Multiple sequence alignment - TraesCS2D01G098200

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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 TraesCS2D01G098200 chr2D 100.000 3346 0 0 1 3346 50236426 50239771 0.000000e+00 6180.0
1 TraesCS2D01G098200 chr2D 89.464 2724 177 59 5 2683 39322638 39319980 0.000000e+00 3339.0
2 TraesCS2D01G098200 chr2D 91.048 525 26 6 1961 2481 50158065 50157558 0.000000e+00 689.0
3 TraesCS2D01G098200 chr2D 91.160 362 25 3 2749 3110 39310581 39310227 5.020000e-133 484.0
4 TraesCS2D01G098200 chr2D 89.785 372 27 7 2930 3301 50228600 50228240 1.820000e-127 466.0
5 TraesCS2D01G098200 chr2D 95.472 265 12 0 1633 1897 50160455 50160191 1.110000e-114 424.0
6 TraesCS2D01G098200 chr2D 86.505 289 32 5 2645 2931 50157501 50157218 9.010000e-81 311.0
7 TraesCS2D01G098200 chr2D 86.957 207 17 5 2353 2550 50160193 50159988 1.210000e-54 224.0
8 TraesCS2D01G098200 chr2D 87.413 143 18 0 2977 3119 39309951 39309809 7.430000e-37 165.0
9 TraesCS2D01G098200 chr2D 85.714 119 13 1 2645 2763 50155212 50155098 4.530000e-24 122.0
10 TraesCS2D01G098200 chr2A 92.042 2199 92 29 329 2481 51943823 51945984 0.000000e+00 3014.0
11 TraesCS2D01G098200 chr2A 93.722 1131 59 5 1034 2164 44123267 44124385 0.000000e+00 1685.0
12 TraesCS2D01G098200 chr2A 79.759 1077 111 53 5 1038 44108342 44109354 0.000000e+00 682.0
13 TraesCS2D01G098200 chr2A 88.679 371 35 5 2749 3119 44151934 44152297 2.370000e-121 446.0
14 TraesCS2D01G098200 chr2A 94.182 275 12 3 2461 2733 44131354 44131626 1.860000e-112 416.0
15 TraesCS2D01G098200 chr2A 87.405 262 22 6 2685 2941 51946072 51946327 1.170000e-74 291.0
16 TraesCS2D01G098200 chr2A 85.609 271 26 7 1 269 51943388 51943647 4.250000e-69 272.0
17 TraesCS2D01G098200 chr2A 90.909 88 8 0 2190 2277 44124381 44124468 5.860000e-23 119.0
18 TraesCS2D01G098200 chr2A 95.833 48 2 0 3299 3346 51946453 51946500 9.950000e-11 78.7
19 TraesCS2D01G098200 chr2B 90.506 2075 94 37 436 2473 78070816 78072824 0.000000e+00 2645.0
20 TraesCS2D01G098200 chr2B 91.505 1389 76 20 1078 2450 77995749 77994387 0.000000e+00 1873.0
21 TraesCS2D01G098200 chr2B 91.514 1202 75 13 1189 2379 78012116 78010931 0.000000e+00 1629.0
22 TraesCS2D01G098200 chr2B 94.377 907 42 3 1572 2478 78047843 78046946 0.000000e+00 1384.0
23 TraesCS2D01G098200 chr2B 84.496 516 48 10 2645 3156 78072901 78073388 6.490000e-132 481.0
24 TraesCS2D01G098200 chr2B 95.312 256 12 0 1633 1888 78049649 78049394 1.120000e-109 407.0
25 TraesCS2D01G098200 chr2B 84.694 196 20 5 2353 2539 78049390 78049196 1.590000e-43 187.0
26 TraesCS2D01G098200 chr2B 86.111 180 12 5 3176 3346 78079033 78079208 7.370000e-42 182.0
27 TraesCS2D01G098200 chr2B 78.723 282 33 12 328 602 78070310 78070571 2.670000e-36 163.0
28 TraesCS2D01G098200 chr2B 86.905 84 9 2 1078 1161 78012195 78012114 3.550000e-15 93.5
29 TraesCS2D01G098200 chr5D 92.157 51 4 0 1944 1994 5816828 5816778 4.630000e-09 73.1
30 TraesCS2D01G098200 chr7D 93.478 46 3 0 1388 1433 194224614 194224659 5.990000e-08 69.4
31 TraesCS2D01G098200 chr7B 93.478 46 3 0 1388 1433 158075367 158075412 5.990000e-08 69.4
32 TraesCS2D01G098200 chr7A 93.478 46 3 0 1388 1433 203863713 203863758 5.990000e-08 69.4


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 TraesCS2D01G098200 chr2D 50236426 50239771 3345 False 6180.000000 6180 100.00000 1 3346 1 chr2D.!!$F1 3345
1 TraesCS2D01G098200 chr2D 39319980 39322638 2658 True 3339.000000 3339 89.46400 5 2683 1 chr2D.!!$R1 2678
