Multiple sequence alignment - TraesCS3D01G468100

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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 TraesCS3D01G468100 chr3D 100.000 3272 0 0 1 3272 570558188 570561459 0.000000e+00 6043.0
1 TraesCS3D01G468100 chr3D 83.333 1284 155 32 994 2258 520191927 520190684 0.000000e+00 1131.0
2 TraesCS3D01G468100 chr3D 78.536 1202 225 22 1052 2244 570496343 570495166 0.000000e+00 760.0
3 TraesCS3D01G468100 chr3D 78.082 1241 216 36 991 2224 570379578 570380769 0.000000e+00 734.0
4 TraesCS3D01G468100 chr3D 78.059 1185 212 31 1050 2224 570281079 570282225 0.000000e+00 704.0
5 TraesCS3D01G468100 chr3A 92.005 2289 117 34 595 2865 703394759 703396999 0.000000e+00 3153.0
6 TraesCS3D01G468100 chr3A 83.241 1265 156 32 1010 2258 655637066 655635842 0.000000e+00 1110.0
7 TraesCS3D01G468100 chr3A 80.240 1336 218 34 993 2310 703270274 703271581 0.000000e+00 963.0
8 TraesCS3D01G468100 chr3A 87.591 411 47 1 2864 3270 703398574 703398984 1.060000e-129 473.0
9 TraesCS3D01G468100 chr3A 84.348 115 12 5 303 415 703394311 703394421 1.240000e-19 108.0
10 TraesCS3D01G468100 chr3B 91.602 2179 102 43 714 2865 757807335 757809459 0.000000e+00 2935.0
11 TraesCS3D01G468100 chr3B 80.331 1693 196 63 599 2258 685039615 685038027 0.000000e+00 1155.0
12 TraesCS3D01G468100 chr3B 81.057 1325 211 28 993 2302 757734143 757735442 0.000000e+00 1020.0
13 TraesCS3D01G468100 chr3B 79.026 1273 223 32 1013 2274 757773415 757772176 0.000000e+00 832.0
14 TraesCS3D01G468100 chr3B 89.604 404 40 2 2867 3270 757809650 757810051 2.250000e-141 512.0
15 TraesCS3D01G468100 chr3B 87.617 428 46 4 1 425 757805972 757806395 1.060000e-134 490.0
16 TraesCS3D01G468100 chr3B 97.368 76 2 0 595 670 757807250 757807325 2.650000e-26 130.0
17 TraesCS3D01G468100 chr3B 90.625 64 5 1 473 536 757807039 757807101 2.090000e-12 84.2


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 TraesCS3D01G468100 chr3D 570558188 570561459 3271 False 6043.000000 6043 100.000000 1 3272 1 chr3D.!!$F3 3271
1 TraesCS3D01G468100 chr3D 520190684 520191927 1243 True 1131.000000 1131 83.333000 994 2258 1 chr3D.!!$R1 1264
2 TraesCS3D01G468100 chr3D 570495166 570496343 1177 True 760.000000 760 78.536000 1052 2244 1 chr3D.!!$R2 1192
3 TraesCS3D01G468100 chr3D 570379578 570380769 1191 False 734.000000 734 78.082000 991 2224 1 chr3D.!!$F2 1233
4 TraesCS3D01G468100 chr3D 570281079 570282225 1146 False 704.000000 704 78.059000 1050 2224 1 chr3D.!!$F1 1174
5 TraesCS3D01G468100 chr3A 703394311 703398984 4673 False 1244.666667 3153 87.981333 303 3270 3 chr3A.!!$F2 2967
6 TraesCS3D01G468100 chr3A 655635842 655637066 1224 True 1110.000000 1110 83.241000 1010 2258 1 chr3A.!!$R1 1248
7 TraesCS3D01G468100 chr3A 703270274 703271581 1307 False 963.000000 963 80.240000 993 2310 1 chr3A.!!$F1 1317
8 TraesCS3D01G468100 chr3B 685038027 685039615 1588 True 1155.000000 1155 80.331000 599 2258 1 chr3B.!!$R1 1659
9 TraesCS3D01G468100 chr3B 757734143 757735442 1299 False 1020.000000 1020 81.057000 993 2302 1 chr3B.!!$F1 1309
