCTGAATATTAGATCCTTTCG 59.616 40.741 0.00 0.00 0.00 3.46
144 153 3.694535 TCCTTTCGATCTACGCTTCTC 57.305 47.619 0.00 0.00 42.26 2.87
151 160 3.059529 TCGATCTACGCTTCTCTTCATCG 60.060 47.826 0.00 0.00 42.26 3.84
166 175 0.235665 CATCGTCGCAGTTGCTGTTT 59.764 50.000 2.29 0.00 39.32 2.83
167 176 0.512952 ATCGTCGCAGTTGCTGTTTC 59.487 50.000 2.29 0.00 39.32 2.78
168 177 0.529773 TCGTCGCAGTTGCTGTTTCT 60.530 50.000 2.29 0.00 39.32 2.52
170 179 0.040958 GTCGCAGTTGCTGTTTCTGG 60.041 55.000 2.29 0.00 39.32 3.86
171 180 0.463654 TCGCAGTTGCTGTTTCTGGT 60.464 50.000 2.29 0.00 39.32 4.00
172 181 0.317269 CGCAGTTGCTGTTTCTGGTG 60.317 55.000 2.29 0.00 39.32 4.17
173 182 0.595825 GCAGTTGCTGTTTCTGGTGC 60.596 55.000 0.00 0.00 38.21 5.01
174 183 0.317269 CAGTTGCTGTTTCTGGTGCG 60.317 55.000 0.00 0.00 0.00 5.34
178 191 0.950555 TGCTGTTTCTGGTGCGCTAG 60.951 55.000 9.73 3.91 0.00 3.42
186 199 0.598680 CTGGTGCGCTAGTCCTATGC 60.599 60.000 9.73 0.00 0.00 3.14
209 222 2.349886 GCCTTAGCATGACGACTTTCTG 59.650 50.000 0.00 0.00 39.53 3.02
212 225 4.489810 CTTAGCATGACGACTTTCTGACT 58.510 43.478 0.00 0.00 0.00 3.41
223 236 4.220572 GACTTTCTGACTGTCGACTACAC 58.779 47.826 17.92 6.41 33.45 2.90
227 240 2.552743 TCTGACTGTCGACTACACCAAG 59.447 50.000 17.92 6.19 33.45 3.61
235 248 2.140717 CGACTACACCAAGGTTTGTCC 58.859 52.381 9.14 0.00 0.00 4.02
248 261 0.322456 TTTGTCCGGCTCCAATGAGG 60.322 55.000 0.00 0.00 39.14 3.86
267 280 2.515996 GAAGGGGTGATGACGGCGAA 62.516 60.000 16.62 0.57 0.00 4.70
297 310 7.373778 GTCTACGGACCTGAATGTAATTTTT 57.626 36.000 0.00 0.00 34.75 1.94
298 311 8.483307 GTCTACGGACCTGAATGTAATTTTTA 57.517 34.615 0.00 0.00 34.75 1.52
380 393 2.112297 TTCGTGGTCCCTTGCACC 59.888 61.111 0.00 0.00 0.00 5.01
395 408 0.097150 GCACCGCGATTTTTCCTCTC 59.903 55.000 8.23 0.00 0.00 3.20
425 438 1.816537 CCCTTCGATCTTCCTCGCA 59.183 57.895 0.00 0.00 38.52 5.10
429 442 2.392821 CTTCGATCTTCCTCGCATGAG 58.607 52.381 0.00 0.00 42.18 2.90
729 749 1.745087 CCCAGTGATCAATTGAACCGG 59.255 52.381 13.09 8.74 0.00 5.28
755 775 5.982356 TCTACAAGTTCCAGGATGAGATTG 58.018 41.667 0.00 0.00 39.69 2.67
1065 1086 2.893489 AGGACAGCAAAGAAACCCAATC 59.107 45.455 0.00 0.00 0.00 2.67
1136 1157 5.798132 TCATCACATATATGACTCCTTGCC 58.202 41.667 19.63 0.00 0.00 4.52
1739 1791 4.830046 TGAGGGTGATATTGAGACTAGAGC 59.170 45.833 0.00 0.00 0.00 4.09
