Multiple sequence alignment - TraesCS3A01G156600

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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 TraesCS3A01G156600 chr3A 100.000 1521 0 0 1 1521 151674660 151676180 0.000000e+00 2809.0
1 TraesCS3A01G156600 chr3A 88.336 643 59 7 3 630 405577954 405578595 0.000000e+00 758.0
2 TraesCS3A01G156600 chr3A 100.000 407 0 0 1879 2285 151676538 151676944 0.000000e+00 752.0
3 TraesCS3A01G156600 chr3A 94.030 134 7 1 2150 2283 48365100 48365232 3.850000e-48 202.0
4 TraesCS3A01G156600 chr3A 93.333 135 9 0 2149 2283 24186311 24186177 1.380000e-47 200.0
5 TraesCS3A01G156600 chr3A 87.805 82 8 2 2088 2169 404656912 404656991 6.720000e-16 95.3
6 TraesCS3A01G156600 chr6D 94.386 1425 60 6 3 1412 213077581 213076162 0.000000e+00 2170.0
7 TraesCS3A01G156600 chr1D 92.784 873 45 6 3 860 474221268 474220399 0.000000e+00 1247.0
8 TraesCS3A01G156600 chr1D 90.426 470 30 6 998 1467 474219639 474219185 2.510000e-169 604.0
9 TraesCS3A01G156600 chr1D 91.575 273 21 2 358 630 37783527 37783257 2.140000e-100 375.0
10 TraesCS3A01G156600 chr1D 96.800 125 2 2 882 1005 474220423 474220300 8.270000e-50 207.0
11 TraesCS3A01G156600 chr1D 93.069 101 7 0 3 103 278645121 278645021 5.090000e-32 148.0
12 TraesCS3A01G156600 chrUn 89.869 839 66 7 634 1470 8327704 8326883 0.000000e+00 1061.0
13 TraesCS3A01G156600 chrUn 89.924 655 51 5 3 642 8336597 8335943 0.000000e+00 830.0
14 TraesCS3A01G156600 chr4B 92.130 737 52 4 629 1364 329056949 329056218 0.000000e+00 1035.0
15 TraesCS3A01G156600 chr4B 88.006 642 62 6 4 630 285800159 285799518 0.000000e+00 745.0
16 TraesCS3A01G156600 chr4B 93.525 139 8 1 2146 2283 457459357 457459495 2.980000e-49 206.0
17 TraesCS3A01G156600 chr4B 90.541 148 12 2 2136 2283 355502958 355503103 6.440000e-46 195.0
18 TraesCS3A01G156600 chr4B 90.141 71 6 1 2091 2160 86487010 86487080 8.690000e-15 91.6
19 TraesCS3A01G156600 chr1B 90.698 774 69 3 734 1506 52334137 52333366 0.000000e+00 1027.0
20 TraesCS3A01G156600 chr1B 86.824 296 23 12 1879 2161 52333287 52332995 1.320000e-82 316.0
21 TraesCS3A01G156600 chr6A 87.558 643 64 7 3 630 456678454 456679095 0.000000e+00 730.0
22 TraesCS3A01G156600 chr2A 92.149 484 37 1 734 1216 476461357 476461840 0.000000e+00 682.0
23 TraesCS3A01G156600 chr2A 93.224 428 29 0 789 1216 421058421 421057994 4.140000e-177 630.0
24 TraesCS3A01G156600 chr7B 88.194 576 53 6 666 1241 440657485 440656925 0.000000e+00 673.0
25 TraesCS3A01G156600 chr7B 94.872 78 4 0 629 706 440657564 440657487 3.080000e-24 122.0
26 TraesCS3A01G156600 chr4A 90.083 484 41 4 734 1216 231511649 231511172 2.490000e-174 621.0
27 TraesCS3A01G156600 chr4A 93.333 135 9 0 2149 2283 127174403 127174269 1.380000e-47 200.0
28 TraesCS3A01G156600 chr4A 93.333 135 9 0 2149 2283 293534553 293534687 1.380000e-47 200.0
29 TraesCS3A01G156600 chr7D 90.099 303 30 0 3 305 181740101 181739799 5.920000e-106 394.0
30 TraesCS3A01G156600 chr7D 87.032 347 30 7 299 630 181739271 181738925 5.960000e-101 377.0
31 TraesCS3A01G156600 chr1A 89.259 270 27 2 359 628 348887346 348887613 1.010000e-88 337.0
32 TraesCS3A01G156600 chr1A 91.262 103 8 1 2 103 115259346 115259244 3.060000e-29 139.0
33 TraesCS3A01G156600 chr1A 90.909 66 6 0 2101 2166 56983903 56983968 3.130000e-14 89.8
34 TraesCS3A01G156600 chr7A 90.446 157 10 5 2130 2283 113531236 113531082 3.850000e-48 202.0
