Multiple sequence alignment - TraesCS4A01G354900

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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 TraesCS4A01G354900 chr4A 100.000 3978 0 0 1 3978 629291193 629295170 0.000000e+00 7347.0
1 TraesCS4A01G354900 chr4A 86.866 769 87 8 2235 3002 681919842 681920597 0.000000e+00 848.0
2 TraesCS4A01G354900 chr4A 80.058 692 102 22 1582 2246 681918476 681919158 7.730000e-132 481.0
3 TraesCS4A01G354900 chr4A 86.250 240 22 6 659 890 736464834 736465070 2.370000e-62 250.0
4 TraesCS4A01G354900 chr4A 75.263 190 35 4 3443 3632 175004757 175004580 3.300000e-11 80.5
5 TraesCS4A01G354900 chr5B 88.571 1715 162 20 2235 3940 680994344 680992655 0.000000e+00 2050.0
6 TraesCS4A01G354900 chr5B 84.335 932 104 22 1334 2246 680995936 680995028 0.000000e+00 874.0
7 TraesCS4A01G354900 chr5B 89.714 350 36 0 891 1240 680998336 680997987 7.840000e-122 448.0
8 TraesCS4A01G354900 chr5D 87.851 1745 127 18 2235 3978 539454557 539452897 0.000000e+00 1969.0
9 TraesCS4A01G354900 chr5D 83.671 692 94 15 1571 2246 539455929 539455241 5.610000e-178 634.0
10 TraesCS4A01G354900 chr5D 80.786 458 85 3 3515 3970 384881985 384882441 4.890000e-94 355.0
11 TraesCS4A01G354900 chr3A 90.444 879 70 5 1 874 726857905 726857036 0.000000e+00 1146.0
12 TraesCS4A01G354900 chr3A 89.590 903 81 8 1 890 31545289 31546191 0.000000e+00 1134.0
13 TraesCS4A01G354900 chr1A 88.677 892 74 16 1 890 150737241 150736375 0.000000e+00 1062.0
14 TraesCS4A01G354900 chr7B 89.265 857 74 7 1 853 58872421 58873263 0.000000e+00 1057.0
15 TraesCS4A01G354900 chr7B 89.538 736 63 11 1 735 6165850 6166572 0.000000e+00 920.0
16 TraesCS4A01G354900 chr2D 90.095 737 60 10 1 735 587251561 587252286 0.000000e+00 944.0
17 TraesCS4A01G354900 chr2D 82.398 392 66 3 3516 3906 543527453 543527064 4.920000e-89 339.0
18 TraesCS4A01G354900 chr6D 89.747 751 56 10 1 734 308897576 308898322 0.000000e+00 941.0
19 TraesCS4A01G354900 chr6D 93.082 636 41 3 4 638 421683881 421683248 0.000000e+00 928.0
20 TraesCS4A01G354900 chr3D 92.801 639 43 3 1 638 564941041 564940405 0.000000e+00 922.0
21 TraesCS4A01G354900 chr3D 79.383 810 135 24 106 891 469607336 469608137 3.500000e-150 542.0
22 TraesCS4A01G354900 chr3D 80.795 453 82 5 3491 3940 516072901 516073351 2.270000e-92 350.0
23 TraesCS4A01G354900 chr7D 93.164 629 40 3 1 628 104079727 104080353 0.000000e+00 920.0
24 TraesCS4A01G354900 chr7D 81.124 498 85 5 3444 3940 478368242 478368731 1.340000e-104 390.0
25 TraesCS4A01G354900 chr7D 81.897 348 58 4 3542 3885 230975377 230975031 5.030000e-74 289.0
26 TraesCS4A01G354900 chr6B 90.365 685 55 11 1 683 278149555 278150230 0.000000e+00 889.0
27 TraesCS4A01G354900 chr4D 86.216 769 92 8 2235 3002 475178311 475179066 0.000000e+00 821.0
28 TraesCS4A01G354900 chr4D 79.884 691 105 23 1582 2246 475176945 475177627 3.600000e-130 475.0
29 TraesCS4A01G354900 chr4B 85.566 769 97 8 2235 3002 599886370 599887125 0.000000e+00 793.0
30 TraesCS4A01G354900 chr4B 80.145 690 105 20 1582 2246 599885004 599885686 1.660000e-133 486.0
31 TraesCS4A01G354900 chr3B 80.240 501 93 6 3443 3940 628472741 628472244 4.860000e-99 372.0
32 TraesCS4A01G354900 chr3B 73.861 505 110 10 3443 3928 540097015 540096514 8.780000e-42 182.0
33 TraesCS4A01G354900 chr5A 79.096 531 104 7 3445 3971 22613096 22612569 3.780000e-95 359.0
34 TraesCS4A01G354900 chr5A 78.710 465 98 1 3515 3978 485864410 485864874 3.860000e-80 309.0
35 TraesCS4A01G354900 chr7A 91.250 240 21 0 653 892 149551892 149552131 1.070000e-85 327.0
