Multiple sequence alignment - TraesCS6A01G146800

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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 TraesCS6A01G146800 chr6A 100.000 3887 0 0 1 3887 125884660 125880774 0.000000e+00 7179
1 TraesCS6A01G146800 chr6D 89.308 2357 118 52 566 2885 104301127 104298868 0.000000e+00 2833
2 TraesCS6A01G146800 chr6D 88.958 960 94 11 2931 3886 146943759 146942808 0.000000e+00 1175
3 TraesCS6A01G146800 chr6D 88.425 959 101 8 2931 3886 328617707 328616756 0.000000e+00 1147
4 TraesCS6A01G146800 chr6D 88.150 962 99 14 2928 3886 460841402 460840453 0.000000e+00 1131
5 TraesCS6A01G146800 chr6D 86.301 584 31 13 1 555 104301793 104301230 1.200000e-164 590
6 TraesCS6A01G146800 chr6B 88.603 1790 118 31 1168 2931 189530454 189528725 0.000000e+00 2097
7 TraesCS6A01G146800 chr6B 88.935 958 96 10 2934 3886 162712236 162713188 0.000000e+00 1173
8 TraesCS6A01G146800 chr6B 86.899 977 116 10 2916 3886 55123152 55124122 0.000000e+00 1085
9 TraesCS6A01G146800 chr6B 88.772 570 21 12 13 561 189531633 189531086 0.000000e+00 658
10 TraesCS6A01G146800 chr6B 88.288 555 34 16 566 1118 189530988 189530463 1.520000e-178 636
11 TraesCS6A01G146800 chr6B 83.065 248 38 4 2916 3161 438906390 438906635 5.050000e-54 222
12 TraesCS6A01G146800 chr7D 90.208 960 88 6 2929 3886 585426837 585427792 0.000000e+00 1247
13 TraesCS6A01G146800 chr7D 89.062 960 101 4 2928 3886 4237728 4238684 0.000000e+00 1188
14 TraesCS6A01G146800 chr5A 88.482 955 100 10 2936 3886 494284230 494283282 0.000000e+00 1146
15 TraesCS6A01G146800 chr1D 88.041 970 106 9 2920 3886 58563862 58564824 0.000000e+00 1140
16 TraesCS6A01G146800 chr1D 88.653 943 98 8 2948 3886 250735006 250734069 0.000000e+00 1140


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 TraesCS6A01G146800 chr6A 125880774 125884660 3886 True 7179.000000 7179 100.000000 1 3887 1 chr6A.!!$R1 3886
1 TraesCS6A01G146800 chr6D 104298868 104301793 2925 True 1711.500000 2833 87.804500 1 2885 2 chr6D.!!$R4 2884
2 TraesCS6A01G146800 chr6D 146942808 146943759 951 True 1175.000000 1175 88.958000 2931 3886 1 chr6D.!!$R1 955
3 TraesCS6A01G146800 chr6D 328616756 328617707 951 True 1147.000000 1147 88.425000 2931 3886 1 chr6D.!!$R2 955
4 TraesCS6A01G146800 chr6D 460840453 460841402 949 True 1131.000000 1131 88.150000 2928 3886 1 chr6D.!!$R3 958
5 TraesCS6A01G146800 chr6B 162712236 162713188 952 False 1173.000000 1173 88.935000 2934 3886 1 chr6B.!!$F2 952
6 TraesCS6A01G146800 chr6B 189528725 189531633 2908 True 1130.333333 2097 88.554333 13 2931 3 chr6B.!!$R1 2918
7 TraesCS6A01G146800 chr6B 55123152 55124122 970 False 1085.000000 1085 86.899000 2916 3886 1 chr6B.!!$F1 970
8 TraesCS6A01G146800 chr7D 585426837 585427792 955 False 1247.000000 1247 90.208000 2929 3886 1 chr7D.!!$F2 957
9 TraesCS6A01G146800 chr7D 4237728 4238684 956 False 1188.000000 1188 89.062000 2928 3886 1 chr7D.!!$F1 958
10 TraesCS6A01G146800 chr5A 494283282 494284230 948 True 1146.000000 1146 88.482000 2936 3886 1 chr5A.!!$R1 950
