Multiple sequence alignment - TraesCS3D01G023300

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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 TraesCS3D01G023300 chr3D 100.000 4829 0 0 1 4829 7424893 7420065 0.000000e+00 8918.0
1 TraesCS3D01G023300 chr3D 79.899 398 53 14 4193 4567 277218040 277217647 2.870000e-67 267.0
2 TraesCS3D01G023300 chr3D 80.503 159 27 4 4416 4571 361254886 361255043 8.490000e-23 119.0
3 TraesCS3D01G023300 chr3B 94.072 4622 202 26 1 4566 9421650 9417045 0.000000e+00 6951.0
4 TraesCS3D01G023300 chr3B 83.396 265 20 4 4567 4829 9415614 9415372 1.750000e-54 224.0
5 TraesCS3D01G023300 chr3B 90.476 42 1 3 4680 4718 190483687 190483728 9.000000e-03 52.8
6 TraesCS3D01G023300 chr5B 75.183 2595 551 72 1277 3820 707191200 707193752 0.000000e+00 1138.0
7 TraesCS3D01G023300 chr5B 72.763 2034 473 48 1101 3086 707408045 707410045 3.190000e-171 612.0
8 TraesCS3D01G023300 chr5B 77.399 646 134 12 3181 3820 707430575 707431214 1.640000e-99 374.0
9 TraesCS3D01G023300 chr5B 73.091 799 178 25 1382 2163 707414682 707415460 2.890000e-62 250.0
10 TraesCS3D01G023300 chr6D 73.564 2769 619 84 1113 3809 24225993 24228720 0.000000e+00 953.0
11 TraesCS3D01G023300 chr6D 74.715 2021 457 43 1822 3812 24364496 24362500 0.000000e+00 852.0
12 TraesCS3D01G023300 chr6D 74.667 2029 458 49 1812 3809 24403017 24405020 0.000000e+00 848.0
13 TraesCS3D01G023300 chr6D 74.070 1774 404 43 2099 3837 24353242 24351490 0.000000e+00 676.0
14 TraesCS3D01G023300 chr6D 72.864 398 93 8 1099 1484 24357977 24357583 6.560000e-24 122.0
15 TraesCS3D01G023300 chr6D 80.503 159 27 4 4416 4571 242703327 242703484 8.490000e-23 119.0
16 TraesCS3D01G023300 chr6B 73.546 2786 620 86 1099 3809 39193335 39196078 0.000000e+00 953.0
17 TraesCS3D01G023300 chr6B 86.232 138 18 1 4195 4332 36144917 36144781 1.080000e-31 148.0
18 TraesCS3D01G023300 chr6A 73.424 2807 605 100 1099 3809 22691022 22693783 0.000000e+00 920.0
19 TraesCS3D01G023300 chr6A 73.342 2337 559 50 1496 3797 22816598 22818905 0.000000e+00 806.0
20 TraesCS3D01G023300 chr6A 76.454 1410 277 41 2480 3857 22975546 22976932 0.000000e+00 713.0
21 TraesCS3D01G023300 chr5D 74.596 2102 482 39 1740 3815 565719865 565717790 0.000000e+00 876.0
22 TraesCS3D01G023300 chr5D 73.984 2091 487 43 1763 3820 565729348 565727282 0.000000e+00 795.0
23 TraesCS3D01G023300 chr5D 76.334 1031 206 25 2807 3820 565824709 565823700 7.160000e-143 518.0
24 TraesCS3D01G023300 chr5D 80.952 84 12 4 4143 4225 447976224 447976144 4.030000e-06 63.9
25 TraesCS3D01G023300 chrUn 73.707 2358 546 60 1498 3809 278292886 278295215 0.000000e+00 852.0
26 TraesCS3D01G023300 chrUn 79.109 651 117 12 3167 3809 18015865 18016504 9.600000e-117 431.0
27 TraesCS3D01G023300 chrUn 76.190 210 48 2 1277 1485 18013922 18014130 5.110000e-20 110.0
28 TraesCS3D01G023300 chr7D 79.265 381 72 7 4197 4571 423582885 423582506 4.790000e-65 259.0
29 TraesCS3D01G023300 chr7D 79.452 365 65 9 4206 4564 406911650 406912010 2.890000e-62 250.0
30 TraesCS3D01G023300 chr7D 81.132 159 26 4 4416 4571 487073782 487073625 1.820000e-24 124.0
31 TraesCS3D01G023300 chr7A 82.171 258 37 8 4312 4566 517888673 517888924 3.790000e-51 213.0