10 TraesCS3D01G468100 chr3B 757772176 757773415 1239 True 832.000000 832 79.026000 1013 2274 1 chr3B.!!$R2 1261
11 TraesCS3D01G468100 chr3B 757805972 757810051 4079 False 830.240000 2935 91.363200 1 3270 5 chr3B.!!$F2 3269

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
30 31 0.030908 GCCGTCCGTCATAGAGGAAG 59.969 60.0 0.0 0.0 38.41 3.46 F
86 87 0.034337 GGACACGGTTTGGAGTGCTA 59.966 55.0 0.0 0.0 41.72 3.49 F
572 1295 0.040692 CGGATGCTTGATTGATGGCG 60.041 55.0 0.0 0.0 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1304 2052 1.679944 CCCTGCATACCTTGTGACTGG 60.680 57.143 0.00 0.00 0.00 4.00 R
2214 2980 2.435059 GTGAAGGACGGCAGCCTC 60.435 66.667 10.54 6.11 33.76 4.70 R
2326 3102 1.763120 AGCCACACTGAGCATCCAA 59.237 52.632 0.00 0.00 0.00 3.53 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
30 31 0.030908 GCCGTCCGTCATAGAGGAAG 59.969 60.000 0.00 0.00 38.41 3.46
31 32 0.030908 CCGTCCGTCATAGAGGAAGC 59.969 60.000 0.00 0.00 38.41 3.86
32 33 0.738975 CGTCCGTCATAGAGGAAGCA 59.261 55.000 0.00 0.00 38.41 3.91
52 53 0.535335 GGCGGACATACCTCACTTGA 59.465 55.000 0.00 0.00 36.31 3.02
58 59 3.118629 GGACATACCTCACTTGATGCAGA 60.119 47.826 0.00 0.00 35.41 4.26
78 79 1.961793 TTCTCAAGGGACACGGTTTG 58.038 50.000 0.00 0.00 0.00 2.93
80 81 0.107831 CTCAAGGGACACGGTTTGGA 59.892 55.000 0.00 0.00 0.00 3.53
81 82 0.107831 TCAAGGGACACGGTTTGGAG 59.892 55.000 0.00 0.00 0.00 3.86
82 83 0.179029 CAAGGGACACGGTTTGGAGT 60.179 55.000 0.00 0.00 0.00 3.85
84 85 2.258726 GGGACACGGTTTGGAGTGC 61.259 63.158 0.00 0.00 41.72 4.40
85 86 1.227853 GGACACGGTTTGGAGTGCT 60.228 57.895 0.00 0.00 41.72 4.40
86 87 0.034337 GGACACGGTTTGGAGTGCTA 59.966 55.000 0.00 0.00 41.72 3.49
87 88 1.338769 GGACACGGTTTGGAGTGCTAT 60.339 52.381 0.00 0.00 41.72 2.97
88 89 2.093869 GGACACGGTTTGGAGTGCTATA 60.094 50.000 0.00 0.00 41.72 1.31
89 90 3.431766 GGACACGGTTTGGAGTGCTATAT 60.432 47.826 0.00 0.00 41.72 0.86
90 91 4.202182 GGACACGGTTTGGAGTGCTATATA 60.202 45.833 0.00 0.00 41.72 0.86
91 92 5.510861 GGACACGGTTTGGAGTGCTATATAT 60.511 44.000 0.00 0.00 41.72 0.86
92 93 5.297547 ACACGGTTTGGAGTGCTATATATG 58.702 41.667 0.00 0.00 41.72 1.78
93 94 4.152402 CACGGTTTGGAGTGCTATATATGC 59.848 45.833 0.00 0.00 0.00 3.14
94 95 4.202315 ACGGTTTGGAGTGCTATATATGCA 60.202 41.667 0.00 0.00 38.19 3.96
102 103 2.595386 TGCTATATATGCACGCACTCG 58.405 47.619 0.00 0.00 42.43 4.18
103 104 1.321743 GCTATATATGCACGCACTCGC 59.678 52.381 0.00 0.00 39.84 5.03
104 105 2.868662 CTATATATGCACGCACTCGCT 58.131 47.619 0.00 0.00 39.84 4.93
112 113 2.028190 CGCACTCGCTAGGATGGG 59.972 66.667 0.00 0.00 35.30 4.00
130 131 2.665185 GTCGCCGGACAAGCAACT 60.665 61.111 5.05 0.00 42.91 3.16
145 146 3.381949 AGCAACTCAACACTACGAACTC 58.618 45.455 0.00 0.00 0.00 3.01
146 147 2.475487 GCAACTCAACACTACGAACTCC 59.525 50.000 0.00 0.00 0.00 3.85
153 154 2.224606 ACACTACGAACTCCGACAGAA 58.775 47.619 0.00 0.00 41.76 3.02
160 161 0.458669 AACTCCGACAGAACGTGTGT 59.541 50.000 3.54 3.54 40.56 3.72
164 165 3.503363 ACTCCGACAGAACGTGTGTATTA 59.497 43.478 3.89 0.00 40.56 0.98
182 183 9.332502 TGTGTATTATGTTTACTGTTGTGTCTT 57.667 29.630 0.00 0.00 0.00 3.01
