Multiple sequence alignment - TraesCS2B01G069900

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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 TraesCS2B01G069900 chr2B 100.000 4171 0 0 1 4171 37013774 37017944 0.000000e+00 7703
1 TraesCS2B01G069900 chr2B 92.040 3530 193 41 678 4169 37357513 37360992 0.000000e+00 4881
2 TraesCS2B01G069900 chr2B 89.907 3547 258 49 683 4170 37232367 37235872 0.000000e+00 4475
3 TraesCS2B01G069900 chr2B 89.738 3547 264 49 683 4170 37249525 37253030 0.000000e+00 4442
4 TraesCS2B01G069900 chr2B 92.605 2583 155 17 1270 3827 37215750 37218321 0.000000e+00 3679
5 TraesCS2B01G069900 chr2B 90.612 1651 111 20 678 2301 37123669 37125302 0.000000e+00 2150
6 TraesCS2B01G069900 chr2B 91.276 1238 89 10 2947 4170 37142945 37144177 0.000000e+00 1670
7 TraesCS2B01G069900 chr2B 93.491 169 11 0 4002 4170 37218314 37218482 6.920000e-63 252
8 TraesCS2B01G069900 chr2B 89.017 173 19 0 489 661 37123511 37123683 9.080000e-52 215
9 TraesCS2B01G069900 chr2B 85.612 139 13 1 435 566 37357316 37357454 5.620000e-29 139
10 TraesCS2B01G069900 chr1A 91.783 2215 152 18 1048 3249 534356964 534359161 0.000000e+00 3055
11 TraesCS2B01G069900 chr1A 83.648 899 94 19 3285 4166 534360735 534361597 0.000000e+00 797
12 TraesCS2B01G069900 chr1A 82.385 369 27 15 678 1025 534356624 534356975 1.900000e-73 287
13 TraesCS2B01G069900 chr1A 83.333 198 26 6 471 661 534356441 534356638 4.290000e-40 176
14 TraesCS2B01G069900 chr2A 91.805 2221 139 19 1048 3249 24572004 24569808 0.000000e+00 3053
15 TraesCS2B01G069900 chr2A 91.764 2222 139 20 1048 3249 24601394 24599197 0.000000e+00 3049
16 TraesCS2B01G069900 chr2A 91.629 2222 142 20 1048 3249 25640199 25642396 0.000000e+00 3033
17 TraesCS2B01G069900 chr2A 85.412 1419 137 30 683 2071 24545380 24544002 0.000000e+00 1410
18 TraesCS2B01G069900 chr2A 82.570 786 84 19 3285 4053 24568352 24567603 0.000000e+00 643
19 TraesCS2B01G069900 chr2A 82.570 786 82 20 3285 4053 24597741 24596994 3.520000e-180 641
20 TraesCS2B01G069900 chr2A 85.519 511 59 7 993 1495 24536489 24535986 1.720000e-143 520
21 TraesCS2B01G069900 chr2A 82.385 369 27 15 678 1025 24572344 24571993 1.900000e-73 287
22 TraesCS2B01G069900 chr2A 82.385 369 27 15 678 1025 24601734 24601383 1.900000e-73 287
23 TraesCS2B01G069900 chr2A 82.385 369 27 15 678 1025 25639859 25640210 1.900000e-73 287
24 TraesCS2B01G069900 chr2A 83.333 198 26 6 471 661 24572527 24572330 4.290000e-40 176
25 TraesCS2B01G069900 chr2A 83.333 198 26 6 471 661 24601917 24601720 4.290000e-40 176
26 TraesCS2B01G069900 chr2A 83.333 198 26 6 471 661 25639676 25639873 4.290000e-40 176
27 TraesCS2B01G069900 chr2A 93.636 110 7 0 4057 4166 24558612 24558503 9.280000e-37 165
28 TraesCS2B01G069900 chr2D 85.235 2296 265 44 857 3103 23046616 23044346 0.000000e+00 2294
29 TraesCS2B01G069900 chr2D 82.443 2096 267 58 1141 3199 23026936 23024905 0.000000e+00 1738
30 TraesCS2B01G069900 chr2D 89.189 666 66 4 1 661 23055167 23054503 0.000000e+00 826
31 TraesCS2B01G069900 chr2D 85.990 414 28 10 686 1077 23054509 23054104 2.320000e-112 416
