Multiple sequence alignment - TraesCS1B01G207700

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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 TraesCS1B01G207700 chr1B 100.000 3382 0 0 1 3382 375259403 375256022 0.000000e+00 6246.0
1 TraesCS1B01G207700 chr1D 89.835 3453 137 85 50 3363 275944900 275941523 0.000000e+00 4235.0
2 TraesCS1B01G207700 chr1A 87.232 2984 131 106 123 2945 348401403 348398509 0.000000e+00 3169.0
3 TraesCS1B01G207700 chr1A 86.547 446 32 8 2936 3365 348398267 348397834 1.840000e-127 466.0
4 TraesCS1B01G207700 chr5B 93.182 176 12 0 1693 1868 681847825 681848000 3.350000e-65 259.0
5 TraesCS1B01G207700 chr2A 82.533 229 18 13 1915 2141 697290087 697290295 7.450000e-42 182.0
6 TraesCS1B01G207700 chr2A 81.553 103 13 4 2274 2370 697290595 697290697 2.800000e-11 80.5
7 TraesCS1B01G207700 chr2A 85.714 56 5 2 2089 2141 727305424 727305479 4.710000e-04 56.5
8 TraesCS1B01G207700 chr2A 85.714 56 5 2 2089 2141 727350696 727350751 4.710000e-04 56.5
9 TraesCS1B01G207700 chr2D 81.373 102 13 4 2275 2370 557259391 557259492 1.010000e-10 78.7
10 TraesCS1B01G207700 chr2B 81.188 101 13 4 2275 2369 664934410 664934510 3.620000e-10 76.8


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 TraesCS1B01G207700 chr1B 375256022 375259403 3381 True 6246.0 6246 100.0000 1 3382 1 chr1B.!!$R1 3381
1 TraesCS1B01G207700 chr1D 275941523 275944900 3377 True 4235.0 4235 89.8350 50 3363 1 chr1D.!!$R1 3313
2 TraesCS1B01G207700 chr1A 348397834 348401403 3569 True 1817.5 3169 86.8895 123 3365 2 chr1A.!!$R1 3242

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
84 85 0.035317 TCTCCTCGCTGCACACAAAT 59.965 50.0 0.0 0.0 0.0 2.32 F
650 704 0.037326 ATACCACCACAGACACAGCG 60.037 55.0 0.0 0.0 0.0 5.18 F
1254 1375 0.038067 TGCGTGCGTTACTGTGGTAT 60.038 50.0 0.0 0.0 0.0 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1213 1317 0.179000 CAGTTCCCCTCATTCCTCCG 59.821 60.000 0.0 0.0 0.0 4.63 R
2240 2442 0.032615 GCAGAGGAGAGGAGGAGGAA 60.033 60.000 0.0 0.0 0.0 3.36 R
2541 2746 1.916181 TCCATCCACCTCCCTTTCTTC 59.084 52.381 0.0 0.0 0.0 2.87 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
22 23 4.982241 TTCTTGTGTCATCCTCTCCTTT 57.018 40.909 0.00 0.00 0.00 3.11
23 24 4.277515 TCTTGTGTCATCCTCTCCTTTG 57.722 45.455 0.00 0.00 0.00 2.77
24 25 3.648067 TCTTGTGTCATCCTCTCCTTTGT 59.352 43.478 0.00 0.00 0.00 2.83
25 26 4.838423 TCTTGTGTCATCCTCTCCTTTGTA 59.162 41.667 0.00 0.00 0.00 2.41
26 27 5.306937 TCTTGTGTCATCCTCTCCTTTGTAA 59.693 40.000 0.00 0.00 0.00 2.41
27 28 5.152623 TGTGTCATCCTCTCCTTTGTAAG 57.847 43.478 0.00 0.00 0.00 2.34
28 29 4.593206 TGTGTCATCCTCTCCTTTGTAAGT 59.407 41.667 0.00 0.00 0.00 2.24
29 30 5.071788 TGTGTCATCCTCTCCTTTGTAAGTT 59.928 40.000 0.00 0.00 0.00 2.66
30 31 5.998363 GTGTCATCCTCTCCTTTGTAAGTTT 59.002 40.000 0.00 0.00 0.00 2.66
31 32 5.997746 TGTCATCCTCTCCTTTGTAAGTTTG 59.002 40.000 0.00 0.00 0.00 2.93
32 33 5.412904 GTCATCCTCTCCTTTGTAAGTTTGG 59.587 44.000 0.00 0.00 0.00 3.28
33 34 5.309543 TCATCCTCTCCTTTGTAAGTTTGGA 59.690 40.000 0.00 0.00 0.00 3.53
34 35 5.228945 TCCTCTCCTTTGTAAGTTTGGAG 57.771 43.478 0.00 0.00 44.00 3.86
35 36 4.658901 TCCTCTCCTTTGTAAGTTTGGAGT 59.341 41.667 0.00 0.00 43.34 3.85
36 37 5.842328 TCCTCTCCTTTGTAAGTTTGGAGTA 59.158 40.000 0.00 0.00 43.34 2.59
37 38 6.328148 TCCTCTCCTTTGTAAGTTTGGAGTAA 59.672 38.462 0.00 0.00 43.34 2.24
38 39 7.017254 TCCTCTCCTTTGTAAGTTTGGAGTAAT 59.983 37.037 0.00 0.00 43.34 1.89
