Multiple sequence alignment - TraesCS4D01G200800

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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 TraesCS4D01G200800 chr4D 100.000 6642 0 0 540 7181 348042143 348048784 0.000000e+00 12266.0
1 TraesCS4D01G200800 chr4D 100.000 306 0 0 1 306 348041604 348041909 3.760000e-157 566.0
2 TraesCS4D01G200800 chr4B 95.974 5663 161 25 653 6283 428198998 428204625 0.000000e+00 9132.0
3 TraesCS4D01G200800 chr4B 92.871 519 30 3 6670 7181 428204919 428205437 0.000000e+00 747.0
4 TraesCS4D01G200800 chr4B 95.779 308 8 3 6307 6609 428204619 428204926 6.470000e-135 492.0
5 TraesCS4D01G200800 chr4B 92.473 279 17 2 1 275 428198526 428198804 5.220000e-106 396.0
6 TraesCS4D01G200800 chr4B 89.167 120 3 1 546 655 428198805 428198924 2.700000e-29 141.0
7 TraesCS4D01G200800 chr4A 94.524 3780 131 28 872 4602 117698670 117694918 0.000000e+00 5764.0
8 TraesCS4D01G200800 chr4A 97.389 2489 62 2 4694 7181 117694879 117692393 0.000000e+00 4233.0
9 TraesCS4D01G200800 chr4A 91.379 58 4 1 4655 4711 117694936 117694879 2.150000e-10 78.7
10 TraesCS4D01G200800 chr5D 79.247 877 174 7 2901 3773 295072632 295071760 7.970000e-169 604.0
11 TraesCS4D01G200800 chr5D 81.336 434 81 0 4069 4502 295071502 295071069 3.190000e-93 353.0
12 TraesCS4D01G200800 chr5D 90.667 75 5 2 6596 6668 66982613 66982687 1.650000e-16 99.0
13 TraesCS4D01G200800 chr5D 93.846 65 3 1 6605 6668 560549319 560549255 5.930000e-16 97.1
14 TraesCS4D01G200800 chr5B 79.247 877 174 7 2901 3773 336791965 336791093 7.970000e-169 604.0
15 TraesCS4D01G200800 chr5B 81.797 434 79 0 4069 4502 336790834 336790401 1.470000e-96 364.0
16 TraesCS4D01G200800 chr5B 93.846 65 4 0 6604 6668 597288184 597288120 1.650000e-16 99.0
17 TraesCS4D01G200800 chr5A 78.588 878 180 7 2900 3773 388641234 388640361 2.250000e-159 573.0
18 TraesCS4D01G200800 chr5A 81.106 434 82 0 4069 4502 388640102 388639669 1.480000e-91 348.0
19 TraesCS4D01G200800 chr3B 96.721 61 1 1 6601 6661 446451006 446450947 4.580000e-17 100.0
20 TraesCS4D01G200800 chr1B 96.721 61 1 1 6601 6661 382213176 382213235 4.580000e-17 100.0
21 TraesCS4D01G200800 chr2D 93.939 66 3 1 6604 6668 441760444 441760379 1.650000e-16 99.0
22 TraesCS4D01G200800 chr6D 93.846 65 3 1 6605 6668 259292219 259292283 5.930000e-16 97.1
23 TraesCS4D01G200800 chr1D 83.871 93 8 5 6602 6691 74410468 74410556 1.660000e-11 82.4


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 TraesCS4D01G200800 chr4D 348041604 348048784 7180 False 6416.000000 12266 100.000000 1 7181 2 chr4D.!!$F1 7180
1 TraesCS4D01G200800 chr4B 428198526 428205437 6911 False 2181.600000 9132 93.252800 1 7181 5 chr4B.!!$F1 7180
2 TraesCS4D01G200800 chr4A 117692393 117698670 6277 True 3358.566667 5764 94.430667 872 7181 3 chr4A.!!$R1 6309
3 TraesCS4D01G200800 chr5D 295071069 295072632 1563 True 478.500000 604 80.291500 2901 4502 2 chr5D.!!$R2 1601
4 TraesCS4D01G200800 chr5B 336790401 336791965 1564 True 484.000000 604 80.522000 2901 4502 2 chr5B.!!$R2 1601
5 TraesCS4D01G200800 chr5A 388639669 388641234 1565 True 460.500000 573 79.847000 2900 4502 2 chr5A.!!$R1 1602

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
962 1053 0.112412 AACCCCAAAACCGATCAGCT 59.888 50.000 0.00 0.00 0.00 4.24 F
1668 1764 0.034896 CTGGGTTCGTGTTAGCCTGT 59.965 55.000 0.00 0.00 34.29 4.00 F
2965 3107 0.097499 TGCAGCGATCAAAAGCATCG 59.903 50.000 0.00 0.00 44.94 3.84 F
3214 3356 2.164624 CCTAGGTGGAAGTTCTGACGAG 59.835 54.545 0.00 2.12 38.35 4.18 F