32 TraesCS2B01G069900 chr2D 84.393 173 18 5 688 859 23027610 23027446 1.200000e-35 161
33 TraesCS2B01G069900 chrUn 91.118 1351 90 13 1048 2389 366633769 366635098 0.000000e+00 1803
34 TraesCS2B01G069900 chrUn 92.078 770 47 7 2491 3249 228952553 228951787 0.000000e+00 1072
35 TraesCS2B01G069900 chrUn 83.248 585 52 17 3285 3853 460996577 460996023 2.900000e-136 496
36 TraesCS2B01G069900 chrUn 88.652 282 31 1 3886 4166 338620178 338619897 3.990000e-90 342
37 TraesCS2B01G069900 chrUn 88.652 282 31 1 3886 4166 444705744 444706025 3.990000e-90 342
38 TraesCS2B01G069900 chrUn 89.030 237 25 1 1048 1283 342305920 342305684 4.080000e-75 292
39 TraesCS2B01G069900 chrUn 82.385 369 27 15 678 1025 342306260 342305909 1.900000e-73 287
40 TraesCS2B01G069900 chrUn 82.385 369 27 15 678 1025 366633429 366633780 1.900000e-73 287
41 TraesCS2B01G069900 chrUn 83.333 198 26 6 471 661 342306443 342306246 4.290000e-40 176
42 TraesCS2B01G069900 chrUn 83.333 198 26 6 471 661 366633246 366633443 4.290000e-40 176


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 TraesCS2B01G069900 chr2B 37013774 37017944 4170 False 7703.000000 7703 100.000000 1 4171 1 chr2B.!!$F1 4170
1 TraesCS2B01G069900 chr2B 37232367 37235872 3505 False 4475.000000 4475 89.907000 683 4170 1 chr2B.!!$F3 3487
2 TraesCS2B01G069900 chr2B 37249525 37253030 3505 False 4442.000000 4442 89.738000 683 4170 1 chr2B.!!$F4 3487
3 TraesCS2B01G069900 chr2B 37357316 37360992 3676 False 2510.000000 4881 88.826000 435 4169 2 chr2B.!!$F7 3734
4 TraesCS2B01G069900 chr2B 37215750 37218482 2732 False 1965.500000 3679 93.048000 1270 4170 2 chr2B.!!$F6 2900
5 TraesCS2B01G069900 chr2B 37142945 37144177 1232 False 1670.000000 1670 91.276000 2947 4170 1 chr2B.!!$F2 1223
6 TraesCS2B01G069900 chr2B 37123511 37125302 1791 False 1182.500000 2150 89.814500 489 2301 2 chr2B.!!$F5 1812
7 TraesCS2B01G069900 chr1A 534356441 534361597 5156 False 1078.750000 3055 85.287250 471 4166 4 chr1A.!!$F1 3695
8 TraesCS2B01G069900 chr2A 24544002 24545380 1378 True 1410.000000 1410 85.412000 683 2071 1 chr2A.!!$R2 1388
9 TraesCS2B01G069900 chr2A 25639676 25642396 2720 False 1165.333333 3033 85.782333 471 3249 3 chr2A.!!$F1 2778
10 TraesCS2B01G069900 chr2A 24567603 24572527 4924 True 1039.750000 3053 85.023250 471 4053 4 chr2A.!!$R4 3582
11 TraesCS2B01G069900 chr2A 24596994 24601917 4923 True 1038.250000 3049 85.013000 471 4053 4 chr2A.!!$R5 3582
12 TraesCS2B01G069900 chr2A 24535986 24536489 503 True 520.000000 520 85.519000 993 1495 1 chr2A.!!$R1 502
13 TraesCS2B01G069900 chr2D 23044346 23046616 2270 True 2294.000000 2294 85.235000 857 3103 1 chr2D.!!$R1 2246
14 TraesCS2B01G069900 chr2D 23024905 23027610 2705 True 949.500000 1738 83.418000 688 3199 2 chr2D.!!$R2 2511
15 TraesCS2B01G069900 chr2D 23054104 23055167 1063 True 621.000000 826 87.589500 1 1077 2 chr2D.!!$R3 1076
16 TraesCS2B01G069900 chrUn 228951787 228952553 766 True 1072.000000 1072 92.078000 2491 3249 1 chrUn.!!$R1 758
17 TraesCS2B01G069900 chrUn 366633246 366635098 1852 False 755.333333 1803 85.612000 471 2389 3 chrUn.!!$F2 1918
