Multiple sequence alignment - TraesCS5A01G221500

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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 TraesCS5A01G221500 chr5A 100.000 2937 0 0 1 2937 437595011 437592075 0.000000e+00 5424
1 TraesCS5A01G221500 chr5A 88.186 838 90 8 157 991 501613360 501612529 0.000000e+00 990
2 TraesCS5A01G221500 chr5A 87.828 838 93 8 154 988 501060254 501061085 0.000000e+00 974
3 TraesCS5A01G221500 chr5A 87.663 843 91 10 157 993 246389724 246388889 0.000000e+00 968
4 TraesCS5A01G221500 chr5A 97.656 128 3 0 4 131 601268430 601268303 1.370000e-53 220
5 TraesCS5A01G221500 chr2B 95.369 1490 63 3 993 2481 692692939 692691455 0.000000e+00 2364
6 TraesCS5A01G221500 chr2B 97.222 432 11 1 2507 2937 692691326 692690895 0.000000e+00 730
7 TraesCS5A01G221500 chr4A 95.010 1483 70 1 992 2474 670765222 670766700 0.000000e+00 2326
8 TraesCS5A01G221500 chr4A 97.216 431 12 0 2507 2937 670766836 670767266 0.000000e+00 730
9 TraesCS5A01G221500 chr4A 96.947 131 4 0 1 131 164679675 164679805 1.370000e-53 220
10 TraesCS5A01G221500 chr7A 95.010 1483 59 2 992 2474 730331348 730329881 0.000000e+00 2314
11 TraesCS5A01G221500 chr7A 94.875 1483 61 2 992 2474 730378617 730377150 0.000000e+00 2303
12 TraesCS5A01G221500 chr7A 93.276 1041 56 1 992 2032 654049940 654050966 0.000000e+00 1522
13 TraesCS5A01G221500 chr7A 87.723 839 93 9 154 988 190619182 190620014 0.000000e+00 970
14 TraesCS5A01G221500 chr7A 96.752 431 14 0 2507 2937 630991569 630991999 0.000000e+00 719
15 TraesCS5A01G221500 chr7A 96.520 431 15 0 2507 2937 730329745 730329315 0.000000e+00 713
16 TraesCS5A01G221500 chr7A 96.288 431 16 0 2507 2937 655545775 655546205 0.000000e+00 708
17 TraesCS5A01G221500 chr7A 96.065 432 16 1 2507 2937 654053290 654053721 0.000000e+00 702
18 TraesCS5A01G221500 chr7A 97.692 130 3 0 2 131 96376051 96376180 1.060000e-54 224
19 TraesCS5A01G221500 chr7A 96.947 131 4 0 1 131 512420311 512420181 1.370000e-53 220
20 TraesCS5A01G221500 chr4B 94.003 1484 71 5 991 2474 7101711 7103176 0.000000e+00 2231
21 TraesCS5A01G221500 chr4B 96.010 827 33 0 1648 2474 424430841 424431667 0.000000e+00 1345
22 TraesCS5A01G221500 chr4B 96.520 431 15 0 2507 2937 424431803 424432233 0.000000e+00 713
23 TraesCS5A01G221500 chr4B 96.288 431 15 1 2507 2937 7103312 7103741 0.000000e+00 706
24 TraesCS5A01G221500 chr3A 95.425 1224 41 2 1252 2474 21307079 21308288 0.000000e+00 1936
25 TraesCS5A01G221500 chr3A 88.292 837 90 7 157 991 416662925 416662095 0.000000e+00 996
26 TraesCS5A01G221500 chr3A 96.288 431 15 1 2507 2937 42885452 42885881 0.000000e+00 706
27 TraesCS5A01G221500 chr3A 96.947 131 4 0 1 131 484920833 484920703 1.370000e-53 220
28 TraesCS5A01G221500 chr2A 94.922 1221 48 2 1252 2472 746144550 746143344 0.000000e+00 1899
29 TraesCS5A01G221500 chr2A 94.849 1223 49 1 1252 2474 22312388 22311180 0.000000e+00 1897
30 TraesCS5A01G221500 chr2A 96.947 131 4 0 1 131 480305765 480305635 1.370000e-53 220
31 TraesCS5A01G221500 chr1D 87.683 1161 105 22 992 2148 462746363 462745237 0.000000e+00 1317
32 TraesCS5A01G221500 chr1A 92.473 837 54 7 157 991 123178026 123177197 0.000000e+00 1188
33 TraesCS5A01G221500 chr1A 91.981 823 58 6 171 991 123184933 123184117 0.000000e+00 1147