35 TraesCS3A01G156600 chr7A 94.656 131 6 1 2153 2283 539232650 539232779 3.850000e-48 202.0
36 TraesCS3A01G156600 chr3D 87.574 169 14 5 2120 2283 569061815 569061981 3.000000e-44 189.0


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 TraesCS3A01G156600 chr3A 151674660 151676944 2284 False 1780.5 2809 100.000000 1 2285 2 chr3A.!!$F4 2284
1 TraesCS3A01G156600 chr3A 405577954 405578595 641 False 758.0 758 88.336000 3 630 1 chr3A.!!$F3 627
2 TraesCS3A01G156600 chr6D 213076162 213077581 1419 True 2170.0 2170 94.386000 3 1412 1 chr6D.!!$R1 1409
3 TraesCS3A01G156600 chr1D 474219185 474221268 2083 True 686.0 1247 93.336667 3 1467 3 chr1D.!!$R3 1464
4 TraesCS3A01G156600 chrUn 8326883 8327704 821 True 1061.0 1061 89.869000 634 1470 1 chrUn.!!$R1 836
5 TraesCS3A01G156600 chrUn 8335943 8336597 654 True 830.0 830 89.924000 3 642 1 chrUn.!!$R2 639
6 TraesCS3A01G156600 chr4B 329056218 329056949 731 True 1035.0 1035 92.130000 629 1364 1 chr4B.!!$R2 735
7 TraesCS3A01G156600 chr4B 285799518 285800159 641 True 745.0 745 88.006000 4 630 1 chr4B.!!$R1 626
8 TraesCS3A01G156600 chr1B 52332995 52334137 1142 True 671.5 1027 88.761000 734 2161 2 chr1B.!!$R1 1427
9 TraesCS3A01G156600 chr6A 456678454 456679095 641 False 730.0 730 87.558000 3 630 1 chr6A.!!$F1 627
10 TraesCS3A01G156600 chr7B 440656925 440657564 639 True 397.5 673 91.533000 629 1241 2 chr7B.!!$R1 612
11 TraesCS3A01G156600 chr7D 181738925 181740101 1176 True 385.5 394 88.565500 3 630 2 chr7D.!!$R1 627

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
385 935 0.46187 TCATGCCCATCGTGCACTAC 60.462 55.0 16.19 0.0 42.38 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2092 3436 0.035439 ATTTGAATCACGGCGTCCCT 60.035 50.0 10.85 0.0 0.0 4.2 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
74 75 4.112341 ACGAGTGGTAGCCGACGC 62.112 66.667 0.00 0.00 0.00 5.19
284 285 1.573108 AGGTCAATGTGGTCGGAGAT 58.427 50.000 0.00 0.00 40.67 2.75
297 298 2.124983 GAGATGCAGGAGCGGCAA 60.125 61.111 1.45 0.00 45.60 4.52
373 923 1.608283 GCGGGTTACTAGATCATGCCC 60.608 57.143 0.00 0.00 0.00 5.36
385 935 0.461870 TCATGCCCATCGTGCACTAC 60.462 55.000 16.19 0.00 42.38 2.73
400 950 4.505191 GTGCACTACGAAACTGAACTAACA 59.495 41.667 10.32 0.00 0.00 2.41
726 1318 7.672983 AGTACGTACTACTAGTTAGCACAAA 57.327 36.000 26.36 0.00 33.53 2.83
771 1363 6.368779 ACAACCTAGTTGCCTGAACTTATA 57.631 37.500 7.36 0.00 46.20 0.98
861 1453 4.779733 TCGGGGCCTCCTCCAGTC 62.780 72.222 0.84 0.00 0.00 3.51
868 1460 0.971447 GCCTCCTCCAGTCGTAGGTT 60.971 60.000 0.00 0.00 34.30 3.50
871 1463 2.379972 CTCCTCCAGTCGTAGGTTGAT 58.620 52.381 0.00 0.00 34.30 2.57
880 1472 4.580995 CAGTCGTAGGTTGATGTCTCCTAT 59.419 45.833 0.00 0.00 36.43 2.57
1033 2340 2.982130 GGGGCATCACTCGTCAGT 59.018 61.111 0.00 0.00 0.00 3.41
1123 2431 0.331954 AGAGGTAGACGAAGGCCAGA 59.668 55.000 5.01 0.00 0.00 3.86
1177 2485 3.731728 GCAGGTGGAGGATGGCCA 61.732 66.667 8.56 8.56 36.29 5.36
1181 2489 3.717294 GTGGAGGATGGCCACGGT 61.717 66.667 8.16 0.00 45.50 4.83
1207 2515 1.122632 TTGTTGTGGTAGGAGGCCGA 61.123 55.000 0.00 0.00 0.00 5.54
1237 2545 1.609210 TCATGCTCCTCGTCCACCA 60.609 57.895 0.00 0.00 0.00 4.17
1259 2567 1.759445 GATGCTCCAGCTCAACTCCTA 59.241 52.381 0.00 0.00 42.66 2.94
1971 3311 2.111878 CCCCGGGTGAGATCATGC 59.888 66.667 21.85 0.00 0.00 4.06
