Multiple sequence alignment - TraesCS1D01G030400

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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 TraesCS1D01G030400 chr1D 100.000 5387 0 0 1 5387 11848875 11854261 0.000000e+00 9949
1 TraesCS1D01G030400 chr1D 78.519 270 53 5 262 531 105970905 105971169 7.170000e-39 172
2 TraesCS1D01G030400 chr1B 92.810 3171 171 26 2249 5381 17683392 17686543 0.000000e+00 4540
3 TraesCS1D01G030400 chr1B 85.836 1059 82 31 595 1619 17680860 17681884 0.000000e+00 1062
4 TraesCS1D01G030400 chr1B 86.070 201 23 5 292 491 17680557 17680753 1.520000e-50 211
5 TraesCS1D01G030400 chr1B 84.729 203 27 4 301 502 471198658 471198857 3.290000e-47 200
6 TraesCS1D01G030400 chr1B 85.366 205 14 11 1 196 17680159 17680356 1.180000e-46 198
7 TraesCS1D01G030400 chr1B 81.633 245 38 7 260 502 172388416 172388655 4.260000e-46 196
8 TraesCS1D01G030400 chr1A 89.130 3643 286 60 384 3958 13971269 13974869 0.000000e+00 4433
9 TraesCS1D01G030400 chr1A 87.291 299 31 4 4214 4510 13975115 13975408 8.650000e-88 335
10 TraesCS1D01G030400 chr1A 91.758 182 8 4 1 175 13970579 13970760 4.170000e-61 246
11 TraesCS1D01G030400 chr1A 90.789 76 6 1 4036 4110 13974884 13974959 3.430000e-17 100
12 TraesCS1D01G030400 chr5D 83.519 807 115 14 2331 3130 423266034 423266829 0.000000e+00 737
13 TraesCS1D01G030400 chr5D 88.050 318 31 6 1027 1339 423263138 423263453 2.370000e-98 370
14 TraesCS1D01G030400 chr5D 80.000 300 48 7 3642 3935 423374618 423374911 1.520000e-50 211
15 TraesCS1D01G030400 chr5D 82.500 160 28 0 2800 2959 423373688 423373847 2.020000e-29 141
16 TraesCS1D01G030400 chr5D 84.962 133 18 2 302 433 563589570 563589701 3.380000e-27 134
17 TraesCS1D01G030400 chr5B 82.630 806 123 14 2331 3130 510883037 510883831 0.000000e+00 697
18 TraesCS1D01G030400 chr5B 93.361 241 16 0 1099 1339 510880342 510880582 1.850000e-94 357
19 TraesCS1D01G030400 chr5B 78.233 317 59 5 3642 3953 511075990 511076301 1.530000e-45 195
20 TraesCS1D01G030400 chr5A 84.268 642 101 0 2331 2972 536884306 536884947 1.270000e-175 627
21 TraesCS1D01G030400 chr5A 91.701 241 20 0 1099 1339 536768593 536768833 8.650000e-88 335
22 TraesCS1D01G030400 chr5A 83.793 290 43 3 1051 1339 536878970 536879256 6.880000e-69 272
23 TraesCS1D01G030400 chr5A 78.616 318 56 7 3642 3953 536885824 536886135 3.290000e-47 200
24 TraesCS1D01G030400 chr3B 87.755 245 30 0 1098 1342 795810126 795809882 2.460000e-73 287
25 TraesCS1D01G030400 chr3D 86.400 250 33 1 1100 1348 593226635 593226386 6.880000e-69 272
26 TraesCS1D01G030400 chr3D 73.884 605 146 11 2331 2929 593223095 593222497 1.170000e-56 231
27 TraesCS1D01G030400 chr3A 86.066 244 32 2 1100 1342 724496641 724496399 1.490000e-65 261
28 TraesCS1D01G030400 chr4A 82.627 236 35 6 260 494 628931232 628931462 2.540000e-48 204
29 TraesCS1D01G030400 chr7D 82.684 231 36 4 301 530 59859822 59859595 9.150000e-48 202
30 TraesCS1D01G030400 chr2B 81.933 238 35 8 259 494 131102140 131101909 1.530000e-45 195
31 TraesCS1D01G030400 chr6B 83.673 196 29 3 336 531 591571293 591571485 1.190000e-41 182


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 TraesCS1D01G030400 chr1D 11848875 11854261 5386 False 9949.00 9949 100.0000 1 5387 1 chr1D.!!$F1 5386
1 TraesCS1D01G030400 chr1B 17680159 17686543 6384 False 1502.75 4540 87.5205 1 5381 4 chr1B.!!$F3 5380
2 TraesCS1D01G030400 chr1A 13970579 13975408 4829 False 1278.50 4433 89.7420 1 4510 4 chr1A.!!$F1 4509
3 TraesCS1D01G030400 chr5D 423263138 423266829 3691 False 553.50 737 85.7845 1027 3130 2 chr5D.!!$F2 2103
4 TraesCS1D01G030400 chr5B 510880342 510883831 3489 False 527.00 697 87.9955 1099 3130 2 chr5B.!!$F2 2031