232 235 3.791973 CTCAACATAGAGAGGACGCTT 57.208 47.619 0.00 0.00 37.87 4.68
248 251 4.201920 GGACGCTTGGGAGAATGAAAATAC 60.202 45.833 0.00 0.00 0.00 1.89
254 257 4.349365 TGGGAGAATGAAAATACCCAACC 58.651 43.478 0.00 0.00 43.34 3.77
261 264 0.876399 AAAATACCCAACCGACACGC 59.124 50.000 0.00 0.00 0.00 5.34
276 279 1.000955 ACACGCGATGGAAGAACTCTT 59.999 47.619 15.93 0.00 39.23 2.85
278 281 2.092838 CACGCGATGGAAGAACTCTTTC 59.907 50.000 15.93 0.00 36.11 2.62
285 288 5.466728 CGATGGAAGAACTCTTTCAAAGTGA 59.533 40.000 6.21 0.00 44.04 3.41
291 294 7.812669 GGAAGAACTCTTTCAAAGTGAAAAACA 59.187 33.333 6.21 0.00 44.69 2.83
310 313 3.014623 ACACGTCCATAGTGAGATCGAA 58.985 45.455 3.20 0.00 41.83 3.71
332 337 6.310956 CGAATATTAACACGTACACCCAAAGA 59.689 38.462 0.00 0.00 0.00 2.52
336 341 4.877378 AACACGTACACCCAAAGATAGA 57.123 40.909 0.00 0.00 0.00 1.98
362 367 2.518949 CACTGCCATGCGAAACATTAC 58.481 47.619 0.00 0.00 36.64 1.89
386 391 8.709386 ACTAGTTCTTACAACAAGATGCATAG 57.291 34.615 0.00 0.00 0.00 2.23
416 421 2.386661 AACTCGAATGCGATTCACCT 57.613 45.000 0.00 0.00 46.80 4.00
485 1086 0.590682 TGCACACTTACCATGCAACG 59.409 50.000 0.00 0.00 45.96 4.10
522 1123 9.701098 TTTCAGATTTGAGAATTTCAGATTTGG 57.299 29.630 0.00 0.00 34.86 3.28
538 1261 0.251916 TTGGGCCGAGTACTCATTGG 59.748 55.000 22.37 15.87 0.00 3.16
545 1268 3.130693 GCCGAGTACTCATTGGTAGTCTT 59.869 47.826 22.37 0.00 38.98 3.01
552 1275 7.777095 AGTACTCATTGGTAGTCTTGATTCTC 58.223 38.462 0.00 0.00 0.00 2.87
562 1285 2.611292 GTCTTGATTCTCCGGATGCTTG 59.389 50.000 3.57 0.00 0.00 4.01
563 1286 2.501316 TCTTGATTCTCCGGATGCTTGA 59.499 45.455 3.57 0.00 0.00 3.02
564 1287 3.135348 TCTTGATTCTCCGGATGCTTGAT 59.865 43.478 3.57 0.00 0.00 2.57
565 1288 3.565764 TGATTCTCCGGATGCTTGATT 57.434 42.857 3.57 0.00 0.00 2.57
566 1289 3.208594 TGATTCTCCGGATGCTTGATTG 58.791 45.455 3.57 0.00 0.00 2.67
567 1290 3.118298 TGATTCTCCGGATGCTTGATTGA 60.118 43.478 3.57 0.00 0.00 2.57
568 1291 3.565764 TTCTCCGGATGCTTGATTGAT 57.434 42.857 3.57 0.00 0.00 2.57
569 1292 2.842457 TCTCCGGATGCTTGATTGATG 58.158 47.619 3.57 0.00 0.00 3.07
570 1293 1.878088 CTCCGGATGCTTGATTGATGG 59.122 52.381 3.57 0.00 0.00 3.51
571 1294 0.313043 CCGGATGCTTGATTGATGGC 59.687 55.000 0.00 0.00 0.00 4.40
572 1295 0.040692 CGGATGCTTGATTGATGGCG 60.041 55.000 0.00 0.00 0.00 5.69
573 1296 1.027357 GGATGCTTGATTGATGGCGT 58.973 50.000 0.00 0.00 0.00 5.68
574 1297 1.268896 GGATGCTTGATTGATGGCGTG 60.269 52.381 0.00 0.00 0.00 5.34
575 1298 0.101759 ATGCTTGATTGATGGCGTGC 59.898 50.000 0.00 0.00 0.00 5.34
576 1299 1.242665 TGCTTGATTGATGGCGTGCA 61.243 50.000 0.00 0.00 0.00 4.57
577 1300 0.109179 GCTTGATTGATGGCGTGCAA 60.109 50.000 0.00 0.00 0.00 4.08
578 1301 1.621107 CTTGATTGATGGCGTGCAAC 58.379 50.000 0.00 0.00 0.00 4.17
579 1302 0.243365 TTGATTGATGGCGTGCAACC 59.757 50.000 0.00 0.00 0.00 3.77
580 1303 1.139520 GATTGATGGCGTGCAACCC 59.860 57.895 4.63 0.86 0.00 4.11
581 1304 2.283472 GATTGATGGCGTGCAACCCC 62.283 60.000 4.63 0.00 34.61 4.95
582 1305 2.786512 ATTGATGGCGTGCAACCCCT 62.787 55.000 4.63 0.00 35.26 4.79
583 1306 2.676471 GATGGCGTGCAACCCCTT 60.676 61.111 4.63 0.00 35.26 3.95