39 40 7.119846 CCTCTCCTTTGTAAGTTTGGAGTAATG 59.880 40.741 0.00 0.00 43.34 1.90
40 41 7.514721 TCTCCTTTGTAAGTTTGGAGTAATGT 58.485 34.615 0.00 0.00 43.34 2.71
41 42 7.444183 TCTCCTTTGTAAGTTTGGAGTAATGTG 59.556 37.037 0.00 0.00 43.34 3.21
42 43 6.488683 TCCTTTGTAAGTTTGGAGTAATGTGG 59.511 38.462 0.00 0.00 0.00 4.17
43 44 6.264518 CCTTTGTAAGTTTGGAGTAATGTGGT 59.735 38.462 0.00 0.00 0.00 4.16
44 45 7.446013 CCTTTGTAAGTTTGGAGTAATGTGGTA 59.554 37.037 0.00 0.00 0.00 3.25
45 46 7.972832 TTGTAAGTTTGGAGTAATGTGGTAG 57.027 36.000 0.00 0.00 0.00 3.18
46 47 7.069877 TGTAAGTTTGGAGTAATGTGGTAGT 57.930 36.000 0.00 0.00 0.00 2.73
47 48 8.192743 TGTAAGTTTGGAGTAATGTGGTAGTA 57.807 34.615 0.00 0.00 0.00 1.82
48 49 8.308931 TGTAAGTTTGGAGTAATGTGGTAGTAG 58.691 37.037 0.00 0.00 0.00 2.57
54 55 8.598202 TTGGAGTAATGTGGTAGTAGTAATGA 57.402 34.615 0.00 0.00 0.00 2.57
60 61 9.084164 GTAATGTGGTAGTAGTAATGAGTGTTG 57.916 37.037 0.00 0.00 0.00 3.33
72 73 1.813178 TGAGTGTTGCTACTCTCCTCG 59.187 52.381 21.84 0.00 45.70 4.63
74 75 0.528470 GTGTTGCTACTCTCCTCGCT 59.472 55.000 0.00 0.00 0.00 4.93
82 83 1.005748 CTCTCCTCGCTGCACACAA 60.006 57.895 0.00 0.00 0.00 3.33
84 85 0.035317 TCTCCTCGCTGCACACAAAT 59.965 50.000 0.00 0.00 0.00 2.32
85 86 0.877071 CTCCTCGCTGCACACAAATT 59.123 50.000 0.00 0.00 0.00 1.82
87 88 2.076100 TCCTCGCTGCACACAAATTAG 58.924 47.619 0.00 0.00 0.00 1.73
88 89 2.076100 CCTCGCTGCACACAAATTAGA 58.924 47.619 0.00 0.00 0.00 2.10
90 91 2.738846 CTCGCTGCACACAAATTAGAGT 59.261 45.455 0.00 0.00 0.00 3.24
91 92 3.920446 TCGCTGCACACAAATTAGAGTA 58.080 40.909 0.00 0.00 0.00 2.59
92 93 3.926527 TCGCTGCACACAAATTAGAGTAG 59.073 43.478 0.00 0.00 0.00 2.57
93 94 3.679980 CGCTGCACACAAATTAGAGTAGT 59.320 43.478 0.00 0.00 0.00 2.73
94 95 4.862574 CGCTGCACACAAATTAGAGTAGTA 59.137 41.667 0.00 0.00 0.00 1.82
95 96 5.220228 CGCTGCACACAAATTAGAGTAGTAC 60.220 44.000 0.00 0.00 0.00 2.73
96 97 5.637810 GCTGCACACAAATTAGAGTAGTACA 59.362 40.000 2.52 0.00 0.00 2.90
97 98 6.401153 GCTGCACACAAATTAGAGTAGTACAC 60.401 42.308 2.52 0.00 0.00 2.90
101 102 8.027771 GCACACAAATTAGAGTAGTACACTAGT 58.972 37.037 2.52 0.05 37.72 2.57
109 110 5.655893 GAGTAGTACACTAGTCTTAGCCG 57.344 47.826 14.40 0.00 42.70 5.52
120 121 0.459585 TCTTAGCCGTCATCAACCGC 60.460 55.000 0.00 0.00 32.93 5.68
121 122 1.429148 CTTAGCCGTCATCAACCGCC 61.429 60.000 0.00 0.00 33.17 6.13
232 241 0.105224 TGACCCAAAGAGAAACGCGA 59.895 50.000 15.93 0.00 0.00 5.87
333 346 4.478203 TCAAATCAAATCAAGTGGGGTGA 58.522 39.130 0.00 0.00 0.00 4.02
345 370 0.768622 TGGGGTGAAAATGTCCGTCT 59.231 50.000 0.00 0.00 0.00 4.18
375 400 1.826487 GAACACGTGCCCAAACCCT 60.826 57.895 17.22 0.00 0.00 4.34
376 401 0.535553 GAACACGTGCCCAAACCCTA 60.536 55.000 17.22 0.00 0.00 3.53
378 403 0.111639 ACACGTGCCCAAACCCTAAT 59.888 50.000 17.22 0.00 0.00 1.73
382 407 0.532115 GTGCCCAAACCCTAATGCAG 59.468 55.000 0.00 0.00 0.00 4.41
455 503 1.595882 CTGAGGTCACAGAGCAGGG 59.404 63.158 0.00 0.00 39.94 4.45
496 548 1.635663 AATCCGGCACTTCGCTTTCG 61.636 55.000 0.00 0.00 41.91 3.46
507 559 2.288961 TCGCTTTCGATCCCTGTTAC 57.711 50.000 0.00 0.00 40.21 2.50
515 569 4.563337 TCGATCCCTGTTACGTAATCAG 57.437 45.455 21.23 21.23 0.00 2.90
523 577 3.702330 TGTTACGTAATCAGATGCGAGG 58.298 45.455 11.86 0.00 0.00 4.63
525 579 1.399714 ACGTAATCAGATGCGAGGGA 58.600 50.000 12.84 0.00 0.00 4.20
526 580 1.338337 ACGTAATCAGATGCGAGGGAG 59.662 52.381 12.84 0.00 0.00 4.30