11 TraesCS6A01G146800 chr1D 58563862 58564824 962 False 1140.000000 1140 88.041000 2920 3886 1 chr1D.!!$F1 966
12 TraesCS6A01G146800 chr1D 250734069 250735006 937 True 1140.000000 1140 88.653000 2948 3886 1 chr1D.!!$R1 938

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
101 102 0.177141 GCCGTCTTGCCATACTGGTA 59.823 55.0 0.00 0.00 40.46 3.25 F
397 421 0.533755 GGTCCTGCCCGATCTTGATG 60.534 60.0 0.00 0.00 0.00 3.07 F
1552 1697 0.874390 TGAGAATCACTTTGGCGTGC 59.126 50.0 0.00 0.00 42.56 5.34 F
2692 2866 0.230515 CGTGCTATGTACATGCTGCG 59.769 55.0 18.81 19.71 0.00 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1122 1260 0.180171 CGGGCAGAGAGAGAGAGAGA 59.820 60.0 0.00 0.00 0.00 3.10 R
2247 2421 0.171231 TCCAGCTCGATGAACGACTG 59.829 55.0 0.00 0.00 46.45 3.51 R
2720 2894 0.320374 CAGGCGTCAACTGGACCTAA 59.680 55.0 0.00 0.00 43.95 2.69 R
3652 3846 0.826715 CGTGGAGGACATGATGACCT 59.173 55.0 16.06 16.06 44.85 3.85 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
81 82 1.738099 CTCGTCTGCTTTGTCGGGG 60.738 63.158 0.00 0.00 0.00 5.73
99 100 3.813596 GCCGTCTTGCCATACTGG 58.186 61.111 0.00 0.00 41.55 4.00
100 101 1.078426 GCCGTCTTGCCATACTGGT 60.078 57.895 0.00 0.00 40.46 4.00
101 102 0.177141 GCCGTCTTGCCATACTGGTA 59.823 55.000 0.00 0.00 40.46 3.25
135 136 2.574018 CCTGCGGACTGGTCTGTGA 61.574 63.158 10.69 0.00 38.23 3.58
149 154 2.676839 GTCTGTGAACTCATGCATGGAG 59.323 50.000 25.97 21.69 38.36 3.86
150 155 2.568509 TCTGTGAACTCATGCATGGAGA 59.431 45.455 25.97 11.74 36.26 3.71
151 156 3.008266 TCTGTGAACTCATGCATGGAGAA 59.992 43.478 25.97 6.24 36.26 2.87
152 157 3.340928 TGTGAACTCATGCATGGAGAAG 58.659 45.455 25.97 17.73 36.26 2.85
307 312 1.889573 GCTGCTAATCAGACGGGGC 60.890 63.158 0.00 0.00 45.72 5.80
395 419 3.309582 GGTCCTGCCCGATCTTGA 58.690 61.111 0.00 0.00 0.00 3.02
396 420 1.832912 GGTCCTGCCCGATCTTGAT 59.167 57.895 0.00 0.00 0.00 2.57
397 421 0.533755 GGTCCTGCCCGATCTTGATG 60.534 60.000 0.00 0.00 0.00 3.07
398 422 1.146930 TCCTGCCCGATCTTGATGC 59.853 57.895 0.00 0.00 0.00 3.91
402 426 2.247437 GCCCGATCTTGATGCGACC 61.247 63.158 0.00 0.00 0.00 4.79
439 463 2.311542 AGAGGTGCCCATGTTGGATTTA 59.688 45.455 0.00 0.00 40.96 1.40
441 465 1.136891 GGTGCCCATGTTGGATTTAGC 59.863 52.381 0.00 0.00 40.96 3.09
442 466 1.824230 GTGCCCATGTTGGATTTAGCA 59.176 47.619 0.00 0.00 40.96 3.49
443 467 2.101783 TGCCCATGTTGGATTTAGCAG 58.898 47.619 0.00 0.00 40.96 4.24
444 468 2.102578 GCCCATGTTGGATTTAGCAGT 58.897 47.619 0.00 0.00 40.96 4.40
445 469 3.287222 GCCCATGTTGGATTTAGCAGTA 58.713 45.455 0.00 0.00 40.96 2.74
446 470 3.066760 GCCCATGTTGGATTTAGCAGTAC 59.933 47.826 0.00 0.00 40.96 2.73
450 474 6.349300 CCATGTTGGATTTAGCAGTACTACT 58.651 40.000 0.31 0.31 40.96 2.57
564 599 5.108385 GCACTTGCACTTACATTAACAGT 57.892 39.130 0.00 0.00 41.59 3.55
591 723 3.129502 CAGTGGCATGGGAGCACG 61.130 66.667 0.00 0.00 35.83 5.34
672 804 3.131478 GCCCCCGTTGAACCGATG 61.131 66.667 0.00 0.00 0.00 3.84
673 805 2.437716 CCCCCGTTGAACCGATGG 60.438 66.667 0.00 0.00 0.00 3.51
674 806 2.349755 CCCCGTTGAACCGATGGT 59.650 61.111 0.00 0.00 37.65 3.55
675 807 1.743995 CCCCGTTGAACCGATGGTC 60.744 63.158 0.00 0.00 33.12 4.02