5 TraesCS1D01G030400 chr5A 536884306 536886135 1829 False 413.50 627 81.4420 2331 3953 2 chr5A.!!$F3 1622
6 TraesCS1D01G030400 chr3D 593222497 593226635 4138 True 251.50 272 80.1420 1100 2929 2 chr3D.!!$R1 1829

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
973 1560 0.673644 CGGAAACCAACGCTCTCCAT 60.674 55.0 0.00 0.0 0.00 3.41 F
1699 3684 0.040157 TGTAGCAAGTCGTACGCGTT 60.040 50.0 20.78 0.8 39.49 4.84 F
2427 8199 0.320050 TCTACATGCAACGCTCCACA 59.680 50.0 0.00 0.0 0.00 4.17 F
3257 9054 0.176219 TACCCGGCCTCAACATAACG 59.824 55.0 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2670 8442 0.178767 TGTAGACGGCGAGGTAGCTA 59.821 55.000 16.62 2.19 37.29 3.32 R
3241 9038 0.390603 TCACGTTATGTTGAGGCCGG 60.391 55.000 0.00 0.00 0.00 6.13 R
4088 10219 1.070758 ACTACTGTGTGCCCTGTTGAG 59.929 52.381 0.00 0.00 0.00 3.02 R
4954 11152 0.466124 CCCCTAGCTACAAGGAGCAC 59.534 60.000 7.10 0.00 45.43 4.40 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
18 19 3.702802 CCCACAGGCCACGTACTA 58.297 61.111 5.01 0.00 0.00 1.82
19 20 2.208527 CCCACAGGCCACGTACTAT 58.791 57.895 5.01 0.00 0.00 2.12
192 201 9.940166 GAAAAAGAAACGTAGGAATTTCTGTTA 57.060 29.630 0.00 0.00 42.89 2.41
195 204 9.726232 AAAGAAACGTAGGAATTTCTGTTAAAC 57.274 29.630 0.00 0.00 42.89 2.01
196 205 7.570161 AGAAACGTAGGAATTTCTGTTAAACG 58.430 34.615 4.75 4.75 42.27 3.60
197 206 5.851047 ACGTAGGAATTTCTGTTAAACGG 57.149 39.130 10.06 0.00 32.47 4.44
198 207 5.540911 ACGTAGGAATTTCTGTTAAACGGA 58.459 37.500 10.06 0.00 32.47 4.69
199 208 5.636543 ACGTAGGAATTTCTGTTAAACGGAG 59.363 40.000 10.06 0.00 34.53 4.63
211 380 4.641094 TGTTAAACGGAGGTGAAACATGTT 59.359 37.500 4.92 4.92 39.98 2.71
223 392 5.163499 GGTGAAACATGTTACAAACCTGGAA 60.163 40.000 12.39 0.00 39.98 3.53
230 399 4.448210 TGTTACAAACCTGGAACTCAGAC 58.552 43.478 0.00 0.00 45.45 3.51
232 401 3.644966 ACAAACCTGGAACTCAGACAA 57.355 42.857 0.00 0.00 46.18 3.18
250 422 2.348605 AAAATTGGCGTGCGTGCACT 62.349 50.000 21.36 0.72 44.16 4.40
259 431 2.435586 GCGTGCACTGGAGCAGAT 60.436 61.111 16.19 0.00 46.69 2.90
260 432 2.037136 GCGTGCACTGGAGCAGATT 61.037 57.895 16.19 0.00 46.69 2.40
290 462 9.979578 TTGTGAACAATATTTTTATTGCTCAGT 57.020 25.926 10.48 0.00 40.81 3.41
311 483 7.833786 TCAGTAATAAGGAGTTACAATCACGT 58.166 34.615 0.00 0.00 35.11 4.49
343 516 2.236395 CAAGTACTTCCTTGGTCCCGAT 59.764 50.000 4.77 0.00 38.51 4.18
424 945 7.706281 AGCTAGATTTTGAGTATGTCGAATG 57.294 36.000 0.00 0.00 0.00 2.67
433 954 8.771920 TTTGAGTATGTCGAATGTGAGTAATT 57.228 30.769 0.00 0.00 0.00 1.40
468 989 7.507616 ACGTTCCTCTAGATTATCCTTGATCTT 59.492 37.037 0.00 0.00 34.60 2.40
471 992 9.667607 TTCCTCTAGATTATCCTTGATCTTCTT 57.332 33.333 0.00 0.00 34.60 2.52
624 1175 2.677337 TCACATGCACCATATGACGTTG 59.323 45.455 3.65 0.00 0.00 4.10
628 1179 1.670295 TGCACCATATGACGTTGCATC 59.330 47.619 3.65 0.00 0.00 3.91
635 1186 3.554692 GACGTTGCATCTCGGCCG 61.555 66.667 22.12 22.12 0.00 6.13
637 1188 2.202690 CGTTGCATCTCGGCCGTA 60.203 61.111 27.15 15.53 0.00 4.02
641 1192 1.600511 TTGCATCTCGGCCGTACTCA 61.601 55.000 27.15 14.71 0.00 3.41
642 1193 1.589196 GCATCTCGGCCGTACTCAC 60.589 63.158 27.15 8.07 0.00 3.51
704 1255 3.139077 GGGTGAGGTGTTACAGTTTCTG 58.861 50.000 0.00 0.00 37.52 3.02
816 1367 1.237285 GGTTTCTGTGATGCTGCGGT 61.237 55.000 0.00 0.00 0.00 5.68
875 1432 4.344865 AGTTGGCGCCGGGTGATT 62.345 61.111 23.90 0.00 0.00 2.57
900 1463 2.590092 CCCATCCCCGTGTCTTCC 59.410 66.667 0.00 0.00 0.00 3.46
910 1473 1.451067 CGTGTCTTCCTCTACCTCGT 58.549 55.000 0.00 0.00 0.00 4.18
935 1522 1.267087 GCGTTGCGTTCATAAGAGAGC 60.267 52.381 0.00 0.00 0.00 4.09