2 TraesCS2D01G098200 chr2D 50155098 50160455 5357 True 354.000000 689 89.13920 1633 2931 5 chr2D.!!$R4 1298
3 TraesCS2D01G098200 chr2D 39309809 39310581 772 True 324.500000 484 89.28650 2749 3119 2 chr2D.!!$R3 370
4 TraesCS2D01G098200 chr2A 51943388 51946500 3112 False 913.925000 3014 90.22225 1 3346 4 chr2A.!!$F5 3345
5 TraesCS2D01G098200 chr2A 44123267 44124468 1201 False 902.000000 1685 92.31550 1034 2277 2 chr2A.!!$F4 1243
6 TraesCS2D01G098200 chr2A 44108342 44109354 1012 False 682.000000 682 79.75900 5 1038 1 chr2A.!!$F1 1033
7 TraesCS2D01G098200 chr2B 77994387 77995749 1362 True 1873.000000 1873 91.50500 1078 2450 1 chr2B.!!$R1 1372
8 TraesCS2D01G098200 chr2B 78070310 78073388 3078 False 1096.333333 2645 84.57500 328 3156 3 chr2B.!!$F2 2828
9 TraesCS2D01G098200 chr2B 78010931 78012195 1264 True 861.250000 1629 89.20950 1078 2379 2 chr2B.!!$R2 1301
10 TraesCS2D01G098200 chr2B 78046946 78049649 2703 True 659.333333 1384 91.46100 1572 2539 3 chr2B.!!$R3 967

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
799 1344 0.248661 AGTCAACGGAGCGATCGATG 60.249 55.0 21.57 3.89 0.0 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2448 3115 0.523966 ACGGCTGAAACGAGAGAGAG 59.476 55.0 0.0 0.0 34.93 3.2 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
160 164 6.202762 CCAAAGCCAAATTTCCTGTTTTCTAC 59.797 38.462 0.00 0.00 0.00 2.59
196 200 4.696479 TCTCTATGAATCAAAGAGGCCC 57.304 45.455 0.00 0.00 37.84 5.80
204 208 2.270434 TCAAAGAGGCCCTACCATCT 57.730 50.000 0.00 0.00 43.14 2.90
205 209 1.839994 TCAAAGAGGCCCTACCATCTG 59.160 52.381 0.00 0.00 43.14 2.90
217 221 3.832704 CCATCTGGTGACTACGCAA 57.167 52.632 0.00 0.00 0.00 4.85
218 222 2.093306 CCATCTGGTGACTACGCAAA 57.907 50.000 0.00 0.00 0.00 3.68
219 223 2.632377 CCATCTGGTGACTACGCAAAT 58.368 47.619 0.00 0.00 0.00 2.32
221 225 3.261580 CATCTGGTGACTACGCAAATGA 58.738 45.455 0.00 0.00 0.00 2.57
229 233 2.928116 GACTACGCAAATGAGGGTACAC 59.072 50.000 0.00 0.00 36.07 2.90
232 236 1.273048 ACGCAAATGAGGGTACACGTA 59.727 47.619 0.00 0.00 32.43 3.57
235 239 2.677037 GCAAATGAGGGTACACGTAGCT 60.677 50.000 6.38 0.00 34.26 3.32
241 245 2.490903 GAGGGTACACGTAGCTGAGAAA 59.509 50.000 0.00 0.00 34.26 2.52
247 251 3.243336 ACACGTAGCTGAGAAAACGATC 58.757 45.455 11.18 0.00 38.64 3.69
257 261 0.521242 GAAAACGATCGCTTGCGCAT 60.521 50.000 12.75 0.00 35.30 4.73
277 288 6.250819 CGCATATGTCTTTTTAGTTGACTGG 58.749 40.000 4.29 0.00 0.00 4.00
293 311 7.212274 AGTTGACTGGGAATTCATTTTTCAAG 58.788 34.615 7.93 0.00 0.00 3.02
316 396 0.667184 GCACATTCCCCGCAAAACAG 60.667 55.000 0.00 0.00 0.00 3.16
321 401 0.748729 TTCCCCGCAAAACAGAACGT 60.749 50.000 0.00 0.00 0.00 3.99
324 404 1.538075 CCCCGCAAAACAGAACGTAAT 59.462 47.619 0.00 0.00 0.00 1.89
325 405 2.743126 CCCCGCAAAACAGAACGTAATA 59.257 45.455 0.00 0.00 0.00 0.98
326 406 3.425227 CCCCGCAAAACAGAACGTAATAC 60.425 47.826 0.00 0.00 0.00 1.89
333 459 9.858247 CGCAAAACAGAACGTAATACATAATAT 57.142 29.630 0.00 0.00 0.00 1.28
374 500 6.183361 ACCCATGTTGTAACAATTTGTCCATT 60.183 34.615 1.83 0.00 43.03 3.16
421 555 4.063998 TCATAGCTTGAGAACATGCGAT 57.936 40.909 0.00 0.00 46.91 4.58
452 607 4.612943 TGGAATTTTGAAGCAACCGTAAC 58.387 39.130 0.00 0.00 0.00 2.50
572 1104 2.047274 ACGTGGACATGCCTTCGG 60.047 61.111 18.80 0.00 38.37 4.30
791 1336 2.022129 CGTGGTCAGTCAACGGAGC 61.022 63.158 5.68 5.68 38.66 4.70
799 1344 0.248661 AGTCAACGGAGCGATCGATG 60.249 55.000 21.57 3.89 0.00 3.84
906 1458 2.104170 CCCTCGCTATATCCCTCTTCC 58.896 57.143 0.00 0.00 0.00 3.46
