Multiple sequence alignment - TraesCS4A01G052300

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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 TraesCS4A01G052300 chr4A 100.000 3748 0 0 1 3748 43289945 43286198 0.000000e+00 6922.0
1 TraesCS4A01G052300 chr4D 91.489 3043 177 36 2 2998 420918947 420921953 0.000000e+00 4109.0
2 TraesCS4A01G052300 chr4D 78.788 297 38 16 3462 3746 420922627 420922910 3.850000e-40 176.0
3 TraesCS4A01G052300 chr4B 89.133 1914 142 36 88 1993 518078392 518080247 0.000000e+00 2322.0
4 TraesCS4A01G052300 chr4B 92.288 778 48 4 2022 2787 518080246 518081023 0.000000e+00 1094.0
5 TraesCS4A01G052300 chr4B 77.835 970 113 42 2823 3746 518081011 518081924 1.200000e-139 507.0
6 TraesCS4A01G052300 chr4B 87.778 180 17 2 351 530 564748335 564748161 4.910000e-49 206.0
7 TraesCS4A01G052300 chr7D 87.978 183 17 1 348 530 67745489 67745312 1.050000e-50 211.0
8 TraesCS4A01G052300 chr7D 87.978 183 17 2 348 530 490745277 490745100 1.050000e-50 211.0
9 TraesCS4A01G052300 chr7D 87.978 183 17 2 348 530 490778668 490778491 1.050000e-50 211.0
10 TraesCS4A01G052300 chr7D 100.000 32 0 0 589 620 67745274 67745243 4.040000e-05 60.2
11 TraesCS4A01G052300 chr5D 87.978 183 17 2 348 530 546420108 546420285 1.050000e-50 211.0
12 TraesCS4A01G052300 chr5D 100.000 31 0 0 590 620 546420324 546420354 1.450000e-04 58.4
13 TraesCS4A01G052300 chr2D 87.978 183 17 2 348 530 574646105 574645928 1.050000e-50 211.0
14 TraesCS4A01G052300 chr1D 87.978 183 17 2 348 530 446661197 446661020 1.050000e-50 211.0
15 TraesCS4A01G052300 chr1D 100.000 30 0 0 589 618 446660984 446660955 5.230000e-04 56.5
16 TraesCS4A01G052300 chr5B 87.568 185 16 5 348 531 299946015 299945837 1.360000e-49 207.0
17 TraesCS4A01G052300 chr5B 96.875 32 1 0 589 620 299945800 299945769 2.000000e-03 54.7
18 TraesCS4A01G052300 chr6A 86.339 183 19 2 348 530 159240312 159240136 1.060000e-45 195.0
19 TraesCS4A01G052300 chr1B 86.022 186 21 1 345 530 77722659 77722839 1.060000e-45 195.0
20 TraesCS4A01G052300 chr3A 85.246 183 22 2 348 530 462638251 462638428 2.300000e-42 183.0
21 TraesCS4A01G052300 chr6D 89.091 55 4 1 3629 3683 225649696 225649748 2.420000e-07 67.6
22 TraesCS4A01G052300 chr7A 97.059 34 1 0 589 622 636677151 636677118 1.450000e-04 58.4
23 TraesCS4A01G052300 chr3D 80.519 77 11 3 3581 3655 540884691 540884765 5.230000e-04 56.5
24 TraesCS4A01G052300 chr3D 80.519 77 11 3 3581 3655 607900483 607900557 5.230000e-04 56.5
25 TraesCS4A01G052300 chr3B 87.234 47 6 0 3626 3672 133378531 133378485 2.000000e-03 54.7


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 TraesCS4A01G052300 chr4A 43286198 43289945 3747 True 6922.000000 6922 100.000000 1 3748 1 chr4A.!!$R1 3747
1 TraesCS4A01G052300 chr4D 420918947 420922910 3963 False 2142.500000 4109 85.138500 2 3746 2 chr4D.!!$F1 3744
2 TraesCS4A01G052300 chr4B 518078392 518081924 3532 False 1307.666667 2322 86.418667 88 3746 3 chr4B.!!$F1 3658

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
590 610 0.542702 CTGCCATGTTCTTTGGGGGT 60.543 55.0 0.00 0.0 34.66 4.95 F
1293 1340 0.322816 GAACATGAAGCTGGAGGCCA 60.323 55.0 5.01 0.0 43.05 5.36 F
1941 1988 0.167470 CAATGCTGGCAAGTCTGACG 59.833 55.0 1.52 0.0 30.46 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1640 1687 0.173708 GCGTGACCTCCTGGAAGTAG 59.826 60.0 0.00 0.0 37.04 2.57 R
2245 2295 0.251519 TGCAGCCTCTGACTCTGAGA 60.252 55.0 12.44 0.0 32.44 3.27 R
3425 3755 0.453390 GCAACATCTACCTGCTTGGC 59.547 55.0 0.00 0.0 40.22 4.52 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
