Multiple sequence alignment - TraesCS2A01G081900

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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 TraesCS2A01G081900 chr2A 100.000 6014 0 0 506 6519 36938697 36932684 0.000000e+00 11106.0
1 TraesCS2A01G081900 chr2A 99.381 485 3 0 5901 6385 705994088 705993604 0.000000e+00 880.0
2 TraesCS2A01G081900 chr2A 100.000 231 0 0 1 231 36939202 36938972 1.680000e-115 427.0
3 TraesCS2A01G081900 chr2A 97.576 165 3 1 6356 6519 705993592 705993428 1.380000e-71 281.0
4 TraesCS2A01G081900 chr2A 97.260 73 2 0 5828 5900 705994312 705994240 2.470000e-24 124.0
5 TraesCS2A01G081900 chr2D 90.072 2377 128 52 506 2841 33956256 33953947 0.000000e+00 2983.0
6 TraesCS2A01G081900 chr2D 92.346 1790 72 21 4060 5828 33953949 33952204 0.000000e+00 2486.0
7 TraesCS2A01G081900 chr2D 83.951 243 37 2 2842 3083 21006977 21007218 1.410000e-56 231.0
8 TraesCS2A01G081900 chr2D 90.533 169 6 7 64 231 33956452 33956293 1.420000e-51 215.0
9 TraesCS2A01G081900 chr2D 97.674 43 1 0 24 66 33956519 33956477 2.520000e-09 75.0
10 TraesCS2A01G081900 chrUn 87.635 2313 139 60 536 2841 293692824 293690652 0.000000e+00 2551.0
11 TraesCS2A01G081900 chrUn 87.635 2313 139 60 536 2841 297417088 297414916 0.000000e+00 2551.0
12 TraesCS2A01G081900 chrUn 87.635 2313 139 60 536 2841 327633354 327631182 0.000000e+00 2551.0
13 TraesCS2A01G081900 chrUn 92.018 1804 85 25 4060 5828 293690654 293688875 0.000000e+00 2479.0
14 TraesCS2A01G081900 chrUn 93.293 656 30 5 4060 4704 297414918 297414266 0.000000e+00 955.0
15 TraesCS2A01G081900 chrUn 93.293 656 30 5 4060 4704 327631184 327630532 0.000000e+00 955.0
16 TraesCS2A01G081900 chrUn 85.083 181 7 6 63 231 370764748 370764920 4.040000e-37 167.0
17 TraesCS2A01G081900 chrUn 94.872 39 2 0 24 62 370764687 370764725 1.960000e-05 62.1
18 TraesCS2A01G081900 chr6B 100.000 1218 0 0 2842 4059 56332284 56331067 0.000000e+00 2250.0
19 TraesCS2A01G081900 chr6B 93.789 161 8 2 6040 6199 664307766 664307925 2.350000e-59 241.0
20 TraesCS2A01G081900 chr6B 94.737 76 4 0 5829 5904 664306269 664306344 1.150000e-22 119.0
21 TraesCS2A01G081900 chr6A 99.675 616 2 0 5904 6519 60427655 60427040 0.000000e+00 1127.0
22 TraesCS2A01G081900 chr6A 84.332 434 59 7 5901 6329 162912812 162912383 3.640000e-112 416.0
23 TraesCS2A01G081900 chr6A 98.684 76 1 0 5829 5904 60427880 60427805 1.140000e-27 135.0
24 TraesCS2A01G081900 chr6A 94.737 76 4 0 5829 5904 162913034 162912959 1.150000e-22 119.0
25 TraesCS2A01G081900 chr7A 98.714 622 8 0 5898 6519 419012739 419013360 0.000000e+00 1105.0
26 TraesCS2A01G081900 chr7A 97.468 79 2 0 5826 5904 419012517 419012595 1.140000e-27 135.0
27 TraesCS2A01G081900 chr1D 90.860 186 16 1 3874 4059 32520376 32520192 1.400000e-61 248.0
28 TraesCS2A01G081900 chr5B 84.184 196 31 0 2842 3037 606467973 606467778 2.400000e-44 191.0
29 TraesCS2A01G081900 chr5B 91.139 79 6 1 6437 6514 679387331 679387253 8.940000e-19 106.0
30 TraesCS2A01G081900 chr5A 84.672 137 19 2 2902 3037 613747397 613747262 1.140000e-27 135.0


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 TraesCS2A01G081900 chr2A 36932684 36939202 6518 True 5766.500000 11106 100.000000 1 6519 2 chr2A.!!$R1 6518
1 TraesCS2A01G081900 chr2A 705993428 705994312 884 True 428.333333 880 98.072333 5828 6519 3 chr2A.!!$R2 691
2 TraesCS2A01G081900 chr2D 33952204 33956519 4315 True 1439.750000 2983 92.656250 24 5828 4 chr2D.!!$R1 5804