907 1459 2.104170 CCTCGCTATATCCCTCTTCCC 58.896 57.143 0.00 0.00 0.00 3.97
913 1465 3.445805 GCTATATCCCTCTTCCCTCTTCG 59.554 52.174 0.00 0.00 0.00 3.79
961 1518 0.984230 TTGGATCAACCGGAGCTCTT 59.016 50.000 9.46 0.00 42.61 2.85
977 1538 3.003173 TTCAGCGCCTGGGTAGCT 61.003 61.111 2.29 0.00 42.64 3.32
1223 1797 0.951040 GCACCTCCAACTCCAACTCG 60.951 60.000 0.00 0.00 0.00 4.18
1377 1960 1.004918 ACCAAGAACTTCGGCTCCG 60.005 57.895 1.14 1.14 41.35 4.63
1521 2107 2.530151 AGAGCTTCCAGGGCCACA 60.530 61.111 6.18 0.00 0.00 4.17
1796 2403 0.249868 TCAAGTCCTCCAACGTGCTG 60.250 55.000 0.00 0.00 0.00 4.41
2257 2901 4.643387 AAGCGCCGCCAAGTCCTT 62.643 61.111 4.98 0.00 0.00 3.36
2280 2924 2.812609 CCTCCTCGACGACGACGA 60.813 66.667 20.18 20.18 43.81 4.20
2352 3003 3.446161 TCGAAACAAAGCCTAGCTAGCTA 59.554 43.478 22.85 22.85 40.49 3.32
2353 3004 3.799420 CGAAACAAAGCCTAGCTAGCTAG 59.201 47.826 35.39 35.39 44.07 3.42
2448 3115 8.522830 TGTAGATTGGAAATTGGACATCTTTTC 58.477 33.333 0.00 0.00 0.00 2.29
2530 3197 3.764434 GGGTCAAGATTTTCTTTCCTCCC 59.236 47.826 7.63 0.00 33.78 4.30
2540 3207 1.705186 TCTTTCCTCCCTTCTGTTGGG 59.295 52.381 0.00 0.00 45.90 4.12
2694 3364 0.318955 GCTGGCAGCATCAACGTTTT 60.319 50.000 33.33 0.00 41.89 2.43
2733 3403 3.136443 TGAACACTTCCTAGCCCCATATG 59.864 47.826 0.00 0.00 0.00 1.78
2734 3404 2.057922 ACACTTCCTAGCCCCATATGG 58.942 52.381 15.41 15.41 0.00 2.74
2742 3412 3.520623 GCCCCATATGGCCATATCC 57.479 57.895 31.50 17.62 46.11 2.59
2747 3417 3.770933 CCCCATATGGCCATATCCAAAAG 59.229 47.826 31.50 20.04 39.96 2.27
2821 3496 4.329545 TGGTGCGCAAGAGGGTCC 62.330 66.667 14.00 8.03 43.02 4.46
2872 3551 1.038681 TCCCCATAACGAGCGCTACA 61.039 55.000 11.50 0.00 0.00 2.74
2942 3621 4.685165 CGGATGCTCAATCTCTAACATCAG 59.315 45.833 0.00 0.00 36.49 2.90
2990 3669 4.350620 CGATCTCCCTCGCCATTG 57.649 61.111 0.00 0.00 0.00 2.82
3008 3687 1.357334 GACGCACCTCTCTCGGATC 59.643 63.158 0.00 0.00 0.00 3.36
3018 3697 1.070445 TCTCTCGGATCGGTAGTCCTC 59.930 57.143 0.00 0.00 33.46 3.71
3028 3707 1.031235 GGTAGTCCTCGGCTAGAACC 58.969 60.000 0.00 0.00 0.00 3.62
3063 3742 4.318760 CGTCGAGAAAAACAAGCTGAATGA 60.319 41.667 0.00 0.00 0.00 2.57
3064 3743 4.906437 GTCGAGAAAAACAAGCTGAATGAC 59.094 41.667 0.00 0.00 0.00 3.06
3068 3747 6.395426 AGAAAAACAAGCTGAATGACATGA 57.605 33.333 0.00 0.00 0.00 3.07
3133 3883 8.496751 GTTAGAGTGTTTGAGAATAGGTTCAAC 58.503 37.037 0.00 0.00 36.79 3.18
3140 3890 6.605471 TTGAGAATAGGTTCAACTAGCTCA 57.395 37.500 0.00 0.00 36.94 4.26
3141 3891 6.798427 TGAGAATAGGTTCAACTAGCTCAT 57.202 37.500 0.00 0.00 35.35 2.90
3159 3909 6.951971 AGCTCATTCTTGTTATAGACCTTGT 58.048 36.000 0.00 0.00 0.00 3.16
3160 3910 8.079211 AGCTCATTCTTGTTATAGACCTTGTA 57.921 34.615 0.00 0.00 0.00 2.41
3162 3912 9.162764 GCTCATTCTTGTTATAGACCTTGTAAA 57.837 33.333 0.00 0.00 0.00 2.01
3167 3917 8.827177 TCTTGTTATAGACCTTGTAAAGTGTG 57.173 34.615 0.00 0.00 44.25 3.82
3168 3918 7.876068 TCTTGTTATAGACCTTGTAAAGTGTGG 59.124 37.037 0.00 0.00 44.25 4.17
3169 3919 7.069877 TGTTATAGACCTTGTAAAGTGTGGT 57.930 36.000 0.00 0.00 44.25 4.16
3170 3920 6.932400 TGTTATAGACCTTGTAAAGTGTGGTG 59.068 38.462 0.00 0.00 44.25 4.17
3171 3921 2.572290 AGACCTTGTAAAGTGTGGTGC 58.428 47.619 0.00 0.00 44.25 5.01
3172 3922 2.172717 AGACCTTGTAAAGTGTGGTGCT 59.827 45.455 0.00 0.00 44.25 4.40
3173 3923 3.389983 AGACCTTGTAAAGTGTGGTGCTA 59.610 43.478 0.00 0.00 44.25 3.49
3174 3924 4.041691 AGACCTTGTAAAGTGTGGTGCTAT 59.958 41.667 0.00 0.00 44.25 2.97