36 37 5.670792 AATATGAAGGAACACGTGTAGGA 57.329 39.130 23.69 3.43 0.00 2.94
63 64 3.821421 AGTAGGATGCTCTAAAACCCG 57.179 47.619 0.00 0.00 0.00 5.28
83 84 1.265365 GGGAGTATAGTCGTACGCACC 59.735 57.143 11.24 3.33 0.00 5.01
84 85 1.070309 GGAGTATAGTCGTACGCACCG 60.070 57.143 11.24 0.00 0.00 4.94
184 195 0.607217 TCGTGGCACGAGGAGAAGTA 60.607 55.000 36.29 13.33 46.73 2.24
244 262 0.604073 TCACCACGACCAAAGCGATA 59.396 50.000 0.00 0.00 0.00 2.92
245 263 0.999406 CACCACGACCAAAGCGATAG 59.001 55.000 0.00 0.00 0.00 2.08
246 264 0.606604 ACCACGACCAAAGCGATAGT 59.393 50.000 0.00 0.00 39.35 2.12
256 274 1.481871 AAGCGATAGTTTCCTCGGGA 58.518 50.000 0.00 0.00 32.53 5.14
259 277 1.605712 GCGATAGTTTCCTCGGGATGG 60.606 57.143 0.00 0.00 35.48 3.51
302 320 2.579787 CACGGCGCCTCGTCTTAG 60.580 66.667 26.68 8.67 41.86 2.18
308 327 2.583593 GCCTCGTCTTAGCCGCTG 60.584 66.667 2.16 0.00 0.00 5.18
311 330 3.068691 TCGTCTTAGCCGCTGCCT 61.069 61.111 2.16 0.00 38.69 4.75
313 332 2.202946 GTCTTAGCCGCTGCCTCC 60.203 66.667 2.16 0.00 38.69 4.30
316 335 3.003173 TTAGCCGCTGCCTCCTGT 61.003 61.111 2.16 0.00 38.69 4.00
317 336 3.315142 TTAGCCGCTGCCTCCTGTG 62.315 63.158 2.16 0.00 38.69 3.66
335 354 1.044611 TGGCAGTATATGTAGCGCCA 58.955 50.000 2.29 7.48 46.80 5.69
346 365 3.047718 TAGCGCCACTCGTTCCTCG 62.048 63.158 2.29 0.00 41.07 4.63
380 399 2.476854 CGCTGCTCTCTTTGGCATTTAC 60.477 50.000 0.00 0.00 37.83 2.01
384 403 3.753272 TGCTCTCTTTGGCATTTACAGTC 59.247 43.478 0.00 0.00 33.23 3.51
389 408 4.469657 TCTTTGGCATTTACAGTCTTGGT 58.530 39.130 0.00 0.00 0.00 3.67
394 413 4.202461 TGGCATTTACAGTCTTGGTCTCTT 60.202 41.667 0.00 0.00 0.00 2.85
397 416 5.551233 CATTTACAGTCTTGGTCTCTTGGA 58.449 41.667 0.00 0.00 0.00 3.53
400 419 2.630580 ACAGTCTTGGTCTCTTGGACTC 59.369 50.000 0.00 0.00 43.97 3.36
401 420 1.889829 AGTCTTGGTCTCTTGGACTCG 59.110 52.381 0.00 0.00 43.97 4.18
402 421 0.603569 TCTTGGTCTCTTGGACTCGC 59.396 55.000 0.00 0.00 43.97 5.03
403 422 0.734253 CTTGGTCTCTTGGACTCGCG 60.734 60.000 0.00 0.00 43.97 5.87
404 423 2.154798 TTGGTCTCTTGGACTCGCGG 62.155 60.000 6.13 0.00 43.97 6.46
408 427 3.997064 CTCTTGGACTCGCGGGCTG 62.997 68.421 5.51 0.00 0.00 4.85
460 479 3.667282 CAGCAGCAAGGCAACGCT 61.667 61.111 0.00 0.00 46.39 5.07
497 516 3.492311 GATCGAGTGAGCCGCCTCC 62.492 68.421 0.00 0.00 37.29 4.30
499 518 4.504916 CGAGTGAGCCGCCTCCTG 62.505 72.222 0.00 0.00 37.29 3.86
500 519 4.154347 GAGTGAGCCGCCTCCTGG 62.154 72.222 0.00 0.00 37.29 4.45
530 549 7.165460 TCAAGGTACGATCTCTTGTTGATTA 57.835 36.000 8.17 0.00 38.99 1.75
544 564 4.744570 TGTTGATTAGACGTCTCCACATC 58.255 43.478 23.89 18.27 0.00 3.06
554 574 3.321111 ACGTCTCCACATCTGTTGTTACT 59.679 43.478 0.00 0.00 36.00 2.24
555 575 4.521639 ACGTCTCCACATCTGTTGTTACTA 59.478 41.667 0.00 0.00 36.00 1.82
556 576 4.857588 CGTCTCCACATCTGTTGTTACTAC 59.142 45.833 0.00 0.00 36.00 2.73
581 601 3.841643 CAAAGGTGAATCTGCCATGTTC 58.158 45.455 0.00 0.00 0.00 3.18
590 610 0.542702 CTGCCATGTTCTTTGGGGGT 60.543 55.000 0.00 0.00 34.66 4.95
610 630 3.760684 GGTGAATCTGCCATTTGAGAAGT 59.239 43.478 0.00 0.00 0.00 3.01
622 642 5.879223 CCATTTGAGAAGTCAGACTGCTTAT 59.121 40.000 12.84 4.51 33.16 1.73
623 643 7.044181 CCATTTGAGAAGTCAGACTGCTTATA 58.956 38.462 12.84 4.29 33.16 0.98
627 647 7.517614 TGAGAAGTCAGACTGCTTATATAGG 57.482 40.000 12.84 0.00 33.16 2.57
649 669 4.340263 GTTTTTGTGTGTTCCTCGAACTC 58.660 43.478 6.13 3.35 42.39 3.01
654 674 2.094854 GTGTGTTCCTCGAACTCGGTAT 60.095 50.000 6.13 0.00 42.39 2.73
