Multiple sequence alignment - TraesCS2D01G456800

Loading Multiple Alignment...

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 TraesCS2D01G456800 chr2D 100.000 3452 0 0 1 3452 564475284 564478735 0.000000e+00 6375.0
1 TraesCS2D01G456800 chr2D 94.449 2414 104 9 791 3180 564438197 564440604 0.000000e+00 3688.0
2 TraesCS2D01G456800 chr2D 79.586 2415 352 66 465 2803 564418107 564420456 0.000000e+00 1598.0
3 TraesCS2D01G456800 chr2D 89.521 1212 103 14 1890 3087 564071994 564070793 0.000000e+00 1513.0
4 TraesCS2D01G456800 chr2D 95.526 760 26 4 1 754 564437436 564438193 0.000000e+00 1208.0
5 TraesCS2D01G456800 chr2D 93.333 90 5 1 3291 3379 564440609 564440698 7.770000e-27 132.0
6 TraesCS2D01G456800 chr2D 94.366 71 4 0 3378 3448 564440780 564440850 3.640000e-20 110.0
7 TraesCS2D01G456800 chr2B 92.382 3216 198 22 1 3180 675533064 675536268 0.000000e+00 4538.0
8 TraesCS2D01G456800 chr2B 81.147 2721 400 57 465 3114 675524277 675526955 0.000000e+00 2078.0
9 TraesCS2D01G456800 chr2B 88.990 1208 114 12 1890 3087 675334063 675332865 0.000000e+00 1476.0
10 TraesCS2D01G456800 chr2B 93.750 160 9 1 3291 3449 675536273 675536432 4.450000e-59 239.0
11 TraesCS2D01G456800 chr2A 89.972 1795 129 22 1 1757 705267545 705269326 0.000000e+00 2270.0
12 TraesCS2D01G456800 chr2A 82.219 2722 367 58 465 3114 705264057 705266733 0.000000e+00 2237.0
13 TraesCS2D01G456800 chr2A 88.696 1212 113 14 1890 3087 704754679 704753478 0.000000e+00 1458.0
14 TraesCS2D01G456800 chr2A 90.323 589 50 5 2079 2666 705342890 705343472 0.000000e+00 765.0
15 TraesCS2D01G456800 chr2A 94.595 111 4 2 3186 3294 96153111 96153221 1.650000e-38 171.0
16 TraesCS2D01G456800 chr4B 91.260 1087 77 11 1949 3032 22438650 22437579 0.000000e+00 1465.0
17 TraesCS2D01G456800 chr4B 92.702 1014 72 2 941 1953 22440877 22439865 0.000000e+00 1461.0
18 TraesCS2D01G456800 chr4B 89.956 1125 101 9 2058 3180 22488520 22487406 0.000000e+00 1441.0
19 TraesCS2D01G456800 chr4B 96.937 653 12 3 1 652 22442729 22442084 0.000000e+00 1088.0
20 TraesCS2D01G456800 chr4B 92.833 293 13 4 645 933 22441257 22440969 5.330000e-113 418.0
21 TraesCS2D01G456800 chr4B 85.890 163 15 3 3291 3452 22487401 22487246 2.130000e-37 167.0
22 TraesCS2D01G456800 chr4B 95.122 41 2 0 941 981 22440939 22440899 8.000000e-07 65.8
23 TraesCS2D01G456800 chr7A 79.104 1206 189 42 628 1784 9683769 9682578 0.000000e+00 773.0
24 TraesCS2D01G456800 chr7A 80.833 840 139 15 954 1784 9364074 9364900 1.040000e-179 640.0
25 TraesCS2D01G456800 chr7A 96.262 107 3 1 3187 3292 649922437 649922543 1.270000e-39 174.0
26 TraesCS2D01G456800 chr4A 78.518 1201 200 41 628 1784 729654105 729655291 0.000000e+00 736.0
27 TraesCS2D01G456800 chr4A 77.957 1175 200 31 653 1784 729798488 729799646 0.000000e+00 680.0
28 TraesCS2D01G456800 chr4A 77.575 1204 210 42 624 1784 729152151 729153337 0.000000e+00 673.0
29 TraesCS2D01G456800 chr4A 75.920 1196 222 44 628 1784 729213157 729214325 1.400000e-153 553.0