2041 3385 2.723273 GATGGGATCGGGAGTGTTTTT 58.277 47.619 0.00 0.00 0.00 1.94
2074 3418 1.582502 GCTATCGTTTCCGTGAGTTCG 59.417 52.381 0.00 0.00 35.01 3.95
2083 3427 3.888093 CGTGAGTTCGGAGAAACCT 57.112 52.632 0.00 0.00 45.90 3.50
2084 3428 1.699343 CGTGAGTTCGGAGAAACCTC 58.301 55.000 0.00 0.00 45.90 3.85
2085 3429 1.699343 GTGAGTTCGGAGAAACCTCG 58.301 55.000 0.00 0.00 45.90 4.63
2086 3430 1.000496 GTGAGTTCGGAGAAACCTCGT 60.000 52.381 0.00 0.00 45.90 4.18
2087 3431 1.684983 TGAGTTCGGAGAAACCTCGTT 59.315 47.619 0.00 0.00 45.90 3.85
2088 3432 2.886523 TGAGTTCGGAGAAACCTCGTTA 59.113 45.455 0.00 0.00 45.90 3.18
2090 3434 4.701651 TGAGTTCGGAGAAACCTCGTTATA 59.298 41.667 0.00 0.00 45.90 0.98
2091 3435 5.359009 TGAGTTCGGAGAAACCTCGTTATAT 59.641 40.000 0.00 0.00 45.90 0.86
2092 3436 6.543465 TGAGTTCGGAGAAACCTCGTTATATA 59.457 38.462 0.00 0.00 45.90 0.86
2093 3437 6.968250 AGTTCGGAGAAACCTCGTTATATAG 58.032 40.000 0.00 0.00 45.90 1.31
2094 3438 5.954296 TCGGAGAAACCTCGTTATATAGG 57.046 43.478 0.00 0.00 38.93 2.57
2095 3439 4.763793 TCGGAGAAACCTCGTTATATAGGG 59.236 45.833 0.00 0.00 37.18 3.53
2096 3440 4.763793 CGGAGAAACCTCGTTATATAGGGA 59.236 45.833 0.00 0.00 37.18 4.20
2097 3441 5.335504 CGGAGAAACCTCGTTATATAGGGAC 60.336 48.000 0.00 0.00 37.18 4.46
2099 3443 3.930634 AACCTCGTTATATAGGGACGC 57.069 47.619 1.38 0.00 37.18 5.19
2100 3444 2.165998 ACCTCGTTATATAGGGACGCC 58.834 52.381 1.38 0.00 37.18 5.68
2106 3457 3.366679 CGTTATATAGGGACGCCGTGATT 60.367 47.826 0.00 0.00 0.00 2.57
2113 3464 2.011222 GGGACGCCGTGATTCAAATAA 58.989 47.619 0.00 0.00 0.00 1.40
2114 3465 2.223180 GGGACGCCGTGATTCAAATAAC 60.223 50.000 0.00 0.00 0.00 1.89
2119 3470 6.431198 ACGCCGTGATTCAAATAACTATTT 57.569 33.333 0.00 0.00 36.39 1.40
2147 3498 8.738645 ATTCTGGAATTAGAATAGTGTTGTCC 57.261 34.615 2.23 0.00 43.63 4.02
2183 3534 7.958053 ATACTAGTAAAAGAGTTTGTGCGTT 57.042 32.000 6.70 0.00 0.00 4.84
2184 3535 6.044512 ACTAGTAAAAGAGTTTGTGCGTTG 57.955 37.500 0.00 0.00 0.00 4.10
2185 3536 3.691498 AGTAAAAGAGTTTGTGCGTTGC 58.309 40.909 0.00 0.00 0.00 4.17
2186 3537 2.645730 AAAAGAGTTTGTGCGTTGCA 57.354 40.000 0.00 0.00 35.60 4.08
2187 3538 2.645730 AAAGAGTTTGTGCGTTGCAA 57.354 40.000 0.00 0.00 41.47 4.08
2188 3539 1.908065 AAGAGTTTGTGCGTTGCAAC 58.092 45.000 19.89 19.89 41.47 4.17
2201 3552 3.414549 GTTGCAACGGAAGAGAAAACA 57.585 42.857 14.90 0.00 0.00 2.83
2202 3553 3.964909 GTTGCAACGGAAGAGAAAACAT 58.035 40.909 14.90 0.00 0.00 2.71
2203 3554 5.103290 GTTGCAACGGAAGAGAAAACATA 57.897 39.130 14.90 0.00 0.00 2.29
2204 3555 5.516090 GTTGCAACGGAAGAGAAAACATAA 58.484 37.500 14.90 0.00 0.00 1.90
2205 3556 5.103290 TGCAACGGAAGAGAAAACATAAC 57.897 39.130 0.00 0.00 0.00 1.89
2206 3557 4.576873 TGCAACGGAAGAGAAAACATAACA 59.423 37.500 0.00 0.00 0.00 2.41
2207 3558 4.909880 GCAACGGAAGAGAAAACATAACAC 59.090 41.667 0.00 0.00 0.00 3.32
2208 3559 5.504994 GCAACGGAAGAGAAAACATAACACA 60.505 40.000 0.00 0.00 0.00 3.72
2209 3560 5.668558 ACGGAAGAGAAAACATAACACAC 57.331 39.130 0.00 0.00 0.00 3.82
2210 3561 4.210537 ACGGAAGAGAAAACATAACACACG 59.789 41.667 0.00 0.00 0.00 4.49
2211 3562 4.464112 GGAAGAGAAAACATAACACACGC 58.536 43.478 0.00 0.00 0.00 5.34
2212 3563 4.213482 GGAAGAGAAAACATAACACACGCT 59.787 41.667 0.00 0.00 0.00 5.07
2213 3564 5.277828 GGAAGAGAAAACATAACACACGCTT 60.278 40.000 0.00 0.00 0.00 4.68
2214 3565 5.751243 AGAGAAAACATAACACACGCTTT 57.249 34.783 0.00 0.00 0.00 3.51
