Multiple sequence alignment - TraesCS4D01G044800

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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 TraesCS4D01G044800 chr4D 100.000 3247 0 0 1 3247 20436881 20433635 0.000000e+00 5997.0
1 TraesCS4D01G044800 chr4D 88.956 1494 76 36 660 2111 20081363 20082809 0.000000e+00 1762.0
2 TraesCS4D01G044800 chr4D 94.017 117 6 1 2107 2222 20083233 20083349 3.330000e-40 176.0
3 TraesCS4D01G044800 chr4D 93.805 113 7 0 1373 1485 20083361 20083473 1.550000e-38 171.0
4 TraesCS4D01G044800 chr4D 93.878 98 6 0 1 98 20136650 20136747 7.260000e-32 148.0
5 TraesCS4D01G044800 chr4D 96.296 81 3 0 6 86 20075443 20075523 2.030000e-27 134.0
6 TraesCS4D01G044800 chr4D 80.263 152 21 6 189 332 20080866 20081016 4.430000e-19 106.0
7 TraesCS4D01G044800 chr4A 88.360 2586 138 64 756 3247 581201671 581199155 0.000000e+00 2957.0
8 TraesCS4D01G044800 chr4A 87.766 188 17 2 2386 2569 581229403 581229218 7.060000e-52 215.0
9 TraesCS4D01G044800 chr4A 77.447 235 28 15 428 649 581201952 581201730 2.050000e-22 117.0
10 TraesCS4D01G044800 chr4B 90.015 1983 95 36 922 2873 32425090 32423180 0.000000e+00 2470.0
11 TraesCS4D01G044800 chr4B 86.992 1230 77 39 922 2111 32277965 32279151 0.000000e+00 1308.0
12 TraesCS4D01G044800 chr4B 96.830 347 9 1 2903 3247 32423180 32422834 2.170000e-161 579.0
13 TraesCS4D01G044800 chr4B 92.381 105 6 2 1 105 32426258 32426156 7.260000e-32 148.0
14 TraesCS4D01G044800 chr4B 78.212 179 20 12 721 880 32425279 32425101 2.670000e-16 97.1
15 TraesCS4D01G044800 chr5A 87.547 530 55 6 2241 2768 491372049 491372569 1.290000e-168 603.0
16 TraesCS4D01G044800 chr5A 84.444 180 20 6 2246 2423 491525530 491525703 1.550000e-38 171.0
17 TraesCS4D01G044800 chr6D 85.929 533 57 8 2246 2770 106895457 106895979 1.320000e-153 553.0
18 TraesCS4D01G044800 chr5D 85.343 539 62 8 2241 2768 388334933 388335465 2.850000e-150 542.0
19 TraesCS4D01G044800 chr6A 83.854 384 46 8 2246 2621 130408715 130409090 5.150000e-93 351.0
20 TraesCS4D01G044800 chr6A 88.235 85 9 1 1461 1544 299336768 299336852 2.060000e-17 100.0
21 TraesCS4D01G044800 chr5B 91.429 105 6 2 359 460 693050113 693050009 1.210000e-29 141.0
22 TraesCS4D01G044800 chr5B 97.619 42 1 0 1466 1507 658464275 658464234 4.490000e-09 73.1
23 TraesCS4D01G044800 chr2B 85.075 134 11 5 331 455 62344301 62344434 9.460000e-26 128.0


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 TraesCS4D01G044800 chr4D 20433635 20436881 3246 True 5997.000 5997 100.00000 1 3247 1 chr4D.!!$R1 3246
1 TraesCS4D01G044800 chr4D 20080866 20083473 2607 False 553.750 1762 89.26025 189 2222 4 chr4D.!!$F3 2033
2 TraesCS4D01G044800 chr4A 581199155 581201952 2797 True 1537.000 2957 82.90350 428 3247 2 chr4A.!!$R2 2819
3 TraesCS4D01G044800 chr4B 32277965 32279151 1186 False 1308.000 1308 86.99200 922 2111 1 chr4B.!!$F1 1189
4 TraesCS4D01G044800 chr4B 32422834 32426258 3424 True 823.525 2470 89.35950 1 3247 4 chr4B.!!$R1 3246
5 TraesCS4D01G044800 chr5A 491372049 491372569 520 False 603.000 603 87.54700 2241 2768 1 chr5A.!!$F1 527
6 TraesCS4D01G044800 chr6D 106895457 106895979 522 False 553.000 553 85.92900 2246 2770 1 chr6D.!!$F1 524
7 TraesCS4D01G044800 chr5D 388334933 388335465 532 False 542.000 542 85.34300 2241 2768 1 chr5D.!!$F1 527

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