3 TraesCS2A01G081900 chrUn 293688875 293692824 3949 True 2515.000000 2551 89.826500 536 5828 2 chrUn.!!$R1 5292
4 TraesCS2A01G081900 chrUn 297414266 297417088 2822 True 1753.000000 2551 90.464000 536 4704 2 chrUn.!!$R2 4168
5 TraesCS2A01G081900 chrUn 327630532 327633354 2822 True 1753.000000 2551 90.464000 536 4704 2 chrUn.!!$R3 4168
6 TraesCS2A01G081900 chr6B 56331067 56332284 1217 True 2250.000000 2250 100.000000 2842 4059 1 chr6B.!!$R1 1217
7 TraesCS2A01G081900 chr6A 60427040 60427880 840 True 631.000000 1127 99.179500 5829 6519 2 chr6A.!!$R1 690
8 TraesCS2A01G081900 chr6A 162912383 162913034 651 True 267.500000 416 89.534500 5829 6329 2 chr6A.!!$R2 500
9 TraesCS2A01G081900 chr7A 419012517 419013360 843 False 620.000000 1105 98.091000 5826 6519 2 chr7A.!!$F1 693

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
688 723 0.883833 CACCCATGCACTCTGTTTCC 59.116 55.000 0.00 0.0 0.00 3.13 F
1525 1586 0.036952 CAGAGGTCTTCATGCACGGT 60.037 55.000 0.00 0.0 0.00 4.83 F
1993 2070 0.537653 TTCTGGGTCAACGTGTGTGA 59.462 50.000 0.00 0.0 0.00 3.58 F
1994 2071 0.756294 TCTGGGTCAACGTGTGTGAT 59.244 50.000 0.00 0.0 0.00 3.06 F
1995 2072 1.140052 TCTGGGTCAACGTGTGTGATT 59.860 47.619 0.00 0.0 0.00 2.57 F
2133 2210 1.323534 AGCAATAATCGCAACGACGAC 59.676 47.619 0.00 0.0 46.28 4.34 F
4329 4421 0.601046 TTGTTCGAGCTGCTGACCTG 60.601 55.000 7.01 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1975 2052 0.756294 ATCACACACGTTGACCCAGA 59.244 50.000 5.01 0.0 0.00 3.86 R
2709 2788 1.696336 AGTGCTATCAGGCGGATCAAT 59.304 47.619 2.64 0.0 37.44 2.57 R
4127 4210 7.121168 TGAACTCATCACCTGGAAAACATAATC 59.879 37.037 0.00 0.0 31.50 1.75 R
4206 4295 1.249469 AACTCTCGTTCGGGGAGGAC 61.249 60.000 15.34 0.0 32.34 3.85 R
4299 4391 2.012673 GCTCGAACAATTGGCTCATCT 58.987 47.619 10.83 0.0 0.00 2.90 R
4398 4490 0.034337 TACCTTCCGGCACTTGTGAC 59.966 55.000 0.00 0.0 0.00 3.67 R
5668 5800 0.032267 GTAGGTAGCTAAGGCAGGCG 59.968 60.000 2.58 0.0 41.70 5.52 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
195 223 2.193248 CTCCCCGCCTCCATTTCC 59.807 66.667 0.00 0.00 0.00 3.13
209 237 2.798148 ATTTCCTCCACGTCACCCGC 62.798 60.000 0.00 0.00 41.42 6.13
676 711 2.436646 GCCGGTCTGTCACCCATG 60.437 66.667 1.90 0.00 43.31 3.66
677 712 2.436646 CCGGTCTGTCACCCATGC 60.437 66.667 0.00 0.00 43.31 4.06
678 713 2.347114 CGGTCTGTCACCCATGCA 59.653 61.111 0.00 0.00 43.31 3.96
686 721 1.133823 TGTCACCCATGCACTCTGTTT 60.134 47.619 0.00 0.00 0.00 2.83
688 723 0.883833 CACCCATGCACTCTGTTTCC 59.116 55.000 0.00 0.00 0.00 3.13
716 751 1.070134 TGGGGATCGAATCATCCGTTC 59.930 52.381 0.00 0.00 43.22 3.95
717 752 1.070134 GGGGATCGAATCATCCGTTCA 59.930 52.381 0.00 0.00 43.22 3.18
719 754 2.544267 GGGATCGAATCATCCGTTCAAC 59.456 50.000 0.00 0.00 43.22 3.18
720 755 2.544267 GGATCGAATCATCCGTTCAACC 59.456 50.000 0.00 0.00 33.13 3.77
721 756 3.458189 GATCGAATCATCCGTTCAACCT 58.542 45.455 0.00 0.00 0.00 3.50
722 757 2.888594 TCGAATCATCCGTTCAACCTC 58.111 47.619 0.00 0.00 0.00 3.85
723 758 2.496070 TCGAATCATCCGTTCAACCTCT 59.504 45.455 0.00 0.00 0.00 3.69
750 786 3.207669 CAGGGCATGCTCCTTCGC 61.208 66.667 21.08 2.45 31.06 4.70
754 790 1.525535 GGCATGCTCCTTCGCTCAT 60.526 57.895 18.92 0.00 0.00 2.90
762 798 1.222936 CCTTCGCTCATTCCAGGCT 59.777 57.895 0.00 0.00 0.00 4.58
766 802 1.227497 CGCTCATTCCAGGCTCTCC 60.227 63.158 0.00 0.00 0.00 3.71