740 763 8.353684 TCAACTGAACTTCTAGACTTACTCAAG 58.646 37.037 0.00 0.00 37.81 3.02
779 802 4.248859 CTGACGGACAAATCTGAAGATGT 58.751 43.478 0.00 0.00 34.49 3.06
797 820 5.821204 AGATGTTTTGACAGTTGTGCTAAC 58.179 37.500 0.00 0.00 0.00 2.34
825 848 3.876274 AGTGTGTGACTAGGCTGTATG 57.124 47.619 0.00 0.00 30.86 2.39
924 950 5.470368 TCAGTATATTACGCTTGAGGCATC 58.530 41.667 0.00 0.00 41.91 3.91
925 951 5.010617 TCAGTATATTACGCTTGAGGCATCA 59.989 40.000 0.00 0.00 41.91 3.07
948 974 1.939934 CTTGTTCAACTCGTGCAGGAA 59.060 47.619 10.76 0.00 0.00 3.36
951 977 1.002792 GTTCAACTCGTGCAGGAAACC 60.003 52.381 10.76 0.00 0.00 3.27
952 978 0.878523 TCAACTCGTGCAGGAAACCG 60.879 55.000 10.76 1.26 0.00 4.44
956 982 3.276091 CGTGCAGGAAACCGCACA 61.276 61.111 24.39 7.20 46.19 4.57
975 1001 2.254459 CAAGGACTGACTGAATCGACG 58.746 52.381 0.00 0.00 0.00 5.12
1071 1101 3.351740 TCTCTTCGAGCAGAGAAGTGAT 58.648 45.455 13.28 0.00 45.28 3.06
1120 1150 3.665745 ACGTACGTGGGTACTCAATTT 57.334 42.857 22.14 0.00 45.52 1.82
1122 1152 3.005684 ACGTACGTGGGTACTCAATTTCA 59.994 43.478 22.14 0.00 45.52 2.69
1129 1159 5.560183 CGTGGGTACTCAATTTCACAACTTC 60.560 44.000 0.00 0.00 0.00 3.01
1131 1161 4.464112 GGTACTCAATTTCACAACTTCGC 58.536 43.478 0.00 0.00 0.00 4.70
1132 1162 4.024387 GGTACTCAATTTCACAACTTCGCA 60.024 41.667 0.00 0.00 0.00 5.10
1133 1163 4.836125 ACTCAATTTCACAACTTCGCAT 57.164 36.364 0.00 0.00 0.00 4.73
1229 1276 4.379243 ACCAAGGAGCTGGCGACG 62.379 66.667 0.00 0.00 40.45 5.12
1264 1311 2.015227 GAGGCCAAGGAGAGCGAGAG 62.015 65.000 5.01 0.00 0.00 3.20
1293 1340 0.322816 GAACATGAAGCTGGAGGCCA 60.323 55.000 5.01 0.00 43.05 5.36
1514 1561 3.141488 CTCGGGGAGGTGGAGTCG 61.141 72.222 0.00 0.00 0.00 4.18
1711 1758 0.622665 ACCATCAGGAAGCAGAAGGG 59.377 55.000 0.00 0.00 38.69 3.95
1722 1769 2.066393 CAGAAGGGGGCGATGGAGA 61.066 63.158 0.00 0.00 0.00 3.71
1754 1801 2.467826 GCTGCTGGCGAAGACCATC 61.468 63.158 0.00 0.00 39.54 3.51
1830 1877 1.142060 TGTCAGAACGGGTCATGGTTT 59.858 47.619 0.00 0.00 0.00 3.27
1941 1988 0.167470 CAATGCTGGCAAGTCTGACG 59.833 55.000 1.52 0.00 30.46 4.35
2009 2059 1.839191 TGGCTGTCCAGAAGTTGCT 59.161 52.632 0.00 0.00 37.47 3.91
2050 2100 3.462678 GCCGAGGGAGGACTGTCC 61.463 72.222 19.20 19.20 36.58 4.02
2076 2126 2.401583 TCAATCTGGTGACGGGAATG 57.598 50.000 0.00 0.00 37.31 2.67
2122 2172 0.536006 GTGCAAGTTCAGGCAGGACT 60.536 55.000 0.00 0.00 41.35 3.85
2132 2182 0.695347 AGGCAGGACTGAAAAGGAGG 59.305 55.000 3.00 0.00 0.00 4.30
2170 2220 0.471617 AGCCCGATGGAGGATTTCAG 59.528 55.000 0.00 0.00 0.00 3.02
2245 2295 0.475906 AACCTGGCAGCAAAGAGAGT 59.524 50.000 9.56 0.00 0.00 3.24
2259 2309 3.634397 AGAGAGTCTCAGAGTCAGAGG 57.366 52.381 22.05 0.00 34.71 3.69
2270 2332 4.383861 TCAGAGGCTGCAGGTGCG 62.384 66.667 17.12 0.00 45.83 5.34
2298 2360 1.729470 CTCCGAGATCGTGGAGGTGG 61.729 65.000 21.97 4.31 46.55 4.61
2300 2362 1.109920 CCGAGATCGTGGAGGTGGAT 61.110 60.000 1.09 0.00 37.74 3.41
2331 2396 3.173390 GATGGCGATGGCGAGTTGC 62.173 63.158 0.00 0.00 45.38 4.17
2428 2493 1.815613 TCTCAAGGACGAGAAGCTGAG 59.184 52.381 0.00 0.00 39.09 3.35
2777 2842 0.030235 GGTTTTGAACCGTGTCAGGC 59.970 55.000 0.00 0.00 42.62 4.85
2801 2866 1.196808 ACAAATTTCGCCTGCGTGTAG 59.803 47.619 11.68 1.37 40.74 2.74
2804 2869 1.076533 ATTTCGCCTGCGTGTAGTCG 61.077 55.000 11.68 0.00 40.74 4.18
2823 2888 1.363744 GCCAAGTCAGAACGATGGAG 58.636 55.000 0.00 0.00 38.70 3.86
2829 2894 2.632996 AGTCAGAACGATGGAGGTGAAA 59.367 45.455 0.00 0.00 0.00 2.69