3750 3892 2.617276 CCTATATACGGTCCTCGCTCCA 60.617 54.545 0.00 0.00 43.89 3.86 F
5371 5667 2.611292 GGATCGCAAGTTGGATCTTCTG 59.389 50.000 22.69 0.00 39.19 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2784 2925 0.322277 AGCTGATGGTGGCTCAACTG 60.322 55.000 0.00 0.0 32.98 3.16 R
3154 3296 0.608130 TCACCGCACTGCATAGTTCT 59.392 50.000 1.11 0.0 34.07 3.01 R
4612 4888 2.614057 GGGTTGATGAAAGGATACAGCG 59.386 50.000 0.00 0.0 41.41 5.18 R
5207 5501 3.553828 TGAATCCACCCTCGGTAAATC 57.446 47.619 0.00 0.0 32.11 2.17 R
5537 5833 0.255890 TGCCTGGGATAGCTCAAACC 59.744 55.000 0.00 0.0 0.00 3.27 R
6286 6582 0.239613 GCACACACACACACACACAA 59.760 50.000 0.00 0.0 0.00 3.33 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
65 66 1.941377 TGGGTGACGTGGTAATAGGT 58.059 50.000 0.00 0.00 0.00 3.08
66 67 2.259012 TGGGTGACGTGGTAATAGGTT 58.741 47.619 0.00 0.00 0.00 3.50
97 98 1.691337 ACGGGCCAGGGCTACAATA 60.691 57.895 13.81 0.00 41.60 1.90
99 100 1.227853 GGGCCAGGGCTACAATACG 60.228 63.158 13.81 0.00 41.60 3.06
109 110 2.159572 GGCTACAATACGGTGCACTTTG 60.160 50.000 17.98 16.52 0.00 2.77
231 236 2.100631 GCGAACACATCCAGGTCCG 61.101 63.158 0.00 0.00 0.00 4.79
243 248 1.482553 CCAGGTCCGGGTCCTACATAT 60.483 57.143 12.62 0.00 33.54 1.78
253 258 1.066605 GTCCTACATATGCGACCGTGT 59.933 52.381 1.58 0.00 0.00 4.49
268 273 2.431771 TGTGGGCGAACATCGTCG 60.432 61.111 1.45 0.00 46.90 5.12
275 280 2.215604 CGAACATCGTCGTCGGCTC 61.216 63.158 1.55 0.00 36.26 4.70
276 281 1.872679 GAACATCGTCGTCGGCTCC 60.873 63.158 1.55 0.00 37.69 4.70
277 282 2.267681 GAACATCGTCGTCGGCTCCT 62.268 60.000 1.55 0.00 37.69 3.69
278 283 2.024871 CATCGTCGTCGGCTCCTC 59.975 66.667 1.55 0.00 37.69 3.71
279 284 3.210528 ATCGTCGTCGGCTCCTCC 61.211 66.667 1.55 0.00 37.69 4.30
290 295 2.835431 CTCCTCCGGCGACTCCAT 60.835 66.667 9.30 0.00 34.01 3.41
291 296 2.833582 TCCTCCGGCGACTCCATC 60.834 66.667 9.30 0.00 34.01 3.51
583 588 0.395862 TAAGGAGCGGGAGAGGACAG 60.396 60.000 0.00 0.00 0.00 3.51
638 653 1.339631 GGTCCATGTTGTCGGAATCCA 60.340 52.381 0.00 0.00 31.67 3.41
665 756 2.288213 GCGGATGTCGACATTAGATGGA 60.288 50.000 30.46 0.17 42.43 3.41
685 776 3.304190 GGATAAAAGTGCGTGAACCGTTT 60.304 43.478 0.00 0.00 39.32 3.60
692 783 1.801771 TGCGTGAACCGTTTAATCCAG 59.198 47.619 0.00 0.00 39.32 3.86
699 790 5.856455 GTGAACCGTTTAATCCAGACATTTG 59.144 40.000 0.00 0.00 0.00 2.32
703 794 3.730662 CGTTTAATCCAGACATTTGCGGG 60.731 47.826 0.00 0.00 0.00 6.13
705 796 1.463674 AATCCAGACATTTGCGGGAC 58.536 50.000 0.00 0.00 0.00 4.46
748 839 1.668419 CTGACCGCTCTAAAATGGGG 58.332 55.000 0.00 0.00 41.34 4.96
769 860 0.308993 GGTGCTGAAGTTGCTCACAC 59.691 55.000 0.00 0.00 31.84 3.82
770 861 1.016627 GTGCTGAAGTTGCTCACACA 58.983 50.000 0.00 0.00 32.39 3.72
776 867 4.023707 GCTGAAGTTGCTCACACATAACTT 60.024 41.667 0.00 0.00 43.71 2.66
875 966 8.647143 AAAATGAAAGTAGATTTGTGGTTGTG 57.353 30.769 0.00 0.00 0.00 3.33
876 967 5.766150 TGAAAGTAGATTTGTGGTTGTGG 57.234 39.130 0.00 0.00 0.00 4.17
877 968 4.037446 TGAAAGTAGATTTGTGGTTGTGGC 59.963 41.667 0.00 0.00 0.00 5.01
878 969 2.514803 AGTAGATTTGTGGTTGTGGCC 58.485 47.619 0.00 0.00 0.00 5.36
889 980 0.671796 GTTGTGGCCTTGTGGGTTAC 59.328 55.000 3.32 0.00 37.43 2.50
962 1053 0.112412 AACCCCAAAACCGATCAGCT 59.888 50.000 0.00 0.00 0.00 4.24
1302 1395 2.261671 CGTTCCACCTCCTCCACG 59.738 66.667 0.00 0.00 0.00 4.94
1323 1419 1.755008 CACCTCGACCTCCTCCTCC 60.755 68.421 0.00 0.00 0.00 4.30
1425 1521 1.254026 CGTCATCTAAGGCCGGGATA 58.746 55.000 2.18 0.00 0.00 2.59
1583 1679 7.435192 CGAAATGTGGCTTCCCTTTATTTATTC 59.565 37.037 0.00 0.00 0.00 1.75