34 TraesCS5A01G221500 chr1A 83.863 1165 105 39 992 2148 554534904 554533815 0.000000e+00 1033
35 TraesCS5A01G221500 chr1A 96.947 131 4 0 1 131 47304434 47304304 1.370000e-53 220
36 TraesCS5A01G221500 chr1A 96.947 131 4 0 1 131 181526181 181526311 1.370000e-53 220
37 TraesCS5A01G221500 chr1B 85.701 1077 110 20 992 2063 637833187 637832150 0.000000e+00 1096
38 TraesCS5A01G221500 chr6A 88.200 839 87 10 154 988 120898886 120899716 0.000000e+00 990
39 TraesCS5A01G221500 chr6A 87.530 842 96 8 154 991 165001457 165002293 0.000000e+00 965
40 TraesCS5A01G221500 chr6A 96.947 131 4 0 1 131 550811760 550811890 1.370000e-53 220


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 TraesCS5A01G221500 chr5A 437592075 437595011 2936 True 5424.0 5424 100.0000 1 2937 1 chr5A.!!$R2 2936
1 TraesCS5A01G221500 chr5A 501612529 501613360 831 True 990.0 990 88.1860 157 991 1 chr5A.!!$R3 834
2 TraesCS5A01G221500 chr5A 501060254 501061085 831 False 974.0 974 87.8280 154 988 1 chr5A.!!$F1 834
3 TraesCS5A01G221500 chr5A 246388889 246389724 835 True 968.0 968 87.6630 157 993 1 chr5A.!!$R1 836
4 TraesCS5A01G221500 chr2B 692690895 692692939 2044 True 1547.0 2364 96.2955 993 2937 2 chr2B.!!$R1 1944
5 TraesCS5A01G221500 chr4A 670765222 670767266 2044 False 1528.0 2326 96.1130 992 2937 2 chr4A.!!$F2 1945
6 TraesCS5A01G221500 chr7A 730377150 730378617 1467 True 2303.0 2303 94.8750 992 2474 1 chr7A.!!$R2 1482
7 TraesCS5A01G221500 chr7A 730329315 730331348 2033 True 1513.5 2314 95.7650 992 2937 2 chr7A.!!$R3 1945
8 TraesCS5A01G221500 chr7A 654049940 654053721 3781 False 1112.0 1522 94.6705 992 2937 2 chr7A.!!$F5 1945
9 TraesCS5A01G221500 chr7A 190619182 190620014 832 False 970.0 970 87.7230 154 988 1 chr7A.!!$F2 834
10 TraesCS5A01G221500 chr4B 7101711 7103741 2030 False 1468.5 2231 95.1455 991 2937 2 chr4B.!!$F1 1946
11 TraesCS5A01G221500 chr4B 424430841 424432233 1392 False 1029.0 1345 96.2650 1648 2937 2 chr4B.!!$F2 1289
12 TraesCS5A01G221500 chr3A 21307079 21308288 1209 False 1936.0 1936 95.4250 1252 2474 1 chr3A.!!$F1 1222
13 TraesCS5A01G221500 chr3A 416662095 416662925 830 True 996.0 996 88.2920 157 991 1 chr3A.!!$R1 834
14 TraesCS5A01G221500 chr2A 746143344 746144550 1206 True 1899.0 1899 94.9220 1252 2472 1 chr2A.!!$R3 1220
15 TraesCS5A01G221500 chr2A 22311180 22312388 1208 True 1897.0 1897 94.8490 1252 2474 1 chr2A.!!$R1 1222
16 TraesCS5A01G221500 chr1D 462745237 462746363 1126 True 1317.0 1317 87.6830 992 2148 1 chr1D.!!$R1 1156
17 TraesCS5A01G221500 chr1A 123177197 123178026 829 True 1188.0 1188 92.4730 157 991 1 chr1A.!!$R2 834
18 TraesCS5A01G221500 chr1A 123184117 123184933 816 True 1147.0 1147 91.9810 171 991 1 chr1A.!!$R3 820
19 TraesCS5A01G221500 chr1A 554533815 554534904 1089 True 1033.0 1033 83.8630 992 2148 1 chr1A.!!$R4 1156
20 TraesCS5A01G221500 chr1B 637832150 637833187 1037 True 1096.0 1096 85.7010 992 2063 1 chr1B.!!$R1 1071
21 TraesCS5A01G221500 chr6A 120898886 120899716 830 False 990.0 990 88.2000 154 988 1 chr6A.!!$F1 834
22 TraesCS5A01G221500 chr6A 165001457 165002293 836 False 965.0 965 87.5300 154 991 1 chr6A.!!$F2 837

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