2871 2936 3.472652 TGTGTTCGTACTTGCAATTCCT 58.527 40.909 0.00 0.00 0.00 3.36
2872 2937 4.633175 TGTGTTCGTACTTGCAATTCCTA 58.367 39.130 0.00 0.00 0.00 2.94
2947 3016 7.540055 CCAAAGAATTCACTTTTGCTACATCTC 59.460 37.037 8.44 0.00 37.91 2.75
2948 3017 7.750229 AAGAATTCACTTTTGCTACATCTCA 57.250 32.000 8.44 0.00 0.00 3.27
2958 3027 3.099141 TGCTACATCTCATCACAGGTGA 58.901 45.455 4.37 4.37 44.59 4.02
2970 3039 4.687901 TCACAGGTGATTCAGTTTCTCA 57.312 40.909 0.00 0.00 34.14 3.27
2998 3067 4.394729 AGTCGATTTCCTTTTGTTAGGCA 58.605 39.130 0.00 0.00 35.15 4.75
3045 3341 6.161381 ACGTCATCCTTCGTAAAATGTAAGT 58.839 36.000 0.00 0.00 38.52 2.24
3048 3344 5.808540 TCATCCTTCGTAAAATGTAAGTCCG 59.191 40.000 0.00 0.00 0.00 4.79
3072 3368 7.598493 CCGGTTTGACTTTGAATTGTATTTGAT 59.402 33.333 0.00 0.00 0.00 2.57
3073 3369 8.427012 CGGTTTGACTTTGAATTGTATTTGATG 58.573 33.333 0.00 0.00 0.00 3.07
3074 3370 8.223100 GGTTTGACTTTGAATTGTATTTGATGC 58.777 33.333 0.00 0.00 0.00 3.91
3075 3371 8.763356 GTTTGACTTTGAATTGTATTTGATGCA 58.237 29.630 0.00 0.00 0.00 3.96
3076 3372 7.872163 TGACTTTGAATTGTATTTGATGCAC 57.128 32.000 0.00 0.00 0.00 4.57
3094 3403 8.744568 TGATGCACACCATTTATCAAACTATA 57.255 30.769 0.00 0.00 33.29 1.31
3095 3404 8.620416 TGATGCACACCATTTATCAAACTATAC 58.380 33.333 0.00 0.00 33.29 1.47
3098 3410 6.905076 GCACACCATTTATCAAACTATACACG 59.095 38.462 0.00 0.00 0.00 4.49
3188 3500 7.809546 TTACACTGATTTTGTGGACATACAA 57.190 32.000 0.00 0.00 39.52 2.41
3191 3503 8.044060 ACACTGATTTTGTGGACATACAATAG 57.956 34.615 0.00 0.00 40.00 1.73
3196 3508 8.892723 TGATTTTGTGGACATACAATAGATGAC 58.107 33.333 0.00 0.00 40.00 3.06
3219 3531 5.412594 ACAGTCATAGTCAAAATTGTGCGAT 59.587 36.000 0.00 0.00 0.00 4.58
3251 3564 8.986477 AAAGCTAAACATGCCTTAGTATTTTG 57.014 30.769 13.78 0.00 0.00 2.44
3252 3565 7.938140 AGCTAAACATGCCTTAGTATTTTGA 57.062 32.000 13.78 0.00 0.00 2.69
3254 3567 7.067494 AGCTAAACATGCCTTAGTATTTTGAGG 59.933 37.037 13.78 0.00 0.00 3.86
3255 3568 7.067008 GCTAAACATGCCTTAGTATTTTGAGGA 59.933 37.037 13.78 0.00 0.00 3.71
3256 3569 7.396540 AAACATGCCTTAGTATTTTGAGGAG 57.603 36.000 0.00 0.00 0.00 3.69
3257 3570 5.440610 ACATGCCTTAGTATTTTGAGGAGG 58.559 41.667 0.00 0.00 0.00 4.30
3258 3571 4.503714 TGCCTTAGTATTTTGAGGAGGG 57.496 45.455 0.00 0.00 0.00 4.30
3259 3572 4.108570 TGCCTTAGTATTTTGAGGAGGGA 58.891 43.478 0.00 0.00 0.00 4.20
3260 3573 4.164221 TGCCTTAGTATTTTGAGGAGGGAG 59.836 45.833 0.00 0.00 0.00 4.30
3261 3574 4.164413 GCCTTAGTATTTTGAGGAGGGAGT 59.836 45.833 0.00 0.00 0.00 3.85
3262 3575 5.365895 GCCTTAGTATTTTGAGGAGGGAGTA 59.634 44.000 0.00 0.00 0.00 2.59
3263 3576 6.463190 GCCTTAGTATTTTGAGGAGGGAGTAG 60.463 46.154 0.00 0.00 0.00 2.57
3264 3577 6.042208 CCTTAGTATTTTGAGGAGGGAGTAGG 59.958 46.154 0.00 0.00 0.00 3.18
3265 3578 3.712218 AGTATTTTGAGGAGGGAGTAGGC 59.288 47.826 0.00 0.00 0.00 3.93
3296 3609 5.622346 AGAATGTGGAGGGAGTAGATTTC 57.378 43.478 0.00 0.00 0.00 2.17
3310 3623 7.079475 GGAGTAGATTTCTGATAAGCTACGTC 58.921 42.308 15.48 13.70 46.38 4.34
3366 3679 3.865446 CCATTCTTGGGAAATTCTTGGC 58.135 45.455 0.00 0.00 39.56 4.52
3368 3681 4.262981 CCATTCTTGGGAAATTCTTGGCAA 60.263 41.667 0.00 0.00 39.56 4.52
3369 3682 5.307204 CATTCTTGGGAAATTCTTGGCAAA 58.693 37.500 0.00 0.00 34.90 3.68
3370 3683 5.565455 TTCTTGGGAAATTCTTGGCAAAT 57.435 34.783 0.00 0.00 0.00 2.32
3372 3685 6.872585 TCTTGGGAAATTCTTGGCAAATAT 57.127 33.333 0.00 0.00 0.00 1.28
3373 3686 7.256494 TCTTGGGAAATTCTTGGCAAATATT 57.744 32.000 0.00 1.02 0.00 1.28