32 TraesCS3D01G023300 chr4D 82.632 190 28 4 4144 4332 8666298 8666113 3.870000e-36 163.0
33 TraesCS3D01G023300 chr5A 81.771 192 31 4 4142 4332 558340298 558340486 1.800000e-34 158.0
34 TraesCS3D01G023300 chr4A 81.579 190 26 3 4143 4332 688485272 688485452 1.080000e-31 148.0
35 TraesCS3D01G023300 chr2D 77.011 261 51 9 4195 4449 463090129 463090386 1.810000e-29 141.0
36 TraesCS3D01G023300 chr2B 81.761 159 25 4 4416 4571 251253158 251253001 3.920000e-26 130.0
37 TraesCS3D01G023300 chr1D 81.457 151 24 4 4424 4571 419857953 419857804 2.360000e-23 121.0
38 TraesCS3D01G023300 chr1D 76.250 160 26 8 4143 4292 363860943 363860786 1.860000e-09 75.0
39 TraesCS3D01G023300 chr7B 80.503 159 27 4 4416 4571 485276170 485276327 8.490000e-23 119.0


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 TraesCS3D01G023300 chr3D 7420065 7424893 4828 True 8918.0 8918 100.0000 1 4829 1 chr3D.!!$R1 4828
1 TraesCS3D01G023300 chr3B 9415372 9421650 6278 True 3587.5 6951 88.7340 1 4829 2 chr3B.!!$R1 4828
2 TraesCS3D01G023300 chr5B 707191200 707193752 2552 False 1138.0 1138 75.1830 1277 3820 1 chr5B.!!$F1 2543
3 TraesCS3D01G023300 chr5B 707408045 707410045 2000 False 612.0 612 72.7630 1101 3086 1 chr5B.!!$F2 1985
4 TraesCS3D01G023300 chr5B 707430575 707431214 639 False 374.0 374 77.3990 3181 3820 1 chr5B.!!$F4 639
5 TraesCS3D01G023300 chr5B 707414682 707415460 778 False 250.0 250 73.0910 1382 2163 1 chr5B.!!$F3 781
6 TraesCS3D01G023300 chr6D 24225993 24228720 2727 False 953.0 953 73.5640 1113 3809 1 chr6D.!!$F1 2696
7 TraesCS3D01G023300 chr6D 24362500 24364496 1996 True 852.0 852 74.7150 1822 3812 1 chr6D.!!$R3 1990
8 TraesCS3D01G023300 chr6D 24403017 24405020 2003 False 848.0 848 74.6670 1812 3809 1 chr6D.!!$F2 1997
9 TraesCS3D01G023300 chr6D 24351490 24353242 1752 True 676.0 676 74.0700 2099 3837 1 chr6D.!!$R1 1738
10 TraesCS3D01G023300 chr6B 39193335 39196078 2743 False 953.0 953 73.5460 1099 3809 1 chr6B.!!$F1 2710
11 TraesCS3D01G023300 chr6A 22691022 22693783 2761 False 920.0 920 73.4240 1099 3809 1 chr6A.!!$F1 2710
12 TraesCS3D01G023300 chr6A 22816598 22818905 2307 False 806.0 806 73.3420 1496 3797 1 chr6A.!!$F2 2301
13 TraesCS3D01G023300 chr6A 22975546 22976932 1386 False 713.0 713 76.4540 2480 3857 1 chr6A.!!$F3 1377
14 TraesCS3D01G023300 chr5D 565717790 565719865 2075 True 876.0 876 74.5960 1740 3815 1 chr5D.!!$R2 2075
15 TraesCS3D01G023300 chr5D 565727282 565729348 2066 True 795.0 795 73.9840 1763 3820 1 chr5D.!!$R3 2057
16 TraesCS3D01G023300 chr5D 565823700 565824709 1009 True 518.0 518 76.3340 2807 3820 1 chr5D.!!$R4 1013
17 TraesCS3D01G023300 chrUn 278292886 278295215 2329 False 852.0 852 73.7070 1498 3809 1 chrUn.!!$F1 2311
18 TraesCS3D01G023300 chrUn 18013922 18016504 2582 False 270.5 431 77.6495 1277 3809 2 chrUn.!!$F2 2532

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
443 484 0.109597 CCAACTGAATTCTGCACCGC 60.110 55.000 11.86 0.0 0.00 5.68 F
2068 2175 0.172803 CAAGCTGCAAGAATCCTGGC 59.827 55.000 1.02 0.0 39.85 4.85 F
2761 2874 1.300963 GGGTCAGCTCCTGATTGCA 59.699 57.895 0.00 0.0 42.73 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2341 2448 1.599518 TTTGCCACCGTAGCCACAG 60.600 57.895 0.00 0.00 0.00 3.66 R