3175 3925 4.725490 ACCTTGTAAAGTGTGGTGCTATT 58.275 39.130 0.00 0.00 44.25 1.73
3177 3927 6.300703 ACCTTGTAAAGTGTGGTGCTATTTA 58.699 36.000 0.00 0.00 44.25 1.40
3178 3928 6.206048 ACCTTGTAAAGTGTGGTGCTATTTAC 59.794 38.462 0.00 0.00 44.25 2.01
3179 3929 6.349033 CCTTGTAAAGTGTGGTGCTATTTACC 60.349 42.308 0.00 0.00 44.25 2.85
3180 3930 5.871834 TGTAAAGTGTGGTGCTATTTACCT 58.128 37.500 0.00 0.00 39.01 3.08
3182 3932 7.101054 TGTAAAGTGTGGTGCTATTTACCTAG 58.899 38.462 0.00 0.00 39.01 3.02
3183 3933 5.757099 AAGTGTGGTGCTATTTACCTAGT 57.243 39.130 0.00 0.00 39.01 2.57
3185 3935 6.218108 AGTGTGGTGCTATTTACCTAGTAC 57.782 41.667 0.00 0.00 39.01 2.73
3186 3936 5.718130 AGTGTGGTGCTATTTACCTAGTACA 59.282 40.000 0.00 0.00 36.42 2.90
3187 3937 5.809051 GTGTGGTGCTATTTACCTAGTACAC 59.191 44.000 0.00 0.00 36.42 2.90
3188 3938 5.039333 GTGGTGCTATTTACCTAGTACACG 58.961 45.833 0.00 0.00 36.42 4.49
3190 3940 4.098501 GGTGCTATTTACCTAGTACACGGT 59.901 45.833 10.45 10.45 36.42 4.83
3191 3941 5.394553 GGTGCTATTTACCTAGTACACGGTT 60.395 44.000 10.81 0.00 36.42 4.44
3192 3942 5.517770 GTGCTATTTACCTAGTACACGGTTG 59.482 44.000 10.81 0.83 35.26 3.77
3193 3943 5.045872 GCTATTTACCTAGTACACGGTTGG 58.954 45.833 10.81 0.00 34.76 3.77
3194 3944 3.959535 TTTACCTAGTACACGGTTGGG 57.040 47.619 10.81 0.00 34.76 4.12
3195 3945 1.851304 TACCTAGTACACGGTTGGGG 58.149 55.000 10.81 0.00 34.76 4.96
3196 3946 1.219935 CCTAGTACACGGTTGGGGC 59.780 63.158 0.00 0.00 0.00 5.80
3197 3947 1.262640 CCTAGTACACGGTTGGGGCT 61.263 60.000 0.00 0.00 0.00 5.19
3198 3948 1.477553 CTAGTACACGGTTGGGGCTA 58.522 55.000 0.00 0.00 0.00 3.93
3199 3949 1.826720 CTAGTACACGGTTGGGGCTAA 59.173 52.381 0.00 0.00 0.00 3.09
3201 3951 1.631898 AGTACACGGTTGGGGCTAAAT 59.368 47.619 0.00 0.00 0.00 1.40
3203 3953 0.111639 ACACGGTTGGGGCTAAATGT 59.888 50.000 0.00 0.00 0.00 2.71
3205 3955 0.323087 ACGGTTGGGGCTAAATGTCC 60.323 55.000 0.00 0.00 40.45 4.02
3220 5520 4.671590 TCCCGAGTCGCTGGTCCA 62.672 66.667 7.12 0.00 0.00 4.02
3221 5521 4.436998 CCCGAGTCGCTGGTCCAC 62.437 72.222 7.12 0.00 0.00 4.02
3222 5522 3.374402 CCGAGTCGCTGGTCCACT 61.374 66.667 7.12 0.00 0.00 4.00
3223 5523 2.044555 CCGAGTCGCTGGTCCACTA 61.045 63.158 7.12 0.00 0.00 2.74
3225 5525 1.810532 GAGTCGCTGGTCCACTAGG 59.189 63.158 0.00 0.00 0.00 3.02
3227 5527 1.982938 GTCGCTGGTCCACTAGGGT 60.983 63.158 6.97 0.00 38.30 4.34
3228 5528 1.229082 TCGCTGGTCCACTAGGGTT 60.229 57.895 6.97 0.00 38.30 4.11
3231 5531 0.400594 GCTGGTCCACTAGGGTTTGT 59.599 55.000 0.00 0.00 38.11 2.83
3232 5532 1.882352 GCTGGTCCACTAGGGTTTGTG 60.882 57.143 0.00 0.00 38.11 3.33
3235 5535 2.242708 TGGTCCACTAGGGTTTGTGTTT 59.757 45.455 0.00 0.00 38.11 2.83
3238 5538 2.092103 TCCACTAGGGTTTGTGTTTGCT 60.092 45.455 0.00 0.00 38.11 3.91
3239 5539 2.693074 CCACTAGGGTTTGTGTTTGCTT 59.307 45.455 0.00 0.00 32.76 3.91
3240 5540 3.490761 CCACTAGGGTTTGTGTTTGCTTG 60.491 47.826 0.00 0.00 32.76 4.01
3241 5541 2.100749 ACTAGGGTTTGTGTTTGCTTGC 59.899 45.455 0.00 0.00 0.00 4.01
3242 5542 0.901124 AGGGTTTGTGTTTGCTTGCA 59.099 45.000 0.00 0.00 0.00 4.08
3243 5543 1.006086 GGGTTTGTGTTTGCTTGCAC 58.994 50.000 0.00 0.00 36.26 4.57
3244 5544 1.405391 GGGTTTGTGTTTGCTTGCACT 60.405 47.619 0.00 0.00 36.63 4.40
3247 5547 2.736192 GTTTGTGTTTGCTTGCACTTGT 59.264 40.909 0.00 0.00 36.63 3.16
3248 5548 1.993542 TGTGTTTGCTTGCACTTGTG 58.006 45.000 0.00 0.00 36.63 3.33
3249 5549 1.280066 GTGTTTGCTTGCACTTGTGG 58.720 50.000 2.81 0.00 33.22 4.17
3250 5550 0.175302 TGTTTGCTTGCACTTGTGGG 59.825 50.000 2.81 0.00 0.00 4.61