3374 3687 7.688343 TCTTGGGAAATTCTTGGCAAATATTT 58.312 30.769 15.16 15.16 0.00 1.40
3375 3688 8.162746 TCTTGGGAAATTCTTGGCAAATATTTT 58.837 29.630 15.92 9.77 0.00 1.82
3376 3689 8.703378 TTGGGAAATTCTTGGCAAATATTTTT 57.297 26.923 15.92 6.77 0.00 1.94
3377 3690 8.334263 TGGGAAATTCTTGGCAAATATTTTTC 57.666 30.769 15.92 12.90 0.00 2.29
3379 3692 7.413988 GGGAAATTCTTGGCAAATATTTTTCGG 60.414 37.037 15.92 0.00 0.00 4.30
3381 3694 8.614469 AAATTCTTGGCAAATATTTTTCGGAA 57.386 26.923 0.00 0.00 0.00 4.30
3384 3697 6.105333 TCTTGGCAAATATTTTTCGGAATGG 58.895 36.000 0.00 0.00 0.00 3.16
3386 3699 5.659463 TGGCAAATATTTTTCGGAATGGAG 58.341 37.500 0.00 0.00 0.00 3.86
3395 3708 5.988310 TTTTCGGAATGGAGTAGTCACTA 57.012 39.130 0.00 0.00 34.21 2.74
3399 3712 6.145338 TCGGAATGGAGTAGTCACTAATTC 57.855 41.667 0.00 0.00 37.29 2.17
3401 3714 5.749109 CGGAATGGAGTAGTCACTAATTCAC 59.251 44.000 0.00 0.00 38.51 3.18
3438 3768 1.002134 GCAAGGCCAAGCAGGTAGA 60.002 57.895 5.01 0.00 40.61 2.59
3445 3775 0.729116 CCAAGCAGGTAGATGTTGCG 59.271 55.000 0.00 0.00 42.47 4.85
3454 3784 2.030946 GGTAGATGTTGCGAGAATGTGC 59.969 50.000 0.00 0.00 0.00 4.57
3476 3806 7.235399 TGTGCCAAGGTGAATGATCTATATCTA 59.765 37.037 0.00 0.00 32.93 1.98
3507 3837 4.949856 ACAACCTCATAGGCGATTCAATTT 59.050 37.500 0.00 0.00 39.63 1.82
3508 3838 6.119536 ACAACCTCATAGGCGATTCAATTTA 58.880 36.000 0.00 0.00 39.63 1.40
3516 3846 8.474025 TCATAGGCGATTCAATTTATTTTTGGT 58.526 29.630 0.00 0.00 0.00 3.67
3582 3920 9.598517 AGAACAATTGTTGTACATTGAACATTT 57.401 25.926 27.85 6.78 44.59 2.32
3583 3921 9.635632 GAACAATTGTTGTACATTGAACATTTG 57.364 29.630 27.85 20.76 44.59 2.32
3584 3922 7.629130 ACAATTGTTGTACATTGAACATTTGC 58.371 30.769 21.58 0.00 42.11 3.68
3585 3923 7.495279 ACAATTGTTGTACATTGAACATTTGCT 59.505 29.630 21.58 12.70 42.11 3.91
3592 3930 8.888332 TGTACATTGAACATTTGCTAAATACG 57.112 30.769 0.00 0.00 0.00 3.06
3595 3933 6.307800 ACATTGAACATTTGCTAAATACGCAC 59.692 34.615 0.00 0.00 37.07 5.34
3600 3938 5.390613 ACATTTGCTAAATACGCACTGAAC 58.609 37.500 0.00 0.00 37.07 3.18
3607 3945 7.585867 TGCTAAATACGCACTGAACAATTTTA 58.414 30.769 0.00 0.00 31.40 1.52
3616 3954 9.900710 ACGCACTGAACAATTTTATAATTTACA 57.099 25.926 0.00 0.00 31.63 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 6.461231 GGTTTTAGAGCATCCTACTATCACGT 60.461 42.308 0.00 0.00 33.66 4.49
47 48 0.544697 TCCCGGGTTTTAGAGCATCC 59.455 55.000 22.86 0.00 33.66 3.51
63 64 1.265365 GGTGCGTACGACTATACTCCC 59.735 57.143 21.65 0.00 0.00 4.30
164 175 1.444553 CTTCTCCTCGTGCCACGAC 60.445 63.158 17.22 0.00 46.73 4.34
172 183 1.313812 CGCCCACTACTTCTCCTCGT 61.314 60.000 0.00 0.00 0.00 4.18
175 186 0.905337 AAGCGCCCACTACTTCTCCT 60.905 55.000 2.29 0.00 0.00 3.69
184 195 3.241530 TCAGTCCAAGCGCCCACT 61.242 61.111 2.29 0.00 0.00 4.00
245 263 0.179018 CCATCCCATCCCGAGGAAAC 60.179 60.000 0.00 0.00 34.34 2.78
246 264 0.327095 TCCATCCCATCCCGAGGAAA 60.327 55.000 0.00 0.00 34.34 3.13
256 274 2.143419 GGGCTCGTCTCCATCCCAT 61.143 63.158 0.00 0.00 36.96 4.00
259 277 3.551407 GGGGGCTCGTCTCCATCC 61.551 72.222 0.00 0.00 0.00 3.51
284 302 3.047718 CTAAGACGAGGCGCCGTGA 62.048 63.158 23.20 2.27 43.49 4.35
311 330 2.296190 CGCTACATATACTGCCACAGGA 59.704 50.000 0.00 0.00 35.51 3.86
313 332 2.061773 GCGCTACATATACTGCCACAG 58.938 52.381 0.00 0.00 37.52 3.66
316 335 3.906660 GGCGCTACATATACTGCCA 57.093 52.632 7.64 0.00 42.03 4.92
317 336 1.000955 AGTGGCGCTACATATACTGCC 59.999 52.381 26.36 0.00 42.76 4.85
318 337 2.329379 GAGTGGCGCTACATATACTGC 58.671 52.381 26.36 0.00 0.00 4.40