36 TraesCS4A01G354900 chr7A 88.421 190 21 1 702 890 717335309 717335120 1.110000e-55 228.0
37 TraesCS4A01G354900 chr7A 80.597 201 37 2 3443 3643 35389384 35389186 1.910000e-33 154.0
38 TraesCS4A01G354900 chr1D 86.383 235 26 6 659 890 445537047 445537278 6.600000e-63 252.0
39 TraesCS4A01G354900 chr2A 84.753 223 26 7 672 891 695480774 695480557 2.410000e-52 217.0
40 TraesCS4A01G354900 chr2A 78.462 130 25 3 3440 3568 750627224 750627351 9.160000e-12 82.4
41 TraesCS4A01G354900 chr2A 78.740 127 24 3 3443 3568 750737815 750737691 9.160000e-12 82.4
42 TraesCS4A01G354900 chr2B 80.620 129 19 2 3440 3568 758396844 758396966 1.180000e-15 95.3
43 TraesCS4A01G354900 chr2B 100.000 32 0 0 2286 2317 73551539 73551570 4.290000e-05 60.2


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 TraesCS4A01G354900 chr4A 629291193 629295170 3977 False 7347.0 7347 100.0000 1 3978 1 chr4A.!!$F1 3977
1 TraesCS4A01G354900 chr4A 681918476 681920597 2121 False 664.5 848 83.4620 1582 3002 2 chr4A.!!$F3 1420
2 TraesCS4A01G354900 chr5B 680992655 680998336 5681 True 1124.0 2050 87.5400 891 3940 3 chr5B.!!$R1 3049
3 TraesCS4A01G354900 chr5D 539452897 539455929 3032 True 1301.5 1969 85.7610 1571 3978 2 chr5D.!!$R1 2407
4 TraesCS4A01G354900 chr3A 726857036 726857905 869 True 1146.0 1146 90.4440 1 874 1 chr3A.!!$R1 873
5 TraesCS4A01G354900 chr3A 31545289 31546191 902 False 1134.0 1134 89.5900 1 890 1 chr3A.!!$F1 889
6 TraesCS4A01G354900 chr1A 150736375 150737241 866 True 1062.0 1062 88.6770 1 890 1 chr1A.!!$R1 889
7 TraesCS4A01G354900 chr7B 58872421 58873263 842 False 1057.0 1057 89.2650 1 853 1 chr7B.!!$F2 852
8 TraesCS4A01G354900 chr7B 6165850 6166572 722 False 920.0 920 89.5380 1 735 1 chr7B.!!$F1 734
9 TraesCS4A01G354900 chr2D 587251561 587252286 725 False 944.0 944 90.0950 1 735 1 chr2D.!!$F1 734
10 TraesCS4A01G354900 chr6D 308897576 308898322 746 False 941.0 941 89.7470 1 734 1 chr6D.!!$F1 733
11 TraesCS4A01G354900 chr6D 421683248 421683881 633 True 928.0 928 93.0820 4 638 1 chr6D.!!$R1 634
12 TraesCS4A01G354900 chr3D 564940405 564941041 636 True 922.0 922 92.8010 1 638 1 chr3D.!!$R1 637
13 TraesCS4A01G354900 chr3D 469607336 469608137 801 False 542.0 542 79.3830 106 891 1 chr3D.!!$F1 785
14 TraesCS4A01G354900 chr7D 104079727 104080353 626 False 920.0 920 93.1640 1 628 1 chr7D.!!$F1 627
15 TraesCS4A01G354900 chr6B 278149555 278150230 675 False 889.0 889 90.3650 1 683 1 chr6B.!!$F1 682
16 TraesCS4A01G354900 chr4D 475176945 475179066 2121 False 648.0 821 83.0500 1582 3002 2 chr4D.!!$F1 1420
17 TraesCS4A01G354900 chr4B 599885004 599887125 2121 False 639.5 793 82.8555 1582 3002 2 chr4B.!!$F1 1420
18 TraesCS4A01G354900 chr5A 22612569 22613096 527 True 359.0 359 79.0960 3445 3971 1 chr5A.!!$R1 526

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
811 867 0.749649 ACATCGAGCCTCACATCTCC 59.250 55.0 0.00 0.00 0.00 3.71 F
1089 1145 0.327480 ATACATGGTGGCCCTCCTCA 60.327 55.0 13.97 0.13 0.00 3.86 F
1170 1226 0.373716 GCGGTCAAATCTTAGTGGCG 59.626 55.0 0.00 0.00 0.00 5.69 F
2201 4262 0.172578 CATGTCGAGGGCGTTGAGTA 59.827 55.0 0.00 0.00 38.98 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1820 3869 0.035458 CGGGCTTCATCCTCCATACC 59.965 60.0 0.0 0.0 0.00 2.73 R
2184 4245 0.038892 GTTACTCAACGCCCTCGACA 60.039 55.0 0.0 0.0 39.41 4.35 R
2657 5414 1.024579 GCGTTGGTGTCAATCCCGAT 61.025 55.0 0.0 0.0 35.10 4.18 R
3774 6546 0.038166 CACCTGCATTGGGTAGTGGT 59.962 55.0 0.0 0.0 35.00 4.16 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