2904 3017 2.354003 CCATGATGGCAAAGTCCCAAAC 60.354 50.000 0.00 0.00 35.67 2.93 R
4450 4622 0.032813 CCACCTCATGGGCCTTGAAT 60.033 55.000 21.08 10.95 45.95 2.57 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
120 121 6.679327 TTCGAAGAATCTCTATCGAAGTCA 57.321 37.500 12.54 0.00 45.94 3.41
166 167 4.766373 TGATGTTGATGTTTGGTACTGCAT 59.234 37.500 0.00 0.00 0.00 3.96
188 189 1.502990 CGTCGGTTGTTGCACCATGA 61.503 55.000 0.00 0.00 36.49 3.07
228 247 6.595772 TTTTTGTTATTGTTGTGTGCATCC 57.404 33.333 0.00 0.00 0.00 3.51
234 253 6.432472 TGTTATTGTTGTGTGCATCCTTGATA 59.568 34.615 0.00 0.00 0.00 2.15
241 260 5.499313 TGTGTGCATCCTTGATATCTTGAA 58.501 37.500 3.98 0.00 0.00 2.69
270 289 4.305769 TGACATTGTATTGTTGCAAAGGC 58.694 39.130 0.00 0.00 41.68 4.35
271 290 3.663025 ACATTGTATTGTTGCAAAGGCC 58.337 40.909 0.00 0.00 40.13 5.19
272 291 2.430546 TTGTATTGTTGCAAAGGCCG 57.569 45.000 0.00 0.00 40.13 6.13
273 292 0.600557 TGTATTGTTGCAAAGGCCGG 59.399 50.000 0.00 0.00 40.13 6.13
274 293 0.885196 GTATTGTTGCAAAGGCCGGA 59.115 50.000 5.05 0.00 40.13 5.14
275 294 1.476488 GTATTGTTGCAAAGGCCGGAT 59.524 47.619 5.05 0.00 40.13 4.18
280 317 0.250945 TTGCAAAGGCCGGATGTACA 60.251 50.000 5.05 0.00 40.13 2.90
291 328 3.368843 GCCGGATGTACATGATATCAGCT 60.369 47.826 14.43 1.04 0.00 4.24
295 332 6.104665 CGGATGTACATGATATCAGCTTGAT 58.895 40.000 14.43 0.72 40.72 2.57
370 411 3.813166 ACCGTGTTGTCAAGAAATACCAG 59.187 43.478 0.00 0.00 0.00 4.00
390 431 6.831976 ACCAGAGCGAATCTAGGAATAAAAT 58.168 36.000 11.01 0.00 36.10 1.82
392 433 6.348050 CCAGAGCGAATCTAGGAATAAAATGC 60.348 42.308 0.00 0.00 36.10 3.56
409 450 2.671130 TGCAGTGCATACGAAGATGA 57.329 45.000 15.37 0.00 31.71 2.92
424 465 5.409826 ACGAAGATGAAAAGAATGTCTGGTC 59.590 40.000 0.00 0.00 0.00 4.02
428 469 5.474876 AGATGAAAAGAATGTCTGGTCCAAC 59.525 40.000 0.00 0.00 0.00 3.77
430 471 4.580167 TGAAAAGAATGTCTGGTCCAACTG 59.420 41.667 0.00 0.00 0.00 3.16
443 484 0.109597 CCAACTGAATTCTGCACCGC 60.110 55.000 11.86 0.00 0.00 5.68
450 491 0.383949 AATTCTGCACCGCACGTTTT 59.616 45.000 0.00 0.00 33.79 2.43
452 493 0.584396 TTCTGCACCGCACGTTTTAG 59.416 50.000 0.00 0.00 33.79 1.85
458 501 0.179051 ACCGCACGTTTTAGGAACCA 60.179 50.000 0.00 0.00 0.00 3.67
567 610 3.060473 GCGTGTTGTACAGTTGAACTCTC 60.060 47.826 0.00 0.00 0.00 3.20
568 611 4.360563 CGTGTTGTACAGTTGAACTCTCT 58.639 43.478 0.00 0.00 0.00 3.10
579 622 4.646945 AGTTGAACTCTCTGACTCACTTGA 59.353 41.667 0.00 0.00 0.00 3.02
596 639 6.734137 TCACTTGAAATTTCACGCACTTTAT 58.266 32.000 20.35 0.00 36.83 1.40
602 645 9.469807 TTGAAATTTCACGCACTTTATGTATTT 57.530 25.926 20.35 0.00 36.83 1.40
628 671 4.348656 GTGGAAGAAACAAAGAAACGGAC 58.651 43.478 0.00 0.00 0.00 4.79
644 687 2.190161 CGGACGAACGCATCTATTCAA 58.810 47.619 0.00 0.00 0.00 2.69
645 688 2.216488 CGGACGAACGCATCTATTCAAG 59.784 50.000 0.00 0.00 0.00 3.02
646 689 2.033662 GGACGAACGCATCTATTCAAGC 60.034 50.000 0.00 0.00 0.00 4.01
647 690 2.860735 GACGAACGCATCTATTCAAGCT 59.139 45.455 0.00 0.00 0.00 3.74
713 756 5.980698 TGCAATTTGTTTGTGGTGTATTG 57.019 34.783 0.00 0.00 37.65 1.90
754 797 4.504858 GTGACGAACACTTGGGATAATCT 58.495 43.478 9.42 0.00 45.13 2.40
779 822 0.523966 CGTCTCACTCACCCAGACTC 59.476 60.000 0.00 0.00 35.37 3.36
800 843 3.552699 TCGTCGAACGTTGAAACAAAGAT 59.447 39.130 5.00 0.00 43.14 2.40