676 808 1.295423 CCCGTTGAACCGATGGTCT 59.705 57.895 0.00 0.00 33.12 3.85
687 824 2.234143 CCGATGGTCTGATGCTCTCTA 58.766 52.381 0.00 0.00 0.00 2.43
732 869 4.803426 GAGGCCTGAGCACGACCG 62.803 72.222 12.00 0.00 42.56 4.79
811 948 3.549471 CCAGTTGTGAGAAGATTCGATCG 59.451 47.826 9.36 9.36 0.00 3.69
814 951 4.623167 AGTTGTGAGAAGATTCGATCGTTG 59.377 41.667 15.94 0.00 0.00 4.10
815 952 3.511699 TGTGAGAAGATTCGATCGTTGG 58.488 45.455 15.94 0.00 0.00 3.77
849 986 2.249844 TCCTGTTCTTTCCAACGACC 57.750 50.000 0.00 0.00 0.00 4.79
863 1000 2.821366 GACCTCCTCCGTCGCGTA 60.821 66.667 5.77 0.00 0.00 4.42
864 1001 3.105852 GACCTCCTCCGTCGCGTAC 62.106 68.421 5.77 1.94 0.00 3.67
1084 1222 3.092511 TCCTGCCCATCCTCTGCC 61.093 66.667 0.00 0.00 0.00 4.85
1110 1248 4.785346 ATCTCTCTTGCTCTCTCTCTCT 57.215 45.455 0.00 0.00 0.00 3.10
1111 1249 4.142609 TCTCTCTTGCTCTCTCTCTCTC 57.857 50.000 0.00 0.00 0.00 3.20
1112 1250 3.776969 TCTCTCTTGCTCTCTCTCTCTCT 59.223 47.826 0.00 0.00 0.00 3.10
1113 1251 4.125703 CTCTCTTGCTCTCTCTCTCTCTC 58.874 52.174 0.00 0.00 0.00 3.20
1114 1252 3.776969 TCTCTTGCTCTCTCTCTCTCTCT 59.223 47.826 0.00 0.00 0.00 3.10
1115 1253 4.125703 CTCTTGCTCTCTCTCTCTCTCTC 58.874 52.174 0.00 0.00 0.00 3.20
1116 1254 3.776969 TCTTGCTCTCTCTCTCTCTCTCT 59.223 47.826 0.00 0.00 0.00 3.10
1117 1255 3.827008 TGCTCTCTCTCTCTCTCTCTC 57.173 52.381 0.00 0.00 0.00 3.20
1118 1256 3.378512 TGCTCTCTCTCTCTCTCTCTCT 58.621 50.000 0.00 0.00 0.00 3.10
1119 1257 3.386078 TGCTCTCTCTCTCTCTCTCTCTC 59.614 52.174 0.00 0.00 0.00 3.20
1120 1258 3.640967 GCTCTCTCTCTCTCTCTCTCTCT 59.359 52.174 0.00 0.00 0.00 3.10
1121 1259 4.261994 GCTCTCTCTCTCTCTCTCTCTCTC 60.262 54.167 0.00 0.00 0.00 3.20
1122 1260 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
1123 1261 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1124 1262 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1125 1263 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1126 1264 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1127 1265 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1128 1266 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1175 1313 2.649349 GACTCTAGCTCGTGCGCG 60.649 66.667 14.79 14.79 45.42 6.86
1460 1598 1.606889 GTCCACGGACTCCTCAGGT 60.607 63.158 9.04 0.00 41.57 4.00
1461 1599 1.606601 TCCACGGACTCCTCAGGTG 60.607 63.158 0.00 0.00 0.00 4.00
1462 1600 2.262915 CACGGACTCCTCAGGTGC 59.737 66.667 0.00 0.00 0.00 5.01
1464 1602 3.374402 CGGACTCCTCAGGTGCGT 61.374 66.667 0.00 0.00 42.05 5.24
1465 1603 2.574399 GGACTCCTCAGGTGCGTC 59.426 66.667 0.00 0.00 0.00 5.19
1486 1624 4.077188 GTGCGCTCGTTGGTGCTC 62.077 66.667 9.73 5.65 42.46 4.26
1494 1639 1.813178 CTCGTTGGTGCTCTCAGTCTA 59.187 52.381 0.00 0.00 0.00 2.59
1495 1640 1.540267 TCGTTGGTGCTCTCAGTCTAC 59.460 52.381 0.00 0.00 0.00 2.59
1496 1641 1.269723 CGTTGGTGCTCTCAGTCTACA 59.730 52.381 0.00 0.00 0.00 2.74
1497 1642 2.094494 CGTTGGTGCTCTCAGTCTACAT 60.094 50.000 0.00 0.00 0.00 2.29
1498 1643 3.257393 GTTGGTGCTCTCAGTCTACATG 58.743 50.000 0.00 0.00 0.00 3.21