584 1307 1.377987 GATGGCGTGCAACCCCTTA 60.378 57.895 4.63 0.00 35.26 2.69
585 1308 0.963355 GATGGCGTGCAACCCCTTAA 60.963 55.000 4.63 0.00 35.26 1.85
586 1309 0.540830 ATGGCGTGCAACCCCTTAAA 60.541 50.000 4.63 0.00 35.26 1.52
587 1310 0.755698 TGGCGTGCAACCCCTTAAAA 60.756 50.000 4.63 0.00 35.26 1.52
588 1311 0.389757 GGCGTGCAACCCCTTAAAAA 59.610 50.000 0.00 0.00 30.19 1.94
709 1438 5.703130 GGACAGATAGATAACATGGGCTTTC 59.297 44.000 0.00 0.00 0.00 2.62
749 1478 1.298638 TCTCACGCTGCATCGATCG 60.299 57.895 18.00 9.36 0.00 3.69
807 1536 0.900182 AGATCCGACACTGTGGCAGA 60.900 55.000 15.00 8.41 35.18 4.26
827 1556 7.136772 GGCAGACGAAAACAATTTAACTACTT 58.863 34.615 0.00 0.00 0.00 2.24
911 1641 2.821366 GCACATGCCTCACCTCCG 60.821 66.667 0.00 0.00 34.31 4.63
917 1650 1.691976 CATGCCTCACCTCCGGTATAA 59.308 52.381 0.00 0.00 32.11 0.98
975 1715 3.702330 GCAAGTTAAGTCAACACCAACC 58.298 45.455 0.00 0.00 39.81 3.77
978 1718 3.284617 AGTTAAGTCAACACCAACCACC 58.715 45.455 0.00 0.00 39.81 4.61
979 1719 1.956297 TAAGTCAACACCAACCACCG 58.044 50.000 0.00 0.00 0.00 4.94
981 1721 0.253610 AGTCAACACCAACCACCGAA 59.746 50.000 0.00 0.00 0.00 4.30
984 1724 1.099689 CAACACCAACCACCGAACTT 58.900 50.000 0.00 0.00 0.00 2.66
986 1726 0.544697 ACACCAACCACCGAACTTCT 59.455 50.000 0.00 0.00 0.00 2.85
989 1729 2.036733 CACCAACCACCGAACTTCTCTA 59.963 50.000 0.00 0.00 0.00 2.43
1047 1795 2.820619 CGTCTCGCTAGCCGTGCTA 61.821 63.158 9.66 5.64 40.44 3.49
1304 2052 1.739562 CTGACAAGCTCTGCGACCC 60.740 63.158 0.00 0.00 0.00 4.46
1743 2503 5.736207 GCACTACATCACGATCAAGTCCATA 60.736 44.000 0.00 0.00 0.00 2.74
1932 2692 0.462047 CGAAAGCGGTGAAGCCCTAT 60.462 55.000 0.00 0.00 38.01 2.57
2321 3093 7.196637 TCTGTATCTCTACTGAAGTCTACCA 57.803 40.000 0.00 0.00 34.15 3.25
2322 3094 7.049133 TCTGTATCTCTACTGAAGTCTACCAC 58.951 42.308 0.00 0.00 34.15 4.16
2326 3102 9.563748 GTATCTCTACTGAAGTCTACCACTTAT 57.436 37.037 0.00 0.00 46.10 1.73
2341 3117 4.611310 CACTTATTGGATGCTCAGTGTG 57.389 45.455 0.00 0.00 0.00 3.82
2342 3118 3.376234 CACTTATTGGATGCTCAGTGTGG 59.624 47.826 0.00 0.00 0.00 4.17
2343 3119 2.042686 TATTGGATGCTCAGTGTGGC 57.957 50.000 4.40 4.40 0.00 5.01
2369 3145 6.328934 TGATCTTGATTATGGTGTTAGGCCTA 59.671 38.462 8.91 8.91 0.00 3.93
2379 3155 2.676342 GTGTTAGGCCTACGACATTTGG 59.324 50.000 18.15 0.00 0.00 3.28
2392 3168 1.976474 ATTTGGCACGCGGTTCCAT 60.976 52.632 12.47 0.00 27.78 3.41
2393 3169 1.933115 ATTTGGCACGCGGTTCCATC 61.933 55.000 12.47 0.00 27.78 3.51
2394 3170 3.545124 TTGGCACGCGGTTCCATCT 62.545 57.895 12.47 0.00 27.78 2.90
2395 3171 2.746277 GGCACGCGGTTCCATCTT 60.746 61.111 12.47 0.00 0.00 2.40
2396 3172 2.480555 GCACGCGGTTCCATCTTG 59.519 61.111 12.47 0.00 0.00 3.02
2400 3176 1.153449 CGCGGTTCCATCTTGCCTA 60.153 57.895 0.00 0.00 0.00 3.93
2416 3192 7.789202 TCTTGCCTAGCTAAGAGATATTCAT 57.211 36.000 0.00 0.00 0.00 2.57
2424 3200 9.956640 CTAGCTAAGAGATATTCATCCCATTTT 57.043 33.333 0.00 0.00 0.00 1.82
2426 3202 9.732130 AGCTAAGAGATATTCATCCCATTTTAC 57.268 33.333 0.00 0.00 0.00 2.01
2457 3239 5.735922 GCACTTGTTTGTGTGTGGTTGATAT 60.736 40.000 0.00 0.00 39.89 1.63