527 581 1.336332 CGTAATCAGATGCGAGGGAGG 60.336 57.143 2.40 0.00 0.00 4.30
528 582 1.001406 GTAATCAGATGCGAGGGAGGG 59.999 57.143 0.00 0.00 0.00 4.30
529 583 0.399091 AATCAGATGCGAGGGAGGGA 60.399 55.000 0.00 0.00 0.00 4.20
530 584 0.831288 ATCAGATGCGAGGGAGGGAG 60.831 60.000 0.00 0.00 0.00 4.30
531 585 1.456518 CAGATGCGAGGGAGGGAGA 60.457 63.158 0.00 0.00 0.00 3.71
649 703 1.442769 CATACCACCACAGACACAGC 58.557 55.000 0.00 0.00 0.00 4.40
650 704 0.037326 ATACCACCACAGACACAGCG 60.037 55.000 0.00 0.00 0.00 5.18
651 705 1.110518 TACCACCACAGACACAGCGA 61.111 55.000 0.00 0.00 0.00 4.93
652 706 1.227527 CCACCACAGACACAGCGAA 60.228 57.895 0.00 0.00 0.00 4.70
663 717 0.891373 CACAGCGAAAGAGGAGAGGA 59.109 55.000 0.00 0.00 0.00 3.71
685 739 2.289820 GGAAGACGACTTGGTTTGGTTC 59.710 50.000 4.51 0.00 36.39 3.62
686 740 1.963172 AGACGACTTGGTTTGGTTCC 58.037 50.000 0.00 0.00 0.00 3.62
772 834 1.151450 CCTCCCATTCCCATTCCCG 59.849 63.158 0.00 0.00 0.00 5.14
823 894 3.871485 TCGTCTACTTCTAGACTCCCAC 58.129 50.000 0.00 0.00 44.87 4.61
825 896 2.944349 GTCTACTTCTAGACTCCCACCG 59.056 54.545 0.00 0.00 44.02 4.94
826 897 1.677052 CTACTTCTAGACTCCCACCGC 59.323 57.143 0.00 0.00 0.00 5.68
827 898 0.971447 ACTTCTAGACTCCCACCGCC 60.971 60.000 0.00 0.00 0.00 6.13
828 899 1.677637 CTTCTAGACTCCCACCGCCC 61.678 65.000 0.00 0.00 0.00 6.13
829 900 3.528370 CTAGACTCCCACCGCCCG 61.528 72.222 0.00 0.00 0.00 6.13
855 926 4.530857 CCTGCCCATCCGTCCGTC 62.531 72.222 0.00 0.00 0.00 4.79
856 927 4.530857 CTGCCCATCCGTCCGTCC 62.531 72.222 0.00 0.00 0.00 4.79
952 1032 4.980702 CAGCAGCAGCCCAACCCA 62.981 66.667 0.00 0.00 43.56 4.51
953 1033 4.673375 AGCAGCAGCCCAACCCAG 62.673 66.667 0.00 0.00 43.56 4.45
975 1057 2.555757 CCCCTTCTTCTGCTTCTTGTTG 59.444 50.000 0.00 0.00 0.00 3.33
981 1063 5.643379 TCTTCTGCTTCTTGTTGTTGTTT 57.357 34.783 0.00 0.00 0.00 2.83
995 1077 2.103340 GTTTTTGGTGCGGTGCGT 59.897 55.556 0.00 0.00 0.00 5.24
996 1078 2.103143 TTTTTGGTGCGGTGCGTG 59.897 55.556 0.00 0.00 0.00 5.34
997 1079 2.407428 TTTTTGGTGCGGTGCGTGA 61.407 52.632 0.00 0.00 0.00 4.35
1044 1136 1.003355 CAAGGAGCTCCGCCTCAAA 60.003 57.895 26.95 0.00 42.08 2.69
1167 1271 4.836736 AGTAGTAGTACTGGTTTCTTGGCA 59.163 41.667 13.29 0.00 38.14 4.92
1187 1291 5.517054 TGGCATGTTTGTACGTTTCTTTTTC 59.483 36.000 0.00 0.00 0.00 2.29
1188 1292 5.331235 GGCATGTTTGTACGTTTCTTTTTCG 60.331 40.000 0.00 0.00 0.00 3.46
1191 1295 7.659159 CATGTTTGTACGTTTCTTTTTCGTTT 58.341 30.769 0.00 0.00 38.69 3.60
1192 1296 7.250839 TGTTTGTACGTTTCTTTTTCGTTTC 57.749 32.000 0.00 0.00 38.69 2.78
1193 1297 6.031210 TGTTTGTACGTTTCTTTTTCGTTTCG 59.969 34.615 0.00 0.00 38.69 3.46
1194 1298 5.202046 TGTACGTTTCTTTTTCGTTTCGT 57.798 34.783 0.00 0.00 38.69 3.85
1195 1299 5.247340 TGTACGTTTCTTTTTCGTTTCGTC 58.753 37.500 0.00 0.00 38.69 4.20
1196 1300 3.673366 ACGTTTCTTTTTCGTTTCGTCC 58.327 40.909 0.00 0.00 34.07 4.79
1197 1301 2.705486 CGTTTCTTTTTCGTTTCGTCCG 59.295 45.455 0.00 0.00 0.00 4.79
1198 1302 3.673366 GTTTCTTTTTCGTTTCGTCCGT 58.327 40.909 0.00 0.00 0.00 4.69
1199 1303 3.307339 TTCTTTTTCGTTTCGTCCGTG 57.693 42.857 0.00 0.00 0.00 4.94
1200 1304 1.004715 TCTTTTTCGTTTCGTCCGTGC 60.005 47.619 0.00 0.00 0.00 5.34
1201 1305 1.004292 CTTTTTCGTTTCGTCCGTGCT 60.004 47.619 0.00 0.00 0.00 4.40
1202 1306 0.578211 TTTTCGTTTCGTCCGTGCTC 59.422 50.000 0.00 0.00 0.00 4.26
1203 1307 1.216941 TTTCGTTTCGTCCGTGCTCC 61.217 55.000 0.00 0.00 0.00 4.70
1204 1308 2.049433 CGTTTCGTCCGTGCTCCT 60.049 61.111 0.00 0.00 0.00 3.69