972 1533 0.038159 CTTCCGACTCACACCTCCAC 60.038 60.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2854 4039 0.317799 ATTTGCGCACTTGAATGGCA 59.682 45.0 11.12 0.0 0.0 4.92 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
17 18 2.968206 GCAAAGCAGAAGCAGGGG 59.032 61.111 0.00 0.00 45.49 4.79
19 20 1.871126 GCAAAGCAGAAGCAGGGGTC 61.871 60.000 0.00 0.00 45.49 4.46
22 23 1.422161 AAGCAGAAGCAGGGGTCACT 61.422 55.000 0.00 0.00 45.49 3.41
26 27 0.908198 AGAAGCAGGGGTCACTGATC 59.092 55.000 4.15 1.81 40.97 2.92
64 65 0.094046 GCATTAACGACGGTGGTTCG 59.906 55.000 11.88 4.13 0.00 3.95
98 99 6.038161 ACTGTGAAAATGACATCGTGAAAAGA 59.962 34.615 0.00 0.00 0.00 2.52
100 101 5.853282 GTGAAAATGACATCGTGAAAAGAGG 59.147 40.000 0.00 0.00 30.94 3.69
102 103 3.981071 ATGACATCGTGAAAAGAGGGA 57.019 42.857 0.00 0.00 28.13 4.20
104 105 2.632996 TGACATCGTGAAAAGAGGGAGT 59.367 45.455 0.00 0.00 28.13 3.85
107 108 3.181454 ACATCGTGAAAAGAGGGAGTTGT 60.181 43.478 0.00 0.00 28.13 3.32
108 109 3.107642 TCGTGAAAAGAGGGAGTTGTC 57.892 47.619 0.00 0.00 0.00 3.18
118 161 1.341531 AGGGAGTTGTCTTCTCACACG 59.658 52.381 0.00 0.00 37.76 4.49
127 170 1.067565 TCTTCTCACACGATGCTCACC 60.068 52.381 0.00 0.00 0.00 4.02
128 171 0.678950 TTCTCACACGATGCTCACCA 59.321 50.000 0.00 0.00 0.00 4.17
129 172 0.897621 TCTCACACGATGCTCACCAT 59.102 50.000 0.00 0.00 36.70 3.55
130 173 1.004595 CTCACACGATGCTCACCATG 58.995 55.000 0.00 0.00 33.29 3.66
131 174 0.321346 TCACACGATGCTCACCATGT 59.679 50.000 0.00 0.00 33.29 3.21
132 175 0.445043 CACACGATGCTCACCATGTG 59.555 55.000 0.00 0.00 38.15 3.21
153 196 5.716703 TGTGATGTCAATCCTAGAGACTGAA 59.283 40.000 0.00 0.00 33.56 3.02
160 203 5.420421 TCAATCCTAGAGACTGAACCAGAAG 59.580 44.000 0.45 0.00 35.18 2.85
161 204 3.093057 TCCTAGAGACTGAACCAGAAGC 58.907 50.000 0.45 0.00 35.18 3.86
162 205 3.096092 CCTAGAGACTGAACCAGAAGCT 58.904 50.000 0.45 0.00 35.18 3.74
164 207 4.020662 CCTAGAGACTGAACCAGAAGCTTT 60.021 45.833 0.00 0.00 35.18 3.51
166 209 5.552870 AGAGACTGAACCAGAAGCTTTTA 57.447 39.130 0.00 0.00 35.18 1.52
167 210 5.301555 AGAGACTGAACCAGAAGCTTTTAC 58.698 41.667 0.00 0.00 35.18 2.01
169 212 4.134563 GACTGAACCAGAAGCTTTTACCA 58.865 43.478 0.00 0.00 35.18 3.25
180 223 3.232213 GCTTTTACCAAGCTTTAGCCC 57.768 47.619 0.00 0.00 43.38 5.19
181 224 2.094182 GCTTTTACCAAGCTTTAGCCCC 60.094 50.000 0.00 0.00 43.38 5.80
182 225 3.431415 CTTTTACCAAGCTTTAGCCCCT 58.569 45.455 0.00 0.00 43.38 4.79
183 226 2.507407 TTACCAAGCTTTAGCCCCTG 57.493 50.000 0.00 0.00 43.38 4.45
184 227 0.623723 TACCAAGCTTTAGCCCCTGG 59.376 55.000 0.00 11.50 43.38 4.45
186 229 0.967380 CCAAGCTTTAGCCCCTGGTG 60.967 60.000 0.00 0.00 43.38 4.17
187 230 0.038166 CAAGCTTTAGCCCCTGGTGA 59.962 55.000 0.00 0.00 43.38 4.02
195 258 2.930826 AGCCCCTGGTGATAATAACG 57.069 50.000 0.00 0.00 0.00 3.18
206 269 8.665685 CCTGGTGATAATAACGATATTAAAGCC 58.334 37.037 8.94 10.67 37.49 4.35
225 288 4.769688 AGCCATGAACGTATGAAATGAGA 58.230 39.130 0.00 0.00 0.00 3.27
226 289 4.813161 AGCCATGAACGTATGAAATGAGAG 59.187 41.667 0.00 0.00 0.00 3.20
227 290 4.024556 GCCATGAACGTATGAAATGAGAGG 60.025 45.833 0.00 0.00 0.00 3.69
276 585 9.667107 AAATATATAGTATGACATTTCGGGTGG 57.333 33.333 0.00 0.00 0.00 4.61
281 600 1.313772 TGACATTTCGGGTGGTGTTG 58.686 50.000 0.00 0.00 0.00 3.33
283 602 0.825840 ACATTTCGGGTGGTGTTGGG 60.826 55.000 0.00 0.00 0.00 4.12
299 618 1.078708 GGGAGAAACGGCCATCGAA 60.079 57.895 2.24 0.00 42.43 3.71
310 630 2.805295 CGGCCATCGAAGTAAAGCCATA 60.805 50.000 2.24 0.00 40.49 2.74
311 631 2.808543 GGCCATCGAAGTAAAGCCATAG 59.191 50.000 0.00 0.00 40.20 2.23