173 174 2.625617 GGACATCTCCTCCTTCCTCAGT 60.626 54.545 0.00 0.00 33.07 3.41
241 246 2.263540 GTACATGGCACCGACGGT 59.736 61.111 15.37 15.37 35.62 4.83
291 296 1.207390 GATGAGCTGACAGACGATGC 58.793 55.000 6.65 0.00 0.00 3.91
329 334 4.358102 AGGAGGCCCTTGACCTTT 57.642 55.556 0.00 0.00 40.78 3.11
513 520 3.731766 AAGTTGTGGCGGCCAAGGT 62.732 57.895 25.70 5.91 34.18 3.50
763 817 7.615757 TGACTATCTGATACCAAGTTGAAGAGA 59.384 37.037 3.87 0.00 0.00 3.10
773 827 6.174049 ACCAAGTTGAAGAGATAGGTTTAGC 58.826 40.000 3.87 0.00 0.00 3.09
789 845 2.409651 GCGTTTTGCGTTGGTGGA 59.590 55.556 0.00 0.00 43.66 4.02
797 853 1.364721 TGCGTTGGTGGATAACATCG 58.635 50.000 0.00 0.00 30.79 3.84
806 862 2.107366 TGGATAACATCGAGCCTCACA 58.893 47.619 0.00 0.00 0.00 3.58
811 867 0.749649 ACATCGAGCCTCACATCTCC 59.250 55.000 0.00 0.00 0.00 3.71
901 957 6.927294 ACCTATTTTACATGCAGAGCTAAC 57.073 37.500 0.00 0.00 0.00 2.34
913 969 1.883732 AGCTAACGCTTCTCTCGCA 59.116 52.632 0.00 0.00 46.47 5.10
924 980 2.591571 TCTCTCGCATGTCTGGATTG 57.408 50.000 0.00 0.00 0.00 2.67
975 1031 1.209127 GCGCCACACACCACAATAC 59.791 57.895 0.00 0.00 0.00 1.89
986 1042 1.066143 ACCACAATACTTCTCCAGCGG 60.066 52.381 0.00 0.00 0.00 5.52
1011 1067 2.353889 CGGCTGAAACATGGATCTTGAG 59.646 50.000 0.00 0.00 0.00 3.02
1013 1069 3.128242 GGCTGAAACATGGATCTTGAGTG 59.872 47.826 0.00 0.00 0.00 3.51
1014 1070 3.128242 GCTGAAACATGGATCTTGAGTGG 59.872 47.826 0.00 0.00 0.00 4.00
1026 1082 2.032681 GAGTGGGCAGTGGTGGTC 59.967 66.667 0.00 0.00 0.00 4.02
1048 1104 1.227380 GCTCGGAGTGGCTATGTGG 60.227 63.158 6.90 0.00 0.00 4.17
1052 1108 1.066430 TCGGAGTGGCTATGTGGAAAC 60.066 52.381 0.00 0.00 0.00 2.78
1053 1109 1.338674 CGGAGTGGCTATGTGGAAACA 60.339 52.381 0.00 0.00 38.70 2.83
1068 1124 2.839474 GAAACATTCCAGAGAAACGCG 58.161 47.619 3.53 3.53 35.09 6.01
1073 1129 2.288961 TTCCAGAGAAACGCGGATAC 57.711 50.000 12.47 0.00 0.00 2.24
1074 1130 1.179152 TCCAGAGAAACGCGGATACA 58.821 50.000 12.47 0.00 0.00 2.29
1089 1145 0.327480 ATACATGGTGGCCCTCCTCA 60.327 55.000 13.97 0.13 0.00 3.86
1130 1186 4.119862 CGGTGATGGTTAGATTTGTCGAT 58.880 43.478 0.00 0.00 0.00 3.59
1135 1191 6.535150 GTGATGGTTAGATTTGTCGATTCAGA 59.465 38.462 0.00 0.00 0.00 3.27
1136 1192 6.535150 TGATGGTTAGATTTGTCGATTCAGAC 59.465 38.462 0.00 2.88 41.30 3.51
1162 1218 2.764314 GCATGCGGCGGTCAAATCT 61.764 57.895 9.78 0.00 0.00 2.40
1164 1220 1.013596 CATGCGGCGGTCAAATCTTA 58.986 50.000 9.78 0.00 0.00 2.10
1170 1226 0.373716 GCGGTCAAATCTTAGTGGCG 59.626 55.000 0.00 0.00 0.00 5.69
1172 1228 0.373716 GGTCAAATCTTAGTGGCGCG 59.626 55.000 0.00 0.00 0.00 6.86
1175 1231 1.024579 CAAATCTTAGTGGCGCGGGT 61.025 55.000 8.83 0.00 0.00 5.28
1190 1246 2.668550 GGTCGAGGTGGTGGCAAC 60.669 66.667 0.00 0.00 0.00 4.17
1210 1266 0.607489 GCAAGGCAGAGGCAAAGAGA 60.607 55.000 0.00 0.00 43.71 3.10
1232 1288 2.103042 GTGCTGACGTGGAGGCATC 61.103 63.158 0.00 0.00 37.16 3.91
1243 1299 2.981859 GGAGGCATCCGAGAAGTTAA 57.018 50.000 0.00 0.00 35.37 2.01
1275 2076 3.949113 AGGGTTCGACTAGAGTTGATCTC 59.051 47.826 0.00 0.74 43.05 2.75
1302 2103 1.522580 GCCATCCCTCAAGTCGAGC 60.523 63.158 0.00 0.00 40.78 5.03
1303 2104 1.144936 CCATCCCTCAAGTCGAGCC 59.855 63.158 0.00 0.00 40.78 4.70
1320 2121 3.421826 CGAGCCATCGTTTACATATTCGC 60.422 47.826 0.00 0.00 44.09 4.70
1395 3408 9.830294 AGTTGATGCTTTTTCTTTTTCTTTTTG 57.170 25.926 0.00 0.00 0.00 2.44
1431 3444 6.019779 CTCAAAGCTTGTGAGTACTCTAGT 57.980 41.667 23.01 6.87 38.16 2.57