1205 1309 2.087009 CGTTTCGTCCGTGCTCCTC 61.087 63.158 0.00 0.00 0.00 3.71
1240 1361 1.966451 GAGGGGAACTGGTTGCGTG 60.966 63.158 0.00 0.00 0.00 5.34
1241 1362 3.670377 GGGGAACTGGTTGCGTGC 61.670 66.667 0.00 0.00 0.00 5.34
1242 1363 4.025401 GGGAACTGGTTGCGTGCG 62.025 66.667 0.00 0.00 0.00 5.34
1244 1365 2.713154 GAACTGGTTGCGTGCGTT 59.287 55.556 0.00 0.00 0.00 4.84
1245 1366 1.500512 GGAACTGGTTGCGTGCGTTA 61.501 55.000 0.00 0.00 0.00 3.18
1246 1367 0.383860 GAACTGGTTGCGTGCGTTAC 60.384 55.000 0.00 0.00 0.00 2.50
1247 1368 0.812412 AACTGGTTGCGTGCGTTACT 60.812 50.000 0.00 0.00 0.00 2.24
1248 1369 1.204062 CTGGTTGCGTGCGTTACTG 59.796 57.895 0.00 0.00 0.00 2.74
1249 1370 1.495584 CTGGTTGCGTGCGTTACTGT 61.496 55.000 0.00 0.00 0.00 3.55
1250 1371 1.083015 GGTTGCGTGCGTTACTGTG 60.083 57.895 0.00 0.00 0.00 3.66
1251 1372 1.083015 GTTGCGTGCGTTACTGTGG 60.083 57.895 0.00 0.00 0.00 4.17
1252 1373 1.521906 TTGCGTGCGTTACTGTGGT 60.522 52.632 0.00 0.00 0.00 4.16
1253 1374 0.249363 TTGCGTGCGTTACTGTGGTA 60.249 50.000 0.00 0.00 0.00 3.25
1254 1375 0.038067 TGCGTGCGTTACTGTGGTAT 60.038 50.000 0.00 0.00 0.00 2.73
1255 1376 0.643820 GCGTGCGTTACTGTGGTATC 59.356 55.000 0.00 0.00 0.00 2.24
1256 1377 1.734707 GCGTGCGTTACTGTGGTATCT 60.735 52.381 0.00 0.00 0.00 1.98
1265 1386 0.388649 CTGTGGTATCTATCGGGCGC 60.389 60.000 0.00 0.00 0.00 6.53
1303 1444 1.800586 CAGTTCGTGTCAATCCTGTGG 59.199 52.381 0.00 0.00 0.00 4.17
1328 1469 1.202114 TGGCGGTCAAAGCATTGATTC 59.798 47.619 7.74 3.17 46.67 2.52
1329 1470 1.474077 GGCGGTCAAAGCATTGATTCT 59.526 47.619 7.74 0.00 46.67 2.40
1343 1492 5.866092 GCATTGATTCTTTTTCCCTGTCTTC 59.134 40.000 0.00 0.00 0.00 2.87
1351 1500 2.743636 TTCCCTGTCTTCTGCGTTAG 57.256 50.000 0.00 0.00 0.00 2.34
1449 1616 2.417239 TCGATGCGTTGGAATTTGGTAC 59.583 45.455 0.00 0.00 0.00 3.34
1450 1617 2.418628 CGATGCGTTGGAATTTGGTACT 59.581 45.455 0.00 0.00 0.00 2.73
1451 1618 3.619483 CGATGCGTTGGAATTTGGTACTA 59.381 43.478 0.00 0.00 0.00 1.82
1452 1619 4.260212 CGATGCGTTGGAATTTGGTACTAG 60.260 45.833 0.00 0.00 0.00 2.57
1516 1683 5.065090 TGGTTGATTGATTGATAACTCGCAG 59.935 40.000 0.00 0.00 0.00 5.18
2184 2386 3.423154 GCAACGACAAGGCGAGGG 61.423 66.667 0.66 0.00 34.83 4.30
2197 2399 4.424711 GAGGGTGATGCGGGCCAA 62.425 66.667 4.39 0.00 0.00 4.52
2229 2431 3.691342 CCAAGGGCTCGTCGGACA 61.691 66.667 9.10 0.00 0.00 4.02
2414 2619 0.171903 GCCATTGACAAAGCTGCGAT 59.828 50.000 6.37 0.00 0.00 4.58
2444 2649 2.551721 CCAGTTGCAGAGTGAATGGAGT 60.552 50.000 0.00 0.00 0.00 3.85
2541 2746 2.044551 GGGAGAAAGCAGGCAGGG 60.045 66.667 0.00 0.00 0.00 4.45
2889 3129 4.789012 AATATGGTGTTGCTCAACCTTG 57.211 40.909 9.92 0.00 40.46 3.61
2931 3172 4.016444 TCAATGGCTGGTTCTGGATTAAC 58.984 43.478 0.00 0.00 0.00 2.01
2932 3173 3.737559 ATGGCTGGTTCTGGATTAACA 57.262 42.857 0.00 0.00 0.00 2.41
2938 3429 6.321181 TGGCTGGTTCTGGATTAACAATTATC 59.679 38.462 0.00 0.00 0.00 1.75
2957 3448 8.689061 CAATTATCATTCATCCCTCTTGTTGAA 58.311 33.333 0.00 0.00 33.06 2.69
2958 3449 9.430399 AATTATCATTCATCCCTCTTGTTGAAT 57.570 29.630 0.00 0.00 38.89 2.57
2971 3462 6.712547 CCTCTTGTTGAATCTTCCTTAACTGT 59.287 38.462 0.00 0.00 0.00 3.55
3093 3584 0.260816 AGGGGCAGCATGAATGTGAT 59.739 50.000 0.00 0.00 39.69 3.06
3101 3592 1.752498 GCATGAATGTGATGGCCTGAA 59.248 47.619 3.32 0.00 0.00 3.02
3102 3593 2.166870 GCATGAATGTGATGGCCTGAAA 59.833 45.455 3.32 0.00 0.00 2.69
3109 3600 7.622713 TGAATGTGATGGCCTGAAAAATTATT 58.377 30.769 3.32 0.00 0.00 1.40