829 873 9.579932 ATTCATTAGGAAAAACTCAAGAGTTCT 57.420 29.630 15.18 10.54 42.38 3.01
863 907 0.459237 GAGTCCTGCATGACGTGAGG 60.459 60.000 15.27 3.14 40.26 3.86
903 951 3.493129 TGCTAGTACTTCAACAGCAAACG 59.507 43.478 13.60 0.00 39.18 3.60
984 1032 7.275560 GCAAAGACATACAAAGTTGTTTCTGTT 59.724 33.333 1.35 0.00 42.35 3.16
1032 1082 1.197492 CTTAGATGCTTGTGCGTGCAA 59.803 47.619 0.00 0.00 42.74 4.08
1046 1096 1.743772 CGTGCAACTAGCCATAGCCTT 60.744 52.381 0.00 0.00 44.83 4.35
1051 1101 2.945668 CAACTAGCCATAGCCTTGTTCC 59.054 50.000 0.00 0.00 41.25 3.62
1074 1124 0.465460 TCACACAAACCAGCTCCACC 60.465 55.000 0.00 0.00 0.00 4.61
1165 1215 0.535102 CTTGTCGGACCCTGCAAACT 60.535 55.000 5.55 0.00 0.00 2.66
1332 1406 3.883669 AGAACGTCTAAGGTACCTCGAT 58.116 45.455 23.22 14.01 0.00 3.59
1835 1939 5.933617 TCCTGACAAGATTGGGAATATGAG 58.066 41.667 0.00 0.00 0.00 2.90
1991 2095 1.880027 ACGGTTGCCTTCTTGTTCATC 59.120 47.619 0.00 0.00 0.00 2.92
1998 2102 6.404734 GGTTGCCTTCTTGTTCATCGAATAAT 60.405 38.462 0.00 0.00 0.00 1.28
2055 2159 1.168714 GAAGCCTACCAACCAAGCTG 58.831 55.000 0.00 0.00 33.18 4.24
2068 2175 0.172803 CAAGCTGCAAGAATCCTGGC 59.827 55.000 1.02 0.00 39.85 4.85
2560 2670 4.082125 CAGTGGTCCAATTCCTAAGCTTT 58.918 43.478 3.20 0.00 0.00 3.51
2568 2678 8.622157 GGTCCAATTCCTAAGCTTTCTATTAAC 58.378 37.037 3.20 2.81 0.00 2.01
2628 2741 5.044105 AGGGCTACCATTAGAATTTGGAACT 60.044 40.000 0.82 0.00 40.13 3.01
2664 2777 8.635765 AAGTACTTCTTCTATTTGGCAATTCA 57.364 30.769 1.12 0.00 0.00 2.57
2689 2802 2.158711 TCTGGCACCATTCCATCATCTC 60.159 50.000 0.00 0.00 32.37 2.75
2761 2874 1.300963 GGGTCAGCTCCTGATTGCA 59.699 57.895 0.00 0.00 42.73 4.08
2871 2984 4.783764 ATTCCTCAAAAATTGTCCCGAC 57.216 40.909 0.00 0.00 0.00 4.79
2904 3017 6.545508 TCTTGATCTCGCACACAATAAATTG 58.454 36.000 1.13 1.13 43.26 2.32
3077 3190 6.039717 TCAGGAAGCATACCAAAATCTATTGC 59.960 38.462 0.00 0.00 0.00 3.56
3089 3202 6.314018 CAAAATCTATTGCTAACTTCACGCA 58.686 36.000 0.00 0.00 0.00 5.24
3126 3251 9.798994 AGCAAAGATAAATCTGATGAATTCAAC 57.201 29.630 13.09 10.68 37.19 3.18
3162 3290 5.545658 TTGAAGATGTTGTTTATCGCTCC 57.454 39.130 0.00 0.00 0.00 4.70
3178 3316 1.402456 GCTCCGACGTTGACTACACAT 60.402 52.381 3.74 0.00 0.00 3.21
3450 3588 4.760757 GGCTTATCGGCTCTCACC 57.239 61.111 0.00 0.00 34.85 4.02
3748 3909 5.183904 AGGAAATGGAGAATTTTCTGGTTCG 59.816 40.000 0.00 0.00 41.77 3.95
3896 4061 7.068103 GTCATGTGTGGGGATTTTATGATGTAA 59.932 37.037 0.00 0.00 0.00 2.41
3986 4151 0.028505 CGTATGTACCCAGTCGACCG 59.971 60.000 13.01 0.70 0.00 4.79
3988 4153 1.332997 GTATGTACCCAGTCGACCGAG 59.667 57.143 13.01 3.16 0.00 4.63
3993 4158 1.374252 CCCAGTCGACCGAGTTTGG 60.374 63.158 13.01 12.01 0.00 3.28
4137 4302 1.923204 CGAGCAGTTGTAGCTAGCTTG 59.077 52.381 24.88 15.69 43.58 4.01
4166 4331 0.036732 GCATCTCCAACACTCACCCA 59.963 55.000 0.00 0.00 0.00 4.51
4168 4333 0.693049 ATCTCCAACACTCACCCACC 59.307 55.000 0.00 0.00 0.00 4.61
4225 4396 4.467084 GAGCCGGCCATCCAACGA 62.467 66.667 26.15 0.00 0.00 3.85
4228 4399 3.585990 CCGGCCATCCAACGATGC 61.586 66.667 2.24 0.00 44.00 3.91
4234 4405 1.105167 CCATCCAACGATGCCTGCAT 61.105 55.000 3.90 3.90 44.00 3.96
4244 4415 6.384224 CAACGATGCCTGCATATATTTCAAT 58.616 36.000 4.30 0.00 36.70 2.57