787 823 7.185565 TCTCCCTCTAGCTAATAATATGTGCT 58.814 38.462 0.00 5.77 37.72 4.40
795 831 7.602517 AGCTAATAATATGTGCTCGGAAATC 57.397 36.000 0.00 0.00 0.00 2.17
874 915 1.066587 CTCCGCTCCATTCGAGGAC 59.933 63.158 0.00 0.00 39.22 3.85
887 928 1.136305 TCGAGGACACGATTCATTCCC 59.864 52.381 0.00 0.00 37.37 3.97
890 931 1.436983 GGACACGATTCATTCCCGCC 61.437 60.000 0.00 0.00 0.00 6.13
901 942 2.257409 ATTCCCGCCGCAGTCTCAAT 62.257 55.000 0.00 0.00 0.00 2.57
903 944 2.892425 CCGCCGCAGTCTCAATCC 60.892 66.667 0.00 0.00 0.00 3.01
917 958 3.450457 TCTCAATCCCTTGCTCTTCTCTC 59.550 47.826 0.00 0.00 32.11 3.20
923 964 2.353605 CCCTTGCTCTTCTCTCTGTGTC 60.354 54.545 0.00 0.00 0.00 3.67
949 991 4.513000 TGCGTTTTGTTTCTTGATTTGC 57.487 36.364 0.00 0.00 0.00 3.68
1019 1076 0.806102 ATGCGACCGAGGTTCGATTG 60.806 55.000 14.84 0.00 43.74 2.67
1023 1080 2.805845 CGACCGAGGTTCGATTGTTAT 58.194 47.619 0.00 0.00 43.74 1.89
1078 1135 4.862823 CCTCCTCCCTCCCCGTCC 62.863 77.778 0.00 0.00 0.00 4.79
1098 1155 2.548295 CCACCAAACGACCCCAACG 61.548 63.158 0.00 0.00 0.00 4.10
1155 1212 0.744414 CATGGACCGTCATCACCACC 60.744 60.000 0.00 0.00 35.19 4.61
1156 1213 1.198094 ATGGACCGTCATCACCACCA 61.198 55.000 0.00 0.00 35.19 4.17
1157 1214 1.375523 GGACCGTCATCACCACCAC 60.376 63.158 0.00 0.00 0.00 4.16
1158 1215 1.375523 GACCGTCATCACCACCACC 60.376 63.158 0.00 0.00 0.00 4.61
1159 1216 2.107041 GACCGTCATCACCACCACCA 62.107 60.000 0.00 0.00 0.00 4.17
1160 1217 1.671054 CCGTCATCACCACCACCAC 60.671 63.158 0.00 0.00 0.00 4.16
1161 1218 1.671054 CGTCATCACCACCACCACC 60.671 63.158 0.00 0.00 0.00 4.61
1162 1219 1.454104 GTCATCACCACCACCACCA 59.546 57.895 0.00 0.00 0.00 4.17
1163 1220 0.606401 GTCATCACCACCACCACCAG 60.606 60.000 0.00 0.00 0.00 4.00
1329 1386 1.167851 CCACTGCATGTACCAAGGTG 58.832 55.000 1.07 0.00 0.00 4.00
1335 1392 1.743394 GCATGTACCAAGGTGCTTACC 59.257 52.381 8.76 0.00 34.85 2.85
1374 1435 5.180492 GCTACTACCAGTGTTAATTTGCACA 59.820 40.000 12.52 0.00 38.02 4.57
1398 1459 0.100682 CGGTCGTCATGGAGGTACTG 59.899 60.000 0.00 0.00 41.55 2.74
1425 1486 0.380378 GCGTTGGTTGTGTGTCATGT 59.620 50.000 0.00 0.00 0.00 3.21
1525 1586 0.036952 CAGAGGTCTTCATGCACGGT 60.037 55.000 0.00 0.00 0.00 4.83
1528 1589 2.690778 GGTCTTCATGCACGGTGGC 61.691 63.158 10.60 3.04 0.00 5.01
1531 1592 2.672651 TTCATGCACGGTGGCCTG 60.673 61.111 10.60 5.99 0.00 4.85
1606 1667 1.471676 CCCGTCATCAGTAAGCACCTC 60.472 57.143 0.00 0.00 0.00 3.85
1607 1668 1.550065 CGTCATCAGTAAGCACCTCG 58.450 55.000 0.00 0.00 0.00 4.63
1611 1672 2.362397 TCATCAGTAAGCACCTCGATCC 59.638 50.000 0.00 0.00 0.00 3.36
1617 1678 3.399181 GCACCTCGATCCACCCCA 61.399 66.667 0.00 0.00 0.00 4.96
1859 1927 7.133513 CGTAAGTTACTATCTCTGATGGTGTC 58.866 42.308 11.17 1.31 0.00 3.67
1862 1930 6.191315 AGTTACTATCTCTGATGGTGTCTGT 58.809 40.000 6.79 0.00 0.00 3.41
1863 1931 6.665680 AGTTACTATCTCTGATGGTGTCTGTT 59.334 38.462 6.79 0.00 0.00 3.16
1864 1932 5.590530 ACTATCTCTGATGGTGTCTGTTC 57.409 43.478 0.00 0.00 0.00 3.18
1865 1933 5.268387 ACTATCTCTGATGGTGTCTGTTCT 58.732 41.667 0.00 0.00 0.00 3.01
1866 1934 3.949842 TCTCTGATGGTGTCTGTTCTG 57.050 47.619 0.00 0.00 0.00 3.02
1867 1935 3.234353 TCTCTGATGGTGTCTGTTCTGT 58.766 45.455 0.00 0.00 0.00 3.41
1869 1937 3.993081 CTCTGATGGTGTCTGTTCTGTTC 59.007 47.826 0.00 0.00 0.00 3.18
1870 1938 3.643320 TCTGATGGTGTCTGTTCTGTTCT 59.357 43.478 0.00 0.00 0.00 3.01