18 TraesCS2B01G069900 chrUn 460996023 460996577 554 True 496.000000 496 83.248000 3285 3853 1 chrUn.!!$R3 568
19 TraesCS2B01G069900 chrUn 342305684 342306443 759 True 251.666667 292 84.916000 471 1283 3 chrUn.!!$R4 812

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
648 690 0.249073 AGCATCGACGTCAGTATGGC 60.249 55.000 17.16 9.64 37.35 4.40 F
863 943 0.717224 ACACGGCTTAATTACACGCG 59.283 50.000 3.53 3.53 0.00 6.01 F
1123 1506 1.142097 TAATTCATGGCGCGGTCGA 59.858 52.632 8.83 0.00 38.10 4.20 F
1242 1643 1.225704 CCTTGATGCCTCACTCCCC 59.774 63.158 0.00 0.00 0.00 4.81 F
2392 2865 0.647410 CTGAATTACTGCAGGACGCG 59.353 55.000 19.93 3.53 46.97 6.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1636 2084 1.000163 CTGTAGCACTCTGTCGTGGTT 60.000 52.381 9.08 0.0 42.42 3.67 R
2354 2826 1.165270 GTTCCAGCGCAAGTGGTAAT 58.835 50.000 11.47 0.0 38.89 1.89 R
2392 2865 1.350193 CGCGTATGATCATGTAGGCC 58.650 55.000 18.72 0.0 0.00 5.19 R
2665 3138 2.203640 ACGAGGCTCTCACACCCA 60.204 61.111 13.50 0.0 0.00 4.51 R
3670 5719 0.104672 TTGAAGACTGGTCCAGGGGA 60.105 55.000 23.06 0.0 35.51 4.81 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
26 29 8.540388 AGAAGTGAAGCTAATCAATAGTGGTTA 58.460 33.333 0.00 0.00 33.87 2.85
30 33 9.595823 GTGAAGCTAATCAATAGTGGTTACTTA 57.404 33.333 9.46 1.04 38.36 2.24
33 36 8.320338 AGCTAATCAATAGTGGTTACTTACCT 57.680 34.615 0.00 0.00 38.70 3.08
52 55 0.396435 TGTTCGTGAAGAGCCATGGT 59.604 50.000 14.67 0.00 0.00 3.55
63 66 4.196372 CCATGGTTGGGCACAGTT 57.804 55.556 2.57 0.00 39.56 3.16
68 71 1.034838 TGGTTGGGCACAGTTGTCAC 61.035 55.000 0.00 0.00 0.00 3.67
112 117 2.058798 GAAGCTAAAACTTTTGGCGCC 58.941 47.619 22.73 22.73 0.00 6.53
116 121 2.869801 GCTAAAACTTTTGGCGCCTTTT 59.130 40.909 29.70 25.15 0.00 2.27
125 130 4.592485 TTTGGCGCCTTTTGAGAAATTA 57.408 36.364 29.70 0.00 0.00 1.40
135 140 7.905493 CGCCTTTTGAGAAATTATGTAGAGTTC 59.095 37.037 0.00 0.00 0.00 3.01
144 149 9.965902 AGAAATTATGTAGAGTTCAAAGGTCAT 57.034 29.630 0.00 0.00 0.00 3.06
150 155 7.921786 TGTAGAGTTCAAAGGTCATTAATGG 57.078 36.000 15.36 0.00 0.00 3.16
154 159 6.656693 AGAGTTCAAAGGTCATTAATGGACAG 59.343 38.462 15.36 2.16 37.00 3.51
157 162 4.943705 TCAAAGGTCATTAATGGACAGAGC 59.056 41.667 15.36 5.51 37.00 4.09
164 169 6.294731 GGTCATTAATGGACAGAGCAAAGTTT 60.295 38.462 15.36 0.00 37.00 2.66
166 171 6.489700 TCATTAATGGACAGAGCAAAGTTTCA 59.510 34.615 15.36 0.00 0.00 2.69
167 172 4.574599 AATGGACAGAGCAAAGTTTCAC 57.425 40.909 0.00 0.00 0.00 3.18
180 185 5.708948 CAAAGTTTCACTGTTTCCTGTTGA 58.291 37.500 0.00 0.00 0.00 3.18
193 198 6.979817 TGTTTCCTGTTGATTTGTCATTCTTG 59.020 34.615 0.00 0.00 0.00 3.02
202 207 6.680810 TGATTTGTCATTCTTGCCTTGTAAG 58.319 36.000 0.00 0.00 0.00 2.34
222 227 4.016113 AGACTTTGTCAAAACTGTTCGC 57.984 40.909 0.00 0.00 34.60 4.70
223 228 2.776225 GACTTTGTCAAAACTGTTCGCG 59.224 45.455 0.00 0.00 32.09 5.87
231 236 3.680842 AACTGTTCGCGGTTTCTCT 57.319 47.368 6.13 0.00 43.70 3.10
235 240 0.937699 TGTTCGCGGTTTCTCTCGTG 60.938 55.000 6.13 0.00 38.12 4.35
240 245 1.439679 GCGGTTTCTCTCGTGGAAAT 58.560 50.000 5.03 0.00 35.55 2.17