4265 4436 9.834628 TTCAATCATTATTTGAACTAAACGGAC 57.165 29.630 0.00 0.00 37.97 4.79
4273 4444 5.987777 TTGAACTAAACGGACGAAATTCA 57.012 34.783 0.00 0.00 0.00 2.57
4285 4456 1.386412 CGAAATTCATGCAAACACGGC 59.614 47.619 0.00 0.00 0.00 5.68
4287 4458 0.595588 AATTCATGCAAACACGGCGA 59.404 45.000 16.62 0.00 0.00 5.54
4324 4495 8.519492 AACAGGACAAAATTCATTACATTTCG 57.481 30.769 0.00 0.00 0.00 3.46
4362 4533 3.396570 CGGCCCGGTCCTAAACCT 61.397 66.667 0.00 0.00 46.87 3.50
4371 4542 3.480470 CGGTCCTAAACCTATCCTACGA 58.520 50.000 0.00 0.00 46.87 3.43
4375 4546 2.030451 CCTAAACCTATCCTACGACGGC 60.030 54.545 0.00 0.00 0.00 5.68
4376 4547 1.477553 AAACCTATCCTACGACGGCA 58.522 50.000 0.00 0.00 0.00 5.69
4391 4562 2.617274 GGCAGCCGTTGTCCACTTC 61.617 63.158 0.00 0.00 0.00 3.01
4414 4585 2.665649 TGTATTCCGCATCAACGACT 57.334 45.000 0.00 0.00 34.06 4.18
4430 4601 2.186076 CGACTACGTTCTTCATCTGCC 58.814 52.381 0.00 0.00 34.56 4.85
4446 4618 3.107447 CCGTTCCATAAAGGCGGC 58.893 61.111 0.00 0.00 36.45 6.53
4447 4619 2.707039 CGTTCCATAAAGGCGGCG 59.293 61.111 0.51 0.51 37.29 6.46
4448 4620 2.819552 CGTTCCATAAAGGCGGCGG 61.820 63.158 9.78 0.00 37.29 6.13
4449 4621 2.124487 TTCCATAAAGGCGGCGGG 60.124 61.111 9.78 0.00 37.29 6.13
4450 4622 2.671164 TTCCATAAAGGCGGCGGGA 61.671 57.895 9.78 1.12 37.29 5.14
4457 4629 3.995506 AAGGCGGCGGGATTCAAGG 62.996 63.158 9.78 0.00 0.00 3.61
4462 4634 2.123726 GCGGGATTCAAGGCCCAT 60.124 61.111 0.00 0.00 44.94 4.00
4508 4680 4.447138 ACGAGAGTAGAAGATGGGAGAT 57.553 45.455 0.00 0.00 46.88 2.75
4510 4682 4.141367 ACGAGAGTAGAAGATGGGAGATGA 60.141 45.833 0.00 0.00 46.88 2.92
4512 4684 5.278266 CGAGAGTAGAAGATGGGAGATGAAC 60.278 48.000 0.00 0.00 0.00 3.18
4513 4685 5.776358 AGAGTAGAAGATGGGAGATGAACT 58.224 41.667 0.00 0.00 0.00 3.01
4538 4710 1.072266 ACTTGGGACACAATGCCCTA 58.928 50.000 0.00 0.00 44.96 3.53
4566 4738 0.319728 CATGCCCTACTCATCCTCGG 59.680 60.000 0.00 0.00 0.00 4.63
4567 4739 0.105453 ATGCCCTACTCATCCTCGGT 60.105 55.000 0.00 0.00 0.00 4.69
4627 6230 6.791303 ACACGTGTTCAACATTGTTTTCTAT 58.209 32.000 17.22 0.00 0.00 1.98
4629 6232 7.853929 ACACGTGTTCAACATTGTTTTCTATAC 59.146 33.333 17.22 0.00 0.00 1.47
4796 6400 9.621629 AAACACATAATATAAAGAATCACCCGA 57.378 29.630 0.00 0.00 0.00 5.14
4816 6420 4.851558 CCGACGATCCTTTTTCAAACATTC 59.148 41.667 0.00 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 2.670229 GCTCCGTTGTCGTCTGATACAA 60.670 50.000 4.91 4.91 33.35 2.41
40 41 1.460504 AGCTCCGTTGTCGTCTGATA 58.539 50.000 0.00 0.00 35.01 2.15
53 54 2.967076 ACACACGCACAAGCTCCG 60.967 61.111 0.00 0.00 39.10 4.63
120 121 6.209192 TCAACTGCCATCTTTGACAACATATT 59.791 34.615 0.00 0.00 0.00 1.28
166 167 2.174969 GGTGCAACAACCGACGACA 61.175 57.895 0.00 0.00 39.98 4.35
210 211 5.119931 TCAAGGATGCACACAACAATAAC 57.880 39.130 0.00 0.00 0.00 1.89
213 214 5.889853 AGATATCAAGGATGCACACAACAAT 59.110 36.000 5.32 0.00 0.00 2.71
258 277 1.112315 ACATCCGGCCTTTGCAACAA 61.112 50.000 0.00 0.00 40.13 2.83
259 278 0.250945 TACATCCGGCCTTTGCAACA 60.251 50.000 0.00 0.00 40.13 3.33
260 279 0.170339 GTACATCCGGCCTTTGCAAC 59.830 55.000 0.00 0.00 40.13 4.17
262 281 0.034574 ATGTACATCCGGCCTTTGCA 60.035 50.000 1.41 0.00 40.13 4.08