3251 5551 0.530431 GTTTGCTTGCACTTGTGGGG 60.530 55.000 2.81 0.00 0.00 4.96
3253 5553 2.521708 GCTTGCACTTGTGGGGGT 60.522 61.111 2.81 0.00 0.00 4.95
3256 5556 1.000993 TTGCACTTGTGGGGGTGTT 59.999 52.632 2.81 0.00 36.03 3.32
3257 5557 1.326213 TTGCACTTGTGGGGGTGTTG 61.326 55.000 2.81 0.00 36.03 3.33
3258 5558 1.756561 GCACTTGTGGGGGTGTTGT 60.757 57.895 2.81 0.00 36.03 3.32
3259 5559 1.326951 GCACTTGTGGGGGTGTTGTT 61.327 55.000 2.81 0.00 36.03 2.83
3260 5560 1.190643 CACTTGTGGGGGTGTTGTTT 58.809 50.000 0.00 0.00 0.00 2.83
3261 5561 1.134848 CACTTGTGGGGGTGTTGTTTG 60.135 52.381 0.00 0.00 0.00 2.93
3262 5562 1.190643 CTTGTGGGGGTGTTGTTTGT 58.809 50.000 0.00 0.00 0.00 2.83
3263 5563 1.552792 CTTGTGGGGGTGTTGTTTGTT 59.447 47.619 0.00 0.00 0.00 2.83
3264 5564 0.898320 TGTGGGGGTGTTGTTTGTTG 59.102 50.000 0.00 0.00 0.00 3.33
3266 5566 1.276705 GTGGGGGTGTTGTTTGTTGTT 59.723 47.619 0.00 0.00 0.00 2.83
3267 5567 1.276421 TGGGGGTGTTGTTTGTTGTTG 59.724 47.619 0.00 0.00 0.00 3.33
3269 5569 1.406205 GGGGTGTTGTTTGTTGTTGGG 60.406 52.381 0.00 0.00 0.00 4.12
3273 5573 3.394719 GTGTTGTTTGTTGTTGGGTTGT 58.605 40.909 0.00 0.00 0.00 3.32
3274 5574 4.557205 GTGTTGTTTGTTGTTGGGTTGTA 58.443 39.130 0.00 0.00 0.00 2.41
3275 5575 4.623595 GTGTTGTTTGTTGTTGGGTTGTAG 59.376 41.667 0.00 0.00 0.00 2.74
3276 5576 3.512033 TGTTTGTTGTTGGGTTGTAGC 57.488 42.857 0.00 0.00 0.00 3.58
3277 5577 2.166664 TGTTTGTTGTTGGGTTGTAGCC 59.833 45.455 0.00 0.00 36.00 3.93
3285 5585 3.564262 GGGTTGTAGCCCTTGTACC 57.436 57.895 0.00 0.00 45.22 3.34
3286 5586 0.034767 GGGTTGTAGCCCTTGTACCC 60.035 60.000 0.00 0.00 45.22 3.69
3287 5587 0.034767 GGTTGTAGCCCTTGTACCCC 60.035 60.000 0.00 0.00 0.00 4.95
3288 5588 0.989602 GTTGTAGCCCTTGTACCCCT 59.010 55.000 0.00 0.00 0.00 4.79
3289 5589 1.065636 GTTGTAGCCCTTGTACCCCTC 60.066 57.143 0.00 0.00 0.00 4.30
3290 5590 0.117541 TGTAGCCCTTGTACCCCTCA 59.882 55.000 0.00 0.00 0.00 3.86
3291 5591 0.831307 GTAGCCCTTGTACCCCTCAG 59.169 60.000 0.00 0.00 0.00 3.35
3293 5593 0.910088 AGCCCTTGTACCCCTCAGAC 60.910 60.000 0.00 0.00 0.00 3.51
3294 5594 0.910088 GCCCTTGTACCCCTCAGACT 60.910 60.000 0.00 0.00 0.00 3.24
3295 5595 1.657804 CCCTTGTACCCCTCAGACTT 58.342 55.000 0.00 0.00 0.00 3.01
3296 5596 1.985895 CCCTTGTACCCCTCAGACTTT 59.014 52.381 0.00 0.00 0.00 2.66
3297 5597 2.290323 CCCTTGTACCCCTCAGACTTTG 60.290 54.545 0.00 0.00 0.00 2.77
3298 5598 2.427506 CTTGTACCCCTCAGACTTTGC 58.572 52.381 0.00 0.00 0.00 3.68
3299 5599 1.429930 TGTACCCCTCAGACTTTGCA 58.570 50.000 0.00 0.00 0.00 4.08
3301 5601 1.348036 GTACCCCTCAGACTTTGCACT 59.652 52.381 0.00 0.00 0.00 4.40
3304 5604 2.310538 CCCCTCAGACTTTGCACTTTT 58.689 47.619 0.00 0.00 0.00 2.27
3315 5615 7.116805 CAGACTTTGCACTTTTGTTTTCTCTTT 59.883 33.333 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 81 9.479549 AAAAAGGCATATAGAAAAGAGGATGAA 57.520 29.630 0.00 0.00 0.00 2.57
110 114 5.657745 TGGCACAATGTATCCATTTGATTCT 59.342 36.000 2.95 0.00 39.28 2.40
160 164 9.447157 GATTCATAGAGAAATGGAGGGAAATAG 57.553 37.037 0.00 0.00 40.22 1.73
204 208 1.338674 CCCTCATTTGCGTAGTCACCA 60.339 52.381 0.00 0.00 0.00 4.17
205 209 1.338769 ACCCTCATTTGCGTAGTCACC 60.339 52.381 0.00 0.00 0.00 4.02
210 214 1.924524 CGTGTACCCTCATTTGCGTAG 59.075 52.381 0.00 0.00 0.00 3.51
217 221 2.427453 CTCAGCTACGTGTACCCTCATT 59.573 50.000 0.00 0.00 0.00 2.57
218 222 2.025155 CTCAGCTACGTGTACCCTCAT 58.975 52.381 0.00 0.00 0.00 2.90
219 223 1.003928 TCTCAGCTACGTGTACCCTCA 59.996 52.381 0.00 0.00 0.00 3.86