1826 1879 8.653191 TGGTAAGTTAATCTGAGGTTCAAGTAA 58.347 33.333 0.00 0.00 0.00 2.24
1838 1893 7.722363 TGAGGTTCAAGTAATTTTTCTTTCCC 58.278 34.615 0.00 0.00 0.00 3.97
1927 1992 8.394121 GCTACCTGAGTTATTTCTTGAAGAATG 58.606 37.037 8.64 0.00 33.67 2.67
2006 2091 9.857957 CTTAGTTAGAAAACAGACCTACCTAAG 57.142 37.037 0.00 0.00 38.12 2.18
2133 2235 6.126156 ACTCCCCTCACTCTCAGTATATTGTA 60.126 42.308 0.00 0.00 0.00 2.41
2205 2308 7.714377 TGCTTTTGTTCATTTCCATTTGTATGT 59.286 29.630 0.00 0.00 0.00 2.29
2361 2464 4.324099 GGAAGGCATCATGGCATATACTCT 60.324 45.833 14.65 0.00 46.46 3.24
2382 2485 5.205821 TCTCTCCGTCCCACAATATAAGAA 58.794 41.667 0.00 0.00 0.00 2.52
2456 2581 6.042208 GGAGGGAGTAGTAAATAAGTGCAGAT 59.958 42.308 0.00 0.00 0.00 2.90
2599 2724 3.455737 CTTCCTTTTGGCAGGGGAA 57.544 52.632 14.12 14.12 40.12 3.97
2710 2836 8.682936 AGCACTTTTATTAGGTCCATTGATAG 57.317 34.615 0.00 0.00 0.00 2.08
2742 2868 3.330701 TGGAGAACTGAAAGCCCTTGTAT 59.669 43.478 0.00 0.00 37.60 2.29
2785 2911 0.039035 TTTTTGAGCGTATGGGGGCT 59.961 50.000 0.00 0.00 43.42 5.19
2793 2920 1.149401 GTATGGGGGCTCTTCTGGC 59.851 63.158 0.00 0.00 0.00 4.85
2986 3117 4.991056 AGCATACCATATCGCAGTTAGTTG 59.009 41.667 0.00 0.00 0.00 3.16
3263 5529 6.045106 GGGGGAGTAGGAATTCAATGGTATAA 59.955 42.308 7.93 0.00 0.00 0.98
3266 5532 8.218488 GGGAGTAGGAATTCAATGGTATAACTT 58.782 37.037 7.93 0.00 0.00 2.66
3326 5593 9.883142 TTGATGGTCAAACTTAAACTTGAAATT 57.117 25.926 1.49 0.00 32.71 1.82
3339 5606 4.870363 ACTTGAAATTCATTGGTTCCACG 58.130 39.130 0.00 0.00 0.00 4.94
3366 5633 1.636988 GGACACCGTAGTACATGCAC 58.363 55.000 0.38 0.00 0.00 4.57
3368 5635 2.259618 GACACCGTAGTACATGCACAG 58.740 52.381 0.00 0.00 0.00 3.66
3427 5695 4.796231 CTTGTCGGCGTCCTCCCG 62.796 72.222 6.85 0.00 46.88 5.14
3436 5704 4.699522 GTCCTCCCGTTGCGGCTT 62.700 66.667 0.00 0.00 46.86 4.35
3457 5725 3.068881 CCCCGGTGCTCTGAAAGA 58.931 61.111 0.00 0.00 43.69 2.52
3468 5736 0.324614 TCTGAAAGATGCGCCCTTCA 59.675 50.000 4.18 7.62 38.67 3.02
3482 5750 0.251519 CCTTCAGGCTTCCTTGGCTT 60.252 55.000 0.00 0.00 41.04 4.35
3483 5751 0.886563 CTTCAGGCTTCCTTGGCTTG 59.113 55.000 0.00 0.00 41.04 4.01
3493 5761 3.498401 CTTGGCTTGCCGGCGTTTT 62.498 57.895 23.90 0.00 42.02 2.43
3494 5762 3.781770 TTGGCTTGCCGGCGTTTTG 62.782 57.895 23.90 10.64 42.02 2.44
3501 5769 2.050442 CCGGCGTTTTGGCAACTC 60.050 61.111 6.01 0.00 45.16 3.01