111 112 0.036875 CAAGCGGACTTCTTCCCCTT 59.963 55.0 0.0 0.0 42.45 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1991 2034 0.171231 TGATGAGCCTCACGAACTCG 59.829 55.0 0.0 0.0 46.33 4.18 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
21 22 2.538512 TCATCAAGATCATCCTGCCG 57.461 50.000 0.00 0.00 0.00 5.69
22 23 2.041701 TCATCAAGATCATCCTGCCGA 58.958 47.619 0.00 0.00 0.00 5.54
23 24 2.435437 TCATCAAGATCATCCTGCCGAA 59.565 45.455 0.00 0.00 0.00 4.30
24 25 3.072038 TCATCAAGATCATCCTGCCGAAT 59.928 43.478 0.00 0.00 0.00 3.34
25 26 3.117491 TCAAGATCATCCTGCCGAATC 57.883 47.619 0.00 0.00 0.00 2.52
26 27 1.797046 CAAGATCATCCTGCCGAATCG 59.203 52.381 0.00 0.00 0.00 3.34
27 28 0.320247 AGATCATCCTGCCGAATCGC 60.320 55.000 0.00 0.00 0.00 4.58
28 29 1.294659 GATCATCCTGCCGAATCGCC 61.295 60.000 0.00 0.00 0.00 5.54
29 30 3.341043 CATCCTGCCGAATCGCCG 61.341 66.667 0.00 0.00 0.00 6.46
30 31 3.536917 ATCCTGCCGAATCGCCGA 61.537 61.111 0.00 0.00 0.00 5.54
31 32 3.792053 ATCCTGCCGAATCGCCGAC 62.792 63.158 0.00 0.00 0.00 4.79
32 33 4.812476 CCTGCCGAATCGCCGACA 62.812 66.667 0.00 0.00 0.00 4.35
33 34 3.257561 CTGCCGAATCGCCGACAG 61.258 66.667 0.00 0.00 34.07 3.51
36 37 2.586079 CCGAATCGCCGACAGCAT 60.586 61.111 0.00 0.00 44.04 3.79
37 38 2.589492 CCGAATCGCCGACAGCATC 61.589 63.158 0.00 0.00 44.04 3.91
38 39 2.589492 CGAATCGCCGACAGCATCC 61.589 63.158 0.00 0.00 44.04 3.51
39 40 1.521457 GAATCGCCGACAGCATCCA 60.521 57.895 0.00 0.00 44.04 3.41
40 41 1.493950 GAATCGCCGACAGCATCCAG 61.494 60.000 0.00 0.00 44.04 3.86
41 42 2.244117 AATCGCCGACAGCATCCAGT 62.244 55.000 0.00 0.00 44.04 4.00
42 43 2.635229 ATCGCCGACAGCATCCAGTC 62.635 60.000 0.00 0.00 44.04 3.51
46 47 2.512515 GACAGCATCCAGTCGCCC 60.513 66.667 0.00 0.00 0.00 6.13
47 48 3.005539 ACAGCATCCAGTCGCCCT 61.006 61.111 0.00 0.00 0.00 5.19
48 49 2.513204 CAGCATCCAGTCGCCCTG 60.513 66.667 0.00 0.00 41.15 4.45
55 56 2.989639 CAGTCGCCCTGGATCCAA 59.010 61.111 17.00 0.00 37.54 3.53
56 57 1.528824 CAGTCGCCCTGGATCCAAT 59.471 57.895 17.00 0.00 37.54 3.16
57 58 0.533755 CAGTCGCCCTGGATCCAATC 60.534 60.000 17.00 6.69 37.54 2.67
70 71 3.063704 CAATCCTTGGGCAGCGCA 61.064 61.111 11.47 8.34 0.00 6.09
71 72 2.753043 AATCCTTGGGCAGCGCAG 60.753 61.111 11.47 1.31 0.00 5.18
72 73 3.574074 AATCCTTGGGCAGCGCAGT 62.574 57.895 11.47 0.00 0.00 4.40
73 74 3.984193 ATCCTTGGGCAGCGCAGTC 62.984 63.158 11.47 1.58 0.00 3.51
75 76 4.711949 CTTGGGCAGCGCAGTCCT 62.712 66.667 24.55 0.00 0.00 3.85
76 77 4.704833 TTGGGCAGCGCAGTCCTC 62.705 66.667 24.55 9.23 0.00 3.71
81 82 3.443925 CAGCGCAGTCCTCGAGGA 61.444 66.667 30.49 30.49 43.08 3.71
89 90 3.843304 TCCTCGAGGAAGATCCGC 58.157 61.111 31.91 0.00 42.75 5.54
90 91 1.828660 TCCTCGAGGAAGATCCGCC 60.829 63.158 31.91 0.00 42.75 6.13
91 92 2.731374 CTCGAGGAAGATCCGCCC 59.269 66.667 3.91 0.00 42.75 6.13
92 93 2.838225 TCGAGGAAGATCCGCCCC 60.838 66.667 0.00 0.00 42.75 5.80
93 94 3.154473 CGAGGAAGATCCGCCCCA 61.154 66.667 0.00 0.00 42.75 4.96
94 95 2.731571 CGAGGAAGATCCGCCCCAA 61.732 63.158 0.00 0.00 42.75 4.12
95 96 1.147153 GAGGAAGATCCGCCCCAAG 59.853 63.158 0.00 0.00 42.75 3.61
96 97 2.517166 GGAAGATCCGCCCCAAGC 60.517 66.667 0.00 0.00 38.52 4.01
105 106 2.034221 GCCCCAAGCGGACTTCTT 59.966 61.111 0.00 0.00 32.29 2.52
106 107 2.041115 GCCCCAAGCGGACTTCTTC 61.041 63.158 0.00 0.00 32.29 2.87