3111 3602 8.947055 AATGTGATGGCCTGAAAAATTATTAC 57.053 30.769 3.32 0.00 0.00 1.89
3112 3603 7.473735 TGTGATGGCCTGAAAAATTATTACA 57.526 32.000 3.32 0.00 0.00 2.41
3113 3604 8.076910 TGTGATGGCCTGAAAAATTATTACAT 57.923 30.769 3.32 0.00 0.00 2.29
3229 3727 4.074526 GACCGAGCAGAGCAGCCA 62.075 66.667 0.00 0.00 34.23 4.75
3297 3807 2.027385 GAGGGGAGATGCCACATTTTC 58.973 52.381 0.00 0.00 45.20 2.29
3298 3808 1.642762 AGGGGAGATGCCACATTTTCT 59.357 47.619 0.00 0.00 45.20 2.52
3299 3809 1.753073 GGGGAGATGCCACATTTTCTG 59.247 52.381 0.00 0.00 41.00 3.02
3300 3810 1.135721 GGGAGATGCCACATTTTCTGC 59.864 52.381 0.00 0.00 38.95 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.103153 ACAAAGGAGAGGATGACACAAGAA 59.897 41.667 0.00 0.00 0.00 2.52
2 3 3.648067 ACAAAGGAGAGGATGACACAAGA 59.352 43.478 0.00 0.00 0.00 3.02
3 4 4.013267 ACAAAGGAGAGGATGACACAAG 57.987 45.455 0.00 0.00 0.00 3.16
4 5 5.071788 ACTTACAAAGGAGAGGATGACACAA 59.928 40.000 0.00 0.00 0.00 3.33
5 6 4.593206 ACTTACAAAGGAGAGGATGACACA 59.407 41.667 0.00 0.00 0.00 3.72
6 7 5.153950 ACTTACAAAGGAGAGGATGACAC 57.846 43.478 0.00 0.00 0.00 3.67
10 11 5.560724 TCCAAACTTACAAAGGAGAGGATG 58.439 41.667 0.00 0.00 0.00 3.51
11 12 5.310857 ACTCCAAACTTACAAAGGAGAGGAT 59.689 40.000 13.23 0.00 46.89 3.24
12 13 4.658901 ACTCCAAACTTACAAAGGAGAGGA 59.341 41.667 13.23 0.00 46.89 3.71
13 14 4.974399 ACTCCAAACTTACAAAGGAGAGG 58.026 43.478 13.23 0.00 46.89 3.69
14 15 7.661847 ACATTACTCCAAACTTACAAAGGAGAG 59.338 37.037 13.23 0.00 46.89 3.20
15 16 7.444183 CACATTACTCCAAACTTACAAAGGAGA 59.556 37.037 13.23 0.00 46.89 3.71
17 18 6.488683 CCACATTACTCCAAACTTACAAAGGA 59.511 38.462 0.00 0.00 0.00 3.36
18 19 6.264518 ACCACATTACTCCAAACTTACAAAGG 59.735 38.462 0.00 0.00 0.00 3.11
19 20 7.272037 ACCACATTACTCCAAACTTACAAAG 57.728 36.000 0.00 0.00 0.00 2.77
20 21 7.994334 ACTACCACATTACTCCAAACTTACAAA 59.006 33.333 0.00 0.00 0.00 2.83
21 22 7.511268 ACTACCACATTACTCCAAACTTACAA 58.489 34.615 0.00 0.00 0.00 2.41
22 23 7.069877 ACTACCACATTACTCCAAACTTACA 57.930 36.000 0.00 0.00 0.00 2.41
23 24 8.309656 ACTACTACCACATTACTCCAAACTTAC 58.690 37.037 0.00 0.00 0.00 2.34
24 25 8.426569 ACTACTACCACATTACTCCAAACTTA 57.573 34.615 0.00 0.00 0.00 2.24
25 26 7.312415 ACTACTACCACATTACTCCAAACTT 57.688 36.000 0.00 0.00 0.00 2.66
26 27 6.930068 ACTACTACCACATTACTCCAAACT 57.070 37.500 0.00 0.00 0.00 2.66
27 28 9.095065 CATTACTACTACCACATTACTCCAAAC 57.905 37.037 0.00 0.00 0.00 2.93
28 29 9.038072 TCATTACTACTACCACATTACTCCAAA 57.962 33.333 0.00 0.00 0.00 3.28
29 30 8.598202 TCATTACTACTACCACATTACTCCAA 57.402 34.615 0.00 0.00 0.00 3.53
30 31 7.837689 ACTCATTACTACTACCACATTACTCCA 59.162 37.037 0.00 0.00 0.00 3.86
31 32 8.136165 CACTCATTACTACTACCACATTACTCC 58.864 40.741 0.00 0.00 0.00 3.85
32 33 8.684520 ACACTCATTACTACTACCACATTACTC 58.315 37.037 0.00 0.00 0.00 2.59
33 34 8.591114 ACACTCATTACTACTACCACATTACT 57.409 34.615 0.00 0.00 0.00 2.24
34 35 9.084164 CAACACTCATTACTACTACCACATTAC 57.916 37.037 0.00 0.00 0.00 1.89
35 36 7.762615 GCAACACTCATTACTACTACCACATTA 59.237 37.037 0.00 0.00 0.00 1.90
36 37 6.594159 GCAACACTCATTACTACTACCACATT 59.406 38.462 0.00 0.00 0.00 2.71
37 38 6.070767 AGCAACACTCATTACTACTACCACAT 60.071 38.462 0.00 0.00 0.00 3.21
38 39 5.245301 AGCAACACTCATTACTACTACCACA 59.755 40.000 0.00 0.00 0.00 4.17
39 40 5.721232 AGCAACACTCATTACTACTACCAC 58.279 41.667 0.00 0.00 0.00 4.16
40 41 5.995565 AGCAACACTCATTACTACTACCA 57.004 39.130 0.00 0.00 0.00 3.25