1499 1644 2.529632 TGGTGCTCTCAGTCTACATGT 58.470 47.619 2.69 2.69 0.00 3.21
1500 1645 2.493675 TGGTGCTCTCAGTCTACATGTC 59.506 50.000 0.00 0.00 0.00 3.06
1501 1646 2.757868 GGTGCTCTCAGTCTACATGTCT 59.242 50.000 0.00 0.00 0.00 3.41
1502 1647 3.948473 GGTGCTCTCAGTCTACATGTCTA 59.052 47.826 0.00 0.00 0.00 2.59
1503 1648 4.036262 GGTGCTCTCAGTCTACATGTCTAG 59.964 50.000 0.00 0.00 0.00 2.43
1522 1667 3.878160 AGTTACAGCTAGCCTCTGTTC 57.122 47.619 12.13 6.71 41.61 3.18
1536 1681 3.437428 CTCTGTTCGCTGAATCTCTGAG 58.563 50.000 0.00 0.00 0.00 3.35
1540 1685 4.428209 TGTTCGCTGAATCTCTGAGAATC 58.572 43.478 12.00 13.38 36.78 2.52
1542 1687 4.039151 TCGCTGAATCTCTGAGAATCAC 57.961 45.455 18.93 14.79 42.56 3.06
1543 1688 3.698539 TCGCTGAATCTCTGAGAATCACT 59.301 43.478 18.93 0.00 42.56 3.41
1546 1691 5.220434 CGCTGAATCTCTGAGAATCACTTTG 60.220 44.000 18.93 11.78 42.56 2.77
1552 1697 0.874390 TGAGAATCACTTTGGCGTGC 59.126 50.000 0.00 0.00 42.56 5.34
1559 1704 2.339348 CTTTGGCGTGCCATTGCA 59.661 55.556 15.40 0.00 46.64 4.08
1567 1712 3.863543 TGCCATTGCATCGTCGCG 61.864 61.111 0.00 0.00 44.23 5.87
1598 1743 2.796651 CAGCAGGATGGAAAGCGC 59.203 61.111 0.00 0.00 35.86 5.92
1669 1814 1.118965 TGTTCCTCCTCGCCAAGACA 61.119 55.000 0.00 0.00 0.00 3.41
1808 1953 4.681978 AGTGCCACGCTTCGTCCC 62.682 66.667 0.00 0.00 38.32 4.46
1893 2038 1.135053 TCGCCATTTCCGTCGTGATAA 60.135 47.619 0.00 0.00 0.00 1.75
1897 2042 0.928229 ATTTCCGTCGTGATAAGCGC 59.072 50.000 0.00 0.00 0.00 5.92
1909 2054 3.982372 TAAGCGCGCTGGACGGAAG 62.982 63.158 37.24 0.00 43.93 3.46
2064 2230 3.743017 GGGCTTCATGGCTGGGGA 61.743 66.667 0.00 0.00 41.48 4.81
2071 2237 1.304713 CATGGCTGGGGAGCAGTTT 60.305 57.895 0.00 0.00 36.33 2.66
2121 2291 3.081061 CACCCGAGGTTTGAATGATTGA 58.919 45.455 0.00 0.00 31.02 2.57
2130 2300 5.587844 AGGTTTGAATGATTGATTCCTCTCG 59.412 40.000 0.00 0.00 40.00 4.04
2131 2301 5.269313 GTTTGAATGATTGATTCCTCTCGC 58.731 41.667 0.00 0.00 40.00 5.03
2139 2309 3.079960 TGATTCCTCTCGCGAATACAC 57.920 47.619 11.33 0.00 30.08 2.90
2140 2310 2.688446 TGATTCCTCTCGCGAATACACT 59.312 45.455 11.33 0.00 30.08 3.55
2144 2314 1.471964 CTCTCGCGAATACACTGAGC 58.528 55.000 11.33 0.00 0.00 4.26
2220 2394 3.296943 CGTGTTGTGTTTCTTTGTGTTCG 59.703 43.478 0.00 0.00 0.00 3.95
2226 2400 4.452795 TGTGTTTCTTTGTGTTCGTCTGAA 59.547 37.500 0.00 0.00 0.00 3.02
2309 2483 1.680989 TAGAGGCGGCTACAGTGCA 60.681 57.895 13.24 0.00 34.04 4.57
2341 2515 0.461961 GATTCAGAGGACGGACAGGG 59.538 60.000 0.00 0.00 0.00 4.45
2342 2516 0.978146 ATTCAGAGGACGGACAGGGG 60.978 60.000 0.00 0.00 0.00 4.79
2343 2517 3.077556 CAGAGGACGGACAGGGGG 61.078 72.222 0.00 0.00 0.00 5.40
2344 2518 3.273654 AGAGGACGGACAGGGGGA 61.274 66.667 0.00 0.00 0.00 4.81
2345 2519 2.760385 GAGGACGGACAGGGGGAG 60.760 72.222 0.00 0.00 0.00 4.30
2346 2520 4.400251 AGGACGGACAGGGGGAGG 62.400 72.222 0.00 0.00 0.00 4.30
2353 2527 2.540910 ACAGGGGGAGGAGGAGGA 60.541 66.667 0.00 0.00 0.00 3.71
2362 2536 2.018086 AGGAGGAGGAGGAGGAGGG 61.018 68.421 0.00 0.00 0.00 4.30
2594 2768 4.751600 TGATCAATATCGACCGTACGTAGT 59.248 41.667 15.21 5.63 38.83 2.73