2458 3240 6.514212 GCACTTGTTTGTGTGTGGTTGATATA 60.514 38.462 0.00 0.00 39.89 0.86
2459 3241 7.592938 CACTTGTTTGTGTGTGGTTGATATAT 58.407 34.615 0.00 0.00 33.61 0.86
2460 3242 8.081633 CACTTGTTTGTGTGTGGTTGATATATT 58.918 33.333 0.00 0.00 33.61 1.28
2461 3243 8.296713 ACTTGTTTGTGTGTGGTTGATATATTC 58.703 33.333 0.00 0.00 0.00 1.75
2462 3244 7.751768 TGTTTGTGTGTGGTTGATATATTCA 57.248 32.000 0.00 0.00 0.00 2.57
2483 3265 4.739137 TCAAACAATTGGGCAAGTAGCAAC 60.739 41.667 10.83 0.00 39.16 4.17
2507 3289 6.155827 CACTGTTACTCTCTTTCCTTCTCTG 58.844 44.000 0.00 0.00 0.00 3.35
2710 3494 6.152638 TCAGGAAAATTAATCTGGAACCCT 57.847 37.500 2.94 0.00 0.00 4.34
2722 3506 1.428912 TGGAACCCTGCAGGATTTCTT 59.571 47.619 34.91 15.69 39.89 2.52
2739 3523 7.039714 AGGATTTCTTAGGCGATTTTTCTGTTT 60.040 33.333 0.00 0.00 0.00 2.83
2801 3599 5.523588 TCTCTCTCTCTCTCTCTCTCTCTT 58.476 45.833 0.00 0.00 0.00 2.85
2816 3614 7.335673 TCTCTCTCTCTTGTTATGTGTGTCTAG 59.664 40.741 0.00 0.00 0.00 2.43
2817 3615 5.955488 TCTCTCTTGTTATGTGTGTCTAGC 58.045 41.667 0.00 0.00 0.00 3.42
2818 3616 5.712446 TCTCTCTTGTTATGTGTGTCTAGCT 59.288 40.000 0.00 0.00 0.00 3.32
2819 3617 6.209589 TCTCTCTTGTTATGTGTGTCTAGCTT 59.790 38.462 0.00 0.00 0.00 3.74
2865 5240 1.471684 GTGAGGCAAGCAGGATTCAAG 59.528 52.381 0.00 0.00 0.00 3.02
2869 5244 2.097825 GGCAAGCAGGATTCAAGATGT 58.902 47.619 0.00 0.00 0.00 3.06
2888 5263 2.302733 TGTGGCACTAGAAGAGATGCAA 59.697 45.455 19.83 0.00 39.92 4.08
2938 5313 0.544357 AGGTGGTGGGTCATCTCGAA 60.544 55.000 0.00 0.00 0.00 3.71
2947 5322 4.267928 GTGGGTCATCTCGAAGTAAAATCG 59.732 45.833 0.00 0.00 41.53 3.34
2970 5345 7.162761 TCGAACCACTTTTTCATAGTATTCCA 58.837 34.615 0.00 0.00 0.00 3.53
2971 5346 7.662258 TCGAACCACTTTTTCATAGTATTCCAA 59.338 33.333 0.00 0.00 0.00 3.53
3057 5432 3.314541 ACTCGTGCTTAAGTTACCAGG 57.685 47.619 4.02 0.00 0.00 4.45
3062 5437 3.187842 CGTGCTTAAGTTACCAGGTTTCC 59.812 47.826 0.00 0.00 0.00 3.13
3065 5440 5.410746 GTGCTTAAGTTACCAGGTTTCCTAC 59.589 44.000 0.00 0.00 29.64 3.18
3076 5451 7.666063 ACCAGGTTTCCTACGTTATAGTTAT 57.334 36.000 0.00 0.00 29.64 1.89
3091 5466 3.272574 AGTTATCAGTCTGCCCATGTG 57.727 47.619 0.00 0.00 0.00 3.21
3106 5481 3.136443 CCCATGTGGAAGTTATCAGGCTA 59.864 47.826 0.00 0.00 37.39 3.93
3128 5503 6.093495 GCTAATCATGTTGTAGTTACCAAGCA 59.907 38.462 0.00 0.00 0.00 3.91
3129 5504 6.500684 AATCATGTTGTAGTTACCAAGCAG 57.499 37.500 0.00 0.00 0.00 4.24
3148 5523 7.443272 CCAAGCAGATCATGTCATAGTTATCAA 59.557 37.037 0.00 0.00 0.00 2.57
3169 5544 8.854614 ATCAAACTTCTCATGCTAAAGTTACT 57.145 30.769 15.64 4.23 41.17 2.24
3175 5550 4.714802 TCTCATGCTAAAGTTACTAGGCCA 59.285 41.667 5.01 0.00 0.00 5.36
3199 5574 5.357878 ACCCATGCTACATTTATCAACACAG 59.642 40.000 0.00 0.00 0.00 3.66
3218 5593 4.453478 CACAGCGATTATGTGGCTATCATT 59.547 41.667 0.00 0.00 43.47 2.57
3270 5649 8.041143 AGATAAATATAGTTACCAGTTGCCCA 57.959 34.615 0.00 0.00 0.00 5.36
3271 5650 8.669571 AGATAAATATAGTTACCAGTTGCCCAT 58.330 33.333 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.351336 CTATGACGGACGGCCACCTC 62.351 65.000 8.76 0.00 0.00 3.85