319 338 2.031069 ACGAGTGGCGCTACATATACTG 60.031 50.000 26.36 9.18 46.04 2.74
320 339 2.228059 ACGAGTGGCGCTACATATACT 58.772 47.619 26.36 3.42 46.04 2.12
335 354 2.833631 AAATGAACCGAGGAACGAGT 57.166 45.000 0.00 0.00 45.77 4.18
346 365 3.003480 AGAGCAGCGAGTAAAATGAACC 58.997 45.455 0.00 0.00 0.00 3.62
389 408 3.760035 GCCCGCGAGTCCAAGAGA 61.760 66.667 8.23 0.00 0.00 3.10
404 423 3.355957 ATTGGCCAGAGGAGCAGCC 62.356 63.158 5.11 0.00 45.96 4.85
408 427 1.751927 CACCATTGGCCAGAGGAGC 60.752 63.158 26.93 0.00 0.00 4.70
464 483 1.658717 GATCACGGGAGCACGATCG 60.659 63.158 14.88 14.88 37.61 3.69
497 516 1.448540 CGTACCTTGAGCAGCCCAG 60.449 63.158 0.00 0.00 0.00 4.45
499 518 0.530870 GATCGTACCTTGAGCAGCCC 60.531 60.000 0.00 0.00 0.00 5.19
500 519 0.461961 AGATCGTACCTTGAGCAGCC 59.538 55.000 0.00 0.00 0.00 4.85
544 564 2.411031 CCTTTGCGCGTAGTAACAACAG 60.411 50.000 8.43 3.15 0.00 3.16
554 574 1.075542 CAGATTCACCTTTGCGCGTA 58.924 50.000 8.43 0.00 0.00 4.42
555 575 1.868997 CAGATTCACCTTTGCGCGT 59.131 52.632 8.43 0.00 0.00 6.01
556 576 1.512734 GCAGATTCACCTTTGCGCG 60.513 57.895 0.00 0.00 0.00 6.86
581 601 0.251742 TGGCAGATTCACCCCCAAAG 60.252 55.000 0.00 0.00 0.00 2.77
590 610 4.654915 TGACTTCTCAAATGGCAGATTCA 58.345 39.130 0.00 0.00 0.00 2.57
610 630 8.100791 ACACAAAAACCTATATAAGCAGTCTGA 58.899 33.333 3.32 0.00 0.00 3.27
622 642 5.856156 TCGAGGAACACACAAAAACCTATA 58.144 37.500 0.00 0.00 0.00 1.31
623 643 4.710324 TCGAGGAACACACAAAAACCTAT 58.290 39.130 0.00 0.00 0.00 2.57
627 647 4.340263 GAGTTCGAGGAACACACAAAAAC 58.660 43.478 10.74 0.00 44.11 2.43
714 737 7.818997 TGAGTAAGTCTAGAAGTTCAGTTGA 57.181 36.000 5.50 0.00 0.00 3.18
740 763 3.303132 CGTCAGTTAGCCAACAACTTCAC 60.303 47.826 0.00 0.00 37.10 3.18
779 802 3.759086 TGTGGTTAGCACAACTGTCAAAA 59.241 39.130 15.16 0.00 0.00 2.44
808 831 1.482593 AGCCATACAGCCTAGTCACAC 59.517 52.381 0.00 0.00 0.00 3.82
825 848 8.782339 TTACAGGTTACTAGTAATGAAAAGCC 57.218 34.615 18.03 12.26 0.00 4.35
876 899 5.990120 AAAATAATGCCAGATGCCTATCC 57.010 39.130 0.00 0.00 40.16 2.59
919 945 3.189287 ACGAGTTGAACAAGAATGATGCC 59.811 43.478 0.00 0.00 0.00 4.40
924 950 3.548587 CTGCACGAGTTGAACAAGAATG 58.451 45.455 0.00 0.00 0.00 2.67
925 951 2.549754 CCTGCACGAGTTGAACAAGAAT 59.450 45.455 0.00 0.00 0.00 2.40
948 974 0.532862 CAGTCAGTCCTTGTGCGGTT 60.533 55.000 0.00 0.00 0.00 4.44
951 977 1.728971 GATTCAGTCAGTCCTTGTGCG 59.271 52.381 0.00 0.00 0.00 5.34
952 978 1.728971 CGATTCAGTCAGTCCTTGTGC 59.271 52.381 0.00 0.00 0.00 4.57
956 982 1.402984 GCGTCGATTCAGTCAGTCCTT 60.403 52.381 0.00 0.00 0.00 3.36
975 1001 0.040425 CGTACAACTGGTTGCCTTGC 60.040 55.000 12.65 0.00 44.03 4.01
989 1015 0.736636 CTCGGCCATCTGTACGTACA 59.263 55.000 25.88 25.88 34.56 2.90
1068 1098 0.397564 TGCTGAACCTGCTGTGATCA 59.602 50.000 0.00 0.00 0.00 2.92
1071 1101 1.598962 GCTGCTGAACCTGCTGTGA 60.599 57.895 0.00 0.00 32.04 3.58
1120 1150 4.061596 TGTGTGATTATGCGAAGTTGTGA 58.938 39.130 0.00 0.00 0.00 3.58
1122 1152 4.515191 AGTTGTGTGATTATGCGAAGTTGT 59.485 37.500 0.00 0.00 0.00 3.32
1129 1159 2.898181 TGCAGTTGTGTGATTATGCG 57.102 45.000 0.00 0.00 36.47 4.73
1131 1161 8.599055 ACTAGATATGCAGTTGTGTGATTATG 57.401 34.615 0.00 0.00 0.00 1.90
1132 1162 9.265901 GAACTAGATATGCAGTTGTGTGATTAT 57.734 33.333 0.00 0.00 35.17 1.28
1133 1163 7.710907 GGAACTAGATATGCAGTTGTGTGATTA 59.289 37.037 0.00 0.00 35.17 1.75
1202 1249 1.658114 CTCCTTGGTCACGACGTCA 59.342 57.895 17.16 0.00 0.00 4.35
1264 1311 0.455633 CTTCATGTTCGCCTGCTTGC 60.456 55.000 0.00 0.00 0.00 4.01