245 250 2.257974 TTCTCTCGTGGAAATCGACG 57.742 50.000 11.10 11.10 46.93 5.12
249 254 1.965990 TCGTGGAAATCGACGGGAA 59.034 52.632 16.10 0.00 45.87 3.97
250 255 0.533491 TCGTGGAAATCGACGGGAAT 59.467 50.000 16.10 0.00 45.87 3.01
271 276 4.888326 TGCCCTTTAATTTGTTCAGCAT 57.112 36.364 0.00 0.00 0.00 3.79
300 305 5.897377 AATATTGTGTGCAAGGTTACCTC 57.103 39.130 3.62 0.00 38.10 3.85
302 307 0.882927 TGTGTGCAAGGTTACCTCGC 60.883 55.000 7.49 7.49 33.52 5.03
322 327 6.292542 CCTCGCACAAATATCAGTTGAGTATG 60.293 42.308 0.00 0.00 0.00 2.39
331 336 9.499479 AAATATCAGTTGAGTATGAATGCCTAG 57.501 33.333 0.00 0.00 0.00 3.02
341 346 8.677300 TGAGTATGAATGCCTAGTTTTTCATTC 58.323 33.333 13.32 11.46 42.89 2.67
358 363 4.703897 TCATTCAATCCGACCCATTCTAC 58.296 43.478 0.00 0.00 0.00 2.59
363 368 1.046472 TCCGACCCATTCTACCGCAT 61.046 55.000 0.00 0.00 0.00 4.73
427 432 6.010219 GCCACATTGGTTAGATATTGGGTAT 58.990 40.000 0.00 0.00 40.46 2.73
451 456 1.292992 CCGCGTAAAGGTTGTATCCC 58.707 55.000 4.92 0.00 0.00 3.85
506 518 3.700538 TGCCTAGCTTTCCATTTGATGT 58.299 40.909 0.00 0.00 0.00 3.06
536 548 5.724370 TGTTTCTTCCATGTAGATCCTACCA 59.276 40.000 0.00 0.00 0.00 3.25
586 622 1.526225 GAGGTATCCGCCAAAGCCC 60.526 63.158 0.00 0.00 34.57 5.19
645 687 2.665056 CGTAGCATCGACGTCAGTAT 57.335 50.000 17.16 2.70 35.58 2.12
646 688 2.299170 CGTAGCATCGACGTCAGTATG 58.701 52.381 17.16 15.76 35.58 2.39
647 689 2.651701 GTAGCATCGACGTCAGTATGG 58.348 52.381 17.16 0.00 36.16 2.74
648 690 0.249073 AGCATCGACGTCAGTATGGC 60.249 55.000 17.16 9.64 37.35 4.40
657 699 2.802787 GTCAGTATGGCGCTGTAGAT 57.197 50.000 7.64 0.00 36.16 1.98
658 700 2.398498 GTCAGTATGGCGCTGTAGATG 58.602 52.381 7.64 0.00 36.16 2.90
659 701 2.031870 TCAGTATGGCGCTGTAGATGT 58.968 47.619 7.64 0.00 36.16 3.06
660 702 3.004419 GTCAGTATGGCGCTGTAGATGTA 59.996 47.826 7.64 0.00 36.16 2.29
661 703 3.826729 TCAGTATGGCGCTGTAGATGTAT 59.173 43.478 7.64 0.00 36.16 2.29
662 704 4.280929 TCAGTATGGCGCTGTAGATGTATT 59.719 41.667 7.64 0.00 36.16 1.89
663 705 4.991056 CAGTATGGCGCTGTAGATGTATTT 59.009 41.667 7.64 0.00 0.00 1.40
664 706 5.466728 CAGTATGGCGCTGTAGATGTATTTT 59.533 40.000 7.64 0.00 0.00 1.82
665 707 6.017934 CAGTATGGCGCTGTAGATGTATTTTT 60.018 38.462 7.64 0.00 0.00 1.94
716 760 3.369147 CACGCAGATTTGACCTAAGACTG 59.631 47.826 0.00 0.00 0.00 3.51
717 761 3.258372 ACGCAGATTTGACCTAAGACTGA 59.742 43.478 0.00 0.00 0.00 3.41
748 792 3.240670 CCTGGCCCAGGTCAGTATA 57.759 57.895 22.48 0.00 45.54 1.47
863 943 0.717224 ACACGGCTTAATTACACGCG 59.283 50.000 3.53 3.53 0.00 6.01
959 1311 2.481009 CTCGACGCGCAAGAGAGA 59.519 61.111 17.56 2.10 40.82 3.10
978 1346 8.172352 AGAGAGACAGTATATATTCACACCAC 57.828 38.462 0.00 0.00 0.00 4.16
991 1361 4.906065 TCACACCACCGTATACAGATAC 57.094 45.455 3.32 0.00 35.49 2.24
1031 1402 3.008485 AGCTAGCTCTGCCTAACTTGTTT 59.992 43.478 12.68 0.00 0.00 2.83
1083 1466 3.201353 TCGATTCCACCTGTTTTCACA 57.799 42.857 0.00 0.00 0.00 3.58
1123 1506 1.142097 TAATTCATGGCGCGGTCGA 59.858 52.632 8.83 0.00 38.10 4.20
1149 1532 1.270305 CCTCTCGTCAACAAGGCTTCA 60.270 52.381 0.00 0.00 0.00 3.02