30 TraesCS2D01G456800 chr4A 92.500 120 5 4 3178 3294 593739138 593739020 5.930000e-38 169.0
31 TraesCS2D01G456800 chr7D 78.705 1174 195 37 653 1785 10056654 10057813 0.000000e+00 732.0
32 TraesCS2D01G456800 chr1A 97.222 108 1 2 3186 3291 556786980 556786873 7.610000e-42 182.0
33 TraesCS2D01G456800 chr5A 95.413 109 3 2 3185 3291 16499953 16500061 4.580000e-39 172.0
34 TraesCS2D01G456800 chr6A 93.913 115 4 3 3180 3291 475435048 475435162 1.650000e-38 171.0
35 TraesCS2D01G456800 chr6A 93.103 116 6 2 3181 3294 250834628 250834513 5.930000e-38 169.0
36 TraesCS2D01G456800 chr6D 90.476 126 9 3 3176 3299 435974338 435974462 2.760000e-36 163.0
37 TraesCS2D01G456800 chr3A 90.476 126 6 5 3175 3297 336604526 336604648 9.910000e-36 161.0


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 TraesCS2D01G456800 chr2D 564475284 564478735 3451 False 6375.00 6375 100.0000 1 3452 1 chr2D.!!$F2 3451
1 TraesCS2D01G456800 chr2D 564418107 564420456 2349 False 1598.00 1598 79.5860 465 2803 1 chr2D.!!$F1 2338
2 TraesCS2D01G456800 chr2D 564070793 564071994 1201 True 1513.00 1513 89.5210 1890 3087 1 chr2D.!!$R1 1197
3 TraesCS2D01G456800 chr2D 564437436 564440850 3414 False 1284.50 3688 94.4185 1 3448 4 chr2D.!!$F3 3447
4 TraesCS2D01G456800 chr2B 675533064 675536432 3368 False 2388.50 4538 93.0660 1 3449 2 chr2B.!!$F2 3448
5 TraesCS2D01G456800 chr2B 675524277 675526955 2678 False 2078.00 2078 81.1470 465 3114 1 chr2B.!!$F1 2649
6 TraesCS2D01G456800 chr2B 675332865 675334063 1198 True 1476.00 1476 88.9900 1890 3087 1 chr2B.!!$R1 1197
7 TraesCS2D01G456800 chr2A 705264057 705269326 5269 False 2253.50 2270 86.0955 1 3114 2 chr2A.!!$F3 3113
8 TraesCS2D01G456800 chr2A 704753478 704754679 1201 True 1458.00 1458 88.6960 1890 3087 1 chr2A.!!$R1 1197
9 TraesCS2D01G456800 chr2A 705342890 705343472 582 False 765.00 765 90.3230 2079 2666 1 chr2A.!!$F2 587
10 TraesCS2D01G456800 chr4B 22437579 22442729 5150 True 899.56 1465 93.7708 1 3032 5 chr4B.!!$R1 3031
11 TraesCS2D01G456800 chr4B 22487246 22488520 1274 True 804.00 1441 87.9230 2058 3452 2 chr4B.!!$R2 1394
12 TraesCS2D01G456800 chr7A 9682578 9683769 1191 True 773.00 773 79.1040 628 1784 1 chr7A.!!$R1 1156
13 TraesCS2D01G456800 chr7A 9364074 9364900 826 False 640.00 640 80.8330 954 1784 1 chr7A.!!$F1 830
14 TraesCS2D01G456800 chr4A 729654105 729655291 1186 False 736.00 736 78.5180 628 1784 1 chr4A.!!$F3 1156
15 TraesCS2D01G456800 chr4A 729798488 729799646 1158 False 680.00 680 77.9570 653 1784 1 chr4A.!!$F4 1131
16 TraesCS2D01G456800 chr4A 729152151 729153337 1186 False 673.00 673 77.5750 624 1784 1 chr4A.!!$F1 1160
17 TraesCS2D01G456800 chr4A 729213157 729214325 1168 False 553.00 553 75.9200 628 1784 1 chr4A.!!$F2 1156
18 TraesCS2D01G456800 chr7D 10056654 10057813 1159 False 732.00 732 78.7050 653 1785 1 chr7D.!!$F1 1132

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