1666 1762 0.320697 GTCTGGGTTCGTGTTAGCCT 59.679 55.000 0.00 0.00 34.29 4.58
1667 1763 0.320374 TCTGGGTTCGTGTTAGCCTG 59.680 55.000 0.00 0.00 34.29 4.85
1668 1764 0.034896 CTGGGTTCGTGTTAGCCTGT 59.965 55.000 0.00 0.00 34.29 4.00
1669 1765 0.470766 TGGGTTCGTGTTAGCCTGTT 59.529 50.000 0.00 0.00 34.29 3.16
1670 1766 1.693062 TGGGTTCGTGTTAGCCTGTTA 59.307 47.619 0.00 0.00 34.29 2.41
1671 1767 2.303600 TGGGTTCGTGTTAGCCTGTTAT 59.696 45.455 0.00 0.00 34.29 1.89
1672 1768 3.244630 TGGGTTCGTGTTAGCCTGTTATT 60.245 43.478 0.00 0.00 34.29 1.40
1673 1769 3.126343 GGGTTCGTGTTAGCCTGTTATTG 59.874 47.826 0.00 0.00 0.00 1.90
1674 1770 3.126343 GGTTCGTGTTAGCCTGTTATTGG 59.874 47.826 0.00 0.00 0.00 3.16
1675 1771 3.688694 TCGTGTTAGCCTGTTATTGGT 57.311 42.857 0.00 0.00 0.00 3.67
1676 1772 3.331150 TCGTGTTAGCCTGTTATTGGTG 58.669 45.455 0.00 0.00 0.00 4.17
1741 1838 2.331132 GCCAGTGGCTTGTCTCAGC 61.331 63.158 27.48 0.00 46.69 4.26
1792 1895 9.753674 TCATATGGAATTTACTTTCCTTGAGTT 57.246 29.630 2.13 0.00 44.63 3.01
1836 1939 1.908619 TGATATGTGGTGACCAGCTGT 59.091 47.619 13.81 0.11 32.34 4.40
1929 2034 7.141100 TGCAGTGATATATTGCATGAATCAG 57.859 36.000 6.49 0.00 45.65 2.90
2015 2120 3.806625 ATGGTTGCTTAATGATGGTGC 57.193 42.857 0.00 0.00 0.00 5.01
2083 2196 3.508840 GCGGGATTGGCAACGGAG 61.509 66.667 0.00 0.00 42.51 4.63
2121 2234 1.722011 ACCTTGTATTCGGTTCTGCG 58.278 50.000 0.00 0.00 0.00 5.18
2128 2241 5.252969 TGTATTCGGTTCTGCGTATAAGT 57.747 39.130 0.00 0.00 0.00 2.24
2129 2242 5.653507 TGTATTCGGTTCTGCGTATAAGTT 58.346 37.500 0.00 0.00 0.00 2.66
2169 2282 8.026026 TGTTGTGCGTGTAATATGAAATCAAAT 58.974 29.630 0.00 0.00 0.00 2.32
2253 2368 6.605594 TGTTTCCTAAGGTGAACTGTTCAAAT 59.394 34.615 23.55 14.91 42.15 2.32
2259 2374 4.936891 AGGTGAACTGTTCAAATTTCAGC 58.063 39.130 23.55 10.60 43.57 4.26
2262 2377 5.343249 GTGAACTGTTCAAATTTCAGCTGT 58.657 37.500 23.55 0.00 42.15 4.40
2265 2380 3.054878 CTGTTCAAATTTCAGCTGTGGC 58.945 45.455 14.67 2.27 39.06 5.01
2375 2490 8.762645 TGTATCAGTCCTTCATTCTTATCACTT 58.237 33.333 0.00 0.00 0.00 3.16
2457 2576 9.236006 CATAGCTAGGCAATAATAACCTGAATT 57.764 33.333 0.00 0.00 34.92 2.17
2489 2608 7.705325 GCAGAAACTGAGCATTGAAATCATAAT 59.295 33.333 2.81 0.00 32.44 1.28
2512 2631 6.596309 TCAATATATGCTCTACCTGTGAGG 57.404 41.667 0.00 0.00 42.49 3.86
2540 2659 7.169140 GTGGACACACTGAAAAATGGAATTTAC 59.831 37.037 0.00 0.00 44.39 2.01
2558 2677 9.379791 GGAATTTACTATTTATATCCCACTCGG 57.620 37.037 0.00 0.00 0.00 4.63
2597 2716 8.239681 GGTACCTTTGATTCTTATTTTGTTGC 57.760 34.615 4.06 0.00 0.00 4.17
2598 2717 8.088365 GGTACCTTTGATTCTTATTTTGTTGCT 58.912 33.333 4.06 0.00 0.00 3.91
2647 2787 9.388506 CCTTTTAGACATATCAGACATGAACTT 57.611 33.333 0.00 0.00 39.39 2.66
2692 2833 9.543231 TTCTTTAAGATAGAGGAAGTTGGTAGA 57.457 33.333 0.00 0.00 0.00 2.59
2739 2880 2.015736 AGCTCTAACACTGGCAATCG 57.984 50.000 0.00 0.00 0.00 3.34
2754 2895 6.072175 ACTGGCAATCGTTCTATTTTAGCAAA 60.072 34.615 0.00 0.00 0.00 3.68
2784 2925 8.767478 TTACTTAGAGCACCATTAACTTGTAC 57.233 34.615 0.00 0.00 0.00 2.90
2956 3098 1.474330 TAGAGTTCCTGCAGCGATCA 58.526 50.000 8.66 0.00 0.00 2.92
2965 3107 0.097499 TGCAGCGATCAAAAGCATCG 59.903 50.000 0.00 0.00 44.94 3.84
3074 3216 3.760151 TCCCTTGAGCAAATCAGACATTG 59.240 43.478 0.00 0.00 39.68 2.82
3088 3230 5.490159 TCAGACATTGATGCACAGACATTA 58.510 37.500 0.00 0.00 0.00 1.90
3154 3296 3.440173 GGAAGAACTTGGAATCGATGCAA 59.560 43.478 5.57 3.91 36.98 4.08
3211 3353 2.234168 GTCCCTAGGTGGAAGTTCTGAC 59.766 54.545 8.29 0.00 35.80 3.51
3214 3356 2.164624 CCTAGGTGGAAGTTCTGACGAG 59.835 54.545 0.00 2.12 38.35 4.18