1275 1322 0.333993 ATGGCCTCCAGCTTCATGTT 59.666 50.000 3.32 0.00 43.05 2.71
1293 1340 2.412323 CCTGCATGGACTTGCGCAT 61.412 57.895 12.75 0.00 45.77 4.73
1298 1345 0.322277 ACAGCTCCTGCATGGACTTG 60.322 55.000 0.00 5.60 40.56 3.16
1490 1537 2.754658 ACCTCCCCGAGCACGTAG 60.755 66.667 2.18 0.00 37.88 3.51
1514 1561 4.286320 ATCCGCCGCGTCTCCATC 62.286 66.667 12.58 0.00 0.00 3.51
1640 1687 0.173708 GCGTGACCTCCTGGAAGTAG 59.826 60.000 0.00 0.00 37.04 2.57
1702 1749 3.801997 CCATCGCCCCCTTCTGCT 61.802 66.667 0.00 0.00 0.00 4.24
1711 1758 2.281345 CCATGCTCTCCATCGCCC 60.281 66.667 0.00 0.00 29.71 6.13
1722 1769 3.095163 CAGCTCCCCCTCCATGCT 61.095 66.667 0.00 0.00 0.00 3.79
1754 1801 2.202362 CGCAGACACTCGACCTCG 60.202 66.667 0.00 0.00 41.45 4.63
2009 2059 6.591062 GCAATTCAATGTCAAAATAGGCTTCA 59.409 34.615 0.00 0.00 0.00 3.02
2050 2100 3.366273 CCCGTCACCAGATTGAATGTTTG 60.366 47.826 0.00 0.00 0.00 2.93
2122 2172 3.284793 TGAAACGAACCCTCCTTTTCA 57.715 42.857 0.00 0.00 0.00 2.69
2170 2220 0.315568 ACACTCAGAGTTCACGCTCC 59.684 55.000 0.00 0.00 36.20 4.70
2245 2295 0.251519 TGCAGCCTCTGACTCTGAGA 60.252 55.000 12.44 0.00 32.44 3.27
2270 2332 0.528684 CGATCTCGGAGACAAAGCCC 60.529 60.000 10.41 0.00 35.37 5.19
2298 2360 1.312815 CCATCGGCCTCTTTGGAATC 58.687 55.000 0.00 0.00 38.35 2.52
2300 2362 1.378514 GCCATCGGCCTCTTTGGAA 60.379 57.895 12.68 0.00 44.06 3.53
2321 2386 1.165907 CCTTCTTGTGCAACTCGCCA 61.166 55.000 0.00 0.00 41.33 5.69
2331 2396 1.192146 TCCCCGACCTCCTTCTTGTG 61.192 60.000 0.00 0.00 0.00 3.33
2335 2400 2.362632 CGTCCCCGACCTCCTTCT 60.363 66.667 0.00 0.00 35.63 2.85
2406 2471 1.815613 CAGCTTCTCGTCCTTGAGAGA 59.184 52.381 0.00 0.00 45.23 3.10
2441 2506 1.846007 ACTTCAGGTCGCTGATCTCT 58.154 50.000 0.00 0.00 32.91 3.10
2594 2659 2.583593 CTCTCCACGCGCCTTAGC 60.584 66.667 5.73 0.00 0.00 3.09
2777 2842 1.059657 CGCAGGCGAAATTTGTGACG 61.060 55.000 8.15 0.00 42.83 4.35
2801 2866 0.716108 CATCGTTCTGACTTGGCGAC 59.284 55.000 0.00 0.00 34.36 5.19
2804 2869 1.363744 CTCCATCGTTCTGACTTGGC 58.636 55.000 0.00 0.00 30.79 4.52
2805 2870 1.276421 ACCTCCATCGTTCTGACTTGG 59.724 52.381 0.00 0.00 0.00 3.61
2806 2871 2.029020 TCACCTCCATCGTTCTGACTTG 60.029 50.000 0.00 0.00 0.00 3.16
2807 2872 2.248248 TCACCTCCATCGTTCTGACTT 58.752 47.619 0.00 0.00 0.00 3.01
2808 2873 1.924731 TCACCTCCATCGTTCTGACT 58.075 50.000 0.00 0.00 0.00 3.41
2809 2874 2.737252 GTTTCACCTCCATCGTTCTGAC 59.263 50.000 0.00 0.00 0.00 3.51
2823 2888 6.308766 GCAGATGACATTACATTTGTTTCACC 59.691 38.462 0.00 0.00 35.65 4.02
2829 2894 6.016024 ACACAAGCAGATGACATTACATTTGT 60.016 34.615 0.00 0.00 35.65 2.83
2958 3027 8.608844 AATCGACTTAAACTGAGAAACTGAAT 57.391 30.769 0.00 0.00 0.00 2.57
2970 3039 8.565416 CCTAACAAAAGGAAATCGACTTAAACT 58.435 33.333 0.00 0.00 39.15 2.66
3006 3302 6.942976 AGGATGACGTATCTTAGAAACCAAA 58.057 36.000 0.00 0.00 36.03 3.28
3023 3319 6.237755 CGGACTTACATTTTACGAAGGATGAC 60.238 42.308 0.00 0.00 0.00 3.06
3024 3320 5.808540 CGGACTTACATTTTACGAAGGATGA 59.191 40.000 0.00 0.00 0.00 2.92
3045 3341 6.642707 AATACAATTCAAAGTCAAACCGGA 57.357 33.333 9.46 0.00 0.00 5.14
3048 3344 8.223100 GCATCAAATACAATTCAAAGTCAAACC 58.777 33.333 0.00 0.00 0.00 3.27
3060 3356 9.316730 GATAAATGGTGTGCATCAAATACAATT 57.683 29.630 0.00 0.00 0.00 2.32
3072 3368 7.413548 CGTGTATAGTTTGATAAATGGTGTGCA 60.414 37.037 0.00 0.00 0.00 4.57
3073 3369 6.905076 CGTGTATAGTTTGATAAATGGTGTGC 59.095 38.462 0.00 0.00 0.00 4.57
3074 3370 7.970384 ACGTGTATAGTTTGATAAATGGTGTG 58.030 34.615 0.00 0.00 0.00 3.82