939 1870 0.179045 CATCCCCTCGTCCATTGACC 60.179 60.0 0.0 0.0 38.32 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2558 4831 1.033202 TCTCGTACGCCATGTAGCCA 61.033 55.0 11.24 0.0 32.51 4.75 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
193 195 6.259167 AGGATAATTGAAAATACGCGCACTAA 59.741 34.615 5.73 0.00 0.00 2.24
410 419 0.253044 GTTCAGGGCTGGCACTATCA 59.747 55.000 2.88 0.00 0.00 2.15
695 1576 3.555956 ACTGTTCTACTTGTTCAACAGCG 59.444 43.478 17.25 0.00 46.49 5.18
700 1581 0.928229 ACTTGTTCAACAGCGTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
759 1644 4.080072 AGAGAAGAAAAGGGGATGATCACC 60.080 45.833 5.33 5.33 41.37 4.02
846 1740 5.534654 ACAATTGGTAACTTTTCTGCAGCTA 59.465 36.000 9.47 0.00 37.61 3.32
865 1759 4.344102 AGCTACAGAAATAGTATTGGCCGA 59.656 41.667 0.00 0.00 0.00 5.54
871 1765 5.408604 CAGAAATAGTATTGGCCGATGTACC 59.591 44.000 16.45 0.96 0.00 3.34
873 1767 2.910688 AGTATTGGCCGATGTACCTG 57.089 50.000 16.45 0.00 0.00 4.00
874 1769 2.394632 AGTATTGGCCGATGTACCTGA 58.605 47.619 16.45 0.00 0.00 3.86
876 1771 0.908910 ATTGGCCGATGTACCTGACA 59.091 50.000 4.07 0.00 43.97 3.58
921 1823 6.706270 GTCTCTTCCAAGTATTTGTCAACTCA 59.294 38.462 0.00 0.00 32.21 3.41
938 1869 0.830648 TCATCCCCTCGTCCATTGAC 59.169 55.000 0.00 0.00 38.18 3.18
939 1870 0.179045 CATCCCCTCGTCCATTGACC 60.179 60.000 0.00 0.00 38.32 4.02
944 1875 1.406069 CCCTCGTCCATTGACCTGAAG 60.406 57.143 0.00 0.00 38.32 3.02
1027 2020 2.123428 CCCAATACCAGCAGCCTGC 61.123 63.158 9.13 9.13 45.46 4.85
1293 2300 4.645535 TCAACTCCTTCAGGACAGATTTG 58.354 43.478 0.00 0.00 39.78 2.32
1440 2466 2.582687 GTGAAGACGAACCGAGTAGTG 58.417 52.381 0.00 0.00 0.00 2.74
1525 2551 4.330894 TCGACATCAACAGCATCAAATCTC 59.669 41.667 0.00 0.00 0.00 2.75
1617 2643 2.843401 ACCACGGCACATTACAGTTA 57.157 45.000 0.00 0.00 0.00 2.24
1744 2776 2.738521 CAGGTTCCACAGGCGACG 60.739 66.667 0.00 0.00 0.00 5.12
1842 2880 1.959282 AGAAAGGTGCTTTTGGCTCTG 59.041 47.619 0.00 0.00 42.39 3.35
2046 4303 1.377994 CAGAGGAGGCTTTGGCACT 59.622 57.895 0.00 0.00 40.87 4.40
2073 4330 2.823747 CCTTGGATACGTCGATGGGATA 59.176 50.000 9.90 0.00 42.51 2.59
2084 4341 2.438021 TCGATGGGATAAACTTGGAGGG 59.562 50.000 0.00 0.00 0.00 4.30
2178 4441 0.033920 ACACGATCAGCAAGCTGTCA 59.966 50.000 20.34 4.01 43.96 3.58
2322 4594 3.336715 CTCGTCCATGTCGGCGTCA 62.337 63.158 9.58 9.58 36.21 4.35
3180 5467 6.289834 TGACTACGGTTTCCTTGTGAAATTA 58.710 36.000 0.00 0.00 44.44 1.40
3182 6367 7.094975 TGACTACGGTTTCCTTGTGAAATTATG 60.095 37.037 0.00 0.00 44.44 1.90
3185 6370 4.858692 CGGTTTCCTTGTGAAATTATGCAG 59.141 41.667 0.00 0.00 44.44 4.41
3188 6373 6.806739 GGTTTCCTTGTGAAATTATGCAGTAC 59.193 38.462 0.00 0.00 44.44 2.73
3189 6374 7.309194 GGTTTCCTTGTGAAATTATGCAGTACT 60.309 37.037 0.00 0.00 44.44 2.73
3190 6375 6.985188 TCCTTGTGAAATTATGCAGTACTC 57.015 37.500 0.00 0.00 0.00 2.59
3191 6376 5.880332 TCCTTGTGAAATTATGCAGTACTCC 59.120 40.000 0.00 0.00 0.00 3.85