956 1543 1.142748 GAGAGTGGATCACTGCCGG 59.857 63.158 5.20 0.00 45.44 6.13
962 1549 1.002624 GGATCACTGCCGGAAACCA 60.003 57.895 5.05 0.00 0.00 3.67
965 1552 1.234615 ATCACTGCCGGAAACCAACG 61.235 55.000 5.05 0.00 0.00 4.10
973 1560 0.673644 CGGAAACCAACGCTCTCCAT 60.674 55.000 0.00 0.00 0.00 3.41
975 1564 1.087501 GAAACCAACGCTCTCCATCC 58.912 55.000 0.00 0.00 0.00 3.51
1040 1633 1.510480 GACACCACCAAGCTGCAGAC 61.510 60.000 20.43 9.11 0.00 3.51
1124 1744 4.899239 GAGCATCCTGGGCGACGG 62.899 72.222 0.00 0.00 36.08 4.79
1342 1962 1.202533 CCTACGGCCTCATGGTAAGTG 60.203 57.143 0.00 0.00 35.27 3.16
1349 1970 2.743183 GCCTCATGGTAAGTGCCACTAG 60.743 54.545 0.00 0.00 41.94 2.57
1368 1989 1.272769 AGGTCTCTCAGTTAACCACGC 59.727 52.381 0.88 0.00 34.09 5.34
1369 1990 1.272769 GGTCTCTCAGTTAACCACGCT 59.727 52.381 0.88 0.00 0.00 5.07
1520 2641 0.455295 CTTATCTCGCGATCCGGCTC 60.455 60.000 10.36 0.00 37.59 4.70
1592 2717 7.678947 TGTGTTCACCTACTAACTACTACTC 57.321 40.000 0.37 0.00 0.00 2.59
1594 2719 6.883756 GTGTTCACCTACTAACTACTACTCCT 59.116 42.308 0.00 0.00 0.00 3.69
1595 2720 8.043710 GTGTTCACCTACTAACTACTACTCCTA 58.956 40.741 0.00 0.00 0.00 2.94
1628 2754 5.918576 TGGATTCTATATTTGTAGCGTGTCG 59.081 40.000 0.00 0.00 0.00 4.35
1655 3640 4.323417 TGCGTTACATCTGTCCATTTCTT 58.677 39.130 0.00 0.00 0.00 2.52
1674 3659 0.781787 TCTTTGACGCGTGTGAATCG 59.218 50.000 20.70 0.00 0.00 3.34
1699 3684 0.040157 TGTAGCAAGTCGTACGCGTT 60.040 50.000 20.78 0.80 39.49 4.84
1704 3689 1.136446 GCAAGTCGTACGCGTTTGAAT 60.136 47.619 20.78 12.64 36.59 2.57
1793 4558 6.106648 TCTTTCATCACTCACTCTTGTCAT 57.893 37.500 0.00 0.00 0.00 3.06
1826 4591 9.369904 CATTTATTGGTAATTCTTTCTGGTTGG 57.630 33.333 0.00 0.00 0.00 3.77
1847 6225 2.610232 GCCCTATGTTGGTTTTGCACAG 60.610 50.000 0.00 0.00 0.00 3.66
1886 6264 4.939509 TTGCAACTAAAGCGACTTATCC 57.060 40.909 0.00 0.00 33.85 2.59
1989 6367 2.084610 ACATGTCACCTCATCACACG 57.915 50.000 0.00 0.00 0.00 4.49
1990 6368 1.344438 ACATGTCACCTCATCACACGT 59.656 47.619 0.00 0.00 0.00 4.49
1991 6369 2.560981 ACATGTCACCTCATCACACGTA 59.439 45.455 0.00 0.00 0.00 3.57
1992 6370 2.717580 TGTCACCTCATCACACGTAC 57.282 50.000 0.00 0.00 0.00 3.67
1993 6371 1.271379 TGTCACCTCATCACACGTACC 59.729 52.381 0.00 0.00 0.00 3.34
1995 6373 1.271379 TCACCTCATCACACGTACCAC 59.729 52.381 0.00 0.00 0.00 4.16
1997 6375 0.895530 CCTCATCACACGTACCACCT 59.104 55.000 0.00 0.00 0.00 4.00
1998 6376 1.275291 CCTCATCACACGTACCACCTT 59.725 52.381 0.00 0.00 0.00 3.50
2066 6470 4.145876 ACTAATTGTGTCAACATGCACG 57.854 40.909 0.00 0.00 38.36 5.34
2092 6496 7.065803 GCATCACGTAAAGCCCAATATATATGT 59.934 37.037 0.00 0.00 0.00 2.29
2168 6611 8.546597 TTCGTGTCATATTCAAATTCAAGAGA 57.453 30.769 0.00 0.00 0.00 3.10
2169 6612 8.546597 TCGTGTCATATTCAAATTCAAGAGAA 57.453 30.769 0.00 0.00 38.31 2.87
2170 6613 8.998377 TCGTGTCATATTCAAATTCAAGAGAAA 58.002 29.630 0.00 0.00 37.29 2.52
2171 6614 9.611284 CGTGTCATATTCAAATTCAAGAGAAAA 57.389 29.630 0.00 0.00 37.29 2.29
2190 6633 3.963383 AAAAATTCACGTGTTCTCGCT 57.037 38.095 16.51 0.00 0.00 4.93
2197 6640 0.880278 ACGTGTTCTCGCTGCAACAT 60.880 50.000 7.21 0.00 35.05 2.71
2204 6647 2.985282 CGCTGCAACATGTGGGGT 60.985 61.111 0.00 0.00 0.00 4.95
2227 6691 1.135689 CCACACTAGGCATCGTTTTGC 60.136 52.381 0.00 0.19 42.01 3.68
2237 6701 5.222631 AGGCATCGTTTTGCTTTCTTTTAG 58.777 37.500 7.47 0.00 42.38 1.85
2362 8134 4.148825 GGAGCGCGGTGGAGACAT 62.149 66.667 18.92 0.00 46.14 3.06
2427 8199 0.320050 TCTACATGCAACGCTCCACA 59.680 50.000 0.00 0.00 0.00 4.17
2431 8203 0.952497 CATGCAACGCTCCACAGTCT 60.952 55.000 0.00 0.00 0.00 3.24
2490 8262 2.286121 TTCTCCCGGCCCATCCTT 60.286 61.111 0.00 0.00 0.00 3.36