1872 1940 4.380531 TGATGGTGTCTGTTCTGTTCTTC 58.619 43.478 0.00 0.00 0.00 2.87
1873 1941 3.194005 TGGTGTCTGTTCTGTTCTTCC 57.806 47.619 0.00 0.00 0.00 3.46
1874 1942 2.503765 TGGTGTCTGTTCTGTTCTTCCA 59.496 45.455 0.00 0.00 0.00 3.53
1875 1943 2.872858 GGTGTCTGTTCTGTTCTTCCAC 59.127 50.000 0.00 0.00 0.00 4.02
1876 1944 3.531538 GTGTCTGTTCTGTTCTTCCACA 58.468 45.455 0.00 0.00 0.00 4.17
1877 1945 3.557595 GTGTCTGTTCTGTTCTTCCACAG 59.442 47.826 0.00 0.00 44.96 3.66
1878 1946 3.197766 TGTCTGTTCTGTTCTTCCACAGT 59.802 43.478 0.97 0.00 44.10 3.55
1920 1997 1.471684 GAAATACTGCTGCTGCTGCTT 59.528 47.619 27.67 18.47 41.07 3.91
1953 2030 4.703897 TCCTAGTTTCACTTGTGTCCTTG 58.296 43.478 0.46 0.00 0.00 3.61
1971 2048 2.315925 TGCAGCTTACTAGTGCATCC 57.684 50.000 5.39 0.00 42.20 3.51
1975 2052 3.691609 GCAGCTTACTAGTGCATCCTTTT 59.308 43.478 5.39 0.00 37.16 2.27
1980 2057 3.356529 ACTAGTGCATCCTTTTCTGGG 57.643 47.619 0.00 0.00 0.00 4.45
1981 2058 2.644798 ACTAGTGCATCCTTTTCTGGGT 59.355 45.455 0.00 0.00 0.00 4.51
1982 2059 2.206576 AGTGCATCCTTTTCTGGGTC 57.793 50.000 0.00 0.00 0.00 4.46
1983 2060 1.425066 AGTGCATCCTTTTCTGGGTCA 59.575 47.619 0.00 0.00 0.00 4.02
1984 2061 2.158475 AGTGCATCCTTTTCTGGGTCAA 60.158 45.455 0.00 0.00 0.00 3.18
1985 2062 2.029918 GTGCATCCTTTTCTGGGTCAAC 60.030 50.000 0.00 0.00 0.00 3.18
1986 2063 1.200020 GCATCCTTTTCTGGGTCAACG 59.800 52.381 0.00 0.00 0.00 4.10
1987 2064 2.504367 CATCCTTTTCTGGGTCAACGT 58.496 47.619 0.00 0.00 0.00 3.99
1988 2065 1.961793 TCCTTTTCTGGGTCAACGTG 58.038 50.000 0.00 0.00 0.00 4.49
1989 2066 1.210967 TCCTTTTCTGGGTCAACGTGT 59.789 47.619 0.00 0.00 0.00 4.49
1991 2068 2.014128 CTTTTCTGGGTCAACGTGTGT 58.986 47.619 0.00 0.00 0.00 3.72
1992 2069 1.374560 TTTCTGGGTCAACGTGTGTG 58.625 50.000 0.00 0.00 0.00 3.82
1993 2070 0.537653 TTCTGGGTCAACGTGTGTGA 59.462 50.000 0.00 0.00 0.00 3.58
1994 2071 0.756294 TCTGGGTCAACGTGTGTGAT 59.244 50.000 0.00 0.00 0.00 3.06
1995 2072 1.140052 TCTGGGTCAACGTGTGTGATT 59.860 47.619 0.00 0.00 0.00 2.57
1996 2073 2.365941 TCTGGGTCAACGTGTGTGATTA 59.634 45.455 0.00 0.00 0.00 1.75
1997 2074 3.007506 TCTGGGTCAACGTGTGTGATTAT 59.992 43.478 0.00 0.00 0.00 1.28
1998 2075 3.745799 TGGGTCAACGTGTGTGATTATT 58.254 40.909 0.00 0.00 0.00 1.40
1999 2076 4.895961 TGGGTCAACGTGTGTGATTATTA 58.104 39.130 0.00 0.00 0.00 0.98
2009 2086 9.595823 AACGTGTGTGATTATTATACTAAAGCT 57.404 29.630 0.00 0.00 0.00 3.74
2133 2210 1.323534 AGCAATAATCGCAACGACGAC 59.676 47.619 0.00 0.00 46.28 4.34
2277 2354 7.272244 TCAGACAAGACTGAACAGAACAATTA 58.728 34.615 8.87 0.00 42.79 1.40
2340 2417 2.060050 TCTCCTAGTGCACTAGAGGC 57.940 55.000 42.26 7.80 46.80 4.70
2355 2432 5.240183 CACTAGAGGCCAATTTGTCCATATG 59.760 44.000 5.01 0.00 0.00 1.78
2358 2435 2.138596 GCCAATTTGTCCATATGGCG 57.861 50.000 17.58 0.00 46.11 5.69
2402 2479 7.306953 AGAACATGACTTACTCTCTTCGTTAC 58.693 38.462 0.00 0.00 0.00 2.50
2549 2627 4.037923 ACATGCTAGTTGTTTGGACTTTGG 59.962 41.667 0.00 0.00 0.00 3.28
2552 2630 5.626142 TGCTAGTTGTTTGGACTTTGGATA 58.374 37.500 0.00 0.00 0.00 2.59
2555 2633 7.232534 TGCTAGTTGTTTGGACTTTGGATAAAT 59.767 33.333 0.00 0.00 0.00 1.40
2561 2639 9.672673 TTGTTTGGACTTTGGATAAATTTGAAA 57.327 25.926 0.00 0.00 0.00 2.69
2562 2640 9.844257 TGTTTGGACTTTGGATAAATTTGAAAT 57.156 25.926 0.00 0.00 0.00 2.17
2566 2644 9.936759 TGGACTTTGGATAAATTTGAAATAACC 57.063 29.630 0.00 0.00 0.00 2.85
2568 2646 9.634163 GACTTTGGATAAATTTGAAATAACCGT 57.366 29.630 0.00 0.00 0.00 4.83