2215 3566 6.131544 AGAGAAAACATAACACACGCTTTT 57.868 33.333 0.00 0.00 0.00 2.27
2216 3567 7.254227 AGAGAAAACATAACACACGCTTTTA 57.746 32.000 0.00 0.00 0.00 1.52
2217 3568 7.699566 AGAGAAAACATAACACACGCTTTTAA 58.300 30.769 0.00 0.00 0.00 1.52
2218 3569 7.642586 AGAGAAAACATAACACACGCTTTTAAC 59.357 33.333 0.00 0.00 0.00 2.01
2219 3570 7.477494 AGAAAACATAACACACGCTTTTAACT 58.523 30.769 0.00 0.00 0.00 2.24
2220 3571 7.642586 AGAAAACATAACACACGCTTTTAACTC 59.357 33.333 0.00 0.00 0.00 3.01
2221 3572 5.994887 ACATAACACACGCTTTTAACTCA 57.005 34.783 0.00 0.00 0.00 3.41
2222 3573 6.366315 ACATAACACACGCTTTTAACTCAA 57.634 33.333 0.00 0.00 0.00 3.02
2223 3574 6.196571 ACATAACACACGCTTTTAACTCAAC 58.803 36.000 0.00 0.00 0.00 3.18
2224 3575 4.688511 AACACACGCTTTTAACTCAACA 57.311 36.364 0.00 0.00 0.00 3.33
2225 3576 4.688511 ACACACGCTTTTAACTCAACAA 57.311 36.364 0.00 0.00 0.00 2.83
2226 3577 4.408694 ACACACGCTTTTAACTCAACAAC 58.591 39.130 0.00 0.00 0.00 3.32
2227 3578 3.789224 CACACGCTTTTAACTCAACAACC 59.211 43.478 0.00 0.00 0.00 3.77
2228 3579 3.440872 ACACGCTTTTAACTCAACAACCA 59.559 39.130 0.00 0.00 0.00 3.67
2229 3580 4.097286 ACACGCTTTTAACTCAACAACCAT 59.903 37.500 0.00 0.00 0.00 3.55
2230 3581 4.675114 CACGCTTTTAACTCAACAACCATC 59.325 41.667 0.00 0.00 0.00 3.51
2231 3582 4.336993 ACGCTTTTAACTCAACAACCATCA 59.663 37.500 0.00 0.00 0.00 3.07
2232 3583 4.675114 CGCTTTTAACTCAACAACCATCAC 59.325 41.667 0.00 0.00 0.00 3.06
2233 3584 5.505654 CGCTTTTAACTCAACAACCATCACT 60.506 40.000 0.00 0.00 0.00 3.41
2234 3585 5.915196 GCTTTTAACTCAACAACCATCACTC 59.085 40.000 0.00 0.00 0.00 3.51
2235 3586 6.459573 GCTTTTAACTCAACAACCATCACTCA 60.460 38.462 0.00 0.00 0.00 3.41
2236 3587 7.397892 TTTTAACTCAACAACCATCACTCAA 57.602 32.000 0.00 0.00 0.00 3.02
2237 3588 6.618287 TTAACTCAACAACCATCACTCAAG 57.382 37.500 0.00 0.00 0.00 3.02
2238 3589 4.422073 ACTCAACAACCATCACTCAAGA 57.578 40.909 0.00 0.00 0.00 3.02
2239 3590 4.130118 ACTCAACAACCATCACTCAAGAC 58.870 43.478 0.00 0.00 0.00 3.01
2240 3591 3.476552 TCAACAACCATCACTCAAGACC 58.523 45.455 0.00 0.00 0.00 3.85
2241 3592 3.118075 TCAACAACCATCACTCAAGACCA 60.118 43.478 0.00 0.00 0.00 4.02
2242 3593 2.851195 ACAACCATCACTCAAGACCAC 58.149 47.619 0.00 0.00 0.00 4.16
2243 3594 2.172505 ACAACCATCACTCAAGACCACA 59.827 45.455 0.00 0.00 0.00 4.17
2244 3595 3.213506 CAACCATCACTCAAGACCACAA 58.786 45.455 0.00 0.00 0.00 3.33
2245 3596 3.795688 ACCATCACTCAAGACCACAAT 57.204 42.857 0.00 0.00 0.00 2.71
2246 3597 4.908601 ACCATCACTCAAGACCACAATA 57.091 40.909 0.00 0.00 0.00 1.90
2247 3598 4.836825 ACCATCACTCAAGACCACAATAG 58.163 43.478 0.00 0.00 0.00 1.73
2248 3599 4.532126 ACCATCACTCAAGACCACAATAGA 59.468 41.667 0.00 0.00 0.00 1.98
2249 3600 5.190528 ACCATCACTCAAGACCACAATAGAT 59.809 40.000 0.00 0.00 0.00 1.98
2250 3601 5.757320 CCATCACTCAAGACCACAATAGATC 59.243 44.000 0.00 0.00 0.00 2.75
2251 3602 5.344743 TCACTCAAGACCACAATAGATCC 57.655 43.478 0.00 0.00 0.00 3.36
2252 3603 4.777366 TCACTCAAGACCACAATAGATCCA 59.223 41.667 0.00 0.00 0.00 3.41
2253 3604 5.426509 TCACTCAAGACCACAATAGATCCAT 59.573 40.000 0.00 0.00 0.00 3.41
2254 3605 5.757320 CACTCAAGACCACAATAGATCCATC 59.243 44.000 0.00 0.00 0.00 3.51
2255 3606 5.664908 ACTCAAGACCACAATAGATCCATCT 59.335 40.000 0.00 0.00 40.86 2.90
2256 3607 6.166984 TCAAGACCACAATAGATCCATCTC 57.833 41.667 0.00 0.00 38.32 2.75