221 225 2.211250 TTCTCAGCTACGTGTACCCT 57.789 50.000 0.00 0.00 0.00 4.34
229 233 1.253034 GCGATCGTTTTCTCAGCTACG 59.747 52.381 17.81 0.00 35.46 3.51
232 236 1.728971 CAAGCGATCGTTTTCTCAGCT 59.271 47.619 14.93 0.00 34.70 4.24
235 239 0.438445 CGCAAGCGATCGTTTTCTCA 59.562 50.000 14.93 0.00 42.83 3.27
257 261 8.934023 AATTCCCAGTCAACTAAAAAGACATA 57.066 30.769 0.00 0.00 34.80 2.29
277 288 5.461737 TGTGCGAACTTGAAAAATGAATTCC 59.538 36.000 2.27 0.00 0.00 3.01
293 311 2.136196 TTTGCGGGGAATGTGCGAAC 62.136 55.000 0.00 0.00 0.00 3.95
325 405 8.395633 GGTGAGCACGTTTTTAGAATATTATGT 58.604 33.333 0.00 0.00 0.00 2.29
326 406 7.855904 GGGTGAGCACGTTTTTAGAATATTATG 59.144 37.037 0.00 0.00 0.00 1.90
333 459 2.920524 TGGGTGAGCACGTTTTTAGAA 58.079 42.857 0.00 0.00 0.00 2.10
418 552 7.488792 TGCTTCAAAATTCCAATGTTGATATCG 59.511 33.333 5.85 0.00 41.09 2.92
421 555 7.387397 GGTTGCTTCAAAATTCCAATGTTGATA 59.613 33.333 5.85 0.00 41.09 2.15
452 607 2.287009 GGAGAAAGGAACGTGCAACAAG 60.287 50.000 0.00 0.00 35.74 3.16
572 1104 2.434884 TGTTCCGCTAGCTGCTGC 60.435 61.111 13.43 12.66 40.11 5.25
791 1336 0.315951 CAGCTTGCTTGCATCGATCG 60.316 55.000 9.36 9.36 34.99 3.69
900 1452 1.107945 GGAGGACGAAGAGGGAAGAG 58.892 60.000 0.00 0.00 0.00 2.85
913 1465 1.612463 ACAAGTCACAGTACGGAGGAC 59.388 52.381 0.00 7.18 0.00 3.85
966 1523 4.537433 CCGCTCAGCTACCCAGGC 62.537 72.222 0.00 0.00 0.00 4.85
977 1538 1.153369 GGTGCAGCTTATCCGCTCA 60.153 57.895 9.07 0.00 38.41 4.26
991 1552 3.758931 GTTTCCCATGGCCGGTGC 61.759 66.667 6.09 0.00 0.00 5.01
992 1553 1.184970 AAAGTTTCCCATGGCCGGTG 61.185 55.000 6.09 0.00 0.00 4.94
1377 1960 3.217743 CTCCCCGAGGTAGGACGC 61.218 72.222 0.00 0.00 0.00 5.19
1521 2107 2.681778 CTCGGTGAGCCACTCCCT 60.682 66.667 5.48 0.00 34.40 4.20
1625 2219 1.299926 GCGGGGCATGTACTCGTAG 60.300 63.158 12.27 0.00 0.00 3.51
2257 2901 1.221293 GTCGTCGAGGAGGAGGAGA 59.779 63.158 8.30 0.00 32.07 3.71
2311 2958 4.269523 GGTGGCCTCTGTGCACCA 62.270 66.667 15.69 0.00 34.56 4.17
2352 3003 2.445682 ATGAACCGAGTCTCCTAGCT 57.554 50.000 0.00 0.00 0.00 3.32
2353 3004 3.528597 AAATGAACCGAGTCTCCTAGC 57.471 47.619 0.00 0.00 0.00 3.42
2354 3005 8.414778 AGTAATTAAATGAACCGAGTCTCCTAG 58.585 37.037 0.00 0.00 0.00 3.02
2355 3006 8.195436 CAGTAATTAAATGAACCGAGTCTCCTA 58.805 37.037 0.00 0.00 0.00 2.94
2448 3115 0.523966 ACGGCTGAAACGAGAGAGAG 59.476 55.000 0.00 0.00 34.93 3.20
2733 3403 8.177119 TGTACATAATTCTTTTGGATATGGCC 57.823 34.615 0.00 0.00 0.00 5.36
2770 3445 6.636850 ACTTTTTGTTTACTGCATCGACATTC 59.363 34.615 0.00 0.00 0.00 2.67
2872 3551 0.322975 AGCACGACAGAGCAAAGGAT 59.677 50.000 0.00 0.00 36.39 3.24
2990 3669 1.357334 GATCCGAGAGAGGTGCGTC 59.643 63.158 0.00 0.00 0.00 5.19
3008 3687 0.662085 GTTCTAGCCGAGGACTACCG 59.338 60.000 0.00 0.00 41.83 4.02
3028 3707 1.158484 TCTCGACGACTAGGATGCCG 61.158 60.000 0.00 0.00 0.00 5.69
3063 3742 4.080129 ACCAAGCAACTAGGATGATCATGT 60.080 41.667 14.30 1.31 0.00 3.21
3064 3743 4.458397 ACCAAGCAACTAGGATGATCATG 58.542 43.478 14.30 0.59 0.00 3.07
3068 3747 2.846206 TGGACCAAGCAACTAGGATGAT 59.154 45.455 0.00 0.00 0.00 2.45
3133 3883 8.200792 ACAAGGTCTATAACAAGAATGAGCTAG 58.799 37.037 0.00 0.00 32.92 3.42
3141 3891 9.268268 CACACTTTACAAGGTCTATAACAAGAA 57.732 33.333 0.00 0.00 0.00 2.52
3159 3909 7.248743 ACTAGGTAAATAGCACCACACTTTA 57.751 36.000 0.00 0.00 38.62 1.85
3160 3910 6.123045 ACTAGGTAAATAGCACCACACTTT 57.877 37.500 0.00 0.00 38.62 2.66
3162 3912 5.718130 TGTACTAGGTAAATAGCACCACACT 59.282 40.000 0.00 0.00 38.62 3.55