2496 8268 1.376466 CCGGCCCATCCTTATCCTG 59.624 63.158 0.00 0.00 0.00 3.86
2670 8442 2.641559 GTCGTCCACGTCGTCCTT 59.358 61.111 0.00 0.00 40.80 3.36
2978 8751 4.813697 GCTCTCCATCTGGTAATCACTTTC 59.186 45.833 0.00 0.00 36.34 2.62
3203 9000 7.161773 TCATCAAAGGGAATTTCACTCAATC 57.838 36.000 0.69 0.00 0.00 2.67
3241 9038 1.094785 AACCGCACTGCATGAATACC 58.905 50.000 0.00 0.00 0.00 2.73
3257 9054 0.176219 TACCCGGCCTCAACATAACG 59.824 55.000 0.00 0.00 0.00 3.18
3384 9181 0.178992 CTGGAAACCCCAAGTCAGCA 60.179 55.000 0.00 0.00 46.07 4.41
3492 9289 3.068165 TCAGTTACATCTATGCTGACGGG 59.932 47.826 0.00 0.00 32.09 5.28
3558 9355 2.838202 ACTAACCGTCATCCTCAATGGT 59.162 45.455 0.00 0.00 36.31 3.55
3638 9757 1.596603 CTGCCATTGTGACACTGACA 58.403 50.000 7.20 0.00 0.00 3.58
3810 9929 4.160814 TCCGTGCAAGGCTCTTTATAACTA 59.839 41.667 14.54 0.00 0.00 2.24
3823 9942 2.433868 ATAACTATACACCGCCTGCG 57.566 50.000 4.20 4.20 39.44 5.18
3824 9943 1.105457 TAACTATACACCGCCTGCGT 58.895 50.000 10.94 0.00 37.81 5.24
3829 9950 2.304901 ATACACCGCCTGCGTGCATA 62.305 55.000 10.94 0.00 37.81 3.14
3945 10073 2.756760 CCATCAGGACAAATTGGGACAG 59.243 50.000 0.00 0.00 36.82 3.51
3946 10074 1.909700 TCAGGACAAATTGGGACAGC 58.090 50.000 0.00 0.00 42.39 4.40
3958 10086 1.061570 GGACAGCGAGGTACGTACG 59.938 63.158 18.98 15.01 44.60 3.67
3975 10106 3.303229 CGTACGTACGTTTGGGATTTACC 59.697 47.826 33.95 0.00 44.13 2.85
3997 10128 5.986135 ACCTCGATTGTAATGAATCACTAGC 59.014 40.000 0.00 0.00 32.67 3.42
3998 10129 6.183360 ACCTCGATTGTAATGAATCACTAGCT 60.183 38.462 0.00 0.00 32.67 3.32
3999 10130 7.014326 ACCTCGATTGTAATGAATCACTAGCTA 59.986 37.037 0.00 0.00 32.67 3.32
4000 10131 7.540400 CCTCGATTGTAATGAATCACTAGCTAG 59.460 40.741 19.44 19.44 32.67 3.42
4095 10226 9.113838 ACAGAACAATAATATTAGGCTCAACAG 57.886 33.333 1.02 0.00 0.00 3.16
4205 10368 7.221838 CAGTTAAACAACCAAATAACACCAGTG 59.778 37.037 0.00 0.00 32.10 3.66
4389 10581 6.507900 TCTATTAGCTGTCGAGGAATGAAAG 58.492 40.000 0.00 0.00 0.00 2.62
4439 10631 5.912149 TCATAAGCAGGATTGGAAGGTAT 57.088 39.130 0.00 0.00 0.00 2.73
4457 10649 8.787852 GGAAGGTATGTAATCCAAGATCATTTC 58.212 37.037 0.00 0.00 32.08 2.17
4497 10689 2.997303 TCGTTGTCCAAACACATATCCG 59.003 45.455 0.00 0.00 34.35 4.18
4510 10702 0.472471 ATATCCGATGGTGGGCGTTT 59.528 50.000 0.00 0.00 0.00 3.60
4511 10703 0.462937 TATCCGATGGTGGGCGTTTG 60.463 55.000 0.00 0.00 0.00 2.93
4512 10704 3.439540 CCGATGGTGGGCGTTTGG 61.440 66.667 0.00 0.00 0.00 3.28
4567 10759 5.464168 CATCTTTGTGATGTCCCTTTTCAC 58.536 41.667 0.00 0.00 45.55 3.18
4627 10819 1.873591 TCTCGCTTCTTTTGGCAGTTC 59.126 47.619 0.00 0.00 0.00 3.01
4690 10882 1.005924 CCTAAGGACCATGGCAACCTT 59.994 52.381 28.79 28.79 43.75 3.50
4717 10909 8.210265 GGGATTCAAGAATCAGAAGTAGAGAAT 58.790 37.037 20.73 0.00 46.77 2.40
4785 10982 4.695455 TGAGTTTGGTATAGTTGCTCTTGC 59.305 41.667 0.00 0.00 40.20 4.01
4834 11032 4.847990 ATATCGGTTAAGTTCCACCCAA 57.152 40.909 0.00 0.00 0.00 4.12
4835 11033 2.259266 TCGGTTAAGTTCCACCCAAC 57.741 50.000 0.00 0.00 0.00 3.77
4844 11042 0.037139 TTCCACCCAACGGACATACG 60.037 55.000 0.00 0.00 40.31 3.06
4858 11056 3.558533 GGACATACGTTTTGGAAGGGTCT 60.559 47.826 0.00 0.00 0.00 3.85
4866 11064 4.570930 GTTTTGGAAGGGTCTACTGAGAG 58.429 47.826 0.00 0.00 30.20 3.20
4872 11070 4.142116 GGAAGGGTCTACTGAGAGTTAAGC 60.142 50.000 0.00 0.00 30.20 3.09
4885 11083 5.706833 TGAGAGTTAAGCATGCATTCTTTCA 59.293 36.000 21.98 17.82 0.00 2.69
4895 11093 6.537301 AGCATGCATTCTTTCAATTTGGTATG 59.463 34.615 21.98 0.00 0.00 2.39
4905 11103 9.743057 TCTTTCAATTTGGTATGTTTGTTGTAG 57.257 29.630 0.00 0.00 0.00 2.74