2257 3608 5.070981 TCAAGACCACAATAGATCCATCTCC 59.929 44.000 0.00 0.00 38.32 3.71
2258 3609 4.825445 AGACCACAATAGATCCATCTCCT 58.175 43.478 0.00 0.00 38.32 3.69
2259 3610 5.222870 AGACCACAATAGATCCATCTCCTT 58.777 41.667 0.00 0.00 38.32 3.36
2260 3611 5.669447 AGACCACAATAGATCCATCTCCTTT 59.331 40.000 0.00 0.00 38.32 3.11
2261 3612 6.846505 AGACCACAATAGATCCATCTCCTTTA 59.153 38.462 0.00 0.00 38.32 1.85
2262 3613 7.515514 AGACCACAATAGATCCATCTCCTTTAT 59.484 37.037 0.00 0.00 38.32 1.40
2263 3614 8.050316 ACCACAATAGATCCATCTCCTTTATT 57.950 34.615 0.00 0.00 38.32 1.40
2264 3615 8.506083 ACCACAATAGATCCATCTCCTTTATTT 58.494 33.333 0.00 0.00 38.32 1.40
2265 3616 9.359653 CCACAATAGATCCATCTCCTTTATTTT 57.640 33.333 0.00 0.00 38.32 1.82
2268 3619 9.688592 CAATAGATCCATCTCCTTTATTTTTGC 57.311 33.333 0.00 0.00 38.32 3.68
2269 3620 6.382869 AGATCCATCTCCTTTATTTTTGCG 57.617 37.500 0.00 0.00 29.30 4.85
2270 3621 6.122277 AGATCCATCTCCTTTATTTTTGCGA 58.878 36.000 0.00 0.00 29.30 5.10
2271 3622 5.818136 TCCATCTCCTTTATTTTTGCGAG 57.182 39.130 0.00 0.00 0.00 5.03
2272 3623 4.640201 TCCATCTCCTTTATTTTTGCGAGG 59.360 41.667 0.00 0.00 0.00 4.63
2273 3624 4.354587 CATCTCCTTTATTTTTGCGAGGC 58.645 43.478 0.00 0.00 0.00 4.70
2274 3625 3.417101 TCTCCTTTATTTTTGCGAGGCA 58.583 40.909 0.00 0.00 36.47 4.75
2275 3626 4.016444 TCTCCTTTATTTTTGCGAGGCAT 58.984 39.130 0.00 0.00 38.76 4.40
2276 3627 4.096382 TCTCCTTTATTTTTGCGAGGCATC 59.904 41.667 0.00 0.00 38.76 3.91
2277 3628 3.761218 TCCTTTATTTTTGCGAGGCATCA 59.239 39.130 0.00 0.00 38.76 3.07
2278 3629 4.402155 TCCTTTATTTTTGCGAGGCATCAT 59.598 37.500 0.00 0.00 38.76 2.45
2279 3630 5.592282 TCCTTTATTTTTGCGAGGCATCATA 59.408 36.000 0.00 0.00 38.76 2.15
2280 3631 6.265196 TCCTTTATTTTTGCGAGGCATCATAT 59.735 34.615 0.00 0.00 38.76 1.78
2281 3632 6.925165 CCTTTATTTTTGCGAGGCATCATATT 59.075 34.615 0.00 0.00 38.76 1.28
2282 3633 7.439056 CCTTTATTTTTGCGAGGCATCATATTT 59.561 33.333 0.00 0.00 38.76 1.40
2283 3634 7.928908 TTATTTTTGCGAGGCATCATATTTC 57.071 32.000 0.00 0.00 38.76 2.17
2284 3635 5.581126 TTTTTGCGAGGCATCATATTTCT 57.419 34.783 0.00 0.00 38.76 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 0.884704 CCGTTGTGCCAGCAGTTAGT 60.885 55.000 0.00 0.00 0.00 2.24
19 20 4.954970 CCCCGTTGTGCCAGCAGT 62.955 66.667 0.00 0.00 0.00 4.40
74 75 2.956987 CAAGCTTCCCTTGTGCGG 59.043 61.111 0.00 0.00 44.74 5.69
150 151 2.117423 TCTCCGCCCTCTGTCACA 59.883 61.111 0.00 0.00 0.00 3.58
284 285 4.728110 AGCATTGCCGCTCCTGCA 62.728 61.111 4.70 0.00 37.91 4.41
297 298 2.985282 CGGCCACCACACAAGCAT 60.985 61.111 2.24 0.00 0.00 3.79
354 889 1.691976 TGGGCATGATCTAGTAACCCG 59.308 52.381 0.00 0.00 38.79 5.28
385 935 4.377431 GCCTGATGTGTTAGTTCAGTTTCG 60.377 45.833 0.00 0.00 36.06 3.46
400 950 0.905357 AGGTTAGCTTCGCCTGATGT 59.095 50.000 0.00 0.00 0.00 3.06
492 1042 1.470098 GTCAGTTTCGCCTGATGCATT 59.530 47.619 0.00 0.00 43.03 3.56
713 1305 5.542779 ACCTTCTCTGTTTGTGCTAACTAG 58.457 41.667 0.00 0.00 0.00 2.57
714 1306 5.546621 ACCTTCTCTGTTTGTGCTAACTA 57.453 39.130 0.00 0.00 0.00 2.24
715 1307 4.423625 ACCTTCTCTGTTTGTGCTAACT 57.576 40.909 0.00 0.00 0.00 2.24
726 1318 5.130477 TGTTCACTAGGAAAACCTTCTCTGT 59.870 40.000 0.00 0.00 37.23 3.41
771 1363 7.091443 TGACACCGTATTTGTTTTTGTTCTTT 58.909 30.769 0.00 0.00 0.00 2.52
860 1452 4.760715 GCTATAGGAGACATCAACCTACGA 59.239 45.833 1.04 0.00 38.79 3.43
861 1453 4.762765 AGCTATAGGAGACATCAACCTACG 59.237 45.833 1.04 0.00 38.79 3.51