1432 3445 7.147143 CTCAAAGCTTGTGAGTACTCTAGTA 57.853 40.000 23.01 0.19 38.16 1.82
1455 3468 3.873361 CAGTACATCCGTGCTCAATGAAT 59.127 43.478 0.00 0.00 35.69 2.57
1458 3471 4.142609 ACATCCGTGCTCAATGAATACT 57.857 40.909 5.44 0.00 0.00 2.12
1459 3472 4.122776 ACATCCGTGCTCAATGAATACTC 58.877 43.478 5.44 0.00 0.00 2.59
1460 3473 3.885724 TCCGTGCTCAATGAATACTCA 57.114 42.857 0.00 0.00 35.56 3.41
1462 3475 4.574892 TCCGTGCTCAATGAATACTCAAA 58.425 39.130 0.00 0.00 34.49 2.69
1463 3476 4.631377 TCCGTGCTCAATGAATACTCAAAG 59.369 41.667 0.00 0.00 34.49 2.77
1464 3477 4.337763 CGTGCTCAATGAATACTCAAAGC 58.662 43.478 1.08 1.08 36.74 3.51
1467 3480 5.798934 GTGCTCAATGAATACTCAAAGCTTG 59.201 40.000 0.00 0.00 36.95 4.01
1470 3483 6.348786 GCTCAATGAATACTCAAAGCTTGTGA 60.349 38.462 0.00 5.48 34.91 3.58
1471 3484 7.137490 TCAATGAATACTCAAAGCTTGTGAG 57.863 36.000 24.71 24.71 46.59 3.51
1483 3496 8.492673 TCAAAGCTTGTGAGTACTTATTATGG 57.507 34.615 0.00 0.00 0.00 2.74
1484 3497 8.100791 TCAAAGCTTGTGAGTACTTATTATGGT 58.899 33.333 0.00 0.00 0.00 3.55
1485 3498 8.391106 CAAAGCTTGTGAGTACTTATTATGGTC 58.609 37.037 0.00 0.00 0.00 4.02
1486 3499 6.273825 AGCTTGTGAGTACTTATTATGGTCG 58.726 40.000 0.00 0.00 0.00 4.79
1487 3500 6.040878 GCTTGTGAGTACTTATTATGGTCGT 58.959 40.000 0.00 0.00 0.00 4.34
1488 3501 6.019801 GCTTGTGAGTACTTATTATGGTCGTG 60.020 42.308 0.00 0.00 0.00 4.35
1489 3502 5.345702 TGTGAGTACTTATTATGGTCGTGC 58.654 41.667 0.00 0.00 0.00 5.34
1550 3571 5.401674 GCTTCATTTTTCTTCTTCAGCTGTG 59.598 40.000 14.67 8.33 0.00 3.66
1584 3606 2.595463 GTGGCTGGACTTGCTGCA 60.595 61.111 0.00 0.00 0.00 4.41
1675 3712 3.946907 ACGCTTCCGTCCTTTTCG 58.053 55.556 0.00 0.00 46.39 3.46
1705 3748 3.353600 CGTGAAGCACCATTGGCA 58.646 55.556 1.54 0.00 0.00 4.92
1761 3810 1.594293 CTCCGCAAACCACGAGTGT 60.594 57.895 2.36 0.00 0.00 3.55
1777 3826 0.460284 GTGTGACCGAGATGCCGATT 60.460 55.000 0.00 0.00 0.00 3.34
1919 3980 1.676635 TCGTCGGGGTTGATCGTCT 60.677 57.895 0.00 0.00 0.00 4.18
2020 4081 1.453197 TCTGCTCGGTATCTCGCCA 60.453 57.895 0.00 0.00 0.00 5.69
2068 4129 3.188786 GACAGTGCCGGCATCGTC 61.189 66.667 35.23 33.49 33.95 4.20
2119 4180 1.330655 GGTTGCTCCCGAGGATCAGA 61.331 60.000 0.00 0.00 29.27 3.27
2131 4192 3.815569 GATCAGAGACGCGAGCCGG 62.816 68.421 15.93 0.00 42.52 6.13
2145 4206 4.129737 CCGGTGGCACGAGACGAT 62.130 66.667 12.17 0.00 35.47 3.73
2201 4262 0.172578 CATGTCGAGGGCGTTGAGTA 59.827 55.000 0.00 0.00 38.98 2.59
2266 5023 2.042944 GGGATGGGGCCTTCCAAC 60.043 66.667 22.13 10.16 40.71 3.77
2268 5025 2.626467 GGATGGGGCCTTCCAACCT 61.626 63.158 17.05 0.00 43.80 3.50
2367 5124 1.940294 GCCGATGATGATCTGCTCCAG 60.940 57.143 1.41 0.00 36.25 3.86
2400 5157 0.687757 AATAGCACAGCCGGGAGAGA 60.688 55.000 2.18 0.00 0.00 3.10
2496 5253 1.977293 GAGAAGAAGCCGCCCCTGAT 61.977 60.000 0.00 0.00 0.00 2.90
2508 5265 1.513158 CCCTGATGTCGAGCGTCTT 59.487 57.895 0.00 0.00 34.29 3.01
2578 5335 3.411351 CCGGACGCGTTGAAGTGG 61.411 66.667 15.53 5.56 0.00 4.00
2588 5345 4.704833 TGAAGTGGGCCAGCGAGC 62.705 66.667 6.40 0.00 0.00 5.03
2644 5401 2.354188 CCGTTGTCGCTGACGTCA 60.354 61.111 18.88 18.88 41.18 4.35
2657 5414 2.342279 CGTCAAACTCCCGGAGCA 59.658 61.111 14.86 0.00 32.04 4.26
2679 5436 1.964373 GGATTGACACCAACGCCGT 60.964 57.895 0.00 0.00 34.72 5.68
2782 5539 2.825836 CTCAGGTTCATGCCCGCC 60.826 66.667 0.00 0.00 0.00 6.13
3000 5757 8.698973 TGAGAAGAAGACTAAGAAGAAGAAGA 57.301 34.615 0.00 0.00 0.00 2.87
3003 5760 9.362151 AGAAGAAGACTAAGAAGAAGAAGAAGA 57.638 33.333 0.00 0.00 0.00 2.87