107 108 1.377333 CCCCAAGCGGACTTCTTCC 60.377 63.158 0.00 0.00 41.75 3.46
108 109 1.377333 CCCAAGCGGACTTCTTCCC 60.377 63.158 0.00 0.00 42.27 3.97
109 110 1.377333 CCAAGCGGACTTCTTCCCC 60.377 63.158 0.00 0.00 42.27 4.81
110 111 1.679898 CAAGCGGACTTCTTCCCCT 59.320 57.895 0.00 0.00 42.27 4.79
111 112 0.036875 CAAGCGGACTTCTTCCCCTT 59.963 55.000 0.00 0.00 42.45 3.95
112 113 0.325272 AAGCGGACTTCTTCCCCTTC 59.675 55.000 0.00 0.00 37.95 3.46
113 114 1.078356 GCGGACTTCTTCCCCTTCC 60.078 63.158 0.00 0.00 42.27 3.46
114 115 1.602771 CGGACTTCTTCCCCTTCCC 59.397 63.158 0.00 0.00 42.27 3.97
115 116 1.911702 CGGACTTCTTCCCCTTCCCC 61.912 65.000 0.00 0.00 42.27 4.81
116 117 0.550393 GGACTTCTTCCCCTTCCCCT 60.550 60.000 0.00 0.00 38.70 4.79
117 118 0.621082 GACTTCTTCCCCTTCCCCTG 59.379 60.000 0.00 0.00 0.00 4.45
118 119 1.304617 CTTCTTCCCCTTCCCCTGC 59.695 63.158 0.00 0.00 0.00 4.85
119 120 1.465188 TTCTTCCCCTTCCCCTGCA 60.465 57.895 0.00 0.00 0.00 4.41
120 121 1.789576 TTCTTCCCCTTCCCCTGCAC 61.790 60.000 0.00 0.00 0.00 4.57
121 122 3.264845 TTCCCCTTCCCCTGCACC 61.265 66.667 0.00 0.00 0.00 5.01
141 142 3.339093 CGCCTTCCCCTTCCCCTT 61.339 66.667 0.00 0.00 0.00 3.95
142 143 2.684104 GCCTTCCCCTTCCCCTTC 59.316 66.667 0.00 0.00 0.00 3.46
143 144 2.997584 GCCTTCCCCTTCCCCTTCC 61.998 68.421 0.00 0.00 0.00 3.46
144 145 2.680370 CCTTCCCCTTCCCCTTCCG 61.680 68.421 0.00 0.00 0.00 4.30
145 146 2.612746 TTCCCCTTCCCCTTCCGG 60.613 66.667 0.00 0.00 0.00 5.14
146 147 3.196872 TTCCCCTTCCCCTTCCGGA 62.197 63.158 0.00 0.00 0.00 5.14
147 148 2.368329 CCCCTTCCCCTTCCGGAT 60.368 66.667 4.15 0.00 0.00 4.18
148 149 2.006991 CCCCTTCCCCTTCCGGATT 61.007 63.158 4.15 0.00 0.00 3.01
149 150 1.580994 CCCCTTCCCCTTCCGGATTT 61.581 60.000 4.15 0.00 0.00 2.17
150 151 0.106669 CCCTTCCCCTTCCGGATTTC 60.107 60.000 4.15 0.00 0.00 2.17
151 152 0.106669 CCTTCCCCTTCCGGATTTCC 60.107 60.000 4.15 0.00 0.00 3.13
152 153 0.919710 CTTCCCCTTCCGGATTTCCT 59.080 55.000 4.15 0.00 0.00 3.36
153 154 1.285078 CTTCCCCTTCCGGATTTCCTT 59.715 52.381 4.15 0.00 0.00 3.36
154 155 1.378732 TCCCCTTCCGGATTTCCTTT 58.621 50.000 4.15 0.00 0.00 3.11
155 156 1.714217 TCCCCTTCCGGATTTCCTTTT 59.286 47.619 4.15 0.00 0.00 2.27
189 190 5.197451 TGTTGTGACACCCTAGAATTTTGT 58.803 37.500 2.45 0.00 0.00 2.83
202 203 9.423061 CCCTAGAATTTTGTCCTTGTTTTAATG 57.577 33.333 0.00 0.00 0.00 1.90
319 322 7.428282 TTCCCAAAGTGAAAACTTTTCAAAC 57.572 32.000 16.79 7.44 37.80 2.93
338 341 9.442047 TTTCAAACATGTTATTGGACTTGTTTT 57.558 25.926 12.39 0.00 46.70 2.43
359 362 9.675464 TGTTTTACCTCTCAAGAAAAACTCTTA 57.325 29.630 14.73 0.00 42.84 2.10
450 454 5.480073 TCCAAGGTTATATGGCCATATTTGC 59.520 40.000 36.85 26.16 36.62 3.68
513 517 7.317390 CAAAATTTGGAGATGTCATGTGATGA 58.683 34.615 0.00 0.00 36.84 2.92
686 691 5.872070 GGTAGTAGCATATGATTCAGCTTCC 59.128 44.000 6.97 1.39 38.47 3.46
858 864 4.338795 TCCTAAGTCCAGGAGAGTGAAT 57.661 45.455 0.00 0.00 39.89 2.57
922 928 8.215050 TCCTTTCTGTCCAGAATTGTAGTTTTA 58.785 33.333 10.34 0.00 45.78 1.52
977 983 4.261197 GCAAACTAACTTCACCACCTTCTG 60.261 45.833 0.00 0.00 0.00 3.02
1009 1015 4.473520 CGGCGGCCATGGAGAACT 62.474 66.667 18.40 0.00 0.00 3.01
1056 1062 3.755628 GCCTACACGGTGCTCGGA 61.756 66.667 8.30 0.00 44.45 4.55
1063 1069 3.680786 CGGTGCTCGGAGACCACA 61.681 66.667 19.63 3.90 44.31 4.17