863 1455 5.953571 TCAGCTATAGGAGACATCAACCTA 58.046 41.667 1.04 0.00 39.99 3.08
868 1460 4.809193 ACCTTCAGCTATAGGAGACATCA 58.191 43.478 17.72 0.00 35.45 3.07
871 1463 3.215151 CGACCTTCAGCTATAGGAGACA 58.785 50.000 17.72 0.00 35.45 3.41
880 1472 4.143333 GGCCGCGACCTTCAGCTA 62.143 66.667 8.23 0.00 0.00 3.32
977 1617 2.281761 AGCCACGGCAAGTCCAAG 60.282 61.111 11.35 0.00 44.88 3.61
1123 2431 3.681835 GACCGCCTCCACGACACT 61.682 66.667 0.00 0.00 34.06 3.55
1177 2485 2.177580 CACAACAAGCGACCACCGT 61.178 57.895 0.00 0.00 41.15 4.83
1181 2489 0.250124 CCTACCACAACAAGCGACCA 60.250 55.000 0.00 0.00 0.00 4.02
1237 2545 1.065564 GGAGTTGAGCTGGAGCATCTT 60.066 52.381 0.00 0.00 45.16 2.40
1259 2567 2.380410 GCGTTCTTGTCGCGTCCAT 61.380 57.895 5.77 0.00 43.94 3.41
1301 2609 1.228894 AGCTGACTTGACCTCCGGA 60.229 57.895 2.93 2.93 0.00 5.14
1302 2610 1.079543 CAGCTGACTTGACCTCCGG 60.080 63.158 8.42 0.00 0.00 5.14
1470 2810 3.461773 CCATCCCCGAGCGACACT 61.462 66.667 0.00 0.00 0.00 3.55
1954 3294 2.111878 GCATGATCTCACCCGGGG 59.888 66.667 27.92 12.73 0.00 5.73
1958 3298 2.969238 CGCCGCATGATCTCACCC 60.969 66.667 0.00 0.00 0.00 4.61
2074 3418 5.335504 CGTCCCTATATAACGAGGTTTCTCC 60.336 48.000 0.08 0.00 38.65 3.71
2076 3420 4.022503 GCGTCCCTATATAACGAGGTTTCT 60.023 45.833 9.15 0.00 38.65 2.52
2077 3421 4.233005 GCGTCCCTATATAACGAGGTTTC 58.767 47.826 9.15 0.00 38.65 2.78
2080 3424 2.165998 GGCGTCCCTATATAACGAGGT 58.834 52.381 9.15 0.00 38.65 3.85
2083 3427 1.536766 CACGGCGTCCCTATATAACGA 59.463 52.381 10.85 0.00 38.65 3.85
2084 3428 1.536766 TCACGGCGTCCCTATATAACG 59.463 52.381 10.85 1.84 39.33 3.18
2085 3429 3.863142 ATCACGGCGTCCCTATATAAC 57.137 47.619 10.85 0.00 0.00 1.89
2086 3430 3.827876 TGAATCACGGCGTCCCTATATAA 59.172 43.478 10.85 0.00 0.00 0.98
2087 3431 3.423749 TGAATCACGGCGTCCCTATATA 58.576 45.455 10.85 0.00 0.00 0.86
2088 3432 2.244695 TGAATCACGGCGTCCCTATAT 58.755 47.619 10.85 0.00 0.00 0.86
2090 3434 0.828022 TTGAATCACGGCGTCCCTAT 59.172 50.000 10.85 0.00 0.00 2.57
2091 3435 0.609151 TTTGAATCACGGCGTCCCTA 59.391 50.000 10.85 0.00 0.00 3.53
2092 3436 0.035439 ATTTGAATCACGGCGTCCCT 60.035 50.000 10.85 0.00 0.00 4.20
2093 3437 1.658994 TATTTGAATCACGGCGTCCC 58.341 50.000 10.85 0.00 0.00 4.46
2094 3438 2.676342 AGTTATTTGAATCACGGCGTCC 59.324 45.455 10.85 0.00 0.00 4.79
2095 3439 5.652744 ATAGTTATTTGAATCACGGCGTC 57.347 39.130 10.85 0.00 0.00 5.19
2096 3440 6.431198 AAATAGTTATTTGAATCACGGCGT 57.569 33.333 6.77 6.77 34.79 5.68
2097 3441 8.829514 TTAAAATAGTTATTTGAATCACGGCG 57.170 30.769 4.80 4.80 36.14 6.46
2124 3475 7.496346 AGGACAACACTATTCTAATTCCAGA 57.504 36.000 0.00 0.00 0.00 3.86
2161 3512 5.503520 GCAACGCACAAACTCTTTTACTAGT 60.504 40.000 0.00 0.00 0.00 2.57
2162 3513 4.904154 GCAACGCACAAACTCTTTTACTAG 59.096 41.667 0.00 0.00 0.00 2.57
2163 3514 4.333095 TGCAACGCACAAACTCTTTTACTA 59.667 37.500 0.00 0.00 31.71 1.82
2164 3515 3.127895 TGCAACGCACAAACTCTTTTACT 59.872 39.130 0.00 0.00 31.71 2.24
2165 3516 3.430931 TGCAACGCACAAACTCTTTTAC 58.569 40.909 0.00 0.00 31.71 2.01
2166 3517 3.766676 TGCAACGCACAAACTCTTTTA 57.233 38.095 0.00 0.00 31.71 1.52
2167 3518 2.645730 TGCAACGCACAAACTCTTTT 57.354 40.000 0.00 0.00 31.71 2.27
2168 3519 2.258755 GTTGCAACGCACAAACTCTTT 58.741 42.857 14.90 0.00 38.71 2.52
2169 3520 1.793714 CGTTGCAACGCACAAACTCTT 60.794 47.619 35.89 0.00 46.06 2.85