328 648 4.937620 GCCATAGACACAAGACAAAGATGA 59.062 41.667 0.00 0.00 0.00 2.92
329 649 5.163814 GCCATAGACACAAGACAAAGATGAC 60.164 44.000 0.00 0.00 0.00 3.06
341 784 4.832248 ACAAAGATGACATCTAGGCGAAA 58.168 39.130 18.24 0.00 39.08 3.46
355 798 3.909137 CGAAACGTTCTTCGCTCAG 57.091 52.632 9.23 0.00 41.46 3.35
368 822 1.717937 GCTCAGGCATAACAGCACG 59.282 57.895 0.00 0.00 38.54 5.34
409 863 3.733960 TCGCGGTCGACAGTCCTG 61.734 66.667 18.91 5.56 40.21 3.86
460 921 4.500127 CAGCAAATGATCTGCAAAATCCA 58.500 39.130 8.02 0.00 42.48 3.41
462 923 5.234329 CAGCAAATGATCTGCAAAATCCATC 59.766 40.000 8.02 0.00 42.48 3.51
463 924 4.510340 GCAAATGATCTGCAAAATCCATCC 59.490 41.667 6.35 0.00 39.69 3.51
464 925 5.684030 GCAAATGATCTGCAAAATCCATCCT 60.684 40.000 6.35 0.00 39.69 3.24
465 926 5.786264 AATGATCTGCAAAATCCATCCTC 57.214 39.130 6.35 0.00 0.00 3.71
466 927 4.515028 TGATCTGCAAAATCCATCCTCT 57.485 40.909 6.35 0.00 0.00 3.69
467 928 4.458397 TGATCTGCAAAATCCATCCTCTC 58.542 43.478 6.35 0.00 0.00 3.20
468 929 4.080186 TGATCTGCAAAATCCATCCTCTCA 60.080 41.667 6.35 0.00 0.00 3.27
469 930 3.614092 TCTGCAAAATCCATCCTCTCAC 58.386 45.455 0.00 0.00 0.00 3.51
470 931 3.009363 TCTGCAAAATCCATCCTCTCACA 59.991 43.478 0.00 0.00 0.00 3.58
471 932 3.760151 CTGCAAAATCCATCCTCTCACAA 59.240 43.478 0.00 0.00 0.00 3.33
472 933 3.760151 TGCAAAATCCATCCTCTCACAAG 59.240 43.478 0.00 0.00 0.00 3.16
473 934 4.012374 GCAAAATCCATCCTCTCACAAGA 58.988 43.478 0.00 0.00 0.00 3.02
475 936 3.557228 AATCCATCCTCTCACAAGAGC 57.443 47.619 0.00 0.00 46.59 4.09
476 937 0.820226 TCCATCCTCTCACAAGAGCG 59.180 55.000 0.00 0.00 46.59 5.03
477 938 0.809241 CCATCCTCTCACAAGAGCGC 60.809 60.000 0.00 0.00 46.59 5.92
478 939 0.809241 CATCCTCTCACAAGAGCGCC 60.809 60.000 2.29 0.00 46.59 6.53
479 940 2.290122 ATCCTCTCACAAGAGCGCCG 62.290 60.000 2.29 0.00 46.59 6.46
480 941 2.568612 CTCTCACAAGAGCGCCGA 59.431 61.111 2.29 0.00 42.54 5.54
481 942 1.080501 CTCTCACAAGAGCGCCGAA 60.081 57.895 2.29 0.00 42.54 4.30
482 943 0.667487 CTCTCACAAGAGCGCCGAAA 60.667 55.000 2.29 0.00 42.54 3.46
483 944 0.944311 TCTCACAAGAGCGCCGAAAC 60.944 55.000 2.29 0.00 41.81 2.78
484 945 2.170985 CACAAGAGCGCCGAAACG 59.829 61.111 2.29 0.00 0.00 3.60
485 946 2.279918 ACAAGAGCGCCGAAACGT 60.280 55.556 2.29 0.00 34.88 3.99
486 947 2.308039 ACAAGAGCGCCGAAACGTC 61.308 57.895 2.29 0.00 34.88 4.34
487 948 2.022129 CAAGAGCGCCGAAACGTCT 61.022 57.895 2.29 0.00 34.88 4.18
488 949 2.022129 AAGAGCGCCGAAACGTCTG 61.022 57.895 2.29 0.00 34.88 3.51
489 950 3.479269 GAGCGCCGAAACGTCTGG 61.479 66.667 2.29 0.00 34.88 3.86
490 951 3.909258 GAGCGCCGAAACGTCTGGA 62.909 63.158 2.29 0.00 34.88 3.86
507 1007 1.292541 GATATCCCCTCGAACCGGC 59.707 63.158 0.00 0.00 0.00 6.13
593 1101 1.956802 GGTTGCCCGTCAAAAGAGG 59.043 57.895 0.00 0.00 36.26 3.69
607 1115 2.355717 AAGAGGAGAAGAAGAACGCG 57.644 50.000 3.53 3.53 0.00 6.01
641 1152 1.268948 GCCCTGAGAATCGTACGTACC 60.269 57.143 19.67 5.89 38.61 3.34
705 1216 3.373226 TCGAAACCCGACCCTCAG 58.627 61.111 0.00 0.00 43.23 3.35
706 1217 2.264794 CGAAACCCGACCCTCAGG 59.735 66.667 0.00 0.00 41.76 3.86
707 1218 2.046217 GAAACCCGACCCTCAGGC 60.046 66.667 0.00 0.00 36.11 4.85
708 1219 2.852075 AAACCCGACCCTCAGGCA 60.852 61.111 0.00 0.00 36.11 4.75
709 1220 2.198304 GAAACCCGACCCTCAGGCAT 62.198 60.000 0.00 0.00 36.11 4.40
710 1221 2.198304 AAACCCGACCCTCAGGCATC 62.198 60.000 0.00 0.00 36.11 3.91
711 1222 2.765807 CCCGACCCTCAGGCATCT 60.766 66.667 0.00 0.00 36.11 2.90