3005 5762 8.122472 AGAAGACTAAGAAGAAGAAGAAGAGG 57.878 38.462 0.00 0.00 0.00 3.69
3006 5763 7.947890 AGAAGACTAAGAAGAAGAAGAAGAGGA 59.052 37.037 0.00 0.00 0.00 3.71
3007 5764 8.485578 AAGACTAAGAAGAAGAAGAAGAGGAA 57.514 34.615 0.00 0.00 0.00 3.36
3008 5765 8.122472 AGACTAAGAAGAAGAAGAAGAGGAAG 57.878 38.462 0.00 0.00 0.00 3.46
3013 5770 2.028567 AGAAGAAGAAGAGGAAGCGTGG 60.029 50.000 0.00 0.00 0.00 4.94
3056 5813 1.381056 ACTCGCCATGCTCCTCTCT 60.381 57.895 0.00 0.00 0.00 3.10
3065 5827 0.707024 TGCTCCTCTCTCCTCCTTCA 59.293 55.000 0.00 0.00 0.00 3.02
3080 5842 5.187967 TCCTCCTTCAATTCTTCACTCCTAC 59.812 44.000 0.00 0.00 0.00 3.18
3088 5850 6.441924 TCAATTCTTCACTCCTACTCCTTGAT 59.558 38.462 0.00 0.00 0.00 2.57
3091 5853 4.707448 TCTTCACTCCTACTCCTTGATCAC 59.293 45.833 0.00 0.00 0.00 3.06
3092 5854 4.323569 TCACTCCTACTCCTTGATCACT 57.676 45.455 0.00 0.00 0.00 3.41
3095 5857 6.253758 TCACTCCTACTCCTTGATCACTTAA 58.746 40.000 0.00 0.00 0.00 1.85
3096 5858 6.897966 TCACTCCTACTCCTTGATCACTTAAT 59.102 38.462 0.00 0.00 0.00 1.40
3097 5859 7.400339 TCACTCCTACTCCTTGATCACTTAATT 59.600 37.037 0.00 0.00 0.00 1.40
3098 5860 8.696374 CACTCCTACTCCTTGATCACTTAATTA 58.304 37.037 0.00 0.00 0.00 1.40
3099 5861 9.268282 ACTCCTACTCCTTGATCACTTAATTAA 57.732 33.333 0.00 0.00 0.00 1.40
3138 5900 5.772825 ACAAGCTTGTTTGAAGCAATAGA 57.227 34.783 26.36 0.00 45.30 1.98
3145 5907 7.040201 AGCTTGTTTGAAGCAATAGAGAAATGA 60.040 33.333 8.98 0.00 45.30 2.57
3298 6061 1.204312 GCGTTTCGAGTTGACTGCC 59.796 57.895 0.00 0.00 0.00 4.85
3300 6063 0.784778 CGTTTCGAGTTGACTGCCTC 59.215 55.000 0.00 0.00 0.00 4.70
3410 6173 1.620323 AGATTCACCCAGCAAAAAGGC 59.380 47.619 0.00 0.00 0.00 4.35
3472 6235 2.032071 CGCCGACCCTCAAACCTT 59.968 61.111 0.00 0.00 0.00 3.50
3488 6251 2.767505 ACCTTCCGCAACTGTTCTAAG 58.232 47.619 0.00 0.00 0.00 2.18
3494 6258 1.226746 GCAACTGTTCTAAGTGCGGT 58.773 50.000 0.00 0.00 0.00 5.68
3572 6340 2.286713 CGCAAACCGAAGACAAACATGA 60.287 45.455 0.00 0.00 40.02 3.07
3609 6377 4.424711 GCACCGATCCCAAGCCCA 62.425 66.667 0.00 0.00 0.00 5.36
3613 6381 1.000896 CCGATCCCAAGCCCACTTT 60.001 57.895 0.00 0.00 32.29 2.66
3624 6392 1.657751 GCCCACTTTTGATCGCCCTC 61.658 60.000 0.00 0.00 0.00 4.30
3636 6405 2.915137 GCCCTCGCCCACCAAAAA 60.915 61.111 0.00 0.00 0.00 1.94
3662 6432 2.663852 CCTCCCGCGTGTTTTCGT 60.664 61.111 4.92 0.00 0.00 3.85
3711 6482 0.622136 ATTCATGCCCAGACAGAGCA 59.378 50.000 0.00 0.00 41.50 4.26
3713 6484 1.196766 TCATGCCCAGACAGAGCAGT 61.197 55.000 0.00 0.00 40.40 4.40
3741 6513 4.789075 CACTGGCGCTGGCATTGC 62.789 66.667 7.64 0.00 42.47 3.56
3785 6557 4.338710 GCCCGCACCACTACCCAA 62.339 66.667 0.00 0.00 0.00 4.12
3792 6564 0.038166 CACCACTACCCAATGCAGGT 59.962 55.000 1.32 1.32 41.64 4.00
3866 6638 2.497107 GCATTGATAGCATGCGGTTT 57.503 45.000 13.01 0.00 0.00 3.27
3913 6685 2.737180 CGTCCCTATGCCGCTCAT 59.263 61.111 0.00 0.00 39.17 2.90
3930 6702 5.473931 CGCTCATGAGTGCTATATAAACCT 58.526 41.667 22.52 0.00 31.68 3.50
3931 6703 5.928839 CGCTCATGAGTGCTATATAAACCTT 59.071 40.000 22.52 0.00 31.68 3.50
3943 6715 2.360439 TAAACCTTTGCCCCGGTGCT 62.360 55.000 11.12 0.00 32.86 4.40
3963 6735 2.492088 CTCCGACCATAGACACAGTCAA 59.508 50.000 0.00 0.00 34.60 3.18
3965 6737 2.231478 CCGACCATAGACACAGTCAACT 59.769 50.000 0.00 0.00 34.60 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
173 174 2.338620 CGGCGTCAACTCCAGACA 59.661 61.111 0.00 0.00 35.77 3.41
241 246 2.125310 CGCAGGCGGTATGGACAA 60.125 61.111 5.63 0.00 35.56 3.18
285 290 2.446848 CCATGGAGGAGGGCATCGT 61.447 63.158 5.56 0.00 41.22 3.73