3163 3913 5.809051 GTGTACTAGGTAAATAGCACCACAC 59.191 44.000 0.00 0.00 38.62 3.82
3164 3914 5.393352 CGTGTACTAGGTAAATAGCACCACA 60.393 44.000 0.00 0.00 38.62 4.17
3165 3915 5.039333 CGTGTACTAGGTAAATAGCACCAC 58.961 45.833 0.00 0.00 38.62 4.16
3167 3917 4.098501 ACCGTGTACTAGGTAAATAGCACC 59.901 45.833 10.43 0.00 39.30 5.01
3168 3918 5.254339 ACCGTGTACTAGGTAAATAGCAC 57.746 43.478 10.43 0.00 39.30 4.40
3169 3919 5.394443 CCAACCGTGTACTAGGTAAATAGCA 60.394 44.000 12.11 0.00 40.37 3.49
3170 3920 5.045872 CCAACCGTGTACTAGGTAAATAGC 58.954 45.833 12.11 0.00 40.37 2.97
3171 3921 5.452356 CCCCAACCGTGTACTAGGTAAATAG 60.452 48.000 12.11 2.60 40.37 1.73
3172 3922 4.405358 CCCCAACCGTGTACTAGGTAAATA 59.595 45.833 12.11 0.00 40.37 1.40
3173 3923 3.198417 CCCCAACCGTGTACTAGGTAAAT 59.802 47.826 12.11 0.00 40.37 1.40
3174 3924 2.566724 CCCCAACCGTGTACTAGGTAAA 59.433 50.000 12.11 0.00 40.37 2.01
3175 3925 2.178580 CCCCAACCGTGTACTAGGTAA 58.821 52.381 12.11 0.00 40.37 2.85
3177 3927 1.547472 GCCCCAACCGTGTACTAGGT 61.547 60.000 6.96 6.96 43.68 3.08
3178 3928 1.219935 GCCCCAACCGTGTACTAGG 59.780 63.158 5.78 5.78 0.00 3.02
3179 3929 1.477553 TAGCCCCAACCGTGTACTAG 58.522 55.000 0.00 0.00 0.00 2.57
3180 3930 1.935799 TTAGCCCCAACCGTGTACTA 58.064 50.000 0.00 0.00 0.00 1.82
3182 3932 1.741145 CATTTAGCCCCAACCGTGTAC 59.259 52.381 0.00 0.00 0.00 2.90
3183 3933 1.351683 ACATTTAGCCCCAACCGTGTA 59.648 47.619 0.00 0.00 0.00 2.90
3185 3935 0.808755 GACATTTAGCCCCAACCGTG 59.191 55.000 0.00 0.00 0.00 4.94
3186 3936 0.323087 GGACATTTAGCCCCAACCGT 60.323 55.000 0.00 0.00 0.00 4.83
3187 3937 1.035385 GGGACATTTAGCCCCAACCG 61.035 60.000 0.00 0.00 39.89 4.44
3188 3938 1.035385 CGGGACATTTAGCCCCAACC 61.035 60.000 0.00 0.00 41.50 3.77
3190 3940 0.254747 CTCGGGACATTTAGCCCCAA 59.745 55.000 0.00 0.00 41.50 4.12
3191 3941 0.912487 ACTCGGGACATTTAGCCCCA 60.912 55.000 0.00 0.00 41.50 4.96
3192 3942 0.179054 GACTCGGGACATTTAGCCCC 60.179 60.000 0.00 0.00 41.50 5.80
3193 3943 0.529992 CGACTCGGGACATTTAGCCC 60.530 60.000 0.00 0.00 41.11 5.19
3194 3944 1.152383 GCGACTCGGGACATTTAGCC 61.152 60.000 0.00 0.00 0.00 3.93
3195 3945 0.179108 AGCGACTCGGGACATTTAGC 60.179 55.000 0.00 0.00 0.00 3.09
3196 3946 1.560923 CAGCGACTCGGGACATTTAG 58.439 55.000 0.00 0.00 0.00 1.85
3197 3947 0.174845 CCAGCGACTCGGGACATTTA 59.825 55.000 0.00 0.00 31.00 1.40
3198 3948 1.079127 CCAGCGACTCGGGACATTT 60.079 57.895 0.00 0.00 31.00 2.32
3199 3949 2.227089 GACCAGCGACTCGGGACATT 62.227 60.000 0.00 0.00 33.91 2.71
3201 3951 3.371063 GACCAGCGACTCGGGACA 61.371 66.667 0.00 0.00 33.91 4.02
3203 3953 4.671590 TGGACCAGCGACTCGGGA 62.672 66.667 0.00 0.00 33.91 5.14
3205 3955 1.994507 CTAGTGGACCAGCGACTCGG 61.995 65.000 0.00 0.00 36.84 4.63
3206 3956 1.429825 CTAGTGGACCAGCGACTCG 59.570 63.158 0.00 0.00 36.84 4.18
3207 3957 1.668101 CCCTAGTGGACCAGCGACTC 61.668 65.000 0.00 0.00 36.84 3.36
3209 3959 1.542187 AACCCTAGTGGACCAGCGAC 61.542 60.000 0.00 0.00 38.00 5.19
3210 3960 0.834687 AAACCCTAGTGGACCAGCGA 60.835 55.000 0.00 0.00 38.00 4.93
3220 5520 2.100749 GCAAGCAAACACAAACCCTAGT 59.899 45.455 0.00 0.00 0.00 2.57
3221 5521 2.100584 TGCAAGCAAACACAAACCCTAG 59.899 45.455 0.00 0.00 0.00 3.02
3222 5522 2.103373 TGCAAGCAAACACAAACCCTA 58.897 42.857 0.00 0.00 0.00 3.53
3223 5523 0.901124 TGCAAGCAAACACAAACCCT 59.099 45.000 0.00 0.00 0.00 4.34
3225 5525 2.008752 AGTGCAAGCAAACACAAACC 57.991 45.000 0.00 0.00 39.30 3.27
3227 5527 2.735663 CACAAGTGCAAGCAAACACAAA 59.264 40.909 0.00 0.00 39.30 2.83