712 1223 2.370445 CCCGACCCTCAGGCATCTT 61.370 63.158 0.00 0.00 36.11 2.40
752 1263 2.664436 CCGCGTCGTTGGTCTTTCC 61.664 63.158 4.92 0.00 0.00 3.13
754 1265 1.662446 GCGTCGTTGGTCTTTCCGA 60.662 57.895 0.00 0.00 39.52 4.55
795 1316 3.295273 TGTCAGCTCGCTCGTGGT 61.295 61.111 0.00 0.00 0.00 4.16
796 1317 2.505118 GTCAGCTCGCTCGTGGTC 60.505 66.667 0.00 0.00 0.00 4.02
797 1318 4.103103 TCAGCTCGCTCGTGGTCG 62.103 66.667 0.00 0.00 38.55 4.79
798 1319 4.406173 CAGCTCGCTCGTGGTCGT 62.406 66.667 0.00 0.00 38.33 4.34
799 1320 4.406173 AGCTCGCTCGTGGTCGTG 62.406 66.667 0.00 0.00 38.33 4.35
944 1505 1.292061 TCCCGCGTCCGAATTAATTG 58.708 50.000 5.17 0.00 36.29 2.32
971 1532 1.185618 CCTTCCGACTCACACCTCCA 61.186 60.000 0.00 0.00 0.00 3.86
972 1533 0.038159 CTTCCGACTCACACCTCCAC 60.038 60.000 0.00 0.00 0.00 4.02
973 1534 0.757561 TTCCGACTCACACCTCCACA 60.758 55.000 0.00 0.00 0.00 4.17
974 1535 1.006102 CCGACTCACACCTCCACAC 60.006 63.158 0.00 0.00 0.00 3.82
978 1539 1.071471 CTCACACCTCCACACCACC 59.929 63.158 0.00 0.00 0.00 4.61
981 1542 4.329545 CACCTCCACACCACCCCG 62.330 72.222 0.00 0.00 0.00 5.73
1036 1632 0.110486 AAAACCGCCTCATCACCACT 59.890 50.000 0.00 0.00 0.00 4.00
1041 1637 1.679311 GCCTCATCACCACTCACCA 59.321 57.895 0.00 0.00 0.00 4.17
1045 1641 1.301637 CATCACCACTCACCACGCA 60.302 57.895 0.00 0.00 0.00 5.24
1168 1796 2.993853 GCCTCAAGTCCCTCCTGG 59.006 66.667 0.00 0.00 0.00 4.45
1758 2431 3.767230 GACGACGACGACGACCGA 61.767 66.667 25.15 0.00 42.66 4.69
2216 3347 8.201554 TGTATTGATTGATAGCAGTTGAACTC 57.798 34.615 0.00 0.00 0.00 3.01
2243 3374 6.257193 TGCAGCTATATATTGCAGATCATTCG 59.743 38.462 19.16 0.60 42.41 3.34
2340 3475 2.565841 AGAACAGAGAGCAAACACCAC 58.434 47.619 0.00 0.00 0.00 4.16
2391 3528 7.492669 CGCCTCGATATAATTTAAGATGGTGAT 59.507 37.037 0.00 0.00 0.00 3.06
2453 3590 9.141400 CAAACCTCAGATAAACTACTACTGAAC 57.859 37.037 0.00 0.00 37.20 3.18
2468 3605 3.358118 ACTGAACCTACCAGCTAGAGTC 58.642 50.000 0.00 0.00 35.14 3.36
2530 3688 4.081365 TCTGTCTGGACAAACTACAACACA 60.081 41.667 4.94 0.00 41.33 3.72
2531 3689 3.936453 TGTCTGGACAAACTACAACACAC 59.064 43.478 0.51 0.00 38.56 3.82
2532 3690 3.000925 GTCTGGACAAACTACAACACACG 59.999 47.826 0.00 0.00 0.00 4.49
2533 3691 2.281517 TGGACAAACTACAACACACGG 58.718 47.619 0.00 0.00 0.00 4.94
2534 3692 1.003223 GGACAAACTACAACACACGGC 60.003 52.381 0.00 0.00 0.00 5.68
2551 3709 1.207329 CGGCCTGCCTAAGAAACTAGT 59.793 52.381 6.60 0.00 0.00 2.57
2560 3718 8.044908 CCTGCCTAAGAAACTAGTAAAACCATA 58.955 37.037 0.00 0.00 0.00 2.74
2579 3761 4.883585 CCATAGAGCTGTTTGGCTGATAAA 59.116 41.667 7.41 0.00 43.20 1.40
2581 3763 4.773323 AGAGCTGTTTGGCTGATAAAAC 57.227 40.909 0.00 0.00 43.20 2.43
2582 3764 4.401925 AGAGCTGTTTGGCTGATAAAACT 58.598 39.130 0.00 0.00 43.20 2.66
2583 3765 4.217118 AGAGCTGTTTGGCTGATAAAACTG 59.783 41.667 0.00 0.00 43.20 3.16
2584 3766 4.144297 AGCTGTTTGGCTGATAAAACTGA 58.856 39.130 8.69 0.00 41.43 3.41
2585 3767 4.768968 AGCTGTTTGGCTGATAAAACTGAT 59.231 37.500 8.69 0.99 41.43 2.90
2586 3768 4.860907 GCTGTTTGGCTGATAAAACTGATG 59.139 41.667 8.69 0.00 37.39 3.07
2587 3769 5.565439 GCTGTTTGGCTGATAAAACTGATGT 60.565 40.000 8.69 0.00 37.39 3.06
2588 3770 6.349280 GCTGTTTGGCTGATAAAACTGATGTA 60.349 38.462 8.69 0.00 37.39 2.29
2589 3771 7.517614 TGTTTGGCTGATAAAACTGATGTAA 57.482 32.000 0.00 0.00 37.22 2.41
2590 3772 8.121305 TGTTTGGCTGATAAAACTGATGTAAT 57.879 30.769 0.00 0.00 37.22 1.89
2591 3773 9.237187 TGTTTGGCTGATAAAACTGATGTAATA 57.763 29.630 0.00 0.00 37.22 0.98