3502 5770 2.050442 CGGCGTTTTGGCAACTCC 60.050 61.111 0.00 0.00 45.16 3.85
3503 5771 2.050442 GGCGTTTTGGCAACTCCG 60.050 61.111 0.00 3.60 44.08 4.63
3504 5772 2.050442 GCGTTTTGGCAACTCCGG 60.050 61.111 0.00 0.00 37.80 5.14
3505 5773 2.050442 CGTTTTGGCAACTCCGGC 60.050 61.111 0.00 0.00 37.80 6.13
3512 5780 4.070552 GCAACTCCGGCCTCGTCT 62.071 66.667 0.00 0.00 33.95 4.18
3513 5781 2.125912 CAACTCCGGCCTCGTCTG 60.126 66.667 0.00 0.00 33.95 3.51
3514 5782 2.282958 AACTCCGGCCTCGTCTGA 60.283 61.111 0.00 0.00 33.95 3.27
3515 5783 2.637383 AACTCCGGCCTCGTCTGAC 61.637 63.158 0.00 0.00 33.95 3.51
3516 5784 2.752238 CTCCGGCCTCGTCTGACT 60.752 66.667 0.00 0.00 33.95 3.41
3517 5785 1.451567 CTCCGGCCTCGTCTGACTA 60.452 63.158 0.00 0.00 33.95 2.59
3518 5786 1.440938 CTCCGGCCTCGTCTGACTAG 61.441 65.000 0.00 4.27 33.95 2.57
3519 5787 1.451567 CCGGCCTCGTCTGACTAGA 60.452 63.158 10.60 0.00 33.95 2.43
3520 5788 0.820074 CCGGCCTCGTCTGACTAGAT 60.820 60.000 10.60 0.00 34.94 1.98
3521 5789 0.589223 CGGCCTCGTCTGACTAGATC 59.411 60.000 10.60 2.80 34.94 2.75
3522 5790 1.812324 CGGCCTCGTCTGACTAGATCT 60.812 57.143 10.60 0.00 34.94 2.75
3523 5791 1.606668 GGCCTCGTCTGACTAGATCTG 59.393 57.143 10.60 0.00 34.94 2.90
3524 5792 1.001815 GCCTCGTCTGACTAGATCTGC 60.002 57.143 10.60 2.40 34.94 4.26
3525 5793 1.262950 CCTCGTCTGACTAGATCTGCG 59.737 57.143 10.60 0.00 34.94 5.18
3526 5794 1.937223 CTCGTCTGACTAGATCTGCGT 59.063 52.381 5.18 2.02 34.94 5.24
3527 5795 1.934525 TCGTCTGACTAGATCTGCGTC 59.065 52.381 16.00 16.00 34.94 5.19
3528 5796 1.937223 CGTCTGACTAGATCTGCGTCT 59.063 52.381 20.70 0.00 34.94 4.18
3529 5797 2.033236 CGTCTGACTAGATCTGCGTCTC 60.033 54.545 20.70 13.25 34.94 3.36
3530 5798 3.202906 GTCTGACTAGATCTGCGTCTCT 58.797 50.000 20.70 0.00 34.94 3.10
3531 5799 3.247648 GTCTGACTAGATCTGCGTCTCTC 59.752 52.174 20.70 11.26 34.94 3.20
3532 5800 2.548057 CTGACTAGATCTGCGTCTCTCC 59.452 54.545 20.70 3.43 0.00 3.71
3533 5801 2.092914 TGACTAGATCTGCGTCTCTCCA 60.093 50.000 20.70 5.40 0.00 3.86
3534 5802 2.946329 GACTAGATCTGCGTCTCTCCAA 59.054 50.000 5.18 0.00 0.00 3.53
3535 5803 3.357203 ACTAGATCTGCGTCTCTCCAAA 58.643 45.455 5.18 0.00 0.00 3.28
3536 5804 3.957497 ACTAGATCTGCGTCTCTCCAAAT 59.043 43.478 5.18 0.00 0.00 2.32
3537 5805 3.451141 AGATCTGCGTCTCTCCAAATC 57.549 47.619 0.00 0.00 0.00 2.17
3538 5806 2.102252 AGATCTGCGTCTCTCCAAATCC 59.898 50.000 0.00 0.00 0.00 3.01