11 12 0.030908 CTTCCTCTATGACGGACGGC 59.969 60.000 0.00 0.00 0.00 5.68
12 13 0.030908 GCTTCCTCTATGACGGACGG 59.969 60.000 0.00 0.00 0.00 4.79
30 31 1.521681 GTGAGGTATGTCCGCCTGC 60.522 63.158 0.00 0.00 41.99 4.85
31 32 0.537188 AAGTGAGGTATGTCCGCCTG 59.463 55.000 0.00 0.00 41.99 4.85
32 33 0.537188 CAAGTGAGGTATGTCCGCCT 59.463 55.000 0.00 0.00 41.99 5.52
52 53 2.679059 CGTGTCCCTTGAGAATCTGCAT 60.679 50.000 0.00 0.00 34.92 3.96
58 59 2.504367 CAAACCGTGTCCCTTGAGAAT 58.496 47.619 0.00 0.00 0.00 2.40
82 83 2.595386 CGAGTGCGTGCATATATAGCA 58.405 47.619 0.00 5.94 40.19 3.49
97 98 1.742768 GACCCCATCCTAGCGAGTG 59.257 63.158 0.00 0.00 0.00 3.51
98 99 1.828660 CGACCCCATCCTAGCGAGT 60.829 63.158 0.00 0.00 0.00 4.18
99 100 3.043419 CGACCCCATCCTAGCGAG 58.957 66.667 0.00 0.00 0.00 5.03
100 101 3.224324 GCGACCCCATCCTAGCGA 61.224 66.667 0.00 0.00 0.00 4.93
102 103 4.301027 CGGCGACCCCATCCTAGC 62.301 72.222 0.00 0.00 0.00 3.42
103 104 3.616721 CCGGCGACCCCATCCTAG 61.617 72.222 9.30 0.00 0.00 3.02
104 105 4.146156 TCCGGCGACCCCATCCTA 62.146 66.667 9.30 0.00 0.00 2.94
112 113 3.723348 GTTGCTTGTCCGGCGACC 61.723 66.667 9.30 0.00 38.32 4.79
130 131 1.948834 TGTCGGAGTTCGTAGTGTTGA 59.051 47.619 0.00 0.00 40.32 3.18
145 146 4.171005 ACATAATACACACGTTCTGTCGG 58.829 43.478 0.00 0.00 34.94 4.79
146 147 5.756950 AACATAATACACACGTTCTGTCG 57.243 39.130 0.00 0.00 0.00 4.35
153 154 7.225145 ACACAACAGTAAACATAATACACACGT 59.775 33.333 0.00 0.00 0.00 4.49
164 165 9.120538 ACATAGAAAAGACACAACAGTAAACAT 57.879 29.630 0.00 0.00 0.00 2.71
229 232 4.023291 TGGGTATTTTCATTCTCCCAAGC 58.977 43.478 0.00 0.00 41.38 4.01
232 235 4.349365 GGTTGGGTATTTTCATTCTCCCA 58.651 43.478 0.00 0.00 42.41 4.37
248 251 3.487202 CATCGCGTGTCGGTTGGG 61.487 66.667 5.77 0.00 39.05 4.12
254 257 0.732880 AGTTCTTCCATCGCGTGTCG 60.733 55.000 5.77 0.00 40.15 4.35
261 264 5.466728 TCACTTTGAAAGAGTTCTTCCATCG 59.533 40.000 12.53 0.00 34.61 3.84
276 279 4.768130 TGGACGTGTTTTTCACTTTGAA 57.232 36.364 0.00 0.00 44.16 2.69
278 281 5.681105 CACTATGGACGTGTTTTTCACTTTG 59.319 40.000 0.00 0.00 44.16 2.77
285 288 4.625742 CGATCTCACTATGGACGTGTTTTT 59.374 41.667 0.00 0.00 34.14 1.94
291 294 6.576662 AATATTCGATCTCACTATGGACGT 57.423 37.500 0.00 0.00 0.00 4.34
310 313 8.698210 TCTATCTTTGGGTGTACGTGTTAATAT 58.302 33.333 0.00 0.00 0.00 1.28
332 337 2.015588 GCATGGCAGTGCAGTGTCTAT 61.016 52.381 25.57 16.04 44.43 1.98
336 341 3.359523 CGCATGGCAGTGCAGTGT 61.360 61.111 22.22 0.01 45.30 3.55
357 362 8.935844 TGCATCTTGTTGTAAGAACTAGTAATG 58.064 33.333 0.00 0.00 0.00 1.90
362 367 7.278646 TGCTATGCATCTTGTTGTAAGAACTAG 59.721 37.037 0.19 0.00 31.71 2.57
386 391 2.796032 GCATTCGAGTTTGGCCTAATGC 60.796 50.000 3.32 4.64 41.44 3.56
416 421 7.952671 AGAAGAGTAGCATGGTTATCGAATTA 58.047 34.615 1.12 0.00 0.00 1.40
459 674 4.875536 TGCATGGTAAGTGTGCAAGTATAG 59.124 41.667 0.00 0.00 44.99 1.31
460 675 4.837972 TGCATGGTAAGTGTGCAAGTATA 58.162 39.130 0.00 0.00 44.99 1.47
462 677 3.133141 TGCATGGTAAGTGTGCAAGTA 57.867 42.857 0.00 0.00 44.99 2.24
463 678 1.979855 TGCATGGTAAGTGTGCAAGT 58.020 45.000 0.00 0.00 44.99 3.16