4919 11117 6.775142 TGTTTGTTGTAGGGAATGAAGAATCA 59.225 34.615 0.00 0.00 40.57 2.57
4926 11124 5.972327 AGGGAATGAAGAATCAGTGAGAT 57.028 39.130 0.00 0.00 39.39 2.75
4954 11152 2.961062 GAGGACAAATGGATTGGGGATG 59.039 50.000 0.00 0.00 43.66 3.51
4979 11177 4.287326 GCTCCTTGTAGCTAGGGGATAATT 59.713 45.833 4.97 0.00 39.50 1.40
4984 11182 9.043548 TCCTTGTAGCTAGGGGATAATTAATAC 57.956 37.037 0.00 0.00 33.41 1.89
4985 11183 7.980099 CCTTGTAGCTAGGGGATAATTAATACG 59.020 40.741 0.00 0.00 0.00 3.06
4986 11184 8.426569 TTGTAGCTAGGGGATAATTAATACGT 57.573 34.615 0.00 0.00 0.00 3.57
4987 11185 9.532494 TTGTAGCTAGGGGATAATTAATACGTA 57.468 33.333 0.00 0.00 0.00 3.57
4988 11186 9.705103 TGTAGCTAGGGGATAATTAATACGTAT 57.295 33.333 1.14 1.14 0.00 3.06
5024 11222 4.218417 GGATGCCACTGTAATTGTTGTTCT 59.782 41.667 0.00 0.00 0.00 3.01
5050 11248 3.935818 TGGAAAACCCACTAGTTGACA 57.064 42.857 0.00 0.00 40.82 3.58
5066 11264 2.238521 TGACATTTTGTTGGGCTCTCC 58.761 47.619 0.00 0.00 0.00 3.71
5070 11268 1.770294 TTTTGTTGGGCTCTCCGTTT 58.230 45.000 0.00 0.00 38.76 3.60
5078 11276 0.673644 GGCTCTCCGTTTTAGCAGCA 60.674 55.000 0.00 0.00 38.01 4.41
5105 11303 2.545742 CGGAGTGCAATGATATCGTCCA 60.546 50.000 0.00 0.00 0.00 4.02
5111 11309 2.031682 GCAATGATATCGTCCACAAGGC 60.032 50.000 0.00 0.00 33.74 4.35
5134 11332 5.672321 GCTGTGAAGATGCAACTAACTTAGC 60.672 44.000 0.00 2.25 0.00 3.09
5167 11365 6.316390 GTCATTTAAGTGGGACCTTCATACAG 59.684 42.308 0.00 0.00 0.00 2.74
5176 11374 3.264964 GGACCTTCATACAGTTGGGGTTA 59.735 47.826 0.00 0.00 0.00 2.85
5217 11415 8.373048 TGTACTTTGCTTTAATGGATATACGG 57.627 34.615 0.00 0.00 0.00 4.02
5265 11463 6.693315 TGGTGCCTTAAATTACATCTAAGC 57.307 37.500 0.00 0.00 0.00 3.09
5268 11466 7.341769 TGGTGCCTTAAATTACATCTAAGCATT 59.658 33.333 0.00 0.00 0.00 3.56
5301 11499 7.474190 TCCTTAAGAACAACTTGTTTAAACGG 58.526 34.615 13.45 10.88 41.28 4.44
5317 11515 2.632987 ACGGGAAACACAAAGTAGCT 57.367 45.000 0.00 0.00 0.00 3.32
5350 11548 8.812147 TGTATATGAAACTATCATCCAACGTC 57.188 34.615 0.00 0.00 45.91 4.34
5372 11570 2.853731 TTTTACTGTGGTTTGGCACG 57.146 45.000 0.00 0.00 0.00 5.34
5381 11579 3.437395 TGTGGTTTGGCACGTATTGTATC 59.563 43.478 0.00 0.00 0.00 2.24
5382 11580 3.437395 GTGGTTTGGCACGTATTGTATCA 59.563 43.478 0.00 0.00 0.00 2.15
5383 11581 4.095782 GTGGTTTGGCACGTATTGTATCAT 59.904 41.667 0.00 0.00 0.00 2.45
5384 11582 4.095632 TGGTTTGGCACGTATTGTATCATG 59.904 41.667 0.00 0.00 0.00 3.07
5385 11583 3.961477 TTGGCACGTATTGTATCATGC 57.039 42.857 0.00 0.00 0.00 4.06
5386 11584 1.864082 TGGCACGTATTGTATCATGCG 59.136 47.619 0.00 0.00 33.85 4.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
178 187 5.935789 CACCTCCGTTTAACAGAAATTCCTA 59.064 40.000 0.00 0.00 0.00 2.94
179 188 4.760204 CACCTCCGTTTAACAGAAATTCCT 59.240 41.667 0.00 0.00 0.00 3.36
182 191 6.095720 TGTTTCACCTCCGTTTAACAGAAATT 59.904 34.615 0.00 0.00 0.00 1.82
192 201 4.200874 TGTAACATGTTTCACCTCCGTTT 58.799 39.130 17.78 0.00 0.00 3.60
195 204 4.533222 GTTTGTAACATGTTTCACCTCCG 58.467 43.478 17.78 0.00 0.00 4.63
196 205 4.583073 AGGTTTGTAACATGTTTCACCTCC 59.417 41.667 17.78 17.24 0.00 4.30
197 206 5.507315 CCAGGTTTGTAACATGTTTCACCTC 60.507 44.000 17.78 9.95 41.30 3.85
198 207 4.340950 CCAGGTTTGTAACATGTTTCACCT 59.659 41.667 17.78 17.16 41.30 4.00
199 208 4.339814 TCCAGGTTTGTAACATGTTTCACC 59.660 41.667 17.78 15.26 41.30 4.02
211 380 4.764050 TTGTCTGAGTTCCAGGTTTGTA 57.236 40.909 0.00 0.00 43.12 2.41
223 392 1.001378 GCACGCCAATTTTGTCTGAGT 60.001 47.619 0.00 0.00 0.00 3.41
230 399 1.948138 TGCACGCACGCCAATTTTG 60.948 52.632 0.00 0.00 0.00 2.44
232 401 2.354539 GTGCACGCACGCCAATTT 60.355 55.556 6.38 0.00 37.19 1.82