3192 6377 5.066505 CCTTGTGAAATTATGCAGTACTCCC 59.933 44.000 0.00 0.00 0.00 4.30
3193 6378 5.435686 TGTGAAATTATGCAGTACTCCCT 57.564 39.130 0.00 0.00 0.00 4.20
3194 6379 5.428253 TGTGAAATTATGCAGTACTCCCTC 58.572 41.667 0.00 0.00 0.00 4.30
3195 6380 4.816925 GTGAAATTATGCAGTACTCCCTCC 59.183 45.833 0.00 0.00 0.00 4.30
3196 6381 3.753294 AATTATGCAGTACTCCCTCCG 57.247 47.619 0.00 0.00 0.00 4.63
3197 6382 2.154567 TTATGCAGTACTCCCTCCGT 57.845 50.000 0.00 0.00 0.00 4.69
3198 6383 2.154567 TATGCAGTACTCCCTCCGTT 57.845 50.000 0.00 0.00 0.00 4.44
3199 6384 0.824759 ATGCAGTACTCCCTCCGTTC 59.175 55.000 0.00 0.00 0.00 3.95
3200 6385 1.255667 TGCAGTACTCCCTCCGTTCC 61.256 60.000 0.00 0.00 0.00 3.62
3201 6386 1.807886 CAGTACTCCCTCCGTTCCG 59.192 63.158 0.00 0.00 0.00 4.30
3202 6387 0.679002 CAGTACTCCCTCCGTTCCGA 60.679 60.000 0.00 0.00 0.00 4.55
3203 6388 0.038744 AGTACTCCCTCCGTTCCGAA 59.961 55.000 0.00 0.00 0.00 4.30
3204 6389 1.109609 GTACTCCCTCCGTTCCGAAT 58.890 55.000 0.00 0.00 0.00 3.34
3205 6390 1.479730 GTACTCCCTCCGTTCCGAATT 59.520 52.381 0.00 0.00 0.00 2.17
3206 6391 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
3207 6392 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
3208 6393 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
3209 6394 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
3210 6395 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
3211 6396 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
3212 6397 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
3213 6398 2.597305 CTCCGTTCCGAATTACTTGTCG 59.403 50.000 0.00 0.00 37.01 4.35
3214 6399 1.060122 CCGTTCCGAATTACTTGTCGC 59.940 52.381 0.00 0.00 35.93 5.19
3215 6400 1.722464 CGTTCCGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 35.93 5.10
3216 6401 2.222508 CGTTCCGAATTACTTGTCGCAG 60.223 50.000 0.00 0.00 35.93 5.18
3217 6402 2.004583 TCCGAATTACTTGTCGCAGG 57.995 50.000 0.00 0.00 35.93 4.85
3218 6403 1.274167 TCCGAATTACTTGTCGCAGGT 59.726 47.619 0.00 0.91 35.93 4.00
3219 6404 2.492881 TCCGAATTACTTGTCGCAGGTA 59.507 45.455 0.00 0.00 35.93 3.08
3220 6405 3.131577 TCCGAATTACTTGTCGCAGGTAT 59.868 43.478 3.46 0.00 35.93 2.73
3221 6406 3.245284 CCGAATTACTTGTCGCAGGTATG 59.755 47.826 3.46 0.00 35.93 2.39
3222 6407 4.109766 CGAATTACTTGTCGCAGGTATGA 58.890 43.478 3.46 0.00 0.00 2.15
3223 6408 4.565166 CGAATTACTTGTCGCAGGTATGAA 59.435 41.667 3.46 0.00 0.00 2.57
3224 6409 5.234329 CGAATTACTTGTCGCAGGTATGAAT 59.766 40.000 3.46 0.00 0.00 2.57
3225 6410 5.991328 ATTACTTGTCGCAGGTATGAATG 57.009 39.130 3.46 0.00 0.00 2.67
3226 6411 3.334583 ACTTGTCGCAGGTATGAATGT 57.665 42.857 0.00 0.00 0.00 2.71
3227 6412 4.465632 ACTTGTCGCAGGTATGAATGTA 57.534 40.909 0.00 0.00 0.00 2.29
3228 6413 5.023533 ACTTGTCGCAGGTATGAATGTAT 57.976 39.130 0.00 0.00 0.00 2.29
3229 6414 4.811024 ACTTGTCGCAGGTATGAATGTATG 59.189 41.667 0.00 0.00 0.00 2.39
3230 6415 4.400529 TGTCGCAGGTATGAATGTATGT 57.599 40.909 0.00 0.00 0.00 2.29