3075 3371 8.447833 CAACGTGTATAGTTTGATAAATGGTGT 58.552 33.333 0.00 0.00 0.00 4.16
3076 3372 8.661257 TCAACGTGTATAGTTTGATAAATGGTG 58.339 33.333 0.00 0.00 28.07 4.17
3171 3483 8.892723 TGTCATCTATTGTATGTCCACAAAATC 58.107 33.333 0.00 0.00 41.50 2.17
3188 3500 9.896645 ACAATTTTGACTATGACTGTCATCTAT 57.103 29.630 25.35 12.85 42.95 1.98
3191 3503 6.744537 GCACAATTTTGACTATGACTGTCATC 59.255 38.462 25.35 13.85 42.95 2.92
3196 3508 5.281693 TCGCACAATTTTGACTATGACTG 57.718 39.130 0.00 0.00 0.00 3.51
3230 3543 8.506168 TCCTCAAAATACTAAGGCATGTTTAG 57.494 34.615 14.00 14.00 34.92 1.85
3234 3547 5.440610 CCTCCTCAAAATACTAAGGCATGT 58.559 41.667 0.00 0.00 0.00 3.21
3246 3559 2.852130 AGCCTACTCCCTCCTCAAAAT 58.148 47.619 0.00 0.00 0.00 1.82
3273 3586 6.325028 CAGAAATCTACTCCCTCCACATTCTA 59.675 42.308 0.00 0.00 0.00 2.10
3279 3592 6.732896 TTATCAGAAATCTACTCCCTCCAC 57.267 41.667 0.00 0.00 0.00 4.02
3319 3632 3.052262 TGGCCCAAGATATTCCATTCCAA 60.052 43.478 0.00 0.00 0.00 3.53
3320 3633 2.517553 TGGCCCAAGATATTCCATTCCA 59.482 45.455 0.00 0.00 0.00 3.53
3321 3634 3.160269 CTGGCCCAAGATATTCCATTCC 58.840 50.000 0.00 0.00 0.00 3.01
3346 3659 4.540359 TGCCAAGAATTTCCCAAGAATG 57.460 40.909 0.00 0.00 0.00 2.67
3353 3666 7.413988 CCGAAAAATATTTGCCAAGAATTTCCC 60.414 37.037 0.39 0.00 0.00 3.97
3355 3668 8.250538 TCCGAAAAATATTTGCCAAGAATTTC 57.749 30.769 0.39 0.00 0.00 2.17
3360 3673 6.071108 TCCATTCCGAAAAATATTTGCCAAGA 60.071 34.615 0.39 0.00 0.00 3.02
3364 3677 5.660460 ACTCCATTCCGAAAAATATTTGCC 58.340 37.500 0.39 0.00 0.00 4.52
3365 3678 7.480810 ACTACTCCATTCCGAAAAATATTTGC 58.519 34.615 0.39 0.00 0.00 3.68
3366 3679 8.673711 TGACTACTCCATTCCGAAAAATATTTG 58.326 33.333 0.39 0.00 0.00 2.32
3368 3681 8.047310 AGTGACTACTCCATTCCGAAAAATATT 58.953 33.333 0.00 0.00 28.79 1.28
3369 3682 7.565680 AGTGACTACTCCATTCCGAAAAATAT 58.434 34.615 0.00 0.00 28.79 1.28
3370 3683 6.942976 AGTGACTACTCCATTCCGAAAAATA 58.057 36.000 0.00 0.00 28.79 1.40
3372 3685 5.223449 AGTGACTACTCCATTCCGAAAAA 57.777 39.130 0.00 0.00 28.79 1.94
3373 3686 4.884668 AGTGACTACTCCATTCCGAAAA 57.115 40.909 0.00 0.00 28.79 2.29
3374 3687 5.988310 TTAGTGACTACTCCATTCCGAAA 57.012 39.130 0.00 0.00 38.36 3.46
3375 3688 6.153851 TGAATTAGTGACTACTCCATTCCGAA 59.846 38.462 10.57 0.00 36.65 4.30
3376 3689 5.655090 TGAATTAGTGACTACTCCATTCCGA 59.345 40.000 10.57 0.00 36.65 4.55
3377 3690 5.749109 GTGAATTAGTGACTACTCCATTCCG 59.251 44.000 10.57 0.00 36.65 4.30
3425 3755 0.453390 GCAACATCTACCTGCTTGGC 59.547 55.000 0.00 0.00 40.22 4.52
3438 3768 1.200716 CTTGGCACATTCTCGCAACAT 59.799 47.619 0.00 0.00 39.30 2.71
3445 3775 3.084039 TCATTCACCTTGGCACATTCTC 58.916 45.455 0.00 0.00 39.30 2.87
3476 3806 4.825085 TCGCCTATGAGGTTGTTTCTTTTT 59.175 37.500 0.00 0.00 37.80 1.94
3485 3815 5.505173 AAATTGAATCGCCTATGAGGTTG 57.495 39.130 0.00 0.00 37.80 3.77
3488 3818 8.971321 CAAAAATAAATTGAATCGCCTATGAGG 58.029 33.333 0.00 0.00 38.80 3.86
3493 3823 9.495572 AAAACCAAAAATAAATTGAATCGCCTA 57.504 25.926 0.00 0.00 0.00 3.93
3555 3888 9.598517 AATGTTCAATGTACAACAATTGTTCTT 57.401 25.926 20.85 13.10 42.22 2.52
3556 3889 9.598517 AAATGTTCAATGTACAACAATTGTTCT 57.401 25.926 20.85 12.41 42.22 3.01
3558 3891 8.121708 GCAAATGTTCAATGTACAACAATTGTT 58.878 29.630 18.13 18.13 42.01 2.83
3582 3920 5.621197 AATTGTTCAGTGCGTATTTAGCA 57.379 34.783 0.00 0.00 42.99 3.49
3583 3921 6.927933 AAAATTGTTCAGTGCGTATTTAGC 57.072 33.333 0.00 0.00 0.00 3.09


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

AutoCloner maintained by Alex Coulton.