466 681 0.590682 CGTTGCATGGTAAGTGTGCA 59.409 50.000 0.00 0.00 46.15 4.57
467 682 0.729140 GCGTTGCATGGTAAGTGTGC 60.729 55.000 0.00 0.00 39.26 4.57
468 683 0.590682 TGCGTTGCATGGTAAGTGTG 59.409 50.000 0.00 0.00 31.71 3.82
469 684 1.313772 TTGCGTTGCATGGTAAGTGT 58.686 45.000 0.00 0.00 38.76 3.55
484 1085 8.506140 TCTCAAATCTGAAAGTTTTATTTGCG 57.494 30.769 18.12 14.93 33.81 4.85
522 1123 1.755380 ACTACCAATGAGTACTCGGCC 59.245 52.381 17.85 0.00 0.00 6.13
538 1261 3.068873 AGCATCCGGAGAATCAAGACTAC 59.931 47.826 11.34 0.00 36.25 2.73
545 1268 3.118298 TCAATCAAGCATCCGGAGAATCA 60.118 43.478 11.34 0.00 36.25 2.57
552 1275 0.313043 GCCATCAATCAAGCATCCGG 59.687 55.000 0.00 0.00 0.00 5.14
562 1285 1.139520 GGGTTGCACGCCATCAATC 59.860 57.895 8.55 0.00 0.00 2.67
563 1286 3.287445 GGGTTGCACGCCATCAAT 58.713 55.556 8.55 0.00 0.00 2.57
570 1293 3.969995 TTTTTAAGGGGTTGCACGC 57.030 47.368 0.00 0.00 0.00 5.34
589 1312 3.598019 ATGCACGCCATCAATCTTTTT 57.402 38.095 0.00 0.00 0.00 1.94
666 1389 1.068055 CCATTTCTGTGCACAGGAAGC 60.068 52.381 36.73 3.97 44.07 3.86
712 1441 0.674534 ACTGACTGACCGAGTGGAAC 59.325 55.000 0.00 0.00 39.21 3.62
713 1442 0.959553 GACTGACTGACCGAGTGGAA 59.040 55.000 0.00 0.00 39.21 3.53
827 1556 5.010415 TCGACGATGAGGAGTGTACTATAGA 59.990 44.000 6.78 0.00 0.00 1.98
911 1641 3.119743 GGGTGCGACCTTGTTTTTATACC 60.120 47.826 5.48 0.00 38.64 2.73
917 1650 1.388837 GGTGGGTGCGACCTTGTTTT 61.389 55.000 5.48 0.00 38.64 2.43
975 1715 2.231478 TCTTGGCTAGAGAAGTTCGGTG 59.769 50.000 0.00 0.00 0.00 4.94
978 1718 4.810790 TCTTTCTTGGCTAGAGAAGTTCG 58.189 43.478 14.81 0.00 34.84 3.95
979 1719 5.584251 CCATCTTTCTTGGCTAGAGAAGTTC 59.416 44.000 14.81 0.00 34.84 3.01
981 1721 5.096443 CCATCTTTCTTGGCTAGAGAAGT 57.904 43.478 14.81 5.95 34.84 3.01
1015 1763 4.131088 GACGGCCAGGACGAGGAC 62.131 72.222 25.69 5.92 35.20 3.85
1304 2052 1.679944 CCCTGCATACCTTGTGACTGG 60.680 57.143 0.00 0.00 0.00 4.00
2214 2980 2.435059 GTGAAGGACGGCAGCCTC 60.435 66.667 10.54 6.11 33.76 4.70
2244 3010 2.918131 GCTGCGAGTGGTGAAATTGAAC 60.918 50.000 0.00 0.00 0.00 3.18
2321 3093 3.614092 CCACACTGAGCATCCAATAAGT 58.386 45.455 0.00 0.00 0.00 2.24
2322 3094 2.357009 GCCACACTGAGCATCCAATAAG 59.643 50.000 0.00 0.00 0.00 1.73
2326 3102 1.763120 AGCCACACTGAGCATCCAA 59.237 52.632 0.00 0.00 0.00 3.53
2341 3117 5.471456 CCTAACACCATAATCAAGATCAGCC 59.529 44.000 0.00 0.00 0.00 4.85
2342 3118 5.049129 GCCTAACACCATAATCAAGATCAGC 60.049 44.000 0.00 0.00 0.00 4.26
2343 3119 5.471456 GGCCTAACACCATAATCAAGATCAG 59.529 44.000 0.00 0.00 0.00 2.90
2354 3130 2.737544 TGTCGTAGGCCTAACACCATA 58.262 47.619 15.83 0.00 0.00 2.74
2369 3145 3.722295 CCGCGTGCCAAATGTCGT 61.722 61.111 4.92 0.00 0.00 4.34
2379 3155 2.480555 CAAGATGGAACCGCGTGC 59.519 61.111 4.92 0.00 0.00 5.34
2392 3168 7.093552 GGATGAATATCTCTTAGCTAGGCAAGA 60.094 40.741 0.00 0.00 33.68 3.02
2393 3169 7.041107 GGATGAATATCTCTTAGCTAGGCAAG 58.959 42.308 0.00 0.00 33.68 4.01
2394 3170 6.070538 GGGATGAATATCTCTTAGCTAGGCAA 60.071 42.308 0.00 0.00 30.74 4.52
2395 3171 5.423610 GGGATGAATATCTCTTAGCTAGGCA 59.576 44.000 0.00 0.00 30.74 4.75