3539 5807 1.561643 TCTGCGTCTCTCCAAATCCT 58.438 50.000 0.00 0.00 0.00 3.24
3540 5808 1.205655 TCTGCGTCTCTCCAAATCCTG 59.794 52.381 0.00 0.00 0.00 3.86
3542 5810 1.092345 GCGTCTCTCCAAATCCTGGC 61.092 60.000 0.00 0.00 45.98 4.85
3543 5811 0.539051 CGTCTCTCCAAATCCTGGCT 59.461 55.000 0.00 0.00 45.98 4.75
3544 5812 1.472376 CGTCTCTCCAAATCCTGGCTC 60.472 57.143 0.00 0.00 45.98 4.70
3545 5813 0.826715 TCTCTCCAAATCCTGGCTCG 59.173 55.000 0.00 0.00 45.98 5.03
3546 5814 0.813210 CTCTCCAAATCCTGGCTCGC 60.813 60.000 0.00 0.00 45.98 5.03
3547 5815 1.821332 CTCCAAATCCTGGCTCGCC 60.821 63.158 0.00 0.00 45.98 5.54
3548 5816 3.204827 CCAAATCCTGGCTCGCCG 61.205 66.667 3.14 0.00 38.76 6.46
3549 5817 3.204827 CAAATCCTGGCTCGCCGG 61.205 66.667 9.83 9.83 42.03 6.13
3550 5818 3.717294 AAATCCTGGCTCGCCGGT 61.717 61.111 15.19 0.00 40.80 5.28
3551 5819 3.976701 AAATCCTGGCTCGCCGGTG 62.977 63.158 9.28 9.28 40.80 4.94
3559 5827 4.988598 CTCGCCGGTGTTGCTGGT 62.989 66.667 16.01 0.00 45.57 4.00
3560 5828 4.555709 TCGCCGGTGTTGCTGGTT 62.556 61.111 16.01 0.00 45.57 3.67
3561 5829 4.326766 CGCCGGTGTTGCTGGTTG 62.327 66.667 6.91 0.00 45.57 3.77
3562 5830 4.645921 GCCGGTGTTGCTGGTTGC 62.646 66.667 1.90 0.00 45.57 4.17
3563 5831 2.906897 CCGGTGTTGCTGGTTGCT 60.907 61.111 0.00 0.00 43.37 3.91
3564 5832 2.332514 CGGTGTTGCTGGTTGCTG 59.667 61.111 0.00 0.00 43.37 4.41
3565 5833 2.480610 CGGTGTTGCTGGTTGCTGT 61.481 57.895 0.00 0.00 43.37 4.40
3566 5834 1.360192 GGTGTTGCTGGTTGCTGTC 59.640 57.895 0.00 0.00 43.37 3.51
3567 5835 1.009675 GTGTTGCTGGTTGCTGTCG 60.010 57.895 0.00 0.00 43.37 4.35
3568 5836 2.050985 GTTGCTGGTTGCTGTCGC 60.051 61.111 0.00 0.00 43.37 5.19
3569 5837 2.515757 TTGCTGGTTGCTGTCGCA 60.516 55.556 0.00 0.00 46.24 5.10
3577 5845 4.002506 TGCTGTCGCATCCCGTGT 62.003 61.111 0.00 0.00 42.25 4.49
3578 5846 3.490759 GCTGTCGCATCCCGTGTG 61.491 66.667 0.00 0.00 39.73 3.82
3579 5847 3.490759 CTGTCGCATCCCGTGTGC 61.491 66.667 0.00 0.00 38.23 4.57
3584 5852 4.760047 GCATCCCGTGTGCCGACT 62.760 66.667 0.00 0.00 39.56 4.18
3585 5853 2.509336 CATCCCGTGTGCCGACTC 60.509 66.667 0.00 0.00 39.56 3.36
3586 5854 2.680352 ATCCCGTGTGCCGACTCT 60.680 61.111 0.00 0.00 39.56 3.24
3587 5855 2.711922 ATCCCGTGTGCCGACTCTC 61.712 63.158 0.00 0.00 39.56 3.20
3588 5856 3.374402 CCCGTGTGCCGACTCTCT 61.374 66.667 0.00 0.00 39.56 3.10
3589 5857 2.651361 CCGTGTGCCGACTCTCTT 59.349 61.111 0.00 0.00 39.56 2.85