41 42 7.067251 AGAGTAGCAACACTCATTACTACTACC 59.933 40.741 13.54 0.00 46.15 3.18
42 43 7.987649 AGAGTAGCAACACTCATTACTACTAC 58.012 38.462 13.54 0.00 46.15 2.73
43 44 7.282675 GGAGAGTAGCAACACTCATTACTACTA 59.717 40.741 13.54 0.00 46.15 1.82
44 45 6.095720 GGAGAGTAGCAACACTCATTACTACT 59.904 42.308 13.54 0.00 46.15 2.57
45 46 6.095720 AGGAGAGTAGCAACACTCATTACTAC 59.904 42.308 13.54 0.00 46.15 2.73
46 47 6.188407 AGGAGAGTAGCAACACTCATTACTA 58.812 40.000 13.54 0.00 46.15 1.82
47 48 5.020132 AGGAGAGTAGCAACACTCATTACT 58.980 41.667 13.54 0.00 46.15 2.24
48 49 5.331876 AGGAGAGTAGCAACACTCATTAC 57.668 43.478 13.54 0.00 46.15 1.89
54 55 0.528470 GCGAGGAGAGTAGCAACACT 59.472 55.000 0.00 0.00 0.00 3.55
60 61 1.226831 GTGCAGCGAGGAGAGTAGC 60.227 63.158 0.00 0.00 0.00 3.58
68 69 2.076100 TCTAATTTGTGTGCAGCGAGG 58.924 47.619 0.00 0.00 0.00 4.63
72 73 5.637810 TGTACTACTCTAATTTGTGTGCAGC 59.362 40.000 5.10 0.00 0.00 5.25
74 75 6.755206 AGTGTACTACTCTAATTTGTGTGCA 58.245 36.000 5.10 0.00 33.17 4.57
82 83 9.341078 GGCTAAGACTAGTGTACTACTCTAATT 57.659 37.037 0.00 0.00 40.89 1.40
84 85 6.983307 CGGCTAAGACTAGTGTACTACTCTAA 59.017 42.308 0.00 0.00 40.89 2.10
85 86 6.097554 ACGGCTAAGACTAGTGTACTACTCTA 59.902 42.308 0.00 0.00 40.89 2.43
87 88 5.115480 ACGGCTAAGACTAGTGTACTACTC 58.885 45.833 0.00 0.00 40.89 2.59
88 89 5.096443 ACGGCTAAGACTAGTGTACTACT 57.904 43.478 0.00 0.00 43.56 2.57
90 91 5.089970 TGACGGCTAAGACTAGTGTACTA 57.910 43.478 0.00 0.00 0.00 1.82
91 92 3.947868 TGACGGCTAAGACTAGTGTACT 58.052 45.455 0.00 0.00 0.00 2.73
92 93 4.334759 TGATGACGGCTAAGACTAGTGTAC 59.665 45.833 0.00 0.00 0.00 2.90
93 94 4.520179 TGATGACGGCTAAGACTAGTGTA 58.480 43.478 0.00 0.00 0.00 2.90
94 95 3.353557 TGATGACGGCTAAGACTAGTGT 58.646 45.455 0.00 0.00 0.00 3.55
95 96 4.106197 GTTGATGACGGCTAAGACTAGTG 58.894 47.826 0.00 0.00 0.00 2.74
96 97 3.130693 GGTTGATGACGGCTAAGACTAGT 59.869 47.826 0.00 0.00 0.00 2.57
97 98 3.707793 GGTTGATGACGGCTAAGACTAG 58.292 50.000 0.00 0.00 0.00 2.57
101 102 3.733236 CGGTTGATGACGGCTAAGA 57.267 52.632 0.00 0.00 0.00 2.10
135 136 6.656270 TCGAATAAATATAGGTCACGGCTAGA 59.344 38.462 0.00 0.00 0.00 2.43
170 177 1.843368 TTAGGCGGCGGCTATATAGT 58.157 50.000 38.04 18.18 40.30 2.12
232 241 2.933573 AGTATAGTGCTAGCTCCACGT 58.066 47.619 17.23 3.43 38.22 4.49
333 346 3.208747 ACTTGGACAGACGGACATTTT 57.791 42.857 0.00 0.00 0.00 1.82
345 370 1.069513 CACGTGTTCCCTACTTGGACA 59.930 52.381 7.58 0.00 38.35 4.02
375 400 0.912487 ACCCCGGTCCTTCTGCATTA 60.912 55.000 0.00 0.00 0.00 1.90
376 401 2.231380 ACCCCGGTCCTTCTGCATT 61.231 57.895 0.00 0.00 0.00 3.56
378 403 3.636231 CACCCCGGTCCTTCTGCA 61.636 66.667 0.00 0.00 0.00 4.41
382 407 4.717313 GGTGCACCCCGGTCCTTC 62.717 72.222 26.31 0.00 0.00 3.46
468 520 4.909880 GCGAAGTGCCGGATTAATTAATTC 59.090 41.667 5.05 9.13 37.76 2.17
496 548 4.686554 GCATCTGATTACGTAACAGGGATC 59.313 45.833 24.64 14.25 33.19 3.36
507 559 1.336332 CCTCCCTCGCATCTGATTACG 60.336 57.143 3.99 3.99 0.00 3.18
515 569 1.152652 TCTCTCCCTCCCTCGCATC 60.153 63.158 0.00 0.00 0.00 3.91
523 577 1.595058 TTCCCTCCCTCTCTCCCTCC 61.595 65.000 0.00 0.00 0.00 4.30
525 579 1.031112 AATTCCCTCCCTCTCTCCCT 58.969 55.000 0.00 0.00 0.00 4.20
526 580 1.135960 CAATTCCCTCCCTCTCTCCC 58.864 60.000 0.00 0.00 0.00 4.30
527 581 2.182516 TCAATTCCCTCCCTCTCTCC 57.817 55.000 0.00 0.00 0.00 3.71
528 582 2.437651 CCTTCAATTCCCTCCCTCTCTC 59.562 54.545 0.00 0.00 0.00 3.20