1242 1643 1.225704 CCTTGATGCCTCACTCCCC 59.774 63.158 0.00 0.00 0.00 4.81
1280 1720 1.672030 CGGTGTTGCAGCAGGATGA 60.672 57.895 2.40 0.00 39.69 2.92
1283 1723 1.672030 TGTTGCAGCAGGATGACGG 60.672 57.895 0.00 0.00 39.69 4.79
1284 1724 2.747460 TTGCAGCAGGATGACGGC 60.747 61.111 0.00 0.00 39.69 5.68
1286 1726 4.819761 GCAGCAGGATGACGGCGA 62.820 66.667 16.62 0.00 45.49 5.54
1287 1727 2.887568 CAGCAGGATGACGGCGAC 60.888 66.667 16.62 8.59 45.49 5.19
1288 1728 3.381983 AGCAGGATGACGGCGACA 61.382 61.111 16.62 15.80 45.49 4.35
1289 1729 2.202932 GCAGGATGACGGCGACAT 60.203 61.111 23.65 23.65 39.69 3.06
1290 1730 2.240500 GCAGGATGACGGCGACATC 61.241 63.158 33.47 33.47 39.69 3.06
1291 1731 1.946156 CAGGATGACGGCGACATCG 60.946 63.158 33.54 22.72 43.24 3.84
1292 1732 2.104331 GGATGACGGCGACATCGT 59.896 61.111 33.54 16.47 43.24 3.73
1305 1745 2.202932 ATCGTCGCTGCCACCATC 60.203 61.111 0.00 0.00 0.00 3.51
1306 1746 3.740128 ATCGTCGCTGCCACCATCC 62.740 63.158 0.00 0.00 0.00 3.51
1315 1755 1.225704 GCCACCATCCCTCTGAAGG 59.774 63.158 0.00 0.00 42.95 3.46
1329 1769 3.960102 CTCTGAAGGGAGATGCTACTCTT 59.040 47.826 9.70 0.00 37.13 2.85
1508 1956 2.983791 GCTACGGCAACCCCACTA 59.016 61.111 0.00 0.00 38.54 2.74
1818 2268 6.889595 TCAAGGGATCCATATGCATGTATA 57.110 37.500 15.23 5.94 0.00 1.47
1925 2378 3.113322 GTGCATCGACATTAAGCTCGTA 58.887 45.455 0.00 0.00 0.00 3.43
2366 2838 8.665685 ACTAGATTTTAAAGATTACCACTTGCG 58.334 33.333 0.00 0.00 0.00 4.85
2392 2865 0.647410 CTGAATTACTGCAGGACGCG 59.353 55.000 19.93 3.53 46.97 6.01
2665 3138 2.363306 TCATTGCAACCTCACTTGGT 57.637 45.000 0.00 0.00 43.11 3.67
2718 3191 2.105134 TCATGTCCTTTTGGTACGTGGT 59.895 45.455 0.00 0.00 41.38 4.16
2928 3407 1.685148 GATGACATTCTCCAAGCCCC 58.315 55.000 0.00 0.00 0.00 5.80
2941 3420 2.165641 CCAAGCCCCGGAGAAAATTTAC 59.834 50.000 0.73 0.00 0.00 2.01
3066 3552 7.916914 TCCTAAGAAAAGGTAATTAGTGTGC 57.083 36.000 0.00 0.00 37.91 4.57
3125 3615 8.786937 TTGATGATAAGAAATATTTGCTTCGC 57.213 30.769 5.17 5.75 0.00 4.70
3127 3626 6.358118 TGATAAGAAATATTTGCTTCGCGT 57.642 33.333 5.77 0.00 0.00 6.01
3135 3634 2.804421 TTTGCTTCGCGTCATATGTG 57.196 45.000 5.77 0.00 0.00 3.21
3271 5050 3.145286 GGTAGATCACTCGGTAGGGTAC 58.855 54.545 0.00 0.00 0.00 3.34
3450 5497 8.435931 TGGCTTATGTATAAGATACTGTGGAT 57.564 34.615 14.21 0.00 41.72 3.41
3521 5568 1.620819 TCACTCTGGCTTCCTTGTCTC 59.379 52.381 0.00 0.00 0.00 3.36
3551 5598 1.065782 GGCCTTCAGAGACTTCCTTCC 60.066 57.143 0.00 0.00 0.00 3.46
3553 5600 2.238395 GCCTTCAGAGACTTCCTTCCAT 59.762 50.000 0.00 0.00 0.00 3.41
3603 5651 3.502356 GGAGGAAATCGATCTAGGAGGT 58.498 50.000 0.00 0.00 0.00 3.85
3604 5652 3.257127 GGAGGAAATCGATCTAGGAGGTG 59.743 52.174 0.00 0.00 0.00 4.00
3606 5654 5.063017 AGGAAATCGATCTAGGAGGTGTA 57.937 43.478 0.00 0.00 0.00 2.90
3670 5719 7.254164 ACCCCTAGGCTATAACACATAAGTAT 58.746 38.462 2.05 0.00 36.11 2.12
3738 5792 0.454600 TACTACCTTCTCGCTTGCCG 59.545 55.000 0.00 0.00 38.61 5.69
3752 5806 2.606108 CTTGCCGAGGTTTAAATTGGC 58.394 47.619 11.70 11.70 44.97 4.52
3758 5812 3.756434 CCGAGGTTTAAATTGGCTCTTCA 59.244 43.478 0.00 0.00 0.00 3.02