3590 5858 1.444553 CCGTGTGCCGACTCTCTTC 60.445 63.158 0.00 0.00 39.56 2.87
3591 5859 1.797933 CGTGTGCCGACTCTCTTCG 60.798 63.158 0.00 0.00 39.56 3.79
3592 5860 2.089349 GTGTGCCGACTCTCTTCGC 61.089 63.158 0.00 0.00 37.70 4.70
3593 5861 2.258591 GTGCCGACTCTCTTCGCA 59.741 61.111 0.00 0.00 37.70 5.10
3594 5862 2.089349 GTGCCGACTCTCTTCGCAC 61.089 63.158 0.00 0.00 38.17 5.34
3595 5863 2.258591 GCCGACTCTCTTCGCACA 59.741 61.111 0.00 0.00 37.70 4.57
3596 5864 1.372997 GCCGACTCTCTTCGCACAA 60.373 57.895 0.00 0.00 37.70 3.33
3597 5865 1.618640 GCCGACTCTCTTCGCACAAC 61.619 60.000 0.00 0.00 37.70 3.32
3598 5866 1.009389 CCGACTCTCTTCGCACAACC 61.009 60.000 0.00 0.00 37.70 3.77
3599 5867 1.337817 CGACTCTCTTCGCACAACCG 61.338 60.000 0.00 0.00 31.03 4.44
3600 5868 1.618640 GACTCTCTTCGCACAACCGC 61.619 60.000 0.00 0.00 0.00 5.68
3601 5869 2.357034 TCTCTTCGCACAACCGCC 60.357 61.111 0.00 0.00 0.00 6.13
3602 5870 3.777925 CTCTTCGCACAACCGCCG 61.778 66.667 0.00 0.00 0.00 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 1.660917 GACCGATCCCACGAGATCC 59.339 63.158 0.00 0.00 39.67 3.36
69 70 1.569493 CACTGAGGACAAAACGCCG 59.431 57.895 0.00 0.00 0.00 6.46
81 82 1.276421 ACAAAGACCGGATCCACTGAG 59.724 52.381 9.46 6.75 0.00 3.35
84 85 1.337823 CGAACAAAGACCGGATCCACT 60.338 52.381 9.46 4.92 0.00 4.00
99 100 3.610040 ATATTCAGACACAGGCGAACA 57.390 42.857 0.00 0.00 0.00 3.18
105 106 7.383572 CGAAAGGATCTAATATTCAGACACAGG 59.616 40.741 0.00 0.00 0.00 4.00
125 134 3.701532 AGAGAAGCGTAGATCGAAAGG 57.298 47.619 0.00 0.00 42.86 3.11
126 135 4.663166 TGAAGAGAAGCGTAGATCGAAAG 58.337 43.478 0.00 0.00 42.86 2.62
130 139 3.222361 CGATGAAGAGAAGCGTAGATCG 58.778 50.000 0.00 0.00 43.12 3.69
131 140 4.215965 GACGATGAAGAGAAGCGTAGATC 58.784 47.826 0.00 0.00 35.09 2.75
166 175 1.032794 CATAGGACTAGCGCACCAGA 58.967 55.000 11.47 0.33 0.00 3.86
167 176 0.598680 GCATAGGACTAGCGCACCAG 60.599 60.000 11.47 6.11 0.00 4.00
168 177 1.441729 GCATAGGACTAGCGCACCA 59.558 57.895 11.47 0.00 0.00 4.17
170 179 3.923614 CGCATAGGACTAGCGCAC 58.076 61.111 11.47 0.00 45.14 5.34
186 199 0.460284 AAGTCGTCATGCTAAGGCCG 60.460 55.000 0.00 0.00 37.74 6.13
209 222 1.612463 ACCTTGGTGTAGTCGACAGTC 59.388 52.381 19.50 7.95 39.29 3.51
212 225 2.168936 ACAAACCTTGGTGTAGTCGACA 59.831 45.455 19.50 0.48 32.71 4.35
223 236 1.971695 GGAGCCGGACAAACCTTGG 60.972 63.158 5.05 0.00 36.31 3.61