3568 3710 4.041198 ACGGGTTGGACAGAGAAAAGATTA 59.959 41.667 0.00 0.00 0.00 1.75
3750 3892 2.617276 CCTATATACGGTCCTCGCTCCA 60.617 54.545 0.00 0.00 43.89 3.86
3942 4084 4.692625 ACATCACTAATCACTGTCAGCAAC 59.307 41.667 0.00 0.00 0.00 4.17
4094 4362 3.113824 AGAGAATGGATGAGGCAGACTT 58.886 45.455 0.00 0.00 0.00 3.01
4260 4528 6.295236 CCCTTCATTCTTGCTTTGGTAATGAA 60.295 38.462 0.00 0.00 41.68 2.57
4666 4942 8.810652 TTACCTTTGCAAGCTTTTATAGTTTG 57.189 30.769 0.00 0.00 45.01 2.93
4805 5099 7.378995 GCAATTGCATATCTTTCTTGAGTGATC 59.621 37.037 25.36 0.00 41.59 2.92
5207 5501 9.511144 AGCTTATTTTCCCGTAAAATTATTTCG 57.489 29.630 10.01 0.00 43.75 3.46
5349 5645 2.625737 CCACATGCTCTTCTGAATCGT 58.374 47.619 0.00 0.00 0.00 3.73
5371 5667 2.611292 GGATCGCAAGTTGGATCTTCTG 59.389 50.000 22.69 0.00 39.19 3.02
5499 5795 4.215185 TGCTTGCGAAACAGTGAATTATCA 59.785 37.500 0.00 0.00 0.00 2.15
5664 5960 1.375396 GTATGTCGGTGGTGCTGCA 60.375 57.895 0.00 0.00 0.00 4.41
5760 6056 0.389391 CGCGGGACCATCTCATAACT 59.611 55.000 0.00 0.00 0.00 2.24
5793 6089 2.919602 AGCTTCCTTTGATGGGTTCCTA 59.080 45.455 0.00 0.00 0.00 2.94
6285 6581 2.135139 CGCTGATAAGTGTGTGTGTGT 58.865 47.619 0.00 0.00 0.00 3.72
6286 6582 2.543848 CGCTGATAAGTGTGTGTGTGTT 59.456 45.455 0.00 0.00 0.00 3.32
6305 6601 0.239613 TTGTGTGTGTGTGTGTGTGC 59.760 50.000 0.00 0.00 0.00 4.57
6486 6786 7.118723 AGGAAAGGATGATATGTTTTGTGCTA 58.881 34.615 0.00 0.00 0.00 3.49
6608 6975 6.809630 AGAAAGGCATTCTGAAAAGTACTC 57.190 37.500 3.86 0.00 46.71 2.59
6609 6976 5.707764 AGAAAGGCATTCTGAAAAGTACTCC 59.292 40.000 3.86 0.00 46.71 3.85
6610 6977 3.956744 AGGCATTCTGAAAAGTACTCCC 58.043 45.455 0.00 0.00 0.00 4.30
6611 6978 3.589288 AGGCATTCTGAAAAGTACTCCCT 59.411 43.478 0.00 0.00 0.00 4.20
6612 6979 3.942115 GGCATTCTGAAAAGTACTCCCTC 59.058 47.826 0.00 0.00 0.00 4.30
6613 6980 3.942115 GCATTCTGAAAAGTACTCCCTCC 59.058 47.826 0.00 0.00 0.00 4.30
6614 6981 3.955650 TTCTGAAAAGTACTCCCTCCG 57.044 47.619 0.00 0.00 0.00 4.63
6615 6982 2.885616 TCTGAAAAGTACTCCCTCCGT 58.114 47.619 0.00 0.00 0.00 4.69
6616 6983 2.824341 TCTGAAAAGTACTCCCTCCGTC 59.176 50.000 0.00 0.00 0.00 4.79
6617 6984 1.897802 TGAAAAGTACTCCCTCCGTCC 59.102 52.381 0.00 0.00 0.00 4.79
6618 6985 1.206610 GAAAAGTACTCCCTCCGTCCC 59.793 57.143 0.00 0.00 0.00 4.46
6619 6986 0.115745 AAAGTACTCCCTCCGTCCCA 59.884 55.000 0.00 0.00 0.00 4.37
6620 6987 0.338814 AAGTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
6621 6988 1.229131 AGTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
6622 6989 1.572415 AGTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
6623 6990 2.179424 AGTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
6624 6991 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
6625 6992 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
6626 6993 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
6627 6994 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
6628 6995 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
6629 6996 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
6630 6997 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
6631 6998 3.386726 CCTCCGTCCCATAATGTAAGACA 59.613 47.826 0.00 0.00 0.00 3.41
6632 6999 4.040461 CCTCCGTCCCATAATGTAAGACAT 59.960 45.833 0.00 0.00 41.31 3.06
6634 7001 5.996644 TCCGTCCCATAATGTAAGACATTT 58.003 37.500 9.92 0.00 45.80 2.32
6635 7002 6.419791 TCCGTCCCATAATGTAAGACATTTT 58.580 36.000 9.92 0.33 45.80 1.82
6636 7003 6.887545 TCCGTCCCATAATGTAAGACATTTTT 59.112 34.615 9.92 0.00 45.80 1.94