529 583 2.486716 CCTTCAATTCCCTCCCTCTCT 58.513 52.381 0.00 0.00 0.00 3.10
530 584 1.133945 GCCTTCAATTCCCTCCCTCTC 60.134 57.143 0.00 0.00 0.00 3.20
531 585 0.922626 GCCTTCAATTCCCTCCCTCT 59.077 55.000 0.00 0.00 0.00 3.69
590 644 6.911250 AACCCCGGATTAATTAATTGATCC 57.089 37.500 29.41 29.41 44.82 3.36
649 703 2.425668 GTCTTCCTCCTCTCCTCTTTCG 59.574 54.545 0.00 0.00 0.00 3.46
650 704 2.425668 CGTCTTCCTCCTCTCCTCTTTC 59.574 54.545 0.00 0.00 0.00 2.62
651 705 2.041891 TCGTCTTCCTCCTCTCCTCTTT 59.958 50.000 0.00 0.00 0.00 2.52
652 706 1.636519 TCGTCTTCCTCCTCTCCTCTT 59.363 52.381 0.00 0.00 0.00 2.85
663 717 1.489230 ACCAAACCAAGTCGTCTTCCT 59.511 47.619 0.00 0.00 0.00 3.36
853 924 2.924290 GCGGAAGAAGCGATATATGGAC 59.076 50.000 0.00 0.00 0.00 4.02
854 925 2.094182 GGCGGAAGAAGCGATATATGGA 60.094 50.000 0.00 0.00 35.00 3.41
855 926 2.271800 GGCGGAAGAAGCGATATATGG 58.728 52.381 0.00 0.00 35.00 2.74
856 927 1.920574 CGGCGGAAGAAGCGATATATG 59.079 52.381 0.00 0.00 35.00 1.78
908 984 1.338136 GGGGGAATCGAAGAGCAGGA 61.338 60.000 0.00 0.00 43.63 3.86
944 1024 2.788210 GAAGAAGGGGCTGGGTTGGG 62.788 65.000 0.00 0.00 0.00 4.12
945 1025 1.304464 GAAGAAGGGGCTGGGTTGG 60.304 63.158 0.00 0.00 0.00 3.77
946 1026 0.610232 CAGAAGAAGGGGCTGGGTTG 60.610 60.000 0.00 0.00 0.00 3.77
947 1027 1.770324 CAGAAGAAGGGGCTGGGTT 59.230 57.895 0.00 0.00 0.00 4.11
949 1029 2.044551 GCAGAAGAAGGGGCTGGG 60.045 66.667 0.00 0.00 0.00 4.45
951 1031 0.327591 AGAAGCAGAAGAAGGGGCTG 59.672 55.000 0.00 0.00 36.58 4.85
952 1032 1.071434 AAGAAGCAGAAGAAGGGGCT 58.929 50.000 0.00 0.00 38.45 5.19
953 1033 1.172175 CAAGAAGCAGAAGAAGGGGC 58.828 55.000 0.00 0.00 0.00 5.80
975 1057 1.747686 CGCACCGCACCAAAAACAAC 61.748 55.000 0.00 0.00 0.00 3.32
981 1063 3.276091 CTCACGCACCGCACCAAA 61.276 61.111 0.00 0.00 0.00 3.28
995 1077 2.190313 GGTCGATGGCCATGCTCA 59.810 61.111 26.56 0.00 0.00 4.26
996 1078 2.182842 GTGGTCGATGGCCATGCTC 61.183 63.158 26.56 9.19 38.40 4.26
997 1079 2.124570 GTGGTCGATGGCCATGCT 60.125 61.111 26.56 0.00 38.40 3.79
1044 1136 6.078456 TCAATTACCATGATCCTCCTGTTT 57.922 37.500 0.00 0.00 0.00 2.83
1167 1271 7.253060 CGAAACGAAAAAGAAACGTACAAACAT 60.253 33.333 0.00 0.00 39.31 2.71
1187 1291 2.049433 AGGAGCACGGACGAAACG 60.049 61.111 0.00 0.00 37.36 3.60
1188 1292 0.733223 GAGAGGAGCACGGACGAAAC 60.733 60.000 0.00 0.00 0.00 2.78
1191 1295 2.750637 GGAGAGGAGCACGGACGA 60.751 66.667 0.00 0.00 0.00 4.20
1192 1296 4.180946 CGGAGAGGAGCACGGACG 62.181 72.222 0.00 0.00 0.00 4.79
1213 1317 0.179000 CAGTTCCCCTCATTCCTCCG 59.821 60.000 0.00 0.00 0.00 4.63
1240 1361 3.562505 CCGATAGATACCACAGTAACGC 58.437 50.000 0.00 0.00 39.76 4.84
1241 1362 3.611057 GCCCGATAGATACCACAGTAACG 60.611 52.174 0.00 0.00 39.76 3.18
1242 1363 3.611057 CGCCCGATAGATACCACAGTAAC 60.611 52.174 0.00 0.00 39.76 2.50
1244 1365 2.156917 CGCCCGATAGATACCACAGTA 58.843 52.381 0.00 0.00 39.76 2.74
1245 1366 0.959553 CGCCCGATAGATACCACAGT 59.040 55.000 0.00 0.00 39.76 3.55
1246 1367 0.388649 GCGCCCGATAGATACCACAG 60.389 60.000 0.00 0.00 39.76 3.66
1247 1368 1.663739 GCGCCCGATAGATACCACA 59.336 57.895 0.00 0.00 39.76 4.17
1248 1369 1.443872 CGCGCCCGATAGATACCAC 60.444 63.158 0.00 0.00 36.29 4.16
1249 1370 2.959372 CGCGCCCGATAGATACCA 59.041 61.111 0.00 0.00 36.29 3.25
1250 1371 2.506438 GCGCGCCCGATAGATACC 60.506 66.667 23.24 0.00 36.29 2.73
1251 1372 2.874780 CGCGCGCCCGATAGATAC 60.875 66.667 27.72 0.00 36.29 2.24
1252 1373 4.111016 CCGCGCGCCCGATAGATA 62.111 66.667 27.36 0.00 36.29 1.98