2683 3868 2.283298 CTCGCCAGCATTTCACTGTAT 58.717 47.619 0.00 0.00 33.09 2.29
2814 3999 0.516439 GCTGACTGACAAGAAGCAGC 59.484 55.000 0.00 0.00 38.43 5.25
2819 4004 0.788995 CTGACAAGAAGCAGCGACAG 59.211 55.000 0.00 0.00 0.00 3.51
2840 4025 7.518370 CGACAGCAAATGAACTAAACAACTACT 60.518 37.037 0.00 0.00 0.00 2.57
2841 4026 8.671384 ACAGCAAATGAACTAAACAACTACTA 57.329 30.769 0.00 0.00 0.00 1.82
2842 4027 8.557029 ACAGCAAATGAACTAAACAACTACTAC 58.443 33.333 0.00 0.00 0.00 2.73
2854 4039 4.158015 ACAACTACTACCAGTTACAGCCT 58.842 43.478 0.00 0.00 36.61 4.58
2868 4053 2.180017 GCCTGCCATTCAAGTGCG 59.820 61.111 0.00 0.00 0.00 5.34
2874 4083 0.717224 GCCATTCAAGTGCGCAAATG 59.283 50.000 20.55 20.55 0.00 2.32
2877 4086 3.058450 CCATTCAAGTGCGCAAATGAAA 58.942 40.909 30.78 19.72 35.62 2.69
2878 4087 3.493877 CCATTCAAGTGCGCAAATGAAAA 59.506 39.130 30.78 17.54 35.62 2.29
2880 4089 3.706802 TCAAGTGCGCAAATGAAAAGA 57.293 38.095 20.39 5.41 0.00 2.52
2881 4090 4.039151 TCAAGTGCGCAAATGAAAAGAA 57.961 36.364 20.39 1.12 0.00 2.52
2883 4092 4.267452 TCAAGTGCGCAAATGAAAAGAAAC 59.733 37.500 20.39 1.12 0.00 2.78
2884 4093 3.779759 AGTGCGCAAATGAAAAGAAACA 58.220 36.364 14.00 0.00 0.00 2.83
2885 4094 4.370917 AGTGCGCAAATGAAAAGAAACAT 58.629 34.783 14.00 0.00 0.00 2.71
2886 4095 5.527951 AGTGCGCAAATGAAAAGAAACATA 58.472 33.333 14.00 0.00 0.00 2.29
2887 4096 6.158598 AGTGCGCAAATGAAAAGAAACATAT 58.841 32.000 14.00 0.00 0.00 1.78
2888 4097 7.312154 AGTGCGCAAATGAAAAGAAACATATA 58.688 30.769 14.00 0.00 0.00 0.86
2889 4098 7.975616 AGTGCGCAAATGAAAAGAAACATATAT 59.024 29.630 14.00 0.00 0.00 0.86
2890 4099 8.261908 GTGCGCAAATGAAAAGAAACATATATC 58.738 33.333 14.00 0.00 0.00 1.63
2891 4100 7.972832 TGCGCAAATGAAAAGAAACATATATCA 59.027 29.630 8.16 0.00 0.00 2.15
2892 4101 8.971321 GCGCAAATGAAAAGAAACATATATCAT 58.029 29.630 0.30 0.00 0.00 2.45
2974 4183 1.209504 TGGTCTTTGGGGCTATTCTCG 59.790 52.381 0.00 0.00 0.00 4.04
3030 4239 1.968493 TCGCTTTCTCCACTGGTTAGT 59.032 47.619 0.00 0.00 37.75 2.24
3161 4370 3.671008 TGAGCTCTGCCGTTAAAACTA 57.329 42.857 16.19 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.813161 ACCATCGATTGATTGATCAGTGAC 59.187 41.667 3.08 0.00 38.19 3.67
19 20 5.277683 GGAACCATCGATTGATTGATCAGTG 60.278 44.000 3.08 0.00 38.19 3.66
22 23 4.818005 CAGGAACCATCGATTGATTGATCA 59.182 41.667 3.08 0.00 30.49 2.92
26 27 2.684374 TGCAGGAACCATCGATTGATTG 59.316 45.455 3.08 0.00 30.49 2.67
86 87 3.403038 ACAACTCCCTCTTTTCACGATG 58.597 45.455 0.00 0.00 0.00 3.84
98 99 1.341531 CGTGTGAGAAGACAACTCCCT 59.658 52.381 0.00 0.00 33.95 4.20
100 101 2.795175 TCGTGTGAGAAGACAACTCC 57.205 50.000 0.00 0.00 33.95 3.85
102 103 2.036475 AGCATCGTGTGAGAAGACAACT 59.964 45.455 0.00 0.00 0.00 3.16
104 105 2.035832 TGAGCATCGTGTGAGAAGACAA 59.964 45.455 0.00 0.00 38.61 3.18
107 108 1.067565 GGTGAGCATCGTGTGAGAAGA 60.068 52.381 0.00 0.00 38.61 2.87
108 109 1.337167 TGGTGAGCATCGTGTGAGAAG 60.337 52.381 0.00 0.00 38.61 2.85
118 161 2.635714 TGACATCACATGGTGAGCATC 58.364 47.619 0.00 3.48 46.04 3.91
127 170 5.984323 CAGTCTCTAGGATTGACATCACATG 59.016 44.000 0.00 0.00 34.15 3.21
128 171 5.896106 TCAGTCTCTAGGATTGACATCACAT 59.104 40.000 0.00 0.00 36.08 3.21
129 172 5.264395 TCAGTCTCTAGGATTGACATCACA 58.736 41.667 0.00 0.00 36.08 3.58
130 173 5.843673 TCAGTCTCTAGGATTGACATCAC 57.156 43.478 0.00 0.00 36.08 3.06
131 174 5.127845 GGTTCAGTCTCTAGGATTGACATCA 59.872 44.000 6.10 0.00 39.77 3.07
132 175 5.127845 TGGTTCAGTCTCTAGGATTGACATC 59.872 44.000 6.10 2.45 39.77 3.06