6660 7027 7.821595 TTGACACTAACGTCTTACATTATGG 57.178 36.000 0.00 0.00 36.82 2.74
6661 7028 7.160547 TGACACTAACGTCTTACATTATGGA 57.839 36.000 0.00 0.00 36.82 3.41
6662 7029 7.604549 TGACACTAACGTCTTACATTATGGAA 58.395 34.615 0.00 0.00 36.82 3.53
6663 7030 8.255206 TGACACTAACGTCTTACATTATGGAAT 58.745 33.333 0.00 0.00 36.82 3.01
6664 7031 8.420374 ACACTAACGTCTTACATTATGGAATG 57.580 34.615 0.00 0.00 46.77 2.67
6665 7032 7.494625 ACACTAACGTCTTACATTATGGAATGG 59.505 37.037 0.00 0.00 45.83 3.16
6666 7033 7.709182 CACTAACGTCTTACATTATGGAATGGA 59.291 37.037 0.00 0.00 45.83 3.41
6667 7034 7.926555 ACTAACGTCTTACATTATGGAATGGAG 59.073 37.037 0.00 1.17 45.83 3.86
6668 7035 6.235231 ACGTCTTACATTATGGAATGGAGT 57.765 37.500 0.00 0.00 45.83 3.85
6669 7036 7.356089 ACGTCTTACATTATGGAATGGAGTA 57.644 36.000 0.00 0.00 45.83 2.59
6670 7037 7.434492 ACGTCTTACATTATGGAATGGAGTAG 58.566 38.462 0.00 0.00 45.83 2.57
6671 7038 6.868864 CGTCTTACATTATGGAATGGAGTAGG 59.131 42.308 0.00 0.00 45.83 3.18
6672 7039 7.255836 CGTCTTACATTATGGAATGGAGTAGGA 60.256 40.741 0.00 0.00 45.83 2.94
6676 7043 5.370880 ACATTATGGAATGGAGTAGGAGCTT 59.629 40.000 0.00 0.00 45.83 3.74
6700 7067 9.884465 CTTTAAACTTACCAGAAGTCAGAAATG 57.116 33.333 0.00 0.00 0.00 2.32
6900 7270 3.925379 TCATCACGCTGTTCTTGTATGT 58.075 40.909 0.00 0.00 0.00 2.29
6947 7320 2.727123 TGTTGCCGAATCCCATGTAT 57.273 45.000 0.00 0.00 0.00 2.29
7017 7391 3.866651 GCAGACAGCAGATTTAAGAGGA 58.133 45.455 0.00 0.00 44.79 3.71
7018 7392 3.870419 GCAGACAGCAGATTTAAGAGGAG 59.130 47.826 0.00 0.00 44.79 3.69
7022 7396 4.512484 ACAGCAGATTTAAGAGGAGCTTC 58.488 43.478 0.00 0.00 38.05 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.135315 CCAAGAATCGCCGCAACAG 59.865 57.895 0.00 0.00 0.00 3.16
65 66 1.002624 CCCGTCCAGCTAAAGCCAA 60.003 57.895 0.00 0.00 43.38 4.52
66 67 2.668632 CCCGTCCAGCTAAAGCCA 59.331 61.111 0.00 0.00 43.38 4.75
97 98 1.167851 CATCATCCAAAGTGCACCGT 58.832 50.000 14.63 0.00 0.00 4.83
99 100 1.203052 CACCATCATCCAAAGTGCACC 59.797 52.381 14.63 0.00 0.00 5.01
109 110 0.107703 TCAAGCCGACACCATCATCC 60.108 55.000 0.00 0.00 0.00 3.51
132 134 4.770874 TTAGAAGGCGGTGGCGGC 62.771 66.667 0.00 0.00 41.24 6.53
135 137 0.036294 AAGACTTAGAAGGCGGTGGC 60.036 55.000 0.00 0.00 39.71 5.01
200 205 3.787676 TTCGCCTGCAATGTCGCG 61.788 61.111 0.00 0.00 45.76 5.87
203 208 0.523072 ATGTGTTCGCCTGCAATGTC 59.477 50.000 0.00 0.00 0.00 3.06
206 211 0.608856 TGGATGTGTTCGCCTGCAAT 60.609 50.000 0.00 0.00 0.00 3.56
231 236 0.038526 CGGTCGCATATGTAGGACCC 60.039 60.000 24.46 14.12 44.80 4.46
253 258 2.126228 GACGACGATGTTCGCCCA 60.126 61.111 0.00 0.00 45.12 5.36
559 564 0.748729 CTCTCCCGCTCCTTACGTCT 60.749 60.000 0.00 0.00 0.00 4.18
583 588 0.939106 GTCATTTGCACAACCACGCC 60.939 55.000 0.00 0.00 0.00 5.68
638 653 0.107703 ATGTCGACATCCGCCACAAT 60.108 50.000 25.18 0.00 38.37 2.71
685 776 2.639065 GTCCCGCAAATGTCTGGATTA 58.361 47.619 0.00 0.00 0.00 1.75
692 783 0.386731 CCAAACGTCCCGCAAATGTC 60.387 55.000 0.00 0.00 0.00 3.06
703 794 2.604174 CCACTGCGGACCAAACGTC 61.604 63.158 0.00 0.00 41.15 4.34
705 796 2.280524 TCCACTGCGGACCAAACG 60.281 61.111 0.00 0.00 39.64 3.60
748 839 2.253758 TGAGCAACTTCAGCACCGC 61.254 57.895 0.00 0.00 0.00 5.68
769 860 6.423182 TGGGGGAGAATTAGACAAAGTTATG 58.577 40.000 0.00 0.00 0.00 1.90
770 861 6.652205 TGGGGGAGAATTAGACAAAGTTAT 57.348 37.500 0.00 0.00 0.00 1.89
776 867 8.909423 AAAAATTATGGGGGAGAATTAGACAA 57.091 30.769 0.00 0.00 0.00 3.18
804 895 8.557450 ACTTCTATTTTCCCTTAGAATTAGGCA 58.443 33.333 0.00 0.00 34.76 4.75