2614 2693 5.186603 TGTGAGAAGTATCTGCATCTGAACT 59.813 40.000 0.00 0.00 35.54 3.01
2709 2788 3.196469 GGACATGTCTCCAGATCAGTCAA 59.804 47.826 24.50 0.00 0.00 3.18
2771 2850 4.186926 TGAAGTCAGAGATATGCAGCAAC 58.813 43.478 0.00 0.00 0.00 4.17
4059 4138 7.595604 TCGTAATATCAACTGTGTTGTAGTGA 58.404 34.615 9.78 0.00 0.00 3.41
4060 4139 7.753580 TCGTAATATCAACTGTGTTGTAGTGAG 59.246 37.037 9.78 0.00 0.00 3.51
4061 4140 7.541091 CGTAATATCAACTGTGTTGTAGTGAGT 59.459 37.037 9.78 0.00 0.00 3.41
4094 4173 2.423185 TCACTGTGCAACTGAACCAAAG 59.577 45.455 2.12 0.00 39.30 2.77
4104 4187 1.410153 CTGAACCAAAGGCTGCTTGTT 59.590 47.619 0.00 0.00 0.00 2.83
4115 4198 3.834231 AGGCTGCTTGTTCCATTTTGTAT 59.166 39.130 0.00 0.00 0.00 2.29
4127 4210 9.619316 TGTTCCATTTTGTATTGACTAAATTCG 57.381 29.630 0.00 0.00 38.45 3.34
4206 4295 7.381766 TGGTAATTTGAACACAGATGATCAG 57.618 36.000 0.09 0.00 38.69 2.90
4299 4391 9.473007 TCCAATGATACAGTTATGGAAAATTCA 57.527 29.630 0.00 0.00 34.21 2.57
4329 4421 0.601046 TTGTTCGAGCTGCTGACCTG 60.601 55.000 7.01 0.00 0.00 4.00
4332 4424 0.610174 TTCGAGCTGCTGACCTGATT 59.390 50.000 7.01 0.00 0.00 2.57
4398 4490 3.573598 CATAGATGCTCCTAACTGCTCG 58.426 50.000 0.00 0.00 0.00 5.03
4490 4582 2.810012 CGAGATCGACCGCAGACGA 61.810 63.158 0.00 0.00 41.52 4.20
4491 4583 1.297745 GAGATCGACCGCAGACGAC 60.298 63.158 0.00 0.00 43.93 4.34
4527 4619 1.344763 CAGGAGGAACAGAGGAACGTT 59.655 52.381 0.00 0.00 0.00 3.99
4536 4628 0.314302 AGAGGAACGTTGTGAGACGG 59.686 55.000 5.00 0.00 46.77 4.79
4673 4765 2.115291 GCGGTCTCCAATCAAGGCC 61.115 63.158 0.00 0.00 35.06 5.19
4675 4767 2.115291 GGTCTCCAATCAAGGCCGC 61.115 63.158 0.00 0.00 0.00 6.53
4840 4932 2.546789 CGCCGGTGGAAATAATAAGGTC 59.453 50.000 7.26 0.00 0.00 3.85
4846 4938 4.448210 GTGGAAATAATAAGGTCTCGCCA 58.552 43.478 0.00 0.00 40.61 5.69
4935 5027 3.057245 GGGAAAGACAAGGCTGATGAAAC 60.057 47.826 0.00 0.00 0.00 2.78
4951 5043 2.877786 TGAAACGAGCAAGAAGAATGCA 59.122 40.909 0.00 0.00 46.22 3.96
4957 5049 1.271656 AGCAAGAAGAATGCAGCAACC 59.728 47.619 0.00 0.00 46.22 3.77
4981 5079 4.759564 GCAGCAGCGAAAGACATG 57.240 55.556 0.00 0.00 0.00 3.21
4982 5080 2.165380 GCAGCAGCGAAAGACATGA 58.835 52.632 0.00 0.00 0.00 3.07
5011 5109 1.529244 ACAGAGCAAACACCCCTGC 60.529 57.895 0.00 0.00 38.91 4.85
5064 5165 1.079266 GAGGCACTGCTCAGTCCAG 60.079 63.158 15.65 0.00 41.55 3.86
5066 5167 1.072159 GGCACTGCTCAGTCCAGTT 59.928 57.895 0.00 0.00 41.34 3.16
5077 5178 2.441375 TCAGTCCAGTTTGGTCAATCCA 59.559 45.455 0.00 0.00 45.60 3.41
5164 5268 3.775654 GGGAGCACCGCAGCTACT 61.776 66.667 9.09 0.00 46.75 2.57
5165 5269 2.510238 GGAGCACCGCAGCTACTG 60.510 66.667 2.60 0.00 46.75 2.74
5322 5432 3.825014 GGGAAGAAGGTACTGGGTTTTTC 59.175 47.826 0.00 0.00 40.86 2.29
5323 5433 3.825014 GGAAGAAGGTACTGGGTTTTTCC 59.175 47.826 0.00 0.00 40.86 3.13
5335 5452 2.592194 GGTTTTTCCGAAAGCCGATTC 58.408 47.619 0.00 0.00 41.76 2.52
5371 5488 8.088365 TCTGTTCTTCGTTTCATTCTTCTGATA 58.912 33.333 0.00 0.00 0.00 2.15
5375 5492 5.677319 TCGTTTCATTCTTCTGATAGGGT 57.323 39.130 0.00 0.00 0.00 4.34
5383 5500 6.371548 TCATTCTTCTGATAGGGTTTTGTTCG 59.628 38.462 0.00 0.00 0.00 3.95
5388 5505 4.935205 TCTGATAGGGTTTTGTTCGTGATG 59.065 41.667 0.00 0.00 0.00 3.07
5404 5521 3.735820 CGTGATGGCTGATGAAAAATGGG 60.736 47.826 0.00 0.00 0.00 4.00
5406 5523 4.402155 GTGATGGCTGATGAAAAATGGGTA 59.598 41.667 0.00 0.00 0.00 3.69