2595 2769 5.925969 TGATCAATATCGACCGTACGTAGTA 59.074 40.000 15.21 0.39 37.08 1.82
2596 2770 6.128822 TGATCAATATCGACCGTACGTAGTAC 60.129 42.308 15.21 0.57 46.40 2.73
2638 2812 2.820197 TGCGACAGTGAGTAGTGAATCT 59.180 45.455 0.00 0.00 0.00 2.40
2639 2813 3.119814 TGCGACAGTGAGTAGTGAATCTC 60.120 47.826 0.00 0.00 0.00 2.75
2640 2814 3.127895 GCGACAGTGAGTAGTGAATCTCT 59.872 47.826 0.00 0.00 0.00 3.10
2679 2853 2.882876 GAGAGCCCGAACGTGCTA 59.117 61.111 4.07 0.00 38.11 3.49
2692 2866 0.230515 CGTGCTATGTACATGCTGCG 59.769 55.000 18.81 19.71 0.00 5.18
2720 2894 1.170290 CGGGTGAACGGGAAAAGCTT 61.170 55.000 0.00 0.00 0.00 3.74
2735 2910 2.457366 AGCTTTAGGTCCAGTTGACG 57.543 50.000 0.00 0.00 45.46 4.35
2779 2954 0.107410 CTTGGTGCTGGCGGGTATAA 60.107 55.000 0.00 0.00 0.00 0.98
2788 2963 3.149196 CTGGCGGGTATAATGCAGAAAT 58.851 45.455 0.00 0.00 0.00 2.17
2790 2965 4.069304 TGGCGGGTATAATGCAGAAATAC 58.931 43.478 0.00 0.00 0.00 1.89
2845 3020 5.156355 AGCGCTGATCAAACAATTACTTTG 58.844 37.500 10.39 2.61 41.36 2.77
2861 3036 9.698617 CAATTACTTTGTTAATACGTTAGCTCC 57.301 33.333 0.00 0.00 0.00 4.70
2885 3063 8.536175 TCCTGTGACATAAAATGTGTATCACTA 58.464 33.333 0.00 0.00 45.03 2.74
2886 3064 8.604035 CCTGTGACATAAAATGTGTATCACTAC 58.396 37.037 0.00 0.00 45.03 2.73
2890 3068 9.936759 TGACATAAAATGTGTATCACTACAGAA 57.063 29.630 0.00 0.00 45.03 3.02
2896 3074 7.724305 AATGTGTATCACTACAGAAACGTTT 57.276 32.000 14.57 14.57 38.51 3.60
2900 3078 6.018507 GTGTATCACTACAGAAACGTTTGGTT 60.019 38.462 20.10 4.20 38.51 3.67
2901 3079 6.539464 TGTATCACTACAGAAACGTTTGGTTT 59.461 34.615 20.10 1.05 40.90 3.27
2902 3080 7.466185 TGTATCACTACAGAAACGTTTGGTTTG 60.466 37.037 20.10 15.16 39.62 2.93
2970 3148 1.281656 CCAAACGGACGGCACTTTC 59.718 57.895 0.00 0.00 0.00 2.62
3067 3245 1.606350 GACGGCCGCGATCTATTTCG 61.606 60.000 28.58 0.00 41.99 3.46
3070 3248 1.201825 GCCGCGATCTATTTCGTGC 59.798 57.895 8.23 0.00 45.67 5.34
3311 3504 0.443869 GCACACTTGCCGACATACAG 59.556 55.000 0.00 0.00 43.66 2.74
3323 3516 3.270027 CGACATACAGAAAAGGATGGCA 58.730 45.455 0.00 0.00 0.00 4.92
3342 3535 3.792053 CTCGCCGCCATAGGTCACC 62.792 68.421 0.00 0.00 0.00 4.02
3352 3545 1.094073 ATAGGTCACCCGTCGTCGAG 61.094 60.000 2.98 0.00 39.71 4.04
3439 3633 1.842562 CACCTTCATGATCTCCACCCT 59.157 52.381 0.00 0.00 0.00 4.34
3518 3712 4.642437 TCGATCTCTAGCATCTTGACTTGT 59.358 41.667 0.00 0.00 0.00 3.16
3545 3739 1.133853 GCCTCCATCTCAAGCATCCTT 60.134 52.381 0.00 0.00 0.00 3.36
3652 3846 2.927007 TCTCCTCCCTTGAGTCCTTCTA 59.073 50.000 0.00 0.00 36.86 2.10
3886 4080 1.234821 GACTTGCCATCGTGTTGGAA 58.765 50.000 1.13 0.00 39.25 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.761802 GACTCTGATCCATCACCCCC 59.238 60.000 0.00 0.00 32.50 5.40
135 136 1.918262 TCCCTTCTCCATGCATGAGTT 59.082 47.619 28.31 0.00 0.00 3.01
149 154 2.044946 ACTTGCCGCCATCCCTTC 60.045 61.111 0.00 0.00 0.00 3.46
150 155 2.044946 GACTTGCCGCCATCCCTT 60.045 61.111 0.00 0.00 0.00 3.95
151 156 4.473520 CGACTTGCCGCCATCCCT 62.474 66.667 0.00 0.00 0.00 4.20
202 207 0.383860 GGACAAAGAAAACCGTCGCG 60.384 55.000 0.00 0.00 0.00 5.87
387 411 1.203928 GTCAGGTCGCATCAAGATCG 58.796 55.000 0.00 0.00 0.00 3.69