263 282 0.381801 CATGTACATCCGGCCTTTGC 59.618 55.000 5.07 0.00 0.00 3.68
264 283 2.036958 TCATGTACATCCGGCCTTTG 57.963 50.000 5.07 0.00 0.00 2.77
268 287 3.525537 CTGATATCATGTACATCCGGCC 58.474 50.000 5.07 0.00 0.00 6.13
270 289 4.462508 AGCTGATATCATGTACATCCGG 57.537 45.455 5.07 0.00 0.00 5.14
271 290 5.473039 TCAAGCTGATATCATGTACATCCG 58.527 41.667 5.07 0.00 0.00 4.18
272 291 9.610705 AATATCAAGCTGATATCATGTACATCC 57.389 33.333 5.07 0.00 46.26 3.51
322 363 1.275010 TGGCGCTTCTGTGTATCAAGA 59.725 47.619 7.64 0.00 0.00 3.02
327 368 0.108138 GAGGTGGCGCTTCTGTGTAT 60.108 55.000 7.64 0.00 0.00 2.29
370 411 6.203723 ACTGCATTTTATTCCTAGATTCGCTC 59.796 38.462 0.00 0.00 0.00 5.03
390 431 2.671130 TCATCTTCGTATGCACTGCA 57.329 45.000 6.09 6.09 44.86 4.41
392 433 5.784750 TCTTTTCATCTTCGTATGCACTG 57.215 39.130 0.00 0.00 0.00 3.66
409 450 4.792068 TCAGTTGGACCAGACATTCTTTT 58.208 39.130 0.00 0.00 0.00 2.27
424 465 0.109597 GCGGTGCAGAATTCAGTTGG 60.110 55.000 8.44 0.00 0.00 3.77
428 469 1.133253 CGTGCGGTGCAGAATTCAG 59.867 57.895 8.44 0.00 40.08 3.02
430 471 0.040425 AAACGTGCGGTGCAGAATTC 60.040 50.000 0.00 0.00 40.08 2.17
482 525 2.344950 CAAGTGCTCTAGAACTGCCAG 58.655 52.381 0.00 0.00 33.24 4.85
543 586 2.350498 AGTTCAACTGTACAACACGCAC 59.650 45.455 0.00 0.00 0.00 5.34
567 610 4.214437 GCGTGAAATTTCAAGTGAGTCAG 58.786 43.478 27.40 11.45 39.21 3.51
568 611 3.625313 TGCGTGAAATTTCAAGTGAGTCA 59.375 39.130 27.40 17.22 39.21 3.41
596 639 8.610248 TCTTTGTTTCTTCCACGATAAATACA 57.390 30.769 0.00 0.00 0.00 2.29
602 645 5.049954 CCGTTTCTTTGTTTCTTCCACGATA 60.050 40.000 0.00 0.00 0.00 2.92
628 671 3.426859 CCTAGCTTGAATAGATGCGTTCG 59.573 47.826 0.00 0.00 0.00 3.95
644 687 0.621571 TCATCTTGGGTGGCCTAGCT 60.622 55.000 3.32 0.00 0.00 3.32
645 688 0.464554 GTCATCTTGGGTGGCCTAGC 60.465 60.000 3.32 0.00 0.00 3.42
646 689 1.207791 AGTCATCTTGGGTGGCCTAG 58.792 55.000 3.32 0.00 0.00 3.02
647 690 1.281867 CAAGTCATCTTGGGTGGCCTA 59.718 52.381 3.32 0.00 45.02 3.93
672 715 2.417924 GCATGGTCAGACCTGTAGACTG 60.418 54.545 20.82 7.65 39.58 3.51
713 756 2.614057 CACCTTTGACAACTGACCTGAC 59.386 50.000 0.00 0.00 0.00 3.51
754 797 2.734591 GTGAGTGAGACGTGGGCA 59.265 61.111 0.00 0.00 0.00 5.36
760 803 0.523966 GAGTCTGGGTGAGTGAGACG 59.476 60.000 0.00 0.00 40.92 4.18
779 822 4.780946 ACATCTTTGTTTCAACGTTCGACG 60.781 41.667 0.00 5.97 39.45 5.12
800 843 9.793259 ACTCTTGAGTTTTTCCTAATGAATACA 57.207 29.630 0.00 0.00 31.67 2.29
824 868 3.554934 TCATGCTTGTGTGGAAAGAACT 58.445 40.909 0.00 0.00 0.00 3.01
825 869 3.316308 ACTCATGCTTGTGTGGAAAGAAC 59.684 43.478 6.51 0.00 0.00 3.01
827 871 3.141398 GACTCATGCTTGTGTGGAAAGA 58.859 45.455 11.52 0.00 30.04 2.52
828 872 2.227388 GGACTCATGCTTGTGTGGAAAG 59.773 50.000 11.52 0.00 30.04 2.62
829 873 2.158623 AGGACTCATGCTTGTGTGGAAA 60.159 45.455 11.52 0.00 30.04 3.13
830 874 1.421268 AGGACTCATGCTTGTGTGGAA 59.579 47.619 11.52 0.00 30.04 3.53
831 875 1.059098 AGGACTCATGCTTGTGTGGA 58.941 50.000 11.52 0.00 30.04 4.02
883 931 6.807230 AGTATCGTTTGCTGTTGAAGTACTAG 59.193 38.462 0.00 0.00 0.00 2.57
886 934 5.389516 CCAGTATCGTTTGCTGTTGAAGTAC 60.390 44.000 5.77 0.00 36.41 2.73
888 936 3.498397 CCAGTATCGTTTGCTGTTGAAGT 59.502 43.478 5.77 0.00 36.41 3.01