5408 5525 4.799564 TGGCTGATGAAAAATGGGTAAC 57.200 40.909 0.00 0.00 0.00 2.50
5552 5677 5.163258 ACACACCTAGCTATACCTAGTACGT 60.163 44.000 0.00 0.00 34.34 3.57
5553 5678 6.042093 ACACACCTAGCTATACCTAGTACGTA 59.958 42.308 0.00 0.00 34.34 3.57
5554 5679 6.931281 CACACCTAGCTATACCTAGTACGTAA 59.069 42.308 0.00 0.00 34.34 3.18
5666 5798 5.862678 AGAATAACAAGCTACTCCTCCTC 57.137 43.478 0.00 0.00 0.00 3.71
5667 5799 4.651962 AGAATAACAAGCTACTCCTCCTCC 59.348 45.833 0.00 0.00 0.00 4.30
5668 5800 1.574263 AACAAGCTACTCCTCCTCCC 58.426 55.000 0.00 0.00 0.00 4.30
5743 5875 4.817464 AGAGTACATAGTAGAAGTGCGGAG 59.183 45.833 0.00 0.00 0.00 4.63
5744 5876 4.525024 AGTACATAGTAGAAGTGCGGAGT 58.475 43.478 0.00 0.00 0.00 3.85
5745 5877 4.575645 AGTACATAGTAGAAGTGCGGAGTC 59.424 45.833 0.00 0.00 0.00 3.36
5746 5878 2.355132 ACATAGTAGAAGTGCGGAGTCG 59.645 50.000 0.00 0.00 39.81 4.18
5847 5984 9.704098 GAGTATTCGATAAAGCCTTTTACTTTG 57.296 33.333 0.00 0.00 37.86 2.77
6222 6515 4.323569 AGAGTATGTGGGAGAGACAGAA 57.676 45.455 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
518 546 0.178947 AGGGGGAGAGATCGATGGAC 60.179 60.000 0.54 0.00 0.00 4.02
598 626 0.106469 TGGAGGAGGAGGATGACGAG 60.106 60.000 0.00 0.00 0.00 4.18
604 638 0.031616 GTCAGGTGGAGGAGGAGGAT 60.032 60.000 0.00 0.00 0.00 3.24
662 697 0.674895 GAGTGCATGGGTGACAGACC 60.675 60.000 0.00 0.00 45.28 3.85
672 707 0.957395 AGCGGAAACAGAGTGCATGG 60.957 55.000 0.00 0.00 0.00 3.66
674 709 1.016130 CGAGCGGAAACAGAGTGCAT 61.016 55.000 0.00 0.00 0.00 3.96
676 711 0.737715 ATCGAGCGGAAACAGAGTGC 60.738 55.000 0.00 0.00 0.00 4.40
677 712 1.391485 CAATCGAGCGGAAACAGAGTG 59.609 52.381 0.00 0.00 0.00 3.51
678 713 1.673033 CCAATCGAGCGGAAACAGAGT 60.673 52.381 0.00 0.00 0.00 3.24
686 721 3.138625 GATCCCCAATCGAGCGGA 58.861 61.111 4.49 0.09 0.00 5.54
716 751 1.339438 CCTGGATCCACACAGAGGTTG 60.339 57.143 11.44 0.00 36.86 3.77
717 752 0.987294 CCTGGATCCACACAGAGGTT 59.013 55.000 11.44 0.00 36.86 3.50
719 754 1.910722 CCCTGGATCCACACAGAGG 59.089 63.158 11.44 9.51 36.86 3.69
720 755 1.222936 GCCCTGGATCCACACAGAG 59.777 63.158 11.44 0.00 36.86 3.35
721 756 0.915872 ATGCCCTGGATCCACACAGA 60.916 55.000 11.44 0.00 36.86 3.41
722 757 0.750546 CATGCCCTGGATCCACACAG 60.751 60.000 11.44 0.24 34.54 3.66
723 758 1.303948 CATGCCCTGGATCCACACA 59.696 57.895 11.44 9.70 0.00 3.72
750 786 0.758123 GAGGGAGAGCCTGGAATGAG 59.242 60.000 0.00 0.00 0.00 2.90
754 790 0.397816 GCTAGAGGGAGAGCCTGGAA 60.398 60.000 0.00 0.00 32.25 3.53
762 798 7.185565 AGCACATATTATTAGCTAGAGGGAGA 58.814 38.462 0.00 0.00 33.06 3.71
766 802 6.095580 TCCGAGCACATATTATTAGCTAGAGG 59.904 42.308 0.00 8.13 35.36 3.69
787 823 3.454375 GTTAATCTCCAGCGATTTCCGA 58.546 45.455 0.00 0.00 41.76 4.55
795 831 0.876342 GAGCCGGTTAATCTCCAGCG 60.876 60.000 1.90 0.00 34.01 5.18
857 893 1.680989 TGTCCTCGAATGGAGCGGA 60.681 57.895 0.00 0.00 41.71 5.54
874 915 3.014036 CGGCGGGAATGAATCGTG 58.986 61.111 0.00 0.00 0.00 4.35
887 928 2.859273 AAGGGATTGAGACTGCGGCG 62.859 60.000 0.51 0.51 0.00 6.46
890 931 0.392193 AGCAAGGGATTGAGACTGCG 60.392 55.000 0.00 0.00 0.00 5.18
901 942 1.898472 CACAGAGAGAAGAGCAAGGGA 59.102 52.381 0.00 0.00 0.00 4.20
903 944 2.562298 AGACACAGAGAGAAGAGCAAGG 59.438 50.000 0.00 0.00 0.00 3.61
917 958 4.901866 AACAAAACGCAAAAAGACACAG 57.098 36.364 0.00 0.00 0.00 3.66
923 964 7.459991 GCAAATCAAGAAACAAAACGCAAAAAG 60.460 33.333 0.00 0.00 0.00 2.27