329 334 3.354948 CATTGGTGGACTCAGGATCAA 57.645 47.619 0.00 0.00 0.00 2.57
624 632 3.385749 TTTCCTCCTCATCCGCCGC 62.386 63.158 0.00 0.00 0.00 6.53
625 633 1.521681 GTTTCCTCCTCATCCGCCG 60.522 63.158 0.00 0.00 0.00 6.46
626 634 0.179070 GAGTTTCCTCCTCATCCGCC 60.179 60.000 0.00 0.00 0.00 6.13
636 653 1.446272 CGCCTCCACGAGTTTCCTC 60.446 63.158 0.00 0.00 34.06 3.71
739 793 7.962995 TCTCTTCAACTTGGTATCAGATAGT 57.037 36.000 0.00 0.00 0.00 2.12
783 838 1.412710 GAGGCTCGATGTTATCCACCA 59.587 52.381 0.00 0.00 0.00 4.17
789 845 3.006323 GGAGATGTGAGGCTCGATGTTAT 59.994 47.826 10.42 0.00 31.95 1.89
797 853 7.505248 TCATCTATATATGGAGATGTGAGGCTC 59.495 40.741 18.67 7.79 46.14 4.70
878 934 5.523916 CGTTAGCTCTGCATGTAAAATAGGT 59.476 40.000 0.00 0.00 0.00 3.08
901 957 1.144565 CCAGACATGCGAGAGAAGCG 61.145 60.000 0.00 0.00 37.44 4.68
913 969 2.804572 CGGAGATTCGCAATCCAGACAT 60.805 50.000 5.57 0.00 38.71 3.06
929 985 4.704833 GCACTTGGGCAGCGGAGA 62.705 66.667 0.00 0.00 0.00 3.71
957 1013 1.209127 GTATTGTGGTGTGTGGCGC 59.791 57.895 0.00 0.00 0.00 6.53
958 1014 1.196808 GAAGTATTGTGGTGTGTGGCG 59.803 52.381 0.00 0.00 0.00 5.69
969 1025 0.460284 CGCCGCTGGAGAAGTATTGT 60.460 55.000 0.00 0.00 0.00 2.71
986 1042 4.481112 CCATGTTTCAGCCGCCGC 62.481 66.667 0.00 0.00 0.00 6.53
1026 1082 2.786495 ATAGCCACTCCGAGCACCG 61.786 63.158 0.00 0.00 38.18 4.94
1048 1104 2.412847 CCGCGTTTCTCTGGAATGTTTC 60.413 50.000 4.92 0.00 0.00 2.78
1052 1108 1.656652 ATCCGCGTTTCTCTGGAATG 58.343 50.000 4.92 0.00 33.48 2.67
1053 1109 2.167693 TGTATCCGCGTTTCTCTGGAAT 59.832 45.455 4.92 0.00 33.48 3.01
1068 1124 1.062488 AGGAGGGCCACCATGTATCC 61.062 60.000 22.59 9.42 40.13 2.59
1073 1129 1.150081 GATGAGGAGGGCCACCATG 59.850 63.158 22.59 0.00 40.13 3.66
1074 1130 2.446848 CGATGAGGAGGGCCACCAT 61.447 63.158 22.59 7.68 40.13 3.55
1130 1186 0.310543 GCATGCCGTTGTTGTCTGAA 59.689 50.000 6.36 0.00 0.00 3.02
1135 1191 4.341502 GCCGCATGCCGTTGTTGT 62.342 61.111 13.15 0.00 34.38 3.32
1162 1218 4.124351 CTCGACCCGCGCCACTAA 62.124 66.667 0.00 0.00 40.61 2.24
1172 1228 3.948719 TTGCCACCACCTCGACCC 61.949 66.667 0.00 0.00 0.00 4.46
1175 1231 4.980805 GCGTTGCCACCACCTCGA 62.981 66.667 0.00 0.00 0.00 4.04
1184 1240 2.979676 CTCTGCCTTGCGTTGCCA 60.980 61.111 0.00 0.00 0.00 4.92
1190 1246 1.919956 CTCTTTGCCTCTGCCTTGCG 61.920 60.000 0.00 0.00 36.33 4.85
1210 1266 4.363990 CTCCACGTCAGCACCGCT 62.364 66.667 0.00 0.00 40.77 5.52
1232 1288 4.215613 CCTCAAAAGGGTTTAACTTCTCGG 59.784 45.833 0.00 0.00 39.21 4.63
1261 2062 3.974719 TGGAGCTGAGATCAACTCTAGT 58.025 45.455 11.81 0.00 45.13 2.57
1275 2076 1.153005 GAGGGATGGCTTGGAGCTG 60.153 63.158 0.00 0.00 41.99 4.24
1302 2103 4.913345 TCTACGCGAATATGTAAACGATGG 59.087 41.667 15.93 0.00 0.00 3.51
1303 2104 6.612855 ATCTACGCGAATATGTAAACGATG 57.387 37.500 15.93 0.00 0.00 3.84
1314 2115 8.752254 CACTTAGAAATCAAATCTACGCGAATA 58.248 33.333 15.93 0.00 0.00 1.75
1370 3383 9.824534 TCAAAAAGAAAAAGAAAAAGCATCAAC 57.175 25.926 0.00 0.00 0.00 3.18
1372 3385 9.434420 TCTCAAAAAGAAAAAGAAAAAGCATCA 57.566 25.926 0.00 0.00 0.00 3.07
1395 3408 9.155975 TCACAAGCTTTGAGTATTAATCTTCTC 57.844 33.333 0.00 0.14 0.00 2.87
1427 3440 3.626217 TGAGCACGGATGTACTGTACTAG 59.374 47.826 17.98 9.43 36.20 2.57
1430 3443 2.933495 TGAGCACGGATGTACTGTAC 57.067 50.000 10.98 10.98 36.20 2.90
1431 3444 3.445805 TCATTGAGCACGGATGTACTGTA 59.554 43.478 0.00 0.00 36.20 2.74
1432 3445 2.233676 TCATTGAGCACGGATGTACTGT 59.766 45.455 0.00 0.00 38.85 3.55
1433 3446 2.892374 TCATTGAGCACGGATGTACTG 58.108 47.619 0.00 0.00 0.00 2.74