398 422 0.926155 CAATCTCATGCGTCAGGTCG 59.074 55.000 0.00 0.00 0.00 4.79
402 426 2.159128 ACCTCTCAATCTCATGCGTCAG 60.159 50.000 0.00 0.00 0.00 3.51
439 463 7.948034 AGTCTTGAAAGATAGTAGTACTGCT 57.052 36.000 17.94 17.94 37.39 4.24
445 469 9.617523 GTCCTACTAGTCTTGAAAGATAGTAGT 57.382 37.037 25.10 19.92 41.22 2.73
446 470 9.841295 AGTCCTACTAGTCTTGAAAGATAGTAG 57.159 37.037 23.18 23.18 41.66 2.57
555 590 5.237996 CCACTGCTGATATCCACTGTTAATG 59.762 44.000 0.00 0.00 0.00 1.90
556 591 5.371526 CCACTGCTGATATCCACTGTTAAT 58.628 41.667 0.00 0.00 0.00 1.40
561 596 1.134310 TGCCACTGCTGATATCCACTG 60.134 52.381 0.00 0.00 38.71 3.66
562 597 1.206878 TGCCACTGCTGATATCCACT 58.793 50.000 0.00 0.00 38.71 4.00
564 599 1.202842 CCATGCCACTGCTGATATCCA 60.203 52.381 0.00 0.00 38.71 3.41
591 723 0.036732 TTGTGACATCCTCCTGTGCC 59.963 55.000 0.00 0.00 0.00 5.01
658 790 1.019278 CAGACCATCGGTTCAACGGG 61.019 60.000 0.00 0.00 35.25 5.28
660 792 1.660607 CATCAGACCATCGGTTCAACG 59.339 52.381 0.00 0.00 35.25 4.10
661 793 1.398390 GCATCAGACCATCGGTTCAAC 59.602 52.381 0.00 0.00 35.25 3.18
663 795 0.904649 AGCATCAGACCATCGGTTCA 59.095 50.000 0.00 0.00 35.25 3.18
666 798 0.749649 GAGAGCATCAGACCATCGGT 59.250 55.000 0.00 0.00 36.36 4.69
667 799 1.039068 AGAGAGCATCAGACCATCGG 58.961 55.000 0.00 0.00 37.82 4.18
668 800 3.899734 CTTAGAGAGCATCAGACCATCG 58.100 50.000 0.00 0.00 37.82 3.84
687 824 1.672356 GCTCACATCACGGTGGCTT 60.672 57.895 8.50 0.00 39.27 4.35
811 948 4.452455 CAGGATATAATGGCTCGAACCAAC 59.548 45.833 12.35 0.14 44.65 3.77
814 951 4.273148 ACAGGATATAATGGCTCGAACC 57.727 45.455 0.00 0.00 0.00 3.62
815 952 5.542779 AGAACAGGATATAATGGCTCGAAC 58.457 41.667 0.00 0.00 0.00 3.95
886 1023 5.067283 ACAACATTCCCTATACAAAATCCGC 59.933 40.000 0.00 0.00 0.00 5.54
1063 1201 4.899239 GAGGATGGGCAGGACGCG 62.899 72.222 3.53 3.53 43.84 6.01
1064 1202 3.474570 AGAGGATGGGCAGGACGC 61.475 66.667 0.00 0.00 41.28 5.19
1084 1222 4.978099 AGAGAGAGCAAGAGAGATAGAGG 58.022 47.826 0.00 0.00 0.00 3.69
1110 1248 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1111 1249 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1112 1250 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1113 1251 5.009911 CAGAGAGAGAGAGAGAGAGAGAGAG 59.990 52.000 0.00 0.00 0.00 3.20
1114 1252 4.892345 CAGAGAGAGAGAGAGAGAGAGAGA 59.108 50.000 0.00 0.00 0.00 3.10
1115 1253 4.501229 GCAGAGAGAGAGAGAGAGAGAGAG 60.501 54.167 0.00 0.00 0.00 3.20
1116 1254 3.386078 GCAGAGAGAGAGAGAGAGAGAGA 59.614 52.174 0.00 0.00 0.00 3.10
1117 1255 3.494048 GGCAGAGAGAGAGAGAGAGAGAG 60.494 56.522 0.00 0.00 0.00 3.20
1118 1256 2.435805 GGCAGAGAGAGAGAGAGAGAGA 59.564 54.545 0.00 0.00 0.00 3.10
1119 1257 2.486191 GGGCAGAGAGAGAGAGAGAGAG 60.486 59.091 0.00 0.00 0.00 3.20
1120 1258 1.490490 GGGCAGAGAGAGAGAGAGAGA 59.510 57.143 0.00 0.00 0.00 3.10
1121 1259 1.811558 CGGGCAGAGAGAGAGAGAGAG 60.812 61.905 0.00 0.00 0.00 3.20
1122 1260 0.180171 CGGGCAGAGAGAGAGAGAGA 59.820 60.000 0.00 0.00 0.00 3.10
1123 1261 1.447317 GCGGGCAGAGAGAGAGAGAG 61.447 65.000 0.00 0.00 0.00 3.20