1072 1129 2.975799 CGTTTGGTGGTGGACGGG 60.976 66.667 0.00 0.00 32.29 5.28
1078 1135 1.454111 TTGGGGTCGTTTGGTGGTG 60.454 57.895 0.00 0.00 0.00 4.17
1098 1155 1.528129 CTGGCTCCAAGAGGAAACAC 58.472 55.000 0.00 0.00 45.19 3.32
1155 1212 3.362797 CTGCTGCTGCTGGTGGTG 61.363 66.667 17.00 0.00 40.48 4.17
1158 1215 3.738246 CTGCTGCTGCTGCTGGTG 61.738 66.667 27.67 13.98 40.48 4.17
1235 1292 0.393537 CCCTGATGGTCTTCCTGTGC 60.394 60.000 0.00 0.00 34.23 4.57
1329 1386 3.491792 GCTGAGACAGAGTATGGGTAAGC 60.492 52.174 2.81 0.00 32.44 3.09
1335 1392 4.517453 GGTAGTAGCTGAGACAGAGTATGG 59.483 50.000 0.00 0.00 32.44 2.74
1374 1435 2.362503 TCCATGACGACCGAGCCT 60.363 61.111 0.00 0.00 0.00 4.58
1398 1459 1.202475 ACACAACCAACGCCCAAATTC 60.202 47.619 0.00 0.00 0.00 2.17
1525 1586 4.770362 TCGATCCCGGACAGGCCA 62.770 66.667 5.01 0.00 39.21 5.36
1528 1589 2.442272 AGGTCGATCCCGGACAGG 60.442 66.667 0.73 0.00 40.63 4.00
1531 1592 3.140225 GAGCAGGTCGATCCCGGAC 62.140 68.421 0.73 0.00 36.75 4.79
1606 1667 3.849951 CCGAGGTGGGGTGGATCG 61.850 72.222 0.00 0.00 0.00 3.69
1607 1668 4.176752 GCCGAGGTGGGGTGGATC 62.177 72.222 0.00 0.00 38.63 3.36
1617 1678 1.467342 GAAACATTTTAGCGCCGAGGT 59.533 47.619 2.29 0.00 0.00 3.85
1804 1868 3.129502 CTCCACACATGCGCCCAG 61.130 66.667 4.18 0.00 0.00 4.45
1865 1933 8.818622 ATACATACTACTACTGTGGAAGAACA 57.181 34.615 0.00 0.00 0.00 3.18
1866 1934 8.900781 TGATACATACTACTACTGTGGAAGAAC 58.099 37.037 0.00 0.00 0.00 3.01
1867 1935 9.642343 ATGATACATACTACTACTGTGGAAGAA 57.358 33.333 0.00 0.00 0.00 2.52
1869 1937 9.067986 TGATGATACATACTACTACTGTGGAAG 57.932 37.037 0.00 0.00 0.00 3.46
1870 1938 8.990163 TGATGATACATACTACTACTGTGGAA 57.010 34.615 0.00 0.00 0.00 3.53
1872 1940 9.847706 GAATGATGATACATACTACTACTGTGG 57.152 37.037 0.00 0.00 0.00 4.17
1920 1997 4.632153 GTGAAACTAGGAACTGAAGCAGA 58.368 43.478 0.82 0.00 41.52 4.26
1953 2030 2.611225 AGGATGCACTAGTAAGCTGC 57.389 50.000 6.73 1.43 33.21 5.25
1971 2048 2.014128 ACACACGTTGACCCAGAAAAG 58.986 47.619 5.01 0.00 0.00 2.27
1975 2052 0.756294 ATCACACACGTTGACCCAGA 59.244 50.000 5.01 0.00 0.00 3.86
1982 2059 9.632969 GCTTTAGTATAATAATCACACACGTTG 57.367 33.333 0.00 0.00 0.00 4.10
1983 2060 9.595823 AGCTTTAGTATAATAATCACACACGTT 57.404 29.630 0.00 0.00 0.00 3.99
1999 2076 9.569122 TCCAAGAAAACAACTTAGCTTTAGTAT 57.431 29.630 0.00 0.00 0.00 2.12
2009 2086 6.317893 GGACTGAGTTCCAAGAAAACAACTTA 59.682 38.462 0.00 0.00 35.49 2.24
2067 2144 5.470098 GCTCTTTGATTTGGTACACTTCTGA 59.530 40.000 0.00 0.00 39.29 3.27
2106 2183 3.057999 CGTTGCGATTATTGCTGTTGTTG 59.942 43.478 5.97 0.00 0.00 3.33
2109 2186 2.840176 GTCGTTGCGATTATTGCTGTTG 59.160 45.455 5.97 0.00 38.42 3.33
2213 2290 8.868522 AGTAGTATACCTTAAGTACACACACA 57.131 34.615 0.97 0.00 44.47 3.72
2340 2417 3.381272 AGTTCGCCATATGGACAAATTGG 59.619 43.478 26.47 0.00 37.39 3.16
2355 2432 6.736123 TCTAGTCACAGATAATTAGTTCGCC 58.264 40.000 0.00 0.00 0.00 5.54
2505 2582 8.243426 GCATGTGTTTCAAATCTTACTATCCAA 58.757 33.333 0.00 0.00 0.00 3.53
2552 2630 8.138712 TCTGCTTACAACGGTTATTTCAAATTT 58.861 29.630 0.00 0.00 0.00 1.82
2555 2633 6.621316 TCTGCTTACAACGGTTATTTCAAA 57.379 33.333 0.00 0.00 0.00 2.69
2561 2639 8.416485 GTAAGTATTCTGCTTACAACGGTTAT 57.584 34.615 9.38 0.00 44.46 1.89
2562 2640 7.816945 GTAAGTATTCTGCTTACAACGGTTA 57.183 36.000 9.38 0.00 44.46 2.85
2589 2668 5.259832 TCAGATGCAGATACTTCTCACAG 57.740 43.478 0.00 0.00 0.00 3.66