1117 1123 3.664025 CTGCCGTCCATCGCCTTCA 62.664 63.158 0.00 0.00 38.35 3.02
1223 1229 3.515286 CTGCCCAGCTTGGATGCG 61.515 66.667 8.31 0.00 40.96 4.73
1277 1283 3.323403 GGTCTAGCTATGCTTGGATCTGT 59.677 47.826 0.00 0.00 40.44 3.41
1287 1293 2.362077 GCTTGGATCTGTGGTTGTTGTT 59.638 45.455 0.00 0.00 0.00 2.83
1408 1422 3.758425 GCTAGGAAGCTAGCTAGGTACT 58.242 50.000 24.93 24.68 46.32 2.73
1409 1423 4.909001 GCTAGGAAGCTAGCTAGGTACTA 58.091 47.826 24.93 24.51 46.32 1.82
1410 1424 4.696877 GCTAGGAAGCTAGCTAGGTACTAC 59.303 50.000 24.93 11.96 46.32 2.73
1411 1425 5.513614 GCTAGGAAGCTAGCTAGGTACTACT 60.514 48.000 24.93 18.25 46.32 2.57
1412 1426 6.295802 GCTAGGAAGCTAGCTAGGTACTACTA 60.296 46.154 24.93 18.38 46.32 1.82
1413 1427 6.117975 AGGAAGCTAGCTAGGTACTACTAG 57.882 45.833 24.93 0.00 41.31 2.57
1554 1591 6.276832 TCTCAGTACAAGTGGGTATACAAC 57.723 41.667 5.01 2.60 0.00 3.32
1584 1621 3.042887 GCGGTTCTGTGTTTTGACATTC 58.957 45.455 0.00 0.00 0.00 2.67
1596 1633 5.124776 TGTTTTGACATTCGAACTCCTTTGT 59.875 36.000 0.00 0.00 0.00 2.83
1600 1637 2.800544 ACATTCGAACTCCTTTGTCACG 59.199 45.455 0.00 0.00 0.00 4.35
1719 1758 2.035321 TCCATTTTGGCGTCCTGTTTTC 59.965 45.455 0.00 0.00 37.47 2.29
1730 1770 4.438200 GCGTCCTGTTTTCTTTTTCTGACA 60.438 41.667 0.00 0.00 0.00 3.58
1957 2000 1.860641 TGAGGGGCTCTCGTGATAAA 58.139 50.000 10.34 0.00 45.32 1.40
1968 2011 5.446473 GCTCTCGTGATAAAAGTGAACCATG 60.446 44.000 0.00 0.00 0.00 3.66
2009 2052 0.452184 TCGAGTTCGTGAGGCTCATC 59.548 55.000 21.84 12.51 40.80 2.92
2389 4179 5.247792 CCCATCTCTCTCACCATCATATCAA 59.752 44.000 0.00 0.00 0.00 2.57
2416 4206 1.971695 GCGGGCAGCCTACAAACTT 60.972 57.895 12.43 0.00 40.81 2.66
2474 4264 1.602668 GCAGCAAGCATTTCGTTTCCA 60.603 47.619 0.00 0.00 44.79 3.53
2475 4265 2.053627 CAGCAAGCATTTCGTTTCCAC 58.946 47.619 0.00 0.00 0.00 4.02
2476 4266 1.956477 AGCAAGCATTTCGTTTCCACT 59.044 42.857 0.00 0.00 0.00 4.00
2477 4267 3.058293 CAGCAAGCATTTCGTTTCCACTA 60.058 43.478 0.00 0.00 0.00 2.74
2481 4271 5.163754 GCAAGCATTTCGTTTCCACTACTAT 60.164 40.000 0.00 0.00 0.00 2.12
2483 4273 6.663944 AGCATTTCGTTTCCACTACTATTC 57.336 37.500 0.00 0.00 0.00 1.75
2484 4274 5.585047 AGCATTTCGTTTCCACTACTATTCC 59.415 40.000 0.00 0.00 0.00 3.01
2485 4275 5.353123 GCATTTCGTTTCCACTACTATTCCA 59.647 40.000 0.00 0.00 0.00 3.53
2487 4277 5.988310 TTCGTTTCCACTACTATTCCAGA 57.012 39.130 0.00 0.00 0.00 3.86
2488 4278 5.320549 TCGTTTCCACTACTATTCCAGAC 57.679 43.478 0.00 0.00 0.00 3.51
2489 4279 5.014858 TCGTTTCCACTACTATTCCAGACT 58.985 41.667 0.00 0.00 0.00 3.24
2490 4280 5.125097 TCGTTTCCACTACTATTCCAGACTC 59.875 44.000 0.00 0.00 0.00 3.36
2491 4281 5.105877 CGTTTCCACTACTATTCCAGACTCA 60.106 44.000 0.00 0.00 0.00 3.41
2493 4283 6.716934 TTCCACTACTATTCCAGACTCATC 57.283 41.667 0.00 0.00 0.00 2.92
2495 4285 6.065374 TCCACTACTATTCCAGACTCATCTC 58.935 44.000 0.00 0.00 30.42 2.75
2496 4286 6.068010 CCACTACTATTCCAGACTCATCTCT 58.932 44.000 0.00 0.00 30.42 3.10
2497 4287 6.549364 CCACTACTATTCCAGACTCATCTCTT 59.451 42.308 0.00 0.00 30.42 2.85
2498 4288 7.069331 CCACTACTATTCCAGACTCATCTCTTT 59.931 40.741 0.00 0.00 30.42 2.52
2500 4290 6.478512 ACTATTCCAGACTCATCTCTTTCC 57.521 41.667 0.00 0.00 30.42 3.13