284 456 7.043325 CGTGATTGTAACTCCTTATTACTGAGC 60.043 40.741 0.00 0.00 34.28 4.26
286 458 7.833786 ACGTGATTGTAACTCCTTATTACTGA 58.166 34.615 0.00 0.00 34.28 3.41
287 459 7.044249 CGACGTGATTGTAACTCCTTATTACTG 60.044 40.741 0.00 0.00 34.28 2.74
288 460 6.971184 CGACGTGATTGTAACTCCTTATTACT 59.029 38.462 0.00 0.00 34.28 2.24
289 461 6.749118 ACGACGTGATTGTAACTCCTTATTAC 59.251 38.462 0.00 0.00 33.85 1.89
290 462 6.855836 ACGACGTGATTGTAACTCCTTATTA 58.144 36.000 0.00 0.00 0.00 0.98
291 463 5.717119 ACGACGTGATTGTAACTCCTTATT 58.283 37.500 0.00 0.00 0.00 1.40
292 464 5.320549 ACGACGTGATTGTAACTCCTTAT 57.679 39.130 0.00 0.00 0.00 1.73
293 465 4.771590 ACGACGTGATTGTAACTCCTTA 57.228 40.909 0.00 0.00 0.00 2.69
294 466 3.655276 ACGACGTGATTGTAACTCCTT 57.345 42.857 0.00 0.00 0.00 3.36
311 483 5.717078 AGGAAGTACTTGACATTGTACGA 57.283 39.130 14.14 0.00 42.53 3.43
343 516 2.235155 TCAAACTGCGGTATAGCTTGGA 59.765 45.455 0.00 0.00 38.13 3.53
413 934 8.407457 TCTTGAATTACTCACATTCGACATAC 57.593 34.615 0.00 0.00 33.91 2.39
416 937 6.147164 GGTTCTTGAATTACTCACATTCGACA 59.853 38.462 0.00 0.00 33.91 4.35
424 945 5.333875 GGAACGTGGTTCTTGAATTACTCAC 60.334 44.000 8.25 0.00 41.70 3.51
433 954 3.493334 TCTAGAGGAACGTGGTTCTTGA 58.507 45.455 8.25 0.00 41.70 3.02
591 1142 3.623060 GGTGCATGTGAACTTACGATCAT 59.377 43.478 0.00 0.00 0.00 2.45
624 1175 1.589196 GTGAGTACGGCCGAGATGC 60.589 63.158 35.90 13.89 0.00 3.91
628 1179 1.592400 TTCTGGTGAGTACGGCCGAG 61.592 60.000 35.90 16.53 0.00 4.63
635 1186 3.428870 CACATCACGTTTCTGGTGAGTAC 59.571 47.826 0.99 0.00 46.55 2.73
637 1188 2.158957 ACACATCACGTTTCTGGTGAGT 60.159 45.455 8.89 0.00 46.55 3.41
641 1192 2.613026 TCACACATCACGTTTCTGGT 57.387 45.000 0.00 0.00 0.00 4.00
642 1193 2.160219 CCATCACACATCACGTTTCTGG 59.840 50.000 0.00 0.00 0.00 3.86
704 1255 2.109126 CCAGCTAAGCCTTGCGACC 61.109 63.158 0.00 0.00 0.00 4.79
816 1367 4.082845 CTGTCTTCTCTCCTACTCCACAA 58.917 47.826 0.00 0.00 0.00 3.33
900 1463 2.023461 CGCGAGCACGAGGTAGAG 59.977 66.667 8.01 0.00 42.66 2.43
935 1522 0.102120 GGCAGTGATCCACTCTCTCG 59.898 60.000 0.00 0.00 43.43 4.04
951 1538 2.975799 GAGCGTTGGTTTCCGGCA 60.976 61.111 0.00 0.00 0.00 5.69
956 1543 1.087501 GGATGGAGAGCGTTGGTTTC 58.912 55.000 0.00 0.00 0.00 2.78
962 1549 4.162690 GCGGGGATGGAGAGCGTT 62.163 66.667 0.00 0.00 0.00 4.84
965 1552 3.036429 AACTGCGGGGATGGAGAGC 62.036 63.158 0.00 0.00 0.00 4.09
1008 1601 3.470567 GTGTCGTTGCTCTCCGCG 61.471 66.667 0.00 0.00 43.27 6.46
1023 1616 2.263741 GGTCTGCAGCTTGGTGGTG 61.264 63.158 9.47 0.00 46.12 4.17
1024 1617 2.113986 GGTCTGCAGCTTGGTGGT 59.886 61.111 9.47 0.00 0.00 4.16
1025 1618 2.674380 GGGTCTGCAGCTTGGTGG 60.674 66.667 9.47 0.00 0.00 4.61
1131 1751 4.458829 ATCCTCCTCGCCCACGGA 62.459 66.667 0.00 0.00 40.63 4.69
1342 1962 3.119065 GGTTAACTGAGAGACCTAGTGGC 60.119 52.174 5.42 0.00 36.63 5.01
1349 1970 1.272769 AGCGTGGTTAACTGAGAGACC 59.727 52.381 5.42 0.00 0.00 3.85
1368 1989 0.804989 GGGGCGATCAACTGTTTGAG 59.195 55.000 0.00 0.00 45.07 3.02
1369 1990 0.400213 AGGGGCGATCAACTGTTTGA 59.600 50.000 0.00 0.00 45.93 2.69
1520 2641 3.646715 TGGCTCCCCGAAACCCAG 61.647 66.667 0.00 0.00 0.00 4.45
1623 2749 0.780002 ATGTAACGCAACGTCGACAC 59.220 50.000 17.16 3.88 39.99 3.67
1628 2754 1.389106 GGACAGATGTAACGCAACGTC 59.611 52.381 0.00 2.51 39.99 4.34
1655 3640 0.781787 CGATTCACACGCGTCAAAGA 59.218 50.000 9.86 1.45 0.00 2.52
1674 3659 3.481388 GCGTACGACTTGCTACAAGTATC 59.519 47.826 21.65 1.65 0.00 2.24
1826 4591 1.342819 TGTGCAAAACCAACATAGGGC 59.657 47.619 0.00 0.00 0.00 5.19
1966 6344 3.310774 GTGTGATGAGGTGACATGTATGC 59.689 47.826 0.00 0.00 0.00 3.14