227 240 0.608035 TCATTGGAGCCGGACAAACC 60.608 55.000 5.05 0.18 0.00 3.27
248 261 2.511600 CGCCGTCATCACCCCTTC 60.512 66.667 0.00 0.00 0.00 3.46
255 268 2.809174 CACGCTTCGCCGTCATCA 60.809 61.111 0.00 0.00 39.83 3.07
360 373 2.671963 GCAAGGGACCACGAACCC 60.672 66.667 0.00 0.00 45.88 4.11
380 393 1.584308 GAGTCGAGAGGAAAAATCGCG 59.416 52.381 0.00 0.00 40.69 5.87
395 408 1.153939 CGAAGGGCTGAGTGAGTCG 60.154 63.158 0.00 0.00 0.00 4.18
429 442 4.728021 GCTTCGTTAGGTCAAAGCATTAGC 60.728 45.833 1.33 0.00 42.80 3.09
729 749 2.501723 TCATCCTGGAACTTGTAGAGGC 59.498 50.000 0.00 0.00 0.00 4.70
755 775 2.820787 CAGGGTCGGATCTAGATGTACC 59.179 54.545 10.74 13.54 0.00 3.34
833 853 7.007367 CGCACAGCAAAATGTTAACTACTTATG 59.993 37.037 7.22 1.11 0.00 1.90
950 971 5.241403 AGGGTGAAATGACATAGTCACAA 57.759 39.130 23.51 0.00 45.65 3.33
956 977 4.402474 GGGGAAAAGGGTGAAATGACATAG 59.598 45.833 0.00 0.00 0.00 2.23
1042 1063 3.140325 TGGGTTTCTTTGCTGTCCTAG 57.860 47.619 0.00 0.00 0.00 3.02
1065 1086 2.582728 TAAATACGCTGTACCCACCG 57.417 50.000 0.00 0.00 0.00 4.94
1211 1232 2.885266 CCCATGCCATTCTTCTCATGAG 59.115 50.000 17.07 17.07 38.77 2.90
1826 1879 5.072193 ACAGATTGCCAAGGGAAAGAAAAAT 59.928 36.000 0.00 0.00 0.00 1.82
1838 1893 6.900568 TTTACAACAAAACAGATTGCCAAG 57.099 33.333 0.00 0.00 33.52 3.61
1927 1992 2.560105 AGAGAACAAAAATCAGCAGGGC 59.440 45.455 0.00 0.00 0.00 5.19
2006 2091 3.228017 GAGCTAGTCCCGCTCCCC 61.228 72.222 0.74 0.00 46.22 4.81
2012 2097 0.457851 CAACAGGAGAGCTAGTCCCG 59.542 60.000 10.44 3.97 34.21 5.14
2133 2235 9.848710 AAATGACATGAATTCAGAGATGATAGT 57.151 29.630 14.54 1.46 0.00 2.12
2175 2277 8.468399 ACAAATGGAAATGAACAAAAGCAAAAT 58.532 25.926 0.00 0.00 0.00 1.82
2361 2464 4.960469 ACTTCTTATATTGTGGGACGGAGA 59.040 41.667 0.00 0.00 0.00 3.71
2456 2581 2.942796 AACGCTGCCTGTCCGATGA 61.943 57.895 0.00 0.00 0.00 2.92
2599 2724 2.238898 AGGTCGCAACTAAAATAGCCCT 59.761 45.455 0.00 0.00 0.00 5.19
2710 2836 4.602340 TTCAGTTCTCCAGTCCAGTTAC 57.398 45.455 0.00 0.00 0.00 2.50
2785 2911 3.244215 ACTCGATTTCAACAGCCAGAAGA 60.244 43.478 0.00 0.00 0.00 2.87
2793 2920 8.607459 AGCTCAATATAAACTCGATTTCAACAG 58.393 33.333 0.00 0.00 0.00 3.16
2986 3117 7.859875 GCAGATAAGTAAATTCAGATTTGAGCC 59.140 37.037 0.00 0.00 36.22 4.70
3326 5593 1.336440 CAGTTTGCGTGGAACCAATGA 59.664 47.619 0.00 0.00 29.48 2.57