2503 4293 3.784178 TCCAGACTCATCTCTTTCCACT 58.216 45.455 0.00 0.00 30.42 4.00
2542 4435 3.132824 GCCCTGCAGTTATATTTTGGCTT 59.867 43.478 13.81 0.00 33.64 4.35
2754 4647 4.337763 GTTGATTCATCTTGCTAGCAACG 58.662 43.478 26.06 20.29 0.00 4.10
2789 4682 4.960938 TGCATACTTCTGTCAACAACTCT 58.039 39.130 0.00 0.00 0.00 3.24
2859 4753 8.166422 TCTGTTATACATCATACAGTGACGAT 57.834 34.615 0.00 0.00 40.28 3.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.636403 TCGGCAGGATGATCTTGATGAT 59.364 45.455 8.88 0.00 39.69 2.45
2 3 2.041701 TCGGCAGGATGATCTTGATGA 58.958 47.619 8.88 2.19 39.69 2.92
3 4 2.538512 TCGGCAGGATGATCTTGATG 57.461 50.000 8.88 0.00 39.69 3.07
4 5 3.672808 GATTCGGCAGGATGATCTTGAT 58.327 45.455 8.88 0.00 39.69 2.57
5 6 2.546584 CGATTCGGCAGGATGATCTTGA 60.547 50.000 8.88 0.00 39.69 3.02
6 7 1.797046 CGATTCGGCAGGATGATCTTG 59.203 52.381 0.00 0.00 39.69 3.02
7 8 1.875576 GCGATTCGGCAGGATGATCTT 60.876 52.381 8.34 0.00 39.69 2.40
8 9 0.320247 GCGATTCGGCAGGATGATCT 60.320 55.000 8.34 0.00 39.69 2.75
9 10 2.157421 GCGATTCGGCAGGATGATC 58.843 57.895 8.34 0.00 39.69 2.92
10 11 4.368391 GCGATTCGGCAGGATGAT 57.632 55.556 8.34 0.00 39.69 2.45
19 20 2.586079 ATGCTGTCGGCGATTCGG 60.586 61.111 14.79 7.50 45.43 4.30
20 21 2.589492 GGATGCTGTCGGCGATTCG 61.589 63.158 14.79 5.74 45.43 3.34
21 22 1.493950 CTGGATGCTGTCGGCGATTC 61.494 60.000 14.79 0.69 45.43 2.52
22 23 1.522355 CTGGATGCTGTCGGCGATT 60.522 57.895 14.79 0.00 45.43 3.34
23 24 2.107750 CTGGATGCTGTCGGCGAT 59.892 61.111 14.79 0.00 45.43 4.58
24 25 3.356639 GACTGGATGCTGTCGGCGA 62.357 63.158 4.99 4.99 45.43 5.54
25 26 2.887568 GACTGGATGCTGTCGGCG 60.888 66.667 8.42 0.00 45.43 6.46
29 30 2.512515 GGGCGACTGGATGCTGTC 60.513 66.667 13.25 13.25 0.00 3.51
30 31 3.005539 AGGGCGACTGGATGCTGT 61.006 61.111 0.00 0.00 0.00 4.40
31 32 2.513204 CAGGGCGACTGGATGCTG 60.513 66.667 0.00 0.00 43.70 4.41
39 40 1.832912 GATTGGATCCAGGGCGACT 59.167 57.895 15.53 0.00 0.00 4.18
40 41 4.464262 GATTGGATCCAGGGCGAC 57.536 61.111 15.53 0.80 0.00 5.19
54 55 2.753043 CTGCGCTGCCCAAGGATT 60.753 61.111 9.73 0.00 0.00 3.01
55 56 3.984193 GACTGCGCTGCCCAAGGAT 62.984 63.158 14.80 0.00 0.00 3.24
56 57 4.704833 GACTGCGCTGCCCAAGGA 62.705 66.667 14.80 0.00 0.00 3.36
58 59 4.711949 AGGACTGCGCTGCCCAAG 62.712 66.667 21.00 5.50 0.00 3.61
59 60 4.704833 GAGGACTGCGCTGCCCAA 62.705 66.667 21.00 0.00 0.00 4.12
64 65 2.880719 CTTCCTCGAGGACTGCGCTG 62.881 65.000 33.75 13.23 45.39 5.18
65 66 2.676822 TTCCTCGAGGACTGCGCT 60.677 61.111 33.75 0.00 45.39 5.92
66 67 2.010582 ATCTTCCTCGAGGACTGCGC 62.011 60.000 33.75 0.00 45.39 6.09
67 68 0.030101 GATCTTCCTCGAGGACTGCG 59.970 60.000 33.75 20.66 45.39 5.18
68 69 0.387565 GGATCTTCCTCGAGGACTGC 59.612 60.000 33.75 21.20 45.39 4.40
69 70 0.665835 CGGATCTTCCTCGAGGACTG 59.334 60.000 33.75 26.61 45.39 3.51
70 71 1.104577 GCGGATCTTCCTCGAGGACT 61.105 60.000 33.75 20.61 45.39 3.85
71 72 1.360911 GCGGATCTTCCTCGAGGAC 59.639 63.158 33.75 21.26 45.39 3.85
72 73 1.828660 GGCGGATCTTCCTCGAGGA 60.829 63.158 30.49 30.49 43.73 3.71
73 74 2.731374 GGCGGATCTTCCTCGAGG 59.269 66.667 26.32 26.32 33.30 4.63
74 75 2.731374 GGGCGGATCTTCCTCGAG 59.269 66.667 5.13 5.13 33.30 4.04
75 76 2.838225 GGGGCGGATCTTCCTCGA 60.838 66.667 0.00 0.00 33.30 4.04
76 77 2.650813 CTTGGGGCGGATCTTCCTCG 62.651 65.000 0.00 0.00 33.30 4.63