805 896 8.982091 ACTTCTATTTTCCCTTAGAATTAGGC 57.018 34.615 0.00 0.00 34.76 3.93
855 946 4.546570 GCCACAACCACAAATCTACTTTC 58.453 43.478 0.00 0.00 0.00 2.62
871 962 0.259065 TGTAACCCACAAGGCCACAA 59.741 50.000 5.01 0.00 40.58 3.33
872 963 0.466555 GTGTAACCCACAAGGCCACA 60.467 55.000 5.01 0.00 43.92 4.17
873 964 1.512156 CGTGTAACCCACAAGGCCAC 61.512 60.000 5.01 0.00 44.78 5.01
874 965 1.228003 CGTGTAACCCACAAGGCCA 60.228 57.895 5.01 0.00 44.78 5.36
875 966 3.663202 CGTGTAACCCACAAGGCC 58.337 61.111 0.00 0.00 44.78 5.19
878 969 0.179040 ACCACCGTGTAACCCACAAG 60.179 55.000 0.00 0.00 44.78 3.16
889 980 0.995728 GTTTGCAACAAACCACCGTG 59.004 50.000 11.26 0.00 0.00 4.94
1302 1395 2.053277 GGAGGAGGTCGAGGTGGAC 61.053 68.421 0.00 0.00 36.18 4.02
1583 1679 0.454957 CAGCGAAACAAGCAATCGGG 60.455 55.000 0.00 0.00 37.08 5.14
1666 1762 5.594725 ACACACCAATAACACACCAATAACA 59.405 36.000 0.00 0.00 0.00 2.41
1667 1763 5.918011 CACACACCAATAACACACCAATAAC 59.082 40.000 0.00 0.00 0.00 1.89
1668 1764 5.828328 TCACACACCAATAACACACCAATAA 59.172 36.000 0.00 0.00 0.00 1.40
1669 1765 5.377478 TCACACACCAATAACACACCAATA 58.623 37.500 0.00 0.00 0.00 1.90
1670 1766 4.211125 TCACACACCAATAACACACCAAT 58.789 39.130 0.00 0.00 0.00 3.16
1671 1767 3.621558 TCACACACCAATAACACACCAA 58.378 40.909 0.00 0.00 0.00 3.67
1672 1768 3.283259 TCACACACCAATAACACACCA 57.717 42.857 0.00 0.00 0.00 4.17
1673 1769 4.545610 CAATCACACACCAATAACACACC 58.454 43.478 0.00 0.00 0.00 4.16
1674 1770 4.037446 ACCAATCACACACCAATAACACAC 59.963 41.667 0.00 0.00 0.00 3.82
1675 1771 4.211125 ACCAATCACACACCAATAACACA 58.789 39.130 0.00 0.00 0.00 3.72
1676 1772 4.846779 ACCAATCACACACCAATAACAC 57.153 40.909 0.00 0.00 0.00 3.32
1741 1838 5.942236 TCTTCCAAATCTCAAGATCACCAAG 59.058 40.000 0.00 0.00 32.75 3.61
1792 1895 7.766738 TCAGTTGCGATCTTAACCAACATAATA 59.233 33.333 0.00 0.00 39.86 0.98
1793 1896 6.597672 TCAGTTGCGATCTTAACCAACATAAT 59.402 34.615 0.00 0.00 39.86 1.28
1794 1897 5.935206 TCAGTTGCGATCTTAACCAACATAA 59.065 36.000 0.00 0.00 39.86 1.90
1795 1898 5.483811 TCAGTTGCGATCTTAACCAACATA 58.516 37.500 0.00 0.00 39.86 2.29
1796 1899 4.323417 TCAGTTGCGATCTTAACCAACAT 58.677 39.130 0.00 0.00 39.86 2.71
1797 1900 3.734463 TCAGTTGCGATCTTAACCAACA 58.266 40.909 0.00 0.00 39.86 3.33
1798 1901 4.946784 ATCAGTTGCGATCTTAACCAAC 57.053 40.909 5.61 0.00 38.20 3.77
1929 2034 4.423625 AGGGAATAGGTACTTGCATCAC 57.576 45.455 0.00 0.00 41.75 3.06
2015 2120 3.588955 GCCCCATGTAAAAGCAAGAAAG 58.411 45.455 0.00 0.00 0.00 2.62
2090 2203 4.635765 CGAATACAAGGTTGACATGGTCAT 59.364 41.667 0.00 0.00 42.40 3.06
2093 2206 3.244770 ACCGAATACAAGGTTGACATGGT 60.245 43.478 0.00 0.00 37.49 3.55
2106 2219 5.252969 ACTTATACGCAGAACCGAATACA 57.747 39.130 0.00 0.00 0.00 2.29
2190 2303 0.532573 TCAGAGCTTGACGGGATCAC 59.467 55.000 0.00 0.00 36.92 3.06
2192 2305 0.820871 ACTCAGAGCTTGACGGGATC 59.179 55.000 0.00 0.00 0.00 3.36
2253 2368 0.591170 GCTAAACGCCACAGCTGAAA 59.409 50.000 23.35 0.00 36.60 2.69
2259 2374 2.095853 CCATAACTGCTAAACGCCACAG 59.904 50.000 0.00 0.00 38.05 3.66
2262 2377 2.483014 ACCATAACTGCTAAACGCCA 57.517 45.000 0.00 0.00 38.05 5.69
2286 2401 9.761504 CAGTTCACAGAGATTGTATCAGATAAT 57.238 33.333 0.00 0.00 38.16 1.28
2344 2459 6.865834 AGAATGAAGGACTGATACAAGTCT 57.134 37.500 4.50 0.00 44.98 3.24
2457 2576 5.247862 TCAATGCTCAGTTTCTGCTAATCA 58.752 37.500 0.00 0.00 0.00 2.57
2489 2608 6.596309 CCTCACAGGTAGAGCATATATTGA 57.404 41.667 0.00 0.00 0.00 2.57
2553 2672 4.094830 ACCCAAACAAATCTTACCGAGT 57.905 40.909 0.00 0.00 0.00 4.18