3231 6416 5.523438 TGTCGCAGGTATGAATGTATGTA 57.477 39.130 0.00 0.00 0.00 2.29
3232 6417 5.528870 TGTCGCAGGTATGAATGTATGTAG 58.471 41.667 0.00 0.00 0.00 2.74
3233 6418 5.300792 TGTCGCAGGTATGAATGTATGTAGA 59.699 40.000 0.00 0.00 0.00 2.59
3234 6419 6.015434 TGTCGCAGGTATGAATGTATGTAGAT 60.015 38.462 0.00 0.00 0.00 1.98
3235 6420 6.309009 GTCGCAGGTATGAATGTATGTAGATG 59.691 42.308 0.00 0.00 0.00 2.90
3236 6421 6.015434 TCGCAGGTATGAATGTATGTAGATGT 60.015 38.462 0.00 0.00 0.00 3.06
3237 6422 7.175990 TCGCAGGTATGAATGTATGTAGATGTA 59.824 37.037 0.00 0.00 0.00 2.29
3238 6423 7.976175 CGCAGGTATGAATGTATGTAGATGTAT 59.024 37.037 0.00 0.00 0.00 2.29
3239 6424 9.658799 GCAGGTATGAATGTATGTAGATGTATT 57.341 33.333 0.00 0.00 0.00 1.89
3265 6450 9.647797 TTTAGTTCTAGATACATCTTTTTGCGA 57.352 29.630 0.00 0.00 38.32 5.10
3266 6451 7.527084 AGTTCTAGATACATCTTTTTGCGAC 57.473 36.000 0.00 0.00 38.32 5.19
3267 6452 6.253727 AGTTCTAGATACATCTTTTTGCGACG 59.746 38.462 0.00 0.00 38.32 5.12
3268 6453 5.886992 TCTAGATACATCTTTTTGCGACGA 58.113 37.500 0.00 0.00 38.32 4.20
3269 6454 5.971792 TCTAGATACATCTTTTTGCGACGAG 59.028 40.000 0.00 0.00 38.32 4.18
3270 6455 4.495422 AGATACATCTTTTTGCGACGAGT 58.505 39.130 0.00 0.00 31.97 4.18
3271 6456 5.647589 AGATACATCTTTTTGCGACGAGTA 58.352 37.500 0.00 0.00 31.97 2.59
3272 6457 6.097356 AGATACATCTTTTTGCGACGAGTAA 58.903 36.000 0.00 0.00 31.97 2.24
3273 6458 6.757010 AGATACATCTTTTTGCGACGAGTAAT 59.243 34.615 0.00 0.00 31.97 1.89
3274 6459 5.607119 ACATCTTTTTGCGACGAGTAATT 57.393 34.783 0.00 0.00 0.00 1.40
3275 6460 5.997385 ACATCTTTTTGCGACGAGTAATTT 58.003 33.333 0.00 0.00 0.00 1.82
3276 6461 5.851177 ACATCTTTTTGCGACGAGTAATTTG 59.149 36.000 0.00 0.00 0.00 2.32
3277 6462 5.660629 TCTTTTTGCGACGAGTAATTTGA 57.339 34.783 0.00 0.00 0.00 2.69
3278 6463 6.050454 TCTTTTTGCGACGAGTAATTTGAA 57.950 33.333 0.00 0.00 0.00 2.69
3279 6464 6.487960 TCTTTTTGCGACGAGTAATTTGAAA 58.512 32.000 0.00 0.00 0.00 2.69
3280 6465 6.412653 TCTTTTTGCGACGAGTAATTTGAAAC 59.587 34.615 0.00 0.00 0.00 2.78
3281 6466 3.427516 TGCGACGAGTAATTTGAAACG 57.572 42.857 0.00 0.00 0.00 3.60
3282 6467 2.156117 TGCGACGAGTAATTTGAAACGG 59.844 45.455 0.00 0.00 0.00 4.44
3283 6468 2.409378 GCGACGAGTAATTTGAAACGGA 59.591 45.455 0.00 0.00 0.00 4.69
3284 6469 3.481467 GCGACGAGTAATTTGAAACGGAG 60.481 47.826 0.00 0.00 0.00 4.63
3285 6470 3.060363 CGACGAGTAATTTGAAACGGAGG 59.940 47.826 0.00 0.00 0.00 4.30
3286 6471 3.332034 ACGAGTAATTTGAAACGGAGGG 58.668 45.455 0.00 0.00 0.00 4.30
3287 6472 3.007182 ACGAGTAATTTGAAACGGAGGGA 59.993 43.478 0.00 0.00 0.00 4.20
3288 6473 3.617263 CGAGTAATTTGAAACGGAGGGAG 59.383 47.826 0.00 0.00 0.00 4.30
3289 6474 4.576879 GAGTAATTTGAAACGGAGGGAGT 58.423 43.478 0.00 0.00 0.00 3.85
3290 6475 5.622914 CGAGTAATTTGAAACGGAGGGAGTA 60.623 44.000 0.00 0.00 0.00 2.59
3291 6476 6.309389 AGTAATTTGAAACGGAGGGAGTAT 57.691 37.500 0.00 0.00 0.00 2.12