77 78 1.147153 CTTGGGGCGGATCTTCCTC 59.853 63.158 0.00 0.00 33.30 3.71
78 79 3.049080 GCTTGGGGCGGATCTTCCT 62.049 63.158 0.00 0.00 33.30 3.36
79 80 2.517166 GCTTGGGGCGGATCTTCC 60.517 66.667 0.00 0.00 0.00 3.46
88 89 2.034221 AAGAAGTCCGCTTGGGGC 59.966 61.111 0.00 0.00 42.41 5.80
89 90 1.377333 GGAAGAAGTCCGCTTGGGG 60.377 63.158 0.00 0.00 36.40 4.96
90 91 4.303257 GGAAGAAGTCCGCTTGGG 57.697 61.111 0.00 0.00 36.40 4.12
98 99 0.621082 CAGGGGAAGGGGAAGAAGTC 59.379 60.000 0.00 0.00 0.00 3.01
99 100 1.501654 GCAGGGGAAGGGGAAGAAGT 61.502 60.000 0.00 0.00 0.00 3.01
100 101 1.304617 GCAGGGGAAGGGGAAGAAG 59.695 63.158 0.00 0.00 0.00 2.85
101 102 1.465188 TGCAGGGGAAGGGGAAGAA 60.465 57.895 0.00 0.00 0.00 2.52
102 103 2.209809 TGCAGGGGAAGGGGAAGA 59.790 61.111 0.00 0.00 0.00 2.87
103 104 2.356667 GTGCAGGGGAAGGGGAAG 59.643 66.667 0.00 0.00 0.00 3.46
104 105 3.264845 GGTGCAGGGGAAGGGGAA 61.265 66.667 0.00 0.00 0.00 3.97
124 125 3.339093 AAGGGGAAGGGGAAGGCG 61.339 66.667 0.00 0.00 0.00 5.52
125 126 2.684104 GAAGGGGAAGGGGAAGGC 59.316 66.667 0.00 0.00 0.00 4.35
126 127 2.680370 CGGAAGGGGAAGGGGAAGG 61.680 68.421 0.00 0.00 0.00 3.46
127 128 2.998949 CGGAAGGGGAAGGGGAAG 59.001 66.667 0.00 0.00 0.00 3.46
134 135 7.576751 CCTAAAAGGAAATCCGGAAGGGGAA 62.577 48.000 9.01 0.00 45.84 3.97
135 136 6.165636 CCTAAAAGGAAATCCGGAAGGGGA 62.166 50.000 9.01 0.00 45.84 4.81
136 137 3.939884 CCTAAAAGGAAATCCGGAAGGGG 60.940 52.174 9.01 0.00 45.84 4.79
137 138 3.288092 CCTAAAAGGAAATCCGGAAGGG 58.712 50.000 9.01 0.00 45.84 3.95
138 139 3.288092 CCCTAAAAGGAAATCCGGAAGG 58.712 50.000 9.01 7.21 46.83 3.46
139 140 3.288092 CCCCTAAAAGGAAATCCGGAAG 58.712 50.000 9.01 0.00 37.67 3.46
140 141 2.024751 CCCCCTAAAAGGAAATCCGGAA 60.025 50.000 9.01 0.00 37.67 4.30
141 142 1.567175 CCCCCTAAAAGGAAATCCGGA 59.433 52.381 6.61 6.61 37.67 5.14
142 143 2.067365 CCCCCTAAAAGGAAATCCGG 57.933 55.000 0.00 0.00 37.67 5.14
223 224 6.015434 GGAGCCCAGAAAATCAAAGTTCTAAA 60.015 38.462 0.00 0.00 32.79 1.85
227 228 3.056536 GGGAGCCCAGAAAATCAAAGTTC 60.057 47.826 0.00 0.00 35.81 3.01
319 322 8.110860 AGAGGTAAAACAAGTCCAATAACATG 57.889 34.615 0.00 0.00 0.00 3.21
421 425 5.669164 TGGCCATATAACCTTGGAAAAAC 57.331 39.130 0.00 0.00 34.81 2.43
422 426 8.560124 AATATGGCCATATAACCTTGGAAAAA 57.440 30.769 33.47 7.39 34.81 1.94
450 454 9.912634 AAGTGATTTTATCAAATGGTTGTAGTG 57.087 29.630 0.00 0.00 41.69 2.74
564 568 6.712547 CCAGAGAAGAAAATTTGGTGTAGAGT 59.287 38.462 0.00 0.00 0.00 3.24
623 628 7.758820 TTGGTGGAGGGTAGAAAGAAATATA 57.241 36.000 0.00 0.00 0.00 0.86
637 642 3.396685 TCCCATAATTTTGGTGGAGGG 57.603 47.619 13.13 0.00 34.94 4.30
856 862 7.850935 AGCATTTAGAATCATCCAATGGATT 57.149 32.000 12.91 0.00 39.79 3.01
858 864 6.461927 GCAAGCATTTAGAATCATCCAATGGA 60.462 38.462 3.67 3.67 35.55 3.41
977 983 0.861837 CGCCGGTCTTTAGATGCATC 59.138 55.000 19.37 19.37 0.00 3.91
1009 1015 3.116300 GCTTATTGACGAGCGAGATCAA 58.884 45.455 0.00 0.00 36.81 2.57
1043 1049 3.681835 GGTCTCCGAGCACCGTGT 61.682 66.667 0.00 0.00 36.31 4.49
1049 1055 4.056125 CGCTGTGGTCTCCGAGCA 62.056 66.667 9.28 0.00 37.74 4.26
1056 1062 2.347322 GCTCTCCTCGCTGTGGTCT 61.347 63.158 0.00 0.00 0.00 3.85
1114 1120 2.989639 CACCTGGCCTCCGATGAA 59.010 61.111 3.32 0.00 0.00 2.57