1967 6345 3.553105 CGTGTGATGAGGTGACATGTATG 59.447 47.826 0.00 0.00 0.00 2.39
1989 6367 6.171213 AGCAGTAAAGTTGATAAGGTGGTAC 58.829 40.000 0.00 0.00 0.00 3.34
1990 6368 6.368779 AGCAGTAAAGTTGATAAGGTGGTA 57.631 37.500 0.00 0.00 0.00 3.25
1991 6369 5.242795 AGCAGTAAAGTTGATAAGGTGGT 57.757 39.130 0.00 0.00 0.00 4.16
1992 6370 6.575162 AAAGCAGTAAAGTTGATAAGGTGG 57.425 37.500 0.00 0.00 0.00 4.61
2041 6430 6.344936 CGTGCATGTTGACACAATTAGTTTTC 60.345 38.462 0.00 0.00 36.16 2.29
2066 6470 5.880054 ATATATTGGGCTTTACGTGATGC 57.120 39.130 9.40 9.40 0.00 3.91
2075 6479 7.233144 TGCATGTTGACATATATATTGGGCTTT 59.767 33.333 0.00 0.00 34.26 3.51
2078 6482 6.513806 TGCATGTTGACATATATATTGGGC 57.486 37.500 0.00 0.00 34.26 5.36
2142 6585 9.166173 TCTCTTGAATTTGAATATGACACGAAT 57.834 29.630 0.00 0.00 0.00 3.34
2145 6588 9.611284 TTTTCTCTTGAATTTGAATATGACACG 57.389 29.630 0.00 0.00 31.56 4.49
2170 6613 3.617669 CAGCGAGAACACGTGAATTTTT 58.382 40.909 25.01 5.11 35.59 1.94
2171 6614 2.602217 GCAGCGAGAACACGTGAATTTT 60.602 45.455 25.01 5.56 35.59 1.82
2172 6615 1.069906 GCAGCGAGAACACGTGAATTT 60.070 47.619 25.01 5.99 35.59 1.82
2173 6616 0.512952 GCAGCGAGAACACGTGAATT 59.487 50.000 25.01 6.87 35.59 2.17
2174 6617 0.599991 TGCAGCGAGAACACGTGAAT 60.600 50.000 25.01 10.71 35.59 2.57
2180 6623 0.588252 ACATGTTGCAGCGAGAACAC 59.412 50.000 0.00 0.00 34.98 3.32
2190 6633 1.304052 GGCTACCCCACATGTTGCA 60.304 57.895 0.00 0.00 36.40 4.08
2237 6701 8.466617 TGATTAGAACTAGTAGAAGGATGTCC 57.533 38.462 3.59 0.00 0.00 4.02
2362 8134 2.749839 GTATGCCTGCCCGCACAA 60.750 61.111 0.00 0.00 42.70 3.33
2391 8163 4.343231 TGTAGATGCCCAACATGTCAAAT 58.657 39.130 0.00 0.00 39.84 2.32
2427 8199 1.078848 GGTCGCCATGAGCAAGACT 60.079 57.895 0.00 0.00 44.60 3.24
2490 8262 1.453197 TGACTCGCCGAGCAGGATA 60.453 57.895 15.20 0.00 45.00 2.59
2622 8394 2.336809 GAGATGTAGGCGCTCGGG 59.663 66.667 7.64 0.00 0.00 5.14
2670 8442 0.178767 TGTAGACGGCGAGGTAGCTA 59.821 55.000 16.62 2.19 37.29 3.32
2724 8496 2.265739 CACCAGCTGGCGCTAAGA 59.734 61.111 33.06 0.00 46.99 2.10
2847 8619 1.002624 GGAGGCAATGGACAACCGA 60.003 57.895 0.00 0.00 39.42 4.69
3203 9000 5.003214 GCGGTTGTATTAGCTCGATATAACG 59.997 44.000 16.41 13.95 34.09 3.18
3241 9038 0.390603 TCACGTTATGTTGAGGCCGG 60.391 55.000 0.00 0.00 0.00 6.13
3257 9054 1.663643 CAAATTGGCTGCATGCATCAC 59.336 47.619 22.97 14.61 45.15 3.06
3384 9181 1.556911 CCTACCACCACTGAGAATGCT 59.443 52.381 0.00 0.00 0.00 3.79
3558 9355 4.188937 ACCTGATAGTACGGGTTGGATA 57.811 45.455 0.00 0.00 46.02 2.59
3638 9757 5.954150 GCCATCCCTAATTATGAACATCCAT 59.046 40.000 0.00 0.00 0.00 3.41
3810 9929 2.304901 TATGCACGCAGGCGGTGTAT 62.305 55.000 18.63 18.00 44.69 2.29
3945 10073 4.552797 CGTACGTACGTACCTCGC 57.447 61.111 38.76 22.63 45.80 5.03
3958 10086 3.848726 TCGAGGTAAATCCCAAACGTAC 58.151 45.455 0.00 0.00 36.75 3.67
3975 10106 7.540400 CCTAGCTAGTGATTCATTACAATCGAG 59.460 40.741 19.31 0.00 35.78 4.04
3997 10128 8.634475 GGTTACGTACCATAACTAAAACCTAG 57.366 38.462 12.19 0.00 46.92 3.02
4088 10219 1.070758 ACTACTGTGTGCCCTGTTGAG 59.929 52.381 0.00 0.00 0.00 3.02
4095 10226 4.575885 TGATCTTTAACTACTGTGTGCCC 58.424 43.478 0.00 0.00 0.00 5.36
4389 10581 9.958234 GCTCTGGAATTCTTATTTAAATCCTTC 57.042 33.333 3.39 2.58 0.00 3.46
4419 10611 5.653255 ACATACCTTCCAATCCTGCTTAT 57.347 39.130 0.00 0.00 0.00 1.73
4439 10631 7.201522 CGTTTCTCGAAATGATCTTGGATTACA 60.202 37.037 5.85 0.00 42.86 2.41
4457 10649 4.706527 ACGAACTACTAAGACGTTTCTCG 58.293 43.478 0.00 0.00 46.00 4.04
4497 10689 0.893727 AAGACCAAACGCCCACCATC 60.894 55.000 0.00 0.00 0.00 3.51
4510 10702 6.601613 ACTCAACACTGAATTAAACAAGACCA 59.398 34.615 0.00 0.00 0.00 4.02