160 203 2.094182 GGGGCTAAAGCTTGGTAAAAGC 60.094 50.000 0.00 1.82 43.31 3.51
161 204 3.193479 CAGGGGCTAAAGCTTGGTAAAAG 59.807 47.826 0.00 0.00 41.70 2.27
162 205 3.161866 CAGGGGCTAAAGCTTGGTAAAA 58.838 45.455 0.00 0.00 41.70 1.52
164 207 1.005450 CCAGGGGCTAAAGCTTGGTAA 59.995 52.381 0.00 0.00 41.70 2.85
166 209 1.384191 CCAGGGGCTAAAGCTTGGT 59.616 57.895 0.00 0.00 41.70 3.67
167 210 0.967380 CACCAGGGGCTAAAGCTTGG 60.967 60.000 0.00 14.71 41.70 3.61
169 212 1.002857 ATCACCAGGGGCTAAAGCTT 58.997 50.000 0.00 0.00 41.70 3.74
176 219 2.404559 TCGTTATTATCACCAGGGGCT 58.595 47.619 0.00 0.00 0.00 5.19
178 221 9.162764 CTTTAATATCGTTATTATCACCAGGGG 57.837 37.037 6.75 0.00 31.86 4.79
179 222 8.665685 GCTTTAATATCGTTATTATCACCAGGG 58.334 37.037 6.75 0.00 31.86 4.45
180 223 8.665685 GGCTTTAATATCGTTATTATCACCAGG 58.334 37.037 6.75 0.00 31.86 4.45
181 224 9.214957 TGGCTTTAATATCGTTATTATCACCAG 57.785 33.333 6.75 1.89 31.86 4.00
182 225 9.733556 ATGGCTTTAATATCGTTATTATCACCA 57.266 29.630 16.18 16.18 34.06 4.17
183 226 9.988350 CATGGCTTTAATATCGTTATTATCACC 57.012 33.333 6.75 8.50 31.86 4.02
206 269 5.812127 TGTCCTCTCATTTCATACGTTCATG 59.188 40.000 0.00 0.00 0.00 3.07
225 288 2.664402 AAGTGGTTGCAGATTGTCCT 57.336 45.000 0.00 0.00 0.00 3.85
226 289 2.029918 GGAAAGTGGTTGCAGATTGTCC 60.030 50.000 0.00 0.00 0.00 4.02
227 290 2.887152 AGGAAAGTGGTTGCAGATTGTC 59.113 45.455 0.00 0.00 0.00 3.18
270 579 1.149627 TTTCTCCCAACACCACCCG 59.850 57.895 0.00 0.00 0.00 5.28
273 582 1.792118 GCCGTTTCTCCCAACACCAC 61.792 60.000 0.00 0.00 0.00 4.16
276 585 0.893727 ATGGCCGTTTCTCCCAACAC 60.894 55.000 0.00 0.00 31.43 3.32
281 600 1.078708 TTCGATGGCCGTTTCTCCC 60.079 57.895 0.00 0.00 39.75 4.30
283 602 2.288961 TACTTCGATGGCCGTTTCTC 57.711 50.000 0.00 0.00 39.75 2.87
299 618 5.483685 TGTCTTGTGTCTATGGCTTTACT 57.516 39.130 0.00 0.00 0.00 2.24
310 630 5.862845 AGATGTCATCTTTGTCTTGTGTCT 58.137 37.500 9.68 0.00 35.76 3.41
311 631 6.312426 CCTAGATGTCATCTTTGTCTTGTGTC 59.688 42.308 20.27 0.00 40.76 3.67
328 648 3.251571 GAAGAACGTTTCGCCTAGATGT 58.748 45.455 0.46 0.00 34.02 3.06
329 649 2.279136 CGAAGAACGTTTCGCCTAGATG 59.721 50.000 9.23 0.00 42.74 2.90
341 784 0.530744 TATGCCTGAGCGAAGAACGT 59.469 50.000 0.00 0.00 44.31 3.99
352 795 0.541392 ATCCGTGCTGTTATGCCTGA 59.459 50.000 0.00 0.00 0.00 3.86
354 797 0.541392 TGATCCGTGCTGTTATGCCT 59.459 50.000 0.00 0.00 0.00 4.75
355 798 1.331756 CTTGATCCGTGCTGTTATGCC 59.668 52.381 0.00 0.00 0.00 4.40
368 822 2.482839 GCTGCTCCTAGTGTCTTGATCC 60.483 54.545 0.00 0.00 0.00 3.36
405 859 0.314935 GTTTCGTACGGTCCACAGGA 59.685 55.000 16.52 0.00 0.00 3.86
408 862 4.632037 CGTTTCGTACGGTCCACA 57.368 55.556 16.52 0.00 46.42 4.17
464 925 0.944311 GTTTCGGCGCTCTTGTGAGA 60.944 55.000 7.64 0.00 42.73 3.27
465 926 1.493311 GTTTCGGCGCTCTTGTGAG 59.507 57.895 7.64 0.00 42.96 3.51
466 927 2.307309 CGTTTCGGCGCTCTTGTGA 61.307 57.895 7.64 0.00 0.00 3.58
467 928 2.170985 CGTTTCGGCGCTCTTGTG 59.829 61.111 7.64 0.00 0.00 3.33
468 929 2.279918 ACGTTTCGGCGCTCTTGT 60.280 55.556 7.64 0.00 34.88 3.16
469 930 2.022129 AGACGTTTCGGCGCTCTTG 61.022 57.895 7.64 0.00 41.28 3.02
470 931 2.022129 CAGACGTTTCGGCGCTCTT 61.022 57.895 7.64 0.00 41.28 2.85
471 932 2.430921 CAGACGTTTCGGCGCTCT 60.431 61.111 7.64 0.00 41.28 4.09
472 933 3.479269 CCAGACGTTTCGGCGCTC 61.479 66.667 7.64 0.00 41.28 5.03
473 934 1.940883 TATCCAGACGTTTCGGCGCT 61.941 55.000 7.64 0.00 41.28 5.92