890 938 2.225491 GCCAGTATCGTTTGCTGTTGAA 59.775 45.455 5.77 0.00 36.41 2.69
903 951 1.821332 GCACAGCCCAGCCAGTATC 60.821 63.158 0.00 0.00 0.00 2.24
933 981 2.477375 TGGCGACTTTGTTGTTCGATAC 59.523 45.455 0.00 0.00 0.00 2.24
965 1013 9.567848 ACTTTGTAACAGAAACAACTTTGTATG 57.432 29.630 0.00 0.00 41.31 2.39
984 1032 7.075121 CGATGCTCATTGTGTTTAACTTTGTA 58.925 34.615 0.00 0.00 0.00 2.41
1032 1082 2.171448 CAGGAACAAGGCTATGGCTAGT 59.829 50.000 0.00 0.00 37.50 2.57
1046 1096 1.340502 TGGTTTGTGTGAGCAGGAACA 60.341 47.619 0.00 0.00 0.00 3.18
1051 1101 0.590195 GAGCTGGTTTGTGTGAGCAG 59.410 55.000 0.00 0.00 43.55 4.24
1074 1124 0.387202 TGTTGTTGGCATGGGTTTCG 59.613 50.000 0.00 0.00 0.00 3.46
1165 1215 2.356553 CCGCCACGTCGAAAGGAA 60.357 61.111 0.00 0.00 0.00 3.36
1991 2095 6.799512 AGATCCAAGGCTGAAAAATTATTCG 58.200 36.000 0.00 0.00 31.80 3.34
1998 2102 7.402054 TGTTAGATAGATCCAAGGCTGAAAAA 58.598 34.615 0.00 0.00 0.00 1.94
2055 2159 2.358267 CAGATTGAGCCAGGATTCTTGC 59.642 50.000 0.00 0.00 32.40 4.01
2068 2175 6.985645 CCAAGATAGAGAAAGGTCAGATTGAG 59.014 42.308 0.00 0.00 0.00 3.02
2341 2448 1.599518 TTTGCCACCGTAGCCACAG 60.600 57.895 0.00 0.00 0.00 3.66
2352 2459 4.056050 CGAGGTATATAGGTGTTTGCCAC 58.944 47.826 0.00 0.00 43.74 5.01
2560 2670 9.725206 AAGATCCAAGTAGGTTAGGTTAATAGA 57.275 33.333 0.00 0.00 39.02 1.98
2568 2678 7.893124 TGTACTAAGATCCAAGTAGGTTAGG 57.107 40.000 5.27 0.00 39.02 2.69
2664 2777 2.242965 TGATGGAATGGTGCCAGAGATT 59.757 45.455 0.00 0.00 39.11 2.40
2689 2802 2.874086 TCAGTGATGTCAACTTGCACAG 59.126 45.455 0.00 0.00 32.16 3.66
2761 2874 7.882791 TGTGTTTGTAGTGGATTGATTGACTAT 59.117 33.333 0.00 0.00 0.00 2.12
2770 2883 6.377327 ACTTTCTGTGTTTGTAGTGGATTG 57.623 37.500 0.00 0.00 0.00 2.67
2871 2984 5.050499 GTGTGCGAGATCAAGAAATATGAGG 60.050 44.000 0.00 0.00 0.00 3.86
2904 3017 2.354003 CCATGATGGCAAAGTCCCAAAC 60.354 50.000 0.00 0.00 35.67 2.93
3077 3190 6.292061 GCTTAGAATCATCTGCGTGAAGTTAG 60.292 42.308 0.00 0.00 37.10 2.34
3123 3248 6.539649 TCTTCAAAATTGAGTACTCCGTTG 57.460 37.500 20.11 16.54 38.61 4.10
3126 3251 6.727824 ACATCTTCAAAATTGAGTACTCCG 57.272 37.500 20.11 2.33 38.61 4.63
3162 3290 4.903638 ATTCAATGTGTAGTCAACGTCG 57.096 40.909 0.00 0.00 0.00 5.12
3178 3316 7.437862 GCCTTTTGTGACTATTGTGAAATTCAA 59.562 33.333 0.00 0.00 0.00 2.69
3450 3588 3.181471 ACAGGTTCAAGTGACTCAGTGAG 60.181 47.826 18.83 18.83 35.52 3.51
3502 3640 5.520376 AGTGTTTGAAGTTGATTTCCAGG 57.480 39.130 0.00 0.00 0.00 4.45
3748 3909 2.807967 TGTACAAGCTGTCACAGAATGC 59.192 45.455 9.70 0.00 42.53 3.56
3858 4023 3.811497 CCACACATGACAGCATATACCAG 59.189 47.826 0.00 0.00 32.27 4.00
3986 4151 6.047231 ACATAGCGAAGGTAATACCAAACTC 58.953 40.000 12.54 2.02 46.26 3.01
3988 4153 6.757947 TGTACATAGCGAAGGTAATACCAAAC 59.242 38.462 12.54 1.76 46.26 2.93
3993 4158 7.998753 AACTTGTACATAGCGAAGGTAATAC 57.001 36.000 0.00 0.00 46.26 1.89
4066 4231 4.778143 AGGCCCGGACGACATTGC 62.778 66.667 0.73 0.00 0.00 3.56
4093 4258 2.078849 TGTATTGAGACAGCGGTGTG 57.921 50.000 27.15 0.00 36.88 3.82
4094 4259 2.037251 ACTTGTATTGAGACAGCGGTGT 59.963 45.455 22.06 22.06 40.71 4.16
4101 4266 4.217767 ACTGCTCGTACTTGTATTGAGACA 59.782 41.667 13.48 10.59 0.00 3.41
4137 4302 2.027192 TGTTGGAGATGCCCTTAGTCAC 60.027 50.000 0.00 0.00 34.97 3.67