1303 1444 1.322538 ATGCTTTGACCGCCATTCCC 61.323 55.000 0.00 0.00 0.00 3.97
1310 1451 2.927553 AGAATCAATGCTTTGACCGC 57.072 45.000 16.45 9.31 44.36 5.68
1328 1469 2.222027 ACGCAGAAGACAGGGAAAAAG 58.778 47.619 0.00 0.00 0.00 2.27
1329 1470 2.341846 ACGCAGAAGACAGGGAAAAA 57.658 45.000 0.00 0.00 0.00 1.94
1343 1492 1.646189 GAGAAGAAGGGCTAACGCAG 58.354 55.000 0.00 0.00 38.10 5.18
1351 1500 4.491409 GCGGGGGAGAAGAAGGGC 62.491 72.222 0.00 0.00 0.00 5.19
1429 1591 2.418628 AGTACCAAATTCCAACGCATCG 59.581 45.455 0.00 0.00 0.00 3.84
1449 1616 3.643792 ACATAAAGGCTAGGACTGGCTAG 59.356 47.826 7.60 0.00 39.47 3.42
1450 1617 3.654273 ACATAAAGGCTAGGACTGGCTA 58.346 45.455 7.60 0.00 39.47 3.93
1451 1618 2.482494 ACATAAAGGCTAGGACTGGCT 58.518 47.619 7.60 0.56 42.26 4.75
1452 1619 3.283259 AACATAAAGGCTAGGACTGGC 57.717 47.619 0.00 0.00 36.25 4.85
1516 1683 5.448360 GCTGACAAGATTGCCAGAAATCTAC 60.448 44.000 12.37 0.00 44.35 2.59
1557 1732 4.346730 TGGCATCCTGACAATCAAGAAAT 58.653 39.130 0.00 0.00 28.38 2.17
2184 2386 3.443045 CCTGTTGGCCCGCATCAC 61.443 66.667 0.00 0.00 0.00 3.06
2240 2442 0.032615 GCAGAGGAGAGGAGGAGGAA 60.033 60.000 0.00 0.00 0.00 3.36
2360 2562 4.320641 GCCTAGTAGTCGATGATGAGGTTC 60.321 50.000 0.00 0.00 0.00 3.62
2444 2649 2.281484 GTGGTGGCCGCTTTCTCA 60.281 61.111 17.49 1.65 0.00 3.27
2541 2746 1.916181 TCCATCCACCTCCCTTTCTTC 59.084 52.381 0.00 0.00 0.00 2.87
2674 2900 5.360144 GTGTGGTAGAAATAGTAGAGCAGGA 59.640 44.000 0.00 0.00 0.00 3.86
2889 3129 7.255730 CCATTGACCCATATGGAAAGAAGATTC 60.256 40.741 24.00 5.56 43.25 2.52
2931 3172 8.229253 TCAACAAGAGGGATGAATGATAATTG 57.771 34.615 0.00 0.00 0.00 2.32
2932 3173 8.827832 TTCAACAAGAGGGATGAATGATAATT 57.172 30.769 0.00 0.00 0.00 1.40
2938 3429 6.183360 GGAAGATTCAACAAGAGGGATGAATG 60.183 42.308 4.72 0.00 41.29 2.67
2946 3437 6.712547 ACAGTTAAGGAAGATTCAACAAGAGG 59.287 38.462 0.00 0.00 0.00 3.69
2957 3448 4.472833 AGATGCCTCACAGTTAAGGAAGAT 59.527 41.667 3.24 0.00 34.35 2.40
2958 3449 3.840666 AGATGCCTCACAGTTAAGGAAGA 59.159 43.478 3.24 0.00 34.35 2.87
3084 3575 5.486735 AATTTTTCAGGCCATCACATTCA 57.513 34.783 5.01 0.00 0.00 2.57
3093 3584 9.249053 TCAGTAATGTAATAATTTTTCAGGCCA 57.751 29.630 5.01 0.00 0.00 5.36
3109 3600 8.304596 AGAACAAGAAGACGATTCAGTAATGTA 58.695 33.333 7.65 0.00 0.00 2.29
3111 3602 7.588143 AGAACAAGAAGACGATTCAGTAATG 57.412 36.000 7.65 0.00 0.00 1.90
3112 3603 7.360438 GCAAGAACAAGAAGACGATTCAGTAAT 60.360 37.037 7.65 0.00 0.00 1.89
3113 3604 6.073765 GCAAGAACAAGAAGACGATTCAGTAA 60.074 38.462 7.65 0.00 0.00 2.24
3115 3606 4.212214 GCAAGAACAAGAAGACGATTCAGT 59.788 41.667 7.65 3.68 0.00 3.41
3116 3607 4.450419 AGCAAGAACAAGAAGACGATTCAG 59.550 41.667 7.65 3.18 0.00 3.02
3117 3608 4.380531 AGCAAGAACAAGAAGACGATTCA 58.619 39.130 7.65 0.00 0.00 2.57
3118 3609 4.143009 GGAGCAAGAACAAGAAGACGATTC 60.143 45.833 0.00 0.00 0.00 2.52
3124 3622 3.470709 CACAGGAGCAAGAACAAGAAGA 58.529 45.455 0.00 0.00 0.00 2.87
3229 3727 4.330074 GCGTCGGCTTCAGCAATAATATAT 59.670 41.667 0.30 0.00 44.36 0.86
3297 3807 2.163818 TTACTCGGTTCCAACTGCAG 57.836 50.000 13.48 13.48 35.25 4.41
3298 3808 2.695359 GATTACTCGGTTCCAACTGCA 58.305 47.619 0.00 0.00 35.25 4.41
3299 3809 1.659098 CGATTACTCGGTTCCAACTGC 59.341 52.381 0.00 0.00 41.27 4.40
3300 3810 1.659098 GCGATTACTCGGTTCCAACTG 59.341 52.381 4.55 0.00 45.15 3.16


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

AutoCloner maintained by Alex Coulton.