474 935 0.874607 ATATCCAGACGTTTCGGCGC 60.875 55.000 0.00 0.00 41.28 6.53
475 936 1.129326 GATATCCAGACGTTTCGGCG 58.871 55.000 0.00 0.00 41.28 6.46
476 937 1.499049 GGATATCCAGACGTTTCGGC 58.501 55.000 17.34 0.00 35.64 5.54
477 938 1.270147 GGGGATATCCAGACGTTTCGG 60.270 57.143 23.27 0.00 37.91 4.30
478 939 1.687123 AGGGGATATCCAGACGTTTCG 59.313 52.381 23.27 0.00 37.91 3.46
479 940 2.288273 CGAGGGGATATCCAGACGTTTC 60.288 54.545 23.27 8.27 37.91 2.78
480 941 1.687123 CGAGGGGATATCCAGACGTTT 59.313 52.381 23.27 0.31 37.91 3.60
481 942 1.133575 TCGAGGGGATATCCAGACGTT 60.134 52.381 23.27 1.70 37.91 3.99
482 943 0.477204 TCGAGGGGATATCCAGACGT 59.523 55.000 23.27 7.68 37.91 4.34
483 944 1.269998 GTTCGAGGGGATATCCAGACG 59.730 57.143 23.27 21.36 37.91 4.18
484 945 1.619332 GGTTCGAGGGGATATCCAGAC 59.381 57.143 23.27 12.43 37.91 3.51
485 946 1.822062 CGGTTCGAGGGGATATCCAGA 60.822 57.143 23.27 13.08 37.91 3.86
486 947 0.603569 CGGTTCGAGGGGATATCCAG 59.396 60.000 23.27 11.07 37.91 3.86
487 948 0.830444 CCGGTTCGAGGGGATATCCA 60.830 60.000 23.27 0.00 37.91 3.41
488 949 1.972978 CCGGTTCGAGGGGATATCC 59.027 63.158 13.87 13.87 0.00 2.59
489 950 1.186267 AGCCGGTTCGAGGGGATATC 61.186 60.000 1.90 0.00 0.00 1.63
490 951 1.152312 AGCCGGTTCGAGGGGATAT 60.152 57.895 1.90 0.00 0.00 1.63
507 1007 1.079543 CTGCGGGTGGAGACTTGAG 60.080 63.158 0.00 0.00 35.14 3.02
529 1029 3.116531 GGGAAAACGACGGCGAGG 61.117 66.667 22.49 7.21 41.64 4.63
562 1062 2.604174 GCAACCGTGACTTCGTGGG 61.604 63.158 0.00 0.00 0.00 4.61
593 1101 1.782181 GTGGCGCGTTCTTCTTCTC 59.218 57.895 8.43 0.00 0.00 2.87
621 1129 1.268948 GGTACGTACGATTCTCAGGGC 60.269 57.143 24.41 0.00 0.00 5.19
622 1130 2.770699 GGTACGTACGATTCTCAGGG 57.229 55.000 24.41 0.00 0.00 4.45
688 1199 2.280552 CCTGAGGGTCGGGTTTCGA 61.281 63.158 0.00 0.00 46.77 3.71
691 1202 2.198304 GATGCCTGAGGGTCGGGTTT 62.198 60.000 0.00 0.00 44.85 3.27
698 1209 0.394565 GCGATAAGATGCCTGAGGGT 59.605 55.000 0.00 0.00 34.45 4.34
699 1210 0.394192 TGCGATAAGATGCCTGAGGG 59.606 55.000 0.00 0.00 0.00 4.30
700 1211 2.344950 GATGCGATAAGATGCCTGAGG 58.655 52.381 0.00 0.00 0.00 3.86
701 1212 1.991264 CGATGCGATAAGATGCCTGAG 59.009 52.381 0.00 0.00 0.00 3.35
702 1213 1.936656 GCGATGCGATAAGATGCCTGA 60.937 52.381 0.00 0.00 0.00 3.86
703 1214 0.441533 GCGATGCGATAAGATGCCTG 59.558 55.000 0.00 0.00 0.00 4.85
704 1215 2.832931 GCGATGCGATAAGATGCCT 58.167 52.632 0.00 0.00 0.00 4.75
752 1263 3.110178 GTTCGTTCGGCTGGGTCG 61.110 66.667 0.00 0.00 0.00 4.79
754 1265 4.675029 CCGTTCGTTCGGCTGGGT 62.675 66.667 7.89 0.00 43.96 4.51
779 1300 2.505118 GACCACGAGCGAGCTGAC 60.505 66.667 0.84 0.00 0.00 3.51
944 1505 2.296471 TGTGAGTCGGAAGGAGAAAGAC 59.704 50.000 0.00 0.00 0.00 3.01
987 1548 1.408969 TTTATACCCCCGTCCCGTAC 58.591 55.000 0.00 0.00 0.00 3.67
988 1549 1.760029 GTTTTATACCCCCGTCCCGTA 59.240 52.381 0.00 0.00 0.00 4.02
989 1550 0.541392 GTTTTATACCCCCGTCCCGT 59.459 55.000 0.00 0.00 0.00 5.28
1054 1661 1.227823 TGAGTGCTGACGGTTTGGG 60.228 57.895 0.00 0.00 0.00 4.12
1851 2524 2.802667 CGTGGCAGCCGATTCGAAG 61.803 63.158 7.03 0.00 0.00 3.79
2071 2753 1.807573 CCTGCTCTTCTCCGCGTTC 60.808 63.158 4.92 0.00 0.00 3.95
2216 3347 6.980051 TGATCTGCAATATATAGCTGCAAG 57.020 37.500 18.11 13.64 44.94 4.01
2340 3475 7.459486 GTCTTATCACTGACAACATAAGCTTG 58.541 38.462 9.86 0.00 33.75 4.01
2453 3590 1.600023 CGAGGACTCTAGCTGGTAGG 58.400 60.000 13.43 7.29 0.00 3.18
2468 3605 7.282332 TGATGATAATATATCTGCTCCGAGG 57.718 40.000 0.00 0.00 0.00 4.63