2396 3172 5.423610 TGGGATGAATATCTCTTAGCTAGGC 59.576 44.000 0.00 0.00 34.73 3.93
2400 3176 9.732130 GTAAAATGGGATGAATATCTCTTAGCT 57.268 33.333 0.00 0.00 34.73 3.32
2416 3192 6.352516 ACAAGTGCAATTTTGTAAAATGGGA 58.647 32.000 9.89 0.00 38.53 4.37
2424 3200 5.928839 ACACACAAACAAGTGCAATTTTGTA 59.071 32.000 14.53 0.00 43.23 2.41
2426 3202 5.080731 CACACACAAACAAGTGCAATTTTG 58.919 37.500 9.19 9.19 43.23 2.44
2457 3239 5.244851 TGCTACTTGCCCAATTGTTTGAATA 59.755 36.000 4.43 0.00 42.00 1.75
2458 3240 4.040217 TGCTACTTGCCCAATTGTTTGAAT 59.960 37.500 4.43 0.00 42.00 2.57
2459 3241 3.386078 TGCTACTTGCCCAATTGTTTGAA 59.614 39.130 4.43 0.00 42.00 2.69
2460 3242 2.961741 TGCTACTTGCCCAATTGTTTGA 59.038 40.909 4.43 0.00 42.00 2.69
2461 3243 3.383620 TGCTACTTGCCCAATTGTTTG 57.616 42.857 4.43 0.00 42.00 2.93
2462 3244 3.133721 TGTTGCTACTTGCCCAATTGTTT 59.866 39.130 4.43 0.00 42.00 2.83
2483 3265 6.155827 CAGAGAAGGAAAGAGAGTAACAGTG 58.844 44.000 0.00 0.00 0.00 3.66
2641 3425 9.295825 TGTTATTGTGGATGTTGAGACTTTTAT 57.704 29.630 0.00 0.00 0.00 1.40
2706 3490 1.064389 GCCTAAGAAATCCTGCAGGGT 60.064 52.381 32.23 24.65 36.25 4.34
2710 3494 3.281727 AATCGCCTAAGAAATCCTGCA 57.718 42.857 0.00 0.00 0.00 4.41
2722 3506 4.825085 AGAACCAAACAGAAAAATCGCCTA 59.175 37.500 0.00 0.00 0.00 3.93
2755 3539 0.759346 AGATAACATCGCCTGGACCC 59.241 55.000 0.00 0.00 0.00 4.46
2756 3540 1.689273 AGAGATAACATCGCCTGGACC 59.311 52.381 0.00 0.00 0.00 4.46
2762 3546 4.072131 AGAGAGAGAGAGATAACATCGCC 58.928 47.826 0.00 0.00 0.00 5.54
2850 3648 2.159282 CCACATCTTGAATCCTGCTTGC 60.159 50.000 0.00 0.00 0.00 4.01
2865 5240 3.129871 GCATCTCTTCTAGTGCCACATC 58.870 50.000 0.00 0.00 0.00 3.06
2869 5244 3.198417 TGATTGCATCTCTTCTAGTGCCA 59.802 43.478 0.00 0.00 33.74 4.92
2888 5263 2.324541 GACATGCCCTACCTCTCTGAT 58.675 52.381 0.00 0.00 0.00 2.90
2938 5313 9.063615 ACTATGAAAAAGTGGTTCGATTTTACT 57.936 29.630 0.00 0.00 0.00 2.24
2947 5322 9.573133 CATTGGAATACTATGAAAAAGTGGTTC 57.427 33.333 0.00 0.00 0.00 3.62
2970 5345 0.620410 TCCCCGACCCATCTCACATT 60.620 55.000 0.00 0.00 0.00 2.71
2971 5346 1.002921 TCCCCGACCCATCTCACAT 59.997 57.895 0.00 0.00 0.00 3.21
3057 5432 9.448294 CAGACTGATAACTATAACGTAGGAAAC 57.552 37.037 0.00 0.00 0.00 2.78
3062 5437 6.016527 TGGGCAGACTGATAACTATAACGTAG 60.017 42.308 6.65 0.00 0.00 3.51
3065 5440 5.196341 TGGGCAGACTGATAACTATAACG 57.804 43.478 6.65 0.00 0.00 3.18
3076 5451 0.325933 CTTCCACATGGGCAGACTGA 59.674 55.000 6.65 0.00 36.21 3.41
3091 5466 6.543831 ACAACATGATTAGCCTGATAACTTCC 59.456 38.462 0.00 0.00 0.00 3.46
3106 5481 6.237901 TCTGCTTGGTAACTACAACATGATT 58.762 36.000 0.00 0.00 37.61 2.57
3148 5523 6.819146 GCCTAGTAACTTTAGCATGAGAAGTT 59.181 38.462 18.88 18.88 43.68 2.66
3169 5544 1.221635 AATGTAGCATGGGTGGCCTA 58.778 50.000 3.32 0.00 0.00 3.93
3175 5550 5.260424 TGTGTTGATAAATGTAGCATGGGT 58.740 37.500 0.00 0.00 0.00 4.51
3199 5574 5.065090 TGCATAATGATAGCCACATAATCGC 59.935 40.000 0.00 0.00 0.00 4.58
3218 5593 9.382275 CATATTGGTAACTATAGCATGTGCATA 57.618 33.333 7.83 0.00 39.15 3.14


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

AutoCloner maintained by Alex Coulton.