2709 2788 1.696336 AGTGCTATCAGGCGGATCAAT 59.304 47.619 2.64 0.00 37.44 2.57
4127 4210 7.121168 TGAACTCATCACCTGGAAAACATAATC 59.879 37.037 0.00 0.00 31.50 1.75
4206 4295 1.249469 AACTCTCGTTCGGGGAGGAC 61.249 60.000 15.34 0.00 32.34 3.85
4299 4391 2.012673 GCTCGAACAATTGGCTCATCT 58.987 47.619 10.83 0.00 0.00 2.90
4329 4421 2.993220 GTTTTTGGCCATCGAACCAATC 59.007 45.455 6.09 8.42 45.08 2.67
4332 4424 1.403814 TGTTTTTGGCCATCGAACCA 58.596 45.000 6.09 0.00 0.00 3.67
4398 4490 0.034337 TACCTTCCGGCACTTGTGAC 59.966 55.000 0.00 0.00 0.00 3.67
4416 4508 1.210931 CTCACGGTCGGCGTCTTTA 59.789 57.895 6.85 0.00 0.00 1.85
4527 4619 1.970114 GAGGTCCGACCGTCTCACA 60.970 63.158 12.04 0.00 44.90 3.58
4675 4767 4.796231 CTCCCGACGAACCCTGCG 62.796 72.222 0.00 0.00 0.00 5.18
4846 4938 1.008995 GTGCGTGTTGCCGTTGATT 60.009 52.632 0.00 0.00 45.60 2.57
4935 5027 0.800631 TGCTGCATTCTTCTTGCTCG 59.199 50.000 0.00 0.00 40.77 5.03
4964 5056 0.096628 CTCATGTCTTTCGCTGCTGC 59.903 55.000 5.34 5.34 0.00 5.25
4965 5057 1.128136 CACTCATGTCTTTCGCTGCTG 59.872 52.381 0.00 0.00 0.00 4.41
4980 5078 0.250038 GCTCTGTGCTTCACCACTCA 60.250 55.000 0.00 0.00 38.95 3.41
4981 5079 0.250038 TGCTCTGTGCTTCACCACTC 60.250 55.000 3.20 0.00 43.37 3.51
4982 5080 0.181114 TTGCTCTGTGCTTCACCACT 59.819 50.000 3.20 0.00 43.37 4.00
5077 5178 1.896122 GACCTTCAACCGGACCCGAT 61.896 60.000 9.46 0.00 42.83 4.18
5166 5270 3.738246 CAGCAGCAGCACCAGCAG 61.738 66.667 3.17 0.00 45.49 4.24
5169 5273 3.738246 CAGCAGCAGCAGCACCAG 61.738 66.667 12.92 0.00 45.49 4.00
5170 5274 3.181238 TACAGCAGCAGCAGCACCA 62.181 57.895 12.92 0.00 45.49 4.17
5171 5275 2.359107 TACAGCAGCAGCAGCACC 60.359 61.111 12.92 0.00 45.49 5.01
5172 5276 1.303799 ATGTACAGCAGCAGCAGCAC 61.304 55.000 12.92 2.18 45.49 4.40
5322 5432 3.395669 GACGGAATCGGCTTTCGG 58.604 61.111 0.00 0.00 42.13 4.30
5335 5452 2.287668 ACGAAGAACAGAGAACAGACGG 60.288 50.000 0.00 0.00 0.00 4.79
5371 5488 0.958822 GCCATCACGAACAAAACCCT 59.041 50.000 0.00 0.00 0.00 4.34
5375 5492 3.145286 TCATCAGCCATCACGAACAAAA 58.855 40.909 0.00 0.00 0.00 2.44
5383 5500 3.196254 ACCCATTTTTCATCAGCCATCAC 59.804 43.478 0.00 0.00 0.00 3.06
5388 5505 4.462483 TGAGTTACCCATTTTTCATCAGCC 59.538 41.667 0.00 0.00 0.00 4.85
5404 5521 2.031157 ACGCACCTGCAAAATGAGTTAC 60.031 45.455 0.00 0.00 42.21 2.50
5406 5523 1.032014 ACGCACCTGCAAAATGAGTT 58.968 45.000 0.00 0.00 42.21 3.01
5408 5525 2.584791 GTAACGCACCTGCAAAATGAG 58.415 47.619 0.00 0.00 42.21 2.90
5435 5552 2.492090 CTCCGCCAGTCTCTTCCG 59.508 66.667 0.00 0.00 0.00 4.30
5554 5679 9.539825 CACAAGAATCAGCTGTCTAAATAGTAT 57.460 33.333 14.67 0.00 0.00 2.12
5666 5798 2.109181 GTAGCTAAGGCAGGCGGG 59.891 66.667 0.00 0.00 41.70 6.13
5667 5799 1.113517 TAGGTAGCTAAGGCAGGCGG 61.114 60.000 0.00 0.00 41.70 6.13
5668 5800 0.032267 GTAGGTAGCTAAGGCAGGCG 59.968 60.000 2.58 0.00 41.70 5.52
5717 5849 5.333187 CCGCACTTCTACTATGTACTCTACG 60.333 48.000 0.00 0.00 0.00 3.51
5743 5875 1.226717 GCCTGTCTGATCGACCGAC 60.227 63.158 12.89 0.00 42.13 4.79
5744 5876 1.377366 GAGCCTGTCTGATCGACCGA 61.377 60.000 12.89 0.00 42.13 4.69
5745 5877 1.064946 GAGCCTGTCTGATCGACCG 59.935 63.158 12.89 8.11 42.13 4.79
5746 5878 1.439644 GGAGCCTGTCTGATCGACC 59.560 63.158 12.89 0.00 42.13 4.79
6222 6515 3.006728 TTTCCGCCCTCCGTCCAT 61.007 61.111 0.00 0.00 34.38 3.41


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

AutoCloner maintained by Alex Coulton.