2530 3688 1.207329 CTAGTTTCTTAGGCAGGCCGT 59.793 52.381 4.37 0.00 41.95 5.68
2531 3689 1.207329 ACTAGTTTCTTAGGCAGGCCG 59.793 52.381 4.37 0.00 41.95 6.13
2532 3690 4.482952 TTACTAGTTTCTTAGGCAGGCC 57.517 45.455 0.00 0.97 0.00 5.19
2533 3691 5.123502 GGTTTTACTAGTTTCTTAGGCAGGC 59.876 44.000 0.00 0.00 0.00 4.85
2534 3692 6.235664 TGGTTTTACTAGTTTCTTAGGCAGG 58.764 40.000 0.00 0.00 0.00 4.85
2551 3709 4.458989 CAGCCAAACAGCTCTATGGTTTTA 59.541 41.667 9.32 0.00 42.61 1.52
2560 3718 4.217118 CAGTTTTATCAGCCAAACAGCTCT 59.783 41.667 0.00 0.00 42.61 4.09
2591 3773 8.052748 GGGAGTATCTCAGATCAGATGTAGTAT 58.947 40.741 5.94 0.00 33.91 2.12
2592 3774 7.017651 TGGGAGTATCTCAGATCAGATGTAGTA 59.982 40.741 5.94 0.00 43.69 1.82
2593 3775 6.183361 TGGGAGTATCTCAGATCAGATGTAGT 60.183 42.308 5.94 0.00 43.69 2.73
2594 3776 6.244654 TGGGAGTATCTCAGATCAGATGTAG 58.755 44.000 5.94 0.00 43.69 2.74
2814 3999 5.510671 AGTTGTTTAGTTCATTTGCTGTCG 58.489 37.500 0.00 0.00 0.00 4.35
2819 4004 7.867752 TGGTAGTAGTTGTTTAGTTCATTTGC 58.132 34.615 0.00 0.00 0.00 3.68
2840 4025 1.285280 ATGGCAGGCTGTAACTGGTA 58.715 50.000 17.16 0.00 36.48 3.25
2841 4026 0.405585 AATGGCAGGCTGTAACTGGT 59.594 50.000 17.16 0.00 36.48 4.00
2842 4027 1.098050 GAATGGCAGGCTGTAACTGG 58.902 55.000 17.16 0.00 36.48 4.00
2854 4039 0.317799 ATTTGCGCACTTGAATGGCA 59.682 45.000 11.12 0.00 0.00 4.92
2889 4098 9.223099 CCTGACACTTGATTAATGCATATATGA 57.777 33.333 17.10 2.36 0.00 2.15
2890 4099 9.006839 ACCTGACACTTGATTAATGCATATATG 57.993 33.333 8.45 8.45 0.00 1.78
2893 4102 8.978874 TTACCTGACACTTGATTAATGCATAT 57.021 30.769 0.00 0.00 0.00 1.78
2894 4103 8.800370 TTTACCTGACACTTGATTAATGCATA 57.200 30.769 0.00 0.00 0.00 3.14
2895 4104 7.701539 TTTACCTGACACTTGATTAATGCAT 57.298 32.000 0.00 0.00 0.00 3.96
2896 4105 7.013750 TGTTTTACCTGACACTTGATTAATGCA 59.986 33.333 0.00 0.00 0.00 3.96
2897 4106 7.367285 TGTTTTACCTGACACTTGATTAATGC 58.633 34.615 0.00 0.00 0.00 3.56
2898 4107 9.398170 CTTGTTTTACCTGACACTTGATTAATG 57.602 33.333 0.00 0.00 0.00 1.90
2899 4108 9.349713 TCTTGTTTTACCTGACACTTGATTAAT 57.650 29.630 0.00 0.00 0.00 1.40
2900 4109 8.740123 TCTTGTTTTACCTGACACTTGATTAA 57.260 30.769 0.00 0.00 0.00 1.40
2901 4110 8.740123 TTCTTGTTTTACCTGACACTTGATTA 57.260 30.769 0.00 0.00 0.00 1.75
2902 4111 7.201821 CCTTCTTGTTTTACCTGACACTTGATT 60.202 37.037 0.00 0.00 0.00 2.57
2903 4112 6.263168 CCTTCTTGTTTTACCTGACACTTGAT 59.737 38.462 0.00 0.00 0.00 2.57
2904 4113 5.588648 CCTTCTTGTTTTACCTGACACTTGA 59.411 40.000 0.00 0.00 0.00 3.02
2905 4114 5.221048 CCCTTCTTGTTTTACCTGACACTTG 60.221 44.000 0.00 0.00 0.00 3.16
2906 4115 4.887655 CCCTTCTTGTTTTACCTGACACTT 59.112 41.667 0.00 0.00 0.00 3.16
2907 4116 4.461198 CCCTTCTTGTTTTACCTGACACT 58.539 43.478 0.00 0.00 0.00 3.55
2908 4117 3.568430 CCCCTTCTTGTTTTACCTGACAC 59.432 47.826 0.00 0.00 0.00 3.67
2909 4118 3.827722 CCCCTTCTTGTTTTACCTGACA 58.172 45.455 0.00 0.00 0.00 3.58
2910 4119 2.557056 GCCCCTTCTTGTTTTACCTGAC 59.443 50.000 0.00 0.00 0.00 3.51
2911 4120 2.175931 TGCCCCTTCTTGTTTTACCTGA 59.824 45.455 0.00 0.00 0.00 3.86
2912 4121 2.593026 TGCCCCTTCTTGTTTTACCTG 58.407 47.619 0.00 0.00 0.00 4.00
2974 4183 6.156949 TCAAGGAGCTATGGGATAATATCACC 59.843 42.308 0.00 1.00 0.00 4.02
3134 4343 1.726853 ACGGCAGAGCTCATGTTTAC 58.273 50.000 17.77 0.00 0.00 2.01
3161 4370 4.016444 ACATGAGTGTGTTTGTTCAACCT 58.984 39.130 0.00 0.00 37.14 3.50


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

AutoCloner maintained by Alex Coulton.