1124 1262 1.453015 GCGGGCAGAGAGAGAGAGA 60.453 63.158 0.00 0.00 0.00 3.10
1125 1263 2.833533 CGCGGGCAGAGAGAGAGAG 61.834 68.421 0.00 0.00 0.00 3.20
1126 1264 2.826287 CGCGGGCAGAGAGAGAGA 60.826 66.667 0.00 0.00 0.00 3.10
1127 1265 4.567385 GCGCGGGCAGAGAGAGAG 62.567 72.222 20.76 0.00 39.62 3.20
1175 1313 1.302033 CCCTACTGCCGATGCCATC 60.302 63.158 0.00 0.00 36.33 3.51
1187 1325 2.690881 TCAATGCCGCCCCCTACT 60.691 61.111 0.00 0.00 0.00 2.57
1445 1583 2.262915 GCACCTGAGGAGTCCGTG 59.737 66.667 4.99 7.04 0.00 4.94
1448 1586 1.979693 AGACGCACCTGAGGAGTCC 60.980 63.158 4.99 0.00 32.70 3.85
1463 1601 4.415501 CAACGAGCGCACGCAGAC 62.416 66.667 26.86 7.24 44.88 3.51
1484 1622 7.466725 GCTGTAACTAGACATGTAGACTGAGAG 60.467 44.444 0.00 0.00 0.00 3.20
1486 1624 6.317642 AGCTGTAACTAGACATGTAGACTGAG 59.682 42.308 0.00 0.00 0.00 3.35
1494 1639 4.657436 GGCTAGCTGTAACTAGACATGT 57.343 45.455 15.72 0.00 46.04 3.21
1498 1643 3.949113 ACAGAGGCTAGCTGTAACTAGAC 59.051 47.826 15.72 0.00 46.98 2.59
1499 1644 4.237976 ACAGAGGCTAGCTGTAACTAGA 57.762 45.455 15.72 0.00 44.27 2.43
1500 1645 4.496673 CGAACAGAGGCTAGCTGTAACTAG 60.497 50.000 15.72 1.98 45.27 2.57
1501 1646 3.377485 CGAACAGAGGCTAGCTGTAACTA 59.623 47.826 15.72 0.00 45.27 2.24
1502 1647 2.164624 CGAACAGAGGCTAGCTGTAACT 59.835 50.000 15.72 1.91 45.27 2.24
1503 1648 2.531206 CGAACAGAGGCTAGCTGTAAC 58.469 52.381 15.72 8.30 45.27 2.50
1522 1667 4.044336 AGTGATTCTCAGAGATTCAGCG 57.956 45.455 20.67 0.00 35.89 5.18
1536 1681 1.956043 TGGCACGCCAAAGTGATTC 59.044 52.632 8.67 0.00 44.12 2.52
1669 1814 4.122776 CCATCTTGTTTAGCTCTACGCAT 58.877 43.478 0.00 0.00 42.61 4.73
1675 1820 1.555075 TCGGCCATCTTGTTTAGCTCT 59.445 47.619 2.24 0.00 0.00 4.09
1872 2017 0.806102 ATCACGACGGAAATGGCGAG 60.806 55.000 0.00 0.00 0.00 5.03
1873 2018 0.456628 TATCACGACGGAAATGGCGA 59.543 50.000 0.00 0.00 0.00 5.54
1996 2141 2.268920 GCGGTCTCCATGGCAGAA 59.731 61.111 6.96 0.00 0.00 3.02
2048 2202 2.123982 CTCCCCAGCCATGAAGCC 60.124 66.667 0.00 0.00 0.00 4.35
2052 2206 1.792757 AAACTGCTCCCCAGCCATGA 61.793 55.000 0.00 0.00 46.26 3.07
2121 2291 2.688446 TCAGTGTATTCGCGAGAGGAAT 59.312 45.455 9.59 1.56 43.69 3.01
2130 2300 0.926846 GCAGAGCTCAGTGTATTCGC 59.073 55.000 17.77 0.25 0.00 4.70
2131 2301 1.923204 GTGCAGAGCTCAGTGTATTCG 59.077 52.381 17.77 0.00 0.00 3.34
2206 2379 4.437820 GCATTCAGACGAACACAAAGAAAC 59.562 41.667 0.00 0.00 32.81 2.78
2220 2394 0.985549 GACGACGACTGCATTCAGAC 59.014 55.000 0.00 0.00 42.95 3.51
2226 2400 2.178521 GTCCGACGACGACTGCAT 59.821 61.111 9.28 0.00 42.66 3.96
2247 2421 0.171231 TCCAGCTCGATGAACGACTG 59.829 55.000 0.00 0.00 46.45 3.51
2309 2483 2.125106 GAATCTCGCCACCGCCTT 60.125 61.111 0.00 0.00 0.00 4.35
2341 2515 2.015726 TCCTCCTCCTCCTCCTCCC 61.016 68.421 0.00 0.00 0.00 4.30
2342 2516 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
2343 2517 1.541672 CCTCCTCCTCCTCCTCCTC 59.458 68.421 0.00 0.00 0.00 3.71
2344 2518 2.018086 CCCTCCTCCTCCTCCTCCT 61.018 68.421 0.00 0.00 0.00 3.69
2345 2519 2.612251 CCCTCCTCCTCCTCCTCC 59.388 72.222 0.00 0.00 0.00 4.30
2346 2520 2.612251 CCCCTCCTCCTCCTCCTC 59.388 72.222 0.00 0.00 0.00 3.71