3292 6477 6.718294 AGTAATTTGAAACGGAGGGAGTATT 58.282 36.000 0.00 0.00 0.00 1.89
3306 6491 3.489785 GGGAGTATTTATGTTCGTCGCTG 59.510 47.826 0.00 0.00 0.00 5.18
3316 6501 1.649390 TTCGTCGCTGCTCTCCTCTC 61.649 60.000 0.00 0.00 0.00 3.20
3375 8050 9.975218 AAAGTTTGTAATCTACCCTAATGACAT 57.025 29.630 0.00 0.00 0.00 3.06
3412 8170 0.863119 GCATTGTCGGCATCTTTCGC 60.863 55.000 0.00 0.00 0.00 4.70
3435 8193 4.320861 CCGTTACATTGTTGAAGGCATTGA 60.321 41.667 0.00 0.00 0.00 2.57
3449 8207 2.578495 GCATTGACTTGAACTTGCTCG 58.422 47.619 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
380 389 1.074951 CCCTGAACAACCTGGGTCC 59.925 63.158 0.00 0.00 39.61 4.46
695 1576 1.212229 GTCTGGGAGGAACGACGAC 59.788 63.158 0.00 0.00 0.00 4.34
700 1581 2.432628 GCGTGTCTGGGAGGAACG 60.433 66.667 0.00 0.00 37.32 3.95
759 1644 6.618811 ACTCGCCGGTAATATATTTGACTAG 58.381 40.000 1.90 0.00 0.00 2.57
846 1740 5.036117 ACATCGGCCAATACTATTTCTGT 57.964 39.130 2.24 0.00 0.00 3.41
865 1759 2.567615 GGGACTTGTCTGTCAGGTACAT 59.432 50.000 0.00 0.00 38.53 2.29
871 1765 3.070018 GTCAATGGGACTTGTCTGTCAG 58.930 50.000 0.00 0.00 43.46 3.51
873 1767 2.224523 TGGTCAATGGGACTTGTCTGTC 60.225 50.000 0.61 0.00 46.16 3.51
874 1769 1.774254 TGGTCAATGGGACTTGTCTGT 59.226 47.619 0.61 0.00 46.16 3.41
876 1771 2.376518 ACATGGTCAATGGGACTTGTCT 59.623 45.455 0.00 0.00 46.16 3.41
921 1823 0.326618 AGGTCAATGGACGAGGGGAT 60.327 55.000 0.00 0.00 45.28 3.85
944 1875 3.375699 TCAGGGAAGAGGAAGATACCAC 58.624 50.000 0.00 0.00 0.00 4.16
1027 2020 1.202510 AGCTATGCAGAAGAAGCTCGG 60.203 52.381 3.11 0.00 41.35 4.63
1154 2161 2.087646 GCAGGGAGTTGTTGGAGATTC 58.912 52.381 0.00 0.00 0.00 2.52
1274 2281 4.841422 CATCAAATCTGTCCTGAAGGAGT 58.159 43.478 0.00 0.00 46.49 3.85
1525 2551 1.658994 TTAAGCGGGTATTGCCGAAG 58.341 50.000 0.00 0.00 38.44 3.79
1617 2643 6.883217 TGTACTGGACTAGAAATACTCGAAGT 59.117 38.462 0.00 0.00 0.00 3.01
1687 2719 4.155462 GTCGTCCACTAGATACTGTGACAA 59.845 45.833 0.00 0.00 36.38 3.18
1744 2776 1.609208 ATCTGGTTCAGTTGTGTGGC 58.391 50.000 0.00 0.00 32.61 5.01
1842 2880 6.743575 ATAGAGAACACAAGCAATGTAACC 57.256 37.500 0.00 0.00 41.46 2.85
2046 4303 4.426416 CATCGACGTATCCAAGGTAAACA 58.574 43.478 0.00 0.00 0.00 2.83
2073 4330 3.182996 ACGGCCCCCTCCAAGTTT 61.183 61.111 0.00 0.00 0.00 2.66
2178 4441 1.366366 CTTCACGAGGTTCCGGTGT 59.634 57.895 0.00 0.00 0.00 4.16
2326 4598 2.959484 ATGTGAGCTCCGGGGTGTG 61.959 63.158 12.15 0.00 0.00 3.82
2477 4750 4.658786 AGGCCGAAGTCCCCCAGT 62.659 66.667 0.00 0.00 0.00 4.00
2558 4831 1.033202 TCTCGTACGCCATGTAGCCA 61.033 55.000 11.24 0.00 32.51 4.75
3087 5374 2.266055 CGTGAGGGAAGTGGAGGC 59.734 66.667 0.00 0.00 0.00 4.70
3180 5467 0.824759 GAACGGAGGGAGTACTGCAT 59.175 55.000 16.81 9.33 0.00 3.96
3182 6367 1.516423 GGAACGGAGGGAGTACTGC 59.484 63.158 5.70 5.70 0.00 4.40
3196 6381 2.093783 CCTGCGACAAGTAATTCGGAAC 59.906 50.000 0.00 0.00 35.02 3.62
3197 6382 2.289195 ACCTGCGACAAGTAATTCGGAA 60.289 45.455 0.00 0.00 35.02 4.30