3228 5528 2.335752 CACAAGTGCAAGCAAACACAA 58.664 42.857 0.00 0.00 39.30 3.33
3231 5531 0.175302 CCCACAAGTGCAAGCAAACA 59.825 50.000 0.00 0.00 0.00 2.83
3232 5532 0.530431 CCCCACAAGTGCAAGCAAAC 60.530 55.000 0.00 0.00 0.00 2.93
3235 5535 2.521465 CCCCCACAAGTGCAAGCA 60.521 61.111 0.00 0.00 0.00 3.91
3238 5538 1.000993 AACACCCCCACAAGTGCAA 59.999 52.632 0.00 0.00 37.51 4.08
3239 5539 1.756172 CAACACCCCCACAAGTGCA 60.756 57.895 0.00 0.00 37.51 4.57
3240 5540 1.326951 AACAACACCCCCACAAGTGC 61.327 55.000 0.00 0.00 37.51 4.40
3241 5541 1.134848 CAAACAACACCCCCACAAGTG 60.135 52.381 0.00 0.00 39.93 3.16
3242 5542 1.190643 CAAACAACACCCCCACAAGT 58.809 50.000 0.00 0.00 0.00 3.16
3243 5543 1.190643 ACAAACAACACCCCCACAAG 58.809 50.000 0.00 0.00 0.00 3.16
3244 5544 1.276421 CAACAAACAACACCCCCACAA 59.724 47.619 0.00 0.00 0.00 3.33
3247 5547 1.276421 CAACAACAAACAACACCCCCA 59.724 47.619 0.00 0.00 0.00 4.96
3248 5548 1.406205 CCAACAACAAACAACACCCCC 60.406 52.381 0.00 0.00 0.00 5.40
3249 5549 1.406205 CCCAACAACAAACAACACCCC 60.406 52.381 0.00 0.00 0.00 4.95
3250 5550 1.276705 ACCCAACAACAAACAACACCC 59.723 47.619 0.00 0.00 0.00 4.61
3251 5551 2.739379 CAACCCAACAACAAACAACACC 59.261 45.455 0.00 0.00 0.00 4.16
3253 5553 3.753294 ACAACCCAACAACAAACAACA 57.247 38.095 0.00 0.00 0.00 3.33
3256 5556 2.166664 GGCTACAACCCAACAACAAACA 59.833 45.455 0.00 0.00 0.00 2.83
3257 5557 2.816689 GGCTACAACCCAACAACAAAC 58.183 47.619 0.00 0.00 0.00 2.93
3269 5569 0.989602 AGGGGTACAAGGGCTACAAC 59.010 55.000 0.00 0.00 0.00 3.32
3273 5573 0.714180 TCTGAGGGGTACAAGGGCTA 59.286 55.000 0.00 0.00 0.00 3.93
3274 5574 0.910088 GTCTGAGGGGTACAAGGGCT 60.910 60.000 0.00 0.00 0.00 5.19
3275 5575 0.910088 AGTCTGAGGGGTACAAGGGC 60.910 60.000 0.00 0.00 0.00 5.19
3276 5576 1.657804 AAGTCTGAGGGGTACAAGGG 58.342 55.000 0.00 0.00 0.00 3.95
3277 5577 2.876079 GCAAAGTCTGAGGGGTACAAGG 60.876 54.545 0.00 0.00 0.00 3.61
3279 5579 1.771854 TGCAAAGTCTGAGGGGTACAA 59.228 47.619 0.00 0.00 0.00 2.41
3280 5580 1.071699 GTGCAAAGTCTGAGGGGTACA 59.928 52.381 0.00 0.00 0.00 2.90
3282 5582 1.729586 AGTGCAAAGTCTGAGGGGTA 58.270 50.000 0.00 0.00 0.00 3.69
3283 5583 0.846693 AAGTGCAAAGTCTGAGGGGT 59.153 50.000 0.00 0.00 0.00 4.95
3284 5584 1.986882 AAAGTGCAAAGTCTGAGGGG 58.013 50.000 0.00 0.00 0.00 4.79
3285 5585 2.689983 ACAAAAGTGCAAAGTCTGAGGG 59.310 45.455 0.00 0.00 0.00 4.30
3286 5586 4.376340 AACAAAAGTGCAAAGTCTGAGG 57.624 40.909 0.00 0.00 0.00 3.86
3287 5587 6.095377 AGAAAACAAAAGTGCAAAGTCTGAG 58.905 36.000 0.00 0.00 0.00 3.35
3288 5588 6.024552 AGAAAACAAAAGTGCAAAGTCTGA 57.975 33.333 0.00 0.00 0.00 3.27
3289 5589 6.095377 AGAGAAAACAAAAGTGCAAAGTCTG 58.905 36.000 0.00 0.00 0.00 3.51
3290 5590 6.272822 AGAGAAAACAAAAGTGCAAAGTCT 57.727 33.333 0.00 0.00 0.00 3.24
3291 5591 6.951256 AAGAGAAAACAAAAGTGCAAAGTC 57.049 33.333 0.00 0.00 0.00 3.01
3293 5593 8.498358 AGAAAAAGAGAAAACAAAAGTGCAAAG 58.502 29.630 0.00 0.00 0.00 2.77
3294 5594 8.281893 CAGAAAAAGAGAAAACAAAAGTGCAAA 58.718 29.630 0.00 0.00 0.00 3.68
3295 5595 7.440856 ACAGAAAAAGAGAAAACAAAAGTGCAA 59.559 29.630 0.00 0.00 0.00 4.08
3296 5596 6.928492 ACAGAAAAAGAGAAAACAAAAGTGCA 59.072 30.769 0.00 0.00 0.00 4.57
3297 5597 7.351414 ACAGAAAAAGAGAAAACAAAAGTGC 57.649 32.000 0.00 0.00 0.00 4.40
3304 5604 9.950680 GTGATCATAACAGAAAAAGAGAAAACA 57.049 29.630 0.00 0.00 0.00 2.83
3315 5615 6.402442 CGAGTTGCATGTGATCATAACAGAAA 60.402 38.462 0.00 0.00 32.47 2.52


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

AutoCloner maintained by Alex Coulton.