2478 2652 1.137872 CTCCTTCTCCATCACCTTCCG 59.862 57.143 0.00 0.00 0.00 4.30
2638 2812 2.787473 AGATTCGGAAATGCACCAGA 57.213 45.000 0.00 0.00 0.00 3.86
2639 2813 2.874701 CCTAGATTCGGAAATGCACCAG 59.125 50.000 0.00 0.00 0.00 4.00
2640 2814 2.917933 CCTAGATTCGGAAATGCACCA 58.082 47.619 0.00 0.00 0.00 4.17
2692 2866 4.307908 GTTCACCCGTGCACGTGC 62.308 66.667 34.81 33.11 42.50 5.34
2706 2880 2.486982 GGACCTAAAGCTTTTCCCGTTC 59.513 50.000 18.47 3.80 0.00 3.95
2720 2894 0.320374 CAGGCGTCAACTGGACCTAA 59.680 55.000 0.00 0.00 43.95 2.69
2788 2963 9.999660 ACCAAACAAAAAGTTCTTTAAAAGGTA 57.000 25.926 0.00 0.00 40.26 3.08
2790 2965 9.820229 GAACCAAACAAAAAGTTCTTTAAAAGG 57.180 29.630 0.00 0.00 40.26 3.11
2845 3020 5.404946 TGTCACAGGAGCTAACGTATTAAC 58.595 41.667 0.00 0.00 0.00 2.01
2848 3023 4.737855 ATGTCACAGGAGCTAACGTATT 57.262 40.909 0.00 0.00 0.00 1.89
2849 3024 5.847111 TTATGTCACAGGAGCTAACGTAT 57.153 39.130 0.00 0.00 0.00 3.06
2860 3035 7.615582 AGTGATACACATTTTATGTCACAGG 57.384 36.000 4.75 0.00 42.70 4.00
2861 3036 9.150348 TGTAGTGATACACATTTTATGTCACAG 57.850 33.333 4.75 0.00 42.70 3.66
2885 3063 3.305398 TTGCAAACCAAACGTTTCTGT 57.695 38.095 11.37 8.70 42.98 3.41
2886 3064 4.576678 CAATTGCAAACCAAACGTTTCTG 58.423 39.130 11.37 8.02 42.98 3.02
2902 3080 5.220340 GCATGATAACAAGACTTGCAATTGC 60.220 40.000 23.69 23.69 42.50 3.56
2903 3081 5.290158 GGCATGATAACAAGACTTGCAATTG 59.710 40.000 15.24 4.50 36.75 2.32
2904 3082 5.186409 AGGCATGATAACAAGACTTGCAATT 59.814 36.000 15.24 5.06 36.75 2.32
2905 3083 4.708421 AGGCATGATAACAAGACTTGCAAT 59.292 37.500 15.24 8.66 36.75 3.56
2917 3095 4.513318 GGAGTTGCTCTTAGGCATGATAAC 59.487 45.833 0.00 0.00 42.09 1.89
2970 3148 0.738412 AACGGACAAATAGGCGGACG 60.738 55.000 0.00 0.00 0.00 4.79
2976 3154 1.735571 CGACCCAAACGGACAAATAGG 59.264 52.381 0.00 0.00 34.64 2.57
3048 3226 1.606350 CGAAATAGATCGCGGCCGTC 61.606 60.000 28.70 16.94 35.85 4.79
3059 3237 4.195308 GTGCGGGCACGAAATAGA 57.805 55.556 15.48 0.00 44.60 1.98
3067 3245 1.953642 AAAATTTGCGTGCGGGCAC 60.954 52.632 13.61 13.61 43.82 5.01
3070 3248 1.212616 TTTCAAAATTTGCGTGCGGG 58.787 45.000 0.00 0.00 0.00 6.13
3323 3516 2.758327 TGACCTATGGCGGCGAGT 60.758 61.111 12.98 0.00 0.00 4.18
3342 3535 2.874010 ATGCTCAAGCTCGACGACGG 62.874 60.000 7.55 0.00 42.66 4.79
3352 3545 2.482374 GTGCCGACATGCTCAAGC 59.518 61.111 0.00 0.00 42.50 4.01
3439 3633 1.265365 CTCTCGCTAGCATGATGACGA 59.735 52.381 16.45 9.34 0.00 4.20
3471 3665 1.187567 GCCAATGCCAAGACCAAGGT 61.188 55.000 0.00 0.00 0.00 3.50
3518 3712 1.208052 CTTGAGATGGAGGCGGAGAAA 59.792 52.381 0.00 0.00 0.00 2.52
3545 3739 1.302511 GGAGGCGGAGAAGCAAACA 60.303 57.895 0.00 0.00 39.27 2.83
3652 3846 0.826715 CGTGGAGGACATGATGACCT 59.173 55.000 16.06 16.06 44.85 3.85
3695 3889 0.842030 AGGAGGACAAGTGGGATGCA 60.842 55.000 0.00 0.00 0.00 3.96
3784 3978 2.895372 CCCTTATGTCGCGTGGGC 60.895 66.667 5.77 0.00 0.00 5.36
3797 3991 3.595758 GCGCAATATGCCGCCCTT 61.596 61.111 0.30 0.00 41.12 3.95


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

AutoCloner maintained by Alex Coulton.