3805 5865 3.320610 TCTCCTATAGCCTGACTGCTT 57.679 47.619 0.00 0.00 42.75 3.91
3807 5867 3.117322 TCTCCTATAGCCTGACTGCTTCT 60.117 47.826 0.00 0.00 42.75 2.85
3853 5916 6.814146 GGTCTTGACTTTTCGATGAAGATAGT 59.186 38.462 13.97 0.00 0.00 2.12
3898 5961 0.874175 CAACTGACTTCCACGCGTCA 60.874 55.000 9.86 1.51 37.79 4.35
3905 5968 3.187700 GACTTCCACGCGTCATATTCTT 58.812 45.455 9.86 0.00 0.00 2.52
3930 5993 7.897920 TGCGTAATACTAGTTAAATTGTTCGG 58.102 34.615 0.00 0.00 0.00 4.30
3944 6007 0.461339 GTTCGGCCCGATTTGCTCTA 60.461 55.000 6.69 0.00 35.23 2.43
3948 6011 1.002468 CGGCCCGATTTGCTCTAAATG 60.002 52.381 0.00 0.00 39.06 2.32
4047 6111 1.528824 CACCTAGGCCACATCCCAG 59.471 63.158 9.30 0.00 0.00 4.45
4053 6117 2.352422 GCCACATCCCAGCTCACA 59.648 61.111 0.00 0.00 0.00 3.58
4112 6176 1.770658 CCCCTTGATCCTCATGCACTA 59.229 52.381 0.00 0.00 0.00 2.74
4170 6234 1.125711 ACGTGGAGGGGCTTTACTGT 61.126 55.000 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 29 2.288886 GGCTCTTCACGAACAGGTAAGT 60.289 50.000 0.00 0.00 0.00 2.24
30 33 0.687354 ATGGCTCTTCACGAACAGGT 59.313 50.000 0.00 0.00 0.00 4.00
33 36 0.396435 ACCATGGCTCTTCACGAACA 59.604 50.000 13.04 0.00 0.00 3.18
52 55 1.102154 CTTGTGACAACTGTGCCCAA 58.898 50.000 0.00 0.00 0.00 4.12
84 87 6.483307 GCCAAAAGTTTTAGCTTCCATTCTTT 59.517 34.615 10.97 0.00 0.00 2.52
87 90 4.385748 CGCCAAAAGTTTTAGCTTCCATTC 59.614 41.667 15.25 0.00 0.00 2.67
92 95 2.058798 GGCGCCAAAAGTTTTAGCTTC 58.941 47.619 24.80 7.87 0.00 3.86
93 96 1.686587 AGGCGCCAAAAGTTTTAGCTT 59.313 42.857 31.54 8.70 0.00 3.74
107 110 4.110036 ACATAATTTCTCAAAAGGCGCC 57.890 40.909 21.89 21.89 0.00 6.53
116 121 9.436957 GACCTTTGAACTCTACATAATTTCTCA 57.563 33.333 0.00 0.00 0.00 3.27
125 130 8.328758 TCCATTAATGACCTTTGAACTCTACAT 58.671 33.333 17.23 0.00 0.00 2.29
135 140 4.701651 TGCTCTGTCCATTAATGACCTTTG 59.298 41.667 17.23 4.42 0.00 2.77
144 149 6.072112 GTGAAACTTTGCTCTGTCCATTAA 57.928 37.500 0.00 0.00 0.00 1.40
164 169 4.946772 TGACAAATCAACAGGAAACAGTGA 59.053 37.500 0.00 0.00 0.00 3.41
166 171 6.322201 AGAATGACAAATCAACAGGAAACAGT 59.678 34.615 0.00 0.00 38.69 3.55
167 172 6.742109 AGAATGACAAATCAACAGGAAACAG 58.258 36.000 0.00 0.00 38.69 3.16
180 185 6.491403 AGTCTTACAAGGCAAGAATGACAAAT 59.509 34.615 0.00 0.00 36.86 2.32
193 198 5.743872 CAGTTTTGACAAAGTCTTACAAGGC 59.256 40.000 0.10 0.00 33.15 4.35
202 207 2.776225 CGCGAACAGTTTTGACAAAGTC 59.224 45.455 0.00 0.00 0.00 3.01
222 227 1.654105 CGATTTCCACGAGAGAAACCG 59.346 52.381 0.00 0.00 34.18 4.44
223 228 2.666994 GTCGATTTCCACGAGAGAAACC 59.333 50.000 0.00 0.00 40.37 3.27
231 236 0.533491 ATTCCCGTCGATTTCCACGA 59.467 50.000 0.00 0.00 38.32 4.35
235 240 1.444917 GGGCATTCCCGTCGATTTCC 61.445 60.000 0.00 0.00 43.94 3.13
249 254 4.888326 TGCTGAACAAATTAAAGGGCAT 57.112 36.364 0.00 0.00 0.00 4.40
250 255 4.282957 TCATGCTGAACAAATTAAAGGGCA 59.717 37.500 0.00 0.00 0.00 5.36
267 272 7.493320 CCTTGCACACAATATTATTTTCATGCT 59.507 33.333 0.00 0.00 34.61 3.79
268 273 7.278424 ACCTTGCACACAATATTATTTTCATGC 59.722 33.333 0.00 0.00 34.61 4.06