1434 3447 3.610040 TTCATTGAGCACGGATGTACT 57.390 42.857 0.00 0.00 0.00 2.73
1435 3448 5.050490 AGTATTCATTGAGCACGGATGTAC 58.950 41.667 0.00 0.00 0.00 2.90
1458 3471 8.100791 ACCATAATAAGTACTCACAAGCTTTGA 58.899 33.333 0.00 3.72 0.00 2.69
1459 3472 8.268850 ACCATAATAAGTACTCACAAGCTTTG 57.731 34.615 0.00 0.00 0.00 2.77
1460 3473 7.277981 CGACCATAATAAGTACTCACAAGCTTT 59.722 37.037 0.00 0.00 0.00 3.51
1462 3475 6.127423 ACGACCATAATAAGTACTCACAAGCT 60.127 38.462 0.00 0.00 0.00 3.74
1463 3476 6.019801 CACGACCATAATAAGTACTCACAAGC 60.020 42.308 0.00 0.00 0.00 4.01
1464 3477 6.019801 GCACGACCATAATAAGTACTCACAAG 60.020 42.308 0.00 0.00 0.00 3.16
1467 3480 5.231568 GTGCACGACCATAATAAGTACTCAC 59.768 44.000 0.00 0.00 0.00 3.51
1470 3483 4.142315 ACGTGCACGACCATAATAAGTACT 60.142 41.667 42.94 14.05 43.02 2.73
1471 3484 4.027132 CACGTGCACGACCATAATAAGTAC 60.027 45.833 42.94 0.00 43.02 2.73
1472 3485 4.106909 CACGTGCACGACCATAATAAGTA 58.893 43.478 42.94 0.00 43.02 2.24
1474 3487 2.285602 GCACGTGCACGACCATAATAAG 60.286 50.000 42.94 19.07 43.02 1.73
1475 3488 1.661617 GCACGTGCACGACCATAATAA 59.338 47.619 42.94 0.00 43.02 1.40
1476 3489 1.134936 AGCACGTGCACGACCATAATA 60.135 47.619 42.94 0.00 45.16 0.98
1477 3490 0.391130 AGCACGTGCACGACCATAAT 60.391 50.000 42.94 18.38 45.16 1.28
1480 3493 2.738521 GAGCACGTGCACGACCAT 60.739 61.111 42.94 25.31 45.16 3.55
1481 3494 4.961511 GGAGCACGTGCACGACCA 62.962 66.667 42.94 0.00 45.16 4.02
1482 3495 3.277211 TAGGAGCACGTGCACGACC 62.277 63.158 42.94 33.35 45.16 4.79
1483 3496 2.087009 GTAGGAGCACGTGCACGAC 61.087 63.158 42.94 31.99 45.16 4.34
1484 3497 2.257371 GTAGGAGCACGTGCACGA 59.743 61.111 42.94 25.21 45.16 4.35
1485 3498 3.172575 CGTAGGAGCACGTGCACG 61.173 66.667 39.21 35.99 45.16 5.34
1486 3499 2.537792 TAGCGTAGGAGCACGTGCAC 62.538 60.000 39.21 33.13 43.79 4.57
1487 3500 1.663379 ATAGCGTAGGAGCACGTGCA 61.663 55.000 39.21 18.73 43.79 4.57
1488 3501 0.935366 GATAGCGTAGGAGCACGTGC 60.935 60.000 32.79 32.79 43.79 5.34
1489 3502 0.657659 CGATAGCGTAGGAGCACGTG 60.658 60.000 12.28 12.28 43.79 4.49
1550 3571 1.614317 CCACCCCTCATGAAGTGGTTC 60.614 57.143 22.47 0.00 43.91 3.62
1567 3588 2.595463 TGCAGCAAGTCCAGCCAC 60.595 61.111 0.00 0.00 0.00 5.01
1584 3606 3.654414 GTCAAGGAGAACAACATCGTCT 58.346 45.455 0.00 0.00 0.00 4.18
1689 3732 1.134946 GGTATGCCAATGGTGCTTCAC 59.865 52.381 0.00 0.00 34.09 3.18
1691 3734 1.473258 TGGTATGCCAATGGTGCTTC 58.527 50.000 0.00 0.00 42.83 3.86
1692 3735 3.687847 TGGTATGCCAATGGTGCTT 57.312 47.368 0.00 0.00 42.83 3.91
1750 3793 1.105167 TCTCGGTCACACTCGTGGTT 61.105 55.000 1.77 0.00 43.79 3.67
1751 3794 0.894184 ATCTCGGTCACACTCGTGGT 60.894 55.000 1.77 0.00 43.79 4.16
1761 3810 1.521457 GCAATCGGCATCTCGGTCA 60.521 57.895 0.00 0.00 43.97 4.02
1820 3869 0.035458 CGGGCTTCATCCTCCATACC 59.965 60.000 0.00 0.00 0.00 2.73
1999 4060 1.227639 GCGAGATACCGAGCAGACTA 58.772 55.000 0.00 0.00 0.00 2.59
2002 4063 1.448119 CTGGCGAGATACCGAGCAGA 61.448 60.000 0.00 0.00 0.00 4.26
2003 4064 1.007964 CTGGCGAGATACCGAGCAG 60.008 63.158 0.00 0.00 0.00 4.24
2020 4081 2.903135 CCTCTCCAACAACTTCCTCTCT 59.097 50.000 0.00 0.00 0.00 3.10
2109 4170 1.278337 CTCGCGTCTCTGATCCTCG 59.722 63.158 5.77 0.00 0.00 4.63
2140 4201 3.843117 GATCCCGACCGGCATCGTC 62.843 68.421 12.83 1.52 40.59 4.20
2141 4202 3.912907 GATCCCGACCGGCATCGT 61.913 66.667 12.83 0.00 40.59 3.73
2184 4245 0.038892 GTTACTCAACGCCCTCGACA 60.039 55.000 0.00 0.00 39.41 4.35
2195 4256 2.945615 GCGGTTGCGCGTTACTCAA 61.946 57.895 8.43 0.00 0.00 3.02