2170 3521 0.248054 CGTTGCAACGCACAAACTCT 60.248 50.000 35.89 0.00 46.06 3.24
2171 3522 2.194733 CGTTGCAACGCACAAACTC 58.805 52.632 35.89 2.57 46.06 3.01
2172 3523 4.375723 CGTTGCAACGCACAAACT 57.624 50.000 35.89 0.00 46.06 2.66
2181 3532 3.414549 TGTTTTCTCTTCCGTTGCAAC 57.585 42.857 19.89 19.89 0.00 4.17
2182 3533 5.066634 TGTTATGTTTTCTCTTCCGTTGCAA 59.933 36.000 0.00 0.00 0.00 4.08
2183 3534 4.576873 TGTTATGTTTTCTCTTCCGTTGCA 59.423 37.500 0.00 0.00 0.00 4.08
2184 3535 4.909880 GTGTTATGTTTTCTCTTCCGTTGC 59.090 41.667 0.00 0.00 0.00 4.17
2185 3536 5.907391 GTGTGTTATGTTTTCTCTTCCGTTG 59.093 40.000 0.00 0.00 0.00 4.10
2186 3537 5.277154 CGTGTGTTATGTTTTCTCTTCCGTT 60.277 40.000 0.00 0.00 0.00 4.44
2187 3538 4.210537 CGTGTGTTATGTTTTCTCTTCCGT 59.789 41.667 0.00 0.00 0.00 4.69
2188 3539 4.698276 CGTGTGTTATGTTTTCTCTTCCG 58.302 43.478 0.00 0.00 0.00 4.30
2189 3540 4.213482 AGCGTGTGTTATGTTTTCTCTTCC 59.787 41.667 0.00 0.00 0.00 3.46
2190 3541 5.344207 AGCGTGTGTTATGTTTTCTCTTC 57.656 39.130 0.00 0.00 0.00 2.87
2191 3542 5.751243 AAGCGTGTGTTATGTTTTCTCTT 57.249 34.783 0.00 0.00 0.00 2.85
2192 3543 5.751243 AAAGCGTGTGTTATGTTTTCTCT 57.249 34.783 0.00 0.00 0.00 3.10
2193 3544 7.642586 AGTTAAAAGCGTGTGTTATGTTTTCTC 59.357 33.333 0.00 0.00 29.75 2.87
2194 3545 7.477494 AGTTAAAAGCGTGTGTTATGTTTTCT 58.523 30.769 0.00 0.00 29.75 2.52
2195 3546 7.429920 TGAGTTAAAAGCGTGTGTTATGTTTTC 59.570 33.333 0.00 0.00 29.75 2.29
2196 3547 7.251994 TGAGTTAAAAGCGTGTGTTATGTTTT 58.748 30.769 0.00 0.00 31.07 2.43
2197 3548 6.787225 TGAGTTAAAAGCGTGTGTTATGTTT 58.213 32.000 0.00 0.00 0.00 2.83
2198 3549 6.366315 TGAGTTAAAAGCGTGTGTTATGTT 57.634 33.333 0.00 0.00 0.00 2.71
2199 3550 5.994887 TGAGTTAAAAGCGTGTGTTATGT 57.005 34.783 0.00 0.00 0.00 2.29
2200 3551 6.195868 TGTTGAGTTAAAAGCGTGTGTTATG 58.804 36.000 0.00 0.00 0.00 1.90
2201 3552 6.366315 TGTTGAGTTAAAAGCGTGTGTTAT 57.634 33.333 0.00 0.00 0.00 1.89
2202 3553 5.798015 TGTTGAGTTAAAAGCGTGTGTTA 57.202 34.783 0.00 0.00 0.00 2.41
2203 3554 4.688511 TGTTGAGTTAAAAGCGTGTGTT 57.311 36.364 0.00 0.00 0.00 3.32
2204 3555 4.408694 GTTGTTGAGTTAAAAGCGTGTGT 58.591 39.130 0.00 0.00 0.00 3.72
2205 3556 3.789224 GGTTGTTGAGTTAAAAGCGTGTG 59.211 43.478 0.00 0.00 0.00 3.82
2206 3557 3.440872 TGGTTGTTGAGTTAAAAGCGTGT 59.559 39.130 0.00 0.00 0.00 4.49
2207 3558 4.022464 TGGTTGTTGAGTTAAAAGCGTG 57.978 40.909 0.00 0.00 0.00 5.34
2208 3559 4.336993 TGATGGTTGTTGAGTTAAAAGCGT 59.663 37.500 0.00 0.00 0.00 5.07
2209 3560 4.675114 GTGATGGTTGTTGAGTTAAAAGCG 59.325 41.667 0.00 0.00 0.00 4.68
2210 3561 5.831997 AGTGATGGTTGTTGAGTTAAAAGC 58.168 37.500 0.00 0.00 0.00 3.51
2211 3562 7.026631 TGAGTGATGGTTGTTGAGTTAAAAG 57.973 36.000 0.00 0.00 0.00 2.27
2212 3563 7.338196 TCTTGAGTGATGGTTGTTGAGTTAAAA 59.662 33.333 0.00 0.00 0.00 1.52
2213 3564 6.826231 TCTTGAGTGATGGTTGTTGAGTTAAA 59.174 34.615 0.00 0.00 0.00 1.52
2214 3565 6.260050 GTCTTGAGTGATGGTTGTTGAGTTAA 59.740 38.462 0.00 0.00 0.00 2.01
2215 3566 5.758296 GTCTTGAGTGATGGTTGTTGAGTTA 59.242 40.000 0.00 0.00 0.00 2.24
2216 3567 4.576463 GTCTTGAGTGATGGTTGTTGAGTT 59.424 41.667 0.00 0.00 0.00 3.01
2217 3568 4.130118 GTCTTGAGTGATGGTTGTTGAGT 58.870 43.478 0.00 0.00 0.00 3.41
2218 3569 3.499918 GGTCTTGAGTGATGGTTGTTGAG 59.500 47.826 0.00 0.00 0.00 3.02
2219 3570 3.118075 TGGTCTTGAGTGATGGTTGTTGA 60.118 43.478 0.00 0.00 0.00 3.18