271 276 9.632807 GTAACCTTGCACACAATATTATTTTCA 57.367 29.630 0.00 0.00 34.61 2.69
300 305 6.588348 TCATACTCAACTGATATTTGTGCG 57.412 37.500 0.00 0.00 0.00 5.34
302 307 7.859377 GGCATTCATACTCAACTGATATTTGTG 59.141 37.037 0.00 0.00 0.00 3.33
322 327 6.473455 CGGATTGAATGAAAAACTAGGCATTC 59.527 38.462 0.00 0.00 44.12 2.67
331 336 4.513198 TGGGTCGGATTGAATGAAAAAC 57.487 40.909 0.00 0.00 0.00 2.43
341 346 1.865865 CGGTAGAATGGGTCGGATTG 58.134 55.000 0.00 0.00 0.00 2.67
342 347 0.106149 GCGGTAGAATGGGTCGGATT 59.894 55.000 0.00 0.00 0.00 3.01
358 363 5.580691 TGTAATCTCAGTCTGTTTTATGCGG 59.419 40.000 0.00 0.00 0.00 5.69
405 410 8.690203 TTCATACCCAATATCTAACCAATGTG 57.310 34.615 0.00 0.00 0.00 3.21
408 413 7.447238 CGGTTTCATACCCAATATCTAACCAAT 59.553 37.037 0.00 0.00 44.70 3.16
427 432 1.666054 ACAACCTTTACGCGGTTTCA 58.334 45.000 12.47 0.00 42.63 2.69
451 456 2.033194 GGTCTTGGAGGCGGTTTCG 61.033 63.158 0.00 0.00 39.81 3.46
506 518 0.537143 ACATGGAAGAAACAGCGGCA 60.537 50.000 1.45 0.00 0.00 5.69
536 548 3.277142 AGGAACAAACGAAACCAGTCT 57.723 42.857 0.00 0.00 0.00 3.24
609 645 2.202676 GCGCTGGAGAAGACCTCG 60.203 66.667 0.00 0.00 42.89 4.63
637 679 0.380733 TCTACAGCGCCATACTGACG 59.619 55.000 2.29 0.00 38.55 4.35
638 680 2.223829 ACATCTACAGCGCCATACTGAC 60.224 50.000 2.29 0.00 38.55 3.51
639 681 2.031870 ACATCTACAGCGCCATACTGA 58.968 47.619 2.29 0.00 38.55 3.41
674 716 1.327764 GTTTACATCTACAGCGCCAGC 59.672 52.381 2.29 0.00 45.58 4.85
675 717 2.348666 GTGTTTACATCTACAGCGCCAG 59.651 50.000 2.29 0.00 0.00 4.85
676 718 2.343101 GTGTTTACATCTACAGCGCCA 58.657 47.619 2.29 0.00 0.00 5.69
681 723 6.090763 TCAAATCTGCGTGTTTACATCTACAG 59.909 38.462 0.00 0.00 0.00 2.74
716 760 1.539280 GGCCAGGACGAATCTAAGCTC 60.539 57.143 0.00 0.00 0.00 4.09
717 761 0.466124 GGCCAGGACGAATCTAAGCT 59.534 55.000 0.00 0.00 0.00 3.74
748 792 1.559682 ACGTGCCAGTGGGATTAAGAT 59.440 47.619 12.15 0.00 35.59 2.40
808 880 7.931015 TGTACTAGTGGATCCATTATTCCTT 57.069 36.000 19.62 3.19 32.95 3.36
809 881 7.958583 AGATGTACTAGTGGATCCATTATTCCT 59.041 37.037 19.62 11.57 32.95 3.36
810 882 8.140112 AGATGTACTAGTGGATCCATTATTCC 57.860 38.462 19.62 3.99 0.00 3.01
863 943 0.179089 ATCCATGCTCAGTCTCGCAC 60.179 55.000 0.00 0.00 39.21 5.34
959 1311 5.864418 ACGGTGGTGTGAATATATACTGT 57.136 39.130 0.00 0.00 0.00 3.55
991 1361 1.657538 GCTGCTCGTTTGTGTTCTTCG 60.658 52.381 0.00 0.00 0.00 3.79
1031 1402 4.504514 GCCAAGCTCAGATAGGATCAATGA 60.505 45.833 0.00 0.00 0.00 2.57
1083 1466 1.289380 GTGCGGTCGAGGAAGAGTT 59.711 57.895 0.00 0.00 0.00 3.01
1123 1506 1.267261 CTTGTTGACGAGAGGAGACGT 59.733 52.381 0.00 0.00 45.32 4.34
1170 1568 3.437795 GAACGGCGAGGTCGGAGA 61.438 66.667 16.62 0.00 40.23 3.71
1176 1574 1.228657 GCTTTGAAGAACGGCGAGGT 61.229 55.000 16.62 0.00 0.00 3.85
1285 1725 3.188786 GGTGGCAGCGACGATGTC 61.189 66.667 11.38 11.38 0.00 3.06
1286 1726 3.315142 ATGGTGGCAGCGACGATGT 62.315 57.895 15.31 0.00 0.00 3.06
1287 1727 2.512286 ATGGTGGCAGCGACGATG 60.512 61.111 9.11 9.11 0.00 3.84
1288 1728 2.202932 GATGGTGGCAGCGACGAT 60.203 61.111 12.58 4.70 0.00 3.73
1289 1729 4.451150 GGATGGTGGCAGCGACGA 62.451 66.667 12.58 0.00 0.00 4.20