2196 4257 3.408020 GCGGTTGCGCGTTACTCA 61.408 61.111 8.43 0.00 0.00 3.41
2400 5157 2.980233 GCAACAACCTCAGCGGCT 60.980 61.111 0.00 0.00 35.61 5.52
2458 5215 2.190578 GGCACGATCCCCAAGAGG 59.809 66.667 0.00 0.00 0.00 3.69
2496 5253 1.210413 GAGCTCAAGACGCTCGACA 59.790 57.895 9.40 0.00 43.69 4.35
2508 5265 2.666190 GCAACGCCACAGAGCTCA 60.666 61.111 17.77 0.00 0.00 4.26
2560 5317 2.355363 CACTTCAACGCGTCCGGA 60.355 61.111 14.44 8.32 39.22 5.14
2644 5401 2.584608 CCGATGCTCCGGGAGTTT 59.415 61.111 24.30 12.63 45.43 2.66
2657 5414 1.024579 GCGTTGGTGTCAATCCCGAT 61.025 55.000 0.00 0.00 35.10 4.18
2715 5472 4.421479 CCGCGCTCAACTCGGTCT 62.421 66.667 5.56 0.00 41.84 3.85
2782 5539 2.358737 GTCACCGGCCTTGACCTG 60.359 66.667 19.17 0.00 37.93 4.00
3000 5757 1.968540 GCAAGCCACGCTTCCTCTT 60.969 57.895 0.00 0.00 46.77 2.85
3003 5760 2.670934 CAGCAAGCCACGCTTCCT 60.671 61.111 0.00 0.00 46.77 3.36
3005 5762 3.319926 GAGCAGCAAGCCACGCTTC 62.320 63.158 0.00 0.00 46.77 3.86
3051 5808 5.187576 AGTGAAGAATTGAAGGAGGAGAGAG 59.812 44.000 0.00 0.00 0.00 3.20
3056 5813 4.171234 AGGAGTGAAGAATTGAAGGAGGA 58.829 43.478 0.00 0.00 0.00 3.71
3065 5827 6.441924 TGATCAAGGAGTAGGAGTGAAGAATT 59.558 38.462 0.00 0.00 0.00 2.17
3080 5842 9.831737 CACAAAGTTAATTAAGTGATCAAGGAG 57.168 33.333 6.31 0.00 31.87 3.69
3095 5857 9.030301 GCTTGTTGATGTAAACACAAAGTTAAT 57.970 29.630 0.00 0.00 40.26 1.40
3096 5858 8.247562 AGCTTGTTGATGTAAACACAAAGTTAA 58.752 29.630 0.00 0.00 40.26 2.01
3097 5859 7.767261 AGCTTGTTGATGTAAACACAAAGTTA 58.233 30.769 0.00 0.00 40.26 2.24
3098 5860 6.630071 AGCTTGTTGATGTAAACACAAAGTT 58.370 32.000 0.00 0.00 43.89 2.66
3099 5861 6.207691 AGCTTGTTGATGTAAACACAAAGT 57.792 33.333 0.00 0.00 39.70 2.66
3138 5900 5.635120 AGCTGTTAGTTTCCCTTCATTTCT 58.365 37.500 0.00 0.00 0.00 2.52
3145 5907 4.367039 TGCTTAGCTGTTAGTTTCCCTT 57.633 40.909 5.60 0.00 0.00 3.95
3275 6038 2.032894 CAGTCAACTCGAAACGCAACAT 60.033 45.455 0.00 0.00 0.00 2.71
3298 6061 1.512310 GAGTCGTCAACTCGGCGAG 60.512 63.158 33.42 33.42 44.79 5.03
3410 6173 7.701809 TTTTTACGAAATTTACAGGCTTTGG 57.298 32.000 0.00 0.00 0.00 3.28
3472 6235 1.508632 GCACTTAGAACAGTTGCGGA 58.491 50.000 0.00 0.00 0.00 5.54
3488 6251 2.461110 CGTTGGATGGCTACCGCAC 61.461 63.158 0.00 0.00 38.10 5.34
3494 6258 1.069090 GGATCGCGTTGGATGGCTA 59.931 57.895 5.77 0.00 0.00 3.93
3572 6340 2.154462 CGGACTCATGCAAACCTTCTT 58.846 47.619 0.00 0.00 0.00 2.52
3584 6352 2.797278 GGGATCGGTGCGGACTCAT 61.797 63.158 7.11 0.00 0.00 2.90
3585 6353 3.458163 GGGATCGGTGCGGACTCA 61.458 66.667 7.11 0.00 0.00 3.41
3609 6377 1.745489 GGCGAGGGCGATCAAAAGT 60.745 57.895 0.00 0.00 41.24 2.66
3613 6381 4.467084 GTGGGCGAGGGCGATCAA 62.467 66.667 0.00 0.00 41.24 2.57
3662 6432 2.722487 GCTCTAGAGCGGCGCTAA 59.278 61.111 36.55 24.25 45.29 3.09
3702 6473 4.427661 GCCGCGACTGCTCTGTCT 62.428 66.667 8.23 0.00 39.65 3.41
3774 6546 0.038166 CACCTGCATTGGGTAGTGGT 59.962 55.000 0.00 0.00 35.00 4.16
3777 6549 1.003580 CAGTCACCTGCATTGGGTAGT 59.996 52.381 0.00 0.00 35.00 2.73
3780 6552 4.828409 CAGTCACCTGCATTGGGT 57.172 55.556 0.00 0.00 37.59 4.51
3792 6564 0.380378 GTTTGAACGCAAGGCAGTCA 59.620 50.000 0.00 0.00 46.39 3.41
3889 6661 2.750350 GCATAGGGACGGATGGGG 59.250 66.667 0.00 0.00 0.00 4.96
3913 6685 5.130350 GGGCAAAGGTTTATATAGCACTCA 58.870 41.667 0.00 0.00 0.00 3.41
3943 6715 2.209690 TGACTGTGTCTATGGTCGGA 57.790 50.000 0.00 0.00 33.15 4.55


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

AutoCloner maintained by Alex Coulton.