3198 6383 1.274167 ACCTGCGACAAGTAATTCGGA 59.726 47.619 0.00 0.00 35.73 4.55
3199 6384 1.722011 ACCTGCGACAAGTAATTCGG 58.278 50.000 0.00 0.00 35.73 4.30
3200 6385 4.109766 TCATACCTGCGACAAGTAATTCG 58.890 43.478 0.00 0.00 38.31 3.34
3201 6386 6.037172 ACATTCATACCTGCGACAAGTAATTC 59.963 38.462 0.00 0.00 0.00 2.17
3202 6387 5.880332 ACATTCATACCTGCGACAAGTAATT 59.120 36.000 0.00 0.00 0.00 1.40
3203 6388 5.428253 ACATTCATACCTGCGACAAGTAAT 58.572 37.500 0.00 0.00 0.00 1.89
3204 6389 4.827692 ACATTCATACCTGCGACAAGTAA 58.172 39.130 0.00 0.00 0.00 2.24
3205 6390 4.465632 ACATTCATACCTGCGACAAGTA 57.534 40.909 0.00 0.00 0.00 2.24
3206 6391 3.334583 ACATTCATACCTGCGACAAGT 57.665 42.857 0.00 0.00 0.00 3.16
3207 6392 4.811024 ACATACATTCATACCTGCGACAAG 59.189 41.667 0.00 0.00 0.00 3.16
3208 6393 4.765273 ACATACATTCATACCTGCGACAA 58.235 39.130 0.00 0.00 0.00 3.18
3209 6394 4.400529 ACATACATTCATACCTGCGACA 57.599 40.909 0.00 0.00 0.00 4.35
3210 6395 5.769367 TCTACATACATTCATACCTGCGAC 58.231 41.667 0.00 0.00 0.00 5.19
3211 6396 6.015434 ACATCTACATACATTCATACCTGCGA 60.015 38.462 0.00 0.00 0.00 5.10
3212 6397 6.159293 ACATCTACATACATTCATACCTGCG 58.841 40.000 0.00 0.00 0.00 5.18
3213 6398 9.658799 AATACATCTACATACATTCATACCTGC 57.341 33.333 0.00 0.00 0.00 4.85
3239 6424 9.647797 TCGCAAAAAGATGTATCTAGAACTAAA 57.352 29.630 0.00 0.00 35.76 1.85
3240 6425 9.084164 GTCGCAAAAAGATGTATCTAGAACTAA 57.916 33.333 0.00 0.00 35.76 2.24
3241 6426 7.431376 CGTCGCAAAAAGATGTATCTAGAACTA 59.569 37.037 0.00 0.00 35.76 2.24
3242 6427 6.253727 CGTCGCAAAAAGATGTATCTAGAACT 59.746 38.462 0.00 0.00 35.76 3.01
3243 6428 6.252869 TCGTCGCAAAAAGATGTATCTAGAAC 59.747 38.462 0.00 0.00 35.76 3.01
3244 6429 6.327154 TCGTCGCAAAAAGATGTATCTAGAA 58.673 36.000 0.00 0.00 35.76 2.10
3245 6430 5.886992 TCGTCGCAAAAAGATGTATCTAGA 58.113 37.500 0.00 0.00 35.76 2.43
3246 6431 5.744345 ACTCGTCGCAAAAAGATGTATCTAG 59.256 40.000 0.00 0.00 35.76 2.43
3247 6432 5.647589 ACTCGTCGCAAAAAGATGTATCTA 58.352 37.500 0.00 0.00 35.76 1.98
3248 6433 4.495422 ACTCGTCGCAAAAAGATGTATCT 58.505 39.130 0.00 0.00 39.22 1.98
3249 6434 4.842139 ACTCGTCGCAAAAAGATGTATC 57.158 40.909 0.00 0.00 0.00 2.24
3250 6435 6.903883 ATTACTCGTCGCAAAAAGATGTAT 57.096 33.333 0.00 0.00 0.00 2.29
3251 6436 6.715344 AATTACTCGTCGCAAAAAGATGTA 57.285 33.333 0.00 0.00 0.00 2.29
3252 6437 5.607119 AATTACTCGTCGCAAAAAGATGT 57.393 34.783 0.00 0.00 0.00 3.06
3253 6438 6.077197 TCAAATTACTCGTCGCAAAAAGATG 58.923 36.000 0.00 0.00 0.00 2.90
3254 6439 6.236017 TCAAATTACTCGTCGCAAAAAGAT 57.764 33.333 0.00 0.00 0.00 2.40
3255 6440 5.660629 TCAAATTACTCGTCGCAAAAAGA 57.339 34.783 0.00 0.00 0.00 2.52
3256 6441 6.560166 GTTTCAAATTACTCGTCGCAAAAAG 58.440 36.000 0.00 0.00 0.00 2.27
3257 6442 5.169915 CGTTTCAAATTACTCGTCGCAAAAA 59.830 36.000 0.00 0.00 0.00 1.94
3258 6443 4.667061 CGTTTCAAATTACTCGTCGCAAAA 59.333 37.500 0.00 0.00 0.00 2.44