1291 1731 4.101448 AGGGATGGTGGCAGCGAC 62.101 66.667 12.58 8.19 0.00 5.19
1292 1732 3.785859 GAGGGATGGTGGCAGCGA 61.786 66.667 12.58 1.70 0.00 4.93
1293 1733 3.790437 AGAGGGATGGTGGCAGCG 61.790 66.667 12.58 0.00 0.00 5.18
1294 1734 2.124403 CAGAGGGATGGTGGCAGC 60.124 66.667 10.30 10.30 0.00 5.25
1295 1735 0.107312 CTTCAGAGGGATGGTGGCAG 60.107 60.000 0.00 0.00 0.00 4.85
1296 1736 1.565390 CCTTCAGAGGGATGGTGGCA 61.565 60.000 0.00 0.00 39.55 4.92
1297 1737 1.225704 CCTTCAGAGGGATGGTGGC 59.774 63.158 0.00 0.00 39.55 5.01
1306 1746 2.627699 GAGTAGCATCTCCCTTCAGAGG 59.372 54.545 0.00 0.00 43.15 3.69
1428 1876 4.821589 GGTCGCCCGAGCTCTTGG 62.822 72.222 12.85 13.14 39.31 3.61
1636 2084 1.000163 CTGTAGCACTCTGTCGTGGTT 60.000 52.381 9.08 0.00 42.42 3.67
1925 2378 4.363990 CGGTGACACAGCTCCGCT 62.364 66.667 8.08 0.00 40.77 5.52
1983 2436 2.306805 TGAGTGGCTTCTGATTGATGGT 59.693 45.455 0.00 0.00 0.00 3.55
2354 2826 1.165270 GTTCCAGCGCAAGTGGTAAT 58.835 50.000 11.47 0.00 38.89 1.89
2366 2838 2.421424 CCTGCAGTAATTCAGTTCCAGC 59.579 50.000 13.81 0.00 0.00 4.85
2392 2865 1.350193 CGCGTATGATCATGTAGGCC 58.650 55.000 18.72 0.00 0.00 5.19
2665 3138 2.203640 ACGAGGCTCTCACACCCA 60.204 61.111 13.50 0.00 0.00 4.51
3125 3615 9.558648 TTGAATTTCTTTCAATCACATATGACG 57.441 29.630 10.38 0.00 46.80 4.35
3187 3690 5.125417 CCCGAATAAAAGTGATTGACATGGT 59.875 40.000 0.00 0.00 0.00 3.55
3271 5050 2.505982 CTACTGACCATGCCGGGG 59.494 66.667 2.18 0.00 40.22 5.73
3352 5393 7.725251 TCACAATATACATGAGCATGAGTACA 58.275 34.615 16.70 0.00 41.20 2.90
3450 5497 4.202441 GACTAGGTCGTGTAACCCTATGA 58.798 47.826 0.00 0.00 40.42 2.15
3521 5568 2.168521 TCTCTGAAGGCCTTGTTATCCG 59.831 50.000 26.25 4.40 0.00 4.18
3551 5598 2.510906 CGGTCCAAGGGCCCTATG 59.489 66.667 28.96 23.84 0.00 2.23
3670 5719 0.104672 TTGAAGACTGGTCCAGGGGA 60.105 55.000 23.06 0.00 35.51 4.81
3738 5792 5.635280 GCTTTGAAGAGCCAATTTAAACCTC 59.365 40.000 0.00 0.00 36.66 3.85
3744 5798 3.763897 GGGAGCTTTGAAGAGCCAATTTA 59.236 43.478 0.00 0.00 43.74 1.40
3752 5806 4.646572 ACTGTTAAGGGAGCTTTGAAGAG 58.353 43.478 0.00 0.00 0.00 2.85
3758 5812 4.003648 CGATGAACTGTTAAGGGAGCTTT 58.996 43.478 0.00 0.00 0.00 3.51
3805 5865 2.231478 GAGTGGTTCATCCGACTTCAGA 59.769 50.000 0.00 0.00 39.52 3.27
3807 5867 1.275291 GGAGTGGTTCATCCGACTTCA 59.725 52.381 0.00 0.00 39.52 3.02
3853 5916 5.221106 GCCTAAATATCAATGTGCAGCTCAA 60.221 40.000 0.32 0.00 0.00 3.02
3905 5968 7.464444 GCCGAACAATTTAACTAGTATTACGCA 60.464 37.037 0.00 0.00 0.00 5.24
3928 5991 1.002468 CATTTAGAGCAAATCGGGCCG 60.002 52.381 22.51 22.51 34.49 6.13
3930 5993 4.370364 TTTCATTTAGAGCAAATCGGGC 57.630 40.909 0.00 0.00 34.49 6.13
3944 6007 4.834496 TGAAGAGACCAGCCAATTTCATTT 59.166 37.500 0.00 0.00 0.00 2.32
3948 6011 2.489722 GGTGAAGAGACCAGCCAATTTC 59.510 50.000 0.00 0.00 35.88 2.17
3998 6062 3.064820 ACACGTCATTTTGACTGGTTGTC 59.935 43.478 6.13 0.00 44.85 3.18
4053 6117 0.767375 AGATCAAGGCACACACCACT 59.233 50.000 0.00 0.00 0.00 4.00
4112 6176 3.983410 ACATCCCCACTAATGCCTCTTAT 59.017 43.478 0.00 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.