1223 1229 3.906879 AAACCGTGGCCAAACCGC 61.907 61.111 7.24 0.00 46.23 5.68
1249 1255 0.605589 AGCATAGCTAGACCGCATCC 59.394 55.000 0.00 0.00 36.99 3.51
1277 1283 1.617947 GCCAACCCCAACAACAACCA 61.618 55.000 0.00 0.00 0.00 3.67
1287 1293 0.704076 AAATCTAGCTGCCAACCCCA 59.296 50.000 0.00 0.00 0.00 4.96
1411 1425 8.290185 GTTGATCCCAAGTGGTAGTAGTACCTA 61.290 44.444 24.16 10.60 40.24 3.08
1412 1426 7.537686 GTTGATCCCAAGTGGTAGTAGTACCT 61.538 46.154 24.16 5.60 40.24 3.08
1413 1427 5.394993 GTTGATCCCAAGTGGTAGTAGTACC 60.395 48.000 18.51 18.51 40.12 3.34
1505 1542 4.516698 CACTTGAACCACTCTTAACAGCAT 59.483 41.667 0.00 0.00 0.00 3.79
1584 1621 0.508641 CAGCGTGACAAAGGAGTTCG 59.491 55.000 0.00 0.00 0.00 3.95
1596 1633 1.880894 CCCGAACTCTACAGCGTGA 59.119 57.895 0.00 0.00 0.00 4.35
1600 1637 1.666189 GATTTGCCCGAACTCTACAGC 59.334 52.381 0.00 0.00 0.00 4.40
1719 1758 9.480538 CAAAACAAATCAATGTGTCAGAAAAAG 57.519 29.630 0.00 0.00 32.81 2.27
1730 1770 8.103948 TCAAACCAAACAAAACAAATCAATGT 57.896 26.923 0.00 0.00 34.24 2.71
1991 2034 0.171231 TGATGAGCCTCACGAACTCG 59.829 55.000 0.00 0.00 46.33 4.18
2009 2052 8.284693 GGTTCTGACATCAAATTGGAATTTTTG 58.715 33.333 0.00 0.33 36.52 2.44
2082 3872 6.573664 ATTGCAGTGCTTCAGTTATGTTTA 57.426 33.333 17.60 0.00 0.00 2.01
2337 4127 5.738909 AGCAGCGAAAGATAAGCCATATAT 58.261 37.500 0.00 0.00 0.00 0.86
2412 4202 8.196378 AGAACAGTAGTGGAAAGAGATAAGTT 57.804 34.615 1.92 0.00 0.00 2.66
2416 4206 8.107729 TGTCTAGAACAGTAGTGGAAAGAGATA 58.892 37.037 1.92 0.00 32.81 1.98
2474 4264 7.286775 GGAAAGAGATGAGTCTGGAATAGTAGT 59.713 40.741 0.00 0.00 33.97 2.73
2475 4265 7.286546 TGGAAAGAGATGAGTCTGGAATAGTAG 59.713 40.741 0.00 0.00 33.97 2.57
2476 4266 7.068839 GTGGAAAGAGATGAGTCTGGAATAGTA 59.931 40.741 0.00 0.00 33.97 1.82
2477 4267 5.960811 TGGAAAGAGATGAGTCTGGAATAGT 59.039 40.000 0.00 0.00 33.97 2.12
2481 4271 4.163427 AGTGGAAAGAGATGAGTCTGGAA 58.837 43.478 0.00 0.00 33.97 3.53
2483 4273 4.709397 AGTAGTGGAAAGAGATGAGTCTGG 59.291 45.833 0.00 0.00 33.97 3.86
2484 4274 5.913137 AGTAGTGGAAAGAGATGAGTCTG 57.087 43.478 0.00 0.00 33.97 3.51
2485 4275 8.474025 CAAATAGTAGTGGAAAGAGATGAGTCT 58.526 37.037 0.00 0.00 37.42 3.24
2487 4277 8.140112 ACAAATAGTAGTGGAAAGAGATGAGT 57.860 34.615 0.00 0.00 0.00 3.41
2493 4283 9.372369 CCTCTTAACAAATAGTAGTGGAAAGAG 57.628 37.037 11.59 11.59 37.42 2.85
2495 4285 7.065923 GCCCTCTTAACAAATAGTAGTGGAAAG 59.934 40.741 0.00 0.00 0.00 2.62
2496 4286 6.882678 GCCCTCTTAACAAATAGTAGTGGAAA 59.117 38.462 0.00 0.00 0.00 3.13
2497 4287 6.412214 GCCCTCTTAACAAATAGTAGTGGAA 58.588 40.000 0.00 0.00 0.00 3.53
2498 4288 5.104652 GGCCCTCTTAACAAATAGTAGTGGA 60.105 44.000 0.00 0.00 0.00 4.02
2500 4290 5.104485 AGGGCCCTCTTAACAAATAGTAGTG 60.104 44.000 22.28 0.00 0.00 2.74
2503 4293 4.384868 GCAGGGCCCTCTTAACAAATAGTA 60.385 45.833 25.77 0.00 0.00 1.82
2542 4435 5.104982 ACACAAAAATGAAGGAGCAAAAGGA 60.105 36.000 0.00 0.00 0.00 3.36
2649 4542 6.994496 AGCAGTTAAGCTATGCATCATTCTTA 59.006 34.615 0.19 4.26 44.50 2.10
2693 4586 7.560626 GGTTGGAGTCTAGAAAGGTATTCTCTA 59.439 40.741 0.00 0.00 0.00 2.43
2696 4589 6.265304 AGGTTGGAGTCTAGAAAGGTATTCT 58.735 40.000 0.00 0.00 0.00 2.40
2859 4753 0.908910 ATGGTTGGTGTATGCGGAGA 59.091 50.000 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.