3339 5606 0.250166 ACTACGGTGTCCCAGTTTGC 60.250 55.000 0.00 0.00 0.00 3.68
3443 5711 1.712081 CGCATCTTTCAGAGCACCG 59.288 57.895 0.00 0.00 0.00 4.94
3444 5712 1.427020 GCGCATCTTTCAGAGCACC 59.573 57.895 0.30 0.00 0.00 5.01
3452 5720 2.101700 CCTGAAGGGCGCATCTTTC 58.898 57.895 10.83 5.60 0.00 2.62
3468 5736 2.283460 GGCAAGCCAAGGAAGCCT 60.283 61.111 6.14 0.00 42.01 4.58
3495 5763 4.070552 AGACGAGGCCGGAGTTGC 62.071 66.667 5.05 0.00 40.78 4.17
3496 5764 2.125912 CAGACGAGGCCGGAGTTG 60.126 66.667 5.05 0.00 40.78 3.16
3497 5765 2.282958 TCAGACGAGGCCGGAGTT 60.283 61.111 5.05 0.00 40.78 3.01
3498 5766 2.194388 TAGTCAGACGAGGCCGGAGT 62.194 60.000 5.05 0.00 40.78 3.85
3499 5767 1.440938 CTAGTCAGACGAGGCCGGAG 61.441 65.000 5.05 0.00 40.78 4.63
3500 5768 1.451567 CTAGTCAGACGAGGCCGGA 60.452 63.158 5.05 0.00 40.78 5.14
3501 5769 0.820074 ATCTAGTCAGACGAGGCCGG 60.820 60.000 10.50 0.00 40.78 6.13
3502 5770 0.589223 GATCTAGTCAGACGAGGCCG 59.411 60.000 10.50 0.00 42.50 6.13
3503 5771 1.606668 CAGATCTAGTCAGACGAGGCC 59.393 57.143 10.50 0.00 32.25 5.19
3504 5772 1.001815 GCAGATCTAGTCAGACGAGGC 60.002 57.143 10.50 2.91 32.25 4.70
3505 5773 1.262950 CGCAGATCTAGTCAGACGAGG 59.737 57.143 10.50 0.00 32.25 4.63
3506 5774 1.937223 ACGCAGATCTAGTCAGACGAG 59.063 52.381 4.33 4.33 32.25 4.18
3507 5775 1.934525 GACGCAGATCTAGTCAGACGA 59.065 52.381 19.68 0.00 35.19 4.20
3508 5776 1.937223 AGACGCAGATCTAGTCAGACG 59.063 52.381 23.93 10.83 37.36 4.18
3509 5777 3.202906 AGAGACGCAGATCTAGTCAGAC 58.797 50.000 23.93 16.88 37.36 3.51
3510 5778 3.462982 GAGAGACGCAGATCTAGTCAGA 58.537 50.000 23.93 0.00 37.36 3.27
3511 5779 2.548057 GGAGAGACGCAGATCTAGTCAG 59.452 54.545 23.93 3.49 37.36 3.51
3512 5780 2.092914 TGGAGAGACGCAGATCTAGTCA 60.093 50.000 23.93 8.31 37.36 3.41
3513 5781 2.566913 TGGAGAGACGCAGATCTAGTC 58.433 52.381 17.89 17.89 35.30 2.59
3514 5782 2.719531 TGGAGAGACGCAGATCTAGT 57.280 50.000 0.00 0.00 0.00 2.57
3515 5783 4.545610 GATTTGGAGAGACGCAGATCTAG 58.454 47.826 0.00 0.00 0.00 2.43
3516 5784 3.319405 GGATTTGGAGAGACGCAGATCTA 59.681 47.826 0.00 0.00 0.00 1.98
3517 5785 2.102252 GGATTTGGAGAGACGCAGATCT 59.898 50.000 0.00 0.00 0.00 2.75
3518 5786 2.102252 AGGATTTGGAGAGACGCAGATC 59.898 50.000 0.00 0.00 0.00 2.75
3519 5787 2.114616 AGGATTTGGAGAGACGCAGAT 58.885 47.619 0.00 0.00 0.00 2.90
3520 5788 1.205655 CAGGATTTGGAGAGACGCAGA 59.794 52.381 0.00 0.00 0.00 4.26