4511 10703 7.027778 ACTCAACACTGAATTAAACAAGACC 57.972 36.000 0.00 0.00 0.00 3.85
4512 10704 8.827677 ACTACTCAACACTGAATTAAACAAGAC 58.172 33.333 0.00 0.00 0.00 3.01
4585 10777 8.512138 CGAGACCAATAAAAACTTATCCACTTT 58.488 33.333 0.00 0.00 0.00 2.66
4590 10782 6.679327 AGCGAGACCAATAAAAACTTATCC 57.321 37.500 0.00 0.00 0.00 2.59
4596 10788 6.143919 CCAAAAGAAGCGAGACCAATAAAAAC 59.856 38.462 0.00 0.00 0.00 2.43
4690 10882 6.669591 TCTCTACTTCTGATTCTTGAATCCCA 59.330 38.462 17.50 4.63 0.00 4.37
4750 10947 9.227777 ACTATACCAAACTCAACCTTCATTAAC 57.772 33.333 0.00 0.00 0.00 2.01
4792 10989 7.067008 CGATATAAGTGGTTTTGACCCAAAGAT 59.933 37.037 0.00 0.00 34.72 2.40
4794 10991 6.404293 CCGATATAAGTGGTTTTGACCCAAAG 60.404 42.308 0.00 0.00 34.72 2.77
4800 10997 8.260270 ACTTAACCGATATAAGTGGTTTTGAC 57.740 34.615 10.71 0.00 43.23 3.18
4834 11032 2.419667 CCTTCCAAAACGTATGTCCGT 58.580 47.619 0.00 0.00 44.23 4.69
4835 11033 1.735571 CCCTTCCAAAACGTATGTCCG 59.264 52.381 0.00 0.00 0.00 4.79
4844 11042 4.040584 ACTCTCAGTAGACCCTTCCAAAAC 59.959 45.833 0.00 0.00 0.00 2.43
4858 11056 5.982356 AGAATGCATGCTTAACTCTCAGTA 58.018 37.500 20.33 0.00 0.00 2.74
4866 11064 7.095102 ACCAAATTGAAAGAATGCATGCTTAAC 60.095 33.333 20.58 16.76 0.00 2.01
4872 11070 7.837202 ACATACCAAATTGAAAGAATGCATG 57.163 32.000 0.00 0.00 0.00 4.06
4885 11083 7.604657 TTCCCTACAACAAACATACCAAATT 57.395 32.000 0.00 0.00 0.00 1.82
4895 11093 7.040409 ACTGATTCTTCATTCCCTACAACAAAC 60.040 37.037 0.00 0.00 0.00 2.93
4905 11103 7.401955 AAAATCTCACTGATTCTTCATTCCC 57.598 36.000 0.00 0.00 43.99 3.97
4919 11117 6.208204 CCATTTGTCCTCTGAAAAATCTCACT 59.792 38.462 0.00 0.00 36.47 3.41
4926 11124 5.011943 CCCAATCCATTTGTCCTCTGAAAAA 59.988 40.000 0.00 0.00 32.32 1.94
4954 11152 0.466124 CCCCTAGCTACAAGGAGCAC 59.534 60.000 7.10 0.00 45.43 4.40
4984 11182 7.173218 AGTGGCATCCTTATAATGAACAATACG 59.827 37.037 0.00 0.00 0.00 3.06
4985 11183 8.292448 CAGTGGCATCCTTATAATGAACAATAC 58.708 37.037 0.00 0.00 0.00 1.89
4986 11184 7.998383 ACAGTGGCATCCTTATAATGAACAATA 59.002 33.333 0.00 0.00 0.00 1.90
4987 11185 6.835488 ACAGTGGCATCCTTATAATGAACAAT 59.165 34.615 0.00 0.00 0.00 2.71
4988 11186 6.186957 ACAGTGGCATCCTTATAATGAACAA 58.813 36.000 0.00 0.00 0.00 2.83
4989 11187 5.754782 ACAGTGGCATCCTTATAATGAACA 58.245 37.500 0.00 0.00 0.00 3.18
5001 11199 4.218417 AGAACAACAATTACAGTGGCATCC 59.782 41.667 0.00 0.00 0.00 3.51
5050 11248 1.995376 AACGGAGAGCCCAACAAAAT 58.005 45.000 0.00 0.00 34.14 1.82
5066 11264 2.095213 TCCGCTAAATGCTGCTAAAACG 59.905 45.455 0.00 0.00 40.11 3.60
5070 11268 2.279741 CACTCCGCTAAATGCTGCTAA 58.720 47.619 0.00 0.00 40.11 3.09
5078 11276 4.389992 CGATATCATTGCACTCCGCTAAAT 59.610 41.667 3.12 0.00 43.06 1.40
5090 11288 2.031682 GCCTTGTGGACGATATCATTGC 60.032 50.000 3.12 0.00 34.57 3.56
5105 11303 1.610522 GTTGCATCTTCACAGCCTTGT 59.389 47.619 0.00 0.00 38.31 3.16
5111 11309 5.409520 TGCTAAGTTAGTTGCATCTTCACAG 59.590 40.000 11.51 0.00 0.00 3.66
5134 11332 4.095483 GTCCCACTTAAATGACTCATGCTG 59.905 45.833 0.00 0.00 0.00 4.41
5167 11365 5.131475 TGGAGTATACAGGAATAACCCCAAC 59.869 44.000 5.50 0.00 40.05 3.77
5176 11374 6.992715 GCAAAGTACATGGAGTATACAGGAAT 59.007 38.462 5.50 0.00 34.67 3.01
5236 11434 8.995027 AGATGTAATTTAAGGCACCATAATCA 57.005 30.769 0.00 0.00 0.00 2.57
5287 11485 5.388408 TGTGTTTCCCGTTTAAACAAGTT 57.612 34.783 18.07 0.00 45.56 2.66
5288 11486 5.388408 TTGTGTTTCCCGTTTAAACAAGT 57.612 34.783 18.07 0.00 45.56 3.16
5301 11499 8.512138 ACATAACATAAGCTACTTTGTGTTTCC 58.488 33.333 12.76 0.00 34.95 3.13


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

AutoCloner maintained by Alex Coulton.