2558 2677 7.279750 TCAAAGGTACCCAAACAAATCTTAC 57.720 36.000 8.74 0.00 0.00 2.34
2597 2716 6.446781 AGACATGCATTTGACCTGAAATAG 57.553 37.500 0.00 0.00 0.00 1.73
2598 2717 5.357878 GGAGACATGCATTTGACCTGAAATA 59.642 40.000 0.00 0.00 0.00 1.40
2668 2808 9.589111 GTTCTACCAACTTCCTCTATCTTAAAG 57.411 37.037 0.00 0.00 0.00 1.85
2671 2811 8.840200 ATGTTCTACCAACTTCCTCTATCTTA 57.160 34.615 0.00 0.00 0.00 2.10
2711 2852 4.130118 CCAGTGTTAGAGCTTGACAAGTT 58.870 43.478 16.39 10.73 0.00 2.66
2754 2895 9.686683 AAGTTAATGGTGCTCTAAGTAATTCAT 57.313 29.630 0.00 0.00 0.00 2.57
2761 2902 6.765403 TGTACAAGTTAATGGTGCTCTAAGT 58.235 36.000 0.00 0.00 0.00 2.24
2765 2906 5.228945 ACTGTACAAGTTAATGGTGCTCT 57.771 39.130 0.00 0.00 34.57 4.09
2784 2925 0.322277 AGCTGATGGTGGCTCAACTG 60.322 55.000 0.00 0.00 32.98 3.16
2956 3098 3.085952 TCAGGGAAATCCGATGCTTTT 57.914 42.857 0.00 0.00 41.52 2.27
2965 3107 3.117738 ACTCATGTGGATCAGGGAAATCC 60.118 47.826 0.00 0.00 42.62 3.01
3074 3216 4.033990 TCTCTCGTAATGTCTGTGCATC 57.966 45.455 0.00 0.00 0.00 3.91
3088 3230 9.674068 TCATATGCTCTACTTATTATCTCTCGT 57.326 33.333 0.00 0.00 0.00 4.18
3118 3260 4.461198 AGTTCTTCCCGTTTTGAAGTGAT 58.539 39.130 0.00 0.00 40.10 3.06
3154 3296 0.608130 TCACCGCACTGCATAGTTCT 59.392 50.000 1.11 0.00 34.07 3.01
3211 3353 0.738762 CATCTGCCCAGTGACACTCG 60.739 60.000 4.74 0.00 0.00 4.18
3214 3356 2.042831 GCCATCTGCCCAGTGACAC 61.043 63.158 0.00 0.00 0.00 3.67
3568 3710 7.575720 GCATTGAAAGTTTCATGGTAAGCTAGT 60.576 37.037 18.69 0.00 39.84 2.57
3750 3892 6.884280 AACTTACTTGAGCAAAAGCAGTAT 57.116 33.333 0.00 0.00 0.00 2.12
3983 4126 7.607615 AAGGCCAATATTAAGATCAAGCATT 57.392 32.000 5.01 0.00 0.00 3.56
3984 4127 7.607615 AAAGGCCAATATTAAGATCAAGCAT 57.392 32.000 5.01 0.00 0.00 3.79
4094 4362 5.059161 CAGGATTCCTTGATGATCGCTTTA 58.941 41.667 1.28 0.00 0.00 1.85
4260 4528 3.055891 GCCCAACCATAAATTGCTTCAGT 60.056 43.478 0.00 0.00 0.00 3.41
4612 4888 2.614057 GGGTTGATGAAAGGATACAGCG 59.386 50.000 0.00 0.00 41.41 5.18
5207 5501 3.553828 TGAATCCACCCTCGGTAAATC 57.446 47.619 0.00 0.00 32.11 2.17
5349 5645 2.237143 AGAAGATCCAACTTGCGATCCA 59.763 45.455 12.85 0.00 36.36 3.41
5371 5667 1.373570 CATCCTTCCGACTTTCCAGC 58.626 55.000 0.00 0.00 0.00 4.85
5425 5721 3.133003 ACCTCAGTTCGGATGTAATGGAG 59.867 47.826 0.00 0.00 0.00 3.86
5499 5795 0.998928 TGGTGCCATTACCATCCTGT 59.001 50.000 0.00 0.00 45.46 4.00
5510 5806 1.285667 TCATTCCATCAGTGGTGCCAT 59.714 47.619 0.00 0.00 46.16 4.40
5537 5833 0.255890 TGCCTGGGATAGCTCAAACC 59.744 55.000 0.00 0.00 0.00 3.27
5577 5873 2.109538 CTGTTGCGTCACACAGCTGG 62.110 60.000 19.93 9.66 0.00 4.85
5664 5960 0.779997 AAGGCTCCACCCTGTTTGAT 59.220 50.000 0.00 0.00 40.58 2.57
5760 6056 1.896220 AGGAAGCTTTCATCAACGCA 58.104 45.000 7.68 0.00 0.00 5.24
6285 6581 1.335415 GCACACACACACACACACAAA 60.335 47.619 0.00 0.00 0.00 2.83
6286 6582 0.239613 GCACACACACACACACACAA 59.760 50.000 0.00 0.00 0.00 3.33
6305 6601 1.060553 GAAGACACACACACACACACG 59.939 52.381 0.00 0.00 0.00 4.49
6486 6786 4.081642 ACAACTCAGATATTACAGGTGCGT 60.082 41.667 0.00 0.00 0.00 5.24
6606 6973 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
6607 6974 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
6608 6975 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
6609 6976 3.386726 TGTCTTACATTATGGGACGGAGG 59.613 47.826 0.00 0.00 0.00 4.30
6610 6977 4.665833 TGTCTTACATTATGGGACGGAG 57.334 45.455 0.00 0.00 0.00 4.63
6611 6978 5.623956 AATGTCTTACATTATGGGACGGA 57.376 39.130 3.51 0.00 46.11 4.69
6634 7001 8.714179 CCATAATGTAAGACGTTAGTGTCAAAA 58.286 33.333 0.00 0.00 41.41 2.44