3521 5789 1.649664 CAGGATTTGGAGAGACGCAG 58.350 55.000 0.00 0.00 0.00 5.18
3522 5790 3.840831 CAGGATTTGGAGAGACGCA 57.159 52.632 0.00 0.00 0.00 5.24
3532 5800 3.204827 CCGGCGAGCCAGGATTTG 61.205 66.667 9.30 0.00 35.37 2.32
3533 5801 3.717294 ACCGGCGAGCCAGGATTT 61.717 61.111 24.18 6.44 35.07 2.17
3534 5802 4.473520 CACCGGCGAGCCAGGATT 62.474 66.667 24.18 7.01 35.07 3.01
3542 5810 4.988598 ACCAGCAACACCGGCGAG 62.989 66.667 9.30 2.48 36.08 5.03
3543 5811 4.555709 AACCAGCAACACCGGCGA 62.556 61.111 9.30 0.00 36.08 5.54
3544 5812 4.326766 CAACCAGCAACACCGGCG 62.327 66.667 0.00 0.00 36.08 6.46
3545 5813 4.645921 GCAACCAGCAACACCGGC 62.646 66.667 0.00 0.00 44.79 6.13
3561 5829 3.490759 CACACGGGATGCGACAGC 61.491 66.667 0.00 0.00 45.41 4.40
3562 5830 3.490759 GCACACGGGATGCGACAG 61.491 66.667 0.00 0.00 32.45 3.51
3567 5835 4.760047 AGTCGGCACACGGGATGC 62.760 66.667 0.00 0.00 44.45 3.91
3568 5836 2.509336 GAGTCGGCACACGGGATG 60.509 66.667 0.00 0.00 44.45 3.51
3569 5837 2.680352 AGAGTCGGCACACGGGAT 60.680 61.111 0.00 0.00 44.45 3.85
3570 5838 3.371063 GAGAGTCGGCACACGGGA 61.371 66.667 0.00 0.00 44.45 5.14
3571 5839 2.820767 GAAGAGAGTCGGCACACGGG 62.821 65.000 0.00 0.00 44.45 5.28
3572 5840 1.444553 GAAGAGAGTCGGCACACGG 60.445 63.158 0.00 0.00 44.45 4.94
3573 5841 1.797933 CGAAGAGAGTCGGCACACG 60.798 63.158 0.00 0.00 46.11 4.49
3574 5842 2.089349 GCGAAGAGAGTCGGCACAC 61.089 63.158 0.00 0.00 41.40 3.82
3575 5843 2.258591 GCGAAGAGAGTCGGCACA 59.741 61.111 0.00 0.00 41.40 4.57
3576 5844 2.089349 GTGCGAAGAGAGTCGGCAC 61.089 63.158 9.36 9.36 41.40 5.01
3577 5845 2.082629 TTGTGCGAAGAGAGTCGGCA 62.083 55.000 0.00 0.00 41.40 5.69
3578 5846 1.372997 TTGTGCGAAGAGAGTCGGC 60.373 57.895 0.00 0.00 41.40 5.54
3579 5847 1.009389 GGTTGTGCGAAGAGAGTCGG 61.009 60.000 0.00 0.00 41.40 4.79
3580 5848 1.337817 CGGTTGTGCGAAGAGAGTCG 61.338 60.000 0.00 0.00 43.98 4.18
3581 5849 1.618640 GCGGTTGTGCGAAGAGAGTC 61.619 60.000 0.00 0.00 0.00 3.36
3582 5850 1.664965 GCGGTTGTGCGAAGAGAGT 60.665 57.895 0.00 0.00 0.00 3.24
3583 5851 2.383527 GGCGGTTGTGCGAAGAGAG 61.384 63.158 0.00 0.00 35.06 3.20
3584 5852 2.357034 GGCGGTTGTGCGAAGAGA 60.357 61.111 0.00 0.00 35.06 3.10
3585 5853 3.777925 CGGCGGTTGTGCGAAGAG 61.778 66.667 0.00 0.00 35.06 2.85


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

AutoCloner maintained by Alex Coulton.