3259 6444 4.205334 CGTTTCAAATTACTCGTCGCAAA 58.795 39.130 0.00 0.00 0.00 3.68
3260 6445 3.363182 CCGTTTCAAATTACTCGTCGCAA 60.363 43.478 0.00 0.00 0.00 4.85
3261 6446 2.156117 CCGTTTCAAATTACTCGTCGCA 59.844 45.455 0.00 0.00 0.00 5.10
3262 6447 2.409378 TCCGTTTCAAATTACTCGTCGC 59.591 45.455 0.00 0.00 0.00 5.19
3263 6448 3.060363 CCTCCGTTTCAAATTACTCGTCG 59.940 47.826 0.00 0.00 0.00 5.12
3264 6449 3.370061 CCCTCCGTTTCAAATTACTCGTC 59.630 47.826 0.00 0.00 0.00 4.20
3265 6450 3.007182 TCCCTCCGTTTCAAATTACTCGT 59.993 43.478 0.00 0.00 0.00 4.18
3266 6451 3.592059 TCCCTCCGTTTCAAATTACTCG 58.408 45.455 0.00 0.00 0.00 4.18
3267 6452 4.576879 ACTCCCTCCGTTTCAAATTACTC 58.423 43.478 0.00 0.00 0.00 2.59
3268 6453 4.635699 ACTCCCTCCGTTTCAAATTACT 57.364 40.909 0.00 0.00 0.00 2.24
3269 6454 6.997239 AATACTCCCTCCGTTTCAAATTAC 57.003 37.500 0.00 0.00 0.00 1.89
3270 6455 9.116067 CATAAATACTCCCTCCGTTTCAAATTA 57.884 33.333 0.00 0.00 0.00 1.40
3271 6456 7.614192 ACATAAATACTCCCTCCGTTTCAAATT 59.386 33.333 0.00 0.00 0.00 1.82
3272 6457 7.116736 ACATAAATACTCCCTCCGTTTCAAAT 58.883 34.615 0.00 0.00 0.00 2.32
3273 6458 6.478129 ACATAAATACTCCCTCCGTTTCAAA 58.522 36.000 0.00 0.00 0.00 2.69
3274 6459 6.057321 ACATAAATACTCCCTCCGTTTCAA 57.943 37.500 0.00 0.00 0.00 2.69
3275 6460 5.687166 ACATAAATACTCCCTCCGTTTCA 57.313 39.130 0.00 0.00 0.00 2.69
3276 6461 5.233689 CGAACATAAATACTCCCTCCGTTTC 59.766 44.000 0.00 0.00 0.00 2.78
3277 6462 5.114081 CGAACATAAATACTCCCTCCGTTT 58.886 41.667 0.00 0.00 0.00 3.60
3278 6463 4.161001 ACGAACATAAATACTCCCTCCGTT 59.839 41.667 0.00 0.00 0.00 4.44
3279 6464 3.703052 ACGAACATAAATACTCCCTCCGT 59.297 43.478 0.00 0.00 0.00 4.69
3280 6465 4.296690 GACGAACATAAATACTCCCTCCG 58.703 47.826 0.00 0.00 0.00 4.63
3281 6466 4.296690 CGACGAACATAAATACTCCCTCC 58.703 47.826 0.00 0.00 0.00 4.30
3282 6467 3.734735 GCGACGAACATAAATACTCCCTC 59.265 47.826 0.00 0.00 0.00 4.30
3283 6468 3.383825 AGCGACGAACATAAATACTCCCT 59.616 43.478 0.00 0.00 0.00 4.20
3284 6469 3.489785 CAGCGACGAACATAAATACTCCC 59.510 47.826 0.00 0.00 0.00 4.30
3285 6470 3.060473 GCAGCGACGAACATAAATACTCC 60.060 47.826 0.00 0.00 0.00 3.85
3286 6471 3.797256 AGCAGCGACGAACATAAATACTC 59.203 43.478 0.00 0.00 0.00 2.59
3287 6472 3.782046 AGCAGCGACGAACATAAATACT 58.218 40.909 0.00 0.00 0.00 2.12
3288 6473 3.797256 AGAGCAGCGACGAACATAAATAC 59.203 43.478 0.00 0.00 0.00 1.89
3289 6474 4.041740 AGAGCAGCGACGAACATAAATA 57.958 40.909 0.00 0.00 0.00 1.40
3290 6475 2.860735 GAGAGCAGCGACGAACATAAAT 59.139 45.455 0.00 0.00 0.00 1.40
3291 6476 2.259618 GAGAGCAGCGACGAACATAAA 58.740 47.619 0.00 0.00 0.00 1.40
3292 6477 1.469251 GGAGAGCAGCGACGAACATAA 60.469 52.381 0.00 0.00 0.00 1.90
3316 6501 4.063534 CGTTTCGAATAACAAACTCGTCG 58.936 43.478 0.00 0.00 34.27 5.12
3375 8050 7.144234 ACAATGCCAGGTATAACCAACTATA 57.856 36.000 0.00 0.00 41.95 1.31
3412 8170 3.848272 ATGCCTTCAACAATGTAACGG 57.152 42.857 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.