6635 7002 8.089597 TCCATAATGTAAGACGTTAGTGTCAAA 58.910 33.333 0.00 0.00 41.41 2.69
6636 7003 7.604549 TCCATAATGTAAGACGTTAGTGTCAA 58.395 34.615 0.00 0.00 41.41 3.18
6637 7004 7.160547 TCCATAATGTAAGACGTTAGTGTCA 57.839 36.000 0.00 0.00 41.41 3.58
6638 7005 8.540492 CATTCCATAATGTAAGACGTTAGTGTC 58.460 37.037 0.00 0.00 38.15 3.67
6639 7006 7.494625 CCATTCCATAATGTAAGACGTTAGTGT 59.505 37.037 0.00 0.00 40.84 3.55
6640 7007 7.709182 TCCATTCCATAATGTAAGACGTTAGTG 59.291 37.037 0.00 0.00 40.84 2.74
6641 7008 7.788026 TCCATTCCATAATGTAAGACGTTAGT 58.212 34.615 0.00 0.00 40.84 2.24
6642 7009 7.926555 ACTCCATTCCATAATGTAAGACGTTAG 59.073 37.037 0.00 0.00 40.84 2.34
6643 7010 7.788026 ACTCCATTCCATAATGTAAGACGTTA 58.212 34.615 0.00 0.00 40.84 3.18
6644 7011 6.650120 ACTCCATTCCATAATGTAAGACGTT 58.350 36.000 0.00 0.00 40.84 3.99
6645 7012 6.235231 ACTCCATTCCATAATGTAAGACGT 57.765 37.500 0.00 0.00 40.84 4.34
6646 7013 6.868864 CCTACTCCATTCCATAATGTAAGACG 59.131 42.308 0.00 0.00 40.84 4.18
6647 7014 7.963532 TCCTACTCCATTCCATAATGTAAGAC 58.036 38.462 0.00 0.00 40.84 3.01
6648 7015 7.256332 GCTCCTACTCCATTCCATAATGTAAGA 60.256 40.741 0.00 0.00 40.84 2.10
6649 7016 6.876257 GCTCCTACTCCATTCCATAATGTAAG 59.124 42.308 0.00 0.00 40.84 2.34
6650 7017 6.558775 AGCTCCTACTCCATTCCATAATGTAA 59.441 38.462 0.00 0.00 40.84 2.41
6651 7018 6.084738 AGCTCCTACTCCATTCCATAATGTA 58.915 40.000 0.00 0.00 40.84 2.29
6652 7019 4.910304 AGCTCCTACTCCATTCCATAATGT 59.090 41.667 0.00 0.00 40.84 2.71
6653 7020 5.495926 AGCTCCTACTCCATTCCATAATG 57.504 43.478 0.00 0.00 41.90 1.90
6654 7021 6.521527 AAAGCTCCTACTCCATTCCATAAT 57.478 37.500 0.00 0.00 0.00 1.28
6655 7022 5.975988 AAAGCTCCTACTCCATTCCATAA 57.024 39.130 0.00 0.00 0.00 1.90
6656 7023 7.127339 AGTTTAAAGCTCCTACTCCATTCCATA 59.873 37.037 0.00 0.00 0.00 2.74
6657 7024 5.975988 TTAAAGCTCCTACTCCATTCCAT 57.024 39.130 0.00 0.00 0.00 3.41
6658 7025 5.250774 AGTTTAAAGCTCCTACTCCATTCCA 59.749 40.000 0.00 0.00 0.00 3.53
6659 7026 5.746284 AGTTTAAAGCTCCTACTCCATTCC 58.254 41.667 0.00 0.00 0.00 3.01
6660 7027 7.280428 GGTAAGTTTAAAGCTCCTACTCCATTC 59.720 40.741 0.00 0.00 0.00 2.67
6661 7028 7.110810 GGTAAGTTTAAAGCTCCTACTCCATT 58.889 38.462 0.00 0.00 0.00 3.16
6662 7029 6.214819 TGGTAAGTTTAAAGCTCCTACTCCAT 59.785 38.462 0.00 0.00 0.00 3.41
6663 7030 5.544948 TGGTAAGTTTAAAGCTCCTACTCCA 59.455 40.000 0.00 0.00 0.00 3.86
6664 7031 6.046290 TGGTAAGTTTAAAGCTCCTACTCC 57.954 41.667 0.00 0.00 0.00 3.85
6665 7032 6.932947 TCTGGTAAGTTTAAAGCTCCTACTC 58.067 40.000 0.00 0.00 0.00 2.59
6666 7033 6.930068 TCTGGTAAGTTTAAAGCTCCTACT 57.070 37.500 0.00 0.00 0.00 2.57
6667 7034 7.160049 ACTTCTGGTAAGTTTAAAGCTCCTAC 58.840 38.462 0.00 0.00 0.00 3.18
6668 7035 7.015877 TGACTTCTGGTAAGTTTAAAGCTCCTA 59.984 37.037 0.00 0.00 0.00 2.94
6669 7036 6.183361 TGACTTCTGGTAAGTTTAAAGCTCCT 60.183 38.462 0.00 0.00 0.00 3.69
6670 7037 5.995897 TGACTTCTGGTAAGTTTAAAGCTCC 59.004 40.000 0.00 0.00 0.00 4.70
6671 7038 6.929606 TCTGACTTCTGGTAAGTTTAAAGCTC 59.070 38.462 0.00 0.00 0.00 4.09
6672 7039 6.827727 TCTGACTTCTGGTAAGTTTAAAGCT 58.172 36.000 0.00 0.00 0.00 3.74
6676 7043 7.040686 GCCATTTCTGACTTCTGGTAAGTTTAA 60.041 37.037 0.00 0.00 0.00 1.52
6753 7120 4.242475 CGAGTTGTATTTGCTAGTCACCA 58.758 43.478 0.00 0.00 0.00 4.17
7016 7390 4.888917 GGTCTCATACCCAATAGAAGCTC 58.111 47.826 0.00 0.00 43.16 4.09
7017 7391 4.965200 GGTCTCATACCCAATAGAAGCT 57.035 45.455 0.00 0.00 43.16 3.74


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

AutoCloner maintained by Alex Coulton.