4166 4331 0.179018 GGATGCCGGAGCTAATTGGT 60.179 55.000 5.05 0.00 40.80 3.67
4168 4333 2.238353 CGGATGCCGGAGCTAATTG 58.762 57.895 5.05 0.00 44.15 2.32
4217 4388 2.574006 ATATGCAGGCATCGTTGGAT 57.426 45.000 10.48 0.00 37.82 3.41
4244 4415 7.655236 TTCGTCCGTTTAGTTCAAATAATGA 57.345 32.000 0.00 0.00 35.85 2.57
4253 4424 4.786575 GCATGAATTTCGTCCGTTTAGTTC 59.213 41.667 0.00 0.00 0.00 3.01
4260 4431 2.292016 TGTTTGCATGAATTTCGTCCGT 59.708 40.909 0.00 0.00 0.00 4.69
4261 4432 2.656422 GTGTTTGCATGAATTTCGTCCG 59.344 45.455 0.00 0.00 0.00 4.79
4262 4433 2.656422 CGTGTTTGCATGAATTTCGTCC 59.344 45.455 0.00 0.00 33.58 4.79
4265 4436 1.386412 GCCGTGTTTGCATGAATTTCG 59.614 47.619 0.00 0.00 33.58 3.46
4273 4444 2.147436 AAAATTCGCCGTGTTTGCAT 57.853 40.000 0.00 0.00 0.00 3.96
4302 4473 8.356657 TGTTCGAAATGTAATGAATTTTGTCCT 58.643 29.630 0.00 0.00 32.44 3.85
4362 4533 2.549198 CGGCTGCCGTCGTAGGATA 61.549 63.158 31.72 0.00 42.73 2.59
4375 4546 0.535102 AAGGAAGTGGACAACGGCTG 60.535 55.000 0.00 0.00 0.00 4.85
4376 4547 0.182775 AAAGGAAGTGGACAACGGCT 59.817 50.000 0.00 0.00 0.00 5.52
4382 4553 3.670625 CGGAATACAAAGGAAGTGGACA 58.329 45.455 0.00 0.00 0.00 4.02
4383 4554 2.418976 GCGGAATACAAAGGAAGTGGAC 59.581 50.000 0.00 0.00 0.00 4.02
4387 4558 3.950397 TGATGCGGAATACAAAGGAAGT 58.050 40.909 0.00 0.00 0.00 3.01
4391 4562 2.675844 TCGTTGATGCGGAATACAAAGG 59.324 45.455 0.00 0.00 0.00 3.11
4414 4585 2.602878 GAACGGCAGATGAAGAACGTA 58.397 47.619 0.00 0.00 33.85 3.57
4422 4593 2.917933 CCTTTATGGAACGGCAGATGA 58.082 47.619 0.00 0.00 38.35 2.92
4430 4601 2.707039 CGCCGCCTTTATGGAACG 59.293 61.111 0.00 0.00 38.35 3.95
4446 4618 0.820891 CTCATGGGCCTTGAATCCCG 60.821 60.000 21.08 7.29 45.60 5.14
4447 4619 0.468771 CCTCATGGGCCTTGAATCCC 60.469 60.000 21.08 0.00 42.93 3.85
4448 4620 0.259938 ACCTCATGGGCCTTGAATCC 59.740 55.000 21.08 0.00 39.10 3.01
4449 4621 1.396653 CACCTCATGGGCCTTGAATC 58.603 55.000 21.08 0.00 39.10 2.52
4450 4622 0.032813 CCACCTCATGGGCCTTGAAT 60.033 55.000 21.08 10.95 45.95 2.57
4462 4634 1.899437 GAATCCGCACCTCCACCTCA 61.899 60.000 0.00 0.00 0.00 3.86
4499 4671 0.179006 GGGGCAGTTCATCTCCCATC 60.179 60.000 0.00 0.00 37.59 3.51
4538 4710 2.122413 TAGGGCATGGGAGGCGAT 60.122 61.111 0.00 0.00 34.40 4.58
4597 6200 7.639162 AACAATGTTGAACACGTGTTTAAAA 57.361 28.000 32.15 28.84 36.73 1.52
4606 6209 6.031003 GCGTATAGAAAACAATGTTGAACACG 59.969 38.462 0.00 6.63 0.00 4.49
4627 6230 8.994429 ATTTTGAAAAATATTCACCATGCGTA 57.006 26.923 0.00 0.00 36.88 4.42
4711 6314 9.755064 CGTGTATTTTAAAAGAGTTCATCGAAT 57.245 29.630 6.79 0.00 0.00 3.34
4712 6315 8.980610 TCGTGTATTTTAAAAGAGTTCATCGAA 58.019 29.630 6.79 0.00 0.00 3.71
4713 6316 8.523523 TCGTGTATTTTAAAAGAGTTCATCGA 57.476 30.769 6.79 6.17 0.00 3.59
4714 6317 9.199184 CATCGTGTATTTTAAAAGAGTTCATCG 57.801 33.333 6.79 4.34 0.00 3.84
4786 6389 2.311124 AAAGGATCGTCGGGTGATTC 57.689 50.000 0.00 0.00 0.00 2.52
4790 6393 1.803334 TGAAAAAGGATCGTCGGGTG 58.197 50.000 0.00 0.00 0.00 4.61
4795 6399 6.129088 GCTTGAATGTTTGAAAAAGGATCGTC 60.129 38.462 0.00 0.00 0.00 4.20
4796 6400 5.691754 GCTTGAATGTTTGAAAAAGGATCGT 59.308 36.000 0.00 0.00 0.00 3.73


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

AutoCloner maintained by Alex Coulton.