2220 3571 3.003689 GTGGTCTTGAGTGATGGTTGTTG 59.996 47.826 0.00 0.00 0.00 3.33
2221 3572 3.214328 GTGGTCTTGAGTGATGGTTGTT 58.786 45.455 0.00 0.00 0.00 2.83
2222 3573 2.172505 TGTGGTCTTGAGTGATGGTTGT 59.827 45.455 0.00 0.00 0.00 3.32
2223 3574 2.849942 TGTGGTCTTGAGTGATGGTTG 58.150 47.619 0.00 0.00 0.00 3.77
2224 3575 3.576078 TTGTGGTCTTGAGTGATGGTT 57.424 42.857 0.00 0.00 0.00 3.67
2225 3576 3.795688 ATTGTGGTCTTGAGTGATGGT 57.204 42.857 0.00 0.00 0.00 3.55
2226 3577 5.089970 TCTATTGTGGTCTTGAGTGATGG 57.910 43.478 0.00 0.00 0.00 3.51
2227 3578 5.757320 GGATCTATTGTGGTCTTGAGTGATG 59.243 44.000 0.00 0.00 0.00 3.07
2228 3579 5.426509 TGGATCTATTGTGGTCTTGAGTGAT 59.573 40.000 0.00 0.00 0.00 3.06
2229 3580 4.777366 TGGATCTATTGTGGTCTTGAGTGA 59.223 41.667 0.00 0.00 0.00 3.41
2230 3581 5.089970 TGGATCTATTGTGGTCTTGAGTG 57.910 43.478 0.00 0.00 0.00 3.51
2231 3582 5.664908 AGATGGATCTATTGTGGTCTTGAGT 59.335 40.000 0.00 0.00 34.85 3.41
2232 3583 6.172136 AGATGGATCTATTGTGGTCTTGAG 57.828 41.667 0.00 0.00 34.85 3.02
2233 3584 5.070981 GGAGATGGATCTATTGTGGTCTTGA 59.929 44.000 0.00 0.00 37.25 3.02
2234 3585 5.071519 AGGAGATGGATCTATTGTGGTCTTG 59.928 44.000 0.00 0.00 37.25 3.02
2235 3586 5.222870 AGGAGATGGATCTATTGTGGTCTT 58.777 41.667 0.00 0.00 37.25 3.01
2236 3587 4.825445 AGGAGATGGATCTATTGTGGTCT 58.175 43.478 0.00 0.00 37.25 3.85
2237 3588 5.559148 AAGGAGATGGATCTATTGTGGTC 57.441 43.478 0.00 0.00 37.25 4.02
2238 3589 5.983333 AAAGGAGATGGATCTATTGTGGT 57.017 39.130 0.00 0.00 37.25 4.16
2239 3590 8.930846 AAATAAAGGAGATGGATCTATTGTGG 57.069 34.615 0.00 0.00 37.25 4.17
2242 3593 9.688592 GCAAAAATAAAGGAGATGGATCTATTG 57.311 33.333 0.00 0.00 37.25 1.90
2243 3594 8.571336 CGCAAAAATAAAGGAGATGGATCTATT 58.429 33.333 0.00 0.00 37.25 1.73
2244 3595 7.939039 TCGCAAAAATAAAGGAGATGGATCTAT 59.061 33.333 0.00 0.00 37.25 1.98
2245 3596 7.279615 TCGCAAAAATAAAGGAGATGGATCTA 58.720 34.615 0.00 0.00 37.25 1.98
2246 3597 6.122277 TCGCAAAAATAAAGGAGATGGATCT 58.878 36.000 0.00 0.00 40.50 2.75
2247 3598 6.377327 TCGCAAAAATAAAGGAGATGGATC 57.623 37.500 0.00 0.00 0.00 3.36
2248 3599 5.300286 CCTCGCAAAAATAAAGGAGATGGAT 59.700 40.000 0.00 0.00 0.00 3.41
2249 3600 4.640201 CCTCGCAAAAATAAAGGAGATGGA 59.360 41.667 0.00 0.00 0.00 3.41
2250 3601 4.734695 GCCTCGCAAAAATAAAGGAGATGG 60.735 45.833 0.00 0.00 0.00 3.51
2251 3602 4.142403 TGCCTCGCAAAAATAAAGGAGATG 60.142 41.667 0.00 0.00 34.76 2.90
2252 3603 4.016444 TGCCTCGCAAAAATAAAGGAGAT 58.984 39.130 0.00 0.00 34.76 2.75
2253 3604 3.417101 TGCCTCGCAAAAATAAAGGAGA 58.583 40.909 0.00 0.00 34.76 3.71
2254 3605 3.848272 TGCCTCGCAAAAATAAAGGAG 57.152 42.857 0.00 0.00 34.76 3.69
2255 3606 3.761218 TGATGCCTCGCAAAAATAAAGGA 59.239 39.130 0.00 0.00 43.62 3.36
2256 3607 4.108699 TGATGCCTCGCAAAAATAAAGG 57.891 40.909 0.00 0.00 43.62 3.11
2257 3608 7.935338 AATATGATGCCTCGCAAAAATAAAG 57.065 32.000 0.00 0.00 43.62 1.85
2258 3609 8.196771 AGAAATATGATGCCTCGCAAAAATAAA 58.803 29.630 0.00 0.00 43.62 1.40
2259 3610 7.715657 AGAAATATGATGCCTCGCAAAAATAA 58.284 30.769 0.00 0.00 43.62 1.40
2260 3611 7.275888 AGAAATATGATGCCTCGCAAAAATA 57.724 32.000 0.00 0.00 43.62 1.40
2261 3612 6.152932 AGAAATATGATGCCTCGCAAAAAT 57.847 33.333 0.00 0.00 43.62 1.82
2262 3613 5.581126 AGAAATATGATGCCTCGCAAAAA 57.419 34.783 0.00 0.00 43.62 1.94


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

AutoCloner maintained by Alex Coulton.